# hmmscan :: search sequence(s) against a profile database
# HMMER 3.2.1 (June 2018); http://hmmer.org/
# Copyright (C) 2018 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query sequence file:             /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Euryarchaeota/Thermococcus_sibiricus_MM_739_uid59399/NC_012883.faa
# target HMM database:             /oak/stanford/groups/akundaje/marinovg/genomes/PFam/PFam32.0/Pfam-A.hmm
# output directed to file:         /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Euryarchaeota/Thermococcus_sibiricus_MM_739_uid59399/NC_012883.PFam32-A
# per-seq hits tabular output:     /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Euryarchaeota/Thermococcus_sibiricus_MM_739_uid59399/NC_012883.PFam32-A.tblout
# number of worker threads:        20
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       gi|242397998|ref|YP_002993422.1|  [L=377]
Description: hypothetical protein TSIB_0001 [Thermococcus sibiricus MM 739]
Scores for complete 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-08   33.3   0.1    6.1e-08   32.1   0.1    1.6  1  DUF354           Protein of unknown function (DUF354)
     0.0049   16.9   0.0      0.013   15.5   0.0    1.7  1  Glyco_transf_4   Glycosyltransferase Family 4
      0.005   16.9   0.0      0.012   15.6   0.0    1.7  1  Glyco_trans_4_2  Glycosyl transferase 4-like
  ------ inclusion threshold ------
      0.093   12.3   0.1        3.5    7.2   0.0    2.6  3  PrpR_N           Propionate catabolism activator
       0.14   10.9   0.0       0.26   10.1   0.0    1.3  1  Epimerase_2      UDP-N-acetylglucosamine 2-epimerase


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 !   32.1   0.1   1.7e-11   6.1e-08       5     278 ..      10     285 ..       6     353 .. 0.73

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 1.7e-11
                            DUF354   5 idltnaphvryfrdlikkfekeGievlltardsGdlaklvklynfvfksiGkhGvtlkekliesakrvin....lsk 77 
                                       i +      ++++++ + ++++G  v+l ar++Gd   l++ ++f +          ++kl++ a+  ++    l k
  gi|242397998|ref|YP_002993422.1|  10 IVVNTPAQAHFYKNIYTALKDKGHSVFLLARNYGDTIELLNSFGFDYIMYSD-PLVSSNKLLKTAQFPLDvmsaLLK 85 
                                       5444444789***********************************9987765.556689999999864431112666 PP

                            DUF354  78 liae.vkpdvalakhsvelprvafGlnipvvyvldnehae..aankltlpladeiikpividendlkktGadpnrir 151
                                        i +  kpdv +         ++  ln+p ++ +d e        +l + +   i + i++ +   + +G +  ++ 
  gi|242397998|ref|YP_002993422.1|  86 TIKNkIKPDVIVGGGGYG-AIISEILNVPNIWYMDGEPMFysGLYQLEFKMFSRIPRAIITPKAFRQSLGNQHIKVD 161
                                       6665279**999887765.567888************8761145678888889998888888888888999977777 PP

                            DUF354 152 ryeGtsevinvqsyeideeilkdlnlkledektilmrpepslasyldad....chkdvltkiveklkdridilvipr 224
                                        y+  s +   + y+ + +il++l+ + +++  +l+r +    +  d +    +++d +  +++kl++      i  
  gi|242397998|ref|YP_002993422.1| 162 SYKELSYL-SPKYYNPNPDILHELG-VSKHDTYLLLRFNA-FDALHDVNlyglSYEDKI-YLIKKLEKLGIKFFISS 234
                                       77766654.3466999*********.56666777888777.444444440000444433.34566655433333444 PP

                            DUF354 225 deeqkeiyeevdnviviketvdalsllkrsdlviGaGGtmnreaallGipvvsc 278
                                       +       e+++   ++k+ +    +++ s +++   Gtm  eaa+lG+p+v  
  gi|242397998|ref|YP_002993422.1| 235 ELPLPAPLEKYK-LSIPKHRIH--DVIYYSSMLVADTGTMVTEAAVLGVPAVMI 285
                                       444555678888.99****997..579999********************9965 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   3.6e-06     0.013       9     107 ..      22     122 ..      17     156 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.6e-06
                    Glyco_transf_4   9 leLaraLarrGheVtvvtpgddgpleeev..elvvrvprvplpllkrllrslaf....lrrlrrllkre.kpDvvHa 78 
                                        ++  aL ++Gh V ++++++++ +e        + + + pl+++++ll++ +f    +++l + +k+  kpDv+  
  gi|242397998|ref|YP_002993422.1|  22 KNIYTALKDKGHSVFLLARNYGDTIELLNsfGFDYIMYSDPLVSSNKLLKTAQFpldvMSALLKTIKNKiKPDVIVG 98 
                                       67889*******************9999999444455555555555555555551111666777777668*****44 PP

                    Glyco_transf_4  79 hspaalgaallalrrrlgiplVltvHgly 107
                                            +g++++ +   l++p ++++ g  
  gi|242397998|ref|YP_002993422.1|  99 ----GGGYGAIISEI-LNVPNIWYMDGEP 122
                                       ....45666665555.8899888876665 PP

>> Glyco_trans_4_2  Glycosyl transferase 4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   3.4e-06     0.012       2     100 ..       8     112 ..       7     139 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.4e-06
                   Glyco_trans_4_2   2 illlanls..svhtlrlakeLakrgyeVhvitpkkga.kdeleaegihvhrlkvdrkgpleylk.a........fkl 66 
                                       il+++n++    +++++  +L+++g+ V ++ ++ g   + l++ g+  +   ++  ++ ++lk a        + l
  gi|242397998|ref|YP_002993422.1|   8 ILIVVNTPaqAHFYKNIYTALKDKGHSVFLLARNYGDtIELLNSFGFDYIMYSDPLVSSNKLLKtAqfpldvmsALL 84 
                                       99****99744578999****************88866888888888888888784444444442344566653455 PP

                   Glyco_trans_4_2  67 kklikkikPDvvhahyakpygllgslaarlsgvi 100
                                       k + +kikPDv+      + g +g++++ +++ +
  gi|242397998|ref|YP_002993422.1|  85 KTIKNKIKPDVIV-----GGGGYGAIISEILN-V 112
                                       99999*******3.....33445666666666.4 PP

>> PrpR_N  Propionate catabolism activator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0   0.00097       3.5      26      50 ..      90     114 ..      76     116 .. 0.80
   2 ?    2.0   0.0     0.038   1.4e+02       5      34 ..     204     233 ..     200     236 .. 0.90
   3 ?   -2.6   0.0         1   3.6e+03     127     146 ..     269     288 ..     263     290 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00097
                            PrpR_N  26 aegvdviiSrGgtaellrkhvsvPV 50 
                                       + + dvi+ +Gg ++++++ ++vP 
  gi|242397998|ref|YP_002993422.1|  90 KIKPDVIVGGGGYGAIISEILNVPN 114
                                       3689*******************95 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.038
                            PrpR_N   5 ldievvegdleeavelakeleaegvdviiS 34 
                                        d+ ++  ++e+ + l+k+le+ g++ +iS
  gi|242397998|ref|YP_002993422.1| 204 HDVNLYGLSYEDKIYLIKKLEKLGIKFFIS 233
                                       58899999*********************9 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 1
                            PrpR_N 127 gvvadlAekaGlksvlltsg 146
                                       g++++ A+ +G+++v++ s+
  gi|242397998|ref|YP_002993422.1| 269 GTMVTEAAVLGVPAVMINSS 288
                                       46677888899999999996 PP

>> Epimerase_2  UDP-N-acetylglucosamine 2-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   7.3e-05      0.26     251     294 ..     252     294 ..     245     299 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 7.3e-05
                                       HHHHHHHHC-SEEEES-HHHHHHHHHCT--EEESSSS-S-THHH CS
                       Epimerase_2 251 ldflsllknaklvltdSgGiqeEapslgvpvvnlReeteRpegv 294
                                        +++ ++  + +++ d g++  Ea++lgvp+v + ++  +  gv
  gi|242397998|ref|YP_002993422.1| 252 HRIHDVIYYSSMLVADTGTMVTEAAVLGVPAVMI-NSSAWKVGV 294
                                       6677788899********9999************.777777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); 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: 0.63u 0.38s 00:00:01.01 Elapsed: 00:00:00.55
# Mc/sec: 2064.00
//
Query:       gi|242397999|ref|YP_002993423.1|  [L=180]
Description: Glycosyltransferase, partial [Thermococcus sibiricus MM 739]
Scores for complete 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   58.1   0.0      1e-15   57.7   0.0    1.2  1  Glycos_transf_1  Glycosyl transferases group 1
    1.8e-10   41.4   0.0    2.3e-10   41.0   0.0    1.1  1  Glyco_trans_1_4  Glycosyl transferases group 1
    2.9e-08   34.0   0.0    5.7e-08   33.0   0.0    1.5  2  Glyco_trans_1_2  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.7   0.0   1.7e-19     1e-15      26     171 ..       3     151 ..       1     152 [. 0.92

  Alignments for each domain:
  == domain 1  score: 57.7 bits;  conditional E-value: 1.7e-19
                                       TTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHHHCESEEEEEESS CS
                   Glycos_transf_1  26 keKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleellknadifvlpsis 102
                                       + ++++++i a+++lk++ n  +k++ia +g+ +++l+kla+e  l d vif+g ++r++ +e+++ + + +++   
  gi|242397999|ref|YP_002993423.1|   3 HAQDLKNVILAIEQLKER-NIGIKFLIARDGDVREYLEKLAKEKCLTDVVIFTGLLPRDRTPEIMSESLVGIANLKE 78 
                                       66899**********998.************************************************8888887777 PP

                                       .....BSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHHHHHHHHHHH CS
                   Glycos_transf_1 103 .....EgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeelrerlgenark 171
                                             ++++ ++E+ ++ lpv  s ++ ++  +k+ + G++v +n ++ +a++i  l e+++ r+++g+++r+
  gi|242397999|ref|YP_002993423.1|  79 lesleYAMPTKAYEYASCELPVMGSGSKELLAFIKESKGGIFVSTN-PHGIADEILFLFENPKIRVKMGKRGRR 151
                                       7777589*******************************66666655.************************996 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 !   41.0   0.0   3.8e-14   2.3e-10      16     134 .]       6     138 ..       1     138 [. 0.83

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 3.8e-14
                                       THHHHHHHHHHHH.HH..EEEEEES---...HHHHHHHT..T-T.TEEEE---..THHHHHHHH-SEEEE--...-. CS
                   Glyco_trans_1_4  16 gvdllleavpllrkkd..vrlvivGdgp.rpeeleelaa..gleerveftGfv..edlaellaaadvfvaPs...e. 81 
                                        ++ ++ a+++l++++  ++++i+ dg+ r+  le+la+   l++ v+ftG +  +  +e+++++ v +a +   e 
  gi|242397999|ref|YP_002993423.1|   6 DLKNVILAIEQLKERNigIKFLIARDGDvRE-YLEKLAKekCLTDVVIFTGLLprDRTPEIMSESLVGIANLkelEs 81 
                                       567788899999999778**********775.99988866567788*****998555**************997635 PP

                                       ...--SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHHHH- CS
                   Glyco_trans_1_4  82 ...gfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailrLled 134
                                           ++ k++E+++++lpv  +  + + +++   + g+ v+  +p+ +a++il L+e+
  gi|242397999|ref|YP_002993423.1|  82 leyAMPTKAYEYASCELPVMGSGSKELLAFIkeSKGGIFVS-TNPHGIADEILFLFEN 138
                                       5588******************8877666677446678885.68*********99876 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       1.7     1e+04      58      67 ..      26      35 ..      10      48 .. 0.55
   2 !   33.0   0.0   9.6e-12   5.7e-08      11      87 ..      86     163 ..      67     168 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.7
                   Glyco_trans_1_2 58 yllanpeerr 67
                                      +l+a +++ r
  gi|242397999|ref|YP_002993423.1| 26 FLIARDGDVR 35
                                      3333333322 PP

  == domain 2  score: 33.0 bits;  conditional E-value: 9.6e-12
                   Glyco_trans_1_2  11 pnlrlfEaaacGafaltddaegleelftpgkevilfe.dleelaekiryllanpeerraiaeaarervlaehtydhr 86 
                                       + ++ +E+a c  +++ + +++l  ++++ k +i+++ +++ +a+ i +l +np+ r ++++++r++v+++++ +  
  gi|242397999|ref|YP_002993423.1|  86 MPTKAYEYASCELPVMGSGSKELLAFIKESKGGIFVStNPHGIADEILFLFENPKIRVKMGKRGRRFVKRHYDRKEI 162
                                       45699****************************************************************99976655 PP

                   Glyco_trans_1_2  87 a 87 
                                       a
  gi|242397999|ref|YP_002993423.1| 163 A 163
                                       5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); 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:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.51
# Mc/sec: 1056.27
//
Query:       gi|242398000|ref|YP_002993424.1|  [L=72]
Description: Capsular polysaccharide biosynthesis protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       293  (0.0163422); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 537.71
//
Query:       gi|242398001|ref|YP_002993425.1|  [L=332]
Description: probable glycosyltransferase [Thermococcus sibiricus MM 739]
Scores for complete 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   0.0    2.3e-35  121.9   0.0    1.3  1  Glycos_transf_2  Glycosyl transferase family 2
      1e-23   84.5   0.0    1.5e-23   83.9   0.0    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    1.5e-10   41.0   0.0    1.8e-09   37.5   0.0    2.1  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
    2.7e-08   33.5   0.0    4.3e-08   32.8   0.0    1.2  1  Glyco_transf_21  Glycosyl transferase family 21
    2.9e-05   24.1   0.0    4.5e-05   23.5   0.0    1.3  1  Glyco_trans_2_3  Glycosyl transferase family group 2
    6.5e-05   23.4   0.0    0.00015   22.2   0.0    1.6  1  Glyco_tranf_2_4  Glycosyl transferase family 2
    8.8e-05   22.1   0.1    0.00019   21.0   0.1    1.5  1  Glyco_transf_7C  N-terminal domain of galactosyltransferase
  ------ inclusion threshold ------
       0.17   11.3   0.3       0.23   10.9   0.3    1.3  1  GlcNAc           Glycosyltransferase (GlcNAc)


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 !  121.9   0.0     1e-38   2.3e-35       1     164 [.       8     169 ..       8     174 .. 0.98

  Alignments for each domain:
  == domain 1  score: 121.9 bits;  conditional E-value: 1e-38
                                       EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglra 77 
                                       sv+++tyN ek+++++l+s+l++     +e+ivvD+gStD+t+e++e+    +p+v++i++++n G++g+ n g+r+
  gi|242398001|ref|YP_002993425.1|   8 SVIVVTYNHEKYIRACLTSVLDN---NPLEVIVVDNGSTDGTAELVEKE---FPQVKLIKNPRNLGYGGGNNLGVRH 78 
                                       8**********************...***********************...69*********************** PP

                                       --SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SS....EEEECCHCCCCHCCCCCC CS
                   Glycos_transf_2  78 atgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrv....generlyfkerkrslkgn 150
                                       a+g+y+++l+ D+ ++++wle+l+++lek+++ +  +++  ++g++ +   n ++    ++   l++  rk+ ++  
  gi|242398001|ref|YP_002993425.1|  79 ARGEYVVILNPDTKVEKGWLEELLKPLEKEQKLITTPKILTYDGSKINTCGNIEHftglTFVRGLNGDPRKFDEFEY 155
                                       ****************************************************999********************** PP

                                       STTCSTCCCEEEEH CS
                   Glycos_transf_2 151 lsfeigsaallrre 164
                                       ls+ +g ++++rr+
  gi|242398001|ref|YP_002993425.1| 156 LSGLSGACFAMRRS 169
                                       ************97 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.9   0.0   6.5e-27   1.5e-23       5     212 ..       8     212 ..       5     232 .. 0.85

  Alignments for each domain:
  == domain 1  score: 83.9 bits;  conditional E-value: 6.5e-27
                   Glyco_tranf_2_3   5 avlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralne 81 
                                       +v+V+t+n e++++++l+s+l   + ++ev+vv+++s+++t+e +e    ++p+v  +++ n+rnlg  g  +  n 
  gi|242398001|ref|YP_002993425.1|   8 SVIVVTYNHEKYIRACLTSVLD--NNPLEVIVVDNGSTDGTAELVEK---EFPQV--KLIKNPRNLGY-GGGN--NL 74 
                                       8*********************..89*****************9976...9*996..9*******995.4445..79 PP

                   Glyco_tranf_2_3  82 alravksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfllnrstlvsalgalefaerhlrflaar...... 152
                                       ++r++++++v++++ Dt ve++ l+ ll  +  ++ + ++tp+ l ++ + ++  g++e   +++   ++r      
  gi|242398001|ref|YP_002993425.1|  75 GVRHARGEYVVILNPDTKVEKGWLEELLKPL-EKEQKLITTPKILTYDGSKINTCGNIE---HFTGLTFVRglngdp 147
                                       ******************************9.9999*******8888887777777764...333333333444557 PP

                   Glyco_tranf_2_3 153 ...ralg.vltlnGsgslirrevlkelegldp.lflltdDyelglrlrragfrtayvpgaavrev 212
                                          +++     l+G+++++rr+ + el+g+d+  f+  +D+el+ r+ + gf++ yvp ++v++ 
  gi|242398001|ref|YP_002993425.1| 148 rkfDEFEyLSGLSGACFAMRRSEYFELGGFDEnFFSYMEDAELSWRAHAKGFKILYVPTSIVYHD 212
                                       7676666468999*******************888999************************996 PP

>> Glyco_tranf_2_2  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.5   0.0   8.1e-13   1.8e-09       1     218 [.       8     213 ..       8     220 .. 0.73

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 8.1e-13
                   Glyco_tranf_2_2   1 svviplraseerhyieervlqkakyyd.eeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarNrG 76 
                                       sv++  +++e+   i+  +       d + +e+ivvd+gS++ ++e v++   + +l+   +   +  + +   N+G
  gi|242398001|ref|YP_002993425.1|   8 SVIVVTYNHEKY--IRACLTS---VLDnNPLEVIVVDNGSTDGTAELVEKEFPQVKLIK--NP--RNLGYGGGNNLG 75 
                                       577777777764..7766644...3440557***************9976544444444..22..346788889*** PP

                   Glyco_tranf_2_2  77 askaesdlvlFlDaDcfissDkfekilklitikklrenidaavvlpvvdlnkedsevlkdvedltassrvledllaa 153
                                       + +a +++v+ l+ D  +    +e +lk     k ++ i ++ +l++     +    + +   lt    +  d   +
  gi|242398001|ref|YP_002993425.1|  76 VRHARGEYVVILNPDTKVEKGWLEELLK--PLEKEQKLITTPKILTYDGSKINTCGNIEHFTGLTFVRGLNGDPRKF 150
                                       ****************************..77777888888877765544444444444444444444444444442 PP

                   Glyco_tranf_2_2 154 kstlvkffapss.ssilinrraflevGGyDErfrGhgaEDfdlllRlakaikslekmpvellykar 218
                                            +++   s   + ++r  + e+GG+DE+f     ED +l  R  ++  ++   p+ + y++ 
  gi|242398001|ref|YP_002993425.1| 151 D--EFEYLSGLSgACFAMRRSEYFELGGFDENF-FSYMEDAELSWRAHAKGFKILYVPTSIVYHDY 213
                                       2..2345666555999*****************.5678********988877777999**999875 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 !   32.8   0.0   1.9e-11   4.3e-08      25     151 ..      75     209 ..      70     221 .. 0.79

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 1.9e-11
                   Glyco_transf_21  25 aleaakydllvisDsdvrvkpdyLeellaaledpkvglVtslpv.gsdak..glaaaleaaflntlagvlqa..... 93 
                                       +++ a+ +++vi+  d+ v++  Leell++le+ + +l+t + + ++d +  + ++++e     t+ + l       
  gi|242398001|ref|YP_002993425.1|  75 GVRHARGEYVVILNPDTKVEKGWLEELLKPLEK-EQKLITTPKIlTYDGSkiNTCGNIEHFTGLTFVRGLNGdprkf 150
                                       67889***************************6.9******988455555223445555544434433333334422 PP

                   Glyco_transf_21  94 .klsglgfavGksmalrreaLeaiGGfealadeLAeDyalgkllraaGlkvvlspapia 151
                                        +++ l+   G++ a+rr+   ++GGf +      eD++l+++ +a+G+k+  +p+ i+
  gi|242398001|ref|YP_002993425.1| 151 dEFEYLSGLSGACFAMRRSEYFELGGFDENFFSYMEDAELSWRAHAKGFKILYVPTSIV 209
                                       3367888899*****************99999999****************99999877 PP

>> Glyco_trans_2_3  Glycosyl transferase family group 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0     2e-08   4.5e-05       1     130 [.      83     217 ..      83     266 .. 0.70

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 2e-08
                   Glyco_trans_2_3   1 iilllDaDtvlppdclreiaaelaspevaivqgp.vl.vm....nvanwleelaalffaedhgkdilvrealgrvvp 71 
                                       ++++l  Dt +    l+e++  l+  e +++++p +l ++    n    +e++  l+f +  + d + ++ +     
  gi|242398001|ref|YP_002993425.1|  83 YVVILNPDTKVEKGWLEELLKPLEK-EQKLITTPkILtYDgskiNTCGNIEHFTGLTFVRGLNGDPRKFDEFEYLSG 158
                                       5777777777777777777777775.556666663332334444444555555555566556666555666666666 PP

                   Glyco_trans_2_3  72 svGsgaflrrsalqevggwdgdessvsEDfdmglrlqrkGyrvrfvpeslvkekspltl 130
                                       + G++++ rrs   e+gg+d +++s  ED +++ r+ +kG+++ +vp s+v+   +l +
  gi|242398001|ref|YP_002993425.1| 159 LSGACFAMRRSEYFELGGFDENFFSYMEDAELSWRAHAKGFKILYVPTSIVYHDYELKV 217
                                       889********999***********************************9988776654 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   6.6e-08   0.00015       1      52 [.      14      66 ..      14     101 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 6.6e-08
                   Glyco_tranf_2_4  1 rneadiLpeflahhlalgfdrilvydndstDgtrailkel.pevkllhvdksy 52
                                      +n ++++ ++l+  l++   +++v+dn+stDgt++++++  p+vkl++++ + 
  gi|242398001|ref|YP_002993425.1| 14 YNHEKYIRACLTSVLDNNPLEVIVVDNGSTDGTAELVEKEfPQVKLIKNPRNL 66
                                      58999**********999999****************7755*****9998654 PP

>> Glyco_transf_7C  N-terminal domain of galactosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.1   8.5e-08   0.00019      17      75 ..     157     213 ..     147     217 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 8.5e-08
                   Glyco_transf_7C  17 ekyfgGvlalrkedfekiNGfsntfwgWGgEDdelyaRlakkgleierpekgtgryhml 75 
                                       +++ g  +a+r++++ +++Gf+++f+ +  ED el  R  +kg++i  ++ ++  yh +
  gi|242398001|ref|YP_002993425.1| 157 SGLSGACFAMRRSEYFELGGFDENFFSY-MEDAELSWRAHAKGFKILYVPTSIV-YHDY 213
                                       5788999*********************.9****************99888776.6766 PP

>> GlcNAc  Glycosyltransferase (GlcNAc)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.3    0.0001      0.23     216     283 ..     159     225 ..      80     255 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0001
                            GlcNAc 216 fvaagFlfadaefvrdvpfD.phlpylfdGEevlysvRlwtaGydlysParavvfhiYsRne.apkvwse 283
                                          a F++ ++e +    fD  +++y+   E+  +s R +++G+++    +++v+h Y+ +  ++k+++ 
  gi|242398001|ref|YP_002993425.1| 159 LSGACFAMRRSEYFELGGFDeNFFSYM---EDAELSWRAHAKGFKILYVPTSIVYHDYELKVpSKKIYHL 225
                                       566889999999999999994588888...66779**********8777789******954314455555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); 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: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2402.27
//
Query:       gi|242398002|ref|YP_002993426.1|  [L=290]
Description: Glycosyl transferase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-26   92.3   0.0    3.8e-26   91.9   0.0    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
    0.00084   19.8   0.0     0.0013   19.2   0.0    1.2  1  Glyco_tranf_2_4  Glycosyl transferase family 2
    0.00093   19.2   0.0     0.0013   18.7   0.0    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
  ------ inclusion threshold ------
      0.029   13.8   0.0      0.044   13.3   0.0    1.3  1  Glyco_transf_21  Glycosyl transferase family 21


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.9   0.0   8.5e-30   3.8e-26       2     123 ..       5     119 ..       4     161 .. 0.92

  Alignments for each domain:
  == domain 1  score: 91.9 bits;  conditional E-value: 8.5e-30
                                       EEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH- CS
                   Glycos_transf_2   2 vviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraa 78 
                                       +vip+yNee t+  +++ l++       +++vvDDgS D+t ei++e+     +  vir+e n+Gk+ al++g+++a
  gi|242398002|ref|YP_002993426.1|   5 IVIPAYNEELTIGSVVA-LAKK----FGDVLVVDDGSFDRTSEIAREA-----GAVVIRHEVNKGKGQALRTGFEYA 71 
                                       8****************.5555....69********************.....9*********************** PP

                                       -SS...EEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCC CS
                   Glycos_transf_2  79 tgd...yilflDaDdepdpdwleklvealekdgadvvlgqrprifget 123
                                        ++   ++++lDaD +++pd ++ l+e++ k+ ad+v+g+r+ +++++
  gi|242398002|ref|YP_002993426.1|  72 LSKeydVVVTLDADGQHNPDEIPLLLEPIVKGKADLVIGSRYLNGSKK 119
                                       *****************************************9887665 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   2.9e-07    0.0013       1      81 [.      10      85 ..      10      91 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 2.9e-07
                   Glyco_tranf_2_4  1 rneadiLpeflahhlalgfdrilvydndstDgtrailkelpevkllhvdksyederrqvellkallaryaeadwvlvvD 79
                                      +ne+ ++++++a ++++   ++lv+d++s D+t++i +e  +v + h +++ ++++       al ++y   d v+++D
  gi|242398002|ref|YP_002993426.1| 10 YNEELTIGSVVALAKKF--GDVLVVDDGSFDRTSEIAREAGAVVIRHEVNKGKGQALRTGFEYALSKEY---DVVVTLD 83
                                      699999*****999988..78*********************999999999988888877888888777...9999999 PP

                   Glyco_tranf_2_4 80 aD 81
                                      aD
  gi|242398002|ref|YP_002993426.1| 84 AD 85
                                      98 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   2.9e-07    0.0013       5     122 ..       4     110 ..       2     132 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.9e-07
                   Glyco_tranf_2_3   5 avlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralne 81 
                                       ++++p++nee ++g+v++ +        +v vv+d+s + t e a+e+       + +v++ +     +gk +al  
  gi|242398002|ref|YP_002993426.1|   4 LIVIPAYNEELTIGSVVALA----KKFGDVLVVDDGSFDRTSEIAREA-------GAVVIRHE--VN-KGKGQALRT 66 
                                       799******77777776533....3457899999***********993.......44555333..33.69******* PP

                   Glyco_tranf_2_3  82 alravk...sdlvllvDdDtvvePdtlkrllqffltpkvgavgt 122
                                       +++ +    +d+v+ +D+D    Pd ++ ll  +   k++ v +
  gi|242398002|ref|YP_002993426.1|  67 GFEYALskeYDVVVTLDADGQHNPDEIPLLLEPIVKGKADLVIG 110
                                       ***65446799******************999884445666655 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 ?   13.3   0.0   9.8e-06     0.044      26      73 ..      68     118 ..      50     154 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.8e-06
                   Glyco_transf_21  26 lea...akydllvisDsdvrvkpdyLeellaaledpkvglVtslpvgsdak 73 
                                       +e+    +yd++v++D+d   +pd +  ll+++ + k+ lV +  +  + k
  gi|242398002|ref|YP_002993426.1|  68 FEYalsKEYDVVVTLDADGQHNPDEIPLLLEPIVKGKADLVIGSRYLNGSK 118
                                       55545579*********************************9987755544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.51
# Mc/sec: 1701.39
//
Query:       gi|242398003|ref|YP_002993427.1|  [L=765]
Description: Oligosaccharyl transferase, STT3 subunit [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-15   55.6  25.0    1.1e-14   54.3  25.0    1.7  1  STT3      Oligosaccharyl transferase STT3 subunit
    3.3e-06   27.4  18.8    3.3e-06   27.4  18.8    3.7  3  PMT_2     Dolichyl-phosphate-mannose-protein mannosyltransfer


Domain annotation for each model (and alignments):
>> STT3  Oligosaccharyl transferase STT3 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.3  25.0   1.2e-18   1.1e-14      29     481 ..      32     507 ..      29     513 .. 0.71

  Alignments for each domain:
  == domain 1  score: 54.3 bits;  conditional E-value: 1.2e-18
                                       S--SSCHHHHHHHCCCHHHT-C.....CCHHSSEETTSSTTT-EEEST.TCCHCCC.CHHHHHHCCHHC...HHHHH CS
                              STT3  29 ylsefDpYYnyRltenllnnGfpGdvvikkknwfdhsqyyPpGsrvdy.gplivlLamlasaiinhsld...vsire 101
                                       y++  DpY+ +  +e  l+ G      +     f+  +  P G+ ++   pl +++   + a+++ +l+   vs+ +
  gi|242398003|ref|YP_002993427.1|  32 YILGYDPYFHLAYIEEALKAGD----WF----NFLTIAGGPWGRQINNaHPLGLWM---TPAYVYKVLKvfgVSLYN 97 
                                       5666666666666666666654....22....233333356775554313444455...5555555555555***** PP

                                       HHHCCHHHHHHHHCHHHHHHHHHHS-CCCHHHHHHHCCC-CCCCCTTSTT--STCCCCHHHHHHHHHHHHHHHHCCS CS
                              STT3 102 vclwlpallgsLlaIpiyflvrelksdiaGllAAlllaiaPgYlsrtvaGfyDtdmfeivlllfvlffflkaiktks 178
                                       +  + p ++g L+++  y+ + +l ++  +++A l+lai+ g + r++a +y  d   +++  ++l     ai  k+
  gi|242398003|ref|YP_002993427.1|  98 AFRITPVIFGVLTVVFLYLALLKLYDEKKAFFASLFLAISFGHVFRSMANYYRGDNYMLFWYSVALLGVALAISMKD 174
                                       *999999************99999999*************************9999999999999999999998888 PP

                                       ....TTCHHHHHHHHHHHHHHTTSCCGG.HHHHCCHHHHHHHHHCTTTS-CCHHHHH....HHHHHHHHHH..CCCC CS
                              STT3 179 ....nkislaviaaliiflivlaWggya.iliyallllfilalLiigrfelklkiav....tfsviiaflviaiivl 246
                                            + +l ++ a++    ++ W +y  i ++ ll+  +++ + +    +k +++      +s+++++++  ++  
  gi|242398003|ref|YP_002993427.1| 175 klgnLRFALYLVPAFASGFASIFWQAYYpI-FIFLLANAVFLAVGAFILDKKENLLDalalVLSTVLGAFMANSLGG 250
                                       8887788999999*************9742.3333333333333333334444444400124444444444455544 PP

                                       CCCTTCHHH......STTTCH..HCCCCHHHH.HHHHCCCHHC..CCCCCHHCCCHHTT.HHHHTT--GGGHHHHHH CS
                              STT3 247 lflgfqvva......vseiig..algifgllq.lvafgsvvvlvaelkfyqfislfqpgilsevlgligevvtalav 314
                                        f              +++++  +++ fg++   +++++v  l   l+   +i +f  g + +  +    v+  lav
  gi|242398003|ref|YP_002993427.1| 251 KFGY----GmlgydqLGKRVAekLMLEFGTIKdAYLLVHVKYL-VPLGLAFIILIFILGKFIKDRKARAGVLIGLAV 322
                                       4432....11222343333321122233444313333443333.456666666666655455555554666777777 PP

                                       HHHHHHCCCCCCTS-----TTHHHHHHHHHS---S--CCHHHCCSSSTTTTCCCHH.HCHHCCHHCTCHHHHHHHHH CS
                              STT3 315 lglialwlgilyslldleyaklkikiiilvsvwlpvgllaltkglrfliftvPlgi.ifvgllleflavfvkiysvs 390
                                       lg+  l+    ++ l+     + i i + +++ +p +++ l k   + +f++Pl +  f    +++   ++ + +  
  gi|242398003|ref|YP_002993427.1| 323 LGVFVLFH--RFEALKELSTGFGIFIEAPIQETQPSSFSDLWKAFSISLFLAPLFFlRFDPNRVNMSDFLILGLIFP 397
                                       77776665..4455555678899********************************9888888999999999999999 PP

                                       HHHHCCC-SCHCCCCCHHHHHHHCCCHHHHHHHHCCHHHHHHHHHHHHHH......................HHHHC CS
                              STT3 391 qilfsgvvvillmltllpvlallaavkiskifstykdekeakikvaakav......................aptks 445
                                       +i++ ++  +  ++  ++++al+a++ + ++++t +     k+++   ++                       p  +
  gi|242398003|ref|YP_002993427.1| 398 SIYMIKTWTR-FLFIGSAAIALMAGIGVVELYETLNRLDGRKVSA---VGigllvllpmvnggfsiketyslRPYAN 470
                                       **********.888889******************9986666665...123566777788899999999999***** PP

                                       T.TTTTHHH.TTHHHCHHHHHHHHHHHHHHHHHHHHH CS
                              STT3 446 nglkeslew.kantnrdsvvitwwdyghilaveadrp 481
                                       ++++e+l w ++n+n+++vv twwdygh+++++a+r 
  gi|242398003|ref|YP_002993427.1| 471 EHWEEALTWlRENSNQNDVVLTWWDYGHFVTYYARRS 507
                                       **********************************995 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 !   27.4  18.8   3.7e-10   3.3e-06      13     153 ..      87     239 ..      73     244 .. 0.83
   2 !    3.4   0.9    0.0088        79      77     153 ..     291     323 ..     280     341 .. 0.57
   3 !    3.5   0.1    0.0086        78      29      66 ..     417     454 ..     408     463 .. 0.88

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 3.7e-10
                             PMT_2  13 ftklfgf.selairlvsalagvltilllyllarrlfgkraallaalllavvplfvalsa..lftpdaplvllwalal 86 
                                       ++k+fg     a+r+ ++++gvlt+++lyl + +l++++ a++a+l+la+++  v+ s    ++ d+ +++ ++ al
  gi|242398003|ref|YP_002993427.1|  87 VLKVFGVsLYNAFRITPVIFGVLTVVFLYLALLKLYDEKKAFFASLFLAISFGHVFRSManYYRGDNYMLFWYSVAL 163
                                       7899999566799*************************************998777776535566************ PP

                             PMT_2  87 ylllrale.knklkyw...llagvlfGlgflsKytaallliaall...yllis.arrilkekkpyl.alllalllf 153
                                       + ++ a+  k+kl  +   l++ ++f+ gf s +++a+++i ++l   ++++  +  il +k  +l al+l+l  +
  gi|242398003|ref|YP_002993427.1| 164 LGVALAISmKDKLGNLrfaLYLVPAFASGFASIFWQAYYPIFIFLlanAVFLAvGAFILDKKENLLdALALVLSTV 239
                                       *******98666666666699*******************954446764444466779999999999999998766 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.0088
                             PMT_2  77 plvllwalalylllraleknklkywllagvlfGlgflsKytaallliaallyllisarrilkekkpylalllalllf 153
                                       pl l+ ++++++l +                                             +k++k+ +++l++l++ 
  gi|242398003|ref|YP_002993427.1| 291 PLGLAFIILIFILGK--------------------------------------------FIKDRKARAGVLIGLAVL 323
                                       333444444444444............................................555555555555555443 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.0086
                             PMT_2  29 alagvltilllyllarrlfgkraallaalllavvplfv 66 
                                       al++ ++++ ly ++ rl g++++++++ ll ++p+++
  gi|242398003|ref|YP_002993427.1| 417 ALMAGIGVVELYETLNRLDGRKVSAVGIGLLVLLPMVN 454
                                       788999999***********************999654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (765 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       776  (0.0432818); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.74u 0.34s 00:00:01.08 Elapsed: 00:00:00.58
# Mc/sec: 3941.00
//
Query:       gi|242398004|ref|YP_002993428.1|  [L=178]
Description: hypothetical protein TSIB_0008 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1150.93
//
Query:       gi|242398005|ref|YP_002993429.1|  [L=432]
Description: DUF58 domain containing protein [Thermococcus sibiricus MM 739]
Scores for complete 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-19   68.2   0.1    1.2e-18   67.1   0.1    1.6  1  DUF58     Protein of unknown function DUF58


Domain annotation for each model (and alignments):
>> DUF58  Protein of unknown function DUF58
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.1   0.1   6.8e-23   1.2e-18       1      80 [.     182     260 ..     182     265 .. 0.91

  Alignments for each domain:
  == domain 1  score: 67.1 bits;  conditional E-value: 6.8e-23
                             DUF58   1 gldfaglReYvpgDplrrIdWkatARtgelyvrefeaerartvllvldlspemslgstgdekletavsaaaslarql 77 
                                       g+++++lReY+ gD+++rIdWka+ R+gel++re+ +e++++v++++d+++em++g +   k+++a ++a+ la++l
  gi|242398005|ref|YP_002993429.1| 182 GVEIKDLREYRHGDDFKRIDWKASVRLGELIIREMLKESDADVYIFVDNTNEMRKGIKM-AKVDYASTLALQLAATL 257
                                       57899*************************************************99975.99999999999999988 PP

                             DUF58  78 lde 80 
                                       +++
  gi|242398005|ref|YP_002993429.1| 258 IKS 260
                                       874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (432 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 3171.48
//
Query:       gi|242398006|ref|YP_002993430.1|  [L=309]
Description: Methanol dehydrogenase regulator [Thermococcus sibiricus MM 739]
Scores for complete 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-62  209.4   0.0    2.1e-62  208.7   0.0    1.3  1  AAA_3            ATPase family associated with various cellul
    3.6e-21   74.8   0.1    6.8e-21   73.9   0.1    1.5  1  AAA_lid_2        AAA lid domain
    5.7e-16   58.8   0.0    1.4e-15   57.5   0.0    1.7  2  AAA_5            AAA domain (dynein-related subfamily)
    1.8e-08   33.8   0.0    4.6e-08   32.4   0.0    1.6  1  MCM              MCM P-loop domain
    1.6e-06   27.7   0.2      0.013   14.9   0.1    2.5  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    3.2e-06   27.6   0.0    9.4e-06   26.1   0.0    1.8  2  AAA              ATPase family associated with various cellul
    1.3e-05   25.0   0.2    0.00024   20.8   0.2    2.3  1  Sigma54_activat  Sigma-54 interaction domain
    0.00012   21.9   0.1    0.00094   19.0   0.1    2.1  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
  ------ inclusion threshold ------
      0.026   14.9   0.0        0.1   12.9   0.0    1.8  1  AAA_16           AAA ATPase domain
      0.058   13.3   0.0       0.12   12.2   0.0    1.5  1  AAA_lid_8        AAA lid domain


Domain annotation for each model (and alignments):
>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  208.7   0.0   1.2e-65   2.1e-62       1     131 []      37     167 ..      37     167 .. 1.00

  Alignments for each domain:
  == domain 1  score: 208.7 bits;  conditional E-value: 1.2e-65
                             AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvfanllladeinrappk 77 
                                       hvl+eg+PG+akt+++ka+++a++l+f+riq+tpdllP+di+G+ ++++k+ e+++k+Gp+fan++lade+nra+pk
  gi|242398006|ref|YP_002993430.1|  37 HVLIEGIPGVAKTTIAKAFSNAIGLKFSRIQLTPDLLPADIIGIFYYDQKTGEWTIKHGPIFANVILADEVNRAQPK 113
                                       9**************************************************************************** PP

                             AAA_3  78 tqsalleameerqvtvegethklpepflvlatqnPieqeGtyplpeaqldrfll 131
                                       tqsalleam+e+qvt+eg thklpepflv+at nP+e+eG+y lpeaqldrf+l
  gi|242398006|ref|YP_002993430.1| 114 TQSALLEAMQEKQVTIEGVTHKLPEPFLVIATMNPLEHEGVYILPEAQLDRFML 167
                                       ****************************************************97 PP

>> AAA_lid_2  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.9   0.1   3.8e-24   6.8e-21       2      72 ..     229     300 ..     228     301 .. 0.97

  Alignments for each domain:
  == domain 1  score: 73.9 bits;  conditional E-value: 3.8e-24
                         AAA_lid_2   2 atrahlaielgvsgrRadlallraArAlAalegrdyVtpeDvkeaaplVLaHRlr..repeaegetteeivee 72 
                                       +tr+++++ +g+s+r a  +ll aA+A A+l+grdyV+p+Dvk++ap VLaHRl    e e eg+tt+ei++e
  gi|242398006|ref|YP_002993430.1| 229 KTRSDERLLFGASPR-AGEHLLYAAKASAFLDGRDYVIPDDVKKVAPAVLAHRLLlkAEYELEGVTTKEIIRE 300
                                       6999***********.***************************************9999************98 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.5   0.0   7.8e-19   1.4e-15       1     138 []      37     165 ..      37     165 .. 0.86
   2 ?   -3.2   0.0       4.4   7.9e+03      69      83 ..     264     278 ..     244     290 .. 0.70

  Alignments for each domain:
  == domain 1  score: 57.5 bits;  conditional E-value: 7.8e-19
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--...........--------G-SEEEEESGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslv..dsplvraaregeilvlDEve 75 
                                       +vl+ G pG++K+++a+ ++ a++ ++  +qlt d+ ++d++g   ++++t +++   +p+      + +++ DEv+
  gi|242398006|ref|YP_002993430.1|  37 HVLIEGIPGVAKTTIAKAFSNAIGLKFSRIQLTPDLLPADIIGIFYYDQKTGEWTikHGPIF-----ANVILADEVN 108
                                       79*********************************************977777752267777.....99******** PP

                                       G--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--..-TT-TTHHHHTT- CS
                             AAA_5  76 raesevlnsLlslleerrllleeggelvkaknddllerfrviatanpld.rslnelspalrsRf 138
                                       ra+++++++Ll  + e+++   eg +    ++      f viat+npl+  ++  l +a ++Rf
  gi|242398006|ref|YP_002993430.1| 109 RAQPKTQSALLEAMQEKQVT-IEGVTHKLPEP------FLVIATMNPLEhEGVYILPEAQLDRF 165
                                       ********************.55555555666......***********555555566666666 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 4.4
                                       EEEESGGG--HHHHH CS
                             AAA_5  69 lvlDEveraesevln 83 
                                       ++ D+v+++ ++vl+
  gi|242398006|ref|YP_002993430.1| 264 VIPDDVKKVAPAVLA 278
                                       444778888777765 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.0   2.6e-11   4.6e-08      36     174 ..      14     149 ..       2     156 .. 0.80

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 2.6e-11
                                       HHHHHH---EBBBSSSSBBCSS-EEEEEESSTSTHHHHHHHHHHHS..SSEEEEESSSSSSSHSSSEEEEESSSSSE CS
                               MCM  36 illqlfggvkkkledktklrgdinvllvgdpgtaKsqlLkyvekla..pravytsgkgssaagLtaavvrdeetgef 110
                                       i  +++g  +  +   + l ++ +vl+ g pg+aK+++ k+ ++ +  + +          a++      d++tge+
  gi|242398006|ref|YP_002993430.1|  14 ISKAVVGKEDVIELLTIALLSEGHVLIEGIPGVAKTTIAKAFSNAIglKFSRIQLTPDLLPADIIGIFYYDQKTGEW 90 
                                       55555555554444556678899******************99665112333344444556888888999******* PP

                                       EEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEESSSCEEEEE--EEEEEEE--S CS
                               MCM 111 vleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisiaKaGivatLnartsvlaAanpk 174
                                       +++ G +      v++ De+++ + +++sal+Eam +++++i   G++ +L+    v+a +np 
  gi|242398006|ref|YP_002993430.1|  91 TIKHGPIFAN---VILADEVNRAQPKTQSALLEAMQEKQVTIE--GVTHKLPEPFLVIATMNPL 149
                                       *****98764...9****************************7..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 !   14.9   0.1     7e-06     0.013       4      43 ..      17      56 ..      15      64 .. 0.93
   2 !   10.3   0.0   0.00019      0.34     109     159 ..     101     149 ..      77     171 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 7e-06
                      Mg_chelatase  4 dvkGqeeakraleiaaaGgHnlllvGppGsGKtmlakrlp 43
                                       v+G+e+  + l+ia   + ++l+ G pG  Kt +ak+++
  gi|242398006|ref|YP_002993430.1| 17 AVVGKEDVIELLTIALLSEGHVLIEGIPGVAKTTIAKAFS 56
                                      799*********************************9986 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00019
                      Mg_chelatase 109 vLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpc 159
                                       v++ DE+   + k+  +L e +++++vti+  ++k   p  f ++a+mNp 
  gi|242398006|ref|YP_002993430.1| 101 VILADEVNRAQPKTQSALLEAMQEKQVTIEGVTHK--LPEPFLVIATMNPL 149
                                       7889*************************998876..5888********95 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0   5.3e-09   9.4e-06       1     130 [.      38     171 ..      38     173 .. 0.79
   2 ?   -3.1   0.0       5.3   9.5e+03      38      51 ..     237     250 ..     205     275 .. 0.56

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 5.3e-09
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEET.TTCSSSSTTHHHHHHHHHHHHHHHTS.........TSEEEEEETG CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisg.sellskyvgesekkirelfkeakeka.........kpsilfiDEi 67 
                                       vl+ G pG+ KT++aka  + +g +f +i++ ++ll       +++i ++f   ++              +++ DE+
  gi|242398006|ref|YP_002993430.1|  38 VLIEGIPGVAKTTIAKAFSNAIGLKFSRIQLtPDLL-------PADIIGIFYYDQKTGewtikhgpiFANVILADEV 107
                                       6899*************************9825666.......666666665533333566666555449******* PP

                                       GGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS........SSTEEEEEEESS.....GGGSTHHHHSTTSSEEEET CS
                               AAA  68 dalaksrsgseseeeervvnqLlteldgvkkk........eskvivigatnr.....pdkldpallrgRfdrkiei 130
                                        +  ++            +++Ll+++++ +           ++++vi++ n      +  l++a l +Rf  kie+
  gi|242398006|ref|YP_002993430.1| 108 NRAQPKT-----------QSALLEAMQEKQVTiegvthklPEPFLVIATMNPlehegVYILPEAQL-DRFMLKIEV 171
                                       ***9999...........9********99999999999997779***9999865555556777777.888888776 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 5.3
                                       STTHHHHHHHHHHH CS
                               AAA  38 yvgesekkirelfk 51 
                                       ++g+s++  ++l+ 
  gi|242398006|ref|YP_002993430.1| 237 LFGASPRAGEHLLY 250
                                       34444444444444 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.2   1.3e-07   0.00024      10     142 ..      23     147 ..      15     154 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.3e-07
                                       HHHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHEBS.SSSSTTTSS-B CS
                   Sigma54_activat  10 elleqikkvaktdlsvlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFGhe.kGaFtGAekek 85 
                                       +++e ++ +  ++ +vli+G  G+ K+++a+a  +a      +f ++   +++++ll +++ G+      tG  + k
  gi|242398006|ref|YP_002993430.1|  23 DVIELLTIALLSEGHVLIEGIPGVAKTTIAKAFSNAIG---LKFSRI---QLTPDLLPADIIGIFyYDQKTGEWTIK 93 
                                       67888888899999*****************9877665...334444...567777777777754134456666677 PP

                                       EHHHHHTTTSEEEEETGGGS-HHHHHHHHHHHHHSEEESBTSSSEEE--EEEEEEES CS
                   Sigma54_activat  86 kGlfekadgGtlfLDeigelplelQekLlrvlqegevervGsskeikvdvriiaatn 142
                                       +G + +    +++ De+++ ++++Q+ Ll+++qe++v+  G +++ +  + +ia+ n
  gi|242398006|ref|YP_002993430.1|  94 HGPIFA---NVILADEVNRAQPKTQSALLEAMQEKQVTIEGVTHKLPEPFLVIATMN 147
                                       777653...58999****************************999999888887655 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 !   19.0   0.1   5.3e-07   0.00094      34     115 ..      36     129 ..      16     136 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 5.3e-07
                            RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvkl.kitsgPvlekagdlaallt........nleek....dvlfideihrls 97 
                                        hvl+ G PG+ ktt+ak  ++ +g k+ +i  +P l  ++d+++++         +++++    +v++ de+ r +
  gi|242398006|ref|YP_002993430.1|  36 GHVLIEGIPGVAKTTIAKAFSNAIGLKFsRIQLTPDLL-PADIIGIFYydqktgewTIKHGpifaNVILADEVNRAQ 111
                                       6************************9984566788875.77888887521111111233323333789999999999 PP

                            RuvB_N  98 raveevlysamedfrldi 115
                                       ++++  l  am++ ++ i
  gi|242398006|ref|YP_002993430.1| 112 PKTQSALLEAMQEKQVTI 129
                                       999999999999988766 PP

>> AAA_16  AAA ATPase 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       0.1       2      51 ..      18      62 ..      17     138 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.8e-05
                            AAA_16  2 lvGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekd 51
                                      +vG+e+ +e L+ al      +++ vl+ G +Gv K+++++++ +a+  +
  gi|242398006|ref|YP_002993430.1| 18 VVGKEDVIELLTIALL-----SEGHVLIEGIPGVAKTTIAKAFSNAIGLK 62
                                      6888888888888776.....3479*******************999877 PP

>> AAA_lid_8  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   6.9e-05      0.12       1      51 [.     218     269 ..     218     275 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.9e-05
                         AAA_lid_8   1 evlelileiknkleeeeea.iyvSDRRwkkivkllkasAylngrdevnlsDl 51 
                                       e++e+i++i  k  + e+  +  S R     +   kasA+l+grd v ++D+
  gi|242398006|ref|YP_002993430.1| 218 EIIEYIYSIASKTRSDERLlFGASPRAGEHLLYAAKASAFLDGRDYVIPDDV 269
                                       68889999998884433323688999999999999***************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.53
# Mc/sec: 1762.53
//
Query:       gi|242398007|ref|YP_002993431.1|  [L=339]
Description: hypothetical protein TSIB_0011 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-10   41.1   0.0    5.3e-10   39.6   0.0    1.8  2  DUF4350         Domain of unknown function (DUF4350)
  ------ inclusion threshold ------
      0.023   14.2   0.0      0.036   13.5   0.0    1.3  1  ABC_transp_aux  ABC-type uncharacterized transport system


Domain annotation for each model (and alignments):
>> DUF4350  Domain of unknown function (DUF4350)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   0.0   5.9e-14   5.3e-10       1      69 []      36     105 ..      36     105 .. 0.89
   2 ?   -2.4   0.0      0.74   6.7e+03      37      49 ..     201     213 ..     192     230 .. 0.57

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 5.9e-14
                           DUF4350   1 skspnGtralaelLeaqGvevrrvrkpfd..alegedgtllvvapdlrlteeelaallewvarGntlvlaa 69 
                                       ++++nG + + +lL ++G  +  v +++d   l +++gtl++v+p+l +t+ee+ +l++++++Gn l+la+
  gi|242398007|ref|YP_002993431.1|  36 NTDWNGVSSFGKLLYSKGEITP-VLSTYDsvNLGERKGTLIIVGPNLDFTNEEIVELRKFLENGNALILAD 105
                                       799***********99887777.555555489999*********************************986 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.74
                           DUF4350  37 tllvvapdlrlte 49 
                                       ++l+ +pdl +++
  gi|242398007|ref|YP_002993431.1| 201 VILISDPDLFTNS 213
                                       6777777744433 PP

>> ABC_transp_aux  ABC-type uncharacterized transport system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0     4e-06     0.036     192     229 ..      69     106 ..      31     126 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4e-06
                    ABC_transp_aux 192 edidvlviakptkdlseeelykldqflmnGgkllvfld 229
                                       e+  +l+i++p  d+++ee+  l++fl+nG+ l+++ d
  gi|242398007|ref|YP_002993431.1|  69 ERKGTLIIVGPNLDFTNEEIVELRKFLENGNALILADD 106
                                       555689***********************999988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       937  (0.0522617); expected 358.6 (0.02)
Passed bias filter:                      739  (0.0412181); 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):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.52
# Mc/sec: 1971.45
//
Query:       gi|242398008|ref|YP_002993432.1|  [L=587]
Description: hypothetical protein TSIB_0012 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-05   25.2   0.0     0.0018   18.5   0.0    3.1  3  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
    0.00037   20.4   0.2      0.058   13.4   0.0    3.0  3  CarbopepD_reg_2  CarboxypepD_reg-like domain
     0.0035   17.5   0.0      0.098   12.9   0.0    2.8  3  Big_3_5          Bacterial Ig-like domain (group 3)
  ------ inclusion threshold ------
      0.042   13.9   0.0      0.094   12.7   0.0    1.5  1  Big_1            Bacterial Ig-like domain (group 1)
       0.09   12.8   0.1       0.77    9.8   0.0    2.4  2  CooC_C           CS1-pili formation C-terminal
       0.22   11.3   0.1        2.2    8.1   0.0    2.2  2  zf-ZPR1          ZPR1 zinc-finger 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 ?   -1.8   0.0       1.3   3.9e+03      37      63 ..     236     265 ..     218     283 .. 0.64
   2 !   18.5   0.0     6e-07    0.0018       1      65 [.     291     354 ..     291     371 .. 0.87
   3 ?    2.7   0.0     0.051   1.5e+02      33      65 ..     410     443 ..     385     453 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.3
                   CarboxypepD_reg  37 dGafrlrglpp..gtysvtvsa.pGyatat 63 
                                       +G frlr      g y+v ++a +G + +t
  gi|242398008|ref|YP_002993432.1| 236 NGGFRLRYSFNetGLYEVYAQAmNGSHVVT 265
                                       566666644333477888775403333334 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 6e-07
                   CarboxypepD_reg   1 tisGrVtdasgapiagatVtvtnadtgtvastttdadGafrlrglpp..gtysvtvsapGyatatre 65 
                                       t++G+  d  g p++g +++++   +g+++   td++G+f+++ l     + +vt+s+ G ++++ +
  gi|242398008|ref|YP_002993432.1| 291 TVEGYLLDYFGSPLKGKEIILE--MDGENYKSLTDENGTFSFD-LGEfyEEKNVTMSFLGDDEHEGT 354
                                       799*******************..89****************8.87778999999999998888754 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.051
                   CarboxypepD_reg  33 ttdadGafrlrglpp..gtysvtvsapGyatatre 65 
                                       t +a G+f+l  l    g++ v v +pG ++++ +
  gi|242398008|ref|YP_002993432.1| 410 TINARGNFTLL-LRFdrGEHAVYVKFPGNEEFAES 443
                                       6699*****97.54458***********9998864 PP

>> CarbopepD_reg_2  CarboxypepD_reg-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   1.9e-05     0.058      11      63 ..     301     356 ..     292     384 .. 0.76
   2 ?    3.6   0.0     0.022        65      12      61 ..     395     443 ..     386     455 .. 0.76
   3 ?   -2.7   0.0       2.1   6.2e+03      48      66 ..     468     488 ..     467     504 .. 0.49

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.9e-05
                   CarbopepD_reg_2  11 keplpgatVyv..kgtkkgtvTdenGnFelknlpa.gkytLvvsyvGyktqekkvt 63 
                                       + pl g  +++   g + +  TdenG+F+++  +  ++  +++s++G ++ e ++t
  gi|242398008|ref|YP_002993432.1| 301 GSPLKGKEIILemDGENYKSLTDENGTFSFDLGEFyEEKNVTMSFLGDDEHEGTIT 356
                                       478888888883356789999*********9666546789*******999998887 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.022
                   CarbopepD_reg_2  12 eplpgatVyvkgtkkgtvTdenGnFelk.nlpagkytLvvsyvGyktqekk 61 
                                       +++p   Vyv ++ + t+ ++ GnF+l  + ++g++ + v++ G ++  ++
  gi|242398008|ref|YP_002993432.1| 395 DEIPL-EVYVDDKLTETI-NARGNFTLLlRFDRGEHAVYVKFPGNEEFAES 443
                                       45665.788888877776.9******9757788999999999998776555 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 2.1
                   CarbopepD_reg_2  48 LvvsyvGyktqek..kvtvsk 66 
                                       Lv  ++Gyk  ++  kv v++
  gi|242398008|ref|YP_002993432.1| 468 LVLGFIGYKLLTRrpKVVVET 488
                                       566688888555411333332 PP

>> Big_3_5  Bacterial Ig-like domain (group 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.65     2e+03      28      66 ..     221     256 ..     205     275 .. 0.71
   2 ?    0.6   0.0      0.22   6.6e+02      41      74 ..     320     352 ..     286     359 .. 0.80
   3 !   12.9   0.0   3.3e-05     0.098      40      84 ..     409     451 ..     378     456 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.65
                                       EEEEETTEE-SS-EE--TTSEEEEEEE-SS-EEEEEEEE CS
                           Big_3_5  28 VtftdggttlgtavllsanGtAtltvsalaaGthsitAt 66 
                                       V++ ++++++ t+  +  nG   l +s+ ++G +++ A+
  gi|242398008|ref|YP_002993432.1| 221 VKVIINNASY-TPEII--NGGFRLRYSFNETGLYEVYAQ 256
                                       4444455555.33333..588999999999999999886 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.22
                                       EE--TTSEEEEEEE-SS-EEEEEEEEEE-TTS-- CS
                           Big_3_5  41 vllsanGtAtltvsalaaGthsitAtYsGdanya 74 
                                       +l+++nGt ++++      + ++t ++ Gd+ ++
  gi|242398008|ref|YP_002993432.1| 320 SLTDENGTFSFDLGEF-YEEKNVTMSFLGDDEHE 352
                                       3557799999999776.68999*******99765 PP

  == domain 3  score: 12.9 bits;  conditional E-value: 3.3e-05
                                       -EE--TTSEEEEEEE-SS-EEEEEEEEEE-TTS---S--EEEEEE CS
                           Big_3_5  40 avllsanGtAtltvsalaaGthsitAtYsGdanyaastssavtvt 84 
                                        + ++  G+ tl +++   G+h++ +++ G+  +a s s+ v v+
  gi|242398008|ref|YP_002993432.1| 409 ETINA-RGNFTLLLRFD-RGEHAVYVKFPGNEEFAESVSNIVEVQ 451
                                       34344.79999999997.9********************977665 PP

>> Big_1  Bacterial Ig-like domain (group 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.1e-05     0.094       7      52 ..     290     332 ..     287     333 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.1e-05
                             Big_1   7 ntltatvkDangnpvagatVtfsvsggalsassgtTdanGkatvtl 52 
                                       +t+   + D +g p++g+++ ++++g++    ++ Td+nG++++ l
  gi|242398008|ref|YP_002993432.1| 290 VTVEGYLLDYFGSPLKGKEIILEMDGENY---KSLTDENGTFSFDL 332
                                       56777789******************888...89********9976 PP

>> CooC_C  CS1-pili formation C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.63   1.9e+03      35      60 ..     223     248 ..     216     261 .. 0.77
   2 ?    9.8   0.0   0.00026      0.77      16      64 ..     289     341 ..     280     345 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.63
                            CooC_C  35 kilnhagvavteedGvFtlevdakap 60 
                                        i+n+a+ + +  +G+F l  +  ++
  gi|242398008|ref|YP_002993432.1| 223 VIINNASYTPEIINGGFRLRYSFNET 248
                                       4789999999999****998766555 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00026
                            CooC_C  16 tvtviGrlvdedgqplanakil....nhagvavteedGvFtlevdakapsltv 64 
                                       +vtv G l d  g+pl++ +i+    ++  +++t+e+G F++++ + ++++ v
  gi|242398008|ref|YP_002993432.1| 289 IVTVEGYLLDYFGSPLKGKEIIlemdGENYKSLTDENGTFSFDLGEFYEEKNV 341
                                       79***************9876433339999************99887777666 PP

>> zf-ZPR1  ZPR1 zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.18   5.5e+02      83     111 ..     160     186 ..     156     209 .. 0.75
   2 ?    8.1   0.0   0.00074       2.2      68     105 ..     261     298 ..     250     345 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.18
                           zf-ZPR1  83 leleippgtlegrlttvEGlLeqikeele 111
                                       l++e+++  +   l  +EGl+e+ +e+l+
  gi|242398008|ref|YP_002993432.1| 160 LNFELEE--TYEALEKLEGLIERYEERLN 186
                                       6777777..6677999**********996 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00074
                           zf-ZPR1  68 rqvlkSetatveipeleleippgtlegrlttvEGlLeq 105
                                        +v+ S+  ++e++++  +i + +++g++ tvEG L +
  gi|242398008|ref|YP_002993432.1| 261 SHVVTSNVIRIEVQKIPTQIIALEKTGTIVTVEGYLLD 298
                                       57999*****************************8865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (587 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       690  (0.0384851); expected 358.6 (0.02)
Passed bias filter:                      578  (0.0322383); 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: 0.67u 0.30s 00:00:00.97 Elapsed: 00:00:00.47
# Mc/sec: 3752.30
//
Query:       gi|242398009|ref|YP_002993433.1|  [L=246]
Description: hypothetical protein TSIB_0013 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.26s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1596.45
//
Query:       gi|242398010|ref|YP_002993434.1|  [L=475]
Description: archaeal ATPase, fused to C-terminal DUF234 domain [Thermococcus sibiricus MM 739]
Scores for 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   0.7    8.7e-24   83.9   0.0    2.3  2  DUF234    Archaea bacterial proteins of unknown function
    1.2e-14   54.8   6.2    9.1e-14   51.9   2.8    2.8  2  ATPase_2  ATPase domain predominantly from Archaea
    1.4e-09   38.1   0.6    3.2e-09   36.9   0.2    1.8  2  AAA_14    AAA domain
    1.1e-05   25.9   0.2    0.00011   22.6   0.0    2.1  2  AAA_16    AAA ATPase domain
    0.00038   20.8   0.0      0.001   19.3   0.0    1.7  1  AAA_22    AAA domain
  ------ inclusion threshold ------
        0.1   12.4   0.3       0.37   10.6   0.1    2.1  2  HTH_38    Helix-turn-helix domain
       0.12   12.3   0.0        1.6    8.6   0.0    2.4  2  HTH_5     Bacterial regulatory protein, arsR family
       0.14   12.1   0.1       0.55   10.2   0.1    1.9  1  MarR      MarR family


Domain annotation for each model (and alignments):
>> DUF234  Archaea bacterial proteins of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1       1.1   2.5e+03      18      40 ..      74      98 ..      57     110 .. 0.65
   2 !   83.9   0.0   3.9e-27   8.7e-24       1      98 [.     315     419 ..     315     420 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.1
                            DUF234 18 eevlekik..eelneyvgkvFEelv 40
                                      + v++k +  ++++e++g  FE++ 
  gi|242398010|ref|YP_002993434.1| 74 KGVITKYEslSTWDEFFGVLFERFN 98
                                      3444333322578999999999875 PP

  == domain 2  score: 83.9 bits;  conditional E-value: 3.9e-27
                            DUF234   1 wfrfvypnrseielgeseevlekikeelneyvgkvFEelvrelllelnkagklpfrftkvGrwW........kkeee 69 
                                       wfrf++p+ se+e  + e++ +++ + l +yvgk+F+ ++rell+ ln++g+lpf+ft++Gr+W        ++  e
  gi|242398010|ref|YP_002993434.1| 315 WFRFIHPRLSEYEAMR-EDLGKEVMSMLPDYVGKRFDFISRELLWILNHKGELPFKFTQMGRHWgyyreegvRRVYE 390
                                       *************998.67779******************************************999988877999* PP

                            DUF234  70 iDivaldeeekkalfgEvKwknsekeakk 98 
                                       iD+va++ + kkalfgE+Kw+ +  + kk
  gi|242398010|ref|YP_002993434.1| 391 IDLVAVSRDRKKALFGECKWRGKPVDGKK 419
                                       ********************996666655 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 !   51.9   2.8     4e-17   9.1e-14       1     230 [.       3     203 ..       3     206 .. 0.82
   2 ?   -1.8   0.1       1.1   2.4e+03      84     136 ..     413     466 ..     380     472 .. 0.59

  Alignments for each domain:
  == domain 1  score: 51.9 bits;  conditional E-value: 4e-17
                          ATPase_2   1 FfdRekelkeleeilerepneiy..fiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeek 75 
                                       F++Re e++ l +  e ++++ y  +iYG +++GKt+Ll e++e+      +  ++ +  + s+s l+e+      +
  gi|242398010|ref|YP_002993434.1|   3 FVNREHEIEVLHKARELSKRKLYtvVIYGMRRVGKTRLLLEFLEEN-----DLYFFVNKTKTSESLLREY------E 68 
                                       9************9999888875449******************99.....4466777777788888888......2 PP

                          ATPase_2  76 kklekalgiavpkaeleeilkeksklvfkaielllekikkkgkkiiiiiDelqklidlglngaellvkeLlnliesl 152
                                       + + +++g ++ k e             + +++++  + ++    ++ +De+q+    +++   ++   L++li+  
  gi|242398010|ref|YP_002993434.1|  69 E-ILRKKG-VITKYES-----------LSTWDEFFGVLFERFN-GAVAFDEFQEFQ--KVD--PSVFPLLQKLIDTN 127
                                       2.333332.2333222...........3668888888877744.689*********..888..9************* PP

                          ATPase_2 153 tkekhlcvviclsSeglfie.rvyneselegrhky.ilvddldketalnflkegfkeleelskedfeeiyryvGGkP 227
                                        ++  l++++ +s  g++ +   +++ +l+gr k  i+++ l  + a +++ke+  ++     +df ++y ++GG P
  gi|242398010|ref|YP_002993434.1| 128 ENRAGLMLIFTGSTIGMMEKlFKDSKEPLYGRIKReIHLKELGIKGAYEMTKEL--KIG--DLDDFMTLYALFGGFP 200
                                       ********************55577889****9999*****************7..444..667************* PP

                          ATPase_2 228 kal 230
                                       k+ 
  gi|242398010|ref|YP_002993434.1| 201 KYY 203
                                       985 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.1
                          ATPase_2  84 iavpkaeleeilkeksklvfkaielllekikkkgkk...iiiiiDelqklidlgln 136
                                       ++v  +++ e lk+ks+l   + ++++  i k+ k     +i++De + l+   l+
  gi|242398010|ref|YP_002993434.1| 413 KPVDGKKVFEELKKKSELTGWKGDKYYLIIAKRVKNapeEAIVLDEKAILK--VLD 466
                                       444444444444566666666667777777777666666677888766666..554 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.2   1.4e-12   3.2e-09       5     121 ..      27     165 ..      24     172 .. 0.65
   2 ?   -3.1   0.0       3.4   7.7e+03      51      72 ..     437     458 ..     421     460 .. 0.61

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 1.4e-12
                            AAA_14   5 lvitGaRrvGKTtllkqlikell....vkkesilyinldderd........kkladpekllelileklke....... 62 
                                       +vi G+RrvGKT ll ++++e+     v+k ++ +  l + ++        +                 +       
  gi|242398010|ref|YP_002993434.1|  27 VVIYGMRRVGKTRLLLEFLEENDlyffVNKTKTSESLLREYEEilrkkgviT-----------------Kyeslstw 86 
                                       89*****************888744443333333333333333222222221.................12233334 PP

                            AAA_14  63 .........ekktylflDEiqev....pewekalkslvdegkn...ldvivtGSnskllsk...eiatslagrva.e 119
                                                + +  + +DE qe     p+++  l++l+d+++n   l +i+tGS  +++ k   + ++ l gr++ e
  gi|242398010|ref|YP_002993434.1|  87 deffgvlfeRFNGAVAFDEFQEFqkvdPSVFPLLQKLIDTNENragLMLIFTGSTIGMMEKlfkDSKEPLYGRIKrE 163
                                       45555665545667*********888888999999***966443448********9998653337778888887644 PP

                            AAA_14 120 ie 121
                                       i+
  gi|242398010|ref|YP_002993434.1| 164 IH 165
                                       55 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.4
                            AAA_14  51 kllelileklkeekktylflDE 72 
                                       k++ +i +++k+  ++ ++lDE
  gi|242398010|ref|YP_002993434.1| 437 KYYLIIAKRVKNAPEEAIVLDE 458
                                       3444555556666677799998 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0     5e-08   0.00011       1      63 [.       2      60 ..       2      95 .. 0.75
   2 ?    0.6   0.0      0.29   6.4e+02     141     170 .]     103     136 ..      99     136 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 5e-08
                            AAA_16  1 rlvGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdql 63
                                      r+v Re+e+e L+ a e +++     v+++G++ vGK++l+ e+l+   +++ +f+  k++ +
  gi|242398010|ref|YP_002993434.1|  2 RFVNREHEIEVLHKARE-LSKRKLYTVVIYGMRRVGKTRLLLEFLE---ENDLYFFVNKTKTS 60
                                      6999*****99999876.66666699***************99996...55566644444433 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.29
                            AAA_16 141 lDdlq...wadeaslqllaaLlrllesk.pllvv 170
                                       +D++q   ++d++   ll+ L ++ e++  l+++
  gi|242398010|ref|YP_002993434.1| 103 FDEFQefqKVDPSVFPLLQKLIDTNENRaGLMLI 136
                                       5655544499999999999999998887788776 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   4.6e-07     0.001       8     131 ..      27     141 ..      21     148 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 4.6e-07
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.sskdllrellralglelkaerlsseelleale 83 
                                       +v++G   +GKT+ll ++le+          ++ ++fv+ ++ + s+   ++e+lr+ g+ +k+   +s   ++ + 
  gi|242398010|ref|YP_002993434.1|  27 VVIYGMRRVGKTRLLLEFLEE----------NDLYFFVNKTKTSeSLLREYEEILRKKGVITKY---ESLSTWDEFF 90 
                                       799*****************9..........688999999999966666699999999999999...8888888888 PP

                            AAA_22  84 qalraravielliiDEaqhlr..seealeeLrsllnl..srkgvqliLvGtp 131
                                         l +r+  +++  DE+q +    + ++  L +l +   +r g+ li+ G +
  gi|242398010|ref|YP_002993434.1|  91 GVLFERFN-GAVAFDEFQEFQkvDPSVFPLLQKLIDTneNRAGLMLIFTGST 141
                                       88888888.9**********65435555555555555458999999999876 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       2.7     6e+03      11      19 ..       8      16 ..       8      23 .. 0.66
   2 ?   10.6   0.1   0.00016      0.37      17      42 ..     257     283 ..     251     284 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.7
                            HTH_38 11 eeIerllae 19
                                      +eIe l+++
  gi|242398010|ref|YP_002993434.1|  8 HEIEVLHKA 16
                                      689999864 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00016
                            HTH_38  17 laeG.lslreIArrLgrspsTIsRElk 42 
                                        a G  s+++IA +L+r+ ++  R+lk
  gi|242398010|ref|YP_002993434.1| 257 VANGaTSISKIAGYLNRKETSLTRHLK 283
                                       5667689******************98 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.22     5e+02      23      47 .]      55      79 ..      39      79 .. 0.85
   2 ?    8.6   0.0   0.00072       1.6       6      39 ..     252     285 ..     251     287 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.22
                                      HHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5 23 eelglsqstvShHLkkLreaGLVek 47
                                      ++++ s+s ++++  +Lr+ G+++k
  gi|242398010|ref|YP_002993434.1| 55 NKTKTSESLLREYEEILRKKGVITK 79
                                      6788899999999999****99986 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00072
                                       HHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHH CS
                             HTH_5   6 kILklLaegelcvcelaeelglsqstvShHLkkL 39 
                                       +IL ++a+g ++++ +a +l+  +  + +HLk L
  gi|242398010|ref|YP_002993434.1| 252 DILEAVANGATSISKIAGYLNRKETSLTRHLKEL 285
                                       59******************************88 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00024      0.55      15      42 ..     259     286 ..     252     287 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00024
                                       STTEEHHHHHHHHTS-HHHHHHHHHHHH CS
                              MarR  15 qgplsvseLakklgvskstvtrvldrLe 42 
                                       +g+ s+s++a  l+ + +++tr l++L 
  gi|242398010|ref|YP_002993434.1| 259 NGATSISKIAGYLNRKETSLTRHLKELT 286
                                       6899**********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.46
# Mc/sec: 3113.96
//
Query:       gi|242398011|ref|YP_002993435.1|  [L=80]
Description: hypothetical protein TSIB_0015 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.048   13.7   2.8       0.06   13.4   2.8    1.1  1  SirB       Invasion gene expression up-regulator, SirB
        5.3    7.7   7.8       0.94   10.1   0.7    2.2  2  OAD_gamma  Oxaloacetate decarboxylase, gamma chain


Domain annotation for each model (and alignments):
>> SirB  Invasion gene expression up-regulator, SirB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   2.8   6.7e-06      0.06      47     111 ..       7      70 ..       4      76 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.7e-06
                              SirB  47 tlLllsgiaLlvllglspftkaWltaKlvllvvyivlgvvalkrakskklrllafvlAlvvflyi 111
                                        lL+ls  +L+  l +  + + +lt  l++l++ + +g ++l ++++++l+ l+ +l +++ +++
  gi|242398011|ref|YP_002993435.1|   7 MLLFLSSWVLISALAVGTV-DVFLTLTLIGLLITLEVGSFFLSKEQKESLKPLVELLLVIFAIIV 70 
                                       5899999999999988777.45********************66666666655444433333322 PP

>> OAD_gamma  Oxaloacetate decarboxylase, gamma chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.7    0.0001      0.94       9      40 ..      22      55 ..      15      60 .. 0.76
   2 ?    2.0   1.2     0.037   3.3e+02      18      32 ..      61      75 ..      58      79 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0001
                         OAD_gamma  9 lGmgvVFvvLilLslvisl..fskiikkkakkkk 40
                                      +G + VF+ L+l+ l+i+l   s++ +k++k++ 
  gi|242398011|ref|YP_002993435.1| 22 VGTVDVFLTLTLIGLLITLevGSFFLSKEQKESL 55
                                      455569************9866777777777764 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.037
                         OAD_gamma 18 LilLslvislfskii 32
                                      L+l +++i +++k+ 
  gi|242398011|ref|YP_002993435.1| 61 LLLVIFAIIVMKKVY 75
                                      89999******9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       879  (0.0490267); 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:                         2  (0.000111551); expected 0.2 (1e-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: 508.64
//
Query:       gi|242398012|ref|YP_002993436.1|  [L=125]
Description: HEPN domain protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.9e-22   78.0   0.8    6.6e-22   77.9   0.8    1.0  1  HEPN           HEPN domain
    0.00086   19.8   0.0     0.0014   19.1   0.0    1.3  1  HEPN_SAV_6107  SAV_6107-like HEPN
  ------ inclusion threshold ------
       0.11   11.9   0.0       0.67    9.3   0.0    2.1  2  GatD_N         GatD N-terminal domain


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 !   77.9   0.8   1.1e-25   6.6e-22       2     117 ..      10     123 ..       9     124 .. 0.97

  Alignments for each domain:
  == domain 1  score: 77.9 bits;  conditional E-value: 1.1e-25
                                       HHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHTT--.SSCCHHHHHHCCHHHT...-HHHHHHHH CS
                              HEPN   2 eewlrrAeedleaAellleegdydlacfhaqqaaekalKAlllkkggeppkthdlreLleelkkelkeseelreele 78 
                                       +  +++A+++l++Ae+ +e gdy ++  +a+ +a+++++All++kg++  ++ +l   ++el +  +++ el ++++
  gi|242398012|ref|YP_002993436.1|  10 KSSIEIARRFLKSAERTFEIGDYVMVEIAAYNSAFHSVRALLFAKGYKERSHQCLVIAVRELYRTNPKIVELMNIFD 86 
                                       6689************************************************************************* PP

                                       HHHCCCHHCCCTSS--S--HHHHHHHHHHHHHHHHHHHH CS
                              HEPN  79 eLekayiesrYpdakeeyteedaeealkdaeevlelvee 117
                                       +L+  +++++Y+ a +  +ee+ae +l++a+evle+ve+
  gi|242398012|ref|YP_002993436.1|  87 KLRISRHNVQYGGALV--DEEEAEFVLRFAREVLEIVEQ 123
                                       ****************..******************986 PP

>> HEPN_SAV_6107  SAV_6107-like HEPN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   2.3e-07    0.0014      13      98 .]      38     122 ..      33     122 .. 0.96

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 2.3e-07
                     HEPN_SAV_6107  13 aahlaAlraAaAvLaargrperrrrrprsaWelLaevaPelaewaalFaagaarraaieaGieravtareaddllre 89 
                                       aa+ +A  +  A+L a+g +er+++    a + L ++ P++ e  ++F++    r +++ G +  v+++ea+ +lr 
  gi|242398012|ref|YP_002993436.1|  38 AAYNSAFHSVRALLFAKGYKERSHQCLVIAVRELYRTNPKIVELMNIFDKLRISRHNVQYGGA-LVDEEEAEFVLRF 113
                                       68999********************************************************98.9************ PP

                     HEPN_SAV_6107  90 aeeFlrlVe 98 
                                       a e l+ Ve
  gi|242398012|ref|YP_002993436.1| 114 AREVLEIVE 122
                                       *****9997 PP

>> GatD_N  GatD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0     0.098   5.9e+02       1      10 [.      27      36 ..      27      41 .. 0.86
   2 ?    9.3   0.0   0.00011      0.67       1      25 [.      82     106 ..      82     111 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.098
                                      --TT-EEEEE CS
                            GatD_N  1 ievGDlikve 10
                                      +e+GD++ ve
  gi|242398012|ref|YP_002993436.1| 27 FEIGDYVMVE 36
                                      689****997 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00011
                                       --TT-EEEEE-SS-EEEEEE----T CS
                            GatD_N   1 ievGDlikvekkgreyeGilmPrse 25 
                                       ++++D++++ + +++y G l +++e
  gi|242398012|ref|YP_002993436.1|  82 MNIFDKLRISRHNVQYGGALVDEEE 106
                                       689******************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); 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: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 789.30
//
Query:       gi|242398013|ref|YP_002993437.1|  [L=183]
Description: nucleotidytransferase [Thermococcus sibiricus MM 739]
Scores for complete 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-08   32.5   0.5    1.6e-07   31.5   0.3    1.7  2  NTP_transf_2   Nucleotidyltransferase domain
    9.1e-07   28.9   0.5    1.6e-06   28.1   0.3    1.6  1  Polbeta        Polymerase beta, Nucleotidyltransferase
  ------ inclusion threshold ------
      0.062   13.2   0.0      0.083   12.8   0.0    1.2  1  Adenyl_cycl_N  Adenylate cyclase NT domain
      0.068   13.3   0.1       0.17   12.0   0.1    1.8  1  RAP            RAP 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 ?   -1.7   0.0      0.82   3.7e+03      58      67 ..      71      80 ..      39     102 .. 0.56
   2 !   31.5   0.3   3.6e-11   1.6e-07      16      80 ..     102     158 ..      89     178 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.82
                                      HHCCCEEECT CS
                      NTP_transf_2 58 eiikfleell 67
                                       + ++++e++
  gi|242398013|ref|YP_002993437.1| 71 NDDFAVKEIK 80
                                      2222222222 PP

  == domain 2  score: 31.5 bits;  conditional E-value: 3.6e-11
                                       EEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEEEEECEEECC CS
                      NTP_transf_2  16 kvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleellglevdlvtrekle 80 
                                       +++++GS+a G++ + SD+D+lv++++e          + l+ei++++      +  +++++k e
  gi|242398013|ref|YP_002993437.1| 102 SLAIYGSFASGEFDEKSDLDILVIGNKED------INYQLLHEIEDKVGV--RFQLTVIPFYKWE 158
                                       6899************************2......444666777766666..5555555555544 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.3   3.6e-10   1.6e-06      13      66 ..     100     149 ..      87     179 .. 0.72

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 3.6e-10
                                       HHSTTEEEEEE-S------EEEEEEEESS---HHHHHHHHHHHHHH.SSSEEEE CS
                           Polbeta  13 ielaylFGSrakgkareeSDiDlavllkekldleeelelaaelediklgkkvDl 66 
                                        + + ++GS+a+g++ e+SD+D+ v+ +++   +  ++l +e+ed   g ++ l
  gi|242398013|ref|YP_002993437.1| 100 CSSLAIYGSFASGEFDEKSDLDILVIGNKE---DINYQLLHEIEDK-VGVRFQL 149
                                       467789**********************99...3444555555555.4444443 PP

>> Adenyl_cycl_N  Adenylate cyclase NT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.9e-05     0.083      91     134 ..      99     143 ..      59     149 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.9e-05
                     Adenyl_cycl_N  91 aieglylmGStgsiaqsekSDlDiWvc.hrselsaeelelLekKl 134
                                       + ++l   GS++s  + ekSDlDi v+  +++++ + l+++e+K+
  gi|242398013|ref|YP_002993437.1|  99 NCSSLAIYGSFASGEFDEKSDLDILVIgNKEDINYQLLHEIEDKV 143
                                       45667777******************9889999999999999996 PP

>> RAP  RAP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   3.8e-05      0.17      32      56 ..     147     169 ..     132     171 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.8e-05
                               RAP  32 ykvinIpyfeWnqlknkedkveylk 56 
                                       +++  Ip+++W+++  ke+k ++++
  gi|242398013|ref|YP_002993437.1| 147 FQLTVIPFYKWEKM--KEEKDHFTE 169
                                       66677*********..999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); 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: 0.58u 0.35s 00:00:00.93 Elapsed: 00:00:00.54
# Mc/sec: 1016.03
//
Query:       gi|242398014|ref|YP_002993438.1|  [L=328]
Description: hypothetical protein TSIB_0018 [Thermococcus sibiricus MM 739]
Scores for 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-96  321.8   0.0    4.7e-96  321.6   0.0    1.0  1  DUF1616        Protein of unknown function (DUF1616)
  ------ inclusion threshold ------
        1.6    8.6   9.9        1.2    9.0   6.7    2.0  2  7TMR-DISM_7TM  7TM diverse intracellular signalling


Domain annotation for each model (and alignments):
>> DUF1616  Protein of unknown function (DUF1616)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  321.6   0.0  5.2e-100   4.7e-96       2     274 ..      11     290 ..      10     323 .. 0.95

  Alignments for each domain:
  == domain 1  score: 321.6 bits;  conditional E-value: 5.2e-100
                           DUF1616   2 lvlalllllailvpvlnetplRivlglplvLflPGYaliaaLFPekrdidgieRlaLSfglSiaivpliglvlnvtp 78 
                                       ++++l+lll +l++++++++lR +lgl++vLf+PGY++i+aLFPek+++d++eRlaLSfglSiaivpligl+ln+tp
  gi|242398014|ref|YP_002993438.1|  11 TIITLSLLLDLLIAFYPDSLLRKALGLAFVLFFPGYVFITALFPEKKELDNLERLALSFGLSIAIVPLIGLGLNYTP 87 
                                       689999*********************************************************************** PP

                           DUF1616  79 wgirlepilvslslftlllalvAivrRsrlpeeerfsvplralieslkeeleeksesrldkalnvlLvvsivlavaa 155
                                       wgirl pilvsl++f l++ ++Ai+rR +  +++  +++     e+lkeele+ ++s+ldkal+v+L+++i+ ++a+
  gi|242398014|ref|YP_002993438.1|  88 WGIRLIPILVSLTVFNLIFGIAAIYRRANAVDPWIPRIS----SEKLKEELEWGKSSKLDKALTVILIIAIISSIAT 160
                                       ************************************997....899********99********************* PP

                           DUF1616 156 lgyavvaPkegekfTelyllgedgdelvaenypteltagesqevivgieNhEheevnYtvvvllqev.......... 222
                                       lgy++++Pk gekfTe+y+lg++g   +a++yptel +ge+ +vi+gi NhE+++v+Y v+v+l ++          
  gi|242398014|ref|YP_002993438.1| 161 LGYVITHPKPGEKFTEFYILGPEG---KAADYPTELFVGEKARVILGIANHEYRDVTYHVEVWLVNLtydfetneti 234
                                       ************************...*********************************************99999 PP

                           DUF1616 223 tdeeevevlerteldrrevtladnet..weqelevepeatgenlrleflLYkd...e 274
                                         ++++ ++ + +l  ++v+++ n+t  we++++++++++g +++l+flL+kd    
  gi|242398014|ref|YP_002993438.1| 235 IYNMYIVDYFNVTLPHKPVDIEGNWTpqWETNYTFTINRAG-KWQLWFLLFKDersP 290
                                       788899999******************************99.**********94332 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 ?    9.0   6.7   0.00014       1.2      48     148 ..      18     115 ..       9     119 .. 0.63
   2 ?    0.1   0.1     0.068   6.1e+02     127     157 ..     147     180 ..     138     181 .. 0.46

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00014
                     7TMR-DISM_7TM  48 lngllfqylwpnappalnnkllyltlllllilfllFarsflelkkkp.rllklllllavllslllll.lpllpytes 122
                                       l  ll+ +     p +l  k+l l++ l++   ++F+  ++  kk    l +l l + + ++++ l+ l l ++++ 
  gi|242398014|ref|YP_002993438.1|  18 LLDLLIAFY----PDSLLRKALGLAFVLFF-PGYVFITALFPEKKELdNLERLALSFGLSIAIVPLIgLGLNYTPWG 89 
                                       344444444....45799999999999999.8889****99996644655555544444433333331255599999 PP

                     7TMR-DISM_7TM 123 lslaqllallvillllligikawrkg 148
                                       ++l+ +l+ l+++ l++ + +++r+ 
  gi|242398014|ref|YP_002993438.1|  90 IRLIPILVSLTVFNLIFGIAAIYRRA 115
                                       99998888877666666666666664 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.068
                     7TMR-DISM_7TM 127 qllallvillllligikaw...rkgnkparyfli 157
                                       +++++++i+++++++ +++   + g+k   ++++
  gi|242398014|ref|YP_002993438.1| 147 TVILIIAIISSIATLGYVIthpKPGEKFTEFYIL 180
                                       3333333333333333333344555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       676  (0.0377043); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.36s 00:00:00.99 Elapsed: 00:00:00.53
# Mc/sec: 1849.47
//
Query:       gi|242398015|ref|YP_002993439.1|  [L=399]
Description: hypothetical protein TSIB_0019 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00044   20.2   1.3       0.76    9.8   0.1    3.8  4  tRNA_anti-codon  OB-fold nucleic acid binding domain
  ------ inclusion threshold ------
       0.16   12.2   0.1        1.6    9.0   0.0    2.4  3  Ig_GlcNase       Exo-beta-D-glucosaminidase Ig-fold domain
       0.18   12.2   0.0        1.1    9.6   0.0    2.3  4  Rep_fac-A_3      Replication factor A protein 3


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 ?    1.3   0.0     0.057   3.4e+02      44      72 ..      37      64 ..      35      69 .. 0.80
   2 !    5.1   0.0    0.0039        23      42      64 ..      70      92 ..      60     102 .. 0.81
   3 !    9.8   0.1   0.00013      0.76      22      72 ..     189     231 ..     188     238 .. 0.83
   4 ?   -3.2   0.0       1.5   8.9e+03      48      66 ..     297     314 ..     283     319 .. 0.64

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.057
                                      TTS-TTSEEEEEEEEEECTTSSEEEEEEE CS
                   tRNA_anti-codon 44 enlkeGdvvrvtGrvkrrpggelelkvee 72
                                      e+ k+Gd+++ tG    ++++ + + ++ 
  gi|242398015|ref|YP_002993439.1| 37 EEAKKGDLIEFTGICVNSKEN-FAVLYNG 64
                                      56799*********9999988.7777665 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0039
                                      HHTTS-TTSEEEEEEEEEECTTS CS
                   tRNA_anti-codon 42 laenlkeGdvvrvtGrvkrrpgg 64
                                      ++e+l+ G+v++++G+++  ++ 
  gi|242398015|ref|YP_002993439.1| 70 VFETLESGKVYKIRGKLTDPDKS 92
                                      5799*************988665 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.00013
                                       EEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEEEEEEECTTSSEEEEEEE CS
                   tRNA_anti-codon  22 dlrDgtgriqvvlfreeatklaenlkeGdvvrvtGrvkrrpggelelkvee 72 
                                       ++ Dg+ +++v+l        +++l++Gd+v+v G+ k +    l+++v++
  gi|242398015|ref|YP_002993439.1| 189 TIWDGEEEVRVYLPY------KQTLEVGDYVEVIGTAKLYS-T-LTIYVND 231
                                       677899999999999......9****************995.4.6777776 PP

  == domain 4  score: -3.2 bits;  conditional E-value: 1.5
                                       TTSEEEEEEEEEECTTSSE CS
                   tRNA_anti-codon  48 eGdvvrvtGrvkrrpggel 66 
                                       +++++  +++v+r ++  l
  gi|242398015|ref|YP_002993439.1| 297 KNSLYCLECKVSRPREA-L 314
                                       44455555888887665.5 PP

>> Ig_GlcNase  Exo-beta-D-glucosaminidase Ig-fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0   0.00026       1.6      38     102 ..      85     148 ..      54     150 .. 0.83
   2 ?   -1.4   0.0      0.45   2.7e+03      65      89 ..     181     204 ..     180     218 .. 0.61
   3 ?   -1.1   0.0      0.36   2.2e+03      33      53 ..     361     381 ..     347     385 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00026
                        Ig_GlcNase  38 tLenkss..vpAffvrlnlvdaa.geevlPvlwsDNyvtLlPgEsltltveypaaalkgkkpkvevsG 102
                                       +L+ + +  v Af ++ +  +a   e v+ ++w D+y +Ll  +++ l+   +a++ +    +v v+G
  gi|242398015|ref|YP_002993439.1|  85 KLTDPDKsyVQAFEINQTSPKALpLETVTGAYWVDDYCQLLTPQRISLNTCLNASKGE----RVIVEG 148
                                       5555555447799999999999999*********************999988777776....677776 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.45
                        Ig_GlcNase  65 vlwsDNyvtLlPgEsltltveypaa 89 
                                       v++  N  t++ gE+ +++v  p +
  gi|242398015|ref|YP_002993439.1| 181 VIYGGNPATIWDGEE-EVRVYLPYK 204
                                       7888999999*9986.344444333 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.36
                        Ig_GlcNase  33 tkvtvtLenkssvpAffvrln 53 
                                       +++ vtLe  ++v+Af  + +
  gi|242398015|ref|YP_002993439.1| 361 KSIGVTLEEGGHVVAFGFHTT 381
                                       67889**********987765 PP

>> Rep_fac-A_3  Replication factor A protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.98   5.8e+03      55      74 ..      38      58 ..      26      82 .. 0.69
   2 ?   -2.6   0.0       1.2     7e+03      55      73 ..      73      92 ..      63     103 .. 0.73
   3 ?    9.6   0.0   0.00019       1.1      36      74 ..     188     227 ..     180     236 .. 0.78
   4 ?   -2.7   0.0       1.3   7.7e+03      18      36 ..     232     250 ..     223     253 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.98
                                      SS---SEEEEEEEE-T.TS-E CS
                       Rep_fac-A_3 55 tleiskwvEvvGkvsd.dlgi 74
                                      +++ + ++E++G+  + +  +
  gi|242398015|ref|YP_002993439.1| 38 EAKKGDLIEFTGICVNsKENF 58
                                      344477889988766544444 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.2
                                      SS---SEEEEEEEE-T.TS- CS
                       Rep_fac-A_3 55 tleiskwvEvvGkvsd.dlg 73
                                      tle +k++ + Gk +d d++
  gi|242398015|ref|YP_002993439.1| 73 TLESGKVYKIRGKLTDpDKS 92
                                      78889999999998886444 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00019
                                       EEEE-TTS-EEEEEESS--SS---SEEEEEEEE-T..TS-E CS
                       Rep_fac-A_3  36 lilqstdggsvtvrlsedstleiskwvEvvGkvsd..dlgi 74 
                                       +++ ++ +++v v l  ++tle++ +vEv+G+++    l+i
  gi|242398015|ref|YP_002993439.1| 188 ATIWDG-EEEVRVYLPYKQTLEVGDYVEVIGTAKLysTLTI 227
                                       555555.677999999****************987555555 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 1.3
                                       TSEEEEEEEEEEETTSSEE CS
                       Rep_fac-A_3  18 grtvrivgkvesvpsgktl 36 
                                        + +r++g++ + p g++ 
  gi|242398015|ref|YP_002993439.1| 232 RSDIRVLGRARKCPIGEEK 250
                                       5679999999999887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); 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: 0.62u 0.35s 00:00:00.97 Elapsed: 00:00:00.55
# Mc/sec: 2203.56
//
Query:       gi|242398016|ref|YP_002993440.1|  [L=383]
Description: hypothetical protein TSIB_0020 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-38  132.0  34.4    3.3e-38  131.5  34.4    1.2  1  TctA      Tripartite tricarboxylate transporter TctA family


Domain annotation for each model (and alignments):
>> TctA  Tripartite tricarboxylate transporter TctA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.5  34.4   1.8e-42   3.3e-38       4     408 ..       5     373 ..       2     374 .. 0.84

  Alignments for each domain:
  == domain 1  score: 131.5 bits;  conditional E-value: 1.8e-42
                              TctA   4 vllGvllGtliGllPGlhatlavalllpltfgldpeaalilllgiyvgaifggsipaillgvPGtpssvatvldgyp 80 
                                       ++lG+l Gtl+Gl P lh+++ ++l+  l f l+  + ++l  ++ ++++f++++p++++gvP ++ ++++vl++++
  gi|242398016|ref|YP_002993440.1|   5 LILGMLGGTLTGLTPSLHVNTLASLINNLDFPLEGFSFVVLAYAMGLTHTFLDAFPSTFFGVP-DEGTALSVLPAHR 80 
                                       579************************************************************.************* PP

                              TctA  81 lakqGrageAlrlaaigSfiGglvsvllllllapllakvalkfgpaeyfalillglvliailsek..sllkgliall 155
                                       la+qG++ e ++l++ +S++++++s+ l+ l  ++ +      +++e    i++ l+++++++ek  + l +l++ll
  gi|242398016|ref|YP_002993440.1|  81 LALQGKGLEVINLSLRASLLAAIFSIALIPLYLIIAP-----YYTPEIGRAIVFFLAFLIVVTEKgiKKLYALFVLL 152
                                       *************************998877766666.....44677777777777777777765114566777777 PP

                              TctA 156 lglllgtvgldpnsgtpRftfgsielldgislvpvliGlFgiselltsleskskip..lslkdlkkslptilrgsli 230
                                       l+++lg+v                      ++  +++GlFg++ +l sl +++ki+  +  + ++ s  +++  s++
  gi|242398016|ref|YP_002993440.1| 153 LAGALGIVSDLLP--------------LREPFYHLFVGLFGVPAILLSLDNNNKISggN--DTIEMSQSQLVGFSFL 213
                                       7777777765433..............456799****************9998887663..3333333334444555 PP

                              TctA 231 GtivG....ilPgvGasiaaflayavakrlskkpekfgkgaiegvaapeaannaaaggaliplltlgipgsgvaavl 303
                                       Gti+G    +lP +++s aa+++ ++a+            ++++++ + a+n+a+ ++ l   ++ g +++g+ +++
  gi|242398016|ref|YP_002993440.1| 214 GTIFGmmasLLPTFTSSQAALIGSFIAR-----------SERTFLTITFAVNTANFVFGLGNFYSTGKTRNGILVLI 279
                                       555555555*****************87...........5799*******************************999 PP

                              TctA 304 lgallihglqpgpeLftenpelvyallasllianvlllvlgllliklfakll.kipkelLlpiilvllvigayalnn 379
                                        +++        p       e++++lla+l++a+++  + gl+l+k ++ l+ +i+++ L ++il  +v+g+  l +
  gi|242398016|ref|YP_002993440.1| 280 RELY-------YPIS---LQEFLILLLATLAVAAIVN-LYGLWLSKKLVTLIeRIDYRTLNALILTTTVLGSLFLDG 345
                                       9987.......3442...2357777777777777766.578889999999777************************ PP

                              TctA 380 slfdvlvmlifgvlGlllrrlgvplaplv 408
                                         f++lv+++++++Gl    lgv++ +++
  gi|242398016|ref|YP_002993440.1| 346 L-FGLLVLIAATLVGLTAVFLGVKRTACM 373
                                       *.************************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       729  (0.0406604); 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:                         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: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 2253.81
//
Query:       gi|242398017|ref|YP_002993441.1|  [L=436]
Description: ATPase of the AAA superfamily [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-23   82.3   0.0    5.1e-23   81.6   0.0    1.3  1  AAA_14    AAA domain
      0.001   19.0   0.1     0.0018   18.2   0.1    1.4  1  HTH_36    Helix-turn-helix domain
     0.0058   16.2   0.1      0.011   15.3   0.1    1.5  1  HTH_24    Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.039   14.3   0.4          1    9.7   0.1    2.5  3  AAA_16    AAA ATPase domain
      0.041   13.8   0.0      0.079   12.8   0.0    1.4  1  HTH_5     Bacterial regulatory protein, arsR family
      0.058   13.3   0.0        6.9    6.5   0.0    2.9  2  ATPase_2  ATPase domain predominantly from Archaea
       0.11   12.5   0.0       0.24   11.3   0.0    1.6  1  MarR_2    MarR family
       0.15   12.0   0.0       0.46   10.5   0.0    1.8  1  HTH_11    HTH domain
       0.23   11.4   2.2        0.3   11.0   0.1    2.2  2  PT-TG     Pre-toxin TG


Domain annotation for each model (and alignments):
>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.6   0.0   2.5e-26   5.1e-23       5     131 .]      54     175 ..      52     175 .. 0.91

  Alignments for each domain:
  == domain 1  score: 81.6 bits;  conditional E-value: 2.5e-26
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqevpewek 81 
                                       +++ G+R +GKTtll ql+      +++++y+ +d+ ++  ++   +  e +le +++ ++ +l+lDE+q+ ++w  
  gi|242398017|ref|YP_002993441.1|  54 VFLPGLRATGKTTLLGQLYFYTHSLSSEVIYLPVDELKLLGFTLI-EAVERYLEIFRP-ERPVLLLDEVQYDEKWPL 128
                                       7899***********99964444579*************999977.478899998888.99**************** PP

                            AAA_14  82 alkslvdegknldvivtGSnskllskeiatslagrvaeielyplsfaEfl 131
                                       +lk l d++ ++ +i+tGS++++l++  + +la+r+++i+++pl+f+E+l
  gi|242398017|ref|YP_002993441.1| 129 TLKVLNDRK-QFLIIATGSSALNLKE--SPDLARRAEHIHVHPLTFREYL 175
                                       *******99.99************77..8*******************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 !   18.2   0.1   9.1e-07    0.0018      15      55 .]     267     306 ..     258     306 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 9.1e-07
                            HTH_36  15 asfanknggcfpsqetlakrlglsknTvsraikeLeqlGyi 55 
                                         +an +g+  +s+e+l+k lg+ k Tv++ i+ L+++G++
  gi|242398017|ref|YP_002993441.1| 267 FLLANPKGE-RFSYERLSKILGMAKGTVISTINALIKAGIL 306
                                       555544444.479**************************97 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   5.5e-06     0.011       5      47 ..     262     306 ..     259     307 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5.5e-06
                            HTH_24   5 drkILelLqk..nprisqreLAerlglSpstvnrrlkrLeeeGlI 47 
                                       ++k+L lL      r s+  L++ lg+ ++tv   ++ L+++G++
  gi|242398017|ref|YP_002993441.1| 262 TLKLLFLLANpkGERFSYERLSKILGMAKGTVISTINALIKAGIL 306
                                       56677777777555689999***********************96 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1   0.00051         1      20      45 ..      47      72 ..      29      92 .. 0.72
   2 ?    1.6   0.0      0.16   3.2e+02     119     158 ..      97     133 ..      87     143 .. 0.72
   3 ?   -3.2   0.0       4.8   9.6e+03      41      63 ..     399     421 ..     390     430 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00051
                            AAA_16 20 rsgrpelvllsGesGvGKsslvrell 45
                                        gr+  v+l G +++GK++l+ +l+
  gi|242398017|ref|YP_002993441.1| 47 GGGRCATVFLPGLRATGKTTLLGQLY 72
                                      3455599***************8886 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.16
                            AAA_16 119 llellkrllallsrderplvlvlDdlqwadeaslql.laaL 158
                                       l e++ r l+  ++ er  vl+lD++q  +   + l l+ L
  gi|242398017|ref|YP_002993441.1|  97 LIEAVERYLEIFRP-ER-PVLLLDEVQYDE--KWPLtLKVL 133
                                       67788888888888.88.8********433..344444555 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 4.8
                            AAA_16  41 vrellralekdggiflrgkcdql 63 
                                       vr+ ++++++dggi++ +k+  +
  gi|242398017|ref|YP_002993441.1| 399 VRRSMERVSADGGIVIGEKFYAN 421
                                       36666778888888888888777 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 ?   12.8   0.0     4e-05     0.079       5      45 ..     263     306 ..     260     307 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4e-05
                                       HHHHHHHTT..SSEEHHH.HHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5   5 lkILklLae..gelcvce.laeelglsqstvShHLkkLreaGLV 45 
                                       lk+L+lLa+  ge+ + e l+++lg+ ++tv    ++L +aG++
  gi|242398017|ref|YP_002993441.1| 263 LKLLFLLANpkGERFSYErLSKILGMAKGTVISTINALIKAGIL 306
                                       899**********998888***********************85 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 ?    6.5   0.0    0.0034       6.9      12      54 ..      43      85 ..      36      92 .. 0.85
   2 ?    3.3   0.0     0.034        68     153     200 ..     133     177 ..      90     202 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0034
                          ATPase_2 12 eeilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyy 54
                                      ++ +  ++   +f+ G +  GKt+Ll +++   ++++ +viy+
  gi|242398017|ref|YP_002993441.1| 43 NSFMGGGRCATVFLPGLRATGKTTLLGQLYFYTHSLSSEVIYL 85
                                      556666777789999***************9999999999996 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.034
                          ATPase_2 153 tkekhlcvviclsSeglfiervyneselegrhkyilvddldketalnf 200
                                       +++++ +++i++ S  l ++   ++  l  r+++i+v++l++ + l +
  gi|242398017|ref|YP_002993441.1| 133 LNDRKQFLIIATGSSALNLK---ESPDLARRAEHIHVHPLTFREYLYL 177
                                       34566677777777777777...6667778888888888887766655 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00012      0.24      10      55 ..     265     310 ..     258     313 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00012
                                       HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2  10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55 
                                       +L+ L++  g++++   l + lg+ k++v  +++ L +aG +++ p
  gi|242398017|ref|YP_002993441.1| 265 LLFLLANPKGERFSYERLSKILGMAKGTVISTINALIKAGILVEIP 310
                                       45555555555*****************************998766 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00023      0.46       3      47 ..     263     308 ..     261     314 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00023
                            HTH_11   3 lqilelLleargp.isgeeLAeeLnvSrrtvrrdIkaLeelgvpIe 47 
                                       l++l lL + +g  +s e+L++ L++ + tv   I aL ++g+ +e
  gi|242398017|ref|YP_002993441.1| 263 LKLLFLLANPKGErFSYERLSKILGMAKGTVISTINALIKAGILVE 308
                                       78899998889999****************************5544 PP

>> PT-TG  Pre-toxin TG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.2      0.93   1.9e+03      51      63 ..     308     322 ..     273     332 .. 0.65
   2 ?   11.0   0.1   0.00015       0.3       8      51 ..     373     415 ..     370     432 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.93
                             PT-TG  51 g..gvgkvgkkakka 63 
                                           +g+ +kk+kk+
  gi|242398017|ref|YP_002993441.1| 308 EipSIGGMTKKVKKG 322
                                       244677777776654 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00015
                             PT-TG   8 vldfvpevggvkdaieaitGrDpiTGeklsdwdRllaavalvpg 51 
                                       + dfv+ v g k ++e+  G+D +T+   s ++R+ a +++v g
  gi|242398017|ref|YP_002993441.1| 373 GADFVLTVDGRKYVVEVGLGKDRVTQVRRS-MERVSADGGIVIG 415
                                       5799**************************.******9999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); 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: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 2601.78
//
Query:       gi|242398018|ref|YP_002993442.1|  [L=204]
Description: Methyltransferase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-09   37.5   1.0    4.1e-09   36.6   1.0    1.6  1  Peptidase_M73  Camelysin metallo-endopeptidase
  ------ inclusion threshold ------
      0.037   14.0   0.0      0.092   12.7   0.0    1.6  1  CusF_Ec        Copper binding periplasmic protein CusF


Domain annotation for each model (and alignments):
>> Peptidase_M73  Camelysin metallo-endopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   1.0   4.6e-13   4.1e-09      22     190 ..      28     203 ..       6     204 .] 0.58

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 4.6e-13
                     Peptidase_M73  22 GGtyayfsDseta.nnsfaaGtldlsvd........ptviidvknlkPGDtvtrefklenkGtLdikkvlleteyev 89 
                                       GG  a fsD + + nn+ a+G++d+ +         +  +++ ++lkPGD ++ ef ++n+G  +i+k+l+  + + 
  gi|242398018|ref|YP_002993442.1|  28 GG--ALFSDISISeNNEIATGEFDVRISktgssfynDLKLFEFNDLKPGDEIKAEFYIKNSGDFNISKILIIPHVQD 102
                                       33..789**88652789*********9877777776889*******************************9865433 PP

                     Peptidase_M73  90 ...kdvkkdnegeDfgkhi...rvefLvnedkeeevisettLaeLkemspdvveedvlallleeegddleagesdkl 160
                                           d+++ ++  D +++i     + +  +   ++  ++ tL++ + +s + ++++ ++ll            s+ l
  gi|242398018|ref|YP_002993442.1| 103 lesGDLNGAEALVDNTTEIgelSQNLILEWIVITQSNQTYTLSDYSGKSLHELNNQSISLLTAP------FAPSEVL 173
                                       1112222222222222221110222222233333333333444444444444444333333222......2356677 PP

                     Peptidase_M73 161 kvkfefvdndedqnkfqgdsLklewtfeak 190
                                       kv + f  n e  n+ q+d   ++ ++ a+
  gi|242398018|ref|YP_002993442.1| 174 KVTMFFLVNPEAGNEIQKDLCLISMQIYAE 203
                                       777777777777777777766666666655 PP

>> CusF_Ec  Copper binding periplasmic protein CusF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0     1e-05     0.092      40      66 ..      68      94 ..      66      95 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1e-05
                                      ESS-STT-EEEEEEEEETTCEEEEEEE CS
                           CusF_Ec 40 laglkaGdkVrFefekrdggeyvitki 66
                                      +++lk+Gd+++ ef  +++g++ i+ki
  gi|242398018|ref|YP_002993442.1| 68 FNDLKPGDEIKAEFYIKNSGDFNISKI 94
                                      689*********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       562  (0.0313459); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); 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: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1313.45
//
Query:       gi|242398019|ref|YP_002993443.1|  [L=283]
Description: sugar-catabolism phosphotransferase [Thermococcus sibiricus MM 739]
Scores for complete 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  108.9   0.0    4.4e-31  107.0   0.0    2.0  3  Hydrolase_6      Haloacid dehalogenase-like hydrolase
    3.5e-20   71.8   0.1    9.1e-20   70.5   0.0    1.7  2  Hydrolase_like   HAD-hyrolase-like
    5.8e-08   33.0   4.7     0.0016   18.6   0.1    3.4  3  HAD_2            Haloacid dehalogenase-like hydrolase
    2.6e-07   31.1   0.7       0.12   12.6   0.0    3.5  4  Hydrolase        haloacid dehalogenase-like hydrolase
    2.3e-06   27.3   0.0    1.9e-05   24.3   0.0    2.5  3  PGP_phosphatase  Mitochondrial PGP phosphatase
     0.0023   17.7   0.0     0.0034   17.1   0.0    1.3  1  Hydrolase_3      haloacid dehalogenase-like hydrolase
     0.0063   16.3   0.0        3.4    7.5   0.1    3.5  4  DRTGG            DRTGG domain
  ------ inclusion threshold ------
      0.024   15.1   0.0       0.13   12.7   0.0    2.2  3  DUF3293          Protein of unknown function (DUF3293)
      0.039   14.7   0.1         42    5.0   0.0    3.2  3  GARS_N           Phosphoribosylglycinamide synthetase, N doma


Domain annotation for each model (and alignments):
>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.0   0.0   2.2e-34   4.4e-31       1      99 [.      22     120 ..      22     122 .. 0.98
   2 ?   -2.2   0.0       2.3   4.5e+03      14      28 ..     179     193 ..     177     209 .. 0.80
   3 ?   -2.2   0.0       2.3   4.5e+03      66      89 ..     205     228 ..     184     242 .. 0.70

  Alignments for each domain:
  == domain 1  score: 107.0 bits;  conditional E-value: 2.2e-34
                                       EEEESTTTSEETTEE-TTHHHHHHHHHHTT-EEEEEE---SS-HHHHHHHHHHTT----GGGEEEHHHHHHHHHHHH CS
                       Hydrolase_6   1 flfDidGvLwrgdkaipgaaealnalraagkpvvllTNnsskseeeyakkleklgvditeeqvvtsataaaeylkkr 77 
                                       ++fD+dGv++rg+++i+g++e++++l+++++p+v+lTNns++  + y +kl+ +g++++e++++ts+ a+a+ylkk+
  gi|242398019|ref|YP_002993443.1|  22 IIFDMDGVIYRGNQPIDGVKEVIEFLKSNKIPFVFLTNNSTRDAKMYREKLQGMGIEVEEDRIITSGHATAQYLKKH 98 
                                       69*************************************************************************** PP

                                       SXXXEEEEESXHHHHHHHHHTT CS
                       Hydrolase_6  78 kadkkvlvigeeglreelkeag 99 
                                        ++++v+v+g++gl ee+k+ +
  gi|242398019|ref|YP_002993443.1|  99 FEKGNVFVVGGKGLVEEIKSID 120
                                       *****************99876 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.3
                                       EE-TTHHHHHHHHHH CS
                       Hydrolase_6  14 kaipgaaealnalra 28 
                                        ++pga  ++ al+ 
  gi|242398019|ref|YP_002993443.1| 179 GILPGAGSIIAALKV 193
                                       679999999999985 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 2.3
                                       HHHHHHHHHHHHSXXXEEEEESXH CS
                       Hydrolase_6  66 sataaaeylkkrkadkkvlvigee 89 
                                       + +++ e+++++ + + ++v+g  
  gi|242398019|ref|YP_002993443.1| 205 PNEPVFEVVREKLNADEIWVVGDR 228
                                       556677777777888888888875 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       3.7   7.3e+03      18      28 ..      98     108 ..      67     108 .. 0.64
   2 !   70.5   0.0   4.6e-23   9.1e-20       2      75 .]     202     273 ..     201     273 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 3.7
                                       ---GGGEEEEE CS
                    Hydrolase_like  18 gsdpeevlmiG 28 
                                       + ++++v+++G
  gi|242398019|ref|YP_002993443.1|  98 HFEKGNVFVVG 108
                                       34466677776 PP

  == domain 2  score: 70.5 bits;  conditional E-value: 4.6e-23
                                       .STTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESSSSS-TTTHHHHHHHHT---SEEES- CS
                    Hydrolase_like   2 lgKPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVltGvtrpedleepehkptyvaddlaea 75 
                                       +gKP+ ++++  +e+l++  +e++++GDrl+tDia+A+++G+k ++VltGv++ ed e+ e kp++v+++++e+
  gi|242398019|ref|YP_002993443.1| 202 IGKPNEPVFEVVREKLNA--DEIWVVGDRLDTDIAFAKKIGAKAIMVLTGVNTLEDIEKSEVKPDIVLPSIKEL 273
                                       7**************855..89************************************************9985 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.5     0.027        53       1      10 [.      22      31 ..      22      35 .. 0.88
   2 !   11.3   0.0   0.00013      0.27      79     128 ..      35      87 ..      31      98 .. 0.75
   3 !   18.6   0.1     8e-07    0.0016     129     178 .]     198     246 ..     186     246 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.027
                             HAD_2  1 iiFDlDgTll 10
                                      iiFD+Dg+++
  gi|242398019|ref|YP_002993443.1| 22 IIFDMDGVIY 31
                                      8*******97 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00013
                             HAD_2  79 kpydgvkelLeeLkeagyklgivTsksreav...eekleqlgiesyFdvivts 128
                                       +p+dgvke++e Lk++++     T++s++ +   +ekl+ +gie   d i+ts
  gi|242398019|ref|YP_002993443.1|  35 QPIDGVKEVIEFLKSNKIPFVFLTNNSTRDAkmyREKLQGMGIEVEEDRIITS 87 
                                       79***********************9665541115666666666666666665 PP

  == domain 3  score: 18.6 bits;  conditional E-value: 8e-07
                             HAD_2 129 edvekkKPdpeviekaleklklkkeeviyvGDsp.tDieaakkagikviav 178
                                       e     KP+  v+e + ekl+  ++e+++vGD   tDi  akk+g k+i+v
  gi|242398019|ref|YP_002993443.1| 198 EPLIIGKPNEPVFEVVREKLN--ADEIWVVGDRLdTDIAFAKKIGAKAIMV 246
                                       555567999999999988765..689***********************97 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0      0.01        20       4      16 ..      22      34 ..      20      38 .. 0.88
   2 !   10.5   0.0   0.00027      0.53     119     156 ..      36      74 ..      34     108 .. 0.70
   3 !   12.6   0.0   6.3e-05      0.12     155     210 .]     184     240 ..     125     240 .. 0.76
   4 ?   -2.7   0.0       2.9   5.8e+03     168     186 ..     255     273 ..     245     279 .. 0.63

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.01
                                      EEEESBTTTBCHH CS
                                      xxxxxxxxxxxxx RF
                         Hydrolase  4 vvfDkdGTLttge 16
                                      ++fD+dG++++g+
  gi|242398019|ref|YP_002993443.1| 22 IIFDMDGVIYRGN 34
                                      89********998 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00027
                                       BHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHH.TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx RF
                         Hydrolase 119 vkpeaaeavasLkaagievvlltgdnpetaeraanq.lG 156
                                       + ++++e+++ Lk+++i+ v lt+++ + a+   ++  G
  gi|242398019|ref|YP_002993443.1|  36 PIDGVKEVIEFLKSNKIPFVFLTNNSTRDAKMYREKlQG 74 
                                       6799********************999877755444233 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 6.3e-05
                                       TTGGGE.SEEEEHHCES..STTTSHHHHHHHHHHHTSTGGGEEEEESSHH.HHHHHHHTT CS
                                       xxxxxx.xxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                         Hydrolase 155 lGddyf.daviasdiet..vakpspegkvaaireLqgkpeevamVGDgvn.DaaalaaAg 210
                                       +G  ++ + ++a++ e   ++kp+   ++ + ++L+++   + +VGD++  D+a++++ g
  gi|242398019|ref|YP_002993443.1| 184 AG-SIIaALKVATEKEPliIGKPNEPVFEVVREKLNADE--IWVVGDRLDtDIAFAKKIG 240
                                       66.3333556666666688****************8777..***************9876 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 2.9
                                       CESSTTTSHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 168 ietvakpspegkvaaireL 186
                                       + + ++++p++++  i+eL
  gi|242398019|ref|YP_002993443.1| 255 DIEKSEVKPDIVLPSIKEL 273
                                       4445777777777777777 PP

>> PGP_phosphatase  Mitochondrial PGP phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.65   1.3e+03      23      56 ..     113     151 ..     110     154 .. 0.81
   2 !   24.3   0.0   9.8e-09   1.9e-05     127     167 ..     213     250 ..     165     251 .. 0.81
   3 ?   -2.5   0.0       1.7   3.3e+03      14      31 ..     258     275 ..     256     280 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.65
                   PGP_phosphatase  23 vptfrqlpieig.....kkkektikavvlDKDnclaapk 56 
                                       v++++++++++      k+k ++i +vv+  D  l+++k
  gi|242398019|ref|YP_002993443.1| 113 VEEIKSIDWPVIsleeaKEKWREIGYVVVGMDPQLTYEK 151
                                       678899999988788878888999999999998888765 PP

  == domain 2  score: 24.3 bits;  conditional E-value: 9.8e-09
                   PGP_phosphatase 127 fkerkvveeadeiavvgDRllTdvllanmmGslgvwlrdgv 167
                                        +e+    +adei vvgDRl Td+ +a+++G+ ++++  gv
  gi|242398019|ref|YP_002993443.1| 213 VREK---LNADEIWVVGDRLDTDIAFAKKIGAKAIMVLTGV 250
                                       4444...689*************************999888 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 1.7
                   PGP_phosphatase  14 pslvlPhltvptfrqlpi 31 
                                       +s v P++ +p++++l +
  gi|242398019|ref|YP_002993443.1| 258 KSEVKPDIVLPSIKELLE 275
                                       678899999999988855 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.7e-06    0.0034       1      53 [.      22      73 ..      22     102 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.7e-06
                                      EEEEIIIIIS-TTS---HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCC CS
                       Hydrolase_3  1 ialDlDGTLlnsdkkisektkeaikklkekgikvviATGRslravlpvleelg 53
                                      i++D+DG + + ++ i +  ke+i+ lk++ i +v+ T +s+r+++ + e+l+
  gi|242398019|ref|YP_002993443.1| 22 IIFDMDGVIYRGNQPI-DGVKEVIEFLKSNKIPFVFLTNNSTRDAKMYREKLQ 73
                                      89*****998888887.99*******************************997 PP

>> DRTGG  DRTGG domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.2   2.3e+03      75      97 ..      41      63 ..      24      72 .. 0.68
   2 ?    1.3   0.0      0.15   2.9e+02      27      48 ..      88     109 ..      70     110 .. 0.78
   3 ?    2.4   0.0     0.065   1.3e+02      17      50 ..     131     164 ..     116     165 .. 0.78
   4 !    7.5   0.1    0.0017       3.4      34      71 ..     213     251 ..     209     260 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.2
                                      HHHHHHHHHHT--EEE-SS-HHH CS
                             DRTGG 75 eevlklaeeaglpvlsveldtft 97
                                      +ev+++++ +++p +  + ++  
  gi|242398019|ref|YP_002993443.1| 41 KEVIEFLKSNKIPFVFLTNNSTR 63
                                      67888888888886666555554 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.15
                                       -SS-HHHHHHHHHTSEEEEEET CS
                             DRTGG  27 gamsvenmlerlkegdlvivpG 48 
                                       g  +++ + +++++g++ +v+G
  gi|242398019|ref|YP_002993443.1|  88 GHATAQYLKKHFEKGNVFVVGG 109
                                       5567778889999999999987 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.065
                                       SS--E-EEEE-SS-HHHHHHHHHTSEEEEEETT- CS
                             DRTGG  17 elrrvekvvvgamsvenmlerlkegdlvivpGDR 50 
                                       e+ r   +vv+ m ++ + e+lk g+l i  G R
  gi|242398019|ref|YP_002993443.1| 131 EKWREIGYVVVGMDPQLTYEKLKYGCLAIRNGAR 164
                                       33347789999******************88866 PP

  == domain 4  score: 7.5 bits;  conditional E-value: 0.0017
                                       HHHHHHTSEEEEEETT-HHHHHHHTT-T..EEEEEEETT- CS
                             DRTGG  34 mlerlkegdlvivpGDRediqlaaleag..iaalilTggl 71 
                                       + e+l+ +++ +v GDR d+ +a +++    a+++lTg  
  gi|242398019|ref|YP_002993443.1| 213 VREKLNADEIWVV-GDRLDTDIAFAKKIgaKAIMVLTGVN 251
                                       6788999******.******99998887766788888754 PP

>> DUF3293  Protein of unknown function (DUF3293)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       2.7   5.3e+03      56      70 ..      87     101 ..      59     104 .. 0.65
   2 ?   12.7   0.0   6.6e-05      0.13      23      59 ..     112     146 ..     109     153 .. 0.82
   3 ?   -3.9   0.0         9   1.8e+04      37      51 ..     165     180 ..     162     181 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.7
                           DUF3293  56 lslaeakeLakkFgQ 70 
                                        + a+a+ L k+F+ 
  gi|242398019|ref|YP_002993443.1|  87 SGHATAQYLKKHFEK 101
                                       466777777777765 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 6.6e-05
                           DUF3293  23 LleelkklglpvlpavgadedgeWsEesflVlglsla 59 
                                       L ee+k+  +pv++ + a+e+  W+E++++V g++++
  gi|242398019|ref|YP_002993443.1| 112 LVEEIKSIDWPVISLEEAKEK--WREIGYVVVGMDPQ 146
                                       889999999999988776555..********998765 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 9
                           DUF3293  37 avgadedgeWs.Eesf 51 
                                        +g+++d++++ Ee++
  gi|242398019|ref|YP_002993443.1| 165 FIGTNPDTTYPgEEGI 180
                                       5788999999888876 PP

>> GARS_N  Phosphoribosylglycinamide synthetase, N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.079   1.6e+02      30      59 ..      30      59 ..      26      73 .. 0.87
   2 ?    5.0   0.0     0.021        42      13      64 ..      89     148 ..      86     169 .. 0.79
   3 ?    2.6   0.0      0.12   2.4e+02      32      81 ..     175     226 ..     164     231 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.079
                                      EEE--CGGTTHHHHHHHHHHCTESEEEE-S CS
                            GARS_N 30 vapgNagtedlealvefakeekidlvvvGp 59
                                      ++ gN+ ++ +++++ef k++ki +v+  +
  gi|242398019|ref|YP_002993443.1| 30 IYRGNQPIDGVKEVIEFLKSNKIPFVFLTN 59
                                      567899998899************999876 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.021
                                       HHHHHHHTTSTTESEEEEEE--CGGTTHHH.......HHHHHHH..CTESEEEE-SHHHHH CS
                            GARS_N  13 halawklaqspkvekvyvapgNagtedlea.......lvefake..ekidlvvvGpeapLv 64 
                                       ha a+ l+++ +  +v+v+ g + +e++++       l e ake  ++i +vvvG + +L+
  gi|242398019|ref|YP_002993443.1|  89 HATAQYLKKHFEKGNVFVVGGKGLVEEIKSidwpvisLEE-AKEkwREIGYVVVGMDPQLT 148
                                       999*******9999*******9999777744455442444.444236799*****988775 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.12
                                       E--CGG....TTHHHHHHHHHHCTESEEEE-SHHHHHTTHHHHHHHHHT-EEES CS
                            GARS_N  32 pgNagt....edlealvefakeekidlvvvGpeapLvaGvadaleeekgikvfG 81 
                                       pg +g+     ++ a +++a+e++  l++  p++p+++ v ++l+++ +i v+G
  gi|242398019|ref|YP_002993443.1| 175 PGEEGIlpgaGSIIAALKVATEKE-PLIIGKPNEPVFEVVREKLNAD-EIWVVG 226
                                       555555544422334455555554.688888*************666.999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); 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:                         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 0.27s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 1865.85
//
Query:       gi|242398020|ref|YP_002993444.1|  [L=54]
Description: hypothetical protein TSIB_0024, partial [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       252  (0.0140554); expected 358.6 (0.02)
Passed bias filter:                      191  (0.0106531); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 405.78
//
Query:       gi|242398021|ref|YP_002993445.1|  [L=184]
Description: Inorganic pyrophosphatase [Thermococcus sibiricus MM 739]
Scores for complete 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-56  189.3   0.4    4.5e-56  189.1   0.4    1.0  1  Pyrophosphatase  Inorganic pyrophosphatase


Domain annotation for each model (and alignments):
>> Pyrophosphatase  Inorganic pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.1   0.4   2.5e-60   4.5e-56       2     160 .]      28     179 ..      27     179 .. 0.97

  Alignments for each domain:
  == domain 1  score: 189.1 bits;  conditional E-value: 2.5e-60
                                       EEEE-TTCSEEEEEETTTTEEEEEEE-SSSB-BSSEEEEETT--BTCCBEETSSSEEEEEESSS---TTEEEEEEEE CS
                   Pyrophosphatase   2 vvEiprgsnaKyeidkeegklrldrvlftskgypanYGfipqTledtelkGDgDPlDvlvlgeeplspgevvevkvl 78 
                                       ++Eip+gs++Kye+dk++g ++ldrvl++ + yp++YG+ipqT+ d     D+DP D++v+++ep++p +++e++++
  gi|242398021|ref|YP_002993445.1|  28 LIEIPKGSRNKYELDKKTGLIKLDRVLYSPFYYPVDYGVIPQTWYD-----DDDPFDIMVIMREPTYPLTIIEARPI 99 
                                       79********************************************.....************************** PP

                                       EEEEEEETTEEEEEEEEEETTSGGGTT-SSGGGSTHHHHHHHHHHHHHTTTTSCCT-SEEEEEEEEHHHHHHHHHHH CS
                   Pyrophosphatase  79 GvlamiDegetDdKiiavpvkdprlkkindiedlpgllleeiehfFetykdlegkkknvkveewkdkeeAekvieea 155
                                       G+++miD+g +D K++avpv+dp +k+++d++d+p+ +l+ei hfF+ yk+l+gk  +  ve+w+++++A+++i +a
  gi|242398021|ref|YP_002993445.1| 100 GLFKMIDSGDRDYKVLAVPVEDPYFKDWKDLDDVPKAFLDEIAHFFRRYKELQGK--EIIVEGWENADKAKQEILRA 174
                                       ***********************88****************************55..78999*************** PP

                                       HHHHH CS
                   Pyrophosphatase 156 heryk 160
                                       +e yk
  gi|242398021|ref|YP_002993445.1| 175 IELYK 179
                                       99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        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 0.24s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 1393.80
//
Query:       gi|242398022|ref|YP_002993446.1|  [L=187]
Description: DNA-directed RNA polymerase, subunit E' [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.6e-19   68.3   0.2    1.2e-18   67.2   0.2    1.6  1  SHS2_Rpb7-N  SHS2 domain found in N terminus of Rpb7p/Rpc25p/
    2.6e-15   56.5   2.3    2.6e-15   56.5   2.3    1.8  2  S1           S1 RNA binding domain
  ------ inclusion threshold ------
       0.64   10.2   5.5        2.8    8.2   0.2    2.9  3  CSD2         Cold shock domain


Domain annotation for each model (and alignments):
>> SHS2_Rpb7-N  SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.2   0.2     2e-22   1.2e-18       1      70 []       8      77 ..       8      77 .. 0.99

  Alignments for each domain:
  == domain 1  score: 67.2 bits;  conditional E-value: 2e-22
                                      EEEEEE-GGGTTSTHHHHHHHHHHHHHTTBEETTTEEEEEEEEEEEECCEEE-TTTSSEEEEEEEEEEEE CS
                       SHS2_Rpb7-N  1 edtvrlePsylgstledallerllekyegkvvpslGvivavldiaeysegkvlggsGsvyvrVtfralvF 70
                                      +d+vr++P ++  ++++a++  l+e+yeg ++++ Gv++avl++ e+seg +++g+G++y++V+f++lv+
  gi|242398022|ref|YP_002993446.1|  8 KDIVRIPPKMFTLDPKEAAKIVLREAYEGIYNKDEGVVLAVLEVHEISEGVIIPGDGATYHDVVFDVLVW 77
                                      599******************************************************************9 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       1.5   8.7e+03       3      13 ..      50      60 ..      42      64 .. 0.67
   2 !   56.5   2.3   4.3e-19   2.6e-15       1      70 [.      78     155 ..      78     159 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.5
                                      TTTCEEEEEEE CS
                                S1  3 ekgevveGeVt 13
                                      e++e+ eG+++
  gi|242398022|ref|YP_002993446.1| 50 EVHEISEGVII 60
                                      45666666665 PP

  == domain 2  score: 56.5 bits;  conditional E-value: 4.3e-19
                                       HSTTTCEEEEEEEEEETTEEEEEETTTEEEEEEGGGSSSS..........CEESCHHHCEETTEEEEEEEEEEETTT CS
                                S1   1 kpekgevveGeVtsvtkgGafVelgngvegfvpaselsrd..........arvedpdevlkvGdevkvkvlkvdkdr 67 
                                       kpe +evveGeV++v+++Gaf+++g +++g+v++s+l++d            +++++ vlk Gd v+++++ + ++ 
  gi|242398022|ref|YP_002993446.1|  78 KPEMHEVVEGEVIDVVPYGAFIRIG-PMDGLVHISQLMDDyvvfdeknaqFVGKEKGHVLKLGDVVRARIIAISEKS 153
                                       68999********************.**********************9966888999**************99987 PP

                                       TEE CS
                                S1  68 rri 70 
                                       + i
  gi|242398022|ref|YP_002993446.1| 154 K-I 155
                                       7.5 PP

>> CSD2  Cold shock domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1      0.17     1e+03      12      50 ..       9      49 ..       6      60 .. 0.63
   2 ?    3.3   0.3     0.016        96       9      49 ..      54      92 ..      47      94 .. 0.65
   3 ?    8.2   0.2   0.00048       2.8       1      39 [.     117     152 ..     117     161 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.17
                              CSD2 12 dif.ipkeklk.gakdGdkVvveiteypdkkn.peGevievL 50
                                      di+ ip++    ++k+  k+v +   y++ +n  eG v+ vL
  gi|242398022|ref|YP_002993446.1|  9 DIVrIPPKMFTlDPKEAAKIVLR-EAYEGIYNkDEGVVLAVL 49
                                      55558877555477777777776.334433333677777776 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.016
                              CSD2  9 lkqdifipkeklkgakdGdkVvveitey.pdkkn.peGeviev 49
                                      +++ ++ip +   ga   d Vv +++ + p+ ++ +eGevi+v
  gi|242398022|ref|YP_002993446.1| 54 ISEGVIIPGD---GATYHD-VVFDVLVWkPEMHEvVEGEVIDV 92
                                      5566677744...444444.5566666636666679****998 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.00048
                              CSD2   1 FVvpddkrlkqdifipkeklkgakdGdkVvveiteypdk 39 
                                       +Vv d+k+ +   f+ kek + +k Gd+V ++i+   +k
  gi|242398022|ref|YP_002993446.1| 117 YVVFDEKNAQ---FVGKEKGHVLKLGDVVRARIIAISEK 152
                                       8999999999...89***9999***********987654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 1433.21
//
Query:       gi|242398023|ref|YP_002993447.1|  [L=61]
Description: DNA-directed RNA polymerase, subunit e'' [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.7e-15   56.2   0.0    3.1e-15   56.0   0.0    1.1  1  Spt4          Spt4/RpoE2 zinc finger
      0.009   15.6   3.8      0.013   15.1   3.8    1.3  1  RecR          RecR protein
  ------ inclusion threshold ------
       0.02   14.4   1.7      0.027   14.0   1.7    1.2  1  zn-ribbon_14  Zinc-ribbon
      0.022   14.2   2.7       0.09   12.2   0.1    2.1  2  zf-ribbon_3   zinc-ribbon domain
        0.1   12.6   2.4       0.14   12.1   2.4    1.1  1  HypA          Hydrogenase/urease nickel incorporation, metall
       0.11   11.3   1.0       0.11   11.2   1.0    1.0  1  NRDD          Anaerobic ribonucleoside-triphosphate reductase
       0.33   10.7   0.1       0.33   10.7   0.1    2.2  2  zf-RRN7       Zinc-finger of RNA-polymerase I-specific TFIIB,
        1.3    9.0   7.2        3.7    7.5   7.2    1.7  1  DUF35_N       Rubredoxin-like zinc ribbon domain (DUF35_N)
        1.3    9.2   5.5         17    5.6   5.4    2.1  2  Zn-ribbon_8   Zinc ribbon domain


Domain annotation for each model (and alignments):
>> Spt4  Spt4/RpoE2 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.0   0.0   1.6e-18   3.1e-15       1      77 []       3      61 .]       3      61 .] 0.98

  Alignments for each domain:
  == domain 1  score: 56.0 bits;  conditional E-value: 1.6e-18
                              Spt4  1 lrACllCklvktedqFeeegCpnCeilelkgdkekvsectseefeGlvaildpekSwvAkwqrldkkvpglYAlkve 77
                                      ++AC++C+++++ed+     Cp C           +s+++s+e+ +lv+ildpe+S +A+   l+ k+pg+YA++v+
  gi|242398023|ref|YP_002993447.1|  3 EKACRHCHYITNEDR-----CPAC-----------GSRDLSDEWFDLVIILDPENSRIAQT--LGVKKPGKYAIRVR 61
                                      69*************.....****...........**************************..************96 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   3.8   6.5e-06     0.013      17      35 ..       4      22 ..       3      25 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 6.5e-06
                                      EE-TTT--EESSSS-CCCC CS
                              RecR 17 rhCsrCgnlteedlCaICs 35
                                      + C+ C+ +t ed C+ C 
  gi|242398023|ref|YP_002993447.1|  4 KACRHCHYITNEDRCPACG 22
                                      57****************6 PP

>> zn-ribbon_14  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   1.7   1.3e-05     0.027       2      18 ..       5      21 ..       4      22 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.3e-05
                      zn-ribbon_14  2 kCerCGylSSqkiCkAC 18
                                       C+ C y+++ + C AC
  gi|242398023|ref|YP_002993447.1|  5 ACRHCHYITNEDRCPAC 21
                                      6**************** PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.4     0.057   1.1e+02      17      22 ..       4       9 ..       2      11 .. 0.83
   2 ?   12.2   0.1   4.5e-05      0.09       2      14 ..      15      28 ..      14      30 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.057
                       zf-ribbon_3 17 nvCpyC 22
                                      ++C +C
  gi|242398023|ref|YP_002993447.1|  4 KACRHC 9 
                                      68**** PP

  == domain 2  score: 12.2 bits;  conditional E-value: 4.5e-05
                       zf-ribbon_3  2 tvrCPnCGa.plss 14
                                      + rCP+CG+  ls+
  gi|242398023|ref|YP_002993447.1| 15 EDRCPACGSrDLSD 28
                                      679*****965666 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   2.4   7.2e-05      0.14      72      97 ..       5      26 ..       2      29 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.2e-05
                                      EETTTS-EEECHHHHHS-TTTSSS-E CS
                              HypA 72 rCreCgkefeleekalrCpkCgsadv 97
                                       Cr+C++ ++++    rCp+Cgs+d+
  gi|242398023|ref|YP_002993447.1|  5 ACRHCHYITNED----RCPACGSRDL 26
                                      7*****888866....8******986 PP

>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.0   5.6e-05      0.11     508     529 ..       4      25 ..       1      33 [. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5.6e-05
                                       EEETT.--EESSSB-TTT--BE CS
                              NRDD 508 dvCnecgykgeiekCpkCgsee 529
                                       + C++c+y    ++Cp Cgs++
  gi|242398023|ref|YP_002993447.1|   4 KACRHCHYITNEDRCPACGSRD 25 
                                       57******666666*****876 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   3.0     0.095   1.9e+02      24      28 ..       6      10 ..       6      12 .. 0.96
   2 ?   10.7   0.1   0.00016      0.33       4      14 ..      15      25 ..      13      31 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.095
                           zf-RRN7 24 CrrCh 28
                                      Cr+Ch
  gi|242398023|ref|YP_002993447.1|  6 CRHCH 10
                                      ***** PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00016
                           zf-RRN7  4 gppCgvCgcrs 14
                                      + +C++Cg+r+
  gi|242398023|ref|YP_002993447.1| 15 EDRCPACGSRD 25
                                      579******76 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   7.2    0.0018       3.7      15      36 ..       4      26 ..       4      27 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0018
                           DUF35_N 15 pdCGtvqfPPr.avCphCgsddl 36
                                      ++C + ++      Cp Cgs+dl
  gi|242398023|ref|YP_002993447.1|  4 KACRHCHYITNeDRCPACGSRDL 26
                                      589999999999*********98 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.5      0.11   2.2e+02      26      33 ..       3      10 ..       1      13 [. 0.76
   2 ?    5.6   5.4    0.0087        17      26      36 ..      15      26 ..       5      28 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.11
                       Zn-ribbon_8 26 ltaCPeCg 33
                                      ++aC +C+
  gi|242398023|ref|YP_002993447.1|  3 EKACRHCH 10
                                      56799997 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0087
                       Zn-ribbon_8 26 ltaCPeCgs.ev 36
                                      +  CP+Cgs ++
  gi|242398023|ref|YP_002993447.1| 15 EDRCPACGSrDL 26
                                      455*****9665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       731  (0.0407719); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); 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: 00:00:00.45
# Mc/sec: 404.61
//
Query:       gi|242398024|ref|YP_002993448.1|  [L=180]
Description: Ribosomal protein S24E [Thermococcus sibiricus MM 739]
Scores for complete 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  133.9   0.1      3e-39  133.5   0.1    1.2  1  DUF359    Protein of unknown function (DUF359)
  ------ inclusion threshold ------
      0.026   14.3   0.5       0.06   13.1   0.5    1.6  1  DUF3903   Domain of unknown function (DUF3903)


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 !  133.5   0.1   3.3e-43     3e-39       1     126 []      53     174 ..      53     174 .. 0.94

  Alignments for each domain:
  == domain 1  score: 133.5 bits;  conditional E-value: 3.3e-43
                            DUF359   1 vtknllkagikPdlaivDgktkReeveeeekeeekekekekevievkNpaGtiteelieaikeal...eseekvlil 74 
                                       vt+n+lk gikP++ai+D ktkR+e+e        + e ++ v++ kNp+Gtit+ l++a+k+++   +++++v + 
  gi|242398024|ref|YP_002993448.1|  53 VTENVLKVGIKPSVAIYDYKTKRKEYEP-------DIEFGAVVLTTKNPPGTITKALLNAVKKSFelaKKGKRVYLK 122
                                       8***********************3333.......23557899**********************9999******** PP

                            DUF359  75 VdGEEDLavlpaillapegsvvvYGqpdeGvvlvkvteeakeeaeellekfe 126
                                       V+GEEDLa++pa+++apeg++v+YGqpdeG+vl+kvt+e+k+++ +ll+k+e
  gi|242398024|ref|YP_002993448.1| 123 VNGEEDLAAIPAVIYAPEGALVIYGQPDEGIVLIKVTSECKRRCAKLLRKME 174
                                       **************************************************96 PP

>> DUF3903  Domain of unknown function (DUF3903)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.5   6.7e-06      0.06      11      23 ..     156     168 ..     153     177 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.7e-06
                           DUF3903  11 eKVeaECKRRFGK 23 
                                        KV+ ECKRR  K
  gi|242398024|ref|YP_002993448.1| 156 IKVTSECKRRCAK 168
                                       5*********877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); 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: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1196.89
//
Query:       gi|242398025|ref|YP_002993449.1|  [L=98]
Description: 30S ribosomal protein S24e [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.8e-26   90.0   0.1    8.2e-26   89.8   0.1    1.1  1  Ribosomal_S24e  Ribosomal protein S24e


Domain annotation for each model (and alignments):
>> Ribosomal_S24e  Ribosomal protein S24e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.8   0.1   4.6e-30   8.2e-26       2      78 ..      21      97 ..      20      98 .] 0.98

  Alignments for each domain:
  == domain 1  score: 89.8 bits;  conditional E-value: 4.6e-30
                                      EEEE-SSS-S--HHHHHHHHHHHHTS-CTTEEEEEEEE-SSSSEEEEEEEEES-HHHHHHHS-HHHHHHTTSS---S CS
                    Ribosomal_S24e  2 vdvlHpgkatpskteireklakmykvdpdlvvvfgfrthfGggkttGfakiYdsleaakkfEpkhrlaRnglaekkk 78
                                      ++v+H+g++tps+++++ kl++m++ +p+ +vv+ +r+ fG + ++G+ak Y+s+e++  +Ep+++l+R g+ ++++
  gi|242398025|ref|YP_002993449.1| 21 FEVIHEGEPTPSRADVKGKLVAMLDLNPEATVVQYIRSYFGSHVSEGYAKAYESKERMLYIEPEYVLRREGIIQEQE 97
                                      89**********************************************************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 745.67
//
Query:       gi|242398026|ref|YP_002993450.1|  [L=55]
Description: 30S ribosomal protein S27ae [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-22   78.6   2.0    3.2e-22   78.4   2.0    1.1  1  Ribosomal_S27   Ribosomal protein S27a
     0.0016   18.6   2.5     0.0016   18.6   2.5    1.5  2  Ribosomal_L37e  Ribosomal protein L37e
     0.0041   16.8   0.8     0.0041   16.8   0.8    2.4  2  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
      0.008   16.1   7.1      0.052   13.5   7.1    2.0  1  Nudix_N_2       Nudix N-terminal
     0.0096   16.2   1.6      0.083   13.2   0.1    2.0  2  GFA             Glutathione-dependent formaldehyde-activating
  ------ inclusion threshold ------
      0.022   14.8   2.4      0.062   13.3   2.4    1.6  1  DZR             Double zinc ribbon
      0.034   14.1   5.5      0.057   13.4   5.4    1.5  1  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
      0.046   13.6   3.7       0.13   12.1   3.7    1.7  1  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
       0.06   13.3   2.1      0.075   13.0   2.1    1.4  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
        0.1   12.3   0.3        0.1   12.3   0.3    2.3  2  zinc_ribbon_2   zinc-ribbon domain
       0.13   11.9   1.9        5.9    6.6   0.1    2.2  2  zf_UBZ          Ubiquitin-Binding Zinc Finger


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 !   78.4   2.0   1.9e-25   3.2e-22       3      45 .]      11      51 ..       9      51 .. 0.98

  Alignments for each domain:
  == domain 1  score: 78.4 bits;  conditional E-value: 1.9e-25
                                      SSCCESSSSSEEESS-B-SS-S-TTSBEEECTTEEEESSTTTE CS
                     Ribosomal_S27  3 kyYkvddsgkverlrkeCpreCGaGvfMAehkdRkyCGkCglT 45
                                      k+Y+v+d gk++r+++ Cpr CG+GvfMA+hk+R++CG+Cg+T
  gi|242398026|ref|YP_002993450.1| 11 KLYEVKD-GKISRKNRFCPR-CGPGVFMADHKNRWTCGRCGYT 51
                                      89*****.************.*********************9 PP

>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       4.7   7.7e+03       9      14 ..       4       9 ..       2      12 .. 0.48
   2 !   18.6   2.5   9.8e-07    0.0016       8      43 ..      18      54 ..      15      55 .] 0.76

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 4.7
                    Ribosomal_L37e  9 krqkkk 14
                                      k++++k
  gi|242398026|ref|YP_002993450.1|  4 KKTSQK 9 
                                      443333 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 9.8e-07
                    Ribosomal_L37e  8 GkrqkkktHilCrrCgkrsy...hvqkktCascGypsak 43
                                      Gk ++     +C rCg   +   h ++ tC+ cGy + k
  gi|242398026|ref|YP_002993450.1| 18 GKISR--KNRFCPRCGPGVFmadHKNRWTCGRCGYTEWK 54
                                      56632..3568*******99666777889******7654 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 !   16.8   0.8   2.5e-06    0.0041       1      11 [.      22      32 ..      22      39 .. 0.79
   2 ?    3.0   2.6     0.051        84       6      10 ..      45      49 ..      45      50 .. 0.96

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.5e-06
                     zf-NADH-PPase  1 rthrFCgrCGa 11
                                      r++rFC+rCG 
  gi|242398026|ref|YP_002993450.1| 22 RKNRFCPRCGP 32
                                      789*******5 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.051
                     zf-NADH-PPase  6 CgrCG 10
                                      CgrCG
  gi|242398026|ref|YP_002993450.1| 45 CGRCG 49
                                      ****9 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   7.1   3.2e-05     0.052       1      31 [.      25      51 ..      25      54 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.2e-05
                                      -B-TTT--B-EEE--TT-SS-EEEETTTTEE CS
                         Nudix_N_2  1 kFCsqCGtpvelripdgDnreRlvCpaCgti 31
                                      +FC+ CG  v       D++ R +C +Cg++
  gi|242398026|ref|YP_002993450.1| 25 RFCPRCGPGVF----MADHKNRWTCGRCGYT 51
                                      8******9955....469***********97 PP

>> GFA  Glutathione-dependent formaldehyde-activating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.1   5.1e-05     0.083      33      63 ..       9      38 ..       2      42 .. 0.67
   2 ?    4.0   0.2     0.038        63      46      60 ..      39      53 ..      37      55 .] 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.1e-05
                               GFA 33 elkeykktadsgnkvtrsfCpeCgsplysee 63
                                      + k y+  +d +   +++fCp+Cg  +++  
  gi|242398026|ref|YP_002993450.1|  9 KWKLYEV-KDGKISRKNRFCPRCGPGVFMAD 38
                                      5566663.4555555669*******999854 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.038
                               GFA 46 kvtrsfCpeCgsply 60
                                      +++r+ C +Cg + +
  gi|242398026|ref|YP_002993450.1| 39 HKNRWTCGRCGYTEW 53
                                      5789*******8755 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   2.4   3.8e-05     0.062       7      36 ..      19      50 ..      17      54 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.8e-05
                               DZR  7 elppdarfCseCgtklkavaa..edrCpsCge 36
                                      +++ ++rfC++Cg  +  + +    +C +Cg+
  gi|242398026|ref|YP_002993450.1| 19 KISRKNRFCPRCGPGVFMADHknRWTCGRCGY 50
                                      5778999*****99987555577889999997 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 ?   13.4   5.4   3.5e-05     0.057      17      46 .]      24      51 ..      16      51 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.5e-05
                     Zn_Tnp_IS1595 17 ngfvCPhCgsrkayrikt.rglfqCkeCrkq 46
                                      n+f CP+Cg     ++++   ++ C +C+++
  gi|242398026|ref|YP_002993450.1| 24 NRF-CPRCG--PGVFMADhKNRWTCGRCGYT 51
                                      455.*****..3334443479*******985 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   3.7     8e-05      0.13       2      31 ..      25      52 ..      25      53 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8e-05
                                      EBESTTTSBEEEEECSCCCEEEESSSS-EE CS
                    RNA_POL_M_15KD  2 kFCpkCgNlLlpkedkegknfeCrqCgYee 31
                                      +FCp Cg     ++ k  +   C  CgY e
  gi|242398026|ref|YP_002993450.1| 25 RFCPRCGPGVFMADHKNRWT--CGRCGYTE 52
                                      7******9999999998887..******76 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 ?   13.0   2.1   4.6e-05     0.075      31      55 ..      27      51 ..       4      54 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.6e-05
                    OrfB_Zn_ribbon 31 CseCgsknkealsgrtfkCpnCgfe 55
                                      C++Cg  +  a+++++++C +Cg++
  gi|242398026|ref|YP_002993450.1| 27 CPRCGPGVFMADHKNRWTCGRCGYT 51
                                      ******99999************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 ?   12.3   0.3   6.3e-05       0.1      10      20 ..      21      31 ..      19      31 .. 0.79
   2 ?    2.7   1.7     0.067   1.1e+02      16      21 ..      45      50 ..      44      51 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.3e-05
                     zinc_ribbon_2 10 qdnakFCpyCG 20
                                      + +++FCp+CG
  gi|242398026|ref|YP_002993450.1| 21 SRKNRFCPRCG 31
                                      55789*****9 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.067
                     zinc_ribbon_2 16 CpyCGt 21
                                      C +CG+
  gi|242398026|ref|YP_002993450.1| 45 CGRCGY 50
                                      777775 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1    0.0036       5.9       3       9 ..      25      31 ..      23      38 .. 0.86
   2 ?    5.2   0.3      0.01        16       2       9 ..      42      49 ..      41      51 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0036
                            zf_UBZ  3 ylCerCg 9 
                                       +C+rCg
  gi|242398026|ref|YP_002993450.1| 25 RFCPRCG 31
                                      59****9 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.01
                            zf_UBZ  2 tylCerCg 9 
                                       ++C rCg
  gi|242398026|ref|YP_002993450.1| 42 RWTCGRCG 49
                                      69*****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); 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: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 381.06
//
Query:       gi|242398027|ref|YP_002993451.1|  [L=199]
Description: N5-glutamine methyltransferase, HemK family [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.6e-17   62.1   0.1    3.4e-16   59.2   0.1    1.9  1  MTS              Methyltransferase small domain
    2.5e-16   59.8   0.0    3.3e-16   59.5   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    5.3e-12   45.7   0.8    6.9e-12   45.4   0.1    1.4  2  PrmA             Ribosomal protein L11 methyltransferase (Prm
    5.2e-10   39.9   0.0    1.1e-09   38.9   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
    3.4e-08   33.5   0.0      5e-08   32.9   0.0    1.3  1  Met_10           Met-10+ like-protein
    8.1e-08   32.8   0.0    1.5e-07   32.0   0.0    1.6  1  Methyltransf_11  Methyltransferase domain
    1.7e-07   31.2   0.0    2.7e-07   30.6   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    4.2e-06   26.7   0.0    5.7e-06   26.2   0.0    1.1  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    1.9e-05   25.3   0.0    4.9e-05   24.0   0.0    1.6  1  Methyltransf_12  Methyltransferase domain
    0.00025   21.0   0.0    0.00046   20.1   0.0    1.4  1  Methyltransf_18  Methyltransferase domain
     0.0004   19.7   0.0     0.0024   17.1   0.0    1.8  2  TRM              N2,N2-dimethylguanosine tRNA methyltransfera
     0.0035   16.9   0.0     0.0037   16.9   0.0    1.2  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
     0.0051   16.3   0.1      0.037   13.5   0.0    1.9  2  Methyltransf_4   Putative methyltransferase
     0.0052   16.1   0.1     0.0078   15.6   0.1    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
     0.0056   16.4   0.0     0.0077   15.9   0.0    1.2  1  UPF0020          Putative RNA methylase family UPF0020
  ------ inclusion threshold ------
      0.014   15.1   0.0      0.024   14.3   0.0    1.3  1  Cons_hypoth95    Conserved hypothetical protein 95
      0.022   14.4   0.0      0.033   13.8   0.0    1.2  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
      0.028   14.7   0.0       0.04   14.2   0.0    1.3  1  DUF2431          Domain of unknown function (DUF2431)
      0.028   13.7   0.0      0.054   12.8   0.0    1.5  1  CMAS             Mycolic acid cyclopropane synthetase
      0.064   13.2   0.0       0.16   12.0   0.0    1.6  2  rRNA_methylase   Putative rRNA methylase
      0.067   12.8   0.0      0.093   12.4   0.0    1.3  1  TPMT             Thiopurine S-methyltransferase (TPMT)
        0.1   11.6   0.1       0.15   11.0   0.1    1.2  1  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
       0.12   11.7   0.0       0.17   11.2   0.0    1.2  1  N6_Mtase         N-6 DNA Methylase
       0.12   12.1   0.1       0.28   10.9   0.1    1.6  2  Methyltransf_16  Lysine methyltransferase
       0.12   11.9   0.0       0.17   11.4   0.0    1.3  1  DOT1             Histone methylation protein DOT1
       0.22   11.0   0.0       0.38   10.2   0.0    1.4  1  AviRa            RRNA methyltransferase AviRa


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 !   59.2   0.1     5e-19   3.4e-16      20     154 ..      22     166 ..       6     181 .. 0.80

  Alignments for each domain:
  == domain 1  score: 59.2 bits;  conditional E-value: 5e-19
                                       HHHHHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTSTT CS
                               MTS  20 sklLletlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvleevee 95 
                                       + lL+e+l  +  + +lD+G+G+G++++ +ak+ +   v  vdv+  A+e+aken++ n++  v++ +sd++++v  
  gi|242398027|ref|YP_002993451.1|  22 TFLLAENLMIKDGDFALDMGTGTGIIALLMAKKAKF--VLGVDVNPIAVELAKENARLNGITnVKFKQSDLFQNVG- 95 
                                       779999999998999*****************8877..99*********************99*************. PP

                                       S-EEEEEE---STTTCHCH............HHHHHHHHHHHHHHEEEEEEEEEEEETTSCHHHHHHHHHS CS
                               MTS  96 kkfdlivsNPPfhagkate............lavaeeliaeAkeaLkegGeLliVanrklgyeslleelfg 154
                                       +kfd+i  N P+  g+ +e             +v +++i+e   +L+e+G ++iV ++  g+++++ +l +
  gi|242398027|ref|YP_002993451.1|  96 GKFDIITFNAPYLPGEPEElidlalvggregREVLDRFIEEVDGYLTENGIIQIVQSSITGVDKTIGKLTS 166
                                       ***********986653321111111111117899***********************9999999766654 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.5   0.0   4.7e-19   3.3e-16       7     113 ..      37     153 ..      31     185 .. 0.78

  Alignments for each domain:
  == domain 1  score: 59.5 bits;  conditional E-value: 4.7e-19
                   Methyltransf_31   7 vlDlGCGtGeltfelaeelgpkae.vvGiDiseeaielArenaqklgldnveFeqgdiee.leklledekfDlilsn 81 
                                        lD G+GtG +++ +a++    a+ v G+D ++ a+elA+ena+ +g++nv+F+q+d ++         kfD+i+ n
  gi|242398027|ref|YP_002993451.1|  37 ALDMGTGTGIIALLMAKK----AKfVLGVDVNPIAVELAKENARLNGITNVKFKQSDLFQnVG-----GKFDIITFN 104
                                       79**************65....444***********************************666.....99******* PP

                   Methyltransf_31  82 .........evl.........naladpdkileeiervlkpggilliedpr 113
                                                e l              +d ++ee+  +l+++gi+ i + +
  gi|242398027|ref|YP_002993451.1| 105 apylpgepeE-LidlalvggrEGREVLDRFIEEVDGYLTENGIIQIVQSS 153
                                       5555555551.045555677777777777788999999999999887776 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.4   0.1     1e-14   6.9e-12     158     233 ..      30     104 ..      22     105 .. 0.85
   2 ?   -2.8   0.0       4.7   3.2e+03     239     257 ..     130     149 ..     128     178 .. 0.47

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 1e-14
                              PrmA 158 lvkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkvea.klevalseellk..eekadviv 231
                                       ++k g+  lD+GtG+Gi+a+  ak  ak v++vD++++Av+ akeNa+lN++++ k++   +++l++   +k+d+i 
  gi|242398027|ref|YP_002993451.1|  30 MIKDGDFALDMGTGTGIIALLMAK-KAKFVLGVDVNPIAVELAKENARLNGITNvKFK---QSDLFQnvGGKFDIIT 102
                                       57888999************9998.79**************************97774...5666654568999997 PP

                              PrmA 232 aN 233
                                        N
  gi|242398027|ref|YP_002993451.1| 103 FN 104
                                       66 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.7
                              PrmA 239 lielaedikklvkeggll.i 257
                                       l +++e++   + e+g++ i
  gi|242398027|ref|YP_002993451.1| 130 LDRFIEEVDGYLTENGIIqI 149
                                       55666666666666665422 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9   0.0   1.6e-12   1.1e-09       2      71 ..      38     104 ..      37     120 .. 0.87

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 1.6e-12
                                       EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEEE CS
                   Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvss 71 
                                       Ld+G+GtG ++l +ak+   + v+gvD+++ ++e a+e+a+ +g+ nv+f q d+ +     g+fD+++ +
  gi|242398027|ref|YP_002993451.1|  38 LDMGTGTGIIALLMAKKA--KFVLGVDVNPIAVELAKENARLNGItNVKFKQSDLFQN--VGGKFDIITFN 104
                                       9****************6..9********************9************9443..46899999884 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.0   7.2e-11     5e-08      97     152 ..      30      83 ..      23     122 .. 0.92

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 7.2e-11
                                       T--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTC CS
                            Met_10  97 lveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekv 152
                                       ++++g+  +d+  G G  a+ +ak  kak+vl++d+nP +v++ ken +lN + +v
  gi|242398027|ref|YP_002993451.1|  30 MIKDGDFALDMGTGTGIIALLMAK--KAKFVLGVDVNPIAVELAKENARLNGITNV 83 
                                       689*********************..*************************99875 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   0.0   2.1e-10   1.5e-07       1      68 [.      38     104 ..      38     149 .. 0.89

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 2.1e-10
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-TT-EEEEEEE CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl.kvefvvadaeklpfednsfDlvvss 68 
                                       Ld+G+GtG++a  +ak+++ v+gvD+++ +++lake+a+ +g+ +v+f ++d+ +     ++fD+++ +
  gi|242398027|ref|YP_002993451.1|  38 LDMGTGTGIIALLMAKKAKFVLGVDVNPIAVELAKENARLNGItNVKFKQSDLFQ--NVGGKFDIITFN 104
                                       8*****************************************9*99****99997..345699999876 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.0     4e-10   2.7e-07      26      89 ..      37     104 ..      15     105 .. 0.84

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 4e-10
                   Methyltransf_23  26 vLdiGcGtGillevlrengfsvtgvDlspeaveiae.........kakkaqkdqfdeqeaaepqgkfdlIvlr 89 
                                        Ld+G+GtGi + +++++ + v gvD +p+ave+a+         + k+ q+d f     ++  gkfd+I+ +
  gi|242398027|ref|YP_002993451.1|  37 ALDMGTGTGIIALLMAKKAKFVLGVDVNPIAVELAKenarlngitNVKFKQSDLF-----QNVGGKFDIITFN 104
                                       6**************************************9996666666666666.....77888*****976 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 !   26.2   0.0   8.3e-09   5.7e-06      66     167 ..      26     123 ..       6     125 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 8.3e-09
                                       HHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGGTTGGG-S CS
                              PCMT  66 lellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGrkGyeekaP 142
                                        e l +k+g+ +L++G+G+G+ + ++a+  ++k+ v++++  +  ve ak+n + ++++nv+++ +D  + +     
  gi|242398027|ref|YP_002993451.1|  26 AENLMIKDGDFALDMGTGTGIIALLMAK--KAKF-VLGVDVNPIAVELAKENARLNGITNVKFKQSDLFQNVGG--K 97 
                                       57889*****************999997..4556.89******************************8887654..4 PP

                                       EEEEEESSB.BSS--HHHHHTEEEEE CS
                              PCMT 143 Ydaihvgaa.apeiPealidQLkeGG 167
                                       +d i + a   p  Pe+lid    GG
  gi|242398027|ref|YP_002993451.1|  98 FDIITFNAPyLPGEPEELIDLALVGG 123
                                       88888877525777888887666666 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   7.1e-08   4.9e-05       1      72 [.      38     103 ..      38     107 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 7.1e-08
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvva 72 
                                       L+ G+GtG ++  +++k   + ++gvD++p a+e ake  + +     +nv++++ dl++  gg +fD+++ 
  gi|242398027|ref|YP_002993451.1|  38 LDMGTGTGIIALLMAKK--AKFVLGVDVNPIAVELAKENARLN---GITNVKFKQSDLFQNVGG-KFDIITF 103
                                       89999999888888888..77888*********5555554444...4799****9999988887.****986 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   6.7e-07   0.00046      11      86 ..      30     101 ..      24     104 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 6.7e-07
                   Methyltransf_18  11 lvekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGleklkeeevdtv 86 
                                       ++++g+  +D Gt  g++++ ++  +kak v+ +D+n+ ++e aken++ +g++ ++++  sd ++++  +++d++
  gi|242398027|ref|YP_002993451.1|  30 MIKDGDFALDMGTGTGIIALLMA--KKAKFVLGVDVNPIAVELAKENARLNGIT-NVKFKQSDLFQNVG-GKFDII 101
                                       8999************9887766..78889*********************995.69999999999985.446665 PP

>> TRM  N2,N2-dimethylguanosine tRNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   3.5e-06    0.0024      58     139 ..      42     119 ..      35     126 .. 0.80
   2 ?    0.2   0.0      0.46   3.2e+02     307     355 ..     129     174 ..     121     178 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.5e-06
                                       -TTSHHHHHHHHH-S-EEEEEEE-S-HHHHHHHHHHHHHTT--GGEEEE-S-HHHHHC--SS-EEEEEE-.-S..S- CS
                               TRM  58 sasGlRaiRfalEvpgvkevlaNDisekAvelikeNvklneveeivvineddAnvllaekkkrfdviDlD.Pf..Gs 131
                                       +++G+ a+  a+    +k vl  D+++ Avel keN++ln + + v+++++d   l++++  +fd+i    P+  G 
  gi|242398027|ref|YP_002993451.1|  42 TGTGIIALLMAKK---AKFVLGVDVNPIAVELAKENARLNGITN-VKFKQSD---LFQNVGGKFDIITFNaPYlpGE 111
                                       5777777777766...8999999*********************.9999944...7788999999998755776677 PP

                                       -GGGHHHH CS
                               TRM 132 papfldsa 139
                                       p + +d a
  gi|242398027|ref|YP_002993451.1| 112 PEELIDLA 119
                                       77777766 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.46
                                       HHHHHHHHHS--SS-EEHHHHHHHHT-SS---HHHHHHH....TT-EE- CS
                               TRM 307 lLklikeElldaplyydlsqlasvlklsvpplkkvvsalkelgfevsrt 355
                                       +L+   eE   + +y + + + +++++s   ++k + +l + gf+v  t
  gi|242398027|ref|YP_002993451.1| 129 VLDRFIEE---VDGYLTENGIIQIVQSSITGVDKTIGKLTSKGFKVEIT 174
                                       55555555...66788999999***********************9876 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 !   16.9   0.0   5.3e-06    0.0037       4      62 ..      37      94 ..      34     176 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 5.3e-06
                   Methyltransf_15  4 ilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfell 62
                                       lD+ +G+G  +  +a++ + v ++++n+  +++a++Na++ g+  ++++++ d+f+ +
  gi|242398027|ref|YP_002993451.1| 37 ALDMGTGTGIIALLMAKKAKFVLGVDVNPIAVELAKENARLNGIT-NVKFKQSDLFQNV 94
                                      6999999**99*******999*********************996.69*******9955 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   5.4e-05     0.037       5      60 ..      37      90 ..      33      99 .. 0.90
   2 ?    0.6   0.0      0.49   3.4e+02      97     149 ..     131     184 ..     125     192 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.4e-05
                                      EEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-C CS
                    Methyltransf_4  5 vleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgda 60
                                       l++G+G G + + +Akk   k +lG++++   v+ + ++++ ++++N++  ++d 
  gi|242398027|ref|YP_002993451.1| 37 ALDMGTGTGIIALLMAKK--AKFVLGVDVNPIAVELAKENARLNGITNVKFKQSDL 90
                                      6899*****999999998..599***************************999885 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.49
                                       HHHHHHHHHHEEEEEEEEE.EESHHHHHHHHHHHHHCSTTEEESSCCCSCCTCH CS
                    Methyltransf_4  97 pellkelarvLkkgGvlel.aTDveeyaeemlkvleeeplferlskeeeleeep 149
                                       + +++e+   L ++G++++ ++ +  + + + k +++  ++e++ ke +  ee+
  gi|242398027|ref|YP_002993451.1| 131 DRFIEEVDGYLTENGIIQIvQSSITGVDKTIGKLTSKGFKVEITAKERYFFEEI 184
                                       6799999999*****998725668999999999999998999888887766655 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   1.1e-05    0.0078      45     121 ..      31     102 ..      22     105 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.1e-05
                                       S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEE CS
                   Ubie_methyltran  45 vkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvt 121
                                        k g  +lD+ +Gtg +a+ ++++++    v ++D+n+  ++ +++ ++ +g +n++f q++   ++   + fD++t
  gi|242398027|ref|YP_002993451.1|  31 IKDGDFALDMGTGTGIIALLMAKKAK---FVLGVDVNPIAVELAKENARLNGITNVKFKQSDL--FQNVGGKFDIIT 102
                                       5789999*********9999887665...5899*************************98763..344556777776 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.1e-05    0.0077      75     132 ..      53     108 ..      36     132 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.1e-05
                                       HH--.EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--G.GG--STTS---EEEE----- CS
                           UPF0020  75 aelk.lygsDldrrvvqgareNaekagvgdliefsqada.akLrlkegevdvivtnpPYG 132
                                       +++k + g+D ++ +v+ a+eNa+  g+++ ++f+q d  +++    g++d+i  n PY 
  gi|242398027|ref|YP_002993451.1|  53 KKAKfVLGVDVNPIAVELAKENARLNGITN-VKFKQSDLfQNVG---GKFDIITFNAPYL 108
                                       4556689*********************86.6666666504444...79**********6 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   3.5e-05     0.024      45     133 ..      37     116 ..      20     123 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.5e-05
                                       EEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEEEE-- CS
                     Cons_hypoth95  45 vLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdivflDP 121
                                        LD+  G+G ++l  +  +ak ++ v+ ++ av++ ken +  +++    ++k ++++ +++    +++fdi+ ++ 
  gi|242398027|ref|YP_002993451.1|  37 ALDMGTGTGIIAL-LMAKKAKFVLGVDVNPIAVELAKENARLNGIT----NVKFKQSDLFQNV---GGKFDIITFNA 105
                                       5999999999998.57899*********************999966....5777777888777...678******** PP

                                       SSSTTCH.HHHH CS
                     Cons_hypoth95 122 Pyakellieevl 133
                                       Py  ++  ee++
  gi|242398027|ref|YP_002993451.1| 106 PYLPGEP-EELI 116
                                       **88775.6665 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   4.8e-05     0.033       4      88 ..      29     106 ..      26     108 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.8e-05
                                       H---TT-EEEESS-TTSHHHHHHHHHTTTT.SEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC.. CS
                   Methyltr_RsmB-F   4 LapqeeetilDlcaaPGgKTthiaelmknk.gtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlggel 79 
                                       L  +++++ lD+    G  T  ia lm++k + v+ vd+n   ++  +en +  g+tn++  + D+ +    +gg +
  gi|242398027|ref|YP_002993451.1|  29 LMIKDGDFALDM----GTGTGIIALLMAKKaKFVLGVDVNPIAVELAKENARLNGITNVKFKQSDLFQN---VGG-K 97 
                                       667888889998....5567789999766515699***************9999***********9877...565.7 PP

                                       EEEEEEEE- CS
                   Methyltr_RsmB-F  80 fDriLlDaP 88 
                                       fD i   aP
  gi|242398027|ref|YP_002993451.1|  98 FDIITFNAP 106
                                       999999998 PP

>> DUF2431  Domain of unknown function (DUF2431)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   5.8e-05      0.04      44     128 ..      46     151 ..      29     187 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.8e-05
                           DUF2431  44 nieeLeeegvkvlfgVDatkleks.................kl.qeklkkekfdriifnFPhvggkstdvnr....q 98 
                                       +i+ L ++++k++ gVD++ ++                   ++   ++  +kfd i fn P   g+ ++  +     
  gi|242398027|ref|YP_002993451.1|  46 IIALLMAKKAKFVLGVDVNPIAVElakenarlngitnvkfkQSdLFQNVGGKFDIITFNAPYLPGEPEELIDlalvG 122
                                       678899999999*****999995599999***99999988633345666777***********88887766678888 PP

                           DUF2431  99 vranqeLlvsffksakellsekpgeilvtl 128
                                        r+ +e l +f++++  +l+e+ g i +  
  gi|242398027|ref|YP_002993451.1| 123 GREGREVLDRFIEEVDGYLTEN-GIIQIVQ 151
                                       89999*************9999.8777654 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   7.9e-05     0.054      54     131 ..      25     101 ..      17     181 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.9e-05
                                       HHTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG-----SE CS
                              CMAS  54 ileklelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedldekvdr 130
                                       + e l +k+G+  Ld+G+G G ++  ++++    v+g+ +     +lak++    ++++ +  +   ++++ +k+d 
  gi|242398027|ref|YP_002993451.1|  25 LAENLMIKDGDFALDMGTGTGIIALLMAKK-AKFVLGVDVNPIAVELAKENARLNGITNVKFKQSDLFQNVGGKFDI 100
                                       67899******************9999998.5557777777777777777666666555444444456666666665 PP

                                       E CS
                              CMAS 131 v 131
                                       +
  gi|242398027|ref|YP_002993451.1| 101 I 101
                                       4 PP

>> rRNA_methylase  Putative rRNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00023      0.16       1      62 [.      58     115 ..      58     120 .. 0.84
   2 ?   -2.1   0.0         5   3.5e+03      80      89 ..     141     150 ..     122     170 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00023
                                       EEEEES-HHHHHHHHHHHHHTT-GGSEEEEES-GGGGGGT--S-EEEEEEEESB-CTS-TTS CS
                    rRNA_methylase   1 vyafDiQeeAleatkerleeekleervelildsHekleeyvkekvkavifNLGYLPggdksi 62 
                                       v+++D+   A+e +ke+ + ++++ +v++     ++l + v +k+++++fN  YLPg+ +++
  gi|242398027|ref|YP_002993451.1|  58 VLGVDVNPIAVELAKENARLNGIT-NVKF---KQSDLFQNVGGKFDIITFNAPYLPGEPEEL 115
                                       7899**********9999999987.4554...4567888899***************87665 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 5
                                       EEEEEEEEEE CS
                    rRNA_methylase  80 LkkgGlitiv 89 
                                       L ++G+i iv
  gi|242398027|ref|YP_002993451.1| 141 LTENGIIQIV 150
                                       4444444443 PP

>> TPMT  Thiopurine S-methyltransferase (TPMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00013     0.093      47      91 ..      43      86 ..      10     105 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00013
                                      TT-HHHHHH-BTTEEEEEE-S-HHHHHHHHHHHTTSGGGGGEEEE CS
                              TPMT 47 GkaldlvwlAeqgrevvGvelselAvekffeeanlepkvkelsgv 91
                                      G ++ +  +A++ ++v+Gv++ ++Ave + e+a l   ++++++ 
  gi|242398027|ref|YP_002993451.1| 43 GTGIIALLMAKKAKFVLGVDVNPIAVELAKENARL-NGITNVKFK 86
                                      66677788*******************98666666.455555544 PP

>> tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00021      0.15     205     253 ..      37      85 ..      24      90 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00021
                   tRNA_U5-meth_tr 205 llelycGnGnfslalarnfekvlateiakssveaaqyniaankidnvqi 253
                                        l++  G G  +l +a++ + vl  ++   +ve a+ n   n i+nv++
  gi|242398027|ref|YP_002993451.1|  37 ALDMGTGTGIIALLMAKKAKFVLGVDVNPIAVELAKENARLNGITNVKF 85 
                                       4888999****************************************97 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00024      0.17      28     135 ..      15     107 ..       3     114 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00024
                          N6_Mtase  28 ffTPrevsklivellepksgesvyDpacGsggllvqaekvlkeedgktkelsiyGqeknettyrLakmNlllhgiey 104
                                       ++ P e + l++e l  k+g   +D+  G+g + + ++k         k++ + G+++n+ +++Lak N  l gi +
  gi|242398027|ref|YP_002993451.1|  15 VYEPAEDTFLLAENLMIKDGDFALDMGTGTGIIALLMAK---------KAKFVLGVDVNPIAVELAKENARLNGITN 82 
                                       566666677777777777777777777777755444443.........567899*********************98 PP

                          N6_Mtase 105 kkvkirlgdtlekpkfekdkkfdvvvaNppf 135
                                          k +++d +++       kfd++  N p+
  gi|242398027|ref|YP_002993451.1|  83 V--KFKQSDLFQNVGG----KFDIITFNAPY 107
                                       7..5667777776555....59999999998 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1    0.0004      0.28      50      97 ..      37      80 ..      26      98 .. 0.80
   2 ?   -2.4   0.0       4.9   3.4e+03     135     161 ..     153     179 ..     150     187 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0004
                   Methyltransf_16 50 vlELGsGtGlvGlavaellpeakviltDlee.llellkknielnknalk 97
                                      +l++G GtG++ l +a++     v+  D++  ++el k+n  ln+    
  gi|242398027|ref|YP_002993451.1| 37 ALDMGTGTGIIALLMAKK--AKFVLGVDVNPiAVELAKENARLNG---I 80
                                      699*************99..55566678877699******99977...2 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.9
                   Methyltransf_16 135 slelLvkvLkellkkeskvlvaykkrr 161
                                       s++   k++ +l++k  kv ++ k+r+
  gi|242398027|ref|YP_002993451.1| 153 SITGVDKTIGKLTSKGFKVEITAKERY 179
                                       666677888889888888888888885 PP

>> DOT1  Histone methylation protein DOT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00025      0.17      35      88 ..      26      77 ..      13      95 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00025
                                      HHHTT--TT-EEEEES-TTSHHHHHHHHHH--SEEEEEE--HHHHHHHHHHHHH CS
                              DOT1 35 ldkvnlkkedvFvDLGSGvGnvvlqaalevgcklsvGvEimdnaselaekqkee 88
                                       +++ +k+ d  +D+G G G + l++a +++    +Gv++   a ela+++++ 
  gi|242398027|ref|YP_002993451.1| 26 AENLMIKDGDFALDMGTGTGIIALLMAKKAKFV--LGVDVNPIAVELAKENARL 77
                                      567889999999***************998776..9***********9998765 PP

>> AviRa  RRNA methyltransferase AviRa
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00056      0.38      70     113 ..      46      89 ..      41     101 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00056
                             AviRa  70 vlgllhgkkikkvlasDvdeevlelakkNLsLLtkeglakreee 113
                                       +++ll +kk k vl+ Dv+  ++elak+N +L     ++ ++++
  gi|242398027|ref|YP_002993451.1|  46 IIALLMAKKAKFVLGVDVNPIAVELAKENARLNGITNVKFKQSD 89 
                                       799**************************999766666655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 1201.19
//
Query:       gi|242398028|ref|YP_002993452.1|  [L=46]
Description: hypothetical protein TSIB_0032 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.43
# Mc/sec: 322.96
//
Query:       gi|242398029|ref|YP_002993453.1|  [L=247]
Description: Fe-S oxidoreductase [Thermococcus sibiricus MM 739]
Scores for complete 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-22   78.1   0.0    9.2e-22   77.2   0.0    1.5  1  Wyosine_form  Wyosine base formation
    1.8e-17   64.2   0.2    3.8e-17   63.2   0.1    1.5  2  Radical_SAM   Radical SAM superfamily
  ------ inclusion threshold ------
      0.016   14.6   0.0      0.023   14.1   0.0    1.2  1  DUF1776       Fungal family of unknown function (DUF1776)
      0.032   14.0   0.1      0.046   13.6   0.1    1.3  1  DUF4523       Protein of unknown function (DUF4523)
      0.066   13.6   0.0       0.13   12.7   0.0    1.4  1  HAD           haloacid dehalogenase-like hydrolase
       0.11   12.4   0.0       0.22   11.5   0.0    1.4  1  AhpC-TSA      AhpC/TSA family


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 !   77.2   0.0   3.1e-25   9.2e-22       1      62 [.     173     234 ..     173     235 .. 0.97

  Alignments for each domain:
  == domain 1  score: 77.2 bits;  conditional E-value: 3.1e-25
                                       HHT-SEEEEEE------------------HHHHHHHHHHHHTSSS.EEEEEEETTTTEEEEE CS
                      Wyosine_form   1 kaepdFvEvKaytyvGssrsrLtmknvPwheevadfakrlegsaedYellaehrhSrvvlla 62 
                                       ka+p+FvE Kay++vG sr+rLt++n+P+he+++ fa++l +++  Y + +e ++Srvvl+ 
  gi|242398029|ref|YP_002993453.1| 173 KARPMFVEAKAYMFVGFSRNRLTINNMPSHEDIKAFAEELVKNLPGYHIEDEYPPSRVVLIM 234
                                       689*********************************************************97 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.2   0.1   1.3e-20   3.8e-17      38     167 .]      43     171 ..      33     171 .. 0.91
   2 ?   -2.5   0.0       1.9   5.7e+03      60      78 ..     202     219 ..     189     236 .. 0.56

  Alignments for each domain:
  == domain 1  score: 63.2 bits;  conditional E-value: 1.3e-20
                                       HHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT..-SEEEEEEBS CS
                                       xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxx RF
                       Radical_SAM  38 vkelkaekg.vkevilgggepllypdfvellerlaklavpgiritvetngtlpdeeklerllelg..vdrvslglea 111
                                       vk+l + +  ++  i+++gep+lyp + el+e+ +k+   g+++++++ngt    e+le++ + +  + +++++l a
  gi|242398029|ref|YP_002993453.1|  43 VKKLEEAMEpKHAAISLSGEPMLYPMIGELVEEFHKR---GFTTFIVSNGTE--VEVLEKMMKENklPKQLYISLTA 114
                                       4555545555999***********************9...************..5********99************ PP

                                       SSHH...HHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHHHHHHH CS
                                       xxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 112 adde...kvlklmnrghtfeevlealeklreagikrvvdrivglpGendeeleellell 167
                                       +d+e   +v  +m  +++++++ ++le++r++  + +v+r+++++Gen++  e +++l+
  gi|242398029|ref|YP_002993453.1| 115 PDEEtyqRVNVPM-IPDGWDRINKTLELMRDLPTR-TVIRLTLVKGENMHNPEGYAKLI 171
                                       ****888888888.99****************888.*************9999888775 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.9
                                       STTHHHHHHHHHHTCCCTE CS
                                       xxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  60 ypdfvellerlaklavpgi 78 
                                       + d+  ++e+l+k+  pg+
  gi|242398029|ref|YP_002993453.1| 202 HEDIKAFAEELVKN-LPGY 219
                                       33333333444443.2444 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 ?   14.1   0.0   7.5e-06     0.023      12      42 ..      64      94 ..      53     122 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7.5e-06
                           DUF1776 12 ptePltRsialDLerrGFiVfvtvesaeeek 42
                                      +  P++  ++ ++++rGF+ f++++  e e 
  gi|242398029|ref|YP_002993453.1| 64 MLYPMIGELVEEFHKRGFTTFIVSNGTEVEV 94
                                      456*********************9988653 PP

>> DUF4523  Protein of unknown function (DUF4523)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   1.5e-05     0.046      29     102 ..      90     165 ..      86     215 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.5e-05
                           DUF4523  29 selsgleriLarkklPkeinltpkPsrmplwkRkainkisegwkkcklwkknlkdpplstivvrWlkk..nlkpte 102
                                       +e+++le++++++klPk ++++       +++R  +  i +gw +++     ++d+p  t++   l k  n++  e
  gi|242398029|ref|YP_002993453.1|  90 TEVEVLEKMMKENKLPKQLYISLTAPDEETYQRVNVPMIPDGWDRINKTLELMRDLPTRTVIRLTLVKgeNMHNPE 165
                                       68899***************9976666678889999************999********99865554423665555 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   4.3e-05      0.13      48     113 ..      21      92 ..       7     112 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.3e-05
                               HAD  48 rldraglaelleallaglseelaaelerfvaevirpk......lldpgalellaahraaGdrvvvvSgglrp 113
                                       + + ++ ++ll+ +++  ++   + le++++ +++         l+p++ el+++ +++G+++ +vS+g + 
  gi|242398029|ref|YP_002993453.1|  21 EESVKAQRKLLSGYWGVKDQINVKKLEEAMEPKHAAIslsgepMLYPMIGELVEEFHKRGFTTFIVSNGTEV 92 
                                       5667788999999999999999999999996666666778888567********999**********99654 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   7.3e-05      0.22      47     110 ..      68     148 ..      64     160 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.3e-05
                                       HHHHCHHHCCCTTEEEEEEES.SSCHHHHHHHHH-H....................SSEEEE-TTSHHHHHTT-EET CS
                          AhpC-TSA  47 alaklyeefkergvevigvsv.dspeshkkfiekes...................lnfpllsDeegkvakaygvlke 103
                                        + +l+eef++rg++ ++vs  +++e ++k +++++                   +n+p++ D    + k ++++++
  gi|242398029|ref|YP_002993453.1|  68 MIGELVEEFHKRGFTTFIVSNgTEVEVLEKMMKENKlpkqlyisltapdeetyqrVNVPMIPDGWDRINKTLELMRD 144
                                       567899***************45555777777777799999999999999999999999999988888888888855 PP

                                       TTTECSC CS
                          AhpC-TSA 104 ekglalr 110
                                           ++r
  gi|242398029|ref|YP_002993453.1| 145 L---PTR 148
                                       4...444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1641.83
//
Query:       gi|242398030|ref|YP_002993454.1|  [L=740]
Description: squalene-hopene cyclase [Thermococcus sibiricus MM 739]
Scores for complete 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   1.5      0.075   12.1   0.0    5.4  5  SQHop_cyclase_C  Squalene-hopene cyclase C-terminal domain
    2.4e-11   43.2   0.4    2.6e-05   23.9   0.0    4.2  4  Prenyltrans      Prenyltransferase and squalene oxidase repea
    2.9e-11   43.0   0.1     0.0081   15.3   0.0    5.0  5  SQHop_cyclase_N  Squalene-hopene cyclase N-terminal domain
     0.0024   17.0   0.5       0.38    9.7   0.1    3.4  4  TED_complement   A-macroglobulin TED domain


Domain annotation for each model (and alignments):
>> SQHop_cyclase_C  Squalene-hopene cyclase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0   9.1e-05      0.41     197     234 ..      42      79 ..      17      93 .. 0.72
   2 !    4.1   0.0    0.0046        21     155     220 ..     106     171 ..      81     176 .. 0.88
   3 !    6.9   0.1   0.00064       2.9     210     231 ..     293     314 ..     286     328 .. 0.76
   4 !   12.1   0.0   1.7e-05     0.075     149     227 ..     372     447 ..     363     453 .. 0.68
   5 !    8.2   0.0   0.00026       1.2     184     247 ..     458     522 ..     455     561 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 9.1e-05
                                       HHHTT--TTSHHHHHHHHHHHTT--TTSSBB--GGGGT CS
                   SQHop_cyclase_C 197 laavgedleepvirkavdWlksvqnedGGWGesaesyk 234
                                         +++e+l+++ i   v+ l ++qn+dGGWG    s +
  gi|242398030|ref|YP_002993454.1|  42 SYSIAENLTKENITLFVEELLERQNSDGGWGYYEGSIS 79 
                                       3345667788888889999************8776655 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0046
                                       -TTSHHHHHHHHHHHHHS-TTS----SSBSSHHHHHHHHHHHHHHTT--TTSHHHHHHHHHHHTT- CS
                   SQHop_cyclase_C 155 eedsealkraveylkkeqepdGsWfGrWGvnyiyGtwsvlsalaavgedleepvirkavdWlksvq 220
                                       ++ s+al+++++++ k    +G  +    +   y t+++l al + g  +++  +++a+++l+s  
  gi|242398030|ref|YP_002993454.1| 106 RKISKALENGLNFISKSHTLNGWGYIPNTLPEFYPTVMALWALGENGYTEKSRHVNEAIAYLESAE 171
                                       56788999999*******999998999999999****************************99875 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.00064
                                       HHHHHHHHTT--TTSSBB--GG CS
                   SQHop_cyclase_C 210 rkavdWlksvqnedGGWGesae 231
                                       + + + l++vqn+dGGWG  a 
  gi|242398030|ref|YP_002993454.1| 293 EDSCSALEKVQNPDGGWGYRAG 314
                                       56777899**********8764 PP

  == domain 4  score: 12.1 bits;  conditional E-value: 1.7e-05
                                       HHHHT--.TTSHHHHHHHHHHHHHS-TTS----SSBSSHHHHHHHHHHHHHHTT--TTSHHHHHHHHHHHTT--TTS CS
                   SQHop_cyclase_C 149 laqlgee.edsealkraveylkkeqepdGsWfGrWGvnyiyGtwsvlsalaavgedleepvirkavdWlksvqnedG 224
                                       l+ l+ +  ++   +  ++++k+   +dG W    G    y t  +++al a+g+d +++ i ka +Wl s+     
  gi|242398030|ref|YP_002993454.1| 372 LTLLEFNmLNETEKQTHISFIKSL-GEDGKWNTILGPQ-PYETALAIKALLALGVDPSDEDIVKAKEWLLSRP--TD 444
                                       555555523344455567777655.4578888888865.5888888888888888888888888888888764..34 PP

                                       SBB CS
                   SQHop_cyclase_C 225 GWG 227
                                       GWG
  gi|242398030|ref|YP_002993454.1| 445 GWG 447
                                       677 PP

  == domain 5  score: 8.2 bits;  conditional E-value: 0.00026
                                       SSHHHHHH.HHHHHHHHTT--TTSHHHHHHHHHHHTT--TTSSBB--GGGGT-GGGTT-SSBBHH CS
                   SQHop_cyclase_C 184 vnyiyGtw.svlsalaavgedleepvirkavdWlksvqnedGGWGesaesykdpklagkgestas 247
                                       v yi  t+ ++l  l+a++   +++ +++ + Wl +++ ed GW    e y    l+  g+   +
  gi|242398030|ref|YP_002993454.1| 458 VRYIMSTVpTTLEVLEALTPLVTKEEVERHLTWLMEQKIEDDGWPVVKEIYIRDILMYLGAPSVE 522
                                       67888887356888999998999999******************999999987766666555555 PP

>> Prenyltrans  Prenyltransferase and squalene oxidase repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   9.9e-06     0.044      10      37 ..      61      91 ..      61      92 .. 0.73
   2 !   23.9   0.0   5.8e-09   2.6e-05       3      41 ..     292     330 ..     290     330 .. 0.91
   3 ?   -3.8   0.0       2.6   1.2e+04       3      13 ..     339     349 ..     338     350 .. 0.84
   4 ?    0.2   0.0      0.14   6.4e+02       2      13 ..     430     441 ..     429     449 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.9e-06
                                      HHHHSHTTS-BBSSTTS...SBBHHHHHHHH CS
                       Prenyltrans 10 LlscQnedGGwggrpgs...esdtyytywal 37
                                      Ll +Qn dGGwg   gs    +dt+y+ +al
  gi|242398030|ref|YP_002993454.1| 61 LLERQNSDGGWGYYEGSisnVVDTSYAVIAL 91
                                      799**************55555555555444 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 5.8e-09
                                       HHHHHHHHHHHSHTTS-BBSSTTSSBBHHHHHHHHHHHH CS
                       Prenyltrans   3 vekavefLlscQnedGGwggrpgsesdtyytywalaaLa 41 
                                       +e  +  L++ Qn+dGGwg r+g+ sd + ty++l aL+
  gi|242398030|ref|YP_002993454.1| 292 IEDSCSALEKVQNPDGGWGYRAGYSSDDRTTYYVLKALK 330
                                       6777899****************************9995 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 2.6
                                       HHHHHHHHHHH CS
                       Prenyltrans   3 vekavefLlsc 13 
                                       +ek +e+++++
  gi|242398030|ref|YP_002993454.1| 339 IEKGLEWVETR 349
                                       79*****9875 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 0.14
                                       HHHHHHHHHHHH CS
                       Prenyltrans   2 dvekavefLlsc 13 
                                       d+ ka e+Lls+
  gi|242398030|ref|YP_002993454.1| 430 DIVKAKEWLLSR 441
                                       789*******97 PP

>> SQHop_cyclase_N  Squalene-hopene cyclase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.8e-06    0.0081      40      85 ..      47      92 ..      41      96 .. 0.90
   2 ?    1.0   0.0     0.041   1.8e+02      63     283 ..     127     168 ..     103     176 .. 0.58
   3 !    3.8   0.0    0.0057        26      50      84 ..     295     329 ..     289     334 .. 0.80
   4 !   13.4   0.0     7e-06     0.031      44     106 ..     381     441 ..     360     445 .. 0.75
   5 ?    1.8   0.0     0.023     1e+02      38      68 ..     475     505 ..     462     512 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.8e-06
                   SQHop_cyclase_N 40 geddeeeeekiakylrsqqredGgWelypggpgdlsttveaYlALk 85
                                      ++ ++e+++ +++ l+++q++dGgW+ y g+ +++  t  a +ALk
  gi|242398030|ref|YP_002993454.1| 47 ENLTKENITLFVEELLERQNSDGGWGYYEGSISNVVDTSYAVIALK 92
                                      667888999999********************************99 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.041
                   SQHop_cyclase_N  63 gWelypggpgdlsttveaYlALkllGdspdapalarArefilarGGvakvrvfTrilLalfglvpweavpalPpelm 139
                                       gW+ +p+   +   tv a  AL   G                                                   
  gi|242398030|ref|YP_002993454.1| 127 GWGYIPNTLPEFYPTVMALWALGENG--------------------------------------------------- 152
                                       45555555555555555555555555................................................... PP

                   SQHop_cyclase_N 140 lLPkwfpfniykfsswaRttivPllilsakkpvaklprevdldELfveppeevkyelrkekkalswtklflaldkvl 216
                                                                                                                    
  gi|242398030|ref|YP_002993454.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                   SQHop_cyclase_N 217 kllerlplkplrkrAlrkaeewilerqeasgglggifpamvnsvlaLrllgydldhpvvaraleale 283
                                                                                          y+++  +v++a++ le
  gi|242398030|ref|YP_002993454.1| 153 ---------------------------------------------------YTEKSRHVNEAIAYLE 168
                                       ...................................................5555555555555444 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.0057
                   SQHop_cyclase_N  50 iakylrsqqredGgWelypggpgdlsttveaYlAL 84 
                                        +  l++ q++dGgW+   g ++d  tt     AL
  gi|242398030|ref|YP_002993454.1| 295 SCSALEKVQNPDGGWGYRAGYSSDDRTTYYVLKAL 329
                                       5678999**********999999877775555555 PP

  == domain 4  score: 13.4 bits;  conditional E-value: 7e-06
                   SQHop_cyclase_N  44 eeeeekiakylrsqqredGgWelypggp.gdlsttveaYlALkllGdspdapalarArefilar 106
                                       +e+e+++   + ++  edG W+++ g +  +  ++++a   L  lG++p+++ +++A+e++l+r
  gi|242398030|ref|YP_002993454.1| 381 NETEKQTHISFIKSLGEDGKWNTILGPQpYETALAIKA---LLALGVDPSDEDIVKAKEWLLSR 441
                                       4555556666677778********98664777777776...5567***************9986 PP

  == domain 5  score: 1.8 bits;  conditional E-value: 0.023
                   SQHop_cyclase_N  38 flgeddeeeeekiakylrsqqredGgWelyp 68 
                                       +    ++ee e+  ++l++q+ ed gW++++
  gi|242398030|ref|YP_002993454.1| 475 LTPLVTKEEVERHLTWLMEQKIEDDGWPVVK 505
                                       446678999999****************986 PP

>> TED_complement  A-macroglobulin TED domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.2   0.0     0.008        36     153     186 ..      80     113 ..      25     131 .. 0.80
   2 ?   -2.3   0.0      0.38   1.7e+03     176     208 ..     155     189 ..     141     216 .. 0.65
   3 !    9.7   0.1   8.5e-05      0.38     201     248 ..     216     264 ..     200     310 .. 0.85
   4 ?   -3.1   0.0      0.69   3.1e+03     115     295 ..     481     499 ..     466     503 .. 0.57

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.008
                                       HHHHHHHHHHHHHHHHTTCSHHHHHHHHHHHHHH CS
                    TED_complement 153 evtLtAyvliaLleakeilelkkkvelsiskAle 186
                                       +v  t+y++iaL+++ ++  +++++   iskAle
  gi|242398030|ref|YP_002993454.1|  80 NVVDTSYAVIALKRVIDLYYPNENIYRKISKALE 113
                                       566699*********9999977777776666653 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.38
                                       HHHHHHHHHHHHHHHHHHHS---HHH..HHHHHHH CS
                    TED_complement 176 kvelsiskAleyLeekqaeelesvya..lAilaYa 208
                                       + +  +++A++yLe++++ e++++ a  l ilaY 
  gi|242398030|ref|YP_002993454.1| 155 EKSRHVNEAIAYLESAESMEISEAKAvgLKILAYK 189
                                       55667889999999966666655443004455554 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 8.5e-05
                                       HHHHHHHHHHHTT-THH.HHHHHHHHHTTEEEETTEEEE--TTSSSGGG CS
                    TED_complement 201 alAilaYalalakseek.aeellksLkaeakeegnsvyWeedekskeee 248
                                       ++A+l+Y l++++       +ll++L+ +a++++  +yW +++   +++
  gi|242398030|ref|YP_002993454.1| 216 ERALLTYVLTTYEGLTFeVAKLLSRLEDLAESNETLIYWANAPDEWTNR 264
                                       679*********999888*********************8876554443 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 0.69
                                       HHHHHHHHHHHHTTB-TTS-B--SS-SS-TTCSSSTHCHHHHHHHHHHHHHHHHTTCSHHHHHHHHHHHHHHHHHHH CS
                    TED_complement 115 eeeiseslewLlseQkedGsFkeegsllnrkmkggvekevtLtAyvliaLleakeilelkkkvelsiskAleyLeek 191
                                       +ee+++                                                                       
  gi|242398030|ref|YP_002993454.1| 481 KEEVERH---------------------------------------------------------------------- 487
                                       3444444...................................................................... PP

                                       HHHS---HHHHHHHHHHHHHTT-THHHHHHHHHHHTTEEEETTEEEE--TTSSSGGGTSS-B----HHHHHHHHHHH CS
                    TED_complement 192 qaeelesvyalAilaYalalakseekaeellksLkaeakeegnsvyWeedekskeeeklelkekasslevettaYaL 268
                                                                                                                    
  gi|242398030|ref|YP_002993454.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                                       HHHHHTTSCHHHHHHHHHHHHTHTSTS CS
                    TED_complement 269 LallsekdleladkivkWLtkqrnsaG 295
                                                      ++WL++q+ ++ 
  gi|242398030|ref|YP_002993454.1| 488 ---------------LTWLMEQKIEDD 499
                                       ...............555555554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (740 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.72u 0.32s 00:00:01.04 Elapsed: 00:00:00.50
# Mc/sec: 4449.90
//
Query:       gi|242398031|ref|YP_002993455.1|  [L=367]
Description: cell division GTPase [Thermococcus sibiricus MM 739]
Scores for complete 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-31  107.7   0.7    1.1e-28  100.8   0.7    2.2  1  Tubulin       Tubulin/FtsZ family, GTPase domain
  ------ inclusion threshold ------
      0.031   13.5   0.1        0.1   11.8   0.0    1.8  2  Tubulin_2     Tubulin like
       0.13   11.6   0.0       0.23   10.8   0.0    1.4  1  2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, 


Domain annotation for each model (and alignments):
>> Tubulin  Tubulin/FtsZ family, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.8   0.7   1.9e-32   1.1e-28       4     194 ..       5     168 ..       2     171 .. 0.84

  Alignments for each domain:
  == domain 1  score: 100.8 bits;  conditional E-value: 1.9e-32
                                       EEEEHHHHHHHHHHHHH...HHHCH....HHHT.....TTEEEEE....EEESBHHHHHTS-GS......EEEE--C CS
                           Tubulin   4 vigvGqcGnqignelwellakehgiqsdgdslesfFsesgkveyiprsvaidtdpqvlneikagselfnpnklllgk 80 
                                       +igvGqcG +i++ +         +              +  e +    ai+t +++l+ +k      +++++l+g+
  gi|242398031|ref|YP_002993455.1|   5 IIGVGQCGTKIADLFAL-------V--------------D-FEAL----AINTSKSDLDYLKHI---PKERRILIGE 52 
                                       56666666666655555.......1..............1.2333....777777777766666...899******* PP

                                       CCCTTC--TT-HHHHHHHHHHTHHHHHHHHTT-SE....SEEEEEEETTSSHHHHHHHHHHHHHHHTSTTSEEEEEE CS
                           Tubulin  81 egagnngaggypevgkeaaeeileeirkevekcds...lqgffitaslgGGTGSGlgpvilevlkeeypkalvvtvv 154
                                       + +g++g++++p +g+ea++  l +++k+++ +     ++ ff+t ++gGGTGSG +p+++e+lk+eyp+ lvv++ 
  gi|242398031|ref|YP_002993455.1|  53 SLTGGKGVNANPVLGREAMKRDLSMVMKKINAMVGysdVDVFFLTFGFGGGTGSGGTPILAEALKDEYPESLVVAIG 129
                                       ********************999998888875433233699************************************ PP

                                       EE--GG.G-HHHHHHHHHHHHHHHHT-SEEEEEEHHHHHC CS
                           Tubulin 155 vlPsefsevvvepynailalkelieesdavividNdaLlk 194
                                        lP ++ e+++   na+ ++ +l++ +d++i idN++L++
  gi|242398031|ref|YP_002993455.1| 130 ALPLKE-EGIRPTINAAITIDKLSKVADSIIAIDNNKLKE 168
                                       ****99.*******************************97 PP

>> Tubulin_2  Tubulin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   1.7e-05       0.1     115     193 ..      58     128 ..      27     135 .. 0.73
   2 ?   -2.0   0.0      0.27   1.6e+03     275     289 ..     177     192 ..     134     244 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.7e-05
                         Tubulin_2 115 eGAGqiRtvGRlalfanleeirealrdaikrlrgsageeeglnvfVvgSLaGGTGSGiflDvayllrkilkeekqkv 191
                                       +G   ++ +GR a+   l+ ++++++  ++    +        +f+ ++  GGTGSG    +a  l+++++e+   v
  gi|242398031|ref|YP_002993455.1|  58 KGVNANPVLGREAMKRDLSMVMKKINAMVGYSDVD-------VFFLTFGFGGGTGSGGTPILAEALKDEYPESLV-V 126
                                       55566777777777777777777777777766554.......67899**********999999999999999876.4 PP

                         Tubulin_2 192 ki 193
                                        i
  gi|242398031|ref|YP_002993455.1| 127 AI 128
                                       34 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.27
                         Tubulin_2 275 sk.lmelvadniflsl 289
                                       ++ +++ ++++i++ l
  gi|242398031|ref|YP_002993455.1| 177 YEkINRTIVERIASLL 192
                                       3333333333333333 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   0.0   3.9e-05      0.23      39      71 ..       3      35 ..       1      47 [. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3.9e-05
                                      EEEES-SHHHHHHHHHHHHTT-EEEEESSSHHH CS
                      2-Hacid_dh_C 39 vGiiGlGrIGqavakrlkafgmkviaydrskkk 71
                                        iiG+G+ G+++a++++ ++++ +a+++sk++
  gi|242398031|ref|YP_002993455.1|  3 ALIIGVGQCGTKIADLFALVDFEALAINTSKSD 35
                                      67**************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); 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: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 2351.00
//
Query:       gi|242398032|ref|YP_002993456.1|  [L=193]
Description: hypothetical protein TSIB_0036 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score 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   14.6   0.0      0.019   14.3   0.0    1.2  1  MipZ      ATPase MipZ
       0.02   13.7   0.1       0.02   13.7   0.1    1.1  1  DUF2207   Predicted membrane protein (DUF2207)
       0.11   12.6   0.7         17    5.6   0.1    2.3  2  DUF1874   Domain of unknown function (DUF1874)


Domain annotation for each model (and alignments):
>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   3.1e-06     0.019     138     224 ..      25     115 ..      17     161 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.1e-06
                                       CCEEE-SSS--EEEE-HHHHHHHHH.HHTTTTT-SS--EEEEEEESB...-S--HHHHHHHHHHHHHHHHHHT-EEE CS
                              MipZ 138 llgkvdpetlkvkrpslyaelvwea.rkkrakaerkevdWvvlrnrl...salearnkkkveealeeLskrvGfrva 210
                                       +++ +d+e  k++++ ++ e  w+   k+r  ++++++ +      l      +++n+kkv++ ++     +G+ +a
  gi|242398032|ref|YP_002993456.1|  25 IISSIDAERAKIRGEIIHYEDDWDElMKQRVAKGKRHTAFDFYNPSLltiWENKVKNMKKVKNLFKLGLILLGLFIA 101
                                       7899**********9988888886515667666666665544444431113467899999998887666789***** PP

                                       ---B--GGGTTTGG CS
                              MipZ 211 sGlserviyrelfp 224
                                        G++  viyre++ 
  gi|242398032|ref|YP_002993456.1| 102 GGVAVTVIYREFWV 115
                                       ***********864 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   3.4e-06      0.02     358     430 ..      45     130 ..       3     167 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.4e-06
                           DUF2207 358 kkwksavkk................kergyfdkkgkkklkklsalglgliilglilillallllvlllvfllillli 418
                                       ++w + +k+                +    +++k k+ +k  +++ lgli+lgl+++ ++++++   ++  +++l+ 
  gi|242398032|ref|YP_002993456.1|  45 DDWDELMKQrvakgkrhtafdfynpSLLTIWENKVKNMKKVKNLFKLGLILLGLFIAGGVAVTV---IYREFWVLIP 118
                                       5677777777777777777788888888889999999999999999999999999999998887...5555555566 PP

                           DUF2207 419 llliaiivlllf 430
                                       l ++ ++++l+ 
  gi|242398032|ref|YP_002993456.1| 119 LSVVPMVIFLFD 130
                                       666666666654 PP

>> DUF1874  Domain of unknown function (DUF1874)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.1    0.0029        17      34      64 ..       6      36 ..       1      62 [. 0.73
   2 ?    5.5   0.1    0.0031        19      13      35 ..     137     159 ..     128     173 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0029
                                      SSTTEEE----HHHHHHHHHHHT-------- CS
                           DUF1874 34 nneefvsaiGHeataellselldveikvnRi 64
                                      +++e+ s i He++  +++ +  ++ +  +i
  gi|242398032|ref|YP_002993456.1|  6 KEKEVYSHIAHESAEDMIRIISSIDAERAKI 36
                                      567999************9887665554433 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0031
                                       SE......EEEEEEE-HHHHHSS CS
                           DUF1874  13 eeglykiekitieeakellkenn 35 
                                       + g y++ +++iee+kellk+++
  gi|242398032|ref|YP_002993456.1| 137 DIGYYQLTQLFIEELKELLKKYE 159
                                       5689****************974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1088  (0.0606838); expected 358.6 (0.02)
Passed bias filter:                      679  (0.0378716); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.30s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 1282.09
//
Query:       gi|242398033|ref|YP_002993457.1|  [L=205]
Description: hypothetical protein TSIB_0037 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-07   30.4   1.6    4.4e-07   29.7   1.6    1.4  1  Class_IIIsignal  Class III signal peptide
     0.0038   17.0   0.8     0.0074   16.1   0.8    1.4  1  TadF             Putative tight adherence pilin protein F


Domain annotation for each model (and alignments):
>> Class_IIIsignal  Class III signal peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   1.6   4.9e-11   4.4e-07       1      27 []       6      32 ..       6      32 .. 0.96

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 4.9e-11
                   Class_IIIsignal  1 kKGQiSlEyiLLilavlviaiiaiyyy 27
                                      kKGQiSlE+i+++  ++++++++i+++
  gi|242398033|ref|YP_002993457.1|  6 KKGQISLEFIFIFVLFIILLTFSIRNI 32
                                      8***********************985 PP

>> TadF  Putative tight adherence pilin protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.8   8.2e-07    0.0074       5      30 ..       5      30 ..       2      40 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 8.2e-07
                              TadF  5 kqrGsvtielalvllflsllliflvd 30
                                       ++G ++ e++++++++++ll+f++ 
  gi|242398033|ref|YP_002993457.1|  5 MKKGQISLEFIFIFVLFIILLTFSIR 30
                                      69*********************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1120  (0.0624686); expected 358.6 (0.02)
Passed bias filter:                      626  (0.0349155); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1433.64
//
Query:       gi|242398034|ref|YP_002993458.1|  [L=140]
Description: hypothetical protein TSIB_0038 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.033   14.2   0.1      0.055   13.5   0.1    1.3  1  Cpn10     Chaperonin 10 Kd subunit


Domain annotation for each model (and alignments):
>> Cpn10  Chaperonin 10 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   3.1e-06     0.055      31      89 ..      49     108 ..      46     111 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.1e-06
                                       HHSEEEEEEEEE-T........TS-TTS--T-EEEEEGGGTSS-GG....---.EEEEEGGG- CS
                             Cpn10  31 kekpeqGvVvaVGegarnekgedvplevkvgdkVlfpkyagtkvkv....dgkeylilkekdI 89 
                                       + + ++++V aVGeg + ++++   ++++ g+ ++  ++  +k++v    dgk+y i+k++ +
  gi|242398034|ref|YP_002993458.1|  49 EIVDHTAKVYAVGEGYKLKEEA---PQISGGNFTIIFNGTTNKITVsatvDGKSYWIVKNSTV 108
                                       557789*********9998555...99***98777777776766666677********99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 897.44
//
Query:       gi|242398035|ref|YP_002993459.1|  [L=120]
Description: hypothetical protein TSIB_0039 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 812.64
//
Query:       gi|242398036|ref|YP_002993460.1|  [L=481]
Description: hypothetical protein TSIB_0040 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (481 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.31s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2956.93
//
Query:       gi|242398037|ref|YP_002993461.1|  [L=756]
Description: hypothetical protein TSIB_0041 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.078   13.5   0.8        4.4    7.9   0.6    3.1  3  Cadherin-like  Cadherin-like beta sandwich domain


Domain annotation for each model (and alignments):
>> Cadherin-like  Cadherin-like beta sandwich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0     0.025   4.4e+02      19      52 ..     220     257 ..     200     275 .. 0.84
   2 ?    7.9   0.6   0.00025       4.4      13      53 ..     453     498 ..     443     522 .. 0.83
   3 ?   -1.8   0.0      0.26   4.7e+03      59      74 ..     605     625 ..     593     638 .. 0.65

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.025
                     Cadherin-like  19 tvdVdedvdsvtitatae....dsvatvtvngvaveeg 52 
                                       ++  d ++++++  a+++    +s+++++++g++v+ g
  gi|242398037|ref|YP_002993461.1| 220 ELPYDANITKIKWFAQPRwfspSSYMRLFIDGEPVKCG 257
                                       5556788999***********99**********99865 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00025
                     Cadherin-like  13 petteYtvdVdedvdsvtitatae..dsvatvtvngvaveeg...s 53 
                                       ++ ++Y+++ ++d++ ++  +t+e  ++ +++++ ++ ++++   s
  gi|242398037|ref|YP_002993461.1| 453 SASYTYRLKLNYDTSYIRAVYTPEtaKTLYSIDITEEITKDDvidS 498
                                       6789*******************98778899999888777665551 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.26
                     Cadherin-like  59 vsLneGrnkieikv.....ta 74 
                                         L +G+n+i++++     ++
  gi|242398037|ref|YP_002993461.1| 605 RALAPGENYIKVETgndyvIS 625
                                       568899999999874444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (756 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.29s 00:00:00.95 Elapsed: 00:00:00.47
# Mc/sec: 4788.11
//
Query:       gi|242398038|ref|YP_002993462.1|  [L=1096]
Description: hypothetical protein TSIB_0042 [Thermococcus sibiricus MM 739]
Scores for complete 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-26   91.7  16.3    4.3e-15   56.1   6.0    3.0  2  DUF2341   Domain of unknown function (DUF2341)


Domain annotation for each model (and alignments):
>> DUF2341  Domain of unknown function (DUF2341)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   2.6   2.1e-14   3.7e-10       3      83 ..     365     440 ..     363     441 .. 0.80
   2 !   56.1   6.0   2.4e-19   4.3e-15       2      82 ..     542     627 ..     541     629 .. 0.78

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 2.1e-14
                           DUF2341   3 sdiRfvdsdgttLpywieswdantekaliWvkvpsipangnktikiyygnptatsts..ngdatfelFDdfsgteld 77 
                                       + iR++d d++++p+wie+w   +++ liW+k      + ++++ iyy    a + +  n ++ f+l+Ddf+gt++d
  gi|242398038|ref|YP_002993462.1| 365 ASIRVYDVDCNPIPFWIEKW--GNDEILIWIKT-----GVTNQYFIYYTADPAYAIDgyNKETLFDLYDDFDGTSID 434
                                       57****************97..45569***994.....55556667776655544444599999************* PP

                           DUF2341  78 ttkWtv 83 
                                       ttkW++
  gi|242398038|ref|YP_002993462.1| 435 TTKWDI 440
                                       ****85 PP

  == domain 2  score: 56.1 bits;  conditional E-value: 2.4e-19
                           DUF2341   2 gsdiRfvdsdgttLpywieswdantekaliWvkvpsip.......angnktikiyygnptatstsngdatfelFDdf 71 
                                        ++i+++d+++++Lp+wie+w++++ekaliWvk + i           ++t +i y+  ++ +++ng a+fe+FD+f
  gi|242398038|ref|YP_002993462.1| 542 TAEIKIYDNQENELPFWIEYWNTTEEKALIWVKSSFIYdrrqgntYYYHATFYIEYNT-GTLTRGNGTAVFEFFDNF 617
                                       579**********************************965322211122334666655.555599************ PP

                           DUF2341  72 sgteldttkWt 82 
                                       ++++ d +kW+
  gi|242398038|ref|YP_002993462.1| 618 EDSTWD-DKWE 627
                                       **8776.6886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1096 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.27s 00:00:00.90 Elapsed: 00:00:00.46
# Mc/sec: 7230.90
//
Query:       gi|242398039|ref|YP_002993463.1|  [L=258]
Description: hypothetical protein TSIB_0043 [Thermococcus sibiricus MM 739]
Scores for complete 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  245.3  16.3    5.4e-73  245.1  16.3    1.0  1  DUF2101    Predicted membrane protein (DUF2101)
  ------ inclusion threshold ------
        0.1   12.5   0.1       0.24   11.3   0.1    1.7  2  HTH_5      Bacterial regulatory protein, arsR family
       0.16   11.8   0.3       0.16   11.8   0.3    1.8  2  DUF3487    Protein of unknown function (DUF3487)
        2.1    8.3   0.0        2.1    8.3   0.0    3.2  3  RseC_MucC  Positive regulator of sigma(E), RseC/MucC


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 !  245.1  16.3   1.2e-76   5.4e-73       1     206 []      25     232 ..      25     232 .. 0.97

  Alignments for each domain:
  == domain 1  score: 245.1 bits;  conditional E-value: 1.2e-76
                           DUF2101   1 ikelllpiPseeaPks.iliklakrnltehelvsLkLqlifllyliislv.lvflksllvlllaalleflllryili 75 
                                       ik+++ p+P ++ P+  il+kl kr+lt hel+sL+Lql+f+ yl+++l+ +v++ + l l ++++++f++lry+l+
  gi|242398039|ref|YP_002993463.1|  25 IKDIVNPTPFQKPPRFkILKKLIKRELTVHELLSLNLQLSFIFYLLLALLlIVLFGNELYLTIISVVYFIYLRYTLL 101
                                       589999********988****************************977651566999******************** PP

                           DUF2101  76 rniellidfeayrafylavsviailaylgyvllrklslelyyylvyllvivivvlvfryyfksrygrDytyGvveev 152
                                       +n++++i+ e+yr+fy++++ i +l++lgy+l+r++++++yy+++yl +i++vvl+fry++ks+++rD+tyG+ve++
  gi|242398039|ref|YP_002993463.1| 102 KNRDFFIEVEPYRFFYYGLTAIGFLSFLGYLLIRRFAKNVYYFYTYLIAIFVVVLAFRYIYKSKFTRDWTYGIVEDI 178
                                       ***************************************************************************** PP

                           DUF2101 153 kedlvkvfvhdDiaanvkPgyywvpavadveegdivkllveervlrgsrPvril 206
                                       k++lv v vhdDi+anvkPg ywv++  dve+gd+vk+l+eer++r+s P r+l
  gi|242398039|ref|YP_002993463.1| 179 KGELVLVSVHDDIRANVKPGKYWVDNTEDVEVGDVVKILIEERIFRSSLPKRVL 232
                                       **************************************************9986 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 ?   -3.4   0.0       2.2   9.7e+03      17      24 ..       9      16 ..       8      17 .. 0.81
   2 ?   11.3   0.1   5.3e-05      0.24       2      21 ..      37      56 ..      36      64 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 2.2
                                      EHHHHHHH CS
                             HTH_5 17 cvcelaee 24
                                      +++e+ae+
  gi|242398039|ref|YP_002993463.1|  9 KIGEIAEA 16
                                      799***97 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 5.3e-05
                                      HHHHHHHHHHTTSSEEHHHH CS
                             HTH_5  2 ptRlkILklLaegelcvcel 21
                                      p R kILk L ++el+v+el
  gi|242398039|ref|YP_002993463.1| 37 PPRFKILKKLIKRELTVHEL 56
                                      6699***************8 PP

>> DUF3487  Protein of unknown function (DUF3487)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.3   3.6e-05      0.16      17      61 ..      48      92 ..      43     103 .. 0.75
   2 ?   -1.4   0.1      0.47   2.1e+03      38      66 ..     128     156 ..     115     171 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.6e-05
                           DUF3487 17 frGltadEllvla.glglvvglvlglllallvgslaliptialllv 61
                                       r lt++Ell l   l+++++l+l+lll++l+g+ +  +ti+ ++ 
  gi|242398039|ref|YP_002993463.1| 48 KRELTVHELLSLNlQLSFIFYLLLALLLIVLFGNEL-YLTIISVVY 92
                                      57799***9977548******************554.445443333 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.47
                           DUF3487  38 vlglllallvgslaliptialllvllvvl 66 
                                        lg ll+  + + +  +   l+++++vvl
  gi|242398039|ref|YP_002993463.1| 128 FLGYLLIRRFAKNVYYFYTYLIAIFVVVL 156
                                       44555555555444444444444444443 PP

>> RseC_MucC  Positive regulator of sigma(E), RseC/MucC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   1.9     0.069   3.1e+02      76     110 ..      66     100 ..      58     108 .. 0.56
   2 ?    1.0   1.2     0.083   3.7e+02      79     109 ..     128     156 ..     114     175 .. 0.44
   3 ?    8.3   0.0   0.00047       2.1      37      63 ..     197     223 ..     191     227 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.069
                         RseC_MucC  76 lllilgallgsallgssellaalgall.glvlgfli 110
                                       ++ +l all  +l +++el+  +++++ +++l + +
  gi|242398039|ref|YP_002993463.1|  66 IFYLLLALLLIVL-FGNELYLTIISVVyFIYLRYTL 100
                                       3444444444444.5666666665555044455554 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.083
                         RseC_MucC  79 ilgallgsallgssellaalgallglvlgfl 109
                                       +lg+ll+  ++  ++++ + + l+++++ +l
  gi|242398039|ref|YP_002993463.1| 128 FLGYLLIRRFA--KNVYYFYTYLIAIFVVVL 156
                                       34444444442..333333332222222222 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.00047
                         RseC_MucC  37 ekrleveneigakvGdkVevgieeksl 63 
                                       + + +v+n+ +++vGd V++ iee+ +
  gi|242398039|ref|YP_002993463.1| 197 PGKYWVDNTEDVEVGDVVKILIEERIF 223
                                       557789****************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1141  (0.0636399); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1781.53
//
Query:       gi|242398040|ref|YP_002993464.1|  [L=188]
Description: GMP synthase [glutamine-hydrolyzing] subunit A [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.3e-45  153.1   0.0    8.6e-45  152.8   0.0    1.0  1  GATase         Glutamine amidotransferase class-I
    5.9e-14   52.3   0.2    2.2e-12   47.2   0.2    2.6  2  Peptidase_C26  Peptidase C26
     0.0033   17.7   0.0      0.056   13.7   0.0    2.3  2  GST_N_2        Glutathione S-transferase, N-terminal domain
  ------ inclusion threshold ------
       0.15   11.6   0.0       0.19   11.3   0.0    1.3  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
       0.17   11.7   0.1        4.2    7.2   0.1    2.1  1  SNO            SNO glutamine amidotransferase family
       0.23   11.6   0.0       0.32   11.1   0.0    1.2  1  DUF5012        Domain of unknown function (DUF5012)


Domain annotation for each model (and alignments):
>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.8   0.0   2.9e-48   8.6e-45       2     186 ..       4     181 ..       3     184 .. 0.96

  Alignments for each domain:
  == domain 1  score: 152.8 bits;  conditional E-value: 2.9e-48
                                       EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTTTTTHHHHHHHHCTSTS-EEEET CS
                            GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspgvegkieaikearenkiPiLGIC 78 
                                       ++Dn+ ++++ + + l+ lgv+ +++p++++ eei+   +np gi++sgGp    ++++ ++++++ e ++PiLGIC
  gi|242398040|ref|YP_002993464.1|   4 IMDNHGQYVHRIWRTLRYLGVEAKIIPNTTPPEEIK--SMNPRGIIFSGGPTLERTGNCEAILEHYEEFNVPILGIC 78 
                                       68*********************************4..79************************************* PP

                                       HHHHHHHHHTTTEEEEEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEEE CS
                            GATase  79 LGmQllaiefgrkvvkekekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtakseddeelm 155
                                       LG+Ql+a+ fg+kv + ++ e+   + ++ + e+++++gl+++++++ +H +ev++   +p+++e +akse  + ++
  gi|242398040|ref|YP_002993464.1|  79 LGHQLIAKYFGGKVGRGERGEYSLVEVEILE-ENDIFKGLPEKLKVWESHMDEVKE---LPEEFELLAKSEF-CPVE 150
                                       ******************9**********99.77**********************...***********55.79** PP

                                       EEEEETTTEEEESSBTTSTTSTTHHHHHHHH CS
                            GATase 156 eiiekknpfvgvQFHPEststpegpellfnf 186
                                       ++ +kk p++gvQFHPE+ +t++g+ + +nf
  gi|242398040|ref|YP_002993464.1| 151 AMKHKKLPIYGVQFHPEVAHTERGSDIYRNF 181
                                       ****************************998 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.12   3.5e+02      29      71 ..      15      55 ..       4      69 .. 0.74
   2 !   47.2   0.2   7.4e-16   2.2e-12      96     216 .]      62     167 ..      52     167 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.12
                     Peptidase_C26 29 yveavekagglpvllpieedeedvkaildkldgllltGgqdve 71
                                        +  +  g+ + ++p ++++e++k++     g++++Gg+++e
  gi|242398040|ref|YP_002993464.1| 15 IWRTLRYLGVEAKIIPNTTPPEEIKSMNP--RGIIFSGGPTLE 55
                                      55556666677778899999999988754..59******9876 PP

  == domain 2  score: 47.2 bits;  conditional E-value: 7.4e-16
                     Peptidase_C26  96 aLiraalergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhreheqsaashavkv.ekgsllaellgseeievn 171
                                       a++++  e +vPilgiC+G+ql++  +GG++ +  +             +    +v++ e++ +++ l +  + +v 
  gi|242398040|ref|YP_002993464.1|  62 AILEHYEEFNVPILGICLGHQLIAKYFGGKVGRGERG------------EYSLVEVEIlEENDIFKGLPE--KLKVW 124
                                       5677778889*******************98766553............122345665156666666655..***** PP

                     Peptidase_C26 172 slHhqaikelaeelrveAvaeDgviEaieseeakafvlgvQwHPE 216
                                         H   +kel ee++  A +e   +Ea+++++   +++gvQ+HPE
  gi|242398040|ref|YP_002993464.1| 125 ESHMDEVKELPEEFELLAKSEFCPVEAMKHKK--LPIYGVQFHPE 167
                                       *****************************999..67********9 PP

>> GST_N_2  Glutathione S-transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   1.9e-05     0.056       4      49 ..      11      75 ..       8      85 .. 0.82
   2 ?    1.8   0.0     0.098   2.9e+02      14      37 ..     114     138 ..     113     175 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.9e-05
                                      HHHHHHHHHHHCT--EEEEEEH...-TTSHHHHHHHHCTTT.........................SSSEE CS
                           GST_N_2  4 wahRvlialalkglediisvvvlepkgfekseefprlnprg.........................tVPvL 49
                                      ++hR++ +l+++g+e +i++        +++ee +  nprg                          VP+L
  gi|242398040|ref|YP_002993464.1| 11 YVHRIWRTLRYLGVEAKIIPN------TTPPEEIKSMNPRGiifsggptlertgnceailehyeefNVPIL 75
                                      89***************9776......67889999****99888877777777777777777777777776 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.098
                                       HCT--EEEEEE.H...-TTSHHHHH CS
                           GST_N_2  14 lkglediisvv.vlepkgfekseef 37 
                                        kgl+ +++v+ +++++ +e +eef
  gi|242398040|ref|YP_002993464.1| 114 FKGLPEKLKVWeSHMDEVKELPEEF 138
                                       5999999999888888877877777 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   6.3e-05      0.19      59     108 ..      55     103 ..      16     128 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 6.3e-05
                          GATase_3  59 lresgldeaikeaaeaggpvlgiCGGlqmLGeeiedpegvegeagevegl 108
                                       +r  + +  ++++ e ++p+lgiC G q+  +++  + g  ge+ge++ +
  gi|242398040|ref|YP_002993464.1|  55 ERTGNCEAILEHYEEFNVPILGICLGHQLIAKYFGGKVGR-GERGEYSLV 103
                                       34444444566667789***************99887776.666666554 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.1    0.0014       4.2      51      88 ..      54      91 ..      22     186 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0014
                                      HHHTT-HHHHHHHHHTT.--EEEETHHHHHHCCEETTB CS
                               SNO 51 iertglyedllefvknsekvvlGtCaGlillskelene 88
                                      +ertg  e++le  ++ + ++lG C G  l++k  +++
  gi|242398040|ref|YP_002993464.1| 54 LERTGNCEAILEHYEEFNVPILGICLGHQLIAKYFGGK 91
                                      57778788888888888888888888888777766554 PP

>> DUF5012  Domain of unknown function (DUF5012)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00011      0.32      24      97 ..      62     133 ..      46     146 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00011
                                       SS-EEE---EEEEEEEETTEEEES-TTTTTTTTSST--TTSS-EEEEEE-TTS-EEEEEEE-TTS----SEEEE CS
                           DUF5012  24 gavveyagyevtiekiaPGlfyisdflGGyydqraGyGaayamkGyiqlkndnsitllsssvkgwddsldalee 97 
                                       + +++y +++v i  i  G   i+ ++GG    ++G   +y+++    l++++  + l +++k w+  +d+++e
  gi|242398040|ref|YP_002993464.1|  62 AILEHYEEFNVPILGICLGHQLIAKYFGGK--VGRGERGEYSLVEVEILEENDIFKGLPEKLKVWESHMDEVKE 133
                                       45679************************5..5778888999886555555556689************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.30s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1149.56
//
Query:       gi|242398041|ref|YP_002993465.1|  [L=132]
Description: hypothetical protein TSIB_0045 [Thermococcus sibiricus MM 739]
Scores for complete 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   83.2   4.5    1.7e-23   83.0   4.5    1.0  1  HEPN      HEPN domain
    0.00069   19.5   0.3    0.00069   19.5   0.3    1.6  2  PaREP1    Archaeal PaREP1/PaREP8 family
  ------ inclusion threshold ------
      0.098   12.8   0.1        5.5    7.2   0.0    2.2  2  Mrr_N     Mrr N-terminal domain


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 !   83.0   4.5   2.9e-27   1.7e-23       2     117 ..       5     120 ..       4     121 .. 0.97

  Alignments for each domain:
  == domain 1  score: 83.0 bits;  conditional E-value: 2.9e-27
                                       HHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHTT--.SSCCHHHHHHC..CHHHT...-HHHHHH CS
                              HEPN   2 eewlrrAeedleaAellleegdydlacfhaqqaaekalKAlllkkggeppkthdlreLle..elkkelkeseelree 76 
                                       e+++++A++ lea+++ll++g+yd+a+ +a++ +++++ A+ll+k++++ k+++l++L++  ++k+ ++ + +l + 
  gi|242398041|ref|YP_002993465.1|   5 EALIKKAQKSLEASKELLKKGFYDFAAARAYYTMFYCVEAILLTKNISVSKHSSLIALFGreFVKTSEI-PHKLYTH 80 
                                       89***********************************************************99**9999.******* PP

                                       HHHHHCCCHHCCCTSS--S--HHHHHHHHHHHHHHHHHHHH CS
                              HEPN  77 leeLekayiesrYpdakeeyteedaeealkdaeevlelvee 117
                                       l  ++++++e++Y+   e   +e aee++k+ +e+le+ +e
  gi|242398041|ref|YP_002993465.1|  81 LIMAFNLRQEADYEVMLEI-PKERAEEIVKFSKEFLEFTKE 120
                                       ******************7.******************886 PP

>> PaREP1  Archaeal PaREP1/PaREP8 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.3   1.2e-07   0.00069       2      49 ..       7      54 ..       6      92 .. 0.92
   2 ?   -2.3   0.0      0.68   4.1e+03       9      18 ..     107     116 ..      99     126 .. 0.51

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.2e-07
                            PaREP1  2 rleeaekeleeAeellekGdlrqAaeKaykAvkalvkalaeknnlkll 49
                                       ++ a+k le ++ell+kG +  Aa +ay  +  +v a++  +n ++ 
  gi|242398041|ref|YP_002993465.1|  7 LIKKAQKSLEASKELLKKGFYDFAAARAYYTMFYCVEAILLTKNISVS 54
                                      5799************************************99888765 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.68
                            PaREP1   9 eleeAeelle 18 
                                        ++ ++e+le
  gi|242398041|ref|YP_002993465.1| 107 IVKFSKEFLE 116
                                       3333333332 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0   0.00092       5.5      25      69 ..       5      49 ..       3      70 .. 0.91
   2 ?    4.0   0.0    0.0089        53      23      68 ..      77     129 ..      65     132 .] 0.62

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00092
                             Mrr_N 25 ervaerfglseeeraellpsgkqtrfknrvgWartyLkkaglles 69
                                      e+++++++ s e+ +ell++g       r+ + + y+++a ll++
  gi|242398041|ref|YP_002993465.1|  5 EALIKKAQKSLEASKELLKKGFYDFAAARAYYTMFYCVEAILLTK 49
                                      67889999999*****************************99986 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.0089
                             Mrr_N  23 irervaerfglseeeraell...psgkq....trfknrvgWartyLkkaglle 68 
                                       ++  ++  f+l +e+  e+    p+ +     +  k  + + + yL k g+le
  gi|242398041|ref|YP_002993465.1|  77 LYTHLIMAFNLRQEADYEVMleiPKERAeeivKFSKEFLEFTKEYLIKKGFLE 129
                                       55566666666544433333355555545552333444689999******998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       997  (0.0556082); expected 358.6 (0.02)
Passed bias filter:                      603  (0.0336327); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 844.92
//
Query:       gi|242398042|ref|YP_002993466.1|  [L=104]
Description: nucleotidyltransferase [Thermococcus sibiricus MM 739]
Scores for complete 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   43.6   0.3    3.2e-11   43.4   0.3    1.1  1  NTP_transf_2    Nucleotidyltransferase domain
    5.8e-11   42.3   0.3    7.7e-11   41.9   0.3    1.2  1  Polbeta         Polymerase beta, Nucleotidyltransferase
     0.0073   16.5   0.0     0.0089   16.2   0.0    1.2  1  DNA_pol_B_palm  DNA polymerase beta palm
  ------ inclusion threshold ------
        0.1   12.4   0.0       0.12   12.2   0.0    1.2  1  DUF294          Putative nucleotidyltransferase DUF294
       0.14   12.3   0.0       0.31   11.2   0.0    1.6  1  SMODS           Second Messenger Oligonucleotide or Dinucleot
       0.14   12.0   0.0       0.16   11.8   0.0    1.1  1  Adenyl_cycl_N   Adenylate cyclase NT domain


Domain annotation for each model (and alignments):
>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.4   0.3   1.1e-14   3.2e-11       2      73 ..       8      77 ..       7     101 .. 0.79

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 1.1e-14
                                      HHHHHHHHHHTT..TSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEEEE CS
                      NTP_transf_2  2 kklleelkelep..vakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleellglevdl 73
                                      ++l+e++++  +    +++l+GSyarG++   SD+D+l+v++   +     e+ ek++ei  +l++     v +
  gi|242398042|ref|YP_002993466.1|  8 NELREKVRSILGdkLEEIILYGSYARGDYSTRSDVDILLVVKGKLNL----EEYEKIMEIAAELSLKYEKVVSI 77
                                      6899999999999999****************************875....66667777777776655444444 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.9   0.3   2.6e-14   7.7e-11       1      84 [.      12     100 ..      12     103 .. 0.72

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 2.6e-14
                                       -STTTTHHHHHHHHSTTEEEEEE-S------EEEEEEEESS-...--HHHHHHHHHHHHHH.SSSEEEEEE.....T CS
                           Polbeta   1 ekikeilekekeielaylFGSrakgkareeSDiDlavllkek...ldleeelelaaelediklgkkvDlvd.....l 69 
                                       ek+++il ++  +e ++l+GS+a+g++  +SD+D+ +++k k   +++e+ +e+aael+    +k v ++d     +
  gi|242398042|ref|YP_002993466.1|  12 EKVRSILGDK--LEEIILYGSYARGDYSTRSDVDILLVVKGKlnlEEYEKIMEIAAELSLK-YEKVVSIIDypkwiF 85 
                                       6777777777..999***************************7777788888888888877.445555554111212 PP

                                       TTS-HHHHHHHHHS- CS
                           Polbeta  70 neapplllyeilkeg 84 
                                        ++++ +l+++ +eg
  gi|242398042|ref|YP_002993466.1|  86 TSSDSPFLQNVKREG 100
                                       345556666666655 PP

>> DNA_pol_B_palm  DNA polymerase beta palm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0     3e-06    0.0089      13      65 ..       9      63 ..       2      80 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3e-06
                                      HHHHHHHHH-TT..-EEEE-HHHHTT-SEE.SSEEEEEEBTTBSTTSS--HHHHHH CS
                    DNA_pol_B_palm 13 lvkkaakeldpe..vevivcGSYRRgaess.GDvDvlitkkdakseskklkkllek 65
                                       ++++++++  +   e+i  GSY Rg  s+  DvD+l+  k++ +  ++ +k++e 
  gi|242398042|ref|YP_002993466.1|  9 ELREKVRSILGDklEEIILYGSYARGDYSTrSDVDILLVVKGKLNL-EEYEKIMEI 63
                                      45555555543333578899*****9865438*****998877663.455555554 PP

>> DUF294  Putative nucleotidyltransferase DUF294
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0     4e-05      0.12      53      94 ..      26      67 ..       3      76 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4e-05
                            DUF294 53 lvmGSeGReEqtlktDqDnalvledeeeeaareyfaelaerv 94
                                      +  GS +R++   ++D D  lv++ + + ++ e++ e+a+++
  gi|242398042|ref|YP_002993466.1| 26 ILYGSYARGDYSTRSDVDILLVVKGKLNLEEYEKIMEIAAEL 67
                                      678*********************977777777777777665 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 ?   11.2   0.0    0.0001      0.31      28     107 ..       3      74 ..       1      88 [. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0001
                             SMODS  28 vkaitkrLnkdfrel.kskiaesllvGSyardTaikpvsdkdmlfeldvdllvvvnevegdepsdlleklkkalkkt 103
                                       ++a+ ++L+++ r++ ++k++e +l GSyar+         d  +++dvd+l+vv+ + + e  + + ++ + l+ +
  gi|242398042|ref|YP_002993466.1|   3 IQALLNELREKVRSIlGDKLEEIILYGSYARG---------DYSTRSDVDILLVVKGKLNLEEYEKIMEIAAELSLK 70 
                                       5566666666666541669***********97.........334589999999999988888888888888888888 PP

                             SMODS 104 ykss 107
                                       y++ 
  gi|242398042|ref|YP_002993466.1|  71 YEKV 74 
                                       8774 PP

>> Adenyl_cycl_N  Adenylate cyclase NT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   5.5e-05      0.16      91     133 ..      21      63 ..       3      76 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.5e-05
                     Adenyl_cycl_N  91 aieglylmGStgsiaqsekSDlDiWvchrselsaeelelLekK 133
                                       ++e + l GS +   +s++SD+Di ++++ +l+ ee+e++ + 
  gi|242398042|ref|YP_002993466.1|  21 KLEEIILYGSYARGDYSTRSDVDILLVVKGKLNLEEYEKIMEI 63 
                                       577788899****9***********************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       828  (0.0461822); expected 358.6 (0.02)
Passed bias filter:                      634  (0.0353617); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 697.14
//
Query:       gi|242398043|ref|YP_002993467.1|  [L=313]
Description: GMP synthase [glutamine-hydrolyzing] subunit B [Thermococcus sibiricus MM 739]
Scores for complete 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  118.3   0.0    2.3e-34  117.3   0.0    1.5  1  GMP_synt_C     GMP synthase C terminal domain
    1.8e-13   50.2   0.0    3.7e-07   29.5   0.0    2.2  2  NAD_synthase   NAD synthase
    5.5e-05   22.8   0.0     0.0039   16.7   0.0    2.3  1  QueC           Queuosine biosynthesis protein QueC
    7.3e-05   22.4   0.0    0.00015   21.4   0.0    1.5  1  ThiI           Thiamine biosynthesis protein (ThiI)
    7.3e-05   21.7   0.0       0.02   13.7   0.0    2.2  2  tRNA_Me_trans  tRNA methyl transferase
    0.00054   20.0   0.0      0.001   19.2   0.0    1.5  1  PAPS_reduct    Phosphoadenosine phosphosulfate reductase fami
  ------ inclusion threshold ------
      0.035   13.8   0.0      0.079   12.6   0.0    1.5  2  Asn_synthase   Asparagine synthase
      0.035   13.9   0.0      0.088   12.6   0.0    1.7  1  ATP_bind_3     PP-loop family
       0.21   11.5   1.0        5.7    6.8   0.1    2.8  3  DUF2124        Uncharacterized protein conserved in archaea (


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 !  117.3   0.0   1.2e-37   2.3e-34       1      92 []     223     312 ..     223     312 .. 0.96

  Alignments for each domain:
  == domain 1  score: 117.3 bits;  conditional E-value: 1.2e-37
                                       CCCCTTT-GGGSSEEEEEEEEEEE----------EEEEEEEEE---------B----HHHHHHHHHHHHHHSTT--- CS
                        GMP_synt_C   1 eelkkaglykkiwQafavllpvksvGvmgdkRtyeyvvalRaveseDamtadvaelpyevLekissrivnevkgvnr 77 
                                       ee+++agl+   wQafavll vk+vGv+gd R+y++++a+R+ves D+mta+++++p+evL++i+ ri++e+++v r
  gi|242398043|ref|YP_002993467.1| 223 EEIENAGLK--PWQAFAVLLGVKTVGVQGDIRAYKETIAVRVVESLDGMTANAMKVPFEVLQRIAFRITSEIPQVGR 297
                                       577777775..7***************************************************************** PP

                                       EEEE---TTTS-S-- CS
                        GMP_synt_C  78 vvyditskPpatiEw 92 
                                       v+ydit+kPpatiE+
  gi|242398043|ref|YP_002993467.1| 298 VLYDITNKPPATIEF 312
                                       **************7 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.0   1.9e-10   3.7e-07       7      82 ..      10      89 ..       5     109 .. 0.70
   2 !   18.4   0.0   4.5e-07    0.0009     148     177 ..     163     192 ..     161     195 .. 0.95

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 1.9e-10
                                      HHHHHHHHH....CTTSEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHH.HHHHHHHHHTSEEEE-- CS
                      NAD_synthase  7 dflkeyvkk....agakgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedve.dalalaenlgievktid 80
                                      +f++e+vk+     g k++++ lSGGvDSs++a la ka+  ++ +a+ + + +  + + e   +++ e++g++   +d
  gi|242398043|ref|YP_002993467.1| 10 KFIEEKVKEikktVGEKKAIIALSGGVDSSTAAILAYKAI-GDRLHAVFVNTGFLRKGEPEfVIKTFKEEFGLNLIYVD 87
                                      56666665411115779***********************.57888988875555554444134556667777776666 PP

                                      -H CS
                      NAD_synthase 81 ik 82
                                       +
  gi|242398043|ref|YP_002993467.1| 88 AQ 89
                                      55 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 4.5e-07
                                       BETTTTS-HHHHHHHHHHTT--HHHHCS-- CS
                      NAD_synthase 148 lapiaellKtevkeLakelnvPervlkkpP 177
                                       ++p+ +l+K ev+e akel+ Pe+++++ P
  gi|242398043|ref|YP_002993467.1| 163 IEPLRDLYKDEVREVAKELGLPEKIYHRMP 192
                                       78**************************98 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0     2e-06    0.0039       1      61 [.      27      88 ..      27     190 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2e-06
                                      EEEEE--SSHHHHHHHHHHHHH.-SEEEEEEEESS-TTSHHHHHH.HHHHHHT--.-EEEEE- CS
                              QueC  1 kavvllSGGlDSttvlalakke.gkevealtfdYgqrhkkeleaa.kkiakelgveehkildl 61
                                      ka++ lSGG+DS+t+++la k+ g++++a+ ++ g  +k e e + k++ +e+g+ +   +d 
  gi|242398043|ref|YP_002993467.1| 27 KAIIALSGGVDSSTAAILAYKAiGDRLHAVFVNTGFLRKGEPEFViKTFKEEFGL-NLIYVDA 88
                                      79*************99997762699****9999988777777551555566666.5555544 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   7.6e-08   0.00015       4     160 ..      26     182 ..      23     191 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 7.6e-08
                              ThiI   4 gkvlaLlSgGiDSpVaaylllkR.Gcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdfkevlkei 79 
                                        k++  lSgG+DS  aa l+ k  G r ++v+++     + e + ++++      e++    ++l+ vd +e  +  
  gi|242398043|ref|YP_002993467.1|  26 KKAIIALSGGVDSSTAAILAYKAiGDRLHAVFVNTGFLRKGEPEFVIKTFK---EEFG----LNLIYVDAQERFFTA 95 
                                       578899*************998559******99544444444443333333...3454....799999999998888 PP

                              ThiI  80 lekv..kekltivllkrkmlriAekvaeeegakalvtGesL.gqVaSq....tleNlrvisavvnllilrPLigldK 149
                                       l+ v  +e+ + ++ k +++ + e+va+e +a+ l++G      + Sq      +N+  + +  nl +++PL  l K
  gi|242398043|ref|YP_002993467.1|  96 LKGVtdPEEKRKIIGK-TFIDVFEEVANEIDADFLIQGTIApDWIESQgkikSHHNVGGLPERLNLKLIEPLRDLYK 171
                                       8888655666666665.789999***************74313455552222468999******************* PP

                              ThiI 150 eeiiklAkeig 160
                                       +e+ ++Ake+g
  gi|242398043|ref|YP_002993467.1| 172 DEVREVAKELG 182
                                       *********99 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0     1e-05      0.02       2      31 ..      27      57 ..      26      69 .. 0.76
   2 !    5.9   0.0    0.0023       4.6     163     186 ..     161     184 ..     154     190 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1e-05
                     tRNA_Me_trans  2 kvvvalSgGVDSsvaaallkeq.gyevigvf 31
                                      k ++alSgGVDSs aa+l  ++ g  + +vf
  gi|242398043|ref|YP_002993467.1| 27 KAIIALSGGVDSSTAAILAYKAiGDRLHAVF 57
                                      6799************987655144555555 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0023
                     tRNA_Me_trans 163 kllfPlgeltKeevrkiAkeagla 186
                                       kl+ Pl +l K+evr++Ake gl+
  gi|242398043|ref|YP_002993467.1| 161 KLIEPLRDLYKDEVREVAKELGLP 184
                                       5677****************9997 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   5.1e-07     0.001       2      75 ..      28     103 ..      27     133 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 5.1e-07
                                       EEEE--SSCTCHHHHHHHHHHCTTH.EEEEEE-STB-HHHHHHHHHH.HHHTT-EEEEEE-SCHHHHHHHHHH-S- CS
                       PAPS_reduct   2 lvvsvsgGkdslVllhLalkafkpv.pvvfvdtghefpetiefvdel.eeryglrlkvyepeeevaekinaekhgs 75 
                                        +++ sgG ds+   +La ka  ++ + vfv+tg   +   efv ++ +e++gl+l++++ +e++  +++  + ++
  gi|242398043|ref|YP_002993467.1|  28 AIIALSGGVDSSTAAILAYKAIGDRlHAVFVNTGFLRKGEPEFVIKTfKEEFGLNLIYVDAQERFFTALKGVTDPE 103
                                       57899*******************758*********9999999866517777*****9999998877776666655 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0     4e-05     0.079      17      59 ..      25      69 ..      15      97 .. 0.75
   2 ?   -2.6   0.0       1.6   3.3e+03     262     283 ..     168     190 ..     151     191 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4e-05
                      Asn_synthase 17 dvpvGalLSGGlDSSliaalaarqsksplktFsigf..eekgsde 59
                                      + +  + LSGG+DSS+ a la +    +l+++ + +    kg +e
  gi|242398043|ref|YP_002993467.1| 25 EKKAIIALSGGVDSSTAAILAYKAIGDRLHAVFVNTgfLRKGEPE 69
                                      5566688*************9998888888876655224455555 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.6
                      Asn_synthase 262 gieKyiLRealegy.lPeeileR 283
                                       +  K   Re+++ + lPe+i++R
  gi|242398043|ref|YP_002993467.1| 168 DLYKDEVREVAKELgLPEKIYHR 190
                                       56677788888888899999888 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   4.4e-05     0.088       2     158 ..      28     180 ..      27     185 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.4e-05
                                       EEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE--H...HHCTTST CS
                        ATP_bind_3   2 vlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvkelckklnikleiekvdv...akkkgkn 75 
                                       +++A+SgG+DS +   l++k     g +l a+ v+ g+  + +  + ++k++ ++++++l++ +++     + kg +
  gi|242398043|ref|YP_002993467.1|  28 AIIALSGGVDSSTAAILAYKAI---GDRLHAVFVNTGFLRKGEP-EFVIKTFKEEFGLNLIYVDAQErffTALKGVT 100
                                       79*********99888887774...4589999999998766544.46789999999999999999988884444444 PP

                                       CCCHHHHH....HHHHHHHCHHCCT.CEEE---BHHHHHHHHHHHHCCT--CCHHH-S-SEEEETTCCEE-CCCT-- CS
                        ATP_bind_3  76 leeaARel....RYevlkealkkegievlllAhhadDqaEtfllrlargsglaglagikeaseiasirlvRPlLkvs 148
                                         e+ R++      +v++e++++ ++++l+ +  a D +E       + ++ +++ g++e+    + +l+ Pl +++
  gi|242398043|ref|YP_002993467.1| 101 DPEEKRKIigktFIDVFEEVANEIDADFLIQGTIAPDWIESQ----GKIKSHHNVGGLPERL---NLKLIEPLRDLY 170
                                       445555431211578999999999999999999999999964....3333445667777755...788888888888 PP

                                       HHHHHHHHHH CS
                        ATP_bind_3 149 keeleeylke 158
                                       k+e++e++ke
  gi|242398043|ref|YP_002993467.1| 171 KDEVREVAKE 180
                                       8888888877 PP

>> DUF2124  Uncharacterized protein conserved in archaea (DUF2124)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.085   1.7e+02       3      52 ..      12      60 ..      10      83 .. 0.79
   2 ?    6.8   0.1    0.0029       5.7     101     140 ..      97     134 ..      80     135 .. 0.82
   3 ?   -1.0   0.0      0.76   1.5e+03      66     106 ..     245     287 ..     235     305 .. 0.63

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.085
                                      HHHHHHHHHHHTTT-SEEEEEE-TTTTHHHHHHHHHHTTT..SEEEEEET CS
                           DUF2124  3 lsgllrefkelvkesekivfvGspgvCtpfaellayaiRdlekelvfvpd 52
                                      +++ ++e k++v e++ i+ + s gv  + a +lay     + + vfv +
  gi|242398043|ref|YP_002993467.1| 12 IEEKVKEIKKTVGEKKAIIAL-SGGVDSSTAAILAYKAIGDRLHAVFVNT 60
                                      778899999999999888654.5688889999999987777888888865 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0029
                                       HHHHHHHEEEEEEEEEETTHHHHTTHHHHS--SEEEEEEE CS
                           DUF2124 101 keliekiekkkviGvcfmsifekagWldkidFdliidakl 140
                                       k +++  ek+k+iG +f ++fe+    ++id d++i++++
  gi|242398043|ref|YP_002993467.1|  97 KGVTDPEEKRKIIGKTFIDVFEEV--ANEIDADFLIQGTI 134
                                       5555666999***********986..68999999999887 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.76
                                       TEEE..EEEE-.-S-EEEEEEEGGGGSTTTS--HHHHHHHHHH CS
                           DUF2124  66 vGmq..leeeaeeekadvvvllGGlampkikveaedvkeliek 106
                                       vG+q  ++  +e+  + vv  l G++ + +kv  e ++++  +
  gi|242398043|ref|YP_002993467.1| 245 VGVQgdIRAYKETIAVRVVESLDGMTANAMKVPFEVLQRIAFR 287
                                       5553113333445555666668888888888887777766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); 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:                         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 0.27s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2093.51
//
Query:       gi|242398044|ref|YP_002993468.1|  [L=483]
Description: Inosine-5'-monophosphate dehydrogenase [Thermococcus sibiricus MM 739]
Scores for complete 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-148  491.9  12.0     1e-147  491.7  12.0    1.0  1  IMPDH         IMP dehydrogenase / GMP reductase domain
    7.3e-30  103.2   9.4    5.8e-17   61.9   1.9    3.3  3  CBS           CBS domain
    1.6e-07   31.1   9.3    0.00051   19.5   1.3    3.6  4  NMO           Nitronate monooxygenase
      3e-07   29.8  11.1    3.7e-06   26.2  10.2    2.6  2  FMN_dh        FMN-dependent dehydrogenase
    1.2e-06   28.0   7.0    2.2e-06   27.1   6.7    1.6  1  Glu_synthase  Conserved region in glutamate synthase
  ------ inclusion threshold ------
      0.034   13.6   9.5      0.024   14.1   4.8    2.5  3  His_biosynth  Histidine biosynthesis protein
      0.052   12.8   0.7        2.4    7.4   0.0    3.1  3  Zeta_toxin    Zeta toxin
      0.057   12.7  10.3      0.056   12.7   3.6    3.2  3  ThiG          Thiazole biosynthesis protein ThiG
       0.11   12.6   2.1       0.32   11.1   0.1    2.6  3  sCache_3_2    Single cache domain 3


Domain annotation for each model (and alignments):
>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  491.7  12.0  5.1e-151    1e-147       1     345 []      14     468 ..      14     468 .. 0.98

  Alignments for each domain:
  == domain 1  score: 491.7 bits;  conditional E-value: 5.1e-151
                                       E--GGGEEEE---B-S-GGGSB--EESSTTEEESSSEEE-SSTTT-SHHHHHHHHHTTSEEEE-SSS-HHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH   1 gltfddvllvpaksevlpkevdlktkltkkiklniPlvsaamdtvtesemAialareGgigvihknlsieeqaeevk 77 
                                       g+tfddvll+p+ +ev+pk+vd++t++t ki+lniP++saamdtvte emAia+ar Gg+gvih+n+sieeq+++v+
  gi|242398044|ref|YP_002993468.1|  14 GYTFDDVLLIPQGTEVEPKDVDVSTQITPKIRLNIPILSAAMDTVTEWEMAIAMARLGGLGVIHRNMSIEEQVDMVR 90 
                                       79*************************************************************************** PP

                                       HHHTS........................................................................ CS
                                       xxxxx........................................................................ RF
                             IMPDH  78 kvkrs........................................................................ 82 
                                       +vkr+                                                                        
  gi|242398044|ref|YP_002993468.1|  91 RVKREetveevitispeetidyalflmeregidglpviengelvgivtktdittregervkevmtkdvitakesasv 167
                                       ***************************************************************************** PP

                                       .......................................TTSXBXTTSXB-EEEEE-SSTTHHHHHHHHHHTT-SEE CS
                                       .......................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH  83 .......................................pnaakdekgrllvgaavgvkedalervkalveagvdvl 120
                                                                              +na++de+grl+v+aav+  +  ++r+ al +ag+dv+
  gi|242398044|ref|YP_002993468.1| 168 eeimtlmiensidrvpivdddgklvgiitigdllarkkhRNAVRDEEGRLIVAAAVSPFD--IKRALALDKAGADVI 242
                                       ***********************************************************5..9************** PP

                                       EEE-STSSSHHHHHHHHHHHHHTTTSEEEEEEE-SHHHHHHHHHTT-SEEEE-SS-STTBHHHHHCSB---HHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 121 vvdsahghsekvleavkeikkkveeveviaGnvataegakaLieagadavkvGiGpGsiCttrvvagvGvpqltAva 197
                                       v+d+ah+h+ k ++a+keik+kv e e+i+Gn+a+ +++ +L    adavkvGiGpGsiCttr+vagvGvpq+tA++
  gi|242398044|ref|YP_002993468.1| 243 VIDTAHAHNLKAIKAMKEIKNKV-EAELIVGNIANPKAVDDLTF--ADAVKVGIGPGSICTTRIVAGVGVPQITAIS 316
                                       ***********************.79****************86..69***************************** PP

                                       HHHHHHCTCT-EEEEES---SHHHHHHHHHTT-SEEEESCCCTTBTTSSSEEEEETTEEEEEEEETTSHHHHHH-SS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 198 evaeaakkagvpviaDGGikysgdivkAlaaGadavmlGsllagteEspgeviliegrkyKeyrGmgslgamkkgsk 274
                                        va+ a ++g++viaDGGi+ysgdivkA+aaGadavmlG+llagt+E+pg+ ++i+grkyK+yrGmgslgam kg +
  gi|242398044|ref|YP_002993468.1| 317 MVADKAVEYGIRVIADGGIRYSGDIVKAIAAGADAVMLGNLLAGTKEAPGREVTINGRKYKQYRGMGSLGAMMKGGA 393
                                       ************************************************************************99*** PP

                                       -TTS-....-...-SS-SBEEEEEE--B-HHHHHHHHHHHHHHHHHHHT-SSHHHHHHH-EEEEE-HHHHHHHS-- CS
                                       xxxxx..xxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 275 dryfq..kke...klvpeGvegrvpykgsvkevveqlvgglrsgmgylGaktieelkekakfvritaaglkeshvH 345
                                       +ry+q  +     k+vpeG+eg vpykg+v+ev++qlvggl++gmgy+Gak+i+elkek++fv it+ag+kesh+H
  gi|242398044|ref|YP_002993468.1| 394 ERYYQkgH-MktrKFVPEGIEGVVPYKGKVSEVLYQLVGGLKAGMGYVGAKNIKELKEKSEFVIITHAGVKESHPH 468
                                       ***99442.1346**************************************************************9 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.4   0.5   8.4e-15   1.7e-11       7      52 ..      99     143 ..      85     146 .. 0.91
   2 !   61.9   1.9   2.9e-20   5.8e-17       1      54 [.     150     203 ..     150     206 .. 0.96
   3 ?   -1.0   0.0       1.3   2.6e+03      33      56 ..     209     233 ..     201     234 .. 0.71

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 8.4e-15
                                       SSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHH CS
                               CBS   7 rdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDll 52 
                                       ++v+t++p++t+  al lm+++g+++lPV+ e+g+lvGivt++D+ 
  gi|242398044|ref|YP_002993468.1|  99 EEVITISPEETIDYALFLMEREGIDGLPVI-ENGELVGIVTKTDIT 143
                                       367****************9999*******.9************96 PP

  == domain 2  score: 61.9 bits;  conditional E-value: 2.9e-20
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54 
                                       V+++mt+dv+t+++++++ee++ lm+e+ ++r+P+Vd+dgklvGi+t  Dll  
  gi|242398044|ref|YP_002993468.1| 150 VKEVMTKDVITAKESASVEEIMTLMIENSIDRVPIVDDDGKLVGIITIGDLLAR 203
                                       89*************************************************975 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 1.3
                                       EEEEETTTB..EEEEEEHHHHHHHHH CS
                               CBS  33 lPVVdedgk..lvGivtlrDllrall 56 
                                         V de+g+  +   v+  D+ ral+
  gi|242398044|ref|YP_002993468.1| 209 A-VRDEEGRliVAAAVSPFDIKRALA 233
                                       4.669999875668888888888875 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0   0.00019      0.37       5      50 ..      41      85 ..      37     101 .. 0.79
   2 ?    3.9   0.3     0.015        30      90     163 ..     169     245 ..     148     267 .. 0.68
   3 !   19.5   1.3   2.5e-07   0.00051     188     237 ..     319     370 ..     307     382 .. 0.87
   4 ?   -1.7   0.0      0.73   1.5e+03      99     148 ..     415     464 ..     393     466 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00019
                               NMO  5 tellkikppvvqpgmggiskarLaaavsnaGgLGvlasgyltaDrl 50
                                      t ++  + p+  + m  +++ ++a a +  GgLGv+    ++  + 
  gi|242398044|ref|YP_002993468.1| 41 TPKIRLNIPILSAAMDTVTEWEMAIAMARLGGLGVIH-RNMSIEEQ 85
                                      56777899***************************98.44454444 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.015
                               NMO  90 aalelnieegvrfyrkvevvldekvevvsfg....fglpteevvarlkeagvvliptis..svkearkvearGaDal 160
                                       + + l+ie ++    +v +v d +  v +++    ++ +++ +  r +e+ +++   +s   +k a ++ ++GaD++
  gi|242398044|ref|YP_002993468.1| 169 EIMTLMIENSID---RVPIVDDDGKLVGIITigdlLARKKHRNAVRDEEGRLIVAAAVSpfDIKRALALDKAGADVI 242
                                       445556666666...777777775444444411223456666666666666666666662269999*********** PP

                               NMO 161 ivq 163
                                       +++
  gi|242398044|ref|YP_002993468.1| 243 VID 245
                                       986 PP

  == domain 3  score: 19.5 bits;  conditional E-value: 2.5e-07
                               NMO 188 vldavd..iPviAaGGiidrrgvaaaLalGAsgvqigtrfLltkesdakdah 237
                                       + +av+  i viA GGi    ++  a+a+GA +v +g  + +tke++ ++++
  gi|242398044|ref|YP_002993468.1| 319 ADKAVEygIRVIADGGIRYSGDIVKAIAAGADAVMLGNLLAGTKEAPGREVT 370
                                       45788899**************************************988875 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 0.73
                               NMO  99 gvrfyrkvevvldekvevvsfgfglpteevvarlkeagvvliptissvke 148
                                        v++ +kv  vl + v     g+g    +++++lke   ++i+t + vke
  gi|242398044|ref|YP_002993468.1| 415 VVPYKGKVSEVLYQLVGGLKAGMGYVGAKNIKELKEKSEFVIITHAGVKE 464
                                       45588899999999888899999999999999999999999999998887 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2  10.2   1.9e-09   3.7e-06     268     303 ..     304     358 ..     208     372 .. 0.64
   2 ?    1.2   0.0     0.077   1.5e+02     315     344 ..     422     451 ..     418     453 .. 0.90

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 1.9e-09
                                       H.....................SS-EEEESS--SHHHHHHHHHTT-SEEEESHHH CS
                            FMN_dh 268 v...................ggrievlvDgGirrGsDvlkAlalGAdavllGRpf 303
                                       v                   +  i v++DgGir   D++kA+a GAdav+lG  +
  gi|242398044|ref|YP_002993468.1| 304 VagvgvpqitaismvadkavEYGIRVIADGGIRYSGDIVKAIAAGADAVMLGNLL 358
                                       05555555555544444333557*****************************765 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.077
                                       HHHHHHHHHHHHHHHHHHHT-SBHHHHHCG CS
                            FMN_dh 315 vervleilraelertmallGvksvaeldrs 344
                                       v++vl  l   l++ m  +G+k+++el+++
  gi|242398044|ref|YP_002993468.1| 422 VSEVLYQLVGGLKAGMGYVGAKNIKELKEK 451
                                       8899999999*****************875 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 !   27.1   6.7   1.1e-09   2.2e-06     194     304 ..     249     356 ..     240     359 .. 0.87

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 1.1e-09
                                       HHHHHHH-TTSEEEEEEE-STTHHHHHHHHHHTT-SEEEEE-TT---SSE...EHHHHHHB---HHHHHHHHHHHHH CS
                      Glu_synthase 194 iedLkevnkeakvsvKlvaeagvetiaagvakanadiilidGleGGTGAs...pkssikhaGlPlelalaevdqtlk 267
                                        ++Lk ++  +++  K+ ae  v+ ia    ka  d+   d ++ G G      + ++  +G+P ++a++ v  + +
  gi|242398044|ref|YP_002993468.1| 249 AHNLKAIKAMKEIKNKVEAELIVGNIAN--PKAVDDLTFADAVKVGIGPGsicTTRIVAGVGVPQITAISMVADKAV 323
                                       5789**********************99..7777788888888888776511156788999***********99999 PP

                                       HTT-GGG-EEEEESS--SHHHHHHHHHHT-SEEE-SH CS
                      Glu_synthase 268 eeglrdrvsliadGglktgadvvkalalGAdavgigt 304
                                       e+g+r    +iadGg++ + d+vka+a GAdav +g 
  gi|242398044|ref|YP_002993468.1| 324 EYGIR----VIADGGIRYSGDIVKAIAAGADAVMLGN 356
                                       99976....8***********************9986 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       1.6   3.3e+03     135     170 ..     141     176 ..     133     183 .. 0.77
   2 ?    4.4   0.4     0.011        22      34     101 ..     230     293 ..     199     306 .. 0.66
   3 ?   14.1   4.8   1.2e-05     0.024      90     223 ..     233     358 ..     224     363 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.6
                                       EEEETTTTEEEEEEHHHHHHHHHHTT-SEEEEEETT CS
                      His_biosynth 135 kvaikgwreetgldavelakkleelgageilltdid 170
                                       +++++++++ +++ + +++ + e++ ++ei+   i+
  gi|242398044|ref|YP_002993468.1| 141 DITTREGERVKEVMTKDVITAKESASVEEIMTLMIE 176
                                       477788888888888888888888888888887775 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.011
                                       HHHHHHHHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEE CS
                      His_biosynth  34 lakryeeegadelhvvDldaakegreanldlveeiaeevfipvqvGGGIrsledveelleagadkvii 101
                                        a +++++gad ++   +d a++++ + +++++ei ++v++++ vG  I + ++v++l  a a kv i
  gi|242398044|ref|YP_002993468.1| 230 RALALDKAGADVIV---IDTAHAHNLKAIKAMKEIKNKVEAELIVGN-IANPKAVDDLTFADAVKVGI 293
                                       44455566666554...455677777777777777777777777764.66666666666666666555 PP

  == domain 3  score: 14.1 bits;  conditional E-value: 1.2e-05
                                       HHHHCT-SEEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEECEEEEETTTTEEEEEEHHHHHHHHH.HTT-SEEE CS
                      His_biosynth  90 elleagadkviigtaavknpelikelaekfgsqkivvaiDarrgykvaikgwreetgldavelakkle.elgageil 165
                                       +l +agad ++i ta ++n + ik + e  ++      ++     ++ + +  + +++d + +a +++   g g+i 
  gi|242398044|ref|YP_002993468.1| 233 ALDKAGADVIVIDTAHAHNLKAIKAMKEIKNK------VE----AELIVGNIANPKAVDDLTFADAVKvGIGPGSIC 299
                                       55578899999999999999999888886555......33....234555666666777777776654135667777 PP

                                       EEET.TTTTTSS---HHHHHHHHHHHSSEEEEESS--SHHHHHHHHHTTCSEEEESHHH CS
                      His_biosynth 166 ltdi.drdGtlsGpdleltkelaeavkipviasGGvgsledlkelksegvdavivgsal 223
                                        t i + +G+ +   ++++ + a ++ i+via GG++   d+ ++ ++g+dav++g++l
  gi|242398044|ref|YP_002993468.1| 300 TTRIvAGVGVPQITAISMVADKAVEYGIRVIADGGIRYSGDIVKAIAAGADAVMLGNLL 358
                                       7765278999999999**999999*******************************9987 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1      0.52     1e+03     140     190 ..     142     190 ..     137     193 .. 0.76
   2 ?    1.6   0.0     0.072   1.4e+02      85     115 ..     316     346 ..     312     352 .. 0.81
   3 ?    7.4   0.0    0.0012       2.4      17      67 ..     425     475 ..     416     480 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.52
                        Zeta_toxin 140 vldRyeeevaegRlvpkeehdeafeglresvealeeekqldrvkikdrdgk 190
                                       +  R+ e+v+e  ++ k+++ +  ++  e++ +l  e  +drv i+d dgk
  gi|242398044|ref|YP_002993468.1| 142 ITTREGERVKE--VMTKDVITAKESASVEEIMTLMIENSIDRVPIVDDDGK 190
                                       55666666666..77778888888888889999999999999999999885 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.072
                        Zeta_toxin  85 ekllqeaiengyniivegtlrspdvvkklae 115
                                        ++ ++a+e g+ +i +g +r   ++ k++ 
  gi|242398044|ref|YP_002993468.1| 316 SMVADKAVEYGIRVIADGGIRYSGDIVKAIA 346
                                       6899***************998777766554 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0012
                        Zeta_toxin  17 klillgGqpGAGKselaellkdelerqgnvvrldpDdlRelhPeyeeilka 67 
                                       +l++l+G+  AG +++ ++  +el++++++v +    ++e hP+  +i ++
  gi|242398044|ref|YP_002993468.1| 425 VLYQLVGGLKAGMGYVGAKNIKELKEKSEFVIITHAGVKESHPHDIAITNE 475
                                       799*****************************************7776665 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.4      0.36   7.1e+02     189     226 ..     227     267 ..     216     288 .. 0.72
   2 ?   12.7   3.6   2.8e-05     0.056     153     212 ..     301     363 ..     277     367 .. 0.85
   3 ?    1.8   0.0     0.064   1.3e+02     156     187 ..     434     465 ..     396     476 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.36
                                       HHHHHH...HTT-SEEEESHHHHTSSSHHHHHHHHHHHHHH CS
                              ThiG 189 daaqam...elGadavllntavaeakdpvamArafklavea 226
                                       d+  a+   + Gad ++++ta a+    ++  + +k  vea
  gi|242398044|ref|YP_002993468.1| 227 DIKRALaldKAGADVIVIDTAHAHNLKAIKAMKEIKNKVEA 267
                                       44444411245999999999999988888888888888877 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 2.8e-05
                                       SSTTS----S-HHHHHHHHHH-...SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSS CS
                              ThiG 153 apiGsglGllnkealkiiieea...kvPvivDAGigspsdaaqamelGadavllntavaeakd 212
                                       + i +g G+ + +a++++ ++a    + vi D Gi+ + d+++a+  Gadav+l   +a +k+
  gi|242398044|ref|YP_002993468.1| 301 TRIVAGVGVPQITAISMVADKAveyGIRVIADGGIRYSGDIVKAIAAGADAVMLGNLLAGTKE 363
                                       568889999999******9987755799**************************988887765 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.064
                                       TS----S-HHHHHHHHHH-SS-BEEES---SH CS
                              ThiG 156 GsglGllnkealkiiieeakvPvivDAGigsp 187
                                        +g+G + ++++k + e+ +  +i  AG+ ++
  gi|242398044|ref|YP_002993468.1| 434 KAGMGYVGAKNIKELKEKSEFVIITHAGVKES 465
                                       57999***********************9764 PP

>> sCache_3_2  Single cache domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.62   1.2e+03     109     122 ..     125     137 ..     123     146 .. 0.91
   2 ?   11.1   0.1   0.00016      0.32      83     125 ..     157     198 ..     136     203 .. 0.74
   3 ?   -1.8   0.1       1.5   3.1e+03       4      52 ..     207     251 ..     204     260 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.62
                        sCache_3_2 109 lPvfdadgrviGiv 122
                                       lPv++ +g+++Giv
  gi|242398044|ref|YP_002993468.1| 125 LPVIE-NGELVGIV 137
                                       79999.9******9 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00016
                        sCache_3_2  83 taaalkagrayvgtvtgtlgpslrvklPvfdadgrviGivsvG 125
                                       +  ++k+  ++ +++t+ +  s++  +P++d+dg+++Gi+ +G
  gi|242398044|ref|YP_002993468.1| 157 DVITAKESASVEEIMTLMIENSID-RVPIVDDDGKLVGIITIG 198
                                       444555666666777888888888.69***************9 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 1.5
                        sCache_3_2   4 rdlaealeeralalatsvagsrivrvaltdrapesglqalvddvrritg 52 
                                       r++++++e r l +a +v+  +i+r++  d   ++g + +v d++++++
  gi|242398044|ref|YP_002993468.1| 207 RNAVRDEEGR-LIVAAAVSPFDIKRALALD---KAGADVIVIDTAHAHN 251
                                       6788888899.7788899999999888888...7777777755555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (483 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       714  (0.0398237); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); 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: 0.66u 0.32s 00:00:00.98 Elapsed: 00:00:00.50
# Mc/sec: 2889.93
//
Query:       gi|242398045|ref|YP_002993469.1|  [L=333]
Description: probable 5-formaminoimidazole-4-carboxamide-1-(beta)-D- ribofuranosyl 5'-monophosphate synthetase [Thermococcus sibiricus MM 739]
Scores for complete 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-73  245.4   0.1      4e-73  245.0   0.1    1.1  1  DUF1297      Domain of unknown function (DUF1297)
    4.9e-34  116.9   0.0    8.8e-34  116.1   0.0    1.4  1  DUF1246      Protein of unknown function (DUF1246)
  ------ inclusion threshold ------
      0.019   15.0   0.1       0.17   11.9   0.1    2.2  1  ATP-grasp_3  ATP-grasp domain
      0.024   14.1   0.1      0.054   13.0   0.0    1.6  2  CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP bindin


Domain annotation for each model (and alignments):
>> DUF1297  Domain of unknown function (DUF1297)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  245.0   0.1     9e-77     4e-73       8     188 .]     154     333 .]     149     333 .] 0.97

  Alignments for each domain:
  == domain 1  score: 245.0 bits;  conditional E-value: 9e-77
                                       HHHCTTSSSHHHHCCEEEEE---SEEEEEEEEEETTTTEEEEEEEEEEEEEECCCHCCS-HHHHHCCT----EEEEE CS
                           DUF1297   8 ellekglieeedlkkasieeyvvGanfnlnyfysplkeevellgidrRyesnldglvrlpakeqlelevepeyvvvG 84 
                                       +  + g+ ++edlk+++i+eyv+G++++ ++fys+l++e+el+++drRyesn d + r+ a++ql++ v p+y+vvG
  gi|242398045|ref|YP_002993469.1| 154 RASNLGVKNKEDLKEVQIQEYVIGVPVYPHFFYSKLNGELELMSVDRRYESNADAIGRISAEQQLKIGVGPSYTVVG 230
                                       555668889******************************************************************** PP

                                       EEEEEE-GGGHHHHHHHHHHHHHHHHHHSTT---EEEEEEEEE-TTS-EEEEEEESSB-GGGGGGTT--CCHHHTTS CS
                           DUF1297  85 nipvvlREsllekvfelgekfveaakklvppGiiGpFcLqsvvtkdlelvvfdvsaRivggtnvymegspyskllfg 161
                                       nip+vlREsll  ++e+ge++++a++kl+  G++GpFcL++v+t+d+e+vvf++saRiv+gtn +++gspy+++++ 
  gi|242398045|ref|YP_002993469.1| 231 NIPIVLRESLLMGIIEAGENVIRASEKLMG-GLWGPFCLEGVITEDMEFVVFEISARIVAGTNPFINGSPYTWIKYS 306
                                       ***************************997.********************************************** PP

                                       S---HHHHHHHHHHHHHHCT-GGGCEE CS
                           DUF1297 162 eplsmGrrialEikeaiekdrleeivt 188
                                       ep+s+Grria+Eik+aie++rl+ei+t
  gi|242398045|ref|YP_002993469.1| 307 EPMSTGRRIAREIKQAIEEERLDEILT 333
                                       *************************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 !  116.1   0.0     2e-37   8.8e-34       1     121 [.       5     118 ..       5     119 .. 0.94

  Alignments for each domain:
  == domain 1  score: 116.1 bits;  conditional E-value: 2e-37
                                       EEEESSTTHHHHHHHHHHTT--EEEEC-CCCHHHHHTT.TT-SEEEE.S.S..TTSS--HHHHHHTTCEE--BTTHH CS
                           DUF1246   1 iatlaSHsalqilkgAkkegfrtlavcekgreklYekf.kvidevivldkfkdilkeevqeklreenailvPhgsfv 76 
                                       iat aSHsalqil+gAk+egf+tla+ +++ + lY+k+ +v+d++i         +e  +e+l +++ai++P gsfv
  gi|242398045|ref|YP_002993469.1|   5 IATYASHSALQILHGAKQEGFKTLAFGKEKVRPLYTKYfPVADDFIP--------NEYPEEELLKKKAIIIPTGSFV 73 
                                       89***********************************98999*9987........33445789************** PP

                                       HHC-HHHHHC-SS-EES-TTHHHHHCSHHHHHHHHHHTT-BB--B CS
                           DUF1246  77 eYvgiekieelkvpifGnrkllrwEerrekkrkyLekAgiriPkk 121
                                       +Y+giek+e +k  ++Gn+k+lrwE++r+ +rk+L +A+iriP++
  gi|242398045|ref|YP_002993469.1|  74 AYLGIEKVECMKAMYYGNKKVLRWESDRKLERKWLLEAKIRIPEV 118
                                       *******************************************97 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   3.8e-05      0.17       5      75 ..     102     180 ..      98     290 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.8e-05
                                       HHHHHHHTTT.S---....-EESS--SSSEEEEESS-------B--SS--TTE.................EEEE--- CS
                       ATP-grasp_3   5 lktykkLkeagvkvPtkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieeve..........lvqefie 71 
                                           k+L ea++++P     e ++  + +++vKp  + gg + ++++  +e  +   ++            +qe++ 
  gi|242398045|ref|YP_002993469.1| 102 KLERKWLLEAKIRIP--EVIEDPDDIDRPVIVKPHGAKGGRGYFMAKTPKEFWERASNLGvknkedlkevQIQEYVI 176
                                       55568999999****..7788999********************999877665544443345556777766777777 PP

                                       SEEE CS
                       ATP-grasp_3  72 Gkpl 75 
                                       G p+
  gi|242398045|ref|YP_002993469.1| 177 GVPV 180
                                       7766 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 ?   13.0   0.0   1.2e-05     0.054      32      68 ..     120     156 ..     110     177 .. 0.84
   2 ?   -3.5   0.1       1.3   5.8e+03     167     180 ..     274     287 ..     271     289 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.2e-05
                                       HHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHH CS
                       CPSase_L_D2  32 aiakeigyPviikaafglGGkGmrvarneeelaelvk 68 
                                       +  ++i  Pvi+k+  + GG+G  +a++ +e+ e ++
  gi|242398045|ref|YP_002993469.1| 120 EDPDDIDRPVIVKPHGAKGGRGYFMAKTPKEFWERAS 156
                                       55678999*********************99987654 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.3
                                       TTTEEEEEEEESS- CS
                       CPSase_L_D2 167 kskeyyviEvNtRl 180
                                       +++e++v E+ +R+
  gi|242398045|ref|YP_002993469.1| 274 EDMEFVVFEISARI 287
                                       47899******998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 1983.53
//
Query:       gi|242398046|ref|YP_002993470.1|  [L=271]
Description: Membrane-bound phosphoesterase, PAP2 superfamily [Thermococcus sibiricus MM 739]
Scores for 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-09   37.4  13.1      2e-09   37.4  13.1    2.2  2  PAP2_3    PAP2 superfamily
    2.8e-08   33.6   6.9    2.8e-08   33.6   6.9    2.7  3  PAP2      PAP2 superfamily
  ------ inclusion threshold ------
      0.022   15.3   3.1      0.022   15.3   3.1    3.1  3  PAP2_C    PAP2 superfamily C-terminal


Domain annotation for each model (and alignments):
>> PAP2_3  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4  13.1   3.4e-13     2e-09      19     187 ..      63     213 ..      57     216 .. 0.84
   2 ?   -0.2   0.2      0.11   6.8e+02      40      63 ..     241     264 ..     223     270 .. 0.69

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 3.4e-13
                            PAP2_3  19 nklllahpalavilalaYaslhfqvtllvl..vllflrrrerlreflttlllatllgllvyalfPaagPrlleeagf 93 
                                       ++++++ p +++++ ++Y+  +   + l++  +ll++r+ e+ +++l+ +lla +++ lvy+     +P ++     
  gi|242398046|ref|YP_002993470.1|  63 VEFIKGVPPIHTFFTVVYYLGFAGSIALMIayLLLYMRDLEASDRLLARYLLAYAVAGLVYLIAHIHAPHIV----- 134
                                       45999************9876655444443114455*********************************555..... PP

                            PAP2_3  94 vdtvaaaslagalrdgasravllrgtienglaafPSlHvawallvalalwrlrrkrllrvlalllnvlmivatvatg 170
                                             ++l g        +   ++ ++++   +PSlH ++ ++ +++lw++r++   + +++l n l+ +atv +g
  gi|242398046|ref|YP_002993470.1| 135 ------YNLPG--------YTSSNTLLTRQEFVLPSLHNTFIMINIITLWKYRNRL-GGKVLILTNSLISFATVFLG 196
                                       ......44444........45566677789999*******************9998.899999************** PP

                            PAP2_3 171 nHYlvDviaGvalalva 187
                                       +H + Dvi+G++l++++
  gi|242398046|ref|YP_002993470.1| 197 HHWIYDVIVGFFLGIAV 213
                                       ************99886 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.11
                            PAP2_3  40 hfqvtllvlvllflrrrerlrefl 63 
                                        f ++l+v+vl+++ +++r++++ 
  gi|242398046|ref|YP_002993470.1| 241 VFNLFLVVIVLIVATDPARVLAIF 264
                                       455667777777766666666555 PP

>> PAP2  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   2.7      0.05     3e+02      91     129 ..      85     124 ..      22     132 .. 0.47
   2 !   33.6   6.9   4.7e-12   2.8e-08       6     131 ..     113     221 ..     107     226 .. 0.79
   3 ?   -3.1   0.3         1   6.1e+03      85      99 ..     239     253 ..     227     255 .. 0.55

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.05
                              PAP2  91 llllavlvalsRlylgvHflsDvlaG.lliGialaalayr 129
                                       +   a+++a+  ly +    sD l +  l+++a+a l+y 
  gi|242398046|ref|YP_002993470.1|  85 AGSIALMIAYLLLYMRDLEASDRLLArYLLAYAVAGLVYL 124
                                       2233333334444443333344333333334444333333 PP

  == domain 2  score: 33.6 bits;  conditional E-value: 4.7e-12
                              PAP2   6 llalalaalltsvlKdlvgrpRPfflaeetkldtqvstletseskeakesf..PSgHsafafalalllalllrrkrk 80 
                                       lla+a+a+l+      +     P+++ +  +++++ +   t      +  f  PS H +f +   ++l+ + +r+  
  gi|242398046|ref|YP_002993470.1| 113 LLAYAVAGLVY----LIAHIHAPHIVYNLPGYTSSNTL-LT------RQEFvlPSLHNTFIMINIITLWKYRNRLGG 178
                                       44555544442....22333448888888888887544.43......457777************************ PP

                              PAP2  81 kiglvllalillllavlvalsRlylgvHflsDvlaGlliGialaalayrlv 131
                                       k        +l+l   l++++ ++lg+H+  Dv++G+++Gia+  +++ + 
  gi|242398046|ref|YP_002993470.1| 179 K--------VLILTNSLISFATVFLGHHWIYDVIVGFFLGIAVSKVSWEWS 221
                                       *........68888899***************************9999886 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 1
                              PAP2  85 vllalillllavlva 99 
                                       + +++++l+++vl+ 
  gi|242398046|ref|YP_002993470.1| 239 ITVFNLFLVVIVLIV 253
                                       345556666666554 PP

>> PAP2_C  PAP2 superfamily C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.7      0.42   2.5e+03      22      22 ..      99      99 ..      72     129 .. 0.46
   2 ?   15.3   3.1   3.7e-06     0.022       8      68 ..     156     213 ..     153     220 .. 0.82
   3 ?   -0.1   0.7      0.23   1.4e+03      31      49 ..     236     254 ..     216     257 .. 0.55

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.42
                            PAP2_C 22 l 22
                                      +
  gi|242398046|ref|YP_002993470.1| 99 M 99
                                      2 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 3.7e-06
                            PAP2_C   8 SGHtvvltlavlfileyspkklailkvillllallglfliiasrkHYtvDVllglyittlv 68 
                                       S H +++++ ++++++y ++     kv++l+ + l++f  +   +H+  DV++g+++ ++v
  gi|242398046|ref|YP_002993470.1| 156 SLHNTFIMINIITLWKYRNRLG--GKVLILT-NSLISFATVFLGHHWIYDVIVGFFLGIAV 213
                                       669*****************97..6766665.5556677777788***********99877 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.23
                            PAP2_C  31 ilkvillllallglfliia 49 
                                       + +++++ l l+ ++li+a
  gi|242398046|ref|YP_002993470.1| 236 LQRITVFNLFLVVIVLIVA 254
                                       3455555566666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      204  (0.0113782); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 1834.19
//
Query:       gi|242398047|ref|YP_002993471.1|  [L=275]
Description: Nicotinate-nucleotide pyrophosphorylase [Thermococcus sibiricus MM 739]
Scores for complete 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-50  169.1   0.7    9.6e-50  168.7   0.7    1.2  1  QRPTase_C        Quinolinate phosphoribosyl transferase, C-te
    4.3e-32  110.0   0.1    7.5e-32  109.3   0.1    1.4  1  QRPTase_N        Quinolinate phosphoribosyl transferase, N-te
    6.8e-05   22.3   0.0    0.00012   21.5   0.0    1.4  1  TMP-TENI         Thiamine monophosphate synthase
     0.0073   15.7   0.6      0.028   13.8   0.5    1.9  1  Ribul_P_3_epim   Ribulose-phosphate 3 epimerase family
  ------ inclusion threshold ------
       0.01   15.0   0.1      0.015   14.5   0.1    1.2  1  ALAD             Delta-aminolevulinic acid dehydratase
      0.012   15.4   4.5      0.043   13.7   1.2    3.1  2  Biotin_lipoyl_2  Biotin-lipoyl like
      0.015   14.7   0.9      0.045   13.2   0.1    1.9  2  NQRA             Na(+)-translocating NADH-quinone reductase s
      0.015   15.1   0.8       0.11   12.3   0.1    2.5  2  Biotin_lipoyl    Biotin-requiring enzyme
      0.023   14.7   0.7      0.051   13.6   0.1    1.8  2  B12-binding      B12 binding domain
      0.073   12.5   0.5       0.13   11.7   0.1    1.5  2  Lactamase_B_5    Metallo-beta-lactamase superfamily
      0.082   11.9   1.7      0.095   11.7   1.7    1.1  1  IMPDH            IMP dehydrogenase / GMP reductase domain


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 !  168.7   0.7   5.9e-53   9.6e-50       1     169 []     104     272 ..     104     272 .. 0.97

  Alignments for each domain:
  == domain 1  score: 168.7 bits;  conditional E-value: 5.9e-53
                                       HHHHHHHHHHHHHCT..SSEEEE-S---TTTHHHHHHHHHHTTSB--TSSTTTSEEE-HHHHHHHSSHHHHHHHHHH CS
                         QRPTase_C   1 iAtltarmveaaksa..kvrildTRkttPglrllekyAvliGGgdnhrlgLsdmvlikdnhiaaagsiveavksvre 75 
                                       iAt+t+++v +++ +  kvr+++TRkt+  l++l+k+A+liG g+ hr++Lsd++likdnh+a++  ++ea+k++++
  gi|242398047|ref|YP_002993471.1| 104 IATQTRKLVGKVRAVnpKVRVAGTRKTL--LKPLDKKAILIGNGEPHRFSLSDAILIKDNHLALVP-LEEAIKRAKA 177
                                       9**************99**********6..*********************************998.********** PP

                                       HHTTTSEEEEEESSHHHHHHHHHHT-SEEEEES--HHHHHHHHHHHHHHSTT..SEEEEESS--TTTHHHHHCTT-S CS
                         QRPTase_C  76 avdkevkievevesleeleevleaeadiimLDnfsveelkkaveelkeknkr..vlievSGgvtlenveeyaksgvd 150
                                           ++ +evevesle++ ++++a+ad+imLDn+++ ++k+++e lk+   r  v+ievSGg+t+en+++yak ++d
  gi|242398047|ref|YP_002993471.1| 178 FSAYKI-VEVEVESLEDALKAAKAGADVIMLDNMTPGQIKEVLEALKRDRLRdkVKIEVSGGITEENIQDYAKLDID 253
                                       998887.***************************************77777677*********************** PP

                                       EEEECHHCHTB----EEEE CS
                         QRPTase_C 151 visvgalthsvkalDislk 169
                                       vis+galthsvk  D+sl+
  gi|242398047|ref|YP_002993471.1| 254 VISLGALTHSVKNFDVSLE 272
                                       ****************995 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 !  109.3   0.1   4.6e-35   7.5e-32       2      89 .]      16     102 ..      15     102 .. 0.99

  Alignments for each domain:
  == domain 1  score: 109.3 bits;  conditional E-value: 4.6e-35
                                       TT--HHHHHHGCTTSEEEEEEEESSSEEE-SHHHHHHHHHHHTTTEEEESS-TT-EEETTEEEEEEEEEHHHHHHHH CS
                         QRPTase_N   2 grgDlttealipeekkakaeiiakeegvvaGlevaeevfellpglevellvkDGervekgdvlleieGnarallsaE 78 
                                       ++gD+t+ea+ipe+ +a+a+i+ak++gv+aGle+a+++fe++ g++vel+vkDG++v+kg+v+++++Gnar++l +E
  gi|242398047|ref|YP_002993471.1|  16 PFGDVTSEAVIPEDLEAEAVILAKQDGVIAGLEEAKALFEHF-GVKVELKVKDGDEVKKGTVVINLKGNARKILLVE 91 
                                       68****************************************.********************************** PP

                                       HHHHHHHHHHH CS
                         QRPTase_N  79 RvaLnllqrlS 89 
                                       R+aLn++ r+S
  gi|242398047|ref|YP_002993471.1|  92 RTALNIIGRMS 102
                                       **********9 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   7.4e-08   0.00012      87     176 ..     173     256 ..     148     259 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 7.4e-08
                          TMP-TENI  87 aearellgpdliiGlSvhsleeaeeaealgadYigvGpifpTdtKkdaeplgleglkelaealeiPvvaiGGitlen 163
                                       ++ ++ + +++i+ + v+sle+a++a+++gad i++  + p + K+  e+l  ++l++ ++     + + GGit+en
  gi|242398047|ref|YP_002993471.1| 173 KR-AKAFSAYKIVEVEVESLEDALKAAKAGADVIMLDNMTPGQIKEVLEALKRDRLRDKVK-----IEVSGGITEEN 243
                                       33.455899**************************************99999998876544.....6789******* PP

                          TMP-TENI 164 vaevleagadgva 176
                                       +++ ++  +d ++
  gi|242398047|ref|YP_002993471.1| 244 IQDYAKLDIDVIS 256
                                       ****999999886 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 !   13.8   0.5   1.7e-05     0.028     153     194 ..     215     258 ..     167     261 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.7e-05
                                       HHHHHHHHHHHT..---EEEEESS--TTTCHHHHHHT--EEEES CS
                    Ribul_P_3_epim 153 ikkvrklideke..ldlkievDGGvkldnieqiaeagadvlVag 194
                                       ik+v +++++     ++kiev GG++++ni+  a+ ++dv+  g
  gi|242398047|ref|YP_002993471.1| 215 IKEVLEALKRDRlrDKVKIEVSGGITEENIQDYAKLDIDVISLG 258
                                       44444444443332579**********************99877 PP

>> ALAD  Delta-aminolevulinic acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   9.4e-06     0.015     145     181 ..     192     229 ..     183     235 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 9.4e-06
                                       HHHHHHHHCT-SEEEE-S--TTHHHHHHHHHHHTT-.T CS
                              ALAD 145 kvavsqaeaGadivapSdmmDgrvaaireaLdeagf.e 181
                                       + a++ a+aGad++   +m  g+++++ eaL+++ + +
  gi|242398047|ref|YP_002993471.1| 192 EDALKAAKAGADVIMLDNMTPGQIKEVLEALKRDRLrD 229
                                       5699***************************9988734 PP

>> Biotin_lipoyl_2  Biotin-lipoyl like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   1.2   2.6e-05     0.043      14      32 ..      61      79 ..      58      84 .. 0.87
   2 ?    1.0   0.1      0.23   3.7e+02      30      49 ..     183     202 ..     182     203 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.6e-05
                   Biotin_lipoyl_2 14 aqlnVkdGqrVkaGdvLae 32
                                      ++l VkdG++Vk+G v + 
  gi|242398047|ref|YP_002993471.1| 61 VELKVKDGDEVKKGTVVIN 79
                                      689***********98765 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.23
                   Biotin_lipoyl_2  30 LaelDsralqlalaqaeaql 49 
                                       ++e + + l++al+ a+a++
  gi|242398047|ref|YP_002993471.1| 183 IVEVEVESLEDALKAAKAGA 202
                                       6788889999*******986 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 ?   13.2   0.1   2.8e-05     0.045      35      64 ..      55      84 ..      45     117 .. 0.88
   2 ?   -0.2   0.1      0.34   5.5e+02      61     113 ..     199     255 ..     182     265 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.8e-05
                              NQRA 35 dyvglkpklkvkegdkVkkGqvlfedKknp 64
                                      ++ g+k +lkvk gd+VkkG+v+++ K n 
  gi|242398047|ref|YP_002993471.1| 55 EHFGVKVELKVKDGDEVKKGTVVINLKGNA 84
                                      5679********************999775 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.34
                              NQRA  61 Kknpgvlfts.pasGevveinrGekRv.l.qsvvievdgd.eeeefekfskkelasl 113
                                       K+  +v++      G+++e+    kR  l  +v iev+g  +ee++++++k +++ +
  gi|242398047|ref|YP_002993471.1| 199 KAGADVIMLDnMTPGQIKEVLEALKRDrLrDKVKIEVSGGiTEENIQDYAKLDIDVI 255
                                       555555544303469999998888875131478999997558888888888877655 PP

>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.58   9.5e+02      42      56 ..      33      47 ..      31      52 .. 0.82
   2 ?   12.3   0.1     7e-05      0.11      16      36 ..      60      80 ..      53      83 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.58
                                      EEEEEBSSSEEEEEE CS
                     Biotin_lipoyl 42 emeieapkaGvvkei 56
                                      e  i a+++Gv++ +
  gi|242398047|ref|YP_002993471.1| 33 EAVILAKQDGVIAGL 47
                                      6789999****9876 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 7e-05
                                      ECSESSSTTCEE-TTSEEEEE CS
                     Biotin_lipoyl 16 vvevlvkvGdkVkagqvlaev 36
                                       ve +vk+Gd+Vk+g v++ +
  gi|242398047|ref|YP_002993471.1| 60 KVELKVKDGDEVKKGTVVINL 80
                                      4779*************9987 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.5   2.4e+03      65      83 ..     105     123 ..      38     126 .. 0.62
   2 ?   13.6   0.1   3.1e-05     0.051      27     118 ..     176     265 ..     166     268 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.5
                       B12-binding  65 leavkelvellkrirprvk 83 
                                        +++++lv  +++++p+v+
  gi|242398047|ref|YP_002993471.1| 105 ATQTRKLVGKVRAVNPKVR 123
                                       3334444444555555555 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 3.1e-05
                       B12-binding  27 agfeVq.llganven.edivaairaekpdvvglSalltsqleavkelvellkrirprvkvvvGGahpsldpeetlea 101
                                       + f+ + +++++ve  ed ++a++a  +dv++l  +   q+ +v e +++  r r++vk+ v G +   ++e +  +
  gi|242398047|ref|YP_002993471.1| 176 KAFSAYkIVEVEVESlEDALKAAKA-GADVIMLDNMTPGQIKEVLEALKRD-RLRDKVKIEVSGGI---TEENIQDY 247
                                       4554443666677666666665555.5999***998888888888888876.56788999999976...55555557 PP

                       B12-binding 102 k.lgiddvvvgegedale 118
                                       + l id++ +g  ++ + 
  gi|242398047|ref|YP_002993471.1| 248 AkLDIDVISLGALTHSVK 265
                                       779999999998777765 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 ?   11.7   0.1     8e-05      0.13      86     181 ..      52     145 ..      24     152 .. 0.67
   2 ?   -2.6   0.0         2   3.2e+03     136     153 ..     193     210 ..     176     233 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 8e-05
                     Lactamase_B_5  86 aeketfpiacdrwlsdgdelvsglkvlelkgsktpgelallleettlitgdlvrakkagsltllpdekllnreeava 162
                                       a  e f ++ +  ++dgde+  g  v++lkg        ll+e t+l     +    + +  l+ + + +n +  va
  gi|242398047|ref|YP_002993471.1|  52 ALFEHFGVKVELKVKDGDEVKKGTVVINLKGNA---RKILLVERTALNIIGRMSGIATQTRKLVGKVRAVNPKVRVA 125
                                       3447899**********************9975...56799999988544444555555666666666666666666 PP

                     Lactamase_B_5 163 svrr.laalekieavlvgdg 181
                                         r+ l +  + +a+l+g+g
  gi|242398047|ref|YP_002993471.1| 126 GTRKtLLKPLDKKAILIGNG 145
                                       65542222233356666665 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2
                     Lactamase_B_5 136 dlvrakkagsltllpdek 153
                                       d ++a kag+  ++ d+ 
  gi|242398047|ref|YP_002993471.1| 193 DALKAAKAGADVIMLDNM 210
                                       566777777766665553 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.7   5.8e-05     0.095      77     173 ..     113     258 ..      59     264 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.8e-05
                                       HHHHTS..................................................TTSXBXTTSXB-EEEEE-SST CS
                                       xxxxxx..................................................xxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH  77 kkvkrs..................................................pnaakdekgrllvgaavgvke 103
                                        kv+                                                    + +a ++ + +     v+v+ 
  gi|242398047|ref|YP_002993471.1| 113 GKVRAVnpkvrvagtrktllkpldkkailigngephrfslsdailikdnhlalvplE-EAIKRAKAFSAYKIVEVEV 188
                                       444444555666666666666666666666666666666666666666666666321.2222333334444567788 PP

                                       THHHHHHHHHHTT-SEEEEE-.STSSSHHHHHHHHH..HHHHTTTSEEEEEEE-SHHHHHHHHHTT-SEEEE- CS
                                       xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 104 dalervkalveagvdvlvvds.ahghsekvleavke..ikkkveeveviaGnvataegakaLieagadavkvG 173
                                       ++le + + ++ag+dv+++d  + g+ ++vlea+k+  +++kv ++ev +G + t+e +++ ++ ++d++  G
  gi|242398047|ref|YP_002993471.1| 189 ESLEDALKAAKAGADVIMLDNmTPGQIKEVLEALKRdrLRDKV-KIEV-SGGI-TEENIQDYAKLDIDVISLG 258
                                       899999999**********9626799********972245555.4655.5554.8999***********9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       663  (0.0369792); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 1931.69
//
Query:       gi|242398048|ref|YP_002993472.1|  [L=300]
Description: Quinolinate synthetase A [Thermococcus sibiricus MM 739]
Scores for complete 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-111  372.4   0.9   1.7e-111  372.2   0.9    1.0  1  NadA            Quinolinate synthetase A protein
  ------ inclusion threshold ------
      0.023   14.2   0.0       0.06   12.8   0.0    1.7  1  Sua5_yciO_yrdC  Telomere recombination


Domain annotation for each model (and alignments):
>> NadA  Quinolinate synthetase A protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  372.2   0.9  1.9e-115  1.7e-111       1     299 []       5     297 ..       5     297 .. 0.96

  Alignments for each domain:
  == domain 1  score: 372.2 bits;  conditional E-value: 1.9e-115
                                       HHHHHHHHHHTEEEEEETTS-HHHHHH-SEEE-HHHHHHHCCC-SSSEEEEES-HHHHHHHHHHSTTSEEE-SSTT- CS
                              NadA   1 eeikelkkeknavilaHnYqedeiqeiadfvGDSleLarkaaeteaevivfcGVhFMaetakiLspekkvllpdlea 77 
                                       eei +lk+ekna+ilaHnYq +eiq+iadf+GDSleLarka +++a++ivf+GV+FMaetakiL+pekkvllp+++a
  gi|242398048|ref|YP_002993472.1|   5 EEIMRLKEEKNAIILAHNYQLPEIQDIADFLGDSLELARKAVNVDADIIVFAGVDFMAETAKILNPEKKVLLPTKRA 81 
                                       589************************************************************************** PP

                                       --HHHCT--HHHHHHHHHHSTTS-EEEESSS-HHHHTT-SEEE-TTTHHHHHHHSS-SEEEEES-HHHHHHHHHHH. CS
                              NadA  78 gCsladmitaeeveelkeelpdaavvtYvNssaevKalsdivcTSsnavkvvealkekkilflPDqnLgryvakklg 154
                                       +C +a+m++ +++ e+k+++p+a+vv YvN++ae Ka++d+++TS+na+k++ +l+ ++i+f PD+nL+ yva+++g
  gi|242398048|ref|YP_002993472.1|  82 TCAMANMLKVDHILEAKKKHPNAPVVLYVNTTAESKAYADVTVTSANAEKIIAKLDAETIIFGPDNNLAYYVANRTG 158
                                       ****************************************************************************9 PP

                                       SEEEEESS..SS-GCGGG--CHHHHHHHHCSTT-EEEE-TTS-HHHHHCSSEE--HHHHCCCCGTTSSSCEEEES-T CS
                              NadA 155 ekkiilwk..gaCsvHeefkaeeveelkeehpdakvlvHPEckeevveaadvvgSTsqiikavkeseakefiigTel 229
                                       ++ ii ++  g+C+vH++f+ ++ve+++  +p+ak++vHPEc++ev e+ad ++ST ++++ +   +++e+++ Te+
  gi|242398048|ref|YP_002993472.1| 159 KR-IIPIPegGHCYVHRKFTLKDVERARGLYPNAKLMVHPECNPEVQEKADLIVSTGGMVRNAC--QHDEWVVFTEK 232
                                       86.66664479*************************************************9885..5689******* PP

                                       HHHHHHHHH-TTSEEE.....ECSSSSSTTGGG--HHHHHHHHHHT-S.B----HHHHHHHHHHHHHHHH CS
                              NadA 230 glverlkkeapekefialsaeaaeeavCetMkkitleklleaLeeleeeeikvdeevaekAkkalermle 299
                                       ++v+rl+k +p+k+f+     a+e+a C  Mk itl++l+eaL+++++ e+ v+ee+a++A+ka+ermle
  gi|242398048|ref|YP_002993472.1| 233 EMVYRLQKLYPDKKFYP----AIEDAFCIGMKSITLKHLYEALRDEKY-EVDVPEEIAHRARKAIERMLE 297
                                       ****************3....345899*******************99.*******************97 PP

>> Sua5_yciO_yrdC  Telomere recombination
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   6.7e-06      0.06      21      98 ..      83     158 ..      80     171 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.7e-06
                                       EETTSHHHHHHHHHHHTSHCCC--EEEESSCCCCCCCC-.TC--HHHHHHHHCT-SSSCEEEEE..E-TS-HHHHTT CS
                    Sua5_yciO_yrdC  21 cdatneeaverlreiKgrpsdkplavlvasledlkklae.seveeealkllerfwPGpitlllkrskeklpkevapg 96 
                                       c + n   v+ + e+K+   + p+ + v+  ++ k++a+ + ++++a k++++ + +   +  +  +++l+  va++
  gi|242398048|ref|YP_002993472.1|  83 CAMANMLKVDHILEAKKKHPNAPVVLYVNTTAESKAYADvTVTSANAEKIIAK-LDAETIIFGP--DNNLAYYVANR 156
                                       9999999*********************************999******9999.5555554444..44467666666 PP

                                       TT CS
                    Sua5_yciO_yrdC  97 lk 98 
                                       ++
  gi|242398048|ref|YP_002993472.1| 157 TG 158
                                       55 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); 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 0.29s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 1945.53
//
Query:       gi|242398049|ref|YP_002993473.1|  [L=461]
Description: Quinolinate synthetase B [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-64  218.4   0.0    2.2e-64  218.1   0.0    1.1  1  FAD_binding_2   FAD binding domain
    4.6e-13   49.1   0.1    1.4e-07   31.0   0.1    2.6  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
      1e-11   44.9   0.1    2.8e-05   24.1   0.0    2.8  2  Succ_DH_flav_C  Fumarate reductase flavoprotein C-term
    7.1e-08   31.6   0.9      6e-07   28.5   1.0    2.3  2  HI0933_like     HI0933-like protein
    5.8e-07   29.4   0.1     0.0092   15.6   0.0    2.7  3  DAO             FAD dependent oxidoreductase
    5.9e-05   22.3   1.6      0.012   14.7   1.0    2.2  2  GIDA            Glucose inhibited division protein A
  ------ inclusion threshold ------
      0.016   14.5   0.1      0.024   13.9   0.1    1.3  1  FAD_binding_3   FAD binding domain
      0.032   13.8   0.1      0.051   13.1   0.1    1.4  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
      0.033   14.8   1.1       0.14   12.7   0.2    2.4  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
      0.055   12.8   0.9      0.083   12.2   0.9    1.2  1  FAD_oxidored    FAD dependent oxidoreductase
       0.06   13.5   0.0       0.11   12.6   0.0    1.5  1  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
      0.064   13.1   0.1       0.12   12.2   0.1    1.5  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
      0.065   13.2   0.2        6.7    6.7   0.0    2.6  3  NAD_binding_9   FAD-NAD(P)-binding
      0.068   12.4   1.4       0.24   10.6   0.5    2.2  3  Thi4            Thi4 family
      0.093   13.3   0.2       0.21   12.2   0.2    1.6  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
      0.099   12.3   0.1       0.17   11.5   0.1    1.4  1  ApbA            Ketopantoate reductase PanE/ApbA
       0.16   11.2   0.1       0.27   10.5   0.1    1.3  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
       0.19   12.0   0.5       0.43   10.9   0.5    1.6  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
        0.2   10.5   0.6       0.55    9.0   0.4    1.7  2  Trp_halogenase  Tryptophan halogenase
       0.28   10.4   1.9       0.26   10.5   0.3    1.7  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase


Domain annotation for each model (and alignments):
>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  218.1   0.0   2.5e-67   2.2e-64       4     417 .]       5     347 ..       3     347 .. 0.93

  Alignments for each domain:
  == domain 1  score: 218.1 bits;  conditional E-value: 2.5e-67
                                       EE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S-EE-TT..SSGGSTC.CHHHHHHHHHHHHTTT-S-HH CS
                     FAD_binding_2   4 ViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqGgidavlspeqkkagikdspelhrtdtlkaldeladqp 80 
                                       +iG G AGL+AA+++a++G +v +v  + + + ++  +q+gi+++       +++ ds+++h+ dt++a+++l++++
  gi|242398049|ref|YP_002993473.1|   5 IIGNGTAGLTAAISLAKKGNEVYIVGDTIK-KTNSYLAQAGIAFPI------LDE-DSIRKHVLDTINAGRHLNNEE 73 
                                       9************************99997.99*************......555.********************* PP

                                       HHHHHHHTHHHHHHHHHHTT----BCCTSSB-EEE-TT-SSTEEEE-.STT-......HHHHHHHHHHHHHHTCTEE CS
                     FAD_binding_2  81 lveafveaapeavdeLeelgvpfsrtedgpvdvrelGglsatartlhdaadarretlvtghallarlvesarkagvd 157
                                        v  +++++ ea+d+L +lg+ f +           Gg+s + r+     ++      tg+++++ l+ +a+++gv+
  gi|242398049|ref|YP_002993473.1|  74 TVWSVISKSSEAYDFLLSLGLEFEG-------NEIEGGHSFP-RVFT-IKNE------TGKHIIKLLYMRAKELGVQ 135
                                       *************************.......66679*****.8887.8888......******************* PP

                                       EEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----GG..........GSSSBSSGTT-S-HHHHHHH CS
                     FAD_binding_2 158 fqerteadeLivedgrvtGavvenpesgrevrirakavvlatgGfgrallkellgaaaeaettnapavtGdglalal 234
                                       f     a+++ +++++++G+ +      +e+ ++ +a+vlatgG+ +           +++t + p + G+ ++ ++
  gi|242398049|ref|YP_002993473.1| 136 FIKG-LAESVAIKNKKCYGVFLD-----GEF-LKFDATVLATGGYTA----------LFKYTAGSPLNLGTLIGDTV 195
                                       *987.5899999**********9.....444.56779*********9..........9******************* PP

                                       CTTSSEES..TT-EEEEEEEET....TTTB.B--THHHHTT-EEE-TTSSBTHGGGS-HHHHHHHHH.HHHHTTTSC CS
                     FAD_binding_2 235 ragaalnddrmeevqfhPtslvpirdgsgi.LitealrgeGgilvdkdGrrFmnelasrdvvsrailekeiaeggse 310
                                       ++ga  +d  +e+vqfhPt+ ++   ++gi Li+ea+rg G+ l+++dG+rF nel++rd+v+rai    ++ +++ 
  gi|242398049|ref|YP_002993473.1| 196 MKGALARD--LEFVQFHPTGFIG---KNGIkLISEAVRGAGAKLINSDGERFINELEPRDIVARAIY---MQTQEG- 263
                                       *****999..************4...77779************************************...555555. PP

                                       CBEEEE-TT.SSHHHHHHHSHHHHHHHHHCCT......S-TTTSEEE.......EEEEEEEES-EEEBETTSBESTT CS
                     FAD_binding_2 311 anvyldashgldaegleatleaineeaangldkdfgrgidpadrpipgpfyavkvvpaqhytmgGvetdengrvlda 387
                                       + vylda++    e +++++++ ++++ +++       i+p++ +ip       ++p +hy+ gG+ +d+  r+   
  gi|242398049|ref|YP_002993473.1| 264 KEVYLDATD---IEDFKSRFPQ-IYAFLKQEN------INPKRDMIP-------ISPIAHYSIGGLSVDTYYRT--- 320
                                       679******...677*******.666666688......*********.......********************... PP

                                       EEESSBTEEE-STCEESSSSTTS--TTHHH CS
                     FAD_binding_2 388 dgqpipGLYAaGevaaggvhganrlgGnsl 417
                                          ++++LYA+Ge+a  g+hganrl++nsl
  gi|242398049|ref|YP_002993473.1| 321 ---NVENLYAIGEAADNGFHGANRLASNSL 347
                                       ...*************************98 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.1   1.6e-10   1.4e-07       2     115 ..       2     178 ..       1     199 [. 0.75
   2 !   15.1   0.0   1.1e-05      0.01     254     279 ..     308     334 ..     297     346 .. 0.84

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 1.6e-10
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEE....TTHCHHHCSHHHHCHHHHHHHHHHHHH................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxx................. RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlve....legtclnggcllskallgvaedaeias................. 57 
                                       +v +iG G AGl+aa+ la++g +v++v+    +++  l +  +  ++l + + +++++                  
  gi|242398049|ref|YP_002993473.1|   2 KVGIIGNGTAGLTAAISLAKKGNEVYIVGdtikKTNSYLAQAGIAFPILDEDSIRKHVLDtinagrhlnneetvwsv 78 
                                       788*************************8676544444445555555555555555555588888888899999999 PP

                                       ....................................HHHHCHHHHCCCCHC...CT.CEEEEESC.EEEEETEEEC. CS
                                       ....................................xxxxxxxxxxxxxxx...xx.xxxxxxxx.xxxxxxxxxx. RF
                       Pyr_redox_2  58 ....................................evvkklnqgielllg...ee.vvkidpgk.kkvklekkke. 92 
                                                                           +   + +++i++ll    +e +v++++g  + v +++kk+ 
  gi|242398049|ref|YP_002993473.1|  79 isksseaydfllslglefegneiegghsfprvftikN---ETGKHIIKLLYmraKElGVQFIKGLaESVAIKNKKCy 152
                                       999999999999*************999999996651...4455544444344444577777776567777777778 PP

                                       ...TCEEEEEESEEEE---EEE-BCT CS
                                       ...xxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  93 ...gdeekiaydklvlAtGssprdlg 115
                                           d+e +++d+ vlAtG+ + +++
  gi|242398049|ref|YP_002993473.1| 153 gvfLDGEFLKFDATVLATGGYTALFK 178
                                       8887889************9887774 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 1.1e-05
                                       ETTEEE--TTSBESSTTEEE-GGGC.T CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx.x RF
                       Pyr_redox_2 254 erggivvdeflrtnvpgiyaiGDva.g 279
                                       + gg+ vd ++rtnv+++yaiG  a +
  gi|242398049|ref|YP_002993473.1| 308 SIGGLSVDTYYRTNVENLYAIGEAAdN 334
                                       6799*******************9941 PP

>> Succ_DH_flav_C  Fumarate reductase flavoprotein C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   2.4e-06    0.0022       3      34 ..     386     417 ..     384     422 .. 0.90
   2 !   24.1   0.0   3.1e-08   2.8e-05      63      90 ..     423     451 ..     418     460 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.4e-06
                                       HHHHHHHHHSSSSB-HHHHHHHHHHHHHHHHH CS
                    Succ_DH_flav_C   3 eLgkimqkkvgvfRteegLkealkelkelrer 34 
                                       +++++++k++g++R++e+Lke++k+lk+++++
  gi|242398049|ref|YP_002993473.1| 386 QIREVLWKHAGIVRSGEKLKEGIKKLKNIEAD 417
                                       7899***********************99875 PP

  == domain 2  score: 24.1 bits;  conditional E-value: 3.1e-08
                                       HHHHHHHHHHH--S-BTTBEBTTS-.SEE CS
                    Succ_DH_flav_C  63 lAeaiaksAlaRkESrGaHaredfp.erd 90 
                                       lAe i+ksAl R+ESrG H+r dfp +r+
  gi|242398049|ref|YP_002993473.1| 423 LAEGILKSALWREESRGVHYRVDFPfTRE 451
                                       7999********************93343 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   1.0   6.7e-10     6e-07       2     165 ..       2     173 ..       1     176 [. 0.77
   2 ?   -3.3   0.0       3.1   2.8e+03     368     386 ..     315     333 ..     308     334 .. 0.75

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 6.7e-10
                                       SEEEE--SHHHHHHHHHHHHTT--EEEE.-SSSSS-HHHHHCGGGT-EEEETT-SGGGEEES........STTTTHH CS
                       HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlll.ekakklgrKilisGgGrcNvTnlseepeellsryp.....enpkflks 72 
                                       +v +iG G AGl aAis+ak+g++V ++ +  kk+ + ++ +G     +   +   +++l+ ++     +n++++ s
  gi|242398049|ref|YP_002993473.1|   2 KVGIIGNGTAGLTAAISLAKKGNEVYIVgDTIKKTNSYLAQAGIAFPILDE-DSIRKHVLDTINagrhlNNEETVWS 77 
                                       678**********************987588899999******98876666.6666666666651111157777888 PP

                                       HHHHS-HHHHHHHHHHTT--EEE-..STT....EEEETT..-CHHHHHHHHHHHHHHT-EEE-S--EEEEECETTE. CS
                       HI0933_like  73 alsrftnedlialveelgvelkee..dsg....rlFpvsd.kaedivdallkelkeagvklrletevksvekeedgk 142
                                       ++s+  + +  +++ +lg+e++ +  + g    r+F+ ++ + ++i+++l  ++ke gv++    + +sv+ ++++ 
  gi|242398049|ref|YP_002993473.1|  78 VISK--SSEAYDFLLSLGLEFEGNeiEGGhsfpRVFTIKNeTGKHIIKLLYMRAKELGVQFIKGLA-ESVAIKNKKC 151
                                       8886..556677777777777643113443344788876526799***************987765.6666778888 PP

                                       EEEEE.TTEEEEESEEEE----S CS
                       HI0933_like 143 frvktkseeeleadklvlAtGGl 165
                                       + v + ++e l+ d++vlAtGG 
  gi|242398049|ref|YP_002993473.1| 152 YGVFL-DGEFLKFDATVLATGGY 173
                                       *****.9***************6 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.1
                                       TT-BBTTSTTEEE-GGGBS CS
                       HI0933_like 368 ktmeskkvpgLffaGEvlD 386
                                       +t    +v++L+ +GE  D
  gi|242398049|ref|YP_002993473.1| 315 DTYYRTNVENLYAIGEAAD 333
                                       555567899******9765 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.1   0.00036      0.32       2      28 ..       3      31 ..       2      79 .. 0.76
   2 !   15.6   0.0     1e-05    0.0092     149     208 ..     122     179 ..     108     197 .. 0.82
   3 ?   -1.2   0.0       1.3   1.1e+03     246     321 ..     249     330 ..     221     356 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00036
                                      EEEECTSHHHHHHHHHHHHTT..EEEEES CS
                               DAO  2 vviiGGGiiGlstAyeLarrg..Vtllek 28
                                      v iiG G +Gl++A  La++g  V ++  
  gi|242398049|ref|YP_002993473.1|  3 VGIIGNGTAGLTAAISLAKKGneVYIVGD 31
                                      78******************999988865 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 1e-05
                                       HHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEE.EECTEEEEEEEEEEE--GGGHHHH.H CS
                               DAO 149 taalaraaealGveilegtevtgleeedgkvwgve.rttpgendaadavVnaaGawsdll.g 208
                                       ++ l+ +a++lGv++++g  ++++  +++k +gv+ +   ge  ++da V+a+G ++ l+  
  gi|242398049|ref|YP_002993473.1| 122 IKLLYMRAKELGVQFIKG-LAESVAIKNKKCYGVFlD---GEFLKFDATVLATGGYTALFkY 179
                                       5678999***********.77777667789****976...776456**********998733 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.3
                                       EEETTTTEEEEEETTSEEEEEESSEEETTCSSTSCSHHHHHHHHHHHHHHSGGGCGEEE.EEEE......EEEETTS CS
                               DAO 246 tdddgrgvyvtprkdgrvlvGgtadeesgdddpevdeedidellealrklfPqlgdvlr.kwaG......lrplpdg 315
                                       +d  +r +y+   ++ +v++ +t+ e+++   p++ +   +e ++  r+++P  +++ + +  G      +r+++ +
  gi|242398049|ref|YP_002993473.1| 249 RDIVARAIYMQTQEGKEVYLDATDIEDFKSRFPQIYAFLKQENINPKRDMIPI-SPIAHySIGGlsvdtyYRTNVEN 324
                                       55667788888888888999888854444433677776777777777777766.44443244443333333334455 PP

                                       SEEEEE CS
                               DAO 316 lplige 321
                                       l  ige
  gi|242398049|ref|YP_002993473.1| 325 LYAIGE 330
                                       555555 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   1.0   1.4e-05     0.012       2      29 ..       3      33 ..       2      46 .. 0.82
   2 !    6.0   0.0    0.0058       5.2     111     153 ..     134     175 ..     114     209 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.4e-05
                                      EEEE-SSHHHHHHHHHHHHTT--EEEE...E CS
                              GIDA  2 viViGgGhAGceAAlaaarlGakvlLi...t 29
                                      v +iG G AG+ AA+ +a++G +v ++    
  gi|242398049|ref|YP_002993473.1|  3 VGIIGNGTAGLTAAISLAKKGNEVYIVgdtI 33
                                      889*********************9995542 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0058
                                       EEEEES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT-BT CS
                              GIDA 111 leiieeeveeliveekkvkgvvtedgetikakavviatGtflk 153
                                       ++ i++ +e++ +++kk+ gv + dge +k +a+v+atG + +
  gi|242398049|ref|YP_002993473.1| 134 VQFIKGLAESVAIKNKKCYGVFL-DGEFLKFDATVLATGGYTA 175
                                       6778899999*9********998.699************9765 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   2.7e-05     0.024       3      36 ..       2      35 ..       1      48 [. 0.80

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.7e-05
                                      EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSS CS
                     FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlvekrstt 36
                                      +V I+G G aGl++a  L+++G +v +v    ++
  gi|242398049|ref|YP_002993473.1|  2 KVGIIGNGTAGLTAAISLAKKGNEVYIVGDTIKK 35
                                      799************************9655444 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   5.7e-05     0.051       1      30 [.       1      30 [.       1      75 [. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.7e-05
                                      SEEEEE--STTHHHHHHHHHHCTSEEEEE- CS
                    UDPG_MGDP_dh_N  1 mkisviGlGYvGlvtaavlaeighevigvD 30
                                      mk+ +iG G  Gl+ a+ la++g+ev +v 
  gi|242398049|ref|YP_002993473.1|  1 MKVGIIGNGTAGLTAAISLAKKGNEVYIVG 30
                                      89************************9884 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   0.00016      0.14       1      29 [.       2      30 ..       2      41 .. 0.92
   2 ?   -0.8   0.0       2.5   2.3e+03      39      60 ..     118     139 ..     109     150 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00016
                                      EEEEECSSHHHHHHHHHHHHTTSEEEEEE CS
                         Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvve 29
                                      kv ++G G+ gl +A  la+ g++V++v 
  gi|242398049|ref|YP_002993473.1|  2 KVGIIGNGTAGLTAAISLAKKGNEVYIVG 30
                                      688************************96 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.5
                                       SHHHHHHHHHHHHHTTEEEECS CS
                         Pyr_redox  39 Deeaskilqeklekngievlln 60 
                                       ++ + k+l  + +++g++++ +
  gi|242398049|ref|YP_002993473.1| 118 GKHIIKLLYMRAKELGVQFIKG 139
                                       67788999999999****9975 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.9   9.2e-05     0.083       2      30 ..       3      31 ..       2      33 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.2e-05
                      FAD_oxidored  2 vvVvGGgpaGvaAAiaAaraGakvlLvee 30
                                      v ++G g+aG++AAi+ a++G +v +v +
  gi|242398049|ref|YP_002993473.1|  3 VGIIGNGTAGLTAAISLAKKGNEVYIVGD 31
                                      569***********************965 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00013      0.11       1      43 [.       2      49 ..       2     100 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00013
                                      EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT.....E CS
                     NAD_binding_2  1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg.....a 43
                                      k+g+iG G+ G   a  l+k+g +v+++  t +k+++ +a+      +
  gi|242398049|ref|YP_002993473.1|  2 KVGIIGNGTAGLTAAISLAKKGNEVYIVGDTIKKTNSYLAQAgiafpI 49
                                      69*********************************9999887454331 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00014      0.12       1      36 [.       2      37 ..       2      70 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00014
                                      EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHH CS
                           3HCDH_N  1 kvaviGaGtmGagiaavfasagleVvlvdiseeale 36
                                      kv++iG Gt G   a  +a++g eV +v  + ++ +
  gi|242398049|ref|YP_002993473.1|  2 KVGIIGNGTAGLTAAISLAKKGNEVYIVGDTIKKTN 37
                                      79************************9976655555 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.4     0.084        76       2      19 ..       5      22 ..       4      30 .. 0.87
   2 ?    6.7   0.0    0.0075       6.7     111     154 ..     129     171 ..     118     173 .. 0.87
   3 ?   -2.4   0.0       4.8   4.3e+03      81      96 ..     241     257 ..     230     262 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.084
                     NAD_binding_9  2 ivGaGprGlavlerLlar 19
                                      i+G G +Gl+++  L+++
  gi|242398049|ref|YP_002993473.1|  5 IIGNGTAGLTAAISLAKK 22
                                      9**************998 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0075
                     NAD_binding_9 111 lpegvtvevhraevvdleeradgqavlladgaslaadaVvLAlG 154
                                       + +++ v+++++ +++++ ++++ + +  dg+ l++da vLA+G
  gi|242398049|ref|YP_002993473.1| 129 A-KELGVQFIKGLAESVAIKNKKCYGVFLDGEFLKFDATVLATG 171
                                       3.45789****************999999**************9 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 4.8
                     NAD_binding_9  81 e.aeeldpddfvpRaly 96 
                                       + ++el+p+d v Ra+y
  gi|242398049|ref|YP_002993473.1| 241 RfINELEPRDIVARAIY 257
                                       25789999999999998 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.5   0.00027      0.24      20      47 ..       3      29 ..       1      37 [. 0.84
   2 ?   -1.9   0.0       1.8   1.6e+03     187     227 ..      61     103 ..      47     111 .. 0.75
   3 ?   -2.3   0.0       2.3   2.1e+03     210     231 ..     320     342 ..     316     344 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00027
                                      EEEE--SHHHHHHHHHHHHCTTS-EEEE CS
                              Thi4 20 vvivGaGssGLtaayylakkpdlkvail 47
                                      v i+G G++GLtaa  lakk + +v i+
  gi|242398049|ref|YP_002993473.1|  3 VGIIGNGTAGLTAAISLAKK-GNEVYIV 29
                                      779*****************.6677665 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.8
                                       S-----ECB-HHHHHHHHHHHECEEETTEEE-THHH..HHHHT CS
                              Thi4 187 ekvkgeksldaekaedaivkktrevvpnlyvaGmev..aevdg 227
                                       ++++  + l  e++  ++++k+ e ++ l+  G+e   +e++g
  gi|242398049|ref|YP_002993473.1|  61 DTINAGRHLNNEETVWSVISKSSEAYDFLLSLGLEFegNEIEG 103
                                       5677778888888888999999999999999998752255555 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 2.3
                                       EEETTEEE-THHH.HHHHT-EB- CS
                              Thi4 210 evvpnlyvaGmev.aevdganRm 231
                                         v+nly+ G ++ + ++ganR+
  gi|242398049|ref|YP_002993473.1| 320 TNVENLYAIGEAAdNGFHGANRL 342
                                       6799***9997763679***997 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 ?   12.2   0.2   0.00024      0.21       1      47 [.       2      44 ..       2      63 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00024
                                      EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC CS
                     F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg 47
                                      k+giiG G  g + a  l+++g   +e++++   + +k ++  +++g
  gi|242398049|ref|YP_002993473.1|  2 KVGIIGNGTAGLTAAISLAKKG---NEVYIV-GDTIKKTNSYLAQAG 44
                                      79********************...****88.777777777666666 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00019      0.17       1      44 [.       3      48 ..       3      80 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00019
                                      EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHH.HHHHCEEEE CS
                              ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr.rlea.lkknGlrlt 44
                                      + i+G G  G + a +Lak+g++v++++ +  + ++ l ++G+ + 
  gi|242398049|ref|YP_002993473.1|  3 VGIIGNGTAGLTAAISLAKKGNEVYIVGDTIkKTNSyLAQAGIAFP 48
                                      57*************************9998888888888887665 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1    0.0003      0.27      30      67 ..       2      40 ..       1      64 [. 0.76

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0003
                                      EEEEESTSHHHHHHHHHHHHTT-EEEEE.ESSHHHHHHH CS
                       AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvl.Dvrparleql 67
                                      kv +iG G+aGl A+   ++ g +V+++ D+ +++  +l
  gi|242398049|ref|YP_002993473.1|  2 KVGIIGNGTAGLTAAISLAKKGNEVYIVgDTIKKTNSYL 40
                                      799***********9999999999998734444444444 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 ?   10.9   0.5   0.00048      0.43       1      24 [.       5      28 ..       5      30 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00048
                                      EE--SHHHHHHHHHHHCCTEEEEE CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvll 24
                                      I+G G +Gl+aA  Lak+g +v +
  gi|242398049|ref|YP_002993473.1|  5 IIGNGTAGLTAAISLAKKGNEVYI 28
                                      9*****************999865 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.4   0.00062      0.55       1      24 [.       2      25 ..       2      35 .. 0.86
   2 ?   -1.7   0.0       1.1   9.9e+02     157     209 ..     122     172 ..     119     183 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00062
                                      EEEEE--SHHHHHHHHHHHHHTTT CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkg 24
                                      k+ i+G GtaG +aA+ lak +++
  gi|242398049|ref|YP_002993473.1|  2 KVGIIGNGTAGLTAAISLAKKGNE 25
                                      799*****************9954 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS-EEE-SEEEE-SGG CS
                    Trp_halogenase 157 akfLrrvaearGvtrvegkvvevqldedgrveslrledgreveadlfiDcsGf 209
                                        k+L   a++ Gv+ ++g  ++v ++++ +  ++ l dg+ +++d  + ++G 
  gi|242398049|ref|YP_002993473.1| 122 IKLLYMRAKELGVQFIKGLAESVAIKNK-KCYGVFL-DGEFLKFDATVLATGG 172
                                       57888999***********999998865.4455555.6666666666666665 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 ?   10.5   0.3   0.00028      0.26       2      26 ..       5      29 ..       4      41 .. 0.80
   2 ?   -3.4   0.1       4.8   4.3e+03     295     305 .]     319     329 ..     316     329 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00028
                       Pyr_redox_3  2 IiGaGPaGlaaaielkkagledyli 26
                                      IiG G aGl+aai l k+g e y++
  gi|242398049|ref|YP_002993473.1|  5 IIGNGTAGLTAAISLAKKGNEVYIV 29
                                      9******************976655 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 4.8
                       Pyr_redox_3 295 etnvpglflaG 305
                                        tnv++l+ +G
  gi|242398049|ref|YP_002993473.1| 319 RTNVENLYAIG 329
                                       69******998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (461 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); 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: 0.68u 0.33s 00:00:01.01 Elapsed: 00:00:00.52
# Mc/sec: 2689.16
//
Query:       gi|242398050|ref|YP_002993474.1|  [L=713]
Description: Phosphoribosylformylglycinamidine synthase II [Thermococcus sibiricus MM 739]
Scores for complete 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  204.1   2.9    1.3e-35  122.9   0.1    2.4  2  AIRS_C          AIR synthase related protein, C-terminal doma
      1e-47  160.7   0.2    7.6e-25   87.4   0.1    2.3  2  AIRS            AIR synthase related protein, N-terminal doma
    2.8e-07   30.9   1.5    4.7e-07   30.2   0.3    2.1  2  FGAR-AT_linker  Formylglycinamide ribonucleotide amidotransfe
  ------ inclusion threshold ------
       0.16   12.0   0.0         24    4.9   0.0    2.4  2  DUF3801         Protein of unknown function (DUF3801)


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 !  122.9   0.1   2.8e-39   1.3e-35       3     155 ..     186     340 ..     184     341 .. 0.93
   2 !   80.9   0.8   2.3e-26   1.1e-22       3     147 ..     547     680 ..     545     684 .. 0.91

  Alignments for each domain:
  == domain 1  score: 122.9 bits;  conditional E-value: 2.8e-39
                                       TEEEEEEET....SSCTCCHHHHHHHCHHHCTSHTT.TSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHH CS
                            AIRS_C   3 Gdvliltgs....lGlggagtslkrkileeegldds.avqlgdvlleptliyvkralaalkglvkaahDvTgGGLlg 74 
                                       G +l+l+g+    +G++g++ ++++++ e ++++d+ avq+ d++ e+ li++ +++ +  g+vka++D++gGGL++
  gi|242398050|ref|YP_002993474.1| 186 GLLLVLVGNktgrDGIHGVT-FASEELSENAEEEDRsAVQIPDPFTEKLLIEATLEAVHT-GKVKALKDLGGGGLTC 260
                                       78899999999*********.6666677766666667**********************6.**************** PP

                                       HHHHHHHTTTEEEEEECGTHHHHHHHHHHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEEEESSSE CS
                            AIRS_C  75 alaemapasgvgaeidldkvpifdelesplemllsensGrllvavppeeadavlaileeeglpeaavIGevtakeel 151
                                       a +ema + g+ga+i++d+vp +++ ++p+e+++se+++r+l+av++e+ +++++i+e+++l e++v+Ge++++++ 
  gi|242398050|ref|YP_002993474.1| 261 ASSEMAGKKGFGAVIYADRVPQREPNMNPMEIMISESQERMLFAVRKEDLNEITKIFEKYDL-EWTVVGETIEEPRY 336
                                       **************************************************************.8**********998 PP

                                       EEEE CS
                            AIRS_C 152 sviv 155
                                        v++
  gi|242398050|ref|YP_002993474.1| 337 IVYW 340
                                       7765 PP

  == domain 2  score: 80.9 bits;  conditional E-value: 2.3e-26
                                       TEEEEEEET..SSCTCCHHHHHHHCHHHCTSHTTTSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHHHHH CS
                            AIRS_C   3 Gdvliltgs..lGlggagtslkrkileeeglddsavqlgdvlleptliyvkralaalkglvkaahDvTgGGLlgala 77 
                                       Gd++ ++g+    lgg+ ++ + +i++  +      +++d+++e+  ++  +++++l +lvka+hDv+ GGL+ al 
  gi|242398050|ref|YP_002993474.1| 547 GDLIAVVGTtkKELGGSELYRIFGINKGIA------PRVDLEREKQNVEGILKAIEL-KLVKAVHDVSKGGLAIALI 616
                                       999999999999999999777665554444......59******************9.******************* PP

                                       HHHHTTTEEEEEECGTHHHHHHHHHHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEEEE CS
                            AIRS_C  78 emapasgvgaeidldkvpifdelesplemllsensGrllvavppeeadavlaileeeglpeaavIGevta 147
                                       ema  ++ g+e+d++kvp+   l sple+l+se+ Gr l+++++++ ++++ai++e     +avIG+v +
  gi|242398050|ref|YP_002993474.1| 617 EMAISGNKGFEVDIEKVPAEGGL-SPLEVLFSESHGRFLISFEEKNLEKIKAIFDE-----FAVIGRVAE 680
                                       ***************99999998.*******************************5.....789***987 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 !   87.4   0.1   1.7e-28   7.6e-25       1      94 []      67     172 ..      58     172 .. 0.94
   2 !   71.2   0.0   1.9e-23   8.3e-20       5      94 .]     429     533 ..     416     533 .. 0.93

  Alignments for each domain:
  == domain 1  score: 87.4 bits;  conditional E-value: 1.7e-28
                                       SSSEEEEEEEEEE.EECCTCCCCHHHHHHHHHHHHHHTTTEEEEEEEEEEEEC.........HHHHHHHHHHHHHHH CS
                              AIRS   1 dDaavvvttdshnrpvlvepvhfiGakavavnlsDlaamGArPlalllslalp.........wleevvrglaeaaee 68 
                                       d+ a+vv ++shn+p++vep+ + +a++v+++++D+++mGArP+all+ + ++          +e vv+g+a+++++
  gi|242398050|ref|YP_002993474.1|  67 DNTAIVVGIESHNHPSAVEPYGG-AATGVGGIVRDILCMGARPIALLDPIRFGplgkernryLFEYVVKGIADYGNR 142
                                       45668******************.***************************************************** PP

                                       TT-EEEEEEEEEESS....EEEEEEEEEEE CS
                              AIRS  69 lgvplvgGdtsfsne....ptisvtavGlv 94 
                                       +gvp+vgG+t+f+++     +++v+++Gl+
  gi|242398050|ref|YP_002993474.1| 143 IGVPTVGGETEFDESldnyTLVNVACIGLM 172
                                       ************999999999*******86 PP

  == domain 2  score: 71.2 bits;  conditional E-value: 1.9e-23
                                       EEEEEEEEE.EECCTCCCCHHHHHHHHHHHHHHTTTEEEEEEEEEEEEC.........HHHHHHHHHHHHHHHTT-E CS
                              AIRS   5 vvvttdshnrpvlvepvhfiGakavavnlsDlaamGArPlalllslalp.........wleevvrglaeaaeelgvp 72 
                                       +++  d++++++ ++p+h+ +  ava+++++la++GArPlal+++l++           + e ++gla+aa+++g +
  gi|242398050|ref|YP_002993474.1| 429 LAFVSDGNPSYSHLNPYHG-AMSAVAEVVRNLASVGARPLALVDNLNFAsperpevywSFIETIKGLADAAKAFGLA 504
                                       6999***************.*************************************999***************** PP

                                       EEEEEEEEESS.......EEEEEEEEEEE CS
                              AIRS  73 lvgGdtsfsne.......ptisvtavGlv 94 
                                        v+G++sf+ne       pt++v+ +G v
  gi|242398050|ref|YP_002993474.1| 505 YVSGNVSFYNEvgkkpikPTPVVAGLGKV 533
                                       ************************99986 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 !   30.2   0.3   1.1e-10   4.7e-07      16      50 .]       5      36 ..       1      36 [. 0.88
   2 ?   -2.6   0.0       1.9   8.7e+03       2      26 ..     295     319 ..     294     326 .. 0.73

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 1.1e-10
                    FGAR-AT_linker 16 EidylqeafeklgrnPtdvElemfaqvwSEHCrHK 50
                                      E + ++e    lgr+P+ vE  m+ ++wSEH ++K
  gi|242398050|ref|YP_002993474.1|  5 EEKLIKER---LGREPNEVEKAMLEVMWSEHASYK 36
                                      55667777...***********************9 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.9
                    FGAR-AT_linker   2 eeankelglaLsdeEidylqeafek 26 
                                       +e ++++ +a  +e+ + ++++fek
  gi|242398050|ref|YP_002993474.1| 295 SESQERMLFAVRKEDLNEITKIFEK 319
                                       5667777788888888888888854 PP

>> DUF3801  Protein of unknown function (DUF3801)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0    0.0054        24      24      74 ..     290     340 ..     276     353 .. 0.78
   2 ?    4.2   0.0    0.0092        41      67     103 ..     650     699 ..     645     704 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0054
                           DUF3801  24 lkkLlkkggdlkvlqlddsdlkefkkeAkkyGilYavkkdkndkgqteiif 74 
                                       ++ ++ + ++   + ++++dl+e++k   ky +  +v+ +  ++++++++ 
  gi|242398050|ref|YP_002993474.1| 290 MEIMISESQERMLFAVRKEDLNEITKIFEKYDLEWTVVGETIEEPRYIVYW 340
                                       556777777777888888888888888888888888887655778887765 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0092
                           DUF3801  67 kgqteiifraedadainrafqrmkl.............vdkadvsqdaek 103
                                        g++ i+f  +  ++i+++f+++               ++k ++ +d  +
  gi|242398050|ref|YP_002993474.1| 650 HGRFLISFEEKNLEKIKAIFDEFAVigrvaeemlifkhENKEVINSDLRQ 699
                                       699********************997777777777777667777666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (713 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.71u 0.31s 00:00:01.02 Elapsed: 00:00:00.50
# Mc/sec: 4259.02
//
Query:       gi|242398051|ref|YP_002993475.1|  [L=225]
Description: Phosphoribosylformylglycinamidine synthase 1 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-50  171.7   0.0    1.9e-50  171.4   0.0    1.1  1  GATase_5       CobB/CobQ-like glutamine amidotransferase doma
    3.1e-09   36.9   0.0    6.2e-09   35.9   0.0    1.4  1  GATase         Glutamine amidotransferase class-I
    3.7e-09   36.6   0.0    5.8e-09   36.0   0.0    1.3  1  DJ-1_PfpI      DJ-1/PfpI family
    8.2e-09   35.3   0.0    1.7e-08   34.3   0.0    1.5  2  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
      2e-07   31.1   0.0    2.6e-06   27.4   0.0    2.0  2  SNO            SNO glutamine amidotransferase family
     0.0002   21.2   0.0    0.00065   19.5   0.0    1.8  1  Peptidase_C26  Peptidase C26
    0.00087   19.0   0.0     0.0014   18.3   0.0    1.3  1  DUF4131        Domain of unknown function (DUF4131)


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 !  171.4   0.0   7.4e-54   1.9e-50       2     260 .]       5     223 ..       4     223 .. 0.91

  Alignments for each domain:
  == domain 1  score: 171.4 bits;  conditional E-value: 7.4e-54
                          GATase_5   2 pkvailreeGvngeyemaaafekaGfeavdvhmsdllegrvslddfqilalpGGfsygDelgsgkgwakslllnekl 78 
                                       pk a+++++G+n++ e+ +a++kaG +a++v  +       sl+df +++lpGGfsy+D l +g++ a   +  +++
  gi|242398051|ref|YP_002993475.1|   5 PKFAVIVFPGTNCDFETVEAIKKAGGKAERVWYK------SSLKDFDGVVLPGGFSYADYLRAGAISA---R--AEI 70 
                                       899***************************9874......56**********************9988...3..678 PP

                          GATase_5  79 realekflnredtlaLGiCnGfqlLvklglvpggeieeaeksptltrNksgrfesrlvsvvvsekspsvfl..kgme 153
                                        e+++++ ++ d+ +LGiCnGfq+L++ gl+pg          +l  Nk+ rf +++v+++v++++ ++    +++e
  gi|242398051|ref|YP_002993475.1|  71 MEEVKALASE-DKPILGICNGFQILTESGLLPG----------ALRPNKVPRFLCKWVYLRVNDTQTAFTKfyEEGE 136
                                       9***999999.**********************..........9****************76665555533369999 PP

                          GATase_5 154 glslpvahGeGrfvfkseevlkeleangqvalrYvdeegkpteeyplNPNgSpegiagitspdGRvlalmpHpervv 230
                                       ++++p+ah+eG+  ++s+        +  ++++Y de+gk+te+  +NPNgS  +iagi +++G vl++mpHper++
  gi|242398051|ref|YP_002993475.1| 137 VIRMPIAHAEGNYYTDSP--------KVRIVFQYSDEKGKITED--ANPNGSILNIAGISNEKGNVLGMMPHPERAS 203
                                       ***************665........4589***********996..7****************************** PP

                          GATase_5 231 eavqksiipeeeeeevspwlrlFenavkyv 260
                                       +++  s          +++l++F+++v+yv
  gi|242398051|ref|YP_002993475.1| 204 DKWLGS----------EDGLKVFKSMVEYV 223
                                       ***999..........46788999998886 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   0.0   2.4e-12   6.2e-09      19     127 ..      27     161 ..      17     206 .. 0.54

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 2.4e-12
                                       HTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT..TTTHHHHHHHHCT.......STS-EEEETHHHHHHHH CS
                            GATase  19 elgvkvevvpidasaeeilellknpdgilvsgGpgspg..vegkieaikeare.......nkiPiLGICLGmQllai 86 
                                       ++g k e v++++        lk++dg++++gG+ +    + g+i+a  e++e       +++PiLGIC G+Q+l++
  gi|242398051|ref|YP_002993475.1|  27 KAGGKAERVWYKS-------SLKDFDGVVLPGGFSYADylRAGAISARAEIMEevkalasEDKPILGICNGFQILTE 96 
                                       4444555555553.......37899************99*666666666666656666667*************998 PP

                                       HTTT.............................EEEEEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEE CS
                            GATase  87 efgr.............................kvvkekekehhggtmrlgddetallyglknevierhr 127
                                       +                                k      +e     m++ + e + +y ++++v+  ++
  gi|242398051|ref|YP_002993475.1|  97 SGLLpgalrpnkvprflckwvylrvndtqtaftK----FYEEGEVIRMPIAHAE-GNYYTDSPKVRIVFQ 161
                                       7554665666655555555444444433222221....1122233344444422.333333333333333 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 !   36.0   0.0   2.3e-12   5.8e-09      49     115 ..      31     102 ..      10     105 .. 0.85

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 2.3e-12
                                       E-SEEGGGCTCCG-SEEEE--BHHHHHHHHTSH.....HHHHHHHHHHHTT-EEEEETTTHHHHHHTTTTTT CS
                         DJ-1_PfpI  49 tvdaslddvkaaeyDalvlpGGragperlrene.....kvvelvkefaekgklvaaICagpqlLaaagvlkg 115
                                       ++++++ + + +++D +vlpGG + +++lr+ +     +++e vk  a+++k++  IC g q+L + g+l+g
  gi|242398051|ref|YP_002993475.1|  31 KAERVWYKSSLKDFDGVVLPGGFSYADYLRAGAisaraEIMEEVKALASEDKPILGICNGFQILTESGLLPG 102
                                       5666777778899****************975544444899****************************987 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.0   6.8e-12   1.7e-08      18      91 ..      24      97 ..       6     105 .. 0.76
   2 ?   -3.3   0.0       2.3   5.8e+03     169     185 ..     181     195 ..     161     199 .. 0.57

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 6.8e-12
                          GATase_3 18 pLeaepevrvrfvplkdeslgedadlvilpGgkdtiqdl...allresgldeaikeaaeaggpvlgiCGGlqmLGee 91
                                      ++++++ +  r+    ++sl +d d v+lpGg+++++ l   a++++ ++ e++k++a++++p+lgiC G+q+L e+
  gi|242398051|ref|YP_002993475.1| 24 AIKKAGGKAERVWY--KSSL-KDFDGVVLPGGFSYADYLragAISARAEIMEEVKALASEDKPILGICNGFQILTES 97
                                      44444444444443..6778.56*********987655511177888999************************985 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.3
                          GATase_3 169 ekdGavkksedgnvlGt 185
                                       +  G+   +e+gnvlG 
  gi|242398051|ref|YP_002993475.1| 181 NIAGIS--NEKGNVLGM 195
                                       555666..567777775 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0     1e-09   2.6e-06      10      83 ..      20      96 ..      14     104 .. 0.88
   2 ?    1.6   0.0     0.082   2.1e+02     140     174 ..     163     204 ..     142     224 .. 0.69

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 1e-09
                                      HHHHHHHHTTSEEEEE-SGGGGCC-SEEEE-SS-HHH....HHHHHHHTT-HHHHHHHHHTT.--EEEETHHHHHHCC CS
                               SNO 10 ehveaikkclaenktvkrkedlaevdaliiPGGesta....mskliertglyedllefvknsekvvlGtCaGlillsk 83
                                      e veaikk++ ++  v  k  l++ d++++PGG s a     + +  r +++e++++ + +  k++lG C G+ +l++
  gi|242398051|ref|YP_002993475.1| 20 ETVEAIKKAGGKAERVWYKSSLKDFDGVVLPGGFSYAdylrAGAISARAEIMEEVKALASED-KPILGICNGFQILTE 96
                                      7899******************************9884433567999999999999988776.*********988865 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.082
                                       .TTTCEEEEECT..T...EEEEEE..ETTEEEESS-GGGSTT CS
                               SNO 140 ddeavkvlyeld..g...eivvak..qkkilatsfhPelaed 174
                                       +de+ k+  + +  g   +i ++   ++++l++  hPe a d
  gi|242398051|ref|YP_002993475.1| 163 SDEKGKITEDANpnGsilNIAGISneKGNVLGMMPHPERASD 204
                                       46666777776666633334444442559*********8866 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   2.6e-07   0.00065      31     118 ..      23      94 ..      12     107 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 2.6e-07
                     Peptidase_C26  31 eavekagglpvllpieedeedvkaildkldgllltGgqdvePslygeepsekeeeadpeRdalelaLiraalergvP 107
                                       ea++kagg +  ++++       + l+ +dg++l+Gg       y+     + ++++++ +++e   ++a  ++++P
  gi|242398051|ref|YP_002993475.1|  23 EAIKKAGGKAERVWYK-------SSLKDFDGVVLPGGFS-----YADY--LRAGAISARAEIMEE--VKALASEDKP 83 
                                       5666666655555555.......7889999999999987.....4444..455666655555554..789999**** PP

                     Peptidase_C26 108 ilgiCrGlqll 118
                                       ilgiC G+q+l
  gi|242398051|ref|YP_002993475.1|  84 ILGICNGFQIL 94 
                                       *********99 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   5.6e-07    0.0014     124     162 ..      33      71 ..      24      75 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 5.6e-07
                           DUF4131 124 drlrltgrlkrprpatNpggFDyraYLarqgIfatlyvk 162
                                       +r++ + +lk + +   pggF y+ YL++  I+a++ + 
  gi|242398051|ref|YP_002993475.1|  33 ERVWYKSSLKDFDGVVLPGGFSYADYLRAGAISARAEIM 71 
                                       89*******************************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1491.12
//
Query:       gi|242398052|ref|YP_002993476.1|  [L=81]
Description: phosphoribosylformylglycinamidine synthase subunit PurS [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-25   88.5   0.0    2.7e-25   88.3   0.0    1.0  1  PurS      Phosphoribosylformylglycinamidine (FGAM) synthase
  ------ inclusion threshold ------
      0.029   14.0   0.0      0.029   14.0   0.0    1.0  1  FrpC      RTX iron-regulated protein FrpC


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 !   88.3   0.0     3e-29   2.7e-25       1      77 []       4      76 ..       4      76 .. 0.96

  Alignments for each domain:
  == domain 1  score: 88.3 bits;  conditional E-value: 3e-29
                                      EEEEEEEE-TTS--HHHHHHHHHHHHTTHTTEEEEEEEEEEEEEEE-SSHHHHHHHHHHHHHHTTS-TTTEEEEEEE CS
                              PurS  1 kakveVtlKkgvlDpqGkavkkalkslgyeevedvrvgkyieleleaedeeeaeeeveemceklLaNpviedyeiel 77
                                      kak++V lK+g+ Dp+G+++ kalk+lgy+ + +++v ky+el++e+e+ e   ++veemc++lLaNpvi++y++e+
  gi|242398052|ref|YP_002993476.1|  4 KAKIIVHLKEGLNDPEGRVIGKALKNLGYK-IGELKVPKYFELTFESENPE---KDVEEMCRRLLANPVIHTYSYEI 76
                                      79***************************9.***************87765...7*******************996 PP

>> FrpC  RTX iron-regulated protein FrpC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   3.2e-06     0.029     125     195 ..       3      74 ..       1      81 [] 0.91

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.2e-06
                                       THHHHHHHHHHS-SSEEEEEEEE------TTHHH.HHHHTT-EEE--SSTTEEEEEE---BTTBTT--EEEE CS
                              FrpC 125 nkahfiqflrdgldsvddivirkdacslsttmge.rlltygvkkmpsaypeyeayedkrhipenpyfhefyy 195
                                        ka++i  l++gl+  +  vi k    l   +ge ++  y    + s  pe +  e  r +  np +h + y
  gi|242398052|ref|YP_002993476.1|   3 YKAKIIVHLKEGLNDPEGRVIGKALKNLGYKIGElKVPKYFELTFESENPEKDVEEMCRRLLANPVIHTYSY 74 
                                       699*******************************4456799999************************9977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 576.03
//
Query:       gi|242398053|ref|YP_002993477.1|  [L=383]
Description: 5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase [Thermococcus sibiricus MM 739]
Scores for complete 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-81  270.3   0.0    9.9e-81  269.8   0.0    1.2  1  DUF1297   Domain of unknown function (DUF1297)
    3.5e-44  149.7   0.0    5.5e-44  149.0   0.0    1.3  1  DUF1246   Protein of unknown function (DUF1246)


Domain annotation for each model (and alignments):
>> DUF1297  Domain of unknown function (DUF1297)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  269.8   0.0   1.1e-84   9.9e-81       1     188 []     192     383 .]     192     383 .] 0.99

  Alignments for each domain:
  == domain 1  score: 269.8 bits;  conditional E-value: 1.1e-84
                                       HHHHHHHHHHCTTSSSHHHHCCEEEEE---SEEEEEEEEEETTTTEEEEEEEEEEEEEECCCHCCS-HHHHHCCT-. CS
                           DUF1297   1 efeekleellekglieeedlkkasieeyvvGanfnlnyfysplkeevellgidrRyesnldglvrlpakeqlelev. 76 
                                       ef+ek+e+l++ g+i+eedl+ka+ie+y++G  fn+++fysp+++++ellgid+R+e++ldg+vrlpa +ql+l + 
  gi|242398053|ref|YP_002993477.1| 192 EFKEKAERLMKLGVITEEDLNKARIERYIIGPVFNFDFFYSPIDGDIELLGIDWRFETSLDGHVRLPAPQQLTLPEh 268
                                       79**********************************************************************99877 PP

                                       ..---EEEEEEEEEEE-GGGHHHHHHHHHHHHHHHHHHSTT---EEEEEEEEE-TTS-EEEEEEESSB-GGGGGGTT CS
                           DUF1297  77 ..epeyvvvGnipvvlREsllekvfelgekfveaakklvppGiiGpFcLqsvvtkdlelvvfdvsaRivggtnvyme 151
                                         epey+v+G+ + +lREsllekvf+++e++vea+kk+++pG+iGpF+Lq+ v+kdl+++++dv++R++ggtn++m+
  gi|242398053|ref|YP_002993477.1| 269 qfEPEYTVCGHASSTLRESLLEKVFDMAERYVEATKKYYSPGVIGPFTLQTTVDKDLNFYIYDVAPRTGGGTNIHMA 345
                                       789************************************************************************** PP

                                       .--CCHHHTTSS---HHHHHHHHHHHHHHCT-GGGCEE CS
                           DUF1297 152 .gspyskllfgeplsmGrrialEikeaiekdrleeivt 188
                                        g+py + l+++++s+GrrialEik+aie ++le++vt
  gi|242398053|ref|YP_002993477.1| 346 mGHPYGNALWRKQMSTGRRIALEIKRAIELGELEKVVT 383
                                       *************************************8 PP

>> DUF1246  Protein of unknown function (DUF1246)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.0   0.0   6.2e-48   5.5e-44       1     120 [.      24     156 ..      24     158 .. 0.98

  Alignments for each domain:
  == domain 1  score: 149.0 bits;  conditional E-value: 6.2e-48
                                       EEEESSTTHHHHHHHHHHTT--EEEEC-CCCHHHHHTT............TT-SEEEE.S.S..TTSS--HHHHHHT CS
                           DUF1246   1 iatlaSHsalqilkgAkkegfrtlavcekgreklYekf............kvidevivldkfkdilkeevqeklree 65 
                                       i++++SHsal+i++gAk egf+t++v +kgr+++Y ++            ++idevivl+kf++i+  e+qe+lr++
  gi|242398053|ref|YP_002993477.1|  24 IGAIGSHSALDIADGAKVEGFKTIIVSQKGRHRTYAEYfkqkttkdglakGFIDEVIVLEKFAQII--EIQEELRKK 98 
                                       899***************************************************************..678****** PP

                                       TCEE--BTTHHHHC-HHHHH.C-SS-EES-TTHHHHHCSHHHHHHH..HHHTT-BB-- CS
                           DUF1246  66 nailvPhgsfveYvgiekie.elkvpifGnrkllrwEerrekkrky..LekAgiriPk 120
                                       n+i++P++sfv+Y+gi+k+e e+ vp+fG+r+llr+Eer+e+k++y  LekAg+++P+
  gi|242398053|ref|YP_002993477.1|  99 NVIFIPNRSFVVYTGIDKVEnEFLVPLFGSRNLLRSEERSEEKSYYwlLEKAGLPYPE 156
                                       *********************************************99**********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 2409.14
//
Query:       gi|242398054|ref|YP_002993478.1|  [L=435]
Description: Phosphoribosylamine--glycine ligase [Thermococcus sibiricus MM 739]
Scores for complete 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-60  203.0   0.1    5.8e-60  202.4   0.1    1.3  1  GARS_A           Phosphoribosylglycinamide synthetase, ATP-gr
    2.9e-27   95.3   0.2    1.4e-25   89.9   0.1    2.3  2  GARS_N           Phosphoribosylglycinamide synthetase, N doma
    5.3e-14   52.3   1.4    1.3e-12   47.9   0.2    3.1  3  GARS_C           Phosphoribosylglycinamide synthetase, C doma
    2.1e-05   24.7   0.0    6.8e-05   23.0   0.0    1.8  1  ATP-grasp_3      ATP-grasp domain
    4.9e-05   23.0   0.0     0.0001   21.9   0.0    1.5  1  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
    0.00033   20.3   0.1    0.00067   19.3   0.1    1.5  1  ATP-grasp        ATP-grasp domain
    0.00038   20.0   0.0     0.0017   17.9   0.1    2.0  2  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
    0.00053   19.6   0.2     0.0014   18.2   0.2    1.7  1  ATP-grasp_2      ATP-grasp domain
     0.0013   18.4   0.3       0.02   14.5   0.7    2.6  2  ATP-grasp_4      ATP-grasp domain
  ------ inclusion threshold ------
      0.028   14.1   0.0      0.073   12.7   0.0    1.8  1  Peripla_BP_6     Periplasmic binding protein
      0.051   12.8   0.0       0.18   11.1   0.1    1.8  2  ATPgrasp_ST      Sugar-transfer associated ATP-grasp
      0.059   12.8   0.4       0.15   11.5   0.1    1.8  2  ATP-grasp_5      ATP-grasp domain


Domain annotation for each model (and alignments):
>> GARS_A  Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  202.4   0.1   3.9e-63   5.8e-60       1     194 []     105     299 ..     105     299 .. 0.97

  Alignments for each domain:
  == domain 1  score: 202.4 bits;  conditional E-value: 3.9e-63
                                       HBHHHHHHHHHHTT--B-.-EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT-EEEE....SSHHHHHHHHHHHCT CS
                            GARS_A   1 asKsfakdllkkagipta.eyeaftdpeeakeyieeatakalVvKadglaagKgviva....kseeealkavkeile 72 
                                       ++K+fa+++++k++ip+   +++f+d++e+k++i+e+++++ VvK+ gl++gKgv+v+    k++eea +++k ++e
  gi|242398054|ref|YP_002993478.1| 105 TNKAFARQIMEKYKIPGRkLFKVFDDVAEMKTWIDEFGKPV-VVKPLGLTGGKGVKVVgyqlKDNEEAKEYAKALIE 180
                                       68***************96799*******************.****************99999*************7 PP

                                       S-TTCCCCSSEEEEE---SEEEEEEEEECTTEEEE---BEEEEEEECCCEEEEECECEEEE....S-TTS-HHHHHH CS
                            GARS_A  73 kkkfGeagekvviEelleGeEvsllalvdgktvkplplaqdhkrvlegDkgpnTGGmGays....papvvteellek 145
                                         k G    kv++Ee+ +G E+++++++dgk+v+p+plaqd+++++egD gp+TGGmG+ys     +p+++ e+++k
  gi|242398054|ref|YP_002993478.1| 181 --KDG----KVLVEERTDGVEFTFQVFTDGKKVIPMPLAQDYPHAYEGDVGPITGGMGSYScedhLLPFIPREDYHK 251
                                       ..556....9***************************************************999899********** PP

                                       HHHHTHHHHHHHHHCTT---EEEEEEEEEEETTEEEEEEEESS--TTCH CS
                            GARS_A 146 ikeeileptveglkkegipfkGvLyaglmlvedgpkvlefnvRfgDpet 194
                                       + e  l++tv+++ keg+p+kG+Ly+++ml +d pk++efn+RfgDpe+
  gi|242398054|ref|YP_002993478.1| 252 ALE-TLKKTVKAMYKEGTPYKGILYGQFMLANDEPKIIEFNARFGDPEA 299
                                       **9.89*****************************************97 PP

>> GARS_N  Phosphoribosylglycinamide synthetase, N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.9   0.1   9.1e-29   1.4e-25       1      90 []       5     104 ..       5     104 .. 0.94
   2 ?    3.3   0.0     0.096   1.4e+02      49      83 ..     370     404 ..     325     410 .. 0.79

  Alignments for each domain:
  == domain 1  score: 89.9 bits;  conditional E-value: 9.1e-29
                                       EEEEEEESSHHHHHHHHHHTTSTTESEEEEEE--CGG............TTHHHHHHHHHHCTESEEEE-SHHHHHT CS
                            GARS_N   1 mkvLvvGsGGRehalawklaqspkvekvyvapgNagt............edlealvefakeekidlvvvGpeapLva 65 
                                       m+vL+vG+GGRe+a+a++l+ + ++  v++ ++N+g+            +d++++++fa + ++d++++Gpe+pL +
  gi|242398054|ref|YP_002993478.1|   5 MRVLLVGGGGRENAIAEALSTDAELY-VVAKHKNPGIkritkeygltkeTDVQKVLDFALKWNVDMAFIGPESPLEK 80 
                                       9********************97765.67777*******99999999998899************************ PP

                                       THHHHHHHHHT-EEES--CCCCHHH CS
                            GARS_N  66 GvadaleeekgikvfGpskeaAqlE 90 
                                       G++d lee+ gi+++GpskeaAqlE
  gi|242398054|ref|YP_002993478.1|  81 GIVDVLEEN-GIPTVGPSKEAAQLE 104
                                       ******877.**************9 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.096
                                       HCTESEEEE-SHHHHHTTHHHHHHHHHT-EEES-- CS
                            GARS_N  49 eekidlvvvGpeapLvaGvadaleeekgikvfGps 83 
                                       + + d+++ G  a  + G++d lee+++i+  G +
  gi|242398054|ref|YP_002993478.1| 370 SIDEDFTMLGSRALAIVGISDSLEEAEKIASAGIK 404
                                       4556899****************888899888865 PP

>> GARS_C  Phosphoribosylglycinamide synthetase, C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.78   1.2e+03      36      64 ..     151     180 ..      99     192 .. 0.76
   2 ?    1.1   0.0      0.33     5e+02       7      23 ..     212     229 ..     207     266 .. 0.80
   3 !   47.9   0.2   8.4e-16   1.3e-12       2      80 .]     333     419 ..     332     419 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.78
                                       EE-SSEEEEEEEE.ESSHHHHHHHHHHHHT CS
                            GARS_C  36 vtsGGRvlavvav.getleeArakayeavk 64 
                                         +GG+ + vv++  ++ eeA++ a + ++
  gi|242398054|ref|YP_002993478.1| 151 GLTGGKGVKVVGYqLKDNEEAKEYAKALIE 180
                                       568999999998745788899888887776 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.33
                                       EETTTTSS--.ST-EEBS CS
                            GARS_C   7 askGYPgsye.kgkeitg 23 
                                        +++YP++ye    +itg
  gi|242398054|ref|YP_002993478.1| 212 LAQDYPHAYEgDVGPITG 229
                                       5899*****944567776 PP

  == domain 3  score: 47.9 bits;  conditional E-value: 8.4e-16
                                       EEEEEEETTTTSS--ST-EEBS.......TTEEEEESSEE..EEE-SSEEEEEEEEESSHHHHHHHHHHHHTTCB-T CS
                            GARS_C   2 vgvvlaskGYPgsyekgkeitg.......egvkvfhagtk..lvtsGGRvlavvavgetleeArakayeavkkikfe 69 
                                       v  ++a+kGYP+++ kg +++        eg+k+++a+    + + G+R la+v++ ++leeA++ a +++k++k  
  gi|242398054|ref|YP_002993478.1| 333 VVKYVAPKGYPTDPIKGVKVQIsedkikkEGAKIYYASIDedFTMLGSRALAIVGISDSLEEAEKIASAGIKHVKG- 408
                                       7899**************9977889999988899999977889*****************************9975. PP

                                       TEE--STTTHH CS
                            GARS_C  70 glfyRkDIGar 80 
                                       ++fyR D+G++
  gi|242398054|ref|YP_002993478.1| 409 EIFYRADVGTK 419
                                       7********85 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   4.5e-08   6.8e-05       9     159 ..     111     295 ..     104     297 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 4.5e-08
                                       HHHTTT.S---.............-EESS--.SSSEEEEESS-------B--SS--TTE.................E CS
                       ATP-grasp_3   9 kkLkeagvkvP.........tkleaeeleee.ekklvvKprdGaggesvrvveekeeaeaaieeve..........l 65 
                                       ++++e+ +k+P         + +e++ +  e  k++vvKp    gg++v vv  + ++++  +e +          l
  gi|242398054|ref|YP_002993478.1| 111 RQIMEK-YKIPgrklfkvfdDVAEMKTWIDEfGKPVVVKPLGLTGGKGVKVVGYQLKDNEEAKEYAkaliekdgkvL 186
                                       556666.67777766666654444444433359****************9998887777766666669999****** PP

                                       EEE---SEEEEEEEEE.SSSEEEEEEEEEEEET..............TEEEEEEES----H.HHHHHHHHHHHHTTS CS
                       ATP-grasp_3  66 vqefieGkplSvsllsdgekvlvlavnrqliekaeke..........fvyaGnvtpietel.keevvelaeevvekl 131
                                       v e  +G +++ ++  dg+kv ++ + + + +  e +          ++    + p+  ++  +++ e+ +++v+++
  gi|242398054|ref|YP_002993478.1| 187 VEERTDGVEFTFQVFTDGKKVIPMPLAQDYPHAYEGDvgpitggmgsYSCEDHLLPFIPREdYHKALETLKKTVKAM 263
                                       ***************************99997655559888888855444556677654444899999999999999 PP

                                       T.T--EEEEE...EEEESS.SEEEEEEESS-- CS
                       ATP-grasp_3 132 e.glaGyvGv...DlvlkdeepyviEvNPRlt 159
                                         +   y G+    ++l+++ep +iE N+R+ 
  gi|242398054|ref|YP_002993478.1| 264 YkEGTPYKGIlygQFMLANDEPKIIEFNARFG 295
                                       77556666665559****************95 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 !   21.9   0.0     7e-08    0.0001      29      98 ..     135     208 ..     122     220 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 7e-08
                                       HHHHHHC-SSEEEEESSSSTTTTEEEE....SSGGGHHHHHHHHHTT-SCEEEEE--ESEEEEEEEEETSSCEE CS
                   Dala_Dala_lig_C  29 ekveeelgypvfVKpareGSSvGvskv....eseeelkeaieeafkydekvlvEeaiegreievavlgneklev 98 
                                       +  ++e+g pv+VKp  +    Gv+ v    + +ee ke+ ++ +++d kvlvEe  +g e++  v  ++k  +
  gi|242398054|ref|YP_002993478.1| 135 KTWIDEFGKPVVVKPLGLTGGKGVKVVgyqlKDNEEAKEYAKALIEKDGKVLVEERTDGVEFTFQVFTDGKKVI 208
                                       5667899********99888888887644447899*******************************99887655 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1   4.5e-07   0.00067      11      71 ..     125     190 ..     114     201 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 4.5e-07
                                       EEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEE....CTCCGHHCHHHHC..GTTCEEEEE- CS
                         ATP-grasp  11 flaveskeeleeaaeelglpvvvKarrlgydGkGqsvv....rseedleqaleal..keekvivEef 71 
                                       f + ++ +e++  ++e+g pvvvK + +   GkG +vv    +++e++++ ++al  k++kv+vEe+
  gi|242398054|ref|YP_002993478.1| 125 FKVFDDVAEMKTWIDEFGKPVVVK-PLGLTGGKGVKVVgyqlKDNEEAKEYAKALieKDGKVLVEER 190
                                       67788999****************.99999*****99844446777777777777999*******97 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 !   17.9   0.1   1.1e-06    0.0017       2     103 ..     107     204 ..     106     209 .. 0.74
   2 ?   -1.3   0.0      0.83   1.2e+03     159     180 ..     275     294 ..     242     300 .. 0.63

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.1e-06
                                       HHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEE....SSHHHHHHHHHHHHHHH CS
                       CPSase_L_D2   2 kesakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrva....rneeelaelvkkalaea 74 
                                       k  a+++++k ++p  + +++  +++ e  +  +e+g Pv++k+    GGkG +v+    +++ee  + ++kal e 
  gi|242398054|ref|YP_002993478.1| 107 KAFARQIMEKYKIPGRKLFKV-FDDVAEMKTWIDEFGKPVVVKPLGLTGGKGVKVVgyqlKDNEEA-KEYAKALIEK 181
                                       566889999999999999988.99*******************************93322233333.3334444444 PP

                                       HHHHSTS-EEEEE--SSSEEEEEEEEEET CS
                       CPSase_L_D2  75 kaafgnkqvlvekslkgpkeiEvevlrDa 103
                                            + +vlve+  +g  e  ++v  D 
  gi|242398054|ref|YP_002993478.1| 182 -----DGKVLVEERTDGV-EFTFQVFTDG 204
                                       .....5788888877765.5666666665 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.83
                                       EEEEEEETTTTEEEEEEEESS- CS
                       CPSase_L_D2 159 tveflldpkskeyyviEvNtRl 180
                                         +f+l   ++e  +iE N+R 
  gi|242398054|ref|YP_002993478.1| 275 YGQFMLA--NDEPKIIEFNARF 294
                                       4478887..588899****996 PP

>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.2   9.4e-07    0.0014       7      79 ..     110     182 ..     107     197 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 9.4e-07
                                       HHHHHHCTT----S.EEEESSHHHHHHHHHHHTSSSEEEEE--SSSTCC.CTTCEEEESSHHHHHHHHHCCTTSE CS
                       ATP-grasp_2   7 akeilakygvkvpe.gevaesaeeaeeaakklgekelvvKaQvlaGGRG.KagGvklvkskeeakeaakellgke 79 
                                       a++i++ky ++  + ++v ++  e+++ ++++g+ + vvK   l+GG+G K  G +l k++eeake+ak+l+ k+
  gi|242398054|ref|YP_002993478.1| 110 ARQIMEKYKIPGRKlFKVFDDVAEMKTWIDEFGKPV-VVKPLGLTGGKGvKVVGYQL-KDNEEAKEYAKALIEKD 182
                                       79*********87637899999***********999.***********967788776.699**********9764 PP

>> ATP-grasp_4  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.7   1.4e-05      0.02       3      81 ..     143     209 ..     141     221 .. 0.76
   2 ?   -0.6   0.0       0.6     9e+02      24      47 ..     246     266 ..     241     280 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.4e-05
                       ATP-grasp_4   3 lPvviKPsvgffSlGVykinneeewkaavaaieeeleqakeeykeevve.eesflvEeyieGeEfavdayfdeeGep 78 
                                        Pvv+KP   ++  GV ++  +         ++++ e+a +ey+++ +e ++++lvEe  +G Ef   ++   +G++
  gi|242398054|ref|YP_002993478.1| 143 KPVVVKPLGLTGGKGVKVVGYQ---------LKDN-EEA-KEYAKALIEkDGKVLVEERTDGVEFTFQVFT--DGKK 206
                                       6999999999999999988643.........3333.233.447777776589*****************98..8999 PP

                       ATP-grasp_4  79 vil 81 
                                       vi 
  gi|242398054|ref|YP_002993478.1| 207 VIP 209
                                       985 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.6
                       ATP-grasp_4  24 eeewkaavaaieeeleqakeeyke 47 
                                       +e++++a++++++ +   k++yke
  gi|242398054|ref|YP_002993478.1| 246 REDYHKALETLKKTV---KAMYKE 266
                                       689********9886...444444 PP

>> Peripla_BP_6  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   4.9e-05     0.073      45     110 ..      42     107 ..      35     200 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.9e-05
                                       EEEEE-TTSHHHHHHHHHHHHHCT--SEEEE-BSHHHHHHHHHHHHHHT-EEEESS-HHCCTTSTT CS
                      Peripla_BP_6  45 lverDdaydpdraaeaarrlvdqdgvdalvgplssavaaavaevlakdgvpvigpagltgekcspy 110
                                        ++ +++ + ++ ++++ ++  + +vd+ + +  s+  +++++vl+++g+p +gp+  + +  +  
  gi|242398054|ref|YP_002993478.1|  42 RITKEYGLTKETDVQKVLDFALKWNVDMAFIGPESPLEKGIVDVLEENGIPTVGPSKEAAQLETNK 107
                                       57889999999******************999**********************995554333222 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 ?   11.1   0.1   0.00012      0.18      16      85 ..     101     167 ..      91     188 .. 0.75
   2 ?   -1.6   0.0      0.87   1.3e+03     239     266 ..     268     294 ..     251     298 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00012
                       ATPgrasp_ST  16 fplvddKlkfkelalraglkvpkllgvikeqaeiseleafvkeleegvviKpakgsgGkGilviteredq 85 
                                       ++l  +K   ++++++  ++ +kl+ v+   ++++e++  + e+ + vv+Kp    gGkG+ v+  + ++
  gi|242398054|ref|YP_002993478.1| 101 AQLETNKAFARQIMEKYKIPGRKLFKVF---DDVAEMKTWIDEFGKPVVVKPLGLTGGKGVKVVGYQLKD 167
                                       4555699999999999999999988888...5777788889999667**************998543332 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.87
                       ATPgrasp_ST 239 lpglgylGwDivldeekgplllElNarp 266
                                       +p+ g+l   + l++++ p ++E Nar 
  gi|242398054|ref|YP_002993478.1| 268 TPYKGILYGQFMLANDE-PKIIEFNARF 294
                                       45555666667777777.*******995 PP

>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1    0.0001      0.15      12     100 ..     107     194 ..      97     206 .. 0.85
   2 ?   -2.5   0.0       1.9   2.8e+03      48      73 ..     331     356 ..     321     370 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0001
                       ATP-grasp_5  12 eaeakelleaygipvve.trlassaeeaveaaeeigypvvlKivspdilhKtdvgGvrlnlkdaeevraaaeeiler 87 
                                       +a a++++e y ip  + +++ ++++e    ++e+g pvv+K    +++  + v+ v  +lkd+ee ++ a++++e+
  gi|242398054|ref|YP_002993478.1| 107 KAFARQIMEKYKIPGRKlFKVFDDVAEMKTWIDEFGKPVVVKPL--GLTGGKGVKVVGYQLKDNEEAKEYAKALIEK 181
                                       55689*********98746889********************98..789999999999999************9999 PP

                       ATP-grasp_5  88 vkekspeariegv 100
                                         +   e+r +gv
  gi|242398054|ref|YP_002993478.1| 182 DGKVLVEERTDGV 194
                                       7777666666666 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.9
                       ATP-grasp_5  48 pvvlKivspdilhKtdvgGvrlnlkd 73 
                                         v+K v p+      ++Gv++++++
  gi|242398054|ref|YP_002993478.1| 331 ATVVKYVAPKGYPTDPIKGVKVQISE 356
                                       46777777777777777777777654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (435 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2749.73
//
Query:       gi|242398055|ref|YP_002993479.1|  [L=414]
Description: Archaeal ATPase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-05   25.4   0.0    2.6e-05   24.3   0.0    1.6  1  AAA_14           AAA domain
  ------ inclusion threshold ------
       0.01   16.1   0.2       0.38   11.0   0.2    2.5  1  AAA_22           AAA domain
      0.012   15.4   0.0      0.023   14.5   0.0    1.4  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.025   15.0   0.2        3.3    8.0   0.0    2.5  2  AAA_16           AAA ATPase domain
       0.13   11.9   0.0       0.23   11.2   0.0    1.3  1  AAA_24           AAA domain


Domain annotation for each model (and alignments):
>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   7.1e-09   2.6e-05       4      89 ..      18      99 ..      15     120 .. 0.66

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 7.1e-09
                            AAA_14  4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderd....kkladpekllelileklkeekktylflDEiqevpe 78
                                       +++ G R++GKT+l++++++        + ++n d   +     k+ +++++ +++l++l   +k+ +++DE +++p+
  gi|242398055|ref|YP_002993479.1| 18 WKMLYGRRKTGKTFLVQHFLEYDR-----FYFVNRDGTILdltsGKYMNYDEFRREFLDHL---GKEKIVIDEFHRLPD 88
                                      57899**************95555.....55555555333211122223334567777764...5667*********99 PP

                            AAA_14 79 wekalkslvde 89
                                       +  l + + +
  gi|242398055|ref|YP_002993479.1| 89 GFLDLLHAHST 99
                                      77666665554 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.2   0.00011      0.38       9      92 ..      20     102 ..      12     113 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00011
                            AAA_22   9 vvtGesGtGKTtllrrlleqldeeakaee....erpevvfvtlpsst..sskdllrellralglelkaerlsseell 79 
                                       +++G   tGKT+l++ +le +       +    +r+++   +l+s++  + ++++re+l  lg e+    ++ ++l 
  gi|242398055|ref|YP_002993479.1|  20 MLYGRRKTGKTFLVQHFLEYD-------RfyfvNRDGT-ILDLTSGKymNYDEFRREFLDHLGKEKIV-IDEFHRLP 87 
                                       688999999999999999976.......1233334443.44555554559999999999999988877.66666666 PP

                            AAA_22  80 ealeqalrarav..i 92 
                                       + + + l+a+++   
  gi|242398055|ref|YP_002993479.1|  88 DGFLDLLHAHSTldS 102
                                       777777777766554 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   6.3e-06     0.023      10      89 ..      28     101 ..      27     107 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.3e-06
                   Viral_helicase1  10 GKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEylllhaGyilllaal 85 
                                       GK+ l++++l+ +   ++    t+ +lt g       +  + d+f   ++++ +++ +++DE+ +l+ G ++ll+a+
  gi|242398055|ref|YP_002993479.1|  28 GKTFLVQHFLEYDrFYFVNRDGTILDLTSG-------KYMNYDEFRREFLDHLGKEKIVIDEFHRLPDGFLDLLHAH 97 
                                       999999999988554444444444444544.......44445555555555555789*******************9 PP

                   Viral_helicase1  86 skak 89 
                                       s+++
  gi|242398055|ref|YP_002993479.1|  98 STLD 101
                                       9875 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0   0.00093       3.3      28      57 ..      20      46 ..      10      66 .. 0.82
   2 ?    4.3   0.1     0.013        47     125     159 ..      68      98 ..      56     107 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00093
                            AAA_16 28 llsGesGvGKsslvrellralekdggiflr 57
                                      +l+G + +GK+ lv+++l+    d+++f++
  gi|242398055|ref|YP_002993479.1| 20 MLYGRRKTGKTFLVQHFLE---YDRFYFVN 46
                                      699***************6...55566655 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.013
                            AAA_16 125 rllallsrderplvlvlDdlqwadeaslqllaaLl 159
                                       ++l+ l + e+   +v+D+++++ ++ l+ll a  
  gi|242398055|ref|YP_002993479.1|  68 EFLDHLGK-EK---IVIDEFHRLPDGFLDLLHAHS 98 
                                       45577777.77...9***************87654 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   6.4e-05      0.23       6      54 ..      20      67 ..      18      93 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6.4e-05
                            AAA_24  6 liyGpsgiGKTtlakel..gpkplfidtekGlksldadkfpdieswedfld 54
                                      ++yG  ++GKT l+ ++   +++ f++ ++   +l   k+    ++++f+ 
  gi|242398055|ref|YP_002993479.1| 20 MLYGRRKTGKTFLVQHFleYDRFYFVNRDGTILDLTSGKYM---NYDEFRR 67
                                      79****************99**********99998888887...5555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       655  (0.036533); expected 358.6 (0.02)
Passed bias filter:                      572  (0.0319036); 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: 0.69u 0.32s 00:00:01.01 Elapsed: 00:00:00.53
# Mc/sec: 2335.61
//
Query:       gi|242398056|ref|YP_002993480.1|  [L=429]
Description: Phosphoribosylglycinamide formyltransferase 2 [Thermococcus sibiricus MM 739]
Scores for complete 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-55  186.5   0.0    5.8e-55  185.5   0.0    1.4  1  ATP-grasp        ATP-grasp domain
    3.1e-08   33.4   0.0    5.3e-08   32.6   0.0    1.4  1  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
    3.4e-08   33.3   0.0    5.5e-08   32.6   0.0    1.3  1  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
    0.00038   19.9   0.0    0.00088   18.7   0.0    1.6  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
    0.00081   19.2   0.0      0.002   17.9   0.0    1.7  1  GARS_A           Phosphoribosylglycinamide synthetase, ATP-gr
      0.005   16.3   0.0     0.0091   15.5   0.0    1.5  1  Epimerase        NAD dependent epimerase/dehydratase family
  ------ inclusion threshold ------
       0.11   12.6   0.0        0.2   11.7   0.0    1.6  1  ATP-grasp_3      ATP-grasp domain
       0.17   12.5   0.3        1.3    9.6   0.0    2.5  3  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas


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 !  185.5   0.0   2.6e-58   5.8e-55       2     170 ..     127     303 ..     126     304 .. 0.96

  Alignments for each domain:
  == domain 1  score: 185.5 bits;  conditional E-value: 2.6e-58
                                       HTTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC......GTTCEEEEE-- CS
                         ATP-grasp   2 eklglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal......keekvivEefv 72 
                                       +++++p++r++++++ +el +a+e++g+p++ K ++++++GkG+++v+ +ed+++a+e++      ++ k+ivEe++
  gi|242398056|ref|YP_002993480.1| 127 KEAKVPTSRYAYATTLDELYDACEKIGYPCHTK-AIMSSSGKGSYFVKGPEDIPKAWEVAkkkargSADKIIVEEHI 202
                                       6899*****************************.9*************************999999999******** PP

                                       --SEEEEEEEEE..ETTC-..EEE--EEEEEEETTEEEEEEECEE-SCHHHHHHHHHHHHHHHHHTSSEEEEEEEEE CS
                         ATP-grasp  73 pfekElsvlvvr..saeGe..tafypvvetvqedgilrlsvapaevsekaqkkaeeiakkiveeLggvGvfavElFv 145
                                       +f+ E++ l+vr  +++G+  t+f ++v+++q +g+++ s++pae+seka++++ +iak i++ Lgg+G+f+vE+Fv
  gi|242398056|ref|YP_002993480.1| 203 NFDIEITELAVRhfDENGKivTTFPKPVGHYQIEGDYHSSWQPAEISEKAEREVYRIAKAITDVLGGLGIFGVEMFV 279
                                       ************88889997778999*************************************************** PP

                                       ETTCT.EEEEEEESS--GGGGGHHHH CS
                         ATP-grasp 146 ledge.llvnElapRpHnsGhvtlda 170
                                       +  g+ +++nE++pRpH++G+vt+++
  gi|242398056|ref|YP_002993480.1| 280 K--GDkVWANEVSPRPHDTGMVTMAS 303
                                       *..555*****************986 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 !   32.6   0.0   2.4e-11   5.3e-08       7      95 ..     124     208 ..     118     268 .. 0.84

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 2.4e-11
                                       HHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHHHSTS-E CS
                       CPSase_L_D2   7 ealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaafgnkqv 83 
                                       +++k+++vp+ + + a  +tl+e +++ ++igyP+  ka ++  GkG+ +++  e++ ++ + a ++a+   + +++
  gi|242398056|ref|YP_002993480.1| 124 TLAKEAKVPTSRYAYA--TTLDELYDACEKIGYPCHTKAIMSSSGKGSYFVKGPEDIPKAWEVAKKKAR--GSADKI 196
                                       4567777777776666..9*************************************************7..67899* PP

                                       EEEE--SSSEEE CS
                       CPSase_L_D2  84 lvekslkgpkei 95 
                                        ve+ ++   ei
  gi|242398056|ref|YP_002993480.1| 197 IVEEHINFDIEI 208
                                       ***999865555 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 !   32.6   0.0   2.5e-11   5.5e-08      28     197 ..     145     317 ..     125     320 .. 0.81

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 2.5e-11
                                       HHHHHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHHHHTT....-SCEEEEE--..ESEEEEEEEEE.TSSCE CS
                   Dala_Dala_lig_C  28 lekveeelgypvfVKpareGSSvGvskveseeelkeaieeafky....dekvlvEeai..egreievavlg.nekle 97 
                                       l + +e++gyp+  K+  + S  G   v+  e++ +a e a k+      k++vEe i  +++  e av   +e+ +
  gi|242398056|ref|YP_002993480.1| 145 LYDACEKIGYPCHTKAIMSSSGKGSYFVKGPEDIPKAWEVAKKKargsADKIIVEEHInfDIEITELAVRHfDENGK 221
                                       4567899****************************9998877762222579******94333333566666445555 PP

                                       EEEEEEEE-SSSSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEEETTTEEEEEEEES CS
                   Dala_Dala_lig_C  98 vsevgeivvkkgfydyeakysddkaqlevpaklekeveekiqelalkaykaldlrGlaRvDfflteegeivlnEvNt 174
                                       +       +  g y++e  y     +   pa+++++ e+++  +a+ + ++l++ G+  v +f++  ++++ nEv +
  gi|242398056|ref|YP_002993480.1| 222 IV--TTFPKPVGHYQIEGDYH----SSWQPAEISEKAEREVYRIAKAITDVLGGLGIFGVEMFVK-GDKVWANEVSP 291
                                       43..345556699*******5....5677***********************************9.899******** PP

                                       S-...--STTSHHHHHHHCTT--HHH CS
                   Dala_Dala_lig_C 175 lP...GfTeiSlfpklakasGlefkk 197
                                        P   G+ ++   p+ +++ Gl+ ++
  gi|242398056|ref|YP_002993480.1| 292 RPhdtGMVTMASHPTGFSEFGLHVRA 317
                                       *9888999999999999999988766 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 !   18.7   0.0   3.9e-07   0.00088      38      74 ..      18      55 ..       6      75 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 3.9e-07
                                      EEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH.C CS
                      2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlkafgmkviaydrskkkee.e 74
                                      ++ ++G G++G+++a  ++ +g++via+dr++++ + +
  gi|242398056|ref|YP_002993480.1| 18 KIMLLGSGELGKEIAIEAQRLGVEVIAVDRYPNAPAmQ 55
                                      67789**************************9977622 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 !   17.9   0.0   8.9e-07     0.002       8      99 ..     124     213 ..     120     286 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 8.9e-07
                                       HHHHHTT--B--EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT-EEEESSHHHHHHHHHHHCTS-TTCCCCSSEE CS
                            GARS_A   8 dllkkagiptaeyeaftdpeeakeyieeatakalVvKadglaagKgvivakseeealkavkeilekkkfGeagekvv 84 
                                       +l k+a++pt++y+  t  +e+ +  e+ + +    Ka   ++gKg + +k  e+ +  + e+ +kk+ G + +k++
  gi|242398056|ref|YP_002993480.1| 124 TLAKEAKVPTSRYAYATTLDELYDACEKIGYPC-HTKAIMSSSGKGSYFVKGPED-IPKAWEVAKKKARG-SADKII 197
                                       57899***************************9.99*************998766.556678999999**.557889 PP

                                       EEE---.SEEEEEEEE CS
                            GARS_A  85 iEelle.GeEvsllal 99 
                                       +Ee ++  +E++ la+
  gi|242398056|ref|YP_002993480.1| 198 VEEHINfDIEITELAV 213
                                       9998752334443333 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0     4e-06    0.0091       6      70 ..      23      85 ..      19     158 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4e-06
                                      TTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE CS
                         Epimerase  6 atGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavih 70
                                      ++G +G+ ++ + ++ g+evi++dr+++a + +  +  + + ++++d++ l  ++++e+pda++ 
  gi|242398056|ref|YP_002993480.1| 23 GSGELGKEIAIEAQRLGVEVIAVDRYPNAPAMQVAH--KAYVGNMKDKDFLWSIVERENPDAIVP 85
                                      56999*********************9999988877..899**********************96 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   8.9e-05       0.2     104     158 ..     238     293 ..     120     296 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 8.9e-05
                                       EEEEEEES----H..HHHHHHHHHHHHTTSTT--EEEEEEEEESS.SEEEEEEESS- CS
                       ATP-grasp_3 104 vyaGnvtpietel..keevvelaeevvekleglaGyvGvDlvlkdeepyviEvNPRl 158
                                        y  +  p+e ++  ++ev+++a+ ++  l g +G++Gv++ +k ++    Ev PR+
  gi|242398056|ref|YP_002993480.1| 238 DYHSSWQPAEISEkaEREVYRIAKAITDVL-GGLGIFGVEMFVKGDKVWANEVSPRP 293
                                       556666666665544899************.999**********************8 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0    0.0006       1.3       1      32 [.      18      49 ..      18      58 .. 0.91
   2 ?   -2.7   0.0       4.2   9.4e+03      38      54 ..     204     220 ..     196     225 .. 0.80
   3 ?   -1.3   0.0       1.5   3.3e+03      51      73 ..     382     404 ..     379     413 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0006
                                      EEEEECSSHHHHHHHHHHHHTTSEEEEEESSS CS
                         Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversd 32
                                      k++ +G+G +g E A ++++lg +V  v+r +
  gi|242398056|ref|YP_002993480.1| 18 KIMLLGSGELGKEIAIEAQRLGVEVIAVDRYP 49
                                      57889*********************999865 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4.2
                                       SSHHHHHHHHHHHHHTT CS
                         Pyr_redox  38 lDeeaskilqeklekng 54 
                                       +D e+ ++  +++ +ng
  gi|242398056|ref|YP_002993480.1| 204 FDIEITELAVRHFDENG 220
                                       89999999999999987 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.5
                                       HHTTEEEECSEEEEEEEEETTSE CS
                         Pyr_redox  51 ekngievllntkveeiegsedgv 73 
                                       +++g+++ ++++v+  + ++++v
  gi|242398056|ref|YP_002993480.1| 382 RRLGVTLAWDSNVQVAKRKAEQV 404
                                       56799999999999888877763 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 2745.45
//
Query:       gi|242398057|ref|YP_002993481.1|  [L=350]
Description: phosphoribosylaminoimidazole synthetase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-25   90.2   0.0      3e-25   89.2   0.0    1.5  1  AIRS_C    AIR synthase related protein, C-terminal domain
    8.6e-19   68.0   1.1    1.4e-18   67.3   1.1    1.3  1  AIRS      AIR synthase related protein, N-terminal domain
  ------ inclusion threshold ------
      0.097   12.6   0.0        2.1    8.3   0.0    2.3  2  DUF4478   Pyrimidine/purine nucleotide 5'-monophosphate nucle


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 !   89.2   0.0     5e-29     3e-25       2     151 ..     188     341 ..     187     344 .. 0.87

  Alignments for each domain:
  == domain 1  score: 89.2 bits;  conditional E-value: 5e-29
                                       TTEEEEEEETSSCTCCHHHHHHHCHHHCTSHTT...TSEHHHHHHHHHHHHHHHHHHHH.HTTECEEEE--TTHHHH CS
                            AIRS_C   2 pGdvliltgslGlggagtslkrkileeegldds...avqlgdvlleptliyvkralaal.kglvkaahDvTgGGLlg 74 
                                       pGd++i++ s+G++++g+ l+rk+l ++   +    +++l ++llept+iyvk+ l +l + +v++++++TgGGLl+
  gi|242398057|ref|YP_002993481.1| 188 PGDAVIGISSSGIHSNGLTLARKLLIPKYGLEYefeGKKLWEHLLEPTRIYVKAVLELLkRVEVHGLAHITGGGLLN 264
                                       9*************************99765448*8888************************************95 PP

                                       HHHHHHHTTTEEEEEECG....THHHHHHHH.....HHHHHHHCSTTTEEEEEEEHGGH.HHHHHHHHHTTCCCEEE CS
                            AIRS_C  75 alaemapasgvgaeidld....kvpifdele.....splemllsensGrllvavppeea.davlaileeeglpeaav 141
                                        l+++      g+ ++++      ++             em++++n+G+++v+v+ e++ + +l++l+++  p   +
  gi|242398057|ref|YP_002993481.1| 265 -LKRLTS---YGFSLEMPpisgIFKL----IhengvPLDEMFKVFNMGVGFVVVVDEKDkEDALETLNKHY-P-SFE 331
                                       .899955...6788888844444444....44555999*******************************95.5.*** PP

                                       EEEEEESSSE CS
                            AIRS_C 142 IGevtakeel 151
                                       IG+vt++++ 
  gi|242398057|ref|YP_002993481.1| 332 IGKVTEDKGI 341
                                       ******9854 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 !   67.3   1.1   2.4e-22   1.4e-18       5      94 .]      73     175 ..      57     175 .. 0.91

  Alignments for each domain:
  == domain 1  score: 67.3 bits;  conditional E-value: 2.4e-22
                                       EEEEEEEEE.EECCTCCCC....HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC.....HHHHHHHHHHHHHHHTT-E CS
                              AIRS   5 vvvttdshnrpvlvepvhf....iGakavavnlsDlaamGArPlalllslalp.....wleevvrglaeaaeelgvp 72 
                                       +++ttd++++++lv++  +    iG  ++a+n++Dl++ GA+P+al+++la+       ++e+++g+ e+a++ g++
  gi|242398057|ref|YP_002993481.1|  73 LAMTTDGVGTKTLVAEAVGkydnIGVDMIAMNVNDLICLGAEPVALVDYLAVRepdeeVFQEIAKGIYEGAKQSGIA 149
                                       599***********887778888****************************************************** PP

                                       EEEEEEEEESS....EEEEEEEEEEE CS
                              AIRS  73 lvgGdtsfsne....ptisvtavGlv 94 
                                       +vgG+t++ +e    + ++ ta+G+v
  gi|242398057|ref|YP_002993481.1| 150 IVGGETAVLPElvngFDLAGTAIGVV 175
                                       *******9999999999*******97 PP

>> DUF4478  Pyrimidine/purine nucleotide 5'-monophosphate nucleosidases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.04   2.4e+02       2      36 ..     236     270 ..     235     273 .. 0.86
   2 ?    8.3   0.0   0.00035       2.1      39      72 ..     310     343 ..     287     346 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.04
                                       EE--SSS-----HHHHHTTSTSSSCHHHHHHHHHH CS
                           DUF4478   2 kispkgslellsqleverlkdsseselyelfRnca 36 
                                       +i  k  lell ++ev+ l + + ++l +l R ++
  gi|242398057|ref|YP_002993481.1| 236 RIYVKAVLELLKRVEVHGLAHITGGGLLNLKRLTS 270
                                       5777889**************99999999988665 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00035
                                       HHTTT----SSSTTCGTTTT-EEEEEEETTEEEE CS
                           DUF4478  39 vLnsgsetDdskellekykdFdikvlqkerGikl 72 
                                       v++   ++D  ++l ++y +F+i  +++++Gi +
  gi|242398057|ref|YP_002993481.1| 310 VVDEKDKEDALETLNKHYPSFEIGKVTEDKGIIV 343
                                       566677889999999****************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); 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: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 2222.67
//
Query:       gi|242398058|ref|YP_002993482.1|  [L=233]
Description: Phosphoribosylaminoimidazole-succinocarboxamide synthase [Thermococcus sibiricus MM 739]
Scores for complete 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  234.6   0.3    1.4e-69  234.5   0.3    1.0  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 !  234.5   0.3     8e-74   1.4e-69       2     250 ..       7     229 ..       6     231 .. 0.96

  Alignments for each domain:
  == domain 1  score: 234.5 bits;  conditional E-value: 8e-74
                                       EEE-SSEEEEE-SSTTEEEEEEESEEEECCCTEEEEETTHHHHHHHHHHHHHHHHHH..--BSEEEE.....-SSSE CS
                       SAICAR_synt   2 lyeGKvrdvYeledddklllvakDrisAfdvvlkeeipgKGkvltqlsafwfeklek..ipnhliksldpeqlegrs 76 
                                       +yeGK+++v  l dd k+++++kD+++Af++++k +++gKG ++ q+sa++f++le+  i++h+i         +++
  gi|242398058|ref|YP_002993482.1|   7 IYEGKAKKVIPL-DDGKVIIEFKDDATAFNGKKKAQFKGKGWLNAQISAILFKVLEEkgIKTHFIGV-----AGDNK 77 
                                       8**********9.888****************************************558******44.....689** PP

                                       EEEE-EEEESEEEEEEEE--HHH.......HH....HH..T--TT-EEEEEEEEEEE--CCCT.S-EE-HHHHH.HT CS
                       SAICAR_synt  77 mlvkklkmlpvEvvvRgyltGslwkeykksgkvcgirlpeglkegeklpepiftpstKaeegehDeniseeevveal 153
                                       ++v+klkm+pvEvvvR++++Gsl       +k    rl   lkeg++l+epi+++++K+++++ D++i++ ++   l
  gi|242398058|ref|YP_002993482.1|  78 LIVEKLKMYPVEVVVRNVIAGSL-------KK----RL--PLKEGTELSEPIVELYYKNDDLG-DPMINHYHAK-VL 139
                                       ***********************.......88....89..9*********************9.*********8.89 PP

                                       T.-HHHHHHHHHHHHHHHHHHHHHHHHTTEEEEEEEEEEEEETTTTEEEEES--.STTTEEEEETTT.....GGGB- CS
                       SAICAR_synt 154 g.teeeaeeieelalavyekaaelaaergiilvDtKlEFGldeedgelvLaDevltpDssRfwdaetyeegkeqesl 229
                                       g +e+e++eie++al+v+++++e++a+rgiilvD+KlEFG++e  ge++L+De+ +pD++Rfwdaet      +esl
  gi|242398058|ref|YP_002993482.1| 140 GvSERELKEIENIALKVNNILKEYFAQRGIILVDFKLEFGKNE-RGEIILGDEI-SPDTCRFWDAET------KESL 208
                                       999***************************************6.9*********.************......9*** PP

                                       STHHHHTT-STHHHHHHHHHH CS
                       SAICAR_synt 230 DKqfvRdwleeveekwkekle 250
                                       DK+++R + +e  ++++e  +
  gi|242398058|ref|YP_002993482.1| 209 DKDVFRFDKGELINAYEELYK 229
                                       ************999998665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); 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: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1515.76
//
Query:       gi|242398059|ref|YP_002993483.1|  [L=443]
Description: Amidophosphoribosyltransferase [Thermococcus sibiricus MM 739]
Scores for complete 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-19   68.6   0.0    6.7e-19   68.0   0.0    1.3  1  GATase_7      Glutamine amidotransferase domain
      3e-17   63.1   0.0    7.8e-17   61.7   0.0    1.7  2  GATase_6      Glutamine amidotransferase domain
      1e-08   34.4   0.0    1.6e-08   33.8   0.0    1.3  1  GATase_4      Glutamine amidotransferases class-II
    1.6e-08   34.2   0.0    3.4e-08   33.2   0.0    1.5  1  Pribosyltran  Phosphoribosyl transferase domain
  ------ inclusion threshold ------
      0.045   13.2   0.2       0.15   11.5   0.0    1.8  2  PRTase_2      Phosphoribosyl transferase
       0.13   11.0   0.0        9.2    4.8   0.0    2.6  3  GATase_2      Glutamine amidotransferases class-II


Domain annotation for each model (and alignments):
>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.0   0.0   2.2e-22   6.7e-19       1     122 [.      72     199 ..      72     200 .. 0.90

  Alignments for each domain:
  == domain 1  score: 68.0 bits;  conditional E-value: 2.2e-22
                          GATase_7   1 hrrlsiidseagaQPmvs.sedgrlvivfnGeiyNykelreeLeakghrfrtksDtevllallea.........ewg 67 
                                       h r s+  s ++ QP+ +  +++++++++nG+++N+  lr+++e+kg++fr + D+e+l   + +         e +
  gi|242398059|ref|YP_002993483.1|  72 HVRYSTSGSLNETQPLETsCHGKKIAVAHNGTLTNFLPLRRKYEKKGVKFRHSVDSELLGISFLWhlretgdefEAM 148
                                       678888889999*****9668999**********************************744333357889******* PP

                          GATase_7  68 eealerlnGmfAfaiwdeeekrlllaRDrlGikPLyygedkgdallfaSelkall 122
                                       +e++++++G +++a + + +  +l+aRD++G++PL yg  +  + +faSe +al+
  gi|242398059|ref|YP_002993483.1| 149 REVFNEVKGAYSVAFLFDGK--ILVARDPVGFRPLSYGIGD--GHYFASEDSALR 199
                                       ****************9988..*****************95..79******9995 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.7   0.0   2.6e-20   7.8e-17      11     134 .]      65     194 ..      52     194 .. 0.88
   2 ?   -3.2   0.0       2.9   8.8e+03     102     125 ..     207     230 ..     204     241 .. 0.74

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 2.6e-20
                          GATase_6  11 edevalaHvRlaivglaeeegaqPf..psedgrlllvhNGeiynykelreelpalkglafrsrsDtevllall.... 81 
                                       ++++++aHvR +++g    ++ qP+  + + ++++++hNG+  n+  lr+++++ kg++fr  +D+e+l   +    
  gi|242398059|ref|YP_002993483.1|  65 KSNMVIAHVRYSTSGSL--NETQPLetSCHGKKIAVAHNGTLTNFLPLRRKYEK-KGVKFRHSVDSELLGISFlwhl 138
                                       5679************6..667***76667777*********************.*************988555799 PP

                          GATase_6  82 eelG......eevlerlrGmfafaiwdkrentlilardrlgvkplyyavdesglafase 134
                                       +e+G       ev+++++G++++a+     +++ +ard +g +pl+y++ ++g +fase
  gi|242398059|ref|YP_002993483.1| 139 RETGdefeamREVFNEVKGAYSVAFLF--DGKILVARDPVGFRPLSYGI-GDGHYFASE 194
                                       899989889888999****99999876..899999*************8.99999**98 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2.9
                          GATase_6 102 dkrentlilardrlgvkplyyavd 125
                                       d ++++++l+ d++ +k l+   +
  gi|242398059|ref|YP_002993483.1| 207 DVAPGEVFLISDDVENKVLVKEKH 230
                                       557889999999999998876654 PP

>> GATase_4  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.0   5.5e-12   1.6e-08      60     166 ..      52     155 ..      43     175 .. 0.69

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 5.5e-12
                          GATase_4  60 laelvreyp...iksknvvaHiRkatqGevklenthpFvRelwgrewifAHnGdlkeykpklegrfePvG.....sT 128
                                       ++e+ r ++   +ks++v+aH+R  t G+  l++t+p   + +g+++  AHnG+l+++ p +  ++e  G     s 
  gi|242398059|ref|YP_002993483.1|  52 VSEVFRGNElsrLKSNMVIAHVRYSTSGS--LNETQPLETSCHGKKIAVAHNGTLTNFLPLR-RKYEKKGvkfrhSV 125
                                       6666666654458**************97..679***********************98877.23333332222267 PP

                          GATase_4 129 DsElafCelleelasrfekaepsaeeleralaelakei 166
                                       DsEl    +l +l+++         + ++a++e+++e+
  gi|242398059|ref|YP_002993483.1| 126 DSELLGISFLWHLRETG--------DEFEAMREVFNEV 155
                                       88877777776666655........2344444444444 PP

>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   0.0   1.1e-11   3.4e-08      79     120 ..     320     368 ..     258     374 .. 0.71

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 1.1e-11
                                       ........EE----TTSEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEE CS
                      Pribosyltran  79 s.......rlledpagkkVliVDDildtGgTllaalelLkekgpeevri 120
                                                  e++ gk+V+++DD +  G+T+++++  L+++g++ev++
  gi|242398059|ref|YP_002993483.1| 320 LkvklklsPVREIVSGKRVVLIDDSIVRGTTMRRIVAMLRKAGAKEVHV 368
                                       3445555567899********************************8875 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.55   1.7e+03      94     118 ..     222     246 ..     217     254 .. 0.76
   2 ?   11.5   0.0     5e-05      0.15     120     155 ..     334     370 ..     323     372 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.55
                          PRTase_2  94 elleFeEeHSHAtdhllyaedeell 118
                                       + +  +E+H H +   +y ++++ +
  gi|242398059|ref|YP_002993483.1| 222 NKVLVKEKHHHCVFEYIYFARPDSV 246
                                       556679*******999997777655 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 5e-05
                          PRTase_2 120 aakelvLvDDEistGktalnliralqeklpr.kryvv 155
                                       + k++vL+DD i  G+t+ +++  l+++  +  ++ +
  gi|242398059|ref|YP_002993483.1| 334 SGKRVVLIDDSIVRGTTMRRIVAMLRKAGAKeVHVRI 370
                                       5678*******************99998766355555 PP

>> GATase_2  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.22   6.5e+02      13      36 ..      11      34 ..       5      37 .. 0.80
   2 ?    4.8   0.0    0.0031       9.2     198     234 ..      61     103 ..      47     128 .. 0.72
   3 ?    2.7   0.0     0.014        42     336     404 ..     164     228 ..     143     236 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.22
                                      -BSHHHHHHHHHHHHGGGGS-B-T CS
                          GATase_2 13 kshkivekalealenleHRGavga 36
                                      k+++  +ka  al  l+HRG  +a
  gi|242398059|ref|YP_002993483.1| 11 KTENASKKAYYALIALQHRGQESA 34
                                      55666789999*********8776 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0031
                                       STT--BSEEEEEE---S.....SSS--GGGSSS-SS.EEEEE- CS
                          GATase_2 198 deelesalalvHsRfst.....ntfPsWelaqPlRl.laHnGE 234
                                        ++l+s++++ H R+st      t P  +  +  ++ +aHnG 
  gi|242398059|ref|YP_002993483.1|  61 LSRLKSNMVIAHVRYSTsgslnETQPLETSCHGKKIaVAHNGT 103
                                       5789************933333356666666655543567765 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.014
                                       EE-SSEEEEEE-TT--S--EEEEETT--EEEESSTTSS---GGGEEEEEE--TT-EEEE..ETTTTEEEEH CS
                          GATase_2 336 ftdGkvvgavLDRnGLRPaRylvtkddlvvlasEvGvldleeeevvekgrlqPGrmllv..dleegriled 404
                                       + dGk++ a  D  G RP  y + + ++  +asE   l l  e++     + PG+++l+  d+e++ ++++
  gi|242398059|ref|YP_002993483.1| 164 LFDGKILVAR-DPVGFRPLSYGIGDGHY--FASEDSALRLFVEDIR---DVAPGEVFLIsdDVENKVLVKE 228
                                       4699999886.99*********988775..69********999996...599****999655666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (443 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); 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:                         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: 00:00:00.50
# Mc/sec: 2674.94
//
Query:       gi|242398060|ref|YP_002993484.1|  [L=676]
Description: Formate dehydrogenase [Thermococcus sibiricus MM 739]
Scores for complete 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-89  301.2   0.0    1.5e-89  300.9   0.0    1.1  1  Molybdopterin    Molybdopterin oxidoreductase
    2.6e-21   75.7   0.0    4.6e-21   74.9   0.0    1.4  1  Molydop_binding  Molydopterin dinucleotide binding domain
    7.7e-08   32.2   0.2    1.6e-07   31.2   0.2    1.5  1  Molybdop_Fe4S4   Molybdopterin oxidoreductase Fe4S4 domain


Domain annotation for each model (and alignments):
>> Molybdopterin  Molybdopterin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  300.9   0.0   2.6e-93   1.5e-89       1     431 [.      58     479 ..      58     480 .. 0.92

  Alignments for each domain:
  == domain 1  score: 300.9 bits;  conditional E-value: 2.6e-93
                                       B--S-EEECTTTTTSEEEE--HHHHHHHHHHHHHHHHHHCSGGGEEEEEBTSSCSHHHHHHHHHHHHHTT-EEE-BE CS
                     Molybdopterin   1 RlkyPmvRkqargeGkFvrvsWdeAleliaaslkytikkygpdrvagfssgplmsmeslaslkkllsllggknlsfy 77 
                                       R+k+P++R   + ++ +++++W +A e+i+++l+++++ ygpd+va f+s++ +s+e+ ++l+k ++l+g    +++
  gi|242398060|ref|YP_002993484.1|  58 RVKRPLKR---N-RNALKPITWGQAIEEISHKLLEIREVYGPDAVA-FISSSKISNEENYLLQKIARLFGT---NNI 126
                                       9*******...6.8********************************.88889999**************99...899 PP

                                       ECCGGGTTHHHH....CHHCCCCCTTTS-SS-CCGGGG-SEEEEESS-HHHHSHHHHHHHHHHHHTTC-EEEEECSS CS
                     Molybdopterin  78 dwyadlppasaq....qtigsdsrsnyessnpledlensdliilwGsNvreerpilnarirkaalkkkakvivigpr 150
                                       d++a+ ++ + +    +tig++ +     +np ed+en ++i++wG N++e++p+  ++ +k+a+k++ak+iv++ r
  gi|242398060|ref|YP_002993484.1| 127 DNCARICHEASVhalkTTIGTGTQ-----TNPYEDIENFGAILIWGYNPAETHPVI-IHYIKKAKKRGAKIIVVDIR 197
                                       999999998888566666666544.....779************************.9********9********** PP

                                       B-HCGGGCSEEEEEHTTTHHHHHHHHHHHHHHCCCCTCHHHHHHEECHHHCCCCCCCEECCSHHHHHHCCHHHHHHH CS
                     Molybdopterin 151 yaellkfadewlaikpgtdaalalamghvilqelkvdkeflrkytygkeetdmpllvtleeetgkkkevvariarel 227
                                        + +++ ad    ikpgtd  la+a+++vi++e ++++ef++++t+g+ e++m + ++++e  ++k + v ++ ++ 
  gi|242398060|ref|YP_002993484.1| 198 ETITMNLADYKFVIKPGTDIVLANAIMNVIIREELYNEEFIKNRTTGFSEVRMAVMKYTPE-YAEKVTGVPATLIQK 273
                                       ***8899******************************************************.566666666666666 PP

                                       HHHHHHHTSSEEEEECHHHHTSTTHHHHHHHHHHHHHHCTHCSSTTCEEEEESSCTTHHHCHHHHTCCTTCCCCCCC CS
                     Molybdopterin 228 arnaaktagksmiivGaglnhrqdgdaiyravinLallvgnvgqpgGgwahlnGqlilagaaekvgalpvllsvksl 304
                                       a++ ++ ag+ +i++G+g++++ +g +++ a+in+all+g +g+ gG    ++Gq++++g a+ +gal+  l+ +  
  gi|242398060|ref|YP_002993484.1| 274 AAREFALAGSGAIMWGMGVTQHVSGVENVLAIINIALLLGYIGNRGGL-YPMRGQNNVQG-AAYMGALSEFLPGYIP 348
                                       6666667777*********************************97655.56699******.9999999877777777 PP

                                       TT....HHHHHCCCTTTCSTSS--ECGGCHHHHHHTTSSSEEEEESH.HHHHSTTSCCCHCHHHCSSEEEEEESCSS CS
                     Molybdopterin 305 ke....ekikfaaeqpgnlgnfprnlfversnllkssgkkvlyllgnnpevdhadenevekalekldlvvvldgrlt 377
                                        e    +k  +  ++ +n++   +  ++e  +++++ ++k+ly++g+np v+ a+ ++v kal+kldl++v d ++t
  gi|242398060|ref|YP_002993484.1| 349 LEdekfRKRVASLWGVENIPIERGLYLTEVWDAIERDDIKALYIIGENPAVSEANFGRVRKALRKLDLLIVQDLFIT 425
                                       7798888888889**************************************************************** PP

                                       HHHHTSSEEEEBE-CCGSEEEEE-TTSEEEEEEESSS-STT-BEHHHHHHHHHH CS
                     Molybdopterin 378 stalyaDiiLPaatwyEkedlytndegrfqhlkqavsppgeaksdwkIlkaLak 431
                                       +ta+ya++iLPa+++ Ek++ y+n+e+r+q  +++ +p  ++k+dwkIl  L k
  gi|242398060|ref|YP_002993484.1| 426 KTARYAHYILPASAFCEKDGSYMNSERRIQWSEKVLEPLNDSKPDWKILTMLGK 479
                                       ************************************************998865 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.9   0.0   7.7e-25   4.6e-21       1     108 [.     558     656 ..     558     659 .. 0.92

  Alignments for each domain:
  == domain 1  score: 74.9 bits;  conditional E-value: 7.7e-25
                                       EEEEEE-BTTBSTTTTTCGCCHHHHCSSS.-EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEESSB-TTEEEE CS
                   Molydop_binding   1 lrLitgrsldqlhsqtrtrpvlrlakpep.evveinpedAaalGikdGdlVevesrrGsvevrakvtervrpGvvfm 76 
                                       ++L+t+r   +++++ +t ++++l k  + + ++in+edA+ l+i+d+dlVe+e+rrG++++rak+ + v++Gvv++
  gi|242398060|ref|YP_002993484.1| 558 FALTTVRLISHYNTGEMTLRSPSLTKLMGePKILINAEDAKYLEIEDNDLVEIETRRGKIRMRAKIGK-VARGVVAV 633
                                       78*******************9999999999*************************************.******** PP

                                       ESSHCC.....S-GHCTS--SCSTTT--CSTT CS
                   Molydop_binding  77 pfgwweagekggnaNaltddatdplsgtpefk 108
                                       pf++ +        N++t   +   +gtpefk
  gi|242398060|ref|YP_002993484.1| 634 PFHFKA--------NKIT-NNALNKAGTPEFK 656
                                       ****66........9999.5555567888887 PP

>> Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.2   2.7e-11   1.6e-07       7      52 ..      11      52 ..       6      55 .. 0.81

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 2.7e-11
                                      E-SSBTT--EEEEEEETTEEEEEEE-TTSTTTTT---HHHHTCHHC CS
                    Molybdop_Fe4S4  7 aCpyCgvgCglevhvkdgkivkvegdpdhpvnegrlCvKGrtller 52
                                      +CpyCg gC+l+v +++  ++  +g p    n+grlC+KG  ++e+
  gi|242398060|ref|YP_002993484.1| 11 VCPYCGFGCKLLVDPQTLIVKPYRGEP----NRGRLCPKGLYAMEF 52
                                      7************99877666555555....9********999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (676 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       655  (0.036533); expected 358.6 (0.02)
Passed bias filter:                      602  (0.0335769); 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: 0.72u 0.36s 00:00:01.08 Elapsed: 00:00:00.53
# Mc/sec: 3823.70
//
Query:       gi|242398061|ref|YP_002993485.1|  [L=256]
Description: metal-dependent phosphohydrolase, HD superfamily [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.1e-09   35.6   0.1    1.5e-08   34.9   0.1    1.4  1  HD        HD domain
  ------ inclusion threshold ------
       0.16   12.4   0.2       0.49   10.8   0.1    1.8  2  DUF1935   Domain of unknown function (DUF1935)


Domain annotation for each model (and alignments):
>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.1   1.7e-12   1.5e-08       5     121 ..      63     171 ..      59     172 .. 0.90

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 1.7e-12
                                       HHHHHHHHHHHHHHHHH.......HHHHHHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHHHH CS
                                HD   5 sleVaklarrlaedlge.......eedrellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevekrl 74 
                                        leV+k++++++++          e  + ++ ++aL+HDiG++ ++d        +++ l  e + +e+++e+ek +
  gi|242398061|ref|YP_002993485.1|  63 ALEVLKILKKFGIETTAekldksiEWSKFIVAFGALFHDIGNMIHRD-----NHYQFSVLLAEPIIYELVKEFEKED 134
                                       68999999999999988999999999999***************998.....3337788999*************** PP

                                       HHH.HHHHHHHHHTTCCHHHHHHHHHHHHCCTSCHHHHHHHHHHHHHH CS
                                HD  75 gld.ledvaklirehheswegkkrprglaerqlslearivklaDrlaa 121
                                       +l    + +++i  h e  +             ++e  +vk+aD +++
  gi|242398061|ref|YP_002993485.1| 135 WLLlKALTLNAIYTHDEAVP-----------CTTIEGSCVKIADGCDM 171
                                       99999999999999999999...........99***********9986 PP

>> DUF1935  Domain of unknown function (DUF1935)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   5.4e-05      0.49      20      64 ..      17      61 ..       7      73 .. 0.87
   2 ?   -2.3   0.0      0.67     6e+03      20      34 ..     120     135 ..     106     137 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 5.4e-05
                                      ..SEEEEEETTTTEEEEEE--SSEEEEEEEEEETT-EEEE-TT-E CS
                           DUF1935 20 nglLfrivdekekrWaFYNDtkdyemkvtvsfgpksevkalgktt 64
                                      n  L+ + ++  k++  Y Dt++y +   ++f+++  +++l +t+
  gi|242398061|ref|YP_002993485.1| 17 NENLYSLYERAYKKYKHYFDTTNYIVLNIYQFNDHGAIHVLLTTR 61
                                      4679***********************99****999999887665 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.67
                                       ..SEEEEEETTT.TEE CS
                           DUF1935  20 nglLfrivdeke.krW 34 
                                       +++++++v+e e + W
  gi|242398061|ref|YP_002993485.1| 120 EPIIYELVKEFEkEDW 135
                                       4789999998752447 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       699  (0.0389871); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1733.51
//
Query:       gi|242398062|ref|YP_002993486.1|  [L=222]
Description: hypothetical protein TSIB_0069 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-43  148.1   0.0    2.6e-43  147.7   0.0    1.1  1  DUF5616   Domain of unknown function (DUF5616)
    6.7e-24   83.3   3.8    1.2e-23   82.5   3.8    1.4  1  DUF434    Protein of unknown function (DUF434)


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 !  147.7   0.0   2.9e-47   2.6e-43       3     139 ..      64     197 ..      62     198 .. 0.97

  Alignments for each domain:
  == domain 1  score: 147.7 bits;  conditional E-value: 2.9e-47
                           DUF5616   3 elkgkelliDGfNvlitlesalsgevlllcdDgviRDlagvrgkyklveeteealelilellkelkvkkvifllDkp 79 
                                        l+g+ + iDGfNvlitles+l+g+ ++lc+Dg++RDl++ rg y+l+e+t+++lel++ +l++++vk+v fl+D+p
  gi|242398062|ref|YP_002993486.1|  64 GLRGEIIGIDGFNVLITLESLLEGK-AILCEDGFLRDLKHQRG-YRLHENTSKILELLVGFLSNIGVKEVWFLYDSP 138
                                       58999********************.99***********8877.********************************* PP

                           DUF5616  80 vSnSgelaklireileeaglegevelvknvDkeLkeseeivatsDsvildkvksvldlaa 139
                                       vS+Sge+a+l++ei+ + +++g+vel+k +D++Lk++e  va+sD ++++kv  v+d+++
  gi|242398062|ref|YP_002993486.1| 139 VSRSGEIANLTEEIMVNFKVPGKVELSKAPDHDLKRFEV-VASSDIAVIQKVPLVVDIPK 197
                                       *************************************98.******************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 !   82.5   3.8   1.3e-27   1.2e-23       2      56 .]       4      58 ..       3      58 .. 0.97

  Alignments for each domain:
  == domain 1  score: 82.5 bits;  conditional E-value: 1.3e-27
                            DUF434  2 LkeAaeDlryLLnRGYpkksalelVgnhYqLskrqRlaLaRcvssdeeiearksK 56
                                      L  A+eDl+yLLnRGY+kk ale+V+nhY+L++++R +L Rcv+sd+eie+rk+K
  gi|242398062|ref|YP_002993486.1|  4 LLLAYEDLKYLLNRGYRKKYALEFVANHYLLTSKERYFLMRCVFSDREIEERKRK 58
                                      778**************************************************98 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:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1506.89
//
Query:       gi|242398063|ref|YP_002993487.1|  [L=362]
Description: hypothetical protein TSIB_0070 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       897  (0.0500307); expected 358.6 (0.02)
Passed bias filter:                      598  (0.0333538); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 2575.66
//
Query:       gi|242398064|ref|YP_002993488.1|  [L=213]
Description: hypothetical protein TSIB_0071 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-24   86.4   0.0    2.4e-24   85.8   0.0    1.3  1  DUF432    Protein of unknown function (DUF432)


Domain annotation for each model (and alignments):
>> DUF432  Protein of unknown function (DUF432)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.8   0.0   1.3e-28   2.4e-24       1     123 []      51     165 ..      51     165 .. 0.94

  Alignments for each domain:
  == domain 1  score: 85.8 bits;  conditional E-value: 1.3e-28
                            DUF432   1 PvnlpkeitkyllveleeplvvepkseveiyvkvpveigvfikskkeveliDvfslskkkYaLYGspesGviaryvk 77 
                                       P  + ++ +++l+v+++epl+v+p+++   +++ p+ei v +        +D + + ++kYaLYG  e Gvi+ry+ 
  gi|242398064|ref|YP_002993488.1|  51 PAPATGYGVRLLMVKFKEPLIVSPHDSLAGFIEAPIEIDVKVG----GLSVDHLLVGREKYALYGALEAGVICRYHV 123
                                       5566778899*******************************77....367*************************** PP

                            DUF432  78 sevyseppeldpleeavveleikNetdevvevskivfdalglklyy 123
                                       s  y ++    p + + ++l ++N + e++++++++++++++++yy
  gi|242398064|ref|YP_002993488.1| 124 SPFYLKE----PDSIGAAKLIVSNPSPEWKSLERVIIPIWKTSMYY 165
                                       *****95....567899****************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1503.38
//
Query:       gi|242398065|ref|YP_002993489.1|  [L=356]
Description: Small-conductance mechanosensitive channel [Thermococcus sibiricus MM 739]
Scores for complete 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-61  206.8   0.2      5e-61  205.9   0.2    1.5  1  MS_channel  Mechanosensitive ion channel
    1.5e-05   24.9   5.9     0.0012   18.7   1.9    3.4  3  TM_helix    Conserved TM helix
  ------ inclusion threshold ------
       0.41   10.9   2.6        1.9    8.8   0.2    2.9  3  DUF2530     Protein of unknown function (DUF2530)
        4.3    7.2  10.1         15    5.4   3.9    2.5  2  DUF2062     Uncharacterized protein conserved in bacteria (DU


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 !  205.9   0.2   1.1e-64     5e-61       2     206 .]     137     336 ..     136     336 .. 0.99

  Alignments for each domain:
  == domain 1  score: 205.9 bits;  conditional E-value: 1.1e-64
                                       .HHHHHHHHHHHHHHHHTTT--..SCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESSSEEEEE CS
                        MS_channel   2 kilkiliivvgilivlsllgvn..vsallavlGalglalglalkdlisnlvaGiillfekpfkiGDlveigdieGtV 76 
                                       ki+++l+i++++ i+l   g++  +s+lla++G++g++lg+ +++++sn+++Gi+++f+kp+kiGD ve+++ +G+V
  gi|242398065|ref|YP_002993489.1| 137 KIFYYLVITLAFFIALNIAGFSgkLSTLLAAAGITGIVLGFSAQTVVSNFISGIFMYFDKPLKIGDPVEVAGYSGIV 213
                                       89*************************************************************************** PP

                                       EEE-SSEEEEEETTSEEEEEEHHHHHTS-EEESSS.SSEEEEEEEEEE-TTS-...HHHHHHHHHHHHHH-TTB-TT CS
                        MS_channel  77 ediglrttkirtfdgrivtiPnsslvtsnieNlsresgtrrikvsigvtyssdvkklekvleelkealkekpevlkd 153
                                        di +++t+irt+dg +v iPn++l++s+i+Nl++  ++rr+++ +g++y++d   ++k+++++k+ l+e+p+vl +
  gi|242398065|ref|YP_002993489.1| 214 HDIRILSTRIRTWDGLLVRIPNEKLFNSEIKNLQK-YPARRVDIIVGIAYKED---AQKAIDVIKKTLDEMPYVLAE 286
                                       ***********************************.*****************...********************* PP

                                       S-EEEEEEEE-SSSEEEEEEEEEET...TTHHHHHHHHHHHHHHHHHHHT--- CS
                        MS_channel 154 kellvvldefgdsslnfevrvfvktvvpeeylsvqseinlrikkileeegiei 206
                                       +e++v++d++g+ss+++ vr+++++   e++++v+  i++r+kk+l+e+giei
  gi|242398065|ref|YP_002993489.1| 287 PEPMVFVDKLGASSVDIAVRAWAPS---EKWFEVRWRIVQRVKKALDEAGIEI 336
                                       *************************...***********************97 PP

>> TM_helix  Conserved TM helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   1.9   2.7e-07    0.0012      14      42 ..      23      51 ..      18      56 .. 0.84
   2 !    5.9   0.0    0.0028        12      15      37 ..      97     119 ..      94     125 .. 0.86
   3 ?   -2.1   0.4      0.91   4.1e+03      25      38 ..     174     187 ..     149     191 .. 0.60

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.7e-07
                                      HSHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          TM_helix 14 lPnLvgAilILlvGwiiAkfvsrlvtkll 42
                                      l+ +v A+l+L++G++iAk+++r + +l 
  gi|242398065|ref|YP_002993489.1| 23 LGAVVKALLVLVIGLLIAKLLRRYILNLS 51
                                      677899*****************997765 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0028
                                       SHHHHHHHHHHHHHHHHHHHHHH CS
                          TM_helix  15 PnLvgAilILlvGwiiAkfvsrl 37 
                                        nL+ A l++   +i+Ak  ++ 
  gi|242398065|ref|YP_002993489.1|  97 SNLLTAFLVFYFSYILAKKTKDY 119
                                       59****************87766 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.91
                                       HHHHHHHHHHHHHH CS
                          TM_helix  25 lvGwiiAkfvsrlv 38 
                                       ++G++  ++vs+ +
  gi|242398065|ref|YP_002993489.1| 174 VLGFSAQTVVSNFI 187
                                       33555555555555 PP

>> DUF2530  Protein of unknown function (DUF2530)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       1.2   5.6e+03      25      38 ..      71      84 ..      64     102 .. 0.56
   2 ?    8.8   0.2   0.00043       1.9      17      59 ..     141     183 ..     126     185 .. 0.81
   3 ?    0.4   0.0      0.17   7.6e+02       5      20 ..     279     294 ..     275     318 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.2
                           DUF2530 25 lvalvvllvvgdal 38
                                      l+a+++++ + dal
  gi|242398065|ref|YP_002993489.1| 71 LIAIIAVVYSLDAL 84
                                      55555555444443 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00043
                           DUF2530  17 ivvgtllWlvalvvllvvgdaleswlpvclaGlvvGllGlaif 59 
                                        +v+tl++++al ++ ++g+  + +    ++G+v+G+ + +++
  gi|242398065|ref|YP_002993489.1| 141 YLVITLAFFIALNIAGFSGKLSTLLAAAGITGIVLGFSAQTVV 183
                                       5799************9977777788889*******9988875 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.17
                           DUF2530   5 eLprrLtdprpvivvg 20 
                                       e+p +L++p+p++ v 
  gi|242398065|ref|YP_002993489.1| 279 EMPYVLAEPEPMVFVD 294
                                       89**********9885 PP

>> DUF2062  Uncharacterized protein conserved in bacteria (DUF2062)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.4    0.0039        18     110     142 ..      15      47 ..       3      53 .. 0.84
   2 ?    5.4   3.9    0.0035        15      55      93 ..      87     145 ..      69     195 .. 0.59

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0039
                           DUF2062 110 leiglplllGslilglilallgYflvlllwrly 142
                                       ++++l+l lG+++ +l++ ++g ++++ll r+ 
  gi|242398065|ref|YP_002993489.1|  15 ENLFLTLTLGAVVKALLVLVIGLLIAKLLRRYI 47 
                                       57899*****************99999988776 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0035
                           DUF2062  55 lpaavagtwisnPltlppiyylayklGalllgeeaeal.........................s 93 
                                       l   +agt +sn lt ++++y++y l +       +++                          
  gi|242398065|ref|YP_002993489.1|  87 LSYKIAGTSLSNLLTAFLVFYFSYILAKKT-----KDYlvrsssqkklpeaqikakifyylviT 145
                                       4566899*****************998877.....11224444444445555544444444432 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       937  (0.0522617); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); 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):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 2278.50
//
Query:       gi|242398066|ref|YP_002993490.1|  [L=205]
Description: DNA methylase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-14   53.5   0.0      3e-14   52.9   0.0    1.3  1  MTS              Methyltransferase small domain
    3.7e-14   52.8   0.2    5.2e-14   52.3   0.2    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
      3e-10   40.0   0.0    4.2e-10   39.6   0.0    1.3  1  Cons_hypoth95    Conserved hypothetical protein 95
    4.3e-10   39.6   0.0    5.6e-10   39.2   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    2.6e-07   31.2   0.0      8e-07   29.7   0.0    1.8  2  Methyltransf_25  Methyltransferase domain
    8.8e-07   28.8   0.3    2.8e-06   27.1   0.3    1.8  1  UPF0020          Putative RNA methylase family UPF0020
    2.7e-05   24.0   0.5    0.00014   21.7   0.1    1.8  2  Met_10           Met-10+ like-protein
    0.00011   22.8   0.0    0.00041   20.9   0.0    1.9  2  Methyltransf_11  Methyltransferase domain
    0.00025   20.5   0.0    0.00047   19.6   0.0    1.4  1  DNA_methylase    C-5 cytosine-specific DNA methylase
    0.00061   19.1   0.0    0.00097   18.4   0.0    1.3  1  DUF43            Branched-chain polyamine synthase A C-termin
    0.00086   18.9   0.0     0.0016   18.0   0.0    1.5  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
     0.0015   18.6   0.0     0.0018   18.3   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
     0.0015   18.5   0.1      0.003   17.5   0.1    1.4  1  Methyltransf_18  Methyltransferase domain
     0.0016   17.5   0.1     0.0026   16.8   0.1    1.3  1  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
      0.003   16.9   0.1     0.0046   16.3   0.1    1.2  1  GidB             rRNA small subunit methyltransferase G
     0.0078   15.5   0.0      0.018   14.3   0.0    1.5  1  N6_Mtase         N-6 DNA Methylase
     0.0092   15.3   0.0      0.011   15.1   0.0    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
  ------ inclusion threshold ------
      0.022   14.4   0.0      0.029   14.0   0.0    1.3  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
      0.023   15.4   0.0      0.048   14.4   0.0    1.6  1  Methyltransf_12  Methyltransferase domain
      0.047   13.4   0.1      0.066   12.9   0.1    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
      0.055   13.2   0.1      0.099   12.3   0.1    1.3  1  DUF3236          Protein of unknown function (DUF3236)
      0.059   13.2   1.3        0.2   11.4   1.3    1.7  2  N6-adenineMlase  Probable N6-adenine methyltransferase
      0.062   13.3   3.5         10    6.2   0.0    2.9  3  DUF4315          Domain of unknown function (DUF4315)
      0.081   12.7   0.1       0.14   11.9   0.1    1.4  1  Methyltransf_16  Lysine methyltransferase
       0.12   11.9   0.0       0.18   11.3   0.0    1.3  1  DOT1             Histone methylation protein DOT1


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 !   52.9   0.0   4.2e-17     3e-14      26     112 ..      42     126 ..      32     138 .. 0.82

  Alignments for each domain:
  == domain 1  score: 52.9 bits;  conditional E-value: 4.2e-17
                                       HCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTSTTS-EEEE CS
                               MTS  26 tlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvleeveekkfdli 101
                                        + + + + ++DlG+G+Gvl++ +  +  + +v +v++d++Ale+aken+e+ +++ +e+++ +v e ++ +++d++
  gi|242398066|ref|YP_002993490.1|  42 SMGDIEGKIIADLGAGTGVLSIGASLMGAK-KVYAVEKDKKALEIAKENAETLNIKnIEFLEVSVKE-FD-ARVDTV 115
                                       44444555689***********99887777.8***********************989999888754.55.8***** PP

                                       EE---STTTCH CS
                               MTS 102 vsNPPfhagka 112
                                       ++NPPf +++ 
  gi|242398066|ref|YP_002993490.1| 116 IMNPPFGSQNP 126
                                       ******88764 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.3   0.2   7.3e-17   5.2e-14     161     233 ..      47     118 ..      35     119 .. 0.87

  Alignments for each domain:
  == domain 1  score: 52.3 bits;  conditional E-value: 7.3e-17
                              PrmA 161 egeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseellkeekadvivaN 233
                                       eg+ + D+G+G+G+L+i+a+++gakkv+av  D+ A+++akeNae  ++++   + +s + ++ +++d ++ N
  gi|242398066|ref|YP_002993490.1|  47 EGKIIADLGAGTGVLSIGASLMGAKKVYAVEKDKKALEIAKENAETLNIKNIEFLEVSVKEFD-ARVDTVIMN 118
                                       567888****************************************99*99554666666666.889999988 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   0.0   5.9e-13   4.2e-10      37     127 ..      40     125 ..      32     169 .. 0.87

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 5.9e-13
                                       CCC...HCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--S CS
                     Cons_hypoth95  37 aae...iegarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakk 110
                                       a+    ieg+ + Dl aG+G+l++ A   gakk+++vekdk+a++i ken e+l++++   e+ e ++++++ +   
  gi|242398066|ref|YP_002993490.1|  40 AHSmgdIEGKIIADLGAGTGVLSIGASLMGAKKVYAVEKDKKALEIAKENAETLNIKN--IEFLEVSVKEFDAR--- 111
                                       55455599999********************************************997..77777777778666... PP

                                       S-EEEEEEE--SSSTTC CS
                     Cons_hypoth95 111 keefdivflDPPyakel 127
                                          +d v ++PP+ +++
  gi|242398066|ref|YP_002993490.1| 112 ---VDTVIMNPPFGSQN 125
                                       ...8*********9986 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2   0.0   7.8e-13   5.6e-10       5      84 ..      49     121 ..      46     174 .. 0.85

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 7.8e-13
                   Methyltransf_31   5 lrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsn 81 
                                       + + DlG+GtG l++ +  ++g  ++v+ ++ +++a+e A+ena+ l+++n+eF + ++ e++     +++D ++ n
  gi|242398066|ref|YP_002993490.1|  49 KIIADLGAGTGVLSIGAS-LMG-AKKVYAVEKDKKALEIAKENAETLNIKNIEFLEVSVKEFD-----ARVDTVIMN 118
                                       5689************99.665.699***********************************99.....889*99998 PP

                   Methyltransf_31  82 evl 84 
                                        ++
  gi|242398066|ref|YP_002993490.1| 119 PPF 121
                                       555 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.0   1.1e-09     8e-07       1      76 [.      51     123 ..      51     140 .. 0.83
   2 ?   -1.5   0.0       6.1   4.4e+03      66      90 ..     141     161 ..     129     163 .. 0.73

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 1.1e-09
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEEEST.GG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvssga.lh 75 
                                       + dlG+GtG l++ ++   g++kv++v+ ++++le+a+e+ae  ++ n+ef++ ++++++   +++D v+++   + 
  gi|242398066|ref|YP_002993490.1|  51 IADLGAGTGVLSIGASLM-GAKKVYAVEKDKKALEIAKENAETLNIkNIEFLEVSVKEFD---ARVDTVIMN-PpFG 122
                                       78***********99977.79********************998889********99985...678999995.4466 PP

                                       G CS
                   Methyltransf_25  76 h 76 
                                        
  gi|242398066|ref|YP_002993490.1| 123 S 123
                                       5 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 6.1
                                       EEEEEESTGGGSSHHHHHHHHHHHH CS
                   Methyltransf_25  66 Dlvvssgalhhlsdedlekalkeia 90 
                                       D+v+s+    hl +e+++k+++ + 
  gi|242398066|ref|YP_002993490.1| 141 DVVYSI----HLAKEEVRKFIEAFT 161
                                       667773....556778888888765 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.3     4e-09   2.8e-06      77     133 ..      71     123 ..      31     130 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 4e-09
                                       --EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE------ CS
                           UPF0020  77 lklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnpPYGe 133
                                        k+y++++d+++++ a+eNae  ++++ ief +  ++++    + vd+++ npP+G 
  gi|242398066|ref|YP_002993490.1|  71 KKVYAVEKDKKALEIAKENAETLNIKN-IEFLEVSVKEFD---ARVDTVIMNPPFGS 123
                                       358**********************87.566666999888...56***********7 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.1   1.9e-07   0.00014     100     177 ..      47     120 ..      38     125 .. 0.89
   2 ?   -0.1   0.0      0.95   6.8e+02      76      93 ..     137     154 ..     133     167 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.9e-07
                                       TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG---TT-EEEEEE-- CS
                            Met_10 100 egevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpileDgrevireqladrvvmnl 176
                                       eg+++ d+ AG G ++i ++    ak+v+a++++ ++ +  ken +  ++++ ++ ++  ++e+  +  +d v+mn 
  gi|242398066|ref|YP_002993490.1|  47 EGKIIADLGAGTGVLSIGASL-MGAKKVYAVEKDKKALEIAKENAETLNIKN-IEFLEVSVKEF--DARVDTVIMNP 119
                                       78999**************97.66788******************9888866.6799999****..6999*****97 PP

                                       T CS
                            Met_10 177 p 177
                                       p
  gi|242398066|ref|YP_002993490.1| 120 P 120
                                       6 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.95
                                       EETTTS---GGGHHHHHH CS
                            Met_10  76 lDvskvyfsskleaErer 93 
                                       +++s+v +s +l++E  r
  gi|242398066|ref|YP_002993490.1| 137 FEISDVVYSIHLAKEEVR 154
                                       788999999999988766 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   5.7e-07   0.00041       2      67 ..      53     117 ..      52     128 .. 0.92
   2 ?   -1.7   0.0       6.5   4.7e+03      69      86 ..     181     198 ..     173     202 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 5.7e-07
                                       EET-TTSHHHHHHHHTT.SEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-TT-EEEEEE CS
                   Methyltransf_11   2 dvGcGtGrlaealakrg.arvvgvDlskemlklakekaseegl.kvefvvadaeklpfednsfDlvvs 67 
                                       d+G+GtG l+      g ++v++v+ +k++l++ake+a++ ++ ++ef++ ++++  f d+ +D v++
  gi|242398066|ref|YP_002993490.1|  53 DLGAGTGVLSIGASLMGaKKVYAVEKDKKALEIAKENAETLNIkNIEFLEVSVKE--F-DARVDTVIM 117
                                       99************999************************9999*****99998..3.668888876 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 6.5
                                       S-CCC-CCHHHHHHHHHH CS
                   Methyltransf_11  69 evlhhvedpekalkeiaR 86 
                                       ++++h +++e++l  i+R
  gi|242398066|ref|YP_002993490.1| 181 QFFFHKKRLEQILVDIYR 198
                                       578888999999999999 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 !   19.6   0.0   6.6e-07   0.00047       4      70 ..      52     120 ..      50     121 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 6.6e-07
                                       EEES-TT-HHHHHHHHTT-EEEEEEE--TTTHHHHHHH-.-SEEEES-TTTS-..GS--.-SEEEE--- CS
                     DNA_methylase   4 idLfaGiGGfrlgleaagfecvaaseidkkaaktYeanfkkvsigDitkidkk..klpediDlLvgGfP 70 
                                        dL aG G +++g +  g + v+a+e+dkka ++ + n +  +i++i+ ++ +  ++ + +D ++  +P
  gi|242398066|ref|YP_002993490.1|  52 ADLGAGTGVLSIGASLMGAKKVYAVEKDKKALEIAKENAETLNIKNIEFLEVSvkEFDARVDTVIMNPP 120
                                       79**************************************99999999888777788888998887766 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 !   18.4   0.0   1.3e-06   0.00097      33     123 ..      36     122 ..      13     136 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.3e-06
                                       HHHHHHHTT-STT-EEEEES.-TT-HHHHHHHHT--SEEEEE-S-HHHHHHHHHHHHHHT--.EEEE---TTS---T CS
                             DUF43  33 RvallyerGDLegkeilvlG.dDDLtslalaLtglpkkvvvvDiDeRlikfiervakelglk.ieaivyDlrkplpe 107
                                        + l+++ GD+egk i  lG    + s+ ++L g +kkv  v+ D++ +++ ++ a+ l++k ie +   ++     
  gi|242398066|ref|YP_002993490.1|  36 LLWLAHSMGDIEGKIIADLGaGTGVLSIGASLMG-AKKVYAVEKDKKALEIAKENAETLNIKnIEFLEVSVK----- 106
                                       356899********9999**77889*******98.899********************99999998877775..... PP

                                       TTSS-BSEEEE---SS CS
                             DUF43 108 elkekFdvfitDPpet 123
                                       e+  + d++i +Pp +
  gi|242398066|ref|YP_002993490.1| 107 EFDARVDTVIMNPPFG 122
                                       5777788888888765 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   2.2e-06    0.0016       3      96 ..      50     136 ..      48     179 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.2e-06
                   Methyltransf_15   3 vilDlfsGaGGnviqfalv.fekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklklekikvdlvflS 78 
                                       +i Dl +G+G  +i   l+  +kv+a+e++++ l++a++Nae  +++ +i +   +v+e         ++vd v++ 
  gi|242398066|ref|YP_002993490.1|  50 IIADLGAGTGVLSIGASLMgAKKVYAVEKDKKALEIAKENAETLNIK-NIEFLEVSVKE-------FDARVDTVIMN 118
                                       67788888888888888875689*********************775.46665554443.......33346899999 PP

                   Methyltransf_15  79 pPwGGpsYkkqekfdlkk 96 
                                       pP G  + k +  f lk 
  gi|242398066|ref|YP_002993490.1| 119 PPFGSQNPKADRPFLLKA 136
                                       999988888887777744 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   2.5e-06    0.0018      27      95 ..      49     111 ..      33     170 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.5e-06
                   Methyltransf_32  27 ltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkrlsfaelsieeatss 95 
                                       + ++D+GaG g Ls   +l       kv++++  ++  e a++ ae l+  + k+++f e s++e ++ 
  gi|242398066|ref|YP_002993490.1|  49 KIIADLGAGTGVLSIGASL---MGAKKVYAVEKDKKALEIAKENAETLN--I-KNIEFLEVSVKEFDAR 111
                                       6699**************9...6689***********************..8.9********9998753 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   4.1e-06     0.003      14      87 ..      47     116 ..      39     118 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4.1e-06
                   Methyltransf_18  14 kgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGleklkeeevdtvv 87 
                                       +g+++aD G+  g+l+i +   g akkv+a++  +++le aken+e+ +++ +ie+     +++++   vdtv+
  gi|242398066|ref|YP_002993490.1|  47 EGKIIADLGAGTGVLSIGASLMG-AKKVYAVEKDKKALEIAKENAETLNIK-NIEFL-EVSVKEFD-ARVDTVI 116
                                       4889*************998655.78*********************9995.57764.34445553.3366665 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 !   16.8   0.1   3.7e-06    0.0026     187     263 ..      33     110 ..      22     117 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.7e-06
                   tRNA_U5-meth_tr 187 nekmleWalevtqeskg.dllelycGnGnfslalarn.fekvlateiakssveaaqyniaankidnvqiirlsaeel 261
                                       + ++l W  + + + +g  + +l  G G +s+  + +  +kv a e  k ++e a+ n ++ +i+n++++ +s  e+
  gi|242398066|ref|YP_002993490.1|  33 AAELL-WLAHSMGDIEGkIIADLGAGTGVLSIGASLMgAKKVYAVEKDKKALEIAKENAETLNIKNIEFLEVSVKEF 108
                                       55544.555555666651456899999*9999877542799***********************************9 PP

                   tRNA_U5-meth_tr 262 te 263
                                         
  gi|242398066|ref|YP_002993490.1| 109 DA 110
                                       76 PP

>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   6.5e-06    0.0046      51     120 ..      49     116 ..      30     119 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 6.5e-06
                                       ..EEEETSTTTTTHHHHHHH-TTSEEEEEES-HHHHHHHHHHHHHCT-SSEEEEES-CCCTTTTT-EEEEE CS
                              GidB  51 k.viDvGsGaGlPGipLaiarpelkltLleslekkiaFLeevkeelklenveivearaeekqeeekydvvt 120
                                       k ++D+G+G G+ +i  +++ ++ k++ +e+++k  +  +e  e+l+++n+e++e  + e      +d+v+
  gi|242398066|ref|YP_002993490.1|  49 KiIADLGAGTGVLSIGASLMGAK-KVYAVEKDKKALEIAKENAETLNIKNIEFLEVSVKE--FDARVDTVI 116
                                       349*************9998875.66899****************************999..555566665 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   2.5e-05     0.018      27     139 ..      25     125 ..      13     132 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.5e-05
                          N6_Mtase  27 effTPrevsklivell...epksgesvyDpacGsggllvqaekvlkeedgktkelsiyGqeknettyrLakmNlllh 100
                                       ++ TP +v   +  l+    + +g+ + D  +G+g l + a+ +         ++++y +ek++++ ++ak N    
  gi|242398066|ref|YP_002993490.1|  25 QYKTPGNVAAELLWLAhsmGDIEGKIIADLGAGTGVLSIGASLM--------GAKKVYAVEKDKKALEIAKENAETL 93 
                                       66677777654433333336667778999999999888887763........5788999*********999997666 PP

                          N6_Mtase 101 gieykkvkirlgdtlekpkfekdkkfdvvvaNppfnqke 139
                                       +i++        + le   +e d ++d+v+ Nppf++++
  gi|242398066|ref|YP_002993490.1|  94 NIKNI-------EFLEVSVKEFDARVDTVIMNPPFGSQN 125
                                       66555.......5566666677899***********985 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.6e-05     0.011      41     117 ..      41     115 ..      36     167 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.6e-05
                                       HH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-E CS
                   Ubie_methyltran  41 klvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsf 117
                                       + +++ +g+ + D+ +Gtg l++    s+    kv  ++ +++ L+++++ ++    +niefl  + +e++   d+ 
  gi|242398066|ref|YP_002993490.1|  41 HSMGDIEGKIIADLGAGTGVLSIGA--SLMGAKKVYAVEKDKKALEIAKENAETLNIKNIEFLEVSVKEFDARVDTV 115
                                       5689999************988764..555666999****************************9999887766654 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 ?   14.0   0.0   4.1e-05     0.029      27      75 ..      65     112 ..      41     164 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.1e-05
                                       HHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHH CS
                   Methyltr_RsmB-F  27 aelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvl 75 
                                       a lm  +++v+Av+++k+ l+  +en + L+++n+  le+ ++++d  +
  gi|242398066|ref|YP_002993490.1|  65 ASLM-GAKKVYAVEKDKKALEIAKENAETLNIKNIEFLEVSVKEFDARV 112
                                       4554.5678*********************************9997544 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   6.7e-05     0.048       2      73 ..      53     118 ..      52     137 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 6.7e-05
                   Methyltransf_12   2 eiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvas 73 
                                       ++G+GtG l+         +++++v+ +++a+e ake     + +n +++e+ +++ +     + +D+v+++
  gi|242398066|ref|YP_002993490.1|  53 DLGAGTGVLSIGASLM-GAKKVYAVEKDKKALEIAKENAETLNIKNIEFLEVSVKEFD-----ARVDTVIMN 118
                                       89*****999887666.899999******************99999999999999865.....39****997 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 ?   12.9   0.1   9.3e-05     0.066      74     129 ..      48     101 ..      27     112 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.3e-05
                                       T-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEE CS
                              PCMT  74 garvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivv 129
                                       g+ + ++G+G+G l+ + a l+g+k  v ++e+ k+  e ak+n ++l+++n+ + 
  gi|242398066|ref|YP_002993490.1|  48 GKIIADLGAGTGVLS-IGASLMGAKK-VYAVEKDKKALEIAKENAETLNIKNIEFL 101
                                       566889******997.6778888887.99**********************77654 PP

>> DUF3236  Protein of unknown function (DUF3236)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00014     0.099      27      75 ..      62     110 ..      56     119 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00014
                                       HHHHHHHT-SEEEES-SSHHHHHHHHHHHTTTT--EEEEESSTGGGGGG CS
                           DUF3236  27 aireyiknakkivvatknkkkvkvinkvlsklglkeiekleietnsaDl 75 
                                       +i   +  akk++ ++k+kk +++ ++  ++l++k+ie le++ + +D+
  gi|242398066|ref|YP_002993490.1|  62 SIGASLMGAKKVYAVEKDKKALEIAKENAETLNIKNIEFLEVSVKEFDA 110
                                       67778899***********************************999996 PP

>> N6-adenineMlase  Probable N6-adenine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.3   0.00028       0.2      50     106 ..      71     129 ..      51     187 .. 0.67
   2 ?   -0.6   0.0       1.4     1e+03       6      18 ..     180     192 ..     177     203 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00028
                   N6-adenineMlase  50 ekvlLleiDkrFealygeekfvfYdlnnpe..elp.eelkgkfdviviDPPF......lseeclkk 106
                                       +kv+  e Dk+  ++++e+     +++n e  e++ +e++  +d +++ PPF              
  gi|242398066|ref|YP_002993490.1|  71 KKVYAVEKDKKALEIAKEN-AETLNIKNIEflEVSvKEFDARVDTVIMNPPFgsqnpkA------D 129
                                       7899999999998887766.9999****99654436889*************5544442......3 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.4
                   N6-adenineMlase   6 sQfwysdetaeal 18 
                                       +Qf++ ++ +e++
  gi|242398066|ref|YP_002993490.1| 180 AQFFFHKKRLEQI 192
                                       7*****9997765 PP

>> DUF4315  Domain of unknown function (DUF4315)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1       1.4   9.9e+02      47      71 ..       1      25 [.       1      31 [. 0.81
   2 ?    5.8   0.8      0.02        14      14      40 ..      71      97 ..      69     111 .. 0.88
   3 ?    6.2   0.0     0.014        10      36      66 ..     137     167 ..     134     177 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.4
                           DUF4315 47 lspeeLaallkamkegaapgpeaqk 71
                                      ++++ La +l+++k+ + p+pe ++
  gi|242398066|ref|YP_002993490.1|  1 MKKKHLAMILSNLKGFKEPKPELEQ 25
                                      7788999999999998888887665 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.02
                           DUF4315 14 eKiselqarlkelekqktEaENleIvq 40
                                      +K+ ++++  k+le +k  aE l+I +
  gi|242398066|ref|YP_002993490.1| 71 KKVYAVEKDKKALEIAKENAETLNIKN 97
                                      6888899999**************966 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.014
                           DUF4315  36 leIvqlVramklspeeLaallkamkegaapg 66 
                                        eI ++V +++l +ee++++++a+  ++  +
  gi|242398066|ref|YP_002993490.1| 137 FEISDVVYSIHLAKEEVRKFIEAFTRDNSFK 167
                                       69********************987776655 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00019      0.14      44      93 ..      45      94 ..      29     117 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00019
                   Methyltransf_16 44 elsklsvlELGsGtGlvGlavaellpeakviltDlee.llellkknielnk 93
                                      + +++ + +LG+GtG+  + + ++ +  kv+    ++ +le+ k+n e  +
  gi|242398066|ref|YP_002993490.1| 45 DIEGKIIADLGAGTGVLSIGASLM-GAKKVYAVEKDKkALEIAKENAETLN 94
                                      567788999********9999888.788888777766599******99733 PP

>> DOT1  Histone methylation protein DOT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00025      0.18      43      90 ..      48      94 ..      33     118 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00025
                                      T-EEEEES-TTSHHHHHHHHHH--SEEEEEE--HHHHHHHHHHHHHHH CS
                              DOT1 43 edvFvDLGSGvGnvvlqaalevgcklsvGvEimdnaselaekqkeelk 90
                                       ++  DLG G G + + a+l +g k+ + vE+ ++a e+a++++e+l+
  gi|242398066|ref|YP_002993490.1| 48 GKIIADLGAGTGVLSIGASL-MGAKKVYAVEKDKKALEIAKENAETLN 94
                                      57889*******99988777.78899***************9998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       860  (0.047967); expected 358.6 (0.02)
Passed bias filter:                      607  (0.0338558); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); 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: 0.66u 0.35s 00:00:01.01 Elapsed: 00:00:00.55
# Mc/sec: 1114.31
//
Query:       gi|242398067|ref|YP_002993491.1|  [L=124]
Description: hypothetical protein TSIB_0074 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
        1.5    8.2  18.8        3.6    6.9  18.8    1.6  1  ABC2_membrane  ABC-2 type transporter
          8    6.8  16.8       0.76   10.0   4.3    2.2  2  Spore_YabQ     Spore cortex protein YabQ (Spore_YabQ)


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 ?    6.9  18.8    0.0004       3.6      78     152 ..      25     104 ..       1     106 [. 0.75

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0004
                     ABC2_membrane  78 ergvlerelvsplyslsayvlakvlvelpvsllqalifllivyflvgldls.....rf...flflllllltalaass 146
                                       e  + ++el+s  ys  a+ +a v+v+l ++l++++++l++v+ l+ l+l+     +f   f fll ++++++++++
  gi|242398067|ref|YP_002993491.1|  25 EVFT-YKELRS--YSILAISIAEVVVSLGINLFLGVLMLFTVLKLLKLNLKeafvvAFtaeFGFLLGIIVVMFILTT 98 
                                       3333.444444..677************************999999****996666448888888999999998888 PP

                     ABC2_membrane 147 lgllis 152
                                        g +++
  gi|242398067|ref|YP_002993491.1|  99 AGTMFG 104
                                       888887 PP

>> Spore_YabQ  Spore cortex protein YabQ (Spore_YabQ)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   4.3   8.4e-05      0.76      29      69 ..       3      43 ..       1      52 [. 0.87
   2 ?    2.6   5.2     0.017   1.5e+02      10      50 ..      57      97 ..      45     105 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 8.4e-05
                        Spore_YabQ 29 vltfieDilfwllaallvflfllrinygelrlylflgillG 69
                                      ++ +i  ilf +l  l++ ++l +++y elr y +l+i + 
  gi|242398067|ref|YP_002993491.1|  3 FIDIIIYILFVVLYYLFLKTALEVFTYKELRSYSILAISIA 43
                                      56778889*****************************9875 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.017
                        Spore_YabQ 10 lgllydlfrilrrllkhkkvltfieDilfwllaallvflfl 50
                                      + +l+ ++++l+  lk   v+ f  ++ f l + +++f++ 
  gi|242398067|ref|YP_002993491.1| 57 VLMLFTVLKLLKLNLKEAFVVAFTAEFGFLLGIIVVMFILT 97
                                      36788999999999887777888888888888887777764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1206  (0.0672653); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 860.84
//
Query:       gi|242398068|ref|YP_002993492.1|  [L=350]
Description: Diphthine synthase, DPH2 subunit [Thermococcus sibiricus MM 739]
Scores for complete 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-77  260.1   0.0    3.5e-77  259.8   0.0    1.0  1  Diphthamide_syn  Putative diphthamide synthesis protein
    0.00048   19.8   1.5        1.6    8.3   0.0    3.2  3  DUF1847          Protein of unknown function (DUF1847)
  ------ inclusion threshold ------
      0.078   11.8   1.0        2.8    6.7   0.2    2.6  3  Fe-ADH           Iron-containing alcohol dehydrogenase
       0.14   12.4   0.0         19    5.5   0.0    2.6  2  UPF0180          Uncharacterised protein family (UPF0180)


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 !  259.8   0.0   7.9e-81   3.5e-77       2     298 ..      31     324 ..      30     329 .. 0.96

  Alignments for each domain:
  == domain 1  score: 259.8 bits;  conditional E-value: 7.9e-81
                   Diphthamide_syn   2 PegllpdsaeiadileefgaevvilgDttYGaCcvdevaaehlgadllvHyGhsclspvdrlpvlYvfveieldveh 78 
                                       Pegl++ ++ +a+ le+ ++e +i+gD+ YGaC+  + +a+ lg+d+l+H Ghs ++   ++p++++++  +++v +
  gi|242398068|ref|YP_002993492.1|  31 PEGLKREAQFLAEFLEKNSIESLISGDINYGACDPADKEAKMLGCDALIHLGHSYMVLNLEVPTIFIPAFAKVNVVK 107
                                       9********************************************************989**************999 PP

                   Diphthamide_syn  79 lvetlkknfke.kkkivlvstiqyahaleevkeeleeegyevv.kvpqsekplspgevlgctspklkeeeeevdail 153
                                        +++  +++k+ +kki+lv+t+q+   l+++ke le+eg+ev   +++  ++  pg+vlgc+++++k    e++ +l
  gi|242398068|ref|YP_002993492.1| 108 ALSKNIEEIKKlGKKIALVTTVQHIRELNKAKEFLEKEGFEVKvGKGDG-RISFPGQVLGCNFSAAK---VEAEGVL 180
                                       999999999666999*************************888667777.99**************4...5799*** PP

                   Diphthamide_syn 154 yigdgrfhllslmlsnpklpvyrydpyskklteesydakkllrrRyaaiekakdakkvGiivgtlgvqgrlelverl 230
                                       +ig g fh+ +++l+++k p+++++pys++   ++ ++++++r+R a+i+ka dakk+G+i +t+++q r+  ++++
  gi|242398068|ref|YP_002993492.1| 181 FIGAGYFHPVGVALATKK-PTLAINPYSGDAIWMNRETERFIRKRWAQIAKAYDAKKFGVITSTKKGQLRIGEARKI 256
                                       ****************77.********************************************************** PP

                   Diphthamide_syn 231 kkllkeagkksylvlvgelnpakLanfaeidafVlvaCprlsiddgkeFekPvltpyElevalg.erew 298
                                        kll+e gk++ l+++++++ + L+ f ++da+V+vaCpr++idd +++ kPvltp Ele++lg ++++
  gi|242398068|ref|YP_002993492.1| 257 VKLLREYGKEVQLIVMNHISYQALEGF-DFDAYVVVACPRVPIDDVENWRKPVLTPRELEILLGlKEDY 324
                                       ***************************.************************************66655 PP

>> DUF1847  Protein of unknown function (DUF1847)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0   0.00036       1.6      45      84 ..      13      52 ..       8      56 .. 0.92
   2 !    5.0   0.1    0.0039        18      54      84 ..     120     149 ..      99     152 .. 0.84
   3 !    3.9   0.0    0.0086        39      48      88 ..     227     271 ..     215     281 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00036
                           DUF1847 45 eiiefakrmgykkiGiafCvglleeakalakileakgfev 84
                                      e++e  ++++++k+ i +  gl++ea+ la++le++ +e 
  gi|242398068|ref|YP_002993492.1| 13 EVLEKLRELNVRKVLIQTPEGLKREAQFLAEFLEKNSIES 52
                                      78888999****************************9985 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0039
                           DUF1847  54 gykkiGiafCvglleeakalakileakgfev 84 
                                       g kki + + v  ++e ++ +++le++gfev
  gi|242398068|ref|YP_002993492.1| 120 G-KKIALVTTVQHIRELNKAKEFLEKEGFEV 149
                                       3.789999**********************8 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.0086
                           DUF1847  48 efakrmgykkiGiafCvg...l.leeakalakileakgfevvsvi 88 
                                       + ak  ++kk G+ + +    l + ea++++k+l+++g ev  ++
  gi|242398068|ref|YP_002993492.1| 227 QIAKAYDAKKFGVITSTKkgqLrIGEARKIVKLLREYGKEVQLIV 271
                                       6789999999999998742222257*************9998776 PP

>> Fe-ADH  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.011        50      13      83 ..      13      76 ..       9      82 .. 0.67
   2 ?    6.7   0.2   0.00061       2.8      10      57 ..     108     151 ..     103     155 .. 0.89
   3 ?   -2.0   0.0      0.26   1.2e+03      16      56 ..     227     268 ..     221     277 .. 0.66

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.011
                                      GHHHHHTTT-..EEEEEEEHHHH.HH.THHHHHHHHHCTT-EEEE.EEE-S---HHHHHHHHTTS-TT.-- CS
                            Fe-ADH 13 elgellkklgakralivtdkgslkksglldkvlesleeagievtvfdgvepnptleeveeaaalareegad 83
                                      e+ e l++l+++++li t +g+ +++++l+++le+   + ie  +    +++  +  ++ a + a+  g+d
  gi|242398068|ref|YP_002993492.1| 13 EVLEKLRELNVRKVLIQTPEGLKREAQFLAEFLEK---NSIESLI----SGDINYGACDPADKEAKMLGCD 76
                                      6778899**************99887777776655...4666664....4444555555555555555555 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.00061
                                       GGGGHHHHHTTT-..EEEEEEEHHHH.HH.THHHHHHHHHCTT-EEEE CS
                            Fe-ADH  10 aleelgellkklgakralivtdkgslkksglldkvlesleeagievtv 57 
                                       al++  e++kklg k++ +vt+ + +   + l+k++e le++g+ev+v
  gi|242398068|ref|YP_002993492.1| 108 ALSKNIEEIKKLG-KKIALVTTVQHI---RELNKAKEFLEKEGFEVKV 151
                                       7888999******.9********999...778************9986 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.26
                                       HHHTTT-..EEEEEE..EHHHH.HH.THHHHHHHHHCTT-EEE CS
                            Fe-ADH  16 ellkklgakralivt..dkgslkksglldkvlesleeagievt 56 
                                       + +k++ ak+  ++t   kg l + g ++k+++ l+e g ev+
  gi|242398068|ref|YP_002993492.1| 227 QIAKAYDAKKFGVITstKKGQL-RIGEARKIVKLLREYGKEVQ 268
                                       5556666667667763344444.66788888888888888777 PP

>> UPF0180  Uncharacterised protein family (UPF0180)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.013        58      30      72 ..      70     118 ..      60     121 .. 0.66
   2 ?    5.5   0.0    0.0043        19       8      24 ..     134     150 ..     128     158 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.013
                           UPF0180  30 edaqsvdaiVvtG.....qdtnvmgied.tetkapvInAsgktaeeIlq 72 
                                       +++ ++da++  G      + +v +i   +  k+ v+ A  k +eeI++
  gi|242398068|ref|YP_002993492.1|  70 AKMLGCDALIHLGhsymvLNLEVPTIFIpAFAKVNVVKALSKNIEEIKK 118
                                       55667777777773333323333333333567999************86 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0043
                           UPF0180   8 gLsnvkeaLrekGYeVv 24 
                                       +L++ ke+L+++G+eV 
  gi|242398068|ref|YP_002993492.1| 134 ELNKAKEFLEKEGFEVK 150
                                       79999**********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       707  (0.0394333); expected 358.6 (0.02)
Passed bias filter:                      613  (0.0341904); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2276.78
//
Query:       gi|242398069|ref|YP_002993493.1|  [L=369]
Description: hypothetical protein TSIB_0076 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-10   41.9   0.4      2e-10   41.3   0.4    1.3  1  DUF3887   Protein of unknown function (DUF3887)
    1.5e-09   37.6  10.0    0.00017   21.1   0.1    2.2  2  YhfC      YhfC intramembrane metalloprotease


Domain annotation for each model (and alignments):
>> DUF3887  Protein of unknown function (DUF3887)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.3   0.4   2.3e-14     2e-10       1      84 [.      31     113 ..      31     123 .. 0.94

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 2.3e-14
                           DUF3887   1 AeeiiellnsgdyeeaqdlfsedlkealseetleeawkalkeelGefesieeyeveetseeyavvtveakfekgsad 77 
                                       Ae+ +e+l+sgdy  +q ++++d+k+a +e++++++ + l+ + G +++++ ++  ++s+ +   ++  +fek++++
  gi|242398069|ref|YP_002993493.1|  31 AEATFEALKSGDYSILQPYLDDDMKKAFDEKQFNAFREDLISKYGQLKDYTFVKEGRSSG-FILGYYSFEFEKADVT 106
                                       7899***************************************************99999.**************** PP

                           DUF3887  78 lefaFde 84 
                                       l+++F e
  gi|242398069|ref|YP_002993493.1| 107 LRLVFRE 113
                                       *****65 PP

>> YhfC  YhfC intramembrane metalloprotease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   5.7   8.3e-08   0.00074      18     123 ..     162     267 ..     148     275 .. 0.77
   2 !   21.1   0.1   1.8e-08   0.00017     155     216 ..     273     335 ..     268     342 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 8.3e-08
                              YhfC  18 klslkvvglGalvFalfal....vlerplhla.llkqneatakalsapllfavygaLtAGlfEevgrylalrfllkr 89 
                                       k+ ++ ++lG+++ a+       + + p+ ++ +++++ ++ak ++ ++l a++++ +AG+f e      l++ + r
  gi|242398069|ref|YP_002993493.1| 162 KIGVAEIILGIILVAITLGiqplIQNAPFLAVgIKSNSDIIAKGTAFVILTAIWLGFVAGFFQES-----LKYAFSR 233
                                       366778889988888776633423355655542777777888889999****************7.....5666778 PP

                              YhfC  90 ksekkdalayGlGhGGleaiLvgvlsllnlvlla 123
                                        +  ++al  G+G+G  eaiLv +l+++++ +l 
  gi|242398069|ref|YP_002993493.1| 234 SKYLNEALFIGIGFGLGEAILVPALQAIQISVLG 267
                                       889999***********************98765 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 1.8e-08
                              YhfC 155 pltillgvlERlaalvvqialsvlvlqavrak..rvlllllaillhaliDllaalyqaglvana 216
                                       + t+++++lER +a +++ + +v++ +  r++  +++ll l++ +h +iD +aa+yq +  +  
  gi|242398069|ref|YP_002993493.1| 273 LSTAFVSMLERYLAALFHAGTTVVLAYSYRNGfgKRALLGLSV-AHGIIDTFAAYYQFKPSTIV 335
                                       67899*************************9876888888887.6************9974433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       814  (0.0454013); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.33s 00:00:00.95 Elapsed: 00:00:00.52
# Mc/sec: 2151.81
//
Query:       gi|242398070|ref|YP_002993494.1|  [L=115]
Description: transcriptional regulator [Thermococcus sibiricus MM 739]
Scores for complete 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   77.5   0.1      8e-22   77.0   0.1    1.3  1  PadR             Transcriptional regulator PadR-like family
    1.4e-05   23.7   0.2    1.7e-05   23.4   0.2    1.1  1  DUF505           Protein of unknown function (DUF505)
    0.00014   21.9   0.2    0.00032   20.8   0.2    1.7  1  HTH_34           Winged helix DNA-binding domain
     0.0081   16.0   0.1       0.01   15.7   0.1    1.3  1  HxlR             HxlR-like helix-turn-helix
  ------ inclusion threshold ------
      0.016   15.9   0.2      0.026   15.2   0.2    1.4  1  RTP              Replication terminator protein
      0.032   14.0   0.1      0.072   12.8   0.0    1.6  1  DUF4364          Domain of unknown function (DUF4364)
      0.054   13.7   0.0        0.1   12.7   0.0    1.5  1  B-block_TFIIIC   B-block binding subunit of TFIIIC
        0.1   12.8   0.1       0.49   10.6   0.0    1.8  2  FPRL1_inhibitor  Formyl peptide receptor-like 1 inhibitory pr
        5.4    6.7  10.0         27    4.4   5.0    2.6  2  VASP_tetra       VASP tetramerisation domain


Domain annotation for each model (and alignments):
>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.0   0.1     4e-25     8e-22       1      75 []      26      99 ..      26      99 .. 0.97

  Alignments for each domain:
  == domain 1  score: 77.0 bits;  conditional E-value: 4e-25
                                      HHHHHCCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHHHH CS
                              PadR  1 iLalleeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrelae 75
                                      iL+ l+++ s+Gy+i+k+lee s+g + +se++lY +Lk+Lek++l+++ew e+  g+prk+Y++T +G++ l+e
  gi|242398070|ref|YP_002993494.1| 26 ILSFLSRERSHGYAIKKALEEVSDGKFVPSESTLYGILKTLEKHELIKGEWMET-GGRPRKCYTITLNGEEVLKE 99
                                      89**************************************************96.9***************9985 PP

>> DUF505  Protein of unknown function (DUF505)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.2   8.7e-09   1.7e-05     343     411 ..      37     107 ..      24     109 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 8.7e-09
                            DUF505 343 keeiakkfeeakdlekWyednfdlreaLysLesfeLieseveekg...kevyvlTeyGekvledqekklrev 411
                                          i+k  ee+ d + +  ++ +l   L++Le +eLi+ e  e g   ++ y++T +Ge+vl++++k+++ v
  gi|242398070|ref|YP_002993494.1|  37 GYAIKKALEEVSDGK-FVPSESTLYGILKTLEKHELIKGEWMETGgrpRKCYTITLNGEEVLKELKKEINLV 107
                                       557999999999995.99**********************9888879999**************99887655 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 !   20.8   0.2   1.6e-07   0.00032      27      76 ..      55     104 ..      17     110 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.6e-07
                            HTH_34  27 tdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreafkkyvkaL 76 
                                       +++ L+  lk+Lek + i+ +    g++pr  ++iT +G e  k+ +k++
  gi|242398070|ref|YP_002993494.1|  55 SESTLYGILKTLEKHELIKGEWMETGGRPRKCYTITLNGEEVLKELKKEI 104
                                       45679999*********************************999988876 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   5.1e-06      0.01      32      88 ..      55     112 ..      21     115 .] 0.82

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 5.1e-06
                                       -HHHHHHHHHHHHHTTSEEEEEESSSS.-EEEEEE-TCGGGGHHHHHHHHHHHHHHHH CS
                              HxlR  32 sqkmLaqrLreLeqdglierevypevP.pkveYsltekGrslepvlqelkkwgeeyle 88 
                                       s+++L   L+ Le+++li+ e +++ + p+  Y++t +G+++ + l++  ++++e le
  gi|242398070|ref|YP_002993494.1|  55 SESTLYGILKTLEKHELIKGEWMETGGrPRKCYTITLNGEEVLKELKKEINLVKELLE 112
                                       67899999*************99887648999*********99888877777777666 PP

>> RTP  Replication terminator protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.2   1.3e-05     0.026      13      97 ..      25     105 ..      12     114 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.3e-05
                                       HHHHHHHTT-EBCTCHHHHHHHHHTTTT----HHHHHHHHHHHHHTTSEEEEEEEBTSSSSSEEEEEEESS..HHHH CS
                               RTP  13 ylitlvekkklyglklldelkkeFkelgykPnhseiyralhelvedgilkrrkelkekaklqevviYsltdeGkeka 89 
                                        ++ ++ +++ +g+ +   l  e  +  + P++s++y  l+ l ++ ++k +     + + +   +Y++t +G+e +
  gi|242398070|ref|YP_002993494.1|  25 LILSFLSRERSHGYAIKKALE-EVSDGKFVPSESTLYGILKTLEKHELIKGEWMET-GGRPR--KCYTITLNGEEVL 97 
                                       356889999999999988885.678888***************9999887665544.44444..379999999***9 PP

                                       HHHHHHHH CS
                               RTP  90 klykkqvk 97 
                                       k +kk++ 
  gi|242398070|ref|YP_002993494.1|  98 KELKKEIN 105
                                       99999864 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   3.6e-05     0.072      39      78 ..      62     105 ..      57     112 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.6e-05
                           DUF4364  39 alseLvesglieee.ek...enktlykiTekGketlelfenrip 78 
                                       +l+ L++++li+ e  +   + +++y+iT +G+e+l++++++i 
  gi|242398070|ref|YP_002993494.1|  62 ILKTLEKHELIKGEwMEtggRPRKCYTITLNGEEVLKELKKEIN 105
                                       578888888888876333557799*****************996 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 ?   12.7   0.0   5.2e-05       0.1       4      50 ..      23      74 ..      20      82 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.2e-05
                    B-block_TFIIIC  4 qfklLelIassRysGitqsdLakesk.....qdprslfyrlksLekkgLIvk 50
                                      ++ +L+ +++ R +G++ +    e+       + + l+++lk+Lek+ LI++
  gi|242398070|ref|YP_002993494.1| 23 AYLILSFLSRERSHGYAIKKALEEVSdgkfvPSESTLYGILKTLEKHELIKG 74
                                      6899************988877666658888899****************86 PP

>> FPRL1_inhibitor  Formyl peptide receptor-like 1 inhibitory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.28   5.7e+02      35      70 ..       8      50 ..       3      58 .. 0.56
   2 ?   10.6   0.0   0.00025      0.49      46      96 ..      57     109 ..      38     113 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.28
                   FPRL1_inhibitor 35 knltpykaetvndl..ylivkklsq....g.dvkkavvrikdg 70
                                      k l  +k e    +  yli+  ls+    g  +kka+  + dg
  gi|242398070|ref|YP_002993494.1|  8 KSLEKFKKEIRTGIyaYLILSFLSRershGyAIKKALEEVSDG 50
                                      5566666665444311566666654111132467777777666 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00025
                   FPRL1_inhibitor  46 ndlylivkklsqgdvkkavvrikdggprdyytfdlt..rpleenrknikvvkn 96 
                                         ly i+k l + ++ k       g pr  yt+ l     l+e +k+i++vk+
  gi|242398070|ref|YP_002993494.1|  57 STLYGILKTLEKHELIKGEWMETGGRPRKCYTITLNgeEVLKELKKEINLVKE 109
                                       4699*************999999999******9996336799*******9995 PP

>> VASP_tetra  VASP tetramerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.2     0.015        30       3      11 ..       9      17 ..       7      21 .. 0.79
   2 ?    4.4   5.0     0.014        27       9      24 ..      94     109 ..      94     111 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.015
                        VASP_tetra  3 DlErlKqEI 11
                                       lE++K+EI
  gi|242398070|ref|YP_002993494.1|  9 SLEKFKKEI 17
                                      588888887 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.014
                        VASP_tetra   9 qEILeEvrkELqKvKe 24 
                                       +E L+E++kE++ vKe
  gi|242398070|ref|YP_002993494.1|  94 EEVLKELKKEINLVKE 109
                                       599********99997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 748.99
//
Query:       gi|242398071|ref|YP_002993495.1|  [L=38]
Description: hypothetical protein TSIB_0078 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.053   13.4   4.4      0.086   12.7   4.4    1.3  1  NUFIP1    Nuclear fragile X mental retardation-interacting pr
       0.12   11.6   0.3       0.13   11.4   0.3    1.0  1  DUF2950   Protein of unknown function (DUF2950)


Domain annotation for each model (and alignments):
>> NUFIP1  Nuclear fragile X mental retardation-interacting protein 1 (NUFIP1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   4.4   9.6e-06     0.086      20      31 ..      18      29 ..      17      29 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.6e-06
                            NUFIP1 20 eIakWreERkKn 31
                                       I+kWr ERkKn
  gi|242398071|ref|YP_002993495.1| 18 AIEKWRFERKKN 29
                                      6**********9 PP

>> DUF2950  Protein of unknown function (DUF2950)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.3   1.5e-05      0.13      78     105 ..       7      34 ..       5      37 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1.5e-05
                           DUF2950  78 dewtlpiPlvkkgkkWaFdtkagkeEil 105
                                       +ew+   P v++ +kW+F+ k+ k E  
  gi|242398071|ref|YP_002993495.1|   7 NEWKAKCPFVRAIEKWRFERKKNKFEFK 34 
                                       58*******************9998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (38 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.33s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 243.10
//
Query:       gi|242398072|ref|YP_002993496.1|  [L=437]
Description: Histidyl-tRNA synthetase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-64  217.8   0.0    2.7e-64  217.4   0.0    1.1  1  tRNA-synt_His   Histidyl-tRNA synthetase
    3.8e-17   62.2   3.4    3.8e-17   62.2   3.4    1.8  2  HGTP_anticodon  Anticodon binding domain
      4e-15   56.2   0.0    8.9e-14   51.8   0.0    2.4  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
    1.2e-07   31.1   0.3    4.9e-05   22.6   0.2    2.5  2  tRNA-synt_2     tRNA synthetases class II (D, K and N)
     0.0061   16.1   0.0      0.026   14.0   0.0    2.0  2  tRNA-synt_2d    tRNA synthetases class II core domain (F)
  ------ inclusion threshold ------
      0.055   13.7   0.2        7.8    6.8   0.1    2.7  2  ALS_ss_C        Small subunit of acetolactate synthase


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 !  217.4   0.0     9e-68   2.7e-64       1     310 []      12     326 ..      12     326 .. 0.93

  Alignments for each domain:
  == domain 1  score: 217.4 bits;  conditional E-value: 9e-68
                                       T---EETCHHHHHHHHHHHHHHHHHHTT-EEEE--SEEEHHHHCTTSTCC.HHHS-EEE-TTSSEEEE-SSSHHHHH CS
                     tRNA-synt_His   1 glrdllpeeaekieelrrrlldlfeswGYelVspPllEyldslltgaged.ldqtfklvDqsgrllglRaDiTpqva 76 
                                       g+rdllpe++ k++ + +r+ ++fe +G++++ +P++Ey+  ++ ++ge+  +q++ + D+ gr+l+lR+D+T +va
  gi|242398072|ref|YP_002993496.1|  12 GTRDLLPEDMIKRRYVFERIREVFEVYGFKEILTPTFEYTKLFELRSGEEvVEQLYAFEDKGGRNLSLRPDLTSSVA 88 
                                       79*****************************************9999999456************************ PP

                                       HHHHHHHH.TSS-EEEEEEEEEEESS-SSTT--CCEEEEEEEEESS-SHHHHHHHHHHHHHHHHHHCTSSSEEEEEE CS
                     tRNA-synt_His  77 Riaahrln.rerplRlcYaGsvlrtrpdglgrsreplQvGaEliGaegleadlEvlslllealeaaagvkelrldlg 152
                                       R+  + ++ +++p +++Y+ +++r ++ + gr re+ Q+G+EliG++++ead+Ev+ ll+e+   + g+ke+++ +g
  gi|242398072|ref|YP_002993496.1|  89 RLFVNAFQtAPKPIKWYYITNMFRYEEPQSGRLREFWQAGVELIGSSNIEADAEVIALLIESYL-STGLKEFTVNVG 164
                                       *******99******************************************************5.************ PP

                                       ETCHHHHHHHHTT--HHHHHHHHHHHHCT-...HHHHHHHHHCCTTHHHCCHCC....HCCHCCCHHHHCHCCHCTH CS
                     tRNA-synt_His 153 hvglvralleaaglsesleeallaalarkd...laelkelaaeaglkealrellkal.elygdaevleealealaaa 225
                                       +  l+++ ++ +g++++    l++++++kd   + e+ + ++e gl+e+ ++ + +l el+g+++ +  ++++l ++
  gi|242398072|ref|YP_002993496.1| 165 DRILLDEFAKMIGVKDD--IGLMRLIDKKDkmeRGEFVKALQEFGLNEEDINKVFTLiELKGKPDDVLPKARELFTS 239
                                       *************8875..679999999982224567777778999999999999999****99999988899*9** PP

                                       HHHHHHHHHHHHHHHHHHHHHHH-TTEEE-TT--TTTTT--SEEEEEEETT-SS..-SEEEEEECTTTGGG.T---E CS
                     tRNA-synt_His 226 palqaaldeleelaallealakpevrvtlDlaelrgyeYytGlvFaayaegvgq..aiarGGrYdelgaaf.grarp 299
                                       + +++ l+++eel +ll+a++  +    +D++  rg++Yyt +vF+a+a++      i++GGrYd+l+++f g++ p
  gi|242398072|ref|YP_002993496.1| 240 EIAKEELKKIEELFELLKAYG-IKDYALIDFGIARGFDYYTSIVFEAIADNDLGigSIGGGGRYDNLIEVFgGKPTP 315
                                       9******************98.678899**********************977556********************* PP

                                       EEEEEEEHHHH CS
                     tRNA-synt_His 300 AtGfsldleal 310
                                       AtGf++ +e+l
  gi|242398072|ref|YP_002993496.1| 316 ATGFAIGIERL 326
                                       ********987 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1       3.4     1e+04      78      93 ..     190     205 ..     188     205 .. 0.82
   2 !   62.2   3.4   1.3e-20   3.8e-17       1      93 [.     344     435 ..     344     436 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 3.4
                                       EEEEEETTHHHHHHHH CS
                    HGTP_anticodon  78 eqervsldelveklke 93 
                                       ++ ++++ e+v++l+e
  gi|242398072|ref|YP_002993496.1| 190 KKDKMERGEFVKALQE 205
                                       4678999999999986 PP

  == domain 2  score: 62.2 bits;  conditional E-value: 1.3e-20
                                       SEEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTC CS
                    HGTP_anticodon   1 qvvviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtr 77 
                                       +v+v+ +++ + e+++ a ++ + Lr+a+i++e+d +++++gk++ +a+ + + +a+++G ++l +g+vt+rd++++
  gi|242398072|ref|YP_002993496.1| 344 DVFVAYIGN-ELEIKKKAIEVTQTLRKANIKAEYDIQGRKLGKALDYANSIEVKVAIILGRRDLSEGKVTIRDMKSG 419
                                       699999999.77799************************************************************** PP

                                       EEEEEETTHHHHHHHH CS
                    HGTP_anticodon  78 eqervsldelveklke 93 
                                       eq +v+++++ve++k+
  gi|242398072|ref|YP_002993496.1| 420 EQKQVAIESIVEEVKK 435
                                       **************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 !   51.8   0.0     3e-17   8.9e-14       1     175 [.      67     330 ..      67     334 .. 0.89

  Alignments for each domain:
  == domain 1  score: 51.8 bits;  conditional E-value: 3e-17
                                       EEEEETTSEEEEE-SSSHHHHHHHHHHHEEEB.GGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEESGGGH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b   1 YkledrndreyiLkPtneetfvelirdevlrs.krLPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfhaeasl 76 
                                       Y +ed+ +r++ L+P  +  +++l+ +      k  P+k y+i+ ++R+E++ ++G  R+reF q + + +++ +  
  gi|242398072|ref|YP_002993496.1|  67 YAFEDKGGRNLSLRPDLTSSVARLFVNAFQTApK--PIKWYYITNMFRYEEP-QSG--RLREFWQAGVELIGSSN-- 136
                                       89*************************9554446..****************.***..***************99.. PP

                                       HHHHHHHHHHHHHHHHHTT.SCEEEEEE....GTTSC........................................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxx........................................ RF
                      tRNA-synt_2b  77 ddslrdlikaisriferlglefraiiel....msaks........................................ 109
                                        + ++++i +  + + + gl+++ +           +                                        
  gi|242398072|ref|YP_002993496.1| 137 IEADAEVIALLIESYLSTGLKEFTVNVGdrilL---Defakmigvkddiglmrlidkkdkmergefvkalqefglne 210
                                       9*******************8753332223331...14456777888999*************************** PP

                                       ................................................................BTTSEEEEEEEEE CS
                                       ................................................................xxxxxxxxxxxxx RF
                      tRNA-synt_2b 110 ................................................................adykdkkefeavs 122
                                                                                                       +dy+ + +fea+ 
  gi|242398072|ref|YP_002993496.1| 211 edinkvftlielkgkpddvlpkarelftseiakeelkkieelfellkaygikdyalidfgiargFDYYTSIVFEAIA 287
                                       ****************************************************************************9 PP

                                       TTTSEEEEEEEEEE..EETHHHHHTTEEEECTTSSEEEEEEEEEEEEHHHHHHHH CS
                                       xxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b 123 esltkgieigtiqk..lgtrlserlgatvldennreksvimicaaigveRllsai 175
                                             + ig+i++  ++++l e +g++         ++ ++++aig+eRl+ ++
  gi|242398072|ref|YP_002993496.1| 288 D---NDLGIGSIGGggRYDNLIEVFGGKP--------TP-ATGFAIGIERLIPIL 330
                                       9...5555888875226789999999988........99.99*********9765 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 !   22.6   0.2   1.6e-08   4.9e-05      21     187 ..      20     213 ..       6     256 .. 0.80
   2 !    6.0   0.0    0.0018       5.4     270     298 ..     302     330 ..     299     337 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.6e-08
                                       HHHHHHHHHHHHHHHHHHTT-EE----SEESS--SSSS--EEEEETTT..TEEE..............-E-S-.SHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx..............xxxxx.xxx RF
                       tRNA-synt_2  21 vlrlrstvtkavrkyleengfieietPiLsksdteegarlFkvksrek.ekeff..............aLtqs.pql 81 
                                        +  r  v + +r+++e  gf ei tP++  +      +lF + s e+  ++++               Lt s   l
  gi|242398072|ref|YP_002993496.1|  20 DMIKRRYVFERIREVFEVYGFKEILTPTFEYT------KLFELRSGEEvVEQLYafedkggrnlslrpDLTSSvARL 90 
                                       5678999*********************9999......777776666542244445666666666889888884589 PP

                                       HHHHHHHCT.HSEEEEEEEEE--S--BTTB-S-CEEEEEEEE...ET-SCHH..HHHHHHHHHHHHHHHHHHCSCCC CS
                                       xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2  82 ylellivag.idrvfqiaraFRaEdsrtdrhlaEFtqieaem...sfieeed..imqvleelikslvkevlessakd 152
                                       +  +   a    + + i+++FR E+ ++ r   EF+q  +e+   s ie +   i  ++e  +++ +ke++ ++ + 
  gi|242398072|ref|YP_002993496.1|  91 FVNAFQTAPkPIKWYYITNMFRYEEPQSGRLR-EFWQAGVELigsSNIEADAevIALLIESYLSTGLKEFTVNVGDR 166
                                       99999888536799*************99877.********988766665555677889999999999999999888 PP

                                       CCHTTTTTS............EE-SSS-EEEEHHHHHHHHHTS-SS- CS
                                       xxxxxxxxx............xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 153 iefvirrns............kdlkkpfkrltykeaieklneigkdl 187
                                       i  +   ++             d k++++r ++++a++++  +++d+
  gi|242398072|ref|YP_002993496.1| 167 ILLDEFAKMigvkddiglmrlIDKKDKMERGEFVKALQEFGLNEEDI 213
                                       88887777789999999988877778888999999998865555555 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0018
                                       GHHHHHHHHCT--SEEEEEEEHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 270 fswylealeyGapphgGlglGldRlvmll 298
                                       +++++e++     p  G+++G++Rl+ +l
  gi|242398072|ref|YP_002993496.1| 302 YDNLIEVFGGKPTPATGFAIGIERLIPIL 330
                                       7788999999999************9877 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 !   14.0   0.0   8.8e-06     0.026      21     129 ..      26     129 ..      18     152 .. 0.78
   2 ?   -3.5   0.0       1.9   5.6e+03     207     222 ..     312     327 ..     298     330 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 8.8e-06
                                       HHHHHHHHHHHCTTCEESSTTSEEEHHHHTSTTTSTTTSHHHCHTTSEBTCTSSS-ECESEEE-SSTHHHHHHHH.. CS
                      tRNA-synt_2d  21 kvleeikeiflelgfeevegpevesefynfdaLnvpqdhpaRdmqdtFylkkpekaveekllLRthttavqirtl.. 95 
                                        v e+i+e+f  +gf+e+  p  e        L+  +  +  ++ + +y  +++    ++l LR   t+  +r    
  gi|242398072|ref|YP_002993496.1|  26 YVFERIREVFEVYGFKEILTPTFEYTK-----LF--ELRSGEEVVEQLYAFEDKG--GRNLSLRPDLTSSVARLFvn 93 
                                       578999999999999999999884332.....22..2223334444455545555..689************99999 PP

                                       ..TTS-SSEEEEEEEEEEBSST-SSSB-SEEEEEEE CS
                      tRNA-synt_2d  96 ..ekkkppikiisigrvfRrdavDathlaeFhqveg 129
                                         ++  +pik   i ++fR ++  + +l eF q+  
  gi|242398072|ref|YP_002993496.1|  94 afQTAPKPIKWYYITNMFRYEEPQSGRLREFWQAGV 129
                                       999999**************************9865 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.9
                                       TTSEEEEEEEEHHHHH CS
                      tRNA-synt_2d 207 eevsgfafGlGveRla 222
                                       + +++ +f +G+eRl 
  gi|242398072|ref|YP_002993496.1| 312 KPTPATGFAIGIERLI 327
                                       4566778889999985 PP

>> ALS_ss_C  Small subunit of acetolactate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.021        62      12      47 ..     192     228 ..     181     230 .. 0.87
   2 ?    6.8   0.1    0.0026       7.8      39      63 ..     239     264 ..     229     265 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.021
                                       SC.HHHHHHHHHHHTT-EEEEEETTEEEEEEEE-HHH CS
                          ALS_ss_C  12 ke.erseileiaeifrakivdvspdsliieltgteek 47 
                                       ++ er e  +  + f  +  d+++ + +iel g++++
  gi|242398072|ref|YP_002993496.1| 192 DKmERGEFVKALQEFGLNEEDINKVFTLIELKGKPDD 228
                                       34499999*************************9986 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0026
                                       EEEEE-H.HHHHHHHHHS-GGGEEEE CS
                          ALS_ss_C  39 ieltgte.ekidaliellkpfgilev 63 
                                        e++++e +ki++l+ellk +gi+++
  gi|242398072|ref|YP_002993496.1| 239 SEIAKEElKKIEELFELLKAYGIKDY 264
                                       5555544389*************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (437 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 2647.23
//
Query:       gi|242398073|ref|YP_002993497.1|  [L=204]
Description: hypothetical protein TSIB_0080 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.6e-30  105.3  22.0      3e-30  105.1  22.0    1.0  1  MarC         MarC family integral membrane protein
  ------ inclusion threshold ------
        2.7    8.8  13.2        4.4    8.2   0.6    3.4  3  HKR_ArcB_TM  Histidine kinase receptor ArcB trans-membrane do


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 !  105.1  22.0   3.4e-34     3e-30       3     203 .]       4     195 ..       2     195 .. 0.90

  Alignments for each domain:
  == domain 1  score: 105.1 bits;  conditional E-value: 3.4e-34
                              MarC   3 aiikafvsLlaiinplgnvpvflslleevskeerkrialkasilallillvfllfGelilk.lfgisidalkiaGgi 78 
                                       +i++++++++++i+p  ++ ++  l e ++ e  k+ +++a+++++++l++f+l+G++il+ +f i ++al++aGg 
  gi|242398073|ref|YP_002993497.1|   4 EILSSALLMIIMIDPSDKILLVSLLREDFHIEDIKQLIVRANLIGFFLLILFALAGKIILQdIFHIDLNALRVAGGF 80 
                                       6889999*****************************************************549************** PP

                              MarC  79 llfliaidmlkakqkkekkkkseeeeseekdeiavvPLAlPliaGPgaittvlvlaseassivekvavvlaillaal 155
                                       +lf+i+++ l++      + k+e++    +   a vP+A+PliaGP+aitt + l++e+   v+ +a+v+ail  al
  gi|242398073|ref|YP_002993497.1|  81 VLFKIGLEALEGGGMV--TLKKEKN----ILALAAVPVATPLIAGPAAITTAITLTAEYGIKVSALAIVIAILTTAL 151
                                       ************9995..4444444....6689***************************98888888888888887 PP

                              MarC 156 itllilllsslilrllgktginaleRlmGllLvalavqlivdGikeil 203
                                       i++++l  ++     + kt + ++ R++Gl+ +a++ q++v+G+ +i+
  gi|242398073|ref|YP_002993497.1| 152 IMIITLYATEN----ISKTTLGVFIRIIGLFTMAIGAQMMVEGVGGIF 195
                                       77777777665....5689999*********************99886 PP

>> HKR_ArcB_TM  Histidine kinase receptor ArcB trans-membrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1     0.016   1.4e+02      14      45 ..      10      41 ..       5      42 .. 0.84
   2 ?    8.2   0.6   0.00049       4.4       7      37 ..      42      72 ..      41      83 .. 0.87
   3 ?    3.9   2.7      0.01        94       8      41 ..     136     168 ..     121     189 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.016
                       HKR_ArcB_TM 14 vlllivlalliqillslllsgeveiedllrsi 45
                                      +l++i+++   +ill  ll+++++ied+ + i
  gi|242398073|ref|YP_002993497.1| 10 LLMIIMIDPSDKILLVSLLREDFHIEDIKQLI 41
                                      457788888999***************98877 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00049
                       HKR_ArcB_TM  7 vrfSlllvlllivlalliqillslllsgeve 37
                                      vr  l++++lli++al+++i+l+ +++ +++
  gi|242398073|ref|YP_002993497.1| 42 VRANLIGFFLLILFALAGKIILQDIFHIDLN 72
                                      8999******************999886665 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.01
                       HKR_ArcB_TM   8 rfSlllvlllivlalliqillslllsgeveiedl 41 
                                       ++S l ++++++l++++ ++++l+ +++++ + l
  gi|242398073|ref|YP_002993497.1| 136 KVSAL-AIVIAILTTALIMIITLYATENISKTTL 168
                                       55654.5566666677778888888888876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1167  (0.0650901); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1280.76
//
Query:       gi|242398074|ref|YP_002993498.1|  [L=40]
Description: hypothetical protein TSIB_0081 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      199  (0.0110993); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.48
# Mc/sec: 249.63
//
Query:       gi|242398075|ref|YP_002993499.1|  [L=367]
Description: hypothetical protein TSIB_0082 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-19   69.1   0.1    2.1e-17   63.2   0.0    2.3  2  Peptidase_M78  IrrE N-terminal-like domain
      7e-11   42.0   1.0    2.6e-08   33.8   0.3    2.7  2  HTH_3          Helix-turn-helix
    8.4e-09   35.7   0.0    5.5e-08   33.0   0.0    2.2  2  HTH_31         Helix-turn-helix domain
      2e-07   30.9   4.5    4.2e-07   29.9   0.1    3.3  4  HTH_19         Helix-turn-helix domain
    0.00012   21.9   0.1    0.00038   20.3   0.1    2.0  1  HTH_25         Helix-turn-helix domain
    0.00082   19.1   0.0      0.032   14.1   0.0    2.8  2  HTH_23         Homeodomain-like domain
      0.001   18.9   1.0       0.13   12.1   0.1    2.7  2  IF2_N          Translation initiation factor IF-2, N-terminal
     0.0017   18.2   0.3      0.034   14.0   0.0    2.7  2  HTH_AsnC-type  AsnC-type helix-turn-helix domain
     0.0017   18.8   0.0      0.039   14.4   0.0    2.6  2  HTH_26         Cro/C1-type HTH DNA-binding domain
      0.002   18.0   0.1      0.031   14.2   0.1    2.7  2  HTH_11         HTH domain
     0.0083   15.7   0.2      0.087   12.4   0.0    2.7  3  HTH_24         Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.012   15.9   0.0        3.2    8.1   0.0    2.7  2  HTH_Tnp_1      Transposase
      0.021   14.4   0.1       0.47   10.1   0.1    2.7  2  CENP-B_N       CENP-B N-terminal DNA-binding domain
      0.031   14.5   0.9       0.71   10.1   0.0    3.3  2  HTH_17         Helix-turn-helix domain
      0.033   14.3   0.0      0.095   12.9   0.0    1.8  1  Death          Death domain
      0.036   14.0   2.1          1    9.4   0.1    3.5  3  RHH_1          Ribbon-helix-helix protein, copG family
      0.042   13.7   0.0       0.16   11.8   0.0    2.0  1  HTH_5          Bacterial regulatory protein, arsR family
      0.043   13.3   0.1        0.9    9.1   0.0    2.7  2  Sigma70_r4     Sigma-70, region 4
      0.054   13.6   0.1         12    6.0   0.0    3.3  3  MerR_1         MerR HTH family regulatory protein
      0.066   13.0   0.0         16    5.4   0.0    3.1  2  MerR           MerR family regulatory protein
      0.079   12.9   0.1         15    5.6   0.0    3.0  2  DUF3606        Protein of unknown function (DUF3606)
      0.085   12.5   0.1       0.33   10.7   0.1    2.1  1  Sigma70_r4_2   Sigma-70, region 4
       0.09   12.6   0.0        2.8    7.8   0.0    2.7  2  HTH_10         HTH DNA binding domain
      0.091   12.8   0.1        4.3    7.4   0.0    3.0  3  HTH_29         Winged helix-turn helix
      0.092   12.5   0.5        0.5   10.1   0.1    2.5  2  UPF0175        Uncharacterised protein family (UPF0175)
       0.12   12.5   0.0       0.65   10.1   0.0    2.2  2  DUF2623        Protein of unknown function (DUF2623)
       0.13   12.2   0.0          1    9.3   0.0    2.4  3  MarR           MarR family


Domain annotation for each model (and alignments):
>> Peptidase_M78  IrrE N-terminal-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.095        63      92     118 ..      14      39 ..      12      41 .. 0.86
   2 !   63.2   0.0   3.1e-20   2.1e-17       2     122 ..     162     284 ..     161     285 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.095
                     Peptidase_M78  92 flalaatqrkdleerlaeyfgVSkeav 118
                                       +++l +++++  ee la+++gVS++ +
  gi|242398075|ref|YP_002993499.1|  14 LRKLRENSGYSVEE-LAKKLGVSEKKI 39 
                                       577889999999*8.********9765 PP

  == domain 2  score: 63.2 bits;  conditional E-value: 3.1e-20
                     Peptidase_M78   2 erlgidvlaldlgakdldgfrfdnsetkvivlnsnhsptrqrftlaHElgHlllhherdkfreegdskaqerlerea 78 
                                       e+lgi +++ +l++ +++ f+ ++    vivln+++ p  + f+l HE++Hll ++e+++  e   ++++ ++er +
  gi|242398075|ref|YP_002993499.1| 162 EKLGILIIEYPLKNDNVRAFSLKRD-LAVIVLNESDEPKVKLFSLFHEIAHLLKGSEGIC--EIDVDSEKFEIERFC 235
                                       89********************998.********************************99..55555566689999* PP

                     Peptidase_M78  79 nafAaelllPeeaflalaatqrkdlee.....rlaeyfgVSkeavavrl 122
                                       + fAae+l+P  +++  +++  k + +     +la+++gVSk ++  rl
  gi|242398075|ref|YP_002993499.1| 236 DKFAAEFLVPASDLKLEIEKKAKRELSddiisELARRYGVSKHVMMLRL 284
                                       ***************9999999998889****************98887 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.3   3.9e-11   2.6e-08       1      53 [.      14      66 ..      14      68 .. 0.97
   2 ?    6.0   0.0     0.019        13      29      51 ..     253     276 ..     252     278 .. 0.85

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 3.9e-11
                                      HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSEHH CS
                             HTH_3  1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgvsld 53
                                      l++lR+  g+s eeLA+klGvs   i + E+ + + +++ lk lak ++++l+
  gi|242398075|ref|YP_002993499.1| 14 LRKLRENSGYSVEELAKKLGVSEKKIEDVESSKDSFTITQLKSLAKIYKIPLA 66
                                      89************************************************997 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.019
                                       HHTT.SSCSBHHHHHHHHHHHTSE CS
                             HTH_3  29 iEnG.ernPsletlkklakaLgvs 51 
                                       iE+  +r+ s +++ +la+ +gvs
  gi|242398075|ref|YP_002993499.1| 253 IEKKaKRELSDDIISELARRYGVS 276
                                       677779999999999999999998 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.0   8.3e-11   5.5e-08       6      57 ..      14      64 ..      13      68 .. 0.95
   2 ?   -0.9   0.0       3.3   2.2e+03      19      28 ..     268     277 ..     253     280 .. 0.62

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 8.3e-11
                            HTH_31  6 LralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralgld 57
                                      Lr lRe +G s ee+A+ lgvse ++ ++E+ +    +  +l +la ++  +
  gi|242398075|ref|YP_002993499.1| 14 LRKLRENSGYSVEELAKKLGVSEKKIEDVESSKD-SFTITQLKSLAKIYKIP 64
                                      9*********************************.6************9987 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 3.3
                            HTH_31  19 evAerlgvse 28 
                                       e+A+r gvs+
  gi|242398075|ref|YP_002993499.1| 268 ELARRYGVSK 277
                                       5555555554 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.1   6.3e-10   4.2e-07       4      60 ..      14      69 ..      13      72 .. 0.93
   2 ?    0.4   0.0      0.98   6.5e+02      26      54 ..     184     215 ..     160     218 .. 0.78
   3 ?   -1.3   0.0       3.4   2.3e+03      32      55 ..     253     276 ..     251     287 .. 0.73
   4 ?   -2.2   0.0       6.7   4.4e+03      31      50 ..     340     363 ..     334     365 .. 0.75

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 6.3e-10
                            HTH_19  4 LkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealgidleyll 60
                                      L+++Re+ g++ eela++lg+s +ki   E+  kd +++  l+++a++++i+l +++
  gi|242398075|ref|YP_002993499.1| 14 LRKLRENSGYSVEELAKKLGVSEKKIEDVESS-KDSFTITQLKSLAKIYKIPLAAFF 69
                                      9*****************************87.56999**************98887 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.98
                            HTH_19  26 rskisaiEngkkdvps...aelllkiaealgi 54 
                                       ++ ++ i  +++d+p+    +l+  ia++l+ 
  gi|242398075|ref|YP_002993499.1| 184 KRDLAVIVLNESDEPKvklFSLFHEIAHLLKG 215
                                       66789999999999995555555999998876 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 3.4
                            HTH_19  32 iEng.kkdvpsaelllkiaealgid 55 
                                       iE+  k+ ++s + +  +a+ +g++
  gi|242398075|ref|YP_002993499.1| 253 IEKKaKR-ELSDDIISELARRYGVS 276
                                       7777555.88888888888888887 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 6.7
                            HTH_19  31 aiEngkkdvpsaell....lkiae 50 
                                       a+E g++  ++a+++     k+ae
  gi|242398075|ref|YP_002993499.1| 340 AYERGEISFFEASRIlnmkIKYAE 363
                                       788898888888887666666666 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.1   5.7e-07   0.00038       2      33 ..      14      45 ..      13      62 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 5.7e-07
                                      HHHHHHTTT--HHHHHHHSS--HHHHHHHHCT CS
                            HTH_25  2 LraaRearglsleevaketkIrkdylealEed 33
                                      Lr+ Re  g+s+ee+ak++ ++++ +e  E+ 
  gi|242398075|ref|YP_002993499.1| 14 LRKLRENSGYSVEELAKKLGVSEKKIEDVESS 45
                                      9**************************99975 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   4.8e-05     0.032      10      34 ..      13      39 ..      12      45 .. 0.88
   2 ?    1.6   0.0      0.39   2.6e+02      20      32 ..     266     278 ..     256     278 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.8e-05
                            HTH_23 10 illllae..GlsvreIAreLgvsrrTv 34
                                      il+ l+e  G+sv+e A++Lgvs+  +
  gi|242398075|ref|YP_002993499.1| 13 ILRKLREnsGYSVEELAKKLGVSEKKI 39
                                      789999999**************9766 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.39
                            HTH_23  20 vreIAreLgvsrr 32 
                                       ++e Ar++gvs++
  gi|242398075|ref|YP_002993499.1| 266 ISELARRYGVSKH 278
                                       7899*******86 PP

>> IF2_N  Translation initiation factor IF-2, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.1   0.00019      0.13       2      20 ..      21      39 ..      20      40 .. 0.90
   2 ?    4.7   0.1      0.04        26       6      30 ..     266     289 ..     248     293 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00019
                             IF2_N  2 skirVyeLAkeLgvkskev 20
                                      s  +V eLAk+Lgv+ k++
  gi|242398075|ref|YP_002993499.1| 21 SGYSVEELAKKLGVSEKKI 39
                                      5689***********9987 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.04
                             IF2_N   6 VyeLAkeLgvkskevikkLfkelGi 30 
                                       ++eLA++ gv+ +  + +L + lG+
  gi|242398075|ref|YP_002993499.1| 266 ISELARRYGVSKHVMMLRLLN-LGY 289
                                       677788888877777777766.776 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   5.1e-05     0.034       8      32 ..      13      37 ..      12      40 .. 0.94
   2 ?    1.0   0.0      0.58   3.8e+02      21      31 ..     267     277 ..     266     287 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.1e-05
                     HTH_AsnC-type  8 ILeaLqedaRisyaeLAervGlSes 32
                                      IL+ L+e++  s++eLA+++G+Se 
  gi|242398075|ref|YP_002993499.1| 13 ILRKLRENSGYSVEELAKKLGVSEK 37
                                      9**********************96 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.58
                     HTH_AsnC-type  21 aeLAervGlSe 31 
                                       +eLA+r G+S 
  gi|242398075|ref|YP_002993499.1| 267 SELARRYGVSK 277
                                       79*******97 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   5.9e-05     0.039       2      53 ..      14      64 ..      14      69 .. 0.93
   2 ?    1.0   0.0       0.9     6e+02      14      27 ..     267     280 ..     265     286 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.9e-05
                            HTH_26  2 LrelmadrgitkseLargtgisaatlsrlvkgkpervsldtLdkiCdaLgct 53
                                      Lr+l    g+++ eLa+++g+s+ +++   + k ++ +++ L  ++++ ++ 
  gi|242398075|ref|YP_002993499.1| 14 LRKLRENSGYSVEELAKKLGVSEKKIEDVESSK-DSFTITQLKSLAKIYKIP 64
                                      8999999************************99.9***********998775 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.9
                            HTH_26  14 seLargtgisaatl 27 
                                       seLar++g+s+  +
  gi|242398075|ref|YP_002993499.1| 267 SELARRYGVSKHVM 280
                                       89********9876 PP

>> HTH_11  HTH 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       5      30 ..      13      37 ..      12      40 .. 0.90
   2 ?   -0.1   0.0       1.4   9.3e+02      19      29 ..     267     277 ..     266     279 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.7e-05
                            HTH_11  5 ilelLleargpisgeeLAeeLnvSrr 30
                                      il+ L+e+ g  s eeLA++L+vS++
  gi|242398075|ref|YP_002993499.1| 13 ILRKLRENSG-YSVEELAKKLGVSEK 37
                                      8999*99999.7************85 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.4
                            HTH_11  19 eeLAeeLnvSr 29 
                                       +eLA++ +vS+
  gi|242398075|ref|YP_002993499.1| 267 SELARRYGVSK 277
                                       79********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 !   12.4   0.0   0.00013     0.087       8      32 ..      13      37 ..      13      40 .. 0.90
   2 ?   -1.4   0.0       2.7   1.8e+03      21      30 ..     267     276 ..     266     277 .. 0.87
   3 ?   -2.1   0.0       4.4   2.9e+03      38      48 .]     281     291 ..     278     291 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00013
                            HTH_24  8 ILelLqknprisqreLAerlglSps 32
                                      IL+ L++n++ s  eLA++lg+S  
  gi|242398075|ref|YP_002993499.1| 13 ILRKLRENSGYSVEELAKKLGVSEK 37
                                      78889******************76 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.7
                            HTH_24  21 reLAerlglS 30 
                                       +eLA+r g+S
  gi|242398075|ref|YP_002993499.1| 267 SELARRYGVS 276
                                       79****9999 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 4.4
                            HTH_24  38 lkrLeeeGlIk 48 
                                       + rL + G+I+
  gi|242398075|ref|YP_002993499.1| 281 MLRLLNLGYIT 291
                                       66999****96 PP

>> HTH_Tnp_1  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0    0.0048       3.2      12      38 ..      13      37 ..      10      41 .. 0.81
   2 ?    4.9   0.0      0.05        33      26      39 ..     266     279 ..     259     281 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0048
                         HTH_Tnp_1 12 KariVreslepgksvsevArrhgvspn 38
                                      ++r +re   +g+sv e+A+++gvs++
  gi|242398075|ref|YP_002993499.1| 13 ILRKLREN--SGYSVEELAKKLGVSEK 37
                                      55556666..9**************97 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.05
                         HTH_Tnp_1  26 vsevArrhgvspnq 39 
                                       +se+Arr+gvs++ 
  gi|242398075|ref|YP_002993499.1| 266 ISELARRYGVSKHV 279
                                       79*********985 PP

>> CENP-B_N  CENP-B N-terminal DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00072      0.47      18      49 ..      16      49 ..      13      51 .. 0.85
   2 ?    0.6   0.0      0.66   4.4e+02      27      36 ..     268     277 ..     267     279 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00072
                                      HHHCTT..-HHHHHHHHT--CCHHHHHHHCHHHH CS
                          CENP-B_N 18 rleege..SkaelarrfnvpestlsdilknKkkl 49
                                      +l e+   S++ela++++v e  + d+   K+++
  gi|242398075|ref|YP_002993499.1| 16 KLRENSgySVEELAKKLGVSEKKIEDVESSKDSF 49
                                      55666677*******************9999986 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.66
                                       HHHHHHT--C CS
                          CENP-B_N  27 elarrfnvpe 36 
                                       elarr++v +
  gi|242398075|ref|YP_002993499.1| 268 ELARRYGVSK 277
                                       8******975 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0    0.0011      0.71       2      18 ..      23      39 ..      23      47 .. 0.92
   2 ?    0.9   0.0      0.78   5.2e+02       4      27 ..     266     290 ..     266     306 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0011
                            HTH_17  2 ltveEaAelLgvsrstv 18
                                      ++veE+A+ Lgvs++++
  gi|242398075|ref|YP_002993499.1| 23 YSVEELAKKLGVSEKKI 39
                                      89************998 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.78
                            HTH_17   4 veEaAelLgvsrstvy.rlirrgel 27 
                                       ++E+A+  gvs++    rl++ g +
  gi|242398075|ref|YP_002993499.1| 266 ISELARRYGVSKHVMMlRLLNLGYI 290
                                       6899*******98766666665555 PP

>> Death  Death domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00014     0.095       4      40 ..      14      47 ..      12      63 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00014
                                      HHHHHCCSTCCSCCHHHHHHHTTSHHHHHHHHHHSSS CS
                             Death  4 larildhpdplgkdWkelarkLglseeeidriekenn 40
                                      l +++++    g + +ela+kLg+se +i+ +e++ +
  gi|242398075|ref|YP_002993499.1| 14 LRKLREN---SGYSVEELAKKLGVSEKKIEDVESSKD 47
                                      6788898...899********************9983 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 ?    1.8   0.0      0.38   2.5e+02      14      24 ..      25      35 ..      15      36 .. 0.92
   2 ?    9.4   0.1    0.0016         1      11      34 ..     263     286 ..     250     290 .. 0.91
   3 ?   -0.9   0.1       2.7   1.8e+03      11      23 ..     304     317 ..     303     321 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.38
                                      HHHHHHHHTSS CS
                             RHH_1 14 LdelarrrgrS 24
                                      ++ela+++g+S
  gi|242398075|ref|YP_002993499.1| 25 VEELAKKLGVS 35
                                      89*******98 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0016
                                       HHHHHHHHHHHTSSHHHHHHHHHH CS
                             RHH_1  11 lerLdelarrrgrSrSelIReAlr 34 
                                       ++ + elarr g+S++ ++ ++l 
  gi|242398075|ref|YP_002993499.1| 263 DDIISELARRYGVSKHVMMLRLLN 286
                                       57899**************99986 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 2.7
                                       HHHHHHHHHHHT.S CS
                             RHH_1  11 lerLdelarrrg.r 23 
                                       +++L+el+++    
  gi|242398075|ref|YP_002993499.1| 304 KAKLEELKKKKVsG 317
                                       689****9986655 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00025      0.16       7      32 ..      13      39 ..      13      41 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00025
                                      HHHHHTTSS.EEHHHHHHHHTS-HHHH CS
                             HTH_5  7 ILklLaege.lcvcelaeelglsqstv 32
                                      IL+ L+e++ ++v ela++lg+s+ ++
  gi|242398075|ref|YP_002993499.1| 13 ILRKLRENSgYSVEELAKKLGVSEKKI 39
                                      99*****888*************9887 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0    0.0014       0.9      15      37 ..      17      39 ..      12      44 .. 0.82
   2 ?    0.7   0.0      0.59   3.9e+02      24      34 ..     267     277 ..     266     278 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0014
                                      HHHTTT--HHHHHHHHTS-HHHH CS
                        Sigma70_r4 15 lrfgeglTleEIgerlgiSrerV 37
                                      lr   g++ eE++++lg+S+  +
  gi|242398075|ref|YP_002993499.1| 17 LRENSGYSVEELAKKLGVSEKKI 39
                                      445899*************9765 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.59
                                       HHHHHHHTS-H CS
                        Sigma70_r4  24 eEIgerlgiSr 34 
                                       +E+++r+g+S+
  gi|242398075|ref|YP_002993499.1| 267 SELARRYGVSK 277
                                       79*******96 PP

>> MerR_1  MerR HTH family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.019        12       1      17 [.      23      39 ..      23      44 .. 0.92
   2 ?   -2.7   0.0       9.7   6.5e+03      13      21 ..     149     157 ..     129     162 .. 0.71
   3 ?    3.5   0.0      0.12        78       3      16 ..     266     279 ..     265     283 .. 0.94

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.019
                                      EEHHHHHHHHTS-HHHH CS
                            MerR_1  1 ysigevakilgvtthtl 17
                                      ys+ e+ak+lgv+ + +
  gi|242398075|ref|YP_002993499.1| 23 YSVEELAKKLGVSEKKI 39
                                      99***********9887 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 9.7
                                       -HHHHHHHH CS
                            MerR_1  13 tthtlrywe 21 
                                       +++tl ++ 
  gi|242398075|ref|YP_002993499.1| 149 SYRTLEFYK 157
                                       678888886 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.12
                                       HHHHHHHHTS-HHH CS
                            MerR_1   3 igevakilgvttht 16 
                                       i+e+a++ gv++h+
  gi|242398075|ref|YP_002993499.1| 266 ISELARRYGVSKHV 279
                                       9***********97 PP

>> MerR  MerR family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.024        16       2      16 ..      25      39 ..      24      40 .. 0.88
   2 ?    4.0   0.0     0.066        44       2      14 ..     266     278 ..     266     279 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.024
                                      HHHHHHHHTTTHHHH CS
                              MerR  2 IgevAeltGvsprtL 16
                                      + e+A+++Gvs +++
  gi|242398075|ref|YP_002993499.1| 25 VEELAKKLGVSEKKI 39
                                      579********9987 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.066
                                       HHHHHHHHTTTHH CS
                              MerR   2 IgevAeltGvspr 14 
                                       I+e+A++ Gvs +
  gi|242398075|ref|YP_002993499.1| 266 ISELARRYGVSKH 278
                                       99*********76 PP

>> DUF3606  Protein of unknown function (DUF3606)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.022        15      19      36 ..      23      40 ..      20      42 .. 0.88
   2 ?    3.7   0.1     0.088        58       1      27 [.     303     329 ..     303     340 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.022
                           DUF3606 19 yevayWakklgvteeqLr 36
                                      y v+ +akklgv+e +++
  gi|242398075|ref|YP_002993499.1| 23 YSVEELAKKLGVSEKKIE 40
                                      88999*********9987 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.088
                           DUF3606   1 dktkrgprDrsrInldeeyevayWakk 27 
                                       dk+k++ + +++++ +  +e++y+ ++
  gi|242398075|ref|YP_002993499.1| 303 DKAKLEELKKKKVSGSRNWERTYFNRA 329
                                       789999999**************9875 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00049      0.33      21      43 ..      17      39 ..      16      40 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00049
                                      HHHTS---HHHHHHHHT--HHHH CS
                      Sigma70_r4_2 21 lryleglsykEIAellgisegtV 43
                                      lr+  g+s +E A++lg+se+ +
  gi|242398075|ref|YP_002993499.1| 17 LRENSGYSVEELAKKLGVSEKKI 39
                                      67778***************876 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0    0.0042       2.8      25      41 ..      24      40 ..      22      42 .. 0.85
   2 ?    1.4   0.0      0.43   2.8e+02      26      40 ..     266     280 ..     265     286 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0042
                            HTH_10 25 tlkeLAkelGIskstls 41
                                      +++eLAk+lG+s+  ++
  gi|242398075|ref|YP_002993499.1| 24 SVEELAKKLGVSEKKIE 40
                                      689*********98876 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.43
                            HTH_10  26 lkeLAkelGIskstl 40 
                                       ++eLA + G+sk  +
  gi|242398075|ref|YP_002993499.1| 266 ISELARRYGVSKHVM 280
                                       579********9766 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0    0.0064       4.3       9      29 ..      20      39 ..      13      42 .. 0.78
   2 ?   -0.1   0.0       1.5   9.8e+02      15      26 ..     266     277 ..     255     281 .. 0.86
   3 ?    0.9   0.1      0.73   4.9e+02      29      53 ..     295     319 ..     269     324 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0064
                            HTH_29  9 aeGvstvsqiAkllglsrrtv 29
                                      + G s v ++Ak lg+s++++
  gi|242398075|ref|YP_002993499.1| 20 NSGYS-VEELAKKLGVSEKKI 39
                                      45665.************987 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.5
                            HTH_29  15 vsqiAkllglsr 26 
                                       +s++A+++g+s+
  gi|242398075|ref|YP_002993499.1| 266 ISELARRYGVSK 277
                                       799*******96 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.73
                            HTH_29  29 vyrwlkrfeegGlaalldrrrsgrp 53 
                                        +r+++ f++  l+ l++++ sg  
  gi|242398075|ref|YP_002993499.1| 295 YRRFKESFDKAKLEELKKKKVSGSR 319
                                       5788999999999999996556654 PP

>> UPF0175  Uncharacterised protein family (UPF0175)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       3.2   2.1e+03      56      71 ..     216     231 ..     208     233 .. 0.82
   2 ?   10.1   0.1   0.00075       0.5      27      52 ..     339     364 ..     325     367 .] 0.82

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 3.2
                           UPF0175  56 rrgiplinydeeelee 71 
                                       ++gi+ i++d e +e 
  gi|242398075|ref|YP_002993499.1| 216 SEGICEIDVDSEKFEI 231
                                       789**9*****99985 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00075
                           UPF0175  27 klYeegrlSlgkAaelaglsrvefle 52 
                                        +Ye+g++S+ +A+++++++    ++
  gi|242398075|ref|YP_002993499.1| 339 RAYERGEISFFEASRILNMKIKYAER 364
                                       68*****************8765555 PP

>> DUF2623  Protein of unknown function (DUF2623)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       6.4   4.3e+03      64      77 ..     171     184 ..     162     203 .. 0.56
   2 ?   10.1   0.0   0.00098      0.65      22      72 ..     229     281 ..     212     296 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 6.4
                           DUF2623  64 yGlerdavaeffke 77 
                                       y l+ d v  f  +
  gi|242398075|ref|YP_002993499.1| 171 YPLKNDNVRAFSLK 184
                                       55555555555333 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00098
                           DUF2623  22 adirkycadyrrGyvlGyshrl..aekkgdrqlaafeaGelarryGlerdava 72 
                                        +i+++c+ +   +++  s     +ekk +r+l+     elarryG+++++++
  gi|242398075|ref|YP_002993499.1| 229 FEIERFCDKFAAEFLVPASDLKleIEKKAKRELSDDIISELARRYGVSKHVMM 281
                                       58999*********9998864412689999******************99877 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0    0.0016         1       8      30 ..      13      35 ..       9      38 .. 0.94
   2 ?   -1.5   0.0       3.8   2.5e+03       2      15 ..      50      63 ..      49      64 .. 0.84
   3 ?   -2.4   0.0         7   4.6e+03      20      31 ..     266     277 ..     265     280 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0016
                                      HHHHHHHSTTEEHHHHHHHHTS- CS
                              MarR  8 iLrilyeqgplsvseLakklgvs 30
                                      iLr+l+e+ + sv eLakklgvs
  gi|242398075|ref|YP_002993499.1| 13 ILRKLRENSGYSVEELAKKLGVS 35
                                      9********************98 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.8
                                      -HHHHHHHHHHHHS CS
                              MarR  2 tltqfviLrilyeq 15
                                      t tq++ L+++y  
  gi|242398075|ref|YP_002993499.1| 50 TITQLKSLAKIYKI 63
                                      899***9*999975 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 7
                                       HHHHHHHHTS-H CS
                              MarR  20 vseLakklgvsk 31 
                                       +seLa++ gvsk
  gi|242398075|ref|YP_002993499.1| 266 ISELARRYGVSK 277
                                       689****99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       776  (0.0432818); expected 358.6 (0.02)
Passed bias filter:                      589  (0.0328518); expected 358.6 (0.02)
Passed Vit filter:                        97  (0.00541023); 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: 0.61u 0.35s 00:00:00.96 Elapsed: 00:00:00.51
# Mc/sec: 2146.65
//
Query:       gi|242398076|ref|YP_002993500.1|  [L=108]
Description: hypothetical protein TSIB_0083 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.9e-11   42.3   0.2    1.5e-10   41.2   0.2    1.5  1  DUF4411   Domain of unknown function (DUF4411)


Domain annotation for each model (and alignments):
>> DUF4411  Domain of unknown function (DUF4411)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.2   0.2   8.6e-15   1.5e-10      55     159 ..       3     107 ..       1     108 [] 0.78

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 8.6e-15
                           DUF4411  55 skWakenesieklesaedlavveevgkvakwvivesekyskaakkeflsvaDpfliAaAlakna....tvVTkEvk. 126
                                        +W+k++++   ++ ++d + ++++++v+   + +++  +k  +++ +++aDp+++ +A++ +       V  +vk 
  gi|242398076|ref|YP_002993500.1|   3 VEWCKNHKK---MFIDPDNHQIKIFKSVRGA-YEKDQWNKK--ITQPGPWADPWIVTLAIQLRErskiLGVQGNVKi 73 
                                       58*******...9******************.677777777..45888***********984433333224444445 PP

                           DUF4411 127 ..kpnkkknkvkIPdvcealgikcidlfellrelg 159
                                         ++nk+k +  IP+++e +gi+ ++l+e++re g
  gi|242398076|ref|YP_002993500.1|  74 itQENKNK-RNNIPKIAESFGIESLNLIEFFREIG 107
                                       53333344.789*******************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 687.40
//
Query:       gi|242398077|ref|YP_002993501.1|  [L=148]
Description: transcriptional regulatory protein [Thermococcus sibiricus MM 739]
Scores for complete 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   81.7   0.1      4e-23   81.2   0.1    1.2  1  TFX_C         DNA_binding protein, TFX, C-term
    3.3e-08   32.9   1.2    6.8e-08   31.9   1.2    1.5  1  Sigma70_r4    Sigma-70, region 4
    1.1e-07   31.3   1.3    1.8e-07   30.6   1.3    1.4  1  GerE          Bacterial regulatory proteins, luxR family
    7.5e-06   25.5   0.5    7.5e-06   25.5   0.5    1.6  1  Sigma70_r4_2  Sigma-70, region 4
    0.00056   19.6   0.1     0.0011   18.7   0.1    1.5  1  HTH_23        Homeodomain-like domain
     0.0014   18.6   0.3     0.0036   17.2   0.3    1.7  1  HTH_37        Helix-turn-helix domain
     0.0018   18.5   0.5     0.0031   17.7   0.5    1.5  1  KORA          TrfB plasmid transcriptional repressor
     0.0026   17.5   0.1     0.0051   16.5   0.1    1.4  1  HTH_38        Helix-turn-helix domain
  ------ inclusion threshold ------
      0.013   15.6   0.1      0.023   14.8   0.1    1.4  1  HTH_28        Helix-turn-helix domain
      0.019   15.2   1.0      0.019   15.2   1.0    1.7  2  UPF0122       Putative helix-turn-helix protein, YlxM / p13 l
      0.023   14.8   0.1      0.044   13.9   0.1    1.5  1  HTH_7         Helix-turn-helix domain of resolvase
      0.024   14.7   0.0       0.05   13.6   0.0    1.6  1  KorB          KorB domain
      0.024   14.2   0.4       0.11   12.1   0.3    2.2  3  HTH_24        Winged helix-turn-helix DNA-binding
      0.031   14.3   0.2      0.064   13.3   0.2    1.6  1  HTH_19        Helix-turn-helix domain
      0.034   14.2   0.1      0.054   13.5   0.1    1.4  1  HTH_29        Winged helix-turn helix
      0.045   14.4   0.2      0.076   13.7   0.3    1.5  1  Pex14_N       Peroxisomal membrane anchor protein (Pex14p) co
      0.047   13.7   0.0       0.11   12.4   0.0    1.7  1  HTH_Crp_2     Crp-like helix-turn-helix domain
      0.053   13.4   0.0       0.11   12.4   0.0    1.5  1  MarR_2        MarR family
      0.059   13.4   0.4       0.14   12.2   0.3    1.8  1  HTH_3         Helix-turn-helix
      0.067   13.1   0.1       0.16   11.9   0.1    1.7  1  MarR          MarR family
       0.11   12.8   0.3       0.22   11.8   0.3    1.5  1  SAM_DrpA      DNA processing protein A sterile alpha motif do
       0.97    9.3   3.3         35    4.3   3.3    2.4  1  HTH_10        HTH DNA binding domain


Domain annotation for each model (and alignments):
>> TFX_C  DNA_binding protein, TFX, C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.2   0.1   4.9e-26     4e-23       1      83 []      54     134 ..      54     134 .. 0.98

  Alignments for each domain:
  == domain 1  score: 81.2 bits;  conditional E-value: 4.9e-26
                                       SS-HHHHHHHH---EEEEE--GGGHHHHHHHHHHHHHHHS-S----HHHHHHHHHHH-SSS-----SSS-EEEEESS CS
                             TFX_C   1 AreTlaflealdapvlvtieeGtdlfdipkiiyaeadkagikvkydtieLikllreeapeaikgrvvkedlevyite 77 
                                       A++Tl ++e+l+++  v++++G+d+f++p+ i+++adk gikv+y+t+e+i +l e+ap  i++r  ked+  ++++
  gi|242398077|ref|YP_002993501.1|  54 AKNTLLLWEQLNSKAAVEVKKGEDIFKVPEEIFKQADKVGIKVPYTTAEIIAFLVENAP--IEERIAKEDFILFLDS 128
                                       8**********************************************************..9*************** PP

                                       SSSEEE CS
                             TFX_C  78 dGeirv 83 
                                       ++++r+
  gi|242398077|ref|YP_002993501.1| 129 HDKLRI 134
                                       *99986 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   1.2   8.3e-11   6.8e-08       5      48 ..       9      51 ..       8      53 .. 0.94

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 8.3e-11
                                      S-HHHHHHHHHHHTTT--HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                        Sigma70_r4  5 LpererevlelrfgeglTleEIgerlgiSrerVrqiekrAlrkL 48
                                      L+e++ ++l+lr  +gl ++EI+e+lg Sr  V+ +ekrA++k+
  gi|242398077|ref|YP_002993501.1|  9 LTEQQLKILQLRA-KGLKQSEIAEILGTSRANVSILEKRAMEKI 51
                                      99**********6.7789************************97 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   1.3   2.3e-10   1.8e-07       3      46 ..       9      52 ..       7      59 .. 0.95

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 2.3e-10
                                      S-HHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHHHHT CS
                              GerE  3 LskRErevLrllaeGksnkeIAeelniSekTVkvhksnimkKLn 46
                                      L+++++++L+l a+G++  eIAe+l+ S  +V++  +++m+K++
  gi|242398077|ref|YP_002993501.1|  9 LTEQQLKILQLRAKGLKQSEIAEILGTSRANVSILEKRAMEKIE 52
                                      9*****************************************96 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.5   9.2e-09   7.5e-06      11      54 .]       9      51 ..       4      51 .. 0.93

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 9.2e-09
                                      S-HHHHHHHHHHHTS---HHHHHHHHT--HHHHHHHHHHHHHHH CS
                      Sigma70_r4_2 11 LperqreifllryleglsykEIAellgisegtVksrlsRArkkL 54
                                      L+e+q +i+ l + +gl++ EIAe+lg+s ++V    +RA++k+
  gi|242398077|ref|YP_002993501.1|  9 LTEQQLKILQL-RAKGLKQSEIAEILGTSRANVSILEKRAMEKI 51
                                      89*********.68*******************99999999885 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   1.4e-06    0.0011       8      40 ..      14      46 ..      10      54 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.4e-06
                            HTH_23  8 lrillllaeGlsvreIAreLgvsrrTvyrwlkr 40
                                      l+il+l a+Gl ++eIA++Lg sr  v+   kr
  gi|242398077|ref|YP_002993501.1| 14 LKILQLRAKGLKQSEIAEILGTSRANVSILEKR 46
                                      79**********************877776666 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.3   4.5e-06    0.0036      27      57 ..      19      49 ..       9      55 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4.5e-06
                                      HHHCT--HHHHHHHHT--HHHHHHHHTT--T CS
                            HTH_37 27 iekrelsqseaaqllgiaqPkvsrllrgkls 57
                                      +++++l+qse+a++lg+++++vs l++   +
  gi|242398077|ref|YP_002993501.1| 19 LRAKGLKQSEIAEILGTSRANVSILEKRAME 49
                                      5789*********************997665 PP

>> KORA  TrfB plasmid transcriptional repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.5   3.9e-06    0.0031      26      62 ..      18      54 ..       4      74 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.9e-06
                              KORA 26 gvLVegkkqadvatelgltkqavsqavkrvwaahaer 62
                                      ++  +g kq+++a+ lg ++ +vs ++kr+++  ++ 
  gi|242398077|ref|YP_002993501.1| 18 QLRAKGLKQSEIAEILGTSRANVSILEKRAMEKIEKA 54
                                      5667899************************987764 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   6.3e-06    0.0051       9      35 ..      12      38 ..       9      41 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.3e-06
                            HTH_38  9 eReeIerllaeGlslreIArrLgrsps 35
                                      +  +I +l+a+Gl ++eIA +Lg s+ 
  gi|242398077|ref|YP_002993501.1| 12 QQLKILQLRAKGLKQSEIAEILGTSRA 38
                                      5678********************986 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1   2.8e-05     0.023       2      29 ..      13      40 ..      12      47 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.8e-05
                            HTH_28  2 RleiikllaaGhsvreaArelgisrrtv 29
                                       l+i++l a+G  ++e+A++lg+sr  v
  gi|242398077|ref|YP_002993501.1| 13 QLKILQLRAKGLKQSEIAEILGTSRANV 40
                                      699*********************9766 PP

>> UPF0122  Putative helix-turn-helix protein, YlxM / p13 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   1.0   2.3e-05     0.019      15      79 ..       6      69 ..       1      91 [. 0.87
   2 ?   -1.7   0.0       4.1   3.4e+03      51      65 ..     129     143 ..     113     145 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.3e-05
                           UPF0122 15 qsLLTekqanylelyyadDlSlsEiAeefnvsrqavydnikrtekllekyEekLkllekykkree 79
                                      ++ LTe+q + l+l  a+ l  sEiAe   +sr  v+   kr+ + +ek  + L l e+ + +  
  gi|242398077|ref|YP_002993501.1|  6 KTFLTEQQLKILQLR-AKGLKQSEIAEILGTSRANVSILEKRAMEKIEKAKNTLLLWEQLNSKAA 69
                                      679*********995.789*************************************998877655 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 4.1
                           UPF0122  51 ydnikrtekllekyE 65 
                                       +d+++ te+lle+++
  gi|242398077|ref|YP_002993501.1| 129 HDKLRITESLLEELD 143
                                       777888888887765 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   5.4e-05     0.044      10      36 ..      12      38 ..       6      40 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.4e-05
                                      HHGGGGSSTTTT--STTTSSSS---SS CS
                             HTH_7 10 dinrvvkLleeGisiskIAkevnisRs 36
                                      ++  +++L+++G + s+IA+++++sR+
  gi|242398077|ref|YP_002993501.1| 12 QQLKILQLRAKGLKQSEIAEILGTSRA 38
                                      78899*********************8 PP

>> KorB  KorB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   6.1e-05      0.05       2      22 ..      22      42 ..      21      59 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.1e-05
                              KorB  2 kgvkqadIAkaLGksksfvsl 22
                                      kg+kq++IA++LG s++ vs 
  gi|242398077|ref|YP_002993501.1| 22 KGLKQSEIAEILGTSRANVSI 42
                                      89**************99996 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.3   0.00013      0.11       9      35 ..      14      41 ..       9      42 .. 0.80
   2 ?   -2.4   0.0       4.4   3.6e+03      24      32 ..      89      97 ..      89     101 .. 0.80
   3 ?   -2.8   0.0       5.8   4.7e+03       7      17 ..     102     112 ..      97     113 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00013
                            HTH_24  9 LelLqk.nprisqreLAerlglSpstvn 35
                                      L++Lq    ++ q+e+Ae lg S+++v+
  gi|242398077|ref|YP_002993501.1| 14 LKILQLrAKGLKQSEIAEILGTSRANVS 41
                                      5566662346**************9996 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.4
                            HTH_24 24 AerlglSps 32
                                      A+++g+ ++
  gi|242398077|ref|YP_002993501.1| 89 ADKVGIKVP 97
                                      899**9887 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 5.8
                            HTH_24   7 kILelLqknpr 17 
                                       +I+  L +n+ 
  gi|242398077|ref|YP_002993501.1| 102 EIIAFLVENAP 112
                                       68888888876 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2   7.9e-05     0.064      11      40 ..      22      51 ..      19      74 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.9e-05
                            HTH_19 11 lgltqeelaerlgisrskisaiEngkkdvp 40
                                      +gl+q e+ae lg+sr+  s +E+  ++++
  gi|242398077|ref|YP_002993501.1| 22 KGLKQSEIAEILGTSRANVSILEKRAMEKI 51
                                      8**************999999987644444 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   6.6e-05     0.054       2      29 ..      14      40 ..      13      56 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.6e-05
                            HTH_29  2 aqallllaeGvstvsqiAkllglsrrtv 29
                                      +++l+l a+G++  s+iA++lg sr  v
  gi|242398077|ref|YP_002993501.1| 14 LKILQLRAKGLK-QSEIAEILGTSRANV 40
                                      689********9.************866 PP

>> Pex14_N  Peroxisomal membrane anchor protein (Pex14p) conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.3   9.3e-05     0.076      26      56 ..      16      46 ..      10     100 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 9.3e-05
                           Pex14_N 26 vaFLesKGLtqeEIeeaLkraereeeasesa 56
                                      +  L+ KGL+q EI e L+ ++ + +  e++
  gi|242398077|ref|YP_002993501.1| 16 ILQLRAKGLKQSEIAEILGTSRANVSILEKR 46
                                      5569****************77666655432 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00014      0.11      22      39 ..      24      41 ..       7      50 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00014
                                      HHHHHHHHHTTSSHHHHH CS
                         HTH_Crp_2 22 ltqeelAsmlGltretvs 39
                                      l q e+A++lG++r  vs
  gi|242398077|ref|YP_002993501.1| 24 LKQSEIAEILGTSRANVS 41
                                      89**************98 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00013      0.11      16      45 ..      20      47 ..      15      50 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00013
                                      CTTTSEEEHHHHHHHHTSSHHHHHHHHHHH CS
                            MarR_2 16 rrpgrdltvgelarrlglsksavsrilkrL 45
                                      r+ g  l ++e+a+ lg s+++vs + kr+
  gi|242398077|ref|YP_002993501.1| 20 RAKG--LKQSEIAEILGTSRANVSILEKRA 47
                                      4455..99***************9776665 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.3   0.00018      0.14       6      28 ..      20      42 ..      15      58 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00018
                                      HHTTHHHHHHHHHHTSSHHHHHH CS
                             HTH_3  6 kqlglsqeeLAeklGvsrstisr 28
                                       ++gl q e+Ae lG sr+ +s 
  gi|242398077|ref|YP_002993501.1| 20 RAKGLKQSEIAEILGTSRANVSI 42
                                      369***************99985 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00019      0.16       1      35 [.       9      41 ..       9      50 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00019
                                      --HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHH CS
                              MarR  1 ltltqfviLrilyeqgplsvseLakklgvskstvt 35
                                      lt++q++iL +  +  +l++se+a+ lg+s+++v+
  gi|242398077|ref|YP_002993501.1|  9 LTEQQLKILQL--RAKGLKQSEIAEILGTSRANVS 41
                                      68888888886..8899****************98 PP

>> SAM_DrpA  DNA processing protein A sterile alpha motif domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.3   0.00027      0.22       5      54 ..      15      64 ..      12      69 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00027
                          SAM_DrpA  5 elykLKkAGLtNlnilnildYqekneksLsLrdmavvSkcknpalFiekY 54
                                       +++L+  GL+  +i +il  ++ n + L  r+m ++ k kn +l +e+ 
  gi|242398077|ref|YP_002993501.1| 15 KILQLRAKGLKQSEIAEILGTSRANVSILEKRAMEKIEKAKNTLLLWEQL 64
                                      6899*******************************************975 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   3.3     0.043        35      21      51 ..      21      51 ..       9      53 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.043
                            HTH_10 21 PRrvtlkeLAkelGIskstlsehLrkaeskl 51
                                       +  + +e+A++lG s++++s   ++a++k+
  gi|242398077|ref|YP_002993501.1| 21 AKGLKQSEIAEILGTSRANVSILEKRAMEKI 51
                                      4566778999999999999998888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       868  (0.0484132); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); 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: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 908.96
//
Query:       gi|242398078|ref|YP_002993502.1|  [L=224]
Description: effector of murein hydrolase [Thermococcus sibiricus MM 739]
Scores for complete 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-74  249.1  14.8    3.6e-74  248.9  14.8    1.0  1  LrgB             LrgB-like family
  ------ inclusion threshold ------
      0.042   13.6   0.7      0.042   13.6   0.7    1.8  2  AGTRAP           Angiotensin II, type I receptor-associated p
       0.54    9.8   4.1       0.63    9.6   0.8    2.3  3  TRAP-gamma       Translocon-associated protein, gamma subunit
       0.91    9.8   5.8       0.53   10.5   1.1    2.7  3  Phage_r1t_holin  Putative lactococcus lactis phage r1t holin
        7.2    6.7  11.8       0.53   10.4   4.8    2.2  2  FUSC_2           Fusaric acid resistance protein-like


Domain annotation for each model (and alignments):
>> LrgB  LrgB-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  248.9  14.8     1e-77   3.6e-74       1     213 [.       9     221 ..       9     222 .. 0.99

  Alignments for each domain:
  == domain 1  score: 248.9 bits;  conditional E-value: 1e-77
                              LrgB   1 TllaYllakalykklkkpllnPvlvaivliillllllgisyetYkegakllsllLgpatVaLAvpLYkqrellkknl 77 
                                       T+ +++l  ++y+k k+ +lnPvl++i+ i+l+l +++i+yetY+e+a++ls+lLgpa+V+LA+pLYkqr ++k++ 
  gi|242398078|ref|YP_002993502.1|   9 TIGTFYLFSKIYEKRKTFYLNPVLLSIITIALFLHITEIKYETYMESAQILSFLLGPAVVSLAIPLYKQRGIIKAYS 85 
                                       899************************************************************************** PP

                              LrgB  78 laillgllvgslvsllsavllakllglseelllsllpkSvTtpiAmevseelgGipsltavlviltGilGallgell 154
                                       ++i++g+++g ++++lsa+++ak+lg ++e+lls++pkS+Tt+iA++vse++gGip+ltavlviltGilG+++g  +
  gi|242398078|ref|YP_002993502.1|  86 KQIFFGIVFGGALAILSAFYVAKILGGTPEVLLSIAPKSITTAIAIGVSEKIGGIPALTAVLVILTGILGNAVGIEI 162
                                       ***************************************************************************** PP

                              LrgB 155 lkllrikdpvarGlalGtashaiGtakalelgeeagafsslamvlaGiltallaplllk 213
                                       l++ ++kd+varGla+G++sh++Gta+++  +e +ga+s+lam+l+Gi+t+l++p+l+k
  gi|242398078|ref|YP_002993502.1| 163 LNISKVKDKVARGLAMGVTSHGLGTARIILDDELSGAVSGLAMALNGIFTSLILPYLIK 221
                                       *******************************************************9986 PP

>> AGTRAP  Angiotensin II, type I receptor-associated protein (AGTRAP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.7   1.2e-05     0.042      58     108 ..      30      79 ..      24      93 .. 0.89
   2 ?   -2.3   0.1      0.96   3.5e+03      48      85 ..     143     178 ..     127     183 .. 0.55

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.2e-05
                            AGTRAP  58 tillDiihlsiyyprkalsdvkrfsagmailsLllkPvscflvyrmyreRG 108
                                        +ll ii+++++ + ++++  + +  +  ils ll P  + l+   y++RG
  gi|242398078|ref|YP_002993502.1|  30 PVLLSIITIALFLHITEIK-YETYMESAQILSFLLGPAVVSLAIPLYKQRG 79 
                                       6899***********8887.89999999**********************9 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.96
                            AGTRAP  48 ismfliglvltillDiihlsiyyprkalsdvkrfsagm 85 
                                       ++ +l++ ++ il + + + i   + +++d    +++m
  gi|242398078|ref|YP_002993502.1| 143 LTAVLVI-LTGILGNAVGIEILNIS-KVKDKVARGLAM 178
                                       4444433.34566666666665444.445544445555 PP

>> TRAP-gamma  Translocon-associated protein, gamma subunit (TRAP-gamma)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.8   0.00018      0.63      18      57 ..      23      62 ..      16      87 .. 0.78
   2 ?    1.4   0.4     0.059   2.1e+02      22      62 ..      63     101 ..      53     110 .. 0.70
   3 ?    0.1   0.1      0.14   5.1e+02     134     164 ..      97     127 ..      74     131 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00018
                        TRAP-gamma 18 salfyvnalivsaipiwlfwrihqmelleslilfvivtll 57
                                      ++ fy+n +++s+i i lf  i +++  + + +  i++ l
  gi|242398078|ref|YP_002993502.1| 23 RKTFYLNPVLLSIITIALFLHITEIKYETYMESAQILSFL 62
                                      578**********************998888777666543 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.059
                        TRAP-gamma  22 yvnalivsaipiwlfwrihqmelleslilfvivtllstyll 62 
                                        + a++  aip++ + +i  ++ +++ i+f iv   + ++l
  gi|242398078|ref|YP_002993502.1|  63 LGPAVVSLAIPLYKQRGI--IKAYSKQIFFGIVFGGALAIL 101
                                       466788889999999888..667888888888765554444 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.14
                        TRAP-gamma 134 alllvlsfyllksfsptvnyilsvvvasglv 164
                                       al ++++fy+ k +  t  ++ls++  s  +
  gi|242398078|ref|YP_002993502.1|  97 ALAILSAFYVAKILGGTPEVLLSIAPKSITT 127
                                       5778888998888888888888887666555 PP

>> Phage_r1t_holin  Putative lactococcus lactis phage r1t holin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.25     9e+02      36      51 ..      55      70 ..      51      74 .. 0.84
   2 ?   10.5   1.1   0.00015      0.53      38      61 ..     136     159 ..     117     161 .. 0.91
   3 ?   -2.5   0.0       1.7   6.2e+03      40      54 ..     198     213 ..     192     215 .. 0.65

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.25
                   Phage_r1t_holin 36 waaaasvaalaAvvSv 51
                                       a+++s   ++AvvS+
  gi|242398078|ref|YP_002993502.1| 55 SAQILSFLLGPAVVSL 70
                                      5789999999****97 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00015
                   Phage_r1t_holin  38 aaasvaalaAvvSvltSivsaavg 61 
                                       +++++ al+Av+ +lt i++ avg
  gi|242398078|ref|YP_002993502.1| 136 KIGGIPALTAVLVILTGILGNAVG 159
                                       799*****************9987 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 1.7
                   Phage_r1t_holin  40 asvaalaAvv.SvltS 54 
                                       ++v++la ++  + tS
  gi|242398078|ref|YP_002993502.1| 198 GAVSGLAMALnGIFTS 213
                                       7888888655246666 PP

>> FUSC_2  Fusaric acid resistance protein-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.5      0.32   1.1e+03      69      97 ..       7      36 ..       2      46 .. 0.41
   2 ?   10.4   4.8   0.00015      0.53      17      99 ..      66     153 ..      62     168 .. 0.68

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.32
                            FUSC_2 69 llvfliafflkrnyal.afifltllallly 97
                                       +++ ++++ ++ y    +++l++++l+++
  gi|242398078|ref|YP_002993502.1|  7 FITIGTFYLFSKIYEKrKTFYLNPVLLSII 36
                                      233333344444443312233333333333 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00015
                            FUSC_2  17 alitaaivlsptlgasltravqRilGtvlGavlalllly....llpgnlalallvfllvfliaffl.krnyalafif 88 
                                       a+++ ai l + +g    + +q ++G v+G +la+l+ +    +l g+  ++l ++  ++++a+ +  +   +++ +
  gi|242398078|ref|YP_002993502.1|  66 AVVSLAIPLYKQRGIIKAYSKQIFFGIVFGGALAILSAFyvakILGGTPEVLLSIAPKSITTAIAIgVSEKIGGIPA 142
                                       789999******************************88723333334333333333334444444404445666667 PP

                            FUSC_2  89 ltllalllysl 99 
                                       lt+++++l+ +
  gi|242398078|ref|YP_002993502.1| 143 LTAVLVILTGI 153
                                       77777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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 0.28s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1620.86
//
Query:       gi|242398079|ref|YP_002993503.1|  [L=113]
Description: effector of murein hydrolase LrgA [Thermococcus sibiricus MM 739]
Scores for complete 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-31  107.0   7.1    4.2e-31  106.8   7.1    1.1  1  LrgA       LrgA family
     0.0019   17.8   2.7     0.0023   17.6   2.7    1.2  1  CbiQ       Cobalt transport protein
  ------ inclusion threshold ------
      0.022   14.9   1.9      0.023   14.8   0.3    1.8  2  Pox_A14    Poxvirus virion envelope protein A14
      0.028   13.0   5.9      0.033   12.8   5.9    1.0  1  2HCT       2-hydroxycarboxylate transporter family
      0.085   12.5   0.0       0.12   12.0   0.0    1.1  1  RanGAP1_C  RanGAP1 C-terminal domain
       0.21   11.5   1.1       0.35   10.8   0.3    1.6  2  DUF5134    Domain of unknown function (DUF5134)


Domain annotation for each model (and alignments):
>> LrgA  LrgA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.8   7.1   1.4e-34   4.2e-31       2      93 ..      13     104 ..      12     105 .. 0.98

  Alignments for each domain:
  == domain 1  score: 106.8 bits;  conditional E-value: 1.4e-34
                              LrgA   2 llGellsrllplpiPgsviGlllLlllLltkivklekveeaadfllkhlallFvPagvgvmeyldllkaellailva 78 
                                       ++Ge +s+ll+lpiPg+viG++lL+l+L++k++ +++ve+ a+f++k+++++F+P+gvgv++y++l+ka+l++i+va
  gi|242398079|ref|YP_002993503.1|  13 FIGEGISELLHLPIPGNVIGMILLTLALISKLIDISDVEREAEFFIKNMSVMFIPPGVGVIAYWGLIKAQLIPIFVA 89 
                                       89*************************************************************************** PP

                              LrgA  79 lvvstllvlvvtglv 93 
                                       lvvs +l+lv t+ +
  gi|242398079|ref|YP_002993503.1|  90 LVVSFALTLVLTAKF 104
                                       ************976 PP

>> CbiQ  Cobalt transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   2.7   7.6e-07    0.0023      64     129 ..      29     110 ..       3     113 .] 0.71

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 7.6e-07
                                       HHHHHHHHHE........................EECTTEEE...E-TTHHHHHHHHHHHHHHHHHHHHHHHHHS-H CS
                              CbiQ  64 lllgllillf.................qlittegefvfagggqisitseGllrglllalRiltllslllllalTTpp 123
                                       +++g+++l++                 ++i+ +  ++f + g   i ++Gl+++ l+ ++++ ++s++l l+lT ++
  gi|242398079|ref|YP_002993503.1|  29 NVIGMILLTLalisklidisdvereaeFFIK-NMSVMFIPPGVGVIAYWGLIKAQLIPIFVALVVSFALTLVLTAKF 104
                                       4555555555557778899999999974443.33333333333599******************************* PP

                                       HHHHHH CS
                              CbiQ 124 eeltss 129
                                        e++s+
  gi|242398079|ref|YP_002993503.1| 105 VEILSG 110
                                       ***987 PP

>> Pox_A14  Poxvirus virion envelope protein A14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.3   7.7e-06     0.023      16      53 ..      30      66 ..      27      83 .. 0.82
   2 ?   -0.9   0.2      0.62   1.8e+03      48      59 ..      90     101 ..      69     107 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 7.7e-06
                           Pox_A14 16 iaGiiLLilacifafvdfskststtdkawralsivsFi 53
                                      ++G+iLL+la+i   +d+s ++ +++   + +s++ Fi
  gi|242398079|ref|YP_002993503.1| 30 VIGMILLTLALISKLIDISDVEREAEFFIKNMSVM-FI 66
                                      68*****************************9987.55 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.62
                           Pox_A14  48 sivsFilgivil 59 
                                        +vsF l++v++
  gi|242398079|ref|YP_002993503.1|  90 LVVSFALTLVLT 101
                                       355566655554 PP

>> 2HCT  2-hydroxycarboxylate transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   5.9   1.1e-05     0.033     250     356 ..       2     105 ..       1     110 [. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.1e-05
                              2HCT 250 gaglllalslyllgvllekligvkipalvlmiilvvivkllnlipeeleegakqlykfisknltlall.vgiGvalt 325
                                        +gl +++ + ++g+ +++l++ +ip+ v+ +il+ ++ +++li+    + +++  +f++kn+ ++ +  g+Gv   
  gi|242398079|ref|YP_002993503.1|   2 YKGLTIVFGFLFIGEGISELLHLPIPGNVIGMILLTLALISKLIDI--SD-VEREAEFFIKNMSVMFIpPGVGVI-A 74 
                                       6899****************9999**77776666777778888863..23.33334555555554444269**99.7 PP

                              2HCT 326 dlkeliaaltvqyviiilvtVvgavlgaalv 356
                                        +  + a l + +v +++++ +++vl+a +v
  gi|242398079|ref|YP_002993503.1|  75 YWGLIKAQLIPIFVALVVSFALTLVLTAKFV 105
                                       8888888888888888888888888888776 PP

>> RanGAP1_C  RanGAP1 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0     4e-05      0.12      27      73 ..      18      64 ..      15      66 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4e-05
                         RanGAP1_C 27 vssFlafPspeKLlkLGakraelieqqvdvsdaekvveaflkissvy 73
                                      +s+ l+ P p  ++ +      li++ +d+sd+e+ +e+f+k  sv+
  gi|242398079|ref|YP_002993503.1| 18 ISELLHLPIPGNVIGMILLTLALISKLIDISDVEREAEFFIKNMSVM 64
                                      5677888888888888888999***********************97 PP

>> DUF5134  Domain of unknown function (DUF5134)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.51   1.5e+03     104     121 ..       5      22 ..       1      45 [. 0.66
   2 ?   10.8   0.3   0.00012      0.35      16      51 ..      61     101 ..      59     111 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.51
                           DUF5134 104 vtgvlavyFaaaalvwla 121
                                       +t+v+ ++F++ ++  l+
  gi|242398079|ref|YP_002993503.1|   5 LTIVFGFLFIGEGISELL 22 
                                       778888888887776664 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00012
                           DUF5134  16 MaaMawpagvalpsagq.....lavvfalaalwflvlavvr 51 
                                       M +M++p+gv + + +      l+ +f+++++ f++++v  
  gi|242398079|ref|YP_002993503.1|  61 MSVMFIPPGVGVIAYWGlikaqLIPIFVALVVSFALTLVLT 101
                                       99***********9995567789999999999999988764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 889.49
//
Query:       gi|242398080|ref|YP_002993504.1|  [L=136]
Description: translation initiation inhibitor, yjgF family [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.2e-45  152.7   0.1    4.7e-45  152.5   0.1    1.0  1  Ribonuc_L-PSP  Endoribonuclease L-PSP
  ------ inclusion threshold ------
      0.061   13.7   0.4        0.1   12.9   0.4    1.4  1  TAL_effector   TAL effector repeat
       0.18   11.6   0.0       0.24   11.2   0.0    1.1  1  HAD_SAK_1      HAD domain family 1 in Swiss Army Knife RNA re


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 !  152.5   0.1   7.9e-49   4.7e-45       1     120 [.      14     134 ..      14     135 .. 0.97

  Alignments for each domain:
  == domain 1  score: 152.5 bits;  conditional E-value: 7.9e-49
                                       STTSTTTSSS-BSEEE...ETTEEEEEEE-SB-TTTSCB.-SSHHHHHHHHHHHHHHHHHHTT--GGGEEEEEEEES CS
                     Ribonuc_L-PSP   1 teaapaaaapYsqavk...agnlvyvsGqlpldpetgelvegdveeqtrqalenlkavLaaagaslsdvVkvtvFla 74 
                                       te+ap++++pYsq++     ++++++sGq+p+dpetgelv+gd++ q+rqa+enl avL+aaga+++dvVkv+v+l 
  gi|242398080|ref|YP_002993504.1|  14 TENAPQPIGPYSQGILvenPDKILFISGQIPIDPETGELVKGDITRQARQAIENLLAVLEAAGATVDDVVKVNVYLD 90 
                                       579**********887567789******************************************************* PP

                                       SGGGHHHHHHHHHHHSSSSTS--EEEEEE-SBSGGG-SEEEEEEEE CS
                     Ribonuc_L-PSP  75 diedfaevnevyaeafdelkeaParsaveVaaLpkgakvEIeaiav 120
                                       d++df e+n+vy+e+f + k  Par++v+Va+Lpk++k+EIeaia+
  gi|242398080|ref|YP_002993504.1|  91 DMNDFGEFNKVYEEYFGHSK--PARAVVQVARLPKDVKIEIEAIAM 134
                                       *******************8..**********************97 PP

>> TAL_effector  TAL effector repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.4   1.7e-05       0.1       5      30 ..      60      85 ..      56      85 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.7e-05
                                      HHHHHHHHHHHHHHHTT--HHHHHHH CS
                      TAL_effector  5 QALeAVlahgpaLrqrGfSradIVkI 30
                                      QA++A+ +++ +L   G + +d+Vk+
  gi|242398080|ref|YP_002993504.1| 60 QARQAIENLLAVLEAAGATVDDVVKV 85
                                      9***********************95 PP

>> HAD_SAK_1  HAD domain family 1 in Swiss Army Knife RNA repair proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0     4e-05      0.24     130     191 ..      71     131 ..      54     135 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4e-05
                         HAD_SAK_1 130 fledlletyksleeitiYedrpkhvkkfkefleklnkkkkpikaeviqvaelskyldpekEv 191
                                       +le    t++++ ++++Y d  +   +f++  e++  + kp    v+qva+l k ++ e+E+
  gi|242398080|ref|YP_002993504.1|  71 VLEAAGATVDDVVKVNVYLDDMNDFGEFNKVYEEYFGHSKP-ARAVVQVARLPKDVKIEIEA 131
                                       5555556788999***********************99998.899*********99999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); 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 0.24s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 972.36
//
Query:       gi|242398081|ref|YP_002993505.1|  [L=263]
Description: hypothetical protein TSIB_0088 [Thermococcus sibiricus MM 739]
Scores for complete 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-50  170.7   6.3    5.4e-37  127.0   0.8    2.1  2  DUF2666   Protein of unknown function (DUF2666)
  ------ inclusion threshold ------
      0.033   13.7   0.0      0.054   13.0   0.0    1.2  1  DUF4846   Domain of unknown function (4846)
      0.038   14.4   0.0        0.3   11.5   0.0    2.3  2  PDZ_4     PDZ domain
       0.13   12.4   0.1        3.9    7.7   0.0    2.4  2  zf-DBF    DBF zinc finger
       0.15   12.4   0.0       0.56   10.5   0.0    1.9  2  HalOD1    Halobacterial output domain 1


Domain annotation for each model (and alignments):
>> DUF2666  Protein of unknown function (DUF2666)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.7   0.5   9.7e-16   3.5e-12       1     115 [.       4     115 ..       4     124 .. 0.72
   2 !  127.0   0.8   1.5e-40   5.4e-37       2     134 ..     139     262 ..     138     263 .] 0.96

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 9.7e-16
                                       SSEEEEEEEETTEEEEEEEE--TTS-HHHHHHHHHHHHHHHHHHHHHHTT--HHHHHHHTTT--S--S....HHHHH CS
                           DUF2666   1 edkieftakkgkWivvkklkiDektedleiarlLasieetvskkikdylpfDlekleeiadeikkkkkgrvkeedis 77 
                                       ed+i fta +++W v  kl      +d +ia  La + +tv+ k+++yl   + ++ +i++         ++e+d+ 
  gi|242398081|ref|YP_002993505.1|   4 EDHIAFTANHKNWKVGDKLLA---MDDRQIAHFLAMVSNTVTLKLPEYLTE-VMNVAGIMS---LAE--EMTEKDVW 71 
                                       8**************999864...45679*******************963.333333333...222..36789*** PP

                                       HHHHHHHT-...............---HHH....HHHHHHHHHH CS
                           DUF2666  78 evleklkspattkklnki..tdskegkeil....kvilarivLe 115
                                       e+l+ lksp+t++kln +  +++k+ k++l    k++l+r++L+
  gi|242398081|ref|YP_002993505.1|  72 ELLKTLKSPGTSRKLNPMifEENKKLKNHLlnvaKALLTREALS 115
                                       ****************7533567777776511114444454444 PP

  == domain 2  score: 127.0 bits;  conditional E-value: 1.5e-40
                                       SEEEEEEEETTEEEEEEEE--TTS-HHHHHHHHHHHHHHHHHHHHHHTT--HHHHHHHTTT--S--S....HHHHHH CS
                           DUF2666   2 dkieftakkgkWivvkklkiDektedleiarlLasieetvskkikdylpfDlekleeiadeikkkkkgrvkeedise 78 
                                       ++i+ftak+g+Wivvk+l+iD+kt+  +iar+Lasi+et++ ki+ y ++Dl+ +++ +++ikk +     e +i+ 
  gi|242398081|ref|YP_002993505.1| 139 EHINFTAKNGSWIVVKRLIIDNKTPMADIARILASINETAVSKIPLYGKIDLDGIRKWFGDIKKARS----EAEIKT 211
                                       8**************************************************************9999....****** PP

                                       HHHHHHT-.............---HHHHHHHHHHHHHTTT--SS--HHHHHHHH-X CS
                           DUF2666  79 vleklkspattkklnkitdskegkeilkvilarivLerlGiktkveskllekylek 134
                                       ++ek+      +     ++ +e+k+++k+++ r++Le++G+++++++k lekylek
  gi|242398081|ref|YP_002993505.1| 212 LVEKFFHIPVEN-----YAPNEFKDHAKIYALRVALEKVGLTIDIPAKPLEKYLEK 262
                                       ****98885554.....899***********************************9 PP

>> DUF4846  Domain of unknown function (4846)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.5e-05     0.054      96     157 ..       9      71 ..       3      75 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.5e-05
                           DUF4846  96 feadyskwaeGkrikvkgnk.vswvkkaekdksyksfrkYLdlvfayagtlsLekelkkvkle 157
                                       f+a++++w+ G ++   +++  + + +  +++   ++ +YL+ v++ ag +sL +e++++++ 
  gi|242398081|ref|YP_002993505.1|   9 FTANHKNWKVGDKLLAMDDRqIAHFLAMVSNTVTLKLPEYLTEVMNVAGIMSLAEEMTEKDVW 71 
                                       67899*******987766550555677777778889*********************998765 PP

>> PDZ_4  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   8.3e-05       0.3      24      52 ..      11      39 ..       3      56 .. 0.85
   2 ?   -0.3   0.0      0.38   1.4e+03      39      77 ..      66     110 ..      58     141 .. 0.48

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8.3e-05
                                      SSSSSS-TT-EEEEETTEEHHHHHHTTS- CS
                             PDZ_4 24 eeklelkvGDellefdgkpvkevveelke 52
                                       ++ ++kvGD ll++d++++  +++ + +
  gi|242398081|ref|YP_002993505.1| 11 ANHKNWKVGDKLLAMDDRQIAHFLAMVSN 39
                                      57789****************99987765 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.38
                                       TTEEHHHHHHTTS-TT----......HHHHHHHHHHHTEEEGGGT CS
                             PDZ_4  39 dgkpvkevveelkesehkns......atdqslaevkLtsRegalg 77 
                                        +k+v e++++lk+ ++  +      +++++l +  L   ++ l+
  gi|242398081|ref|YP_002993505.1|  66 TEKDVWELLKTLKSPGTSRKlnpmifEENKKLKNHLLNVAKALLT 110
                                       567777888888776553331223322333333333333333333 PP

>> zf-DBF  DBF zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0011       3.9      23      43 ..       4      24 ..       1      25 [. 0.89
   2 ?    2.3   0.0     0.052   1.9e+02      22      42 ..     137     157 ..     132     159 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0011
                            zf-DBF 23 ekHrkFaenssnfeelDelis 43
                                      e H +F  n++n++  D+l++
  gi|242398081|ref|YP_002993505.1|  4 EDHIAFTANHKNWKVGDKLLA 24
                                      79*************999985 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.052
                            zf-DBF  22 sekHrkFaenssnfeelDeli 42 
                                        ++H +F  ++ ++  + +li
  gi|242398081|ref|YP_002993505.1| 137 HDEHINFTAKNGSWIVVKRLI 157
                                       689***********9998887 PP

>> HalOD1  Halobacterial output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       0.8   2.9e+03       9      38 ..      30      60 ..      28      69 .. 0.73
   2 ?   10.5   0.0   0.00016      0.56       2      52 ..     160     207 ..     159     216 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.8
                            HalOD1  9 Vveavaavegvdptelep.LydaiDpdALda 38
                                      +++ +a v+++   +l+  L ++ +   + +
  gi|242398081|ref|YP_002993505.1| 30 IAHFLAMVSNTVTLKLPEyLTEVMNVAGIMS 60
                                      7888999999999999555888877655555 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00016
                            HalOD1   2 eespstaVveavaavegvdptelepLydaiDpdALdaLfasradgearadg 52 
                                       +++p   +++ +a+++++ + ++ pLy  iD d + + f +   ++ar+++
  gi|242398081|ref|YP_002993505.1| 160 NKTPMADIARILASINETAVSKI-PLYGKIDLDGIRKWFGD--IKKARSEA 207
                                       678999****************8.9********99999999..44444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       740  (0.0412739); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1584.31
//
Query:       gi|242398082|ref|YP_002993506.1|  [L=1112]
Description: ATP-dependent protease [Thermococcus sibiricus MM 739]
Scores for complete 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  123.0   3.8      2e-35  122.2   3.8    1.4  1  Lon_C            Lon protease (S16) C-terminal proteolytic do
    1.5e-25   90.0   0.0    1.6e-18   66.8   0.0    3.0  3  AAA_32           AAA domain
    2.1e-17   63.3   0.1    1.2e-10   41.3   0.0    2.5  2  Sigma54_activat  Sigma-54 interaction domain
    1.3e-16   60.6   0.1    3.8e-09   36.2   0.0    2.4  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    3.6e-11   43.2   0.0    0.00025   21.1   0.0    2.7  2  AAA_5            AAA domain (dynein-related subfamily)
      9e-11   41.7   1.8    1.7e-10   40.8   0.9    2.1  1  ChlI             Subunit ChlI of Mg-chelatase
      5e-08   33.2   1.2    0.00015   22.0   0.1    3.6  2  LAGLIDADG_3      LAGLIDADG-like domain
    3.4e-07   30.8   0.0      0.074   13.5   0.0    3.2  2  AAA              ATPase family associated with various cellul
    3.7e-07   29.5   0.4      0.023   13.8   0.0    3.1  3  MCM              MCM P-loop domain
    5.7e-06   26.2   0.1      0.076   12.8   0.1    2.5  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    1.8e-05   25.0   0.0     0.0014   18.9   0.0    2.7  2  AAA_22           AAA domain
    3.2e-05   24.1   0.0       0.24   11.5   0.0    2.8  2  Sigma54_activ_2  Sigma-54 interaction domain
    8.6e-05   22.5   0.2    0.00021   21.2   0.2    1.7  1  Intein_splicing  Intein splicing domain
    0.00046   19.5   0.2        0.5    9.5   0.0    2.7  3  TIP49            TIP49 P-loop domain
    0.00055   19.8   0.1       0.39   10.6   0.0    2.5  2  AAA_3            ATPase family associated with various cellul
    0.00058   19.4   0.0     0.0012   18.4   0.0    1.4  1  AAA_7            P-loop containing dynein motor region
    0.00077   18.5   0.9       0.12   11.3   0.0    3.1  3  AAA_PrkA         PrkA AAA domain
     0.0011   18.7   0.1      0.069   12.9   0.0    2.6  2  AAA_30           AAA domain
      0.002   18.5   0.0        1.8    8.9   0.0    2.4  2  AAA_19           AAA domain
     0.0023   18.3   0.0     0.0097   16.3   0.0    2.1  1  AAA_16           AAA ATPase domain
     0.0084   16.0   0.0      0.023   14.6   0.0    1.8  1  NACHT            NACHT domain
     0.0088   15.4   0.3      0.034   13.5   0.0    2.0  2  S_4TM            SMODS-associating 4TM effector domain
  ------ inclusion threshold ------
      0.031   14.6   0.1       0.12   12.6   0.1    2.1  1  HTH_Tnp_1        Transposase
      0.043   13.3   0.0       0.13   11.7   0.0    1.8  1  PhoH             PhoH-like protein
      0.083   13.4   0.0       0.41   11.2   0.0    2.2  1  ABC_tran         ABC transporter
       0.11   12.3   0.0       0.33   10.7   0.0    1.8  1  IstB_IS21        IstB-like ATP binding protein
       0.11   12.6   0.0         20    5.3   0.0    2.7  2  MMR_HSR1         50S ribosome-binding GTPase
       0.15   11.9   0.1        2.5    8.0   0.0    2.7  2  HTH_23           Homeodomain-like domain
       0.16   11.5   0.9       0.29   10.7   0.9    1.3  1  Ac81             Baculoviridae AC81
       0.19   11.5   0.0       0.47   10.2   0.0    1.6  1  AAA_29           P-loop containing region of AAA 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 !  122.2   3.8   3.3e-38     2e-35      22     204 ..     912    1092 ..     892    1093 .. 0.85

  Alignments for each domain:
  == domain 1  score: 122.2 bits;  conditional E-value: 3.3e-38
                                        SS--BSSEEEEEEE.ETTEEEEEEEEEEEES....S-S-EEEEES--HHHHHHHHHHHHHHTSS-GGGSS-SS-T CS
                             Lon_C   22 ekedqvGvvtGlaw.tevGGdlltieavllp....gkgklkltGklgdvmkesaqaalsyvrsraeelgidkevf 91  
                                         +  ++G v Gla   e  G +l ie ++ p     +gk+++tGklg++ ke++q   ++++   +         
  gi|242398082|ref|YP_002993506.1|  912 TEGGEIGRVNGLAViSEQSGIVLPIEGMVAPaaskEEGKIIVTGKLGEIAKEAIQNVSAIIKR-YKGE-----DI 980 
                                        34568*******9735789*******998773333579****************987777764.3322.....34 PP

                                        TT-EEEEEE-S-B-GGGGGGGHHHHHHHHHHHHTS--B-TTBEE--EE-TT-BEE--S-HHHHHHHHHHTT-SBE CS
                             Lon_C   92 ekkdihihvPeGavPkdGPsaGvtlatalvslltgkkvrkdvamtGeitLrGrvlpiGGlkekllaakragikkv 166 
                                        +++dih+ + +     +G sa +++ata++s+l g++v+++vamtG +++rG+vlp+GG+  k+ aa  agik+v
  gi|242398082|ref|YP_002993506.1|  981 SRYDIHVQFLQTYEGVEGDSASISVATAVISALEGIPVKQNVAMTGSLSVRGEVLPVGGVTPKIEAAIEAGIKQV 1055
                                        578************************************************************************ PP

                                        EEEGGGGGGTTTS-HHHHTS-B--EESBHHHHHHHHB- CS
                             Lon_C  167 ilPkenekdlediPeevreeleiilveevdevlkaalv 204 
                                        i+Pk+ne+d+  +  +  e++ei +ve++d+vl+ al+
  gi|242398082|ref|YP_002993506.1| 1056 IIPKANEQDVF-LSADKAEKIEINPVETIDQVLQIALE 1092
                                        *********97.66677899****************96 PP

>> AAA_32  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   6.9e-07   0.00041       7      95 ..      43     126 ..      38     135 .. 0.85
   2 ?   -3.8   0.0       6.7     4e+03     281     311 ..     186     216 ..     185     219 .. 0.92
   3 !   66.8   0.0   2.7e-21   1.6e-18     319     509 ..     700     887 ..     692     890 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 6.9e-07
                            AAA_32   7 leeiigqeRAvealefglkikkkgYNifvlGesgtGrttlvkrlleeiakkeptpdDwcYvnnfdnpeePkalsLpa 83 
                                       ++++igqe Ave ++++ k k+   ++ ++Ge+gtG+++l + + e      +  +D++   n ++++ Pk+ s+pa
  gi|242398082|ref|YP_002993506.1|  43 IDQVIGQEHAVEVIKTAAKQKR---HVLLIGEPGTGKSMLGQAMAELL-P-TEDLEDILVFPNPEDENMPKIKSVPA 114
                                       589*************987655...9***********99888887665.3.455789999***************** PP

                            AAA_32  84 GkGkelkkdmee 95 
                                        +Gk+  ++ ++
  gi|242398082|ref|YP_002993506.1| 115 CQGKQIIERYRQ 126
                                       ****98776655 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 6.7
                            AAA_32 281 nvlvdnsetegaPVvvednptyanLfGkiey 311
                                       ++l+dn  +++aP v  +  +   L+G + +
  gi|242398082|ref|YP_002993506.1| 186 KLLIDNCGRRKAPFVDATGAHAGALLGDVRH 216
                                       689************************9987 PP

  == domain 3  score: 66.8 bits;  conditional E-value: 2.7e-21
                            AAA_32 319 vtdftlIkaGaLhkAnGGyLildaedlLeeplaWeaLkraLrskeikiesleeqlglistvsLkPepipldvKViLi 395
                                       +  ++++++G +h+An G+L +d    L+   + ++L  a+++k++ i     q +l+s    + ep+p+d   +  
  gi|242398082|ref|YP_002993506.1| 700 TPAHERVEPGMIHRANKGVLFIDEVATLN-IKMQQNLLTAMQEKKMPITG---QSELSSGAMVRTEPVPCDFVLVAA 772
                                       556899*****************988885.56679999***********5...46699999**************** PP

                            AAA_32 396 GsrelYylLseyDpdfkklFkvkadFddemerteenekkyarfias.ivkkekllpfdrsavarlieyssrlaedqe 471
                                       G+ ++ + ++ +     + +  ++ + ++m+ t en +k++rf+a+ ++k+ k+++f+++av+++++++ + a+++ 
  gi|242398082|ref|YP_002993506.1| 773 GNLDTVDKMHPALRSRIRGYGYEVYMRTTMPDTIENRRKLVRFVAQeVAKDGKIPHFTKDAVEEIVREAQKRAGRKG 849
                                       *****9999999999999999***********************9725667789*********************** PP

                            AAA_32 472 klstrfseiadllrEAdywakkegaevveaehVekAle 509
                                       +l++r++++  ++r A  ++ +ega++v++ehV kAl+
  gi|242398082|ref|YP_002993506.1| 850 HLTLRLRDLGGIIRAAGDISIREGAKYVTREHVFKALQ 887
                                       ************************************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 !   19.5   0.0   1.1e-06   0.00064       9      46 ..      50      87 ..      42      98 .. 0.87
   2 !   41.3   0.0   2.1e-13   1.2e-10      50     129 ..     670     751 ..     655     781 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.1e-06
                                      HHHHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHS CS
                   Sigma54_activat  9 kelleqikkvaktdlsvlitGesGtGKellaraiheas 46
                                      ++++e ik++ak++ +vl+ Ge GtGK++l +a+ e  
  gi|242398082|ref|YP_002993506.1| 50 EHAVEVIKTAAKQKRHVLLIGEPGTGKSMLGQAMAELL 87
                                      578999***************************98765 PP

  == domain 2  score: 41.3 bits;  conditional E-value: 2.1e-13
                                       TS-EEEEETTTS-TTCHHHHHHEBSSSSS.TTTSS-BE.HHHHHTTTSEEEEETGGGS-HHHHHHHHHHHHHSEEES CS
                   Sigma54_activat  50 ekpfvavncaaipeelleseLFGhekGaF.tGAekekk.GlfekadgGtlfLDeigelplelQekLlrvlqegever 124
                                       e+  v+ n++  + +ll+  LF  ++G   t A+++ + G++++a++G+lf+De+++l++++Q++Ll+++qe+++  
  gi|242398082|ref|YP_002993506.1| 670 EEVEVTYNVTTETGNLLANGLFVKNSGGLgTPAHERVEpGMIHRANKGVLFIDEVATLNIKMQQNLLTAMQEKKMPI 746
                                       45558899999999***********99983566666558***********************************988 PP

                                       BTSSS CS
                   Sigma54_activat 125 vGssk 129
                                        G+s+
  gi|242398082|ref|YP_002993506.1| 747 TGQSE 751
                                       88765 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   0.0   6.3e-12   3.8e-09       3      55 ..      44      96 ..      42     112 .. 0.93
   2 !   21.8   0.0   1.7e-07    0.0001      95     158 ..     704     775 ..     695     801 .. 0.78

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 6.3e-12
                      Mg_chelatase  3 kdvkGqeeakraleiaaaGgHnlllvGppGsGKtmlakrlpsllpplseeeal 55
                                       +v+Gqe+a ++++ aa  + ++ll+G pG+GK+ml +++++llp  + e++l
  gi|242398082|ref|YP_002993506.1| 44 DQVIGQEHAVEVIKTAAKQKRHVLLIGEPGTGKSMLGQAMAELLPTEDLEDIL 96
                                      68*******************************************98877765 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 1.7e-07
                      Mg_chelatase  95 skpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisraka........kvefparfqlvaamNp 158
                                       ++++pG i +a++GvLf+DE++ ++ k+ + L + ++++++ i+ +++        +   p++f lvaa N+
  gi|242398082|ref|YP_002993506.1| 704 ERVEPGMIHRANKGVLFIDEVATLNIKMQQNLLTAMQEKKMPITGQSElssgamvrTEPVPCDFVLVAAGNL 775
                                       5789*********************************99999975543111111113357888888888886 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   1.5e-06    0.0009       1      25 [.      65      89 ..      65      99 .. 0.89
   2 !   21.1   0.0   4.2e-07   0.00025      64     137 ..     711     788 ..     667     789 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.5e-06
                                      EEEEE--SSSSHHHHHHHGGGGBS- CS
                             AAA_5  1 dvlLvGppGtgKselaerlaaalnr 25
                                      +vlL+G+pGtgKs+l + +a++l +
  gi|242398082|ref|YP_002993506.1| 65 HVLLIGEPGTGKSMLGQAMAELLPT 89
                                      79********************944 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 4.2e-07
                                       -...G-SEEEEESGGG--HHHHHHHHHHHHSSEEE..-SSSEEE---..........-EEEEEESS--.-TT-TTHH CS
                             AAA_5  64 r...egeilvlDEveraesevlnsLlslleerrllleeggelvkaknddller....frviatanpldrslnelspa 133
                                           ++ +l++DEv +++ ++++ Ll+ + e+++++    el + +   ++e+    f ++a++n     + ++ pa
  gi|242398082|ref|YP_002993506.1| 711 IhraNKGVLFIDEVATLNIKMQQNLLTAMQEKKMPITGQSELSSGAMV-RTEPvpcdFVLVAAGNLDT--VDKMHPA 784
                                       0445889****************************8888888877764.344489**********988..99999** PP

                                       HHTT CS
                             AAA_5 134 lrsR 137
                                       lrsR
  gi|242398082|ref|YP_002993506.1| 785 LRSR 788
                                       ***9 PP

>> ChlI  Subunit ChlI of Mg-chelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.8   0.9   2.9e-13   1.7e-10       7     121 .]     946    1061 ..     940    1061 .. 0.95

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 2.9e-13
                              ChlI    7 kglpkftivGlpdtavkeskervrsalkn.sgfefpakkitvnLaPadlkkeGsafDLpiAigilaaleqieaee 80  
                                        k   k+ ++G + +  ke+ + v +++k   g ++ +  i v         eG + ++++A ++++ale i++++
  gi|242398082|ref|YP_002993506.1|  946 KEEGKIIVTGKLGEIAKEAIQNVSAIIKRyKGEDISRYDIHVQFLQTYEGVEGDSASISVATAVISALEGIPVKQ 1020
                                        555678899999***************99799******************************************* PP

                              ChlI   81 etlflGeLsldGslrpvkgvlpialaakkegikkvivpken 121 
                                        ++ + G Ls  G++ pv gv+p + aa ++gik+vi+pk+n
  gi|242398082|ref|YP_002993506.1| 1021 NVAMTGSLSVRGEVLPVGGVTPKIEAAIEAGIKQVIIPKAN 1061
                                        ***************************************98 PP

>> LAGLIDADG_3  LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0    0.0067         4       9      47 ..     429     464 ..     422     494 .. 0.82
   2 !   22.0   0.1   2.5e-07   0.00015       4      82 ..     525     615 ..     523     616 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0067
                                       HHHHHCCECCECSTTTTSEEEEES-HHHHHHHHHHHHHC CS
                       LAGLIDADG_3   9 GlfdaDGsvskskkkgvsisltssskelledvqrlLlrl 47 
                                       G   +DG ++k+ ++   +s+ ss++e +e++ r+L +l
  gi|242398082|ref|YP_002993506.1| 429 GILFSDGNIDKNLNT---LSFVSSEREAIEKFVRILGNL 464
                                       66669********99...******************966 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 2.5e-07
                                       HHHHHHHHHHCCECCECSTTTTSEEEEES-............HHHHHHHHHHHHHCT.HSCEEEEEEE-SCCCCECC CS
                       LAGLIDADG_3   4 aafLrGlfdaDGsvskskkkgvsisltsss............kelledvqrlLlrlGIestiyekkkakgrgvyrll 68 
                                       +af+ Gl+++DGsv  + +++ +i++  +             + + e+++  L  +GIe++++ +k +++  v  +l
  gi|242398082|ref|YP_002993506.1| 525 LAFIDGLYSGDGSVPRFAHYRDGIKFNGTLeiaqltdelekkLPFFEEIAWHLGLFGIEAKVRVDKADGKYKV--RL 599
                                       59********************988888888888999****9***********************43333333..34 PP

                                       CHCH..CTTCGGGTTT CS
                       LAGLIDADG_3  69 iisg..enlkrFleki 82 
                                       i s+  +n+ +Fle i
  gi|242398082|ref|YP_002993506.1| 600 IFSQsiDNVLNFLEFI 615
                                       4433236777887776 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 !   13.5   0.0   0.00013     0.075       1      23 [.      66      88 ..      66     142 .. 0.66
   2 !   13.5   0.0   0.00012     0.074      58     124 ..     715     789 ..     702     793 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00013
                                      EEEESSTTSSHHHHHHHHHHHHT CS
                               AAA  1 vllyGppGtGKTllakavakelg 23
                                      vll+G pGtGK++l +a+a+ l 
  gi|242398082|ref|YP_002993506.1| 66 VLLIGEPGTGKSMLGQAMAELLP 88
                                      79****************99873 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.00012
                                       TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS..................SSTEEEEEEESS..GGG CS
                               AAA  58 kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkk..................eskvivigatnr..pdk 114
                                       ++ +lfiDE+  l+ +            ++ Llt++++ k                      ++++++a+n   +dk
  gi|242398082|ref|YP_002993506.1| 715 NKGVLFIDEVATLNIKM-----------QQNLLTAMQEKKMPitgqselssgamvrtepvPCDFVLVAAGNLdtVDK 780
                                       369**********8888...........99*******99999999************999667********999*** PP

                                       STHHHHSTTS CS
                               AAA 115 ldpallrgRf 124
                                       + pal+ +R+
  gi|242398082|ref|YP_002993506.1| 781 MHPALR-SRI 789
                                       ******.897 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   3.9e-05     0.023      40      83 ..      46      89 ..      11      93 .. 0.83
   2 ?   -1.3   0.1       1.6   9.8e+02     186     202 ..     333     349 ..     324     359 .. 0.78
   3 !   12.0   0.0   0.00013     0.079     112     152 ..     706     746 ..     686     752 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.9e-05
                                      HH---EBBBSSSSBBCSS-EEEEEESSTSTHHHHHHHHHHHSSS CS
                               MCM 40 lfggvkkkledktklrgdinvllvgdpgtaKsqlLkyveklapr 83
                                      ++g  +  +  kt  + + +vll+g+pgt+Ks l +++++l+p+
  gi|242398082|ref|YP_002993506.1| 46 VIGQEHAVEVIKTAAKQKRHVLLIGEPGTGKSMLGQAMAELLPT 89
                                      445555445556778999****************9999998875 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.6
                                       HHSSSSHHHHHHSSEEE CS
                               MCM 186 eninlsaalLsrFDlif 202
                                       e i+++  +L+rFD+  
  gi|242398082|ref|YP_002993506.1| 333 EIIRVPVIILDRFDVAR 349
                                       5689999*******975 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 0.00013
                                       EEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEE CS
                               MCM 112 leaGalvladkGvcciDefdkmkeedrsalhEamEqqtisi 152
                                       +e G +  a+kGv+ iDe+   + + ++ l+ am ++++ i
  gi|242398082|ref|YP_002993506.1| 706 VEPGMIHRANKGVLFIDEVATLNIKMQQNLLTAMQEKKMPI 746
                                       799*******************************9998877 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.1   0.00013     0.076       6      56 ..      43      86 ..      38      91 .. 0.73
   2 !   10.6   0.0   0.00057      0.34      84     119 ..     715     750 ..     705     790 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00013
                            RuvB_N  6 leeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiake 56
                                      +++ igqe+  e   ++ +aak++     hvll+G PG Gk+ l + +a+ 
  gi|242398082|ref|YP_002993506.1| 43 IDQVIGQEHAVE---VIKTAAKQK----RHVLLIGEPGTGKSMLGQAMAEL 86
                                      566777776554...444555554....5***************9999875 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00057
                            RuvB_N  84 ekdvlfideihrlsraveevlysamedfrldivigk 119
                                       +k vlfide+  l+ ++++ l +am++ ++ i+ ++
  gi|242398082|ref|YP_002993506.1| 715 NKGVLFIDEVATLNIKMQQNLLTAMQEKKMPITGQS 750
                                       678*************************99987332 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   2.3e-06    0.0014       3      33 ..      61      91 ..      57     133 .. 0.82
   2 ?    3.2   0.0      0.17     1e+02      81     117 ..     705     740 ..     641     753 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.3e-06
                            AAA_22  3 ktagilvvtGesGtGKTtllrrlleqldeea 33
                                      k++++++++Ge+GtGK++l + ++e l+ e 
  gi|242398082|ref|YP_002993506.1| 61 KQKRHVLLIGEPGTGKSMLGQAMAELLPTED 91
                                      5899*********************998654 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.17
                            AAA_22  81 aleqalraravielliiDEaqhlrseealeeLrslln 117
                                       ++e  + +ra +++l iDE+  l + ++ ++L + + 
  gi|242398082|ref|YP_002993506.1| 705 RVEPGMIHRANKGVLFIDEVATL-NIKMQQNLLTAMQ 740
                                       555555555556***********.6666666655554 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 !   11.5   0.0    0.0004      0.24      14      43 ..      56      85 ..      51     111 .. 0.86
   2 !    9.2   0.0     0.002       1.2      64      97 ..     710     743 ..     693     777 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0004
                                      HHHHHT-SS-EEEEEETT--HHHHHHCC-- CS
                   Sigma54_activ_2 14 LeqaaqsklpvfltGekGsgkelvArlLhk 43
                                      ++ aa++k  v+l+Ge+G+gk++  +++++
  gi|242398082|ref|YP_002993506.1| 56 IKTAAKQKRHVLLIGEPGTGKSMLGQAMAE 85
                                      7899*******************9999876 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.002
                                       HHHHTTTSEEEEEE-TT--HHHHHHHHHHHHHHT CS
                   Sigma54_activ_2  64 lleqakggtLylkdiadlskaeqkeLlellakae 97 
                                       ++ +a+ g+L++ ++a l+ + q++Ll ++++++
  gi|242398082|ref|YP_002993506.1| 710 MIHRANKGVLFIDEVATLNIKMQQNLLTAMQEKK 743
                                       67899***********************999864 PP

>> Intein_splicing  Intein splicing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.2   3.5e-07   0.00021       4     134 .]     232     694 ..     228     694 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 3.5e-07
                                       CTTCEE.EEHHHHCC...........ECTTEEEEEETTTTEEEEEE....EEEEEEEEEE...EEEEEE.ETTS-EE CS
                                       xxxxxx.xxxxxxxx...........xxxxxxxxxxxxxxxxxxxx....xxxxxxxxxx...xxxxxx.xxxxxxx RF
                   Intein_splicing   4 edgeek.vkieelve...........kegeevlslnledlklevks....vkkliklklk...elyeik.lesgrki 60 
                                       +dge + v+++e+v+           + + +v+  ++ + k++  +    vk l   + +   +l +i  le+ + +
  gi|242398082|ref|YP_002993506.1| 232 KDGERRvVTLKEFVDsalkepsgegvDGEINVIYKDFRNDKVKILTkdgfVKLLYANRREgkqNLRRIVnLEKDYWL 308
                                       566666888999999888888776644444444434433333333377885555444433335777764599***** PP

                                       EEETT-EEEECCTTEEEEEECCC--TT-EEEEE............................................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................................ RF
                   Intein_splicing  61 kaTpeHkllvvrdegivEkradeLkegdliavp............................................ 93 
                                        +TpeHk+ +   eg+  k++deL++ d i+ +                                            
  gi|242398082|ref|YP_002993506.1| 309 TVTPEHKVYTA--EGL--KEMDELTKDDEIIRVpviildrfdvartyneekklkdyfrwkdyyektgngykrvakel 381
                                       ***********..9**..************9999******************************************* PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                   Intein_splicing  94 ............................................................................. 93 
                                                                                                                    
  gi|242398082|ref|YP_002993506.1| 382 gikestlrwwtqgakpkslkmaeeleklgllplknederleeiakvmgilfsdgnidknlntlsfvssereaiekfv 458
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                   Intein_splicing  94 ............................................................................. 93 
                                                                                                                    
  gi|242398082|ref|YP_002993506.1| 459 rilgnlfgefeyeikenreamgesilfrtwdrrvirffvalgapvgnktmvklelpwwiklkpslflafidglysgd 535
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                   Intein_splicing  94 ............................................................................. 93 
                                                                                                                    
  gi|242398082|ref|YP_002993506.1| 536 gsvprfahyrdgikfngtleiaqltdelekklpffeeiawhlglfgieakvrvdkadgkykvrlifsqsidnvlnfl 612
                                       ***************************************************************************** PP

                                       ........................................HSCEEEEEEEE......EEEEECEEEEEEEEETTT-E CS
                                       ........................................xxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxx RF
                   Intein_splicing  94 ........................................dadvvwdkvks......ievedeeeyVYdltvednhN 124
                                                                               +    ++++k+      ie ++e e  Y +t+e + N
  gi|242398082|ref|YP_002993506.1| 613 efiqislspskrerflgevekyinavpdsslaeklkefkeR----FERIKKeerrnfIESSEEVEVTYNVTTE-TGN 684
                                       ********************************999966440....5555551122226667788888999998.999 PP

                                       EEECTTEEE- CS
                                       xxxxxxxxxx RF
                   Intein_splicing 125 FvangiivHN 134
                                        +ang++v N
  gi|242398082|ref|YP_002993506.1| 685 LLANGLFVKN 694
                                       9999999876 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0   0.00083       0.5      25      74 ..      45      87 ..      24      95 .. 0.67
   2 !    7.0   0.0    0.0049         3     279     309 ..     716     746 ..     707     752 .. 0.92
   3 ?   -3.2   0.0       6.3   3.8e+03     247     274 ..     953     980 ..     949     987 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00083
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49 25 glvGqkkareaagvivelikekklaGravLlaGpsgtGktalaiaiskel 74
                                       ++Gq++a       ve+ik+     r vLl G++gtGk+ l  a+++ l
  gi|242398082|ref|YP_002993506.1| 45 QVIGQEHA-------VEVIKTAAKQKRHVLLIGEPGTGKSMLGQAMAELL 87
                                      34444433.......4555555555689**************99998766 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0049
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49 279 pGvlfiDevhmlDiecfsylnraleselaPi 309
                                       +GvlfiDev  l+i +   l  a+ ++  Pi
  gi|242398082|ref|YP_002993506.1| 716 KGVLFIDEVATLNIKMQQNLLTAMQEKKMPI 746
                                       6*******************99999998887 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 6.3
                                       .XXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49 247 lkskkteiteklreeinkkvakyveegk 274
                                       +++k +ei ++  +++  ++++y+ e++
  gi|242398082|ref|YP_002993506.1| 953 VTGKLGEIAKEAIQNVSAIIKRYKGEDI 980
                                       578999****************998876 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 ?    6.6   0.0     0.011       6.8       1      24 [.      65      88 ..      65      99 .. 0.91
   2 !   10.6   0.0   0.00065      0.39      64      97 ..     717     750 ..     702     768 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.011
                             AAA_3  1 hvllegvPGlaktllvkalakald 24
                                      hvll g PG++k +l +a+a+ l 
  gi|242398082|ref|YP_002993506.1| 65 HVLLIGEPGTGKSMLGQAMAELLP 88
                                      9*******************9885 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00065
                             AAA_3  64 nllladeinrappktqsalleameerqvtveget 97 
                                        +l+ de+   + k+q  ll am+e+++ ++g++
  gi|242398082|ref|YP_002993506.1| 717 GVLFIDEVATLNIKMQQNLLTAMQEKKMPITGQS 750
                                       58999***********************999886 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0     2e-06    0.0012      25      62 ..      55      92 ..      36      98 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2e-06
                             AAA_7 25 llelllknkkpvllvGptGtGKtviikdllkkldkeky 62
                                      ++++  k+k++vll+G+ GtGK+++ + + + l++e++
  gi|242398082|ref|YP_002993506.1| 55 VIKTAAKQKRHVLLIGEPGTGKSMLGQAMAELLPTEDL 92
                                      688999*********************99999998776 PP

>> AAA_PrkA  PrkA AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.09        54      80     115 ..      55      90 ..      33     114 .. 0.74
   2 ?    0.8   0.1       0.3   1.8e+02     297     321 ..     294     318 ..     284     356 .. 0.78
   3 !   11.3   0.0   0.00019      0.12     227     268 ..     709     750 ..     706     759 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.09
                          AAA_PrkA  80 aaqrleerkqilyllGPvggGksslverlkklleaa 115
                                         +   ++k+ ++l+G  g+Gks l +++ +ll ++
  gi|242398082|ref|YP_002993506.1|  55 VIKTAAKQKRHVLLIGEPGTGKSMLGQAMAELLPTE 90 
                                       34455567888889***********99999888665 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.3
                          AAA_PrkA 297 alldrivvvkvPyclrvseekkiye 321
                                         l riv ++  y l v+ e+k+y 
  gi|242398082|ref|YP_002993506.1| 294 QNLRRIVNLEKDYWLTVTPEHKVYT 318
                                       4578********************5 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.00019
                          AAA_PrkA 227 GalnranrGllefvemfkadikvlhplltatqegnykstekl 268
                                       G + ran+G+l   e+   +ik+  +llta qe++++ t++ 
  gi|242398082|ref|YP_002993506.1| 709 GMIHRANKGVLFIDEVATLNIKMQQNLLTAMQEKKMPITGQS 750
                                       7889*******************************9998875 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   0.00012     0.069       6      45 ..      49      90 ..      47     100 .. 0.75
   2 ?    2.8   0.0      0.14        86      86     117 ..     713     744 ..     644     748 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00012
                            AAA_30  6 Qaaave..alltsgdrvavltGpAGtGKttalkalreaweaa 45
                                      Q++ave  +++++++r ++l G +GtGK+++ +a++e++ ++
  gi|242398082|ref|YP_002993506.1| 49 QEHAVEviKTAAKQKRHVLLIGEPGTGKSMLGQAMAELLPTE 90
                                      56665522345566679******************9998776 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.14
                            AAA_30  86 lepgtllivDEagmvdtkqlaallkaaekaga 117
                                        +++ +l +DE++ +++k+ ++ll+a++++++
  gi|242398082|ref|YP_002993506.1| 713 RANKGVLFIDEVATLNIKMQQNLLTAMQEKKM 744
                                       4566899********************99776 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0     0.003       1.8       7      33 ..      60      86 ..      49      98 .. 0.73
   2 ?    7.0   0.0     0.012       7.1     103     130 ..     715     744 ..     668     749 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.003
                            AAA_19  7 alkekvllvtaGpGtGKTrvlkhival 33
                                      a +++++l+++ pGtGK+ + +++ +l
  gi|242398082|ref|YP_002993506.1| 60 AKQKRHVLLIGEPGTGKSMLGQAMAEL 86
                                      568899***********9765555544 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.012
                            AAA_19 103 ee.llivDEfqdvd.elqyrLlkallgekk 130
                                       ++ +l++DE+  ++ ++q++Ll a+ ++k+
  gi|242398082|ref|YP_002993506.1| 715 NKgVLFIDEVATLNiKMQQNLLTAMQEKKM 744
                                       4459*********************96665 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   1.6e-05    0.0097      19      63 ..      58     105 ..      45     138 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.6e-05
                            AAA_16  19 vrsgrpelvllsGesGvGKsslvrellralekd...ggiflrgkcdql 63 
                                       +++ + + vll+Ge+G+GKs l ++ ++ l ++   +++++    d++
  gi|242398082|ref|YP_002993506.1|  58 TAAKQKRHVLLIGEPGTGKSMLGQAMAELLPTEdleDILVFPNPEDEN 105
                                       3445669****************9999887777675566666666666 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   3.9e-05     0.023       1      84 [.      64     159 ..      64     196 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.9e-05
                                       SCEEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-.....-HCHHHCCCCTS--SSS-C.... CS
                             NACHT   1 rlvilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgna..rsladllfsqlpepaapvse.... 71 
                                       r v+l Ge+G GK++L q +a+++ +++l+     lvF  +  e   + ++   +  +++ + + ++a+++++    
  gi|242398082|ref|YP_002993506.1|  64 RHVLLIGEPGTGKSMLGQAMAELLPTEDLED---ILVFPNPEDENMPKIKSvpACQGKQIIERYRQKAKEQENiksy 137
                                       5699************************999...5777777655444333357788888999999998888887777 PP

                                       .........CHHHHCCSCCCEE CS
                             NACHT  72 .........vwavllelperlL 84 
                                                + avl+ +  ++L
  gi|242398082|ref|YP_002993506.1| 138 illfvlfvvMLAVLMDRSAQTL 159
                                       7777766665566666666655 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 !   13.5   0.0   5.7e-05     0.034     137     213 ..     101     177 ..      83     184 .. 0.90
   2 ?   -1.8   0.1       2.6   1.5e+03     112     137 ..     880     902 ..     870     909 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.7e-05
                             S_4TM 137 eevedlprplavllCqrqNlsWdsrlrrryaklllfalvlwillvlvvgliknlslsdlllsvivpllpllllalke 213
                                       +e e++p+ ++v +Cq + +    r++ + ++ +   ++l++l+v++++++++ s ++ll+ v+v +++l++l    
  gi|242398082|ref|YP_002993506.1| 101 PEDENMPKIKSVPACQGKQIIERYRQKAKEQENIKSYILLFVLFVVMLAVLMDRSAQTLLFGVFVLIVSLMALSNMR 177
                                       5668899999999********99**********************************************99887655 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.6
                             S_4TM 112 eeiarlakkykkkkkdeerlkdWYpe 137
                                       e ++++ +    +k+ e++l dWY e
  gi|242398082|ref|YP_002993506.1| 880 EHVFKALQL---AKPLEKQLADWYIE 902
                                       555555444...5999********64 PP

>> HTH_Tnp_1  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   0.00021      0.12      22      66 ..     370     420 ..     364     428 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00021
                         HTH_Tnp_1  22 pgksvsevArrhgvspnqLykWrrqyr.......egeeaspae....feltaleee 66 
                                       +g  +++vA+++g+++++L+ W + ++       e     ++e      l+++ e+
  gi|242398082|ref|YP_002993506.1| 370 TGNGYKRVAKELGIKESTLRWWTQGAKpkslkmaE-----ELEklglLPLKNEDER 420
                                       577789*****************999875433322.....2223222244444444 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00022      0.13       8      50 ..      48      93 ..      43     107 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00022
                                      HHHHHHHHHH....H-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-S CS
                              PhoH  8 eQkeylealk....kndivfaiGpaGtGKtylavalavealkkkkvk 50
                                      +Q++++e++k    ++  v  iG+ GtGK++l  a+a e+l  ++++
  gi|242398082|ref|YP_002993506.1| 48 GQEHAVEVIKtaakQKRHVLLIGEPGTGKSMLGQAMA-ELLPTEDLE 93
                                      699999999988767779***************9998.455555555 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00068      0.41       6      37 ..      58      89 ..      53     134 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00068
                                      EEEETTSEEEEEESTTSSHHHHHHHHTTSS-- CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  6 lklkegekvaivGenGaGKStLlkllagllkp 37
                                         k+ + v ++Ge G+GKS L +++a+ll  
  gi|242398082|ref|YP_002993506.1| 58 TAAKQKRHVLLIGEPGTGKSMLGQAMAELLPT 89
                                      56688999******************998754 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00055      0.33      45      69 ..      61      85 ..      29      93 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00055
                         IstB_IS21 45 ekkenivllGpsGvGKshlaialgv 69
                                      ++k  ++l+G +G+GKs l  a++ 
  gi|242398082|ref|YP_002993506.1| 61 KQKRHVLLIGEPGTGKSMLGQAMAE 85
                                      567889****************986 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.071        43       2      20 ..      66      84 ..      65      96 .. 0.87
   2 ?    5.3   0.0     0.034        20      19     110 ..     816     909 ..     810     913 .. 0.61

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.071
                                      EEEEESTTSSHHHHHHHHH CS
                          MMR_HSR1  2 vaivGrpNvGKStLinalt 20
                                      v+++G p +GKS L +a+ 
  gi|242398082|ref|YP_002993506.1| 66 VLLIGEPGTGKSMLGQAMA 84
                                      89**********9988876 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.034
                                       HHTSTEEESSSTTSSSSEEEEEEE...ETTEE........EEEEECGGCSSHHHHHH..HHHHHHHHHHCTSEEEEE CS
                          MMR_HSR1  19 ltgekaivsdkpgtTrdinegrvk...lkgke........ielvDtpGliegaseek..glgkaflaleeadlillv 82 
                                         +e+a+ +++p  T+d +e+ v+   +   +        ++l D+ G+i  a  +   ++g ++    + ++++  
  gi|242398082|ref|YP_002993506.1| 816 VAQEVAKDGKIPHFTKDAVEEIVReaqK---RagrkghltLRLRDLGGIIR-AAGDIsiREGAKYV--TR-EHVFKA 885
                                       455689999************9994440...245555555********886.33344123344443..33.334444 PP

                                       EETTTTCSHHHHHHHHHHHHHTTSEEEE CS
                          MMR_HSR1  83 vdaseeklkpldeeleelleeakkplil 110
                                       ++      kpl+++l+++  e+kk++ +
  gi|242398082|ref|YP_002993506.1| 886 LQ----LAKPLEKQLADWYIERKKEYQV 909
                                       43....2356677777776666666555 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0    0.0042       2.5      17      35 ..     371     389 ..     364     399 .. 0.80
   2 ?    0.1   0.0       1.3   7.7e+02       2      29 ..     403     430 ..     402     430 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0042
                            HTH_23  17 GlsvreIAreLgvsrrTvy 35 
                                       G  ++++A+eLg+ ++T++
  gi|242398082|ref|YP_002993506.1| 371 GNGYKRVAKELGIKESTLR 389
                                       7889*************97 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.3
                            HTH_23   2 asereRlrillllaeGlsvreIAreLgv 29 
                                       a+e+e+l  l l  e  + +eIA+ +g+
  gi|242398082|ref|YP_002993506.1| 403 AEELEKLGLLPLKNEDERLEEIAKVMGI 430
                                       678888888888888999*******997 PP

>> Ac81  Baculoviridae AC81
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.9   0.00048      0.29     124     166 ..     131     175 ..     119     182 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00048
                              Ac81 124 gvsvqtvlil.iliavlllaiikfsafllLfi.lfllviLlifns 166
                                       +  +++ ++l +l++v+l  ++ +sa++lLf  ++l+v+L+  ++
  gi|242398082|ref|YP_002993506.1| 131 QENIKSYILLfVLFVVMLAVLMDRSAQTLLFGvFVLIVSLMALSN 175
                                       55567777777********************96667777777665 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00078      0.47      22      46 ..      63      87 ..      49      93 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00078
                            AAA_29 22 kgatlltGpsGsGKSTllDAiqalL 46
                                      k  +ll+G+ G+GKS l  A++ lL
  gi|242398082|ref|YP_002993506.1| 63 KRHVLLIGEPGTGKSMLGQAMAELL 87
                                      2379*************99999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1026  (0.0572257); expected 358.6 (0.02)
Passed bias filter:                      786  (0.0438396); expected 358.6 (0.02)
Passed Vit filter:                       151  (0.00842211); expected 17.9 (0.001)
Passed Fwd filter:                        31  (0.00172904); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              30  [number of targets reported over threshold]
# CPU time: 0.95u 0.36s 00:00:01.31 Elapsed: 00:00:00.50
# Mc/sec: 6705.46
//
Query:       gi|242398083|ref|YP_002993507.1|  [L=136]
Description: hypothetical protein TSIB_0090 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.057   13.5   0.0        0.1   12.8   0.0    1.4  1  DUF3378   Domain of unknown function (DUF3378)


Domain annotation for each model (and alignments):
>> DUF3378  Domain of unknown function (DUF3378)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   5.6e-06       0.1      21      51 ..      78     108 ..      64     109 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.6e-06
                           DUF3378  21 klrskkppyavfaakkndttItaYtSgKVlF 51 
                                       +++++ +p ++  a +++  +++Y SgK+++
  gi|242398083|ref|YP_002993507.1|  78 YQIKSVIPKMLAIAVVEKYEVSIYPSGKIIV 108
                                       78999***********************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 961.15
//
Query:       gi|242398084|ref|YP_002993508.1|  [L=348]
Description: glycosyltransferase, family 2 [Thermococcus sibiricus MM 739]
Scores for complete 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-32  111.0   0.0    7.6e-32  110.5   0.0    1.3  1  Glycos_transf_2  Glycosyl transferase family 2
    5.6e-29  101.7   0.0    6.7e-29  101.4   0.0    1.1  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    1.2e-13   51.4   0.1    2.2e-13   50.6   0.1    1.4  1  Glyco_trans_2_3  Glycosyl transferase family group 2
      3e-12   46.6   0.0    5.6e-12   45.7   0.0    1.4  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
    3.9e-10   39.5   0.0    5.9e-10   38.9   0.0    1.2  1  Glyco_transf_21  Glycosyl transferase family 21
    0.00014   20.7   0.0       0.38    9.3   0.0    2.5  3  Chitin_synth_2   Chitin synthase
  ------ inclusion threshold ------
      0.014   15.9   0.0      0.026   15.0   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 !  110.5   0.0     3e-35   7.6e-32       1     169 [.      39     199 ..      39     200 .. 0.91

  Alignments for each domain:
  == domain 1  score: 110.5 bits;  conditional E-value: 3e-35
                                       EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglra 77 
                                       ++ ip+yNe+ t+l +++s+l+q +yp++e+ivvDDgS+D+t e + ++   d r++v+r+++  Gka+aln gl++
  gi|242398084|ref|YP_002993508.1|  39 TILIPAYNESGTILHSIKSALSQ-DYPKLEVIVVDDGSEDDTFEKANSIK--DSRLKVFRKKHE-GKAKALNFGLQR 111
                                       589********************.*************************5..8********977.************ PP

                                       --SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTTC CS
                   Glycos_transf_2  78 atgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnlsfe 154
                                       ++g++i+++DaD+  +p+ +++lv+++   +  ++ gq+++ +++  e+ +      +       r+ ++  +ls+ 
  gi|242398084|ref|YP_002993508.1| 112 TSGEIITTIDADTLLAPNAIRELVKRIYSKEIVGAGGQIRVLGSSFLERAQDV----EHFRIAMFRRAKELEDLSVA 184
                                       *****************************999888888888888888888874....4666666677788889999* PP

                                       STCCCEEEEHHHHHC CS
                   Glycos_transf_2 155 igsaallrrealeel 169
                                        g+ +++r+ +l+e+
  gi|242398084|ref|YP_002993508.1| 185 PGPLSAFRKTILREI 199
                                       *********999987 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 !  101.4   0.0   2.6e-32   6.7e-29       1     229 [.      36     250 ..      35     251 .. 0.87

  Alignments for each domain:
  == domain 1  score: 101.4 bits;  conditional E-value: 2.6e-32
                   Glyco_tranf_2_3   1 prdlavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksr 77 
                                       p+ +++l+p++ne+ +++  + s+l+q+yp +ev+vv+d+s+++t e a       +d r++v ++++     gk+ 
  gi|242398084|ref|YP_002993508.1|  36 PS-VTILIPAYNESGTILHSIKSALSQDYPKLEVIVVDDGSEDDTFEKANS----IKDSRLKVFRKKH----EGKAK 103
                                       56.9****************************************9998876....6889***876666....48999 PP

                   Glyco_tranf_2_3  78 alnealravksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfllnrstlvsalgal.efaerhlrflaarr 153
                                       aln +l+++++++++ +D+Dt++ P++++ l+  + ++++  +g++ ++  +s+++ +++++ +f +  +r+ +  +
  gi|242398084|ref|YP_002993508.1| 104 ALNFGLQRTSGEIITTIDADTLLAPNAIRELVKRIYSKEIVGAGGQIRV-LGSSFLERAQDVeHFRIAMFRRAKELE 179
                                       ***********************************88877777777776.589999999998344444444444445 PP

                   Glyco_tranf_2_3 154 algvltlnGsgslirrevlkelegldplflltdDyelglrlrragfrtayvpgaavrevfpsslkayikqrnRwvy 229
                                        l+v++  G +s++r ++l+e++g+ +  ++++Dy ++  +++ g +++y+p+a  +   ps+l++++ qr Rw  
  gi|242398084|ref|YP_002993508.1| 180 DLSVAP--GPLSAFRKTILREIGGFVE--SKVEDYATTKAIKKLG-KVVYAPKAKAYVKMPSKLSELWVQRKRWFL 250
                                       556666..9****************99..*******997777765.9***************************76 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 !   50.6   0.1   8.6e-17   2.2e-13       1     192 [.     116     328 ..     116     342 .. 0.70

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 8.6e-17
                   Glyco_trans_2_3   1 iilllDaDtvlppdclreiaaelaspevaivqgpvlvmnvanwleelaalf.faedhgkdilvrealgrvvpsvGsg 76 
                                       ii+ +DaDt+l p+ +re++  + s e+  + g++ v  ++++le+ ++++ f  +++ +++  + l +    +G  
  gi|242398084|ref|YP_002993508.1| 116 IITTIDADTLLAPNAIRELVKRIYSKEIVGAGGQIRVL-GSSFLERAQDVEhF--RIAMFRRA-KELEDLSVAPGPL 188
                                       79**********************99999999999999.579*******9966..56667777.6899999999*** PP

                   Glyco_trans_2_3  77 aflrrsalqevggwdgdessvsEDfdmglrlqrkGyrvrfvpeslvkekspltlraalrQrkRwayGcel....... 146
                                       +++r   l+e+gg+    +s  ED+    ++ +k  +v+++p +  + k p+ l   + QrkRw++G  l       
  gi|242398084|ref|YP_002993508.1| 189 SAFRKTILREIGGFV---ESKVEDYAT-TKAIKKLGKVVYAPKAKAYVKMPSKLSELWVQRKRWFLGD-Lehlgggf 260
                                       **************9...7788***99.677777789999****9**********************5.23445554 PP

                   Glyco_trans_2_3 147 ..eklil....................lvrllgylgsllwsalplhlallllfslla..lalvlllllll 192
                                         e  +l                    l+  +g+l +++   ++ +l+ +l+ + +    ++++++l+++
  gi|242398084|ref|YP_002993508.1| 261 ekE--LLflilgdfiafldiiipialtLTGKFGLLLLFIGYEILTALIPTLVEGGSLlnAMFFPIFLWFW 328
                                       321..21345555555555555555443333333333333333333333333333333322222222222 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 !   45.7   0.0   2.2e-15   5.6e-12       1     127 [.      39     159 ..      39     210 .. 0.81

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 2.2e-15
                   Glyco_tranf_2_2   1 svviplraseerhyieervlqkakyydeeielivvddgSsekfleevssiidlnllv.ylkdeddkayslaaarNrG 76 
                                       +++ip +++ ++  i   ++   ++  +++e+ivvddgS +++ e+ +si+d +l+v   k+e     ++a+a N G
  gi|242398084|ref|YP_002993508.1|  39 TILIPAYNESGT--ILHSIKSALSQDYPKLEVIVVDDGSEDDTFEKANSIKDSRLKVfRKKHE-----GKAKALNFG 108
                                       6899*******9..9999*988888679*****************************444555.....9******** PP

                   Glyco_tranf_2_2  77 askaesdlvlFlDaDcfissDkfekilklitikklrenidaavvlpvvdln 127
                                        +++ ++++  +DaD + +++ +  ++k i +k++        vl    l 
  gi|242398084|ref|YP_002993508.1| 109 LQRTSGEIITTIDADTLLAPNAIRELVKRIYSKEIVGAGGQIRVLGSSFLE 159
                                       ****************************99999987665555555555555 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 !   38.9   0.0   2.3e-13   5.9e-10      17     171 ..     100     248 ..      87     249 .. 0.80

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 2.3e-13
                   Glyco_transf_21  17 pKvnnllqaleaakydllvisDsdvrvkpdyLeellaaledpkvglVtslpvgsdakglaaaleaafl..ntlagvl 91 
                                        K  +l+ +l++   +++++ D+d++++p++++el++++ ++++    + +++ +  ++  + + + +   ++ +++
  gi|242398084|ref|YP_002993508.1| 100 GKAKALNFGLQRTSGEIITTIDADTLLAPNAIRELVKRIYSKEIVGAGGQIRVLGS-SFLERAQDVEHfrIAMFRRA 175
                                       466668899999****************************9766666666666655.55555555555234667777 PP

                   Glyco_transf_21  92 qaklsglgfavGksmalrreaLeaiGGfealadeLAeDyalgkllraaGlkvvlspapiaqtsvprrsslrallaRq 168
                                       +  l+ l+ a G   a+r+ +L++iGGf +      eDya++k++++ G+ v+  +a  a +++p+  +l++l+ + 
  gi|242398084|ref|YP_002993508.1| 176 KE-LEDLSVAPGPLSAFRKTILREIGGFVE---SKVEDYATTKAIKKLGKVVYAPKA-KAYVKMPS--KLSELWVQR 245
                                       77.*************************99...789*************76666665.57677774..799999999 PP

                   Glyco_transf_21 169 lrW 171
                                        rW
  gi|242398084|ref|YP_002993508.1| 246 KRW 248
                                       998 PP

>> Chitin_synth_2  Chitin synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.44   1.1e+03      27      64 ..      38      72 ..      27      78 .. 0.73
   2 !    8.6   0.0   0.00024      0.61     196     258 ..     108     167 ..      99     200 .. 0.77
   3 !    9.3   0.0   0.00015      0.38     337     426 ..     217     307 ..     204     340 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.44
                    Chitin_synth_2 27 ticlvtaysegeeglrttldslastdyddkrklllvvc 64
                                      + +l++ay e+   l +++ s+ s dy++ +  ++vv 
  gi|242398084|ref|YP_002993508.1| 38 VTILIPAYNESGTIL-HSIKSALSQDYPKLE--VIVVD 72
                                      457899999987655.678899999998654..34444 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00024
                    Chitin_synth_2 196 GvspdfyeivlmvdadtkvapdsltrlvaalvkdpeilglcGetkiankkeswvtaiqvfeyy 258
                                       G++ +  ei+ ++dadt +ap+++++lv  + + +ei+g  G+ ++    +s++   q  e++
  gi|242398084|ref|YP_002993508.1| 108 GLQRTSGEIITTIDADTLLAPNAIRELVKRIYS-KEIVGAGGQIRVL--GSSFLERAQDVEHF 167
                                       77788889********************99876.6899999987664..56777777666665 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.00015
                    Chitin_synth_2 337 ktfpkrktvfvpqakcktvaPdtfkvllsqrrrwinstvhnl...lelvlvrdlcGtfcfsmrfvvfieligtvvlP 410
                                       k+    k v+ p+ak+   +P + + l  qr+rw    +  l   +e  l+  + G f+  +  ++ i l+ t    
  gi|242398084|ref|YP_002993508.1| 217 KKL--GKVVYAPKAKAYVKMPSKLSELWVQRKRWFLGDLEHLgggFEKELLFLILGDFIAFLDIIIPIALTLTGKFG 291
                                       443..3789*************************9988877744445555555566666666666666666666666 PP

                    Chitin_synth_2 411 vaiaftlylivasilk 426
                                       + ++f+ y i+++++ 
  gi|242398084|ref|YP_002993508.1| 292 LLLLFIGYEILTALIP 307
                                       6666666666666554 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 ?   15.0   0.0     1e-05     0.026       2      86 ..      46     128 ..      45     135 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1e-05
                   Glyco_tranf_2_4   2 neadiLpeflahhlalgf..drilvydndstDgtrailkelpevkllhvdksyederrqvellkallaryaeadwvl 76 
                                       ne  ++ + ++ +l+ ++   +++v+d++s+D+t +   + ++ +l  ++k+ e    + ++l+  l+r   ++ + 
  gi|242398084|ref|YP_002993508.1|  46 NESGTILHSIKSALSQDYpkLEVIVVDDGSEDDTFEKANSIKDSRLKVFRKKHE---GKAKALNFGLQRT-SGEIIT 118
                                       88888899999999999843369***************9999988888888654...4788999999885.899*** PP

                   Glyco_tranf_2_4  77 vvDaDEflvv 86 
                                       ++DaD +l+ 
  gi|242398084|ref|YP_002993508.1| 119 TIDADTLLAP 128
                                       *****88875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); 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: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 2234.17
//
Query:       gi|242398085|ref|YP_002993509.1|  [L=306]
Description: Sodium/phosphate symporter [Thermococcus sibiricus MM 739]
Scores for complete 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-53  181.3  32.6    1.6e-52  178.6  32.6    1.9  1  PHO4      Phosphate transporter family
  ------ inclusion threshold ------
        0.1   13.0   1.6       0.51   10.7   0.1    2.2  2  DUF1689   Protein of unknown function (DUF1689)


Domain annotation for each model (and alignments):
>> PHO4  Phosphate transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.6  32.6   1.8e-56   1.6e-52       1     336 [.      15     297 ..      15     298 .. 0.91

  Alignments for each domain:
  == domain 1  score: 178.6 bits;  conditional E-value: 1.8e-56
                              PHO4   1 iGanDvanafatsvgskaltlrqAvilaaifeflGavllGaeVaetirkgivdvelfdpselmlgmlaallgaavwl 77 
                                       +G+nD a+ ++t+vgs+ l  ++Av++  +f ++Gav+ G+ V+ ti++             ++ + ++l++aav +
  gi|242398085|ref|YP_002993509.1|  15 VGVNDSAKVVGTAVGSGLLGFKKAVFVIVVFTTMGAVFGGGGVSGTISELAK-------GLDAYSIGIILFSAAVAV 84 
                                       69*********************************************98443.......333478999********* PP

                              PHO4  78 llatvlglPvStthslvGaliGaalaaeggeavkwkklvkivlswvlsPllggiiaallfllvkrlilvkeklknal 154
                                       +la++ glP+Stt+s+vG+l+Gaal+   + +vkw+ l+kivl+wvlsPl ++++a++++ +  +l  +     +++
  gi|242398085|ref|YP_002993509.1|  85 TLASIRGLPISTTQSIVGGLAGAALTF--NLMVKWEILFKIVLAWVLSPLAAAFLAIMVYEVYVKL--F-----KKI 152
                                       **************************6..469*************************999888888..2.....122 PP

                              PHO4 155 ralpvlvlvtiailalsilfkgeskkddeeteklfkflqvvsaalvsfahGanDvanaiGpllaalisiykaskevp 231
                                       +                           +  e ++k+l+ ++ a+ +f  Gan+ +n++G++ a+ i+        p
  gi|242398085|ref|YP_002993509.1| 153 KQ-------------------------IQLLEAMYKWLVFIAVAFSAFNLGANELSNVVGLMEAIGID-------GP 197
                                       22.........................2344788****************************664443.......35 PP

                              PHO4 232 lwvlllgglaialGlllgGkrviktvGekitkkltpsrGfaaelaaaltvllasklglPvStThvlvgavvGvGlak 308
                                           l+  l +++G l++ ++vi  +G+k+t  l+p ++f+ ++a+a+ v +a+ +glPvS+ +++vg+v+G G   
  gi|242398085|ref|YP_002993509.1| 198 --FKLVLSLTLGFGALTFSHEVIMSIGKKLTP-LDPLSAFSSQFASAIAVTTANLFGLPVSSGQAVVGGVAGLGYHL 271
                                       ..78999************************5.*******************************************9 PP

                              PHO4 309 kresavnwklvrnivlaWvlTlpvsall 336
                                       +  + +nw+l+r+ivl+W++   +s++l
  gi|242398085|ref|YP_002993509.1| 272 G--NPINWGLIRSIVLSWIFAPLISGIL 297
                                       5..7*********************987 PP

>> DUF1689  Protein of unknown function (DUF1689)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1     0.054   4.8e+02      33      85 ..      63     117 ..      59     124 .. 0.79
   2 ?   10.7   0.1   5.7e-05      0.51      21      83 ..     147     219 ..     145     241 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.054
                           DUF1689  33 qllggwlgfsavflaptayrryktgaikgvkvpr..sfllGlvalvvssqlaaky 85 
                                       +l  g+ + s++++++ a+  ++  +i+g  +++  s++ Gl++ +++ +l+ k+
  gi|242398085|ref|YP_002993509.1|  63 ELAKGLDAYSIGIILFSAAVAVTLASIRGLPISTtqSIVGGLAGAALTFNLMVKW 117
                                       6667778888888899999999999999987766669999999998888888775 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 5.7e-05
                           DUF1689  21 eLakklqsiaraqllggwlgfsavflaptayrryktgaikgvkvpr..........sfllGlvalvvssqlaa 83 
                                       +L kk+++i+  ++++ wl f+av ++ + +   + +++ g    +          s+ lG++al +s+++ +
  gi|242398085|ref|YP_002993509.1| 147 KLFKKIKQIQLLEAMYKWLVFIAVAFSAFNLGANELSNVVGLMEAIgidgpfklvlSLTLGFGALTFSHEVIM 219
                                       799**************************999988888877755559999*****************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       842  (0.046963); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.56
# Mc/sec: 1656.03
//
Query:       gi|242398086|ref|YP_002993510.1|  [L=584]
Description: archaeosine tRNA-guanine transglycosylase [Thermococcus sibiricus MM 739]
Scores for complete 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  261.4   0.0    1.6e-77  261.0   0.0    1.1  1  TGT       Queuine tRNA-ribosyltransferase
      6e-33  113.0   1.2      6e-33  113.0   1.2    1.9  2  TGT_C1    C1 domain of tRNA-guanine transglycosylase dimerisa
    4.3e-22   78.0   0.0    1.9e-21   75.9   0.0    2.2  1  TGT_C2    Patch-forming domain C2 of tRNA-guanine transglycos
    1.1e-15   57.3   0.1    3.2e-15   55.8   0.1    1.9  1  PUA       PUA domain
    0.00023   21.4   0.1      0.045   14.0   0.0    2.7  2  UPF0113   UPF0113 PUA domain
    0.00047   19.9   0.1      0.058   13.2   0.0    3.4  3  PUA_3     PUA-like domain


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 !  261.0   0.0   5.5e-81   1.6e-77       3     349 ..      19     340 ..      16     341 .. 0.96

  Alignments for each domain:
  == domain 1  score: 261.0 bits;  conditional E-value: 5.5e-81
                                       EEEEEEEETTEEEEESEEEEBETTSSBTTB-HHHHH.HTTES-EEEEHHHHHHTTTHHHHHHTTHHHHHHT--S-EE CS
                               TGT   3 aRlGklelphgtietPafmpvgtqgtvkgltpdelkeelgaqiilsntyhlelrpgeelvakagglhkflgwdkpil 79 
                                       +R+Gk+e++++++etPa+mpv  +++   +tp+el e++g  ii++n+y++++ ++ +  a ++g+h++lg+++ i 
  gi|242398086|ref|YP_002993510.1|  19 GRIGKMEVNGKKLETPAIMPV-VNPKQLIVTPKEL-EQMGFGIIITNSYIIYKDETLKEKALEKGIHRLLGYNGIIE 93 
                                       8********************.66666669*****.699*****************9999999************** PP

                                       EE-SHHHHHHHEEEESSEEEEE-TTTS-EEEE-HHHHHHHHHHHT-SEEE-------SS--HHHHHHHHHHHHHHHH CS
                               TGT  80 tdsggfqvfslkkiteegvsfqsridGskvlltpeesieiqeklgsDiimalddvvpspaskkrveksverTlrwld 156
                                        dsg+fq++              r+ G  + +t++e+ie+q+++g Di + ld ++ ++a ++++e  ++ Tl++++
  gi|242398086|ref|YP_002993510.1|  94 VDSGSFQLM--------------RY-GG-IDVTNREIIEFQHRIGVDIGTFLDIPTIPDAPREKAEDDLKITLERAK 154
                                       *******66..............46.99.************************************************ PP

                                       HHHHHHSE.EEEEE--TT-HHHHHHHHHHHHHH--SEEEE-S.SSSSS..HHHHHHHHHHHHGGGS-TTS-EEETTB CS
                               TGT 157 rcleahqa.lfgivqGglyedlreesaeelakrdfdgyaigG.lsvge..ekeellevveavtellpedkprylmGv 229
                                       ++ + +++ + + +qG++y+dlr ++a++l++++f++ +ig+ ++++e  ++++l++vv a++  l  d+p++l+G+
  gi|242398086|ref|YP_002993510.1| 155 EAERIKEIaMNAAIQGSTYPDLRIRAAKQLSEMNFEVHPIGAvVPLMEayRYRDLVDVVIASKIGLRPDRPVHLFGA 231
                                       **9999888*********************************888***9999************************* PP

                                       -SHHHHHHHHHTT--EEEESHHHHHHHTTEEEETTEEEETTSGGGTT--SBSSSS--SHHHHH-BHHHHHHHHHTT- CS
                               TGT 230 gtPedlleavalGvDmfdcvyptrtarngraltsegelnlknakyaedfspldegCsCytCknytraylhhllktke 306
                                       g+P+ ++ ava+GvD+fd++ ++++a+++r++t+eg+ +l++ +y     p    CsC++C++yt++ l+++ k+++
  gi|242398086|ref|YP_002993510.1| 232 GHPMVFALAVAMGVDLFDSASYALYAKDDRYMTPEGTKRLEELEYF----P----CSCPVCSSYTPQDLKEMPKEER 300
                                       ********************************************99....9....******************9999 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHT CS
                               TGT 307 mlgaiLltiHNlhyylelfkriReaIkegtfeefveefarkye 349
                                          ++Ll++HNl++++e+++r+++a+kegt++e+v+e+ar+++
  gi|242398086|ref|YP_002993510.1| 301 ---TRLLALHNLWIIREELNRVKQAVKEGTLWELVDERARSHP 340
                                       ...*************************************997 PP

>> TGT_C1  C1 domain of tRNA-guanine transglycosylase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.2         4   1.2e+04      21      32 ..     150     160 ..     141     162 .. 0.69
   2 !  113.0   1.2     2e-36     6e-33       1      69 [.     361     429 ..     361     430 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 4
                            TGT_C1  21 verakeraekvk 32 
                                        erake ae++k
  gi|242398086|ref|YP_002993510.1| 150 LERAKE-AERIK 160
                                       478887.78876 PP

  == domain 2  score: 113.0 bits;  conditional E-value: 2e-36
                            TGT_C1   1 pvtkksaffkvseealkwpiverakeraekvkakfpesishpifGeipkylslsypfaqseseedftve 69 
                                       pvtk+saffk+see lk p+  rak rae+v+ kf +++ hpifGeipkyl l++pfaqse+eedf ++
  gi|242398086|ref|YP_002993510.1| 361 PVTKASAFFKISEEILKTPVPLRAKIRAERVRRKFQNTLEHPIFGEIPKYLILTFPFAQSEGEEDFSIK 429
                                       9*****************************************************************996 PP

>> TGT_C2  Patch-forming domain C2 of tRNA-guanine transglycosylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.9   0.0   6.5e-25   1.9e-21       3      71 .]     440     507 ..     439     507 .. 0.97

  Alignments for each domain:
  == domain 1  score: 75.9 bits;  conditional E-value: 6.5e-25
                            TGT_C2   3 lraiadYqFGagagdaLfpedvtitrs.atgrirqvlvdgerlatlraqdgrltLsleGarrlheslppP 71 
                                       ++a+a+YqFG+ga +a+   dv +++s +tg +rq+ ++g+++at+ra+dg+ltL++eGa+rlh +lp+P
  gi|242398086|ref|YP_002993510.1| 440 VQAVAEYQFGEGASEAFK--DVFVELSrKTGMPRQIKAKGQHVATFRADDGFLTLGIEGAKRLHAILPYP 507
                                       899*************98..6***********************************************98 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.8   0.1   1.1e-18   3.2e-15       2      73 ..     510     581 ..     509     582 .. 0.98

  Alignments for each domain:
  == domain 1  score: 55.8 bits;  conditional E-value: 1.1e-18
                                       EEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEEEE CS
                               PUA   2 rvvvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksveierv 73 
                                       rv+v+d A  + ++g+s++a++v+++++ +++ d+V +v++++el+a G +++++ el+ ++ g +++++r 
  gi|242398086|ref|YP_002993510.1| 510 RVIVNDDAEPFAKKGKSVFAKFVIGADERIRPYDEVLVVNKNDELLATGQSLLNGRELKVFQQGLAIKVRRG 581
                                       8********************************************************************996 PP

>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.015        46      33      56 ..      42      67 ..      29      82 .. 0.78
   2 !   14.0   0.0   1.5e-05     0.045      15      55 ..     524     564 ..     511     577 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.015
                           UPF0113 33 nqvvvVlnengeplGiGkirkdt..k 56
                                       ++++V  ++ e +G+G+i+ ++   
  gi|242398086|ref|YP_002993510.1| 42 PKQLIVTPKELEQMGFGIIITNSyiI 67
                                      46799**************9887541 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 1.5e-05
                           UPF0113  15 GrdvlkesilkitesvkenqvvvVlnengeplGiGkirkdt 55 
                                       G+ v+ + ++  +e ++  + v+V+n+n+e+l+ G +  ++
  gi|242398086|ref|YP_002993510.1| 524 GKSVFAKFVIGADERIRPYDEVLVVNKNDELLATGQSLLNG 564
                                       99*********************************997766 PP

>> PUA_3  PUA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.23     7e+02      13      25 ..     231     243 ..     226     263 .. 0.81
   2 !   13.2   0.0   1.9e-05     0.058       9      43 ..     302     336 ..     297     339 .. 0.84
   3 ?    1.5   0.0      0.09   2.7e+02      18      49 ..     527     558 ..     511     559 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.23
                             PUA_3  13 qGhPwvfsneias 25 
                                       +GhP vf+ ++a 
  gi|242398086|ref|YP_002993510.1| 231 AGHPMVFALAVAM 243
                                       79*****988875 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 1.9e-05
                             PUA_3   9 krlrqGhPwvfsneiasvegeledGdvVdvfsekg 43 
                                       + l  + +w+ ++e+++v++++++G + ++++e+ 
  gi|242398086|ref|YP_002993510.1| 302 RLLALHNLWIIREELNRVKQAVKEGTLWELVDERA 336
                                       45556789************************975 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.09
                             PUA_3  18 vfsneiasvegeledGdvVdvfsekgkflGtG 49 
                                       vf++ +   ++ +++ d V v++++++ l+tG
  gi|242398086|ref|YP_002993510.1| 527 VFAKFVIGADERIRPYDEVLVVNKNDELLATG 558
                                       6777777778899999***************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (584 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.27s 00:00:00.91 Elapsed: 00:00:00.46
# Mc/sec: 3824.57
//
Query:       gi|242398087|ref|YP_002993511.1|  [L=555]
Description: bipolar DNA helicase [Thermococcus sibiricus MM 739]
Scores for complete 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  149.0   0.6    3.3e-43  148.4   0.6    1.3  1  DUF87            Helicase HerA, central domain
    5.1e-11   42.6   1.4    3.7e-10   39.8   1.1    2.5  2  HAS-barrel       HAS barrel domain
      7e-08   31.5   0.2    4.1e-05   22.4   0.0    2.1  2  DUF853           Bacterial protein of unknown function (DUF85
     0.0062   15.5   0.0      0.055   12.4   0.0    2.1  2  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
  ------ inclusion threshold ------
      0.075   13.6   0.0       0.16   12.5   0.0    1.7  1  ABC_tran         ABC transporter
      0.093   11.5   0.0       0.14   10.9   0.0    1.2  1  T4SS-DNA_transf  Type IV secretory system Conjugative DNA tra


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 !  148.4   0.6   1.1e-46   3.3e-43       1     226 [.     139     372 ..     139     373 .. 0.91

  Alignments for each domain:
  == domain 1  score: 148.4 bits;  conditional E-value: 1.1e-46
                             DUF87   1 ieiGrllsgsevpvyldlnklvtrHlAilgsTGsGKSntvavLleellekkgatililDpHGEYgkalekllsekvk 77 
                                       i+iGrll +++v+v ld+nklv+rH+A+l+ TG+GKSnt+avL +e++   ++ti+ilDpHGEY++++     +++k
  gi|242398087|ref|YP_002993511.1| 139 IKIGRLLARENVEVGLDVNKLVSRHFAVLAVTGAGKSNTIAVLSKEIVDNTKGTIVILDPHGEYSRLS----WKNAK 211
                                       79**********************************************999*****************....99999 PP

                             DUF87  78 vitpspsakdkelkinpwsldpeelldlleeddkpaaavqrsvleealdqaka..keekeklssdepveklleelk. 151
                                       v t+       + +i+p+++++ e+++ll++   ++a+ qr++l  a+ ++k   +++ + l + ++v  l+++++ 
  gi|242398087|ref|YP_002993511.1| 212 VNTI-------KATIDPAKIKVSEFATLLGV--AENASLQRRFLSLAYYTVKWeaRNSSKILGGIAFVDALEQKIEe 279
                                       9999.......57******************..999999*********9999655555555666777777777777* PP

                             DUF87 152 ........................kekeelrklknqaiarlldkledllrkggsfsnsstdliallleklekegkit 204
                                                                  +++++++ ++  rl+d l++l+ + ++f  +  ++++++      +  ++
  gi|242398087|ref|YP_002993511.1| 280 wirayesrergedvvinyydpqgnLLPRKIQSKDLDSLIRLKDYLQELKANFREF-IKLGNILSEI-----TPAMVN 350
                                       *********************8876666888888888999999999999888888.99999999**.....****** PP

                             DUF87 205 iidlsgvdelaqqlvvsvilrr 226
                                       +idlsg++e+++ +++s++lr 
  gi|242398087|ref|YP_002993511.1| 351 VIDLSGMEEDQMIALASYLLRG 372
                                       ********************95 PP

>> HAS-barrel  HAS barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.8   1.1   1.2e-13   3.7e-10       1      89 [.       4      93 ..       4      96 .. 0.75
   2 ?   -0.6   0.0      0.51   1.5e+03      13      31 ..     105     124 ..     100     146 .. 0.69

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 1.2e-13
                        HAS-barrel  1 iGevigestssslifrvegskdvkvGeyVeielpdgeivlGmvtdirrgn.....selsndlalvlsleeleeangdde 74
                                      +G+v+ges+ + ++f v+++ ++ +Ge+V+++++ g++vl +v  +r++n     +  s d+ +      ++ +   +e
  gi|242398087|ref|YP_002993511.1|  4 VGIVYGESSTDYFTFIVDPQNMPNFGEFVVVKNRNGDEVLAVVKGVRNINwlmgvGKGSYDYIEKTVNVFSKGVLDKSE 82
                                      79**********************************************9999887333333333333334444444445 PP

                        HAS-barrel 75 valatedtgvkvlGe 89
                                       ++a +    kvlG 
  gi|242398087|ref|YP_002993511.1| 83 SIIASA----KVLGV 93
                                      555555....66665 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.51
                        HAS-barrel  13 lifrvegsk.dvkvGeyVei 31 
                                       ++fr ++   ++k Ge Ve 
  gi|242398087|ref|YP_002993511.1| 105 FEFRQRPNRvPIKPGEVVER 124
                                       56666665569999999973 PP

>> DUF853  Bacterial protein of unknown function (DUF853)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.1   0.00057       1.7      17      82 ..     157     223 ..     143     233 .. 0.77
   2 !   22.4   0.0   1.4e-08   4.1e-05     255     361 ..     403     503 ..     396     515 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00057
                            DUF853  17 lklanrhGliaGatGtGktvtLqvlaeslsea.GvpvfladvkGdLsgiakaGevkdklaarleeig 82 
                                        kl+ rh  +   tG+Gk  t+ vl++++ +    ++++ d  G+ s ++      + ++a ++  +
  gi|242398087|ref|YP_002993511.1| 157 NKLVSRHFAVLAVTGAGKSNTIAVLSKEIVDNtKGTIVILDPHGEYSRLSWKNAKVNTIKATIDPAK 223
                                       46899*********************99876514467778999999999988888888887776555 PP

  == domain 2  score: 22.4 bits;  conditional E-value: 1.4e-08
                            DUF853 255 dkPklvfffdeahLLfndapk.allekveqvvrLirskGvGvyfvtqnPldlPdtvLaqLGnrvqhalraftpkdqk 330
                                        kP lv+  +eah++     k    + + ++ r  r  G+G+  v+q P  l d++L+q  +++   lr   p+dq+
  gi|242398087|ref|YP_002993511.1| 403 TKPILVI-VEEAHIFAPREYKtQAAHWLGKIAREGRKFGIGLGIVSQRPKKLDDDILSQTNTKI--ILRLVEPHDQR 476
                                       6888876.689998865444414556688999999*************************9999..69********* PP

                            DUF853 331 avkaaadtfranpefdveeaiteLgvGealv 361
                                        v++a++ + ++  +d    i +Lg+Gea++
  gi|242398087|ref|YP_002993511.1| 477 YVQQASEQISEDLLLD----IASLGIGEAVI 503
                                       ******9998866555....779******98 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   1.8e-05     0.055      13      56 ..     159     203 ..     151     214 .. 0.85
   2 ?    0.4   0.0     0.081   2.4e+02     263     310 ..     431     470 ..     424     488 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.8e-05
                     TrwB_AAD_bind  13 retqhilivGttGsGKtqalekllrairarg.draivlDltGafv 56 
                                          +h++++  tG+GK++++  l ++i      ++++lD++G++ 
  gi|242398087|ref|YP_002993511.1| 159 LVSRHFAVLAVTGAGKSNTIAVLSKEIVDNTkGTIVILDPHGEYS 203
                                       5689*********************9876651678899****985 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.081
                     TrwB_AAD_bind 263 sllaegRkfGgavvlglqsiaqlrevYGedaaqsilslvntklilrvs 310
                                       +++ egRkfG+ + +  q  ++l +         ils +ntk+ilr  
  gi|242398087|ref|YP_002993511.1| 431 KIAREGRKFGIGLGIVSQRPKKLDD--------DILSQTNTKIILRLV 470
                                       5667778888777777777777753........466666666666632 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.5e-05      0.16      15      67 ..     165     218 ..     152     371 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.5e-05
                                       EEEESTTSSHHHHHHHHTTSS.--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS CS
                                       xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  15 aivGenGaGKStLlkllagll.kpteGeilldgkdlkeqeleslrkeigvlpqe 67 
                                       a++  +GaGKS  +++l+++  ++t+G+i + + + ++ +l++ ++++ +++ +
  gi|242398087|ref|YP_002993511.1| 165 AVLAVTGAGKSNTIAVLSKEIvDNTKGTIVILDPHGEYSRLSWKNAKVNTIKAT 218
                                       666679************986166*****7776666665666666666655544 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 ?   10.9   0.0   4.7e-05      0.14      45     111 ..     162     229 ..     120     244 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 4.7e-05
                   T4SS-DNA_transf  45 ehvlvvAptrsgKgvgvvi.Pn.llkwkq.siVvlDpkgElaeltskiRkkqgrkV.fvlePanlktsdrf 111
                                        h  v A t++gK+  + +    +   ++ +iV+lDp gE   l   ++ ++ + +    +Pa++k s  f
  gi|242398087|ref|YP_002993511.1| 162 RHFAVLAVTGAGKSNTIAVlSKeIVDNTKgTIVILDPHGEYSRLS--WKNAKVNTIkATIDPAKIKVS-EF 229
                                       699**********98875524414444445**********98874..666666644245677777766.55 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (555 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:01.81
# Mc/sec: 931.54
//
Query:       gi|242398088|ref|YP_002993512.1|  [L=442]
Description: DNA double-strand break repair protein mre11 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.8e-16   59.9   0.3    4.8e-16   59.9   0.3    2.0  2  Metallophos    Calcineurin-like phosphoesterase
    1.8e-12   47.8   0.0    1.5e-11   44.7   0.0    2.1  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 !   59.9   0.3   5.3e-20   4.8e-16       1     203 [.       3     212 ..       3     213 .. 0.67
   2 ?   -0.4   0.2      0.15   1.4e+03      61      75 ..     282     291 ..     223     410 .. 0.50

  Alignments for each domain:
  == domain 1  score: 59.9 bits;  conditional E-value: 5.3e-20
                                       EEEEEEESBTB....TTCCTHHHHHHHHHHHH...HHHTTESEEEEESTSSSSSHHHHHHHHH.HHHHHHH...TSE CS
                       Metallophos   1 lrilvigDlHl....algggqlddllkllddl...lreekpdlvllaGDlvdrgdlekellel.laalvky...pip 66 
                                       +++++i+D+Hl      ++ +++d+l++++++   + eek+d++llaGDl++ + ++ + ++  ++ l+     +ip
  gi|242398088|ref|YP_002993512.1|   3 MKFAHIADPHLgreqFQQPFRYRDYLEAFKQAierAIEEKVDFILLAGDLFHVSKPSPRAIRDaVEVLGVAkkkDIP 79 
                                       89*************778888888888887775665558***************777777777666666667778** PP

                                       EEEEC-TTS.......CHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEEESECEEETHHHHHHHH CS
                       Metallophos  67 vylllGNHe.......gfeeellnkygylgifsepwrsdaevfnnlplaslgsgslkvlllhGgspellvsldklgs 136
                                       ++++ GNH+          ++ll+  g +++ +  +       ++    s+ +g  +++l++G + ++     ++ +
  gi|242398088|ref|YP_002993512.1|  80 IFAIEGNHDktiretsI--YDLLEHLGLIYTIGIKKTPR----EGEFQRSIKKG--NLYLVYGVFGDI-----EIYG 143
                                       *********65554220..13333333322222222222....44444556777..777777773223.....4444 PP

                                       HHHSCHHHHCCHHHHHH.....HHHHTTCSEEEEEESSESSCSSSCSCCHHHHH.HH.HHHTTESEEEEESSSS CS
                       Metallophos 137 lnleleapepgdewlkd.....lekrekadwvivlgHsplyrgsgylfgdeale.dl.lkkygvdlvisGHtHv 203
                                       l ++ +     ++++k+     +  +++++  i++ H  + + ++ +   +a++ +l +   g  ++  GH+H 
  gi|242398088|ref|YP_002993512.1| 144 LRHNNR-----WQLIKNgqnilKTLFKGRPNSILMLHQAIDYLAEGTPYKDAFDlKLsEIPDGFGYYALGHIHM 212
                                       444444.....455555555555599***************6666666666666677566666999******96 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.15
                                       HHHTSEEEEEC-TTS CS
                       Metallophos  61 vkypipvylllGNHe 75 
                                       ++     +l++GN  
  gi|242398088|ref|YP_002993512.1| 282 YN-----VLIKGNSK 291
                                       33.....55555555 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 !   44.7   0.0   1.7e-15   1.5e-11       1     151 [.       3     238 ..       3     250 .. 0.75

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 1.7e-15
                     Metallophos_2   1 MklaiiSDlH.............snldaleavlealkevgvdaiihaGDl...eeeepevleellela........p 53 
                                       Mk+a+i+D H             + l+a ++++e++ e++vd i++aGDl    + +p +++++ e++        p
  gi|242398088|ref|YP_002993512.1|   3 MKFAHIADPHlgreqfqqpfryrDYLEAFKQAIERAIEEKVDFILLAGDLfhvSKPSPRAIRDAVEVLgvakkkdiP 79 
                                       ********************999999999999*****************98666666667887777778888999** PP

                     Metallophos_2  54 vlaVrGNnD.............................................eevveedvlreaaelgtdl.... 81 
                                       + a+ GN+D                                             +                 +    
  gi|242398088|ref|YP_002993512.1|  80 IFAIEGNHDktiretsiydllehlgliytigikktpregefqrsikkgnlylvyG-----------------Vfgdi 139
                                       **************99999999999999998876666655555555555554441.................04444 PP

                     Metallophos_2  82 ...............peeaelel..agek..vlliHgdpl......gvkdalaellkeaeegsd.vvvcGHtHvpev 132
                                                        +  l+   +g+   +l++H+  +       +kda++  l+e   + + ++++GH+H+++ 
  gi|242398088|ref|YP_002993512.1| 140 eiyglrhnnrwqlikNGQNILKTlfKGRPnsILMLHQAIDylaegtPYKDAFDLKLSE-IPDGFgYYALGHIHMKKE 215
                                       44444443444444323333332235555679999998559***99899999888888.555557**********88 PP

                     Metallophos_2 133 ekeggv....lvvnPGsvgeprd 151
                                        k+g+      +++PGs+++   
  gi|242398088|ref|YP_002993512.1| 216 LKKGESglsgDIIYPGSLERTEI 238
                                       888744446699******98754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (442 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); 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: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 2769.05
//
Query:       gi|242398089|ref|YP_002993513.1|  [L=895]
Description: DNA double-strand break repair rad50 ATPase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.7e-11   43.3  22.8    3.7e-11   43.3  22.8    4.3  1  AAA_15         AAA ATPase domain
    8.8e-09   35.1   0.3    8.8e-09   35.1   0.3    2.7  2  SMC_N          RecF/RecN/SMC N terminal domain
    2.2e-07   31.0  31.2    6.4e-05   22.9   2.0    4.0  3  AAA_21         AAA domain, putative AbiEii toxin, Type IV TA 
    3.2e-06   26.9   0.6    3.2e-06   26.9   0.6    3.9  5  AAA_27         AAA domain
    4.4e-06   26.3   0.0    7.8e-06   25.5   0.0    1.4  1  AAA_29         P-loop containing region of AAA domain
    1.7e-05   24.5   4.3    1.7e-05   24.5   4.3    8.6  9  Rad50_zn_hook  Rad50 zinc hook motif
     0.0018   18.5   0.0      0.004   17.3   0.0    1.6  1  SbcCD_C        Putative exonuclease SbcCD, C subunit
  ------ inclusion threshold ------
      0.013   16.0 154.1    1.8e+04  -23.6  41.3    7.8  0  AAA_23         AAA domain
      0.016   15.6   1.7       0.16   12.4   0.0    3.2  3  AAA_16         AAA ATPase domain
       0.22   11.2   3.0        1.4    8.5   3.0    2.4  1  DUF3440        Domain of unknown function (DUF3440)
        1.8    8.8   0.0        1.8    8.8   0.0    4.5  5  AAA_22         AAA domain
          5    7.2  14.9        3.6    7.7   1.8    4.6  5  Flagellin_N    Bacterial flagellin N-terminal helical region


Domain annotation for each model (and alignments):
>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.3  22.8   2.5e-14   3.7e-11       1     262 [.       9     260 ..       9     279 .. 0.68

  Alignments for each domain:
  == domain 1  score: 43.3 bits;  conditional E-value: 2.5e-14
                            AAA_15   1 MkIkkikikNFRslkdveidlseeltvliGkNnsGKSsilealdlFlnnkekkn...kkvikiekedleifenises 74 
                                       M+I+++kikNFR++++ ++++++ ++++iG N+sGKSsilea   F +         +         +++ + +  +
  gi|242398089|ref|YP_002993513.1|   9 MRIRSLKIKNFRAHENSHVEFNDGINLIIGQNGSGKSSILEAV--FASLYL--GhgsF------PRGYKKVNTRIGK 75 
                                       9*****************************************9..777542..12331......3456677777888 PP

                            AAA_15  75 kdikIdvefaek.ekakeyektlkskekkkadlllkkkesdlkktikdkklklkknelsdekisvekkks....kke 146
                                         +++ ++f+ + ++ ++  k++ ++  k++ + l +k+sd+   ++   + l+  +   +  ++ + +       e
  gi|242398089|ref|YP_002993513.1|  76 SGFELVLKFEHNgKNYEIVRKSNGESYLKENGGVLHEKDSDIARWSERYLYPLHVFR---NALYIRQGEIenilVDE 149
                                       899999999433444455555555555555556667777777777777766666332...22222222222345666 PP

                            AAA_15 147 lpkekeeklekekeelkidkedlkklikkleeslkkeeelknvlksaiiklllisakRnvsdedsekkssllgklke 223
                                       +  ek   + + +e+++   +++++++++l+++ ++ e             +li+a  +++++ +e+ ++ lg+++ 
  gi|242398089|ref|YP_002993513.1| 150 DVREKVLRKVLGIEDFENSANNAQEVLRELRKKREYLE-------------KLIQASGDIQNKIKEQ-EKRLGEVIH 212
                                       66666666677777777777777777777766666666.............8999999999888887.888999999 PP

                            AAA_15 224 kileealqekleeelteklkeiqeklkeidkklaeelk.........k 262
                                       ki+e  ++e  + e+ ++ ++  e+lkei+++l++++k         k
  gi|242398089|ref|YP_002993513.1| 213 KINELRKKEIETAEKLSAVSKRYEELKEIKEILTQKEKeklsvegsmK 260
                                       999976665557777777788888889999999888884433332222 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 !   35.1   0.3   5.9e-12   8.8e-09       2      46 ..      11      52 ..      10      63 .. 0.91
   2 ?   -1.2  49.7      0.74   1.1e+03     135     213 ..     449     880 ..     173     886 .. 0.75

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 5.9e-12
                                      EEEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  2 lkrleienFksyagktvilpfsksftaivGpNGSGKsnlldAilF 46
                                      +++l+i+nF+    ++  ++f+++++ i+G+NGSGKs++l+A+ F
  gi|242398089|ref|YP_002993513.1| 11 IRSLKIKNFRAH--ENSHVEFNDGINLIIGQNGSGKSSILEAV-F 52
                                      789********9..79999***********************9.4 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.74
                                       T............................................................................ CS
                                       x............................................................................ RF
                             SMC_N 135 e............................................................................ 135
                                                                                                                    
  gi|242398089|ref|YP_002993513.1| 449 Ckrpieeheegeikreytaelakiekkkeeiaealrkalkrktelekirnneskliklhktleflenvesklekyni 525
                                       05555555555555555555555555555555555555555555555555555555555555555555555666666 PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|242398089|ref|YP_002993513.1| 526 eelkkkteefekvrervievkkeiirvnkeleklnefkneketllrklgdlerkkaevlheieekgfesfedvekrl 602
                                       66677777777777777777777777777777777777777777777777777788999999999999999999999 PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|242398089|ref|YP_002993513.1| 603 keleplykeyislsnvpqeiqirekrqellettlkdkekdlnltknvfkmlskeieelkvrftveefekiskeylsl 679
                                       99999999999999999999999999999999999999999999999999999999999999999999999999999 PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|242398089|ref|YP_002993513.1| 680 sslhaavlkeiegnenlkeevarnledlkrqleaikkakeeseliekmmadmkvlrekllklkaeaerrglseverv 756
                                       9999999999999999999999999999999********************************************** PP

                                       ...........................................CS-HHHHHHHHHHHHHH..HHCCS--SEEEECTT CS
                                       ...........................................xxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxx RF
                             SMC_N 136 ...........................................lLSgGektLvalaLlfA..iqkvkpaplyllDei 167
                                                                                   LSgGe+  + l++++A  ++kvk   l +lDe 
  gi|242398089|ref|YP_002993513.1| 757 aselfsdmterkyqgikiirekkfgreririvvlyqgqeeeidFLSGGERIALGLSFRLAlsLYKVKNMELLILDEP 833
                                       ********************************************************99997778999999******* PP

                                       TTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-SCEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 168 daaLDeknvkkvaellkekskn.aQfivislreemlekadklvgvtk 213
                                          LDe+++kk++e++ ++  +  Q+i++s++ee+   ad +++v+ 
  gi|242398089|ref|YP_002993513.1| 834 TPFLDEERRKKLVEIITQHLRKiPQVIIVSHDEELKDAADYVIRVSL 880
                                       ****************98766549******************99975 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 !   22.9   2.0   4.3e-08   6.4e-05       1     107 [.      33     123 ..      33     226 .. 0.77
   2 ?   -0.5   0.5      0.57   8.5e+02      37     136 ..     288     388 ..     276     404 .. 0.57
   3 !   18.3  12.4   1.1e-06    0.0016      95     301 ..     620     868 ..     485     870 .. 0.71

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 4.3e-08
                            AAA_21   1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglr 77 
                                       +n++iG NgsGKS++L+a  ++           +   g+g+++   ++ +++  ++ fe+ +  f+ +g++y+   +
  gi|242398089|ref|YP_002993513.1|  33 INLIIGQNGSGKSSILEAV-FA-----------SLYLGHGSFPRGYKKVNTRIGKSGFELVLK-FEHNGKNYEIVRK 96 
                                       79*****************.33...........367888899999999999999999999999.8888888888777 PP

                            AAA_21  78 lersqveeklssvetllesgllldkrslee 107
                                        + + +   l++++ +l     +  r+ e+
  gi|242398089|ref|YP_002993513.1|  97 SNGESY---LKENGGVLHEKDSDIARWSER 123
                                       777777...555555555555555555544 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.57
                            AAA_21  37 sggggirkipslldlydpeipfefeieeflsqgvryryglrlersqveeklssvetlle.sgllldkrsleeedvfn 112
                                       ++ ++i ++ +++ + +  +  + e+ e +++++r + ++++ ++q++e  s +e+l+e + l ++ ++++   +++
  gi|242398089|ref|YP_002993513.1| 288 GRLKEIEWVKKEYETLNALMVKRKELQEIELRKSRLEERIKVLQKQIQELESKSEELEEtKKLEKKLLDDYNVLKTF 364
                                       55555566666666666666666666777777777777777777777444444444433034444445555555666 PP

                            AAA_21 113 peargirggvsvfslkelsvsepn 136
                                       +e ++   ++ v+++k ++  e  
  gi|242398089|ref|YP_002993513.1| 365 AETYDMVRQLVVEKEKYSTELEKA 388
                                       665555555555555555555555 PP

  == domain 3  score: 18.3 bits;  conditional E-value: 1.1e-06
                            AAA_21  95 esgllldkrsleeedvfnpeargirggvsvfslkelsvsepndlqfgkaltditsrawsllllldglrke....rig 167
                                       +   ++ kr +  e    +++++   ++ vf+  +++++e   ++ ++ + +i++++ sl +l+ + +ke    + +
  gi|242398089|ref|YP_002993513.1| 620 QEIQIREKRQELLETTLKDKEKDLNLTKNVFKMLSKEIEELKVRFTVEEFEKISKEYLSLSSLHAAVLKEiegnENL 696
                                       44455555555555566666666666666666666666666666666666666666666666665555544443222 PP

                            AAA_21 168 llnifadyfgfakekrllqrlvrslklveielsdlgegeeliasvderlrer......................... 219
                                         + ++++   ++ ++ +++   ++ l+e    d+++  e           +                         
  gi|242398089|ref|YP_002993513.1| 697 KEEVARNLEDLKRQLEAIKKAKEESELIEKMMADMKVLRE-----------Kllklkaeaerrglsevervaselfs 762
                                       2222222222222222222222222222222222222222...........12333334444566667777777778 PP

                            AAA_21 220 .....................gvvflengdgqelparelSdGtkrllalltallralkkg...sllliDEpEngLHP 272
                                                             +++++  +gqe  ++ lS G + +l+l   l+  l k     ll++DEp  +L+ 
  gi|242398089|ref|YP_002993513.1| 763 dmterkyqgikiirekkfgreRIRIVVLYQGQEEEIDFLSGGERIALGLSFRLALSLYKVknmELLILDEPTPFLDE 839
                                       888888888888888888888**************************8888888888888889************** PP

                            AAA_21 273 kllrrllellkelsrngaQviltTHSpll 301
                                       ++ ++l+e++ ++ r+  Qvi+++H+ +l
  gi|242398089|ref|YP_002993513.1| 840 ERRKKLVEIITQHLRKIPQVIIVSHDEEL 868
                                       **********999999*********9877 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.6   2.2e-09   3.2e-06       1      99 [.       9     107 ..       9     210 .. 0.75
   2 ?   -1.3   0.3      0.95   1.4e+03     143     198 ..     223     281 ..     214     300 .. 0.63
   3 ?   -3.5   0.1       4.3   6.4e+03     179     200 ..     391     412 ..     364     427 .. 0.64
   4 ?   -3.0   1.0         3   4.4e+03     180     180 ..     511     511 ..     466     582 .. 0.59
   5 ?   -3.9   0.7       5.8   8.6e+03     159     191 ..     701     732 ..     693     746 .. 0.51

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 2.2e-09
                            AAA_27   1 MrlerLdLeryGkftdrsldfsaeeadlhliyGpNEAGKstalrAisdllfGipertkd.....nflhdakkLriga 72 
                                       Mr+++L+++ +   ++++++f+   +++ li+G N +GKs++l+A+ + l+  + + ++     n +  ++  ++  
  gi|242398089|ref|YP_002993513.1|   9 MRIRSLKIKNFRAHENSHVEFN---DGINLIIGQNGSGKSSILEAVFASLYLGHGSFPRgykkvNTRIGKSGFELVL 82 
                                       *********************9...8********************9999954444444000014444555555555 PP

                            AAA_27  73 vleeadgeelefaRrkgrkktlldadd 99 
                                        + e++g++ e++R+ + ++  l++++
  gi|242398089|ref|YP_002993513.1|  83 KF-EHNGKNYEIVRKSNGES-YLKENG 107
                                       55.77777888887554444.444444 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.95
                            AAA_27 143 elgqlLfeasaGlaslrevleaLeaeadelfkprkskk...rainealeeleeakkelr 198
                                       e ++ L + s  +++l+e+ e L+++ +e  + ++s k   + i++++++++e++kelr
  gi|242398089|ref|YP_002993513.1| 223 ETAEKLSAVSKRYEELKEIKEILTQKEKEKLSVEGSMKkleADIKNTRDRIAELEKELR 281
                                       55555656666666666666666655555444444433233566666777777776665 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 4.3
                            AAA_27 179 kkrainealeeleeakkelrea 200
                                       +k+++ ++ +++e+akkel+e 
  gi|242398089|ref|YP_002993513.1| 391 TKEKLVNEIKNVEKAKKELKEV 412
                                       3335555566666666666554 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 3
                            AAA_27 180 k 180
                                       +
  gi|242398089|ref|YP_002993513.1| 511 E 511
                                       1 PP

  == domain 5  score: -3.9 bits;  conditional E-value: 5.8
                            AAA_27 159 revleaLeaeadelfkprkskkrainealeele 191
                                       ++ le+L+++ +++ k +++++  i + +++++
  gi|242398089|ref|YP_002993513.1| 701 ARNLEDLKRQLEAIKKAKEESE-LIEKMMADMK 732
                                       4445555555555544444444.4444444444 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   5.2e-09   7.8e-06       3      47 ..      13      56 ..      11      62 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 5.2e-09
                            AAA_29  3 rlqlvNWgtfdghtieidlkgatlltGpsGsGKSTllDAiqalLv 47
                                      +l++ N    ++  +e++ +g+ l++G++GsGKS++l A+ a L+
  gi|242398089|ref|YP_002993513.1| 13 SLKIKNFRAHENSHVEFN-DGINLIIGQNGSGKSSILEAVFASLY 56
                                      567777777788889998.779*****************987665 PP

>> Rad50_zn_hook  Rad50 zinc hook motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.4      0.57   8.6e+02      32      50 ..     170     188 ..     167     190 .. 0.82
   2 ?   -3.4   0.3       6.2   9.2e+03      10      19 ..     233     242 ..     227     250 .. 0.67
   3 ?   -2.1   3.7       2.3   3.5e+03      35      51 ..     327     343 ..     323     354 .. 0.70
   4 ?   -3.1   0.7       4.8   7.2e+03      39      51 ..     403     415 ..     393     416 .. 0.65
   5 !   24.5   4.3   1.1e-08   1.7e-05       8      51 ..     433     475 ..     428     479 .. 0.93
   6 ?   -1.3   0.5       1.3   1.9e+03      38      50 ..     525     537 ..     524     540 .. 0.70
   7 ?   -2.4   1.1       3.1   4.6e+03      39      49 ..     702     712 ..     692     726 .. 0.53
   8 ?   -1.7   0.8       1.8   2.7e+03      33      46 ..     719     732 ..     700     738 .. 0.57
   9 ?    1.3   0.1       0.2     3e+02      29      50 ..     837     858 ..     835     860 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.57
                                       HHHHHHHHHHHHHHHHHH. CS
                     Rad50_zn_hook  32 ehrseLikelqsklerlpe 50 
                                       ++++e+++el++k e l++
  gi|242398089|ref|YP_002993513.1| 170 NNAQEVLRELRKKREYLEK 188
                                       4589********9888876 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 6.2
                                       HHHHHHTT-S CS
                     Rad50_zn_hook  10 kkieelkeak 19 
                                       k++eelke k
  gi|242398089|ref|YP_002993513.1| 233 KRYEELKEIK 242
                                       5566666654 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 2.3
                                       HHHHHHHHHHHHHHH.. CS
                     Rad50_zn_hook  35 seLikelqsklerlpee 51 
                                        ++++++ ++le++ ee
  gi|242398089|ref|YP_002993513.1| 327 IKVLQKQIQELESKSEE 343
                                       56666666666666666 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 4.8
                                       HHHHHHHHHHH.. CS
                     Rad50_zn_hook  39 kelqsklerlpee 51 
                                       ++ +++l++++++
  gi|242398089|ref|YP_002993513.1| 403 EKAKKELKEVEDK 415
                                       4566666666665 PP

  == domain 5  score: 24.5 bits;  conditional E-value: 1.1e-08
                                       HHHHHHHHTT-SEE-TTT--EE-HHHHHHHHHHHHHHHHHHH.. CS
                     Rad50_zn_hook   8 lnkkieelkeakgcCPlCgReldeehrseLikelqsklerlpee 51 
                                       l+ + ++l+ ak  CPlC+R+++e++  e+ +e+ ++l +++++
  gi|242398089|ref|YP_002993513.1| 433 LRDNVSKLEGAK-ECPLCKRPIEEHEEGEIKREYTAELAKIEKK 475
                                       6778899*****.***************************9987 PP

  == domain 6  score: -1.3 bits;  conditional E-value: 1.3
                                       HHHHHHHHHHHH. CS
                     Rad50_zn_hook  38 ikelqsklerlpe 50 
                                       i+el++k+e++++
  gi|242398089|ref|YP_002993513.1| 525 IEELKKKTEEFEK 537
                                       5677777777664 PP

  == domain 7  score: -2.4 bits;  conditional E-value: 3.1
                                       HHHHHHHHHHH CS
                     Rad50_zn_hook  39 kelqsklerlp 49 
                                       + l++  ++l+
  gi|242398089|ref|YP_002993513.1| 702 RNLEDLKRQLE 712
                                       44444333333 PP

  == domain 8  score: -1.7 bits;  conditional E-value: 1.8
                                       HHHHHHHHHHHHHH CS
                     Rad50_zn_hook  33 hrseLikelqskle 46 
                                       + seLi+++ + ++
  gi|242398089|ref|YP_002993513.1| 719 EESELIEKMMADMK 732
                                       24555555555555 PP

  == domain 9  score: 1.3 bits;  conditional E-value: 0.2
                                       E-HHHHHHHHHHHHHHHHHHH. CS
                     Rad50_zn_hook  29 ldeehrseLikelqsklerlpe 50 
                                       ldee+r++L++ + + l+++p+
  gi|242398089|ref|YP_002993513.1| 837 LDEERRKKLVEIITQHLRKIPQ 858
                                       78999******99999999986 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   2.7e-06     0.004      28      89 ..     796     850 ..     783     851 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.7e-06
                           SbcCD_C  28 rssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                       +++  lSGGe+     +al+++++ ++s    + ++++l++LDE    lDee++++l+e+++
  gi|242398089|ref|YP_002993513.1| 796 EEIDFLSGGER-----IALGLSFRLALSLY--KVKNMELLILDEPTPFLDEERRKKLVEIIT 850
                                       677889*****.....88888888888886..4899**********************9986 PP

>> AAA_23  AAA domain
   [No individual domains that satisfy reporting thresholds (although complete target did)]

>> 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    0.0001      0.16      26      59 ..      33      66 ..      17      93 .. 0.82
   2 ?   -1.8   0.1       2.5   3.7e+03     127     127 ..     487     487 ..     392     586 .. 0.67
   3 ?   -0.2   0.1      0.78   1.2e+03      44     126 ..     653     741 ..     645     756 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0001
                            AAA_16 26 lvllsGesGvGKsslvrellralekdggiflrgk 59
                                      + l++G+ G+GKss++++++ +l   +g f rg 
  gi|242398089|ref|YP_002993513.1| 33 INLIIGQNGSGKSSILEAVFASLYLGHGSFPRGY 66
                                      569*****************98876666666665 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.5
                            AAA_16 127 l 127
                                       l
  gi|242398089|ref|YP_002993513.1| 487 L 487
                                       2 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.78
                            AAA_16  44 llralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekleealaavpelagaea.... 116
                                       l +++e+ ++ f+ +++++   + +y+ l ++ a+  l + +++e  + e+++  e l+++l+a+++++ +++    
  gi|242398089|ref|YP_002993513.1| 653 LSKEIEELKVRFTVEEFEKI--SKEYLSLSSLHAA-VLKEIEGNENLKEEVARNLEDLKRQLEAIKKAKEESEliek 726
                                       44555555777877788888..6678777777744.67777777766777777777777777766666666555655 PP

                            AAA_16 117 .....srllellkrl 126
                                            + l+e+l +l
  gi|242398089|ref|YP_002993513.1| 727 mmadmKVLREKLLKL 741
                                       665555555555554 PP

>> DUF3440  Domain of unknown function (DUF3440)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   3.0   0.00096       1.4      80     149 ..     494     566 ..     486     570 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00096
                           DUF3440  80 eelrenylk..klkvsikfWrekGgalseetikelkeaeikieveeksnyktekkvvrlkeylddid.ikefk 149
                                       e++r+n  k  kl+++++f ++  + l++  i+elk+++ ++e+  ++  + +k+++r+++ l++++ +k+ k
  gi|242398089|ref|YP_002993513.1| 494 EKIRNNESKliKLHKTLEFLENVESKLEKYNIEELKKKTEEFEKVRERVIEVKKEIIRVNKELEKLNeFKNEK 566
                                       56666544333999*********************************************99999988777766 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0    0.0012       1.8       4      29 ..      30      55 ..      27      67 .. 0.89
   2 ?   -3.3   0.0       6.8     1e+04     106     114 ..     173     181 ..     149     216 .. 0.58
   3 ?   -1.0   0.7       1.3     2e+03      25      71 ..     452     505 ..     448     530 .. 0.65
   4 ?   -0.7   0.7       1.1   1.6e+03      57     109 ..     628     677 ..     595     739 .. 0.63
   5 ?   -1.3   0.0       1.6   2.4e+03      70      97 ..     836     862 ..     812     866 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0012
                            AAA_22  4 tagilvvtGesGtGKTtllrrlleql 29
                                      ++gi +++G+ G+GK+  l+ ++ +l
  gi|242398089|ref|YP_002993513.1| 30 NDGINLIIGQNGSGKSSILEAVFASL 55
                                      67899**************9998775 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 6.8
                            AAA_22 106 eealeeLrs 114
                                       +e+l+eLr+
  gi|242398089|ref|YP_002993513.1| 173 QEVLRELRK 181
                                       444444432 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 1.3
                            AAA_22  25 lleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka.......e 71 
                                         e+++e +  +e  +e+++++ ++++  + l+++l r+++le+ +       +
  gi|242398089|ref|YP_002993513.1| 452 PIEEHEEGEIKREYTAELAKIEKKKEEIAEALRKALKRKTELEKIRnneskliK 505
                                       555555555555577777888888888888888888888888887733333333 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 1.1
                            AAA_22  57 lrellralglelkaerlsseellealeqalraravielliiDEaqhlrseeal 109
                                       ++ell+ +  ++++  + ++ ++++l + +++ +v   + ++E++++ s+e l
  gi|242398089|ref|YP_002993513.1| 628 RQELLETTLKDKEKDLNLTKNVFKMLSKEIEELKV--RFTVEEFEKI-SKEYL 677
                                       44444444444444455555555555555555555..5555555555.33322 PP

  == domain 5  score: -1.3 bits;  conditional E-value: 1.6
                            AAA_22  70 a.erlsseellealeqalraraviellii 97 
                                          + +++ l+e ++q+lr+     ++i+
  gi|242398089|ref|YP_002993513.1| 836 FlDEERRKKLVEIITQHLRKIPQ--VIIV 862
                                       35667888888888888888877..5554 PP

>> Flagellin_N  Bacterial flagellin N-terminal helical region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1     0.021        31      49      92 ..     178     221 ..     168     227 .. 0.89
   2 ?    7.7   1.8    0.0024       3.6      48     121 ..     198     275 ..     195     282 .. 0.84
   3 ?   -0.9   0.1       1.1   1.6e+03      70     102 ..     315     348 ..     298     363 .. 0.68
   4 ?    4.3   0.1     0.027        41      51     120 ..     355     424 ..     349     429 .. 0.91
   5 ?   -1.3   0.2       1.5   2.2e+03      75     122 ..     694     741 ..     672     749 .. 0.61

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.021
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Flagellin_N  49 slrsqiaglsqlvrnnslgisrlqtaqgalselsdilqrlkela 92 
                                       +lr++ + l++l++++++ +++++  +++l e++  + +l+++ 
  gi|242398089|ref|YP_002993513.1| 178 ELRKKREYLEKLIQASGDIQNKIKEQEKRLGEVIHKINELRKKE 221
                                       68999999*****************************9999875 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0024
                                       HHHHHHHHHHHHHH.HHHHHHHHHHHHHHH..HHHHHHHHHHHHHHHHHHHT-TTTS-S.HHHHHHHHHHHHHHHHH CS
                       Flagellin_N  48 vslrsqiaglsqlv.rnnslgisrlqtaqg..alselsdilqrlkelavaasndsnsde.drqslqaelqqLtdeln 120
                                       +++++q ++l+ ++ + n+l  + ++ta++  a+s+  + l+++ke ++++ +++ s e + ++l+a++++ +d + 
  gi|242398089|ref|YP_002993513.1| 198 NKIKEQEKRLGEVIhKINELRKKEIETAEKlsAVSKRYEELKEIKEILTQKEKEKLSVEgSMKKLEADIKNTRDRIA 274
                                       666777777766551558889999*****999*************************9999*********9999886 PP

                                       H CS
                       Flagellin_N 121 r 121
                                       +
  gi|242398089|ref|YP_002993513.1| 275 E 275
                                       5 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHHHHHHHH.HHHHHHHHT-TTTS- CS
                       Flagellin_N  70 rlqtaqgalselsdilqr.lkelavaasndsnsd 102
                                        ++  +++l+e +++lq+ ++el   + + + ++
  gi|242398089|ref|YP_002993513.1| 315 EIELRKSRLEERIKVLQKqIQELESKSEELEETK 348
                                       4566667777777777777777766555555544 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.027
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-TTTS-SHHHHHHHHHHHHHHHHH CS
                       Flagellin_N  51 rsqiaglsqlvrnnslgisrlqtaqgalselsdilqrlkelavaasndsnsdedrqslqaelqqLtdeln 120
                                         +++ l++++++  ++ +++   ++  +el+++  + ++l+   +n ++ +++ +++++++ +L++eln
  gi|242398089|ref|YP_002993513.1| 355 LDDYNVLKTFAETYDMVRQLVVEKEKYSTELEKAGYTKEKLVNEIKNVEKAKKELKEVEDKILTLKGELN 424
                                       567788888999999999999999*********************************************9 PP

  == domain 5  score: -1.3 bits;  conditional E-value: 1.5
                                       HHHHHHHHHHHHH.HHHHHHHHT-TTTS-SHHHHHHHHHHHHHHHHHHH CS
                       Flagellin_N  75 qgalselsdilqr.lkelavaasndsnsdedrqslqaelqqLtdelnri 122
                                       ++  +e++ +l++  ++l + ++ ++ s+   +++ a+++ L+++l ++
  gi|242398089|ref|YP_002993513.1| 694 ENLKEEVARNLEDlKRQLEAIKKAKEESE-LIEKMMADMKVLREKLLKL 741
                                       44456666677773344444444444443.3667777777777777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (895 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3292  (0.183613); expected 358.6 (0.02)
Passed bias filter:                      645  (0.0359752); expected 358.6 (0.02)
Passed Vit filter:                       213  (0.0118802); expected 17.9 (0.001)
Passed Fwd filter:                        90  (0.0050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 2.41u 0.42s 00:00:02.83 Elapsed: 00:00:00.74
# Mc/sec: 3651.63
//
Query:       gi|242398090|ref|YP_002993514.1|  [L=403]
Description: 5'-3' nuclease, encoded next to Rad50 and Mre11-like protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-34  119.5   2.8    3.1e-34  118.7   2.8    1.4  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 !  118.7   2.8   1.7e-38   3.1e-34       2     242 .]      39     368 ..      38     368 .. 0.94

  Alignments for each domain:
  == domain 1  score: 118.7 bits;  conditional E-value: 1.7e-38
                                       EEEEEEEEEEEEEETTCEEEEEEEEEEECCEEECCCEEEECEBTCCHHEEEEEHHHHHHHHHHHHHHHHHHHCGGCC CS
                              NurA   2 rvaAvDGSngvvrlsggilyilsayavvgggkerleealslasvdsispsdelerrirllmetlElklgallleekg 78 
                                       +v+AvDGS+ v+rlsg i+y +s+++++  +   +e  l+ ++++        ++rirl+me lE++ ga + e kg
  gi|242398090|ref|YP_002993514.1|  39 KVFAVDGSRMVKRLSGAIVYGVSSVSIGDDILQWHEIGLVSPYKHV-------DERIRLHMEMLENRIGAMTFELKG 108
                                       69************************99999998998888888888.......9*********************** PP

                                       SCEEEEECSHHCCCH.............................................................. CS
                              NurA  79 edllllDGsligslv.............................................................. 93 
                                       +dl+l+DG+l+gs+                                                               
  gi|242398090|ref|YP_002993514.1| 109 ADLILMDGTLSGSIArppaylesstrqfyeedkigtintvkaflellesewdkwkesleeegvinystvvarreeif 185
                                       ***************************************************************************** PP

                                       .....................HHHHHHHHHHHHHHHHHHHHHTT-TTCEEEEESS-SCTCCHCCC........S--H CS
                              NurA  94 .....................efdelheeleyeeylyslsrlleaglnlvgvaKsfrskellnll..letlligesi 147
                                                             ++   + ley+eyl+s+++ll+    +++vaK+f++ ++++ +    + ++   i
  gi|242398090|ref|YP_002993514.1| 186 ehlksyvvekeflekiennpnYKEDFIIFLEYLEYLHSIDKLLN--GTVAFVAKTFYTDDIIKQVteGKEESKYALI 260
                                       ***************998885444444558**************..9******************99999999999* PP

                                       HHHCCHHCCHCH---STTS-HHHHTT...................-HCCHHHHHH-.EEEEEEESSTTTTEEEEEHH CS
                              NurA 148 sDiallgallrkpgytspllkilrek...................pllrealidke.iyfaYvrlegggsilrleip 204
                                       +D+ +++++ +k gy +  ++  r++                   +l+ ++ +  + i  aYvr++ +g+i++le  
  gi|242398090|ref|YP_002993514.1| 261 PDVPVIDSISKKRGYMKFKYRESRKWalpeviqravggkylqrvvELFPKEGNPVQnIQPAYVRFMDNGVIYLLE-- 335
                                       ***************99888888888******************8666666666667******************.. PP

                                       HHHHCCHHHHHHHHHH..TTB-SSSBCCHHHHHHHHCC CS
                              NurA 205 aevstakdedvlsllasqrlsisGYprpLalAhelaki 242
                                          +t++ +++ls+++     ++ Y  pL++Ah+ ++i
  gi|242398090|ref|YP_002993514.1| 336 ---TTNLTDELLSAIL--SVAEDEYIIPLEYAHHTVVI 368
                                       ...99***********..*****************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       659  (0.0367561); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.35s 00:00:00.99 Elapsed: 00:00:00.53
# Mc/sec: 2309.79
//
Query:       gi|242398091|ref|YP_002993515.1|  [L=120]
Description: ribosomal protein-alanine acetyltransferase RimI like protein [Thermococcus sibiricus MM 739]
Scores for complete 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-26   92.2   0.1      3e-26   91.9   0.1    1.1  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    1.1e-17   64.2   0.2    1.4e-17   63.9   0.2    1.1  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    1.3e-17   63.9   0.1    1.4e-17   63.8   0.1    1.1  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    2.2e-12   46.8   0.1    2.8e-12   46.4   0.1    1.1  1  FR47             FR47-like protein
    3.8e-11   43.4   0.1    4.5e-11   43.1   0.1    1.0  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
      5e-07   29.5   0.0    1.2e-06   28.3   0.0    1.7  1  Acetyltransf_8   Acetyltransferase (GNAT) domain
    6.8e-06   26.8   0.0    8.3e-06   26.5   0.0    1.1  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
    1.1e-05   25.6   0.1    1.5e-05   25.1   0.1    1.2  1  Acetyltransf_6   Acetyltransferase (GNAT) domain
    4.2e-05   23.6   0.0     0.0002   21.4   0.0    1.9  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
      7e-05   22.9   0.0    0.00011   22.3   0.0    1.3  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
    8.7e-05   22.2   0.0    0.00011   21.9   0.0    1.1  1  GNAT_acetyltran  GNAT acetyltransferase
  ------ inclusion threshold ------
      0.015   14.8   0.0      0.031   13.7   0.0    1.5  1  Acetyltransf_15  Putative acetyl-transferase
       0.13   12.1   0.1       0.38   10.6   0.1    1.7  1  Acetyltransf_18  Acetyltransferase (GNAT) domain
       0.14   11.9   0.0        0.2   11.4   0.0    1.3  1  FlgO             FlgO protein


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.9   0.1   2.4e-29     3e-26      26     117 .]       5      90 ..       1      90 [. 0.93

  Alignments for each domain:
  == domain 1  score: 91.9 bits;  conditional E-value: 2.4e-29
                                       HHHHSTTCEEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEE CS
                    Acetyltransf_1  26 esfsleaegllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikkivlave 102
                                       +s   + e++lvae+ g+++G+++++++pd    +++i s+aV+p yrg+G+G++L+ea+++r+ ++g+++i l+v+
  gi|242398091|ref|YP_002993515.1|   5 DS---NRETFLVAEYSGQVVGYVMGYIRPD---MEGHIMSIAVDPLYRGNGIGRLLMEAVIDRLIKRGARYIGLEVR 75 
                                       33...4558889******************...79****************************************** PP

                                       TTEHHHHHHHHHTTE CS
                    Acetyltransf_1 103 edndaairlYeklGF 117
                                       ++n++ai+lYeklGF
  gi|242398091|ref|YP_002993515.1|  76 VSNKGAIKLYEKLGF 90 
                                       **************9 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.9   0.2   1.1e-20   1.4e-17       2      76 .]       8      92 ..       7      92 .. 0.80

  Alignments for each domain:
  == domain 1  score: 63.9 bits;  conditional E-value: 1.1e-20
                                      TEEEEEEEETTEEEEEEEEEEES...TCTEEEEE-GGGTTSSHHHHHHHH....TT.SEEE.EE.EEEETHHHHHHHHH CS
                    Acetyltransf_7  2 kgevfVaeddgkivGfialslld...aeitrlaVdpeyrgkGiGraLlea....ae.kgii.le.qlelnaekaikfYe 70
                                      +++++Vae  g++vG++  +++    ++i  +aVdp yrg+GiGr L+ea     + +g + +  +++++++ aik+Ye
  gi|242398091|ref|YP_002993515.1|  8 RETFLVAEYSGQVVGYVMGYIRPdmeGHIMSIAVDPLYRGNGIGRLLMEAvidrLIkRGARyIGlEVRVSNKGAIKLYE 86
                                      689**************99999988666666******************855541155533323556677679****** PP

                                      HTTEEE CS
                    Acetyltransf_7 71 klGFee 76
                                      klGF++
  gi|242398091|ref|YP_002993515.1| 87 KLGFKK 92
                                      ****95 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.8   0.1   1.1e-20   1.4e-17      27     110 ..       5      94 ..       1     113 [. 0.82

  Alignments for each domain:
  == domain 1  score: 63.8 bits;  conditional E-value: 1.1e-20
                   Acetyltransf_10  27 eegealllvaeeggkivGvi....elrdgs..hisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnasp. 95 
                                       ++++ ++lvae +g++vG++    + +     hi  ++Vdp yrg+Gig+ L+eav++++ k+g +   l+v+ s+ 
  gi|242398091|ref|YP_002993515.1|   5 DSNRETFLVAEYSGQVVGYVmgyiRPD--MegHIMSIAVDPLYRGNGIGRLLMEAVIDRLIKRGARYiGLEVRVSNk 79 
                                       678899***********8776311444..256***************************99**9999*********9 PP

                   Acetyltransf_10  96 yavpfYeklGFkavg 110
                                        a+++YeklGFk+++
  gi|242398091|ref|YP_002993515.1|  80 GAIKLYEKLGFKKMK 94 
                                       ************983 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.4   0.1   2.2e-15   2.8e-12       8      80 ..      19      93 ..      14      99 .. 0.89

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 2.2e-15
                                      TT--EEEEEEE-TT.SSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EE.EEEETT-HHHHHHHHHHT-EEE CS
                              FR47  8 elgelaawilrkdg.gelgalqvlpehrrrGlgsrlvkalakeiaergktvl.lvvvasNtpsirlyeklGfeki 80
                                      +++  + + +r+d+ g + ++ v+p  r+ G g++l +a++ ++++rg   + l v+ sN+ +i+lyeklGf+k+
  gi|242398091|ref|YP_002993515.1| 19 QVVGYVMGYIRPDMeGHIMSIAVDPLYRGNGIGRLLMEAVIDRLIKRGARYIgLEVRVSNKGAIKLYEKLGFKKM 93
                                      555667788999999********************************98765389*****************997 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.1   0.1   3.5e-14   4.5e-11      48     154 ..       7     110 ..       2     111 .. 0.92

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 3.5e-14
                    Acetyltransf_4  48 keyvflvae.sdrivGyaylgqfkkrakdwkaelsvylaerdnnkeglgrelidaleqvlkeqnienllaeiaspne 123
                                       ++  flvae s+++vGy  +  +++    +  ++s+ ++  + + +g+gr l++a++++l + + +++  e+ ++n+
  gi|242398091|ref|YP_002993515.1|   7 NRETFLVAEySGQVVGYVMGY-IRP--DMEGHIMSIAVD-PLYRGNGIGRLLMEAVIDRLIKRGARYIGLEVRVSNK 79 
                                       4667999999*******9988.888..779999*****6.8************************************ PP

                    Acetyltransf_4 124 nsiqfhkalGFelvgifkkcikkngrwiDmi 154
                                        +i+++++lGF++++i ++++ ++   + m+
  gi|242398091|ref|YP_002993515.1|  80 GAIKLYEKLGFKKMKIIRGYYSDGEDAYYMM 110
                                       ***********************99999988 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.0   9.4e-10   1.2e-06      86     143 ..      39      96 ..       2      97 .. 0.87

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 9.4e-10
                                       ES.SHHHCTTTCHHHHHHHHHHHHHCCTT--EEEE--BTT-HHHHHHHHHTT-EEEEEE CS
                    Acetyltransf_8  86 ig.eaeargkglttallralvhylfadprtrrvvvEPdvrNerairllekaGfekekev 143
                                       i+ ++ +rg g+++ l++a++++l+++ ++r + +E +v+N+ ai+l+ek+Gf+k k +
  gi|242398091|ref|YP_002993515.1|  39 IAvDPLYRGNGIGRLLMEAVIDRLIKR-GARYIGLEVRVSNKGAIKLYEKLGFKKMKII 96 
                                       5557789******************99.**************************99866 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0   6.5e-09   8.3e-06      54     138 .]       9      91 ..       2      91 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 6.5e-09
                    Acetyltransf_3  54 ygwaivlkdtgviGsvglrdleeedeeaelgymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSir 130
                                        ++++ + +++v+G+v+ + +++ ++   +++ ++p ++g+G+++  ++a+++ + ++  ++++  ++  +N++ i+
  gi|242398091|ref|YP_002993515.1|   9 ETFLVAEYSGQVVGYVMGYIRPDMEG-HIMSIAVDPLYRGNGIGRLLMEAVIDRLIKRG-ARYIGLEVRVSNKGAIK 83 
                                       468886655547****5553433333.6677888899******************8777.***************** PP

                    Acetyltransf_3 131 vleklGfe 138
                                       ++eklGf+
  gi|242398091|ref|YP_002993515.1|  84 LYEKLGFK 91 
                                       *******7 PP

>> Acetyltransf_6  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.1   1.2e-08   1.5e-05      73     131 ..      11      70 ..       3      76 .. 0.92

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.2e-08
                    Acetyltransf_6  73 lyvlrldgrpvAvalglrsgd.rlyywlggydpelaklspgllllweliedaaeeGlrrf 131
                                       ++v++  g++v++++g++  d   + + +++dp +++ ++g+ll+  +i++++ +G r++
  gi|242398091|ref|YP_002993515.1|  11 FLVAEYSGQVVGYVMGYIRPDmEGHIMSIAVDPLYRGNGIGRLLMEAVIDRLIKRGARYI 70 
                                       6788999**************7799********************************987 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   1.6e-07    0.0002      74     127 ..      34      92 ..       5      93 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.6e-07
                                       EEEEEEEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--.....SSHHHHHTTT-EE CS
                    Acetyltransf_9  74 agvtgVavapehrgrgvlskLlaraleemreegqplsllfP.....ssipiYrrfGyei 127
                                       + ++++av+p +rg+g+ + L++++++++ ++g++ + l        +i++Y+++G+++
  gi|242398091|ref|YP_002993515.1|  34 GHIMSIAVDPLYRGNGIGRLLMEAVIDRLIKRGARYIGLEVrvsnkGAIKLYEKLGFKK 92 
                                       689*********************************99998876554579999999976 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 !   22.3   0.0   8.5e-08   0.00011      11      59 ..      20      68 ..      10      71 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 8.5e-08
                   Acetyltransf_CG 11 evafl.eYevrkegvldfthTeVpeelrGkGiAkkLvkaalddareeglk 59
                                       v+++  Y  r++ + +++ + V++ +rG Gi++ L++a++d   ++g +
  gi|242398091|ref|YP_002993515.1| 20 VVGYVmGYI-RPDMEGHIMSIAVDPLYRGNGIGRLLMEAVIDRLIKRGAR 68
                                      555443786.8888999**************************9999876 PP

>> GNAT_acetyltran  GNAT acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   8.2e-08   0.00011     161     237 ..      13      93 ..      11      99 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 8.2e-08
                   GNAT_acetyltran 161 vilkngeivsgasSysvye.kgieieidTkedyrrkgLAtivaaalileclkrg.lyPsWDaa..neaSvaLaekLG 233
                                       v+ + g++v  ++ y++ + +g+ ++i+ ++ yr++g  +++ +a i++ +krg  y     +  n+ +++L+ekLG
  gi|242398091|ref|YP_002993515.1|  13 VAEYSGQVVGYVMGYIRPDmEGHIMSIAVDPLYRGNGIGRLLMEAVIDRLIKRGaRYIGLEVRvsNKGAIKLYEKLG 89 
                                       5677899999999999754389*******************************956999999999************ PP

                   GNAT_acetyltran 234 Yefe 237
                                       ++  
  gi|242398091|ref|YP_002993515.1|  90 FKKM 93 
                                       *976 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   0.0   2.4e-05     0.031      75     140 ..      36      94 ..      31     111 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.4e-05
                   Acetyltransf_15  75 iYtlyvsekyrgkGlakklLeeslkelkknYkvdnelllaLHlnpkDksMnisfalYyslgFrkgl 140
                                       i ++ v++ yrg G+ + l+e  +++l+k+       ++ L +  + k    +  lY +lgF+k+ 
  gi|242398091|ref|YP_002993515.1|  36 IMSIAVDPLYRGNGIGRLLMEAVIDRLIKR----GARYIGLEVRVSNK---GAIKLYEKLGFKKMK 94 
                                       67899******************9999764....46788888877665...478888888888765 PP

>> Acetyltransf_18  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1    0.0003      0.38      27     102 ..      10      93 ..       2     101 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0003
                   Acetyltransf_18  27 klvvveedgeivGy..glarktrkglk....iGPlvAen...eeiAeaLlkalvanaegkkvridvpeenkaliell 94 
                                       + +v e  g++vGy  g +r+ ++g++    + Pl+  n   +   ea++++l+++  +  + + v  +nk +i+l 
  gi|242398091|ref|YP_002993515.1|  10 TFLVAEYSGQVVGYvmGYIRPDMEGHImsiaVDPLYRGNgigRLLMEAVIDRLIKRGARY-IGLEVRVSNKGAIKLY 85 
                                       556666667777773334666666665333355777655222234566777777777777.**************** PP

                   Acetyltransf_18  95 eklgfkev 102
                                       eklgfk+ 
  gi|242398091|ref|YP_002993515.1|  86 EKLGFKKM 93 
                                       *****986 PP

>> FlgO  FlgO protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00015       0.2      29      60 ..      41      72 ..      27      89 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00015
                              FlgO 29 lddlqktstLGrqlaEsliselqqrgykvvel 60
                                      +d l++ + +Gr+l+E++i +l +rg + + l
  gi|242398091|ref|YP_002993515.1| 41 VDPLYRGNGIGRLLMEAVIDRLIKRGARYIGL 72
                                      789999********************987633 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.51
# Mc/sec: 707.37
//
Query:       gi|242398092|ref|YP_002993516.1|  [L=175]
Description: tRNA-splicing endonuclease subunit alpha [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-29  101.7   1.2    2.7e-29  101.0   1.2    1.3  1  tRNA_int_endo    tRNA intron endonuclease, catalytic C-termin
    4.5e-18   64.7   1.6      1e-17   63.6   1.4    1.7  2  tRNA_int_endo_N  tRNA intron endonuclease, N-terminal domain
  ------ inclusion threshold ------
      0.011   16.0   0.1      0.018   15.3   0.1    1.5  1  Sen15            Sen15 protein


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 !  101.0   1.2   4.6e-33   2.7e-29       1      85 []      84     167 ..      84     167 .. 0.98

  Alignments for each domain:
  == domain 1  score: 101.0 bits;  conditional E-value: 4.6e-33
                                       HHHHHHHHHHHHHTT-EEEECGGGTSSEEEETSCTTTSSCSEEEEEEETTSEEEHHHHHHHHHHHHHTTSEEEEEEE CS
                     tRNA_int_endo   1 falkyavyrdLrekGyvvrsGlkFGadFrvYqrrpslehseylVvvvsedeeldwpdlsaavrlahsvkKklilaiv 77 
                                       f+lk+ vy+dLr++Gy+v++ lk+G++FrvY r+  ++h+++l+ vv+e++++ +++l+a vr+ah+v+Kk++la+v
  gi|242398092|ref|YP_002993516.1|  84 FDLKFLVYKDLRDRGYTVKTALKYGSHFRVY-RKGMEDHADWLIWVVNESQRMYPNELTARVRVAHGVRKKMVLAVV 159
                                       899****************************.9999***************************************** PP

                                       TTTSCEEE CS
                     tRNA_int_endo  78 daegdvty 85 
                                       d++ dv y
  gi|242398092|ref|YP_002993516.1| 160 DEDNDVVY 167
                                       *****987 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 !   63.6   1.4   1.7e-21     1e-17       2      66 ..      10      73 ..       9      74 .. 0.97
   2 ?   -2.9   0.0      0.96   5.7e+03      11      22 ..     125     136 ..     123     139 .. 0.82

  Alignments for each domain:
  == domain 1  score: 63.6 bits;  conditional E-value: 1.7e-21
                                      EEEEETTEEEESSHHHHHHHHHTTT-SEECCTSSEEEEHHHHHHHHHTTSEEEETTSEEE-HHHH CS
                   tRNA_int_endo_N  2 egeLsgdrvlvedeeaakrlyekgfYGkplidepLqLslvEAlYLlekGklevvkggeplsfeel 66
                                      + +Lsg+rv    e+a ++ly+k++YG+   + +L+Lsl+EA+YLlek++++v +g+++l++ee+
  gi|242398092|ref|YP_002993516.1| 10 KFYLSGERVFSTMESALNKLYNKRHYGE-VVNGKLFLSLIEAAYLLEKEWIKVFDGEKELTLEEV 73
                                      579*************************.**********************************97 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.96
                                       EESSHHHHHHHH CS
                   tRNA_int_endo_N  11 lvedeeaakrly 22 
                                       l++  ++++r+y
  gi|242398092|ref|YP_002993516.1| 125 LIWVVNESQRMY 136
                                       689999999988 PP

>> Sen15  Sen15 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.1   3.1e-06     0.018      70      90 ..     150     170 ..      89     172 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.1e-06
                             Sen15  70 rkkrivLaivddDsTvvYYkv 90 
                                         k++vLa+vd+D  vvYY+v
  gi|242398092|ref|YP_002993516.1| 150 VRKKMVLAVVDEDNDVVYYQV 170
                                       4799***************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); 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:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 1208.64
//
Query:       gi|242398093|ref|YP_002993517.1|  [L=395]
Description: 8-amino-7-oxononanoate synthase [Thermococcus sibiricus MM 739]
Scores for complete 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-72  244.2   0.0    2.5e-72  244.0   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    7.9e-06   24.6   0.0    1.2e-05   24.1   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    4.8e-05   22.8   0.0      8e-05   22.1   0.0    1.3  1  Beta_elim_lyase  Beta-eliminating lyase
    7.9e-05   21.8   0.0    0.00012   21.2   0.0    1.2  1  Aminotran_5      Aminotransferase class-V
      0.001   18.5   0.0      0.015   14.6   0.0    2.2  2  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
     0.0015   17.4   0.0     0.0022   16.8   0.0    1.2  1  OKR_DC_1         Orn/Lys/Arg decarboxylase, major domain
  ------ inclusion threshold ------
        0.1   11.8   0.0        0.6    9.3   0.0    2.0  2  YcaO             YcaO cyclodehydratase, ATP-ad Mg2+-binding


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 !  244.0   0.0   9.9e-76   2.5e-72       1     362 [.      39     383 ..      39     384 .. 0.93

  Alignments for each domain:
  == domain 1  score: 244.0 bits;  conditional E-value: 9.9e-76
                                       SEEEESSSSSTTSTTSSHHHHHHHHHHHH..HHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEES CS
                     Aminotran_1_2   1 tdvinLgsneylgdsgkptlpevakaeke..galaggtlneygpidglpeleealakflgrseklklkreaavvvgs 75 
                                       ++v+n++sn+ylg++++p ++e+a +++   g++ag  +++ g+++++ elee+lakf +        reaa+++ s
  gi|242398093|ref|YP_002993517.1|  39 KKVLNMCSNNYLGLAAHPKIKEAAIRAILdyGVGAGAVRTIAGTMELHVELEEKLAKFKK--------REAAILFQS 107
                                       589**************7776655444445******************************........********* PP

                                       HHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEE CS
                     Aminotran_1_2  76 Gagaliealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvi 152
                                       G++a++ al +l+k+  + ++++ ++++as++++ rlsg+e v y+       hl++e+l++ l+e +  +kk+k+i
  gi|242398093|ref|YP_002993517.1| 108 GYNANLGALSALIKKGEDGVFVSEELNHASIIDGMRLSGAEKVIYK-------HLNMEDLKKRLEEVK--DKKKKLI 175
                                       *************866666688899*********************.......*************55..5556*** PP

                                       EEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSS..HTHHH..HGGSTTSTTEEEEEESSSTTSS CS
                     Aminotran_1_2 153 lvesphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsl..davat..ranveeepnllivgslsKafGl 225
                                       ++ ++++++G++a+l+e+ +l   a++y ++++vD+a++++v+g++  +   +  ++n+ ++++ + +g+lsKafG+
  gi|242398093|ref|YP_002993517.1| 176 VTDGVFSMDGDLAPLPEIAEL---AEQYDAIVYVDDAHGEGVLGDSgrG---IvdHFNLHDRVD-FEMGTLSKAFGV 245
                                       *********************...********************98633...135*********.************ PP

                                       GGG-EEEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECC CS
                     Aminotran_1_2 226 aGeRvGyilgnaavvsqlrklsrpflsssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlas 302
                                        G   Gy++g ++ +++lr+  rpfl+ss+l +  +aa+ ++ ++ ++ +e +++l++++ +l ++L++lg +    
  gi|242398093|ref|YP_002993517.1| 246 IG---GYVAGPEEAIDYLRQRGRPFLFSSALNPPDVAAAIASVEILQHSDELVKKLWDNTNFLQKGLRDLGYDLGNT 319
                                       **...**********************88888888888888888889****************************** PP

                                       SCSSEEEEEETHHCHHHHHHHHHHTCTEEEEEGGGGTS...TTEEEEEC.TTS-HHHHHHHHHH CS
                     Aminotran_1_2 303 qsgmflltdlsaetakelskkLleevgvyvtpgtsftv...pgrlRitv.Aglteeeleelvea 362
                                       ++ + +++++++++a+e+sk L ee+++  +++ ++tv   ++r+R+ + A++++e+l+++++a
  gi|242398093|ref|YP_002993517.1| 320 KHPITPVMLYEEKRAQEFSKRLYEEYNIFAQAIVYPTVplgTARIRLEPsAAHSKEDLQYVIDA 383
                                       *************************************************************998 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 !   24.1   0.0   4.6e-09   1.2e-05      56     181 ..      88     215 ..      81     218 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 4.6e-09
                                       HHHHHHHHHHT-SEEEEESSHHHHHHHHHHTTS-TTEE.EEEESTSSHHHHHHHHHTHHHTTCEEEEESTTSHHH.H CS
                   Cys_Met_Meta_PP  56 vleeriaaLeggeaalavssGmaAiaaailallkaGde.ivvsddlYggtqrllkkvlkklgievkfvdtsdlee.l 130
                                        lee++a+ ++ eaa+++ sG  A   a+ al+k+G++ + vs++l   +     ++    ++ +k+ +++dl++ l
  gi|242398093|ref|YP_002993517.1|  88 ELEEKLAKFKKREAAILFQSGYNANLGALSALIKKGEDgVFVSEELNHASIIDGMRLSGAEKVIYKHLNMEDLKKrL 164
                                       69**********************************88466777777777766677777788999999998876526 PP

                                       HHHCCTTEEEEEEESS-TTTT----HHHHHHHHHHTT-EEEEEGTTTHTTT CS
                   Cys_Met_Meta_PP 131 ekaikentklvylEtptnpllkvvDiekiaklakkagvlvvvDntfaspll 181
                                       e++ +++ kl+ ++ + +   +++ +++ia+la + +++v vD +   ++l
  gi|242398093|ref|YP_002993517.1| 165 EEVKDKKKKLIVTDGVFSMDGDLAPLPEIAELAEQYDAIVYVDDAHGEGVL 215
                                       666666999**********************************98877765 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   3.1e-08     8e-05      35     224 ..      87     265 ..      77     321 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 3.1e-08
                                       HHHHHHHHHHTT-SEEEEES-HHHHHHHHHHHH--TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTTTBE-H CS
                   Beta_elim_lyase  35 nrLedavaelfgkeaalfvpqGtaAnsillkillqrgeevivtepahihfdetgaiaelagvklrdlknkeaGkmdl 111
                                        +Le+++a+    eaa+ + +G  An  +l++l+++ge         +   e   ++ + g++l  +++     +++
  gi|242398093|ref|YP_002993517.1|  87 VELEEKLAKFKKREAAILFQSGYNANLGALSALIKKGEDG------VFVSEELNHASIIDGMRLSGAEKVIYKHLNM 157
                                       6899******************************775543......33333334444446665555555555669** PP

                                       HHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHHTS-CHHHH.. CS
                   Beta_elim_lyase 112 ekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaakslgeivkemf.. 186
                                       e+l++ ++ev++  +k kli++     +  G   +   l e+a++a++y+  + +D A        +g  + + f  
  gi|242398093|ref|YP_002993517.1| 158 EDLKKRLEEVKD--KKKKLIVTDGVFSM-DGDLAP---LPEIAELAEQYDAIVYVDDAHGEGVLGDSGRGIVDHFnl 228
                                       *********999..88898888877775.676555...6678899*************8776665555555555524 PP

                                       .TTSSEEEEESSSTT--SS-EEEEE-HH....HHHHHHH CS
                   Beta_elim_lyase 187 .syvDsvtmslkKdllanvGgvlafrddeledylaerve 224
                                        + vD  +  l+K  ++ +Gg +a+ ++ + dyl++r +
  gi|242398093|ref|YP_002993517.1| 229 hDRVDFEMGTLSKAFGV-IGGYVAGPEE-AIDYLRQRGR 265
                                       46678888899******.********99.9999998855 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   4.6e-08   0.00012      40     177 ..      81     209 ..      49     213 .. 0.71

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 4.6e-08
                                       HHHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEE CS
                       Aminotran_5  40 eatkaveearekvaelinaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakv 116
                                        +++   e +ek+a++ + e    i+f sG     nl als++ +  ++  +v  e++h + +    +     ga+ 
  gi|242398093|ref|YP_002993517.1|  81 GTMELHVELEEKLAKFKKREA--AILFQSGYN--ANLGALSALIKKGEDGVFVSEELNHASII-DGMR---LSGAEK 149
                                       367778899999999998885..9***99976..78888888765666666777777777777.3333...445544 PP

                                       EEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-T CS
                       Aminotran_5 117 kvipldeegeldldelekllnektklvaithvsnvtGtiqpveeigklakkkgalvlvDaa 177
                                       ++++  +   l+ ++le+  ++k kl+    v ++ G + p++ei++la +++a+v vD a
  gi|242398093|ref|YP_002993517.1| 150 VIYKHLNMEDLK-KRLEEVKDKKKKLIVTDGVFSMDGDLAPLPEIAELAEQYDAIVYVDDA 209
                                       444443334444.55566668999***********************************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 !   14.6   0.0   5.9e-06     0.015      26     150 ..      87     213 ..      73     224 .. 0.77
   2 ?    1.2   0.0     0.069   1.8e+02     224     271 ..     277     325 ..     268     361 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.9e-06
                                       HHHHHHHHHHHT-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEE.SSS-THHHHHHHHTT-EEEEE.-B-TTTSSB- CS
                   DegT_DnrJ_EryC1  26 eeFEkafaaylgvkhaiavssGtaAlhlaLralgvgpgdeVIvp.sltFvatanavlelgakpvfv.Dvdpdtynid 100
                                        e+E+++a++ + + ai + sG +A++ aL+al  + +d V v   l+ ++ +   + +ga+ v     + +++   
  gi|242398093|ref|YP_002993517.1|  87 VELEEKLAKFKKREAAILFQSGYNANLGALSALIKKGEDGVFVSeELNHASIIDGMRLSGAEKVIYkHLNMEDLKK- 162
                                       589*****************************65555666666615666667789999999877641445455444. PP

                                       GGGCGGG--TTEEEEE...EB-GGGB---HHHHHHHHHHCT-EEEEE-TT-TT CS
                   DegT_DnrJ_EryC1 101 paaieaaitertkaIl...pVhlyGqvadmdalkaiaakhglkvieDaAhAlG 150
                                         ++e++  ++ k I+   +  + G+ a ++++ ++a++++ +v  D Ah+ G
  gi|242398093|ref|YP_002993517.1| 163 --RLEEVKDKKKKLIVtdgVFSMDGDLAPLPEIAELAEQYDAIVYVDDAHGEG 213
                                       ..44444456777777333356889**********************999877 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.069
                                       HHHHHHHHHH.HCTHHHHHHHHHHHHHHHHHHHHTCCCCEESCGGTTSS CS
                   DegT_DnrJ_EryC1 224 eiqAAiglaq.LerldelvarRreiaelykeeLaelegtaelttpketk 271
                                       +++AAi  +  L++ delv++  ++++ ++++L++l++ +  t ++ t 
  gi|242398093|ref|YP_002993517.1| 277 DVAAAIASVEiLQHSDELVKKLWDNTNFLQKGLRDLGYDLGNTKHPITP 325
                                       7899998665499***********************9887776666654 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 !   16.8   0.0   8.6e-07    0.0022     123     207 ..     119     211 ..      98     214 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 8.6e-07
                                       HHHS-EEEEEE--EB-TTS-BE---G........GGGSHHHHHHHHHHSTTTGSESEEEEESS-T..TSEEE-HHHH CS
                          OKR_DC_1 123 lvlsgatPvylepernalgiiggidl........kefeeetlkekikevpdakaprlavitnsTY..dGvlynakei 189
                                       l+  g   v+++ e n+  ii g+ l        k ++ e lk++++ev d+k+   +++t + +  dG l+ + ei
  gi|242398093|ref|YP_002993517.1| 119 LIKKGEDGVFVSEELNHASIIDGMRLsgaekviyKHLNMEDLKKRLEEVKDKKK--KLIVTDGVFsmDGDLAPLPEI 193
                                       555556666666666666665554331111111157899************999..899999976559********* PP

                                       HHHHTTSESEEEEE-TT- CS
                          OKR_DC_1 190 vdkleklsdrilfDeAwv 207
                                        +++e+++  +++D+A++
  gi|242398093|ref|YP_002993517.1| 194 AELAEQYDAIVYVDDAHG 211
                                       ****************97 PP

>> YcaO  YcaO cyclodehydratase, ATP-ad Mg2+-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00023       0.6     163     229 ..       8      76 ..       2     178 .. 0.60
   2 ?    0.2   0.0      0.14   3.6e+02     258     299 ..     353     390 ..     261     394 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00023
                              YcaO 163 rellerlreagievrlldatldlgipvvaavlvdpk.....lllvagaGahldpevAlerAltElaqsrltl 229
                                        e l++l+e+g+ vr+  +++  g p v++     k        ++g +ah+++++A++rA++    +  ++
  gi|242398093|ref|YP_002993517.1|   8 TEELNELKEKGLYVRIRVLQSSQG-PWVVVDGK--KvlnmcSNNYLGLAAHPKIKEAAIRAILDYGVGAGAV 76 
                                       555666666665555555555443.33333333..2233432245799999999999999998866555555 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.14
                              YcaO 258 lwlpeaaakrldfllfaewassgdleedletllerlkaagld 299
                                       ++ p+ +  +++ +l  e+ s+   +edl+++++++++ g +
  gi|242398093|ref|YP_002993517.1| 353 VY-PTVPLGTARIRL--EP-SAAHSKEDLQYVIDAFEDLGKK 390
                                       22.444443333333..33.4468899999999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       804  (0.0448435); expected 358.6 (0.02)
Passed bias filter:                      704  (0.039266); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.49
# Mc/sec: 2421.92
//
Query:       gi|242398094|ref|YP_002993518.1|  [L=766]
Description: Replication factor C small subunit [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-20   72.3   0.1    9.6e-20   70.8   0.1    1.9  1  Rep_fac_C        Replication factor C C-terminal domain
    2.6e-15   56.5   0.0    5.3e-15   55.5   0.0    1.5  1  Intein_splicing  Intein splicing domain
    1.5e-14   54.1   0.1    1.9e-10   40.7   0.1    2.4  2  DNA_pol3_delta2  DNA polymerase III, delta subunit
    3.3e-14   53.4   0.0    1.4e-06   28.7   0.1    2.6  2  AAA              ATPase family associated with various cellul
    6.6e-09   35.7   0.1    2.8e-07   30.4   0.0    3.0  3  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    9.1e-09   35.5   0.5     0.0064   16.8   0.0    2.8  2  LAGLIDADG_3      LAGLIDADG-like domain
    2.8e-07   31.1   0.0    0.00015   22.2   0.0    2.4  2  AAA_16           AAA ATPase domain
      2e-06   27.9   0.0    6.2e-06   26.3   0.0    1.8  1  Rad17            Rad17 P-loop domain
    4.9e-05   22.8   0.0      0.007   15.8   0.0    2.4  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0001   22.5   1.4    0.00042   20.6   0.2    2.6  2  AAA_assoc_2      AAA C-terminal domain
    0.00019   21.7   0.0       0.49   10.7   0.0    2.6  2  AAA_22           AAA domain
    0.00027   21.5   0.1     0.0069   16.9   0.0    2.9  2  AAA_18           AAA domain
    0.00028   20.7   0.2     0.0021   17.9   0.0    2.3  2  DNA_pol3_delta   DNA polymerase III, delta subunit
    0.00048   20.2   0.0     0.0046   17.0   0.0    2.2  2  ResIII           Type III restriction enzyme, res subunit
    0.00072   19.7   0.0       0.16   12.1   0.0    2.5  2  Hom_end          Homing endonuclease
  ------ inclusion threshold ------
      0.016   14.8   0.2      0.086   12.4   0.0    2.3  3  AAA_25           AAA domain
      0.019   14.5   0.0      0.047   13.2   0.0    1.6  1  AAA_7            P-loop containing dynein motor region
      0.022   14.7   0.0       0.59   10.1   0.0    2.6  2  AAA_5            AAA domain (dynein-related subfamily)
      0.028   13.5   0.0      0.056   12.5   0.0    1.4  1  T2SSE            Type II/IV secretion system protein
       0.04   13.7   0.0      0.083   12.7   0.0    1.4  1  AAA_11           AAA domain
      0.043   13.0   0.0       0.13   11.4   0.0    1.7  2  TIP49            TIP49 P-loop domain
      0.046   13.9   0.0       0.12   12.5   0.0    1.7  1  AAA_33           AAA domain
       0.13   12.5   0.0       0.38   11.0   0.0    1.8  1  AAA_28           AAA domain
       0.14   12.0   0.0         12    5.7   0.0    2.4  2  AAA_3            ATPase family associated with various cellul
       0.18   11.5   0.0        4.6    6.9   0.0    2.5  3  AAA_24           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 !   70.8   0.1   1.3e-22   9.6e-20       2      88 .]     674     759 ..     673     759 .. 0.97

  Alignments for each domain:
  == domain 1  score: 70.8 bits;  conditional E-value: 1.3e-22
                                       -HHHHHHHHHHHHHT-HHHHHHHHHHHHHHC---HHHHHHHHHHHGCCS..S-HHHHHHHHHHHHHHHHHHHCTH-H CS
                         Rep_fac_C   2 hpteieeileaclngdfeeaykklrellvekGysaediltqlhrvvkeqeelpeaqkleilellgeiekrlveGase 78 
                                       +p++++e++  +l+g+f +a++klre l ++G+s+ed+l q+h+ v++   ++e  k+ + +++ge+ +rlveG++e
  gi|242398094|ref|YP_002993518.1| 674 RPEDVREMMLLALEGNFLKARDKLREILLKQGLSGEDVLIQMHKEVFNL-PISEPKKVALADKIGEYNFRLVEGSNE 749
                                       799*********9***********************************6.6************************** PP

                                       HHHHHHHHHH CS
                         Rep_fac_C  79 hlqlsallar 88 
                                        +ql+alla+
  gi|242398094|ref|YP_002993518.1| 750 MIQLEALLAQ 759
                                       ********96 PP

>> Intein_splicing  Intein splicing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.5   0.0   7.4e-18   5.3e-15      19     134 .]     129     523 ..     101     523 .. 0.96

  Alignments for each domain:
  == domain 1  score: 55.5 bits;  conditional E-value: 7.4e-18
                                       CTTEEEEEETTTTEEEEEEEEEEEEEEEEEEEEEEETTS-EEEEETT-EEEECCTTEEEEEECCC--TT-EEEEE.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                   Intein_splicing  19 egeevlslnledlklevksvkkliklklkelyeiklesgrkikaTpeHkllvvrdegivEkradeLkegdliavp.. 93 
                                       ++ evl ++ e++ +++++v+k+i++++  +++++le g k+ +T++H+++v++++g+  ++a+eLkeg ++     
  gi|242398094|ref|YP_002993518.1| 129 SNLEVLTVD-ENYCVKWAQVSKIIRHHVPVILHVHLEGGGKLELTGNHSVMVLTENGLETVKASELKEGTILLSFtt 204
                                       455666666.788899999************************************999889********9999879* PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                   Intein_splicing  94 ............................................................................. 93 
                                                                                                                    
  gi|242398094|ref|YP_002993518.1| 205 niegfldvldmsdysikesartrtfkglsvdeelsyifglyaaegavgfngntsgqviytlgshegqlierikafve 281
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                   Intein_splicing  94 ............................................................................. 93 
                                                                                                                    
  gi|242398094|ref|YP_002993518.1| 282 nlgvsvyenytssgfdrsrksayqfrllntqlarffeesfydgngrrannkrlpgfvfefpireriaflkgladgdg 358
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                   Intein_splicing  94 ............................................................................. 93 
                                                                                                                    
  gi|242398094|ref|YP_002993518.1| 359 tgewggvirvssvsrdllidtvwlarvsgieaslferearliwkggmkwskaellpaepivkmleaienaiegnwry 435
                                       ***************************************************************************** PP

                                       .............................................HSCEEEEEEEEEEEEECEEEEEEEEETTT-EE CS
                                       .............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Intein_splicing  94 .............................................dadvvwdkvksievedeeeyVYdltvednhNF 125
                                                                                    + d+    v++ie  ++++ VYd++v++n+ F
  gi|242398094|ref|YP_002993518.1| 436 efrhqlyegkkrvrkatlrkaiemvneekldekgkrilevlkklaNTDLHALLVRKIELVEYNDFVYDVSVPGNEMF 512
                                       ***************************************************************************** PP

                                       EE..CTTEEE- CS
                                       xx..xxxxxxx RF
                   Intein_splicing 126 va..ngiivHN 134
                                       +a    +++HN
  gi|242398094|ref|YP_002993518.1| 513 FAgeIPVLLHN 523
                                       *9633445998 PP

>> DNA_pol3_delta2  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0   0.00036      0.26       1      47 [.      32      77 ..      32      89 .. 0.91
   2 !   40.7   0.1   2.7e-13   1.9e-10      78     162 ..     526     608 ..     440     609 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00036
                   DNA_pol3_delta2  1 gqeealkilskalksgrlahayLfeGdegigkkelalnlakallcee 47
                                      gq++++k l++ +k+  + h +Lf+G+ g+gk ++ l+la++l+ e+
  gi|242398094|ref|YP_002993518.1| 32 GQDHIVKRLKHYVKTASMPH-LLFAGPPGTGKTTSSLALARELFGEH 77
                                      688999***********999.8*********************9886 PP

  == domain 2  score: 40.7 bits;  conditional E-value: 2.7e-13
                   DNA_pol3_delta2  78 ekersikldqir.elieelsrkpre.skkkiiiiedaekmtksAaNalLktlEEPsenaifiLitsdtnklLktirS 152
                                       e      ++ ir +++e++  kp+   + kii +++a+ +t+ A+ al +t+E  s+n+ fiL  + ++k++++i+S
  gi|242398094|ref|YP_002993518.1| 526 E----RGINVIReKVKEFARTKPIGgVSFKIIFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQS 598
                                       3....378889945566666677764578************************************************ PP

                   DNA_pol3_delta2 153 Rcqelkfspl 162
                                       Rc +++f+pl
  gi|242398094|ref|YP_002993518.1| 599 RCAIFRFRPL 608
                                       ********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 !   22.0   0.0   2.4e-07   0.00017       1      34 [.      52      90 ..      52     141 .. 0.76
   2 !   28.7   0.1     2e-09   1.4e-06      57     130 ..     540     606 ..     509     608 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 2.4e-07
                                      EEEESSTTSSHHHHHHHHHHHH.....THEEEEEETTTC CS
                               AAA  1 vllyGppGtGKTllakavakel.....gvefleisgsel 34
                                      +l+ GppGtGKT+   a+a+el       +fle+++s  
  gi|242398094|ref|YP_002993518.1| 52 LLFAGPPGTGKTTSSLALARELfgehwRHNFLELNASVS 90
                                      699******************865544588888888754 PP

  == domain 2  score: 28.7 bits;  conditional E-value: 2e-09
                                       S........TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSS CS
                               AAA  57 a........kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRfd 125
                                       a        + +i+f+DE+dal+++            +++L + ++ +++   +v +i+ +n+ +k+ +++  +R+ 
  gi|242398094|ref|YP_002993518.1| 540 ArtkpiggvSFKIIFLDEADALTQDA-----------QQALRRTMEMFSS---NVRFILSCNYSSKIIEPIQ-SRCA 601
                                       222246675569**********9888...........*************...6******************.9**9 PP

                                       EEEET CS
                               AAA 126 rkiei 130
                                       +  + 
  gi|242398094|ref|YP_002993518.1| 602 IFRFR 606
                                       87665 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.0   3.9e-10   2.8e-07       2      57 ..      23      73 ..      22      81 .. 0.93
   2 ?    1.3   0.0      0.37   2.6e+02      86     114 ..     551     579 ..     548     594 .. 0.87
   3 ?   -1.2   0.0       2.1   1.5e+03     103     141 ..     636     674 ..     626     716 .. 0.66

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 3.9e-10
                            RuvB_N  2 rPksleeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakel 57
                                      rP++l++ +gq+++ ++lk ++++a     ++ h+l++GpPG Gktt +  +a+el
  gi|242398094|ref|YP_002993518.1| 23 RPERLDDIVGQDHIVKRLKHYVKTA-----SMPHLLFAGPPGTGKTTSSLALAREL 73
                                      9*********************988.....579********************998 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.37
                            RuvB_N  86 dvlfideihrlsraveevlysamedfrld 114
                                       +++f+de   l++ +++ l  +me f+ +
  gi|242398094|ref|YP_002993518.1| 551 KIIFLDEADALTQDAQQALRRTMEMFSSN 579
                                       699*********************98755 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 2.1
                            RuvB_N 103 vlysamedfrldivigkGpsarsikldlpkftlvgattr 141
                                       +ly a  d r  i + + ++a  ++++ ++  lv++ +r
  gi|242398094|ref|YP_002993518.1| 636 ILYVAEGDLRRAINVLQAAAALDTRITDENVFLVASRAR 674
                                       556666666666655555555555555555555544443 PP

>> LAGLIDADG_3  LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.2   1.4e-05      0.01       2      61 ..     236     300 ..     235     320 .. 0.74
   2 !   16.8   0.0   8.9e-06    0.0064       4      61 ..     347     397 ..     344     450 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.4e-05
                                       HHHHHHHHHHHHCCECCECSTTTTS..EEEEES-HHHHHHHHHHHHHCT.HSCEEEE...EEE-S CS
                       LAGLIDADG_3   2 vkaafLrGlfdaDGsvskskkkgvs..isltssskelledvqrlLlrlGIestiyek...kkakg 61 
                                       +++ ++ Gl++a+G v  +++++++   +l+s++ +l+e ++   ++lG+  +   +     +++
  gi|242398094|ref|YP_002993518.1| 236 EELSYIFGLYAAEGAVGFNGNTSGQviYTLGSHEGQLIERIKAFVENLGVSVYENYTssgFDRSR 300
                                       57889***********9999988889999********************9877665544433333 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 8.9e-06
                                       HHHHHHHHHHCCECCECSTTTTSEEEEES-HHHHHHHHHHHHHCT.HSCEEEEEEE-S CS
                       LAGLIDADG_3   4 aafLrGlfdaDGsvskskkkgvsisltssskelledvqrlLlrlGIestiyekkkakg 61 
                                        afL+Gl d+DG+ ++ +     i+++s s++ll d   l    GIe+++ e+   + 
  gi|242398094|ref|YP_002993518.1| 347 IAFLKGLADGDGTGEWGGV----IRVSSVSRDLLIDTVWLARVSGIEASLFER---EA 397
                                       79****************4....**************************9999...33 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0     2e-07   0.00015       3      54 ..      31      79 ..      29     148 .. 0.80
   2 ?    6.4   0.0     0.015        11      93     164 ..     464     578 ..     422     584 .. 0.63

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 2e-07
                            AAA_16  3 vGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekdggi 54
                                      vG ++ +++L+++++++++   + +l+ G++G+GK++   +l+r+l ++++ 
  gi|242398094|ref|YP_002993518.1| 31 VGQDHIVKRLKHYVKTASM---PHLLFAGPPGTGKTTSSLALARELFGEHWR 79
                                      89*************9977...58***************9999999998644 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.015
                            AAA_16  93 eleawrekleeala......................................avpelagaea.......srllellk 124
                                       +l++  ++++e+l+                                      ++       +       +r  ++++
  gi|242398094|ref|YP_002993518.1| 464 KLDEKGKRILEVLKklantdlhallvrkielveyndfvydvsvpgnemffagEI-------PvllhnsdERGINVIR 533
                                       555555555555555555666666666666666666666666644444444422.......1333444466666666 PP

                            AAA_16 125 rll.allsrder.....plvlvlDdlqwadeaslqllaaLlrlles 164
                                       + + +++++ ++       +++lD+++ + ++ +q+l+ +++  +s
  gi|242398094|ref|YP_002993518.1| 534 EKVkEFART-KPiggvsFKIIFLDEADALTQDAQQALRRTMEMFSS 578
                                       666444444.4445554689*****************999987665 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   8.7e-09   6.2e-06       7      70 ..      16      74 ..      12     114 .. 0.88

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 8.7e-09
                             Rad17  7 elWfekykPekaeelavhkkkieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLskelg 70
                                      ++W+eky+Pe ++++    + ++ +k+++k+ ++++     LL +GP+G gk+t    L++el 
  gi|242398094|ref|YP_002993518.1| 16 KPWVEKYRPERLDDIVGQDHIVKRLKHYVKTASMPH-----LLFAGPPGTGKTTSSLALARELF 74
                                      69*******************************997.....5*************999999974 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   0.0   9.8e-06     0.007       2      60 ..      27      88 ..      26     106 .. 0.80
   2 ?    4.6   0.0     0.026        18     109     134 ..     552     577 ..     545     594 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 9.8e-06
                      Mg_chelatase  2 lkdvkGqeeakrale..iaaaGgHnlllvGppGsGKtmlakrlp.sllpplseeealevaki 60
                                      l d++Gq++  + l+  +  a   +ll++GppG+GKt    +l+ +l+ +  +++ le ++ 
  gi|242398094|ref|YP_002993518.1| 27 LDDIVGQDHIVKRLKhyVKTASMPHLLFAGPPGTGKTTSSLALArELFGEHWRHNFLELNAS 88
                                      68999**998887765589999***************9887775256677777777776655 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.026
                      Mg_chelatase 109 vLfLDElpefkrkvlevLRePledge 134
                                       ++fLDE+  +++++ ++LR+ +e  +
  gi|242398094|ref|YP_002993518.1| 552 IIFLDEADALTQDAQQALRRTMEMFS 577
                                       79********************9765 PP

>> AAA_assoc_2  AAA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1       2.5   1.8e+03      30      66 ..     422     469 ..     418     489 .. 0.64
   2 !   20.6   0.2   5.8e-07   0.00042       3      38 ..     624     659 ..     622     699 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 2.5
                                       XXXXXXXXXX...........XXXXXXXXXXXXXXX.XXXXXXXXXXX CS
                       AAA_assoc_2  30 LElaaeaaeak..........egkieitledleeal.qrkalryDkag 66 
                                       LE++ +a e +          egk+++ +++l++a+   +  + D++g
  gi|242398094|ref|YP_002993518.1| 422 LEAIENAIEGNwryefrhqlyEGKKRVRKATLRKAIeMVNEEKLDEKG 469
                                       444444444444456777777778888888888777333444555555 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 5.8e-07
                                       X.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       AAA_assoc_2   3 kklkleddalealaeladGDaRkaLnlLElaaeaae 38 
                                       + l+l+++ l+a++ +a+GD R+a+n+L++aa+   
  gi|242398094|ref|YP_002993518.1| 624 EGLELTEEGLQAILYVAEGDLRRAINVLQAAAALDT 659
                                       67899************************8887654 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   0.00068      0.49       7      29 ..      51      73 ..      47     138 .. 0.78
   2 !    8.3   0.0    0.0036       2.6      74     128 ..     528     585 ..     453     590 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00068
                            AAA_22  7 ilvvtGesGtGKTtllrrlleql 29
                                      +l+  G++GtGKTt+   l+++l
  gi|242398094|ref|YP_002993518.1| 51 HLLFAGPPGTGKTTSSLALAREL 73
                                      67889**********99999887 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0036
                            AAA_22  74 sseellealeqalrarav....ielliiDEaqhlrseealeeLrsllnlsrkgvqliLv 128
                                           ++e++ + +r++       +++ +DEa+ l +++a + Lr+ ++  +++v++iL 
  gi|242398094|ref|YP_002993518.1| 528 GINVIREKVKEFARTKPIggvsFKIIFLDEADAL-TQDAQQALRRTMEMFSSNVRFILS 585
                                       4555556666666666667777789*********.999999**9999999999999996 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   9.7e-06    0.0069       3      44 ..      54      94 ..      52     164 .. 0.79
   2 ?    1.0   0.1      0.81   5.8e+02      28      77 ..     424     472 ..     410     490 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 9.7e-06
                            AAA_18  3 ltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpe 44
                                       +G+pG+GKtt + +L+++l fg++ r+++ e + + + d +
  gi|242398094|ref|YP_002993518.1| 54 FAGPPGTGKTTSSLALAREL-FGEHWRHNFLELNASVSKDTP 94
                                      79***************998.899999999988877777766 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.81
                            AAA_18  28 lrdvakenglllevdpealdeskrldedkldklldaleenssaleegknl 77 
                                        +++a e+++++e+ ++ ++ +kr+++  l k+++ ++e     e+gk +
  gi|242398094|ref|YP_002993518.1| 424 AIENAIEGNWRYEFRHQLYEGKKRVRKATLRKAIEMVNEEKL-DEKGKRI 472
                                       67889999*********9999999999999999999999876.7777775 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 ?   -0.6   0.1       1.4   9.7e+02      22      47 ..     452     477 ..     438     494 .. 0.53
   2 !   17.9   0.0   2.9e-06    0.0021      59     170 ..     551     652 ..     532     654 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.4
                                       HHTTTEEEEEEEE-STTS-HHH.HTT CS
                    DNA_pol3_delta  22 alkqgfedlnyikfdlnedwiddvle 47 
                                       +l++ +e  n +k+d + + i +vl+
  gi|242398094|ref|YP_002993518.1| 452 TLRKAIEMVNEEKLDEKGKRILEVLK 477
                                       44444444444444444433333333 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 2.9e-06
                                       EEEEEE--.....TT-S-TTHHHHHHHHTTT--SSEEEEEEES.S--HHHHHHHHHTTTEEEEEE----TTTHHHHH CS
                    DNA_pol3_delta  59 rivvlknpklltkesklnekllkeLeeylsnlpedtlLiliapkklderkklvklLkkkatvveaktlkeeelkkwi 135
                                       +i++l+ +      + l+++ +++L ++++  + ++ +il ++       k++  ++++  ++++ +lk e++ + +
  gi|242398094|ref|YP_002993518.1| 551 KIIFLDEA------DALTQDAQQALRRTMEMFSSNVRFILSCN----YSSKIIEPIQSRCAIFRFRPLKDEDVARRL 617
                                       66666666......66899999*********************....557899************************ PP

                                       HHHHHHTT-EE-HHHHHHHHHHHTT-HHHHHHHHH CS
                    DNA_pol3_delta 136 qkraqelglkiekealelLlelvennlsaikqele 170
                                       +++a+++gl++++e l+ +l+  e++l+++ + l+
  gi|242398094|ref|YP_002993518.1| 618 KYIAENEGLELTEEGLQAILYVAEGDLRRAINVLQ 652
                                       ****************************9998776 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   6.4e-06    0.0046       8      58 ..      33      83 ..      30      90 .. 0.92
   2 ?   -0.0   0.0       1.1   7.6e+02     129     165 ..     546     584 ..     507     587 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 6.4e-06
                                      HHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EE CS
                            ResIII  8 QeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekfl 58
                                      Q +++++l+  +k     ++l++ + GtGKT  +++l+++l+ ++++ +fl
  gi|242398094|ref|YP_002993518.1| 33 QDHIVKRLKHYVKTASMPHLLFAGPPGTGKTTSSLALARELFGEHWRHNFL 83
                                      888999999999988888****************************99998 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1.1
                                       HTTT-SEEEEETGGGTTS...TTTHHHHHT---SEEEEE CS
                            ResIII 129 lrdrfdviiiDEaHrlgak..kswreilekfkeavllgl 165
                                       +  +f++i+ DEa  l+++  ++ r+ +e+f+++v++ l
  gi|242398094|ref|YP_002993518.1| 546 GGVSFKIIFLDEADALTQDaqQALRRTMEMFSSNVRFIL 584
                                       455678999999999999644477777999998887765 PP

>> Hom_end  Homing endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.046        33      16      64 ..     239     291 ..     233     315 .. 0.82
   2 !   12.1   0.0   0.00023      0.16      12      67 ..     344     397 ..     335     404 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.046
                           Hom_end  16 aFlaGLvdsdgyvkkeked....satvktedksvmegivklarsLGikasvkt 64 
                                       +++ GL  ++g v  + +       t+ + + +++e+i ++ + LG+++  + 
  gi|242398094|ref|YP_002993518.1| 239 SYIFGLYAAEGAVGFNGNTsgqvIYTLGSHEGQLIERIKAFVENLGVSVYENY 291
                                       7999*********988777788999**********************997665 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00023
                           Hom_end  12 evREaFlaGLvdsdgyvkkekedsatvktedksvmegivklarsLGikasvktkee 67 
                                       + R aFl GL d+dg+ +    +++ v+++++ ++ ++v lar  Gi+as  ++e+
  gi|242398094|ref|YP_002993518.1| 344 RERIAFLKGLADGDGTGEWG--GVIRVSSVSRDLLIDTVWLARVSGIEASLFEREA 397
                                       44558**********98877..8**************************9988766 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00012     0.086      37      65 ..      53      80 ..      27      97 .. 0.87
   2 ?   -3.5   0.0         9   6.5e+03      80     186 ..     462     489 ..     452     494 .. 0.56
   3 ?   -1.7   0.0       2.5   1.8e+03      70      96 ..     677     703 ..     622     734 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00012
                            AAA_25 37 llaGapgtGKttlaldlalavatGkpwlg 65
                                      l+aG+pgtGKtt  l la ++  G++w +
  gi|242398094|ref|YP_002993518.1| 53 LFAGPPGTGKTTSSLALARELF-GEHWRH 80
                                      789***************9998.777765 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 9
                            AAA_25  80 EdsedelrrRlravgealrddarllvldlagveslpLfakdrggtlltadvdaleaaieevegvrlvviDplsralg 156
                                       E++ d                                                                        
  gi|242398094|ref|YP_002993518.1| 462 EEKLD------------------------------------------------------------------------ 466
                                       33333........................................................................ PP

                            AAA_25 157 gdensnsdvgalvealeriarrtgaavllv 186
                                             ++ ++++e l+++ ++t+ + llv
  gi|242398094|ref|YP_002993518.1| 467 ------EKGKRILEVLKKL-ANTDLHALLV 489
                                       ......3346666666666.4666666655 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 2.5
                            AAA_25  70 eqgkVlyvsaEdsedelrrRlravgea 96 
                                         +  +++++E++    r +lr+++ +
  gi|242398094|ref|YP_002993518.1| 677 DVREMMLLALEGNFLKARDKLREILLK 703
                                       333344455555555555555555544 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 ?   13.2   0.0   6.6e-05     0.047      34      74 ..      50      90 ..      36      95 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.6e-05
                             AAA_7 34 kpvllvGptGtGKtviikdllkkldkekylsltinfsaqts 74
                                       ++l+ Gp GtGKt+    l ++l  e++  ++++++a+ s
  gi|242398094|ref|YP_002993518.1| 50 PHLLFAGPPGTGKTTSSLALARELFGEHWRHNFLELNASVS 90
                                      589*********************************99877 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00082      0.59       1      34 [.      51      87 ..      51     125 .. 0.80
   2 ?    1.4   0.0       0.4   2.9e+02      65      89 ..     549     573 ..     525     577 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00082
                                      EEEEE--SSSSHHHHHHHGGGGB...S--EEEEE--T CS
                             AAA_5  1 dvlLvGppGtgKselaerlaaal...nreveyvqltr 34
                                      ++l  GppGtgK++ +  la+ l    ++ +   l++
  gi|242398094|ref|YP_002993518.1| 51 HLLFAGPPGTGKTTSSLALARELfgeHWRHNFLELNA 87
                                      68999***********999998876655555555555 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.4
                                       G-SEEEEESGGG--HHHHHHHHHHH CS
                             AAA_5  65 egeilvlDEveraesevlnsLlsll 89 
                                       + +i++lDE + + ++++++L + +
  gi|242398094|ref|YP_002993518.1| 549 SFKIIFLDEADALTQDAQQALRRTM 573
                                       5589**************9997665 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   7.9e-05     0.056     104     188 ..      26     108 ..      16     113 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.9e-05
                             T2SSE 104 tlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeinksderivtvEDpvEiqleganqvqln 180
                                       +ldd++ + +  +++++ +++a  +   +l++G+ g+GKtt+  al  e+  ++ r   +E  + +  + +  v++n
  gi|242398094|ref|YP_002993518.1|  26 RLDDIVGQDHIVKRLKHYVKTA--SMPHLLFAGPPGTGKTTSSLALARELFGEHWRHNFLELNASVSKDTPILVRIN 100
                                       6889999999999999999999..8999**************99999888766666666666666666666666666 PP

                             T2SSE 181 akkakvtf 188
                                        +  + tf
  gi|242398094|ref|YP_002993518.1| 101 GRVMRTTF 108
                                       66555555 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00012     0.083      17      42 ..      50      74 ..      35     102 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00012
                            AAA_11 17 seitliqGPPGtgKTktivellsqll 42
                                      ++  l+ GPPGtgKT+  ++l ++l 
  gi|242398094|ref|YP_002993518.1| 50 PH-LLFAGPPGTGKTTSSLALARELF 74
                                      44.799***************99996 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00018      0.13      45      85 ..      46      87 ..      25      93 .. 0.74
   2 ?   -3.0   0.0       4.5   3.2e+03     280     309 ..     551     580 ..     527     593 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00018
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XX..XXXXXXXX CS
                             TIP49 45 ekklaGravLlaGpsgtGktalaiaiskelg.ed..vpfvalsg 85
                                      +  +    +L+aGp+gtGkt  ++a+++el  e+    f  l++
  gi|242398094|ref|YP_002993518.1| 46 TASMP--HLLFAGPPGTGKTTSSLALARELFgEHwrHNFLELNA 87
                                      44444..79********************952431134555555 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4.5
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49 280 GvlfiDevhmlDiecfsylnraleselaPi 309
                                        ++f+De+  l  ++   l r++e   + +
  gi|242398094|ref|YP_002993518.1| 551 KIIFLDEADALTQDAQQALRRTMEMFSSNV 580
                                       468999999999999999999999766655 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00017      0.12       3      27 ..      53      77 ..      52     133 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00017
                            AAA_33  3 llvGlpGsGKstlaerllkklgavl 27
                                      l+ G+pG+GK+t +  l+++l +++
  gi|242398094|ref|YP_002993518.1| 53 LFAGPPGTGKTTSSLALARELFGEH 77
                                      799***************9998776 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00054      0.38       4      24 ..      54      76 ..      51      92 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00054
                            AAA_28  4 itGgestGKTtlleaLaar..gy 24
                                      + G+++tGKTt + aLa++  g 
  gi|242398094|ref|YP_002993518.1| 54 FAGPPGTGKTTSSLALARElfGE 76
                                      78***************875654 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.017        12       1      29 [.      51      79 ..      51      84 .. 0.86
   2 ?    3.6   0.0     0.079        57      38      87 ..     523     574 ..     517     582 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.017
                             AAA_3  1 hvllegvPGlaktllvkalakaldlefkr 29
                                      h+l+ g PG++kt+   ala+ l  e  r
  gi|242398094|ref|YP_002993518.1| 51 HLLFAGPPGTGKTTSSLALARELFGEHWR 79
                                      99******************998666555 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.079
                             AAA_3  38 PsdilGtevfeekekefefkk..Gpvfanllladeinrappktqsalleame 87 
                                        sd  G++v++ek kef  +k  G v  ++++ de +  +  +q al  +me
  gi|242398094|ref|YP_002993518.1| 523 NSDERGINVIREKVKEFARTKpiGGVSFKIIFLDEADALTQDAQQALRRTME 574
                                       578899**********987755699**********************99997 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0    0.0065       4.6       5      24 ..      52      70 ..      49      99 .. 0.85
   2 ?   -3.1   0.0       7.5   5.4e+03      24      55 ..     174     212 ..     169     235 .. 0.63
   3 ?    1.4   0.0      0.32   2.3e+02      53      92 ..     533     576 ..     515     582 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0065
                            AAA_24  5 iliyGpsgiGKTtlakelgp 24
                                      +l  Gp+g+GKTt+ + l  
  gi|242398094|ref|YP_002993518.1| 52 LLFAGPPGTGKTTSSLAL-A 70
                                      5678*********99887.4 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 7.5
                            AAA_24  24 pkplfidtekGlksldadkfpdie.......swedflde 55 
                                       ++ +++ te+Gl  ++a ++++ +       ++e fld 
  gi|242398094|ref|YP_002993518.1| 174 NHSVMVLTENGLETVKASELKEGTillsfttNIEGFLDV 212
                                       567888899999988888877655666666544444444 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.32
                            AAA_24  53 ldevvel....aaeladyktlviDtideleelclaevirqneka 92 
                                       +++v+e+    +     +k++++D +d l + + + ++r  e +
  gi|242398094|ref|YP_002993518.1| 533 REKVKEFartkPIGGVSFKIIFLDEADALTQDAQQALRRTMEMF 576
                                       55555554444555678**************9999998776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (766 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       684  (0.0381505); expected 358.6 (0.02)
Passed bias filter:                      592  (0.0330191); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); 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: 0.78u 0.33s 00:00:01.11 Elapsed: 00:00:00.50
# Mc/sec: 4613.66
//
Query:       gi|242398095|ref|YP_002993519.1|  [L=487]
Description: Replication factor C large subunit [Thermococcus sibiricus MM 739]
Scores for complete 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-14   52.7   0.0    1.8e-13   51.1   0.0    1.9  1  AAA             ATPase family associated with various cellula
      3e-10   40.3   3.8    3.8e-10   40.0   0.1    2.8  3  Rad17           Rad17 P-loop domain
      3e-07   30.5   1.1    6.7e-07   29.4   0.0    2.2  2  AAA_14          AAA domain
    1.3e-05   25.5   0.1     0.0032   17.7   0.0    3.0  3  AAA_22          AAA domain
    1.3e-05   25.0   0.0      3e-05   23.8   0.0    1.6  1  RuvB_N          Holliday junction DNA helicase RuvB P-loop do
    4.7e-05   23.4   0.0    0.00027   20.9   0.0    2.3  2  AAA_5           AAA domain (dynein-related subfamily)
    0.00019   21.8   0.0     0.0059   17.0   0.0    2.7  3  AAA_16          AAA ATPase domain
    0.00032   20.3   0.0    0.00097   18.8   0.0    1.8  1  AAA_25          AAA domain
    0.00035   19.7   0.0    0.00088   18.4   0.0    1.6  1  T2SSE           Type II/IV secretion system protein
    0.00039   19.4   0.0    0.00065   18.7   0.0    1.3  1  PPV_E1_C        Papillomavirus helicase
    0.00042   19.6   0.0      0.001   18.4   0.0    1.7  1  Zeta_toxin      Zeta toxin
    0.00043   19.5   0.0      0.001   18.3   0.0    1.6  1  DUF815          Protein of unknown function (DUF815)
     0.0012   18.7   0.2      0.022   14.6   0.0    2.9  2  DNA_pol3_delta  DNA polymerase III, delta subunit
     0.0027   17.5   1.5     0.0034   17.1   0.0    1.9  2  AAA_24          AAA domain
     0.0028   18.1   2.0     0.0075   16.7   0.0    2.6  2  AAA_17          AAA domain
     0.0028   17.5   9.4      0.012   15.5   0.0    2.5  2  AAA_11          AAA domain
     0.0028   18.0   0.1       0.01   16.2   0.1    2.0  1  AAA_assoc_2     AAA C-terminal domain
     0.0029   17.8   0.0     0.0076   16.4   0.0    1.9  1  AAA_33          AAA domain
     0.0063   16.9   0.1      0.065   13.6   0.1    2.4  2  AAA_19          AAA domain
  ------ inclusion threshold ------
      0.014   15.9   0.6       0.09   13.3   0.0    2.3  2  ABC_tran        ABC transporter
      0.016   15.5   0.1      0.048   13.9   0.0    1.9  2  AAA_28          AAA domain
      0.022   14.3   0.0      0.042   13.4   0.0    1.4  1  AAA_7           P-loop containing dynein motor region
      0.023   15.2   0.0      0.023   15.2   0.0    3.0  2  AAA_18          AAA domain
      0.025   14.2   0.0      0.059   13.0   0.0    1.6  1  SRP54           SRP54-type protein, GTPase domain
      0.048   13.4   0.0       0.12   12.0   0.0    1.7  1  AAA_30          AAA domain
      0.049   13.6   2.2      0.066   13.2   0.0    2.2  2  ResIII          Type III restriction enzyme, res subunit
      0.054   13.5   0.0       0.12   12.4   0.0    1.6  1  TsaE            Threonylcarbamoyl adenosine biosynthesis prot
      0.057   12.4   0.1       0.15   11.0   0.0    1.7  2  AAA_6           Hydrolytic ATP binding site of dynein motor r
       0.11   12.3   0.0       0.21   11.4   0.0    1.4  1  AAA_29          P-loop containing region of AAA domain
       0.73   10.1   0.0       0.73   10.1   0.0    2.1  2  Hydin_ADK       Hydin Adenylate kinase-like domain
        4.8    7.6   8.8         32    4.9   0.1    2.7  2  DUF1840         Domain of unknown function (DUF1840)


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 !   51.1   0.0   3.1e-16   1.8e-13       1     129 [.      43     152 ..      43     155 .. 0.82

  Alignments for each domain:
  == domain 1  score: 51.1 bits;  conditional E-value: 3.1e-16
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS....TSEEEEEETGGGHHHH CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakeka....kpsilfiDEidalaks 73 
                                       +ll GppG GKT+++ a+a+e ++e++e+++s+ +  ++g+ e+    ++++a ++     + + +f+DE+d++ +s
  gi|242398095|ref|YP_002993519.1|  43 LLLAGPPGSGKTTTVYALANEYKFEVIELNASDDR--TFGKIER----YLNAAYTMDvfgrRRKLIFLDEVDNIEPS 113
                                       69*********************************..5555555....555555555555456*************9 PP

                                       HTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSSEEEE CS
                               AAA  74 rsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRfdrkie 129
                                                   ++++ + + + ++      +++ +nr+++++ +++ ++++++++
  gi|242398095|ref|YP_002993519.1| 114 G-----------AKEIAKLIGKAQN-----PIMMSANRYWEVPIEIR-NKAEIVQY 152
                                       9...........8888888888888.....58889999999998888.88887766 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   0.1   6.5e-13   3.8e-10       8      75 ..       3      70 ..       1      81 [. 0.93
   2 ?   -2.5   0.1       6.9     4e+03      92     112 ..     364     384 ..     345     413 .. 0.64
   3 ?   -0.3   0.4       1.5   8.4e+02      19      40 ..     405     425 ..     394     433 .. 0.78

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 6.5e-13
                             Rad17  8 lWfekykPekaeelavhkkkieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLskelgiklre 75
                                      +W eky+P+ + ++    k +e++k w++       kk+ LL++GP+G gk+t+v  L+ e+ ++++e
  gi|242398095|ref|YP_002993519.1|  3 PWTEKYRPKRLVDIVNQDKALEKIKPWIEEWLHGIPKKKALLLAGPPGSGKTTTVYALANEYKFEVIE 70
                                      7***************************98888888889***********************999987 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 6.9
                             Rad17  92 fkgltekesrflsqiesfkel 112
                                       fk+++  +    s i++f el
  gi|242398095|ref|YP_002993519.1| 364 FKSIFSSNLDVASHIAVFLEL 384
                                       555555555566677777666 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 1.5
                             Rad17  19 eelavhkkkieevkewlkadvL 40 
                                       + l++hk k++evk+ l+  v 
  gi|242398095|ref|YP_002993519.1| 405 KMLSIHK-KLKEVKTELEIRVE 425
                                       5688997.89****99987764 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   1.2e-09   6.7e-07       2      77 ..      40     111 ..      39     134 .. 0.77
   2 ?   -2.7   0.2       9.9   5.8e+03      36      71 ..     448     483 ..     434     483 .. 0.62

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 1.2e-09
                            AAA_14   2 rkilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqevp 77 
                                       +k+l++ G+  +GKTt ++ l++e+     +++++n  d+r+  + +   l+ ++   + +++++++flDE+ +++
  gi|242398095|ref|YP_002993519.1|  40 KKALLLAGPPGSGKTTTVYALANEYK---FEVIELNASDDRTFGKIER-YLNAAYTMDVFGRRRKLIFLDEVDNIE 111
                                       7999******************8888...8999999988888654433.24444444444569*********9984 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 9.9
                            AAA_14  36 inldderdkkladpekllelileklkeekktylflD 71 
                                       +++++++++k++d  + +++  ek  +++k++ ++D
  gi|242398095|ref|YP_002993519.1| 448 VEIEEPEESKEEDLGSKDQITEEKKDKKGKQVTLFD 483
                                       556666666666554444555555434588888887 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   5.6e-06    0.0032       5      56 ..      40      82 ..      38      92 .. 0.84
   2 ?    5.3   0.0     0.037        22      78     106 ..      78     115 ..      70     132 .. 0.75
   3 ?   -1.0   0.0       3.5     2e+03      52      88 ..     156     189 ..     146     212 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 5.6e-06
                            AAA_22  5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdl 56
                                      ++ l++ G++G+GKTt++  l++++         + ev++ +++ + +  ++
  gi|242398095|ref|YP_002993519.1| 40 KKALLLAGPPGSGKTTTVYALANEY---------KFEVIELNASDDRTFGKI 82
                                      6889*********************.........999999999888776655 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.037
                            AAA_22  78 llealeqalrarav.......ielliiDEaqhlr.s.e 106
                                        + ++e++l+a+++       ++l+ +DE++++  s +
  gi|242398095|ref|YP_002993519.1|  78 TFGKIERYLNAAYTmdvfgrrRKLIFLDEVDNIEpSgA 115
                                       56778888888888889999999*********954243 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 3.5
                            AAA_22  52 sskdllrellralglelkaerlsseellealeqalra 88 
                                       s++d+l++l+r+++ e+       +e+l++++q +r 
  gi|242398095|ref|YP_002993519.1| 156 SQRDILKALFRITKAEGIF---VPKEVLQMIAQRARG 189
                                       7899999999999999988...666666666666554 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   5.1e-08     3e-05       2      97 ..       9     111 ..       8     123 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 5.1e-08
                            RuvB_N   2 rPksleeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakelgvklkitsgP......vleka 72 
                                       rPk+l + + q+k  ek+k  ie   +   +   +ll+GpPG Gktt    +a+e + ++    +        +e+ 
  gi|242398095|ref|YP_002993519.1|   9 RPKRLVDIVNQDKALEKIKPWIEEWLHGIPKKKALLLAGPPGSGKTTTVYALANEYKFEVIELNASddrtfgKIERY 85 
                                       9**************************9999************************9987644333201111145555 PP

                            RuvB_N  73 gdlaalltnl.eekdvlfideihrls 97 
                                        + a  +  + ++++++f+de+  ++
  gi|242398095|ref|YP_002993519.1|  86 LNAAYTMDVFgRRRKLIFLDEVDNIE 111
                                       55444444432456677888887765 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   4.7e-07   0.00027       2      90 ..      43     123 ..      42     140 .. 0.86
   2 ?   -1.6   0.0       4.3   2.5e+03      45     105 ..     330     391 ..     319     423 .. 0.69

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 4.7e-07
                                       EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG-- CS
                             AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEverae 78 
                                       +lL GppG+gK++ +  la  ++ ev + + ++d t  ++   ++      +++  ++    r+ ++++lDEv+++e
  gi|242398095|ref|YP_002993519.1|  43 LLLAGPPGSGKTTTVYALANEYKFEVIELNASDDRTFGKIERYLNA-----AYTMDVFG---RRRKLIFLDEVDNIE 111
                                       89************************99999999999999999994.....56655555...89************* PP

                                       HHHHHHHHHHHH CS
                             AAA_5  79 sevlnsLlslle 90 
                                       ++ +++  +l+ 
  gi|242398095|ref|YP_002993519.1| 112 PSGAKEIAKLIG 123
                                       *99988888775 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 4.3
                                       B--.........--------G-SEEEEESGGG--..HHHHHHHHHHHHSSEEE..-SSSEEE- CS
                             AAA_5  45 reikngttslvdsplvraaregeilvlDEverae..sevlnsLlslleerrllleeggelvka 105
                                       r++ ++++s +ds++++ ++  ++  l+ +e+++  +++++s l + ++  + le g++++ +
  gi|242398095|ref|YP_002993519.1| 330 RDT-KEERSIRDSIVKKIMKGMHMSKLEAIETMRifKSIFSSNLDVASHIAVFLELGDKEIEF 391
                                       443.67788889999888888888888877776666777777766666666666666666655 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0     1e-05    0.0059       6      49 ..      20      65 ..      16      89 .. 0.81
   2 ?    0.5   0.0       1.2   6.9e+02     137     163 ..     100     126 ..      73     132 .. 0.82
   3 ?   -0.7   0.1       2.8   1.6e+03      41      91 ..     161     200 ..     158     258 .. 0.55

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1e-05
                            AAA_16  6 eeeleqLlsalervrsgrp..elvllsGesGvGKsslvrellrale 49
                                      ++ le+++  +e +  g p   ++ll G++G+GK++ v +l+++++
  gi|242398095|ref|YP_002993519.1| 20 DKALEKIKPWIEEWLHGIPkkKALLLAGPPGSGKTTTVYALANEYK 65
                                      6667778888888888888999****************99998766 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1.2
                            AAA_16 137 lvlvlDdlqwadeaslqllaaLlrlle 163
                                        +++lD+++ ++++ ++ +a L   ++
  gi|242398095|ref|YP_002993519.1| 100 KLIFLDEVDNIEPSGAKEIAKLIGKAQ 126
                                       489**********99999998887766 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 2.8
                            AAA_16  41 vrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaes 91 
                                       +++l+ +++k++gif+  +  q         +aq + r + lr+  +++++
  gi|242398095|ref|YP_002993519.1| 161 LKALF-RITKAEGIFVPKEVLQM--------IAQRA-R-GDLRAAINDLQT 200
                                       56666.57777778877777777........77777.5.444444444333 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.7e-06   0.00097      14      54 ..      22      61 ..       7      64 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.7e-06
                            AAA_25 14 dlaapppprrwlvkgllpagelallaGapgtGKttlaldla 54
                                      +l++  p  + +++g+ p+++  llaG+pg+GKtt ++ la
  gi|242398095|ref|YP_002993519.1| 22 ALEKIKPWIEEWLHGI-PKKKALLLAGPPGSGKTTTVYALA 61
                                      3444455556666776.*******************99998 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 !   18.4   0.0   1.5e-06   0.00088     115     153 ..      27      64 ..       8      75 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.5e-06
                             T2SSE 115 kekiaevlrkavrerglilvsGgTgsGKttllyallkei 153
                                       k+ i+e l+    +++ +l++G+ gsGKtt++yal +e 
  gi|242398095|ref|YP_002993519.1|  27 KPWIEEWLHGI-PKKKALLLAGPPGSGKTTTVYALANEY 64 
                                       44555556554.899*******************98875 PP

>> PPV_E1_C  Papillomavirus helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   1.1e-06   0.00065     252     292 ..      30      70 ..      19      79 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.1e-06
                          PPV_E1_C 252 lkefLkgvPkknclvllGppntGkslfamslikfLkGkvls 292
                                       + e+L+g+Pkk++l+l Gpp +Gk++  ++l +  k +v+ 
  gi|242398095|ref|YP_002993519.1|  30 IEEWLHGIPKKKALLLAGPPGSGKTTTVYALANEYKFEVIE 70 
                                       579**********************9999998877777765 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.8e-06     0.001      14      56 ..      38      78 ..       9      87 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.8e-06
                        Zeta_toxin 14 erPklillgGqpGAGKselaellkdelerqgnvvrldpDdlRe 56
                                       ++k++ll+G pG+GK+++  +l++e   + +v++l++ d R+
  gi|242398095|ref|YP_002993519.1| 38 PKKKALLLAGPPGSGKTTTVYALANEY--KFEVIELNASDDRT 78
                                      5899**********************9..89999999877666 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.7e-06     0.001      22     103 ..       8      87 ..       2     108 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.7e-06
                            DUF815  22 vdevklddLvgidkqkealventeqfleglpannv.LLwGarGtGKSslvkallneyaeegLrlievekedlkelpk 97 
                                       +++ +l d+v+ dk  e+++  +e++l+g p +++ LL G  G+GK ++v al ney+     +ie++ +d +++ k
  gi|242398095|ref|YP_002993519.1|   8 YRPKRLVDIVNQDKALEKIKPWIEEWLHGIPKKKAlLLAGPPGSGKTTTVYALANEYKF---EVIELNASDDRTFGK 81 
                                       556678899999999999999*********998761578*****************975...577777777777777 PP

                            DUF815  98 lvellr 103
                                       + + l+
  gi|242398095|ref|YP_002993519.1|  82 IERYLN 87 
                                       766665 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 !   14.6   0.0   3.8e-05     0.022      36     171 ..      76     200 ..      55     202 .. 0.77
   2 ?   -2.1   0.0       4.9   2.8e+03      97     140 ..     328     369 ..     317     382 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.8e-05
                                       STTS-HHH.HTTTSTTTTSSSSE.EEEEEE--.....TT-S-TTHHHHHHHHTTT--SSEEEEEEES.S--HHHHHH CS
                    DNA_pol3_delta  36 dlnedwiddvleecetlpffsdk.rivvlknpklltkesklnekllkeLeeylsnlpedtlLiliapkklderkklv 111
                                       d +  +i+  l+++ t++ f+ + ++++l+        ++   + +ke+ +++ +  +++ + + a+    +  ++ 
  gi|242398095|ref|YP_002993519.1|  76 DRTFGKIERYLNAAYTMDVFGRRrKLIFLDEV------DNIEPSGAKEIAKLIGK--AQNPIMMSAN----RYWEVP 140
                                       55556677778888888866654156666666......33455566666666666..5555556666....566788 PP

                                       HHHTTTEEEEEE----TTTHHHHHHHHHHHTT-EE-HHHHHHHHHHHTT-HHHHHHHHHH CS
                    DNA_pol3_delta 112 klLkkkatvveaktlkeeelkkwiqkraqelglkiekealelLlelvennlsaikqelek 171
                                        ++ +ka +v++k+l++ ++ k + ++++++g+   ke+l++++++  ++l+a+ + l+ 
  gi|242398095|ref|YP_002993519.1| 141 IEIRNKAEIVQYKRLSQRDILKALFRITKAEGIFVPKEVLQMIAQRARGDLRAAINDLQT 200
                                       99999***************************************************9986 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.9
                                       EEEES..S--HHHHHHHHHTTTEEEEEE----TTTHHHHHHHHHH CS
                    DNA_pol3_delta  97 iliap.kklderkklvklLkkkatvveaktlkeeelkkwiqkraq 140
                                       il  + ++ + r ++vk++ k    +++++l+  e+ + ++++++
  gi|242398095|ref|YP_002993519.1| 328 ILRDTkEERSIRDSIVKKIMKG---MHMSKLEAIETMRIFKSIFS 369
                                       4444423333344488888874...45666666666666666665 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   5.9e-06    0.0034       2      78 ..      40     111 ..      39     129 .. 0.77
   2 ?   -2.6   0.7       6.5   3.7e+03     144     148 ..     444     448 ..     385     480 .. 0.55

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 5.9e-06
                            AAA_24   2 klkiliyGpsgiGKTtlakel..gpkplfidtekGlksldadkfpdieswedfldevvelaaeladyktlviDtide 76 
                                       k+ +l+ Gp+g+GKTt+++ l  ++k+ +i ++++     ++ f +i   e  l+++ + +   ++ k +++D +d 
  gi|242398095|ref|YP_002993519.1|  40 KKALLLAGPPGSGKTTTVYALanEYKFEVIELNASD----DRTFGKI---ERYLNAAYTMDVFGRRRKLIFLDEVDN 109
                                       67899****************999999999999966....5555533...566677777777777777777777777 PP

                            AAA_24  77 le 78 
                                       +e
  gi|242398095|ref|YP_002993519.1| 110 IE 111
                                       65 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 6.5
                            AAA_24 144 kytrl 148
                                        +  +
  gi|242398095|ref|YP_002993519.1| 444 VKEEV 448
                                       22333 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.3e-05    0.0075       2      25 ..      47      70 ..      46      75 .. 0.92
   2 ?   -1.7   1.5       6.3   3.6e+03     123     127 ..     437     441 ..     392     480 .. 0.59

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.3e-05
                                      E-TTSSHHHHHHHHHHHHTEEEEE CS
                            AAA_17  2 GgPGsGKgtqceklvekygfthls 25
                                      G+PGsGK+t +  l+ +y+f++++
  gi|242398095|ref|YP_002993519.1| 47 GPPGSGKTTTVYALANEYKFEVIE 70
                                      9********************986 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 6.3
                                       TTST- CS
                            AAA_17 123 rtrgr 127
                                       +tr+ 
  gi|242398095|ref|YP_002993519.1| 437 DTREK 441
                                       22222 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0     2e-05     0.012      15      41 ..      38      64 ..      27      99 .. 0.80
   2 ?   -1.3  10.1       2.6   1.5e+03      90     165 ..     399     473 ..     317     483 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2e-05
                            AAA_11 15 seseitliqGPPGtgKTktivellsql 41
                                       +++  l+ GPPG+gKT+t+ +l ++ 
  gi|242398095|ref|YP_002993519.1| 38 PKKKALLLAGPPGSGKTTTVYALANEY 64
                                      4555689***************99987 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.6
                            AAA_11  90 ivRvgneeeriseavksvsleekvekrlekeekaqlakeiskeleklakelrafeeeeekeklkkskekskskleq 165
                                       + ++  +  +i++++k+v++e +++ +  +e k++ ++e ++e+e++++e++ +e ee+ke+ + sk++  ++++ 
  gi|242398095|ref|YP_002993519.1| 399 VGKIKGKMLSIHKKLKEVKTELEIRVEEVME-KIERVEEDTREKEEVKEEVEIEEPEESKEEDLGSKDQITEEKKD 473
                                       3334444467888888888888888777776.67777777777777777777666666554444443333333332 PP

>> AAA_assoc_2  AAA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   1.7e-05      0.01       5      52 ..     173     219 ..     169     239 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.7e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXX CS
                       AAA_assoc_2   5 lkleddalealaeladGDaRkaLnlLElaaeaaeakegkieitledle 52 
                                       + + +++l+++a+ a GD R+a+n L+++++   + + +  +   d+e
  gi|242398095|ref|YP_002993519.1| 173 IFVPKEVLQMIAQRARGDLRAAINDLQTVVSGGVE-DAELILAYRDVE 219
                                       66889**********************99988765.444444444444 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.3e-05    0.0076       3      39 ..      44      80 ..      43     197 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.3e-05
                            AAA_33  3 llvGlpGsGKstlaerllkklgavllssdtlrrrlfg 39
                                      ll G+pGsGK+t +  l+++ ++++++ ++  +r fg
  gi|242398095|ref|YP_002993519.1| 44 LLAGPPGSGKTTTVYALANEYKFEVIELNASDDRTFG 80
                                      789*********************9998885445444 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   0.00011     0.065       9      34 ..      39      64 ..      34      92 .. 0.85
   2 ?   -0.2   0.0       1.9   1.1e+03     101     124 ..      97     121 ..      74     131 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00011
                            AAA_19  9 kekvllvtaGpGtGKTrvlkhivall 34
                                      k+k ll+ ++pG+GKT+++ +  +++
  gi|242398095|ref|YP_002993519.1| 39 KKKALLLAGPPGSGKTTTVYALANEY 64
                                      5678899999********98877665 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.9
                            AAA_19 101 qeeellivDEfqdvd.elqyrLlka 124
                                       ++++l++ DE+ +++   ++++ k 
  gi|242398095|ref|YP_002993519.1|  97 RRRKLIFLDEVDNIEpSGAKEIAKL 121
                                       45669*********94444444443 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   0.00016      0.09       8      37 ..      37      66 ..      34     109 .. 0.87
   2 ?   -0.9   0.8       3.6   2.1e+03      51      70 ..     415     440 ..     382     478 .. 0.47

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00016
                                      EETTSEEEEEESTTSSHHHHHHHHTTSS-- CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  8 lkegekvaivGenGaGKStLlkllagllkp 37
                                      + + + + + G+ G+GK+t + +la+++k 
  gi|242398095|ref|YP_002993519.1| 37 IPKKKALLLAGPPGSGKTTTVYALANEYKF 66
                                      67788999******************9985 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 3.6
                                       G......B-HHHCCHCEEEE-SS--S CS
                                       x......xxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  51 e......qeleslrkeigvlpqepql 70 
                                       e      ++ e++ ++i+ ++++++ 
  gi|242398095|ref|YP_002993519.1| 415 EvkteleIRVEEVMEKIERVEEDTRE 440
                                       12222222333333333333333221 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   8.3e-05     0.048       3      28 ..      44      70 ..      42      92 .. 0.87
   2 ?   -1.9   0.1       6.1   3.6e+03     146     157 ..     418     428 ..     386     483 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 8.3e-05
                            AAA_28  3 vitGgestGKTtlleaLaar.gypvvp 28
                                       + G++++GKTt++ aLa++ +++v++
  gi|242398095|ref|YP_002993519.1| 44 LLAGPPGSGKTTTVYALANEyKFEVIE 70
                                      578***************876888874 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 6.1
                            AAA_28 146 relgipviivps 157
                                       +el i+v +v  
  gi|242398095|ref|YP_002993519.1| 418 TELEIRVEEV-M 428
                                       4444444443.2 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   7.2e-05     0.042      31      77 ..      38      81 ..      33     111 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.2e-05
                             AAA_7 31 knkkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanq 77
                                       +kk +ll Gp G+GKt+++  l ++++   + ++ +n s   +  +
  gi|242398095|ref|YP_002993519.1| 38 PKKKALLLAGPPGSGKTTTVYALANEYK---FEVIELNASDDRTFGK 81
                                      67999*****************999888...7777777766655555 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0     4e-05     0.023       2      25 ..      44      74 ..      43     159 .. 0.76
   2 ?   -2.2   2.9       9.5   5.5e+03     105     127 ..     429     451 ..     329     461 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4e-05
                            AAA_18  2 lltGtpGvGKttlakeLskrlgf.......g 25
                                      ll+G+pG+GKtt   +L+++ +f       +
  gi|242398095|ref|YP_002993519.1| 44 LLAGPPGSGKTTTVYALANEYKFevielnaS 74
                                      69***************99866565544441 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 9.5
                            AAA_18 105 elleRlekRgyeeakikeneeae 127
                                       e +eR+e++ +e+ + ke+ e+e
  gi|242398095|ref|YP_002993519.1| 429 EKIERVEEDTREKEEVKEEVEIE 451
                                       45677777777777766666655 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0    0.0001     0.059       3      27 ..      42      66 ..      40      79 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.0001
                                      EEEEEESTTSSHHHHHHHHHHHHHH CS
                             SRP54  3 villvGlqGaGKTttlaKLaallkk 27
                                       +ll+G+ G+GKTtt+  La+ +k 
  gi|242398095|ref|YP_002993519.1| 42 ALLLAGPPGSGKTTTVYALANEYKF 66
                                      689*****************99985 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      0.12      20      43 ..      42      65 ..      36     132 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00021
                            AAA_30 20 vavltGpAGtGKttalkalreawe 43
                                        +l Gp+G+GKtt++ al++ ++
  gi|242398095|ref|YP_002993519.1| 42 ALLLAGPPGSGKTTTVYALANEYK 65
                                      67899***********99988776 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 ?   13.2   0.0   0.00011     0.066       8      49 ..      19      65 ..      16      73 .. 0.80
   2 ?   -2.4   1.6       7.3   4.2e+03      94     117 ..     436     459 ..     387     483 .. 0.47

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00011
                                      HHHHHHHHT...........TTSEEEEEESTTSTHHHHHHHHHHHH- CS
                            ResIII  8 Qeeaienlleklks.....krdkrglikmaTGtGKTlvaaklierll 49
                                      Q +a+e+++  +++      ++k +l++ + G+GKT + ++l+ +++
  gi|242398095|ref|YP_002993519.1| 19 QDKALEKIKPWIEEwlhgiPKKKALLLAGPPGSGKTTTVYALANEYK 65
                                      5666666665555566667999********************99986 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 7.3
                                       B--.......-SEEEEEHHHHHHT CS
                            ResIII  94 kkakekdstnkkilvttiqsldad 117
                                       ++ +ek++ + ++ +++ ++ +++
  gi|242398095|ref|YP_002993519.1| 436 EDTREKEEVKEEVEIEEPEESKEE 459
                                       222222333333333333333322 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   0.00021      0.12      13      70 ..      29      93 ..      17     120 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00021
                                      HHHHCH.....TEEEEEEESTTSSHHHHHHHHHHHTT--.....----TTTTSEEEEEE..SSEEEEE CS
                              TsaE 13 klakal.....gdvilLeGdLGaGKTtlvrglakalgve.....evkSPTFtlveeYelekeglyHfD 70
                                       + + l     ++++lL G+ G+GKTt v +la+++++e     +    TF  +e+Y +   + y +D
  gi|242398095|ref|YP_002993519.1| 29 WIEEWLhgipkKKALLLAGPPGSGKTTTVYALANEYKFEvielnASDDRTFGKIERYLN---AAYTMD 93
                                      44444444455678********************9988755332333457777777733...345555 PP

>> AAA_6  Hydrolytic ATP binding site of dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00026      0.15      37      78 ..      45      86 ..      37     133 .. 0.91
   2 ?   -2.4   0.1         3   1.7e+03     238     264 ..     342     369 ..     329     432 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00026
                             AAA_6 37 paGpagtGKtEtvkdLakalakqvvvfncsdqldykslgkif 78
                                      +aGp g GKt tv  La++    v+ +n sd+ ++ ++++ +
  gi|242398095|ref|YP_002993519.1| 45 LAGPPGSGKTTTVYALANEYKFEVIELNASDDRTFGKIERYL 86
                                      68*****************************99998888876 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3
                             AAA_6 238 lllralrdvnlpklva.eDvplfkglis 264
                                       ++ + ++ ++++kl a e + +fk++ s
  gi|242398095|ref|YP_002993519.1| 342 IVKKIMKGMHMSKLEAiETMRIFKSIFS 369
                                       4555555555555544123445555543 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00036      0.21      22      42 ..      40      60 ..      32      62 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00036
                            AAA_29 22 kgatlltGpsGsGKSTllDAi 42
                                      k a ll+Gp GsGK+T + A+
  gi|242398095|ref|YP_002993519.1| 40 KKALLLAGPPGSGKTTTVYAL 60
                                      4479************98776 PP

>> Hydin_ADK  Hydin Adenylate kinase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0    0.0013      0.73       1      26 [.      42      67 ..      42      73 .. 0.87
   2 ?   -1.9   1.7       5.8   3.4e+03      60      81 ..     436     457 ..     387     481 .. 0.43

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0013
                         Hydin_ADK  1 aiivhGaPlsGKtatavtLakkYeaA 26
                                      a+++ G+P sGKt+t  +La +Y+  
  gi|242398095|ref|YP_002993519.1| 42 ALLLAGPPGSGKTTTVYALANEYKFE 67
                                      67889******************865 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 5.8
                         Hydin_ADK  60 qaekekeeaaeeaekkegqlsv 81 
                                       + ++ekee +ee+e +e + s+
  gi|242398095|ref|YP_002993519.1| 436 EDTREKEEVKEEVEIEEPEESK 457
                                       1111222222222211111111 PP

>> DUF1840  Domain of unknown function (DUF1840)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1     0.055        32      19      48 ..     156     185 ..     142     210 .. 0.80
   2 ?    3.0   5.4      0.22   1.3e+02      31      83 ..     416     479 ..     387     483 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.055
                           DUF1840  19 vakqllkllgkslterGaitaedlpaaiak 48 
                                       +++ +lk+l + ++++G++ ++++ ++ia+
  gi|242398095|ref|YP_002993519.1| 156 SQRDILKALFRITKAEGIFVPKEVLQMIAQ 185
                                       5788*********************99986 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.22
                           DUF1840  31 lterGaitaedlpaaiakLeaaiaaekaeeaeeeeeeeeeek...........eeekeeeeeev 83 
                                       ++++  i +e++ + i+++e+ + ++++ ++e e ee ee+k           ee+k ++ ++v
  gi|242398095|ref|YP_002993519.1| 416 VKTELEIRVEEVMEKIERVEEDTREKEEVKEEVEIEEPEESKeedlgskdqitEEKKDKKGKQV 479
                                       4455568999************999999988887777766665677777776655555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (487 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2093  (0.116738); expected 358.6 (0.02)
Passed bias filter:                      779  (0.0434492); expected 358.6 (0.02)
Passed Vit filter:                       138  (0.00769703); expected 17.9 (0.001)
Passed Fwd filter:                        31  (0.00172904); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              31  [number of targets reported over threshold]
# CPU time: 0.82u 0.35s 00:00:01.17 Elapsed: 00:00:00.53
# Mc/sec: 2773.93
//
Query:       gi|242398096|ref|YP_002993520.1|  [L=333]
Description: Met-10+ like-protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.1e-38  131.1   0.6    6.9e-38  130.4   0.6    1.5  1  Met_10           Met-10+ like-protein
    4.2e-08   32.9   4.3    1.4e-07   31.3   4.3    2.0  1  Trm5_N           tRNA methyltransferase 5 N-terminal domain
  ------ inclusion threshold ------
      0.059   12.7   0.0      0.093   12.0   0.0    1.3  1  Peptidase_C4     Peptidase family C4
       0.17   11.4   0.0       0.29   10.7   0.0    1.3  1  MTS              Methyltransferase small domain
       0.19   12.5   0.0       0.48   11.2   0.0    1.8  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 !  130.4   0.6   1.9e-41   6.9e-38       2     187 ..      86     272 ..      85     317 .. 0.91

  Alignments for each domain:
  == domain 1  score: 130.4 bits;  conditional E-value: 1.9e-41
                                       EEEEETTEEEEEB-TTSSHHHHHHHHHHHHHSS-SCEEEE-S-SBTTTTB--EEEEEES-.SEEEEEETTEEEEEET CS
                            Met_10   2 kfeiiGdvvilnlreelkeykkvigevildktkvktvlrkvsevegefRtfelevlaGsdstetihkEngcrfklDv 78 
                                       +++iiGd+++++++ e+++ +k+i+e +  + +   v+ k++  +g fR +++ ++ G+++++tihkEng+++k+D+
  gi|242398096|ref|YP_002993520.1|  86 RYDIIGDIAVIQIPPEIEHREKEIVEGLRRVYPFLKVVAKKGFHTGAFRIRRYSIIWGEKRLTTIHKENGIKIKVDL 162
                                       79*************************99999777777777777********************************* PP

                                       TTS---GGGHHHHHHHHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT..-TTCE CS
                            Met_10  79 skvyfsskleaErerlaklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNk..vekvv 153
                                       s+v+f+++ + Er rla++v++ge +  +fAG+ p+a++ia+y k++ + +++ln e+vk+  en+klNk  ++ ++
  gi|242398096|ref|YP_002993520.1| 163 SRVFFNPRMKGERYRLAQTVKDGEKIFLMFAGVLPYALVIARY-KNVDITTVELNEEAVKLGLENLKLNKdkLKGRI 238
                                       *****************************************95.7888*********************544999** PP

                                       EEEES-GGG---.TT-EEEEEE--TTTGGGGHHHH CS
                            Met_10 154 kpileDgrevir.eqladrvvmnlpksaieFldkv 187
                                       + i++ + ev +  +++drv+ + pk  ++ l  +
  gi|242398096|ref|YP_002993520.1| 239 HLIKGNVFEVGPkLETFDRVISPTPK-GVNALRLA 272
                                       **********9967899****99984.44445555 PP

>> Trm5_N  tRNA methyltransferase 5 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   4.3     4e-11   1.4e-07       3      41 ..       2      40 ..       1      44 [. 0.97

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 4e-11
                                      EEEGGGHHHHHHHHHHTT-B-TTS--EEETTEEEEEB-S CS
                            Trm5_N  3 kVpkkegEkvRkkLlekglLdrnyKIksdddylyIPvke 41
                                      kV+k+e+Ek++k+L+++++ d  +++++  +y+++P+++
  gi|242398096|ref|YP_002993520.1|  2 KVKKNEAEKIKKLLKKEEIYDGKRRPQRVKNYILFPITD 40
                                      9************************************98 PP

>> Peptidase_C4  Peptidase family C4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.6e-05     0.093       1      67 [.     104     168 ..     104     190 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.6e-05
                      Peptidase_C4   1 aedksiakglrdyhpvasrlaileyycgdmkteiyGvfyGdkllttahlikekgGnlkvrskrGlyd 67 
                                       + +k i +glr  +p    +a   +++g  +   y +++G+k ltt+h  ke+g ++kv   r +++
  gi|242398096|ref|YP_002993520.1| 104 HREKEIVEGLRRVYPFLKVVAKKGFHTGAFRIRRYSIIWGEKRLTTIH--KENGIKIKVDLSRVFFN 168
                                       56899******************************************9..78888888877776665 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   8.1e-05      0.29      43     103 ..     194     260 ..     187     273 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 8.1e-05
                                       SHHHHH.HHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC....EEEEE-STTTTST.TS-EEEEEE CS
                               MTS  43 Gvlgaa.lakespeaevtlvdvdarAlesakenleankle....vevvasdvleeve.ekkfdlivs 103
                                       Gvl  a + ++++++++t v+ + +A+++  enl+ nk +    +++++ +v+e  +  + fd ++s
  gi|242398096|ref|YP_002993520.1| 194 GVLPYAlVIARYKNVDITTVELNEEAVKLGLENLKLNKDKlkgrIHLIKGNVFEVGPkLETFDRVIS 260
                                       5554331456789999******************999877778899999999986552578888887 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00013      0.48      15      70 ..     202     260 ..     194     306 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00013
                                       HHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT....TEEEEESBCCGBSSSTTTEEEEEE CS
                   Methyltransf_25  15 lakrlgkakvtgvDiseemleaareraeeegl....nvefvqgdaedlpfedgsfDlvvs 70 
                                       +a+  ++ ++t v+++ee+++   e+++ ++     ++++++g++ ++  + ++fD v+s
  gi|242398096|ref|YP_002993520.1| 202 IARY-KNVDITTVELNEEAVKLGLENLKLNKDklkgRIHLIKGNVFEVGPKLETFDRVIS 260
                                       4544.6899*************99999773334588***********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       946  (0.0527637); expected 358.6 (0.02)
Passed bias filter:                      632  (0.0352502); 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: 0.62u 0.33s 00:00:00.95 Elapsed: 00:00:00.52
# Mc/sec: 1945.46
//
Query:       gi|242398097|ref|YP_002993521.1|  [L=290]
Description: hypothetical protein TSIB_0104 [Thermococcus sibiricus MM 739]
Scores for 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-35  119.3   0.2    1.5e-34  118.7   0.2    1.3  1  DUF835    Protein of unknown function (DUF835)
  ------ inclusion threshold ------
      0.073   13.2   0.1       0.21   11.7   0.0    1.7  2  MCU       Mitochondrial calcium uniporter


Domain annotation for each model (and alignments):
>> DUF835  Protein of unknown function (DUF835)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.7   0.2   1.7e-38   1.5e-34      14     136 .]     133     256 ..     121     256 .. 0.95

  Alignments for each domain:
  == domain 1  score: 118.7 bits;  conditional E-value: 1.7e-38
                            DUF835  14 dlvkegvkvlaitRenpkkirekvkienvkviwltkveeentvsPtnlekltetivkflkeaekg.vvliDgleyLv 89 
                                        lv+++  +lai+R +++ + +k++ie  k++wl+++e++++ +P++l++l++t  +flke++ + vv+ +g+eyL+
  gi|242398097|ref|YP_002993521.1| 133 FLVRHSNGLLAISRMQKELWVKKYQIEPDKFVWLSRIETNDSTDPSKLHVLQDTTLRFLKEKGGKsVVYFEGIEYLI 209
                                       57889999***************************************************9988666*********** PP

                            DUF835  90 lengFesvlkflltlkDavllkngtlilvidkealeekelalLkref 136
                                       l+n+F+sv+kfl ++kD+++++n++lil +  ++le+++ ++L +ef
  gi|242398097|ref|YP_002993521.1| 210 LYNDFNSVAKFLFSIKDYIISTNSLLILYLSSNILEKSQESILLKEF 256
                                       *********************************************98 PP

>> MCU  Mitochondrial calcium uniporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   2.3e-05      0.21      85     146 ..      37      97 ..      24     112 .. 0.79
   2 ?   -1.8   0.0      0.31   2.8e+03      39      62 ..     244     267 ..     198     285 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.3e-05
                                       GGCHHHHGGGHHHHHHHHTH.HHHHHHTTTS-S----HHHHHHHHHHHHHHHTTTHHHHGGCT CS
                               MCU  85 errtrrllwagLallavqlg.ilarLTwweysWDvmEPvtYfvtygtamafyaYflltkqeys 146
                                       ++ +r++l+++L++++  ++ il  LT +++ W v+E ++Y ++y ++++  +Y+l+ +++ s
  gi|242398097|ref|YP_002993521.1|  37 KSLARTFLVSTLLFTIGSTAvILDSLTKIQL-W-VIEAICYTLSYLHMVLSVTYYLRIQKSES 97 
                                       5667777777777776665515678888888.6.99*********************998765 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.31
                                       XXXXX-SSSSSSTSSSSSHHHHHH CS
                               MCU  39 vkalesalnveeeqlkkereleek 62 
                                       +++ ++++ ++e ++k+e++l+++
  gi|242398097|ref|YP_002993521.1| 244 LEKSQESILLKEFEQKSEEDLTRE 267
                                       334444444555555555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       732  (0.0408277); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 1946.35
//
Query:       gi|242398098|ref|YP_002993522.1|  [L=267]
Description: Probable molybdenum cofactor biosynthesis protein A [Thermococcus sibiricus MM 739]
Scores for complete 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-24   84.9   0.2    1.6e-23   84.0   0.2    1.5  1  Radical_SAM  Radical SAM superfamily
      7e-22   77.7   0.2    9.8e-22   77.2   0.2    1.2  1  Mob_synth_C  Molybdenum Cofactor Synthesis C
    0.00035   20.8   0.0    0.00077   19.8   0.0    1.6  1  Fer4_12      4Fe-4S single cluster domain
     0.0072   16.4   0.0      0.018   15.2   0.0    1.7  1  Fer4_14      4Fe-4S single cluster domain
      0.009   16.0   0.1      0.017   15.1   0.1    1.4  1  BSD          BSD 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 !   84.0   0.2   4.3e-27   1.6e-23      29     166 ..       1     131 [.       1     132 [. 0.97

  Alignments for each domain:
  == domain 1  score: 84.0 bits;  conditional E-value: 4.3e-27
                                       HHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT-SEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  29 lsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritvetngtlpdeeklerllelgvdrv 105
                                       +s+eei+ +vk++  + g++ v l+ggep+ + d ve+++r++      + ++++tngt++ +   ++l+++g+drv
  gi|242398098|ref|YP_002993522.1|   1 MSPEEIEIIVKIA-SKLGIRKVKLTGGEPTIRNDVVEIVRRIKPY---VVDLSMTTNGTTI-KSLGRALKDAGLDRV 72 
                                       89***********.599***************************8...*************.*************** PP

                                       EEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 106 slgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGendeeleellel 166
                                       +++l+++d+ek+++++ + +++++vl+++ ++ e+  + v+ ++v+++G nd e+++++++
  gi|242398098|ref|YP_002993522.1|  73 NISLDTLDKEKYKQIT-GFDSLSQVLDGINTAVELFYP-VKLNMVVMKGLNDNEIWDMIDY 131
                                       ****************.66****************777.******************9985 PP

>> Mob_synth_C  Molybdenum Cofactor Synthesis C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.2   0.2   2.7e-25   9.8e-22       3     126 ..     139     266 ..     137     267 .] 0.80

  Alignments for each domain:
  == domain 1  score: 77.2 bits;  conditional E-value: 2.7e-25
                                       EEEEE---B-TT.SSB--SSB--HHHHHHHHHHHS-EEEE-..-SST-SSEEEEETTT-..-EEEEE-TTTS-.-GG CS
                       Mob_synth_C   3 lrfIElmpvgeg.eewrekkvvsadeilerieerlalleak..ketkgpakrykikdgk..geiglIapvsep.FCa 73 
                                       l++IE+   +e+ ++w+ kk++ +   l+ +ee+++++++k  +++++ +k+y i+      e+++++++ ++ FCa
  gi|242398098|ref|YP_002993522.1| 139 LQLIEIEVPREMeNSWFFKKYFYS---LKPLEEEFEKIAIKikERKMHRRKKYFIPTRYgtAEVEVVRSMHNTiFCA 212
                                       789998655554156666666655...5566666666555531556999999*9977652367************** PP

                                       G--EEEE-TTSEEESSSS-SS-.EEHHHHHHTT--HHHHHHHHHHHHHT----H CS
                       Mob_synth_C  74 sCnRlRltadGklktCLfaeee.idlrdllregaseeeLkelikealarkkekh 126
                                       +C+R+Rlt++G+lktCL ++++ id+ + +r+gase e+ e++k+a+  +++++
  gi|242398098|ref|YP_002993522.1| 213 NCTRIRLTSTGHLKTCLLKRDDlIDVITPIRNGASEGEIIEIFKKAILMREPYW 266
                                       *********************99************************9999876 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   2.1e-07   0.00077      40     116 ..       5      77 ..       1      92 [. 0.82

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 2.1e-07
                           Fer4_12  40 lleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpekdiwlytgytleelskkekeellkeidvlvd 116
                                        +e i++ ++k  i+++ l+GGEP     +++++e+v+++k   ++   + ++g+t++ l ++ k+  l+ +++ +d
  gi|242398098|ref|YP_002993522.1|   5 EIEIIVKIASKLGIRKVKLTGGEPTI---RNDVVEIVRRIKPYVVD-LSMTTNGTTIKSLGRALKDAGLDRVNISLD 77 
                                       45666777777899************...999************96.89*********9998877777777777776 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 !   15.2   0.0   5.1e-06     0.018      41      96 ..      11      61 ..       2      80 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.1e-06
                           Fer4_14 41 lkkseikiqglvltGGePLhyenkkellklvkrlkeeypekkiwletngtleiele 96
                                      + +s+  i+++ ltGGeP +    ++++++v+r+k  +  ++  + tngt  ++l 
  gi|242398098|ref|YP_002993522.1| 11 KIASKLGIRKVKLTGGEPTIR---NDVVEIVRRIKPYV--VDLSMTTNGTTIKSLG 61
                                      4455666788********966...899**********9..99*******9887766 PP

>> BSD  BSD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   4.7e-06     0.017      32      55 ..     146     169 ..     130     172 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.7e-06
                               BSD  32 VPskvseeqFWsrYfyllrahaie 55 
                                       VP++++++ F ++Yfy+l  +++e
  gi|242398098|ref|YP_002993522.1| 146 VPREMENSWFFKKYFYSLKPLEEE 169
                                       ******************999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       905  (0.0504769); expected 358.6 (0.02)
Passed bias filter:                      680  (0.0379274); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 1952.22
//
Query:       gi|242398099|ref|YP_002993523.1|  [L=252]
Description: hypothetical protein TSIB_0106 [Thermococcus sibiricus MM 739]
Scores for complete 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   0.4    0.00054   19.8   0.1    2.9  2  TrmB          Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.073   13.5   0.0       0.17   12.3   0.0    1.6  1  DUF4288       Domain of unknown function (DUF4288)
      0.096   13.2   0.0       0.18   12.3   0.0    1.4  1  Cucumo_2B     Cucumovirus protein 2B
       0.11   12.5   0.0          2    8.4   0.1    2.8  2  HLH           Helix-loop-helix DNA-binding domain
       0.12   13.0   1.8        1.2    9.7   0.2    2.5  2  Syntaxin-6_N  Syntaxin 6, N-terminal


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 ?    1.8   0.0     0.064   2.3e+02      35      47 ..     105     117 ..     100     119 .. 0.87
   2 !   19.8   0.1   1.5e-07   0.00054      24      63 ..     205     245 ..     203     247 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.064
                                       SCHCHHHHHHHHH CS
                              TrmB  35 prskvYevLrsLe 47 
                                       +rs+v+ +L++L+
  gi|242398099|ref|YP_002993523.1| 105 ERSRVNASLQRLL 117
                                       79**********7 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 1.5e-07
                                       HHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.TTEEE CS
                              TrmB  24 tadeiaeelgvprskvYevLrsLedkGlVerekgr.pklYr 63 
                                       +++ i +++gv+r  + ++L+ L+  G+Ve++++   ++Y+
  gi|242398099|ref|YP_002993523.1| 205 EVRNIEKNSGVEREHATRILEGLMLIGVVEKRERGgEYVYK 245
                                       6899**************************99955588997 PP

>> DUF4288  Domain of unknown function (DUF4288)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   4.7e-05      0.17      35      80 ..       7      53 ..       4      62 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.7e-05
                           DUF4288 35 eeAyekaeklgkeeeepyknadgetvtwellavldvfel.ydelddg 80
                                      +e+++kae l ke ++ +   +    +w++ +++dv ++ y+ ++++
  gi|242398099|ref|YP_002993523.1|  7 REVVKKAETLHKEFQKFFLELYSLSSNWSFEELRDVLSSlYSVIEKK 53
                                      6899********************************99878777764 PP

>> Cucumo_2B  Cucumovirus protein 2B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   5.1e-05      0.18      33      68 ..     100     135 ..      76     141 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.1e-05
                         Cucumo_2B  33 hkspserarsnlrlfrflpfyqvdgseltgscrhvn 68 
                                       + s ser+r n  l r+l fy++    +t s +++n
  gi|242398099|ref|YP_002993523.1| 100 KISFSERSRVNASLQRLLQFYRIYDYSVTQSIQKLN 135
                                       6689*******************9999999999887 PP

>> HLH  Helix-loop-helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.23   8.2e+02      17      28 ..      33      44 ..      32      65 .. 0.74
   2 ?    8.4   0.1   0.00055         2      28      46 ..     121     169 ..     106     172 .. 0.62

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.23
                                      HHHHHHHHHCST CS
                               HLH 17 NsaleeLrellP 28
                                      N ++eeLr+ l 
  gi|242398099|ref|YP_002993523.1| 33 NWSFEELRDVLS 44
                                      55899***9987 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00055
                                       T...........................CSTTSS...-STHHHHHHHHH CS
                               HLH  28 P...........................slppsk...KlsKaeiLekAv 46 
                                                                   +lpp     K+ K+eiLek+v
  gi|242398099|ref|YP_002993523.1| 121 RiydysvtqsiqklngeleglifiseerKLPPTNilnKMQKIEILEKTV 169
                                       3455555555555555555777777666444444566***********9 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 ?    9.7   0.2   0.00035       1.2       9      84 ..       5      81 ..       3      92 .. 0.77
   2 ?    2.3   0.1      0.07   2.5e+02       7      35 ..     106     144 ..     103     199 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00035
                      Syntaxin-6_N  9 eVqkslnkaeslyrrwerlledtss.stseeldetrteLrkalrsiewdledLeetvriveknpskfkidekelsrr 84
                                      ++++ ++kae+l++++++   +  s s++++++e+r+ L + ++ ie++ +   e v++++    +f++ ++el++ 
  gi|242398099|ref|YP_002993523.1|  5 KIREVVKKAETLHKEFQKFFLELYSlSSNWSFEELRDVLSSLYSVIEKKFDTASEIVSMASLVGGRFEVFARELQKN 81
                                      56677777777777776444443444789**********************99999999988888888888888765 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.07
                      Syntaxin-6_N   7 keeVqkslnkaeslyrrwerlledtsss..........t 35 
                                       ++ V+ sl+++ + yr +    ++++++           
  gi|242398099|ref|YP_002993523.1| 106 RSRVNASLQRLLQFYRIYDYSVTQSIQKlngeleglifI 144
                                       678999999999999999643333333322334444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       975  (0.0543812); expected 358.6 (0.02)
Passed bias filter:                      652  (0.0363657); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1763.26
//
Query:       gi|242398100|ref|YP_002993524.1|  [L=463]
Description: RNA-binding protein FAU-1 [Thermococcus sibiricus MM 739]
Scores for complete 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-15   56.1   5.5    2.2e-14   53.4   3.0    2.6  2  DUF402     Protein of unknown function (DUF402)
    1.5e-11   44.2   0.0    2.4e-11   43.6   0.0    1.3  1  RNase_E_G  Ribonuclease E/G family


Domain annotation for each model (and alignments):
>> DUF402  Protein of unknown function (DUF402)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.023     2e+02      23      35 ..      96     108 ..      73     128 .. 0.75
   2 !   53.4   3.0   2.5e-18   2.2e-14       2      68 .]     369     435 ..     368     435 .. 0.95

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.023
                                       TEEEEEEEEEES- CS
                            DUF402  23 grlqglYvDiatp 35 
                                        +++++YvDi + 
  gi|242398100|ref|YP_002993524.1|  96 RDDRYVYVDIGSA 108
                                       3789******985 PP

  == domain 2  score: 53.4 bits;  conditional E-value: 2.5e-18
                                       -EEEEE-TT-SEEEEEEEETTTEEEEEEEEEES--EE..E.EEE-EEEEEEESEEE......-HHHH CS
                            DUF402   2 lelwllplglwynvfhfldgdgrlqglYvDiatppevgegawktiDlyLDlvvspdgevevlDedEL 68 
                                       ++++ + +g+w+  + ++d++g+l+g Y +i+tp ev++++ ++iDl++D+v +pdg+ e++D +EL
  gi|242398100|ref|YP_002993524.1| 369 YAITEIEEGKWWFKHSYYDKEGNLKGEYYNICTPVEVYPDKARYIDLEVDIVKWPDGNKEIIDKEEL 435
                                       67777889*****************************9999*************************8 PP

>> RNase_E_G  Ribonuclease E/G family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.6   0.0   2.6e-15   2.4e-11       1     109 [.     144     255 ..     144     295 .. 0.87

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 2.6e-15
                         RNase_E_G   1 slaGrylVllp....egkkvgvSkkiedeeererlkelleelkpeevGlIvRtaaegaseeelekdleelkkkweei 73 
                                       +++G y+Vl+p    ++k+v++S+ki+d++ererl+ l  ++   + G++ Rtaa+ ++ + l+++l +l+k  ++i
  gi|242398100|ref|YP_002993524.1| 144 TIPGDYAVLIPkpigTQKHVKISRKIRDQNERERLRILGLSVDLGDWGVLWRTAAAYKDWNLLKDELIKLSKIAQKI 220
                                       699********98855566************************99******************************** PP

                         RNase_E_G  74 lekakkrkapsllyeeedlllrvlrdllnedieeiv 109
                                       ++  k  +ap+ + e +d+++       ++++++i 
  gi|242398100|ref|YP_002993524.1| 221 KDIDK-YSAPAQIVEGRDVYEVEFGGATKSKLDDIR 255
                                       99887.779999999999998887777777777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (463 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 2964.79
//
Query:       gi|242398101|ref|YP_002993525.1|  [L=228]
Description: DNA repair and recombination protein radB [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-39  135.2   0.1    3.5e-39  134.6   0.1    1.2  1  Rad51     Rad51
    5.3e-13   48.9   0.6    7.3e-13   48.4   0.6    1.2  1  ATPase    KaiC
    1.3e-09   37.9   0.1    1.1e-08   34.9   0.1    2.0  1  AAA_25    AAA domain
    1.4e-09   37.8   0.0    1.9e-09   37.4   0.0    1.2  1  RecA      recA bacterial DNA recombination protein
    3.2e-08   33.5   0.1    4.5e-08   33.0   0.1    1.2  1  AAA_24    AAA domain
     0.0012   19.4   0.1     0.0028   18.2   0.1    1.7  2  AAA_18    AAA domain
     0.0078   15.6   2.3        0.5    9.7   0.2    2.1  2  DnaB_C    DnaB-like helicase C terminal domain
  ------ inclusion threshold ------
      0.027   14.0   0.4       0.15   11.6   0.4    1.9  1  CobU      Cobinamide kinase / cobinamide phosphate guanyltran
      0.054   13.6   0.4        4.9    7.4   0.0    2.3  2  DUF1296   Protein of unknown function (DUF1296)
       0.26   11.7   1.4       0.59   10.5   1.4    1.6  1  AAA       ATPase family associated with various cellular acti


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 !  134.6   0.1   1.9e-42   3.5e-39      19     254 ..       2     217 ..       1     218 [. 0.93

  Alignments for each domain:
  == domain 1  score: 134.6 bits;  conditional E-value: 1.9e-42
                                       E--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEEEESSS---GGGGHHHHHHT CS
                             Rad51  19 lttGskklDelLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgGgegkavyidtegtfrperlveiaery 95 
                                       lttGsk+lD+lLgGGi+ g +t ++G f +Gkt l++++ +           egk++yidteg+f perl ++ e  
  gi|242398101|ref|YP_002993525.1|   2 LTTGSKNLDALLGGGIDKGILTQVYGPFATGKTTLAMQIGLL---------NEGKVAYIDTEGGFSPERLAKMVESR 69 
                                       8***********************************999986.........489*********************** PP

                                       T--HHHHGGGEEEEE--STTHHHHHHHHTHHHHHHS-EEEEEEETTTGGGCH-------THHHHHHHHHHHHHHHHH CS
                             Rad51  96 kldkeevlenvayaRaytiehqeellqqaaallaedkfallivDsvtalyRtdfsgrgelakRqqklgkllrtLrkl 172
                                       ++d++++l++  +  a+   +q++ ++++ + ++++kf++++vDs+t++yR++     + ++  + lgk l+ L  l
  gi|242398101|ref|YP_002993525.1|  70 GMDSNSTLQKFLIFEAFDFKEQKKTISNLKK-IVNEKFSMIVVDSITNHYRVEE----KKSSMTTDLGKQLQVLLWL 141
                                       ***************************9976.56789***************94....44677899*********** PP

                                       HHHH--EEEEEEE-------.------------HHHHHHHH-SEEEEEEE-STTEEEEEEES-SSS-S-E.EEEEEE CS
                             Rad51 173 adefevavvitnqvvaqvdgqaalfsadpkkPigGlvlahasttRlalrkgkgeeRivkvvdsPnlpele.avfaig 248
                                       a ++++av++tnqv  +  +       ++ kP   ++++ + +  l l k +   Ri+ +      pe   + f i+
  gi|242398101|ref|YP_002993525.1| 142 ARKYNLAVIVTNQVYFDSKQ-------NALKPLAEHIMGYKCKDILRLEKLRPGLRIAVLERHRFKPEGGiVHFEIT 211
                                       **************977666.......999**************************************8735799** PP

                                       TTEEE- CS
                             Rad51 249 eeGied 254
                                       ++Gied
  gi|242398101|ref|YP_002993525.1| 212 DKGIED 217
                                       ****98 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.4   0.6   4.1e-16   7.3e-13       2     225 ..       3     216 ..       2     222 .. 0.76

  Alignments for each domain:
  == domain 1  score: 48.4 bits;  conditional E-value: 4.1e-16
                            ATPase   2 ktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtvee..paedlrenakslGwdlek 76 
                                        tg + lD +l gGi +g  + ++G   tGKt++a+q    g+ + + ++ ++ +e   ++e l + ++s G+d + 
  gi|242398101|ref|YP_002993525.1|   3 TTGSKNLDALLGGGIDKGILTQVYGPFATGKTTLAMQI---GLLN-EGKVAYIDTEGgfSPERLAKMVESRGMDSNS 75 
                                       6999********************************95...6666.678*******73367**************** PP

                            ATPase  77 leeegklaiidasesaeesaeekdkedleelieelaeaikeikakrvviDsitgl..ayeekeav...aReilrqlv 148
                                         ++  + i +a+  +e+          ++ i++l+++++e k + +v+Dsit++   +e+k+++   + ++l+ l+
  gi|242398101|ref|YP_002993525.1|  76 TLQK--FLIFEAFDFKEQ----------KKTISNLKKIVNE-KFSMIVVDSITNHyrVEEKKSSMttdLGKQLQVLL 139
                                       **99..*******99876..........6678888888887.6899********97434444444233455565555 PP

                            ATPase 149 rvlkklgvTailvsekssseeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeIteegik 225
                                          +k+++  i ++++  +++++    ++e+i+    +  l++++ +    + ++   + k +  ++ feIt++gi+
  gi|242398101|ref|YP_002993525.1| 140 WLARKYNLAVIVTNQVYFDSKQNALKPLAEHIMGYKCKDILRLEKLRPGLRIAVLERHRFKPEGGIVHFEITDKGIE 216
                                       55599999999999988866666666666656533333333333445555566666666777788889999999997 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.1     6e-12   1.1e-08      22     188 ..       9     154 ..       3     159 .. 0.84

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 6e-12
                            AAA_25  22 rrwlvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgealr 98 
                                       ++ l++g + +g l+ ++G+ +tGKttla++++l                gkV y+++E++    ++Rl+++ e + 
  gi|242398101|ref|YP_002993525.1|   9 LDALLGGGIDKGILTQVYGPFATGKTTLAMQIGLL-------------NEGKVAYIDTEGGF--SPERLAKMVESRG 70 
                                       677899999**********************9862.............3589**********..9********9987 PP

                            AAA_25  99 ddarllvldlagveslpLfakdrggtlltadvdaleaaieevegvrlvviDplsralggdensnsdv...galveal 172
                                        d++ ++ +        L+++ ++ +  +  + +l + ++e +   ++v+D+++  ++ +e+++s +   g+ ++ l
  gi|242398101|ref|YP_002993525.1|  71 MDSNSTLQK-------FLIFEAFDFKEQKKTISNLKKIVNE-K-FSMIVVDSITNHYRVEEKKSSMTtdlGKQLQVL 138
                                       677765555.......3666777777777889999999999.5.***************999887753337777778 PP

                            AAA_25 173 eriarrtgaavllvhH 188
                                        ++ar+++ av+++ +
  gi|242398101|ref|YP_002993525.1| 139 LWLARKYNLAVIVTNQ 154
                                       889*********9876 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   0.0     1e-12   1.9e-09      34     171 ..       2     144 ..       1     159 [. 0.75

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 1e-12
                                       E--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEESS----HHHHHHT....T--GG CS
                              RecA  34 issGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaqkkggvaafidaehaldpkyakkl....Gvdid 106
                                       +++Gs  ld  lG GG+ kG ++++yGp ++Gkttla+++      + g +a+id+e  + p+  +k+    G+d +
  gi|242398101|ref|YP_002993525.1|   2 LTTGSKNLDALLG-GGIDKGILTQVYGPFATGKTTLAMQIG---LLNEGKVAYIDTEGGFSPERLAKMvesrGMDSN 74 
                                       689**********.***********************9974...3467889**********9865443344499865 PP

                                       G.....-EEE--SSHHHHHHHHHH.HHTTT--SEEEEE-TTT---STT-----------HHHHHHHHHHHH CS
                              RecA 107 e.....llvsqpdtGeqaleiada.lvrsgaidlivvdsvaalvpkaeieGemgdskvglqarlmsqalrk 171
                                       +     l+    d  eq   i +   +      +ivvds++      e +  m+ + +g+q +++    rk
  gi|242398101|ref|YP_002993525.1|  75 StlqkfLIFEAFDFKEQKKTISNLkKIVNEKFSMIVVDSITNHYRVEEKKSSMT-TDLGKQLQVLLWLARK 144
                                       422233455678999*9999987424667889********99887777777775.4566666665555555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.1   2.5e-11   4.5e-08       5      79 ..      23     119 ..      19     133 .. 0.81

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 2.5e-11
                            AAA_24   5 iliyGpsgiGKTtlakel....gpkplfidtekGlksldadkfpdie.................swedfldevvel. 59 
                                        ++yGp  +GKTtla ++    + k+++idte+G+     +k+++ +                  +++ +++   + 
  gi|242398101|ref|YP_002993525.1|  23 TQVYGPFATGKTTLAMQIgllnEGKVAYIDTEGGFSPERLAKMVESRgmdsnstlqkflifeafDFKEQKKT---Is 96 
                                       579********************************8888888887779998896666666654444444444...15 PP

                            AAA_24  60 ...aaeladyktlviDtidelee 79 
                                          +  +++++ +v+D+i+  ++
  gi|242398101|ref|YP_002993525.1|  97 nlkKIVNEKFSMIVVDSITNHYR 119
                                       557778999**********9887 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   1.6e-06    0.0028       3      93 ..      25     125 ..      24     152 .. 0.78
   2 ?   -1.4   0.0       1.8   3.2e+03      17      34 ..     166     182 ..     124     199 .. 0.54

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.6e-06
                            AAA_18   3 ltGtpGvGKttlakeLskrlgf.............gvnlrdvakenglllevdpealdeskrldedkldklldalee 66 
                                       + G+ ++GKttla  +  ++                ++l +++  +g+    + +++  ++ +d + ++k +++l++
  gi|242398101|ref|YP_002993525.1|  25 VYGPFATGKTTLAMQIGLLN-EgkvayidteggfsPERLAKMVESRGMDSNSTLQKFLIFEAFDFKEQKKTISNLKK 100
                                       68*************94443.122455788875565666666666666666666699******************** PP

                            AAA_18  67 nssaleegknlvidghlaeleseaakd 93 
                                       + +  e+ + +v+d++ ++++ e+ k 
  gi|242398101|ref|YP_002993525.1| 101 IVN--EKFSMIVVDSITNHYRVEEKKS 125
                                       *75..9**************9998775 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.8
                            AAA_18  17 eLskrlgfgvnlrdvake 34 
                                        L+++  +g++++d+++ 
  gi|242398101|ref|YP_002993525.1| 166 PLAEHI-MGYKCKDILRL 182
                                       233331.25555555444 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.2   0.00028       0.5       2      42 ..       2      43 ..       2     101 .. 0.67
   2 !    6.1   0.6    0.0034       6.1     123     178 ..      97     155 ..      73     169 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00028
                                      BXSSTHHHHHHCT.SBXTTXEEEEEEXTTSSHHHHHHHHHHH CS
                                      xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C  2 lstgfkdLDklts.GlqkgdliiiAarpsmGktalalniaen 42
                                      l+tg k+LD+l++ G+ kg l+ + +  ++Gkt+la++i   
  gi|242398101|ref|YP_002993525.1|  2 LTTGSKNLDALLGgGIDKGILTQVYGPFATGKTTLAMQIGLL 43
                                      57999****99862799*********************9743 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0034
                                       HHHHH..TTEEEEEEEEGGGTBTS.CSSSCCCHHHHHHHHHHHHHHHHCTSXEEEEEEX CS
                                       xxxxx..xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C 123 rlkke..kglgliviDyLqlmegs.eekenreqevseisrsLkalakelnvpvialsqL 178
                                       +lkk   ++ ++iv+D +       e+k++ ++++ +  + L  la+  n+ vi+  q+
  gi|242398101|ref|YP_002993525.1|  97 NLKKIvnEKFSMIVVDSITNHYRVeEKKSSMTTDLGKQLQVLLWLARKYNLAVIVTNQV 155
                                       3333344899*******9887755244667788888888888899**********9997 PP

>> CobU  Cobinamide kinase / cobinamide phosphate guanyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.4   8.4e-05      0.15       3     127 ..      25     156 ..      23     164 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.4e-05
                              CobU   3 vtGgarSGKSefAeklaeeskekvvYiATaealDee.maeRiarHrerR...paeWetvee......pldlaealke 69 
                                       v G+   GK ++A ++   +++kv Yi T   +  e +a+ ++    +     +++  +e+      ++ ++++ k 
  gi|242398101|ref|YP_002993525.1|  25 VYGPFATGKTTLAMQIGLLNEGKVAYIDTEGGFSPErLAKMVESRGMDSnstLQKFLIFEAfdfkeqKKTISNLKKI 101
                                       8899999********9999999*****99999965513333333222222223444444442222214444443333 PP

                              CobU  70 eek.kevvLvDcltlwltnllleeeaekveekleeeveellealkelkatvvlVsnEvg 127
                                        ++  ++++vD++t         e++++++++l ++++ ll  +++ +   v+V+n v 
  gi|242398101|ref|YP_002993525.1| 102 VNEkFSMIVVDSITNHYRVE---EKKSSMTTDLGKQLQVLLWLARKYNL-AVIVTNQVY 156
                                       33346899999998765443...33344789999999999888888765.678999986 PP

>> DUF1296  Protein of unknown function (DUF1296)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0    0.0027       4.9      22      48 ..      60      86 ..      52      90 .. 0.82
   2 ?    4.2   0.3     0.027        49       4      18 ..      90     104 ..      88     110 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0027
                           DUF1296 22 eeIyamLkecnmDpneavqkLLsqDtf 48
                                      e   +m +  +mD n + qk L  ++f
  gi|242398101|ref|YP_002993525.1| 60 ERLAKMVESRGMDSNSTLQKFLIFEAF 86
                                      55667888889***********98887 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.027
                           DUF1296   4 svrkviqsikEivgk 18 
                                       + +k+i ++k iv++
  gi|242398101|ref|YP_002993525.1|  90 EQKKTISNLKKIVNE 104
                                       679**********95 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   1.4   0.00033      0.59       3      98 ..      25     144 ..      23     171 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00033
                                       EESSTTSSHHHHHHHHH..HHHTHEEEEEETTTCSSS...........................STTHHHHHHHHHH CS
                               AAA   3 lyGppGtGKTllakava..kelgvefleisgsellsk...........................yvgesekkirelf 50 
                                       +yGp  tGKT+la ++   +e +v ++ ++g                                  ++e++k i++l 
  gi|242398101|ref|YP_002993525.1|  25 VYGPFATGKTTLAMQIGllNEGKVAYIDTEGGFS--PerlakmvesrgmdsnstlqkflifeafDFKEQKKTISNLK 99 
                                       79***********998611443333332222111..11122233333333334466676666655556666666666 PP

                                       HHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTT CS
                               AAA  51 keakekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkk 98 
                                       k + ek   s +++D i +  + + +++s+ ++++ +qL   l   +k
  gi|242398101|ref|YP_002993525.1| 100 KIVNEK--FSMIVVDSITNHYRVE-EKKSSMTTDLGKQLQVLLWLARK 144
                                       555554..4888888888887777.56666666666666555554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       849  (0.0473534); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 1412.89
//
Query:       gi|242398102|ref|YP_002993526.1|  [L=195]
Description: metallo-beta-lactamase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.6e-22   78.1   0.1    8.2e-22   77.8   0.1    1.1  1  Lactamase_B_3  Beta-lactamase superfamily domain
    1.8e-18   66.8   0.0    2.6e-18   66.3   0.0    1.2  1  Lactamase_B_2  Beta-lactamase superfamily domain
    1.1e-11   45.2   0.1    1.3e-11   44.9   0.1    1.1  1  Lactamase_B    Metallo-beta-lactamase superfamily


Domain annotation for each model (and alignments):
>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.8   0.1   1.4e-25   8.2e-22      18     163 .]       2     159 ..       1     159 [. 0.82

  Alignments for each domain:
  == domain 1  score: 77.8 bits;  conditional E-value: 1.4e-25
                     Lactamase_B_3  18 rilvDPfkanlgyeppaeeaDlvlisqaledHahletlkql....................aenvkvleegeslevg 74 
                                       +il+DP+++ ++ +   + +D +l++++++dH+  ++l +                      ++vk +e+ge++e++
  gi|242398102|ref|YP_002993526.1|   2 KILIDPYEY-VNDD-AIDGIDYILVTHEHTDHYGKTPLLARlrdatvigpktvylmaindgVTKVKEIEGGEEIELE 76 
                                       79*****95.3322.3389**************9888766647777777777777777777777777777999**96 PP

                     Lactamase_B_3  75 .gleiravatshdavggsergenngflleqdgltiyhlGhlahelsseelkelgrvDvvltPvggpltlgqeealel 150
                                        ++++ra+  +h ++     +   g+++++++ +i+h+G++++ + +++l   g++D++++P+ g  t + +ea+++
  gi|242398102|ref|YP_002993526.1|  77 nNVKVRAIFVEH-PS----SQYPLGYIISDGKRRIFHPGDTYYSPIFKNL--RGKIDIFFVPISGRSTANIREAANI 146
                                       59******9999.22....233478******************4444444..579********************** PP

                     Lactamase_B_3 151 akrLkpklvlPmh 163
                                       ++ ++pk+ +Pmh
  gi|242398102|ref|YP_002993526.1| 147 IETMRPKITIPMH 159
                                       ************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 !   66.3   0.0   4.3e-22   2.6e-18      26     201 .]      14     160 ..       2     160 .. 0.88

  Alignments for each domain:
  == domain 1  score: 66.3 bits;  conditional E-value: 4.3e-22
                                       --..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTTTTEEEEEE-TTSEEEECSTT CS
                     Lactamase_B_2  26 delppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleeepavnvheldwgesfelgdgg 102
                                       d ++ id +l+th+H DH+   + l++lr+  +++++pk v+    + +          ++v+e++ ge++el+  +
  gi|242398102|ref|YP_002993526.1|  14 DAIDGIDYILVTHEHTDHYGKTPLLARLRD--ATVIGPKTVYLMAINDG---------VTKVKEIEGGEEIELE-NN 78 
                                       56789**************99999999876..79999999988777774.........46899**********8.58 PP

                                       EEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---HHHHHHHCT.-SEEEEE-S-SSTTHHHHHHT- CS
                     Lactamase_B_2 103 leitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyipeeigerlgg.adllllditayeddemirhmgH 178
                                       ++++a+ ++h s +         lG++i +g++r+++ gDt y p  i + l+g +d+ +++i          + ++
  gi|242398102|ref|YP_002993526.1|  79 VKVRAIFVEHPSSQ-------YPLGYIISDGKRRIFHPGDTYYSP--IFKNLRGkIDIFFVPIS---------GRST 137
                                       9*************.......9********************999..55555555*******99.........8899 PP

                                       --STSHHHHCTTSSSSEEEEESB CS
                     Lactamase_B_2 179 ltpeeaveaaadlgakrlvliHi 201
                                       ++++ea+ +++ +++k+++++H+
  gi|242398102|ref|YP_002993526.1| 138 ANIREAANIIETMRPKITIPMHY 160
                                       **********************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 !   44.9   0.1   2.2e-15   1.3e-11      38     195 ..      12     157 ..       4     159 .. 0.86

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 2.2e-15
                                       HTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTE CS
                       Lactamase_B  38 lglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmeeaddaasrkglllagvsadkpdvdeeeld 114
                                       ++  ++ +d++++TH H+DH+G  + l++ +d+ v+  + ++ + +++++               ++  +  ee++ 
  gi|242398102|ref|YP_002993526.1|  12 NDDAIDGIDYILVTHEHTDHYGKTPLLARLRDATVIGPKTVYLMAINDGV-------------TKVKEIEGGEEIEL 75 
                                       5678899*******************************************.............7788899******* PP

                                       ECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCCCCC.TTCEEE-SHCHHHHHH.HHHHHHHHHCH CS
                       Lactamase_B 115 gnaggrralyvtggpghghghgvveygggkvlftGDallagetgridltlrgaevrdpsdaekyl.dsllklaglka 190
                                       +n   +ra  v +     ++++++++g +++   GD+ +++    ++ ++++++v+  +  +  + +++  ++++++
  gi|242398102|ref|YP_002993526.1|  76 ENNVKVRAIFVEHPSSQYPLGYIISDGKRRIFHPGDTYYSPIFKNLRGKIDIFFVPISGRSTANIrEAANIIETMRP 152
                                       ***************************************99999999977777777666555554044555555555 PP

                                       SEEEE CS
                       Lactamase_B 191 evlvp 195
                                       ++ +p
  gi|242398102|ref|YP_002993526.1| 153 KITIP 157
                                       55555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 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:                        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: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1369.72
//
Query:       gi|242398103|ref|YP_002993527.1|  [L=48]
Description: hypothetical protein TSIB_0110 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       221  (0.0123264); expected 358.6 (0.02)
Passed bias filter:                      200  (0.0111551); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 345.10
//
Query:       gi|242398104|ref|YP_002993528.1|  [L=64]
Description: hypothetical protein TSIB_0111 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.23s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 499.29
//
Query:       gi|242398105|ref|YP_002993529.1|  [L=188]
Description: hypothetical protein TSIB_0112 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-59  199.3   9.7    4.9e-59  199.2   9.7    1.0  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 !  199.2   9.7   2.7e-63   4.9e-59       1     170 []      10     187 ..      10     187 .. 0.96

  Alignments for each domain:
  == domain 1  score: 199.2 bits;  conditional E-value: 2.7e-63
                           DUF1614   1 llgslinipvaelkskeelve...vkvlgisykvpvleeeekktvvavNvGGaviPlllslylllrlavs.....ll 69 
                                       l+gs+inip++e+ks  ++v+   v+++gi+y+vp+++  e+ktvv++NvGGa++Pl ++ly ++rl v      ++
  gi|242398105|ref|YP_002993529.1|  10 LIGSFINIPIKEIKSYGPVVRmtkVSFFGITYPVPYVDWGEQKTVVSINVGGALVPLSVVLYEVVRLLVLdetflFT 86 
                                       79*************775533357******************************************98778899899 PP

                           DUF1614  70 aallavlivaavvyllarpvpgvGivvpllipplvaalaalllaeeeaaavaYisgvlGtLiGadllnlkkieklga 146
                                       ++++a+li ++v+++++rpv+g+Gi++p++ipplvaa++alll  ++++ +aY+sg++G+LiGadlln++k+++lga
  gi|242398105|ref|YP_002993529.1|  87 RMATAILISTIVSKAFSRPVRGLGIAIPTFIPPLVAAILALLLGGDNRPLIAYASGTMGVLIGADLLNWNKLKELGA 163
                                       ***************************************************************************** PP

                           DUF1614 147 pvvsIGGaGtFdGifltgilavll 170
                                       p+vsIGGaGtFdGifl+gi+avll
  gi|242398105|ref|YP_002993529.1| 164 PMVSIGGAGTFDGIFLAGIIAVLL 187
                                       **********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1348.88
//
Query:       gi|242398106|ref|YP_002993530.1|  [L=286]
Description: ribose-phosphate pyrophosphokinase [Thermococcus sibiricus MM 739]
Scores for complete 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-26   90.6   0.0    1.7e-22   79.5   0.0    2.2  2  Pribosyltran_N  N-terminal domain of ribose phosphate pyropho
    1.1e-18   67.2   0.5    2.6e-17   62.8   0.3    2.3  2  Pribosyltran    Phosphoribosyl transferase domain
    2.3e-15   57.1   0.3    3.4e-15   56.6   0.3    1.3  1  Pribosyl_synth  Phosphoribosyl synthetase-associated domain
    4.2e-07   29.6   0.1    8.6e-07   28.6   0.1    1.5  1  UPRTase         Uracil phosphoribosyltransferase
  ------ inclusion threshold ------
      0.011   15.2   0.0      0.017   14.6   0.0    1.3  1  PRTase_2        Phosphoribosyl transferase
      0.073   13.3   0.2        2.9    8.2   0.0    2.8  3  EIIA-man        PTS system fructose IIA component


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 !   79.5   0.0   5.7e-26   1.7e-22       2     112 ..       4     116 ..       3     118 .. 0.94
   2 !    9.1   0.0   0.00041       1.2      11      57 ..     172     219 ..     162     253 .. 0.87

  Alignments for each domain:
  == domain 1  score: 79.5 bits;  conditional E-value: 5.7e-26
                    Pribosyltran_N   2 kifagssskeLaekiakrl...gvelgkakvsrfadgEikveieesvrgkdvfiiqslskpvndnlmelllmidalr 75 
                                       +i+ gs + ++ae+i++++   +  l++++v++f+dgE +v++     gk+v ++qs+ +p n++l+elll+ dalr
  gi|242398106|ref|YP_002993530.1|   4 RIVLGSGASHMAEEIKNKVekfDKLLIESEVKTFPDGEKYVRVLG--DGKEVLVVQSMFRPQNEHLVELLLLGDALR 78 
                                       6899999*********99977788899***************986..6***************************** PP

                    Pribosyltran_N  76 rasakritaViPylgysrqdrk.ksrepisaklvaklL 112
                                       ++  k+  aV+Pyl+ysrqdr  k+ epis + ++k +
  gi|242398106|ref|YP_002993530.1|  79 EKGFKHLKAVVPYLAYSRQDRVtKEGEPISVRAIMKAI 116
                                       **********************888*******999876 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00041
                    Pribosyltran_N  11 eLaekiakrlgvelgkakvsrfadgEikveiee.svrgkdvfiiqsls 57 
                                       e a+ +a+ lg+e    + +r +  Ei+++  e +v +k+v i+ ++ 
  gi|242398106|ref|YP_002993530.1| 172 ERAKTVANILGLEFSYFEKKRISPTEIQMRPVEvDVEEKNVLIVDDII 219
                                       6699**************************8887**********9986 PP

>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.034     1e+02     106     141 ..      73     110 ..      70     122 .. 0.77
   2 !   62.8   0.3   8.6e-21   2.6e-17      16     124 ..     147     246 ..     133     283 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.034
                                       HHHHHHCC-BSEEEEEEEE..E-HHHHHHHHHH-TTS. CS
                      Pribosyltran 106 alelLkekgpeevriavlv..dkpateeevdknakrvf 141
                                         ++L+ekg + ++++v++  + ++++  ++ ++++v 
  gi|242398106|ref|YP_002993530.1|  73 LGDALREKGFKHLKAVVPYlaYSRQDRVTKEGEPISVR 110
                                       5789***************8877777777777777765 PP

  == domain 2  score: 62.8 bits;  conditional E-value: 8.6e-21
                                       EETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........EE----TTSEEEE CS
                      Pribosyltran  16 arlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdesrlledpagkkVli 92 
                                       a+++a+++++ +  + +v++++rg++ +ak +a+ L++++ y +k++ +p   +  +         + d++ k Vli
  gi|242398106|ref|YP_002993530.1| 147 AKAIANYFKD-KLGEGLVLAPDRGALERAKTVANILGLEFSYFEKKRISPTEIQMRP--------VEVDVEEKNVLI 214
                                       5666666666.66679***************************99876665555554........7889******** PP

                                       E-SEESSSHHHHHHHHHHHCC-BSEEEEEEEE CS
                      Pribosyltran  93 VDDildtGgTllaalelLkekgpeevriavlv 124
                                       VDDi++tGgT+++a+++Lk  g+ +v +++ +
  gi|242398106|ref|YP_002993530.1| 215 VDDIISTGGTMIKAANILKGMGASKVFVVATH 246
                                       ************************77666555 PP

>> Pribosyl_synth  Phosphoribosyl synthetase-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.6   0.3   1.1e-18   3.4e-15      78     152 ..     204     277 ..     164     283 .. 0.90

  Alignments for each domain:
  == domain 1  score: 56.6 bits;  conditional E-value: 1.1e-18
                                       ES--TTSEEEEEEEEE-S-HHHHHHHHHHHHTT--EEEEEEEEE---TTHHHHHHHSS--EEEEESSS--HHHHH CS
                    Pribosyl_synth  78 vGdvgGriaiivddliddvesfvaaaevlkerGaykiyvlathGllssdaprlleesaidevvvtntipheiqkl 152
                                         dv+ +  +ivdd+i    ++++aa++lk  Ga k++v+athG++++ a +++ + a+de+ vtn+ip  + k+
  gi|242398106|ref|YP_002993530.1| 204 EVDVEEKNVLIVDDIISTGGTMIKAANILKGMGASKVFVVATHGVFAEGAIERVSK-AVDELAVTNSIPTPVSKI 277
                                       359**************************************************976.79**********998775 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.1   2.9e-10   8.6e-07     114     179 ..     202     267 ..     172     272 .. 0.82

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 2.9e-10
                           UPRTase 114 kLPkkiaertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvlaseegvkrlaeefpkvkvv 179
                                        +  +++e++vl++D +i+TGg++++a ++Lk  g+ +  ++    + +e +++r+++++ ++ v+
  gi|242398106|ref|YP_002993530.1| 202 PVEVDVEEKNVLIVDDIISTGGTMIKAANILKGMGASKVFVVATHGVFAEGAIERVSKAVDELAVT 267
                                       35667799*************************888777777777899**********99998875 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   5.7e-06     0.017     120     157 ..     208     245 ..     186     281 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.7e-06
                          PRTase_2 120 aakelvLvDDEistGktalnliralqeklprkryvvvs 157
                                       ++k++++vDD istG t+++ ++ l+    +k +vv++
  gi|242398106|ref|YP_002993530.1| 208 EEKNVLIVDDIISTGGTMIKAANILKGMGASKVFVVAT 245
                                       578999**************999998877777777665 PP

>> EIIA-man  PTS system fructose IIA component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.72   2.2e+03      15      54 ..      12      25 ..       4      55 .. 0.60
   2 ?    1.5   0.0      0.11   3.3e+02      51      77 ..     203     231 ..     184     237 .. 0.78
   3 ?    8.2   0.0   0.00096       2.9       2      24 ..     241     263 ..     240     276 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.72
                                      HHHHHCCHSSS-SCEEEEEC-TTS-CCCHHHHHHHHHCTS CS
                          EIIA-man 15 aelleelagedqekviavggtpdesigtlaekikeaieev 54
                                       ++                          ae+ik+++e++
  gi|242398106|ref|YP_002993530.1| 12 SHM--------------------------AEEIKNKVEKF 25
                                      333..........................33333333333 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.11
                                       HCTS--TTEEEEEESSCC..CHHHHHHHH CS
                          EIIA-man  51 ieevdsedevlvLvDlgg..atpfneaal 77 
                                       +e + +e++vl+  D+++  +t+ ++a++
  gi|242398106|ref|YP_002993530.1| 203 VEVDVEEKNVLIVDDIIStgGTMIKAANI 231
                                       56666899********8533788777765 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.00096
                                       EEEEESBCHHHHHHHHHHCCHSS CS
                          EIIA-man   2 ivivsHgelAeglaelleelage 24 
                                       +v+++Hg +Aeg+ e +++ + e
  gi|242398106|ref|YP_002993530.1| 241 FVVATHGVFAEGAIERVSKAVDE 263
                                       69*************99998877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.29s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1784.66
//
Query:       gi|242398107|ref|YP_002993531.1|  [L=170]
Description: magnesium-dependent phosphatase-1 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-10   40.0   0.1    5.2e-10   39.4   0.1    1.3  1  Acid_PPase       Acid Phosphatase
    4.7e-08   33.3   0.8    3.1e-05   24.1   0.0    2.6  3  HAD_2            Haloacid dehalogenase-like hydrolase
    1.1e-05   25.3   0.9    1.4e-05   24.9   0.9    1.1  1  NIF              NLI interacting factor-like phosphatase
    2.5e-05   24.8   0.7     0.0036   17.7   0.0    2.2  2  HAD              haloacid dehalogenase-like hydrolase
     0.0023   17.5   2.1      0.012   15.1   0.1    2.2  2  DUF2608          Protein of unknown function (DUF2608)
     0.0054   17.0   0.0       0.47   10.7   0.0    2.2  2  Hydrolase        haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
       0.11   12.5   0.0       0.18   11.8   0.0    1.3  1  DUF1804          Protein of unknown function (DUF1804)
       0.22   11.8   0.0       0.35   11.1   0.0    1.3  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma


Domain annotation for each model (and alignments):
>> Acid_PPase  Acid Phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.4   0.1   2.3e-13   5.2e-10       3     128 ..       1     141 [.       1     149 [. 0.80

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 2.3e-13
                                       -SEEEE-STTTSSSS-TTTSS-S-EEE-TTS.-EEETT--EE---TTHHHHHHHHHHTT--EEEEE--S-HHHHHHH CS
                        Acid_PPase   3 pklivFDLDyTLWpfevdtlvsaplkkeskksevvDrrgeelklypdveeileelkskevklavaSrtdepdlarel 79 
                                       ++l++FDLD+TLW+ +    + +p++ + ++  ++D+ g++lkl++ v e l++ k +   l +aS  +  +l r +
  gi|242398107|ref|YP_002993531.1|   1 MRLLIFDLDKTLWDHYDASQLVPPFRTHGTE--LIDALGNKLKLFDGVVEFLDWAK-ERFVLSIASW-NLEKLVRPI 73 
                                       6899**********999999*****998887..********************999.6677999997.556899*** PP

                                       HHHTT-G.......................GGESE.EEESS....S-HHHHHHHHHH.HH---GGGEE CS
                        Acid_PPase  80 Lkllein.............dakekekklldvfdd.veiyk....gsktkhfeklkk.ktgieyedml 128
                                       L+ ++i              +a+   ++l+++ ++  ei +     ++t h+ k+kk   +i++ +m+
  gi|242398107|ref|YP_002993531.1|  74 LEEFNIWhyfvfpkienhpdKADMIVRTLQELKNSgYEIEEviyiDDRTLHLDKIKKrIPDIRFIQMW 141
                                       ****9998888888877776555555556665555556555444468888888888844678888876 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.2    0.0027       6.1       1      16 [.       4      19 ..       4      22 .. 0.87
   2 !   24.1   0.0   1.4e-08   3.1e-05      76     162 ..      38     122 ..      25     130 .. 0.86
   3 ?   -1.5   0.0         1   2.3e+03     138     155 ..     148     165 ..     125     166 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0027
                             HAD_2  1 iiFDlDgTlldteeli 16
                                      +iFDlD Tl d  +++
  gi|242398107|ref|YP_002993531.1|  4 LIFDLDKTLWDHYDAS 19
                                      69*********98775 PP

  == domain 2  score: 24.1 bits;  conditional E-value: 1.4e-08
                             HAD_2  76 kevkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekkKPdpeviekalekl...k 149
                                       +++k++dgv e+L++  ++++ l i++ + ++ v+  le+++i +yF +  ++++  k    +++i ++l++l   +
  gi|242398107|ref|YP_002993531.1|  38 NKLKLFDGVVEFLDWA-KERFVLSIASWNLEKLVRPILEEFNIWHYFVFPKIENHPDK----ADMIVRTLQELknsG 109
                                       479************8.889***************************88766665433....699999999997778 PP

                             HAD_2 150 lkkeeviyvGDsp 162
                                        + eeviy+ D +
  gi|242398107|ref|YP_002993531.1| 110 YEIEEVIYIDDRT 122
                                       999********86 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1
                             HAD_2 138 peviekaleklklkkeev 155
                                        e+ e ++++l++kk+e+
  gi|242398107|ref|YP_002993531.1| 148 EELREYLMKELEVKKDEA 165
                                       556667788888888876 PP

>> NIF  NLI interacting factor-like phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.9   6.2e-09   1.4e-05       2     149 ..       3     158 ..       2     165 .. 0.71

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 6.2e-09
                               NIF   2 tLVLDLDetLv.hskleksk...klkvegek....vevsvlkRpgldefLkelsklyevvifTasseeyaeavidil 70 
                                       +L++DLD+tL+ h  ++  +    ++++g++    ++  +++  g+ efL+ + + + + i + + e+ ++++++++
  gi|242398107|ref|YP_002993531.1|   3 LLIFDLDKTLWdHYDAS--QlvpPFRTHGTElidaLGNKLKLFDGVVEFLDWAKERFVLSIASWNLEKLVRPILEEF 77 
                                       79*********655542..223444444333344478889999********************************** PP

                               NIF  71 dpekkllshrlyrescvkkkgeyvKdLsllgr...dlsrvvivDdspdsfelqpengipiksffsdkkD.neLlkll 143
                                       +  + ++     +++   k  + v+ L+ l++   + ++v+ +Dd++    +  ++ ip  +f++ + D +++++l 
  gi|242398107|ref|YP_002993531.1|  78 NIWH-YFVFPKIENHP-DKADMIVRTLQELKNsgyEIEEVIYIDDRTLHLDK-IKKRIPDIRFIQMWVDvKNFEELR 151
                                       9998.57777777777.346789999999955556***********998876.444455555655333313444566 PP

                               NIF 144 pllk.el 149
                                       ++l  el
  gi|242398107|ref|YP_002993531.1| 152 EYLMkEL 158
                                       6655344 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.5   0.7    0.0091        20       2      12 ..       5      15 ..       4      31 .. 0.84
   2 !   17.7   0.0   1.6e-06    0.0036      73     177 ..      36     118 ..      16     122 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0091
                               HAD  2 lfDfDgTLldg 12
                                      +fD+D+TL+d 
  gi|242398107|ref|YP_002993531.1|  5 IFDLDKTLWDH 15
                                      8********96 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 1.6e-06
                               HAD  73 lerfvaevirpklldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelglegkpv 149
                                       l+  +      kl+  g++e+l+++ ++ + + + S +l+ lv+p+l+e++    + +      ++    ++e++p 
  gi|242398107|ref|YP_002993531.1|  36 LGNKL------KLF-DGVVEFLDWA-KERFVLSIASWNLEKLVRPILEEFN----IWH------YFVFP-KIENHPD 93 
                                       33333......367.9*******66.666**********************....999......66655.6677776 PP

                               HAD 150 rgegkvaalrewlaaegegidleevvay 177
                                       + +  v+ l+e l+  g++i  eev+++
  gi|242398107|ref|YP_002993531.1|  94 KADMIVRTLQE-LKNSGYEI--EEVIYI 118
                                       66666666666.55555554..446665 PP

>> DUF2608  Protein of unknown function (DUF2608)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.2     0.045     1e+02      20      30 ..       3      13 ..       1      18 [. 0.87
   2 !   15.1   0.1   5.5e-06     0.012     172     200 ..     104     132 ..      89     157 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.045
                           DUF2608 20 LvvfDiDdtLl 30
                                      L++fD+D tL 
  gi|242398107|ref|YP_002993531.1|  3 LLIFDLDKTLW 13
                                      9********95 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 5.5e-06
                           DUF2608 172 lLdkigrepksviFiDDkkknlasveeal 200
                                        L+  g+e+++vi+iDD + +l+++++ +
  gi|242398107|ref|YP_002993531.1| 104 ELKNSGYEIEEVIYIDDRTLHLDKIKKRI 132
                                       3677899******************9876 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1     0.018        41       1      16 [.       1      16 [.       1      35 [. 0.85
   2 !   10.7   0.0   0.00021      0.47     115     199 ..      38     121 ..      30     123 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.018
                                      SSEEEEESBTTTBCHH CS
                                      xxxxxxxxxxxxxxxx RF
                         Hydrolase  1 iktvvfDkdGTLttge 16
                                      +++++fD+d TL++  
  gi|242398107|ref|YP_002993531.1|  1 MRLLIFDLDKTLWDHY 16
                                      6899*********876 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00021
                                       HTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTTGGGESEEEEHHCESSTTTSHHHHHHHHHHHT...S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...x RF
                         Hydrolase 115 dplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlGddyfdaviasdietvakpspegkvaaireLq...g 188
                                       ++lk++++++e++ + k++ + + +++ + ++ ++ ++++++  + +  +   ie +   + ++ v++++eL+    
  gi|242398107|ref|YP_002993531.1|  38 NKLKLFDGVVEFLDWAKERFV-LSIASWNLEKLVRPILEEFN--IWHYFVFPKIENHP-DKADMIVRTLQELKnsgY 110
                                       567899***********9988.9999999999********99..44445555555522.36799********87767 PP

                                       TGGGEEEEESS CS
                                       xxxxxxxxxxx RF
                         Hydrolase 189 kpeevamVGDg 199
                                       ++eev+ ++D+
  gi|242398107|ref|YP_002993531.1| 111 EIEEVIYIDDR 121
                                       7********96 PP

>> DUF1804  Protein of unknown function (DUF1804)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   8.1e-05      0.18      49     102 ..      51      99 ..      48     114 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.1e-05
                           DUF1804  49 DWDklRaakrlaeggieevakqlledfvvqvqetleelrentelsaedkveiLa 102
                                       DW k R + ++a+ ++e++++ +le+f + ++ ++ +++++      dk+++++
  gi|242398107|ref|YP_002993531.1|  51 DWAKERFVLSIASWNLEKLVRPILEEFNIWHYFVFPKIENHP-----DKADMIV 99 
                                       9*************************************9887.....5666554 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00016      0.35      25      68 ..     112     155 ..      97     160 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00016
                                       G.EEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHT CS
                   Sacchrp_dh_NADP  25 a.eitvadrskeklealaakalgvrfeaialdaenyeavLaallk 68 
                                         e++ +d    +l+++++ +  +rf+++ +d++n e+ L ++l 
  gi|242398107|ref|YP_002993531.1| 112 IeEVIYIDDRTLHLDKIKKRIPDIRFIQMWVDVKNFEE-LREYLM 155
                                       34788888888889************************.777643 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1128.83
//
Query:       gi|242398108|ref|YP_002993532.1|  [L=183]
Description: hypothetical protein TSIB_0115 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-64  216.6   1.9      2e-64  216.4   1.9    1.0  1  DUF366    Domain of unknown function (DUF366)


Domain annotation for each model (and alignments):
>> DUF366  Domain of unknown function (DUF366)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  216.4   1.9   1.1e-68     2e-64       6     183 .]       2     180 ..       1     180 [. 0.99

  Alignments for each domain:
  == domain 1  score: 216.4 bits;  conditional E-value: 1.1e-68
                            DUF366   6 leekikYdGsqlsslwaykefgiqgdsivafrGecevkleelvDleDvkeeeeIksedmlhfivehFdstdlklavl 82 
                                        +++i+YdGs ++s+way++fg+ g+siv+frG+c++k+ee++D+eD+++++eIksedm+h+i+e F++ ++ la +
  gi|242398108|ref|YP_002993532.1|   2 KDKRIDYDGSAIKSHWAYRNFGVLGNSIVIFRGRCDIKIEEMIDIEDLRQQKEIKSEDMIHYIIEIFEVPNVFLASV 78 
                                       5799************************************************************************* PP

                            DUF366  83 rQrllvaivkevleekgvklkreGdDlyvndkKLsvsiataslvsvkiHlglNvesegtp..vetigLkdlgieedi 157
                                       +Q+l++a + e+l e+++k++r GdD+yv+dkKLs+siat+s+vs+kiH+g+Nve++g+p  v++igLk+lgi  di
  gi|242398108|ref|YP_002993532.1|  79 LQKLFIAKLGEILGEYDIKTSRYGDDIYVGDKKLSISIATVSPVSIKIHIGVNVEAKGVPmgVNAIGLKELGI-FDI 154
                                       *************************************************************************.*** PP

                            DUF366 158 eelaeevakkyaeeiediekdirKvr 183
                                       ++++e   k  +ee+ + +kd+ Kvr
  gi|242398108|ref|YP_002993532.1| 155 DQFMELSGKLLVEEFLKAKKDSLKVR 180
                                       ************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1293.97
//
Query:       gi|242398109|ref|YP_002993533.1|  [L=56]
Description: hypothetical protein TSIB_0116 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.29s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 378.37
//
Query:       gi|242398110|ref|YP_002993534.1|  [L=145]
Description: hypothetical protein TSIB_0117 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       581  (0.0324056); 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: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 963.86
//
Query:       gi|242398111|ref|YP_002993535.1|  [L=79]
Description: hypothetical protein TSIB_0118 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 546.23
//
Query:       gi|242398112|ref|YP_002993536.1|  [L=526]
Description: Lysyl-tRNA synthetase [Thermococcus sibiricus MM 739]
Scores for complete 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-130  434.6   0.5   3.4e-130  434.2   0.5    1.1  1  tRNA-synt_1f     tRNA synthetases class I (K)
    5.9e-06   25.3   1.5     0.0081   14.9   0.0    2.9  3  tRNA-synt_1g     tRNA synthetases class I (M)
    0.00028   20.4   0.0       0.51    9.6   0.0    2.7  3  tRNA-synt_1e     tRNA synthetases class I (C) catalytic domai
    0.00055   19.3   0.0      0.027   13.8   0.0    2.2  2  tRNA-synt_1b     tRNA synthetases class I (W and Y)
     0.0048   16.9   0.1       0.01   15.8   0.1    1.5  1  HypA             Hydrogenase/urease nickel incorporation, met
  ------ inclusion threshold ------
      0.058   13.7   0.5         15    5.9   0.2    2.2  2  zf-LITAF-like    LITAF-like zinc ribbon domain
      0.077   13.0   3.7       0.16   12.0   3.7    1.5  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
      0.082   13.4   0.2       0.16   12.5   0.2    1.4  1  Phage_connect_1  Phage gp6-like head-tail connector protein
       0.19   11.5   3.1        0.6    9.9   0.2    2.6  3  DUF1195          Protein of unknown function (DUF1195)
       0.24   11.1   2.4       0.71    9.6   2.4    1.7  1  zinc_ribbon_10   Predicted integral membrane zinc-ribbon meta


Domain annotation for each model (and alignments):
>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  434.2   0.5  1.9e-133  3.4e-130       2     359 ..       3     362 ..       2     363 .. 0.97

  Alignments for each domain:
  == domain 1  score: 434.2 bits;  conditional E-value: 1.9e-133
                      tRNA-synt_1f   2 aWadklaeklieerkkkkaekdevvvesGispSGliHiGnlrevltadlvaralrkrgeevrlilisDdmDglRkvp 78 
                                       +Wad +aek+i+e+ +    k+ +vvesGi+pSG +HiGn+re +t+++v +al++rg++vr+i+++Dd+D++Rkvp
  gi|242398112|ref|YP_002993536.1|   3 HWADYMAEKIIREKGD----KEFYVVESGITPSGYVHIGNFRELFTTYIVGHALEDRGKKVRHIHMWDDYDRFRKVP 75 
                                       9**********66644....699****************************************************** PP

                      tRNA-synt_1f  79 enlpekllekylgkpltsiPdpkgkhesyaehfnaelvesLdelgievefisatelYksglydeaikealenrekik 155
                                       +n+p++ +++yl++p++++Pdp g+h+sya+hf+  ++e++++lgi+v+f +a+elYksg y++ +++ale+reki 
  gi|242398112|ref|YP_002993536.1|  76 KNVPKE-WQEYLTMPVSEVPDPWGCHDSYADHFRLLFEEEVKKLGIKVDFLRASELYKSGEYAHDVRTALEKREKIV 151
                                       ******.********************************************************************** PP

                      tRNA-synt_1f 156 eilekyrgee....reetyspylpvcekcgrvdttevvevdaeeeeieYkceecGeeeevdiregngKLqWkvdwam 228
                                       eil+++r+      + +++ p++++c+kc++  +++ ve+d  e++i+Ykc++c  e  +diregn+KL+W+vdw+m
  gi|242398112|ref|YP_002993536.1| 152 EILNRFRDMAkqphLPKDWQPIQIYCPKCRK--EAQFVEWD-GEWRIKYKCAHCESEDVTDIREGNVKLRWRVDWPM 225
                                       ******998855666788*************..********.*********************************** PP

                      tRNA-synt_1f 229 rWaalgVdfEpaGkDhaaaGgSvdvsskia.eilggeaPekvvYelillkgge.kmssSkGnvltledwlevaepev 303
                                       rWa+++VdfEpaGkDh aaG+ ++++ +i+  ++g e+P++++Ye++++kg++ kms SkGnv+ l+d++ev+ep v
  gi|242398112|ref|YP_002993536.1| 226 RWAHFDVDFEPAGKDHLAAGSGYETGMEIIkAVYGKEPPIPLMYEFVGIKGQKgKMSGSKGNVILLSDLYEVLEPGV 302
                                       ******************************9********************999*********************** PP

                      tRNA-synt_1f 304 lrflilrrkPkkakkldldleilrlvdeYdklerkyf....aeqeeeeekekrvyelsav 359
                                       +rf+++r++P+k++k+dl+l++l+l+de+dk+er yf     ++ ee+e+ kr+yels++
  gi|242398112|ref|YP_002993536.1| 303 IRFIYARHRPNKEIKIDLGLGLLNLYDEFDKIERLYFgleeLRNLEEAEELKRTYELSMP 362
                                       *************************************998766778889999****9975 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1      0.25   4.5e+02      11      48 ..      31      68 ..      23      70 .. 0.89
   2 !    7.5   0.3   0.00083       1.5      66     147 ..     103     185 ..      99     210 .. 0.87
   3 !   14.9   0.0   4.5e-06    0.0081     319     361 ..     270     314 ..     261     320 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.25
                                      SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE--- CS
                      tRNA-synt_1g 11 ngklHlGhllevisaDifaRykrlrgeevlfvcgtDeh 48
                                      +g +H+G+ +e   + i+      rg++v ++   D +
  gi|242398112|ref|YP_002993536.1| 31 SGYVHIGNFRELFTTYIVGHALEDRGKKVRHIHMWDDY 68
                                      6889*************************999877765 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00083
                                       HHHHHHHHHHHHHHHTT---SEEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GGG..-EE... CS
                      tRNA-synt_1g  66 lvekvheeikelfkklnisfdkygrttseehkelvqeifkklkekgliyekeieqlycpkderflpdry..vegtCP 140
                                       ++++++  ++e  kkl+i+ d    ++  +  e ++++ ++l+++++i e   + + + +++  lp     ++  CP
  gi|242398112|ref|YP_002993536.1| 103 YADHFRLLFEEEVKKLGIKVDFLRASELYKSGEYAHDVRTALEKREKIVE-ILNRFRDMAKQPHLPKDWqpIQIYCP 178
                                       5677777889999********99999999999****************97.57789999999***987778****** PP

                                       .....-T CS
                      tRNA-synt_1g 141 kckseea 147
                                       kc++e +
  gi|242398112|ref|YP_002993536.1| 179 KCRKEAQ 185
                                       ***8765 PP

  == domain 3  score: 14.9 bits;  conditional E-value: 4.5e-06
                                       --EEE---..-----------HHHHHHHH-HHHHHHHHHHHS-TT CS
                      tRNA-synt_1g 319 eyltvegk..KlSkSrgvvvkakealerldadllRYylaaeapek 361
                                       e++ ++g+  K+S S+g+v+  +++ e l++ ++R+ +a+++p+k
  gi|242398112|ref|YP_002993536.1| 270 EFVGIKGQkgKMSGSKGNVILLSDLYEVLEPGVIRFIYARHRPNK 314
                                       67777765237*****************************99976 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 !    9.6   0.0   0.00029      0.51      12      58 ..      23      69 ..      12     136 .. 0.83
   2 !    7.5   0.0    0.0012       2.2     246     287 ..     271     314 ..     256     320 .. 0.82
   3 ?   -1.6   0.0      0.74   1.3e+03      72     132 ..     416     477 ..     372     486 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00029
                                      EEEEEEBTTS--BHHHHHHHHHHHHHHHHHHHTT-EEEEEEEBB--S CS
                      tRNA-synt_1e 12 lYvCGptvydashlGhaRslvafDilrrilqalgYdvqfvqnvtDid 58
                                      +   G+t   ++h+G+ R+l ++ i+ + l+++g +v++++   D d
  gi|242398112|ref|YP_002993536.1| 23 VVESGITPSGYVHIGNFRELFTTYIVGHALEDRGKKVRHIHMWDDYD 69
                                      33469**********************************99877766 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0012
                                       -EEETTB..E--TTTT---BHHHHHTTS-HHHHHHHHHSS-TTS CS
                      tRNA-synt_1e 246 hlkiege..kmsksLknfitikdvlkkfdprqlRllllsahyrs 287
                                       ++ i+g+  kms s +n+i++ d+ +  +p ++R++ + ++ ++
  gi|242398112|ref|YP_002993536.1| 271 FVGIKGQkgKMSGSKGNVILLSDLYEVLEPGVIRFIYARHRPNK 314
                                       6666666337************************9988776655 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.74
                                       HHHHHHHHHHHHHHHHHHTT----SB--BGGGGHHHHHHHHHHHHHTTSEEE-TT.S-EEE- CS
                      tRNA-synt_1e  72 vkelaekfieefkkdleaLnvlkptleprvsekvdeiielvekliekgyaYavsd.gdvyfd 132
                                         +la++++e++  d  + +++    e  + e++      v+  +e+   ++++d +++ f+
  gi|242398112|ref|YP_002993536.1| 416 RIKLAKNWVEKYAPDDVKFEIQDQLPEIEIDEEIRTALLEVADWLEEKTRFTIDDlNTTLFN 477
                                       56889999999999999999998888888888886655444444444445555544555555 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 ?    3.2   0.0     0.026        46       8      23 ..      24      39 ..      18      45 .. 0.83
   2 !   13.8   0.0   1.5e-05     0.027     148     218 ..     229     298 ..     226     371 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.026
                                      EEEEEETSSS-BGGGH CS
                      tRNA-synt_1b  8 vysGidPTgklHlGyl 23
                                      v sGi P+g +H+G++
  gi|242398112|ref|YP_002993536.1| 24 VESGITPSGYVHIGNF 39
                                      679***********87 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 1.5e-05
                                       HTCHSEEEEEGGGHHH...HHHHHHHHHHHHHHSTTSS-EEEEET-BBSTTSSSBTTCETTCGC-BTTCCHHHH CS
                      tRNA-synt_1b 148 llkadlvpgGsDQkqn...ielgrdlarrfnkkevfkkpegltvplltgldGekKmSKSagnsaIfLddekesv 218
                                       ++++d++p G+D        e g ++++++  k   ++p +l+ +++    ++ KmS S+gn +I L+d  e  
  gi|242398112|ref|YP_002993536.1| 229 HFDVDFEPAGKDHLAAgsgYETGMEIIKAVYGK---EPPIPLMYEFVGIKGQKGKMSGSKGN-VILLSDLYEVL 298
                                       566667777777543222278999*****9999...99*******987666666********.***99976654 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   0.1   5.7e-06      0.01      57      99 ..     161     209 ..     134     218 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5.7e-06
                                       TTT-EEEEEEE--EEEETTTS-EEECHH...H...HHS-TTTSSS-EEE CS
                              HypA  57 legaeLeieevpvkvrCreCgkefelee...k...alrCpkCgsadvei 99 
                                       +++ +L  + +p++++C +C+ke +  e   +   +++C +C+s+dv+ 
  gi|242398112|ref|YP_002993536.1| 161 AKQPHLPKDWQPIQIYCPKCRKEAQFVEwdgEwriKYKCAHCESEDVTD 209
                                       66677888899************99665444134666********9864 PP

>> zf-LITAF-like  LITAF-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.2    0.0084        15       2      14 ..     171     183 ..     168     186 .. 0.82
   2 ?    5.7   0.0    0.0099        18       5      28 ..     196     219 ..     192     225 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0084
                     zf-LITAF-like   2 eptqvdCpaCqqr 14 
                                       +p q++Cp+C+++
  gi|242398112|ref|YP_002993536.1| 171 QPIQIYCPKCRKE 183
                                       6889999999886 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0099
                     zf-LITAF-like   5 qvdCpaCqqrvvTsveyksgkltw 28 
                                       + +C +C+ + vT +++ + kl w
  gi|242398112|ref|YP_002993536.1| 196 KYKCAHCESEDVTDIREGNVKLRW 219
                                       679************998877776 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   3.7   8.8e-05      0.16      20      44 ..     175     203 ..     168     205 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.8e-05
                     Zn_Tnp_IS1595  20 v.CPhCgsr.kayrikt..rglfqCkeCr 44 
                                       + CP+C ++ ++ +  +  r +++C++C 
  gi|242398112|ref|YP_002993536.1| 175 IyCPKCRKEaQFVEWDGewRIKYKCAHCE 203
                                       44*****997777777799*********7 PP

>> Phage_connect_1  Phage gp6-like head-tail connector protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   8.8e-05      0.16      17      70 ..     408     465 ..     392     482 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.8e-05
                   Phage_connect_1  17 ddDalLesliqaAeeyikdylgrkl....eadedgielpedlktavlelaahryenre 70 
                                       +d + +++ i+ A++++++y  ++     +   + ie++e+++ta+le+a +  e+  
  gi|242398112|ref|YP_002993536.1| 408 EDLERIKLRIKLAKNWVEKYAPDDVkfeiQDQLPEIEIDEEIRTALLEVADWLEEKTR 465
                                       78899*****************99999996678999**************99998874 PP

>> DUF1195  Protein of unknown function (DUF1195)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.2   0.00033       0.6      80     109 ..      52      85 ..      47      93 .. 0.84
   2 ?    1.1   0.0      0.17   3.1e+02      79     107 ..     143     171 ..     133     174 .. 0.87
   3 ?   -2.6   0.1       2.3   4.2e+03      63      82 ..     428     447 ..     416     458 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00033
                           DUF1195  80 leereklvk..rmWdvytrsrri..rlprfWqea 109
                                       le+r k v+  +mWd y r r++   +p+ Wqe 
  gi|242398112|ref|YP_002993536.1|  52 LEDRGKKVRhiHMWDDYDRFRKVpkNVPKEWQEY 85 
                                       89**99998446*******99885579*****96 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.17
                           DUF1195  79 eleereklvkrmWdvytrsrrirlprfWq 107
                                        le+rek+v+ +      +++ +lp+ Wq
  gi|242398112|ref|YP_002993536.1| 143 ALEKREKIVEILNRFRDMAKQPHLPKDWQ 171
                                       589******999888888899999*9999 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 2.3
                           DUF1195  63 lsddldapladdldvlelee 82 
                                       + dd++++++d+l  +e++e
  gi|242398112|ref|YP_002993536.1| 428 APDDVKFEIQDQLPEIEIDE 447
                                       46889999999999888877 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 ?    9.6   2.4    0.0004      0.71      22      52 ..     174     204 ..     168     205 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0004
                    zinc_ribbon_10  22 alICskChshnGlapkeeleevkyrCpkCga 52 
                                        + C+kC++    ++ +   ++ky+C++C +
  gi|242398112|ref|YP_002993536.1| 174 QIYCPKCRKEAQFVEWDGEWRIKYKCAHCES 204
                                       678***********98888899*******75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (526 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       824  (0.0459591); expected 358.6 (0.02)
Passed bias filter:                      692  (0.0385967); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); 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: 0.67u 0.28s 00:00:00.95 Elapsed: 00:00:00.46
# Mc/sec: 3424.21
//
Query:       gi|242398113|ref|YP_002993537.1|  [L=202]
Description: Indolepyruvate: ferredoxin oxidoreductase (IOR), subunit beta [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.4e-34  117.6   0.0    7.4e-34  117.3   0.0    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 !  117.3   0.0   4.1e-38   7.4e-34       1     176 [.      20     198 ..      20     199 .. 0.92

  Alignments for each domain:
  == domain 1  score: 117.3 bits;  conditional E-value: 4.1e-38
                                       CTSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHHHHGGGEE CS
                               POR   1 GGqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetlsehldglk 77 
                                       GGqG +t+++i+++aa+++Gy+v   ++ g+++r g++ s++r+++e+ +p ie geadl++al+++++ ++   l 
  gi|242398113|ref|YP_002993537.1|  20 GGQGGLTLSRIIGNAAMKEGYNVRIGETLGMSQRYGSVLSYLRFGEEVYSPLIEEGEADLMLALEPAEALRNSRFLS 96 
                                       9*****************************************************************9999******* PP

                                       EEEEEEEECTCGTT-CCHHHCTS-HHHHHHH.....T-EEEEE-HHHHHHHCCC.CCHHHHHHHHHHHHHHTS-H.. CS
                               POR  78 pggiiiynseelkpdelkkakeeerelkerl.....gvrvygvdatkiakeiggneraaNtvmlGalaallglpl.. 147
                                         +++i+n+  + +++    kee+++++e        + v  +++++ a++i  n+r++ ++mlG++ + + +pl  
  gi|242398113|ref|YP_002993537.1|  97 GKSYAIVNAYPIHTATTLIGKEEYPAMEEIHkalvkICTVEIMNFQEEADKI--NPRTLGVLMLGYAHGRGLIPLkk 171
                                       ***************************9999996655555666666666554..38**********98888888888 PP

                                       HHHHHHHHCCS-CH.HHHHHHHHHHHHHH CS
                               POR 148 ealeeaikkrfpkkkeviekNlkafragy 176
                                       e+l e+ik++++   +++e N++a+++g+
  gi|242398113|ref|YP_002993537.1| 172 ESLVEGIKETLKS--KLWEINIQALERGI 198
                                       ************8..5***********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1359.52
//
Query:       gi|242398114|ref|YP_002993538.1|  [L=141]
Description: Manganese-dependent transcription regulator [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-19   68.9   0.3    5.3e-19   68.2   0.3    1.4  1  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
    1.5e-18   66.7   0.1    2.4e-18   66.0   0.1    1.4  1  Fe_dep_repr_C    Iron dependent repressor, metal binding and 
    2.9e-08   33.5   0.0    4.8e-08   32.8   0.0    1.3  1  MarR_2           MarR family
    1.2e-06   28.3   0.4    1.8e-06   27.7   0.4    1.4  1  TrmB             Sugar-specific transcriptional regulator Trm
    3.5e-06   26.9   0.0    6.3e-06   26.0   0.0    1.4  1  MarR             MarR family
    3.6e-05   23.2   0.0    6.6e-05   22.4   0.0    1.5  1  HTH_24           Winged helix-turn-helix DNA-binding
    4.3e-05   23.3   0.0     0.0001   22.1   0.0    1.6  1  HTH_5            Bacterial regulatory protein, arsR family
    0.00032   21.0   0.0    0.00054   20.3   0.0    1.4  1  Rrf2             Transcriptional regulator
    0.00065   19.5   0.1    0.00088   19.0   0.1    1.4  1  DUF4423          Domain of unknown function (DUF4423)
      0.001   18.8   0.0     0.0042   16.8   0.0    2.1  2  LexA_DNA_bind    LexA DNA binding domain
     0.0011   18.8   2.7     0.0028   17.5   0.3    2.0  2  TFIIE_alpha      TFIIE alpha subunit
     0.0013   18.5   0.0      0.002   17.9   0.0    1.3  1  HTH_IclR         IclR helix-turn-helix domain
     0.0013   17.6   0.8     0.0019   17.1   0.3    1.5  2  HTH_micro        HTH-like
     0.0015   18.4   0.0     0.0025   17.7   0.0    1.4  1  HTH_Crp_2        Crp-like helix-turn-helix domain
     0.0034   17.5   0.6     0.0059   16.7   0.6    1.4  1  DUF2250          Uncharacterized protein conserved in archaea
     0.0092   16.3   0.6      0.056   13.8   0.1    2.0  2  Penicillinase_R  Penicillinase repressor
     0.0097   15.8   0.0      0.018   15.0   0.0    1.5  1  HTH_36           Helix-turn-helix domain
  ------ inclusion threshold ------
      0.013   15.4   0.1      0.029   14.3   0.1    1.6  1  HTH_11           HTH domain
      0.015   15.1   0.1      0.054   13.3   0.0    2.0  1  IF2_N            Translation initiation factor IF-2, N-termin
      0.015   15.8   0.0      0.023   15.2   0.0    1.3  1  HTH_27           Winged helix DNA-binding domain
      0.016   15.0   0.0      0.037   13.8   0.0    1.6  1  HTH_23           Homeodomain-like domain
      0.017   14.9   0.0       0.38   10.6   0.0    2.3  2  HTH_10           HTH DNA binding domain
      0.025   14.8   0.3       0.24   11.6   0.1    2.0  2  Rio2_N           Rio2, N-terminal
      0.043   14.1   0.4       0.24   11.7   0.0    2.3  2  Mnd1             Mnd1 HTH domain
      0.047   13.8   0.0      0.078   13.0   0.0    1.3  1  HTH_20           Helix-turn-helix domain
      0.054   13.7   0.0        3.5    7.9   0.0    2.1  2  LPD22            Large polyvalent protein associated domain 2
      0.064   12.9   0.0        0.1   12.2   0.0    1.3  1  GntR             Bacterial regulatory proteins, gntR family
      0.086   12.9   0.0       0.14   12.2   0.0    1.3  1  HTH_29           Winged helix-turn helix
        0.1   12.8   0.0       0.16   12.1   0.0    1.3  1  HTH_28           Helix-turn-helix domain
       0.12   12.3   0.0       0.18   11.7   0.0    1.3  1  HTH_AsnC-type    AsnC-type helix-turn-helix domain
       0.13   11.8   0.0       0.26   10.9   0.0    1.6  1  HTH_CodY         CodY helix-turn-helix domain
       0.15   11.9   2.5       0.13   12.1   1.3    1.6  2  DUF4422          Domain of unknown function (DUF4422)


Domain annotation for each model (and alignments):
>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.2   0.3   9.5e-22   5.3e-19       2      57 ..       3      58 ..       2      61 .. 0.96

  Alignments for each domain:
  == domain 1  score: 68.2 bits;  conditional E-value: 9.5e-22
                                      --HHHHHHHHHHHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT CS
                    Fe_dep_repress  2 LvestEdYLetIYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyveyeky 57
                                      ++++ E+YLe+IY l+++k+v+++kd+++rL+++p+sV   lkkL+++G+veyeky
  gi|242398114|ref|YP_002993538.1|  3 ISKREEEYLEVIYLLQKNKGVIRVKDISKRLGIRPPSVVDALKKLSEKGFVEYEKY 58
                                      57899**************************************************9 PP

>> Fe_dep_repr_C  Iron dependent repressor, metal binding and dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.0   0.1   4.3e-21   2.4e-18       1      65 [.      64     129 ..      64     133 .. 0.96

  Alignments for each domain:
  == domain 1  score: 66.0 bits;  conditional E-value: 4.3e-21
                                       -HHHHHHHHHHHHHHHHHHHHHHHHCT--CCCHHHHCCCCGGGS-HHHHHHHHHHCT-.SB.-TTS CS
                     Fe_dep_repr_C   1 TekGrelAkrlvrrhrllerfLvdvlgvdweeaheeAerlEhalseelierldellgfpee.cPhg 65 
                                       T+kG e+A++++++h l+ +f++++lg+++++a+e+A+++Eh+++e ++e++ e+ ++++  cP+ 
  gi|242398114|ref|YP_002993538.1|  64 TKKGIEVAESTYQKHILIAKFFTEILGIPPDIAEEDACQFEHYVHEITAEKMKEFAQYIQDqCPYV 129
                                       99*******************************************************999879975 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.0   8.5e-11   4.8e-08      10      55 ..      13      57 ..       9      60 .. 0.89

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 8.5e-11
                                      HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2 10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                      v++ L  + g  ++v+++ +rlg+ +++v  +lk+L+++G+ve+++
  gi|242398114|ref|YP_002993538.1| 13 VIYLLQKNKGV-IRVKDISKRLGIRPPSVVDALKKLSEKGFVEYEK 57
                                      78889999995.6******************************986 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.4   3.2e-09   1.8e-06      16      56 ..      15      57 ..       2      73 .. 0.88

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 3.2e-09
                                      HHH..HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                              TrmB 16 aLl..klgpatadeiaeelgvprskvYevLrsLedkGlVerek 56
                                      +Ll  ++g  ++++i+++lg+  ++v ++L++L++kG+Ve ek
  gi|242398114|ref|YP_002993538.1| 15 YLLqkNKGVIRVKDISKRLGIRPPSVVDALKKLSEKGFVEYEK 57
                                      5667688999******************************987 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   1.1e-08   6.3e-06      14      48 ..      19      54 ..       9      58 .. 0.85

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 1.1e-08
                                      HSTT.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR 14 eqgp.lsvseLakklgvskstvtrvldrLekkGlie 48
                                       + + ++v+++ k+lg+ +++v  +l++L +kG++e
  gi|242398114|ref|YP_002993538.1| 19 KNKGvIRVKDISKRLGIRPPSVVDALKKLSEKGFVE 54
                                      44444******************************8 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   1.2e-07   6.6e-05       7      48 .]      12      54 ..      11      54 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.2e-07
                            HTH_24  7 kILelLqknpr.isqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      +++ lLqkn + i  +++++rlg+ p+ v   lk+L e+G+++
  gi|242398114|ref|YP_002993538.1| 12 EVIYLLQKNKGvIRVKDISKRLGIRPPSVVDALKKLSEKGFVE 54
                                      67889***9999*****************************96 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   1.8e-07    0.0001       5      47 .]      11      55 ..       9      55 .. 0.96

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.8e-07
                                      HHHHHHHTT..SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5  5 lkILklLae..gelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                      l++++lL++  g   v ++++ lg+ ++ v   LkkL e G+Ve+
  gi|242398114|ref|YP_002993538.1| 11 LEVIYLLQKnkGVIRVKDISKRLGIRPPSVVDALKKLSEKGFVEY 55
                                      799******8888******************************96 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   9.7e-07   0.00054       1      56 [.       1      54 [.       1      57 [. 0.89

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 9.7e-07
                                      X---HHHHHHHHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2  1 MklsskteyalhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvk 56
                                      M++s++ e  l +++ L+k+++   +++++i++r +i p+ +   l+kL+++g+v+
  gi|242398114|ref|YP_002993538.1|  1 MEISKREEEYLEVIYLLQKNKG--VIRVKDISKRLGIRPPSVVDALKKLSEKGFVE 54
                                      7888888888888888888887..69*****************************8 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.1   1.6e-06   0.00088      22      91 ..      10      76 ..       3     140 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.6e-06
                           DUF4423 22 yypvirellplkdfkadpeelakrlrpkisaeevekalefLlklgllkkdedgkyrqtekslttssevks 91
                                      y  vi+ ll+ +++   ++ ++krl+  i    v +al+ L + g+++ ++ +++  t+k +++ +++ +
  gi|242398114|ref|YP_002993538.1| 10 YLEVIY-LLQKNKGVIRVKDISKRLG--IRPPSVVDALKKLSEKGFVEYEKYDRILLTKKGIEVAESTYQ 76
                                      445555.5555555599*********..**********************************97776544 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   7.6e-06    0.0042      27      59 ..      25      56 ..       2      59 .. 0.76
   2 ?   -2.7   0.0       9.4   5.3e+03      22      30 ..      89      97 ..      76      97 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 7.6e-06
                                      -HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE-G CS
                     LexA_DNA_bind 27 sireiaralglkSpsaveehLkaLerKGyierd 59
                                       +++i+++lg++ p +v   Lk+L+ KG++e +
  gi|242398114|ref|YP_002993538.1| 25 RVKDISKRLGIR-PPSVVDALKKLSEKGFVEYE 56
                                      5899********.8889999**********975 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 9.4
                                      HSS---HHH CS
                     LexA_DNA_bind 22 tgypPsire 30
                                       g pP i+e
  gi|242398114|ref|YP_002993538.1| 89 LGIPPDIAE 97
                                      588998887 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.3     5e-06    0.0028      12      62 ..       7      58 ..       3      79 .. 0.84
   2 ?    1.6   0.1      0.45   2.5e+02      64      99 ..      98     133 ..      94     140 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 5e-06
                                      -HHHHHHHHHHHC.TTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEE CS
                       TFIIE_alpha 12 geeavlvldvLle.kgevteedlakelkidlnelrklLnrLyearlvkykrr 62
                                      +ee  +v+  L + kg++   d++k l+i ++ +  +L +L e+++v+y + 
  gi|242398114|ref|YP_002993538.1|  7 EEEYLEVIYLLQKnKGVIRVKDISKRLGIRPPSVVDALKKLSEKGFVEYEKY 58
                                      67899999999862699999*****************************985 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.45
                                       ETTTEEEEEEEEEECCCHCCCHHHHHHHHHHHHHHH CS
                       TFIIE_alpha  64 deekswykyywrinyeklvdvvkrkleevvkkLeek 99 
                                       ++  + ++y + i+ ek+ +  ++  ++    L++ 
  gi|242398114|ref|YP_002993538.1|  98 EDACQFEHYVHEITAEKMKEFAQYIQDQCPYVLKQF 133
                                       688899999999999999887766666655555554 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   3.5e-06     0.002       7      51 ..      12      56 ..      10      57 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3.5e-06
                                      HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                          HTH_IclR  7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveqd 51
                                      +++ +l +  +  +++++++r+g+ +++v   L+ L e G+ve++
  gi|242398114|ref|YP_002993538.1| 12 EVIYLLQKNKGVIRVKDISKRLGIRPPSVVDALKKLSEKGFVEYE 56
                                      5666777778878*****************************985 PP

>> HTH_micro  HTH-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.3   3.3e-06    0.0019      89     142 ..       6      59 ..       2      86 .. 0.89
   2 ?   -2.3   0.0       2.6   1.5e+03     355     384 ..      93     123 ..      85     129 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.3e-06
                         HTH_micro  89 tskeyykivdflvkakdyvkaaelraklnidpKklfYvikkLakkglieqktke 142
                                        ++ey +++ +l k+k  + ++++ ++l i p  +  ++kkL++kg++e+++ +
  gi|242398114|ref|YP_002993538.1|   6 REEEYLEVIYLLQKNKGVIRVKDISKRLGIRPPSVVDALKKLSEKGFVEYEKYD 59 
                                       6789999999999999*********************************88765 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.6
                         HTH_micro 355 kdvdesdivl.nnyvnkkeaekenkfqkkvk 384
                                       +d+ e+d  +  +yv + +aek+ +f + ++
  gi|242398114|ref|YP_002993538.1|  93 PDIAEEDACQfEHYVHEITAEKMKEFAQYIQ 123
                                       5666666655134555678888888877665 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   4.5e-06    0.0025      24      59 ..      26      63 ..      13      67 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4.5e-06
                                      HHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ETEE.EEE CS
                         HTH_Crp_2 24 qeelAsmlGltretvsrilseLkreglis.rgrr.iri 59
                                       ++++ +lG+++ +v  +l++L+++g ++  +++ i +
  gi|242398114|ref|YP_002993538.1| 26 VKDISKRLGIRPPSVVDALKKLSEKGFVEyEKYDrILL 63
                                      589**************************644322655 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.6     1e-05    0.0059       4      77 ..       4      78 ..       1      80 [. 0.87

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1e-05
                           DUF2250  4 leedelalkvlkhlkka.nvdYaksiakeleipleevrellkkLeelGLlervegktikrteaklKkksevhkhH 77
                                       +++e++l+v++ l+k  +v   k i+k+l i+   v ++lkkL e G +e+ +   i  t++    ++ + ++H
  gi|242398114|ref|YP_002993538.1|  4 SKREEEYLEVIYLLQKNkGVIRVKDISKRLGIRPPSVVDALKKLSEKGFVEYEKYDRILLTKKGIEVAESTYQKH 78
                                      5788999*****99876267889******************************9999999998888888888888 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.1    0.0001     0.056       1      59 [.       3      61 ..       3      78 .. 0.77
   2 ?    1.0   0.1      0.94   5.3e+02      70     100 ..     109     138 ..     104     141 .] 0.77

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.0001
                                      ---S-SHHHHHHHHHS-....EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEETTE CS
                   Penicillinase_R  1 lgelEaevmeilwekge....atvkevveeleeekelaysTVktllrrLvkKgllsrekegra 59
                                      ++++E+e +e+++ +++    + vk++ ++l  +    + +V   l++L +Kg+++ ek  r 
  gi|242398114|ref|YP_002993538.1|  3 ISKREEEYLEVIYLLQKnkgvIRVKDISKRLGIR----PPSVVDALKKLSEKGFVEYEKYDRI 61
                                      6788888888887655421135566666666555....99******************99885 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.94
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                   Penicillinase_R  70 eavasavkqlldklfegsvkelvaafveeek 100
                                       e++a+++k++ + +   + + ++ +f++e+k
  gi|242398114|ref|YP_002993538.1| 109 EITAEKMKEFAQYIQ-DQCPYVLKQFLKEQK 138
                                       677888888887766.488999999998864 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   3.2e-05     0.018      27      54 ..      25      52 ..      11      53 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.2e-05
                            HTH_36 27 sqetlakrlglsknTvsraikeLeqlGy 54
                                       +++++krlg+   +v+ a+k+L ++G+
  gi|242398114|ref|YP_002993538.1| 25 RVKDISKRLGIRPPSVVDALKKLSEKGF 52
                                      799************************7 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   5.1e-05     0.029       5      44 ..      13      52 ..      10      69 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.1e-05
                            HTH_11  5 ilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                      ++ lL +++g i  ++++++L++    v+  +k+L+e+g+
  gi|242398114|ref|YP_002993538.1| 13 VIYLLQKNKGVIRVKDISKRLGIRPPSVVDALKKLSEKGF 52
                                      78899999999****************************3 PP

>> IF2_N  Translation initiation factor IF-2, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   9.7e-05     0.054       4      28 ..      24      47 ..      21      54 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.7e-05
                             IF2_N  4 irVyeLAkeLgvkskevikkLfkel 28
                                      irV+++ k+Lg+++  v++ L+k l
  gi|242398114|ref|YP_002993538.1| 24 IRVKDISKRLGIRPPSVVDALKK-L 47
                                      9******************9944.6 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 ?   15.2   0.0   4.1e-05     0.023      10      68 .]      12      67 ..       4      67 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.1e-05
                            HTH_27 10 hlir..hrrrrkkl.adlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                      ++i+    + +++  +d+++rl +   +++ +lkkL ekG+ve +++       r+ lT kG
  gi|242398114|ref|YP_002993538.1| 12 EVIYllQKNKGVIRvKDISKRLGIRPPSVVDALKKLSEKGFVEYEKY------DRILLTKKG 67
                                      5555543444444459**************************55544......477777776 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   6.6e-05     0.037       8      46 ..      11      52 ..       4      54 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.6e-05
                            HTH_23  8 lrillllae...GlsvreIAreLgvsrrTvyrwlkryreeGl 46
                                      l++++ll++    ++v++I+++Lg+ +  v   lk+  e+G+
  gi|242398114|ref|YP_002993538.1| 11 LEVIYLLQKnkgVIRVKDISKRLGIRPPSVVDALKKLSEKGF 52
                                      789*****999*****************99999999999995 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00069      0.38      24      50 ..      24      50 ..      23      52 .. 0.90
   2 ?    1.6   0.0      0.43   2.4e+02      33      47 ..      68      82 ..      64      83 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00069
                            HTH_10 24 vtlkeLAkelGIskstlsehLrkaesk 50
                                      +++k+++k+lGI ++++ + L+k  +k
  gi|242398114|ref|YP_002993538.1| 24 IRVKDISKRLGIRPPSVVDALKKLSEK 50
                                      5789*****************997665 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.43
                            HTH_10 33 lGIskstlsehLrka 47
                                      + +++st+++h+  a
  gi|242398114|ref|YP_002993538.1| 68 IEVAESTYQKHILIA 82
                                      6799*******9665 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00043      0.24       5      70 ..       4      67 ..       1      71 [. 0.85
   2 ?    1.1   0.0      0.86   4.8e+02      25      51 ..     110     136 ..     100     137 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00043
                            Rio2_N  5 skedfrvLtavEmgmrnhevVptelieeisrlkeeevkkrlsrllkaklisrktakydGYkLtyeG 70
                                      sk++   L+ + +  +n  v+ ++ i+++ +++  +v ++l++l ++++++++  kyd   Lt +G
  gi|242398114|ref|YP_002993538.1|  4 SKREEEYLEVIYLLQKNKGVIRVKDISKRLGIRPPSVVDALKKLSEKGFVEYE--KYDRILLTKKG 67
                                      555666688999999*************************************8..57766666665 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.86
                            Rio2_N  25 Vptelieeisrlkeeevkkrlsrllka 51 
                                       +  e+++e++++ ++++ ++l++ lk+
  gi|242398114|ref|YP_002993538.1| 110 ITAEKMKEFAQYIQDQCPYVLKQFLKE 136
                                       456789999999999999999998875 PP

>> Mnd1  Mnd1 HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00043      0.24      19      49 ..      27      57 ..      13      59 .. 0.92
   2 ?   -0.5   0.1       2.7   1.5e+03      14      33 ..     115     135 ..     106     139 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00043
                              Mnd1 19 klapkekgivsqsVkdvlqsLvdDglveveK 49
                                      k ++k  gi++ sV d l++L + g ve eK
  gi|242398114|ref|YP_002993538.1| 27 KDISKRLGIRPPSVVDALKKLSEKGFVEYEK 57
                                      6688999**********************99 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 2.7
                              Mnd1  14 lKeleklapk.ekgivsqsVk 33 
                                       +Ke+ + ++  ++ + +q  k
  gi|242398114|ref|YP_002993538.1| 115 MKEFAQYIQDqCPYVLKQFLK 135
                                       667766666655555555555 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   0.00014     0.078      28      57 ..      27      56 ..      21      58 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00014
                                      HHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                            HTH_20 28 selaerldlskntlsyHLrvLeeagLvevv 57
                                      +++ +rl++++ ++ + L++L+e g+ve +
  gi|242398114|ref|YP_002993538.1| 27 KDISKRLGIRPPSVVDALKKLSEKGFVEYE 56
                                      6899***********************987 PP

>> LPD22  Large polyvalent protein associated domain 22
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0      0.11        60      20      45 ..      25      50 ..      23      69 .. 0.77
   2 ?    7.9   0.0    0.0062       3.5      25      56 ..      86     120 ..      82     138 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.11
                             LPD22 20 ralrlaeelGlppdvvernleafera 45
                                      r+++++++lG+ p++v + l+++ ++
  gi|242398114|ref|YP_002993538.1| 25 RVKDISKRLGIRPPSVVDALKKLSEK 50
                                      6899***********99998777655 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0062
                             LPD22  25 aeelGlppdvvernleaferaa...eaedwdalle 56 
                                       +e lG+ppd++e++  +fe      +ae+++++++
  gi|242398114|ref|YP_002993538.1|  86 TEILGIPPDIAEEDACQFEHYVheiTAEKMKEFAQ 120
                                       689***********966665554448888887775 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00019       0.1      26      57 ..      25      56 ..      21      61 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00019
                                      -HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              GntR 26 sereLaaefgVsrttvReALrrLeaeglverr 57
                                      +++++++++g+  ++v  AL++L+++g ve +
  gi|242398114|ref|YP_002993538.1| 25 RVKDISKRLGIRPPSVVDALKKLSEKGFVEYE 56
                                      7899************************9965 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00025      0.14      10      40 ..      21      51 ..      12      56 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00025
                            HTH_29 10 eGvstvsqiAkllglsrrtvyrwlkrfeegG 40
                                      +Gv +v++i k+lg+ +++v ++lk   e+G
  gi|242398114|ref|YP_002993538.1| 21 KGVIRVKDISKRLGIRPPSVVDALKKLSEKG 51
                                      55559**********************9998 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00028      0.16       8      41 ..      16      52 ..      11      60 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00028
                            HTH_28  8 lla..aGh.svreaArelgisrrtvyrWikryeegGi 41
                                      ll+  +G+ +v++++++lgi + +v + +k++ e G+
  gi|242398114|ref|YP_002993538.1| 16 LLQknKGViRVKDISKRLGIRPPSVVDALKKLSEKGF 52
                                      44432699**********************9988876 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   0.0   0.00032      0.18       9      41 ..      14      47 ..      11      48 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00032
                     HTH_AsnC-type  9 LeaLqed.aRisyaeLAervGlSestvlrRvrrL 41
                                      + +Lq++ + i ++++++r+G+ ++ v   +++L
  gi|242398114|ref|YP_002993538.1| 14 IYLLQKNkGVIRVKDISKRLGIRPPSVVDALKKL 47
                                      669************************9888887 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 ?   10.9   0.0   0.00046      0.26       3      35 ..      22      54 ..      20      67 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00046
                          HTH_CodY  3 GrLtaskiaDriGitrsvivnaLrkLesaGiie 35
                                      G +    i+ r+Gi    +v+aL+kL   G +e
  gi|242398114|ref|YP_002993538.1| 22 GVIRVKDISKRLGIRPPSVVDALKKLSEKGFVE 54
                                      556667899******************999998 PP

>> DUF4422  Domain of unknown function (DUF4422)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       9.8   5.5e+03      44      63 ..       3      20 ..       2      27 .. 0.70
   2 ?   12.1   1.3   0.00022      0.13     107     167 ..      81     140 ..      42     141 .] 0.68

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 9.8
                           DUF4422 44 ISeknksycELTalYWawkn 63
                                      IS++ ++y E  ++Y + kn
  gi|242398114|ref|YP_002993538.1|  3 ISKREEEYLE--VIYLLQKN 20
                                      7777777765..56766666 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00022
                           DUF4422 107 iekllkkydiilpkkrklkieslyeqYkkahhiedldllreiikekypeyleafekvlkkk 167
                                       i+k+++++  i p+  + +     e+Y +  ++e+++++ ++i++++p +l++f k  k+k
  gi|242398114|ref|YP_002993538.1|  81 IAKFFTEILGIPPDIAE-EDACQFEHYVHEITAEKMKEFAQYIQDQCPYVLKQFLKEQKEK 140
                                       45555555555555555.345889****************************998877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       854  (0.0476323); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                        32  (0.00178482); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              32  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 850.13
//
Query:       gi|242398115|ref|YP_002993539.1|  [L=453]
Description: Xanthine/uracilpermease [Thermococcus sibiricus MM 739]
Scores for complete 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-46  157.0  38.9    6.8e-46  156.7  38.9    1.1  1  Xan_ur_permease  Permease family


Domain annotation for each model (and alignments):
>> Xan_ur_permease  Permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.7  38.9   3.8e-50   6.8e-46       3     384 ..      28     408 ..      26     413 .. 0.91

  Alignments for each domain:
  == domain 1  score: 156.7 bits;  conditional E-value: 3.8e-50
                                       HHHHHHHHHHHHHHHHHHHHHTTTS-.........H.HHHHHHHHHHHHHHHHHTTT-----EEE-GGGHHHHHGGG CS
                   Xan_ur_permease   3 llllglQhllamfaalvvvPllvgdalglaeelrqlisatllasGiatllqllifgirlpillgssfafvtalmial 79 
                                       ++l+g++++++m + l v+P +++da+g+   +++l+++t lasGi+t+++ l+++ + +++ g++++++ a+ +++
  gi|242398115|ref|YP_002993539.1|  28 EVLAGVTTFMTMAYILFVNPAILSDAMGK-DAFSSLVAVTALASGISTIIMGLYAKKPFALAPGMGLNAYFAYNVVI 103
                                       799***********************875.9999******************************************* PP

                                       -....HHHHHHHHHHHHHHHHHHHHHHHTT-SH.HHHHH--HHHHHHHHHHHHHHHHHHHHHHTTSS-...BTT... CS
                   Xan_ur_permease  80 GsaedieialagllgallvagvlfilisltglrgrlarlipPvvtgpvvlliGlslaqiavkkvgggwaa.veg..l 153
                                       G+    ++  +++l a++v g+lfi++s+t++r+ ++ +ip    ++v  +iGl+l+ i++++vg + a   e+  l
  gi|242398115|ref|YP_002993539.1| 104 GM----GYDWRVALAAVFVEGILFIILSVTKIRSAIIHAIPLSQKYAVGAGIGLFLTFIGLNDVGFLTAVvNEAgvL 176
                                       *6....************************************************************99885555653 PP

                                       B--...-HHHHHHHHHHHHHHHHHHHSSSTTTTTHHHHHHHHHHHHHHHHHHHTTSSHHHHS-SS-----------H CS
                   Xan_ur_permease 154 tvv...slkllllavvvllvilllsvflkglfsqlpiLigiiagwllalfmgivnlspevseapwfqlpsplkfgtp 227
                                       +++   ++ l++ +  + l++l l+  l+ l  ++++Li i+++ +l +++g  +  ++++++p ++ +  lk+   
  gi|242398115|ref|YP_002993539.1| 177 QLTglnASALVTKQGLLFLFGLFLAAILISLRIKGALLISILVTSILGWITGAAPWPSQIFSTPNISYT-FLKLDLK 252
                                       333010223333455677888999999*************************9999999*******996.5577776 PP

                                       H...H.HHHHTHHH.HHHHHHHHHHHHHHHHHHTS-TII..IIIHHHHHHHHHHHHHHHHHHT---EEE-HHHHHHH CS
                   Xan_ur_permease 228 l.fnlgliltvlavalvavvesvGdiravakvvgrslkp..kpdlrralladGlatllsgllGalpvttyaeniGvv 301
                                         +n g+i +v+a+++v +++++G++++++  +g   k+   pd ++ ll+d ++t +++llG++ vtty+e+++++
  gi|242398115|ref|YP_002993539.1| 253 GlLNVGAIGVVFAFFMVDFFDTLGTVTGLSAKAGFLTKEgkVPDAEKVLLTDAIGTSFGALLGTSTVTTYIESAAGI 329
                                       67*************************999888866666779*********************************** PP

                                       HHHTB--HHHHHHHHHHHHHHT--H.HHHHHHTTS-HHHHHHHHHHHHHHHHHHHHHHHHHTTS-SHHHHHHHHHHH CS
                   Xan_ur_permease 302 altkvasrrvmvtagvilillglip.klaallssIPepvlgGvllvvfgmiaasgvsnlqtvdldsarnllivavsl 377
                                       + +    +r+++ta v  +l+  ++ ++a+l+++IP+++ ++++lv++g  ++s+++ +++ d  +a  +++v +++
  gi|242398115|ref|YP_002993539.1| 330 EEG----GRTGMTALVTGLLFLAVGlFIAPLAQAIPAFA-TAPALVIVGYYMLSAIRGVDFDDASEAIPAFLVLMTI 401
                                       ***....**********99988775389***********.*******************************999999 PP

                                       HHHHH-- CS
                   Xan_ur_permease 378 vlGlgva 384
                                         + ++a
  gi|242398115|ref|YP_002993539.1| 402 PYTYSIA 408
                                       9888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (453 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 2907.19
//
Query:       gi|242398116|ref|YP_002993540.1|  [L=440]
Description: Malate oxidoreductase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.6e-29  101.8   1.3    5.7e-27   94.7   1.3    2.5  1  malic          Malic enzyme, N-terminal domain
    1.2e-26   93.6   3.8    9.2e-26   90.6   3.8    2.2  1  Malic_M        Malic enzyme, NAD binding domain
    0.00033   20.7   0.8     0.0017   18.5   1.0    2.2  3  Shikimate_DH   Shikimate / quinate 5-dehydrogenase
    0.00078   19.2   0.4     0.0021   17.8   0.1    1.8  2  ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydro
      0.003   16.8   0.1     0.0045   16.3   0.1    1.2  1  FAD_binding_3  FAD binding domain
     0.0052   16.2   1.0      0.011   15.1   1.0    1.5  1  ThiF           ThiF family
     0.0068   15.7   3.3      0.017   14.4   1.6    2.0  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
      0.049   13.9   0.2       0.12   12.6   0.2    1.6  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
       0.23   11.0   1.6       0.39   10.2   1.6    1.3  1  DAO            FAD dependent oxidoreductase


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 !   94.7   1.3   2.9e-30   5.7e-27       2     182 .]      31     162 ..      30     162 .. 0.95

  Alignments for each domain:
  == domain 1  score: 94.7 bits;  conditional E-value: 2.9e-30
                                       TTECCCCCCHHCCCHHHHHHHHSTTCHHHHHHHHHHHGGCHHSCCCEGGGETCHHHHHTTSS.SS..EEEEE-SSSB CS
                             malic   2 eknetlfykllkekleellpivYtPtvgeacqeyseeyrkarglylsikdkekikeilknlpeedvkvivvtdgeri 78 
                                       +k+e++++  +++    +l+++YtP+v+e+c+++++  ++ +  y+ i ++                v+v++dg+++
  gi|242398116|ref|YP_002993540.1|  31 GKIEIIPKVKVEDP--YDLSLAYTPGVAEPCKAIANGESYEN--YTIIPNT----------------VAVISDGSAV 87 
                                       67888888888888..9******************9888777..*******................********** PP

                                       TTTBS-G.HHHHHHHHHHHHHHHHHHS-EGGGEEEEEECS-BS.HHHHC.TT..S.SSB...SHHHHHHHHHHHHHH CS
                             malic  79 LGlGdlG.vagvgimvGKlaLytalagidPekvlpvvldvgtnneelledplYlGlrkkRvkgeeydefvdefveav 154
                                       LGlGd+G +ag+++ +GK +L++alag+d   ++p+ +d++                           ++de+v++v
  gi|242398116|ref|YP_002993540.1|  88 LGLGDVGiLAGMPVLEGKCVLFKALAGVD---AFPILIDTK---------------------------DIDEIVNTV 134
                                       *****************************...*********...........................9******** PP

                                       HHHHGCTSEEEE-S--CCHHHHHHHHHC CS
                             malic 155 kelfppkaliqfEDfkaknafeileryr 182
                                       k +   +++i++ED++a+++fei+e+++
  gi|242398116|ref|YP_002993540.1| 135 KLISKGFGGINLEDISAPRCFEIEEKLK 162
                                       *************************986 PP

>> Malic_M  Malic enzyme, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.6   3.8   4.6e-29   9.2e-26       3     238 ..     176     377 ..     174     396 .. 0.85

  Alignments for each domain:
  == domain 1  score: 90.6 bits;  conditional E-value: 4.6e-29
                                       HHHHHHHHHHHHHHHHH-S-GGG--EEEEC-SHHHHHHHHHHHHHHHTTTS-HHHHHTTEEEEETTEE-BTT-S--- CS
                           Malic_M   3 gTaavalagllaalkitgkklseqkivvlGaGsagiGiaeqivealvkeGlseeeakkkiylvDrkGLltedrekle 79 
                                       gTa+v+lagl++alki gkk+++ k+v+ GaG+agi ia+ +++    +G       ++i +vDrkG+++e+re+l+
  gi|242398116|ref|YP_002993540.1| 176 GTAVVTLAGLINALKIVGKKFADIKVVIKGAGAAGIAIAKILHQ----RG------IREILIVDRKGIIHEGREDLN 242
                                       9***********************************99987764....56......4679****************9 PP

                                       TTTGGGSBS--SS--S....SHHHHHHHH--SEEEE-SSSSS-S-HHHHHHHHHHSSS-EEEE--SSGGGSSS-HHH CS
                           Malic_M  80 eekkpfakkkeelkeakdkltLeevvkkvkptvliGlsgvagafteeivremaksterPiilplSNPtskaEataed 156
                                       ++k++ ak + +      + +L ++++   ++v iG+s v+++ ++e++r m++     i+++l NP    E ++e+
  gi|242398116|ref|YP_002993540.1| 243 PYKREVAKFNINGI----EGELIDAING--ADVFIGVS-VGESVSKEVIRRMSDD---AIVFALANPIP--EIMPEK 307
                                       98888777655544....4578888875..69*****8.78899********865...6********86..789999 PP

                                       HHHHTTT-SEEEESS----EEETSEEE--EE--GGGTHHHHHHHHHHTT-SS--HHHHHHHHHHHHTT--HHHHHTT CS
                           Malic_M 157 vlkwtdgkalvasGsPfkpvelngktyeigQaNNayifPglglgvivarakritdemllaaaealaelvseeelkeg 233
                                       + +   g+ ++a+G          +  +++Q NN++ fPg+  g++ +ra++it +m  aaaea+a+++se+el e+
  gi|242398116|ref|YP_002993540.1| 308 AKE--AGARIIATG----------RSDYPNQINNVLGFPGIFRGALDVRAREITFNMNIAAAEAIANTISEDELFED 372
                                       876..589999998..........57789*********************************************999 PP

                                       -SS-- CS
                           Malic_M 234 sllPe 238
                                        + P+
  gi|242398116|ref|YP_002993540.1| 373 YIIPT 377
                                       99996 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       2.9   5.8e+03     110     124 ..     148     164 ..     132     173 .. 0.72
   2 !   18.5   1.0   8.4e-07    0.0017       5      45 ..     190     231 ..     187     316 .. 0.78
   3 ?   -3.2   0.0         4   7.9e+03      21      50 ..     407     436 ..     406     437 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.9
                                       E--SS-..SB-TTGGGS CS
                      Shikimate_DH 110 DiavPR..dvepevael 124
                                       Di+ PR  ++e+++++ 
  gi|242398116|ref|YP_002993540.1| 148 DISAPRcfEIEEKLKKE 164
                                       99999966667666655 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 8.4e-07
                                       HHHS...TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESS CS
                      Shikimate_DH   5 kkle.slkekkvlliGaGemaelvakhLlakgvkkvvvaNRt 45 
                                       k+++ ++++ kv++ GaG  +  +ak L+++g+++++++ R 
  gi|242398116|ref|YP_002993540.1| 190 KIVGkKFADIKVVIKGAGAAGIAIAKILHQRGIREILIVDRK 231
                                       5666589999*******************************7 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 4
                                       SHHHHHHHHHHHCCT-CEEEEEESSHHHHH CS
                      Shikimate_DH  21 GemaelvakhLlakgvkkvvvaNRtlerak 50 
                                       Ge  e+ +k+L +   + ++ +NR +++ k
  gi|242398116|ref|YP_002993540.1| 407 GEWVEEHIKKLRSFYWHYIAPINRKRRKFK 436
                                       788888999999999999999999998876 PP

>> ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.2   2.4e+03     119     146 ..      58      85 ..       7     131 .. 0.66
   2 !   17.8   0.1     1e-06    0.0021      24      70 ..     188     236 ..     171     262 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.2
                                       E-.SSTTSB-HHHHTHTHHTT-SEEE-SS CS
                     ELFV_dehydrog 119 Pc.AtqneideenakalikngvklvvEgA 146
                                       Pc A+ n  + en    i n+v ++  g+
  gi|242398116|ref|YP_002993540.1|  58 PCkAIANGESYENYT-IIPNTVAVISDGS 85 
                                       555555555555544.4444444444443 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 1e-06
                                       HTTTS..-STTEEEEEE--SHHHHHHHHHHHHCT-EEEEEEESSEEEEE CS
                     ELFV_dehydrog  24 klkld..slegkrvaisGsGnvgsyaallltelgakvvavsDssGviyd 70 
                                        lk+   ++++ +v+i G G  g + a++l+++g + + ++D +G+i++
  gi|242398116|ref|YP_002993540.1| 188 ALKIVgkKFADIKVVIKGAGAAGIAIAKILHQRGIREILIVDRKGIIHE 236
                                       333333379999***********************************96 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   2.3e-06    0.0045       2      34 ..     199     231 ..     198     244 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.3e-06
                                       EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSS CS
                     FAD_binding_3   2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrs 34 
                                       ++V+I GaG aG+  a++L+++G+r +l+  r+
  gi|242398116|ref|YP_002993540.1| 199 IKVVIKGAGAAGIAIAKILHQRGIREILIVDRK 231
                                       68***********************77665554 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   1.0   5.5e-06     0.011      14      50 ..     194     230 ..     186     233 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5.5e-06
                                       HHHHTSEEEEE--SHHHHHHHHHHHHHTTTEEEEEES CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF  14 ekLrdskvllvGaGglGsellknLalsGvgkltlvDn 50 
                                       +k +d kv++ GaG+ G  ++k L   G++++ +vD 
  gi|242398116|ref|YP_002993540.1| 194 KKFADIKVVIKGAGAAGIAIAKILHQRGIREILIVDR 230
                                       78999*******************************6 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   1.6   8.4e-06     0.017       1      32 [.     202     233 ..     202     240 .. 0.91
   2 ?    0.1   0.0      0.19   3.8e+02     127     142 ..     313     328 ..     306     340 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 8.4e-06
                       Pyr_redox_3   1 iIiGaGPaGlaaaielkkagledylilEkgni 32 
                                       +I GaG+aG+a+a  l + g+ ++li++++ i
  gi|242398116|ref|YP_002993540.1| 202 VIKGAGAAGIAIAKILHQRGIREILIVDRKGI 233
                                       577*************************9866 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.19
                       Pyr_redox_3 127 kviiAtGefdkPnkln 142
                                         iiAtG+ d+Pn+ n
  gi|242398116|ref|YP_002993540.1| 313 ARIIATGRSDYPNQIN 328
                                       559*********9865 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 ?   12.6   0.2   6.1e-05      0.12       3      28 ..     205     231 ..     203     234 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.1e-05
                                       --SHHHHHHHHHHHCCTE.EEEEE-SS CS
                     NAD_binding_8   3 GaGlsGlvaAylLakagf.dvlllekr 28 
                                       GaG++G ++A  L+++g+ ++l++++ 
  gi|242398116|ref|YP_002993540.1| 205 GAGAAGIAIAKILHQRGIrEILIVDRK 231
                                       9***************9967***9985 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   1.6    0.0002      0.39       1      33 [.     200     235 ..     200     239 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0002
                                       EEEEECTSHHHHHHHHHHHHTT...EEEEESSSSTT CS
                               DAO   1 dvviiGGGiiGlstAyeLarrg...Vtllekgdiag 33 
                                       +vvi G+G +G+++A  L +rg   +++++++ i++
  gi|242398116|ref|YP_002993540.1| 200 KVVIKGAGAAGIAIAKILHQRGireILIVDRKGIIH 235
                                       599******************9*********97766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (440 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.50
# Mc/sec: 2627.11
//
Query:       gi|242398117|ref|YP_002993541.1|  [L=268]
Description: Diphthine synthase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.4e-21   75.5   0.0    6.8e-21   75.2   0.0    1.1  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
     0.0047   16.9   0.1     0.0099   15.9   0.1    1.5  1  DUF1788       Domain of unknown function (DUF1788)
  ------ inclusion threshold ------
       0.15   11.9   0.2       0.15   11.9   0.2    1.9  2  KH_2          KH domain


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.2   0.0   1.1e-24   6.8e-21       2     199 ..       7     215 ..       6     227 .. 0.77

  Alignments for each domain:
  == domain 1  score: 75.2 bits;  conditional E-value: 1.1e-24
                      TP_methylase   2 lylVGvGpGdpellTvrAlralktadvvlgddsraleil.ldllaeeleleapmgke.kepleeayeeiaealaeal 76 
                                       +y++G+G+ d +++T+++l++ k++d+v+++   ++++l    +++   +e++ gk+ k  ++e+ e + e+++  +
  gi|242398117|ref|YP_002993541.1|   7 IYFIGLGLYDEKDITLKGLEIAKNCDLVFAEF--YTSLLaGTTIEK---IEQQIGKPiKLLSREDVELNFEKIVLNN 78 
                                       8***************************8555..333330222222...3333444424455555666777778888 PP

                      TP_methylase  77 ragkdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvllpglakeeere 153
                                       ++ +dV++l++GDP+v++t++ l   +ra++ g++  vi ++s+  +a++ +g+ ++++g++ +v +p +++ + ++
  gi|242398117|ref|YP_002993541.1|  79 AKERDVAFLTAGDPMVATTHADLR--IRAKQMGVRSYVIHAPSIY-SAISITGLQIYKFGKSATVAYPEKNWFPTSH 152
                                       88889******************6..99999*********98766.6789****************99999****** PP

                      TP_methylase 154 leallan....gdtlvllkaprk.............laelaelLkea.lyddttpvavveragt 199
                                       +e + +n     +tl++l+   +             l ++ e  ke+ +  ++t v++ +rag 
  gi|242398117|ref|YP_002993541.1| 153 YEVIKENkergLHTLLFLDIKAEqkkymtaneamniLLQVEEMKKEEiF-TEDTLVVILARAGS 215
                                       ******9999999999995544234566655556656666666677755.55669999999885 PP

>> DUF1788  Domain of unknown function (DUF1788)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   1.7e-06    0.0099      34     103 ..     182     247 ..     153     262 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.7e-06
                           DUF1788  34 llealkkvlkseeelikkikekieekeadvvfltgvGkvyPllRshtlLnnlqsvvkkvpvvlfyPGeyd 103
                                       ++ea++ +l++ ee+    ke+i ++++ vv+l ++G++ P l++  + + +++ + k p +l+ PG+ +
  gi|242398117|ref|YP_002993541.1| 182 ANEAMNILLQV-EEMK---KEEIFTEDTLVVILARAGSLTPTLKAGYVREMIKEDFGKQPHILIVPGKLH 247
                                       23333333333.2221...2233333456**************************************986 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   2.5e-05      0.15      44      73 ..      45      74 ..      44      79 .. 0.91
   2 ?   -2.8   0.1      0.97   5.8e+03      53      77 ..     175     199 ..     171     200 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.5e-05
                                      GHHHHHHHHHHHHHHHHHHTTCEEEEEEEE CS
                              KH_2 44 GsnikkigkelrkdieklegkkVklnivkV 73
                                      G +i+ki+++++k i+ l   +V+ln +k+
  gi|242398117|ref|YP_002993541.1| 45 GTTIEKIEQQIGKPIKLLSREDVELNFEKI 74
                                      899***********************9987 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.97
                                       HHHHHHHHHHTTCEEEEEEEETTTG CS
                              KH_2  53 elrkdieklegkkVklnivkVkkpe 77 
                                       e +k + + e  ++ l++++ kk e
  gi|242398117|ref|YP_002993541.1| 175 EQKKYMTANEAMNILLQVEEMKKEE 199
                                       4555565666667888888888765 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:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1665.86
//
Query:       gi|242398118|ref|YP_002993542.1|  [L=41]
Description: hypothetical protein TSIB_0125 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       206  (0.0114898); expected 358.6 (0.02)
Passed bias filter:                      179  (0.00998383); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 263.42
//
Query:       gi|242398119|ref|YP_002993543.1|  [L=350]
Description: methyltransferase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.3e-117  391.3   0.3   1.7e-117  390.9   0.3    1.1  1  DUF43            Branched-chain polyamine synthase A C-termin
      0.002   18.0   0.0     0.0029   17.4   0.0    1.3  1  N6-adenineMlase  Probable N6-adenine methyltransferase
  ------ inclusion threshold ------
      0.042   13.9   0.0      0.094   12.8   0.0    1.6  1  DUF1217          Protein of unknown function (DUF1217)
      0.052   13.2   0.0       0.11   12.2   0.0    1.5  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
       0.12   12.2   0.0       0.27   11.0   0.0    1.7  1  Methyltransf_31  Methyltransferase domain
       0.17   11.2   0.0       0.33   10.2   0.0    1.4  1  GidB             rRNA small subunit methyltransferase G


Domain annotation for each model (and alignments):
>> 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 !  390.9   0.3  5.7e-121  1.7e-117       1     243 []     105     349 ..     105     349 .. 0.99

  Alignments for each domain:
  == domain 1  score: 390.9 bits;  conditional E-value: 5.7e-121
                                       HHHHHHHHHHTT-----GGGT---B-HHHHHHHHHHHHHTT-STT-EEEEES-TT-HHHHHHHHT--SEEEEE-S-H CS
                             DUF43   1 dllekfreiakdRPeaieeyDqgfvtpettvaRvallyerGDLegkeilvlGdDDLtslalaLtglpkkvvvvDiDe 77 
                                       dlle+frei+k+RPe+++e+Dq++vtpett+aRval+++rGDL++ke++vlGdDDLts+al+L+ lpk+++v+DiD+
  gi|242398119|ref|YP_002993543.1| 105 DLLEQFREIVKERPEPKHEFDQAYVTPETTIARVALMHTRGDLKNKEVFVLGDDDLTSIALMLSSLPKRIAVLDIDD 181
                                       79*************************************************************************** PP

                                       HHHHHHHHHHHHHT--.EEEE---TTS---TTTSS-BSEEEE---SSHHHHHHHHHHHHHTB-STT-EEEEEE-TTT CS
                             DUF43  78 Rlikfiervakelglk.ieaivyDlrkplpeelkekFdvfitDPpetvealkaFlgRGiaaLkgegcagYlgltrre 153
                                       Rl++fi++ a+elg++ +e++++Dlrkplpe++ +kFd+fitDPpetvea++aF+gRGia+Lkg gcagY+g+trre
  gi|242398119|ref|YP_002993543.1| 182 RLTNFIKKTAEELGYNnVEIFTFDLRKPLPEYAIRKFDTFITDPPETVEAIRAFVGRGIATLKGPGCAGYFGITRRE 258
                                       ***************************************************************************** PP

                                       --HHHHHHHHHHHH.TS--EEEEEEEEEEEB---S-GGGSHHHHHSSS----SS---EEEEEEEE--TT----SSS- CS
                             DUF43 154 ssldkWkeiqklll.emgvvitdlirnFneYenweykeetraikllpvkkkpekiwyksalfrietlkgkrkveeev 229
                                       ss+dkW++i kll+ e++v itd+irnFneY+nw+y eetra+kllp+k  p+++wy+s++fri+t++g+r++eee+
  gi|242398119|ref|YP_002993543.1| 259 SSVDKWHQIEKLLItEFNVAITDIIRNFNEYVNWGYVEETRAWKLLPIKTMPTYNWYTSYMFRIQTIEGSRGYEEEI 335
                                       ************999************************************************************** PP

                                       -S.S-S--XXXXXX CS
                             DUF43 230 kkvedlykdeesst 243
                                       +  ++ly deesst
  gi|242398119|ref|YP_002993543.1| 336 TVGQELYDDEESST 349
                                       ***********986 PP

>> N6-adenineMlase  Probable N6-adenine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   9.8e-07    0.0029      49     157 ..     171     291 ..     122     294 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 9.8e-07
                   N6-adenineMlase  49 kekvlLleiDkrFealyge.........ekfvfYdlnnpeelpeelkgkfdviviDPPFlseeclkklaktaklllk 116
                                        +++ +l+iD+r ++++++          + + +dl++p+  pe    kfd +++DPP  +e +   + + + +l+ 
  gi|242398119|ref|YP_002993543.1| 171 PKRIAVLDIDDRLTNFIKKtaeelgynnVEIFTFDLRKPL--PEYAIRKFDTFITDPPETVEAIRAFVGRGIATLKG 245
                                       38999*******9999888888888888558999999995..467799**********9999998888887777744 PP

                   N6-adenineMlase 117 .......klilctgevmee.lekll...gvkktkfepehenklsnefrlYan 157
                                                  +t  + e+ ++k     ++ +t+f++ ++  + ++f+ Y n
  gi|242398119|ref|YP_002993543.1| 246 pgcagyfG---IT--RRESsVDKWHqieKLLITEFNVAITD-IIRNFNEYVN 291
                                       76664321...33..22222333332224555677776665.6666666666 PP

>> DUF1217  Protein of unknown function (DUF1217)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   3.2e-05     0.094      72     137 ..     124     189 ..      48     205 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.2e-05
                                       HHHHHHTT-HHH.HHHHHHHHHSTT--SHHHHHTSHHHHHHHHTTTT----------TTHHHHHHHS CS
                           DUF1217  72 leeevgekdegv.rlAlyfkrkaptltsaydiLgdkaLskvvntvlgLpatsgaadldkqaalikkk 137
                                       ++++    ++++ r Al  +r   + +++  +Lgd+ L++++ +   Lp+ ++ +d+d + + + kk
  gi|242398119|ref|YP_002993543.1| 124 FDQAYVTPETTIaRVALMHTRGDLKNKEV-FVLGDDDLTSIALMLSSLPKRIAVLDIDDRLTNFIKK 189
                                       44444444445458899888876666665.59************************99987654444 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 ?   12.2   0.0   3.5e-05      0.11      29      89 ..     167     227 ..     159     234 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.5e-05
                                       HTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC..EEEEEEEE-- CS
                   Methyltr_RsmB-F  29 lmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlggelfDriLlDaPC 89 
                                       l +  +++  +d++++ ++ ++++ + Lg +n+ +++ D+rk+    + ++fD  + D P 
  gi|242398119|ref|YP_002993543.1| 167 LSSLPKRIAVLDIDDRLTNFIKKTAEELGYNNVEIFTFDLRKPLPEYAIRKFDTFITDPPE 227
                                       44556788999***999*************************977777789**99999885 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   8.9e-05      0.27      31      81 ..     174     224 ..     160     288 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 8.9e-05
                   Methyltransf_31  31 vvGiDiseeaielArenaqklgldnveFeqgdiee.leklledekfDlilsn 81 
                                       +  +Di+ +  ++ ++ a++lg++nve    d  + l++ ++ +kfD  +++
  gi|242398119|ref|YP_002993543.1| 174 IAVLDIDDRLTNFIKKTAEELGYNNVEIFTFDLRKpLPE-YAIRKFDTFITD 224
                                       6678999999999*************************8.8889***99987 PP

>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00011      0.33      64     109 ..     163     208 ..     160     223 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00011
                                       HHHHHH-TTSEEEEEES-HHHHHHHHHHHHHCT-SSEEEEES-CCC CS
                              GidB  64 ipLaiarpelkltLleslekkiaFLeevkeelklenveivearaee 109
                                       i L +    +++++l+ + + ++F+++  eel+ +nvei   ++ +
  gi|242398119|ref|YP_002993543.1| 163 IALMLSSLPKRIAVLDIDDRLTNFIKKTAEELGYNNVEIFTFDLRK 208
                                       5556666667899*************************98877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 2197.61
//
Query:       gi|242398120|ref|YP_002993544.1|  [L=108]
Description: hypothetical protein TSIB_0127 [Thermococcus sibiricus MM 739]
Scores for complete 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-22   77.9   0.1    6.4e-22   77.5   0.1    1.2  1  FeS_assembly_P  Iron-sulfur cluster assembly protein
  ------ inclusion threshold ------
      0.011   15.9   0.2      0.078   13.1   0.1    2.1  2  NifU            NifU-like domain
       0.41   11.1   2.2        1.1    9.8   0.1    2.6  2  HMA             Heavy-metal-associated domain


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 !   77.5   0.1   1.1e-25   6.4e-22       1      73 [.      12      85 ..      12      86 .. 0.97

  Alignments for each domain:
  == domain 1  score: 77.5 bits;  conditional E-value: 1.1e-25
                                      HHHHHHHHTT-B-TTTSSBCCCCT---EEEE-T.-EEEEEE--SSTT-TTHHHHHHHHHHHHC.STT--EEEEE CS
                    FeS_assembly_P  1 keavlaaLrtVtDPelgvdlvslglvreidieg.gkVsvditltypacslaeairadaeaalralpgvevveVe 73
                                      ke vl+ L++V+DPe+g+d+v+lgl++e++i+  ++V+v++t+t+p+c+l   + +++e+++  +pgv+++e+e
  gi|242398120|ref|YP_002993544.1| 12 KEMVLEKLKEVIDPEIGIDVVNLGLIYELKINPdNTVYVKMTMTTPGCPLTMWLLQAVEQKILEIPGVKDAEIE 85
                                      689*****************************99************************************9998 PP

>> NifU  NifU-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1     0.042   2.5e+02      48      64 ..      11      27 ..       3      30 .. 0.77
   2 ?   13.1   0.1   1.3e-05     0.078      24      58 ..      41      75 ..      15      83 .. 0.69

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.042
                                      HHHHHHHHHHHH-TT-- CS
                              NifU 48 lkegiekaLkeevpevk 64
                                      +ke++ ++Lke +++++
  gi|242398120|ref|YP_002993544.1| 11 TKEMVLEKLKEVIDPEI 27
                                      68999999999998765 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 1.3e-05
                                      EEETT.EEEEEEESGGGG-....THHHHHHHHHHHH CS
                              NifU 24 dvdeg.vVkvrlqGaCsgCpsstvtlkegiekaLke 58
                                      +++ + +V+v+++    gCp     l +++e+++ e
  gi|242398120|ref|YP_002993544.1| 41 KINPDnTVYVKMTMTTPGCPLTMWLL-QAVEQKILE 75
                                      444445**************865555.*****9986 PP

>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.3      0.16   9.7e+02      21      56 ..      17      23 ..       6      55 .. 0.58
   2 ?    9.8   0.1   0.00018       1.1      15      33 ..      68      86 ..      67     106 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.16
                               HMA 21 selpgVesvkvdlatktvtVegdaestklrkiieai 56
                                      ++l++V                             i
  gi|242398120|ref|YP_002993544.1| 17 EKLKEV-----------------------------I 23
                                      444444.............................2 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00018
                               HMA 15 kvekvLselpgVesvkvdl 33
                                      +ve+ ++e+pgV+++++ l
  gi|242398120|ref|YP_002993544.1| 68 AVEQKILEIPGVKDAEIEL 86
                                      79**************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 708.20
//
Query:       gi|242398121|ref|YP_002993545.1|  [L=67]
Description: 4Fe-4S ferredoxin [Thermococcus sibiricus MM 739]
Scores for complete 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-19   68.4   7.3    6.4e-19   68.3   7.3    1.0  1  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
      3e-16   59.9   8.4    3.4e-16   59.7   8.4    1.1  1  Fer4_15   4Fe-4S single cluster domain
    0.00068   19.4   8.7     0.0032   17.2   1.6    2.3  2  Fer4      4Fe-4S binding domain
     0.0014   18.7   2.5     0.0021   18.1   2.5    1.3  1  Fer4_19   Divergent 4Fe-4S mono-cluster
     0.0068   16.5   4.0      0.011   15.8   4.0    1.4  1  Fer4_10   4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.014   15.5   7.6      0.045   13.9   7.8    1.7  1  Fer4_21   4Fe-4S dicluster domain
      0.051   13.7   0.6      0.051   13.7   0.6    2.4  2  Fer4_6    4Fe-4S binding domain
       0.13   12.8   4.3        1.1    9.9   0.3    2.1  3  Fer4_7    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 !   68.3   7.3   2.9e-22   6.4e-19       1      56 [.       8      62 ..       8      64 .. 0.97

  Alignments for each domain:
  == domain 1  score: 68.3 bits;  conditional E-value: 2.9e-22
                           Fer4_13  1 VDrdtCiacgaCvelaPdvFeeddeggasvvaeqptseeekadaeeAadaCPvesI 56
                                      VD+d Ci++++C++l+PdvFe++de g+s+v  +  +e+++++a+eAa+aCPv++I
  gi|242398121|ref|YP_002993545.1|  8 VDQDVCIGDAICASLCPDVFEMNDE-GKSQVIVEIIGEDLIDCAREAAEACPVSCI 62
                                      9***********************9.899**************************9 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.7   8.4   1.5e-19   3.4e-16       1      66 []       6      64 ..       6      64 .. 0.97

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 1.5e-19
                           Fer4_15  1 VvvDrdaCigcglCvaeapevfeldedglasvllddgeiaegevpddeeeaaqeAaraCPvdAIrv 66
                                      V+vD+d Cig++ C+ ++p+vfe++++g+++v++       + +++d++++a+eAa+aCPv +I +
  gi|242398121|ref|YP_002993545.1|  6 VRVDQDVCIGDAICASLCPDVFEMNDEGKSQVIV-------EIIGEDLIDCAREAAEACPVSCIYI 64
                                      89*******************************7.......69*********************87 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   1.6   1.4e-06    0.0032       2      19 ..       7      24 ..       6      26 .. 0.93
   2 !    6.4   0.9    0.0038       8.6      15      24 .]      54      63 ..      54      63 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.4e-06
                                      EEETTTSSS-THHHHHST CS
                              Fer4  2 videekCigCGaCvevCP 19
                                       +d++ Cig  +C++ CP
  gi|242398121|ref|YP_002993545.1|  7 RVDQDVCIGDAICASLCP 24
                                      79**************** PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0038
                                      HHHSTTTEEE CS
                              Fer4 15 vevCPvgAIt 24
                                      +e+CPv +I+
  gi|242398121|ref|YP_002993545.1| 54 AEACPVSCIY 63
                                      69*****996 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 !   18.1   2.5   9.2e-07    0.0021       7      55 ..       5      58 ..       2      64 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 9.2e-07
                           Fer4_19  7 tiednrelCihsgnCvkglpevFdpkrk...pwi..kpdeasteeiievverCP 55
                                      ++  ++++Ci+ + C    p+vF+++++   + i     e  ++ ++e++e CP
  gi|242398121|ref|YP_002993545.1|  5 KVRVDQDVCIGDAICASLCPDVFEMNDEgksQVIveIIGEDLIDCAREAAEACP 58
                                      678899******************998833333355556666799999999999 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   4.0     5e-06     0.011       1      52 [.       5      58 ..       5      63 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5e-06
                           Fer4_10  1 kvvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtg..cgaCv 52
                                      kv++d+d Ci+ + C + CP  +++++  + + + e + +++ +C +   +aC 
  gi|242398121|ref|YP_002993545.1|  5 KVRVDQDVCIGDAICASLCPDVFEMNDEGKSQVIVEIIGEDLIDCAReaAEACP 58
                                      5889*****************999999999999999998888888763334554 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   7.8     2e-05     0.045       2      57 ..       7      62 ..       6      64 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2e-05
                           Fer4_21  2 ridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnl.CssvCPvedci 57
                                      r+d+d Cig   C+  C+d      e++++ +++++ ++ + C+   ++ CPv  ci
  gi|242398121|ref|YP_002993545.1|  7 RVDQDVCIGDAICASLCPDVFEMNDEGKSQVIVEIIGEDLIDCAReAAEACPV-SCI 62
                                      79****************9555555677777889999******863789***9.999 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.6   2.3e-05     0.051       1      20 [.       5      24 ..       5      38 .. 0.89
   2 ?   -1.0   2.8      0.98   2.2e+03      17      23 ..      55      61 ..      47      62 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.3e-05
                            Fer4_6  1 vveidpdkCigCgdCvrvCP 20
                                      +v++d+d Cig   C++ CP
  gi|242398121|ref|YP_002993545.1|  5 KVRVDQDVCIGDAICASLCP 24
                                      699***************** PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.98
                            Fer4_6 17 rvCPega 23
                                       +CP   
  gi|242398121|ref|YP_002993545.1| 55 EACPVSC 61
                                      5798765 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.3   0.00048       1.1      30      49 ..       5      24 ..       2      27 .. 0.90
   2 ?    8.6   5.2    0.0013       2.8       2      51 ..      13      60 ..      12      61 .. 0.83
   3 ?    3.7   0.7     0.043        96       9      21 ..      54      66 ..      47      67 .] 0.75

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00048
                            Fer4_7 30 kveidpekClgCgaCvavCP 49
                                      kv++d++ C+g   C++ CP
  gi|242398121|ref|YP_002993545.1|  5 KVRVDQDVCIGDAICASLCP 24
                                      689999*************9 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0013
                            Fer4_7  2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCga.CvavCPtg 51
                                      Cig   C++ Cp +++e+++e   k +  vei  e+ ++C +  +++CP+ 
  gi|242398121|ref|YP_002993545.1| 13 CIGDAICASLCP-DVFEMNDEG--KSQVIVEIIGEDLIDCAReAAEACPVS 60
                                      99999*******.999999984..344678888899999988899999985 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.043
                            Fer4_7  9 vaaCpvkaielde 21
                                      ++aCpv++i+++e
  gi|242398121|ref|YP_002993545.1| 54 AEACPVSCIYIEE 66
                                      4789999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.49u 0.34s 00:00:00.83 Elapsed: 00:00:00.53
# Mc/sec: 382.25
//
Query:       gi|242398122|ref|YP_002993546.1|  [L=59]
Description: Ferredoxin [Thermococcus sibiricus MM 739]
Scores for 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   71.5   6.7    7.6e-20   71.2   6.7    1.1  1  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
    1.4e-16   61.0   7.7    2.1e-16   60.4   7.7    1.3  1  Fer4_15   4Fe-4S single cluster domain
    1.9e-08   33.7   7.6    1.5e-06   27.8   5.7    2.3  2  Fer4      4Fe-4S binding domain
    2.9e-07   30.3   2.0    2.9e-07   30.3   2.0    2.2  2  Fer4_6    4Fe-4S binding domain
    2.7e-06   27.4   1.7    3.2e-06   27.1   1.7    1.1  1  Fer4_19   Divergent 4Fe-4S mono-cluster
    2.7e-06   27.4   3.4    3.9e-06   26.9   0.9    2.2  2  Fer4_4    4Fe-4S binding domain
    3.4e-06   27.5  17.4    0.00079   20.0   2.3    1.9  2  Fer4_7    4Fe-4S dicluster domain
    6.5e-06   25.9   2.8    6.5e-06   25.9   2.8    2.0  2  Fer4_2    4Fe-4S binding domain
    3.8e-05   23.7   6.6    8.5e-05   22.6   6.6    1.6  1  Fer4_10   4Fe-4S dicluster domain
    4.9e-05   23.4  14.5     0.0036   17.4   5.3    1.6  2  Fer4_9    4Fe-4S dicluster domain
    0.00014   21.9   7.2    0.00031   20.8   7.2    1.6  1  Fer4_21   4Fe-4S dicluster domain
     0.0042   17.5   4.9     0.0076   16.7   4.9    1.5  1  Fer4_8    4Fe-4S dicluster domain
     0.0083   16.6   3.0      0.017   15.7   3.0    1.5  1  Fer4_17   4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.022   15.7   8.0       0.32   11.9   5.5    2.2  2  Fer4_16   4Fe-4S double cluster binding domain
      0.052   14.4   2.5      0.052   14.4   2.5    1.5  2  Fer4_22   4Fe-4S dicluster domain
       0.14   13.2   9.0       0.61   11.1   4.6    2.3  2  Fer4_3    4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.2   6.7   6.8e-23   7.6e-20       1      58 []       5      58 ..       5      58 .. 0.91

  Alignments for each domain:
  == domain 1  score: 71.2 bits;  conditional E-value: 6.8e-23
                           Fer4_13  1 VDrdtCiacgaCvelaPdvFeeddeggasvvaeqptseeekadaeeAadaCPvesIgv 58
                                      VD+dtCi+cg+C++++PdvFe+ddeg+a +     ++e++ ++a+eAa++CP+ sI+v
  gi|242398122|ref|YP_002993546.1|  5 VDKDTCIGCGVCASICPDVFEMDDEGKAQA----LVTETDLECAKEAAESCPTGSITV 58
                                      9************************77644....4778899***************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 !   60.4   7.7   1.9e-19   2.1e-16       1      66 []       3      58 ..       3      58 .. 0.95

  Alignments for each domain:
  == domain 1  score: 60.4 bits;  conditional E-value: 1.9e-19
                           Fer4_15  1 VvvDrdaCigcglCvaeapevfeldedglasvllddgeiaegevpddeeeaaqeAaraCPvdAIrv 66
                                      V vD+d+Cigcg+C+  +p+vfe+d++g+a+ l          v++++ e+a+eAa++CP++ I+v
  gi|242398122|ref|YP_002993546.1|  3 VSVDKDTCIGCGVCASICPDVFEMDDEGKAQAL----------VTETDLECAKEAAESCPTGSITV 58
                                      89****************************555..........899*****************997 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   5.7   1.3e-09   1.5e-06       2      19 ..       4      21 ..       3      23 .. 0.93
   2 ?    5.8   0.0     0.012        13      15      24 .]      48      57 ..      48      57 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 1.3e-09
                                      EEETTTSSS-THHHHHST CS
                              Fer4  2 videekCigCGaCvevCP 19
                                       +d++ CigCG C+++CP
  gi|242398122|ref|YP_002993546.1|  4 SVDKDTCIGCGVCASICP 21
                                      69**************** PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.012
                                      HHHSTTTEEE CS
                              Fer4 15 vevCPvgAIt 24
                                      +e CP+g It
  gi|242398122|ref|YP_002993546.1| 48 AESCPTGSIT 57
                                      589****996 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   2.0   2.6e-10   2.9e-07       1      20 [.       2      21 ..       2      35 .. 0.84
   2 ?    2.0   0.2      0.22   2.5e+02      18      24 .]      50      56 ..      42      56 .. 0.69

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 2.6e-10
                            Fer4_6  1 vveidpdkCigCgdCvrvCP 20
                                      +v +d+d CigCg C+++CP
  gi|242398122|ref|YP_002993546.1|  2 KVSVDKDTCIGCGVCASICP 21
                                      689***************** PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.22
                            Fer4_6 18 vCPegai 24
                                       CP+g i
  gi|242398122|ref|YP_002993546.1| 50 SCPTGSI 56
                                      4**9865 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 !   27.1   1.7   2.8e-09   3.2e-06       7      61 ..       2      58 ..       1      59 [] 0.87

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 2.8e-09
                           Fer4_19  7 tiednrelCihsgnCvkglpevFdpkrkpwikp..deasteeiievverCPSGALsy 61
                                      +++ +++ Ci+ g+C    p+vF++++++  +    e++ e ++e++e+CP G +++
  gi|242398122|ref|YP_002993546.1|  2 KVSVDKDTCIGCGVCASICPDVFEMDDEGKAQAlvTETDLECAKEAAESCPTGSITV 58
                                      7999***********************9888542267777*************9875 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.9   3.5e-09   3.9e-06       1      16 [.       7      22 ..       7      36 .. 0.90
   2 ?    0.6   0.1      0.95   1.1e+03      13      17 .]      50      54 ..      48      54 .. 0.76

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 3.5e-09
                            Fer4_4  1 qerCigCgsCvaaCPq 16
                                      +++CigCg+C ++CP+
  gi|242398122|ref|YP_002993546.1|  7 KDTCIGCGVCASICPD 22
                                      699************4 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.95
                            Fer4_4 13 aCPqg 17
                                      +CP+g
  gi|242398122|ref|YP_002993546.1| 50 SCPTG 54
                                      79975 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   2.3   7.1e-07   0.00079      30      49 ..       2      21 ..       1      24 [. 0.86
   2 !   18.4   7.4   2.2e-06    0.0025       1      51 [.       9      54 ..       9      55 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 7.1e-07
                            Fer4_7 30 kveidpekClgCgaCvavCP 49
                                      kv +d ++C+gCg+C++ CP
  gi|242398122|ref|YP_002993546.1|  2 KVSVDKDTCIGCGVCASICP 21
                                      67889999999999999999 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 2.2e-06
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCga.CvavCPtg 51
                                      +CigCg C++ Cp +++e+d+e +++     +++ e+ l C +  ++ CPtg
  gi|242398122|ref|YP_002993546.1|  9 TCIGCGVCASICP-DVFEMDDEGKAQ-----ALVTETDLECAKeAAESCPTG 54
                                      6************.999999984333.....344455556655577888876 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   2.8   5.8e-09   6.5e-06       3      21 ..       3      21 ..       1      22 [. 0.93
   2 ?   -0.2   0.3       1.2   1.3e+03      18      22 .]      49      53 ..      42      53 .. 0.74

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 5.8e-09
                            Fer4_2  3 vvvdtdrCigCgaCvsaCP 21
                                      v vd d+CigCg C s CP
  gi|242398122|ref|YP_002993546.1|  3 VSVDKDTCIGCGVCASICP 21
                                      679**************** PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.2
                            Fer4_2 18 saCPa 22
                                       +CP+
  gi|242398122|ref|YP_002993546.1| 49 ESCPT 53
                                      46986 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   6.6   7.6e-08   8.5e-05       1      56 []       2      52 ..       2      57 .. 0.63

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 7.6e-08
                           Fer4_10  1 kvvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcg.aCveaCP 56
                                      kv +d+dtCi+Cg C + CP  +      + ++e++a+  + e   +c  + +e+CP
  gi|242398122|ref|YP_002993546.1|  2 KVSVDKDTCIGCGVCASICPDVF------EMDDEGKAQALVTETDLECAkEAAESCP 52
                                      5789****************944......3333333333333333344334555554 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   1.7     6e-06    0.0067      34      48 ..       8      22 ..       3      25 .. 0.81
   2 !   17.4   5.3   3.3e-06    0.0036       2      49 ..      10      54 ..       9      56 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 6e-06
                            Fer4_9 34 eaCigCgaCveaCpk 48
                                      + CigCg C+ +Cp 
  gi|242398122|ref|YP_002993546.1|  8 DTCIGCGVCASICPD 22
                                      369999999999995 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 3.3e-06
                            Fer4_9  2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkg 49
                                      C+gCg C + Cp    ++d+++  a +++++  +C   ++ +e Cp+g
  gi|242398122|ref|YP_002993546.1| 10 CIGCGVCASICPDVFEMDDEGKAQALVTETDL-ECA--KEAAESCPTG 54
                                      ************99999999999999998877.566..4567777776 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   7.2   2.8e-07   0.00031       3      58 ..       5      57 ..       3      58 .. 0.63

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.8e-07
                           Fer4_21  3 idedkCigCgkCliaCedtshqaieidaktvlkv.vedeCvGC.nlCssvCPvedcie 58
                                      +d+d+CigCg C+  C+d      e+d++ +++  v+++   C +  ++ CP+ + i+
  gi|242398122|ref|YP_002993546.1|  5 VDKDTCIGCGVCASICPD----VFEMDDEGKAQAlVTETDLECaKEAAESCPT-GSIT 57
                                      799999999999999996....5666655433321455445551456778885.7665 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   4.9   6.8e-06    0.0076       3      51 ..       8      51 ..       6      56 .. 0.61

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 6.8e-06
                            Fer4_8  3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsC 51
                                      + Ci+Cg C s Cp + +++      +g+a++ v e++ + ++ea++sC
  gi|242398122|ref|YP_002993546.1|  8 DTCIGCGVCASICPDVFEMD-----DEGKAQALVTETDLECAKEAAESC 51
                                      68************555543.....333333323333333335666666 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   3.0   1.5e-05     0.017       2      28 ..      10      38 ..       9      56 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.5e-05
                           Fer4_17  2 CiqCgyClpeCpsyeaydnepk..kllra 28
                                      Ci+Cg C+  Cp   ++d+e k   l+ +
  gi|242398122|ref|YP_002993546.1| 10 CIGCGVCASICPDVFEMDDEGKaqALVTE 38
                                      99*********987777765431134444 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   5.5   0.00029      0.32       1      14 [.       9      22 ..       9      48 .. 0.77
   2 ?    4.7   0.2     0.054        61       8      19 ..      47      58 ..      41      59 .] 0.76

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00029
                           Fer4_16  1 rCgtCgkCaevCPt 14
                                      +C++Cg Ca++CP 
  gi|242398122|ref|YP_002993546.1|  9 TCIGCGVCASICPD 22
                                      59999999999995 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.054
                           Fer4_16  8 CaevCPtnaike 19
                                       ae+CPt+ i+ 
  gi|242398122|ref|YP_002993546.1| 47 AAESCPTGSITV 58
                                      5799****9985 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   2.5   4.7e-05     0.052      76      94 ..       4      22 ..       1      24 [. 0.83
   2 ?    9.6   6.4    0.0015       1.7       2      19 ..      10      27 ..       9      57 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.7e-05
                           Fer4_22 76 kfgesgCvGCgRCieacpv 94
                                      ++++ +C+GCg C + cp 
  gi|242398122|ref|YP_002993546.1|  4 SVDKDTCIGCGVCASICPD 22
                                      568899***********95 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0015
                           Fer4_22  2 ClsCgaCtlvCptCsCfd 19
                                      C++Cg C+ +Cp  + +d
  gi|242398122|ref|YP_002993546.1| 10 CIGCGVCASICPDVFEMD 27
                                      888888888888654444 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   4.6   0.00055      0.61       1      12 [.      10      21 ..      10      23 .. 0.97
   2 ?    4.3   0.1     0.086        96       8      14 ..      48      54 ..      41      55 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00055
                            Fer4_3  1 CtgCgaCvevCP 12
                                      C+gCg C   CP
  gi|242398122|ref|YP_002993546.1| 10 CIGCGVCASICP 21
                                      ***********9 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.086
                            Fer4_3  8 vevCPvg 14
                                       e+CP+g
  gi|242398122|ref|YP_002993546.1| 48 AESCPTG 54
                                      589**98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.42u 0.32s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 383.86
//
Query:       gi|242398123|ref|YP_002993547.1|  [L=390]
Description: nicotinate phosphoribosyltransferase [Thermococcus sibiricus MM 739]
Scores for complete 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-27   94.8   0.0    6.6e-27   94.3   0.0    1.2  1  QRPTase_C       Quinolinate phosphoribosyl transferase, C-ter
    3.2e-07   30.8   0.0    1.2e-06   28.9   0.0    1.9  1  NAPRTase_C      Nicotinate phosphoribosyltransferase C-termin
    0.00013   22.0   0.0    0.00026   21.0   0.0    1.5  1  QRPTase_N       Quinolinate phosphoribosyl transferase, N-ter
  ------ inclusion threshold ------
      0.011   15.8   1.1      0.041   14.0   0.4    2.2  2  Zn-ribbon_8     Zinc ribbon domain
      0.031   14.1   0.0      0.092   12.6   0.0    1.7  1  NIR_SIR_ferr    Nitrite/Sulfite reductase ferredoxin-like hal
       0.11   12.9   0.0        1.5    9.2   0.0    2.2  2  NAPRTase_N      Nicotinate phosphoribosyltransferase (NAPRTas
       0.13   12.3   1.7       0.43   10.6   0.6    2.1  2  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai


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 !   94.3   0.0   2.6e-30   6.6e-27       1     169 []     115     303 ..     115     303 .. 0.97

  Alignments for each domain:
  == domain 1  score: 94.3 bits;  conditional E-value: 2.6e-30
                                       HHHHHHHHHHHHHCTSSEEEE-S---TTTHHHHHHHHHHTTSB.......--TSSTTTSEEE-HHHHHHHSSHHHHH CS
                         QRPTase_C   1 iAtltarmveaaksakvrildTRkttPglrllekyAvliGGgd.......nhrlgLsdmvlikdnhiaaagsiveav 70 
                                       iAt++ r + aak + v++++ R ++P+++++  +++ iGG+d          +g + + +++++ i  +g++v+a+
  gi|242398123|ref|YP_002993547.1| 115 IATAALRTKIAAKFKPVYSFGIRHMHPAIAPMIDRSAFIGGCDgvsgvlgAEMIGEKAVGTMPHALILTVGDQVKAW 191
                                       8*************************************************99************************* PP

                                       HHHHHHHTTTSE..EEEEESSHHHHHHHHHHT.....-SEEEEES--H..HHHHHHHHHH.HHHSTT....SEEEEE CS
                         QRPTase_C  71 ksvreavdkevk..ievevesleeleevleae.....adiimLDnfsv..eelkkaveel.keknkr....vlievS 133
                                       k ++e ++ ev+    v++  +e++e+v++ae      + ++LD++s+   ++k++vee+ +e + r    v+i+ S
  gi|242398123|ref|YP_002993547.1| 192 KYFDEIMPPEVPrtALVDTLCDEKFEAVMAAEtlgerLNAVRLDTPSSrrGNFKRIVEEVrWELDLRgyehVKIFLS 268
                                       *******99998899***************87777779********997799*******9999999999******** PP

                                       SS--TTTHHHHHCTT-SEEEECHHCHTB----EEEE CS
                         QRPTase_C 134 GgvtlenveeyaksgvdvisvgalthsvkalDislk 169
                                       Gg+ +e+++e+a+   d+++vg  + s+k++D+sl+
  gi|242398123|ref|YP_002993547.1| 269 GGLDEESLKELADVA-DAFGVGGSIASAKPVDFSLD 303
                                       ***************.******************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 !   28.9   0.0   4.8e-10   1.2e-06      42      86 ..     341     385 ..     328     388 .. 0.86

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 4.8e-10
                        NAPRTase_C  42 kkrveitpsrvekLlkkvfkdGklvyelpsleeireyvkeqlael 86 
                                        +++ +  ++ve+Llk+++++G++v elp+ +eireyv eq +++
  gi|242398123|ref|YP_002993547.1| 341 LEKCPVCGAKVEPLLKPLIENGEIVAELPKAKEIREYVLEQAKKF 385
                                       4566666799*******************************9987 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 !   21.0   0.0     1e-07   0.00026      26      89 .]      52     113 ..      43     113 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1e-07
                                       SSEEE-SHHHHHHHHHHHTTTEEEESS-TT-EEETTEEEEEEEEEHHHHHHHHHHHHHHHHHHH CS
                         QRPTase_N  26 eegvvaGlevaeevfellpglevellvkDGervekgdvlleieGnarallsaERvaLnllqrlS 89 
                                       ++gv+aG+e++++++e    ++v  + ++G+ +++ + +++ieG ++++   E  +L +l+++S
  gi|242398123|ref|YP_002993547.1|  52 NWGVLAGVEEVAKLLEGH-PVNVYSM-PEGTIFHPFESVMQIEGYYKEFGIFETALLGMLSQAS 113
                                       589*************77.6666555.*********************************9987 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.66   1.7e+03      11      19 ..     212     220 ..     210     225 .. 0.77
   2 ?   14.0   0.4   1.6e-05     0.041       6      37 ..     325     352 ..     324     355 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.66
                       Zn-ribbon_8  11 Cghefevlq 19 
                                       C+++fe+++
  gi|242398123|ref|YP_002993547.1| 212 CDEKFEAVM 220
                                       ******875 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 1.6e-05
                       Zn-ribbon_8   6 YrCeeCghefevlqsisdapltaCPeCgsevr 37 
                                       YrCe+ gh + v +   +++l++CP Cg++v+
  gi|242398123|ref|YP_002993547.1| 325 YRCEN-GHYHRVPA---EKKLEKCPVCGAKVE 352
                                       9****.87777555...677999******986 PP

>> NIR_SIR_ferr  Nitrite/Sulfite reductase ferredoxin-like half domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   3.6e-05     0.092       8      39 ..     259     289 ..     256     292 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.6e-05
                      NIR_SIR_ferr   8 gyymvrlrvpnGritaeqlraladiaekygsg 39 
                                       gy +v +++  G ++ e l++lad+a+++g g
  gi|242398123|ref|YP_002993547.1| 259 GYEHVKIFLS-GGLDEESLKELADVADAFGVG 289
                                       6789999998.99*****************76 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 ?    1.7   0.0      0.13   3.3e+02       3      52 ..      18      67 ..      17      71 .. 0.93
   2 ?    9.2   0.0    0.0006       1.5      88     125 .]      73     110 ..      64     110 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.13
                        NAPRTase_N  3 tDlYkltmaqavfkkgpdvevvfelffRkkpfkgeyaivagleevieyle 52
                                      tD+Y +   +++ +kg +++v  +    + p++ + +++ag+eev + le
  gi|242398123|ref|YP_002993547.1| 18 TDVYFIRTKKILEEKGIHKKVFADISTTSLPKGWNWGVLAGVEEVAKLLE 67
                                      99*****************************999**********999886 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0006
                        NAPRTase_N  88 evaveeeevvfpgepeirveGpwieaillEtplLaivn 125
                                       +++++e+++++p e  +++eG   e  ++Et+lL +++
  gi|242398123|ref|YP_002993547.1|  73 VYSMPEGTIFHPFESVMQIEGYYKEFGIFETALLGMLS 110
                                       478999999*************************8875 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.44   1.1e+03      17      22 ..     324     329 ..     317     331 .. 0.84
   2 ?   10.6   0.6   0.00017      0.43       1      10 [.     343     352 ..     343     355 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.44
                    DNA_ligase_ZBD  17 iyRCtn 22 
                                       +yRC n
  gi|242398123|ref|YP_002993547.1| 324 VYRCEN 329
                                       8***87 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00017
                    DNA_ligase_ZBD   1 hCPvCGsavv 10 
                                       +CPvCG++v+
  gi|242398123|ref|YP_002993547.1| 343 KCPVCGAKVE 352
                                       6*******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.51
# Mc/sec: 2319.88
//
Query:       gi|242398124|ref|YP_002993548.1|  [L=115]
Description: 6-pyruvoyl tetrahydropterin synthase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-24   85.6   0.0      3e-24   85.3   0.0    1.0  1  PTPS      6-pyruvoyl tetrahydropterin synthase


Domain annotation for each model (and alignments):
>> PTPS  6-pyruvoyl tetrahydropterin synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.3   0.0   1.7e-28     3e-24       2     120 ..       5     113 ..       4     114 .. 0.96

  Alignments for each domain:
  == domain 1  score: 85.3 bits;  conditional E-value: 1.7e-28
                                       EEEEEEEEEEE--TTTTGGGGSTEEEEEEEEEEEEEC-STCTTBSS-HHHHHHHHHHHHHCTTTEECCCC-CCHHCC CS
                              PTPS   2 iskefeFdaaHrlrkhegkcrnlHGHnykvevtvegeeldetgmvvdfgelkealkeileelDhkflnaddpeleel 78 
                                       i+ +f FdaaH ++  +g+ +++HGH+++ e+ +ege   ++g+++df el+++l++ +++l hk+ln     +e+ 
  gi|242398124|ref|YP_002993548.1|   5 IREKFVFDAAHAIK-INGELEEIHGHTFRGEIFIEGE--VREGYIMDFLELRKILNDAIAPLRHKNLN---RLFEN- 74 
                                       8899*********9.8899******************..899**************************...88986. PP

                                       S.--HHHHHHHHHHHHHHHHGCCCGCEEEEEEEEETTEEEEE CS
                              PTPS  79 lspTaEnlaklifeelkerlqekevklskvrvwEtpnswaey 120
                                         pT+En+a +i+e++k  l +++++l+k+ +wE +++ +e+
  gi|242398124|ref|YP_002993548.1|  75 --PTTENIALWIAEQVKMDL-PQGIRLHKIVLWEGEENGVEF 113
                                       ..******************.****************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 787.40
//
Query:       gi|242398125|ref|YP_002993549.1|  [L=93]
Description: hypothetical protein TSIB_0132 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       258  (0.0143901); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.48
# Mc/sec: 576.71
//
Query:       gi|242398126|ref|YP_002993550.1|  [L=732]
Description: Methionyl-tRNA synthetase [Thermococcus sibiricus MM 739]
Scores for complete 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-160  534.7   0.1   1.4e-160  534.4   0.1    1.1  1  tRNA-synt_1g   tRNA synthetases class I (M)
      3e-31  107.4   0.1    5.4e-31  106.6   0.1    1.4  1  tRNA_bind      Putative tRNA binding domain
    1.9e-15   56.2   0.1      2e-08   33.0   0.1    3.5  3  tRNA-synt_1    tRNA synthetases class I (I, L, M and V)
    4.6e-14   52.6   0.1    9.5e-14   51.6   0.1    1.6  1  Anticodon_1    Anticodon-binding domain of tRNA
      8e-05   22.1   0.0       0.32   10.3   0.0    2.5  2  tRNA-synt_1e   tRNA synthetases class I (C) catalytic domain
  ------ inclusion threshold ------
      0.049   13.7   4.5      0.092   12.8   4.5    1.4  1  DZR            Double zinc ribbon
        2.6    7.6  11.3         17    5.0   1.2    3.3  3  zf-ribbon_3    zinc-ribbon domain
        4.2    7.2   9.6          6    6.7   0.3    3.4  3  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 !  534.4   0.1  6.1e-164  1.4e-160       2     390 ..       9     412 ..       8     413 .. 0.98

  Alignments for each domain:
  == domain 1  score: 534.4 bits;  conditional E-value: 6.1e-164
                                       EEEE--B--SS---HHHHH.HHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHTTS-HHHHHHHHHHHHHHH CS
                      tRNA-synt_1g   2 lvttalpYangklHlGhll.evisaDifaRykrlrgeevlfvcgtDehGtpielkAekegvtpeelvekvheeikel 77 
                                        vt+alpYang++H Ghl+  +++aDif+Ry rl+ge+v+f+cgtDehGtpi+ +A keg +p+e+v+ +he+ik++
  gi|242398126|ref|YP_002993550.1|   9 TVTSALPYANGPIHAGHLAgAYLPADIFVRYLRLKGEDVVFICGTDEHGTPITFRALKEGKSPREIVDYYHEHIKTT 85 
                                       79*************************************************************************** PP

                                       HHHTT---SEEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GGG-EE........-TTS-EE-T CS
                      tRNA-synt_1g  78 fkklnisfdkygrttseehkelvqeifkklkekgliyekeieqlycpkderflpdryvegtCPkckseeargdqcee 154
                                       f++ +isfd++grt+   h++++qe+f k  e++++ +k  +q+yc++d++flpdryv gtCP+c++ee+rgdqce 
  gi|242398126|ref|YP_002993550.1|  86 FERAKISFDYFGRTELPVHYRISQEFFLKALENEYLIKKVEKQAYCEHDKMFLPDRYVIGTCPYCGAEEQRGDQCEV 162
                                       ***************************************************************************** PP

                                       TSSB-E................EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ESS- CS
                      tRNA-synt_1g 155 cgkkleptelinpksaisgskpevketehlffklskfekklkewieeeekeleenvkkivkewlkegLkdlaisrdl 231
                                       cg+ l+p++linpk+ i+g++ +++++ h++ ++++f++klk+w+  +++++++nv+++v+ w++egL+++ai+rdl
  gi|242398126|ref|YP_002993550.1| 163 CGHPLTPEKLINPKCNICGNSITFRDSAHYYIRMQEFQEKLKDWV-LRQEHWKSNVRNTVLGWINEGLEERAITRDL 238
                                       *********************************************.55559************************** PP

                                       SSS-EET....TECCEEE-HHHHHHHHHHHTTTTT-...TTSGGGG.G-.-S......EEEEEGGGHHHHHTHHHHH CS
                      tRNA-synt_1g 232 dwGipvP....gaekkvlYVWldAligYisatkelakkkgeeekwkeyW.akdkevelvhfigkdiikFHtifwPai 303
                                        wGipvP    + ++kvlYVW++A+igYis+t e +kk g+e++wk+yW + d e++++hfigkd+++FH+ifwPa+
  gi|242398126|ref|YP_002993550.1| 239 GWGIPVPledeDVKGKVLYVWFEAPIGYISITIEHFKKLGKEDEWKKYWfNIDGETRVIHFIGKDNVPFHAIFWPAF 315
                                       ********9888899**********************************9999************************ PP

                                       HHH..........TT----S-EEEE--EEE--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE-HHH CS
                      tRNA-synt_1g 304 llg..........aelklpkkvvaheyltvegkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfswed 370
                                       l++           e++lp  + a+eyl++eg+K+S+Sr+++++++e+l+ ++ad+lRYyl+a  pe++D+dfs+ d
  gi|242398126|ref|YP_002993550.1| 316 LMAygkykdekgeFEWNLPYDIPANEYLNLEGRKFSTSRNWAIWVHEFLDAFPADYLRYYLTAIMPETRDSDFSLGD 392
                                       ***98988888777888************************************************************ PP

                                       HHHHHHHHCCCHHHHHHHHH CS
                      tRNA-synt_1g 371 fvervNseLadklgnlvnRv 390
                                       f +++N+eL+++lgn+v+R+
  gi|242398126|ref|YP_002993550.1| 393 FKKKINEELVNNLGNFVHRA 412
                                       *******************8 PP

>> tRNA_bind  Putative tRNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.6   0.1   2.4e-34   5.4e-31       1      95 [.     638     729 ..     638     730 .. 0.98

  Alignments for each domain:
  == domain 1  score: 106.6 bits;  conditional E-value: 2.4e-34
                                       EEEEEEEEEEEETTSSTEEEEEEEESSSSEEEEEESCTTTSTHHHHTTEEEEEETTSESEEETTEEESSEE-EEECC CS
                         tRNA_bind   1 lrvGkvleaeehpnadkLlvlkvdvGeeeprqivsgaknvyepeelvakkvvvvanlkpkklrGveSeGMilsaeel 77 
                                       +r+Gk++ +e+hpnadkL+ +kvd+G+e  rq v+g+k++y++eel+++ v+v+ nl+pkklrG+eS+GMil+a+  
  gi|242398126|ref|YP_002993550.1| 638 IRIGKIIGVEDHPNADKLYLIKVDLGDEV-RQLVAGLKKYYKKEELLNRYVAVITNLEPKKLRGIESQGMILAAD-- 711
                                       79***************************.*********************************************.. PP

                                       ESSCEEEEEESST--TTC CS
                         tRNA_bind  78 dekevgilelpadveaGe 95 
                                       d+k+v +l+++++v++G+
  gi|242398126|ref|YP_002993550.1| 712 DGKDVALLTPEKEVKLGA 729
                                       9***************97 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 !   33.0   0.1   9.1e-12     2e-08      24      83 ..       7      67 ..       3      96 .. 0.84
   2 !   15.9   0.1   1.4e-06     0.003     361     435 ..     173     248 ..     166     276 .. 0.83
   3 ?    2.8   0.0     0.012        27     560     601 ..     346     388 ..     342     389 .. 0.90

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 9.1e-12
                       tRNA-synt_1 24 efilvdgPPyvtGslHiGhalaktl.kdivirykrmkGkevlyvpGwDhaGlaieakvekk 83
                                      +f+++   Py++G +H Gh     l  di +ry r+kG++v +  G+D +G +i     k+
  gi|242398126|ref|YP_002993550.1|  7 RFTVTSALPYANGPIHAGHLAGAYLpADIFVRYLRLKGEDVVFICGTDEHGTPITFRALKE 67
                                      69999999***********99998857**************************98765555 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1.4e-06
                       tRNA-synt_1 361 svpfcerskkpiiyrateqWfvrvkeladaalkave.kvqfvpkskekryaswl.eniqdWciSRqrwWGhriplfv 435
                                         p c+  ++ i +r +  +++r++e+++++ + v  + +++ + +++    w+ e  ++ +i R++ WG ++pl  
  gi|242398126|ref|YP_002993550.1| 173 INPKCNICGNSITFRDSAHYYIRMQEFQEKLKDWVLrQEHWKSNVRNTV-LGWInEGLEERAITRDLGWGIPVPLED 248
                                       56999999*************************9985777777776655.5566156899**************855 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.012
                       tRNA-synt_1 560 eGrKmSKslgNvidpldvikkygadalRltli.lsdvgrdinl 601
                                       eGrK S s    i   + +++  ad lR++l    + +rd ++
  gi|242398126|ref|YP_002993550.1| 346 EGRKFSTSRNWAIWVHEFLDAFPADYLRYYLTaIMPETRDSDF 388
                                       8******************************988888888766 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 !   51.6   0.1   4.2e-17   9.5e-14       1     108 [.     434     541 ..     434     622 .. 0.80

  Alignments for each domain:
  == domain 1  score: 51.6 bits;  conditional E-value: 4.2e-17
                       Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedk.ra..aqevllevletll 74 
                                       dr +l+e++k+ +ev++ + +y+f++a+++++ +    + + y++  +p+   ++  dk r+  + +v l ++++l 
  gi|242398126|ref|YP_002993550.1| 434 DRKALKEIEKTFEEVNRLISRYQFKEALKRVMAL--AIFGNQYFDYQRPWKTAKT--DKvRTgtTINVSLQIVKALG 506
                                       899******************************8..89************97665..455444466*********** PP

                       Anticodon_1  75 rllaPfmPfitEelwqr.eeeelgkkesimlaewp 108
                                       +ll+Pf+P  +E++w+  + ee+++ e+i l++  
  gi|242398126|ref|YP_002993550.1| 507 ILLEPFLPDASEKIWHLlNIEEVKRWEFIPLEAGQ 541
                                       ***************55755556667777665533 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0   0.00014      0.32      23      89 ..      21      88 ..      10      98 .. 0.89
   2 !    9.0   0.0   0.00037      0.82     244     282 ..     340     378 ..     335     389 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00014
                                      -BHHH.HHHHHHHHHHHHHHHHTT-EEEEEEEBB--SHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHH CS
                      tRNA-synt_1e 23 shlGh.aRslvafDilrrilqalgYdvqfvqnvtDidDkiikrareeeksvkelaekfieefkkdlea 89
                                      +h Gh a +++  Di+ r+l+ +g dv f+    +    i  ra +e+ks +e+++++ e+ k+ +e 
  gi|242398126|ref|YP_002993550.1| 21 IHAGHlAGAYLPADIFVRYLRLKGEDVVFICGTDEHGTPITFRALKEGKSPREIVDYYHEHIKTTFER 88
                                      799996678999*******************99999999*******************9999888775 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00037
                                       E--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHS CS
                      tRNA-synt_1e 244 nghlkiegekmsksLknfitikdvlkkfdprqlRlllls 282
                                       n++l++eg+k s s +  i ++++l  f +  lR++l+ 
  gi|242398126|ref|YP_002993550.1| 340 NEYLNLEGRKFSTSRNWAIWVHEFLDAFPADYLRYYLTA 378
                                       689*********************************975 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   4.5   4.1e-05     0.092       1      35 [.     147     181 ..     129     189 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.1e-05
                               DZR   1 CpqCgeelppdarfCseCgtklkavaa.edrCpsCg 35 
                                       Cp Cg+e +++   C+ Cg++l +++  + +C  Cg
  gi|242398126|ref|YP_002993550.1| 147 CPYCGAE-EQRGDQCEVCGHPLTPEKLiNPKCNICG 181
                                       5555555.4444445555555553333555555555 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   1.2    0.0074        17      19      24 ..     147     152 ..     146     153 .. 0.64
   2 ?    2.6   0.3     0.044        99       4      14 ..     159     169 ..     156     172 .. 0.84
   3 ?    4.9   0.2    0.0082        18       4      17 ..     176     189 ..     175     190 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0074
                       zf-ribbon_3  19 CpyCGt 24 
                                       CpyCG+
  gi|242398126|ref|YP_002993550.1| 147 CPYCGA 152
                                       777775 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.044
                       zf-ribbon_3   4 rCPnCGaplss 14 
                                       +C  CG+pl++
  gi|242398126|ref|YP_002993550.1| 159 QCEVCGHPLTP 169
                                       6999***9887 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.0082
                       zf-ribbon_3   4 rCPnCGaplssddn 17 
                                       +C+ CG+ ++ +d+
  gi|242398126|ref|YP_002993550.1| 176 KCNICGNSITFRDS 189
                                       6******7799886 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.3    0.0027         6      16      22 ..     147     153 ..     139     153 .. 0.85
   2 ?    4.1   0.1     0.017        39      16      23 .]     160     167 ..     158     167 .. 0.90
   3 ?   -0.1   0.6      0.36   8.1e+02       1       9 [.     176     184 ..     176     185 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0027
                     zinc_ribbon_2  16 CpyCGtp 22 
                                       CpyCG++
  gi|242398126|ref|YP_002993550.1| 147 CPYCGAE 153
                                       9999986 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.017
                     zinc_ribbon_2  16 CpyCGtpl 23 
                                       C+ CG+pl
  gi|242398126|ref|YP_002993550.1| 160 CEVCGHPL 167
                                       ******97 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.36
                     zinc_ribbon_2   1 fCpnCGael 9  
                                       +C  CG+ +
  gi|242398126|ref|YP_002993550.1| 176 KCNICGNSI 184
                                       799999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (732 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       797  (0.0444531); expected 358.6 (0.02)
Passed bias filter:                      635  (0.0354175); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); 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: 0.74u 0.33s 00:00:01.07 Elapsed: 00:00:00.51
# Mc/sec: 4344.97
//
Query:       gi|242398127|ref|YP_002993551.1|  [L=281]
Description: Sugar-specific transcriptional regulator TrmB family [Thermococcus sibiricus MM 739]
Scores for complete 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   37.4   0.0    3.7e-09   36.3   0.0    1.5  1  TrmB            Sugar-specific transcriptional regulator TrmB
    9.1e-08   31.5   0.0    2.1e-07   30.4   0.0    1.6  1  HTH_24          Winged helix-turn-helix DNA-binding
    1.5e-05   24.8   0.0    2.6e-05   24.0   0.0    1.3  1  MarR_2          MarR family
    0.00026   21.1   0.3     0.0027   17.8   0.0    2.3  2  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
     0.0009   19.5   0.0     0.0018   18.6   0.0    1.4  1  Rrf2            Transcriptional regulator
     0.0025   17.7   0.0     0.0049   16.8   0.0    1.4  1  MarR            MarR family
     0.0076   16.0   0.0      0.014   15.2   0.0    1.4  1  HTH_IclR        IclR helix-turn-helix domain
  ------ inclusion threshold ------
      0.012   16.1   0.0      0.024   15.1   0.0    1.5  1  HTH_27          Winged helix DNA-binding domain
      0.015   15.1   0.2      0.028   14.3   0.2    1.5  1  DUF4897         Domain of unknown function (DUF4897)
        0.1   12.5   0.1        0.2   11.5   0.1    1.5  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
       0.11   12.4   0.1       0.21   11.5   0.1    1.4  1  HTH_11          HTH domain
       0.11   12.3   0.1       0.22   11.4   0.1    1.5  1  HTH_23          Homeodomain-like domain
       0.19   11.0   0.0       0.34   10.2   0.0    1.4  1  CcmH            Cytochrome C biogenesis protein
          9    7.0   9.6        1.1    9.9   2.0    2.8  2  LPAM_1          Prokaryotic membrane lipoprotein lipid attach


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 !   36.3   0.0   2.9e-12   3.7e-09       1      59 [.     214     273 ..     214     279 .. 0.94

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 2.9e-12
                                       HHHCHHHHHCCCHCHHHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTT CS
                              TrmB   1 LqklGLseyEakvYlaLl.klgpatadeiaeelgvprskvYevLrsLedkGlVerekgrp 59 
                                       L+ ++L+e E ++ l++l k g+a+  e+  +l++p++++ ++ ++Le+ GlV+++kgr+
  gi|242398127|ref|YP_002993551.1| 214 LEFFNLNEDERRALLYILeKGGRASQAEVRTALEIPKTTAWRMFKRLEKQGLVKIIKGRK 273
                                       789***************77788999*******************************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 !   30.4   0.0   1.7e-10   2.1e-07       6      48 .]     225     267 ..     224     267 .. 0.96

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 1.7e-10
                            HTH_24   6 rkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                                       r++L +L+k +r sq+e+  +l ++++t +r  krLe++Gl+k
  gi|242398127|ref|YP_002993551.1| 225 RALLYILEKGGRASQAEVRTALEIPKTTAWRMFKRLEKQGLVK 267
                                       7899*************************************97 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   2.1e-08   2.6e-05       7      53 ..     223     268 ..     218     274 .. 0.91

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 2.1e-08
                                       HHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                            MarR_2   7 qarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53 
                                       ++r+L+++   +gr  +++e+  +l ++k ++ r+ krL+++GLv  
  gi|242398127|ref|YP_002993551.1| 223 ERRALLYILEKGGR-ASQAEVRTALEIPKTTAWRMFKRLEKQGLVKI 268
                                       89**********98.7*****************************75 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 ?    0.7   0.1       0.5   6.3e+02      38      55 ..      22      39 ..      18      41 .. 0.84
   2 !   17.8   0.0   2.1e-06    0.0027      12      54 ..     226     268 ..     220     273 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.5
                                      HHHHHHHHHHHTTSEEEE CS
                    Fe_dep_repress 38 sVsemlkkLekdGyveye 55
                                      +Vsem      dGyv+++
  gi|242398127|ref|YP_002993551.1| 22 TVSEMELTVYTDGYVKVH 39
                                      889998888899**9986 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 2.1e-06
                                       HHHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                    Fe_dep_repress  12 tIYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyvey 54 
                                       +++ + e+++ ++++++  +L++ + ++  m k+Lek+G+v+ 
  gi|242398127|ref|YP_002993551.1| 226 ALLYILEKGGRASQAEVRTALEIPKTTAWRMFKRLEKQGLVKI 268
                                       66667889999******************************86 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.4e-06    0.0018      12      62 ..     225     273 ..     223     277 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.4e-06
                                       HHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT- CS
                              Rrf2  12 hallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvrGkg 62 
                                       +ally+ ++ ++  +s +e+ +  +i+++ + +++++L+k+glvk ++G++
  gi|242398127|ref|YP_002993551.1| 225 RALLYILEKGGR--ASQAEVRTALEIPKTTAWRMFKRLEKQGLVKIIKGRK 273
                                       678888777775..69*********************************97 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   3.8e-06    0.0049       8      48 ..     227     267 ..     222     270 .. 0.95

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.8e-06
                                       HHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR   8 iLrilyeqgplsvseLakklgvskstvtrvldrLekkGlie 48 
                                       +L+il+  g +s++e   +l++ k+t+ r+ +rLek+Gl++
  gi|242398127|ref|YP_002993551.1| 227 LLYILEKGGRASQAEVRTALEIPKTTAWRMFKRLEKQGLVK 267
                                       899************************************95 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.1e-05     0.014       9      49 ..     228     267 ..     225     268 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.1e-05
                                       HCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR   9 LdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49 
                                       L ++ e +++ + +e+  ++ +pk+t+ R+ + L+++G+v+
  gi|242398127|ref|YP_002993551.1| 228 L-YILEKGGRASQAEVRTALEIPKTTAWRMFKRLEKQGLVK 267
                                       3.4445555569***************************97 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   1.9e-05     0.024       7      49 ..     226     267 ..     219     275 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.9e-05
                            HTH_27   7 lvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLve 49 
                                       ++L  ++  ++r+++a+++ +l + ++++  + k+L+++GLv+
  gi|242398127|ref|YP_002993551.1| 226 ALLYILE-KGGRASQAEVRTALEIPKTTAWRMFKRLEKQGLVK 267
                                       4566666.99********************************4 PP

>> DUF4897  Domain of unknown function (DUF4897)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.2   2.2e-05     0.028     106     145 ..     109     148 ..      66     160 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.2e-05
                           DUF4897 106 iklnlagdselvvslPkdaklisvePtPtkivenellWkg 145
                                        +ln++ ds++ v lP++a+++++   P ki+ n++   +
  gi|242398127|ref|YP_002993551.1| 109 WTLNMSMDSSFNVILPENAVIVDLSEVPLKIASNVITMPP 148
                                       579999****************************997665 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00015       0.2       6      42 .]     225     261 ..     225     261 .. 0.97

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00015
                     HTH_AsnC-type   6 rkILeaLqedaRisyaeLAervGlSestvlrRvrrLe 42 
                                       r++L +L++ +R+s ae+  ++ +  +t++r  +rLe
  gi|242398127|ref|YP_002993551.1| 225 RALLYILEKGGRASQAEVRTALEIPKTTAWRMFKRLE 261
                                       89*****************************999998 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00017      0.21       2      49 ..     224     271 ..     223     274 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00017
                            HTH_11   2 llqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg.vpIese 49 
                                       ++++l +L e+ g  s +e    L++ ++t +r  k+Le++g v+I++ 
  gi|242398127|ref|YP_002993551.1| 224 RRALLYIL-EKGGRASQAEVRTALEIPKTTAWRMFKRLEKQGlVKIIKG 271
                                       57888999.99999****************************9888764 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00017      0.22       6      46 ..     223     265 ..     218     268 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00017
                            HTH_23   6 eRlrillllae..GlsvreIAreLgvsrrTvyrwlkryreeGl 46 
                                       eR   l+ l +  ++s++e+ ++L +++ T +r  kr ++ Gl
  gi|242398127|ref|YP_002993551.1| 223 ERRALLYILEKggRASQAEVRTALEIPKTTAWRMFKRLEKQGL 265
                                       5555555555599************************977886 PP

>> CcmH  Cytochrome C biogenesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00027      0.34      90     130 ..     163     214 ..     159     231 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00027
                                       --XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...........X CS
                              CcmH  90 PpvkastllLWlgPllllllgllvlllllrrrkkkkaeee...........e 130
                                       P+ +++++  +l+Pl +l++ ll+ ++l+r+r+k+ +++e            
  gi|242398127|ref|YP_002993551.1| 163 PTEEGQSYSKYLLPLGILVVILLISIVLARNRRKEPKRTEihidkeeflkkL 214
                                       8888999999****************99999998888877644444444440 PP

>> LPAM_1  Prokaryotic membrane lipoprotein lipid attachment site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   2.0   0.00082       1.1       1      14 [.       1      14 [.       1      14 [. 0.98
   2 ?    0.5   1.1      0.82   1.1e+03       3      13 ..     172     182 ..     171     191 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00082
                            LPAM_1  1 MKKillalgalllL 14
                                      MKKil+++++l++L
  gi|242398127|ref|YP_002993551.1|  1 MKKILSLISILAIL 14
                                      ************98 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.82
                            LPAM_1   3 Killalgalll 13 
                                       K+ll lg+l++
  gi|242398127|ref|YP_002993551.1| 172 KYLLPLGILVV 182
                                       78888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       660  (0.0368119); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1867.03
//
Query:       gi|242398128|ref|YP_002993552.1|  [L=384]
Description: hypothetical protein TSIB_0135 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0028   17.6   8.8       0.74    9.7   8.8    2.6  1  YfdX      YfdX protein
  ------ inclusion threshold ------
      0.013   15.2   3.9        0.2   11.3   0.2    2.6  2  GARP      Glutamic acid/alanine-rich protein of Trypanosoma
      0.053   13.6   7.9       0.37   10.9   2.2    3.9  3  PTS_IIA   PTS system, Lactose/Cellobiose specific IIA subunit
      0.085   13.5   0.3       0.26   11.9   0.3    1.9  1  YtkA      YtkA-like
      0.094   12.9  14.5        3.8    7.9   0.1    5.8  7  TPR_2     Tetratricopeptide repeat
        1.8    9.0  19.2       0.31   11.4   0.4    5.9  7  TPR_8     Tetratricopeptide repeat
        9.7    6.2  13.2         20    5.2   1.4    4.9  6  TPR_1     Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> YfdX  YfdX protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   8.8   0.00029      0.74       8     147 ..     174     377 ..     169     378 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00029
                                       HHHHHCTT-HHHHHHHHHHHHHHHTS-HHHHHCCB-.....S--SSSS............................. CS
                              YfdX   8 ArlaldqgdtkeAkkllekAqgkleaaladdpklvk.....kapasad............................. 50 
                                        +  +++g+ +eAk  lekA++k  ++  ++ +l+            +                             
  gi|242398128|ref|YP_002993552.1| 174 VLEYIENGNLEEAKISLEKAKQKKMELDIETRDLTTkltskN-----Aemivksfliktnqsittaekaieyaksrg 245
                                       57889*****************99999999999976455550.....244555555555555556677788888888 PP

                                       ...............................-EEEEEEEEEEE--.----HHHHHHHHHHHHHH...HTT-HHHHHH CS
                              YfdX  51 ...............................alvPvdaevividd.ladtpekkaaikkanell...kkgdtqaAre 92 
                                                                      al  +++  +     + +++++k++  +++  l   +++ +++A +
  gi|242398128|ref|YP_002993552.1| 246 retgeaekamekikgiylqvtylanegkwidALRVIGENADYMKNfFMTIEKVKSEKMNTEVFLmmtRERIRKDATA 322
                                       88888899999999999999999999977766666666666655555666666555444443331213444677777 PP

                                       HHHHTT-EEEEEEEEEEHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHT-EEEE CS
                              YfdX  93 lLkllgseidittallPLatypaavkkAaelleegkyyeAkeaLkealntlvfvs 147
                                       l  l +++i +t a + L    +    A++l+++++++ A + L++a + l +v+
  gi|242398128|ref|YP_002993552.1| 323 LATLRKKGIQTTRAEIQLRGAINEFSIAISLIKKNDVNSAILHLQRANRLLTEVE 377
                                       77777899*************************************9998887765 PP

>> GARP  Glutamic acid/alanine-rich protein of Trypanosoma
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.4     0.011        27      24      75 ..     125     176 ..     111     208 .. 0.77
   2 ?   11.3   0.2   7.8e-05       0.2      21      75 ..     213     267 ..     205     305 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.011
                              GARP  24 leeeaaaaaskaskAkarseeaverAesaaendteakelvkrakeaaaeate 75 
                                       l++++++++++ + + +  e+ +e A+s++   ++  ++  +ak+a++e+ e
  gi|242398128|ref|YP_002993552.1| 125 LRTQIQEESTRVFAYFTYVEKLIEVAKSKGIDVENLTKAYVEAKTAYVEVLE 176
                                       56788999999999999999********999977777777777777777765 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 7.8e-05
                              GARP  21 vssleeeaaaaaskaskAkarseeaverAesaaendteakelvkrakeaaaeate 75 
                                        +++e  +++   k+ +  + +e+a+e A+s+++++ ea++++++ k  + ++t 
  gi|242398128|ref|YP_002993552.1| 213 SKNAEMIVKSFLIKTNQSITTAEKAIEYAKSRGRETGEAEKAMEKIKGIYLQVTY 267
                                       566777777778889999999*************************988888775 PP

>> PTS_IIA  PTS system, Lactose/Cellobiose specific IIA subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.17   4.2e+02      28      50 ..      74      96 ..      70     105 .. 0.73
   2 ?   10.9   2.2   0.00014      0.37      12      82 ..     166     237 ..     165     246 .. 0.68
   3 ?    1.5   0.0      0.12   3.1e+02      17      45 ..     347     375 ..     342     379 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.17
                           PTS_IIA 28 dfeeaeellkeAeeelkeAhkaq 50
                                      d+++a+el ++A +e++++  +q
  gi|242398128|ref|YP_002993552.1| 74 DYDKAKELKEKALTEYQNGNYLQ 96
                                      67777777777777777776665 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00014
                           PTS_IIA  12 eArslameAlkaakegdfeeaeellkeAeeelkeAhkaqteliqkea.sgekvevslllvHAqDhLmtaell 82 
                                       eA++ ++e l+ +++g++eea+  l++A+++  e      +l +k + ++ ++ v+ +l+  +  + tae +
  gi|242398128|ref|YP_002993552.1| 166 EAKTAYVEVLEYIENGNLEEAKISLEKAKQKKMELDIETRDLTTKLTsKNAEMIVKSFLIKTNQSITTAEKA 237
                                       69**************************99866544333333333331223444555666666666666555 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.12
                           PTS_IIA  17 ameAlkaakegdfeeaeellkeAeeelke 45 
                                       +  A++ +k++d++ a  +l+ A++ l+e
  gi|242398128|ref|YP_002993552.1| 347 FSIAISLIKKNDVNSAILHLQRANRLLTE 375
                                       5569*******************998876 PP

>> YtkA  YtkA-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.3    0.0001      0.26      16      82 ..     210     275 ..     192     278 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0001
                              YtkA  16 epkagentivvt..vtqggkpVedadvkvefwmpameGmeemttkvelkesedGvYeaevnfsmeGtWq 82 
                                       +++  +++ +v+    ++++ ++ a+  +e  +    G e+ + ++ +++  +G Y   +++  eG+W+
  gi|242398128|ref|YP_002993552.1| 210 KLTSKNAEMIVKsfLIKTNQSITTAEKAIEYAKSR--GRETGEAEKAMEK-IKGIYLQVTYLANEGKWI 275
                                       345555565554457799****************5..9998777777777.*****************6 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.5     0.032        81      14      31 ..      72      89 ..      71      91 .. 0.83
   2 ?    4.1   1.0     0.024        62       2      23 ..      79     100 ..      78     100 .. 0.87
   3 ?    1.3   0.1      0.19   4.8e+02      17      30 ..     164     177 ..     161     180 .. 0.85
   4 ?    7.9   0.1    0.0015       3.8      11      29 ..     177     195 ..     175     198 .. 0.90
   5 ?   -2.9   0.0       4.3   1.1e+04      25      30 ..     235     240 ..     229     242 .. 0.61
   6 ?   -3.2   0.0         5   1.3e+04      19      26 ..     250     257 ..     247     258 .. 0.72
   7 ?    4.5   0.0     0.018        45       7      28 ..     349     370 ..     346     373 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.032
                             TPR_2 14 lgdyeeAleafekAleld 31
                                      l+dy++A+e+ ekAl  +
  gi|242398128|ref|YP_002993552.1| 72 LKDYDKAKELKEKALTEY 89
                                      79*******999998765 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.024
                             TPR_2   2 ealynlGlayyklgdyeeAlea 23 
                                       + l + +l  y++g+y +A+++
  gi|242398128|ref|YP_002993552.1|  79 KELKEKALTEYQNGNYLQAIQY 100
                                       667889999**********987 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.19
                             TPR_2  17 yeeAleafekAlel 30 
                                       y eA+ a+ ++le+
  gi|242398128|ref|YP_002993552.1| 164 YVEAKTAYVEVLEY 177
                                       88*********997 PP

  == domain 4  score: 7.9 bits;  conditional E-value: 0.0015
                             TPR_2  11 yyklgdyeeAleafekAle 29 
                                       y+++g++eeA+  +ekA +
  gi|242398128|ref|YP_002993552.1| 177 YIENGNLEEAKISLEKAKQ 195
                                       999*************965 PP

  == domain 5  score: -2.9 bits;  conditional E-value: 4.3
                             TPR_2  25 ekAlel 30 
                                       ekA+e+
  gi|242398128|ref|YP_002993552.1| 235 EKAIEY 240
                                       555554 PP

  == domain 6  score: -3.2 bits;  conditional E-value: 5
                             TPR_2  19 eAleafek 26 
                                       eA++a+ek
  gi|242398128|ref|YP_002993552.1| 250 EAEKAMEK 257
                                       78888776 PP

  == domain 7  score: 4.5 bits;  conditional E-value: 0.018
                             TPR_2   7 lGlayyklgdyeeAleafekAl 28 
                                       ++ +++k++d + A+ ++++A 
  gi|242398128|ref|YP_002993552.1| 349 IAISLIKKNDVNSAILHLQRAN 370
                                       7999****************95 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       6.7   1.7e+04      13      30 ..      35      52 ..      32      53 .. 0.76
   2 ?    4.2   1.0     0.024        60      14      29 ..      72      87 ..      70      91 .. 0.88
   3 ?    0.8   0.1       0.3   7.6e+02       8      24 ..      85     101 ..      83     109 .. 0.78
   4 ?   11.4   0.4   0.00012      0.31      10      27 ..     176     193 ..     166     195 .. 0.90
   5 ?    1.5   0.1      0.18   4.6e+02      18      32 ..     228     242 ..     225     244 .. 0.82
   6 ?   -1.7   0.1       1.9   4.8e+03      18      26 ..     249     257 ..     246     261 .. 0.68
   7 ?   -0.0   0.0      0.55   1.4e+03       7      27 ..     349     369 ..     347     372 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 6.7
                                      HTT-HHHHHHHHHHHHHH CS
                             TPR_8 13 klgdyeeAkeyyekalel 30
                                      ++++ e A e +++ ++l
  gi|242398128|ref|YP_002993552.1| 35 EQNNEEIAGEIINQLTKL 52
                                      567888888888888887 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.024
                                      TT-HHHHHHHHHHHHH CS
                             TPR_8 14 lgdyeeAkeyyekale 29
                                      l+dy++Ake  ekal+
  gi|242398128|ref|YP_002993552.1| 72 LKDYDKAKELKEKALT 87
                                      89*******9999986 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.3
                                       HHHHHHTT-HHHHHHHH CS
                             TPR_8   8 gsiylklgdyeeAkeyy 24 
                                       +++  + g+y +A++y 
  gi|242398128|ref|YP_002993552.1|  85 ALTEYQNGNYLQAIQYS 101
                                       6666799*******996 PP

  == domain 4  score: 11.4 bits;  conditional E-value: 0.00012
                                       HHHHTT-HHHHHHHHHHH CS
                             TPR_8  10 iylklgdyeeAkeyyeka 27 
                                        y++ g++eeAk ++eka
  gi|242398128|ref|YP_002993552.1| 176 EYIENGNLEEAKISLEKA 193
                                       69***************9 PP

  == domain 5  score: 1.5 bits;  conditional E-value: 0.18
                                       HHHHHHHHHHHHHHH CS
                             TPR_8  18 eeAkeyyekaleldp 32 
                                       ++++ + eka+e+++
  gi|242398128|ref|YP_002993552.1| 228 NQSITTAEKAIEYAK 242
                                       788999999999986 PP

  == domain 6  score: -1.7 bits;  conditional E-value: 1.9
                                       HHHHHHHHH CS
                             TPR_8  18 eeAkeyyek 26 
                                        eA++++ek
  gi|242398128|ref|YP_002993552.1| 249 GEAEKAMEK 257
                                       467777776 PP

  == domain 7  score: -0.0 bits;  conditional E-value: 0.55
                                       HHHHHHHTT-HHHHHHHHHHH CS
                             TPR_8   7 lgsiylklgdyeeAkeyyeka 27 
                                       ++  ++k++d ++A+  +++a
  gi|242398128|ref|YP_002993552.1| 349 IAISLIKKNDVNSAILHLQRA 369
                                       5667899********999888 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.7     0.027        69      14      29 ..      72      87 ..      70      91 .. 0.73
   2 ?    5.2   1.4    0.0078        20       1      23 [.      78     100 ..      78     100 .. 0.93
   3 ?   -0.3   0.0      0.44   1.1e+03      16      29 ..     163     176 ..     161     180 .. 0.84
   4 ?    3.2   0.1     0.034        86      10      27 ..     176     193 ..     175     196 .. 0.88
   5 ?   -3.1   0.2       3.2   8.3e+03      18      23 ..     235     240 ..     235     242 .. 0.72
   6 ?    1.5   0.0      0.11   2.9e+02       6      27 ..     348     369 ..     346     369 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.027
                                      TT-HHHHHHHHHHHHH CS
                             TPR_1 14 lgkydeAleyyekALe 29
                                      l++yd+A e  ekAL+
  gi|242398128|ref|YP_002993552.1| 72 LKDYDKAKELKEKALT 87
                                      7888888887777775 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0078
                                       HHHHHHHHHHHHHTT-HHHHHHH CS
                             TPR_1   1 akalynlGnayfklgkydeAley 23 
                                       ak l+ ++++ +++g+y +A++y
  gi|242398128|ref|YP_002993552.1|  78 AKELKEKALTEYQNGNYLQAIQY 100
                                       678999***************98 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.44
                                       -HHHHHHHHHHHHH CS
                             TPR_1  16 kydeAleyyekALe 29 
                                        y eA  +y ++Le
  gi|242398128|ref|YP_002993552.1| 163 AYVEAKTAYVEVLE 176
                                       5899*******998 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.034
                                       HHHHTT-HHHHHHHHHHH CS
                             TPR_1  10 ayfklgkydeAleyyekA 27 
                                        y ++g+++eA    ekA
  gi|242398128|ref|YP_002993552.1| 176 EYIENGNLEEAKISLEKA 193
                                       5999********999999 PP

  == domain 5  score: -3.1 bits;  conditional E-value: 3.2
                                       HHHHHH CS
                             TPR_1  18 deAley 23 
                                       ++A+ey
  gi|242398128|ref|YP_002993552.1| 235 EKAIEY 240
                                       678887 PP

  == domain 6  score: 1.5 bits;  conditional E-value: 0.11
                                       HHHHHHHHTT-HHHHHHHHHHH CS
                             TPR_1   6 nlGnayfklgkydeAleyyekA 27 
                                        ++  + k+++ + A+ + ++A
  gi|242398128|ref|YP_002993552.1| 348 SIAISLIKKNDVNSAILHLQRA 369
                                       5789999*************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1471  (0.0820458); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2446.99
//
Query:       gi|242398129|ref|YP_002993553.1|  [L=254]
Description: permease [Thermococcus sibiricus MM 739]
Scores for complete 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-61  206.9  28.8      4e-61  206.7  28.8    1.0  1  TauE      Sulfite exporter TauE/SafE
  ------ inclusion threshold ------
      0.013   14.8   0.6      0.013   14.8   0.6    1.7  2  DUF2705   Protein of unknown function (DUF2705)
       0.23   11.4   0.1       0.23   11.4   0.1    2.1  2  YajC      Preprotein translocase subunit


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 !  206.7  28.8   6.7e-65     4e-61       2     236 .]       8     244 ..       7     244 .. 0.95

  Alignments for each domain:
  == domain 1  score: 206.7 bits;  conditional E-value: 6.7e-65
                              TauE   2 llagllaGfvagllGiGggliavPlLlll.lppavavatsllavvatslsgalahrrrgnvdwrlllllllgsliGa 77 
                                       + +g+++G++a+l+G+Ggg+++vP L ll + +++av+ts +avv+tsls+a+a++r+++++++++lll+  ++iGa
  gi|242398129|ref|YP_002993553.1|   8 FSIGIFVGILAALFGLGGGFLVVPTLNLLgVEIHHAVGTSSAAVVFTSLSSAIAYHRQRRIHYKAGLLLASTAVIGA 84 
                                       679*************************559********************************************** PP

                              TauE  78 llGallllllpsellkllfgvlllllallmllrkkr..srakgrerrptaillvligglvGllsGllGiGgGfllvp 152
                                       ++Ga++ ++++++ lk++fgv+l l+a++++++k+r  ++ + ++ + ++ ++++ g+++G++sGllGiGgG++ vp
  gi|242398129|ref|YP_002993553.1|  85 YIGAWMTSYISASQLKVIFGVVLFLVAIRIYRKKSRepHEVDLNQVKLDYKIVPIGGFIAGIASGLLGIGGGAINVP 161
                                       *******************************9888755444478888888877777777****************** PP

                              TauE 153 llllllglplkkavatslllilvislagalgyalagavdwpllllllpgallGallGarlarrlsertlrrlfalll 229
                                       +l++ +glp++ avats+++i++++++gal ++++g+v +++l+ll+pg ++Ga+lGa++a+r ++  l ++fa+++
  gi|242398129|ref|YP_002993553.1| 162 FLTY-MGLPIHYAVATSSFAIVFTAISGALKHYMLGNVEVEWLILLVPGLIVGAQLGAKIAKRTKASNLTKAFAVIM 237
                                       ***9.7*********************************************************************** PP

                              TauE 230 lvlgvkl 236
                                       ++l++++
  gi|242398129|ref|YP_002993553.1| 238 AFLAIRM 244
                                       *****98 PP

>> DUF2705  Protein of unknown function (DUF2705)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.2      0.27   1.6e+03     177     213 ..      76     112 ..      51     118 .. 0.60
   2 ?   14.8   0.6   2.2e-06     0.013     154     216 ..     182     245 ..     165     248 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.27
                           DUF2705 177 lfpnlmfglrnGllssedikteyeigililiillili 213
                                       l    ++g+  G+   + i+++ +  i+ +++ l++i
  gi|242398129|ref|YP_002993553.1|  76 LASTAVIGAYIGAWMTSYISASQLKVIFGVVLFLVAI 112
                                       4445555666666666656655555555555555544 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 2.2e-06
                           DUF2705 154 vYlvvSlllgnkl.lkdskllkvllfpnlmfglrnGllssedikteyeigililiillililil 216
                                       v+  +S  l + +  +  + + +ll p l++g++ G+   + +k++++++ +++i+++++i ++
  gi|242398129|ref|YP_002993553.1| 182 VFTAISGALKHYMlGNVEVEWLILLVPGLIVGAQLGAKIAKRTKASNLTKAFAVIMAFLAIRMI 245
                                       56666655544442444556889************************************99886 PP

>> YajC  Preprotein translocase subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   3.8e-05      0.23       8      52 ..     101     147 ..      96     150 .. 0.75
   2 ?   -1.7   0.7      0.46   2.7e+03       8      19 ..     232     243 ..     229     245 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.8e-05
                              YajC   8 lifvifyfll.irpqqkkqke.hkemlasLkkGdeVvtigGivGkvv 52 
                                       +if+++ fl+ ir  +kk +e h+  l+++k + ++v igG+++ ++
  gi|242398129|ref|YP_002993553.1| 101 VIFGVVLFLVaIRIYRKKSREpHEVDLNQVKLDYKIVPIGGFIAGIA 147
                                       667555555547776665555277779***************99885 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.46
                              YajC   8 lifvifyfllir 19 
                                       ++ vi+ fl ir
  gi|242398129|ref|YP_002993553.1| 232 AFAVIMAFLAIR 243
                                       567999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       928  (0.0517597); 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:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 1634.59
//
Query:       gi|242398130|ref|YP_002993554.1|  [L=332]
Description: Endoglucanase (intracellular) [Thermococcus sibiricus MM 739]
Scores for complete 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-88  296.7   0.2    1.6e-88  296.5   0.2    1.0  1  Peptidase_M42  M42 glutamyl aminopeptidase
    2.8e-11   43.5   0.1    1.3e-10   41.4   0.0    2.0  2  Peptidase_M20  Peptidase family M20/M25/M40
    8.4e-05   22.4   0.0     0.0015   18.3   0.0    2.3  2  Peptidase_M28  Peptidase family M28
    0.00044   19.2   0.1       0.47    9.2   0.0    2.1  2  Peptidase_M18  Aminopeptidase I zinc metalloprotease (M18)


Domain annotation for each model (and alignments):
>> Peptidase_M42  M42 glutamyl aminopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  296.5   0.2   3.6e-92   1.6e-88       1     292 []      42     323 ..      42     323 .. 0.97

  Alignments for each domain:
  == domain 1  score: 296.5 bits;  conditional E-value: 3.6e-92
                                       S-EEEEEESSTTSSEEEEEEE--B-EEEEEEEETTSEEEEEEESS--GGGTTTEEEEEEETTEEEEEEEEE--CGGC CS
                     Peptidase_M42   1 GnliakkkgkekepkvmiaAHmDeiGfmVkeIkedGflrfekvGGvdpkvlegqrvkiltkkgkisGvigskppHll 77 
                                       Gnli ++ +   e k +++AHmDeiG++++ I++dG+l+f+kvGG+d++ l g++v++ t++g+++Gvig++p Hl+
  gi|242398130|ref|YP_002993554.1|  42 GNLITELGE--GEEKAIFMAHMDEIGLLITGITSDGKLKFRKVGGIDDRLLLGRHVEVITEEGTLDGVIGVTPVHLN 116
                                       889988887..899**************************************************************9 PP

                                       HHHHHHCT--GCGEEEEGSGSSHHHHHHTTS-TT-EEEES---EEETTECEEETTHHHHHHHHHHHHHHHHHCTSS- CS
                     Peptidase_M42  78 keeerkkaleikelfiDigakskeeaeelGisvGdivvfdkefvelangkivskalDdragvavllellkelkeeel 154
                                         e++ ++++++ l iDiga+skeeae++G++v d++vf+k+f++l+n++i+++ lDdr+gv++l+e++k l +++l
  gi|242398130|ref|YP_002993554.1| 117 I-ERKFDTIPWNALEIDIGAESKEEAEKMGVKVLDFAVFKKHFSVLNNRYIAARSLDDRFGVVALVEAIKDLVDHDL 192
                                       9.57778899******************************************************************* PP

                                       SSEEEEEEESTCTTTSHHHHHHHHHH--SEEEEEEEEEE-CSTTSTTTTSSTTS-CEEEEEETTCCSHHHHHHHHHH CS
                     Peptidase_M42 155 eatvylvatvqEEvGlrGaktsaekikpdiaiavDvtaagdtpgskekeaklgkGpvirvkDasgiyhpklrkklle 231
                                       + + ++++tvqEE+Gl+Ga+++a++++p++aiavD  a++     + k    g+G+vir++D+s iy p l +k le
  gi|242398130|ref|YP_002993554.1| 193 DGKYIFAFTVQEEIGLKGARFLANTYSPKYAIAVDSFACCSFLTGDVKP---GNGAVIRAVDNSAIYTPSLARKTLE 266
                                       ************************************9998877777666...************************* PP

                                       HHHHTT--EEEEEESSSSSTHHHHHTSTTTSEEEEEEEEEBSTTSTTEEEEHHHHHHHHHH CS
                     Peptidase_M42 232 lAkknnipyqlevlsgggtDAgaihltgegvptalisiptryiHspvevahlddleatvkL 292
                                       +A+knnip+q+  ++gggtDA+ +  +    +t+++s+p+ry+Hs++e++h++dl+a++kL
  gi|242398130|ref|YP_002993554.1| 267 IAQKNNIPIQI-GVTGGGTDASVFEAK---SQTLALSVPLRYLHSEAEMLHISDLKALIKL 323
                                       ***********.999*******99888...89**************************998 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 ?   -0.7   0.0      0.22   9.9e+02      94     128 ..      94     126 ..      51     155 .. 0.66
   2 !   41.4   0.0   2.8e-14   1.3e-10      29     205 ..     165     328 ..     145     330 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.22
                                       EEEEEEESSSBTCHSTETEEEEEEEEEEEEEESHE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20  94 vfelhieepgileagklaigvvkvevelleggapv 128
                                        +e+ i e+g l+ g +++++v+ ++e+  +  p+
  gi|242398130|ref|YP_002993554.1|  94 HVEV-ITEEGTLD-GVIGVTPVHLNIERKFDTIPW 126
                                       4444.45566666.677777776666655544444 PP

  == domain 2  score: 41.4 bits;  conditional E-value: 2.8e-14
                                       EEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTTTHHHHHHHHHHTTTCESEEEEEEEESSSBT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20  29 klyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggrgGakallegleerekvdavfelhieepgil 105
                                       ++ +r + d+  gv+a++ea++ l d+   ++g+  ++f++ EE+g +Ga+ l++     + +++++++        
  gi|242398130|ref|YP_002993554.1| 165 YIAAR-SLDDRFGVVALVEAIKDLVDHD--LDGKYIFAFTVQEEIGLKGARFLAN----TYSPKYAIAVDSF--ACC 232
                                       45555.99*******************8..599***********999********....4555554433322..222 PP

                                       CHSTETEEEEE.EEEEEEEEESHEEECCHHHHHHHHHHHHHHHTSCEEEE.EESSSBHTHHHH.TTTEEEEEEESSG CS
                                       xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx.xxxxxxxxxxxxx RF
                     Peptidase_M20 106 eagklaigvvk.vevelleggapvtlndsplvkalaeaaeelfgekveli.vsgpggtdarff.agiptvmifgpgs 179
                                       +  + ++++++ + ++ + ++a +t   + l+++  e+a++  +  + +i v+g ggtda+ f a+ +t+ + +p  
  gi|242398130|ref|YP_002993554.1| 233 SFLTGDVKPGNgAVIRAVDNSAIYT---PSLARKTLEIAQKN-NI-PIQIgVTG-GGTDASVFeAKSQTLALSVPL- 302
                                       2233345566635666443333333...45666666676773.44.45555***.********5555677666688. PP

                                       GCTTSTTTEEEHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20 180 glaHspnEyvdledlekgikvlarll 205
                                          Hs+ E ++++dl++ ik++++l+
  gi|242398130|ref|YP_002993554.1| 303 RYLHSEAEMLHISDLKALIKLIEALV 328
                                       9********************99887 PP

>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.049   2.2e+02       1      28 [.      43      72 ..      43      88 .. 0.66
   2 !   18.3   0.0   3.4e-07    0.0015      37      92 ..     172     225 ..     166     320 .. 0.65

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.049
                                      EEEEEESTTCESEEEEEEEE--B-TTT....T CS
                     Peptidase_M28  1 NviatlegkatdevlllgAHyDsvgvg....r 28
                                      N+i +l g+  +e  +++AH+D +g       
  gi|242398130|ref|YP_002993554.1| 43 NLITEL-GEG-EEKAIFMAHMDEIGLLitgiT 72
                                      677777.444.57889******9987555551 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 3.4e-07
                                       TTHHHHHHHHHHHHHCHHGGCCSSEEEEEEEESSCSGSSHHHHHHHH.HHCCCTTEE CS
                     Peptidase_M28  37 DnAsgvaalLelarvlaasgsrpkrgvrflffdaEEagllGSkafak.akpelkkia 92 
                                       D+  gv+al+e ++ l++  ++++ + +f+f+  EE gl G++++a+  + ++++ia
  gi|242398130|ref|YP_002993554.1| 172 DDRFGVVALVEAIKDLVD--HDLDGKYIFAFTVQEEIGLKGARFLANtYS-PKYAIA 225
                                       7889*************9..79************************7533.444442 PP

>> Peptidase_M18  Aminopeptidase I zinc metalloprotease (M18)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0   0.00024       1.1     224     281 ..     161     215 ..     135     224 .. 0.84
   2 !    9.2   0.0    0.0001      0.47     336     430 ..     240     326 ..     236     328 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00024
                                       TTT-EEEESSHHHHHHHHHHHHHHCCCCHT-TTTS-SEEEEEEESSCCGTS-STTSGG CS
                     Peptidase_M18 224 iekeflfaprlDnkvscfaaleallesaedsleeedkvrivalfDnEEvGStsaqGad 281
                                       +++ +++a  lD++ ++ a +ea+ ++ +++l+ +    i a+  +EE+G ++a+ + 
  gi|242398130|ref|YP_002993554.1| 161 LNNRYIAARSLDDRFGVVALVEAIKDLVDHDLDGK---YIFAFTVQEEIGLKGARFLA 215
                                       57889**********************99966555...78888899****99887655 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0001
                                       -TTSEEEEEEETTSSSTT-HHHHHHHHHHHHHHC-EEEEEEE-TTS----HCHHHHHHHHT-EEEEEE-EEBSTTSS CS
                     Peptidase_M18 336 llnkGvvikvnanqryatnsagaallkevaqkanvklQelvvrndspcGstigpilaaktGirtiDlGaaqlsmHSi 412
                                       ++++G vi+   n    t s   + l e+aqk+n+++Q  v      +G+t   ++ ak   +t+ l  +   +HS 
  gi|242398130|ref|YP_002993554.1| 240 KPGNGAVIRAVDNSAIYTPSLARKTL-EIAQKNNIPIQIGV-----TGGGTDASVFEAKS--QTLALSVPLRYLHSE 308
                                       578999***99999999999888777.69*********865.....68999999**9996..9************** PP

                                       SEEEECCHHHHHHHHHHH CS
                     Peptidase_M18 413 reltgskdveeavklfka 430
                                        e+  ++d++  +kl +a
  gi|242398130|ref|YP_002993554.1| 309 AEMLHISDLKALIKLIEA 326
                                       **********99998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.54
# Mc/sec: 1841.46
//
Query:       gi|242398131|ref|YP_002993555.1|  [L=185]
Description: Transcription factor TFIID [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-57  190.8   0.0    3.5e-28   97.4   0.0    2.0  2  TBP       Transcription factor TFIID (or TATA-binding protein
    3.9e-08   33.3   0.0    0.00012   22.2   0.0    2.3  2  DUF3378   Domain of unknown function (DUF3378)
  ------ inclusion threshold ------
      0.057   13.5   0.0        1.7    8.7   0.0    2.1  2  AIRS_C    AIR synthase related protein, C-terminal 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 !   91.9   0.0   3.1e-30   1.9e-26       2      84 ..       6      86 ..       5      87 .. 0.96
   2 !   97.4   0.0   5.9e-32   3.5e-28       2      84 ..      97     177 ..      96     178 .. 0.96

  Alignments for each domain:
  == domain 1  score: 91.9 bits;  conditional E-value: 3.1e-30
                                      EEEEEEEEEEE-SSCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHHHH CS
                               TBP  2 fkiqNvvasanlgleldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakkiap 80
                                      ++i+N+vas++l  +ldLek+ + +   +++Y+pe+fpg+++r++epkv++l+FssGk+v+tGaks++++++a+ k+++
  gi|242398131|ref|YP_002993555.1|  6 LRIENIVASVDLFASLDLEKVIEIC--PHSKYNPEEFPGIICRFDEPKVALLVFSSGKLVVTGAKSVDDIQAAVSKLVE 82
                                      69*******************7677..**************************************************** PP

                                      HHHH CS
                               TBP 81 ilkk 84
                                      +l+k
  gi|242398131|ref|YP_002993555.1| 83 MLSK 86
                                      **98 PP

  == domain 2  score: 97.4 bits;  conditional E-value: 5.9e-32
                                       EEEEEEEEEEE-SSCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHH CS
                               TBP   2 fkiqNvvasanlgleldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakki 78 
                                       + iqN+v+s +l++e++L+++al +   n+eYepe+fpg++yr+++pk+++l+FssGk+v+ Gakse ++ ea+kk+
  gi|242398131|ref|YP_002993555.1|  97 IDIQNMVFSGDLKMEFNLDAVALVL--PNCEYEPEQFPGVIYRVKDPKAVILLFSSGKIVCSGAKSEHDAWEAVKKL 171
                                       78*******************9777..************************************************** PP

                                       HHHHHH CS
                               TBP  79 apilkk 84 
                                       +  l k
  gi|242398131|ref|YP_002993555.1| 172 LHELDK 177
                                       999987 PP

>> DUF3378  Domain of unknown function (DUF3378)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0   0.00025       1.5      21      55 ..      34      68 ..      21      86 .. 0.88
   2 !   22.2   0.0   1.9e-08   0.00012      24      60 ..     128     164 ..     124     175 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00025
                           DUF3378 21 klrskkppyavfaakkndttItaYtSgKVlFQGkn 55
                                      k + ++ p+++ + +++++   ++ SgK+++ G++
  gi|242398131|ref|YP_002993555.1| 34 KYNPEEFPGIICRFDEPKVALLVFSSGKLVVTGAK 68
                                      4566789************************9986 PP

  == domain 2  score: 22.2 bits;  conditional E-value: 1.9e-08
                           DUF3378  24 skkppyavfaakkndttItaYtSgKVlFQGknaeaeA 60 
                                        ++ p+++++ k+++++I ++ SgK++  G++ e++A
  gi|242398131|ref|YP_002993555.1| 128 PEQFPGVIYRVKDPKAVILLFSSGKIVCSGAKSEHDA 164
                                       5789*****************************9998 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 ?    2.9   0.0     0.018   1.1e+02      95     143 ..      42      88 ..      10      95 .. 0.66
   2 ?    8.7   0.0   0.00029       1.7      76     133 ..      99     174 ..      97     181 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.018
                                       HHHHHHHHHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEE CS
                            AIRS_C  95 pifdelesplemllsensGrllvavppeeadavlaileeeglpeaavIG 143
                                        i++   +p  +ll+++sG+l+v+ ++  +  + a++++  +   + IG
  gi|242398131|ref|YP_002993555.1|  42 GIICRFDEPKVALLVFSSGKLVVTGAKSVD-DIQAAVSKLVE-MLSKIG 88 
                                       445555578889999****99776666555.44444444444.356666 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00029
                                       HHHHHHTTTEEEEEECGTHHHHHHHH...............HHHHHHHCSTTTEEEEEEEHGGH...HHHHHHHHH CS
                            AIRS_C  76 laemapasgvgaeidldkvpifdele...............splemllsensGrllvavppeea...davlailee 133
                                       +++m++ +++++e++ld+v ++ + +               +p  + l ++sG+ +++ ++ e+   +av+++l+e
  gi|242398131|ref|YP_002993555.1|  99 IQNMVFSGDLKMEFNLDAVALVLPNCeyepeqfpgviyrvkDPKAVILLFSSGKIVCSGAKSEHdawEAVKKLLHE 174
                                       789**************88888888777665555555555566666666999999998887777566666666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); 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: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1263.18
//
Query:       gi|242398132|ref|YP_002993556.1|  [L=143]
Description: hypothetical protein TSIB_0139 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0059   16.4   0.0     0.0068   16.2   0.0    1.2  1  FAM209    FAM209 family
  ------ inclusion threshold ------
       0.02   14.6   0.3      0.024   14.3   0.3    1.1  1  MAGE      MAGE family


Domain annotation for each model (and alignments):
>> FAM209  FAM209 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   7.5e-07    0.0068      27      69 ..      24      66 ..       7     108 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.5e-07
                            FAM209 27 qnlpehaqgWLgskllWllfvvvlyvilkfrgdsekskeqtpp 69
                                      +n peh ++WL      +l++ ++y i +++g++e ske  + 
  gi|242398132|ref|YP_002993556.1| 24 ENHPEHWEDWLRAGRRRFLLLNIIYYIQHVQGKEEVSKEDLKM 66
                                      79*********999999******************99997655 PP

>> MAGE  MAGE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.3   2.7e-06     0.024     136     212 ..      56     138 ..      41     139 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.7e-06
                              MAGE 136 ggsiseqeLekyLkrlgldenstskeitklklkldelLkklvkqgYlvreke.....s.kasdeeeekveyrvGpRa 206
                                       ++++s ++L+  L +l+  +++   +i k   +ld++Lk+l  q+ +v++ e     + +  ++ee+ + ++  +++
  gi|242398132|ref|YP_002993556.1|  56 KEEVSKEDLKMFLGELYYVDREMFSNIIKPWKSLDDTLKELLEQKLIVQVSEgaylvNeQRIQDEEDLIYWEGIRKT 132
                                       67899**********966555454557788889***********************955778889999999988999 PP

                              MAGE 207 kvEige 212
                                       + E+g+
  gi|242398132|ref|YP_002993556.1| 133 LDEVGR 138
                                       999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1037.23
//
Query:       gi|242398133|ref|YP_002993557.1|  [L=513]
Description: metallo-beta-lactamase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-08   34.2   0.0    9.7e-05   22.0   0.0    2.5  3  Lactamase_B_2  Beta-lactamase superfamily domain
    1.5e-05   24.9   0.0    0.00013   21.8   0.1    2.2  2  RMMBL          Zn-dependent metallo-hydrolase RNA specificity
     0.0001   22.4   1.1    0.00053   20.0   1.0    2.2  1  Lactamase_B    Metallo-beta-lactamase superfamily
     0.0037   17.2   0.0       0.14   12.0   0.0    2.7  3  Lactamase_B_3  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
        0.1   11.7   0.1       0.19   10.8   0.1    1.3  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 !   22.0   0.0   2.7e-08   9.7e-05      30      75 ..      88     129 ..      75     149 .. 0.84
   2 !    9.5   0.0   0.00018      0.65      98     187 ..     207     293 ..     182     300 .. 0.75
   3 ?   -3.9   0.0       2.2   7.9e+03     176     200 ..     463     487 ..     456     487 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 2.7e-08
                                       SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCG CS
                     Lactamase_B_2  30 pidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfv 75 
                                       p +aVl++haH DH+ ++  l e    ++ +++++ ++a+l+a  +
  gi|242398133|ref|YP_002993557.1|  88 PANAVLISHAHLDHVGNVALLDE----NISIVGSPTTIAILKALND 129
                                       789************99999999....499***********98765 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00018
                                       ECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---......HHHHHHHCT-SEEEEE-S-SS CS
                     Lactamase_B_2  98 lgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyip......eeigerlggadllllditaye 168
                                        +d g+ei+a+ + h+           + +++ie g+ +++y+gD            +  ++ ++a +l+ ++t++ 
  gi|242398133|ref|YP_002993557.1| 207 DEDLGFEIKAFSVDHSIYG--------ATAYIIE-GDVSLAYTGDFRLHGksgnetRKFIREAKNASILITEGTRTG 274
                                       467899**********999........9******.99**********77756533333557889999*******999 PP

                                       TTHHHHHHT---S...TSHHHH CS
                     Lactamase_B_2 169 ddemirhmgHltp...eeavea 187
                                        +e   h+  + +   e+a+++
  gi|242398133|ref|YP_002993557.1| 275 REE---HENVSEQevyENALKI 293
                                       988...3333333335555555 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 2.2
                                       HT---STSHHHHCTTSSSSEEEEES CS
                     Lactamase_B_2 176 mgHltpeeaveaaadlgakrlvliH 200
                                        gH++ ee   +++++++   +++H
  gi|242398133|ref|YP_002993557.1| 463 SGHISREELRGIIDEVNPDYIIPVH 487
                                       6899999999999999999999999 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 ?   -0.2   0.0      0.28   9.9e+02      19      36 ..     250     267 ..     248     277 .. 0.84
   2 !   21.8   0.1   3.6e-08   0.00013      12      41 ..     461     490 ..     458     492 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.28
                             RMMBL  19 knellelirklkprnvil 36 
                                        ne++++ir  k+  + +
  gi|242398133|ref|YP_002993557.1| 250 GNETRKFIREAKNASILI 267
                                       69********99988765 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 3.6e-08
                             RMMBL  12 dfSgHadknellelirklkprnvilvHGee 41 
                                       + SgH  ++el+ +i  ++p ++i+vH e 
  gi|242398133|ref|YP_002993557.1| 461 HASGHISREELRGIIDEVNPDYIIPVHTEN 490
                                       67*************************996 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   1.0   1.5e-07   0.00053      44      71 ..      88     115 ..      81     302 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.5e-07
                                       GEEEEE-SBSSHHHHTTGGGCTTHHCCE CS
                       Lactamase_B  44 dvdavilTHlHlDHiGglgglveatdvp 71 
                                       +  av+++H+HlDH+G+++ l e   ++
  gi|242398133|ref|YP_002993557.1|  88 PANAVLISHAHLDHVGNVALLDENISIV 115
                                       5679*****************9987766 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 !   12.0   0.0   3.9e-05      0.14      29      73 ..      81     123 ..      71     165 .. 0.73
   2 ?   -2.5   0.0       1.2   4.2e+03      95     115 ..     225     244 ..     201     269 .. 0.73
   3 ?    1.8   0.0     0.055     2e+02     143     163 .]     467     487 ..     458     487 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.9e-05
                     Lactamase_B_3  29 gyeppaeeaDlvlisqaledHahletlkqlaenvkvleegeslev 73 
                                        +++p++ a++vlis+a+ dH    +l    en+ ++ ++ ++++
  gi|242398133|ref|YP_002993557.1|  81 VTRYPKVPANAVLISHAHLDHVGNVALLD--ENISIVGSPTTIAI 123
                                       578999***************87766655..79999998877664 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.2
                     Lactamase_B_3  95 enngflleqdgltiyhlGhla 115
                                       + +++++ ++++++++ G+  
  gi|242398133|ref|YP_002993557.1| 225 GATAYII-EGDVSLAYTGDFR 244
                                       4566777.4588999999864 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.055
                     Lactamase_B_3 143 gqeealelakrLkpklvlPmh 163
                                       ++ee   ++ +++p++++P+h
  gi|242398133|ref|YP_002993557.1| 467 SREELRGIIDEVNPDYIIPVH 487
                                       678888999***********9 PP

>> PDEase_II  cAMP phosphodiesterases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   5.2e-05      0.19      84     122 ..      92     122 ..      78     127 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 5.2e-05
                                       EE-S---GGGTHHHHHHGGGGGS-S.--EEEEE-HHHHH CS
                         PDEase_II  84 ylItHsHLDHvsglvinSaefykaqlkkktivGlpytIn 122
                                        lI+H+HLDHv+ + +      +    +  ivG+p tI 
  gi|242398133|ref|YP_002993557.1|  92 VLISHAHLDHVGNVALL----DE----NISIVGSPTTIA 122
                                       59*********988654....23....234666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (513 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); 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:                         5  (0.000278878); expected 0.2 (1e-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 0.31s 00:00:00.94 Elapsed: 00:00:00.51
# Mc/sec: 3045.94
//
Query:       gi|242398134|ref|YP_002993558.1|  [L=106]
Description: daunorubicin ABC transporter ATP-binding protein [Thermococcus sibiricus MM 739]
Scores for complete 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   61.4   0.0    1.4e-16   61.3   0.0    1.0  1  ABC_tran         ABC transporter
    1.4e-05   25.1   0.0    1.4e-05   25.1   0.0    1.1  1  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    0.00013   22.5   1.3    0.00025   21.6   0.7    1.6  2  AAA_23           AAA domain
    0.00034   20.5   0.2    0.00035   20.4   0.2    1.1  1  AAA_15           AAA ATPase domain
    0.00051   20.0   0.1     0.0011   18.9   0.0    1.5  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
    0.00067   20.1   0.0    0.00067   20.1   0.0    1.2  1  AAA              ATPase family associated with various cellul
      0.002   17.9   0.0     0.0028   17.3   0.0    1.3  1  AAA_29           P-loop containing region of AAA domain
      0.002   18.0   0.0     0.0025   17.7   0.0    1.3  1  RsgA_GTPase      RsgA GTPase
     0.0022   18.5   0.0     0.0028   18.2   0.0    1.3  1  AAA_18           AAA domain
     0.0027   18.0   0.0     0.0027   18.0   0.0    1.2  1  AAA_28           AAA domain
     0.0037   17.2   0.0      0.005   16.8   0.0    1.4  1  ATPase_2         ATPase domain predominantly from Archaea
     0.0046   16.7   0.0     0.0057   16.4   0.0    1.1  1  Thymidylate_kin  Thymidylate kinase
     0.0073   16.6   0.0     0.0079   16.5   0.0    1.3  1  AAA_22           AAA domain
     0.0091   15.7   0.0     0.0091   15.7   0.0    1.1  1  AAA_30           AAA domain
  ------ inclusion threshold ------
      0.011   16.1   0.0      0.011   16.1   0.0    1.1  1  AAA_16           AAA ATPase domain
      0.019   14.9   0.0      0.028   14.4   0.0    1.4  1  Rad17            Rad17 P-loop domain
      0.026   13.2   0.0      0.026   13.2   0.0    1.2  1  AAA_13           AAA domain
      0.031   13.9   0.0      0.042   13.5   0.0    1.2  1  SRP54            SRP54-type protein, GTPase domain
      0.042   14.0   0.1      0.058   13.5   0.1    1.2  1  SKI              Shikimate kinase
      0.043   14.0   0.0      0.093   12.9   0.0    1.6  2  AAA_33           AAA domain
      0.046   13.6   0.0      0.062   13.2   0.0    1.2  1  NACHT            NACHT domain
      0.059   13.4   0.0       0.08   12.9   0.0    1.2  1  AAA_5            AAA domain (dynein-related subfamily)
      0.074   12.8   0.0        0.1   12.3   0.0    1.2  1  Cytidylate_kin   Cytidylate kinase
        0.1   12.4   0.0       0.11   12.2   0.0    1.2  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
       0.13   12.7   0.0       0.14   12.5   0.0    1.3  1  RNA_helicase     RNA helicase
       0.15   11.7   0.0       0.17   11.4   0.0    1.2  1  cobW             CobW/HypB/UreG, nucleotide-binding domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.3   0.0     2e-19   1.4e-16       2      98 ..       2     103 ..       1     106 [] 0.90

  Alignments for each domain:
  == domain 1  score: 61.3 bits;  conditional E-value: 2e-19
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       k ++l+++ege+ a++G+nGaGK+tL+++la+ lk ++G+i++ +++l++    ++ + ig++pqe+   + ltv+e
  gi|242398134|ref|YP_002993558.1|   2 KGINLEIEEGEIFALLGPNGAGKTTLIRILAEGLKFDSGDIEVFEEKLSK----KTARLIGYVPQESISYDLLTVEE 74 
                                       789**************************************888888877....99999*******99999999*** PP

                                       H.........HHHTCHHHHHHHSTTGGTT CS
                                       x.........xxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n.........esdeeiekalsklglkelk 98 
                                       n         +  e++++++++++l+ +k
  gi|242398134|ref|YP_002993558.1|  75 NlgfyadlynAPMEKVKELIKRFDLPSKK 103
                                       ****9999887777788888888887744 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0     2e-08   1.4e-05       1      63 [.      13      70 ..      13     100 .. 0.79

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 2e-08
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeie 63
                                      + +l GpNg+GK++L+++l       +  ++++d++    +++k + +l +y p +++ + + 
  gi|242398134|ref|YP_002993558.1| 13 IFALLGPNGAGKTTLIRILA-----EGLKFDSGDIEVFEEKLSKKTARLIGYVPQESISYDLL 70
                                      579****************5.....45556777777777777777777777777777766655 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.7   3.6e-07   0.00025      18      41 ..      10      33 ..       2      58 .. 0.78
   2 ?   -0.1   0.0       1.7   1.1e+03     131     162 ..      53      97 ..      32     105 .. 0.43

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 3.6e-07
                            AAA_23 18 skgltlItGpNGaGKTTildAikl 41
                                      +  ++++ GpNGaGKTT+++ +  
  gi|242398134|ref|YP_002993558.1| 10 EGEIFALLGPNGAGKTTLIRILAE 33
                                      4579***************98765 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.7
                            AAA_23 131 ilnlilflgqer.........feefel........kdkkerleelekel 162
                                         +li + +qe+         +    +        +++ e+++el+k +
  gi|242398134|ref|YP_002993558.1|  53 TARLIGYVPQESisydlltveE----NlgfyadlyNAPMEKVKELIKRF 97 
                                       3333333444442222222110....01122222233333555555554 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.2     5e-07   0.00035      19     127 ..       6     102 ..       1     106 [] 0.74

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 5e-07
                            AAA_15  19 idlsee.ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifeniseskdikIdvefaekekakeyek 94 
                                       ++++e  +  l G+N++GK++++++l            + +k+++ d+e+fe++  +k+ ++  +   ++++++y  
  gi|242398134|ref|YP_002993558.1|   6 LEIEEGeIFALLGPNGAGKTTLIRIL-----------AEGLKFDSGDIEVFEEKLSKKTARLIGYV--PQESISYDL 69 
                                       4444445999****************...........3346899******************9999..555666666 PP

                            AAA_15  95 tlkskekkkadlllkkkesdlkktikdkklklk 127
                                       +  +++  ++  l++   ++ k++ik ++l  k
  gi|242398134|ref|YP_002993558.1|  70 LTVEENLGFYADLYNAPMEKVKELIKRFDLPSK 102
                                       666666666666666666667777776666555 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   1.7e-06    0.0011      19      46 ..      11      38 ..       2      45 .. 0.82
   2 ?   -1.9   0.0       4.4     3e+03      49      73 ..      63      84 ..      47      97 .. 0.51

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.7e-06
                                      TEEEEEEESTTSSHHHHHHHHHHHTT-- CS
                              TsaE 19 gdvilLeGdLGaGKTtlvrglakalgve 46
                                      g++++L G+ GaGKTtl+r la++l+++
  gi|242398134|ref|YP_002993558.1| 11 GEIFALLGPNGAGKTTLIRILAEGLKFD 38
                                      7889********************9875 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.4
                                      --TTTTSEEEEEE..SSEEEEE-TT CS
                              TsaE 49 kSPTFtlveeYelekeglyHfDlYR 73
                                      +S ++ l++  e+     + +DlY 
  gi|242398134|ref|YP_002993558.1| 63 ESISYDLLTVEEN---LGFYADLYN 84
                                      4444444443321...123455554 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 !   20.1   0.0   9.7e-07   0.00067       3      39 ..      16      57 ..      14     104 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 9.7e-07
                                      EESSTTSSHHHHHHHHHHHHT.....HEEEEEETTTCSSSST CS
                               AAA  3 lyGppGtGKTllakavakelg.....vefleisgsellskyv 39
                                      l Gp G GKT+l++ +a+ l+     +e++e ++s+ +  ++
  gi|242398134|ref|YP_002993558.1| 16 LLGPNGAGKTTLIRILAEGLKfdsgdIEVFEEKLSKKTARLI 57
                                      89*****************97444446677777777665543 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   4.1e-06    0.0028      16      39 ..       5      28 ..       1      32 [. 0.84

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.1e-06
                            AAA_29 16 tieidlkgatlltGpsGsGKSTll 39
                                       +ei++ +++ l Gp+G+GK+Tl+
  gi|242398134|ref|YP_002993558.1|  5 NLEIEEGEIFALLGPNGAGKTTLI 28
                                      567876669**************8 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   3.6e-06    0.0025      99     131 ..      10      43 ..       1      64 [. 0.81

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.6e-06
                                       T.SEEEEECSTTSSHHHHHHHHCTT-----S--- CS
                       RsgA_GTPase  99 d.ktsvlvGqSGvGKStLinallpelelktgevs 131
                                       + ++ +l+G+ G+GK+tLi  l++ l+   g++ 
  gi|242398134|ref|YP_002993558.1|  10 EgEIFALLGPNGAGKTTLIRILAEGLKFDSGDIE 43 
                                       44999******************99998888876 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0     4e-06    0.0028       3      25 ..      16      47 ..      15     103 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 4e-06
                            AAA_18  3 ltGtpGvGKttlakeLskrlgf.........g 25
                                      l G+ G+GKttl + L++ l+f          
  gi|242398134|ref|YP_002993558.1| 16 LLGPNGAGKTTLIRILAEGLKFdsgdievfeE 47
                                      78****************99888766655551 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   3.9e-06    0.0027       2      35 ..      14      49 ..      13      93 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3.9e-06
                            AAA_28  2 ivitGgestGKTtlleaLaar.gypvv.pEaareil 35
                                      ++++G+ ++GKTtl++ La+  ++     E++ e l
  gi|242398134|ref|YP_002993558.1| 14 FALLGPNGAGKTTLIRILAEGlKFDSGdIEVFEEKL 49
                                      589****************86544433344444444 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 !   16.8   0.0   7.2e-06     0.005      16      61 ..       7      53 ..       4      98 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 7.2e-06
                          ATPase_2 16 erepneiyfiYGpegsGKtaLlkeiienl.edkdkyviyyialrees 61
                                      e e+ ei  + Gp g GKt+L++ ++e l  d+++  ++  +l+++ 
  gi|242398134|ref|YP_002993558.1|  7 EIEEGEIFALLGPNGAGKTTLIRILAEGLkFDSGDIEVFEEKLSKKT 53
                                      6677899999*****************99557778999998888765 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   8.2e-06    0.0057       3      79 ..      18      96 ..      17      99 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 8.2e-06
                                      ESTTSSHHHHHHHHHHHHHHTTE.EEEESSSTTSHHHHHHHHHHHTCS---HHH..HHHHHHHHHHHTTHHHHHHHHHT CS
                   Thymidylate_kin  3 GlDGaGKttqaellkerlkeegikvvltrepggteiGekirelllkeeeleeqt..eallfaadriehleekikpalkq 79
                                      G +GaGKtt +++l+e lk     + +  e+ + +++++i  + +++  ++ +t  e+l f+ad + +  ek+k+ +k+
  gi|242398134|ref|YP_002993558.1| 18 GPNGAGKTTLIRILAEGLKFDSGDIEVFEEKLSKKTARLIGYVPQESISYDLLTveENLGFYADLYNAPMEKVKELIKR 96
                                      899***************999877667778889999999999999777777777769999***9999988999988775 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.1e-05    0.0079       5      30 ..      11      36 ..       7     104 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.1e-05
                            AAA_22  5 agilvvtGesGtGKTtllrrlleqld 30
                                        i ++ G+ G+GKTtl+r l+e l+
  gi|242398134|ref|YP_002993558.1| 11 GEIFALLGPNGAGKTTLIRILAEGLK 36
                                      678899***************99984 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   1.3e-05    0.0091      19      46 ..      12      40 ..       5     102 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.3e-05
                            AAA_30 19 rvavltGpAGtGKttalkalreaweaa.g 46
                                       + +l Gp G+GKtt+++ l+e ++ + g
  gi|242398134|ref|YP_002993558.1| 12 EIFALLGPNGAGKTTLIRILAEGLKFDsG 40
                                      478999**************999887734 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.1   0.0   1.6e-05     0.011      23      51 ..      10      38 ..       5      96 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.6e-05
                            AAA_16 23 rpelvllsGesGvGKsslvrellralekd 51
                                      ++e+  l G+ G GK++l+r l++ l+ d
  gi|242398134|ref|YP_002993558.1| 10 EGEIFALLGPNGAGKTTLIRILAEGLKFD 38
                                      458999**************999855544 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0     4e-05     0.028      38      69 ..       4      35 ..       1      57 [. 0.86

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4e-05
                             Rad17 38 dvLesrkkriLLisGPsGCgkstvvkvLskel 69
                                        Le ++ +i  + GP G gk+t +++L+  l
  gi|242398134|ref|YP_002993558.1|  4 INLEIEEGEIFALLGPNGAGKTTLIRILAEGL 35
                                      567888888999****************9765 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   3.8e-05     0.026      22      53 ..      17      42 ..      11      95 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.8e-05
                            AAA_13 22 YGwNGaGKTtLSrllrslelgetepkfangsi 53
                                       G NGaGKTtL r+l++        kf +g i
  gi|242398134|ref|YP_002993558.1| 17 LGPNGAGKTTLIRILAEG------LKFDSGDI 42
                                      59*************995......35555555 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   6.1e-05     0.042       3      26 ..      13      36 ..      11      45 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.1e-05
                                      EEEEEESTTSSHHHHHHHHHHHHH CS
                             SRP54  3 villvGlqGaGKTttlaKLaallk 26
                                      +++l+G++GaGKTt +  La+ lk
  gi|242398134|ref|YP_002993558.1| 13 IFALLGPNGAGKTTLIRILAEGLK 36
                                      6789************99998776 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   8.4e-05     0.058       1      35 [.      20      54 ..      20      59 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.4e-05
                                      TTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHTS-H CS
                               SKI  1 mGaGKstvGkllAkklglefiDlDeliekrtgksi 35
                                      +GaGK+t+ ++lA+ l+++  D+  + ek  +k++
  gi|242398134|ref|YP_002993558.1| 20 NGAGKTTLIRILAEGLKFDSGDIEVFEEKLSKKTA 54
                                      59********************9887777777665 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00014     0.093       4      24 ..      16      36 ..      13      68 .. 0.85
   2 ?   -1.4   0.0       3.6   2.5e+03     127     143 .]      84     100 ..      74     100 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00014
                            AAA_33  4 lvGlpGsGKstlaerllkklg 24
                                      l G++G+GK+tl++ l++ l+
  gi|242398134|ref|YP_002993558.1| 16 LLGPNGAGKTTLIRILAEGLK 36
                                      78************9987665 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.6
                            AAA_33 127 evpeealdrqkarferp 143
                                       ++p+e +++ ++rf++p
  gi|242398134|ref|YP_002993558.1|  84 NAPMEKVKELIKRFDLP 100
                                       78999999999999876 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   8.9e-05     0.062       3      25 ..      14      36 ..      12      46 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.9e-05
                                      EEEEC-TTTCHHHHHHHHHHHHC CS
                             NACHT  3 vilqGeaGsGKTtLlqklalawa 25
                                       +l G++G GKTtL++ la+ ++
  gi|242398134|ref|YP_002993558.1| 14 FALLGPNGAGKTTLIRILAEGLK 36
                                      5799*************999887 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00012      0.08       3      34 ..      15      51 ..      13      56 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00012
                                      EEE--SSSSHHHHHHHGGGGB.....S--EEEEE--T CS
                             AAA_5  3 lLvGppGtgKselaerlaaal.....nreveyvqltr 34
                                       L+Gp G gK++l++ la+ l       ev++  l++
  gi|242398134|ref|YP_002993558.1| 15 ALLGPNGAGKTTLIRILAEGLkfdsgDIEVFEEKLSK 51
                                      59****************9986655555555555555 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00015       0.1       2      25 ..      15      38 ..      14      45 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00015
                                      EEE-STTSSHHHHHHHHHHHHT-E CS
                    Cytidylate_kin  2 aiDGPagsGKssvaralaeklglk 25
                                      a+ GP g+GK ++ r+lae l++ 
  gi|242398134|ref|YP_002993558.1| 15 ALLGPNGAGKTTLIRILAEGLKFD 38
                                      677****************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 ?   12.2   0.0   0.00016      0.11      37      59 ..      15      37 ..       7      74 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00016
                            RuvB_N 37 llyGpPGlGkttlakiiakelgv 59
                                       l Gp G Gkttl +i+a+ l+ 
  gi|242398134|ref|YP_002993558.1| 15 ALLGPNGAGKTTLIRILAEGLKF 37
                                      589***************98865 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00021      0.14       3      26 ..      16      39 ..      14      98 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00021
                      RNA_helicase  3 lyGpsgeGKStlakeLakallkkl 26
                                      l Gp+g GK+tl++ La+ l  ++
  gi|242398134|ref|YP_002993558.1| 16 LLGPNGAGKTTLIRILAEGLKFDS 39
                                      78**************99998444 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00025      0.17       4      21 ..      15      32 ..      12      57 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00025
                                      EEEESTTCCHHHHHHHHH CS
                              cobW  4 vltGflGsGKTtLlnhll 21
                                       l G+ G+GKTtL++ l 
  gi|242398134|ref|YP_002993558.1| 15 ALLGPNGAGKTTLIRILA 32
                                      6889**********9776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 677.81
//
Query:       gi|242398135|ref|YP_002993559.1|  [L=173]
Description: Daunorubicin resistance ATP-binding protein, partial [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.7e-09   36.9   1.1    7.6e-09   36.2   1.1    1.4  1  DUF4162          Domain of unknown function (DUF4162)
    2.3e-06   27.7   0.0    3.8e-06   26.9   0.0    1.4  1  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    8.4e-06   26.3   0.0    2.1e-05   25.0   0.0    1.7  1  ABC_tran         ABC transporter
  ------ inclusion threshold ------
      0.012   15.1   0.9      0.014   14.8   0.9    1.2  1  DUF2117          Uncharacterized protein conserved in archaea
      0.024   14.8   0.0      0.048   13.8   0.0    1.4  1  Cob_adeno_trans  Cobalamin adenosyltransferase
       0.13   12.7   0.0       0.39   11.2   0.0    1.8  2  ILEI             Interleukin-like EMT inducer


Domain annotation for each model (and alignments):
>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   1.1   2.6e-12   7.6e-09       1      81 []      82     166 ..      82     166 .. 0.84

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 2.6e-12
                                       E-HHHHHTTS-SSEEE.EE-------..--.-EEEE-TTS-EEEEE--.-----------.----EEEEEEEE---H CS
                           DUF4162   1 GtleeiKrsygknrie.veadaeelleepg.veeveeeggelelkled.eeaanellkal.tsgveirsFeeeePsL 73 
                                       Gt +e+K+ +g++ i  ve+  + ++++ + +  + e+ g+l++++++ +e+ +++l+ l + g ei+ +++eeP+L
  gi|242398135|ref|YP_002993559.1|  82 GTADELKALIGEESIIqVEGILKGVERIREvFPRLIEKSGTLRIHVRNsKEVLSKILELLiSVGSEIKAIKVEEPTL 158
                                       899*******8877776995555555555545566777799******99***********889999*********** PP

                                       HHHHHHHH CS
                           DUF4162  74 ndIFiekv 81 
                                       +d+F++++
  gi|242398135|ref|YP_002993559.1| 159 EDVFLKLT 166
                                       *****975 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0   1.3e-09   3.8e-06     237     298 ..       1      59 [.       1      64 [. 0.91

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 1.3e-09
                            AAA_21 237 lSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHS 298
                                       +S G+kr l ++ +ll+ +   ++l++DEp +gL+    r l++l+k  +  g  +il+TH 
  gi|242398135|ref|YP_002993559.1|   1 MSGGFKRRLNIAISLLYEP---KILILDEPSTGLDVTSRRQLWDLIKGFKVDGKTIILATHY 59 
                                       799**************99...9***********************66666699*******6 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   7.1e-09   2.1e-05     109     136 ..       1      28 [.       1      29 [. 0.96

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 7.1e-09
                                       S-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 109 LSgGqkqrvalarallkkpkllllDEpt 136
                                       +SgG k+r+ +a +ll +pk+l+lDEp+
  gi|242398135|ref|YP_002993559.1|   1 MSGGFKRRLNIAISLLYEPKILILDEPS 28 
                                       7**************************7 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 ?   14.8   0.9   4.8e-06     0.014      86     161 ..      54     132 ..      24     158 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.8e-06
                           DUF2117  86 v......rkiagvspgenilvnGiviGkaeseevtivaedgkivdikggeiKehGvekLgkvdlekaivktgllRrs 156
                                       +       +++++    +i+ +G v++  + +e++  + +  i++++g+    +Gve++ +v   + i k+g+lR +
  gi|242398135|ref|YP_002993559.1|  54 IlathymEEVEALADRIAIINEGRVVAVGTADELKALIGEESIIQVEGIL---KGVERIREV-FPRLIEKSGTLRIH 126
                                       4444444778888888889999**************************94...7*******8.567899******98 PP

                           DUF2117 157 .kvkek 161
                                        + +++
  gi|242398135|ref|YP_002993559.1| 127 vRNSKE 132
                                       433333 PP

>> Cob_adeno_trans  Cobalamin adenosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.6e-05     0.048      24      73 ..      76     150 ..      73     169 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.6e-05
                                       HHHHHHHHHHHHHHHHHHHHHHCTTT..........................THHHHHHHHHHHHHHHHHHHHHHT CS
                   Cob_adeno_trans  24 prveayGtvDelnsaiglarallaee..........................eeelkeaLeeiqneLfdlgaelat 73 
                                        rv a+Gt Del+++ig    +++ e                           ++ ke+L++i + L+++g+e+ +
  gi|242398135|ref|YP_002993559.1|  76 GRVVAVGTADELKALIGEES-IIQVEgilkgverirevfprlieksgtlrihVRNSKEVLSKILELLISVGSEIKA 150
                                       699**************877.4444468899899999999999999988888778888899999999999998853 PP

>> ILEI  Interleukin-like EMT inducer
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00013      0.39      23      61 ..      57      96 ..      24     111 .. 0.85
   2 ?   -1.6   0.0       1.3     4e+03      54      73 ..     131     149 ..     124     156 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00013
                              ILEI 23 ty.eeeskrlveflksipdgsiVlvavkdeassnlsdear 61
                                      t+  ee ++l++ +  i++g++V+v + de +  + +e +
  gi|242398135|ref|YP_002993559.1| 57 THyMEEVEALADRIAIINEGRVVAVGTADELKALIGEESI 96
                                      44337999**********************9877777665 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.3
                              ILEI  54 snlsdearkaleslGskkik 73 
                                       +++ +++ ++l s+Gs+ ik
  gi|242398135|ref|YP_002993559.1| 131 KEVLSKILELLISVGSE-IK 149
                                       45566788889999987.44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); 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 0.25s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1137.98
//
Query:       gi|242398136|ref|YP_002993560.1|  [L=126]
Description: ABC transporter [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      6e-06   25.6   0.3    6.9e-06   25.4   0.3    1.0  1  ABC2_membrane_3  ABC-2 family transporter protein
     0.0016   17.9   0.1     0.0021   17.5   0.1    1.2  1  ABC2_membrane    ABC-2 type transporter
  ------ inclusion threshold ------
       0.11   11.8   0.0       0.14   11.6   0.0    1.2  1  SBP_bac_3        Bacterial extracellular solute-binding prote


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 !   25.4   0.3   1.2e-09   6.9e-06       4      87 ..      24     112 ..      21     122 .. 0.74

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 1.2e-09
                   ABC2_membrane_3   4 liitlllPiilvlllglifsnsveddentpiavvdednsslsqqlv..........ealeaspsvelvyevdseeea 70 
                                       l++++++P+  ++l+g+i++ +++ + ++ i+v + +    s  ++            le+++ + +v  +++e++a
  gi|242398136|ref|YP_002993560.1|  24 LFWIFIFPLMWITLFGTIWGGESP-PITVDIGVFYTNE---SAPFTaydiveimrnVTLEETNLF-NVLDFKDENSA 95 
                                       89****************999885.8888887766653...223333334444444444445555.5********** PP

                   ABC2_membrane_3  71 kkalkngdidgilvipk 87 
                                        + lk+g+id+++v  k
  gi|242398136|ref|YP_002993560.1|  96 LEVLKSGKIDAVVVRLK 112
                                       ***********998754 PP

>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   3.5e-07    0.0021       5      42 ..       8      44 ..       5      75 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.5e-07
                     ABC2_membrane  5 allkreflqrwrdpslgllwrliqplllalvfgtvfgn 42
                                       ++ ++++   r ++ + +w +i+pl+++++fgt++g+
  gi|242398136|ref|YP_002993560.1|  8 GIILKDLKELRREKMAL-FWIFIFPLMWITLFGTIWGG 44
                                      57788999999999888.******************95 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 ?   11.6   0.0   2.3e-05      0.14     134     167 ..      85     118 ..      57     124 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.3e-05
                                       EEEEESSHHHHHHHHHTTSSSEEEEEHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SBP_bac_3 134 eivefdtleealqaLkngrvdavvadspvlaylv 167
                                       ++  f++ ++al+ Lk+g++davv+    ++ l+
  gi|242398136|ref|YP_002993560.1|  85 NVLDFKDENSALEVLKSGKIDAVVVRLKFIYTLI 118
                                       56679*******************9876666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 940.80
//
Query:       gi|242398137|ref|YP_002993561.1|  [L=261]
Description: ABC transporter [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.6e-18   64.9  15.1    7.8e-18   64.7  15.1    1.0  1  ABC2_membrane_3  ABC-2 family transporter protein
    3.5e-17   62.5  16.9    3.5e-17   62.5  16.9    2.0  2  ABC2_membrane    ABC-2 type transporter
    2.6e-08   33.5  11.8    3.3e-08   33.2  11.8    1.1  1  ABC2_membrane_2  ABC-2 family transporter protein
  ------ inclusion threshold ------
      0.017   15.1  19.2      0.056   13.4  15.3    2.6  2  ABC2_membrane_4  ABC-2 family transporter protein
          9    6.3  13.4        2.2    8.3   8.9    2.1  2  MARVEL           Membrane-associating domain


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 !   64.7  15.1   2.2e-21   7.8e-18     120     344 ..      31     249 ..       9     250 .. 0.77

  Alignments for each domain:
  == domain 1  score: 64.7 bits;  conditional E-value: 2.2e-21
                   ABC2_membrane_3 120 lns.llqqlnasalvlqseatstsaninvestqleeelsnvasflvg.liliilifitasfiavsiveEkesrikel 194
                                       l++ +            + ++ ++ +i +e+ + e+++    +f+v+ +i i l+f t++ + ++ +eE +++++ +
  gi|242398137|ref|YP_002993561.1|  31 LTTeM----------IRKYMLASAEPIVIEEKEVESKTATPIQFYVTsFIGIQLLFATMLTVGSGTLEEIQKGTLRR 97 
                                       23333..........344567788999999999999997777777777***************************** PP

                   ABC2_membrane_3 195 qlvsgvsplqywlskilgdflvyllqlllill...lafglgipfgnlglllllfllfglayialgyllsslfknset 268
                                       ++ s+ +++ ++++k+l++flv ++++++ l+   l+fg  i  + lg+  + +++ +l + +lg+++   +++ ++
  gi|242398137|ref|YP_002993561.1|  98 IVASPATAWDFLMGKMLSTFLVIMFSIVVGLGyakLLFGETIIPSLLGW--VIIFIASLFSMSLGLAIAMGTRSIKS 172
                                       ***************************9999833447773222223333..44444455555666666666777777 PP

                   ABC2_membrane_3 269 aqilifivilllsgffgglfpledlpsalkwifsiiPffapglgllrl.itgdplweillsliilalfavvylllal 344
                                       + +++ +v+++l+++ g+++p + lp++++ i+ ++P+    + +  l i+  + +ei++++++l l ++++l++a+
  gi|242398137|ref|YP_002993561.1| 173 TTAVVNFVSMPLLFLAGIVVPESVLPKWVRPIANYFPLGRALKDFRLLeIYKRSASEIAPDILWLSLATLITLIIAV 249
                                       8889******555555555556669***************99999877778889*********************97 PP

>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.5  16.9   9.8e-21   3.5e-17      54     202 ..      68     214 ..      52     222 .. 0.88
   2 ?    3.1   0.7     0.015        55      98     127 ..     227     256 ..     212     259 .. 0.87

  Alignments for each domain:
  == domain 1  score: 62.5 bits;  conditional E-value: 9.8e-21
                     ABC2_membrane  54 gllffsvlflafsaltsvapvferergvlerelvsplyslsayvlakvlvelpvsllqalifllivyflvgldlsrf 130
                                        ++++ +lf + +++ +++++ e+++g+l r  +sp  ++++++++k+l+ ++v+++ +++ l  + +l+g ++  +
  gi|242398137|ref|YP_002993561.1|  68 SFIGIQLLFAT-MLTVGSGTLEEIQKGTLRRIVASPA-TAWDFLMGKMLSTFLVIMFSIVVGLGYAKLLFGETI--I 140
                                       34444555555.7778888******************.*****************999999999******9999..5 PP

                     ABC2_membrane 131 ..flflllllltalaasslgllisalapsfedasqlaslvllpllllsGffipidsmpkwlqwiaylnPltyav 202
                                         +l ++++++ +l+++slgl+i++ ++s++  + ++++v +pll+l+G+++p + +pkw++ ia + Pl  a+
  gi|242398137|ref|YP_002993561.1| 141 psLLGWVIIFIASLFSMSLGLAIAMGTRSIKSTTAVVNFVSMPLLFLAGIVVPESVLPKWVRPIANYFPLGRAL 214
                                       58*****************************************************************9996665 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.015
                     ABC2_membrane  98 lakvlvelpvsllqalifllivyflvgldl 127
                                       ++ ++ ++++  l++li l+i+++l ++ +
  gi|242398137|ref|YP_002993561.1| 227 ASEIAPDILWLSLATLITLIIAVVLYNWAV 256
                                       5788999*****************988876 PP

>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2  11.8   9.2e-12   3.3e-08      58     283 ..      17     252 ..       2     257 .. 0.66

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 9.2e-12
                   ABC2_membrane_2  58 veaasasdeaedtdqdlkv.............................vstimavlipviaalfgadaia.gEkerg 104
                                       +e   +++++++++   ++                             ++t+++++  ++a+++++ + + +E   g
  gi|242398137|ref|YP_002993561.1|  17 MESYLPKEIIAEYNLTTEMirkymlasaepivieekevesktatpiqfYVTSFIGIQLLFATMLTVGSGTlEEIQKG 93 
                                       444444444444444443355566666667777777777788888888999999999999***999996537889** PP

                   ABC2_membrane_2 105 TlkllLskPvsRdeillgKfigglaiglaiavallatvllalaiilalgivlaledllllvvasvlllllvvflalg 181
                                       Tl++  ++P++ ++ l+gK+++ +++   i+ +++++ l    +  +  i ++l  ++++++as+      + ++lg
  gi|242398137|ref|YP_002993561.1|  94 TLRRIVASPATAWDFLMGKMLSTFLV---IMFSIVVG-LGYAKLLFGETIIPSLLGWVIIFIASL------FSMSLG 160
                                       **************************...77777777.443455567777888888888888888......348899 PP

                   ABC2_membrane_2 182 lllSsvarssreaaalalglfvvlailvpivlygvaellagpavpqeindflsllsptsay.ntllneilagsdlna 257
                                       l++++ +r s +++++++ ++ + +++  +++ + + l+        ++++ ++++ ++a  ++ l ei+++s+   
  gi|242398137|ref|YP_002993561.1| 161 LAIAMGTR-SIKSTTAVVNFVSMPLLFLAGIVVPESVLPK------WVRPIANYFPLGRALkDFRLLEIYKRSA--- 227
                                       99999999.5555555555555555555555544333333......2455555665555542355556666664... PP

                   ABC2_membrane_2 258 lgstatnllilllllavllvlgyvlF 283
                                           a  +l l l +++ l+++ vl+
  gi|242398137|ref|YP_002993561.1| 228 -SEIAPDILWLSLATLITLIIAVVLY 252
                                       .4455566666666666666666554 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 ?   13.4  15.3   1.6e-05     0.056      34     152 ..      52     167 ..      35     204 .. 0.63
   2 ?   -1.1   0.1      0.44   1.6e+03      17      31 ..     237     250 ..     222     258 .. 0.54

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.6e-05
                   ABC2_membrane_4  34 nllgktgldpaefyslsvfgftlllllplilgiiasylifrEeqndtlknLltiPvsrtklllaKlivllllsvllm 110
                                       + ++++++ p +fy  s +g++  ll+ ++l++ +++l  +E q++tl+ ++  P +   +l++K++ ++l++++ +
  gi|242398137|ref|YP_002993561.1|  52 KEVESKTATPIQFYVTSFIGIQ--LLFATMLTVGSGTL--EEIQKGTLRRIVASPATAWDFLMGKMLSTFLVIMFSI 124
                                       5566777788899888777765..57888888777776..9******************************999666 PP

                   ABC2_membrane_4 111 lvtf.litvlfallsgfvgfsvklvlellkkclelgllvffav 152
                                       +v +  + +lf+  +  + + +  ++++   ++ lgl +++ +
  gi|242398137|ref|YP_002993561.1| 125 VVGLgYAKLLFGETIIPSLLGWVIIFIASLFSMSLGLAIAMGT 167
                                       6655223333444444333444433333333333333333222 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.44
                   ABC2_membrane_4  17 llvlaallvpllall 31 
                                       l+++ ++++ + a++
  gi|242398137|ref|YP_002993561.1| 237 LSLATLITLII-AVV 250
                                       32222222222.222 PP

>> MARVEL  Membrane-associating domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   8.9   0.00061       2.2      11     106 ..      71     172 ..      64     200 .. 0.87
   2 ?   -2.2   0.1       1.1   3.8e+03      73      88 ..     234     249 ..     219     255 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00061
                            MARVEL  11 ilqlvfaiiilgliaslia....kldqllgspssalnfavfvavfsflyalfllvlylfk..nsaftsilwplidli 81 
                                       ++ql+fa +    +++l      +l+ ++ sp +a+ f +     +fl+++f +v+ l++    + + i++ l+ ++
  gi|242398137|ref|YP_002993561.1|  71 GIQLLFATMLTVGSGTLEEiqkgTLRRIVASPATAWDFLMGKMLSTFLVIMFSIVVGLGYakLLFGETIIPSLLGWV 147
                                       5677777666666666666888988999*********************************88888999999999** PP

                            MARVEL  82 vdalaallwlvafialaaglrdisc 106
                                       + ++a+l+ +  + a+a g+r+i+ 
  gi|242398137|ref|YP_002993561.1| 148 IIFIASLFSMSLGLAIAMGTRSIKS 172
                                       ********************99664 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.1
                            MARVEL  73 ilwplidlivdalaal 88 
                                       ilw  +  ++++++a+
  gi|242398137|ref|YP_002993561.1| 234 ILWLSLATLITLIIAV 249
                                       4444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1054  (0.0587874); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 1780.33
//
Query:       gi|242398138|ref|YP_002993562.1|  [L=202]
Description: iorB indolepyruvate ferredoxin oxidoreductase, subunit beta [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-40  137.6   0.2    5.1e-40  137.4   0.2    1.0  1  POR       Pyruvate ferredoxin/flavodoxin oxidoreductase
  ------ inclusion threshold ------
       0.13   11.6   0.0       0.21   11.0   0.0    1.2  1  DUF4159   Domain of unknown function (DUF4159)
       0.19   11.3   0.0        0.4   10.2   0.0    1.5  2  FGGY_N    FGGY family of carbohydrate kinases, N-terminal dom


Domain annotation for each model (and alignments):
>> POR  Pyruvate ferredoxin/flavodoxin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.4   0.2   8.5e-44   5.1e-40       1     176 [.      12     193 ..      12     194 .. 0.96

  Alignments for each domain:
  == domain 1  score: 137.4 bits;  conditional E-value: 8.5e-44
                                       CTSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHHHHGGGEE CS
                               POR   1 GGqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetlsehldglk 77 
                                       GGqGv+ta++il+ aa +aGy+v   +++g+++r g+++s+vr+++++  ++++ g+a++++ +++ ++ +++++lk
  gi|242398138|ref|YP_002993562.1|  12 GGQGVLTAANILGWAALHAGYKVRLGEVHGMSQRFGSVISYVRFGEDVYGSMVPEGKANVMLSFEPVEALRYVNYLK 88 
                                       9**********************************************999****************9999******* PP

                                       EEEEEEEECTCGTT-CCHHHCTS-HHHHHHH.......T-EEEEE-HHHHHHHCCC.CCHHHHHHHHHHHHHHTS-H CS
                               POR  78 pggiiiynseelkpdelkkakeeerelkerl.......gvrvygvdatkiakeiggneraaNtvmlGalaallglpl 147
                                       +gg +++n++ + p ++      ++ l+e +       +++ +g++a+++a+++g   +++Ntv++Gal ++  +pl
  gi|242398138|ref|YP_002993562.1|  89 EGGMVVVNTKPIVPVQVSMGMAKYPSLEEIRkvfeeefKAKWIGFNAEELAEQAGH-VVTTNTVLIGALTQIPEFPL 164
                                       **************************999999*******************88777.***************99666 PP

                                       ..HHHHHHHHCCS-CH.HHHHHHHHHHHHHH CS
                               POR 148 ..ealeeaikkrfpkkkeviekNlkafragy 176
                                         e+++e+ik ++p k  ++++N+kaf++g+
  gi|242398138|ref|YP_002993562.1| 165 daEHVREVIKISVPPK--AVDMNMKAFDLGI 193
                                       66************95..9*********996 PP

>> DUF4159  Domain of unknown function (DUF4159)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   3.5e-05      0.21      60     101 ..      68     118 ..      64     127 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.5e-05
                                       SS------HHHHHHH..HHHHTT-EEEEEE-.......SSSSHHHHHHHHH CS
                           DUF4159  60 hgnvkfssaeakaLr..aYlrkGGfLliDdr.......gygaaeaerlrre 101
                                       ++nv +s + ++aLr  +Yl++GG++++ ++        +g+a++ +l+++
  gi|242398138|ref|YP_002993562.1|  68 KANVMLSFEPVEALRyvNYLKEGGMVVVNTKpivpvqvSMGMAKYPSLEEI 118
                                       566666667777777558************999999998888888888654 PP

>> FGGY_N  FGGY family of carbohydrate kinases, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       0.5     3e+03     188     223 ..      32      70 ..      17      74 .. 0.74
   2 ?   10.2   0.0   6.8e-05       0.4     134     167 ..     126     167 ..     112     197 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.5
                                       E-HHHHHHTT--GG...GS-EEE-TCCEEEEEECCCCCC CS
                            FGGY_N 188 wdeellailgipee...lLPklvesseiigelkpelaak 223
                                       ++  l ++ g++++   +++ ++ ++ ++g + pe +a+
  gi|242398138|ref|YP_002993562.1|  32 YKVRLGEVHGMSQRfgsVISYVRFGEDVYGSMVPEGKAN 70 
                                       566666777777777778888899999999998887765 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 6.8e-05
                                       HHHHHHHHHSCCHHCCHCEEEEHHHHHHHHHCT........- CS
                            FGGY_N 134 sklkWlkenepevfekiekflliddyLiwrLtg........q 167
                                       +k kW+  n +e +e++  ++++++ Li  Lt+        +
  gi|242398138|ref|YP_002993562.1| 126 FKAKWIGFNAEELAEQAGHVVTTNTVLIGALTQipefpldaE 167
                                       799*****************************9774444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1454.14
//
Query:       gi|242398139|ref|YP_002993563.1|  [L=646]
Description: indolepyruvate: ferredoxin oxidoreductase, alpha subunit [Thermococcus sibiricus MM 739]
Scores for complete 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  101.7   0.2    6.1e-29  100.8   0.2    1.5  1  TPP_enzyme_C    Thiamine pyrophosphate enzyme, C-terminal TPP
    2.1e-15   57.1   0.2    3.2e-15   56.5   0.2    1.2  1  POR_N           Pyruvate flavodoxin/ferredoxin oxidoreductase
    1.7e-08   34.9  11.5    5.1e-07   30.2  11.2    3.0  3  Fer4_7          4Fe-4S dicluster domain
    3.2e-08   33.1  18.6    4.5e-06   26.2   2.6    3.2  2  Fer4            4Fe-4S binding domain
    1.3e-06   28.4  10.7    1.3e-06   28.4  10.7    2.0  2  Fer4_10         4Fe-4S dicluster domain
    1.5e-06   28.3  11.1    2.4e-06   27.6  10.2    1.9  1  Fer4_9          4Fe-4S dicluster domain
    4.4e-05   23.5   8.8    0.00042   20.4   9.0    2.3  2  Fer4_21         4Fe-4S dicluster domain
    4.9e-05   23.2   2.5    4.9e-05   23.2   2.5    3.1  3  Fer4_2          4Fe-4S binding domain
    0.00024   21.1  17.5      0.005   16.9   2.5    3.1  3  Fer4_6          4Fe-4S binding domain
  ------ inclusion threshold ------
      0.016   14.4   0.1      0.054   12.7   0.1    1.8  2  DXP_synthase_N  1-deoxy-D-xylulose-5-phosphate synthase
      0.022   14.4   0.5       0.22   11.2   0.2    2.3  2  Transket_pyr    Transketolase, pyrimidine binding domain
      0.077   13.6  12.5       0.34   11.5   1.7    3.7  3  Fer4_13         4Fe-4S single cluster domain of Ferredoxin I
        0.1   13.5  12.7       0.24   12.4   2.0    3.4  4  Fer4_16         4Fe-4S double cluster binding domain
       0.28   11.9   4.8         18    6.1   0.7    3.1  3  Fer4_15         4Fe-4S single cluster domain
        2.1    8.9  14.0        2.4    8.7   1.8    2.9  2  Fer4_17         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 !  100.8   0.2   5.1e-32   6.1e-29       1     152 [.     410     562 ..     410     563 .. 0.92

  Alignments for each domain:
  == domain 1  score: 100.8 bits;  conditional E-value: 5.1e-32
                                       ESSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHH..........ST.TSEEEEEEEHHHHHHT.GGGH CS
                      TPP_enzyme_C   1 diGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGakla..........kp.drevvaivGDGgflmi.lqel 65 
                                       diGc+tl      ++ +p ++++  ++++mG ++++++G+++a           p ++ vva++GD++f+++ l++l
  gi|242398139|ref|YP_002993563.1| 410 DIGCYTL------GLLPPLKTVD--TTVAMGASIGIGHGLSIAqngslseeqqGPeKQVVVATIGDSTFYHTgLPAL 478
                                       89*****......99********..9****************5555666665445357889**************** PP

                                       HHHHHTT-SEEEEEEE-SBCCCHHHHHHHHTCCTTTTSBB.BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHH CS
                      TPP_enzyme_C  66 atavrrnlpitvvvlnNegygmtggqqepfggkrksgpagkdlkpvdfaklaealGak.garvekadveeleealke 141
                                       a+a++++ ++++vvl+N +++mtg q++p +g++ +g     +k + ++ +a+a+Ga+ +a+v+++d++ + e++k+
  gi|242398139|ref|YP_002993563.1| 479 ANAIYNRSNVLIVVLDNLVTAMTGDQPNPSTGQTPHGM----GKRIPIEDVAKAMGADfVAVVDPYDIKTTYETVKK 551
                                       ********************************999884....6899************999**************** PP

                                       HHCSSSEEEEE CS
                      TPP_enzyme_C 142 alekkgpalie 152
                                       ale +g+++i+
  gi|242398139|ref|YP_002993563.1| 552 ALEVEGVSVIV 562
                                       *********96 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   0.2   2.7e-18   3.2e-15       2     185 ..      28     207 ..      27     240 .. 0.85

  Alignments for each domain:
  == domain 1  score: 56.5 bits;  conditional E-value: 2.7e-18
                                       HHHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCC CS
                             POR_N   2 aaiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmien 78 
                                       +a++a++ v+aaYP TPsse+ +++a   +k +v   ++    +E  a+++++ Aa++G ra+Ta    Gl  + ++
  gi|242398139|ref|YP_002993563.1|  28 GALEANIAVYAAYPGTPSSELTDTMAIVSKKAGV---YMEYSTNEKVAFETALAAAWSGLRAMTAMKHVGLNVAADT 101
                                       899*************************999997...777889********************************** PP

                                       HHHHHHTT--EEEEEEEEE-STTBEEEEE--TTCHHHHS---EEEE-SSHHHHHHHHHHHHHHHHHCTSEEEEEEEH CS
                             POR_N  79 lglaageelPvvivvvaRalpstglsirtdqsDlmaardtglivlasenvqeafdlalvAfnlAekvrvPvivlfDg 155
                                       ++ a+g+ +   +v++    ps  +s +++q   ++a   ++ vl + +  ea +++  Af l+ek++  vi l   
  gi|242398139|ref|YP_002993563.1| 102 FMSAVGMGVEGGFVIMVADDPSM-WSSQNEQDTRVYAKFANVPVLEPTSPHEAKEMTKYAFELSEKFKHFVI-LRTT 176
                                       ******99988877777788999.*******************************************98555.5668 PP

                                       HHH.HEEEEEEC-SGG..GS-----SBXXXX CS
                             POR_N 156 fllshevekvelpdee.delklikekleeye 185
                                       +++sh++ +v l +   ++++ ++++ + ++
  gi|242398139|ref|YP_002993563.1| 177 TRTSHARGDVVLGELPeEIKERKRKFGKFNK 207
                                       999*******999888334444444443333 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.44   5.2e+02      10      23 ..     238     251 ..     237     267 .. 0.84
   2 !    9.2   3.1    0.0016       1.9      18      49 ..     573     605 ..     565     606 .. 0.67
   3 !   30.2  11.2   4.2e-10   5.1e-07       1      52 []     591     637 ..     591     637 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.44
                            Fer4_7  10 aaCpvkaieldeee 23 
                                       ++Cp ++ie +e++
  gi|242398139|ref|YP_002993563.1| 238 NNCPFNWIEGKEDA 251
                                       79*******99864 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0016
                            Fer4_7  18 eldeeenekgtekveidpekClgCgaCva..vCP 49 
                                           + + ++ + ++++++kC+gC+ C++   CP
  gi|242398139|ref|YP_002993563.1| 573 GQMRR-RGEKWPIYYVNEDKCTGCRICINayGCP 605
                                       44444.3345688999***********9844466 PP

  == domain 3  score: 30.2 bits;  conditional E-value: 4.2e-10
                            Fer4_7   1 rCigCgaCvaa..CpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                       +C+gC+ C +a  Cp  ai++dee     +++++++p++C+gCg C++vCP+ga
  gi|242398139|ref|YP_002993563.1| 591 KCTGCRICINAygCP--AIYWDEE-----KKQARVEPTMCWGCGGCAQVCPFGA 637
                                       7********997788..****998.....56789******************98 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   2.0   2.3e-06    0.0027       1      17 [.     585     601 ..     585     601 .. 0.92
   2 !   26.2   2.6   3.8e-09   4.5e-06       3      23 ..     618     638 ..     616     639 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.3e-06
                                       EEEETTTSSS-THHHHH CS
                              Fer4   1 vvideekCigCGaCvev 17 
                                       ++++e+kC+gC +C+++
  gi|242398139|ref|YP_002993563.1| 585 YYVNEDKCTGCRICINA 601
                                       68************986 PP

  == domain 2  score: 26.2 bits;  conditional E-value: 3.8e-09
                                       EETTTSSS-THHHHHSTTTEE CS
                              Fer4   3 ideekCigCGaCvevCPvgAI 23 
                                       + + +C gCG C++vCP+gA 
  gi|242398139|ref|YP_002993563.1| 618 VEPTMCWGCGGCAQVCPFGAF 638
                                       7899****************7 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       9.7   1.2e+04      18      23 ..     239     244 ..     231     257 .. 0.65
   2 !   28.4  10.7   1.1e-09   1.3e-06       3      56 .]     586     634 ..     584     634 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 9.7
                           Fer4_10  18 aCPadl 23 
                                        CP+++
  gi|242398139|ref|YP_002993563.1| 239 NCPFNW 244
                                       488765 PP

  == domain 2  score: 28.4 bits;  conditional E-value: 1.1e-09
                           Fer4_10   3 vidddtCirCgkCvka..CPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       ++++d+C++C+ C +a  CPa       ++ ++e+++ r+ +  C gcg C+++CP
  gi|242398139|ref|YP_002993563.1| 586 YVNEDKCTGCRICINAygCPA-------IYWDEEKKQARVEPTMCWGCGGCAQVCP 634
                                       6799***********889***.......***************************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 !   27.6  10.2     2e-09   2.4e-06       1      50 [.     591     637 ..     591     638 .. 0.89

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 2e-09
                            Fer4_9   1 kCtgCgaCvea..CpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50 
                                       kCtgC+ C++a  Cpa  + e++++  ++ ++     C+gCg C+++Cp ga
  gi|242398139|ref|YP_002993563.1| 591 KCTGCRICINAygCPAIYWDEEKKQARVEPTM-----CWGCGGCAQVCPFGA 637
                                       7*******88777******9999999988865.....************876 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   1.9   0.00024      0.29      34      52 ..     585     605 ..     566     608 .. 0.80
   2 !   20.4   9.0   3.5e-07   0.00042       3      53 ..     587     635 ..     585     639 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00024
                           Fer4_21  34 lkvvedeCvGCnlCssv..CP 52 
                                       + v ed+C+GC +C++   CP
  gi|242398139|ref|YP_002993563.1| 585 YYVNEDKCTGCRICINAygCP 605
                                       46789*********9754477 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 3.5e-07
                           Fer4_21   3 idedkCigCgkCliaCedtshqaieidak.tvlkvvedeCvGCnlCssvCPv 53 
                                       ++edkC gC  C+ a       ai  d++ ++++v    C GC  C++vCP 
  gi|242398139|ref|YP_002993563.1| 587 VNEDKCTGCRICINAYG---CPAIYWDEEkKQARVEPTMCWGCGGCAQVCPF 635
                                       799*********98843...559*98866156677789*************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 ?   -2.7   1.5       7.1   8.4e+03      16      22 .]     385     390 ..     383     390 .. 0.73
   2 !   23.2   2.5   4.1e-08   4.9e-05       2      22 .]     584     606 ..     582     606 .. 0.90
   3 !    9.5   2.3   0.00092       1.1       5      21 ..     618     634 ..     614     635 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 7.1
                            Fer4_2  16 CvsaCPa 22 
                                       C  aCP+
  gi|242398139|ref|YP_002993563.1| 385 C-PACPH 390
                                       6.78986 PP

  == domain 2  score: 23.2 bits;  conditional E-value: 4.1e-08
                            Fer4_2   2 pvvvdtdrCigCgaCvsa..CPa 22 
                                        ++v++d+C+gC++C++a  CPa
  gi|242398139|ref|YP_002993563.1| 584 IYYVNEDKCTGCRICINAygCPA 606
                                       499*************9999**8 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.00092
                            Fer4_2   5 vdtdrCigCgaCvsaCP 21 
                                       v++ +C gCg C ++CP
  gi|242398139|ref|YP_002993563.1| 618 VEPTMCWGCGGCAQVCP 634
                                       6788999********** PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.4       7.5     9e+03       7      12 ..     383     388 ..     382     391 .. 0.65
   2 !   16.9   2.5   4.2e-06     0.005       4      21 ..     587     606 ..     586     610 .. 0.93
   3 !   14.1   1.5   3.1e-05     0.037       3      24 .]     617     638 ..     616     638 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 7.5
                            Fer4_6   7 dkCigC 12 
                                       ++C  C
  gi|242398139|ref|YP_002993563.1| 383 SLCPAC 388
                                       566666 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 4.2e-06
                            Fer4_6   4 idpdkCigCgdCvrv..CPe 21 
                                       +++dkC+gC+ C+++  CP+
  gi|242398139|ref|YP_002993563.1| 587 VNEDKCTGCRICINAygCPA 606
                                       89*************9**97 PP

  == domain 3  score: 14.1 bits;  conditional E-value: 3.1e-05
                            Fer4_6   3 eidpdkCigCgdCvrvCPegai 24 
                                       ++ p  C gCg C+ vCP+ga+
  gi|242398139|ref|YP_002993563.1| 617 RVEPTMCWGCGGCAQVCPFGAF 638
                                       67889999************95 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 ?   12.7   0.1   4.5e-05     0.054     115     173 ..     433     497 ..     425     504 .. 0.75
   2 ?   -1.8   0.0       1.2   1.4e+03     233     267 ..     525     559 ..     500     563 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.5e-05
                    DXP_synthase_N 115 tsisaalGlava......rdlkg.ekkkvvaviGDgaltgGmafealnnigelkkkllvilNdNem 173
                                       +si +++Gl++a      ++++g ek+ vva iGD+++     + al n+  +++++l+++ dN  
  gi|242398139|ref|YP_002993563.1| 433 ASIGIGHGLSIAqngslsEEQQGpEKQVVVATIGDSTFYH-TGLPALANAIYNRSNVLIVVLDNLV 497
                                       56666777776644444344455467999*******9964.5689****************99965 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.2
                    DXP_synthase_N 233 lfeelgfkYlGpidGhdleelikvleevkklkgpv 267
                                       + +++g +++  +d  d+++  ++++++ +++g  
  gi|242398139|ref|YP_002993563.1| 525 VAKAMGADFVAVVDPYDIKTTYETVKKALEVEGVS 559
                                       55789999****************99999988754 PP

>> Transket_pyr  Transketolase, pyrimidine binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   0.00018      0.22      46     171 ..      41     176 ..      12     181 .. 0.72
   2 ?    0.7   0.0      0.31   3.7e+02     128     170 ..     523     562 ..     495     568 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00018
                                       T.................TEGEEE--S-HHHHHHHHHHHHHHCTTEEEEEEEEHHHHGGGHHGGHHHHHCHHHHHT- CS
                      Transket_pyr  46 g.................egrvidsgisEqavlgfavGaalagpllviveaqFgdFangAqiyadqairsgeakgkl 105
                                       +                 +g +++++  E+ +  +a++aa +g  l+ + a+  + +n   + ad +++  + ++++
  gi|242398139|ref|YP_002993563.1|  41 PgtpsseltdtmaivskkAGVYMEYSTNEKVAFETALAAAWSG--LRAMTAMKHVGLN---VAADTFMS--AVGMGV 110
                                       4444444444444444448999999999999999999999999..9999999999999...66666666..556666 PP

                                       -EEEEESBSGGGSTTGTTTSBSSHHHHHHTSTTEEEE--SSHHHHHHHHHHHHHS..SS.SEEEEEE- CS
                      Transket_pyr 106 kvgvvtrlpigvgedGpehqsaeleaflrlipglkvvrPsdpaetkhllrrairr..edrkPvvlrlp 171
                                       + g v+  ++  + +  + q  +++++++  +++ v+ P++p e+k++ + a +   ++++ v+lr++
  gi|242398139|ref|YP_002993563.1| 111 EGGFVI--MVADDPSMWSSQNEQDTRVYAKFANVPVLEPTSPHEAKEMTKYAFELseKFKHFVILRTT 176
                                       655333..334466678889999******************************997778888888776 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.31
                                       SHHHHHHTSTTEEEE--SSHHHHHHHHHHHHHSSS.SEEEEEE CS
                      Transket_pyr 128 eleaflrlipglkvvrPsdpaetkhllrrairredrkPvvlrl 170
                                       e++a     + + vv P+d   t++ +++a++ e+   v ++ 
  gi|242398139|ref|YP_002993563.1| 523 EDVAKAMGADFVAVVDPYDIKTTYETVKKALEVEG---VSVIV 562
                                       455555555558899****************9664...44444 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.38   4.5e+02      34      56 ..     223     245 ..     206     246 .. 0.78
   2 ?   11.5   1.7   0.00029      0.34       1      28 [.     587     616 ..     587     621 .. 0.84
   3 ?    4.2   2.8     0.053        63       1      17 [.     618     634 ..     618     644 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.38
                           Fer4_13  34 qptseeekadaeeAadaCPvesI 56 
                                       +p   e++++++e +++CP + I
  gi|242398139|ref|YP_002993563.1| 223 HPAILEKIEKIREELNNCPFNWI 245
                                       455568899**********9887 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00029
                           Fer4_13   1 VDrdtCiacgaCvel..aPdvFeeddegga 28 
                                       V++d+C++c +C ++  +P ++  +++++a
  gi|242398139|ref|YP_002993563.1| 587 VNEDKCTGCRICINAygCPAIYWDEEKKQA 616
                                       899**********98889***988877543 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.053
                           Fer4_13   1 VDrdtCiacgaCvelaP 17 
                                       V+   C +cg C++++P
  gi|242398139|ref|YP_002993563.1| 618 VEPTMCWGCGGCAQVCP 634
                                       66778***********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 ?   -0.7   0.0       2.4   2.9e+03      10      25 ..     238     253 ..     237     266 .. 0.82
   2 ?    2.9   3.0      0.18   2.2e+02      52      63 ..     590     601 ..     564     607 .. 0.70
   3 ?   12.3   2.3   0.00021      0.25      44      66 ..     613     635 ..     606     636 .. 0.73
   4 ?   12.4   2.0    0.0002      0.24       2      20 ..     623     641 ..     622     645 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 2.4
                           Fer4_16  10 evCPtnaikekkekei 25 
                                       + CP n i++k++++i
  gi|242398139|ref|YP_002993563.1| 238 NNCPFNWIEGKEDAKI 253
                                       5799999999977665 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.18
                           Fer4_16  52 eaitgCdiCqdv 63 
                                        ++tgC+iC ++
  gi|242398139|ref|YP_002993563.1| 590 DKCTGCRICINA 601
                                       478888888764 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 0.00021
                           Fer4_16  44 deekckkqeaitgCdiCqdvCPa 66 
                                       +++++ + + + gC+ C++vCP+
  gi|242398139|ref|YP_002993563.1| 613 KKQARVEPTMCWGCGGCAQVCPF 635
                                       334444567899**********8 PP

  == domain 4  score: 12.4 bits;  conditional E-value: 0.0002
                           Fer4_16   2 CgtCgkCaevCPtnaikek 20 
                                       C +Cg Ca+vCP +a++  
  gi|242398139|ref|YP_002993563.1| 623 CWGCGGCAQVCPFGAFEPM 641
                                       8899999999999998765 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       3.7   4.4e+03      48      64 ..     229     245 ..     227     246 .. 0.84
   2 ?    6.1   0.7     0.015        18       2      17 ..     586     601 ..     586     613 .. 0.88
   3 ?    5.6   0.4     0.023        27       3      19 ..     618     634 ..     616     644 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 3.7
                           Fer4_15  48 eeeaaqeAaraCPvdAI 64 
                                       ++e+++e   +CP   I
  gi|242398139|ref|YP_002993563.1| 229 KIEKIREELNNCPFNWI 245
                                       689999*******9876 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.015
                           Fer4_15   2 vvDrdaCigcglCvae 17 
                                       +v++d+C+gc  C+ +
  gi|242398139|ref|YP_002993563.1| 586 YVNEDKCTGCRICINA 601
                                       5899*********976 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.023
                           Fer4_15   3 vDrdaCigcglCvaeap 19 
                                       v+ + C gcg C++++p
  gi|242398139|ref|YP_002993563.1| 618 VEPTMCWGCGGCAQVCP 634
                                       78899***********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 ?    3.9  10.5     0.064        77       2      58 ..     592     635 ..     591     638 .. 0.65
   2 ?    8.7   1.8     0.002       2.4       2      15 ..     623     636 ..     622     643 .. 0.61

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.064
                           Fer4_17   2 CiqCgyClp..eCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPq 58 
                                       C++C+ C++   Cp  ++ +++++               ++ +   C +Cg+C+++CP 
  gi|242398139|ref|YP_002993563.1| 592 CTGCRICINayGCPAIYWDEEKKQ---------------ARVEPTMCWGCGGCAQVCPF 635
                                       777777777555666666555333...............222345799*********96 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.002
                           Fer4_17   2 CiqCgyClpeCpsy 15 
                                       C +Cg C+++Cp++
  gi|242398139|ref|YP_002993563.1| 623 CWGCGGCAQVCPFG 636
                                       55555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (646 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.77u 0.29s 00:00:01.06 Elapsed: 00:00:00.50
# Mc/sec: 3910.33
//
Query:       gi|242398140|ref|YP_002993564.1|  [L=457]
Description: Acetyl-CoA synthetase II (ACSII, ADP-forming), subunit alpha [Thermococcus sibiricus MM 739]
Scores for complete 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-58  195.4   2.4      1e-56  190.5   1.0    2.7  3  Succ_CoA_lig    Succinyl-CoA ligase like flavodoxin domain
    3.1e-29  101.8   0.2    3.6e-26   91.9   0.1    2.5  2  CoA_binding_2   CoA binding domain
    7.9e-16   58.5   0.3    2.6e-15   56.9   0.3    2.0  1  CoA_binding     CoA binding domain
  ------ inclusion threshold ------
      0.026   14.5   0.5      0.058   13.4   0.1    1.8  2  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
      0.035   14.9   0.8        3.9    8.3   0.1    3.1  4  GFO_IDH_MocA    Oxidoreductase family, NAD-binding Rossmann f


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 !  190.5   1.0   2.9e-60     1e-56       1     138 []     152     289 ..     152     289 .. 0.99
   2 ?   -2.4   0.0       1.1   3.8e+03       3      29 ..     298     324 ..     296     326 .. 0.87
   3 ?    3.1   0.0     0.021        76      68      89 ..     393     414 ..     388     447 .. 0.76

  Alignments for each domain:
  == domain 1  score: 190.5 bits;  conditional E-value: 2.9e-60
                      Succ_CoA_lig   1 pGkialisqSGalalalldwaasrglgfskvvslGneadvdvadlleylaedpetkvillylEsirdgrkflsaarr 77 
                                       +G++a++sqSGal++ ++ ++ ++++gfsk++s+Gn+advd+adl+eylaed++ k+i+ly+E+i++g+kf+++a++
  gi|242398140|ref|YP_002993564.1| 152 KGSVAFVSQSGALGAGIVYKTIKEDIGFSKFISVGNMADVDFADLMEYLAEDNNSKSIALYIEGIKNGKKFMEIAKK 228
                                       699************************************************************************** PP

                      Succ_CoA_lig  78 aarkkpvvvlksGrseagaraaashtgalagsdavvdaafrqaGvlrvdsleelfdaaell 138
                                       +++kkp+++lk+G+se+garaa+shtg+lags+a++daafrq+Gvl+++++++l+++a+++
  gi|242398140|ref|YP_002993564.1| 229 VSKKKPIIALKAGKSESGARAASSHTGSLAGSYAIYDAAFRQSGVLVAETIDDLLSMARAF 289
                                       **********************************************************986 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.1
                      Succ_CoA_lig   3 kialisqSGalalalldwaasrglgfs 29 
                                       k+a+++  G+ ++  +d++ +rgl+++
  gi|242398140|ref|YP_002993564.1| 298 KVAIMTNAGGPGVLTADQLDKRGLKLA 324
                                       699999999999999999999999875 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.021
                      Succ_CoA_lig  68 grkflsaarraarkkpvvvlks 89 
                                       ++  ++a+++++++kpv++l +
  gi|242398140|ref|YP_002993564.1| 393 AEGIARAVKEVNNRKPVLALFM 414
                                       567899************9854 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.9   0.1     1e-29   3.6e-26       1     114 [.      13     136 ..      13     138 .. 0.96
   2 !    7.6   0.0    0.0015       5.2      63     105 ..     388     433 ..     346     437 .. 0.79

  Alignments for each domain:
  == domain 1  score: 91.9 bits;  conditional E-value: 1e-29
                                       --EEEET--S-TTSHHHHHHHHHHHHT--EEEESSS-SEETTEES----T....T--EEEE-S-HHHHGGGHHHHHH CS
                     CoA_binding_2   1 rtiaVvGasdnpgkfgykvlryllehglpvvpVnpkeeeilgekvyaslaedpepvdlvdvftppeatpeivkeala 77 
                                       ++iaV+Gas++p k gy v+++l++ + +v+p+n kee+++g+k+y+++++ pe+vdl+++++p   + + + ++++
  gi|242398140|ref|YP_002993564.1|  13 KSIAVLGASNDPLKLGYEVFKNLKDYEGKVYPINIKEETVQGVKAYKNVKNIPEDVDLAVIVVPKRFVKQALMDCGE 89 
                                       79***********************555**********************758************************ PP

                                       H--SEEEE-TT..........---HHHHHHHHHTT-EEE.ES-HHHH CS
                     CoA_binding_2  78 lgakavwlqpg..........sedeeaaelaeeagirvvgdrCilve 114
                                       +g+k++++  +           e++e++e+a+++gir++g++C++v+
  gi|242398140|ref|YP_002993564.1|  90 KGVKGAIIITAgfgemgeegkREERELVEIAQKYGIRIIGPNCVGVM 136
                                       *****9999999*********************************97 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0015
                                       S-HHHHGGGHHHHHHH...--SEEEE-TT---HHHHHHHHHTT-EE CS
                     CoA_binding_2  63 tppeatpeivkealal...gakavwlqpgsedeeaaelaeeagirv 105
                                       tp e+++ i+++++++   ++  + +++g ++e+a el+e++gi+ 
  gi|242398140|ref|YP_002993564.1| 388 TPTEHAEGIARAVKEVnnrKPVLALFMAGYVSEKARELLEKEGIPA 433
                                       66666666666666554338***********************986 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.9   0.3   7.4e-19   2.6e-15       3      96 .]      12     101 ..      10     101 .. 0.94

  Alignments for each domain:
  == domain 1  score: 56.9 bits;  conditional E-value: 7.4e-19
                                       TEEEEEETTTSHHHHHHHHHHHHHHECEEEEEEC-TTTTTCEETTEEEESCHHHHHHHCTTTEEEEES-HHHHHHHH CS
                       CoA_binding   3 dtkviviGagglgiaglyhfkeklkygikavfgvnprkvgtevlglpvyksvdeleektevdvavitvPaesaqeav 79 
                                       +++++v Ga++   +++y ++++lk    +v+++n +   ++v+g+++yk+v++++e+  vd avi+vP++++++a 
  gi|242398140|ref|YP_002993564.1|  12 PKSIAVLGASNDPLKLGYEVFKNLKDYEGKVYPINIK--EETVQGVKAYKNVKNIPED--VDLAVIVVPKRFVKQAL 84 
                                       689**************8888888866679*******..*******************..***************** PP

                                       HHHHHTT-SEEEEESST CS
                       CoA_binding  80 delveagikgiviiteg 96 
                                       +++ e+g+kg++iit+g
  gi|242398140|ref|YP_002993564.1|  85 MDCGEKGVKGAIIITAG 101
                                       ***************86 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 ?   13.4   0.1   1.6e-05     0.058      55     134 ..      53     131 ..      44     143 .. 0.79
   2 ?   -3.5   0.1       2.5   8.8e+03     101     127 ..     211     235 ..     197     244 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.6e-05
                                       TTEEEES-HHHHHTT--EEEE---HHHHHHHHHHHCCC--TT-EEEE---SEET.TTEEHHHHHHHHH-S--EEEEE CS
                    NAD_Gly3P_dh_N  55 enlvattdlaealkgadiivlvvPsqalrevlkklkgllkkkailvsliKGieegtlkllsevieeelkeekvavls 131
                                       + ++a++++++  +++d+ v+vvP+ ++++ l ++ ++  k ai++ +  G   ++ k+ +  + e+ +++    + 
  gi|242398140|ref|YP_002993564.1|  53 QGVKAYKNVKNIPEDVDLAVIVVPKRFVKQALMDCGEKGVKGAIIITAGFGEMGEEGKREERELVEIAQKY-GIRII 128
                                       6799*******************************998877777776655545556666666666666666.33455 PP

                                       SS- CS
                    NAD_Gly3P_dh_N 132 Gps 134
                                       Gp+
  gi|242398140|ref|YP_002993564.1| 129 GPN 131
                                       665 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.5
                                       E---SEET.TTEEHHHHHHHHH-S--E CS
                    NAD_Gly3P_dh_N 101 sliKGieegtlkllsevieeelkeekv 127
                                         i Gi++   k + e+++++ k++++
  gi|242398140|ref|YP_002993564.1| 211 LYIEGIKN--GKKFMEIAKKVSKKKPI 235
                                       45666666..44555677766666663 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 ?    8.3   0.1    0.0011       3.9      47      89 ..      54      96 ..      45     126 .. 0.89
   2 ?   -2.6   0.0       2.7   9.5e+03      18      39 ..     115     143 ..      99     164 .. 0.55
   3 ?    3.4   0.1     0.037   1.3e+02      43      97 ..     352     411 ..     315     430 .. 0.74
   4 ?   -1.6   0.0       1.3   4.5e+03      36      59 ..     419     442 ..     397     447 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0011
                                      THEEESSHHHHHTCTTESEEEE-S-GGGHHHHHHHHHHTT-..EE CS
                      GFO_IDH_MocA 47 gveaysdleelladpeidavivatpngtheelakaaleagk..hv 89
                                      gv+ay++++++++  ++d++++++p +  ++  +++ e+g+  ++
  gi|242398140|ref|YP_002993564.1| 54 GVKAYKNVKNIPE--DVDLAVIVVPKRFVKQALMDCGEKGVkgAI 96
                                      7889********9..99*********9999999988888875555 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.7
                                       HHHHTTTTE.......EEEEEECSSHHHH CS
                      GFO_IDH_MocA  18 plnesqrle.......evvalldpdaera 39 
                                        l e  +++       + v+++d++++  
  gi|242398140|ref|YP_002993564.1| 115 ELVEIAQKYgiriigpNCVGVMDTHSNMN 143
                                       44443333344444445566666665544 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.037
                                       HHHTTHEEESSHHHHHTCTTESE.EEE-S-G....GGHHHHHHHHHHTT-EEEEESSS-S CS
                      GFO_IDH_MocA  43 aesfgveaysdleelladpeida.vivatpn....gtheelakaaleagkhvllEKPlat 97 
                                       a + g + y+  + ll+d+++d+ v++++ +     t  e+a+ +++a k v   KP+ +
  gi|242398140|ref|YP_002993564.1| 352 ASARGEDYYKTAKLLLEDENVDMlVTICVVPtfagMTPTEHAEGIARAVKEVNNRKPVLA 411
                                       555556688889999999999963678887778888888999999999999888888854 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 1.3
                                       HHHHHHHHHHTTHEEESSHHHHHT CS
                      GFO_IDH_MocA  36 aeraeavaesfgveaysdleella 59 
                                       +e+a+++ e+ g++ay+  e++++
  gi|242398140|ref|YP_002993564.1| 419 SEKARELLEKEGIPAYERPEDVAS 442
                                       578888899999999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (457 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); 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: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 2981.28
//
Query:       gi|242398141|ref|YP_002993565.1|  [L=210]
Description: probable thymidylate kinase [Thermococcus sibiricus MM 739]
Scores for 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-52  175.4   0.0    1.1e-51  175.1   0.0    1.0  1  Thymidylate_kin  Thymidylate kinase
    9.7e-07   29.2   0.0    2.1e-06   28.1   0.0    1.5  1  AAA_28           AAA domain
    8.4e-06   25.8   0.2       0.18   11.6   0.1    2.6  2  dNK              Deoxynucleoside kinase
    0.00095   19.5   0.0     0.0028   17.9   0.0    1.8  2  AAA_22           AAA domain
     0.0029   17.7   0.2          1    9.5   0.1    2.2  2  SKI              Shikimate kinase
     0.0039   17.3   0.0     0.0084   16.3   0.0    1.7  1  AAA_33           AAA domain
     0.0042   16.6   0.0       0.01   15.4   0.0    1.7  2  PPK2             Polyphosphate kinase 2 (PPK2)
     0.0056   16.3   0.0      0.012   15.2   0.0    1.5  1  SRP54            SRP54-type protein, GTPase domain
  ------ inclusion threshold ------
      0.012   16.1   0.0      0.046   14.3   0.0    2.1  1  AAA_18           AAA domain
      0.013   16.0   0.1      0.038   14.4   0.0    1.9  1  AAA_17           AAA domain
      0.013   15.4   0.3       0.18   11.7   0.0    2.4  3  APS_kinase       Adenylylsulphate kinase
      0.017   14.6   0.1      0.049   13.1   0.0    1.7  3  KTI12            Chromatin associated protein KTI12
      0.024   14.7   0.0      0.031   14.3   0.0    1.4  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
      0.027   14.2   0.1      0.038   13.7   0.1    1.4  1  AAA_30           AAA domain
      0.047   13.5   0.1      0.065   13.1   0.1    1.2  1  BBP1_C           Spindle pole body component BBP1, C-terminal
      0.075   13.3   0.5       0.11   12.8   0.5    1.2  1  zf-C4H2          Zinc finger-containing protein
      0.088   13.8   0.0       0.15   13.1   0.0    1.4  1  LytR_C           LytR cell envelope-related transcriptional a
       0.12   11.3   0.0        0.2   10.6   0.0    1.3  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 


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 !  175.1   0.0   1.1e-54   1.1e-51       1     185 []       7     196 ..       7     196 .. 0.93

  Alignments for each domain:
  == domain 1  score: 175.1 bits;  conditional E-value: 1.1e-54
                                       EEESTTSSHHHHHHHHHHHHHHTTE.EEEESSSTTSHHHHHHHHHHH........TCS---HHHHHHHHHHHHHHTT CS
                   Thymidylate_kin   1 iEGlDGaGKttqaellkerlkeegikvvltrepggteiGekirelll........keeeleeqteallfaadriehl 69 
                                       +EG+DGaGK+tqa++l+++++++g++vvlt+ep++t +G++ir+l+l        +  ++++++eallfaadr+eh+
  gi|242398141|ref|YP_002993565.1|   7 LEGIDGAGKSTQAKMLAKWFENRGYEVVLTKEPTDTAFGKLIRRLVLiggkegiiDGARISKEAEALLFAADRAEHV 83 
                                       6*********************************************999876666677888999************* PP

                                       HHHHHHHHHTT-EEEEES-HHHHHHHHHTTTTTTCHHHHHHGGGTTSE-SEEEEEESSHHHHHTSCCTTSSTTTSHH CS
                   Thymidylate_kin  70 eekikpalkqgktvivdRylfSslaYqgakegvdldlvlslnedvllkPdltflldvdpevalkRlakrdeldeeee 146
                                        ++i+p++k gk+vi+dRy +SslaYq a +g+dl+++ +ln +++ + dl++lld++++++++R++ r+ + +e  
  gi|242398141|ref|YP_002993565.1|  84 KKLIEPSIKAGKVVISDRYFYSSLAYQWA-RGLDLNWLINLNAFAP-RADLVILLDLPVKESINRINGRSIR-SEFD 157
                                       ****************************6.66*************9.************************4.4444 PP

                                       HHHHHHHHHHHHHHHHHHTTSTEEEEETTS-HHHHHHHH CS
                   Thymidylate_kin 147 eqldflrkvrerylelakederiliidasksieevheeI 185
                                       +  + ++kvr++yl+la++ ++i ii+a  ++e++h++I
  gi|242398141|ref|YP_002993565.1| 158 KIVELQKKVRKNYLKLAEKFNEIRIINALAPVEDIHNDI 196
                                       5567799***********9999***************98 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   2.1e-09   2.1e-06       2     146 ..       5     171 ..       4     182 .. 0.72

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 2.1e-09
                            AAA_28   2 ivitGgestGKTtlleaLa....argypvv..pEaareileeklakge............dalpwvedllafaervl 60 
                                       iv+ G  ++GK+t ++ La    +rgy+vv  +E+  + + ++ ++              +++++ +++l fa+ + 
  gi|242398141|ref|YP_002993565.1|   5 IVLEGIDGAGKSTQAKMLAkwfeNRGYEVVltKEPTDTAFGKLIRRLVliggkegiidgaRISKE-AEALLFAADRA 80 
                                       899****************777666***9999999999988887665544444544443233333.48888887766 PP

                            AAA_28  61 eeqleeeaaa.aankvlfcDrglldtlaYarayggeaeaeleaaar.ekrydlvfllp.papei.dddgeR..redl 131
                                       e+ ++  +   +a+kv+++Dr +  +laY  a+g +  + l +  + + r dlv+ll+ p++e   + + R  r ++
  gi|242398141|ref|YP_002993565.1|  81 EHVKKLIEPSiKAGKVVISDRYFYSSLAYQWARGLD-LNWLINLNAfAPRADLVILLDlPVKESiNRINGRsiRSEF 156
                                       66555444446*************************.9998885554999******997666544333333235566 PP

                            AAA_28 132 eereaiderlrealr 146
                                       ++  ++++++r+ + 
  gi|242398141|ref|YP_002993565.1| 157 DKIVELQKKVRKNYL 171
                                       676666666666655 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   0.00018      0.18       1      23 [.       5      27 ..       5      51 .. 0.78
   2 !   11.6   0.1   0.00018      0.18     112     174 ..     119     181 ..      72     204 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00018
                                      EEEEESTTSSHHHHHHHHHCCST CS
                               dNK  1 ivveGnIgaGKstlvklLskklg 23
                                      iv+eG  gaGKst +k+L+k ++
  gi|242398141|ref|YP_002993565.1|  5 IVLEGIDGAGKSTQAKMLAKWFE 27
                                      89*****************9876 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00018
                                       HHHHHHHHCCH-SEEEEEE--HHHHHHHHHHCTTCCCTTS-HHHHHHHHHHHHHHHTSGGCS- CS
                               dNK 112 lldnlleelakpdlliYLkasletclerikkRgreeekkieldYlekLhekyeewlkklnevp 174
                                       +l nl+  +++ dl+i L++++++  +ri+ R+   e     +  +k+ ++y +  +k+ne+ 
  gi|242398141|ref|YP_002993565.1| 119 WLINLNAFAPRADLVILLDLPVKESINRINGRSIRSEFDKIVELQKKVRKNYLKLAEKFNEIR 181
                                       555566666779***********************9997667777888888888888877773 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   2.8e-06    0.0028       7      63 ..       4      54 ..       2      99 .. 0.74
   2 ?   -0.8   0.0       1.7   1.7e+03      38      69 ..     129     165 ..      91     200 .. 0.63

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.8e-06
                            AAA_22  7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellra 63
                                      ++v+ G  G+GK+t +++l+++++++      + evv+ + p +t   +l r+l+ +
  gi|242398141|ref|YP_002993565.1|  4 FIVLEGIDGAGKSTQAKMLAKWFENR------GYEVVLTKEPTDTAFGKLIRRLVLI 54
                                      7999*******************876......8888888777777666666666544 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.7
                            AAA_22  38 erpevvfvtlpsst.....sskdllrellralglelk 69 
                                       + + v++ +lp+++     + +++++e+ ++++l++k
  gi|242398141|ref|YP_002993565.1| 129 RADLVILLDLPVKEsinriNGRSIRSEFDKIVELQKK 165
                                       4445557777777644444555555555555555444 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.5   0.0    0.0086       8.6       2      15 ..      12      25 ..      11      46 .. 0.91
   2 !    9.5   0.1     0.001         1      84     155 ..     129     198 ..     118     201 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0086
                                      TSSHHHHHHHHHHH CS
                               SKI  2 GaGKstvGkllAkk 15
                                      GaGKst +k+lAk 
  gi|242398141|ref|YP_002993565.1| 12 GAGKSTQAKMLAKW 25
                                      9***********85 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.001
                                       HHSEEEEEE--HHHHHHHHHHTTSSGGGCSCHHHHHHHHHHH.HHHHHHCCSSCEEEECTSSHHHHHHHHHHH CS
                               SKI  84 ekgiviyLdvsleellerlkadkeRPllqekskeeelleela.ereplyeeaadvvvdeseeskeevaeeile 155
                                       +  +vi+Ld++++e ++r++ ++ R   +e +k  el+++ + +  +l e+++ + + ++ ++ e + + i++
  gi|242398141|ref|YP_002993565.1| 129 RADLVILLDLPVKESINRINGRSIR---SEFDKIVELQKKVRkNYLKLAEKFNEIRIINALAPVEDIHNDITA 198
                                       5678*****************9998...555555566666666678999999999999999998888888776 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   8.5e-06    0.0084       2     136 ..       5     170 ..       4     197 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 8.5e-06
                            AAA_33   2 vllvGlpGsGKstlaerl...lkklgavllssdt........lrrrlfg.........tdqqsktdytr...vldrl 55 
                                       ++l G  G+GKst a+ l    +++g++++ + +        l+rrl+              ++++ ++   ++ + 
  gi|242398141|ref|YP_002993565.1|   5 IVLEGIDGAGKSTQAKMLakwFENRGYEVVLTKEptdtafgkLIRRLVLiggkegiidG--ARISKEAEallFAADR 79 
                                       6899************9944455666877766664577777744444445555446422..3333333321222334 PP

                            AAA_33  56 yqilnelarkalsagrnvildatnls....rrer....arflklarrlgvp....vrivvvetdeetlkeRlakRaa 120
                                        +++++l++   +ag+ vi d  + s    +++r     ++++l           ++++ ++ + ++   R+  R+ 
  gi|242398141|ref|YP_002993565.1|  80 AEHVKKLIEPSIKAGKVVISDRYFYSslayQWARgldlNWLINLNA----FapraDLVILLDLPVKESINRINGRSI 152
                                       4588999999999999999998866655436666544322333222....123347889999999999999999998 PP

                            AAA_33 121 ng..ddrsevpeealdrq 136
                                       ++  d+ +e+ +++ +++
  gi|242398141|ref|YP_002993565.1| 153 RSefDKIVELQKKVRKNY 170
                                       765556666666666655 PP

>> PPK2  Polyphosphate kinase 2 (PPK2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0     1e-05      0.01      32      71 ..       3      42 ..       1      51 [. 0.93
   2 ?   -3.7   0.0       7.1     7e+03      88     100 ..      93     105 ..      83     107 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1e-05
                                      EEEEEEESTTS-HHHHHHHHHTTS-GGG-EEEE--S--HH CS
                              PPK2 32 lvvifegrDaAGKgGaikrvtealnprvarvvalkaPtee 71
                                      + +++eg D+AGK    k + + ++ r+++vv  k+Pt++
  gi|242398141|ref|YP_002993565.1|  3 IFIVLEGIDGAGKSTQAKMLAKWFENRGYEVVLTKEPTDT 42
                                      679***********************************97 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 7.1
                                       TT-EEEEES-GGG CS
                              PPK2  88 kgeivlFdRswYn 100
                                       +g++v+ dR +Y 
  gi|242398141|ref|YP_002993565.1|  93 AGKVVISDRYFYS 105
                                       6899999999986 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.2e-05     0.012       4      35 ..       5      36 ..       3      44 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.2e-05
                                      EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEE CS
                             SRP54  4 illvGlqGaGKTttlaKLaallkkegkkvllv 35
                                      i+l G+ GaGK t +  La++++++g++v+l 
  gi|242398141|ref|YP_002993565.1|  5 IVLEGIDGAGKSTQAKMLAKWFENRGYEVVLT 36
                                      7899*************************996 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   4.6e-05     0.046       1      25 [.       5      36 ..       5     161 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.6e-05
                            AAA_18  1 IlltGtpGvGKttlakeLskrlgf.......g 25
                                      I+l G+ G+GK+t ak L+k  ++        
  gi|242398141|ref|YP_002993565.1|  5 IVLEGIDGAGKSTQAKMLAKWFENrgyevvlT 36
                                      89****************99874444444441 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   3.8e-05     0.038       2     126 ..       9     154 ..       8     164 .. 0.54

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.8e-05
                                       E-TTSSHHHHHHHHHHHH...TEEEEEH........HHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHH.. CS
                            AAA_17   2 GgPGsGKgtqceklveky...gfthlsa........Gdllreeakrgglakardemrklpleekkelqkeaaeki.. 65 
                                       G+ G+GK+tq++ l++ +   g++++ +        G l+r  +  gg +   d  r  ++ e   + +  ae++  
  gi|242398141|ref|YP_002993565.1|   9 GIDGAGKSTQAKMLAKWFenrGYEVVLTkeptdtafGKLIRRLVLIGGKEGIIDGARISKEAEALLFAADRAEHVkk 85 
                                       899***********974444466665332333333399999988777654444444433333333333222222200 PP

                                       .HHHH..HSSEEEEEE-SEEEETTEEEESSHHHHH...HHH....SEEEEEE--HHHHHHHHHHHTTST CS
                            AAA_17  66 .aeea..kkkgvlvdghprikeqagfldglpkevl...eelkp..daiilleadpeeilerrlkdrtrg 126
                                         e +  + k v+ d ++      +   gl+ + l   + + p  d++ill+ + +e ++r   +  r+
  gi|242398141|ref|YP_002993565.1|  86 lIEPSikAGKVVISDRYFYSSLAYQWARGLDLNWLinlNAFAPraDLVILLDLPVKESINRINGRSIRS 154
                                       033334223456666666555455555666655541113444444778888888888888887775555 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00018      0.18       2      34 ..       2      34 ..       1      40 [. 0.91
   2 ?   -2.0   0.0       2.9   2.9e+03      30      63 ..      55      86 ..      38      97 .. 0.65
   3 ?    0.9   0.0      0.38   3.8e+02      34      97 ..     145     201 ..     137     207 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00018
                                      -EEEEEESSTTSSHHHHHHHHHHHHHHTT--EE CS
                        APS_kinase  2 gvvvwltGlsgsGKstianalekkLvekgisvy 34
                                      g+ + l G+ g+GKst a++l+k  +++g++v+
  gi|242398141|ref|YP_002993565.1|  2 GIFIVLEGIDGAGKSTQAKMLAKWFENRGYEVV 34
                                      77899***********************99886 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.9
                                      T--EEEEEHHHHTTTTTTT--SSHHHHHHHHHHH CS
                        APS_kinase 30 gisvylLdGdnvRhgLnkdLgfseedRkenirrv 63
                                      g +  ++dG  + ++ +  L f ++dR+e+++++
  gi|242398141|ref|YP_002993565.1| 55 GGKEGIIDGARISKEAE-ALLF-AADRAEHVKKL 86
                                      55555666666655533.3434.57888888776 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.38
                                       EEEEHHHHTTTTTTT--SSHHHHHHHHHHHHHHHHHHHHTT-EEEEE----SHHHHHHHHHHHH CS
                        APS_kinase  34 ylLdGdnvRhgLnkdLgfseedRkenirrvaevaklladaglivlvafisPyreeReaarelle 97 
                                        +++G ++R +  k +  +++ Rk+ ++    +a+++   + i ++ +++P ++  +++ +l+e
  gi|242398141|ref|YP_002993565.1| 145 NRINGRSIRSEFDKIVELQKKVRKNYLK----LAEKF---NEIRIINALAPVEDIHNDITALIE 201
                                       5667777777777777777777764442....34444...456667777777777777776666 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   4.9e-05     0.049       4      37 ..       5      38 ..       3      45 .. 0.91
   2 ?   -3.4   0.0       5.1   5.1e+03      60      80 ..      83     103 ..      79     105 .. 0.76
   3 ?   -3.5   0.0       5.7   5.7e+03     239     252 ..     161     175 ..     148     185 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.9e-05
                                      EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-T CS
                             KTI12  4 vvltGlPssGKstrakeLakaleeekrsvvvidd 37
                                      +vl G+  +GKst ak Lak +e+++++vv+ ++
  gi|242398141|ref|YP_002993565.1|  5 IVLEGIDGAGKSTQAKMLAKWFENRGYEVVLTKE 38
                                      8999*************************98765 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 5.1
                                       HHHHHHHHHTT.SEEEE-S-- CS
                             KTI12  60 lrsavkrdLskekvVIvDsln 80 
                                       +++ ++ +++  kvVI D   
  gi|242398141|ref|YP_002993565.1|  83 VKKLIEPSIKAGKVVISDRYF 103
                                       566778888899999999765 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 5.7
                                       HHH.HHHHHHHHHHT CS
                             KTI12 239 eLs.rlrrqFvklnk 252
                                       eL+ ++r++++kl +
  gi|242398141|ref|YP_002993565.1| 161 ELQkKVRKNYLKLAE 175
                                       443134555555544 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   0.0   3.1e-05     0.031       9      35 ..      12      38 ..       4     203 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.1e-05
                                      TSSHHHHHHHHHHHHHHTT--EEEEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  9 GvGKTtlaanLaralarrglrVllvDa 35
                                      G+GK+t a  La+ + +rg++V+l + 
  gi|242398141|ref|YP_002993565.1| 12 GAGKSTQAKMLAKWFENRGYEVVLTKE 38
                                      9***********************983 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   3.8e-05     0.038      21      52 ..       5      36 ..       2     100 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.8e-05
                            AAA_30 21 avltGpAGtGKttalkalreaweaaggrvigl 52
                                       vl+G  G+GK+t  k l++ +e++g++v++ 
  gi|242398141|ref|YP_002993565.1|  5 IVLEGIDGAGKSTQAKMLAKWFENRGYEVVLT 36
                                      689*************************9975 PP

>> BBP1_C  Spindle pole body component BBP1, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   6.5e-05     0.065      47      93 ..     151     199 ..     142     210 .] 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.5e-05
                            BBP1_C  47 elraeLinelkqskklydnYykLysKYqeLkkiskesl..dlqskianl 93 
                                       ++r e+ +     kk+  nY kL +K++e++ i   +   d+++ i+ l
  gi|242398141|ref|YP_002993565.1| 151 SIRSEFDKIVELQKKVRKNYLKLAEKFNEIRIINALAPveDIHNDITAL 199
                                       7899999989999******************998544444777777765 PP

>> zf-C4H2  Zinc finger-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.5   0.00011      0.11      72     127 ..     153     208 ..     141     210 .] 0.91

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00011
                           zf-C4H2  72 eeekekslekakklyeeykklkeevnelrselglekledleeeeeellkeeifekq 127
                                       ++e +k +e  kk+ ++y kl e+ ne+r  + l ++ed +++ + l+++e+fek 
  gi|242398141|ref|YP_002993565.1| 153 RSEFDKIVELQKKVRKNYLKLAEKFNEIRIINALAPVEDIHNDITALIEHELFEKA 208
                                       66778889999*****************************************9986 PP

>> LytR_C  LytR cell envelope-related transcriptional attenuator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00015      0.15       8      43 ..      11      50 ..      10      98 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00015
                            LytR_C  8 NgtgvsGlAarvadaLeerGftvgevgnagnadee......t 43
                                      +g+g+s +A+ +a+++e+rG++v+ +++ +++          
  gi|242398141|ref|YP_002993565.1| 11 DGAGKSTQAKMLAKWFENRGYEVVLTKEPTDT--AfgklirR 50
                                      799******************99985543333..13445542 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0    0.0002       0.2      33      70 ..       6      42 ..       2      49 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0002
                                      EEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE----- CS
                              MeaB 33 GltGvPGaGkstlvealglelrrrGkrvavlavDPssp 70
                                       l G+ GaGkst  + l+  + +rG+ v vl  +P+ +
  gi|242398141|ref|YP_002993565.1|  6 VLEGIDGAGKSTQAKMLAKWFENRGYEV-VLTKEPTDT 42
                                      578***********************99.666677665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       958  (0.053433); expected 358.6 (0.02)
Passed bias filter:                      734  (0.0409393); 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: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 1354.05
//
Query:       gi|242398142|ref|YP_002993566.1|  [L=238]
Description: phosphomannomutase-related protein [Thermococcus sibiricus MM 739]
Scores for complete 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   27.9   0.0    2.3e-06   27.3   0.0    1.3  1  PGM_PMM_I  Phosphoglucomutase/phosphomannomutase, alpha/beta/


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 !   27.3   0.0   1.3e-10   2.3e-06      14      82 ..       8      71 ..       3     101 .. 0.89

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 1.3e-10
                                      CHCTBSCCHHHHHHHHHHHHCHHCSTS-EEEEEE-S-TTHHHHHHHHHHHHHCCT-CEEEEEEB-HHHH CS
                         PGM_PMM_I 14 gegeltpelveklgqaiaeylkaeakkkkvvvGrDtRvssrelaealaaglaanGvevillgllptPav 82
                                        +e++pe ++ lg+ai+++ +      +++vGrD+R+ sr  ++al+ g++++G +++++ l+p  ++
  gi|242398142|ref|YP_002993566.1|  8 RSEEFNPEELALLGRAIGTVAQG-----TIIVGRDGRAISRYGKRALVVGIVSTGSSTMDVRLIPLIVL 71
                                      5688**************99986.....8*********************************9997655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1603.87
//
Query:       gi|242398143|ref|YP_002993567.1|  [L=361]
Description: Nucleotidyl transferase [Thermococcus sibiricus MM 739]
Scores for complete 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-52  176.2   0.0    1.2e-51  175.7   0.0    1.2  1  NTP_transferase  Nucleotidyl transferase
    1.5e-17   62.5   9.5    1.3e-06   27.9   1.4    3.8  3  Hexapep          Bacterial transferase hexapeptide (six repea
    1.9e-10   41.3   0.0    2.8e-10   40.8   0.0    1.3  1  NTP_transf_3     MobA-like NTP transferase domain
     0.0016   18.4   0.0     0.0032   17.4   0.0    1.4  1  CTP_transf_3     Cytidylyltransferase
     0.0027   15.9   1.0     0.0045   15.2   1.0    1.3  1  DUF4954          Domain of unknown function (DUF4954)
  ------ inclusion threshold ------
      0.012   14.6   0.1        0.4    9.6   0.1    2.2  2  Fucokinase       L-fucokinase
       0.11   12.3  16.5       0.12   12.1   8.2    4.1  3  Hexapep_2        Hexapeptide repeat of succinyl-transferase


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.7   0.0   4.5e-55   1.2e-51       2     244 ..       3     231 ..       2     233 .. 0.97

  Alignments for each domain:
  == domain 1  score: 175.7 bits;  conditional E-value: 4.5e-55
                                       EEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEE CS
                   NTP_transferase   2 avILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlia 78 
                                       avILaGG+GtRL PLt  ++k+++p+ +k +++++++ +l+n+g+ee i++l  + ++++ +++++gs+fgve++++
  gi|242398143|ref|YP_002993567.1|   3 AVILAGGKGTRLLPLTVYRPKPMIPFFNK-PMMEYVVRELVNAGVEE-IFILVGYLKERIINYFGDGSDFGVEIKYS 77 
                                       8****************************.*****************.***************************** PP

                                       EESS--.BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEEC CS
                   NTP_transferase  79 lepegk.gtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGviead 154
                                         ++ k gtA+A +++a+ ++d++     +v ++D+l++ +++++ + ++ k+a  ++t+++++ve++++yG++ +d
  gi|242398143|ref|YP_002993567.1|  78 NGENIKlGTAGATKKVADRINDTF-----IVASSDVLTNLDIKTLYDYHKRKKA--LATIALSRVEDPSQYGIAIVD 147
                                       9998888*************9877.....9************************..********************* PP

                                       TTSBEEEEECS-SSHSH.CSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EE CS
                   NTP_transferase 155 eegrverfvEKPkeaka.selassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWs 230
                                       +++r+ +f+EKP+ ++a s+l+++G+Y+f++ev++       +  +  d+  +++pk+lee  + + f f+   yW+
  gi|242398143|ref|YP_002993567.1| 148 SNNRILKFKEKPRLEEAfSNLVNAGVYIFEPEVFDLV-----PRGQNFDFSLNLFPKMLEENLPLYGFPFEE--YWN 217
                                       ****************99******************9.....889**************************9..9** PP

                                       EXSSHHHHHHHHHH CS
                   NTP_transferase 231 DvGtldslleanek 244
                                       DvG ++s+l+a+++
  gi|242398143|ref|YP_002993567.1| 218 DVGRPSSYLQATAD 231
                                       **********9886 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.1   4.5e-08   0.00012       7      33 ..     267     293 ..     263     296 .. 0.89
   2 !   25.9   3.7   2.2e-09   5.6e-06       1      35 [.     296     329 ..     291     330 .. 0.84
   3 !   27.9   1.4   4.9e-10   1.3e-06       1      36 []     319     354 ..     319     354 .. 0.94

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 4.5e-08
                                       TEEE-TTEEEETTEEE-TTEEEETTEE CS
                           Hexapep   7 nvlIgpfaviggnVkIGdnvkIgagvv 33 
                                       + +I+ fav+g+nV+I +nvkI++ v 
  gi|242398143|ref|YP_002993567.1| 267 KPQIRGFAVLGDNVEISRNVKIERSVI 293
                                       678999*****************9775 PP

  == domain 2  score: 25.9 bits;  conditional E-value: 2.2e-09
                                       TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                           Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                       +++I++++ I   a+ig+nV IG++v+I++g+vig
  gi|242398143|ref|YP_002993567.1| 296 NVTIEEGTEIY-EAIIGENVYIGKGVIIESGSVIG 329
                                       45666666666.**********************8 PP

  == domain 3  score: 27.9 bits;  conditional E-value: 4.9e-10
                                       TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEEES CS
                           Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvigg 36 
                                       +++I+s+++Ig ++vi + +kIG nvkI+  ++ig+
  gi|242398143|ref|YP_002993567.1| 319 GVIIESGSVIGDNSVIEDFTKIGANVKIWTESRIGR 354
                                       589**************************9999985 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 !   40.8   0.0   1.1e-13   2.8e-10       1     120 [.       3     130 ..       3     180 .. 0.76

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 1.1e-13
                                       EEEEEESS-TTT.....TTTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHH...TTCTS-EEE-TT CS
                      NTP_transf_3   1 aviLAGGrSsRm.....ggdKallplggkpllervldalraagvdevvvvggd..eevlaal...arlgvrvveded 67 
                                       aviLAGG+++R+      ++K+++p+ +kp++e+v++ l  agv+e+++ +g+  e + +++    ++gv++ +   
  gi|242398143|ref|YP_002993567.1|   3 AVILAGGKGTRLlpltvYRPKPMIPFFNKPMMEYVVRELVNAGVEEIFILVGYlkERIINYFgdgSDFGVEIKYSNG 79 
                                       79**********5554447*********************************9866666655333455666544433 PP

                                       S..S-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEE CS
                      NTP_transf_3  68 p..gkgplaslaaalraaadadavlvlacDmPlltpelverllaaaaasgadvvv 120
                                       +    g++++ +  ++++  +d ++v++ D+  lt   +++l + +++++a +++
  gi|242398143|ref|YP_002993567.1|  80 EniKLGTAGATKKVADRI--NDTFIVASSDV--LTNLDIKTLYDYHKRKKALATI 130
                                       312678888888888877..58888888887..5677777777776655554444 PP

>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   1.2e-06    0.0032      16      45 ..      23      51 ..      18      52 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.2e-06
                                      GGGSEETTEEHHHHHHHHHHHTTTTSEEEE CS
                      CTP_transf_3 16 Knlldlggkpliayvleaalkskafekviv 45
                                      K+++++++kp+++yv+++++++++ e++++
  gi|242398143|ref|YP_002993567.1| 23 KPMIPFFNKPMMEYVVRELVNAGV-EEIFI 51
                                      9********************998.77776 PP

>> DUF4954  Domain of unknown function (DUF4954)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   1.0   1.8e-06    0.0045     217     272 ..     279     335 ..     269     354 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.8e-06
                           DUF4954 217 pveiGegViledfiissGskikdgavisrcfvGqavklkkqfsae.dsllfaNcqge 272
                                        vei ++V +e ++i s  +i++g+ i ++++G++v ++k+  +e  s++++N+ +e
  gi|242398143|ref|YP_002993567.1| 279 NVEISRNVKIERSVIFSNVTIEEGTEIYEAIIGENVYIGKGVIIEsGSVIGDNSVIE 335
                                       466777777777777777777777777777777777777766554146677776555 PP

>> Fucokinase  L-fucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.017        45      45     121 ..      94     163 ..      84     181 .. 0.73
   2 ?    9.6   0.1   0.00015       0.4     270     320 ..     282     332 ..     243     357 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.017
                        Fucokinase  45 pkrmkpGvlvtssDvlllfdseeisfdka..gvtalavpstldigtnHGVfvlddqsseeeeleirsvkkflhKpse 119
                                         r++ +++v+ssDvl   d +++   ++  ++ a    s ++  ++ G+ ++d++         +++ kf  Kp  
  gi|242398143|ref|YP_002993567.1|  94 ADRINDTFIVASSDVLTNLDIKTLYDYHKrkKALATIALSRVEDPSQYGIAIVDSN---------NRILKFKEKPRL 161
                                       448899***********886666555444244444444567777788888888888.........777777777777 PP

                        Fucokinase 120 ee 121
                                       ee
  gi|242398143|ref|YP_002993567.1| 162 EE 163
                                       76 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00015
                        Fucokinase 270 kkesavvinSvlessvsvgegsviehsslkgnvsigsnsivsglelessee 320
                                       +++++ +  Sv+ s+v+++eg+ i++  +++nv ig++ i+ + ++  +++
  gi|242398143|ref|YP_002993567.1| 282 ISRNVKIERSVIFSNVTIEEGTEIYEAIIGENVYIGKGVIIESGSVIGDNS 332
                                       38899999********************************97666665544 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1      0.62   1.6e+03      26      32 ..     169     175 ..     168     177 .. 0.84
   2 ?    2.4   0.1     0.053   1.4e+02      20      32 ..     276     288 ..     272     290 .. 0.84
   3 ?   12.1   8.2   4.8e-05      0.12       3      27 ..     309     335 ..     307     346 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.62
                                       E-TT-EE CS
                         Hexapep_2  26 vgaGvvi 32 
                                       v aGv+i
  gi|242398143|ref|YP_002993567.1| 169 VNAGVYI 175
                                       78****9 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.053
                                       E-TT-EE-TT-EE CS
                         Hexapep_2  20 lGdncvvgaGvvi 32 
                                       lGdn+ ++ +v i
  gi|242398143|ref|YP_002993567.1| 276 LGDNVEISRNVKI 288
                                       9******999866 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 4.8e-05
                                       EE-TT-EE-TT-EE..SEEE-TT-EE- CS
                         Hexapep_2   3 iIGdnCliGanagi..GvslGdncvvg 27 
                                       iIG+n+ iG+  +i  G  +Gdn+v++
  gi|242398143|ref|YP_002993567.1| 309 IIGENVYIGKGVIIesGSVIGDNSVIE 335
                                       899999999999988999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2559.50
//
Query:       gi|242398144|ref|YP_002993568.1|  [L=622]
Description: phosphoenolpyruvate carboxykinase [Thermococcus sibiricus MM 739]
Scores for complete 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-106  354.3   0.0   7.3e-106  354.0   0.0    1.1  1  PEPCK_GTP  Phosphoenolpyruvate carboxykinase C-terminal P-loo
    1.1e-59  201.7   0.0    1.5e-59  201.3   0.0    1.2  1  PEPCK_N    Phosphoenolpyruvate carboxykinase N-terminal domai


Domain annotation for each model (and alignments):
>> PEPCK_GTP  Phosphoenolpyruvate carboxykinase C-terminal P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  354.0   0.0  8.2e-110  7.3e-106       1     358 []     244     605 ..     244     605 .. 0.93

  Alignments for each domain:
  == domain 1  score: 354.0 bits;  conditional E-value: 8.2e-110
                                       -EEES-EEEEEE-TTS-EEEEEEE-TTTSSHHHHHT---SSTT-EEEEEESS-EEEEE-TTSBEEEE---SEEEEE- CS
                         PEPCK_GTP   1 wLaEhmlilgvtspegkkkyvaaafpsacGKtnlamleptlegwkvetvgdDiawlkfgedgrlraiNpeaGfFgva 77 
                                       wL+Ehm++++++ p+g+k+y+++a+ps+cGKt++am++ +      ++vgdD++++    +g+ r+ N+e+G+Fg++
  gi|242398144|ref|YP_002993568.1| 244 WLSEHMFLMRINGPNGRKTYFTGAYPSMCGKTSTAMISWE------NIVGDDLTFIVDM-KGEARGANVEKGVFGII 313
                                       9************************************987......9*********876.9**************** PP

                                       TT-STTT-HHHHHHT.TBS.-EEES-EEETTS-EE-TT--------EE-TTSSEE-T.T-S.......SS-TT-EEE CS
                         PEPCK_GTP  78 pgtnektnpnalktl.kkn.tiftNvaltedgdvwWegleeeapaelidwkgkkwtkekek.......aahpnsrft 145
                                       +g+n++++p ++++l + n +if+Nv++ +dg+++W++++   p+e+ +++gk w+ + ++        +h+n+rft
  gi|242398144|ref|YP_002993568.1| 314 QGVNQEDDPIIWEVLhSPNeIIFSNVLV-KDGKPYWNEMGIPIPDEGENHSGKWWRGK-KDsegneisPSHKNARFT 388
                                       ***************86667******99.79*********************555554.3346788999******** PP

                                       EEGGGSTTB-.TTTT-TT-EEEEEEEEEEB-SSSS-SEEE-SSHHHHHHH.HHT-EEE--TTSSS-TT-EEE-GGG- CS
                         PEPCK_GTP 146 vpakqlpiia.pewedpeGvpisaiifggrrsetvplvleafdwehGvfl.gatlesetTaaaegkvgvvrrdPfam 220
                                       v+++ +p+++ +++e+p Gv +  +ifggr+++t+p+v eafdw+hGv++ ga+lesetTaa+ gk+gv   +P+a+
  gi|242398144|ref|YP_002993568.1| 389 VSLDAFPNTDlEALETPCGVRVGGMIFGGRDADTWPPVREAFDWAHGVITmGAALESETTAATLGKEGVRAFNPMAI 465
                                       *********73678**********************************877************************** PP

                                       GGG-SS-HHHHHHHHHHHTTSTT-B--EEEEEES--B-TTSSBSS--GGGHHHHHHHHHHHHTT..S-EEETTEEEE CS
                         PEPCK_GTP 221 lpFlgynlgdYlehwlelgkklekklPkifsvNwfrkdeegkflWPGfgenlrvlkWilkrvegeakavetpiGlvP 297
                                       l+Fl++++g+Yl+++le++kk  + +Pkif vN+f+++++gk+l     + +  lkW+  rv+g+++a++tp+G++P
  gi|242398144|ref|YP_002993568.1| 466 LDFLSVHIGKYLKNYLEFEKK-LRIKPKIFAVNYFLREKDGKWLN-HKLDKSVWLKWMELRVHGDVDAIKTPVGYIP 540
                                       ********************9.999*******************6.44566777*********************** PP

                                       -BTTC--TT-.........TT--HHHHS---HHHHHHHHHHHHHHHHHTGGGS-HHHHHHHHHHHHHH CS
                         PEPCK_GTP 298 kkedldlkgl.......dlskedleellsvdkeewkeeveeieelfeklgeklPkelleeleelekrl 358
                                       k+edl+  +l       d+s+ed+e+++ +++ e+++++e+ie++++++g ++P+el++ lee ++rl
  gi|242398144|ref|YP_002993568.1| 541 KYEDLK--RLfkevlnkDYSREDYEKQFVIRVPEFLAKIERIEKIYRDVG-NIPEELFKVLEEERHRL 605
                                       ****65..555566899*******************************88.9**********999986 PP

>> PEPCK_N  Phosphoenolpyruvate carboxykinase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  201.3   0.0   1.6e-63   1.5e-59       1     217 [.      29     239 ..      29     240 .. 0.96

  Alignments for each domain:
  == domain 1  score: 201.3 bits;  conditional E-value: 1.6e-63
                                       HHHHHHHHHH--SEEEE----HHHHHHHHHHHHHTTSEEE-TTSBS-EEE---TTSSS--GGGEEEE-SSHHHH-SS CS
                           PEPCK_N   1 efveevaelcqPdkvvvcdgseeeneellkelvekgeliklekypnsylarsdpkDvARvesrTfictekeedagpl 77 
                                       ef+++++el++P++v++c++s+e++++++++++e ge+++l ++++++++ + + D+AR++ rT i+++k  ++ p+
  gi|242398144|ref|YP_002993568.1|  29 EFLAKYIELLNPARVFICTDSKEDENYIRRRAIEYGEEKSL-AMEGHTIHYDGYYDQARDKARTKILVPKGVEI-PF 103
                                       699**************************************.********************************.** PP

                                       --EE-HHHHHHHHHHHSTTTTTTSEEEEEEEEES-TTSTT-EEEEEEES-HHHHHHHHHHSEESHHHHTT-SS..TS CS
                           PEPCK_N  78 nnwmdpeemkeelkelfkgcmkGrtmyVipfsmGpvgsplskigveiTdsaYVvlsmrimtrvgkkvleklgeeeef 154
                                        n+md+e+  +e++e++k++ kG++++V++f++Gp +s ++ ++v++TdsaYV++s+ i++r g++++++lg+e++f
  gi|242398144|ref|YP_002993568.1| 104 INTMDREKGLKEIHEIMKDIAKGKELFVCFFVLGPKNSVFTIPAVQLTDSAYVAHSEFILYRKGYEEFKRLGREAKF 180
                                       ***************************************************************************** PP

                                       EEEEEE-S-..-SS-SS-BTB---GG-EEEEEGGGTEEEEES--SHHHH-TCCHHHHCHHHHHHH CS
                           PEPCK_N 155 vkclHsvga..plegqkdvkWpcnekkyivhfpeereilsvgsgYgGNaLlgKkcfalRiasvia 217
                                       +k++Hs+g+  +++++k+      +k++++++ e ++++s +++YgGN++++Kk +a+R++++ a
  gi|242398144|ref|YP_002993568.1| 181 LKFVHSAGEldERKTSKNI-----DKRRVYIDLEGETVYSANTQYGGNTIGLKK-LAFRLTIKRA 239
                                       ********95333455553.....5*****************************.*****99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (622 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.46
# Mc/sec: 4076.58
//
Query:       gi|242398145|ref|YP_002993569.1|  [L=117]
Description: magnesium transporter [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 678.09
//
Query:       gi|242398146|ref|YP_002993570.1|  [L=278]
Description: magnesium transporter [Thermococcus sibiricus MM 739]
Scores for complete 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-28   98.2  27.7    1.9e-19   70.3   7.4    3.1  3  MgtE      Divalent cation transporter


Domain annotation for each model (and alignments):
>> MgtE  Divalent cation transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   5.0     1e-12   1.8e-08      68     123 ..      10      67 ..       2      68 .. 0.83
   2 !    4.3   0.7    0.0028        49      39      85 ..      79     129 ..      74     145 .. 0.60
   3 !   70.3   7.4     1e-23   1.9e-19       1     123 [.     146     271 ..     146     272 .. 0.89

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 1e-12
                                       HHHHHHHHHHHHHHHHHH....HHHHHHHHHHTTS-GGGSHHHHHHHHHHHHHHHHHH CS
                              MgtE  68 alvvglalvlvllaaall..ilgvllplllwklglDPdnaaiPlltalgDllgtlllv 123
                                       a++v l +++  l+++ll  + ++l +++ +k+g+DPd +a+P++t+++Dl+++ llv
  gi|242398146|ref|YP_002993570.1|  10 AVAVFLIVITSTLFTSLLlgYSTALATIIPFKKGIDPDAVAAPIVTSIADLITIPLLV 67 
                                       445666666666666666899999999*****************************98 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0028
                                       HHHHHHHHHHHHHHHHHHHHHHHT-......CTSHHHHHHHHHHHHHHHHHH CS
                              MgtE  39 elrvvlllgvilgllifllalllgw.....slllalvvglalvlvllaaall 85 
                                        + ++l+lgvil+l+++    +  +      + ++ +vg+  ++  ++ +ll
  gi|242398146|ref|YP_002993570.1|  79 TFYLLLVLGVILSLIVSKGSKIG-KrerkiFVEVLSIVGALAFISSISGTLL 129
                                       56778888888888888775553.3466554444445555555566666655 PP

  == domain 3  score: 70.3 bits;  conditional E-value: 1e-23
                                       HHHHHHHHHHHHHHHHHHHHHHHHTTSS-GGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-....CTSHHHHHHH CS
                              MgtE   1 iPvilglgGnlgaqlasristalhlgelekklkkvllkelrvvlllgvilgllifllalllgw...slllalvvgla 74 
                                       +P+il+  Gnlg++  + +st +hlge+ek ++k  + e+ +  +l++ilg+l+ l+a+ + +   + +++lv  + 
  gi|242398146|ref|YP_002993570.1| 146 YPAILDSTGNLGSVIGAKTSTRIHLGEIEKLFNKTTAIEISLYTILAAILGILANLIAIGVVKltlNTQIGLVKPFL 222
                                       59**************************888**************************88776677677777776666 PP

                                       HHHHHHHHHHH..HHHHHHHHHHTTS-GGGSHHHHHHHHHHHHHHHHHH CS
                              MgtE  75 lvlvllaaallilgvllplllwklglDPdnaaiPlltalgDllgtlllv 123
                                       l+  ll+  ++ ++++l++ + +lglDPdna++P +t+l+D+++tl+ v
  gi|242398146|ref|YP_002993570.1| 223 LLYPLLTFGVMWMAYFLAITFDRLGLDPDNATVPTITTLADIFSTLFTV 271
                                       666666666669999999***************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       748  (0.0417201); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 1752.73
//
Query:       gi|242398147|ref|YP_002993571.1|  [L=205]
Description: probable phosphate transport regulator [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-13   49.9   0.0      4e-13   49.0   0.0    1.5  1  TrkA_C    TrkA-C domain
    2.7e-13   50.2   3.4    4.9e-13   49.4   3.4    1.4  1  PhoU      PhoU domain
      0.001   18.4   2.7     0.0013   18.1   2.7    1.2  1  PhoU_div  Protein of unknown function DUF47


Domain annotation for each model (and alignments):
>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.0   0.0   6.8e-17     4e-13       2      67 ..     124     191 ..     123     194 .. 0.91

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 6.8e-17
                                       EEEEEE--GGGTTSBHHHHTHHHH.S-EEEEEE-T.-EEES--TT-B--TT-EEEEEEEHHHHHHHHH CS
                            TrkA_C   2 vevtvpagsplvGktlkelnlrar.gvlvvairRg.geliipsgdtvLeeGDvllvvgspsdlaelre 67 
                                       + +tv+ +s lvGktl++l+l  + gv ++a+rRg  +++ p+ d+++++GDvl+  g++ ++ +l+e
  gi|242398147|ref|YP_002993571.1| 124 AKITVTQESILVGKTLGDLKLASNtGVWIIAVRRGkRWIFAPDKDFKIKPGDVLIGRGTQTSVGHLKE 191
                                       569***************************************************98888877777766 PP

>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.4   3.4   8.2e-17   4.9e-13       2      88 ..      19     101 ..      18     102 .. 0.92

  Alignments for each domain:
  == domain 1  score: 49.4 bits;  conditional E-value: 8.2e-17
                                       HHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHH CS
                              PhoU   2 rrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlERi 78 
                                        +m++ive m+d+a++++  +d+e+a+ev+++++++d l + +  +++ a+  r+p++   ++++s+l++a+++E i
  gi|242398147|ref|YP_002993571.1|  19 IEMKNIVELMVDLAYTSILFGDKEIAEEVLDLEERMDLLNYHLMTHAVLAA--RNPKE--AEQITSVLQMANSIEDI 91 
                                       59*****************************************99977766..77774..689************** PP

                                       HHHHHHHHHH CS
                              PhoU  79 gDhavniaer 88 
                                       +  a ++a+ 
  gi|242398147|ref|YP_002993571.1|  92 SNAAGDLAKM 101
                                       *******996 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 !   18.1   2.7   2.2e-07    0.0013     114     207 ..       5     101 ..       1     109 [. 0.80

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.2e-07
                          PhoU_div 114 deflallkktveaiealaevieeleklleta..lskkdiveeieslEdeiDqlqrklikklfs.redasnplevlll 187
                                       +ef    k + e++ ++++++e +  l  t+  +  k+i+ee+ +lE+++D+l+ +l+++      +     ++  +
  gi|242398147|ref|YP_002993571.1|   5 EEFEYQPKSVKEIFIEMKNIVELMVDLAYTSilFGDKEIAEEVLDLEERMDLLNYHLMTHAVLaARNPKEAEQITSV 81 
                                       4666667778889999999999999888887446677********************99765524555666678888 PP

                          PhoU_div 188 veiieklenvsdraedvadr 207
                                        ++ + +e +s++a d+a+ 
  gi|242398147|ref|YP_002993571.1|  82 LQMANSIEDISNAAGDLAKM 101
                                       99999999999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       759  (0.0423336); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); 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: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1341.21
//
Query:       gi|242398148|ref|YP_002993572.1|  [L=197]
Description: probable phosphate transport regulator [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-15   55.5   0.3    6.4e-15   54.7   0.3    1.4  1  TrkA_C    TrkA-C domain
    4.3e-09   36.7   5.6    7.3e-09   36.0   5.6    1.4  1  PhoU      PhoU domain
  ------ inclusion threshold ------
      0.068   13.5   0.1         10    6.5   0.0    2.3  2  DUF3642   Bacterial lipoprotein


Domain annotation for each model (and alignments):
>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.7   0.3   1.1e-18   6.4e-15       3      59 ..     118     176 ..     116     188 .. 0.92

  Alignments for each domain:
  == domain 1  score: 54.7 bits;  conditional E-value: 1.1e-18
                                       EEEEE--GGGTTSBHHHHTHHHH.S-EEEEEE-T.-EEES--TT-B--TT-EEEEEEEH CS
                            TrkA_C   3 evtvpagsplvGktlkelnlrar.gvlvvairRg.geliipsgdtvLeeGDvllvvgsp 59 
                                       +v+v++gs l+G +lk+l+l+++ g++++ai+Rg   +++ps d ++eeGD+l+ vgs 
  gi|242398148|ref|YP_002993572.1| 118 RVKVNKGSILIGNPLKQLKLPTKvGIRLIAIKRGsRYIYNPSKDEIIEEGDILIAVGSG 176
                                       799*****************************************************985 PP

>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   5.6   1.2e-12   7.3e-09       1      88 [.      11      94 ..      11      95 .. 0.90

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 1.2e-12
                                      HHHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHHH CS
                              PhoU  1 lrrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlERig 79
                                      l +m+++++ m+d+a +++  + +++a+ev+ +++++d+l  ++++ +l+a+ k+++   d + lls++++a+  E i+
  gi|242398148|ref|YP_002993572.1| 11 LIEMKNLSSLMVDLAFSSVMYDSEDIADEVYILEEKMDELTLKVKKLALRAA-KYEE---DPEKLLSIIEMANINEQIS 85
                                      679***************999999********************99988777.3333...67889************** PP

                                      HHHHHHHHH CS
                              PhoU 80 Dhavniaer 88
                                      D a +i++ 
  gi|242398148|ref|YP_002993572.1| 86 DSAYEISDL 94
                                      ******975 PP

>> DUF3642  Bacterial lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.006        36       8      38 ..      40      70 ..      33      85 .. 0.77
   2 ?    6.5   0.0    0.0017        10      30      62 ..     106     136 ..      92     142 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.006
                           DUF3642  8 tYvladendqlTlkkegetglieleesdgdk 38
                                       Y+l+++ d+lTlk+++      + e d +k
  gi|242398148|ref|YP_002993572.1| 40 VYILEEKMDELTLKVKKLALRAAKYEEDPEK 70
                                      69999999*******9988777777777666 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0017
                           DUF3642  30 eleesdgdkpidpvtldadnklilvGddvktyk 62 
                                        +   d+d++i +v+++  +  il+G+ +k  k
  gi|242398148|ref|YP_002993572.1| 106 RKIMHDVDEEIGRVKVN--KGSILIGNPLKQLK 136
                                       555689******99999..99******988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       746  (0.0416086); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.37s 00:00:00.92 Elapsed: 00:00:00.53
# Mc/sec: 1117.30
//
Query:       gi|242398149|ref|YP_002993573.1|  [L=156]
Description: hypothetical protein TSIB_0156 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); 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: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1178.81
//
Query:       gi|242398150|ref|YP_002993574.1|  [L=504]
Description: phosphohydrolase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.1e-29  102.5   9.0    2.7e-20   73.7   4.0    2.4  2  Metallophos    Calcineurin-like phosphoesterase
    2.5e-23   83.1   0.1    1.4e-12   48.1   0.1    2.5  2  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    0.00011   21.6   0.8        0.9    8.8   0.0    3.4  3  Metallophos_3  Metallophosphoesterase, calcineurin superfamil
     0.0092   15.0   0.0        3.4    6.6   0.0    3.0  3  PhoD           PhoD-like phosphatase


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 !   73.7   4.0   6.1e-24   2.7e-20       1     204 []       2     185 ..       2     185 .. 0.76
   2 !   31.2   0.2   6.3e-11   2.8e-07      21     200 ..     278     434 ..     257     437 .. 0.74

  Alignments for each domain:
  == domain 1  score: 73.7 bits;  conditional E-value: 6.1e-24
                                       EEEEEEESBTB....TTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHH.HHHHHHHTSEEEEEC- CS
                       Metallophos   1 lrilvigDlHl....algggqlddllkllddllreekpdlvllaGDlvdrgdlekellel.laalvkypipvylllG 72 
                                       ++i++i+D+H+    a+ g+ +d +++ ++ l    + +lv+++GD++++g  e+ +++  ++ +    +p+++l+G
  gi|242398150|ref|YP_002993574.1|   2 IKIAHISDTHItsgeAYKGYAYDLIANEINTL----DYNLVIHTGDVTNDGLREE-YERAsYELKKI-QKPLIVLPG 72 
                                       59*********777766667777777777666....***************6666.66664555555.37******* PP

                                       TTSCHHH.HHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEEESECEEETHHHHHHHHHHHSCHHHHCC. CS
                       Metallophos  73 NHegfee.ellnkygylgifsepwrsdaevfnnlplaslgsgslkvlllhGgspellvsldklgslnleleapepg. 147
                                       NH+  ++ +++ +++y+g         ++ +++  l+ + ++  ++  l+ g                  +    g 
  gi|242398150|ref|YP_002993574.1|  73 NHD-ARNvGYELFQKYIGPL-------NGIYEWKDLVIIWTD-STIPDLNDG------------------R--I-Gg 119
                                       ***.7777777777776665.......444455555553333.133333333..................1..1.12 PP

                                       ..HHHHHH.HHHHTTCSEEEEEESSESS......CSSSCSCCHHHHHHHHHHTTESEEEEESSSSE CS
                       Metallophos 148 ..dewlkd.lekrekadwvivlgHsply......rgsgylfgdealedllkkygvdlvisGHtHvy 204
                                           wlk+ le+ ++++++iv +H+ l       r    lf+   + +ll k++v l+++GH Hv+
  gi|242398150|ref|YP_002993574.1| 120 ykFRWLKEkLEEYSHKKFKIVASHHHLVplpdtgRERNVLFNAGDVLELLLKHEVNLYLCGHKHVP 185
                                       3499*********************999999*********************************86 PP

  == domain 2  score: 31.2 bits;  conditional E-value: 6.3e-11
                                       HHHHHHHHHHHTTESEEEEESTSSSSS..HHHHHHHHHHHHHHHHTSEEEEEC-TTSCHHH.HHHHHHHHHHHHHHH CS
                       Metallophos  21 llkllddllreekpdlvllaGDlvdrg..dlekellellaalvkypipvylllGNHegfee.ellnkygylgifsep 94 
                                       l+++++ ++++ kpdlv+++GD+v+ g   + k+   l+++      ++++++G  +  ++ +++ +++y+   +ep
  gi|242398150|ref|YP_002993574.1| 278 LKNAIKAINERYKPDLVVHCGDIVEVGieRYYKKAYALWEKIKG---KKIIVPGHND-ITYlGYELFREYF---GEP 347
                                       67888999999****************75555544444555555...99********.6665666665555...455 PP

                                       HEHHHCEEETSEEEEEETTEEEEEEEESECEEETHHHHHHHHHHHSCHHHHCC...HHHHHH.HHHHTTCSEEEEEE CS
                       Metallophos  95 wrsdaevfnnlplaslgsgslkvlllhGgspellvsldklgslnleleapepg...dewlkd.lekrekadwvivlg 167
                                          ++e f ++p++s        +  + g                       g   +++l++ l+k e++  vi+++
  gi|242398150|ref|YP_002993574.1| 348 EIIENENFTFIPIIS------AQYETPIG---------------------VVGrigQKILREhLKKYEDTFRVIIMH 397
                                       666678899999999......44444444.....................111122677777566666666777777 PP

                                       SSESS....CSSSCSCCHHHHHHHHHHTTESEEEEES CS
                       Metallophos 168 Hsply....rgsgylfgdealedllkkygvdlvisGH 200
                                       H   +    r +g l +   + ++l + ++ lv+ GH
  gi|242398150|ref|YP_002993574.1| 398 HNITPipksREIGFLEDGGNVLKILTDEKANLVLTGH 434
                                       76666899999999999999999*************9 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 !   48.1   0.1   3.1e-16   1.4e-12       2     164 ..       3     221 ..       2     222 .. 0.71
   2 !   32.3   0.0   2.3e-11     1e-07      18     163 ..     281     473 ..     273     475 .. 0.72

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 3.1e-16
                     Metallophos_2   2 klaiiSDlH......snldaleavlealkevgvdaiihaGDl....eeeep...e.vleellela.pvlaVrGNnD. 62 
                                       k+a+iSD+H       ++ a + ++++++  +++++ih+GD+            e + +el+++  p+++ +GN+D 
  gi|242398150|ref|YP_002993574.1|   3 KIAHISDTHitsgeaYKGYAYDLIANEINTLDYNLVIHTGDVtndgL---ReeyErASYELKKIQkPLIVLPGNHDa 76 
                                       89********999887888899999****************864332...2222347777777778**********8 PP

                     Metallophos_2  63 ........................eevveedvlreaaelgtdl........................peeaelelag 91 
                                                                                 +                        ++ +e + ++
  gi|242398150|ref|YP_002993574.1|  77 rnvgyelfqkyigplngiyewkdlV-----------------IiwtdstipdlndgriggykfrwlkEKLEEYSHKK 136
                                       8887777777777777666554330.................03333333333333346666666533455555588 PP

                     Metallophos_2  92 ekvlliHgdpl.............gvkdalaellkeaeegsdvvvcGHtHvpevekeggvlvvnPG..svgeprdgd 153
                                       +k+   H++               ++ d l+ llk    ++++++cGH Hvp++   +g++v n G  s +  r+gd
  gi|242398150|ref|YP_002993574.1| 137 FKIVASHHHLVplpdtgrernvlfNAGDVLELLLK---HEVNLYLCGHKHVPNIYSVEGLVVANSGctSCRKTRKGD 210
                                       99999999944999999999666554444444444...4888**********************9933444556666 PP

                     Metallophos_2 154 petyaildtde 164
                                         +y ++++++
  gi|242398150|ref|YP_002993574.1| 211 VNSYNMIKIKD 221
                                       66998888876 PP

  == domain 2  score: 32.3 bits;  conditional E-value: 2.3e-11
                     Metallophos_2  18 avlealkevgvdaiihaGDl....eeeep...evleellela.pvlaVrGNnD.....................eev 65 
                                       a+ ++ ++ ++d+++h+GD+       e    ++ + +++++ + ++V+G nD                     e+ 
  gi|242398150|ref|YP_002993574.1| 281 AIKAINERYKPDLVVHCGDIvevgI--ERyykKAYALWEKIKgKKIIVPGHNDitylgyelfreyfgepeiienENF 355
                                       4555566789*********854221..223334666666666999************99999999999988876333 PP

                     Metallophos_2  66 ....veedvlreaaelgtdlpeeaele.l....agekvlliHgdpl............gvkdalaellkeaeegsdv 121
                                           ++++  + + ++ +++ ++   e l    + ++v ++H+               ++  ++ + l +  e++++
  gi|242398150|ref|YP_002993574.1| 356 tfipIISAQYETPIGVVGRIGQKILREhLkkyeDTFRVIIMHHN-ItpipksreigflEDGGNVLKILTD--EKANL 429
                                       43455566666666666666433333313444356668888886.4489999999887666666666666..7888* PP

                     Metallophos_2 122 vvcGHtHvpevekeggvlvvnPGsvgeprdgdpe..tyaildtd 163
                                       v+ GH +     k++++ +vn+Gs+++  ++ p   ++ ++d+ 
  gi|242398150|ref|YP_002993574.1| 430 VLTGHGGNSLGMKIEQTPIVNAGSISWELHRNPFgnSFNLIDIY 473
                                       ****************************9999988888888875 PP

>> Metallophos_3  Metallophosphoesterase, calcineurin superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0   0.00053       2.4      26      68 ..      28      69 ..      21      92 .. 0.76
   2 !    8.8   0.0    0.0002       0.9      19      83 ..     276     341 ..     258     350 .. 0.72
   3 ?    1.7   0.0      0.03   1.3e+02     169     238 ..     385     455 ..     378     459 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00053
                                      HHHHHH--SEEEEES-----HHHHHHHHHHHHTT----THHHH CS
                     Metallophos_3 26 eviedkdpDllvlvGdlvkaeakadeyesaqeerrepdkkeil 68
                                      + i+  d +l++ +Gd+  +++  +eye+a  e ++ +k  i 
  gi|242398150|ref|YP_002993574.1| 28 NEINTLDYNLVIHTGDV-TNDGLREEYERASYELKKIQKPLIV 69
                                      568888999*******9.999*********9999888877664 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0002
                                       GGHHHHHHHHHHH.--SEEEEES-----HHHHHHHHHHHHTT---.-THHHHHHHHHHHHHHHHHHH CS
                     Metallophos_3  19 ellerlveviedk.dpDllvlvGdlvkaeakadeyesaqeerrep.dkkeileekneiiklldklfr 83 
                                        +l++ +++i+++ +pDl+v  Gd+v+  + +  y++a     +   kk i   +n+i  l  +lfr
  gi|242398150|ref|YP_002993574.1| 276 KVLKNAIKAINERyKPDLVVHCGDIVEV-GIERYYKKAYALWEKIkGKKIIVPGHNDITYLGYELFR 341
                                       56888999*****9***********765.55667777765444332566666665555555555555 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.03
                                       GGS---EEEEEESS-..-S-SSTBTTBS---S-HHHHHHHHHH--SEEEE-SS--EE.EEETTEEEEE--BGG CS
                     Metallophos_3 169 kelkdrrkvlllatp..PigelvadkglkekgsevvaelvktlnPevvvvghavkeh.eelgktlvvnPGale 238
                                       k+  d  +v++++    Pi +   + g+ e g +v+ +++ + + ++v+ gh + +   ++++t +vn G+++
  gi|242398150|ref|YP_002993574.1| 385 KKYEDTFRVIIMHHNitPIPK-SREIGFLEDGGNVL-KILTDEKANLVLTGHGGNSLgMKIEQTPIVNAGSIS 455
                                       555566667776654113322.35668888888877.5778999********99988899*********9975 PP

>> PhoD  PhoD-like phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.6   0.0    0.0063        28       4      47 ..      13      56 ..      10      73 .. 0.69
   2 ?    0.5   0.0     0.053   2.4e+02     195     222 ..     118     146 ..     101     166 .. 0.79
   3 !    6.6   0.0   0.00076       3.4      15      56 ..     280     320 ..     272     335 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.0063
                              PhoD  4 vSCqnyeagyfnayrelaee..e.dlDlvlhlGDyiYeygpgeyase 47
                                      +S+  y+ gy  ay+ +a+e  + d++lv+h GD+     ++ey+++
  gi|242398150|ref|YP_002993574.1| 13 TSGEAYK-GY--AYDLIANEinTlDYNLVIHTGDVTNDGLREEYERA 56
                                      5676776.54..677777766435999*******8755556666665 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.053
                              PhoD 195 GeeQeqwLkaeLka.srarWkvlaqqvlm 222
                                       G    +wLk++L++ s++++k++a++  +
  gi|242398150|ref|YP_002993574.1| 118 GGYKFRWLKEKLEEySHKKFKIVASHHHL 146
                                       666679******9726666*****98765 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.00076
                              PhoD  15 nayrelaeeedlDlvlhlGDyiYeygpgeyaseaaelgreve 56 
                                       na +++ e+ ++Dlv+h+GD++ e g ++y ++a +l+++ +
  gi|242398150|ref|YP_002993574.1| 280 NAIKAINERYKPDLVVHCGDIV-EVGIERYYKKAYALWEKIK 320
                                       6778888889**********76.6666666666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (504 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       688  (0.0383736); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.27s 00:00:00.89 Elapsed: 00:00:00.44
# Mc/sec: 3462.29
//
Query:       gi|242398151|ref|YP_002993575.1|  [L=139]
Description: inosine-5'-monophosphate dehydrogenase related [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-28   98.1   4.7    9.7e-14   51.6   0.2    2.1  2  CBS       CBS domain


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.5   0.7     5e-17   8.9e-13       4      55 ..      14      64 ..      11      66 .. 0.93
   2 !   51.6   0.2   5.4e-18   9.7e-14       1      54 [.      75     127 ..      75     130 .. 0.96

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 5e-17
                                      HSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS  4 imtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55
                                      +mt++++ v+pd+t+ ea + m+e ++++l VV ++g++vG +t++D++r +
  gi|242398151|ref|YP_002993575.1| 14 YMTKKLIAVKPDDTIQEACRVMVEFDIGSLVVV-DNGNVVGFFTKSDIIRRV 64
                                      4**********************999****888.6**************975 PP

  == domain 2  score: 51.6 bits;  conditional E-value: 5.4e-18
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54 
                                       V++im+++++tv+ + +l+++le+m+ k++ ++  ++e+gk+vGi+tl+Dll+a
  gi|242398151|ref|YP_002993575.1|  75 VAEIMSKELITVNANVPLKKVLEIMAAKRIKHM-LIEEEGKVVGIFTLSDLLEA 127
                                       789**********************9999****.889***************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.51
# Mc/sec: 824.56
//
Query:       gi|242398152|ref|YP_002993576.1|  [L=300]
Description: 2-phosphoglycerate kinase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.4e-09   36.1   1.6    1.9e-08   34.7   0.1    2.4  2  ATP-cone         ATP cone domain
      1e-05   26.1   0.0    2.3e-05   24.9   0.0    1.6  1  AAA_18           AAA domain
    1.9e-05   25.0   0.1    0.00019   21.7   0.0    2.3  2  AAA_28           AAA domain
    2.1e-05   24.7   0.0    0.00019   21.6   0.0    2.1  2  AAA_33           AAA domain
      6e-05   22.4   0.0    0.00018   20.8   0.0    1.8  2  Zeta_toxin       Zeta toxin
     0.0055   17.1   0.0      0.011   16.2   0.0    1.5  1  AAA_16           AAA ATPase domain
     0.0073   16.2   0.0      0.017   15.0   0.0    1.7  1  DUF1533          Protein of unknown function (DUF1533)
  ------ inclusion threshold ------
       0.01   15.8   0.5       0.15   12.0   0.0    2.4  2  AAA_5            AAA domain (dynein-related subfamily)
      0.019   14.9   0.0      0.033   14.1   0.0    1.4  1  RsgA_GTPase      RsgA GTPase
      0.022   15.2   0.0      0.067   13.6   0.0    1.9  1  AAA_17           AAA domain
      0.032   13.8   0.0      0.062   12.9   0.0    1.4  1  AAA_25           AAA domain
      0.032   14.0   0.8      0.072   12.8   0.0    1.9  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      0.036   14.4   0.1       0.12   12.7   0.0    1.9  1  AAA_22           AAA domain
      0.047   13.8   0.1      0.083   13.0   0.1    1.7  1  Cytidylate_kin2  Cytidylate kinase-like family
      0.057   13.3   0.6        0.3   11.0   0.3    2.2  3  NACHT            NACHT domain
      0.059   12.8   0.6       0.14   11.6   0.1    1.8  2  ParA             NUBPL iron-transfer P-loop NTPase
      0.066   12.3   1.2       0.11   11.5   0.1    1.8  2  T2SSE            Type II/IV secretion system protein
      0.067   13.6   0.0       0.17   12.3   0.0    1.7  1  RNA_helicase     RNA helicase
      0.076   12.6   0.1       0.14   11.8   0.1    1.4  1  GTP_cyclohydro2  GTP cyclohydrolase II
      0.085   12.2   0.2         10    5.3   0.0    2.2  2  DnaB_C           DnaB-like helicase C terminal domain
       0.12   12.4   3.9      0.051   13.6   1.0    1.9  2  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
       0.12   12.3   0.8       0.98    9.4   0.0    2.2  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
       0.13   12.0   0.0       0.25   11.1   0.0    1.4  1  AAA_29           P-loop containing region of AAA 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 !   34.7   0.1   2.5e-11   1.9e-08       7      85 ..       9      86 ..       3      87 .. 0.92
   2 ?   -1.0   0.1       3.4   2.7e+03      30      47 ..     272     289 ..     250     298 .. 0.58

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 2.5e-11
                                      TS-EEE--HHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHIIT-BHHHHHHHHHHHHHHSS-HHHHHHHHHHHHHHH CS
                          ATP-cone  7 dGtvepfdvekIkraiekAcegseeeideiaeeveaevrkrlrdgisteeIqdlvektliehpdyavaaayilyrnlrk 85
                                      ++t+ pf+++ ++r+i+         ++ ia e+++++++++ + i+ eeI+++  ++li h+  + a++y+++ +lr+
  gi|242398152|ref|YP_002993576.1|  9 KNTRIPFSRGILTRSITTTGVD-VGIAYSIATEIVKDLQRKKIKLITKEEIRKITYEKLIGHGLKDAARKYLFWHELRR 86
                                      57999**************444.5569***********************************************99985 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3.4
                                       HHHHHHHHHHHHHHHHHH CS
                          ATP-cone  30 eeeideiaeeveaevrkr 47 
                                       e  i++i + + +++ kr
  gi|242398152|ref|YP_002993576.1| 272 ERSINNIMAHLMEDISKR 289
                                       334566666666666555 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0     3e-08   2.3e-05       1     102 [.      93     219 ..      93     246 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 3e-08
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf.........gvnlrdvakenglllevdpe.......aldeskrldedkldkll 61 
                                       Il+ G+ GvGK+tla eL+ rlg+          ++ r+++ ++ l     p        a++e k l +++ d l+
  gi|242398152|ref|YP_002993576.1|  93 ILIGGATGVGKSTLATELAFRLGIrtvigtdtiREVMRKMINKELL-----PSihtssflAWKELKNLPRNV-DPLI 163
                                       99********************999999655544444444444333.....334444588888888888888.8888 PP

                            AAA_18  62 daleenss............aleegknlvidghlaeleseaakdikk...vvLtas 102
                                        ++e + +            ++ eg n +i+g++  + + ++ d+ +   + L+ +
  gi|242398152|ref|YP_002993576.1| 164 YGFETQVRytsvginavierSYKEGFNTIIEGIHLVPGYVSLNDRSFmylISLKSP 219
                                       88888888999999999999999999999999999999999988888666666544 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.87   6.8e+02      13      43 ..      39      70 ..      38      89 .. 0.78
   2 !   21.7   0.0   2.5e-07   0.00019       2      39 ..      93     137 ..      92     158 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.87
                            AAA_28 13 TtlleaLaargypvv.pEaareileeklakge 43
                                      T +++ L++++++ + +E  r+i+ ekl  ++
  gi|242398152|ref|YP_002993576.1| 39 TEIVKDLQRKKIKLItKEEIRKITYEKLIGHG 70
                                      78899999999999999999999999985544 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 2.5e-07
                            AAA_28   2 ivitGgestGKTtlleaLaar.......gypvvpEaareileekl 39 
                                       i i G+ + GK+tl+ +La r       g+ +++E++r++++++l
  gi|242398152|ref|YP_002993576.1|  93 ILIGGATGVGKSTLATELAFRlgirtviGTDTIREVMRKMINKEL 137
                                       678899*************55544457888899999999988775 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   2.4e-07   0.00019       2      50 ..      93     142 ..      92     194 .. 0.74
   2 ?    0.7   0.0      0.67   5.2e+02      28      74 ..     216     266 ..     202     286 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 2.4e-07
                            AAA_33   2 vllvGlpGsGKstlaerllkklg.avllssdtlrrrlfgtdqqsktdytr 50 
                                       +l+ G+ G+GKstla++l+ +lg  +++ +dt+r+ +++  ++ +  +++
  gi|242398152|ref|YP_002993576.1|  93 ILIGGATGVGKSTLATELAFRLGiRTVIGTDTIREVMRKMINKELLPSIH 142
                                       7888*******************999******999888844444443333 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.67
                            AAA_33  28 lssdtlrrrlfg....tdqqsktdytrvldrlyqilnelarkalsagrnvi 74 
                                       l s++++++ f+       ++ ++y++  ++++ i++ l++ka++ ++++i
  gi|242398152|ref|YP_002993576.1| 216 LKSPDALEARFYerahYSLRPAEYYIKNIEEIIHIQEYLIKKAREYEIPII 266
                                       667777776666343322335669999999999999999998888777766 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   2.3e-07   0.00018      13      60 ..      86     131 ..      78     148 .. 0.85
   2 ?   -3.4   0.0       6.3   4.9e+03      86     102 ..     179     195 ..     173     196 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.3e-07
                        Zeta_toxin  13 q.erPklillgGqpGAGKselaellkdelerqgnvvrldpDdlRelhPe 60 
                                       + ++P +il+gG++G GKs+la++l+ +l   g   ++ +D++Re  ++
  gi|242398152|ref|YP_002993576.1|  86 RlKYPMIILIGGATGVGKSTLATELAFRL---GIRTVIGTDTIREVMRK 131
                                       4499**********************999...56667999999998765 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 6.3
                        Zeta_toxin  86 kllqeaiengyniiveg 102
                                        +++  +++g+n i+eg
  gi|242398152|ref|YP_002993576.1| 179 AVIERSYKEGFNTIIEG 195
                                       57788899999999997 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.4e-05     0.011      24      51 ..      90     117 ..      82     170 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.4e-05
                            AAA_16  24 pelvllsGesGvGKsslvrellralekd 51 
                                       p ++l+ G+ GvGKs+l++el+ +l  +
  gi|242398152|ref|YP_002993576.1|  90 PMIILIGGATGVGKSTLATELAFRLGIR 117
                                       5799****************99877666 PP

>> DUF1533  Protein of unknown function (DUF1533)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   2.2e-05     0.017      19      48 ..     235     265 ..     202     268 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.2e-05
                           DUF1533  19 ennkyslssigk.LklkasvfnkaGentIvI 48 
                                        ++ y++++i++ +++++ +++ka+e++I I
  gi|242398152|ref|YP_002993576.1| 235 RPAEYYIKNIEEiIHIQEYLIKKAREYEIPI 265
                                       7899*************************77 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 ?   12.0   0.0    0.0002      0.15       2      26 ..      93     117 ..      92     144 .. 0.83
   2 ?    1.4   0.1      0.36   2.8e+02      56      96 ..     251     290 ..     237     298 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0002
                                       EEEE--SSSSHHHHHHHGGGGBS-- CS
                             AAA_5   2 vlLvGppGtgKselaerlaaalnre 26 
                                       +l+ G++G+gKs+la +la +l+ +
  gi|242398152|ref|YP_002993576.1|  93 ILIGGATGVGKSTLATELAFRLGIR 117
                                       46679***************99543 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.36
                                       .--------G-SEEEEESGGG--HHHHHHHHHHHHSSEEE. CS
                             AAA_5  56 dsplvraaregeilvlDEveraesevlnsLlslleerrlll 96 
                                       +  l ++are ei +++ +e +e+++ n++  l+e+   +l
  gi|242398152|ref|YP_002993576.1| 251 QEYLIKKAREYEIPIIENIE-LERSINNIMAHLMEDISKRL 290
                                       56788999***********9.99******999999876555 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   4.2e-05     0.033      55     124 ..      49     115 ..      20     130 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.2e-05
                                       -GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTTSEEEEECSTTSSHHHHHHHHCTT-- CS
                       RsgA_GTPase  55 KiDlleeeeeleelkeelealgyevllvsaktkegleelkellkdktsvlvGqSGvGKStLinallpele 124
                                       Ki l+++ee     k ++e+l  + l+  a++   ++el++l    ++++ G +GvGKStL  +l+ +l 
  gi|242398152|ref|YP_002993576.1|  49 KIKLITKEE---IRKITYEKLIGHGLKDAARKYLFWHELRRLKYPMIILIGGATGVGKSTLATELAFRLG 115
                                       444444444...23333444433444444444555666666666678888899********999986655 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   8.6e-05     0.067       2      37 ..      97     132 ..      96     154 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.6e-05
                                       E-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTT CS
                            AAA_17   2 GgPGsGKgtqceklvekygfthlsaGdllreeakrg 37 
                                       G  G+GK+t++ +l+ ++g+  +   d +re++++ 
  gi|242398152|ref|YP_002993576.1|  97 GATGVGKSTLATELAFRLGIRTVIGTDTIREVMRKM 132
                                       889****************************99875 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   7.9e-05     0.062      36      55 ..      93     112 ..      80     117 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.9e-05
                            AAA_25  36 allaGapgtGKttlaldlal 55 
                                       +l+ Ga+g+GK+tla++la+
  gi|242398152|ref|YP_002993576.1|  93 ILIGGATGVGKSTLATELAF 112
                                       7999**************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 ?   12.8   0.0   9.3e-05     0.072      35     105 ..      92     164 ..      65     176 .. 0.88
   2 ?   -1.6   0.4       2.6   2.1e+03      82     111 ..     258     286 ..     244     290 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.3e-05
                            RuvB_N  35 hvllyGpPGlGkttlakiiakelgvklkitsgPvlekagdla..alltnleekdvlfideihrlsraveevly 105
                                        +l+ G+ G+Gk+tla+ +a  lg++  i +  + e  + ++   ll +++++  l   e+  l r+v+ ++y
  gi|242398152|ref|YP_002993576.1|  92 IILIGGATGVGKSTLATELAFRLGIRTVIGTDTIREVMRKMInkELLPSIHTSSFLAWKELKNLPRNVDPLIY 164
                                       4788999******************999998888777777762269***********************9999 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.6
                            RuvB_N  82 leekdvlfideihrlsraveevlysamedf 111
                                        +e ++  i++i  l+r++++++   med+
  gi|242398152|ref|YP_002993576.1| 258 AREYEIPIIENI-ELERSINNIMAHLMEDI 286
                                       455666666666.58999999999999996 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00015      0.12       4      29 ..      89     114 ..      85     144 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00015
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleql 29 
                                       +  i+++ G +G+GK+tl+ +l+ +l
  gi|242398152|ref|YP_002993576.1|  89 YPMIILIGGATGVGKSTLATELAFRL 114
                                       567999*************9998666 PP

>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   0.00011     0.083       1      39 [.      92     131 ..      92     247 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00011
                   Cytidylate_kin2   1 iITIsreyGsgGetigeaLAekLglpfy.dreiieevake 39 
                                       iI I++  G g++t++ +LA +Lg++ +   + i+ev+++
  gi|242398152|ref|YP_002993576.1|  92 IILIGGATGVGKSTLATELAFRLGIRTViGTDTIREVMRK 131
                                       788**********************975255888887765 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       5.5   4.3e+03      33      46 ..      75      88 ..      66      90 .. 0.76
   2 ?   11.0   0.3   0.00039       0.3       3      25 ..      93     115 ..      91     125 .. 0.86
   3 ?   -1.0   0.0       1.9   1.4e+03     104     122 ..     124     142 ..     116     165 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 5.5
                                      C-SEEEEEETTTTT CS
                             NACHT 33 afklvFflslrels 46
                                      a k++F+++lr+l+
  gi|242398152|ref|YP_002993576.1| 75 ARKYLFWHELRRLK 88
                                      35899****99986 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00039
                                       EEEEC-TTTCHHHHHHHHHHHHC CS
                             NACHT   3 vilqGeaGsGKTtLlqklalawa 25 
                                       +++ G+ G+GK+tL+ +la+ + 
  gi|242398152|ref|YP_002993576.1|  93 ILIGGATGVGKSTLATELAFRLG 115
                                       7899**************99876 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 1.9
                                       .....HHHHHCTTTTT--E CS
                             NACHT 104 pvrtlLselirkkllpeas 122
                                        +r++++++i+k+llp+ +
  gi|242398152|ref|YP_002993576.1| 124 TIREVMRKMINKELLPSIH 142
                                       5788999999999999876 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 ?   11.6   0.1   0.00018      0.14       6      29 ..      92     115 ..      89     122 .. 0.87
   2 ?   -2.4   0.0       3.4   2.6e+03     196     219 ..     256     279 ..     244     291 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00018
                              ParA   6 iavlSgKGGVGKStvavnlAlaLa 29 
                                       i+ + g  GVGKSt+a++lA+ L 
  gi|242398152|ref|YP_002993576.1|  92 IILIGGATGVGKSTLATELAFRLG 115
                                       77788999************9985 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.4
                              ParA 196 klaeelgvpllgeipldpeireas 219
                                       k a+e+++p++ +i l+ +i++ +
  gi|242398152|ref|YP_002993576.1| 256 KKAREYEIPIIENIELERSINNIM 279
                                       667888999999999988887655 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 ?   11.5   0.1   0.00015      0.11      97     147 ..      55     108 ..      28     122 .. 0.72
   2 ?   -1.1   0.1         1   7.9e+02      34      65 ..     258     289 ..     237     292 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00015
                             T2SSE  97 kksakeltlddlgaeealkekiaevlrkav...rerglilvsGgTgsGKttlly 147
                                       k++ +++t+++l+ ++  +++ + +  + +   +  ++il+ G+Tg GK+tl+ 
  gi|242398152|ref|YP_002993576.1|  55 KEEIRKITYEKLIGHGLKDAARKYLFWHELrrlKYPMIILIGGATGVGKSTLAT 108
                                       556666777777766666655555444433000445799************975 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1
                             T2SSE  34 ielreveelekaalerlisriaalakldisee 65 
                                        +  e++ +e+ +ler i++i+a+  +dis++
  gi|242398152|ref|YP_002993576.1| 258 AREYEIPIIENIELERSINNIMAHLMEDISKR 289
                                       44567778888888888888888888888875 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   0.00022      0.17       1      23 [.      93     115 ..      92     161 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00022
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakall 23 
                                       i++ G++g+GKStla+eLa +l 
  gi|242398152|ref|YP_002993576.1|  93 ILIGGATGVGKSTLATELAFRLG 115
                                       5677899***********98887 PP

>> GTP_cyclohydro2  GTP cyclohydrolase II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00018      0.14     123     148 ..      35      61 ..      32      76 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00018
                                       -HHHHHHHHHTT--EEEEE-S-H.HHH CS
                   GTP_cyclohydro2 123 ygiaaqILkdlgvkkirLlTnnp.ekv 148
                                       y+ia++I kdl  kki+L+T+++ +k+
  gi|242398152|ref|YP_002993576.1|  35 YSIATEIVKDLQRKKIKLITKEEiRKI 61 
                                       99******************8632333 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.013        10      21      44 ..      92     115 ..      84     142 .. 0.83
   2 ?    4.8   0.1      0.02        15     152     183 ..     245     276 ..     235     288 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.013
                                       EEEEEEXTTSSHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C  21 liiiAarpsmGktalalniaenaa 44 
                                       +i+i++  ++Gk++la+++a +  
  gi|242398152|ref|YP_002993576.1|  92 IILIGGATGVGKSTLATELAFRLG 115
                                       789***************997655 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.02
                                       HHHHHHHHHHHHHHHHCTSXEEEEEEXSGGGC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C 152 qevseisrsLkalakelnvpvialsqLsrave 183
                                       +e+ +i   L + a+e ++p+i    L+r+++
  gi|242398152|ref|YP_002993576.1| 245 EEIIHIQEYLIKKAREYEIPIIENIELERSIN 276
                                       689999999********************987 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   1.0   6.6e-05     0.051       1      24 [.      92     115 ..      92     194 .. 0.92
   2 ?   -2.1   0.1       4.8   3.7e+03      92     119 ..     249     276 ..     235     286 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.6e-05
                                       EEEEESSTTSSHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA   1 iaiastkGGvGKTtlaanLarala 24 
                                       i+++++  GvGK+tla+ La+ l 
  gi|242398152|ref|YP_002993576.1|  92 IILIGGATGVGKSTLATELAFRLG 115
                                       6889****************9775 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.8
                                       TCHHHHHHHHHHCTS-EEEEEE--CCHC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  92 llkealeelkqrygvpvlgviprdeava 119
                                       +++e l +  ++y++p++  i    +++
  gi|242398152|ref|YP_002993576.1| 249 HIQEYLIKKAREYEIPIIENIELERSIN 276
                                       5566677777777888888766655554 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0    0.0013      0.98      18      48 ..      88     119 ..      69     128 .. 0.78
   2 ?    1.1   0.1      0.47   3.6e+02      58      88 ..     239     274 ..     232     300 .] 0.58

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0013
                                       H.TEEEEEEESTTSSHHHHHHHHHHHTT---- CS
                              TsaE  18 l.gdvilLeGdLGaGKTtlvrglakalgveev 48 
                                           +il+ G  G+GK+tl+ +la  lg+++v
  gi|242398152|ref|YP_002993576.1|  88 KyPMIILIGGATGVGKSTLATELAFRLGIRTV 119
                                       2355799999*****************99743 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.47
                                       EEEE..SSEEEEE-TT-SSTHH.....HHHCTTCCC CS
                              TsaE  58 eYelekeglyHfDlYRledeee.....leelgleey 88 
                                        Y ++ e+++H+  Y +++++e     +e+++le  
  gi|242398152|ref|YP_002993576.1| 239 YYIKNIEEIIHIQEYLIKKAREyeipiIENIELERS 274
                                       344444459999999999988823333333333333 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 ?   11.1   0.0   0.00033      0.25      24      38 ..      92     106 ..      76     108 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00033
                            AAA_29  24 atlltGpsGsGKSTl 38 
                                       ++l+ G++G+GKSTl
  gi|242398152|ref|YP_002993576.1|  92 IILIGGATGVGKSTL 106
                                       589***********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       895  (0.0499191); expected 358.6 (0.02)
Passed bias filter:                      612  (0.0341346); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); 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: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.50
# Mc/sec: 1814.18
//
Query:       gi|242398153|ref|YP_002993577.1|  [L=434]
Description: cyclic 2,3-diphospoglycerate synthetase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.048   13.7   0.1       0.31   11.1   0.0    2.4  2  DUF4974          Domain of unknown function (DUF4974)
       0.19   11.7   0.0        1.4    8.8   0.0    2.2  2  Glyco_tran_WecB  Glycosyl transferase WecB/TagA/CpsF family


Domain annotation for each model (and alignments):
>> DUF4974  Domain of unknown function (DUF4974)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.29   2.6e+03      43      58 ..     291     306 ..     286     313 .. 0.74
   2 ?   11.1   0.0   3.5e-05      0.31       9      34 ..     339     364 ..     336     387 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.29
                                       .-.HHHHHHHHHHHH- CS
                           DUF4974  43 nesleevLelLektgg 58 
                                       +e++e++ +++e++++
  gi|242398153|ref|YP_002993577.1| 291 KEKIEKIQKIIESINP 306
                                       5778888888877764 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 3.5e-05
                                       HHHHHHHHHHHHT--EEE-TTS---- CS
                           DUF4974   9 LeeilkkLerwYnveivieneelkny 34 
                                       Le  ++ Le++Y+veiv ++ +l+n 
  gi|242398153|ref|YP_002993577.1| 339 LEKAARHLENRYDVEIVGKSANLANR 364
                                       8999*************999998875 PP

>> Glyco_tran_WecB  Glycosyl transferase WecB/TagA/CpsF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0     0.084   7.5e+02      95     120 ..     147     172 ..      95     184 .. 0.74
   2 ?    8.8   0.0   0.00016       1.4      37      96 ..     320     375 ..     292     390 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.084
                   Glyco_tran_WecB  95 skpdlllvglGapkqEkwiarlkeel 120
                                       skp ++ +g G p+  ++i+ +k e+
  gi|242398153|ref|YP_002993577.1| 147 SKPIIVTMGRGGPEEPEIIEGNKLEI 172
                                       58888999999998888888777665 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00016
                   Glyco_tran_WecB  37 leraeee.glrvfllGgkpevlekaaerlrekypglriagthdgykeeeeeaiieainask 96 
                                       l+++  + ++ + ++ + pe lekaa++l+++y +++i+g ++    ++ +++ie++++ k
  gi|242398153|ref|YP_002993577.1| 320 LSEI--KgKKAILVMTAPPEGLEKAARHLENRY-DVEIVGKSANL--ANRPKLIEDLSRFK 375
                                       5555..22689999*******************.9*****98886..88888888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2702.30
//
Query:       gi|242398154|ref|YP_002993578.1|  [L=352]
Description: ABC-type molybdate transport system, periplasmic component [Thermococcus sibiricus MM 739]
Scores for complete 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  114.0   0.0    1.1e-32  113.7   0.0    1.1  1  SBP_bac_11  Bacterial extracellular solute-binding protein
      9e-10   39.0   0.0    1.7e-09   38.1   0.0    1.5  1  SBP_bac_1   Bacterial extracellular solute-binding protein


Domain annotation for each model (and alignments):
>> SBP_bac_11  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.7   0.0   1.2e-36   1.1e-32       1     227 [.      44     326 ..      44     328 .. 0.86

  Alignments for each domain:
  == domain 1  score: 113.7 bits;  conditional E-value: 1.2e-36
                                       .EEEE-SSTHHHHHHHHHHHHHHH-......--EEEEESSHHHHHHHHHHH...-SEEEESSH.HHHHHHHHGGGGG CS
                        SBP_bac_11   1 ltvaaagslaaalrelaaaFeahtg......vkvevsaggsgklarqiadga.rpDvwipassawlellaaaglvqa 70 
                                       l+++ agsl ++l+++ +aF+++++      ++++ +a gs  ++r+++d   ++D+++ a+ + + +l   ++++ 
  gi|242398154|ref|YP_002993578.1|  44 LKIFHAGSLSEPLNDVSEAFKEYSKrslgydLEIQAEASGSVMAVRKVTDLGkKADIVAVADYTLIPQLLLPNFTD- 119
                                       7899****************99877789999999999999999999**99766***********************. PP

                                       GG-EEEEEEEEEEEESTT-..TT..---SHHH.HHHSS--EEEE--T-TTTTHH.HHHHGGG....--......... CS
                        SBP_bac_11  71 esavplassplviavpkgn..pk..kikgwad.LlkpglklavadPttspsGlaalalleaa....ga......... 129
                                         +v +a++ +via    +  ++  ++ +w + L++++++++++dP+++p G++ +++++ a    g+         
  gi|242398154|ref|YP_002993578.1| 120 -FYVLFATNEIVIAFTDKSkyADeiTSENWYEiLAREDVSFGFSDPNQDPCGYRSIMVMKLAdlyyGKpifktlvek 195
                                       .**************8888653323566776647779***********************99555522333333444 PP

                                       .............HHHHHHHHHTEEEEESSHHHHHHHHHTTT-SEEEEEHHHHH..HSTTSSEEEE--TTT--.... CS
                        SBP_bac_11 130 .............qellkalekkvvklgessrqlltaveageadagivyeseakaaengdkleavylpeglnl.d.. 190
                                                    ++ ++   +kvv  ++ +++l+  ve+g+ d++++y+s a+    +++l++++lp ++nl +  
  gi|242398154|ref|YP_002993578.1| 196 ntniyaegsniiaPKDIQIKTDKVV-IRPKETDLTGLVESGSLDYYFIYKSVAM----QHNLRFIALPREINLkEfs 267
                                       4444555556666555555566666.66777***********************....9**************66** PP

                                       ........................EEEEEEEE-TT--HHHHHHHHHTTSHHHHHHHHHT CS
                        SBP_bac_11 191 ......................pldypaavlkkaakreaAraFlafLrspeaqailrky 227
                                                             p++y+++vlk+++ re A  +l+f++s+++++i++k+
  gi|242398154|ref|YP_002993578.1| 268 laehyerisitlgstgntikaePIVYGITVLKDTSGRELALQYLRFMLSEKGKEIFEKN 326
                                       *********************************************************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 !   38.1   0.0   1.9e-13   1.7e-09      12     314 ..      61     320 ..      49     321 .. 0.74

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 1.9e-13
                                       HHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHHHHTTSSSCSEEEE.CGGHHHHHHHTTSBECCHHHHHH..TTECT CS
                         SBP_bac_1  12 alvakafekehpgikVeiesvgsgslaqkltlaiaaGdgpaDviav.dndwiarlakaglllpldpyvka..ylapg 85 
                                       +++ k++ k+  g++ ei+   sgs++  +++++  G+++ D++av d++ i+     +lllp  +++     + ++
  gi|242398154|ref|YP_002993578.1|  61 EAF-KEYSKRSLGYDLEIQAEASGSVMA-VRKVTDLGKKA-DIVAVaDYTLIP-----QLLLPNFTDFYVlfATNEI 129
                                       566.88999999****************.*********77.*****4444444.....4444443332220022222 PP

                                       TCCTEEEEHHHHTHHHHCEEEESEEEEEEEEEEEETTTHH...CTTGGGSHBHH.HHHHHHHHHHHHCTCT...HCC CS
                         SBP_bac_1  86 vkdaadklsssvlpkildskvlyvPlyaargliYNkdlfe...kagldppwtWd.elveaakklkekgkkp...igg 155
                                       v                               +++k++++          ++W   l++ ++ ++ ++++    +++
  gi|242398154|ref|YP_002993578.1| 130 VIA-----------------------------FTDKSKYAdeiT-----SENWYeILAREDVSFGFSDPNQdpcGYR 172
                                       222.............................335555553331.....55999899**************977666 PP

                                       HCCEEHHHHHHHHHHHHHHHHTGGGEECCCTHHCSHHHHS..HHHHHHHHHHHH.HHHHHHHTTEEECSSHHHHHHH CS
                         SBP_bac_1 156 arggsasgtayyfalalakslggkvfdkdgggldnpegvt..aatylvklyava.nltkelkgkgaenkdgaaalal 229
                                       + +   + ++yy         g++ f+         + v+  ++ y++ ++ +a ++ + +++k++   +++++++l
  gi|242398154|ref|YP_002993578.1| 173 SIMVMKLADLYY---------GKPIFK---------TLVEknTNIYAEGSNIIApKDIQIKTDKVVIRPKETDLTGL 231
                                       666666666666.........323332.........222234444444444433033448999************** PP

                                       HHTTSCSEEEEEHHHHHHHHCEEEEE..CHHCHHHHTTSTEEEECEEBETTTTSEE..EEEEEEEEBTTCSTHHHHH CS
                         SBP_bac_1 230 feaGeaamaivglwaalaamkvapkv..afaadkekpkeelgvaplPagkggkpgi..lgayglaipkgsknpeaAk 302
                                       +e+G  + ++++ + a ++++  ++     + +  ++ e+++ + + +g +g++    +++yg++++k+++ +e A 
  gi|242398154|ref|YP_002993578.1| 232 VESGSLDYYFIYKSVAMQHNLRFIALprEINLKEFSLAEHYERISITLGSTGNTIKaePIVYGITVLKDTSGRELAL 308
                                       *******************9986665337788888899****************99********************* PP

                                       HHHHHHTSHHHH CS
                         SBP_bac_1 303 kFldfllspeaq 314
                                       ++l+f+ls++++
  gi|242398154|ref|YP_002993578.1| 309 QYLRFMLSEKGK 320
                                       *********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); 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: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2427.68
//
Query:       gi|242398155|ref|YP_002993579.1|  [L=248]
Description: sulfate ABC transporter permease [Thermococcus sibiricus MM 739]
Scores for complete 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-22   79.5  12.2    2.5e-22   79.5  12.2    2.0  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
        5.1    6.4   6.9       0.65    9.3   1.0    2.3  2  DUF4191       Domain of unknown function (DUF4191)


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 ?   -3.1   3.6      0.62   5.5e+03      62      71 ..      20      29 ..       4      69 .. 0.51
   2 !   79.5  12.2   2.8e-26   2.5e-22       1     176 [.      70     242 ..      70     246 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.62
                      BPD_transp_1 62 lsaapyvrli 71
                                      + ++p+v+++
  gi|242398155|ref|YP_002993579.1| 20 YILLPLVVIV 29
                                      2222222222 PP

  == domain 2  score: 79.5 bits;  conditional E-value: 2.8e-26
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalr 77 
                                       g++lG+++a ++ +k++ +++ +++v+  +P+ v++i+l++   +++++ ++ l++i+++l+ +ap+++   r+++ 
  gi|242398155|ref|YP_002993579.1|  70 GVPLGYILA-RKEFKGKSFVQAVVDVPIVIPHSVVGIMLLV--TFSNKILDSYLGIIMAMLFVSAPFTINAARDGFL 143
                                       89*******.****************************997..5777799*************************** PP

                      BPD_transp_1  78 slpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG.lgtllleailgydysei 153
                                       ++++ l+ +ar+lGas+ + f+++ lP+a+++i++g+i+++++++ +  +++++  +p   + l++e  ++y + + 
  gi|242398155|ref|YP_002993579.1| 144 AVDEKLEHVARTLGASKLRAFFTISLPMAMSSILSGAIMTWARAISEVGAILIISYYPKtAQILVMEYFNNYGLRAS 220
                                       *******************************************************9997777778888888888877 PP

                      BPD_transp_1 154 snggvlalviavlllnlvadilq 176
                                          ++++lv++ l + +++++l+
  gi|242398155|ref|YP_002993579.1| 221 R-PISVILVLLSLSIFVILRWLV 242
                                       7.999999999999999999987 PP

>> DUF4191  Domain of unknown function (DUF4191)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.2     0.044   3.9e+02      28      65 ..      37      78 ..      27      90 .. 0.56
   2 ?    9.3   1.0   7.2e-05      0.65      33     101 ..      97     167 ..      75     210 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.044
                           DUF4191 28 lllaaflvvvvvfvvlglllg....slilllilgillgllva 65
                                       +l+  l   +v+++l   l     ++++ l++g++lg ++a
  gi|242398155|ref|YP_002993579.1| 37 EMLMRTLKDELVLIALRNSLLtstaTMLISLFFGVPLGYILA 78
                                      555555555555555443332011135555666666666655 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 7.2e-05
                           DUF4191  33 flvvvvvfvvlglllgslilllilgillgllvalivltrraekaayaqiegqpGaaaavl..enlrrgwrv 101
                                       ++   vv+++l + +++ il   lgi++++l++   +t  a +  +  ++++    a  l  ++lr  +++
  gi|242398155|ref|YP_002993579.1|  97 VIPHSVVGIMLLVTFSNKILDSYLGIIMAMLFVSAPFTINAARDGFLAVDEKLEHVARTLgaSKLRAFFTI 167
                                       34445666677777789***************************999999887776666633445555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       819  (0.0456802); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.58u 0.34s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 1497.52
//
Query:       gi|242398156|ref|YP_002993580.1|  [L=344]
Description: ABC transporter, ATP-binding protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-32  113.2   0.0    2.3e-32  112.3   0.0    1.4  1  ABC_tran     ABC transporter
    8.5e-16   58.0   0.0    1.5e-15   57.2   0.0    1.4  1  TOBE         TOBE domain
    3.5e-10   39.9   0.0    3.3e-09   36.8   0.0    2.2  2  TOBE_2       TOBE domain
    7.8e-07   28.7   0.0    1.4e-06   27.9   0.0    1.4  1  AAA_29       P-loop containing region of AAA domain
     0.0002   21.3   3.3      0.093   12.5   0.3    2.3  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
     0.0011   19.5   0.6     0.0028   18.2   0.1    1.8  2  AAA_23       AAA domain
     0.0011   19.1   0.1      0.026   14.8   0.1    2.3  1  SbcCD_C      Putative exonuclease SbcCD, C subunit
     0.0047   16.4   0.0      0.064   12.7   0.0    2.1  1  SMC_N        RecF/RecN/SMC N terminal domain
  ------ inclusion threshold ------
      0.013   15.9   0.0      0.021   15.2   0.0    1.3  1  AAA_16       AAA ATPase domain
      0.031   15.1   0.6       0.18   12.6   0.7    2.3  1  OB_MalK      MalK OB fold domain
      0.048   13.9   0.0       0.13   12.6   0.0    1.6  2  AAA_22       AAA domain
      0.081   12.8   0.0       0.16   11.9   0.0    1.4  1  RsgA_GTPase  RsgA GTPase
      0.099   12.4   0.0       0.32   10.7   0.0    1.8  2  IstB_IS21    IstB-like ATP binding protein
       0.12   11.9   0.0        0.2   11.2   0.0    1.2  1  AAA_27       AAA domain
       0.15   12.1   0.0       0.41   10.6   0.0    1.8  2  AAA_5        AAA domain (dynein-related subfamily)


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.3   0.0     2e-35   2.3e-32       1     137 []      16     159 ..      16     159 .. 0.95

  Alignments for each domain:
  == domain 1  score: 112.3 bits;  conditional E-value: 2e-35
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l+++++++k+ e + i+G++GaGK+ Ll+l+ag   p++G+i ++g+d++   l+  +++++++pq+  lfp+++v+
  gi|242398156|ref|YP_002993580.1|  16 LHDITFEVKNREYLIILGPSGAGKTLLLELIAGIFVPDSGRIFMNGNDITF--LPPEKRKLAYIPQNYALFPHMKVY 90 
                                       789************************************************..************************ PP

                                       HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       +n             e d++++++ + lg+++l +++     ++LSgG+ qrva+aral+ +pkllllDEp+a
  gi|242398156|ref|YP_002993580.1|  91 DNiayglklkkipknEIDKKVKEIGEILGISHLLHRKP----KTLSGGEAQRVAIARALVLEPKLLLLDEPFA 159
                                       ***********888888888999999999999888887....*****************************85 PP

>> TOBE  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.2   0.0   1.2e-18   1.5e-15       1      64 []     281     343 ..     281     343 .. 0.99

  Alignments for each domain:
  == domain 1  score: 57.2 bits;  conditional E-value: 1.2e-18
                              TOBE   1 ssarNqlpgtVvvveplgseveVrvdlgggatLtArvtrrsaeeLgLapGeeVfalikaakvhl 64 
                                       ssarN ++++V++ve+lgs v++++d+gg + L A +tr s  e++++ ++eV++++ka+++h+
  gi|242398156|ref|YP_002993580.1| 281 SSARNEFKAKVLAVEDLGSLVRLTLDIGGIE-LRAFITRSSLLEMEIKEDKEVYLSFKATAIHV 343
                                       79*****************************.******************************97 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.58   6.9e+02      46      67 ..     182     204 ..     177     208 .. 0.79
   2 !   36.8   0.0   2.8e-12   3.3e-09       1      76 []     265     344 .]     265     344 .] 0.89

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.58
                            TOBE_2  46 vvrqpnadr.dsalapGdtVels 67 
                                       +++ ++++  ++a+  Gd+V++ 
  gi|242398156|ref|YP_002993580.1| 182 FTALHVTHSfEEAVSLGDRVGVM 204
                                       5667778888899*******985 PP

  == domain 2  score: 36.8 bits;  conditional E-value: 2.8e-12
                            TOBE_2   1 laiRPEklrla....aagganglsGtVedveylGsstryvvelaggqlvvvrqpnadrdsalapGdtVelswdpdda 73 
                                       ++iRPE++ ++    + +++n ++++V  ve lGs +r++++++g +l +  + ++  +  ++++ +V ls+++ ++
  gi|242398156|ref|YP_002993580.1| 265 IGIRPEDIIISsepiKSSARNEFKAKVLAVEDLGSLVRLTLDIGGIELRAFITRSSLLEMEIKEDKEVYLSFKATAI 341
                                       58*********9998777779************************9996666666654679**************** PP

                            TOBE_2  74 vvl 76 
                                       +v+
  gi|242398156|ref|YP_002993580.1| 342 HVF 344
                                       **9 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0   1.2e-09   1.4e-06       8      55 ..      10      60 ..       5      62 .. 0.90

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 1.2e-09
                            AAA_29  8 NWgtfdghtieidlkg..atlltGpsGsGKSTllDAiqalLvpak.kvrfN 55
                                      NWg+f+ h+i++++k+    ++ GpsG+GK+ ll  i+ ++vp++ ++  N
  gi|242398156|ref|YP_002993580.1| 10 NWGEFKLHDITFEVKNreYLIILGPSGAGKTLLLELIAGIFVPDSgRIFMN 60
                                      ***********999999778889********************99676666 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 !   12.5   0.3   7.8e-05     0.093       3      41 ..      30      60 ..      29      82 .. 0.71
   2 !    9.1   0.2   0.00087         1     251     287 ..     145     178 ..     120     192 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.8e-05
                            AAA_21  3 vliGpNgsGKSnLLdaldllarldrdvegltdelsgggg 41
                                      ++ Gp g+GK+ LL+++ +++          d+ + + +
  gi|242398156|ref|YP_002993580.1| 30 IILGPSGAGKTLLLELIAGIFV--------PDSGRIFMN 60
                                      799**************99963........333333333 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00087
                            AAA_21 251 llralkkgsllliDEpEngLHPkllrrllellkelsr 287
                                       l   +   +lll+DEp ++L+ +  ++l++ +k+ ++
  gi|242398156|ref|YP_002993580.1| 145 LVLEP---KLLLLDEPFANLDIQTRSKLIQEMKYWHK 178
                                       33333...9*********************9976444 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   2.3e-06    0.0028       5      43 ..       9      50 ..       7      67 .. 0.87
   2 ?   -2.3   0.0       4.5   5.4e+03      60     121 ..     248     301 ..     218     332 .. 0.51

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.3e-06
                            AAA_23  5 enfrsfrdqeidF...skgltlItGpNGaGKTTildAiklaL 43
                                      +n++ f+  +i F   ++   +I Gp GaGKT +l+ i  ++
  gi|242398156|ref|YP_002993580.1|  9 KNWGEFKLHDITFevkNREYLIILGPSGAGKTLLLELIAGIF 50
                                      89****999999999999999***************998766 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4.5
                            AAA_23  60 ksdveiesegkvkayveltfenkdgrytrsiererelskkkgkttkkaklelleideleqfi 121
                                       ++ + ie   +vk+ v++ ++ +d         + e +k+++  +++ k + l +++l  ++
  gi|242398156|ref|YP_002993580.1| 248 TNGILIELPIEVKGKVRIGIRPEDI------IISSEPIKSSA--RNEFKAKVLAVEDLGSLV 301
                                       4444444444444444444433322......12222222222..222223333334444444 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 !   14.8   0.1   2.2e-05     0.026      26      86 ..     124     171 ..     106     174 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.2e-05
                           SbcCD_C  26 lsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatlle 86 
                                       l+r+ +tlSGGe+q    +a+a     ++         ++l++LDE F++lD +++++l++
  gi|242398156|ref|YP_002993580.1| 124 LHRKPKTLSGGEAQR---VAIA----RALVL------EPKLLLLDEPFANLDIQTRSKLIQ 171
                                       678888899999943...3333....33333......378***************999987 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   5.4e-05     0.064      26     194 ..      28     184 ..       7     210 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.4e-05
                                       EEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  26 ftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrr 102
                                         +i+Gp G+GK+ ll+ i  ++  +s + + +   +d+ +     ++ k a++   +    +  + ++  + ++ +
  gi|242398156|ref|YP_002993580.1|  28 YLIILGPSGAGKTLLLELIAGIFVPDSGRIFMN--GNDITFL--PPEKRKLAYIPQNYALFPHMKVYDNIAYGLKLK 100
                                       456677777777777777776666666655543..3344443..334555666666665555554555555555555 PP

                                       EETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 103 vkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkv 179
                                       ++ k+e    i++k  +  e+  + +  + ++++LSgGe + va+a  + ++   p  l llDe  a+LD + ++k+
  gi|242398156|ref|YP_002993580.1| 101 KIPKNE----IDKKVKEIGEILGISHLLHRKPKTLSGGEAQRVAIARALVLE---P-KLLLLDEPFANLDIQTRSKL 169
                                       555555....77777777777777777777899*******999998775543...4.4899**************** PP

                                       HHHHHHHCTTSEEEE CS
                                       xxxxxxxxxxxxxxx RF
                             SMC_N 180 aellkeksknaQfiv 194
                                        + +k  +k+  f  
  gi|242398156|ref|YP_002993580.1| 170 IQEMKYWHKELNFTA 184
                                       *99997777766644 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   1.8e-05     0.021      25      63 ..      27      66 ..      16     101 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.8e-05
                            AAA_16 25 elvllsGesGvGKsslvrellralekd.ggiflrgkcdql 63
                                      e++++ G+sG GK+ l++ ++  +  d g if++g+   +
  gi|242398156|ref|YP_002993580.1| 27 EYLIILGPSGAGKTLLLELIAGIFVPDsGRIFMNGNDITF 66
                                      789*****************98888774577777776655 PP

>> OB_MalK  MalK OB fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.7   0.00015      0.18      18      53 .]     245     272 ..     235     272 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00015
                           OB_MalK  18 lvegggvtlplpeeqklalklyagkevilGiRPEhi 53 
                                       +++ +g+ ++lp e           +v +GiRPE+i
  gi|242398156|ref|YP_002993580.1| 245 VLKTNGILIELPIEV--------KGKVRIGIRPEDI 272
                                       566677777777665........99**********8 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00011      0.13       4      26 ..      25      47 ..      22      83 .. 0.87
   2 ?   -1.9   0.0       3.2   3.8e+03      91      99 ..     145     156 ..      88     187 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00011
                            AAA_22  4 tagilvvtGesGtGKTtllrrll 26
                                      ++  l++ G+sG+GKT+ll+ ++
  gi|242398156|ref|YP_002993580.1| 25 NREYLIILGPSGAGKTLLLELIA 47
                                      567799************99775 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.2
                            AAA_22  91 v...ielliiDE 99 
                                           ++ll++DE
  gi|242398156|ref|YP_002993580.1| 145 LvlePKLLLLDE 156
                                       234455677776 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00013      0.16      89     121 ..      15      48 ..       3      57 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00013
                                       THHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  89 gleelkellkd.ktsvlvGqSGvGKStLinallp 121
                                       +l++++ ++k+ +  +++G+SG+GK+ L++ +++
  gi|242398156|ref|YP_002993580.1|  15 KLHDITFEVKNrEYLIILGPSGAGKTLLLELIAG 48 
                                       577889999998999***********99998865 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00027      0.32      44      64 ..      23      43 ..      13      58 .. 0.85
   2 ?   -2.5   0.0         3   3.6e+03     106     132 ..     146     171 ..     135     196 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00027
                         IstB_IS21 44 iekkenivllGpsGvGKshla 64
                                      ++++e +++lGpsG+GK+ l 
  gi|242398156|ref|YP_002993580.1| 23 VKNREYLIILGPSGAGKTLLL 43
                                      78999*************985 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3
                         IstB_IS21 106 llkvdllilDdlgllpldqaeaellfe 132
                                       +l+++ll+lD+  + +ld + +++l +
  gi|242398156|ref|YP_002993580.1| 146 VLEPKLLLLDEP-FANLDIQTRSKLIQ 171
                                       566788888883.55666666666654 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00017       0.2      10      44 ..      10      44 ..       3      50 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00017
                            AAA_27 10 ryGkftdrsldfsaeeadlhliyGpNEAGKstalr 44
                                       +G+f+ + ++f+ ++++  +i+Gp  AGK+ +l+
  gi|242398156|ref|YP_002993580.1| 10 NWGEFKLHDITFEVKNREYLIILGPSGAGKTLLLE 44
                                      69****************************98876 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00034      0.41       2      35 ..      29      63 ..      28      66 .. 0.81
   2 ?   -2.6   0.0       4.2     5e+03      65      95 ..     148     176 ..     133     197 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00034
                                      EEEE--SSSSHHHHHHHGGGGB.S--EEEEE--TT CS
                             AAA_5  2 vlLvGppGtgKselaerlaaal.nreveyvqltrd 35
                                      ++++Gp+G gK+ l e +a  +  ++  + ++  d
  gi|242398156|ref|YP_002993580.1| 29 LIILGPSGAGKTLLLELIAGIFvPDSGRIFMNGND 63
                                      799****************9988666666665555 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4.2
                                       G-SEEEEESGGG--HHHHHHHHHHHHSSEEE CS
                             AAA_5  65 egeilvlDEveraesevlnsLlslleerrll 95 
                                       e+++l+lDE + a+ +++ +  +l+ e +++
  gi|242398156|ref|YP_002993580.1| 148 EPKLLLLDEPF-ANLDIQTRS-KLIQEMKYW 176
                                       66677777766.666666554.444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 2122.32
//
Query:       gi|242398157|ref|YP_002993581.1|  [L=202]
Description: Tryptophan/tyrosine permease [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.1e-20   71.6  13.2    7.1e-20   71.4  13.2    1.1  1  Trp_Tyr_perm  Tryptophan/tyrosine permease family
    1.8e-07   30.3  10.8    2.1e-07   30.0  10.8    1.1  1  Aa_trans      Transmembrane amino acid transporter protein
    1.1e-06   27.6  15.5    1.3e-06   27.3  15.5    1.1  1  AA_permease   Amino acid permease
    7.7e-05   21.7   6.1    9.1e-05   21.5   6.1    1.1  1  CstA          Carbon starvation protein CstA
     0.0023   16.9   7.8     0.0027   16.7   7.5    1.3  1  Nramp         Natural resistance-associated macrophage protei
  ------ inclusion threshold ------
      0.022   15.1   1.1      0.049   14.0   1.1    1.5  1  EbsA          EbsA-like protein


Domain annotation for each model (and alignments):
>> Trp_Tyr_perm  Tryptophan/tyrosine permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.4  13.2   2.4e-23   7.1e-20       7     175 ..       8     168 ..       2     197 .. 0.88

  Alignments for each domain:
  == domain 1  score: 71.4 bits;  conditional E-value: 2.4e-23
                      Trp_Tyr_perm   7 ggvlliagtviGaGmlalPvatagagfipsllllilswvlmlasgllllEvllaakeeasfttlakkllGkkgniiv 83 
                                        ++ +++gt iGaG+l+lP a  gagf+  l  l+ + ++ l+++l++lEv ++ + + s++ l+++ lGk g +++
  gi|242398157|ref|YP_002993581.1|   8 EASAMLIGTQIGAGVLGLPYALRGAGFLEFL-WLLNLGLMTLLTALFVLEVASK-NLGKSLSKLTEEHLGKMGGVVM 82 
                                       5677889********************9765.55667788999********986.5699****************** PP

                      Trp_Tyr_perm  84 alvllfllyiLlvAyisggGsilselleeasgialsarlavliftlvlgalvvlstkavdrinrvllflklvafvll 160
                                        l++  l y  l+Ayi+g+ +i+s+l+  +      +++a ++f  +++ +v ++ k+       l  ++l+a+vl+
  gi|242398157|ref|YP_002993581.1|  83 FLSISALAYGALIAYIAGSADIISSLVGIR------PEIAAIVFWSLMSLIVFMGLKVSGEAELTLTGVLLLALVLS 153
                                       ************************977654......6999************************************* PP

                      Trp_Tyr_perm 161 lalllskvksdvLls 175
                                       ++l+l k+++++L +
  gi|242398157|ref|YP_002993581.1| 154 ISLVLGKINEKNLTH 168
                                       *************98 PP

>> Aa_trans  Transmembrane amino acid transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0  10.8   6.9e-11   2.1e-07       4     207 ..       5     195 ..       2     201 .. 0.75

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 6.9e-11
                          Aa_trans   4 salsavlnlikaivGaGvLaLPyAfkqlGlivGlillllvallslytlllLvkcsktlasgkrnksYgdlgyrllGp 80 
                                       +  +a++ li + +GaGvL+LPyA++ +G + +l  ll  +l++l+t+l  ++++ +    +  ks ++l +  lG+
  gi|242398157|ref|YP_002993581.1|   5 TLAEASAMLIGTQIGAGVLGLPYALRGAGFLEFL-WLLNLGLMTLLTALFVLEVASK----NLGKSLSKLTEEHLGK 76 
                                       677899*************************555.5667899999999888888864....468999********** PP

                          Aa_trans  81 kgkliidlailvqlfGvgvsyliligdllpaifesffdtlllsnvyfilisaliiipLslipnls.kLsylSllalv 156
                                        g +++ l+i     G+ ++y+   +d ++++++   +      v ++l+s ++++ L +  + +  L+ + llalv
  gi|242398157|ref|YP_002993581.1|  77 MGGVVMFLSISALAYGALIAYIAGSADIISSLVGI--RPEIAAIVFWSLMSLIVFMGLKVSGEAElTLTGVLLLALV 151
                                       ***************************99999995..3235689999********9999777766358888888888 PP

                          Aa_trans 157 sslyyivilvlvvaelvklelkgvseetvkkasklkglflaigiivFAftg 207
                                       +s+   ++l  ++ ++++++ ++   ++     + ++lf+ +  ++F f++
  gi|242398157|ref|YP_002993581.1| 152 LSIS--LVLGKINEKNLTHRVRSPLPKG-----QGSSLFSVVFLLIFNFVS 195
                                       8875..3444444444444433333322.....223455555555555555 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3  15.5   4.4e-10   1.3e-06       4     189 ..      11     177 ..       8     200 .. 0.70

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 4.4e-10
                       AA_permease   4 vialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviGl 80 
                                        +++g  iG+g+ +gl ++l+ aG    +l +l  g++++l++l + e+a+++  + +     s+ ++++lG + G 
  gi|242398157|ref|YP_002993581.1|  11 AMLIGTQIGAGV-LGLPYALRGAGF-LEFLWLLNLGLMTLLTALFVLEVASKNL-GKSL----SKLTEEHLGKMGGV 80 
                                       5899*******8.5***********.5569********************9875.4454....55666777777777 PP

                       AA_permease  81 nylfswitvlaleltaasiliq...fwelvtdlpkawvtgavflvvlliinlvgvkvygeaefilalikiiaiiafi 154
                                         +f++i +la +  +a ++ +   +++++  +   ++ ++vf+ ++++i ++g+kv+geae+ l+ ++++a++  i
  gi|242398157|ref|YP_002993581.1|  81 V-MFLSISALAYGALIA-YIAGsadIISSLVGIR-PEIAAIVFWSLMSLIVFMGLKVSGEAELTLTGVLLLALVLSI 154
                                       7.666677777763333.3333000333334444.456699*******************************99988 PP

                       AA_permease 155 ivgiillaggkpnkgagfrflgdngsifknnlppg 189
                                        +    + +++++++         +      lp+g
  gi|242398157|ref|YP_002993581.1| 155 SLVLGKINEKNLTHR---------V---RSPLPKG 177
                                       877655566666655.........2...2344444 PP

>> CstA  Carbon starvation protein CstA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   6.1   3.1e-08   9.1e-05      86     215 ..      37     170 ..      18     197 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 3.1e-08
                              CstA  86 llWilvGavfagavhDfvvlvasvrrkgkslgelakkelgkvakllallailli....lilvlavlalvvvkalaes 158
                                       +lW+l  + ++     + vl ++ ++ gksl++l++++lgk+++++++l i ++    li  +a  a+++++ +   
  gi|242398157|ref|YP_002993581.1|  37 FLWLLNLG-LMTLLTALFVLEVASKNLGKSLSKLTEEHLGKMGGVVMFLSISALaygaLIAYIAGSADIISSLVGIR 112
                                       56655322.4556667889999**********************99887765432222677899999****999888 PP

                              CstA 159 paavfsv.iltipialllGvllrklrkgvleasvigvvllllavvvgseveealaell 215
                                       p  + +v   ++ + +++G+ +    + +l+ +++  ++l +++v+g+  e++l++ +
  gi|242398157|ref|YP_002993581.1| 113 PEIAAIVfWSLMSLIVFMGLKVSGEAELTLTGVLLLALVLSISLVLGKINEKNLTHRV 170
                                       76555550566778999**998876666555555555556677777765555555544 PP

>> Nramp  Natural resistance-associated macrophage protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   7.5   9.1e-07    0.0027      41     158 ..      63     180 ..      28     189 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 9.1e-07
                             Nramp  41 gkglaelirerlpkkvsillwilaelaiiatdlaeviGaAialnllfgipllvgvlitavlvllllflekggyrklE 117
                                       gk+l++l++e+l+k  ++++++ +   + ++ +a ++G+A  ++ l+gi   ++++++  l+ l++f+  +     E
  gi|242398157|ref|YP_002993581.1|  63 GKSLSKLTEEHLGKMGGVVMFLSISALAYGALIAYIAGSADIISSLVGIRPEIAAIVFWSLMSLIVFMGLKVSGEAE 139
                                       79*********************************************998888888888888888885555555555 PP

                             Nramp 118 aliialvlvialsFiaelflvkpdwgevlkglvvPslpg.ke 158
                                         + + vl++al+  ++l+l k++ +++ + +  P  +g  +
  gi|242398157|ref|YP_002993581.1| 140 LTLTG-VLLLALVLSISLVLGKINEKNLTHRVRSPLPKGqGS 180
                                       55555.555559999999999999999988887776666333 PP

>> EbsA  EbsA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   1.1   1.6e-05     0.049      10      57 ..     113     159 ..     111     167 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.6e-05
                              EbsA  10 PelataiiyWSitfiilfislilllEntriylksnlvlllflvlvilg 57 
                                       Pe+a ai++WS+  +i+f++l ++ E     + ++l++l+  + ++lg
  gi|242398157|ref|YP_002993581.1| 113 PEIA-AIVFWSLMSLIVFMGLKVSGEAELTLTGVLLLALVLSISLVLG 159
                                       6666.799****************998776666666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       831  (0.0463495); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); 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):               6  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 1374.05
//
Query:       gi|242398158|ref|YP_002993582.1|  [L=863]
Description: DEAD/H associated family [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.5e-56  189.7   0.1    8.5e-56  188.8   0.1    1.5  1  DEAD_assoc  DEAD/H associated
    1.5e-28   99.8   0.2    2.7e-27   95.7   0.0    2.7  3  DEAD        DEAD/DEAH box helicase
    1.3e-16   60.9   0.1    4.9e-16   59.1   0.0    2.0  2  Helicase_C  Helicase conserved C-terminal domain
    2.7e-11   43.7   0.0    1.2e-10   41.7   0.0    2.1  2  ResIII      Type III restriction enzyme, res subunit
  ------ inclusion threshold ------
      0.019   13.7   0.0      0.043   12.5   0.0    1.6  1  SNF2_N      SNF2 family N-terminal domain
      0.043   14.1   0.0       0.84   10.0   0.0    2.6  2  AAA_19      AAA domain
      0.045   12.8   0.2       0.36    9.9   0.0    2.2  2  T2SSE       Type II/IV secretion system protein
      0.064   12.2   0.1       0.17   10.8   0.0    1.7  2  DUF1424     Putative rep protein (DUF1424)


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 !  188.8   0.1   3.8e-59   8.5e-56       1     191 []     639     827 ..     639     827 .. 0.97

  Alignments for each domain:
  == domain 1  score: 188.8 bits;  conditional E-value: 3.8e-59
                        DEAD_assoc   1 lPtdrtllvErfrdelgdwrlvvhspfGrrvnealalllaarlsrrfgidvqvaanDdgivlllpleerlpllldel 77 
                                       +P+d+ llvE ++de  + ++++h++ Grr+neal++++a+ +s++ +++v++a++D+g++l+lp+e+ l+   +e+
  gi|242398158|ref|YP_002993582.1| 639 IPDDELLLVEGIFDER-RVKYFFHTLIGRRANEALSRAFAYIISKKKKTNVGIAISDNGFMLILPKEKILN--EEEI 712
                                       7***********9988.99*******************************************999988875..689* PP

                        DEAD_assoc  78 lellspdeleedleaalnaselfkrrFrevAaralllprrypgkrkplwqqrlraaqLldvar.eypdfpllleavr 153
                                        el++ ++++e l++al+++el+krrFr+vA+r ll++rry g++k+l++q+l+a+ Ll+ ++ +ypdfpll+e +r
  gi|242398158|ref|YP_002993582.1| 713 RELFQIENVRETLKRALDNTELLKRRFRHVANRGLLILRRYMGRKKSLSRQQLNAQTLLRLLKkNYPDFPLLKEVYR 789
                                       *************************************************************983577********** PP

                        DEAD_assoc 154 evledqlDlerlaellrriaageirvvevetprpSpfA 191
                                       e++ed++D+e+++ +l+++++g+i+vv  + + pSpfA
  gi|242398158|ref|YP_002993582.1| 790 EIMEDKMDIENAELFLSWVKEGKIKVVVEHNELPSPFA 827
                                       ****************************99*******9 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.7   0.0   1.2e-30   2.7e-27       1     170 [.      34     217 ..      34     225 .. 0.88
   2 ?    0.1   0.0      0.27   6.1e+02      51      95 ..     260     304 ..     245     345 .. 0.63
   3 ?   -0.7   0.0      0.47   1.1e+03      48      70 ..     836     858 ..     670     861 .. 0.72

  Alignments for each domain:
  == domain 1  score: 95.7 bits;  conditional E-value: 1.2e-30
                                       -HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHS....TTSTS-EEEEEESSHHHHHHHHHHHHHHTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   1 tdiQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyet....kgktgpkalivePtreLaeqtlnnlkkfkky 73 
                                       t+ Q+ a+ +i +g++vl++ +TGsGKTl ++++++++++      k +++  +l+v+P+r+L +++ +nl + +++
  gi|242398158|ref|YP_002993582.1|  34 TPPQRYAVVEIHKGENVLISSPTGSGKTLSAFLAAINELVLLgkegKLEDKIYVLYVSPLRALNNDIRRNLDEPLSE 110
                                       6889********************************99977699999************************999997 PP

                                       ST............SEEEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSH..CTTEEEEEEETHHHHHHT CS
                                       xx............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxx RF
                              DEAD  74 id............lrvlliiggvaardqlskldngvdivvgtpgrlddllstgkln..lsqvrflVlDEadrlldq 136
                                       i+            +rv + +++++  ++++ +++ ++i+++tp+ l+  l+  k++  l+ v+++++DE++ l ++
  gi|242398158|ref|YP_002993582.1| 111 IRqiykelgyelpeIRVAVRTSDTSSYKKQKMVKKPPHILITTPESLAIALNAPKFSqrLKTVKYVIVDEVHALAEN 187
                                       666777788888888888777777777777777677*************9988887777****************** PP

                                       TTHHHHHHHHHHSHHHCTTSTTTSEEEEEESSBS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 137 gfsdfinrilnqlpqitcdgklqrqvivlSATlp 170
                                       +++ ++   l++l++   d       i lSAT++
  gi|242398158|ref|YP_002993582.1| 188 KRGTHLALSLERLQNLAGDFV----RIGLSATIH 217
                                       *************87777766....9*******9 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.27
                                       EEEESSHHHHHHHHHHHHHHTTTSTSEEEEEET..TSSHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxx RF
                              DEAD  51 livePtreLaeqtlnnlkkfkkyidlrvlliig..gvaardqlskld 95 
                                       li +P  eL    +++l +++++   r+ li++   + a++   +l+
  gi|242398158|ref|YP_002993582.1| 260 LIYAPANELSGALYKRLDELIEQ--HRTTLIFTntRSGAERVAYHLK 304
                                       78888888888888888888886..3444444411333344444443 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.47
                                       -EEEEEESSHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  48 pkalivePtreLaeqtlnnlkkf 70 
                                         ++++e  reL++q ++++ k+
  gi|242398158|ref|YP_002993582.1| 836 SDVVLMEDRRELIKQLHSKIMKL 858
                                       67888888999999988887665 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         8   1.8e+04      40      62 ..     124     146 ..     109     153 .. 0.67
   2 !   59.1   0.0   2.2e-19   4.9e-16       8     108 ..     274     379 ..     268     381 .. 0.89

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 8
                                       TSTEEEESTTSTHHHHHHHHHHH CS
                        Helicase_C  40 gikvavlhgelpqnereeileqf 62 
                                       +i+vav ++++++ ++++++++ 
  gi|242398158|ref|YP_002993582.1| 124 EIRVAVRTSDTSSYKKQKMVKKP 146
                                       78888888888888888877765 PP

  == domain 2  score: 59.1 bits;  conditional E-value: 2.2e-19
                                       HHH.HHTTTTSEEEEEESSHHHHHHHHHHHHHT....TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSS CS
                        Helicase_C   8 ell.kleeeggkilifvntidrlekvklllekk....gikvavlhgelpqnereeileqfnkgesdvLiatdvaerG 79 
                                       + l +l e+++++lif+nt++ +e+v + l+kk    +  + ++h++l+ + r+e+ e+ ++ge + +i+++ +e G
  gi|242398158|ref|YP_002993582.1| 274 KRLdELIEQHRTTLIFTNTRSGAERVAYHLKKKypkyAELIETHHSSLSRDVRLEVEEKLKRGELKSVISSTSLELG 350
                                       44444559999**********8888777777777877788999********************************** PP

                                       STSTTESEEEESSSSSSHHHHHHHHTTSS CS
                        Helicase_C  80 idipkvnlVinfdlprnvtsyiqriGRtg 108
                                       idi  ++lV+ ++ p++v ++ qriGR+g
  gi|242398158|ref|YP_002993582.1| 351 IDIGTIDLVVLIGSPKSVNRALQRIGRAG 379
                                       ****************************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 !   41.7   0.0   5.3e-14   1.2e-10      22     169 ..      45     216 ..       4     218 .. 0.75
   2 ?   -2.3   0.0       1.7   3.8e+03      56      80 ..     837     861 ..     831     863 .] 0.84

  Alignments for each domain:
  == domain 1  score: 41.7 bits;  conditional E-value: 5.3e-14
                                       .TTSEEEEEESTTSTHHHHH.HHHHHHH-S...........-EEEEESSHHHHHHHHHHGGGGTGG........... CS
                            ResIII  22 krdkrglikmaTGtGKTlva.aklierllkkgkee......kflflvprkslleqtleefkkflseayke....... 84 
                                       ++ +++li  +TG+GKTl a +++i +l   gke        +l + p ++l +  ++++ + lse ++        
  gi|242398158|ref|YP_002993582.1|  45 HKGENVLISSPTGSGKTLSAfLAAINELVLLGKEGkledkiYVLYVSPLRALNNDIRRNLDEPLSEIRQIykelgye 121
                                       67889***************9999999999888778999999999************99977777766544445555 PP

                                       ........GEEEESSS-B--...............-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTT CS
                            ResIII  85 ........igkkvsgdkkka........kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlg 145
                                                                   ++  ++  +il+tt +sl  ++   +  + +++ ++ +++i+DE+H l+
  gi|242398158|ref|YP_002993582.1| 122 lpeirvavR----------TsdtssykkQKMVKKPPHILITTPESLAIAL---NAPKFSQRLKTVKYVIVDEVHALA 185
                                       544433321..........02223333345667899**************...7788888888889*********** PP

                                       S.T.......TTHHHHHT---SEEEEEESS- CS
                            ResIII 146 akk.......swreilekfkeavllglTATp 169
                                       ++k       s +++ +   ++v++gl+AT+
  gi|242398158|ref|YP_002993582.1| 186 ENKrgthlalSLERLQNLAGDFVRIGLSATI 216
                                       *96565566677777777777*********7 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.7
                                       -EEEEESSHHHHHHHHHHGGGGTGG CS
                            ResIII  56 kflflvprkslleqtleefkkflse 80 
                                        ++++ +r++l++q+ ++++k++ e
  gi|242398158|ref|YP_002993582.1| 837 DVVLMEDRRELIKQLHSKIMKLIGE 861
                                       689999*********9999888776 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 ?   12.5   0.0   1.9e-05     0.043     124     201 ..     125     196 ..      27     215 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.9e-05
                                       EEE--SSHHHH-----------------EEEE-HHHHHHHT......TTS-S-S-SEEEES-GGGT--TTSHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N 124 lrvlvyggqkkmkkkntkvapklladydvvittYdvlsreaelqkkrsvlkqvewkrvvlDEghtlknstskaaeav 200
                                       +rv v ++++    +  k ++ + +  +++itt + l+   + +k  + lk v  k+v++DE h l  +++ ++ a+
  gi|242398158|ref|YP_002993582.1| 125 IRVAVRTSDT----SSYKKQKMVKKPPHILITTPESLAIALNAPKFSQRLKTV--KYVIVDEVHALAENKRGTHLAL 195
                                       4444544443....22334566677789*************999999999987..69*********99987776666 PP

                                       H CS
                                       x RF
                            SNF2_N 201 s 201
                                       s
  gi|242398158|ref|YP_002993582.1| 196 S 196
                                       5 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   0.00038      0.84       1     115 [.      37     185 ..      37     204 .. 0.63
   2 ?    1.0   0.0      0.21   4.7e+02      35      84 ..     280     327 ..     269     418 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00038
                            AAA_19   1 qreave.alkekvllvtaGpGtGKTr..vlkhivallvelggvkp...eeillvaftgrAakelrerlaalgaeatT 71 
                                       qr av   +k +++l+  + G+GKT    l +i +l++  ++ k+     +l v++ +   + +r +l++ + e++ 
  gi|242398158|ref|YP_002993582.1|  37 QRYAVVeIHKGENVLISSPTGSGKTLsaFLAAINELVLLGKEGKLedkIYVLYVSPLRALNNDIRRNLDEPLSEIRQ 113
                                       77888559999**************6223444444443333333332245666777777778899999666666555 PP

                            AAA_19  72 iH.rlal..............................ldfddlltealelleeaeeekklqeeellivDEfqdvd 115
                                       i  +l+                               +++ + l   + +l+  + ++ l+  +++ivDE+  + 
  gi|242398158|ref|YP_002993582.1| 114 IYkELGYelpeirvavrtsdtssykkqkmvkkpphilITTPESL---AIALNAPKFSQRLKTVKYVIVDEVHALA 185
                                       54344446666666666666666566666666665432222222...2334566788889666799999997765 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.21
                            AAA_19  35 velggvkpeeillvaftgrAakelrerlaalgae.......atTiHrlalldfddll 84 
                                       +e++    ++ l+ + t+  a++++  l++   +       ++T H+   l  d +l
  gi|242398158|ref|YP_002993582.1| 280 IEQH----RTTLIFTNTRSGAERVAYHLKK---KypkyaelIETHHSS--LSRDVRL 327
                                       3333....7899999999999999988833...233688889999976..4444433 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 ?    9.9   0.0   0.00016      0.36     127     151 ..      45      67 ..      31      80 .. 0.78
   2 ?   -0.2   0.0      0.19   4.2e+02      14      59 ..     240     285 ..     236     294 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00016
                             T2SSE 127 rerglilvsGgTgsGKttllyallk 151
                                       ++  ++l+s +TgsGKt ++   l+
  gi|242398158|ref|YP_002993582.1|  45 HKGENVLISSPTGSGKTLSAF--LA 67 
                                       56689************8763..33 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.19
                             T2SSE  14 vsdihvekpervkvrervdgielreveelekaalerlisriaalak 59 
                                       v+d+ + k+ ++kv+  v+++ +++++el+ a+ +rl + i ++  
  gi|242398158|ref|YP_002993582.1| 240 VVDVSFAKQTEIKVESVVEDLIYAPANELSGALYKRLDELIEQHRT 285
                                       89*********************************99999988765 PP

>> DUF1424  Putative rep protein (DUF1424)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   7.7e-05      0.17      36     137 ..     275     375 ..     263     384 .. 0.84
   2 ?   -3.2   0.1       1.4   3.2e+03     211     246 ..     444     479 ..     440     485 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 7.7e-05
                           DUF1424  36 rfeswyddqrdtqivveeetlgervgfdtpnrftpeyremlyakaqslerglreewgdllhtamvtltassteeegr 112
                                       r++   ++ r t i  +  +  erv +++ +++ p+y e++ ++  sl r +r e  + l+ + +    sst  e +
  gi|242398158|ref|YP_002993582.1| 275 RLDELIEQHRTTLIFTNTRSGAERVAYHLKKKY-PKYAELIETHHSSLSRDVRLEVEEKLKRGELKSVISSTSLELG 350
                                       5566667778888888888888******99887.9***********************9999999888888887777 PP

                           DUF1424 113 lrpllehlrdllesweavrdalarv 137
                                       +      l  l+ s ++v +al+r+
  gi|242398158|ref|YP_002993582.1| 351 IDIGTIDLVVLIGSPKSVNRALQRI 375
                                       7666666888999999999999986 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.4
                           DUF1424 211 avsvrrsarpdredgvenlgaylaaymagey.gveal 246
                                       a ++ r a p r+   +++ + l  y+agey g e  
  gi|242398158|ref|YP_002993582.1| 444 AYNLVRRAYPYRNLSFDDFVSVL-RYLAGEYaGLEEK 479
                                       55666778899999988887766.699***9445555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (863 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.78u 0.30s 00:00:01.08 Elapsed: 00:00:00.49
# Mc/sec: 5333.28
//
Query:       gi|242398159|ref|YP_002993583.1|  [L=58]
Description: hypothetical protein TSIB_0166 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       226  (0.0126053); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 393.21
//
Query:       gi|242398160|ref|YP_002993584.1|  [L=214]
Description: hypothetical protein TSIB_0167 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-06   28.1   0.7    4.2e-05   23.2   0.2    2.1  2  PQQ_2     PQQ-like domain
     0.0038   16.7   0.0     0.0055   16.2   0.0    1.2  1  DUF2117   Uncharacterized protein conserved in archaea (DUF21


Domain annotation for each model (and alignments):
>> PQQ_2  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.6   0.0    0.0047        42      54      80 ..      58      81 ..      52      89 .. 0.59
   2 !   23.2   0.2   4.7e-09   4.2e-05       2     104 ..      89     183 ..      87     214 .] 0.71

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.0047
                             PQQ_2 54 atGkvlWettlegpvvgaplvaegrvv 80
                                       tG++lW+++++++ +++   a++ +v
  gi|242398160|ref|YP_002993584.1| 58 PTGSELWRKEFNVTSLST---AGDLIV 81
                                      467777777776665554...444444 PP

  == domain 2  score: 23.2 bits;  conditional E-value: 4.7e-09
                             PQQ_2   2 egvvsaldaatGaelWrvdlarplgggvsravlsggtlfvatgggrlvaldaatGkvlWettlegpvvgaplvaegr 78 
                                       ++vv+++d   G+elW +d    +g+ v  a+  g+t++va ++ +++ ++  +G ++ + ++ + +vg+ ++++++
  gi|242398160|ref|YP_002993584.1|  89 GSVVKVFDI-GGNELWGLD----FGEKV--AT-NGKTVAVA-EKSKIYIFS-RDGNIIRTIEPWKGAVGSVELTDDE 155
                                       5677****8.6*******7....7999*..99.99999998.9*****998.9**********66677776666666 PP

                             PQQ_2  79 vvvva..sdg.qlialdaedGkrlWstqq 104
                                        +vv+  s++ +++++ +e+G +lW+   
  gi|242398160|ref|YP_002993584.1| 156 KLVVTfySKEaSYLRVYSENGSLLWTK-N 183
                                       667777877777777777********2.2 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 !   16.2   0.0   6.1e-07    0.0055      81     125 ..      88     138 ..      63     145 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 6.1e-07
                           DUF2117  81 kgkrvv......rkiagvspgenilvnGiviGkaeseevtivaedgkivdi 125
                                       +g++v+       ++ g++ ge++  nG  ++ ae++++ i ++dg i++ 
  gi|242398160|ref|YP_002993584.1|  88 NGSVVKvfdiggNELWGLDFGEKVATNGKTVAVAEKSKIYIFSRDGNIIRT 138
                                       4554445566667899********************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        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 0.32s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 1234.74
//
Query:       gi|242398161|ref|YP_002993585.1|  [L=96]
Description: hypothetical protein TSIB_0168 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
        1.3    9.1   3.2        2.2    8.4   2.5    1.7  2  EF-hand_6  EF-hand domain


Domain annotation for each model (and alignments):
>> EF-hand_6  EF-hand domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   2.5   0.00012       2.2       8      21 ..      31      44 ..      31      44 .. 0.92
   2 ?   -2.3   0.0      0.34   6.1e+03      20      27 ..      86      93 ..      85      94 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00012
                         EF-hand_6  8 lfDkdgdGkidaeE 21
                                      lfD+d+dG id ++
  gi|242398161|ref|YP_002993585.1| 31 LFDHDKDGIIDEDD 44
                                      7**********986 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.34
                         EF-hand_6 20 eElrkalr 27
                                      eE+++al 
  gi|242398161|ref|YP_002993585.1| 86 EEIKNALD 93
                                      79999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1338  (0.0746277); expected 358.6 (0.02)
Passed bias filter:                      903  (0.0503653); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.52
# Mc/sec: 558.37
//
Query:       gi|242398162|ref|YP_002993586.1|  [L=641]
Description: Prolyl endopeptidase [Thermococcus sibiricus MM 739]
Scores for complete 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-56  189.4   0.0    7.9e-56  188.9   0.0    1.2  1  Peptidase_S9    Prolyl oligopeptidase family
    1.2e-23   83.7   0.0    2.1e-23   82.8   0.0    1.3  1  Peptidase_S9_N  Prolyl oligopeptidase, N-terminal beta-propel
     0.0016   17.8   0.0      0.014   14.7   0.0    2.1  2  Hydrolase_4     Serine aminopeptidase, S33
  ------ inclusion threshold ------
      0.024   14.5   0.0       0.15   11.9   0.0    1.9  1  Abhydrolase_3   alpha/beta hydrolase fold
      0.056   13.1   0.0        1.1    8.8   0.0    2.2  2  Abhydrolase_1   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 !  188.9   0.0   2.2e-59   7.9e-56       3     210 ..     434     638 ..     432     640 .. 0.95

  Alignments for each domain:
  == domain 1  score: 188.9 bits;  conditional E-value: 2.2e-59
                                       --.HHHHHHHCCT-EEEEE--TTSSTTHCHHHHTTSGGGGHHHHHHHHHHHHHHHHTTS--GGGEEEEEETHHHHHH CS
                      Peptidase_S9   3 fs.selqlladrGyvvvvanirGsggyGeafhdagkrklgqnefdDfiaaaealakegyvdserlaitGgSyGGylt 78 
                                       f  +++ +  ++G  +++an+rG+++yGe++h+ag r+++qn fdDfia++e+l +e+y    ++a++G S+GG+l+
  gi|242398162|ref|YP_002993586.1| 434 FFpHVIPFI-EMGGTFAMANLRGGSEYGEEWHKAGMRENKQNVFDDFIAVLEKLKEEDY----KVAAWGRSNGGLLV 505
                                       665778888.***********************************************99....5************* PP

                                       HHHHHH-GGG-SEEEEESE---CCCHHCSTTSTHH.HCCCC--TTTCHHHHHHHHHH-CGGG--...---EEEEEEE CS
                      Peptidase_S9  79 gaalnqrpdlFkaavaevpvvdvlrydsdtdllte.eymewgnpeeneegykelspyspldnvk...aypplLlihG 151
                                        ++l qrpd+ +aa++++pv+d+lr+++    ++  ++ e+gnp +++ +++ l +ysp++n+    +ypp+L+ +G
  gi|242398162|ref|YP_002993586.1| 506 STVLVQRPDVMDAALIGYPVIDMLRFHKLY--IGSvWVPEYGNP-DDPRDREFLLKYSPYHNIDptkKYPPTLIYTG 579
                                       *****************************7..9999********.777779999********99999********** PP

                                       TT-SSS-THHHHHHHHHHH--S-SEEEEEETTS-SSTTSSHHHHHHHHHHHHHHHHHCT CS
                      Peptidase_S9 152 laDdrvppaealklvaaLqkkgknvlllifpdegHgvgkprakveelarllaFlkealg 210
                                       l+Ddrv+p +alk++++L++ g +v l++++++gH +++p+++++ela++l+F+ ++l+
  gi|242398162|ref|YP_002993586.1| 580 LHDDRVHPGHALKFAKRLRDMGAPVYLRVETKSGHMGASPETRIRELADMLSFVVKTLE 638
                                       *******************************************************9986 PP

>> Peptidase_S9_N  Prolyl oligopeptidase, N-terminal beta-propeller domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.8   0.0   5.8e-27   2.1e-23      18     402 ..      22     374 ..       5     382 .. 0.88

  Alignments for each domain:
  == domain 1  score: 82.8 bits;  conditional E-value: 5.8e-27
                                       EE-TTGGGGSTTSHHHHHHHHHHHHHHHHHHCTST.CHHHHHHHHHHHT-S-EE---EEETTEEEEEEE-SS-SS-E CS
                    Peptidase_S9_N  18 vsDpYrWLeDddspetkayleaenkyteevlaqlkelrekikeeitklikeddisapfrkgkyyyysrneggknqsv 94 
                                       ++DpY W+e  +++ + +++++en  ++e++ +l+   ++++++++k +  ++i   +  +k ++   neggk+  +
  gi|242398162|ref|YP_002993586.1|  22 MEDPYIWMENLTDERVLKFVNEENTRFREFIGELP---DRLIDKVKKYYYLPNIVEARITKKGTFVKVNEGGKQ--I 93 
                                       58*********************************...*****************9999999999999999985..3 PP

                                       EEEECSTS-TTS-EEEEE-GGGGST..TS-.EEEEEEEE-TTSSEEEEEEEETTSSEEEEEEEETTTTEEEEEEEEE CS
                    Peptidase_S9_N  95 lyrqdalskegeeeevlLDpNtlse..dgtfvalgefavsedgkllAyslsksGsdwytirvkdietgedlpdeled 169
                                       + +        e+ ev++ + tl +  +++ + l++f v edgk lAy +s +Gsd    r++d e+g+ + +e++ 
  gi|242398162|ref|YP_002993586.1|  94 IKVL-------ETNEVIITSETLEKelKDE-ILLQSFTVDEDGKRLAYNFSIGGSDEGITRIIDFENGK-IVEEIKP 161
                                       3333.......4679********9975566.**************************************.6677777 PP

                                       EESEEEEECTTSSEE..EEEESS-SSS-TSTSB-S-BEEEEEETTS-GGG-EEEES-TTGTTBEEEEEE-TTSSEEE CS
                    Peptidase_S9_N 170 vkfsgivWaadekgf..fYtrydkedersdtdtnlnqkvyrhkLGtaqseDelvfeeeeepkwllgaersedgkylf 244
                                          + i+ ++d+ +f  fY +++++d+ +       +++      ++++e ++vf e     +++++++++d+k  +
  gi|242398162|ref|YP_002993586.1| 162 SLWN-ITFLEDGYYFarFYRKEKTPDGIDA----PAERIFL---KKGKEE-KMVFGEGLGSGYFMSIQKTKDKKHAL 229
                                       7777.9999**7666666666666666666....5555554...577777.99***888888888************ PP

                                       EEEESSSS--EEEEEEGGGTSS--EEEEESSSSS.-EEEEEEETTEEEEEE-TT-TT-EEEEEETTSSSGGGEEEEE CS
                    Peptidase_S9_N 245 issasgtdtnelyvldlekeskkvlklvdnrfda.eysvehnegdrfliltndgapnfrlvsvdlndpspsewkelv 320
                                       ++ + g+++n++y  +l++++ k++k+ + ++ a  ++++ +   +++i t +g   +++++ +  ++     +e++
  gi|242398162|ref|YP_002993586.1| 230 VTLSFGWNKNDIYFGPLSEPE-KWKKVYSSEVPAhPIEYVNE---KLYIYTREGRGLGKVIALENGET-----REII 297
                                       ********************9.********999988999988...7***************9876666.....59** PP

                                       --.SSCEEEEEEECTTEEEEEEEETTEEEEEEEETTTS-.EEEEEB-SSSSEEEEEE--TT-SEEEEEEEETTCEEE CS
                    Peptidase_S9_N 321 perekvvleeitvfknylvvsyrkdvlsrvqvvdlkngkvllfevplpgvgsvssasgekedselfysfsSfltPst 397
                                       pe e  + e + + k++++++y+ ++ s ++v++  +g+ l+ e++   +g+v    ++ ++    ++++Sf+ P +
  gi|242398162|ref|YP_002993586.1| 298 PEGEFPL-EWVIIVKDKILAAYLVHASSLLKVFT-LDGE-LIEEIKFDMPGQVYPLDNNGKT--AILRYESFTIPYR 369
                                       **99998.688899999*****************.6688.9999999999999988877777..58999******** PP

                                       EEEEE CS
                    Peptidase_S9_N 398 iykld 402
                                       +yk+d
  gi|242398162|ref|YP_002993586.1| 370 LYKFD 374
                                       ***99 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   3.9e-06     0.014      47     106 ..     464     521 ..     444     534 .. 0.82
   2 ?    0.2   0.0       0.1   3.6e+02     193     218 ..     573     598 ..     563     605 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.9e-06
                       Hydrolase_4  47 gkrghvpsfddyvdDlaafvekvkeehpelplfllGhSmGGliallyllrypdkvaglil 106
                                        k g  ++ + + dD+ a++ek+ke  ++ ++  +G S GGl++ ++l ++pd ++++ +
  gi|242398162|ref|YP_002993586.1| 464 HKAGMRENKQNVFDDFIAVLEKLKE--EDYKVAAWGRSNGGLLVSTVLVQRPDVMDAALI 521
                                       55666678899*************5..55788*********************8885544 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.1
                       Hydrolase_4 193 PllllhGeaDkvvdpeasrelyerlg 218
                                       P+l++ G +D  v+p+ + ++++rl+
  gi|242398162|ref|YP_002993586.1| 573 PTLIYTGLHDDRVHPGHALKFAKRLR 598
                                       9*******************999986 PP

>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   4.1e-05      0.15      49     207 ..     476     614 ..     471     617 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.1e-05
                                       HHHHHHHHHHHHHTHHHHTETTCEEEEEEETHHHHHHHHHHHHHHHTT---EEEEEEESE-SSTSSTTSHHHHHCHH CS
                     Abhydrolase_3  49 vedalaalrwlaeqawelgadpsrivlaGdSaGGnlaaavalrardegepkvagqvliyPvtdlertesesikkaee 125
                                       ++d +a+l+ l+e+         +++  G S GG l+  v+++  d     + + ++ yPv d+ r+ ++ +     
  gi|242398162|ref|YP_002993586.1| 476 FDDFIAVLEKLKEE-------DYKVAAWGRSNGGLLVSTVLVQRPDV----MDAALIGYPVIDMLRF-HKLY----- 535
                                       66777777777776.......46788888888888888777666554....7778888887777333.2222..... PP

                                       TTTSSSSCHHHHHHHHHHHSSGGGGGST...TTSGGGCS-.SST---EEEEEETT-TTHH..HHHHHHHHHHHTT-- CS
                     Abhydrolase_3 126 ladgplltraaldlfwrlylpeadrddp...laspllaed.lsglpptlvvvaefDplrd..egeayaerlraagve 196
                                          g+++       + ++  p++ rd+     +sp ++ d  +++pptl++++ +D   +   + ++a+rlr++g +
  gi|242398162|ref|YP_002993586.1| 536 --IGSVW-------VPEYGNPDDPRDREfllKYSPYHNIDpTKKYPPTLIYTGLHDDRVHpgHALKFAKRLRDMGAP 603
                                       ..23332.......2233334555555555556777663459***********99966651156679********** PP

                                       EEEEEETTEET CS
                     Abhydrolase_3 197 velieyegmvH 207
                                       v l++  +  H
  gi|242398162|ref|YP_002993586.1| 604 VYLRVETKSGH 614
                                       **999888888 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.038   1.4e+02      72     100 ..     490     518 ..     398     532 .. 0.84
   2 ?    8.8   0.0   0.00032       1.1     202     251 ..     557     615 ..     537     620 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.038
                                       TSSEEEEEETHHHHHHHHHHHHHGGGEEE CS
                     Abhydrolase_1  72 ddkltlvGhSmGGmialayaaeyperVka 100
                                       d k++ +G S GG+++++++ + p+ ++a
  gi|242398162|ref|YP_002993586.1| 490 DYKVAAWGRSNGGLLVSTVLVQRPDVMDA 518
                                       447889**************999997766 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00032
                                       HHHHCTHHHHS.....EEEEEEETTCSSSCHHHHHHHHHCHTS....EEEEEEETCSSS CS
                     Abhydrolase_1 202 lrlrelknvla.....ptlvisgtsDplvppkaledlaqllpk....krlvvisdagHl 251
                                       l++   +n+       ptl++ g +D  v p++  ++a+ l++    ++l+v+ ++gH+
  gi|242398162|ref|YP_002993586.1| 557 LKYSPYHNIDPtkkypPTLIYTGLHDDRVHPGHALKFAKRLRDmgapVYLRVETKSGHM 615
                                       4444455555566677***************99999999988889999**********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (641 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       596  (0.0332422); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); 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: 0.69u 0.32s 00:00:01.01 Elapsed: 00:00:00.46
# Mc/sec: 4151.47
//
Query:       gi|242398163|ref|YP_002993587.1|  [L=154]
Description: hypothetical protein TSIB_0170 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-22   81.1   0.0    1.6e-22   80.9   0.0    1.0  1  ATC_hydrolase  L-2-amino-thiazoline-4-carboxylic acid hydrola


Domain annotation for each model (and alignments):
>> ATC_hydrolase  L-2-amino-thiazoline-4-carboxylic acid hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.9   0.0   8.9e-27   1.6e-22       3     144 ..      13     150 ..       9     151 .. 0.87

  Alignments for each domain:
  == domain 1  score: 80.9 bits;  conditional E-value: 8.9e-27
                     ATC_hydrolase   3 lleaailvalyealkkeigkeeakeiirkalerlgkergkklaekakakkdkadvekflaly....seifekenalk 75 
                                       +++a  ++ + ++++ ++g +e++ ++rka+e++g erg++++++   ++ + ++e++ ++y    +e +      k
  gi|242398163|ref|YP_002993587.1|  13 EIMALLFYHISKEVIDTFG-DEGERVLRKAIENFGSERGENIRKEVLSRGLPPTMENLSKYYdmplKEAW------K 82 
                                       5666677888888888875.89************************************999944444444......4 PP

                     ATC_hydrolase  76 fevleedkdeleidvtrCpyceawkkeGlpelgkllCeiDkavaeginpkvklertktlaeGgdcCdfr 144
                                         + + d+  ++ +v  Cp++++wk+ G +e+g ++Ce D a+++++np+++++r k++ +G++ C f 
  gi|242398163|ref|YP_002993587.1|  83 G-TSKVDEVTYYSEVSFCPFAKVWKEKGAEEIGLIYCEQDIALMKAYNPNINFKRPKNVLKGDEICLFD 150
                                       3.44447999********************************************************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1167.12
//
Query:       gi|242398164|ref|YP_002993588.1|  [L=223]
Description: hypothetical protein TSIB_0171 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.5e-10   40.9   8.7    6.5e-10   38.8   5.1    2.2  2  DUF4097     Putative adhesin
     0.0051   17.1  15.6     0.0051   17.1   8.0    3.5  4  Bactofilin  Polymer-forming cytoskeletal
  ------ inclusion threshold ------
       0.31   10.9   3.7       0.64    9.9   0.1    2.6  3  DUF2154     Cell wall-active antibiotics response 4TMS YvqF


Domain annotation for each model (and alignments):
>> DUF4097  Putative adhesin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.9   0.3     0.005        30      11      66 ..      24      83 ..      13     109 .. 0.63
   2 !   38.8   5.1   1.1e-13   6.5e-10     129     252 .]      98     221 ..      86     221 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.005
                           DUF4097 11 advtikesddekitveystakklkkqkve....etggtLsitqkekngvstgfikelssg 66
                                        ++i+ +d+++i+++++++  l  ++ +    ++g+ L+i+ k  +++ + ++++ +++
  gi|242398164|ref|YP_002993588.1| 24 GRIRIEGYDGDTIKLKAEKKWGLLGTEPKikvkKEGNILKIEAKHGKSFGVSMGESAVNF 83
                                      467888888888887777765543333223345999999999999888888777543333 PP

  == domain 2  score: 38.8 bits;  conditional E-value: 1.1e-13
                           DUF4097 129 sesGdvtiegseakk.lklqltsGdieleslsletldltsssGdltlsntklegsltitassGdvdlslpeekkaav 204
                                         +G ++++++e  k  k+++ +G i +e++ ++  ++ +  G ++++  +++g l i++  G++++ l+++++++v
  gi|242398164|ref|YP_002993588.1|  98 NVNGSISLKNIE--KvGKVATVNGSITAENVFAG--KISTVNGSIKAMLSSINGDLVISTVNGSIEVYLSKDSDIEV 170
                                       556777777765..449*************9998..9**************************************** PP

                           DUF4097 205 dassesGdvslpk...kreeeekesnsisaseknakkkvsvstssGDitvk 252
                                       +a+s +G++ +       +   +  +s+++  +++k++v++st +G+i++k
  gi|242398164|ref|YP_002993588.1| 171 NAHSVNGKIASEIpgeLSKAPFHGPKSFKGVLGEGKYNVKISTVNGNISIK 221
                                       *********98887787778889999***********************97 PP

>> Bactofilin  Polymer-forming cytoskeletal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1      0.13   7.9e+02      19      21 ..      26      28 ..       4      83 .. 0.67
   2 !   17.1   8.0   8.6e-07    0.0051      25      92 ..      81     150 ..      52     154 .. 0.86
   3 ?    3.2   0.2     0.019   1.1e+02      17      49 ..     147     181 ..     142     190 .. 0.55
   4 ?   -1.3   0.0      0.46   2.7e+03      75      81 ..     213     219 ..     196     223 .] 0.54

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.13
                        Bactofilin 19 lri 21
                                      +ri
  gi|242398164|ref|YP_002993588.1| 26 IRI 28
                                      222 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 8.6e-07
                        Bactofilin  25 veGdieakgklvvgeggkvegnikaeevvvaGt...vkGnveaeekvelkktakveGdikaksleieegav 92 
                                       v+ di   +++ vg+ g+v+g+i+ ++++  G+   v+G+++ae +v   k ++v+G+ika   +i+ + v
  gi|242398164|ref|YP_002993588.1|  81 VNFDILVPKSVEVGKVGNVNGSISLKNIEKVGKvatVNGSITAE-NVFAGKISTVNGSIKAMLSSINGDLV 150
                                       5667777889**********************966667*****9.***************98888877665 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.019
                        Bactofilin  17 gdlridGkveGdi....eakgklvvgeggkvegnika 49 
                                       gdl+i+  v+G+i    ++++++ v+ ++ v+g+i +
  gi|242398164|ref|YP_002993588.1| 147 GDLVIST-VNGSIevylSKDSDIEVNAHS-VNGKIAS 181
                                       4555432.444443333666666666555.6666654 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 0.46
                        Bactofilin  75 kveGdik 81 
                                       +v+G+i+
  gi|242398164|ref|YP_002993588.1| 213 TVNGNIS 219
                                       2333333 PP

>> DUF2154  Cell wall-active antibiotics response 4TMS YvqF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1     0.053   3.2e+02      50      74 ..      82     105 ..      69     126 .. 0.76
   2 ?    9.9   0.1   0.00011      0.64      33      73 ..     140     180 ..     137     186 .. 0.90
   3 ?   -3.3   0.1       1.3   7.9e+03      41      51 ..     208     218 ..     200     220 .. 0.43

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.053
                           DUF2154  50 dvkilVPedvevsveasvifGdvkv 74 
                                       + +ilVP+ vev    +v  G++++
  gi|242398164|ref|YP_002993588.1|  82 NFDILVPKSVEVGKVGNVN-GSISL 105
                                       5689******998766653.55555 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00011
                           DUF2154  33 avlpegetvivirkliGdvkilVPedvevsveasvifGdvk 73 
                                       a+l+  +  +vi+ + G++++++ +d +++v+a ++ G++ 
  gi|242398164|ref|YP_002993588.1| 140 AMLSSINGDLVISTVNGSIEVYLSKDSDIEVNAHSVNGKIA 180
                                       6777778889**************************99985 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 1.3
                           DUF2154  41 vivirkliGdv 51 
                                        + i+ + G++
  gi|242398164|ref|YP_002993588.1| 208 NVKISTVNGNI 218
                                       23333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.48
# Mc/sec: 1399.43
//
Query:       gi|242398165|ref|YP_002993589.1|  [L=198]
Description: Membrane-associated metalloprotease, CaaX family [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-09   38.2   0.5    1.4e-09   38.2   0.5    1.9  2  CPBP      CPBP intramembrane metalloprotease


Domain annotation for each model (and alignments):
>> CPBP  CPBP intramembrane metalloprotease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.2      0.14   2.5e+03      65      75 ..      22      32 ..       6      58 .. 0.56
   2 !   38.2   0.5   7.9e-14   1.4e-09      14      88 ..     111     185 ..      95     189 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.14
                                      HHHHHHHHHHH CS
                              CPBP 65 aGlvlgylylk 75
                                       G ++ ++ ++
  gi|242398165|ref|YP_002993589.1| 22 GGNIYEWALYN 32
                                      33333333333 PP

  == domain 2  score: 38.2 bits;  conditional E-value: 7.9e-14
                                       HHHHHHHHHHTTCHHHHHHHH.S-HHHHHHHHHHHHHCSGGGHHH.HHHHHHHHHHHHHHHHHTT-HHHHHHHHHH CS
                              CPBP  14 lapllEEllfRglllqllqergsstlailissilFglaHlpngps.vllaalaGlvlgylylktgsllaaillHal 88 
                                       +  ++ E+++Rg+ll  l+++ +++l i+++ i ++l+H+   p  + + ++aG+v++ + lk+ s+l+++llH++
  gi|242398165|ref|YP_002993589.1| 111 VIMFAHEAFYRGILLFPLAKK-NEWLGIIVQNIPYTLVHIGKPPLeIPYSFIAGIVFAKIDLKSESFLPSFLLHWI 185
                                       456799*******99999999.446*****************9999****************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1292.03
//
Query:       gi|242398166|ref|YP_002993590.1|  [L=314]
Description: peptidyl-prolyl cis-trans isomerase, FKBP-type domain protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-17   63.5   0.0    4.3e-17   62.2   0.0    1.8  1  FKBP_C    FKBP-type peptidyl-prolyl cis-trans isomerase
    6.9e-07   29.3   2.0    1.4e-06   28.3   0.8    2.2  2  FKBP26_C  FKBP26_C-terminal


Domain annotation for each model (and alignments):
>> FKBP_C  FKBP-type peptidyl-prolyl cis-trans isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.2   0.0   4.8e-21   4.3e-17       5      93 ..      27     177 ..      24     178 .. 0.74

  Alignments for each domain:
  == domain 1  score: 62.2 bits;  conditional E-value: 4.8e-21
                                       B-TTCEEEEEEEEEET.TSSEEEEH..........CC...HTSEEEEETTSSSSCHHHHHHHTTSBTT-EEEEEEEG CS
                            FKBP_C   5 akegdtVtvhykgkle.dgkvfdss..........rs...rakplefkvGsgqvikGfeealegmkvGekrtltipp 67 
                                       ++++d++++hy+gk++  g++fd++          ++    + p+ + vG+g+vikG++e leg++vG k t++ipp
  gi|242398166|ref|YP_002993590.1|  27 VAKKDVIKLHYTGKIKeTGEIFDTTyddvakeagiYNekgIYGPVPIAVGAGHVIKGLDETLEGLEVGKKYTIEIPP 103
                                       67899**********978*******7777777777336779************************************ PP

                                       GGTTTT.....................................TTBCTTTB.TT....................SEE CS
                            FKBP_C  68 elaYge.....................................kglaggvippn....................atL 87 
                                       e a+g+                                     k         +                    +t 
  gi|242398166|ref|YP_002993590.1| 104 EKAFGKrdpkliktftigqfrrqgiypfpgldveietdsgkklK---------GrvmsvssgrvrvdfnhpfagKTA 171
                                       ******66666666666666666666666666665555553330.........033333344444445555555888 PP

                                       EEEEEE CS
                            FKBP_C  88 vFeveL 93 
                                       v+eve+
  gi|242398166|ref|YP_002993590.1| 172 VYEVEI 177
                                       888887 PP

>> FKBP26_C  FKBP26_C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0      0.87   7.8e+03      28      40 ..      95     107 ..      91     118 .. 0.77
   2 !   28.3   0.8   1.5e-10   1.4e-06       3      39 ..     186     222 ..     184     251 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.87
                                       TEEEEE--TTGGG CS
                          FKBP26_C  28 ktvtIelpeeakF 40 
                                       k+ tIe+p e +F
  gi|242398166|ref|YP_002993590.1|  95 KKYTIEIPPEKAF 107
                                       6778999988877 PP

  == domain 2  score: 28.3 bits;  conditional E-value: 1.5e-10
                                       HHHHHHHHHH-TT--..--EEEEETTEEEEE--TTGG CS
                          FKBP26_C   3 ekikelIkryiPnidlekfkieiedktvtIelpeeak 39 
                                       ek+k+lI+++iP+id ek++ie+ ++ v++e  ++++
  gi|242398166|ref|YP_002993590.1| 186 EKVKALIELRIPRIDFEKVEIEVGEEDVKVEFKDQTI 222
                                       9*****************************9988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1187  (0.0662056); expected 358.6 (0.02)
Passed bias filter:                      572  (0.0319036); 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: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2134.13
//
Query:       gi|242398167|ref|YP_002993591.1|  [L=468]
Description: Cysteinyl-tRNA synthetase [Thermococcus sibiricus MM 739]
Scores for complete 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-138  458.9   0.0   1.3e-137  458.1   0.0    1.3  1  tRNA-synt_1e     tRNA synthetases class I (C) catalytic domai
      4e-22   78.5   1.1    5.1e-11   42.0   0.2    2.4  2  tRNA-synt_1g     tRNA synthetases class I (M)
    1.4e-15   57.5   0.7    5.9e-15   55.5   0.2    2.3  2  DALR_2           DALR domain
      2e-09   36.3   0.5    2.4e-06   26.1   0.0    3.1  3  tRNA-synt_1      tRNA synthetases class I (I, L, M and V)
    1.5e-08   33.9   3.6    2.6e-06   26.6   0.0    3.0  3  tRNA-synt_1f     tRNA synthetases class I (K)
  ------ inclusion threshold ------
       0.17   11.8   1.8       0.27   11.1   0.2    2.2  2  NleF_casp_inhib  NleF caspase inhibitor
        1.4    9.4   5.2       0.45   10.9   0.1    2.8  3  EntA_Immun       Enterocin A Immunity
        1.4    8.7  11.9        3.2    7.6   0.2    3.6  4  CdvA             CdvA-like coiled-coil 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 !  458.1   0.0    6e-141  1.3e-137       2     301 .]       8     306 ..       7     306 .. 0.99

  Alignments for each domain:
  == domain 1  score: 458.1 bits;  conditional E-value: 6e-141
                                       ---SBTTEEEEEEEEEBTTS--BHHHHHHHHHHHHHHHHHHHTT-EEEEEEEBB--SHHHHHHHHHTTS-HHHHHHH CS
                      tRNA-synt_1e   2 vkpleekkvtlYvCGptvydashlGhaRslvafDilrrilqalgYdvqfvqnvtDidDkiikrareeeksvkelaek 78 
                                       +kpl+++++ +YvCGptvyd++hlGhaR+++afD++rr+l+++gY v  v n+tDidDkii+ra+e ++  kelaek
  gi|242398167|ref|YP_002993591.1|   8 FKPLRDDEIRMYVCGPTVYDYTHLGHARTYIAFDVIRRYLEHKGYTVLMVMNFTDIDDKIIRRANETGEDPKELAEK 84 
                                       6889999********************************************************************** PP

                                       HHHHHHHHHHHTT----SB--BGGGGHHHHHHHHHHHHHTTSEEE-TTS-EEE-GGG-TTTTTTTT--HHHHHHT-- CS
                      tRNA-synt_1e  79 fieefkkdleaLnvlkptleprvsekvdeiielvekliekgyaYavsdgdvyfdvskkeeYgklskqnleelelgae 155
                                       f + f +d++aL+v+++++ prv+e++++iie+v kl ekgyaY +s + vyf+v+k+e+Ygklsk nle+l++g +
  gi|242398167|ref|YP_002993591.1|  85 FLKYFLEDMKALKVKPADIYPRVTEHIQDIIEFVRKLEEKGYAYGSS-DGVYFEVRKYEKYGKLSKVNLEDLRKGVR 160
                                       **********************************************9.89*************************** PP

                                       --S--S-SSTT-EEEEEE--TTS--B--TTSSEEE-SSHHHHHHHHHHH-SSEEEEEEEGGGTTTHHHHHHHHHHHH CS
                      tRNA-synt_1e 156 gevseekkdkkDfaLWkaskegepswdsPwgkGRPGWhieCsvmaskllgseidihsGGiDLafPhhenelaqseaa 232
                                       +e  e+kk+++DfaLWk++k+gep+w+sPwg+GRPGWhieCs+m++k+lg+++dih+GG+DL+fPhhene+aq+ea 
  gi|242398167|ref|YP_002993591.1| 161 VEPGEGKKNPEDFALWKKAKPGEPKWESPWGEGRPGWHIECSTMSTKYLGESFDIHGGGNDLIFPHHENEIAQTEAC 237
                                       ***************************************************************************** PP

                                       SSS--EEEEEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHSS-TTS-EEE-HHHHHHHHH CS
                      tRNA-synt_1e 233 fdkqlvkyflhnghlkiegekmsksLknfitikdvlkkfdprqlRllllsahyrsqldfkeelleeaks 301
                                       ++k++vky++h+g++++ gekmsksL+nf+ti+++l++++p+++R+++l++hyrs+ld++ee +++ak+
  gi|242398167|ref|YP_002993591.1| 238 TGKEWVKYWFHTGFVMVSGEKMSKSLGNFVTIRELLQRYSPEVIRFFVLQKHYRSPLDYTEEGIQHAKN 306
                                       *****************************************************************9985 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 !   42.0   0.2   2.3e-14   5.1e-11      12     126 ..      27     140 ..      18     147 .. 0.89
   2 !   34.8   0.0   3.4e-12   7.6e-09     307     383 ..     238     315 ..     219     319 .. 0.77

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 2.3e-14
                                       S---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHTT--.-SE CS
                      tRNA-synt_1g  12 gklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAekegvtpeelvekvheeikelfkklnis.fdk 87 
                                       + +HlGh++++i+ D++ Ry   +g+ vl+v        +i  +A++ g +p+el+ek+ + + e++k l+++  d 
  gi|242398167|ref|YP_002993591.1|  27 DYTHLGHARTYIAFDVIRRYLEHKGYTVLMVMNFTDIDDKIIRRANETGEDPKELAEKFLKYFLEDMKALKVKpADI 103
                                       568*****************************999999**********************************85699 PP

                                       EEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTT CS
                      tRNA-synt_1g  88 ygrttseehkelvqeifkklkekgliyekeieqlycpkd 126
                                       y r t+  h +   e+++kl+ekg+ y ++  +++ +++
  gi|242398167|ref|YP_002993591.1| 104 YPRVTE--HIQDIIEFVRKLEEKGYAYGSSDGVYFEVRK 140
                                       999886..6666779***********9998888777665 PP

  == domain 2  score: 34.8 bits;  conditional E-value: 3.4e-12
                                       TT----S-EEEE--EEE--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE-HHHHHHHHHH..HCCC CS
                      tRNA-synt_1g 307 aelklpkkvvaheyltvegkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfswedfvervNs..eLad 381
                                       ++ + +k  + +++++v+g+K+SkS g++v+++e+l+r++++++R++++++    + ld+++e +++  N+   L +
  gi|242398167|ref|YP_002993591.1| 238 TGKEWVKYWFHTGFVMVSGEKMSKSLGNFVTIRELLQRYSPEVIRFFVLQK-HYRSPLDYTEEGIQHAKNNleRLYN 313
                                       556677788999**********************************99875.5667899999999987774224555 PP

                                       HH CS
                      tRNA-synt_1g 382 kl 383
                                       ++
  gi|242398167|ref|YP_002993591.1| 314 TI 315
                                       55 PP

>> DALR_2  DALR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.5   0.2   2.6e-18   5.9e-15       2      57 ..     349     407 ..     348     420 .. 0.81
   2 ?   -0.7   0.0      0.93   2.1e+03      32      49 ..     434     451 ..     418     460 .. 0.51

  Alignments for each domain:
  == domain 1  score: 55.5 bits;  conditional E-value: 2.6e-18
                                       HHHHHTBT--HHHHHHHHHHHHHHHHHHHHTT-HHHHHHHH...HHHHHHHGGGT-S-S CS
                            DALR_2   2 FeeaMdDDFNTaeAiavlFelakeiNralkeedkaaasalk...allrelaevLGllqe 57 
                                        +eaMdDDFNTaeA+  +Fe+a+++N++l++ +k ++s l+   +++r ++ev+G+++e
  gi|242398167|ref|YP_002993591.1| 349 LYEAMDDDFNTAEAMKPIFEVANAVNAYLTKVEKPKESVLRkalEFFRIISEVFGIFEE 407
                                       68*************************77777666665553222888888*******98 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.93
                                       TT-HHHHHHHHHHHHHHH CS
                            DALR_2  32 eedkaaasalkallrela 49 
                                       +++ + a++ +a+lrel+
  gi|242398167|ref|YP_002993591.1| 434 QKNFELADKIRAQLRELG 451
                                       334444444455555553 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 !    5.9   0.0    0.0014       3.1      27      67 ..      18      58 ..       3      65 .. 0.85
   2 !   26.1   0.0   1.1e-09   2.4e-06     517     595 ..     213     290 ..     200     297 .. 0.90
   3 ?    0.2   0.1     0.076   1.7e+02     111     163 ..     314     366 ..     293     389 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0014
                       tRNA-synt_1 27 lvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvp 67
                                      +++  P v    H+Gha + +  d++ ry + kG++vl v+
  gi|242398167|ref|YP_002993591.1| 18 MYVCGPTVYDYTHLGHARTYIAFDVIRRYLEHKGYTVLMVM 58
                                      556668888899************************99765 PP

  == domain 2  score: 26.1 bits;  conditional E-value: 1.1e-09
                       tRNA-synt_1 517 admlleGlDiirgWvarlillslaltgsePfkevlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltlils 593
                                       +d+   G D i+   ++ i ++ a tg+e  k  + +g+v+   G KmSKslgN +   +++++y+ +++R+++++ 
  gi|242398167|ref|YP_002993591.1| 213 FDIHGGGNDLIFPHHENEIAQTEACTGKEWVKYWFHTGFVMV-SGEKMSKSLGNFVTIRELLQRYSPEVIRFFVLQK 288
                                       567778999999999999**********************96.6******************************987 PP

                       tRNA-synt_1 594 dv 595
                                       ++
  gi|242398167|ref|YP_002993591.1| 289 HY 290
                                       66 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.076
                       tRNA-synt_1 111 yaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkgliyrgkklv 163
                                        +e+ir +++++ v + +++e + l++ + +a k+ +  + d+    ++ k++
  gi|242398167|ref|YP_002993591.1| 314 TIENIRIAMEKVEVPFKWEKEEFELYETIRDAKKKLYEAMDDDFNTAEAMKPI 366
                                       56788889999999999***************999999998887777777766 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 !    5.9   0.0    0.0023       5.1      30      93 ..      22      89 ..       2     137 .. 0.81
   2 !   26.6   0.0   1.2e-09   2.6e-06     274     338 ..     252     314 ..     243     327 .. 0.83
   3 ?    0.5   0.4       0.1   2.3e+02     261     351 ..     329     418 ..     318     427 .. 0.66

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0023
                      tRNA-synt_1f 30 GispSGliHiGnlrevltadlvaralrkrgeevrlilisDdmDg..lRkvpe..nlpekllekylgkp 93
                                      G ++    H+G +r  +  d+++r l+++g +v +++   d+D   +R+  e  + p++l+ek+l++ 
  gi|242398167|ref|YP_002993591.1| 22 GPTVYDYTHLGHARTYIAFDVIRRYLEHKGYTVLMVMNFTDIDDkiIRRANEtgEDPKELAEKFLKYF 89
                                      56666678*************************99999999995346777765444555677776655 PP

  == domain 2  score: 26.6 bits;  conditional E-value: 1.2e-09
                      tRNA-synt_1f 274 illkggekmssSkGnvltledwlevaepevlrflilrrkPkkakkldldleilrlvdeYdklerk 338
                                       ++   gekms+S Gn++t++++l+ ++pev+rf++l+++ ++ ++ + + +i+++ ++ ++l + 
  gi|242398167|ref|YP_002993591.1| 252 VM-VSGEKMSKSLGNFVTIRELLQRYSPEVIRFFVLQKHYRSPLDYTEE-GIQHAKNNLERLYNT 314
                                       34.4556******************************998888888877.888888877776655 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.1
                      tRNA-synt_1f 261 lggeaPekvvYelillkgge...kmssSkGnvltledwlevaepevlrflilrrkPkkakkldldleilrlvdeYdk 334
                                       +++e+ e   Ye i + +++   +m     +  +++ ++eva+  v ++l+  +kPk++  l   le+ r++ e   
  gi|242398167|ref|YP_002993591.1| 329 FKWEKEEFELYETIRDAKKKlyeAMDDDFNTAEAMKPIFEVAN-AVNAYLTKVEKPKES-VLRKALEFFRIISEVFG 403
                                       5666666778888888888755555555555555555555554.466777777788765.57777799999999999 PP

                      tRNA-synt_1f 335 lerkyfaeqeeeeekek 351
                                       + ++yf+e++e++  e+
  gi|242398167|ref|YP_002993591.1| 404 IFEEYFKEAKETK--EE 418
                                       9999993333333..33 PP

>> NleF_casp_inhib  NleF caspase inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       1.7   3.7e+03      35      55 ..     299     319 ..     294     326 .. 0.63
   2 ?   11.1   0.2   0.00012      0.27       7      59 ..     336     388 ..     330     425 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.7
                   NleF_casp_inhib  35 ekikElsdkltklknsvlser 55 
                                       e i+  +++l+ l+n +++ r
  gi|242398167|ref|YP_002993591.1| 299 EGIQHAKNNLERLYNTIENIR 319
                                       445556666777776666554 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00012
                   NleF_casp_inhib   7 eetektlkdIkdklklifereiastTaeekikElsdkltklknsvlseredlY 59 
                                        e  +t++d k+kl ++++ + ++  a + i E+++ ++++  +v++ +e + 
  gi|242398167|ref|YP_002993591.1| 336 FELYETIRDAKKKLYEAMDDDFNTAEAMKPIFEVANAVNAYLTKVEKPKESVL 388
                                       56779******************************************999875 PP

>> EntA_Immun  Enterocin A Immunity
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1       1.7   3.8e+03       4      14 ..     307     317 ..     304     323 .. 0.64
   2 ?   -1.4   0.1       1.4   3.2e+03      31      39 ..     346     354 ..     332     392 .. 0.59
   3 ?   10.9   0.1    0.0002      0.45      15      56 ..     413     452 ..     399     458 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.7
                        EntA_Immun   4 llnelynlild 14 
                                        l++lyn i++
  gi|242398167|ref|YP_002993591.1| 307 NLERLYNTIEN 317
                                       55666666665 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.4
                        EntA_Immun  31 knklekgkn 39 
                                       k+kl +  +
  gi|242398167|ref|YP_002993591.1| 346 KKKLYEAMD 354
                                       444333322 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.0002
                        EntA_Immun  15 peikeneelrevLltaknklekgknvsvvasrLeqelrsyal 56 
                                       +e+ke+e l e+L +++ +l k+kn++  a ++  +lr + +
  gi|242398167|ref|YP_002993591.1| 413 KETKEEE-LIELLIEVRSALRKQKNFEL-ADKIRAQLRELGI 452
                                       4577777.******************99.9999999988876 PP

>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.2    0.0014       3.2      11      61 ..      73     123 ..      65     127 .. 0.93
   2 ?    4.1   0.1     0.017        39      78     111 ..     288     322 ..     285     334 .. 0.76
   3 ?   -3.5   0.1       3.9   8.7e+03      35      45 ..     343     353 ..     337     365 .. 0.45
   4 ?    3.6   0.6     0.024        54      32      60 ..     430     458 ..     404     463 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0014
                              CdvA  11 segdipkstyeeikekleealkklkekakelkeklkkrlkeledqikslek 61 
                                       ++g+ pk+ +e++ + + e +k+lk k +++  +++++++++ + +++le+
  gi|242398167|ref|YP_002993591.1|  73 ETGEDPKELAEKFLKYFLEDMKALKVKPADIYPRVTEHIQDIIEFVRKLEE 123
                                       67999*************************************999999985 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.017
                              CdvA  78 eaYksaieairellesaleekeeikkllekl.skl 111
                                       + Y+s  ++++e++++a++ +e + +++e++  ++
  gi|242398167|ref|YP_002993591.1| 288 KHYRSPLDYTEEGIQHAKNNLERLYNTIENIrIAM 322
                                       67888899999999999999999888888873344 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 3.9
                              CdvA  35 kekakelkekl 45 
                                       ++ +k+l e +
  gi|242398167|ref|YP_002993591.1| 343 RDAKKKLYEAM 353
                                       22222222222 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.024
                              CdvA  32 kklkekakelkeklkkrlkeledqiksle 60 
                                       +  k+k  el++k++++l+el  q++ ++
  gi|242398167|ref|YP_002993591.1| 430 ALRKQKNFELADKIRAQLRELGIQLEDTP 458
                                       334788899************99998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (468 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1074  (0.059903); expected 358.6 (0.02)
Passed bias filter:                      620  (0.0345808); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.77u 0.35s 00:00:01.12 Elapsed: 00:00:00.57
# Mc/sec: 2486.52
//
Query:       gi|242398168|ref|YP_002993592.1|  [L=447]
Description: ArgE/DapE-related deacylase [Thermococcus sibiricus MM 739]
Scores for complete 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-33  114.0   0.0    9.6e-33  113.6   0.0    1.2  1  Peptidase_M20  Peptidase family M20/M25/M40
    1.9e-05   24.4   0.0    0.00027   20.7   0.0    2.1  2  Peptidase_M28  Peptidase family M28
    0.00013   21.1   0.0     0.0038   16.3   0.0    2.7  3  Peptidase_M42  M42 glutamyl aminopeptidase
  ------ inclusion threshold ------
       0.06   13.7   0.0       0.11   12.8   0.0    1.4  1  Aconitase_C    Aconitase C-terminal domain


Domain annotation for each model (and alignments):
>> Peptidase_M20  Peptidase family M20/M25/M40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.6   0.0   2.1e-36   9.6e-33       1     205 [.      75     441 ..      75     443 .. 0.88

  Alignments for each domain:
  == domain 1  score: 113.6 bits;  conditional E-value: 2.1e-36
                                       EEEEES-BSS.TTCGGGSSS.TTSEEETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTT CS
                                       xxxxxxxxxx.xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20   1 llgsHlDvVp.eeetdgwtt.pfslteedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggr 75 
                                       l+++H DvVp + e+  w+t pf+l ++ +k yGrG++d+kg v++++ a+++l +    ++g++ +++++dEE+  
  gi|242398168|ref|YP_002993592.1|  75 LFMAHFDVVPvNREE--WNTePFKLVIKGNKAYGRGSADDKGNVASVMLAIKELSKMD--LEGKVLFAVTGDEEI-- 145
                                       79********88888..***********99************************9997..69************9.. PP

                                       THH..HHHHHHHH.TTTCESEEEEEE.EESSSBTCHSTETEEEE................................. CS
                                       xxx..xxxxxxxx.xxxxxxxxxxxx.xxxxxxxxxxxxxxxxx................................. RF
                     Peptidase_M20  76 gGa..kallegle.erekvdavfelh.ieepgileagklaigvv................................. 115
                                       gG    +++e l+ e++ +++++ +  ++  +i    ++++gv+                                 
  gi|242398168|ref|YP_002993592.1| 146 GGVlaMHIAEKLRdEGKMPEYMINADgVGMKPIIR-RRKGFGVTirmpsekvklkgtlkeqkfrintpivetrhaay 221
                                       67744666668887777777766333455555555.3335555566******************************* PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                     Peptidase_M20 116 ............................................................................. 115
                                                                                                                    
  gi|242398168|ref|YP_002993592.1| 222 flpgvdthpmiavshflrnsnvavvslegkflkgnivpsevtlkylevgdgeeievdlgltrllkaiiplvrapikt 298
                                       ***************************************************************************** PP

                                       ...................................................EEEEEEE.EEESHEEEC..CHHHHHH CS
                                       ...................................................xxxxxxx.xxxxxxxxx..xxxxxxx RF
                     Peptidase_M20 116 ...................................................kvevell.eggapvtln..dsplvka 138
                                                                                          ++e++ +  + a + +   d+ +v +
  gi|242398168|ref|YP_002993592.1| 299 ekysdygvsitpnlysyqgnkhvlrldiramsysqeaiettlkeiirfnipNAEITIRsNEKAGYLFTppDEGIVTT 375
                                       **************************************************96777755555555555567******* PP

                                       HHHHHHHHHTSCEEEEEESSSBHTHHHH..TTTEEEEEEESSGGCTTSTTTEEEHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20 139 laeaaeelfgekvelivsgpggtdarff..agiptvmifgpgsglaHspnEyvdledlekgikvlarll 205
                                       + +++e +   k e++  + g+ d+rff   g+  ++ fgp +g++H+pnEyvd+e+l+   +v+++++
  gi|242398168|ref|YP_002993592.1| 376 MLKILEGF-DQKAEPVEGP-GAADSRFFtpYGV-KAIDFGPKGGNIHGPNEYVDIESLKVLPDVYKEVA 441
                                       *****995.6567777777.********88888.4444**888*****************999999886 PP

>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   5.9e-08   0.00027      12     103 ..      71     176 ..      62     216 .. 0.84
   2 ?    1.5   0.0     0.047   2.1e+02     142     177 ..     390     423 ..     370     441 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 5.9e-08
                                       SEEEEEEEE--B-TTT................TCC.T---TTTTHHHHHHHHHHHHHCHHGGCCSSEEEEEEEESSC CS
                     Peptidase_M28  12 devlllgAHyDsvgvg................rgp.ifvGAdDnAsgvaalLelarvlaasgsrpkrgvrflffdaE 71 
                                       +  +l++AH+D v+v+                +   +   AdD +  ++++L + ++ +    +++ +v f++++ E
  gi|242398168|ref|YP_002993592.1|  71 KPKILFMAHFDVVPVNreewntepfklvikgnK-AyGRGSADDKGNVASVMLAIKELSKM---DLEGKVLFAVTGDE 143
                                       4579***********9*****999999996542.14556689999888888888777775...89************ PP

                                       SGSSHHHHHHHH.HHCCCTTEEEEEEECS-SSS CS
                     Peptidase_M28  72 EagllGSkafak.akpelkkiaavlnlDmvgsg 103
                                       E g + + + a+  ++e k  ++++n D vg +
  gi|242398168|ref|YP_002993592.1| 144 EIGGVLAMHIAEkLRDEGKMPEYMINADGVGMK 176
                                       ***********7655699999********9976 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.047
                                       ESSTT-STTHHHHTTT--EEEECTSSS-TTTTSTTS CS
                     Peptidase_M28 142 rsgrgrsDhspflkagvpvldlaetgfpevyHtprD 177
                                        +g+g  D + f+ +gv+++d+   + + ++H p+ 
  gi|242398168|ref|YP_002993592.1| 390 VEGPGAADSRFFTPYGVKAIDF--GPKGGNIHGPNE 423
                                       458999***************9..445555565554 PP

>> Peptidase_M42  M42 glutamyl aminopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.07   3.1e+02      11      25 ..      69      83 ..      61      85 .. 0.80
   2 !   16.3   0.0   8.5e-07    0.0038     132     215 ..     109     192 ..      94     209 .. 0.78
   3 ?   -0.0   0.0     0.079   3.5e+02     256     287 ..     400     431 ..     390     435 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.07
                                      TTSSEEEEEEE--B- CS
                     Peptidase_M42 11 ekepkvmiaAHmDei 25
                                      e +pk++++AH D +
  gi|242398168|ref|YP_002993592.1| 69 EGKPKILFMAHFDVV 83
                                      5799*********76 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 8.5e-07
                                       THHHHHHHHHHHHHHHHHCTSS-SSEEEEEEESTCTTTSHHHHHHHHHH--SEEEEEEEEEE-CSTTSTTTTSS.TT CS
                     Peptidase_M42 132 alDdragvavllellkelkeeeleatvylvatvqEEvGlrGaktsaekikpdiaiavDvtaagdtpgskekeak.lg 207
                                         Dd+  va ++ ++kel++ +le +v +++t  EE+G   a  +aek++ d+    + ++ +d  g+k   ++  g
  gi|242398168|ref|YP_002993592.1| 109 SADDKGNVASVMLAIKELSKMDLEGKVLFAVTGDEEIGGVLAMHIAEKLR-DEGKMPEYMINADGVGMKPIIRRrKG 184
                                       57************************************999999999954.66666677777777777766655667 PP

                                       S-CEEEEE CS
                     Peptidase_M42 208 kGpvirvk 215
                                        G++ir+ 
  gi|242398168|ref|YP_002993592.1| 185 FGVTIRMP 192
                                       77777765 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.079
                                       HTSTTTSEEEEEEEEEBSTTSTTEEEEHHHHH CS
                     Peptidase_M42 256 hltgegvptalisiptryiHspvevahlddle 287
                                        +t  gv+++  ++   +iH+p+e +++++l+
  gi|242398168|ref|YP_002993592.1| 400 FFTPYGVKAIDFGPKGGNIHGPNEYVDIESLK 431
                                       5677899*********************9986 PP

>> Aconitase_C  Aconitase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.4e-05      0.11      21      96 ..      33     117 ..      20     126 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.4e-05
                                       GCCGHCCHHHCCCGGTTTCCCCTTTSBBSEEEETTTTEEE.........EHHHHHHHHHHTT--EEEE--SSBTBS- CS
                       Aconitase_C  21 tdlkipkqfegtianiglgnelveekrankttdlddgeke.........dvvdaaerykkegaklvviagknfGeGS 88 
                                       + +  pk + +++   g++ el+e+  + +++++  + k+          v+ + e++++e+ klv+ ++k +G GS
  gi|242398168|ref|YP_002993592.1|  33 PSKDCPKFVMDILSSWGIETELIEKDGYYAVYGELGEGKPkilfmahfdVVPVNREEWNTEPFKLVIKGNKAYGRGS 109
                                       5555666666666777777777766655555555443344567777775677899********************** PP

                                       --THHHHH CS
                       Aconitase_C  89 SRehAAka 96 
                                       + ++   a
  gi|242398168|ref|YP_002993592.1| 110 ADDKGNVA 117
                                       98876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       270  (0.0150594); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 2878.98
//
Query:       gi|242398169|ref|YP_002993593.1|  [L=215]
Description: Phosphoribosyl transferase domain protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.4e-20   70.9   0.0    1.4e-19   70.2   0.0    1.3  1  Pribosyltran  Phosphoribosyl transferase domain


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 !   70.2   0.0   7.8e-24   1.4e-19      14     154 ..      17     152 ..       8     156 .. 0.78

  Alignments for each domain:
  == domain 1  score: 70.2 bits;  conditional E-value: 7.8e-24
                                       EEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-.EE-EEEEEE-TTT--EE........EE----TTSE CS
                      Pribosyltran  14 avarlaaeileeyngkpdvvvgiargGvpfakiladeLevp.layvrkvkyrpdgseeaargssdesrlledpagkk 89 
                                        +++ + +il+e n+ pdvvvg argG++ a  + d+L+++ l+ + ++      +++ +  ++       d++gkk
  gi|242398169|ref|YP_002993593.1|  17 WAKEGSIKILKE-NWIPDVVVGLARGGWVAARLYCDYLGIKeLVSIKVEHWGVTATPDGKARLKY--GTQYDFEGKK 90 
                                       455566678888.9************************966344444444444444444444433..5899****** PP

                                       EEEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE-HHHHHHHHHH-TTS.....EEEEEEE-S CS
                      Pribosyltran  90 VliVDDildtGgTllaalelLkekgpeevriavlvdkpateeevdknakrvfslspdnfvavvgf 154
                                       VliVDDi dtG +l+ a + +++k+p+e+++a+l+  +++++++d+   ++ ++   ++v++++f
  gi|242398169|ref|YP_002993593.1|  91 VLIVDDIADTGESLTLAKNYIESKNPAEIKVAALLVIKTSKFRPDY---FGEEIDWAWIVFPWNF 152
                                       ************************************9999999966...5554447788888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 1274.83
//
Query:       gi|242398170|ref|YP_002993594.1|  [L=109]
Description: hypothetical protein TSIB_0177 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 711.02
//
Query:       gi|242398171|ref|YP_002993595.1|  [L=323]
Description: ABC transporter, periplasmic binding protein [Thermococcus sibiricus MM 739]
Scores for complete 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  100.1   2.0    1.6e-28   99.9   2.0    1.1  1  ZnuA      Zinc-uptake complex component A periplasmic
    0.00034   20.1   0.0    0.00062   19.3   0.0    1.3  1  DUF4618   Domain of unknown function (DUF4618)


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 !   99.9   2.0   1.7e-32   1.6e-28       1     255 [.      27     282 ..      27     283 .. 0.83

  Alignments for each domain:
  == domain 1  score: 99.9 bits;  conditional E-value: 1.7e-32
                                       EEESSHHHHHHHHHHHGGGCEEEECS-TTSTTTT----HHHHHHHHHSSEEEESS.TTTSGTHHHHHHHHTTCCCE. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx. RF
                              ZnuA   1 VvattsplgdlvrqvaGdrvevtvLvppgadpHsyeptprdvrklaeAdllvyng.lelEtwldkllasssqatrv. 75 
                                       V++++ p++++vr+  G+ v+v+ Lvpp +dpH+y++tp++++k+++Ad+++++  l +E+ +++l ++ +   ++ 
  gi|242398171|ref|YP_002993595.1|  27 VITSIAPIAEIVREAFGESVQVEYLVPPSVDPHQYQLTPEQIEKIQKADVILTIAhLPVEEKIEEL-EKEG---VLk 99 
                                       89**************************************************98547788777777.3333...223 PP

                                       .EEEETTTTCCSEBCSS..............EST.GGGSHHHHHHHHHHHHHHHHHHTGGGHHHHHHHHHHHHHHHH CS
                                       .xxxxxxxxxxxxxxxx..............xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ZnuA  76 .evidlsegveeeeeee..............DpH.iWlspknaiamveniadaLveadpanadtyeanaaayiekLe 136
                                        ++++ ++      +++              +pH iWl+p+na a++e++++ L      +++ ++a++  +++k+e
  gi|242398171|ref|YP_002993595.1| 100 gKILEIEDY-----QRHgfrylperwynnkyNPHgIWLDPYNALAIAETTKESLKTR-YSGKNIFDAQYSLFKAKVE 170
                                       366654431.....11234456666677778***********************885.5699*************** PP

                                       HHHHHHHHHHTTSSGTEGEEEESSSTTHHHHHHTT-EEEEEESSSSS..HHHHHHHHHHHHHTT-SEEEEET.TS-T CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx.xxxx RF
                              ZnuA 137 eldaeireelaeipeekrklvtthdafgylarayglevagiagiste..aaqiaalieeikeagvkaifvep.lasp 210
                                       ++   +++    + e++   +   ++ +y  + +g+ev+++++ ++e  a+ + +l e++k  +v +  v++  + +
  gi|242398171|ref|YP_002993595.1| 171 TIILAYQKMN--LSEKQ--AIIELPSQQYALEWMGIEVIASIKPEEEipAKSVDELLEMAKTVDVIVYSVDSpESLK 243
                                       **99999873..45555..9*******************98877777*************99999999999977789 PP

                                       HHHHHHHHHHT-EEEEE-STSSSTSTTSTTSHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ZnuA 211 klaetlaeeagvkvatlysldslgdegsaetYidmmranleslke 255
                                       ++a +l +++gv  +++ +   +  e+    Y +++ +n  +++ 
  gi|242398171|ref|YP_002993595.1| 244 NAALELSRKTGVPAIEVST---IWSEK---EYTEVLIQNSANIVS 282
                                       99999999***99888888...44455...899999999988876 PP

>> DUF4618  Domain of unknown function (DUF4618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   6.9e-08   0.00062       4     118 ..     183     295 ..     181     299 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 6.9e-08
                           DUF4618   4 rkksleelkkheaeLtklnkeLvkeIqdtedstakkvrklLqqyeklktvisileksskkqleqakaeLqeweekee 80 
                                       +k+++ el +++ +L+    e ++ I+  e+  ak+v +lL+  +++  ++  ++  s + l++a  eL  ++   +
  gi|242398171|ref|YP_002993595.1| 183 EKQAIIELPSQQYALEWMGIEVIASIKPEEEIPAKSVDELLEMAKTVDVIVYSVD--SPESLKNAALELSRKTGVPA 257
                                       68999*************************************9999998887776..56789*************** PP

                           DUF4618  81 kklekLeqqleqlnakvqklqeelnvLstYkDkeYpvk 118
                                        +++ +  + e+ +  +q++ + ++  +tY  +e p +
  gi|242398171|ref|YP_002993595.1| 258 IEVSTIWSEKEYTEVLIQNSANIVSAFRTYIPQEVPSQ 295
                                       ********************************999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       962  (0.0536561); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2163.08
//
Query:       gi|242398172|ref|YP_002993596.1|  [L=301]
Description: ABC-type transport system, permease component [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.6e-39  133.9  31.3    7.1e-39  133.6  31.3    1.2  1  BPD_transp_2    Branched-chain amino acid transport system / 
  ------ inclusion threshold ------
        1.9    8.5   7.1       0.29   11.1   0.5    2.9  3  Gly-zipper_Omp  Glycine zipper


Domain annotation for each model (and alignments):
>> BPD_transp_2  Branched-chain amino acid transport system / permease component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.6  31.3   7.9e-43   7.1e-39       2     259 ..       9     264 ..       8     286 .. 0.89

  Alignments for each domain:
  == domain 1  score: 133.6 bits;  conditional E-value: 7.9e-43
                      BPD_transp_2   2 ilnlltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsllllallvallvgaavglllgllvl 78 
                                       ++  lt   +l+++++G +++  +aGv+n+g +g++++ a+  a+ +   +s ++++l+ +  +g+++g+l g++++
  gi|242398172|ref|YP_002993596.1|   9 LIGALTAMVPLVLTSVGATVSE-RAGVVNIGYEGILLMTAFFGAMFAEISGS-PWIGLIGGAFIGMLLGMLHGFITV 83 
                                       56789999**************.*****************************.************************ PP

                      BPD_transp_2  79 rlkvdeliitllllsvlvgltllll..tgitsgvkgqssvkellgfagallsflsavivllalllvlavllllrrtr 153
                                       +lk d++i +++++++++g++++     ++t g+ +++s  +++ +  +    ls   v+++++++++ +++l rt+
  gi|242398172|ref|YP_002993596.1|  84 YLKGDHVIPGIGVNLLALGVVAFGIpaYWGTAGQHQVPSNFRITPIIKTAYGSLS-PMVFVTIVIAVLTHWVLFRTP 159
                                       **********************775224666666666666666666666666664.456999*************** PP

                      BPD_transp_2 154 fGralravgeneeaaralGinvkrvklltfvisgalAglaGallalllgsipp.nigvglgfnaiaavvlGgagsll 229
                                       +G+++r vgen+eaa+alGinv+r+++l+ v ++ lAgl Ga++++   +  + + + g gf a+a +v  g+ ++l
  gi|242398172|ref|YP_002993596.1| 160 LGLRIRSVGENPEAADALGINVERYRFLATVYGATLAGLGGAFMSVDWLGTVTkQLSAGRGFIALANMVFSGW-NPL 235
                                       *********************************************876555556*******************.*** PP

                      BPD_transp_2 230 gtviGaliigvvksllltllgiptelarvl 259
                                        +++G++i+g+ ++ l+ ++   ++ ++++
  gi|242398172|ref|YP_002993596.1| 236 RALLGGFIFGFFDN-LSVWVRTTPAIQKIV 264
                                       **************.666666666666665 PP

>> Gly-zipper_Omp  Glycine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.2   0.1         2   1.8e+04      26      28 ..      10      12 ..       8      15 .. 0.48
   2 ?   11.1   0.5   3.3e-05      0.29       7      39 ..      47      79 ..      44      82 .. 0.89
   3 ?   -0.4   0.1      0.13   1.2e+03      31      40 ..     192     201 ..     183     206 .. 0.54

  Alignments for each domain:
  == domain 1  score: -4.2 bits;  conditional E-value: 2
                    Gly-zipper_Omp 26 iGA 28
                                      iGA
  gi|242398172|ref|YP_002993596.1| 10 IGA 12
                                      333 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 3.3e-05
                    Gly-zipper_Omp  7 AaaGaliGgavggrgtGaliGAavGaavGgliG 39
                                      A+ Ga ++ ++g + +G ++GA +G ++G l G
  gi|242398172|ref|YP_002993596.1| 47 AFFGAMFAEISGSPWIGLIGGAFIGMLLGMLHG 79
                                      899*********999**********99997655 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.13
                    Gly-zipper_Omp  31 GaavGgliGa 40 
                                       Ga++ gl Ga
  gi|242398172|ref|YP_002993596.1| 192 GATLAGLGGA 201
                                       3333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1828.24
//
Query:       gi|242398173|ref|YP_002993597.1|  [L=343]
Description: ABC transporter, ATP-binding protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      1e-40  139.6  31.4      1e-40  139.6  31.4    1.9  2  BPD_transp_2  Branched-chain amino acid transport system / pe


Domain annotation for each model (and alignments):
>> BPD_transp_2  Branched-chain amino acid transport system / permease component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.5     0.011     2e+02      56      72 ..      16      32 ..       8      44 .. 0.61
   2 !  139.6  31.4   5.6e-45     1e-40       4     267 ..      57     328 ..      54     329 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.011
                      BPD_transp_2 56 llallvallvgaavgll 72
                                      l+a+++++lvga++ ++
  gi|242398173|ref|YP_002993597.1| 16 LIAVIIGILVGAIILAF 32
                                      34444455554444444 PP

  == domain 2  score: 139.6 bits;  conditional E-value: 5.6e-45
                      BPD_transp_2   4 nlltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsllllallvallvgaavglllgllvlrl 80 
                                       ++l+ a+++ ++Al + l   ++G++n+g +g + +Ga++a++l + +++ +l++ll ++++g+a++++ +ll+++ 
  gi|242398173|ref|YP_002993597.1|  57 MTLSAATPIMLTALTFGLGA-KTGLFNIGGEGTVYFGAIAALILTNIWGN-ILMGLLGGIIAGIAWMAIPALLKVFR 131
                                       68999***************.****************************9.************************** PP

                      BPD_transp_2  81 kvdeliitllllsvlvgltlllltgitsgvkgqs.svkellgfagallsflsaviv..llalllvlavllllrrtrf 154
                                       +v+e+++t++l++v+++l+l++  + +  +k ++ ++  +l     +++ + +  +  ++ ++++l+++++l +t +
  gi|242398173|ref|YP_002993597.1| 132 GVNEVVSTIMLNWVAYFLALYIIIQKIPNPKDPNkTIAIPLSARFPIIIKGTELSWafAISVIAALVAYYILWHTTI 208
                                       ********************999888888887773555555555666666666666768889999************ PP

                      BPD_transp_2 155 GralravgeneeaaralGinvkrvklltfvisgalAglaGallalllgsipp.nigvg....lgfnaiaavvlGgag 226
                                       G+ lr+ g ne+aar++Gin+k++ +++fv++g+++glaGa+  +    +++ + g+     +gf++i + ++G + 
  gi|242398173|ref|YP_002993597.1| 209 GYELRVSGYNERAARYAGINPKKTVIWSFVLGGIMSGLAGAIEMMGRPPSYAiSQGMAniygYGFDGIGVSLVGRN- 284
                                       ******************************************99987777755333325555**************. PP

                      BPD_transp_2 227 sllgtviGaliigvvksllltllgi....ptelarvllgallilv 267
                                       ++lg+++ ++ +g++k+ + t+++i    p e+ rv++g++++ v
  gi|242398173|ref|YP_002993597.1| 285 HPLGIIFSGIFFGMLKA-GATAMQIeagvPLEMVRVVQGIIVVTV 328
                                       *****************.888888989999**********99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       694  (0.0387082); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 2203.06
//
Query:       gi|242398174|ref|YP_002993598.1|  [L=509]
Description: ABC transporter, ATP-binding protein [Thermococcus sibiricus MM 739]
Scores for complete 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-46  156.0   0.1    1.3e-26   93.8   0.0    2.2  2  ABC_tran     ABC transporter
    1.7e-08   34.6   0.1     0.0014   18.5   0.0    2.3  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    0.00062   19.7   3.6     0.0011   18.8   0.1    3.0  4  Bac_DnaA     Bacterial dnaA  protein
     0.0016   18.1   1.4      0.027   14.2   0.2    2.6  2  AAA_29       P-loop containing region of AAA domain
      0.009   15.7   0.1      0.052   13.3   0.0    2.2  2  AAA_30       AAA domain
  ------ inclusion threshold ------
      0.023   14.4   0.5       0.16   11.6   0.1    2.0  2  AAA_15       AAA ATPase domain
      0.024   15.1   0.6      0.024   15.1   0.6    2.0  2  AAA_23       AAA domain
      0.036   14.0   2.1       0.61   10.0   0.0    3.3  4  RsgA_GTPase  RsgA GTPase
      0.066   13.4   1.0        4.3    7.6   0.1    2.4  2  ArlS_N       ArlS sensor domain
       0.15   11.7   0.1       0.28   10.7   0.1    1.4  1  AAA_27       AAA domain
       0.21   11.9   0.8        2.3    8.5   0.6    2.6  2  AAA_22       AAA domain
       0.25   11.1   4.9         33    4.1   4.9    3.0  1  AAA_24       AAA domain
       0.59   10.6   2.5        2.7    8.4   0.7    2.8  2  AAA          ATPase family associated with various cellular a
       0.85    9.0   5.5         10    5.5   0.1    3.2  4  SMC_N        RecF/RecN/SMC N terminal domain
        2.1    8.1   5.0        5.6    6.7   0.2    3.5  5  PduV-EutP    Ethanolamine utilisation - propanediol utilisati
        2.6    7.6   4.7        9.1    5.8   0.0    2.8  3  cobW         CobW/HypB/UreG, nucleotide-binding domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.8   0.0   1.1e-29   1.3e-26       1     137 []      23     173 ..      23     173 .. 0.90
   2 !   60.3   0.0   2.4e-19   2.7e-16       2     136 ..     278     434 ..     277     435 .. 0.90

  Alignments for each domain:
  == domain 1  score: 93.8 bits;  conditional E-value: 1.1e-29
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltv 76 
                                       lk v++++k+ge+++++GenGaGK+tL+k+l+g+l+pt G+i +++k+++  ++   l + ig+++q+ +l +    
  gi|242398174|ref|YP_002993598.1|  23 LKGVDFSVKQGEIHGLLGENGAGKTTLMKILSGMLHPTDGKIFVNNKEVRFkTPADALANGIGMVHQHFTLVDVFDG 99 
                                       789**********************************************998999*************999999887 PP

                                       HHH.................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxx.................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  77 ren.................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                         n                 ++ ++++k+++ l+ +   d +v    ++L  G +qr+++ ++l ++ ++l+lDEpt
  gi|242398174|ref|YP_002993598.1| 100 LHNiilgmeghglfskidveKAMKKLQKLMDDLNFQVPLDVPV----ETLPVGVQQRIEILKTLYRDVDVLILDEPT 172
                                       788899*******887666555555777777777777666666....*****************************9 PP

                                       T CS
                                       x RF
                          ABC_tran 137 a 137
                                       a
  gi|242398174|ref|YP_002993598.1| 173 A 173
                                       7 PP

  == domain 2  score: 60.3 bits;  conditional E-value: 2.4e-19
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS...--S-TTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx...xxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqe...pqlfpel 74 
                                       k +++++k+ge+ +i G  G G + L+++++gl k ++G++ l+gk+++   ++e ++  ++ +p++     l  e+
  gi|242398174|ref|YP_002993598.1| 278 KGLTFNVKAGEIFGIAGVEGNGQTELIEAISGLRKIEKGKVILNGKEITGrPPKELYDLGVAHIPEDrihMGLVAEM 354
                                       789**********************************************9889999***********99999***** PP

                                       BHHHH.....................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEE CS
                                       xxxxx.....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  75 tvren.....................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkll 130
                                       +v en                     +++e+++k+++ ++        ++   +sLSgG +q++ +ar   k+p+++
  gi|242398174|ref|YP_002993598.1| 355 SVTENsilglhwretfrgpigmlrwnKAKEHAAKIVKDFEVLV---PSIDAPVKSLSGGNQQKLIVARETSKQPEFI 428
                                       *************999999999987666666777777777544...4555556************************ PP

                                       EEESTT CS
                                       xxxxxx RF
                          ABC_tran 131 llDEpt 136
                                       ++  pt
  gi|242398174|ref|YP_002993598.1| 429 IASQPT 434
                                       998887 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 !   18.5   0.0   1.2e-06    0.0014       2      25 ..      36      59 ..      35      91 .. 0.73
   2 !   13.8   0.0   3.4e-05     0.039     232     297 ..     140     202 ..     115     207 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.2e-06
                            AAA_21  2 nvliGpNgsGKSnLLdaldllarl 25
                                       +l G Ng+GK++L+++l+++   
  gi|242398174|ref|YP_002993598.1| 36 HGLLGENGAGKTTLMKILSGMLHP 59
                                      689***************999653 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 3.4e-05
                            AAA_21 232 lparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                       +p+  l+ G+++ + +l  l+r+    ++l++DEp + L P  +++l+++lk+l++ g  +i+ +H
  gi|242398174|ref|YP_002993598.1| 140 VPVETLPVGVQQRIEILKTLYRDV---DVLILDEPTAVLTPIEVKELFDVLKKLKSQGKTIIFISH 202
                                       667777888888889999999999...9***********************888888********* PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.2       1.6   1.8e+03      40      54 ..      39      53 ..      37      61 .. 0.85
   2 !   18.8   0.1   9.9e-07    0.0011      86     161 ..     151     224 ..     143     262 .. 0.76
   3 ?   -0.7   0.0      0.94     1e+03     137     168 ..     326     359 ..     292     363 .. 0.65
   4 ?   -3.5   0.0       6.8   7.6e+03     124     166 ..     450     490 ..     443     498 .. 0.59

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.6
                                      E-SSSSSHHHHHHHH CS
                          Bac_DnaA 40 ygevGlGktHLlkai 54
                                       ge G Gkt L+k +
  gi|242398174|ref|YP_002993598.1| 39 LGENGAGKTTLMKIL 53
                                      6999********865 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 9.9e-07
                                       T-HHHHHHHHTT-SEEEEE-GGGGTT-HHHHHHHHHHHHHHHTTT-EEEEEESS-TTT-SS--HHHHHHHHSSEEE CS
                          Bac_DnaA  86 kkaeefkeklrkvDvLliDDiqflagkektqeelfhtfnalleegkqvvlssDrsPkeleeledrlrsrfeaGlvv 161
                                       +++e +k  +r+vDvL++D+   + +  ++ +elf ++ +l  +gk +++ s +  ke+ e++dr+    +  l+ 
  gi|242398174|ref|YP_002993598.1| 151 QRIEILKTLYRDVDVLILDEPTAVLTPIEV-KELFDVLKKLKSQGKTIIFISHKL-KEVMEITDRVTVLRKGELIG 224
                                       577889**************8887776655.689******************986.77888999986544433443 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.94
                                       ESS-TTT-SS--.HHH.HHHHHSSEEEE-----H CS
                          Bac_DnaA 137 sDrsPkeleele.drl.rsrfeaGlvvdieppdl 168
                                       + r+Pkel +l  +++ + r+++Glv++++ +++
  gi|242398174|ref|YP_002993598.1| 326 TGRPPKELYDLGvAHIpEDRIHMGLVAEMSVTEN 359
                                       4588888888752344367999999999887665 PP

  == domain 4  score: -3.5 bits;  conditional E-value: 6.8
                                       HHHHTTT-EEEEEESS-TTT-SS--HHHHHHHHSSEEEE---- CS
                          Bac_DnaA 124 nalleegkqvvlssDrsPkeleeledrlrsrfeaGlvvdiepp 166
                                        +l +e+k v+l s     e+ +l dr+   +e G  v i +p
  gi|242398174|ref|YP_002993598.1| 450 IKLRDENKAVLLVSADL-DEVLQLSDRMAIMYE-GKFVGIVKP 490
                                       56778888877655433.456667777765544.444555555 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.2   2.4e-05     0.027      14      55 ..      25      67 ..      20      69 .. 0.77
   2 ?    2.0   0.1      0.15   1.7e+02      15      43 ..     280     308 ..     275     320 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.4e-05
                            AAA_29 14 ghtieidlkgatlltGpsGsGKSTllDAiqalLvpak.kvrfN 55
                                      g ++++++ +++ l G++G+GK+Tl+  ++ +L p+  k+  N
  gi|242398174|ref|YP_002993598.1| 25 GVDFSVKQGEIHGLLGENGAGKTTLMKILSGMLHPTDgKIFVN 67
                                      5566777555999*************88888888887666555 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.15
                            AAA_29  15 htieidlkgatlltGpsGsGKSTllDAiq 43 
                                        t++++  +++ ++G  G+G + l+ Ai+
  gi|242398174|ref|YP_002993598.1| 280 LTFNVKAGEIFGIAGVEGNGQTELIEAIS 308
                                       566777555999**************997 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   4.6e-05     0.052      19     121 ..      34     199 ..      26     203 .. 0.66
   2 ?   -1.3   0.2       1.4   1.6e+03      20      51 ..     289     320 ..     276     325 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.6e-05
                            AAA_30  19 rvavltGpAGtGKttalkalreaweaa.g......grviglAptgkaAkvLa......................... 63 
                                        ++ l G  G+GKtt++k l  +++   g      ++v   +p  + A+ ++                         
  gi|242398174|ref|YP_002993598.1|  34 EIHGLLGENGAGKTTLMKILSGMLHPTdGkifvnnKEVRFKTPADALANGIGmvhqhftlvdvfdglhniilgmegh 110
                                       478899**************999998856888888888888888888888886666666666665555555555332 PP

                            AAA_30  64 ...e..elgieastiakllkrlk.......................grarlepg.tllivDEagmv....dtkqlaa 107
                                             +++ + + ++kl++ l+                       +  +l ++ ++li DE   v      k+l +
  gi|242398174|ref|YP_002993598.1| 111 glfSkiDVEKAMKKLQKLMDDLNfqvpldvpvetlpvgvqqrieilK--TLYRDvDVLILDEPTAVltpiEVKELFD 185
                                       22211122224444555554444888888888888888888887532..4445558888888777766666677777 PP

                            AAA_30 108 llkaaekagakvil 121
                                       +lk+++++g ++i+
  gi|242398174|ref|YP_002993598.1| 186 VLKKLKSQGKTIIF 199
                                       77777777777776 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.4
                            AAA_30  20 vavltGpAGtGKttalkalreaweaaggrvig 51 
                                       +  + G+ G G t +++a+  + + ++g+vi+
  gi|242398174|ref|YP_002993598.1| 289 IFGIAGVEGNGQTELIEAISGLRKIEKGKVIL 320
                                       5668899999******9999999988888875 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00014      0.16      25      65 ..      35      71 ..      21      82 .. 0.77
   2 ?    0.4   0.1      0.39   4.3e+02     323     362 ..     162     200 ..     114     204 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00014
                            AAA_15 25 ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedl 65
                                      +  l G+N++GK++++++l  +l  +    + +i+++++++
  gi|242398174|ref|YP_002993598.1| 35 IHGLLGENGAGKTTLMKILSGMLHPT----DGKIFVNNKEV 71
                                      55688***************999988....56666666655 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.39
                            AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnktQviit 362
                                       + ++l+++EP a L p   k+l++ lk+l +++kt +i+ 
  gi|242398174|ref|YP_002993598.1| 162 DVDVLILDEPTAVLTPIEVKELFDVLKKLKSQGKT-IIFI 200
                                       4578999**********************999984.4444 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.6   2.1e-05     0.024      15      44 ..      26      58 ..       7     209 .. 0.85
   2 ?   -2.8   0.5       6.8   7.6e+03      20      40 ..     288     308 ..     277     310 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.1e-05
                            AAA_23 15 idF...skgltlItGpNGaGKTTildAiklaLy 44
                                      +dF      +  + G+NGaGKTT++  +  +L 
  gi|242398174|ref|YP_002993598.1| 26 VDFsvkQGEIHGLLGENGAGKTTLMKILSGMLH 58
                                      45544444678899***********98877665 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 6.8
                            AAA_23  20 gltlItGpNGaGKTTildAik 40 
                                        ++ I G  G G T +++Ai 
  gi|242398174|ref|YP_002993598.1| 288 EIFGIAGVEGNGQTELIEAIS 308
                                       5999***************95 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   0.00054      0.61      91     124 ..      24      58 ..      11      80 .. 0.78
   2 ?   -0.9   0.0       1.2   1.3e+03      52      98 ..     112     161 ..     107     168 .. 0.69
   3 ?    0.9   0.1      0.34   3.8e+02      87     130 ..     274     318 ..     254     328 .. 0.82
   4 ?   -3.0   0.0       5.2   5.8e+03      58      85 ..     439     465 ..     397     478 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00054
                                       HHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-- CS
                       RsgA_GTPase  91 eelkellkd.ktsvlvGqSGvGKStLinallpele 124
                                       + +   +k+ ++  l+G+ G+GK+tL++ l + l+
  gi|242398174|ref|YP_002993598.1|  24 KGVDFSVKQgEIHGLLGENGAGKTTLMKILSGMLH 58 
                                       55556666669999**************9998765 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.2
                                       EEE-GGG--HHHHHHHHHHHHH...HTTSEEEE--TTTHTTHHHHHHHCT CS
                       RsgA_GTPase  52 vlnKiDlleeeeeleelkeele...algyevllvsaktkegleelkellk 98 
                                       +++KiD+ + +++l++l+++l+    l+++v ++ +  ++ +e lk+l +
  gi|242398174|ref|YP_002993598.1| 112 LFSKIDVEKAMKKLQKLMDDLNfqvPLDVPVETLPVGVQQRIEILKTLYR 161
                                       58999999999988888877652225667777777776677766666555 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.34
                                       HTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S-- CS
                       RsgA_GTPase  87 kegleelkellkd.ktsvlvGqSGvGKStLinallpelelktgev 130
                                       +++++ l+ ++k  ++  ++G  G G + Li+a+ +  +++ g+v
  gi|242398174|ref|YP_002993598.1| 274 QDAVKGLTFNVKAgEIFGIAGVEGNGQTELIEAISGLRKIEKGKV 318
                                       466777888888779999****************99877776665 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 5.2
                                       G--HHHHHHHHHHHHHHTTSEEEE--TT CS
                       RsgA_GTPase  58 lleeeeeleelkeelealgyevllvsak 85 
                                       ++++e  ++++  +l++ + +vllvsa+
  gi|242398174|ref|YP_002993598.1| 439 VASTEY-IRNYLIKLRDENKAVLLVSAD 465
                                       444444.555555555555555555544 PP

>> ArlS_N  ArlS sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.1    0.0038       4.3       8      73 ..     151     217 ..     147     251 .. 0.75
   2 ?    4.3   0.1     0.039        43      14      71 ..     419     477 ..     411     499 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0038
                            ArlS_N   8 qEeeeversltevttyleekkls.lteeelqesdsllekinekdqtirildkdgkevlevsndspei 73 
                                       q  e ++   ++v  ++  ++++ lt+ e++e  ++l+k++ +  ti+ + ++ kev+e++++++  
  gi|242398174|ref|YP_002993598.1| 151 QRIEILKTLYRDVDVLILDEPTAvLTPIEVKELFDVLKKLKSQGKTIIFISHKLKEVMEITDRVTVL 217
                                       5555666777899999999999999***********************************8876654 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.039
                            ArlS_N  14 ersltevttyleekkls.lteeelqesdsllekinekdqtirildkdgkevlevsndsp 71 
                                       +++ ++ +  + +++++ ++ +  ++ +++l k+ +++  + +  +d +evl+ s++++
  gi|242398174|ref|YP_002993598.1| 419 RETSKQPEFIIASQPTRgVDVASTEYIRNYLIKLRDENKAVLLVSADLDEVLQLSDRMA 477
                                       5566666667788888899999999*****************************99765 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00025      0.28      19      50 ..      26      57 ..      19      69 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00025
                            AAA_27 19 ldfsaeeadlhliyGpNEAGKstalrAisdll 50
                                      +dfs ++ ++h ++G N AGK+t+++ +s +l
  gi|242398174|ref|YP_002993598.1| 26 VDFSVKQGEIHGLLGENGAGKTTLMKILSGML 57
                                      899*9********************9888877 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.6    0.0021       2.3      10      30 ..      38      58 ..      31     208 .. 0.68
   2 ?   -2.3   0.0       4.3   4.8e+03      38      85 ..     218     266 ..     193     272 .. 0.61

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0021
                            AAA_22 10 vtGesGtGKTtllrrlleqld 30
                                      + Ge G+GKTtl++ l   l+
  gi|242398174|ref|YP_002993598.1| 38 LLGENGAGKTTLMKILSGMLH 58
                                      67************9988885 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4.3
                            AAA_22  38 erpevvfvtlpsstsskdllre.llralglelkaerlsseellealeqa 85 
                                       ++ e++    +++ts+k+l+++ + r++ l+ ++++++ e  + ++++ 
  gi|242398174|ref|YP_002993598.1| 218 RKGELIGTVNTNETSPKELAKMmVGREVVLRIEKPPKEAENPVLQVQDL 266
                                       5556666666788889999554155666666666666666666666655 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   4.9      0.03        33       7      77 ..      38     174 ..      35     239 .. 0.57

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.03
                            AAA_24   7 iyGpsgiGKTtlakel.......gpkplfi............................dtekGlksldadkfpdie. 47 
                                       + G++g+GKTtl+k l           +f+                            d+++Gl+++          
  gi|242398174|ref|YP_002993598.1|  38 LLGENGAGKTTLMKILsgmlhptDG-KIFVnnkevrfktpadalangigmvhqhftlvDVFDGLHNI--------Il 105
                                       7899999999999998666665322.22223444444444444444444444444444333333222........02 PP

                            AAA_24  48 ..................swedfldevvel.....................aaeladyktlviDtidel 77 
                                                         ++++++d++++                      ++ ++d ++l++D  + +
  gi|242398174|ref|YP_002993598.1| 106 gmeghglfskidvekamkKLQKLMDDLNFQvpldvpvetlpvgvqqrieilKTLYRDVDVLILDEPTAV 174
                                       222223333333333333444444444444666666666666666666666666666666666665554 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 ?    8.4   0.7    0.0024       2.7       3      35 ..      38      72 ..      37     207 .. 0.60
   2 ?   -1.9   0.0       3.8   4.3e+03       4      22 ..     293     311 ..     291     335 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0024
                                      EESSTTSSHHHHHHHHHHHHTHE..EEEEETTTCS CS
                               AAA  3 lyGppGtGKTllakavakelgve..fleisgsell 35
                                      l G  G GKT+l+k +   l+ +   + ++ +e++
  gi|242398174|ref|YP_002993598.1| 38 LLGENGAGKTTLMKILSGMLHPTdgKIFVNNKEVR 72
                                      789**************999522222333333333 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.8
                                       ESSTTSSHHHHHHHHHHHH CS
                               AAA   4 yGppGtGKTllakavakel 22 
                                        G  G G T l++a+    
  gi|242398174|ref|YP_002993598.1| 293 AGVEGNGQTELIEAISGLR 311
                                       6888999999999987654 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   0.1    0.0093        10      25      44 ..      34      53 ..      12      69 .. 0.76
   2 ?    4.3   0.0     0.021        23     161     208 ..     165     214 ..     158     224 .. 0.75
   3 ?   -0.5   0.2      0.61   6.8e+02      27      45 ..     290     308 ..     277     324 .. 0.87
   4 ?   -2.9   0.0       3.3   3.7e+03     134     143 ..     404     413 ..     380     477 .. 0.66

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0093
                                      SEEEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 25 sftaivGpNGSGKsnlldAi 44
                                      ++  ++G+NG+GK+ l+  +
  gi|242398174|ref|YP_002993598.1| 34 EIHGLLGENGAGKTTLMKIL 53
                                      477899*********99765 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.021
                                       EEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-.SCE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx.xxx RF
                             SMC_N 161 lyllDeidaaLDeknvkkvaellkekskn.aQfivislreemleka.dkl 208
                                       + +lDe  a L   +vk++ ++lk+ +++   +i is++ + + +  d++
  gi|242398174|ref|YP_002993598.1| 165 VLILDEPTAVLTPIEVKELFDVLKKLKSQgKTIIFISHKLKEVMEItDRV 214
                                       679*********************99887466777999865544441444 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.61
                                       EEEEESTTSSHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxx RF
                             SMC_N  27 taivGpNGSGKsnlldAil 45 
                                         i G  G G + l++Ai+
  gi|242398174|ref|YP_002993598.1| 290 FGIAGVEGNGQTELIEAIS 308
                                       5699*************95 PP

  == domain 4  score: -2.9 bits;  conditional E-value: 3.3
                                       TTCS-HHHHH CS
                                       xxxxxxxxxx RF
                             SMC_N 134 kelLSgGekt 143
                                        ++LSgG+++
  gi|242398174|ref|YP_002993598.1| 404 VKSLSGGNQQ 413
                                       5566666543 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.2     0.005       5.6       6      23 ..      38      55 ..      35      78 .. 0.90
   2 ?   -1.9   0.0       2.3   2.6e+03      67     113 ..      84     130 ..      59     134 .. 0.73
   3 ?    0.3   0.1      0.48   5.4e+02      39     102 ..     166     232 ..     149     247 .. 0.72
   4 ?   -3.4   0.0       6.4   7.2e+03       8      22 ..     294     308 ..     286     311 .. 0.55
   5 ?   -0.3   0.0       0.7   7.9e+02      57     102 ..     449     494 ..     439     502 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.005
                         PduV-EutP  6 liGkvgsGKttLtqalkg 23
                                      l+G+ g+GKttL++ l+g
  gi|242398174|ref|YP_002993598.1| 38 LLGENGAGKTTLMKILSG 55
                                      79************9987 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.3
                         PduV-EutP  67 ialvqdateeesvfppgfasvfnkeviGiitkidlaedeenieavee 113
                                       i++v++  +   vf      ++  e  G+  kid+ + ++++++  +
  gi|242398174|ref|YP_002993598.1|  84 IGMVHQHFTLVDVFDGLHNIILGMEGHGLFSKIDVEKAMKKLQKLMD 130
                                       55555555555566656666666677789999999999988887655 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.48
                         PduV-EutP  39 eviDtPGey...lenrklysalivtsaeadvialvqdateeesvfppgfasvfnkeviGiitkidla 102
                                        ++D P      +e ++l  +l+ +  + + i ++ +  +e   +++ ++ + + e+iG +   +++
  gi|242398174|ref|YP_002993598.1| 166 LILDEPTAVltpIEVKELFDVLKKLKSQGKTIIFISHKLKEVMEITDRVTVLRKGELIGTVNTNETS 232
                                       5555555432226889999999999999999999999999999999999998888999988655554 PP

  == domain 4  score: -3.4 bits;  conditional E-value: 6.4
                         PduV-EutP   8 GkvgsGKttLtqalk 22 
                                       G  g G+t L +a++
  gi|242398174|ref|YP_002993598.1| 294 GVEGNGQTELIEAIS 308
                                       445556666666555 PP

  == domain 5  score: -0.3 bits;  conditional E-value: 0.7
                         PduV-EutP  57 livtsaeadvialvqdateeesvfppgfasvfnkeviGiitkidla 102
                                       li +  e + + lv +  +e   +++ +a + + + +Gi+   +++
  gi|242398174|ref|YP_002993598.1| 449 LIKLRDENKAVLLVSADLDEVLQLSDRMAIMYEGKFVGIVKPEEVT 494
                                       5666667778888888888889999999999999999998665555 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0    0.0082       9.1       4      21 ..      37      54 ..      34      96 .. 0.80
   2 ?   -1.1   0.1       1.1   1.3e+03      91      99 ..     172     180 ..     111     246 .. 0.53
   3 ?    2.6   0.3      0.08        90       3      34 ..     290     321 ..     288     327 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0082
                                      EEEESTTCCHHHHHHHHH CS
                              cobW  4 vltGflGsGKTtLlnhll 21
                                      +l G  G+GKTtL++ l 
  gi|242398174|ref|YP_002993598.1| 37 GLLGENGAGKTTLMKILS 54
                                      677889*******98765 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.1
                                       CTTTTHHHH CS
                              cobW  91 tGlaePapv 99 
                                       t +++P +v
  gi|242398174|ref|YP_002993598.1| 172 TAVLTPIEV 180
                                       334444444 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.08
                                       EEEEESTTCCHHHHHHHHHCT--SS-EEEEES CS
                              cobW   3 tvltGflGsGKTtLlnhllenraglklavivN 34 
                                       ++++G  G G T L++++   r+ +k  vi+N
  gi|242398174|ref|YP_002993598.1| 290 FGIAGVEGNGQTELIEAISGLRKIEKGKVILN 321
                                       6799***************9999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (509 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       756  (0.0421663); expected 358.6 (0.02)
Passed bias filter:                      662  (0.0369234); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); 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: 0.65u 0.33s 00:00:00.98 Elapsed: 00:00:00.47
# Mc/sec: 3249.88
//
Query:       gi|242398175|ref|YP_002993599.1|  [L=414]
Description: sugar binding protein [Thermococcus sibiricus MM 739]
Scores for 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-53  180.8   2.5    4.8e-53  180.1   2.5    1.3  1  Bmp       ABC transporter substrate-binding protein PnrA-like
  ------ inclusion threshold ------
      0.053   12.9   2.2      0.083   12.3   2.2    1.2  1  Not3      Not1 N-terminal domain, CCR4-Not complex component
       0.18   11.9   0.5       0.53   10.4   0.0    2.0  2  LPD11     Large polyvalent protein-associated domain 11


Domain annotation for each model (and alignments):
>> Bmp  ABC transporter substrate-binding protein PnrA-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.1   2.5     8e-57   4.8e-53       3     286 ..      38     340 ..      36     353 .. 0.88

  Alignments for each domain:
  == domain 1  score: 180.1 bits;  conditional E-value: 8e-57
                                       EEEEECSS-TTTSCHHHHHHHHHHHHHHHCTTEEEEEEEEC.GGGHHHHHHHHHHCTT.-SEEEEESCCHHHHHHHH CS
                               Bmp   3 kvavlvegtidDksfnessyeGirrlkkeqnieliskesslltdedyiadlknlkeeg.sdlivatgfalqdalqev 78 
                                       +++v ++g + D sfn ++y G ++++k++n+e+++ +s +  ++dy+ +l+ l++ g +d+iva+gf+++da+++v
  gi|242398175|ref|YP_002993599.1|  38 VAVVYDVGGRGDLSFNDMAYLGASKAAKDFNLEIKEVQSNT--ESDYLPNLRSLAQTGeYDIIVAVGFMMTDAVIQV 112
                                       68999******************************999999..8********9988655****************** PP

                                       HHH-TTS-EEEESS--TT-STTEEEEEE-HHHHHHHHHHHHHHHHHCTTTTEEC...SS-SCCCHHCHHHHHHHH.. CS
                               Bmp  79 ssdfpkvkFliiDavvekeyknvlsvaFrseegaFLaGvaaAlmsktnkigfvg...GveipvvksfingFeaGi.. 150
                                       +++fp++kF+i+D++++++  nv+s+ F+++eg+ L G +a+l+++   +  vg   G+eipv+ +f+ g+  G+  
  gi|242398175|ref|YP_002993599.1| 113 ADEFPDQKFAIVDGFIPDKP-NVVSILFKENEGSALIGALAGLIAANDGKDKVGivlGIEIPVLYKFEGGYHFGVvw 188
                                       *******************5.***********************9987777777777******************44 PP

                                       ......HHH..-TT-EEEEEE-SSSS-HHHHHHHHHHHHHCT--EEEEE-GGGHHHHHHHHHHHCHCT.......EE CS
                               Bmp 151 ......kyv..npdievvvkvagtfsDakkgkslAsslykegvdvifpaagkagkgvieaakelglsn.......yv 212
                                             +++  + +iev + ++g+f D++kgk++A+    +g+ +i+++ag+ g gv++a+ e   s+       ++
  gi|242398175|ref|YP_002993599.1| 189 aedyykQKTgnDVNIEVLYTYTGSFTDPAKGKTAAQAQLGQGAWIIYQVAGAVGLGVFDAVDEYLESQgkemgppFA 265
                                       4433332223245799999******************************************99887777889***** PP

                                       EEEES--CGCSTTCCEEEEEEEHHHHHHHHHHHHHCCT---TTEEEEE-CCCTSEEE-...S--TCCHHHHCHHHHH CS
                               Bmp 213 Igvdkdqsylapenvitsiiknvedlvvsiiekvakgevlaggevitlglkegvvgld...eesdvledekvkeqlk 286
                                       +gvd+ q  + p  +i s +k v+  v+  +e ++kg+  ++g+++ lgl+eg+vg++   ++ +++++ + + + +
  gi|242398175|ref|YP_002993599.1| 266 VGVDSAQDWIKPGVIIASMMKRVDVGVYRTVEMAVKGN--WQGGIMELGLNEGGVGVStieDVREIFNSLPEDTKQQ 340
                                       ******************99999999999999999999..9*****************8985555554443333322 PP

>> Not3  Not1 N-terminal domain, CCR4-Not complex component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   2.2   1.4e-05     0.083      81     155 ..     322     395 ..     320     413 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.4e-05
                              Not3  81 liEeamerFkavEkesKtKafSkeglakaaaekldpkekekeearewlkdaideLneqvekleaeieklsskkkk 155
                                       +iE+  e F ++  ++K  +  + gl+ +++e   + e++++++ +w+ +a++eL++++++ e ei +  ++++ 
  gi|242398175|ref|YP_002993599.1| 322 TIEDVREIFNSLPEDTKQQKLEELGLN-SEEELFTKLEETRSQVPDWIWQAVSELESKIKSGEIEIPSALTSEQI 395
                                       7999999********************.333345999****************************9876555433 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 ?   10.4   0.0   8.9e-05      0.53      36      57 ..     321     342 ..     309     353 .. 0.86
   2 ?   -2.7   0.0       1.1   6.4e+03      57      64 ..     390     397 ..     385     411 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 8.9e-05
                             LPD11  36 eqieemkelynslpedeKPewl 57 
                                        +ie ++e++nslped K + l
  gi|242398175|ref|YP_002993599.1| 321 STIEDVREIFNSLPEDTKQQKL 342
                                       58***************98866 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.1
                             LPD11  57 ltleqiae 64 
                                       lt eqi+ 
  gi|242398175|ref|YP_002993599.1| 390 LTSEQIEA 397
                                       55555543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       754  (0.0420548); expected 358.6 (0.02)
Passed bias filter:                      638  (0.0355848); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.52
# Mc/sec: 2417.05
//
Query:       gi|242398176|ref|YP_002993600.1|  [L=153]
Description: hypothetical protein TSIB_0183 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.50
# Mc/sec: 918.40
//
Query:       gi|242398177|ref|YP_002993601.1|  [L=454]
Description: Phosphoglucomutase/phosphomannomutase, C-terminal domain family, partial [Thermococcus sibiricus MM 739]
Scores for complete 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-46  155.4   0.0    1.3e-45  154.5   0.0    1.4  1  PGM_PMM_I    Phosphoglucomutase/phosphomannomutase, alpha/bet
    8.7e-21   74.5   0.0    2.2e-20   73.2   0.0    1.7  1  PGM_PMM_II   Phosphoglucomutase/phosphomannomutase, alpha/bet
    4.3e-19   68.8   0.0      1e-18   67.5   0.0    1.6  1  PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/bet
    1.1e-07   31.9   0.0    2.8e-07   30.6   0.0    1.6  1  PGM_PMM_IV   Phosphoglucomutase/phosphomannomutase, C-termina
  ------ inclusion threshold ------
      0.015   15.4   0.3      0.075   13.2   0.1    2.3  3  CinA_KH      Damage-inducible protein CinA KH domain


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 !  154.5   0.0   3.5e-49   1.3e-45       2     137 ..       8     138 ..       7     139 .. 0.97

  Alignments for each domain:
  == domain 1  score: 154.5 bits;  conditional E-value: 3.5e-49
                                       GGBBTTCEEEECCHCTBSCCHHHHHHHHHHHHCHHCSTS-EEEEEE-S-TTHHHHHHHHHHHHHCCT-CEEEEEEB- CS
                         PGM_PMM_I   2 qkfgtsGlRgkvgegeltpelveklgqaiaeylkaeakkkkvvvGrDtRvssrelaealaaglaanGvevillgllp 78 
                                       ++fgtsG+R +v+ + ltp+l++k+g+a+++yl +    +kvvvG+DtR+s+++l++al++gl+++Gv+vi+++l p
  gi|242398177|ref|YP_002993601.1|   8 KYFGTSGIREVVN-ERLTPDLALKVGKALGTYLGE----GKVVVGKDTRTSGEMLKNALISGLLSTGVDVIDIDLSP 79 
                                       68***********.55******************9....9************************************* PP

                                       HHHHHHHHHHCCECEEEEE--TTS-TTCCCEEEEETTTCE--CHHHHHHHHHHCCT-EE CS
                         PGM_PMM_I  79 tPavsfairklkadagimitaSHnppeyngiKvylsnGgpispeveekIeaiiekeeea 137
                                       tP   fai+ ++adag+ itaSHnppeyngiKv ++nG+ +++e+e+++e+i+ek +++
  gi|242398177|ref|YP_002993601.1|  80 TPLTGFAIKLYEADAGVTITASHNPPEYNGIKVWQPNGMAYTSEMENELERILEKGKFQ 138
                                       ******************************************************99875 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 !   73.2   0.0     6e-24   2.2e-20       2     103 .]     156     251 ..     155     251 .. 0.92

  Alignments for each domain:
  == domain 1  score: 73.2 bits;  conditional E-value: 6e-24
                                       HHHHHGGGTS-HHHHHHHT-EEEEE-TT-TTHHHHHHHHHHTT-EEEES-----TT-TTSS----TT-TTTTHHHHG CS
                        PGM_PMM_II   2 aYiealkekvdseaikksglkvvidplhGaggeilkellkelgvdvvelnaepdpdfptkapnpeekealkllielv 78 
                                       +Yi++ +e +      ++g kvv+d+++Gag+ + + l +elg +vv+ln++p++ f+ +  +p++ ++l +l+++v
  gi|242398177|ref|YP_002993601.1| 156 EYIKKALEMIE----LSKGYKVVVDCGNGAGSILSPYLQRELGNKVVSLNSHPSGFFV-RELEPNA-KSLLALSKAV 226
                                       68888888887....67789***********************************999.7899999.8999999*** PP

                                       GGGG-SEEEEE-TTS-BEEEEETTE CS
                        PGM_PMM_II  79 kkegadlglafDgDaDRlgvvderG 103
                                       k+ gad+g+a+DgDaDR+gv+d++G
  gi|242398177|ref|YP_002993601.1| 227 KSLGADVGIAHDGDADRIGVIDDQG 251
                                       *********************9987 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 !   67.5   0.0   2.9e-22     1e-18       5     112 ..     259     362 ..     256     364 .. 0.91

  Alignments for each domain:
  == domain 1  score: 67.5 bits;  conditional E-value: 2.9e-22
                                       HHHHHHHHHHCHCSTTTCEEEEETTS-THHHHHHHHTT-EEEEESSSCHHHHHHHHHTTECEEEETTCEEEETTTBS CS
                       PGM_PMM_III   5 llallakylleeklkpgagvvktvmtslalervakklgiklvetkvGdkyvleemkeegavlGgEeSghiifldeat 81 
                                       +l l++ y+l++   +g ++++tv    al++++k lg+++ ++kvGd  v+e + +e+av+GgE Sg++i+++ + 
  gi|242398177|ref|YP_002993601.1| 259 MLSLISSYMLRK-FGKG-KIITTVDAGFALDDYIKPLGGEVARVKVGDVAVAEGIVRENAVFGGEPSGTWIIPQWNL 333
                                       67899999*995.4444.6********************************************************** PP

                                       S--HHHHHHHHHHHHHHHTS-HHHHHHHHHH CS
                       PGM_PMM_III  82 tkDGilaallvleilaetgkslselleellk 112
                                       t DGi a +lvle++ + g +lse+++  ++
  gi|242398177|ref|YP_002993601.1| 334 TPDGIFAGVLVLEMIDKLG-PLSEIAKG-VP 362
                                       ***************9987.*****954.44 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 !   30.6   0.0   7.7e-11   2.8e-07       6      72 ..     373     446 ..     369     448 .. 0.68

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 7.7e-11
                                       HCC-TT...EECCCCCTTHHCCCCCCCCGCCEEEE........EEEETTCCEEEEEEEESSHHHHHHHHHHHHHH CS
                        PGM_PMM_IV   6 veekak.vvaalaallkvasikeglkilledGrrla.......vRpSGTepllrvyvEaksdeelarlaeevael 72 
                                       +++++k +  ++ ++    ++ e  +i + dG+r++        RpSGTep  r+ +Ea++++++++l e+  e+
  gi|242398177|ref|YP_002993601.1| 373 CPNEKKaKAMEFIKREVL-ENFEYKRIIDIDGIRIEndewwilFRPSGTEPIMRITLEAHTKKKAEELMEKAEEV 446
                                       555555444444444333.445555666666666666666666************************99987665 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 ?   -3.0   0.0       2.3   8.3e+03      14      38 ..      19      44 ..      11      46 .. 0.63
   2 ?   -2.9   0.0       2.3   8.1e+03      38      55 ..     365     382 ..     362     390 .. 0.79
   3 ?   13.2   0.1   2.1e-05     0.075      34      68 ..     418     452 ..     405     454 .] 0.88

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.3
                                      HHHHHGG.GS-BSSSEEEEEEETTEE CS
                           CinA_KH 14 vaeklad.lidrenptlAiyakegev 38
                                      v+e+l + l+ +    l++y  eg+v
  gi|242398177|ref|YP_002993601.1| 19 VNERLTPdLALKVGKALGTYLGEGKV 44
                                      45555432666667788888888877 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.3
                                       EEEEEE...EEHHHHHHH CS
                           CinA_KH  38 vtvRltakaaneeeaeal 55 
                                       vt+R      ne++a+a+
  gi|242398177|ref|YP_002993601.1| 365 VTLRAKIPCPNEKKAKAM 382
                                       778888888888888887 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 2.1e-05
                                       ETTEEEEEEE...EEHHHHHHHHH....HHHHHTT CS
                           CinA_KH  34 kegevtvRltakaaneeeaealiapveeeirerlg 68 
                                       +  e   R+t +a ++++ae+l++++ee ++++++
  gi|242398177|ref|YP_002993601.1| 418 SGTEPIMRITLEAHTKKKAEELMEKAEEVVKRAIK 452
                                       5566678*********************9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); 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: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2814.64
//
Query:       gi|242398178|ref|YP_002993602.1|  [L=151]
Description: Flavodoxin [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-09   38.1   0.0    2.3e-09   37.6   0.0    1.2  1  Flavodoxin_5  Flavodoxin domain
    7.9e-09   35.4   0.0    1.8e-05   24.5   0.0    2.2  2  Flavodoxin_3  Flavodoxin domain


Domain annotation for each model (and alignments):
>> Flavodoxin_5  Flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.6   0.0   2.6e-13   2.3e-09       1      86 [.       4      85 ..       4     106 .. 0.85

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 2.6e-13
                      Flavodoxin_5  1 lilYsS.rdGqTkkiaeriaeelreegelvdvedvekesedlesydavvigasvyygkllpelakFvekhreaLstkpv 78
                                      li+Y S ++ +T+k+a+ +a++l++e  l++  ++  + e+l +yd + +g+++yy+k++++l k+ve   ++++ k+ 
  gi|242398178|ref|YP_002993602.1|  4 LIIYVSiHHRNTEKVAKIMAKTLEAE--LTKPWEI--KPEELLKYDLIGFGSGIYYWKHHRALFKLVES-LPRMKGKKA 77
                                      79999967789*************66..5555555..5689***************************5.9999**999 PP

                      Flavodoxin_5 79 alfsvslt 86
                                       +fs+  +
  gi|242398178|ref|YP_002993602.1| 78 FIFSTAGI 85
                                      99998765 PP

>> Flavodoxin_3  Flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0     2e-09   1.8e-05       2     111 ..       5     114 ..       4     127 .. 0.74
   2 !    9.2   0.0    0.0001      0.92     144     160 ..     128     144 ..     116     145 .. 0.88

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 2e-09
                      Flavodoxin_3   2 ilysS.ltGNTkkvAeaikealeeekeivsikeakekveeadvvfvGfwvdkgtadeealkfletl...knkkillf 74 
                                       i+y S +  NT+kvA+ ++++le+ +   + + + e++ ++d++  G  ++  +  +++ k++e+l   k+kk ++f
  gi|242398178|ref|YP_002993602.1|   5 IIYVSiHHRNTEKVAKIMAKTLEA-ELTKPWEIKPEELLKYDLIGFGSGIYYWKHHRALFKLVESLprmKGKKAFIF 80 
                                       555442567***************.44555555555599********99988888887777666543339******* PP

                      Flavodoxin_3  75 gTlGagkdseyakkilekvkallekn.nevlgeflcqG 111
                                        T+G++          +k++++l k+  e++gef c+G
  gi|242398178|ref|YP_002993602.1|  81 STAGINIPFINH----RKLRSALRKKgFEIVGEFSCRG 114
                                       ****97654333....455566666659********99 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0001
                      Flavodoxin_3 144 AasHPdeeDlekakevv 160
                                       +++HP+e+Dle+a++++
  gi|242398178|ref|YP_002993602.1| 128 SKEHPNEKDLENARRFA 144
                                       689**********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); 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: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 852.20
//
Query:       gi|242398179|ref|YP_002993603.1|  [L=245]
Description: Cyclopropane-fatty-acyl-phospholipid synthase superfamily [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-22   80.3   0.0    2.4e-22   79.4   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
    2.5e-22   79.3   0.0    3.6e-22   78.8   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    1.9e-19   70.1   0.0    3.8e-19   69.1   0.0    1.5  1  Methyltransf_11  Methyltransferase domain
    1.2e-15   57.8   0.0    1.6e-15   57.4   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    1.4e-14   54.6   0.0    2.3e-14   53.9   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
    2.8e-12   46.5   0.0    4.2e-12   45.9   0.0    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    2.6e-11   43.4   0.0    5.1e-11   42.4   0.0    1.5  1  MTS              Methyltransferase small domain
    6.1e-11   42.1   0.0    7.6e-11   41.8   0.0    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
    1.7e-09   37.4   0.0    2.3e-09   36.9   0.0    1.3  1  TehB             Tellurite resistance protein TehB
    2.9e-09   36.8   0.0    4.3e-09   36.3   0.0    1.2  1  NodS             Nodulation protein S (NodS)
    2.1e-07   30.9   0.0    3.3e-07   30.2   0.0    1.4  1  TPMT             Thiopurine S-methyltransferase (TPMT)
    1.1e-05   25.4   0.0    3.2e-05   23.9   0.0    1.7  1  Methyltransf_18  Methyltransferase domain
    1.3e-05   25.2   0.0    1.6e-05   24.9   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
    1.4e-05   24.4   0.0    1.8e-05   24.0   0.0    1.2  1  Pox_MCEL         mRNA capping enzyme
    1.6e-05   24.8   0.0    4.3e-05   23.4   0.0    1.6  2  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    4.6e-05   22.6   0.0    5.7e-05   22.3   0.0    1.1  1  RrnaAD           Ribosomal RNA adenine dimethylase
    0.00014   21.2   0.0    0.00042   19.7   0.0    1.7  1  Methyltransf_2   O-methyltransferase domain
    0.00019   20.9   0.0     0.0004   19.9   0.0    1.5  1  Methyltransf_4   Putative methyltransferase
    0.00026   20.8   0.0    0.00038   20.2   0.0    1.2  1  UPF0020          Putative RNA methylase family UPF0020
    0.00032   20.2   0.0    0.00064   19.2   0.0    1.6  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    0.00038   19.7   0.0    0.00056   19.2   0.0    1.3  1  N2227            N2227-like protein
     0.0019   17.7   0.1      0.003   17.0   0.1    1.2  1  adh_short        short chain dehydrogenase
     0.0025   17.4   0.0     0.0038   16.8   0.0    1.2  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
     0.0043   16.8   0.0     0.0055   16.5   0.0    1.2  1  Met_10           Met-10+ like-protein
     0.0083   15.1   0.0      0.031   13.2   0.0    1.8  2  Methyltransf_9   Protein of unknown function (DUF1698)
  ------ inclusion threshold ------
       0.01   15.4   0.0      0.024   14.2   0.0    1.5  2  Methyltransf_5   MraW methylase family
      0.011   15.3   0.1      0.017   14.7   0.1    1.2  1  MetW             Methionine biosynthesis protein MetW
      0.022   15.0   0.0      0.038   14.2   0.0    1.4  1  TrkA_N           TrkA-N domain
      0.031   14.3   0.0      0.058   13.4   0.0    1.5  1  DUF1327          Protein of unknown function (DUF1327)
      0.034   14.5   0.0      0.067   13.5   0.0    1.4  1  Mur_ligase       Mur ligase family, catalytic domain
      0.038   13.0   0.0      0.051   12.6   0.0    1.1  1  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
      0.058   12.9   0.0       0.57    9.6   0.0    2.5  2  CheR             CheR methyltransferase, SAM binding domain
      0.068   12.8   0.0        0.1   12.3   0.0    1.2  1  CmcI             Cephalosporin hydroxylase
      0.075   13.0   0.2        3.8    7.5   0.1    2.6  3  ADH_zinc_N       Zinc-binding dehydrogenase
       0.11   12.0   0.2       0.19   11.3   0.2    1.3  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
       0.11   12.3   0.0        0.2   11.5   0.0    1.4  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
       0.14   11.5   0.0       0.22   10.8   0.0    1.3  1  GidB             rRNA small subunit methyltransferase G


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 !   79.4   0.0     5e-25   2.4e-22       1      97 []      45     145 ..      45     145 .. 0.83

  Alignments for each domain:
  == domain 1  score: 79.4 bits;  conditional E-value: 5e-25
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEEST..GG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssga..lh 75 
                                       +Ld+GcG Gr++l+lakr+  ++vtgvDis++mle+a+era++eg++vef+++da+++  + ++fD+ v+  +  ++
  gi|242398179|ref|YP_002993603.1|  45 ILDVGCGVGRHSLELAKRG--YRVTGVDISQKMLEKAEERAQKEGVEVEFIKADATKFARN-EKFDAAVCLCEgaFS 118
                                       8*****************5..*************************************955.6****9994333355 PP

                                       GSSHHHH.....HHHHHHHHHHEEEEE CS
                   Methyltransf_25  76 hlsdedl.....ekalkeiarvLkpgG 97 
                                       +l  +d       ++l+++++ LkpgG
  gi|242398179|ref|YP_002993603.1| 119 LLGSSDDpiehdLAILRNVYKSLKPGG 145
                                       543332212222579***********9 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.8   0.0   7.4e-25   3.6e-22       4     125 ..      42     165 ..      40     195 .. 0.85

  Alignments for each domain:
  == domain 1  score: 78.8 bits;  conditional E-value: 7.4e-25
                   Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlils 80 
                                       g ++lD+GCG G+ ++ela++   + +v+G+Dis++++e+A+e+aqk g++ veF ++d++++  +   ekfD  ++
  gi|242398179|ref|YP_002993603.1|  42 GAKILDVGCGVGRHSLELAKR---GYRVTGVDISQKMLEKAEERAQKEGVE-VEFIKADATKFARN---EKFDAAVC 111
                                       679****************76...457***********************7.**********8866...9***9887 PP

                   Methyltransf_31  81 n..evl.......naladpdkileeiervlkpggilliedprllaelpakveee 125
                                          +++       + + +  +il+++ + lkpgg ++++  ++l+++++   e+
  gi|242398179|ref|YP_002993603.1| 112 LceGAFsllgssdDPIEHDLAILRNVYKSLKPGGKFILTALSALSRVKKATNED 165
                                       644333666999999**************************9888877555544 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.1   0.0   7.7e-22   3.8e-19       1      96 []      46     149 ..      46     149 .. 0.89

  Alignments for each domain:
  == domain 1  score: 69.1 bits;  conditional E-value: 7.7e-22
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES..-CCC-. CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvsse..vlhhv. 74 
                                       LdvGcG Gr++ +lakrg+rv+gvD+s++ml+ a+e+a++eg++vef++ada+k+  ++++fD+ v+    ++  + 
  gi|242398179|ref|YP_002993603.1|  46 LDVGCGVGRHSLELAKRGYRVTGVDISQKMLEKAEERAQKEGVEVEFIKADATKF-ARNEKFDAAVCLCegAFSLLg 121
                                       8****************************************************95.3557***99887766666667 PP

                                       ......CCHHHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  75 ......edpekalkeiaRvLkpgGllvi 96 
                                             e   ++l+++++ LkpgG++++
  gi|242398179|ref|YP_002993603.1| 122 ssddpiEHDLAILRNVYKSLKPGGKFIL 149
                                       77766667789**************985 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.4   0.0   3.2e-18   1.6e-15      10     162 ..      27     213 ..      11     216 .. 0.76

  Alignments for each domain:
  == domain 1  score: 57.4 bits;  conditional E-value: 3.2e-18
                   Methyltransf_23  10 sdklerllpk..lraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae..........kakkaqkdqfdeq 74 
                                       ++++++ll++  l++g+++Ld+GcG+G+ + +l+++g+ vtgvD+s ++ e+ae          +++ka  ++f   
  gi|242398179|ref|YP_002993603.1|  27 KKEIDFLLEEfkLPEGAKILDVGCGVGRHSLELAKRGYRVTGVDISQKMLEKAEeraqkegvevEFIKADATKF--- 100
                                       57788888555599***************************************988777777777777777777... PP

                   Methyltransf_23  75 eaaepqgkfdlIvl.....revlehvpdpp....ellrqiatllkpgGylllseplasl......kedrllld.... 132
                                            ++kfd +v+     + +l++ +dp     + lr++++ lkpgG ++l+   a +             +    
  gi|242398179|ref|YP_002993603.1| 101 ---ARNEKFDAAVClcegaFSLLGSSDDPIehdlAILRNVYKSLKPGGKFILTALSALSrvkkatN------Ediak 168
                                       ...688899998864444479*******9999999***************9999865444444440......13333 PP

                   Methyltransf_23 133 ...........wlylvpagrhi....sffsarslkelleeaGlev 162
                                                   ++++p+g+++    +++  ++l  +++  G+ev
  gi|242398179|ref|YP_002993603.1| 169 glfdpntmtfyEELEAPDGTKVaireRVYVPTELYLMFRMVGFEV 213
                                       444443333322445777777777788888888888888888887 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.9   0.0   4.8e-17   2.3e-14       1      99 []      46     147 ..      46     147 .. 0.85

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 4.8e-17
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvas..nv 75 
                                       L++GcG+G+ + +l+++  + ++tgvDis++++e+a+e+ +k++     +ve+ + d+ + + +++fD+ v++  ++
  gi|242398179|ref|YP_002993603.1|  46 LDVGCGVGRHSLELAKR--GYRVTGVDISQKMLEKAEERAQKEG----VEVEFIKADATKFARNEKFDAAVCLceGA 116
                                       8****************..**************77777766666....46777777766666778****99776799 PP

                   Methyltransf_12  76 lhhl.......kdirevldnirklLkpgGrl 99 
                                       ++ l       ++  ++l+n++k LkpgG++
  gi|242398179|ref|YP_002993603.1| 117 FSLLgssddpiEHDLAILRNVYKSLKPGGKF 147
                                       ***9***987777779*************86 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.9   0.0   8.6e-15   4.2e-12      38     156 ..      32     154 ..      19     173 .. 0.78

  Alignments for each domain:
  == domain 1  score: 45.9 bits;  conditional E-value: 8.6e-15
                                       HHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS- CS
                   Ubie_methyltran  38 fveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfed 114
                                       f+ +     +gak+lDv +G g  +++l++   + ++v+++Di+++mL+ +e+++++eg+ ++ef++a+a ++  ++
  gi|242398179|ref|YP_002993603.1|  32 FLLEEFKLPEGAKILDVGCGVGRHSLELAK---RGYRVTGVDISQKMLEKAEERAQKEGV-EVEFIKADATKFARNE 104
                                       55555566789************9999875...5679*********************97.7*********998765 PP

                                       T-EEE.EEE...ES-GGG-S-H.....HHHHHHHHHHEEEEEEEEEEEE-- CS
                   Ubie_methyltran 115 dsfDv.vtv...sfGlrnvtDk.....lkaLkeayrvlkpGGrlvvlefsk 156
                                         fD  v +   +f l   +D      l  L+++y+ lkpGG+++   +s 
  gi|242398179|ref|YP_002993603.1| 105 -KFDAaVCLcegAFSLLGSSDDpiehdLAILRNVYKSLKPGGKFILTALSA 154
                                       .34431333223799998888622222478*************98776664 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.4   0.0     1e-13   5.1e-11      21     137 ..      31     149 ..      23     163 .. 0.80

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 1e-13
                                       HHHHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS- CS
                               MTS  21 klLletlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekk 97 
                                       ++Lle ++  +  k+lD+GcG+G  +++lak+  +  vt vd++ + le a+e ++++++eve+++ d+++ + ++k
  gi|242398179|ref|YP_002993603.1|  31 DFLLEEFKLPEGAKILDVGCGVGRHSLELAKRGYR--VTGVDISQKMLEKAEERAQKEGVEVEFIKADATKFARNEK 105
                                       589*****999********************9888..9*************************************** PP

                                       EEEEEE..---STTTCHCHHHHHH..HHHHHHHHHEEEEEEEEE CS
                               MTS  98 fdlivs..NPPfhagkatelavae..eliaeAkeaLkegGeLli 137
                                       fd+ v+     f      ++ + +  +++++  + Lk+gG++++
  gi|242398179|ref|YP_002993603.1| 106 FDAAVClcEGAFSLLGSSDDPIEHdlAILRNVYKSLKPGGKFIL 149
                                       **876511555555555444444411345666666666666655 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.8   0.0   1.6e-13   7.6e-11      40     178 ..      15     163 ..       8     210 .. 0.77

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 1.6e-13
                                       T--HHHH....HHHHHHHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS CS
                              CMAS  40 dmtLeeA....qlaKldlileklelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldler 112
                                       d  L+eA     ++ +d +le  +l +G ++Ld+GcG G    + ++r + +v g+ +S++  ++a++r +++++e 
  gi|242398179|ref|YP_002993603.1|  15 DYYLQEAftkhTKKEIDFLLEEFKLPEGAKILDVGCGVGRHSLELAKR-GYRVTGVDISQKMLEKAEERAQKEGVE- 89 
                                       5556666221134568999*****************************.*************************65. PP

                                       -EEEEES-GGG---..--SEEEEE..S-GGGTSGGG....HH.HHHHHHHHHS-TT-EEEEEEEEE--HHHHHCT CS
                              CMAS 113 kvevklldyedlde..kvdrvvsv..gafehvgken....yd.tffkklkkllkedGllllhtitslhkkelaer 178
                                        ve   +d   ++   k+d+ v +  gaf  +g +     +d +  ++++k lk++G ++l ++ +l++ ++a++
  gi|242398179|ref|YP_002993603.1|  90 -VEFIKADATKFARneKFDAAVCLceGAFSLLGSSDdpieHDlAILRNVYKSLKPGGKFILTALSALSRVKKATN 163
                                       .566666666665444****99987799**9987541111322678999************99988876655533 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.0   4.8e-12   2.3e-09       4     128 ..      12     145 ..       9     165 .. 0.72

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 4.8e-12
                                       CGCCHHHHHHT-----HHH...HHHCCCS-S-EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHTT- CS
                              TehB   4 kkedyfskkynltathsev...veavkivkpgkvldlgcgqgrnslylsllgydvtawdknensiafleeikekenl 77 
                                       ++ dy+ +   + +t+ e+   +e  k+ + +k+ld+gcg gr sl l+  gy vt +d  ++ ++  ee ++ke +
  gi|242398179|ref|YP_002993603.1|  12 READYYLQEAFTKHTKKEIdflLEEFKLPEGAKILDVGCGVGRHSLELAKRGYRVTGVDISQKMLEKAEERAQKEGV 88 
                                       6778888877777777765333788899999********************************99999999999999 PP

                                       TTEEEEE--GGG----S-EEEEEE..ESSGGGS..-GGGHHH...HHHHHHHTEEEEE CS
                              TehB  78 knistalydineaklderydfils..tvvlmfl..eaerips...iienmqectkvgg 128
                                       + ++    d  +   +e++d  +      + +l    + i +   i++n+ +  k+gg
  gi|242398179|ref|YP_002993603.1|  89 E-VEFIKADATKFARNEKFDAAVClcEGAFSLLgsSDDPIEHdlaILRNVYKSLKPGG 145
                                       8.77777777777777888865441133444441123334333335666666666666 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   0.0   8.9e-12   4.3e-09      45     145 ..      43     150 ..      22     159 .. 0.82

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 8.9e-12
                              NodS  45 adalevGcaaGalterlapyckrltvvdvveeaiararervke.sshiswivsdvqqfstdekfdlivv.aevlyyi 119
                                       a++l+vGc  G  + +la    r+t vd+ ++ +++a er ++   ++ +i++d ++f  +ekfd  v+ +e  + +
  gi|242398179|ref|YP_002993603.1|  43 AKILDVGCGVGRHSLELAKRGYRVTGVDISQKMLEKAEERAQKeGVEVEFIKADATKFARNEKFDAAVClCEGAFSL 119
                                       689*************************************8751579******************999745655554 PP

                              NodS 120 ....ed.vaelraavrnlvsllapdgqlvfG 145
                                           +d +++  a +rn+ + l+p+g++++ 
  gi|242398179|ref|YP_002993603.1| 120 lgssDDpIEHDLAILRNVYKSLKPGGKFILT 150
                                       2221232344456789999999999999875 PP

>> TPMT  Thiopurine S-methyltransferase (TPMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0   6.9e-10   3.3e-07       1      90 [.       1      92 [.       1     119 [. 0.76

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 6.9e-10
                                      HHHHHHHHHHHTT--TT--SS--HHHHH....HHHT.T-S--EEEEEET-TT-HHHHHH-BTTEEEEEE-S-HHHHHHH CS
                              TPMT  1 veedfWekrweeeqipfhqeevnpllkk....fldalkakaglrvlvPlCGkaldlvwlAeqgrevvGvelselAvekf 75
                                      +++ +We+ + +e   + qe  ++  kk    +l++ k+++g+++l  +CG +     lA++g++v Gv++s++ +ek+
  gi|242398179|ref|YP_002993603.1|  1 MKKHEWEEFFDREADYYLQEAFTKHTKKeidfLLEEFKLPEGAKILDVGCGVGRHSLELAKRGYRVTGVDISQKMLEKA 79
                                      577899999999988888887766655533326677999***************************************6 PP

                                      HHHHTTSGGGGGEEE CS
                              TPMT 76 feeanlepkvkelsg 90
                                       e a+   +  e+++
  gi|242398179|ref|YP_002993603.1| 80 EERAQ--KEGVEVEF 92
                                      43333..33333333 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   6.5e-08   3.2e-05      13      88 ..      40     111 ..      37     167 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 6.5e-08
                   Methyltransf_18  13 ekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGleklkeeevdtvvi 88 
                                       ++g++++D+G+  g  +++l+k+g   +v+ +Di+++ leka+e ++k+g+  ++e++ +d  +  ++e++d++v+
  gi|242398179|ref|YP_002993603.1|  40 PEGAKILDVGCGVGRHSLELAKRGY--RVTGVDISQKMLEKAEERAQKEGV--EVEFIKADATKFARNEKFDAAVC 111
                                       7899*****************9886..6**********************9..69999999999888777886664 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   3.4e-08   1.6e-05      24      92 ..      40     100 ..      23     168 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 3.4e-08
                   Methyltransf_32  24 sgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkrlsfaelsieea 92 
                                        +  +++DvG+G g  s  la      +++v+g+d+++++ ekae+ra+k g  +  +++f++++ ++ 
  gi|242398179|ref|YP_002993603.1|  40 PEGAKILDVGCGVGRHSLELAK----RGYRVTGVDISQKMLEKAEERAQKEG--V--EVEFIKADATKF 100
                                       45678************99999....59**********************99..5..455555554443 PP

>> Pox_MCEL  mRNA capping enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   3.7e-08   1.8e-05      63     190 ..      40     155 ..      17     184 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 3.7e-08
                          Pox_MCEL  63 snklkvLdldcgkGgDLeKyekgeIsklvatDiaeesieeckeRYnklrsekkskyykFdaelirsdsfvssvrevf 139
                                       ++  k+Ld++cg G       k +  +  ++Di+++ +e+++eR      +k+      ++e+i++d+++   +e+f
  gi|242398179|ref|YP_002993603.1|  40 PEGAKILDVGCGVGRHSLELAKRG-YRVTGVDISQKMLEKAEERA-----QKEG----VEVEFIKADATKFARNEKF 106
                                       566799********8766666655.4678***************8.....2333....4789*************** PP

                          Pox_MCEL 140 edyelkfdivslQFaiHYsF.eseekartvlrNvaellasGGkvlgTtpdgd 190
                                          ++ + +++  F++  s  ++ e+   +lrNv ++l++GGk++ T  ++ 
  gi|242398179|ref|YP_002993603.1| 107 ---DAAVCLCEGAFSLLGSSdDPIEHDLAILRNVYKSLKPGGKFILTALSAL 155
                                       ...68999*******98766156666669******************98874 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   8.8e-08   4.3e-05      65     134 ..      33      98 ..      15     112 .. 0.84
   2 ?   -1.9   0.0       4.9   2.4e+03     160     172 ..     138     150 ..     133     168 .. 0.68

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 8.8e-08
                                       HHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GG CS
                              PCMT  65 alellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGr 134
                                       +le  +l +ga++L+vG+G G ++     l ++  rv +++ ++++ e+a+++ +k+++e v ++ +D +
  gi|242398179|ref|YP_002993603.1|  33 LLEEFKLPEGAKILDVGCGVGRHSLE---LAKRGYRVTGVDISQKMLEKAEERAQKEGVE-VEFIKADAT 98 
                                       567778****************9975...557889999****************999985.788888865 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.9
                                       HHTEEEEEEEEEE CS
                              PCMT 160 idQLkeGGrlvvP 172
                                        + Lk+GG++++ 
  gi|242398179|ref|YP_002993603.1| 138 YKSLKPGGKFILT 150
                                       5779999999974 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   1.2e-07   5.7e-05      17      92 ..      28     104 ..      18     149 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.2e-07
                                       HHHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTT.TCCCEEEE-S-CCGHHHHH CS
                            RrnaAD  17 kvineIldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkkls.kdeklkvvhqDflkfetpe 92 
                                       k i+  l++ +l e  ++l++g G+G  + eLakr   v+ + + +++++  +++ + ++  ++ +++D+ kf+  e
  gi|242398179|ref|YP_002993603.1|  28 KEIDFLLEEFKLPEGAKILDVGCGVGRHSLELAKRGYRVTGVDISQKMLEKAEERAQkEGVEVEFIKADATKFARNE 104
                                       5677778899999*****************************************99867778889*******98776 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   8.6e-07   0.00042      34     168 ..      13     153 ..       4     181 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 8.6e-07
                                       HHHHHHHHHHHTTHHHHHHHHHHSS-GGG-SEEEEET-TTSHHHHHHHHH-TT-EEEEEE-H.HHHHHHHHHS---- CS
                    Methyltransf_2  34 eerakfnkglqessslvakkvleafdleglkslvDvGGGtGalakaivsayPtikvivfDlp.eVveaAkehlsage 109
                                       e +   +++++++++   + +le+f+l +  +++DvG G+G    + ++   + +v+  D++ +  e+A+e+  ++e
  gi|242398179|ref|YP_002993603.1|  13 EADYYLQEAFTKHTKKEIDFLLEEFKLPEGAKILDVGCGVGRHSLELAKR--GYRVTGVDISqKMLEKAEER-AQKE 86 
                                       55566678899999999999*********************998888876..67888999983588999999.7778 PP

                                       -TTEEEEES-TTTS---.--SE.EEEES...SGGGS-H...HHHHHHHHHHHHH--TT-EEEEEE-- CS
                    Methyltransf_2 110 eervefvgGdffkdslP.eaDa.illkr...vlhDwsd...ekcvklLkrvkkalpagGkvivveav 168
                                         +vef++ d  k +   + Da + l      l   sd   e+   +L++v+k+l++gGk i+    
  gi|242398179|ref|YP_002993603.1|  87 GVEVEFIKADATKFARNeKFDAaVCLCEgafSLLGSSDdpiEHDLAILRNVYKSLKPGGKFILTALS 153
                                       88999999997653333244541444331113445556122455679*************9997543 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   8.2e-07    0.0004       4      64 ..      44     101 ..      41     110 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 8.2e-07
                                       EEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCCHH CS
                    Methyltransf_4   4 vvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgdalkvl 64 
                                        +l++GcG G++ ++lAk+     + G++i++k+++k+ +++++++++ ++ ++ da+k+ 
  gi|242398179|ref|YP_002993603.1|  44 KILDVGCGVGRHSLELAKRG--YRVTGVDISQKMLEKAEERAQKEGVE-VEFIKADATKFA 101
                                       579***************96..6778*****************99986.888999987765 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   7.8e-07   0.00038      72     127 ..      59     111 ..      25     112 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 7.8e-07
                                       HHHHH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE CS
                           UPF0020  72 earaelklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivt 127
                                        a++ +++ g+D+ ++++++a+e a+k gv+  +ef +ada+k+  +++++d+ v+
  gi|242398179|ref|YP_002993603.1|  59 LAKRGYRVTGVDISQKMLEKAEERAQKEGVE--VEFIKADATKFA-RNEKFDAAVC 111
                                       55677889*******************9986..89**********.8889*99887 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   1.3e-06   0.00064     155     232 ..      34     111 ..      24     172 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.3e-06
                              PrmA 155 leklvk.egeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveakleval.seellkeekadv 229
                                       le++   eg+++lDvG+G G  ++  ak g  +v++vDi +  ++ a+e a++ +ve ++ +++ + +  ++ek+d 
  gi|242398179|ref|YP_002993603.1|  34 LEEFKLpEGAKILDVGCGVGRHSLELAKRGY-RVTGVDISQKMLEKAEERAQKEGVEVEF-IKAdATKFARNEKFDA 108
                                       6666541567******************996.79************************99.4330334445899998 PP

                              PrmA 230 iva 232
                                        v+
  gi|242398179|ref|YP_002993603.1| 109 AVC 111
                                       887 PP

>> N2227  N2227-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   1.2e-06   0.00056      54      92 ..      38      76 ..       5      80 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.2e-06
                                      ....T-EEEEET-TT-HHHHHHHHTT-EEEEEE--HHHH CS
                             N2227 54 kerekvkilvPGaGlGrlavelatkgyqvegnEfsyfml 92
                                      k  e +kil  G+G+Gr ++ela+ gy+v g+++s  ml
  gi|242398179|ref|YP_002993603.1| 38 KLPEGAKILDVGCGVGRHSLELAKRGYRVTGVDISQKML 76
                                      44567899999************************9997 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   6.3e-06     0.003      11      67 ..      51     106 ..      45     112 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 6.3e-06
                                       HHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHH CS
                         adh_short  11 GIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreeveal 67 
                                       G+Gr  + elak+G++v+ vd+s++ le++ +  ++eg ++ +i++D t+ ++ e++
  gi|242398179|ref|YP_002993603.1|  51 GVGRH-SLELAKRGYRVTGVDISQKMLEKAEERAQKEGVEVEFIKADATKFARNEKF 106
                                       55554.679****************************************99988776 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 !   16.8   0.0   7.8e-06    0.0038       3      70 ..      44     109 ..      42     117 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 7.8e-06
                   Methyltransf_15   3 vilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklkleki 70 
                                        ilD+ +G G  + ++a+ + +v +++i+++ l+ a++ a+  gv+  + ++++d ++  ++ k++++
  gi|242398179|ref|YP_002993603.1|  44 KILDVGCGVGRHSLELAKRGYRVTGVDISQKMLEKAEERAQKEGVE--VEFIKADATKFARNEKFDAA 109
                                       69***************************************99885..88999999988888777665 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.1e-05    0.0055      98     171 ..      39     120 ..      15     166 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.1e-05
                                       --TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG---TT-EE.... CS
                            Met_10  98 veegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpileDgrevireqlad.... 170
                                         eg  ++dv  G+G +++ +ak  ++ rv ++d+  +  +  +e  +   ve  v+ i++D+ +++r++++d    
  gi|242398179|ref|YP_002993603.1|  39 LPEGAKILDVGCGVGRHSLELAK--RGYRVTGVDISQKMLEKAEERAQKEGVE--VEFIKADATKFARNEKFDaavc 111
                                       348999*****************..*********9665555555555555554..778**********999995555 PP

                                       ........E CS
                            Met_10 171 ........r 171
                                                
  gi|242398179|ref|YP_002993603.1| 112 lcegafslL 120
                                       555555550 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   6.3e-05     0.031     116     220 ..      42     152 ..      29     161 .. 0.73
   2 ?   -1.2   0.0       1.5   7.4e+02     128     143 ..     203     218 ..     199     220 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.3e-05
                                       T-EEEEET-TTSHHHHHHHHCT-SEEEEE---HHHHHHHHHHHCCTTTTSSEEEE---GGGS-T---EEEEEEE..S CS
                    Methyltransf_9 116 grtildvGcgnGyhlwrmvgegaklvvGidPselfliqfeavrkllgedqrahllplgieqlpeleafdtvfsm..G 190
                                       g +ildvGcg G h   ++ +g   v G+d s+  l + e  ++   e  ++  +     ++ + e fd+   +  G
  gi|242398179|ref|YP_002993603.1|  42 GAKILDVGCGVGRHSLELAKRG-YRVTGVDISQKMLEKAE--ERAQKEGVEVEFIKADATKFARNEKFDAAVCLceG 115
                                       678************9987665.6789******9997654..55555666666777788888888889876543222 PP

                                       ...-GGG-S-HHHH....HHHHHCTEEEEEEEEEEEE CS
                    Methyltransf_9 191 ...vlyhrrsPldh....llqlkdqlvkgGelvletl 220
                                          +l     P++h    l+++ ++l+ gG+++l +l
  gi|242398179|ref|YP_002993603.1| 116 afsLLGSSDDPIEHdlaiLRNVYKSLKPGGKFILTAL 152
                                       2226777788888864444555667888888888766 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.5
                                       HHHHHHHHCT-SEEEE CS
                    Methyltransf_9 128 yhlwrmvgegaklvvG 143
                                       y ++rmvg + k + G
  gi|242398179|ref|YP_002993603.1| 203 YLMFRMVGFEVKAIWG 218
                                       99******99887655 PP

>> Methyltransf_5  MraW methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   4.9e-05     0.024      12      84 ..      33     103 ..      23     125 .. 0.82
   2 ?   -2.2   0.0       4.6   2.2e+03     223     264 ..     134     174 ..     127     191 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.9e-05
                                       HHHHT---TT-EEEES--TTSHHHHHHHTT--TTEEEEEES-HHHHHHHTT.....---EEEEES-GGGHHHH CS
                    Methyltransf_5  12 vvellepkedgvyiDaTlGaggHsealLeqlselrligidrDksalarakerLkefekrltlvkgnfkelkea 84 
                                       ++e ++  e++  +D+  G g Hs +l +  +  r++g+d+ +++l++a+er ++   +++++k+  +++++ 
  gi|242398179|ref|YP_002993603.1|  33 LLEEFKLPEGAKILDVGCGVGRHSLELAK--RGYRVTGVDISQKMLEKAEERAQKEGVEVEFIKADATKFARN 103
                                       5667777889999***********88754..4559********************9999***99998777654 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 4.6
                                       HHHHHHHEEEEEEEEEEESSHHHHHHHHHHHHHTT------- CS
                    Methyltransf_5 223 leaalellakggrlavisFhSledrivkkvfkeaskkeevPa 264
                                       l+++ + l++gg++ + +  S   r+ k + ++ +k    P+
  gi|242398179|ref|YP_002993603.1| 134 LRNVYKSLKPGGKFILTA-LSALSRVKKATNEDIAKGLFDPN 174
                                       667777888888875444.44445655555555555544455 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   3.4e-05     0.017      11      80 ..      39     110 ..      29     115 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.4e-05
                              MetW  11 ikpgsrvldlGcGdGellellkeekqvdgrGleldeegvaecvak....Glsviqgdldkdlenfedksfdyvv 80 
                                       +++g+++ld+GcG G     l+ +++ +  G++++++ + ++ ++    G++v    +d   ++ ++++fd +v
  gi|242398179|ref|YP_002993603.1|  39 LPEGAKILDVGCGVGRHSLELA-KRGYRVTGVDISQKMLEKAEERaqkeGVEVEFIKADAT-KFARNEKFDAAV 110
                                       6899***********8755553.47888888888888877654431112777655444432.334566777665 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   7.9e-05     0.038       9      96 ..      52     151 ..      48     169 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.9e-05
                                       HHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTT.SEEEES-TTSHHHHHHTTGGGESEEEE-SS.........SH.. CS
                            TrkA_N   9 vGrslaeeLseggkdvvvidkdeerveelreeg.levvvgdatdeevLeeagiekadaviaatg.........dd.. 73 
                                       vGr+ +e  ++g+ +v+++d +++ +e+++e+   e v  +  + ++ + a  ek+da +++++         dd  
  gi|242398179|ref|YP_002993603.1|  52 VGRHSLELAKRGY-RVTGVDISQKMLEKAEERAqKEGVEVEFIKADATKFARNEKFDAAVCLCEgafsllgssDDpi 127
                                       5677777777789.5********998888766644466666666666688899999999999887888888865568 PP

                                       HHHHHHHHHH.HHHTSSSEEEEEE CS
                            TrkA_N  74 eanilavlla.kelnpkkkiiara 96 
                                       e  ++++ ++ k+l p+ k i  a
  gi|242398179|ref|YP_002993603.1| 128 EHDLAILRNVyKSLKPGGKFILTA 151
                                       888888888878888886666554 PP

>> DUF1327  Protein of unknown function (DUF1327)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   0.00012     0.058      44      89 ..      84     129 ..      68     148 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00012
                           DUF1327  44 rveGaalefyeaeakksvkqvfldvaaglcegdeklsekrevilea 89 
                                       + eG  +ef +a+a k +++  +d a+ lceg   l    +  +e+
  gi|242398179|ref|YP_002993603.1|  84 QKEGVEVEFIKADATKFARNEKFDAAVCLCEGAFSLLGSSDDPIEH 129
                                       469*****************************98876666655555 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 ?   13.5   0.0   0.00014     0.067       9      49 ..      49      97 ..      46     111 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00014
                                      SCCHHHHHHHHHHTTSEEEEEESSHC........HHHTT-EEEES-HGG CS
                        Mur_ligase  9 grgmsagalflalkGykvdGsdfies........lialGaaavvghdaa 49
                                      g g++  +l la++Gy+v+G d+ ++        + ++G+++ +  ++a
  gi|242398179|ref|YP_002993603.1| 49 GCGVGRHSLELAKRGYRVTGVDISQKmlekaeerAQKEGVEVEFIKADA 97
                                      6688888999****************99999999999999887777666 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 ?   12.6   0.0    0.0001     0.051     187     262 ..      26     101 ..       6     108 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.0001
                   tRNA_U5-meth_tr 187 nekmleWalevtqeskg.dllelycGnGnfslalarnfekvlateiakssveaaqyniaankidnvqiirlsaeelt 262
                                       ++k +++ le  +  +g  +l++ cG G  sl la++  +v   +i++  +e a    +++ ++ v++i+  a  ++
  gi|242398179|ref|YP_002993603.1|  26 TKKEIDFLLEEFKLPEGaKILDVGCGVGRHSLELAKRGYRVTGVDISQKMLEKAEERAQKEGVE-VEFIKADATKFA 101
                                       56666666666666555589**********************************9998888775.788888777775 PP

>> CheR  CheR methyltransferase, SAM binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0    0.0012      0.57      26      83 ..      36      82 ..      12     105 .. 0.70
   2 ?    0.2   0.0      0.88   4.3e+02     154     173 ..     130     149 ..      83     165 .. 0.57

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0012
                                      HHHTSSSEEEEEES-TTTHHHHHHHHHHHCHSTTTSSS-EEEEEEESSCHHHHHHHHT CS
                              CheR 26 kaknekrvriwsagcssGeEpYslAmllketlpkaaklkvkilAtDidlkvlekAkag 83
                                      + k  +  +i+ +gc+ G  +  lA          ++  ++++++Di++k+lekA++ 
  gi|242398179|ref|YP_002993603.1| 36 EFKLPEGAKILDVGCGVGRHSLELA----------KR-GYRVTGVDISQKMLEKAEER 82
                                      5555555666666666666543333..........23.589**************875 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.88
                                       HHHHHHHHHCCEEEEEEEEE CS
                              CheR 154 qekvlerfaeklkpgglLll 173
                                         ++l++++++lkpgg  +l
  gi|242398179|ref|YP_002993603.1| 130 DLAILRNVYKSLKPGGKFIL 149
                                       34567777777777776666 PP

>> CmcI  Cephalosporin hydroxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00021       0.1      55     149 ..      58     154 ..      52     175 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00021
                              CmcI  55 allkskrkvlaididireknrqaieahplasrieliegssvdpeiveqvkslakekekvlvilD.sdHthehvlaeL 130
                                       +l+k   +v ++di+++  ++++ +a++   ++e+i+++++  +  e+ ++     e  +  l  sd   eh la L
  gi|242398179|ref|YP_002993603.1|  58 ELAKRGYRVTGVDISQKMLEKAEERAQKEGVEVEFIKADATKFARNEKFDAAVCLCEGAFSLLGsSDDPIEHDLAIL 134
                                       56677789******************************************999998888877752678899999999 PP

                              CmcI 131 e.ayaplvsaGsYivveDtv 149
                                       + +y++l   G++i+   + 
  gi|242398179|ref|YP_002993603.1| 135 RnVYKSLKPGGKFILTALSA 154
                                       64799999999998766555 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       6.6   3.2e+03      33      64 ..       4      35 ..       1      36 [. 0.71
   2 ?    7.5   0.1    0.0078       3.8       1      33 [.      51      82 ..      51     120 .. 0.79
   3 ?    2.7   0.0      0.25   1.2e+02      71      90 ..     133     152 ..     129     181 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 6.6
                                      TTESEEEETTTC.HHHHHHHHHTTTSSEEEEEE CS
                        ADH_zinc_N 33 lGadevinykea.dlverikeltggegvdvvfe 64
                                         +e+++++ +  l+e+  ++t ++ +d+ +e
  gi|242398179|ref|YP_002993603.1|  4 HEWEEFFDREADyYLQEAFTKHT-KKEIDFLLE 35
                                      55567788877666889999999.668887765 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0078
                                      HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHT CS
                        ADH_zinc_N  1 gvGlaavqlAkalGaeviavdsseeklelakkl 33
                                      gvG + ++lAk  G +v++vd+s++ le+a++ 
  gi|242398179|ref|YP_002993603.1| 51 GVGRHSLELAK-RGYRVTGVDISQKMLEKAEER 82
                                      89999999998.69**************99985 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.25
                                       HHHHHHHCEEEEEEEEECSC CS
                        ADH_zinc_N  71 tleaalkllkpgGrlvvvGg 90 
                                        l++ +k+lkpgG++ + ++
  gi|242398179|ref|YP_002993603.1| 133 ILRNVYKSLKPGGKFILTAL 152
                                       57899**********99997 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   0.00039      0.19      12      57 ..      57     104 ..      48     111 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00039
                                       HHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSEE..EE--TTSHHHHH CS
                      adh_short_C2  12 kalaeeGaevvltdlneeakkrveelaeelgaev..lecDVtdeeqve 57 
                                        +la++G++v  +d++++  +++ee a++ g ev  +++D+t+ +  e
  gi|242398179|ref|YP_002993603.1|  57 LELAKRGYRVTGVDISQKMLEKAEERAQKEGVEVefIKADATKFARNE 104
                                       5799***************99999999999988666*****9977655 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 ?   11.5   0.0   0.00041       0.2      18      45 ..      59      86 ..      48     115 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00041
                                      HHHTT-EEEEE-S-HHHHHHHHHHHHHH CS
                           3HCDH_N 18 fasagleVvlvdiseealekalekieks 45
                                      +a++g++V+ vdis++ leka+e+++k+
  gi|242398179|ref|YP_002993603.1| 59 LAKRGYRVTGVDISQKMLEKAEERAQKE 86
                                      799*********************9983 PP

>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00045      0.22      47     121 ..      41     111 ..      19     120 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00045
                                       CCC-.EEEETSTTTTTHHHHHHH-TTSEEEEEES-HHHHHHHHHHHHHCT-SSEEEEES-CCCTTTTT-EEEEEE CS
                              GidB  47 ekrdkviDvGsGaGlPGipLaiarpelkltLleslekkiaFLeevkeelklenveivearaeekqeeekydvvts 121
                                       e   k++DvG G G  ++   +a+  +++t ++ ++k  +  ee  ++ ++e ve+++a+a ++ ++ek+d++++
  gi|242398179|ref|YP_002993603.1|  41 EGA-KILDVGCGVGRHSL--ELAKRGYRVTGVDISQKMLEKAEERAQKEGVE-VEFIKADATKFARNEKFDAAVC 111
                                       333.5*********9875..667999***********999989989999999.9*****************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       731  (0.0407719); expected 358.6 (0.02)
Passed bias filter:                      640  (0.0356964); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); expected 17.9 (0.001)
Passed Fwd filter:                        37  (0.0020637); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              37  [number of targets reported over threshold]
# CPU time: 0.62u 0.34s 00:00:00.96 Elapsed: 00:00:00.49
# Mc/sec: 1491.59
//
Query:       gi|242398180|ref|YP_002993604.1|  [L=191]
Description: hypothetical protein TSIB_0187 [Thermococcus sibiricus MM 739]
Scores for 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   32.1   0.0      2e-07   31.1   0.0    1.4  1  DUF523    Protein of unknown function (DUF523)
  ------ inclusion threshold ------
      0.038   14.1   0.2      0.061   13.4   0.2    1.3  1  DUF2096   Uncharacterized protein conserved in archaea (DUF20


Domain annotation for each model (and alignments):
>> DUF523  Protein of unknown function (DUF523)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.0   2.2e-11     2e-07       1     133 [.       4     169 ..       4     172 .. 0.76

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 2.2e-11
                            DUF523   1 ilvSaCLlgekvrydgkakksevleeelkelvke.....elvpv.CPEvaggLptPRepaelakrvlkkeg.edvte 70 
                                       ++++ CLl     y g + k+ ++++el +l+++     ++++  CPE +  ++ PR+p+  +   l+k g ++  +
  gi|242398180|ref|YP_002993604.1|   4 VVLAPCLLSPFYVYRGPKDKEYTTSRELLNLLAKhvreiRVLTYpCPEYKL-IGWPRPPMSRE--ALEKLGiSETAR 77 
                                       567889999999999988887777777666664434326555557****96.788*****997..566666589999 PP

                            DUF523  71 alekgaeealeelkeeeikgailkekSPSCGvekiY................................dgtfskklv 115
                                       ++ +++e++l e k e   +++  ++SP+CG+  +                                 + +f  k +
  gi|242398180|ref|YP_002993604.1|  78 KILDFIERVLTEEKPE-KVIFVGVKGSPTCGIFYTTssdpekfpyriieefsclnkkerielskelmeEQNF--KVI 151
                                       **********998875.5577899*******97662556666677999999999999888888776543343..459 PP

                            DUF523 116 egeGvfaallkeegievp 133
                                       +geGv+ ++lk++++e +
  gi|242398180|ref|YP_002993604.1| 152 PGEGVLFQILKRRFPEAI 169
                                       999999999999998865 PP

>> DUF2096  Uncharacterized protein conserved in archaea (DUF2096)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   6.8e-06     0.061     115     169 .]     133     190 ..     110     190 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.8e-06
                           DUF2096 115 tirvklkkpleeerlqeiaEyegvIiefeeddv...vvvyGdkedikkaLkelselfk 169
                                         r++l k+l ee   ++   egv++++ + +    + ++ dk++i+k+Lk+l + fk
  gi|242398180|ref|YP_002993604.1| 133 KERIELSKELMEEQNFKVIPGEGVLFQILKRRFpeaIYLEFDKDNIEKSLKQLEKHFK 190
                                       569***********************9988876677*****************98886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       703  (0.0392102); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); 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: 0.62u 0.34s 00:00:00.96 Elapsed: 00:00:00.55
# Mc/sec: 1041.13
//
Query:       gi|242398181|ref|YP_002993605.1|  [L=201]
Description: dephospho-CoA kinase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-19   69.9   0.1    4.2e-19   69.4   0.1    1.2  1  AAA_18           AAA domain
    2.3e-05   24.9   0.2    6.4e-05   23.4   0.2    1.7  1  AAA_17           AAA domain
    0.00012   21.8   0.1     0.0027   17.4   0.0    2.3  2  CoaE             Dephospho-CoA kinase
    0.00015   21.7   0.5        0.2   11.5   0.0    2.4  2  dNK              Deoxynucleoside kinase
     0.0024   18.0   0.1       0.03   14.5   0.1    2.2  1  AAA_33           AAA domain
  ------ inclusion threshold ------
      0.059   12.8   0.1       0.91    8.9   0.0    2.1  2  Glyco_tranf_2_2  Glycosyltransferase like family 2


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 !   69.4   0.1   1.4e-22   4.2e-19       1     121 [.      11     146 ..      11     162 .. 0.93

  Alignments for each domain:
  == domain 1  score: 69.4 bits;  conditional E-value: 1.4e-22
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....gvnlrdvakenglllevdpealdeskrldedkldklldaleenss... 69 
                                       +++ G++++GKtt+ak  +++ gf     ++ l+d++++n + +++ pe ++e+ +  +dkl +  + l++      
  gi|242398181|ref|YP_002993605.1|  11 VGVVGKIAAGKTTVAKFFEEK-GFcrvscSDPLIDLLTHNLSKYSWLPE-IPEKSEPTRDKLIEYGRHLKKTFGedi 85 
                                       6899****************9.67799**********************.**********************99*** PP

                            AAA_18  70 .......aleegknlvidghlaeleseaakdikk..vvLtaspeelleRlekRgyeeakik 121
                                              + +++kn+vidg++++ e ea k+ ++  ++++a+p++++eRl++R+  ++k  
  gi|242398181|ref|YP_002993605.1|  86 lirlaldKKRNCKNVVIDGVRSKGEIEAIKKQGGfiIYVEARPKIRYERLKRRNAGKDKAI 146
                                       *******9**********************9999********************9998854 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.2   2.1e-08   6.4e-05       2     128 ..      15     143 ..      14     152 .. 0.73

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 2.1e-08
                                       E-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTT..T..........SHSSHHHHCTSHHHHHHHHHHHHHHHHH CS
                            AAA_17   2 GgPGsGKgtqceklvekygfthlsaGdllreeakrg..g..........lakardemrklpleekkelqkeaaekia 66 
                                       G   +GK+t++ k  e+ gf  +s +d l++  +++  +          ++++rd++ +     kk + + +  ++a
  gi|242398181|ref|YP_002993605.1|  15 GKIAAGKTTVA-KFFEEKGFCRVSCSDPLIDLLTHNlsKyswlpeipekSEPTRDKLIEYGRHLKKTFGEDILIRLA 90 
                                       55679******.999999*********99999988865156776676656888999988777777777766665554 PP

                                       HHH..HSSEEEEEE-SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHHTTST-T CS
                            AAA_17  67 eea..kkkgvlvdghprikeqagfldglpkevleelkpdaiilleadpeeilerrlkdrtrgrd 128
                                        ++  + k+v++dg  +    +g+++ ++k      +  +ii++ea p+ i+ +rlk+r+ g d
  gi|242398181|ref|YP_002993605.1|  91 LDKkrNCKNVVIDGVRS----KGEIEAIKK------QGGFIIYVEARPK-IRYERLKRRNAGKD 143
                                       443235599*****985....788888887......3569********8.55566666555443 PP

>> CoaE  Dephospho-CoA kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0     9e-07    0.0027       1      28 [.       9      36 ..       9      49 .. 0.90
   2 ?    2.0   0.0     0.047   1.4e+02     123     178 ..     119     183 ..     110     184 .. 0.60

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 9e-07
                                      EEEEEEESTTSSHHHHHHHHHHTT-EEE CS
                              CoaE  1 livgltGgiasGKstvanlfadlgvpiv 28
                                      +ivg+ G ia+GK+tva+ f++ g+  v
  gi|242398181|ref|YP_002993605.1|  9 MIVGVVGKIAAGKTTVAKFFEEKGFCRV 36
                                      69*******************9887655 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.047
                                       SEEEEEE--HHHHHHHHHHCCTSTHHHH...HHHHHHS--HHH....H..HHH-SEEEE-.SSHH CS
                              CoaE 123 ervlvvdvelelqveRlvardgvseeev...kaiiaaQlseee....r..laladvvldNdssla 178
                                         ++ v++ ++ + eRl +r+  + + +   ++ ++a  +ee+    r  + lad+++ N++sl+
  gi|242398181|ref|YP_002993605.1| 119 GFIIYVEARPKIRYERLKRRNAGKDKAIksfEDFLNADEAEEKlyhtRmlKDLADFLIVNEGSLE 183
                                       56788888888888888888854444440114556665555432222211357888888888876 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   6.7e-05       0.2       3      22 ..      13      32 ..      11      56 .. 0.83
   2 !    8.3   0.2   0.00064       1.9     125     152 ..     120     147 ..     110     194 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.7e-05
                                      EEESTTSSHHHHHHHHHCCS CS
                               dNK  3 veGnIgaGKstlvklLskkl 22
                                      v G+I+aGK+t++k++++k 
  gi|242398181|ref|YP_002993605.1| 13 VVGKIAAGKTTVAKFFEEKG 32
                                      67**************9875 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00064
                                       EEEEEE--HHHHHHHHHHCTTCCCTTS- CS
                               dNK 125 lliYLkasletclerikkRgreeekkie 152
                                       ++iY++a ++  +er+k+R+  ++k i+
  gi|242398181|ref|YP_002993605.1| 120 FIIYVEARPKIRYERLKRRNAGKDKAIK 147
                                       79******************99998665 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1     1e-05      0.03       2     126 ..      11     146 ..      10     160 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1e-05
                            AAA_33   2 vllvGlpGsGKstlaerllkklgavllssdt..................lrrrlfgtdqqskt............dy 48 
                                       v +vG  ++GK+t+a+   ++ g++++s  +                  +                         + 
  gi|242398181|ref|YP_002993605.1|  11 VGVVGKIAAGKTTVAKFF-EEKGFCRVSCSDplidllthnlskyswlpeI------------PekseptrdklieYG 74 
                                       5589************85.5899****96665555544444444433321............022222233333233 PP

                            AAA_33  49 trvldr.lyqilnelarkalsagrnvildatnlsrrerarflklarrlgvpvrivvvetdeetlkeRlakRaangdd 124
                                        ++++    +il +la ++ +  +nv++d + +s+ e +++ k     g    i++ve+ ++   eRl++R+a +d+
  gi|242398181|ref|YP_002993605.1|  75 RHLKKTfGEDILIRLALDKKRNCKNVVID-GVRSKGEIEAIKKQG---G---FIIYVEARPKIRYERLKRRNAGKDK 144
                                       33444433446667776666666677776.566666666554444...4...6788888888888888888886665 PP

                            AAA_33 125 rs 126
                                       ++
  gi|242398181|ref|YP_002993605.1| 145 AI 146
                                       54 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 ?    8.9   0.0    0.0003      0.91      28      92 ..      95     157 ..      70     169 .. 0.80
   2 ?    2.3   0.0     0.031        93      27      52 ..     169     194 ..     157     198 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0003
                   Glyco_tranf_2_2  28 eeielivvddgSsekfleevssiidlnllv.ylkdeddkayslaaarNrGaskaesdlvlFlDaDc 92 
                                        + + +v+d+  s+    e+++i+++ + + y++  ++  y   + rN G +ka+  +  Fl+aD 
  gi|242398181|ref|YP_002993605.1|  95 RNCKNVVIDGVRSKG---EIEAIKKQGGFIiYVEARPKIRYERLKRRNAGKDKAIKSFEDFLNADE 157
                                       577888999998888...999**9999999576777777********************9*99996 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.031
                   Glyco_tranf_2_2  27 deeielivvddgSsekfleevssiid 52 
                                        +  ++++v++gS e++ + v+++i 
  gi|242398181|ref|YP_002993605.1| 169 KDLADFLIVNEGSLEDLKKRVNTVIT 194
                                       56678***********9999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       724  (0.0403815); expected 358.6 (0.02)
Passed bias filter:                      586  (0.0326845); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1258.13
//
Query:       gi|242398182|ref|YP_002993606.1|  [L=266]
Description: hypothetical protein TSIB_0189 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); 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:                         0  (0); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 1692.91
//
Query:       gi|242398183|ref|YP_002993607.1|  [L=82]
Description: hypothetical protein TSIB_0190 [Thermococcus sibiricus MM 739]
Scores for complete 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   22.2   0.1    0.00012   22.0   0.1    1.1  1  TBP        Transcription factor TFIID (or TATA-binding protei
  ------ inclusion threshold ------
      0.065   13.4   0.0      0.088   13.0   0.0    1.3  1  UPF0180    Uncharacterised protein family (UPF0180)
      0.082   12.8   0.2        1.6    8.7   0.0    2.2  2  Fanconi_A  Fanconi anaemia group A protein


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 !   22.0   0.1   1.9e-08   0.00012      14      81 ..      11      75 ..       2      79 .. 0.73

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.9e-08
                                      SSCE-HHHHHHHCC.TTTEEE-TT.TSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHHHHH CS
                               TBP 14 gleldLeklalkae.krnaeYepe.rfpglvyrlrepkvtaliFssGkvvitGakseeelreaakkiapi 81
                                      +++ldLe++  ++  +r+ + ++  rf +lv +     + ++iF sGk+++  + ++ee+ + a++i++ 
  gi|242398183|ref|YP_002993607.1| 11 KFDLDLEEVC-ECLaERGYQIKRVtRFLALVRKA----YDISIFPSGKIIVKETDNKEEALKIAQEIYEC 75
                                      6889999994.33224444444433555555555....559*************************9975 PP

>> UPF0180  Uncharacterised protein family (UPF0180)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.5e-05     0.088       8      29 ..      15      38 ..      13      74 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.5e-05
                           UPF0180  8 gLsnvkeaLrekGYeVvdlet..e 29
                                      +L++v e L+e+GY++ +++    
  gi|242398183|ref|YP_002993607.1| 15 DLEEVCECLAERGYQIKRVTRflA 38
                                      79**************99887542 PP

>> Fanconi_A  Fanconi anaemia group A protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1     0.028   1.7e+02      36      46 ..      17      27 ..       3      37 .. 0.70
   2 ?    8.7   0.0   0.00026       1.6      17      48 ..      51      82 .]      49      82 .] 0.87

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.028
                         Fanconi_A 36 aeiLecLekrk 46
                                       e+ ecL +r+
  gi|242398183|ref|YP_002993607.1| 17 EEVCECLAERG 27
                                      57889999887 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00026
                         Fanconi_A 17 sskltpkeavdslkalevcaeiLecLekrkvs 48
                                      s k+  ke+ + ++al++++ei ec +  +vs
  gi|242398183|ref|YP_002993607.1| 51 SGKIIVKETDNKEEALKIAQEIYECAKAYRVS 82
                                      5678889999***************8887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       938  (0.0523175); expected 358.6 (0.02)
Passed bias filter:                      674  (0.0375927); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 512.07
//
Query:       gi|242398184|ref|YP_002993608.1|  [L=194]
Description: hypothetical protein TSIB_0191 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score 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   1.6       0.54   10.3   1.5    2.3  1  DUF5643   Family of unknown function (DUF5643)


Domain annotation for each model (and alignments):
>> DUF5643  Family of unknown function (DUF5643)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   1.5     3e-05      0.54      28      67 ..      31      74 ..      15      95 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 3e-05
                           DUF5643 28 strisy...sgdvenskeikek.sldfevvDdkGnelegisggg 67
                                      +++i++    ++++ +++  ++ + d++v+D++Gn le++ +g 
  gi|242398184|ref|YP_002993608.1| 31 TVEIEMpvdDYTTQVTSSLLGDhYEDIFVIDENGNPLEYSINGN 74
                                      45555555555666666666667888***********9855543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1430.35
//
Query:       gi|242398185|ref|YP_002993609.1|  [L=404]
Description: hypothetical protein TSIB_0192 [Thermococcus sibiricus MM 739]
Scores for complete 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-05   23.4   9.8       0.03   14.2   0.0    3.3  2  YfdX            YfdX protein
     0.0049   17.0   0.5        9.2    6.8   0.0    3.7  2  PPR             PPR repeat
  ------ inclusion threshold ------
      0.016   15.1   4.2        4.1    7.3   0.0    3.8  4  Sec8_exocyst    Sec8 exocyst complex component specific domai
      0.042   13.8   0.8        2.2    8.3   0.0    2.5  2  PX              PX domain
      0.084   13.0   0.2        1.4    9.1   0.0    2.8  3  T2SS_PulS_OutS  Type II secretion system pilotin lipoprotein 
      0.093   12.9   0.2        5.3    7.3   0.0    2.7  2  PPR_2           PPR repeat family
      0.094   12.8   2.0       0.22   11.6   0.4    2.3  2  DUF4070         Domain of unknown function (DUF4070)
       0.13   11.2   2.5       0.12   11.3   0.3    2.0  2  Lyase_8_N       Polysaccharide lyase family 8, N terminal alp
       0.19   12.0   4.6         29    5.1   0.1    4.6  4  TPR_2           Tetratricopeptide repeat
       0.26   11.4   6.2       0.39   10.9   0.3    3.3  2  DUF4363         Domain of unknown function (DUF4363)
       0.47   10.0  20.6      0.017   14.6   8.7    3.3  4  4HB_MCP_1       Four helix bundle sensory module for signal t
        1.1    9.7   4.3        2.8    8.3   0.5    3.8  3  Nif11           Nif11 domain
        1.2    8.9   4.3         17    5.2   0.1    2.6  2  PPR_1           PPR repeat


Domain annotation for each model (and alignments):
>> YfdX  YfdX protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   7.7     0.011        16       8      96 ..     185     294 ..     175     301 .. 0.72
   2 !   14.2   0.0   2.2e-05      0.03      92     144 ..     341     394 ..     331     398 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.011
                                       HHHHHCTT-HHHHHHHHHHHHHHHTS-HHHHHCCB-...S--SSSS....................-EEEEEEE..E CS
                              YfdX   8 ArlaldqgdtkeAkkllekAqgkleaaladdpklvk...kapasad....................alvPvdae..v 59 
                                        + +++++d ++A++ le A++k +a+ ++  +  k   +    a+                    + v  ++e  +
  gi|242398185|ref|YP_002993609.1| 185 VLEDIKAKDLEKAREDLEIAREKKAALDEELRRIRKelvE----ANadkivneflekgargietaeKVVEMAEEkgY 257
                                       5678999999999999999999999999999999334331....224455666777777777777655555543236 PP

                                       EEE------HHHHHHHHHHHHHHHTT-HHHHHHHHHH CS
                              YfdX  60 ividdladtpekkaaikkanellkkgdtqaArelLkl 96 
                                       ++++  + +++ k++  ++++l ++g+ ++A +++++
  gi|242398185|ref|YP_002993609.1| 258 DAHELQERLEAFKEIYSEVKALADEGKYDEALQVMRE 294
                                       7777788888888888888888888888888888876 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 2.2e-05
                                       HHHHHT.T-EEEEEEEEEEHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHT-E CS
                              YfdX  92 elLkll.gseidittallPLatypaavkkAaelleegkyyeAkeaLkealntlv 144
                                       ++L++l + ++d+  a l L+t  + +   +ell+++k+ eAk   + al+ l 
  gi|242398185|ref|YP_002993609.1| 341 RELRELgRRGVDTRRAELQLKTSIQEIRLGIELLKNRKPAEAKMHFAIALDMLH 394
                                       4444441579*********************************99999999875 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.0    0.0067       9.2       3      25 ..     109     131 ..     108     135 .. 0.90
   2 !    6.3   0.0    0.0093        13       8      25 ..     277     294 ..     276     294 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0067
                               PPR   3 ynslIsgycknGkleeAlelfke 25 
                                       yn++I+g+     ++e+l+ f++
  gi|242398185|ref|YP_002993609.1| 109 YNTIINGLTAMHHYREVLKSFER 131
                                       9*****************99987 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0093
                               PPR   8 sgycknGkleeAlelfke 25 
                                       ++++ +Gk++eAl++++e
  gi|242398185|ref|YP_002993609.1| 277 KALADEGKYDEALQVMRE 294
                                       68999*********9987 PP

>> Sec8_exocyst  Sec8 exocyst complex component specific domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1      0.53   7.3e+02     119     139 ..     109     129 ..      56     162 .. 0.64
   2 ?   -1.1   0.0       1.1   1.6e+03      91     109 ..     189     208 ..     168     226 .. 0.48
   3 ?    6.3   0.1    0.0062       8.5      49     108 ..     220     278 ..     209     301 .. 0.81
   4 ?    7.3   0.0    0.0029       4.1      83     120 ..     317     354 ..     293     369 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.53
                      Sec8_exocyst 119 ykevieiLdaieelkkvpdki 139
                                       y+ +i+ L a+ + ++v + +
  gi|242398185|ref|YP_002993609.1| 109 YNTIINGLTAMHHYREVLKSF 129
                                       233333333333333332222 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.1
                      Sec8_exocyst  91 lK.esleeakkklstkkkeL 109
                                       +K ++le+a+++l+  +++ 
  gi|242398185|ref|YP_002993609.1| 189 IKaKDLEKAREDLEIAREKK 208
                                       33123444444443333332 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.0062
                      Sec8_exocyst  49 kkqieeaLqevvnehhqaFnssiasYskilssiqesqekvselKesleeakkklstkkke 108
                                       k+ +e++ +++vne+ ++ +++i + +k++++ +e   + +el+e+le+ k+ +  + k 
  gi|242398185|ref|YP_002993609.1| 220 KELVEANADKIVNEFLEKGARGIETAEKVVEMAEEKGYDAHELQERLEAFKE-IYSEVKA 278
                                       566889999**************************************87654.4444444 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.0029
                      Sec8_exocyst  83 esqekvselKesleeakkklstkkkeLkelnarsakyk 120
                                       e qe++ +lK  l+e +  +++++ eL+el  r +  +
  gi|242398185|ref|YP_002993609.1| 317 EVQERLGDLKGFLREMTIRIQKDSRELRELGRRGVDTR 354
                                       57999*************************99876655 PP

>> PX  PX domain
   #    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      58     111 ..     184     236 ..     134     237 .. 0.86
   2 ?    3.5   0.1      0.05        69      57      94 ..     296     332 ..     258     335 .. 0.58

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0016
                                       STSTSSSTSGSSSSSCTTSHHHHHHHHHHHHHHHHHHHTSCHHHH.SHHHHHHHH CS
                                PX  58 vkiPplPkkvlfgsvrkkdeefiekrrkgLeeyLqrllnhpelrn.sevlteFLe 111
                                        ++  +  k+l +   ++d e++++++++L+e L+r+ +  +  n ++++ eFLe
  gi|242398185|ref|YP_002993609.1| 184 AVLEDIKAKDLEKA--REDLEIAREKKAALDEELRRIRKELVEANaDKIVNEFLE 236
                                       45555556666665..99************************************8 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.05
                                       TSTSTSSSTSGSSSSSCTTSHHHHHHHHHHHHHHHHHH CS
                                PX  57 rvkiPplPkkvlfgsvrkkdeefiekrrkgLeeyLqrl 94 
                                       + +i ++ ++  f + +k++e+ +++r  +L+ +L+++
  gi|242398185|ref|YP_002993609.1| 296 TETIKEFHRAMAFLQ-KKFHEREVQERLGDLKGFLREM 332
                                       334444444454543.9******************998 PP

>> T2SS_PulS_OutS  Type II secretion system pilotin lipoprotein (PulS_OutS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       1.4   1.9e+03      41      52 ..      75      86 ..      35     115 .. 0.56
   2 ?    9.1   0.0     0.001       1.4      52      89 ..     154     191 ..     145     199 .. 0.88
   3 ?   -0.4   0.0      0.96   1.3e+03      51      80 ..     244     273 ..     239     288 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.4
                                      --TTS--HHHHH CS
                    T2SS_PulS_OutS 41 nrsdLpddatil 52
                                      n  +Lp++++i+
  gi|242398185|ref|YP_002993609.1| 75 NNVNLPENSSIM 86
                                      333344444443 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.001
                                       HHHHHHHHHHTT--GGG-TTHHHHHHHHHHHHHHSSS- CS
                    T2SS_PulS_OutS  52 lkvalkvakqrgWdtdeyqslpqrserlYqgLlkdstp 89 
                                       +++ +++a+++g d+++  +l q+ +  Y+++l+d   
  gi|242398185|ref|YP_002993609.1| 154 AEKTIEIAQRQGIDVGNTTTLLQETKDAYKAVLEDIKA 191
                                       567899**9*************************9554 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.96
                                       HHHHHHHHHHHTT--GGG-TTHHHHHHHHH CS
                    T2SS_PulS_OutS  51 ilkvalkvakqrgWdtdeyqslpqrserlY 80 
                                       ++++++++a ++g+d+ e q      +++Y
  gi|242398185|ref|YP_002993609.1| 244 TAEKVVEMAEEKGYDAHELQERLEAFKEIY 273
                                       5678999********988876666666666 PP

>> PPR_2  PPR repeat family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0    0.0038       5.3       6      27 ..     109     130 ..     108     135 .. 0.92
   2 ?    2.6   0.0      0.12   1.6e+02      11      28 ..     277     294 ..     276     294 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0038
                             PPR_2   6 yNtlIsglckkgkveeAfklfn 27 
                                       yNt+I+gl    +++e +k f+
  gi|242398185|ref|YP_002993609.1| 109 YNTIINGLTAMHHYREVLKSFE 130
                                       9***************999887 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.12
                             PPR_2  11 sglckkgkveeAfklfne 28 
                                       ++l+ +gk++eA++++ e
  gi|242398185|ref|YP_002993609.1| 277 KALADEGKYDEALQVMRE 294
                                       57889*********9976 PP

>> DUF4070  Domain of unknown function (DUF4070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.4   0.00016      0.22      22      67 ..      78     123 ..      63     153 .. 0.76
   2 ?   -0.2   0.1      0.74     1e+03      43      67 ..     253     276 ..     214     319 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00016
                           DUF4070  22 sltnfiPtmpleelakeyvevleqlYspeayleRvdklllklkpar 67 
                                       +l +    m + +la++y+ev +++Y+ + y++ + + l+ +++ r
  gi|242398185|ref|YP_002993609.1|  78 NLPENSSIMRHYQLAEQYKEVATNAYESDDYYNTIINGLTAMHHYR 123
                                       444445569999********************99988877777554 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.74
                           DUF4070  43 leqlYspeayleRvdklllklkpar 67 
                                        e+ Y+++++ eR++++ ++++++ 
  gi|242398185|ref|YP_002993609.1| 253 EEKGYDAHELQERLEAF-KEIYSEV 276
                                       45678888888888887.4444332 PP

>> Lyase_8_N  Polysaccharide lyase family 8, N terminal alpha-helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.3   8.7e-05      0.12      58     101 ..      79     124 ..      28     132 .. 0.75
   2 ?   -1.5   0.1      0.65     9e+02      59     101 ..     270     314 ..     198     324 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8.7e-05
                                       H..HHHHHHHHHHHHHHC-TTSTTTT-HHHHHHHHHHHHHHHHHTS CS
                         Lyase_8_N  58 l..tktyrrletlakaytepgselyqdekllaaiveglaflsetky 101
                                       l  ++++ r ++la +y+e  ++ y++++ +++i++gl  +++ + 
  gi|242398185|ref|YP_002993609.1|  79 LpeNSSIMRHYQLAEQYKEVATNAYESDDYYNTIINGLTAMHHYRE 124
                                       344566778899*****************************99765 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.65
                                       HHHHHHHHHHHH..HHC-TTSTTTT-HHHHHHHHHHHHHHHHHTS CS
                         Lyase_8_N  59 tktyrrletlak..aytepgselyqdekllaaiveglaflsetky 101
                                       ++ y++++ la    y e    + ++ + +++  +++afl++++ 
  gi|242398185|ref|YP_002993609.1| 270 KEIYSEVKALADegKYDEALQVMRENTETIKEFHRAMAFLQKKFH 314
                                       333444444443113444445556666666666666666666655 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       2.2     3e+03      20      29 ..     118     127 ..     117     133 .. 0.70
   2 ?    2.4   0.4      0.15   2.1e+02      13      28 ..     190     205 ..     188     208 .. 0.84
   3 ?    5.1   0.1     0.021        29      10      25 ..     278     293 ..     277     294 .. 0.85
   4 ?    1.8   0.0      0.25   3.4e+02       6      27 ..     368     389 ..     367     392 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.2
                             TPR_2  20 AleafekAle 29 
                                       A ++++++l+
  gi|242398185|ref|YP_002993609.1| 118 AMHHYREVLK 127
                                       6677777776 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.15
                             TPR_2  13 klgdyeeAleafekAl 28 
                                       k++d+e+A+e++e A 
  gi|242398185|ref|YP_002993609.1| 190 KAKDLEKAREDLEIAR 205
                                       789********99775 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.021
                             TPR_2  10 ayyklgdyeeAleafe 25 
                                       a++  g+y+eAl+ ++
  gi|242398185|ref|YP_002993609.1| 278 ALADEGKYDEALQVMR 293
                                       78899*******9877 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.25
                             TPR_2   6 nlGlayyklgdyeeAleafekA 27 
                                       +lG  ++k+ +++eA+ +f  A
  gi|242398185|ref|YP_002993609.1| 368 RLGIELLKNRKPAEAKMHFAIA 389
                                       79*************8666655 PP

>> DUF4363  Domain of unknown function (DUF4363)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   1.1      0.28   3.8e+02      12      41 ..     176     205 ..     168     226 .. 0.71
   2 ?   10.9   0.3   0.00028      0.39       6      75 ..     261     330 ..     257     333 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.28
                           DUF4363  12 delsekleeleeaienedweeakekleele 41 
                                       +e+++  + + e i+++d e+a e+le ++
  gi|242398185|ref|YP_002993609.1| 176 QETKDAYKAVLEDIKAKDLEKAREDLEIAR 205
                                       445555555556667888888877777554 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00028
                           DUF4363   6 ylkkstdelsekleeleeaienedweeakekleelekeWekkkkklsifiehdeldeietslaklkayie 75 
                                        l+   + ++e  +e+++ +++++++ea + ++e  ++ ++ ++ ++++      +e+++ l +lk++++
  gi|242398185|ref|YP_002993609.1| 261 ELQERLEAFKEIYSEVKALADEGKYDEALQVMRENTETIKEFHRAMAFLQKKFHEREVQERLGDLKGFLR 330
                                       566677788899999***************************************************9986 PP

>> 4HB_MCP_1  Four helix bundle sensory module for signal transduction
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.3      0.36     5e+02     105     145 ..      50      90 ..      32     124 .. 0.72
   2 ?   -1.4   2.7         1   1.4e+03      97     159 ..     125     189 ..      98     206 .. 0.56
   3 ?    1.9   5.1       0.1   1.4e+02      42     138 ..     162     258 ..     151     260 .. 0.80
   4 ?   14.6   8.7   1.3e-05     0.017      74     154 ..     220     301 ..     189     311 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.36
                         4HB_MCP_1 105 eeEkelleefkeqlnaYrevrkkvlelakegkkdeAyqlye 145
                                       ++E ++++++  +l++ +++  k+++ ++  ++   +++y+
  gi|242398185|ref|YP_002993609.1|  50 TQEEKIANQIVVALERLSNITTKLINNVNLPENSSIMRHYQ 90 
                                       56777777777777777777777777777777775555553 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1
                         4HB_MCP_1  97 kyektilteeE.kelleefkeqlnaYrevrkkvlelakegkkd..eAyqlyetegrpareklieal 159
                                         ++    +eE ke+l e  + +++Y +  +k++e a+++  d  +  + + +e++ a++++ e +
  gi|242398185|ref|YP_002993609.1| 125 VLKSFERGKEElKERLPEEIKRMEGYFRMAEKTIEIAQRQGIDvgN-TTTLLQETKDAYKAVLEDI 189
                                       4555555556545566666777777777777777777777777320.1222222223333333322 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.1
                         4HB_MCP_1  42 edrllpikdlgeikanlrelradlleliltkdkaekdellkdieeleaeidkllekyektilteeEkelleefkeql 118
                                       + + + ++  + + +++++   ++le i +kd ++ +e l+   e++a +d++l++++k  ++++  ++++ef e+ 
  gi|242398185|ref|YP_002993609.1| 162 QRQGIDVGNTTTLLQETKDAYKAVLEDIKAKDLEKAREDLEIAREKKAALDEELRRIRKELVEANADKIVNEFLEKG 238
                                       55555555555566666666666777777778888888888789********************************* PP

                         4HB_MCP_1 119 naYrevrkkvlelakegkkd 138
                                       ++  e  +kv+e a+e+ +d
  gi|242398185|ref|YP_002993609.1| 239 ARGIETAEKVVEMAEEKGYD 258
                                       *************9999887 PP

  == domain 4  score: 14.6 bits;  conditional E-value: 1.3e-05
                         4HB_MCP_1  74 kaekdellkdi.eeleaeidkllekyektilteeEke.lleefkeqlnaYrevrkkvlelakegkkdeAyqlyeteg 148
                                       k+  ++ +++i +e+ ++    +e  ek    +eEk   + e++e l+a++e+ ++v +la egk+deA q++++++
  gi|242398185|ref|YP_002993609.1| 220 KELVEANADKIvNEFLEKGARGIETAEKVVEMAEEKGyDAHELQERLEAFKEIYSEVKALADEGKYDEALQVMRENT 296
                                       555555555555899999999999999********999**************************************9 PP

                         4HB_MCP_1 149 rparek 154
                                       ++  ++
  gi|242398185|ref|YP_002993609.1| 297 ET-IKE 301
                                       54.444 PP

>> Nif11  Nif11 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       6.5     9e+03      30      40 ..     155     165 ..     153     168 .. 0.82
   2 ?    8.3   0.5     0.002       2.8      24      42 ..     240     258 ..     194     262 .. 0.90
   3 ?   -1.4   0.0       2.2   3.1e+03      18      29 ..     261     272 ..     259     286 .. 0.60

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 6.5
                             Nif11  30 eevvalAkeaG 40 
                                       e  +++A+++G
  gi|242398185|ref|YP_002993609.1| 155 EKTIEIAQRQG 165
                                       66789999998 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.002
                             Nif11  24 kacsdheevvalAkeaGye 42 
                                       + ++++e vv++A e+Gy+
  gi|242398185|ref|YP_002993609.1| 240 RGIETAEKVVEMAEEKGYD 258
                                       5689**************8 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 2.2
                             Nif11  18 alreqlkacsdh 29 
                                       +l+e+l a ++ 
  gi|242398185|ref|YP_002993609.1| 261 ELQERLEAFKEI 272
                                       788888887643 PP

>> PPR_1  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   1.5     0.042        58      10      17 ..     109     116 ..     108     116 .. 0.95
   2 ?    5.2   0.1     0.012        17      16      32 ..     278     294 ..     276     294 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.042
                                       HHHHHHHH CS
                             PPR_1  10 YNtLIdGl 17 
                                       YNt+I+Gl
  gi|242398185|ref|YP_002993609.1| 109 YNTIINGL 116
                                       *******8 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.012
                                       HHHHTS-HHHHHHHHHH CS
                             PPR_1  16 GlCkaGrvdeAfelfde 32 
                                       +l  +G+ deA+++++e
  gi|242398185|ref|YP_002993609.1| 278 ALADEGKYDEALQVMRE 294
                                       67789**********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2095  (0.11685); expected 358.6 (0.02)
Passed bias filter:                      713  (0.039768); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.66u 0.32s 00:00:00.98 Elapsed: 00:00:00.47
# Mc/sec: 2586.74
//
Query:       gi|242398186|ref|YP_002993610.1|  [L=402]
Description: cysteine desulfurase [Thermococcus sibiricus MM 739]
Scores for complete 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-137  456.2   0.0   8.6e-137  456.0   0.0    1.0  1  Aminotran_5      Aminotransferase class-V
    6.3e-05   22.3   0.0    0.00019   20.7   0.0    1.7  2  Aminotran_1_2    Aminotransferase class I and II
    0.00017   20.3   0.0    0.00034   19.3   0.0    1.5  2  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    0.00068   19.0   0.0    0.00086   18.7   0.0    1.2  1  Beta_elim_lyase  Beta-eliminating lyase
    0.00091   18.6   0.0     0.0014   18.0   0.0    1.3  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family


Domain annotation for each model (and alignments):
>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  456.0   0.0  2.4e-140  8.6e-137       1     371 []      22     390 ..      22     390 .. 0.99

  Alignments for each domain:
  == domain 1  score: 456.0 bits;  conditional E-value: 2.4e-140
                                       EEEBTTTS----HHHHHHHHHHHHCTCCSSSSSSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHH CS
                       Aminotran_5   1 iyldsaAttqkpqeVldalqeyytdynanvhrsvhhlgkeatkaveearekvaelinaeseeeiiftsGtteainlv 77 
                                       iy+d++At+ +p+ V++a++eyy +y anvhr+vh+l+++at+ +e+ re  a++i+a+  eeiift++t+e++nl+
  gi|242398186|ref|YP_002993610.1|  22 IYFDNTATSLTPKPVVEAMDEYYLKYRANVHRGVHRLSQKATHEYEKSREITAKFIGAKF-EEIIFTKNTSESLNLA 97 
                                       8**********************************************************8.**************** PP

                                       HHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTE CS
                       Aminotran_5  78 alslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsnvtGt 154
                                       al+l+  lk+gd+iv+t  ehh+ l+pwq+lak+  +k+++i+ d+eg+ldl ++ek+  +++k+va++hvsn++G+
  gi|242398186|ref|YP_002993610.1|  98 ALGLEGVLKKGDKIVTTPYEHHSDLLPWQRLAKKLDLKLEIIEGDNEGNLDLADAEKKT-KRAKIVAVQHVSNALGV 173
                                       ****999************************************************9985.9**************** PP

                                       B--HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTT.TTSSTT-EEEEEEHHHHHTS..SS.STTS CS
                       Aminotran_5 155 iqpveeigklakkkgalvlvDaaqavghipidvkklgvDflafsghK.llgPtGiGvlyvrkellekleplllggem 230
                                       i++vee+gk+ak++ga+++vDaaq+vgh+++dv+kl +DflafsghK  +gPtGiGvly+r+e    +ep l+gg++
  gi|242398186|ref|YP_002993610.1| 174 IHEVEELGKMAKDEGAIFVVDAAQSVGHMEVDVNKLHADFLAFSGHKgPMGPTGIGVLYIREEFFDVFEPPLIGGGT 250
                                       ***************************************************************************** PP

                                       EEEEETTEEEEHCTTGGGS.SS--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-CT CS
                       Aminotran_5 231 veevsleettfaeapskfeaGTpnvagiiglgaaleyleeigleaiekhekelaeyllerlkslpgvrlygpdkaer 307
                                       +e+v+l +++++e+p +feaGTpn+ g igl+a ++y+e+ig+++iek+e++l ++++e+l +l+   +ygp++ ++
  gi|242398186|ref|YP_002993610.1| 251 IEDVDLYDYKLTEPPERFEAGTPNIGGTIGLAAGIKYIEKIGIDKIEKQEHKLVKRTTEGLTELEVP-WYGPRDLKK 326
                                       ****************************************************************988.78******* PP

                                       CBSEEEEEETTCSHHHHHHHHHHTTEEEEEE-TTTHHHHHHTT.S-EEEEE--TTS-HHHHHHH CS
                       Aminotran_5 308 rasivsfnfkgvhaedvatlLdeegIavrsGhhcaqplmkrlalegtvRaSlyiynteeevdrl 371
                                       +a++vsfn++ +h++dva +Lde++I+vrsGhhca p+mk l+++gtvRaS+++yn+ eev+ +
  gi|242398186|ref|YP_002993610.1| 327 HAGVVSFNVPPLHPHDVAAVLDEHKIMVRSGHHCALPVMKKLGINGTVRASFHVYNSLEEVETF 390
                                       *************************************************************976 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 !   20.7   0.0   5.3e-08   0.00019      41     195 ..      61     202 ..      18     238 .. 0.77
   2 ?   -1.4   0.0      0.28   9.9e+02     284     341 ..     303     371 ..     284     389 .. 0.62

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 5.3e-08
                                       -BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHH..HTTT-EEEEEESS-THHHHHHHHTTS CS
                     Aminotran_1_2  41 gpidglpeleealakflgrseklklkreaavvvgsGagaliealifllk..lnpgdeilvpdptyasyknilrlsgg 115
                                         ++ + + +e +akf+g       k e +++++  +++ +++++  l+  l +gd+i+     y+++++ l + ++
  gi|242398186|ref|YP_002993610.1|  61 KATHEYEKSREITAKFIG------AKFE-EIIFTKNTSESLNLAALGLEgvLKKGDKIVTTP--YEHHSDLLPWQRL 128
                                       44666778889999****......6667.999999999999998888877788****99766..6778888888887 PP

                                       E.EEEEEBEET...TTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEE CS
                     Aminotran_1_2 116 e.vvryplyse...edfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDe 188
                                       +     +l+     ++ +ldl + e++ k       + k+++v  ++N  G++   eel k+   ak  +++ +vD 
  gi|242398186|ref|YP_002993610.1| 129 AkKLDLKLEIIegdNEGNLDLADAEKKTK-------RAKIVAVQHVSNALGVIHEVEELGKM---AKDEGAIFVVDA 195
                                       76666665544666999999999999777.......569***********************...9999*******9 PP

                                       TTTTCBS CS
                     Aminotran_1_2 189 aYagfvf 195
                                       a +++ +
  gi|242398186|ref|YP_002993610.1| 196 AQSVGHM 202
                                       9777665 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.28
                                       HHHHHHHHHHHS.....TEEEECCSCSSEEEEEETHHCHHHHHHHHHHTCTEEEEEGGGGTS........T CS
                     Aminotran_1_2 284 rrkelrdeLael.....glkvlasqsgmflltdlsaetakelskkLleevgvyvtpgtsftv........p 341
                                       + k+ +++L+el     g   l++++g++++ + + +  ++++   l+e+++ v+ g ++ +         
  gi|242398186|ref|YP_002993610.1| 303 LVKRTTEGLTELevpwyGPRDLKKHAGVVSFNVPPLH-PHDVAA-VLDEHKIMVRSGHHCALpvmkklgiN 371
                                       4555556666663334444445566777777655555.444444.56666999999988887555444444 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   9.4e-08   0.00034      44     180 ..      64     202 ..      40     221 .. 0.74
   2 ?   -3.9   0.0         1   3.6e+03     293     322 ..     323     353 ..     322     355 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 9.4e-08
                                       -SBTTT--HHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEE CS
                   Cys_Met_Meta_PP  44 yeYsRsgnptrsvleeriaaLeggeaalavssGmaAiaaailallkaGdeivvsddlYggtqrllkkvlkklgievk 120
                                       +eY +s   t + + ++  ++  ++++   s  +aA+   +  +lk+Gd+iv++ + + +     ++++kkl ++ +
  gi|242398186|ref|YP_002993610.1|  64 HEYEKSREITAKFIGAKFEEIIFTKNTS-ESLNLAAL--GLEGVLKKGDKIVTTPYEHHSDLLPWQRLAKKLDLKLE 137
                                       5666666666666665555555554432.34445555..78899*********9987777777789*********** PP

                                       EESTTSHHHHHHHCCT....TEEEEEEESS-TTTT----HHHHHHHHHHTT-EEEEEGTTTHT.T CS
                   Cys_Met_Meta_PP 121 fvdtsdleelekaike....ntklvylEtptnpllkvvDiekiaklakkagvlvvvDntfasp.l 180
                                       +++ +++ +l  a  e    + k+v +  ++n l  ++ +e++ k+ak++g++ vvD++ + + +
  gi|242398186|ref|YP_002993610.1| 138 IIEGDNEGNLDLADAEkktkRAKIVAVQHVSNALGVIHEVEELGKMAKDEGAIFVVDAAQSVGhM 202
                                       ****9999986543332233789**********************************98877734 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 1
                                       HSSSG-SEEEEEESSHH.HHHHHHHHC-SSS CS
                   Cys_Met_Meta_PP 293 qlkgaggvlsFelksee.ekakkfvdnlklf 322
                                       +lk+ +gv+sF++   + + +++++d+ k++
  gi|242398186|ref|YP_002993610.1| 323 DLKKHAGVVSFNVPPLHpHDVAAVLDEHKIM 353
                                       5677889999999876667777777777765 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   2.4e-07   0.00086      96     241 ..     134     319 ..      54     374 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.4e-07
                                       -EEEEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHH CS
                   Beta_elim_lyase  96 vklrdlknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfa 172
                                        kl  ++++++G++dl++ e++ k+  a     k++ +    n+  G    + e++e+ ++ak++g  +++D+A  +
  gi|242398186|ref|YP_002993610.1| 134 LKLEIIEGDNEGNLDLADAEKKTKR--A-----KIVAVQHVSNA-LG---VIHEVEELGKMAKDEGAIFVVDAAQSV 199
                                       55667888899*********99999..3.....34555544453.23...4788899999*************9655 PP

                                       HHHHHHTS-CHHHHTTSSEEEEESSSTT--SS-.EEEEE-HH................................... CS
                   Beta_elim_lyase 173 naakslgeivkemfsyvDsvtmslkKdllanvG.gvlafrddel................................. 215
                                           +++++v ++  ++D + +s+ K+ + + G gvl +r++                                   
  gi|242398186|ref|YP_002993610.1| 200 ---GHMEVDVNKL--HADFLAFSGHKGPMGPTGiGVLYIREEFFdvfeppligggtiedvdlydykltepperfeag 271
                                       ...5678888887..69************************955888888888888888888888888888888888 PP

                                       .......................HH.HHHHHHHHHHT---SSTHHHHH CS
                   Beta_elim_lyase 216 .....................edyl.aerveqrkylggglrqagvlaa 241
                                                             d + ++ ++++k+  +gl++ +v+  
  gi|242398186|ref|YP_002993610.1| 272 tpniggtiglaagikyiekigIDKIeKQEHKLVKRTTEGLTELEVPWY 319
                                       888888888888888888888444414556678888888888888777 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 !   18.0   0.0     4e-07    0.0014      33     150 ..      74     200 ..      40     217 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 4e-07
                                       HHHHT-S..EEEEESSHHHHHHHHHHHTTTT....TT-EEEEESSS-THHHHH....HHHTT-EEEEE-B-TTTSSB CS
                   DegT_DnrJ_EryC1  33 aaylgvk..haiavssGtaAlhlaLralgvg....pgdeVIvpsltFvatana....vlelgakpvfvDvdpdtyni 99 
                                       a+++g+k    i + + +++l la  alg++    +gd+++++++   +   +    + +l +k   ++ d +  n+
  gi|242398186|ref|YP_002993610.1|  74 AKFIGAKfeEIIFTKNTSESLNLA--ALGLEgvlkKGDKIVTTPYEHHSDLLPwqrlAKKLDLKLEIIEGD-NEGNL 147
                                       667775411577788888887765..33333333699******9999998765111156667777788888.89*** PP

                                       -GGGCGGG--TTEEEEEEB-G...GGB---HHHHHHHHHHCT-EEEEE-TT-TT CS
                   DegT_DnrJ_EryC1 100 dpaaieaaitertkaIlpVhl...yGqvadmdalkaiaakhglkvieDaAhAlG 150
                                       d a++e++ t+r k + + h+   +G + ++++l ++a++ g +++ DaA+++G
  gi|242398186|ref|YP_002993610.1| 148 DLADAEKK-TKRAKIVAVQHVsnaLGVIHEVEELGKMAKDEGAIFVVDAAQSVG 200
                                       ******99.67777666655422289999************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); 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: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 2577.06
//
Query:       gi|242398187|ref|YP_002993611.1|  [L=40]
Description: hypothetical protein TSIB_0194 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       156  (0.00870099); expected 358.6 (0.02)
Passed bias filter:                      112  (0.00624686); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 282.49
//
Query:       gi|242398188|ref|YP_002993612.1|  [L=194]
Description: hypothetical protein TSIB_0195 [Thermococcus sibiricus MM 739]
Scores for complete 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-05   22.8  20.5    9.6e-05   22.5  20.5    1.1  1  ECF_trnsprt  ECF transporter, substrate-specific component
    0.00098   18.9   8.1    0.00098   18.9   8.1    1.6  2  7tm_3        7 transmembrane sweet-taste receptor of 3 GCPR


Domain annotation for each model (and alignments):
>> ECF_trnsprt  ECF transporter, substrate-specific component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5  20.5   1.1e-08   9.6e-05       1     171 [.       4     185 ..       4     186 .. 0.70

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.1e-08
                                       HHHHHHHHHHHHHHHHHH.H.HEEE.STSEEESHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHCHT-SSTTHHHH.. CS
                       ECF_trnsprt   1 kklvitglliAisivlsl.l.gyiplpnikitiihipvllggllfGpikGailgiitsvlkailtggtgalssfv.. 73 
                                       ++++++gll+ +s+vl + +  ++     +i+++ +p++++ +++G ++ + + i+  ++++ l+    +++  +  
  gi|242398188|ref|YP_002993612.1|   4 REIALIGLLLSLSLVLEVsPlKVPTQWGMSIDLVAVPMVIIYVIMGFWSSVTALILL-FVGLSLVSSA-SWL--Gas 76 
                                       689**************987566666677*****************99998888763.4444443222.232..334 PP

                                       ..HHHHHHHHCHHHHHHHHHHCC.CHTTHHHH.....HHHHHHHHCCCCCHHHHHHHCCCHHHHS............ CS
                       ECF_trnsprt  74 ..piaflsriligliagllykkg.kkknlkei.....vvsfilagvlgtivatllvlliilplylklktakaiaiag 142
                                         ++a+ls +l   +a  + k+  k+ n k +     v+++ +++ +   v++++++++++pl+l +++ ++i  ++
  gi|242398188|ref|YP_002993612.1|  77 mkFFATLSLVLGLELAKRITKFDfKNFNEK-KfvifvVLAYSMGIAIRIPVMVIMNYYYAIPLWLGIPKEQVIPTIE 152
                                       668888888888888886665541344444.34777666666666666678888899999****9888888888888 PP

                                       .....--HHHHHHHHHCCTTCCHHHHHHHHHHC CS
                       ECF_trnsprt 143 ....kallaailgpiivkglieaiiaaiivvll 171
                                             ++++i +p  ++++++ ++ +++ +++
  gi|242398188|ref|YP_002993612.1| 153 ewfhIPFWLVIGIPNAIQSAVDVLVGVLVSLPV 185
                                       666666666666666666666666666666665 PP

>> 7tm_3  7 transmembrane sweet-taste receptor of 3 GCPR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   3.6       0.4   3.6e+03     136     136 ..      44      44 ..       4      70 .. 0.43
   2 !   18.9   8.1   1.1e-07   0.00098     101     211 ..      36     133 ..      18     143 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.4
                             7tm_3 136 i 136
                                       i
  gi|242398188|ref|YP_002993612.1|  44 I 44 
                                       1 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 1.1e-07
                             7tm_3 101 lvlllvlvqviillvwtlidplstrekseeereevileC..ssssysdiffllllgy.kglllllgtflafktrkvp 174
                                       lv++ +++  +i+ +w+ ++ l              l +  s   +s  ++++++ +   l l+lg+ la ++ k  
  gi|242398188|ref|YP_002993612.1|  36 LVAVPMVIIYVIMGFWSSVTALIL------------LFVglSL-VSSASWLGASMKFfATLSLVLGLELAKRITKFD 99 
                                       455555666778888876654332............1124322.234578888887725556899************ PP

                             7tm_3 175 .snfneakfitlsilnvlliwlvfiplylllnskpdaa 211
                                        +nfne kf+++++l++ + +++ ip+++++n+     
  gi|242398188|ref|YP_002993612.1| 100 fKNFNEKKFVIFVVLAYSMGIAIRIPVMVIMNY----Y 133
                                       *****************************9994....3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       908  (0.0506442); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1331.20
//
Query:       gi|242398189|ref|YP_002993613.1|  [L=371]
Description: D-glucuronyl C5-epimerase [Thermococcus sibiricus MM 739]
Scores for 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-42  142.7   8.2    1.8e-41  141.7   8.2    1.4  1  C5-epim_C  D-glucuronyl C5-epimerase C-terminus


Domain annotation for each model (and alignments):
>> C5-epim_C  D-glucuronyl C5-epimerase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.7   8.2     1e-45   1.8e-41       7     188 .]     194     365 ..     188     365 .. 0.92

  Alignments for each domain:
  == domain 1  score: 141.7 bits;  conditional E-value: 1e-45
                         C5-epim_C   7 wrinveyklyegkklspGWlsamaqgqaisvllrAYeltgdekYlkaakkalksfkipvekGGvlktledkkiwyee 83 
                                       + +  +y + e+   s +W+s+ aqg  + ++++AY+ t++e Ylk+ak +l+sf+ip ++GG++ ++ + ++w+ e
  gi|242398189|ref|YP_002993613.1| 194 YALFLNYFHFEN--SSIPWVSGYAQGMGAGLYAKAYQITKNETYLKTAKLLLNSFQIPYKEGGFVVESPY-GLWILE 267
                                       455556666443..889*****************************************************.****** PP

                         C5-epim_C  84 YptspksyvLNGfiysligLydlstakkseeakelfkkglkslkallpkydtgswslYdlrhvtlgkapnlarwdYh 160
                                       Y  + +  vLNG+i++l gLy + + +k+  akelf++g  s+ + lp +d   wslY+     ++ ++     +Yh
  gi|242398189|ref|YP_002993613.1| 268 YGYNSNELVLNGHIIALQGLYYYWEVTKDPYAKELFDNGTISVAKALPDFDKEGWSLYSN----IHGKAMR---KYH 337
                                       ***********************************************************5....5444444...6** PP

                         C5-epim_C 161 klhiellkaLakitndkvfkkyaerwks 188
                                       +lhi+ll++L++ t++++fk yaerwk+
  gi|242398189|ref|YP_002993613.1| 338 ELHIQLLEWLYEKTKNEIFKGYAERWKK 365
                                       **************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); 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 0.29s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2454.40
//
Query:       gi|242398190|ref|YP_002993614.1|  [L=512]
Description: hypothetical protein TSIB_0197 [Thermococcus sibiricus MM 739]
Scores for complete 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  145.3  13.8    1.5e-42  145.3  13.8    1.8  2  C5-epim_C       D-glucuronyl C5-epimerase C-terminus
  ------ inclusion threshold ------
      0.034   13.2   4.8        0.5    9.4   0.9    2.3  2  Glyco_hydro_88  Glycosyl Hydrolase Family 88


Domain annotation for each model (and alignments):
>> C5-epim_C  D-glucuronyl C5-epimerase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1      0.29   2.6e+03      42      58 ..     189     205 ..     183     250 .. 0.44
   2 !  145.3  13.8   1.6e-46   1.5e-42      10     187 ..     331     498 ..     320     499 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.29
                         C5-epim_C  42 YeltgdekYlkaakkal 58 
                                       Y  tg+  Yl++ + + 
  gi|242398190|ref|YP_002993614.1| 189 YSKTGNITYLRSYRDSF 205
                                       55555555555443332 PP

  == domain 2  score: 145.3 bits;  conditional E-value: 1.6e-46
                         C5-epim_C  10 nveyklyegkklspGWlsamaqgqaisvllrAYeltgdekYlkaakkalksfkipvekGGvlktledkkiwyeeYpt 86 
                                         +y + e+   s +W+s+ aqg  + ++++AY+ t++e Ylk+ak +l+sf+++ ++ G+++++++ ++wy eY+ 
  gi|242398190|ref|YP_002993614.1| 331 FLNYFHFEN--SSIPWVSGYAQGMGAGLYAKAYQITKNETYLKTAKLLLNSFDLSLKENGFVSNTKY-GPWYLEYNY 404
                                       455555443..889*****************************************************.********* PP

                         C5-epim_C  87 spksyvLNGfiysligLydlstakkseeakelfkkglkslkallpkydtgswslYdlrhvtlgkapnlarwdYhklh 163
                                       + +  vLNG+i++l gLy + + +k+e+a +lf++g++s+k+ lp +dt+sws Y+        +   a+++Yh+lh
  gi|242398190|ref|YP_002993614.1| 405 NSNELVLNGHIIALQGLYYYWEVTKDEKAWQLFQAGVESTKKTLPIFDTNSWSKYSN-------IHGDASEFYHRLH 474
                                       ********************************************************4.......44445589***** PP

                         C5-epim_C 164 iellkaLakitndkvfkkyaerwk 187
                                       i+llk+L+ +t+d++f +ya +w+
  gi|242398190|ref|YP_002993614.1| 475 IQLLKWLYDVTGDEYFFNYARKWN 498
                                       ***********************8 PP

>> Glyco_hydro_88  Glycosyl Hydrolase Family 88
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.2    0.0013        12      29      60 ..     348     379 ..     329     408 .. 0.67
   2 ?    9.4   0.9   5.6e-05       0.5      34     105 ..     417     502 ..     412     505 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0013
                                       HHHHHHHHHHHHHHHHH--HHHHHHHHHHHHH CS
                    Glyco_hydro_88  29 wtnGvflsglleayeatgdkeyldyakawads 60 
                                       + +G+  +  ++ay++t++++yl+ ak   +s
  gi|242398190|ref|YP_002993614.1| 348 YAQGMGAGLYAKAYQITKNETYLKTAKLLLNS 379
                                       55564443334677777777777666654444 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 5.6e-05
                                       HHHHHHHHHHHH--HHHHHHHHH..........HHHHCCCTTS-CTTSGGGTGHHHHHHH.....HHHHH-THHHHH CS
                    Glyco_hydro_88  34 flsglleayeatgdkeyldyaka..........wadslideggktelelDdidiglllll.....lyeltkderyke 95 
                                       +l+gl++++e t+d++  ++ +a          ++d++ + + + +++ D+ +  + l +     ly  t+de + +
  gi|242398190|ref|YP_002993614.1| 417 ALQGLYYYWEVTKDEKAWQLFQAgvestkktlpIFDTNSWSKYS-NIHGDASEFYHRLHIqllkwLYDVTGDEYFFN 492
                                       689********************999999999999999999999.999999998887755566679*******9999 PP

                                       HHHHHHHHHH CS
                    Glyco_hydro_88  96 aaeeladyvl 105
                                        a+++ +y++
  gi|242398190|ref|YP_002993614.1| 493 YARKWNNYLI 502
                                       9999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (512 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       828  (0.0461822); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); 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: 0.65u 0.33s 00:00:00.98 Elapsed: 00:00:00.50
# Mc/sec: 3076.70
//
Query:       gi|242398191|ref|YP_002993615.1|  [L=298]
Description: phosphomethylpyrimidine kinase [Thermococcus sibiricus MM 739]
Scores for 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-49  167.4   0.0    3.3e-49  166.7   0.0    1.3  1  ThiP_synth      Thiamine-phosphate synthase
    2.8e-05   24.0   0.0    5.3e-05   23.1   0.0    1.4  1  HTH_37          Helix-turn-helix domain
    3.8e-05   23.6   0.1    9.2e-05   22.4   0.1    1.7  1  HTH_3           Helix-turn-helix
    0.00011   22.1   0.0    0.00042   20.3   0.0    2.0  1  HTH_19          Helix-turn-helix domain
     0.0025   17.7   0.0     0.0047   16.8   0.0    1.4  1  Terminase_5     Putative ATPase subunit of terminase (gpP-lik
     0.0042   16.8   0.0      0.025   14.4   0.0    2.2  2  HTH_23          Homeodomain-like domain
     0.0051   16.4   0.1      0.089   12.4   0.0    2.8  3  HTH_24          Winged helix-turn-helix DNA-binding
     0.0056   17.0   0.0      0.012   16.0   0.0    1.5  1  HTH_31          Helix-turn-helix domain
     0.0056   16.4   0.0      0.014   15.1   0.0    1.7  1  HTH_38          Helix-turn-helix domain
     0.0087   15.6   0.0      0.019   14.4   0.0    1.6  1  Sigma70_r4      Sigma-70, region 4
  ------ inclusion threshold ------
      0.011   15.8   0.0       0.22   11.6   0.1    2.4  2  HTH_7           Helix-turn-helix domain of resolvase
      0.024   14.5   0.0      0.048   13.5   0.0    1.4  1  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox
      0.026   14.4   0.0      0.061   13.3   0.0    1.6  1  MarR            MarR family
      0.057   13.4   0.1        0.4   10.7   0.0    2.4  3  HTH_Crp_2       Crp-like helix-turn-helix domain
      0.073   13.1   0.1       0.17   12.0   0.1    1.5  1  Cro             Cro
      0.075   13.5   0.0       0.17   12.4   0.0    1.6  1  HTH_26          Cro/C1-type HTH DNA-binding domain
       0.11   12.7   0.0       0.47   10.6   0.0    2.0  2  HTH_28          Helix-turn-helix domain
       0.12   12.4   0.1       0.42   10.6   0.1    1.9  1  HTH_11          HTH domain
       0.12   12.1   0.2       0.33   10.7   0.0    1.8  2  Sigma70_r4_2    Sigma-70, region 4
       0.14   12.3   0.0       0.22   11.6   0.0    1.3  1  RepB            RepB plasmid partitioning protein
       0.15   12.1   0.2       0.69   10.0   0.0    2.3  2  KorB            KorB domain


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 !  166.7   0.0   3.9e-52   3.3e-49       2     164 ..     134     292 ..     133     293 .. 0.96

  Alignments for each domain:
  == domain 1  score: 166.7 bits;  conditional E-value: 3.9e-52
                                       HHHHHHHHHCC--.GCC--TT-B-EEEE-ST--SGGGEEEETT-EEE-TSSEEE-S-EEETS-CHHHHHHHHHHCC- CS
                        ThiP_synth   2 leralelleeeeefakliPevgsNiayalpdAksieDvaavpGRIvrvkgrvkvvgepefgasshvarvllaamkfd 78 
                                       l+ al  l ++++f kliPe++sN+ay+lpd+k+ eDvaavpGRI+ vk+++  + +pefgas+h+a vl+a+ +++
  gi|242398191|ref|YP_002993615.1| 134 LNLALGGLLRNKGFLKLIPEIRSNFAYSLPDPKEKEDVAAVPGRITHVKDKAY-ALPPEFGASEHMAGVLIALSNVF 209
                                       777899999******************************************97.789******************** PP

                                       TT--EEEEEE--HHHHHHHCCTTSEEEE--CCCS-CCCT-HHHHHHHHHHHCCS-ECEEEE--BCTB--EEEEEESS CS
                        ThiP_synth  79 pevraainirydekilealeelglkvvefdreeepeevgstmewgvaeaieelevpdviydeGgvGkEpmiyvlgkd 155
                                       p +r+++ni+yde+i +al+++g+k+  ++++e++e+  +t++  v+e  ++    d+++d+Gg+G+Ep++y++gk+
  gi|242398191|ref|YP_002993615.1| 210 PGIRSVLNIKYDENIFRALKKAGFKFGVIEKSERSED--ETVRLIVEEFKKKG-SLDAVVDRGGFGIEPCVYIFGKN 283
                                       *************************************..99999999987766.69********************* PP

                                       HHHHHHHHH CS
                        ThiP_synth 156 aeevvekvl 164
                                       + evvekv+
  gi|242398191|ref|YP_002993615.1| 284 PIEVVEKVK 292
                                       *******97 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   6.3e-08   5.3e-05      21      58 ..      18      55 ..      10      59 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 6.3e-08
                                      HHHHHHHHHCT--HHHHHHHHT--HHHHHHHHTT--TT CS
                            HTH_37 21 laiaeliekrelsqseaaqllgiaqPkvsrllrgklsr 58
                                      + ia+++ +++l+q+++a++lgi+q+ vs+ l gk +r
  gi|242398191|ref|YP_002993615.1| 18 ADIARILYSKGLTQAKIAEHLGITQAMVSKYLTGKYKR 55
                                      559*****************************999877 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.1   1.1e-07   9.2e-05       7      34 ..      26      53 ..      20      64 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.1e-07
                                      HTTHHHHHHHHHHTSSHHHHHHHHTTSS CS
                             HTH_3  7 qlglsqeeLAeklGvsrstisriEnGer 34
                                       +gl+q+++Ae lG++++ +s++  G+ 
  gi|242398191|ref|YP_002993615.1| 26 SKGLTQAKIAEHLGITQAMVSKYLTGKY 53
                                      79************************53 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   4.9e-07   0.00042      10      43 ..      26      59 ..      20      73 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 4.9e-07
                            HTH_19 10 elgltqeelaerlgisrskisaiEngkkdvpsae 43
                                       +gltq+++ae+lgi++++ s++ +gk++ ++ +
  gi|242398191|ref|YP_002993615.1| 26 SKGLTQAKIAEHLGITQAMVSKYLTGKYKRLGGD 59
                                      68*************************9998844 PP

>> Terminase_5  Putative ATPase subunit of terminase (gpP-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   5.5e-06    0.0047       5      33 ..      20      48 ..      18      58 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.5e-06
                       Terminase_5  5 qArlLYwqGyrvaeIAeelglkeatVysW 33
                                       Ar LY +G + a+IAe+lg+ +a V  +
  gi|242398191|ref|YP_002993615.1| 20 IARILYSKGLTQAKIAEHLGITQAMVSKY 48
                                      69**********************99877 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   2.9e-05     0.025      13      38 ..      24      49 ..      16      57 .. 0.83
   2 ?   -1.3   0.0       2.4     2e+03      33      47 ..     248     263 ..     247     265 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.9e-05
                            HTH_23 13 llaeGlsvreIAreLgvsrrTvyrwl 38
                                      l+ +Gl++++IA++Lg+++  v+++l
  gi|242398191|ref|YP_002993615.1| 24 LYSKGLTQAKIAEHLGITQAMVSKYL 49
                                      3445******************9885 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.4
                            HTH_23  33 TvyrwlkryreeG.le 47 
                                       Tv+ +++ ++++G l+
  gi|242398191|ref|YP_002993615.1| 248 TVRLIVEEFKKKGsLD 263
                                       99*******9888565 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0    0.0001     0.089      17      38 ..      28      49 ..      22      50 .. 0.93
   2 ?    0.2   0.0      0.65   5.5e+02      19      36 ..     126     143 ..     123     144 .. 0.80
   3 ?   -2.3   0.0       3.9   3.3e+03       2      17 ..     246     261 ..     245     262 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0001
                            HTH_24 17 risqreLAerlglSpstvnrrl 38
                                      +++q+ +Ae+lg++++ v+++l
  gi|242398191|ref|YP_002993615.1| 28 GLTQAKIAEHLGITQAMVSKYL 49
                                      79*****************997 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.65
                            HTH_24  19 sqreLAerlglSpstvnr 36 
                                       s +++ e+l+l ++ ++r
  gi|242398191|ref|YP_002993615.1| 126 SRTQILEELNLALGGLLR 143
                                       567899999999998766 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 3.9
                            HTH_24   2 detdrkILelLqknpr 17 
                                       det r I e+ +k+++
  gi|242398191|ref|YP_002993615.1| 246 DETVRLIVEEFKKKGS 261
                                       7888889888888775 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.4e-05     0.012      13      40 ..      27      54 ..      15      66 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.4e-05
                            HTH_31 13 aGLsqeevAerlgvsestlsrlEqGrrg 40
                                       GL+q+  Ae+lg++++ +s++ +G+  
  gi|242398191|ref|YP_002993615.1| 27 KGLTQAKIAEHLGITQAMVSKYLTGKYK 54
                                      49***********************875 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.7e-05     0.014      10      35 ..      17      43 ..      14      50 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.7e-05
                            HTH_38 10 ReeIerl.laeGlslreIArrLgrsps 35
                                      R  I+r  +++Gl++++IA +Lg    
  gi|242398191|ref|YP_002993615.1| 17 RADIARIlYSKGLTQAKIAEHLGITQA 43
                                      7777776489************97665 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   2.3e-05     0.019      18      39 ..      26      47 ..      20      56 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.3e-05
                                      TTT--HHHHHHHHTS-HHHHHH CS
                        Sigma70_r4 18 geglTleEIgerlgiSrerVrq 39
                                       +glT++ I+e+lgi++  V+ 
  gi|242398191|ref|YP_002993615.1| 26 SKGLTQAKIAEHLGITQAMVSK 47
                                      579**************99985 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00026      0.22      11      43 ..      18      50 ..      11      52 .. 0.86
   2 ?    1.2   0.0      0.45   3.8e+02      22      34 ..     125     137 ..     120     143 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00026
                                      HGGGGSSTTTT--STTTSSSS---SSSS--SS- CS
                             HTH_7 11 inrvvkLleeGisiskIAkevnisRsTvYRyla 43
                                       + ++ L+++G + +kIA+ ++i+ + v +yl+
  gi|242398191|ref|YP_002993615.1| 18 ADIARILYSKGLTQAKIAEHLGITQAMVSKYLT 50
                                      567899******************998888886 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.45
                                       --STTTSSSS--- CS
                             HTH_7  22 isiskIAkevnis 34 
                                        s+++I +e+n++
  gi|242398191|ref|YP_002993615.1| 125 PSRTQILEELNLA 137
                                       589********97 PP

>> YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   5.7e-05     0.048      10      32 ..      30      52 ..      26      66 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.7e-05
                    YdaS_antitoxin 10 gqkaLAealgvsqqaVsqWlkgk 32
                                      +q++ Ae+lg++q+ Vs+ l gk
  gi|242398191|ref|YP_002993615.1| 30 TQAKIAEHLGITQAMVSKYLTGK 52
                                      699****************9987 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   7.1e-05     0.061      12      38 ..      23      49 ..      20      51 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.1e-05
                                      HHHSTTEEHHHHHHHHTS-HHHHHHHH CS
                              MarR 12 lyeqgplsvseLakklgvskstvtrvl 38
                                      + ++ +l+++++a++lg+++++v++ l
  gi|242398191|ref|YP_002993615.1| 23 ILYSKGLTQAKIAEHLGITQAMVSKYL 49
                                      667889******************876 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00047       0.4      22      43 ..      29      50 ..      15      51 .. 0.89
   2 ?   -2.8   0.0       7.6   6.5e+03      39      54 ..      73      89 ..      63      96 .. 0.57
   3 ?   -1.7   0.0       3.4   2.9e+03      36      52 ..     247     263 ..     244     273 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00047
                                      HHHHHHHHHTTSSHHHHHHHHH CS
                         HTH_Crp_2 22 ltqeelAsmlGltretvsrils 43
                                      ltq+ +A++lG+t+  vs+ l+
  gi|242398191|ref|YP_002993615.1| 29 LTQAKIAEHLGITQAMVSKYLT 50
                                      8*****************9885 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 7.6
                                      HHHHHHHHHTTSEE.ET CS
                         HTH_Crp_2 39 srilseLkreglis.rg 54
                                      s il   k+e +i+  +
  gi|242398191|ref|YP_002993615.1| 73 SLILYGAKKEDIIRfLN 89
                                      44444445555555434 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 3.4
                                       HHHHHHHHHHHHTTSEE CS
                         HTH_Crp_2  36 etvsrilseLkreglis 52 
                                       etv  i  e+k++g ++
  gi|242398191|ref|YP_002993615.1| 247 ETVRLIVEEFKKKGSLD 263
                                       89999999****99776 PP

>> Cro  Cro
   #    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       9      34 ..      25      50 ..      21      55 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00019
                                      HHHHHHHHHHHHHHTS-HHHHHHHHH CS
                               Cro  9 yvtkvGQaktAkdlgvkqsaIsKAlk 34
                                      y +   Qak A+ lg++q+ +sK l 
  gi|242398191|ref|YP_002993615.1| 25 YSKGLTQAKIAEHLGITQAMVSKYLT 50
                                      556677*****************875 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0    0.0002      0.17       4      38 ..      22      56 ..      19      62 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0002
                            HTH_26  4 elmadrgitkseLargtgisaatlsrlvkgkperv 38
                                      +++  +g+t+++ a+++gi++a +s++++gk +r+
  gi|242398191|ref|YP_002993615.1| 22 RILYSKGLTQAKIAEHLGITQAMVSKYLTGKYKRL 56
                                      5677899************************9887 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00055      0.47       7      31 ..      23      47 ..      16      58 .. 0.83
   2 ?   -2.1   0.0       5.3   4.5e+03      11      24 ..     122     136 ..     119     137 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00055
                            HTH_28  7 kllaaGhsvreaArelgisrrtvyr 31
                                       l+ +G +++ +A++lgi++ +v++
  gi|242398191|ref|YP_002993615.1| 23 ILYSKGLTQAKIAEHLGITQAMVSK 47
                                      5788999*************99965 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 5.3
                            HTH_28  11 aGh.svreaArelgi 24 
                                       +G+ s++++ +el++
  gi|242398191|ref|YP_002993615.1| 122 SGEpSRTQILEELNL 136
                                       799999999999997 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1    0.0005      0.42       4      36 ..      19      49 ..      16      50 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0005
                            HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrrdI 36
                                      +i ++L+ ++g ++ +++Ae+L+++ + v +++
  gi|242398191|ref|YP_002993615.1| 19 DIARILY-SKG-LTQAKIAEHLGITQAMVSKYL 49
                                      5667774.444.9****************9997 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00039      0.33      25      47 ..      27      49 ..      18      50 .. 0.92
   2 ?   -2.6   0.0       5.5   4.7e+03      47      53 ..     224     230 ..     223     230 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00039
                                      S---HHHHHHHHT--HHHHHHHH CS
                      Sigma70_r4_2 25 eglsykEIAellgisegtVksrl 47
                                      +gl+++ IAe lgi+ + V ++l
  gi|242398191|ref|YP_002993615.1| 27 KGLTQAKIAEHLGITQAMVSKYL 49
                                      69*****************9987 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 5.5
                                       HHHHHHH CS
                      Sigma70_r4_2  47 lsRArkk 53 
                                       ++RA+kk
  gi|242398191|ref|YP_002993615.1| 224 IFRALKK 230
                                       89***98 PP

>> RepB  RepB plasmid partitioning protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00026      0.22      14      54 ..      21      64 ..      15      81 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00026
                              RepB 14 aarleerGvdreeiasalgldkqtvskmva...raipegicaee 54
                                      a  l  +G+++++ia +lg+++++vsk+++   +++ +++++e 
  gi|242398191|ref|YP_002993615.1| 21 ARILYSKGLTQAKIAEHLGITQAMVSKYLTgkyKRLGGDLSKEI 64
                                      5556789***********************99999999996664 PP

>> KorB  KorB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00081      0.69       2      24 ..      27      49 ..      26      75 .. 0.93
   2 ?   -1.6   0.0       3.3   2.8e+03      55      74 ..     242     261 ..     238     268 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00081
                              KorB  2 kgvkqadIAkaLGksksfvslyl 24
                                      kg++qa IA+ LG  ++ vs yl
  gi|242398191|ref|YP_002993615.1| 27 KGLTQAKIAEHLGITQAMVSKYL 49
                                      89********************8 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.3
                              KorB  55 aekhpaevrafvaengeagl 74 
                                        + +++ vr +v+e++++g+
  gi|242398191|ref|YP_002993615.1| 242 ERSEDETVRLIVEEFKKKGS 261
                                       57788899999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); 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: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1834.04
//
Query:       gi|242398192|ref|YP_002993616.1|  [L=99]
Description: hypothetical protein TSIB_0199 [Thermococcus sibiricus MM 739]
Scores for complete 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-10   39.6   0.5    1.1e-09   39.0   0.5    1.3  1  VanZ      VanZ like family


Domain annotation for each model (and alignments):
>> VanZ  VanZ like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   0.5   6.1e-14   1.1e-09      55     125 ..      27      91 ..       3      92 .. 0.79

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 6.1e-14
                              VanZ  55 i.vgnvalfvplGfllplllkkkflkvlllgfllslsiElhQlfvpgRsfdvdDvilntlGallGillylll 125
                                           ++++f+++ +l  l+ + k        +++ +++E +QlfvpgRsf++ D+  n +G  +G+ll++++
  gi|242398192|ref|YP_002993616.1|  27 AgGDKIVHFLEFLIL-GLVSRDK------SYMIFPVIFESLQLFVPGRSFSFLDMGANLIGFGVGYLLWRWW 91 
                                       35779******9666.4444232......35789**********************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 631.86
//
Query:       gi|242398193|ref|YP_002993617.1|  [L=135]
Description: hypothetical protein TSIB_0200 [Thermococcus sibiricus MM 739]
Scores for complete 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-35  120.2   0.0    5.5e-35  120.0   0.0    1.0  1  UPF0047   Uncharacterised protein family UPF0047


Domain annotation for each model (and alignments):
>> UPF0047  Uncharacterised protein family UPF0047
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.0   0.0   3.1e-39   5.5e-35       1     115 []      18     132 ..      18     132 .. 0.96

  Alignments for each domain:
  == domain 1  score: 120.0 bits;  conditional E-value: 3.1e-39
                                       E-HHHHHHHHHHHT.SEEEEEEEESSSSEEEEEEESSSHHHHHHHHHHHHHHSTTT.T-GGGTTS..THHHHHHHHH CS
                           UPF0047   1 diteeveeavkesgvkeGlvlvfsrhttasltinEnadpdvqeDleealeklvpee.eYrhnaegpdnadaHlkssl 76 
                                       dit+++ee+v++s++k+G vlvf++ +t ++++ E+ ++d+ eD++++l++lvp+   Y+h++  ++na++Hl++sl
  gi|242398193|ref|YP_002993617.1|  18 DITRDIEEIVEKSEIKNGQVLVFVPGATGAIVTIEH-ENDLLEDFKRVLRELVPKGaGYKHDI-IDNNAHSHLRASL 92 
                                       8**********************************9.******************9******4.346********** PP

                                       H-SEEEEEEETTEE---TTEEEEEEESS.-SSEEEEEEEE CS
                           UPF0047  77 lgssltipvedgklalGtwqsiylveld.gpreRkvvvqv 115
                                       lgssl++p++dgk++ G wq+i++veld +pr+R++vvq+
  gi|242398193|ref|YP_002993617.1|  93 LGSSLVLPIVDGKVVRGLWQQIFFVELDvRPRRRRLVVQI 132
                                       ****************************888******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 812.35
//
Query:       gi|242398194|ref|YP_002993618.1|  [L=260]
Description: metallo-beta-lactamase superfamily protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.1e-24   85.2   0.0    5.4e-24   84.8   0.0    1.1  1  Lactamase_B_2  Beta-lactamase superfamily domain
    5.8e-12   46.0   0.2    8.8e-12   45.4   0.2    1.2  1  Lactamase_B    Metallo-beta-lactamase superfamily
    5.9e-06   26.3   0.0    8.2e-06   25.8   0.0    1.2  1  Lactamase_B_3  Beta-lactamase superfamily domain
    7.3e-05   22.0   0.0     0.0015   17.7   0.4    2.2  2  PDEase_II      cAMP phosphodiesterases class-II
  ------ inclusion threshold ------
       0.15   11.5   0.0       0.29   10.6   0.0    1.5  1  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 !   84.8   0.0   1.5e-27   5.4e-24       3     201 .]      56     231 ..      55     231 .. 0.88

  Alignments for each domain:
  == domain 1  score: 84.8 bits;  conditional E-value: 1.5e-27
                                       EEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHC CS
                     Lactamase_B_2   3 iLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylal 79 
                                        LiD++pdl  + +++l         ++i+ V++th H+DH+ gl+ l+ ++  k+++y +k++l+ l+++++  +l
  gi|242398194|ref|YP_002993618.1|  56 ALIDPSPDLYYH-MSYL--------NERIENVFITHPHFDHIGGLPELQVFK--KVRFYSHKKILD-LAKHLQETFL 120
                                       59*******999.7776........359**********************85..59***9999986.6666688999 PP

                                       HTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---...HHHHHH CS
                     Lactamase_B_2  80 eeepavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyip...eeiger 153
                                       +   + + + l+ +   ++g  +++++ +p+ h+ g         + G+++e +gkr++ +gDtg      +e+ e+
  gi|242398194|ref|YP_002993618.1| 121 GIR-EWEYVSLEFNRWYDFG--KFKVKQFPVVHQPGD-------VAGGFILEVKGKRIVITGDTGPEIlrnHELLEE 187
                                       999.8999999999999999..689************.......9********************4334679999** PP

                                       HCT-SEEEEE-S-SSTTHHHHHHT---STSHHHHCTTSSSSEEEEESB CS
                     Lactamase_B_2 154 lggadllllditayeddemirhmgHltpeeaveaaadlgakrlvliHi 201
                                       ++gadll+ ++t  ++ + i   +Hl +e+a+++a++++a +++++Hi
  gi|242398194|ref|YP_002993618.1| 188 IRGADLLVSEMT--HK-YSI-PKTHLGVEDAIKFAQKVEANKTLFVHI 231
                                       ********9977..33.333.69************************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 !   45.4   0.2   2.5e-15   8.8e-12      40     153 ..      70     176 ..      51     202 .. 0.90

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 2.5e-15
                                       SGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEEC CS
                       Lactamase_B  40 lkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmeeaddaasrkglllagvsadkpdvdeeeldgn 116
                                       +  ++++ v++TH+H+DHiGgl++l    +v  + +++++   ++  + +   r       +++  + ++   +d++
  gi|242398194|ref|YP_002993618.1|  70 YLNERIENVFITHPHFDHIGGLPELQVFKKVRFYSHKKILDLAKHLQETFLGIR-------EWEYVSLEFNRWYDFG 139
                                       557899**************************************9999777666.......89999999******** PP

                                       CCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTS CS
                       Lactamase_B 117 aggrralyvtggpghghghgvveygggkvlftGDall 153
                                        + ++ ++v++ pg  +g++++e +g+++++tGD+++
  gi|242398194|ref|YP_002993618.1| 140 KFKVKQFPVVHQPGDVAGGFILEVKGKRIVITGDTGP 176
                                       ***********************************97 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 !   25.8   0.0   2.3e-09   8.2e-06      16     157 ..      53     224 ..      45     230 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 2.3e-09
                     Lactamase_B_3  16 garilvDPfka.nlgyeppaeeaDlvlisqaledHahletlkqlaenvkvlee...................ges.. 70 
                                         + l+DP    + ++ + +e+++ v i++ + dH    +  q++++v++ ++                   +e   
  gi|242398194|ref|YP_002993618.1|  53 QINALIDPSPDlYYHMSYLNERIENVFITHPHFDHIGGLPELQVFKKVRFYSHkkildlakhlqetflgireWEYvs 129
                                       56889***998899999999***************998888888777777777666666666655666555532255 PP

                     Lactamase_B_3  71 ......levggleiravatshdavggsergenngflleqdgltiyhlGhlahe..lsseelkelgrvDvvltPvgg. 138
                                             +++g++++++++  h  ++g + g   gf+le++g +i+  G+++ e  ++ e l+e+  +D+++      
  gi|242398194|ref|YP_002993618.1| 130 lefnrwYDFGKFKVKQFPVVH--QPGDVAG---GFILEVKGKRIVITGDTGPEilRNHELLEEIRGADLLVSEMTHk 201
                                       555566999999999999999..4666666...8*****************9854466777**********999998 PP

                     Lactamase_B_3 139 ....pltlgqeealelakrLkpk 157
                                           +  lg e+a++ a++++++
  gi|242398194|ref|YP_002993618.1| 202 ysipKTHLGVEDAIKFAQKVEAN 224
                                       9997678999*******999986 PP

>> PDEase_II  cAMP phosphodiesterases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.4   4.2e-07    0.0015      72      97 ..      66      91 ..      28     109 .. 0.79
   2 ?    2.4   0.0     0.019        69     135     233 ..      92     188 ..      91     192 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4.2e-07
                                      HHHHHHHHTEEEEE-S---GGGTHHH CS
                         PDEase_II 72 kktyeiknniksylItHsHLDHvsgl 97
                                       ++  ++++i++ +ItH+H DH++gl
  gi|242398194|ref|YP_002993618.1| 66 YHMSYLNERIENVFITHPHFDHIGGL 91
                                      46667899****************97 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.019
                                       --GGGSTT-....-EEEEE--.TT--EE-SSSSEEEEE................EEEEEEE-TTT--EEEEEEEEEE CS
                         PDEase_II 135 Pnlpsfkrvnlislvkliele.pkelnkltettldvvanefsfs.....vkvktfevnhgslikknsevlSsaflft 205
                                       P+l+ fk+v+++s  k+ +l  + + + l + +++ v  ef         kvk f+v h+       +v    f+  
  gi|242398194|ref|YP_002993618.1|  92 PELQVFKKVRFYSHKKILDLAkHLQETFLGIREWEYVSLEFNRWydfgkFKVKQFPVVHQP-----GDVA-GGFI-- 160
                                       8888899998888888888851445556788888888888877744444555555555544.....3443.4455.. PP

                                       ETTT--EEEEE-S-----TTTS-HHHHH CS
                         PDEase_II 206 devskesilvfgDvesdlssseslnlki 233
                                       +ev ++ i++ gD++++   + +l ++i
  gi|242398194|ref|YP_002993618.1| 161 LEVKGKRIVITGDTGPEILRNHELLEEI 188
                                       5889999999999999988877777666 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 ?   10.6   0.0     8e-05      0.29      30      80 ..      69     113 ..      51     134 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 8e-05
                     Lactamase_B_6  30 ekviptvdliLLshatlehlGayallyakfksklllnipvyatlpvvkLGr 80 
                                       +   ++++ + ++h+  +h+G+++ l       ++++++ y+ + +  L++
  gi|242398194|ref|YP_002993618.1|  69 SYLNERIENVFITHPHFDHIGGLPELQ------VFKKVRFYSHKKILDLAK 113
                                       333468999*************87554......567788888887777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       663  (0.0369792); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); 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: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1612.19
//
Query:       gi|242398195|ref|YP_002993619.1|  [L=220]
Description: zinc-dependent protease [Thermococcus sibiricus MM 739]
Scores for complete 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-46  158.2   2.9    1.9e-45  155.5   2.9    1.9  1  DUF45     Protein of unknown function DUF45
  ------ inclusion threshold ------
      0.023   14.8   0.1      0.051   13.6   0.1    1.5  1  WLM       WLM domain
      0.028   13.8   0.5      0.028   13.8   0.5    1.7  2  TilS_C    TilS substrate C-terminal domain


Domain annotation for each model (and alignments):
>> DUF45  Protein of unknown function DUF45
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.5   2.9   3.1e-49   1.9e-45       1     206 [.      21     201 ..      21     202 .. 0.93

  Alignments for each domain:
  == domain 1  score: 155.5 bits;  conditional E-value: 3.1e-49
                             DUF45   1 knlrlrvepdgsvevsaPkgvseeeiedfvkkkakwiekklakleerakeaekelesgesfpllGkkyrlkvekgke 77 
                                       +++r+ v p+g++e++ P++    ++e f++ k+kwi +k++ +e+         ++ + fp+lG+ y+    ++  
  gi|242398195|ref|YP_002993619.1|  21 RYMRIYVTPSGKLEIVSPTR----RVEPFLRAKEKWIITKIEAIEK--------AKQLSGFPYLGRFYNTGSGEKF- 84 
                                       689**************995....**********************........89999*********99888888. PP

                             DUF45  78 asvklkreelelavkkeeeeeklrkaleewlrkeakeeleerlaklaaklgvkprsvsikdmktrWGscsskgkirl 154
                                             + + +++++++      +k+le  lr +++e++++++++ ++kl+v++++v i+++ktrWGscs+kg++++
  gi|242398195|ref|YP_002993619.1|  85 ------KVNDNMIKLPH------NKKLESTLRVRLREIITPLIQEKTKKLNVNVNKVFIRKQKTRWGSCSPKGNLNF 149
                                       ......44444444444......5789************************************************** PP

                             DUF45 155 nwrLvkappevidYVvvHElaHlleknHskrFwalvekllPdwkeakkeLkr 206
                                       n+ ++ +pp++idY v HE+aHl+e+nHskrFw+lvek+ Pdwk+ ++eLk+
  gi|242398195|ref|YP_002993619.1| 150 NLAMLALPPQLIDYLVSHEVAHLVEMNHSKRFWKLVEKFHPDWKRKRRELKE 201
                                       **************************************************96 PP

>> WLM  WLM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   8.6e-06     0.051      87     113 ..     165     191 ..     155     200 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.6e-06
                               WLM  87 llHELaHnvygpHdakFyallkeLeke 113
                                         HE aH v  +H ++F++l+++ + +
  gi|242398195|ref|YP_002993619.1| 165 VSHEVAHLVEMNHSKRFWKLVEKFHPD 191
                                       56******************9987655 PP

>> TilS_C  TilS substrate 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   6.2e+03      36      50 ..      40      53 ..      36      54 .. 0.58
   2 ?   13.8   0.5   4.7e-06     0.028       4      28 ..     180     204 ..     177     207 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1
                                      HCCCSEEEEETTEEE CS
                            TilS_C 36 lRdriPLlfygdelv 50
                                      +R + P+l + ++++
  gi|242398195|ref|YP_002993619.1| 40 RRVE-PFLRAKEKWI 53
                                      4443.7777777665 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 4.7e-06
                                       EC-.TTSEEEBTTSSSEEEHHHHHH CS
                            TilS_C   4 rfrrggerlqpagrggsrkLKklfq 28 
                                       rf++  e+++p+ ++++r+LK++++
  gi|242398195|ref|YP_002993619.1| 180 RFWKLVEKFHPDWKRKRRELKEWWI 204
                                       899999******************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); 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: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1354.52
//
Query:       gi|242398196|ref|YP_002993620.1|  [L=349]
Description: hypothetical protein TSIB_0203 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-06   28.4   0.0      5e-06   26.7   0.0    1.8  2  Lactamase_B    Metallo-beta-lactamase superfamily
    3.2e-06   27.1   0.0    8.6e-06   25.7   0.0    1.6  2  Lactamase_B_3  Beta-lactamase superfamily domain
    0.00011   21.8   0.0       0.15   11.6   0.0    2.4  2  Lactamase_B_2  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
       0.12   12.2   0.4        4.4    7.2   0.0    2.5  2  SHOCT          Short 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 !   26.7   0.0   1.1e-09     5e-06       6      59 ..      17      81 ..      14      82 .. 0.97
   2 ?   -1.6   0.0      0.52   2.3e+03     137     152 ..     231     246 ..     182     308 .. 0.63

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 1.1e-09
                                      SEEEEEEETTCEEEES--SCHHHHHHHH...........HHHHHTSGGGGEEEEE-SBSSHHHHT CS
                       Lactamase_B  6 vnsyliegdggviLiDtGtsteaaraal...........elaalglkpkdvdavilTHlHlDHiG 59
                                      ++++l+ +++  ++iD+G+   ++ +               +a++   k+ d ++++H+H+DH++
  gi|242398196|ref|YP_002993620.1| 17 SSCVLVKTPDISVIIDPGIAIMQPSFPAseekkiewlieGEKAIKNASKEADVLVISHYHYDHYF 81
                                      79*************************************************************95 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.52
                                       EEEETTCCEEEECTTT CS
                       Lactamase_B 137 vveygggkvlftGDal 152
                                       v+ey+++k++ + D+ 
  gi|242398196|ref|YP_002993620.1| 231 VIEYEDEKLIHSSDLN 246
                                       4455555555544443 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 !   25.7   0.0   1.9e-09   8.6e-06       7      65 ..      17      94 ..      15     130 .. 0.81
   2 ?   -2.4   0.0      0.87   3.9e+03     145     160 ..     289     304 ..     256     317 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 1.9e-09
                     Lactamase_B_3  7 hnsflletagarilvDPf....................kanlgyeppaeeaDlvlisqaledHahletlkqlaenvkvl 65
                                      ++++l++t++ ++++DP+                    ++++  ++  +eaD+++is+ + dH+ +  l+  ++  ++l
  gi|242398196|ref|YP_002993620.1| 17 SSCVLVKTPDISVIIDPGiaimqpsfpaseekkiewliEGEKAIKNASKEADVLVISHYHYDHYFPGDLEV-YRGKRLL 94
                                      79****************999988887777666666654455666666****************9998886.5544554 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.87
                     Lactamase_B_3 145 eealelakrLkpklvl 160
                                       e+a+++++++++++++
  gi|242398196|ref|YP_002993620.1| 289 ENAVKIVRKIDAEIII 304
                                       6788888888888876 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 !   11.6   0.0   3.2e-05      0.15      25      47 ..      61      85 ..      28     101 .. 0.65
   2 !    7.9   0.0   0.00043       1.9      89     201 .]     195     308 ..     160     308 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.2e-05
                                      S--..SEEEEE-SS--HHHH..GGG CS
                     Lactamase_B_2 25 rdelppidaVllthaHyDHl..agl 47
                                      ++  ++ d+++++h HyDH+   +l
  gi|242398196|ref|YP_002993620.1| 61 KNASKEADVLVISHYHYDHYfpGDL 85
                                      3444789************965555 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00043
                                       EE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S.---HHHHHHHCT..-SEEEE CS
                     Lactamase_B_2  89 eldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtg.yipeeigerlgg..adllll 162
                                        ++ g +f++gd++  i++t  + ++g  + ++ g +++ +ie +++++ ++ D++  i e+ +e++ +  +++l+l
  gi|242398196|ref|YP_002993620.1| 195 HFADGREFQFGDTK--IRFT-GPMFHGI-EFSRVGWVISTVIEYEDEKLIHSSDLNgPIIEDYAEWIIKenPNILIL 267
                                       24479999999876..5554.5666666.56899999******************9433366666664445999999 PP

                                       E-S-SSTTHHHH..HHT---STSHHHHCTTSSSSEEEEESB CS
                     Lactamase_B_2 163 ditayeddemir..hmgHltpeeaveaaadlgakrlvliHi 201
                                       d+ ++    +     +    +e+av+++++++a++ ++ H+
  gi|242398196|ref|YP_002993620.1| 268 DGPMTYMLGYLLnkINLRRAVENAVKIVRKIDAEIIIYDHH 308
                                       97644433322234555555688888888888888887775 PP

>> SHOCT  Short C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1     0.027   1.2e+02      19      28 .]     155     164 ..     155     164 .. 0.96
   2 ?    7.2   0.0   0.00099       4.4       7      21 ..     326     340 ..     326     343 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.027
                             SHOCT  19 EFeakKakLL 28 
                                       E+++++++LL
  gi|242398196|ref|YP_002993620.1| 155 EYNTRRKQLL 164
                                       9********8 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.00099
                             SHOCT   7 keLyarGeIteEEFe 21 
                                       +e++++ ++t +EF 
  gi|242398196|ref|YP_002993620.1| 326 AERLDKNLLTAAEFL 340
                                       59************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); 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 0.35s 00:00:00.92 Elapsed: 00:00:00.52
# Mc/sec: 2003.96
//
Query:       gi|242398197|ref|YP_002993621.1|  [L=139]
Description: Polyketide Cyclase Snoal [Thermococcus sibiricus MM 739]
Scores for complete 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-38  130.2   0.2      4e-38  130.1   0.2    1.0  1  SnoaL           SnoaL-like polyketide cyclase
      7e-23   81.2   0.0    8.1e-23   81.0   0.0    1.1  1  SnoaL_2         SnoaL-like domain
  ------ inclusion threshold ------
      0.015   15.3   0.0      0.026   14.6   0.0    1.3  1  Spo0A_C         Sporulation initiation factor Spo0A C termina
      0.027   14.0   0.0      0.052   13.1   0.0    1.5  1  Lipoprotein_15  Secreted repeat of unknown function
        0.1   12.4   0.2       0.13   12.1   0.2    1.1  1  NMT             Myristoyl-CoA:protein N-myristoyltransferase,


Domain annotation for each model (and alignments):
>> SnoaL  SnoaL-like polyketide cyclase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.1   0.2   1.1e-41     4e-38       3     126 .]       8     133 ..       6     133 .. 0.98

  Alignments for each domain:
  == domain 1  score: 130.1 bits;  conditional E-value: 1.1e-41
                                       HHHHHHHHHHTT-HHHHHGTEEEEEEETCCTTTCECHHHHHHHHHHHHHHHCTTCEEEEEEEEEETTEEEEEEEEEE CS
                             SnoaL   3 vlrfyeevwnsgdldaldelvaedvvdhnpeeeparGlegfrafveelfkafPDlkvevedlvaegdkvaarltftG 79 
                                       +++ ++evwn+g++++lde++a+++v+h+p++ + + le+f++ v  + k+fPD++v++ed+++egd ++ r+++tG
  gi|242398197|ref|YP_002993621.1|   8 IQQIVDEVWNKGNVNTLDEFYAQNFVNHDPANPDVTNLEKFKEWVLFNHKTFPDFHVTIEDTITEGDEIVKRWKVTG 84 
                                       78999***************************9999***************************************** PP

                                       EESSEBTT..BE-TT-EEEEEEEEEEEEETTEEEEEEEEECHHHHHHHC CS
                             SnoaL  80 thtgeflG..ipptGkkvkfeeitllrvedGkIveewdviDllgllrQl 126
                                       t +ge++G  ipptGk+v++e++ ++r+e +kI+e w+ +Dll++l+Ql
  gi|242398197|ref|YP_002993621.1|  85 TQKGEMMGgkIPPTGKQVTIEGTSIYRFEGDKIAEMWWGYDLLSMLQQL 133
                                       ************************************************8 PP

>> SnoaL_2  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.0   0.0   2.2e-26   8.1e-23       6     101 ..      14     119 ..       8     120 .. 0.95

  Alignments for each domain:
  == domain 1  score: 81.0 bits;  conditional E-value: 2.2e-26
                                       HHHHTTCHHHHHHTEEEEEEEEETTSE.EESHHHHHHHHHHHHHHEEEEEEEEEEEEEETTEEEEEEEEEEE..... CS
                           SnoaL_2   6 aalnagdldalaalfapdvvwedpgge.lrGreairaffralfaafpdlrfeihdvvadgdrvavewtvtgt..... 76 
                                       +++n+g++ +l++++a ++v +dp+++ ++  e +++++   +++fpd++++i+d +++gd+++ +w vtgt     
  gi|242398197|ref|YP_002993621.1|  14 EVWNKGNVNTLDEFYAQNFVNHDPANPdVTNLEKFKEWVLFNHKTFPDFHVTIEDTITEGDEIVKRWKVTGTqkgem 90 
                                       49**********************5555**********999999********************************* PP

                                       ....EETTSSEEEEEEEEEEEEETTEEEE CS
                           SnoaL_2  77 ....ipatgrgvtvrgvdvfrvrdGkive 101
                                           ip+tg++vt++g++++r++++ki+e
  gi|242398197|ref|YP_002993621.1|  91 mggkIPPTGKQVTIEGTSIYRFEGDKIAE 119
                                       ****************************9 PP

>> Spo0A_C  Sporulation initiation factor Spo0A C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   7.2e-06     0.026      57      91 ..       5      37 ..       2      45 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 7.2e-06
                           Spo0A_C 57 eraIrhaIevaWekgnkekleelfgysinsekgkP 91
                                      er I+++++ +W+kgn ++l+e++ +++ +  + P
  gi|242398197|ref|YP_002993621.1|  5 ERIIQQIVDEVWNKGNVNTLDEFYAQNFVN--HDP 37
                                      899*******************99955443..333 PP

>> Lipoprotein_15  Secreted repeat of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.4e-05     0.052      10      29 ..     100     119 ..      95     125 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.4e-05
                    Lipoprotein_15  10 kqvaykGmPLYtFakDkkpg 29 
                                       kqv+ +G  +Y+F++Dk + 
  gi|242398197|ref|YP_002993621.1| 100 KQVTIEGTSIYRFEGDKIAE 119
                                       9***************9665 PP

>> NMT  Myristoyl-CoA:protein N-myristoyltransferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   3.7e-05      0.13      29      83 ..      15      69 ..       8      87 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.7e-05
                                      TTSHHHHHHHHHHHHHHSSCTTTSTEEE---HHHHHHHCTSTT--GGGEEEEEET CS
                               NMT 29 ledeeelkevyelLsenYvedddamfrfkyskeflkWalkppgykkewhvgvrvk 83
                                      + ++ +++ + e+  +n+v++d a   ++  ++f +W l   ++ +++hv++  +
  gi|242398197|ref|YP_002993621.1| 15 VWNKGNVNTLDEFYAQNFVNHDPANPDVTNLEKFKEWVLFNHKTFPDFHVTIEDT 69
                                      56788999999****************************************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 990.71
//
Query:       gi|242398198|ref|YP_002993622.1|  [L=235]
Description: Acetyl-CoA synthetase II (ACSII, ADP-forming) and succinyl-CoA synthetase (SCS, ADP-forming), subunit beta [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-77  260.4   0.2    1.2e-77  260.3   0.2    1.0  1  ATP-grasp_5  ATP-grasp domain
    5.9e-05   22.7   0.1     0.0002   21.0   0.1    1.8  2  ATP-grasp_2  ATP-grasp domain
     0.0041   16.6   0.0     0.0078   15.7   0.0    1.7  1  CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP bindin


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 !  260.3   0.2   2.1e-81   1.2e-77       2     222 .]      12     234 ..      11     234 .. 0.97

  Alignments for each domain:
  == domain 1  score: 260.3 bits;  conditional E-value: 2.1e-81
                       ATP-grasp_5   2 alaegrtlLteaeakelleaygipvvetrlassaeeaveaaeeigypvvlKivspdilhKtdvgGvrlnlkdaeevr 78 
                                       +l++gr+ L e+eak++l+ay++p++e +la++ +ea+++a+eigypvv+K++sp+ilhK+d++ v+l++k++ee++
  gi|242398198|ref|YP_002993622.1|  12 VLTQGRKALVEYEAKQVLKAYDLPLPEEKLAKNLDEAIKYANEIGYPVVMKLMSPQILHKSDAKVVMLKIKNDEELK 88 
                                       7899************************************************************************* PP

                       ATP-grasp_5  79 aaaeeilervkekspeariegvlVqemakrggrElivgvteDpvFGpvilfGlGGtavevlkdvavalpplnstlar 155
                                       +++eei e++++++p+a+i gvl+ +m k  grE+i+gvteDp+FG  ++fGlGG+ ve+lkdv++++ p+++++a 
  gi|242398198|ref|YP_002993622.1|  89 QKWEEIHENARKYKPDAEILGVLIAPMLK-PGREIIIGVTEDPQFGHALMFGLGGIFVEILKDVTFRIIPIEEKDAW 164
                                       ***************************88.8********************************************** PP

                       ATP-grasp_5 156 eliertkaskllkgvrgekkadlaaleellvrlsqLvvdlpe.IreldinPllveeeg..vvalDarirl 222
                                       ++i+++k +++l g rge++ad++a++++++++sqL++dl+  I+e+d+nP++v++eg  +v++Dari l
  gi|242398198|ref|YP_002993622.1| 165 AMIKSIKGYPILAGARGEAPADMKAIVDMMLKVSQLIDDLKDyIKEMDLNPIFVYPEGegAVIVDARIIL 234
                                       ***************************************9877***********995555*******976 PP

>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.1   3.3e-08    0.0002       2      45 ..      20      62 ..      19     129 .. 0.83
   2 ?   -1.5   0.0      0.26   1.6e+03      48      57 ..     175     189 ..     161     217 .. 0.62

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 3.3e-08
                                      E-HHHHHHHHHCTT----SEEEESSHHHHHHHHHHHTSSSEEEE CS
                       ATP-grasp_2  2 lhEyqakeilakygvkvpegevaesaeeaeeaakklgekelvvK 45
                                      l Ey+ak++l+ y+++ pe ++a++ +ea + a+++g  + v+K
  gi|242398198|ref|YP_002993622.1| 20 LVEYEAKQVLKAYDLPLPEEKLAKNLDEAIKYANEIGYPV-VMK 62
                                      89***********************************998.666 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.26
                                       -SSSTCCCT.....T CS
                       ATP-grasp_2  48 vlaGGRGKa.....g 57 
                                       +laG+RG a     +
  gi|242398198|ref|YP_002993622.1| 175 ILAGARGEApadmkA 189
                                       677888877544431 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 !   15.7   0.0   1.3e-06    0.0078       4      44 ..      24      62 ..      22     130 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.3e-06
                                      HHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEE CS
                       CPSase_L_D2  4 sakealkkinvpvvpssaapvetleealaiakeigyPviik 44
                                      +ak+ lk+ + p+ + + a  ++l+ea++ a+eigyPv++k
  gi|242398198|ref|YP_002993622.1| 24 EAKQVLKAYDLPLPEEKLA--KNLDEAIKYANEIGYPVVMK 62
                                      5788889999999888877..******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       961  (0.0536003); expected 358.6 (0.02)
Passed bias filter:                      732  (0.0408277); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 1690.67
//
Query:       gi|242398199|ref|YP_002993623.1|  [L=473]
Description: Acyl-CoA synthetase, subunit alpha [Thermococcus sibiricus MM 739]
Scores for complete 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-56  188.9   5.9    1.2e-54  183.8   0.8    2.9  4  Succ_CoA_lig    Succinyl-CoA ligase like flavodoxin domain
    2.6e-28   98.9   0.8    2.4e-25   89.3   0.0    3.3  3  CoA_binding_2   CoA binding domain
    1.5e-15   57.6   5.0    2.7e-15   56.8   0.9    2.6  2  CoA_binding     CoA binding domain
     0.0024   17.7   0.2     0.0063   16.3   0.1    1.8  2  Ligase_CoA      CoA-ligase
     0.0088   16.1   0.2       0.16   12.0   0.0    2.8  3  B12-binding     B12 binding domain
  ------ inclusion threshold ------
      0.016   15.3   0.0       0.79    9.8   0.0    2.6  2  Hpr_kinase_N    HPr Serine kinase N terminus
      0.025   14.8   0.3       0.42   10.9   0.0    3.0  4  Asparaginase_C  Glutaminase/Asparaginase C-terminal domain
      0.076   13.8   0.1          4    8.3   0.0    2.7  2  GFO_IDH_MocA    Oxidoreductase family, NAD-binding Rossmann f
      0.077   13.4   0.7        9.8    6.5   0.2    3.1  3  Radical_SAM     Radical SAM superfamily


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 ?   -3.5   0.0         4     8e+03      75      96 ..      94     117 ..      92     123 .. 0.74
   2 !  183.8   0.8   6.2e-58   1.2e-54       2     138 .]     168     304 ..     167     304 .. 0.99
   3 ?   -3.0   0.0         3   5.9e+03       3      28 ..     314     339 ..     313     342 .. 0.81
   4 !    6.9   0.0    0.0025       5.1      45      95 ..     378     433 ..     366     445 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 4
                      Succ_CoA_lig  75 arraark..kpvvvlksGrseaga 96 
                                       ++++a+k  k v+++  G  e g+
  gi|242398199|ref|YP_002993623.1|  94 MKEIAEKgiKSVIIITGGFGELGE 117
                                       667777778999999998766655 PP

  == domain 2  score: 183.8 bits;  conditional E-value: 6.2e-58
                      Succ_CoA_lig   2 GkialisqSGalalalldwaasrglgfskvvslGneadvdvadlleylaedpetkvillylEsirdgrkflsaarra 78 
                                       G+ia+++qSGa+a+a+ldwaa  g+g+ k+vs+Gn++dvd adl++y+  d+++k+++ly+E++++grkf++aa+r+
  gi|242398199|ref|YP_002993623.1| 168 GSIAFVTQSGAFAAAMLDWAAGAGIGIGKMVSYGNKLDVDDADLMDYFIYDESIKAVTLYIEGVKEGRKFIEAAKRI 244
                                       99*************************************************************************** PP

                      Succ_CoA_lig  79 arkkpvvvlksGrseagaraaashtgalagsdavvdaafrqaGvlrvdsleelfdaaell 138
                                       ++ kpv++lksG++e ga+aa+shtg+lag d ++da+f+q+G+lr++++e +fd+a+++
  gi|242398199|ref|YP_002993623.1| 245 TKVKPVIALKSGKTEYGAKAASSHTGSLAGADIIYDAVFKQTGILRAEDFEHMFDVAKAF 304
                                       *********************************************************986 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 3
                      Succ_CoA_lig   3 kialisqSGalalalldwaasrglgf 28 
                                       +i++i+  G+ +++  d++a+ gl++
  gi|242398199|ref|YP_002993623.1| 314 RIGIITDGGGAGVMASDAVAKFGLKM 339
                                       68999999999999999888877665 PP

  == domain 4  score: 6.9 bits;  conditional E-value: 0.0025
                      Succ_CoA_lig  45 lleylaedpetkvillyl...Esirdgrkflsaarraark..kpvvvlksGrseag 95 
                                        +e++ +dp++++i++ +     + + ++ ++++ + a+k  kp+v++ +G +++ 
  gi|242398199|ref|YP_002993623.1| 378 AIEAFVNDPNVDAIVIIVlfqVPLLNEEEIIEILAEYAKKseKPIVAVAMGGKKTE 433
                                       68899999999987654411156778999***9999998889********987665 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.3   0.0   1.2e-28   2.4e-25       1     114 [.      17     146 ..      17     148 .. 0.97
   2 ?    2.5   0.0       0.1     2e+02      82     105 ..     171     194 ..     163     203 .. 0.86
   3 ?    3.7   0.1     0.042        83      16     106 ..     343     447 ..     331     450 .. 0.65

  Alignments for each domain:
  == domain 1  score: 89.3 bits;  conditional E-value: 1.2e-28
                                       --EEEET--S-TTSHHHHHHHHHHH.......HT--EEEESSS-SEETTEES----T....T--EEEE-S-HHHHGG CS
                     CoA_binding_2   1 rtiaVvGasdnpgkfgykvlrylle.......hglpvvpVnpkeeeilgekvyaslaedpepvdlvdvftppeatpe 70 
                                       + +a++Ga +++gk g+ +++++++       +g  ++pVnpk +ei+g kvy+ ++e pe+ dl+++ +p+  +p+
  gi|242398199|ref|YP_002993623.1|  17 KAVAIIGATNKKGKVGNVIFENFKKnkeqgifKG-SIYPVNPKLDEIEGYKVYKGVKELPEDTDLAVISIPAPFVPQ 92 
                                       679****************************999.**********************847***************** PP

                                       GHHHHHHH--SEEEE-TT..........---HHHHHHHHHTT-EEE.ES-HHHH CS
                     CoA_binding_2  71 ivkealalgakavwlqpg..........sedeeaaelaeeagirvvgdrCilve 114
                                       ++ke++++g+k+v++  g            +ee++++a+e+gir++g++C++v 
  gi|242398199|ref|YP_002993623.1|  93 TMKEIAEKGIKSVIIITGgfgelgeegrKMEEEILKIAKENGIRIIGPNCVGVY 146
                                       ****************************************************96 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.1
                                       EEEE-TT---HHHHHHHHHTT-EE CS
                     CoA_binding_2  82 avwlqpgsedeeaaelaeeagirv 105
                                       a++ q+g++ ++++++a+ agi +
  gi|242398199|ref|YP_002993623.1| 171 AFVTQSGAFAAAMLDWAAGAGIGI 194
                                       7899****************9966 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.042
                                       HHHHHHHHHHHT--EEEESSS-SEETTEES----T..........T--...EEEE-....S-HHHHGGGHHHHHHH. CS
                     CoA_binding_2  16 gykvlryllehglpvvpVnpkeeeilgekvyasla...ed...pepvd...lvdvf....tppeatpeivkealal. 78 
                                       +  +++yl+eh  p ++V  + + + g +  ++ +   e+   + +vd   ++++f    ++ e++ ei+ e +++ 
  gi|242398199|ref|YP_002993623.1| 343 SEEIIKYLKEHF-PPHAVAGNPTDVVGDTDAQRYKyaiEAfvnDPNVDaivIIVLFqvplLNEEEIIEILAEYAKKs 418
                                       677888888876.8888877777777766444444222212334455554433332222257888888888885554 PP

                                       .--SEEEE-TT---HHHHHHHHHTT-EEE CS
                     CoA_binding_2  79 .gakavwlqpgsedeeaaelaeeagirvv 106
                                        ++ +++ + g   e  a+++e++g++v 
  gi|242398199|ref|YP_002993623.1| 419 eKPIVAVAMGGKKTEYYAKMLENKGVPVY 447
                                       47999999999999999999999999885 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.8   0.9   1.4e-18   2.7e-15       2      95 ..      15     110 ..      14     111 .. 0.87
   2 ?    2.0   0.2      0.17   3.5e+02      32      95 ..     357     427 ..     335     428 .. 0.74

  Alignments for each domain:
  == domain 1  score: 56.8 bits;  conditional E-value: 1.4e-18
                                       TTEEEEEETTTSHHHHHH.H...HHHHHHHECEE..EEEEC-TTTTTCEETTEEEESCHHHHHHHCTTTEEEEES-H CS
                       CoA_binding   2 kdtkviviGagglgiagl.y...hfkeklkygik..avfgvnprkvgtevlglpvyksvdeleektevdvavitvPa 72 
                                       +++ v++iGa+++ ++++ +   +fk++++ gi   ++++vnp+   +e++g +vyk v+el+e+   d avi +Pa
  gi|242398199|ref|YP_002993623.1|  15 EPKAVAIIGATNKKGKVGnVifeNFKKNKEQGIFkgSIYPVNPK--LDEIEGYKVYKGVKELPED--TDLAVISIPA 87 
                                       5788*********9988755222455666666655889******..*******************..********** PP

                                       HHHHHHHHHHHHTT-SEEEEESS CS
                       CoA_binding  73 esaqeavdelveagikgiviite 95 
                                       +++ ++++e +e+gik ++iit 
  gi|242398199|ref|YP_002993623.1|  88 PFVPQTMKEIAEKGIKSVIIITG 110
                                       *********************95 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.17
                                       EEEEC-TT.TTTCEETTEEEESCHHHHHHHCTTTEEEEES.......-HHHHHHHHHHHHHTT-SEEEEESS CS
                       CoA_binding  32 avfgvnpr.kvgtevlglpvyksvdeleektevdvavitv.......Paesaqeavdelveagikgiviite 95 
                                       +++  np+  vg++      y +++  +++ +vd+ vi v        +e++ e+  e ++++ k+iv+++ 
  gi|242398199|ref|YP_002993623.1| 357 HAVAGNPTdVVGDTDAQRYKY-AIEAFVNDPNVDAIVIIVlfqvpllNEEEIIEILAEYAKKSEKPIVAVAM 427
                                       566666664566666666666.88888888779999999999998888899999999999999999998875 PP

>> Ligase_CoA  CoA-ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.0       5.6   1.1e+04      95     118 ..     237     257 ..     230     275 .. 0.65
   2 !   16.3   0.1   3.2e-06    0.0063      57     149 ..     371     456 ..     365     460 .. 0.79

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 5.6
                                       HHHHHHHTT...--S-EEEEEECT CS
                        Ligase_CoA  95 llkaikeakaegrelpvvarvaGt 118
                                       +++a+k++    + +pv+a   G 
  gi|242398199|ref|YP_002993623.1| 237 FIEAAKRIT---KVKPVIALKSGK 257
                                       566666666...666777766664 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 3.2e-06
                                       .HHHHHHHHHHHHS-TT-SEEEEE..EEESSSEHHHHHHHHHHHHHHTT...--S-EEEEEECTTHH.....HHHHH CS
                        Ligase_CoA  57 Dptkriealkklaadpevkvilld..ivlGygahedpaaellkaikeakaegrelpvvarvaGteadpqelseqaka 131
                                       D +++  a++ +++dp+v++i++   + +   ++e++++ l++ +k+ +     +p+va  +G ++     +  ak+
  gi|242398199|ref|YP_002993623.1| 371 DAQRYKYAIEAFVNDPNVDAIVIIvlFQVPLLNEEEIIEILAEYAKKSE-----KPIVAVAMGGKKT----EYYAKM 438
                                       7889999***********9876551055666677777766666666665.....9999999999998....8999** PP

                                       HHTTTSSEEE-SSHHHHH CS
                        Ligase_CoA 132 leeagveiasskaqalra 149
                                       le+ gv ++s+ +  +ra
  gi|242398199|ref|YP_002993623.1| 439 LENKGVPVYSTPERGVRA 456
                                       *********998877776 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1      0.36   7.1e+02      67      89 ..      89     112 ..      80     122 .. 0.77
   2 ?   -1.3   0.1       1.1   2.1e+03      41      56 ..     124     139 ..      98     151 .. 0.57
   3 !   12.0   0.0   8.2e-05      0.16      33     103 ..     369     442 ..     342     456 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.36
                       B12-binding  67 avkelvel..lkrirprvkvvvGGa 89 
                                       +v +++++  +k+i + v++++GG 
  gi|242398199|ref|YP_002993623.1|  89 FVPQTMKEiaEKGI-KSVIIITGGF 112
                                       66677777767777.679*****94 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.1
                       B12-binding  41 edivaairaekpdvvg 56 
                                       e+i++ ++++  +++g
  gi|242398199|ref|YP_002993623.1| 124 EEILKIAKENGIRIIG 139
                                       5566666666666665 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 8.2e-05
                       B12-binding  33 llganvenedivaairaekpdvvglSalltsqleavkelvel.....lkrirprvkvvvGGahpsldpeetleakl 103
                                       +++a+  + +i+a + + ++d++++ +l++  l + +e++e      +k+++p v v++GG   ++++++ le+  
  gi|242398199|ref|YP_002993623.1| 369 DTDAQRYKYAIEAFVNDPNVDAIVIIVLFQVPLLNEEEIIEIlaeyaKKSEKPIVAVAMGGKKTEYYAKM-LEN-K 442
                                       667777778999*************99999999999999999999****************998888887.665.3 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 ?    2.4   0.0     0.075   1.5e+02      74     108 ..      95     138 ..      91     142 .. 0.70
   2 ?    9.8   0.0    0.0004      0.79      64     124 ..     402     463 ..     399     463 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.075
                                       HHHHTT--.S-EEEETTT-........--HHHHHHHHHH---EE CS
                      Hpr_kinase_N  74 eklfskki.pciiltrgle........ppeellelaeeygvpll 108
                                       +++ +k+i  +ii+t g+         ++ee+l++a+e+g+ ++
  gi|242398199|ref|YP_002993623.1|  95 KEIAEKGIkSVIIITGGFGelgeegrkMEEEILKIAKENGIRII 138
                                       55555555234555666666666666699***********9987 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0004
                                       -HHHHH..HHHHHHT.T--S-EEEETTT---HHHHHHHHHH---EEEESS-HHHHHTTHHHH CS
                      Hpr_kinase_N  64 lseeerkerleklfs.kkipciiltrgleppeellelaeeygvpllrtklstsefiaeliry 124
                                       l+eee +e+l ++ + ++ p++ ++ g + +e+ +++ e++gvp+++t+++  + +a l +y
  gi|242398199|ref|YP_002993623.1| 402 LNEEEIIEILAEYAKkSEKPIVAVAMGGKKTEYYAKMLENKGVPVYSTPERGVRAMAGLVQY 463
                                       6889999999999963679********************************99999988776 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 ?   -2.0   0.0         2     4e+03      20      53 ..      14      47 ..       8      48 .. 0.83
   2 ?   10.9   0.0   0.00021      0.42      10      55 ..      88     137 ..      80     187 .. 0.83
   3 ?   -0.2   0.0      0.58   1.2e+03      25      41 ..     315     331 ..     209     353 .. 0.83
   4 ?   -2.2   0.0       2.4   4.7e+03      22      57 ..     385     424 ..     368     430 .. 0.55

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2
                                      HHTT--EEEEEEBTTTB--HHHHHHHHHHHTTT- CS
                    Asparaginase_C 20 lkkgakGvvlegtGvGnlpsallealkeakargi 53
                                      ++ +a +++ ++   G++ +++ e +k+ k++gi
  gi|242398199|ref|YP_002993623.1| 14 FEPKAVAIIGATNKKGKVGNVIFENFKKNKEQGI 47
                                      5677788899999999999999999999999998 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00021
                                       T--HHHHHHHHHTT--EEEEEEBTTTB--H...HHH.HHHHHHHTTT-EE CS
                    Asparaginase_C  10 gmdtkvlkallkkgakGvvlegtGvGnlps...all.ealkeakargivv 55 
                                        + ++++k++ +kg+k v++ ++G G l +   ++  e lk ak++gi +
  gi|242398199|ref|YP_002993623.1|  88 PFVPQTMKEIAEKGIKSVIIITGGFGELGEegrKMEeEILKIAKENGIRI 137
                                       56799***********************9877755404455555666644 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.58
                                       -EEEEEEBTTTB--HHH CS
                    Asparaginase_C  25 kGvvlegtGvGnlpsal 41 
                                        G++  g+G+G + s+ 
  gi|242398199|ref|YP_002993623.1| 315 IGIITDGGGAGVMASDA 331
                                       48999999999888833 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 2.4
                                       T.T--EEEE.EEBTTTB--H.HHHHHHHHHH.TTT-EEEE CS
                    Asparaginase_C  22 k.gakGvvl.egtGvGnlps.allealkeak.argivvva 57 
                                         +++++v+  ++ v  l++ +++e l+e   +++ ++va
  gi|242398199|ref|YP_002993623.1| 385 DpNVDAIVIiVLFQVPLLNEeEIIEILAEYAkKSEKPIVA 424
                                       4466776651333444444345555444433144566655 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 ?    8.3   0.0     0.002         4       3      90 ..      19     106 ..      17     108 .. 0.66
   2 ?    2.9   0.0     0.096   1.9e+02      53      96 ..     377     423 ..     322     448 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.002
                                       EEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHH.HHHHHTTHEEESSHHHHHTCTTESEEEE-S-GGGHHHH CS
                      GFO_IDH_MocA   3 vaiiGaGkigskhlrplnesqrleevvalldpdaerae.avaesfgveaysdleelladpeidavivatpngtheel 78 
                                       vaiiGa +   k ++ + e++++ +  ++++ +      ++ e  g ++y+ ++el++  + d++++ +p+    + 
  gi|242398199|ref|YP_002993623.1|  19 VAIIGATNKKGKVGNVIFENFKKNKEQGIFKGSIYPVNpKLDEIEGYKVYKGVKELPE--DTDLAVISIPAPFVPQT 93 
                                       7899996665555666666666666666665554433303344478889*********..77999999999666666 PP

                                       HHHHHHTT-.EEE CS
                      GFO_IDH_MocA  79 akaaleagk.hvl 90 
                                       +k+++e+g+ +v+
  gi|242398199|ref|YP_002993623.1|  94 MKEIAEKGIkSVI 106
                                       6666666665555 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.096
                                       S.HHHHHTCTTESEEEE-S-G....GGHHHHHHHHHHTT-EEEEESSS- CS
                      GFO_IDH_MocA  53 d.leelladpeidavivatpn....gtheelakaaleagkhvllEKPla 96 
                                         +e+ ++dp++da+++++         ee+++ ++e  k+   EKP++
  gi|242398199|ref|YP_002993623.1| 377 YaIEAFVNDPNVDAIVIIVLFqvplLNEEEIIEILAEYAKK--SEKPIV 423
                                       25889999999999999875533322233333333333333..566665 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.2    0.0049       9.8      36      68 ..      92     124 ..      82     148 .. 0.61
   2 ?   -2.3   0.0       2.5     5e+03     110     149 ..     276     315 ..     262     322 .. 0.72
   3 ?    3.6   0.0      0.04        80      48     101 ..     391     442 ..     341     454 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0049
                                       HHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHH CS
                                       xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  36 eevkelkaekg.vkevilgggepllypdfvelle 68 
                                       + +ke+ aekg + ++i++gg   l  +  +  e
  gi|242398199|ref|YP_002993623.1|  92 QTMKEI-AEKGiKSVIIITGGFGELGEEGRKMEE 124
                                       555566.566666666666666666544333333 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.5
                                       BSSSHHHHHHHHT..CTSHHHHHHHHHHHHHHTTSETEEEEE CS
                                       xxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 110 eaaddekvlklmn..rghtfeevlealeklreagikrvvdri 149
                                       +++ d  v k ++  r ++fe+  ++ +++++  ++   dri
  gi|242398199|ref|YP_002993623.1| 276 DIIYDA-VFKQTGilRAEDFEHMFDVAKAFAKCKLP-KGDRI 315
                                       555555.55555556888999999999999988887.34444 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.04
                                       EEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  48 kevilgggepllypdfvellerlaklavpgiritvetngtlpdeeklerllelg 101
                                        ++i++ + pll+ +++ +++++ +++ ++  i+ ++ g++   e+ +++le  
  gi|242398199|ref|YP_002993623.1| 391 IVIIVLFQVPLLNEEEIIEILAEYAKK-SEKPIVAVAMGGKK-TEYYAKMLENK 442
                                       567777788888866555555555553.78888888888886.77777777755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (473 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); 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:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.62u 0.26s 00:00:00.88 Elapsed: 00:00:00.45
# Mc/sec: 3130.49
//
Query:       gi|242398200|ref|YP_002993624.1|  [L=258]
Description: xylose isomerase domain-containing protein [Thermococcus sibiricus MM 739]
Scores for complete 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   0.0      3e-24   85.6   0.0    1.1  1  AP_endonuc_2  Xylose isomerase-like TIM barrel
  ------ inclusion threshold ------
       0.12   10.7   0.0       0.15   10.4   0.0    1.1  1  PTPS_related  6-pyruvoyl-tetrahydropterin synthase related do


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 !   85.6   0.0   3.4e-28     3e-24      37     210 .]      54     220 ..      21     220 .. 0.85

  Alignments for each domain:
  == domain 1  score: 85.6 bits;  conditional E-value: 3.4e-28
                                       HHHTTSEEEEEEECCCHSTCTHCHTTCS.HHHHHHHHHHHHHHHHHHTBSEEEEEBCCGBCTTTSGHHHHHHHHHHH CS
                      AP_endonuc_2  37 ldelglriaslslftrfgypdederear.reesvdalkraielaaaLGapllvlhpGtagagpkgseeeawerlaes 112
                                       l+e+ l+   + +f++ +       +++ r+ s++ l ++ e+a+++G  l+v+hpG+++ ++++ +++  +   +s
  gi|242398200|ref|YP_002993624.1|  54 LEEAKLKNIIHAPFSDVNMGSL---NEKiRRISLELLFETFEIAHEMGSALVVIHPGHYSPLSSRFPKAYEKVQKRS 127
                                       6666677666666666666544...56678999************************8877777777777777788* PP

                                       HHHHHHHHHHHTSEEEEE--TTTTSSSTCHHHHHHHHHHTTTTEEEEEEHHHHHHHTTTHHHHHHHHHGGEEEEEE. CS
                      AP_endonuc_2 113 lneladyaekegvklalEtlagsgvelgdeelarlldavdspnvgvclDtgHlliaeedvddalraladrikhvHik 189
                                       l+e+ ++ +k g+++alE++++ ++ +g ++ +r+ + vd + + v++D+gHl+   +++d++++ l+dri + H++
  gi|242398200|ref|YP_002993624.1| 128 LEEISKISQKIGITVALENMPSYPILDG-QTPERIKELVDGTEILVTFDIGHLNTVNAQFDRFIELLEDRIIYAHLS 203
                                       ****************************.88888888888888********************************** PP

                                       EESSTTTTSSTTEESTTSSSS CS
                      AP_endonuc_2 190 DakgdlgagrdrhvpigeGei 210
                                       D+ g      d h+ +geG+i
  gi|242398200|ref|YP_002993624.1| 204 DNHG----ANDSHLALGEGNI 220
                                       ****....***********87 PP

>> PTPS_related  6-pyruvoyl-tetrahydropterin synthase related domain; membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   1.6e-05      0.15     414     490 ..      77     162 ..      36     182 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 1.6e-05
                      PTPS_related 414 etlkaldksaavsgYklytevddgnvyv.........rpvpkpfevvkereglaigkssldivllfpsfesgsssyl 481
                                       e +  ++ ++ +  +++  e++++ v           +  pk++e v++r  + i k s+ i + ++ ++++s+ +l
  gi|242398200|ref|YP_002993624.1|  77 EKIRRISLELLFETFEIAHEMGSALVVIhpghysplsSRFPKAYEKVQKRSLEEISKISQKIGITVALENMPSYPIL 153
                                       4566677788999999999999999877677776665559************************************* PP

                      PTPS_related 482 eDytleelk 490
                                       +  t+e +k
  gi|242398200|ref|YP_002993624.1| 154 DGQTPERIK 162
                                       988999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       674  (0.0375927); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); 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: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1638.93
//
Query:       gi|242398201|ref|YP_002993625.1|  [L=210]
Description: hypothetical protein TSIB_0209 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-59  201.4   0.6    1.4e-59  201.3   0.6    1.0  1  AIM24     Mitochondrial biogenesis AIM24


Domain annotation for each model (and alignments):
>> AIM24  Mitochondrial biogenesis AIM24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  201.3   0.6   7.9e-64   1.4e-59      10     201 .]       1     192 [.       1     192 [. 0.98

  Alignments for each domain:
  == domain 1  score: 201.3 bits;  conditional E-value: 7.9e-64
                                       EEEEEE-TT-EEEE-CCGEEEEETTEEEEE...--------.------EEEEEEES.SS-EEEEE--SSSEEEEEEE CS
                             AIM24  10 llsvtLspgeelyaerGalvamsgkvemet...gllkalkr.lltgeslfllkftakissgtvllapklpgtivtle 82 
                                       +++v+L++ge++ ae+Ga+v ms+++++et   g++kalkr +l+ges+f+++f+a++++g++ lap + g+i  le
  gi|242398201|ref|YP_002993625.1|   1 MVEVELEEGEAIKAEPGAMVHMSPTIKIETktgGVFKALKRsMLGGESIFINTFRAEEGKGNIGLAPAYMGDIEALE 77 
                                       79*************************************************************************** PP

                                       GGTT.EEEEEGGGEEEEETT-EEEEEEEE--SSGGGTS-EEEEEEESSSEEEEEEECSEEEEEEE.EEEEEEEGGGE CS
                             AIM24  83 lgggdwlivqkdafLAatgnveldikfqkglkglfggeglflqkltGrGlvalsgyGaiyeielkageelvvdpghl 159
                                       + +g +l++q++afLA+++++e+++kf  g k++f++eglfl+kl+G+G+v+ls++G+iy++el ++e +++d+ghl
  gi|242398201|ref|YP_002993625.1|  78 I-RG-TLYAQSGAFLASSETIEINTKFG-GAKTFFSREGLFLLKLSGEGTVFLSSFGGIYKKEL-RNERFIIDTGHL 150
                                       9.55.7**********************.5799*******************************.78********** PP

                                       EEEETTEEEEEEEETT---STTTTS-EEEEEEEEEEEEEESS CS
                             AIM24 160 vafsgslkfdiervgglkrrligGeglflkltGpgtvllqsr 201
                                       vaf+++l+f ++rvgglk++++gGegl++++ G gt+++q+r
  gi|242398201|ref|YP_002993625.1| 151 VAFTEGLDFRVKRVGGLKSTIFGGEGLVAEFYGSGTLYIQTR 192
                                       ****************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       247  (0.0137766); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1600.20
//
Query:       gi|242398202|ref|YP_002993626.1|  [L=233]
Description: Endonuclease III [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.1e-17   63.0   0.0    5.2e-17   62.3   0.0    1.4  1  HhH-GPD        HhH-GPD superfamily base excision DNA repair p
    1.5e-07   30.9   0.1    4.2e-07   29.5   0.0    1.8  2  HHH            Helix-hairpin-helix motif
    1.9e-05   24.7   0.0     0.0096   16.0   0.0    2.4  2  HHH_2          Helix-hairpin-helix motif
     0.0074   16.9   0.0        1.5    9.5   0.0    2.7  3  HHH_5          Helix-hairpin-helix domain
  ------ inclusion threshold ------
      0.011   15.3   0.1      0.011   15.3   0.1    1.2  1  DUF4238        Protein of unknown function (DUF4238)
      0.015   13.7   0.2      0.019   13.4   0.2    1.1  1  Nic96          Nup93/Nic96
      0.045   13.7   0.1       0.15   12.0   0.0    1.8  2  DUF2400        Protein of unknown function (DUF2400)
      0.074   13.4   3.3       0.12   12.7   3.3    1.4  1  EndIII_4Fe-2S  Iron-sulfur binding domain of endonuclease III


Domain annotation for each model (and alignments):
>> HhH-GPD  HhH-GPD superfamily base excision DNA repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.3   0.0   2.3e-20   5.2e-17       3     107 ..      50     185 ..      48     186 .. 0.96

  Alignments for each domain:
  == domain 1  score: 62.3 bits;  conditional E-value: 2.3e-20
                                       HHHHTTS-HHHHHHHHHHHHHHHSHCSHHHHHHSHHHHHHHHHTT..STTHHHHHHHHHHHHHHHH........... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxx........... RF
                           HhH-GPD   3 ailsqqtsderanriierlferfgfptpedladadeekLrelire..lGfyrrKakyikelArilv........... 66 
                                       +i+sq+ +de++n++ + lf++++  + e +a+a+ e+++e +r   +G++++K + i  +++i++           
  gi|242398202|ref|YP_002993626.1|  50 CIISQRMRDEVTNKVGKMLFKKYK--NIENIANAPVEEMQEFLRNngVGLWKTKGEWIVRTSQIILreyrgrvpnki 124
                                       8*********************99..******************999****************************** PP

                                       ......................S-SSS--TTSHHHHHHHHHHTTSSSSTTHHHHHHHHHHHHH CS
                                       ......................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           HhH-GPD  67 ......................gkpdvlivvDvhvrrilkrlrsikekktkkkvekkleelle 107
                                                             g  + +i+vD+hv ri krl+++ ++  ++kve++l++l++
  gi|242398202|ref|YP_002993626.1| 125 eelmklpgigrkcanivlaygfG--KQTIPVDTHVNRISKRLGLAPPTVAPEKVEEYLKKLIP 185
                                       ********************665..579******************************99987 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       3.8   8.5e+03       3      14 ..      76      87 ..      75      88 .. 0.79
   2 !   29.5   0.0   1.9e-10   4.2e-07       2      30 .]     116     144 ..     115     144 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3.8
                                      HHHHTSSHHHHH CS
                               HHH  3 eglipasreeLl 14
                                      e++ +a +ee +
  gi|242398202|ref|YP_002993626.1| 76 ENIANAPVEEMQ 87
                                      899999899875 PP

  == domain 2  score: 29.5 bits;  conditional E-value: 1.9e-10
                                       HHHHHTSSHHHHHTSTT-SHHHHHHHHHH CS
                               HHH   2 leglipasreeLlalPGVGpktAeaIlsy 30 
                                       + g +p+ +eeL++lPG+G+k A+ +l+y
  gi|242398202|ref|YP_002993626.1| 116 YRGRVPNKIEELMKLPGIGRKCANIVLAY 144
                                       78999*******************99998 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   4.3e-06    0.0096      13      39 ..      62      88 ..      58      92 .. 0.90
   2 !    6.1   0.0    0.0051        12      33      54 ..     123     144 ..     121     149 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4.3e-06
                             HHH_2 13 ektAklLakrFksldaLkkasleeLle 39
                                      +k+ k L k++k+++++++a +ee++e
  gi|242398202|ref|YP_002993626.1| 62 NKVGKMLFKKYKNIENIANAPVEEMQE 88
                                      68889********************87 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0051
                             HHH_2  33 sleeLlevddiGeeiAqsivef 54 
                                       ++eeL ++++iG + A+ +  +
  gi|242398202|ref|YP_002993626.1| 123 KIEELMKLPGIGRKCANIVLAY 144
                                       589*************988765 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       3.6   8.2e+03      14      34 ..      25      43 ..      20      47 .. 0.62
   2 ?    4.3   0.0     0.028        62      10      39 ..      60      88 ..      58      97 .. 0.81
   3 !    9.5   0.0   0.00068       1.5       2      22 ..     125     145 ..     122     152 .. 0.68

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 3.6
                                      HHHHHHTTT--SHHHHHHS-H CS
                             HHH_5 14 tAlallsaGiesvedlaaadv 34
                                      ++++l+++   + e+l+  d+
  gi|242398202|ref|YP_002993626.1| 25 IVKRLINH--YQREKLLTGDP 43
                                      45566666..56677776665 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.028
                                      --HHHHHHHHTTT--SHHHHHHS-HHHHHT CS
                             HHH_5 10 iGpktAlallsaGiesvedlaaadveeLak 39
                                      +  k+ + l ++ ++ +e +a+a vee ++
  gi|242398202|ref|YP_002993626.1| 60 VTNKVGKMLFKK-YKNIENIANAPVEEMQE 88
                                      566888999999.**********9998654 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.00068
                                       HHHHTSTT--HHHHHHHHTTT CS
                             HHH_5   2 eeLlsvsGiGpktAlallsaG 22 
                                       eeL++++GiG+k A  +l  G
  gi|242398202|ref|YP_002993626.1| 125 EELMKLPGIGRKCANIVLAYG 145
                                       567777777777666666555 PP

>> DUF4238  Protein of unknown function (DUF4238)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.1   4.8e-06     0.011      57     147 ..       8      94 ..       2     203 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.8e-06
                           DUF4238  57 pnhiEktlaklEskaakiirkilkegkstrtltreerkqlrkflfllkyRtprfreeydtedkeelesymrekkkfe 133
                                          +E+ + +   +a++i+++++++ + ++ lt    k+l + + ++ +R +       ++ k ++++y++ ++  +
  gi|242398202|ref|YP_002993626.1|   8 SFTFEENWEEKKRRAKEIVKRLINHYQREKLLTGDPYKTLIYCIISQRMRDEVTN----KVGKMLFKKYKNIENIAN 80 
                                       56788888888899*************************************4444....7***************** PP

                           DUF4238 134 kpldelldelkvil 147
                                       +p++e+ + l+ + 
  gi|242398202|ref|YP_002993626.1|  81 APVEEMQEFLRNNG 94 
                                       ****8877666555 PP

>> Nic96  Nup93/Nic96
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   8.5e-06     0.019     148     196 ..      11      55 ..       2      85 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.5e-06
                                       HHHCTTTTSS---TCCCHHHHHHHHHHTTT.-TTS-HHHHHHHHHHHT- CS
                             Nic96 148 lkayassedrrlpseleerlkleYnqrirnasedsDpykkavYkiigrc 196
                                       +++  ++++rr  +e+ +rl ++Y+++    +  +Dpyk ++Y+ii++ 
  gi|242398202|ref|YP_002993626.1|  11 FEENWEEKKRRA-KEIVKRLINHYQREKLL-T--GDPYKTLIYCIISQR 55 
                                       555555555555.99999999999887665.4..4***********875 PP

>> DUF2400  Protein of unknown function (DUF2400)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1      0.85   1.9e+03      80      80 ..      38      38 ..       2      94 .. 0.55
   2 ?   12.0   0.0   6.7e-05      0.15     172     210 ..     150     184 ..     147     193 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.85
                           DUF2400 80 l 80
                                      l
  gi|242398202|ref|YP_002993626.1| 38 L 38
                                      2 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 6.7e-05
                           DUF2400 172 iiPlDvHvarvarklgllkrkqadlkaaleltealrkld 210
                                       +iP+D+Hv+r++++lgl   +     a ++++e l+kl 
  gi|242398202|ref|YP_002993626.1| 150 TIPVDTHVNRISKRLGLAPPT----VAPEKVEEYLKKLI 184
                                       59***************7433....33444555555555 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 ?   12.7   3.3   5.5e-05      0.12       6      17 .]     209     220 ..     204     220 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.5e-05
                     EndIII_4Fe-2S   6 PkCeaCPLaDlC 17 
                                       PkC +C+ +DlC
  gi|242398202|ref|YP_002993626.1| 209 PKCHECFFQDLC 220
                                       ************ PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       935  (0.0521501); expected 358.6 (0.02)
Passed bias filter:                      688  (0.0383736); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 1647.59
//
Query:       gi|242398203|ref|YP_002993627.1|  [L=144]
Description: Cell division protein 48 (CDC48), domain 2 [Thermococcus sibiricus MM 739]
Scores for complete 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   30.0   0.1    5.2e-07   29.3   0.1    1.3  1  CDC48_2   Cell division protein 48 (CDC48), domain 2
  ------ inclusion threshold ------
      0.066   13.2   0.2       0.19   11.8   0.0    1.8  2  DUF2375   Protein of unknown function (DUF2375)


Domain annotation for each model (and alignments):
>> 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 !   29.3   0.1   5.8e-11   5.2e-07       2      60 ..      13      70 ..      12      72 .. 0.94

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 5.8e-11
                                      .SCCCCHHHHCCCTTEEE-TTEEEEECCTCCCEEEEEEEECCCCSCEEECTSCCEEEST CS
                           CDC48_2  2 idgdemaylkrqFlgrpvtkGdlvvfefkgqeiklvVvstePkgpvgitetTeielgtk 60
                                      +  d+++ ++ ++ g+ v +Gd+v ++ +g++++++V   ePk   +++ +T+iel ++
  gi|242398203|ref|YP_002993627.1| 13 LTPDFIEVIRAKLIGKEVKEGDTVEIDLLGKALQFKVIYSEPK-LIRVNKDTKIELTEE 70
                                      6789999************************************.788********9876 PP

>> DUF2375  Protein of unknown function (DUF2375)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   2.1e-05      0.19      46      69 .]      91     114 ..      87     114 .. 0.94
   2 ?   -3.5   0.0       1.3   1.1e+04      47      52 ..     127     132 ..     122     137 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.1e-05
                           DUF2375  46 KsiiaVlEGeikilNslGervlsq 69 
                                       K i+  lE e+ ilN+ G ++++q
  gi|242398203|ref|YP_002993627.1|  91 KWIVILLENEVLILNQKGHKIFNQ 114
                                       789*******************97 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.3
                           DUF2375  47 siiaVl 52 
                                        iiaV+
  gi|242398203|ref|YP_002993627.1| 127 GIIAVI 132
                                       578876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 918.74
//
Query:       gi|242398204|ref|YP_002993628.1|  [L=158]
Description: Transcription regulator, PadR-like family [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-18   65.3   1.5      5e-18   64.8   0.8    1.6  2  PadR      Transcriptional regulator PadR-like family
    0.00013   21.7   1.9    0.00075   19.3   0.1    2.3  2  DUF4364   Domain of unknown function (DUF4364)
     0.0013   19.4   0.2     0.0053   17.4   0.1    1.9  2  RTP       Replication terminator protein
     0.0013   18.6   0.1      0.003   17.5   0.1    1.8  1  HTH_45    Winged helix-turn-helix
     0.0058   16.8   0.0      0.017   15.3   0.0    1.8  2  HTH_34    Winged helix DNA-binding domain
  ------ inclusion threshold ------
      0.089   12.6   0.3       0.26   11.1   0.0    1.8  2  DUF1495   Winged helix DNA-binding domain (DUF1495)
       0.09   12.8   0.3       0.34   10.9   0.0    1.9  2  PsbU      Photosystem II 12 kDa extrinsic protein (PsbU)


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 !   64.8   0.8     2e-21     5e-18       1      74 [.      21      90 ..      21      91 .. 0.95
   2 ?   -3.6   0.0       4.6   1.2e+04      12      22 ..     114     124 ..     110     128 .. 0.73

  Alignments for each domain:
  == domain 1  score: 64.8 bits;  conditional E-value: 2e-21
                                      HHHHHCCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHHH CS
                              PadR  1 iLalleeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrela 74
                                      iL+ll+e+p++Gy i+ ele+++ g+ ++s+G +Yp+L+ L+++gl+    +    ++++k+Y++Td+G+++l 
  gi|242398204|ref|YP_002993628.1| 21 ILYLLKEKPQHGYGIMYELETRY-GIPTPSPGAIYPILSGLKRNGLIRVAGK---GKREKKLYQITDRGKEYLD 90
                                      8*********************8.9**********************99977...479*************997 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 4.6
                                       HHHHHHHHHCC CS
                              PadR  12 Gyeiikeleel 22 
                                       G e++++++e 
  gi|242398204|ref|YP_002993628.1| 114 GNELKEAIKEV 124
                                       66778877775 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.3     0.065   1.7e+02       2      11 ..      18      27 ..      17      31 .. 0.88
   2 !   19.3   0.1   2.9e-07   0.00075      39      82 ..      56     101 ..      52     127 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.065
                           DUF4364  2 KllilYllkk 11
                                      KllilYllk+
  gi|242398204|ref|YP_002993628.1| 18 KLLILYLLKE 27
                                      9*******86 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 2.9e-07
                           DUF4364  39 alseLvesglieee..ekenktlykiTekGketlelfenripksir 82 
                                       +ls L  +gli++    k++k+ly+iT++Gke l++ +n++ + ir
  gi|242398204|ref|YP_002993628.1|  56 ILSGLKRNGLIRVAgkGKREKKLYQITDRGKEYLDEHKNELFEVIR 101
                                       6899********9964569**********************99887 PP

>> RTP  Replication terminator protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   2.1e-06    0.0053       6      95 ..      13      95 ..      10     108 .. 0.84
   2 ?    0.1   0.0      0.47   1.2e+03      28      58 ..     102     134 ..      94     153 .. 0.58

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.1e-06
                                      HHHHHHHHHHHHHHTT-EBCTCHHHHHHHHHTTTT----HHHHHHHHHHHHHTTSEEEEEEEBTSSSSSEEEEEEESS. CS
                               RTP  6 qrAFlklylitlvekkklyglklldelkkeFkelgykPnhseiyralhelvedgilkrrkelkekaklqevviYsltde 84
                                       +  lkl ++ l+++k+++g+ ++ el +++     +P++  iy  l  l  +g+++   + k     +e  +Y++td 
  gi|242398204|ref|YP_002993628.1| 13 YKGHLKLLILYLLKEKPQHGYGIMYELETRYGI--PTPSPGAIYPILSGLKRNGLIRVAGKGK-----REKKLYQITDR 84
                                      56789**********************987654..57999**************998776666.....45568****** PP

                                      .HHHHHHHHHH CS
                               RTP 85 Gkekaklykkq 95
                                      Gke +   k++
  gi|242398204|ref|YP_002993628.1| 85 GKEYLDEHKNE 95
                                      **998887765 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.47
                                       HHHHHHHHHTTTT...----HHHHHHHHHHHHHT CS
                               RTP  28 lldelkkeFkelg...ykPnhseiyralhelved 58 
                                       +++++k eF++lg    k +  e++ a+  l+e+
  gi|242398204|ref|YP_002993628.1| 102 MIESFK-EFRSLGgneLKEAIKEVFMAIPSLTEE 134
                                       444443.455555444444445555555555544 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   1.2e-06     0.003      40      71 ..      57      94 ..      19     102 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.2e-06
                            HTH_45 40 LdmLvekgli......kkskekYvlTekGlelleklke 71
                                      L+ L  +gli      k +k+ Y++T++G+e+l++ k+
  gi|242398204|ref|YP_002993628.1| 57 LSGLKRNGLIrvagkgKREKKLYQITDRGKEYLDEHKN 94
                                      78899******9**9999***************98764 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   6.5e-06     0.017      29      79 ..      51      99 ..      47     100 .. 0.81
   2 ?   -1.7   0.0       1.3   3.4e+03      59      76 ..     129     146 ..     118     150 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 6.5e-06
                            HTH_34 29 gnLsvhlkkLekagYievdkefkgkkprtllriTpeGreafkkyvkaLksl 79
                                      g+++  l+ L+ +g i v  + kgk+++ l++iT+ G+e  ++++++L ++
  gi|242398204|ref|YP_002993628.1| 51 GAIYPILSGLKRNGLIRV--AGKGKREKKLYQITDRGKEYLDEHKNELFEV 99
                                      666777777777777765..56899999******************99765 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.3
                            HTH_34  59 lriTpeGreafkkyvkaL 76 
                                        ++T+e ++a ++++++ 
  gi|242398204|ref|YP_002993628.1| 129 PSLTEEQKKALSDEIEEF 146
                                       578888888888887775 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 ?   -1.9   0.0       1.2     3e+03      17      23 ..      23      29 ..       3      45 .. 0.52
   2 ?   11.1   0.0    0.0001      0.26      59      88 ..      60      90 ..      51      91 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.2
                           DUF1495 17 yLysiyp 23
                                      yL++  p
  gi|242398204|ref|YP_002993628.1| 23 YLLKEKP 29
                                      2222222 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0001
                           DUF1495 59 LielGLveeeee.seglklYklteeGieive 88
                                      L   GL++   + +++ klY++t++G+e+ +
  gi|242398204|ref|YP_002993628.1| 60 LKRNGLIRVAGKgKREKKLYQITDRGKEYLD 90
                                      667899975533599************9876 PP

>> PsbU  Photosystem II 12 kDa extrinsic protein (PsbU)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.58   1.5e+03      55      75 ..      79     100 ..      71     111 .. 0.67
   2 ?   10.9   0.0   0.00013      0.34      49      74 ..     122     148 ..     115     155 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.58
                                       TT--HHHHHHHHHHGGG.EE-- CS
                              PsbU  55 PgLsekqkelleknlek.ftvt 75 
                                        +++++ ke l++++++ f v 
  gi|242398204|ref|YP_002993628.1|  79 YQITDRGKEYLDEHKNElFEVI 100
                                       4568888888887765425555 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00013
                                       GGG.GG-TT--HHHHHHHHHHGGGEE- CS
                              PsbU  49 edv.lniPgLsekqkelleknlekftv 74 
                                       ++v + iP L+e+qk+ l++  e+ft 
  gi|242398204|ref|YP_002993628.1| 122 KEVfMAIPSLTEEQKKALSDEIEEFTR 148
                                       555258*******************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       964  (0.0537676); expected 358.6 (0.02)
Passed bias filter:                      769  (0.0428914); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); 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 0.28s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1054.46
//
Query:       gi|242398205|ref|YP_002993629.1|  [L=326]
Description: ABC-type multidrug transport system, ATPase component [Thermococcus sibiricus MM 739]
Scores for complete 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  119.4   0.0    3.1e-34  118.4   0.0    1.5  1  ABC_tran     ABC transporter
    5.3e-11   42.9   0.4    4.4e-07   30.0   0.1    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    7.9e-09   36.1   0.0    2.3e-08   34.6   0.0    1.9  1  DUF4162      Domain of unknown function (DUF4162)
    1.4e-06   28.3   0.2      0.028   14.1   0.3    2.2  2  AAA_15       AAA ATPase domain
    0.00027   21.5   1.2    0.00062   20.3   1.2    1.7  1  AAA_23       AAA domain
     0.0034   17.1   0.2     0.0066   16.1   0.2    1.4  1  SRP54        SRP54-type protein, GTPase domain
     0.0063   16.0   0.0      0.018   14.5   0.0    1.7  1  SMC_N        RecF/RecN/SMC N terminal domain
     0.0065   16.2   0.1      0.012   15.3   0.1    1.4  1  AAA_29       P-loop containing region of AAA domain
     0.0067   16.0   0.1      0.014   15.0   0.1    1.4  1  AAA_27       AAA domain
     0.0077   16.7   0.7       0.18   12.2   0.7    2.8  1  AAA          ATPase family associated with various cellular a
  ------ inclusion threshold ------
      0.074   11.7   0.0        3.2    6.3   0.0    2.2  2  AAA_13       AAA domain
       0.11   12.3   0.1       0.32   10.7   0.0    1.7  2  AAA_30       AAA domain
       0.12   12.3   0.0       0.29   11.0   0.0    1.7  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 !  118.4   0.0   2.2e-37   3.1e-34       2     136 ..      20     162 ..      19     163 .. 0.97

  Alignments for each domain:
  == domain 1  score: 118.4 bits;  conditional E-value: 2.2e-37
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       k +s+k+++ge+ a++G+nGaGK+t + +l+ ll+ t+G+  + g+d+ + e  ++rk+ig+++q+p+l++elt++e
  gi|242398205|ref|YP_002993629.1|  20 KGISFKVNKGEIFAFLGPNGAGKTTTVHVLTTLLRLTSGKAIVAGHDVVK-EPMEVRKKIGIVFQDPSLDRELTAYE 95 
                                       789***********************************************.666789******************** PP

                                       H.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       n             + +e+ie++l+ ++l e+kd++v    + +SgG+++r+++ar+ll +p++l+lDEpt
  gi|242398205|ref|YP_002993629.1|  96 NmyihgriygltgnKLEEKIERLLKFVELWEFKDKPV----KMFSGGMQRRLEIARSLLHEPEILFLDEPT 162
                                       *************9999********************....*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   0.00016      0.22       2      63 ..      32      85 ..      31     132 .. 0.73
   2 !   30.0   0.1   3.2e-10   4.4e-07     237     297 ..     135     193 ..     121     196 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00016
                            AAA_21  2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeie 63
                                       ++ GpNg+GK++    l  l rl        ++   ++   ++ +++ +  ++i ++f+++
  gi|242398205|ref|YP_002993629.1| 32 FAFLGPNGAGKTTTVHVLTTLLRL--------TSGKAIVAGHDVVKEPMEVRKKIGIVFQDP 85
                                      6899*********99999999874........444444455555555555555555555555 PP

  == domain 2  score: 30.0 bits;  conditional E-value: 3.2e-10
                            AAA_21 237 lSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell...kelsrngaQviltTH 297
                                       +S G++r l ++ +ll  +    +l++DEp  gL+P+  +++++ +   ke+  ++  ++ltTH
  gi|242398205|ref|YP_002993629.1| 135 FSGGMQRRLEIARSLLHEP---EILFLDEPTIGLDPQTRAHIWDYIkamKEE--HNMTIFLTTH 193
                                       6999999999999999988...9********************888433555..55******** PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   0.0   1.7e-11   2.3e-08       1      80 [.     217     302 ..     217     303 .. 0.86

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 1.7e-11
                                       E-HHHHHTTS-SSEEEEE...-------..---EEEE-TT.S-EEEEE--.-----------.----EEEEEEEE-- CS
                           DUF4162   1 GtleeiKrsygknrieve...adaeelleepgveeveeeg.gelelkled.eeaanellkal.tsgveirsFeeeeP 71 
                                       Gt +e+K+  g++ ++++    ++ + l+ + ++  +    g+++l++e+  ea ++l++ + + gv+i +++ ++P
  gi|242398205|ref|YP_002993629.1| 217 GTANELKKLVGNDVVYLKleaLEEVKCLKAEFIKGCKILSdGKVQLEVENaAEALPKLFTLVqHLGVKILEVTYHRP 293
                                       999*************997665566666666677775555588*******9***********66************* PP

                                       -HHHHHHHH CS
                           DUF4162  72 sLndIFiek 80 
                                       +Lnd+F+++
  gi|242398205|ref|YP_002993629.1| 294 TLNDVFLHL 302
                                       ******987 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   9.3e-05      0.13      21      55 ..      24      65 ..       3     118 .. 0.73
   2 !   14.1   0.3     2e-05     0.028     323     364 ..     152     193 ..     107     194 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9.3e-05
                            AAA_15 21 lsee...ltvliGkNnsGKSsilealdlFlnnkekkn....k 55
                                      ++ +   +  + G+N++GK++ +++l  +l  ++ k     +
  gi|242398205|ref|YP_002993629.1| 24 FKVNkgeIFAFLGPNGAGKTTTVHVLTTLLRLTSGKAivagH 65
                                      3333445999******************99977443365551 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 2e-05
                            AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                       ++ il+++EP + L pq   ++++++k + +++++ +++tTH
  gi|242398205|ref|YP_002993629.1| 152 EPEILFLDEPTIGLDPQTRAHIWDYIKAMKEEHNMTIFLTTH 193
                                       5689************************************** PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   1.2   4.5e-07   0.00062       9      44 ..      12      54 ..       4     242 .. 0.66

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 4.5e-07
                            AAA_23  9 sfrdqe....idF...skgltlItGpNGaGKTTildAiklaLy 44
                                      +++d+e    i F   +  ++++ GpNGaGKTT +  ++  L 
  gi|242398205|ref|YP_002993629.1| 12 KYGDFEavkgISFkvnKGEIFAFLGPNGAGKTTTVHVLTTLLR 54
                                      4444433337889885557**************9999988774 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.2   4.8e-06    0.0066       3      39 ..      31      67 ..      29      70 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.8e-06
                                      EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEEST CS
                             SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvllvaaDt 39
                                      +++++G++GaGKTtt+  L  ll+    k++++  D+
  gi|242398205|ref|YP_002993629.1| 31 IFAFLGPNGAGKTTTVHVLTTLLRLTSGKAIVAGHDV 67
                                      6789*********************999999999887 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   1.3e-05     0.018      26     207 ..      31     200 ..       4     213 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.3e-05
                                       EEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEE.SSSSSSCEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx RF
                             SMC_N  26 ftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkk.lkiekeevsisr 101
                                       + a +GpNG+GK+  +  +  +L  +s k++ +   +d+++    ++   + ++ i+f++++ + + +  e+++i  
  gi|242398205|ref|YP_002993629.1|  31 IFAFLGPNGAGKTTTVHVLTTLLRLTSGKAIVAG--HDVVK----EPMEVRKKIGIVFQDPSLDrELTAYENMYIHG 101
                                       55779********988777555555555444432..34554....46667778999998887662445555566665 PP

                                       EEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 102 rvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkk 178
                                       r++       k+++k  +  +  el e ++   +++SgG +  + +    A    +   + +lDe    LD + ++ 
  gi|242398205|ref|YP_002993629.1| 102 RIYGLTG--NKLEEKIERLLKFVELWEFKDKPVKMFSGGMQRRLEI----ARSLLHEPEILFLDEPTIGLDPQTRAH 172
                                       5553333..4666777777777777777777788*****7764444....4444455557789************** PP

                                       HHHHHHHHCTT..SEEEEE-SSHHHCCC-SC CS
                                       xxxxxxxxxxx..xxxxxxxxxxxxxxxxxx RF
                             SMC_N 179 vaellkekskn..aQfivislreemlekadk 207
                                       + +++k+ +++  + ++ +++  +   +a++
  gi|242398205|ref|YP_002993629.1| 173 IWDYIKAMKEEhnMTIFLTTHYMD---EAEQ 200
                                       ******766541155555555444...4433 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 !   15.3   0.1   8.7e-06     0.012      16      46 ..      23      53 ..      10      60 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 8.7e-06
                            AAA_29 16 tieidlkg.atlltGpsGsGKSTllDAiqalL 46
                                      +++++  g ++ + Gp+G+GK+T +  +++lL
  gi|242398205|ref|YP_002993629.1| 23 SFKVNK-GeIFAFLGPNGAGKTTTVHVLTTLL 53
                                      445553.369**************99999988 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   9.9e-06     0.014       9      50 ..      11      53 ..       6      55 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 9.9e-06
                            AAA_27  9 eryGkftd.rsldfsaeeadlhliyGpNEAGKstalrAisdll 50
                                      ++yG f+  + ++f+ ++ ++   +GpN AGK+t+++ ++ ll
  gi|242398205|ref|YP_002993629.1| 11 KKYGDFEAvKGISFKVNKGEIFAFLGPNGAGKTTTVHVLTTLL 53
                                      79****98357**************************999987 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.7   0.00013      0.18       3      66 ..      34     160 ..      32     225 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                                       EESSTTSSHHHHHHHHHHHHTHE..EEEEETTTCSSS........................................ CS
                               AAA   3 lyGppGtGKTllakavakelgve..fleisgsellsk........................................ 37 
                                       + Gp G GKT++++ + + l  +     + g++++++                                        
  gi|242398205|ref|YP_002993629.1|  34 FLGPNGAGKTTTVHVLTTLLRLTsgKAIVAGHDVVKEpmevrkkigivfqdpsldreltayenmyihgriygltgnk 110
                                       78**************9998643223445555555223333333333333333333344444444444444433333 PP

                                       ....................STTHHHHHHHHHHHHHHHTS.TSEEEEEET CS
                               AAA  38 ....................yvgesekkirelfkeakeka.kpsilfiDE 66 
                                                            v+  +  ++  ++ a++   +p ilf+DE
  gi|242398205|ref|YP_002993629.1| 111 leekierllkfvelwefkdkPVKMFSGGMQRRLEIARSLLhEPEILFLDE 160
                                       44445555555555554444555555555555555555555566777776 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0    0.0023       3.2      22      39 ..      35      52 ..      24     133 .. 0.84
   2 ?    3.5   0.0     0.016        22     524     577 ..     150     201 ..     141     222 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0023
                            AAA_13 22 YGwNGaGKTtLSrllrsl 39
                                       G NGaGKTt   +l  l
  gi|242398205|ref|YP_002993629.1| 35 LGPNGAGKTTTVHVLTTL 52
                                      69********99999887 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.016
                            AAA_13 524 igkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleffkev 577
                                       + + +i ++D P   LD +   ++  +ik+    +++   +f+ TH ++   ++
  gi|242398205|ref|YP_002993629.1| 150 LHEPEILFLDEPTIGLDPQTRAHIWDYIKAMK--EEHNMTIFLTTHYMDEAEQL 201
                                       56889************************997..899999******87655555 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00023      0.32      20      49 ..      31      61 ..      23      86 .. 0.82
   2 ?   -1.8   0.0       1.5   2.1e+03      39      69 ..     178     214 ..     173     241 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00023
                            AAA_30 20 vavltGpAGtGKttalkalreaweaa.ggrv 49
                                      + +  Gp G+GKtt++ +l+ +++   g+ +
  gi|242398205|ref|YP_002993629.1| 31 IFAFLGPNGAGKTTTVHVLTTLLRLTsGKAI 61
                                      67788**************999987745444 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.5
                            AAA_30  39 reaweaaggrviglAptgkaAkvLaeelgi......e 69 
                                       +++ e++++++++ ++    A++La+ + i       
  gi|242398205|ref|YP_002993629.1| 178 KAMKEEHNMTIFLTTHYMDEAEQLADRIAIidhgkiI 214
                                       4455555788888888888888888777654433332 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00021      0.29      80     122 ..       9      52 ..       1      63 [. 0.77

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00021
                                       EE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase  80 llvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallpe 122
                                       l+ +  + e+++ ++ ++++ ++ +++G+ G+GK+t + +l+  
  gi|242398205|ref|YP_002993629.1|   9 LVKKYGDFEAVKGISFKVNKgEIFAFLGPNGAGKTTTVHVLTTL 52 
                                       555555667788888888777****************9999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       722  (0.04027); expected 358.6 (0.02)
Passed bias filter:                      617  (0.0344135); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 2063.88
//
Query:       gi|242398206|ref|YP_002993630.1|  [L=232]
Description: ABC-type multidrug transport system, permease component [Thermococcus sibiricus MM 739]
Scores for complete 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  18.1    1.1e-37  129.6  18.1    1.7  2  ABC2_membrane    ABC-2 type transporter
    4.1e-15   55.7  25.8    4.8e-15   55.5  25.8    1.2  1  ABC2_membrane_3  ABC-2 family transporter protein
  ------ inclusion threshold ------
      0.033   13.9   0.7       0.37   10.5   0.7    2.2  1  DUF2585          Protein of unknown function (DUF2585)


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 !  129.6  18.1   1.8e-41   1.1e-37      26     208 ..       2     193 ..       1     195 [. 0.92
   2 ?    0.8   0.4     0.047   2.8e+02     120     144 ..     192     223 ..     192     226 .. 0.49

  Alignments for each domain:
  == domain 1  score: 129.6 bits;  conditional E-value: 1.8e-41
                     ABC2_membrane  26 liqplllalvfgtvfgnlgnsedglnr.................pgllffsvlflafsaltsvapvferergvlere 85 
                                       +i+pl+++++fg+ ++++       n+                 pg++++++++ +  ++++v+++++++ g+l++ 
  gi|242398206|ref|YP_002993630.1|   2 IINPLIWLVFFGLGWSKVF------NNpmartifggvdyltflaPGIFAMTIFNQS--FVSGVSVIWDKQFGFLKEV 70 
                                       89**************844......22333344566677999**************..9999999************ PP

                     ABC2_membrane  86 lvsplyslsayvlakvlvelpvsllqalifllivyflv.gldlsrf.flflllllltalaasslgllisalapsfed 160
                                       lv+p  s+++ +l++++++ +++++q+li+ll++++l  +l++s + + +ll+ +l+a+a+s++g  ++  ++s+e 
  gi|242398206|ref|YP_002993630.1|  71 LVAPA-SRKETILGRLAGDSLLTTVQGLIILLLTFLLAeNLKIS-GiIPALLIGFLLAIAFSGFGTSLALKMESMEG 145
                                       *****.****************************9998899998.55****************************** PP

                     ABC2_membrane 161 asqlaslvllpllllsGffipidsmpkwlqwiaylnPltyavealrsn 208
                                       +++++++++lpl++lsG+++pi++mp+w++++ay+nPltyav++ r+ 
  gi|242398206|ref|YP_002993630.1| 146 FQMIMMVLMLPLTFLSGAIYPIEAMPSWMKALAYINPLTYAVDGARYY 193
                                       *********************************************986 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.047
                     ABC2_membrane 120 yflvgldlsrf.......flflllllltalaa 144
                                       y+lvg ++++f       +l ll+++l++la+
  gi|242398206|ref|YP_002993630.1| 192 YYLVGANVTKFsitidwaVLSLLAVVLVSLAM 223
                                       66677777744443322244455555544444 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 !   55.5  25.8   8.1e-19   4.8e-15     158     344 ..      33     223 ..       5     224 .. 0.89

  Alignments for each domain:
  == domain 1  score: 55.5 bits;  conditional E-value: 8.1e-19
                   ABC2_membrane_3 158 nvasflvg.liliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilll..afgl 231
                                       ++  fl++ ++++ ++  +++   vs++ +k+ + ++  lv++ s+ + +l+++ gd l+  +q l+illl  +++ 
  gi|242398206|ref|YP_002993630.1|  33 DYLTFLAPgIFAMTIFNQSFV-SGVSVIWDKQFGFLKEVLVAPASRKETILGRLAGDSLLTTVQGLIILLLtfLLAE 108
                                       577788884555555555555.6669*********99999*****************************96557777 PP

                   ABC2_membrane_3 232 gipfgnlglllllfllfglayialgyllsslfknsetaqilifivilllsgffgglfpledlpsalkwifsiiPffa 308
                                       ++ +++++ +ll  +l ++a++ +g+ l   + ++e  q ++++++l+l +++g+++p+e++ps++k +++i+P+++
  gi|242398206|ref|YP_002993630.1| 109 NLKISGIIPALLIGFLLAIAFSGFGTSLALKMESMEGFQMIMMVLMLPLTFLSGAIYPIEAMPSWMKALAYINPLTY 185
                                       9**************************************************************************** PP

                   ABC2_membrane_3 309 pglgllrlitgd..plweillsliilalfavvylllal 344
                                         +g    + g+  + ++i +++++l l+avv++ la+
  gi|242398206|ref|YP_002993630.1| 186 AVDGARYYLVGAnvTKFSITIDWAVLSLLAVVLVSLAM 223
                                       ****9888855522555699***************996 PP

>> DUF2585  Protein of unknown function (DUF2585)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.7   6.1e-05      0.37      86     132 ..      76     123 ..      56     176 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 6.1e-05
                           DUF2585  86 yreatialdyaGdsilnsvadtvamvlGfllaarlpvlltv.alaill 132
                                        r++ti    aGds+l +v+  ++++l flla +l++  ++ al i +
  gi|242398206|ref|YP_002993630.1|  76 SRKETILGRLAGDSLLTTVQGLIILLLTFLLAENLKISGIIpALLIGF 123
                                       6889999999*************************9987763444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       654  (0.0364772); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1402.50
//
Query:       gi|242398207|ref|YP_002993631.1|  [L=413]
Description: 3-phosphoglycerate kinase (PGK) [Thermococcus sibiricus MM 739]
Scores for complete 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-109  363.9   0.0   9.8e-109  363.7   0.0    1.0  1  PGK       Phosphoglycerate kinase
  ------ inclusion threshold ------
      0.029   13.4   0.0        4.6    6.2   0.0    2.3  2  LuxE      Acyl-protein synthetase, LuxE
      0.066   13.1   0.0       0.21   11.5   0.0    1.9  1  VacA2     Putative vacuolating cytotoxin


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 !  363.7   0.0  1.6e-112  9.8e-109       2     377 ..       5     389 ..       4     390 .. 0.93

  Alignments for each domain:
  == domain 1  score: 363.7 bits;  conditional E-value: 1.6e-112
                                       GGS--TT-EEEEEE-----EECTTEES--HHHHHHHHHHHHHHHTT-EEEEEE--S--TTS-GGG-SHHHHHHHHHH CS
                               PGK   2 kdldlkgkrvlvRvDfNvplkkegkitddtriraalpTikyllekgakvvllsHlgrpkgekeklslkpvaerLsel 78 
                                       +d++ ++k +++R+D+N+p+k+ gki +d r+ra l+Ti+ylle++akvv+ +H+++p  e++ l+++++ae Ls+l
  gi|242398207|ref|YP_002993631.1|   5 SDFNYHDKVIFLRADLNSPVKD-GKIISDARFRAVLHTIRYLLEHKAKVVIGTHQSKPY-EEDYLTTEQHAEILSSL 79 
                                       7999****************87.***********************************5.8999************* PP

                                       HTT-EEEESSTTSHHHHHHHHT-TTT-EEEES-GGGSTTTTTT-H.......HHHHHHHHT-SEEEE--GGGTTS-- CS
                               PGK  79 lgkeVkfvedvvgeeveeaiaelkegevllLeNvrfykeEeknde.......elakklasladvyVnDAFgtahrah 148
                                       lg +Vk+v+d++g+ +++ai++lk+ evl+LeN+rf +eE+k+++       ++++kl+ l+d+ Vn+AF++ahr++
  gi|242398207|ref|YP_002993631.1|  80 LGVKVKYVDDIFGKCARDAIKALKPSEVLMLENLRFAAEETKQNPleycertHFVRKLSPLIDYVVNEAFAAAHRSQ 156
                                       *****************************************998887777666************************ PP

                                       TTTTHHHHCSEEEE-HHHHHHHHHHHHHHHS--SSEEEEEEES-HHHCHHHHHHHTT..T-SEEEEETCHHHHHHHH CS
                               PGK 149 aStvgiakvlsaaaGllmekElealskvlenperplvailGGakvsdkikvienLle..kvdkliigGgmantFlka 223
                                        S+vg+a++ + + G+lmekE++al+++ e+ erp +++lGGakv+d ++v en+l+  k+d +++gG++  +F  a
  gi|242398207|ref|YP_002993631.1| 157 PSLVGFARIRPMIPGFLMEKEIKALTRAYESLERPKIYVLGGAKVEDSLNVAENVLRneKADLILTGGLVGHVFTLA 233
                                       *********998*******************************************962266**************** PP

                                       TT-B-TTSS-...-GGG....HHHHHHHHHHHHHHT-EEE--SEEEEESSSSTTS..EEEECCG--TT-EEEEE-HH CS
                               PGK 224 qgleigkslv...eedk....lelakellekakkkgvkillpvDvvvakeeaeke.akvveveaipedemalDigpk 292
                                       +g+++g+  +   +e+     ++ a+ +l+++      i +pvD++v+ + ++ e   + +++ i ++  +lDig++
  gi|242398207|ref|YP_002993631.1| 234 KGFDLGDANIsflDEKGliklVDRAEIILNEFY---PYIRTPVDFAVEYKGERVEiDLLSDKQWIFDERPILDIGSR 307
                                       ******876644344324445999999999998...89**********975555535566888899*********** PP

                                       HHHHHHHHHCC-SEEEEES-SS-TTSGCCCHHHHHHHHHHHHHCHTSEEEEESHHHHHHHHHTT-GGGSSEEESSSH CS
                               PGK 293 tielfaeaikeaktvvwnGpmGvfeiekfakGTkaiakalaeatkgalsivGGgdsaaaveklgladkvshvStGGg 369
                                       tie+++e++kea+++v nGpmGvfeie+fakGT ++ ka+ e++  a+sivGGg+s+a + ++++ + +sh+StGGg
  gi|242398207|ref|YP_002993631.1| 308 TIEKYSEILKEASIIVANGPMGVFEIEEFAKGTVEVFKAIGESK--AFSIVGGGHSIASIYQYNI-KGISHISTGGG 381
                                       ******************************************84..6*****************9.68********* PP

                                       HHHHHHCT CS
                               PGK 370 AsLelLeg 377
                                       A+L+++ g
  gi|242398207|ref|YP_002993631.1| 382 AMLTFFAG 389
                                       *****998 PP

>> LuxE  Acyl-protein synthetase, LuxE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0    0.0021        13     227     272 ..      48      93 ..      36     100 .. 0.86
   2 ?    6.2   0.0   0.00077       4.6     185     230 ..     203     251 ..     198     256 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0021
                              LuxE 227 dknlqvitiGGWkklekekldkidfnrdladvlnlsiddvvdiygf 272
                                        k   vi +   k +e++ l  ++    l + l+++++ v di+g 
  gi|242398207|ref|YP_002993631.1|  48 HKAKVVIGTHQSKPYEEDYLTTEQHAEILSSLLGVKVKYVDDIFGK 93 
                                       46666777778899******************************95 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.00077
                              LuxE 185 kklvellrikasek.dliliG....fiyllyqtvyktlkdknisfqldknl 230
                                         l+  ++++ +ek dlil G     ++ l +  +  l d nisf  +k+l
  gi|242398207|ref|YP_002993631.1| 203 DSLNVAENVLRNEKaDLILTGglvgHVFTLAK-GF-DLGDANISFLDEKGL 251
                                       567777887655543999987777799*9*99.77.8**********9997 PP

>> VacA2  Putative vacuolating cytotoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   3.5e-05      0.21      26      48 ..     375     397 ..     365     409 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.5e-05
                             VacA2  26 awktGGgAsltFnaadnitlnga 48 
                                        ++tGGgA ltF a +++ + +a
  gi|242398207|ref|YP_002993631.1| 375 HISTGGGAMLTFFAGQSLPVLQA 397
                                       589************99954443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.65u 0.33s 00:00:00.98 Elapsed: 00:00:00.54
# Mc/sec: 2288.73
//
Query:       gi|242398208|ref|YP_002993632.1|  [L=717]
Description: type II restriction endonuclease [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.6e-11   43.1   0.0    6.5e-11   42.3   0.0    1.5  1  Mrr_cat     Restriction endonuclease
    1.8e-06   28.4   9.6     0.0067   17.0   0.3    5.1  6  PepSY       Peptidase propeptide and YPEB domain
  ------ inclusion threshold ------
      0.027   14.7   0.3      0.027   14.7   0.3    3.2  3  PBP5_C      Penicillin-binding protein 5, C-terminal domain
      0.049   14.2   0.1      0.049   14.2   0.1    4.1  5  PepSY_like  Putative beta-lactamase-inhibitor-like, PepSY-lik


Domain annotation for each model (and alignments):
>> Mrr_cat  Restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   0.0   1.5e-14   6.5e-11      11     113 ..      18     123 ..       8     125 .. 0.86

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 1.5e-14
                                       HHHHHHHHHHSSSEEE---B-TTSSB--EEEE.TTE.EEEEEEEEEE--TS-B-HHHHHHHHHHCTTS..SEEEEEE CS
                           Mrr_cat  11 klvaellealGykeveltgrsgDggiDliakk.dpl.gserilvqaKryknkvgvkeVqeligalkkrgadkgifvt 85 
                                       + + +ll ++G+++ve  +  ++ g++++a + dp  g e+++v +K+ ++  ++++++++  a++  +adkgif  
  gi|242398208|ref|YP_002993632.1|  18 EALINLLDKMGFNNVEKIENPKEWGVEILALRdDPIaGFEKYVVKIKH-EALASSQDIESFGEAIMRSKADKGIFLA 93 
                                       56789***********************975514442568********.77889*********************** PP

                                       SS-B-HHHHHHHHT.T-.-EEEE-HHHHHH CS
                           Mrr_cat  86 tsdftkaAreeaee.ln.kieLldgdeLae 113
                                       +++ftk+A+  + +  + +++ +dg++++e
  gi|242398208|ref|YP_002993632.1|  94 IHGFTKDAKLLVGKeYKgRMITWDGEKFIE 123
                                       ***********96634458********987 PP

>> PepSY  Peptidase propeptide and YPEB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.47   2.1e+03       1      14 [.     333     346 ..     333     371 .. 0.78
   2 ?   -4.0   0.0         4   1.8e+04      55      61 ..     385     391 ..     382     392 .. 0.82
   3 ?   -3.5   0.0       3.6   1.6e+04      44      61 ..     495     512 ..     488     513 .. 0.68
   4 !    6.9   0.1     0.002       9.1       2      37 ..     517     559 ..     516     569 .. 0.71
   5 !   17.0   0.3   1.5e-06    0.0067       4      62 ..     576     630 ..     574     631 .. 0.94
   6 !    6.2   0.1    0.0034        15      15      61 ..     651     694 ..     639     696 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.47
                                       SS-HHHHHHHHHHH CS
                             PepSY   1 kiseeqAlaiAlaa 14 
                                       ++++e+ ++iA+++
  gi|242398208|ref|YP_002993632.1| 333 PLPKEKLIEIAREE 346
                                       5899*******987 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 4
                                       TT--EEE CS
                             PepSY  55 kTGkvlk 61 
                                       ++G vlk
  gi|242398208|ref|YP_002993632.1| 385 YSGRVLK 391
                                       9****98 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 3.6
                                       TTEEEEEEEETTT--EEE CS
                             PepSY  44 egpeyevfiDAkTGkvlk 61 
                                       e++ +  + D k+G++ +
  gi|242398208|ref|YP_002993632.1| 495 EDGKVLLKADGKSGDIMD 512
                                       566666677888888865 PP

  == domain 4  score: 6.9 bits;  conditional E-value: 0.002
                                       S-HHHHHHHHHHHSTTE.EEEEEEEEEE......TTEEEEEEE CS
                             PepSY   2 iseeqAlaiAlaavpgk.iieieleded......dgrlvYeve 37 
                                       is+++A++i l++++g  i++ie  +++      ++rl  +++
  gi|242398208|ref|YP_002993632.1| 517 ISPKKARKIILEKYSGWrIKKIEELKDNykaeleNDRLLLRIS 559
                                       9*************99955556665554655555666555555 PP

  == domain 5  score: 17.0 bits;  conditional E-value: 1.5e-06
                                       HHHHHHHHHHHSTTEEEEEEEEEEETTEEEEEEEEE.EE.TTEEEEEEEETTT--EEEE CS
                             PepSY   4 eeqAlaiAlaavpgkiieielededdgrlvYevelstaepegpeyevfiDAkTGkvlkk 62 
                                       ee A++iA++++ gk i++e+ +  + ++ ++v++    +e +  e++i   +Gkvlk+
  gi|242398208|ref|YP_002993632.1| 576 EEVAREIAEKFLDGKGISAEIKEI-KLDANWQVRFA---GEERVGEILIEKISGKVLKS 630
                                       7889********************.***********...699999999*********97 PP

  == domain 6  score: 6.2 bits;  conditional E-value: 0.0034
                                       STTEEEEEEEEEEETTEEEEEEEEE.EE.TTEEEEEEEETTT--EEE CS
                             PepSY  15 vpgkiieielededdgrlvYevelstaepegpeyevfiDAkTGkvlk 61 
                                       +++k +++e     ++++   ++ls   ++ ++y+ + D  TGk l+
  gi|242398208|ref|YP_002993632.1| 651 FNDKNLKTETIIVHKEKGYATIKLS---GDEAFYYAKLDLRTGKLLE 694
                                       4444444444443366777779999...7****************98 PP

>> PBP5_C  Penicillin-binding protein 5, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1      0.13   5.8e+02      20      53 ..     420     455 ..     412     473 .. 0.84
   2 ?   14.7   0.3   6.1e-06     0.027      25      90 ..     514     579 ..     494     580 .. 0.87
   3 ?   -1.6   0.3      0.72   3.2e+03      13      38 ..     656     684 ..     643     711 .. 0.49

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.13
                                       SSSSSEEEEEESSXEEEEEETTHCCTEEEEEEE..S CS
                            PBP5_C  20 kgkekeVplvakediyvtvkkgekkklkakvel..k 53 
                                       k+++  ++++++e i v+ ++ e+ ++++kvel  +
  gi|242398208|ref|YP_002993632.1| 420 KEDKAIIDVLTPEGIVVLEFNLENGEYNIKVELlhP 455
                                       566778999**********************99433 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 6.1e-06
                                       EEEEEESSXEEEEEETTHCCTEEEEEEESSSEESGBGTTSEEEEEEEEETTEEEEEEEEEESSXBX CS
                            PBP5_C  25 eVplvakediyvtvkkgekkklkakvelkksleapikkGqkvGklkvyldgkliakvplvakedve 90 
                                       +V++++k+  +++++k +   +k+  elk++ +a ++ +  + ++++++dgk++ +++   ke+v 
  gi|242398208|ref|YP_002993632.1| 514 FVEISPKKARKIILEKYSGWRIKKIEELKDNYKAELENDRLLLRISLSKDGKILEETDKHLKEEVA 579
                                       89******************************************************9988888885 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.72
                                       SEEEEEESSSSS...EEEEEESSXEEEEE CS
                            PBP5_C  13 vktvsvlkgkek...eVplvakediyvtv 38 
                                       +kt +++  kek   +++l+ +e +y+  
  gi|242398208|ref|YP_002993632.1| 656 LKTETIIVHKEKgyaTIKLSGDEAFYYAK 684
                                       34444444444444556666666665554 PP

>> PepSY_like  Putative beta-lactamase-inhibitor-like, PepSY-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.92   4.1e+03      32      62 ..      12      42 ..       5      47 .. 0.71
   2 ?   -1.0   0.1      0.59   2.6e+03      38      67 ..     399     428 ..     395     450 .. 0.77
   3 ?   14.2   0.1   1.1e-05     0.049      37      82 ..     519     567 ..     503     568 .. 0.90
   4 ?   -3.2   0.0       2.9   1.3e+04      63      75 ..     597     609 ..     573     612 .. 0.60
   5 ?   -0.9   0.6      0.56   2.5e+03      37      75 ..     644     682 ..     626     686 .. 0.65

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.92
                                      SGGGS-HHHHHHHHHH.TTTEEEEEEEECS.SE CS
                        PepSY_like 32 plsilpkavlkaikns.ypdekvtkierkk.ke 62
                                      +++il +a ++ +++  ++  +v+kie++k  +
  gi|242398208|ref|YP_002993632.1| 12 SREILVEALINLLDKMgFN--NVEKIENPKeWG 42
                                      5667777777777776666..999999998544 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.59
                                       HHHHHHHHHHTTTEEEEEEEECSSEEEEEE CS
                        PepSY_like  38 kavlkaiknsypdekvtkierkkkeyeiel 67 
                                       +a+l+ ++  yp+ kv   ++k+ + +i++
  gi|242398208|ref|YP_002993632.1| 399 EAILSEVSDRYPGGKVISFTEKEDKAIIDV 428
                                       689999999999988888888877777776 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 1.1e-05
                                       -HHHHHHHHHHTTTEEEEEEEECSSEEEEEETT...SEEEEEETTS-EE CS
                        PepSY_like  37 pkavlkaiknsypdekvtkierkkkeyeielen...eielyfdedGnll 82 
                                       pk+  k i ++y++  ++kie+ k +y+ elen    + + +++dG++l
  gi|242398208|ref|YP_002993632.1| 519 PKKARKIILEKYSGWRIKKIEELKDNYKAELENdrlLLRISLSKDGKIL 567
                                       8899999**************************9887888999999998 PP

  == domain 4  score: -3.2 bits;  conditional E-value: 2.9
                                       EEEEETTSEEEEE CS
                        PepSY_like  63 yeieleneielyf 75 
                                        ei+l+ ++++ f
  gi|242398208|ref|YP_002993632.1| 597 KEIKLDANWQVRF 609
                                       3566666666655 PP

  == domain 5  score: -0.9 bits;  conditional E-value: 0.56
                                       -HHHHHHHHHHTTTEEEEEEEECSSEEEEEETTSEEEEE CS
                        PepSY_like  37 pkavlkaiknsypdekvtkierkkkeyeieleneielyf 75 
                                       +k vl+ ++ +  ++++  + ++k    i+l+ +   y+
  gi|242398208|ref|YP_002993632.1| 644 QKHVLEKFNDKNLKTETIIVHKEKGYATIKLSGDEAFYY 682
                                       344555555554447777888888888899887666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (717 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       762  (0.042501); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.70u 0.30s 00:00:01.00 Elapsed: 00:00:00.48
# Mc/sec: 4446.89
//
Query:       gi|242398209|ref|YP_002993633.1|  [L=203]
Description: hypothetical protein TSIB_0217 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       920  (0.0513135); expected 358.6 (0.02)
Passed bias filter:                      620  (0.0345808); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 1346.95
//
Query:       gi|242398210|ref|YP_002993634.1|  [L=685]
Description: Metallophosphoesterase, calcineurin superfamily [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.6e-13   50.5   2.3    6.9e-13   49.6   2.3    1.5  1  Metallophos    Calcineurin-like phosphoesterase
    0.00022   21.5   0.0    0.00069   19.9   0.0    1.8  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
  ------ inclusion threshold ------
      0.021   15.1   0.0       0.11   12.8   0.0    2.2  2  DUF4625        Domain of unknown function (DUF4625)
       0.66   10.0  20.0       0.28   11.2  17.1    1.8  2  Mucin          Mucin-like glycoprotein
        1.9    6.6  16.6        2.8    6.0  16.6    1.1  1  SSP160         Special lobe-specific silk protein SSP160
        6.8    6.6   7.5         14    5.6   7.5    1.4  1  MSA-2c         Merozoite surface antigen 2c


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.6   2.3   2.3e-16   6.9e-13       1     204 []     123     361 ..     123     361 .. 0.68

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 2.3e-16
                                       EEEEEEESBTB...........TTCCTHHHHHHHHHHHH...................HHHTTESEEEEESTSSSSS CS
                       Metallophos   1 lrilvigDlHl...........algggqlddllkllddl...................lreekpdlvllaGDlvdrg 47 
                                       lri++++D+H+           ++  g++++++kl d                      +  ++++++ +GD+vd+ 
  gi|242398210|ref|YP_002993634.1| 123 LRIAHLSDTHVisgakfgyvcrEYFQGSIQKIQKLCDGGmiiplhsyvatdsaytywsMD-DRVNVIITTGDVVDTA 198
                                       69*************999777766667777777777555776666666555555555322.799************9 PP

                                       HHHHHHHHHHHHHHHH....TSEEEEEC-TTSCHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEE CS
                       Metallophos  48 dlekellellaalvky....pipvylllGNHegfeeellnkygylgifsepwrsdaevfnnlplaslgsgslkvlll 120
                                       + +k   ++l   ++     + p ++++GNH+    + +n y++l    + +    ++f ++ l s           
  gi|242398210|ref|YP_002993634.1| 199 GDSK-AYKMLFDIISTttaaGRPTIIVKGNHD----DPPNYYPKLIGPTDYYI-TIGKFLIIALDS----------- 258
                                       8888.66665555555588899**********....88888776554333333.345554555544........... PP

                                       ESECEEETHHHHHHHHHHHSCHHHHCC...HHHHHHHHHHTTCSEEEEEESSESS...................... CS
                       Metallophos 121 hGgspellvsldklgslnleleapepg...dewlkdlekrekadwvivlgHsply...................... 172
                                       hG++++                         ew+++  ++ ++++ ivl H+p +                      
  gi|242398210|ref|YP_002993634.1| 259 HGDEAHP-------------------SmqqLEWMENILEEHPDKIPIVLVHHPYWysgsegwiggyiegtafddksw 316
                                       5552222...................122399999966667777777777777776999999999666666666666 PP

                                       .....CSSSCSCCHHHHH.........HHHHHTTESEEEEESSSSE CS
                       Metallophos 173 .....rgsgylfgdeale.........dllkkygvdlvisGHtHvy 204
                                            +gs y+fg+++           d  +ky+++l+ sGH+H++
  gi|242398210|ref|YP_002993634.1| 317 eemiqYGSFYWFGRNQEFldiarrflqD-VEKYNIKLIMSGHIHHD 361
                                       6665544444444444448999977533.58888**********85 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 !   19.9   0.0   2.3e-07   0.00069       2     131 ..     124     366 ..     123     393 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2.3e-07
                     Metallophos_2   2 klaiiSDlH..................................snldaleav.........lealkevgvdaiihaG 35 
                                       ++a++SD+H                                                    +  + + +v+ ii +G
  gi|242398210|ref|YP_002993634.1| 124 RIAHLSDTHvisgakfgyvcreyfqgsiqkiqklcdggmiiplH-------SyvatdsaytYWSM-DDRVNVIITTG 192
                                       68888888888888888888888885444444444444444443.......04444444442222.34479999*** PP

                     Metallophos_2  36 Dl..eeeepevleellela........pvlaVrGNnD......................eevveedvlreaaelgtd 80 
                                       D+   +++ ++ + l+++         p ++V+GN+D                       +++ +  ++ea++ +++
  gi|242398210|ref|YP_002993634.1| 193 DVvdTAGDSKAYKMLFDIIstttaagrPTIIVKGNHDdppnyypkligptdyyitigkfLIIALDSHGDEAHPSMQQ 269
                                       *86644444455555555555688889***********************999888544333777788888888888 PP

                     Metallophos_2  81 lp.eeaelel..agek..vlliHgdpl.....................................gvkdalaellkea 115
                                       l+  e  le   +  k  + l+H+  +                                     +   ++a+++ + 
  gi|242398210|ref|YP_002993634.1| 270 LEwMENILEEhpD--KipIVLVHHPYWysgsegwiggyiegtafddksweemiqygsfywfgrnQEFLDIARRFLQD 344
                                       8766666664234..356******855*********************************97764445555555553 PP

                     Metallophos_2 116 eegsd..vvvcGHtHvp....e 131
                                        e+ +  ++++GH+H      +
  gi|242398210|ref|YP_002993634.1| 345 VEKYNikLIMSGHIHHDklhvY 366
                                       3334456********9844443 PP

>> DUF4625  Domain of unknown function (DUF4625)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       3.3   9.8e+03      94     113 ..      81     100 ..      77     101 .. 0.77
   2 ?   12.8   0.0   3.5e-05      0.11      10      60 ..     518     563 ..     513     582 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 3.3
                           DUF4625  94 lheeieiPadaeaGdYhlvi 113
                                       ++ +++iP+++ +  Y l++
  gi|242398210|ref|YP_002993634.1|  81 ATLKVKIPENVVPDVYFLQV 100
                                       567899****9998887765 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 3.5e-05
                           DUF4625  10 edtekPvidllevsaepeeeevlkiGetlhfeaklsdnealasykvdihnn 60 
                                       +dtekP id+  +++     ++ ++G+ +++ + l+dn  +++++v+i++n
  gi|242398210|ref|YP_002993634.1| 518 KDTEKPQIDIPYITP-----SKPTKGKPFKVFISLKDNLGVKDIYVEIEAN 563
                                       69********96655.....78899***********************998 PP

>> Mucin  Mucin-like glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.4   4.2e+03      85     117 ..     378     410 ..     375     413 .. 0.75
   2 ?   11.2  17.1   9.5e-05      0.28      32      92 ..     606     667 ..     587     678 .. 0.66

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.4
                             Mucin  85 tttateaPsdavttaeaPtttttrapsrlrevd 117
                                       t t+t aP +  +    P+ + t   s++ e+d
  gi|242398210|ref|YP_002993634.1| 378 TLTTTGAPDKEPNPPSKPNYSPTWYGSNVVEID 410
                                       567788888888888888888777777777777 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 9.5e-05
                             Mucin  32 daavveaaegqskltttttttkppttttttttasttittkttkatttttttttttt.ateaP 92 
                                       ++a+ e + g+ ++ tt  tt++pt++ tt++ stt   +t+ +t t+t+++ttt+  t  P
  gi|242398210|ref|YP_002993634.1| 606 NKATSEMTVGEIETSTTPSTTESPTSSSTTSSPSTTSPETTSPTTETPTSSSTTTSgGTCGP 667
                                       56777888888888888888888888888885555544444444444443333333033444 PP

>> SSP160  Special lobe-specific silk protein SSP160
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0  16.6   0.00093       2.8     104     160 ..     616     673 ..     595     680 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.00093
                            SSP160 104 sasssssssatstssststtssssttssnstttt.snstsssnstssgltssasvvsl 160
                                          +s++ s+t + +s+sttss stts ++t+ t    tsss +ts g    a+++sl
  gi|242398210|ref|YP_002993634.1| 616 EIETSTTPSTTESPTSSSTTSSPSTTSPETTSPTtETPTSSSTTTSGGTCGPAAIISL 673
                                       4445555566666667788888888888877655055677777777777778999997 PP

>> MSA-2c  Merozoite surface antigen 2c
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   7.5    0.0046        14     139     199 ..     607     661 ..     592     672 .. 0.56

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0046
                            MSA-2c 139 kdvteeLlke.lqekkPsrtssaetPaPsdaesaaaqPPeskpaqaPaPtspsqseesssnl 199
                                       k ++e  + e +++ +Ps+t+s+     +++ s+++  P ++++++ +Pt+ +++  s++  
  gi|242398210|ref|YP_002993634.1| 607 KATSEMTVGEiETSTTPSTTESP-----TSS-STTSS-PSTTSPETTSPTTETPTSSSTTTS 661
                                       55555444331344566666554.....444.33333.446677777777666666666543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (685 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.70u 0.29s 00:00:00.99 Elapsed: 00:00:00.43
# Mc/sec: 4775.08
//
Query:       gi|242398211|ref|YP_002993635.1|  [L=200]
Description: hypothetical protein TSIB_0219 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-22   79.0   0.0    4.1e-22   78.8   0.0    1.0  1  DUF447    Protein of unknown function (DUF447)


Domain annotation for each model (and alignments):
>> DUF447  Protein of unknown function (DUF447)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.8   0.0   2.3e-26   4.1e-22       1     171 [.      10     185 ..      10     190 .. 0.85

  Alignments for each domain:
  == domain 1  score: 78.8 bits;  conditional E-value: 2.3e-26
                                       EEEEEEEE-TT-EEEEEEEEEESSSEEEEEEETTSHHHHHHHHHSEEEEEE---HHHHHHHHHS---GGGEEEETT. CS
                            DUF447   1 yEvivtTksekrpnaaPiGvivkgdkvvlrlfkgsrTleNllengelvinvtdDpllfakaalgdleesdfdsetk. 76 
                                       yE ++ Tks    n++P+Gv++kg k+ ++lf+g +++++++e+++ v+++t+D+ +++++al+   e + ++ ++ 
  gi|242398211|ref|YP_002993635.1|  10 YELLLLTKS----NVTPVGVVKKGSKFYFKLFEG-KSAKDIKEHPYGVLHITWDVDILVRTALNLPCELEWEDSKTi 81 
                                       899999*99....********************9.*****************************7655555444444 PP

                                       TC.TT....EETT-SEEEEEEEEEECTCECCEEEEEEEEEEEEETTB---B-HHHHHHHHHHHHHHCCCC....... CS
                            DUF447  77 pa.kia...vlksaeawveveveevegdsealelelepvkeeileervkpfnRgdaaviEaaVlatRldi....... 142
                                       p+ ki+    +++   ++e  +++  g+ + l++ l+p + e+     +p++R+d  ++E+a+++tRl +       
  gi|242398211|ref|YP_002993635.1|  82 PLkKIKnlpNIEGKIEFQEDLIKDSLGEARILRCSLTPSRIEVFPISNPPLSRADFYLLEMAINLTRLYVatrklhv 158
                                       8888884445555566666667888********************99*********************777777666 PP

                                       SHHHHHHHHHHHHHHHHHHH--HHHHHHH CS
                            DUF447 143 edkeklleeieylssvikktggerekeal 171
                                       ++ +++ ++i   ++++k++gg++e  ++
  gi|242398211|ref|YP_002993635.1| 159 KEAQNIYSKIWVGYRTYKRLGGKNE--LA 185
                                       888888899999999*******998..33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1479.99
//
Query:       gi|242398212|ref|YP_002993636.1|  [L=353]
Description: Fructose-1,6-bisphosphate aldolase (FBA) [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.4e-33  116.3   0.0    2.2e-33  115.7   0.0    1.3  1  ABC_tran     ABC transporter
    3.8e-08   33.5   0.1     0.0029   17.4   0.0    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    2.4e-05   24.4   0.6    0.00012   22.2   0.0    2.4  3  TOBE_2       TOBE domain
     0.0015   18.5   0.0     0.0021   18.0   0.0    1.3  1  Rad17        Rad17 P-loop domain
     0.0087   15.7   0.0       0.41   10.2   0.0    2.2  2  AAA_25       AAA domain
  ------ inclusion threshold ------
      0.046   13.6   2.0      0.059   13.2   0.1    2.2  2  Myosin_N     Myosin N-terminal SH3-like domain
      0.049   13.5   0.1       0.18   11.7   0.0    1.8  2  RsgA_GTPase  RsgA GTPase
      0.049   13.9   0.8       0.36   11.1   0.8    2.1  1  AAA_22       AAA domain
       0.05   14.1   0.3      0.072   13.6   0.3    1.5  1  AAA_23       AAA domain
      0.088   13.6   0.5       0.37   11.7   0.1    2.3  2  OB_MalK      MalK OB fold domain
      0.099   13.1   0.0       0.63   10.5   0.0    2.1  2  AAA          ATPase family associated with various cellular a
       0.11   12.3   0.1       0.25   11.1   0.1    1.5  1  AAA_29       P-loop containing region of AAA domain
       0.14   12.6   0.0       0.28   11.6   0.0    1.5  1  AAA_16       AAA ATPase domain
       0.16   12.2   0.0        2.2    8.5   0.0    2.2  2  AAA_28       AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.7   0.0   1.7e-36   2.2e-33       1     136 [.      19     161 ..      19     162 .. 0.97

  Alignments for each domain:
  == domain 1  score: 115.7 bits;  conditional E-value: 1.7e-36
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       lk ++l++k ge+  ++G++G+GKSt l+++agl   ++G++ +d++d+++  ++s+++    ++q+  l+p++tv+
  gi|242398212|ref|YP_002993636.1|  19 LKGINLHVKDGELFTLLGPSGCGKSTTLRIIAGLDFADSGHLYFDDDDVTY--KSSSERGAVLVFQNYALWPHMTVY 93 
                                       789************************************************..99999999**************** PP

                                       HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       +n             e d++++ al+ ++l++ +d+      ++LSgGq+qrva+aral+ +pkllllDEp 
  gi|242398212|ref|YP_002993636.1|  94 DNvayglkvkklpkqEIDRKVKWALELVKLQGYEDRYP----TQLSGGQQQRVAIARALVVEPKLLLLDEPL 161
                                       **************9999**************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 !   14.0   0.0   2.6e-05     0.034       2      33 ..      32      64 ..      31      85 .. 0.72
   2 !   17.4   0.0   2.3e-06    0.0029     223     299 ..     120     194 ..      91     198 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.6e-05
                            AAA_21  2 nvliGpNgsGKSnLLdaldllarl.drdveglt 33
                                        l Gp g+GKS+ L+++ +l ++  +++ ++ 
  gi|242398212|ref|YP_002993636.1| 32 FTLLGPSGCGKSTTLRIIAGLDFAdSGHLYFDD 64
                                      5799****************9554533333333 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 2.3e-06
                            AAA_21 223 flengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHS 298
                                       +++  ++ ++ +++lS G+++  a++ al   +   +lll+DEp ++L+ kl  +    +++ +r  g+ vi +TH+
  gi|242398212|ref|YP_002993636.1| 120 LVKLQGYEDRYPTQLSGGQQQRVAIARALVVEP---KLLLLDEPLSNLDAKLRLEMRSEIRRIQReLGITVIYVTHD 193
                                       55566777888999******9999999999988...9*************999888877755555589********8 PP

                            AAA_21 299 p 299
                                        
  gi|242398212|ref|YP_002993636.1| 194 Q 194
                                       5 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.8   2.4e+03      26      48 ..     121     143 ..     113     149 .. 0.80
   2 ?   -3.4   0.0       8.9   1.1e+04      60      68 ..     248     256 ..     243     257 .. 0.81
   3 !   22.2   0.0   9.3e-08   0.00012       1      76 []     275     349 ..     275     349 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.8
                            TOBE_2  26 veylGsstryvvelaggqlvvvr 48 
                                       v  +G + ry  +l ggq+++v+
  gi|242398212|ref|YP_002993636.1| 121 VKLQGYEDRYPTQLSGGQQQRVA 143
                                       56678888999999999998886 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 8.9
                            TOBE_2  60 pGdtVelsw 68 
                                        Gd+V++++
  gi|242398212|ref|YP_002993636.1| 248 DGDKVTVRF 256
                                       599999988 PP

  == domain 3  score: 22.2 bits;  conditional E-value: 9.3e-08
                            TOBE_2   1 laiRPEklrlaaagg.an..glsGtVedveylGsstryvvelaggqlvvvrqpnadrdsalapGdtVelswdpddav 74 
                                       ++iRPE+++l+   + +n  +++G+V+ +ey G ++++ v l g+ +++ r+ n ++   l+p   V+  ++ +d++
  gi|242398212|ref|YP_002993636.1| 275 VVIRPERISLH---PiENavSITGKVDLIEYYGFFIEV-VGLFGEMRIISRTINDRDVIGLRPQGDVTFYIEREDIL 347
                                       78********5...44443589**************95.68888888888888888535788888888888888888 PP

                            TOBE_2  75 vl 76 
                                       vl
  gi|242398212|ref|YP_002993636.1| 348 VL 349
                                       86 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   0.0   1.6e-06    0.0021      35      66 ..      19      50 ..       5     120 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.6e-06
                             Rad17 35 lkadvLesrkkriLLisGPsGCgkstvvkvLs 66
                                      lk   L  +  ++  + GPsGCgkst++++++
  gi|242398212|ref|YP_002993636.1| 19 LKGINLHVKDGELFTLLGPSGCGKSTTLRIIA 50
                                      5666677777789999*************987 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0   0.00032      0.41      29      78 ..      25      82 ..      20      83 .. 0.77
   2 ?    3.2   0.0     0.045        57     170     188 ..     174     192 ..     157     198 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00032
                            AAA_25 29 llpagelallaGapgtGKttla.ldlalava.tGkpwlg......pvapeqgkVlyvs 78
                                      ++  gel  l G++g+GK+t + +  +l+ a +G+  ++      +  +e+g+Vl+ +
  gi|242398212|ref|YP_002993636.1| 25 HVKDGELFTLLGPSGCGKSTTLrIIAGLDFAdSGHLYFDdddvtyKSSSERGAVLVFQ 82
                                      67789*************8754266778888888888888888654445888888765 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.045
                            AAA_25 170 ealeriarrtgaavllvhH 188
                                       + ++ri+r++g++v+ v H
  gi|242398212|ref|YP_002993636.1| 174 SEIRRIQRELGITVIYVTH 192
                                       6799*************** PP

>> Myosin_N  Myosin N-terminal SH3-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   4.6e-05     0.059      14      30 ..     240     256 ..     240     258 .. 0.89
   2 ?   -3.3   0.2       6.8   8.7e+03      22      29 ..     269     276 ..     268     277 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.6e-05
                                       EEEEEEEEESSEEEEEE CS
                          Myosin_N  14 vkGeIkeeeGdkvtVet 30 
                                       + +e++e++GdkvtV+ 
  gi|242398212|ref|YP_002993636.1| 240 IPAEVVERDGDKVTVRF 256
                                       679************85 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 6.8
                                       ESSEEEEE CS
                          Myosin_N  22 eGdkvtVe 29 
                                       e+dkv+V 
  gi|242398212|ref|YP_002993636.1| 269 ENDKVVVV 276
                                       67999985 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00014      0.18      90     121 ..      19      51 ..       4      63 .. 0.81
   2 ?   -1.4   0.0       1.5   1.9e+03      63      90 ..     171     198 ..     146     208 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00014
                                       HHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  90 leelkellkd.ktsvlvGqSGvGKStLinallp 121
                                       l+ ++ ++kd ++ +l+G+SG GKSt +  +++
  gi|242398212|ref|YP_002993636.1|  19 LKGINLHVKDgELFTLLGPSGCGKSTTLRIIAG 51 
                                       55666677777999************9987765 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.5
                                       HHHHHHHHHHHHTTSEEEE--TTTHTTH CS
                       RsgA_GTPase  63 eeleelkeelealgyevllvsaktkegl 90 
                                       e  +e++   ++lg++v++v  +++e++
  gi|242398212|ref|YP_002993636.1| 171 EMRSEIRRIQRELGITVIYVTHDQEEAM 198
                                       4456778888899999999977655443 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.8   0.00028      0.36       6      29 ..      30      53 ..      25     197 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00028
                            AAA_22  6 gilvvtGesGtGKTtllrrlleql 29
                                       + ++ G+sG+GK+t+lr ++  +
  gi|242398212|ref|YP_002993636.1| 30 ELFTLLGPSGCGKSTTLRIIAGLD 53
                                      567899***********9877665 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.3   5.6e-05     0.072       3      40 ..       5      50 ..       3     184 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.6e-05
                            AAA_23  3 kienfrsf.rdqe....idF...skgltlItGpNGaGKTTildAik 40
                                      k+en+ +  +++     i++   +  l+ + Gp G+GK+T l+ i 
  gi|242398212|ref|YP_002993636.1|  5 KLENIVKTfGETValkgINLhvkDGELFTLLGPSGCGKSTTLRIIA 50
                                      66666444233222234566777778***************99886 PP

>> OB_MalK  MalK OB fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00029      0.37       6      53 .]     238     282 ..     237     282 .. 0.76
   2 ?   -2.2   0.0       6.2   7.9e+03      45      50 ..     328     333 ..     320     334 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00029
                           OB_MalK   6 Nflpatveedg...vlvegggvtlplpeeqklalklyagkevilGiRPEhi 53 
                                       N +pa+v+e +   v+v ++g++l+  +         ++++v++ iRPE i
  gi|242398212|ref|YP_002993636.1| 238 NVIPAEVVERDgdkVTVRFEGFKLDGLTYT------GENDKVVVVIRPERI 282
                                       99****997765666666666666655544......889999999****87 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 6.2
                           OB_MalK  45 ilGiRP 50 
                                       ++G+RP
  gi|242398212|ref|YP_002993636.1| 328 VIGLRP 333
                                       89***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 ?   10.5   0.0   0.00049      0.63       3      20 ..      34      51 ..      32      85 .. 0.89
   2 ?   -0.1   0.0      0.92   1.2e+03      45      69 ..     137     162 ..      97     205 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00049
                                      EESSTTSSHHHHHHHHHH CS
                               AAA  3 lyGppGtGKTllakavak 20
                                      l Gp G+GK+++ + +a 
  gi|242398212|ref|YP_002993636.1| 34 LLGPSGCGKSTTLRIIAG 51
                                      89*************996 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.92
                                       HHHHHHHHHHHTS.TSEEEEEETGGG CS
                               AAA  45 kirelfkeakeka.kpsilfiDEida 69 
                                         ++ ++ a++   +p+ l++DE  +
  gi|242398212|ref|YP_002993636.1| 137 GQQQRVAIARALVvEPKLLLLDEPLS 162
                                       44444444444445578888887433 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 ?   11.1   0.1    0.0002      0.25      18      39 ..      25      46 ..      16      50 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0002
                            AAA_29 18 eidlkg.atlltGpsGsGKSTll 39
                                      +++  g  + l GpsG GKST l
  gi|242398212|ref|YP_002993636.1| 25 HVKD-GeLFTLLGPSGCGKSTTL 46
                                      4443.3588899*********65 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   0.00022      0.28      24      44 ..      29      49 ..      18      86 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00022
                            AAA_16 24 pelvllsGesGvGKsslvrel 44
                                      +el  l G+sG+GKs+ +r +
  gi|242398212|ref|YP_002993636.1| 29 GELFTLLGPSGCGKSTTLRII 49
                                      47889************9866 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0    0.0017       2.2       3      20 ..      33      50 ..      31      84 .. 0.87
   2 ?    1.5   0.0      0.24   3.1e+02     130     161 ..     165     195 ..     122     197 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0017
                            AAA_28  3 vitGgestGKTtlleaLa 20
                                       ++G++++GK+t+l+ +a
  gi|242398212|ref|YP_002993636.1| 33 TLLGPSGCGKSTTLRIIA 50
                                      689***********9887 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.24
                            AAA_28 130 dleereaiderlrealrelgipviivpsgdve 161
                                       d + r ++   +r + relgi vi v + d e
  gi|242398212|ref|YP_002993636.1| 165 DAKLRLEMRSEIRRIQRELGITVIYV-THDQE 195
                                       677899999***************99.76655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); 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: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 2180.20
//
Query:       gi|242398213|ref|YP_002993637.1|  [L=614]
Description: ABC transporter, permease [Thermococcus sibiricus MM 739]
Scores for complete 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-24   84.3  34.6    1.3e-13   51.1  16.4    4.2  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 ?    0.4   2.2     0.026   4.6e+02      19      44 ..      15      50 ..       7     116 .. 0.68
   2 !   47.7  10.2   8.3e-17   1.5e-12       1     179 [.     117     313 ..     117     317 .. 0.86
   3 ?   -0.9   5.8     0.067   1.2e+03      98     172 ..     342     418 ..     335     424 .. 0.65
   4 !   51.1  16.4   7.5e-18   1.3e-13       7     173 ..     419     597 ..     411     609 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.026
                      BPD_transp_1 19 llrpliivllslPsfvlaillvlvf..........v 44
                                      l+ pli + + +P + l+++l++ +           
  gi|242398213|ref|YP_002993637.1| 15 LFEPLIAFSYLFPLLYLVMFLIVPVismlliaftyD 50
                                      667777777777777777776655444444444440 PP

  == domain 2  score: 47.7 bits;  conditional E-value: 8.3e-17
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf.................vilsilghlilpviill 60 
                                       g+++++++a ++n+k+++l+r+  +++l + +fv a ++  +f                   + i  ++  +v+++ 
  gi|242398213|ref|YP_002993637.1| 117 GTVFAFVMA-RYNFKGKNLFRIALFIPLLVTPFVNAYVIKQMFsefglinyifhevlhllP-FRIKIDGLAGVVLAQ 191
                                       7899*****.************************888888888888888888899999742.3233357777***** PP

                      BPD_transp_1  61 llsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGl 137
                                        + + p+v+l+ +a + +++  l+e a+ lG + +++fr+v++P+alp i++g+ l+f+++l + +++  + ++p l
  gi|242398213|ref|YP_002993637.1| 192 SMAYYPIVYLNAYASFINIDPTLEEQAENLGSKSFRLFRTVTFPLALPGIAAGATLVFIFSLEDLAAPVVFHADP-L 267
                                       ************************************************************************998.7 PP

                      BPD_transp_1 138 gtllleailgydyseis....nggvlalviavlllnlvadilqrll 179
                                          l++ ++ + + +++      +++  +i++ l ++++  + +++
  gi|242398213|ref|YP_002993637.1| 268 AKKLMSYQIFSKFIYGLgersPEIAALSIIMLTLAIIAFLGIRKYV 313
                                       7777777777777777788887777777777777777777777766 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.067
                      BPD_transp_1  98 frkvvlPnalppiitgli...lafggllggavlleflgswpGlgtllleailgydyseisnggvlalviavlllnlv 171
                                       ++ v+lP++l++i+++l+   laf   ++ +vl+  ++ +  +  ++l++   + + + +  + +a++++v+l +++
  gi|242398213|ref|YP_002993637.1| 342 IYLVLLPALLITIFPQLGvimLAFSERWTTTVLPQGFTIDY-IKEMILNPDVRRFIVNSLTYSGAAVILIVILSITS 417
                                       55688888888888887622245555588888887666333.88888888877777666645556666666655555 PP

                      BPD_transp_1 172 a 172
                                       +
  gi|242398213|ref|YP_002993637.1| 418 S 418
                                       5 PP

  == domain 4  score: 51.1 bits;  conditional E-value: 7.5e-18
                      BPD_transp_1   7 laalnrnkkldkllrpliivllslPsfvlaillvlvf..........vilsilghlilp.viillllsaapyvrlir 72 
                                       +a  ++++ l+ +l  ++i++ ++P +v+a+  +++f             s  g+     +i+++ +  +p++ + +
  gi|242398213|ref|YP_002993637.1| 419 YASSRFKGALSPVLESIVILPIAVPGIVVAMGYFYFFsvitpensplNPTSLYGFNPALvLILAYSIRRLPFAARSV 495
                                       333899999**************************9*********9544444455544446777788889******* PP

                      BPD_transp_1  73 raalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgyd 149
                                       +a+l+++  +l+e +  lGasrw+++  +++P++   ++ g +l+f++++ ++++  +lgs + + +  ++a +   
  gi|242398213|ref|YP_002993637.1| 496 YAGLQQVHISLEESSINLGASRWRTITGILMPLISLNVFGGSMLSFVYSMSETSVGITLGSIN-MEQAPITAFMKEV 571
                                       ************************************************************999.5555555555555 PP

                      BPD_transp_1 150 yseis...nggvlalviavlllnlvad 173
                                       + +++   n +++al+++++++ + a 
  gi|242398213|ref|YP_002993637.1| 572 LMSAAgsiN-LAAALGVLLIVVQITAI 597
                                       555554642.33333333333333222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (614 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       923  (0.0514808); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.45
# Mc/sec: 4060.78
//
Query:       gi|242398214|ref|YP_002993638.1|  [L=489]
Description: iron ABC transporter substrate-binding protein [Thermococcus sibiricus MM 739]
Scores for complete 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   76.3   1.0    1.8e-20   73.9   0.0    2.3  2  SBP_bac_8     Bacterial extracellular solute-binding protein
    1.1e-19   70.8   0.2    1.8e-19   70.2   0.2    1.3  1  SBP_bac_6     Bacterial extracellular solute-binding protein
    6.9e-13   49.2   0.8    6.9e-13   49.2   0.8    1.8  2  SBP_bac_1     Bacterial extracellular solute-binding protein
    0.00011   22.1   0.6     0.0096   15.7   0.0    3.1  3  SBP_bac_11    Bacterial extracellular solute-binding protein
     0.0056   17.1   0.2      0.015   15.8   0.2    1.7  1  DUF3644       Protein of unknown function (DUF3644)
  ------ inclusion threshold ------
      0.063   13.0   0.0       0.16   11.7   0.0    1.7  1  HeH           HeH/LEM domain
       0.55    9.6  10.8        0.9    8.9  10.8    1.2  1  Orthopox_A5L  Orthopoxvirus A5L protein-like
        4.1    5.5  10.3        5.7    5.0  10.3    1.1  1  SSP160        Special lobe-specific silk protein SSP160


Domain annotation for each model (and alignments):
>> SBP_bac_8  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.9   0.0     8e-24   1.8e-20      41     281 ..     117     361 ..      41     363 .. 0.81
   2 ?   -0.2   0.1      0.32   7.2e+02     141     176 ..     391     420 ..     369     433 .. 0.68

  Alignments for each domain:
  == domain 1  score: 73.9 bits;  conditional E-value: 8e-24
                                       E.EEE-HHH.HHHHHHTTSB--GGGSTTHHH....-HHHHHTT.....--TS.----EEEEEEE-EEEEEHHHHHH. CS
                         SBP_bac_8  41 dvvwaneda.latlaeeglladlsdldnldd....ltdalaav.....gydgklygvPyasetpyvliynkdllek. 106
                                       dv w+ +   ++ l+ +++l++++d + l      ++ ++a++     g dgk+y++  a ++  ++ +n d+l+  
  gi|242398214|ref|YP_002993638.1| 117 DVGWGGGPTlFDSLFRNNYLVPIEDQKVLGLignqIQETIAGMpmirkGDDGKIYWIAAALSS-FGFTVNHDVLKRw 192
                                       45555544347788888888888854444444455566666668888778************8.9**********75 PP

                                       S..---BHHHHHHHHHHH...HHH-SEGG---G..GGGGGTHHETTEE---H..HHH.HHHHHHHHHHHHTT-EE-S CS
                         SBP_bac_8 107 a.edpktwdellaaakkl...kgkfglpdpasg..wlqaallakdgksldddggkdglkealellkklkdngktydt 177
                                       +  +p+ w++l +  +++   + ++g++dp+ +  + ++++++ + + +       g++e +++l+ + +n k+yd+
  gi|242398214|ref|YP_002993638.1| 193 NlPVPQRWEDLAS--ETFamdPPQVGIADPTRStsNTRIYQII-L-QAF-------GWDEGWKILTLIAANSKIYDA 258
                                       399********99..7776677999**9888663344555555.4.222.......69******************* PP

                                       ..--SSTTTTTSBSEEEE-TTHHHHHH-TTTSEEEE--S--EEEEEEEEEEBTTS-HHHHHHHHHHHHHTTSHHHHH CS
                         SBP_bac_8 178 gadavsefanGevaftingswdiaaaqkagkklgaivpkqgsfaggkglavpknaknedlaAldFlkwltspenqaa 254
                                       ++++ +++  G++  + + +     a k ++  ++i+pk +s+++g+++av+ ++ +++ aA++F+ w+++ e+q+ 
  gi|242398214|ref|YP_002993638.1| 259 SDAVREAVIGGDIGVGNTIDFYGYIAMKSNPSCEYIIPKGQSIINGDPIAVLVKSQHKE-AAQAFIYWVLT-EGQRI 333
                                       ************987666555544555889*****************************.6*****99997.79999 PP

                                       HHH.HH---BS-S-TTTHHHHHH-HHH. CS
                         SBP_bac_8 255 lae.ktgyipvnksaalspevkkdpalp 281
                                       + + +++ +pvn+++ ++pe ++ p+l+
  gi|242398214|ref|YP_002993638.1| 334 WLDeQINRLPVNPDVFNTPEGQNRPDLK 361
                                       9999***************999988765 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.32
                                       THHETTEE---H..HHH.HHHHHHHHHHHHTT-EE- CS
                         SBP_bac_8 141 llakdgksldddggkdglkealellkklkdngktyd 176
                                       ++a     l d   +++l +a++ l k ++ gk+ +
  gi|242398214|ref|YP_002993638.1| 391 FKA-T---LVD--ANQELHRAWTALVKAYKEGKISE 420
                                       333.2...223..37889999999999999999774 PP

>> SBP_bac_6  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.2   0.2   7.9e-23   1.8e-19       4     231 ..     116     367 ..     113     379 .. 0.80

  Alignments for each domain:
  == domain 1  score: 70.2 bits;  conditional E-value: 7.9e-23
                         SBP_bac_6   4 pdlilsfdkdflekfieeglfqpld............panlpnvnkdfaeeglkdp.dgkyy..pygvgplvlavnk 65 
                                       +d++++ ++ +++ +  ++++ p++            ++ ++ ++      +++++ dgk+y  + + + +++ vn+
  gi|242398214|ref|YP_002993638.1| 116 ADVGWGGGPTLFDSLFRNNYLVPIEdqkvlglignqiQETIAGMP------MIRKGdDGKIYwiAAALSSFGFTVNH 186
                                       899999****************************99988899998......344333444443499*********** PP

                         SBP_bac_6  66 drlkgrpv..PksWaDLldPeykg...kvalpgnngsdlfealllalykdfgedgvkkllrnlkanlhpaq.mvkaa 136
                                       d+lk  ++  P++W+DL +++++    +v++ ++ +s++++ +  ++ + fg+d+++k+l  ++an + +  ++   
  gi|242398214|ref|YP_002993638.1| 187 DVLKRWNLpvPQRWEDLASETFAMdppQVGIADPTRSTSNTRIYQIILQAFGWDEGWKILTLIAANSKIYDaSDAVR 263
                                       ***97766558************9999********************************************777777 PP

                         SBP_bac_6 137 gslesgepavsvvpyffadilpekkkgknlkvvwPedGalvs..pifmlvkkgkkkelakafidfllspevqailak 211
                                        +++ g+  + v+ + ++  + + k++ + + ++P+  ++++  pi++lvk++ +ke a+afi + l + +q+i+ +
  gi|242398214|ref|YP_002993638.1| 264 EAVIGGD--IGVGNTIDFYGYIAMKSNPSCEYIIPKGQSIINgdPIAVLVKSQ-HKEAAQAFIYWVLTE-GQRIWLD 336
                                       7888888..66665555555555555589********9999966777888888.**********99997.6776665 PP

                         SBP_bac_6 212 agg.vfPvv..........tnpavlnelpeg 231
                                       ++   +Pv+            p++++ +++ 
  gi|242398214|ref|YP_002993638.1| 337 EQInRLPVNpdvfntpegqNRPDLKKAYESA 367
                                       55549**966666655555445555555555 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 !   49.2   0.8   3.1e-16   6.9e-13      14     314 ..      89     332 ..      72     333 .. 0.84
   2 ?   -2.8   0.1       2.1   4.7e+03     187     202 ..     438     454 ..     387     470 .. 0.51

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 3.1e-16
                                       HHHHHHHHHTTEEEEEEEECHHHHHHHHHHHHHTTSSSCSEEEE.CGGHHHHHHHTTSBECCHHHHHHTTECTTCCT CS
                         SBP_bac_1  14 vakafekehpgikVeiesvgsgslaqkltlaiaaGdgpaDviav.dndwiarlakaglllpldpyvkaylapgvkda 89 
                                       +     k+++  ++++++++ + +       i++G+   Dv ++ +++ ++ l ++++l p+ +  +  l+  + + 
  gi|242398214|ref|YP_002993638.1|  89 I----AKQYNIKDIRFIPIPESLWPS----YIEKGA---DVGWGgGPTLFDSLFRNNYLVPIEDQKVLGLIGNQIQE 154
                                       3....455677888888888888888....888888...99999888888888888999999999999877776665 PP

                                       EEEEHHHHTHHHHCE.EE.ES.EEEE.EEEEEEEETTTHHCTTGGGSHBHHHHHHHHHHHHHHCTCTHCCHCCEEHH CS
                         SBP_bac_1  90 adklsssvlpkilds.kv.ly.vPly.aargliYNkdlfekagldppwtWdelveaakklkekgkkpiggarggsas 162
                                       +        p i+ +  + +y +    ++ g+ +N+d+++ + l++p  W++l+        + +    g++  + s
  gi|242398214|ref|YP_002993638.1| 155 TIA----GMPMIRKGdDGkIYwIAAAlSSFGFTVNHDVLKRWNLPVPQRWEDLASETF--AMDPPQV--GIADPTRS 223
                                       555....55666665555********77*************************95544..4444444..56778888 PP

                                       HHHHHHHHHHHHHHTGGGEECCCTHHCSHHHHSHHHHHHHHHHHHHHHHHHHTTEEECSSHHHHHHHHHTTSCSEEE CS
                         SBP_bac_1 163 gtayyfalalakslggkvfdkdgggldnpegvtaatylvklyavanltkelkgkgaenkdgaaalalfeaGeaamai 239
                                       + +   ++ +++ +g                  +++ ++ l          + +++    ++a++ ++  G+++++ 
  gi|242398214|ref|YP_002993638.1| 224 TSNTRIYQIILQAFG------------------WDEGWKILT-------LIAANSKIYDASDAVREAVIGGDIGVGN 275
                                       889999999999999..................999999999.......9999************************ PP

                                       EEHHHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEEEEEEEEEEBTTCSTHHHHHHHHHHHTSHHHH CS
                         SBP_bac_1 240 vglwaalaamkvapkvafaadkekpkeelgvaplPagkggkpgilgayglaipkgsknpeaAkkFldfllspeaq 314
                                          ++ ++amk++p   ++++k +  +                  +++++a++ +s+++eaA++F+ ++l++++ 
  gi|242398214|ref|YP_002993638.1| 276 TIDFYGYIAMKSNPSCEYIIPKGQSII------------------NGDPIAVLVKSQHKEAAQAFIYWVLTEGQR 332
                                       *************************87..................**************************9985 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.1
                                       HHCSHHHHS.HHHHHHH CS
                         SBP_bac_1 187 gldnpegvt.aatylvk 202
                                         d+++ vt +++y++k
  gi|242398214|ref|YP_002993638.1| 438 DPDTGNTVTlTIEYAKK 454
                                       23334444444444444 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 ?   -1.9   0.0      0.98   2.2e+03     166     189 ..      86     109 ..      42     115 .. 0.66
   2 !   15.7   0.0   4.3e-06    0.0096      93     224 ..     197     334 ..     174     337 .. 0.79
   3 ?    2.4   0.0     0.048   1.1e+02      64     130 ..     392     470 ..     370     488 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.98
                                       HHHHH..HSTTSSEEEE--TTT-- CS
                        SBP_bac_11 166 eseakaaengdkleavylpeglnl 189
                                       +s+++ + n ++++++++pe+l+ 
  gi|242398214|ref|YP_002993638.1|  86 QSDIAKQYNIKDIRFIPIPESLWP 109
                                       333344568889999999999884 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 4.3e-06
                                       --SHHHHHHSS-.....-EEEE--T-TTTTHH.HHHHGGG....--HHHHHHHHHTEEEEESSHHHHHHHHHTTT-S CS
                        SBP_bac_11  93 ikgwadLlkpgl.....klavadPttspsGlaalalleaa....gaqellkalekkvvklgessrqlltaveagead 160
                                       ++ w+dL+ + +     ++++adPt+s+s +++++++ +a    ++ ++l+ ++ +     ++s+ + +av  g++ 
  gi|242398214|ref|YP_002993638.1| 197 PQRWEDLASETFamdppQVGIADPTRSTSNTRIYQIILQAfgwdEGWKILTLIAANSK-IYDASDAVREAVIGGDIG 272
                                       578*******99889899*************999999988666632558888888886.667788999999998888 PP

                                       EEEEEHHHHH...HSTTSSEEEE--TTT--...EEEEEEEE-TT--HHHHHHHHHTTSHHHHHHH CS
                        SBP_bac_11 161 agivyeseakaa.engdkleavylpeglnldpldypaavlkkaakreaAraFlafLrspeaqail 224
                                       +g +     + a +  +  e++ ++ +  +     p+avl k++++eaA+aF+ +++  e+q+i+
  gi|242398214|ref|YP_002993638.1| 273 VGNTIDFYGYIAmKSNPSCEYIIPKGQSII-N-GDPIAVLVKSQHKEAAQAFIYWVL-TEGQRIW 334
                                       887776666555467888888877666665.2.4499****************9999.5677765 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.048
                                       HHGGGGGGG-EEEEEEEEEEEESTT-TT---SHHHHHHSS--.EEEE--T-TTTTHH.HHHHGGG--.......... CS
                        SBP_bac_11  64 aaglvqaesavplassplviavpkgnpkkikgwadLlkpglk.lavadPttspsGlaalalleaaga.......... 129
                                       +a lv+a ++   a + lv a+++g+  + +  ++L+++ l+ + + dP t ++ + +++++++ ++          
  gi|242398214|ref|YP_002993638.1| 392 KATLVDANQELHRAWTALVKAYKEGK-ISESKYNELKAKLLEpVRFKDPDTGNTVTLTIEYAKKINDkledpafrdt 467
                                       55556644444457788888888888.788889999999995599***********999999988766666666534 PP

                                       ..H CS
                        SBP_bac_11 130 ..q 130
                                         q
  gi|242398214|ref|YP_002993638.1| 468 lmQ 470
                                       431 PP

>> DUF3644  Protein of unknown function (DUF3644)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.2   6.6e-06     0.015       5      66 ..     403     472 ..     402     476 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 6.6e-06
                           DUF3644   5 vnAWelLLkakllkkgiksiy...kkkr.......ykknrdGnpktisLeeclkkvdkekddpvrkNleaLi 66 
                                       ++AW+ L ka+ + k  +s y   k          +k+ + Gn  t+ +e++ k+ dk +d++ r++l  ++
  gi|242398214|ref|YP_002993638.1| 403 HRAWTALVKAYKEGKISESKYnelK--AkllepvrFKDPDTGNTVTLTIEYAKKINDKLEDPAFRDTLMQIW 472
                                       68***********996666665542..3468999999999************999999999******99987 PP

>> HeH  HeH/LEM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0     7e-05      0.16      12      30 ..      68      86 ..      66      87 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7e-05
                               HeH 12 iLvehgveyPsnaKKadLv 30
                                      +L+ h+v + + aKKa L+
  gi|242398214|ref|YP_002993638.1| 68 VLTRHDVTIQTIAKKAFLQ 86
                                      8****************98 PP

>> Orthopox_A5L  Orthopoxvirus A5L protein-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9  10.8    0.0004       0.9     144     202 ..      27      81 ..      19      99 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0004
                      Orthopox_A5L 144 ttttpstqpsqtlPtttcvrqsdas.istttdivtppqppivatvctptPvdgtvctvad 202
                                       +t+tpst  s+t Pttt ++ s  + +st++++      pi   v   t  d t+ t+a+
  gi|242398214|ref|YP_002993638.1|  27 STSTPSTTSSETEPTTTSTQSSTQTtSSTSSPTP---TGPITLVVL--TRHDVTIQTIAK 81 
                                       799****************988654044555544...445544444..455666777666 PP

>> SSP160  Special lobe-specific silk protein SSP160
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0  10.3    0.0026       5.7     283     327 ..      25      65 ..      10      91 .. 0.50

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0026
                            SSP160 283 anstssststststttststtttnsttstnstsssnsstiagsid 327
                                        +    stst ++t++ t  ttt + +st++tss+ s t +g i 
  gi|242398214|ref|YP_002993638.1|  25 GE----STSTPSTTSSETEPTTTSTQSSTQTTSSTSSPTPTGPIT 65 
                                       33....333333333333333333334444444444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (489 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       981  (0.0547158); expected 358.6 (0.02)
Passed bias filter:                      698  (0.0389313); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); 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: 0.75u 0.34s 00:00:01.09 Elapsed: 00:00:00.54
# Mc/sec: 2730.78
//
Query:       gi|242398215|ref|YP_002993639.1|  [L=380]
Description: amylopullulanase, GH57 family [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00027   20.5   0.0    0.00046   19.7   0.0    1.4  1  ABC_transp_aux  ABC-type uncharacterized transport system
  ------ inclusion threshold ------
      0.024   13.5   0.0      0.041   12.7   0.0    1.4  1  DDOST_48kD      Oligosaccharyltransferase 48 kDa subunit beta
       0.12   11.7   4.8       0.11   11.9   2.0    1.9  2  DUF5305         Family of unknown function (DUF5305)


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 !   19.7   0.0   7.7e-08   0.00046     188     229 ..      90     130 ..      25     156 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 7.7e-08
                    ABC_transp_aux 188 dilpedidvlviakptkdlseeelykldqflmnGgkllvfld 229
                                       d l +++d+l++ +pt++++++e++++ ++ ++Ggk+l+ + 
  gi|242398215|ref|YP_002993639.1|  90 DAL-ANVDMLILGQPTSPFQPDEIQAIVNWFNQGGKVLWIAG 130
                                       234.89*********************************875 PP

>> DDOST_48kD  Oligosaccharyltransferase 48 kDa subunit beta
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   6.9e-06     0.041      52     180 ..      98     232 ..      90     343 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.9e-06
                        DDOST_48kD  52 illapkvkelgksltpkallefvnkggniLvalsssk.......lpesirsllselgielsergskvvDhfnydses 121
                                       ++l + ++ ++++ + +a+++ +n+gg +L ++++s+       + + ++s+l++lg el  ++ ++ D +++    
  gi|242398215|ref|YP_002993639.1|  98 LILGQPTSPFQPD-EIQAIVNWFNQGGKVLWIAGDSDygssgvnAIDIVNSVLEQLGSELRLDQCQIQDPVSNAG-- 171
                                       5555556777777.889**************98877655544455577899999999999999999999999864.. PP

                        DDOST_48kD 122 daekhdvlllsspeellakvknifsekkkeeevlf..rgvgallgnnplllpiLra..pstsy 180
                                         + + v+ l +p++ +++++ i++  k +++vl+   gv a++++n    p++ +  p++ y
  gi|242398215|ref|YP_002993639.1| 172 --QPYRVIGLVQPDDETPDKEMITNGFKYGGKVLYhgPGVVAWVNENGEWQPLIDGnvPENVY 232
                                       ..5677899999999999999999999999*****7778889999999999999762245555 PP

>> DUF5305  Family of unknown function (DUF5305)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0     0.089   5.3e+02     116     138 ..       5      27 ..       1      48 [. 0.69
   2 ?   11.9   2.0   1.8e-05      0.11      82     133 ..     321     372 ..     317     379 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.089
                           DUF5305 116 gilliilgllaliglvvlirrii 138
                                        il+++++l++l+g++++  +++
  gi|242398215|ref|YP_002993639.1|   5 SILISVFVLFGLFGAAFASATTV 27 
                                       47778888888888887766655 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 1.8e-05
                           DUF5305  82 lteqtyeikkdetdeengeitetvtvkespslaegilliilgllaliglvvl 133
                                       ++++t++++ +et +++++ tetvt+++ ++++e + + i+g +aligl+++
  gi|242398215|ref|YP_002993639.1| 321 VSKETITVTVTETITKTETKTETVTETKTETTTETVQGGICGPAALIGLALI 372
                                       578999****************************999999999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       979  (0.0546043); expected 358.6 (0.02)
Passed bias filter:                      712  (0.0397122); 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: 0.67u 0.34s 00:00:01.01 Elapsed: 00:00:00.52
# Mc/sec: 2210.20
//
Query:       gi|242398216|ref|YP_002993640.1|  [L=375]
Description: Tyrosyl-tRNA synthetase [Thermococcus sibiricus MM 739]
Scores for complete 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-43  148.6   0.1    6.7e-43  147.1   0.1    1.6  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 !  147.1   0.1   3.7e-47   6.7e-43       5     293 .]      33     352 ..      30     352 .. 0.88

  Alignments for each domain:
  == domain 1  score: 147.1 bits;  conditional E-value: 3.7e-47
                                       --EEEEEEETSSS-BGG.GHHHHHHHHHHHHTTSEEEEEEEHHHHHTTTTT-SSHHHHHHHHHHHHHH.HHHHH.HH CS
                      tRNA-synt_1b   5 plrvysGidPTgklHlG.ylvplkklvelqkaghevffliaDlhAiigdpskaeerklrkreevlena.ikaql.ak 78 
                                       pl+ y G++ +g +HlG  l++  k++++qkag+++ +++aD+h  i+d+   +++ ++k +  + +  +k+ +   
  gi|242398216|ref|YP_002993640.1|  33 PLQHYIGFEISGYIHLGtGLMAGAKIADFQKAGIKTRVFLADWHSWINDKLGGDLEVIQKVALGYFKEgMKQSIkVM 109
                                       6788***********************************************99*******99999888866555156 PP

                                       TCHTTTEEEEETHHHHTTHHHHHHHHHHHTTCBHHHHHHHHHCCHHCSSSC--BHHHHHHHHHHHHHHHHTCHSEEE CS
                      tRNA-synt_1b  79 gldpekaevvlqsewlehlelaellrdlgklgslnrmlqfksvkkrleegegislgeftYplLqaaDilllkadlvp 155
                                       g dpek+e+vl se+le  +++  + d++k ++l+rm++  +++ r    e i ++ ++Yp +q aDi++  +++  
  gi|242398216|ref|YP_002993640.1| 110 GGDPEKVEFVLASEILERGDYWRTIIDISKNVTLARMMRSITIMGRQMG-EAIDFAKLIYPAMQVADIFYQGVNIAH 185
                                       7*****************************************7776665.59************************* PP

                                       EEGGGHHHHHHHHHHHHHHHHH.........STTSS-EEEEET.................-BBSTTSSSBTTCETTC CS
                      tRNA-synt_1b 156 gGsDQkqnielgrdlarrfnkk.........evfkkpegltvp.................lltgldGekKmSKSagn 206
                                        G+DQ++  +++r++a+++++          +    p ++ ++                   + ++ + KmSKS++ 
  gi|242398216|ref|YP_002993640.1| 186 AGMDQRKAHVIAREVAEKLKYHplvwdgkkvK----PIAVHHHlllglqeppkwpiegeeEFKEIKAQMKMSKSKPY 258
                                       **************************965553....444444444557777888888999788888888******** PP

                                       GC-BTTCCHHHHHHHHHHCHCSTTC..SHHHHHHHHHTHHH........CHHHHHHHHCCSEEESSHHHHHHHHHCC CS
                      tRNA-synt_1b 207 saIfLddekesvkkkiqkavtdsde..evekllklktelsn........elierleavsgkkpkreaeellaeevtk 273
                                       sa+f+ d +e++k+k +ka++  +e       + l    ++        ++i r  +++g  +++++eel+ +++++
  gi|242398216|ref|YP_002993640.1| 259 SAVFIHDTPEEIKQKLRKAFCPAGEvnY---NPVLDWAEHIifreepteFTIHRPAKFGGDVTYTTFEELKRDFAEG 332
                                       *********************9999532...3333333333445888899**********999************** PP

                                       CCHHHHHHHHHHHHHHHHHH CS
                      tRNA-synt_1b 274 lvhggdlkkalaealnelle 293
                                       ++h+ dlk+a+ae l ell+
  gi|242398216|ref|YP_002993640.1| 333 KLHPLDLKNAVAEYLVELLK 352
                                       **************999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); 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: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 2224.37
//
Query:       gi|242398217|ref|YP_002993641.1|  [L=213]
Description: Alanyl-tRNA synthetase-related protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-12   46.9   0.0      2e-12   46.4   0.0    1.1  1  tRNA-synt_2c  tRNA synthetases class II (A)
    6.6e-11   42.1   0.8    3.7e-10   39.7   0.3    2.2  2  tRNA_SAD      Threonyl and Alanyl tRNA synthetase second addi


Domain annotation for each model (and alignments):
>> tRNA-synt_2c  tRNA synthetases class II (A)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.4   0.0   2.2e-16     2e-12     473     552 .]      13      88 ..       6      88 .. 0.92

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 2.2e-16
                                       SEEEEEEEEEETTEEEESEEXXXXSSSSCSXXXEEEEESSEEEEESEEEEET.TEEEEEXSS.XSXXXTTSEEEEEE CS
                      tRNA-synt_2c 473 kefveeveegeevgvvLdrTpfYaesGGqigDeGliekegaefrvkdvqkak.gvvlhkgkleegklkvgdkvkaev 548
                                       ke +++v +++e++++L++T fY+++GGq  D+G+i++     +v dv k + + + h++++  + ++vgd+v++++
  gi|242398217|ref|YP_002993641.1|  13 KEATAKVLQIKENALLLNQTIFYPTGGGQPHDTGTINGV----KVLDVYKDEeENIWHVVENP-EMFRVGDEVELKL 84 
                                       678999******************************975....59999888879********8.9************ PP

                                       XHHH CS
                      tRNA-synt_2c 549 deer 552
                                       d++r
  gi|242398217|ref|YP_002993641.1|  85 DWDR 88 
                                       *986 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 ?   -0.1   0.0      0.11     1e+03      20      33 ..      43      61 ..      36      64 .. 0.74
   2 !   39.7   0.3   4.2e-14   3.7e-10       5      44 .]     170     209 ..     166     209 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.11
                                      SBGGGC-SEEEE.....CC CS
                          tRNA_SAD 20 pnTgeIgafkil.....se 33
                                      + Tg I+ +k+l     +e
  gi|242398217|ref|YP_002993641.1| 43 HDTGTINGVKVLdvykdEE 61
                                      679*******998885433 PP

  == domain 2  score: 39.7 bits;  conditional E-value: 4.2e-14
                                       EETT.EEEEESS---SBGGGC-SEEEECCECCCTCEEEEE CS
                          tRNA_SAD   5 siGdisvelCgGtHvpnTgeIgafkilseesiakglrRIy 44 
                                       +i d+ + +CgGtHv+ ++eIg+ k l+ +si+kg +RI+
  gi|242398217|ref|YP_002993641.1| 170 QIRDFEILPCGGTHVKDIKEIGHLKKLKRSSIGKGAQRIE 209
                                       567788889******************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1640.52
//
Query:       gi|242398218|ref|YP_002993642.1|  [L=60]
Description: hypothetical protein TSIB_0226 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.025   14.4   0.1      0.041   13.7   0.1    1.4  1  CoatB            Bacteriophage coat protein B
      0.069   13.1   1.0      0.097   12.6   1.0    1.2  1  Gram_pos_anchor  LPXTG cell wall anchor motif


Domain annotation for each model (and alignments):
>> CoatB  Bacteriophage coat protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   4.6e-06     0.041      18      44 ..      36      60 .]      32      60 .] 0.84

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.6e-06
                             CoatB 18 AkadiaaiGaaVLvvlVgvavfkWvRR 44
                                        + ia iG+a+  +l+g avf+  RR
  gi|242398218|ref|YP_002993642.1| 36 TNTQIAGIGGAI--ILIGLAVFMLKRR 60
                                      5799*******8..689*****98777 PP

>> Gram_pos_anchor  LPXTG cell wall anchor motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   1.0   1.1e-05     0.097      16      39 ..      37      60 .]      35      60 .] 0.90

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.1e-05
                                      XXXXXXXXXXXXXXXXXXXXXXXX CS
                   Gram_pos_anchor 16 gnifltaaGllallggllLlvkrR 39
                                      ++ +  ++G+++l+g +++ +krR
  gi|242398218|ref|YP_002993642.1| 37 NTQIAGIGGAIILIGLAVFMLKRR 60
                                      788899*************99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); 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: 0.52u 0.33s 00:00:00.85 Elapsed: 00:00:00.53
# Mc/sec: 339.14
//
Query:       gi|242398219|ref|YP_002993643.1|  [L=361]
Description: hypothetical protein TSIB_0227 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
       0.03   14.4   0.0      0.085   12.9   0.0    1.7  1  DUF3858       Domain of Unknown Function with PDB structure (
       0.16   11.9   0.1       0.35   10.8   0.1    1.5  1  Pro-MCH       Pro-melanin-concentrating hormone (Pro-MCH)
        2.7    8.3   6.5        2.9    8.2   1.5    2.5  2  PG_binding_4  Putative peptidoglycan binding domain


Domain annotation for each model (and alignments):
>> DUF3858  Domain of Unknown Function with PDB structure (DUF3858)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.4e-05     0.085      31      91 ..     154     214 ..     151     231 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.4e-05
                                       -SS-EEEEEEEEEEE-TT-EE-S--S-EEEEETTEEEEEEEEEETTEEEEEEEEEE--SEE CS
                           DUF3858  31 LpylvdetytytvkvpeglklvtkpvekkisnkvGsveitvkkegnkveivrslklkkqli 91 
                                       Lp +++    +++++peg +lv  p+  + + +  ++ ++ k egn+++i+  l l+++l 
  gi|242398219|ref|YP_002993643.1| 154 LPQKMELHNMFIIELPEGAELVDYPQAYTREFNQSKFYVRSKVEGNTITITSDLYLEENLS 214
                                       7889999999***********************************************9984 PP

>> Pro-MCH  Pro-melanin-concentrating hormone (Pro-MCH)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   5.9e-05      0.35      12      63 ..      27      80 ..      19      89 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 5.9e-05
                           Pro-MCH 12 shglplnlgikql..pylalkgslafpaenevqniesvqekreigdeensakfp 63
                                      +   +l++ i q     +++k s+  p +   q+i s+ ++ +++dee  akf 
  gi|242398219|ref|YP_002993643.1| 27 KEEFTLKIKILQNgdAQITVKTSILGPKDIINQEIASILNQTNLSDEEAIAKFE 80
                                      44444444444431156789********************************96 PP

>> PG_binding_4  Putative peptidoglycan binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   1.5   0.00048       2.9      33      84 ..      52     105 ..      23     112 .. 0.77
   2 ?    2.0   0.2     0.041   2.5e+02      15      95 ..     248     328 ..     241     331 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00048
                      PG_binding_4  33 rlsetiaawk..evdlrvsldeeklkeyldeiakeidtepkdasfklkggsvkv 84 
                                        ++++i++++   +++    dee++ ++ +e++++++ + ++a +k++++++k 
  gi|242398219|ref|YP_002993643.1|  52 GPKDIINQEIasILNQTNLSDEEAIAKFEKEQLDNYIASLANAGIKTENQTFKL 105
                                       44555666556445577788*****************************99985 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.041
                      PG_binding_4  15 eeyvaealtygrkgnelerlsetiaawk.evd.lrvsldeeklkeyldeiakeidtepkdasfklkggsvkvspeky 89 
                                       e+y+++ ++     n    ++et    k +++ ++++++   +++  + i++++ +  +   +++++ + ++ + ++
  gi|242398219|ref|YP_002993643.1| 248 EQYLKAEISEDGTTNL--LVRETYFEPKdQIElMKLQINLLGVQNVTNMILQNYLQGMVAQGIQVENANATILGLEK 322
                                       5666665554444333..35555555455777899999999999999999999999999999**********99999 PP

                      PG_binding_4  90 Gwkidk 95 
                                       G++i++
  gi|242398219|ref|YP_002993643.1| 323 GRTINN 328
                                       999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       675  (0.0376485); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2544.93
//
Query:       gi|242398220|ref|YP_002993644.1|  [L=428]
Description: Proton/glutamate symporter, SDF family [Thermococcus sibiricus MM 739]
Scores for 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-125  417.3  40.7   6.7e-125  417.1  40.7    1.0  1  SDF       Sodium:dicarboxylate symporter family


Domain annotation for each model (and alignments):
>> SDF  Sodium:dicarboxylate symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  417.1  40.7  3.8e-129  6.7e-125       3     389 ..      17     418 ..      15     419 .. 0.95

  Alignments for each domain:
  == domain 1  score: 417.1 bits;  conditional E-value: 3.8e-129
                               SDF   3 lqiliglvlGlviGll...elvkelaalisplgdlfinllkmlivPlvfasiisgiaslgdakklgklglktllyfl 76 
                                        +i+iglvlG+v Gl+      + +a+ i+plgdlf++llkml++P+v+as+++g as++ +++lg++g+k+++y+l
  gi|242398220|ref|YP_002993644.1|  17 RKIFIGLVLGAVYGLIvgaIGHPGAATAIKPLGDLFVRLLKMLVMPIVLASLVVGAASIS-PARLGRVGVKIVIYYL 92 
                                       589***********99996679*************************************6.**************** PP

                               SDF  77 lttliAaiiglilalllkpgselaleassakeaekketdslldlilslipsnifealaegnvlavivfailfGiala 153
                                       +t+++A++igli+a+l+kpg +l+l  + + +a +++++sl d++l+++p+n+f al++g vl+ i+fai++Gial+
  gi|242398220|ref|YP_002993644.1|  93 ITSAFAVFIGLIMANLFKPGLGLELG-TGEGKAIEATAPSLVDTLLNIVPTNPFGALSSGAVLPTIFFAIVLGIALS 168
                                       ********************555555.555555555899************************************** PP

                               SDF 154 algekg........epllkffeslnevvmkvvkivmklaPigvfaliaslvaskglgalsslakflltvylglaihl 222
                                        l +++         +l + f+ l+e++ k+v+ vm++aPigvfalia+++a++g++++++la ++l+vylgl+i++
  gi|242398220|ref|YP_002993644.1| 169 YLMTSEneriknsaTTLYNAFDGLAEAMYKIVRGVMQYAPIGVFALIAYIMATQGVKVVGPLAEVTLAVYLGLIIQI 245
                                       998887889999999999*********************************************************** PP

                               SDF 223 livlpllllvltkknplkflkkilpalltAfsTaSSaAtLPvtlecaeknlgvsesiasfvlPlGatinmdGtalye 299
                                        +v+ +ll+++ ++  +kfl k+ +a++tAf+T+SS++tLPvt++ ae+n+gv++si+sf+lPlGatinmdGtaly+
  gi|242398220|ref|YP_002993644.1| 246 ALVYGILLKFF-GLDLIKFLNKAKDAMITAFVTRSSSGTLPVTMRVAEENMGVPRSIYSFTLPLGATINMDGTALYQ 321
                                       *********55.57*************************************************************** PP

                               SDF 300 avaaifiaqlfgvelslgqllllvlvatlasiGaagvPgaglvalllvlsalglp.......vegialilaidrllD 369
                                       +v+a+fia ++g +l ++q+l++vl+a+lasiG+agvPgag ++l++vl+++gl        + ++a+il+id++lD
  gi|242398220|ref|YP_002993644.1| 322 GVCAMFIAFAIGQPLPFSQQLVIVLTAVLASIGTAGVPGAGAIMLAMVLESVGLSlepgtavALAYAMILGIDAILD 398
                                       *****************************************************9966666543449*********** PP

                               SDF 370 mfrTavNvtGdavaalivak 389
                                       m+rT+vNvtGd+v+++iv k
  gi|242398220|ref|YP_002993644.1| 399 MGRTMVNVTGDLVGTTIVTK 418
                                       ******************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       938  (0.0523175); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 2698.59
//
Query:       gi|242398221|ref|YP_002993645.1|  [L=248]
Description: Biotin-(Acetyl-coA carboxylase) ligase [Thermococcus sibiricus MM 739]
Scores for complete 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   70.3   0.0    1.9e-19   69.9   0.0    1.2  1  BPL_LplA_LipB    Biotin/lipoate A/B protein ligase family
    4.2e-12   45.8   0.1      1e-11   44.5   0.1    1.6  1  BPL_C            Biotin protein ligase C terminal domain
  ------ inclusion threshold ------
      0.016   14.8   0.0      0.019   14.5   0.0    1.3  1  BPL_LplA_LipB_2  Biotin/lipoate A/B protein ligase family


Domain annotation for each model (and alignments):
>> BPL_LplA_LipB  Biotin/lipoate A/B protein ligase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.9   0.0   3.1e-23   1.9e-19       2     131 .]      16     138 ..      15     138 .. 0.92

  Alignments for each domain:
  == domain 1  score: 69.9 bits;  conditional E-value: 3.1e-23
                                       EEEES-HHHHHH..GCGGG--TT-EEEEEEESS-B....-B--B-TTSEEEEEEEEESS...-CCGTHHHHHHHHHH CS
                     BPL_LplA_LipB   2 gevikstntllkeslnsselesgglvvvrrqtgGr....nvwhspkgeltyslllspeqktfqnrvlelyvsllvla 74 
                                       ++ i+stn+++k  +  +  e g++ v++ q  G     + w sp+g+l++s++l+p     ++  +  +v l +la
  gi|242398221|ref|YP_002993645.1|  16 FKKIDSTNEYAK--RIAAHEEEGTVIVADVQETGYgrkfRAWASPQGGLWMSVILKPNT---TPEHMIKLVFLGALA 87 
                                       677999999999..5666679999**********999*******************664...87888888******* PP

                                       HHHHH......HHTT-TTEEEETTTEEEETTEEEEEEEEEEEE.TTS-EEEEEEEEEE CS
                     BPL_LplA_LipB  75 vlealgyrdskpgiegipvfikwpnDlyvngrKlaGiavtstr.gktlhhivigvgvn 131
                                       v+e+l       ++ gi  +ikwpnD++vn +K+ Gi+v+    +k++++iv+g+g+n
  gi|242398221|ref|YP_002993645.1|  88 VVETL-------EQLGIEGKIKWPNDVLVNEKKICGILVEGSFsEKEVYYIVLGIGMN 138
                                       *****.......*****************************99999**********99 PP

>> BPL_C  Biotin protein ligase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.5   0.1   1.7e-15     1e-11       5      48 .]     203     246 ..     202     246 .. 0.97

  Alignments for each domain:
  == domain 1  score: 44.5 bits;  conditional E-value: 1.7e-15
                                       EEEEEETSCEEEEEEEEE-TTSEEEEEETTE.EEEESSCCEEEE CS
                             BPL_C   5 eVtlededgkveGiavGIdddGaLllktddglqpdinsGdislr 48 
                                        V+l++ed++++G+a +Id++GaL+l+++dg+ ++i  Gd+slr
  gi|242398221|ref|YP_002993645.1| 203 KVKLITEDKTLTGKALDIDEFGALILELEDGKKEKILYGDVSLR 246
                                       69****************************************97 PP

>> BPL_LplA_LipB_2  Biotin/lipoate A/B protein ligase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   3.3e-06     0.019      36     127 ..      56     142 ..      21     196 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.3e-06
                   BPL_LplA_LipB_2  36 slaadlleaAlvlaPevplakAaamlpvlmvalqdAlgalaPPevavhlewpgtilvngarvGgvrlaaseadeeev 112
                                       +  +  l ++++l+P+++ ++  ++++++++a+ + l+ l+      +++wp+++lvn+ ++ g+ ++ s ++  ++
  gi|242398221|ref|YP_002993645.1|  56 ASPQGGLWMSVILKPNTTPEHMIKLVFLGALAVVETLEQLGI---EGKIKWPNDVLVNEKKICGILVEGSFSE--KE 127
                                       5556667899******************************95...77899********998887777666543..34 PP

                   BPL_LplA_LipB_2 113 Pdwlvvglelaleke 127
                                         ++v+g+ ++++++
  gi|242398221|ref|YP_002993645.1| 128 VYYIVLGIGMNVNNS 142
                                       467777777776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1670.49
//
Query:       gi|242398222|ref|YP_002993646.1|  [L=282]
Description: fructose-1,6-bisphosphate aldolase (FBA) [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-34  118.7   0.0    3.4e-34  118.5   0.0    1.0  1  DeoC      DeoC/LacD family aldolase


Domain annotation for each model (and alignments):
>> DeoC  DeoC/LacD family aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.5   0.0   1.9e-38   3.4e-34       2     235 .]      24     252 ..      23     252 .. 0.94

  Alignments for each domain:
  == domain 1  score: 118.5 bits;  conditional E-value: 1.9e-38
                                       EEEEECCSHHHHHHHHCTSSHHHHHHHHHHHHHHGGGSSEEEEETTTHHHHHHCS.CTTSEEEEETECSSCCTTSTT CS
                              DeoC   2 vilavDqrvankddtasaqneqledlkalvkealtpgasavlldpgviasaskey.akdiallvkldkgtyllkskq 77 
                                       +i+a+D++ ++++ +++ ++   +++ +++++++++g++ v++ pg++++a  e+ +k+++l vkl ++t l ++++
  gi|242398222|ref|YP_002993646.1|  24 LIFAMDHGFEHGPTDFE-ETWEHINPSVIIRKVARAGIDGVMMLPGIARIAGNELiGKEVGLMVKLTSKTELRPKEE 99 
                                       699**********9998.788999**************************99887477******************9 PP

                                       EEEE.TTCHHHHHHHTT-SEEEEEEEEHTTTTCHHHHHHHHHHHHHHHHHHHTEEEEEEEEE-CTTBSSTT...CHH CS
                              DeoC  78 rdvd.evasveeakalGAdavkvvvyyradgseeeqqklaeikrvkeacheeglplilelylrdeaikdek...vdp 150
                                        ++  ++  ve a++lGAdav ++vy+   gs +e  ++++++++++ +h++g p++  +y+r++ i++++    d 
  gi|242398222|ref|YP_002993646.1| 100 WLMQdQLGFVEDAIKLGADAVAATVYW---GSPYEGAMMRQFAEIASYAHDLGYPVVQFAYPRGPYINEKYgkkEDY 173
                                       888889999******************...*************************************9999999999 PP

                                       HHHHHHHHHHTCCT-SEEEE--SSCC.B.HHHHHHHHHHHHHC.HSSTEEEEETTS...SHHHHHHHHHHHHHHHTH CS
                              DeoC 151 dlvaeAarvsaelGaDiiKvevpkevvnateedaevfkdvika.apvpgvvlsGGv...seedfletvedAvkeaga 223
                                       ++v  +ar++ae+GaD iK+  +        ++ e+f +vi+a + vp v+lsGG+   +  dfl+ v + + eag+
  gi|242398222|ref|YP_002993646.1| 174 RVVMYGARAAAEIGADMIKTYWT--------GSRETFAKVIDAaSGVP-VLLSGGAktdNPLDFLKLVWEVI-EAGG 240
                                       9**********************........88889988886515799.*******9877789*********.**** PP

                                       CEEEESHHHHTT CS
                              DeoC 224 sGvlsGRaifqk 235
                                       sG+++GR+ifq+
  gi|242398222|ref|YP_002993646.1| 241 SGAVVGRNIFQR 252
                                       **********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 2120.71
//
Query:       gi|242398223|ref|YP_002993647.1|  [L=590]
Description: Oxaloacetate decarboxylase, alpha subunit [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-58  198.3   1.0    2.6e-58  197.0   0.1    2.0  3  PYC_OADA         Conserved carboxylase domain
    9.9e-43  146.6   0.0    1.3e-42  146.2   0.0    1.1  1  HMGL-like        HMGL-like
    4.1e-24   84.2   2.4    4.1e-24   84.2   2.4    1.9  2  Biotin_lipoyl    Biotin-requiring enzyme
    3.6e-14   52.3   1.5    4.1e-06   26.5   0.0    2.6  2  Biotin_lipoyl_2  Biotin-lipoyl like
    5.2e-05   23.9   0.3       0.21   12.3   0.0    2.6  2  HlyD_3           HlyD family secretion protein
    0.00046   19.5   0.2       0.22   10.7   0.0    2.4  2  HlyD_D23         Barrel-sandwich domain of CusB or HlyD membr
     0.0053   16.7   0.6       0.33   10.9   0.1    2.8  2  RnfC_N           RnfC Barrel sandwich hybrid domain
  ------ inclusion threshold ------
      0.011   15.5   0.5        1.9    8.2   0.0    2.8  3  PTS_EIIA_1       phosphoenolpyruvate-dependent sugar phosphot
      0.038   13.4   0.9       0.41   10.0   0.3    2.1  2  NQRA             Na(+)-translocating NADH-quinone reductase s
      0.062   13.6   0.1        1.5    9.1   0.0    2.4  2  zf-C4H2          Zinc finger-containing protein
      0.065   12.7   0.2        4.2    6.8   0.2    2.4  1  ComA             (2R)-phospho-3-sulfolactate synthase (ComA)


Domain annotation for each model (and alignments):
>> PYC_OADA  Conserved carboxylase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1      0.91   1.5e+03     142     163 ..      83     116 ..      62     205 .. 0.58
   2 ?   -2.0   0.0       1.5   2.5e+03     118     149 ..     174     205 ..     110     235 .. 0.62
   3 !  197.0   0.1   1.6e-61   2.6e-58       1     193 [.     290     475 ..     290     479 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.91
                                       HHHHHHHHSHH.HHHHHHHHHH...........H CS
                          PYC_OADA 142 edvlsyalypk.vaekflkfre...........e 163
                                       ++v+ y  yp+ v+ekf++  +           +
  gi|242398223|ref|YP_002993647.1|  83 QNVVGYKHYPDdVVEKFVELAHkngidifrvfdA 116
                                       5555555555413344444333233333332222 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.5
                                       GGGG---.-HHHHHHHTTTTSSSHHHHHHHHH CS
                          PYC_OADA 118 padslepedleklrkeleekakteedvlsyal 149
                                        a++l+p+   +l ke++++++ + +v ++a 
  gi|242398223|ref|YP_002993647.1| 174 MAALLDPQTAYELVKEIKNRYGVKVNVHTHAT 205
                                       33445555555555555555555555555554 PP

  == domain 3  score: 197.0 bits;  conditional E-value: 1.6e-61
                                       HHCCT--CCHHHHHHHHHHHTT-GGGHHHHHHHHHHHHHHTT----STTHHHHHHHHHHHHHHH........TS.TT CS
                          PYC_OADA   1 VykheiPGGqltnlkeqakeqglldkfeevlkeyaevnkllGdivkVTPsSkvvgdlAvfnvlnklteedvleegry 77 
                                       V+ h+iPGG+++nl +q+ e+ +ldk++evl+e+++v+++lG++++VTP+S++vg++Avfnvl+          gry
  gi|242398223|ref|YP_002993647.1| 290 VLIHQIPGGMYSNLIKQLSELKALDKLDEVLEEVPKVREDLGYPPLVTPTSQIVGTQAVFNVLF----------GRY 356
                                       899*************************************************************..........79* PP

                                       SS--HHHHHHHTTSS---SS---HHHHHHHHT.-----S-GGGG---.-HHHHHHHTTTTS..SSHHHHHHHHHSHH CS
                          PYC_OADA  78 kdipdsvvdllkGelGkppggfpeelvkkvlkgeepitsrpadslepedleklrkeleeka..kteedvlsyalypk 152
                                       k i++++++++kG +G+pp++++ee+ k +l +ee i++rpad+lep  lek+rkeleek   + eedv++y+l+p+
  gi|242398223|ref|YP_002993647.1| 357 KMITEETKNYVKGLYGRPPAPIKEEIKKLILGDEESISVRPADLLEP-MLEKARKELEEKGylEREEDVVTYCLFPQ 432
                                       ***********************************************.89*********9955699*********** PP

                                       HHHHHHHHHH..HHHHHH..CTTTS......-SEEEEEETTEE CS
                          PYC_OADA 153 vaekflkfre..eygdvsvlptkvffeglkvgeeveveveggk 193
                                       va +f++ r+  +   v+  p+ ++++    g+e+ev veg k
  gi|242398223|ref|YP_002993647.1| 433 VALEFFELRKqgKLRPVEEKPKGKVIKVYVGGREYEVGVEGVK 475
                                       *******888556667777888888888888999999999876 PP

>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.2   0.0   7.7e-46   1.3e-42       2     263 ..       2     266 ..       1     267 [. 0.95

  Alignments for each domain:
  == domain 1  score: 146.2 bits;  conditional E-value: 7.7e-46
                                       -EEEE-TTTHHHHTS.SS---HHHHHHHHHHHHHHT-SEE--........TSGGGT.THHHHHHHS---TT-B.... CS
                         HMGL-like   2 vkivdttLRDGeqal.kaalsveeklaiakaLdeagvdeiEv........gfpaaseddfevvraiakavkkar... 66 
                                       v+i+dttLRD++q+l +++ls++++l+ia+++de+g+ ++Ev          +++ ed++e++r + +++ k++   
  gi|242398223|ref|YP_002993647.1|   2 VRIIDTTLRDAHQSLiATRLSTSDMLPIAEKMDEIGFYSMEVwggatfdaALRFLREDPWERLRVLREHIRKTKfqm 78 
                                       79************9999******************************9999*********************6667 PP

                                       .......--EE-SSHHHHHHHHH....TT-SEEEEEEES-HHHHHHHHSSTHHHHHHHHHHHHHHHHHTT-E..TTT CS
                         HMGL-like  67 ......ilalvrarekdikaavealkgagakrvhvfiatselhlkaklkkdreevakkaeeavkaarslgkd..vel 135
                                             ++++ ++ +++++++ve ++++g ++++vf+a ++              ++++e+a+k a++ g++   ++
  gi|242398223|ref|YP_002993647.1|  79 llrgqnVVGYKHYPDDVVEKFVELAHKNGIDIFRVFDALND--------------VRNMEKAIKKAKEVGAEvqGAI 141
                                       777788***********************************..............9****************55567 PP

                                       -BTTTBS--HHHHHHHHHHHHHHT-SEEEEEETTS---HHHHHHHHHHHHHHS-.GGGEEEEEB-TTS-HHHHHHHH CS
                         HMGL-like 136 sledasrtdleflaevveaaeeaGatriniaDtvGvltPneaaelisalkervkdkvilsvHcHndlGlAvantlaA 212
                                       s+++ +  +le+ ++ v++++e+ +++i i+D+  +l+P+ a+el++++k+r+   v+++vH+H++ GlA a  l+A
  gi|242398223|ref|YP_002993647.1| 142 SYTTGKIFTLEYYLQKVDELIELDVDYITIKDMAALLDPQTAYELVKEIKNRYG--VKVNVHTHATSGLASATYLKA 216
                                       88888999**********************************************..********************* PP

                                       HHTT--EEEEBTTS--SSBBB-BHHHHHHHHHHTT-B----HHHHHHHHHH CS
                         HMGL-like 213 veaGadrvdgtvnGlGeraGnaaleelvaalealgvdtgldlqklrsiaal 263
                                       veaGad +d+++  l  ++  +a+  + + l+    ++++d++ + +i+++
  gi|242398223|ref|YP_002993647.1| 217 VEAGADYIDTAIYPLANGTAQPAIQSIYYSLREED-KPKIDMKLIFEISRY 266
                                       **************************999998765.788888888888765 PP

>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   0.2       9.1   1.5e+04      49      62 ..     453     465 ..     449     470 .. 0.67
   2 !   84.2   2.4   2.5e-27   4.1e-24       2      73 .]     523     589 ..     522     589 .. 0.97

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 9.1
                                       SSEEEEEESSTTTE CS
                     Biotin_lipoyl  49 kaGvvkeilvkeGd 62 
                                        +G+v +++v  G 
  gi|242398223|ref|YP_002993647.1| 453 PKGKVIKVYVG-GR 465
                                       57888888886.55 PP

  == domain 2  score: 84.2 bits;  conditional E-value: 2.5e-27
                                       EEEESSSEEEEEE.ECSESSSTTCEE-TTSEEEEEECTTEEEEEEBSSSEEEEEESSTTTEEE-TTCEEEEE CS
                     Biotin_lipoyl   2 eiksPmiGesveegvvevlvkvGdkVkagqvlaeveamKmemeieapkaGvvkeilvkeGdtvevgdllaki 73 
                                        +++Pm+G++ +     vlv +Gd+Vk gq l+++eamKme+ei++pk+Gvvk+ilvkeGdtv++g+ l+++
  gi|242398223|ref|YP_002993647.1| 523 VVTAPMPGKILR-----VLVREGDQVKVGQGLLVLEAMKMENEIPSPKDGVVKKILVKEGDTVDTGQTLIEL 589
                                       699*********.....****************************************************986 PP

>> Biotin_lipoyl_2  Biotin-lipoyl like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0   2.5e-09   4.1e-06       5      41 ..     524     560 ..     523     563 .. 0.91
   2 !   24.9   0.3     8e-09   1.3e-05       5      33 ..     561     589 ..     559     590 .] 0.93

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 2.5e-09
                   Biotin_lipoyl_2   5 IaapvsGrVaqlnVkdGqrVkaGdvLaelDsralqla 41 
                                       ++ap +G++ +++V++G++Vk G+ L++l+  + +++
  gi|242398223|ref|YP_002993647.1| 524 VTAPMPGKILRVLVREGDQVKVGQGLLVLEAMKMENE 560
                                       789**************************98887776 PP

  == domain 2  score: 24.9 bits;  conditional E-value: 8e-09
                   Biotin_lipoyl_2   5 IaapvsGrVaqlnVkdGqrVkaGdvLael 33 
                                       I +p +G+V++++Vk+G+ V +G++L+el
  gi|242398223|ref|YP_002993647.1| 561 IPSPKDGVVKKILVKEGDTVDTGQTLIEL 589
                                       66899**********************98 PP

>> HlyD_3  HlyD family secretion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0    0.0013         2       1      30 [.     523     552 ..     523     558 .. 0.91
   2 !   12.3   0.0   0.00013      0.21       2      30 ..     561     589 ..     560     590 .] 0.92

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0013
                            HlyD_3   1 tlrApvdGvvvelnveegevvqagdellei 30 
                                       +++Ap  G++  + v+eg+ v  g+ ll +
  gi|242398223|ref|YP_002993647.1| 523 VVTAPMPGKILRVLVREGDQVKVGQGLLVL 552
                                       699**********************99876 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00013
                            HlyD_3   2 lrApvdGvvvelnveegevvqagdellei 30 
                                       + +p dGvv+++ v+eg+ v  g++l e+
  gi|242398223|ref|YP_002993647.1| 561 IPSPKDGVVKKILVKEGDTVDTGQTLIEL 589
                                       569***********************987 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 !    6.9   0.0     0.002       3.3      21      55 ..     523     556 ..     518     560 .. 0.77
   2 !   10.7   0.0   0.00013      0.22     110     139 ..     560     589 ..     554     590 .] 0.85

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.002
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          HlyD_D23  21 rvsarveGwveklyvnatgdkVkkGqpLaelyspe 55 
                                       +v+a + G + ++ v+ +gd+Vk Gq L+ l++ +
  gi|242398223|ref|YP_002993647.1| 523 VVTAPMPGKILRVLVR-EGDQVKVGQGLLVLEAMK 556
                                       5778888888888888.888888888888877655 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00013
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          HlyD_D23 110 tvkapisGvVteknvreGqyvqpgdtlfti 139
                                       ++ +p +GvV +  v eG++v++g+tl+++
  gi|242398223|ref|YP_002993647.1| 560 EIPSPKDGVVKKILVKEGDTVDTGQTLIEL 589
                                       678999999999999999999999999875 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 !   10.9   0.1   0.00021      0.33      39      80 ..     530     572 ..     518     573 .. 0.85
   2 !    6.0   0.2    0.0071        12      40      58 ..     568     586 ..     565     590 .] 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00021
                            RnfC_N  39 GapakplvkvgdkVlkGqkiaeaeg.fvsapvhasvsGtVkai 80 
                                       G+  ++lv +gd+V+ Gq +   e+  +  ++ ++  G Vk+i
  gi|242398223|ref|YP_002993647.1| 530 GKILRVLVREGDQVKVGQGLLVLEAmKMENEIPSPKDGVVKKI 572
                                       666789************8877766456999**********98 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0071
                            RnfC_N  40 apakplvkvgdkVlkGqki 58 
                                          k+lvk+gd+V +Gq +
  gi|242398223|ref|YP_002993647.1| 568 VVKKILVKEGDTVDTGQTL 586
                                       56789************87 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 ?   -3.4   0.0       4.6   7.5e+03      95     110 ..     156     171 ..     149     175 .. 0.81
   2 ?    8.2   0.0    0.0012       1.9      76     111 ..     525     560 ..     522     569 .. 0.85
   3 ?    4.9   0.0     0.013        21      85     103 ..     571     589 ..     563     590 .] 0.87

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 4.6
                                       -SEEEEEEE-HHHHGG CS
                        PTS_EIIA_1  95 kagdklvevdleaikk 110
                                       ++ d+l+e+d+++i+ 
  gi|242398223|ref|YP_002993647.1| 156 QKVDELIELDVDYITI 171
                                       677999****999975 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0012
                                       TTTTTTTTEEES----SEE-SEEEEEEE-HHHHGGG CS
                        PTS_EIIA_1  76 tvklkgegFellvkegdkVkagdklvevdleaikka 111
                                       t  + g+  ++lv+egd+Vk g+ l+ ++  +++++
  gi|242398223|ref|YP_002993647.1| 525 TAPMPGKILRVLVREGDQVKVGQGLLVLEAMKMENE 560
                                       566889999****************99998888876 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.013
                                       EES----SEE-SEEEEEEE CS
                        PTS_EIIA_1  85 ellvkegdkVkagdklvev 103
                                       ++lvkegd+V +g++l+e+
  gi|242398223|ref|YP_002993647.1| 571 KILVKEGDTVDTGQTLIEL 589
                                       789*************985 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 ?   10.0   0.3   0.00025      0.41      36      79 ..     528     572 ..     512     574 .. 0.80
   2 ?    4.9   0.1    0.0096        16      38      59 ..     567     588 ..     566     589 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00025
                              NQRA  36 yvglkpklkvkegdkVkkGqvlfe.dKknpgvlftspasGevvei 79 
                                         g  ++++v+egd+Vk Gq l+  +  + +  + sp +G+v++i
  gi|242398223|ref|YP_002993647.1| 528 MPGKILRVLVREGDQVKVGQGLLVlEAMKMENEIPSPKDGVVKKI 572
                                       55666889************876515556688899*******998 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0096
                              NQRA  38 glkpklkvkegdkVkkGqvlfe 59 
                                       g+  k++vkegd+V +Gq+l+e
  gi|242398223|ref|YP_002993647.1| 567 GVVKKILVKEGDTVDTGQTLIE 588
                                       567799*************986 PP

>> zf-C4H2  Zinc finger-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.14   2.2e+02      59      94 ..     118     153 ..     107     206 .. 0.81
   2 ?    9.1   0.0   0.00089       1.5      29     110 ..     256     337 ..     246     530 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.14
                           zf-C4H2  59 aDinalEsvikeaeeekekslekakklyeeykklke 94 
                                       +D+ ++E+ ik+a+e   +   +++ ++ ++  l +
  gi|242398223|ref|YP_002993647.1| 118 NDVRNMEKAIKKAKEVGAEVQGAISYTTGKIFTLEY 153
                                       6999*********99887777777766666666554 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00089
                           zf-C4H2  29 eekcleeykkelelLeqEkmaHveeLrlIhaDinalEsvike.aeeekekslekakklyeeykklkeevnelrselg 104
                                         k + e+++ l +L  Ek +H+ + r +h D n l + i     ++  k+l++ k +++++++++eev ++r++lg
  gi|242398223|ref|YP_002993647.1| 256 DMKLIFEISRYLRKLLDEKYEHLLNKRALHGDPNVLIHQIPGgMYSNLIKQLSELK-ALDKLDEVLEEVPKVREDLG 331
                                       568899999*************************9988887615566777777765.66899*************** PP

                           zf-C4H2 105 lekled 110
                                         +l +
  gi|242398223|ref|YP_002993647.1| 332 YPPLVT 337
                                       998866 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 ?    6.8   0.2    0.0026       4.2      51      97 ..      93     136 ..      86     228 .. 0.55

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0026
                                       CHHHHHHHHHHHCTT-EEEE-HHHHHHHHHTT-HHHHHHHHHHCT-S CS
                              ComA  51 eeilrekielahehgvyvstGgtlfEaalaqgkvdeyleeckelgfd 97 
                                       ++++++++elah++g++++    +f+a+    ++++ ++++ke+g +
  gi|242398223|ref|YP_002993647.1|  93 DDVVEKFVELAHKNGIDIFR---VFDALNDVRNMEKAIKKAKEVGAE 136
                                       55555555555555555552...444444444444444444444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (590 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       792  (0.0441742); expected 358.6 (0.02)
Passed bias filter:                      654  (0.0364772); 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: 0.78u 0.31s 00:00:01.09 Elapsed: 00:00:00.51
# Mc/sec: 3498.19
//
Query:       gi|242398224|ref|YP_002993648.1|  [L=577]
Description: Carbon starvation protein A [Thermococcus sibiricus MM 739]
Scores for complete 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-109  365.6  29.2   2.5e-109  365.6  29.2    2.1  2  CstA      Carbon starvation protein CstA
    1.4e-29  102.8  13.5    1.4e-29  102.8  13.5    3.1  4  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 !  365.6  29.2  2.8e-113  2.5e-109       1     350 [.       1     359 [.       1     375 [. 0.93
   2 ?   -3.1   6.3      0.31   2.8e+03     160     233 ..     453     523 ..     397     558 .. 0.54

  Alignments for each domain:
  == domain 1  score: 365.6 bits;  conditional E-value: 2.8e-113
                              CstA   1 mnavllvvvavvvfviayrfYgkfiakkvlklddkraTPaerledgkdyvptnklvlfghhFasiagagPlvGpvlA 77 
                                       mn+++++++a++++v  y +Ygk +++kv+k+d++r+TPa++l dg+dyvp++ +vl+ghhFasiagagP++Gp++A
  gi|242398224|ref|YP_002993648.1|   1 MNSAVIILAAAIIYVAMYFTYGKALQNKVVKADPNRPTPAHKLYDGVDYVPAHPVVLYGHHFASIAGAGPITGPAIA 77 
                                       8**************************************************************************** PP

                              CstA  78 aqfGylPgllWilvGavfagavhDfvvlvasvrrkgkslgelakkelgkvakllallaillililvlavlalvvvka 154
                                       + +G+lP+llW+ +G+vf+gavhD+++l+asvr +gks+  +a k ++k++++++ + i+++l+lv+a+++ vv++ 
  gi|242398224|ref|YP_002993648.1|  78 MAWGWLPSLLWVWFGNVFIGAVHDYLALMASVRYDGKSIQWIAGKIMSKRTGVAFEVYIWFTLLLVVAAFVAVVARL 154
                                       ***************************************************************************** PP

                              CstA 155 laespaavfsviltipialllGvllrklrkgvleasvigvvllllavvvgse.....veealaell......tlske 220
                                       ++ +p a+++++l++++a++lG+l++k++ + + a++ig++ll++av++g +     v    ++++        + +
  gi|242398224|ref|YP_002993648.1| 155 VVLTPEAATATLLFLLVAIILGWLMYKMNVNFYVATIIGLILLVVAVWIGFKnplifV---QGQTVdgspeyLQAYH 228
                                       **************************************************86332212...2222244444245567 PP

                              CstA 221 tlaivlivYvfvAsvlPvwlllaPrdYlstflligtivllalgilvvapelklpavtef.vdgegpvfagslfPllf 296
                                        + i+l++Y++vA+ lPvw+ll+PrdYl++++l  ++++  ++ +  a  +++p +t+f ++       ++++P++ 
  gi|242398224|ref|YP_002993648.1| 229 YWNIILMIYIIVAASLPVWILLQPRDYLNAYILWFGLLIGGIAFIALAKPFEAPGFTTFsANVVVVGQPSPFWPTVP 305
                                       8*******************************************999999*********555544445689****** PP

                              CstA 297 itiACGaiSGFHslvssgttskllekesdarlvgygamllEslvailalvaaav 350
                                       ++iACGa+SGFHslvssgt+sk+l+ke +  lvgyg+m++E++++ +++ a+av
  gi|242398224|ref|YP_002993648.1| 306 LVIACGALSGFHSLVSSGTSSKQLDKEIHGLLVGYGGMFTEGFLSTIVITAIAV 359
                                       *********************************************999988775 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.31
                              CstA 160 aavfsviltipialllGvllrklrkg.vleasvigvvllllavvvgseveea..laelltlsketlaivlivYvfvA 233
                                       + + ++i+++   ++ G   + l +  + ++++++ + +l a + + ++++a  ++ ++ +       +l++++ v 
  gi|242398224|ref|YP_002993648.1| 453 WVASIIIAVLGTWMAWGASYKVLWPAfAGMNQLLASIAMLTAALWAYKIQKAgiWSYAVLI------PALFLWITVT 523
                                       3333333334444444444444444444444444444444444444444222222222221......1111111111 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 ?   -4.4   0.9         2   1.8e+04      62      74 ..      79      92 ..      68      94 .. 0.64
   2 ?    1.2   2.2     0.053   4.7e+02       4      64 ..     144     204 ..     138     250 .. 0.76
   3 ?   -4.1   0.0         2   1.8e+04      48      59 ..     349     360 ..     341     373 .. 0.59
   4 !  102.8  13.5   1.6e-33   1.4e-29       3     114 ..     403     523 ..     401     524 .. 0.89

  Alignments for each domain:
  == domain 1  score: -4.4 bits;  conditional E-value: 2
                          CstA_5TM 62 lwg.gintlWplFG 74
                                      +wg   + lW  FG
  gi|242398224|ref|YP_002993648.1| 79 AWGwLPSLLWVWFG 92
                                      45523478999998 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.053
                          CstA_5TM   4 aytfailfvalfalTtlDtatRlaRyilqellgelkkkaltnkyvatliavalavllllwg 64 
                                       +++f++++  l +lT   +++ l  +++  +lg+l +k   n yvat+i ++l v+++ +g
  gi|242398224|ref|YP_002993648.1| 144 VAAFVAVVARLVVLTPEAATATLLFLLVAIILGWLMYKMNVNFYVATIIGLILLVVAVWIG 204
                                       5677777777777777766666777777777788777776788899999888888874443 PP

  == domain 3  score: -4.1 bits;  conditional E-value: 2
                          CstA_5TM  48 vatliavalavl 59 
                                       ++t++++a+av+
  gi|242398224|ref|YP_002993648.1| 349 LSTIVITAIAVY 360
                                       444554444444 PP

  == domain 4  score: 102.8 bits;  conditional E-value: 1.6e-33
                          CstA_5TM   3 vaytfailfvalfalTtlDtatRlaRyilqellgelk......kkaltnkyvatliavalavllllwg.gintlWpl 72 
                                       +++tfa+l+v++falT+lDtatRl+R+++qe++g++        k+ltnk+va++i+++l++ + +wg ++++lWp+
  gi|242398224|ref|YP_002993648.1| 403 LGKTFATLWVSAFALTSLDTATRLGRFAWQEVFGMVVdtsqgiWKSLTNKWVASIIIAVLGTWM-AWGaSYKVLWPA 478
                                       789*******************************999766666556******************.5665******** PP

                          CstA_5TM  73 FGaaNQlLAalaLlvvtvwllktgr...kalvtliPmvfmlvvtl 114
                                       F+  NQlLA++a+l++++w +k ++   + +++liP++f++++++
  gi|242398224|ref|YP_002993648.1| 479 FAGMNQLLASIAMLTAALWAYKIQKagiWSYAVLIPALFLWITVT 523
                                       *********************7777666667778*******9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (577 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1117  (0.0623013); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.74u 0.34s 00:00:01.08 Elapsed: 00:00:00.51
# Mc/sec: 3399.27
//
Query:       gi|242398225|ref|YP_002993649.1|  [L=95]
Description: hypothetical protein TSIB_0233 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.17   12.0   0.0       0.19   11.8   0.0    1.1  1  RhoGEF67_u2  Unstructured region two on RhoGEF 6 and 7


Domain annotation for each model (and alignments):
>> RhoGEF67_u2  Unstructured region two on RhoGEF 6 and 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   1.1e-05      0.19      27      58 ..      57      89 ..      39      94 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.1e-05
                       RhoGEF67_u2 27 papplrpsaa.lgykermsyilkdsskspktvk 58
                                      p pp+  s+  l y  r  yi++++s  p t+k
  gi|242398225|ref|YP_002993649.1| 57 PNPPVDISYRlLPYMLREMYIMQEKSLNPLTMK 89
                                      99****9997268*******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       239  (0.0133304); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 650.71
//
Query:       gi|242398226|ref|YP_002993650.1|  [L=89]
Description: hypothetical protein TSIB_0234 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 571.60
//
Query:       gi|242398227|ref|YP_002993651.1|  [L=330]
Description: Arsenical pump-driving ATPase [Thermococcus sibiricus MM 739]
Scores for complete 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-77  260.9   0.7    1.8e-77  260.6   0.7    1.1  1  ArsA_ATPase  Anion-transporting ATPase
    4.5e-18   65.8   0.2    1.9e-17   63.8   0.0    1.9  2  AAA_31       AAA domain
    2.7e-11   43.6   0.0    8.7e-11   42.0   0.0    1.8  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    3.6e-06   26.6   0.2    2.2e-05   24.1   0.0    2.0  2  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
    2.5e-05   23.9   2.6    0.00011   21.8   0.0    2.6  3  ParA         NUBPL iron-transfer P-loop NTPase
    5.3e-05   23.1   0.7      0.002   18.0   0.1    2.8  2  ATP_bind_1   Conserved hypothetical ATP binding protein
    5.6e-05   22.9   0.0    0.00021   21.0   0.0    1.9  2  SRP54        SRP54-type protein, GTPase domain
    0.00057   19.4   0.0     0.0012   18.4   0.0    1.7  1  CBP_BcsQ     Cellulose biosynthesis protein BcsQ
     0.0028   16.7   0.0     0.0053   15.8   0.0    1.4  1  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
  ------ inclusion threshold ------
      0.014   15.0   0.0      0.049   13.2   0.0    1.9  2  AAA_25       AAA domain
      0.016   14.7   0.8      0.082   12.3   0.8    2.1  1  PhoH         PhoH-like protein
       0.02   14.2   0.4        0.5    9.6   0.3    2.3  2  MipZ         ATPase MipZ
      0.034   13.9   0.0      0.061   13.0   0.0    1.4  1  AAA_30       AAA domain
      0.052   12.7   0.3       0.14   11.3   0.2    1.9  2  NB-ARC       NB-ARC domain
       0.12   12.5   0.0        0.2   11.8   0.0    1.5  1  AAA_33       AAA domain
       0.14   12.5   0.5       0.14   12.5   0.5    2.8  3  FlaC_arch    Flagella accessory protein C (FlaC)
       0.17   12.2   0.2        0.3   11.5   0.2    1.6  1  AAA_16       AAA ATPase 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 !  260.6   0.7   1.7e-80   1.8e-77       2     303 ..      12     327 ..      11     329 .. 0.89

  Alignments for each domain:
  == domain 1  score: 260.6 bits;  conditional E-value: 1.7e-80
                                       EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STTTHHHHHHTS--BSS-EEETSSEEEEE--HHHHHHHHHC CS
                       ArsA_ATPase   2 kvilvgGKGGVGKttvsaatavklsekgkkvllistDPAhslsDsfdqklgkeptkvkeNLsavEidpeveleeakq 78 
                                       +v+++ GKGGVGKtt+saa+++ ls+ g+k+l++s DPAh+l D+f+ kl+ +p+++ e L+a+E+d+e+ ++ + +
  gi|242398227|ref|YP_002993651.1|  12 RVLFFIGKGGVGKTTSSAAVSAALSKRGYKTLIVSIDPAHNLGDVFEVKLNDKPKQIAESLYAMELDMEKLIKTYLK 88 
                                       89*******************************************************************66666655 PP

                                       ...CHHGGGSCCHHHHHHHHHHHHHHTSSTTHHHHHHHHHHHHHHH.CSSSSEEEEESBSCCHTCGGGGHHHHHHHH CS
                       ArsA_ATPase  79 ...evqkeeeallgleeledvlaeelaslPGideilsfeellkyvk.eeeydvvvlDtaPTGhtlrllslpevlekl 151
                                          e  k++ + l++  le+ ++  + s PGi+e +++e++ + ++ ++e+dv+++Dt+PTG tlr++ lp++   +
  gi|242398227|ref|YP_002993651.1|  89 hleENLKHMYRYLTVINLEKYFEVLSFS-PGIEEYATLEAIREILQkGDEWDVIIFDTPPTGLTLRVMALPHIALIW 164
                                       0104455666677999999***999999.*************99875899*************************** PP

                                       HHHHHHHHHHHHHHHHHHCCCSHCHHHHHH.............HHHHHHHHHHHHHHHHHHHHTSTTTEEEEEEEES CS
                       ArsA_ATPase 152 leklvklkeklsplakqlvkllglggvsie.............ealeeleetkeeikkveeiltdpertsfrlVvip 215
                                       ++kl+++++k+ +  +++ ++ g  ++ ++              +++el + keei+ v++i+t+ +rts+++V+++
  gi|242398227|ref|YP_002993651.1| 165 VNKLIEVRRKILDKRRTIENIQGERKFMVDgeeyelpsreredPVMKELLAYKEEIEFVRDIITNRDRTSVVAVMNA 241
                                       *******99776666666665554444433333445588777679******************************** PP

                                       SHHHHHHHHHHHHHHHHTT-EEEEEEEEEE-TTCSSSTSHHHHHHHHHHHHHHHHHHHHTTTSEEEEEE--SS-S-S CS
                       ArsA_ATPase 216 EklslkEteRaikeLkkygikvdavivNkllpeeeqenCeflearkkiqkkylkeieelfedlevvklplleeEvvG 292
                                       E l+l+EteRa+++Lkk++i  ++v+vNk+++ ee+   ++++ r ++qkk+l ei+++f+d+ +vk+p++eeE +G
  gi|242398227|ref|YP_002993651.1| 242 EMLPLYETERAHESLKKFKIPFNLVVVNKIIEFEEE--VSKIKVRMDTQKKVLGEIHKKFRDVDIVKVPMFEEEPRG 316
                                       ******************************987777..599************************************ PP

                                       HHHHHHHHHHH CS
                       ArsA_ATPase 293 lekleklsell 303
                                       l+ le++  l+
  gi|242398227|ref|YP_002993651.1| 317 LKWLERIGGLI 327
                                       ******98776 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.8   0.0   1.8e-20   1.9e-17       9     130 ..      18     150 ..      12     169 .. 0.74
   2 ?   -0.5   0.1      0.93   9.8e+02      84     118 ..     265     299 ..     222     308 .. 0.62

  Alignments for each domain:
  == domain 1  score: 63.8 bits;  conditional E-value: 1.8e-20
                            AAA_31   9 qKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgiekneiektlyevl....ieeknikeaiiktkvenl 81 
                                        KGGvGKTT+s +++aal+k+g+k+L+v +Dp  n+   ++++ n++ k++ e l    ++ +++ +++ k+  enl
  gi|242398227|ref|YP_002993651.1|  18 GKGGVGKTTSSAAVSAALSKRGYKTLIVSIDPAHNLGDVFEVKLNDKPKQIAESLyameLDMEKLIKTYLKHLEENL 94 
                                       6*************************************999988886665555552111544444444446778999 PP

                            AAA_31  82 dlipssidLaeaeielvelekk....eeilkellekvk...deYDyiiiDcpPsLg 130
                                       + +  ++ ++++e+ +  l+ +    e++  e+++++    de+D+ii+D+pP+  
  gi|242398227|ref|YP_002993651.1|  95 KHMYRYLTVINLEKYFEVLSFSpgieEYATLEAIREILqkgDEWDVIIFDTPPTGL 150
                                       9999999999999999888888667633344444444411167**********844 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.93
                            AAA_31  84 ipssidLaeaeielvelekkeeilkellekvkdeY 118
                                       ++   +++e+e e+ +++ + ++ k++l ++++++
  gi|242398227|ref|YP_002993651.1| 265 LVVVNKIIEFEEEVSKIKVRMDTQKKVLGEIHKKF 299
                                       23334567788888888888888888888888876 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 !   42.0   0.0   8.2e-14   8.7e-11       4     114 ..      16     297 ..      13     310 .. 0.75

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 8.2e-14
                                       EESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH.......................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......................... RF
                              CbiA   4 astkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep.......................... 54 
                                         +kGGvGKTt +a+  +al++rg+++l v  Dp  n+  ++e + nd+ +                          
  gi|242398227|ref|YP_002993651.1|  16 FIGKGGVGKTTSSAAVSAALSKRGYKTLIVSIDPAHNLGDVFEVKLNDKPKqiaeslyameldmekliktylkhlee 92 
                                       569***********************************99988888887779999*******888888888888888 PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|242398227|ref|YP_002993651.1|  93 nlkhmyryltvinlekyfevlsfspgieeyatleaireilqkgdewdviifdtpptgltlrvmalphialiwvnkli 169
                                       88888888888888888888888888888888888888888888888888888888888888888888888888888 PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|242398227|ref|YP_002993651.1| 170 evrrkildkrrtieniqgerkfmvdgeeyelpsreredpvmkellaykeeiefvrdiitnrdrtsvvavmnaemlpl 246
                                       88888888888888888888888888888888888888888888888888888888888777777777777777777 PP

                                       .CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHC..TS-EEEEEE- CS
                                       .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxx RF
                              CbiA  55 .dlkrllellealgkkkalllkiagvvlnrvdgeneetllkealeelkqry..gvpvlgvipr 114
                                          +r  e+l+++++++        vv+n++ + +ee + ++        +    +vlg+i++
  gi|242398227|ref|YP_002993651.1| 247 yETERAHESLKKFKIPF------NLVVVNKIIEFEEEVSKIKVR------MdtQKKVLGEIHK 297
                                       76666666666666664......357777754432222222222......1225677777765 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0     2e-08   2.2e-05       5      41 ..      16      52 ..      12      87 .. 0.84
   2 ?    0.2   0.1       0.4   4.2e+02     142     180 ..     233     272 ..     226     305 .. 0.68

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 2e-08
                         Fer4_NifH  5 iyGkGGiGksttsqnlsaalaemgkkvlivGCDPkaD 41
                                      + GkGG+Gk+t+s+ +saal+++g k liv  DP ++
  gi|242398227|ref|YP_002993651.1| 16 FIGKGGVGKTTSSAAVSAALSKRGYKTLIVSIDPAHN 52
                                      67********************************986 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.4
                         Fer4_NifH 142 qevyivtsgelmalyaanniakgiekyaksgg.vrlgGli 180
                                        +v+ v+++e+  ly   +  ++++k++   + v +  +i
  gi|242398227|ref|YP_002993651.1| 233 TSVVAVMNAEMLPLYETERAHESLKKFKIPFNlVVVNKII 272
                                       5678889999999999999999998886544423333333 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 !   21.8   0.0     1e-07   0.00011      10      41 ..      17      48 ..      12      88 .. 0.83
   2 ?    0.9   0.0      0.24   2.6e+02     110     122 ..     136     148 ..     123     163 .. 0.79
   3 ?   -1.3   0.1       1.1   1.2e+03     136     173 ..     232     269 ..     222     302 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1e-07
                              ParA 10 SgKGGVGKStvavnlAlaLakkglkvgllDaD 41
                                       gKGGVGK+t ++ +++aL+k+g+k+ ++ +D
  gi|242398227|ref|YP_002993651.1| 17 IGKGGVGKTTSSAAVSAALSKRGYKTLIVSID 48
                                      69************************999998 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.24
                              ParA 110 gelDyLiiDlPPG 122
                                       +e D++i D+PP 
  gi|242398227|ref|YP_002993651.1| 136 DEWDVIIFDTPPT 148
                                       578*********4 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.1
                              ParA 136 lagaviVttpqevaladvkkaiemfkkvkvkvlGvveN 173
                                        + +v V   + + l ++++a e +kk k++   vv N
  gi|242398227|ref|YP_002993651.1| 232 RTSVVAVMNAEMLPLYETERAHESLKKFKIPFNLVVVN 269
                                       56677788888888888888888888888887766666 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 !   18.0   0.1   1.9e-06     0.002       2      36 ..      17      51 ..      16      61 .. 0.95
   2 ?    2.4   0.1       0.1   1.1e+02      78      99 ..     124     146 ..      71     147 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.9e-06
                        ATP_bind_1  2 vGpaGsGKttfvgalseilelrgrsvavvNLDPAa 36
                                      +G  G+GKtt   a+s  l++rg++  +v +DPA 
  gi|242398227|ref|YP_002993651.1| 17 IGKGGVGKTTSSAAVSAALSKRGYKTLIVSIDPAH 51
                                      899*******************************6 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.1
                        ATP_bind_1  78 sldwldeelekeed.dyllfDtP 99 
                                       +l+ ++e l+k ++ d ++fDtP
  gi|242398227|ref|YP_002993651.1| 124 TLEAIREILQKGDEwDVIIFDTP 146
                                       45666777766655688888887 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0     2e-07   0.00021       3      38 ..      13      48 ..      11      52 .. 0.95
   2 ?   -2.1   0.0       2.4   2.5e+03      77      91 ..     133     145 ..     108     146 .. 0.70

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2e-07
                                      EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                             SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvllvaaD 38
                                      v+ ++G  G+GKTt+ a ++a l+k+g+k+l+v+ D
  gi|242398227|ref|YP_002993651.1| 13 VLFFIGKGGVGKTTSSAAVSAALSKRGYKTLIVSID 48
                                      7899******************************99 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.4
                                       HHHHHTTSSEEEEEE CS
                             SRP54  77 ekakeekidvvlvDT 91 
                                       +k   ++ dv++ DT
  gi|242398227|ref|YP_002993651.1| 133 QKG--DEWDVIIFDT 145
                                       333..4599****99 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.1e-06    0.0012      10      55 ..      19      64 ..      12     159 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.1e-06
                          CBP_BcsQ 10 RGGvGttsllaaLawalhelgesvlviDlspdnlLrlhFnvdieqr 55
                                      +GGvG+t+ +aa + al + g++ l++ + p+  L   F+v+++++
  gi|242398227|ref|YP_002993651.1| 19 KGGVGKTTSSAAVSAALSKRGYKTLIVSIDPAHNLGDVFEVKLNDK 64
                                      7***************************************998765 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 !   15.8   0.0     5e-06    0.0053      31      69 ..      13      51 ..       3      60 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5e-06
                                      EEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE---- CS
                              MeaB 31 vvGltGvPGaGkstlvealglelrrrGkrvavlavDPss 69
                                      v+ + G  G+Gk t   a+ + l +rG++  ++++DP+ 
  gi|242398227|ref|YP_002993651.1| 13 VLFFIGKGGVGKTTSSAAVSAALSKRGYKTLIVSIDPAH 51
                                      56678999*****************************85 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.6e-05     0.049      35     106 ..      13      97 ..       3     146 .. 0.65
   2 ?   -2.1   0.0       2.3   2.5e+03      98     125 ..     228     255 ..     192     259 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.6e-05
                            AAA_25  35 lallaGapgtGKttlaldlalava.tGkpwlg....pvapeqgkVlyvsaEdsedelrrRlravgeal......... 97 
                                       +  ++G +g+GKtt    +++a++ +G + l     p a+  g V  v + d+ +++++ l+a+  ++         
  gi|242398227|ref|YP_002993651.1|  13 VLFFIGKGGVGKTTSSAAVSAALSkRGYKTLIvsidP-AHNLGDVFEVKLNDKPKQIAESLYAMELDMekliktylk 88 
                                       44568*******************9999999898854.5799*************************9777777776 PP

                            AAA_25  98 ....rddarllvl 106
                                           +    l  +
  gi|242398227|ref|YP_002993651.1|  89 hleeN----LKHM 97 
                                       44431....3222 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.3
                            AAA_25  98 rddarllvldlagveslpLfakdrggtl 125
                                       + ++r  v+ +++ e lpL++++r ++ 
  gi|242398227|ref|YP_002993651.1| 228 TNRDRTSVVAVMNAEMLPLYETERAHES 255
                                       5567777777777777888888877765 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.8   7.8e-05     0.082      20      92 ..      12      99 ..       3     135 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.8e-05
                                      SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S--T...............T----SS---------TTTHHH CS
                              PhoH 20 divfaiGpaGtGKtylavalavealkkkkvkriiltrpavea...............geelGflpgdleekvdpylrpl 83
                                       ++f iG+ G GKt  + a+ +++ k++  + i+ + pa +                 e+l +++ d+e+ ++ yl+ l
  gi|242398227|ref|YP_002993651.1| 12 RVLFFIGKGGVGKTTSSAAVSAALSKRGYKTLIVSIDPAHNLgdvfevklndkpkqiAESLYAMELDMEKLIKTYLKHL 90
                                      5899**********99999999888888888888899998776666677787777777888888888888888888888 PP

                                      HHHHTTTS- CS
                              PhoH 84 ydaLkdllg 92
                                       ++Lk+++ 
  gi|242398227|ref|YP_002993651.1| 91 EENLKHMYR 99
                                      888888874 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.3   0.00048       0.5       7      38 ..      17      48 ..      11      53 .. 0.86
   2 ?    2.2   0.0     0.089        94      88     112 ..     124     150 ..      69     163 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00048
                                      -SSTTSSHHHHHHHHHHHHHTTT--EEEEE-- CS
                              MipZ  7 nekGGsGksttavhvavaLlkkGarvaaidld 38
                                        kGG Gk+t +  v  aL+k+G +   + +d
  gi|242398227|ref|YP_002993651.1| 17 IGKGGVGKTTSSAAVSAALSKRGYKTLIVSID 48
                                      57**********************98877777 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.089
                                       HHHHHHH..HHHHH-SEEEEE--SS-- CS
                              MipZ  88 eleelva..dleaeldfividtPGsds 112
                                       +le++ +  +   e d+i++dtP +  
  gi|242398227|ref|YP_002993651.1| 124 TLEAIREilQKGDEWDVIIFDTPPTGL 150
                                       444443311345689********7655 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   5.8e-05     0.061      17      53 ..      10      46 ..       5      95 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.8e-05
                            AAA_30 17 gdrvavltGpAGtGKttalkalreaweaaggrviglA 53
                                      g rv +  G  G GKtt+ +a+ +a+ ++g++ ++++
  gi|242398227|ref|YP_002993651.1| 10 GFRVLFFIGKGGVGKTTSSAAVSAALSKRGYKTLIVS 46
                                      56788999**********************9988765 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   0.00014      0.14      10      43 ..       3      34 ..       1     105 [. 0.76
   2 ?   -1.9   0.0       1.5   1.5e+03     212     249 ..      78     116 ..      67     116 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00014
                                      HHHHCTTTSCSEEEEEEESTTSSHHHHHHHHCCS CS
                            NB-ARC 10 ekLlekdelqslvvalvGmgGvGKttlakqilnk 43
                                      e L  k+++   v+++ G+gGvGKtt ++ +   
  gi|242398227|ref|YP_002993651.1|  3 EYLIPKEGFR--VLFFIGKGGVGKTTSSAAVSAA 34
                                      5567677778..9*************77766554 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.5
                                       CSCCHHHHHHHHHHCTGCC.TS--SSSSSSSHHHHHHHH CS
                            NB-ARC 212 ktveewkkvleklesklle.vekstskslesvasilqls 249
                                       ++++  k +l++le++l +  +  t  +le+ +++l++s
  gi|242398227|ref|YP_002993651.1|  78 DMEKLIKTYLKHLEENLKHmYRYLTVINLEKYFEVLSFS 116
                                       556666777777777776667777777888888877776 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00019       0.2       1      93 [.      13     133 ..      13     156 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00019
                            AAA_33   1 lvllvGlpGsGKstlaerllkklg.....avllssdtlrr..rlfg...tdqqskt...................dy 48 
                                       +++++G  G+GK+t +  + ++l      + ++s d +++   +f+   +d++  +                   ++
  gi|242398227|ref|YP_002993651.1|  13 VLFFIGKGGVGKTTSSAAVSAALSkrgykTLIVSIDPAHNlgDVFEvklNDKP--KqiaeslyameldmekliktYL 87 
                                       789***************97776666677666777775554455544332222..1123344444444444444455 PP

                            AAA_33  49 trvldrlyqilnelarkalsagrnvildatnlsr.rerarflklar 93 
                                       ++++++l+ + + l  ++l++ + v+  ++ +++ ++ ++++++++
  gi|242398227|ref|YP_002993651.1|  88 KHLEENLKHMYRYLTVINLEKYFEVLSFSPGIEEyATLEAIREILQ 133
                                       5555555555555555555555555555555555455555555555 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 ?   -0.7   0.1       1.9     2e+03      26      44 ..      68      86 ..      60     101 .. 0.57
   2 ?   -1.5   0.1       3.2   3.4e+03      37      46 ..     235     249 ..     209     249 .. 0.57
   3 ?   12.5   0.5   0.00014      0.14       1      33 [.     270     302 ..     270     304 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.9
                         FlaC_arch 26 lsksveelkenVkdllsLY 44
                                      + +s+  ++ + ++l++ Y
  gi|242398227|ref|YP_002993651.1| 68 IAESLYAMELDMEKLIKTY 86
                                      4445545555555554444 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.2
                         FlaC_arch  37 V.....kdllsLYEv 46 
                                       V      ++l LYE+
  gi|242398227|ref|YP_002993651.1| 235 VvavmnAEMLPLYET 249
                                       245555678888886 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 0.00014
                         FlaC_arch   1 ridelEnklsklsteletvkkeneelsksveel 33 
                                       +i e+E+++sk++++++t kk + e+ k+  ++
  gi|242398227|ref|YP_002993651.1| 270 KIIEFEEEVSKIKVRMDTQKKVLGEIHKKFRDV 302
                                       7889**********************9987665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   0.00028       0.3      24      52 ..      11      39 ..       5     181 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00028
                            AAA_16 24 pelvllsGesGvGKsslvrellralekdg 52
                                       ++++++G  GvGK++   ++  al+k+g
  gi|242398227|ref|YP_002993651.1| 11 FRVLFFIGKGGVGKTTSSAAVSAALSKRG 39
                                      4899******************9999994 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1200  (0.0669307); expected 358.6 (0.02)
Passed bias filter:                      761  (0.0424452); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); 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: 0.71u 0.37s 00:00:01.08 Elapsed: 00:00:00.55
# Mc/sec: 1800.64
//
Query:       gi|242398228|ref|YP_002993652.1|  [L=96]
Description: hypothetical protein TSIB_0236 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-05   24.6   0.6    7.6e-05   22.8   0.5    1.9  1  FeS_assembly_P  Iron-sulfur cluster assembly protein
  ------ inclusion threshold ------
        1.4    8.6   5.0        0.3   10.7   0.6    2.1  3  VASP_tetra      VASP tetramerisation domain


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 !   22.8   0.5   8.5e-09   7.6e-05       2      42 ..       4      44 ..       3      81 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 8.5e-09
                                      HHHHHHHTT-B-TTTSSBCCCCT---EEEE-T-EEEEEE-- CS
                    FeS_assembly_P  2 eavlaaLrtVtDPelgvdlvslglvreidieggkVsvditl 42
                                      e++++ L++V+ P +g d+vslg v+ i+ e++kV + + l
  gi|242398228|ref|YP_002993652.1|  4 EEIYQELKKVKEPISGEDIVSLGIVSLIRKEDNKVIIFLGL 44
                                      689999*****************************886655 PP

>> VASP_tetra  VASP tetramerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.6   3.4e-05       0.3      12      26 ..       3      17 ..       3      18 .. 0.91
   2 ?   -1.8   0.0      0.27   2.4e+03      15      22 ..      31      38 ..      27      38 .. 0.73
   3 ?   -4.0   0.0       1.3   1.2e+04      22      28 ..      77      83 ..      76      84 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 3.4e-05
                        VASP_tetra 12 LeEvrkELqKvKeEI 26
                                      +eE+  EL+KvKe I
  gi|242398228|ref|YP_002993652.1|  3 IEEIYQELKKVKEPI 17
                                      69**********966 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.27
                        VASP_tetra 15 vrkELqKv 22
                                      +rkE +Kv
  gi|242398228|ref|YP_002993652.1| 31 IRKEDNKV 38
                                      78997776 PP

  == domain 3  score: -4.0 bits;  conditional E-value: 1.3
                        VASP_tetra 22 vKeEIIe 28
                                      v  EI++
  gi|242398228|ref|YP_002993652.1| 77 VNFEIVD 83
                                      5557775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); 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: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 668.99
//
Query:       gi|242398229|ref|YP_002993653.1|  [L=218]
Description: hypothetical protein TSIB_0237 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.052   14.1   0.0        0.1   13.2   0.0    1.6  1  RPAP3_C   Potential Monad-binding region of RPAP3


Domain annotation for each model (and alignments):
>> RPAP3_C  Potential Monad-binding region of RPAP3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   5.6e-06       0.1      22      60 ..     134     173 ..     120     211 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.6e-06
                           RPAP3_C  22 lka.vllqinpkqlpkiFknsledeilsdildalnerlqe 60 
                                       l + ++ +in kq++ +F+++ ++e+l ++l+ ++   ++
  gi|242398229|ref|YP_002993653.1| 134 LLQrEIVEINGKQYEALFEKKRDVELLKEFLQGFSRIENV 173
                                       22236677***********************966554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1592.63
//
Query:       gi|242398230|ref|YP_002993654.1|  [L=310]
Description: TRNA/rRNA cytosine-C5-methylase, NOL1/NOP2/Sun family [Thermococcus sibiricus MM 739]
Scores for complete 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-58  196.9   0.0    3.5e-58  196.6   0.0    1.1  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
    1.7e-18   66.9   0.0    3.5e-18   65.9   0.0    1.5  1  Methyltr_RsmF_N  N-terminal domain of 16S rRNA methyltransfer
    1.4e-06   28.5   0.0    2.6e-06   27.7   0.0    1.4  1  FtsJ             FtsJ-like methyltransferase
    5.4e-05   23.0   0.0    8.3e-05   22.4   0.0    1.3  1  Methyltransf_31  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  196.6   0.0   7.7e-62   3.5e-58       2     199 ..     106     306 ..     105     307 .. 0.91

  Alignments for each domain:
  == domain 1  score: 196.6 bits;  conditional E-value: 7.7e-62
                                       HHH---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC. CS
                   Methyltr_RsmB-F   2 llLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlgge 78 
                                       ++L+p+++e i D++aaPGgKT+++a+lmknkg+++A d+ + Rlk+   nl+rLgvtnti+++    ++ +    +
  gi|242398230|ref|YP_002993654.1| 106 VALEPKPGEIIADMAAAPGGKTSYMAQLMKNKGVIYAFDVGRDRLKETRLNLSRLGVTNTILIHKSSLYMGELG--I 180
                                       68*************************************************************99888775544..5 PP

                                       .EEEEEEEE--CCGGGTTT-TCHHHH--HHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEES--STTTTHHHHHHHHH CS
                   Methyltr_RsmB-F  79 lfDriLlDaPCsgtgvirrdpdvklrrkekdiaqlaklqkellsaaidllkkgGvlvYsTCsvlveEneevieeaLk 155
                                        fD+iLlDaPC+g g+i+++p+ k  r+ +d++ +++lq ++++ a++ lk gGvlvYsTCs+++eEne vi+ aL 
  gi|242398230|ref|YP_002993654.1| 181 EFDKILLDAPCTGSGTIHKNPERKADRTIEDVKFCQNLQMQMIKVALENLKVGGVLVYSTCSLEPEENEFVIQWALD 257
                                       6***************************************************************************9 PP

                                       H-TTEEEESSBSTTSTTSSECEEC......TSEEE-TTTTSS-SEEEEEE CS
                   Methyltr_RsmB-F 156 kredvelvetelsepkglklgeea......gtlrllPhtenkdgffiakl 199
                                       +  d++l ++++ ep  ++    +      +++r++P+++n+ gff+ak+
  gi|242398230|ref|YP_002993654.1| 258 NF-DIALLPLRFGEPALTSPFDIElsselaKARRFYPDEHNTSGFFVAKI 306
                                       98.99999998888654433222234555689****************98 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 !   65.9   0.0   7.9e-22   3.5e-18       3      90 .]      12     102 ..      11     102 .. 0.95

  Alignments for each domain:
  == domain 1  score: 65.9 bits;  conditional E-value: 7.9e-22
                                       HHHHHHHHHHHGGGHHHHHHHHH-----EEE--TTS..TTHHHHHHH..-SS--B-TT-TTEEES---....TTSHH CS
                   Methyltr_RsmF_N   3 eeFiekmkellgeeaeaflaaleeprkkglRvNtlKisveeleklse..efelepvpwceeGfyleeee.rpgkhpl 76 
                                       +eF e++ +l ge+a ++ +a+e+p ++ +RvNtl+++ ++++k+++  +f+++++ w++eGf l++e+ + + +p+
  gi|242398230|ref|YP_002993654.1|  12 KEFAERYFDLWGERAVRIAEAMERPLPRCFRVNTLRTEISTITKIMNkkGFQFKRISWAREGFCLTREPfSITSTPE 88 
                                       69******************************************988899***************9987366***** PP

                                       HHTTS-EE--TTTH CS
                   Methyltr_RsmF_N  77 heaGlyYiQEpSam 90 
                                       +  Gl+YiQE+S+m
  gi|242398230|ref|YP_002993654.1|  89 YLGGLIYIQEASSM 102
                                       *************9 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.0   5.7e-10   2.6e-06      20     147 ..     111     254 ..      93     262 .. 0.81

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 5.7e-10
                                       -TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSSHHH.TTEEEECS-CCCSSHHHHHCHCHHH..SSEEEEEE CS
                              FtsJ  20 kpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpmapl.pgvttiqgditdpetiekikealse..rkvdlvvs 93 
                                       kpg+ + D +aaPGg + +++q +++kg+++a+D++  ++   ++++ +  +t+   i k + +++e   ++d ++ 
  gi|242398230|ref|YP_002993654.1| 111 KPGEIIADMAAAPGGKTSYMAQLMKNKGVIYAFDVGRDRLKeTRLNLSRLGVTNTILIHKSSLYMGElgIEFDKILL 187
                                       478889******************99***********98888999999999999999999998887766789***** PP

                                       --S-SS-CH.HHHHHHHH..........CCCCHHHHCCHCCCCECCCEEEECCCH..CCCHHHHHHH CS
                              FtsJ  94 Dgapdvsgv.hdldeylq..........sqLllaalelalkllkpggtfvlkifr..geeteallkq 147
                                       D     sg+ h+ +e ++           +L ++ +++al+ lk gg++v  ++    ee e++++ 
  gi|242398230|ref|YP_002993654.1| 188 DAPCTGSGTiHKNPERKAdrtiedvkfcQNLQMQMIKVALENLKVGGVLVYSTCSlePEENEFVIQW 254
                                       *876666663555444448888899997799*******************88888633333355554 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   1.8e-08   8.3e-05       5     114 ..     114     243 ..     110     264 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.8e-08
                   Methyltransf_31   5 lrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieelekl.ledekfDlils 80 
                                         + D +++ G +t  +a+++  k+ ++ +D   + ++  r n+++lg++n  + + +   + +l +e   fD il 
  gi|242398230|ref|YP_002993654.1| 114 EIIADMAAAPGGKTSYMAQLMKNKGVIYAFDVGRDRLKETRLNLSRLGVTNTILIHKSSLYMGELgIE---FDKILL 187
                                       5688**************999999********************************999999999899...****** PP

                   Methyltransf_31  81 n......................evlnaladpdkileeiervlkpggilliedprl 114
                                       +                      +v  +++ + + ++ + ++lk gg+l+ ++++l
  gi|242398230|ref|YP_002993654.1| 188 DapctgsgtihknperkadrtieDVKFCQNLQMQMIKVALENLKVGGVLVYSTCSL 243
                                       *66666666666666666633333336666666777788899************93 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2214.33
//
Query:       gi|242398231|ref|YP_002993655.1|  [L=212]
Description: hypothetical protein TSIB_0239 [Thermococcus sibiricus MM 739]
Scores for complete 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-25   88.3   0.1    6.4e-25   88.2   0.1    1.1  1  DUF257     Pyrococcus protein of unknown function, DUF257
  ------ inclusion threshold ------
       0.05   13.7   0.8        0.4   10.8   0.0    2.4  2  ssDBP_DBD  Single stranded DNA-binding protein ss DNA binding


Domain annotation for each model (and alignments):
>> DUF257  Pyrococcus protein of unknown function, DUF257
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.2   0.1   7.1e-29   6.4e-25       1     128 [.       7     138 ..       7     200 .. 0.89

  Alignments for each domain:
  == domain 1  score: 88.2 bits;  conditional E-value: 7.1e-29
                            DUF257   1 elletlrpGetvLiEyssssvpevllyliakyskeknvPllvdDvlDtllivlkhlkllGldvpe.esikviKigGt 76 
                                       e+l+++r Ge ++iEy+s + pe+ l  ++k s+e+++P+l++D+lD + + +++l++lG ++ + e+  viK gG 
  gi|242398231|ref|YP_002993655.1|   7 EFLNDIREGERIFIEYESTTHPELFLDGLVKWSNEEGIPILIIDMLDIFHLFVQQLRFLGYKTHHlENLCVIKGGGR 83 
                                       79**************************************************************99*********** PP

                            DUF257  77 kevgnvvkkidfdkdpsiylskykravekvsve...etvinlvlglerllllldn 128
                                        e+g+v+ ++   ++  + l++y+ av+    +   ++ + + lg e++l   ++
  gi|242398231|ref|YP_002993655.1|  84 VEFGKVIGRVRIMEEFYVQLKEYTDAVRLFFEKaksDKAVIVFLGTEKFLYSFQE 138
                                       *************************9987765532244488889****9975544 PP

>> ssDBP_DBD  Single stranded DNA-binding protein ss DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   4.5e-05       0.4      64     106 ..       9      57 ..       5      72 .. 0.75
   2 ?    0.9   0.1     0.053   4.7e+02      62      92 ..      88     117 ..      68     135 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 4.5e-05
                         ssDBP_DBD  64 fnrirdsek.f....retsrelf.dglkkwffeeavprynlergdifmi 106
                                       +n ir+ e+ f      t  elf dgl kw  ee +p   ++  dif +
  gi|242398231|ref|YP_002993655.1|   9 LNDIREGERiFieyeSTTHPELFlDGLVKWSNEEGIPILIIDMLDIFHL 57 
                                       566777765222211235668877**********************976 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.053
                         ssDBP_DBD  62 nifnrirdsekfretsrelfdglkkwffeea 92 
                                       +++ r+r  e+f    +e  d ++  ffe+a
  gi|242398231|ref|YP_002993655.1|  88 KVIGRVRIMEEFYVQLKEYTDAVR-LFFEKA 117
                                       467888999999999999888875.567766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 1259.94
//
Query:       gi|242398232|ref|YP_002993656.1|  [L=226]
Description: hypothetical protein TSIB_0240 [Thermococcus sibiricus MM 739]
Scores for complete 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-33  114.4   3.0    6.7e-33  114.2   3.0    1.0  1  DUF257    Pyrococcus protein of unknown function, DUF257


Domain annotation for each model (and alignments):
>> DUF257  Pyrococcus protein of unknown function, DUF257
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.2   3.0   3.7e-37   6.7e-33       1     203 [.      11     213 ..      11     215 .. 0.93

  Alignments for each domain:
  == domain 1  score: 114.2 bits;  conditional E-value: 3.7e-37
                            DUF257   1 elletlrpGetvLiEyssssvpevllyliakyskeknvPllvdDvlDtllivlkhlkllGldvpe.esikviKigGt 76 
                                       e+ +++   e ++iEysss + ++ ++ ++ +s++    +lv DvlD l++++  l ++G d++   +  viKigG+
  gi|242398232|ref|YP_002993656.1|  11 EYAKSVMWKEGIVIEYSSSEPIHLIFKWLVGISEKITDNILVLDVLDILSMLKLNLDIAGKDTSFtHELDVIKIGGN 87 
                                       57778888899**********************998888*************************978********** PP

                            DUF257  77 kevgnvvkkidfdkdpsiylskykravekvsveetv.inlvlglerllllldnrrdlyklvksikkyl.gnknRkaf 151
                                        ++g+++  +d+++d+ +y s+y +++++    ++  +  ++g+erl+ l++++  + + + +  +y+ g+++R  +
  gi|242398232|ref|YP_002993656.1|  88 IKLGKMIGYLDPHQDITVYASRYSKILREYYETHKNiVYFIFGIERLVHLQEREEVFELYATNYTRYVfGDEERVGI 164
                                       ******************************998777699****************999988888887659******* PP

                            DUF257 152 ylinrnllesikPellplLEeiassvieiesekealivrilKslnldivgtt 203
                                       y+inr+++ +     l  LEe+as+v+e+ +e+ +l ++i Ks  l+  g++
  gi|242398232|ref|YP_002993656.1| 165 YFINRDIATKAL---LLQLEEAASRVLEVIHEEGTLKIKIRKSPRLEDYGKE 213
                                       *******99877...9**************************9998888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1660.88
//
Query:       gi|242398233|ref|YP_002993657.1|  [L=323]
Description: hypothetical protein TSIB_0241 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.14   12.0   0.2         28    4.6   0.0    2.7  3  DUF3148   Protein of unknown function (DUF3148)


Domain annotation for each model (and alignments):
>> DUF3148  Protein of unknown function (DUF3148)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0    0.0016        28      32      59 ..      35      64 ..      32      66 .. 0.74
   2 ?   -2.1   0.0      0.19   3.4e+03       4      21 ..      88     106 ..      85     107 .. 0.63
   3 ?    4.4   0.0    0.0017        31      36      60 ..     131     155 ..     127     157 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0016
                           DUF3148 32 geeGviidrrpgdywa..VrfarGaFLlds 59
                                      ge  +i+   p + w+    ++rGaFL++ 
  gi|242398233|ref|YP_002993657.1| 35 GELNTIVFVTPSEEWKtiLDLRRGAFLIEM 64
                                      6666788888888887334689******96 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.19
                           DUF3148   4 kVrlvelpp.ylKTAdpmP 21 
                                       ++ l + p+   KTA+ +P
  gi|242398233|ref|YP_002993657.1|  88 QIILLRVPKeAEKTAEIVP 106
                                       5556555541569999887 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.0017
                           DUF3148  36 viidrrpgdywaVrfarGaFLldsk 60 
                                       +++d +  d ++++  +G+FL+ ++
  gi|242398233|ref|YP_002993657.1| 131 IVTDKKLVDHVNIKDIKGSFLIKKN 155
                                       68999*****************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       734  (0.0409393); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); 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 0.29s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2099.70
//
Query:       gi|242398234|ref|YP_002993658.1|  [L=196]
Description: metallophosphoesterase, calcineurin superfamily [Thermococcus sibiricus MM 739]
Scores for complete 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-08   33.1   0.0    1.2e-07   32.5   0.0    1.3  1  Metallophos    Calcineurin-like phosphoesterase
    2.7e-07   30.9   0.0    3.5e-07   30.6   0.0    1.1  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
  ------ inclusion threshold ------
      0.015   15.1   0.1      0.022   14.5   0.1    1.2  1  YqgF           Holliday-junction resolvase-like of SPT6
      0.046   13.3   0.0       0.08   12.5   0.0    1.4  1  DUF2268        Predicted Zn-dependent protease (DUF2268)
      0.055   13.8   0.0       0.13   12.6   0.0    1.6  1  DUF2183        Uncharacterized conserved protein (DUF2183)


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 !   32.5   0.0   3.2e-11   1.2e-07       2     109 ..      25     130 ..      24     177 .. 0.63

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 3.2e-11
                                       EEEEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSS..........HHHHHHHHHHHHHHHHTSEEE CS
                       Metallophos   2 rilvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrg..........dlekellellaalvkypipvy 68 
                                       +i++i+D+       +++ ++  l   +++++p +++++GDlvd             + k++++ll+ l +++  vy
  gi|242398234|ref|YP_002993658.1|  25 KIMHISDTP-----DNIYPFILNL---IEKSRPAYIIHTGDLVDNIklerrpelkeRYKKRVQKLLDILENSNATVY 93 
                                       899*****9.....5555555444...34449**************9*99998888777777777777777799*** PP

                                       EEC-TTSCHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEE CS
                       Metallophos  69 lllGNHegfeeellnkygylgifsepwrsdaevfnnlplas 109
                                       +++GN +    + + +++++++ + ++ +d    +++ la 
  gi|242398234|ref|YP_002993658.1|  94 IVPGNED----DPKILRKFSKKAKIVKPRDIIDIEGIRLAL 130
                                       *******....555555555444444444444444444444 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 !   30.6   0.0   9.7e-11   3.5e-07       2     103 ..      25     136 ..      25     165 .. 0.79

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 9.7e-11
                     Metallophos_2   2 klaiiSDlHsnldaleavlealkevgvdaiihaGDl.eeeep...........evleellela.....pvlaVrGNn 61 
                                       k+++iSD+ +  ++ + +l+ +++ ++ +iih+GDl  ++++           + +++ll+++      v++V+GN 
  gi|242398234|ref|YP_002993658.1|  25 KIMHISDTPD--NIYPFILNLIEKSRPAYIIHTGDLvDNIKLerrpelkerykKRVQKLLDILensnaTVYIVPGNE 99 
                                       7899****96..5667789999999999*******653333344456666665566666666688889********* PP

                     Metallophos_2  62 DeevveedvlreaaelgtdlpeeaelelagekvlliHgdplg 103
                                       D    + ++lr++ + ++ ++ ++ ++++g +++l H+  ++
  gi|242398234|ref|YP_002993658.1| 100 D----DPKILRKFSKKAKIVKPRDIIDIEGIRLALAHEP-YE 136
                                       *....999*****************************97.42 PP

>> YqgF  Holliday-junction resolvase-like of SPT6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   6.1e-06     0.022      24      81 ..      50     107 ..      47     129 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.1e-06
                                       EEE-TTS-EEEEEEE-S-TT-SS-SHHHHHHHHHHHHHH--SEEEE--SSTHHHHHHH CS
                              YqgF  24 vlvngeGevvdslklaareedrekkakfvetlkkfllskkPdvigvsGenrdaqklie 81 
                                       +++ + G++vd++kl  r+e +e+ +k v++l ++l++ +  v  v G++ d + l++
  gi|242398234|ref|YP_002993658.1|  50 AYIIHTGDLVDNIKLERRPELKERYKKRVQKLLDILENSNATVYIVPGNEDDPKILRK 107
                                       688899******************************************9999887766 PP

>> DUF2268  Predicted Zn-dependent protease (DUF2268)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.2e-05      0.08       2      51 ..      71     120 ..      70     134 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.2e-05
                           DUF2268   2 kelieealekliealkkpdvdvfilpvneenrklieekgykgglaipdki 51 
                                       ke+ ++ ++kl ++l++ + +v+i+p ne+ +k+ +++  k ++  p +i
  gi|242398234|ref|YP_002993658.1|  71 KERYKKRVQKLLDILENSNATVYIVPGNEDDPKILRKFSKKAKIVKPRDI 120
                                       578899******************************99999888777766 PP

>> DUF2183  Uncharacterized conserved protein (DUF2183)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   3.5e-05      0.13       2      87 ..      27     111 ..      26     121 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.5e-05
                           DUF2183   2 fYvSaspwnlyplleeFleenglPkgslllrdlsltlksllkekstaehKraeiekiletfpe.rkfiliGDsgqkd 77 
                                       + +S +p n+yp++ + +e++  P+  +++ dl  ++ +l ++++ +e+ +++++k+l+ + +    ++i    ++d
  gi|242398234|ref|YP_002993658.1|  27 MHISDTPDNIYPFILNLIEKS-RPAYIIHTGDLV-DNIKLERRPELKERYKKRVQKLLDILENsNATVYIVPGNEDD 101
                                       679*****************9.9*********98.444455544555555666666666665523456666667889 PP

                           DUF2183  78 peiYaeiake 87 
                                       p+i +++ k+
  gi|242398234|ref|YP_002993658.1| 102 PKILRKFSKK 111
                                       9988887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 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:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 1456.96
//
Query:       gi|242398235|ref|YP_002993659.1|  [L=364]
Description: Saccharopine reductase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-31  109.9   0.0    3.6e-31  109.3   0.0    1.3  1  Sacchrp_dh_C     Saccharopine dehydrogenase C-terminal domain
    1.3e-17   64.3   0.0      2e-17   63.7   0.0    1.3  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
    9.7e-06   25.0   0.1    1.5e-05   24.4   0.1    1.3  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
    0.00011   22.3   0.1    0.00033   20.7   0.0    1.9  2  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
    0.00014   22.6   0.0    0.00026   21.8   0.0    1.5  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
    0.00024   21.4   0.1    0.00074   19.8   0.1    2.0  1  TrkA_N           TrkA-N domain
     0.0008   19.8   0.2     0.0018   18.7   0.1    1.6  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
      0.002   18.6   0.1     0.0077   16.8   0.1    2.0  2  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
     0.0037   17.4   0.1     0.0067   16.5   0.1    1.5  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
     0.0041   17.8   0.1      0.077   13.7   0.0    2.3  2  CoA_binding      CoA binding domain
  ------ inclusion threshold ------
      0.055   13.1   0.0      0.099   12.3   0.0    1.4  1  ApbA             Ketopantoate reductase PanE/ApbA
      0.068   14.0   0.0       0.16   12.8   0.0    1.8  1  GARS_N           Phosphoribosylglycinamide synthetase, N doma
       0.09   12.3   0.0       0.56    9.8   0.0    2.0  2  IlvN             Acetohydroxy acid isomeroreductase, NADPH-bi
      0.099   12.0   0.0       0.16   11.3   0.0    1.4  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
       0.13   12.1   0.0       0.82    9.5   0.1    2.3  3  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
       0.19   12.4   0.0       0.62   10.7   0.0    1.8  2  NAD_binding_3    Homoserine dehydrogenase, NAD binding domain


Domain annotation for each model (and alignments):
>> Sacchrp_dh_C  Saccharopine dehydrogenase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.3   0.0   3.2e-34   3.6e-31       1     263 [.     117     347 ..     117     349 .. 0.83

  Alignments for each domain:
  == domain 1  score: 109.3 bits;  conditional E-value: 3.2e-34
                                       BTTTBHHHHHHHHHHHCCCHTTBECCCCCCCCCCCCECCCCESTTCEEESS-HHHHHHHCCSEEEEEETTEEEECT. CS
                      Sacchrp_dh_C   1 GldPGidhllamkaidevkakggkiesflsycgglpapeasdnplgYkfsWspegvlreltnpakvlengqvkevp. 76 
                                       G++PG++h++  ++++e+++     e+ ++y+gglp  e++  pl Y ++Wsp  +++e+t+pa+v+++g++++v+ 
  gi|242398235|ref|YP_002993659.1| 117 GFAPGLSHIFLGRIYQEMDE----LEEAYIYVGGLP-KEPKP-PLYYRITWSPYDLIEEYTRPARVIRDGKIVSVDp 187
                                       9***************9877....899*********.88885.****************************999995 PP

                                       CCCSGCC.TCEEECCCCCEECTTECEEECTHCHHHHHHC.SCSEEEEEEEEEHHHHHHHHHHHTTT--SCECCCCCC CS
                      Sacchrp_dh_C  77 gsellkgakkpiyilpglslegypnrdslpyeelyglpeaktlfrgtlrypgfsellkslkelGllseepkeealka 153
                                       ++      +k+++i ++ ++e++   d+l+   l+++  ak l   tlr+pg+ + +k l+elG++s+e+       
  gi|242398235|ref|YP_002993659.1| 188 LEG-----IKNVNIGNR-EFEAFV-SDGLRS-LLENIN-AKRLEEWTLRWPGHLAKMKILRELGFFSSEN------- 248
                                       555.....589999666.899996.668887.566777.899**************************97....... PP

                                       HHSTTCEHHHHHHHHCCHHCCCCTTEEEEEEEEEEEEEE.TTSEEEEEEEEEEEEEE.HH.SSSHHHHHHHHHHHHH CS
                      Sacchrp_dh_C 154 wlsegespldvlaalLekklalepgerDlvvlqhefgie.sdgkkkekktstlvgyd.ee.gssamaktvGvpaaia 227
                                               l+   ++++   ++  ++ D  ++++  +++ +d +  e  ++ l   d e+ g ++ma+++G+++ai+
  gi|242398235|ref|YP_002993659.1| 249 --------LENTLNVISPLTTY--ESPDFSIMEVIGKGRiNDRSM-E-VRYFLY--DeEKdGFTSMARVTGFTTAIV 311
                                       ........34334444444455..588999999999777665553.2.223333..32336**************** PP

                                       HHHHHTTSCTSSEEEEGGGS..CHHHHHHHHHHHHHC CS
                      Sacchrp_dh_C 228 aklildgkikkrGvvtpeelv.dpeiyeplleeLeke 263
                                       a+++++g +   Gv++pe l  +++ y +++ eL+k+
  gi|242398235|ref|YP_002993659.1| 312 ARIVAKGLCA-YGVIPPEVLGmREDTYIEIMRELKKR 347
                                       ******9644.7********9888***********97 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 !   63.7   0.0   1.8e-20     2e-17       1     130 []       3     113 ..       3     113 .. 0.95

  Alignments for each domain:
  == domain 1  score: 63.7 bits;  conditional E-value: 1.8e-20
                                       EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-S CS
                   Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnls 77 
                                       vli+GaG+vG+a+a++l+++f+    + v d s+++le+l      + +e+i++da+n  + L++++++ +lv+ ++
  gi|242398235|ref|YP_002993659.1|   3 VLILGAGNVGKAIAWDLKDEFE----VSVGDVSERRLEELS-----KFAETIKIDASNFNE-LVEIMRQFELVIGAL 69 
                                       89*****************985....59********88885.....4589***********.*************** PP

                                       SGGGHHHHHHHHHHHT-EEEESS-BCGCCSCHCCSHHHHHTHHHHHHCTSEEE CS
                   Sacchrp_dh_NADP  78 ppissldvlkaCietgvhyvdtsiskeertnyalreavlklkekakeagvtav 130
                                       p  ++ + +ka+i++gv+ vd+s+         + e+ ++l +ka++a+vt+v
  gi|242398235|ref|YP_002993659.1|  70 PGRFGYSTVKAAIKAGVDIVDVSF---------MPENPMELYDKAEKAQVTVV 113
                                       ************************.........******************97 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 !   24.4   0.1   1.3e-08   1.5e-05      30     101 ..       2      69 ..       1      93 [. 0.92

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 1.3e-08
                                       EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHCHHHHHHHHHHHH-SEEEE---B CS
                       AlaDh_PNT_C  30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvevlksqeellaeavkeadvvigtvli 101
                                       kvl++G+G +G +Aia   + + +V v Dv+++rle+l+++ ++ +++ +s+ ++l e +++ ++vig+  +
  gi|242398235|ref|YP_002993659.1|   2 KVLILGAGNVG-KAIAWDLKDEFEVSVGDVSERRLEELSKFAET-IKIDASNFNELVEIMRQFELVIGA--L 69 
                                       8**********.5888888889*********************9.***********************9..3 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0     3e-07   0.00033      14      82 ..       2      68 ..       1      93 [. 0.82
   2 ?   -2.4   0.0         4   4.5e+03      35      48 ..     190     203 ..     188     224 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 3e-07
                                      EEEEES-SHHHHHHHHHHHCC.T-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE- CS
                      Shikimate_DH 14 kvlliGaGemaelvakhLlak.gvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisa 82
                                      kvl++GaG++++ +a  L ++ +v    v  R le  +++ae +   +i a +++el e+++++++vi a
  gi|242398235|ref|YP_002993659.1|  2 KVLILGAGNVGKAIAWDLKDEfEVSVGDVSERRLEELSKFAETI---KIDASNFNELVEIMRQFELVIGA 68
                                      8*****************96644444445555555555555555...788*****************987 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4
                                       T-CEEEEEESSHHH CS
                      Shikimate_DH  35 gvkkvvvaNRtler 48 
                                       g+k+v + NR++e 
  gi|242398235|ref|YP_002993659.1| 190 GIKNVNIGNREFEA 203
                                       78999999999875 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 !   21.8   0.0   2.4e-07   0.00026       1      90 [.       1      89 [.       1     115 [. 0.76

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 2.4e-07
                                      EEEEEETTSHHHHHHHHHHHHTTTTE.EEEEEECSSHHHHHHHHHHTTHE..EESSHHHHHTCTTESEEEE-S-GGGHH CS
                      GFO_IDH_MocA  1 lrvaiiGaGkigskhlrplnesqrle.evvalldpdaeraeavaesfgve..aysdleelladpeidavivatpngthe 76
                                      ++v+i GaG++g+  +  +  ++++e  v  + +++ e+  ++ae+ +++   +++l e+++  + ++vi a p + ++
  gi|242398235|ref|YP_002993659.1|  1 MKVLILGAGNVGKAIA--WDLKDEFEvSVGDVSERRLEELSKFAETIKIDasNFNELVEIMR--QFELVIGALPGRFGY 75
                                      689**********997..77776677566668888899999999999999555555555555..9************** PP

                                      HHHHHHHHTT-EEE CS
                      GFO_IDH_MocA 77 elakaaleagkhvl 90
                                        +kaa++ag++++
  gi|242398235|ref|YP_002993659.1| 76 STVKAAIKAGVDIV 89
                                      ***********765 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.1   6.6e-07   0.00074       1      57 [.       3      57 ..       3     113 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 6.6e-07
                                      EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHH CS
                            TrkA_N  1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeglevvvgdatdeevLee 57
                                      ++i+G+G+vG+++a  L+++ + v+v d +e+r+eel+ +++e+++ da++ + L e
  gi|242398235|ref|YP_002993659.1|  3 VLILGAGNVGKAIAWDLKDEFE-VSVGDVSERRLEELS-KFAETIKIDASNFNELVE 57
                                      68*****************995.*************97.999*******99877766 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   1.6e-06    0.0018       1      97 [.       2      92 ..       2      94 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.6e-06
                                      EEEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEEGGGGGCTT-SEEEE-SCHHHH CS
                    Semialdhyde_dh  1 kvaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavkaleegkdlkvedvdeeelkevdivflalpagvs 79
                                      kv i+G  G+vG++++  L++++ev++  ++ ++ ++ +k+ae  k    +   ++++   e++++ ++v+ alp+   
  gi|242398235|ref|YP_002993659.1|  2 KVLILG-AGNVGKAIAWDLKDEFEVSVGDVSERRLEELSKFAETIK----IDASNFNE-LVEIMRQFELVIGALPGRFG 74
                                      799***.8*********************99999977777777766....66666666.66788*************** PP

                                      HHHHHHHHHTTSEEEESS CS
                    Semialdhyde_dh 80 kelapklaeagvkviDls 97
                                       + ++++++agv ++D s
  gi|242398235|ref|YP_002993659.1| 75 YSTVKAAIKAGVDIVDVS 92
                                      ****************98 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   6.8e-06    0.0077       1      87 [.       2      84 ..       2      94 .. 0.72
   2 ?   -2.2   0.0       5.7   6.3e+03      11      35 ..     312     334 ..     310     357 .. 0.54

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 6.8e-06
                                      EEEEETTSHHHHHHHHHHHHTTS-GGCEEEE..EESSCCCHHHHHHHHC-EEECEC.HHHHHHH-SEEEE-S-HHHHHH CS
                     F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivva..nsrnpekaeelaeelgvkvtavd.neeaaeeadvvvlavkpedvee 76
                                      k+ i+GaGn+g+a+a  l  +     e+ v+  ++r  e++ ++ae+++++++  +   e +++ + v+ a++ +   +
  gi|242398235|ref|YP_002993659.1|  2 KVLILGAGNVGKAIAWDLKDEF----EVSVGdvSERRLEELSKFAETIKIDASNFNeLVEIMRQFELVIGALPGRFGYS 76
                                      56799***********988774....55543114899999999999999888874314577778899998888777777 PP

                                      HHHHCGHHHHT CS
                     F420_oxidored 77 vlselakdalk 87
                                      +++++    ++
  gi|242398235|ref|YP_002993659.1| 77 TVKAA---IKA 84
                                      77666...445 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 5.7
                                       HHHHHHHHHHTTS-GGCEEEEEESS CS
                     F420_oxidored  11 gealasgllaagaqpheivvansrn 35 
                                       ++ +a+gl a g+ p e++ +  r+
  gi|242398235|ref|YP_002993659.1| 312 ARIVAKGLCAYGVIPPEVL-G-MRE 334
                                       5666777777776555555.4.333 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1     6e-06    0.0067       1      96 [.       1      90 [.       1     118 [. 0.85

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6e-06
                                      EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEBSSHHHHHHH-SEEEE-S-HHH CS
                            DapB_N  1 ikvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglgklgvavtddleevlekadvliDFTtpea 79
                                      +kv+++Ga G +Gk+++  ++++ ++ ++ + +r+      +++++++++ k++   +++l e++++++ +i       
  gi|242398235|ref|YP_002993659.1|  1 MKVLILGA-GNVGKAIAWDLKDEFEVSVGDVSERRL-----EELSKFAETIKIDASNFNELVEIMRQFELVIGALPGRF 73
                                      89*****9.************988888888888876.....89999****************************99999 PP

                                      HHHHHHHHHHTT-EEEE CS
                            DapB_N 80 vlenlklalekgvklVi 96
                                       ++++k+a+++gv++V 
  gi|242398235|ref|YP_002993659.1| 74 GYSTVKAAIKAGVDIVD 90
                                      9************9994 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   6.9e-05     0.077       5      89 ..       2      88 ..       1      94 [. 0.82
   2 ?    1.4   0.0      0.47   5.3e+02      26      60 ..     106     140 ..      99     144 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.9e-05
                                      EEEEETTTSHHHHHHHHHHHHHHECEEEEEEC-TT...TTTCEETTEEEES.CHHHHHHHC.TTTEEEEES-HHHHHHH CS
                       CoA_binding  5 kviviGagglgiaglyhfkeklkygikavfgvnpr...kvgtevlglpvyk.svdeleekt.evdvavitvPaesaqea 78
                                      kv++ Gag+ g+a++ + k++ +   ++v++v++r    +++  +++++   + +el+e + + +  + ++P ++ +++
  gi|242398235|ref|YP_002993659.1|  2 KVLILGAGNVGKAIAWDLKDEFE---VSVGDVSERrleELSKFAETIKIDAsNFNELVEIMrQFELVIGALPGRFGYST 77
                                      89*******************99...6788888872224555566776653167888888866**************** PP

                                      HHHHHHTT-SE CS
                       CoA_binding 79 vdelveagikg 89
                                      v+++++ag+  
  gi|242398235|ref|YP_002993659.1| 78 VKAAIKAGVDI 88
                                      ********976 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.47
                                       HHECEEEEEEC-TTTTTCEETTEEEESCHHHHHHH CS
                       CoA_binding  26 lkygikavfgvnprkvgtevlglpvyksvdeleek 60 
                                        k ++++vf+ +   + + +    +y+++delee 
  gi|242398235|ref|YP_002993659.1| 106 EKAQVTVVFDAGFAPGLSHIFLGRIYQEMDELEEA 140
                                       56789999999999999999999*********986 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   8.8e-05     0.099       1      46 [.       3      48 ..       3      66 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.8e-05
                                      EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHCEEEEET CS
                              ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr.rlealkknGlrltse 46
                                      ++ilGaG +G  +a+ L k   +v + + s+ rle+l+k   +++++
  gi|242398235|ref|YP_002993659.1|  3 VLILGAGNVGKAIAWDL-KDEFEVSVGDVSErRLEELSKFAETIKID 48
                                      68***************.66778888777777899998887777766 PP

>> GARS_N  Phosphoribosylglycinamide synthetase, N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00014      0.16       1      26 [.       1      26 [.       1     114 [. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00014
                                      EEEEEEESSHHHHHHHHHHTTSTTES CS
                            GARS_N  1 mkvLvvGsGGRehalawklaqspkve 26
                                      mkvL++G G   +a+aw l+++ +v+
  gi|242398235|ref|YP_002993659.1|  1 MKVLILGAGNVGKAIAWDLKDEFEVS 26
                                      9******************9986665 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 ?    9.8   0.0    0.0005      0.56       6      81 ..       2      82 ..       1      93 [. 0.71
   2 ?   -0.2   0.0      0.56   6.3e+02      24      91 ..     279     350 ..     276     352 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0005
                                      -EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-......HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHHHHHHHH CS
                              IlvN  6 kiaviGyGsqGhaqalnlrdsgldvvvglregs......ksvkkAkeegfevltvaeavkkadvvmiliPDelqkevye 78
                                      k+ ++G G+ G+a a  l+d  ++v vg  +++      k +++ k ++ +  ++ e++++ ++v+  +P ++  + ++
  gi|242398235|ref|YP_002993659.1|  2 KVLILGAGNVGKAIAWDLKDE-FEVSVGDVSERrleelsKFAETIKIDASNFNELVEIMRQFELVIGALPGRFGYSTVK 79
                                      799****************96.899999877763433223334444455566666677777888888777776666665 PP

                                      HHT CS
                              IlvN 79 eei 81
                                      ++i
  gi|242398235|ref|YP_002993659.1| 80 AAI 82
                                      555 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.56
                                       HHTT--EEEEE-TT-H..HHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHH...HHHHHHHHTGGG--TT-EE CS
                              IlvN  24 rdsgldvvvglregsk..svkkAkeegfevltvaeavkkadvvmiliPDel...qkevyeeeiepnlkegkal 91 
                                        d  ++v + l++++k   ++ A+ +gf+++ va +v+k      +iP e+   +++ y  ei+ +lk+ ++l
  gi|242398235|ref|YP_002993659.1| 279 NDRSMEVRYFLYDEEKdgFTSMARVTGFTTAIVARIVAKGLCAYGVIPPEVlgmREDTY-IEIMRELKKRDIL 350
                                       67788888888877764468899999****99999999999999999988633245566.6777778777766 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00015      0.16      38      91 ..       2      61 ..       1      73 [. 0.68

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00015
                                      EEEEES-SHHHHHHHHHHH.HTT-EEEEESSSHHHHH....CHHHHTC.EECSHHHHHHH CS
                      2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlk.afgmkviaydrskkkee....eeeelgv.elvsleellae 91
                                      +v i+G+G++G+a+a  lk +f++ v  ++ ++ +e     e+ +  + ++ +l e++++
  gi|242398235|ref|YP_002993659.1|  2 KVLILGAGNVGKAIAWDLKdEFEVSVGDVSERRLEELskfaETIKIDAsNFNELVEIMRQ 61
                                      799****************99999999988888766554331222222244455555555 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1   0.00073      0.82       1      44 [.       2      44 ..       2      89 .. 0.78
   2 ?   -1.2   0.0       1.4   1.6e+03       4      44 ..      65     107 ..      63     117 .. 0.78
   3 ?   -2.3   0.0       3.1   3.5e+03      16      73 ..     202     262 ..     196     266 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00073
                                      EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHH CS
                           3HCDH_N  1 kvaviGaGtmGagiaavfasagleVvlvdiseealekalekiek 44
                                      kv ++GaG +G+ ia   ++ ++eV + d+se++le+  + +e+
  gi|242398235|ref|YP_002993659.1|  2 KVLILGAGNVGKAIAWD-LKDEFEVSVGDVSERRLEELSKFAET 44
                                      6889**********987.5789**********999987765554 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.4
                                       EE--..SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHH CS
                           3HCDH_N   4 viGa..GtmGagiaavfasagleVvlvdiseealekalekiek 44 
                                       viGa  G  G +  +++++ag+++v v   +e   +  +k+ek
  gi|242398235|ref|YP_002993659.1|  65 VIGAlpGRFGYSTVKAAIKAGVDIVDVSFMPENPMELYDKAEK 107
                                       7888889999999999999999998877777766666666555 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 3.1
                                       HHHHHTT-EEEEE-S-HHHHHHHHHHHHH...HHHCCTTTTSS-HHHHCCCHHCEEEES-H CS
                           3HCDH_N  16 avfasagleVvlvdiseealekalekiek...sleklvekgklkeeeveaalarisfttdl 73 
                                       ++f+s gl+  l +i++++le+ + +      +++ l e g ++ e+ e++l+ is+ t +
  gi|242398235|ref|YP_002993659.1| 202 EAFVSDGLRSLLENINAKRLEEWTLRWPGhlaKMKILRELGFFSSENLENTLNVISPLTTY 262
                                       5677778888888888888887776666522234445566677788888888888777666 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 ?   10.7   0.0   0.00055      0.62       1     116 [.       7     114 ..       7     115 .. 0.78
   2 ?   -2.0   0.0       4.8   5.4e+03      56      67 ..     342     354 ..     326     359 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00055
                                       --SHHHHHHHHHHHH---SSEEEEEEEEESS.EEE-TTHHHHHT--CB---HHHHHHHH.S-EEEEE-S--HHHHTT CS
                     NAD_binding_3   1 GlGaiGsavleqlkrqqseielelvavadrd.sllskdrkallasealtldlddliahl.dpdvvVEcasseavael 75 
                                       G+G++G+a++  lk++    e+ +  v +r+  +lsk ++   + +   +++ +l++ + +  +v+ + + +   ++
  gi|242398235|ref|YP_002993659.1|   7 GAGNVGKAIAWDLKDEF---EVSVGDVSERRlEELSKFAE---TIKIDASNFNELVEIMrQFELVIGALPGRFGYST 77 
                                       99***********9987...69*********444444444...444445666666666637**************** PP

                                       HHHHHHTTEEEE-S--CGGG-HHHHHHHTSSSTTS--.EE- CS
                     NAD_binding_3  76 vlkaLkagkdvvtankgaladealyeeLreaaeangakiyv 116
                                       v +a+kag+d+v ++   ++ ++   eL+++ae++++++ +
  gi|242398235|ref|YP_002993659.1|  78 VKAAIKAGVDIVDVS---FM-PENPMELYDKAEKAQVTVVF 114
                                       ***********9888...44.56677888888888887766 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.8
                                       HHH.S-EEEEE-S CS
                     NAD_binding_3  56 ahl.dpdvvVEca 67 
                                       ++l + d++VE+ 
  gi|242398235|ref|YP_002993659.1| 342 RELkKRDILVEVN 354
                                       3334699999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 2666.87
//
Query:       gi|242398236|ref|YP_002993660.1|  [L=220]
Description: Probable ribosome biogenesis protein NEP1-like protein [Thermococcus sibiricus MM 739]
Scores for complete 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-49  167.1   0.0      4e-49  166.9   0.0    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 !  166.9   0.0   2.2e-53     4e-49       2     194 .]       5     215 ..       4     215 .. 0.92

  Alignments for each domain:
  == domain 1  score: 166.9 bits;  conditional E-value: 2.2e-53
                                       EEEEES--B--GG................SCGGSB--HHHHCGG.TTSTTGGGSS-CHHHHHHHHHHHCSCHHCTT. CS
                              EMG1   2 vLeeasLelvkvk................kkseqLLnsddhkkilkklkreakeaRpDIvHqcLlalldspLnkagl 62 
                                       ++++++Lelv+++                k++e LL+s++h+++lk+lk+ ++++RpDIvH cL+++l+s+Lnk+g+
  gi|242398236|ref|YP_002993660.1|   5 IIADSELELVPKElqnhpsiishakrrfkKPEEILLDSTYHHTALKSLKDGERRGRPDIVHLCLINALESILNKEGK 81 
                                       899************************************************************************** PP

                                       EEEEEEETTSEEEEE-TT----SSHHHHHHHHHHHHCCSEEEETTEE.SCEEEECS-HHHHCCC...SEEEEE-TTS CS
                              EMG1  63 lqvyihttknvlIevnpqtRiPrtfkrFagLmvqLLkklsirategeekLlkviknpitdhlpp..gskiillsesa 137
                                       l+vy+ht++n++I+++p+tR+Pr+++rF+gLm++L+k++ i+++     Ll++ ++++++++ +     +++++e++
  gi|242398236|ref|YP_002993660.1|  82 LRVYVHTRNNEVIYIKPETRLPRNYNRFVGLMESLFKNRVIPKDL---ALLRIENKTLSEIIGDigPDAVFIMHENG 155
                                       *****************************************9875...69*************99778899999999 PP

                                       EE-..................EEEE-SSSS....---HHEEESSSS---HHHHHHHHHHHCH CS
                              EMG1 138 ekklvdleefv.....vkpvvfvigamskgsvkidykeeeisisnypLsaavvcskiltafE 194
                                          l+++++f       ++ ++++g++++g+    ++ e+isi+++pL a+ v++++l ++E
  gi|242398236|ref|YP_002993660.1| 156 V--LMSPQSFGrklneYISPAVIVGGFPHGDFLSVLEGEKISIYKEPLMAWSVVNEVLINYE 215
                                       9..5567777666655557789********555566669*****************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); 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: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1440.97
//
Query:       gi|242398237|ref|YP_002993661.1|  [L=138]
Description: Translation initiation factor 5A [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.9e-12   46.1   0.7      6e-12   45.5   0.7    1.3  1  eIF-5a       Eukaryotic elongation factor 5A hypusine, DNA-bi
    0.00058   19.8   0.0     0.0015   18.5   0.0    1.8  1  EFP_N        Elongation factor P (EF-P) KOW-like domain
  ------ inclusion threshold ------
       0.11   12.6   0.3       0.22   11.6   0.3    1.5  1  EFP          Elongation factor P (EF-P) OB domain
       0.14   12.4   0.0       0.24   11.6   0.0    1.5  1  DNA_pol_B_3  DNA polymerase family B viral insert


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 !   45.5   0.7   1.3e-15     6e-12       1      69 []      70     134 ..      70     134 .. 0.96

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 1.3e-15
                                       --EEEEEEEEEE-SS.EEEEEE.TT--EEE.EEGG..GB-HHHHTT--TT-E..EEEEEETTEEEEEEE- CS
                            eIF-5a   1 nVkrkeyqLidIqdDgflsLmd.ddgetkeDlklpegelgkqikekfeegkdvlVtVlsamGeekiiavK 69 
                                       ++++k+ q+i+I++D +++Lmd +++++++ +++  + + ++ik+k++eg +  V++++++G+ ki+++K
  gi|242398237|ref|YP_002993661.1|  70 IIDKKTGQIIAITPD-TVQLMDmETYDLFD-VPIA-TGVNEEIKDKLKEGIN--VEYWETLGRIKIMKLK 134
                                       599************.*************9.8888.9*************99..*************988 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 !   18.5   0.0   3.3e-07    0.0015       2      33 ..       9      40 ..       8      59 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 3.3e-07
                                      GGG--TT-EEEETTEEEEEEEEEEEEETTS-- CS
                             EFP_N  2 aselkkGlvieidgklyvVlefehvkpGkGqa 33
                                      +s lk+G  i id++++++  +  + pGk ++
  gi|242398237|ref|YP_002993661.1|  9 VSKLKPGRYILIDDEPCRIANITVSSPGKHGS 40
                                      689*************************8553 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 ?   11.6   0.3   4.8e-05      0.22      11      44 ..      84     119 ..      82     123 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.8e-05
                                       TEEEEEETTT--EEEEEHH.HHTTGC.GG--TT-EE CS
                               EFP  11 deyvFMdnetYeqielpke.qlgdaa.kfLkEgmev 44 
                                       d++ +Md+etY+ + +p +  + +++ + LkEg +v
  gi|242398237|ref|YP_002993661.1|  84 DTVQLMDMETYDLFDVPIAtGVNEEIkDKLKEGINV 119
                                       67889*********9997744555555778887777 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 ?   11.6   0.0   5.3e-05      0.24      31      61 ..       3      51 ..       1     109 [. 0.63

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.3e-05
                       DNA_pol_B_3 31 dkisiFsevlstgnYvtiddnvlkilekki..................n 61
                                      dk+++  + l+ g Y+ idd++++i++ ++                   
  gi|242398237|ref|YP_002993661.1|  3 DKTRVQVSKLKPGRYILIDDEPCRIANITVsspgkhgsakarieavgiF 51
                                      7888888999****************99986666666666666655551 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 896.20
//
Query:       gi|242398238|ref|YP_002993662.1|  [L=288]
Description: Agmatinase [Thermococcus sibiricus MM 739]
Scores for complete 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-62  209.1   0.0      1e-61  208.9   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 !  208.9   0.0   5.8e-66     1e-61       2     279 ..      26     283 ..      25     284 .. 0.90

  Alignments for each domain:
  == domain 1  score: 208.9 bits;  conditional E-value: 5.8e-66
                                       EEEEEEEE--TTTSSSGGGGGHHHHHHHHHHTSBT.HCHEETTTTESCCSEEEEEEEEE--SSCHHHHHHHHHHHHH CS
                          Arginase   2 dvallGvPfdaagsgrpGarfGPraireasarlee.aleynlelgvleelkivdlgdvavtpvdneevleqieeava 77 
                                       d+++lG+Pfd+++s++pG+rfGP+ ir+a+ +le+  l y+++   l e++i+d+gd+a+ ++++ e++++   +v+
  gi|242398238|ref|YP_002993662.1|  26 DFVILGIPFDGTTSYKPGTRFGPTLIRQATLNLESyILDYDVD---LAEVRIADVGDLAIVAGNPLETIKRGVGTVE 99 
                                       689*******************************867777775...55************99888888888888888 PP

                                       HHHHT..TCEEEEEESSGGGHHHHHHHHHHHHSTTEEEEEESSS----SSCTTTBSSSTTSHHHHHHHHTSECGCEE CS
                          Arginase  78 eilka..gklpivlGGDHsialgilralaekygkplgvihfDAHaDlrtpetegsgnshGtpfrraaeegllkpkkl 152
                                       ei k   +++p+vlGG+Hs++++ ++al  k     + + fDAH+Dlr+++ e++ ++h+++ rr++ e  +   k+
  gi|242398238|ref|YP_002993662.1| 100 EIKKInpNAMPVVLGGEHSMTYAPVKALNPK-----SYVVFDAHLDLRESY-EENPWNHACVARRIS-ELGI---KV 166
                                       77554569********************976.....5699***********.99*************.4445...59 PP

                                       EEEEE-STCSHHHHHHHHTTSEEEEHHHHHHHHHHHHHHHHHHHHTCTTSEEEEEEEGGGBBTTTSTSSSS-BSS-B CS
                          Arginase 153 vqiGirsvdneeyelakelgirvitmreidelglkavveeilervgaeedpvylSfDiDvlDpavaPGtGtpepgGl 229
                                       + +Girs ++ee+e+a+e  i ++++r+    +     +ei +++   ++p+y+S+D+Dv+D +++P+tGtpe+gGl
  gi|242398238|ref|YP_002993662.1| 167 TEFGIRSGTKEEVEYARENDIPWVHARDYSITNF----KEIVKKL---PEPIYISIDVDVFDLSMVPSTGTPEAGGL 236
                                       ****************************998775....5666666...57*************************** PP

                                       -HHHHHHHHHHHHCHSEEEEEEEE-B-GGGSSTTTHHHHHHHHHHHHHHH CS
                          Arginase 230 tlrellallrelaeklnlvgaDvvEvnPaldteaeqtarlaarlvrelll 279
                                        + e++++l+ l e+++++g+D++Ev+   +  ++ ta++aa+l++  ++
  gi|242398238|ref|YP_002993662.1| 237 GFWEVIEALEWLVEHKRVIGFDIMEVAGM-EL-GDVTALTAAKLLFY-MI 283
                                       ***********9999************98.44.569********998.55 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1760.13
//
Query:       gi|242398239|ref|YP_002993663.1|  [L=572]
Description: Voltage-gated chloride channel protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.1e-81  273.9  43.7    2.7e-81  273.6  36.1    2.0  2  Voltage_CLC  Voltage gated chloride channel
    4.9e-14   52.5   0.0    3.1e-06   27.5   0.0    2.7  2  CBS          CBS domain


Domain annotation for each model (and alignments):
>> Voltage_CLC  Voltage gated chloride channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.3   0.8    0.0011        10     164     192 ..      14      42 ..       4      64 .. 0.81
   2 !  273.6  36.1     3e-85   2.7e-81       2     353 ..      68     410 ..      67     411 .. 0.96

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0011
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Voltage_CLC 164 lilfvllGilgGllgalfvrlllkverlf 192
                                       l+l +++Gi+gG+ +++f +l   ++ lf
  gi|242398239|ref|YP_002993663.1|  14 LLLSLIIGIVGGFGAVIFRKLISLMRGLF 42 
                                       677899************99998887665 PP

  == domain 2  score: 273.6 bits;  conditional E-value: 3e-85
                                       HHHHHHHCCCCC-GGGSC-SHHHHHHHCTTSS---HHHHHHHHHHHHHHHHCTT-S-BTHHHHHHHHHHHHHHHHHH CS
                       Voltage_CLC   2 ggllagllvklvapeaagsGipevkaalngvkgplslrvllvkflasvltvgsGlslGreGplvqiGAavgsglsrl 78 
                                       g+++++ ++k++ pe +g Gipev++a+  +kg+++   +l+k+la+ +t+gsG+s+GreGp+  iGA+++s ls+ 
  gi|242398239|ref|YP_002993663.1|  68 GSIMVAPIIKKY-PELKGNGIPEVIEAVIFKKGEIKGILALLKTLATSITIGSGGSVGREGPIGFIGASLASELSQY 143
                                       7889999*****.**************************************************************** PP

                                       TT.--SHHHHHHHHHHHHHHHHHHHT-HHHHHHHHCTTTSTSS--TTHHHHHHHHHHHHHHHHHHCTTS-S-.T--- CS
                       Voltage_CLC  79 lklsrndrdrrlvaaGaAAGiAAaFnaPlgGvlfalEevsrefslrallpvfvasvvaalvlrlllgeepafgeves 155
                                       ++ls++  ++ l ++G AAGiA +Fn+P +G++falE+v+  + + +l+p+f+++v+++ v+ lllge ++++ ++ 
  gi|242398239|ref|YP_002993663.1| 144 FNLSPEM-KKLLTTCGLAAGIAGTFNTPFAGAIFALEVVYMGIFSINLVPIFLSAVIGNTVTLLLLGEAFEVN-IPL 218
                                       **99888.999***************************999999999************************98.775 PP

                                       ...--GGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHCHHHHHHHHHHHHHHHHHHHCCCSCC..CSSSSCCH CS
                       Voltage_CLC 156 lfalsllelilfvllGilgGllgalfvrlllkverlfrkleklkikkrlepalvgllvgllglllpa.svlgggyel 231
                                       +  +   el++++++G+++G+l+a +++ l +++ +f+++   k++ +++++l+gl vg++g+++p+  +lg gye 
  gi|242398239|ref|YP_002993663.1| 219 QIVHAHIELLFLFFMGLIFGILAAYWAKFLFWLTDIFENV---KTPLWIKLLLGGLSVGFIGMFFPNyGILGVGYEG 292
                                       5556667*******************************99...899999*****************99********* PP

                                       HHHHCTT-S-HHHHHH...HHHHHHHHHHHHHCTT-CSBSHHHHHHHHHHHHHHHHHHHHHH-CTSSC...HHHHHH CS
                       Voltage_CLC 232 iasllegstlllsllllllllllkllataltlgsgvpgGifaPsLviGAalGrlvglvlalllpgaassdpgafalv 308
                                       ++ +++g    l+l+ll+ll + k+lat++ ++sg +gGifaPsL+iGA+lG ++g++l+ll+p+    +p+++al+
  gi|242398239|ref|YP_002993663.1| 293 MELAIAGL---LPLTLLILLGIGKMLATSIMISSGHSGGIFAPSLYIGALLGTAYGTILNLLFPNI-GINPAVYALA 365
                                       *******5...*****************************************************65.4479****** PP

                                       CCTHHHHHCCS-HHHHHHHHHHCC--GCCHHHHHHHHHHHHHHHC CS
                       Voltage_CLC 309 GmaaflagvtrapltaiviviEltgdlelllplmlavliAkavad 353
                                       Gmaaf++g ++ap+  i++v E+t++++ll+ ++++++++ ++a+
  gi|242398239|ref|YP_002993663.1| 366 GMAAFFSGLIQAPINQILMVAEITKGYTLLPGVITSATTSFLTAR 410
                                       ****************************************99987 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   1.9e-08   0.00017       1      53 [.     443     495 ..     443     498 .. 0.92
   2 !   27.5   0.0   3.5e-10   3.1e-06      13      54 ..     517     560 ..     505     562 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.9e-08
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53 
                                       V++imt ++v+v+   tl  + e+  ++g++++PVVde+ +++G+v  +D l+
  gi|242398239|ref|YP_002993663.1| 443 VKEIMTINPVFVYKWNTLNYVEEMVGKTGHDCFPVVDENMEVLGVVGVKDFLN 495
                                       89999999999999999999999998888*********************997 PP

  == domain 2  score: 27.5 bits;  conditional E-value: 3.5e-10
                                       ETTSBHHHHHHH.HHHHTSSEEEEE..ETTTBEEEEEEHHHHHHH CS
                               CBS  13 ppdttleealel.mrekgvsrlPVV..dedgklvGivtlrDllra 54 
                                       +p++t ++a+e+ m +++ + lP+V  +e+++l+G+vt+rD+ +a
  gi|242398239|ref|YP_002993663.1| 517 YPTETAHDAFEKlM-KYDQNLLPIVesPESKRLIGVVTKRDIYKA 560
                                       699*********56.9889888***999999***********886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (572 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.27s 00:00:00.87 Elapsed: 00:00:00.44
# Mc/sec: 3864.23
//
Query:       gi|242398240|ref|YP_002993664.1|  [L=457]
Description: Phosphoglucomutase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.9e-45  153.9   0.0    4.3e-45  152.8   0.0    1.6  1  PGM_PMM_I    Phosphoglucomutase/phosphomannomutase, alpha/bet
      1e-30  106.4   0.0    2.7e-30  105.0   0.0    1.8  1  PGM_PMM_II   Phosphoglucomutase/phosphomannomutase, alpha/bet
    3.7e-27   94.8   0.1    7.1e-27   93.9   0.1    1.5  1  PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/bet
    1.2e-14   54.2   0.1    3.9e-14   52.6   0.1    1.9  1  PGM_PMM_IV   Phosphoglucomutase/phosphomannomutase, C-termina


Domain annotation for each model (and alignments):
>> PGM_PMM_I  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.8   0.0   9.5e-49   4.3e-45       2     137 ..       3     139 ..       2     140 .. 0.97

  Alignments for each domain:
  == domain 1  score: 152.8 bits;  conditional E-value: 9.5e-49
                                       GGBBTTCEEEECCHCTBSCCHHHHHHHHHHHHCHHC..STS-EEEEEE-S-TTHHHHHHHHHHHHHCCT-CEEEEEE CS
                         PGM_PMM_I   2 qkfgtsGlRgkvgegeltpelveklgqaiaeylkae..akkkkvvvGrDtRvssrelaealaaglaanGvevillgl 76 
                                       ++fgt G+Rg+++ +++tpe+++k+g+a+++ lk+e  +k+  vv+GrDtRvs+++l++al++gl++ Gv+vi++++
  gi|242398240|ref|YP_002993664.1|   3 RIFGTFGVRGIAN-EKITPEFALKIGMAFGTLLKREqpDKELWVVIGRDTRVSGEMLKNALISGLLSVGVNVIDVEV 78 
                                       68***********.56*******************99999999********************************** PP

                                       B-HHHHHHHHHHCCECEEEEE--TTS-TTCCCEEEEETTTCE--CHHHHHHHHHHCCT-EE CS
                         PGM_PMM_I  77 lptPavsfairklkadagimitaSHnppeyngiKvylsnGgpispeveekIeaiiekeeea 137
                                       +ptPa++fa+++++ d+g +itaSHnppeyngiK++ +nG  +++e e+ +e+ ++k+e++
  gi|242398240|ref|YP_002993664.1|  79 APTPAIQFACKYFGTDGGAVITASHNPPEYNGIKLLEPNGLGLKKEREAIVEELFFKKEFY 139
                                       ********************************************************99987 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 !  105.0   0.0   5.9e-34   2.7e-30       2     103 .]     157     257 ..     156     257 .. 0.98

  Alignments for each domain:
  == domain 1  score: 105.0 bits;  conditional E-value: 5.9e-34
                                       HHHHHGGGTS-HHHHHHHT-EEEEE-TT-TTHHHHHHHHHHTT-EEEES-----TT-TTSS----TT-TTTTHHHHG CS
                        PGM_PMM_II   2 aYiealkekvdseaikksglkvvidplhGaggeilkellkelgvdvvelnaepdpdfptkapnpeekealkllielv 78 
                                       +Yi+ +k+kvd eaikk++  vv+d+ +Gag+ +l+ ll+elg++vv++na+pd++fp ++p+p+e e+l+ ++++v
  gi|242398240|ref|YP_002993664.1| 157 PYIDTIKAKVDVEAIKKRNPFVVVDTSNGAGSLVLPYLLRELGCKVVSVNAQPDGHFPARNPEPNE-ENLQGFMKIV 232
                                       7**********9999999888*********************************************.********** PP

                                       GGGG-SEEEEE-TTS-BEEEEETTE CS
                        PGM_PMM_II  79 kkegadlglafDgDaDRlgvvderG 103
                                       k+ +ad+g+a DgDaDR +++de+G
  gi|242398240|ref|YP_002993664.1| 233 KSLKADFGVAQDGDADRSVFIDENG 257
                                       ***********************98 PP

>> PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.9   0.1   1.6e-30   7.1e-27       2     112 ..     262     370 ..     261     372 .. 0.95

  Alignments for each domain:
  == domain 1  score: 93.9 bits;  conditional E-value: 1.6e-30
                                       HHHHHHHHHHHHHCHCSTTTCEEEEETTS-THHHHHHHHTT-EEEEESSSCHHHHHHHHHTTECEEEETTCEEEETT CS
                       PGM_PMM_III   2 gdqllallakylleeklkpgagvvktvmtslalervakklgiklvetkvGdkyvleemkeegavlGgEeSghiifld 78 
                                       gd+++al+ k++lee +k+g  vv+t+ ts+++++ ak +g+k+++tkvGd  v +++ e++ ++GgEe+g++if+d
  gi|242398240|ref|YP_002993664.1| 262 GDKTFALVVKAMLEE-NKGGL-VVTTIATSHIIDELAKMYGGKVLKTKVGDLIVSRALLEHNGLVGGEENGGVIFPD 336
                                       9************95.66565.******************************************************* PP

                                       TBSS--HHHHHHHHHHHHHHHTS-HHHHHHHHHH CS
                       PGM_PMM_III  79 eattkDGilaallvleilaetgkslselleellk 112
                                       ++  +DG++++++++ei a++gk+ sel+eel+k
  gi|242398240|ref|YP_002993664.1| 337 HVLGRDGAMTVAKIVEIFAKRGKKFSELIEELPK 370
                                       *****************************99886 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 !   52.6   0.1   8.7e-18   3.9e-14      10      65 ..     384     443 ..     373     447 .. 0.88

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 8.7e-18
                                       TT...EECCCCCTTH....HCCCCCCCCGCCEEEE.EEEETTCCEEEEEEEESSHHHHHHH CS
                        PGM_PMM_IV  10 ak.vvaalaallkva....sikeglkilledGrrlavRpSGTepllrvyvEaksdeelarl 65 
                                       +k +va++a++++++    ++ +g kil+edG++l +R+SGTep +r+ +Eaks+++++++
  gi|242398240|ref|YP_002993664.1| 384 RKaIVAKVAEIAEKEglkiDTTDGTKILFEDGWVL-IRASGTEPIIRIFAEAKSEKRAKEY 443
                                       345788888988888999*****************.********************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (457 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); 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: 0.69u 0.31s 00:00:01.00 Elapsed: 00:00:00.54
# Mc/sec: 2546.56
//
Query:       gi|242398241|ref|YP_002993665.1|  [L=460]
Description: Mannose-6-phosphate isomerase/mannose-1-phosphate guanylyl transferase [Thermococcus sibiricus MM 739]
Scores for 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-66  221.6   0.6    8.5e-66  220.5   0.6    1.6  1  MannoseP_isomer  Mannose-6-phosphate isomerase
      9e-62  208.9   0.1    1.5e-61  208.1   0.0    1.4  2  NTP_transferase  Nucleotidyl transferase
    4.2e-12   45.6   0.4    1.2e-11   44.1   0.1    1.8  2  Cupin_2          Cupin domain
    1.1e-07   32.4   0.0    2.4e-07   31.3   0.0    1.5  1  NTP_transf_3     MobA-like NTP transferase domain
    2.9e-05   24.0   0.0    5.4e-05   23.1   0.0    1.3  1  AraC_binding     AraC-like ligand binding domain
  ------ inclusion threshold ------
        0.1   12.6   0.1        0.3   11.1   0.1    1.7  1  Nit_Regul_Hom    Uncharacterized protein, homolog of nitrogen


Domain annotation for each model (and alignments):
>> MannoseP_isomer  Mannose-6-phosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  220.5   0.6   2.9e-69   8.5e-66       1     151 []     305     455 ..     305     455 .. 0.99

  Alignments for each domain:
  == domain 1  score: 220.5 bits;  conditional E-value: 2.9e-69
                   MannoseP_isomer   1 vGvedlvvvetkdavlvadkdkvqdvkkvveelkaegreeaelhrevyrPWGsyevldegeryqvkritvkPgekls 77 
                                       vGvedlv+++t da+lva+k + q+vk+v+++l ++++e+a +hr++yrPWGsy+vl+egery++kr+tv Pg +ls
  gi|242398241|ref|YP_002993665.1| 305 VGVEDLVIIDTGDALLVAKKGETQKVKEVYKKLIEKHDERALVHRTAYRPWGSYTVLEEGERYKIKRLTVLPGMRLS 381
                                       79*************************************************************************** PP

                   MannoseP_isomer  78 lqkhhhraehWvvvkGtakvtvddevlllkenestyiplgaihrlenpGkiplelievqsGsylgeddivrled 151
                                       +q+h+hr+ehWvvv+Gtakv+++d++lll+  est+ip+g+ihrlenpGk++le+ie q+G+ylgeddi r++d
  gi|242398241|ref|YP_002993665.1| 382 VQRHYHRSEHWVVVRGTAKVKIGDKELLLRPGESTFIPAGVIHRLENPGKVTLEVIETQIGEYLGEDDIERFQD 455
                                       ************************************************************************97 PP

>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  208.1   0.0   5.1e-65   1.5e-61       1     246 [.       2     272 ..       2     274 .. 0.93
   2 ?   -3.6   0.0       2.3   6.8e+03     203     220 ..     329     346 ..     319     370 .. 0.63

  Alignments for each domain:
  == domain 1  score: 208.1 bits;  conditional E-value: 5.1e-65
                                       EEEEE--S--GGGTTCCTTSSGGGSEETTET.ETTHHHHHHHHH.TT-SEEEEEEETTTHHHHHHHHTTSGGGTSEE CS
                   NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgke.rliqatlsrlan.sgieeiivvltqehsflveeqlkegskfgvev 75 
                                       k++ILaGG+GtRLwPL+r+l++k++    ++ +l+q+t++r+++ s+ +ei +v+++e +f+v + l+e      ++
  gi|242398241|ref|YP_002993665.1|   2 KTLILAGGKGTRLWPLSRKLMPKQFIRIFDNtSLFQKTMERALKfSNPKEIFIVTNREYNFRVLDDLNELGIDVPKE 78 
                                       579**********************9998888**********999***********************99844469* PP

                                       EEEEESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEEST..THHHHHHHHHTHSSTTSEEEEEEESS-CTTSEE CS
                   NTP_transferase  76 lialepegkgtAdAvalaaelledeksdelvlvLggDhlikd..ayeeavkkaiekaakgtvtfgivpveeateyGv 150
                                       +i+lep gk+t +A++++ +++e+++ +  v vL++Dhlik   +y +a++ka++ a ++ +tfgi+p++++t+yG+
  gi|242398241|ref|YP_002993665.1|  79 NILLEPVGKNTLPAIYWGMKIIEENYGKSKVAVLPSDHLIKVneDYIKAFEKAKKLATNYFITFGIKPTRPHTGYGY 155
                                       *****************************************999********************************* PP

                                       EEEC...TTS.BEEEEECS-SSHSHCSEECCSEEEEETTHHHHHHH.CCHHHTTSSCHHHHHHHHHHHTTEEEEEEC CS
                   NTP_transferase 151 iead...eeg.rverfvEKPkeakaselassGiYvfnsevllflak.dleelkrgedeitdilpkaleegkvalafl 222
                                       i+++   e+g +v +f+EKP+ ++a+ +++ G Y++ns+++lf  + ++ee kr ++e+++++++a e+ ++a++ +
  gi|242398241|ref|YP_002993665.1| 156 IKPGerlEGGyKVDEFKEKPDYETAKRYVENG-YYWNSGMFLFDSRlFIEEVKRVNPEVYQAFEEA-EDVEKAYEKV 230
                                       ****7663337*********************.********************************9.6667777755 PP

                                       STTEE...................-EEEXSSHHHHHHHHHHHH CS
                   NTP_transferase 223 fkdae...................yWsDvGtldslleanekla 246
                                        +  +                   yW+D+G++d+l+ea ek++
  gi|242398241|ref|YP_002993665.1| 231 PEV-SvdygvmektdkaaivplniYWNDLGSFDALYEAFEKDE 272
                                       555.34899*******************************997 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 2.3
                                       HHHHHHHHHHHTTEEEEE CS
                   NTP_transferase 203 eitdilpkaleegkvala 220
                                       +++++ +k++e++++ + 
  gi|242398241|ref|YP_002993665.1| 329 KVKEVYKKLIEKHDERAL 346
                                       445555555555544443 PP

>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       2.1   6.1e+03      33      49 ..     304     321 ..     300     325 .. 0.60
   2 !   44.1   0.1     4e-15   1.2e-11       5      68 ..     374     437 ..     371     439 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.1
                                       EEC.TEEEEEETTEEEEE CS
                           Cupin_2  33 tvd.geeveleaGdsvyf 49 
                                       tv+ +  v++ +Gd++++
  gi|242398241|ref|YP_002993665.1| 304 TVGvEDLVIIDTGDALLV 321
                                       455233567777777765 PP

  == domain 2  score: 44.1 bits;  conditional E-value: 4e-15
                                       EETTE..EEEEECSSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEEEE-SSS-EEEE CS
                           Cupin_2   5 lppGe..sapshrHpgedeffyVleGegeltvdgeeveleaGdsvyfpagtpHrfrNtgdeparll 68 
                                       + pG   s ++h+H+   e  +V++G+++++++++e  l++G+s ++pag+ Hr++N+g+  ++++
  gi|242398241|ref|YP_002993665.1| 374 VLPGMrlSVQRHYHRS--EHWVVVRGTAKVKIGDKELLLRPGESTFIPAGVIHRLENPGKVTLEVI 437
                                       4555524566777777..6999*************************************9888876 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 !   31.3   0.0   7.9e-11   2.4e-07       2     107 ..       4     128 ..       3     146 .. 0.83

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 7.9e-11
                                       EEEEESS-TTT....TT..THHHHCC.CCCCHHHHHHHHHCTT..-CEEEEECSHC...HHHHHHTTCTS-E....E CS
                      NTP_transf_3   2 viLAGGrSsRm....gg..dKallpl.ggkpllervldalraa.gvdevvvvggde...evlaalarlgvrv....v 63 
                                       +iLAGG+++R+     +  +K+++++ ++++l++ +++++ +  + +e+++v+++e    vl++l++lg++v    +
  gi|242398241|ref|YP_002993665.1|   4 LILAGGKGTRLwplsRKlmPKQFIRIfDNTSLFQKTMERALKFsNPKEIFIVTNREynfRVLDDLNELGIDVpkenI 80 
                                       7**********66642278********************9999569*********877789999*****99954444 PP

                                       E-TTSS-SHHHHHHHHHHHH....SSSCEEEEETT-TT.--HHHHHHH CS
                      NTP_transf_3  64 ededpgkgplaslaaalraaa...dadavlvlacDmPl.ltpelverl 107
                                         e+ gk++l +++ +++ ++   +++ v+vl+ D+   ++++ ++++
  gi|242398241|ref|YP_002993665.1|  81 LLEPVGKNTLPAIYWGMKIIEenyGKSKVAVLPSDHLIkVNEDYIKAF 128
                                       44777************88666679999*******8654666666665 PP

>> AraC_binding  AraC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   1.8e-08   5.4e-05      15      65 ..     381     430 ..     376     442 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1.8e-08
                                       SEEEETT-SEEEEEEEEE-EEEEETTEEEEE-TT-EEEE-TTS-EEEEE-T CS
                      AraC_binding  15 sfpphvhdeyvihyvteGtgrlrlngrtydlgpGdlfLlppgepHdyesds 65 
                                       s+++h h   ++ +v++Gt+++++++++  l+pG+  ++p g++H++e  +
  gi|242398241|ref|YP_002993665.1| 381 SVQRHYHRSEHW-VVVRGTAKVKIGDKELLLRPGESTFIPAGVIHRLENPG 430
                                       678888888887.578******************************99766 PP

>> Nit_Regul_Hom  Uncharacterized protein, homolog of nitrogen regulatory protein PII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   9.9e-05       0.3      29      63 ..     201     235 ..     198     245 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9.9e-05
                     Nit_Regul_Hom  29 fylieYkGlsPqewkgflleedpesaikiikdlse 63 
                                        ++ e k + P+ ++ f+ +ed e+a++ + ++s 
  gi|242398241|ref|YP_002993665.1| 201 LFIEEVKRVNPEVYQAFEEAEDVEKAYEKVPEVSV 235
                                       6999*************************999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (460 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       632  (0.0352502); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.66u 0.29s 00:00:00.95 Elapsed: 00:00:00.49
# Mc/sec: 2816.73
//
Query:       gi|242398242|ref|YP_002993666.1|  [L=243]
Description: Mannosyl-3-phosphoglycerate phosphatase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.1e-18   66.0   0.0    4.4e-16   59.4   0.0    2.1  1  Hydrolase_3  haloacid dehalogenase-like hydrolase
    0.00024   21.5   0.5      0.084   13.1   0.0    2.9  2  Hydrolase    haloacid dehalogenase-like hydrolase
    0.00057   20.3   0.0      0.034   14.6   0.0    2.5  2  HAD          haloacid dehalogenase-like hydrolase
     0.0022   17.5   0.0        2.6    7.5   0.0    2.6  2  S6PP         Sucrose-6F-phosphate phosphohydrolase
  ------ inclusion threshold ------
      0.074   13.2   0.0       0.27   11.4   0.0    1.9  2  Hydrolase_6  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 !   59.4   0.0   1.2e-19   4.4e-16       1     238 [.       4     232 ..       4     239 .. 0.74

  Alignments for each domain:
  == domain 1  score: 59.4 bits;  conditional E-value: 1.2e-19
                                       EEEEIIIIIS-TTS---HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEEEEGGGTEEECTTTEEEEE- CS
                       Hydrolase_3   1 ialDlDGTLlnsdkkisektkeaikklkekgikvviATGRslravlpvleelgldlpvialNGaliddekgkilyks 77 
                                       i+lDlD TL+ +d + +e +ke+++ lke+g+k+++ +     + +++   l+++ p+i  NG+ ++  k+   ++ 
  gi|242398242|ref|YP_002993666.1|   4 IFLDLDKTLIGDDYS-PEPAKETVNFLKERGFKIIFNSSKTRLEQEYYRSTLEVKDPFIVENGSAVYIPKNYFPFEF 79 
                                       89*********9999.6889**********************************************88877777888 PP

                                       -B-HHHHH.HHHHHHHHTT.CEEEEEESSEEEESTT.THHHHHHHHHCHCTCEEEESHHHHHCHCSESEEEEES-HH CS
                       Hydrolase_3  78 tiskedvk.eiikllkenn.veillytedkvyvlnkeksekkkkeeektkkkkeeidseeeledeeiakililkdke 152
                                       ++++ + + +ii+l   ++ ++ +l + ++ ++l++           + +++ eei  +++l++  +ak+   +++e
  gi|242398242|ref|YP_002993666.1|  80 PFTRGTQDyKIIELGTPYEiIKRILDKISTEFGLKY-----------YGNSSIEEIVRFTDLPR-RLAKL--ATQRE 142
                                       888655541566666665544444443333333333...........44444444444444444.55555..44555 PP

                                       HHHHHHHHHHHHCTTTE...EEEEESTTEEEEEETT-SHHHHHHHHHHHC.T--GGGEEEEESSGGGHHHHHHSSEE CS
                       Hydrolase_3 153 kldelekelksklnkll...titssskgyleimpkgvsKgtalkklakel.nisleeviafGDgeNDieMLeaaglg 225
                                        ++ l+k+ ks ++++l       s+++ +  +   ++Kg+a++ l++ + ++++ e +a+GDgeNDi+MLe++++ 
  gi|242398242|ref|YP_002993666.1| 143 YSETLFKWNKSGFEEKLkknGLKVSKGSRFYTVTGPTDKGKATRVLLNLYsKLEKVESYAVGDGENDIPMLEVVDNP 219
                                       5555555555555555555456666666666778889*********987736899999******************* PP

                                       EEETTS-HHHHHH CS
                       Hydrolase_3 226 vAmgnaseevkka 238
                                       +A+g + +++k++
  gi|242398242|ref|YP_002993666.1| 220 FAIGLSYNRAKNI 232
                                       ****888888876 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.5   0.1    0.0052        19     121     150 ..      20      49 ..       3      69 .. 0.77
   2 !   13.1   0.0   2.4e-05     0.084     187     210 .]     194     217 ..     128     217 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0052
                                       TTHHHHHHHHHHTTEEEEEEESSEHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 121 peaaeavasLkaagievvlltgdnpetaer 150
                                       + a+e+v+ Lk++g++++  ++  +  +e 
  gi|242398242|ref|YP_002993666.1|  20 EPAKETVNFLKERGFKIIFNSSKTRLEQEY 49 
                                       4577************99998887766665 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 2.4e-05
                                       TSTGGGEEEEESSHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 187 qgkpeevamVGDgvnDaaalaaAg 210
                                       + ++ e  +VGDg nD+++l+ ++
  gi|242398242|ref|YP_002993666.1| 194 KLEKVESYAVGDGENDIPMLEVVD 217
                                       36777899************9765 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.025        89       1      13 [.       4      16 ..       4      67 .. 0.81
   2 !   14.6   0.0   9.4e-06     0.034     149     188 .]     178     214 ..     152     214 .. 0.67

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.025
                               HAD  1 alfDfDgTLldgd 13
                                      +++D+D+TL+ +d
  gi|242398242|ref|YP_002993666.1|  4 IFLDLDKTLIGDD 16
                                      799******9886 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 9.4e-06
                               HAD 149 vrgegkvaalrewlaaegegidleevvayGDspsDlpllr 188
                                         ++gk++++   l+ + e+    e++a+GD+++D+p+l+
  gi|242398242|ref|YP_002993666.1| 178 PTDKGKATRVLLNLYSKLEKV---ESYAVGDGENDIPMLE 214
                                       334456666666555555555...59************96 PP

>> S6PP  Sucrose-6F-phosphate phosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.0   0.00073       2.6       3      61 ..       2      59 ..       1      76 [. 0.79
   2 !    7.4   0.0    0.0008       2.9     142     198 ..     161     214 ..     120     237 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00073
                                      EEEEE-TBTTTB.S-HHHHHHHHHHHH.GGGGGEEEEEE-SS-HHHHHHHHHHHT---- CS
                              S6PP  3 lllvsdLDntlvdgdnealarlnelleaeerkdvllvfaTGRsldsakellkeknllkP 61
                                      +++  dLD+tl+ gd+ + +  +e ++  +++ ++++f++ ++  +++  +   ++  P
  gi|242398242|ref|YP_002993666.1|  2 KVIFLDLDKTLI-GDDYSPEPAKETVNFLKERGFKIIFNSSKTRLEQEYYRSTLEVKDP 59
                                      68999*******.***9999999999999999999999998877776666666666655 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0008
                                       TTTS-EEEEEETTTEEEEEETT-SHHHHHHHHHHHH.T--GGGEEEEE-SGGGHHHHT CS
                              S6PP 142 kreldvkviyssgkdlDvlPkraskgeAlryLakkl.eleleqilvcGdsgnDeelli 198
                                       k++l+v    s g+ +  +   ++kg+A r L++ + +le  +   +Gd +nD+ +l+
  gi|242398242|ref|YP_002993666.1| 161 KNGLKV----SKGSRFYTVTGPTDKGKATRVLLNLYsKLEKVESYAVGDGENDIPMLE 214
                                       555544....5566666677789********99988468999************9994 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   7.6e-05      0.27       1      48 [.       4      51 ..       4      63 .. 0.86
   2 ?   -1.7   0.0      0.91   3.3e+03      87     101 .]     151     165 ..     134     175 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7.6e-05
                                      EEEESTTTSEETTEE-TTHHHHHHHHHHTT-EEEEEE---SS-HHHHH CS
                       Hydrolase_6  1 flfDidGvLwrgdkaipgaaealnalraagkpvvllTNnsskseeeya 48
                                      +++D+d +L+ +d   + a+e++n+l+++g ++++ + +++  +e y 
  gi|242398242|ref|YP_002993666.1|  4 IFLDLDKTLIGDDYSPEPAKETVNFLKERGFKIIFNSSKTRLEQEYYR 51
                                      579********************************9987776655555 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.91
                                       SXHHHHHHHHHTTXE CS
                       Hydrolase_6  87 geeglreelkeagfk 101
                                        + g++e lk++g+k
  gi|242398242|ref|YP_002993666.1| 151 NKSGFEEKLKKNGLK 165
                                       444555555555543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 1833.02
//
Query:       gi|242398243|ref|YP_002993667.1|  [L=394]
Description: Mannosyl-3-phosphoglycerate synthase [Thermococcus sibiricus MM 739]
Scores for 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-153  511.6   0.3   1.2e-153  511.4   0.3    1.0  1  Osmo_MPGsynth  Mannosyl-3-phosphoglycerate synthase (osmo_MPG


Domain annotation for each model (and alignments):
>> 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 !  511.4   0.3  6.6e-158  1.2e-153       4     387 ..       8     381 ..       5     382 .. 0.97

  Alignments for each domain:
  == domain 1  score: 511.4 bits;  conditional E-value: 6.6e-158
                     Osmo_MPGsynth   4 kserlgsvkihdvqrvleLdagkskksnksessetvsvseeeleevesklaivvpiknEelkvlegvlsgiPhdclv 80 
                                       + e +g+vki+++q+v+++d+++    +     +++++++e++++   +++ vvp+knE+l++++gvl++iPh++ +
  gi|242398243|ref|YP_002993667.1|   8 YKEIFGAVKIYELQKVIKMDTET----EDVPMFTVQNIPREDIYKTIGEMTTVVPMKNEKLHLVDGVLKAIPHKSPI 80 
                                       6789****************996....6777788999**************************************** PP

                     Osmo_MPGsynth  81 ilvSnssreevdkykaevellkefcraterqaiiihQkdpalaeafkaaglkelldetgklirnGKgEgmllgilla 157
                                       i+vSns+r++ +++k+ev+l+k+fc+ t+ ++i+ihQkdp+laeafk+ag++++lde+g l+r+GKgEgm++gilla
  gi|242398243|ref|YP_002993667.1|  81 IIVSNSKRKGPNRFKQEVDLVKHFCNLTHSKVIMIHQKDPGLAEAFKEAGYNDILDEKG-LVRSGKGEGMIVGILLA 156
                                       ***********************************************************.***************** PP

                     Osmo_MPGsynth 158 kllgkkyvgFiDaDnyvpgavnEYckafaaglalaksekphamvRikWasKpKvredelvfekeGRvSrvvNrwlNk 234
                                       k++g kyvgF+DaDny+pgavnEY+k +aag+ +++s  +++mvR++W++KpKv++++l+f+k+GRvS+++Nr+lN+
  gi|242398243|ref|YP_002993667.1| 157 KAIGAKYVGFVDADNYIPGAVNEYVKDYAAGFLMSES--EYTMVRLHWRHKPKVSKGTLYFKKWGRVSEITNRYLNQ 231
                                       *************************************..************************************** PP

                     Osmo_MPGsynth 235 llseieslaaeaeteiikTgnaGEhAmtleLalklrfatGyaiEpfelidllekfeskkpae.ekeaaekeveilQi 310
                                       l+se     +++et+i+ TgnaGEhAmt++La+ l f+tGy+iEp+e+++lle+f++ ++ae ++++ ++++ei+Q+
  gi|242398243|ref|YP_002993667.1| 232 LISEK----TTFETNIMVTGNAGEHAMTMKLAEILPFSTGYSIEPYEIVYLLERFGTWENAEeAQDVFDQGIEIFQL 304
                                       ****9....**********************************************7766655167789********* PP

                     Osmo_MPGsynth 311 etrNPHlHeekgeeHikemlaqglgtiyhsklaeeelkeelleelkeekvleegeeppkervypplekldlevfrev 387
                                       et+NPH+He+kg+eH+kem + +l tiyhskl++++lk+++le l+ +++++e+eeppk+ v++p++++d+++ +++
  gi|242398243|ref|YP_002993667.1| 305 ETLNPHFHEDKGQEHVKEMALLSLTTIYHSKLTSKRLKNSILEDLRMHGIIKENEEPPKPMVMKPIKDIDIKKWMKT 381
                                       ***********************************************************************998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); 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: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2501.42
//
Query:       gi|242398244|ref|YP_002993668.1|  [L=467]
Description: ADP-dependent glucokinase (GLK) [Thermococcus sibiricus MM 739]
Scores for complete 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-90  303.1   0.0    2.9e-90  302.9   0.0    1.0  1  ADP_PFK_GK  ADP-specific Phosphofructokinase/Glucokinase cons
  ------ inclusion threshold ------
       0.16   11.7   1.1        9.8    5.9   0.0    3.1  3  DUF2299     Uncharacterized conserved protein (DUF2299)


Domain annotation for each model (and alignments):
>> ADP_PFK_GK  ADP-specific Phosphofructokinase/Glucokinase conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  302.9   0.0   3.3e-94   2.9e-90       2     423 ..      32     459 ..      31     460 .. 0.92

  Alignments for each domain:
  == domain 1  score: 302.9 bits;  conditional E-value: 3.3e-94
                                       EEEEES--EEEEE.....HHHHHHHHCC-HH.HHHHHHC--SSBSSHHHHHHHHHHHHHHT--EEEEB--HHHHHHH CS
                        ADP_PFK_GK   2 kvavGynanvDai.....vdavelleklgleevkekseedhdeikskedlletfayffkkGaaaErfvenkelfeel 73 
                                        v+++yn+n+D+i     +d+++ ++++g e+v e  + + + i+s e l+ +++ ++k G+a E+fven+e+ + l
  gi|242398244|ref|YP_002993668.1|  32 GVLLAYNTNIDVIkylnkDDLERRINQIGKERVFEVIKAPTERISSLEHLFGGILRSIKLGKAIEWFVENEEIRRYL 108
                                       589**************99********************************************************** PP

                                       H....CC--SEEEEESHHHHHHHHHCC.TT-EEEEE-.---HHHHTTS-SS......EE....EEEEGGG-S-..-- CS
                        ADP_PFK_GK  74 vkaakklkkaelrmGGnagimanrlak.egakvllga.klskklkellsek......iv....vlgkpseaske.kd 137
                                            ++ ++elr+GG+agiman++    ++  ++++ +  k +++l+ +        +     l +p+ea ke ++
  gi|242398244|ref|YP_002993668.1| 109 R----EWGWDELRIGGQAGIMANLIGGvYRIPTIVHVpQNPKLQADLFVDGpiyvpiFEgkelKLVHPKEAVKEeNE 181
                                       *....5*********************556688899978888999******87766511666777889999998888 PP

                                       -EEEEEEE-TT-EETEEE-SS-EEEEEE--STCGGTS--HHHCTTHHHHH..-SEEEE--GGG--TB-TTSTCHHHH CS
                        ADP_PFK_GK 138 eiHlIlEykkgekwgeieapraNRfIissdpenlrlsileefkealkefk..pdllvlsGlqmleeqykegkereer 212
                                        iH+I E+++g ++ +i+apr+NRfI++ d+ n r+ + +efke+++++   ++l+++sGlq l+e+y++g+++++ 
  gi|242398244|ref|YP_002993668.1| 182 LIHYIYEFPRGFQVFDIQAPRENRFIANADDYNARVYMRKEFKESFEKIAkgVELAIISGLQVLKEYYSDGTTYRDV 258
                                       9***********************************************8889************************* PP

                                       HHHHHHHHHHHCC.T-EEEEE----S-HHHHHHHHHHCGGG-SEEEE-HHHHHHHHHHTT-HHHCCSS...CC--HH CS
                        ADP_PFK_GK 213 lekvkeqlkslkn.kikiHlElAsfqdeellkeilekilpyvdslGlnEqElanllsvlggeekeltevsdkepria 288
                                       l++v+++l+ l++  ++ H+E+A + ++ +++e++  il+++ s+GlnE Ela +++++g  e+  +ev   e ++ 
  gi|242398244|ref|YP_002993668.1| 259 LDRVESHLNILNRyGVRSHFEFAYTPNRLVREELIG-ILSKFTSVGLNEVELASIVEIIGD-ETLAKEV--LEGHVF 331
                                       ************99*********************9.**********************66.3333455..458999 PP

                                       HHHHHHHHHHH.....HHTT-SEEEEEETTEEEEEEETTSSS-HHHHHHHHHHHHHHHHHHHHH-SHHHHHHHH... CS
                        ADP_PFK_GK 289 kvlealrkllkllkkskkrkltrihvHtlayqiiltkkesewkneaakkalakaallAarkacnsdleklelkldds 365
                                        +++a+  l++     ++ ++ rih+Ht++y+++ltk    +++e+ ++al +a+l+Aa+ka + ++ek+  +  d 
  gi|242398244|ref|YP_002993668.1| 332 PIIDAINLLMD-----ET-GIDRIHLHTYGYYLALTK----YRSEEVRDALLFASLAAAAKAMKGNIEKIDHVK-DA 397
                                       9**********.....88.*****************4....67788889***************9888888777.67 PP

                                       ........HS-B-TT..HHHHHHHHCC.EETTEEEEEEE-B--SS-S--TTHHHHHHHHHHH CS
                        ADP_PFK_GK 366 fsvsks.kkiplnek..epvscweeei.eleevevclaPvlvckkpkkTvGlGDtISaaglv 423
                                       +sv ++ + i ++e+  ++++++e+   ++ + +++++P++++++pk+TvG+GDtIS++++v
  gi|242398244|ref|YP_002993668.1| 398 LSVPTNeRAIVFEEEleKEFTEFENGLiDMVDRQLAFVPTKIVTSPKSTVGIGDTISSSAFV 459
                                       777777799999999888888888888888999****************************8 PP

>> DUF2299  Uncharacterized conserved protein (DUF2299)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1      0.14   1.2e+03      71     116 ..       6      53 ..       1      68 [. 0.65
   2 ?    5.9   0.0    0.0011       9.8      14      45 ..     174     204 ..     164     208 .. 0.87
   3 ?    2.5   0.0     0.012   1.1e+02     101     129 ..     239     267 ..     222     270 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.14
                                       HHHHHHHHHHHHHHTTTT-EEEEE-TTS--.....-EEEEEEEEEGGG-- CS
                           DUF2299  71 eerkeflselkrdLlrlcvdfqlipqdeel....pqsiqvskeiykdglt 116
                                       +er ++ ++l ++  +++  + +ip+ e +     ++i v+k + kd+l+
  gi|242398244|ref|YP_002993668.1|   6 KERIKLWKNLYMN--AFENAVNAIPNVEGVllayNTNIDVIKYLNKDDLE 53 
                                       5666665555444..34444455555555556777889999999999885 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0011
                                       EE---TTEEEEEEEE-STT..-EEEEEEETT- CS
                           DUF2299  14 eevpdanaefhilveppqpggvvvdvikpkgk 45 
                                       e v+++n+  h++ e+p  g +v+d++ p+++
  gi|242398244|ref|YP_002993668.1| 174 EAVKEENELIHYIYEFPR-GFQVFDIQAPREN 204
                                       678899************.8*********986 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.012
                                       .-EEEEEEEEEGGG--HHHHHHHHHHHHH CS
                           DUF2299 101 pqsiqvskeiykdgltknelldavkrvrn 129
                                        + +qv ke y+dg t +++ld v+   n
  gi|242398244|ref|YP_002993668.1| 239 ISGLQVLKEYYSDGTTYRDVLDRVESHLN 267
                                       46789*****************9987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (467 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); 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 0.26s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 3407.84
//
Query:       gi|242398245|ref|YP_002993669.1|  [L=288]
Description: mRNA 3'-end processing factor [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0017   17.9   0.3      0.031   13.8   0.4    2.5  2  Lactamase_B_2  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.023   14.6   0.1      0.072   13.0   0.0    1.8  2  RMMBL          Zn-dependent metallo-hydrolase RNA specificity
       0.11   12.8   0.0       0.19   11.9   0.0    1.4  1  Sigma_reg_C    Sigma factor regulator C-terminal


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 !   13.8   0.4   5.2e-06     0.031      35     166 ..      17     120 ..       9     126 .. 0.82
   2 ?   -2.0   0.0      0.36   2.1e+03      69     113 ..     187     220 ..     161     229 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.2e-06
                                       E-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE- CS
                     Lactamase_B_2  35 llthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleeepavnvheldwgesfelgdggleitatpar 111
                                       + +haH DH+  ++ +  +rp         + l++l++ + y                + sf +g  + + ++ pa 
  gi|242398245|ref|YP_002993669.1|  17 FQSHAHSDHFVSADIIISTRP--------TKFLSHLKKAGFYKTYS-----------FERSFYVG--DYKAKLYPAG 72 
                                       668999999977777777665........46788888887664444...........44999999..5679999999 PP

                                       EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---..HHHHHHHCT-SEEEEE-S- CS
                     Lactamase_B_2 112 hksgrrldrnagdtlGlriegggkrvyyigDtgyip..eeigerlggadlllldita 166
                                       h+ g          + l i+ ++ +++y+gD++ ++   + + ++++ad+l++++t+
  gi|242398245|ref|YP_002993669.1|  73 HMLGS---------AQLYIKFDEFSLLYTGDVKWFKlrTAEKSEFRKADVLIIEATY 120
                                       99999.........9999******************9877789***********996 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.36
                                       HCCTTCGHHHCHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE CS
                     Lactamase_B_2  69 vleanfvylaleeepavnvheldwgesfelgdggleitatparhk 113
                                       v e+          ++v+++ ++ ++++ + +++ + +++ a h 
  gi|242398245|ref|YP_002993669.1| 187 VYEK----------FGVKFNNIEEDGEVVVRGFK-TKKPFDAIHP 220
                                       2222..........55666666666666665444.4455555554 PP

>> RMMBL  Zn-dependent metallo-hydrolase RNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.1       1.8   1.1e+04      15      30 ..      21      36 ..      18      40 .. 0.62
   2 ?   13.0   0.0   1.2e-05     0.072      12      36 ..     232     256 ..     229     266 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 1.8
                             RMMBL 15 gHadknellelirklk 30
                                      +H+d+    ++i +++
  gi|242398245|ref|YP_002993669.1| 21 AHSDHFVSADIIISTR 36
                                      8888755555555555 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 1.2e-05
                             RMMBL  12 dfSgHadknellelirklkprnvil 36 
                                        +S Had+ el ++i+k++p++++ 
  gi|242398245|ref|YP_002993669.1| 232 KLSNHADFWELVKIIEKVSPEKIYT 256
                                       5899******************986 PP

>> Sigma_reg_C  Sigma factor regulator C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   3.2e-05      0.19      33     128 ..      92     194 ..      76     207 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.2e-05
                       Sigma_reg_C  33 nlkllWyavdteeeekkeedkliseteaiGfkvnpsssekddkkkypkele......kaeehfislLkylsdqeeiv 103
                                         ++ W+ ++t e++++ +++++  ++ +G+++++    k+++kk   + e      k+ + + +++ + ++  +i+
  gi|242398245|ref|YP_002993669.1|  92 TGDVKWFKLRTAEKSEFRKADVLIIEATYGLPMYNFPTPKEAEKKLIAFVEevldrkKVPTLYANQMGKAQELLKIL 168
                                       66889*******************************88888888666666578888866666666666666666666 PP

                       Sigma_reg_C 104 ktleeslekek.lkerydyvkkngvk 128
                                       +   +s    + + ++ +  +k gvk
  gi|242398245|ref|YP_002993669.1| 169 DIHGYSARVSNgIRKVAKVYEKFGVK 194
                                       66655555555566666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); 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 0.28s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1864.97
//
Query:       gi|242398246|ref|YP_002993670.1|  [L=138]
Description: Probable glycine cleavage system H protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-47  159.6   2.6    3.3e-47  159.4   2.6    1.0  1  GCV_H            Glycine cleavage H-protein
      6e-08   32.4   2.1    6.1e-08   32.4   0.8    1.6  2  Biotin_lipoyl    Biotin-requiring enzyme
    2.9e-05   24.0   0.0    3.7e-05   23.6   0.0    1.3  1  RnfC_N           RnfC Barrel sandwich hybrid domain
  ------ inclusion threshold ------
      0.049   13.5   0.2        1.5    8.7   0.0    2.6  3  Biotin_lipoyl_2  Biotin-lipoyl like
       0.14   12.0   0.0       0.39   10.5   0.0    1.7  2  DnaA_N           DnaA N-terminal domain
       0.14   12.5   0.6        2.2    8.6   0.6    2.2  1  RNaseH_C         T4 RNase H, C terminal
        1.2    9.4   4.4          2    8.7   0.8    2.6  2  MazG             MazG nucleotide pyrophosphohydrolase domain


Domain annotation for each model (and alignments):
>> GCV_H  Glycine cleavage H-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.4   2.6   1.3e-50   3.3e-47       1     120 [.      17     136 ..      17     138 .] 0.97

  Alignments for each domain:
  == domain 1  score: 159.4 bits;  conditional E-value: 1.3e-50
                                       -EE-TTSEEEEEETT.EEEEEE-HHHHHHH-SEEEEE---TT-EE-TT-EEEEEEESS-EEEEE-SSSEEEEEE-GG CS
                             GCV_H   1 lyytkehewvkveedgvatvGitdfaqeelgdvvfvelpevgtkvkkgeslaavEsvKaasevyapvsGevvevNek 77 
                                       lyytk+hew +  edg++ vGi+d+aq+elgd+ +velpevg++v+kg+ l  vEsvKa+sevyapvsGev+evNe+
  gi|242398246|ref|YP_002993670.1|  17 LYYTKDHEWAQIMEDGTVLVGISDYAQKELGDLAYVELPEVGKEVSKGDVLCEVESVKAVSEVYAPVSGEVIEVNEE 93 
                                       79*************************************************************************** PP

                                       GTT-TTHHHH-TTTTT--EEEEES-GGGGGG.SEEHHHHHHHHH CS
                             GCV_H  78 leeepeliNkdpyeegWliklklsnleelee.Llsaeeyekllk 120
                                       lee pe iN+dpy ++W++k+k+snlee+ + L++ae+y+++l+
  gi|242398246|ref|YP_002993670.1|  94 LEEAPEKINEDPY-DAWIAKIKPSNLEEELKdLMTAEKYAEYLE 136
                                       *************.9**********9988777*********997 PP

>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       2.8   7.1e+03      25      25 ..      10      10 ..       2      19 .. 0.46
   2 !   32.4   0.8   2.4e-11   6.1e-08      22      58 ..      56      92 ..      50      98 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.8
                                      C CS
                     Biotin_lipoyl 25 d 25
                                      +
  gi|242398246|ref|YP_002993670.1| 10 E 10
                                      2 PP

  == domain 2  score: 32.4 bits;  conditional E-value: 2.4e-11
                                      STTCEE-TTSEEEEEECTTEEEEEEBSSSEEEEEESS CS
                     Biotin_lipoyl 22 kvGdkVkagqvlaeveamKmemeieapkaGvvkeilv 58
                                      +vG +V++g+vl+eve+ K++ e+ ap++G v e+  
  gi|242398246|ref|YP_002993670.1| 56 EVGKEVSKGDVLCEVESVKAVSEVYAPVSGEVIEVNE 92
                                      79*******************************9975 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 !   23.6   0.0   1.5e-08   3.7e-05      46      91 ..      55     101 ..      12     104 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 1.5e-08
                            RnfC_N  46 vkvgdkVlkGqkiaeaeg.fvsapvhasvsGtVkaiekrlvahgsgv 91 
                                        +vg +V kG+++ e e+    ++v+a+vsG+V+++++ l   ++++
  gi|242398246|ref|YP_002993670.1|  55 PEVGKEVSKGDVLCEVESvKAVSEVYAPVSGEVIEVNEELEEAPEKI 101
                                       479*************99556789*************9988877765 PP

>> Biotin_lipoyl_2  Biotin-lipoyl like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0   0.00059       1.5      21      36 ..      58      73 ..      56      75 .. 0.88
   2 ?    1.8   0.0     0.082   2.1e+02       3      17 ..      77      91 ..      75      92 .. 0.83
   3 ?   -3.0   0.0       2.7     7e+03      30      43 ..     110     123 ..     110     125 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00059
                   Biotin_lipoyl_2 21 GqrVkaGdvLaelDsr 36
                                      G++V +GdvL e +s 
  gi|242398246|ref|YP_002993670.1| 58 GKEVSKGDVLCEVESV 73
                                      99********999886 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.082
                   Biotin_lipoyl_2  3 vsIaapvsGrVaqln 17
                                       ++ apvsG V ++n
  gi|242398246|ref|YP_002993670.1| 77 SEVYAPVSGEVIEVN 91
                                      56889****999887 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 2.7
                   Biotin_lipoyl_2  30 LaelDsralqlala 43 
                                       +a + +++l+ +l+
  gi|242398246|ref|YP_002993670.1| 110 IAKIKPSNLEEELK 123
                                       78888888887775 PP

>> DnaA_N  DnaA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00015      0.39      14      36 ..     100     121 ..      90     127 .. 0.85
   2 ?    0.1   0.0      0.27   6.8e+02       9      27 ..     120     138 .]     117     138 .] 0.84

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00015
                            DnaA_N  14 elgeqsfdtWikplklfalknng 36 
                                       +++e+ +d Wi+++k+ +l +++
  gi|242398246|ref|YP_002993670.1| 100 KINEDPYDAWIAKIKPSNL-EEE 121
                                       799999**********999.544 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.27
                            DnaA_N   9 erLkkelgeqsfdtWikpl 27 
                                       e+Lk+ ++++++ ++++ l
  gi|242398246|ref|YP_002993670.1| 120 EELKDLMTAEKYAEYLESL 138
                                       6799999999999999876 PP

>> RNaseH_C  T4 RNase H, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.6   0.00086       2.2      52      73 ..     116     137 ..      53     138 .] 0.62

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00086
                                       HH-GGGHHHHS-HHHHHHHHHH CS
                          RNaseH_C  52 asdreelkkllteeeyaryken 73 
                                       ++ +eelk l+t e+ya y e 
  gi|242398246|ref|YP_002993670.1| 116 SNLEEELKDLMTAEKYAEYLES 137
                                       456799************9885 PP

>> MazG  MazG nucleotide pyrophosphohydrolase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1      0.14   3.7e+02      30      36 ..      43      49 ..      27      80 .. 0.83
   2 ?    8.7   0.8   0.00076         2      10      37 ..      90     126 ..      78     129 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.14
                                      HHHHHHH CS
                              MazG 30 eeELGDv 36
                                      ++ELGD+
  gi|242398246|ref|YP_002993670.1| 43 QKELGDL 49
                                      6888886 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00076
                                       HHHHHHHHHHHHHTT-HH.........HHHHHHHHHH CS
                              MazG  10 lleEvgEvaeaIkkedrd.........eleeELGDvL 37 
                                       + eE +E  e+I+++  d         +leeEL D++
  gi|242398246|ref|YP_002993670.1|  90 VNEELEEAPEKINEDPYDawiakikpsNLEEELKDLM 126
                                       457777777777774444556666666******9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 829.77
//
Query:       gi|242398247|ref|YP_002993671.1|  [L=37]
Description: hypothetical protein TSIB_0255 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 244.60
//
Query:       gi|242398248|ref|YP_002993672.1|  [L=458]
Description: MATE efflux family protein [Thermococcus sibiricus MM 739]
Scores for complete 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-64  215.8  35.6    6.6e-38  129.9   9.2    2.8  4  MatE             MatE
    9.4e-09   35.5  54.7    7.2e-07   29.4  24.6    4.8  4  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai
    5.5e-08   32.5  12.7    5.5e-08   32.5  12.7    3.1  3  Polysacc_synt    Polysaccharide biosynthesis protein


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 !  129.9   9.2   1.1e-41   6.6e-38       1     161 []      26     186 ..      26     186 .. 0.99
   2 ?   -2.5   0.3      0.58   3.5e+03      74      89 ..     200     215 ..     190     223 .. 0.51
   3 !   99.9  18.4   1.9e-32   1.1e-28       1     161 []     248     413 ..     248     413 .. 0.98
   4 ?   -3.9   0.2       1.6   9.8e+03      76      90 ..     425     439 ..     421     446 .. 0.57

  Alignments for each domain:
  == domain 1  score: 129.9 bits;  conditional E-value: 1.1e-41
                              MatE   1 PialenllesllslidtllvgrlgskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqgli 77 
                                       P+++ +l++sl++l+d ++v++lgs+al a++++++i++ l++++ gl++++++ +++++Ga n+k+a +++ +++i
  gi|242398248|ref|YP_002993672.1|  26 PMMVGMLVQSLYNLVDGIWVAGLGSNALVAIGLFFPIFMGLIALASGLGVGASSAISRRIGAQNKKGADNVADHAVI 102
                                       99*************************************************************************** PP

                              MatE  78 lllllsliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislislll 154
                                       ++l+l++++++l++  +e i+  +++++e++ela +y rililg+ ++++++v++gilrg g+tk+++y++++++ l
  gi|242398248|ref|YP_002993672.1| 103 TGLFLGVLLSVLLFPVIETIFVEMGATQEIVELAVKYSRILILGASVIVFNNVANGILRGEGDTKRSMYAMVLGSGL 179
                                       ***************************************************************************** PP

                              MatE 155 niplnyl 161
                                       ni+l+++
  gi|242398248|ref|YP_002993672.1| 180 NIILDPI 186
                                       ****986 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.58
                              MatE  74 qglilllllsliiall 89 
                                       ++++l++++   + ++
  gi|242398248|ref|YP_002993672.1| 200 YATLLSMIITSGFLIF 215
                                       3333333333333333 PP

  == domain 3  score: 99.9 bits;  conditional E-value: 1.9e-32
                              MatE   1 Pialenllesllslidtllvgrl.gskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqgl 76 
                                       P+al++l++s+  ++++ ++ r+ +s+a+A  + a++i++l +v+llg++ta+t++vg ++Gak+ ++++ a+ +++
  gi|242398248|ref|YP_002993672.1| 248 PSALAQLAMSFAMFFINTIIIRIgSSDAVAIFTSAWRIIMLGTVPLLGMATATTAIVGASYGAKDIEKLEIAYLYAI 324
                                       99*********************99**************************************************** PP

                              MatE  77 illlllsliiallvllfseqilslftqdee...vlelakrylrililgipalalqlvlsgilrgagktkvplyisli 150
                                       +l++l+ l++++++++f+ +i +lft++e    +++   r lril+l++p+  + +++ +++rg+g  + +l+++ +
  gi|242398248|ref|YP_002993672.1| 325 KLGFLVELLVTMFIFIFASPITYLFTYSEGaeqLANGLVRALRILALFLPFVPFGMLTGAMFRGIGQGEKSLIVTTL 401
                                       ****************************997889999999************************************* PP

                              MatE 151 sl.llniplnyl 161
                                       ++ + ++ ++y+
  gi|242398248|ref|YP_002993672.1| 402 RTiIMQVGFAYI 413
                                       **9999999997 PP

  == domain 4  score: -3.9 bits;  conditional E-value: 1.6
                              MatE  76 lilllllsliiallv 90 
                                       ++++++l+  ia+lv
  gi|242398248|ref|YP_002993672.1| 425 VWIGVALGNMIAALV 439
                                       555555555555553 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 ?    0.6   2.9     0.092   5.5e+02     100     139 ..      28      68 ..       5      85 .. 0.65
   2 ?   -1.1   0.2       0.3   1.8e+03      35      55 ..     101     121 ..      93     129 .. 0.71
   3 !   29.4  24.6   1.2e-10   7.2e-07       3     124 ..     141     279 ..     139     350 .. 0.83
   4 !   17.3   6.5   6.2e-07    0.0037       1      75 [.     365     442 ..     365     455 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.092
                   Polysacc_synt_C 100 vmgivvylllllllgllllaal..alllavlvgalvYlllll 139
                                       ++g++v  l++l+ g++    l  + l+a+++   ++++l+ 
  gi|242398248|ref|YP_002993672.1|  28 MVGMLVQSLYNLVDGIWVAG-LgsNALVAIGLFFPIFMGLIA 68 
                                       22222455666666666655.446777777777777766654 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.3
                   Polysacc_synt_C  35 lvigalvklilnllliplfgi 55 
                                       ++ g+++ ++l++ll p + +
  gi|242398248|ref|YP_002993672.1| 101 VITGLFLGVLLSVLLFPVIET 121
                                       566777777777777776654 PP

  == domain 3  score: 29.4 bits;  conditional E-value: 1.2e-10
                   Polysacc_synt_C   3 ailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplf..givGaaiatvlallvvavln..ly 75 
                                       +il+l++ ++++++v ++iL g g +k+ ++a+v+g  +++il  ++i+ +  g+vGaa+at+l++++++ ++  + 
  gi|242398248|ref|YP_002993672.1| 141 RILILGASVIVFNNVANGILRGEGDTKRSMYAMVLGSGLNIILDPIFIYTLglGVVGAAYATLLSMIITSGFLifWL 217
                                       79**********************************************8773367*************998884455 PP

                   Polysacc_synt_C  76 alrrllgikl.............ellrrllkpllaalvmgivvylllllllgllllaalall 124
                                       + +r + +++             ++lr  l  +la l+m+ ++++++ +++ + ++ a+a++
  gi|242398248|ref|YP_002993672.1| 218 FFKRDTYVDItlkdfdpnreifiDILRVGLPSALAQLAMSFAMFFINTIIIRIGSSDAVAIF 279
                                       66888888888899987776665555555688888888888888788887777777743333 PP

  == domain 4  score: 17.3 bits;  conditional E-value: 6.2e-07
                   Polysacc_synt_C   1 vLailalsiiflslstvlssiLqglgrqkialkalvi.galvklilnllli..plfgivGaaiatvlallvvavlnl 74 
                                       +L+ilal ++f  + +++++++ g+g+  + l+++ + ++++++++ +++     +g+ G+ i+ +l+ +++a++ +
  gi|242398248|ref|YP_002993672.1| 365 ALRILALFLPFVPFGMLTGAMFRGIGQGEKSLIVTTLrTIIMQVGFAYIFAfySDIGLSGVWIGVALGNMIAALVSF 441
                                       69*************************888777766526779*********66677999999999999998888876 PP

                   Polysacc_synt_C  75 y 75 
                                        
  gi|242398248|ref|YP_002993672.1| 442 T 442
                                       5 PP

>> Polysacc_synt  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.4   0.1    0.0034        20     205     235 ..      18      49 ..      14      60 .. 0.85
   2 !   32.5  12.7   9.2e-12   5.5e-08      54     265 ..      75     300 ..      57     302 .. 0.81
   3 !    3.2   9.8    0.0082        49      85     186 ..     332     442 ..     308     458 .] 0.64

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0034
                     Polysacc_synt 205 rellsfsapltisslaillytyidsi.llgll 235
                                       r  ++ s+p++++ l+ +ly+ +d i ++gl 
  gi|242398248|ref|YP_002993672.1|  18 RAVIKLSLPMMVGMLVQSLYNLVDGIwVAGLG 49 
                                       567889********************888865 PP

  == domain 2  score: 32.5 bits;  conditional E-value: 9.2e-12
                     Polysacc_synt  54 lGlnaalvreiakyrek...kelvslillnvllvllvlvllfllllliaaflglp....elavlylilalmllllvg 123
                                        G + a++r+i  +++k   +      +  ++l++l++vllf ++ +i++ +g++    elav y  + + ++ ++ 
  gi|242398248|ref|YP_002993672.1|  75 VGASSAISRRIGAQNKKgadNVADHAVITGLFLGVLLSVLLFPVIETIFVEMGATqeivELAVKYSRILILGASVIV 151
                                       577889********99998866666777778889999999999999999966655333389*****9******9999 PP

                     Polysacc_synt 124 vasfrrglfqglermkyaavsqvveqlsrvilvliavflfld.ivaavlgavlaalvg.givslavlrkkfr..... 193
                                       ++ + +g+++g  + k  +  +v+ +   +il  i++++ +  +v+a+ +++l+++++ g++ +++++k  r     
  gi|242398248|ref|YP_002993672.1| 152 FNNVANGILRGEGDTKRSMYAMVLGSGLNIILDPIFIYTLGLgVVGAAYATLLSMIITsGFLIFWLFFK--Rdtyvd 226
                                       999****************************97777777664466666666666655513444444443..255789 PP

                     Polysacc_synt 194 .prfvils.lklvrellsfsapltisslaillytyidsillglllgaeavGiYnaayqllvaisgllapivtaa 265
                                          + +   ++ + ++l++++p  + +la ++  ++   ++ ++ +++av+i++ a ++ ++ ++ l  ++ta+
  gi|242398248|ref|YP_002993672.1| 227 iTLKDFDPnREIFIDILRVGLPSALAQLAMSFAMFFINTIIIRIGSSDAVAIFTSAWRIIMLGTVPLLGMATAT 300
                                       8666666669************************99999999**********************9999999865 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.0082
                     Polysacc_synt  85 llvlvllfllllliaa........flglpelavlylilalmllllvgvas...frrglfqglermkyaavsqvveql 150
                                       llv++ +f+++ +i +           +  l+  ++ilal+l++++++++   ++rg+ qg +    +++++++ q+
  gi|242398248|ref|YP_002993672.1| 332 LLVTMFIFIFASPITYlftysegaEQLANGLVRALRILALFLPFVPFGMLtgaMFRGIGQGEKSLIVTTLRTIIMQV 408
                                       44555555555555447768888877777788888899988888877775222577778888888888888888888 PP

                     Polysacc_synt 151 srvilvliavflfldivaavlgavlaalvggivsla 186
                                       +++ +++++   ++ + ++ +g +l+++++++vs++
  gi|242398248|ref|YP_002993672.1| 409 GFA-YIFAFYSDIG-LSGVWIGVALGNMIAALVSFT 442
                                       877.4444444444.556666666666666555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (458 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       730  (0.0407162); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 2977.83
//
Query:       gi|242398249|ref|YP_002993673.1|  [L=43]
Description: hypothetical protein TSIB_0257 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       173  (0.00964917); expected 358.6 (0.02)
Passed bias filter:                      160  (0.00892409); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.47
# Mc/sec: 275.71
//
Query:       gi|242398250|ref|YP_002993674.1|  [L=958]
Description: Leucyl-tRNA synthetase [Thermococcus sibiricus MM 739]
Scores for complete 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  220.6   2.1      1e-64  218.9   2.1    1.8  1  tRNA-synt_1    tRNA synthetases class I (I, L, M and V)
    2.7e-29  102.1   0.7    7.1e-29  100.7   0.7    1.7  1  Anticodon_1    Anticodon-binding domain of tRNA
    7.4e-23   80.9   0.5    3.3e-10   39.3   0.0    2.5  2  tRNA-synt_1g   tRNA synthetases class I (M)
    5.8e-10   39.0   0.3    1.8e-09   37.4   0.2    1.8  1  tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
    6.1e-09   35.6   1.1    0.00064   19.2   0.0    3.0  3  tRNA-synt_1e   tRNA synthetases class I (C) catalytic domain
     0.0012   17.9   0.0      0.045   12.7   0.0    2.4  2  tRNA-synt_1f   tRNA synthetases class I (K)


Domain annotation for each model (and alignments):
>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  218.9   2.1   3.5e-68     1e-64       1     601 [.      10     681 ..      10     682 .. 0.87

  Alignments for each domain:
  == domain 1  score: 218.9 bits;  conditional E-value: 3.5e-68
                       tRNA-synt_1   1 klyekWeeedvfkkelekekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaie 77 
                                       k+++kW ee+vf+++   +++ ++f +++  Py  G+lH+Gha + t+ d++ r+krm+G++vl+ + w   G +i 
  gi|242398250|ref|YP_002993674.1|  10 KWQNKWLEEKVFEPQ--MDEKVPKFYITVAFPYLSGHLHVGHARTYTIPDVIARFKRMQGYNVLFPMAWHITGSPIV 84 
                                       5899***********..8889*******************************************************7 PP

                       tRNA-synt_1  78 akvekklgakekkerkklgr.eef.rekvr......ewkaeyaeeirkqvkrlGvsvDfdreylT..ldkeleeavk 144
                                           +++ +++ ++++ +    +   +  +      +++++++++ r+++ r G svD++re  T  l + +++ ++
  gi|242398250|ref|YP_002993674.1|  85 GI-AERIKHRDPQTVYLYRDiYKVpEDILWsfedpiNIVKYFMKTARETFIRAGFSVDWSREFHTtsLFPPFSKFIE 160
                                       65.556678888887766421222123445111111568899********************998456799****** PP

                       tRNA-synt_1 145 evfvrladkgliyrgkklvnwstklktalselEv.eykdkk.dalihvafpladkee.vklviaTTtPeTllgdtav 218
                                       + f +l +kgl+ +g++ v w++ + t+l + +  e +d++    + ++f l+++ e ++l +aT +PeT+ g t +
  gi|242398250|ref|YP_002993674.1| 161 WQFLKLKEKGLVVKGTHYVRWDPIVGTPLGDHDLiEGEDVQiLDYVLIKFILEENGEvAYLPAATLRPETVYGVTNM 237
                                       *********************************867788873235679999977665489***************** PP

                       tRNA-synt_1 219 avnpeldyv.......itkeklilaeallkslvkkesekkiledergkeLegkevelplvnrkipiiaddyvdkeaG 288
                                        +npe  yv         +e +i+ +    +l  +++e +ile+++g++L+gk v++p+++ +i i+  d+vd ++ 
  gi|242398250|ref|YP_002993674.1| 238 WLNPEATYVkakiknkDIEEVWIITKEAAYKLSFQDKEIEILEEFKGEKLIGKWVKNPVTEDEIIILPADFVDPDNA 314
                                       *********999876444567788888888888888888************************************** PP

                       tRNA-synt_1 289 tGvVkiaPahdedDyevgk..kynlevinildedgtlteea.................................... 327
                                       tGvV   Pah + D+++ +  k n ++++  d d ++ e++                                    
  gi|242398250|ref|YP_002993674.1| 315 TGVVMSVPAHAPFDHAALEdiKKNTNLLVKYDIDPRIVENItyvsliklegygefpavdeseklsvksqkdvekleq 391
                                       ***************987622567788888888889999989999999999************************** PP

                       tRNA-synt_1 328 .................aefeglkvfdarkkvveelkekglllkaekiehsvpfcerskkpiiyrateqWfvrvke. 386
                                                        + ++g  v + ++ v ++++ekg   ++ +++ +  ++  ++  ++  + +qWf+   + 
  gi|242398250|ref|YP_002993674.1| 392 atkniykaeyhrgifkiEPYKGKPVSEVKDLVAKDMTEKGIADRMYEFSDKNVISRFGNRAVVKIIHDQWFIDYGNp 468
                                       ***************************************************99999999**************9886 PP

                       tRNA-synt_1 387 .ladaalkavekvqfvpkskekryaswleniqdWciSRqrwWGhripl...fvsketeevvvreelkelvagreeee 459
                                         +++a +a+ ++++ p+s++++++ +le     +  R+   G+++p    +v ++  + ++      + +++++  
  gi|242398250|ref|YP_002993674.1| 469 eWKAKAREALANMKILPESRRTQFEAILEWLDKKACVRKVGLGTPLPWdpeWVIESLSDSTIYMAYYTISRAINKYG 545
                                       68999999999********************99999**********7545599999999888788888888889999 PP

                       tRNA-synt_1 460 aekkalekeakdklkkekgelekdedvlDvWFsSgswpfstlgypeedteelkkffpadmlleGlDiirgWvarlil 536
                                        + ++l  e+ d l  e+++  ++e+      +   +p   l    e +ee++  +p d   +  D i   ++  i+
  gi|242398250|ref|YP_002993674.1| 546 IKGEQLVPEVFDYLFLEEKSEAREEEL----SEKTDIPKEFLR---EMKEEFEYWYPLDWRCSAKDLIPNHLTFFIF 615
                                       999999999999995554454555554....245556776666...5589*************************** PP

                       tRNA-synt_1 537 lslaltgsePf.kevlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltli.lsdvgrdinl 601
                                         +a++ ++ + + + v+g+ +  eG KmSKs+gNv++ +d i++ gad++Rl+++ l++  +d ++
  gi|242398250|ref|YP_002993674.1| 616 NHVAIFRKKHWpRGIAVNGFGT-LEGAKMSKSKGNVLNFIDAIEENGADVVRLYIMsLAEHDSDFDW 681
                                       ****999886636799999975.68******************************988888887766 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 !  100.7   0.7   2.4e-32   7.1e-29       1     148 [.     717     849 ..     717     854 .. 0.87

  Alignments for each domain:
  == domain 1  score: 100.7 bits;  conditional E-value: 2.4e-32
                       Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkraaqevllevletllrll 77 
                                       d+w+l+++nk++k +tea+ee+r ++a++ +++ ++ndl +wy++ ++ r + ++       +++l++++  ++rl+
  gi|242398250|ref|YP_002993674.1| 717 DKWLLHRVNKAIKGTTEALEEFRTRTAVQWAFYSILNDL-RWYMRRTEGRDDEAK-------RSTLRKLAGVWVRLM 785
                                       9**************************************.********9974433.......39************* PP

                       Anticodon_1  78 aPfmPfitEelwqreeeelgkkesimlaewpekaeel.ekeleeeevellkeivkairklrselkikpssel 148
                                       aPf+P+i+Eelw    e+lg++ +++laewpe  ee+ +k++ e e e+   i ++i++++++  +++ +++
  gi|242398250|ref|YP_002993674.1| 786 APFTPHICEELW----ERLGGEGFVSLAEWPEPVEEWwNKTI-ELEEEY---IKTLIEDIKEIVSVAKLENA 849
                                       ************....9**************96666675555.447777...88888888888888776664 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 !   39.3   0.0   1.1e-13   3.3e-10       2      60 ..      33      91 ..      32     116 .. 0.87
   2 !   39.2   0.1   1.1e-13   3.4e-10     269     371 ..     587     686 ..     575     694 .. 0.84

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 1.1e-13
                                      EEEE--B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHTT CS
                      tRNA-synt_1g  2 lvttalpYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAekeg 60
                                      ++t+a+pY +g+lH+Gh++++ + D++aR+kr++g++vlf  +    G pi   Ae+ +
  gi|242398250|ref|YP_002993674.1| 33 YITVAFPYLSGHLHVGHARTYTIPDVIARFKRMQGYNVLFPMAWHITGSPIVGIAERIK 91
                                      8******************************************9999999998887654 PP

  == domain 2  score: 39.2 bits;  conditional E-value: 1.1e-13
                                       SGGGG.G--S......EEEEEGGGHHHHHTHHHHHHHH..TT----S-EEEE--EEE--------------HHHHHH CS
                      tRNA-synt_1g 269 eekwkeyWakdkevelvhfigkdiikFHtifwPaillg..aelklpkkvvaheyltvegkKlSkSrgvvvkakeale 343
                                       +e+++ ++  d         +kd i+ H  f+     +   + + p+ ++++++ t+eg+K+SkS+g+v    +a+e
  gi|242398250|ref|YP_002993674.1| 587 KEEFEYWYPLD-----WRCSAKDLIPNHLTFFIFNHVAifRKKHWPRGIAVNGFGTLEGAKMSKSKGNVLNFIDAIE 658
                                       55666444221.....344589******9999888888889999********************************* PP

                                       HH-HHHHHHHHHHHS-TTS-EEE-HHHH CS
                      tRNA-synt_1g 344 rldadllRYylaaeapekkDldfswedf 371
                                       +  ad++R y+++ a++++D+d++ +++
  gi|242398250|ref|YP_002993674.1| 659 ENGADVVRLYIMSLAEHDSDFDWKRSEV 686
                                       **************99999999887765 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 !   37.4   0.2   6.1e-13   1.8e-09      22     126 ..     220     329 ..     206     358 .. 0.73

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 6.1e-13
                     tRNA-synt_1_2  22 klevfttrpdtlfGvtfvalapehplvekl..aekkkelaafieevkkk.seserelet.kekeGv.ftglkaihPi 93 
                                        l   t rp+t++Gvt + l pe   v++   +++ +e+   ++e++ k s +++e+e  +e +G    g  + +P+
  gi|242398250|ref|YP_002993674.1| 220 YLPAATLRPETVYGVTNMWLNPEATYVKAKikNKDIEEVWIITKEAAYKlSFQDKEIEIlEEFKGEkLIGKWVKNPV 296
                                       5667799******************999873344445555555555544133333333313456665899******* PP

                     tRNA-synt_1_2  94 tgekipiwvanyvlmeygtgavmavPahdqrDf 126
                                       t+++i i  a++v  +  tg+vm+vPah   D+
  gi|242398250|ref|YP_002993674.1| 297 TEDEIIILPADFVDPDNATGVVMSVPAHAPFDH 329
                                       ****************************87666 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 !   14.1   0.0   7.6e-06     0.023      20      50 ..      42      72 ..      21      90 .. 0.86
   2 !   19.2   0.0   2.2e-07   0.00064     209     296 ..     597     686 ..     587     691 .. 0.84
   3 ?   -2.9   0.2       1.1   3.3e+03     103     135 ..     835     866 ..     816     917 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7.6e-06
                                      TS--BHHHHHHHHHHHHHHHHHHHTT-EEEE CS
                      tRNA-synt_1e 20 ydashlGhaRslvafDilrrilqalgYdvqf 50
                                        + h+GhaR++ + D+++r+ +++gY+v f
  gi|242398250|ref|YP_002993674.1| 42 SGHLHVGHARTYTIPDVIARFKRMQGYNVLF 72
                                      4679*************************88 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 2.2e-07
                                       EEEEEEGGGTTTHHHHHHHHHHHHSS.S--EEEEEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHS.S CS
                      tRNA-synt_1e 209 dihsGGiDLafPhhenelaqseaafd.kqlvkyflhnghlkiegekmsksLknfitikdvlkkfdprqlRlllls.a 283
                                       d  +  +DL+  h    +  + a f  k++ +    ng+ ++eg kmsks +n++   d++++  + ++Rl+++s a
  gi|242398250|ref|YP_002993674.1| 597 DWRCSAKDLIPNHLTFFIFNHVAIFRkKHWPRGIAVNGFGTLEGAKMSKSKGNVLNFIDAIEENGADVVRLYIMSlA 673
                                       666677788777777778888888887889999999**********************************9887636 PP

                                       -TTS-EEE-HHHH CS
                      tRNA-synt_1e 284 hyrsqldfkeell 296
                                       ++ s +d+k +++
  gi|242398250|ref|YP_002993674.1| 674 EHDSDFDWKRSEV 686
                                       8889999988776 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 1.1
                                       GGHHHHHHHHHHHHHTTSEEE-TTS-EEE-GGG CS
                      tRNA-synt_1e 103 ekvdeiielvekliekgyaYavsdgdvyfdvsk 135
                                       e ++ei+  v+kl +   aY  + ++ +++v +
  gi|242398250|ref|YP_002993674.1| 835 EDIKEIVS-VAKLENAKRAYIYTAEEWKWKVAQ 866
                                       34444443.456666555555555555554443 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 ?    2.6   0.0     0.018        53      25      61 ..      34      69 ..       9     109 .. 0.77
   2 !   12.7   0.0   1.5e-05     0.045     266     322 ..     627     682 ..     601     721 .. 0.71

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.018
                      tRNA-synt_1f 25 vvvesGispSGliHiGnlrevltadlvaralrkrgee 61
                                      ++v+  +  SG++H+G +r    +d++ar  r +g +
  gi|242398250|ref|YP_002993674.1| 34 ITVAFPY-LSGHLHVGHARTYTIPDVIARFKRMQGYN 69
                                      4444444.6******************9987777665 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 1.5e-05
                      tRNA-synt_1f 266 PekvvYelillkggekmssSkGnvltledwlevaepevlrflilrrkPkkakkldld 322
                                       P ++  + ++  +g+kms+SkGnvl   d++e    +v+r++i++   ++  ++d +
  gi|242398250|ref|YP_002993674.1| 627 PRGIAVNGFGTLEGAKMSKSKGNVLNFIDAIEENGADVVRLYIMS-LAEHDSDFDWK 682
                                       666666777778899*************************99988.55555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (958 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       885  (0.0493614); 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:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.83u 0.37s 00:00:01.20 Elapsed: 00:00:00.58
# Mc/sec: 4933.06
//
Query:       gi|242398251|ref|YP_002993675.1|  [L=417]
Description: Archaeal ATPase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0025   17.9   0.0      0.012   15.6   0.0    2.1  2  AAA_14    AAA domain
  ------ inclusion threshold ------
      0.025   15.0   0.0       0.13   12.7   0.0    2.2  2  AAA       ATPase family associated with various cellular acti
      0.062   13.8   3.1        1.8    9.0   3.1    2.5  1  DUF234    Archaea bacterial proteins of unknown function


Domain annotation for each model (and alignments):
>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0     2e-06     0.012       3      88 ..      21     103 ..      19     128 .. 0.61
   2 ?   -1.4   0.0      0.37   2.2e+03       3      18 ..     144     159 ..     142     167 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2e-06
                            AAA_14   3 kilvitGaRrvGKTtllkqlikell....vkkesilyinldderdkkladpekllelileklkeekktylflDEiqe 75 
                                       k l++ G R++GKT+++++ +k +     ++ ++i++i+  +   ++++++   ++++  +l   k+  +++DE ++
  gi|242398251|ref|YP_002993675.1|  21 KWLLVYGRRKTGKTFYIRERAKYSHyfivTSGREIFEIKRGE--IYSFSEF---MRVFPLLL---KQGKVVIDEFHR 89 
                                       6789****************9766634322223333332222..2222223...33333332...22339******9 PP

                            AAA_14  76 vpe.wekalkslvd 88 
                                       + e +++a+++l  
  gi|242398251|ref|YP_002993675.1|  90 LGEpFFSAIQGLSG 103
                                       95547777776655 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.37
                            AAA_14   3 kilvitGaRrvGKTtl 18 
                                        i +++G+ ++GKT +
  gi|242398251|ref|YP_002993675.1| 144 AINFVEGLGHSGKTLI 159
                                       578899********87 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.1e-05      0.13       1      71 [.      23      91 ..      23     108 .. 0.72
   2 ?   -1.9   0.0      0.68   4.1e+03      10      50 ..     155     201 ..     150     218 .. 0.49

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.1e-05
                                      EEEESSTTSSHHHHHHHHHHHH.......THEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHH CS
                               AAA  1 vllyGppGtGKTllakavakel.......gvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidala 71
                                      +l+yG   tGKT  ++  ak +       g+e++ei+  e+    ++e ++ +  l+   k+ +    ++iDE+++l+
  gi|242398251|ref|YP_002993675.1| 23 LLVYGRRKTGKTFYIRERAKYShyfivtsGREIFEIKRGEIY--SFSEFMRVFPLLL---KQGK----VVIDEFHRLG 91
                                      699******************633333335777777777777..3333333333333...4444....7899999885 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.68
                                       SHHHHHHHHHHH..........HTHEEEEEETTTCSSSSTTHHHHHHHHHH CS
                               AAA  10 GKTllakavake..........lgvefleisgsellskyvgesekkirelf 50 
                                       GKTl+  av  +          lg +++++ g++l     g+ ++ i e+f
  gi|242398251|ref|YP_002993675.1| 155 GKTLIELAVLVQepwlapaienLGERVFSTFGATLK----GNVPSLIGEIF 201
                                       788877777655454433333333333333333333....33333333333 PP

>> DUF234  Archaea bacterial proteins of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   3.1   0.00031       1.8      67      98 ..     339     371 ..     284     372 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00031
                            DUF234  67 eeeiDivaldeeekkalfgEvKwkn..sekeakk 98 
                                       + e+Di  l++++  +l++E Kwk+  +ek+++k
  gi|242398251|ref|YP_002993675.1| 339 DLEVDIALLRNKK-LYLVAEAKWKEkiKEKDIRK 371
                                       5699*99888888.5**********777777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       684  (0.0381505); expected 358.6 (0.02)
Passed bias filter:                      561  (0.0312901); 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 0.36s 00:00:00.99 Elapsed: 00:00:00.54
# Mc/sec: 2337.90
//
Query:       gi|242398252|ref|YP_002993676.1|  [L=144]
Description: transposase ISTsi3 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.6e-37  125.9   0.0      1e-36  125.7   0.0    1.0  1  Y1_Tnp         Transposase IS200 like
  ------ inclusion threshold ------
      0.041   13.6   0.0      0.074   12.7   0.0    1.4  1  MoCF_biosynth  Probable molybdopterin binding domain


Domain annotation for each model (and alignments):
>> Y1_Tnp  Transposase IS200 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.7   0.0   1.1e-40     1e-36       4     121 .]      18     134 ..      15     134 .. 0.97

  Alignments for each domain:
  == domain 1  score: 125.7 bits;  conditional E-value: 1.1e-40
                            Y1_Tnp   4 lkyhivlvtkyRrkvltgeveerlkeiikeiaekkevkilelelmpDHvHllvelppklsiskivkalkgassrlin 80 
                                       l yh+v+++kyRr +ltg+v+erlk+++ke+a + ++++++le+ pDHvH++++++p+l++++i+++lkg+s+r++ 
  gi|242398252|ref|YP_002993676.1|  18 LAYHFVWIPKYRRDILTGKVAERLKQMLKEFAGEIGCEVISLEVIPDHVHVFLRAKPDLAPARIINHLKGKSARKLL 94 
                                       78*************************************************************************** PP

                            Y1_Tnp  81 kefpelkkkklkkeslWqrgYfvstvgeasletvkrYIenq 121
                                       +efpel+ k    + lW+r+Yfv+++g  + e vk+Y+e+q
  gi|242398252|ref|YP_002993676.1|  95 QEFPELRTKTAH-GRLWSRSYFVASAGYITDEIVKHYVETQ 134
                                       *******99888.77************************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 ?   12.7   0.0   8.3e-06     0.074       9      44 ..      32      67 ..      30      77 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.3e-06
                                      HHTTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHH CS
                     MoCF_biosynth  9 llsgkieDtngpllaellkelgvevskytvvpDdee 44
                                      +l+gk+  +  ++l+e   e+g+ev+ ++v+pD   
  gi|242398252|ref|YP_002993676.1| 32 ILTGKVAERLKQMLKEFAGEIGCEVISLEVIPDHVH 67
                                      799******************************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 867.13
//
Query:       gi|242398253|ref|YP_002993677.1|  [L=402]
Description: transposase ISTsi3 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.7e-32  110.0   0.0    1.4e-31  109.2   0.0    1.4  1  OrfB_IS605      Probable transposase
    4.1e-19   68.3   0.0    7.5e-19   67.4   0.0    1.5  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
  ------ inclusion threshold ------
      0.022   15.1   0.1      0.074   13.4   0.1    1.9  1  RuvX            Holliday junction resolvase
       0.12   11.0   0.1       0.19   10.4   0.1    1.2  1  MAP65_ASE1      Microtubule associated protein (MAP65/ASE1 fa
       0.18   12.5   1.1       0.38   11.5   0.1    2.1  3  Ribosomal_L6    Ribosomal protein L6


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.2   0.0   3.9e-35   1.4e-31       1     119 [.     139     264 ..     139     265 .. 0.97

  Alignments for each domain:
  == domain 1  score: 109.2 bits;  conditional E-value: 3.9e-35
                        OrfB_IS605   1 sipveveve.........lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksk 68 
                                       +i ++ve++         +++pkgn +agiDlG+nnL++v++e+g++fl +gr+lks  +y++k+iae qskl+ks+
  gi|242398253|ref|YP_002993677.1| 139 HISYTVEEKlegnswvklPRTPKGNLVAGIDLGVNNLMAVYVENGESFLVNGRPLKSIGFYWQKRIAEYQSKLNKSG 215
                                       6888888889999999999*********************************************************9 PP

                        OrfB_IS605  69 nykkasrklarlhrkrsrrrkhllhklathliktlkevgvetLnvgnmkdi 119
                                          kasrkl+r+h+k + +  h+++ ++++ +++l+e+gv+ ++vg++k+i
  gi|242398253|ref|YP_002993677.1| 216 --AKASRKLKRMHEKAKLQAGHYINTAVRQTVRRLYELGVSRIVVGYPKEI 264
                                       ..9*********************************************987 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.4   0.0   2.1e-22   7.5e-19       1      69 []     284     353 ..     284     353 .. 0.97

  Alignments for each domain:
  == domain 1  score: 67.4 bits;  conditional E-value: 2.1e-22
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke.alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       f+ ++++l + a+eyGi+v++vn+a+TS+tC+ Cg+ +k  +  + ++ Cp  g+++++D+++a+Nil++
  gi|242398253|ref|YP_002993677.1| 284 FNYVIKRLTEVAEEYGIQVVVVNEAFTSQTCPLCGKPHKGaRFVRGLYMCPVEGLVFNADLVGAFNILRK 353
                                       78899***********************************999************************986 PP

>> RuvX  Holliday junction resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   2.1e-05     0.074      37     101 ..     238     313 ..     211     316 .. 0.55

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.1e-05
                                       HHHHHHHHHHHHHTT--EEEEE------SSS--......-SSTTHHHHHHHHHT.......T-EEEEE--S----X CS
                              RuvX  37 ekdleelkelvkeeeveeiVvGlPlnldgsege......sakkvrkfaeeLakrl.....kklpvelvDErlttve 101
                                       ++++++  + + e  v++iVvG+P++++ +  +         +v +f   +++ +     ++++v++v+E +t+ +
  gi|242398253|ref|YP_002993677.1| 238 NTAVRQTVRRLYELGVSRIVVGYPKEISREPDKgrkqnfVLSHVWRFNYVIKRLTevaeeYGIQVVVVNEAFTSQT 313
                                       455555555666679*********776543322000001223333443333333344566699**********975 PP

>> MAP65_ASE1  Microtubule associated protein (MAP65/ASE1 family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   5.2e-05      0.19     386     438 ..     175     229 ..     172     247 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 5.2e-05
                                       HHHHHHHCTS--EETTEEHHHHHHHHHHHHH......HHHHHHHHHHHHHHHHHHH CS
                        MAP65_ASE1 386 veaweeefgrpFlvdGeklleiieeqweeleeky...qererqksarklkkasqte 438
                                       ++a   e+g+ Flv+G +l + i  +w+++ + y     ++  k++rklk   ++ 
  gi|242398253|ref|YP_002993677.1| 175 LMAVYVENGESFLVNGRPLKS-IGFYWQKRIAEYqskLNKSGAKASRKLKRMHEKA 229
                                       5666779***********976.799******9994444455556666666555444 PP

>> Ribosomal_L6  Ribosomal protein L6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       3.4   1.2e+04      41      67 ..      30      56 ..      20      57 .. 0.68
   2 ?   11.5   0.1    0.0001      0.38       4      56 ..      89     136 ..      88     169 .. 0.82
   3 ?   -4.0   0.0         5   1.8e+04      17      29 ..     257     269 ..     255     272 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3.4
                                      TEEEEEECSESCHHHHHHHHHHHHHHH CS
                      Ribosomal_L6 41 nkvtvivvsgidkekvAligtvrslin 67
                                      +++  ++v+ i ++++  ++++ sli+
  gi|242398253|ref|YP_002993677.1| 30 GEIGSATVQQIARKNAEAWRSFFSLIK 56
                                      556666777777777777888877776 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.0001
                                       TEEEEEETTTEEEEEESSEEEEEE-CTTSEEEEEECSTEEEEEECSESCHHHH CS
                      Ribosomal_L6   4 gvrvsikggqlvlvlGpkgeltreipegvtvevkvegnkvtvivvsgidkekv 56 
                                        +r+ +++  +++ lG+ + l+++++  ++++ k    +++ +++ ++ k k 
  gi|242398253|ref|YP_002993677.1|  89 QYRIDGNK-VILKGLGKFKKLEVQFKGRIHLKGK----QGRLEIIYDDVKRKW 136
                                       59999995.*******************888855....899999988888776 PP

  == domain 3  score: -4.0 bits;  conditional E-value: 5
                                       EEESSEEEEEE-C CS
                      Ribosomal_L6  17 vlGpkgeltreip 29 
                                       v+G+ +e++re  
  gi|242398253|ref|YP_002993677.1| 257 VVGYPKEISREPD 269
                                       7899999998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       966  (0.0538792); expected 358.6 (0.02)
Passed bias filter:                      841  (0.0469072); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.70u 0.36s 00:00:01.06 Elapsed: 00:00:00.53
# Mc/sec: 2266.05
//
Query:       gi|242398254|ref|YP_002993678.1|  [L=182]
Description: hypothetical protein TSIB_0262 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.9e-13   48.6  18.2    8.3e-13   48.3  18.2    1.0  1  DUF998    Protein of unknown function (DUF998)


Domain annotation for each model (and alignments):
>> DUF998  Protein of unknown function (DUF998)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.3  18.2   4.6e-17   8.3e-13       4     175 ..       6     157 ..       3     162 .. 0.91

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 4.6e-17
                            DUF998   4 allalavilaaallrpgydplrhaiSeLgaeg.gpggwlfnaglvllgllvlalavgllraargragragrlllava 79 
                                       +++ l++i++a ll + ++ + +a+S+Lg ++ +p + +fn+gl l g+l++ ++ +++     ++++a +++  + 
  gi|242398254|ref|YP_002993678.1|   6 VAVPLISIAIAILLSDWFSITNNALSDLGHATkSPVAPIFNFGLSLGGALIIYTSTLCIY----KISKAFSVVGFLV 78 
                                       6777899*******9999***********9999**********************99876....5555555555556 PP

                            DUF998  80 glglvlagvfptdpgggspslsglvHglasavaflalavavlllasaarrrawallrlvggvallllvaalvwllaa 156
                                       g+ l+l++vf +  +g        +H ++s+++fl+lav +++++         + +++ + al+++v+a+v ++a 
  gi|242398254|ref|YP_002993678.1|  79 GFTLILVAVFDEVYRG--------LHFAVSVAFFLSLAVFLIAYG-------IYFKSYLPLPALAVAVVAWVIHFAY 140
                                       7**************9........*********************.......************************* PP

                            DUF998 157 aldgslllGlaerllvlai 175
                                         d +++++++e ++v+a 
  gi|242398254|ref|YP_002993678.1| 141 --DVPKGVAIPELISVFAT 157
                                       ..99**********99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       851  (0.047465); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); 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):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1178.24
//
Query:       gi|242398255|ref|YP_002993679.1|  [L=442]
Description: NADPH:elemental sulfur oxidoreductase [Thermococcus sibiricus MM 739]
Scores for complete 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-59  201.1   0.6    3.2e-59  200.6   0.4    1.3  2  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
    3.7e-23   81.9   5.5    1.3e-16   60.9   1.0    3.8  3  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
    1.2e-20   73.8   0.0    2.5e-20   72.8   0.0    1.6  1  Pyr_redox_dim    Pyridine nucleotide-disulphide oxidoreductas
      1e-18   67.7   3.4    3.3e-16   59.4   0.3    2.3  2  Pyr_redox_3      Pyridine nucleotide-disulphide oxidoreductas
    1.4e-08   33.9   0.9     0.0022   16.8   0.0    4.1  4  HI0933_like      HI0933-like protein
    2.4e-07   30.7   0.3       0.11   12.0   0.0    3.8  4  DAO              FAD dependent oxidoreductase
    2.9e-07   30.8   0.7    0.00025   21.5   0.2    2.5  2  NAD_binding_7    Putative NAD(P)-binding
    1.4e-05   24.4   2.4      0.012   14.7   0.0    3.1  3  FAD_binding_2    FAD binding domain
      4e-05   23.8   0.0     0.0022   18.2   0.0    2.5  2  NAD_binding_8    NAD(P)-binding Rossmann-like domain
    5.1e-05   22.5   0.1      0.015   14.3   0.0    2.3  2  Lycopene_cycl    Lycopene cyclase protein
    5.9e-05   22.3   4.3      0.094   11.8   0.1    3.0  3  GIDA             Glucose inhibited division protein A
    0.00023   21.2   0.1       0.65   10.0   0.0    3.3  3  NAD_binding_9    FAD-NAD(P)-binding
    0.00045   19.6   0.0       0.63    9.3   0.0    2.8  3  Amino_oxidase    Flavin containing amine oxidoreductase
    0.00048   19.8   0.1    0.00088   18.9   0.1    1.4  1  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
    0.00052   19.9   0.6     0.0016   18.4   0.1    2.0  2  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
    0.00056   20.1   1.8        2.1    8.6   1.2    3.2  2  TrkA_N           TrkA-N domain
     0.0013   17.7   0.2      0.038   12.8   0.1    2.2  2  Trp_halogenase   Tryptophan halogenase
     0.0016   17.8   1.6      0.031   13.6   0.1    2.3  2  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
     0.0025   17.1   0.4      0.036   13.3   0.0    2.8  3  Thi4             Thi4 family
  ------ inclusion threshold ------
      0.044   12.3   0.0      0.077   11.5   0.0    1.3  1  Mqo              Malate:quinone oxidoreductase (Mqo)
      0.076   13.8   0.1        2.5    8.9   0.0    2.4  2  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
      0.077   13.6   0.7        2.5    8.8   0.2    2.9  2  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
       0.15   11.7   0.8       0.32   10.6   0.1    1.9  2  ApbA             Ketopantoate reductase PanE/ApbA
       0.17   12.0   3.6       0.25   11.4   0.2    2.4  2  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
       0.19   12.0   0.5        1.3    9.3   0.1    2.2  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
       0.44    9.8   2.4        2.2    7.5   0.0    2.6  2  FAD_oxidored     FAD dependent oxidoreductase
       0.62    9.3   3.6        3.6    6.7   0.2    3.0  3  FAD_binding_3    FAD binding domain


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  200.6   0.4   4.8e-62   3.2e-59       1     282 [.       4     293 ..       4     305 .. 0.90
   2 ?   -3.6   0.0       7.9   5.2e+03      20      54 ..     347     381 ..     338     402 .. 0.69

  Alignments for each domain:
  == domain 1  score: 200.6 bits;  conditional E-value: 4.8e-62
                                       CSEEEE--SHHHHHHHHHHHH..HTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH..HHHHCHHHHCCCCHCC CS
                                       xxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxx RF
                       Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaq..agakvtlvelegtclnggcllskallgvaedaeias..evvkklnqgielllge 73 
                                       k+vv+iGgG+AG++aa ++++   + +v ++e+++ + +  c ++++++g++ +++ ++   ++   + gi+l l++
  gi|242398255|ref|YP_002993679.1|   4 KKVVIIGGGAAGMSAASRVKRlkPEWDVKVFEATEWVSHAPCGVPYVVEGISPKEKLMHypPEFFIKKRGIDLHLNA 80 
                                       58*******************755*******999999999999***********99999**445555679******9 PP

                                       TCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-T...SEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxx RF
                       Pyr_redox_2  74 evvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllp...krivv 147
                                       ev+++++g+  v +++k  + e++++ d+lv A G+spr+++i+G   ++++  +   +a a+++ + +   ++++v
  gi|242398255|ref|YP_002993679.1|  81 EVIEVEQGS--VRVREK--DGEHTYEWDYLVFANGASPRIPNIEGIDLKGVFTADLPPDAVAIREYMEKndvRDVLV 153
                                       9****7777..666444..4568***********************8888899899*******999999899999** PP

                                       ES-SHHHHHHHHHHHHHT-EEEEEESSSSSS.TTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 148 vGgGyiGvElAaalaklgkevtlveardrll.raldkelsaaleealekeGvevklgtsvkeidgngeklevvledg 223
                                       +G Gyi++E+A a+   gk+vtl+ + +r+l +++dke+++++e++l+++  +++l++s  +i+g+++ +e v +d 
  gi|242398255|ref|YP_002993679.1| 154 IGTGYIALEMAEAFVVQGKNVTLIGRSERILrKTFDKEITDIVEAKLREH-LNLRLNESTLRIEGKDR-VEKVITDA 228
                                       *************************************************8.9***************8.99888899 PP

                                       CEEEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GGGC.......TECC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxx RF
                       Pyr_redox_2 224 eeidadlvvvavGvrpstelleeklglelderggivvdeflrtnvpgiyaiGDva.......ggkg 282
                                        e++adlv++a+G++p+tel+ e+lg+++ e+g+i ++e+++t+v+++ya+GDva       g++ 
  gi|242398255|ref|YP_002993679.1| 229 GEYKADLVIIATGIKPNTELA-EQLGVKIGETGAIWTNEKMQTSVENVYAAGDVAetrhlitGKRV 293
                                       99*******************.*********************************66666555555 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 7.9
                                       HH.HTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHH CS
                                       xx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  20 aq.agakvtlvelegtclnggcllskallgvaedae 54 
                                       ++ + +k++ + + +t ++  +  +k++l++ +d+e
  gi|242398255|ref|YP_002993679.1| 347 KEgYDVKTAFI-EARTKPHYYPGAKKIWLKAVADKE 381
                                       44567778888.666666666777777777776665 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   0.00034      0.23       1      33 [.       5      39 ..       5      44 .. 0.86
   2 !    8.6   0.0    0.0042       2.8      50      71 ..      69      90 ..      66      97 .. 0.81
   3 !   60.9   1.0   1.9e-19   1.3e-16       2      78 ..     151     226 ..     150     230 .. 0.96

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00034
                                      EEEEECSSHHHHHHHHHHHHTT..SEEEEEESSSS CS
                         Pyr_redox  1 kvvvvGgGyiglElAgalaelg..kkVtvversdk 33
                                      kvv++GgG  g+ +A+  ++l+   +V+v+e+ ++
  gi|242398255|ref|YP_002993679.1|  5 KVVIIGGGAAGMSAASRVKRLKpeWDVKVFEATEW 39
                                      79******************995558888887766 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0042
                                      HHHTTEEEECSEEEEEEEEETT CS
                         Pyr_redox 50 lekngievllntkveeiegsed 71
                                      ++k+gi+++ln++v e+e+ + 
  gi|242398255|ref|YP_002993679.1| 69 IKKRGIDLHLNAEVIEVEQGSV 90
                                      5899**************7664 PP

  == domain 3  score: 60.9 bits;  conditional E-value: 1.9e-19
                                       EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS.TTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEE CS
                         Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkll.rllDeeaskilqeklekngievllntkveeiegsedgvesvk 77 
                                       v+v+G Gyi+lE+A+a+   gk+Vt++ rs+++l + +D+e+ +i++ kl+++  +++ln+++ +ieg+++ ve+v 
  gi|242398255|ref|YP_002993679.1| 151 VLVIGTGYIALEMAEAFVVQGKNVTLIGRSERILrKTFDKEITDIVEAKLREH-LNLRLNESTLRIEGKDR-VEKVI 225
                                       89***************************************************.***************99.99998 PP

                                       E CS
                         Pyr_redox  78 l 78 
                                       +
  gi|242398255|ref|YP_002993679.1| 226 T 226
                                       6 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 !   72.8   0.0   3.8e-23   2.5e-20       3     104 ..     327     428 ..     325     433 .. 0.95

  Alignments for each domain:
  == domain 1  score: 72.8 bits;  conditional E-value: 3.8e-23
                                       EEEESSSEEEEEES-HHHHHHHHSGEEEEEEEEECGHHHCHTTH.TEEEEEEEEETTTTBEEEEEEECTTHHHHHHH CS
                     Pyr_redox_dim   3 tvvftdpevasvGlteeeAkaagieikvgkfpfkangralayae.tkgfvKlvadaktgkvlGahivGpgageliqe 78 
                                        ++f+d+e++ +Glte eA ++g  ++v+++ ++a ++ ++y+  +k+++K vad++tg++lG++ vG +   ++++
  gi|242398255|ref|YP_002993679.1| 327 ITKFMDLEIGKTGLTEGEALKEG--YDVKTAFIEARTKPHYYPGaKKIWLKAVADKETGRLLGLQAVGAEILPRVDA 401
                                       689********************..*******************9******************************** PP

                                       HHHHHHTTSBHH.HHHTSBSSSSSTGG CS
                     Pyr_redox_dim  79 lavaikagltve.dladtihihPtlse 104
                                       la+a++ag t++ ++  +++++P+++ 
  gi|242398255|ref|YP_002993679.1| 402 LAIALQAGFTTKdLFFADLAYAPPFAP 428
                                       *********99966**********994 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 !    8.8   0.3    0.0013      0.87       1      20 [.       7      26 ..       7      43 .. 0.82
   2 !   59.4   0.3     5e-19   3.3e-16      91     305 .]      69     279 ..      46     279 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0013
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkag 20
                                      +IiG+G+aG++aa  +k+++
  gi|242398255|ref|YP_002993679.1|  7 VIIGGGAAGMSAASRVKRLK 26
                                      7*************999876 PP

  == domain 2  score: 59.4 bits;  conditional E-value: 5e-19
                       Pyr_redox_3  91 aksfelpiklfeeVesvkkedegfevetsketyeAkkviiAtGefdkPnklnipGeeklvkhyskv.......kefh 160
                                        k+  ++ +l+ eV +v++ +   + +  ++tye ++++ A G    P+ +ni+G + + + ++         +e++
  gi|242398255|ref|YP_002993679.1|  69 IKKRGIDLHLNAEVIEVEQGSVRVREKDGEHTYEWDYLVFANGA--SPRIPNIEGIDLKGVFTADLppdavaiREYM 143
                                       5677889999999999988766666566667************9..**********965554444322222223333 PP

                       Pyr_redox_3 161 kya.gqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikvlfnaevk 236
                                       + +  ++v+ViG +  a ++A  +v +g++Vt++ r++ i ++  +++ ++  ++e +l+e     ++++  n+++ 
  gi|242398255|ref|YP_002993679.1| 144 EKNdVRDVLVIGTGYIALEMAEAFVVQGKNVTLIGRSERILRK--TFDKEITDIVEAKLRE-----HLNLRLNESTL 213
                                       3332578*******************************99887..5888899999999998.....47899999*** PP

                       Pyr_redox_3 237 eikekeeeykvktedgkkvevkddvvlatGykpdlsflkkslfeldedgrpvlteeteetnvpglflaG 305
                                       +i+ k++  kv t+ g+   + d v++atG kp++++ ++ ++++ e+g +  t+e+++t v++++ aG
  gi|242398255|ref|YP_002993679.1| 214 RIEGKDRVEKVITDAGEY--KADLVIIATGIKPNTELAEQLGVKIGETGAI-WTNEKMQTSVENVYAAG 279
                                       *****9999999999864..56999********************888865.677899*********99 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   3.2e-06    0.0022       2      32 ..       5      37 ..       4      42 .. 0.84
   2 ?    3.8   0.0     0.028        19     119     164 ..      69     112 ..      66     120 .. 0.83
   3 ?    4.0   0.1     0.024        16       2      38 ..     150     186 ..     149     189 .. 0.95
   4 ?    4.7   0.0     0.016        10     110     165 ..     191     243 ..     188     262 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.2e-06
                                      SEEEE--SHHHHHHHHHH..HHTT--EEEE-SS CS
                       HI0933_like  2 dviviGgGaAGlmaAisa..akrgkrVllleka 32
                                      +v++iGgGaAG+ aA ++   k + +V ++e++
  gi|242398255|ref|YP_002993679.1|  5 KVVIIGGGAAGMSAASRVkrLKPEWDVKVFEAT 37
                                      89**************99555778889999876 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.028
                                       HHHHT-EEE-S--EEEEECETTE.EEEEE..TTEEEEESEEEE---- CS
                       HI0933_like 119 lkeagvklrletevksvekeedgkfrvkt.kseeeleadklvlAtGG 164
                                       +k++g++l+l+ ev +ve   +g++rv+  ++e+++e d+lv+A G 
  gi|242398255|ref|YP_002993679.1|  69 IKKRGIDLHLNAEVIEVE---QGSVRVREkDGEHTYEWDYLVFANGA 112
                                       6899*************4...3557777757899**********886 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.024
                                       SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HH CS
                       HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakklgrK 38 
                                       dv+viG G   l  A++   +gk+V+l+ + ++++rK
  gi|242398255|ref|YP_002993679.1| 150 DVLVIGTGYIALEMAEAFVVQGKNVTLIGRSERILRK 186
                                       89**********************************9 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.016
                                       HHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----S CS
                       HI0933_like 110 divdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGGl 165
                                       +i d+ +++l+e + +lrl+++  ++e  +d++ +v t +++e++ad +++AtG +
  gi|242398255|ref|YP_002993679.1| 191 EITDIVEAKLRE-HLNLRLNESTLRIEG-KDRVEKVIT-DAGEYKADLVIIATGIK 243
                                       566666666654.689999999999965.555577777.9************9855 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   0.00017      0.11       1      33 [.       5      41 ..       5      44 .. 0.81
   2 !    8.1   0.0    0.0025       1.7     157     204 ..      70     114 ..      58     143 .. 0.80
   3 ?    0.0   0.1      0.75     5e+02       1      29 [.     150     180 ..     150     188 .. 0.86
   4 ?    5.1   0.1     0.021        14     162     209 ..     205     251 ..     189     289 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00017
                                      EEEEECTSHHHHHHHHHHHHTT....EEEEESSSSTT CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg....Vtllekgdiag 33
                                      +vviiGGG +G+s+A    r +    V ++e+ + ++
  gi|242398255|ref|YP_002993679.1|  5 KVVIIGGGAAGMSAASRVKRLKpewdVKVFEATEWVS 41
                                      59*************9995544489999999986555 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0025
                                       HHTT-EEEESECEEEEEEEETCEEEEEEECTEEE.EEEEEEEE--GGGH CS
                               DAO 157 ealGveilegtevtgleeedgkvwgverttpgen.daadavVnaaGaws 204
                                       +++G+++++++ev ++e+     ++v r+++ge   + d++V a+Ga  
  gi|242398255|ref|YP_002993679.1|  70 KKRGIDLHLNAEVIEVEQG---SVRV-REKDGEHtYEWDYLVFANGASP 114
                                       799************9653...5677.6666665467899******974 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.75
                                       EEEEECTSHHHHHHHHHHHHTT..EEEEESS CS
                               DAO   1 dvviiGGGiiGlstAyeLarrg..Vtllekg 29 
                                       dv++iG G+i l  A +   +g  Vtl+ ++
  gi|242398255|ref|YP_002993679.1| 150 DVLVIGTGYIALEMAEAFVVQGknVTLIGRS 180
                                       8*********999999998777899999776 PP

  == domain 4  score: 5.1 bits;  conditional E-value: 0.021
                                       EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHH.HH.HT CS
                               DAO 162 eilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsd.ll.gl 209
                                       ++++++   ++e + ++v +v   t+ ge  +ad v++a+G+  + +l ++
  gi|242398255|ref|YP_002993679.1| 205 NLRLNESTLRIEGK-DRVEKV--ITDaGEY-KADLVIIATGIKPNtELaEQ 251
                                       55566444556433.467777..6777986.5699******9877744333 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 !    7.6   0.0    0.0076         5       8      36 ..       4      34 ..       1     111 [. 0.77
   2 !   21.5   0.2   3.7e-07   0.00025       8      71 ..     149     242 ..     143     287 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0076
                     NAD_binding_7  8 kkvlvvGgGevAa...rkvrklleagakvtvv 36
                                      kkv+++GgG  ++   ++v++l ++  +v+v 
  gi|242398255|ref|YP_002993679.1|  4 KKVVIIGGGAAGMsaaSRVKRLKPE-WDVKVF 34
                                      89******99864222788888887.777775 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 3.7e-07
                     NAD_binding_7   8 kkvlvvGgGevAarkvrklleagakvtvvapev....keele...........elvklaeeelekd........... 58 
                                       + vlv+G G +A++ ++ ++ +g++vt++        k + +           e           +           
  gi|242398255|ref|YP_002993679.1| 149 RDVLVIGTGYIALEMAEAFVVQGKNVTLIGRSErilrKTFDKeitdiveaklrE-----------Hlnlrlnestlr 214
                                       78**************************98875556633333333333333331...........222222222233 PP

                     NAD_binding_7  59 ..........leg.....adlviaatdd 71 
                                                 +++     adlvi+at  
  gi|242398255|ref|YP_002993679.1| 215 iegkdrvekvITDageykADLVIIATGI 242
                                       2222333333332555669999999953 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   0.0   1.8e-05     0.012       2      20 ..       6      24 ..       5      42 .. 0.80
   2 ?    0.8   0.2       0.3     2e+02       1      30 [.     150     179 ..     150     188 .. 0.88
   3 !    7.1   0.0    0.0038       2.5     373     402 ..     259     282 ..     178     289 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.8e-05
                                      EEEE--SHHHHHHHHHHHH CS
                     FAD_binding_2  2 viViGsGlAGLaAAleaae 20
                                      v++iG+G+AG++AA + ++
  gi|242398255|ref|YP_002993679.1|  6 VVIIGGGAAGMSAASRVKR 24
                                      9*************98876 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.3
                                       SEEEE--SHHHHHHHHHHHHTTT-EEEEES CS
                     FAD_binding_2   1 DviViGsGlAGLaAAleaaeaGlkvavvek 30 
                                       Dv+ViG+G   L  A +   +G++v+++  
  gi|242398255|ref|YP_002993679.1| 150 DVLVIGTGYIALEMAEAFVVQGKNVTLIGR 179
                                       9********999999999999999999865 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0038
                                       S-EEEBETTSBESTTEEESSBTEEE-STCE CS
                     FAD_binding_2 373 mgGvetdengrvldadgqpipGLYAaGeva 402
                                        g + t+e++++       +++ YAaG va
  gi|242398255|ref|YP_002993679.1| 259 TGAIWTNEKMQT------SVENVYAAGDVA 282
                                       333667777777......***********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 !   18.2   0.0   3.3e-06    0.0022       1      28 [.       8      37 ..       8      41 .. 0.89
   2 ?    2.9   0.0       0.2   1.3e+02       1      31 [.     153     183 ..     153     191 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.3e-06
                                      EE--SHHHHHHHHHHHCC..TEEEEEE-SS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLaka..gfdvlllekr 28
                                      I+G+G++G++aA++ ++     dv ++e+ 
  gi|242398255|ref|YP_002993679.1|  8 IIGGGAAGMSAASRVKRLkpEWDVKVFEAT 37
                                      9***************9756789****985 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.2
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSSSS CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrl 31 
                                       ++G+G  +l +A +   +g++v+l+ +++r+
  gi|242398255|ref|YP_002993679.1| 153 VIGTGYIALEMAEAFVVQGKNVTLIGRSERI 183
                                       8***********************9888775 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   2.3e-05     0.015       2      35 ..       6      39 ..       5      46 .. 0.90
   2 !    6.0   0.0    0.0077       5.1       1      38 [.     150     185 ..     150     250 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.3e-05
                     Lycopene_cycl  2 vvviGaGpAglslAarlteakpglkvvlieasps 35
                                      vv+iG+G+Ag+s A r+ + kp+  v + ea + 
  gi|242398255|ref|YP_002993679.1|  6 VVIIGGGAAGMSAASRVKRLKPEWDVKVFEATEW 39
                                      8**********************99999999875 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0077
                     Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvlieaspsllf 38 
                                       Dv+viG G   l +A+      +g +v+li  s+ +l+
  gi|242398255|ref|YP_002993679.1| 150 DVLVIGTGYIALEMAEAF--VVQGKNVTLIGRSERILR 185
                                       9****************9..778889999998988865 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.1   0.00014     0.094       1      21 [.       5      25 ..       5      45 .. 0.88
   2 ?   -1.9   0.0       2.1   1.4e+03       1      28 [.     150     177 ..     150     184 .. 0.88
   3 !   10.6   0.7   0.00032      0.21      92     150 ..     183     242 ..     159     283 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00014
                                      CEEEE-SSHHHHHHHHHHHHT CS
                              GIDA  1 dviViGgGhAGceAAlaaarl 21
                                      +v++iGgG AG+ AA  ++rl
  gi|242398255|ref|YP_002993679.1|  5 KVVIIGGGAAGMSAASRVKRL 25
                                      69**************99987 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.1
                                       CEEEE-SSHHHHHHHHHHHHTT--EEEE CS
                              GIDA   1 dviViGgGhAGceAAlaaarlGakvlLi 28 
                                       dv ViG G   +e A a    G +v+Li
  gi|242398255|ref|YP_002993679.1| 150 DVLVIGTGYIALEMAEAFVVQGKNVTLI 177
                                       799******99****9999999999998 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00032
                                       E-HHHHHHHHHHHHHT..STTEEEEES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT CS
                              GIDA  92 vdrelyskevteklen..epnleiieeeveeliveekkvkgvvtedgetikakavviatGt 150
                                       + r+++ ke+t+ +e+   ++l+++ +e +  i  +++v+ v+t+ ge +ka+ v+iatG 
  gi|242398255|ref|YP_002993679.1| 183 ILRKTFDKEITDIVEAklREHLNLRLNESTLRIEGKDRVEKVITDAGE-YKADLVIIATGI 242
                                       44778888888887776656666666665554466899****999886.89*********6 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 !   10.0   0.0   0.00097      0.65       1      35 [.       7      38 ..       7      48 .. 0.89
   2 ?    1.5   0.0       0.4   2.7e+02     121     154 ..      79     111 ..      70     113 .. 0.72
   3 ?    5.5   0.0     0.023        15     110     154 ..     199     241 ..     180     243 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00097
                     NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpse 35
                                      +i+G+G++G++++ r+ +    k + ++++f+ +e
  gi|242398255|ref|YP_002993679.1|  7 VIIGGGAAGMSAASRVKRL---KPEWDVKVFEATE 38
                                      7**************9999...699******9866 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.4
                     NAD_binding_9 121 raevvdleeradgqavlladg.aslaadaVvLAlG 154
                                       +aev+++e  +++++v+++dg ++++ d++v A G
  gi|242398255|ref|YP_002993679.1|  79 NAEVIEVE--QGSVRVREKDGeHTYEWDYLVFANG 111
                                       55565555..556789998883557********99 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.023
                     NAD_binding_9 110 rlpegvtvevhraevvdleeradgqavlladgaslaadaVvLAlG 154
                                       +l+e++++++ +++ +++e +++ ++ + +d  +++ad V++A+G
  gi|242398255|ref|YP_002993679.1| 199 KLREHLNLRL-NESTLRIEGKDR-VEKVITDAGEYKADLVIIATG 241
                                       5555555553.666677776654.5555889999**********9 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.39   2.6e+02       2      24 ..      14      38 ..      13      40 .. 0.92
   2 !    9.3   0.0   0.00094      0.63     209     259 ..      61     109 ..      29     117 .. 0.83
   3 ?    5.6   0.0     0.012       8.1     221     262 ..     202     242 ..     164     252 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.39
                                      HHHHHHHHHHHTT..EEEEEEESSS CS
                     Amino_oxidase  2 aGLaaArqLlsaG..fdVtvlEard 24
                                      aG++aA++ ++     dV v+Ea++
  gi|242398255|ref|YP_002993679.1| 14 AGMSAASRVKRLKpeWDVKVFEATE 38
                                      9********999999********86 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00094
                                       THHHHHHHHHTTTTEEEETSEEEEEEEEETTCEEEEETTSTEE.EESEEEE- CS
                     Amino_oxidase 209 lsqlpealaeelrgldirlntrVkeikregdgvtvtledgevv.eaDaVvvT 259
                                       ++ +pe + + +rg d++ln++V e+++++  v+v+ +dge++ e D+ v +
  gi|242398255|ref|YP_002993679.1|  61 MHYPPEFFIK-KRGIDLHLNAEVIEVEQGS--VRVREKDGEHTyEWDYLVFA 109
                                       5566777777.9****************55..566667999999*9999977 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.012
                                       TTEEEETSEEEEEEEEETTCEEEEETTSTEEEESEEEE-S-H CS
                     Amino_oxidase 221 rgldirlntrVkeikregdgvtvtledgevveaDaVvvTvpl 262
                                         l++rln+   +i+ ++d v   ++d  +++aD V++++ +
  gi|242398255|ref|YP_002993679.1| 202 EHLNLRLNESTLRIE-GKDRVEKVITDAGEYKADLVIIATGI 242
                                       367889999999998.58888888999999*********976 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   1.3e-06   0.00088       3      83 ..     151     239 ..     149     254 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.3e-06
                                       EEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHH.HCTTS-SS--TTHHHHHHHHCHTT..TEEEES-HHHHHH. CS
                    UDPG_MGDP_dh_N   3 isviGlGYvGlvtaavlaeighevigvDideekvdk.lnsgkipiyepgLeelvkkavesg..rlsfttdvekave. 75 
                                       + viG+GY+ l +a ++  +g++v+++  +e+  +k + ++   i+e +L+e ++ +++++  r++++ +vek +  
  gi|242398255|ref|YP_002993679.1| 151 VLVIGTGYIALEMAEAFVVQGKNVTLIGRSERILRKtFDKEITDIVEAKLREHLNLRLNEStlRIEGKDRVEKVITd 227
                                       78****************************99997625777789********9988776551156677777777652 PP

                                       ....C-SEEEE- CS
                    UDPG_MGDP_dh_N  76 ....eadvifia 83 
                                           +ad+++ia
  gi|242398255|ref|YP_002993679.1| 228 ageyKADLVIIA 239
                                       222235666666 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 ?   -1.1   0.0       2.2   1.5e+03       1      20 [.       5      24 ..       5      41 .. 0.73
   2 !   18.4   0.1   2.4e-06    0.0016       2      78 ..     151     227 ..     150     239 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 2.2
                                      EEEEE--SCCHHHHHHHHHH CS
                           3HCDH_N  1 kvaviGaGtmGagiaavfas 20
                                      kv +iG G  G + a+ + +
  gi|242398255|ref|YP_002993679.1|  5 KVVIIGGGAAGMSAASRVKR 24
                                      6999*****99999987654 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 2.4e-06
                                       EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEEES-HHHHH. CS
                           3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklkeeeveaalarisfttdleeav. 77 
                                       v viG+G +  ++a++f+ +g +V+l+ +se++l+k  +k  + + +++ +++l+    ++   ri+ ++ +e+++ 
  gi|242398255|ref|YP_002993679.1| 151 VLVIGTGYIALEMAEAFVVQGKNVTLIGRSERILRKTFDKEITDIVEAKLREHLN-LRLNESTLRIEGKDRVEKVIt 226
                                       78********************************999877666666666666666.566666667777777776654 PP

                                       C CS
                           3HCDH_N  78 d 78 
                                       d
  gi|242398255|ref|YP_002993679.1| 227 D 227
                                       4 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0     0.013       8.6       1      31 [.       6      38 ..       6      60 .. 0.85
   2 !    8.6   1.2    0.0032       2.1       1      80 [.     151     238 ..     151     279 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.013
                                      EEEES-SHHHHHHHHHHHH.TT.EEEEEEESSH CS
                            TrkA_N  1 iiiiGlGrvGrslaeeLse.gg.kdvvvidkde 31
                                      ++iiG G  G+s a ++++ +  +dv v +  e
  gi|242398255|ref|YP_002993679.1|  6 VVIIGGGAAGMSAASRVKRlKPeWDVKVFEATE 38
                                      79****************955379999999865 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0032
                                       EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTT.SEEEES-TT.......SHHHHHHTTGGGESEEEE- CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeg.levvvgdat.......deevLeeagiekadaviaa 69 
                                       +++iG G ++ ++ae +  +gk+v++i ++e+ +++  +++ +++v +          +e++L+  g ++++ vi+ 
  gi|242398255|ref|YP_002993679.1| 151 VLVIGTGYIALEMAEAFVVQGKNVTLIGRSERILRKTFDKEiTDIVEAKLRehlnlrlNESTLRIEGKDRVEKVITD 227
                                       689***************97768******999988887777455777665422222224566666666666666666 PP

                                       SSSHHHHHHHH CS
                            TrkA_N  70 tgddeanilav 80 
                                       +g+++a ++++
  gi|242398255|ref|YP_002993679.1| 228 AGEYKADLVII 238
                                       66665555554 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.1   5.8e-05     0.038       1      35 [.       5      38 ..       5      46 .. 0.87
   2 ?    2.6   0.0     0.073        49     178     210 ..     212     243 ..     185     264 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.8e-05
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SS CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlvesee 35
                                      k+vi+GGG aG  aA+ +++   +  +v++ e+ e
  gi|242398255|ref|YP_002993679.1|  5 KVVIIGGGAAGMSAASRVKRLKPE-WDVKVFEATE 38
                                      79****************999854.9999988765 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.073
                                       EEEE-TTS-EEEEEETTS-EEE-SEEEE-SGGG CS
                    Trp_halogenase 178 evqldedgrveslrledgreveadlfiDcsGfr 210
                                       + +++ ++rve++ ++ g+ ++adl+i ++G +
  gi|242398255|ref|YP_002993679.1| 212 TLRIEGKDRVEKVITDAGE-YKADLVIIATGIK 243
                                       5678889*******98887.***********87 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 !   13.6   0.1   4.6e-05     0.031      30      52 ..       5      27 ..       2      41 .. 0.83
   2 ?    3.3   0.2     0.066        44      30      69 ..     150     189 ..     145     280 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.6e-05
                                      EEEEESTSHHHHHHHHHHHHTT- CS
                       AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglga 52
                                      kv++iGgG aG++A++  k+l+ 
  gi|242398255|ref|YP_002993679.1|  5 KVVIIGGGAAGMSAASRVKRLKP 27
                                      8*****************99974 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.066
                                       EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH CS
                       AlaDh_PNT_C  30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleqles 69 
                                        vlviG G   l+ +++ +  g +Vt++  +++ l++  +
  gi|242398255|ref|YP_002993679.1| 150 DVLVIGTGYIALEMAEAFVVQGKNVTLIGRSERILRKTFD 189
                                       69************************99999888876544 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   5.5e-05     0.036      18      49 ..       4      36 ..       1      87 [. 0.89
   2 ?   -0.8   0.0       1.1   7.3e+02      13      39 ..     144     170 ..     137     181 .. 0.69
   3 ?   -0.2   0.0      0.75     5e+02      26      51 ..     336     361 ..     330     411 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.5e-05
                                      EEEEEE--SHHHHHHHHHHHHC.TTS-EEEEES CS
                              Thi4 18 sDvvivGaGssGLtaayylakk.pdlkvailer 49
                                        vvi+G+G++G++aa  + +  p+  v ++e+
  gi|242398255|ref|YP_002993679.1|  4 KKVVIIGGGAAGMSAASRVKRLkPEWDVKVFEA 36
                                      679**************999977******9997 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.1
                                       HHHTEEEEEEE--SHHHHHHHHHHHHC CS
                              Thi4  13 lkyaesDvvivGaGssGLtaayylakk 39 
                                        k  + Dv+++G+G   L  a  +  +
  gi|242398255|ref|YP_002993679.1| 144 EKNDVRDVLVIGTGYIALEMAEAFVVQ 170
                                       4445689*******9999888765554 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.75
                                       SHHHHHHHHHHHHCTTS-EEEEESSS CS
                              Thi4  26 GssGLtaayylakkpdlkvailersv 51 
                                       G +GLt +  l +  d+k+a +e++ 
  gi|242398255|ref|YP_002993679.1| 336 GKTGLTEGEALKEGYDVKTAFIEART 361
                                       889********999*********986 PP

>> Mqo  Malate:quinone oxidoreductase (Mqo)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00012     0.077       4      39 ..       5      40 ..       3      45 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00012
                               Mqo  4 dvvliGaGimsatlgvllkelepelsievlerldkv 39
                                       vv+iG+G    + ++ +k+l+pe++++v+e  + v
  gi|242398255|ref|YP_002993679.1|  5 KVVIIGGGAAGMSAASRVKRLKPEWDVKVFEATEWV 40
                                      69*****************************98765 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 ?    2.5   0.0      0.37   2.4e+02       2      28 ..       5      31 ..       4      45 .. 0.84
   2 ?    8.9   0.0    0.0038       2.5       3      81 ..     151     251 ..     149     286 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.37
                                      EEEEETTSHHHHHHHHHHHHTTTTEEE CS
                      GFO_IDH_MocA  2 rvaiiGaGkigskhlrplnesqrleev 28
                                      +v+iiG+G +g   +  +++ +++++v
  gi|242398255|ref|YP_002993679.1|  5 KVVIIGGGAAGMSAASRVKRLKPEWDV 31
                                      89********99999888888887765 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0038
                                       EEEETTSHHHHHHHHHHHHTTTTE................EEEEEECSSHHHHHHH...HHHTTHEEESSHHHHHTC CS
                      GFO_IDH_MocA   3 vaiiGaGkigskhlrplnesqrle................evvalldpdaeraeav...aesfgveaysdleellad 60 
                                       v++iG+G+i+ + ++++  + ++                 e++ +++ +  ++ ++     ++++e  + +e++ +d
  gi|242398255|ref|YP_002993679.1| 151 VLVIGTGYIALEMAEAFVVQGKNVtligrserilrktfdkEITDIVEAKLREHLNLrlnESTLRIEGKDRVEKVITD 227
                                       89*******9999999999988889999999999999999999999999999999988888899999999******9 PP

                                       T...TESEEEE-S-GGGHHHHHHH CS
                      GFO_IDH_MocA  61 p...eidavivatpngtheelaka 81 
                                           ++d+vi+at  +   ela++
  gi|242398255|ref|YP_002993679.1| 228 AgeyKADLVIIATGIKPNTELAEQ 251
                                       99899*******988887777776 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 ?    1.6   0.0      0.65   4.3e+02       1      20 [.       5      24 ..       5      37 .. 0.84
   2 ?    8.8   0.2    0.0037       2.5       4      45 ..     153     190 ..     150     258 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.65
                                      EEEEETTSHHHHHHHHHHHH CS
                     F420_oxidored  1 kigiiGaGnmgealasglla 20
                                      k+ iiG+G  g + as++ +
  gi|242398255|ref|YP_002993679.1|  5 KVVIIGGGAAGMSAASRVKR 24
                                      689********999998766 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0037
                                       EETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHH CS
                     F420_oxidored   4 iiGaGnmgealasgllaagaqpheivvansrnpekaeelaee 45 
                                       +iG+G ++  +a+ ++ +g   ++++++  r++  ++++ ++
  gi|242398255|ref|YP_002993679.1| 153 VIGTGYIALEMAEAFVVQG---KNVTLI-GRSERILRKTFDK 190
                                       8******************...****88.8988888887654 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       4.6   3.1e+03       1      17 [.       6      22 ..       6      31 .. 0.80
   2 ?   10.6   0.1   0.00049      0.32       1      93 [.     151     257 ..     151     264 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 4.6
                                      EEEES-SHHHHHHHHHH CS
                              ApbA  1 iailGaGaiGsllaakL 17
                                      ++i+G Ga G   a + 
  gi|242398255|ref|YP_002993679.1|  6 VVIIGGGAAGMSAASRV 22
                                      689*****998777665 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00049
                                       EEEES-SHHHHHHHHHHHHHTHCEEEE-SCHHHHHHHHHCEEEEETTCEEEEEECEEECCH................ CS
                              ApbA   1 iailGaGaiGsllaakLakagadvtlilrsrrlealkknGlrltseggeeilrppealsae................ 61 
                                       ++++G+G i   +a     +g +vtli+rs+r+   k+ + ++t+   e +lr+  +l+                  
  gi|242398255|ref|YP_002993679.1| 151 VLVIGTGYIALEMAEAFVVQGKNVTLIGRSERIL-RKTFDKEITDIV-EAKLREHLNLRLNestlriegkdrvekvi 225
                                       6899***999999999999************544.355555555555.33333333333333344789999999999 PP

                                       SCCCCS-ESEEEE-SSGGGHHHHHHHHGGGEC CS
                              ApbA  62 ekselepidlvivtvKayqteealeeikplld 93 
                                       +++   ++dlvi+++   ++ e +e++   ++
  gi|242398255|ref|YP_002993679.1| 226 TDAGEYKADLVIIATGIKPNTELAEQLGVKIG 257
                                       9999999*******999999988888766655 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.2      0.72   4.8e+02      12      29 ..       3      20 ..       1      28 [. 0.81
   2 ?   11.4   0.2   0.00037      0.25       9      75 ..     145     210 ..     138     229 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.72
                                      T-EEEEES-SHHHHHHHH CS
                      Shikimate_DH 12 ekkvlliGaGemaelvak 29
                                       kkv++iG G  +  +a+
  gi|242398255|ref|YP_002993679.1|  3 MKKVVIIGGGAAGMSAAS 20
                                      689*****9999887776 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00037
                                       ..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHH.HHHHHT.ET-EEEEGCGHHHHHHT CS
                      Shikimate_DH   9 slkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerake.laeelkgeeiealkleelkellae 75 
                                       + + + vl+iG+G +a ++a++++ +g + v+ ++R+ +  ++ + +e+ +  +ea+  e l+ +l+e
  gi|242398255|ref|YP_002993679.1| 145 KNDVRDVLVIGTGYIALEMAEAFVVQGKN-VTLIGRSERILRKtFDKEITDI-VEAKLREHLNLRLNE 210
                                       556689******************99977.******9876544133334333.555555555555555 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 ?    0.5   0.0         1   6.8e+02       1      21 [.       6      26 ..       6      37 .. 0.85
   2 ?    9.3   0.1    0.0019       1.3       1      70 [.     151     228 ..     151     250 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 1
                                      EEEE--SHHHHHHHHHHHCTC CS
                   Sacchrp_dh_NADP  1 vliiGaGsvGqavaellarhf 21
                                      v+iiG+G+ G ++a  ++r +
  gi|242398255|ref|YP_002993679.1|  6 VVIIGGGAAGMSAASRVKRLK 26
                                      89********99999988865 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0019
                                       EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH............TTTCEEEEE--TTTHHHHHHH CS
                   Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaaka............lgvrfeaialdaenyeavLaa 65 
                                       vl+iG G+++  +ae  + +++   ++t+++rs++ l+++++k+            l+ r++  +l +e ++  +++
  gi|242398255|ref|YP_002993679.1| 151 VLVIGTGYIALEMAEAFVVQGK---NVTLIGRSERILRKTFDKEitdiveaklrehLNLRLNESTLRIEGKDR-VEK 223
                                       89*************9999997...6**************998888887777777766666666666555555.555 PP

                                       HHTTS CS
                   Sacchrp_dh_NADP  66 llkeg 70 
                                       +++++
  gi|242398255|ref|YP_002993679.1| 224 VITDA 228
                                       55554 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0033       2.2       2      20 ..       6      24 ..       5      39 .. 0.91
   2 ?    0.9   0.7      0.34   2.3e+02      83     155 ..     187     255 ..     143     309 .. 0.60

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0033
                      FAD_oxidored  2 vvVvGGgpaGvaAAiaAar 20
                                      vv++GGg+aG+ AA   +r
  gi|242398255|ref|YP_002993679.1|  6 VVIIGGGAAGMSAASRVKR 24
                                      9*************87766 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.34
                      FAD_oxidored  83 tfepevakavleemlaeagvtvllntrlvevekegkriesvtveskegrktirAkvfiDATg...dGdlaalaGvp 155
                                       tf+ e+   ++e+ l+e  +++ ln+   ++e ++ r+e+v++       +++A+++i ATg   + +la++ Gv+
  gi|242398255|ref|YP_002993679.1| 187 TFDKEIT-DIVEAKLRE-HLNLRLNESTLRIEGKD-RVEKVITD----AGEYKADLVIIATGikpNTELAEQLGVK 255
                                       4444443.333444444.56666666666666665.77777774....5677777777777644445666666665 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.2    0.0054       3.6       3      18 ..       5      20 ..       4      25 .. 0.90
   2 ?   -0.0   0.0      0.61     4e+02     138     168 ..      86     116 ..      70     130 .. 0.73
   3 ?    0.7   0.2      0.37   2.5e+02       3      35 ..     150     182 ..     149     188 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0054
                                      EEEEE--SHHHHHHHH CS
                     FAD_binding_3  3 dVlIVGaGpaGlmlal 18
                                      +V+I+G+G aG+++a+
  gi|242398255|ref|YP_002993679.1|  5 KVVIIGGGAAGMSAAS 20
                                      69************96 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.61
                                       CCCEEEECCTTEEEEEEEEEEEE--GTT-HH CS
                     FAD_binding_3 138 vtaevrdketgeeetvrakYlvGaDGgrStv 168
                                       ++  vr +e++ e t + +Ylv a G+  ++
  gi|242398255|ref|YP_002993679.1|  86 EQGSVRVREKDGEHTYEWDYLVFANGASPRI 116
                                       56678878888888************97665 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.37
                                       EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSS CS
                     FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekrst 35 
                                       dVl++G+G   l  a     +G +v+l+ + ++
  gi|242398255|ref|YP_002993679.1| 150 DVLVIGTGYIALEMAEAFVVQGKNVTLIGRSER 182
                                       8***************************99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (442 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); 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: 0.70u 0.35s 00:00:01.04 Elapsed: 00:00:00.50
# Mc/sec: 2684.70
//
Query:       gi|242398256|ref|YP_002993680.1|  [L=355]
Description: hypothetical protein TSIB_0264 [Thermococcus sibiricus MM 739]
Scores for complete 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-132  440.3   1.6   4.8e-132  440.1   1.6    1.0  1  DUF1464      Protein of unknown function (DUF1464)
  ------ inclusion threshold ------
      0.016   15.2   0.0      0.035   14.1   0.0    1.5  1  B12-binding  B12 binding domain


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 !  440.1   1.6  5.3e-136  4.8e-132       1     327 []       5     351 ..       5     351 .. 0.99

  Alignments for each domain:
  == domain 1  score: 440.1 bits;  conditional E-value: 5.3e-136
                           DUF1464   1 GiDPGtksydvvvvddlgkvvlekeiptdevekdpsvlvkaieearadivalpSGyGlPlkriselaereillltla 77 
                                       G+DPGt+s+d +++++ gk++l+ ++p+++v+++ps +vkaie+++adi+++pSGyG+Plk+i+el+er+++++tl+
  gi|242398256|ref|YP_002993680.1|   5 GVDPGTRSFDAIGLEN-GKIKLDLSFPSEVVAEEPSKIVKAIEDFNADIIIGPSGYGVPLKHIKELTERDRFEMTLV 80 
                                       9***************.************************************************************ PP

                           DUF1464  78 eeseegl....vGLrellkelaskelnaftiPgVieLptvPewRKvnkiDmGtADKlasavlavadeaeee..eyre 148
                                       +e+e+++    +GL++++ e+a+k++n+++iPgVi+LptvPewRK+nkiDmGtADK+a++vl+++d+a++   ey+e
  gi|242398256|ref|YP_002993680.1|  81 REEEMKEipvlIGLQKMIDEMAEKNMNVWFIPGVIHLPTVPEWRKYNKIDMGTADKMAITVLGIYDQAKRLgvEYSE 157
                                       *****999999***********************************************************99***** PP

                           DUF1464 149 lsFilvEvGsgfnaviaVknGkivDGlGgtilpG..flsaGalDgEvAyllgkvakiekslifsgGvasiagea... 220
                                       +sF+l+EvG+g+n++ aVknGki+DG+Ggti+pG  ++++GalDgEvAyl+g   +++k+++f+gG+++i++e+   
  gi|242398256|ref|YP_002993680.1| 158 VSFVLLEVGFGYNYAGAVKNGKIIDGIGGTIFPGvgYVNSGALDGEVAYLMG---NVRKQHLFWGGASMIVAEKilp 231
                                       *********************************988****************...99******************** PP

                           DUF1464 221 ..elekklsee....aferlke.vvksvaellsskykleeiivSGrlkrikelgkklesrleev......kllelas 284
                                         e++k+l+ee    a+e++k+ ++k+va+ l+ + +++eii+SGrl+ri+el+k++++ +e+       kl++l++
  gi|242398256|ref|YP_002993680.1| 232 peEFAKRLDEEpfanAWEAMKDgFLKAVASELAVVGDAKEIILSGRLMRIEELKKDVKDLFEDKfdlpvvKLRGLEG 308
                                       *************************************************************9989************ PP

                           DUF1464 285 kaKeaaqGaAiianalaGgryrelvdhleiekssgtvldyvkl 327
                                       kaKeaaqG+Aii+++laGg+++elv+h+ei+ks+g vldyv+l
  gi|242398256|ref|YP_002993680.1| 309 KAKEAAQGSAIIGDGLAGGEFKELVEHVEIKKSYGIVLDYVRL 351
                                       *****************************************86 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   3.9e-06     0.035      39      87 ..      37      93 ..      24      93 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.9e-06
                       B12-binding 39 enedivaairaekpdv.vglSalltsqleavkelvel........lkrirprvkvvvG 87
                                      e+ +iv+ai+++++d+ +g S  ++  l ++kel+e+        ++++ ++++v++G
  gi|242398256|ref|YP_002993680.1| 37 EPSKIVKAIEDFNADIiIGPSG-YGVPLKHIKELTERdrfemtlvREEEMKEIPVLIG 93
                                      4589************889999.**************999999998888899999888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        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 0.32s 00:00:00.97 Elapsed: 00:00:00.56
# Mc/sec: 1924.68
//
Query:       gi|242398257|ref|YP_002993681.1|  [L=389]
Description: Nonsense-mediated mRNA decay NMD3 like protein [Thermococcus sibiricus MM 739]
Scores for complete 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-59  200.2   2.0    3.6e-59  200.2   2.0    1.5  2  NMD3          NMD3 family
  ------ inclusion threshold ------
       0.04   14.2   0.1       0.12   12.7   0.0    1.8  2  DUF555        Protein of unknown function (DUF555)
      0.042   13.9   0.1       0.12   12.4   0.1    1.8  1  EFP           Elongation factor P (EF-P) OB domain
      0.063   13.6   0.4         22    5.5   0.0    3.3  3  GFA           Glutathione-dependent formaldehyde-activating e
        0.1   12.8   0.1        9.1    6.5   0.0    2.8  2  Tudor_RapA    RapA N-terminal Tudor like domain
       0.11   13.4   0.1       0.37   11.6   0.0    1.8  2  Rotamase_2    PPIC-type PPIASE domain
       0.57    9.7   4.7         13    5.3   0.0    3.7  4  zf-ribbon_3   zinc-ribbon domain
        0.7   10.1   3.8        7.4    6.8   0.2    2.9  3  Zn-ribbon_8   Zinc ribbon domain
       0.71   10.2   4.9         17    5.8   0.2    3.1  3  Rpr2          RNAse P Rpr2/Rpp21/SNM1 subunit domain
       0.72    9.9   5.8         18    5.5   3.4    3.0  2  DZR           Double zinc ribbon
        1.2    9.4   4.4         19    5.5   0.1    2.9  3  NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like


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 !  200.2   2.0   2.2e-62   3.6e-59       1     243 []      10     278 ..      10     278 .. 0.94
   2 ?   -2.8   0.1       2.1   3.5e+03      77     105 ..     313     341 ..     303     362 .. 0.60

  Alignments for each domain:
  == domain 1  score: 200.2 bits;  conditional E-value: 2.2e-62
                              NMD3   1 CcrCGkei...eelinglCedCllkevditegiekievevCkeCgrylpkgkWvk.aeleseellaeclkklvekgL 73 
                                       C+rCG+++    +li+glC+ C++ke++++ ++++i++e+C++Cg+y+ kg+Wv+ ++++ eel+ e++ +++ ++L
  gi|242398257|ref|YP_002993681.1|  10 CYRCGISEnegGPLIDGLCQVCFRKENPVLLIEDEINTELCQNCGSYKVKGTWVDpKTYNLEELIFEVADNALIENL 86 
                                       ********888778999*******************************999****9889****************** PP

                              NMD3  74 kvseeveevkvelvdaefiwtephskrikv.......................kvtvqgevrgenetilqqevevev 127
                                        ++e+v+++k+   +  +  +e       +                       +v++++++++++++  ++++ v+v
  gi|242398257|ref|YP_002993681.1|  87 ALNERVKSIKIAPREELEEIEEL-----SIgtahvsfqplewhveyfpaiinyEVEIKARIHEMQKELHHEKKIVTV 158
                                       *9999999999754444333333.....2333566****************************9999********** PP

                              NMD3 128 kvkrqqCprCsriaggyyeaivQvRqk.relteeehkrtfelleqli...lkhdahafiskikevkeGlDfyfgsks 200
                                       +v++++CprC+++ ggy+eai+Q R++ r lt+ee++++ +l+e+ +    k d++ fi+++ e++eGlDfy+gs+ 
  gi|242398257|ref|YP_002993681.1| 159 YVRQTVCPRCQKFLGGYFEAILQARAEdRVLTKEEKDEISKLVEEKVdeiMKRDRMGFIQDTVEKEEGLDFYMGSTA 235
                                       ***********************************************999999************************ PP

                              NMD3 201 aArklveflksevggkvkeseklvsedkksgkevyrltysvrl 243
                                       aArkl++ +++++gg+++e+++l+++d+ ++kevyr+++ +r+
  gi|242398257|ref|YP_002993681.1| 236 AARKLAQIIRDRYGGSISEAYQLIGQDRITSKEVYRTSVRIRI 278
                                       ****************************************998 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.1
                              NMD3  77 eeveevkvelvdaefiwtephskrikvkv 105
                                       +e e+++++  + ++i t +h++   ++ 
  gi|242398257|ref|YP_002993681.1| 313 HESEHKDWKSAKRDEIDTIEHERLEAMTT 341
                                       44566677777777777777666555544 PP

>> DUF555  Protein of unknown function (DUF555)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       3.7     6e+03      59      94 ..      74     112 ..      59     114 .. 0.58
   2 ?   12.7   0.0   7.3e-05      0.12      22      57 ..     138     173 ..     130     204 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 3.7
                            DUF555  59 alvvadtalv...glllemkvfnaeseEhaeriakseig 94 
                                       ++ vad+al+   +l   +k  +   +E+ e i   +ig
  gi|242398257|ref|YP_002993681.1|  74 IFEVADNALIenlALNERVKSIKIAPREELEEIEELSIG 112
                                       566788887632223334455555566666666666665 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 7.3e-05
                            DUF555  22 igiAiseagkrlnpeldfveievgetecPkcgeele 57 
                                       i+  i e+ k l++e + v + v++t cP+c++ l 
  gi|242398257|ref|YP_002993681.1| 138 IKARIHEMQKELHHEKKIVTVYVRQTVCPRCQKFLG 173
                                       677899*************************98775 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 ?   12.4   0.1   7.3e-05      0.12      13      41 ..     348     371 ..     346     383 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.3e-05
                                       EEEEETTT--EEEEEHHHHTTGCGG--TT CS
                               EFP  13 yvFMdnetYeqielpkeqlgdaakfLkEg 41 
                                       + FMd+++Ye +el+k  ++     +kEg
  gi|242398257|ref|YP_002993681.1| 348 VQFMDMKSYETFELEKPRFE-----VKEG 371
                                       67*************99883.....3455 PP

>> GFA  Glutathione-dependent formaldehyde-activating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1      0.25     4e+02      46      57 ..       4      15 ..       2      19 .. 0.86
   2 ?    2.4   0.0      0.13     2e+02      46      66 ..      44      64 ..      39      81 .. 0.75
   3 ?    5.5   0.0     0.013        22       4      36 ..     164     196 ..     161     212 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.25
                               GFA 46 kvtrsfCpeCgs 57
                                      +++++fC +Cg 
  gi|242398257|ref|YP_002993681.1|  4 RMSERFCYRCGI 15
                                      68899*****96 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.13
                               GFA 46 kvtrsfCpeCgsplyseesaa 66
                                      +++++ C++Cgs  +  +  +
  gi|242398257|ref|YP_002993681.1| 44 EINTELCQNCGSYKVKGTWVD 64
                                      678899*****9776555555 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.013
                               GFA   4 hCsdCrkasgsaftanavvkaealellegelke 36 
                                        C +C+k  g+ f a +  +ae+  l+++e  e
  gi|242398257|ref|YP_002993681.1| 164 VCPRCQKFLGGYFEAILQARAEDRVLTKEEKDE 196
                                       6***************99999988877775444 PP

>> Tudor_RapA  RapA N-terminal Tudor like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.064     1e+02       5      34 ..     206     235 ..     203     244 .. 0.81
   2 ?    6.5   0.0    0.0056       9.1       1      22 [.     281     302 ..     281     318 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.064
                        Tudor_RapA   5 DeiesqegwkltVeeveeenGlliYlgkre 34 
                                       Dei +++   ++ ++ve+e+Gl +Y g ++
  gi|242398257|ref|YP_002993681.1| 206 DEIMKRDRMGFIQDTVEKEEGLDFYMGSTA 235
                                       777888888888899***********9987 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0056
                        Tudor_RapA   1 FnvGDeiesqegwkltVeevee 22 
                                       F++GD + +++g+ + Veev+ 
  gi|242398257|ref|YP_002993681.1| 281 FRKGDIVCDKKGNVYRVEEVNG 302
                                       99*****************975 PP

>> Rotamase_2  PPIC-type PPIASE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       3.6   5.9e+03      36      55 ..     190     209 ..     176     254 .. 0.57
   2 ?   11.6   0.0   0.00023      0.37      43     102 ..     311     385 ..     290     386 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3.6
                        Rotamase_2  36 aeaalalakagaekdfaala 55 
                                        + ++ +  +  e+++++++
  gi|242398257|ref|YP_002993681.1| 190 TKEEKDEISKLVEEKVDEIM 209
                                       33333333333333333333 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00023
                        Rotamase_2  43 akagae.kdfaalakgnskkaadlgifesasnlpe..............elakaafalkpgevsgpvetdngyyi 102
                                       + +++e kd++++++++ +++++  + ++++ l +              el+k  f+ k+ge+ +++++ ++yyi
  gi|242398257|ref|YP_002993681.1| 311 LTHESEhKDWKSAKRDEIDTIEHERLEAMTTSLTPrevqfmdmksyetfELEKPRFEVKEGEIYKLIKVKGRYYI 385
                                       4455555899999999999999999999999888899999999*******************************8 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1       0.2   3.2e+02      16      23 ..       7      14 ..       6      15 .. 0.77
   2 ?    2.5   0.1     0.065   1.1e+02       5      12 ..      50      58 ..      47      63 .. 0.64
   3 ?    5.3   0.0    0.0081        13      15      26 .]     161     172 ..     158     172 .. 0.86
   4 ?   -1.5   0.0       1.2   1.9e+03      14      20 ..     283     289 ..     281     290 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.2
                       zf-ribbon_3 16 dnvCpyCG 23
                                       ++C+ CG
  gi|242398257|ref|YP_002993681.1|  7 ERFCYRCG 14
                                      57899999 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.065
                       zf-ribbon_3  5 CPnCGa.pl 12
                                      C nCG+ ++
  gi|242398257|ref|YP_002993681.1| 50 CQNCGSyKV 58
                                      556666555 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.0081
                       zf-ribbon_3  15 ddnvCpyCGtkl 26 
                                       +++vCp C+++l
  gi|242398257|ref|YP_002993681.1| 161 RQTVCPRCQKFL 172
                                       699*****9886 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 1.2
                       zf-ribbon_3  14 sddnvCp 20 
                                       ++d+vC 
  gi|242398257|ref|YP_002993681.1| 283 KGDIVCD 289
                                       79****7 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1         4   6.6e+03      29      33 ..      10      14 ..       3      18 .. 0.65
   2 ?    6.8   0.2    0.0045       7.4       8      37 ..      28      59 ..      22      60 .. 0.80
   3 ?    3.3   0.0     0.054        88      26      33 ..     162     169 ..     147     172 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 4
                       Zn-ribbon_8 29 CPeCg 33
                                      C +Cg
  gi|242398257|ref|YP_002993681.1| 10 CYRCG 14
                                      55555 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0045
                       Zn-ribbon_8  8 CeeCghefevlqsisdaplta.CPeCgs.evr 37
                                      C+ C ++ +++  i d+ +t+ C +Cgs +v+
  gi|242398257|ref|YP_002993681.1| 28 CQVCFRKENPVLLIEDEINTElCQNCGSyKVK 59
                                      8888866667777778888999******8875 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.054
                       Zn-ribbon_8  26 ltaCPeCg 33 
                                       +t+CP+C+
  gi|242398257|ref|YP_002993681.1| 162 QTVCPRCQ 169
                                       678****7 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 ?   -1.5   0.1         2   3.2e+03      42      52 ..       4      14 ..       1      16 [. 0.80
   2 ?    5.8   0.2      0.01        17      39      59 ..      41      61 ..      28      72 .. 0.84
   3 ?    5.3   0.0     0.015        24      39      56 ..     156     173 ..     135     214 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 2
                                      TCCCTB-TTT- CS
                              Rpr2 42 svkrtvCkkCg 52
                                       +++++C +Cg
  gi|242398257|ref|YP_002993681.1|  4 RMSERFCYRCG 14
                                      578899*9998 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.01
                                      -SSTCCCTB-TTT--B--CTT CS
                              Rpr2 39 lppsvkrtvCkkCgsvlipgv 59
                                      ++++++ ++C++Cgs+ ++g 
  gi|242398257|ref|YP_002993681.1| 41 IEDEINTELCQNCGSYKVKGT 61
                                      678999*********999885 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.015
                                       -SSTCCCTB-TTT--B-- CS
                              Rpr2  39 lppsvkrtvCkkCgsvli 56 
                                       +   v++tvC +C+++l 
  gi|242398257|ref|YP_002993681.1| 156 VTVYVRQTVCPRCQKFLG 173
                                       455679********9985 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   3.4     0.011        18      11      35 ..       6      54 ..       3      62 .. 0.66
   2 ?    2.5   0.0     0.089   1.5e+02      28      36 ..     162     170 ..     139     174 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.011
                               DZR 11 darfCseCgtklkavaa........................edrCpsCg 35
                                      + rfC++Cg + ++                            + C +Cg
  gi|242398257|ref|YP_002993681.1|  6 SERFCYRCGISENEGGPlidglcqvcfrkenpvlliedeinTELCQNCG 54
                                      5789999999876433377555556666666666666666666666666 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.089
                               DZR  28 edrCpsCge 36 
                                       +++Cp+C++
  gi|242398257|ref|YP_002993681.1| 162 QTVCPRCQK 170
                                       778888875 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 ?    4.5   0.1     0.023        38      18      30 ..       2      14 ..       1      17 [. 0.86
   2 ?    5.5   0.1     0.011        19      11      34 ..      28      58 ..      26      71 .. 0.83
   3 ?   -3.1   0.1       5.6   9.1e+03      24      30 ..     163     169 ..     156     170 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.023
                      NOB1_Zn_bind 18 tkdmtkkFCpkCG 30
                                      +++m+ +FC +CG
  gi|242398257|ref|YP_002993681.1|  2 VRRMSERFCYRCG 14
                                      6789********9 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.011
                      NOB1_Zn_bind 11 ChaCfk.......vtkdmtkkFCpkCGnktL 34
                                      C+ Cf+       +  + + + C++CG+  +
  gi|242398257|ref|YP_002993681.1| 28 CQVCFRkenpvllIEDEINTELCQNCGSYKV 58
                                      999999888877555779*********9766 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 5.6
                      NOB1_Zn_bind  24 kFCpkCG 30 
                                         Cp+C 
  gi|242398257|ref|YP_002993681.1| 163 TVCPRCQ 169
                                       5699995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1199  (0.0668749); expected 358.6 (0.02)
Passed bias filter:                      725  (0.0404373); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.65u 0.33s 00:00:00.98 Elapsed: 00:00:00.51
# Mc/sec: 2282.87
//
Query:       gi|242398258|ref|YP_002993682.1|  [L=99]
Description: hypothetical protein TSIB_0266 [Thermococcus sibiricus MM 739]
Scores for 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  107.5   0.0    3.4e-31  107.4   0.0    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 !  107.4   0.0   1.9e-35   3.4e-31       1      92 []       8      98 ..       8      98 .. 0.98

  Alignments for each domain:
  == domain 1  score: 107.4 bits;  conditional E-value: 1.9e-35
                                      EEETTE.EEEEEEEGGGTT-EEEETTEEEE--HHHH--EEE-HHHHHHHHHHHEEEEEESHHHHHHHHHTTSS-GGG-E CS
                            DUF424  1 yrtddllklvavcdkellgktfkegelllnvsegfyggelaseeeaikeLekatiaNivgeeavvlavkaGlvdpdsVl 79
                                      yr++++ +lva+cd+ellgktf+egel+l+v+e fy+gel++ + + + Le+atiaN++ge++v++a++ G+vdp++Vl
  gi|242398258|ref|YP_002993682.1|  8 YRVQGE-VLVAACDEELLGKTFREGELKLEVKERFYKGELKEIDVLEELLEDATIANLTGERCVKKAIDLGYVDPERVL 85
                                      7999**.**********************************99999********************************* PP

                                      EETTEEEEEEEE- CS
                            DUF424 80 vidgvphaqigkl 92
                                      +++g+phaq+ kl
  gi|242398258|ref|YP_002993682.1| 86 RVQGIPHAQMAKL 98
                                      **********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); 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 0.32s 00:00:00.86 Elapsed: 00:00:00.54
# Mc/sec: 552.83
//
Query:       gi|242398259|ref|YP_002993683.1|  [L=1870]
Description: pyrolisin-like serine protease [Thermococcus sibiricus MM 739]
Scores for complete 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-29  101.4   0.0    3.1e-28   98.9   0.0    2.1  1  Peptidase_S8  Subtilase family
    6.4e-08   32.8   5.8    5.5e-06   26.6   0.6    3.5  3  CARDB         CARDB
    1.2e-07   32.8   5.0      1e-06   29.7   4.0    3.4  2  PPC           Bacterial pre-peptidase C-terminal domain
  ------ inclusion threshold ------
      0.055   14.2   1.2       0.19   12.4   0.0    2.6  3  fn3_5         Fn3-like domain
       0.14   12.4   5.1         10    6.5   0.0    4.6  4  NPCBM_assoc   NPCBM-associated, NEW3 domain of alpha-galactos


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 !   98.9   0.0   8.6e-32   3.1e-28       1     298 []     246     948 ..     246     948 .. 0.80

  Alignments for each domain:
  == domain 1  score: 98.9 bits;  conditional E-value: 8.6e-32
                                       -TT-EEEEECS-B-TT-TTTGGGEEE..EEEE---TTSG...................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..................................... RF
                      Peptidase_S8   1 gkgvlvavlDtGvdpshpdlsvttdgerklvdvideegag..................................... 40 
                                       g+gv vav+D+Gvd ++pdl++ +  + +l    +                                          
  gi|242398259|ref|YP_002993683.1| 246 GEGVNVAVIDSGVDFGNPDLQDAYAVDTNL----N----Spyygwpiafdgnsmlyyllfgatfldfatfsgylysw 314
                                       79*******************655444443....2....13335889999999************************ PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                      Peptidase_S8  41 ............................................................................. 40 
                                                                                                                    
  gi|242398259|ref|YP_002993683.1| 315 yanteypiepypvygyfgigykgnyttvftsmslanipddyersqlinntlkwvgnvtnillvdddggdllelfyie 391
                                       ************************************************99999999999999999999999999999 PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                      Peptidase_S8  41 ............................................................................. 40 
                                                                                                                    
  gi|242398259|ref|YP_002993683.1| 392 aldylgvnytyyeipdetangpnvtvlsnyslviwftgatytntltnadignltqylenggklwlissdylydvgld 468
                                       99999999999999999999999999999999999888888888888888888888888888888888888888888 PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                      Peptidase_S8  41 ............................................................................. 40 
                                                                                                                    
  gi|242398259|ref|YP_002993683.1| 469 nnfttnylhiadaiedypvptviydyngdayyggevyqglwesptdiaadyivpdanatilltgytvyaydpqlygy 545
                                       88888888888888888888888887777777777777777777777777777777777777777777777777777 PP

                                       .................................................................GGEETT-SS-TT CS
                                       .................................................................xxxxxxxxxxxx RF
                      Peptidase_S8  41 .................................................................fngadsettstn 52 
                                                                                                        f           
  gi|242398259|ref|YP_002993683.1| 546 yvdiklpltkdltiptqsgtmklglhpdlalwydwyggfvlvtdpnanqtydtvyvdltpsvvidF----------- 611
                                       777777777777777777777777777777777777777776555555555555555555555550........... PP

                                       -SC-S........................................................................ CS
                                       xxxxx........................................................................ RF
                      Peptidase_S8  53 wardd........................................................................ 57 
                                           +                                                                        
  gi|242398259|ref|YP_002993683.1| 612 ----Nkdtghtkdnpvvqldfwdtfenwfgqdgyadlsggliyfiadgetpipysdkvaerwglplripgngdlvaf 684
                                       ....055555555555555566666666666699999999999999999999999999999********97777777 PP

                                       .....SS........HHHHHHHHHH-B..SSSSSB-SSTTSEEEEEE-SSTTSB-HH...HHHHHHHHHHHHCT-S. CS
                                       .....xxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx. RF
                      Peptidase_S8  58 .....ngnsie....HGthvAGiaaanapeegekngvapgakilsvkvldtsggsmetg.teliraieeaaedkvd. 123
                                            +         HGt +A  ++a      ++ g+ +g  i+   +  +s+ +  +  + l+ a+e       d 
  gi|242398259|ref|YP_002993683.1| 685 mignvY----IgggdHGTLCAAAVGAR---GRTFLGLTFGNAIGTKIIAEGSLYQGGSWlDYLYFAVEG-----YDg 749
                                       666442....14566***********9...899999999999986555655555554444555555432.....222 PP

                                       .........EEEE-EESCETTCHHCHHHHHH.HHHHHH.CCT-EEEEE--SS-T-HHEEE-TTCEECTTTSTTCEEE CS
                                       .........xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 124 .........vinmslgestslpktgrsieal.ainravnkkgvlvviSaGNngktgsslqagspvgtpstsknvitv 190
                                                v+++s+  s++ +k  +++e    +++ ++  ++ + ++ GN g      +   + +  ++s  vi+v
  gi|242398259|ref|YP_002993683.1| 750 ivatgdealVVSNSYSVSSDIQKGFSWYERFlYYMTEMYAPNTAFLFAMGNGG------PGYGTTHRYASSPAVIGV 820
                                       223344555********************998667777689************......66667777777788**** PP

                                       EEES....................TTSSB-TT--B-TT.......-EEEE-S-CCCCCCCCCHHHTTTHHEEEE-SH CS
                                       xxxx....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 191 gayt....................tegkiapfSsrGpssdgklkpdivapGgnivstwsrqsnnsaglssyqsmsGT 247
                                       ga++                    + g++ +fS rGp++ g++kpd+ a G+  + + + +   ++g    +++sGT
  gi|242398259|ref|YP_002993683.1| 821 GAAVefgyralfgydngpwgyelaNYGDVVWFSDRGPNALGRVKPDVIAVGAYALGSLPVNY-VGDGFWAADLWSGT 896
                                       *****************************************************888888887.33333349****** PP

                                       HHCHHHHHHHHHHHHHHHTT.....--HHHHHHHHHCCS-EE......SSSSSSTT CS
                                       xxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 248 SmAsPnaagaaAlllsalpk.....ltpetvraallntAqdlgkadniesfaqGaG 298
                                       S A+P+aag+aAl+ +a+ +      t+++v+++l+ tA    k+ n+ +f+qGaG
  gi|242398259|ref|YP_002993683.1| 897 SLATPMAAGIAALVYEAFYEshgrwPTAHEVKEILMSTA----KNVNHDVFSQGAG 948
                                       ****************66666**98899***********....56699******99 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.0    0.0023       8.1      31      83 ..     975    1027 ..     974    1031 .. 0.86
   2 ?   -3.0   0.1       2.5     9e+03      61      82 ..    1458    1478 ..    1438    1480 .. 0.68
   3 !   26.6   0.6   1.5e-09   5.5e-06      15      85 ..    1573    1643 ..    1560    1655 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0023
                                        SSS-EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S-S-CEEEEEEE CS
                             CARDB   31 GtaasgatkvalyldgelvgtvtvpsLaagesttvsftwtteategevtltvv 83  
                                        G+ + + +   ly  ++  +t+tv++++++e++tv+++  +  + gev+l vv
  gi|242398259|ref|YP_002993683.1|  975 GKTNYPMFANVLYPGESASKTFTVENINPNENVTVEISAEIFQKIGEVELDVV 1027
                                        6667777777888888889*******************999989999999886 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.5
                                        EEEEEEEEEE-S-S-CEEEEEE CS
                             CARDB   61 esttvsftwtteategevtltv 82  
                                        +++++++t   + t+g++ ++v
  gi|242398259|ref|YP_002993683.1| 1458 ATSDETVTLDFP-TPGQYVIEV 1478
                                        455566666666.889999987 PP

  == domain 3  score: 26.6 bits;  conditional E-value: 1.5e-09
                                        EETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE.EEEEESEE-CTEEEEEEEEEE-S-S-CEEEEEEEES CS
                             CARDB   15 afvgeentitvtvkNqGtaasgatkvalyldgelv.gtvtvpsLaagesttvsftwtteategevtltvvvD 85  
                                        ++v   +++t+ v+N+G  ++++++v+++ d   +  +v++p +a+ge ++v+f+++++  +  +++++vv 
  gi|242398259|ref|YP_002993683.1| 1573 PYVDGIYNVTIYVTNEGLSNATDVEVRVVRDNVPTdIQVSIPTIAPGEIYNVTFSIPMM-DSLLHEYKFVVN 1643
                                        566667899*********************99996556666*****************9.776666666664 PP

>> PPC  Bacterial pre-peptidase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       4.4   1.6e+04       4      31 ..    1238    1270 ..    1235    1279 .. 0.64
   2 !   29.7   4.0   2.9e-10     1e-06       1      70 []    1407    1480 ..    1407    1480 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 4.4
                                        EEEEEE-..TT-E.EEEEES-TT....SEEEEE CS
                               PPC    4 vysfevp..agds.ltididggti..dldLyll 31  
                                        v+ f+ p  + +s + +d+d+ +   d +L ll
  gi|242398259|ref|YP_002993683.1| 1238 VFHFNIPesEEGSyVLVDLDWENEmtDINLHLL 1270
                                        566666633344546688888887445557666 PP

  == domain 2  score: 29.7 bits;  conditional E-value: 2.9e-10
                                        -EEEEEEEE-TT-EEEEEES-TT.......SEEEEE-TT..-SS-EE-STT-TTS-TTS-EE-SSSEEEEEEE.. CS
                               PPC    1 dvDvysfevpagdsltididggti.....dldLylldsngtsvaaydansapsgsdeyieftapqaGtYyvaVss 70  
                                        d+++y ++v+++  l++++++        dldLy+++++ +++   +++s + +sde+++ ++p++G+Y ++V+s
  gi|242398259|ref|YP_002993683.1| 1407 DSHYYAVNVATSPILDVELNSVWDelaglDLDLYVYYNESGTLIE-VGSSTTATSDETVTLDFPTPGQYVIEVYS 1480
                                        789****************999999999***********666666.788899999******************96 PP

>> fn3_5  Fn3-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.1       4.8   1.7e+04      16      79 ..     998    1012 ..     989    1018 .. 0.52
   2 ?   12.4   0.0   5.4e-05      0.19      57      88 ..    1142    1173 ..    1117    1193 .. 0.78
   3 ?   -2.8   0.1       2.7   9.7e+03      13      37 ..    1502    1526 ..    1499    1533 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 4.8
                             fn3_5   16 lkNtsnkaltykvsandvlTdladkeegklilkaaspeikeaaltfetskvtvpAnssktvtvt 79  
                                        ++N                                                 +++n+ +tv++ 
  gi|242398259|ref|YP_002993683.1|  998 VEN-------------------------------------------------INPNENVTVEIS 1012
                                        333.................................................455555555544 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 5.4e-05
                             fn3_5   57 aaltfetskvtvpAnssktvtvtldlpsdakk 88  
                                        + ++++++++tv++n+++t+++t+++psda+ 
  gi|242398259|ref|YP_002993683.1| 1142 TWIKLDKNTLTVEPNQKATFKATASVPSDAEF 1173
                                        678999**********************8764 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 2.7
                             fn3_5   13 tltlkNtsnkaltykvsandvlTdl 37  
                                        +l++kN+++ + ty+++a   lT++
  gi|242398259|ref|YP_002993683.1| 1502 ELQVKNITEFNGTYTITAAYNLTEE 1526
                                        6899999999999999998666655 PP

>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.08   2.9e+02      31      60 ..     969     999 ..     952    1013 .. 0.82
   2 ?    6.5   0.0    0.0028        10      41      70 ..    1148    1176 ..    1128    1184 .. 0.80
   3 ?    2.0   0.2     0.069   2.5e+02       9      57 ..    1581    1626 ..    1579    1630 .. 0.50
   4 ?   -3.1   0.0       2.8   9.9e+03      47      64 ..    1740    1757 ..    1735    1759 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.08
                       NPCBM_assoc  31 PeGWtvvevspasaa.slapGetveatvkVt 60 
                                       P+ W++ ++    +a  l pGe+++ t++V 
  gi|242398259|ref|YP_002993683.1| 969 PSSWQAGKTNYPMFAnVLYPGESASKTFTVE 999
                                       999997766666655699**********995 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0028
                       NPCBM_assoc   41 pasaaslapGetveatvkVtppagaaaGdy 70  
                                          +  +++p+++++++++ ++p++a+ G+y
  gi|242398259|ref|YP_002993683.1| 1148 K-NTLTVEPNQKATFKATASVPSDAEFGTY 1176
                                        3.3348**********************99 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.069
                       NPCBM_assoc    9 ltltvtndgtaaatnvslsls...lPeGWtvvevspasaaslapGetveatv 57  
                                        +t++vtn+g + at+v++++    +P +         s++++apGe   +t+
  gi|242398259|ref|YP_002993683.1| 1581 VTIYVTNEGLSNATDVEVRVVrdnVPTDI------QVSIPTIAPGEIYNVTF 1626
                                        66677777777777777666311122222......24444555555444444 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 2.8
                       NPCBM_assoc   47 lapGetveatvkVtppag 64  
                                        l+  ++++++v++t+pa+
  gi|242398259|ref|YP_002993683.1| 1740 LPETRALKVQVQITSPAN 1757
                                        666677889999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1870 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); 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: 1.13u 0.34s 00:00:01.47 Elapsed: 00:00:00.56
# Mc/sec: 10089.38
//
Query:       gi|242398260|ref|YP_002993684.1|  [L=380]
Description: Bifunctional carboxypeptidase/aminoacylase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-37  129.5   0.2      2e-37  128.9   0.2    1.2  1  Peptidase_M20  Peptidase family M20/M25/M40
    4.8e-12   45.8   0.1    1.3e-11   44.3   0.1    1.7  1  M20_dimer      Peptidase dimerisation domain


Domain annotation for each model (and alignments):
>> Peptidase_M20  Peptidase family M20/M25/M40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.9   0.2   2.2e-41     2e-37       1     199 [.      68     370 ..      68     377 .. 0.88

  Alignments for each domain:
  == domain 1  score: 128.9 bits;  conditional E-value: 2.2e-41
                                       EEEEES-BSS.TTCGGGSSSTTSEEETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTTT CS
                                       xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20   1 llgsHlDvVp.eeetdgwttpfslteedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggrg 76 
                                       +l++++D++p +ee+d    p++++++ Gk++++G+d +++++l+a ++++++k+e    + +++l+fqp+EEgg +
  gi|242398260|ref|YP_002993684.1|  68 ALRADMDALPvQEENDV---PYKSRVP-GKMHACGHDAHTAMLLGASKIIAEHKEEL---PNKVRLIFQPAEEGG-N 136
                                       69********8777755...*****99.****************************8...99***********98.* PP

                                       HHHHHHH.HHHTTTCESEEEEEEEESSSBTCHSTETEEEE..................................... CS
                                       xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..................................... RF
                     Peptidase_M20  77 Gakalle.gleerekvdavfelhieepgileagklaigvv..................................... 115
                                       Ga +++e g++  ++vda+f+lh++   +++ g ++i+ +                                     
  gi|242398260|ref|YP_002993684.1| 137 GALKMIEdGAL--KGVDAIFGLHVW-MELPS-GIVGIREGpfmagvgrfdieiegkgghgasphetidpvpiaaqvi 209
                                       *******8776..59*********9.66666.5544444499999******************************** PP

                                       .......................................................................EEEEEE CS
                                       .......................................................................xxxxxx RF
                     Peptidase_M20 116 .......................................................................kvevel 121
                                                                                                              +++++ 
  gi|242398260|ref|YP_002993684.1| 210 lafqtiisrnlnplesgvvsvgtikageafnvipervymngtyrfftqetkkliekrieevlkgiviannaSYKLK- 285
                                       *********************************************************************8767887. PP

                                       EEEESHEEECCHHHHHHHHHHHHHHHTSCEEEEEESSSBHTHHHH.TTTE.EEEEEE.SSG..GCTTS.TTTEEE.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx.xxxxxx.xxx..xxxxx.xxxxxx.. RF
                     Peptidase_M20 122 leggapvtlndsplvkalaeaaeelfgekvelivsgpggtdarff.agip.tvmifg.pgs..glaHs.pnEyvd.. 190
                                       +e+ ap+t+nds ++ + +++a++l g+kve++++++g++d++f+ +++p +++ +g +++   +++  ++++++  
  gi|242398260|ref|YP_002993684.1| 286 IEEVAPPTINDSSMASLTKRVAQKL-GLKVEEVPKSMGSEDFSFYlQKVPgAFIALGiRNEekRIIYPhHHPKFNvd 361
                                       79**********************9.*9977765558********9999945566**88845755544477776643 PP

                                       HHHHHHHHH CS
                                       xxxxxxxxx RF
                     Peptidase_M20 191 ledlekgik 199
                                       +e l+ g++
  gi|242398260|ref|YP_002993684.1| 362 EEVLPLGTA 370
                                       666766665 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.3   0.1   1.5e-15   1.3e-11       5     102 ..     177     272 ..     175     278 .. 0.95

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 1.5e-15
                                       EEEEEEEEEE-B-EEGG-TTTTB-HHHHHHHHHHCSCTTEEC.....TCCTCCCCCEECCE-CCCCEESSEEEEEEE CS
                         M20_dimer   5 GlaggkitvkgkagHsgapgagaNAieklarllaeledeegdiaeerslprttlnvtgiegGsaknvipdeaeakid 81 
                                       G+  + i+++gk+gH++ p+  ++++ ++a+++ +++   +++   ++l    ++v++i++G a nvip++++++ +
  gi|242398260|ref|YP_002993684.1| 177 GVGRFDIEIEGKGGHGASPHETIDPVPIAAQVILAFQTIISRNL--NPLESGVVSVGTIKAGEAFNVIPERVYMNGT 251
                                       8889***********************************88866..******************************* PP

                                       EEHHHHHHHHHHHHHHHHHHT CS
                         M20_dimer  82 iRllpgedpeevleeieeile 102
                                        R+  +e+ + ++++iee+l+
  gi|242398260|ref|YP_002993684.1| 252 YRFFTQETKKLIEKRIEEVLK 272
                                       ******************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); 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: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2338.92
//
Query:       gi|242398261|ref|YP_002993685.1|  [L=347]
Description: hypothetical protein TSIB_0269 [Thermococcus sibiricus MM 739]
Scores for complete 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   68.9  31.2      9e-19   67.9  31.2    1.6  1  O_anti_polymase  Putative O-antigen polymerase


Domain annotation for each model (and alignments):
>> O_anti_polymase  Putative O-antigen polymerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.9  31.2     5e-23     9e-19       2     322 ..      39     318 ..       7     333 .. 0.77

  Alignments for each domain:
  == domain 1  score: 67.9 bits;  conditional E-value: 5e-23
                   O_anti_polymase   2 lfspliivlllilfiilsaia..vsslliilillglisfilgalllsklvlsieellvknnkkkleikfnekkveki 76 
                                       + s lii l++  +++l + +   + + +  +l++++sf+l+++   +l +      v+       +  +++ +ek 
  gi|242398261|ref|YP_002993685.1|  39 IMSALIIALIFWGVLVLGYLKpiQFPEWVYWLLIFILSFALPIYG--QLAVL-----VMF-----LLSREYNAFEKY 103
                                       556677777777777775544434445555559999999999988..22222.....222.....222333344444 PP

                   O_anti_polymase  77 glilvliGillfiinllivggiPlfdpslraklntkltalsylflpsiailvakvarlrnlilfiiglvllallgYr 153
                                           vl+G +l i+ l++ +giP f+  lr kl + l +l++l  +s ++     + + +++ ++i  vl++l  +r
  gi|242398261|ref|YP_002993685.1| 104 AK-FVLLGSILSILVLYSFEGIPFFQWGLRFKLVKPLVFLAFLSGISLTYCRL--NWKPKILALLILEVLFFLGTFR 177
                                       44.568899999999**********************9999998888888877..556788888888999******* PP

                   O_anti_polymase 154 ttvlaillsilitlYytkkikikeivllilllvllllgigylrsiseqawslnplelllyRadftlsvldkivk..g 228
                                         +l ++l +++ +Yy++k+ +k++++++ ++++    + yl         +  le ll+R +ft  v+  iv+   
  gi|242398261|ref|YP_002993685.1| 178 SLMLLVFLFYILPYYYENKLAFKQVLVAVPIFLV----VIYL---------SGNLESLLVRVGFTFLVFHNIVSvsL 241
                                       ************************9998876666....5555.........345799*****************844 PP

                   O_anti_polymase 229 lqgvthGklllsaitslsssgprvligklilgrevsiTsTlfGpvllDFGllgvliqmlilgllLgilykiikklkd 305
                                         g++hG lll+       s+pr  ++ +    +   T  lfG+ + DFG+lg+ i+  ++g lL+++    + +  
  gi|242398261|ref|YP_002993685.1| 242 PLGFFHGRLLLH-------SDPRWRVAFMFTL-NSRYTYFLFGQPIADFGVLGI-IETYLIGSLLKLSEADERTA-- 307
                                       4599*****987.......8******976555.66789****************.68999999998876544443.. PP

                   O_anti_polymase 306 vllalYsillaytiigi 322
                                             s++la +i  +
  gi|242398261|ref|YP_002993685.1| 308 ------SVVLATLIYAL 318
                                       ......34444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       788  (0.0439511); expected 358.6 (0.02)
Passed bias filter:                      201  (0.0112109); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 2103.65
//
Query:       gi|242398262|ref|YP_002993686.1|  [L=814]
Description: membrane-bound dolichyl-phosphate-mannose-protein mannosyltransferase [Thermococcus sibiricus MM 739]
Scores for complete 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-11   42.5  18.2    3.2e-10   40.4  18.2    2.1  1  PMT_2            Dolichyl-phosphate-mannose-protein mannosylt
    3.1e-06   26.7   1.8      0.021   14.1   0.1    2.2  2  Pec_lyase        Pectic acid lyase
    3.8e-05   23.3   0.0        1.8    8.4   0.0    3.6  3  Prenyltrans      Prenyltransferase and squalene oxidase repea
    9.9e-05   21.6   3.6      0.075   12.1   1.3    2.4  2  Glyco_hydro_88   Glycosyl Hydrolase Family 88
    0.00024   20.3   0.1    0.00079   18.6   0.0    1.8  2  SQHop_cyclase_C  Squalene-hopene cyclase C-terminal domain
      0.002   17.3   0.6      0.012   14.8   0.1    2.4  3  SQHop_cyclase_N  Squalene-hopene cyclase N-terminal domain
     0.0091   15.1   0.2      0.095   11.7   0.0    2.1  2  TED_complement   A-macroglobulin TED domain
  ------ inclusion threshold ------
      0.027   13.0   0.1        1.8    7.1   0.0    2.4  2  LANC_like        Lanthionine synthetase C-like protein
      0.068   11.6   0.2        0.3    9.5   0.2    1.8  1  Glyco_hydro_127  Beta-L-arabinofuranosidase, GH127


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 !   40.4  18.2   1.6e-13   3.2e-10       3     150 ..      68     215 ..      66     222 .. 0.90

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 1.6e-13
                             PMT_2   3 PPliawllalftklfgfselairlvsalagvltilllyllarrlfg.kraallaalllavvplfvalsalftpdapl 78 
                                       PPl+  + alf+ +f ++++ +++++a+ g l+++++y l ++++  ++ a+laall+ + p+f++ + l+ p+++ 
  gi|242398262|ref|YP_002993686.1|  68 PPLFHVIGALFYGIF-KTDYIFFILPAIYGTLSLVAFYYLSKEILEdEKKAFLAALLVGFAPNFLYRTSLYIPENLG 143
                                       9*************8.8999*************************99****************************** PP

                             PMT_2  79 vllwalalylllraleknklkywllagvlfGlgfls.Kytaallliaall.yllisarrilkekkpylalllal 150
                                       +l+ +  ++ll+r+l+++k+ y l + +l+ + + + + ++++++++al+ ++++    ++k+  +yl++l ++
  gi|242398262|ref|YP_002993686.1| 144 ILFFIVGMWLLVRFLKTGKTNYMLSLIILLPIYMVThRGWVFFVGVGALMgFIYFI--PWVKKHLHYLVVLGIV 215
                                       ********************************999835677778888888977777..6999999999554433 PP

>> Pec_lyase  Pectic acid lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.2   5.8e-05      0.11      49      86 ..     561     598 ..     553     609 .. 0.87
   2 !   14.1   0.1   1.1e-05     0.021      41     114 ..     693     763 ..     671     803 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.8e-05
                         Pec_lyase  49 aevykatkdekykdavrkglefllkaqYsnGgwpqfyP 86 
                                       + +y++t+dek+k+     l++l   q +nGg+p   P
  gi|242398262|ref|YP_002993686.1| 561 SYLYQKTGDEKFKERYEWLLKWLAYKQLENGGFPEGIP 598
                                       679*******************************8776 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 1.1e-05
                         Pec_lyase  41 tvtellflaevykatkdekykdavrkglefllkaqYsnGgwpqfyPlkkgY.sehitfnDdamvrvlnllekiae 114
                                       t+     la+ y+ ++de+   a++k+ e++ ++q +nG ++     +kgY ++++t+ D  +v+ +  +e+ +e
  gi|242398262|ref|YP_002993686.1| 693 TIVTAFALARYYQLSEDERVLPAIKKAAEWIREQQEDNGRFK----GEKGYgYSRVTYADVLFVYHIAGMEHEKE 763
                                       7777789********************************976....577775789****9988887777765443 PP

>> Prenyltrans  Prenyltransferase and squalene oxidase repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0   0.00089       1.8       6      35 ..     579     608 ..     577     614 .. 0.85
   2 !    5.9   0.0    0.0055        11       8      28 ..     674     695 ..     669     701 .. 0.80
   3 ?    4.7   0.0     0.013        26       2      18 ..     715     731 ..     714     753 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00089
                                       HHHHHHHHSHTTS-BBSSTTSSBBHHHHHH CS
                       Prenyltrans   6 avefLlscQnedGGwggrpgsesdtyytyw 35 
                                       ++ +L  +Q e GG+ +     ++t yt++
  gi|242398262|ref|YP_002993686.1| 579 LLKWLAYKQLENGGFPEGIPPNDFTLYTAF 608
                                       578************999888888888887 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0055
                                       HHHHHHSHTTS-BBSSTTS.SB CS
                       Prenyltrans   8 efLlscQnedGGwggrpgs.es 28 
                                         +l  Q+ dG+w  + g+  +
  gi|242398262|ref|YP_002993686.1| 674 TKILDEQRNDGSWKKSLGGtIV 695
                                       56999***********998555 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.013
                                       HHHHHHHHHHHHSHTTS CS
                       Prenyltrans   2 dvekavefLlscQnedG 18 
                                        ++ka+e+++  Q + G
  gi|242398262|ref|YP_002993686.1| 715 AIKKAAEWIREQQEDNG 731
                                       689**********7777 PP

>> Glyco_hydro_88  Glycosyl Hydrolase Family 88
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0   0.00029      0.58      75     117 ..     554     594 ..     523     609 .. 0.83
   2 !   12.1   1.3   3.7e-05     0.075      38     132 ..     657     751 ..     622     778 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00029
                                       TGHHHHHHHHHHHH-THHHHHHHHHHHHHHHHCS-B.TTS.B. CS
                    Glyco_hydro_88  75 idigllllllyeltkderykeaaeeladyvlakpprtseGgfw 117
                                       + i+ ++++ly++t+de++ke+ e l +++   ++++++Ggf 
  gi|242398262|ref|YP_002993686.1| 554 ARIAEIYSYLYQKTGDEKFKERYEWLLKWLA--YKQLENGGFP 594
                                       57899***********************998..7777899995 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 3.7e-05
                                       HHHHHHHH--HHHHHHHHHHHHHCCCTTS-CTTSGGGTGHHHHHHHHHHHH-THHHHHHHHHHHHHHHHCS-B.TTS CS
                    Glyco_hydro_88  38 lleayeatgdkeyldyakawadslideggktelelDdidigllllllyeltkderykeaaeeladyvlakpprtseG 114
                                       +l+ ye  ++    ++++++ d++ ++g  ++    +i  ++ l++ y+l +der+  a++++a+++ +++++  +G
  gi|242398262|ref|YP_002993686.1| 657 ILYEYELLNKTVLDNIITKILDEQRNDGSWKKSLGGTIVTAFALARYYQLSEDERVLPAIKKAAEWIREQQED--NG 731
                                       667899999999999999999999998888777778899999999********************87755555..88 PP

                                       .B.S..BTTSTTEEETHHHH CS
                    Glyco_hydro_88 115 gfwh..kkkepeqlWlDgLf 132
                                        f       + + +++D Lf
  gi|242398262|ref|YP_002993686.1| 732 RFKGekGYGYSRVTYADVLF 751
                                       88873344556667888887 PP

>> SQHop_cyclase_C  Squalene-hopene cyclase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       1.5     3e+03     213     226 ..     580     593 ..     561     596 .. 0.48
   2 !   18.6   0.0     4e-07   0.00079     156     238 ..     664     746 ..     645     751 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.5
                                       HHHHHTT--TTSSB CS
                   SQHop_cyclase_C 213 vdWlksvqnedGGW 226
                                       ++Wl  +q e+GG+
  gi|242398262|ref|YP_002993686.1| 580 LKWLAYKQLENGGF 593
                                       33444444444443 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 4e-07
                                       TTSHHHHHHHHHHHHHS-TTS----SSBSSHHHHHHHHHHHHHHTT--.TTSHHHHHHHHHHHTT--TTSSB.B--G CS
                   SQHop_cyclase_C 156 edsealkraveylkkeqepdGsWfGrWGvnyiyGtwsvlsalaavged.leepvirkavdWlksvqnedGGW.Gesa 230
                                        ++ +l + +  +  eq++dGsW    G   +  t  +l    +++ed    p+i+ka++W++++q+++G + Ge+ 
  gi|242398262|ref|YP_002993686.1| 664 LNKTVLDNIITKILDEQRNDGSWKKSLGGTIV--TAFALARYYQLSEDeRVLPAIKKAAEWIREQQEDNGRFkGEKG 738
                                       4566788899999**********999987655..667777777788773567**************99997668888 PP

                                       GGGT-GGG CS
                   SQHop_cyclase_C 231 esykdpkl 238
                                         y+  ++
  gi|242398262|ref|YP_002993686.1| 739 YGYSRVTY 746
                                       88876655 PP

>> SQHop_cyclase_N  Squalene-hopene cyclase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.41   8.2e+02      40      65 ..     569     594 ..     550     635 .. 0.79
   2 !   10.1   0.1   0.00015       0.3      28     105 ..     650     725 ..     623     726 .. 0.84
   3 !   14.8   0.1   5.9e-06     0.012       7      96 ..     675     765 ..     669     772 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.41
                   SQHop_cyclase_N  40 geddeeeeekiakylrsqqredGgWe 65 
                                       +e+ +e+ e + k+l  +q e+Gg++
  gi|242398262|ref|YP_002993686.1| 569 DEKFKERYEWLLKWLAYKQLENGGFP 594
                                       55557778888999999999999997 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00015
                   SQHop_cyclase_N  28 itaeyillreflgeddeeeeekiakylrsqqredGgWelypggpgdlsttveaYlALkllGdspdapalarArefil 104
                                        +a+++ +    +  +++  ++i + ++++qr+dG+W+   gg+    ++   Y+   l  d+   pa+++A+e+i+
  gi|242398262|ref|YP_002993686.1| 650 AEAQMLPILYEYELLNKTVLDNIITKILDEQRNDGSWKKSLGGTIVTAFALARYYQ--LSEDERVLPAIKKAAEWIR 724
                                       5666666666666777889999*********************9999999999985..5678999999999999999 PP

                   SQHop_cyclase_N 105 a 105
                                       +
  gi|242398262|ref|YP_002993686.1| 725 E 725
                                       7 PP

  == domain 3  score: 14.8 bits;  conditional E-value: 5.9e-06
                   SQHop_cyclase_N   7 allslqkpdGhWvgeLeanvtitaeyillrefl.geddeeeeekiakylrsqqredGgWelypggpgdlsttveaYl 82 
                                        +l++q++dG W+  L   +++        ++  +e+    ++k+a+++r+qq+++G ++  +g      t  +  +
  gi|242398262|ref|YP_002993686.1| 675 KILDEQRNDGSWKKSLGGTIVTAFALARYYQLSeDERVLPAIKKAAEWIREQQEDNGRFKGEKGYGYSRVTYADVLF 751
                                       6899************876554444444444443333445899***************9988888877777777777 PP

                   SQHop_cyclase_N  83 ALkllGdspdapal 96 
                                          ++G++ +++++
  gi|242398262|ref|YP_002993686.1| 752 VYHIAGMEHEKEQM 765
                                       77777777777777 PP

>> TED_complement  A-macroglobulin TED domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0     0.089   1.8e+02     120     137 ..     578     595 ..     532     609 .. 0.67
   2 !   11.7   0.0   4.7e-05     0.095      66     140 ..     670     738 ..     602     750 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.089
                                       HHHHHHHTTB-TTS-B-- CS
                    TED_complement 120 eslewLlseQkedGsFke 137
                                         l+wL+ +Q e+G F e
  gi|242398262|ref|YP_002993686.1| 578 WLLKWLAYKQLENGGFPE 595
                                       446677778888888866 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 4.7e-05
                                       HHHHHHHHTCBETTSEBBSSS..SS-BEHHHHHHHHHHHHHCHHHST--HHHHHHHHHHHHTTB-TTS-B--SS- CS
                    TED_complement  66 ekgyqrqlsykkadgsysafgkdssegstWLtAfvlkvlaqakefifideeeiseslewLlseQkedGsFkeegs 140
                                        +   ++l  +++dgs   ++  +s g t +tAf l  ++q +e   +   +i+++ ew+ ++Q+++G Fk e+ 
  gi|242398262|ref|YP_002993686.1| 670 DNIITKILDEQRNDGS---WK--KSLGGTIVTAFALARYYQLSEDERVL-PAIKKAAEWIREQQEDNGRFKGEKG 738
                                       5555666777777776...56..6789999*****99999999988775.57******************97765 PP

>> LANC_like  Lanthionine synthetase C-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.011        22     277     318 ..     557     595 ..     554     606 .. 0.78
   2 ?    7.1   0.0    0.0009       1.8      14     212 ..     696     736 ..     657     808 .. 0.66

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.011
                                       HHHHHHHHHHH--HHHHHHHHHHHHHHHHTCCSHHHTTSSB- CS
                         LANC_like 277 leillllykltndekylerakkfieslldegkkngfetglge 318
                                       +ei+ +ly++t+dek++er +  +++l  ++++ng   g++e
  gi|242398262|ref|YP_002993686.1| 557 AEIYSYLYQKTGDEKFKERYEWLLKWLAYKQLENG---GFPE 595
                                       78999999999999999999999999999998887...4444 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0009
                                       HHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHCCH.-S--STTTSHHHHHHHHHHHHHHCTHHHHHHHHHHHHHCCH CS
                         LANC_like  14 iallllelykvtknekylklahkylekikkelselglesisffsGaagiafalavaskklgnyqellkaldslleli 90 
                                       +                                                                            
  gi|242398262|ref|YP_002993686.1| 696 T---------------------------------------------------------------------------- 696
                                       3............................................................................ PP

                                       HHCTCHT..GHSSTTTSHHHHHHHHHHHHHHH-SGHHHHHHHHHHHHHHHCHHCCTTTCHSCHH-BTTBEB-STTTS CS
                         LANC_like  91 eeekledekkdyDvisGlaGilsyllllneetkieedllkqilkylvelgiksenqvswsplmyepegesnlGlAHG 167
                                                                                                                    
  gi|242398262|ref|YP_002993686.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                                       HHHHHHHHHCCCHT.-HHHHHHHHHHHHHHHHHTS-TGTST--SB CS
                         LANC_like 168 lsGialallalykgtksekllelikkllkylkslkfksegnWpds 212
                                           a+al ++y+  ++e+ l +ikk+++++++++ +++g ++  
  gi|242398262|ref|YP_002993686.1| 697 ----AFALARYYQLSEDERVLPAIKKAAEWIREQQ-EDNGRFKGE 736
                                       ....4455555555555555555555555555555.223333332 PP

>> Glyco_hydro_127  Beta-L-arabinofuranosidase, GH127
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.2   0.00015       0.3      64     166 ..     555     732 ..     506     751 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00015
                                       HHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHCH.SSS-B-GCCTHH.............................. CS
                   Glyco_hydro_127  64 kwleavalllastkdkelekrldrlvdelakaQq.edGYlsavtelk.............................. 109
                                        + e +++l+++t+d+++++r + l++ la  Q  + G+ ++++  +                              
  gi|242398262|ref|YP_002993686.1| 555 RIAEIYSYLYQKTGDEKFKERYEWLLKWLAYKQLeNGGFPEGIPPNDftlytaftieplkrlsfegqektmkylrdr 631
                                       45677899999999999999999999999999996778888888888899999999999999999999999999999 PP

                                       ...............................................SSEETTEESH----HHHHHHHHHHHHHHHH CS
                   Glyco_hydro_127 110 ...............................................neakkeawapdshelYnlgkliegavayyq 139
                                                                                      +++ +++w +    l     +  ++  yyq
  gi|242398262|ref|YP_002993686.1| 632 iqedyimttskdkkgdlfaeaqmlpilyeyellnktvldniitkildEQRNDGSWKK---SLGGTIVTAFALARYYQ 705
                                       999999999999999999999999999999999999999999999988888999999...33222334457899*** PP

                                       HH--HHHHHHHHHHHHHHHHHHCCS-C CS
                   Glyco_hydro_127 140 atgkeklldvatrladyleevleklgd 166
                                       ++++e++l +++++a+++ e +e  g+
  gi|242398262|ref|YP_002993686.1| 706 LSEDERVLPAIKKAAEWIREQQEDNGR 732
                                       ******************666655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (814 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       901  (0.0502538); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.72u 0.31s 00:00:01.03 Elapsed: 00:00:00.47
# Mc/sec: 5184.58
//
Query:       gi|242398263|ref|YP_002993687.1|  [L=788]
Description: Phosphoenolpyruvate synthetase [Thermococcus sibiricus MM 739]
Scores for complete 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-116  388.1   4.3   4.8e-116  387.6   4.3    1.2  1  PPDK_N           Pyruvate phosphate dikinase, PEP/pyruvate bi
    1.3e-95  319.9   0.2    3.2e-95  318.6   0.0    1.7  2  PEP-utilizers_C  PEP-utilising enzyme, TIM barrel domain
    6.7e-28   96.2   1.8    1.9e-27   94.8   1.8    1.9  1  PEP-utilizers    PEP-utilising enzyme, mobile domain
  ------ inclusion threshold ------
      0.023   14.3   0.8      0.061   12.9   0.0    2.1  3  Pep_deformylase  Polypeptide deformylase


Domain annotation for each model (and alignments):
>> PPDK_N  Pyruvate phosphate dikinase, PEP/pyruvate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  387.6   4.3  1.1e-119  4.8e-116       2     326 ..      18     350 ..      17     352 .. 0.96

  Alignments for each domain:
  == domain 1  score: 387.6 bits;  conditional E-value: 1.1e-119
                            PPDK_N   2 elvGGKganLaellneagipvPpgfaitadafrefleeng......leekideelkeldvddvdelrkaskeireli 72 
                                       +lvGGKganL+e+ ++agipvPpgf++ta+a+++f+e+ +      l+e i +++++++vdd ++l++++++ire i
  gi|242398263|ref|YP_002993687.1|  18 PLVGGKGANLGEM-TSAGIPVPPGFCVTAEAYKYFVENVKvedgrtLQEWIMDLISKTNVDDSRQLQENTAKIREKI 93 
                                       69***********.77*********************999999********************************** PP

                            PPDK_N  73 lsaelPeeleeaikeayeelgkkfgdeelpvaVRSSataEDlpkasfaGqqdtyLnvggeeevleaikavfaSlfne 149
                                       +s e+Pee+ ++i++ay++l+++f++ee+ vaVRSSataEDlp+asfaGqq+tyL v g e+v e++k+++aSl+++
  gi|242398263|ref|YP_002993687.1|  94 ISMEMPEEIASEIEQAYKKLSQRFNMEEVYVAVRSSATAEDLPEASFAGQQETYLDVLGVEDVKEKVKKCWASLWTA 170
                                       ***************************************************************************** PP

                            PPDK_N 150 rAilYrkekgldheevalavvvqkmvnsdlgasGVafsldpetGfkdevlinasyGlGeaVVaGrvtpdefvvekst 226
                                       rA++Yr+++g+dh++v l++vvqkmvns+   sGV+f+++p t +++e++ina++GlGeaVV+G+v+pde++vek t
  gi|242398263|ref|YP_002993687.1| 171 RATFYRAKQGFDHSKVYLSAVVQKMVNSE--TSGVMFTANPVTNDRSEIMINAAWGLGEAVVSGAVSPDEYIVEKGT 245
                                       *****************************..********************************************** PP

                            PPDK_N 227 rkilekkigekeikivydekeeg.tkevevpe....eereklaLsdeeveeLaeiakkiekhygtpmdiEfaideee 298
                                        ki+ek +++kei+iv+++++ + t++v++ e    e +ek++L+d+++ e+a+i+ +ie+hyg p+diE+a+d+++
  gi|242398263|ref|YP_002993687.1| 246 WKIKEKFVAKKEIMIVRNPETGRgTVKVSTAEflgpEYVEKQVLTDDQIIEVAQIGARIEEHYGWPQDIEWAYDKDD 322
                                       *****************99886567777744433336778889********************************** PP

                            PPDK_N 299 gklyllQaRpetrtsekkekkaaetlee 326
                                       gkly++Q+Rp t+ +e+ ++++ae+ ee
  gi|242398263|ref|YP_002993687.1| 323 GKLYIVQSRPVTTLKEEVKTEEAEMTEE 350
                                       ****************999999988876 PP

>> PEP-utilizers_C  PEP-utilising enzyme, TIM barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0      0.58   2.6e+03      61      96 ..     103     138 ..      89     161 .. 0.72
   2 !  318.6   0.0   7.2e-99   3.2e-95      17     292 ..     483     767 ..     466     769 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.58
                                       HHHHHHHHHHHHHHTTTSEEEEEXXXSSCCGGSGGC CS
                   PEP-utilizers_C  61 eeeqaeaykkvleamngrpvvvRtlDiggdkelpel 96 
                                        +e  +aykk+ + +n   v v +    + + lpe 
  gi|242398263|ref|YP_002993687.1| 103 ASEIEQAYKKLSQRFNMEEVYVAVRSSATAEDLPEA 138
                                       345667899999999988888877777777777765 PP

  == domain 2  score: 318.6 bits;  conditional E-value: 7.2e-99
                                       CXBCEEEEEESSCHHHHHHHHCTXSSEEEEEHHHHCTTSCC.HHHHHH..........HHHHHHHHHHHTTTSEEEE CS
                   PEP-utilizers_C  17 gkkikvlaNidtpedaekalengaeGiGLlRtEflfmaree.lpteee..........qaeaykkvleamngrpvvv 82 
                                       +++++v aN+++pe ae+a+++ga+G+GLlR+E++++   + + ++++          ++e +++v+ a+++r v++
  gi|242398263|ref|YP_002993687.1| 483 VTATEVKANVSMPEVAERAAATGADGVGLLRAEHMILGIGAhPVKFIKegkeeelierLVEGIRTVATAFYPRRVWY 559
                                       678999*********************************765556666699************************** PP

                                       EXXXSSCC..GGSGGCHHHH.XSXGGGSSXTHHHHCCSHHHHHHHHHHHHHHCCCC..EEEEEESSXXSHHHHHHHH CS
                   PEP-utilizers_C  83 RtlDiggd..kelpelkeepeevNPmlGfRgirlglsepelfetqlrAllrasaag..kleimlPmvasveeleeak 155
                                       RtlD++++  +elp +++epee+NPmlG+Rgir+gl++pel++++++A++r   +g  +l +mlP+v++ve+l+eak
  gi|242398263|ref|YP_002993687.1| 560 RTLDAPTNefRELPGGEDEPEERNPMLGWRGIRRGLDQPELLKAEFKAIKRLVDEGydNLGVMLPLVSHVEQLREAK 636
                                       ********9999***************************************9996666******************* PP

                                       HHHHHHHHHHHHCTCTXXTTXEEEEEEXSHHHHHTHHHHCTT.SSEEEEXHHHHHHHHHTXXCCCHCHHHHSXTTTC CS
                   PEP-utilizers_C 156 kiieevkeelekegvkkkkkvkvGiMiEvpsaalladklake.vdFfSiGtNDLtQytlavdRdneevaklydplep 231
                                       ++++ev       g++ +k+v++G+M+E+ps al++++l+ke  dF+S+GtNDLtQytla+dRdne+v klyd+++p
  gi|242398263|ref|YP_002993687.1| 637 RLAREV-------GLEPHKDVEFGVMVETPSSALIIEDLCKEgLDFISFGTNDLTQYTLAIDRDNERVFKLYDETHP 706
                                       ******.......8999*************************9********************************** PP

                                       HHCCCHHHHHHHHHHCCXEEEEESCCCCSCCCHHHHHHCTXSEEEEXGGGHHHHHHHHHCT CS
                   PEP-utilizers_C 232 avlrlikevikaaeekglkvgiCGelagdpsavellvglGldelSmsaasvpaaraalaqv 292
                                       avl+lik+vik+++++g++++iCG++a+dp+++++lv+lG+d+lS+++++v+ +++++a+ 
  gi|242398263|ref|YP_002993687.1| 707 AVLKLIKHVIKVCKKYGVETSICGQAASDPKMAKILVRLGIDSLSANPDAVQLIKQVVARE 767
                                       *********************************************************9986 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 !   94.8   1.8   4.3e-31   1.9e-27       1      73 []     380     452 ..     380     452 .. 0.98

  Alignments for each domain:
  == domain 1  score: 94.8 bits;  conditional E-value: 4.3e-31
                                       G--S-EEEEES---HHHHTTS-GEEEEEES--TTHHHHHHHHHHTT--EEE--SSHH.HH--TEEEEEETTTT CS
                     PEP-utilizers   1 kleegvILvaeetspsdiagldkaaGivterGGmtSHaAivArelgiPaVvgvgeatielkegdlitvDgstG 73 
                                       k++eg++Lv+++t+p++++++++a++ivt++GG+t+HaAiv+relgiPaVvg+++at++lk+g litvDg++G
  gi|242398263|ref|YP_002993687.1| 380 KVKEGDVLVTTMTNPDMVPAMKRASAIVTDEGGRTCHAAIVSRELGIPAVVGTKDATKVLKDGMLITVDGTRG 452
                                       5799*******************************************************************99 PP

>> Pep_deformylase  Polypeptide deformylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1       1.3     6e+03      19      65 ..      55     101 ..      52     114 .. 0.68
   2 ?   12.9   0.0   1.4e-05     0.061      15      88 ..     329     403 ..     320     423 .. 0.83
   3 ?   -3.5   0.0       1.6   7.1e+03       7      38 ..     514     545 ..     511     548 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.3
                                       --BSSHHHHHHHHHHHHHHHHHCT-SEEEGGGGT--BSEEEEECCSS CS
                   Pep_deformylase  19 vekfeskelekllekmletmkeakgvgLAApQigvnkrlfvielpse 65 
                                       v+ ++ ++l++++ +++++ +  +  +L  +   + ++++ +e+p+e
  gi|242398263|ref|YP_002993687.1|  55 VKVEDGRTLQEWIMDLISKTNVDDSRQLQENTAKIREKIISMEMPEE 101
                                       55556677888888888777777777776666666777777766665 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 1.4e-05
                                       --B---BSSHHHHHHHHHHHHHHHHHC.T-SEEEGGGGT--BSEEEEECCSS-ETT....SEEEEEEEEEE..ECSC CS
                   Pep_deformylase  15 kakpvekfeskelekllekmletmkea.kgvgLAApQigvnkrlfvielpseeeeeeenkeltvliNPkit..skse 88 
                                       +++pv++++++ +++  ++m e+mk   kg+g A p ig  k ++++e ++ ++ +e +  +t++ NP ++   k+ 
  gi|242398263|ref|YP_002993687.1| 329 QSRPVTTLKEE-VKTEEAEMTEEMKVLlKGLG-ASPGIGAGKVVVIFEADEIDKVKEGDVLVTTMTNPDMVpaMKRA 403
                                       68899988766.***************99999.99******************99988888*********9443333 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 1.6
                                       TT-GGGCS--B---BSSHHHHHHHHHHHHHHH CS
                   Pep_deformylase   7 vgdpvLrekakpvekfeskelekllekmletm 38 
                                       +++ +L   a+pv+ +++ + e+l+e ++e +
  gi|242398263|ref|YP_002993687.1| 514 AEHMILGIGAHPVKFIKEGKEEELIERLVEGI 545
                                       56667888899999888778899999998755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (788 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       966  (0.0538792); expected 358.6 (0.02)
Passed bias filter:                      634  (0.0353617); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.79u 0.31s 00:00:01.10 Elapsed: 00:00:00.50
# Mc/sec: 4767.07
//
Query:       gi|242398264|ref|YP_002993688.1|  [L=318]
Description: transposase ISTis2 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-25   89.4   0.0    2.7e-25   88.9   0.0    1.2  1  OrfB_IS605       Probable transposase
    1.8e-23   82.2   2.9    3.4e-23   81.3   2.9    1.5  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
  ------ inclusion threshold ------
      0.011   15.3   4.6      0.044   13.3   3.1    2.3  2  TF_Zn_Ribbon     TFIIB zinc-binding
      0.026   14.6   1.4      0.061   13.4   0.3    2.0  2  Ribosomal_L37ae  Ribosomal L37ae protein family
      0.051   13.9   0.0      0.093   13.1   0.0    1.4  1  RuvX             Holliday junction resolvase
       0.07   13.1   0.0       0.19   11.7   0.0    1.7  1  Bac_rhamnosid    Bacterial alpha-L-rhamnosidase concanavalin-
       0.22   11.9   3.4       0.48   10.8   3.4    1.5  1  C1_2             C1 domain
       0.27   11.0   2.1          1    9.1   0.1    2.3  2  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI
        1.3    8.8   8.1        1.5    8.6   4.8    2.7  2  A2L_zn_ribbon    A2L zinc ribbon domain


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.9   0.0   1.3e-28   2.7e-25       2     119 ..      75     190 ..      74     191 .. 0.98

  Alignments for each domain:
  == domain 1  score: 88.9 bits;  conditional E-value: 1.3e-28
                        OrfB_IS605   2 ipvevevelpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrkla 78 
                                       +++eve++++  + nk ++iDlG+ n+at+v ++gt f+++gr lks +++++ke+ +lqs+++k++   k  rk+a
  gi|242398264|ref|YP_002993688.1|  75 YVYEVEPQKADLDYNKYLSIDLGLDNFATCVPTSGTPFIIEGRGLKSFNRWWNKEKVKLQSIYDKQG--IKMGRKMA 149
                                       79****************************************************************9..9******* PP

                        OrfB_IS605  79 rlhrkrsrrrkhllhklathliktlkevgvetLnvgnmkdi 119
                                        l rkr++ ++++++++ ++++k++ ++ ++++++g++k+i
  gi|242398264|ref|YP_002993688.1| 150 WLLRKRRNVINNFMNQAMNYIVKYCLKNKIGNIVIGELKEI 190
                                       **************************************987 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.3   2.9   1.7e-26   3.4e-23       1      69 []     209     278 ..     209     278 .. 0.95

  Alignments for each domain:
  == domain 1  score: 81.3 bits;  conditional E-value: 1.7e-26
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke.alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       ++ +k++l+ k++ yGi+++ev++ayTS+tCs+Cg +n++ ++ + ++ C++Cg ++++D+n+aiNilk+
  gi|242398264|ref|YP_002993688.1| 209 YGLFKQKLKSKCEYYGINYIEVDEAYTSQTCSVCGDVNRNnRKYRGLYICKKCGNVMNADFNGAINILKK 278
                                       5679************************************88888899********************96 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   1.0    0.0045         9       2      28 ..     219     245 ..     219     250 .. 0.86
   2 ?   13.3   3.1   2.2e-05     0.044       2      30 ..     238     266 ..     237     270 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0045
                                       EETTTTCEECHEETSTTCEEESSSSBE CS
                      TF_Zn_Ribbon   2 kCPnCgstnlveDpergelvCtdCGlV 28 
                                       kC + g  ++++D++ +  +C+ CG V
  gi|242398264|ref|YP_002993688.1| 219 KCEYYGINYIEVDEAYTSQTCSVCGDV 245
                                       5677778899*****9999******77 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 2.2e-05
                                       EETTTTCEECHEETSTTCEEESSSSBEEE CS
                      TF_Zn_Ribbon   2 kCPnCgstnlveDpergelvCtdCGlVle 30 
                                       +C +Cg  n  +   rg ++C++CG+V+ 
  gi|242398264|ref|YP_002993688.1| 238 TCSVCGDVNRNNRKYRGLYICKKCGNVMN 266
                                       7******99888899************96 PP

>> Ribosomal_L37ae  Ribosomal L37ae protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0         1     2e+03      19      44 ..     154     179 ..     134     186 .. 0.72
   2 ?   13.4   0.3     3e-05     0.061      30      61 ..     233     265 ..     224     272 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1
                                       HHHHHHHHHHHHHS-BEESSSSSSEE CS
                   Ribosomal_L37ae  19 lrkrvkkieisqhakytCpfcgktkv 44 
                                        r++v +  ++q  +y  + c k+k+
  gi|242398264|ref|YP_002993688.1| 154 KRRNVINNFMNQAMNYIVKYCLKNKI 179
                                       35556666678888899999988887 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 3e-05
                                       HHS-BEESSSSSS.EEEEEETTEEEETTTTEEE CS
                   Ribosomal_L37ae  30 qhakytCpfcgkt.kvkRkavgiwkCkkcgktv 61 
                                        ++++tC+ cg   + +Rk  g++ Ckkcg+++
  gi|242398264|ref|YP_002993688.1| 233 AYTSQTCSVCGDVnRNNRKYRGLYICKKCGNVM 265
                                       467889*****987999*************987 PP

>> RuvX  Holliday junction resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   4.7e-05     0.093      14     103 ..     141     240 ..     138     254 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.7e-05
                                       EEEEE-S--SS---EEEEE---HHHHHHHHHHHHHHTT--EEEEE--........----SSS---SSTTHHHHHHHH CS
                              RuvX  14 GvAvsdplgilaspletierkskekdleelkelvkeeeveeiVvGlP........lnldgsegesakkvrkfaeeLa 82 
                                       G+ ++ ++ +l ++ +++ ++  +++++ + +++ ++++ +iV+G          l  +++++ +      f ++L+
  gi|242398264|ref|YP_002993688.1| 141 GIKMGRKMAWLLRKRRNVINNFMNQAMNYIVKYCLKNKIGNIVIGELkeikngmnLGRRNNQNFQYIPYGLFKQKLK 217
                                       6666777777777777777776799********************8766666633444555555555568899**** PP

                                       HT....T-EEEEE--S----XXX CS
                              RuvX  83 krl..kklpvelvDErlttveae 103
                                       +++  ++++ + vDE +t+ + +
  gi|242398264|ref|YP_002993688.1| 218 SKCeyYGINYIEVDEAYTSQTCS 240
                                       999778999**********8765 PP

>> Bac_rhamnosid  Bacterial alpha-L-rhamnosidase concanavalin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   9.5e-05      0.19      51      90 ..     196     236 ..     175     246 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.5e-05
                                       G.TT---EEEEE----SSEEE--SS--EEEEEEEEES-SS- CS
                     Bac_rhamnosid  51 l.rkakatdeyilkGreeeawqpsftfhGfrYveieglade 90 
                                       l r+++++ +yi  G  +++ + + +++G  Y+e++++  +
  gi|242398264|ref|YP_002993688.1| 196 LgRRNNQNFQYIPYGLFKQKLKSKCEYYGINYIEVDEAYTS 236
                                       349999*****************************998333 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   3.4   0.00024      0.48      14      39 ..     232     262 ..     216     268 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00024
                              C1_2  14 dssesfnCsaCgrk..idgff.....YsCseCd 39 
                                       + + s +Cs+Cg     +  +     Y+C++C 
  gi|242398264|ref|YP_002993688.1| 232 EAYTSQTCSVCGDVnrNN--RkyrglYICKKCG 262
                                       567889******996533..33479*******5 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.2      0.19   3.7e+02       6      12 ..     238     244 ..     235     251 .. 0.84
   2 ?    9.1   0.1   0.00051         1      20      30 ..     254     264 ..     254     265 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.19
                           zf-RRN7   6 pCgvCgc 12 
                                        C vCg 
  gi|242398264|ref|YP_002993688.1| 238 TCSVCGD 244
                                       6****96 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00051
                           zf-RRN7  20 GfyyCrrChtq 30 
                                       G+y+C+ C+++
  gi|242398264|ref|YP_002993688.1| 254 GLYICKKCGNV 264
                                       9********97 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 ?   -0.6   0.1      0.59   1.2e+03      18      26 ..       7      15 ..       4      15 .. 0.89
   2 ?    8.6   4.8   0.00075       1.5       5      30 ..     238     264 ..     236     266 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.59
                     A2L_zn_ribbon 18 eqgylvCie 26
                                      +++y +Ci+
  gi|242398264|ref|YP_002993688.1|  7 KDSYFICIF 15
                                      699****98 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00075
                     A2L_zn_ribbon   5 vCsvCggngiln.seqgylvCieCgas 30 
                                       +CsvCg  +  n + +g ++C++Cg++
  gi|242398264|ref|YP_002993688.1| 238 TCSVCGDVNRNNrKYRGLYICKKCGNV 264
                                       799999877777999**********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       873  (0.0486921); expected 358.6 (0.02)
Passed bias filter:                      573  (0.0319594); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1981.33
//
Query:       gi|242398265|ref|YP_002993689.1|  [L=459]
Description: multidrug efflux pump protein [Thermococcus sibiricus MM 739]
Scores for complete 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-62  207.7  26.6    8.2e-35  119.8   9.4    2.7  4  MatE             MatE
    5.3e-10   39.5  16.3    6.6e-09   36.0   4.8    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 !  119.8   9.4   9.2e-39   8.2e-35       1     161 []      31     191 ..      31     191 .. 0.99
   2 ?   -3.9   0.1       1.1   9.7e+03      48      61 ..     205     218 ..     195     221 .. 0.64
   3 !  101.8   9.3   3.1e-33   2.8e-29       1     160 [.     256     416 ..     256     417 .. 0.98
   4 ?   -2.9   0.1      0.51   4.5e+03      75      90 ..     427     442 ..     425     455 .. 0.60

  Alignments for each domain:
  == domain 1  score: 119.8 bits;  conditional E-value: 9.2e-39
                              MatE   1 PialenllesllslidtllvgrlgskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqgli 77 
                                       P+++ n++++l++l+d++++grlg+++l+a + a++++++++++++g++ta  ++v+q++Gak++++a++a+     
  gi|242398265|ref|YP_002993689.1|  31 PLIINNMVQVLYNLTDMFWLGRLGTEELSAPGTAWPLVWFFMSIGMGFATAGFAFVSQYIGAKDYEKANRAAGALYS 107
                                       99*************************************************************************** PP

                              MatE  78 lllllsliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislislll 154
                                       l++++s+++a+++l+ +++ l ++  ++ev ++a +y+r++++ ip+ + +++++  lr++g+t++p+ i+++++ l
  gi|242398265|ref|YP_002993689.1| 108 LMMIFSVFVAIFGLIIAPFALDFMRVTPEVYPYALNYIRVIFIEIPFSFTLFAFNFLLRAVGDTRTPVKINMFTVFL 184
                                       ***************************************************************************** PP

                              MatE 155 niplnyl 161
                                       ni+l++l
  gi|242398265|ref|YP_002993689.1| 185 NIILDPL 191
                                       ****985 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 1.1
                              MatE  48 lstalttlvgqalG 61 
                                       +++a++t+ ++++G
  gi|242398265|ref|YP_002993689.1| 205 IGAAVATMFSNSVG 218
                                       45566666666555 PP

  == domain 3  score: 101.8 bits;  conditional E-value: 3.1e-33
                              MatE   1 PialenllesllslidtllvgrlgskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqgli 77 
                                       P+ + + +  + + ++t ++  +g++a A ++i++++++++f+++ g+s+a+ t+vgq++Ga++++rak+++ ++++
  gi|242398265|ref|YP_002993689.1| 256 PSSVGSSTDAFGFVVLTRIIYAYGTVAFATYTIGNRLTNFMFAIADGISMAMGTMVGQNVGAEKYERAKKIAEKAML 332
                                       7777888888999**************************************************************** PP

                              MatE  78 lllllsliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislisl.l 153
                                       ++l++  i +l+v +f+ qi+ +f +de vl+ + +++++ ++++p+++++ + s+++++ g tk ++++ +i+l  
  gi|242398265|ref|YP_002993689.1| 333 TNLVVLSIGTLIVAVFRAQIFGFFINDERVLAESVKFVKYFAFSLPFFGIFSAVSNVFQSSGHTKKSMILGMIRLwA 409
                                       ***************************************************************************** PP

                              MatE 154 lniplny 160
                                       l+ipl+y
  gi|242398265|ref|YP_002993689.1| 410 LRIPLAY 416
                                       *****99 PP

  == domain 4  score: -2.9 bits;  conditional E-value: 0.51
                              MatE  75 glilllllsliiallv 90 
                                       g++l+++ls ++a+l+
  gi|242398265|ref|YP_002993689.1| 427 GVWLGMGLSNFLAALI 442
                                       5666666665555553 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 ?    0.4   2.4     0.071   6.3e+02      47     120 ..      65     104 ..      57     134 .. 0.44
   2 !   36.0   4.8   7.4e-13   6.6e-09       2      85 ..     145     235 ..     144     260 .. 0.87
   3 !   17.3   3.7   4.1e-07    0.0037       3      76 ..     371     446 ..     369     456 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.071
                   Polysacc_synt_C  47 llliplfgivGaaiatvlallvvavlnlyalrrllgiklellrrllkpllaalvmgivvylllllllglllla.... 119
                                       ++l+ +f  +G+ +at+   +v+ ++                                              +    
  gi|242398265|ref|YP_002993689.1|  65 WPLVWFFMSIGMGFATAGFAFVSQYIGAKDY-----------------------------------------Ekanr 100
                                       5555555555555555554444444432222.........................................13333 PP

                   Polysacc_synt_C 120 ...a 120
                                          a
  gi|242398265|ref|YP_002993689.1| 101 aagA 104
                                       3331 PP

  == domain 2  score: 36.0 bits;  conditional E-value: 7.4e-13
                   Polysacc_synt_C   2 LailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllli......plfgivGaaiatvlallvvavl 72 
                                       ++++ + i+f++    ++ +L ++g +++++k++++++++++il  lli      p++g++Gaa+at+++  v++++
  gi|242398265|ref|YP_002993689.1| 145 IRVIFIEIPFSFTLFAFNFLLRAVGDTRTPVKINMFTVFLNIILDPLLIfgwlgfPKLGVIGAAVATMFSNSVGSLI 221
                                       57788889999999***********************************999888899******************9 PP

                   Polysacc_synt_C  73 nlyalrr.llgikl 85 
                                         y+l + ++gi+l
  gi|242398265|ref|YP_002993689.1| 222 GGYLLFKgTVGIHL 235
                                       97776665888888 PP

  == domain 3  score: 17.3 bits;  conditional E-value: 4.1e-07
                   Polysacc_synt_C   3 ailalsiiflslstvlssiLqglgrqkialkalvigal.vklilnllliplf.givGaaiatvlallvvavlnlya 76 
                                        ++a+s++f+++++ +s+++q+ g++k+ ++  +i +  + + l + l  ++  +vG+ +++ l+ +++a++ +++
  gi|242398265|ref|YP_002993689.1| 371 KYFAFSLPFFGIFSAVSNVFQSSGHTKKSMILGMIRLWaLRIPLAYGLGKFMaDTVGVWLGMGLSNFLAALIGFVW 446
                                       579*****************************99998559999999999555479**9999999999999987554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (459 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       752  (0.0419432); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.28s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 3073.86
//
Query:       gi|242398266|ref|YP_002993690.1|  [L=304]
Description: Transcription regulator, SpoVT/AbrB family, containing PhoU domain [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-12   47.0   8.6    3.9e-11   43.2   0.5    2.5  2  PhoU            PhoU domain
      4e-08   33.0   0.1    1.5e-07   31.1   0.1    2.1  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
     0.0011   19.1   0.1     0.0027   17.8   0.1    1.7  1  SRI             SRI (Set2 Rpb1 interacting) domain


Domain annotation for each model (and alignments):
>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.2   0.5   6.6e-15   3.9e-11       1      88 [.     138     230 ..     138     231 .. 0.82
   2 !    7.2   2.3    0.0011       6.9      34      86 ..     256     302 ..     234     304 .] 0.73

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 6.6e-15
                                       HHHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SH.......HHHHHHHHHH CS
                              PhoU   1 lrrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplae.......dlrellsllr 70 
                                       ++r+a+i  +m++d+  + e + +e +r++  +++e+dr++++  r + +al+ + + +e       +  +ll++l 
  gi|242398266|ref|YP_002993690.1| 138 IERLASILVSMIEDLALINEFERKEVLRDINGLENELDRFYFLTLRTVNKALS-GGSIGEdrgfikrN-FDLLGVLF 212
                                       679999999999999888665667999********************777775.45555546778743.33689*** PP

                                       HHHHHHHHHHHHHHHHHH CS
                              PhoU  71 iardlERigDhavniaer 88 
                                       i+r++ERigDh+v+iae 
  gi|242398266|ref|YP_002993690.1| 213 IVRNIERIGDHIVRIAEN 230
                                       ****************96 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0011
                                       HHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              PhoU  34 ddeidrlekeiersllealakrqplaedlrellsllriardlERigDhavnia 86 
                                        ++id++  e++++ ++ +  r++ a+d     s++ri  ++E ig  + n++
  gi|242398266|ref|YP_002993690.1| 256 LKKIDEIMLELKNY-IKSIDYRKSIAMD-----SYRRILEYIENIGETIINMS 302
                                       47888888888888.7777667777774.....4999*********9999885 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 !   31.1   0.1   2.6e-11   1.5e-07       1      44 [.       8      51 ..       8      53 .. 0.89

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 2.6e-11
                                      EEETTEEEEEE-CCCHHHCCEECTCEEEEEECTTCCCCCCCHHS CS
                    MazE_antitoxin  1 fkvGnsgavriPkevrfelgireGdevelevdgdkiilrplksl 44
                                      f++ +s+++++Pk +++e+++++Gd v + +++d+++l+++k++
  gi|242398266|ref|YP_002993690.1|  8 FTGRSSYIISLPKKWVKENELKQGDAVPIAINPDGSLLILPKKP 51
                                      8999******************************7777776665 PP

>> SRI  SRI (Set2 Rpb1 interacting) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   4.6e-07    0.0027      12      53 ..     220     261 ..     217     296 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 4.6e-07
                               SRI  12 lakvVvnvlnkYrkklkkedfKklakeltkklvekElkkdks 53 
                                       +  ++v++ +++  +l+ e +K + +++  +++ek+lkk ++
  gi|242398266|ref|YP_002993690.1| 220 IGDHIVRIAENFDRDLDIEYLKGMIRKVISQITEKDLKKIDE 261
                                       678************************************763 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       896  (0.0499749); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1911.14
//
Query:       gi|242398267|ref|YP_002993691.1|  [L=305]
Description: Asparaginase [Thermococcus sibiricus MM 739]
Scores for complete 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-91  304.7   3.7    6.9e-91  304.5   3.7    1.0  1  Asparaginase_2  Asparaginase
  ------ inclusion threshold ------
      0.064   13.5   0.1         22    5.3   0.0    2.8  3  DUF1612         Protein of unknown function (DUF1612)


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 !  304.5   3.7   7.7e-95   6.9e-91       2     298 ..       3     297 ..       2     303 .. 0.92

  Alignments for each domain:
  == domain 1  score: 304.5 bits;  conditional E-value: 7.7e-95
                                       EEEEEEEEESE-G-HHHHHHHHHCHHHHHHHHHHHHHTT--HHHHHHHHHHHHHCTCCCSSSTTSS-BTTS---EEE CS
                    Asparaginase_2   2 vlvihGGAgsilktkereeavrkalkealeagykvLkeggsaldaVeaavrllEddplfnaGkGsvltedgeveldA 78 
                                       ++++hGGAg+i++ ker  +v +++++a+  g+k Lk+ gsa+daVe+a+++lEd+p fnaG+Gsvlt dg+ve+dA
  gi|242398267|ref|YP_002993691.1|   3 AIIVHGGAGTIKN-KERIPKVMEGVRNAALIGWKELKR-GSAIDAVEEAIKTLEDNPIFNAGTGSVLTLDGKVEMDA 77 
                                       69*********99.**********************97.59************************************ PP

                                       EEEETTTTEEEEEEEESSBS-HHHHHHHHHHHCS-SEEEHHHHHHHHHHTT-----CGGG--HHHHHHHHHHHHCCC CS
                    Asparaginase_2  79 simdgktlraGaVagvkrvknpislArlvmeksehvlLvgegAeefareqglelvdeesllteerlkelekakkeka 155
                                       +im   +l+aGaVag+  vknpis+Ar+vmek++hvlL+gegA +far +g+    e++++ eer+++++k +++  
  gi|242398267|ref|YP_002993691.1|  78 AIMRS-NLEAGAVAGIWGVKNPISIARKVMEKTDHVLLAGEGAVKFARLMGF---GEYNPIIEERIEQWKKLREKLL 150
                                       ***85.678*******************************************...*****************99998 PP

                                       HS..B-S-BS-TTT.......TT---EEEEEE-TTS-EEEEEEE--STTB-TTEE-STTSTTTSEEEETTTEEEEEE CS
                    Asparaginase_2 156 ekkeaknvsekelk.......aklgTvGaValDsegnlAaaTSTgGltnklvGRvGDspiiGaGtYAdnkvgAvsaT 225
                                       ek + ++ ++  ++         + TvGaVa+D +  + a+TSTgG+  k+ GRvGD+piiGaGtYA n++++vs+T
  gi|242398267|ref|YP_002993691.1| 151 EKGIISHWKKI-SElikeypeVLRSTVGAVAFDGKE-IVAGTSTGGVFLKMFGRVGDTPIIGAGTYA-NEFAGVSCT 224
                                       87665554443.2246556544445********985.668***************************.********* PP

                                       E-HHHHCCTTHHHHHHHHHHTTT--HHHHHHHHHHCHHHHTTT.-EEEEEEETTS-EEEEECSCCCEEEEEETT CS
                    Asparaginase_2 226 GkGeeiirellaadivalmeykglsleeAaekvieeklkrvkg.sgGviavdkkGevaaefnsegmlrayaked 298
                                       G Ge+ i+ +la++    ++  gl++++A+e +ie +++ ++  ++G+i vdk+G++++++n+++m++ay+ke+
  gi|242398267|ref|YP_002993691.1| 225 GLGEVAIKLSLAKTATDFVRF-GLNAQKASEAAIELATRYFGSeNMGIIMVDKNGNIGFAKNTKHMSVAYMKES 297
                                       *********************.*************9999998889**************************986 PP

>> DUF1612  Protein of unknown function (DUF1612)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0    0.0032        28      90     114 ..      15      39 ..      10      48 .. 0.90
   2 ?   -2.0   0.0      0.46   4.2e+03      10      21 ..     136     147 ..     135     155 .. 0.82
   3 ?    5.3   0.0    0.0025        22      12      40 ..     154     182 ..     147     198 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0032
                           DUF1612  90 retRllailealeaaaeaglkeldR 114
                                       +++R+  ++e++ +aa +g kel+R
  gi|242398267|ref|YP_002993691.1|  15 NKERIPKVMEGVRNAALIGWKELKR 39 
                                       689********************99 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.46
                           DUF1612  10 eeRLeeWravla 21 
                                       eeR+e+W+++ +
  gi|242398267|ref|YP_002993691.1| 136 EERIEQWKKLRE 147
                                       68999**98755 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.0025
                           DUF1612  12 RLeeWravlaeaeelPpvlaaavlldaWe 40 
                                        +++W+++ + ++e+P vl++ v   a++
  gi|242398267|ref|YP_002993691.1| 154 IISHWKKISELIKEYPEVLRSTVGAVAFD 182
                                       5789****************987665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1932.67
//
Query:       gi|242398268|ref|YP_002993692.1|  [L=388]
Description: permease, major facilitator superfamily [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.7e-48  163.9  56.4    2.4e-42  145.1  49.6    2.0  2  MFS_1          Major Facilitator Superfamily
    3.5e-07   29.0  17.1    4.6e-07   28.6  17.1    1.2  1  MFS_3          Transmembrane secretion effector
    2.4e-05   23.4  33.7     0.0001   21.3  12.6    2.2  2  MFS_1_like     MFS_1 like family
    4.2e-05   22.7   8.1    4.2e-05   22.7   8.1    2.3  2  PUCC           PUCC protein
  ------ inclusion threshold ------
      0.097   12.3   0.8       0.16   11.6   0.1    1.7  2  DUF647         Vitamin B6 photo-protection and homoeostasis


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 !  145.1  49.6   6.7e-46   2.4e-42       2     341 ..       7     335 ..       6     335 .. 0.85
   2 !   29.2   0.8   1.2e-10   4.4e-07     115     175 ..     324     385 ..     322     388 .] 0.92

  Alignments for each domain:
  == domain 1  score: 145.1 bits;  conditional E-value: 6.7e-46
                             MFS_1   2 llaaflsalarsilgpalpl.alaedlgispseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalg. 75 
                                       ++++f +++  + +++a  +  la ++g+sp  +g+++++ +++a+++ +++G l+d+ G    v+++g+++ a++ 
  gi|242398268|ref|YP_002993692.1|   7 WFLHFSAFFFLGYVLVAPLIsPLAITFGASPFIVGIVASVSSIFALILKPLGGILGDK-GKSFeVMMVGAIFGAFAg 82 
                                       5666666666666555555558999*********************************.99999************7 PP

                             MFS_1  76 lllll..fasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg 149
                                       ++++l  f + +  +++v+r+l G++a+++fp++++ +  ++pk + g  +g+ +++fs++ +lgp++gg++a++lg
  gi|242398268|ref|YP_002993692.1|  83 FFYILsfF-IKSLvIFAVGRALHGVAAAFFFPSSLSTAITLAPKGRVGETLGWRGTMFSVSQLLGPAVGGFVAEYLG 158
                                       77777854.55555*************************************************************** PP

                             MFS_1 150 Wravfyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsgl 226
                                       ++++f++  i+sl++f     ++++ ++e k+k +++e    +  + ++ +k+l++  +++ + ++l+++ f++sg+
  gi|242398268|ref|YP_002993692.1| 159 FHSAFILTVILSLIGFF----FVLTAYREIKNKMHVKE----EAEGKIS-YKELVNLSFIF-AAVSLFFMVFAYSGM 225
                                       ***************55....55555555555555555....5556999.999***99886.66666666778888* PP

                             MFS_1 227 ltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavll 303
                                       +t+lp y  + lg++     g++ ++++ +++  ++++gr +d+ g   +  +al++lll+++++a+l  +  ++ +
  gi|242398268|ref|YP_002993692.1| 226 YTFLPAY-YKLLGFG-TSVFGVYASVMGGFSILTRVFGGREADKRG---PVPVALVGLLLSSISYAILVIYLLPPEA 297
                                       *******.*******.566666688888888888**********66...5777777777777777777777777*** PP

                             MFS_1 304 llvlvliGfglgfvfpsllalasdlappeeagtasglf 341
                                       +l+ +++G+g+g+++p+l+ la  ++p++ +g  s+++
  gi|242398268|ref|YP_002993692.1| 298 YLSAAILGMGFGLAVPALQMLALVNLPKSIRGIGSSIY 335
                                       ********************************998876 PP

  == domain 2  score: 29.2 bits;  conditional E-value: 1.2e-10
                             MFS_1 115 pkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafv.lfllllpee 175
                                       pk+ rg + ++++++f lG++ gpl+ g+la+s ++ +vf++l i+++l+++ l++l l+++
  gi|242398268|ref|YP_002993692.1| 324 PKSIRGIGSSIYTMFFDLGYLSGPLVLGYLAESESYKSVFFFLPILTFLSLLnLMILRLWRR 385
                                       8889**********************************************998777777776 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6  17.1   1.3e-10   4.6e-07      33     396 ..      26     383 ..       6     388 .] 0.75

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 1.3e-10
                             MFS_3  33 asWlmtdisasplmvAlvqaaatLPifllsilaGalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlllal 109
                                       +s l  +  asp  v +v   +++  ++l  l G+l D+    +v++++ ++ a +  + +++ +++ l   +  + 
  gi|242398268|ref|YP_002993692.1|  26 ISPLAITFGASPFIVGIVASVSSIFALILKPLGGILGDKGKSFEVMMVGAIFGAFAGFFYILSFFIKSLV--IFAVG 100
                                       566777889**********************************************999988877765443..33345 PP

                             MFS_3 110 tlligiGaalndPaWqAsvgelvkrrdvpaAvaLnsvginiaRsvGPAlgGvlvaavGaalafavnalsyla.liva 185
                                         l g+ aa+  P+   +   l ++  v +        + ++   GPA+gG +   +G   af ++++  l+   ++
  gi|242398268|ref|YP_002993692.1| 101 RALHGVAAAFFFPSSLSTAITLAPKGRVGETLGWRGTMFSVSQLLGPAVGGFVAEYLGFHSAFILTVILSLIgFFFV 177
                                       6789*************************************************************997555505555 PP

                             MFS_3 186 llrwkrevrksslprEkllealraglRftaasreikavlvRaalFglsa.savlaLLPlvardqldgdalvyGillg 261
                                       l++  re++++   +E+  + ++     +++s    av      F ++a s +++ LP    + l+ +++v+G+  +
  gi|242398268|ref|YP_002993692.1| 178 LTAY-REIKNKMHVKEEAEGKISY-KELVNLSFIFAAVS---LFFMVFAySGMYTFLPAYY-KLLGFGTSVFGVYAS 248
                                       5555.5555555555655555542.34466666555553...34444551567899**765.678888999999877 PP

                             MFS_3 262 alGvGAilgalllsrL...Rerlsserl..vllaavalAlvllslalasslwvavlvlllgGaaWitalstlnvavq 333
                                        +G   il+ ++  r    R  +   +l  +ll+++ +A+ ++ l l +++++ +   +++G ++ +a+  l+  + 
  gi|242398268|ref|YP_002993692.1| 249 VMGGFSILTRVFGGREadkRGPVPV-ALvgLLLSSISYAILVIYL-LPPEAYLSA---AILGMGFGLAVPALQMLAL 320
                                       7777777777665543000333333.3312345666666554443.445555544...4457777788888999999 PP

                             MFS_3 334 lavPrWvvgRalavYltvlaGglaaGsllWGavaealsvtlaLlaaaaalllaaaillllklp 396
                                       + +P+ ++g + ++Y + ++ g   G l+ G +ae+ s ++      ++ +l+ + l+ l+l 
  gi|242398268|ref|YP_002993692.1| 321 VNLPKSIRGIGSSIYTMFFDLGYLSGPLVLGYLAESESYKSVFFFLPILTFLSLLNLMILRLW 383
                                       *************************************99998888888888877777777765 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 !    8.3  14.8   0.00026      0.94     255     383 ..      33     163 ..       6     165 .. 0.82
   2 !   21.3  12.6   2.9e-08    0.0001     180     384 ..     160     364 ..     154     365 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00026
                        MFS_1_like 255 lgasntllGslvalgvvaeiplfffaekllekl.Ghvklliiall.ayilrfllyaii.enawlvlpievLhgisfg 328
                                        gas +++G++  +  +  ++l  ++  l +k  +++++++ a++ a++  f +++++ +++++  +  +Lhg++ +
  gi|242398268|ref|YP_002993692.1|  33 FGASPFIVGIVASVSSIFALILKPLGGILGDKGkSFEVMMVGAIFgAFAGFFYILSFFiKSLVIFAVGRALHGVAAA 109
                                       599999***999999999999999999999886255566666666245555677888877777778889******** PP

                        MFS_1_like 329 llwaaaveyvskiapksleatgqgllsglyfglGralGsliGGllwdlksaiflF 383
                                        ++ +  + +  +apk+  + + g   g++f++ + lG  +GG++ ++ + + +F
  gi|242398268|ref|YP_002993692.1| 110 FFFPSSLSTAITLAPKGRVGETLGWR-GTMFSVSQLLGPAVGGFVAEYLGFHSAF 163
                                       ************************75.556**************99888777777 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 2.9e-08
                        MFS_1_like 180 sallyvlaallvisllvvl.ilnetekesklkvtkslqvllnilknpeviifllvalilgmswgiienFlflYLkel 255
                                       + ++++  +l +i +++vl +  e + + ++k  +  +   + l n + i+  + ++++ ++++ +++Fl  Y+k l
  gi|242398268|ref|YP_002993692.1| 160 HSAFILTVILSLIGFFFVLtAYREIKNKMHVKEEAEGKISYKELVNLSFIFAAVSLFFMVFAYSGMYTFLPAYYKLL 236
                                       45666666666666666551567777777888887778888999999999999999********************* PP

                        MFS_1_like 256 gasntllGslvalgvvaeiplfffaeklleklGhvklliiallayilrfllyaiienawlvlpievLhgisfgllwa 332
                                       g+ +++ G++  +    +i + +f+ +  +k G v + +++ll+  + + ++ i+  +  + +  ++ g+ fgl   
  gi|242398268|ref|YP_002993692.1| 237 GFGTSVFGVYASVMGGFSILTRVFGGREADKRGPVPVALVGLLLSSISYAILVIYLLPPEAYLSAAILGMGFGLAVP 313
                                       *******************************************************99999999************99 PP

                        MFS_1_like 333 aaveyvskiapksleatgqgllsglyfglGralGsliGGllwdlksaiflFr 384
                                       a+   +    pks+++ g ++++++ f lG  +G l+ G+l + +s + +F 
  gi|242398268|ref|YP_002993692.1| 314 ALQMLALVNLPKSIRGIGSSIYTMF-FDLGYLSGPLVLGYLAESESYKSVFF 364
                                       99999999**************998.9**************99888888875 PP

>> PUCC  PUCC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   8.1   1.2e-08   4.2e-05     270     365 ..      64     159 ..      50     189 .. 0.88
   2 ?   -2.3   2.5      0.46   1.6e+03     273     313 ..     270     309 ..     164     324 .. 0.68

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.2e-08
                              PUCC 270 glkkarlaslgvllgllsflllilaallenvallvagvlllGlasGlfavaaltlmldlaaeeraglalGaWGaaQa 346
                                       + k + + ++g++ g+ + ++ il+ ++++ +++++g +l G+a+ +f  ++l+ +++la+++r+g  lG  G   +
  gi|242398268|ref|YP_002993692.1|  64 KGKSFEVMMVGAIFGAFAGFFYILSFFIKSLVIFAVGRALHGVAAAFFFPSSLSTAITLAPKGRVGETLGWRGTMFS 140
                                       5567888999******************************************************************* PP

                              PUCC 347 iaaglavllggalrdllka 365
                                       +++ l+ ++gg +++ l  
  gi|242398268|ref|YP_002993692.1| 141 VSQLLGPAVGGFVAEYLGF 159
                                       ************9987764 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.46
                              PUCC 273 karlaslgvllgllsflllilaallenvallvagvlllGla 313
                                       +  +a +g+ll  +s+  ++++ ll   a l a++l +G++
  gi|242398268|ref|YP_002993692.1| 270 PVPVALVGLLLSSISYA-ILVIYLLPPEAYLSAAILGMGFG 309
                                       34455555555555443.33344555555555555555554 PP

>> DUF647  Vitamin B6 photo-protection and homoeostasis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   4.4e-05      0.16     125     220 ..      88     184 ..      59     198 .. 0.74
   2 ?   -3.0   0.1       1.3   4.6e+03     174     208 ..     336     372 ..     331     379 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.4e-05
                            DUF647 125 slfllvlslasvlkslcgvaaga.tkaslsa..hfArkgnlgevnAKdssqetvvsllGlllgivvvslisskaalt 198
                                       s+f+  l++  v+++l gvaa     +sls+    A kg +ge     + +  v +llG ++g +v+++++ ++a+ 
  gi|242398268|ref|YP_002993692.1|  88 SFFIKSLVIFAVGRALHGVAAAFfFPSSLSTaiTLAPKGRVGETLGWRGTMFSVSQLLGPAVGGFVAEYLGFHSAF- 163
                                       7788888888999999999887634455555115688**********************************99994. PP

                            DUF647 199 wlllilllalhllanykavrav 220
                                        +l ++l+++  ++   a r +
  gi|242398268|ref|YP_002993692.1| 164 -ILTVILSLIGFFFVLTAYREI 184
                                       .344444444444444443333 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.3
                            DUF647 174 tvvsllGlllgivvvslisskaa..ltwlllilllal 208
                                       t++  lG l g +v+ +++++ +   +++ l +l++l
  gi|242398268|ref|YP_002993692.1| 336 TMFFDLGYLSGPLVLGYLAESESykSVFFFLPILTFL 372
                                       5566688899999999998877744333333344444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       911  (0.0508115); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.80u 0.36s 00:00:01.16 Elapsed: 00:00:00.54
# Mc/sec: 2154.63
//
Query:       gi|242398269|ref|YP_002993693.1|  [L=320]
Description: Biotin synthase related protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-11   45.3   0.2    9.8e-11   42.3   0.0    2.2  2  Radical_SAM   Radical SAM superfamily
  ------ inclusion threshold ------
       0.13   11.6   0.3       0.83    9.0   0.0    2.2  2  mRNA_decap_C  mRNA-decapping enzyme C-terminus


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 !   42.3   0.0   1.1e-14   9.8e-11       6     165 ..      42     200 ..      39     202 .. 0.91
   2 ?    0.2   0.1     0.099   8.9e+02       8      20 ..     281     297 ..     279     318 .. 0.66

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 1.1e-14
                                       EESS--TTTSCCTT......HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCC CS
                                       xxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   6 gCnlrCsfCarpet......vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavp 76 
                                        C ++C fC + ++      + ++ ++ + ++e+++ ++++ k    ++ +i++ + p l  d v +le l+ +   
  gi|242398269|ref|YP_002993693.1|  42 RCINNCAFCVQARKsradieKLSRITWPVFDLEDVVSKLEKTK-F--ARLCIQTIDYPALKEDVVSILESLSPI--- 112
                                       6*******************999*******************5.5..89*************************... PP

                                       TEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSET..EEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx..xxxxxx RF
                       Radical_SAM  77 giritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikr..vvdriv 150
                                       g+ +++++ ++   e  l+++++lgvd++ +gl+aa++e + ++++   ++++e ++  e   +  + +   ++ ++
  gi|242398269|ref|YP_002993693.1| 113 GLPVSLSITPVE--EASLKTFKKLGVDYIGVGLDAASEE-IYNKVKdSYYSWSEMWNFAEGVIKI-FGEkkAFIHLI 185
                                       ************..9************************.888888877***************9.55548777777 PP

                                       EBTTTSHHHHHHHHH CS
                                       xxxxxxxxxxxxxxx RF
                       Radical_SAM 151 glpGendeeleelle 165
                                        + Ge++e +  +++
  gi|242398269|ref|YP_002993693.1| 186 FGLGETEEAFLSTIQ 200
                                       777799999888876 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.099
                                       SS--TTTSCCTT....H CS
                                       xxxxxxxxxxxx....x RF
                       Radical_SAM   8 nlrCsfCarpet....v 20 
                                       +++C+ C+rp+     +
  gi|242398269|ref|YP_002993693.1| 281 THGCPGCNRPYYnekpS 297
                                       589*******9764443 PP

>> mRNA_decap_C  mRNA-decapping enzyme C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0   9.3e-05      0.83      11      31 ..     179     203 ..     178     204 .. 0.93
   2 ?   -0.5   0.0     0.087   7.8e+02      14      19 ..     240     245 ..     230     246 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 9.3e-05
                      mRNA_decap_C  11 dtLiHLI....knDssFLntIHeAY 31 
                                        ++iHLI     +   FL+tI eAY
  gi|242398269|ref|YP_002993693.1| 179 KAFIHLIfglgETEEAFLSTIQEAY 203
                                       699****98889************* PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.087
                      mRNA_decap_C  14 iHLIkn 19 
                                       ++LIkn
  gi|242398269|ref|YP_002993693.1| 240 LYLIKN 245
                                       8****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2247.81
//
Query:       gi|242398270|ref|YP_002993694.1|  [L=159]
Description: hypothetical protein TSIB_0279 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00056   20.4   0.0     0.0025   18.3   0.0    2.1  2  TPR_19    Tetratricopeptide repeat
  ------ inclusion threshold ------
       0.73   10.2   0.0       0.73   10.2   0.0    3.4  4  TPR_8     Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   2.8e-07    0.0025       2      62 ..      18      82 ..      17      88 .. 0.90
   2 ?   -2.1   0.0      0.64   5.7e+03      47      57 ..     125     135 ..     122     141 .. 0.60

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.8e-07
                            TPR_19  2 laegdyaeAlalleqa..lqedpk...naearllLAeallalgqldeAealLdalpeedpddarya 62
                                      l++++++ A + +e++  l+edp+   + ea  +L++++++  +++ A++   ++++++p+ +++ 
  gi|242398270|ref|YP_002993694.1| 18 LKDKKLDVAKEKFENIirLTEDPHpwlYFEACFGLVKVYIEKEDYKSAMDSAFKALLHAPN-QEVY 82
                                      678999*********745699*************************************999.5554 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.64
                            TPR_19  47 lLdalpeedpd 57 
                                       +L+al +e+ +
  gi|242398270|ref|YP_002993694.1| 125 ALNALARENYK 135
                                       56666666665 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.2     0.054   4.8e+02      15      29 ..       2      16 ..       1      17 [. 0.84
   2 ?   -2.4   0.1      0.91   8.2e+03      15      30 ..      21      36 ..      18      39 .. 0.70
   3 ?   10.2   0.0   8.2e-05      0.73       2      27 ..      47      72 ..      46      78 .. 0.86
   4 ?   -1.0   0.2      0.31   2.8e+03      18      26 ..     128     136 ..     119     146 .. 0.55

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.054
                                      T-HHHHHHHHHHHHH CS
                             TPR_8 15 gdyeeAkeyyekale 29
                                      ++ e A++ +++a +
  gi|242398270|ref|YP_002993694.1|  2 EKEELAISIFKEAQK 16
                                      67899******9965 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.91
                                      T-HHHHHHHHHHHHHH CS
                             TPR_8 15 gdyeeAkeyyekalel 30
                                      ++++ Ake +e  ++l
  gi|242398270|ref|YP_002993694.1| 21 KKLDVAKEKFENIIRL 36
                                      6778888877777766 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 8.2e-05
                                      CHHHHHHHHHHHTT-HHHHHHHHHHH CS
                             TPR_8  2 eayynlgsiylklgdyeeAkeyyeka 27
                                      ea++ l ++y++++dy++A+ +  ka
  gi|242398270|ref|YP_002993694.1| 47 EACFGLVKVYIEKEDYKSAMDSAFKA 72
                                      79*****************9876555 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 0.31
                                       HHHHHHHHH CS
                             TPR_8  18 eeAkeyyek 26 
                                         A e y++
  gi|242398270|ref|YP_002993694.1| 128 ALARENYKE 136
                                       444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1033  (0.0576162); expected 358.6 (0.02)
Passed bias filter:                      571  (0.0318478); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1040.81
//
Query:       gi|242398271|ref|YP_002993695.1|  [L=307]
Description: Serine/threonine protein kinase, RIO1 family [Thermococcus sibiricus MM 739]
Scores for complete 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-47  159.2   0.1    1.1e-46  158.9   0.1    1.1  1  RIO1            RIO1 family
    1.2e-24   86.3   0.0    2.6e-24   85.2   0.0    1.6  1  Rio2_N          Rio2, N-terminal
    2.2e-06   27.2   1.8    1.3e-05   24.7   1.8    1.9  1  Pkinase         Protein kinase domain
    5.6e-06   26.5   0.1      0.017   15.0   0.0    2.5  2  APH             Phosphotransferase enzyme family
     0.0012   17.7   0.0     0.0018   17.1   0.0    1.2  1  Pkinase_fungal  Fungal protein kinase
  ------ inclusion threshold ------
      0.025   14.7   0.0      0.044   13.9   0.0    1.4  1  Opacity         Opacity family porin protein
      0.069   13.2   0.0        0.2   11.8   0.0    1.7  1  La              La domain
       0.11   11.8   0.2       0.32   10.2   0.2    1.8  1  Pkinase_Tyr     Protein tyrosine 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 !  158.9   0.1   4.7e-50   1.1e-46       1     187 [.     111     291 ..     111     292 .. 0.97

  Alignments for each domain:
  == domain 1  score: 158.9 bits;  conditional E-value: 4.7e-50
                                       EEEEEEETTTEEEEEEEE-S---SS-HHHHCTTTSTTSTCG--GS-HHHHHHHHHHHHHHHHHHHHHTT--S--EEE CS
                              RIO1   1 nVyhavsedgkevaiKiyktstteFkkrkkyvsgekrfkdrksktnprklvklwaekEfrnLkrleeagvpvPkpie 77 
                                       +Vy +++ +++ va+K+ ++++t+F+++k y+ +  +    k +++++++++l+a++E+++L+ l+ + ++vPkpi+
  gi|242398271|ref|YP_002993695.1| 111 DVYIGITPNEERVAVKFNRVGRTSFTRIKLYRPNLID----KRHISWLYVSRLVAQREYEALQLLSPI-AKVPKPIA 182
                                       69********************************999....669************************.8******* PP

                                       EETTEEEEE--EETTEEGGBHHHCG.-HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETT.EEEE--GTTE CS
                              RIO1  78 lkrhvlvmefigedgvaapklkdve.eeeeaeelyeevleemrklykeaglvHaDLSeyNvlvded.kvviIDvsQa 152
                                       ++rh++vmefi+  g+++ +l d++ ++eea e++++vlee++k++ e g++H D+S yN++++++ +++iID++Q+
  gi|242398271|ref|YP_002993695.1| 183 WNRHAIVMEFID--GIELIELTDTDlTKEEALEVLNKVLEEYKKIV-EFGIIHSDMSLYNIVLKSNgDILIIDWPQY 256
                                       ************..***********77*******************.*****************999********** PP

                                       EETTSTTHHHHHHHHHHHHHHHHHTTC-----HHH CS
                              RIO1 153 veldhpnalefLerDveniikfFrrkgvekvdeee 187
                                       ++ + p+a+ +LerD++ + + F++k+  +v++++
  gi|242398271|ref|YP_002993695.1| 257 LTSAFPEARYYLERDLQVLLNSFKKKWGVQVEKNK 291
                                       **************************998777665 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.2   0.0   1.2e-27   2.6e-24       3      82 .]      13      93 ..      11      93 .. 0.97

  Alignments for each domain:
  == domain 1  score: 85.2 bits;  conditional E-value: 1.2e-27
                            Rio2_N  3 yLskedfrvLtavEmgmrnhevVptelieeisrlkeeevkkrlsrllkaklisr.ktakydGYkLtyeGyDyLALktlv 80
                                      +L+  dfr+L+++E+ mr++e+Vp e i++++r++ e +++rl +l +++l++r +++ y GY+Lt +GyD+LA++t++
  gi|242398271|ref|YP_002993695.1| 13 NLKDLDFRILRGIELNMRHYEWVPLETIAKFARVDIETTSHRLGKLDNWGLVKRrSDIGYIGYQLTIHGYDALAIRTFA 91
                                      68899*************************************************999*********************9 PP

                            Rio2_N 81 kr 82
                                      ++
  gi|242398271|ref|YP_002993695.1| 92 QK 93
                                      86 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   1.8     6e-09   1.3e-05       5     142 ..     102     253 ..      99     255 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 6e-09
                                       EEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHHHHHHHHHHHHHHHSCTTB--EEEEEEE............ CS
                           Pkinase   5 eklGeGsfGkVykaveketgkivAvKkikkekakkkkekkvlrEikilkklkhpnivrlyevfee............ 69 
                                       +++G G+ + Vy ++ + +++ vAvK  ++ +++ ++ k ++  +   ++++  ++ rl+   e             
  gi|242398271|ref|YP_002993695.1| 102 TQIGVGKEADVYIGI-TPNEERVAVKFNRVGRTSFTRIKLYRPNLIDKRHISWLYVSRLVAQREYealqllspiakv 177
                                       689999999999999.7999999999998888877776544444444555555555555554444566778888888 PP

                                       .....SSEEEEEEE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-S CS
                           Pkinase  70 .....kdelylvleyveggeladllerkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitD 141
                                             ++  +v+e+++g el +l    + l++eea ++++++le  + + + giiH D+   Ni ++++g++ i+D
  gi|242398271|ref|YP_002993695.1| 178 pkpiaWNRHAIVMEFIDGIELIELTD--TDLTKEEALEVLNKVLEEYKKIVEFGIIHSDMSLYNIVLKSNGDILIID 252
                                       88887667779********9999996..68*********************************************** PP

                                       G CS
                           Pkinase 142 F 142
                                       +
  gi|242398271|ref|YP_002993695.1| 253 W 253
                                       8 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.1   0.00024      0.54       3      84 ..     102     203 ..     100     220 .. 0.73
   2 !   15.0   0.0   7.6e-06     0.017     146     193 ..     209     253 ..     198     264 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00024
                                       EEE--.SSCEEEEEEETT.--EEEEE.........................E-TTS-HHHHHHHHHHHHHHHHTT-B CS
                               APH   3 relsggasnrtylvttpa.gryvlrr.........................npparaaeeirrevallrlLakagvp 53 
                                       ++++ g + ++y   tp+  r+++++                         +    +   ++re++ l+lL+   ++
  gi|242398271|ref|YP_002993695.1| 102 TQIGVGKEADVYIGITPNeERVAVKFnrvgrtsftriklyrpnlidkrhisWLYV-SRLVAQREYEALQLLSPI-AK 176
                                       6889999999999999998899999999999999999999999999855553333.556677999999999988.56 PP

                                       --B-CTTBS-EEETTEEEEEEE----EE-SS CS
                               APH  54 vPevlagdtddeeigllfalieyvpgrsllr 84 
                                       vP+++a+    + + +++++i +++   l++
  gi|242398271|ref|YP_002993695.1| 177 VPKPIAW----NRHAIVMEFIDGIELIELTD 203
                                       *****95....44444555555555555544 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 7.6e-06
                                       HHHHHHHHHHHHHH--SSS-EEEE-SS-SGGGEEEC..TTEEEEE--- CS
                               APH 146 eeleeqvlaalaallpgelptvllHgDlhpgNllvdpddgrvtGviDf 193
                                       ee+ e vl++++++  + ++ +++H D ++ N++++++++ +  +iD+
  gi|242398271|ref|YP_002993695.1| 209 EEALE-VLNKVLEEYKKIVEFGIIHSDMSLYNIVLKSNGDIL--IIDW 253
                                       45555.55555555555678****************999999..**** PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   8.1e-07    0.0018     304     341 ..     207     243 ..     200     266 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 8.1e-07
                    Pkinase_fungal 304 spkellealrDaIkghrsLflkagiLHrDiSenNilit 341
                                       +++e+le+l  +++ +++ + + gi+H D S +Ni++ 
  gi|242398271|ref|YP_002993695.1| 207 TKEEALEVLNKVLEEYKKIV-EFGIIHSDMSLYNIVLK 243
                                       789*****************.**************998 PP

>> Opacity  Opacity family porin protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0     2e-05     0.044      54     121 ..      72     140 ..      44     145 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2e-05
                           Opacity  54 yvGvrvasngak...vsasaklpkkeafasetrvGlGvlaGvkykltpnltldtgvrynrlGrleatrvkt 121
                                       y+G +++  g +   +++ a+ + ++a  s+t++G+G  a v   +tpn +    v++nr+Gr   tr+k 
  gi|242398271|ref|YP_002993695.1|  72 YIGYQLTIHGYDalaIRTFAQKGIIKA-ISQTQIGVGKEADVYIGITPNEE-RVAVKFNRVGRTSFTRIKL 140
                                       888888876554111566677777888.9********************76.5789********9999985 PP

>> La  La domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   8.7e-05       0.2      25      44 ..      30      47 ..      26      65 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.7e-05
                                      TTSTTS---HHHHHTSSHHH CS
                                La 25 dkdpegwVplsliasfkrmk 44
                                      ++    wVpl++ia+f r+ 
  gi|242398271|ref|YP_002993695.1| 30 RH--YEWVPLETIAKFARVD 47
                                      44..46************96 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.2   0.00014      0.32      74     147 ..     184     253 ..      99     275 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00014
                                       SSEEEEEE--TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEETTEEEE-ST CS
                       Pkinase_Tyr  74 epllivteyvkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLlsenkvvkisDf 147
                                       +++ iv+e+++g +L +   +     lt ++ l++  +v +  + + +  ++H d++  N++l++n  + i D 
  gi|242398271|ref|YP_002993695.1| 184 NRHAIVMEFIDGIELIELTDT----DLTKEEALEVLNKVLEEYKKIVEFGIIHSDMSLYNIVLKSNGDILIIDW 253
                                       457899999999999876444....6****************************************99999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       715  (0.0398795); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.62u 0.37s 00:00:00.99 Elapsed: 00:00:00.54
# Mc/sec: 1716.67
//
Query:       gi|242398272|ref|YP_002993696.1|  [L=345]
Description: Permease, major facilitator superfamily [Thermococcus sibiricus MM 739]
Scores for complete 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-51  173.5  46.9    2.7e-44  151.5  29.9    2.1  2  MFS_1     Major Facilitator Superfamily
    4.1e-10   39.1  26.8    4.4e-08   32.4   6.2    3.2  2  Sugar_tr  Sugar (and other) transporter
     0.0081   14.5  17.4      0.096   11.0   0.1    3.3  3  OATP      Organic Anion Transporter Polypeptide (OATP) family
  ------ inclusion threshold ------
        3.1    7.7   8.5       0.12   12.3   1.9    2.0  2  DUF5090   Domain of unknown function (DUF5090)


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 !  151.5  29.9     6e-48   2.7e-44      15     353 .]       3     310 ..       1     310 [. 0.85
   2 !   35.5   8.9   1.1e-12     5e-09      96     169 ..     268     341 ..     262     344 .. 0.92

  Alignments for each domain:
  == domain 1  score: 151.5 bits;  conditional E-value: 6e-48
                             MFS_1  15 lgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfasslwlllvl 91 
                                       + p++p +++++lgi+ +++gll+t   l +a++++p+G+++d++Gr+r++++++l+++l++ l++fa ++w l+ +
  gi|242398272|ref|YP_002993696.1|   3 IPPLIP-IIKNELGITNAQAGLLMTSLLLPYALTQVPAGYFGDKIGRKRLVVISILGYSLASSLMVFARQYWHLISV 78 
                                       678899.9*****************************************************777778999******* PP

                             MFS_1  92 rvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlf 168
                                       r+l G++a ++++ + ali++++++ ++g+a+g++++g  +G++++p++   +a +l Wr++f+i+ ++s+l ++  
  gi|242398272|ref|YP_002993696.1|  79 RALYGVFADLYYAPSTALISEVYKE-KKGSALGVFMIGPPVGSAIAPAIVVPIALALEWRYSFVIISLMSALIGI-- 152
                                       ************************9.********************999999999******************99.. PP

                             MFS_1 169 llllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlglsglll 245
                                        +l+   + e + ++ +          ++p  k +++      l ++ +++ ++f+g+lt+lp +   + g s   +
  gi|242398272|ref|YP_002993696.1| 153 -ALIHGVKGEVRHVERVNF--------AIP--KNVFR------LSLMNFIALAAFFGMLTFLPDF-FVDKGRS-IEE 210
                                       .666444333333333222........333..33333......3444444444999********9.9999***.8** PP

                             MFS_1 246 aglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvl.iGfglgfvfpsl 321
                                       a+++++ll++vg+++++ +g + dr+g+     l+ +l++ ++l+++l+ +t      + +lvl +G+++  v p++
  gi|242398272|ref|YP_002993696.1| 211 ASFYFSLLSIVGIFGSIAGGTIYDRVGK---GSLFSALFFNMFLSFLLVKTT------YPILVLpLGLFFYSVGPIV 278
                                       *************************887...555555555555555555555......224444689988889**** PP

                             MFS_1 322 lalasdlappeeagtasglfntagslggalgp 353
                                       +a++s++a pe+ gt++g++n++g +g+ +gp
  gi|242398272|ref|YP_002993696.1| 279 TAYTSEHATPENLGTVMGFVNMMGFFGATIGP 310
                                       *******************************8 PP

  == domain 2  score: 35.5 bits;  conditional E-value: 1.1e-12
                             MFS_1  96 GlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfl 169
                                       Gl+  ++ p++ a++++ +++e+ g ++g+++++  +Ga +gp + gll++ +g++ +fy + +++l+++++f+
  gi|242398272|ref|YP_002993696.1| 268 GLFFYSVGPIVTAYTSEHATPENLGTVMGFVNMMGFFGATIGPYFIGLLIDRVGYEMAFYSISGMYLVSLLIFM 341
                                       667778889************************************************************88644 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   6.2   9.8e-12   4.4e-08      45     184 ..      18     150 ..      10     159 .. 0.85
   2 !   10.1  12.7   5.8e-05      0.26      19     180 ..     187     336 ..     179     344 .. 0.74

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 9.8e-12
                                       ..HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHH CS
                          Sugar_tr  45 svlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasv 121
                                       + + gl++ ++l+  +++++ ag++gd++GRk   +i+++ ++ ++ l+++a    +++ li  R l G+++ l ++
  gi|242398272|ref|YP_002993696.1|  18 NAQAGLLMTSLLLPYALTQVPAGYFGDKIGRKRLVVISILGYSLASSLMVFAR---QYWHLISVRALYGVFADLYYA 91 
                                       56889999999999***************************************...9******************** PP

                                       HHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHH CS
                          Sugar_tr 122 lvPmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpalll 184
                                        ++ +isE+ ++k+ +al++ +  +  +G  +a  + + ++   +   wr+ + + ++++ l+
  gi|242398272|ref|YP_002993696.1|  92 PSTALISEVYKEKKGSALGV-FMIGPPVGSAIAPAIVVPIALALE---WRYSFVIISLMSALI 150
                                       *********99999888876.567777777777777777777777...888887766655443 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 5.8e-05
                                       GGGTHHHHHHHHTSTT--SHHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH- CS
                          Sugar_tr  19 igafltllkfaknfglsksksskeessvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaa 95 
                                       ++af  +l f+ +f+++k +s +e+     ++ +s++++++i+Gs+ +g++ dr+G+  sl  a ++ +  ++l + 
  gi|242398272|ref|YP_002993696.1| 187 LAAFFGMLTFLPDFFVDKGRSIEEA-----SFYFSLLSIVGIFGSIAGGTIYDRVGK-GSLFSALFFNMFLSFLLVK 257
                                       6777788888889999999987776.....9*************************5.3444444444444444444 PP

                                       TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHH.HHHHHHHHTSS-TTHHH CS
                          Sugar_tr  96 akgknsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgalvslyqlaitfGilva.aifglglnktsnadgwr 171
                                       ++    + +l++    +G++   +  +v+ y+sE A+++  g+++++ +++  fG  ++ +++gl +++++++  + 
  gi|242398272|ref|YP_002993696.1| 258 TT----YPILVL---PLGLFFYSVGPIVTAYTSEHATPENLGTVMGFVNMMGFFGATIGpYFIGLLIDRVGYEMAFY 327
                                       44....555554...477777778899************************99999998788999999999854444 PP

                                       HHHHCCHHH CS
                          Sugar_tr 172 illglqlvp 180
                                          g+ lv+
  gi|242398272|ref|YP_002993696.1| 328 SISGMYLVS 336
                                       444443333 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 !   11.0   0.1   2.1e-05     0.096      26      85 ..       9      68 ..       2      80 .. 0.92
   2 !    9.6   4.4   5.4e-05      0.24     300     384 ..     180     263 ..     173     268 .. 0.83
   3 ?    1.3   1.5     0.018        81     152     192 ..     277     318 ..     262     330 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 2.1e-05
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP 26 tiEkrFklpsstsgliassneignillilfvsYfggrghrPrwigigallmalgslllal 85
                                       i  + ++++++ gl+++s  + ++l+ +  +Yfg++  r r++ i++l  +l+s l+++
  gi|242398272|ref|YP_002993696.1|  9 IIKNELGITNAQAGLLMTSLLLPYALTQVPAGYFGDKIGRKRLVVISILGYSLASSLMVF 68
                                      5778899***********************************************999975 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 5.4e-05
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx RF
                              OATP 300 ilssvfeillvaGfitFlpkylEtqFslsaseAnlltGvvvipgaalGillgGllvkkl.klsakklaklvlvvsll 375
                                       +l + + + ++ G+ tFlp +   + + s  eA++++ +++i+g ++G ++gG +  ++ k s  +++++++++s+l
  gi|242398272|ref|YP_002993696.1| 180 SLMNFIALAAFFGMLTFLPDFFVDK-GRSIEEASFYFSLLSIVG-IFGSIAGGTIYDRVgKGSLFSALFFNMFLSFL 254
                                       6777888999***********9777.999********9999976.6899*******998456677889999999998 PP

                                       xxxxxxxxx RF
                              OATP 376 sllllllll 384
                                        + ++ ++l
  gi|242398272|ref|YP_002993696.1| 255 LVKTTYPIL 263
                                       877766665 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.018
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx RF
                              OATP 152 lGisYidDnvkkknsplylgilyalrilGpalG.fllGslll 192
                                       + ++Y  ++++++n  + +g++ ++ ++G  +G +++G l+ 
  gi|242398272|ref|YP_002993696.1| 277 IVTAYTSEHATPENLGTVMGFVNMMGFFGATIGpYFIGLLID 318
                                       4578999999999999************99999788887665 PP

>> DUF5090  Domain of unknown function (DUF5090)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.9   2.7e-05      0.12      40     136 ..     171     270 ..     157     282 .. 0.84
   2 ?   -2.6   0.6      0.98   4.4e+03     105     122 ..     300     317 ..     286     342 .. 0.49

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.7e-05
                           DUF5090  40 klPtevknlklkdiikitlllkavllipiyllviaengnkldflksksriifltlik...ivlsilvdlvvyfsels 113
                                       ++P +v +l+l + i +++++ +++++p + +     +++++f  s ++i+ +       ++ + + + + +    +
  gi|242398272|ref|YP_002993696.1| 171 AIPKNVFRLSLMNFIALAAFFGMLTFLPDFFVDKGRSIEEASFYFSLLSIVGIFGSIaggTIYDRVGKGSLFSALFF 247
                                       7******************************998888888999888777776655336789999999999******* PP

                           DUF5090 114 slfkvflllkiikllitlivlla 136
                                       ++f++fll+k    +++l + l+
  gi|242398272|ref|YP_002993696.1| 248 NMFLSFLLVKTTYPILVLPLGLF 270
                                       *********99887777766665 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.98
                           DUF5090 105 lvvyfselsslfkvflll 122
                                       ++ +f+ ++ ++ + ll+
  gi|242398272|ref|YP_002993696.1| 300 MMGFFGATIGPYFIGLLI 317
                                       444444444444333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      189  (0.0105416); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 2380.92
//
Query:       gi|242398273|ref|YP_002993697.1|  [L=375]
Description: NiFe hydrogenase I, subunit beta [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-27   95.9  13.1    3.3e-27   95.2  10.6    2.2  2  Fer4_22   4Fe-4S dicluster domain
    2.4e-06   27.6   9.9     0.0021   18.2   0.4    2.5  2  Fer4_10   4Fe-4S dicluster domain
      7e-06   26.5  13.2      0.004   17.7   1.7    2.5  2  Fer4_17   4Fe-4S dicluster domain
    8.8e-06   26.2  10.0      0.016   15.8   2.2    2.6  2  Fer4_7    4Fe-4S dicluster domain
    2.2e-05   24.8  12.1    4.5e-05   23.8  11.3    1.9  2  Fer4_8    4Fe-4S dicluster domain
    6.9e-05   22.5  12.7      0.013   15.3   3.7    2.7  2  Fer4      4Fe-4S binding domain
    7.8e-05   22.5  13.7      0.034   14.2   4.7    2.8  2  Fer4_2    4Fe-4S binding domain
    0.00045   20.3  15.3      0.015   15.4   2.5    2.9  2  Fer4_9    4Fe-4S dicluster domain
    0.00057   20.2   1.5    0.00057   20.2   1.5    3.3  3  Fer4_4    4Fe-4S binding domain
     0.0036   18.2   9.2       0.16   12.9   0.8    2.9  2  Fer4_16   4Fe-4S double cluster binding domain
  ------ inclusion threshold ------
      0.013   15.7  13.5       0.24   11.6   2.0    2.5  2  Fer4_21   4Fe-4S dicluster domain
      0.037   14.1  18.5      0.073   13.2   2.7    2.7  2  Fer4_6    4Fe-4S binding domain
      0.057   13.6   2.5        1.8    8.8   0.1    2.3  2  Fer4_18   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.69   9.6e+02      28      57 ..     187     216 ..     177     238 .. 0.72
   2 !   95.2  10.6   2.4e-30   3.3e-27       2      96 .]     241     334 ..     240     334 .. 0.97

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.69
                           Fer4_22  28 skegervrvwdsClleeftkvaggenvrke 57 
                                        k  e v ++d C ++ef++ +++    +e
  gi|242398273|ref|YP_002993697.1| 187 IKLFEEVTTQDVCEFREFENKKHQMFKYHE 216
                                       566788889999999999988877544444 PP

  == domain 2  score: 95.2 bits;  conditional E-value: 2.4e-30
                           Fer4_22   2 ClsCgaCtlvCptCsCfdvedetkeeskegervrvwdsClleeftkvaggenvrkekkerlrqrllhklsefkekfg 78 
                                       Cl+Cg+C+l+CptC C++v+d  + + ++g r+r+wdsC+l+++  vag++n+r++kk+r+ +r+l k ++++ek g
  gi|242398273|ref|YP_002993697.1| 241 CLACGNCNLTCPTCRCYEVQDIPNLDGDTGARIRRWDSCQLRSHGLVAGNHNFRPTKKSRFMNRYLCK-NSYNEKLG 316
                                       ***********************9999*****************************************.567999** PP

                           Fer4_22  79 esgCvGCgRCieacpvki 96 
                                        s CvGCgRC+  cp++i
  gi|242398273|ref|YP_002993697.1| 317 ISYCVGCGRCTYFCPAEI 334
                                       ***************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 !   12.7   3.6   7.5e-05       0.1       3      29 ..     235     262 ..     233     288 .. 0.71
   2 !   18.2   0.4   1.5e-06    0.0021       8      24 ..     319     342 ..     314     368 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.5e-05
                           Fer4_10   3 vidddtCirCgkCvkaCPadl.tsvgak 29 
                                         +++ C+ Cg+C+  CP++   +v+ +
  gi|242398273|ref|YP_002993697.1| 235 NEQSELCLACGNCNLTCPTCRcYEVQDI 262
                                       567899*************666333333 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 1.5e-06
                           Fer4_10   8 tCirCgkCvkaCPadl.......t 24 
                                        C++Cg+C+ +CPa +       t
  gi|242398273|ref|YP_002993697.1| 319 YCVGCGRCTYFCPAEIsfvenlrT 342
                                       7*************7744444440 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   4.1   5.1e-05     0.071      12      57 ..     199     252 ..     196     254 .. 0.62
   2 !   17.7   1.7   2.9e-06     0.004      21      60 ..     297     334 ..     277     335 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.1e-05
                           Fer4_17  12 Cpsyeaydnepkkllraakl........glleeaekeekaslCieCgeCerkCP 57 
                                       C + e  +++ +++ +   +         ++e  + +e+ +lC+ Cg+C+  CP
  gi|242398273|ref|YP_002993697.1| 199 CEFREFENKKHQMFKYHEDWgnlrylleMEMEHPMWNEQSELCLACGNCNLTCP 252
                                       66655555555544444444334433322455556669***************9 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 2.9e-06
                           Fer4_17  21 epkkllraaklglleea.ekeekaslCieCgeCerkCPqgl 60 
                                       ++ ++++++ ++   +  +++  +s C++Cg+C++ CP+++
  gi|242398273|ref|YP_002993697.1| 297 KKSRFMNRYLCK---NSyNEKLGISYCVGCGRCTYFCPAEI 334
                                       444566664443...33034569***************987 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   2.2   1.2e-05     0.016      20      50 ..     202     253 ..     190     254 .. 0.63
   2 !   14.5   1.1     3e-05     0.041       2      15 ..     320     333 ..     294     356 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.2e-05
                            Fer4_7  20 deeenek.....................gtekveidpekClgCgaCvavCPt 50 
                                       +e+en+k                     + + ++ ++e Cl Cg+C  +CPt
  gi|242398273|ref|YP_002993697.1| 202 REFENKKhqmfkyhedwgnlryllememEHPMWNEQSELCLACGNCNLTCPT 253
                                       4444444333444444544444444432336679999**************8 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 3e-05
                            Fer4_7   2 CigCgaCvaaCpvk 15 
                                       C+gCg+C+  Cp++
  gi|242398273|ref|YP_002993697.1| 320 CVGCGRCTYFCPAE 333
                                       77777777777765 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   3.9   0.00053      0.73      44      63 ..     228     253 ..     196     255 .. 0.60
   2 !   23.8  11.3   3.3e-08   4.5e-05       4      65 .]     240     334 ..     237     334 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00053
                            Fer4_8  44 e......eealwsCttcgaCtevCpv 63 
                                       e      +e  + C++cg+C+  Cp+
  gi|242398273|ref|YP_002993697.1| 228 EmehpmwNEQSELCLACGNCNLTCPT 253
                                       23345558888999999999999996 PP

  == domain 2  score: 23.8 bits;  conditional E-value: 3.3e-08
                            Fer4_8   4 kCieCgaCqsaCpvlrr.......................tkkhlldargeaaedvqeeqvlee............. 44 
                                        C  Cg C+ +Cp++r+                       +                                    
  gi|242398273|ref|YP_002993697.1| 240 LCLACGNCNLTCPTCRCyevqdipnldgdtgarirrwdscQ----------------------Lrshglvagnhnfr 294
                                       6************9999444444444444444444433330......................23344444455555 PP

                            Fer4_8  45 ...................eealwsCttcgaCtevCpvgi 65 
                                                          + ++ +C++cg+Ct  Cp +i
  gi|242398273|ref|YP_002993697.1| 295 ptkksrfmnrylcknsyneKLGISYCVGCGRCTYFCPAEI 334
                                       5555555555556666666889***************986 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   1.7   0.00013      0.18       6      20 ..     239     253 ..     237     253 .. 0.93
   2 !   15.3   3.7   9.4e-06     0.013       7      21 ..     319     333 ..     317     334 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00013
                                       TTSSS-THHHHHSTT CS
                              Fer4   6 ekCigCGaCvevCPv 20 
                                       e+C +CG+C   CP+
  gi|242398273|ref|YP_002993697.1| 239 ELCLACGNCNLTCPT 253
                                       89************7 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 9.4e-06
                                       TSSS-THHHHHSTTT CS
                              Fer4   7 kCigCGaCvevCPvg 21 
                                        C+gCG+C   CP +
  gi|242398273|ref|YP_002993697.1| 319 YCVGCGRCTYFCPAE 333
                                       7************76 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   1.6   7.6e-05       0.1       7      22 .]     238     253 ..     230     253 .. 0.80
   2 !   14.2   4.7   2.5e-05     0.034      10      22 .]     320     332 ..     318     332 .. 0.96

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.6e-05
                            Fer4_2   7 tdrCigCgaCvsaCPa 22 
                                       ++ C++Cg C   CP+
  gi|242398273|ref|YP_002993697.1| 238 SELCLACGNCNLTCPT 253
                                       569*******999**7 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 2.5e-05
                            Fer4_2  10 CigCgaCvsaCPa 22 
                                       C+gCg C+  CPa
  gi|242398273|ref|YP_002993697.1| 320 CVGCGRCTYFCPA 332
                                       ************8 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   4.7   0.00072      0.99      12      48 ..     199     253 ..     196     256 .. 0.67
   2 !   15.4   2.5   1.1e-05     0.015       1      24 [.     319     342 ..     319     368 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00072
                            Fer4_9  12 Cpagvvvedaaerkarlraase..................eaCigCgaCveaCpk 48 
                                       C++  +++++ + +  ++ +++                  e C+ Cg C   Cp+
  gi|242398273|ref|YP_002993697.1| 199 CEFREFENKKHQMFKYHEDWGNlryllememehpmwneqsELCLACGNCNLTCPT 253
                                       555555555555555555555566666666666666668899***********97 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 1.1e-05
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaer 24 
                                       +C+gCg+C++ Cpa++   ++ ++
  gi|242398273|ref|YP_002993697.1| 319 YCVGCGRCTYFCPAEISFVENLRT 342
                                       6*************9876666555 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   8.3      0.75     1e+03       2      16 ..     239     253 ..     238     260 .. 0.90
   2 !   20.2   1.5   4.1e-07   0.00057       3      16 ..     319     332 ..     313     337 .. 0.92
   3 ?   -1.7   0.1       4.4     6e+03      11      15 ..     348     352 ..     348     357 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.75
                            Fer4_4   2 erCigCgsCvaaCPq 16 
                                       e C+ Cg C  +CP+
  gi|242398273|ref|YP_002993697.1| 239 ELCLACGNCNLTCPT 253
                                       78***********96 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 4.1e-07
                            Fer4_4   3 rCigCgsCvaaCPq 16 
                                        C+gCg+C+++CP 
  gi|242398273|ref|YP_002993697.1| 319 YCVGCGRCTYFCPA 332
                                       6************6 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 4.4
                            Fer4_4  11 vaaCP 15 
                                       +++CP
  gi|242398273|ref|YP_002993697.1| 348 EDSCP 352
                                       68999 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   2.0    0.0027       3.7      12      65 ..     199     252 ..     195     254 .. 0.51
   2 !   12.9   0.8   0.00012      0.16      52      66 ..     318     332 ..     272     335 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0027
                           Fer4_16  12 CPtnaikekkekeiearecisy...ntaekkdlaedeekckkqeaitgCdiCqdvCP 65 
                                       C  + +++kk+++++++e+  +        +   e+   +++ e +  C++C+ +CP
  gi|242398273|ref|YP_002993697.1| 199 CEFREFENKKHQMFKYHEDWGNlryL---LEMEMEHPMWNEQSELCLACGNCNLTCP 252
                                       55555555555566666655542221...1112222222223455789999999999 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00012
                           Fer4_16  52 eaitgCdiCqdvCPa 66 
                                         + gC++C+  CPa
  gi|242398273|ref|YP_002993697.1| 318 SYCVGCGRCTYFCPA 332
                                       556777777777765 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   4.0    0.0012       1.7      35      56 ..     235     256 ..     225     263 .. 0.75
   2 ?   11.6   2.0   0.00017      0.24      39      53 ..     318     332 ..     306     351 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0012
                           Fer4_21  35 kvvedeCvGCnlCssvCPvedc 56 
                                       + +++ C +C  C   CP+  c
  gi|242398273|ref|YP_002993697.1| 235 NEQSELCLACGNCNLTCPTCRC 256
                                       4557788888888888887666 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00017
                           Fer4_21  39 deCvGCnlCssvCPv 53 
                                       + CvGC  C+  CP 
  gi|242398273|ref|YP_002993697.1| 318 SYCVGCGRCTYFCPA 332
                                       568888888888884 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   8.1     0.011        16       6      21 ..     238     253 ..     237     259 .. 0.91
   2 ?   13.2   2.7   5.3e-05     0.073       8      22 ..     319     333 ..     317     335 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.011
                            Fer4_6   6 pdkCigCgdCvrvCPe 21 
                                        ++C+ Cg+C   CP+
  gi|242398273|ref|YP_002993697.1| 238 SELCLACGNCNLTCPT 253
                                       689************7 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 5.3e-05
                            Fer4_6   8 kCigCgdCvrvCPeg 22 
                                        C+gCg+C+  CP+ 
  gi|242398273|ref|YP_002993697.1| 319 YCVGCGRCTYFCPAE 333
                                       6************86 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.4     0.028        39      55      73 ..     235     253 ..     206     259 .. 0.81
   2 ?    8.8   0.1    0.0013       1.8      50      78 ..     309     337 ..     284     352 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.028
                           Fer4_18  55 ekgagdcidcescvkvcPt 73 
                                       ++++  c++c+ c   cPt
  gi|242398273|ref|YP_002993697.1| 235 NEQSELCLACGNCNLTCPT 253
                                       455667************8 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0013
                           Fer4_18  50 keerkekgagdcidcescvkvcPtgidir 78 
                                       +  +++ g + c+ c+ c   cP +i   
  gi|242398273|ref|YP_002993697.1| 309 NSYNEKLGISYCVGCGRCTYFCPAEISFV 337
                                       44455678899*************99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       655  (0.036533); 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:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 2207.00
//
Query:       gi|242398274|ref|YP_002993698.1|  [L=297]
Description: NiFe hydrogenase I, subunit gamma [Thermococcus sibiricus MM 739]
Scores for complete 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-14   53.7   0.0    4.4e-14   53.0   0.0    1.3  1  NAD_binding_1    Oxidoreductase NAD-binding domain
    1.5e-12   47.1   1.6    2.4e-12   46.4   1.6    1.4  1  DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydr
    6.4e-09   36.1   0.0    9.2e-09   35.6   0.0    1.2  1  FAD_binding_6    Oxidoreductase FAD-binding domain
    0.00022   21.4   0.0       0.08   13.1   0.0    2.2  2  NAD_binding_6    Ferric reductase NAD binding domain
     0.0055   16.8   0.2      0.051   13.7   0.1    2.5  2  FAD_binding_8    FAD-binding domain


Domain annotation for each model (and alignments):
>> NAD_binding_1  Oxidoreductase NAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.0   0.0   1.2e-17   4.4e-14       1     107 [.     130     234 ..     130     236 .. 0.93

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 1.2e-17
                                       EEEEGGGGHHHHHHHHHHHHHCTTCSEEEEEEEESSGCGSTTHHHHHHHHHHCTT.EEEEEEEESSCTTTSSSEESS CS
                     NAD_binding_1   1 miagGtGiaPvrsvlraileeakdktkvvlvyGnrteedllyreeleelakklpg.rlkvvavvsreeagweggkgr 76 
                                       +ia+G G aP+rsv   ++++  + ++++++  +r+ +dll+ +ele+++  ++  ++k+++    ++ +w g kgr
  gi|242398274|ref|YP_002993698.1| 130 LIAAGLGTAPLRSVFLYAMDNRWKYGNITFINTARYGKDLLFYKELEAMKDLAEAeNVKIIQS-VTRDPDWPGLKGR 205
                                       7********************8899************************99999988888888.77788899***** PP

                                       HHHHHHHHHHHHSSTTEEEEEECSHHHHHHH CS
                     NAD_binding_1  77 vqdalleellslkkeethvyvCGppgMikav 107
                                        q+ ++e   +   ++t + vCGpp+M kav
  gi|242398274|ref|YP_002993698.1| 206 PQQFVVEANTN--PKNTAIAVCGPPRMYKAV 234
                                       *****998888..89*************997 PP

>> DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydroorotate dehydrogenase B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.4   1.6   6.7e-16   2.4e-12       1      40 [.     253     288 ..     253     290 .. 0.90

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 6.7e-16
                                       ----SSSSSSS-TTEEEETTCTT.CEEETTTT-CEEECCC CS
                   DHODB_Fe-S_bind   1 eerMaCGvGaClgCvvktkggdggeykrvCkdGPvFdade 40 
                                       e+ M+CG+G C++C v t+++     k++CkdGPvF + +
  gi|242398274|ref|YP_002993698.1| 253 ERKMKCGIGKCGHCNVGTSTS----WKYICKDGPVFGYFD 288
                                       899***************986....79*********8766 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 !   35.6   0.0   2.6e-12   9.2e-09      11      96 ..      36     116 ..      24     118 .. 0.84

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 2.6e-12
                                       CTTEEEEEEEESTTTS-----TT-EEEEEECETTCCEEEEEE.BSSTTECCEEEEEEE--TT-HHHHHHHCS-TT-E CS
                     FAD_binding_6  11 sedtrifrfklpsekqklglpvGqhvflrlkikgeaviRsYtpissenekGelellvkvypgGkmsqaLdelkigdt 87 
                                       +e +  frf+ p+ ++k  + +Gq+v+l+++  ge    + +++ss   kG++el +++   G+++ ++++lk+gdt
  gi|242398274|ref|YP_002993698.1|  36 TEKLFLFRFEDPELAKKWTFKPGQFVQLTIPGVGE---VPISICSSAMRKGFFELCIRK--AGRVTTVIHKLKPGDT 107
                                       33445677777777899*********999997787...5889****************5..7*************** PP

                                       EEEEEEE-S CS
                     FAD_binding_6  88 leikGPlGk 96 
                                       + ++GP+G+
  gi|242398274|ref|YP_002993698.1| 108 VLVRGPYGN 116
                                       *******97 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 !   13.1   0.0   2.2e-05      0.08       4      77 ..     128     196 ..     126     208 .. 0.88
   2 !    6.2   0.0     0.003        11     130     151 ..     213     234 ..     202     238 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.2e-05
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     NAD_binding_6   4 vllvagGiGitpfisilkdllkkskkealktkkikliwvvressslewfkdvLneleeeksegnieihiYlTse 77 
                                       +ll+a+G G +p+ s++   + +      k  +i++i   r  ++l  +k  L+ ++++ +  n++i   +T++
  gi|242398274|ref|YP_002993698.1| 128 LLLIAAGLGTAPLRSVFLYAMDNRW----KYGNITFINTARYGKDLLFYK-ELEAMKDLAEAENVKIIQSVTRD 196
                                       89**************988887776....*****************9999.88888888888999998888876 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.003
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                     NAD_binding_6 130 skhknssvgvfvCGppklvkev 151
                                       ++++ ++++++vCGpp + k v
  gi|242398274|ref|YP_002993698.1| 213 ANTNPKNTAIAVCGPPRMYKAV 234
                                       3667789999********9987 PP

>> FAD_binding_8  FAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.1   1.4e-05     0.051      25      81 ..      50     102 ..      23     117 .. 0.80
   2 ?   -2.1   0.0       1.1   4.1e+03      29      41 ..     151     163 ..     146     171 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.4e-05
                     FAD_binding_8  25 kkslkykaGqyvyinipslsklfwqsHPFtiasape.ddklslvikvksgltkklakk 81 
                                        k++ +k+Gq+v + ip + ++     P +i s++    + +l+i++ + +t+ ++k 
  gi|242398274|ref|YP_002993698.1|  50 AKKWTFKPGQFVQLTIPGVGEV-----PISICSSAMrKGFFELCIRKAGRVTTVIHKL 102
                                       344*****************88.....*****9988799*************999864 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.1
                     FAD_binding_8  29 kykaGqyvyinip 41 
                                       ++k G++ +in  
  gi|242398274|ref|YP_002993698.1| 151 RWKYGNITFINTA 163
                                       7999******984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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 0.35s 00:00:00.96 Elapsed: 00:00:00.55
# Mc/sec: 1617.75
//
Query:       gi|242398275|ref|YP_002993699.1|  [L=267]
Description: NiFe hydrogenase I, subunit delta [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.1e-27   94.0   0.0    9.6e-27   93.4   0.0    1.3  1  Oxidored_q6  NADH ubiquinone oxidoreductase, 20 Kd subunit
     0.0034   17.6   0.0     0.0087   16.3   0.0    1.7  1  eIF2_C       Initiation factor eIF2 gamma, C terminal


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 !   93.4   0.0   1.1e-30   9.6e-27       1     129 [.      21     156 ..      21     158 .. 0.85

  Alignments for each domain:
  == domain 1  score: 93.4 bits;  conditional E-value: 1.1e-30
                                       -SHHHHHHT-TTTTHHHHHHTEEEEEETTT-S--HHHHHHTHTTTSEEEEEESBE...EEEHHHHHHHHGGGSSEEE CS
                       Oxidored_q6   1 CtGcsisllaleedlldllelielryhetlladskeeeieakekeadvlvveGavtrkpkealellkelaekakavi 77 
                                       C Gc+++++ +++++l+ll+ +++++ + ++ + +    + ++ke+d++++eG+v  +++e++el+k+++ekak+vi
  gi|242398275|ref|YP_002993699.1|  21 CYGCQLQFA-MMDEVLQLLDKANIEC-W-FMLERG----SDEDKEVDIAFIEGSV--STQEEVELVKKIREKAKIVI 88 
                                       9******97.5677889999999988.4.445556....57788***********..******************** PP

                                       EESHHHHH-TGGGSTT-TEE................-HHHHHHHC.S-E.EEE-SSS--HHHHHHHHH CS
                       Oxidored_q6  78 avGtCAafGGipaaannpsv................geevgellevvpvdinipGCPphpeailetll 129
                                       avG+CA++GG+++  ++ +                  + +++++++++vd+++ GCPp+++++l++l 
  gi|242398275|ref|YP_002993699.1|  89 AVGSCAVHGGVQSWDKDKEFnelwktvygdahvkfePKMAEPVEKYIKVDYKLYGCPPEKKDFLYALG 156
                                       ************99997733567888887777655537788***********************9986 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 !   16.3   0.0   9.7e-07    0.0087       5      56 ..      59     111 ..      55     122 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 9.7e-07
                                       EEEEE-SBESSSSSCCC.-----TTEEEEEEETTEEEEEEEEEEESSEEEEEE CS
                            eIF2_C   5 ieyellerlvgvkeekk.veklkkkEvLmlniGsastggvvtsvkkdeakvkL 56 
                                       +++ ++e  v+++ee + v+k+++k ++++ +Gs +++g v+s  kd+   +L
  gi|242398275|ref|YP_002993699.1|  59 VDIAFIEGSVSTQEEVElVKKIREKAKIVIAVGSCAVHGGVQSWDKDKEFNEL 111
                                       667777888889999778**************************999765555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       833  (0.046461); expected 358.6 (0.02)
Passed bias filter:                      704  (0.039266); 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: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 1582.38
//
Query:       gi|242398276|ref|YP_002993700.1|  [L=427]
Description: NiFe hydrogenase I, catalytic subunit alpha [Thermococcus sibiricus MM 739]
Scores for complete 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   89.6   0.4    2.7e-11   43.1   0.0    3.1  3  NiFeSe_Hases  Nickel-dependent hydrogenase


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 !   43.1   0.0   1.5e-15   2.7e-11       1      79 [.      40     118 ..      40     124 .. 0.96
   2 !    2.6   0.0    0.0028        50     147     206 ..     124     184 ..     118     198 .. 0.75
   3 !   40.4   0.0   9.6e-15   1.7e-10     398     505 .]     319     423 ..     238     423 .. 0.72

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 1.5e-15
                                       --HHHHTTTS-GGGHHHHHHTT-SSSTTHHHHHHHHHHHHHHT----HHHHHHHHHHHHHHHHHHHHHHHHHTTGGG CS
                      NiFeSe_Hases   1 RGlElilkgrdprdawalvqRiCGVCttvHalasvravedAlgikipknarlirnliaaalllhdhivhFYhLhalD 77 
                                       R +E i  g++ ++a a+  RiC  C  +H l++v+a e+A+g+++  + + +r+l+    ++++h +h+Y L   D
  gi|242398276|ref|YP_002993700.1|  40 RFFEAITLGKKLEEALAVYPRICSFCSAAHKLTAVEAAEKAVGFTPRPEIQDLRDLLYIGDMIESHALHLYLLVLPD 116
                                       5689*********************************************************************9999 PP

                                       TS CS
                      NiFeSe_Hases  78 wv 79 
                                       ++
  gi|242398276|ref|YP_002993700.1| 117 YL 118
                                       97 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.0028
                                       HHHHHHHHHHHHHHHHH....THHHHHHHSSSSS--.EBTTBESSGBGSBSHHHHHHHHHHHHH CS
                      NiFeSe_Hases 147 liavahYLeaLelqrka....akivaifggknPhpqslvvGGvtcaidllnaerlaevkslike 206
                                       l +v +Y++ +e+   +    +ki+  ++++  h+++ + GG       ++ ++++e+k+ +ke
  gi|242398276|ref|YP_002993700.1| 124 LAMVDKYMKEIEYAMALknigSKIMDYLASRAIHQENAILGGFGKL---PTRSQFEELKKELKE 184
                                       77889999877765544111278999****************9888...666666666666655 PP

  == domain 3  score: 40.4 bits;  conditional E-value: 9.6e-15
                                       HHHHTTB---B--TT-SGGGS-.SEEEEEEEEEETTEEEEEEEEEETTEEEEEEEE-HHHHHH--S-TT----HHHH CS
                      NiFeSe_Hases 398 enikkgdtetaneekldkkevp.keakGvglveapRGaLsHwikikdgkienYqavvPsTWnasPrdakgqkgayEa 473
                                       + i   d + a+    +++ev+ k+  Gv ++eapRG L   +++kdgk++  +++ P+  n++  +++ +      
  gi|242398276|ref|YP_002993700.1| 319 RAIDIIDDTLAKWPIKERDEVEiKDGFGVSITEAPRGLLVYALEVKDGKVDYVDIITPTAMNLAIMERHVR------ 389
                                       333444444444443444555556799************************************98877655...... PP

                                       HHTT-B-SSTTS-HHHH..HHHHHT--BHHHHH- CS
                      NiFeSe_Hases 474 aLigtpvadpekPleil..rtihSfDPClACavH 505
                                       ++ +++ +d  + l +l   t++++DPC++C+vH
  gi|242398276|ref|YP_002993700.1| 390 MMAEKHWQDDPETLKLLteMTVRAYDPCISCSVH 423
                                       455666666666666662269************* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       785  (0.0437838); expected 358.6 (0.02)
Passed bias filter:                      643  (0.0358637); 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 0.31s 00:00:00.95 Elapsed: 00:00:00.48
# Mc/sec: 2673.91
//
Query:       gi|242398277|ref|YP_002993701.1|  [L=151]
Description: Hydrogenase-specific maturation endopeptidase [Thermococcus sibiricus MM 739]
Scores for complete 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-20   71.4   0.7    6.7e-20   71.2   0.7    1.1  1  HycI      Hydrogenase maturation 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 !   71.2   0.7   3.7e-24   6.7e-20      12     128 ..      30     147 ..      21     149 .. 0.90

  Alignments for each domain:
  == domain 1  score: 71.2 bits;  conditional E-value: 3.7e-24
                                       C--TTEEEEEECT-SGGGHHHHCC-SEEEEEEE--S.SS-TT-EEEEECCHHHHHHTTC.CGCCCHCHHHHHHHHHH CS
                              HycI  12 efkenvtviDgGtqglelvgtleeadkliivDavdf.glepGevkiikddevpkklkakkmsaHqlplaevlkllee 87 
                                       ++k   +v++ Gt+ ++l +++   +++ii+Da++  + +pG+v+ +k+de ++kl+a+  saH ++  + lkll+ 
  gi|242398277|ref|YP_002993701.1|  30 AEK-GYNVLEVGTDIFRLQRHYSGEERIIIIDAILSeKYKPGQVVHLKGDEAFEKLRAEIRSAHFMGTIDGLKLLRL 105
                                       444.489*****************************999************************************** PP

                                       CCS--SEEEEEEE--S-BST..CCS--HHHHCCHHHHHHHCC CS
                              HycI  88 kgeipkevillgvqpesled.vgielseevkkavekavelil 128
                                        ++  +++ +++v  + +e  +g+elseevk  +++++++i 
  gi|242398277|ref|YP_002993701.1| 106 IDKRLAKAEIHFVGIVAKEIdLGMELSEEVKGNIHNIINIIE 147
                                       9999888888777777777557*****************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1003.08
//
Query:       gi|242398278|ref|YP_002993702.1|  [L=261]
Description: hypothetical protein TSIB_0287 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-51  174.6   0.0    3.5e-51  174.4   0.0    1.0  1  Methyltrn_RNA_3  Putative RNA methyltransferase
    0.00021   21.5   0.0       0.32   11.1   0.0    2.2  2  SpoU_methylase   SpoU rRNA Methylase family


Domain annotation for each model (and alignments):
>> Methyltrn_RNA_3  Putative RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  174.4   0.0   3.9e-55   3.5e-51       3     285 ..       7     254 ..       5     255 .. 0.88

  Alignments for each domain:
  == domain 1  score: 174.4 bits;  conditional E-value: 3.9e-55
                   Methyltrn_RNA_3   3 siaiPssiisnaqsleqktylagqIARaaaiFnVdeivvfddseseeekkekpseflarlLqYletPpYLrkelFpl 79 
                                        i iP s++++ ++++ kty++gqI RaaaiF V++i +++ + +e        +f+  +L+Y+etP+YLrk+l pl
  gi|242398278|ref|YP_002993702.1|   7 HIFIPDSLLEETSDPKIKTYKVGQIGRAAAIFGVEHIWIYKAGGRE-------GKFIKLVLEYMETPQYLRKTLIPL 76 
                                       589*************************************999954.......58********************** PP

                   Methyltrn_RNA_3  80 hkelkyaglLppldaphhl..rsseegeyreGvvvekskekkskkklVniGlkkevklelkqevpegtRVtVklsse 154
                                       +kelkyag+Lppl++phh   r+ + ge+reGv+++k k  +    + +iGl++ + +e     + + R t ++ s 
  gi|242398278|ref|YP_002993702.1|  77 TKELKYAGILPPLRTPHHKlkREPKVGEIREGVIIKKGK--RL---YADIGLDELALVEG----SGEGRMTFEIIS- 143
                                       ******************97555559***********88..44...9*****99998888....7788******33. PP

                   Methyltrn_RNA_3 155 esveakvVspsepreeaglywGYsVrla.kslsavftespfeggydlsigtsergekveeklaelekkkefkhlliv 230
                                         v    V+p++pr     ywGY+V+l+  sl++ ++++    + +l i+ts+ ge+v ++           ++  v
  gi|242398278|ref|YP_002993702.1| 144 --VIPLKVAPTKPR----EYWGYRVHLTrMSLAKTLKKA----KLNLAIATSRMGEDVRKVNLPP----LEGEVGFV 206
                                       ..555556777776....9*******9945888888888....789**********888776655....468999** PP

                   Methyltrn_RNA_3 231 fGg.vrgleaaleadeelklegekaeelFdlwlntvpnqgsrtirtEEavliaLal 285
                                       fG+  +g+ ++l+        + + +  Fdl+lnt+pnq+++t+rtEEavl++La 
  gi|242398278|ref|YP_002993702.1| 207 FGSpRKGIMEILR--------DFNEDYPFDLILNTIPNQKTKTVRTEEAVLVTLAI 254
                                       ***99*******3........3577788**************************85 PP

>> SpoU_methylase  SpoU rRNA Methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0   0.00029       2.6      15      57 ..      28      67 ..      21     107 .. 0.76
   2 !   11.1   0.0   3.6e-05      0.32      62     110 ..     167     216 ..     149     225 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00029
                                      HHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHH CS
                    SpoU_methylase 15 lGaiaRtakafgaselvlvkprsadllnpeakraaagalevle 57
                                      +G i R+a++fg++++++ k  +    + +++++ +++ e+ +
  gi|242398278|ref|YP_002993702.1| 28 VGQIGRAAAIFGVEHIWIYKAGGR---EGKFIKLVLEYMETPQ 67
                                      8****************9885554...7777777776666655 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 3.6e-05
                                       SSHHHHHHHHCCCTEEEEEESTT-SEGCCSHHH...TTEEEEEEBTTTBS-H CS
                    SpoU_methylase  62 dsleealkelkeegfalvatslkgkslseidlk...ekvalvfGnEdkGlsn 110
                                       +sl+++lk+ k +    +ats+ g+++++++l+   ++v +vfG+ +kG+ +
  gi|242398278|ref|YP_002993702.1| 167 MSLAKTLKKAKLN--LAIATSRMGEDVRKVNLPpleGEVGFVFGSPRKGIME 216
                                       4666666666666..5599999******99666666*************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.50
# Mc/sec: 1555.69
//
Query:       gi|242398279|ref|YP_002993703.1|  [L=359]
Description: 50S ribosomal protein L3P [Thermococcus sibiricus MM 739]
Scores for complete 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-89  301.0   0.3    1.2e-89  300.9   0.3    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 !  300.9   0.3   6.7e-94   1.2e-89       6     368 ..       4     359 .]       1     359 [] 0.91

  Alignments for each domain:
  == domain 1  score: 300.9 bits;  conditional E-value: 6.7e-94
                                       SXXXXSSXCCCTTXSBXSXSSXXXSX.XXSBTTTTTXBSEEEEEEEEEEEEEEECHHTTSCCCCCEEEEEEEEEEC- CS
                      Ribosomal_L3   6 feaprhgslGflprkRaerergkvksfPkddtskpvkltaflGyKaGmthiVrevdkpgskldkkevveavtvvetp 82 
                                        ++pr+gsl ++prkRa++ +++++ +P+++    v + +f+GyKaGmth+   +d pg  +++ke+ ++vt+ve p
  gi|242398279|ref|YP_002993703.1|   4 ISRPRRGSLAYSPRKRAKSIVPRIRKWPQEQ---EVRMLGFAGYKAGMTHVLMIDDAPG-LTKGKEIFVPVTIVEAP 76 
                                       589*************************865...57999***********988777776.57899************ PP

                                       -EEEEEEEEEEEETTEEEEEEEEESSS.S.HHHHCCCSTS..TTTSSSSSSHCCCCHCSSCCCCCCHHHHHHHHHHS CS
                      Ribosomal_L3  83 pmvivgvvgyvetprGlrslktvwaehls.eevkrrlykn..wykskkkaftkyskkyeskdvkklieadleeikke 156
                                       p+++ g+++y     Gl + ++v   + + e+   +  kn  +yk   + +    k+y  ++v ++   +le + k 
  gi|242398279|ref|YP_002993703.1|  77 PLMVYGIRAYKRGYFGLETATEVIVPDFKlENYPSKRAKNvtFYKLLERRIKTLPKNYT-EEVFQQKLGELEDLVKT 152
                                       **********************9998775355544444552267777888888999994.44444444589999999 PP

                                       CSCEEEEEEEECCCSS-SCCSSHHEEEEECHCSCHHHHHHHHHHCCTCEEECCCCS-TTSEEEEEEEE---EEE-HH CS
                      Ribosomal_L3 157 asvvrviahtvirktkslaqKkahllEiqvngGtiaekldfarealektvavaavFrqgeliDvigvtkGkGfeGvv 233
                                         vv + a+  ++   ++ +Kk++++E  v+g +i ek+++ +e+l k + v ++ ++gel+D+++vtkGkG++G+v
  gi|242398279|ref|YP_002993703.1| 153 GEVVELRALVATQPWLARIKKKPEVMEYAVGGTSIEEKFNYIKEKLGKEIRVGEILQEGELLDIVAVTKGKGTQGPV 229
                                       999999999888888899*********************************************************** PP

                                       HHCT----STTTSSSSSS-S-SS-SSSSS--TTS--SEEESCCEEEEEEEEEEEEETTTSSTTTSSTTT.SS..SS. CS
                      Ribosomal_L3 234 kRWgvkklprkthrglRkvaaigawdparVsstvaraGqkGyhhRtelnkkiyrigkgedaknastefdltekeitP 310
                                       kRWgvk    k  +g+Rkva+ig+w+parV++tv+raGq+G+hhRte+nk++ rig+     n++   +  + eitP
  gi|242398279|ref|YP_002993703.1| 230 KRWGVKLTSHKDSKGRRKVATIGPWHPARVMWTVPRAGQMGFHHRTEFNKRLLRIGE-----NGKLTLNGEKIEITP 301
                                       *********************************************************.....999999999****** PP

                                       TTTCTTCB..TSCEEEEES--SSSTTEEEEEEE-SSGGGSCCCSS-EEEEEE-TTCTS CS
                      Ribosomal_L3 311 mGGfvhyGevkndfilvkGsvpGpkkrlvklrkslltqtsrkaeeevslkfidtaskf 368
                                        GGf+hyG+vkndfi++ G++pG  kr++++r+++++  +r   e  +  +i+  sk+
  gi|242398279|ref|YP_002993703.1| 302 NGGFPHYGVVKNDFIMIAGTIPGAIKRIIRMRPAVRPPAKRPPAEAPQITYISRESKQ 359
                                       ****************************************9999999999*9999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 2155.96
//
Query:       gi|242398280|ref|YP_002993704.1|  [L=255]
Description: 50S ribosomal protein L4P [Thermococcus sibiricus MM 739]
Scores for complete 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-48  164.3   0.5    2.9e-48  164.1   0.5    1.0  1  Ribosomal_L4  Ribosomal protein L4/L1 family
  ------ inclusion threshold ------
      0.029   14.6   0.1      0.053   13.8   0.1    1.6  1  DUF2149       Uncharacterized conserved protein (DUF2149)


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 !  164.1   0.5   3.3e-52   2.9e-48       1     191 [.      16     252 ..      16     253 .. 0.92

  Alignments for each domain:
  == domain 1  score: 164.1 bits;  conditional E-value: 3.3e-52
                                       EEE-HHHHSS---HHHHHHHHHHHHHSS-EE-----.-TTTSS---S-SS-SSSSSS---S-TT........STTST CS
                      Ribosomal_L4   1 veLspkvFaapirrdlihravvaylanrrqgtastk.arsevsgsgrklwkQKGtGrARvgsir........spiar 68 
                                       ++L pkvF++p+r+dli+rav a +++r q++++++ a+++     ++++k  G+G+ARv +i+        +p+ar
  gi|242398280|ref|YP_002993704.1|  16 ITL-PKVFQTPFRPDLIKRAVIASWTHRIQPQGRDPlAGKRRVT--ENIGK--GRGMARVERIKtsprfaafVPFAR 87 
                                       568.9*******************************77777766..69999..************************ PP

                                       T---SS---S.EEHHHHHHHHHHHHHHHHHHHHHHHTT-EEEES--.-.-S............S--HHHHHHHHHHT CS
                      Ribosomal_L4  69 gGgvahgpkperdystklnkKvrrlAlrsaLsakakqglllvvdnl.eple............esktkelvellkkl 132
                                       gG++ah+pk+e+ +++ +nkK+++lAl sa++a+a+ +l+++++++ ++++              +t + +e++kkl
  gi|242398280|ref|YP_002993704.1|  88 GGRRAHPPKVEKVIWEGINKKEKKLALMSAIAATANYDLVRARGHViDNIPqvplvvenelekVYRTAQTREIFKKL 164
                                       ********************************************6633555566778777767667**********9 PP

                                       T-..........................TTSSEEEEESSSSCHHHHHHTT-TTEEEEESTT--CHHHHHSSE....E CS
                      Ribosomal_L4 133 gl..........................ksksvLivvsekdenlvlaarnlpgvevieveslnvydllkadk....v 179
                                       g+                          k k++Livv + +e++++ arn+pgv+v+ v++l v+ l+++++    +
  gi|242398280|ref|YP_002993704.1| 165 GIwedierakrntkvragkgkmrgrrykKAKGPLIVVAK-NEGIIQGARNHPGVDVVVVDNLGVELLAPGAHpgrlT 240
                                       8888999999999999999999999999999******86.************************************* PP

                                       EEEHHHHHHHHH CS
                      Ribosomal_L4 180 vitksaveklee 191
                                       ++tk+a+e+l+e
  gi|242398280|ref|YP_002993704.1| 241 IWTKGAIERLRE 252
                                       *********987 PP

>> DUF2149  Uncharacterized conserved protein (DUF2149)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   5.9e-06     0.053      48      90 ..     157     201 ..     113     203 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.9e-06
                           DUF2149  48 kmeiivkeg..eelkkakesaekasgkGerlGtayrlkdGkliyV 90 
                                       + ei  k g  e++++ak ++++  gkG+  G  y+ ++G li+V
  gi|242398280|ref|YP_002993704.1| 157 TREIFKKLGiwEDIERAKRNTKVRAGKGKMRGRRYKKAKGPLIVV 201
                                       45564444555899*****************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1671.36
//
Query:       gi|242398281|ref|YP_002993705.1|  [L=86]
Description: 50S ribosomal protein L23P [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-18   67.2  10.1    1.3e-17   63.9  10.1    1.9  1  Ribosomal_L23  Ribosomal protein L23
  ------ inclusion threshold ------
      0.054   13.3   0.4      0.087   12.7   0.4    1.4  1  TusA           Sulfurtransferase TusA


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 !   63.9  10.1   1.5e-21   1.3e-17       1      80 [.       5      72 ..       5      78 .. 0.86

  Alignments for each domain:
  == domain 1  score: 63.9 bits;  conditional E-value: 1.5e-21
                                      SSEEEE--SHHHHHHHTT.E.EEEEE-SS-THHHHHHHHHHHHT--EEEEEEEEE--EBESSSSSEEBE--EEEEEEEE CS
                     Ribosomal_L23  1 dvilkPvitEkstklaek.nkyvFeVakdanKleikkaveklFgVkVekVntlnvkgkkkrvgrkvgrrksyKkaiVtL 78
                                      +vi++Pv+tEk++++ e+ nk++F V+k+a+K++ikkave +++VkV+kVn+++  +               Kka+V+L
  gi|242398281|ref|YP_002993705.1|  5 KVIVRPVVTEKAISMVEReNKLTFIVDKRATKPDIKKAVETVYEVKVDKVNIVITMKG-------------EKKAYVKL 70
                                      69*************99978********************************998764.............45555555 PP

                                      SS CS
                     Ribosomal_L23 79 ke 80
                                      k+
  gi|242398281|ref|YP_002993705.1| 71 KP 72
                                      54 PP

>> TusA  Sulfurtransferase TusA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.4   9.7e-06     0.087      15      48 ..      11      44 ..      10      61 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.7e-06
                                      HHHHHHHCCCGCT-EEEEEESSCHHHHHHHHHHH CS
                              TusA 15 lklkkalekleegevlevladdpaatediprfak 48
                                      + + ka+  +e +++l +++d +a++ di++ ++
  gi|242398281|ref|YP_002993705.1| 11 VVTEKAISMVERENKLTFIVDKRATKPDIKKAVE 44
                                      6799**************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       844  (0.0470746); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.33s 00:00:00.85 Elapsed: 00:00:00.53
# Mc/sec: 490.29
//
Query:       gi|242398282|ref|YP_002993706.1|  [L=241]
Description: 50S ribosomal protein L2P [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.5e-43  145.6   0.8    1.5e-42  144.7   0.8    1.4  1  Ribosomal_L2_C  Ribosomal Proteins L2, C-terminal domain
    5.7e-21   74.3   0.0    1.3e-20   73.1   0.0    1.6  1  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 !  144.7   0.8   1.7e-46   1.5e-42       2     121 ..      95     224 ..      94     229 .. 0.95

  Alignments for each domain:
  == domain 1  score: 144.7 bits;  conditional E-value: 1.7e-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+n+e +pg+ggk++rs G+ya vv++e+++v+v+lpSge + ++  crAtiGvv++g++ e
  gi|242398282|ref|YP_002993706.1|  95 IGNTLPLEKIPEGTYVYNLEASPGDGGKFVRSGGSYALVVSREKNRVIVQLPSGELKGFHPGCRATIGVVAGGGRLE 171
                                       7**************************************************************************** PP

                                       ----STTHHHHT.....TBS----SSSS-TTTSSS--SS...SS..--SSSST CS
                    Ribosomal_L2_C  79 kklgkAgrkrwl.....grrpkvrGvamnpvdHphGGGe...Gk..tksrkap 121
                                       k+++kAg++++      + +pk rGv mn+v+HphGG e   Gk  t+s++ap
  gi|242398282|ref|YP_002993706.1| 172 KPIVKAGKAYYImkarnRFWPKPRGVKMNAVNHPHGGKEhhiGKpsTISKRAP 224
                                       **********999999999********************99988755555555 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 !   73.1   0.0   1.4e-24   1.3e-20       1      76 [.      13      86 ..      13      87 .. 0.96

  Alignments for each domain:
  == domain 1  score: 73.1 bits;  conditional E-value: 1.4e-24
                                      TB-TT.--BSSTT--------EE-B--S---SS--EEEEEEE--TT-SS-EEEEEETTTEEEEEE--SS--SS-EE- CS
                      Ribosomal_L2  1 Grnns.gritvrhrggGhkkkyrlidfkrnkekvkgkVveieyDpgRsApiAlvkyedgekryiiapeglkvGdtvv 76
                                      G++++ +r+++++++g    ky  ++f+++ ++++gkVvei +DpgR+Ap+A+vk+e+g +++i+a egl v ++v+
  gi|242398282|ref|YP_002993706.1| 13 GKGTTtFRAPSHRYRG--AVKYVPLNFTQD-KTLAGKVVEILHDPGRTAPVARVKFENGLEKLILASEGLLVDQEVY 86
                                      99**************..99*******775.6799***************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       255  (0.0142228); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 1386.14
//
Query:       gi|242398283|ref|YP_002993707.1|  [L=133]
Description: 30S ribosomal protein S19P [Thermococcus sibiricus MM 739]
Scores for complete 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  118.1   0.9    1.5e-34  117.7   0.9    1.2  1  Ribosomal_S19   Ribosomal protein S19
     0.0058   17.1   0.4     0.0097   16.4   0.4    1.4  1  bZIP_Maf        bZIP Maf transcription factor
  ------ inclusion threshold ------
      0.012   16.1   1.9      0.031   14.8   1.9    1.7  1  Sas10           Sas10 C-terminal domain
      0.016   15.1   0.0       0.02   14.7   0.0    1.1  1  pPIWI_RE_Z      pPIWI RE three-gene island domain Z
       0.13   12.2   0.3       0.19   11.6   0.3    1.3  1  Myb_DNA-bind_7  Myb DNA-binding like


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 !  117.7   0.9   4.1e-38   1.5e-34       1      81 []      35     116 ..      35     116 .. 0.98

  Alignments for each domain:
  == domain 1  score: 117.7 bits;  conditional E-value: 4.1e-38
                                       .HHHSS.TTCCCHHHHHHHHHHTS-----EEES-TT-B--GGGTT-EEEEE-SSSEEEEE--CCCTTSBCGGGT-SS CS
                     Ribosomal_S19   1 rslkkg.pfvqesllkkvrkakaekkkevikthsRdstIlPemvgltvgVynGktfvpveikeemvGhkLgEFspTr 76 
                                       rslk+g + +q++ll+k+r ak+ k k++i+thsRd++IlPemvg+++ V+nGk+fvpv+i+eem+Gh++gEF++Tr
  gi|242398283|ref|YP_002993707.1|  35 RSLKRGlTPEQKKLLRKIRLAKKGKYKKPIRTHSRDMVILPEMVGMMIYVHNGKEFVPVQIREEMIGHYIGEFALTR 111
                                       899***999*************999**************************************************** PP

                                       ----S CS
                     Ribosomal_S19  77 kpvkh 81 
                                       k+v+h
  gi|242398283|ref|YP_002993707.1| 112 KRVQH 116
                                       ***99 PP

>> bZIP_Maf  bZIP Maf transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.4   2.7e-06    0.0097       4      38 ..      15      58 ..      12      66 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.7e-06
                          bZIP_Maf  4 eellslsvrEfnrfl.........rglteeeverLKqrRRrlKN 38
                                      eel+++s++++ + l         rglt e+ + L+++R  +K 
  gi|242398283|ref|YP_002993707.1| 15 EELINMSLEDLSKLLpsrqrrslkRGLTPEQKKLLRKIRLAKKG 58
                                      9**********999999999999****************88775 PP

>> Sas10  Sas10 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   1.9   8.6e-06     0.031      15      42 ..      39      66 ..      34      74 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 8.6e-06
                             Sas10 15 kGLtpkRkkenrnpRvkkrkkYekakkk 42
                                      +GLtp+ kk  r  R+ k+ kY+k  + 
  gi|242398283|ref|YP_002993707.1| 39 RGLTPEQKKLLRKIRLAKKGKYKKPIRT 66
                                      9**********************97655 PP

>> pPIWI_RE_Z  pPIWI RE three-gene island domain Z
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   5.7e-06      0.02      85     153 ..       8      76 ..       3      83 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.7e-06
                        pPIWI_RE_Z  85 rlrgYeidedgelarrrtptvaaerfe.vyeelLsapppfatrkvkvAeaGryefvakrerktsvripee 153
                                       ++rgY ++e  ++  +  ++++++r    +++ L+ + ++  rk+++A++G+y+ +++++ +  v +p e
  gi|242398283|ref|YP_002993707.1|   8 KYRGYTFEELINMSLEDLSKLLPSRQRrSLKRGLTPEQKKLLRKIRLAKKGKYKKPIRTHSRDMVILP-E 76 
                                       79*************************9*******************************555555555.4 PP

>> Myb_DNA-bind_7  Myb DNA-binding like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.3   5.4e-05      0.19      33      69 ..      25      61 ..      12      73 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.4e-05
                    Myb_DNA-bind_7 33 iaklfpkrtrrqlKlKFkkEerknpeliekalkkrke 69
                                      ++kl+p+r+rr lK+    E++k  ++i+ a k + +
  gi|242398283|ref|YP_002993707.1| 25 LSKLLPSRQRRSLKRGLTPEQKKLLRKIRLAKKGKYK 61
                                      789*************************999776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.52
# Mc/sec: 770.34
//
Query:       gi|242398284|ref|YP_002993708.1|  [L=154]
Description: 50S ribosomal protein L22P [Thermococcus sibiricus MM 739]
Scores for complete 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  105.6   0.0    1.6e-30  105.4   0.0    1.1  1  Ribosomal_L22  Ribosomal protein L22p/L17e
  ------ inclusion threshold ------
       0.25   11.1   1.8         21    4.9   0.0    3.0  4  Sda            Sporulation inhibitor A


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 !  105.4   0.0   1.8e-34   1.6e-30       1     102 [.      19     149 ..      19     150 .. 0.98

  Alignments for each domain:
  == domain 1  score: 105.4 bits;  conditional E-value: 1.8e-34
                                       EEEEEESS-HHHHHHHHHHHTTSBHHHHHHHHHT..-SST...........................THHHHHHHHH CS
                     Ribosomal_L22   1 akgsnlrvsfkklrevarlIrgmkveeAlkyLkf..skkk...........................aakfvlklLk 48 
                                       a++++lr+s+k   ev+r I+gm v++A+k L++  +kk+                           +ak+v klL 
  gi|242398284|ref|YP_002993708.1|  19 ASRRDLRISPKLSIEVCREIKGMMVNDAIKLLDDviAKKRpihlrrfndsqghkrgdgfgpgrypvkVAKEVRKLLL 95 
                                       57899******************************88888************************************* PP

                                       HHHHHHH..HT-GGGEEEEEEEEEEEEEEEEEEEESTTEEEEEEEEEEEEEEEE CS
                     Ribosomal_L22  49 naeanaelkgldvdslvIeeiqvnkgpklkrrtyrArGrinpirkspchievvl 102
                                       n+++nae+kgld+d+l I ++ +++gp l+++ +rA Gr+++++++++hie+++
  gi|242398284|ref|YP_002993708.1|  96 NVRNNAEQKGLDPDRLRIIHVAAHRGPVLRGYIPRAFGRATQFNEQTTHIEIIV 149
                                       *****************************************************8 PP

>> Sda  Sporulation inhibitor A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1      0.81   7.3e+03      34      43 ..      20      29 ..      20      31 .. 0.75
   2 ?   -1.0   0.0      0.17   1.6e+03      24      35 ..      45      56 ..      32      62 .. 0.76
   3 ?    4.0   0.0    0.0045        40       8      30 ..      93     115 ..      92     120 .. 0.89
   4 ?    4.9   0.0    0.0024        21      12      35 ..     131     154 .]     130     154 .] 0.88

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 0.81
                               Sda 34 erRsLshklk 43
                                      +rR L ++ k
  gi|242398284|ref|YP_002993708.1| 20 SRRDLRISPK 29
                                      5999988755 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.17
                               Sda 24 DFIeLieeEier 35
                                      D I+L+ ++i +
  gi|242398284|ref|YP_002993708.1| 45 DAIKLLDDVIAK 56
                                      558899888865 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.0045
                               Sda   8 lLieaYekAlelnLdpDFIeLie 30 
                                       lL+++  +A +  LdpD +++i 
  gi|242398284|ref|YP_002993708.1|  93 LLLNVRNNAEQKGLDPDRLRIIH 115
                                       899999***********999996 PP

  == domain 4  score: 4.9 bits;  conditional E-value: 0.0024
                               Sda  12 aYekAlelnLdpDFIeLieeEier 35 
                                       a+ +A++ n  +  Ie+i eEi r
  gi|242398284|ref|YP_002993708.1| 131 AFGRATQFNEQTTHIEIIVEEIRR 154
                                       67789999999999********87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); 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: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1037.50
//
Query:       gi|242398285|ref|YP_002993709.1|  [L=207]
Description: 30S ribosomal protein S3P [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.8e-24   84.4   1.1    9.7e-24   83.7   1.1    1.4  1  Ribosomal_S3_C  Ribosomal protein S3, C-terminal domain
    4.5e-15   55.2   0.6    1.1e-14   54.0   0.6    1.6  1  KH_2            KH domain
  ------ inclusion threshold ------
      0.032   14.1   2.6      0.061   13.2   0.2    2.6  3  KH_1            KH domain
      0.058   13.4   0.0      0.089   12.8   0.0    1.3  1  Mucin_bdg       Putative mucin or carbohydrate-binding module


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 !   83.7   1.1   2.2e-27   9.7e-24       1      83 []      99     182 ..      99     182 .. 0.99

  Alignments for each domain:
  == domain 1  score: 83.7 bits;  conditional E-value: 2.2e-27
                                       HHHHHHTT--HHHHHHHHHHHHHHCC-SEEEEEEEC-SS.TTT--EEEEEEC----..TCHHHH-EEEEEEEEETTE CS
                    Ribosomal_S3_C   1 iaeqlekrvsfRramkkairramkagakGikiqvsGrLggaeiarsekykeGrvpl..htlradidyavaeaktkyG 75 
                                       +a++le++v+fRra++ air++m++ga+G++i++sG+L+ +e+a+s  + +G++ +  ++++  + +++a+a +k G
  gi|242398285|ref|YP_002993709.1|  99 LAQALERGVHFRRAAYAAIRAIMSNGARGVEIRISGKLT-GERAKSVRFYQGYIAKvgNPAETLVSRGYAQALLKLG 174
                                       699************************************.9************************************ PP

                                       EEEEEEEE CS
                    Ribosomal_S3_C  76 iiGvkVwI 83 
                                       ++GvkV I
  gi|242398285|ref|YP_002993709.1| 175 VLGVKVSI 182
                                       ******98 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.0   0.6   2.4e-18   1.1e-14       2      74 ..      17      86 ..      16      88 .. 0.94

  Alignments for each domain:
  == domain 1  score: 54.0 bits;  conditional E-value: 2.4e-18
                                      HHHHHHHHTECETEEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTCEEEEEEEET CS
                              KH_2  2 ipeslaveikkagvskveIertanrviiviresqpgivIGkgGsnikkigkelrkdieklegkkVklnivkVk 74
                                      i+e+l++e++ ag+++++I++t+ ++++vi +++pg vIG+gG++i++++  l++++ +le+ ++++  +++k
  gi|242398285|ref|YP_002993709.1| 17 IDEYLEKELRRAGYGGLDIKKTPLGTKVVIFVERPGFVIGRGGRKIRELTRILERRF-NLENPQIEV--EEIK 86
                                      889******************************************************.5******95..5555 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   1.4e-05     0.061      12      27 ..      52      67 ..      42      70 .. 0.86
   2 ?   -1.0   0.0      0.36   1.6e+03      22      36 ..     117     133 ..     115     144 .. 0.56
   3 ?   -2.1   0.0       0.8   3.6e+03      30      49 ..     177     194 ..     176     200 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.4e-05
                                      HHHHTGGGHHHHHHHH CS
                              KH_1 12 griIGkgGsnIkeIre 27
                                      g++IG+gG++I+e+ +
  gi|242398285|ref|YP_002993709.1| 52 GFVIGRGGRKIRELTR 67
                                      9************976 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.36
                                       HHHHHHH.H.T-EEEEE CS
                              KH_1  22 IkeIree.t.gakIkvp 36 
                                       I+ I++    g+ I++ 
  gi|242398285|ref|YP_002993709.1| 117 IRAIMSNgArGVEIRIS 133
                                       66777622334444443 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.8
                                       T-EEEEESSTT...T.-EEE CS
                              KH_1  30 gakIkvpksedegsderevt 49 
                                       g+k+ +++++++   ++e++
  gi|242398285|ref|YP_002993709.1| 177 GVKVSIMPPDAR--LPDEIE 194
                                       788998854333..444444 PP

>> Mucin_bdg  Putative mucin or carbohydrate-binding module
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     2e-05     0.089      32      80 ..     106     154 ..      79     162 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2e-05
                         Mucin_bdg  32 hyyfedetYasievkdkdGneklrkeieGtekqtaekeisfkeGdvlki 80 
                                         +f++  Ya i+   ++G   ++  i G+ +    k + f++G++ k+
  gi|242398285|ref|YP_002993709.1| 106 GVHFRRAAYAAIRAIMSNGARGVEIRISGKLTGERAKSVRFYQGYIAKV 154
                                       469**************************776666799*******9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.35s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 1200.48
//
Query:       gi|242398286|ref|YP_002993710.1|  [L=66]
Description: 50S ribosomal protein L29P [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.8e-17   61.0   5.2    8.9e-17   60.8   5.2    1.0  1  Ribosomal_L29  Ribosomal L29 protein
  ------ inclusion threshold ------
      0.032   13.3   0.2      0.093   11.8   0.0    1.7  2  Exonuc_X-T_C   Exonuclease C-terminal


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 !   60.8   5.2     1e-20   8.9e-17       1      57 []       4      61 ..       4      61 .. 0.98

  Alignments for each domain:
  == domain 1  score: 60.8 bits;  conditional E-value: 1e-20
                                      HHHHHS-HHHHHHHHHHHHHHHHHHHHHHHHT.SSS-CHHHHHHHHHHHHHHHHHHHH CS
                     Ribosomal_L29  1 kelrelsdeeLkeklkelkkeLfnLrfqkatg.qlenpsrirkvRkdIARikTvlrer 57
                                      +e+re++ ee+++k+ el+ eL + r    +g +lenp+ ir +R+dIAR++T+ +e+
  gi|242398286|ref|YP_002993710.1|  4 SEIREMNLEEIEKKIIELRLELAKERGMLTMGtSLENPMVIRDLRRDIARLLTIKKEK 61
                                      79*****************************************************997 PP

>> Exonuc_X-T_C  Exonuclease C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0     0.041   3.7e+02      57      80 ..       3      26 ..       1      36 [. 0.68
   2 ?   11.8   0.0     1e-05     0.093      41      71 ..      35      65 ..      30      66 .] 0.87

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.041
                                      -HHHHHS-HHHHHHHHTSTTTTT. CS
                      Exonuc_X-T_C 57 psellelsaeelrerlftkkeela 80
                                      pse+ e++ ee+++++   + ela
  gi|242398286|ref|YP_002993710.1|  3 PSEIREMNLEEIEKKIIELRLELA 26
                                      677777777888777766655554 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 1e-05
                                      -SS-TTEEEEEETTS--HHHHHS-HHHHHHH CS
                      Exonuc_X-T_C 41 hptnknavivvDLaeDpsellelsaeelrer 71
                                        + +n +++ DL++D+++ll+ ++e+lr +
  gi|242398286|ref|YP_002993710.1| 35 GTSLENPMVIRDLRRDIARLLTIKKEKLRSK 65
                                      5667899*********************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 436.92
//
Query:       gi|242398287|ref|YP_002993711.1|  [L=94]
Description: Translation factor SUI1 like protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-19   70.5   0.4    1.5e-19   70.3   0.4    1.1  1  SUI1      Translation initiation factor SUI1
    0.00058   20.1   0.3    0.00082   19.6   0.3    1.3  1  Img2      Mitochondrial large subunit ribosomal protein (Img2


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 !   70.3   0.4   1.7e-23   1.5e-19       1      75 [.      15      85 ..      15      87 .. 0.95

  Alignments for each domain:
  == domain 1  score: 70.3 bits;  conditional E-value: 1.7e-23
                              SUI1  1 akpkihirleqrggrKkvTtvsgleafgidlkklakelkkkfacsgsvvkdggeeiqvQGdqrkkvaelLtekyg 75
                                      ++++i++ +e+ + +K  T+++g++ ++++l+++ak+lk k+ac+g+  k+g   i++QGd+r+kv+ lLt+  g
  gi|242398287|ref|YP_002993711.1| 15 EQQRIRVYIEKARYGKLKTIIEGIDEKEFNLDEIAKKLKAKLACGGTA-KNG--RIELQGDHREKVKRLLTNF-G 85
                                      5899*******************************************6.999..8***************984.6 PP

>> Img2  Mitochondrial large subunit ribosomal protein (Img2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.3   9.1e-08   0.00082      12      80 .]      18      86 ..      11      86 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 9.1e-08
                              Img2 12 slPVYtdvkrggtkkltvirki...eGDiaalredLrkaleelvkvnevtgkieikGdrveevkkfLeskgF 80
                                      ++ VY +  r g+ k t+i  i   e ++ +++++L++ l+  +  + ++g+ie++Gd++e+vk+ L++ gF
  gi|242398287|ref|YP_002993711.1| 18 RIRVYIEKARYGKLK-TIIEGIdekEFNLDEIAKKLKAKLA--CGGTAKNGRIELQGDHREKVKRLLTNFGF 86
                                      566777777766665.4444441114566777888888888..89999*********************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       772  (0.0430587); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); 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: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 603.33
//
Query:       gi|242398288|ref|YP_002993712.1|  [L=122]
Description: Ribonuclease P protein component 1 [Thermococcus sibiricus MM 739]
Scores for complete 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   78.7   0.1    3.1e-22   78.3   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 !   78.3   0.1   1.7e-26   3.1e-22       2      84 .]      42     121 ..      41     121 .. 0.96

  Alignments for each domain:
  == domain 1  score: 78.3 bits;  conditional E-value: 1.7e-26
                                       HHCCSXXSS-EEEEEECSSTTTTTEEEEEEEEETTEEEEEECTTEEEEEESTTCEEEEEE.TTEEEEEECCCCSSXH CS
                           UPF0086   2 kLlkadlhGaeveVvrsknpslvgikGiVvkEtkntlkivtkksrvktvpKegsvFefevkdvlevevdGsqlryrp 78 
                                       +Ll+++l+G++v+Vv+s++p l+gi+G V++Etkntl i    ++v  +pK  + Fefev +  +++++G++l  rp
  gi|242398288|ref|YP_002993712.1|  42 TLLMHELIGLKVKVVKSSHPGLIGIEGYVIDETKNTLTILG--TKVWAIPKIVAEFEFEV-GDKKIRIKGEELVGRP 115
                                       89**************************************7..89***************.7899************ PP

                                       HHHHCH CS
                           UPF0086  79 adRaer 84 
                                       + R ++
  gi|242398288|ref|YP_002993712.1| 116 EMRLKK 121
                                       ***986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 1005.51
//
Query:       gi|242398289|ref|YP_002993713.1|  [L=111]
Description: 30S ribosomal protein S17P [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.9e-24   83.5   0.8      1e-23   83.2   0.8    1.2  1  Ribosomal_S17    Ribosomal protein S17
  ------ inclusion threshold ------
       0.02   15.3   0.0      0.039   14.3   0.0    1.6  1  Ribosomal_S17_N  Ribosomal_S17 N-terminal


Domain annotation for each model (and alignments):
>> Ribosomal_S17  Ribosomal protein S17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.2   0.8   1.1e-27     1e-23       1      67 [.      35     102 ..      35     103 .. 0.99

  Alignments for each domain:
  == domain 1  score: 83.2 bits;  conditional E-value: 1.1e-27
                                       EEEEE--STTEEEEEEEEEEEETTTTEEEEEEEEEEEE-TTTS.--TT-EEEEEEECECSSSEEEEEE CS
                     Ribosomal_S17   1 GvVvsdkmdkTvvVrverlvkhpkykkyvkrrkkylahdenns.vkvGDiVrieecrPlSktkrfvvv 67 
                                       G+Vvsdk   T++V+++++++ +ky++y+ rr++++ah++++  +k GD+V ++e+rPlSktk+fvv+
  gi|242398289|ref|YP_002993713.1|  35 GIVVSDKPRHTITVERQYYHYLRKYERYELRRSRVHAHNPPCVnAKAGDKVIVAETRPLSKTKSFVVI 102
                                       99****************************************************************97 PP

>> Ribosomal_S17_N  Ribosomal_S17 N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   4.3e-06     0.039      34      69 .]       2      33 ..       1      33 [. 0.88

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.3e-06
                                      ----TT----GGGGS-----TTSSSSSS----S-EE CS
                   Ribosomal_S17_N 34 knvglgfktPkeAiegtYiDkKCPFtGnvsirGriL 69
                                      +++gl ++ P+e  +    D KCP+ G+ ++ Gr++
  gi|242398289|ref|YP_002993713.1|  2 RDIGLKIQPPAEKCD----DPKCPWHGHTKVHGRVF 33
                                      788999999988777....99*************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); 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: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 816.52
//
Query:       gi|242398290|ref|YP_002993714.1|  [L=141]
Description: 50S ribosomal protein L14P [Thermococcus sibiricus MM 739]
Scores for complete 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  122.1   1.4    1.6e-35  121.8   1.4    1.0  1  Ribosomal_L14  Ribosomal protein L14p/L23e


Domain annotation for each model (and alignments):
>> Ribosomal_L14  Ribosomal protein L14p/L23e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.8   1.4   8.9e-40   1.6e-35       5     121 ..      24     140 ..      21     141 .] 0.94

  Alignments for each domain:
  == domain 1  score: 121.8 bits;  conditional E-value: 8.9e-40
                                       S-EEE--SSSSBSEEEEEEETT-.....---EE-SSSEEEEEESSS-T...TTSSCEEEEEEEE-SS-EE-TTS-EE CS
                     Ribosomal_L14   5 ktrlkvaDNsgakevecikvlggk....krkaasvGdiivvsvkkakpkgkvkkgdvvkavvvrtkkevrrkdGsvi 77 
                                       +++l+vaDNsgak +++i v+g+k    +  +a vGd+++++vkk++p     +++vv+av+vr++ke++r dG+ +
  gi|242398290|ref|YP_002993714.1|  24 GAYLNVADNSGAKVIQVIGVVGYKgvrrRLASAGVGDMVIATVKKGRP---DIRHQVVRAVIVRQRKEYKRLDGMRV 97 
                                       689******************999885444999***************...899*********************** PP

                                       EESS-EEEEB-TTS-BSS-.B-SBEEHHHHHH.-HHHHHTBSBE CS
                     Ribosomal_L14  78 rfddnaaVllnkkgeplGtrifgpvarelrekkflkivslApev 121
                                       +f+dnaa++ + +g p+Gt+i gpvare++ek + ++ s+A+ +
  gi|242398290|ref|YP_002993714.1|  98 KFEDNAAIITTPEGVPRGTEIRGPVAREAAEK-WVRVGSIASII 140
                                       *******************************9.*******9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        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 0.29s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 864.18
//
Query:       gi|242398291|ref|YP_002993715.1|  [L=120]
Description: 50S ribosomal protein L24P [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.9e-36  122.8   0.5    7.2e-36  122.5   0.5    1.1  1  Ribosomal_L26  Ribosomal proteins L26 eukaryotic, L24P archae
    1.8e-10   40.4   4.7    1.8e-10   40.4   4.7    1.7  2  KOW            KOW motif
  ------ inclusion threshold ------
      0.078   13.4   0.0       0.22   12.0   0.0    1.7  2  hSH3           Helically-extended SH3 domain
       0.13   12.7   1.1        0.3   11.5   0.4    2.1  2  ribosomal_L24  Ribosomal proteins 50S L24/mitochondrial 39S L


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 !  122.5   0.5   1.6e-39   7.2e-36       1      82 []       5     119 ..       5     119 .. 0.99

  Alignments for each domain:
  == domain 1  score: 122.5 bits;  conditional E-value: 1.6e-39
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................xx RF
                     Ribosomal_L26   1 sssrrkqrKahfnapshirrklmsapLskeLrekygvrslpir................................gv 45 
                                       s+++rkqrK ++nap+h r+k++sapLs eLr+kyg+rslpir                                g+
  gi|242398291|ref|YP_002993715.1|   5 SKQPRKQRKFLYNAPLHLRHKIVSAPLSVELRQKYGIRSLPIRsgdkvkvlrgdfkghegkvvevdlkryrvhveGA 81 
                                       89*************************************************************************** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                     Ribosomal_L26  46 trekangttvpvgihpSkvvItklkl.DkdrkkiLerk 82 
                                       t +k  gt+v ++ihpS+v+I++l+l D++rkki+er+
  gi|242398291|ref|YP_002993715.1|  82 TMKKVSGTEVFYPIHPSNVMIVDLNLeDERRKKIIERR 119
                                       ************************************98 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4   4.7   3.9e-14   1.8e-10       2      32 .]      49      79 ..      48      79 .. 0.98
   2 ?   -3.2   0.0       2.2   9.8e+03      18      21 ..     101     104 ..      99     109 .. 0.61

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 3.9e-14
                                      TSEEEESSSTTTTCEEEEEEEETTTTEEEEE CS
                               KOW  2 GdhVkVvsGphkGktGkVvkvdqhkvrVfvd 32
                                      Gd VkV++G +kG +GkVv+vd +++rV+v+
  gi|242398291|ref|YP_002993715.1| 49 GDKVKVLRGDFKGHEGKVVEVDLKRYRVHVE 79
                                      9****************************97 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2.2
                                       EEEE CS
                               KOW  18 kVvk 21 
                                       ++v+
  gi|242398291|ref|YP_002993715.1| 101 MIVD 104
                                       6665 PP

>> hSH3  Helically-extended SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   4.9e-05      0.22       3      45 ..      12      56 ..      10      73 .. 0.85
   2 ?   -0.8   0.0      0.46   2.1e+03      19      32 ..      78      90 ..      56     118 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.9e-05
                              hSH3  3 kkFkyegeikvlysvtvdpnla..skklggkdLpvkrgeildviq 45
                                      +kF y++++++ +++  +p  +   +k g + Lp+++g+++ v++
  gi|242398291|ref|YP_002993715.1| 12 RKFLYNAPLHLRHKIVSAPLSVelRQKYGIRSLPIRSGDKVKVLR 56
                                      79********999998887554226899**************986 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.46
                              hSH3 19 vdpnlaskklggkd 32
                                      v+  +++kk++g +
  gi|242398291|ref|YP_002993715.1| 78 VE-GATMKKVSGTE 90
                                      33.34555555554 PP

>> ribosomal_L24  Ribosomal proteins 50S L24/mitochondrial 39S L24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1      0.41   1.8e+03      40      40 ..      65      65 ..      36      91 .. 0.60
   2 ?   11.5   0.4   6.7e-05       0.3      24      37 ..      93     106 ..      72     118 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.41
                     ribosomal_L24 40 k 40
                                      k
  gi|242398291|ref|YP_002993715.1| 65 K 65
                                      1 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 6.7e-05
                     ribosomal_L24  24 apIhvSnVmlvdpk 37 
                                        pIh SnVm+vd +
  gi|242398291|ref|YP_002993715.1|  93 YPIHPSNVMIVDLN 106
                                       6**********954 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 858.51
//
Query:       gi|242398292|ref|YP_002993716.1|  [L=248]
Description: 30S ribosomal protein S4e [Thermococcus sibiricus MM 739]
Scores for complete 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-24   84.3   0.1    1.5e-23   82.5   0.1    1.8  2  Ribosomal_S4e  Ribosomal family S4e
    1.3e-16   60.4   2.9    2.1e-16   59.7   2.9    1.3  1  RS4NT          RS4NT (NUC023) domain
    5.7e-10   38.8   1.3    7.6e-10   38.3   0.2    1.8  2  S4             S4 domain
  ------ inclusion threshold ------
      0.011   15.5   0.1      0.028   14.3   0.1    1.7  1  S4_2           S4 domain
      0.033   14.1   2.3      0.099   12.6   2.3    1.9  1  KOW            KOW motif
      0.043   13.8   0.0       0.52   10.3   0.0    2.5  3  DUF4920        Domain of unknown function (DUF4920)


Domain annotation for each model (and alignments):
>> Ribosomal_S4e  Ribosomal family S4e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.5   0.1     5e-27   1.5e-23       1      75 []      96     178 ..      96     178 .. 0.97
   2 ?   -1.3   0.0      0.72   2.2e+03      28      47 ..     200     219 ..     182     223 .. 0.83

  Alignments for each domain:
  == domain 1  score: 82.5 bits;  conditional E-value: 5e-27
                                       TTEEEEEEE-TTSSEEEEEE-TTCCCEEEEEECEEEEECCCEEEEEETTS-EEEES........STT-STTEEEEEE CS
                     Ribosomal_S4e   1 tgenyrllydtkgrfalhkItseeakyKLcKikkkttvkkgipqlvthdGrtiryp........dpdikvnDtvkid 69 
                                       tge+yr+l+++ g++ lh+It+eeak+K ++i +k++vk+g++ql++hdG++ +++        +++ ++ Dtv+++
  gi|242398292|ref|YP_002993716.1|  96 TGEHYRVLPNRIGKLILHPITEEEAKLKPLRISNKRMVKGGNLQLNFHDGTNHLVKlssltdetKDSFRTADTVLVK 172
                                       89*****************************************************999******666********** PP

                                       TTTTEE CS
                     Ribosomal_S4e  70 leenkI 75 
                                       ++e++I
  gi|242398292|ref|YP_002993716.1| 173 VPEREI 178
                                       ***998 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.72
                                       EEEEECEEEEECCCEEEEEE CS
                     Ribosomal_S4e  28 KLcKikkkttvkkgipqlvt 47 
                                       ++ Ki +++  ++g p +vt
  gi|242398292|ref|YP_002993716.1| 200 RVGKIVEVRHFPGGWPDVVT 219
                                       67899999999999988876 PP

>> RS4NT  RS4NT (NUC023) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.7   2.9     7e-20   2.1e-16       1      37 []       4      40 ..       4      40 .. 0.97

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 7e-20
                                      -S----EETTTS-TTS---SSSSSEE----SSSS-TT CS
                             RS4NT  1 rGpkkHLKrlaAPkhWpldkkegvfavkPspGPHklr 37
                                      +G k+HLKrlaAP  W +++k  ++av+PspGPH +r
  gi|242398292|ref|YP_002993716.1|  4 KGAKRHLKRLAAPTQWYIERKVFKWAVRPSPGPHDMR 40
                                      699*******************************997 PP

>> S4  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.3   0.2   2.6e-13   7.6e-10      10      48 .]      53      91 ..      44      91 .. 0.94
   2 ?   -3.3   0.1       2.6   7.8e+03      20      31 ..     130     141 ..     130     141 .. 0.80

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 2.6e-13
                                      TTSSSSHHHHHHHHHTTTEEETTEEE--TT-EE-TTCEE CS
                                S4 10 lglassrreArqlIehGrVlVNGkvvkdpsyrVkpgDvi 48
                                      lg+a++ re+r+  ++ +VlV+G+v+kd++++V+ +Dv+
  gi|242398292|ref|YP_002993716.1| 53 LGYAKTGREVRKVLNEEKVLVDGRVRKDYKFPVGIMDVV 91
                                      9************************************98 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.6
                                       HHHHHTTTEEET CS
                                S4  20 rqlIehGrVlVN 31 
                                       ++++++G  ++N
  gi|242398292|ref|YP_002993716.1| 130 KRMVKGGNLQLN 141
                                       589999988877 PP

>> S4_2  S4 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     0.028      17      64 ..      53     102 ..      51     103 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 9.2e-06
                              S4_2  17 aglvesGgeaKafiaegeVkvNGevetrRgkKlraGdvVei..dgetiev 64 
                                       +g++++G e++ +++e++V+v+G v +  +  +   dvV+i   ge+++v
  gi|242398292|ref|YP_002993716.1|  53 LGYAKTGREVRKVLNEEKVLVDGRVRKDYKFPVGIMDVVSIpeTGEHYRV 102
                                       58899******************996555444555577877544666665 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   2.3   3.3e-05     0.099       1      22 [.     186     207 ..     186     221 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.3e-05
                                       TTSEEEESSSTTTTCEEEEEEE CS
                               KOW   1 pGdhVkVvsGphkGktGkVvkv 22 
                                       +G  V Vv+G++  ++Gk+v+v
  gi|242398292|ref|YP_002993716.1| 186 VGAFVFVVQGKNVARVGKIVEV 207
                                       6899*****************9 PP

>> DUF4920  Domain of unknown function (DUF4920)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0         2   5.9e+03      56      68 ..      67      79 ..      62      85 .. 0.55
   2 ?    0.0   0.0      0.28   8.5e+02      23      44 ..     131     152 ..     119     155 .. 0.83
   3 ?   10.3   0.0   0.00018      0.52      14      53 ..     199     240 ..     189     244 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2
                           DUF4920 56 kgkevvveGkafv 68
                                      ++++v+v+G++ +
  gi|242398292|ref|YP_002993716.1| 67 NEEKVLVDGRVRK 79
                                      4555555555443 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.28
                           DUF4920  23 cqkkGcWlkldledgeevrVkf 44 
                                         +kG+ l+l+ +dg++  Vk+
  gi|242398292|ref|YP_002993716.1| 131 RMVKGGNLQLNFHDGTNHLVKL 152
                                       5689999*******99999986 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.00018
                           DUF4920  14 kvkgkveevcqkkGcWlkldledge..evrVkfKdYgffvPk 53 
                                       +  gk+ ev +  G+W  + + +++  e++ ++KdY+f + k
  gi|242398292|ref|YP_002993716.1| 199 ARVGKIVEVRHFPGGWPDVVTIEDRdgELFDTLKDYAFVLGK 240
                                       55799***********986554443358999*******9866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1536.50
//
Query:       gi|242398293|ref|YP_002993717.1|  [L=183]
Description: 50S ribosomal protein L5P [Thermococcus sibiricus MM 739]
Scores for complete 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-25   89.5   0.0    2.8e-25   88.3   0.0    1.6  2  Ribosomal_L5_C  ribosomal L5P family C-terminus
    2.4e-21   75.8   0.3      4e-21   75.1   0.3    1.4  1  Ribosomal_L5    Ribosomal protein L5


Domain annotation for each model (and alignments):
>> Ribosomal_L5_C  ribosomal L5P family C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.63   5.7e+03      73      91 ..      48      66 ..      37      68 .. 0.47
   2 !   88.3   0.0   3.1e-29   2.8e-25       1      94 []      72     171 ..      72     171 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.63
                    Ribosomal_L5_C 73 ivttaktdeearallkelg 91
                                      +v +++++++a++  +++g
  gi|242398293|ref|YP_002993717.1| 48 FVGQKPIRRKAKKTNRDFG 66
                                      3333444444444444443 PP

  == domain 2  score: 88.3 bits;  conditional E-value: 3.1e-29
                    Ribosomal_L5_C   1 piGvkvtLrgekmyefldkllevvlprlrdFkGiskssfdgrGnvsfGikeqiifpeieydkdkgifGmditivtta 77 
                                       pi++kvtLrg+k+ ++l++ll +v +r++       ssfd++Gnv fGi+e+i +p++eyd+++gifGmd+++++++
  gi|242398293|ref|YP_002993717.1|  72 PIALKVTLRGKKASDLLKRLLAAVDNRIK------ISSFDEHGNVCFGIDEHINIPGVEYDPEIGIFGMDVCVTLER 142
                                       89***************************......99**************************************** PP

                    Ribosomal_L5_C  78 ktde.............earallkelgipf 94 
                                       +  +             +++ l+ke+gi f
  gi|242398293|ref|YP_002993717.1| 143 PGHRiairkrrrhhiptKHK-LTKEEGIIF 171
                                       *5555556678899997777.999999866 PP

>> Ribosomal_L5  Ribosomal protein L5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.1   0.3   4.4e-25     4e-21       2      57 .]      16      68 ..      15      68 .. 0.99

  Alignments for each domain:
  == domain 1  score: 75.1 bits;  conditional E-value: 4.4e-25
                                      CTTS-EEEEEEEEEE-SSSSSCHHHHHCCHHHHCCCHSS--EECC--TTCTTTCSC CS
                      Ribosomal_L5  2 vMqvPrleKivinmgvGeagedkkllekaakeLaeItGQkPvvtkakksianFkiR 57
                                      +M++Pr+eK++in+gvGe+ge+   l+ka+k L++ +GQkP+++kakk+ ++F+iR
  gi|242398293|ref|YP_002993717.1| 16 PMRKPRIEKVTINIGVGESGER---LTKAEKMLETFVGQKPIRRKAKKTNRDFGIR 68
                                      8*********************...******************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1165.65
//
Query:       gi|242398294|ref|YP_002993718.1|  [L=58]
Description: 30S ribosomal protein S14P [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-08   33.9   4.8    2.4e-08   33.6   4.8    1.1  1  Ribosomal_S14  Ribosomal protein S14p/S29e
  ------ inclusion threshold ------
       0.22   11.9   2.1        2.5    8.5   0.0    2.0  2  DUF2039        Uncharacterized conserved protein (DUF2039)
       0.38    8.6   0.6       0.42    8.5   0.6    1.0  1  Med16          Mediator complex subunit 16


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 !   33.6   4.8     4e-12   2.4e-08       8      53 ..      15      57 ..       8      58 .] 0.90

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 4e-12
                                      SS..CTTT---SSS--SSSEE-GGG-..EHHHHHHHTTT...TT-EE- CS
                     Ribosomal_S14  8 nssptrirnrCrvtGrprGvirkfgL..sRicfRelAlkgelpGvkKa 53
                                      +   +++ +rC+ +G+   +ir  gL  +R+cfRe A k    G+kK+
  gi|242398294|ref|YP_002993718.1| 15 K--FGKGARRCVRCGQFGPIIRIHGLmlCRHCFREIAPK---LGFKKY 57
                                      3..489*********************************...*****8 PP

>> DUF2039  Uncharacterized conserved protein (DUF2039)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.5     0.016        96      42      62 ..       5      28 ..       3      30 .. 0.72
   2 ?    8.5   0.0   0.00042       2.5      30      48 ..      39      57 ..      31      58 .] 0.90

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.016
                           DUF2039 42 kvkykkYkalt...kkkkCvkCee 62
                                      k +y+k k ++    +++Cv+C +
  gi|242398294|ref|YP_002993718.1|  5 KADYNKRKLRKfgkGARRCVRCGQ 28
                                      567777776665557889999976 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00042
                           DUF2039 30 gvCerCkdkieWkvkykkY 48
                                       +C++C   i  k  +kkY
  gi|242398294|ref|YP_002993718.1| 39 MLCRHCFREIAPKLGFKKY 57
                                      68***************** PP

>> Med16  Mediator complex subunit 16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.6   7.1e-05      0.42     704     723 ..       9      28 ..       2      31 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 7.1e-05
                             Med16 704 rkeqlakkkkqlRrCtRCga 723
                                       +k +l k  k  RrC+RCg+
  gi|242398294|ref|YP_002993718.1|   9 NKRKLRKFGKGARRCVRCGQ 28 
                                       566777777777*******7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 452.09
//
Query:       gi|242398295|ref|YP_002993719.1|  [L=130]
Description: 30S ribosomal protein S8P [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.9e-28   98.4   0.0    3.6e-28   98.1   0.0    1.1  1  Ribosomal_S8  Ribosomal protein S8


Domain annotation for each model (and alignments):
>> Ribosomal_S8  Ribosomal protein S8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.1   0.0     2e-32   3.6e-28       1     127 []       5     130 .]       5     130 .] 0.86

  Alignments for each domain:
  == domain 1  score: 98.1 bits;  conditional E-value: 2e-32
                                       -HHHHHHHHHHHHHHTT-SEEEE.E--HHHHHHHHHHHHCTSEEEEEEE.CCCCCC..EEEEE-BSSS-SBSSSEEE CS
                      Ribosomal_S8   1 DpiadmltrirNaekakkeevev.pasklkeeilkvLkeeGyikdfeve.eekkkk..ikielkynkkkksvikklk 73 
                                       Dp+a++l++i N+ek++k+ev++ paskl+ e+l+v++e+Gyi +fe+  + +  +  +++ +k+nk   ++ik   
  gi|242398295|ref|YP_002993719.1|   5 DPLANALSHITNSEKVGKSEVYIkPASKLIGEVLRVMQENGYIGEFEFIdDGRAGIyrVQLLGKVNK--AGAIKP-- 77 
                                       9***********************************************8544444455777788887..899985.. PP

                                       E-SBTTC--EE-CCC---CGGGTSEEEEEETTEEEEHHHHHHCT--EEEEEEEE CS
                      Ribosomal_S8  74 rvskpgrrvYakvkelpkvlnglGiaivsTskGvmtdkeArkkkvGGevlayvw 127
                                       r+s  +++ Y k ++       +Gi++vsTs+Gvmt+keA +k++GG+++ayv+
  gi|242398295|ref|YP_002993719.1|  78 RFSVKAKE-YEKWEKRFLPAFEFGILVVSTSQGVMTHKEALEKGIGGRLIAYVY 130
                                       56666666.7666665566667*******************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); 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: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 851.46
//
Query:       gi|242398296|ref|YP_002993720.1|  [L=191]
Description: 50S ribosomal protein L6P [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-33  115.5   6.5      2e-17   63.6   0.2    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 !   63.6   0.2   1.1e-21     2e-17       1      76 []      20      92 ..      20      92 .. 0.97
   2 !   54.7   1.6   6.6e-19   1.2e-14       1      76 []     104     178 ..     104     178 .. 0.97

  Alignments for each domain:
  == domain 1  score: 63.6 bits;  conditional E-value: 1.1e-21
                                      CSTTEEEEEETTTEEEEEESSEEEEEE-CTTSEEEEEECSTEEEEEECSESCHHHHHHHHHHHHHHHHHHHHHHTC CS
                      Ribosomal_L6  1 iPvgvrvsikggqlvlvlGpkgeltreipegvtvevkvegnkvtvivvsgidkekvAligtvrslinnmikGVteg 76
                                      iP+g +v+i+g +lv+v+Gpkge+ re+++   +++ +e+nkv+    +  ++  +   +t+r++i+nmikGVt+g
  gi|242398296|ref|YP_002993720.1| 20 IPEGITVEIEG-NLVKVKGPKGEIDRELSYP-GFKLFTEDNKVVIYKGFPRRNDIA-IARTFRAHIANMIKGVTDG 92
                                      8*********8.*******************.99999******9999999999999.*****************98 PP

  == domain 2  score: 54.7 bits;  conditional E-value: 6.6e-19
                                       CSTTEEEEEETTTEEEEEESSEEEEEE-CTTSEEEEEECSTEEEEEECSESCHHHH....HHHHHHHHHHHHHHHHH CS
                      Ribosomal_L6   1 iPvgvrvsikggqlvlvlGpkgeltreipegvtvevkvegnkvtvivvsgidkekv....AligtvrslinnmikGV 73 
                                       +P+ v+v++++++++++lG+k ++ +ei +gvtv+v      + +  v+gidkekv    A+i+++++++ ++ +++
  gi|242398296|ref|YP_002993720.1| 104 FPITVKVQGDKVYIENFLGEKAPRIAEILPGVTVKVM-----GGELLVEGIDKEKVgqtaANIEQATKVVGKDRRVF 175
                                       79*********************************88.....788889***************************** PP

                                       HTC CS
                      Ribosomal_L6  74 teg 76 
                                       ++g
  gi|242398296|ref|YP_002993720.1| 176 QDG 178
                                       *98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1214.78
//
Query:       gi|242398297|ref|YP_002993721.1|  [L=127]
Description: 50S ribosomal protein L32e [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-41  141.0   0.4      2e-41  140.7   0.4    1.1  1  Ribosomal_L32e  Ribosomal protein L32


Domain annotation for each model (and alignments):
>> Ribosomal_L32e  Ribosomal protein L32
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.7   0.4   1.1e-45     2e-41       1     108 []      18     125 ..      18     125 .. 0.99

  Alignments for each domain:
  == domain 1  score: 140.7 bits;  conditional E-value: 1.1e-45
                                       ------TTTTT-TTS-S..S------TT-TTTTT-TTS-----GGG---TTTTT--TTS-EEEEESSGGGGTT--TT CS
                    Ribosomal_L32e   1 tkkFirhqsdryvklke..swrkprGidnrvrrrfkgqilmpkiGYgspkktrgllpsGfkkvlVhnvkeLevllme 75 
                                       ++kF r++++r+ k+k+  +wrkp+G+d+++r ++kg+ + p+iG+ spk++rgl+psG+++vlV+nvk+Le ++ +
  gi|242398297|ref|YP_002993721.1|  18 KPKFLRQEWWRFPKFKNdpKWRKPKGTDSKMRVKLKGKARSPSIGWSSPKAVRGLHPSGYEEVLVYNVKDLELIDSK 94 
                                       68**************889********************************************************** PP

                                       TE..EEEE-TTS-HHHHHHHHHHHHHTT-EBSS CS
                    Ribosomal_L32e  76 nksyaaeiahsVsskkrkeiverAaelgikVtN 108
                                       ++  aa+ia++V++kkr++i+erA+elgikV+N
  gi|242398297|ref|YP_002993721.1|  95 RQ--AARIAATVGKKKRIMIIERARELGIKVLN 125
                                       **..****************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 817.82
//
Query:       gi|242398298|ref|YP_002993722.1|  [L=148]
Description: 50S ribosomal protein L19e [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.1e-56  188.5  16.1    6.8e-56  188.3  16.1    1.0  1  Ribosomal_L19e  Ribosomal protein L19e


Domain annotation for each model (and alignments):
>> Ribosomal_L19e  Ribosomal protein L19e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  188.3  16.1   3.8e-60   6.8e-56       2     142 ..       2     142 ..       1     144 [. 0.98

  Alignments for each domain:
  == domain 1  score: 188.3 bits;  conditional E-value: 3.8e-60
                                       THHHHHHHHHHTTS-GGGEEE-GGGHHHHHH--SHHHHHHHHHTTSEEE-------THHHHHHHHHHHTT-S-SGGG CS
                    Ribosomal_L19e   2 lklqkrlaasvlkvGknrvwldpeeleeiaeAitredirklikdglIikkpkkgnsrararerkekkrkgrrrgsGk 78 
                                       lk+q+r+aa++lk+G+nrvw+dpe++e++++Aitredir+li++g+I+kk  kg+sr+ra+ r+e+k+kgr+rg+G+
  gi|242398298|ref|YP_002993722.1|   2 LKMQRRIAAELLKCGENRVWIDPERIEDVKSAITREDIRRLINEGVIKKKLLKGQSRYRAKIRQEAKKKGRHRGHGN 78 
                                       799************************************************************************** PP

                                       --S-HHHHS-HHHHHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHTT--SSHHHHHHHHT- CS
                    Ribosomal_L19e  79 rkGtkeaRlpekelWikriRalRrlLkelrekkkidkktYrelYrkakGgefknkavLkeyiek 142
                                       rkG+k+aR+ +ke+Wi +iRalR++L++l+++kkid++ Yr+lY +akGg+fk+k++L  ++e+
  gi|242398298|ref|YP_002993722.1|  79 RKGKKTARMGRKERWIMTIRALRKELRKLKAEKKIDEHIYRSLYIRAKGGQFKSKHQLYLFMEE 142
                                       **********************************************************998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1179  (0.0657594); expected 358.6 (0.02)
Passed bias filter:                      573  (0.0319594); 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: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 950.83
//
Query:       gi|242398299|ref|YP_002993723.1|  [L=200]
Description: 50S ribosomal protein L18P [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-27   97.0   0.4    1.3e-15   57.8   0.0    2.7  3  Ribosomal_L5e    Ribosomal large subunit proteins 60S L5, and
    1.8e-11   44.8   0.5    3.4e-11   43.9   0.5    1.4  1  Ribosomal_L18_c  Ribosomal L18 C-terminal region
    3.6e-08   33.8   0.0    5.2e-08   33.3   0.0    1.3  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 !   57.8   0.0   2.1e-19   1.3e-15       2      99 ..       6      97 ..       5     100 .. 0.94
   2 !   36.9   0.0   5.6e-13   3.4e-09     130     163 .]     101     134 ..      96     134 .. 0.94
   3 ?   -1.6   0.0      0.38   2.3e+03     105     137 ..     137     175 ..     135     180 .. 0.61

  Alignments for each domain:
  == domain 1  score: 57.8 bits;  conditional E-value: 2.1e-19
                     Ribosomal_L5e  2 rfqvkfrrrregktdYyarkrliiqdknkyntpkyRlvVrvtnkdiicqiayakiegdkvlaaayskelp.kygvkvgl 79
                                      r++v frrrregkt+Y++r +l+        + k RlvVr t ++ ++qi+    egdk++++a+++el  ++g k   
  gi|242398299|ref|YP_002993723.1|  6 RYRVPFRRRREGKTNYHKRLALLK-------SGKPRLVVRKTLNHHVAQIVLYAPEGDKTVVSAHTRELMrDFGWKGHG 77
                                      9********************985.......5678*********************************9857****999 PP

                     Ribosomal_L5e 80 tnyaaaYatglllarrllkk 99
                                       n  +aY+ gll++ ++l+k
  gi|242398299|ref|YP_002993723.1| 78 GNTPSAYLLGLLIGYKALEK 97
                                      **************999987 PP

  == domain 2  score: 36.9 bits;  conditional E-value: 5.6e-13
                     Ribosomal_L5e 130 kaiLdvGLartttgakvfgalkgavdgglsiphs 163
                                       +aiLd+GL+  t+g+ +f++lkgavd+gl++phs
  gi|242398299|ref|YP_002993723.1| 101 EAILDIGLHPPTKGSSIFAVLKGAVDAGLNVPHS 134
                                       79*******************************7 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.38
                     Ribosomal_L5e 105 iyegqeevtgee......ynveeideekrafkaiLdvGL 137
                                       iy g+e+++g++      +  e+ ++ k+ f  +L  GL
  gi|242398299|ref|YP_002993723.1| 137 IYPGEERINGKHiaeyakMLKEDDENYKKQFGGYLVKGL 175
                                       666666666665444433445555666677777777776 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 !   43.9   0.5   5.8e-15   3.4e-11       6      59 ..     142     194 ..     140     199 .. 0.92

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 5.8e-15
                   Ribosomal_L18_c   6 krIfgkhvaeYmeeLkeedeekykkqFskyikkgieaddleelykkahaaIred 59 
                                       +rI gkh+aeY ++Lke+de +ykkqF  y+ kg+e+++l e ++++ a I e+
  gi|242398299|ref|YP_002993723.1| 142 ERINGKHIAEYAKMLKEDDE-NYKKQFGGYLVKGLEPEKLPEHFEEVKARIIEK 194
                                       79*************98876.9****************************9875 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 !   33.3   0.0   8.8e-12   5.2e-08      14      94 ..      21     107 ..       8     131 .. 0.78

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 8.8e-12
                                       HTTT--.TTSSS-EEEEEE-SS-EEEEEE..-TTT--EEEEECS-SCCCT...S-SSSCHHHHHHHHHHHHHHHCHH CS
                    Ribosomal_L18p  14 irkkls.gtaerprlvvfrsnrhiyaQvi..ddvkgktlasastlekelk...lkstknkeaakkvgeliAerakek 84 
                                        +k+l+  ++ +prlvv ++ +h +aQ++  +   +kt++sa t e       + +++n+ +a  +g li  +a+ek
  gi|242398299|ref|YP_002993723.1|  21 YHKRLAlLKSGKPRLVVRKTLNHHVAQIVlyAPEGDKTVVSAHTRELMRDfgwKGHGGNTPSAYLLGLLIGYKALEK 97 
                                       344454456679***************975578899********9876555588899******************** PP

                                       CHTC-EE--T CS
                    Ribosomal_L18p  85 giekvvfDrg 94 
                                       gie+++ D g
  gi|242398299|ref|YP_002993723.1|  98 GIEEAILDIG 107
                                       *******987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1326.55
//
Query:       gi|242398300|ref|YP_002993724.1|  [L=235]
Description: 30S ribosomal protein S5P [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.5e-22   77.3   1.8    1.4e-21   76.3   1.8    1.5  1  Ribosomal_S5    Ribosomal protein S5, N-terminal domain
    1.1e-20   72.9   0.1    2.2e-20   71.9   0.1    1.5  1  Ribosomal_S5_C  Ribosomal protein S5, C-terminal domain


Domain annotation for each model (and alignments):
>> Ribosomal_S5  Ribosomal protein S5, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.3   1.8   1.5e-25   1.4e-21       3      64 ..      63     124 ..      62     125 .. 0.97

  Alignments for each domain:
  == domain 1  score: 76.3 bits;  conditional E-value: 1.5e-25
                                       EEEEEEEEEEEEETTEEEEEEEEEEEEEETTTEEEEEEEEESSHHHHHHHHHHHHHHTEEE- CS
                      Ribosomal_S5   3 ekvlkikrvqkvtkgGrrtsfsalvvvGdgnGlvGlGvgkakevatAirkAiekAkknlvpv 64 
                                       ++v++i  ++++t++Grr +f++l+vvG+++G+vGlG+g +kev  AirkAi+ Ak n++++
  gi|242398300|ref|YP_002993724.1|  63 QEVIDIALTVRMTDSGRRVRFRVLAVVGNRDGYVGLGIGHGKEVGIAIRKAINYAKMNIIEI 124
                                       69**********************************************************98 PP

>> Ribosomal_S5_C  Ribosomal protein S5, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.9   0.1   2.4e-24   2.2e-20       1      66 [.     146     212 ..     146     217 .. 0.96

  Alignments for each domain:
  == domain 1  score: 71.9 bits;  conditional E-value: 2.4e-24
                                       EEEETTEEEEEEE--TT--EES-HHHHHHHHHHT--SEE---BS.-SSHHHHHHHHHHHHHHTTTT- CS
                    Ribosomal_S5_C   1 tgkfgavkvllkpaprGtGiiaggavravlelaGikDvlakslg.srnpinvvkAtfeALkklrspe 66 
                                       +gk ++vkv+l+p prG G++ g++ +++l laG+kD ++++lg +r+++n++kA+feAL +++s+ 
  gi|242398300|ref|YP_002993724.1| 146 EGKSSSVKVKLMPGPRGLGLVIGDVGKKILTLAGVKDAWSQTLGeTRTTVNFAKAVFEALYNTNSVA 212
                                       599************************************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1716.38
//
Query:       gi|242398301|ref|YP_002993725.1|  [L=154]
Description: 50S ribosomal protein L30P [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.5e-14   52.4   0.3    5.3e-14   51.8   0.3    1.3  1  Ribosomal_L30  Ribosomal protein L30p/L7e
  ------ inclusion threshold ------
      0.033   13.8   0.0      0.057   13.1   0.0    1.4  1  zf-SCNM1       Zinc-finger of sodium channel modifier 1


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 !   51.8   0.3     6e-18   5.3e-14       3      51 .]       6      54 ..       4      54 .. 0.96

  Alignments for each domain:
  == domain 1  score: 51.8 bits;  conditional E-value: 6e-18
                                      EEE-S-STTS-HHHHHHHHHTT-SSTTEEEE--SSHHHHHHHHHCCCGE CS
                     Ribosomal_L30  3 VtrirsiigvppkvrktLqlLgLrkingtvvklntpsirGmLkkVkhlV 51
                                       +r+r+ ++v+  v++tL +L+L+k+n+ v+   +ps++Gm++ Vk+++
  gi|242398301|ref|YP_002993725.1|  6 LIRVRGRVNVKRPVKDTLAMLRLHKVNHLVIIDESPSYNGMIQRVKDYI 54
                                      59*************************99999999*************8 PP

>> zf-SCNM1  Zinc-finger of sodium channel modifier 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   6.4e-06     0.057       6      19 ..      16      29 ..      13      31 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.4e-06
                          zf-SCNM1  6 hrPVfDTilmLsvH 19
                                      +rPV DT++mL +H
  gi|242398301|ref|YP_002993725.1| 16 KRPVKDTLAMLRLH 29
                                      7************* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); 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 0.30s 00:00:00.85 Elapsed: 00:00:00.52
# Mc/sec: 896.23
//
Query:       gi|242398302|ref|YP_002993726.1|  [L=147]
Description: 50S ribosomal protein L15P [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-19   70.2   0.7    3.8e-19   69.6   0.7    1.3  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 !   69.6   0.7   2.1e-23   3.8e-19       2     127 ..      29     145 ..      28     146 .. 0.84

  Alignments for each domain:
  == domain 1  score: 69.6 bits;  conditional E-value: 2.1e-23
                                       GGGTSSTTTTTTTTT-S--......S--.........---.GGG..---EEEEHHHHHHTTTTGTTS.--...---- CS
                    Ribosomal_L27A   2 GktgGrGhkGqkkrsgvkkkpgfeGGqmplyrrlpkrGfk.nskfkkeykvvnlkdLdelideerle.la...deae 73 
                                       G++gG+G++G+ kr+++k    +   ++ +   l krGfk     ++e  +vnl+ +de +de  +   a   +++ 
  gi|242398302|ref|YP_002993726.1|  29 GHKGGKGMAGTGKRKKTKWTWVI---KY-MPEHLGKRGFKrPVEAQNEVMAVNLRFIDEHLDEFMQLgIAyeeEGKI 101
                                       9*************986654334...44.578899*****5433556679************998876668777788 PP

                                       EEEGGGTTTTSSS....SEEEE--S---.--EEEESEE-HHHHHHHHHTT-EEE CS
                    Ribosomal_L27A  74 eidleelaeaglikkkdgvKvlgkgeltkklkvkaskfSkkAkekIeaaGGkve 127
                                       ++d +++            Kvlg+g++tk+l +ka++fS+kA+ekI +aGG++ 
  gi|242398302|ref|YP_002993726.1| 102 VVDTTQF----------ADKVLGSGKITKPLVIKARAFSPKAEEKIVQAGGEAL 145
                                       8999998..........56********************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.51
# Mc/sec: 872.66
//
Query:       gi|242398303|ref|YP_002993727.1|  [L=461]
Description: Preprotein translocase, SecY subunit [Thermococcus sibiricus MM 739]
Scores for complete 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-71  239.4  16.7    6.4e-71  239.1  16.7    1.1  1  SecY             SecY translocase
    1.4e-12   47.2   0.1    5.8e-12   45.2   0.1    2.2  1  Plug_translocon  Plug domain of Sec61p


Domain annotation for each model (and alignments):
>> SecY  SecY translocase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  239.1  16.7   7.1e-75   6.4e-71       1     306 []      72     441 ..      72     441 .. 0.83

  Alignments for each domain:
  == domain 1  score: 239.1 bits;  conditional E-value: 7.1e-75
                                       BTTSSTCHHHHHHHHHHHHH.HHHSSSSSSTS.-S.SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC.......HH CS
                              SecY   1 sifaLGImPyitasIilqLl.tvvipkleelk.ke.geegrkkinqitryltvvlalvqalgialslg.......la 67 
                                       s+++LGI+P++ta+Ii+qLl ++     e+++ +  ++e+r+ ++ ++++++v++++++a +++++ g       ++
  gi|242398303|ref|YP_002993727.1|  72 SLLTLGIGPIVTAGIIMQLLvGS-----EIIRlDLsNPEDRRFYQALQKVFAVFMCFFEAGVYVFA-GafgnpaiAI 142
                                       899*****************999.....666666569***********************997765.56889**978 PP

                                       .HHHHHHHHHHHHHHHHHHHHHHHHSSTTHHHHHHHHHHHHHHCCHSS...................-HHHH..... CS
                              SecY  68 lllivlqltagtvllmwLgEqitekGiGnGisllifagivarlpkals...................gliel..... 120
                                        ll+vlql +g++++m ++E+++++GiG+Gisl+i+ag+++++ +                      g         
  gi|242398303|ref|YP_002993727.1| 143 KLLLVLQLAFGGIMIMIMDELVSKWGIGSGISLFIAAGVSQTILTLSLnplttsaaldpltgepaiiG---Aipafi 216
                                       9*******************************************554436666555555555555551...044434 PP

                                       ...SS...........THHHHHHHHHHHHHHHHHCHHHHBEEEECBBBSTT....S.S-EEEEETTCCCSCHHHHHH CS
                              SecY 121 ...ale.........gilallllllvtllvillvvyveeaerripvqyakrgrkggqssylPlklnyagviPiIfas 185
                                          + +           ++ ++ +l+t++++l+vvy+e+++++ip++y +       ++++P++++y ++iPiI++ 
  gi|242398303|ref|YP_002993727.1| 217 qhiI-QgdllgalyrRGMPDMVSVLATIVIFLIVVYLESMRVEIPLSYGRV----TVRGRYPIRFMYVSNIPIILTF 288
                                       4330.2455555556448*******************************76....79******************** PP

                                       HHHHHHHCCCCS................................TCCCSTHHHHHHHHHHHHHH....HHHHHHTCT CS
                              SecY 186 sllalpstiaqfl...............................lallspsvlyvvlyvlliif....Fayfyteit 227
                                       +l a  + +a++l                               ++++  +++++++y++l+if    F ++++e+t
  gi|242398303|ref|YP_002993727.1| 289 ALYANIQLWARLLqrigypllgrfdesgavvsgfvryvlpprdiFSVM-ADPVRALVYAILTIFfaliFGFLWVELT 364
                                       ****77777777777777777777777666666666666654442222.3345666666666665555********* PP

                                       .THHHHHHHCCHHTBSSSCTTT.TCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS.TT.TTHHHHHHHHHHH CS
                              SecY 228 .fnpkevaenlkksggfipgir.pgketakyLekvlsritliGalflaliavlpdllgasligafggtslLivVgva 302
                                        ++++++a++l++ g +ipg+r + + ++++L+++++ +t++Ga+ la++avl+d+lga  +g  +gt++L++Vg+ 
  gi|242398303|ref|YP_002993727.1| 365 gLDARSIARQLQRAGLQIPGFRrDPRILERVLQRYIPYVTFWGAFTLAVVAVLADFLGA--LG--TGTGILLTVGIL 437
                                       **********************999**********************************..77..9**********9 PP

                                       HHHH CS
                              SecY 303 letv 306
                                       ++++
  gi|242398303|ref|YP_002993727.1| 438 YRFY 441
                                       9875 PP

>> Plug_translocon  Plug domain of Sec61p
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2   0.1   6.4e-16   5.8e-12       1      35 []      38      71 ..      38      71 .. 0.97

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 6.4e-16
                                      HHHHHHCCSB-TT--SSS-TCCHTTTCCCCTSSTT CS
                   Plug_translocon  1 llYlvlsqiPLyGissssssDpfywlRaifAsnrG 35
                                      llY+v+++iPL+Gi+ ++++D f+ lR+++A+ +G
  gi|242398303|ref|YP_002993727.1| 38 LLYFVMAEIPLFGIP-AEVQDYFQTLRVVLAGRNG 71
                                      79*************.****************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (461 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 3227.46
//
Query:       gi|242398304|ref|YP_002993728.1|  [L=196]
Description: Adenylate kinase [Thermococcus sibiricus MM 739]
Scores for complete 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-33  114.8   0.1    5.9e-33  114.2   0.1    1.3  1  AAA_17           AAA domain
    7.6e-10   39.4   0.1    2.6e-09   37.7   0.0    1.7  2  AAA_18           AAA domain
    2.1e-05   24.5   1.8    0.00028   20.9   0.3    2.7  2  AAA_5            AAA domain (dynein-related subfamily)
    0.00093   18.5   0.0     0.0016   17.7   0.0    1.4  1  NB-ARC           NB-ARC domain
     0.0014   19.1   0.2     0.0067   16.9   0.0    2.1  3  AAA              ATPase family associated with various cellul
     0.0014   18.9   0.1     0.0027   18.0   0.0    1.5  2  AAA_28           AAA domain
     0.0018   18.7   0.2     0.0035   17.8   0.2    1.7  1  AAA_16           AAA ATPase domain
     0.0071   15.8   0.0      0.011   15.2   0.0    1.3  1  KTI12            Chromatin associated protein KTI12
     0.0079   16.2   0.3      0.036   14.1   0.0    2.0  2  AAA_14           AAA domain
  ------ inclusion threshold ------
      0.014   15.3   0.6      0.038   13.9   0.3    1.9  1  NTPase_1         NTPase
       0.02   13.9   0.1      0.042   12.8   0.1    1.5  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
       0.02   15.1   1.7       0.14   12.4   1.7    2.1  1  AAA_22           AAA domain
      0.023   15.0   0.0      0.035   14.4   0.0    1.4  1  PAS_9            PAS domain
      0.033   14.3   0.1       0.13   12.3   0.0    2.0  2  MMR_HSR1         50S ribosome-binding GTPase
      0.054   13.7   0.3      0.079   13.1   0.3    1.6  1  AAA_33           AAA domain
      0.071   13.0   0.0       0.92    9.4   0.0    2.3  2  AAA_3            ATPase family associated with various cellul
      0.079   12.2   0.4       0.26   10.6   0.0    1.9  2  Zeta_toxin       Zeta toxin
      0.086   12.7   0.8       0.45   10.4   0.1    2.3  2  APS_kinase       Adenylylsulphate kinase
      0.086   12.6   0.0       0.13   12.0   0.0    1.4  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.089   13.3   0.0       0.14   12.7   0.0    1.5  1  ABC_tran         ABC transporter
       0.98    9.1   4.5       0.53   10.0   0.3    2.4  3  AAA_30           AAA 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 !  114.2   0.1   6.9e-36   5.9e-33       1     136 []       8     145 ..       8     145 .. 0.96

  Alignments for each domain:
  == domain 1  score: 114.2 bits;  conditional E-value: 6.9e-36
                                       EE-TTSSHHHHHHHHHHHH..TEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEE CS
                            AAA_17   1 lGgPGsGKgtqceklveky..gfthlsaGdllreeakrgglakardemrklpleekkelqkeaaekiaeeakkkgvl 75 
                                       +G+PG+GK+t+ +   ++   +f ++++Gd++++ea + g +++rde+rkl+l++++elq +aa++i e ++k+ vl
  gi|242398304|ref|YP_002993728.1|   8 TGIPGVGKSTITRLALQRTraKFRVVNFGDIMFQEAVKAGWVSHRDEVRKLSLKVQRELQLKAAQRILEISQKEPVL 84 
                                       7***********6666654459******************************************************* PP

                                       EEE-SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHHTTST-TS-SHHHHH CS
                            AAA_17  76 vdghprikeqagfldglpkevleelkpdaiilleadpeeilerrlkdrtrgrdddneesik 136
                                       +d+h++ik++ g++ g+p+ev+e ++p +++++ea+p eil rrl+d +r+rd ++e++i+
  gi|242398304|ref|YP_002993728.1|  85 LDTHATIKTPLGYMLGFPREVIEVINPRFMVIIEANPSEILGRRLRDLKRDRDVETEDQIQ 145
                                       *********************************************************9996 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.0     3e-12   2.6e-09       1     117 [.       5     135 ..       5     146 .. 0.74
   2 ?    3.1   0.1      0.15   1.3e+02      25      48 ..     126     152 ..     104     192 .. 0.53

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 3e-12
                            AAA_18   1 IlltGtpGvGKttlakeL.skrl.gf.....gvnlrdvakenglllevdpealdeskrldedkldklldaleenssa 70 
                                       +++tG+pGvGK+t+++   ++   +f     g++  + a + g++  +d+   + s++++++ + k+ + + e+s+ 
  gi|242398304|ref|YP_002993728.1|   5 VVITGIPGVGKSTITRLAlQRTRaKFrvvnfGDIMFQEAVKAGWVSHRDEV-RKLSLKVQRELQLKAAQRILEISQ- 79 
                                       79**************87444434669555566666666666666666666.999999999999999999999976. PP

                            AAA_18  71 leegknlvidghlaeleseaakdikk............vvLtasp.eelleRlekRgyee 117
                                           +++++d h     +  +  +              v+++a+p e+l +Rl++ + ++
  gi|242398304|ref|YP_002993728.1|  80 ---KEPVLLDTHATIKTPLGYMLGFPrevievinprfmVIIEANPsEILGRRLRDLK-RD 135
                                       ...89999999998888877776555888999999999*******666666666644.43 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.15
                            AAA_18  25 gvnlrdvakenglllevdpe...alde 48 
                                       g++lrd+ ++++ ++e++ +   +l++
  gi|242398304|ref|YP_002993728.1| 126 GRRLRDLKRDRDVETEDQIQrhqDLNR 152
                                       455555555555555555553333333 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.3   3.3e-07   0.00028       2     124 ..       5     123 ..       4     135 .. 0.78
   2 ?    0.4   0.1      0.72   6.1e+02      39      90 ..     130     189 ..     127     192 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 3.3e-07
                                       EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG-- CS
                             AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEverae 78 
                                       v++ G pG+gKs++++  ++++++++ +v++ + + +e +k ++    ++ +    ++ r+ + ++  ++ E+ + e
  gi|242398304|ref|YP_002993728.1|   5 VVITGIPGVGKSTITRLALQRTRAKFRVVNFGDIMFQEAVKAGWVSHRDEVRKLSLKVQRELQLKAAQRILEISQKE 81 
                                       7899****************************************975444444455666788888888888888888 PP

                                       HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS-- CS
                             AAA_5  79 sevlnsLlslleerrllleeggelvkaknddllerfrviatanpld 124
                                       +  l++  ++     ++l   +e++ + n+     f+vi +anp +
  gi|242398304|ref|YP_002993728.1|  82 PVLLDTHATIKTPLGYMLGFPREVIEVINPR----FMVIIEANPSE 123
                                       8888887777777777766666777666654....77777777766 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.72
                                       HHHH--B--.........--------.......G-SEEEEESGGG--.HHHHHHHHHHHH CS
                             AAA_5  39 edlkgrreikngttslvdsplvraar.......egeilvlDEverae.sevlnsLlslle 90 
                                       +dlk  r+++ +++  + + l raa+       ++ i +++  e     e++n+L ++l+
  gi|242398304|ref|YP_002993728.1| 130 RDLKRDRDVETEDQIQRHQDLNRAATisyamhsNALIKIIENHEDKGlEEAVNELVKILD 189
                                       588888999988888888999999988888887777777777655555777777777776 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   1.9e-06    0.0016      21      83 ..       3      73 ..       1      96 [. 0.79

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.9e-06
                                      EEEEEEESTTSSHHHHHHHHCCSHCCCCC..CBTEEEEE......EEESXXHHHHHHHXXHHHHHCCCTTS CS
                            NB-ARC 21 lvvalvGmgGvGKttlakqilnksdeveg..rFdsvawv......vvsktdkseeiletilkeLslseddl 83
                                      +vv + G +GvGK+t+ + +l+      +  +F  +++        vs+ d+ +++  ++ +eL+l+ +++
  gi|242398304|ref|YP_002993728.1|  3 FVVVITGIPGVGKSTITRLALQRTRAKFRvvNFGDIMFQeavkagWVSHRDEVRKLSLKVQRELQLKAAQR 73
                                      799*****************99955544445665555548999999******************9986653 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   7.9e-06    0.0067       1      38 [.       5      47 ..       5      85 .. 0.79
   2 ?   -1.7   0.0       4.2   3.5e+03     100     118 ..     110     128 ..      52     139 .. 0.66
   3 ?   -1.0   0.0       2.5   2.1e+03      75      94 ..     170     189 ..     152     194 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 7.9e-06
                                      EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCS.SS....S CS
                               AAA  1 vllyGppGtGKTllakavakelgvefleisgsell.sk....y 38
                                      v+++G pG+GK+++ +   + + ++f  ++  +++ ++     
  gi|242398304|ref|YP_002993728.1|  5 VVITGIPGVGKSTITRLALQRTRAKFRVVNFGDIMfQEavkaG 47
                                      5789*********************999999999955544441 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 4.2
                                       SSTEEEEEEESSGGGSTHH CS
                               AAA 100 eskvivigatnrpdkldpa 118
                                       + +++vi+ +n  + l + 
  gi|242398304|ref|YP_002993728.1| 110 NPRFMVIIEANPSEILGRR 128
                                       4456666666665555555 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 2.5
                                       TTCCCHHHHHHHHHHHHHHH CS
                               AAA  75 sgseseeeervvnqLlteld 94 
                                       +++e++  e++vn+L++ ld
  gi|242398304|ref|YP_002993728.1| 170 ENHEDKGLEEAVNELVKILD 189
                                       55677777888888888877 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   3.2e-06    0.0027       2      82 ..       5      89 ..       4     109 .. 0.66
   2 ?   -2.3   0.0       5.5   4.7e+03     126     131 ..     145     150 ..     115     173 .. 0.60

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3.2e-06
                            AAA_28  2 ivitGgestGKTtlle.aLaar..gypvvpEaareileekl.akgedalpwv.edllafaervleeqleeeaaaaankv 75
                                      +vitG ++ GK+t+++ aL+++  +++vv  ++  +++e   a +  + ++v +  l++++++  +++++  + ++++ 
  gi|242398304|ref|YP_002993728.1|  5 VVITGIPGVGKSTITRlALQRTraKFRVV-NFGDIMFQEAVkAGWVSHRDEVrKLSLKVQRELQLKAAQRILEISQKEP 82
                                      8*************964677655677777.4555555555555555566666333445554432233333344488999 PP

                            AAA_28 76 lfcDrgl 82
                                      +++D+ +
  gi|242398304|ref|YP_002993728.1| 83 VLLDTHA 89
                                      9999875 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 5.5
                            AAA_28 126 eRredl 131
                                       +R +dl
  gi|242398304|ref|YP_002993728.1| 145 QRHQDL 150
                                       222222 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.2     4e-06    0.0035      27     105 ..       5      78 ..       2     194 .. 0.60

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 4e-06
                            AAA_16  27 vllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawreklee 103
                                       v+++G +GvGKs++ r +l++ +++ + +++     +++a+  + +++     + +r+l  + +  ++  ++++++e
  gi|242398304|ref|YP_002993728.1|   5 VVITGIPGVGKSTITRLALQRTRAK-FRVVNFGDIMFQEAVK-AGWVSHR---DEVRKLSLKVQRELQLKAAQRILE 76 
                                       89*****************877776.4444433333333322.1232222...334444444344344444444444 PP

                            AAA_16 104 al 105
                                         
  gi|242398304|ref|YP_002993728.1|  77 IS 78 
                                       43 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.3e-05     0.011       1      83 [.       1      92 [.       1     103 [. 0.60

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.3e-05
                                      E.E.EEEE--TTSSHHHHHHHHHHHHHHTT--EE....EE-THHHH....TTSSS--GGGHHHHHHHHHHHHHHHH..T CS
                             KTI12  1 MpL.vvltGlPssGKstrakeLakaleeekrsvv....viddeslg...iekdsykdsakekalRsslrsavkrdL..s 69
                                      Mp  vv+tG+P +GKst+++   +  ++ k +vv    ++ +e+++   +++ +   + + k  R+ + +a++r L  s
  gi|242398304|ref|YP_002993728.1|  1 MPFvVVITGIPGVGKSTITRLALQRTRA-KFRVVnfgdIMFQEAVKagwVSHRDEVRKLSLKVQRELQLKAAQRILeiS 78
                                      7751679***********9743333333.22222011122234444555555554555566677777777777744226 PP

                                      T.SEEEE-S---SH CS
                             KTI12 70 kekvVIvDslnyik 83
                                      +++ V +D  + ik
  gi|242398304|ref|YP_002993728.1| 79 QKEPVLLDTHATIK 92
                                      77777777777776 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   4.2e-05     0.036       4      46 ..       4      43 ..       2      93 .. 0.73
   2 ?   -0.1   0.1       1.1   9.1e+02      51      87 ..     149     185 ..     116     191 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.2e-05
                            AAA_14  4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkl 46
                                      ++vitG+  vGK+t+ +  +++      ++  +n+ d  ++++
  gi|242398304|ref|YP_002993728.1|  4 VVVITGIPGVGKSTITRLALQRTR---AKFRVVNFGDIMFQEA 43
                                      79*************998887777...9999999999888543 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.1
                            AAA_14  51 kllelileklke.ekktylflDEiqevpewekalkslv 87 
                                       +l+++   ++ + + + ++ + E +e +++e+a+++lv
  gi|242398304|ref|YP_002993728.1| 149 DLNRAATISY-AmHSNALIKIIENHEDKGLEEAVNELV 185
                                       2222222221.123556666667777777777777776 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.3   4.5e-05     0.038       2      24 ..       5      27 ..       4      47 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.5e-05
                                      EEEE--TTSSHHHHHHHHHHHH. CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlellk 24
                                      v+iTG pGvGK+T+ + +l+  +
  gi|242398304|ref|YP_002993728.1|  5 VVITGIPGVGKSTITRLALQRTR 27
                                      89************999888764 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   0.1   4.9e-05     0.042      31      50 ..       4      22 ..       2      35 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.9e-05
                                      EEEEEE-TTSSHHHHHHHHH CS
                              MeaB 31 vvGltGvPGaGkstlvealg 50
                                      vv +tG+PG+Gkst++ +l+
  gi|242398304|ref|YP_002993728.1|  4 VVVITGIPGVGKSTIT-RLA 22
                                      6889**********76.444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   1.7   0.00017      0.14       8      30 ..       5      27 ..       4     195 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00017
                            AAA_22  8 lvvtGesGtGKTtllrrlleqld 30
                                      +v+tG +G+GK+t  r  l++  
  gi|242398304|ref|YP_002993728.1|  5 VVITGIPGVGKSTITRLALQRTR 27
                                      79************999888763 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0     4e-05     0.035       8      50 ..     101     146 ..      94     182 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4e-05
                             PAS_9   8 npdgril.yaNeaalrllGyspeevlgksitdlf...vtdpeanerl 50 
                                        p   ++  +N+ ++ ++  +p e+lg++++dl    + + e++   
  gi|242398304|ref|YP_002993728.1| 101 FPRE-VIeVINPRFMVIIEANPSEILGRRLRDLKrdrDVETEDQIQR 146
                                       4566.566**************************5443333333333 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00016      0.13       2      25 ..       5      29 ..       4      42 .. 0.81
   2 ?   -0.8   0.0       1.8   1.6e+03      59      71 ..     170     182 ..     113     193 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00016
                                      EEEEESTTSSHHHHHHHHHTS.TEE CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltge.kai 25
                                      v+i G p vGKSt+ +  +++ +a+
  gi|242398304|ref|YP_002993728.1|  5 VVITGIPGVGKSTITRLALQRtRAK 29
                                      89************99888765554 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.8
                                       HHHHHHHHHHHHH CS
                          MMR_HSR1  59 gaseekglgkafl 71 
                                       +++e+kgl++a+ 
  gi|242398304|ref|YP_002993728.1| 170 ENHEDKGLEEAVN 182
                                       2334444444444 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.3   9.2e-05     0.079       1      29 [.       4      34 ..       4     156 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.2e-05
                            AAA_33  1 lvllvGlpGsGKstlaerllkklg..avlls 29
                                      +v++ G pG+GKst  +  l+++   + +++
  gi|242398304|ref|YP_002993728.1|  4 VVVITGIPGVGKSTITRLALQRTRakFRVVN 34
                                      7999************999988777655555 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0    0.0011      0.92       2      37 ..       5      39 ..       4      64 .. 0.80
   2 ?    1.0   0.0      0.43   3.6e+02     100     118 ..     109     127 ..     102     138 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0011
                             AAA_3  2 vllegvPGlaktllvkalakaldlefkriqftpdll 37
                                      v+++g+PG++k ++ +   +   ++f+ + f  d++
  gi|242398304|ref|YP_002993728.1|  5 VVITGIPGVGKSTITRLALQRTRAKFRVVNFG-DIM 39
                                      7899************9999******999996.444 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.43
                             AAA_3 100 lpepflvlatqnPieqeGt 118
                                       ++  f+v+   nP e  G 
  gi|242398304|ref|YP_002993728.1| 109 INPRFMVIIEANPSEILGR 127
                                       67789********998884 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0    0.0003      0.26      16      48 ..       2      34 ..       1      44 [. 0.87
   2 ?   -1.3   0.1       1.3   1.1e+03     140     179 ..     124     163 ..     116     177 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0003
                        Zeta_toxin 16 PklillgGqpGAGKselaellkdelerqgnvvr 48
                                      P ++++ G pG GKs++ +l+ ++++++ +vv 
  gi|242398304|ref|YP_002993728.1|  2 PFVVVITGIPGVGKSTITRLALQRTRAKFRVVN 34
                                      889*******************99987777776 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.3
                        Zeta_toxin 140 vldRyeeevaegRlvpkeehdeafeglresvealeeekql 179
                                       +l R + ++++ R v+ e +++ ++ l +++ +    +  
  gi|242398304|ref|YP_002993728.1| 124 ILGRRLRDLKRDRDVETEDQIQRHQDLNRAATISYAMHSN 163
                                       5566666666678888888888888888777665555544 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00053      0.45       2      22 ..       2      22 ..       1      79 [. 0.87
   2 ?    0.6   0.1      0.55   4.7e+02      45      79 ..     132     169 ..     122     172 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00053
                                      -EEEEEESSTTSSHHHHHHHH CS
                        APS_kinase  2 gvvvwltGlsgsGKstianal 22
                                      ++vv +tG+ g GKsti++  
  gi|242398304|ref|YP_002993728.1|  2 PFVVVITGIPGVGKSTITRLA 22
                                      799**************9743 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.55
                                       TTTT--SSHHH...HHHHHHHHHHHHHHHHHTT-EEEE CS
                        APS_kinase  45 LnkdLgfseed...Rkenirrvaevaklladaglivlv 79 
                                       L++d   ++ed   R++++ r a ++  +  ++li ++
  gi|242398304|ref|YP_002993728.1| 132 LKRDRDVETEDqiqRHQDLNRAATISYAMHSNALIKII 169
                                       55555544444333999999******999999999875 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00016      0.13       2      34 ..       6      32 ..       5      64 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00016
                   Viral_helicase1  2 vvhGvpGcGKStlirkllrtsliltvnrptael 34
                                      v+ G+pG GKSt+ r +l+        r  + +
  gi|242398304|ref|YP_002993728.1|  6 VITGIPGVGKSTITRLALQR------TRAKFRV 32
                                      99**********76666655......3333444 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00016      0.14      13      77 ..       4      75 ..       3     188 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00016
                                      EEEEEESTTSSHHHHHHHHTTSS--.....SEEEEEETTCEGGG...B-HHHCCHCEEEE-SS--S-TTSBHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 13 kvaivGenGaGKStLlkllagllkp.....teGeilldgkdlke...qeleslrkeigvlpqepqlfpeltvr 77
                                      +v+i+G  G GKSt+ +l ++ ++      + G+i ++ + +k      + ++rk +  ++ e ql+   ++ 
  gi|242398304|ref|YP_002993728.1|  4 VVVITGIPGVGKSTITRLALQRTRAkfrvvNFGDIMFQ-EAVKAgwvSHRDEVRKLSLKVQRELQLKAAQRIL 75
                                      589**************999999885555555665333.3333334444444444444444444444444443 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.3   0.00063      0.53      20      43 ..       4      27 ..       2      36 .. 0.79
   2 ?    1.0   0.0      0.36     3e+02     112     137 ..      25      50 ..      18      88 .. 0.67
   3 ?   -0.7   0.2       1.1   9.6e+02     134     183 ..     126     174 ..     124     181 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00063
                            AAA_30 20 vavltGpAGtGKttalkalreawe 43
                                      v+v+tG +G GK+t+ + + +  +
  gi|242398304|ref|YP_002993728.1|  4 VVVITGIPGVGKSTITRLALQRTR 27
                                      789***********9988765544 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.36
                            AAA_30 112 aekagakvilvGDerQlasVeaGgvl 137
                                        ++a+ +v+  GD    ++V+aG v 
  gi|242398304|ref|YP_002993728.1|  25 RTRAKFRVVNFGDIMFQEAVKAGWVS 50 
                                       45568999999999999999999764 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.1
                            AAA_30 134 GgvlrdlveaagigtaeLtevvRqke.seeraaalalregdaeealealad 183
                                       G+ lrdl  +++ ++ + ++++R ++ ++ ++++ a+ ++   + +e  +d
  gi|242398304|ref|YP_002993728.1| 126 GRRLRDL--KRDRDVETEDQIQRHQDlNRAATISYAMHSNALIKIIENHED 174
                                       5567777..566677777889999887888888888877766666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       811  (0.045234); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1416.57
//
Query:       gi|242398305|ref|YP_002993729.1|  [L=175]
Description: hypothetical protein TSIB_0314 [Thermococcus sibiricus MM 739]
Scores for complete 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-28   97.2   6.3      1e-27   97.0   6.3    1.0  1  EMC3_TMCO1  Integral membrane protein EMC3/TMCO1-like
    1.1e-06   28.7   1.2    1.4e-06   28.3   1.2    1.2  1  60KD_IMP    60Kd inner membrane protein
    0.00021   21.7   0.9     0.0012   19.3   0.6    1.9  2  DUF4199     Protein of unknown function (DUF4199)
  ------ inclusion threshold ------
      0.012   15.3   1.1      0.016   14.8   1.1    1.2  1  DUF2208     Predicted membrane protein (DUF2208)
      0.014   16.1   0.6      0.025   15.3   0.6    1.3  1  DIOX_N      non-haem dioxygenase in morphine synthesis N-term
       0.25   11.7  12.1       0.37   11.1  12.1    1.1  1  OmpH        Outer membrane protein (OmpH-like)
        1.1    9.4   7.0        1.5    8.9   7.0    1.2  1  Swi5        Swi5


Domain annotation for each model (and alignments):
>> EMC3_TMCO1  Integral membrane protein EMC3/TMCO1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.0   6.3   3.9e-31     1e-27      14     167 ..      21     173 ..       9     175 .] 0.85

  Alignments for each domain:
  == domain 1  score: 97.0 bits;  conditional E-value: 3.9e-31
                        EMC3_TMCO1  14 lPivivillvgiltgllsellqkllidkkkmekeqkrekelqkrarelqkngdklklkklekrqeelmedqsemmmd 90 
                                        P+ +v l  +il g + +l++ +lid++km+k qk++ke+qk+ +++q+ +d++kl kl+++q+el + q e+m+d
  gi|242398305|ref|YP_002993729.1|  21 HPLWVVTLSGAILGG-FFTLVNHFLIDQEKMKKLQKMSKEFQKEWKAAQQAKDEKKLRKLQQKQMELLKLQNEVMKD 96 
                                       577666666555555.5679******************************************************996 PP

                        EMC3_TMCO1  91 .qmkpmivtmipqiliffwlnsffsgfvvaklpfpltg..rfksllqrglesldvrfvssiswYflcsfglsqiirk 164
                                        ++kpm++tm ++++  +w++  + + ++ k pf ++   +f+ + ++    l  +    i wY+l+s+ + q++rk
  gi|242398305|ref|YP_002993729.1|  97 sMFKPMLFTMPIFFIFSGWMRRWYVETAIVKSPFNFFLfdWFHRFYHS---ALPANELGYIGWYILTSMIVGQVLRK 170
                                       488*******************99999******776541166666655...667777889***************** PP

                        EMC3_TMCO1 165 lLg 167
                                       lL+
  gi|242398305|ref|YP_002993729.1| 171 LLD 173
                                       *97 PP

>> 60KD_IMP  60Kd inner membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   1.2   5.4e-10   1.4e-06      17      92 ..      37     131 ..      23     171 .. 0.71

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 5.4e-10
                          60KD_IMP  17 lpltlkqlkssakmqelqPelkeiqekyk.......kdk..qklqqemmklYkkegvnpla.GclplLiqlpifial 83 
                                       + l ++ l  ++km++lq+  ke q+  k       + k   klqq++m+l k ++  +    + p+L ++pif+ +
  gi|242398305|ref|YP_002993729.1|  37 FTLVNHFLIDQEKMKKLQKMSKEFQKEWKaaqqakdE-KklRKLQQKQMELLKLQNEVMKDsMFKPMLFTMPIFFIF 112
                                       667777778899**************99999998532.346889******999777655551556**********99 PP

                          60KD_IMP  84 yrvlrsla..........s 92 
                                          +r+            +
  gi|242398305|ref|YP_002993729.1| 113 SGWMRRWYvetaivkspfN 131
                                       9999985566666555442 PP

>> DUF4199  Protein of unknown function (DUF4199)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.6   4.6e-07    0.0012      75     159 ..      25     113 ..      23     116 .. 0.74
   2 ?    0.3   0.0      0.31     8e+02     150     168 .]     152     170 ..     147     170 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 4.6e-07
                           DUF4199  75 lislvagllsavfqyiyfnfidpdfienyiaeilekleeakeesae.eenaemseeei.kealesls....piiv.a 144
                                       +++l +++l + f+++ + +id++ ++++ ++ +e  +e+k+++++ +e+   +  ++ ++++e l+     +   +
  gi|242398305|ref|YP_002993729.1|  25 VVTLSGAILGGFFTLVNHFLIDQEKMKKLQKMSKEFQKEWKAAQQAkDEK---KLRKLqQKQMELLKlqneVMKDsM 98 
                                       688999************999*********99999999998888774433...333333556664444455333347 PP

                           DUF4199 145 lqsflgnliiGlils 159
                                       ++ +l++++i +i+s
  gi|242398305|ref|YP_002993729.1|  99 FKPMLFTMPIFFIFS 113
                                       788888888888887 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.31
                           DUF4199 150 gnliiGlilsliiAlilkk 168
                                       g++ +++++s+i++ +l+k
  gi|242398305|ref|YP_002993729.1| 152 GYIGWYILTSMIVGQVLRK 170
                                       67789999******99997 PP

>> DUF2208  Predicted membrane protein (DUF2208)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   1.1   6.3e-06     0.016      43     113 ..      49     122 ..      32     143 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 6.3e-06
                           DUF2208  43 tsrsllrerkkleevesgktLfe.EknalkliekDeelqkelkeqlkasmitlll..lliviilffllyryiip 113
                                       ++++l++ +k+ ++  ++ +  + Ek+ +kl++k  el k  +e++k sm+  +l  ++i++i    ++r +++
  gi|242398305|ref|YP_002993729.1|  49 KMKKLQKMSKEFQKEWKAAQQAKdEKKLRKLQQKQMELLKLQNEVMKDSMFKPMLftMPIFFIFSGWMRRWYVE 122
                                       455677778887777777766667***********************999865554788988887666666554 PP

>> DIOX_N  non-haem dioxygenase in morphine synthesis N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.6   9.6e-06     0.025      30      84 ..      35      89 ..      31     100 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 9.6e-06
                            DIOX_N 30 Gffyvvnhg.vpeelidelfeaareFFalPeeeKekl.aksp.sfrGysrlgeektdg 84
                                      Gff +vnh  +++e +++l+++++eF    +e K +  ak++ + r  ++ + e ++ 
  gi|242398305|ref|YP_002993729.1| 35 GFFTLVNHFlIDQEKMKKLQKMSKEFQ---KEWKAAQqAKDEkKLRKLQQKQMELLKL 89
                                      9*******559**************95...4666665433323666666666666655 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1  12.1   0.00014      0.37      31      98 ..      49      93 ..      42     101 .. 0.43

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00014
                                      HHHHHHHHHHHHHHHHHHHHHHTTTS.-HHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHH CS
                              OmpH 31 lqaeleakekelqklqeelqkkakklekeekeqelqkkeqelqqkqqqka.qelqkkqqellkpildki 98
                                        ++l                       ++  +e+qk+ ++ qq++++k+ ++lq+kq ellk +++++
  gi|242398305|ref|YP_002993729.1| 49 KMKKL-----------------------QKMSKEFQKEWKAAQQAKDEKKlRKLQQKQMELLK-LQNEV 93
                                      22333.......................33333444444444443333334444444444444.33333 PP

>> Swi5  Swi5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   7.0    0.0006       1.5       2      49 ..      47      93 ..      46      98 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0006
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHH CS
                              Swi5  2 eaeikeleeqleelekelaelkeelkekkdpeetvkrhIklLheYNEi 49
                                      ++++k+l+++ +e +ke +++++  +ek +  +  +++ +lL+  NE+
  gi|242398305|ref|YP_002993729.1| 47 QEKMKKLQKMSKEFQKEWKAAQQAKDEK-KLRKLQQKQMELLKLQNEV 93
                                      6899******************998876.5****************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2874  (0.160299); expected 358.6 (0.02)
Passed bias filter:                     1180  (0.0658152); expected 358.6 (0.02)
Passed Vit filter:                       164  (0.00914719); 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: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.39
# Mc/sec: 1341.99
//
Query:       gi|242398306|ref|YP_002993730.1|  [L=88]
Description: 50S ribosomal protein L34e [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.1e-22   78.3   3.3    4.8e-22   78.1   3.3    1.0  1  Ribosomal_L34e  Ribosomal protein L34e
     0.0019   18.2   0.4     0.0028   17.7   0.4    1.2  1  DZR             Double zinc ribbon
  ------ inclusion threshold ------
       0.06   12.9   2.2        3.2    7.4   0.1    2.4  2  Sgf11           Sgf11 (transcriptional regulation protein)


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 !   78.1   3.3     8e-26   4.8e-22      12      91 ..       4      82 ..       1      84 [. 0.93

  Alignments for each domain:
  == domain 1  score: 78.1 bits;  conditional E-value: 8e-26
                    Ribosomal_L34e 12 sYntrsnkvrvvktpggklvyqykkkkgkapkCgdckkkLqGipalrpkelsrlsktkktvsRaYGgslcakcvkeriv 90
                                        ++rs ++++v+tpgg++v++ ++kk+k+++C++c++ L+Gip+ rp+el++l+ktkk+++R+    lc++c+++ ++
  gi|242398306|ref|YP_002993730.1|  4 MHRSRSWRRKYVRTPGGRTVIHFERKKPKVAHCAMCGRPLNGIPRGRPNELRKLPKTKKRPERPMP-NLCPSCMRRIMK 81
                                      5789************************************************************85.79*****98776 PP

                    Ribosomal_L34e 91 r 91
                                      +
  gi|242398306|ref|YP_002993730.1| 82 A 82
                                      5 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.4   4.6e-07    0.0028      10      39 ..      31      81 ..      26      86 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4.6e-07
                               DZR 10 pdarfCseCgtklkavaa....................edrCpsCgek.vd 39
                                      p+   C  Cg +l+  ++                    ++ CpsC +  ++
  gi|242398306|ref|YP_002993730.1| 31 PKVAHCAMCGRPLNGIPRgrpnelrklpktkkrperpmPNLCPSCMRRiMK 81
                                      66779*********9999***************************988444 PP

>> Sgf11  Sgf11 (transcriptional regulation protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.1   0.00053       3.2       5      15 ..      34      44 ..      30      45 .. 0.80
   2 ?    4.9   0.4    0.0031        19       7      14 ..      72      79 ..      71      82 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00053
                                      EE-TTTSSEEE CS
                             Sgf11  5 vtCpnCgRqia 15
                                       +C +CgR+ +
  gi|242398306|ref|YP_002993730.1| 34 AHCAMCGRPLN 44
                                      69******875 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0031
                                      -TTTSSEE CS
                             Sgf11  7 CpnCgRqi 14
                                      Cp C+R i
  gi|242398306|ref|YP_002993730.1| 72 CPSCMRRI 79
                                      ******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.30s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 563.45
//
Query:       gi|242398307|ref|YP_002993731.1|  [L=193]
Description: Cytidylate kinase [Thermococcus sibiricus MM 739]
Scores for complete 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-26   91.8   0.8    3.1e-24   86.1   0.8    2.0  1  Cytidylate_kin2  Cytidylate kinase-like family
    1.2e-14   55.0   0.0    1.5e-14   54.6   0.0    1.2  1  AAA_18           AAA domain
    9.5e-14   51.6   4.3    1.4e-08   34.7   1.2    2.1  2  Cytidylate_kin   Cytidylate kinase
    1.1e-12   48.5   0.0    2.3e-12   47.5   0.1    1.5  1  AAA_17           AAA domain
    0.00042   20.5   0.4      0.025   14.7   0.4    2.1  1  AAA_33           AAA domain
    0.00075   19.2   0.8       0.45   10.2   0.0    2.2  2  CoaE             Dephospho-CoA kinase
    0.00093   19.1   0.5       0.29   10.9   0.0    2.9  2  dNK              Deoxynucleoside kinase
     0.0014   18.7   0.0     0.0023   18.1   0.0    1.4  1  ADK              Adenylate kinase
     0.0063   16.8   0.3      0.038   14.2   0.0    1.9  2  AAA_28           AAA domain
  ------ inclusion threshold ------
      0.013   15.3   0.7       0.71    9.7   0.2    2.4  2  SinI             Anti-repressor SinI
      0.015   15.1   0.3       0.41   10.3   0.0    2.1  2  PRK              Phosphoribulokinase / Uridine kinase family
       0.13   11.4   0.0       0.17   11.0   0.0    1.2  1  NB-ARC           NB-ARC domain
       0.16   11.1   0.0       0.17   11.0   0.0    1.1  1  G-alpha          G-protein alpha subunit


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 !   86.1   0.8   2.3e-27   3.1e-24       1     177 [.       7     158 ..       7     160 .. 0.93

  Alignments for each domain:
  == domain 1  score: 86.1 bits;  conditional E-value: 2.3e-27
                   Cytidylate_kin2   1 iITIsreyGsgGetigeaLAekLglpfydr.eiieevakelglseeeveevdersrlssflskllaarvagdtldek 76 
                                       +IT+s+  Gsg +t++++L+  +g++ +    i++++ake+g+s ++++e+ e                     + +
  gi|242398307|ref|YP_002993731.1|   7 VITVSGLAGSGTTTLCRNLSRYYGFKHIYAgLIFRQMAKEMGMSLQQFQEYAEM--------------------HPE 63 
                                       8************************76555499********************2....................356 PP

                   Cytidylate_kin2  77 lddelfeaqervirelaaeesvVivGRgadliLkdrpnvlrvfltapledrvkrvaereglseeearekiketDkrr 153
                                       +d e+ ++q ++ +++    +vVi GR a  ++k+ +  l+v+l+ap ++r++rva+reg+s eea  +i e++ ++
  gi|242398307|ref|YP_002993731.1|  64 IDREVDRRQIEAAEDC----NVVIEGRLAGWMVKEAD--LKVWLEAPIQVRAQRVARREGISIEEAFMQIAEREMQN 134
                                       8888777788877777....9**************77..************************************** PP

                   Cytidylate_kin2 154 akyykkytgqdwgdaenYdlvlnt 177
                                       +k+y +++g d++d++ Ydlv+nt
  gi|242398307|ref|YP_002993731.1| 135 RKRYLNLYGIDINDRSIYDLVINT 158
                                       ***********************8 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.6   0.0   1.1e-17   1.5e-14       1     119 [.       8     121 ..       8     138 .. 0.85

  Alignments for each domain:
  == domain 1  score: 54.6 bits;  conditional E-value: 1.1e-17
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....gvnlrdvakenglllevdpealdeskrldedkldklldaleenssale 72 
                                       I ++G +G+G ttl+++Ls+  gf     g + r++ake g++l +++e  + + ++d++++ + ++a e +     
  gi|242398307|ref|YP_002993731.1|   8 ITVSGLAGSGTTTLCRNLSRYYGFkhiyaGLIFRQMAKEMGMSLQQFQEYAEMHPEIDREVDRRQIEAAEDC----- 79 
                                       89****************999899*************************66777777777777777777776..... PP

                            AAA_18  73 egknlvidghlaeleseaakdikkvvLtaspeelleRlekRgyeeak 119
                                          n+vi+g+la +   +a d+k v+L+a+ +++++R+++R+  + +
  gi|242398307|ref|YP_002993731.1|  80 ---NVVIEGRLAGWMVKEA-DLK-VWLEAPIQVRAQRVARREGISIE 121
                                       ...46*******9998866.467.*****************966554 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   1.1e-06    0.0014       1      38 [.       8      45 ..       8      60 .. 0.90
   2 !   34.7   1.2     1e-11   1.4e-08      92     177 ..      58     137 ..      48     143 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.1e-06
                                      EEEE-STTSSHHHHHHHHHHHHT-EEEEHHHHHHHHHH CS
                    Cytidylate_kin  1 iaiDGPagsGKssvaralaeklglkyldtgalYRalal 38
                                      i++ G agsG  +++r l++  g+k + +g ++R++a 
  gi|242398307|ref|YP_002993731.1|  8 ITVSGLAGSGTTTLCRNLSRYYGFKHIYAGLIFRQMAK 45
                                      8999*******************************985 PP

  == domain 2  score: 34.7 bits;  conditional E-value: 1e-11
                                       HTTSHHHHHHHHHHHHTT-BSSBEEEEESSIIIIISTT-SEEEEEE--HHHHHHHHHHHHHHTT----HHHHHHHHH CS
                    Cytidylate_kin  92 vaaipavRailvkklrelvkkarvvveGRDigtvvfpdaelKifldAsveeRakRRlkqlkakgtsvsleellaeik 168
                                          +p++ +++ +++ e++++ +vv+eGR  g  ++++a+lK++l+A +++Ra+R ++    +g s  +ee   +i+
  gi|242398307|ref|YP_002993731.1|  58 AEMHPEIDREVDRRQIEAAEDCNVVIEGRLAGW-MVKEADLKVWLEAPIQVRAQRVARR---EGIS--IEEAFMQIA 128
                                       456799999********************7765.669*****************98776...3333..666666677 PP

                                       HHHHHHHCT CS
                    Cytidylate_kin 169 eRDklDker 177
                                       eR  + ++r
  gi|242398307|ref|YP_002993731.1| 129 EREMQNRKR 137
                                       777666666 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.5   0.1   1.7e-15   2.3e-12       2     100 ..      12     105 ..      11     137 .. 0.77

  Alignments for each domain:
  == domain 1  score: 47.5 bits;  conditional E-value: 1.7e-15
                                       E-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTS.HSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEEEE CS
                            AAA_17   2 GgPGsGKgtqceklvekygfthlsaGdllreeakrggl.akardemrklpleekkelqkeaaekiaeeakkkgvlvd 77 
                                       G+ GsG +t+c++l + ygf+h+ aG ++r++ak+ g+  ++++e++++  e+++e++++ +e+ ++     +v+++
  gi|242398307|ref|YP_002993731.1|  12 GLAGSGTTTLCRNLSRYYGFKHIYAGLIFRQMAKEMGMsLQQFQEYAEMHPEIDREVDRRQIEAAED----CNVVIE 84 
                                       99***********************************867778888888888888888888765554....589999 PP

                                       E-SEEEETTEEEESSHHHHHHHH CS
                            AAA_17  78 ghprikeqagfldglpkevleel 100
                                       g    +  ++  ++l+++ ++ +
  gi|242398307|ref|YP_002993731.1|  85 GRLAGWMVKE--ADLKVWLEAPI 105
                                       9987544444..34444444433 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.4   1.8e-05     0.025       1     122 [.       7     119 ..       7     140 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.8e-05
                            AAA_33   1 lvllvGlpGsGKstlaerllkklgavllssdtlrrrlfgtdqqskt...dytrvldrlyqilnelarkalsagrnvi 74 
                                       ++ + Gl+GsG +tl ++l +  g+ ++    ++r+++++   s++   +y++  +++ + + ++ ++ +++ +nv+
  gi|242398307|ref|YP_002993731.1|   7 VITVSGLAGSGTTTLCRNLSRYYGFKHIYAGLIFRQMAKEMGMSLQqfqEYAEMHPEIDREV-DRRQIEAAEDCNVV 82 
                                       67889*********************************966666651114444445555554.44444455555555 PP

                            AAA_33  75 ldatnlsrrerarflklarrlgvpvrivvvetdeetlkeRlakRaang 122
                                       +        + a +  ++++++   + v++e++ ++ ++R+a+R+  +
  gi|242398307|ref|YP_002993731.1|  83 IEG------RLAGW--MVKEAD---LKVWLEAPIQVRAQRVARREGIS 119
                                       533......22222..223223...33666666666666666666654 PP

>> CoaE  Dephospho-CoA kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0   0.00033      0.45       1      52 [.       6      57 ..       6      75 .. 0.84
   2 !    8.4   0.6    0.0011       1.5      86     163 ..      60     137 ..      57     151 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00033
                                      EEEEEEESTTSSHHHHHHHHHH.TT-EEEEHHHHHHHTTCCTHHHHHHHHHHH CS
                              CoaE  1 livgltGgiasGKstvanlfad.lgvpivDaDlvArqvvepgsealkkiveeF 52
                                      l++ ++G  +sG +t+++ ++  +g++ + a l+ rq+ ++    l++   e+
  gi|242398307|ref|YP_002993731.1|  6 LVITVSGLAGSGTTTLCRNLSRyYGFKHIYAGLIFRQMAKEMGMSLQQFQ-EY 57
                                      58999***************999****************99999999984.44 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0011
                                       HHHHHHHHHHHHHHH--S.SEEEEE-TTTTTTTGGGGSSEEEEEE--HHHHHHHHHHCCTSTHHHHHHHHHH.S--H CS
                              CoaE  86 lhPlirreikkelakles.kyvlldvPLLvEkqlekliervlvvdvelelqveRlvardgvseeevkaiiaa.Qlse 160
                                       +hP i re+ +++ ++ +   v+++  L     + k ++  + ++++ + + +R+ +r+g+s ee+   ia   +++
  gi|242398307|ref|YP_002993731.1|  60 MHPEIDREVDRRQIEAAEdCNVVIEGRL--AGWMVKEADLKVWLEAPIQVRAQRVARREGISIEEAFMQIAErEMQN 134
                                       7999999987765555551444444433..23445556667778999999************999876665504554 PP

                                       HHH CS
                              CoaE 161 eer 163
                                        +r
  gi|242398307|ref|YP_002993731.1| 135 RKR 137
                                       444 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   0.00021      0.29       1      28 [.       8      35 ..       8      38 .. 0.94
   2 !    5.6   0.2    0.0091        13     102     144 ..      50     116 ..      32     157 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00021
                                      EEEEESTTSSHHHHHHHHHCCSTCEEEE CS
                               dNK  1 ivveGnIgaGKstlvklLskklgvkvfe 28
                                      i+v+G  g+G +tl   Ls+ +g+k+++
  gi|242398307|ref|YP_002993731.1|  8 ITVSGLAGSGTTTLCRNLSRYYGFKHIY 35
                                      89**********************9985 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0091
                                       -HHHHHHHHHHHHHHHHHCCH........................-SEEEEEE--HHHHHHHHHHCT CS
                               dNK 102 seeelkiykelldnlleelak........................pdlliYLkasletclerikkRg 144
                                       s ++++ y+e++  + +e+++                         dl ++L+a++++  +r+ +R+
  gi|242398307|ref|YP_002993731.1|  50 SLQQFQEYAEMHPEIDREVDRrqieaaedcnvviegrlagwmvkeADLKVWLEAPIQVRAQRVARRE 116
                                       5555555555555555444444444444444444444444444448899999999999999998885 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.7e-06    0.0023       2      53 ..      11      59 ..      10      85 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.7e-06
                                      EESTTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHHCT-HHHHHHHHHHHTTS CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               ADK  2 lGaPgaGKGtqaeklvkkyglahlstGdllRaevksgtelGkeakevmdkge 53
                                       G  g+G  t +++l + yg++h+ +G ++R+  k+   +G  ++++ + +e
  gi|242398307|ref|YP_002993731.1| 11 SGLAGSGTTTLCRNLSRYYGFKHIYAGLIFRQMAKE---MGMSLQQFQEYAE 59
                                      6999***************************98875...5555555555554 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   2.8e-05     0.038       2      76 ..       8      82 ..       7      88 .. 0.68
   2 ?    0.7   0.1      0.39   5.3e+02      37      84 ..     110     153 ..      85     156 .. 0.55

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.8e-05
                            AAA_28  2 ivitGgestGKTtlleaLaar.gypvv..pEaareileeklakgedalpwvedllafaervleeqleeeaaaaankvl 76
                                      i ++G  ++G+Ttl+++L++  g++++    ++r++ +e + + ++  +++e   ++ ++v +    + +aa++++v+
  gi|242398307|ref|YP_002993731.1|  8 ITVSGLAGSGTTTLCRNLSRYyGFKHIyaGLIFRQMAKEMGMSLQQFQEYAEMHPEIDREVDRR---QIEAAEDCNVV 82
                                      6789999************988998776566777777777776666544445555555554443...44444555655 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.39
                            AAA_28  37 eklakgedalpwvedllafaervleeqleeeaaaaankvlfcDrglld 84 
                                       ++ a++e+++ + e ++++aer ++++++ +   +  ++ + Dr++ d
  gi|242398307|ref|YP_002993731.1| 110 QRVARREGISIE-EAFMQIAEREMQNRKRYL---NLYGIDINDRSIYD 153
                                       444444443333.345555555444444333...33566666666665 PP

>> SinI  Anti-repressor SinI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.2   0.00052      0.71      12      25 ..      44      57 ..      42      59 .. 0.92
   2 ?    3.5   0.0     0.044        60      12      21 ..     113     122 ..     112     122 .. 0.95

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00052
                                      HHHHT--SHHHHHH CS
                              SinI 12 AkesGlskeEfReF 25
                                      Ake+G+s ++f e+
  gi|242398307|ref|YP_002993731.1| 44 AKEMGMSLQQFQEY 57
                                      9**********998 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.044
                                       HHHHT--SHH CS
                              SinI  12 AkesGlskeE 21 
                                       A+  G+s+eE
  gi|242398307|ref|YP_002993731.1| 113 ARREGISIEE 122
                                       999******9 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0    0.0003      0.41       1      49 [.       7      59 ..       7      80 .. 0.67
   2 ?    3.5   0.1     0.038        52     113     176 ..      81     138 ..      60     141 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0003
                               PRK  1 vIgvagsSGaGkttvarklekifgrekvkaaei....egdsflrldraekdle 49
                                      vI v+g  G+G+tt+ r+l    g +++ a  i         ++l+++++ +e
  gi|242398307|ref|YP_002993731.1|  7 VITVSGLAGSGTTTLCRNLSRYYGFKHIYAGLIfrqmAKEMGMSLQQFQEYAE 59
                                      89*******************99977777655555443333344444444333 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.038
                               PRK 113 lviEGlhalydervaelldlkiyvdisidlelarklqRDiaeRGrsleavldsil.rrkpdyvny 176
                                       +viEG +a++     + +dlk+++ + i+++ a+++ R     G s+e    +i+ r +++ ++y
  gi|242398307|ref|YP_002993731.1|  81 VVIEGRLAGWM---VKEADLKVWLEAPIQVR-AQRVAR---REGISIEEAFMQIAeREMQNRKRY 138
                                       56777666553...34589*******99998.555655...568999888877776888877776 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00012      0.17      19      63 ..       4      47 ..       1      86 [. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00012
                                      CSEEEEEEESTTSSHHHHHHHHCCSHCCCCCCBTEEEEEEEESXX CS
                            NB-ARC 19 qslvvalvGmgGvGKttlakqilnksdevegrFdsvawvvvsktd 63
                                      + lv++++G +G+G ttl ++  +     ++ + ++++ +++k++
  gi|242398307|ref|YP_002993731.1|  4 KCLVITVSGLAGSGTTTLCRNLSRY-YGFKHIYAGLIFRQMAKEM 47
                                      5689****************99887.7788888887777777765 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00012      0.17      24      90 ..       6      93 ..       1     166 [. 0.65

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00012
                                      EEEEEEESTTSSHHHHHHHHHHHCS----HHHHHCCHHHHHHHHHHHHHHHHHHHHHTT.................... CS
                           G-alpha 24 vkllllGqseSGKsTilkqlkllykkgfseeelatwraviqlnivrsiktilealesleselsesf............. 89
                                      + + + G ++SG +T++++l ++y  gf+     ++  +i+ ++ + + + l+++++  + + +++             
  gi|242398307|ref|YP_002993731.1|  6 LVITVSGLAGSGTTTLCRNLSRYY--GFK----HIYAGLIFRQMAKEMGMSLQQFQEYAEMH-PEIdrevdrrqieaae 77
                                      55778899****************..888....45999****************99942222.3333334555555555 PP

                                      ...............H CS
                           G-alpha 90 ...............e 90
                                                     +
  gi|242398307|ref|YP_002993731.1| 78 dcnvviegrlagwmvK 93
                                      5566666666666662 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       744  (0.041497); expected 358.6 (0.02)
Passed bias filter:                      647  (0.0360868); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 1302.26
//
Query:       gi|242398308|ref|YP_002993732.1|  [L=83]
Description: 50S ribosomal protein L14e [Thermococcus sibiricus MM 739]
Scores for complete 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-05   23.3   0.0    9.6e-05   22.8   0.0    1.3  1  Ribosomal_L14e  Ribosomal protein L14
    0.00042   20.2   3.5    0.00066   19.5   3.5    1.3  1  KOW             KOW motif
  ------ inclusion threshold ------
      0.031   14.6   0.0      0.035   14.5   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 !   22.8   0.0   1.6e-08   9.6e-05       1      38 [.      44      81 ..      44      83 .] 0.95

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.6e-08
                    Ribosomal_L14e  1 pRqaiplkrlkLtkivlklprgartgavkkawekadve 38
                                      +R  +++k+l+  + +++++rga  +avk+a+e+a+++
  gi|242398308|ref|YP_002993732.1| 44 KRRRMNIKHLEPLPEKINIERGADDEAVKAALEQAGIS 81
                                      6999*******************************985 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   3.5   1.1e-07   0.00066       2      31 ..       7      35 ..       6      37 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.1e-07
                                      TSEEEESSSTTTTCEEEEEEEETTTTEEEE CS
                               KOW  2 GdhVkVvsGphkGktGkVvkvdqhkvrVfv 31
                                      G+   V++G+ +G++ +Vv++++++ +V+v
  gi|242398308|ref|YP_002993732.1|  7 GRLAVVIAGRRAGQKVVVVDIIDKN-FVLV 35
                                      8899*********************.4444 PP

>> XisI  XisI protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   5.8e-06     0.035      29      89 ..      20      81 ..       9      83 .] 0.89

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.8e-06
                                      EEEEEEETTTTEEEEEE.EEEETTEEEEEEEEEEEEETTEEEEEEE-SS--HHHHHHTTT-- CS
                              XisI 29 eeelifDeerdhYllle.vgwekkkrvygillhldikdgkiwiqedgteegiaeeLveaGvp 89
                                      ++ +++D   ++++l++  g +k kr +  + hl+   +ki i++   +e++ + L +aG++
  gi|242398308|ref|YP_002993732.1| 20 QKVVVVDIIDKNFVLVTgAGLNKVKRRRMNIKHLEPLPEKINIERGADDEAVKAALEQAGIS 81
                                      6778999999999888648999999***********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.32s 00:00:00.79 Elapsed: 00:00:00.51
# Mc/sec: 490.05
//
Query:       gi|242398309|ref|YP_002993733.1|  [L=260]
Description: 3-oxoacyl-[acyl-carrier protein] reductase [Thermococcus sibiricus MM 739]
Scores for complete 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-69  231.9   0.0    8.6e-69  231.7   0.0    1.0  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
    4.2e-58  196.0   0.3      5e-58  195.8   0.3    1.0  1  adh_short        short chain dehydrogenase
    1.8e-12   47.5   0.1    2.6e-12   47.0   0.1    1.2  1  KR               KR domain
    4.1e-05   22.9   0.3    5.5e-05   22.4   0.3    1.1  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    0.00027   20.5   0.3    0.00065   19.2   0.3    1.8  1  Epimerase        NAD dependent epimerase/dehydratase family
    0.00028   20.8   2.4    0.00049   20.0   2.3    1.5  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
     0.0008   18.9   0.0     0.0013   18.2   0.0    1.4  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
     0.0016   17.5   0.7     0.0028   16.7   0.8    1.4  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
     0.0041   17.4   0.4     0.0082   16.4   0.4    1.4  1  TrkA_N           TrkA-N domain
     0.0068   16.4   0.3      0.012   15.6   0.3    1.4  1  ADH_zinc_N       Zinc-binding dehydrogenase
  ------ inclusion threshold ------
      0.011   16.4   0.0      0.029   15.1   0.0    1.7  1  Methyltransf_25  Methyltransferase domain
      0.019   15.2   0.0      0.031   14.4   0.0    1.3  1  Mannitol_dh      Mannitol dehydrogenase Rossmann domain
       0.03   13.4   0.1      0.043   12.9   0.1    1.2  1  RmlD_sub_bind    RmlD substrate binding domain
      0.049   14.3   0.1       0.75   10.5   0.2    2.5  2  Methyltransf_11  Methyltransferase domain
      0.063   12.6   0.2       0.46    9.8   0.0    2.4  3  THF_DHG_CYH_C    Tetrahydrofolate dehydrogenase/cyclohydrolas
      0.063   13.3   0.4       0.11   12.5   0.4    1.4  1  AdoHcyase_NAD    S-adenosyl-L-homocysteine hydrolase, NAD bin
      0.078   13.0   0.5       0.41   10.7   0.0    2.2  2  B12-binding      B12 binding domain
       0.13   12.1   0.9       0.42   10.4   0.9    1.8  1  DFP              DNA / pantothenate metabolism flavoprotein


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 !  231.7   0.0   8.6e-72   8.6e-69       4     234 .]      18     253 ..      13     253 .. 0.94

  Alignments for each domain:
  == domain 1  score: 231.7 bits;  conditional E-value: 8.6e-72
                                       TSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSEE..EE--TTSHHHHHHHHHHHHHHHSSEEEEEE--- CS
                      adh_short_C2   4 sgIGraiAkalaeeGaevvltdlneeakkrveelaeelgaev..lecDVtdeeqvealveevvekfgklDilvnnag 78 
                                       +gIG+aiA+++a++Ga+vv++ ++eea ++ ee+ ++ g +v  +++DV+dee+v+++v+++ve +g++Dilvnna+
  gi|242398309|ref|YP_002993733.1|  18 QGIGAAIAQLFAQNGAKVVIAEIDEEAGREREEMLRKEGFDVtfIKTDVADEESVKNMVKKTVELYGGVDILVNNAA 94 
                                       8**************************66666666666755445********************************* PP

                                       --EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH.HCTSC.CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHH CS
                      adh_short_C2  79 iapklkgpfletsreefdraldvnlyslfllakaalp.lmkeg.gsivnlssvgaervvpnynaygaaKaalealtr 153
                                       i+    +++ e + ee++r++ vnl++ + ++++a++ ++k+g g i+n++s++a ++ p+++ y+a+K++l+alt+
  gi|242398309|ref|YP_002993733.1|  95 IMSV--KSIFERTLEEWERVIRVNLTGPYICSRYAAEeMIKRGgGVIINIASTRAFMSEPDTEPYSASKGGLVALTH 169
                                       ****..*******************************988888899******************************* PP

                                       HHHHHHGGGTEEEEEEEE--BHCTG..GGGSTTHHHHHHHHHHHSTTSS-B-HHHHHHHHHHHC.SGGGTT--SEEE CS
                      adh_short_C2 154 ylAvelgpkgiRvNavspgpikTla..asgikgfdelleelearaplgrlgtpeevaeaalfLa.sdeasyitGqtl 227
                                       +lA +l++++iRv +vspg+i+T     s+++++++l+   ++++p+gr+g+p ++a++++fLa s++a +itG ++
  gi|242398309|ref|YP_002993733.1| 170 SLAISLAKYRIRVVCVSPGWIETSRwkKSRLRKEPNLRPIDHEQHPVGRVGDPMDIAHICAFLAdSEKAGFITGVNF 246
                                       ************************954556778999****************************78999******** PP

                                       EESTTGG CS
                      adh_short_C2 228 vvDgGlt 234
                                       vvDgG+t
  gi|242398309|ref|YP_002993733.1| 247 VVDGGMT 253
                                       *****98 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.8   0.3     5e-61     5e-58       1     191 [.       9     199 ..       9     203 .. 0.98

  Alignments for each domain:
  == domain 1  score: 195.8 bits;  conditional E-value: 5e-61
                                       SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSS CS
                         adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgk 77 
                                       kv++vtG+++GIG aia+ +a++Gakvv++++ ee+ +e  + l++eg ++++i++Dv+d+e+v+++v+k v+ +g+
  gi|242398309|ref|YP_002993733.1|   9 KVAIVTGGGQGIGAAIAQLFAQNGAKVVIAEIDEEAGREREEMLRKEGFDVTFIKTDVADEESVKNMVKKTVELYGG 85 
                                       89*************************************************************************** PP

                                       ESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHH CS
                         adh_short  78 ldvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKa 154
                                       +d+LvnNA+i  ++++ e + eewervi vNltg++ ++r ++++m+k+ +G I+n++S+ ++++ + + +YsAsK+
  gi|242398309|ref|YP_002993733.1|  86 VDILVNNAAIMSVKSIFERTLEEWERVIRVNLTGPYICSRYAAEEMIKRGGGVIINIASTRAFMSEPDTEPYSASKG 162
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHHC CS
                         adh_short 155 avagltrslakelaptgirvnavaPGlvdTdmakelr 191
                                       ++++lt+sla  la+++irv++v PG ++T   k++r
  gi|242398309|ref|YP_002993733.1| 163 GLVALTHSLAISLAKYRIRVVCVSPGWIETSRWKKSR 199
                                       ******************************9998876 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.0   0.1   2.6e-15   2.6e-12       4     154 ..      12     162 ..      10     183 .. 0.85

  Alignments for each domain:
  == domain 1  score: 47.0 bits;  conditional E-value: 2.6e-15
                                       EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS CS
                                KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeep 80 
                                       ++tGG  g+G ++a+  a++ga+ ++    +    e+ +++ + l++ g +v++++ Dv+d+++v++++++  +  +
  gi|242398309|ref|YP_002993733.1|  12 IVTGGGQGIGAAIAQLFAQNGAKVVIAEIDE----EAGREREEMLRKEGFDVTFIKTDVADEESVKNMVKKTVELYG 84 
                                       8*********************988875555....45555668999******************************* PP

                                       ---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTT....S--SEEEEEEEHHHHH--TT-HHHHHHH CS
                                KR  81 pikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelled....esldffvlfSSiagllgsagqanYaaaN 153
                                        +   ++ A ++  k + e t e++e+v++  ++G     ++ ++    +   +++ ++S  +++ ++    Y+a  
  gi|242398309|ref|YP_002993733.1|  85 GVDILVNNAAIMSVKSIFERTLEEWERVIRVNLTGPYICSRYAAEemikRGGGVIINIASTRAFMSEPDTEPYSASK 161
                                       *********************************99888888777744434456788888888888888888888766 PP

                                       H CS
                                KR 154 a 154
                                        
  gi|242398309|ref|YP_002993733.1| 162 G 162
                                       5 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.3   5.5e-08   5.5e-05       2     121 ..      12     133 ..      11     152 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 5.5e-08
                                       EEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT.... CS
                   Polysacc_synt_2   2 lvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleel.. 76 
                                       +vtG+g  iG ++  q+ +++ +k+++ e dE +  e e+ l++e       ++++ + +dv+d+e+++++++++  
  gi|242398309|ref|YP_002993733.1|  12 IVTGGGQGIGAAI-AQLFAQNGAKVVIAEIDEEAGREREEMLRKEG------FDVTFIKTDVADEESVKNMVKKTve 81 
                                       69********986.5777788899*********9999888885333......34446779*******9999997544 PP

                                       ...T-SEEEE------HHHH.HH...SHHHHHHHHHHHHHHHHHHHHHTT-S CS
                   Polysacc_synt_2  77 ...kvdvvfhaAAlKhVPlv.ee...npleaiktNvlgtenvieaaieagvk 121
                                          +vd++++ AA+  V  + e+   ++  +i+ N +g   + + a e  +k
  gi|242398309|ref|YP_002993733.1|  82 lygGVDILVNNAAIMSVKSIfERtleEWERVIRVNLTGPYICSRYAAEEMIK 133
                                       45579*********99976525422145568999999999999999888776 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.3   6.5e-07   0.00065       2     107 ..      12     128 ..      11     194 .. 0.68

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 6.5e-07
                                       EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC.......EEEE--TT-HHHHHHHHHH....H.T-S CS
                         Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledl.......elveldltdrsalerlfke....e.qpd 66 
                                       +VtG+   iG+a+++ ++++g +v+    +++a+++ + e l       ++++ d+ d++++++++k+    + ++d
  gi|242398309|ref|YP_002993733.1|  12 IVTGGGQGIGAAIAQLFAQNGAKVVIAEIDEEAGRERE-EMLrkegfdvTFIKTDVADEESVKNMVKKtvelYgGVD 87 
                                       8****999*************99766666544444332.2224679**************88877776222235789 PP

                                       EEEE--S---HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTC CS
                         Epimerase  67 avihlAavggvaassedpadfieknlqgtlnlleaarkagv 107
                                       + ++ Aa+ +v+  +e+  + +e+ ++++l+    ++++ +
  gi|242398309|ref|YP_002993733.1|  88 ILVNNAAIMSVKSIFERTLEEWERVIRVNLTGPYICSRYAA 128
                                       99999999998887777777666655555544444444444 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 !   20.0   2.3   4.9e-07   0.00049       2      62 ..      10      74 ..       9     111 .. 0.69

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 4.9e-07
                                      EEEE.--SC.CHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHH.HHH.CCTTTTSS-HHHHCC CS
                           3HCDH_N  2 vavi.GaGt.mGagiaavfasagleVvlvdiseealekalekiek.sle.klvekgklkeeevea 62
                                      va++ G G+ +Ga ia++fa++g +Vv+ +i+eea ++ +e+++k  ++  +++   ++ee+v++
  gi|242398309|ref|YP_002993733.1| 10 VAIVtGGGQgIGAAIAQLFAQNGAKVVIAEIDEEAGREREEMLRKeGFDvTFIKTDVADEESVKN 74
                                      55553666559******************************999853331223333333444443 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.3e-06    0.0013       2      96 ..      13     106 ..      12     133 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.3e-06
                                       EETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHH.... CS
                     GDP_Man_Dehyd   2 iTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaev.... 74 
                                       +TG+   iG+ +a+l+ ++g +v+ i + +++   +r e l+k +      +++++k D+ D++s++++++++    
  gi|242398309|ref|YP_002993733.1|  13 VTGGGQGIGAAIAQLFAQNGAKVV-IAEIDEEAGREREEMLRK-EG----FDVTFIKTDVADEESVKNMVKKTvely 83 
                                       8888777****************6.567777777788887764.33....379******************987666 PP

                                       .T-SEEEE--S---HHHHTTSHH CS
                     GDP_Man_Dehyd  75 .qpdevynLAAqshVdvsfekPe 96 
                                         +d  +n AA   V+  fe   
  gi|242398309|ref|YP_002993733.1|  84 gGVDILVNNAAIMSVKSIFERTL 106
                                       67899999999999998888764 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 !   16.7   0.8   2.8e-06    0.0028       1      84 [.      12     103 ..      12     134 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.8e-06
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkk.viegDvtdkdkleeale.......gvdv 69 
                                       +vtGg+  +G+a+ + + + + +  +  +D + + e  e l+k + +  +i++Dv d++++++ ++       gvd+
  gi|242398309|ref|YP_002993733.1|  12 IVTGGGQGIGAAIAQLFAQNGAKVVIAEIDEEAGREREEMLRKEGFDVtFIKTDVADEESVKNMVKktvelygGVDI 88 
                                       69***999*************9999999999999999999999888767**********999987633334446788 PP

                         3Beta_HSD  70 vihlaslvdvagklt 84 
                                       ++  a+++ v++ ++
  gi|242398309|ref|YP_002993733.1|  89 LVNNAAIMSVKSIFE 103
                                       888888877777443 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.4   8.2e-06    0.0082       2      57 ..      12      74 ..      11      84 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 8.2e-06
                                      EEES-SH.HHHHHHHHHHHTTEEEEEEESSH....HHHHHHHHTT..SEEEES-TTSHHHHHH CS
                            TrkA_N  2 iiiGlGr.vGrslaeeLseggkdvvvidkde....erveelreeg..levvvgdatdeevLee 57
                                      i+ G G+ +G ++a+ + ++g +vv+ + de    er e lr+eg  +++++ d++dee +++
  gi|242398309|ref|YP_002993733.1| 12 IVTGGGQgIGAAIAQLFAQNGAKVVIAEIDEeagrEREEMLRKEGfdVTFIKTDVADEESVKN 74
                                      566666559**********7767********4444458888999966669*********9886 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.3   1.2e-05     0.012       1      67 [.      19      94 ..      19     108 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.2e-05
                                      HHHHHHHHHHHHTT-EEEEEESSHH....HHHHHHHTTESEEEET......TTC.HHHHHHHHHTTTSSEEEEEESSC CS
                        ADH_zinc_N  1 gvGlaavqlAkalGaeviavdssee....klelakklGadeviny......kea.dlverikeltggegvdvvfecvG 67
                                      g+G a  ql +  Ga+v+ + ++ee    + e+++k G d+++        ++  ++v++  el   +gvd+ ++ ++
  gi|242398309|ref|YP_002993733.1| 19 GIGAAIAQLFAQNGAKVVIAEIDEEagreREEMLRKEGFDVTFIKtdvadeESVkNMVKKTVELY--GGVDILVNNAA 94
                                      89**********************9555555888888***9998867766433334555555555..49*99998776 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   2.9e-05     0.029       5      94 ..      17     114 ..      13     116 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.9e-05
                                       T-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBS..........SSTTTEEEEEEE CS
                   Methyltransf_25   5 GcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlp..........fedgsfDlvvss 71 
                                       G G G  +++l ++ g akv+  +i+ee+ ++ +e +++eg++v+f++ d+ d +          +  g +D+ v +
  gi|242398309|ref|YP_002993733.1|  17 GQGIGAAIAQLFAQNG-AKVVIAEIDEEAGREREEMLRKEGFDVTFIKTDVADEEsvknmvkktvELYGGVDILVNN 92 
                                       5566666666555545.*********************************955331223333333466677777776 PP

                                       STGGGSSHHHHHHHHHHHHHHEE CS
                   Methyltransf_25  72 galhhlsdedlekalkeiarvLk 94 
                                        a++ ++ +  e++l+e+ rv++
  gi|242398309|ref|YP_002993733.1|  93 AAIMSVK-SIFERTLEEWERVIR 114
                                       5555544.566788888888776 PP

>> Mannitol_dh  Mannitol dehydrogenase Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   3.1e-05     0.031      18      73 ..      23      77 ..      15     102 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.1e-05
                                      HHHHHHTT--TT-EEEEEE-STTHHHHHHHTTTT-EEEEE-SSS---EEEE--EEE CS
                       Mannitol_dh 18 yiddLlaeegldwgivevnlrevdareaLkaqdelyvviekgeeskearlvgsvna 73
                                       i +L+a++g ++ i+e+ ++ +++re++  ++++ v+ +k +++ +++ v+++ +
  gi|242398309|ref|YP_002993733.1| 23 AIAQLFAQNGAKVVIAEIDEEAGREREEMLRKEGFDVTFIK-TDVADEESVKNMVK 77
                                      5899*************************************.88888888888644 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   4.3e-05     0.043       4      91 ..      12     129 ..       9     161 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.3e-05
                                       EEESTTSHHHHHHHHHCTTTSEEEEEE-TT.....................T--TTSHHHHHHHHHHH.....--SE CS
                     RmlD_sub_bind   4 lvtGanGqlGseLakqlaeeglevlaltre.....................eldltdaeavaellkea.....kpdv 54 
                                       +vtG++  +G ++a+++a++g++v+  + +                     ++d++d+e+v++++k++       d+
  gi|242398309|ref|YP_002993733.1|  12 IVTGGGQGIGAAIAQLFAQNGAKVVIAEIDeeagrereemlrkegfdvtfiKTDVADEESVKNMVKKTvelygGVDI 88 
                                       68999999*************9998875556799*******************************987322224689 PP

                                       EEE------HHHH.H...HSHHHHHHHHTHHHHHHHHHHHH CS
                     RmlD_sub_bind  55 vvnaAAytavDka.E...seeeaayavnaeavealAeaaaa 91 
                                       +vn AA   v    E   +e e+  +vn +++   +++aa+
  gi|242398309|ref|YP_002993733.1|  89 LVNNAAIMSVKSIfErtlEEWERVIRVNLTGPYICSRYAAE 129
                                       ******99997652311145677788999998877777764 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.2   0.00075      0.75       4      89 ..      17     114 ..      14     116 .. 0.70
   2 ?   -0.1   0.0       1.5   1.5e+03      13      56 ..     174     215 ..     163     233 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00075
                                       T-TTSHHHHHHH.HTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCC..........TSS-TT-EEEEEEES CS
                   Methyltransf_11   4 GcGtGrlaeala.krgarvvgvDlskemlklakekaseeglkvefvvadaek..........lpfednsfDlvvsse 69 
                                       G G G+  ++l  ++ga+vv  ++++e+ +  +e  ++eg+ v+f++ d+ +          +    + +D+ v + 
  gi|242398309|ref|YP_002993733.1|  17 GQGIGAAIAQLFaQNGAKVVIAEIDEEAGREREEMLRKEGFDVTFIKTDVADeesvknmvkkTVELYGGVDILVNNA 93 
                                       5566666655555888*************999999999999788855555532222221111222224899999999 PP

                                       -CCC-.CCHHHHHHHHHHHEE CS
                   Methyltransf_11  70 vlhhv.edpekalkeiaRvLk 89 
                                       +++ v    e++l+e+ Rv +
  gi|242398309|ref|YP_002993733.1|  94 AIMSVkSIFERTLEEWERVIR 114
                                       999997778999999999987 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.5
                                       HHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTS CS
                   Methyltransf_11  13 alakrgarvvgvDlskemlklakekaseeglkvefvvadaeklp 56 
                                        lak+  rv  v +s+  +++++ k+s+ + + +++  d e+ p
  gi|242398309|ref|YP_002993733.1| 174 SLAKYRIRV--VCVSPGWIETSRWKKSRLRKEPNLRPIDHEQHP 215
                                       344444444..455566665554444443333345666666655 PP

>> THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00046      0.46      33      69 ..       5      41 ..       2      53 .. 0.89
   2 ?   -2.3   0.0       2.5   2.5e+03     112     112 ..     147     147 ..     127     186 .. 0.54
   3 ?   -1.3   0.0       1.2   1.2e+03     127     149 ..     235     258 ..     229     260 .] 0.81

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00046
                                      --TT-EEEEE---TTTHHHHHHHHHCTT-EEEEE-TT CS
                     THF_DHG_CYH_C 33 elegkkvvvvGrsnivgkplallLleknatVtvchsk 69
                                      +le+k ++v G ++ +g ++a+l+++++a V +++  
  gi|242398309|ref|YP_002993733.1|  5 NLEEKVAIVTGGGQGIGAAIAQLFAQNGAKVVIAEID 41
                                      688999*************************998765 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.5
                                       C CS
                     THF_DHG_CYH_C 112 v 112
                                        
  gi|242398309|ref|YP_002993733.1| 147 A 147
                                       2 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.2
                                       CTTSSEE--TTTSC.HHHHHHHHH CS
                     THF_DHG_CYH_C 127 kevasaitPvpgGV.GpmTvamll 149
                                       +e+a++it v   V G mT+ m+ 
  gi|242398309|ref|YP_002993733.1| 235 SEKAGFITGVNFVVdGGMTIKMIY 258
                                       688999999999988899999986 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 ?   12.5   0.4   0.00011      0.11      23      74 ..       8      64 ..       4     100 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
                                      TSEEEEE--SH.HHHHHHHHHHHCT-EEEEE-S-HHHHHHH.HC...TT-EE--HHH CS
                     AdoHcyase_NAD 23 GkvavvaGyGd.vGkGcaaslkglGarvivtevdPicalqa.am...eGfevvtlee 74
                                       kva+v+G G+ +G   a+ + + Ga+v+++e+d  +      m   eGf+v+ +++
  gi|242398309|ref|YP_002993733.1|  8 EKVAIVTGGGQgIGAAIAQLFAQNGAKVVIAEIDEEAGREReEMlrkEGFDVTFIKT 64
                                      699****99965899999999*************86654321223337777777653 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1      0.96   9.5e+02      83     112 ..      12      39 ..       6      47 .. 0.53
   2 ?   10.7   0.0   0.00041      0.41      22      82 ..      50     113 ..      49     140 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.96
                       B12-binding  83 kvvvGGahpsldpeetleaklgiddvvvge 112
                                       +v  GG +  ++ +++ + ++g + vv+ e
  gi|242398309|ref|YP_002993733.1|  12 IVTGGGQGIGAAIAQLFA-QNG-AKVVIAE 39 
                                       455555555555555443.366.4444443 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00041
                       B12-binding  22 aalrdagfeVqllganvenedivaairaekpdvvgl.Sal.ltsqleavkelvel.lkrirprv 82 
                                       ++lr++gf+V+++  +v +e+ v+++ +  +++ g   +l  ++ +  vk + e+ l++  + +
  gi|242398309|ref|YP_002993733.1|  50 EMLRKEGFDVTFIKTDVADEESVKNMVKKTVELYGGvDILvNNAAIMSVKSIFERtLEEWERVI 113
                                       69**********************9999999884431332145555566666666544444444 PP

>> DFP  DNA / pantothenate metabolism flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.9   0.00042      0.42      31      92 ..      20      95 ..      13     104 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00042
                                      HHHHHHHHHHHTT-EEEEEE-S-S..S--.............-TT-EEEE--SHHHHHHHHHHHHTT-SEEEE---S CS
                               DFP 31 mGyalAeaaaarGaeVtlvsgpvs..let.............pegvevvkvesaeemleaveealkeadivimaAAv 92
                                       G+a+A+ +a+ Ga+V +     +    +               +++v + es+++m +++ e +   di++  AA+
  gi|242398309|ref|YP_002993733.1| 20 IGAAIAQLFAQNGAKVVIAEIDEEagR-EreemlrkegfdvtFIKTDVADEESVKNMVKKTVELYGGVDILVNNAAI 95
                                      589*************99865543121.1223344333322112345666788888999999999999********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       806  (0.0449551); expected 358.6 (0.02)
Passed bias filter:                      683  (0.0380947); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1717.01
//
Query:       gi|242398310|ref|YP_002993734.1|  [L=234]
Description: short-chain alcohol dehydrogenase [Thermococcus sibiricus MM 739]
Scores for 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-41  139.8   0.0    8.7e-41  139.5   0.0    1.0  1  adh_short       short chain dehydrogenase
    3.5e-31  108.6   0.0    5.7e-31  107.9   0.0    1.3  1  adh_short_C2    Enoyl-(Acyl carrier protein) reductase
    5.4e-14   52.5   0.1    7.2e-14   52.1   0.1    1.1  1  KR              KR domain
    0.00014   21.8   0.3    0.00016   21.6   0.3    1.3  1  NAD_binding_10  NAD(P)H-binding
    0.00032   20.2   0.1    0.00053   19.5   0.1    1.4  1  Epimerase       NAD dependent epimerase/dehydratase family
  ------ inclusion threshold ------
      0.015   15.4   0.1      0.047   13.8   0.1    1.8  1  Exog_C          Endo/exonuclease (EXOG) C-terminal domain
      0.044   13.3   0.1       0.13   11.8   0.2    1.7  2  NmrA            NmrA-like family
       0.11   13.1   0.1       0.19   12.3   0.1    1.5  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
       0.15    9.9   0.0       0.17    9.7   0.0    1.0  1  Spheroidin      Entomopoxvirus spheroidin protein
       0.21   11.7   3.6        9.6    6.4   0.1    3.7  4  HHH_2           Helix-hairpin-helix motif


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 !  139.5   0.0   4.8e-44   8.7e-41       1     186 [.       2     185 ..       2     192 .. 0.97

  Alignments for each domain:
  == domain 1  score: 139.5 bits;  conditional E-value: 4.8e-44
                                       SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT.TSEEEEEE-TTTSHHHHHHHHHHHHHHHS CS
                         adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkee.gakalaiqvDvtdreevealvekavkklg 76 
                                       kv+++tGas+GIG aia++la++G+ +++ +rs ++le++a el +e g ++++ ++Dv+++e+ve++ +k+ +++g
  gi|242398310|ref|YP_002993734.1|   2 KVAVITGASRGIGEAIARALARDGYALALGARSVDRLEKIAHELMQEqGVEVFYHHLDVSKAESVEEFSKKVLERFG 78 
                                       89******************************************9999***************************** PP

                                       SESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHH CS
                         adh_short  77 kldvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsK 153
                                        +dv+v+NAG+  ++  +elseee+ ++ievNl gv  + +a+l+  lk+ +G    ++S ++    + +  Y ++K
  gi|242398310|ref|YP_002993734.1|  79 DVDVVVANAGLGYFKRLEELSEEEFHEMIEVNLLGVWRTLKAFLDS-LKRTGGLALVTTSDVSARLIPYGGGYVSTK 154
                                       **********************************************.66**************************** PP

                                       HHHHHHHHHHHHHHGGGTEEEEEEEESSBSSHH CS
                         adh_short 154 aavagltrslakelaptgirvnavaPGlvdTdm 186
                                       +a ++l+r+++ e  +  +r   + PG+vdT +
  gi|242398310|ref|YP_002993734.1| 155 WAARALVRTFQIENPD--VRFFELRPGAVDTYF 185
                                       *********9988665..9***********965 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 !  107.9   0.0   3.2e-34   5.7e-31       1     181 [.       8     188 ..       8     214 .. 0.91

  Alignments for each domain:
  == domain 1  score: 107.9 bits;  conditional E-value: 3.2e-34
                                       TTTTSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSEE..EE--TTSHHHHHHHHHHHHHHHSSEEEEE CS
                      adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgaev..lecDVtdeeqvealveevvekfgklDilv 74 
                                       Ga +gIG+aiA+ala+ G+ ++l  ++ ++ +k ++el +e g ev   ++DV++ e+ve++ ++v e+fg +D++v
  gi|242398310|ref|YP_002993734.1|   8 GASRGIGEAIARALARDGYALALGARSVDRlEKIAHELMQEQGVEVfyHHLDVSKAESVEEFSKKVLERFGDVDVVV 84 
                                       999*************************999************996689**************************** PP

                                       E-----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH.HCTSCCEEEEEEEGGGTSBSTTTTHHHHHHHHHHH CS
                      adh_short_C2  75 nnagiapklkgpfletsreefdraldvnlyslfllakaalp.lmkeggsivnlssvgaervvpnynaygaaKaalea 150
                                        nag      ++++e+s+eef+++++vnl ++++++ka+l  l + gg  + ++s  + r +p    y  +K a  a
  gi|242398310|ref|YP_002993734.1|  85 ANAGLGYF--KRLEELSEEEFHEMIEVNLLGVWRTLKAFLDsLKRTGGLALVTTSDVSARLIPYGGGYVSTKWAARA 159
                                       *******9..*******************************555556889999999999****************** PP

                                       HHHHHHHHHGGGTEEEEEEEE--BHCTGGGG CS
                      adh_short_C2 151 ltrylAvelgpkgiRvNavspgpikTlaasg 181
                                       l+r++  e     +R     pg+++T    +
  gi|242398310|ref|YP_002993734.1| 160 LVRTFQIENP--DVRFFELRPGAVDTYFGGS 188
                                       ***9866654..5999999999999976554 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.1   0.1     4e-17   7.2e-14       4     125 ..       5     123 ..       3     153 .. 0.90

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 4e-17
                                       EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS CS
                                KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeep 80 
                                       +itG+  g+G ++ar la++g   l+l +Rs  +d+ +k   + ++++g+ev + ++Dvs++++ve+  +++ ++++
  gi|242398310|ref|YP_002993734.1|   5 VITGASRGIGEAIARALARDGY-ALALGARS--VDRLEKIAHELMQEQGVEVFYHHLDVSKAESVEEFSKKVLERFG 78 
                                       8********************6.59999999..666666677888999***************************** PP

                                       ---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTT CS
                                KR  81 pikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelled 125
                                        +  v+  Ag+   k lee+++e+++++++  + G+w   +++ d
  gi|242398310|ref|YP_002993734.1|  79 DVDVVVANAGLGYFKRLEELSEEEFHEMIEVNLLGVWRTLKAFLD 123
                                       *************************************87777765 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.3   8.8e-08   0.00016       1      71 [.       8      90 ..       8     207 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 8.8e-08
                                      TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHH....CTTTCEEEE..--TT-CCHHHHHHT.......T-SEEEE CS
                    NAD_binding_10  1 GAtGkvGrllvkellargghevtalvRnpeklaele....aeeglevve..gdvtdvedlaealk.......gadaVvs 66
                                      GA+ ++G ++++ l+++ g+++ + +R+ ++l++++    +e+g+ev+   +dv+++e+++e  k       ++d+Vv+
  gi|242398310|ref|YP_002993734.1|  8 GASRGIGEAIARALARD-GYALALGARSVDRLEKIAhelmQEQGVEVFYhhLDVSKAESVEEFSKkvlerfgDVDVVVA 85
                                      9***********99999.6*********999986654455889***986559****99999988888888889999999 PP

                                      S---T CS
                    NAD_binding_10 67 alggg 71
                                      ++g g
  gi|242398310|ref|YP_002993734.1| 86 NAGLG 90
                                      98644 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.1   2.9e-07   0.00053       2     112 ..       5     121 ..       4     182 .. 0.66

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 2.9e-07
                                       EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC.........EEEE--TT-HHHHHHHHHH....H.T CS
                         Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledl.........elveldltdrsalerlfke....e.q 64 
                                       ++tGa+  iG a+++al++ gy +   +r    ++ +++++            ++ld+ +++++e++ k+    + +
  gi|242398310|ref|YP_002993734.1|   5 VITGASRGIGEAIARALARDGYALALGARS--VDRLEKIAHElmqeqgvevFYHHLDVSKAESVEEFSKKvlerFgD 79 
                                       79*******************996665555..2333333333567889**999*********999886652221567 PP

                                       -SEEEE--S---HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEE CS
                         Epimerase  65 pdavihlAavggvaassedpadfieknlqgtlnlleaarkagvkrllf 112
                                       +d+v+  A+ g  ++  e  ++ ++   ++ +nll + r+ ++    f
  gi|242398310|ref|YP_002993734.1|  80 VDVVVANAGLGYFKRLEELSEEEFH--EMIEVNLLGVWRTLKA----F 121
                                       9999999998877765444443222..2444455554444444....3 PP

>> Exog_C  Endo/exonuclease (EXOG) C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   2.6e-05     0.047      17      37 ..      31      52 ..      30      53 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.6e-05
                            Exog_C 17 sArtlkRLekvmkeL.keagie 37
                                      +Ar++ RLek+  eL +e+g+e
  gi|242398310|ref|YP_002993734.1| 31 GARSVDRLEKIAHELmQEQGVE 52
                                      8*************84677776 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   7.3e-05      0.13       2      65 ..       5      73 ..       3      97 .. 0.79
   2 ?   -1.9   0.0       1.1     2e+03     171     204 ..     189     222 ..     182     229 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.3e-05
                                      EESSTTSHHHHHHHHHHHHHT-EEEEEES-S...-SHHHHHHHHSTTEEE..ES-TT-HHHHHHHHTT- CS
                              NmrA  2 lviGaTGrqGksvvrallkaghkvralvRdt...kselakslkeaGvelv..kgdlddkeslvealkgv 65
                                      +++Ga+  +G++++ral+++g+      R +   ++ + + ++e+Gve+   + d+   es++e  k+v
  gi|242398310|ref|YP_002993734.1|  5 VITGASRGIGEAIARALARDGYALALGARSVdrlEKIAHELMQEQGVEVFyhHLDVSKAESVEEFSKKV 73
                                      57899999*****************99**998755556666799*****96566677777777666554 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.1
                                       ESS-TTS-EE-HHHHHHHHHHHHHHHHHHHTTEE CS
                              NmrA 171 gpgnpkavlldaeeDiGafvikilkdprklkgkr 204
                                       +pg+pk++   + ++i+++v  +lk p+++ ++ 
  gi|242398310|ref|YP_002993734.1| 189 KPGKPKEKGYLKPDEIAEAVRCLLKLPKDVRVEE 222
                                       6889999988899999999999988888876655 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 ?   12.3   0.1   0.00011      0.19       2      48 ..       3      51 ..       2      87 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00011
                                      EEEE.TTSH.HHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC....- CS
                     F420_oxidored  2 igii.GaGn.mgealasgllaagaqpheivvansrnpekaeelaeelg....v 48
                                      +++i Ga + +gea+a+ l++ g   + + ++  r+ +++e++a el     v
  gi|242398310|ref|YP_002993734.1|  3 VAVItGASRgIGEAIARALARDG---YALALG-ARSVDRLEKIAHELMqeqgV 51
                                      67776655449************...****88.***********998755442 PP

>> Spheroidin  Entomopoxvirus spheroidin protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   9.7e-05      0.17     213     287 ..      52     125 ..      25     144 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 9.7e-05
                        Spheroidin 213 niavsflsidyevsesaqkkllksLlkkyGefdvynaDtGlvYaknLs.ikenk.tlviqveklpvklkvkaylkde 287
                                        +    l+     +es++ ++ k++l+++G  dv+ a+ Gl Y k L+ + e++    i v+ l+v    ka l  +
  gi|242398310|ref|YP_002993734.1|  52 EVFYHHLD--VSKAESVE-EFSKKVLERFGDVDVVVANAGLGYFKRLEeLSEEEfHEMIEVNLLGVWRTLKAFLDSL 125
                                       43333333..33444443.4567778******************998624433313489999999999999887654 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.2     0.031        56       9      22 ..      11      24 ..       9      49 .. 0.80
   2 ?   -1.7   0.0       1.8   3.2e+03      14      27 ..      68      81 ..      66      88 .. 0.80
   3 ?    6.4   0.1    0.0053       9.6      21      42 ..      90     111 ..      79     114 .. 0.84
   4 ?   -3.2   0.0       5.4   9.6e+03      15      24 ..     156     165 ..     155     166 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.031
                             HHH_2  9 rhVGektAklLakr 22
                                      r +Ge+ A++La+ 
  gi|242398310|ref|YP_002993734.1| 11 RGIGEAIARALARD 24
                                      78999999999985 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.8
                             HHH_2 14 ktAklLakrFksld 27
                                      + +k+  +rF+++d
  gi|242398310|ref|YP_002993734.1| 68 EFSKKVLERFGDVD 81
                                      56789999999998 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0053
                             HHH_2  21 krFksldaLkkasleeLlevdd 42 
                                         Fk l++L++ ++ e++ev+ 
  gi|242398310|ref|YP_002993734.1|  90 GYFKRLEELSEEEFHEMIEVNL 111
                                       68*****************985 PP

  == domain 4  score: -3.2 bits;  conditional E-value: 5.4
                             HHH_2  15 tAklLakrFk 24 
                                       +A++L++ F+
  gi|242398310|ref|YP_002993734.1| 156 AARALVRTFQ 165
                                       6999999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       632  (0.0352502); expected 358.6 (0.02)
Passed bias filter:                      592  (0.0330191); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.60u 0.34s 00:00:00.94 Elapsed: 00:00:00.52
# Mc/sec: 1364.92
//
Query:       gi|242398311|ref|YP_002993735.1|  [L=1058]
Description: Cellobiose phosphorylase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1058 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.88u 0.33s 00:00:01.21 Elapsed: 00:00:00.55
# Mc/sec: 5799.64
//
Query:       gi|242398312|ref|YP_002993736.1|  [L=319]
Description: Laminarinase (endo-beta-1,3-glucanase) (extracellular) [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-40  138.1   0.3    3.3e-40  137.4   0.3    1.3  1  Glyco_hydro_16  Glycosyl hydrolases family 16
      4e-21   75.0   3.2    1.7e-10   39.9   0.9    2.0  2  SKN1            Beta-glucan synthesis-associated protein (SKN


Domain annotation for each model (and alignments):
>> Glyco_hydro_16  Glycosyl hydrolases family 16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.4   0.3   3.6e-44   3.3e-40       9     177 .]     110     312 ..     103     312 .. 0.86

  Alignments for each domain:
  == domain 1  score: 137.4 bits;  conditional E-value: 3.6e-44
                                       E-GGGEEEETTSEEEEEEEE...........EEEEEEEECCEESS...EEEEEEEE---STTEEEEEEE..ET.GG. CS
                    Glyco_hydro_16   9 wsksavsvengetltltldk...........esgsrikskksfly...GkvearikaaksaGvvtafyl..ss.ed. 67 
                                       +s ++ ++eng tl+++++k           +++sr+k++ +++     ++ea++k+++++G+++af++  ++  + 
  gi|242398312|ref|YP_002993736.1| 110 YSPNNTRIENG-TLVIEARKewvtdeygtymYTSSRLKTQGKVEVeppARIEAKMKLPNGKGLWPAFWMlgTNiGEv 185
                                       56788899999.***************************7777763336********************77554447 PP

                                       .TSTTEEEEE.EEETT-TTEEEEEEEBTTBSG.E....EEEEET.SS-TTTS-EEEEEEEETTEEEEEETTEEEEEE CS
                    Glyco_hydro_16  68 .ekahdEiDi.EflGndtgkvqtnvygkGkgk.r....ekrlsl.wfdptedfHtYaieWtpdkikfyVDgkpvrtl 136
                                        +++++EiDi Ef+G+++++v+ +v+g+G+++ r    +++l+  + d+tedfH ++ieW pd+i++yVDgk+++++
  gi|242398312|ref|YP_002993736.1| 186 gWPQCGEIDImEFVGHEPRTVHGTVHGPGYSGgRsitnSYTLPEgVPDFTEDFHVFTIEWFPDRIEWYVDGKLYHVV 262
                                       9*****************************99625545666655789****************************** PP

                                       ESSHHH.HT....-..-EESEEEEEEE.EEEBS.HHHSSE-.EEEEEEEE CS
                    Glyco_hydro_16 137 tkkeae.ev...ky..Pqftpmkvavs.lwpgs.dwateqg.kvkidwar 177
                                       tk++ e ++    +  P++ + ++av+  wpg  +  t++  ++ +d++r
  gi|242398312|ref|YP_002993736.1| 263 TKEQVEtMDnewVFdkPFYIIINLAVGgNWPGVpNARTKFPaRMYVDYVR 312
                                       ****996557554699****************964444443599999986 PP

>> SKN1  Beta-glucan synthesis-associated protein (SKN1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.9   0.9   1.9e-14   1.7e-10      92     230 ..      43     187 ..       8     192 .. 0.80
   2 !   35.6   0.1     4e-13   3.6e-09     363     450 ..     236     315 ..     209     319 .] 0.88

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 1.9e-14
                              SKN1  92 airtslidpdtPesaltrksk.dgkklkLvfsDefn..kegrtfydGdDqfwtavdlhYaatkdlewYdpdavttad 165
                                       +  ++  ++ t ++  t++ + +g++++L++ D+f+  k +  ++  +    +a+ +  ++  +le+Y+p+ +  ++
  gi|242398312|ref|YP_002993736.1|  43 KSPSTQTNSTTETTYITKTIEeNGRTWELIWYDDFEgeKVNENYWTFEIGNGHAYGIPGWGNYELEYYSPNNTRIEN 119
                                       444455566666666666666479***********72245778888888888999999******************* PP

                              SKN1 166 GtLelrldafknhd....LnyrsGmlqsWnklCft.ggalevsvsLpgkgevsGlWPglWtmG.nLgRpGy 230
                                       GtL ++  +    d     +y s  l++  k+ ++  +++e+ ++Lp+    +GlWP++W++G n+g  G+
  gi|242398312|ref|YP_002993736.1| 120 GTLVIEARKEWVTDeygtYMYTSSRLKTQGKVEVEpPARIEAKMKLPNG---KGLWPAFWMLGtNIGEVGW 187
                                       ******998877663333689***********9997899*******985...7*********988888887 PP

  == domain 2  score: 35.6 bits;  conditional E-value: 4e-13
                              SKN1 363 kkfqkygleykpnddekgyitWfvgdektwtlkakalgpngnigqRliseepmsiilnlgisnnfaaidwkelefpa 439
                                       ++f+ +++e+ p+      i+W+v+ +    ++++ ++    +++  +   p +ii+nl++  n+  +  ++ +fpa
  gi|242398312|ref|YP_002993736.1| 236 EDFHVFTIEWFPD-----RIEWYVDGKLYHVVTKEQVE---TMDNEWVFDKPFYIIINLAVGGNWPGVPNARTKFPA 304
                                       6899999999985.....8*******999999888776...5677899***************************** PP

                              SKN1 440 tlriDyvRlyq 450
                                        +++DyvR+y 
  gi|242398312|ref|YP_002993736.1| 305 RMYVDYVRVYR 315
                                       **********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 2033.69
//
Query:       gi|242398313|ref|YP_002993737.1|  [L=121]
Description: nucleic acid-binding protein, containing PIN domain [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); 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 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 891.98
//
Query:       gi|242398314|ref|YP_002993738.1|  [L=71]
Description: hypothetical protein TSIB_0323 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0043   16.7   0.1     0.0046   16.6   0.1    1.0  1  IP_trans      Phosphatidylinositol transfer protein
     0.0049   17.6   5.6     0.0061   17.3   5.6    1.2  1  VAPB_antitox  Putative antitoxin
     0.0087   16.0   1.7       0.13   12.2   0.0    2.6  2  RHH_1         Ribbon-helix-helix protein, copG family
  ------ inclusion threshold ------
      0.089   12.4   2.6       0.07   12.7   1.2    1.5  2  ArsR          ArsR transcriptional regulator


Domain annotation for each model (and alignments):
>> IP_trans  Phosphatidylinositol transfer protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1     1e-06    0.0046      80     135 ..       3      58 ..       1      69 [. 0.88

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1e-06
                                       TTEEEEEEEEETTEEEEEEEETTTGGGEEEEEEEEEESSSS--SSTT---HHHHTT CS
                          IP_trans  80 altveekawnaypytkTvytnplmkekfsikietvhkedngtqeNvfnlskeelkk 135
                                        + v+e+ wn+  + k ++  +   + + i +et+h  + g++ + ++l++ee +k
  gi|242398314|ref|YP_002993738.1|   3 TIAVDEETWNTIKKLKAKLDAKSYDQVLRILLETWHTANLGKKIEKISLDDEESEK 58 
                                       6789****************99667**********************999999554 PP

>> VAPB_antitox  Putative antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   5.6   1.4e-06    0.0061       1      68 [.       2      70 ..       2      71 .] 0.83

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.4e-06
                      VAPB_antitox  1 KtIsIsdevYekLkklKr..egeSFsdvIerLlekkkkgkkkellelfgilseeeadeiekaskelrkef 68
                                      KtI +++e+ +  kklK   + +S++ v++ Lle   + +  +  e +  l++ee ++  +++k+l++++
  gi|242398314|ref|YP_002993738.1|  2 KTIAVDEETWNTIKKLKAklDAKSYDQVLRILLETWHTANLGKKIEKIS-LDDEESEKALDILKKLKEWE 70
                                      9**************998789*************777766544444443.69999999999999999985 PP

>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0     3e-05      0.13       3      37 ..       3      38 ..       3      39 .. 0.95
   2 ?    1.5   1.3     0.071   3.2e+02       8      20 ..      57      69 ..      48      71 .] 0.56

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3e-05
                                      EEEEEHHHHHHHHHHHHHHT.SSHHHHHHHHHHHHH CS
                             RHH_1  3 sirldeellerLdelarrrg.rSrSelIReAlreyl 37
                                      +i +dee+  ++ +l+++++ +S  +++R +l+ ++
  gi|242398314|ref|YP_002993738.1|  3 TIAVDEETWNTIKKLKAKLDaKSYDQVLRILLETWH 38
                                      89******************************9986 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.071
                                      HHHHHHHHHHHHH CS
                             RHH_1  8 eellerLdelarr 20
                                      e+ l+ L +l+++
  gi|242398314|ref|YP_002993738.1| 57 EKALDILKKLKEW 69
                                      4555666666665 PP

>> ArsR  ArsR transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.4    0.0017       7.8      30      52 ..      11      34 ..       5      48 .. 0.53
   2 ?   12.7   1.2   1.6e-05      0.07      14      55 ..      21      67 ..      14      71 .] 0.79

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0017
                              ArsR 30 Wlteeeleeklgee.veealklLk 52
                                      W t ++l+ kl+++  ++ l++L 
  gi|242398314|ref|YP_002993738.1| 11 WNTIKKLKAKLDAKsYDQVLRILL 34
                                      666666666666554444554442 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 1.6e-05
                              ArsR 14 fdsetkkkvyeelskeWlte...eeleeklgee..veealklLkkik 55
                                      +d +++ +v++ l+++W t+   +++e+   ++  +e+al++Lkk k
  gi|242398314|ref|YP_002993738.1| 21 LDAKSYDQVLRILLETWHTAnlgKKIEKISLDDeeSEKALDILKKLK 67
                                      578999*************833347877654333699********87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1019  (0.0568353); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); 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: 0.47u 0.32s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 445.57
//
Query:       gi|242398315|ref|YP_002993739.1|  [L=501]
Description: Beta-galactosidase [Thermococcus sibiricus MM 739]
Scores for 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-66  223.3   2.3    1.2e-56  192.0   0.8    2.7  2  Glyco_hydro_1  Glycosyl hydrolase family 1


Domain annotation for each model (and alignments):
>> Glyco_hydro_1  Glycosyl hydrolase family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.0   1.2e-11   2.1e-07       7      88 ..       3      90 ..       1     101 [. 0.83
   2 !  192.0   0.8   6.9e-61   1.2e-56      92     452 ..     123     486 ..     115     487 .. 0.84

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 1.2e-11
                                      TT-EEEEE--HHHHH--..TTSTT---BHHHHHHHHGGGSTTS--.-SS...TT-HHHHHHHHHHHHHHTT-SEEEEE- CS
                     Glyco_hydro_1  7 edFlwgaataayqiEGa..wnedGkgesiwDtftetpgkvlegsn.gdv...acdsYhrykeDvallkelgvkayrfSi 79
                                      ++Flwg+a + +q E +  +n     +s w ++ + p++  +g   gd+   +++ Y+ y+ D  l k+lg +ay + +
  gi|242398315|ref|YP_002993739.1|  3 KEFLWGVAQSGFQFEMGdrFNRHLDIRSDWWKWVRDPTNLKKGLVsGDLpeeGINNYELYPIDHLLAKKLGANAYSLNL 81
                                      79*************77335666678899999*99999987765544432229************************** PP

                                      -HHHHSTTS CS
                     Glyco_hydro_1 80 sWpRilPkG 88
                                       W+Ri+P  
  gi|242398315|ref|YP_002993739.1| 82 EWSRIFPCA 90
                                      *******76 PP

  == domain 2  score: 192.0 bits;  conditional E-value: 6.9e-61
                                       --HHHHHHHHHHHHHHHHTT-EEEEEEESS--BHHHHH..H..........-GGG-SHHHHHHHHHHHHHHHHHTTT CS
                     Glyco_hydro_1  92 inekGlayYerLidelleagieplvTlyHwdlPqaLqd..e..........Ggwenrsiidafkeyaevvfkrfgdk 156
                                        n + +++Y +++ +l++ g + ++T+ H+  P +L+d  e           gw n++ i +f+++a+++  +fg+ 
  gi|242398315|ref|YP_002993739.1| 123 ANIEEVEHYMSVLSNLKKMGFKVFITIVHYTHPLWLHDpiEsretnlknerNGWVNQRSIIEFTKFAAYLAYKFGHL 199
                                       577889****************************9986422333333333379**9999999*************** PP

                                       --EEEEEE-HHHHHHHHHT..SS-STT-S-TTTHHHHHHHHHHHHHHHHHHHHHHHTTT-EEEEE.EEEEEEEESSS CS
                     Glyco_hydro_1 157 vklwlTfnEpnvvallgyl..tgefaPgkkdleaayeaaHnlllaharavklykevaqkgkigiv.lnlslaeplse 230
                                       v++w+TfnEp+v++ lgyl  ++ f+Pg+ + e+a +a+ n++ ahara++++k+  +k+ +gi+  n+ + +p+++
  gi|242398315|ref|YP_002993739.1| 200 VDMWTTFNEPMVMVELGYLapYSGFPPGVISPENAKKAIINIINAHARAYEAIKNF-SKAPVGIIaNNVGTSYPKDP 275
                                       ******************944579****9999*********************986.578888751578999***** PP

                                       SHHHH.HHHHHHHHHHTHHHHHHHHHSS--HHHHHHHGGG..S----HHHHHHHTT--SEEEEEEEEEEEEEE--.. CS
                     Glyco_hydro_1 231 seedk.eaaeraleflngwfldpvvkGdYpeemkellrergalpeiteedkellkgkadflglnyYtsrlvknkese 306
                                       +++++ +aae  + f++g  l+++ +G+ ++e       +   p++         +  d++g+ yY++++++++e +
  gi|242398315|ref|YP_002993739.1| 276 NNPKDvKAAEMVDFFHSGLLLKALTEGELNAEFDMETMLK--VPHL---------KRLDWIGMTYYSREVITHSEPK 341
                                       999888**********************998764332222..3333.........357**************99955 PP

                                       .-STT---SSGGGGG-.........SBSS-B-SSSS-B-HHHHHHHHHHHHHTS----EEEEE----EE-BSSSHHH CS
                     Glyco_hydro_1 307 easlskteekkleeev.........dpslpktdigwiiepeglrkllellkkeYqklpiyiteNGlgakdeieegkv 374
                                        +++  t+ k++                 p +digw+++peg+++ ++   + Y+ +piyi eNG+++++       
  gi|242398315|ref|YP_002993739.1| 342 FKEIPITAFKGVPGYGyscppnessLDGHPVSDIGWEVYPEGIYNSIKAA-SSYG-KPIYIMENGIADSK------- 409
                                       5555544444443322567777554445789*****************97.89**.9*********9877....... PP

                                       --HHHHHHHHHHHHHHHHHHHTT--EEEEEEE-SB----GGGTTSEE--SEEEETTTTTEEEE.-HHHHHHHHHHH- CS
                     Glyco_hydro_1 375 eDdkRidYlkehlnevkkaiedgvdlkgYvawsllDnfewaegyskrfGlvyvdrnetleRtp.kkSakwykeviek 450
                                        D  R +++++h+  ++kaie+g d++gY+ w+l+Dn+ewa g+++rfGl+ vd   t+eR+p k+S+  y+e+ie+
  gi|242398315|ref|YP_002993739.1| 410 -DLLRPYFIASHIDYIEKAIEEGFDVRGYFHWALTDNYEWAMGFRMRFGLYVVD-MITKERIPrKESVGVYREIIEN 484
                                       .789**************************************************.88888886368*********99 PP

                                       SS CS
                     Glyco_hydro_1 451 ng 452
                                       +g
  gi|242398315|ref|YP_002993739.1| 485 DG 486
                                       76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (501 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); 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: 0.69u 0.29s 00:00:00.98 Elapsed: 00:00:00.50
# Mc/sec: 2991.13
//
Query:       gi|242398316|ref|YP_002993740.1|  [L=491]
Description: beta-agarase (extracellular) [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0003   20.4   0.3    0.00082   19.0   0.0    1.8  2  Glyco_hydro_cc  Glycosyl hydrolase catalytic core
  ------ inclusion threshold ------
      0.032   13.5   0.0        2.8    7.1   0.1    2.3  2  Glyco_hydro_72  Glucanosyltransferase


Domain annotation for each model (and alignments):
>> Glyco_hydro_cc  Glycosyl hydrolase catalytic core
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1      0.26   2.3e+03     178     205 ..      32      59 ..      26      67 .. 0.77
   2 !   19.0   0.0   9.1e-08   0.00082     137     212 ..     355     443 ..     348     466 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.26
                    Glyco_hydro_cc 178 esgdasqeetkeflnevlawldsqeyVe 205
                                       +++++++++t++++++++++ +s+e ++
  gi|242398316|ref|YP_002993740.1|  32 STSKTTEKTTTTYIETSTTTTQSEERIK 59 
                                       4566777779999999999999988876 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 9.1e-08
                    Glyco_hydro_cc 137 kvdflavHwYkgdfeelkehieelheaynkpiWvTEfalqs...........esgdasqeetkeflnevlawldsqe 202
                                        vd++++ +Y +     ke+++ +h+ +++pi +TEf+ +              + ++q+e +e+ ++ ++ + + +
  gi|242398316|ref|YP_002993740.1| 355 YVDVISLNLY-NFEVAPKEYLDHIHNITGRPIMITEFSFRAmdsglpntrgaGITVQTQKERAEYTRKFIESFMKLP 430
                                       6899999999.3344579********************998999*9999988888999999**************** PP

                    Glyco_hydro_cc 203 yVeryawfg...f 212
                                       y   y wf    +
  gi|242398316|ref|YP_002993740.1| 431 YAVGYHWFKwsdQ 443
                                       ********94321 PP

>> Glyco_hydro_72  Glucanosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0    0.0032        28     138     200 ..      22      87 ..      18     102 .. 0.85
   2 ?    7.1   0.1   0.00031       2.8     280     314 ..     449     483 ..     447     484 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.0032
                                       EEEEEEESSS-STT-GG..GHHHHHHHHHHHHHHHHHSSS----EEEEE-.--TTTHHHHHHHTTB CS
                    Glyco_hydro_72 138 lgffaGnevvndksnta..asayvkavvrdvkeyikkkkerkiPvGysaa.ddaelrvelaeylaC 200
                                       lg + Gn+ + ++++t+  +++y+   + ++++  + k + + P Gys     +elrve + y++ 
  gi|242398316|ref|YP_002993740.1|  22 LGCLGGNQTTSTSKTTEktTTTYIETSTTTTQSEERIKPQVEFPEGYSKFgGWKELRVESSGYFRV 87 
                                       7888999999887776655899********9999999999********851578999999999976 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.00031
                                       SB--SSS--SEEE-TTS-EEE-THHHHHHHHHHH- CS
                    Glyco_hydro_72 280 yseeannyGlvkiddddvkkllkdfenlkseykki 314
                                       +  e++nyGlv+i+d+  +++   fe+l++++++i
  gi|242398316|ref|YP_002993740.1| 449 FDGENSNYGLVNIKDEPYEEMVIMFEELNRKLEEI 483
                                       56799************************999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (491 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       648  (0.0361426); expected 358.6 (0.02)
Passed bias filter:                      559  (0.0311785); 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: 0.66u 0.27s 00:00:00.93 Elapsed: 00:00:00.47
# Mc/sec: 3140.23
//
Query:       gi|242398317|ref|YP_002993741.1|  [L=378]
Description: endo-beta 1,4-glucanase (extracellular) [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       858  (0.0478554); expected 358.6 (0.02)
Passed bias filter:                      599  (0.0334096); 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):               0  [number of targets reported over threshold]
# CPU time: 0.63u 0.27s 00:00:00.90 Elapsed: 00:00:00.45
# Mc/sec: 2502.71
//
Query:       gi|242398318|ref|YP_002993742.1|  [L=613]
Description: Endo-beta-1,4-glucanase (intracellular) [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.076   13.1   0.0        0.2   11.7   0.0    1.6  1  KorB          KorB domain


Domain annotation for each model (and alignments):
>> KorB  KorB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   1.1e-05       0.2       7      23 ..     564     580 ..     562     586 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.1e-05
                              KorB   7 adIAkaLGksksfvsly 23 
                                       a+IAk+ Gk++++vs+ 
  gi|242398318|ref|YP_002993742.1| 564 AEIAKIIGKENTWVSMA 580
                                       79*************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (613 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       698  (0.0389313); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.67u 0.30s 00:00:00.97 Elapsed: 00:00:00.47
# Mc/sec: 3886.27
//
Query:       gi|242398319|ref|YP_002993743.1|  [L=507]
Description: endo-beta 1,4-glucanase (extracellular) [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.075   13.0   0.0       0.15   12.1   0.0    1.4  1  DUF2808   Protein of unknown function (DUF2808)
       0.13   12.3   0.2         13    6.0   0.0    2.4  2  Vps51     Vps51/Vps67


Domain annotation for each model (and alignments):
>> DUF2808  Protein of unknown function (DUF2808)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   1.6e-05      0.15      62     111 ..     230     286 ..     202     288 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.6e-05
                           DUF2808  62 veafvgt........trnkgeklpleevvwdkenrtieitfdePippgktvtvvlknv 111
                                         a +gt           k+ ++++ ++ w+ +  +i+ ++ ePi  g +vt+ + ++
  gi|242398319|ref|YP_002993743.1| 230 PPADIGTltatvyvnGAPKEVEFKV-QRAWNADHFVIKFVPTEPITTGGSVTLNVTPF 286
                                       3444433444444434566777777.777***********************998775 PP

>> Vps51  Vps51/Vps67
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0    0.0014        13      47      71 ..      81     104 ..      81     114 .. 0.77
   2 ?    3.8   0.0    0.0067        60      47      61 ..     413     427 ..     413     443 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0014
                             Vps51  47 ydnYskLisasdtIrkmksemdkld 71 
                                       ++nY ++is  dtI+ +  +m++++
  gi|242398319|ref|YP_002993743.1|  81 GENYMRFISSEDTIA-FYANMSNIE 104
                                       58************6.555566665 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.0067
                             Vps51  47 ydnYskLisasdtIr 61 
                                       ++nY ++is  dt++
  gi|242398319|ref|YP_002993743.1| 413 GENYMRFISSEDTVV 427
                                       58***********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (507 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 3297.77
//
Query:       gi|242398320|ref|YP_002993744.1|  [L=682]
Description: cellobiose/beta-glucoside ABC transporter substrate-binding protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.4e-65  220.5   0.9      5e-65  219.9   0.9    1.2  1  SBP_bac_5  Bacterial extracellular solute-binding proteins, f
  ------ inclusion threshold ------
       0.07   13.5   0.3       0.22   12.0   0.0    1.9  2  DUF1935    Domain of unknown function (DUF1935)


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 !  219.9   0.9   5.6e-69     5e-65      14     363 ..      94     481 ..      84     492 .. 0.91

  Alignments for each domain:
  == domain 1  score: 219.9 bits;  conditional E-value: 5.6e-69
                                       ETTTTEEEEEE-TT-B-TTSSB-SHHHHHHHHHHHHTGGGHCTTHHHHHCTCTEEEEEEEETTEEEEEESSETTTTT CS
                         SBP_bac_5  14 sdDgktytfkLRkgvkFsDGtpltAeDvvfsferlldpdtasgyaslleedqdikkveavddytvrftlkkpnalfl 90 
                                         + +t+ ++LR+++k+sDG+p+tAeDv+++++   + ++++ + s  +    i +v+++d++tv+ft  +  +l +
  gi|242398320|ref|YP_002993744.1|  94 LVNETTLLVYLRPEAKWSDGKPITAEDVEYTYKLSREVGSGPAAGSEPY----ISDVKVIDTHTVQFTIGEEKNLPM 166
                                       567899*************************999999999999988886....9******************99888 PP

                                       THCHHHHHHHGC.........................CHTCTCTTTTTGTTTSE-BSSSEEEEEEETTTEEEEEE-T CS
                         SBP_bac_5  91 tllaavpasiak.........................kaaekeddkdkdtnekpvgtGPYklkefkpgqkivlernp 142
                                       +ll+a++ ++a                          +  + ++  d   + + v +GPYkl+ f+   +iv+er +
  gi|242398320|ref|YP_002993744.1| 167 FLLYALQFAPAPkhiieqvyekvgadiinwrncggtcDDIVSTESGDVRIDLPQVVSGPYKLYYFDE-LRIVYERID 242
                                       88888888777778***********************77777777789999999*************.********* PP

                                       TST...TTSCSSSSEEEEEE-.SHHHHHHHHHTTSSSEEESTTCCTHCHHHHHTTEEE.EEEEEEEEEEEEEETTTS CS
                         SBP_bac_5 143 dYw...gggkpkldriefkvipdsdaraaalqsGeiddvaepppsdieqlkeakglkv.lyespgggvtylafNtkk 215
                                       d+w     g+p +++++ +++ +++++++ l++G++ d+++++++++  +ke    ++   ++ +g + +l++N++ 
  gi|242398320|ref|YP_002993744.1| 243 DWWgkdIFGLPGPKYLVHRIYLSNEQALLDLRQGNV-DWSGIFIPNVGNFKEIGTFYKsKPYFRPGAFVMLYLNHRD 318
                                       ***77555999*************************.********************998999999*********** PP

                                       TGGGSHHHHHHHHHHS-HHHHHHHCTTTSS.EEESSSSTTTSTTCCSCHCCCSHH...........SHHHHHHHHHH CS
                         SBP_bac_5 216 ppfddkrvRqAlsyAiDreeivkavlegya.tpansllppsspgadeeykpayka...........ydpekAkklLk 280
                                       p+f+d+++R+A++yAiD++e+++++++gy  +p  sl+ +++p++  + ++                + e Ak++L+
  gi|242398320|ref|YP_002993744.1| 319 PIFQDTNLRKAIAYAIDYQEVLTKAFYGYSeQPSMSLVFTVFPHYRMWLNTTLAQeyfsnpegriqTNKEFAKQILA 395
                                       *****************************86799999************9975449**********99********* PP

                                       HTT-BCSSTSCEETC....EEEEEEEEETTSHHHHHHHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHCTTESEEEE CS
                         SBP_bac_5 281 eaGykdgdggglrek....klkltlllasgspaekaiaeliqqqlkkiGikvevktvdwaatylervkdgdfdmill 353
                                       +aGykd+dg+ + e     k +l++++++g++++  +a+li+++l++iG++v  ++vd   +y+  v++  + ++l+
  gi|242398320|ref|YP_002993744.1| 396 QAGYKDVDGDDYLETptgeKIELNIIIPTGWTDWMIAADLIASDLQDIGLNVVANPVDY-GAYWGMVNSAGYTLALG 471
                                       ************999********************************************.99999999999999988 PP

                                       EEECTTSTTH CS
                         SBP_bac_5 354 gwgadypdpd 363
                                       + ++ ++  +
  gi|242398320|ref|YP_002993744.1| 472 WTSSPSFYHP 481
                                       6655544444 PP

>> DUF1935  Domain of unknown function (DUF1935)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1      0.86   7.7e+03      28      56 ..     336     364 ..     319     379 .. 0.72
   2 ?   12.0   0.0   2.4e-05      0.22      30      56 ..     496     522 ..     484     541 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.86
                                       ETTTTEEEEEE--SSEEEEEEEEEETT-E CS
                           DUF1935  28 dekekrWaFYNDtkdyemkvtvsfgpkse 56 
                                        ++  + aFY  +++ +m   ++++p+ +
  gi|242398320|ref|YP_002993744.1| 336 YQEVLTKAFYGYSEQPSMSLVFTVFPHYR 364
                                       44445568999999999998888887754 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 2.4e-05
                                       TTTEEEEEE--SSEEEEEEEEEETT-E CS
                           DUF1935  30 kekrWaFYNDtkdyemkvtvsfgpkse 56 
                                        +++W FYN++k +e+ v++  +++se
  gi|242398320|ref|YP_002993744.1| 496 PTGNWGFYNNSKALEFLVQAAKAETSE 522
                                       3689***************98888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (682 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); 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: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.52
# Mc/sec: 3915.57
//
Query:       gi|242398321|ref|YP_002993745.1|  [L=335]
Description: cellobiose/beta-glucoside ABC transporter permease [Thermococcus sibiricus MM 739]
Scores for 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  107.0  15.0    1.9e-30  106.0  15.0    1.5  1  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.0  15.0   1.1e-34   1.9e-30       1     184 [.     125     330 ..     125     331 .. 0.98

  Alignments for each domain:
  == domain 1  score: 106.0 bits;  conditional E-value: 1.1e-34
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf........................vilsilghli 53 
                                       g+ lG+ aa++r+  + k+     i+++ +P++++a++l+++f                        +i+s+l h+i
  gi|242398321|ref|YP_002993745.1| 125 GNYLGARAAYRRGTLFEKITVSTGIITSQIPYYWMAMVLIFAFaiklgwvpsgsaydptlapsfsweFIKSYLRHYI 201
                                       6789************************************************************************* PP

                      BPD_transp_1  54 lpviillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavllef 130
                                       lp + ++l+s++++++ +r  a  +l + +v++++ l +s    ++++vl+n+l p +tg+++++g ++ g +++e 
  gi|242398321|ref|YP_002993745.1| 202 LPFLSIALVSTGGWIIGMRVLATMELGSTYVNFSERLNVSNEI-IFRYVLRNSLLPQVTGIAIQLGTVMAGQIITEQ 277
                                       ****************************************866.777****************************** PP

                      BPD_transp_1 131 lgswpGlgtllleailgydyseisnggvlalviavlllnlvadilqrlldprvr 184
                                       +++++G+g ll +a+  +dy++i+ g++l+l+  +ll n+++ +++ l+dpr+r
  gi|242398321|ref|YP_002993745.1| 278 IFNYQGMGILLARALGTRDYPLIQ-GIFLILIGTLLLANFIVEFIYVLIDPRIR 330
                                       ************************.***************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 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:                        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: 0.65u 0.33s 00:00:00.98 Elapsed: 00:00:00.55
# Mc/sec: 1841.05
//
Query:       gi|242398322|ref|YP_002993746.1|  [L=282]
Description: cellobiose/beta-glucoside ABC transporter permease [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.3e-17   62.8  18.5    3.3e-17   62.8  18.5    1.5  2  BPD_transp_1  Binding-protein-dependent transport system inne
    2.4e-05   24.2   0.3    2.4e-05   24.2   0.3    3.7  3  OppC_N        N-terminal TM domain of oligopeptide transport 


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.3      0.89     8e+03     161     179 ..      17      35 ..      14      38 .. 0.52
   2 !   62.8  18.5   3.7e-21   3.3e-17       1     184 [.      92     280 ..      92     281 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 0.89
                      BPD_transp_1 161 lviavlllnlvadilqrll 179
                                       +++a+l + +++ ++ ++l
  gi|242398322|ref|YP_002993746.1|  17 IGFAILMFEILLALFGAYL 35 
                                       4455555555555555555 PP

  == domain 2  score: 62.8 bits;  conditional E-value: 3.7e-21
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilp.viillllsaapyvrlirraal 76 
                                       g+++Gi+a+  +++ +d+ l+ +++v+ ++P ++lai++      l+  +++ +  ++i++l+ +++++r ir++ +
  gi|242398322|ref|YP_002993746.1|  92 GLIIGIVAG-IKGGLIDETLMAFTNVVITIPNVLLAIIIA---TYLGLEHSGLTLvAAIISLTAWPWFARAIRAQLI 164
                                       799******.*****************************9...45666667777778******************** PP

                      BPD_transp_1  77 rslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydysei 153
                                       + +++d+v+++++ G s+ +i +  ++P + +++i +++  + + +++ v l++lg       ++   +lg+++ ++
  gi|242398322|ref|YP_002993746.1| 165 SLRERDFVNFSKMTGYSDLKIAVFDLFPYVTTYTIVSFVTFMNIGINAEVGLSILGLT-----PIQIMTLGKMLYFA 236
                                       ********************************************************44.....55555555555444 PP

                      BPD_transp_1 154 s.............nggvlalviavlllnlvadilqrlldprvr 184
                                       +             + + + lv++   l+l+a  + ++++pr+r
  gi|242398322|ref|YP_002993746.1| 237 AvtqsyflghwwvfIPPGILLVALSTSLLLIATGIEQVFNPRLR 280
                                       45567777889999999999999999999999999999999998 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 !   24.2   0.3   2.7e-09   2.4e-05       5      42 ..       4      42 ..       2      58 .. 0.85
   2 ?  -10.8  12.3         2   1.8e+04      36      36 ..     106     106 ..      80     165 .. 0.59
   3 ?   -2.8   0.1      0.75   6.7e+03      26      34 ..     264     277 ..     255     279 .. 0.50

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 2.7e-09
                            OppC_N  5 dawrrFkrNklAvvglvilllllliaifaPliaPydp.q 42
                                      ++++ ++rN +  +g++il++ +l+a+f+ +++P dp  
  gi|242398322|ref|YP_002993746.1|  4 EILYVLFRNNRFSIGFAILMFEILLALFGAYLYPVDPfK 42
                                      67899****************************998851 PP

  == domain 2  score: -10.8 bits;  conditional E-value: 2
                            OppC_N  36 i 36 
                                       i
  gi|242398322|ref|YP_002993746.1| 106 I 106
                                       1 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 0.75
                            OppC_N  26 lllia.....ifaP 34 
                                       lllia     +f+P
  gi|242398322|ref|YP_002993746.1| 264 LLLIAtgieqVFNP 277
                                       55555445555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 1644.18
//
Query:       gi|242398323|ref|YP_002993747.1|  [L=338]
Description: cellobiose/beta-glucoside ABC transporter ATPase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.8e-25   88.7   0.0    9.4e-25   87.7   0.0    1.5  1  ABC_tran      ABC transporter
    5.7e-21   74.8   0.0      1e-20   74.0   0.0    1.4  1  oligo_HPY     Oligopeptide/dipeptide transporter, C-terminal 
      5e-06   26.5   1.1    0.00026   20.9   0.2    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
     0.0036   17.3   0.1     0.0077   16.2   0.0    1.6  2  Rad17         Rad17 P-loop domain
     0.0038   16.7   0.1       0.31   10.5   0.1    2.2  2  SMC_N         RecF/RecN/SMC N terminal domain
     0.0046   17.2   0.7      0.052   13.8   0.1    2.2  2  AAA_22        AAA domain
  ------ inclusion threshold ------
      0.011   15.4   0.0      0.027   14.2   0.0    1.6  1  AAA_29        P-loop containing region of AAA domain
      0.013   14.7   0.1      0.021   14.0   0.1    1.3  1  NB-ARC        NB-ARC domain
      0.019   15.4   0.0      0.039   14.3   0.0    1.5  1  RNA_helicase  RNA helicase
       0.02   14.8   0.0      0.048   13.6   0.0    1.6  1  RsgA_GTPase   RsgA GTPase
      0.031   14.2   0.0      0.064   13.1   0.0    1.6  1  MobB          Molybdopterin guanine dinucleotide synthesis pr
      0.033   14.2   0.3       0.21   11.6   0.1    2.2  2  AAA_5         AAA domain (dynein-related subfamily)
      0.045   13.9   0.0      0.093   12.9   0.0    1.6  1  AAA_33        AAA domain
      0.049   13.6   0.1       0.14   12.1   0.0    1.8  2  NACHT         NACHT domain
      0.051   14.0   0.1       0.79   10.2   0.0    2.4  2  AAA           ATPase family associated with various cellular 
      0.068   13.6   0.2       0.14   12.6   0.2    1.6  1  AAA_16        AAA ATPase domain
        0.1   12.0   0.1       0.31   10.5   0.1    2.0  2  PhoH          PhoH-like protein
       0.13   11.9   0.3       0.29   10.8   0.0    1.7  2  AAA_24        AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.7   0.0   9.4e-28   9.4e-25       2     137 .]      29     193 ..      28     193 .. 0.88

  Alignments for each domain:
  == domain 1  score: 87.7 bits;  conditional E-value: 9.4e-28
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--....SEEEEEETTCEGGG...........B-HHHCCHCEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxx...........xxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkp....teGeilldgkdlke...........qeleslrkeigv 63 
                                       + v+l++++  ++++vGe+G+GKStL+k+++  l+p      G++++ ++d ++            +++ + k+i +
  gi|242398323|ref|YP_002993747.1|  29 DGVNLEVYKKDILGLVGESGCGKSTLAKTMMIDLTPplqyMGGRLEIISRDGERfeigqfksrdeVKRRLWGKHITY 105
                                       789**************************9999999788766777555555555555666667677899******** PP

                                       E-SS..--S-TTSBHHHH............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHT CS
                                       xxxx..xxxxxxxxxxxx............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  64 lpqe..pqlfpeltvren............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkk 126
                                       +pq+  + l p++++++             + +e +++  ++l   +l+d vv+  p +LSgG++qrv+la+a l +
  gi|242398323|ref|YP_002993747.1| 106 VPQDalNALMPTIRIKKIaydvlrshnndiNFQEAVKTTKERLAELDLPDYVVELYPFQLSGGMRQRVVLAMATLLN 182
                                       ****99999999999998999**9998888777779999999999999***************************** PP

                                       SSEEEEESTTT CS
                                       xxxxxxxxxxx RF
                          ABC_tran 127 pkllllDEpta 137
                                       p++l++DEpt+
  gi|242398323|ref|YP_002993747.1| 183 PEILIVDEPTS 193
                                       *********96 PP

>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.0   0.0     1e-23     1e-20       1      65 []     245     311 ..     245     311 .. 0.99

  Alignments for each domain:
  == domain 1  score: 74.0 bits;  conditional E-value: 1e-23
                         oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekd..klekikgeapslerldeGCpFapRCpfaleeC 65 
                                       vE gp++ ++++plHPYTk+L++sv ++++ek+   +  i+g++p+l + ++GC+F+pRCp+a++ C
  gi|242398323|ref|YP_002993747.1| 245 VEVGPVDSVIRDPLHPYTKGLIDSVTSIEPEKRekGISYIPGQPPNLIDPPKGCRFHPRCPYAMDVC 311
                                       8********************************999*****************************99 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.022        22       2      19 ..      41      58 ..      40      91 .. 0.86
   2 !   20.9   0.2   2.6e-07   0.00026     220     299 ..     148     226 ..      87     230 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.022
                            AAA_21  2 nvliGpNgsGKSnLLdal 19
                                       +l+G  g+GKS+L +++
  gi|242398323|ref|YP_002993747.1| 41 LGLVGESGCGKSTLAKTM 58
                                      579***********8876 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 2.6e-07
                            AAA_21 220 gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.nga.Qvil 294
                                          +  +++  el +++lS G+++   l+ a l  l +  +l++DEp + L+   ++ +l+ l +l++ n++  +i+
  gi|242398323|ref|YP_002993747.1| 148 LAELDLPDYVVELYPFQLSGGMRQRVVLAMATL--LNP-EILIVDEPTSALDVTTQKIVLKSLLKLRKlNLVdSIIF 221
                                       445556678889************844444444..444.9********************98855544444414799 PP

                            AAA_21 295 tTHSp 299
                                        TH+ 
  gi|242398323|ref|YP_002993747.1| 222 ITHDI 226
                                       99985 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   7.7e-06    0.0077      33      71 ..      26      64 ..       7     106 .. 0.84
   2 ?   -3.1   0.1       6.4   6.4e+03     151     174 ..     199     225 ..     176     234 .. 0.52

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.7e-06
                             Rad17 33 ewlkadvLesrkkriLLisGPsGCgkstvvkvLskelgi 71
                                      ++++   Le  kk iL + G sGCgkst  k +   l++
  gi|242398323|ref|YP_002993747.1| 26 KAVDGVNLEVYKKDILGLVGESGCGKSTLAKTMMIDLTP 64
                                      56777889********************99988766665 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 6.4
                             Rad17 151 alrevirkylrsseal...plilvite 174
                                       + + v++  l+ ++     ++i++  +
  gi|242398323|ref|YP_002993747.1| 199 TQKIVLKSLLKLRKLNlvdSIIFITHD 225
                                       333344444444332234555555554 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 ?    4.2   0.0     0.026        26      23      44 ..      37      58 ..      23      63 .. 0.84
   2 !   10.5   0.1   0.00031      0.31     135     210 ..     123     238 ..      76     245 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.026
                                      TSSEEEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 23 sksftaivGpNGSGKsnlldAi 44
                                      +k +  +vG+ G+GKs l   +
  gi|242398323|ref|YP_002993747.1| 37 KKDILGLVGESGCGKSTLAKTM 58
                                      5667789*********998766 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00031
                                       T........................................CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS CS
                                       x........................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 135 e........................................lLSgGektLvalaLlfAiqkvkpaplyllDeidaaL 171
                                                                                +LSgG ++ v la+           + ++De  +aL
  gi|242398323|ref|YP_002993747.1| 123 IaydvlrshnndinfqeavkttkerlaeldlpdyvvelypfQLSGGMRQRVVLAMA----TLLNPEILIVDEPTSAL 195
                                       244455555555555555555555555555555555555559****8886666554....4444457899******* PP

                                       -HHHHHHHHHHHHHHCTT...SEEEEE-SSHHHCCC-.SCEEE CS
                                       xxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxx.xxxxx RF
                             SMC_N 172 Deknvkkvaellkekskn...aQfivislreemleka.dklvg 210
                                       D +  k+v + l + +k      +i i+++  ++++  +++v 
  gi|242398323|ref|YP_002993747.1| 196 DVTTQKIVLKSLLKLRKLnlvDSIIFITHDIATVRQIaNRIVV 238
                                       ******9998776655532435678899998888776244444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.1   5.2e-05     0.052       5      25 ..      38      58 ..      34      64 .. 0.87
   2 ?    1.5   0.1      0.34   3.4e+02      83     133 ..     174     226 ..     122     229 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.2e-05
                            AAA_22  5 agilvvtGesGtGKTtllrrl 25
                                      + il ++GesG+GK+tl++++
  gi|242398323|ref|YP_002993747.1| 38 KDILGLVGESGCGKSTLAKTM 58
                                      678889************987 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.34
                            AAA_22  83 eqalrarav...ielliiDEaqh.lr...seealeeLrsllnlsrkgvqliLvGtpel 133
                                         a+    +   +e+li+DE    l+   ++ +l+ L +l +    +v  i+++t+++
  gi|242398323|ref|YP_002993747.1| 174 VLAMA---TllnPEILIVDEPTSaLDvttQKIVLKSLLKLRK--LNLVDSIIFITHDI 226
                                       33333...2455899*****9888877644777777777777..77777777777766 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   2.7e-05     0.027      13      49 ..      29      65 ..      26      68 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.7e-05
                            AAA_29 13 dghtieidlkgatlltGpsGsGKSTllDAiqalLvpa 49
                                      dg  +e+  k++  l+G+sG GKSTl   +++ L+p+
  gi|242398323|ref|YP_002993747.1| 29 DGVNLEVYKKDILGLVGESGCGKSTLAKTMMIDLTPP 65
                                      56667777777888************98888888876 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   0.1   2.1e-05     0.021      19      41 ..      37      59 ..      21      64 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.1e-05
                                      CSEEEEEEESTTSSHHHHHHHHC CS
                            NB-ARC 19 qslvvalvGmgGvGKttlakqil 41
                                      ++++++lvG  G+GK+tlak ++
  gi|242398323|ref|YP_002993747.1| 37 KKDILGLVGESGCGKSTLAKTMM 59
                                      456****************9876 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   3.9e-05     0.039       3      23 ..      43      63 ..      41      81 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.9e-05
                      RNA_helicase  3 lyGpsgeGKStlakeLakall 23
                                      l+G+sg+GKStlak+++ +l+
  gi|242398323|ref|YP_002993747.1| 43 LVGESGCGKSTLAKTMMIDLT 63
                                      78*************999887 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   4.8e-05     0.048      95     120 ..      34      59 ..       2      79 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.8e-05
                                       HHCTTSEEEEECSTTSSHHHHHHHHC CS
                       RsgA_GTPase  95 ellkdktsvlvGqSGvGKStLinall 120
                                       e+ k+++  lvG+SG GKStL ++++
  gi|242398323|ref|YP_002993747.1|  34 EVYKKDILGLVGESGCGKSTLAKTMM 59 
                                       455678999************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 ?   13.1   0.0   6.5e-05     0.064       1      75 [.      40     119 ..      40     148 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.5e-05
                              MobB   1 vlgivgksgsGKTtLlek....lipelkarglrvgtiKhahhgfdvdk.pgkDsyrhrkAGAkevlvaskerlalik 72 
                                       +lg+vg sg+GK tL +     l p l+  g r+ +i  + + f++ + + +D  + r  G + + v  +   al+ 
  gi|242398323|ref|YP_002993747.1|  40 ILGLVGESGCGKSTLAKTmmidLTPPLQYMGGRLEIISRDGERFEIGQfKSRDEVKRRLWGKHITYVPQDALNALMP 116
                                       799**********98765222267889999***************76538899999999999999998888888887 PP

                              MobB  73 ele 75 
                                        ++
  gi|242398323|ref|YP_002993747.1| 117 TIR 119
                                       764 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00021      0.21       4      30 ..      43      69 ..      40      78 .. 0.84
   2 ?   -0.1   0.0      0.86   8.6e+02      62      97 ..     176     216 ..     163     233 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00021
                                      EE--SSSSHHHHHHHGGGGBS--EEEE CS
                             AAA_5  4 LvGppGtgKselaerlaaalnreveyv 30
                                      LvG++G+gKs+la+ +   l+ +++y+
  gi|242398323|ref|YP_002993747.1| 43 LVGESGCGKSTLAKTMMIDLTPPLQYM 69
                                      9*************9987777666666 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.86
                                       ---...G-SEEEEESGGG--HHHHH..HHHHHHHSSEEE.. CS
                             AAA_5  62 aar...egeilvlDEveraesevln..sLlslleerrllle 97 
                                       a+    ++eil++DE + a + +++  +L sll  r+l l 
  gi|242398323|ref|YP_002993747.1| 176 AMAtllNPEILIVDEPTSALDVTTQkiVLKSLLKLRKLNLV 216
                                       33335588888888888888555542346778888877765 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   9.3e-05     0.093       4      39 ..      43      87 ..      40     150 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.3e-05
                            AAA_33  4 lvGlpGsGKstlaerllkklg.........avllssdtlrrrlfg 39
                                      lvG +G+GKstla+ ++  l+          +++s d +r+ +  
  gi|242398323|ref|YP_002993747.1| 43 LVGESGCGKSTLAKTMMIDLTpplqymggrLEIISRDGERFEIGQ 87
                                      79**************98888777777777777888877666655 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   0.00014      0.14       5      24 ..      43      62 ..      39      70 .. 0.86
   2 ?   -3.7   0.0       9.8   9.7e+03      11      21 ..     321     331 ..     321     333 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00014
                                      EEC-TTTCHHHHHHHHHHHH CS
                             NACHT  5 lqGeaGsGKTtLlqklalaw 24
                                      l Ge+G+GK+tL++ ++ ++
  gi|242398323|ref|YP_002993747.1| 43 LVGESGCGKSTLAKTMMIDL 62
                                      89************999776 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 9.8
                                       TCHHHHHHHHH CS
                             NACHT  11 sGKTtLlqkla 21 
                                       +GKT  +++l 
  gi|242398323|ref|YP_002993747.1| 321 VGKTQVACWLY 331
                                       59******996 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 ?   10.2   0.0   0.00079      0.79       3      22 ..      43      62 ..      41      98 .. 0.78
   2 ?    1.5   0.0      0.38   3.8e+02      23      68 ..     145     192 ..     117     237 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00079
                                      EESSTTSSHHHHHHHHHHHH CS
                               AAA  3 lyGppGtGKTllakavakel 22
                                      l+G  G+GK++lak ++ +l
  gi|242398323|ref|YP_002993747.1| 43 LVGESGCGKSTLAKTMMIDL 62
                                      89************998776 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.38
                                       THEEEEEETTTCSSS...STTHHHHHHHHHHHHHHHTSTSEEEEEETGG CS
                               AAA  23 gvefleisgsellsk...yvgesekkirelfkeakekakpsilfiDEid 68 
                                       + ++ e+++++ + +   ++  + ++ r +++ a   + p il++DE  
  gi|242398323|ref|YP_002993747.1| 145 KERLAELDLPDYVVElypFQLSGGMRQRVVLAMATLLN-PEILIVDEPT 192
                                       55566666666663345556666677777777777776.9999999955 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   0.00014      0.14      28      50 ..      42      64 ..      37     222 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00014
                            AAA_16 28 llsGesGvGKsslvrellralek 50
                                       l+GesG+GKs+l+++ +  l+ 
  gi|242398323|ref|YP_002993747.1| 42 GLVGESGCGKSTLAKTMMIDLTP 64
                                      589***********988766655 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00031      0.31      17      43 ..      36      62 ..      20     142 .. 0.91
   2 ?   -2.9   0.0       3.8   3.8e+03      64      90 ..     246     272 ..     225     279 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00031
                                      HH-SEEEEE--TTSSTTHHHHHHHHHH CS
                              PhoH 17 kkndivfaiGpaGtGKtylavalavea 43
                                       k+di+  +G++G+GK+ la ++ +++
  gi|242398323|ref|YP_002993747.1| 36 YKKDILGLVGESGCGKSTLAKTMMIDL 62
                                      3899*****************999886 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.8
                                       ---SS---------TTTHHHHHHHTTT CS
                              PhoH  64 elGflpgdleekvdpylrplydaLkdl 90 
                                       e+G ++  +++ ++py + l+d+++++
  gi|242398323|ref|YP_002993747.1| 246 EVGPVDSVIRDPLHPYTKGLIDSVTSI 272
                                       455555666777888888888887765 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00029      0.29       5      22 ..      41      58 ..      37      80 .. 0.84
   2 ?   -2.9   0.0       4.7   4.7e+03     118     130 ..     207     224 ..     187     238 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00029
                            AAA_24  5 iliyGpsgiGKTtlakel 22
                                      + ++G+sg GK+tlak++
  gi|242398323|ref|YP_002993747.1| 41 LGLVGESGCGKSTLAKTM 58
                                      5699*************9 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4.7
                            AAA_24 118 lqelrk.....nvifiah 130
                                       l +lrk      +ifi h
  gi|242398323|ref|YP_002993747.1| 207 LLKLRKlnlvdSIIFITH 224
                                       333333333556666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       666  (0.0371465); expected 358.6 (0.02)
Passed bias filter:                      616  (0.0343577); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); 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 0.31s 00:00:00.95 Elapsed: 00:00:00.49
# Mc/sec: 2093.97
//
Query:       gi|242398324|ref|YP_002993748.1|  [L=272]
Description: cellobiose/beta-glucoside ABC transporter ATPase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.7e-27   95.9   0.0    3.9e-27   95.4   0.0    1.2  1  ABC_tran      ABC transporter
    6.3e-07   29.8   0.0    1.1e-06   29.0   0.0    1.4  1  oligo_HPY     Oligopeptide/dipeptide transporter, C-terminal 
    2.8e-05   24.4   0.1    0.00018   21.8   0.1    2.1  1  AAA_22        AAA domain
      0.001   18.9   1.3      0.082   12.7   0.6    2.4  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
     0.0038   16.9   0.1     0.0064   16.2   0.1    1.4  1  AAA_29        P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.011   15.1   0.2       0.22   10.9   0.0    2.3  2  TniB          Bacterial TniB protein
      0.012   14.8   0.1      0.021   14.0   0.1    1.4  1  NB-ARC        NB-ARC domain
      0.013   15.8   0.0      0.019   15.4   0.0    1.3  1  AAA_16        AAA ATPase domain
      0.017   14.3   0.0      0.018   14.2   0.0    1.1  1  G-alpha       G-protein alpha subunit
       0.02   14.4   0.2       0.13   11.7   0.2    2.0  1  SMC_N         RecF/RecN/SMC N terminal domain
      0.033   14.1   0.1      0.056   13.4   0.1    1.4  1  RsgA_GTPase   RsgA GTPase
      0.052   12.9   0.0      0.088   12.2   0.0    1.4  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.054   13.2   0.0        2.4    7.8   0.0    2.1  2  AAA_30        AAA domain
      0.073   13.5   0.1        1.7    9.1   0.0    2.3  2  AAA           ATPase family associated with various cellular 
      0.096   11.8   0.1       0.48    9.5   0.1    2.0  2  PIF1          PIF1-like helicase
       0.11   13.0   0.0       0.23   12.0   0.0    1.6  1  AAA_18        AAA domain
       0.11   11.7   0.0        0.2   10.9   0.0    1.5  1  Zeta_toxin    Zeta toxin
       0.12   12.1   0.0       0.43   10.3   0.0    1.8  2  IstB_IS21     IstB-like ATP binding protein
       0.15   12.1   0.0       0.28   11.2   0.0    1.4  1  TsaE          Threonylcarbamoyl adenosine biosynthesis protei


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.4   0.0   4.2e-30   3.9e-27       1     136 [.      28     183 ..      28     184 .. 0.84

  Alignments for each domain:
  == domain 1  score: 95.4 bits;  conditional E-value: 4.2e-30
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.....B-HHHCCHCEEEE-SS.--S- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxx.xxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.....qeleslrkeigvlpqe.pqlf 71 
                                       ++nvs+++kege++ ++G++G+GK+tL k++++l  pt+G++l+ g+d+ +     +e++++ +++  ++q+    f
  gi|242398324|ref|YP_002993748.1|  28 VDNVSFTVKEGEIISLIGQSGSGKTTLGKIILRLIPPTSGRVLFYGRDIWKeiktkEERKEYWRQVHAVFQNpMGSF 104
                                       58********************************************9998888888888888999999999963344 PP

                                       TTSBHHHH.............HHHTC...HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEE CS
                                       xxxxxxxx.............xxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  72 peltvren.............esdee...iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllll 132
                                       ++    ++             +s+e     e+ l+ +gl+    +++++ p++LSgGq qrv++ r+ + kpkll++
  gi|242398324|ref|YP_002993748.1| 105 NTFYKVDRvlnqaleligvepNSEEGirlKEESLKAVGLNP--GEILGKYPHQLSGGQVQRVMISRSWILKPKLLIA 179
                                       43332222577799999997633333556778888888887..9********************************* PP

                                       ESTT CS
                                       xxxx RF
                          ABC_tran 133 DEpt 136
                                       DE+ 
  gi|242398324|ref|YP_002993748.1| 180 DEAV 183
                                       **96 PP

>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.0   1.2e-09   1.1e-06       1      33 [.     235     267 ..     235     271 .. 0.95

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 1.2e-09
                         oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekd 33 
                                       vE g+ ++++d+p+H YTk+L++svp + r+++
  gi|242398324|ref|YP_002993748.1| 235 VEAGTPQEVIDNPQHEYTKTLVESVPTVYRKWE 267
                                       8*****************************997 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.1   1.9e-07   0.00018       4     128 ..      37     212 ..      34     219 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.9e-07
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee........................erpevvfvtlpsst....s 52 
                                       +  i+ ++G+sG+GKTtl + +l+  +                               ++++ vf ++ +s     +
  gi|242398324|ref|YP_002993748.1|  37 EGEIISLIGQSGSGKTTLGKIILRLIPPT----SgrvlfygrdiwkeiktkeerkeywRQVHAVFQNPMGSFntfyK 109
                                       56799*******************98643....24577*****************9999999999999999897777 PP

                            AAA_22  53 skdllrellralglelka.....................erlsseell.ealeqalrarav...ielliiDEaqh.l 103
                                        + +l++ l+ +g+e ++                      ++  ++l   ++++ + +r+    ++lli DEa   l
  gi|242398324|ref|YP_002993748.1| 110 VDRVLNQALELIGVEPNSeegirlkeeslkavglnpgeiLGKYPHQLSgGQVQRVMISRSWilkPKLLIADEAVSmL 186
                                       77888888888888888899999999999998888888866666666667777777777779999**********77 PP

                            AAA_22 104 r...seealeeLrsllnlsrkgvqliLv 128
                                       +   + +++e +++l n  + g ++i++
  gi|242398324|ref|YP_002993748.1| 187 DvstRGRIVEIFKDLRN--KLGSSIIFI 212
                                       69644999999999999..666666665 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.6   8.7e-05     0.082       3      22 ..      42      61 ..      40     139 .. 0.85
   2 ?    4.9   0.0     0.021        20     270     299 ..     186     216 ..     169     219 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.7e-05
                            AAA_21  3 vliGpNgsGKSnLLdaldll 22
                                       liG  gsGK++L +++  l
  gi|242398324|ref|YP_002993748.1| 42 SLIGQSGSGKTTLGKIILRL 61
                                      69***************887 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.021
                            AAA_21 270 LHPkllrrllellkelsr.ngaQviltTHSp 299
                                       L+ +   r++e++k+l++  g+ +i+ +H+ 
  gi|242398324|ref|YP_002993748.1| 186 LDVSTRGRIVEIFKDLRNkLGSSIIFISHDI 216
                                       66677789*********************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 !   16.2   0.1   6.8e-06    0.0064      13      38 ..      29      54 ..      26      71 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 6.8e-06
                            AAA_29 13 dghtieidlkgatlltGpsGsGKSTl 38
                                      d+ ++++++ +++ l+G+sGsGK+Tl
  gi|242398324|ref|YP_002993748.1| 29 DNVSFTVKEGEIISLIGQSGSGKTTL 54
                                      566788886669*************9 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1       0.2   1.9e+02      38      53 ..      41      56 ..      34      69 .. 0.79
   2 ?   10.9   0.0   0.00023      0.22     118     160 ..     172     212 ..     152     225 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.2
                              TniB 38 lllvGdsnnGKtmive 53
                                      + l+G+s  GKt++ +
  gi|242398324|ref|YP_002993748.1| 41 ISLIGQSGSGKTTLGK 56
                                      5799********9866 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00023
                              TniB 118 lkvrvLiiDEihnllagsarkqreflnalksLgnelkipivlv 160
                                       lk+++Li DE  ++l   ++++ +++++ k L n+l  +i+ +
  gi|242398324|ref|YP_002993748.1| 172 LKPKLLIADEAVSML--DVSTRGRIVEIFKDLRNKLGSSIIFI 212
                                       689************..7888899****************986 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   0.1   2.3e-05     0.021      17      79 ..      37     100 ..      21     120 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.3e-05
                                       TSCSEEEEEEESTTSSHHHHHHHHCCSHCCCCC...CBTEEEEEEEESXXHHHHHHHXXHHHHHCC CS
                            NB-ARC  17 elqslvvalvGmgGvGKttlakqilnksdeveg...rFdsvawvvvsktdkseeiletilkeLsls 79 
                                       e +  +++l G  G+GKttl k il+    + g    + + +w  +  + + +e ++++ +++++ 
  gi|242398324|ref|YP_002993748.1|  37 EGE--IISLIGQSGSGKTTLGKIILRLIPPTSGrvlFYGRDIWKEIKTKEERKEYWRQVHAVFQNP 100
                                       445..9******************999888777443366778888888888888888888877665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.0     2e-05     0.019      20      55 ..      36      69 ..      24     142 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2e-05
                            AAA_16 20 rsgrpelvllsGesGvGKsslvrellralekdggif 55
                                      ++g  e++ l+G+sG+GK++l + +lr +  + g +
  gi|242398324|ref|YP_002993748.1| 36 KEG--EIISLIGQSGSGKTTLGKIILRLIPPTSGRV 69
                                      444..89**************999998888774444 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.9e-05     0.018      26      83 ..      41     116 ..      25     225 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.9e-05
                                       EEEEESTTSSHHHHHHHHHHHCS--...............--HHHHHC.CHHH..HHHHHHHHHHHHHHHHHHTT. CS
                           G-alpha  26 llllGqseSGKsTilkqlkllykkg...............fseeelat.wrav..iqlnivrsiktilealesles 83 
                                       + l+Gqs+SGK+T+ k + +l  ++                ++ee+++ wr+v  +++n + s++t+ +  + l++
  gi|242398324|ref|YP_002993748.1|  41 ISLIGQSGSGKTTLGKIILRLIPPTsgrvlfygrdiwkeiKTKEERKEyWRQVhaVFQNPMGSFNTFYKVDRVLNQ 116
                                       679****************99999999****999999998555566666**9655888888888888776666544 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 ?   11.7   0.2   0.00013      0.13      24     198 ..      38     215 ..      19     234 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00013
                                       SSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTT.TCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  24 ksftaivGpNGSGKsnlldAilFvLGersakkl.rseklsdlihkskekasvkkaeveitfdnedkklkiekeevsi 99 
                                        ++ +++G+ GSGK+ l   il ++  +s + l   +++ + i+  ke+++    +v+ +f+n+  ++++    +++
  gi|242398324|ref|YP_002993748.1|  38 GEIISLIGQSGSGKTTLGKIILRLIPPTSGRVLfYGRDIWKEIKT-KEERKEYWRQVHAVFQNPMGSFNTF---YKV 110
                                       457789999999999999999999998888765245566666776.7888888899999999999993333...333 PP

                                       EEEEETTSE.......EEEEETTEEE-HHHHHHHHHCTT-STT........CS-HHHHHHHHHHHHHHHHCCS--SE CS
                                       xxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 100 srrvkrkge.......seykingkevtkkevsellesagiske........lLSgGektLvalaLlfAiqkvkpapl 161
                                        r + +  e       se  i  ke       e l+ +g+++         +LSgG+ + v+++        kp+ l
  gi|242398324|ref|YP_002993748.1| 111 DRVLNQALEligvepnSEEGIRLKE-------ESLKAVGLNPGeilgkyphQLSGGQVQRVMISRS---WILKPK-L 176
                                       3333222221000011333333333.......33444444444555555559****9887777654...234454.7 PP

                                       EEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxx RF
                             SMC_N 162 yllDeidaaLDeknvkkvaellkekskn..aQfivislr 198
                                        + De  + LD + + +++e++k  +++  + +i is++
  gi|242398324|ref|YP_002993748.1| 177 LIADEAVSMLDVSTRGRIVEIFKDLRNKlgSSIIFISHD 215
                                       899********************9998866778888876 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   5.9e-05     0.056      88     118 ..      26      57 ..      11      88 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.9e-05
                                       TTHHHHHHHCTT.SEEEEECSTTSSHHHHHHH CS
                       RsgA_GTPase  88 egleelkellkd.ktsvlvGqSGvGKStLina 118
                                       +++++++  +k+ +++ l+GqSG GK+tL + 
  gi|242398324|ref|YP_002993748.1|  26 KAVDNVSFTVKEgEIISLIGQSGSGKTTLGKI 57 
                                       56778888888889**************9655 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   9.3e-05     0.088      25      74 ..      41      91 ..      26     106 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.3e-05
                      Mg_chelatase 25 lllvGppGsGKtmlakrlpsllpplseeealevakias.vagkkeeekllk 74
                                      + l+G +GsGKt l k +  l+pp s +  +  + i   +++k+e++++++
  gi|242398324|ref|YP_002993748.1| 41 ISLIGQSGSGKTTLGKIILRLIPPTSGRVLFYGRDIWKeIKTKEERKEYWR 91
                                      679*********************998877766666541334555555554 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0    0.0026       2.4      16      49 ..      36      69 ..      28      75 .. 0.77
   2 ?    3.4   0.0      0.06        56      81     114 ..     157     200 ..     109     212 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0026
                            AAA_30 16 sgdrvavltGpAGtGKttalkalreaweaaggrv 49
                                      ++  +  l G  G+GKtt+ k + +++    grv
  gi|242398324|ref|YP_002993748.1| 36 KEGEIISLIGQSGSGKTTLGKIILRLIPPTSGRV 69
                                      444588899**********999988776665555 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.06
                            AAA_30  81 k.........grarlepg.tllivDEa.gmvdtkqlaallkaaek 114
                                                 +  ++  + +lli DEa +m+d ++  +++++ ++
  gi|242398324|ref|YP_002993748.1| 157 SggqvqrvmiS-RSWILKpKLLIADEAvSMLDVSTRGRIVEIFKD 200
                                       34444555543.23334449******87899**999999998776 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0    0.0018       1.7       3      22 ..      43      62 ..      41     103 .. 0.65
   2 ?    2.1   0.0      0.25   2.4e+02      41      64 ..     189     212 ..     160     214 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0018
                                      EESSTTSSHHHHHHHHHHHH CS
                               AAA  3 lyGppGtGKTllakavakel 22
                                      l+G  G GKT+l k + + +
  gi|242398324|ref|YP_002993748.1| 43 LIGQSGSGKTTLGKIILRLI 62
                                      89*************99875 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.25
                                       HHHHHHHHHHHHHHHTSTSEEEEE CS
                               AAA  41 esekkirelfkeakekakpsilfi 64 
                                        +  +i e+fk++++k + si+fi
  gi|242398324|ref|YP_002993748.1| 189 STRGRIVEIFKDLRNKLGSSIIFI 212
                                       5788999*****9999977****9 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1   0.00051      0.48      10      54 ..      24      70 ..      20      73 .. 0.78
   2 ?   -0.7   0.0      0.67   6.3e+02      89     131 ..     160     203 ..     152     211 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00051
                                      HHHH........HCTS-EEEEESTTSSCHHHHHHHHHHCHCTCCCEE CS
                              PIF1 10 fdaiieavln..ekgklfFvtGsgGtgKtflwkallkklrsegkivl 54
                                      + ++++ v+   ++g+++ + G++G+gKt l k +l  + ++   vl
  gi|242398324|ref|YP_002993748.1| 24 VVKAVDNVSFtvKEGEIISLIGQSGSGKTTLGKIILRLIPPTSGRVL 70
                                      4444455543359************************9998877766 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.67
                                       HHHTSCCCHHHHHC-SEEEEECG.GGSBHHHHHHHHHHHHHHCT CS
                              PIF1  89 kikrgsklaellkktsliiwDEa.pmverecfealdrtlrdilk 131
                                       +++r    ++ + k +l+i DEa +m++ +    + ++++d+++
  gi|242398324|ref|YP_002993748.1| 160 QVQRVMISRSWILKPKLLIADEAvSMLDVSTRGRIVEIFKDLRN 203
                                       56666777788899999****97578877766666666666665 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00025      0.23       1      52 [.      41      96 ..      41     116 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00025
                            AAA_18  1 IlltGtpGvGKttlakeLskrlgf.......gvnlrdvakenglllevdpealdeskrl 52
                                      I l G +G+GKttl+k + ++  +        +  rd++ke  + +e+ ++ +++ + +
  gi|242398324|ref|YP_002993748.1| 41 ISLIGQSGSGKTTLGKIILRL--IpptsgrvLFYGRDIWKEIKTKEERKEY-WRQVHAV 96
                                      6689*************9776..2334655556666666666666666666.5555444 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00021       0.2      18      80 ..      40     101 ..      26     119 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00021
                        Zeta_toxin  18 lillgGqpGAGKselaellkdelerqgnvvrldpDdlRelhPeyeeilkadpkkaseltqkda 80 
                                       +i l Gq+G+GK++l + + + + ++++ v +++ d+ + +   +e +k++ +++ +++q+ +
  gi|242398324|ref|YP_002993748.1|  40 IISLIGQSGSGKTTLGKIILRLIPPTSGRVLFYGRDIWKEIKT-KEERKEYWRQVHAVFQNPM 101
                                       77889*************9999997777777777666666644.3336666666666666655 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00045      0.43      34     104 ..      24      94 ..       8     100 .. 0.72
   2 ?   -1.1   0.0       1.4   1.4e+03     106     130 ..     171     194 ..     158     221 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00045
                         IstB_IS21  34 kvkeLatlsf.iekkenivllGpsGvGKshlaialgveavraglsvlfvrvedLveelkrarrdgklaralk 104
                                        vk++ + sf +++ e i l+G+sG GK+ l   + +    +  +vlf+  +d+ +e+k++++  ++ r+++
  gi|242398324|ref|YP_002993748.1|  24 VVKAVDNVSFtVKEGEIISLIGQSGSGKTTLGKIILRLIPPTSGRVLFYG-RDIWKEIKTKEERKEYWRQVH 94 
                                       4567788888346678888***********99877666556777777765.577777777777777766665 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.4
                         IstB_IS21 106 llkvdllilDdl.gllpldqaeaell 130
                                       +lk++lli D+  ++l+++      +
  gi|242398324|ref|YP_002993748.1| 171 ILKPKLLIADEAvSMLDVSTRG--RI 194
                                       6788999999841444444443..33 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00029      0.28      18      41 ..      35      60 ..      15      68 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00029
                                      H..TEEEEEEESTTSSHHHHHHHHHH CS
                              TsaE 18 l..gdvilLeGdLGaGKTtlvrglak 41
                                      +  g++i L G+ G+GKTtl + +++
  gi|242398324|ref|YP_002993748.1| 35 VkeGEIISLIGQSGSGKTTLGKIILR 60
                                      133788**************999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); expected 358.6 (0.02)
Passed bias filter:                      513  (0.0286129); expected 358.6 (0.02)
Passed Vit filter:                       103  (0.00574488); 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: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 1802.75
//
Query:       gi|242398325|ref|YP_002993749.1|  [L=467]
Description: Beta-glucosidase [Thermococcus sibiricus MM 739]
Scores for 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-63  212.2   0.3    1.4e-55  188.6   0.1    3.1  2  Glyco_hydro_1  Glycosyl hydrolase family 1


Domain annotation for each model (and alignments):
>> Glyco_hydro_1  Glycosyl hydrolase family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.2e-07    0.0021      50      89 ..      33      72 ..       9      79 .. 0.75
   2 !  188.6   0.1   7.6e-60   1.4e-55      95     452 ..     107     450 ..      98     451 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.2e-07
                                      -SSTT-HHHHHHHHHHHHHHTT-SEEEEE--HHHHSTTST CS
                     Glyco_hydro_1 50 gdvacdsYhrykeDvallkelgvkayrfSisWpRilPkGe 89
                                       + +  ++h yk+D ++ ++lg+ a+r  i W+R++Pk++
  gi|242398325|ref|YP_002993749.1| 33 PENGPAYWHLYKQDHDIAEKLGMGAIRGGIEWARLFPKPT 72
                                      34455689*****************************986 PP

  == domain 2  score: 188.6 bits;  conditional E-value: 7.6e-60
                                       HHHHHHHHHHHHHHHTT-EEEEEEESS--BHHHHH.H...........-GGG-SHHHHHHHHHHHHHHHHHTTT--E CS
                     Glyco_hydro_1  95 kGlayYerLidelleagieplvTlyHwdlPqaLqd.e...........Ggwenrsiidafkeyaevvfkrfgdkvkl 159
                                       k l++Y+++    +++g   ++ lyHw lP +L+d              gw +++ + +f ++ ++v  ++ + v++
  gi|242398325|ref|YP_002993749.1| 107 KALEHYRKIYSDWKDRGKVFILNLYHWPLPLWLHDpIkvrrlgpdrapSGWLDERSVVEFAKFVAFVSYHLDELVDM 183
                                       7799*****************************98524566644444459****9999******************* PP

                                       EEEEE-HHHHHHHHHT..SS-STT-S-TTTHHHHHHHHHHHHHHHHHHHHHHHTTT-EEEEEEEEEEEEESSSSHHH CS
                     Glyco_hydro_1 160 wlTfnEpnvvallgyl..tgefaPgkkdleaayeaaHnlllaharavklykevaqkgkigivlnlslaeplseseed 234
                                       w T+nEpnvv+  gy   t+ f+Pg  ++ea+ ++a nl+ ahara++++ke+ +   +g+++++++ + l e+ ed
  gi|242398325|ref|YP_002993749.1| 184 WSTMNEPNVVFENGYSrpTSGFPPGYLSFEASEKVAKNLIQAHARAYDAIKEHSD-KPVGLIYAYTWLDSLREDIED 259
                                       ***************755789******************************9875.58**********999998888 PP

                                       HHHHHHHHHHHTHHHHHHHHHSS--HHHHHHHGGG..S----HHHHHHHTT--SEEEEEEEEEEEEEE--...-STT CS
                     Glyco_hydro_1 235 keaaeraleflngwfldpvvkGdYpeemkellrergalpeiteedkellkgkadflglnyYtsrlvknkeseeasls 311
                                       +   +r +e +++ f+d v+ G+ +      l           e  e lkg +d+lg+nyY++    +     + +s
  gi|242398325|ref|YP_002993749.1| 260 EV--KRIRETNLHRFVDSVYFGSSS------L----------SEGREDLKGRVDWLGVNYYSRLAFDKVGDYIMPVS 318
                                       75..5666666669*****999633......2..........2345789*************999998885555666 PP

                                       ---SSGGGGG-.SBSS-B-SSSS-B-HHHHHHHHHHHHHTS----EEEEE----EE-BSSSHHH--HHHHHHHHHHH CS
                     Glyco_hydro_1 312 kteekkleeev.dpslpktdigwiiepeglrkllellkkeYqklpiyiteNGlgakdeieegkveDdkRidYlkehl 387
                                           +++++ + +   p +d gw+i+pegl kll+ l+++Y+ +p+ i+eNG++++         D +R +Yl +hl
  gi|242398325|ref|YP_002993749.1| 319 GYGFSGVKRGYaKSGRPCSDFGWEIYPEGLEKLLKELHEKYS-VPMIIAENGIADES--------DRYRPYYLVSHL 386
                                       666666666663556799************************.**********9876........99********** PP

                                       HHHHHHHHTT--EEEEEEE-SB----GGGTTSEE--SEEEETTTTTEEEE-HHHHHHHHHHH-SS CS
                     Glyco_hydro_1 388 nevkkaiedgvdlkgYvawsllDnfewaegyskrfGlvyvdrnetleRtpkkSakwykeviekng 452
                                       +++++a++ g+d++gY+ wsl+Dn+ewa+g+++rfGl++vd +et++R+ + Sa  ++e++++++
  gi|242398325|ref|YP_002993749.1| 387 QAIHNAMKAGADVRGYLHWSLTDNYEWAQGFRMRFGLLHVD-FETKKRYLRPSALVFREIATHKE 450
                                       *****************************************.9*****************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (467 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.49
# Mc/sec: 2866.41
//
Query:       gi|242398326|ref|YP_002993750.1|  [L=74]
Description: hypothetical protein TSIB_0335 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.67   10.0   2.2       0.76    9.8   2.2    1.0  1  DUF3043   Protein of unknown function (DUF3043)


Domain annotation for each model (and alignments):
>> DUF3043  Protein of unknown function (DUF3043)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   2.2   4.2e-05      0.76      73     134 ..      13      71 ..      10      74 .] 0.48

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 4.2e-05
                           DUF3043  73 Dsrrnlgelflplalvvlvlllvslvkvpevqavvsllllvllllvvidgillgrkvkkkvr 134
                                       D  r++  +++ ++l+ l ++++  ++v ++   v l++l++   ++i  i l+ k++ k++
  gi|242398326|ref|YP_002993750.1|  13 DRYRHFLFFMVWFFLLSLYTVIALRNEVHTLTFKVGLFMLLI---TLIGIIELAAKIRAKIK 71 
                                       555555555555555555554444444444444444455544...45555555555554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       863  (0.0481343); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); 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):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 493.13
//
Query:       gi|242398327|ref|YP_002993751.1|  [L=48]
Description: hypothetical protein TSIB_0336 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); 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 0.27s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 320.25
//
Query:       gi|242398328|ref|YP_002993752.1|  [L=339]
Description: Probable tRNA pseudouridine synthase B [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.4e-26   91.3   0.6    3.8e-16   59.8   0.1    3.1  2  TruB_N    TruB family pseudouridylate synthase (N terminal do
      1e-24   86.5   0.0    2.3e-24   85.3   0.0    1.7  1  TruB_C_2  tRNA pseudouridylate synthase B C-terminal domain
    3.7e-20   71.7   0.2    7.1e-20   70.8   0.2    1.5  1  PUA       PUA domain
      1e-16   60.7   0.0    2.8e-16   59.3   0.0    1.8  1  DKCLD     DKCLD (NUC011) domain
    0.00017   21.8   0.1    0.00058   20.1   0.0    1.9  2  UPF0113   UPF0113 PUA domain
  ------ inclusion threshold ------
       0.18   11.9   0.0        0.4   10.8   0.0    1.5  1  SIR2_2    SIR2-like domain


Domain annotation for each model (and alignments):
>> TruB_N  TruB family pseudouridylate synthase (N terminal domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.8   0.1   1.3e-19   3.8e-16       1      53 [.      72     124 ..      72     128 .. 0.95
   2 !   27.3   0.1   1.3e-09   3.9e-06      72     149 .]     125     185 ..     122     185 .. 0.96

  Alignments for each domain:
  == domain 1  score: 59.8 bits;  conditional E-value: 1.3e-19
                                       HHHTT-S-EEESS---TT-EEEEEEEEGGGGGGHHHCTTS-EEEEEEEEETEE CS
                            TruB_N   1 krllkakkvGhtGtLDplatGvLvvavgeaTklleylleadKeYeatirlgae 53 
                                       k+ll+ +k+Gh+GtLDp++tGvL+va+++aT++++ ll a KeY+a ++l+ e
  gi|242398328|ref|YP_002993752.1|  72 KKLLNLQKAGHGGTLDPKVTGVLPVALERATRVVQALLPAGKEYVALMHLHGE 124
                                       799*********************************************99866 PP

  == domain 2  score: 27.3 bits;  conditional E-value: 1.3e-09
                                       --HHHHHHHHHHC-EEE---------------------------------EEEEEEEEEEEEEEEEEEEEEESTTTT CS
                            TruB_N  72 lteekleevlkkftGeieqvppmySAvkvnGkrlyelaregeeverkkrkvtiyelelleveepevelevecskGtY 148
                                       + e+k++ v+k+f+Gei q+pp  SAvk                 r+ r+ ++y +++le+e ++v ++v +++GtY
  gi|242398328|ref|YP_002993752.1| 125 VPEDKIRVVMKEFEGEIIQRPPLRSAVK-----------------RRLRTRKVYYIDVLEIEGKDVLFRVGVEAGTY 184
                                       66899***********************.................899***************************** PP

                                       H CS
                            TruB_N 149 i 149
                                       i
  gi|242398328|ref|YP_002993752.1| 185 I 185
                                       8 PP

>> TruB_C_2  tRNA pseudouridylate synthase B C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.3   0.0   7.8e-28   2.3e-24       1      63 [.     186     252 ..     186     253 .. 0.94

  Alignments for each domain:
  == domain 1  score: 85.3 bits;  conditional E-value: 7.8e-28
                                       HHHHHHHHHHTTS-EEEEEEEEEEETTE.GG-..B-HHHHHHHHHHHHT..--H.HHHHEEEGGGGG CS
                          TruB_C_2   1 RtLcdDiGeaLgcgAhveeLRRtrvgpf.deedmvtledLedavllyke..dee.LdrlllPlesal 63 
                                       R+L+++iG+aLg+gAh++eLRRtr+gpf ++e +vtl+dL da++++ke   ee  +r ++P+e+a+
  gi|242398328|ref|YP_002993752.1| 186 RSLIHHIGLALGVGAHMSELRRTRSGPFkEDETLVTLHDLIDAYYFWKEdgIEEyFRRAIQPMEKAV 252
                                       9***************************989999***************885557**********98 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.8   0.2   2.4e-23   7.1e-20       1      73 [.     256     328 ..     256     329 .. 0.98

  Alignments for each domain:
  == domain 1  score: 70.8 bits;  conditional E-value: 2.4e-23
                                       CEEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEEEE CS
                               PUA   1 grvvvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksveierv 73 
                                       ++v++ d+Av a+++ga+L +pG+v+ ++ ++++d Vai++ ++elva+G+a+++++e+ + ++g++v++e+v
  gi|242398328|ref|YP_002993752.1| 256 PKVWIRDSAVAAITHGADLAVPGIVKLHKGIKPDDLVAIMTLKDELVALGKAKMNTQEMLTKTKGIAVDVEKV 328
                                       69********************************************************************997 PP

>> DKCLD  DKCLD (NUC011) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.3   0.0   9.4e-20   2.8e-16       5      58 .]      16      68 ..      12      68 .. 0.87

  Alignments for each domain:
  == domain 1  score: 59.3 bits;  conditional E-value: 9.4e-20
                                      X....XXX-EEESS-.----TTSS--GGG--HHHHHHTEEEEEEE-SSS-HHHHH CS
                             DKCLD  5 pllLknydkllvrte.hytplpaGssPlkRpieeyikyGvinLDKPsnPsSHEVV 58
                                      p +L  +++++++ e ++t+ ++G+ P kRpie ++++G+i LDKP +P+SHEVV
  gi|242398328|ref|YP_002993752.1| 16 PADL--KREIIIKDEkAETNPKWGFPPEKRPIEMHMQFGIISLDKPPGPTSHEVV 68
                                      5555..467888865279************************************9 PP

>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.6   4.8e+03      60      76 .]     171     187 ..     163     187 .. 0.74
   2 !   20.1   0.0   1.9e-07   0.00058       1      62 [.     257     321 ..     257     326 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.6
                           UPF0113  60 gkivvknlaDiGeYlRr 76 
                                       ++++++  +  G+Y+R+
  gi|242398328|ref|YP_002993752.1| 171 KDVLFRVGVEAGTYIRS 187
                                       55666667889999995 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 1.9e-07
                           UPF0113   1 kvvvkekaeklFLYGrdvlkesilkitesvkenqvvvVlnengeplGiGkirkdt..k.aspgki 62 
                                       kv+++ +a   ++ G d+   +i+k+ +++k  + v+++  ++e++++Gk++ +t     ++++i
  gi|242398328|ref|YP_002993752.1| 257 KVWIRDSAVAAITHGADLAVPGIVKLHKGIKPDDLVAIMTLKDELVALGKAKMNTqeMlTKTKGI 321
                                       89*************************************************99987533444444 PP

>> SIR2_2  SIR2-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00013       0.4      36      90 ..     107     160 ..      79     163 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00013
                            SIR2_2  36 elseaesgrtllyklhGslsrpesivltesdYeellarktpiptllkallrsksl 90 
                                       +l +a ++ + l++lhG +  +++i +  +++e  + +++p++ ++k +lr++ +
  gi|242398328|ref|YP_002993752.1| 107 ALLPAGKEYVALMHLHGEVP-EDKIRVVMKEFEGEIIQRPPLRSAVKRRLRTRKV 160
                                       45667778889********7.899999999997777789***********99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); 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: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2283.66
//
Query:       gi|242398329|ref|YP_002993753.1|  [L=195]
Description: Ribosomal RNA small subunit methyltransferase C [Thermococcus sibiricus MM 739]
Scores for complete 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  144.1   0.0    3.4e-42  143.9   0.0    1.0  1  MTS              Methyltransferase small domain
    3.2e-10   39.9   0.2    5.4e-10   39.1   0.2    1.4  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    1.1e-06   28.5   0.0    1.3e-06   28.3   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    5.2e-06   26.2   0.0    6.6e-06   25.9   0.0    1.2  1  Cons_hypoth95    Conserved hypothetical protein 95
    9.5e-06   26.2   0.0    1.5e-05   25.6   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
    1.3e-05   24.4   0.0    1.7e-05   24.0   0.0    1.2  1  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
    3.7e-05   23.5   0.0    5.5e-05   23.0   0.0    1.2  1  Methyltransf_16  Lysine methyltransferase
    5.4e-05   23.2   0.0    8.6e-05   22.5   0.0    1.4  1  Methyltransf_18  Methyltransferase domain
    0.00091   19.1   0.0     0.0022   17.8   0.0    1.8  1  Methyltransf_23  Methyltransferase domain
     0.0068   17.1   0.0      0.011   16.5   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
  ------ inclusion threshold ------
      0.011   16.3   0.0       0.02   15.5   0.0    1.5  1  Methyltransf_11  Methyltransferase domain
      0.013   15.2   0.1       0.02   14.7   0.1    1.4  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
      0.018   14.3   0.0      0.019   14.2   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
      0.038   13.3   0.1      0.054   12.8   0.1    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
      0.066   12.3   0.0      0.094   11.8   0.0    1.2  1  Pox_MCEL         mRNA capping enzyme
      0.097   11.8   0.0       0.13   11.4   0.0    1.2  1  TRM              N2,N2-dimethylguanosine tRNA methyltransfera
       0.11   11.9   0.1        1.5    8.2   0.1    2.0  2  TehB             Tellurite resistance protein TehB
       0.11   12.0   0.0       0.15   11.5   0.0    1.2  1  AviRa            RRNA methyltransferase AviRa


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 !  143.9   0.0   3.4e-45   3.4e-42       2     168 ..      27     191 ..      26     192 .. 0.97

  Alignments for each domain:
  == domain 1  score: 143.9 bits;  conditional E-value: 3.4e-45
                                       EEEEEETTSTTTTS--HHHHHHHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHT CS
                               MTS   2 ltlktlpgvFskdklDkGsklLletlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenlean 78 
                                       ++++t +gvFs +klD G+klL+e++  e++ +vlDlGcG+G++g+++ ++ +    +++d+++rA+ +ak+nl+ n
  gi|242398329|ref|YP_002993753.1|  27 FRFITSSGVFSFGKLDRGTKLLIENMVLEENWQVLDLGCGYGAIGIVASRFVDY--AVMTDINKRAVSIAKKNLKIN 101
                                       5899**********************************************9999..79******************9 PP

                                       TGC.EEEEE-STTTTSTTS-EEEEEE---STTTCHCHHHHHHHHHHHHHHHEEEEEEEEEEEETTSCHHHH...HHH CS
                               MTS  79 kle.vevvasdvleeveekkfdlivsNPPfhagkatelavaeeliaeAkeaLkegGeLliVanrklgyesl...lee 151
                                       ++  +ev++  ++e v+ ++f  i++NPP+hagk+    + +e++ +A+ +L +gG L+iV+++++g++ +   +ee
  gi|242398329|ref|YP_002993753.1| 102 NVMnAEVRWGHLYEPVKGERFHSIITNPPVHAGKD----ILREIVINAPYHLYDGGLLQIVIRTNQGAKYIkglMEE 174
                                       9999*******************************....****************************9998889*** PP

                                       HHS--EEEEEESSEEEE CS
                               MTS 152 lfgnvevvaktkkfkvl 168
                                        f++v+++a+ ++f+v+
  gi|242398329|ref|YP_002993753.1| 175 NFNEVKEIARGSGFRVY 191
                                       ****************8 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1   0.2   5.4e-13   5.4e-10     155     241 ..      49     144 ..      44     193 .. 0.66

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 5.4e-13
                              PrmA 155 leklvkege.evlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkvea.klevalseellkeekadv 229
                                       +e++v e++ +vlD+G+G G + i+a+++  + +v +Di++ Av++ak+N+++N+v + +++     e +k e++  
  gi|242398329|ref|YP_002993753.1|  49 IENMVLEENwQVLDLGCGYGAIGIVASRFV-DYAVMTDINKRAVSIAKKNLKINNVMNaEVRWGHLYEPVKGERFHS 124
                                       5666666555******************96.667789*******************995555444455556688888 PP

                              PrmA 230 ivaN........ILaevlie 241
                                       i+ N        IL e++i+
  gi|242398329|ref|YP_002993753.1| 125 IITNppvhagkdILREIVIN 144
                                       88885544444444444444 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.0   1.3e-09   1.3e-06       2      89 ..      55     136 ..      54     183 .. 0.80

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 1.3e-09
                   Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDli 78 
                                       +++ +vlDlGCG G++++++  +  +    v  Di+++a++ A++n++ +++ n+e++ g   e +  ++ e+f  i
  gi|242398329|ref|YP_002993753.1|  55 EENWQVLDLGCGYGAIGIVAS-RFVD--YAVMTDINKRAVSIAKKNLKINNVMNAEVRWGHLYE-P--VKGERFHSI 125
                                       57889***************9.5544..35678************9998888888888887777.4..456899999 PP

                   Methyltransf_31  79 lsnevlnalad 89 
                                       ++n +++a +d
  gi|242398329|ref|YP_002993753.1| 126 ITNPPVHAGKD 136
                                       99977655444 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   6.6e-09   6.6e-06      41     128 ..      56     136 ..      47     182 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 6.6e-09
                                       CC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEE CS
                     Cons_hypoth95  41 egarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdiv 117
                                       e+ +vLDl +G Ga+g+ A SR ++ av+ + +k+av+i k+nl+  ++ +       +     l ++ k+e+f  +
  gi|242398329|ref|YP_002993753.1|  56 ENWQVLDLGCGYGAIGIVA-SRFVDYAVMTDINKRAVSIAKKNLKINNVMN------AEVRWGHLYEPVKGERFHSI 125
                                       46689************76.***********************98776443......33333444555678899999 PP

                                       EE--SSSTTCH CS
                     Cons_hypoth95 118 flDPPyakell 128
                                         +PP ++++ 
  gi|242398329|ref|YP_002993753.1| 126 ITNPPVHAGKD 136
                                       99999998865 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   1.5e-08   1.5e-05       1      75 [.      60     132 ..      60     153 .. 0.78

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1.5e-08
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEEEST.GG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvssga.lh 75 
                                       vLdlGcG G + + +++ +     +++Di+++++ +a+++++ +++ n+e++ g + + p + ++f+ ++  +  +h
  gi|242398329|ref|YP_002993753.1|  60 VLDLGCGYGAIGIVASRFV--DYAVMTDINKRAVSIAKKNLKINNVmNAEVRWGHLYE-PVKGERFHSIIT-NPpVH 132
                                       9**********99999887..99******************99988899888888766.566778888887.34244 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 !   24.0   0.0   1.7e-08   1.7e-05     199     252 ..      54     107 ..       8     112 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1.7e-08
                   tRNA_U5-meth_tr 199 qeskgdllelycGnGnfslalarnfekvlateiakssveaaqyniaankidnvq 252
                                        e++  +l+l cG+G   +  +r++   + t+i k +v+ a++n++ n++ n +
  gi|242398329|ref|YP_002993753.1|  54 LEENWQVLDLGCGYGAIGIVASRFVDYAVMTDINKRAVSIAKKNLKINNVMNAE 107
                                       4556689*******************************************9976 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   5.5e-08   5.5e-05      46     108 ..      56     111 ..      38     127 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 5.5e-08
                   Methyltransf_16  46 sklsvlELGsGtGlvGlavaellpeakviltDlee.llellkknielnknalkskvkvevLdWg 108
                                       ++ +vl+LG G G +G+++ +       ++tD+++ ++ + kkn+++n+  ++ +v+     Wg
  gi|242398329|ref|YP_002993753.1|  56 ENWQVLDLGCGYGAIGIVASRF--VDYAVMTDINKrAVSIAKKNLKINN-VMNAEVR-----WG 111
                                       6789**************9999..334568**998799*********76.5555554.....44 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   8.6e-08   8.6e-05       8      87 ..      49     126 ..      46     192 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 8.6e-08
                   Methyltransf_18   8 iaslvekgs.rvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGleklkeeev 83 
                                       i ++v +++ +v+D G+  g + i +  ++ ++ ++++Din+ +++ ak+n++ +++  + evr +   e++k e +
  gi|242398329|ref|YP_002993753.1|  49 IENMVLEENwQVLDLGCGYGAIGIVA--SRFVDYAVMTDINKRAVSIAKKNLKINNVM-NAEVRWGHLYEPVKGERF 122
                                       55677666669******999888765..589***********************9995.689999988888875556 PP

                   Methyltransf_18  84 dtvv 87 
                                       + ++
  gi|242398329|ref|YP_002993753.1| 123 HSII 126
                                       6555 PP

>> Methyltransf_23  Methyltransferase 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    0.0022      16      71 ..      48     105 ..      35     192 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.3e-06
                   Methyltransf_23  16 llpk..lraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiaekakkaqkdqf 71 
                                       l ++  l+++  vLd+GcG+G    v+++++   ++ D++ +av+ia+k  k ++++ 
  gi|242398329|ref|YP_002993753.1|  48 LIENmvLEENWQVLDLGCGYGAIGIVASRFVDYAVMTDINKRAVSIAKKNLKINNVMN 105
                                       444444778889*********99999999988999***********985555544444 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.1e-05     0.011       1      98 [.      61     154 ..      61     155 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.1e-05
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieyt.gvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvl 76 
                                       L++GcG G++  +  +    ++y   +Di+++a+   ++k  k++n  n++v++ +l      +g+ f  ++ +  +
  gi|242398329|ref|YP_002993753.1|  61 LDLGCGYGAIGIVASRF---VDYAvMTDINKRAV-SIAKKNLKINNVMNAEVRWGHLYEP--VKGERFHSIITNPPV 131
                                       8*******999888665...88877*********.7777777777788888888877744..344589999998888 PP

                   Methyltransf_12  77 hhlkdir.evldnirklLkpgGr 98 
                                       h+ kdi  e++ n+  +L +gG 
  gi|242398329|ref|YP_002993753.1| 132 HAGKDILrEIVINAPYHLYDGGL 154
                                       88877765777777777777776 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.0     2e-05      0.02       1      58 [.      61     118 ..      61     142 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2e-05
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS- CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl.kvefvvadaeklpfe 58 
                                       Ld+GcG G++     + +   v +D++k+++ +ak++ + +++ + e++ + + + p++
  gi|242398329|ref|YP_002993753.1|  61 LDLGCGYGAIGIVASRFVDYAVMTDINKRAVSIAKKNLKINNVmNAEVRWGHLYE-PVK 118
                                       8********99999999999******************99987755555455544.555 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 ?   14.7   0.1     2e-05      0.02      66     131 ..      49     111 ..      44     175 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2e-05
                                       HHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES CS
                              PCMT  66 lellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvg 131
                                       +e + l++  +vL++G+G G    v +r+v         +  k+ v+ ak+nlk ++++n  v+ g
  gi|242398329|ref|YP_002993753.1|  49 IENMVLEENWQVLDLGCGYGAIGIVASRFVDYAV---MTDINKRAVSIAKKNLKINNVMNAEVRWG 111
                                       6677799***********************9766...67777889999*****9999999888776 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.9e-05     0.019      52     106 ..      46      99 ..      41     179 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.9e-05
                                       HHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHH CS
                              CMAS  52 dlileklelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvd 106
                                       +l++e + l++  ++Ld+GcG+G++ + a +  d  v+   + k     akk+++
  gi|242398329|ref|YP_002993753.1|  46 KLLIENMVLEENWQVLDLGCGYGAIGIVASRFVDYAVMT-DINKRAVSIAKKNLK 99 
                                       78899999****************998887776665553.455555555555554 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   5.4e-05     0.054      26     101 ..      35     107 ..      16     115 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.4e-05
                                       HHHTTTHHHHHHHHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEE CS
                   Ubie_methyltran  26 vlslgihrlWkkfveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinie 101
                                       v+s+g  +   k +++ +   +  +vlD+ +G g + +  s+ v+     v+ Din+  +++++k lk + ++n e
  gi|242398329|ref|YP_002993753.1|  35 VFSFGKLDRGTKLLIENMVLEENWQVLDLGCGYGAIGIVASRFVDY---AVMTDINKRAVSIAKKNLKINNVMNAE 107
                                       788888888888888888999999*************999999986...4789*************9999888543 PP

>> Pox_MCEL  mRNA capping enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   9.5e-05     0.094      64     135 ..      56     126 ..      45     137 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9.5e-05
                          Pox_MCEL  64 nklkvLdldcgkGgDLeKyekgeIsklvatDiaeesieeckeRYnklrsekkskyykFdaelirsdsfvssv 135
                                       ++ +vLdl+cg G+ +       +++ v tDi+++++  +k+  +  + ++++ ++ + +e ++++ f+s +
  gi|242398329|ref|YP_002993753.1|  56 ENWQVLDLGCGYGA-IGIVASRFVDYAVMTDINKRAVSIAKKNLKINNVMNAEVRWGHLYEPVKGERFHSII 126
                                       5779*********9.555677789999*****************9999999999999999999999888876 PP

>> TRM  N2,N2-dimethylguanosine tRNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00013      0.13      74     101 ..      78     105 ..      50     126 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00013
                                       EEEEEEE-S-HHHHHHHHHHHHHTT--G CS
                               TRM  74 vkevlaNDisekAvelikeNvklnevee 101
                                       v  +++ Di+++Av + k+N k+n+v +
  gi|242398329|ref|YP_002993753.1|  78 VDYAVMTDINKRAVSIAKKNLKINNVMN 105
                                       4567899******************986 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.12   1.2e+02      93     120 ..      24      52 ..       7      59 .. 0.78
   2 ?    8.2   0.1    0.0015       1.5      33      89 ..      59     115 ..      53     163 .. 0.71

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.12
                                       -S-EEEEEEESSGGGS-GGGHHH.HHHHH CS
                              TehB  93 derydfilstvvlmfleaerips.iienm 120
                                        er+ fi s+ v+ f + +r ++ +ienm
  gi|242398329|ref|YP_002993753.1|  24 GERFRFITSSGVFSFGKLDRGTKlLIENM 52 
                                       5899***********99888655268998 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0015
                                       EEEEES-TTSHHHHHHHH.TT-EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG CS
                              TehB  33 kvldlgcgqgrnslylsl.lgydvtawdknensiafleeikekenlknistalydine 89 
                                       +vldlgcg g   +  s  + y v   d n+ +++  ++  +++n+ n + +  ++ e
  gi|242398329|ref|YP_002993753.1|  59 QVLDLGCGYGAIGIVASRfVDYAVM-TDINKRAVSIAKKNLKINNVMNAEVRWGHLYE 115
                                       79********999988751567764.57777777777777777777766666555555 PP

>> AviRa  RRNA methyltransferase AviRa
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00015      0.15      56     101 ..      59     100 ..      43     118 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00015
                             AviRa  56 tlyDpCCGgayLltvlgllhgkkikkvlasDvdeevlelakkNLsL 101
                                       ++ D  CG +    ++g++ ++ +   + +D+++ ++++akkNL++
  gi|242398329|ref|YP_002993753.1|  59 QVLDLGCGYG----AIGIVASRFVDYAVMTDINKRAVSIAKKNLKI 100
                                       5666666654....799***************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1194.55
//
Query:       gi|242398330|ref|YP_002993754.1|  [L=156]
Description: 30S ribosomal protein S13P [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-40  139.0   0.1    1.3e-40  138.8   0.1    1.0  1  Ribosomal_S13  Ribosomal protein S13/S18


Domain annotation for each model (and alignments):
>> Ribosomal_S13  Ribosomal protein S13/S18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.8   0.1     7e-45   1.3e-40       1     128 []      17     145 ..      17     145 .. 0.99

  Alignments for each domain:
  == domain 1  score: 138.8 bits;  conditional E-value: 7e-45
                     Ribosomal_S13   1 RilgtdidgkkkveialtaikGiGrrkakiilkkadvdedkrigelteeeiekieeivenkaqykipnwi.nrqkdi 76 
                                       R++++didg+k++++alt i+GiG + a++i++ a++d ++++g ltee+++ ie ++e +a++  p+wi nr kd+
  gi|242398330|ref|YP_002993754.1|  17 RVANVDIDGHKQLRLALTGIRGIGVNFATVICRIAGLDPKMKAGYLTEEQVKAIEAVLEDPAKHGLPSWIlNRPKDY 93 
                                       99*************************************************************************** PP

                     Ribosomal_S13  77 kdGkdshvvendlrrklredieRlkkirsyrGlRHkrGlkvRGQrTkttgRt 128
                                       ++G+d+h++  +l +  red++Rl+kir+yrG+RH+ Gl++RGQrT+++ R+
  gi|242398330|ref|YP_002993754.1|  94 EQGRDMHLIGAKLVMAWREDVNRLRKIRAYRGIRHELGLPLRGQRTRSNFRR 145
                                       *************************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        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 0.25s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1101.27
//
Query:       gi|242398331|ref|YP_002993755.1|  [L=180]
Description: 30S ribosomal protein S4P [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-16   59.2   0.1    2.3e-16   59.2   0.1    2.2  2  S4               S4 domain
  ------ inclusion threshold ------
       0.16   11.6   0.0       0.22   11.2   0.0    1.2  1  Acyltransferase  Acyltransferase


Domain annotation for each model (and alignments):
>> S4  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.4      0.27   2.4e+03      16      25 ..      52      61 ..      51      63 .. 0.82
   2 !   59.2   0.1   2.6e-20   2.3e-16       1      46 [.     103     148 ..     103     150 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.27
                                      HHHHHHHHHT CS
                                S4 16 rreArqlIeh 25
                                      rr Ar+l  +
  gi|242398331|ref|YP_002993755.1| 52 RRRARRLLAA 61
                                      899**99765 PP

  == domain 2  score: 59.2 bits;  conditional E-value: 2.6e-20
                                       EEHHHHHHHTTSSSSHHHHHHHHHTTTEEETTEEE--TT-EE-TTC CS
                                S4   1 rRLdkvlarlglassrreArqlIehGrVlVNGkvvkdpsyrVkpgD 46 
                                       rRL+++++++gla ++++ArqlI hG++ VNG+++++psy V  ++
  gi|242398331|ref|YP_002993755.1| 103 RRLQTLVFKKGLARTIKQARQLIVHGHIEVNGQIIRSPSYLVLKEE 148
                                       8*****************************************8766 PP

>> Acyltransferase  Acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   2.4e-05      0.22      77     125 ..      60     122 ..      16     130 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2.4e-05
                   Acyltransferase  77 raagslenise..lleegklvviFPEGtrsre.............gellpfkkGlvrlaakakk 125
                                        a+g  ++i++  ll++   ++i PEG  + +              ++l fkkGl+r + +a +
  gi|242398331|ref|YP_002993755.1|  60 AARGKQAEIERaqLLQRLARLGILPEGAHLDDvlsltiddilerrLQTLVFKKGLARTIKQA-R 122
                                       33333334444437777677*******999999999999999965666**********9999.3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       730  (0.0407162); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1154.75
//
Query:       gi|242398332|ref|YP_002993756.1|  [L=139]
Description: 30S ribosomal protein S11P [Thermococcus sibiricus MM 739]
Scores for complete 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  166.5   1.8    2.8e-49  166.1   1.8    1.2  1  Ribosomal_S11  Ribosomal protein S11
  ------ inclusion threshold ------
      0.076   13.3   0.0       0.15   12.3   0.0    1.5  1  CBM_25         Carbohydrate binding domain (family 25)
       0.08   12.7   0.2       0.11   12.2   0.2    1.3  1  Pilus_CpaD     Pilus biogenesis CpaD protein (pilus_cpaD)


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 !  166.1   1.8   4.7e-53   2.8e-49       1     110 []      17     135 ..      17     135 .. 0.99

  Alignments for each domain:
  == domain 1  score: 166.1 bits;  conditional E-value: 4.7e-53
                     Ribosomal_S11   1 GvahiqasfnntiititdlkGaevlvksaGglgvkasr.kssPyaaqlaaekaaekvldkGikavevkvkg...... 70 
                                       Gvahi+as+nntii+itdl+Gae+++k +Gg++vka+r +ssPyaa+ aa++aae++++kGi+ v++kv++      
  gi|242398332|ref|YP_002993756.1|  17 GVAHIYASYNNTIIHITDLTGAETISKWSGGMVVKADRdESSPYAAMIAARRAAEEAMEKGINGVHIKVRApggsks 93 
                                       9**************************************************************************** PP

                     Ribosomal_S11  71 ..pGpGreaalralaraGlkigriedvtPiPhdgirrpkkrr 110
                                         pGpG++aa+ralaraGl+igr+edvtPiPhdg+r++++rr
  gi|242398332|ref|YP_002993756.1|  94 knPGPGAQAAIRALARAGLRIGRVEDVTPIPHDGTRPKGGRR 135
                                       ***************************************998 PP

>> CBM_25  Carbohydrate binding domain (family 25)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.6e-05      0.15      13      62 ..      74     123 ..      68     133 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.6e-05
                            CBM_25  13 rkkGftsayihyrpaGGswtavpGvkmrdaeaGyakkdvdlGaassleaa 62 
                                        +kG +  +i+ r  GGs +  pG + ++a    a+  + +G   +++  
  gi|242398332|ref|YP_002993756.1|  74 MEKGINGVHIKVRAPGGSKSKNPGPGAQAAIRALARAGLRIGRVEDVTPI 123
                                       579****************************9999999999988777655 PP

>> Pilus_CpaD  Pilus biogenesis CpaD protein (pilus_cpaD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   1.8e-05      0.11      71     122 ..      43      94 ..      31     111 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.8e-05
                        Pilus_CpaD  71 egagaivisvpsgssneaaaaaaaaeiravlaaaGvpaseisvrayqaaape 122
                                       + +g +v+++ +++s++ aa+ aa++ ++ ++++G+++ +i+vra  +++ +
  gi|242398332|ref|YP_002993756.1|  43 KWSGGMVVKADRDESSPYAAMIAARRAAEEAMEKGINGVHIKVRAPGGSKSK 94 
                                       55788999***********************************997776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.51
# Mc/sec: 821.44
//
Query:       gi|242398333|ref|YP_002993757.1|  [L=271]
Description: DNA-directed RNA polymerase subunit D [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-28   99.9   0.0    2.4e-28   98.8   0.0    1.6  1  RNA_pol_A_bac  RNA polymerase Rpb3/RpoA insert domain
    9.4e-18   63.4   0.0    1.4e-17   62.9   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 !   98.8   0.0   2.7e-32   2.4e-28       1     112 []      57     159 ..      57     159 .. 0.94

  Alignments for each domain:
  == domain 1  score: 98.8 bits;  conditional E-value: 2.7e-32
                                       EEEEECTSSS.HHHHHCHHHCSTCBSSCHHHHHHHHCTT-ETSSSSTTCSEEEEEEEEESSECEEGGGCBESSSSCE CS
                     RNA_pol_A_bac   1 VeieentsvlqDEvvaHrlgliplvsedvleillnlkelveeeeegeeeksvelkLnvkgpgevtagdlkledadve 77 
                                       Ve++en+s+l DE++aHrl+lipl++  +++      el   e+ + e+ +v+l+L+++gp  v++gdlk+ d+dv+
  gi|242398333|ref|YP_002993757.1|  57 VEFYENDSALFDEIIAHRLSLIPLTTPFDRF------EL---ESMELEDYTVTLSLEAEGPAIVYSGDLKSDDPDVK 124
                                       89***********************988888......56...235677777************************** PP

                                       ESSTTSEEEEEETT-EEEEEEEEEEESSEECTTT- CS
                     RNA_pol_A_bac  78 ivnpdilIakLrkgqeleleakvkkGiGkehakfs 112
                                       +vnp+i+I+kL++gq+l ++a++k G Gk+hak++
  gi|242398333|ref|YP_002993757.1| 125 PVNPNIPIVKLAEGQRLVFNAYAKMGKGKDHAKWQ 159
                                       **********************************6 PP

>> RNA_pol_L  RNA polymerase Rpb3/Rpb11 dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.9   0.0   1.6e-21   1.4e-17       1      68 [.      27     258 ..      27     259 .. 0.82

  Alignments for each domain:
  == domain 1  score: 62.9 bits;  conditional E-value: 1.6e-21
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................................... RF
                         RNA_pol_L   1 efllrgvdhtlgNaLRrillsevpgvaiea............................................... 30 
                                       +f l+g+d++++NaLRr+++ evp++ai++                                               
  gi|242398333|ref|YP_002993757.1|  27 RFILEGMDIAFANALRRTIIGEVPTFAIDEvefyendsalfdeiiahrlsliplttpfdrfelesmeledytvtlsl 103
                                       599********************************************************************999999 PP

                                       ............................................................................. RF
                         RNA_pol_L  31 ............................................................................. 30 
                                                                                                                    
  gi|242398333|ref|YP_002993757.1| 104 eaegpaivysgdlksddpdvkpvnpnipivklaegqrlvfnayakmgkgkdhakwqpgfahykyltevhvskevpkw 180
                                       99999999999999999999988888877777777777777777777777777777777777777776666666666 PP

                                       ............xx............................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         RNA_pol_L  31 ............pv............................vkvntdkdklilevetdgslkPeealkeAlkiLke 67 
                                                   pv                            +k + +++ ++++ve++g l++ee+++ AlkiL++
  gi|242398333|ref|YP_002993757.1| 181 edikkaakkkklPVeeteneliittirsfyiprefeqyigekIKEEVVPNTFVFTVESNGELPVEEMISVALKILMR 257
                                       666666555555226666666666666666666666666644445589***************************98 PP

                                       x RF
                         RNA_pol_L  68 k 68 
                                       k
  gi|242398333|ref|YP_002993757.1| 258 K 258
                                       7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 2083.75
//
Query:       gi|242398334|ref|YP_002993758.1|  [L=130]
Description: 50S ribosomal protein L18e [Thermococcus sibiricus MM 739]
Scores for complete 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-16   57.8   0.0    1.5e-15   57.0   0.0    1.3  1  Ribosomal_L18   Ribosomal protein 60S L18 and 50S L18e
    4.1e-09   37.2   1.1    6.2e-09   36.6   1.1    1.4  1  Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27


Domain annotation for each model (and alignments):
>> Ribosomal_L18  Ribosomal protein 60S L18 and 50S L18e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.0   0.0   1.7e-19   1.5e-15      27     138 ..      21     129 ..      11     130 .] 0.90

  Alignments for each domain:
  == domain 1  score: 57.0 bits;  conditional E-value: 1.7e-19
                     Ribosomal_L18  27 LvklyrfLarRtdskFnkv...vlkrLfmsrinrpplslsrlvkkvkkkeeekkiavvvgtvtdDvrllevPklsva 100
                                       L +l r+L ++++++  kv   +  rL   r++++ + +s++ +++k    e+ i+vv g+v+    l +  k+ va
  gi|242398334|ref|YP_002993758.1|  21 LRRLIRYLRKKSNEENVKVwkdIAWRLERPRRQKAEVNISKINRHTK----EGDIIVVPGSVLGAGDLDH--KVIVA 91 
                                       6789999*99998766555444999*******************999....569*********9999986..9**** PP

                     Ribosomal_L18 101 ALrftetararilkaGGeiltlDqLalraPtGkntvLl 138
                                       A +f+e+a+++i++aGGe +t+++L  r+P+G+ ++++
  gi|242398334|ref|YP_002993758.1|  92 AWKFSEKAKEKIIQAGGEAITIEDLIERNPRGSGVIIM 129
                                       **********************************9998 PP

>> Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   1.1     7e-13   6.2e-09      49     127 ..      16     111 ..       1     112 [. 0.67

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 7e-13
                                       -EEEEHHHHHHTTTTGTTS--...............----EEEGGGTTTTSSS........SEEEE--S---.--EE CS
                    Ribosomal_L27A  49 ykvvnlkdLdelideerlela...............deaeeidleelaeaglikk....kdgvKvlgkgeltkklkv 106
                                        + +nl++L +++ ++  e++                +++e++++++  ++ +k+         vlg g+l +k++v
  gi|242398334|ref|YP_002993758.1|  16 PTDINLRRLIRYLRKKSNEENvkvwkdiawrlerprRQKAEVNISKI--NRHTKEgdiiVVPGSVLGAGDLDHKVIV 90 
                                       4555666655555555444223455555555555555789*******..6666665554333379************ PP

                                       EESEE-HHHHHHHHHTT-EEE CS
                    Ribosomal_L27A 107 kaskfSkkAkekIeaaGGkve 127
                                        a kfS+kAkekI +aGG+++
  gi|242398334|ref|YP_002993758.1|  91 AAWKFSEKAKEKIIQAGGEAI 111
                                       ******************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       834  (0.0465168); 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):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 879.23
//
Query:       gi|242398335|ref|YP_002993759.1|  [L=142]
Description: 50S ribosomal protein L13P [Thermococcus sibiricus MM 739]
Scores for complete 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-14   52.1   0.2    1.4e-11   44.7   0.2    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 !   44.7   0.2   7.8e-16   1.4e-11       4     120 ..       3     108 ..       2     113 .. 0.80

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 7.8e-16
                                       EEEETTSBHHHHHHHHHHHHHTTTSTT--TTS--S-EEEEEEGGCBB-SSTHHTT-EEEEE-SSTTSEEEEEHHH.. CS
                     Ribosomal_L13   4 viDAegqvlgrlaskiakvLrGkhkptytphvdcGdyvvvinaekvaltgkkleqkvyyrhtgypgglkevtake.. 78 
                                       +i+Aeg +lgrlask+ak+L              G+ vv+inaek  +tg++    ++ ++++++    +++ ++  
  gi|242398335|ref|YP_002993759.1|   3 IINAEGLILGRLASKVAKMLL------------EGEDVVIINAEKAIITGNRE--FIFEKYKQRTELRTRTNPRKgp 65 
                                       799**************9985............6999*************964..4555555555555555555444 PP

                                       HHCCSHHHHHHHHHHCCS-.SSHHHHHHGCTEEEESSSTTSGG CS
                     Ribosomal_L13  79 llekkpeeilekaVkgmLp.knklgrrrlkrLkvyageehphe 120
                                       +  k+++ei++++++gmLp k+  gr+ +krLkvyag   + e
  gi|242398335|ref|YP_002993759.1|  66 FYPKRSDEIVRRTIRGMLPwKTDRGRKAFKRLKVYAGVPKEFE 108
                                       89999**************777899***********9766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1003.70
//
Query:       gi|242398336|ref|YP_002993760.1|  [L=143]
Description: 30S ribosomal protein S9P [Thermococcus sibiricus MM 739]
Scores for complete 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-30  104.5   0.4      6e-30  104.3   0.4    1.0  1  Ribosomal_S9  Ribosomal protein S9/S16


Domain annotation for each model (and alignments):
>> Ribosomal_S9  Ribosomal protein S9/S16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.3   0.4   3.3e-34     6e-30       1     121 []      16     143 .]      16     143 .] 0.89

  Alignments for each domain:
  == domain 1  score: 104.3 bits;  conditional E-value: 3.3e-34
                                       EECTTEEEEEEEEESSSEEEETTEECCHHSTTSCHHHHHCHHHHHTTTSS..SEEEEEEEESS-HHHHHHHHHHHHH CS
                      Ribosomal_S9   1 GrrKesvArvwikegkgkilvngksleeYfkeeaarekvleplkltgllg..kfdvfvkvkgGGlsgqaeAirlgia 75 
                                       G+rK++vAr++ikeg+g+++vn k++e  ++ e ar +++epl ++g++   k+dv vkv+gGG++gqaeA+r +ia
  gi|242398336|ref|YP_002993760.1|  16 GKRKSAVARATIKEGNGRVRVNYKPVEI-LEPEIARFTIMEPLVIAGEEIlgKVDVDVKVEGGGFMGQAEAARIAIA 91 
                                       8***************************.988*************9975344************************* PP

                                       HHHHHHHHHH..HHHHC..TCCCTS-B--------TTS..SCTTB----S-- CS
                      Ribosomal_S9  76 raLvalekee..kkeLk..kaglltrDpRvvErkKtgk..kkARkkyqwskR 121
                                       raLv+++ ++  k+++   ++++l+ D+R++E++K+++  k+ R+k q+s+R
  gi|242398336|ref|YP_002993760.1|  92 RALVEWTGDMnlKEKFMkyDRTMLVGDSRRTEPHKPNRstKGPRAKRQKSYR 143
                                       ******98432333333589***************98644899*******99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 944.73
//
Query:       gi|242398337|ref|YP_002993761.1|  [L=68]
Description: DNA-directed RNA polymerase subunit N [Thermococcus sibiricus MM 739]
Scores for complete 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  105.3   0.5    1.7e-30  105.1   0.5    1.0  1  RNA_pol_N  RNA polymerases N / 8 kDa subunit


Domain annotation for each model (and alignments):
>> RNA_pol_N  RNA polymerases N / 8 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.1   0.5   9.4e-35   1.7e-30       1      59 []       4      62 ..       4      62 .. 0.98

  Alignments for each domain:
  == domain 1  score: 105.1 bits;  conditional E-value: 9.4e-35
                                      ----SS-TTT--B-STHHHHHHHHHHTT--HHHHHHHHT--SHHHHHHHHTB--THHHH CS
                         RNA_pol_N  1 MiiPVrCFtCGkvigekweeylellekgeepkdaLdaLglkryCCrrmllthvdliekl 59
                                      +i+PVrCFtCGkvig+k+  ++e++ekge+p+++Ld+Lgl+ryCCrrm+l+hv+li+++
  gi|242398337|ref|YP_002993761.1|  4 LIVPVRCFTCGKVIGDKYYIFKERVEKGEDPEKVLDDLGLERYCCRRMFLSHVELIDEI 62
                                      59******************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); 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: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 486.21
//
Query:       gi|242398338|ref|YP_002993762.1|  [L=77]
Description: DNA-directed RNA polymerase subunit K [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.8e-11   42.4   0.1      6e-11   42.1   0.1    1.1  1  RNA_pol_Rpb6  RNA polymerase Rpb6


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb6  RNA polymerase Rpb6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   0.1   3.3e-15     6e-11       8      49 .]      25      71 ..      23      71 .. 0.88

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 3.3e-15
                                      -HHHHHHHHHHHHHHH....HT.........SS-SSSSTTCHHHHTT-S-- CS
                      RNA_pol_Rpb6  8 trYelvriaakRArQieegesl.........etqkpvviAlrEiaegkipi 49
                                      tr+e++ri+++RA+Qi     +         e   p++ A+ E ++g+ipi
  gi|242398338|ref|YP_002993762.1| 25 TRFEKARIIGARALQI----AMgapvlinvpEGASPLDAAIVEFEKGIIPI 71
                                      9***************....66666667786577***************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       253  (0.0141112); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 545.26
//
Query:       gi|242398339|ref|YP_002993763.1|  [L=341]
Description: Enolase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.8e-23   82.1   0.1    4.3e-22   78.7   0.1    2.2  1  Enolase_N  Enolase, N-terminal domain
    0.00012   21.5   0.0    0.00023   20.5   0.0    1.4  1  Enolase_C  Enolase, C-terminal TIM barrel domain


Domain annotation for each model (and alignments):
>> Enolase_N  Enolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.7   0.1   4.8e-26   4.3e-22      50     131 .]      39     119 ..       4     119 .. 0.89

  Alignments for each domain:
  == domain 1  score: 78.7 bits;  conditional E-value: 4.8e-26
                                       -SSTTSGGGT--HHHHHHHHHTHHHHHTTSBTT-HHHHHHHHHHHH-STT-TTT-HHHHHHHHHHHHHHHHHHHTS- CS
                         Enolase_N  50 DgdkkrylgkgvekavenvnekiapaligldvtdqeeiDkllielDgtenksklGaNailavSlAvakaaAkakelp 126
                                       D+d + y     ++av++v e+i p+lig+d ++qe iD++l e+Dgte+ s++GaN++lavS+AvakaaA+ k++p
  gi|242398339|ref|YP_002993763.1|  39 DEDPSLYIV-EAHRAVSEVDEIIGPELIGFDSQEQELIDSYLWEIDGTEDLSHIGANTALAVSVAVAKAAANVKKVP 114
                                       666666665.45789************************************************************** PP

                                       HHHHH CS
                         Enolase_N 127 lyryl 131
                                       ly+y+
  gi|242398339|ref|YP_002993763.1| 115 LYSYI 119
                                       ****8 PP

>> 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 !   20.5   0.0   2.5e-08   0.00023     194     285 ..     247     334 ..     230     340 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.5e-08
                                       HHHHCT--SEEEE-HHHH-SHHHHHHHHHHHHHTT-EEEEE--SC--S--HHHHHHHHCT-SEEE---S-SHHHHHH CS
                         Enolase_C 194 eaiekkaanalllkvnqiGsltesleavklakeagygvvvshrsGetedttiadlavglsaGqiktGaparserlak 270
                                       + ++++  nal +k   +G+lt+  + +++ k+   + +++    e++d  + +lavg ++  i    +     l k
  gi|242398339|ref|YP_002993763.1| 247 NILDRRYYNALSIKPINLGTLTDLYNLINDVKSERIAPILAEAKYESADEALPHLAVGFKCPAI----MFHEGSLVK 319
                                       56789999****************************************************9988....4566789** PP

                                       HHHHHHHHHHHGCC- CS
                         Enolase_C 271 ynqllrieeelgeka 285
                                        n+l+ri e+lge++
  gi|242398339|ref|YP_002993763.1| 320 INELIRIAEDLGERG 334
                                       ************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2337.13
//
Query:       gi|242398340|ref|YP_002993764.1|  [L=204]
Description: 30S ribosomal protein S2P [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.3e-26   92.4   0.0    4.7e-14   52.1   0.1    2.0  2  Ribosomal_S2  Ribosomal protein S2


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 !   38.5   0.0   3.9e-14   7.1e-10       2      95 ..      15     105 ..      14     112 .. 0.93
   2 !   52.1   0.1   2.6e-18   4.7e-14     148     212 ..     113     177 ..     108     179 .. 0.96

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 3.9e-14
                      Ribosomal_S2   2 LeagvhfGhqtrrwnpkmkpyIygern.gihiidlektlaalrraykvvkevaakggkilfvgtkkqakeavkeaak 77 
                                       L+agvh+G q++  +++mk++Iy +r+ g +++d++kt + lr a k++ ++  +  +il v+ +   ++ vk+  +
  gi|242398340|ref|YP_002993764.1|  15 LAAGVHIGTQQK--TKDMKRFIYRVRQdGLYVLDVRKTDERLRAAGKFLAKF--DPDRILAVSVRLYGQKPVKKFGE 87 
                                       89******6666..899******999659********************987..6679******************* PP

                      Ribosomal_S2  78 rangyyvnerWlgGtLTN 95 
                                        +++  +  r+l+G++TN
  gi|242398340|ref|YP_002993764.1|  88 ITGARSIPGRFLPGSMTN 105
                                       ****************** PP

  == domain 2  score: 52.1 bits;  conditional E-value: 2.6e-18
                      Ribosomal_S2 148 lPdlvvvldpkkekiavkEakklgipviaivDtnvdpdlvdypIpaNddsirsiklilgvladai 212
                                        Pd++vv+dp+ ++ a+kEa   gipv+a+vDt+   + vd +Ip N++  +s+ li+ +l++ +
  gi|242398340|ref|YP_002993764.1| 113 EPDVLVVTDPRADHQAMKEAIDIGIPVVALVDTENLLSYVDLAIPTNNKGRKSLALIYWILTREV 177
                                       69**********************************************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 1540.06
//
Query:       gi|242398341|ref|YP_002993765.1|  [L=202]
Description: NAD(P)H-flavin oxidoreductase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-29  102.4   0.0    3.1e-29  102.2   0.0    1.0  1  Nitroreductase  Nitroreductase family
    4.1e-13   49.4   0.6      3e-07   30.2   0.0    2.8  2  TM1586_NiRdase  Putative TM nitroreductase


Domain annotation for each model (and alignments):
>> Nitroreductase  Nitroreductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.2   0.0   3.4e-33   3.1e-29       1     170 []       7     181 ..       7     181 .. 0.94

  Alignments for each domain:
  == domain 1  score: 102.2 bits;  conditional E-value: 3.4e-33
                                       HHH--B---B-S----HHHHHHHHHHHHTS--GGG---EEEEEE.-CCCHHHHHHHHHHHHHHHHTT-SS-GGGGGG CS
                    Nitroreductase   1 irkRrSiRkFddepvpkeelekileaarraPsagnlqpwrfvvvqdkelryklaeaalelllkaeaqaelaqryrke 77 
                                       i +R S+R ++d+ v++++++++++ + raP+a++l++w fvv++dk+ r+++ e + e+  +  ++  l  ++ ++
  gi|242398341|ref|YP_002993765.1|   7 INRRLSVRYYEDREVEEDKIRDLVKVGIRAPTASGLENWLFVVYKDKNFRKRIHETIYEAHAEYYRAHGLPEEKIEK 83 
                                       67899******************************************************999999999999999999 PP

                                       HHHHHHHHHHHHSSEEEEE...---TTS---HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE-GGG..GGHHH CS
                    Nitroreductase  78 elklkaqkalagapvlivi...vatldkserkaaerayryalldagaaaqnllLaAtalGlgscpiggfd..eaaee 149
                                        +     k +++apv+i +     t   + + ++e +  +++ +a++a++nl+L+A +l lg+c+ig +   +++++
  gi|242398341|ref|YP_002993765.1|  84 LRMRIFEKGMYKAPVYIGVfvdKETRFLKGEEYKEIEFLWSIESAAMAIENLMLKAVELELGTCYIGVTSleKYQKK 160
                                       99*****************988666667778999***********************************97655559 PP

                                       HHHHHT-S..SEEEEEEEEE- CS
                    Nitroreductase 150 vrkllglpdeeeivvliavGy 170
                                       +rk+ gl+d++ +v+li+vGy
  gi|242398341|ref|YP_002993765.1| 161 LRKMTGLDDNWYLVGLIPVGY 181
                                       ********************9 PP

>> TM1586_NiRdase  Putative TM nitroreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.3     7e-07    0.0063       2      69 ..       3      71 ..       2      84 .. 0.76
   2 !   30.2   0.0   3.4e-11     3e-07      88     150 ..     132     200 ..     125     202 .] 0.79

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 7e-07
                                      HHHHHHH--B---B--S---HHHHHHHHH-----S...S-----.EE.E.............-SSSSEE CS
                    TM1586_NiRdase  2 lyeaiekRhsvRkYkdealeeelleelkeaieeinkesglelql.videnkafkskvaklgkfkgvpny 69
                                      l++ i+ R svR Y+d+++ee+++ +l +   +  ++sgle  l v  + k+f+ ++++      +++y
  gi|242398341|ref|YP_002993765.1|  3 LKDVINRRLSVRYYEDREVEEDKIRDLVKVGIRAPTASGLENWLfVVYKDKNFRKRIHETIYEAHAEYY 71
                                      7899**********************9999999999997765541444556677777777555555555 PP

  == domain 2  score: 30.2 bits;  conditional E-value: 3.4e-11
                                       HHHHHHHHHHTT-EEEEES--SST................T-S-EEEEE-BS----..-----HHHHBS CS
                    TM1586_NiRdase  88 geqlvLkltalGlgtcWvggtykk.....kkakvelkkgeklvivIalGyaktklv.eakrkpleelce 150
                                        e+l+Lk+++l+lgtc++g t  +      ++ + l ++  lv +I +Gy+++k+v   +rkple++++
  gi|242398341|ref|YP_002993765.1| 132 IENLMLKAVELELGTCYIGVTSLEkyqkkLRKMTGLDDNWYLVGLIPVGYPAEKIVpRPRRKPLEKVLK 200
                                       699****************9976622211233345667778999************66789****9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); 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: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 1182.33
//
Query:       gi|242398342|ref|YP_002993766.1|  [L=382]
Description: Probable thiamine biosynthesis protein thiI [Thermococcus sibiricus MM 739]
Scores for complete 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  205.9   0.1    7.2e-61  205.2   0.1    1.3  1  ThiI           Thiamine biosynthesis protein (ThiI)
    1.3e-25   90.2   5.4    2.7e-25   89.1   5.4    1.6  1  THUMP          THUMP domain
    4.3e-06   26.4   0.1    0.00032   20.2   0.1    2.4  1  QueC           Queuosine biosynthesis protein QueC
    0.00012   21.0   0.0    0.00039   19.3   0.0    1.8  2  tRNA_Me_trans  tRNA methyl transferase
     0.0015   18.6   0.0      0.003   17.6   0.0    1.5  1  PAPS_reduct    Phosphoadenosine phosphosulfate reductase fami
  ------ inclusion threshold ------
      0.014   15.1   0.1      0.034   13.9   0.1    1.6  2  DUF5507        Family of unknown function (DUF5507)
       0.23   11.6   1.7         15    5.9   0.2    3.2  3  DUF2007        Putative prokaryotic signal transducing protei


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 !  205.2   0.1   2.8e-64   7.2e-61       1     194 [.     178     370 ..     178     372 .. 0.94

  Alignments for each domain:
  == domain 1  score: 205.2 bits;  conditional E-value: 2.8e-64
                              ThiI   1 gtqgkvlaLlSgGiDSpVaaylllkRGcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdfk...e 74 
                                       gtqgkv+aLlSg iDS Vaa+l++kRGc+v  vh+    + +e++ ekv+k+ + l +y+ + +  l+v++ +   +
  gi|242398342|ref|YP_002993766.1| 178 GTQGKVMALLSGSIDSSVAAFLMMKRGCEVIPVHI----YVGEKTLEKVRKIWNQLKKYHYGGKSDLIVIKPQereK 250
                                       89*********************************....79****************************98651115 PP

                              ThiI  75 vlkeilekvkekltivllkrkmlriAekvaeeegakalvtGesLgqVaSqtleNlrvisavvnllilrPLigldKee 151
                                       +++ +++  ke++t+v++k +m++ A+++a+e+gak +v G+sLgqVaSqtleN+ ++s++++l+i rPL+g+dKee
  gi|242398342|ref|YP_002993766.1| 251 IIQTLKQLKKENYTCVFCKYMMIKKADEIAREFGAKGIVMGDSLGQVASQTLENMYIVSQASDLPIYRPLVGMDKEE 327
                                       666777777******************************************************************** PP

                              ThiI 152 iiklAkeigtyeisiekedkCsvlakhPttkakleevekaeek 194
                                       i+++Ak i t+e+s+ +ed  ++++khP+++   ee +k +++
  gi|242398342|ref|YP_002993766.1| 328 IVAIAKTIRTFELSTLPEDEVPFIPKHPVIRGSWEEFKKLYKT 370
                                       *************************************998875 PP

>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.1   5.4   1.1e-28   2.7e-25       1     144 []      29     168 ..      29     168 .. 0.97

  Alignments for each domain:
  == domain 1  score: 89.1 bits;  conditional E-value: 1.1e-28
                                       HHHHHHHHHTT.H-SEEEEETTEEEEECTEEEEEETHHHHHHHHHTSTTECEEEEEEEEEESSHHHHHHHHHHHHHH CS
                             THUMP   1 geieellkegkvnverveagkgrivvelkgekpeedeellkealekargiqrvipvcevceadledileaakeivkk 77 
                                       ++i+e+l  ++++++ v a++gri+v+++      ++e+  e l +++gi++++p+ ++++ +l++i++   +++++
  gi|242398342|ref|YP_002993766.1|  29 NNIKEALLSEGIEYKNVFAKHGRIIVKTN------KAEKSVEVLRRVFGIVSLSPA-AEIYVELDKIYRTSLKLFRR 98 
                                       69**************************9......667777999************.******************** PP

                                       HHHHCT-...EEEEEEEESSSTSSSHHHHHHHHHHHHHHCCTT-EE-SSS-SEEEEEEEETTEEEEEEEC CS
                             THUMP  78 kfeeeke...tFaVrvkrrgkhfeftsreinrevGkaivektglkVdlenPdivvrveiikdkayisidr 144
                                       k+++ +    +F+V+v+r  k+f   s+e++ +vG++i e+ ++kVdl+n+di v +e+++ kay+++d+
  gi|242398342|ref|YP_002993766.1|  99 KMRALELespRFRVTVRRITKEFPLKSQELAAKVGEYILENEECKVDLKNYDIEVGIELMEGKAYVYVDK 168
                                       ****9889***********************************************************985 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.1   1.3e-07   0.00032       2     173 ..     183     335 ..     182     343 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.3e-07
                                       EEEE--SSHHHHHHHHHHHHH-SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-E..EEEE-GGGGGGSCGGG---- CS
                              QueC   2 avvllSGGlDSttvlalakkegkevealtfdYgqrhkkeleaakkiakelgveeh..kildldllkelggsaLtdee 76 
                                       ++ llSG +DS+++++l++k+g ev+ +++  g++    le+++ki ++l+   h     dl ++k   ++ ++++ 
  gi|242398342|ref|YP_002993766.1| 183 VMALLSGSIDSSVAAFLMMKRGCEVIPVHIYVGEKT---LEKVRKIWNQLKK-YHygGKSDLIVIKPQEREKIIQTL 255
                                       6789**************************999874...5555666655554.220034455555555555565554 PP

                                       -------...--------TTHHHHHHHHHHHHHHHHT-SEEEE---S-STT--GGGSHHHHHHHHHHHHHHHTS--E CS
                              QueC  77 ievpkeeleeeelpntfVpaRNliflslaasyaealgaeaiiiGvneedfsgYPDcrdefvkalnkalnlgedkkie 153
                                       ++++k     e+   +f      +++  a   a++ ga+ i++G +  ++           ++l++++ +++++++ 
  gi|242398342|ref|YP_002993766.1| 256 KQLKK-----ENYTCVFC---KYMMIKKADEIAREFGAKGIVMGDSLGQV---------ASQTLENMYIVSQASDLP 315
                                       44444.....55555554...5789999***********99999776664.........34667777777777889* PP

                                       EE-TTTT--HHHHHHHHHHT CS
                              QueC 154 ieaPlidlsKaeivklgkel 173
                                       i  Pl+ ++K+eiv+++k +
  gi|242398342|ref|YP_002993766.1| 316 IYRPLVGMDKEEIVAIAKTI 335
                                       *************9999876 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   1.5e-07   0.00039       2      37 ..     182     217 ..     181     232 .. 0.86
   2 ?   -2.1   0.0      0.49   1.3e+03     166     200 ..     318     352 ..     304     358 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.5e-07
                     tRNA_Me_trans   2 kvvvalSgGVDSsvaaallkeqgyevigvflklwee 37 
                                       kv+++lSg +DSsvaa+l+ ++g evi v++ + e+
  gi|242398342|ref|YP_002993766.1| 182 KVMALLSGSIDSSVAAFLMMKRGCEVIPVHIYVGEK 217
                                       899**************************9977666 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.49
                     tRNA_Me_trans 166 fPlgeltKeevrkiAkeagla.vaekkdSqgiCfig 200
                                        Pl  + Kee+ +iAk+++   + + ++  ++ fi+
  gi|242398342|ref|YP_002993766.1| 318 RPLVGMDKEEIVAIAKTIRTFeLSTLPE-DEVPFIP 352
                                       59999**********9987551333333.4555555 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.2e-06     0.003       2     148 ..     183     332 ..     182     337 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.2e-06
                                       EEEE--SSCTCHHHHHHHHHHCTTHEEEEEE-STB-HHHHHHHHHHHHHT....T-EEEEEE-SCHHHHHHHHHH-S CS
                       PAPS_reduct   2 lvvsvsgGkdslVllhLalkafkpvpvvfvdtghefpetiefvdeleery....glrlkvyepeeevaekinaekhg 74 
                                       ++ + sg +ds+V   L++k   +v  v++  g++  e ++ + +  ++y    + +l+v +p+e+++   + ++  
  gi|242398342|ref|YP_002993766.1| 183 VMALLSGSIDSSVAAFLMMKRGCEVIPVHIYVGEKTLEKVRKIWNQLKKYhyggKSDLIVIKPQEREKIIQTLKQLK 259
                                       56789*******************999******999988887776666666886677*******9988777777777 PP

                                       -THHHCHHHHHHTHHHHHHHHHCTTECEEE----CCCTTTTTTSSSEEECTTT-SCEEE-.CCCT--HHHHHHHH CS
                       PAPS_reduct  75 sslyeeaaeriaKveplkkaLekldedalltGaRrdesksraklpiveidedfekslrvf.PllnWteedvwqyi 148
                                       +++y+  +++ + ++++ +  ++++++ +++G    + +s+  ++++ + ++    l ++ Pl+ +++e++ + +
  gi|242398342|ref|YP_002993766.1| 260 KENYTCVFCKYMMIKKADEIAREFGAKGIVMGDSLGQVASQTLENMYIVSQAS--DLPIYrPLVGMDKEEIVAIA 332
                                       899999888888888888888899999*****999999999999988888884..48888899999999998765 PP

>> DUF5507  Family of unknown function (DUF5507)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0         3   7.7e+03      19      32 ..      53      66 ..      35      82 .. 0.57
   2 ?   13.9   0.1   1.3e-05     0.034      58     139 ..     185     269 ..     176     284 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 3
                           DUF5507 19 synenksskhmell 32
                                        + nk+ k +e+l
  gi|242398342|ref|YP_002993766.1| 53 IVKTNKAEKSVEVL 66
                                      23344444444444 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 1.3e-05
                           DUF5507  58 kmmseciyqegnafvimgageqlkrikyevgennlkvfnvhfnnnhelvssgepdviclskqvwenllikl...kle 131
                                        ++s  i     af++m  g ++  ++  vge+ l  +   +n+ ++    g+ d+i++  q  e+++  l   k e
  gi|242398342|ref|YP_002993766.1| 185 ALLSGSIDSSVAAFLMMKRGCEVIPVHIYVGEKTLEKVRKIWNQLKKYHYGGKSDLIVIKPQEREKIIQTLkqlKKE 261
                                       567889999999***********************999999************************987665000556 PP

                           DUF5507 132 nnenvfse 139
                                       n   vf +
  gi|242398342|ref|YP_002993766.1| 262 NYTCVFCK 269
                                       66666654 PP

>> DUF2007  Putative prokaryotic signal transducing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.2    0.0058        15      10      27 ..      25      42 ..      20      70 .. 0.89
   2 ?   -3.1   0.0       3.6   9.2e+03      13      31 ..     130     148 ..     125     154 .. 0.72
   3 ?    3.5   0.0     0.031        79      43      62 ..     206     225 ..     183     230 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0058
                           DUF2007 10 pveaelikslLeeagIea 27
                                      ++++++ik++L ++gIe+
  gi|242398342|ref|YP_002993766.1| 25 SILVNNIKEALLSEGIEY 42
                                      799*************97 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.6
                           DUF2007  13 aelikslLeeagIeavvkd 31 
                                       a+  + +Le++++++ +k+
  gi|242398342|ref|YP_002993766.1| 130 AKVGEYILENEECKVDLKN 148
                                       5555668999998876666 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.031
                           DUF2007  43 gelpvrilVaeedleeArei 62 
                                        ++pv i+V e+ le+ r+i
  gi|242398342|ref|YP_002993766.1| 206 EVIPVHIYVGEKTLEKVRKI 225
                                       6799************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       945  (0.0527079); expected 358.6 (0.02)
Passed bias filter:                      727  (0.0405488); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); 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: 00:00:00.43
# Mc/sec: 2695.25
//
Query:       gi|242398343|ref|YP_002993767.1|  [L=178]
Description: hypothetical protein TSIB_0352 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-16   59.6   4.6    3.7e-16   59.3   4.6    1.0  1  DUF998    Protein of unknown function (DUF998)
  ------ inclusion threshold ------
       0.35   11.3   1.6        1.6    9.1   0.1    2.2  2  DUF2663   Protein of unknown function (DUF2663)
        0.8   10.2   7.4        1.9    8.9   1.1    2.6  3  MerC      MerC mercury resistance protein
        7.6    6.2   6.6        8.8    5.9   3.6    2.2  2  DUF4131   Domain of unknown function (DUF4131)


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 !   59.3   4.6   8.2e-20   3.7e-16       5     184 ..      16     174 ..      13     175 .. 0.84

  Alignments for each domain:
  == domain 1  score: 59.3 bits;  conditional E-value: 8.2e-20
                            DUF998   5 llalavilaaallrpgydplrhaiSeLgaeggpggwlfnaglvllgllvlalavgllraargragragrlllavagl 81 
                                       +la+ +i +   l+p ++++++a+S+ g  + p g++fn+ l+llg+  ++++v +        ++ +++l+ ++ +
  gi|242398343|ref|YP_002993767.1|  16 FLAFGGIFITIHLNPWFSLTENALSDMGSIKNPIGYFFNFLLILLGFVGMVFGVEM------LKEKTVTILFPLGMF 86 
                                       678888999999*****************************************955......669999999999*** PP

                            DUF998  82 glvlagvfptdpgggspslsglvHglasavaflalavavlllasaarrrawallrlvggvallllvaalvwllaaal 158
                                       +l+l+g+fp+            +H ++++ ++++l++ +++++   r+r+    +++++++  + ++++++l  +  
  gi|242398343|ref|YP_002993767.1|  87 SLLLVGIFPEEYK---------PHSFFALSFYILLFADIFIYG--LRKRRKNSSAIAWLLGSPIVFMMMLYLTKV-- 150
                                       ***********99.........9********************..444444444444444555555555555555.. PP

                            DUF998 159 dgslllGlaerllvlaitawllalal 184
                                           +l+++e +++l i aw++ l+l
  gi|242398343|ref|YP_002993767.1| 151 --FEGLAIPELVGALFINAWIIYLTL 174
                                       ..67*****************98865 PP

>> DUF2663  Protein of unknown function (DUF2663)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.3     0.092   4.1e+02      57      77 ..      55      75 ..       2      90 .. 0.57
   2 ?    9.1   0.1   0.00036       1.6      15      68 ..      98     151 ..      95     157 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.092
                           DUF2663 57 lllllllvallyvavkllkkK 77
                                      +ll+ll ++ +++ v++lk+K
  gi|242398343|ref|YP_002993767.1| 55 FLLILLGFVGMVFGVEMLKEK 75
                                      344444555556667777777 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00036
                           DUF2663  15 lekrllllsllallvlllfliyvlikssslssllsallessvlllllllvally 68 
                                       ++ + ++  ++ +l+++  +iy l k  + ss +++ll+s+++++++l ++ ++
  gi|242398343|ref|YP_002993767.1|  98 YKPHSFFALSFYILLFADIFIYGLRKRRKNSSAIAWLLGSPIVFMMMLYLTKVF 151
                                       55555666666677777789999999********************99987665 PP

>> MerC  MerC mercury resistance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.61   2.7e+03      63      84 ..       4      25 ..       3      46 .. 0.71
   2 ?    8.9   1.1   0.00043       1.9      42      87 ..      53      97 ..      27     119 .. 0.71
   3 ?    6.3   4.9    0.0028        13      16      90 ..      79     153 ..      55     175 .. 0.51

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.61
                              MerC 63 ktsvlvlgalGllillvalflg 84
                                      k++v vlg    ++ + + f+ 
  gi|242398343|ref|YP_002993767.1|  4 KKWVKVLGFSFPFLAFGGIFIT 25
                                      5678888888888888777776 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00043
                              MerC 42 llilvvaigllalvvgyrrhrktsvlvlgalGllillvalflgtea 87
                                      + +l +++g++++v+g+   +++ v++l+ lG++ ll+  +++ e+
  gi|242398343|ref|YP_002993767.1| 53 FNFLLILLGFVGMVFGVEMLKEKTVTILFPLGMFSLLLVGIFP-EE 97
                                      4566789999999999999999999999999999888777776.22 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.0028
                              MerC  16 lllPvllallpllglsflasellhqvllilvvaiglla..lvvgyrrhrktsvlvlgalGllillvalflgteaeet 90 
                                       +l+P+ +++l l+g++  ++e+  + +++l+  i l+a  +++g r+ rk s  +  +lG  i+++ +++ t++ e 
  gi|242398343|ref|YP_002993767.1|  79 ILFPLGMFSLLLVGIF--PEEYKPHSFFALSFYILLFAdiFIYGLRKRRKNSSAIAWLLGSPIVFMMMLYLTKVFEG 153
                                       4566666666666654..55553333333333333333224455555555544444444444444444333344444 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.5     0.091   4.1e+02      15      48 ..      16      66 ..       5      76 .. 0.49
   2 ?    5.9   3.6     0.002       8.8       9      64 ..      80     136 ..      53     148 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.091
                           DUF4131 15 llllllllllrr.................rprrrvllllllllllallgfa 48
                                      +l++  +++                     +++   ++ +ll+ll+++g++
  gi|242398343|ref|YP_002993767.1| 16 FLAFGGIFITIHlnpwfsltenalsdmgsIKNPIGYFFNFLLILLGFVGMV 66
                                      333333333222223344446666666654444445555555555555554 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.002
                           DUF4131   9 llalllllllllllllrr..rprrrvllllllllllallgfalrapqpnandlsqlle 64 
                                       l+ l+++ lll +++  +  +p+  ++l++ +ll++  + + lr +++n++ ++ ll 
  gi|242398343|ref|YP_002993767.1|  80 LFPLGMFSLLLVGIF-PEeyKPHSFFALSFYILLFADIFIYGLRKRRKNSSAIAWLLG 136
                                       333444444444444.444788888888888888888888888888888888877664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       632  (0.0352502); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1256.11
//
Query:       gi|242398344|ref|YP_002993768.1|  [L=208]
Description: ThiI thiamin biosynthesis protein thiI [Thermococcus sibiricus MM 739]
Scores for complete 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-58  196.3   0.0    4.4e-58  196.1   0.0    1.0  1  ThiI           Thiamine biosynthesis protein (ThiI)
    1.1e-06   28.4   0.0    0.00041   19.9   0.0    2.4  1  QueC           Queuosine biosynthesis protein QueC
     0.0011   17.8   0.0     0.0043   15.9   0.0    2.0  2  tRNA_Me_trans  tRNA methyl transferase
  ------ inclusion threshold ------
      0.012   15.7   0.0      0.014   15.5   0.0    1.1  1  PAPS_reduct    Phosphoadenosine phosphosulfate reductase fami
      0.043   13.6   0.0        3.3    7.4   0.0    2.2  2  ATP_bind_3     PP-loop family


Domain annotation for each model (and alignments):
>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  196.1   0.0   1.2e-61   4.4e-58       5     194 ..      13     202 ..       9     204 .. 0.90

  Alignments for each domain:
  == domain 1  score: 196.1 bits;  conditional E-value: 1.2e-61
                              ThiI   5 kvlaLlSgGiDSpVaaylllkRGcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdfkevlkeile 81 
                                       k++aLlS GiDSpVa yl+lk+G+ v  +h+    ++se +++kv+++   l e       +l++vd  e++k i +
  gi|242398344|ref|YP_002993768.1|  13 KAVALLSSGIDSPVAIYLMLKKGFTVYPIHF----MQSEVNHQKVRRIWMRLKELYPDSLEELIAVDAFEYQKPIFD 85 
                                       89*****************************....689999999999999888866666667777777777777666 PP

                              ThiI  82 kv....kekltivllkrkmlriAekvaeeegakalvtGesLgqVaSqtleNlrvisavvnllilrPLigldKeeiik 154
                                       k+    kek  ++++k++ml  A ++a+e++a  ++tG+sLgqVaSqtl+Nl +is +++l++lrPLig+dK ei k
  gi|242398344|ref|YP_002993768.1|  86 KLielkKEKWICIFCKFSMLMKAAEIAKEKNAMVIITGDSLGQVASQTLDNLLIISLATDLPVLRPLIGMDKVEIEK 162
                                       6666669**********99888888**************************************************** PP

                              ThiI 155 lAkeigtyeisiekedkCsvlakhPttkakleevekaeek 194
                                       +Akeigt+eisie+e+ C ++++hP ++  l e +k++ +
  gi|242398344|ref|YP_002993768.1| 163 IAKEIGTFEISIEPEESCNFVPRHPIIRGALGEFKKIYRE 202
                                       ******************************9999998866 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   1.1e-07   0.00041       1     183 [.      13     180 ..      13     183 .. 0.67

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.1e-07
                                       EEEEE--SSHHHHHHHHHHHHH-SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEEE-GGGGGGSCGGG----- CS
                              QueC   1 kavvllSGGlDSttvlalakkegkevealtfdYgqrhkkeleaakkiakelgveehkildldllkelggsaLtdeei 77 
                                       kav llS G+DS ++++l++k+g  v+ ++f      +++++++++i  +l+      l  d l+el     ++ ++
  gi|242398344|ref|YP_002993768.1|  13 KAVALLSSGIDSPVAIYLMLKKGFTVYPIHFMQ---SEVNHQKVRRIWMRLK-----ELYPDSLEELIAVDAFEYQK 81 
                                       79****************************964...4444555555554433.....34445555555555555555 PP

                                       ----..--...--------TTHHHHHHHHHHHHHHHHT-SEEEE---S-STT--GGGSHHHHHHHHHHHHHHHTS-- CS
                              QueC  78 evpk..eeleeeelpntfVpaRNliflslaasyaealgaeaiiiGvneedfsgYPDcrdefvkalnkalnlgedkki 152
                                        + +   el++e+       +    +l  aa  a++ +a  ii+G +  ++           ++l+++l ++ ++++
  gi|242398344|ref|YP_002993768.1|  82 PIFDklIELKKEKWICI---FCKFSMLMKAAEIAKEKNAMVIITGDSLGQV---------ASQTLDNLLIISLATDL 146
                                       55551222222333333...3445677788888999999999998666553.........34667777777777789 PP

                                       EEE-TTTT--HHHHHHHHHHTT...HHHHH-B-S CS
                              QueC 153 eieaPlidlsKaeivklgkelg...vpleetlsC 183
                                        +  Pli ++K ei k++ke+g   + +e   sC
  gi|242398344|ref|YP_002993768.1| 147 PVLRPLIGMDKVEIEKIAKEIGtfeISIEPEESC 180
                                       9999999999999999999988666555555555 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.2e-06    0.0043       3      41 ..      14      52 ..      12     123 .. 0.89
   2 ?   -0.6   0.0      0.12   4.4e+02     165     185 ..     149     169 ..     137     186 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.2e-06
                     tRNA_Me_trans  3 vvvalSgGVDSsvaaallkeqgyevigvflklweeedee 41
                                       v++lS+G+DS va +l+ ++g+ v  +++  +e ++++
  gi|242398344|ref|YP_002993768.1| 14 AVALLSSGIDSPVAIYLMLKKGFTVYPIHFMQSEVNHQK 52
                                      5789**********************9987766654443 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.12
                     tRNA_Me_trans 165 lfPlgeltKeevrkiAkeagl 185
                                       l Pl  + K e+ kiAke+g 
  gi|242398344|ref|YP_002993768.1| 149 LRPLIGMDKVEIEKIAKEIGT 169
                                       5699999**********9975 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.0   3.8e-06     0.014       3     106 ..      15     123 ..      13     167 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.8e-06
                                       EEE--SSCTCHHHHHHHHHHCTTH.EEEEEE-STB-HHHHHHHHHHHHHTT-EEEEEE-SCHHHHHHHHHH-S-THH CS
                       PAPS_reduct   3 vvsvsgGkdslVllhLalkafkpv.pvvfvdtghefpetiefvdeleeryglrlkvyepeeevaekinaekhgssly 78 
                                       v + s G+ds V + L+lk    v p+ f++ + +++++ +  ++l+e y   l+     + ++ +   +++  +l 
  gi|242398344|ref|YP_002993768.1|  15 VALLSSGIDSPVAIYLMLKKGFTVyPIHFMQSEVNHQKVRRIWMRLKELYPDSLEELIAVDAFEYQKPIFDKLIELK 91 
                                       778999**************999659************************555667777777777777777666666 PP

                                       HC.......HHHHHHTHHHHHHHHHCTTECEEE-- CS
                       PAPS_reduct  79 ee.......aaeriaKveplkkaLekldedalltG 106
                                       +e       +++ ++K+ ++ k   + ++ +++tG
  gi|242398344|ref|YP_002993768.1|  92 KEkwicifcKFSMLMKAAEIAK---EKNAMVIITG 123
                                       6666777777778888888777...5555666666 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0    0.0096        35       5      39 ..      17      52 ..      13      64 .. 0.74
   2 ?    7.4   0.0   0.00092       3.3     136     158 ..     144     166 ..     102     175 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0096
                                      E--SCHHHHHHHHH.HHHHCTTTTTEEEEEEEE-SS CS
                        ATP_bind_3  5 AvSgGlDSmaLlll.laklkkklgiklvaihvdhgl 39
                                       +S G+DS + ++l l+k  +   i+++   v+h++
  gi|242398344|ref|YP_002993768.1| 17 LLSSGIDSPVAIYLmLKKGFTVYPIHFMQSEVNHQK 52
                                      47******7666550566667777789999999975 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.00092
                                       TTCCEE-CCCT--HHHHHHHHHH CS
                        ATP_bind_3 136 asirlvRPlLkvskeeleeylke 158
                                       ++  ++RPl+ + k e+e+++ke
  gi|242398344|ref|YP_002993768.1| 144 TDLPVLRPLIGMDKVEIEKIAKE 166
                                       46789***************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       742  (0.0413855); expected 358.6 (0.02)
Passed bias filter:                      646  (0.036031); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1451.93
//
Query:       gi|242398345|ref|YP_002993769.1|  [L=38]
Description: hypothetical protein TSIB_0354 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       162  (0.00903564); expected 358.6 (0.02)
Passed bias filter:                      157  (0.00875676); 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: 0.47u 0.34s 00:00:00.81 Elapsed: 00:00:00.53
# Mc/sec: 214.76
//
Query:       gi|242398346|ref|YP_002993770.1|  [L=273]
Description: Cysteine synthase [Thermococcus sibiricus MM 739]
Scores for complete 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  142.8   0.0    9.3e-41  140.1   0.0    1.8  1  PALP      Pyridoxal-phosphate dependent enzyme
  ------ inclusion threshold ------
      0.021   14.7   0.1       0.17   11.7   0.0    2.2  2  DIX       DIX domain
       0.12   11.9   0.0       0.21   11.2   0.0    1.3  1  AIRC      AIR carboxylase


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.1   0.0   1.6e-44   9.3e-41      25     292 ..       3     254 ..       2     256 .. 0.88

  Alignments for each domain:
  == domain 1  score: 140.1 bits;  conditional E-value: 1.6e-44
                                       EEEEGGGST.TSBTTHHHHHHHHHHHHTT...TTTSEEEEEBSSHHHHHHHHHHHHHT-EEEEEEETTS-HHHHHHH CS
                              PALP  25 flKlEslnp.tgSfKdRgaeyllarlkeg...tgaktvveassGNhgralAaaaallGlkvtivvpadaspekvall 97 
                                       f+KlE++np + S+KdR++ ++l+++ e    +g ++++ea+sGN g++lAa + +l + ++ ++p+ ++   + ll
  gi|242398346|ref|YP_002993770.1|   3 FAKLEFFNPfSRSIKDRAVFNMLMKAIERgdiNGVRRLFEATSGNVGISLAALSDVLRIGFRAYLPKPTPMTTQILL 79 
                                       89******99***************77766*********************************************** PP

                                       HHTT-EEEEECCH..HHHHHHHHHHHHHHSTTCEE--TTTSHHHHHH.HHTHHHHHHHHTT...TTEEEEEEE-SSS CS
                              PALP  98 rllGaevvevggd..ydeavaaaaelaaegegaylvsqfdnptvieg.ygtiglEileqlg...gkpdavvvpvGgG 168
                                       + lGaevv ++ +    + v+++ e a++  ga++++qf+n +++++ y  ++ Ei eql+   ++pd++++++G+ 
  gi|242398346|ref|YP_002993770.1|  80 KVLGAEVVMTDFEviDPDMVKYVIEEAKK-AGAVNLNQFENDDNFDAhYRFTAREIDEQLKsigKRPDVIIAGIGTS 155
                                       **********6665466667778888888.9**************************9999999************* PP

                                       HHHHHHHHHHHHHSTT-EEEEEEECTTCGGTTCCS..S.SS..B.SSS.CCSTCSCGTTCCHHHHSEEEEEEEEEEH CS
                              PALP 169 gliaGiaaglkerrpdvrvigvepegsdalarslragrrvtvpvsdtiadglavgspselafelldrlvdeivtvsd 245
                                       g i+Gia+++ker  +++vigv p+ s+++ +                   l+++   ++    ++  +de++++++
  gi|242398346|ref|YP_002993770.1| 156 GHIGGIAKYFKERY-NTKVIGVVPAKSEKIPGIK----------------RLETK---PKW--FFKVEIDEVIEITQ 210
                                       ***********965.57*****999888888777................22222...333..47889********* PP

                                       HHHHHHHHHHHHHHSB-B-HHHHHHHHHHHHHHHHCCTTCEEEEEEE CS
                              PALP 246 eealeamrllarregivvepssaaalaalklreagelkegdrvvvil 292
                                        ea+e+  ++ar+eg++++ ss+a++ a +  +++ l+     v+i+
  gi|242398346|ref|YP_002993770.1| 211 REAIEGSIQVARKEGLLIGLSSGAVVKAFEKIHDKYLGTT---VLIF 254
                                       ****************************944444444433...5555 PP

>> DIX  DIX domain
   #    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       9      53 ..      94     138 ..      87     143 .. 0.91
   2 ?    0.2   0.0      0.12     7e+02      34      60 ..     189     212 ..     167     229 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.9e-05
                               DIX   9 lddeevpyrikipkrpdqiTLkdfKellpkkGnyryffKtldedf 53 
                                       +d + v+y+i+  k+++ + L +f +  +   +yr+  +++de +
  gi|242398346|ref|YP_002993770.1|  94 IDPDMVKYVIEEAKKAGAVNLNQFENDDNFDAHYRFTAREIDEQL 138
                                       678999***********************999********99987 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.12
                               DIX  34 ellpkkGnyryffKtldedfegvVkee 60 
                                       +l +k+   ++ffK + +++ ++ + e
  gi|242398346|ref|YP_002993770.1| 189 RLETKP---KWFFKVEIDEVIEITQRE 212
                                       555555...999999999985555555 PP

>> AIRC  AIR carboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   3.5e-05      0.21      47      96 ..     138     190 ..     123     193 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.5e-05
                                       HHHCHTTTEEEEEEEEESS--HHHHHHHHS...SS-EEEE.EE--STTCCHHHH CS
                              AIRC  47 aeeaeerglkviIagAGgaahLpgvvaslt...tlPVigv.Pvkskalkgldsl 96 
                                       ++++ +   +viIag G + h++g+        ++ Vigv P ks+++ g++ l
  gi|242398346|ref|YP_002993770.1| 138 LKSIGK-RPDVIIAGIGTSGHIGGIAKYFKeryNTKVIGVvPAKSEKIPGIKRL 190
                                       344433.489**************976543333899**9648888888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); 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: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1732.62
//
Query:       gi|242398347|ref|YP_002993771.1|  [L=113]
Description: hypothetical protein TSIB_0356 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      0.009   16.1   2.2      0.013   15.6   2.2    1.2  1  DUF2700   Protein of unknown function (DUF2700)


Domain annotation for each model (and alignments):
>> DUF2700  Protein of unknown function (DUF2700)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   2.2     7e-07     0.013      15      75 ..      10      71 ..       3      75 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 7e-07
                           DUF2700 15 irsivllliss.dtlttalasiislllnlllLfGalknnekalkwaqrvllialilavllll 75
                                      ++s +ll++ss  + ++++  +++ lln+ll  G+++ ++ a+k+a +   +++++a+l l+
  gi|242398347|ref|YP_002993771.1| 10 LQSLFLLYYSSgAENIERYMLLAFALLNFLLAWGIFRGQKRAVKIAVIYKGLDFFFAILMLM 71
                                      55666776665267899****************************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 698.58
//
Query:       gi|242398348|ref|YP_002993772.1|  [L=311]
Description: Sugar kinase [Thermococcus sibiricus MM 739]
Scores for complete 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-53  180.5   0.0    8.4e-53  179.6   0.0    1.4  1  PfkB        pfkB family carbohydrate kinase
  ------ inclusion threshold ------
      0.026   14.9   0.0       0.27   11.6   0.0    2.2  2  NAPRTase_N  Nicotinate phosphoribosyltransferase (NAPRTase) N


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 !  179.6   0.0   9.3e-57   8.4e-53       4     296 ..       2     293 ..       1     298 [. 0.92

  Alignments for each domain:
  == domain 1  score: 179.6 bits;  conditional E-value: 9.3e-57
                                       EEEEEEEEEEEEEECSSHTTSEEEESEEEEEEESHHHHHHHHHHHTT-EEEEEEEEESSHHHHHHHHHHHHTTEEET CS
                              PfkB   4 vvviGealidliavseklegelvevktveksaGGagaNvAvalarlgadvafigavGdDnfGeflleelkkegvdtd 80 
                                       +++iGe+lid+ia++e+    l+ v ++ek++GGa+aNv v+larlg++ a+i+++G D+fGefl++ l+ egv+++
  gi|242398348|ref|YP_002993772.1|   2 IFSIGEVLIDFIAKEEG---ALKDVIEFEKHPGGAPANVSVGLARLGVKCALISKIGADPFGEFLINALEREGVEIK 75 
                                       799*************9...********************************************************* PP

                                       TEEEESSSEEEEEEEEETTTSEEEEEEEEGGGGGHHHHHHHHHHHHHGCTSEEEEES..EECTTSHHHHHHHHHHHH CS
                              PfkB  81 yvkidedtrtglalivvdedgertivfnrgaaadltkeeleededlleeadllyisg..llsselpeavleelaeaa 155
                                       y+ +d +++tg+ ++ + +++   i+++  a  ++++e++     ++e a+l+++++  +  ++++++++e l +a+
  gi|242398348|ref|YP_002993772.1|  76 YISQDIEKHTGIVFVQLIGAKPEFILYDGVAYFNMKPEDM---NVDIEGATLIHFGSvlFAREPSRSTLFEILNKAK 149
                                       ******************9977777777777788888766...7788***********999999*******999999 PP

                                       HHTTE.EEEEECESSSHH....HHHHHHHHHCTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTSSEEEEEE CS
                              PfkB 156 knggt.fdpnlldplgaq....fkeallellaladllkpneeElealtgekledieealaalhklkakgaktvvvtl 227
                                        +    +d n++ +l++     + ++++++l lad++k  +eE e  +++++          ++l+    k++ +t+
  gi|242398348|ref|YP_002993772.1| 150 GKVPIsYDVNIRLDLWKGrenaMFKDIEHALKLADIVKIGDEEVE-YLQKNG----------FNLNDFDFKLIAITK 215
                                       99999***********99****9999*******************.666664..........333333336899*** PP

                                       GGGEEEEEETTEEEEEEE.SSSS-SBGTTHHHHHHHHHHHHHHT..........THHHHHHHHHHHHHHHHHHTSSS CS
                              PfkB 228 GkeGalvvekdgelkvpavpkvkvvDttGAGDsfvggflaalle..........gksleealrfanavAalvvqkkg 294
                                       G++G+ + +++ +++vp+ +k+k+ DttGAGD++++++la+l+            ++lee+ rf n vAal+++k+g
  gi|242398348|ref|YP_002993772.1| 216 GAKGSTIIHRGIKVEVPS-YKIKPTDTTGAGDAYMAALLASLSYmnklktlefsKHELEEIGRFSNLVAALSTTKRG 291
                                       ******************.9********************************************************* PP

                                       SS CS
                              PfkB 295 ai 296
                                       a 
  gi|242398348|ref|YP_002993772.1| 292 AW 293
                                       96 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 ?   11.6   0.0     3e-05      0.27      17      69 ..     147     200 ..     140     217 .. 0.83
   2 ?    0.5   0.0     0.086   7.7e+02      40      62 ..     248     273 ..     221     284 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3e-05
                        NAPRTase_N  17 kgp.dvevvfelffRkkp.fkgeyaivagleevieylenlrfteeeieyLkrklp 69 
                                       k + +v+ ++++  R +  +++e a+++ +e++++    +++ +ee+eyL++  +
  gi|242398348|ref|YP_002993772.1| 147 KAKgKVPISYDVNIRLDLwKGRENAMFKDIEHALKLADIVKIGDEEVEYLQK-NG 200
                                       555588999999999988566799**************************94.44 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.086
                        NAPRTase_N  40 ivagleevieyle...nlrfteeeie 62 
                                       ++a+l + ++y++   +l+f+++e+e
  gi|242398348|ref|YP_002993772.1| 248 YMAALLASLSYMNklkTLEFSKHELE 273
                                       55555555544441115666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); 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: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2310.82
//
Query:       gi|242398349|ref|YP_002993773.1|  [L=435]
Description: maltose ABC transporter substrate-binding protein [Thermococcus sibiricus MM 739]
Scores for complete 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-43  147.8   2.6    6.9e-43  147.8   2.6    1.6  2  SBP_bac_1  Bacterial extracellular solute-binding protein
    1.7e-28  100.2   0.4    2.3e-28   99.8   0.4    1.2  1  SBP_bac_8  Bacterial extracellular solute-binding protein
  ------ inclusion threshold ------
       0.13   12.2   0.6       0.51   10.2   0.0    2.1  2  DUF5572    Family of unknown function (DUF5572)


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 !  147.8   2.6   1.2e-46   6.9e-43       4     314 ..      72     354 ..      69     355 .. 0.95
   2 ?   -2.0   0.4      0.44   2.7e+03      72     119 ..     377     416 ..     359     435 .] 0.52

  Alignments for each domain:
  == domain 1  score: 147.8 bits;  conditional E-value: 1.2e-46
                                       HHHHHHHHHHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHHHHTTSSSCSEEEECGGHHHHHHHTTSBECCHHHHHH CS
                         SBP_bac_1   4 ltegaalqalvakafekehpgikVeiesvgsgslaqkltlaiaaGdgpaDviavdndwiarlakaglllpldpyvka 80 
                                        +e +a+++++ k+fe+ehp+ik+e+++    +l + l l++++Gd paD+i++++++ia++  +g +++l+ ++++
  gi|242398349|ref|YP_002993773.1|  72 GAELDAFNEVI-KEFEAEHPDIKIEYKTYRAEDLSTILPLQFESGDTPADLIFMWGWFIADMGTKGHVMELGQIINP 147
                                       556679*****.***************************************************************** PP

                                       TTECTTCCTEEEEHHHHTHHHHCE.EE...ES.EEEE.E.EEEEEEETTTHHCTTGGGSHBHHHHHHHHHHHHHHCT CS
                         SBP_bac_1  81 ylapgvkdaadklsssvlpkilds.kv...ly.vPly.a.argliYNkdlfekagldppwtWdelveaakklkekgk 150
                                       +               ++p+ild+ +v   +y  P+  a   g++Y+k+ fe+ gl+pp+tWde+v++++ +k   +
  gi|242398349|ref|YP_002993773.1| 148 NE--------------YVPGILDTvTVdgkIYgAPFTaAaKPGFWYRKSFFEEHGLTPPETWDEFVKLLEQIKQIPG 210
                                       95..............*******9999**********************************************9999 PP

                                       CTHCCHCCEEHHHHHHHHHHHHHHHHTGGGEECCCTHHCSHHHHSHHHHHHHHHHHHHHHHHHHTTEEECSSHHHHH CS
                         SBP_bac_1 151 kpiggarggsasgtayyfalalakslggkvfdkdgggldnpegvtaatylvklyavanltkelkgkgaenkdgaaal 227
                                        +  ++ g s ++ ++  +++++  +gg +  +   +l+n+e ++ + +++  + ++++    +g+ +    +++a+
  gi|242398349|ref|YP_002993773.1| 211 IKAPIVSGDSVGWPLSDVTEHFIMTFGGAELQQ---KLINGEVKWQDPQVRSIFEERLVPLLEAGYFSDPIEWTSAV 284
                                       999999999999999999*********777777...56*************************************** PP

                                       HHHHTTSCSEEEEEHHHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEEEEEEEEEEBTTCSTHHHHHHH CS
                         SBP_bac_1 228 alfeaGeaamaivglwaalaamkvapkvafaadkekpkeelgvaplPagkggkpgilgayglaipkgsknpeaAkkF 304
                                        l+ +Ge a++++g+w               + + + + +lg + lP++k      l  +++++pk +++p++A ++
  gi|242398349|ref|YP_002993773.1| 285 ELWWKGEYALYFMGTW--------------LTGMVDDPTDLGLISLPGVKAMV---LAPDYFMVPKYTSHPDEALEL 344
                                       ***************9..............59999999999*****9775554...7******************** PP

                                       HHHHTSHHHH CS
                         SBP_bac_1 305 ldfllspeaq 314
                                        +f++++++ 
  gi|242398349|ref|YP_002993773.1| 345 AKFIATEGQR 354
                                       ******9985 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.44
                                       ECCHHHHHHT.TECTTCCTEEEEHHHHTHHHHCE.EEESEEEEEEEEEEE CS
                         SBP_bac_1  72 lpldpyvkay.lapgvkdaadklsssvlpkilds.kvlyvPlyaargliY 119
                                       +p+ +++k   +++  +d  d+  +++ ++ +d  k          +l++
  gi|242398349|ref|YP_002993773.1| 377 EPMKDVAKVVaNVESAPDLDDSVGGEWQKAFWDQlK----------LLWV 416
                                       444444444434445555555555555555555444..........5555 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 !   99.8   0.4   3.9e-32   2.3e-28       1     274 [.      80     376 ..      80     385 .. 0.82

  Alignments for each domain:
  == domain 1  score: 99.8 bits;  conditional E-value: 3.9e-32
                                       HHHHHHHHH-.TEEEEEEE--SSSHHHHHHHHHHTT---SEE.EEE-HHHHHHHHHTTSB--GGGSTTHHH-.HHHH CS
                         SBP_bac_8   1 klakefekkt.gvkvnvvtaasndleqklkaalaagtapdidvvwanedalatlaeeglladlsdldnlddl.tdal 75 
                                       +++kefe+++ ++k+++ t+  +dl + l  + ++g++p+ d++++++ ++a +  +g + +l ++ n +++ +  l
  gi|242398349|ref|YP_002993773.1|  80 EVIKEFEAEHpDIKIEYKTYRAEDLSTILPLQFESGDTPA-DLIFMWGWFIADMGTKGHVMELGQIINPNEYvPGIL 155
                                       589*****************99****************97.999999*******************777776266** PP

                                       HTT--TS.----EEEEEEE-EEEEEHHHHHHS...---BHHHHHHHHHHHHHH-............SEGG---G.GG CS
                         SBP_bac_8  76 aavgydgklygvPyasetpyvliynkdlleka..edpktwdellaaakklkgkf............glpdpasg.wl 137
                                       ++v++dgk+yg P+++    ++ y+k+ +e++   +p+twde++++++++k+              g+p   s+ + 
  gi|242398349|ref|YP_002993773.1| 156 DTVTVDGKIYGAPFTAAAKPGFWYRKSFFEEHglTPPETWDEFVKLLEQIKQIPgikapivsgdsvGWPL--SDvTE 230
                                       ****************9867**********98999***********999964442225544444334433..33688 PP

                                       GGGTHHETTEE---H....HHH...HHHHHHHHH.HH...HTT-EE.-.S..--SSTTTTTSBSEEEE-TTHHHHHH CS
                         SBP_bac_8 138 qaallakdgksldddg..gkdgl..kealellkk.lk...dngkty.d.tgadavsefanGevaftingswdiaaaq 204
                                       ++++++ +g++l ++   g+ ++  ++++ ++ + l+   ++g++  +  +++av+++ +Ge+a ++ g+w    ++
  gi|242398349|ref|YP_002993773.1| 231 HFIMTF-GGAELQQKLinGEVKWqdPQVRSIFEErLVpllEAGYFSdPiEWTSAVELWWKGEYALYFMGTWLTGMVD 306
                                       999999.99999666555333336688888888766644466666662478899**********************9 PP

                                       -TTTSEEEE.--.S--EEEEEEEEEEBTTS-HHHHHHHHHHHHHTTSHHHHHHHHHH---BS-S-TTTHHHH CS
                         SBP_bac_8 205 kagkklgai.vp.kqgsfaggkglavpknaknedlaAldFlkwltspenqaalaektgyipvnksaalspev 274
                                       +   +lg i +p  +++++  ++++vpk ++++d+ Al+++k+++++ +     + +g + + k+++ ++++
  gi|242398349|ref|YP_002993773.1| 307 D-PTDLGLIsLPgVKAMVLAPDYFMVPKYTSHPDE-ALELAKFIATEGQRIHVGTSSGKLATWKEVTMDDYW 376
                                       9.5699999778545799999*************7.********9977777777799999999998877766 PP

>> DUF5572  Family of unknown function (DUF5572)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1      0.25   1.5e+03       8      22 ..     140     154 ..     139     157 .. 0.86
   2 ?   10.2   0.0   8.6e-05      0.51       3      23 ..     192     212 ..     190     213 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.25
                           DUF5572   8 elveLIesGkpIPgI 22 
                                       el + I+ ++ +PgI
  gi|242398349|ref|YP_002993773.1| 140 ELGQIINPNEYVPGI 154
                                       78889999******9 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 8.6e-05
                           DUF5572   3 plsFaelveLIesGkpIPgIk 23 
                                       p ++ e v+L+e+ k+IPgIk
  gi|242398349|ref|YP_002993773.1| 192 PETWDEFVKLLEQIKQIPGIK 212
                                       8899****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (435 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); 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: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 3231.36
//
Query:       gi|242398350|ref|YP_002993774.1|  [L=293]
Description: maltose ABC transporter permease [Thermococcus sibiricus MM 739]
Scores for 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-22   77.6  19.2    9.8e-22   77.6  19.2    1.8  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
       0.53    9.4   2.9        0.8    8.8   2.9    1.2  1  TipE          Na+ channel auxiliary subunit TipE


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 ?   -0.4   0.5     0.091   8.2e+02      26      40 ..      10      24 ..       4      84 .. 0.64
   2 !   77.6  19.2   1.1e-25   9.8e-22       3     177 ..      89     290 ..      87     293 .] 0.94

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.091
                      BPD_transp_1 26 vllslPsfvlaillv 40
                                      +++ lP ++l++++v
  gi|242398350|ref|YP_002993774.1| 10 LFFLLPALILMVPFV 24
                                      333444444333333 PP

  == domain 2  score: 77.6 bits;  conditional E-value: 1.1e-25
                      BPD_transp_1   3 llGilaa...lnrnkkldkllrpliivllslPsfvlaillvlvf.....................vilsilghlilp 55 
                                       +lG+ +a   +++  k+  ++  +i++++ +P++v ++++ ++f                      +  + +++ ++
  gi|242398350|ref|YP_002993774.1|  89 FLGLGIAlllRRKEIKGASIIKSIIFLGMVIPMIVGGLIIRFLFeegagvipaifkalgieglaiTWTAYPKTALFA 165
                                       677777777889999********************999999999999*****************9999999999999 PP

                      BPD_transp_1  56 viillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflg 132
                                       +i+ +++ ++++ +l+++a+l s+pkd++eaa+++Ga+r+qif++v+ P+++p +i  +++++ + l+ + +++  +
  gi|242398350|ref|YP_002993774.1| 166 AILGSIWIWTGFSMLMYSAGLASIPKDYYEAALIDGANRFQIFKNVTWPLLKPITIVVVAMTLLWDLKIFDVVYVAT 242
                                       ***************************************************************************** PP

                      BPD_transp_1 133 swpGlgtllleailgydyseis...nggvlalviavlllnlvadilqr 177
                                       ++++ g  ++ a+++ dy + +   n +++++v+++ l ++ a +l r
  gi|242398350|ref|YP_002993774.1| 243 GGGPGGASMVLALQMWDYFARAlnyNYAAVVAVLLTTLTLIPALWLIR 290
                                       9999***************99999999999999999999999998876 PP

>> TipE  Na+ channel auxiliary subunit TipE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   2.9   8.9e-05       0.8      28      52 ..      12      36 ..       3      47 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 8.9e-05
                              TipE 28 fslfaflflvpfviepafttifmqf 52
                                      f l a++++vpfvi p f+t+++ f
  gi|242398350|ref|YP_002993774.1| 12 FLLPALILMVPFVIYPVFKTVYLSF 36
                                      56779999**************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1844.20
//
Query:       gi|242398351|ref|YP_002993775.1|  [L=281]
Description: maltose ABC transporter permease [Thermococcus sibiricus MM 739]
Scores for complete 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   78.0  16.3    7.2e-22   78.0  16.3    1.9  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   1.0     0.094   1.7e+03      32      46 ..      23      45 ..      10      77 .. 0.54
   2 !   78.0  16.3     4e-26   7.2e-22       4     179 ..      92     270 ..      89     275 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.094
                      BPD_transp_1 32 sfvlaillvlvf........vil 46
                                       ++l+++l ++         +++
  gi|242398351|ref|YP_002993775.1| 23 LIWLIPFLGVLMasirpyreIVS 45
                                      33333333222234444454333 PP

  == domain 2  score: 78.0 bits;  conditional E-value: 4e-26
                      BPD_transp_1   4 lGilaa...lnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilp.viillllsa.apyvrlirraa 75 
                                       +++laa    ++++++++ l ++i +l++lP    +++l++   +l  ++ l+   ++il+   + ++++++++r++
  gi|242398351|ref|YP_002993775.1|  92 VAALAAyafARYSFPIKNYLFVFIVFLMALPQQMTIVPLYF---LLRNFHLLNKFqGLILVHSAWgLAWIIFFMRNY 165
                                       566677777899**********************9999884...66777755555555554444416899999999* PP

                      BPD_transp_1  76 lrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG...lgtllleailgyd 149
                                       ++ lp+d +eaar++Gas+++if+k+vlP+alp +i+ +il+f++++ +++l++ ++++p     +++l     +y 
  gi|242398351|ref|YP_002993775.1| 166 FSMLPTDVEEAARIDGASDFKIFYKIVLPMALPGLISAAILQFTWVWSDFFLALVFLQNPEkyvATQRLPLLRGQYF 242
                                       ***********************************************************999644444444444444 PP

                      BPD_transp_1 150 yseisnggvlalviavlllnlvadilqrll 179
                                       +++++  +++a + ++l+ +lv+ ++q++ 
  gi|242398351|ref|YP_002993775.1| 243 VDWGI--LTAASIMVMLVPLLVYTLFQKYY 270
                                       44444..88888888899999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1837.27
//
Query:       gi|242398352|ref|YP_002993776.1|  [L=418]
Description: Trehalose synthase [Thermococcus sibiricus MM 739]
Scores for complete 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   98.1   0.1    9.9e-28   96.8   0.1    1.7  1  Glycos_transf_1  Glycosyl transferases group 1
    2.1e-15   57.3   0.0      4e-15   56.4   0.0    1.5  1  Glyco_trans_1_4  Glycosyl transferases group 1
    8.9e-09   35.6   0.0    2.2e-08   34.4   0.0    1.7  1  Glyco_trans_1_2  Glycosyl transferases group 1
  ------ inclusion threshold ------
       0.13   12.3   0.5        1.4    8.9   0.3    2.5  2  Tfb5             Transcription factor TFIIH complex subunit T


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 !   96.8   0.1   2.2e-31   9.9e-28       7     172 .]     227     397 ..     221     397 .. 0.93

  Alignments for each domain:
  == domain 1  score: 96.8 bits;  conditional E-value: 2.2e-31
                                       HHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES..........STTHHHHHHHHHHHCTTCG CS
                   Glycos_transf_1   7 kklgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaG.........ngeeekelkklaeelelsdn 74 
                                       ++  ++ +++i+  v+r++++Kgv  +i++++++k++  p+v+l+++G             ek+l+kl e + ++  
  gi|242398352|ref|YP_002993776.1| 227 ERFDIDPERPIMTQVARFDPWKGVFDVIDVYRKVKEK-IPDVQLLLVGvmahddpegWIYFEKTLRKLGEDYDVKVL 302
                                       56678999****************************9.**************998865567899**********999 PP

                                       GGEEECCHSSSHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHH CS
                   Glycos_transf_1  75 viflgevsredleellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaea 151
                                       ++++g     ++ ++ +++d++++ si+EgfG++++EAm   +pvi  ++gg++ ++ dgetG+lvk+   e++ae+
  gi|242398352|ref|YP_002993776.1| 303 TNLTGVHA-REVNAFQRASDVILQMSIKEGFGLTVTEAMWKEKPVIGRAVGGIKLQIIDGETGFLVKNI--EEAAEK 376
                                       99998887.78*******************************************************976..****** PP

                                       HHHHHHSHHHHHHHHHHHHHH CS
                   Glycos_transf_1 152 irklledeelrerlgenarkr 172
                                        + l++ +e+ +++g++a+++
  gi|242398352|ref|YP_002993776.1| 377 AIYLIKHPETVKDMGKKAKEW 397
                                       ******************987 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 !   56.4   0.0     9e-19     4e-15       2     133 ..     236     382 ..     235     383 .. 0.79

  Alignments for each domain:
  == domain 1  score: 56.4 bits;  conditional E-value: 9e-19
                                       EEEEEES---GG.GTHHHHHHHHHHHH.H..HEEEEEES....---..........HHHHHHHT..T-T.TEEEE-- CS
                   Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkk..dvrlvivG....dgprp........eeleelaa..gleerveftGf 62 
                                       p++  v r+ +++kgv  +++   ++++k  dv+l++vG    d   +        + l++l +  +    v+++  
  gi|242398352|ref|YP_002993776.1| 236 PIMTQVARF-DPWKGVFDVIDVYRKVKEKipDVQLLLVGvmahD---DpegwiyfeKTLRKLGEdyD----VKVLTN 304
                                       778899***.667**************99855*******55432...13456555445543333222....555555 PP

                                       -.....THHHHHHHH-SEEEE--..---SHHHHHHHHTT-EEEE-TGGGT.TT--.TTSSEE--TT-HHHHHHHHHH CS
                   Glyco_trans_1_4  63 v.....edlaellaaadvfvaPs..egfglkllEamaaglpvVatdvggi.aevv.gengllvppgdpealaeailr 130
                                       +      +++++ +a+dv +  s  egfgl++ Eam  ++pv+  +vggi  +++ ge+g+lv+  + e+ ae+ + 
  gi|242398352|ref|YP_002993776.1| 305 LtgvhaREVNAFQRASDVILQMSikEGFGLTVTEAMWKEKPVIGRAVGGIkLQIIdGETGFLVK--NIEEAAEKAIY 379
                                       55555778*****************************************945566********9..9********99 PP

                                       HHH CS
                   Glyco_trans_1_4 131 Lle 133
                                       L++
  gi|242398352|ref|YP_002993776.1| 380 LIK 382
                                       986 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   0.0     5e-12   2.2e-08       2      91 ..     323     412 ..     322     413 .. 0.94

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 5e-12
                   Glyco_trans_1_2   2 vLnpsrsespnlrlfEaaacGafaltddaegleelftpgkevilfedleelaekiryllanpeerraiaeaarervl 78 
                                        L  s +e++ l + Ea+    +++  +  g+   + +g++++l+++ ee+aek  yl+++pe  + ++++a+e+v+
  gi|242398352|ref|YP_002993776.1| 323 ILQMSIKEGFGLTVTEAMWKEKPVIGRAVGGIKLQIIDGETGFLVKNIEEAAEKAIYLIKHPETVKDMGKKAKEWVK 399
                                       57788999*******************99************************************************ PP

                   Glyco_trans_1_2  79 aehtydhraeqll 91 
                                       +++  ++ +e++l
  gi|242398352|ref|YP_002993776.1| 400 ENFIITKHLERYL 412
                                       **98888888776 PP

>> Tfb5  Transcription factor TFIIH complex subunit Tfb5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.18   8.3e+02      37      62 ..      20      45 ..      18      50 .. 0.79
   2 ?    8.9   0.3   0.00032       1.4      17      55 ..     174     213 ..     172     224 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.18
                              Tfb5 37 LDethlfvkeevveelkkeleellek 62
                                      L +   ++ ee ++ +k+++e+l+ k
  gi|242398352|ref|YP_002993776.1| 20 LGDYVGIIGEEGLDRVKEKVEKLQGK 45
                                      5566667889999********99865 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00032
                              Tfb5  17 kqlilkldeqep.sqkfiiedLDethlfvkeevveelkke 55 
                                       kq++ k d+     ++++ edLD + +++ +  ++ l ++
  gi|242398352|ref|YP_002993776.1| 174 KQFVAKYDKYIFhMEEYVQEDLDKNKVVIMPPSIDPLSEK 213
                                       99******9976778***************9999988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       863  (0.0481343); expected 358.6 (0.02)
Passed bias filter:                      649  (0.0361983); 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: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 2494.63
//
Query:       gi|242398353|ref|YP_002993777.1|  [L=338]
Description: Maltose-specific transcriptional repressor TrmB [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.3e-48  163.5   0.4    6.4e-48  163.0   0.4    1.2  1  Regulator_TrmB  Archaeal transcriptional regulator TrmB
    1.4e-21   76.2   0.0    2.3e-21   75.4   0.0    1.4  1  TrmB            Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.094   13.1   0.0       0.48   10.8   0.0    2.1  2  Rrf2            Transcriptional regulator
       0.11   12.6   0.0       0.25   11.5   0.0    1.6  1  HTH_9           RNA polymerase III subunit RPC82 helix-turn-h


Domain annotation for each model (and alignments):
>> Regulator_TrmB  Archaeal transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.0   0.4   1.4e-51   6.4e-48       1     230 [.     110     335 ..     110     337 .. 0.97

  Alignments for each domain:
  == domain 1  score: 163.0 bits;  conditional E-value: 1.4e-51
                                       -EEEESSHHHHHHHHHHHHHH-SSEEEEEE-GGGHHHHHHHHHHHHHTT-EEEEEESS----GGGSSSSEEEEEE-S CS
                    Regulator_TrmB   1 avwvvksretvierieelIesAenelivslpselLeelreeliaaaergvtVllliypdedleeldleevatevrvr 77 
                                       a+w+++s+e+++e+++e ++sA+ne+iv +pse++e++r++l ++ e+gvtV+l+i + ++lee+++ ++  + +++
  gi|242398353|ref|YP_002993777.1| 110 AIWRSQSFEEALEMFRETLRSARNEVIVVTPSEFFEDIRSDLLKTLEKGVTVSLYIDKIPNLEEFRDVGNLFVRQFY 186
                                       59*************************************************************************** PP

                                       ---S.EEEEETTTEEEEE-SSS-......EEEE--HHHHHHHHHHHHHH........HHH-EEEEEEES-TT-EEES CS
                    Regulator_TrmB  78 rsgapllvivDrkrgvvaprevl......rdkeeeyaiifkekelihvlshyFlttlWktseviktdepvekpitfs 148
                                       ++++ l+ ++D+k+++ +++ ++      + k ++ ++if++++li  +        +k+s+  k++  ++++++f+
  gi|242398353|ref|YP_002993777.1| 187 KLNH-LIGMADGKEVINIQNISFrpnlppSFKATYPEVIFSQYSLIIEI--------FKESSLEKEYLINPQDVRFF 254
                                       ****.***********9999777888888999***************99........9******************* PP

                                       -HHHHHHHHHHHT.TTS-EEEEEEEEETTT--EEEEEEEEEEEEEETTTTEEEEEEEETTEEEEEE-TT--SSSEEE CS
                    Regulator_TrmB 149 sirlavedikkllraglkveaeveGrdtetgeevtieGrvveatlnstpgvaslvvetedgevtVGGlgAvlEDiea 225
                                       ++++a + +k+++ +  +++ae+ G++++tge++ti G vv++tl+ +++ +++++ete+g+++VGG  Av+ED+e+
  gi|242398353|ref|YP_002993777.1| 255 AMFHAADFVKRHI-ESIPIMAELIGKNVKTGETETIYGNVVGYTLSFREAINNIHLETENGVIKVGGIFAVIEDYES 330
                                       ************9.888************************************************************ PP

                                       EEEEE CS
                    Regulator_TrmB 226 eeitl 230
                                       +ei++
  gi|242398353|ref|YP_002993777.1| 331 KEIKF 335
                                       ***86 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.4   0.0   5.2e-25   2.3e-21       1      67 [.      11      77 ..      11      78 .. 0.98

  Alignments for each domain:
  == domain 1  score: 75.4 bits;  conditional E-value: 5.2e-25
                                      HHHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE--H CS
                              TrmB  1 LqklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYravdp 67
                                      L+++G+++yE+ +Y++Ll +gp+ta+ei+ ++g+p+++vY++++sL+ +G+V+ ++g+p++Y a +p
  gi|242398353|ref|YP_002993777.1| 11 LSEIGFTKYEILTYWTLLVHGPSTAKEISTKSGIPYNRVYDTISSLKIRGFVTEIDGTPRVYAAYSP 77
                                      789*************************************************************998 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   0.00011      0.48      22      60 ..      30      67 ..      17      70 .. 0.85
   2 ?   -1.7   0.0      0.85   3.8e+03      19      41 ..     194     216 ..     186     218 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00011
                                      TCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT CS
                              Rrf2 22 eeepvsseeiaerqnispsylekilakLrkaglvksvrG 60
                                      + +p +++ei+++ +i+ + +   ++ L+  g+v+ + G
  gi|242398353|ref|YP_002993777.1| 30 H-GPSTAKEISTKSGIPYNRVYDTISSLKIRGFVTEIDG 67
                                      4.4699****************************99988 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.85
                                       HSSTCC-B-HHHHHHHHTS-HHH CS
                              Rrf2  19 keeeeepvsseeiaerqnispsy 41 
                                       + +++e +++++i+ r n++ps+
  gi|242398353|ref|YP_002993777.1| 194 MADGKEVINIQNISFRPNLPPSF 216
                                       45566679999**9999999986 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 ?   11.5   0.0   5.6e-05      0.25      21      57 ..      26      62 ..      24      63 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.6e-05
                                      HHHHHSSBEHHHHHHHHSSTHHHHHHHHHHHHHTTSE CS
                             HTH_9 21 tLlrkgrltlrelvkktkLsldqVkksLvvLiqhrlV 57
                                      tLl +g +t++e+++k++++ + V ++ ++L  +++V
  gi|242398353|ref|YP_002993777.1| 26 TLLVHGPSTAKEISTKSGIPYNRVYDTISSLKIRGFV 62
                                      799***************************9766666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1047  (0.058397); expected 358.6 (0.02)
Passed bias filter:                      829  (0.0462379); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2400.98
//
Query:       gi|242398354|ref|YP_002993778.1|  [L=372]
Description: maltose ABC transporter ATPase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-31  109.7   0.0    2.7e-31  108.9   0.0    1.4  1  ABC_tran         ABC transporter
      4e-19   69.2   0.1      2e-18   67.0   0.0    2.3  2  OB_MalK          MalK OB fold domain
    8.4e-07   29.1   0.0    2.1e-06   27.8   0.0    1.7  1  TOBE_2           TOBE domain
    9.2e-07   29.3   0.1    3.7e-06   27.4   0.0    2.1  2  CysA_C_terminal  CysA C-terminal regulatory domain
    1.3e-05   25.2   0.0       0.14   11.9   0.0    2.2  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    7.9e-05   22.9   0.0    0.00019   21.7   0.0    1.7  1  TOBE             TOBE domain
    9.5e-05   22.4   0.0    0.00014   21.8   0.0    1.4  1  Rad17            Rad17 P-loop domain
    0.00013   21.5   0.1     0.0011   18.4   0.1    2.0  1  SMC_N            RecF/RecN/SMC N terminal domain
      0.001   18.8   0.9      0.002   17.9   0.9    1.5  1  Syntaxin         Syntaxin
     0.0037   17.5   0.3      0.011   16.0   0.3    1.9  1  AAA_22           AAA domain
     0.0046   17.4   0.0     0.0072   16.7   0.0    1.5  1  AAA_16           AAA ATPase domain
  ------ inclusion threshold ------
      0.018   14.9   0.0      0.045   13.7   0.0    1.6  1  RsgA_GTPase      RsgA GTPase
      0.025   15.0   0.1      0.086   13.3   0.0    1.9  2  AAA              ATPase family associated with various cellul
      0.053   13.2   0.0       0.15   11.8   0.0    1.7  1  AAA_30           AAA domain
      0.083   12.6   0.0       0.23   11.2   0.0    1.7  1  AAA_29           P-loop containing region of AAA domain
       0.13   12.8   0.3       0.42   11.1   0.0    1.8  2  AAA_23           AAA domain
       0.15   12.4   0.0       0.33   11.3   0.0    1.5  1  AAA_19           AAA domain
       0.16   11.9   0.2       0.41   10.7   0.1    1.7  2  AAA_5            AAA domain (dynein-related subfamily)


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.9   0.0   2.7e-34   2.7e-31       2     136 ..      20     167 ..      19     168 .. 0.94

  Alignments for each domain:
  == domain 1  score: 108.9 bits;  conditional E-value: 2.7e-34
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS--S-TTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke....qeleslrkeigvlpqepqlfpel 74 
                                       k+++l++k ge + ++G++G+GK+t l++++gl++pt+G+i + +k + +       +  ++ i++++q   l p++
  gi|242398354|ref|YP_002993778.1|  20 KDITLEVKDGEFMILLGPSGCGKTTTLRMISGLEEPTKGQIYIGDKLVADpekgVFVPPKDRDIAMVFQSYALYPHM 96 
                                       89***************************************9998888887666566778999************** PP

                                       BHHHH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  75 tvren.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       tv++n             e d+++ ++++ lgl++l +++     ++LSgGq+qrval ra+++kp+++l+DEp 
  gi|242398354|ref|YP_002993778.1|  97 TVYDNiafplklrkvpkqEIDKRVREVAELLGLSQLLNRKP----RELSGGQRQRVALGRAIVRKPQVFLMDEPL 167
                                       ***************99999999************999998....*****************************7 PP

>> OB_MalK  MalK OB fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.0   0.0     2e-21     2e-18       1      53 []     241     294 ..     241     294 .. 0.97
   2 ?   -2.5   0.0       9.5   9.5e+03       6      43 ..     308     350 ..     308     353 .. 0.42

  Alignments for each domain:
  == domain 1  score: 67.0 bits;  conditional E-value: 2e-21
                           OB_MalK   1 GSPaMNflpatveedgvlvegggvtlplpeeq..klalklyagkevilGiRPEhi 53 
                                       GSP+MNf+++ v+edg +v++g+++l+l ++q  +l++++y+g+evi+GiRPE+i
  gi|242398354|ref|YP_002993778.1| 241 GSPPMNFMDGSVTEDG-FVDFGEFRLKLLPDQfeVLKEQGYVGREVIFGIRPEDI 294
                                       9***************.***********99999888******************8 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 9.5
                           OB_MalK   6 Nflpatveedgvlvegggvtlplpeeq.kl......alklyagke 43 
                                       N+++a ve  +   +gg+  + l++e+ ++      + k ++g++
  gi|242398354|ref|YP_002993778.1| 308 NMVKAMVEIVE--NLGGERIVYLSTEDiSFiakfppESKVKEGQK 350
                                       56666665333..22333333444444322233344455666665 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.0   2.1e-09   2.1e-06       2      76 .]     288     363 ..     287     363 .. 0.92

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 2.1e-09
                            TOBE_2   2 aiRPEklrla.....aagganglsGtVedveylGsstryvvelaggqlvvvrqpnadrdsalapGdtVelswdpdda 73 
                                       +iRPE++  a     +  g+n +++ Ve ve lG +  +++++++ ++ +++ p+++    +++G+++e+ +d  ++
  gi|242398354|ref|YP_002993778.1| 288 GIRPEDIYDAmfaqvKVPGENMVKAMVEIVENLGGERIVYLSTEDISF-IAKFPPES---KVKEGQKIEVVFDMKKI 360
                                       8******99999886555578*************************99.88999999...9**************** PP

                            TOBE_2  74 vvl 76 
                                       +++
  gi|242398354|ref|YP_002993778.1| 361 HIF 363
                                       *98 PP

>> CysA_C_terminal  CysA C-terminal regulatory domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       5.9   5.9e+03       9      22 ..      57      70 ..      56      74 .. 0.79
   2 !   27.4   0.0   3.8e-09   3.7e-06       1      41 [.     246     294 ..     246     295 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 5.9
                   CysA_C_terminal  9 dGklriGglalpvP 22
                                       G++ iG+  ++ P
  gi|242398354|ref|YP_002993778.1| 57 KGQIYIGDKLVADP 70
                                      599****9888887 PP

  == domain 2  score: 27.4 bits;  conditional E-value: 3.8e-09
                   CysA_C_terminal   1 NlFhGrv.edGklriGglalp.vP......elagadgqevvayVRPhDl 41 
                                       N+ +G v edG + +G+++l+ +P      +++g+ g+ev+ ++RP+D+
  gi|242398354|ref|YP_002993778.1| 246 NFMDGSVtEDGFVDFGEFRLKlLPdqfevlKEQGYVGREVIFGIRPEDI 294
                                       888999966************999************************8 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   0.00022      0.22       1      22 [.      31      52 ..      31      81 .. 0.85
   2 !   11.9   0.0   0.00014      0.14     231     299 ..     134     200 ..      97     204 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00022
                            AAA_21  1 lnvliGpNgsGKSnLLdaldll 22
                                      +++l Gp g+GK++ L+ +++l
  gi|242398354|ref|YP_002993778.1| 31 FMILLGPSGCGKTTTLRMISGL 52
                                      789****************999 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00014
                            AAA_21 231 elparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSp 299
                                       ++ +relS G+++  al  a+ r +    ++l DEp ++L+ kl  +    lk+l+r   +  i +TH+ 
  gi|242398354|ref|YP_002993778.1| 134 NRKPRELSGGQRQRVALGRAIVRKP---QVFLMDEPLSNLDAKLRVKMRAELKKLQRqLSVTTIYVTHDQ 200
                                       5668999*****999*******988...9********************999888886888889999985 PP

>> TOBE  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   1.9e-07   0.00019       4      64 .]     307     362 ..     305     362 .. 0.97

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.9e-07
                              TOBE   4 rNqlpgtVvvveplgseveVrvdlgggatLtArvtrrsaeeLgLapGeeVfalikaakvhl 64 
                                       +N +++ V+ ve lg+e  V++ +++    +A+ +++s ++     G+++ +++++ k+h+
  gi|242398354|ref|YP_002993778.1| 307 ENMVKAMVEIVENLGGERIVYLSTEDIS-FIAKFPPESKVK----EGQKIEVVFDMKKIHI 362
                                       89**************************.************....**************96 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   1.4e-07   0.00014      26      67 ..      11      51 ..       5     140 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.4e-07
                             Rad17 26 kkieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLsk 67
                                      kk e+v +++k  +Le +  + +++ GPsGCgk+t+++++s 
  gi|242398354|ref|YP_002993778.1| 11 KKFEDV-TAVKDITLEVKDGEFMILLGPSGCGKTTTLRMISG 51
                                      578888.5778889****999*****************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 !   18.4   0.1   1.1e-06    0.0011      25     213 ..      30     212 ..      11     219 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.1e-06
                                       SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--..BTTCSSTTEEEEEEEEEETTEESSSSSSCEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk..skekasvkkaeveitfdnedkklkiekeevsi 99 
                                       +f +++Gp G+GK+  l  i    G ++ +k +    ++l+    +      k  +++++f+      +  +   +i
  gi|242398354|ref|YP_002993778.1|  30 EFMILLGPSGCGKTTTLRMI---SGLEEPTKGQIYIGDKLVADpeKGVFVPPKDRDIAMVFQSYALY-PHMTVYDNI 102
                                       57888888888888888777...56667767777778888888432333345667777777666655.333333334 PP

                                       EEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 100 srrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknv 176
                                          +k  +  + +i+++  + +e+  l +  + ++ +LSgG+++ val    Ai   ++  ++l+De  ++LD+k +
  gi|242398354|ref|YP_002993778.1| 103 AFPLKLRKVPKQEIDKRVREVAELLGLSQLLNRKPRELSGGQRQRVALG--RAIV--RKPQVFLMDEPLSNLDAKLR 175
                                       444444444455599888888888888888888999*******977664..4554..4455789************* PP

                                       HHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 177 kkvaellkeksknaQfivislreemlekadklvgvtk 213
                                        k+   lk+ + +  +  i ++++++e +    ++  
  gi|242398354|ref|YP_002993778.1| 176 VKMRAELKKLQRQLSVTTIYVTHDQVEAMTMGDKIAV 212
                                       **********988888777788888888765555554 PP

>> Syntaxin  Syntaxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.9     2e-06     0.002     109     158 ..     173     221 ..     113     228 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2e-06
                          Syntaxin 109 elrekireeykerieRrlevtGkevseeeieelietgesevflqkllqeq 158
                                       +lr k+r e k+ ++R+l+vt   v+++++e +   ++  v++q +lq+ 
  gi|242398354|ref|YP_002993778.1| 173 KLRVKMRAELKK-LQRQLSVTTIYVTHDQVEAMTMGDKIAVINQGVLQQV 221
                                       578888888875.8********************************9986 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.3   1.1e-05     0.011       4      29 ..      28      53 ..      24     204 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.1e-05
                            AAA_22  4 tagilvvtGesGtGKTtllrrlleql 29
                                      +  ++++ G+sG+GKTt+lr++    
  gi|242398354|ref|YP_002993778.1| 28 DGEFMILLGPSGCGKTTTLRMISGLE 53
                                      67899***************987655 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   7.2e-06    0.0072      19      51 ..      26      55 ..      14     203 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 7.2e-06
                            AAA_16 19 vrsgrpelvllsGesGvGKsslvrellralekd 51
                                      v++g  e ++l G+sG+GK++ +r++   le+ 
  gi|242398354|ref|YP_002993778.1| 26 VKDG--EFMILLGPSGCGKTTTLRMIS-GLEEP 55
                                      5555..789***************997.44444 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   4.5e-05     0.045      88     123 ..      17      53 ..       6      64 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.5e-05
                                       TTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT- CS
                       RsgA_GTPase  88 egleelkellkd.ktsvlvGqSGvGKStLinallpel 123
                                       +++++++ ++kd ++++l+G+SG GK+t + ++ + +
  gi|242398354|ref|YP_002993778.1|  17 TAVKDITLEVKDgEFMILLGPSGCGKTTTLRMISGLE 53 
                                       5678888888888***************999988754 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   8.6e-05     0.086       1      19 [.      32      50 ..      32      89 .. 0.91
   2 ?   -1.5   0.0       3.2   3.2e+03      58      66 ..     157     165 ..     121     204 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.6e-05
                                      EEEESSTTSSHHHHHHHHH CS
                               AAA  1 vllyGppGtGKTllakava 19
                                      ++l Gp G+GKT++ + + 
  gi|242398354|ref|YP_002993778.1| 32 MILLGPSGCGKTTTLRMIS 50
                                      799***********99885 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.2
                                       TSEEEEEET CS
                               AAA  58 kpsilfiDE 66 
                                       kp ++++DE
  gi|242398354|ref|YP_002993778.1| 157 KPQVFLMDE 165
                                       467777776 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   0.00015      0.15      17      45 ..      29      56 ..      17      64 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00015
                            AAA_30 17 gdrvavltGpAGtGKttalkalreaweaa 45
                                      g  +++l Gp G GKtt+l+ +  + e  
  gi|242398354|ref|YP_002993778.1| 29 G-EFMILLGPSGCGKTTTLRMISGLEEPT 56
                                      4.599***************998776655 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 ?   11.2   0.0   0.00023      0.23      16      39 ..      23      46 ..      10      56 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00023
                            AAA_29 16 tieidlkg.atlltGpsGsGKSTll 39
                                      t+e++  g +++l GpsG GK+T l
  gi|242398354|ref|YP_002993778.1| 23 TLEVKD-GeFMILLGPSGCGKTTTL 46
                                      445553.369************976 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00042      0.42      11      39 ..      20      49 ..      10      51 .. 0.71
   2 ?   -1.4   0.0       2.9   2.8e+03     153     192 ..     114     189 ..      93     193 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00042
                            AAA_23 11 rdqeidF.skgltlItGpNGaGKTTildAi 39
                                      +d +++  +  + ++ Gp G+GKTT l+ i
  gi|242398354|ref|YP_002993778.1| 20 KDITLEVkDGEFMILLGPSGCGKTTTLRMI 49
                                      4455555344566889*********99877 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.9
                            AAA_23 153 erleelekeleeledekkllekl....................................eqekekekeleeleeel 192
                                       +++++  +e  el    +ll+++                                    + + + ++el++l+++l
  gi|242398354|ref|YP_002993778.1| 114 QEIDKRVREVAELLGLSQLLNRKprelsggqrqrvalgraivrkpqvflmdeplsnldaKLRVKMRAELKKLQRQL 189
                                       5555555555555555555555555555555555555555555555555554444433333334455777777666 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00033      0.33      10      30 ..      29      49 ..      20      61 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00033
                            AAA_19 10 ekvllvtaGpGtGKTrvlkhi 30
                                       + ++++++ G+GKT++l++i
  gi|242398354|ref|YP_002993778.1| 29 GEFMILLGPSGCGKTTTLRMI 49
                                      57899*************987 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00041      0.41       2      21 ..      32      51 ..      31      63 .. 0.88
   2 ?   -3.1   0.0       7.2   7.1e+03      85     105 ..     129     148 ..     115     170 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00041
                                      EEEE--SSSSHHHHHHHGGG CS
                             AAA_5  2 vlLvGppGtgKselaerlaa 21
                                      ++L+Gp+G+gK++  + ++ 
  gi|242398354|ref|YP_002993778.1| 32 MILLGPSGCGKTTTLRMISG 51
                                      69***********9998775 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 7.2
                                       HHHHHHSSEEE..-SSSEEE- CS
                             AAA_5  85 Llslleerrllleeggelvka 105
                                       L +ll+++ +   +gg+++++
  gi|242398354|ref|YP_002993778.1| 129 LSQLLNRKPRE-LSGGQRQRV 148
                                       45566666555.334443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      584  (0.0325729); 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: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.53
# Mc/sec: 2124.90
//
Query:       gi|242398355|ref|YP_002993779.1|  [L=494]
Description: L-fucose isomerase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-11   43.4   0.0    3.7e-11   42.9   0.0    1.2  1  Fucose_iso_C  L-fucose isomerase, C-terminal domain
  ------ inclusion threshold ------
       0.17   11.7   0.1       0.27   11.0   0.1    1.2  1  DUF724        Protein of unknown function (DUF724)


Domain annotation for each model (and alignments):
>> Fucose_iso_C  L-fucose isomerase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9   0.0   4.1e-15   3.7e-11       2     138 ..     349     477 ..     348     482 .. 0.89

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 4.1e-15
                                       E-SS---GGGEE-THHHHHHHHT-EEEE--TTT-TT--EEEE-B--TT-EEEEEEEEEETTTEEE.EEEEEEEE--- CS
                      Fucose_iso_C   2 insGnaaldgaarssdvesclkatelkpaareyfrgggfgsvegtikpgpvTllRlnlikgdGkvklqiaeGefvdl 78 
                                        n+G+++l++a+ s+++e++l+a + +  ++  ++gg  g+   ++ p+++T++Rl   ++ G++ l    +e v++
  gi|242398355|ref|YP_002993779.1| 349 ANCGASSLYYAKLSENPEENLRAITIQ--GQCQGAGG--GALTYRTPPTTLTVARLI--RKGGEYYLLYFLAEGVEI 419
                                       6*******************8776655..55555888..9****************9..******99999******* PP

                                       -HHHHHHHHHHH-TTS-BEEEEE---SSHHHHT-SSSEEEEEES--HHHHHHHHHHHT-- CS
                      Fucose_iso_C  79 peetfgslgvrtipewpttffkprltgksvmenwganHvavvyGhvgkdlielakyLrip 138
                                       +ee+  +l+    ++wp+t +k  l+++ +++  ganH  +v G++++++   a++ +i+
  gi|242398355|ref|YP_002993779.1| 420 DEEIESKLKW--GRQWPHTAIKNPLDKEKFLNAMGANHLSAVSGDFRSEIEFSARLWGIR 477
                                       ****888765..578*********************************998777777776 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1     3e-05      0.27      60     105 ..      14      59 ..       2      73 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3e-05
                            DUF724  60 klsiddsrseleslkeslaeLekhGFdVkalqsrlnkLlslkdeqt 105
                                       +ls++ +++ le++k+ ++eL++ GF V  +   l+k  slk+  +
  gi|242398355|ref|YP_002993779.1|  14 SLSLEREKALLEKHKTLINELKASGFTVFDVNGALKKYDSLKNGEN 59 
                                       6899999******************************999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (494 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.49
# Mc/sec: 3023.11
//
Query:       gi|242398356|ref|YP_002993780.1|  [L=637]
Description: Glycogen debranching enzyme [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-15   55.7   0.0    9.6e-15   54.4   0.0    1.6  1  GDE_C            Amylo-alpha-1,6-glucosidase
    5.3e-15   55.5   0.1    1.3e-14   54.3   0.1    1.6  1  GDE_N_bis        N-terminal domain of (some) glycogen debranc
    7.7e-07   28.1   0.0    4.8e-05   22.2   0.0    2.4  3  Glyco_hydro_100  Alkaline and neutral invertase
     0.0088   15.3   0.0      0.014   14.7   0.0    1.3  1  Bac_rhamnosid6H  Bacterial alpha-L-rhamnosidase 6 hairpin gly
  ------ inclusion threshold ------
        0.1   13.1   0.0       0.26   11.8   0.0    1.6  1  Imm42            Immunity protein 42


Domain annotation for each model (and alignments):
>> GDE_C  Amylo-alpha-1,6-glucosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.4   0.0   2.7e-18   9.6e-15      21     381 ..     232     581 ..     217     583 .. 0.79

  Alignments for each domain:
  == domain 1  score: 54.4 bits;  conditional E-value: 2.7e-18
                             GDE_C  21 gvsliAGlpwFsd.WGRDtfIaLsGllLvtgrfeeAreilltFaktlr..........hGliPNlldegqeal.... 82 
                                       g+   AG p+++   GRD++I+     L+++  + A   l+ Fak +            G iP  +  g+       
  gi|242398356|ref|YP_002993780.1| 232 GMVPFAGIPYYACpFGRDSIIT--SWFLLPYYPQYAEGTLKFFAKIQGkqfnpvneeePGKIPHEFRFGELSHsrkm 306
                                       55557*******66******96..789*****************998779999999999****98875432222244 PP

                             GDE_C  83 .....yntvdaslwlieaiekYleyagdaeilrriypvlqeilqkyvqGtky.kigldeedglisagerlnqlTWmD 153
                                            y tvda+  ++    +Yl+ +gd +++++  p l  ++++ ++ ++    ++  + g++        + W D
  gi|242398356|ref|YP_002993780.1| 307 pfapyYGTVDATPLYVILAAEYLRWTGDRNLIEELKPNLTAAVEWILRRLREgGGYIRYKGGFL------ANQGWKD 377
                                       44555***************************99999766666666655541011344445555......4556999 PP

                             GDE_C 154 ....akvkgepvtPRdGkaveinaLwyaaLkileelaekalgeakkssykelaekikesfekkFwdeaaaavakrei 226
                                           + +++   t    + ve+++ +y+aL  +++l  + l+    ++ ++ a+ +k  f++ Fw         ++ 
  gi|242398356|ref|YP_002993780.1| 378 siegIPTEDGTHTKPPVALVEVQGYAYKALVDAASLGLTSLDS---KMLEKEAKALKRRFNRDFWC--------NGF 443
                                       8877667777777778899****************99966666...99*****************9........788 PP

                             GDE_C 227 laDvlksseekdlslRpNflialslapellseekakkvlekaeeeLltplGlktLdpedpeYkgnYdgsedsrdaaY 303
                                       +a  l+ ++   + +  N+   l+   +  ++e a+++    ee++   +G++tL++++++Y++          + Y
  gi|242398356|ref|YP_002993780.1| 444 YALALDGDNVPSKVVSSNMGHLLFTRITEYQKEIAERL---FEEDMFSGWGIRTLSSNEKAYNP----------FSY 507
                                       88888888889999999*99888877777777776665...67899****************98..........68* PP

                             GDE_C 304 HqGtvWvwllgsyveallkfgeklgkskealeevkalLeglekhleeaglgslsElfd.gdaellpkgciaQAWSva 379
                                       H+G +W++  ++    l ++gek    ++a + +++++ +++k+l +++l +l   ++ + + l+p++ + QAWS a
  gi|242398356|ref|YP_002993780.1| 508 HNGSIWPHDNAIIALGLASIGEK----EKAKT-LSEAIFKAAKFLPNSQLPELYSGLEsEYPLLCPRANAPQAWSAA 579
                                       ***********999999999996....33333.44444448888888776666444441555689***********9 PP

                             GDE_C 380 el 381
                                        +
  gi|242398356|ref|YP_002993780.1| 580 SV 581
                                       87 PP

>> GDE_N_bis  N-terminal domain of (some) glycogen debranching enzymes
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.3   0.1   3.5e-18   1.3e-14       3     187 ..       7     173 ..       5     179 .. 0.80

  Alignments for each domain:
  == domain 1  score: 54.3 bits;  conditional E-value: 3.5e-18
                         GDE_N_bis   3 dgdlflvtdtdGdiaeegegsqGlFcrDtRfLsrlelqingespvllsssaekgnsalsvlltnpeledeeggipae 79 
                                        +  f+vt+++Gd++   +  +G++  DtRfL  ++l++n++ + l+ ss+++    +  ++           i++ 
  gi|242398356|ref|YP_002993780.1|   7 YNGAFVVTRQNGDMK---DNYDGFYILDTRFLKGVKLRLNKDGV-LIGSSQDGPR-KAYSHFS----------IED- 67 
                                       5789***********...899*******************8877.7777777777.4444444..........333. PP

                         GDE_N_bis  80 tigirrervv.ng.glfeeleltNynttpvefelslsfdaDFaDlfevrgfr.rekrgkllrleaedeelrlayrgl 153
                                       ++ + r+r + n+ + +eel+  N+++ +++++++  f++   D+fevr+f  ++ r +++  ++ ++e   +y+g 
  gi|242398356|ref|YP_002993780.1|  68 KVVLLRKREIkNNwAYREELQFYNTSNGKIDLRIEYVFKVPIEDIFEVRKFGgQRIRRRIK--SSLGKEGEYSYSGK 142
                                       56677777776778***********************************998446666654..4668999999**** PP

                         GDE_N_bis 154 dgvvretriqfsaqpdtvkggtatwrlkLaphet 187
                                       d   r+ +i+ +    ++++g a  +++L+p ++
  gi|242398356|ref|YP_002993780.1| 143 DRIKRNLKIKTNM---RIEKGLAFAEITLEPFKK 173
                                       *******999954...344666777777777665 PP

>> Glyco_hydro_100  Alkaline and neutral invertase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.1   0.0    0.0085        30     113     140 ..     314     341 ..     296     357 .. 0.82
   2 ?   -3.6   0.0      0.93   3.3e+03     184     231 ..     397     440 ..     396     442 .. 0.64
   3 !   22.2   0.0   1.3e-08   4.8e-05     349     426 ..     500     582 ..     487     589 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.0085
                                       -HHHHHHHHHHHHHHHHHH---HHHHSH CS
                   Glyco_hydro_100 113 pvDsslWWiillraYvkatgdlslaeee 140
                                       +vD++  ++il+  Y ++tgd++l ee 
  gi|242398356|ref|YP_002993780.1| 314 TVDATPLYVILAAEYLRWTGDRNLIEEL 341
                                       6999999****************99864 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 0.93
                                       HHHHHHHHHHHHHHHHHS-STTTHHHHHHHHHHHHHHHHHHHHHHTEE CS
                   Glyco_hydro_100 184 leiqaLlyaalrsakelleeeeeekelleaiekrlkaLrsylreyyWl 231
                                       +e+q   y+al  a++l  ++ ++k     +ek +kaL++  ++ +W 
  gi|242398356|ref|YP_002993780.1| 397 VEVQGYAYKALVDAASLGLTSLDSK----MLEKEAKALKRRFNRDFWC 440
                                       5788888888888888876666533....3445556666666666665 PP

  == domain 3  score: 22.2 bits;  conditional E-value: 1.3e-08
                                       GGG-TTBTTBT-B-GG..GHHHHHHH.HHHTT-HHHHHHHHHHHHTTHTTTT--S-EESTTS-E..E-TT--SSBHH CS
                   Glyco_hydro_100 349 pkntpwsYhngGsWpv..llWllvaa.alkterkelaekaielaekrlskdewaeYydgktgrl..vgkqarkyqtw 420
                                       +   p+sYhng  Wp    + +l +a + ++e+ + +++ai  a+k l++ + +e y g ++++  +  +a++ q+w
  gi|242398356|ref|YP_002993780.1| 500 KAYNPFSYHNGSIWPHdnAIIALGLAsIGEKEKAKTLSEAIFKAAKFLPNSQLPELYSGLESEYplLCPRANAPQAW 576
                                       44579**********63345555555055677889999*********************999754499********* PP

                                       HHHHHH CS
                   Glyco_hydro_100 421 tiagfl 426
                                       + a+++
  gi|242398356|ref|YP_002993780.1| 577 SAASVF 582
                                       *99865 PP

>> Bac_rhamnosid6H  Bacterial alpha-L-rhamnosidase 6 hairpin glycosidase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   3.8e-06     0.014      95     217 ..     313     442 ..     291     493 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.8e-06
                                       --TTTTTHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHTSBT.......TB..--S-S--STT.......... CS
                   Bac_rhamnosid6H  95 etaeWadaivivpwelyetygDkeilkkqYesmkryldylkqrsdd......gle.elskfqlgDWldpe.....ar 159
                                       +t+  + ++vi++ e+ + +gD++++++  +++++ ++++++r ++      ++   l+++++ D          ++
  gi|242398356|ref|YP_002993780.1| 313 GTVDATPLYVILAAEYLRWTGDRNLIEELKPNLTAAVEWILRRLREgggyirYKGgFLANQGWKDS---IegiptED 386
                                       555557789************************************977655322224455555555...24558677 PP

                                       -SS----HHHH.HHHHHHHHHHHHHHHHHHTTS..--HHHHHHHHHHHHHHHHHHB.-T CS
                   Bac_rhamnosid6H 160 dgaaktekalv.ataylvrslklvakiaellgkeedakkyaalaeelkaafnkkyldse 217
                                       + ++k ++alv  + y +++l  +a ++    ++ d+k  +++a++lk++fn+ ++++ 
  gi|242398356|ref|YP_002993780.1| 387 GTHTKPPVALVeVQGYAYKALVDAASLGL---TSLDSKMLEKEAKALKRRFNRDFWCNG 442
                                       77888889999556777777666555554...4569********************654 PP

>> Imm42  Immunity protein 42
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   7.2e-05      0.26      18      75 ..     433     486 ..     430     503 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.2e-05
                             Imm42  18 ewedsawknGlfvfcIdgeiypdykltttLrsevnslkdnksalinkkidkelfnlda 75 
                                       +++ ++w+nG+ ++ +dg+ +p+++ ++ +     +l  +++  ++k i+++lf++d+
  gi|242398356|ref|YP_002993780.1| 433 RFNRDFWCNGFYALALDGDNVPSKVVSSNMG----HLLFTRITEYQKEIAERLFEEDM 486
                                       5789*********************999999....44444788999999999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (637 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 4068.26
//
Query:       gi|242398357|ref|YP_002993781.1|  [L=329]
Description: Glycosidase [Thermococcus sibiricus MM 739]
Scores for complete 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-92  309.7   0.1    2.1e-92  309.5   0.1    1.0  1  Glyco_hydro_130  beta-1,4-mannooligosaccharide phosphorylase
    1.9e-10   40.8   0.0    1.6e-05   24.6   0.0    2.5  2  Glyco_hydro_32N  Glycosyl hydrolases family 32 N-terminal dom
    1.7e-07   30.8   0.0    7.8e-05   22.1   0.1    2.8  3  Glyco_hydro_43   Glycosyl hydrolases family 43
     0.0037   16.6   0.0       0.17   11.1   0.0    2.0  2  BNR_2            BNR repeat-like domain


Domain annotation for each model (and alignments):
>> Glyco_hydro_130  beta-1,4-mannooligosaccharide phosphorylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  309.5   0.1   4.7e-96   2.1e-92       3     313 ..      33     327 ..      31     329 .] 0.94

  Alignments for each domain:
  == domain 1  score: 309.5 bits;  conditional E-value: 4.7e-96
                                       ---TT-------TT--SSEEE-TTS-STTEEEEEEEEEEEETTE......EEEEEEEEE.TTS-E.EEEEEEESSSS CS
                   Glyco_hydro_130   3 rkietidileRvsyitgedvrisnnpvrkpvavFNpavvlvekeLevyaRvvllYrkyv.sdiaslrigledlkdGi 78 
                                       +ki++ +il+ +s ++g+d+r+          ++Npavv +ek+     R+v+lYr+++ +d +++rigl+ ++dGi
  gi|242398357|ref|YP_002993781.1|  33 KKIPQ-PILS-PS-REGFDSRN----------IYNPAVV-KEKD-----RIVMLYRAESkDDNLTGRIGLAISYDGI 90 
                                       78888.8888.77.88999988..........*******.9999.....*********977899************* PP

                                       S-EE-SS---EE-TTS-B--EEEEEEEEETTEEEEEEE.EESSSEEEEEEEESSSSSEEEE--SSSSSE........ CS
                   Glyco_hydro_130  79 kktlepeevvlpedkqellgveDPRvvkinskyyltYtgrdlkgvrievattkdlltvkrleekialielkkdeisl 155
                                       +++++pe+v++pe+ +e+ gveDPRvvk++++yy+tYtg+d k++r+++at+k+llt+k+++++++ ++++k++i++
  gi|242398357|ref|YP_002993781.1|  91 NFFRHPEPVMEPEYPWESAGVEDPRVVKVGKTYYMTYTGYDGKTARLCLATSKNLLTWKKHGPIFKDFKYEKNNIEG 167
                                       ***************************************************************************** PP

                                       ..EEEEE-SS-B.....TTBEEEEEESS-S---EEEEEESSSS-BEEEEEEE---SS-GGGS...SEEEE-S--EEE CS
                   Glyco_hydro_130 156 atkdgalfpkki.....kgkylmfsrvhtvsekifLavsddlvlweneleelassreimfenpfelkigwgtppvet 227
                                       +tk+g ++p+k+     +gky+m+++    +++i++ vs+dl++we+  e+++s+r+  f+n   +++++g+p+v +
  gi|242398357|ref|YP_002993781.1| 168 WTKSGSILPEKLkdgdfRGKYIMYFG----DSHIWMGVSKDLINWEYIEEPVLSPRKENFDN---VLVEPGPPLVSM 237
                                       ************999999********....********************************...************ PP

                                       TTEEEEEEEEEE...TTEEEEEEEEEEE-SS-..SEEEEBSS-SB-S-SHHHHSSSSSSBEEEEEEEE-TT.EEEEE CS
                   Glyco_hydro_130 228 keglLvlihgvd...teklvYrvgaalldleg..kvlartkeyilePeeeyEeyGdrpnvvFpcgalveee.kvlvy 298
                                       +e  ++li++++      l+Yrvgaa++ +++   ++art+++i++Pe+e+E yG+++nvvF ++++ve+e k+ +y
  gi|242398357|ref|YP_002993781.1| 238 DEK-ILLIYNSAgneEGTLKYRVGAAIFSKDDprELIARTENPIMVPEHEWEFYGHVNNVVF-VEGMVEHEnKLFLY 312
                                       **9.6666664423255689************966***************************.*******99***** PP

                                       EEETTTEEEEEEEEH CS
                   Glyco_hydro_130 299 yGaaDtaiglaeisv 313
                                       yG+aD+ igla+++ 
  gi|242398357|ref|YP_002993781.1| 313 YGGADRYIGLAYWTT 327
                                       *************85 PP

>> Glyco_hydro_32N  Glycosyl hydrolases family 32 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   3.7e-09   1.6e-05      59     175 ..      41     157 ..      35     174 .. 0.82
   2 !   13.7   0.0   7.9e-06     0.035      43     120 ..     200     284 ..     187     293 .. 0.76

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 3.7e-09
                                       -SS.SGGCTTEEEEEEEEE-TT-EEEEEEEE-T.CS.EEEEEEEEESSTTSSEEE-TT--SB-.-TTTSTTSEEEEE CS
                   Glyco_hydro_32N  59 apd.eefdsngafSGsavvdddklvllYTgnvk.ee.eqvQnlayskdkgreftkyeenpviaekpeentkhfRDPk 132
                                        p+ e fds  ++   +v ++d++v+lY  ++k ++ +    la+s  +g++f + + +pv++ + + +++ + DP+
  gi|242398357|ref|YP_002993781.1|  41 SPSrEGFDSRNIYNPAVVKEKDRIVMLYRAESKdDNlTGRIGLAIS-YDGINFFR-HPEPVMEPEYPWESAGVEDPR 115
                                       45426789999*****************999994445667778888.77888887.469****87777********* PP

                                       EEEETTTEEEEEEEECCTTCCEEEEEEESSSSSEEEECCESEE CS
                   Glyco_hydro_32N 133 vawkedgkwvmvvgaqdkkkgkillYkskdlkewelaselles 175
                                       v +k  ++++m+    d k+ ++ l +sk+l +w++++ + ++
  gi|242398357|ref|YP_002993781.1| 116 V-VKVGKTYYMTYTGYDGKTARLCLATSKNLLTWKKHGPIFKD 157
                                       *.7888888888888888*****************99877665 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 7.9e-06
                                       EEESSSSSBEE.EEEEE-SS.SGGCTTEEEEEEEEE-TT.-EEEEEEEE-T....CSEEEEEEEEESSTTSSEEE-T CS
                   Glyco_hydro_32N  43 avSkDlvhWee.lpvalapd.eefdsngafSGsavvddd.klvllYTgnvk....eeeqvQnlayskdkgreftkye 112
                                        vSkDl++We  +++ l p+ e+fd+  +  G  +v  d k++l+Y +  +     +  v    +skd+ re+   +
  gi|242398357|ref|YP_002993781.1| 200 GVSKDLINWEYiEEPVLSPRkENFDNVLVEPGPPLVSMDeKILLIYNSAGNeegtLKYRVGAAIFSKDDPRELIART 276
                                       48*******97456778887255666668889888777769*****988775564236777788899999*****99 PP

                                       T--SB-.- CS
                   Glyco_hydro_32N 113 enpviaek 120
                                       enp+++ +
  gi|242398357|ref|YP_002993781.1| 277 ENPIMVPE 284
                                       ****9963 PP

>> Glyco_hydro_43  Glycosyl hydrolases family 43
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.51   2.3e+03      63      97 ..      49      83 ..      33      91 .. 0.57
   2 !   22.1   0.1   1.7e-08   7.8e-05      10      60 ..     111     162 ..     104     199 .. 0.79
   3 !    6.0   0.0    0.0014       6.4      35      84 ..     197     246 ..     184     314 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.51
                                      TEECTEEEEEEEETTEEEEEEE.EEETTCCCSEEEE CS
                    Glyco_hydro_43 63 gknasWAPeiskhdgkyylyyt.atkkgeakqgifv 97
                                      ++n  + P++ k +++  ++y  ++k+++ + +i++
  gi|242398357|ref|YP_002993781.1| 49 SRNI-YNPAVVKEKDRIVMLYRaESKDDNLTGRIGL 83
                                      3333.6666666666666666633344444444555 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 1.7e-08
                                       EESEEEEEETTCEEEEEEEBTEE.SEEEEEEESSSSSCEEEEECEESTTTCS CS
                    Glyco_hydro_43  10 ypDpsilrvgedyYlvtstfewf.pglrifhSkdLvnWkqvgrvlerrsqls 60 
                                        +Dp +++vg++yY++++  +    +l + +Sk+L +Wk++g+++++ + ++
  gi|242398357|ref|YP_002993781.1| 111 VEDPRVVKVGKTYYMTYTGYDGKtARLCLATSKNLLTWKKHGPIFKDFKYEK 162
                                       58*************99987654489999***************98765554 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.0014
                                       EEEEEESSSSSCEEEEECEESTTTCSTTTEECTEEEEEEEETTEEEEEEE CS
                    Glyco_hydro_43  35 lrifhSkdLvnWkqvgrvlerrsqlsmkgknasWAPeiskhdgkyylyyt 84 
                                       + +  SkdL nW+ +++++ +++++++ +  +   P +  +d+k  l+y 
  gi|242398357|ref|YP_002993781.1| 197 IWMGVSKDLINWEYIEEPVLSPRKENFDNVLVEPGPPLVSMDEKILLIYN 246
                                       55567**************9999999888766667777777777666666 PP

>> BNR_2  BNR repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0   3.8e-05      0.17      40     157 ..      41     155 ..      34     192 .. 0.80
   2 ?    3.1   0.0     0.011        50      58     114 ..     235     295 ..     193     303 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.8e-05
                                       TS-...BTTEEEEEEEEEEETTTEEEEEEEEEETT--HHT----EEEESSTTSS----EHHHGGEEEEEE-SS--.. CS
                             BNR_2  40 dreqsrearkklgNPvlfqdpsgtliLfykvgvsvggwagskitrvtSkDdGktWsaprrlpkspflnisgpvknkp 116
                                       +    + ++++  NP++++ +++++++ y   ++  +  g+      S D+   ++ p+++ +  +   +  +  +p
  gi|242398357|ref|YP_002993781.1|  41 SPSREGFDSRNIYNPAVVK-EKDRIVMLYRAESKDDNLTGRI-GLAISYDGINFFRHPEPVMEP-EYPWESAGVEDP 114
                                       5554566788999****99.7888888885666666665555.88*****99999****99976.888888888889 PP

                                       EE--T--EEEEEE..SS--EEEEEEEESSTTSS-EE----S CS
                             BNR_2 117 iqladGrlilPsshelagkwrallelsddggktWkkgrvve 157
                                        +++ G+     ++  +gk + l+  ++++ +tWkk +++ 
  gi|242398357|ref|YP_002993781.1| 115 RVVKVGKTYYMTYTGYDGKTARLCLATSKNLLTWKKHGPIF 155
                                       99999999999999999******************999874 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.011
                                       EETTTEEEEEEEEEETT--HHT----E....EEESSTTSS----E....HHHGGEEEEEE-SS-- CS
                             BNR_2  58 qdpsgtliLfykvgvsvggwagskitr....vtSkDdGktWsapr....rlpkspflnisgpvkn 114
                                       + ++++++L+y  ++  +++ + k +r    + SkDd + + a++     +p+  ++ + g v n
  gi|242398357|ref|YP_002993781.1| 235 VSMDEKILLIY--NSAGNEEGTLK-YRvgaaIFSKDDPRELIARTenpiMVPE-HEWEFYGHVNN 295
                                       34699999999..33333333333.334567*****99999998854433333.46666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2103.36
//
Query:       gi|242398358|ref|YP_002993782.1|  [L=543]
Description: maltooligosaccharide ABC transporter permease [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      4e-22   78.9  47.7    2.7e-14   53.3  22.5    3.6  4  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
      0.036   13.7   3.0      0.048   13.3   1.4    2.0  2  DUF1449       Protein of unknown function (DUF1449)


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   1.2      0.15   1.4e+03     114     141 ..      12      35 ..       6      75 .. 0.44
   2 !   53.3  22.5   3.1e-18   2.7e-14       1     176 [.      74     256 ..      71     260 .. 0.87
   3 ?   -4.3   5.4       1.4   1.3e+04      39     166 ..     306     361 ..     284     372 .. 0.38
   4 !   39.8  17.2   4.4e-14   3.9e-10       4     175 ..     362     534 ..     355     537 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.15
                      BPD_transp_1 114 lilafggllggavlleflgswpGlgtll 141
                                       l+l+f +l+  + l+++l      g++ 
  gi|242398358|ref|YP_002993782.1|  12 LPLVFLFLFFYFPLISILK----EGLWD 35 
                                       3344444444444444444....33333 PP

  == domain 2  score: 53.3 bits;  conditional E-value: 3.1e-18
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf..........vilsilghlilpviillllsaapy 67 
                                       g++++++ a ++ ++++ +l  l  v++ +Ps+ +a+ ++l+f            + ++ +++ ++i++ +++++p+
  gi|242398358|ref|YP_002993782.1|  74 GFPGAYIFA-KYEFPGKGILKALLTVPFVMPSIMVALGFILLFgrvgiitqilGRDLGILYSWKAIILAHAFYNFPV 149
                                       678899999.************************999999999*******988777777788889************ PP

                      BPD_transp_1  68 vrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtlllea 144
                                       v++++++  + ++  ++eaa  lGa+ +++frkv+lP+++p i+++ +l+f++ +  ++++++lg   G ++ ++e+
  gi|242398358|ref|YP_002993782.1| 150 VVRMVSSLWQRINPHYEEAAISLGARGFTLFRKVTLPMLMPAIFASSMLTFVFCFLSFSVPLILG---GYQYATIEV 223
                                       *****************************************************************...557777777 PP

                      BPD_transp_1 145 ilgydyseis.nggvlalviavlllnlvadilq 176
                                        +   +   + + + +al+i+ + l+l+++ l+
  gi|242398358|ref|YP_002993782.1| 224 DIFTSIMTLLdFKTGAALAIIQIFLSLIFMYLY 256
                                       777766666675555666666666666555554 PP

  == domain 3  score: -4.3 bits;  conditional E-value: 1.4
                      BPD_transp_1  39 lvlvf.................................vilsilghlilpviillllsaapyvrlirraalrslpkd 82 
                                       l++v+                                 +i ++l                                 
  gi|242398358|ref|YP_002993782.1| 306 LLAVIyhsftyggsftlewyrrvfspeynpifgansitAIRNSLL-------------------------------- 350
                                       333333555555555555555555555555555543332222222................................ PP

                      BPD_transp_1  83 lveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseisnggvl 159
                                                                                                                +g+ 
  gi|242398358|ref|YP_002993782.1| 351 -------------------------------------------------------------------------FGFS 354
                                       .........................................................................2222 PP

                      BPD_transp_1 160 alviavl 166
                                       a++++++
  gi|242398358|ref|YP_002993782.1| 355 AVILSTF 361
                                       2222222 PP

  == domain 4  score: 39.8 bits;  conditional E-value: 4.4e-14
                      BPD_transp_1   4 lGilaa...lnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilp.viillllsaapyvrlirraal 76 
                                       l++ +a   ++ ++k++++++ ++ ++l+   + l++  + +f        + ++ +i++ ++ a p+v++ ++  l
  gi|242398358|ref|YP_002993782.1| 362 LALSIAyimYRWRFKGKNFFDAIVMLPLASSAITLGLGYIRAFHKPPLEFLGTWYlIIFAHTIIAYPFVLRSVSTSL 438
                                       5555556777999*********************99999999944444445555559999999************** PP

                      BPD_transp_1  77 rslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydysei 153
                                       + ++ +l+eaa  lG+++   f kv lP+a+  ii g+i+af+ ++ +  +++++       ++++++ +++ + + 
  gi|242398358|ref|YP_002993782.1| 439 KKINPNLKEAAMSLGVNELGAFLKVELPLAFGGIIVGAIFAFAMSIAELGATYMIYRP---EYTTITIAIYRFLGSR 512
                                       ********************************************************55...5666666666666666 PP

                      BPD_transp_1 154 snggvlalviavlllnlvadil 175
                                       + g++ a+ ++++l++++a+i+
  gi|242398358|ref|YP_002993782.1| 513 QLGPASAMSVLLILVSTIAFIV 534
                                       6699999999999999999986 PP

>> DUF1449  Protein of unknown function (DUF1449)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   1.4   5.4e-06     0.048      67     136 ..     102     171 ..      90     174 .. 0.81
   2 ?   -3.3   0.0      0.64   5.7e+03     100     134 ..     414     449 ..     403     452 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.4e-06
                           DUF1449  67 vPvLilLvlfLtlFglvGlvlqslvasllgallpallaaaialllalp.lvrvlaallakilpkdetsavs 136
                                       +P +++ + f+ lFg vG+++q l  +l g+l ++  + ++ ++  +p +vr++++l ++i p+ e  a+s
  gi|242398358|ref|YP_002993782.1| 102 MPSIMVALGFILLFGRVGIITQILGRDL-GILYSWKAIILAHAFYNFPvVVRMVSSLWQRINPHYEEAAIS 171
                                       588888899*************999988.6666665555555555665268***************99998 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 0.64
                           DUF1449 100 pallaaaialllalplv.rvlaallakilpkdetsa 134
                                       ++ l+  +  ++a p+v r ++  l+ki p+    a
  gi|242398358|ref|YP_002993782.1| 414 TWYLIIFAHTIIAYPFVlRSVSTSLKKINPNLKEAA 449
                                       566777777888888755888999999988765555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (543 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       726  (0.0404931); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.67u 0.33s 00:00:01.00 Elapsed: 00:00:00.52
# Mc/sec: 3153.32
//
Query:       gi|242398359|ref|YP_002993783.1|  [L=334]
Description: maltooligosaccharide ABC transporter ATPase component [Thermococcus sibiricus MM 739]
Scores for complete 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  113.1   0.0    2.6e-32  112.2   0.0    1.4  1  ABC_tran      ABC transporter
    1.1e-09   38.6   0.1    2.3e-05   24.4   0.0    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
      0.001   19.0   0.0     0.0019   18.2   0.0    1.3  1  Rad17         Rad17 P-loop domain
     0.0099   15.3   0.0       0.17   11.3   0.0    2.1  2  SMC_N         RecF/RecN/SMC N terminal domain
  ------ inclusion threshold ------
      0.017   15.4   0.1      0.083   13.2   0.0    1.9  2  AAA_22        AAA domain
      0.024   15.1   0.8       0.16   12.4   0.8    2.1  1  AAA           ATPase family associated with various cellular 
      0.027   14.9   0.0      0.048   14.0   0.0    1.4  1  RNA_helicase  RNA helicase
      0.048   14.0   0.3       0.11   12.9   0.3    1.7  1  AAA_16        AAA ATPase domain
      0.069   12.5   0.1        1.3    8.4   0.0    2.1  2  TniB          Bacterial TniB protein
       0.14   12.3   0.0       0.22   11.6   0.0    1.2  1  sCache_3_2    Single cache domain 3
       0.15   11.6   0.2        3.4    7.2   0.1    2.2  2  AAA_25        AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.2   0.0   1.6e-35   2.6e-32       5     136 ..      22     160 ..      18     161 .. 0.96

  Alignments for each domain:
  == domain 1  score: 112.2 bits;  conditional E-value: 1.6e-35
                                       EEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                          ABC_tran   5 slklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.. 79 
                                       +l+ k+ge + ++G++G+GK+t l+++ g ++p++G + + +k +++   + ++++ig+++q+  lfp+++v +n  
  gi|242398359|ref|YP_002993783.1|  22 HLEAKAGEFLTLLGPSGCGKTTTLRIIVGFERPDKGAVYFGEKLMNH--VPPYERNIGIVFQDYALFPHMNVFDNia 96 
                                       67899*********************************888888888..**************************** PP

                                       ...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       ...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  80 ...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                  e ++++  al+ +glk+++++      ++LSgGq+qrvalaral+ +p++lllDEp 
  gi|242398359|ref|YP_002993783.1|  97 fglkvrkiprnEIEKRVIWALELVGLKGFEKRYP----EQLSGGQQQRVALARALVIEPQVLLLDEPL 160
                                       **********99999*****************99....*****************************7 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   6.7e-05      0.11       3      72 ..      32      92 ..      30     124 .. 0.76
   2 !   24.4   0.0   1.4e-08   2.3e-05     232     299 ..     128     193 ..     100     197 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.7e-05
                            AAA_21  3 vliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvry 72
                                       l Gp g+GK++ L+++ ++           ++++      k  +  ++y+ +i ++f+++ ++ +++++
  gi|242398359|ref|YP_002993783.1| 32 TLLGPSGCGKTTTLRIIVGFE---------RPDKGAVYFGEKLMNHVPPYERNIGIVFQDYALFPHMNVF 92
                                      699**************8773.........3455555566777777777777777777777666666555 PP

  == domain 2  score: 24.4 bits;  conditional E-value: 1.4e-08
                            AAA_21 232 lparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSp 299
                                       + + +lS G+++  al+ al   +    +ll+DEp ++L+ k+ +rl + +k+ +r  g+  i +TH+ 
  gi|242398359|ref|YP_002993783.1| 128 RYPEQLSGGQQQRVALARALVIEP---QVLLLDEPLSNLDAKIRERLRGEIKRIQReLGITTIYVTHDQ 193
                                       667899****9999*******999...9***********************888888**********85 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.2e-06    0.0019      35      65 ..      18      48 ..       8      55 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.2e-06
                             Rad17 35 lkadvLesrkkriLLisGPsGCgkstvvkvL 65
                                      l+   Le +  + L + GPsGCgk+t+++++
  gi|242398359|ref|YP_002993783.1| 18 LDIPHLEAKAGEFLTLLGPSGCGKTTTLRII 48
                                      666789999999****************986 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0     0.088   1.4e+02      25      41 ..      29      45 ..       9      52 .. 0.85
   2 !   11.3   0.0    0.0001      0.17     134     205 ..     130     199 ..      86     212 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.088
                                      SEEEEEESTTSSHHHHH CS
                                      xxxxxxxxxxxxxxxxx RF
                             SMC_N 25 sftaivGpNGSGKsnll 41
                                      +f  ++Gp G+GK+  l
  gi|242398359|ref|YP_002993783.1| 29 EFLTLLGPSGCGKTTTL 45
                                      68889********9765 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.0001
                                       TTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHHHCCC- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxx RF
                             SMC_N 134 kelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn..aQfivislreemleka 205
                                       +e+LSgG+++ vala  + i   +p+ + llDe  ++LD+k ++++   +k+ + +     i +++++e     
  gi|242398359|ref|YP_002993783.1| 130 PEQLSGGQQQRVALARALVI---EPQ-VLLLDEPLSNLDAKIRERLRGEIKRIQRElgITTIYVTHDQEEAMAI 199
                                       679*********99988665...455.5689*******************987777335566667766554444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   5.1e-05     0.083       5      25 ..      28      48 ..      24      79 .. 0.89
   2 ?   -0.3   0.0      0.71   1.2e+03      61      99 ..     117     158 ..      90     190 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.1e-05
                            AAA_22  5 agilvvtGesGtGKTtllrrl 25
                                        +l++ G+sG+GKTt+lr +
  gi|242398359|ref|YP_002993783.1| 28 GEFLTLLGPSGCGKTTTLRII 48
                                      57999************9965 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.71
                            AAA_22  61 lralglelkaerlsseellealeqalrarav...ielliiDE 99 
                                       l+ +gl++ ++r  ++    + ++ + ara    +++l++DE
  gi|242398359|ref|YP_002993783.1| 117 LELVGLKGFEKRYPEQLSGGQQQRVALARALviePQVLLLDE 158
                                       555555555533333333355555555555568888999998 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.8   9.9e-05      0.16       2      20 ..      32      50 ..      31     203 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9.9e-05
                                      EEESSTTSSHHHHHHHHHH CS
                               AAA  2 llyGppGtGKTllakavak 20
                                       l Gp G+GKT++ + ++ 
  gi|242398359|ref|YP_002993783.1| 32 TLLGPSGCGKTTTLRIIVG 50
                                      589************9976 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     3e-05     0.048       2      58 ..      32      83 ..      31      97 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3e-05
                      RNA_helicase  2 wlyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdgYtgqevvvidDf 58
                                       l Gpsg+GK+t+ +         ++ + k+ vy++++  +++  Y+++  +v++D 
  gi|242398359|ref|YP_002993783.1| 32 TLLGPSGCGKTTTLRI-----IVGFERPDKGAVYFGEKLMNHVPPYERNIGIVFQDY 83
                                      588***********99.....33467999******************9999999997 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.3   6.7e-05      0.11      23      45 ..      27      49 ..      19     193 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.7e-05
                            AAA_16 23 rpelvllsGesGvGKsslvrell 45
                                       +e + l G+sG+GK++ +r + 
  gi|242398359|ref|YP_002993783.1| 27 AGEFLTLLGPSGCGKTTTLRIIV 49
                                      457899************99765 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0     0.087   1.4e+02      38      53 ..      31      46 ..      18      57 .. 0.83
   2 ?    8.4   0.0   0.00077       1.3      97     162 ..     128     191 ..     119     202 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.087
                              TniB 38 lllvGdsnnGKtmive 53
                                      l l+G+s +GKt+ ++
  gi|242398359|ref|YP_002993783.1| 31 LTLLGPSGCGKTTTLR 46
                                      789*********9765 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00077
                              TniB  97 plkararvskleqqvlrllrelkvrvLiiDEihnllagsarkqreflnalksLgnelkipivlvGt 162
                                       ++ ++ +  ++++ +l+    ++++vL++DE  + l   a+ ++++   +k++++el i+ ++v  
  gi|242398359|ref|YP_002993783.1| 128 RYPEQLSGGQQQRVALARALVIEPQVLLLDEPLSNL--DAKIRERLRGEIKRIQRELGITTIYVTH 191
                                       555555555555555555666899*******88877..5666778999************999854 PP

>> sCache_3_2  Single cache domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00014      0.22      10      72 ..     137     203 ..     130     226 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00014
                        sCache_3_2  10 leeralalatsvagsrivrvaltd......rapesglqalvddvrritgvdyvvitDeegrvlahpdpa 72 
                                       +++r +ala++++ +++v  +l +      ++ +++l++ + +++r +g++++++t  + + +a +d+ 
  gi|242398359|ref|YP_002993783.1| 137 QQQR-VALARALVIEPQV-LLLDEplsnldAKIRERLRGEIKRIQRELGITTIYVTHDQEEAMAISDRI 203
                                       4555.99**********9.4444457766666777777777***************9999999998887 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.1    0.0021       3.4      32      49 ..      27      44 ..      22      46 .. 0.90
   2 ?    2.0   0.0      0.08   1.3e+02     159     188 ..     161     191 ..     136     197 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0021
                            AAA_25 32 agelallaGapgtGKttl 49
                                      age+  l G++g+GKtt 
  gi|242398359|ref|YP_002993783.1| 27 AGEFLTLLGPSGCGKTTT 44
                                      799*************96 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.08
                            AAA_25 159 ensnsdv.galvealeriarrtgaavllvhH 188
                                       +n ++++ ++l   ++ri+r++g++++ v H
  gi|242398359|ref|YP_002993783.1| 161 SNLDAKIrERLRGEIKRIQRELGITTIYVTH 191
                                       555666668888899***************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2299.50
//
Query:       gi|242398360|ref|YP_002993784.1|  [L=357]
Description: maltooligosaccharide ABC transporter substrate-binding protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.2e-32  113.3   0.9    1.4e-32  113.1   0.9    1.1  1  SBP_bac_6   Bacterial extracellular solute-binding protein
    2.9e-24   86.3   0.8    3.9e-24   85.9   0.8    1.1  1  SBP_bac_8   Bacterial extracellular solute-binding protein
      3e-19   69.7   0.0    4.4e-19   69.1   0.0    1.2  1  SBP_bac_11  Bacterial extracellular solute-binding protein
    2.5e-17   63.8   3.3    3.6e-17   63.3   3.3    1.2  1  SBP_bac_1   Bacterial extracellular solute-binding protein


Domain annotation for each model (and alignments):
>> SBP_bac_6  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.1   0.9   3.1e-36   1.4e-32       1     220 [.      85     306 ..      85     331 .. 0.90

  Alignments for each domain:
  == domain 1  score: 113.1 bits;  conditional E-value: 3.1e-36
                         SBP_bac_6   1 nplpdlilsfdkdflekfieeglfqpldpanlpnvnkdfaeeglkdpdgkyypygvgplvlavnkdrlkgrpvPksW 77 
                                       np +dl+++ d+++l+k+ie+++++p++p+n++ +++    + + d+  + +py++g++++ + +d + +   Pks 
  gi|242398360|ref|YP_002993784.1|  85 NPRADLVIGIDNSLLAKAIEAEVLEPYKPENINLFPE----SLIFDSTFHLTPYDYGYISINYREDMVQNP--PKSL 155
                                       6789********************************4....667777*********************766..**** PP

                         SBP_bac_6  78 aDLldPeykgkvalpgnngsdlfealllalykdfgedgvkkllrnlkanlhpaq..mvkaagslesgepavsvvpyf 152
                                       +DL++Pe++gk ++ ++++s++ +a+ll +   +g +g+  ++ +lk+n   +    ++a+++   ge  +++v  +
  gi|242398360|ref|YP_002993784.1| 156 EDLTKPEWRGKLVIEDPRTSSPGAAFLLWTIAVYGDEGYLYYWQKLKENDVHIVkgWTEAWTAFMNGE--FPLVLSY 230
                                       *************************************************86666699***********..******* PP

                         SBP_bac_6 153 fadilpekkkgk..nlkvvwPedGalvspifmlvkkg.kkkelakafidfllspevqailakaggvfPvv.....t 220
                                       ++  ++  ++ +   +k + +e+G +  ++ + + kg k+kelak+fi+f+l +e+q ++  ++  +Pv+      
  gi|242398360|ref|YP_002993784.1| 231 ATSPAATVYYDNitYVKAIAFEEGNYMQIEGAGIIKGaKNKELAKKFIEFMLTEEFQDAIPTNQWMYPVNpniklP 306
                                       ********97779999********************************************998888**97444330 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 !   85.9   0.8   8.7e-28   3.9e-24       2     273 ..      52     308 ..      51     315 .. 0.83

  Alignments for each domain:
  == domain 1  score: 85.9 bits;  conditional E-value: 8.7e-28
                                       HHHHHHHH-TEEEEEEE-.-SSSHHHHHHHHHHTT---SEE.EEE-HHHHHHHHHTTSB--GGGSTTHHH-HHHHHT CS
                         SBP_bac_8   2 lakefekktgvkvnvvta.asndleqklkaalaagtapdidvvwanedalatlaeeglladlsdldnlddltdalaa 77 
                                       ++ +fe+k+gvkv+++ + + +++ + l  +     a d+ v+ ++++ la+++e+ +l++ +  +n++ ++    +
  gi|242398360|ref|YP_002993784.1|  52 VIPKFEEKYGVKVELQLIgDAGEVLNRLILEKDNPRA-DL-VIGIDNSLLAKAIEAEVLEPYKP-ENINLFPE---S 122
                                       7889***********9997777777777776544444.44.57777899***********9775.88888877...4 PP

                                       T--TS.----EEEEEEE-EEEEEHHHHHHS.---BHHHHHHHHHHHHHH-SEGG---GGGGGGTHHETTEE---H.. CS
                         SBP_bac_8  78 vgydgklygvPyasetpyvliynkdllekaedpktwdellaaakklkgkfglpdpasgwlqaallakdgksldddgg 154
                                         +d ++   Py+++    + y++d+++ + +pk++++l++  +++ gk  + dp +++  aa+l  +   + +d  
  gi|242398360|ref|YP_002993784.1| 123 LIFDSTFHLTPYDYGY-ISINYREDMVQ-N-PPKSLEDLTK--PEWRGKLVIEDPRTSSPGAAFLL-WTIAVYGD-- 191
                                       446778999******7.9**********.6.**********..*********99998866555555.55555556.. PP

                                       HHH.HHHHHHHHHHHHTT-.EE-S..--SSTTTTTSBSEEEE-TTH..HHHHH-TTTSEEEE--S--EEEEEEEEEE CS
                         SBP_bac_8 155 kdglkealellkklkdngk.tydtgadavsefanGevaftingswd..iaaaqkagkklgaivpkqgsfaggkglav 228
                                           + +l +++klk+n + +++ +++a+ +f nGe+  ++++  +  ++ + ++   ++ai+  +g+  +++g  +
  gi|242398360|ref|YP_002993784.1| 192 ----EGYLYYWQKLKENDVhIVKGWTEAWTAFMNGEFPLVLSYATSpaATVYYDNITYVKAIAFEEGNYMQIEGAGI 264
                                       ....679999*****99873569******************97655314444466666777788************* PP

                                       BTTS-HHHHHHHHHHHHHTTSHHHHHHHHHH---BS-S-TTTHHH CS
                         SBP_bac_8 229 pknaknedlaAldFlkwltspenqaalaektgyipvnksaalspe 273
                                        k+akn++l A++F+++++++e q a  +++ + pvn++  l++ 
  gi|242398360|ref|YP_002993784.1| 265 IKGAKNKEL-AKKFIEFMLTEEFQDAIPTNQWMYPVNPNIKLPEV 308
                                       ********9.*******************99999**999998765 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 !   69.1   0.0   9.9e-23   4.4e-19       3     224 ..      39     290 ..      37     293 .. 0.87

  Alignments for each domain:
  == domain 1  score: 69.1 bits;  conditional E-value: 9.9e-23
                                       EEE-SSTHHHHHHHHHHHHHHH---EEEE.ESSHHHHHHHH...HHH..-SEEEESSH.HHHHHHHHGGGGG..... CS
                        SBP_bac_11   3 vaaagslaaalrelaaaFeahtgvkvevs.aggsgklarqi...adgarpDvwipassawlellaaaglvqa..... 70 
                                       ++++ s++   +e++++Fe+++gvkve++  g++g++++++   +d+ r+D++i  +   l+++++a+++ +     
  gi|242398360|ref|YP_002993784.1|  39 IYSYDSFEYLASEVIPKFEEKYGVKVELQlIGDAGEVLNRLileKDNPRADLVIGIDNSLLAKAIEAEVLEPykpen 115
                                       899999********************9996799********7766666************************99999 PP

                                       .............GG-EEEEEEEEEEEESTT-.TT---SHHHHHHSS-..-EEEE--T-TTTTH....H.HHHHGGG CS
                        SBP_bac_11  71 .............esavplassplviavpkgn.pkkikgwadLlkpgl..klavadPttspsGl....aalalleaa 127
                                                     + +p+ +  + i +++++  +++k+++dL+kp++  kl++ dP+ts+ G      ++a++   
  gi|242398360|ref|YP_002993784.1| 116 inlfpeslifdstFHLTPYDYGYISINYREDMvQNPPKSLEDLTKPEWrgKLVIEDPRTSSPGAafllWTIAVYGDE 192
                                       99999999887766667777777999999999445899**********888********999996666666666676 PP

                                       --HHHHHHHHHTEEEEESSHHHHHHHHHTTT-SEEEEEHHHHH.....HSTTSSEEEE--TTT--...EEEEEEEE- CS
                        SBP_bac_11 128 gaqellkalekkvvklgessrqlltaveageadagivyeseakaa...engdkleavylpeglnldpldypaavlkk 201
                                       g  +++++l+++ v+ +++ + + ta+++ge  ++++y ++ +a+   +n + ++a++  eg +  +   +a+++k+
  gi|242398360|ref|YP_002993784.1| 193 GYLYYWQKLKENDVHIVKGWTEAWTAFMNGEFPLVLSYATSPAATvyyDNITYVKAIAFEEGNY--MQIEGAGIIKG 267
                                       779999********************************99887775556777777777788777..47889****** PP

                                       TT--HHHHHHHHHTTSHHHHHHH CS
                        SBP_bac_11 202 aakreaAraFlafLrspeaqail 224
                                       a+++e A++F++f++++e q+++
  gi|242398360|ref|YP_002993784.1| 268 AKNKELAKKFIEFMLTEEFQDAI 290
                                       ******************99875 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 !   63.3   3.3     8e-21   3.6e-17       9     314 ..      44     287 ..      40     288 .. 0.84

  Alignments for each domain:
  == domain 1  score: 63.3 bits;  conditional E-value: 8e-21
                                       HHHHHHHHH....HHHHHTTEEEEEEEE.CHHHHHHHHHHHHHTTSSSCSEEEE.CGGHHHHHHHTTSBECCHHHHH CS
                         SBP_bac_1   9 alqalvaka....fekehpgikVeiesv.gsgslaqkltlaiaaGdgpaDviav.dndwiarlakaglllpldpyvk 79 
                                       ++++l+  +    fe+ ++g+kVe++ + + g++ +  +l +++ ++ aD++++ dn+ +a+ ++a +l+p  p  +
  gi|242398360|ref|YP_002993784.1|  44 SFEYLA-SEvipkFEE-KYGVKVELQLIgDAGEVLN--RLILEKDNPRADLVIGiDNSLLAKAIEAEVLEPYKPENI 116
                                       444444.444555*99.78*********77777888..99999999999*****************88888888888 PP

                                       HTTECTTCCTEEEEHHHHTHHHHCEEE.ESEEEE.EEEEEEEETTTHHCTTGGGSHBHHHHHHHHHHHHHHCTCTHC CS
                         SBP_bac_1  80 aylapgvkdaadklsssvlpkildskv.lyvPly.aargliYNkdlfekagldppwtWdelveaakklkekgkkpig 154
                                       +  ++                i+ds++ l  P++ ++  + Y+ d +     +pp++ ++l+++  + k   + p  
  gi|242398360|ref|YP_002993784.1| 117 NLFPESL--------------IFDSTFhLT-PYDyGYISINYREDMVQ----NPPKSLEDLTKPEWRGKLVIEDP-- 172
                                       8766554..............344344444.99966************....7889********99999999999.. PP

                                       CHCCEEHHHHHHHHHHHHHHHHTGGGEECCCTHHCSHHHHSHHHHHHHHHHHHHHHHHHHTTEEECSSHHHHHHHHH CS
                         SBP_bac_1 155 garggsasgtayyfalalakslggkvfdkdgggldnpegvtaatylvklyavanltkelkgkgaenkdgaaalalfe 231
                                         r++s +    ++++a++++ g                        +ly   +++k + +++   k++++a ++f 
  gi|242398360|ref|YP_002993784.1| 173 --RTSSPGAAFLLWTIAVYGDEG------------------------YLY---YWQKLKENDVHIVKGWTEAWTAFM 220
                                       ..888888888888888888888........................788...7889******************** PP

                                       TTSCSEEEEEHHHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEEEEEEEEEEBTTCSTHHHHHHHHHHH CS
                         SBP_bac_1 232 aGeaamaivglwaalaamkvapkvafaadkekpkeelgvaplPagkggkpgilgayglaipkgsknpeaAkkFldfl 308
                                       +Ge ++ +++ ++              +++  +++++ +    a++ g+++     g +i kg+kn+e AkkF++f+
  gi|242398360|ref|YP_002993784.1| 221 NGEFPLVLSYATS--------------PAATVYYDNITYVKAIAFEEGNYM--QIEGAGIIKGAKNKELAKKFIEFM 281
                                       *********9988..............666666677777777788888888..************************ PP

                                       TSHHHH CS
                         SBP_bac_1 309 lspeaq 314
                                       l++e q
  gi|242398360|ref|YP_002993784.1| 282 LTEEFQ 287
                                       **9966 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2396.01
//
Query:       gi|242398361|ref|YP_002993785.1|  [L=260]
Description: btpA family protein [Thermococcus sibiricus MM 739]
Scores for complete 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-110  368.3   0.4   2.1e-110  368.1   0.4    1.0  1  BtpA            BtpA family
    0.00087   18.2   0.0     0.0025   16.7   0.0    1.8  2  Trp_syntA       Tryptophan synthase alpha chain
      0.006   15.9   0.0       0.63    9.4   0.0    2.3  2  TMP-TENI        Thiamine monophosphate synthase
  ------ inclusion threshold ------
      0.017   14.6   0.4        1.2    8.6   0.1    2.8  3  PcrB            PcrB family
      0.031   13.7   0.0       0.14   11.5   0.0    1.9  2  Bac_luciferase  Luciferase-like monooxygenase
      0.072   13.1   0.1        1.3    9.1   0.0    2.7  3  B1              Protein L b1 domain


Domain annotation for each model (and alignments):
>> BtpA  BtpA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  368.1   0.4    7e-114  2.1e-110       2     254 .]       5     255 ..       4     255 .. 0.99

  Alignments for each domain:
  == domain 1  score: 368.1 bits;  conditional E-value: 7e-114
                              BtpA   2 ekpvigvvHLkpLPgsaeykanleevidkAvkeakaleegGvDavilenygdaPflkevdpetvaamtvivkevksd 78 
                                       ek +ig+vHLkpLPgs+ y++n++ v+++A++eak++ee+G+Da+++en+ d Pf k+v+p+tva+mt+i++ +k++
  gi|242398361|ref|YP_002993785.1|   5 EKVLIGMVHLKPLPGSYLYDGNFNGVVEHAISEAKKIEEAGFDAIMIENFNDVPFSKTVEPITVASMTLIARTIKEE 81 
                                       799************************************************************************** PP

                              BtpA  79 vsiplGvnvLrndavaalaiAkavgakFiRvnvltgvalsdeGilegkaaellrykkllesrvkiladvavkhavpl 155
                                       + +plG+nvLrnda+aa++iA++v+a+FiRvnvl+gva +d+G++eg a +l+r++kll+s++k++adv+vkha+++
  gi|242398361|ref|YP_002993785.1|  82 IPLPLGINVLRNDAIAAYSIAYTVKADFIRVNVLSGVAYTDQGVIEGIAVQLARLRKLLPSKIKVFADVHVKHAHHF 158
                                       ***************************************************************************** PP

                              BtpA 156 verdlesavkdtvergladavilsGkatGgevdleelklaketvkvkvlvgsGvseenlekllsiadGvivgtsikk 232
                                       ++  +e+a+ d++ergladavi+sGk+tG+evdl++lk+ake+ +v+vlvgsG+++enl +l+++adG+ivgt+ikk
  gi|242398361|ref|YP_002993785.1| 159 GD--FEEALSDAIERGLADAVIISGKRTGNEVDLKKLKRAKELSNVPVLVGSGTTYENLPELWKYADGFIVGTWIKK 233
                                       **..************************************************************************* PP

                              BtpA 233 dGkianaiDkervrkivelaek 254
                                       dGk++n iD er++k+++laek
  gi|242398361|ref|YP_002993785.1| 234 DGKTNNDIDPERAKKLINLAEK 255
                                       ******************9985 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0      0.71   2.1e+03      31     122 ..      39      52 ..      28      81 .. 0.52
   2 !   16.7   0.0   8.3e-07    0.0025     186     256 ..     190     258 ..     175     260 .] 0.84

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.71
                                       HHHHHCT-SSEEEE---S--TTS-HHHHHHHHCCCCTT--HHHHHHHHHHHHHHCSSS-EEEEE-CHHHCCC-HHHH CS
                         Trp_syntA  31 kalekagadviElGlpfsdPladGPvIqaanlraLakgvtlekvlelveevrkkevevPivlltylnlvlsygeerf 107
                                       k+                                                                           
  gi|242398361|ref|YP_002993785.1|  39 KK--------------------------------------------------------------------------- 40 
                                       33........................................................................... PP

                                       CHHHHHCTEEEEEET CS
                         Trp_syntA 108 laelkeagvdglivp 122
                                          ++eag d++++ 
  gi|242398361|ref|YP_002993785.1|  41 ---IEEAGFDAIMIE 52 
                                       ...344444444443 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 8.3e-07
                                       HHHHHHHHHHCTSS-EEEESSS-SHHHHHHHHTT-SEEEE-HHHHHHHHCTTTSHHHHHHHHHHHHHHHHH CS
                         Trp_syntA 186 vdelverlkkltavPvavGFGistkeqvkqvakvadGvivGSalvkkieeeaeekeqalekleelarelke 256
                                       + + ++r k+l++vPv+vG G  t e+  ++ k adG ivG  + k+ +++ +   + ++kl +la++lk+
  gi|242398361|ref|YP_002993785.1| 190 L-KKLKRAKELSNVPVLVGSGT-TYENLPELWKYADGFIVGTWIKKDGKTNNDIDPERAKKLINLAEKLKA 258
                                       3.458999*************5.78999****************999999999999999999998888776 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.1   0.0    0.0083        25     100     152 ..      29      83 ..      22     100 .. 0.90
   2 !    9.4   0.0   0.00021      0.63     133     170 ..     184     221 ..     176     229 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0083
                          TMP-TENI 100 GlSvhsleeaeeaealgadYigvGpifpTdtKkdaeplgleglkelaeale..iP 152
                                       G+  h ++ea+++e++g d i++  +   +  k  ep+ ++ ++ +a++++  iP
  gi|242398361|ref|YP_002993785.1|  29 GVVEHAISEAKKIEEAGFDAIMIENFNDVPFSKTVEPITVASMTLIARTIKeeIP 83 
                                       6667999***********************9999999999999999999887765 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00021
                          TMP-TENI 133 daeplgleglkelaealeiPvvaiGGitlenvaevlea 170
                                         + ++l++lk+++e +++Pv +  G t en++e++++
  gi|242398361|ref|YP_002993785.1| 184 TGNEVDLKKLKRAKELSNVPVLVGSGTTYENLPELWKY 221
                                       457899*****************************975 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1      0.11   3.2e+02      21      52 ..      37      67 ..      31      80 .. 0.75
   2 ?    8.6   0.1   0.00039       1.2      20      67 ..     162     210 ..     158     215 .. 0.65
   3 ?    5.3   0.0    0.0039        12     175     216 ..     196     236 ..     191     246 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.11
                                      HHHHHHHCTT-SEEEEECSTCHHHHHHHHHHH CS
                              PcrB 21 EiveiviesgtDavmigGsqsvtldntvrllk 52
                                      E+ +i  e g Da+mi   + v   +tv+ + 
  gi|242398361|ref|YP_002993785.1| 37 EAKKI-EEAGFDAIMIENFNDVPFSKTVEPIT 67
                                      54444.4999******9999998888887765 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00039
                                       HHHHHHHH.CTT-SEEEEECSTCHHHHHHHHHHHHHCTSSS-EEEEESS CS
                              PcrB  20 dEiveivi.esgtDavmigGsqsvtldntvrllkkvsriklPivlepsn 67 
                                       +E++  +i ++ +Dav+i+G  + ++ +  +l +  +  ++P+++  + 
  gi|242398361|ref|YP_002993785.1| 162 EEALSDAIeRGLADAVIISGKRTGNEVDLKKLKRAKELSNVPVLVGSGT 210
                                       6676665515669*******99555444333333333478999887665 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.0039
                                       HHHHSSSEEEEESS--SHHHHHHHHCCSSEEEE-CHHHHHHH CS
                              PcrB 175 kkklekarlivGGGirsaEkAkevveaADvivvGnvveekde 216
                                        k l++  ++vG G    E+  e  ++AD  +vG+ ++++++
  gi|242398361|ref|YP_002993785.1| 196 AKELSNVPVLVGSGT-TYENLPELWKYADGFIVGTWIKKDGK 236
                                       6889999999**996.579999***************99883 PP

>> Bac_luciferase  Luciferase-like monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   4.8e-05      0.14      20      62 ..      29      72 ..      11      79 .. 0.84
   2 ?   -0.2   0.0      0.18   5.5e+02     167     193 ..     202     229 ..     152     256 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.8e-05
                    Bac_luciferase 20 aslrylvelaraaEelGfdavwvaehhggpgga.ldaftllaal 62
                                        +++++  a+++Ee+Gfda+++     +p+++  +++t++++ 
  gi|242398361|ref|YP_002993785.1| 29 GVVEHAISEAKKIEEAGFDAIMIENFNDVPFSKtVEPITVASMT 72
                                      467889999****************9999999999999999974 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.18
                    Bac_luciferase 167 iPvyvaaas.paglelaarhadglllag 193
                                       +Pv+v++++  ++l   +++adg+++  
  gi|242398361|ref|YP_002993785.1| 202 VPVLVGSGTtYENLPELWKYADGFIVGT 229
                                       7988888888899999999999988765 PP

>> B1  Protein L b1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.32   9.7e+02      25      38 ..      26      39 ..      20      44 .. 0.84
   2 ?    9.1   0.0   0.00045       1.3      15      39 ..     146     170 ..     142     190 .. 0.85
   3 ?   -1.4   0.0      0.81   2.4e+03      28      43 ..     209     224 ..     208     244 .. 0.63

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.32
                                B1 25 efkGtfaeataeay 38
                                      +f G  ++a++ea 
  gi|242398361|ref|YP_002993785.1| 26 NFNGVVEHAISEAK 39
                                      799*********96 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00045
                                B1  15 ifadGktqtaefkGtfaeataeayr 39 
                                       +fad +++ a+  G f+ea ++a  
  gi|242398361|ref|YP_002993785.1| 146 VFADVHVKHAHHFGDFEEALSDAIE 170
                                       6*********************964 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.81
                                B1  28 Gtfaeataeayryadl 43 
                                       Gt  e   e ++yad 
  gi|242398361|ref|YP_002993785.1| 209 GTTYENLPELWKYADG 224
                                       6666777788888884 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); 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:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.63u 0.36s 00:00:00.99 Elapsed: 00:00:00.55
# Mc/sec: 1413.19
//
Query:       gi|242398362|ref|YP_002993786.1|  [L=197]
Description: hypothetical protein TSIB_0371 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-66  222.8   0.5    3.3e-66  222.6   0.5    1.0  1  PIN_5     PINc domain ribonuclease
     0.0072   16.0   0.1      0.018   14.7   0.1    1.8  1  ALC       Phage ALC protein
  ------ inclusion threshold ------
       0.14   12.3   0.1          5    7.2   0.1    2.7  3  BofC_C    BofC C-terminal domain


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 !  222.6   0.5   5.5e-70   3.3e-66       1     205 [.       6     194 ..       6     195 .. 0.96

  Alignments for each domain:
  == domain 1  score: 222.6 bits;  conditional E-value: 5.5e-70
                             PIN_5   1 rfvlDTsaltdpevreklgeeeleeavkklldliaearlklgiscyippsvykElkeflkreeveeeviakldtwlv 77 
                                       rf+lDTs++++pe+r+++g++ + ea+k +l+++++      +++y+pp +ykE+ +f++ eev+++    ++ +++
  gi|242398362|ref|YP_002993786.1|   6 RFILDTSIFVNPEIRNRFGDNPT-EAMKIFLEYAERL--FGRVEFYMPPGIYKEVSHFVELEEVSPD----IELYII 75 
                                       8*********************9.*********9874..455688**********************....****** PP

                             PIN_5  78 kkspdryevkipaeilyeyveevrerinkGlrvaEeavreaaeeseklekeeeeeevgelikklRekYrealRkGil 154
                                       kk p+ ++++ipa ++ye++e++r+ri+kGlrvaE+avre++ +s+         +v+++i+klR++Yr+alR+Gi+
  gi|242398362|ref|YP_002993786.1|  76 KKPPNVHDIRIPAFVVYELIEDIRRRIDKGLRVAEKAVRESVVDSQ---------NVNAIIQKLRRNYRKALREGIV 143
                                       *****************************************99986.........789******************* PP

                             PIN_5 155 DsaeDldvllLAkELdaavvssDeGikkwaeklGlrlveakkfpkvlkeyl 205
                                       Ds+eD++++lLAkELda++vs+D Gi +wa+k+G+++++a +f++vl e++
  gi|242398362|ref|YP_002993786.1| 144 DSKEDFELILLAKELDATIVSADVGILTWAQKMGIKWIDAARFKEVLDELI 194
                                       ************************************************997 PP

>> ALC  Phage ALC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1     3e-06     0.018      65     111 ..      49      95 ..      26     137 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3e-06
                               ALC  65 llaelveeskvfleirlakydlevyvtatlPdvhivsikssvlvnkl 111
                                       + + + +e++ f+e ++   d+e+y+ +  P+vh   i ++v+    
  gi|242398362|ref|YP_002993786.1|  49 MPPGIYKEVSHFVELEEVSPDIELYIIKKPPNVHDIRIPAFVVYELI 95 
                                       5577899******************************9999986544 PP

>> BofC_C  BofC C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.26   1.5e+03      51      70 ..     100     119 ..      91     123 .. 0.79
   2 ?    7.2   0.1   0.00084         5      42      69 ..     127     153 ..     115     157 .. 0.87
   3 ?    1.4   0.0     0.056   3.3e+02      54      71 ..     175     192 ..     171     195 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.26
                                       HHHHH--S---HHHHHHHHH CS
                            BofC_C  51 eqLkkGIrveskeeyesvle 70 
                                        +  kG rv +k+  esv++
  gi|242398362|ref|YP_002993786.1| 100 RRIDKGLRVAEKAVRESVVD 119
                                       67789****99999999887 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.00084
                                       TTTS-HHHHHHHHH--S---HHHHHHHH CS
                            BofC_C  42 veklesslkeqLkkGIrveskeeyesvl 69 
                                       ++kl  + +++L++GI v+ske++e +l
  gi|242398362|ref|YP_002993786.1| 127 IQKLRRNYRKALREGI-VDSKEDFELIL 153
                                       799999999******9.9******9988 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.056
                                       HH--S---HHHHHHHHHH CS
                            BofC_C  54 kkGIrveskeeyesvlet 71 
                                       k GI+  + +++++vl+ 
  gi|242398362|ref|YP_002993786.1| 175 KMGIKWIDAARFKEVLDE 192
                                       67**************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       810  (0.0451782); expected 358.6 (0.02)
Passed bias filter:                      629  (0.0350828); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 1536.53
//
Query:       gi|242398363|ref|YP_002993787.1|  [L=403]
Description: hypothetical protein TSIB_0372 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-05   23.2   0.0    5.2e-05   22.6   0.0    1.2  1  Arabinose_Isome  L-arabinose isomerase


Domain annotation for each model (and alignments):
>> Arabinose_Isome  L-arabinose isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   2.9e-09   5.2e-05     238     308 ..     194     265 ..     159     288 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 2.9e-09
                                       GGGSTTSTTHHHHHHHHHHHHHHHHHHHHHT-SEEE.E-TT--TTSSS-SSHHHHHHHHHT-EEESTT-HHH CS
                   Arabinose_Isome 238 eelkeeeereeslreaarielglrkfLeekgfkaft.ttFedlgglkqlpglavqrLmaeGyGfgaEGDwkt 308
                                       ++++ +e ++e l +  r+ ++l+k++++ ++++f+   Fe l++l+  p la   L aeG   + EG+ ++
  gi|242398363|ref|YP_002993787.1| 194 KAMDIKEPQREDLVKTGRMYVALKKIIQDYKLDGFAiGCFEMLNKLNATPCLALAMLNAEGIPAACEGELNS 265
                                       445556778999***********************7369*****************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2523.45
//
Query:       gi|242398364|ref|YP_002993788.1|  [L=60]
Description: hypothetical protein TSIB_0373 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00011   22.1   4.7    0.00015   21.7   4.7    1.2  1  Class_IIIsignal  Class III signal peptide
     0.0029   17.1   1.7     0.0029   17.1   1.7    1.0  1  MSC              Man1-Src1p-C-terminal domain
     0.0037   17.2   2.6     0.0044   16.9   2.6    1.1  1  DUF4083          Domain of unknown function (DUF4083)
  ------ inclusion threshold ------
      0.043   13.9   0.7      0.053   13.6   0.7    1.1  1  DUF2443          Protein of unknown function (DUF2443)
      0.062   12.9   4.4      0.071   12.7   4.4    1.1  1  Baculo_11_kDa    Baculovirus 11 kDa family
      0.084   12.6   1.9      0.083   12.6   1.9    1.1  1  DUF4736          Domain of unknown function (DUF4736)
       0.32   10.2   0.6       0.29   10.3   0.6    1.0  1  Herpes_LMP1      Herpesvirus latent membrane protein 1 (LMP1)
        1.4    9.2   8.1          4    7.8   8.1    1.7  1  TadE             TadE-like protein


Domain annotation for each model (and alignments):
>> Class_IIIsignal  Class III signal peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   4.7   6.5e-08   0.00015       1      24 [.       3      26 ..       3      28 .. 0.95

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 6.5e-08
                   Class_IIIsignal  1 kKGQiSlEyiLLilavlviaiiai 24
                                      +++Q ++Ey+++i++vl+i+ ++i
  gi|242398364|ref|YP_002993788.1|  3 RNAQAAIEYLMMIAIVLIIIFVVI 26
                                      689*******************98 PP

>> MSC  Man1-Src1p-C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   1.7   1.3e-06    0.0029     221     268 ..       9      56 ..       1      59 [. 0.74

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.3e-06
                               MSC 221 yrllllglllllllilylrsrlrsrraekerveelvkevlerLkkqkk 268
                                        ++l++++++l++++++++   r+  + ++++++l+++++e+L+k+k+
  gi|242398364|ref|YP_002993788.1|   9 IEYLMMIAIVLIIIFVVIQIVRRTVINAAQNIQNLTQTIVEELQKAKE 56 
                                       4555556666666666777777777788999**************986 PP

>> DUF4083  Domain of unknown function (DUF4083)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   2.6     2e-06    0.0044       6      44 ..       9      44 ..       5      53 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2e-06
                           DUF4083  6 iyliivivLilllvfsftlfiRrvvsrsaakkkkskele 44
                                      i ++++i ++l ++f ++ ++Rr+v+  a   ++ ++l 
  gi|242398364|ref|YP_002993788.1|  9 IEYLMMIAIVLIIIFVVIQIVRRTVINAA---QNIQNLT 44
                                      568999999999**************966...5555555 PP

>> DUF2443  Protein of unknown function (DUF2443)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.7   2.4e-05     0.053      14      67 ..       4      59 ..       2      60 .] 0.80

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.4e-05
                                      HHHHHHHHHHHHHT--HHHHHHHHTTSS-.--TTS-HHHHHH.HHHHHHHHHHHHH CS
                           DUF2443 14 dskeeielLLklakislvdyilikrGsld.mPesldvafltq.ideevekLkeaid 67
                                      ++++ ie L+ +a + ++ +++i+      +  + ++ +ltq i ee++k ke i+
  gi|242398364|ref|YP_002993788.1|  4 NAQAAIEYLMMIAIVLIIIFVVIQIVRRTvINAAQNIQNLTQtIVEELQKAKEGIN 59
                                      7999****************9987544431455667778877689********998 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 ?   12.7   4.4   3.1e-05     0.071      27      71 ..       2      46 ..       1      55 [. 0.79

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.1e-05
                     Baculo_11_kDa 27 srNrsflrdFvLvicglvvfvvivlfilLlvvilknaeaeeaeke 71
                                      +rN +   +++++i+ +++++ +v+ i+   vi+  +++++ +++
  gi|242398364|ref|YP_002993788.1|  2 KRNAQAAIEYLMMIAIVLIIIFVVIQIVRRTVINAAQNIQNLTQT 46
                                      688888889*****9999999999999988888887777776654 PP

>> DUF4736  Domain of unknown function (DUF4736)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   1.9   3.7e-05     0.083      29      68 ..       4      42 ..       1      56 [. 0.79

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.7e-05
                           DUF4736 29 lslllvllilslivllililvllsyveptvlsrkirreke 68
                                        ++ +++++++ ++li+i v++++v+ tv+++ ++ + +
  gi|242398364|ref|YP_002993788.1|  4 NAQAAIEYLMMIAIVLIIIFVVIQIVRRTVINAAQNIQ-N 42
                                      5688999***********************99888777.2 PP

>> Herpes_LMP1  Herpesvirus latent membrane protein 1 (LMP1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.6   0.00013      0.29      50      79 ..       7      36 ..       1      52 [. 0.80

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00013
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       Herpes_LMP1 50 gallvlysfallliiiiliififrrdllcp 79
                                       a+  l  +a++liii ++i i+rr ++  
  gi|242398364|ref|YP_002993788.1|  7 AAIEYLMMIAIVLIIIFVVIQIVRRTVINA 36
                                      677788999****************98865 PP

>> TadE  TadE-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   8.1    0.0018         4       2      39 ..       6      38 ..       5      42 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0018
                              TadE  2 aaavEFALvlPlllllllgiiefgrylyarqtlnnAAr 39
                                      +aa+E  + + ++l++++ +i+      +r+t+ nAA+
  gi|242398364|ref|YP_002993788.1|  6 QAAIEYLMMIAIVLIIIFVVIQ-----IVRRTVINAAQ 38
                                      89********************.....56777888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2369  (0.132132); expected 358.6 (0.02)
Passed bias filter:                     1176  (0.0655921); expected 358.6 (0.02)
Passed Vit filter:                       142  (0.00792013); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 393.73
//
Query:       gi|242398365|ref|YP_002993789.1|  [L=766]
Description: TRAP-type transporter, fused permease components [Thermococcus sibiricus MM 739]
Scores for 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-85  284.9  46.0    4.4e-56  190.5  21.7    2.5  2  DctM           Tripartite ATP-independent periplasmic transpo
  ------ inclusion threshold ------
       0.15   12.3   2.1         20    5.5   0.1    2.9  2  Glycophorin_A  Glycophorin A


Domain annotation for each model (and alignments):
>> DctM  Tripartite ATP-independent periplasmic transporter, DctM component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.5  21.7   4.9e-60   4.4e-56       2     294 ..     144     450 ..     143     456 .. 0.82
   2 !   99.7  16.3   1.8e-32   1.7e-28     219     413 ..     462     688 ..     455     691 .. 0.90

  Alignments for each domain:
  == domain 1  score: 190.5 bits;  conditional E-value: 4.9e-60
                              DctM   2 vsllvllalgvpvaislalasllllallgelllgvpleqilaqrvve....glssfalla.ipfFvlaGivlersGl 73 
                                       +++lvl+a+++++++ l l+++++l++  +   g+++ + ++q +++    g+  f++++ + +Fv++G++l ++G+
  gi|242398365|ref|YP_002993789.1| 144 AIILVLEATRRVLGWVLPLVVVVFLLYGINN-IGFNWIRFTQQLYFDegifGIPFFVMTIyVFAFVFFGAFLLKIGI 219
                                       6899******************666555554.599************99996776654431455************* PP

                              DctM  74 akrlidlaaalvGrvrGGlakvsvvgsalfgaiSGsavAnvaavGsitipamkrsGykrefaaaviaasstlgqiiP 150
                                       ++ + +++++l+G  +GG+ak +vv+s l+g++SGs+vAnv+++G++tip+mkr+Gy++e a+av+  +st+gq++P
  gi|242398365|ref|YP_002993789.1| 220 SDYITEFMISLFGARPGGPAKSAVVSSGLMGTVSGSSVANVLTTGTFTIPLMKRAGYPPEVAGAVEPVASTGGQLMP 296
                                       ***************************************************************************** PP

                              DctM 151 Pslglivfama.vlgvsigdlfaaaiipglllavglllavaiaakkenlrsktkaelkrlgqalkeaipalllplii 226
                                       P++g+++f+ma +lg+++ +l++aa++p+l+++ g+ l ++++ k+ +l+++++++   l + +++++ ++llp+ +
  gi|242398365|ref|YP_002993789.1| 297 PIMGAAAFIMAeFLGIPYNKLIIAAVLPALVYYSGVYLFIDLETKRLGLKGMPREKFAPL-RYFIRKL-YILLPIAV 371
                                       *****************************************************9987765.5666666.79999999 PP

                              DctM 227 ligillgiftpteagavavvya.lviallvyrrltlee...vaaallstaktt........aavlfilaaagifagl 291
                                       ++ + l +  p +++a++ ++  + +a + + +++ +e   va +l+st+ ++        +++l++l + g++a+ 
  gi|242398365|ref|YP_002993789.1| 372 IT-VALIWGIPPHISAISSLGIaIWVAWISKDNIKGHEglyVATVLVSTVLMFtgrevaipVTILLVLLTLGLLALG 447
                                       98.56666666666666655442444444444444443222455566666666666666667888888888888887 PP

                              DctM 292 ltl 294
                                       +t 
  gi|242398365|ref|YP_002993789.1| 448 FTK 450
                                       775 PP

  == domain 2  score: 99.7 bits;  conditional E-value: 1.8e-32
                              DctM 219 alllpliiligillgiftpt...eagavavvyalviallv...yrrltleevaaallstakttaavlfilaaagifa 289
                                        ll++++i  + +lg+  +      g++++  +l+++ +    +++l  + +++++++++kt+++v+++ a+ag++ 
  gi|242398365|ref|YP_002993789.1| 462 TLLFIFFIALTKYLGMRKEQillMSGVMGIGFSLIVGYISkseDGKLMYSATYESMIDAGKTSTSVMLAAASAGLIQ 538
                                       6889999999999999776422257899999999999998999999******************************* PP

                              DctM 290 glltltgvplklselllslsggk.llfLilvnllvlvlGmfldttaaiiilvpilaPaaak..lgidp......... 354
                                       g+lt+tg+ +kl++ l+ l++g+ +l+L+l+++++l+lGm+++tta++ii++ ++aPa+ +  lg++          
  gi|242398365|ref|YP_002993789.1| 539 GVLTMTGLVTKLGYRLIDLTAGNlWLLLLLTMVFSLILGMGVPTTANYIITSLVAAPAIYNavLGLQSysspvpgft 615
                                       ***********************9**********************************9772256666********* PP

                              DctM 355 .....ihfgvvivlnlsiglitPPvGlalfvassia.........kvsveeivkalvPflvvlvvalvlitlv 413
                                            +++++++++++ ++++tPPv+la +++s+ a         +++   +  ++ P++    + + lit+ 
  gi|242398365|ref|YP_002993789.1| 616 tpialLAAHFFVFYFGILADVTPPVALASYAGSALAggdfwktamNAVKYALAGYIGPYIYFTHPEMFLITVQ 688
                                       ************************************9999998888888888889999999999988888876 PP

>> Glycophorin_A  Glycophorin A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.2    0.0029        26      69      90 ..      76      97 ..      75     103 .. 0.87
   2 ?    5.5   0.1    0.0022        20      53      72 ..     128     147 ..     123     150 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0029
                                      HHHHHHHHHHHHHHHTHSXXXX CS
                     Glycophorin_A 69 AgvigtillisYlirRliKKss 90
                                      A v+ +illi+Yl+  ++KK +
  gi|242398365|ref|YP_002993789.1| 76 AFVLAMILLITYLLYPIRKKEK 97
                                      67999**************986 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0022
                                       SSSS-TTHHHHHHHHHHHHH CS
                     Glycophorin_A  53 hdFselvitliifgvmAgvi 72 
                                        +F+e+ +t ++fg mA ++
  gi|242398365|ref|YP_002993789.1| 128 AEFAEVYMTDVVFGLMAIIL 147
                                       68***************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (766 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1035  (0.0577277); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.81u 0.33s 00:00:01.14 Elapsed: 00:00:00.50
# Mc/sec: 4579.13
//
Query:       gi|242398366|ref|YP_002993790.1|  [L=149]
Description: hypothetical protein TSIB_0375 [Thermococcus sibiricus MM 739]
Scores for 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-11   42.0   0.0    1.2e-10   41.6   0.0    1.2  1  DUF1850   Domain of unknown function (DUF1850)


Domain annotation for each model (and alignments):
>> DUF1850  Domain of unknown function (DUF1850)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.6   0.0   6.7e-15   1.2e-10       1      80 [.      42     119 ..      42     124 .. 0.84

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 6.7e-15
                           DUF1850   1 ftlswtHSVektpveEdyrvegggLvleetrfksfGaGlpspaeagervedgwfvlrinrp.leelrlrvggiadhr 76 
                                       ++++++HSV+++++ E  + ++ gL++ e++ k+fGaGlp++ +  e   +g++v ++n p  ++l++   + ++ +
  gi|242398366|ref|YP_002993790.1|  42 IEITYIHSVQRSKIVEILKANKTGLYVAEMWWKDFGAGLPEDIQYSE---NGYYVKKVNIPlGKSLSFWFISSNQAK 115
                                       5799************************************9887765...899988899995567877666666666 PP

                           DUF1850  77 lcvd 80 
                                       + v+
  gi|242398366|ref|YP_002993790.1| 116 IAVN 119
                                       6665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); 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 0.33s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 889.92
//
Query:       gi|242398367|ref|YP_002993791.1|  [L=328]
Description: TRAP-type transporter, periplasmic component [Thermococcus sibiricus MM 739]
Scores for complete 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-86  289.5   3.8    3.2e-86  289.3   3.8    1.0  1  NMT1_3          NMT1-like family
    1.6e-11   44.6   0.4      4e-11   43.3   0.3    1.8  2  NMT1            NMT1/THI5 like
    6.9e-08   32.4   4.2      3e-07   30.3   4.1    1.9  1  Phosphonate-bd  ABC transporter, phosphonate, periplasmic sub
    4.7e-06   26.2   0.7    7.8e-06   25.5   0.1    1.6  2  SBP_bac_3       Bacterial extracellular solute-binding protei
     0.0084   15.7   0.3      0.014   15.0   0.3    1.4  1  OpuAC           Substrate binding domain of ABC-type glycine 


Domain annotation for each model (and alignments):
>> NMT1_3  NMT1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  289.3   3.8     9e-90   3.2e-86       1     289 []      37     319 ..      37     319 .. 0.96

  Alignments for each domain:
  == domain 1  score: 289.3 bits;  conditional E-value: 9e-90
                            NMT1_3   1 igTastgGtyYpvGvaiatliseklakdqkvkasaqssaGsveNiqllkkgeadlailqsdvayeAyeGegefegkk 77 
                                       i T++tgG+y+p+G + a+++s     +++v+a+a +s++sv N +++ +g+a+++ilq+dvay+Ay+G   feg +
  gi|242398367|ref|YP_002993791.1|  37 IYTGGTGGVYFPLGSKYAEILS-----KNGVPATAVTSGASVANAKAIGDGTAQAGILQNDVAYYAYKGLYMFEG-Q 107
                                       67*****************985.....568********************************************9.7 PP

                            NMT1_3  78 plknlraitmlyaevfqlvvskdsgigsiadlkgkrvsvGpegsGtegsarailealglsekdlklleelgygesad 154
                                        ++n+r +++ly+e++q++v++ds+i++++dl gk+v++G++gsGt ++a+++l+a+g+  + ++++++ +++e+ +
  gi|242398367|ref|YP_002993791.1| 108 AITNIRGVAALYPETVQFIVRADSDIKTLSDLAGKKVAIGAPGSGTAVAAEQVLRAAGVW-DSIEKVNQ-DFNEASQ 182
                                       9*********************************************************87.46676555.9****** PP

                            NMT1_3 155 alkdgqldgaalvaGvPvsavtqlaasedikliplddeqldkllke.ypvftkyvipagtypq.dedikTiavpnfl 229
                                        lk gq+d+a++v+G+P+ +v q+a +++++++++ d++l+kl++e y ++ ++++p++ty++ d d++Tiav+++l
  gi|242398367|ref|YP_002993791.1| 183 SLKLGQVDAAVIVSGIPTPSVNQIAVQTPVRVLSIPDDTLNKLKEEgYIFYVRQIVPKDTYNGvDVDTPTIAVKAML 259
                                       *******************************************766156899*********99899*********** PP

                            NMT1_3 230 vvradldeelvYeitkaifenldelnsihkaakeislekalaglpvplHpGAerYYkEqG 289
                                       +v adl+e++vY++tk +fen d+l ++h++a++isle+al+g+++plHpGA++YY+E+G
  gi|242398367|ref|YP_002993791.1| 260 AVGADLPEDTVYQMTKILFENVDQLRAVHQKAQAISLETALDGMSIPLHPGAIKYYEEKG 319
                                       ***********************************************************9 PP

>> NMT1  NMT1/THI5 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.51   1.8e+03     110     145 ..      55      88 ..      52     109 .. 0.74
   2 !   43.3   0.3   1.1e-14     4e-11      59     155 ..     108     202 ..      72     246 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.51
                                       HHHHHTT--GGG-EEEE-.TT-HHHHHHCTSSSEEE CS
                              NMT1 110 allakdggdpsdvtlvnvggtslakalltgkvDaai 145
                                       ++l+k+g+ + +vt     + ++ ka+ +g+++a+i
  gi|242398367|ref|YP_002993791.1|  55 EILSKNGVPATAVTSGAS-VANA-KAIGDGTAQAGI 88 
                                       678888888888887444.6664.699999988887 PP

  == domain 2  score: 43.3 bits;  conditional E-value: 1.1e-14
                                       TT--EEEEEEEE-S--EEEEEECCC--SSGGGGTTSEEEE-S.-TTHHHHHHHHHHHTT--GGG-EEEE-.TT-HHH CS
                              NMT1  59 kglpvvsvaallqeplsglivlkdsgikspkDLkGkrigyvg.spfekallkallakdggdpsdvtlvnvggtslak 134
                                       +   ++ vaal+  ++ ++iv++ds+ik+++DL+Gk++++   ++ +    +++l+++g+  ++++ vn ++ ++++
  gi|242398367|ref|YP_002993791.1| 108 AITNIRGVAALY-PETVQFIVRADSDIKTLSDLAGKKVAIGApGSGTAVAAEQVLRAAGV-WDSIEKVNQDFNEASQ 182
                                       445799999999.56789********************9777244455556778888888.9*************** PP

                                       HHHCTSSSEEECEETTTHHHH CS
                              NMT1 135 alltgkvDaaiggyenwegve 155
                                       +l  g+vDaa+ ++ ++ + +
  gi|242398367|ref|YP_002993791.1| 183 SLKLGQVDAAV-IVSGIPTPS 202
                                       **********9.777665555 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 !   30.3   4.1   8.3e-11     3e-07      28     215 ..      61     278 ..      51     285 .. 0.62

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 8.3e-11
                                       SSEEEEE--SSHHHHHHHHHTTS-SEEE--HHHHHHHHHH.S-EEEEEEEEETT-.-S..EEEEEEEEETTSS--SH CS
                    Phosphonate-bd  28 GvevelvvatdyaavvealragqvDiaflgplayvqardq.agveplatrvrsdG.sa..syrsviivradsdiqsl 100
                                       Gv+  +v+     a ++a+  g+++ + l++  ++ a +  +  e  a++   +G +a      ++ivradsdi++l
  gi|242398367|ref|YP_002993791.1|  61 GVPATAVTSGASVANAKAIGDGTAQAGILQNDVAYYAYKGlYMFEGQAITNI-RGvAAlyPETVQFIVRADSDIKTL 136
                                       5555555555555666666666666666665544444443245555555554.552232233578************ PP

                                       HHHGG-EEEE--TT-TTTTHHHHHHTCCCCT--HHHHSSEEEE--HHHHHHHHHTTSSSEEE............... CS
                    Phosphonate-bd 101 edLkgktiafvspsStsGylvpaalLvkeagldpeddfsevfsgshdaavlavlsgdadaaa............... 162
                                       +dL+gk++a+++p S    ++ ++ L + ag+   d +++v  ++ ++a +++  g++daa+               
  gi|242398367|ref|YP_002993791.1| 137 SDLAGKKVAIGAPGSGT-AVAAEQVL-RAAGVW--DSIEKV-NQDFNEASQSLKLGQVDAAVivsgiptpsvnqiav 208
                                       **************977.45555558.899986..344554.4567788899999*******666666666555555 PP

                                       ........EEHHHHHHHHHH-HHHHTTEEEE..........EEEEEE.E--EEEEETTS-HHHHHHHHHHHH CS
                    Phosphonate-bd 163 ........vsadaledlvaegpedkdelrvi..........assppi.pndpvvvrkelseelkekiqdall 215
                                               +++d+l++l++eg + +  +r i            +p i   ++++v ++l+e+++ +++++l+
  gi|242398367|ref|YP_002993791.1| 209 qtpvrvlsIPDDTLNKLKEEGYIFY--VRQIvpkdtyngvdVDTPTIaVKAMLAVGADLPEDTVYQMTKILF 278
                                       5555555555566666665553322..222222222222233666654466666777777777777776665 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 ?   -2.5   0.0      0.77   2.8e+03     118     166 ..      50      97 ..      30     101 .. 0.66
   2 !   25.5   0.1   2.2e-09   7.8e-06      85     158 ..     121     194 ..     114     236 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.77
                                       TSHHHHHHHHHHHCTSEEEEESSHHHHHHHHHTTSSSEEEEEHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SBP_bac_3 118 gstaeellkeelkkgaeivefdtleealqaLkngrvdavvadspvlayl 166
                                       gs ++e+l ++    a++v+     +  +a+ +g ++a +  + v++y+
  gi|242398367|ref|YP_002993791.1|  50 GSKYAEILSKNGV-PATAVTSGASVANAKAIGDGTAQAGILQNDVAYYA 97 
                                       5666666666444.33344333333445668888888888777777775 PP

  == domain 2  score: 25.5 bits;  conditional E-value: 2.2e-09
                                       EEEEEEEEETTSHGTCCHSSCGCGTTSEEEEETTSHHHHHHHHHHHC......TSEE.EEESSHHHHHHHHHTTSSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxx.xxxxxxxxxxxxxxxxxxx RF
                         SBP_bac_3  85 agqvllvrkkdaskissiksladLkgkkvgvqagstaeellkeelkk......gaei.vefdtleealqaLkngrvd 154
                                        +++++vr++     s+ik+l+dL+gkkv++ a  +  + ++e+  +      +  i ++ ++ +ea q Lk g+vd
  gi|242398367|ref|YP_002993791.1| 121 ETVQFIVRAD-----SDIKTLSDLAGKKVAIGAPGSGTAVAAEQVLRaagvwdS--IeKVNQDFNEASQSLKLGQVD 190
                                       678999*944.....4688888********988777666666655554565432..2345799************** PP

                                       EEEE CS
                                       xxxx RF
                         SBP_bac_3 155 avva 158
                                       a+v 
  gi|242398367|ref|YP_002993791.1| 191 AAVI 194
                                       *996 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 !   15.0   0.3     4e-06     0.014      20     174 ..      53     192 ..      48     239 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4e-06
                                       HHHHHHHTTE.EEEEEEEESHHHHHHHHHTTSSSEEEEEEHHHHHHHHHH..HHHHHHEEEEEE.EESEEECEEEEE CS
                             OpuAC  20 lkqllekkGy.kveltnlgstavlfaalasGdiDvypeewtgtayeaykk..aveekkglevlg.plgagnteglav 92 
                                       ++++l+k+G+ ++ +t+++s ++  +a+ +G +++        ay ayk    +e++    + g ++ +  t  ++v
  gi|242398367|ref|YP_002993791.1|  53 YAEILSKNGVpATAVTSGAS-VANAKAIGDGTAQAGI-LQNDVAYYAYKGlyMFEGQAITNIRGvAALYPETVQFIV 127
                                       799*******5555555555.9999999999999999.77778877777743357777777777899999999**** PP

                                       EHHHHHHHTTTBHHHHCTHHGGTEEEEEHHCCHSTTSHHCCHHHHHHHHHHT-.TTCEEEGSCEEEEHHHHHHHHHT CS
                             OpuAC  93 pkyvaekygiksisDLkkpaedlelgakgeflgrpdgwgcekvtegllkaYgl.dkvelvegseaamdaelyaaykr 168
                                       +++     +ik++sDL+ +++            +++g+g+  ++e+ l+a g+ d++e+v    ++   e+ +++k 
  gi|242398367|ref|YP_002993791.1| 128 RADS----DIKTLSDLAGKKV----------AIGAPGSGTAVAAEQVLRAAGVwDSIEKV----NQDFNEASQSLKL 186
                                       9775....********66666..........44555666666666777777773344443....2222245555555 PP

                                       TCSSEE CS
                             OpuAC 169 gepvvv 174
                                       g+++++
  gi|242398367|ref|YP_002993791.1| 187 GQVDAA 192
                                       555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       804  (0.0448435); expected 358.6 (0.02)
Passed bias filter:                      627  (0.0349713); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.51
# Mc/sec: 1930.58
//
Query:       gi|242398368|ref|YP_002993792.1|  [L=42]
Description: hypothetical protein TSIB_0377 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       182  (0.0101512); expected 358.6 (0.02)
Passed bias filter:                      138  (0.00769703); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 295.17
//
Query:       gi|242398369|ref|YP_002993793.1|  [L=280]
Description: hypothetical protein TSIB_0378 [Thermococcus sibiricus MM 739]
Scores for complete 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-66  222.0   0.7    7.5e-66  221.5   0.7    1.1  1  tRNA_deacylase  D-aminoacyl-tRNA deacylase


Domain annotation for each model (and alignments):
>> tRNA_deacylase  D-aminoacyl-tRNA deacylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  221.5   0.7   4.2e-70   7.5e-66       5     204 ..      78     277 ..      75     278 .. 0.97

  Alignments for each domain:
  == domain 1  score: 221.5 bits;  conditional E-value: 4.2e-70
                                       -SEEEEEEEEE-TT---EEEEE--B-SS--TTSS-TT-B--B-HHHHHHHHHHHHGGGGGSTT-EEEE--S-SS--- CS
                    tRNA_deacylase   5 vdliiflSrHssesgkplLTvHvtGnlgeaelGGkpeelapaaPrllkallralkkiaekleefevtlEatHHGPte 81 
                                       +++iif+SrHss+++ p+LT+HvtGn+g+a +GGk+e+la+  P ++k +l +l++++    +++v++EatHHGP+e
  gi|242398369|ref|YP_002993793.1|  78 PKIIIFASRHSSQQKLPALTTHVTGNWGKAMYGGKDESLAIVEPIAMKLALLKLNELN--DLNWTVCYEATHHGPSE 152
                                       579*******************************************************..99*************** PP

                                       --S-EEEEEEEESHHHHT-HHHHHHHHHHHHHHHH--..----EEEEEE-S-TT-HHHHHHHHHBSEEEEEEE-GGG CS
                    tRNA_deacylase  82 lkvPslFvEiGSteeeWkdedaaeavaeavlellese..eekekvlvgiGGgHYaprftklvletevavGhilskya 156
                                       l vPslF+EiGS+eeeWk+e+a+e+vae+++ ++++    ++ k+++giGGgHYap++tk++l++e+a++hi++ky 
  gi|242398369|ref|YP_002993793.1| 153 LGVPSLFIEIGSSEEEWKNEQAGEIVAETIFYVINNYtkIHNFKTVIGIGGGHYAPKQTKAALNSELAFSHIVAKY- 228
                                       ***********************************9988889**********************************. PP

                                       GGG--HHHHHHHHHHH..T-SEEEE-TTT--HHHHHHHHHHHHHHT-EE CS
                    tRNA_deacylase 157 leelkeevikqaleks.egadvalidkkslkseqkeaieelleelgiev 204
                                       ++ +++e++ +a++++ ++++ +++d+k+ k+e+k++ ++++eel++e+
  gi|242398369|ref|YP_002993793.1| 229 AHPISKEMLLKAINRTsGRVHGIYVDWKGSKGETKQMARNIAEELDLEF 277
                                       77888999999999999****************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1872.03
//
Query:       gi|242398370|ref|YP_002993794.1|  [L=378]
Description: Cell division ftsZ like protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.4e-46  158.4   0.4    4.7e-46  157.5   0.4    1.5  1  Tubulin        Tubulin/FtsZ family, GTPase domain
    2.4e-33  114.3   2.7    1.3e-32  111.9   1.1    2.6  2  FtsZ_C         FtsZ family, C-terminal domain
     0.0027   17.4   0.5     0.0092   15.7   0.5    1.9  1  DUF3236        Protein of unknown function (DUF3236)
     0.0038   16.8   3.5       0.16   11.5   0.6    2.4  2  DUF4147        Domain of unknown function (DUF4147)
  ------ inclusion threshold ------
      0.014   14.7   2.0      0.026   13.8   2.0    1.5  1  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
      0.054   12.8   0.1       0.18   11.2   0.0    1.8  2  ThiF           ThiF family
      0.075   12.7   0.1       0.19   11.3   0.1    1.7  2  Peripla_BP_6   Periplasmic binding protein
       0.08   13.4   0.7       0.36   11.3   0.2    2.3  2  NAD_binding_7  Putative NAD(P)-binding
       0.24   10.6   4.0        1.1    8.5   1.7    2.6  2  GCH_III        GTP cyclohydrolase III
        1.4    8.1   7.5        2.2    7.4   1.5    2.4  2  Tubulin_2      Tubulin like


Domain annotation for each model (and alignments):
>> Tubulin  Tubulin/FtsZ family, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.5   0.4   2.6e-49   4.7e-46       1     196 [.      48     208 ..      48     209 .. 0.97

  Alignments for each domain:
  == domain 1  score: 157.5 bits;  conditional E-value: 2.6e-49
                                       EEEEEEEHHHHHHHHHHHHH...HHHCH....HHHT.....TTEEEEE....EEESBHHHHHTS-GS......EEEE CS
                           Tubulin   1 eiivigvGqcGnqignelwellakehgiqsdgdslesfFsesgkveyiprsvaidtdpqvlneikagselfnpnkll 77 
                                       +i vigvG++G++++n+++e      gi             +g ++ i    a++td+q+l +ika+      +k+l
  gi|242398370|ref|YP_002993794.1|  48 KIYVIGVGGAGCNTINRMME-----VGI-------------QG-AKVI----AVNTDAQDLLKIKAH------KKIL 95 
                                       599*****************.....6**.............77.6666....***************......**** PP

                                       --CCCCTTC--TT-HHHHHHHHHHTHHHHHHHHTT-SE.SEEEEEEETTSSHHHHHHHHHHHHHHHTSTTSEEEEEE CS
                           Tubulin  78 lgkegagnngaggypevgkeaaeeileeirkevekcdslqgffitaslgGGTGSGlgpvilevlkeeypkalvvtvv 154
                                       +gk+ ++++gag +p+vg+eaa+e+++ ir+++e++d+   +fit +lgGGTG+G +p+++e++k++  +al+v+vv
  gi|242398370|ref|YP_002993794.1|  96 IGKDLTRGLGAGNNPKVGEEAAKESERDIRDALEGADM---VFITCGLGGGTGTGGAPIVAELAKKM--GALTVSVV 167
                                       **************************************...**************************..******** PP

                                       EE--GG.G-HHHHHHHHHHHHHHHHT-SEEEEEEHHHHHCCS CS
                           Tubulin 155 vlPsefsevvvepynailalkelieesdavividNdaLlkil 196
                                       +lP++  e++++++na+ +l++l+++sd+vivi+Nd+L++++
  gi|242398370|ref|YP_002993794.1| 168 TLPFTV-EGIRRIKNAEYGLERLRKNSDTVIVIPNDKLMEVA 208
                                       *****9.*******************************9986 PP

>> FtsZ_C  FtsZ family, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.37   6.7e+02      27      52 ..      64      89 ..      57     102 .. 0.78
   2 !  111.9   1.1   7.2e-36   1.3e-32       1      94 [.     256     348 ..     256     349 .. 0.98

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.37
                                      GGGT--GGG-SEEEEEEEE-TT--HH CS
                            FtsZ_C 27 pLLdvdlsgAkgvlvnitggsdltlk 52
                                       +++v ++gAk + vn  +   l++k
  gi|242398370|ref|YP_002993794.1| 64 RMMEVGIQGAKVIAVNTDAQDLLKIK 89
                                      578999*****999997766555655 PP

  == domain 2  score: 111.9 bits;  conditional E-value: 7.2e-36
                                       EEEEEEEEEEESTTHHHHHHHHHHTSGGGT--GGG-SEEEEEEEE-TT--HHHHHHHHHHHHHHS-TTSEEEEEEEE CS
                            FtsZ_C   1 GvAmmgvGeasgedraeeaaeaaisspLLdvdlsgAkgvlvnitggsdltlkEveevaetireevdeeanvivGavi 77 
                                       G Am+g+Ge+++e+ra eaa++a++spLLdvd+sgAkg+l++i+ g+d++l+E+++++e +++++d+ea+vi+G ++
  gi|242398370|ref|YP_002993794.1| 256 GIAMIGIGESDSEKRALEAANQALNSPLLDVDISGAKGALISIA-GNDVKLEEAQQIIELVTSKLDPEAQVIWGIQL 331
                                       89*****************************************6.79****************************** PP

                                       -TT--SEEEEEEEEES- CS
                            FtsZ_C  78 deeledeirvtvvatgl 94 
                                       d++le +irv+vv+tg+
  gi|242398370|ref|YP_002993794.1| 332 DPDLEKTIRVMVVVTGV 348
                                       ****************8 PP

>> DUF3236  Protein of unknown function (DUF3236)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.5   5.1e-06    0.0092      17      91 ..      30     101 ..      10     103 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 5.1e-06
                                       --S--HHHHHHHHHHHHT-SEEEES-SSHHHHHHHHHHHTTTT--EEEEESSTGGGGGGSSSHHHHHHHHHHHHS CS
                           DUF3236  17 RkGDkeeeveaireyiknakkivvatknkkkvkvinkvlsklglkeiekleietnsaDltriPalskalialdis 91 
                                          D  ee+++i e+++   ki+v    +   + in ++ ++g++ ++ + ++t++ Dl +i a +k li+ d++
  gi|242398370|ref|YP_002993794.1|  30 PASDIDEELKKILEQVQA--KIYVIGVGGAGCNTINRMM-EVGIQGAKVIAVNTDAQDLLKIKAHKKILIGKDLT 101
                                       567899********9974..7***************976.79****************************99875 PP

>> DUF4147  Domain of unknown function (DUF4147)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.6   8.7e-05      0.16       3     121 ..       7     145 ..       5     168 .. 0.56
   2 !    5.7   0.1    0.0052       9.3      96     142 ..     269     315 ..     262     318 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8.7e-05
                                       HHHHHHHHHTTSHHHHHHTTHHH.....H--..........-SEEEEEESTTHHHHH.HHHH.HHHGEEEEEEETT- CS
                           DUF4147   3 raifeaaveavdpeklvkralsl.....kee...eldlskkkrvvvvgaGKAaaama.aaleeealksgvvvvkkgh 70 
                                        +++e+a+e++++e+ +   +++     + e   ++  + + +++v+g+G A ++ + +++e  + + +v+ v+++ 
  gi|242398370|ref|YP_002993794.1|   7 LKLIESAIERTSAEANTPVEVQTpasdiD-EelkKILEQVQAKIYVIGVGGAGCNTInRMMEVGIQGAKVIAVNTDA 82 
                                       56777888887777777777766444431.134444555789*************9956666344447777777555 PP

                                       --......--TT.......-EEEEE.-SSS--HHHHHHH.HHHHHHHSS--TT-.EEEEEE-TTHHH CS
                           DUF4147  71 ae......eker.......ievlea.ahplPdeesveaa.rkilelaeklkedd.lvlvliSGGgSA 121
                                       ++      + ++       ++ l a ++p   ee+ + + r+i +++e     d +++ +  GGg+ 
  gi|242398370|ref|YP_002993794.1|  83 QDllkikaH-KKiligkdlTRGLGAgNNPKVGEEAAKESeRDIRDALE---GADmVFITCGLGGGTG 145
                                       555555431.22333322223333335555444444433033444444...4441555555566655 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0052
                                       HHHHHHHSS--TT-EEEEEE-TTHHHHS--B-TT--HHHHHHHHHHH CS
                           DUF4147  96 rkilelaeklkeddlvlvliSGGgSAllaaPaegitledkqaltkaL 142
                                       +++le+a+++ +  l+ v iSG   Al++   ++++le+ q+++++ 
  gi|242398370|ref|YP_002993794.1| 269 KRALEAANQALNSPLLDVDISGAKGALISIAGNDVKLEEAQQIIELV 315
                                       68899999999999****************************99865 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 ?   13.8   2.0   1.5e-05     0.026      28      98 ..      46     137 ..      38     166 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.5e-05
                                       --EEEEESTSHHHHHHHHHHHHT...T-EEEEEESSHHHHHHHHHTTTCECEE..................HCHHHH CS
                       AlaDh_PNT_C  28 pakvlviGgGvaGlqAiatakgl...gakVtvlDvrparleqleslgakfvev..................lksqee 83 
                                       +ak+ viG+G aG + i+  +++   gakV +++++++ l ++++ ++  +                     k++e+
  gi|242398370|ref|YP_002993794.1|  46 QAKIYVIGVGGAGCNTINRMMEVgiqGAKVIAVNTDAQDLLKIKAHKKILIGKdltrglgagnnpkvgeeaAKESER 122
                                       69***************99888733369999999999999998885555444466679**********999999999 PP

                                       HHHHHHHH-SEEEE- CS
                       AlaDh_PNT_C  84 llaeavkeadvvigt 98 
                                        +++a++ ad+v  t
  gi|242398370|ref|YP_002993794.1| 123 DIRDALEGADMVFIT 137
                                       9********998655 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   9.8e-05      0.18      14      44 ..      39      72 ..      26      82 .. 0.79
   2 ?   -2.0   0.0         1   1.8e+03      62      97 ..     260     295 ..     232     323 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 9.8e-05
                                      HHHHT...SEEEEE--SHHHHHHHHHHHHHTTTE CS
                                      xxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF 14 ekLrd...skvllvGaGglGsellknLalsGvgk 44
                                      +k+ +   +k+ ++G+Gg G++ +  ++ +G++ 
  gi|242398370|ref|YP_002993794.1| 39 KKILEqvqAKIYVIGVGGAGCNTINRMMEVGIQG 72
                                      333335779**********************975 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1
                                       TTS-GGGTTSBHHHHHHHHHHHT-TTSEEEEEES-C CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF  62 flfreediGkpKaevaaealqeinpdveveavteri 97 
                                       + ++e+d  k   e+a +al++   dv+++  ++ +
  gi|242398370|ref|YP_002993794.1| 260 IGIGESDSEKRALEAANQALNSPLLDVDISGAKGAL 295
                                       556667777777777777777777777777666655 PP

>> Peripla_BP_6  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00011      0.19     164     237 ..      19      90 ..       3     168 .. 0.79
   2 ?   -2.3   0.0       1.6   2.8e+03     114     142 ..     140     168 ..     130     181 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00011
                                       EEEEEEEEE-TTHHHHHHHHHHHHTTT-SE.EEEESSHHHHHHHHHHHHHTT-SSSCEEEECCC-CHHHHHHHHH CS
                      Peripla_BP_6 164 gevvgeepvplgttdfsaqvlqikaagada.vllagtgadlaallkaaaeaGldakrillvswsgseedlkalgg 237
                                        e   +++v+++++d ++ + +i + +++a ++++g+g++ ++ ++ + e+G+++   ++++   +++dl ++++
  gi|242398370|ref|YP_002993794.1|  19 AEANTPVEVQTPASDIDEELKKILE-QVQAkIYVIGVGGAGCNTINRMMEVGIQG--AKVIAVNTDAQDLLKIKA 90 
                                       5544578899999***********9.66777***********************7..788999999999999986 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.6
                                       SS--HHHHHHHHHHHHHHHTTSCEEEEEE CS
                      Peripla_BP_6 114 lgpsysaqasalveylakelggkkvalvy 142
                                       lg+ + + ++ +v  lak+ g+ +v +v+
  gi|242398370|ref|YP_002993794.1| 140 LGGGTGTGGAPIVAELAKKMGALTVSVVT 168
                                       55666777777777788888887777765 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2    0.0002      0.36       8      68 ..      47     137 ..      41     140 .. 0.78
   2 ?   -0.2   0.0      0.76   1.4e+03      56      72 ..     187     203 ..     143     318 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0002
                     NAD_binding_7   8 kkvlvvGgGevAarkvrklleag...akvtvvapevkeele...........................elvklaeee 54 
                                        k+ v+G G  + + +++++e g   akv+ v  + ++ l+                           e  k +e++
  gi|242398370|ref|YP_002993794.1|  47 AKIYVIGVGGAGCNTINRMMEVGiqgAKVIAVNTDAQDLLKikahkkiligkdltrglgagnnpkvgeEAAKESERD 123
                                       6899*****************76655888888888533333666678888888888888888887776666667888 PP

                     NAD_binding_7  55 lekdlegadlviaa 68 
                                       +++ legad+v+++
  gi|242398370|ref|YP_002993794.1| 124 IRDALEGADMVFIT 137
                                       9999*******976 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.76
                     NAD_binding_7  56 ekdlegadlviaatddr 72 
                                       e+  ++ d+vi++++d+
  gi|242398370|ref|YP_002993794.1| 187 ERLRKNSDTVIVIPNDK 203
                                       45555566666666554 PP

>> GCH_III  GTP cyclohydrolase III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   1.7   0.00061       1.1     148     237 ..      24     129 ..      10     137 .. 0.59
   2 ?    1.3   0.0     0.095   1.7e+02     204     230 ..     255     280 ..     193     282 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00061
                                       HHHHHHHHHHHHHHHHHHHHTTT---EEEE....TTEEEEE-T..T--HHHHHHHHHHHHHHHS-..........-E CS
                           GCH_III 148 avrtylevnkvkaklakklekegallqfiG....GDnilavcn..eleeedvldiinevkekvdv..........dl 208
                                       +v+ ++   ++   l k le+ +a ++ iG    G n +      +++  +v  ++++ ++ +++          dl
  gi|242398370|ref|YP_002993794.1|  24 PVEVQTPASDIDEELKKILEQVQAKIYVIGvggaGCNTINRMMevGIQGAKVIAVNTDAQDLLKIkahkkiligkDL 100
                                       555555555555555555555555555554333334444433211233334444444444444444444445555** PP

                                       EEEEEEESSHHHHHHHHHHHHHHHHTTSS CS
                           GCH_III 209 kaGiGiadtaedaaaladeaLeeiRgklv 237
                                         G+G ++ ++     a+e+  +iR +l 
  gi|242398370|ref|YP_002993794.1| 101 TRGLGAGNNPKVGEEAAKESERDIRDALE 129
                                       *************************8875 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.095
                                       HS--EEEEEEEESSHHHHHHHHHHHHH CS
                           GCH_III 204 vdvdlkaGiGiadtaedaaaladeaLe 230
                                        ++++ +GiG +d  + a+  a++aL+
  gi|242398370|ref|YP_002993794.1| 255 GGIAM-IGIGESDSEKRALEAANQALN 280
                                       45554.79***************9997 PP

>> Tubulin_2  Tubulin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.4     0.016        28       2      18 ..      51      67 ..      50      74 .. 0.92
   2 ?    7.4   1.5    0.0012       2.2     156     181 ..     132     157 ..      98     193 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.016
                         Tubulin_2  2 viGLGGtGgkvlaelrr 18
                                      viG+GG G+++++++++
  gi|242398370|ref|YP_002993794.1| 51 VIGVGGAGCNTINRMME 67
                                      8************9975 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0012
                         Tubulin_2 156 lnvfVvgSLaGGTGSGiflDvayllr 181
                                         vf+ ++L GGTG G +  va l +
  gi|242398370|ref|YP_002993794.1| 132 DMVFITCGLGGGTGTGGAPIVAELAK 157
                                       47*************97766665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       713  (0.039768); expected 358.6 (0.02)
Passed bias filter:                      557  (0.031067); 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: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 2418.07
//
Query:       gi|242398371|ref|YP_002993795.1|  [L=65]
Description: Preprotein translocase subunit secE [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-06   28.1   0.5    1.6e-06   27.9   0.5    1.1  1  SecE      SecE/Sec61-gamma subunits of protein translocation 
  ------ inclusion threshold ------
      0.011   16.1   0.3      0.013   15.9   0.3    1.1  1  DUF2839   Protein of unknown function (DUF2839)


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 !   27.9   0.5   1.8e-10   1.6e-06       1      49 [.      13      60 ..      13      64 .. 0.91

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 1.8e-10
                                      HHCHHHHHHHHHCCCCCHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              SecE  1 kkFfkevkaElkKVtWPtrkEllkttvvVlvfvvimglflflvDlvfsk 49
                                      k+F++e+k+ +    +P +kE+   ++++ ++++++g+++ ++ ++ + 
  gi|242398371|ref|YP_002993795.1| 13 KSFISESKRVFLVTKKPGWKEYKLAAKITGIGIILIGVIGMIIRVI-GS 60
                                      58****************************************9854.44 PP

>> DUF2839  Protein of unknown function (DUF2839)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.9   0.3   1.4e-06     0.013      24      62 ..      22      60 ..       2      63 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.4e-06
                           DUF2839 24 wlpltkkqaeqfvklttrgawiGigllvvlWvvvrfiGp 62
                                      ++ +tkk   + +kl  + + iGi+l+ v+ +++r+iG 
  gi|242398371|ref|YP_002993795.1| 22 VFLVTKKPGWKEYKLAAKITGIGIILIGVIGMIIRVIGS 60
                                      4578999999****************************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 419.69
//
Query:       gi|242398372|ref|YP_002993796.1|  [L=155]
Description: NusG transcription antitermination protein [Thermococcus sibiricus MM 739]
Scores for 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-22   76.7   0.1    1.7e-21   75.9   0.1    1.4  1  Spt5-NGN  Early transcription elongation factor of RNA pol II
    5.5e-09   35.7   2.6    7.7e-09   35.2   0.7    2.2  3  KOW       KOW motif


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 !   75.9   0.1   1.9e-25   1.7e-21       1      84 []       8      87 ..       8      87 .. 0.99

  Alignments for each domain:
  == domain 1  score: 75.9 bits;  conditional E-value: 1.9e-25
                          Spt5-NGN  1 siwavkctagqErevalslmkkilelakkenleIkSvfapdelkGyiyvEAdrkaaveralegipnvrgvvqglvpikE 79
                                      +i+av++t gqE ++a  ++ k    ak+ +l I++++ p ++ Gyi+vEA++kaav+++++gi++++g  +g +++ E
  gi|242398372|ref|YP_002993796.1|  8 KIFAVRVTVGQEENTAKLIYSK----AKTYSLPIMAILSPSKVRGYIFVEATEKAAVDEVIRGIRHAKGTLPGPISFIE 82
                                      79********************....9999************************************************* PP

                          Spt5-NGN 80 vedll 84
                                      +e++l
  gi|242398372|ref|YP_002993796.1| 83 IEHFL 87
                                      ***98 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       0.7   6.3e+03       5      10 ..      12      17 ..      11      20 .. 0.70
   2 !   35.2   0.7   8.5e-13   7.7e-09       1      32 []      98     129 ..      98     129 .. 0.96
   3 ?   -2.3   0.0      0.57   5.1e+03       1       9 [.     142     150 ..     142     150 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.7
                                      EEESSS CS
                               KOW  5 VkVvsG 10
                                      V+V+ G
  gi|242398372|ref|YP_002993796.1| 12 VRVTVG 17
                                      677766 PP

  == domain 2  score: 35.2 bits;  conditional E-value: 8.5e-13
                                       TTSEEEESSSTTTTCEEEEEEEETTTTEEEEE CS
                               KOW   1 pGdhVkVvsGphkGktGkVvkvdqhkvrVfvd 32 
                                       pGd+V+ ++Gp+kG+++kVv+vd+ k+ ++v+
  gi|242398372|ref|YP_002993796.1|  98 PGDIVELIAGPFKGEKAKVVRVDESKDEIVVE 129
                                       8*************************999986 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 0.57
                                       TTSEEEESS CS
                               KOW   1 pGdhVkVvs 9  
                                       +G++V+ +s
  gi|242398372|ref|YP_002993796.1| 142 RGEYVRLIS 150
                                       5999*9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1092.75
//
Query:       gi|242398373|ref|YP_002993797.1|  [L=166]
Description: 50S ribosomal protein L11P [Thermococcus sibiricus MM 739]
Scores for complete 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-24   84.7   1.4    2.9e-24   84.7   1.4    1.9  2  Ribosomal_L11_N  Ribosomal protein L11, N-terminal domain
    2.4e-22   79.2   2.4    4.5e-22   78.3   2.4    1.5  1  Ribosomal_L11    Ribosomal protein L11, RNA binding domain
  ------ inclusion threshold ------
       0.11   12.4   0.4       0.11   12.4   0.4    1.8  2  GTP_EFTU_D4      Elongation factor Tu domain 4


Domain annotation for each model (and alignments):
>> Ribosomal_L11_N  Ribosomal protein L11, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.7   1.4   4.8e-28   2.9e-24       4      65 .]       6      68 ..       2      68 .. 0.93
   2 ?   -1.1   0.0      0.28   1.7e+03      14      28 ..     122     136 ..     111     155 .. 0.70

  Alignments for each domain:
  == domain 1  score: 84.7 bits;  conditional E-value: 4.8e-28
                   Ribosomal_L11_N  4 vvkvvklrvpaGkAtpaPplGpaLGplGlnikkfckefnkaTkdkkglripVkitv.yqdrsf 65
                                      ++++v++ v++GkAtp+PplGpa+GplGln+k++++ +n+aTkd++g+++pVki v   +r+f
  gi|242398373|ref|YP_002993797.1|  6 KKQIVEVLVEGGKATPGPPLGPAIGPLGLNVKQVVDRINEATKDFTGMQVPVKIIVdPVTRQF 68
                                      5699****************************************************7777776 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.28
                   Ribosomal_L11_N  14 aGkAtpaPplGpaLG 28 
                                       + kA++   +G aL+
  gi|242398373|ref|YP_002993797.1| 122 GLKAAAKEVIGTALS 136
                                       557778888888875 PP

>> Ribosomal_L11  Ribosomal protein L11, RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.3   2.4   7.6e-26   4.5e-22       2      70 .]      74     141 ..      73     141 .. 0.97

  Alignments for each domain:
  == domain 1  score: 78.3 bits;  conditional E-value: 7.6e-26
                                       --SHHHHHHHHHTXSSXXSSTTTSXXEEEEHHHHHHHHHHHGGGHTXS.SHHHHHHHHHHHHCTTTEEE CS
                     Ribosomal_L11   2 tPptsylLkkaagiekgsgkpgketvGtvslkqvyeIAkiKksdlnaalsleaavksilgtArsmGikV 70 
                                       tPp+s l+kk++g+ekgs++p + +vG+++++qv++IA++Kk+++ aa  l+aa+k+++gtA smG+++
  gi|242398373|ref|YP_002993797.1|  74 TPPVSQLIKKELGLEKGSSEPTRAIVGNLTMEQVVKIARAKKQQMLAA-GLKAAAKEVIGTALSMGVTI 141
                                       9*****************************************999988.9*****************97 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 ?   12.4   0.4   1.8e-05      0.11      13      80 ..       2      69 ..       1      73 [. 0.83
   2 ?   -1.3   0.1      0.36   2.1e+03      26      26 ..     131     131 ..      99     156 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.8e-05
                                      EETCCCEEEEEEEEEEEEETT-EEEETTE.EEE.EEEEEEETTEEESEEETT-EEEEEEESS-TTTS-- CS
                       GTP_EFTU_D4 13 frrsdpaivGvevlgGvikpgvklikedGrevG.eilqiqdkgkkleeakaGqevaisiegkivGrqik 80
                                      +r+++  iv v v gG+ +pg +l  + G  +G +++q+ d+ ++ ++  +G++v + i  + v rq++
  gi|242398373|ref|YP_002993797.1|  2 KRMTKKQIVEVLVEGGKATPGPPLGPAIG-PLGlNVKQVVDRINEATKDFTGMQVPVKIIVDPVTRQFD 69
                                      689999******************77777.555468888888888888889******998887888876 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.36
                                       E CS
                       GTP_EFTU_D4  26 l 26 
                                       +
  gi|242398373|ref|YP_002993797.1| 131 I 131
                                       2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       724  (0.0403815); expected 358.6 (0.02)
Passed bias filter:                      548  (0.030565); 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: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1077.04
//
Query:       gi|242398374|ref|YP_002993798.1|  [L=221]
Description: 50S ribosomal protein L1P [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-47  161.7   0.2    2.2e-47  161.4   0.2    1.1  1  Ribosomal_L1  Ribosomal protein L1p/L10e family


Domain annotation for each model (and alignments):
>> Ribosomal_L1  Ribosomal protein L1p/L10e family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.4   0.2   1.2e-51   2.2e-47       6     204 .]      26     215 ..      16     215 .. 0.96

  Alignments for each domain:
  == domain 1  score: 161.4 bits;  conditional E-value: 1.2e-51
                                       -SSS--EEEEEEEESSS-TTSGGG--EEEEE-STSTSSCS-EEEEE-HHHHH...HHHHTT..-SEEETCHHHHHHT CS
                      Ribosomal_L1   6 kkkfdesveialnlttkkpkkadqrkpgkipLphplgkevkiclitkdpqaeyakeakeagriakviglkklkkkyk 82 
                                        ++f+++ e+a+nl++++ kk+++r++ +++Lph+ gke ki++i+++  ae    ak+ g    vi++++l++  +
  gi|242398374|ref|YP_002993798.1|  26 PRNFTQTLEVAVNLKDIDLKKPENRFKLEVVLPHGRGKEPKIAVIADGAVAE---AAKKLG--LGVISGEELEELGS 97 
                                       35899***********************************************...99****..************** PP

                                       -HHHHHHTCCH-SEEEEEGGGHHHHHHHCHHHHGGGT-S-ECC..CT.BTS-HHHHHHHHCTTEEEEE-TTTSEEEE CS
                      Ribosomal_L1  83 sfeakrkllkefdlfladdrimpllpklLGkvfgkrkkmPipvltkgtvkedvkkevekalkstvvvrldkgtclsv 159
                                       + +  rk++k++d+f+a   +mp++++ LG+ +g+r+kmP+ v    t++ d+++ ve+++k tv ++l+++  +++
  gi|242398374|ref|YP_002993798.1|  98 NPRTARKIAKNYDFFIAAAPLMPKIGRYLGRYLGPRNKMPVVV--PPTIT-DLTSFVERLKK-TVRIQLKNTPAVHA 170
                                       *******************************************..66777.8**********.************** PP

                                       EEEETTSSHHHHHHHHHHHHHHHHHTSTTTSGSEEEEEEEETTS- CS
                      Ribosomal_L1 160 kvGklsftaeelaeNieavvkalvekvpkkwkniksiylkttmsp 204
                                       +vG+ s+++e++aeN+e+v++a++ k++++ ++iks y+kttm+p
  gi|242398374|ref|YP_002993798.1| 171 PVGTESMEDEKIAENVETVLNAIIGKLERGENQIKSAYIKTTMGP 215
                                       ********************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); 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: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1542.58
//
Query:       gi|242398375|ref|YP_002993799.1|  [L=338]
Description: Acidic ribosomal like protein P0 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-23   82.8   0.2    2.9e-23   81.7   0.2    1.6  1  RL10P_insert   Insertion domain in 60S ribosomal protein L10P
    6.7e-22   77.5   1.1    1.1e-21   76.9   0.3    1.8  2  Ribosomal_L10  Ribosomal protein L10
    1.9e-05   25.2  24.0    0.00016   22.2  16.1    3.9  4  Ribosomal_60s  60s Acidic ribosomal protein
      0.005   16.9   6.2       0.98    9.4   3.5    2.4  2  Trigger_C      Bacterial trigger factor protein (TF) C-termin


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 !   81.7   0.2   6.4e-27   2.9e-23       1      71 []     111     181 ..     111     181 .. 1.00

  Alignments for each domain:
  == domain 1  score: 81.7 bits;  conditional E-value: 6.4e-27
                      RL10P_insert   1 AraGtiAtedviipagplelaPgsiepeLrklglptklkkGkivleedylvckkGetltseqaqlLklLgi 71 
                                       A+aG+ A++dv++pagp+ l Pg+++ e+++lg+p++++kGk+ +++d++v k+Ge++t++ a++L++Lgi
  gi|242398375|ref|YP_002993799.1| 111 AKAGAPAPRDVVVPAGPTPLSPGPLVGEMQALGIPARIEKGKVSIQKDTVVLKAGEIITPQLANILNQLGI 181
                                       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 !   76.9   0.3   2.4e-25   1.1e-21       3      99 ..       5     106 ..       3     107 .. 0.93
   2 ?   -3.3   0.0       2.2   9.9e+03      47      61 ..     150     164 ..     146     166 .. 0.79

  Alignments for each domain:
  == domain 1  score: 76.9 bits;  conditional E-value: 2.4e-25
                                       CCCHCCCCCCCCCCCTTSSEEEEEE-TTS-HHHHHHCCCHHHHHGCEEEEESCCCCCCCCHCCTSS.......SSCG CS
                     Ribosomal_L10   3 kekKeelvkelkellkkyksvvvvdyegltvaqlqelRkklrengaelkvvKntlmrrAleetgee......eklke 73 
                                        e+K++ v+el++ll++y ++++vd+++++++ l ++R++lr++ a l+v +ntl+++Al+++++e      ekl e
  gi|242398375|ref|YP_002993799.1|   5 AEWKKKEVEELTKLLQDYPVIALVDVADVPAYPLSKMRESLRDK-AVLRVSRNTLIELALKKAAQElndsnlEKLIE 80 
                                       69*****************************************9.********************855554444*** PP

                                       CCSSSEEEEEESS-TCHHHHCCCCCH CS
                     Ribosomal_L10  74 llkgpvalvftnedpvalakvleefa 99 
                                       +++g +++++t+ +p++l+k lee +
  gi|242398375|ref|YP_002993799.1|  81 HIQGGTGILVTKINPFKLYKFLEESK 106
                                       **********************9974 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.2
                                       GCEEEEESCCCCCCC CS
                     Ribosomal_L10  47 gaelkvvKntlmrrA 61 
                                       ++++ + K t++ +A
  gi|242398375|ref|YP_002993799.1| 150 KGKVSIQKDTVVLKA 164
                                       378899999999988 PP

>> Ribosomal_60s  60s Acidic ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1       2.8   1.2e+04      29      37 ..       6      14 ..       2      20 .. 0.54
   2 !    5.2   0.0    0.0071        32      16      59 ..      56     116 ..      48     122 .. 0.74
   3 ?   -0.9   0.0      0.57   2.5e+03       4      31 ..     169     196 ..     166     199 .. 0.85
   4 !   22.2  16.1   3.6e-08   0.00016       1      88 []     232     337 ..     232     337 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.8
                                      XXXXXXXXX CS
                     Ribosomal_60s 29 alegkdiee 37
                                      + ++k++ee
  gi|242398375|ref|YP_002993799.1|  6 EWKKKEVEE 14
                                      334444444 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0071
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.................XXXXXXXXXXXX CS
                     Ribosomal_60s  16 veveaarvkllvkalegkdieellangaakla.................aaaaaaaaaaaa 59 
                                        ++ + ++k  +++l++ ++e+l++ ++ +                   + ++a+a a+a+
  gi|242398375|ref|YP_002993799.1|  56 NTLIELALKKAAQELNDSNLEKLIEHIQGGTGilvtkinpfklykfleeSKKPAPAKAGAP 116
                                       566678899999*************999886689999999999999976444444444433 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.57
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                     Ribosomal_60s   4 aenikkvlkaagveveaarvkllvkale 31 
                                       + +++++l++ g+e +++ +kll+++ +
  gi|242398375|ref|YP_002993799.1| 169 TPQLANILNQLGIEPLEVGLKLLAAYEH 196
                                       567899***************9998765 PP

  == domain 4  score: 22.2 bits;  conditional E-value: 3.6e-08
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....................XXXXXXXXXX CS
                     Ribosomal_60s   1 eptaenikkvlkaagveveaarvkllvkalegkdieellangaakla....................aaaaaaaaaa 57 
                                       +pt+++i++++++a+    a+ v++++ ++++++  ++l+++   ++                    + a + aa+ 
  gi|242398375|ref|YP_002993799.1| 232 YPTKQTIEAIIQKAFL--GAKNVAVEAGYITKESAGDILGKAFRIALliaqelpeelldektkellnQQAQVIAAQP 306
                                       69**************..88999999999***********997665599****************965555555555 PP

                                       XXXXXXXXXXXXXXXXXX.XX--SS--.STTT CS
                     Ribosomal_60s  58 aaaaaaaaaeekkkeeeeeEeedddmG.fgLF 88 
                                       ++a++a+++ e+++eee+ Eee+  +G ++LF
  gi|242398375|ref|YP_002993799.1| 307 QPAEEAEEKVEEEEEEEK-EEEEALAGlGALF 337
                                       555555555555555555.7999999999999 PP

>> Trigger_C  Bacterial trigger factor protein (TF) C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0   0.00072       3.2      80     125 ..      39      84 ..      29     108 .. 0.87
   2 !    9.4   3.5   0.00022      0.98      39      85 ..     280     326 ..     255     332 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00072
                                       CCHCHHCHHHHHHHHHHHHHHHHHHHHTT----HHHHHHHHHHHCC CS
                         Trigger_C  80 eelreelkeeAekrVklgLvleeiakeekievteeelkeeleelas 125
                                        ++re+l+++A  rV ++ ++e   k+   e ++ +l++ +e +  
  gi|242398375|ref|YP_002993799.1|  39 SKMRESLRDKAVLRVSRNTLIELALKKAAQELNDSNLEKLIEHIQG 84 
                                       589**************************************98865 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00022
                                       EEE-HHHHHHHHHHHHHHHHHCT...TSSHHCHHHHHCTHCCCHCHH CS
                         Trigger_C  39 idiPeslveeeidrllrqakqqleqqGldleeylelsgsseeelree 85 
                                        ++Pe+l++e +++ll+q++q +++q  + ee +e  ++ eee +ee
  gi|242398375|ref|YP_002993799.1| 280 QELPEELLDEKTKELLNQQAQVIAAQPQPAEEAEEKVEEEEEEEKEE 326
                                       49*********************999888888655555433333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1777  (0.0991132); expected 358.6 (0.02)
Passed bias filter:                     1090  (0.0607954); expected 358.6 (0.02)
Passed Vit filter:                       129  (0.00719505); expected 17.9 (0.001)
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: 0.68u 0.32s 00:00:01.00 Elapsed: 00:00:01.04
# Mc/sec: 982.38
//
Query:       gi|242398376|ref|YP_002993800.1|  [L=104]
Description: Ribosomal protein L7/12 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.5e-21   75.6  20.5    4.2e-21   75.3  20.5    1.1  1  Ribosomal_60s  60s Acidic ribosomal protein
    0.00019   21.6   2.4     0.0002   21.5   1.8    1.4  1  TetR_C_31      Tetracyclin repressor-like, C-terminal domain
  ------ inclusion threshold ------
      0.015   15.5   0.6      0.025   14.8   0.0    1.7  2  PhetRS_B1      Phe-tRNA synthetase beta subunit B1 domain
          1    9.7   9.3        3.6    8.0   7.1    2.0  2  DUF1840        Domain of unknown function (DUF1840)
        2.3    8.7   5.5          3    8.4   5.5    1.3  1  DUF3391        Domain of unknown function (DUF3391)


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 !   75.3  20.5   1.2e-24   4.2e-21       1      88 []      16     103 ..      16     103 .. 0.85

  Alignments for each domain:
  == domain 1  score: 75.3 bits;  conditional E-value: 1.2e-24
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXX. CS
                     Ribosomal_60s   1 eptaenikkvlkaagveveaarvkllvkalegkdieellangaakla.aaaaaaaaaaaaaaaaaaaeekkkeeeee 76 
                                       e+t+e ik+vl+aagvev++arvk+lv+aleg++iee+++++a  +a aa++aaa+aa+a a++a+aee+++eee+ 
  gi|242398376|ref|YP_002993800.1|  16 EITEEGIKSVLQAAGVEVDEARVKALVAALEGVNIEEVIEKAAMPVAvAATPAAAPAAEAPAEEAPAEEEEEEEEK- 91 
                                       79****************************************9776677777777777777777777777777776. PP

                                       XX--SS--.STTT CS
                     Ribosomal_60s  77 EeedddmG.fgLF 88 
                                        ee+  +G ++LF
  gi|242398376|ref|YP_002993800.1|  92 -EEEALAGlGALF 103
                                       .788899999999 PP

>> TetR_C_31  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   1.8   5.6e-08    0.0002      52      91 ..      19      65 ..       7      80 .. 0.71

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 5.6e-08
                                      HHHHHHHHHHHCSS-HHHHHHHHHHHHHHHHHHHHHSG.......TS CS
                         TetR_C_31 52 realaallaalGlpdpeeaarllvaaldGllldrLagp.......aa 91
                                      +e +  +l+a+G++ +e+++ +lvaal+G+ ++ +++        aa
  gi|242398376|ref|YP_002993800.1| 19 EEGIKSVLQAAGVEVDEARVKALVAALEGVNIEEVIEKaampvavAA 65
                                      4567889******77888*****************998333333322 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 ?   14.8   0.0   6.9e-06     0.025       6      43 ..       4      41 ..       3      67 .. 0.77
   2 ?   -2.5   0.7       1.8   6.3e+03      40      43 ..      87      90 ..      78      97 .. 0.44

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 6.9e-06
                         PhetRS_B1  6 vkkeaLfkalgkelteeeledllfefGlElDeiveeee 43
                                      v ++ L++a gke+tee ++ +l   G+E+De+  ++ 
  gi|242398376|ref|YP_002993800.1|  4 VYAALLLHAAGKEITEEGIKSVLQAAGVEVDEARVKAL 41
                                      56778999************************977665 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.8
                         PhetRS_B1 40 eeee 43
                                      eeee
  gi|242398376|ref|YP_002993800.1| 87 EEEE 90
                                      1111 PP

>> DUF1840  Domain of unknown function (DUF1840)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1     0.043   1.6e+02      20      38 ..       6      24 ..       1      46 [. 0.75
   2 ?    8.0   7.1     0.001       3.6      30      77 ..      47      94 ..      27     100 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.043
                           DUF1840 20 akqllkllgkslterGait 38
                                      a  ll+++gk++te+G+ +
  gi|242398376|ref|YP_002993800.1|  6 AALLLHAAGKEITEEGIKS 24
                                      56689999***99999744 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.001
                           DUF1840 30 slterGaitaedlpaaiakLeaaiaaekaeeaeeeeeeeeeekeeeke 77
                                       ++ + +i+++ +p a+a+  aa  a++a ++e+ +eeeeee+e+e+e
  gi|242398376|ref|YP_002993800.1| 47 GVNIEEVIEKAAMPVAVAATPAAAPAAEAPAEEAPAEEEEEEEEKEEE 94
                                      4678889*****************999999988888777665543333 PP

>> DUF3391  Domain of unknown function (DUF3391)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   5.5   0.00083         3      40      98 ..      42      93 ..      15      99 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00083
                           DUF3391 40 ierLrasgiqeVwidtdksdeeelagldvpaaeaaeeakaaeesaeleeekqerperle 98
                                      +++L   +i+eV+   +k ++++     v+a +aa++a++a+++++++ee++e++e++e
  gi|242398376|ref|YP_002993800.1| 42 VAALEGVNIEEVI---EK-AAMPV---AVAATPAAAPAAEAPAEEAPAEEEEEEEEKEE 93
                                      6677777888888...44.33333...33333333333333344444433333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1398  (0.0779742); expected 358.6 (0.02)
Passed bias filter:                      814  (0.0454013); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 649.66
//
Query:       gi|242398377|ref|YP_002993801.1|  [L=156]
Description: DUTPase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-13   50.1   0.0    1.6e-11   44.0   0.0    2.0  1  dUTPase   dUTPase
     0.0055   15.5   0.0       0.51    9.1   0.0    2.5  2  DCD       2'-deoxycytidine 5'-triphosphate deaminase (DCD)


Domain annotation for each model (and alignments):
>> dUTPase  dUTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.0   0.0   1.8e-15   1.6e-11      23     120 ..      49     147 ..      13     151 .. 0.89

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 1.8e-15
                                       SEEEETTEEEEEEEEEEEE--TTEEEEEEE-HHHHHHHEEEEEEEEETTBTSEEEEEEEE-SSS-EEE-TT-EEEEE CS
                           dUTPase  23 dltvkpgetvlvptdisiklpdglaalilpRSglaakglivvpgvidsdyrGevkvvlfnltkkdvkikkgdRiAqL 99 
                                       +l+++p+++ l+ t   +klpd++++ +  RS +a+ gl+     +d  + G++ + +fn+++++v ++  +R+ q+
  gi|242398377|ref|YP_002993801.1|  49 KLVIPPKGHALILTLERVKLPDDVMGDMRLRSTFAREGLLGSFAWVDPGWDGNLTLAFFNSSEEEVILHYEERFVQI 125
                                       578999**********************************9999********************************* PP

                                       EEEEBECGEEEEESST.TTESS CS
                           dUTPase 100 ifariltaeleevetl.kater 120
                                        f r+++++ ++++ + + +++
  gi|242398377|ref|YP_002993801.1| 126 AFHRLEEPSKNPYRGIyQGSQH 147
                                       *****99999988887555555 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 !    9.1   0.0   5.7e-05      0.51      22      47 ..      14      38 ..       2      48 .. 0.76
   2 !    4.5   0.0    0.0014        13     240     358 ..      44     152 ..      40     154 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 5.7e-05
                               DCD 22 eepleeeqiqPaslDLrLgkkayrvr 47
                                       ep++e+ +qPa  DLr+gk+a  v 
  gi|242398377|ref|YP_002993801.1| 14 IEPFNEKSLQPAGYDLRVGKEAM-VN 38
                                      4799****************995.55 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0014
                               DCD 240 akegeklildpdeFYilasreavkvppdlaaemvpfdalvGefRvhYaGffDpGFGlaeaggegsravLevRsrevP 316
                                        +e+ kl++ p+   ++ + e+vk+p d+  +m   ++   e       ++DpG+           +     s e  
  gi|242398377|ref|YP_002993801.1|  44 VEEEGKLVIPPKGHALILTLERVKLPDDVMGDMRLRSTFAREGLLGSFAWVDPGWDG-------NLTLAFFNSSEEE 113
                                       555666888888888888888888888888888655544444333333355555432.......2222233455555 PP

                               DCD 317 FiledgqivgrlvyermaekpealYGeelgsnYqg.qglkLsk 358
                                        il+    + ++ ++r++e +++ Y       Yqg q+lkLsk
  gi|242398377|ref|YP_002993801.1| 114 VILHYEERFVQIAFHRLEEPSKNPYR----GIYQGsQHLKLSK 152
                                       56666777777777777777777774....2355326677776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       258  (0.0143901); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); 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: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 969.93
//
Query:       gi|242398378|ref|YP_002993802.1|  [L=82]
Description: DNA-directed RNA polymerase subunit H [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-31  107.2   0.4    3.1e-31  107.1   0.4    1.0  1  RNA_pol_Rpb5_C  RNA polymerase Rpb5, C-terminal domain
  ------ inclusion threshold ------
      0.071   12.8   0.0      0.089   12.4   0.0    1.2  1  HpaB_N          4-hydroxyphenylacetate 3-hydroxylase N termin


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 !  107.1   0.4   3.4e-35   3.1e-31       3      73 .]       9      79 ..       7      79 .. 0.98

  Alignments for each domain:
  == domain 1  score: 107.1 bits;  conditional E-value: 3.4e-35
                                      -TSSSS--EEEEE-HHHHHHHHHHTT--TTCSS-EETTSHHHHCCT--TTSEEEEEEEETTTEEEEEEEEE CS
                    RNA_pol_Rpb5_C  3 itkHelvPkhevlseeekkellkklkikeeqLPkisksDpvarylglkkGdvvkItrksetageavtYRlV 73
                                      i +H+lvP+h+vls+ee++ellkk++ik++qLP+i++sDp++++l++k+Gd+++I rks+tag + +YR+V
  gi|242398378|ref|YP_002993802.1|  9 IFDHVLVPEHRVLSKEETEELLKKYNIKPSQLPQIKTSDPAVQALDAKPGDIIEIKRKSPTAGVYYYYRIV 79
                                      889*******************************************************************9 PP

>> HpaB_N  4-hydroxyphenylacetate 3-hydroxylase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   9.9e-06     0.089     254     271 ..       4      21 ..       1      22 [. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9.9e-06
                                       -EEEEEEEEEEEEGGGEE CS
                            HpaB_N 254 ndalvvfDdVfVPwerVf 271
                                       +++l++fD+V+VP  rV+
  gi|242398378|ref|YP_002993802.1|   4 KKSLTIFDHVLVPEHRVL 21 
                                       5789*************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       776  (0.0432818); expected 358.6 (0.02)
Passed bias filter:                      641  (0.0357521); 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: 0.47u 0.32s 00:00:00.79 Elapsed: 00:00:00.50
# Mc/sec: 497.42
//
Query:       gi|242398379|ref|YP_002993803.1|  [L=1118]
Description: DNA-directed RNA polymerase subunit B [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   1.1e-131  439.5   0.0   1.7e-131  438.9   0.0    1.3  1  RNA_pol_Rpb2_6  RNA polymerase Rpb2, domain 6
      3e-52  177.1   0.0    4.5e-52  176.5   0.0    1.2  1  RNA_pol_Rpb2_1  RNA polymerase beta subunit
    1.1e-34  119.8   0.0    2.2e-34  118.8   0.0    1.6  1  RNA_pol_Rpb2_2  RNA polymerase Rpb2, domain 2
    7.4e-31  106.4   0.2    1.9e-30  105.1   0.2    1.8  1  RNA_pol_Rpb2_7  RNA polymerase Rpb2, domain 7
    6.6e-30  103.1   0.1    1.3e-29  102.1   0.1    1.5  1  RNA_pol_Rpb2_3  RNA polymerase Rpb2, domain 3
      1e-20   73.8   2.0    2.3e-20   72.7   2.0    1.6  1  RNA_pol_Rpb2_4  RNA polymerase Rpb2, domain 4
      4e-08   33.7   3.7    1.9e-07   31.6   3.7    2.2  1  RNA_pol_Rpb2_5  RNA polymerase Rpb2, domain 5
     0.0099   16.0   0.1      0.031   14.5   0.1    1.8  1  NOB1_Zn_bind    Nin one binding (NOB1) Zn-ribbon like
  ------ inclusion threshold ------
       0.16   12.1   0.7       0.31   11.2   0.7    1.5  1  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 
       0.54    9.8   1.9         24    4.6   0.0    2.5  2  TF_Zn_Ribbon    TFIIB zinc-binding


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 !  438.9   0.0  9.7e-135  1.7e-131       2     390 .]     649    1021 ..     648    1021 .. 0.96

  Alignments for each domain:
  == domain 1  score: 438.9 bits;  conditional E-value: 9.7e-135
                                        HHT-SS-TTB-HHHHHHHHHHGGGB-S---TTTTT---SSEEEESS----SSB-S.TTTTTS........GGGS- CS
                    RNA_pol_Rpb2_6    2 aklapvvehvqspriiiqaamekqalgiyslnkfkrsnqktyllcinqkPlvktgdkveagqvldgpatekgela 76  
                                        a+l+p++eh+ +pr+++ a m+kq+lg+ ++n   r++++ +l++++q Plv+++  +ea++        +++ +
  gi|242398379|ref|YP_002993803.1|  649 ASLVPYPEHNAAPRNTYGAGMAKQSLGLGWANFRIRVDTRGHLMHYPQVPLVNSR-IMEAVG--------FEQRP 714 
                                        7899***************************************************.******........***** PP

                                        SEEEEEBBBS--TTTTTTT-EEEBCHHHHTTTT-EEEEEE..EEE--SSSS-.--.-S--..-....-SS-GGGS CS
                    RNA_pol_Rpb2_6   77 lGqnavVAvmsyeGYniEDaiilnerlvdrdvftsihikeyeveardtklge.eeitrdipnv....seealkkL 146 
                                        +Gqn++VAv+sy+GYn+EDa+i+n+++++r++++s+++++ye e +++ +g+ +++    p+v    +e+ +++L
  gi|242398379|ref|YP_002993803.1|  715 AGQNFIVAVLSYSGYNMEDAVIMNKASIERGLARSTFFRTYEAEEKKYMGGQtDKFEIPDPTVrgflGEKYYRNL 789 
                                        ****************************************999999999999555544444559*********** PP

                                        -TTSB--SS-EEETT-EEE---..B-----...-----------..-B---EE--TT-EEEEEEEEE.......E CS
                    RNA_pol_Rpb2_6  147 dedGivrvgaevkegdilvgkvtkgeteltpeekllraifgekarevkdtslrvksgeegvVdkvkvfsrekgde 221 
                                        dedGi  ++++v+ +d+lv ++  ++ ++ +e++ l a   + +   ++ts+++++geeg++dk+++       +
  gi|242398379|ref|YP_002993803.1|  790 DEDGIAFPESKVQGKDVLVART--SPPRFLEEQTSLGAGILQGR---RETSITMRPGEEGIIDKIII-------T 852 
                                        *********************8..99999988888877766654...79******************.......8 PP

                                        E-TT--EEEEEEEEEEE---TT-BEEETTS---BBEEEB-TTTSEEETTS---SEEE-GGGCHHH-BTTHHHHHH CS
                    RNA_pol_Rpb2_6  222 lkagvnklvkvyvaqkRklqvGDKfasrhGqKGvvslilpqeDmPfledGivvDivlNPlgvPSRmtigqllEtl 296 
                                        ++ +++klvkv+v++ R +++GDKfasrhGqKGv++li+pqeDmP++e+Giv+D+++NP+g+PSRmt+gql+E +
  gi|242398379|ref|YP_002993803.1|  853 ETGDGTKLVKVTVRDLRIPEFGDKFASRHGQKGVIGLIVPQEDMPWTENGIVPDLIVNPHGIPSRMTVGQLIEAI 927 
                                        9999*********************************************************************** PP

                                        HHHCCCSSSS--B--TT-...-HHHHHHHHHTTS-TT-EE-EEETTTS-B-SS-EEB-EEEEEEBS--CCCS--- CS
                    RNA_pol_Rpb2_6  297 lgkaaalegkkvdatvFdgakeeeikelLeeagleasGkevlydGrtGekleaeifvGviYylkLkhlvedKiha 371 
                                         gk+a+l+g+++d+t+F g+ ee+++++Lee g+++sG+ev+ydG+tG+k+ea+ifvGviYy++L+h+v+dK+ha
  gi|242398379|ref|YP_002993803.1|  928 GGKVASLKGRRIDGTAFIGEPEEKLRKELEELGFKHSGREVMYDGITGRKFEADIFVGVIYYQRLHHMVADKLHA 1002
                                        *************************************************************************** PP

                                        -SS--B-TTT--B-SCGGG CS
                    RNA_pol_Rpb2_6  372 RstGpyslltqQPlgGkaq 390 
                                        Rs+Gp+++lt+QP++G+a+
  gi|242398379|ref|YP_002993803.1| 1003 RSRGPVQVLTKQPTEGRAR 1021
                                        *****************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 !  176.5   0.0   2.5e-55   4.5e-52       1     188 [.      26     379 ..      26     393 .. 0.97

  Alignments for each domain:
  == domain 1  score: 176.5 bits;  conditional E-value: 2.5e-55
                                       CTTHHHHHHHHHHHHTHHHHHCTTSSECCHCSSSHCSSSCEEEEEEEEEEESCSSECTTSCEEES.HHHHHHCTSBX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb2_1   1 gLvsqqldSFnkfveqdlekiikeeaaieseeeiqssgeelelkfvsirlgkPvvdesdasereiyPkearlrnltY 77 
                                       gLv+q+ldS+n+f+e+ ++++i e + ++ + +       +e+kf+ +rlg+P ++e+ ++++ +yP +ar+rnltY
  gi|242398379|ref|YP_002993803.1|  26 GLVRQHLDSYNAFIEHGMQEVISEFEGVKPDIPD------FEVKFGRVRLGEPEFQEAHGQRKPLYPIDARIRNLTY 96 
                                       69**********************9999999985......9************************************ PP

                                       EEEEEEEEEEEECCCCTCCEEEEEEEEEEEEEXBTTSTTSSSTTS.HHHHHHTTS.TTS..SSEEETTCEEEEXEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb2_1  78 saplyvklklvvyekdnkeeikeeevyiGelPlMlrskacvlseaseeelvelkEcpldqGGyFiinGtekvivaqe 154
                                       sap+++ +  vv    ++ e+++ ev iGelP+Ml+sk c l+++s+eel++++E+p+d+GGyFiinG+e+viv+ e
  gi|242398379|ref|YP_002993803.1|  97 SAPVFLGMIPVV----KGIEQEPVEVRIGELPVMLKSKICRLYNLSDEELIAHGEDPKDPGGYFIINGSERVIVSIE 169
                                       ************....89*********************************************************** PP

                                       E............................................................................ CS
                                       x............................................................................ RF
                    RNA_pol_Rpb2_1 155 k............................................................................ 155
                                       +                                                                            
  gi|242398379|ref|YP_002993803.1| 170 Dlapnrtlveiderqnryiakcfsyrhgyralitverrkdgllyvsipnvpgvlkfvhimralglesdkeivdavgn 246
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                    RNA_pol_Rpb2_1 156 ............................................................................. 155
                                                                                                                    
  gi|242398379|ref|YP_002993803.1| 247 npevqqvlfdnledasdvqtqeealdyigkrampgqpkeyrlrrahsiidnnllphmgvspedrirkayylgmmalk 323
                                       ***************************************************************************** PP

                                       .......................XHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSS CS
                                       .......................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb2_1 156 .......................laGeLlaslfrvllkklerdvkerlqkslekld 188
                                                              laG+Ll++lfrv++ +l++d++ +l k+ +++ 
  gi|242398379|ref|YP_002993803.1| 324 vtelslglreeddkdhyaskrlkLAGDLLKDLFRVAFGQLVKDMQYQLTKTYQRKG 379
                                       ************************************************99987754 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 !  118.8   0.0   1.2e-37   2.2e-34       2     190 .]     173     346 ..     172     346 .. 0.96

  Alignments for each domain:
  == domain 1  score: 118.8 bits;  conditional E-value: 1.2e-37
                                       TSCEEEEE-SSSSSESSSCCEECCCEEEEECCCCSTSCEEEEECTTSSSEEEHHHHHHHTT--STTHHHHHHTSSST CS
                    RNA_pol_Rpb2_2   2 sngiyvekekdknkisatvtsslisqrgsvlklekdgktliwtriskkrkipivivlkAlglvsdreIlericydse 78 
                                        n+ +ve ++++n+++a++ s+++ +r+++++++++++ l+++ +++    ++v +++Algl sd+eI++++    +
  gi|242398379|ref|YP_002993803.1| 173 PNRTLVEIDERQNRYIAKCFSYRHGYRALITVERRKDGLLYVSIPNVPGVLKFVHIMRALGLESDKEIVDAVG---N 246
                                       69999*****************************************************************999...8 PP

                                       THHHHHHHHHHHHHHCTSSSCHHHHHHHHHCSSTTSSSCCCCCHHHHHHHCHHHHHHHTTTTSSTTTTTSSSTCHH. CS
                    RNA_pol_Rpb2_2  79 dsqlleelleeleekeeiqtqeealdyigkvvalrrgeearlqsareilqkrydlgeigreklnkhlglseslenkr 155
                                       ++++++ l+++le+++++qtqeealdyigk+   ++++e rl++a  i+         +++ l+ h+g+s +   +r
  gi|242398379|ref|YP_002993803.1| 247 NPEVQQVLFDNLEDASDVQTQEEALDYIGKRAMPGQPKEYRLRRAHSII---------DNNLLP-HMGVSPE---DR 310
                                       **********************************************997.........677777.*******...44 PP

                                       ..HHHHHHHHHHHHHHHHTTSSSS--TTSGGGEEEE CS
                    RNA_pol_Rpb2_2 156 .lkaqdilymidrLlslklgrrevDDiDhlgnkRvr 190
                                         ka+++++m+ ++ +l+lg re+DD+Dh++ kR++
  gi|242398379|ref|YP_002993803.1| 311 iRKAYYLGMMALKVTELSLGLREEDDKDHYASKRLK 346
                                       47********************************95 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 !  105.1   0.2   1.1e-33   1.9e-30       1      86 [.    1023    1114 ..    1023    1115 .. 0.98

  Alignments for each domain:
  == domain 1  score: 105.1 bits;  conditional E-value: 1.1e-33
                                        BBEEEEHHHHHHHHHHTBHHHHHHHHTTTTTEEEEEEESSSSSCCCEE......EBTTTTCSSSEEEEEEEHHHH CS
                    RNA_pol_Rpb2_7    1 GGlrfGEMErdaliayGaaalLkerltikSDavevdvcgrckllaaan......eCkivkseekiekveipeafk 69  
                                        GGlrfGEMErd+li++Ga++lL erl+++SD++e+++c++c++la+++      +C+++ +ee+i+kve+++afk
  gi|242398379|ref|YP_002993803.1| 1023 GGLRFGEMERDVLIGHGASMLLVERLLEESDKTEAWICESCGHLAVEDkrrdkiYCPVCGEEENISKVEMSYAFK 1097
                                        9*********************************************99*************************** PP

                                        HHHHHHHHTTBEEEEES CS
                    RNA_pol_Rpb2_7   70 lLlqeLqslgialklll 86  
                                        lLl+e++++gi+++l+l
  gi|242398379|ref|YP_002993803.1| 1098 LLLDEIKAMGIRPSLKL 1114
                                        ************99875 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 !  102.1   0.1   7.3e-33   1.3e-29       1      68 []     422     486 ..     422     486 .. 0.98

  Alignments for each domain:
  == domain 1  score: 102.1 bits;  conditional E-value: 7.3e-33
                    RNA_pol_Rpb2_3   1 qvldrlnplselshlrrvsslrgglskerkttevRdlhpshwGriCpveTPEGencGlvksLallarv 68 
                                       q+ldr+n++s+lshlrrv+s+   ls+e+ ++e+Rdlh +hwGriCp eTPEG+ncGlvk+L+l++++
  gi|242398379|ref|YP_002993803.1| 422 QLLDRTNYMSTLSHLRRVTSP---LSREQPHFEARDLHGTHWGRICPTETPEGPNCGLVKNLSLMSQI 486
                                       89*******************...*****************************************997 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 !   72.7   2.0   1.3e-23   2.3e-20       1      62 []     519     580 ..     519     580 .. 0.99

  Alignments for each domain:
  == domain 1  score: 72.7 bits;  conditional E-value: 1.3e-23
                                       EECTT-BEEE-S-HCCHHHHHHHHCCTTSS-TT-EEEE-TTT--EEEE-SSEEB-EEEEE-S CS
                    RNA_pol_Rpb2_4   1 VfvNGrllGvtrdpkklvetlRelRRkgkiseevsivlnekqkevkiatDgGRvcRPliiVe 62 
                                       V++NG+l+G+++d+ +l++++++ RR+g+ise ++++++e+ +e++i++D+GRv+RPliiVe
  gi|242398379|ref|YP_002993803.1| 519 VYLNGVLVGTYKDGVELINKIKTDRREGRISEVINVAYYEDVREIYINSDEGRVRRPLIIVE 580
                                       9************************************************************8 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 !   31.6   3.7     1e-10   1.9e-07       1      56 [.     601     639 ..     601     641 .. 0.85

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 1e-10
                                       HHHHHHTTSEEEEEHHHHTT--EESSTTTCSST-SSTTTSS--TTSSSST-SEEES CS
                    RNA_pol_Rpb2_5   1 wddLlregvvEylDaeEEetamIamtpedleksreekealeekenskshtyTHcEI 56 
                                       w+dL+r gv+EylDaeEEe+a++a  p +++++                 +TH+EI
  gi|242398379|ref|YP_002993803.1| 601 WSDLIRIGVIEYLDAEEEENAYVATWPWEVTEE-----------------HTHLEI 639
                                       ************************999888665.................455555 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   1.7e-05     0.031       9      41 ..    1058    1094 ..    1052    1106 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.7e-05
                      NOB1_Zn_bind    9 lrChaCfkvt...kdmtkkFCpkCGn.ktLkrvavsv 41  
                                          C +C ++    k+ +k +Cp CG+ +++ +v++s+
  gi|242398379|ref|YP_002993803.1| 1058 WICESCGHLAvedKRRDKIYCPVCGEeENISKVEMSY 1094
                                        57*****988666679*********9889***99986 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 ?   11.2   0.7   0.00017      0.31      17      40 .]    1059    1082 ..    1057    1082 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00017
                     Auto_anti-p27   17 tCpvCgvPLmrdrkggkvyCvaCd 40  
                                         C+ Cg   ++d+ + k+yC++C+
  gi|242398379|ref|YP_002993803.1| 1059 ICESCGHLAVEDKRRDKIYCPVCG 1082
                                        5************77899*****6 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.013        24      11      28 ..    1048    1066 ..    1044    1075 .. 0.82
   2 ?    4.2   3.3     0.017        30       3      28 ..    1060    1084 ..    1059    1091 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.013
                                        CHEETSTTCE.EESSSSBE CS
                      TF_Zn_Ribbon   11 lveDpergel.vCtdCGlV 28  
                                        l+e+ + +e  +C++CG +
  gi|242398379|ref|YP_002993803.1| 1048 LLEESDKTEAwICESCGHL 1066
                                        78888999999*****975 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.017
                                        ETTTTCEECHEETSTTCEEESSSSBE CS
                      TF_Zn_Ribbon    3 CPnCgstnlveDpergelvCtdCGlV 28  
                                        C  Cg+   veD  r  ++C+ CG+ 
  gi|242398379|ref|YP_002993803.1| 1060 CESCGHL-AVEDKRRDKIYCPVCGEE 1084
                                        7778873.399************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.73u 0.31s 00:00:01.04 Elapsed: 00:00:00.50
# Mc/sec: 6769.26
//
Query:       gi|242398380|ref|YP_002993804.1|  [L=905]
Description: DNA-directed RNA polymerase subunit alpha [Thermococcus sibiricus MM 739]
Scores for complete 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-108  361.3   0.0   6.1e-108  360.9   0.0    1.1  1  RNA_pol_Rpb1_1  RNA polymerase Rpb1, domain 1
    7.5e-74  247.5   0.1    1.2e-73  246.8   0.1    1.3  1  RNA_pol_Rpb1_2  RNA polymerase Rpb1, domain 2
    6.3e-39  133.4   0.0    1.1e-38  132.7   0.0    1.4  1  RNA_pol_Rpb1_3  RNA polymerase Rpb1, domain 3
    1.1e-29  102.5   0.0    2.5e-29  101.4   0.0    1.6  1  RNA_pol_Rpb1_4  RNA polymerase Rpb1, domain 4
    3.9e-29  101.9   0.1    7.4e-29  101.0   0.1    1.4  1  RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
  ------ inclusion threshold ------
      0.081   13.1   5.2        9.2    6.6   0.0    3.8  4  zf-RING_7       C4-type zinc ribbon domain
        0.3   11.2   1.8        6.3    6.9   0.4    2.3  2  DZR             Double zinc ribbon
       0.52   10.3   3.4          9    6.4   0.1    3.1  2  ADK_lid         Adenylate kinase, active site lid
       0.83    9.2   3.8        1.3    8.5   0.1    2.8  3  zf-ribbon_3     zinc-ribbon domain
        1.7    8.7   3.2        6.5    6.8   0.4    2.4  2  HypA            Hydrogenase/urease nickel incorporation, meta
        5.3    7.1   6.8        1.3    9.0   0.2    3.1  3  Nudix_N_2       Nudix N-terminal


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 !  360.9   0.0  3.7e-111  6.1e-108       2     312 .]       6     319 ..       5     319 .. 0.94

  Alignments for each domain:
  == domain 1  score: 360.9 bits;  conditional E-value: 3.7e-111
                                       E---EEEEEE--HHHHHHH-SBB--STTSTCSTSSSSBBSSSSSSSSS-SSSSSTSTTTSSTTTT-----EEEEEEC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_1   2 kkikeiqfgiaspeeirkwSvvevtkaetieekslkPeegGllDerlgtidkdleCetCgkkkkeCeghfGhieLak 78 
                                       k i +i+fg++sp+eirk+S++e+t ++t++e+   P +gGl+D rlg+id +l+CetCg ++keC+ghfGhieLa+
  gi|242398380|ref|YP_002993804.1|   6 KVIGSIEFGVLSPQEIRKMSAAEITVPDTYSEDG-YPIDGGLMDRRLGVIDPNLRCETCGANYKECPGHFGHIELAR 81 
                                       6799****************************95.9***************************************** PP

                                       EEE-HHHHHHHHHHCTTCETTTTEBSS-TTSH....HHH..HHHCSSSCCCCHHHHHHHHCCS-BE-SSSSB-EEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_1  79 Pvfhigffklilkilecvckecskllldeekkkllsklk..krekleelkkrlkaieelckkinlcekCgavqpkle 153
                                       Pv+h+gf k+i++ le++c+ec+++ l++e+ + ++ +   ++ +  e+   + +i+++ k+ ++c +Cga q +++
  gi|242398380|ref|YP_002993804.1|  82 PVIHVGFAKTIYRTLESTCRECGRIKLTDEEIEDYFGKLniNEARKSEIDALISEIHKKAKERMVCPHCGAPQFSIK 158
                                       ***************************99865544444412333445667999*****************9999999 PP

                                       EETTEEEEEESSSST..SCEEEE-HHHHHHHHHCSTHHHHHHTTSBTTTB-GGGCCECCEEE--GGGS-BEESSSSS CS
                                       xxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_1 154 eegeklkaalkkske..eekeklsaekvkkllkriededvevlgfkssgsrPewliltvlPVpPpeiRPsvqldggr 228
                                        e  +++ +l++++e  e ++ ++++++++ l++i+d+d+ +lg+++++srPew++ltvlPVpP+++RPs++l++g 
  gi|242398380|ref|YP_002993804.1| 159 FERPTIYWELRTDEEgnEYRHRMMPSEIRDRLEKIPDKDLPLLGLNPENSRPEWMVLTVLPVPPVSVRPSITLESGI 235
                                       9999999999999997677799******************************************************* PP

                                       EEBECCCCHHHHHHHHHHHHHHHHHSSSSSTCHHHHHHHHHHHHHHCC-TTSSSSSEEBSTTSSS--THHHHHTSSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_1 229 rsedDlteklrdiikrNnrLkkaeeegapeliieeekelLQehvatlfdneisglkpatqkskrplkslsqrLkGKe 305
                                       r+edDlt+kl+dii++N rLk+++e+gap+liie+ ++lLQ+hv+t+fdne sg++pa++ks+rplk+l qrLkGKe
  gi|242398380|ref|YP_002993804.1| 236 RAEDDLTHKLVDIIRINARLKQNIEAGAPQLIIEDLWDLLQYHVTTYFDNETSGIPPAKHKSGRPLKTLAQRLKGKE 312
                                       ***************************************************************************** PP

                                       SCCCCCT CS
                                       xxxxxxx RF
                    RNA_pol_Rpb1_1 306 GrfRgnL 312
                                       GrfR+nL
  gi|242398380|ref|YP_002993804.1| 313 GRFRKNL 319
                                       ******9 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 !  246.8   0.1   7.3e-77   1.2e-73       1     166 []     321     487 ..     321     487 .. 0.98

  Alignments for each domain:
  == domain 1  score: 246.8 bits;  conditional E-value: 7.3e-77
                                       SEEESSEEEEEEEEESSS-TTEEEEEHHHHTTSEEEEE-STTTHHHHHHHHHHTTTSSSSEEEEESTTSSEEETTTT CS
                    RNA_pol_Rpb1_2   1 GkrvdysaRsvispdpnlkldevgvPisvakkltvpeivtelnikklrklvengpevyPgasyvkredgsekklkak 77 
                                       Gkrv++saR+vispdp ++++evgvP  va+ ltvpe+vt++n +klrk++ ngpe+yPga+yv++ +g++ +l + 
  gi|242398380|ref|YP_002993804.1| 321 GKRVNFSARTVISPDPMISINEVGVPLIVAMELTVPEKVTDFNLEKLRKMILNGPEKYPGANYVIDPQGRRIRLMES 397
                                       9*************************************************************************999 PP

                                       -S.CHHCCTTTTSEEEEE--TTSEEEEE-SSTTSGGGEEEEEEEEESSSSEEEEGGGHCCCT--SSS-EEEEE--SS CS
                    RNA_pol_Rpb1_2  78 kr.klakelekgdiverhvkdgdvvllNRqPsLhklsimahrvkvlekktlrlnlsvttayNaDFDGDemnlhlpqs 153
                                       +  ++a+ + +g++verh+++gdvvl+NRqPsLh++simahrv+v+++kt+rlnl+v+ +yNaDFDGDemnlh+pq+
  gi|242398380|ref|YP_002993804.1| 398 NLeTIADMIDIGWTVERHLMNGDVVLFNRQPSLHRMSIMAHRVRVMPYKTFRLNLAVCPPYNADFDGDEMNLHVPQT 474
                                       8868************************************************************************* PP

                                       HHHHHHHHHCSBT CS
                    RNA_pol_Rpb1_2 154 eearaEaeelllv 166
                                       eea+aEa+ l+ v
  gi|242398380|ref|YP_002993804.1| 475 EEAQAEARILMEV 487
                                       *********9975 PP

>> RNA_pol_Rpb1_3  RNA polymerase Rpb1, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.7   0.0   6.5e-42   1.1e-38       1     156 [.     490     672 ..     490     673 .. 0.92

  Alignments for each domain:
  == domain 1  score: 132.7 bits;  conditional E-value: 6.5e-42
                                       CSEETTTTEESSS--THHHHHHHHHSSTTEEEEHHHHHHHHHHSSSCCSSSSSSSSSBESS.SEBEEHHHHHHCCCH CS
                    RNA_pol_Rpb1_3   1 nilspqsgkPvigivQDsllGvyllTkedvfidreeaqqllykgvgsdsktvtlrpailkp.kelwtgkqtfsrilp 76 
                                       +ilsp+ g P+ig +QD+++G yllT+e+++++++e++++l+   ++   +++++p+ + +  e w+gk++fs++lp
  gi|242398380|ref|YP_002993804.1| 490 HILSPRYGGPIIGGIQDHISGGYLLTREGAYFTKYEVEHMLMFAGVEV--KELPKPDKVENgIEYWSGKTVFSLLLP 564
                                       7*****************************************997774..6799*******9*************** PP

                                       C..CCCEEEE..SSSS...........................STSEEECSSEEEES--SHHHHSSSSTTSHHHHHH CS
                    RNA_pol_Rpb1_3  77 n..einyerk..neek...........................dgkvlikngelikGvidkkvvgkksqgslihvla 122
                                       +  +i y++k     +                           dg+v+i +g l++G idkk++g  + g+l+++++
  gi|242398380|ref|YP_002993804.1| 565 EnlTIWYRNKlcD--DpsqcepieklieeklipsekevkkvatDGFVYILKGKLLSGAIDKKAYG-REDGELLNIIV 638
                                       *998888887552..2335667888888999999999999*************************.899******** PP

                                       HHCHHHHHHHHHHHHHHHHHHHHHHHCEB-TGGG CS
                    RNA_pol_Rpb1_3 123 keygiketvrfldslqrlgfkyllqsgftigigD 156
                                       +eyg++++++fld++++l++ ++++ gft+gi+D
  gi|242398380|ref|YP_002993804.1| 639 REYGVERARQFLDQVTKLAIWVITHKGFTTGIDD 672
                                       *********************************9 PP

>> RNA_pol_Rpb1_4  RNA polymerase Rpb1, domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.4   0.0   1.5e-32   2.5e-29       2     108 .]     699     804 ..     698     804 .. 0.97

  Alignments for each domain:
  == domain 1  score: 101.4 bits;  conditional E-value: 1.5e-32
                                       HHHCTHTCCHHHTTHCHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTTSHHHHHHHCTSSS-HHHHHHHHTB-EEEEB CS
                    RNA_pol_Rpb1_4   2 eeaerygkledlpgksleelfeakinkilnkardkagkiaskslaasNsiliMvksGaKGsiinisqiagclGqqnv 78 
                                       e++++ g+le+lpgk+lee++e++i+ +l++ard+agk+a+++l  +N+ +iM+k+Ga+G i+ni+q+a++lGqq++
  gi|242398380|ref|YP_002993804.1| 699 EAYKN-GELEPLPGKTLEETLESRIMAVLSEARDNAGKVAERYLGMNNHTVIMAKTGARGKILNITQMAAILGQQSI 774
                                       66777.9**************************************88****************************** PP

                                       TTBSS--SSTSCSSTTSSSSESSTTTSSEE CS
                    RNA_pol_Rpb1_4  79 egkripkgfsgrtlphfkkidespesrGFv 108
                                       +gkr  +g++ r+l hfk  d +++++GF+
  gi|242398380|ref|YP_002993804.1| 775 RGKRLYRGYRSRVLSHFKAGDLGARAKGFI 804
                                       *****************************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 !  101.0   0.1   4.5e-32   7.4e-29       1      66 [.     811     876 ..     811     901 .. 0.91

  Alignments for each domain:
  == domain 1  score: 101.0 bits;  conditional E-value: 4.5e-32
                                       B--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTEEEETTSEEEETTS-EEESSGGGTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_5   1 GLkvkefffhtmggReGLiDtAvkTaesGYlqRrlvkaledvvvkyddtvrnsggeivqflygedg 66 
                                       GL+++e+ffh+mggReGL+DtAv+Ta+sGY+qRrl++al+d+ v+yd+tvr+ +g +vqf ygedg
  gi|242398380|ref|YP_002993804.1| 811 GLTPQEYFFHAMGGREGLVDTAVRTAQSGYMQRRLINALQDLKVDYDGTVRDPTGIVVQFRYGEDG 876
                                       9****************************************************************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 ?   -2.7   0.0       4.3   7.1e+03       9      20 ..      16      27 ..      15      32 .. 0.81
   2 ?    1.2   0.1      0.27   4.4e+02      24      31 ..      58      65 ..      45      65 .. 0.82
   3 ?    5.2   0.1     0.015        24      24      32 ..      98     106 ..      87     106 .. 0.88
   4 ?    6.6   0.0    0.0056       9.2      13      31 ..     133     152 ..     131     152 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 4.3
                                      --CCHHHHHCCS CS
                         zf-RING_7  9 lppqvlselrag 20
                                      l+pq+++++ a+
  gi|242398380|ref|YP_002993804.1| 16 LSPQEIRKMSAA 27
                                      99***9998877 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.27
                                      EE-TTT-- CS
                         zf-RING_7 24 vtCpeCGR 31
                                       +C+ CG+
  gi|242398380|ref|YP_002993804.1| 58 LRCETCGA 65
                                      69****96 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.015
                                       EE-TTT--E CS
                         zf-RING_7  24 vtCpeCGRI 32 
                                        tC eCGRI
  gi|242398380|ref|YP_002993804.1|  98 STCRECGRI 106
                                       69******9 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.0056
                                       HHHHHCCS.TB-EE-TTT-- CS
                         zf-RING_7  13 vlselrag.devvtCpeCGR 31 
                                       ++se++++ +e   Cp+CG+
  gi|242398380|ref|YP_002993804.1| 133 LISEIHKKaKERMVCPHCGA 152
                                       6799977767779*****96 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.4    0.0039       6.3      15      37 ..      60     106 ..      55     113 .. 0.90
   2 ?    3.0   0.0     0.064     1e+02      13      21 ..     145     153 ..     134     160 .. 0.64

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0039
                               DZR  15 CseCgtklkavaa........................edrCpsCgek 37 
                                       C++Cg++ k+ +                         e +C +Cg+ 
  gi|242398380|ref|YP_002993804.1|  60 CETCGANYKECPGhfghielarpvihvgfaktiyrtlESTCRECGRI 106
                                       ********988889******************************986 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.064
                               DZR  13 rfCseCgtk 21 
                                        +C++Cg++
  gi|242398380|ref|YP_002993804.1| 145 MVCPHCGAP 153
                                       356666654 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 ?    2.5   1.0     0.091   1.5e+02       4      28 ..      60     104 ..      58     109 .. 0.61
   2 ?    6.4   0.1    0.0055         9       1      10 [.     144     154 ..     136     164 .. 0.70

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.091
                                       -TTT--EE........ETTTB--S............STTB-TTT- CS
                           ADK_lid   4 CpkCGrsY........hvvfnpPk............veglCDkCG 28 
                                       C+ CG+ Y        h++++ P              e  C +CG
  gi|242398380|ref|YP_002993804.1|  60 CETCGANYkecpghfgHIELARPVihvgfaktiyrtLESTCRECG 104
                                       888999997777777754443333344444444555667777776 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0055
                                       EEE-TTT--.E CS
                           ADK_lid   1 RrvCpkCGr.s 10 
                                       R+vCp CG+  
  gi|242398380|ref|YP_002993804.1| 144 RMVCPHCGApQ 154
                                       77777777644 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.2      0.57   9.3e+02       4      11 ..      59      66 ..      56      69 .. 0.81
   2 ?   -0.7   0.0      0.63     1e+03      17      23 ..      98     104 ..      94     110 .. 0.82
   3 ?    8.5   0.1    0.0008       1.3      17      25 ..     145     153 ..     140     154 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.57
                       zf-ribbon_3  4 rCPnCGap 11
                                      rC  CGa+
  gi|242398380|ref|YP_002993804.1| 59 RCETCGAN 66
                                      89999996 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.63
                       zf-ribbon_3  17 nvCpyCG 23 
                                       ++C  CG
  gi|242398380|ref|YP_002993804.1|  98 STCRECG 104
                                       6799998 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0008
                       zf-ribbon_3  17 nvCpyCGtk 25 
                                       +vCp+CG++
  gi|242398380|ref|YP_002993804.1| 145 MVCPHCGAP 153
                                       689999986 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   0.9     0.038        62      68      97 ..      55     108 ..      46     115 .. 0.80
   2 ?    6.8   0.4     0.004       6.5      69      99 ..      96     157 ..      90     161 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.038
                                       --EEEETTTS-EEECHHHHH........................S-TTTSSS-E CS
                              HypA  68 pvkvrCreCgkefeleekal........................rCpkCgsadv 97 
                                       + ++rC++Cg+++++   ++                        +C +Cg+ ++
  gi|242398380|ref|YP_002993804.1|  55 DPNLRCETCGANYKECPGHFghielarpvihvgfaktiyrtlesTCRECGRIKL 108
                                       67899*****99996542335568899999999999999999999999998765 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.004
                                       -EEEETTTS-EEE.CHHHHH................................S-TTTSSS-EEE CS
                              HypA  69 vkvrCreCgkefe.leekal................................rCpkCgsadvei 99 
                                       ++ +CreCg +++ ++e+ +                                 Cp+Cg+ +++i
  gi|242398380|ref|YP_002993804.1|  96 LESTCRECG-RIKlTDEE-IedyfgklninearkseidaliseihkkakermVCPHCGAPQFSI 157
                                       567899999.55514433.234588899999999999999999999999999*******99887 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.2       1.3   2.2e+03      25      29 ..      60      64 ..      58      68 .. 0.61
   2 ?   -0.5   0.2      0.72   1.2e+03      24      31 ..      99     106 ..      98     107 .. 0.72
   3 ?    9.0   0.2   0.00078       1.3      20      29 ..     142     151 ..     136     152 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.3
                                      ETTTT CS
                         Nudix_N_2 25 CpaCg 29
                                      C+ Cg
  gi|242398380|ref|YP_002993804.1| 60 CETCG 64
                                      55555 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.72
                                       EETTTTEE CS
                         Nudix_N_2  24 vCpaCgti 31 
                                       +C  Cg i
  gi|242398380|ref|YP_002993804.1|  99 TCRECGRI 106
                                       58888877 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.00078
                                       S-EEEETTTT CS
                         Nudix_N_2  20 reRlvCpaCg 29 
                                       +eR vCp+Cg
  gi|242398380|ref|YP_002993804.1| 142 KERMVCPHCG 151
                                       89*******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (905 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.83u 0.36s 00:00:01.19 Elapsed: 00:00:00.58
# Mc/sec: 4723.16
//
Query:       gi|242398381|ref|YP_002993805.1|  [L=397]
Description: DNA-directed RNA polymerase subunit A'' [Thermococcus sibiricus MM 739]
Scores for 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-55  188.1   6.4    4.5e-55  187.0   6.4    1.5  1  RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
    0.00059   20.1   0.5      0.025   14.9   0.1    2.5  2  PG_binding_4    Putative peptidoglycan binding domain
  ------ inclusion threshold ------
      0.085   12.8   1.2        1.7    8.7   0.2    2.7  2  KH_7            KH domain
      0.086   13.2   0.6        2.6    8.4   0.0    2.8  3  DUF4277         Domain of unknown function (DUF4277)
       0.12   12.3   3.0       0.49   10.3   0.0    2.4  2  SMC_ScpA        Segregation and condensation protein ScpA


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 !  187.0   6.4   1.2e-58   4.5e-55      61     265 ..      55     336 ..      20     338 .. 0.86

  Alignments for each domain:
  == domain 1  score: 187.0 bits;  conditional E-value: 1.2e-58
                                       SGGGTSB--TT-BHHHHHHHHHHHHHHCCCSSTTSSTCSSTSSSSSSHHHHHHHHTT-SS-SS-EEEEEB-SSSSSC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_5  61 lygedglvepGeavGiiaaQSiGePgTQltlnTFHfaGvasknvtlGvprlkeilnvskniksksltvllvdeeake 137
                                        + e +lvepGeavG++ aQSiGeP+TQ+tlnTFH+aGva+ nvtlG+pr+ ei+++ kn +++ +tv+l +e+  +
  gi|242398381|ref|YP_002993805.1|  55 QEYEQALVEPGEAVGTVTAQSIGEPSTQMTLNTFHYAGVAEINVTLGLPRIIEIVDARKNPSTPIMTVHLDEEHRYN 131
                                       344666********************************************************************999 PP

                                       HHHCHHHHHHHSE................................................................ CS
                                       xxxxxxxxxxxxx................................................................ RF
                    RNA_pol_Rpb1_5 138 lekakkvkkaiek................................................................ 150
                                        eka +v+k+ie                                                                 
  gi|242398381|ref|YP_002993805.1| 132 SEKALEVAKRIEGttleslarsmtldilnmefvvdidperleksgltmekiqakiersfksaeietegttiiirlkk 208
                                       99999999999999999*********************************************999999998885554 PP

                                       ..............CBTTEEEEEEEEEEEEEEET..................EEEEEEECS--HHHHTTSTTTBETT CS
                                       ..............xxxxxxxxxxxxxxxxxxxx..................xxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_5 151 ..............gikkikrilvkeaekgkeee..................kelvletegvnlsevlkveevvdag 195
                                                     +                  +                  +e+v+ teg n+++vlkv++ vd +
  gi|242398381|ref|YP_002993805.1| 209 aknvstlrrladkvK------------------KhrlkglsgvgktvirkegDEYVIYTEGSNFKQVLKVPG-VDPT 266
                                       443333333333221..................134566666677777777799******************.**** PP

                                       TEEESSHHHHHHHHCHHHHHHHHHHHHHHHHHHTTS---HHHHHHHHHHHTTTSS---SSTTCHCCSSSH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_5 196 eilsndiaeileilgieaarkallkeiqevykvqgvsvndrHlelivdqmtkkgeivavnrsGinkaels 265
                                       ++ +n+i+ei+++lgieaar+a+++ei +++++qg++v+ rH++l++d+mt  g + +++r+Gi  ++ s
  gi|242398381|ref|YP_002993805.1| 267 RTKTNNIHEIAQVLGIEAARNAIIEEIVNTMQEQGLEVDVRHIMLVADMMTIDGVVRPIGRHGIVGTKAS 336
                                       ****************************************************************877765 PP

>> PG_binding_4  Putative peptidoglycan binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1     0.036   1.3e+02      26      69 ..      16      60 ..       3      65 .. 0.78
   2 !   14.9   0.1   6.9e-06     0.025      22      84 ..     138     204 ..     122     209 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.036
                      PG_binding_4 26 rkgnelerlsetiaawk.evdlrvsldeeklkeyldeiakeidte 69
                                      + ++  erl+e++  ++ +++ + +l ++ +++++de+ +e++++
  gi|242398381|ref|YP_002993805.1| 16 KASSLPERLREELFERLiHYSGKYKLKKAEIEAIIDEVVQEYEQA 60
                                      445666788888888888999999******************986 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 6.9e-06
                      PG_binding_4  22 ltygrkgnelerlsetiaawk.evdlrvsldeeklke...yldeiakeidtepkdasfklkggsvkv 84 
                                       ++ +++g +le+l   ++  + +++++v++d e+l++    +++i+++i+++ k a+++++g+++ +
  gi|242398381|ref|YP_002993805.1| 138 VAKRIEGTTLESLARSMTLDIlNMEFVVDIDPERLEKsglTMEKIQAKIERSFKSAEIETEGTTIII 204
                                       567789999999999999999999************95555*********************99977 PP

>> KH_7  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.2   0.00047       1.7       7      57 ..     178     224 ..     173     227 .. 0.89
   2 ?    1.9   0.1     0.059   2.1e+02      24      37 ..     238     251 ..     233     259 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00047
                              KH_7   7 lkekieeklPkevkitdveFEGPelViYtknpklfaengdlirklAkelrk 57 
                                       ++eki+ k+ +  k +++e EG +++i  k  k ++     +r+lA +++k
  gi|242398381|ref|YP_002993805.1| 178 TMEKIQAKIERSFKSAEIETEGTTIIIRLKKAKNVS----TLRRLADKVKK 224
                                       5799***********************999988888....78889988888 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.059
                              KH_7  24 veFEGPelViYtkn 37 
                                       ++ EG e ViYt+ 
  gi|242398381|ref|YP_002993805.1| 238 IRKEGDEYVIYTEG 251
                                       5669********85 PP

>> DUF4277  Domain of unknown function (DUF4277)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0   0.00073       2.6      16      60 ..      41      85 ..      38      97 .. 0.87
   2 ?    1.7   0.0      0.09   3.2e+02      34      84 ..     133     183 ..     121     200 .. 0.71
   3 ?   -2.1   0.1       1.3   4.7e+03      28      61 ..     279     312 ..     273     326 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00073
                           DUF4277 16 idelglaelidelipkksqekvsagevvkalilngLgfvsrpLyl 60
                                      +++ +++ +ide++++ +q+ v++ge+v  +  + +g  s++++l
  gi|242398381|ref|YP_002993805.1| 41 LKKAEIEAIIDEVVQEYEQALVEPGEAVGTVTAQSIGEPSTQMTL 85
                                      578899************************999999988887765 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.09
                           DUF4277  34 qekvsagevvkalilngLgfvsrpLy.lfpeffedkplerLlgegveaehln 84 
                                       ++ +++++ ++   l+ L   s +L  l  ef+ d++ erL ++g++ e++ 
  gi|242398381|ref|YP_002993805.1| 133 EKALEVAKRIEGTTLESL-ARSMTLDiLNMEFVVDIDPERLEKSGLTMEKIQ 183
                                       555666666666666666.355555414469***************999985 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1.3
                           DUF4277  28 lipkksqekvsagevvkalilngLgfvsrpLylf 61 
                                       +++ +  ++    e+v+ +  +gL++  r ++l+
  gi|242398381|ref|YP_002993805.1| 279 VLGIEAARNAIIEEIVNTMQEQGLEVDVRHIMLV 312
                                       5555555555566677777777776666665555 PP

>> SMC_ScpA  Segregation and condensation protein ScpA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00014      0.49      66     124 ..      16      75 ..       7      99 .. 0.82
   2 ?    1.3   0.9     0.077   2.8e+02     100     126 ..     203     228 ..     157     313 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00014
                                       XXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          SMC_ScpA  66 deeleleelrdkLiarLleYr.kykeeaklfkeleaerlksfskarsdleefikeveeva 124
                                           + e lr++L++rL+ Y  kyk +   ++    e ++++ +a ++  e + +v +  
  gi|242398381|ref|YP_002993805.1|  16 KASSLPERLREELFERLIHYSgKYKLKKAEIEAIIDEVVQEYEQALVEPGEAVGTVTAQS 75 
                                       34446799************7699999999999998999999999998888888887755 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.077
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          SMC_ScpA 100 aerlksfskarsdleefikeveevavk 126
                                       + rlk+ +k++s+l +++++v++  +k
  gi|242398381|ref|YP_002993805.1| 203 IIRLKK-AKNVSTLRRLADKVKKHRLK 228
                                       456666.89999999999999996554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1023  (0.0570584); expected 358.6 (0.02)
Passed bias filter:                      678  (0.0378158); 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: 0.71u 0.37s 00:00:01.08 Elapsed: 00:00:00.55
# Mc/sec: 2165.37
//
Query:       gi|242398382|ref|YP_002993806.1|  [L=100]
Description: 50S ribosomal protein L30e [Thermococcus sibiricus MM 739]
Scores for complete 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   69.3   0.0    1.8e-19   69.2   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 !   69.2   0.0     1e-23   1.8e-19       5      94 ..       5      94 ..       1      95 [. 0.94

  Alignments for each domain:
  == domain 1  score: 69.2 bits;  conditional E-value: 1e-23
                                      HHHHHHHHHTEEEESHHHHHHHHHTTTESEEEEETTSSSGGHHHHHHHHHH..HTTEEEEEESCHHHHHHHTTSSSECS CS
                    Ribosomal_L7Ae  5 evlkkakkagklvlGlkevtkalergeaklvilAedvepeekkkllealck..ekevpyvkvkskkeLGelvgkkrpvs 81
                                       +l+ka ++gk+v+G +e++++ + geakl+i+A+++++e k + +++++    ++v+ ++++s  eLG+l+gk++  +
  gi|242398382|ref|YP_002993806.1|  5 FELRKAIETGKVVIGSNETMRLARTGEAKLIIMAKNAPKEVKDD-INYYAGlsSIPVYEFEGTS-VELGTLLGKPFVIA 81
                                      5799****************************************.******7777888889999.************** PP

                                      EEEEEESTTTHHH CS
                    Ribosomal_L7Ae 82 alaikdegdskdl 94
                                       +ai+++g+sk+l
  gi|242398382|ref|YP_002993806.1| 82 LMAIVEPGESKIL 94
                                      ***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.35s 00:00:00.87 Elapsed: 00:00:00.54
# Mc/sec: 560.30
//
Query:       gi|242398383|ref|YP_002993807.1|  [L=145]
Description: NusA like protein [Thermococcus sibiricus MM 739]
Scores for complete 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-20   70.6   6.5    4.1e-16   58.6   1.6    2.2  2  KH_2      KH domain
    1.2e-09   38.1   5.8    2.4e-09   37.2   1.2    2.5  3  KH_5      NusA-like KH domain
    3.3e-07   30.1   3.3    8.5e-05   22.4   0.5    2.2  2  KH_4      KH domain
    4.1e-06   26.5   2.7      0.023   14.5   0.9    2.9  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 !   58.6   1.6     9e-20   4.1e-16       3      75 ..      12      98 ..      10     101 .. 0.91
   2 !   15.0   3.2   3.7e-06     0.017       7      55 ..      80     134 ..      74     142 .. 0.69

  Alignments for each domain:
  == domain 1  score: 58.6 bits;  conditional E-value: 9e-20
                                      HHHHHHHTECETEEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTC..............EE CS
                              KH_2  3 peslaveikkagvskveIertanrviiviresqpgivIGkgGsnikkigkelrkdieklegkk..............Vk 67
                                      +++l++++++a+v ++ I+  +nr++iv++++++g+++Gk+Gsn+k++++ ++kdie +e+++              V+
  gi|242398383|ref|YP_002993807.1| 12 YIALFESLTGATVLDCLIDTIKNRLVIVVKNGEMGLALGKRGSNVKRVQSMIGKDIELIEHSEnpeefikniyktmgVR 90
                                      689****************999*****************************************9999999988888877 PP

                                      EEEEEETT CS
                              KH_2 68 lnivkVkk 75
                                      ++ v++++
  gi|242398383|ref|YP_002993807.1| 91 VKKVHITE 98
                                      77666655 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 3.7e-06
                                       HHHT.ECET..EEEEEEEC.CS.CEEE.EEEEESCHHHHHTGGGHHHHHHHHHHH CS
                              KH_2   7 avei.kkag..vskveIer.ta.nrvi.iviresqpgivIGkgGsnikkigkelr 55 
                                        ++i k  g  v+kv+I + ++ ++v  + +    + ++IGkgG+ni+ +++  +
  gi|242398383|ref|YP_002993807.1|  80 IKNIyKTMGvrVKKVHITEkKNgKKVAlLDVNQRDKPRAIGKGGQNINLVKELME 134
                                       44452433366999999884334444414577888*************9998776 PP

>> KH_5  NusA-like KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.2   1.2   5.3e-13   2.4e-09       3      60 ..      34      85 ..      32      96 .. 0.91
   2 ?   -0.8   0.1      0.38   1.7e+03      26      42 ..      87     105 ..      83     113 .. 0.63
   3 ?    2.9   0.1     0.027   1.2e+02      21      37 ..     117     133 ..     104     144 .. 0.81

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 5.3e-13
                              KH_5  3 ertkvaVkshnpnvdpvGaivgkkGsrikavsseLkgekidvvewseDlaefianals 60
                                      +r +++Vk+++     +G ++gk+Gs++k v s + g+ i+++e se+++efi+n+ +
  gi|242398383|ref|YP_002993807.1| 34 NRLVIVVKNGE-----MGLALGKRGSNVKRVQSMI-GKDIELIEHSENPEEFIKNIYK 85
                                      899********.....*******************.*******************855 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.38
                              KH_5  26 kGsrikav..sseLkgeki 42 
                                       +G r+k+v   ++ +g+k+
  gi|242398383|ref|YP_002993807.1|  87 MGVRVKKVhiTEKKNGKKV 105
                                       6778877611344456666 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.027
                              KH_5  21 aivgkkGsrikavsseL 37 
                                        ++gk+G++i+ v++ +
  gi|242398383|ref|YP_002993807.1| 117 RAIGKGGQNINLVKELM 133
                                       579*******9887755 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.1    0.0004       1.8      28      57 ..      33      62 ..      15      65 .. 0.84
   2 !   22.4   0.5   1.9e-08   8.5e-05       1      55 [.      77     130 ..      77     136 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0004
                              KH_4 28 eveielnvegedlGrvIGkrGrtldAlqyl 57
                                      ++++ + v+  ++G+  GkrG +++  q +
  gi|242398383|ref|YP_002993807.1| 33 KNRLVIVVKNGEMGLALGKRGSNVKRVQSM 62
                                      678999999*************99877766 PP

  == domain 2  score: 22.4 bits;  conditional E-value: 1.9e-08
                              KH_4   1 kelvedilkalvddpeevevteeeeeeeveielnvegedlGrvIGkrGrtldAlq 55 
                                       +e++++i k +    ++v +te+ ++ +++  l+v++ d+ r IGk G++++  +
  gi|242398383|ref|YP_002993807.1|  77 EEFIKNIYKTMGVRVKKVHITEK-KNGKKVALLDVNQRDKPRAIGKGGQNINLVK 130
                                       699*********999*******9.55678999******************98555 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.9     5e-06     0.023       3      41 ..      37      76 ..      35     101 .. 0.85
   2 !   10.6   0.0   8.4e-05      0.38       5      27 ..     109     131 ..     105     135 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5e-06
                                      EEEEGGGHHHHHHTGGGHHHHHHHHHH.T-EEEEES.STT. CS
                              KH_1  3 rilvPsslvgriIGkgGsnIkeIreet.gakIkvpk.sede 41
                                      +i v++  +g+ +Gk+Gsn+k+ ++   g  I +++ se++
  gi|242398383|ref|YP_002993807.1| 37 VIVVKNGEMGLALGKRGSNVKRVQS-MiGKDIELIEhSENP 76
                                      7899999******************.669999999866654 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 8.4e-05
                                       EEGGGHHHHHHTGGGHHHHHHHH CS
                              KH_1   5 lvPsslvgriIGkgGsnIkeIre 27 
                                        v+++  +r IGkgG+nI+  +e
  gi|242398383|ref|YP_002993807.1| 109 DVNQRDKPRAIGKGGQNINLVKE 131
                                       5788888999********97665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       753  (0.041999); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); 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: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 868.07
//
Query:       gi|242398384|ref|YP_002993808.1|  [L=147]
Description: 30S ribosomal protein S12P [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.4e-48  161.4   1.4    6.7e-48  161.0   1.4    1.1  1  Ribosom_S12_S23  Ribosomal protein S12/S23


Domain annotation for each model (and alignments):
>> Ribosom_S12_S23  Ribosomal protein S12/S23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.0   1.4   3.7e-52   6.7e-48       1     114 []      32     146 ..      32     146 .. 0.98

  Alignments for each domain:
  == domain 1  score: 161.0 bits;  conditional E-value: 3.7e-52
                                       --------S-TSSTTSSEEEEEEEEEEEE---TT--S-EEEEEEEET.TSEEEEEEE-SSS..----TT-EEEEEE- CS
                   Ribosom_S12_S23   1 rkelrkktksdalegapqkrGvvlekvtveakkPnsAlRkvvrvrLikngkevtafipgegalnfldEhdevlvrGi 77 
                                       r+ lr+k+ksd+legapq+rG+vlek++veak+Pns +Rk+vrv+Likngk +taf+pg+ga++++dEhdevl++Gi
  gi|242398384|ref|YP_002993808.1|  32 RRVLRLKEKSDPLEGAPQARGIVLEKIAVEAKQPNSGMRKAVRVQLIKNGKVITAFTPGDGAIKHIDEHDEVLIEGI 108
                                       678999*********************************************************************** PP

                                       -......BTTSTTEEEEBETS---TSSSTTTTT----T CS
                   Ribosom_S12_S23  78 rrk.gkavkDlpGvrykvvkvagvslkalskykkekpk 114
                                       +++ g +++D+pG+rykvv v++ slk+ +k+kkekp+
  gi|242398384|ref|YP_002993808.1| 109 GGPkGGSMGDIPGIRYKVVIVNRTSLKEIVKGKKEKPR 146
                                       *998********************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 915.62
//
Query:       gi|242398385|ref|YP_002993809.1|  [L=217]
Description: 30S ribosomal protein S7P [Thermococcus sibiricus MM 739]
Scores for complete 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  132.0   3.6    1.8e-38  131.5   3.6    1.2  1  Ribosomal_S7  Ribosomal protein S7p/S5e
  ------ inclusion threshold ------
       0.14   12.4   0.7       0.38   11.0   0.0    2.0  2  DUF1945       Domain of unknown function (DUF1945)
       0.17   12.2   1.5        7.4    7.0   0.2    2.3  2  Prok-TraM     Prokaryotic Transcriptional repressor TraM


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 !  131.5   3.6   3.1e-42   1.8e-38      17     149 .]      60     217 .]      49     217 .] 0.95

  Alignments for each domain:
  == domain 1  score: 131.5 bits;  conditional E-value: 3.1e-42
                                       STTSBHHHHHHHHHSB....................TTBHHHHHHHHHHHHHHHHHHHSS-HHHHHHHHHHHCS-SE CS
                      Ribosomal_S7  17 kynselveklinklmk....................dGkkslAekivygaldiieektkkdplevleeAlenvkPrv 73 
                                       k n ++ve+link+m+                      kk +A+++v++a++iie+ktk++pl+vl++A+en++Pr+
  gi|242398385|ref|YP_002993809.1|  60 KTNIHIVERLINKVMRsgassykigghfmrrehrslMSKKMKAYEVVKEAFKIIENKTKQNPLQVLVKAIENSSPRE 136
                                       47899************************************************************************ PP

                                       EEEEEBSSSSBEEEEEEE-HHHHHHHHHHHHHHHH...STSSSS-HHHHHHHHHHHHHTT-..SHHHHHHHHHHHHH CS
                      Ribosomal_S7  74 evksrrvGGatyqvpvevrpkRrqalAlrwiieaa...rkrkeksmaekLaeElidAaege..gaavkkreethrmA 145
                                       +++++++GG++y+ +v+++p Rr ++Alr+i+ +a     r++ s ae+LaeE+i+Aa+++  + a++k+ee++r+A
  gi|242398385|ref|YP_002993809.1| 137 DTTNIMFGGVRYHLAVDISPMRRLDVALRNIALGAsakCYRNKVSYAEALAEEIIAAANKDtkSFAYSKKEEIERIA 213
                                       ********************************999888889999****************999************** PP

                                       HHTG CS
                      Ribosomal_S7 146 eanr 149
                                       +++r
  gi|242398385|ref|YP_002993809.1| 214 QSSR 217
                                       *987 PP

>> DUF1945  Domain of unknown function (DUF1945)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   6.4e-05      0.38      23      45 ..      16      38 ..       9      40 .. 0.93
   2 ?   -1.9   0.2      0.69   4.1e+03      33      38 ..     103     108 ..      95     118 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6.4e-05
                                      EEEEEEE-SSS-EEETTEEE-TT CS
                           DUF1945 23 sLkvfhnLsGeevvfeGvkmkPy 45
                                       Lkvf   s eevv e   ++Py
  gi|242398385|ref|YP_002993809.1| 16 DLKVFGRWSVEEVVVEDPSLRPY 38
                                      59********************9 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.69
                                       S-EEET CS
                           DUF1945  33 eevvfe 38 
                                        evv e
  gi|242398385|ref|YP_002993809.1| 103 YEVVKE 108
                                       355555 PP

>> Prok-TraM  Prokaryotic Transcriptional repressor TraM
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.1     0.009        54      38      73 ..      90     122 ..      89     142 .. 0.70
   2 ?    7.0   0.2    0.0012       7.4      32      78 ..     167     214 ..     154     217 .] 0.78

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.009
                                       HHHHHHHHHHHHHHHCHHHSCHHHHTTSCHHSHHHH CS
                         Prok-TraM  38 rehRrllaaaeavyeewvrasadekvseavleelqe 73 
                                       rehR+l+ +  ++ye+   +++  k+ e+  ++   
  gi|242398385|ref|YP_002993809.1|  90 REHRSLMSKKMKAYEV---VKEAFKIIENKTKQNPL 122
                                       89*************9...66666666655555544 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0012
                                       HHHHH.HHHHHHHHHHHHHHHHCHHHSCHHHHTTSCHHSHHHHHHHHH CS
                         Prok-TraM  32 LaisA.IrehRrllaaaeavyeewvrasadekvseavleelqeeYvea 78 
                                       +a +A  + +R+ +  aea+ ee ++a++++  s a  ++   e +++
  gi|242398385|ref|YP_002993809.1| 167 IALGAsAKCYRNKVSYAEALAEEIIAAANKDTKSFAYSKKEEIERIAQ 214
                                       555552477**************9999999888888888777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       688  (0.0383736); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1474.39
//
Query:       gi|242398386|ref|YP_002993810.1|  [L=40]
Description: hypothetical protein TSIB_0395 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       133  (0.00741815); expected 358.6 (0.02)
Passed bias filter:                      106  (0.00591221); expected 358.6 (0.02)
Passed Vit filter:                         2  (0.000111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 293.50
//
Query:       gi|242398387|ref|YP_002993811.1|  [L=139]
Description: hypothetical protein TSIB_0396 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 949.00
//
Query:       gi|242398388|ref|YP_002993812.1|  [L=372]
Description: Phosphodiesterase [Thermococcus sibiricus MM 739]
Scores for 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-47  163.5   0.1    1.2e-47  163.3   0.1    1.0  1  Phosphodiest   Type I phosphodiesterase / nucleotide pyrophos
    2.7e-06   26.9   0.0    2.7e-05   23.6   0.0    2.0  2  Metalloenzyme  Metalloenzyme superfamily
    9.2e-05   22.0   0.0       0.11   11.9   0.0    2.4  2  Sulfatase      Sulfatase


Domain annotation for each model (and alignments):
>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.3   0.1   1.9e-51   1.2e-47       2     356 ..       6     322 ..       5     323 .. 0.86

  Alignments for each domain:
  == domain 1  score: 163.3 bits;  conditional E-value: 1.9e-51
                                       EEEEETT-BTTHHHHHGSTSHHHHHHHHHSEEESEEE-SSS-SHHHHHHHHHHSS-HHHHS--SSSEEETTTTEEEE CS
                      Phosphodiest   2 lvislDGlradlldrlaellpnlaaLakegvsapnlrpvfPtlTfpnhaslvTGlyPgeHGivgNtfydrktgeyvv 78 
                                        +is+DG     l++    +p+l++L ++g+    ++++fPtlT   h+s+vTG  P  HG+v N +ydr ++++v+
  gi|242398388|ref|YP_002993812.1|   6 ALISIDGSGVYNLKH----MPFLSELVEKGFFEV-VESIFPTLTDLVHTSVVTGVPPRIHGVVENGYYDRISDRKVN 77 
                                       699****99999976....************777.****************************************** PP

                                       EETTTTGG.GGGCTTS-HHHHHHHTHTTCEE.EESE...TTTTSEBTTCT.SC.TBHHSBTCT.CSTTSCHHHHHHH CS
                      Phosphodiest  79 fvtededa.prwwqgepiwdtaakarglkaa.alfw...pgsevdystyyylvsetppryleddfnakvpledkvdk 150
                                       f  ++ ++ p+ + + +++++  ++rg+++a + ++   p s+ +++        + p++    fn++  +++   +
  gi|242398388|ref|YP_002993812.1|  78 FYDYEIAFnPHKIITTKTVVDILRERGIRSAsVSGYtmpPFSGTHVR--------IFPPF----FNDDTLYREYGRD 142
                                       ****9999977777777777777777***664555545566666664........34444....3555555555556 PP

                                       HHHHHHHHCHTHSHHHHHCTSSESEEEEEECCCHHHHHHH-TTSHHHHHHHHHHHHHHHHHHHHHHHTTGTTTEEEE CS
                      Phosphodiest 151 avlqtwldaafakvvlekelekpdlllvyleetDtvgHkfGpdspevedalrrvDkaigdLlealderglsaetnii 227
                                       +++++w+ +++ ++  e   +kpdlllv+l ++D ++H +Gp s e  +a+++vD a++ L+e l+++     +++i
  gi|242398388|ref|YP_002993812.1| 143 WRKDRWVLNSALYLYEE---CKPDLLLVHLCSIDGMQHDYGPLSDEAMKAVETVDTALNVLWERLRDE-----YAFI 211
                                       67778888887775555...***********************************************9.....**** PP

                                       EEES---EEEHTTSEEEGGGTSTGGH.GEEEEECBHHS.SSEEEEEESTEEE.CCCTTHHHHHHHHHHTCHHCCHST CS
                      Phosphodiest 228 lvSDHGmadvsddkvielndlleekg.llhlkdegkggakaliainpkarelnrvaeaeaeevyaelkakleelrkk 303
                                       +++DHG++ v  ++ ++l+++l++   +  ++++g       +++++k       ++aeaeevy  lk++       
  gi|242398388|ref|YP_002993812.1| 212 IFADHGQENV--HTWVNLKNYLKKHSiETLRVSSG-----GGVHVYLK-------NPAEAEEVYSILKRA------- 267
                                       **********..***********998544444555.....89******.......***************....... PP

                                       HTTTEEEEEGGGS-GGGCHSTTS-SEEEEE-TTEEEESSTTCS.....SBS-SEE--S CS
                      Phosphodiest 304 egealavylkeaipkrlhykkrapdlvlvadpgwsitskdkpd.....eyeikgthGy 356
                                       +g+ +  ++++ +p  l++ + +++l++ a++g+++ s++  d     ++++kg+hG+
  gi|242398388|ref|YP_002993812.1| 268 PGVKYVFFRED-LPH-LNT-PNSGELIVSAKEGYWFCSHRFCDgikgpSHWVKGMHGS 322
                                       67777777766.996.665.******************9999999999********97 PP

>> Metalloenzyme  Metalloenzyme 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   2.7e-05     128     208 ..     158     240 ..      99     259 .. 0.80
   2 ?    1.1   0.0     0.035   2.1e+02     210     248 .]     333     362 ..     327     362 .. 0.73

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 4.6e-09
                                       .CC.-SEEEEEE-HHHHHHHTT-H..HHHHHHHHHHHHHHHHHHTTS-TTTEEEEEE-SSB--TTTSS......... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx RF
                     Metalloenzyme 128 lsgkfdlvvvniknaDmvGHtgdl..eatiaaieaaDeavkeildaieqvdgilvvtADHgnaedmvkr.dkqplTs 201
                                       ++ k dl++v++   D + H+  +   ++++a+e++D a++ + ++++++   +++ ADHg  + ++    k+ l +
  gi|242398388|ref|YP_002993812.1| 158 EECKPDLLLVHLCSIDGMQHDYGPlsDEAMKAVETVDTALNVLWERLRDEY-AFIIFADHGQENVHTWVnLKNYLKK 233
                                       455678999999999999998654236789****************99887.*********7665544305799999 PP

                                       -----EE CS
                                       xxxxxxx RF
                     Metalloenzyme 202 HtlepVP 208
                                       H++e   
  gi|242398388|ref|YP_002993812.1| 234 HSIETLR 240
                                       9998765 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.035
                                       EEESTT----S--SSHHHHTT-TTEEEEGGGHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme 210 livgkglapdkvkegakfrekggLanvaatllnllglea 248
                                       +++g + a           e+ +L ++a+t+l+++g+e+
  gi|242398388|ref|YP_002993812.1| 333 ILWGFEKA---------NLENPTLYDIAPTILKFFGVEK 362
                                       55555422.........346899*************986 PP

>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   1.8e-05      0.11      23     129 ..      18     137 ..       8     149 .. 0.80
   2 !    8.5   0.0    0.0002       1.2     208     308 ..     147     359 ..     117     360 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.8e-05
                                       SCSSHHHHHHHHTSEEESSEE-SSSSHHHHHHHHHHSS-HHHHTHSSCCSTTT................HHCTTTS- CS
                         Sulfatase  23 tattpnldrlaeeglrftnfysaaplcspsraalltgryphnsgvasntevgg................gglpqtea 83 
                                         ++p+l++l+e+g+         +l+  +  ++ tg +p  +gv++n+ +                  +++  t+ 
  gi|242398388|ref|YP_002993812.1|  18 LKHMPFLSELVEKGFFEVVESIFPTLTDLVHTSVVTGVPPRIHGVVENGYYDRisdrkvnfydyeiafnPHKIITTK 94 
                                       3459999999988875333333335********************99998777************************ PP

                                       HHHHHHHHTT-EEEEEEES-SCCSGGGSHHCCTTTSEEEETSSSCH CS
                         Sulfatase  84 tLpellkeaGYntaaigkwhlgwssrqsvyknrgfdrflgfptgsa 129
                                       t++++l+e+G ++a + ++++ ++s ++    r f  f++  t+++
  gi|242398388|ref|YP_002993812.1|  95 TVVDILRERGIRSASVSGYTMPPFSGTH---VRIFPPFFNDDTLYR 137
                                       ****************999998887766...556666666555555 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0002
                                       H.................................HHHHHHHHHHHHHHHHHHHHHHHHHHTTTGGGEEEEEEESSSS CS
                         Sulfatase 208 r.................................qlleaylnsveyvDdligrvlaaLeenglldntlvvftSDhga 251
                                       r                                  l ++   +ve vD +++ + ++L     +d+  +++++Dhg+
  gi|242398388|ref|YP_002993812.1| 147 RwvlnsalylyeeckpdlllvhlcsidgmqhdygPLSDEAMKAVETVDTALNVLWERL-----RDEYAFIIFADHGQ 218
                                       4455555555555555555555555555555555666677789999999999999999.....99************ PP

                                       CCCG......................................................................... CS
                         Sulfatase 252 slee......................................................................... 255
                                       +                                                                            
  gi|242398388|ref|YP_002993812.1| 219 ENVHtwvnlknylkkhsietlrvssgggvhvylknpaeaeevysilkrapgvkyvffredlphlntpnsgelivsak 295
                                       65448999999999999999999999999999999999999999999999999999999999999999999999999 PP

                                       ................HHTTSSSCTTCSSSHHHHBEEEEEEETTTSHCEEECSEEEGGGHHHHHHHHTT CS
                         Sulfatase 256 ................sngplrggkganayeggtrvPllvwwpgekaprvseelvshiDlfptildlag 308
                                                         ++ +g  g + ++  ++vPl++w+ ++       e  ++ D++ptil+ +g
  gi|242398388|ref|YP_002993812.1| 296 egywfcshrfcdgikgPSHWVKGMHG-SLNKPVIKVPLILWGFEKANL----ENPTLYDIAPTILKFFG 359
                                       99999999998886655555556666.777788889988887555444....44456788888888777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2527.81
//
Query:       gi|242398389|ref|YP_002993813.1|  [L=279]
Description: hypothetical protein TSIB_0398 [Thermococcus sibiricus MM 739]
Scores for complete 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-34  118.2   0.2      3e-34  117.7   0.2    1.2  1  DUF835    Protein of unknown function (DUF835)


Domain annotation for each model (and alignments):
>> DUF835  Protein of unknown function (DUF835)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.7   0.2   1.7e-38     3e-34       9     136 .]     141     267 ..     133     267 .. 0.92

  Alignments for each domain:
  == domain 1  score: 117.7 bits;  conditional E-value: 1.7e-38
                            DUF835   9 keilsdlvkegvkvlaitRenpkkirekvkienvkviwltkveeentvsPtnlekltetivkflkeaekg.vvliDg 84 
                                       +e  ++l + g+k+++itR++p+++++k+++e v+viwl+kve ++++ P+nle+  +++++f+++++    ++iDg
  gi|242398389|ref|YP_002993813.1| 141 YEKCKTLLQ-GRKAIIITRQKPEDLKSKLGVE-VPVIWLAKVEVPDAIHPHNLERFAHELISFMRSEKGPkSIIIDG 215
                                       444556666.7******************665.69******************************999778****** PP

                            DUF835  85 leyLvlengFesvlkflltlkDavllkngtlilvidkealeekelalLkref 136
                                       +eyL++engFesv+kfl++lkD+  l++++ ++ +  ealeek++alL ref
  gi|242398389|ref|YP_002993813.1| 216 FEYLMIENGFESVFKFLTSLKDYSTLTDTVTVIPVKREALEEKQYALLLREF 267
                                       ***************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); 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 0.31s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 1637.74
//
Query:       gi|242398390|ref|YP_002993814.1|  [L=434]
Description: hypothetical protein TSIB_0399 [Thermococcus sibiricus MM 739]
Scores for 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-102  343.6   0.0   1.3e-102  343.3   0.0    1.1  1  Nre_N     Archaeal Nre, N-terminal
    5.4e-37  126.1   0.5    8.9e-37  125.4   0.5    1.4  1  Nre_C     Archaeal Nre, C-terminal


Domain annotation for each model (and alignments):
>> Nre_N  Archaeal Nre, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  343.3   0.0  1.4e-106  1.3e-102       1     269 [.      44     309 ..      44     310 .. 0.99

  Alignments for each domain:
  == domain 1  score: 343.3 bits;  conditional E-value: 1.4e-106
                             Nre_N   1 LcglkkcpileklravekakkkisskeleGsspPsvfVGrygYPkVsvgplvppvegdasvldspekwlglsledii 77 
                                       Lcg+++cpile++r +++++++i++++++GsspPs+fVG+ygYPkV++gplvpp+eg++s+ldsp kw +++++di+
  gi|242398390|ref|YP_002993814.1|  44 LCGRPTCPILERFRVAKTIEERINRRDIFGSSPPSIFVGEYGYPKVRIGPLVPPIEGNTSHLDSPLKWENKRIKDIL 120
                                       8**************************************************************************** PP

                             Nre_N  78 klrlslvrgekkvkvkkakedklleeiqelalsekpvdvevelekkpkaklkfdevlaPvGpsaeleklkvaenpkv 154
                                        +r+ lv+ge k++v+  k++++l+e+qela+s +pvd+e+ l+k+p  k+  +e+++PvGp+ael +++++enpk+
  gi|242398390|ref|YP_002993814.1| 121 YYRSLLVMGEMKADVNVRKSERILSEVQELAMSVRPVDSEILLKKRPILKVLPSEFAPPVGPKAELLDFELTENPKI 197
                                       ****************9999********************************************************* PP

                             Nre_N 155 prkveklveDtdlkAeeavveLyrsgvdvykiqrlLSvGlLGekkkrrlVPTrWsITAvddivgkelkkeikdlpei 231
                                       p++ +++v+D +lkAe a+++Ly+  +d+y+i rlLS+GlLG   +r+lVPTrWsITAv+d++gk+l+kei ++++i
  gi|242398390|ref|YP_002993814.1| 198 PKRTDYIVND-ELKAETAIMRLYNWSFDEYYIIRLLSAGLLGI--NRKLVPTRWSITAVQDTIGKRLRKEILHYEPI 271
                                       **********.*******************************9..******************************** PP

                             Nre_N 232 devevfsgeylgNrflviLaPgkwsfelvEawapgslw 269
                                       +e+e++ +e+lgNr++viL+P++++fel+E+w +gsl+
  gi|242398390|ref|YP_002993814.1| 272 NEFELYFHEFLGNRYAVILMPETYAFELLEVWLKGSLF 309
                                       ************************************98 PP

>> Nre_C  Archaeal Nre, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.4   0.5   9.9e-41   8.9e-37       1     110 []     321     430 ..     321     430 .. 0.97

  Alignments for each domain:
  == domain 1  score: 125.4 bits;  conditional E-value: 9.9e-41
                             Nre_C   1 egyegrkeyse.iaGaYyaarlavleaLekikrqakvivlreitpeYwaPvGvWqvReavrkalekkpkefesleea 76 
                                       e+++g k+y+e ++GaYyaarl+vle L++++rqa++iv+re+tp+Y+aPvGvWq+R +v+ka+ +++ +f++l+ea
  gi|242398390|ref|YP_002993814.1| 321 EDFRGIKGYAEeTTGAYYAARLSVLESLRQRRRQARIIVFREVTPKYYAPVGVWQIRVGVKKAMGNPVGRFNTLQEA 397
                                       678999*****9***************************************************************** PP

                             Nre_C  77 leevseklklplkkllkkskllkelkkqktLddF 110
                                       l+e+++ l+l+l+k+l+ks +l+   kq+tLd +
  gi|242398390|ref|YP_002993814.1| 398 LNELKKLLELKLEKYLEKSWILQLR-KQRTLDYY 430
                                       **********************986.8***9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2756.16
//
Query:       gi|242398391|ref|YP_002993815.1|  [L=348]
Description: Threonine synthase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-58  198.1   0.0    2.6e-58  197.8   0.0    1.1  1  PALP      Pyridoxal-phosphate dependent enzyme


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.8   0.0   1.4e-62   2.6e-58      20     294 .]      75     342 ..      62     342 .. 0.93

  Alignments for each domain:
  == domain 1  score: 197.8 bits;  conditional E-value: 1.4e-62
                                       CCCEEEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT-EEEEEEETTS-HHHHHH CS
                              PALP  20 lgvplflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaallGlkvtivvpadaspekval 96 
                                        g+++f+KlE+l p+gSfKdRg +  +++lke+ g   v+  ssGN++++lA+  +  G+k+++++p+++s++k++l
  gi|242398391|ref|YP_002993815.1|  75 KGIKVFFKLEYLMPSGSFKDRGTYVTISKLKEN-GINEVTLDSSGNAALSLALFTKSEGIKAHLFIPDHTSEGKKKL 150
                                       3667*****************************.******************************************* PP

                                       HHHTT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHHHTHHHHHHHHTTTTEEEEEEE-SSSHHHHH CS
                              PALP  97 lrllGaevvevggdydeavaaaaelaaegegaylvsqfdnptviegygtiglEileqlggkpdavvvpvGgGgliaG 173
                                       l++l aev+e++g+ +e  ++   + +  e+ +++s++ np+ ieg + +++E++eq+g ++d+   pvG+G+l+ G
  gi|242398391|ref|YP_002993815.1| 151 LKRLEAEVHEIKGSRMEVHKK---AVSF-EKGLYISHWYNPYFIEGTKVAAYEVYEQIG-NVDYAMTPVGSGSLFLG 222
                                       ***********9977777777...3333.6779999999*******************7.***************** PP

                                       HHHHHHH....HSTT.-EEEEEEECTTCGGTTCCS..S.SS..B.SSS.CCSTCS..CGTTCCHHHHSEEEEEEEEE CS
                              PALP 174 iaaglke....rrpd.vrvigvepegsdalarslragrrvtvpvsdtiadglavg..spselafelldrlvdeivtv 243
                                       +++g+ke    ++++ +++i+v+ +g ++l +          ++++ +a+g+a++     e+ +++l+++ +++++v
  gi|242398391|ref|YP_002993815.1| 223 LYKGFKElhilGNSKiPKMIAVQGKGYESLCEKS--------HEESKLAEGIAIPepPRKEQMLKILEETAGTCISV 291
                                       *******998655558*********999999998........56699********9888999*************** PP

                                       EHHHHHHHHHHHHHHHSB-B-HHHHHHHHHH.HHHHHHCCTTCEEEEEEE-B CS
                              PALP 244 sdeealeamrllarregivvepssaaalaal.klreagelkegdrvvviltg 294
                                        dee+ +a+++l   +g +vep+sa+a+ a   l+e g ++ g++v++ ltg
  gi|242398391|ref|YP_002993815.1| 292 GDEEISSALKELT-SMGFLVEPTSATAYGAFkSLLEEGYFETGSKVLIPLTG 342
                                       *************.**********************************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2275.97
//
Query:       gi|242398392|ref|YP_002993816.1|  [L=277]
Description: Uridine phosphorylase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.2e-46  158.9   0.3    1.4e-46  158.6   0.3    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 !  158.6   0.3     8e-51   1.4e-46       1     228 [.      29     250 ..      29     263 .. 0.89

  Alignments for each domain:
  == domain 1  score: 158.6 bits;  conditional E-value: 8e-51
                                       CEEEEESSHHHHHHHHHHEEEEEEEEEE.TTEEEEEEEETTEEEEEEE--SSHHHHH.HHHHHHHHHHC--SEEEEE CS
                         PNP_UDP_1   1 kiaiivgspgevellaespleetpfgregrgfkfvtGtlkgkpvvivstGiGkpnaa.vvaeirllkefgvkaiiri 76 
                                       +++++ g+p++v+ +++   +e +++  +r+++++tG++kg+p+++vstGiG p+aa  + e++++    ++++ir+
  gi|242398392|ref|YP_002993816.1|  29 RYVLLPGDPERVPRISAL-WDEAKEIAFHREYRTHTGKYKGVPISVVSTGIGGPSAAiAIEELAAIG---ADTFIRV 101
                                       5799**************.**************************************6666666666...******* PP

                                       EEEEESSTTT-TT-EEEEEEEEESSSCCGCCTHHCCTCCCCTTSSEE--HHHHHHHHHCHHTTTTTEEEEEEEEESE CS
                         PNP_UDP_1  77 GtaGglnpdlkvGDvvipddainfdgrsplygpkeegqyfpdsydapadpelrallkeaaealgikvhrGvvatadg 153
                                       G+ G+++p++++GD++i+++a++++g+s+        qy++++y+a ad e + +l eaae lg+k+h+G++a++d+
  gi|242398392|ref|YP_002993816.1| 102 GSTGAIQPGIEIGDLIIAKAAVRLEGTSK--------QYVRAEYPASADIEVTLALIEAAETLGVKYHVGITASTDS 170
                                       *****************************........**************************************** PP

                                       SS-CH.............HHHHHHHHHTC-CEEESSHHHHHHHHHHTT--EEEEEEE.....EETTTBETTCTCH.H CS
                         PNP_UDP_1 154 fyaet.............eaelrllrrlgadaveMEtaavaqlArelgipfaairvv.....sdlaaggadaeathe 212
                                       fy  +             ++ +  lr+  + + eME+a +++lA+ +g++++++++v     ++++++++++ea   
  gi|242398392|ref|YP_002993816.1| 171 FYVGQarpgldgyfpsfaKHLIDDLRQAKVTNFEMEAATLYTLANIYGLRAGCVCAVfanriTNEFGKAGEKEA--- 244
                                       *****999999999987777777999999****************************65555555554444444... PP

                                       CCCHHHHHHHHHHHHH CS
                         PNP_UDP_1 213 eveefaqeaaknaaal 228
                                                 + +a  
  gi|242398392|ref|YP_002993816.1| 245 ----------TLVASE 250
                                       ..........443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 1912.44
//
Query:       gi|242398393|ref|YP_002993817.1|  [L=232]
Description: hypothetical protein TSIB_0402 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-31  110.0   3.7    1.5e-31  109.8   3.7    1.0  1  DUF257          Pyrococcus protein of unknown function, DUF25
     0.0077   15.7   0.0      0.018   14.5   0.0    1.6  1  SHNi-TPR        SHNi-TPR
  ------ inclusion threshold ------
      0.095   13.4   0.1          1   10.0   0.0    2.4  2  CdiI_2          CdiI immunity protein
      0.097   12.5   0.5         15    5.5   0.0    2.4  2  Gln-synt_C-ter  Glutamine synthetase C-terminal domain


Domain annotation for each model (and alignments):
>> DUF257  Pyrococcus protein of unknown function, DUF257
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.8   3.7   3.4e-35   1.5e-31       3     203 ..      12     218 ..      10     220 .. 0.90

  Alignments for each domain:
  == domain 1  score: 109.8 bits;  conditional E-value: 3.4e-35
                            DUF257   3 letlrpGetvLiEyssssvpevllyliakysk...eknvPllvdDvlDtllivlkhlkllGldvpe.esikviKigG 75 
                                       l+++r Ge vL+E++ss + ++++ +i++y k   + n  +l+ D+lD l +++ hl+l+G+d +  e+ +viK gG
  gi|242398393|ref|YP_002993817.1|  12 LKKIRKGEDVLVEHTSSEPIHLTFCTIINYVKqrkQRNTKVLLVDILDQLHLLKAHLELAGIDSSFiENLPVIKFGG 88 
                                       799************************988652116899**************************99********** PP

                            DUF257  76 tkevgnvvkkidfdkdpsiylskykravekvsve..etv.inlvlglerllllldn.rrdlyk.lvksikkylgnkn 147
                                       + ++g+++k+i+ ++++si+ ++y  a+++   e  +++ i +v+g+e+l+ l ++ +r+l       i+ +lgn++
  gi|242398393|ref|YP_002993817.1|  89 IIKTGKILKRIELKSEISIWREQYLEALKEFQREedNEFgIRIVVGIEKLIKLYEDdPRALETfFGTIIRPFLGNEK 165
                                       ******************************9887557789***********99865156666645577899****** PP

                            DUF257 148 RkafylinrnllesikPellplLEeiassvieiesekealivrilKslnldivgtt 203
                                       R+ + lin+ l+++     l ++ e  s+   +  ++ ++ +++ Ks++ +  g+t
  gi|242398393|ref|YP_002993817.1| 166 RILVTLINTSLINEEI---LQEFREHSSRSFLVLLSERKIHFQVIKSIDFEDYGKT 218
                                       ************9876...99**9999999999999999*********99988876 PP

>> SHNi-TPR  SHNi-TPR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   4.1e-06     0.018       9      26 ..     104     121 ..     103     121 .. 0.96

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.1e-06
                          SHNi-TPR   9 EislEnenFpqAveDlrk 26 
                                       Eis+++e++ +A++++++
  gi|242398393|ref|YP_002993817.1| 104 EISIWREQYLEALKEFQR 121
                                       9***************96 PP

>> CdiI_2  CdiI immunity protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00023         1      17      62 ..     105     152 ..      97     164 .. 0.86
   2 ?    0.4   0.0      0.23     1e+03      24      40 ..     178     194 ..     169     226 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00023
                            CdiI_2  17 ydlegdsieeiledYvssespeevaelideieellassldee..leea 62 
                                       ++++ +++ e+l+++ ++e++e   +++  ie+l+++++d+   le+ 
  gi|242398393|ref|YP_002993817.1| 105 ISIWREQYLEALKEFQREEDNEFGIRIVVGIEKLIKLYEDDPraLETF 152
                                       68999999*******************************997644443 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.23
                            CdiI_2  24 ieeiledYvssespeev 40 
                                        eeil+++++ +s+  +
  gi|242398393|ref|YP_002993817.1| 178 NEEILQEFREHSSRSFL 194
                                       46777777777665554 PP

>> Gln-synt_C-ter  Glutamine synthetase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0    0.0033        15      58      84 ..      90     116 ..      79     120 .. 0.89
   2 ?    5.0   0.1    0.0046        20      70      92 ..     205     227 ..     162     232 .] 0.69

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0033
                    Gln-synt_C-ter  58 feklgvlseeElesryeillekYvkki 84 
                                       ++  ++l++ El+s   i  e+Y + +
  gi|242398393|ref|YP_002993817.1|  90 IKTGKILKRIELKSEISIWREQYLEAL 116
                                       56679******************9875 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0046
                    Gln-synt_C-ter  70 esryeillekYvkkieiEaktll 92 
                                       +  + i +e+Y k+ +iEa+ l 
  gi|242398393|ref|YP_002993817.1| 205 QVIKSIDFEDYGKTFSIEAQELQ 227
                                       4557899************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); 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: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 1356.75
//
Query:       gi|242398394|ref|YP_002993818.1|  [L=66]
Description: 50S ribosomal protein L40e [Thermococcus sibiricus MM 739]
Scores for complete 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   21.6   3.8     0.0002   20.9   3.8    1.3  1  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
      0.001   18.9   4.8     0.0013   18.6   4.8    1.2  1  Ribosomal_L40e  Ribosomal L40e family
     0.0014   18.6   0.3     0.0015   18.5   0.3    1.2  1  DZR             Double zinc ribbon
     0.0018   17.9   2.5     0.0029   17.3   2.5    1.3  1  zinc_ribbon_2   zinc-ribbon domain
  ------ inclusion threshold ------
      0.024   14.4   1.4        5.1    6.9   0.2    2.2  2  Rubredoxin_2    Rubredoxin metal binding domain
      0.025   15.0   2.0      0.034   14.5   2.0    1.3  1  Toxin_5         Scorpion short toxin
      0.044   13.5   1.1       0.17   11.7   0.0    2.0  2  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal
      0.054   12.9   2.4      0.083   12.3   2.4    1.3  1  zf-ribbon_3     zinc-ribbon domain
      0.068   13.4   0.8        8.4    6.6   0.0    2.1  2  zinc_ribbon_13  Nucleic-acid-binding protein containing Zn-ri
       0.15   12.4   2.6        1.8    8.9   0.2    2.2  2  zf-nanos        Nanos RNA binding domain


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 !   20.9   3.8   1.1e-07    0.0002       1      26 [.      29      51 ..      29      53 .. 0.96

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.1e-07
                                      -B-SSS--B----SSS----SSS--- CS
                    DNA_RNApol_7kD  1 YiCgeCgaevslkkgdpiRCkeCGhR 26
                                      YiC++Cga +  k++   +C++CG++
  gi|242398394|ref|YP_002993818.1| 29 YICMRCGATNPWKAE---KCRKCGYK 51
                                      ***************...******97 PP

>> Ribosomal_L40e  Ribosomal L40e family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   4.8   7.1e-07    0.0013      14      40 ..      26      50 ..      21      59 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 7.1e-07
                    Ribosomal_L40e 14 cdKmiCrkCYArlpprAtnCrkkkCgh 40
                                      ++K iC +C A  p +A +Cr  kCg 
  gi|242398394|ref|YP_002993818.1| 26 FRKYICMRCGATNPWKAEKCR--KCGY 50
                                      579******************..9*96 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.3   8.4e-07    0.0015      27      49 .]      23      49 ..       6      57 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 8.4e-07
                               DZR 27 a....edrCpsCgekvdpearfCpeCG 49
                                      a    ++ C++Cg+ ++ +a+ C +CG
  gi|242398394|ref|YP_002993818.1| 23 ArifrKYICMRCGATNPWKAEKCRKCG 49
                                      245557788888888888888888887 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   2.5   1.6e-06    0.0029       2      22 ..      31      51 ..      30      52 .. 0.95

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.6e-06
                     zinc_ribbon_2  2 CpnCGaelqdnakFCpyCGtp 22
                                      C +CGa+++ +a  C +CG++
  gi|242398394|ref|YP_002993818.1| 31 CMRCGATNPWKAEKCRKCGYK 51
                                      *******************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 ?    6.7   0.1    0.0034         6       1      10 [.      29      38 ..      29      39 .. 0.87
   2 ?    6.9   0.2    0.0028       5.1       3      10 ..      45      52 ..      44      55 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0034
                      Rubredoxin_2  1 YvCsqCGfes 10
                                      Y+C +CG++ 
  gi|242398394|ref|YP_002993818.1| 29 YICMRCGATN 38
                                      99*****985 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0028
                      Rubredoxin_2  3 CsqCGfes 10
                                      C++CG++ 
  gi|242398394|ref|YP_002993818.1| 45 CRKCGYKG 52
                                      ******86 PP

>> Toxin_5  Scorpion short toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   2.0   1.9e-05     0.034       1      18 [.      31      48 ..      31      58 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.9e-05
                           Toxin_5  1 CgPCFTTdpqmeakCreC 18
                                      C+ C  T+p  ++kCr+C
  gi|242398394|ref|YP_002993818.1| 31 CMRCGATNPWKAEKCRKC 48
                                      999**************9 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   9.3e-05      0.17      42      54 .]      24      38 ..       9      38 .. 0.74
   2 ?    0.6   0.3      0.26   4.6e+02      47      52 ..      45      50 ..      43      52 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.3e-05
                    zinc_ribbon_10 42 ev..kyrCpkCgaln 54
                                      ++  ky+C+ Cga+n
  gi|242398394|ref|YP_002993818.1| 24 RIfrKYICMRCGATN 38
                                      33369*******998 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.26
                    zinc_ribbon_10 47 CpkCga 52
                                      C kCg 
  gi|242398394|ref|YP_002993818.1| 45 CRKCGY 50
                                      888886 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   2.4   4.6e-05     0.083       3      25 ..      29      51 ..      27      51 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.6e-05
                       zf-ribbon_3  3 vrCPnCGa.plssddnvCpyCGtk 25
                                      + C +CGa +    + +C +CG+k
  gi|242398394|ref|YP_002993818.1| 29 YICMRCGAtN-PWKAEKCRKCGYK 51
                                      78999*****.***********97 PP

>> zinc_ribbon_13  Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0047       8.4      19      49 ..      12      42 ..       3      44 .. 0.78
   2 ?    6.0   0.4    0.0072        13       2      11 ..      45      54 ..      42      64 .. 0.62

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0047
                    zinc_ribbon_13 19 GsglskifdvqnkkfitvsCknCgYtelYka 49
                                      G +++++ + + + f   +C +Cg t+ +ka
  gi|242398394|ref|YP_002993818.1| 12 GIKMARFPEAEARIFRKYICMRCGATNPWKA 42
                                      5678888888899999999999998876665 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0072
                    zinc_ribbon_13  2 CpKCgnteae 11
                                      C+KCg +  +
  gi|242398394|ref|YP_002993818.1| 45 CRKCGYKGLR 54
                                      5555555444 PP

>> zf-nanos  Nanos RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.2     0.001       1.8      30      43 ..      25      38 ..      24      42 .. 0.89
   2 ?    3.7   0.2      0.04        72      35      48 ..      44      57 ..      40      60 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.001
                          zf-nanos 30 vLrkyvCpiCgatg 43
                                      + rky C  Cgat 
  gi|242398394|ref|YP_002993818.1| 25 IFRKYICMRCGATN 38
                                      579*********96 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.04
                          zf-nanos 35 vCpiCgatgdkAHt 48
                                      +C+ Cg +g +A  
  gi|242398394|ref|YP_002993818.1| 44 KCRKCGYKGLRAKA 57
                                      8********99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.46
# Mc/sec: 432.11
//
Query:       gi|242398395|ref|YP_002993819.1|  [L=107]
Description: Transcription regulator, PadR-like family [Thermococcus sibiricus MM 739]
Scores for complete 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   65.0   0.7    5.8e-18   64.6   0.7    1.2  1  PadR          Transcriptional regulator PadR-like family
      1e-05   26.1   1.6    1.2e-05   25.9   1.6    1.2  1  RTP           Replication terminator protein
    0.00051   20.1   0.0       0.39   10.9   0.0    2.3  2  Mrr_N         Mrr N-terminal domain
     0.0013   18.6   1.4     0.0022   17.8   1.4    1.5  1  DUF3116       Protein of unknown function (DUF3116)
     0.0063   16.7   0.1     0.0093   16.1   0.1    1.4  1  HTH_34        Winged helix DNA-binding domain
     0.0092   14.4   0.9     0.0093   14.4   0.9    1.1  1  DUF505        Protein of unknown function (DUF505)
  ------ inclusion threshold ------
      0.024   14.7   0.0      0.026   14.6   0.0    1.1  1  Replic_Relax  Replication-relaxation
      0.029   14.3   0.2      0.034   14.1   0.2    1.5  1  HTH_45        Winged helix-turn-helix
      0.031   14.1   0.4      0.057   13.3   0.2    1.7  2  HxlR          HxlR-like helix-turn-helix
      0.065   13.0   0.1      0.088   12.6   0.1    1.5  1  DUF4364       Domain of unknown function (DUF4364)
      0.073   13.6   0.0       0.12   12.9   0.0    1.5  1  HTH_27        Winged helix DNA-binding domain


Domain annotation for each model (and alignments):
>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.6   0.7   3.6e-21   5.8e-18       1      75 []      21      94 ..      21      94 .. 0.95

  Alignments for each domain:
  == domain 1  score: 64.6 bits;  conditional E-value: 3.6e-21
                                      HHHHHCCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-S.TSSS-EEEEEESHCCCHHHHH CS
                              PadR  1 iLalleeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglvesewees.gegpprkyYrlTdaGrrelae 75
                                      iL ll+++p+y ye++++++e + g +e+   s Y +L +Le +g+v+sew+es + +p rkyY+lT++G++ l+e
  gi|242398395|ref|YP_002993819.1| 21 ILRLLKDRPMYAYELKNKIRENF-G-FEPATVSSYVVLYKLEHDGYVTSEWQESeTGRPSRKYYKLTEKGEKLLEE 94
                                      89********************7.7.899999**********************888899***********99875 PP

>> RTP  Replication terminator protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   1.6   7.4e-09   1.2e-05       9      92 ..      16      95 ..       8     107 .] 0.83

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 7.4e-09
                                      HHHHHHHHHHHTT-EBCTCHHHHHHHHHTTTT----HHHHHHHHHHHHHTTSEEEEEEEBTSSSSSEEEEEEESS..HH CS
                               RTP  9 FlklylitlvekkklyglklldelkkeFkelgykPnhseiyralhelvedgilkrrkelkekaklqevviYsltdeGke 87
                                       l +y+++l++ +++y+++l ++++++F   g++P+    y  l  l +dg+++ + +   ++ +    +Y+lt++G+ 
  gi|242398395|ref|YP_002993819.1| 16 VLWMYILRLLKDRPMYAYELKNKIRENF---GFEPATVSSYVVLYKLEHDGYVTSEWQES-ETGRPSRKYYKLTEKGEK 90
                                      5779*********************875...**********************9887776.4555666799****9987 PP

                                      HHHHH CS
                               RTP 88 kakly 92
                                       ++  
  gi|242398395|ref|YP_002993819.1| 91 LLEEG 95
                                      66655 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.0    0.0033       5.3       6      38 ..      19      50 ..      15      55 .. 0.89
   2 !   10.9   0.0   0.00024      0.39      69      86 ..      76      93 ..      69      94 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0033
                             Mrr_N  6 lplLealadgsehrlkeirervaerfglseeer 38
                                        +L+ l+d   +   e++++++e+fg+ +  +
  gi|242398395|ref|YP_002993819.1| 19 MYILRLLKDRPMYA-YELKNKIRENFGFEPATV 50
                                      579**********9.************998876 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00024
                             Mrr_N 69 spkrgvwkiTekGrevlk 86
                                      +p+r ++k+TekG ++l+
  gi|242398395|ref|YP_002993819.1| 76 RPSRKYYKLTEKGEKLLE 93
                                      799*************97 PP

>> DUF3116  Protein of unknown function (DUF3116)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   1.4   1.3e-06    0.0022      11      82 ..      20      94 ..       9      98 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.3e-06
                           DUF3116 11 evLelvkdpnftiknlqleeldeksvkkltkneLLytvYWLElkgyilRk....eekannkkrYelTekGellyke 82
                                       +L+l kd  ++  +l+ +  ++   +  t      ++Y LE  gy+  +    e  + ++k+Y+lTekGe+l++e
  gi|242398395|ref|YP_002993819.1| 20 YILRLLKDRPMYAYELKNKIRENFGFEPATVS-SYVVLYKLEHDGYVTSEwqesETGRPSRKYYKLTEKGEKLLEE 94
                                      46666677666666666555544444444443.35689*********97621113445679***********9976 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   5.7e-06    0.0093      33      79 ..      54     102 ..      21     103 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 5.7e-06
                            HTH_34  33 vhlkkLekagYievdk..efkgkkprtllriTpeGreafkkyvkaLksl 79 
                                       v l kLe  gY++ +   +  g+  r  +++T++G +  ++ +k +++l
  gi|242398395|ref|YP_002993819.1|  54 VVLYKLEHDGYVTSEWqeSETGRPSRKYYKLTEKGEKLLEEGIKFIEEL 102
                                       56789*******987511556777899*************999999887 PP

>> DUF505  Protein of unknown function (DUF505)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.9   5.7e-06    0.0093     367     404 ..      53      95 ..       5     102 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.7e-06
                            DUF505 367 reaLysLesfeLiesev..eekg...kevyvlTeyGekvledq 404
                                          Ly+Le  + ++se   +e g   +++y lTe+Gek+le+ 
  gi|242398395|ref|YP_002993819.1|  53 YVVLYKLEHDGYVTSEWqeSETGrpsRKYYKLTEKGEKLLEEG 95 
                                       457************9954555577799************975 PP

>> Replic_Relax  Replication-relaxation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.6e-05     0.026      25      69 ..      49      92 ..      18     104 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.6e-05
                      Replic_Relax 25 a.tarrrLarLrelgllsr.lrkrvggarggsepyvYaLtpkGarll 69
                                      + + + +L +L+  g++++  +++ +g+ +   +  Y Lt+kG++ll
  gi|242398395|ref|YP_002993819.1| 49 TvSSYVVLYKLEHDGYVTSeWQESETGRPS---RKYYKLTEKGEKLL 92
                                      1578899************99999777777...889**********9 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.2   2.1e-05     0.034      51      73 ..      77      99 ..       9     104 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.1e-05
                            HTH_45 51 kskekYvlTekGlelleklkele 73
                                       s + Y+lTekG++lle+  +++
  gi|242398395|ref|YP_002993819.1| 77 PSRKYYKLTEKGEKLLEEGIKFI 99
                                      46789***********9866665 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       2.1   3.3e+03      26      39 ..       7      20 ..       3      32 .. 0.60
   2 ?   13.3   0.2   3.5e-05     0.057      40      73 ..      56      92 ..      18     106 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.1
                                      HHSTTS-HHHHHHH CS
                              HxlR 26 ralpkisqkmLaqr 39
                                      r   ki++++L   
  gi|242398395|ref|YP_002993819.1|  7 RLKEKITKEVLWMY 20
                                      44556777777544 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 3.5e-05
                                      HHHHHHTTSEEEEEESS...SS-EEEEEE-TCGGGGH CS
                              HxlR 40 LreLeqdglierevype...vPpkveYsltekGrsle 73
                                      L +Le+dg +  e  ++    P +  Y+ltekG++l 
  gi|242398395|ref|YP_002993819.1| 56 LYKLEHDGYVTSEWQESetgRPSRKYYKLTEKGEKLL 92
                                      77899999999775543222699***********985 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   5.4e-05     0.088      39      73 ..      55      95 ..      15     105 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.4e-05
                           DUF4364 39 alseLvesglieee.ek.....enktlykiTekGketlelf 73
                                      +l +L+++g++++e ++      ++++yk+TekG++ le+ 
  gi|242398395|ref|YP_002993819.1| 55 VLYKLEHDGYVTSEwQEsetgrPSRKYYKLTEKGEKLLEEG 95
                                      68899999999999655344445679***********9975 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   0.0   7.2e-05      0.12      21      68 .]      35      88 ..      14      88 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.2e-05
                            HTH_27 21 l.adlcgrlnvedshis.y.slkkLtekGLv..ertgdeadrre..krvrlTdkG 68
                                      l   +++   +e +++s y +l kL+  G+v  e +++e+ r +  k ++lT+kG
  gi|242398395|ref|YP_002993819.1| 35 LkNKIRENFGFEPATVSsYvVLYKLEHDGYVtsEWQESETGR-PsrKYYKLTEKG 88
                                      44678888888889999872578********76556665333.368********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); 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:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 718.86
//
Query:       gi|242398396|ref|YP_002993820.1|  [L=99]
Description: hypothetical protein TSIB_0405 [Thermococcus sibiricus MM 739]
Scores for complete 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   52.9   5.9      5e-14   52.5   5.9    1.2  1  FUN14           FUN14 family
  ------ inclusion threshold ------
      0.024   14.7   2.2      0.024   14.7   2.2    2.1  2  SPC12           Microsomal signal peptidase 12 kDa subunit (S
      0.074   13.5   0.5        0.1   13.1   0.4    1.3  1  TMEM107         Transmembrane protein
       0.73    9.9   4.4       0.56   10.3   0.5    2.1  2  Gly-zipper_Omp  Glycine zipper


Domain annotation for each model (and alignments):
>> FUN14  FUN14 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.5   5.9   1.1e-17     5e-14       2      91 .]      13      96 ..      12      96 .. 0.85

  Alignments for each domain:
  == domain 1  score: 52.5 bits;  conditional E-value: 1.1e-17
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             FUN14  2 giGaviGlvtGfalkkvgKlaaiavGggllllqilasqgyikvnwdkiekdveelldrnkdgklgtedeklltenlpfs 80
                                      +iGav+G++tG+alkk+ K++++++G+ ll l  l+++g+i++n d++ + +e+    + +++l+   ++ +   lp +
  gi|242398396|ref|YP_002993820.1| 13 SIGAVVGFITGYALKKFIKIVLTLIGVYLLSLFWLQQKGVITINTDALFNLAES----ATTSTLTL--ADKVVGILPGT 85
                                      79***********************************************88775....22222222..25577789999 PP

                                      xxxxxxxxxxx RF
                             FUN14 81 agFlaGfllGl 91
                                      ++F+aGf+lG+
  gi|242398396|ref|YP_002993820.1| 86 GAFVAGFYLGF 96
                                      *********98 PP

>> SPC12  Microsomal signal peptidase 12 kDa subunit (SPC12)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   2.2   5.3e-06     0.024      18      50 ..      13      45 ..      10      47 .. 0.91
   2 ?    0.5   0.1      0.14   6.4e+02      18      31 ..      81      94 ..      64      96 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.3e-06
                             SPC12 18 vlsaviafivGyitqdlkltlyillagvvltll 50
                                      +++av++fi+Gy+++++   +++l++ ++l+l+
  gi|242398396|ref|YP_002993820.1| 13 SIGAVVGFITGYALKKFIKIVLTLIGVYLLSLF 45
                                      799********************9999999875 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.14
                             SPC12 18 vlsaviafivGyit 31
                                      +l ++ af++G+++
  gi|242398396|ref|YP_002993820.1| 81 ILPGTGAFVAGFYL 94
                                      45567788888875 PP

>> TMEM107  Transmembrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.4   2.2e-05       0.1      65     101 ..      16      52 ..       8      74 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.2e-05
                           TMEM107  65 lisGislfsatlsllsivlHaigavllslfileswsl 101
                                        ++G+ + +a + +++ivl +ig+ llslf+l++  +
  gi|242398396|ref|YP_002993820.1|  16 AVVGFITGYALKKFIKIVLTLIGVYLLSLFWLQQKGV 52 
                                       456666666777*********************9766 PP

>> Gly-zipper_Omp  Glycine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.5   0.00012      0.56      26      41 ..      14      29 ..       7      33 .. 0.85
   2 ?    1.1   0.2     0.092   4.1e+02      20      27 ..      83      90 ..      67      95 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00012
                    Gly-zipper_Omp 26 iGAavGaavGgliGaa 41
                                      iGA+vG + G++  + 
  gi|242398396|ref|YP_002993820.1| 14 IGAVVGFITGYALKKF 29
                                      89*******9998775 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.092
                    Gly-zipper_Omp 20 rgtGaliG 27
                                      +gtGa+++
  gi|242398396|ref|YP_002993820.1| 83 PGTGAFVA 90
                                      24555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       818  (0.0456244); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); 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: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 652.31
//
Query:       gi|242398397|ref|YP_002993821.1|  [L=440]
Description: hypothetical protein TSIB_0406 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0038   17.3  14.8     0.0038   17.3  14.8    4.5  4  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai
     0.0044   16.7   7.5     0.0044   16.7   7.5    4.1  3  MatE             MatE


Domain annotation for each model (and alignments):
>> Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.7      0.12   1.1e+03      93     120 ..      14      45 ..       3      72 .. 0.46
   2 ?   -3.4   5.8       1.1   9.5e+03      14      39 ..     115     140 ..      82     188 .. 0.51
   3 ?   -0.1   3.5     0.097   8.7e+02      85     109 ..     263     288 ..     216     315 .. 0.47
   4 !   17.3  14.8   4.3e-07    0.0038       4     105 ..     305     409 ..     304     432 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.12
                   Polysacc_synt_C  93 kpllaalvmgivvylllllllglllla.....a 120
                                         ++a ++ g+   ++++ +++ +++      a
  gi|242398397|ref|YP_002993821.1|  14 ASIIALALFGAS-RFIYSAVISRRFGVevlgiA 45 
                                       333333333333.44555555555544433320 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.1
                   Polysacc_synt_C  14 lstvlssiLqglgrqkialkalviga 39 
                                       ++ ++ s + gl+r   +++ +++++
  gi|242398397|ref|YP_002993821.1| 115 FQLTFRSFIYGLHRGEVYAYTMILAF 140
                                       22222222222222222222222222 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.097
                   Polysacc_synt_C  85 l...ellrrllkpllaalvmgivvylll 109
                                           e  +r+   +++a++++i+++ l 
  gi|242398397|ref|YP_002993821.1| 263 KrlaESSTRI-LSFFVAIIVFILIL-LG 288
                                       2232222222.33333333333322.22 PP

  == domain 4  score: 17.3 bits;  conditional E-value: 4.3e-07
                   Polysacc_synt_C   4 ilalsiiflsls.tvlssiLqglgrqkialkalvigalvklilnllliplfgivGaaiatvlallvvavlnlyalrr 79 
                                       +lal++i ++++ +++   L++++++k+ + ++++gal+  i+ llli  fg +Ga+ +   ++l++++    + r+
  gi|242398397|ref|YP_002993821.1| 305 YLALMAIETYIAyNPSIVALNSTKYVKYGTFVALFGALASSIFWLLLIAPFGEYGAVGGLFSGYLIILIGTALISRK 381
                                       5788888888888999999********************************************************** PP

                   Polysacc_synt_C  80 llgikl....ellrrllkpllaalvmgivv 105
                                       +lg+++     + +    ++ + ++m+ ++
  gi|242398397|ref|YP_002993821.1| 382 KLGVSFnsyfPFATA--LLFQSLIFMSKIA 409
                                       ******876422222..2333333333331 PP

>> MatE  MatE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   9.2     0.019   1.7e+02       2     106 ..      15     120 ..      14     153 .. 0.74
   2 !   16.7   7.5   4.9e-07    0.0044      27     154 ..     221     343 ..     210     350 .. 0.74
   3 ?   -3.7   0.2      0.94   8.4e+03       1      23 [.     392     414 ..     392     416 .. 0.64

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.019
                              MatE   2 ialenllesllslidtllvgrl.gskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqgli 77 
                                       ++++ +l+  + +i + +++r  g + l+ ++  +s ++l+ ++l ++++al   ++ +l ++   r++ ++  g+ 
  gi|242398397|ref|YP_002993821.1|  15 SIIALALFGASRFIYSAVISRRfGVEVLGIANSLISQAFLIAIPLSFFAVALGKYASEFLAKGEDSRIRSIATWGFS 91 
                                       67888888899999999999999*****************************************9999999998887 PP

                              MatE  78 lllllsliiallvllfseqilslftqdee 106
                                       + +l  li  + ++l     l+ f+ +  
  gi|242398397|ref|YP_002993821.1|  92 FPFLGILIGPFNIYLALLSTLRAFQLTFR 120
                                       76665555555555555555555555555 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 4.9e-07
                              MatE  27 alAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqgl.illlllsliiallvllfseqilslft 102
                                         + vs++ls ++ll++++  + +a+ +l ++ +G+   + +k+ +  ++ il++++++i+++l+ll +e++  +f+
  gi|242398397|ref|YP_002993821.1| 221 VAGIVSASLSSAFLLTYLPQVFQSAVMPLYSYKYGKDEMDYVKRLAESSTrILSFFVAIIVFILILLGREILSIIFG 297
                                       44568889999999999*****************************9888245566666666665555666555665 PP

                              MatE 103 qdeevlelakry.lrililgipalalqlvlsgilrgagktkvplyislislll 154
                                             +l++++ l ++++    ++ ++++  +l++++++k +++++l+++l 
  gi|242398397|ref|YP_002993821.1| 298 F-----NLGNEFyLALMAIE--TYIAYNPSIVALNSTKYVKYGTFVALFGALA 343
                                       4.....45555404444444..4555899999999999999999999999865 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 0.94
                              MatE   1 Pialenllesllslidtllvgrl 23 
                                       P a + l++sl+++  + +++++
  gi|242398397|ref|YP_002993821.1| 392 PFATALLFQSLIFMSKIAVLAGF 414
                                       55667777777777766666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (440 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       704  (0.039266); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.36s 00:00:01.01 Elapsed: 00:00:00.54
# Mc/sec: 2459.56
//
Query:       gi|242398398|ref|YP_002993822.1|  [L=356]
Description: Aminopeptidase P [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-68  230.7   0.8    1.9e-68  230.3   0.8    1.1  1  Peptidase_M24  Metallopeptidase family M24
    3.5e-17   63.3   0.0    6.2e-17   62.5   0.0    1.4  1  Creatinase_N   Creatinase/Prolidase N-terminal domain
  ------ inclusion threshold ------
       0.13   12.5   0.1       0.37   11.0   0.1    1.8  1  Rio2_N         Rio2, N-terminal


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 !  230.3   0.8   3.1e-72   1.9e-68       2     207 ..     139     338 ..     138     340 .. 0.96

  Alignments for each domain:
  == domain 1  score: 230.3 bits;  conditional E-value: 3.1e-72
                                       HHHHHHHHHHHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHTTTCEESSSSEEEEGGGGGSTTTBCSSSB--TTEEEE CS
                     Peptidase_M24   2 lirkaariasaaleavleaikpgvterelaaeieattlkrhgarglafppivasgenaavlhytpndrvlkegdlvl 78 
                                       l++kaa+ia++++ +++++   g +e+++a eie + l+r+ ++g++f piva+genaa +h+tp++r++++gd+v+
  gi|242398398|ref|YP_002993822.1| 139 LMKKAAQIADEVFYEMISRGLDGKSEKQVALEIE-F-LIREKGDGISFAPIVAAGENAANPHHTPSERKIRRGDIVV 213
                                       7***************8886679***********.5.5888899********************************* PP

                                       EEEEEEETTEEEEEEEEEECSSGSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHHHHHTTBCCGBSSCSEE CS
                     Peptidase_M24  79 idagaeydgyasDitrTvlvGkftpeqrelyeavleaqeaaikavkpGvtlseidaaarevlesaglakffphglGH 155
                                       +d+ga+y+gy+sDitrTv++G+ +++ re+ye+v+eaqe+a++ v++G++++e+d +are++ ++g++++f h++GH
  gi|242398398|ref|YP_002993822.1| 214 LDFGAKYRGYCSDITRTVAIGEINEKLREVYEVVREAQERAFQTVREGIRAREVDSVAREYISAKGYGEYFIHRTGH 290
                                       ***************************************************************************** PP

                                       EESSSSSEEEEEESSSTTCSSB--TTBEEEEEEEEEEETTTEEEEEBEEEEE CS
                     Peptidase_M24 156 gvGlevhdegpsvsresndgrkleeGmvftiEpgiyfapgeggvriedtvlv 207
                                       g+Gl+vh+e p++   s+++r+le Gm+ftiEpgiy + + ggvried+v+v
  gi|242398398|ref|YP_002993822.1| 291 GLGLDVHEE-PYIG--SKNERVLERGMTFTIEPGIY-ISQLGGVRIEDDVVV 338
                                       ********9.***9..678*****************.8899**********9 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 !   62.5   0.0     1e-20   6.2e-17      13     132 .]      13     131 ..       3     131 .. 0.88

  Alignments for each domain:
  == domain 1  score: 62.5 bits;  conditional E-value: 1e-20
                                       T-SEEEEECCHHHHHHHSS....-SSSEEEEEEESSCE.EEEEECTTHHHHHHHH.TTSEEEEEST...HSSHHHHH CS
                      Creatinase_N  13 gldallvtspenlrYltGfa.tetgsrglalvvtadga.lllvdalryteaaeesatveevveydd...pvealadl 84 
                                       +++++l+t+ +nl+YltG   + t++r+++lv+++ g+ +l+ ++l+++e++ es      + ++d   p++ l ++
  gi|242398398|ref|YP_002993822.1|  13 EYSGALITPGTNLYYLTGISpQATEERLFLLVINKGGEsTLIAPKLYENEVDWES-----TIFWSDeedPYKLLKKV 84 
                                       5799************************************************999.....44455533367777777 PP

                                       HHHHHHHT-EEEE-TTSSBHHHHHHHHHHCTTSEEEETHHHHHHHHSC CS
                      Creatinase_N  85 lkellesekrvgveldaltvafyealkealpdaelvdaselieelRvv 132
                                       l  l + ++r+ ve++ + ++f+ ++++ l++ elv++s++ +e+R++
  gi|242398398|ref|YP_002993822.1|  85 LTLLNLTSGRILVEDT-MRASFLINIEKLLRNYELVPLSNVTREMRMR 131
                                       77777777*******9.9****************************95 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   6.3e-05      0.37      12      42 ..     106     136 ..      97     160 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6.3e-05
                            Rio2_N  12 LtavEmgmrnhevVptelieeisrlkeeevk 42 
                                       L  +E   rn+e+Vp + +++  r++++e +
  gi|242398398|ref|YP_002993822.1| 106 LINIEKLLRNYELVPLSNVTREMRMRKDEEE 136
                                       6789*********************966543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 2118.04
//
Query:       gi|242398399|ref|YP_002993823.1|  [L=514]
Description: metal-dependent hydrolase with the TIM-barrel fold [Thermococcus sibiricus MM 739]
Scores for 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-113  378.6   0.0     8e-113  378.4   0.0    1.0  1  Amidohydro_3  Amidohydrolase family
      1e-18   67.8   0.0    2.8e-13   49.9   0.0    2.7  2  Amidohydro_1  Amidohydrolase family
  ------ inclusion threshold ------
       0.16   11.4   0.0       0.46    9.9   0.0    1.7  2  AP_endonuc_2  Xylose isomerase-like TIM barrel


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 !  378.4   0.0  1.3e-116    8e-113       1     470 [.      57     511 ..      57     514 .] 0.95

  Alignments for each domain:
  == domain 1  score: 378.4 bits;  conditional E-value: 1.3e-116
                      Amidohydro_3   1 eviDakGrlvlPGFvDsHtHlagggvnlrllrlpdarvtslegvltavrdqagttpkgrwivgeGwdeaqfaeerfp 77 
                                       e+iD++G++ lPGF+DsHtHl + g+ l +l+l++   ts+++ +++++++a+   k++wi+g+Gwd+  +   r+p
  gi|242398399|ref|YP_002993823.1|  57 EIIDLQGKTILPGFIDSHTHLNSLGQSLHMLDLNG--TTSIDEFKEKLKKYAES-VKTTWILGFGWDQEDL--GRYP 128
                                       68*********************************..****************9.9***********9976..6999 PP

                      Amidohydro_3  78 yalaeldevledapvllaaldtHaavrnsaaldlagiteatpdpaggeilrdangegatgllregafhlvldla..p 152
                                        ++ ++dev++d+pv+l++++ Haav+n++a++l g++e  + +               g+++e+a ++v+d +   
  gi|242398399|ref|YP_002993823.1| 129 -TKEDIDEVIKDRPVFLSRTCFHAAVLNTKAIELIGLEEGEDVD------------LERGIVKENALERVRDVInqN 192
                                       .*********************************8888777776............244667777777777777734 PP

                      Amidohydro_3 153 lareaeaaavaaalaalasyGitsveagggnvsslddleplfeltaeeklplrvi...ikelldaaerlglplspgs 226
                                       l++e+++++++ +++ + s+G+ts+   g  + +++ l +l+el+ e+klp+rv    + +ll+  ++lgl+ + gs
  gi|242398399|ref|YP_002993823.1| 193 LTIEDYKQFIEEGAKFALSQGVTSI---GFVSVNEKSLRALLELDSEGKLPIRVFvylNPSLLEELKKLGLTKNIGS 266
                                       4************************...******************************999**************** PP

                      Amidohydro_3 227 eeltigavklfadgvlgsrtalltepyf....tgwpdfedealaelvaaadergldvaihaigdaavddvldafeaa 299
                                       ++++i ++k++adg+lg rta+l++py     +g p++++e+l+ +v +a++ gl++a+haigd ++d+vld +   
  gi|242398399|ref|YP_002993823.1| 267 KRVKIMGIKILADGSLGARTAWLSKPYEdaptSGHPNISKEELETIVQEAQQLGLQMAVHAIGDRTIDMVLDIY--- 340
                                       **************************************************************************... PP

                      Amidohydro_3 300 aekngnqdrrrlehaegvtesqiervaalqvaagvqpvfnfedelldsrlgperargstpvkellnagvkvalgsDa 376
                                        ek g +   r+eha++++e+qier+++l+v  +vqp+f++ d+++++r+g+era++++p++++l++g+++ +g+D+
  gi|242398399|ref|YP_002993823.1| 341 -EKFGEERY-RIEHASIIREDQIERMKKLGVVVSVQPRFVISDWWAVQRVGKERAKWIYPFNSMLKKGIPIGFGTDS 415
                                       .66687855.******************************************************************* PP

                      Amidohydro_3 377 pvgpfdpwprigaavmrktrrgg..evlrpdeelsleealalyTrgpAkalgledrkGtLevGadADlvvldadpld 451
                                       p+++++pw +++aav+r +++g   + ++++e++sleeal+ly  g+A++++ e + GtLe+ + AD+++ d+dp++
  gi|242398399|ref|YP_002993823.1| 416 PIEVVNPWETVYAAVTRGKFEGIetYKYTEEECVSLEEALHLYIYGSAYIMHSENELGTLEEEKLADFIIVDKDPFE 492
                                       *******************98879999************************************************** PP

                      Amidohydro_3 452 vdppelaearvrltvvdGr 470
                                       v++ el++++v + +v+G 
  gi|242398399|ref|YP_002993823.1| 493 VEERELKNIKVLEAYVGGS 511
                                       *****************96 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   2.2e-06     0.013       1      25 [.      65      88 ..      65     116 .. 0.68
   2 !   49.9   0.0   4.6e-17   2.8e-13      28     322 ..     193     498 ..     170     512 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.2e-06
                                      EEEE-EEEEEEECETTECSSS..GHHH CS
                      Amidohydro_1  1 ivlPGlIDaHvHleqsllrga..tled 25
                                      ++lPG+ID+H+Hl+   ++g+  +++d
  gi|242398399|ref|YP_002993823.1| 65 TILPGFIDSHTHLN---SLGQslHMLD 88
                                      69***********7...4455444444 PP

  == domain 2  score: 49.9 bits;  conditional E-value: 4.6e-17
                                       STTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTHHHHHHHH.HHHT.SSSEEEEEEESSEGGS..........GCCC CS
                      Amidohydro_1  28 vppetaaealesgiktalksGtttvadmgattstgiealle.aaee.lplglrilggkvsldr..........gsae 92 
                                       ++ e++++ +e g+k al+ G+t++  ++ + +++++alle  +e  lp+ + +++    l++          gs  
  gi|242398399|ref|YP_002993823.1| 193 LTIEDYKQFIEEGAKFALSQGVTSIGFVSVN-EKSLRALLElDSEGkLPIRVFVYLNPSLLEElkklgltkniGSKR 268
                                       67789999****************9999996.569999999544448999999998877777699995555443333 PP

                                       SHHHHHHHHHHHHHHHHHHCTTTCEE.EEEEE.......CGTCCSHHHHHHHHHHHHHHHTTEEEEEETSSCHHHHH CS
                      Amidohydro_1  93 tskasreklkagaaetikgkadgvvk.valap.......heapafsdeelkealkeakkrdlpvaiHaletkgeved 161
                                       + +  ++ l++g           +   ++l         +++p +s+eel+ +++ea + +l++a+Ha +++ +  +
  gi|242398399|ref|YP_002993823.1| 269 VKIMGIKILADGS---------LGARtAWLSKpyedaptSGHPNISKEELETIVQEAQQLGLQMAVHAIGDRTID-M 335
                                       3333334343333.........22222333221111112578999999********************5544443.5 PP

                                       HHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEE..HH.......HHHHHHHHHHHHCEEHHHHHHHHSEHHH CS
                      Amidohydro_1 162 aeaafgetiehgthlevaeslglldeiklilahgvhlt..pt.......eaellkerlkeagvahcpfsnsilrsgr 229
                                       +++ + +  e+ +  e   s+   d i  + + gv ++  p         + ++ +                 ++ +
  gi|242398399|ref|YP_002993823.1| 336 VLDIYEKFGEERYRIEH-ASIIREDQIERMKKLGVVVSvqPRfvisdwwAVQRVGKE---------------RAKWI 396
                                       55555555566666666.344555788999********5533555555555555555...............99999 PP

                                       HHHHHHHHHTSCEEEEEECTTSSCCGGHHHH.....HHHHHHHHHHCCTT.......TTHCHCHHHHHHHHHTHHHH CS
                      Amidohydro_1 230 ealrkaldeGvkvglgtDgaasgnslnllee.....lrlalklqrgllye.......deegglslkealrmaTingA 294
                                        +++ +l++G+ +g+gtD+     ++  +e+     +       rg+  +       +ee+ +sl+eal ++ ++ A
  gi|242398399|ref|YP_002993823.1| 397 YPFNSMLKKGIPIGFGTDSPIEVVNP--WETvyaavT-------RGKFEGietykytEEEC-VSLEEALHLYIYGSA 463
                                       ******************99666666..444222222.......22222222233436677.*************** PP

                                       HHTT-TTTSSSS-TTSB--EEEECCCT.......C CS
                      Amidohydro_1 295 kalglddkvGsievGkdADlvvvdldi.......l 322
                                        ++  ++++G++e+ k AD+++vd d+       l
  gi|242398399|ref|YP_002993823.1| 464 YIMHSENELGTLEEEKLADFIIVDKDPfeveereL 498
                                       ***********************996656665552 PP

>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0      0.58   3.4e+03      28      39 ..      93     104 ..      45     138 .. 0.59
   2 ?    9.9   0.0   7.8e-05      0.46      22      83 ..     297     368 ..     281     384 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.58
                                       HHHHHHHHHHHH CS
                      AP_endonuc_2  28 eelrelrkalde 39 
                                       + ++e+++ l++
  gi|242398399|ref|YP_002993823.1|  93 TSIDEFKEKLKK 104
                                       334444444444 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 7.8e-05
                                       HHHC....HHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHC....HTTCS..HHHHHHHHHHHHHHHHHHT CS
                      AP_endonuc_2  22 vsel....sdeelrelrkaldelglriaslslftrfgypded....erear..reesvdalkraielaaaLG 83 
                                        ++     s+eel+++ + +++lgl++a++ +  r  + + d     +e+r   e++    +++ie++++LG
  gi|242398399|ref|YP_002993823.1| 297 PTSGhpniSKEELETIVQEAQQLGLQMAVHAIGDRTIDMVLDiyekFGEERyrIEHASIIREDQIERMKKLG 368
                                       3333566799****************************9999999966666653444444445555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (514 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       770  (0.0429472); expected 358.6 (0.02)
Passed bias filter:                      670  (0.0373696); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.46
# Mc/sec: 3329.73
//
Query:       gi|242398400|ref|YP_002993824.1|  [L=300]
Description: Signal recognition particle GTPase [Thermococcus sibiricus MM 739]
Scores for complete 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-77  258.3   0.2    5.6e-77  257.8   0.2    1.2  1  SRP54            SRP54-type protein, GTPase domain
    1.3e-12   47.7   7.6    1.3e-12   47.7   7.6    1.8  1  SRP54_N          SRP54-type protein, helical bundle domain
    2.3e-07   30.7   0.5    3.6e-07   30.1   0.5    1.3  1  AAA_30           AAA domain
    6.7e-06   26.0   3.2      0.005   16.7   0.2    2.4  2  MobB             Molybdopterin guanine dinucleotide synthesis
    1.2e-05   25.0   3.5      0.042   13.4   0.1    3.0  3  Peripla_BP_4     Periplasmic binding protein domain
    1.5e-05   24.1   0.1    3.5e-05   22.9   0.1    1.6  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
    1.9e-05   24.0   0.1    5.4e-05   22.6   0.1    1.7  2  Zeta_toxin       Zeta toxin
    0.00011   22.4   0.0    0.00021   21.4   0.0    1.5  1  AAA_33           AAA domain
    0.00012   22.1   2.4    0.00045   20.3   0.8    2.4  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
    0.00015   22.2   2.3    0.00027   21.4   0.1    2.2  2  AAA_17           AAA domain
    0.00024   20.7   1.3    0.00061   19.4   1.3    1.6  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
     0.0003   20.2   0.0     0.0006   19.2   0.0    1.4  1  VirC1            VirC1 protein
    0.00055   19.7   0.3      0.003   17.3   0.1    2.3  2  Thymidylate_kin  Thymidylate kinase
    0.00055   20.0   3.8     0.0018   18.4   0.6    2.6  2  MMR_HSR1         50S ribosome-binding GTPase
     0.0013   19.0   0.0     0.0027   18.0   0.0    1.5  1  AAA_22           AAA domain
      0.002   17.6   0.0      0.003   17.1   0.0    1.2  1  CbiJ             Precorrin-6x reductase CbiJ/CobK
     0.0027   17.2   2.9      0.009   15.5   0.1    2.4  3  KdpD             Osmosensitive K+ channel His kinase sensor d
     0.0044   16.3   0.0     0.0091   15.3   0.0    1.5  1  6PF2K            6-phosphofructo-2-kinase
     0.0056   16.6   1.2        0.5   10.2   0.6    3.1  3  RsgA_GTPase      RsgA GTPase
     0.0062   16.8   0.1      0.012   15.8   0.1    1.5  1  AAA_28           AAA domain
     0.0074   16.1   0.2       0.62    9.8   0.0    2.3  2  CLP1_P           mRNA cleavage and polyadenylation factor CLP
     0.0082   15.0   1.0       0.11   11.3   0.3    2.2  2  Fe-ADH           Iron-containing alcohol dehydrogenase
     0.0087   16.0   0.3      0.033   14.1   0.0    2.0  2  APS_kinase       Adenylylsulphate kinase
  ------ inclusion threshold ------
      0.015   15.8   0.4       0.41   11.2   0.0    2.6  2  CoA_binding_2    CoA binding domain
      0.015   14.8   0.1      0.031   13.7   0.0    1.6  1  KTI12            Chromatin associated protein KTI12
      0.017   14.9   0.1      0.028   14.2   0.1    1.4  1  DUF2855          Protein of unknown function (DUF2855)
      0.022   14.6   6.8       0.33   10.9   2.8    3.1  2  NTPase_1         NTPase
      0.027   15.0   0.5       0.23   12.0   0.1    2.6  2  ATPgrasp_N       ATP-grasp N-terminal domain
      0.032   14.6   0.2      0.075   13.4   0.2    1.6  1  AAA_19           AAA domain
      0.035   13.3   0.0      0.058   12.6   0.0    1.4  1  PIF1             PIF1-like helicase
      0.042   13.8   0.0       0.19   11.7   0.0    2.0  1  Glyco_transf_4   Glycosyltransferase Family 4
      0.059   12.6   0.0      0.092   12.0   0.0    1.3  1  UvdE             UV-endonuclease UvdE
      0.059   12.8   0.2       0.94    8.8   0.1    2.3  2  ZnuA             Zinc-uptake complex component A periplasmic
      0.063   13.3   0.1          6    6.9   0.1    2.3  2  Glyco_trans_4_2  Glycosyl transferase 4-like
      0.067   12.9   0.3        6.5    6.5   0.1    2.5  2  TPP_enzyme_M     Thiamine pyrophosphate enzyme, central domai
      0.098   11.5   0.0       0.19   10.6   0.0    1.5  1  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
        0.1   12.5   2.3      0.086   12.7   0.5    1.9  2  AAA_31           AAA domain
       0.11   12.9   0.0       0.23   11.8   0.0    1.6  1  AAA_16           AAA ATPase domain
       0.18   11.9   0.2        0.9    9.6   0.2    2.1  1  Torsin           Torsin
        0.2   12.1   0.0       0.41   11.1   0.0    1.6  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
       0.69    9.8   4.5       0.57   10.0   0.1    2.3  2  ATPase_2         ATPase domain predominantly from Archaea


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 !  257.8   0.2   1.3e-79   5.6e-77       1     195 [.     104     298 ..     104     299 .. 0.99

  Alignments for each domain:
  == domain 1  score: 257.8 bits;  conditional E-value: 1.3e-79
                                       SEEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEESSTTSCHHHHHHHHHH CS
                             SRP54   1 pnvillvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvikkkeeadpaavakeave 77 
                                       p vi++vG++G GKTtt+aKLa++lkk+g +v+++a DtfRa+A+eQ++++a+++gv+vik+  ++dpaava++++e
  gi|242398400|ref|YP_002993824.1| 104 PFVIVFVGFNGGGKTTTIAKLANWLKKNGLSVVIAASDTFRAGAIEQVEEHAKRVGVKVIKHGYKSDPAAVAYDSIE 180
                                       579************************************************************************** PP

                                       HHHHTTSSEEEEEE--SSTTHHHHHHHHHHHHHHHSSSEEEEEEETTBHTHHHHHHHHHHHHSSCSEEEEESTTSSS CS
                             SRP54  78 kakeekidvvlvDTaGrlqndkelmeelkkikkvvkpdevllvldattgqeavkqakaFkeavgitgviltklDgda 154
                                       +ak+++idvvlvDTaGr++ +++lm+e+kki++v+kpd v++v d+++g++ ++qa++F+eav+i+gviltklD+da
  gi|242398400|ref|YP_002993824.1| 181 HAKARGIDVVLVDTAGRNELNRNLMDEMKKIARVTKPDLVIFVGDSLAGNAILEQARQFNEAVKIDGVILTKLDADA 257
                                       ***************************************************************************** PP

                                       STTHHHHHHHHHTS-EEEEE-SSSTTGEEE--HHHHHHHHH CS
                             SRP54 155 kgGaalsiaaelklPikfigvGekiedleefdperlvsrll 195
                                       +gG+als++++++ Pi f+g+G+ ++dl +fd+++++++++
  gi|242398400|ref|YP_002993824.1| 258 RGGTALSVSHAIGAPILFVGIGQGYDDLIPFDEKWILEKIF 298
                                       **************************************997 PP

>> SRP54_N  SRP54-type protein, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.7   7.6   3.1e-15   1.3e-12       1      74 [.       5      80 ..       5      81 .. 0.88

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 3.1e-15
                                      HHHHHHHHHHHHCCSSCGHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHCTTS....S-HHHHHHHHHHHH CS
                           SRP54_N  1 LgkklnsalkklsgkskideedleealkeleeaLleaDVgvkvvkklienvkkkavgekk....lkpkqqvkkivkde 74
                                      L++kl+ ++ k   +++i+e+d+e+al++le  LleaDV+++vv++l e++k+k vg +k    ++++  v+++v+d+
  gi|242398400|ref|YP_002993824.1|  5 LKEKLSLFVDK-VAQTEISEKDVENALWDLELELLEADVALEVVDELKERIKEKLVG-QKvkigTNKRNIVENAVRDA 80
                                      56777777877.45678****************************************.66488888999999999985 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.5   8.1e-10   3.6e-07      19     125 ..     105     226 ..      94     258 .. 0.78

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 8.1e-10
                            AAA_30  19 rvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelgieastiakllkrlk.............g 82 
                                        v v +G  G GKtt++++l++ ++++g +v+++A+    A ++++ ++ +a+++   + +++             +
  gi|242398400|ref|YP_002993824.1| 105 FVIVFVGFNGGGKTTTIAKLANWLKKNGLSVVIAASDTFRAGAIEQ-VEEHAKRVGVKVIKHGyksdpaavaydsiE 180
                                       47899********************************999999984.444555554444444455667888888774 PP

                            AAA_30  83 rarlepgtllivDEagmv..dtkqlaallkaaekag.akvilvGDe 125
                                       +a+ +  ++++vD ag    + + ++++ k+a+ ++   vi+vGD 
  gi|242398400|ref|YP_002993824.1| 181 HAKARGIDVVLVDTAGRNelNRNLMDEMKKIARVTKpDLVIFVGDS 226
                                       4555555*********87557788999999999977699******7 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.2   1.2e-05     0.005       1      31 [.     106     136 ..     106     142 .. 0.93
   2 !    9.6   0.3    0.0019      0.81      24      96 ..     152     222 ..     142     238 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.2e-05
                              MobB   1 vlgivgksgsGKTtLleklipelkarglrvg 31 
                                       v+ +vg++g GKTt + kl ++lk++gl+v 
  gi|242398400|ref|YP_002993824.1| 106 VIVFVGFNGGGKTTTIAKLANWLKKNGLSVV 136
                                       689*************************985 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0019
                              MobB  24 karglrvg..tiKhahhgfdvdkpgkDsyrhrkA.GAkevlvaskerlalikeleeaelsleellarlsevDlvlv 96 
                                       +++  rvg  +iKh   + d      Ds +h+kA G + vlv +  r  l ++l +     ++ +ar+++ Dlv+ 
  gi|242398400|ref|YP_002993824.1| 152 EEHAKRVGvkVIKHGY-KSDPAAVAYDSIEHAKArGIDVVLVDTAGRNELNRNLMD----EMKKIARVTKPDLVIF 222
                                       5554454411677754.456778899*******9899999*******999999744....3455666667888875 PP

>> Peripla_BP_4  Periplasmic binding protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.1   9.6e-05     0.042     135     216 ..      71     165 ..      40     176 .. 0.63
   2 !   10.1   0.1   0.00099      0.44      65      89 ..     170     195 ..     167     204 .. 0.87
   3 ?    2.4   0.1      0.22        98      34      72 ..     223     262 ..     201     287 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.6e-05
                                       HHHHHHHHHHHHHHHHH-TTCEECC............EEESTT.TCHHHHHHHHHHHHHTTTECEEEESSCCHHHCH CS
                      Peripla_BP_4 135 dpnaeeriegfrkvlkeypgikiva............evagan.wdaekaqqalealltanpldgilaandgmaega 198
                                       +   ++  +++ +vl++   i +++            +++g n    +++  +l+++l++n l +++aa+d+   ga
  gi|242398400|ref|YP_002993824.1|  71 NIVENAVRDAVLEVLTPERHIDLLEmikskeekpfviVFVGFNgGGKTTTIAKLANWLKKNGLSVVIAASDTFRAGA 147
                                       44444556666666777334444444445556666554445555777788889******999*************** PP

                                       HHHHHHTTTTSTEEEEEE CS
                      Peripla_BP_4 199 lealeaaglagkvvvtgq 216
                                       +e +e+  ++  v+v+ +
  gi|242398400|ref|YP_002993824.1| 148 IEQVEEHAKRVGVKVIKH 165
                                       ******766433344433 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00099
                                       SHHHHH.HHHHHHHHTT-EEEEESTT CS
                      Peripla_BP_4  65 dstala.palkkakaaGIpVvafdsd 89 
                                       d++a+a + ++ aka+GI Vv +d++
  gi|242398400|ref|YP_002993824.1| 170 DPAAVAyDSIEHAKARGIDVVLVDTA 195
                                       8889999*****************98 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.22
                                       E..ECSTT-HHHHHHHHHHHHHTT-SEEEE--SSHHHHH.HH CS
                      Peripla_BP_4  34 v..gdaendaaeQvaqiedaiakgvdgiivapvdstala.pa 72 
                                       v  + a+n + eQ+ q++ a   + dg+i++  d++a   +a
  gi|242398400|ref|YP_002993824.1| 223 VgdSLAGNAILEQARQFNEA--VKIDGVILTKLDADARGgTA 262
                                       34445777779999999999..5799***9999999866555 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 !   22.9   0.1     8e-08   3.5e-05      16     133 ..      91     198 ..      77     230 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 8e-08
                                       HHHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE------------------HCCCTSTTE CS
                              MeaB  16 kellerllakaGraqvvGltGvPGaGkstlvealglelrrrGkrvavlavDPsspftGGsilGDklRleelavdegv 92 
                                        +lle + +k  +  v+ + G+ G Gk t++ +l+  l+++G  v + a   s +f  G+i     ++ee+a+  gv
  gi|242398400|ref|YP_002993824.1|  91 IDLLEMIKSKEEKPFVIVFVGFNGGGKTTTIAKLANWLKKNGLSVVIAA---SDTFRAGAI----EQVEEHAKRVGV 160
                                       57999999************************************98877...558999*99....468888888887 PP

                                       EEEEE-----HHHHHHHHHHHHHHHHHTT-SEEEEEEESST CS
                              MeaB  93 fiRslpsrGalGGlaaktrevvllleaaGfDvvlietvGvG 133
                                           +   G +   aa + + ++   a G Dvvl++t G  
  gi|242398400|ref|YP_002993824.1| 161 K---VIKHGYKSDPAAVAYDSIEHAKARGIDVVLVDTAGRN 198
                                       5...45689999999999*******************9865 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.1   1.2e-07   5.4e-05       9     117 ..      98     208 ..      91     214 .. 0.77
   2 ?   -1.4   0.0       2.8   1.2e+03       7      28 ..     207     229 ..     201     246 .. 0.72

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.2e-07
                        Zeta_toxin   9 kypsqerPklillgGqpGAGKselaellkdelerqgnvvrl.dpDdlRe.lhPeyeeilka.dpkkaseltqkdase 82 
                                       k  ++e+P +i+ +G  G GK++++++l++ l+++g  v++   D++R+  + ++ee+ k   +k      ++d   
  gi|242398400|ref|YP_002993824.1|  98 K-SKEEKPFVIVFVGFNGGGKTTTIAKLANWLKKNGLSVVIaASDTFRAgAIEQVEEHAKRvGVKVIKHGYKSDPAA 173
                                       3.355****************************77766666167****85688888888866788888888999999 PP

                        Zeta_toxin  83 lvekllqeaiengyniivegtlrspdvvkklaeal 117
                                       ++   +++a  +g+++++  t    +  ++l++++
  gi|242398400|ref|YP_002993824.1| 174 VAYDSIEHAKARGIDVVLVDTAGRNELNRNLMDEM 208
                                       99999999999999988655555555555555555 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.8
                        Zeta_toxin   7 dkk.ypsqerPklillgGqpGAG 28 
                                       + k + +  +P+l++ +G + AG
  gi|242398400|ref|YP_002993824.1| 207 EMKkIARVTKPDLVIFVGDSLAG 229
                                       33435566999999999988777 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   4.9e-07   0.00021       1     104 [.     106     223 ..     106     246 .. 0.68

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 4.9e-07
                            AAA_33   1 lvllvGlpGsGKstlaerl...lkklg..avllssdtlrr.rlfgtdqqskt.........dytrvldrlyqilnel 62 
                                       ++++vG +G GK+t + +l   lkk+g  +v+ +sdt+r  +++  +++ k+         +     ++  +   + 
  gi|242398400|ref|YP_002993824.1| 106 VIVFVGFNGGGKTTTIAKLanwLKKNGlsVVIAASDTFRAgAIEQVEEHAKRvgvkvikhgYK----SDPAAVAYDS 178
                                       89**************99866677777977777888877744444333333355554444332....2333355577 PP

                            AAA_33  63 arkalsagrnvildat....nlsrrerarflklarrlgvpvrivvv 104
                                       ++ a ++g++v+l  t     l+r+ ++++ k+ar  + p+++++v
  gi|242398400|ref|YP_002993824.1| 179 IEHAKARGIDVVLVDTagrnELNRNLMDEMKKIARVTK-PDLVIFV 223
                                       788899****9998884444344666688888887655.7777766 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 !   20.3   0.8     1e-06   0.00045       2      88 ..     108     257 ..     107     291 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1e-06
                                       EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH........................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................ RF
                              CbiA   2 aiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep........................ 54 
                                       +++++ GG GKTt+ a+La  l+++gl V+    D+         g  +++e+                        
  gi|242398400|ref|YP_002993824.1| 108 VFVGFNGG-GKTTTIAKLANWLKKNGLSVVIAASDTF------RAGAIEQVEEhakrvgvkvikhgyksdpaavayd 177
                                       55666666.**********************999988......34444444445667999999************** PP

                                       ...............................................CCHCCCHHHHHHCHCHHHH..EEEEEEEEE CS
                                       ...............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  55 ...............................................dlkrllellealgkkkalllkiagvvlnrv 84 
                                                                                      d   +  +le+ + +++ ++ki gv+l++ 
  gi|242398400|ref|YP_002993824.1| 178 siehakargidvvlvdtagrnelnrnlmdemkkiarvtkpdlvifvgDSLAGNAILEQAR-QFNEAVKIDGVILTKL 253
                                       *****************************9999999999999999996666566666666.455569999*****99 PP

                                       SS.. CS
                                       xxxx RF
                              CbiA  85 dgen 88 
                                       d ++
  gi|242398400|ref|YP_002993824.1| 254 DADA 257
                                       9885 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.2         2   8.9e+02      49      82 ..      38      71 ..      10     102 .. 0.68
   2 !   21.4   0.1   6.2e-07   0.00027       1     110 [.     110     225 ..     110     242 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 2
                                      SHHHHHHHHHHHHHHHHHHHHHSSEEEEEE-SEE CS
                            AAA_17 49 lpleekkelqkeaaekiaeeakkkgvlvdghpri 82
                                      l+ ++  e+ +e++e+i+e+   ++v + +  r+
  gi|242398400|ref|YP_002993824.1| 38 LEADVALEVVDELKERIKEKLVGQKVKIGTNKRN 71
                                      4556666777888888888775555555544444 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 6.2e-07
                                       EE-TTSSHHHHHHHHH...HHHTEEE.EEHHHHHHHHHHTTTSHSSHHHHCTS.HHHHHHHHHHHHHHHHHHHH..H CS
                            AAA_17   1 lGgPGsGKgtqceklv...ekygfth.lsaGdllreeakrgglakardemrkl.pleekkelqkeaaekiaeea..k 70 
                                       +G  G GK+t ++kl+   +k g+++ + a+d +r+ a ++  + a+    k+ ++  k +  + a ++i++++  +
  gi|242398400|ref|YP_002993824.1| 110 VGFNGGGKTTTIAKLAnwlKKNGLSVvIAASDTFRAGAIEQVEEHAKRVGVKViKHGYKSDPAAVAYDSIEHAKarG 186
                                       6999***********955556688862688*****988776433333333344244556666777778887776334 PP

                                       SSEEEEEE-SEEEETTEEEESSHHHHHHHH..SEEEEEE- CS
                            AAA_17  71 kkgvlvdghprikeqagfldglpkevleelkpdaiillea 110
                                        + vlvd+  r++ ++ ++d+++k + +  kpd++i++ +
  gi|242398400|ref|YP_002993824.1| 187 IDVVLVDTAGRNELNRNLMDEMKK-IARVTKPDLVIFVGD 225
                                       4669********999999999986.99*********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 !   19.4   1.3   1.4e-06   0.00061       2     152 ..     106     255 ..     105     268 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.4e-06
                                       EEEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SSCHCCCCCCHCCCT.EEEETTTTECCH.CTT-HHHHHHH CS
                              cobW   2 vtvltGflGsGKTtLlnhll..enraglklavivNefgevsiDaellretgveivelenGciCct.lredllkelea 75 
                                       v+v++Gf G GKTt + +l    +++gl++ +   +       a  +++ ++++  +    i +   ++ +  + ++
  gi|242398400|ref|YP_002993824.1| 106 VIVFVGFNGGGKTTTIAKLAnwLKKNGLSVVIAASDTF----RAGAIEQVEEHAKRVGVKVIKHGyKSDPAAVAYDS 178
                                       799*****************555555555555555555....33344444444444444455555234445555555 PP

                                       HHHHH.TT-SEEEEEECT.TTTHHHHHTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-H CS
                              cobW  76 leere.erldviliEttG.laePapvafteeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnKt 150
                                       +e+ + + +dv+l+ t G +     ++ + +++++ ++ d v++v D+ +  ++  ++++++++ ++  d ++l+K 
  gi|242398400|ref|YP_002993824.1| 179 IEHAKaRGIDVVLVDTAGrNELNRNLMDEMKKIARVTKPDLVIFVGDSLAG-NAILEQARQFNEAVK-IDGVILTKL 253
                                       655555569*********7777777777799*****************554.455556666666665.589999999 PP

                                       HH CS
                              cobW 151 Dl 152
                                       D 
  gi|242398400|ref|YP_002993824.1| 254 DA 255
                                       95 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   1.4e-06    0.0006       4     102 ..     107     204 ..     105     212 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.4e-06
                             VirC1   4 itfcslkGGaGkttalmglcsalasdgkrvalfeadenrP..ltkwkenalrkgawddacevfvadelplleaayee 78 
                                       i f+ + GG Gktt++  l  +l  +g  v +  +d  r   +++  e+a+r g        +++d  ++  ++ e+
  gi|242398400|ref|YP_002993824.1| 107 IVFVGFNGG-GKTTTIAKLANWLKKNGLSVVIAASDTFRAgaIEQVEEHAKRVGVK-VIKHGYKSDPAAVAYDSIEH 181
                                       678888887.9*********************999998853388999999998875.45567999999**9****** PP

                             VirC1  79 aegeGfdyaladtrgGsselnnti 102
                                       a+++G d++l+dt  G  eln  +
  gi|242398400|ref|YP_002993824.1| 182 AKARGIDVVLVDTA-GRNELNRNL 204
                                       ************96.788999765 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       6.9     3e+03      58      80 ..      35      57 ..      19      68 .. 0.68
   2 !   17.3   0.1   6.8e-06     0.003       3      86 ..     111     192 ..     109     242 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 6.9
                                      HHHHHHHHHHTTHHHHHHHHHTT CS
                   Thymidylate_kin 58 allfaadriehleekikpalkqg 80
                                      + l+ ad++ ++++++k+ +k++
  gi|242398400|ref|YP_002993824.1| 35 LELLEADVALEVVDELKERIKEK 57
                                      55666777777776666665553 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 6.8e-06
                                       ESTTSSHHHHHHHHHHHHHHTTE.EEEESSSTTSHHHHHHHHHHHTCS---HHHHHHHHHHHHHHTTHHHHHHHHHT CS
                   Thymidylate_kin   3 GlDGaGKttqaellkerlkeegikvvltrepggteiGekirelllkeeeleeqteallfaadriehleekikpalkq 79 
                                       G +G GKtt +++l+++lk++g++vv+    ++t  +  i ++ ++++++  + +   +  d +  ++++i+ a ++
  gi|242398400|ref|YP_002993824.1| 111 GFNGGGKTTTIAKLANWLKKNGLSVVIAA--SDTFRAGAIEQVEEHAKRVGVKVIKHGYKSDPAAVAYDSIEHAKAR 185
                                       899********************977764..5677888899998888888888888888888888888888888888 PP

                                       T-EEEEE CS
                   Thymidylate_kin  80 gktvivd 86 
                                       g  v++ 
  gi|242398400|ref|YP_002993824.1| 186 GIDVVLV 192
                                       8877754 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.1      0.59   2.6e+02      70      92 ..      34      56 ..       6     104 .. 0.70
   2 !   18.4   0.6     4e-06    0.0018       2      98 ..     107     237 ..     106     253 .. 0.57

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.59
                                      HHHHHCTSEEEEEEETTTTCSHH CS
                          MMR_HSR1 70 flaleeadlillvvdaseeklkp 92
                                       l+l ead++l vvd  +e +k+
  gi|242398400|ref|YP_002993824.1| 34 ELELLEADVALEVVDELKERIKE 56
                                      34567899999999933332222 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 4e-06
                                       EEEEESTTSSHHHHHHHHHT.......STEEESSSTTSSSSEEEEEEEETTEE........................ CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltg.......ekaivsdkpgtTrdinegrvklkgke........................ 47 
                                       +++vG    GK+t i +l +       +++i+++  +    i++ + + k  +                        
  gi|242398400|ref|YP_002993824.1| 107 IVFVGFNGGGKTTTIAKLANwlkknglSVVIAASDTFRAGAIEQVEEHAK--Rvgvkvikhgyksdpaavaydsieh 181
                                       799***************98776655523344444443333333322211..1222333333444555566666666 PP

                                       .......EEEEECGGCSSHHHHHH...HHHHHHHHHHCTSEEEEEEETT..TTCSHHHHHHHH CS
                          MMR_HSR1  48 .......ielvDtpGliegaseek...glgkaflaleeadlillvvdas..eeklkpldeele 98 
                                              ++lvDt+G    ++ ++   ++ k+++++ + dl+++v d+   +    ++ e+  
  gi|242398400|ref|YP_002993824.1| 182 akargidVVLVDTAG-R--NELNRnlmDEMKKIARVTKPDLVIFVGDSLagN----AILEQAR 237
                                       6666666********.3..34444124555556666667********44432....2223333 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   6.3e-06    0.0027       7     115 ..     106     211 ..     100     227 .. 0.63

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 6.3e-06
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka..erlsseellea 81 
                                       ++v +G  G GKTt++++l+++l+        + ++  v ++s+t ++   +++ +  ++ + +  + + +++  + 
  gi|242398400|ref|YP_002993824.1| 106 VIVFVGFNGGGKTTTIAKLANWLK--------KNGLSVVIAASDTFRAGAIEQVEEHAKRVGVKviKHGYKSDPAAV 174
                                       68999******************4........556556666666633333444444444444446645555555555 PP

                            AAA_22  82 leqalrarav..ielliiDEaqh..lrseealeeLrsl 115
                                        ++ ++++++  i ++++D a +  l + +++ e +++
  gi|242398400|ref|YP_002993824.1| 175 AYDSIEHAKArgIDVVLVDTAGRneL-NRNLMDEMKKI 211
                                       55555555555668888887766333.45555555544 PP

>> CbiJ  Precorrin-6x reductase CbiJ/CobK
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0     7e-06     0.003      52     148 ..     121     217 ..     111     243 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 7e-06
                                       HHHHHHHHHHHT--EEEE-S-TT-HHHHHHHHHHHHHHT-EEEEE-------EEEEESSHHHHH........EEE.E CS
                              CbiJ  52 eeglaellreekidlvvDATHPfAaeisanaaeackelgipylrleRpsweakiievdsleeaaella....vll.t 123
                                        ++la++l+++++++v+ A+  f a + +++ e +k++g++++    +s ++ ++ +ds+e+a   ++    vl+ t
  gi|242398400|ref|YP_002993824.1| 121 IAKLANWLKKNGLSVVIAASDTFRAGAIEQVEEHAKRVGVKVIKHGYKS-DPAAVAYDSIEHAK--ARgidvVLVdT 194
                                       789****************************************999887.56899999999996..33688955549 PP

                                       STSTTGGGGSTT...SEEEEEESS- CS
                              CbiJ 124 tGskelaafaealkkerllaRvlpt 148
                                        G++el+    +  + + +aRv ++
  gi|242398400|ref|YP_002993824.1| 195 AGRNELNRNLMD--EMKKIARVTKP 217
                                       9*****998533..23447777665 PP

>> KdpD  Osmosensitive K+ channel His kinase sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.3       1.1   4.8e+02      62      91 ..      20      50 ..       7      75 .. 0.52
   2 ?    0.8   0.2      0.64   2.8e+02     155     198 ..      42      85 ..      34      96 .. 0.78
   3 !   15.5   0.1     2e-05     0.009       7      95 ..     108     199 ..     104     216 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 1.1
                              KdpD 62 eveykgkeleeldld.ailarkpevvlvDel 91
                                      e++ k++e    dl+ ++l+ + ++ +vDel
  gi|242398400|ref|YP_002993824.1| 20 EISEKDVENALWDLElELLEADVALEVVDEL 50
                                      3333333333333332233444444444444 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.64
                              KdpD 155 develvDltpeeLlerLkegkvykkekaeralknffrkgnLtaL 198
                                         +e+vD   e+++e+L   kv   ++ +++++n  r + L+ L
  gi|242398400|ref|YP_002993824.1|  42 VALEVVDELKERIKEKLVGQKVKIGTNKRNIVENAVRDAVLEVL 85 
                                       46788999899999999888888888888888888888877766 PP

  == domain 3  score: 15.5 bits;  conditional E-value: 2e-05
                              KdpD   7 iflGaapGvGktyamLeeaqelkeegvdvviglvethgrketeallegleviprkeveykgk....eleeldldail 79 
                                       +f+G+ +G Gkt ++ + a+ lk++g  vvi++ +t +   +e++ e+ + +  k +++  k    ++   +++++ 
  gi|242398400|ref|YP_002993824.1| 108 VFVGF-NGGGKTTTIAKLANWLKKNGLSVVIAASDTFRAGAIEQVEEHAKRVGVKVIKHGYKsdpaAVAYDSIEHAK 183
                                       67775.688***************************99999999998888887776665433111145555688889 PP

                              KdpD  80 arkpevvlvDelahtn 95 
                                       ar  +vvlvD  + ++
  gi|242398400|ref|YP_002993824.1| 184 ARGIDVVLVDTAGRNE 199
                                       99999****9877664 PP

>> 6PF2K  6-phosphofructo-2-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   2.1e-05    0.0091       6      43 ..      97     134 ..      94     185 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.1e-05
                                       HHHT..S-EEEEEESSTTSSHHHHHHHHHHHHHHTT-- CS
                             6PF2K   6 vtnlknsklvivlvGLpargKtyiskkltrylkwlgvr 43 
                                       +++++++++viv+vG    gKt++  kl  +lk +g++
  gi|242398400|ref|YP_002993824.1|  97 IKSKEEKPFVIVFVGFNGGGKTTTIAKLANWLKKNGLS 134
                                       6677999**************************88875 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.6    0.0012       0.5      27     121 ..      18     126 ..       9     138 .. 0.65
   2 ?   -0.3   0.0       2.1     9e+02      50      85 ..     134     168 ..     127     183 .. 0.80
   3 ?    2.5   0.0      0.27   1.2e+02      84     113 ..     202     231 ..     176     248 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0012
                                       TTT--HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHH..............HHHHHHHHHHHTTSEEEE--TTTHTT CS
                       RsgA_GTPase  27 epelslnlldrfLvlaeekgiepvivlnKiDlleeee..............eleelkeelealgyevllvsaktkeg 89 
                                       + e+s++ ++ +L  +e + +e  ++l  +D l+e+               + + ++++++++ +evl+ + +  + 
  gi|242398400|ref|YP_002993824.1|  18 QTEISEKDVENALWDLELELLEADVALEVVDELKERIkeklvgqkvkigtnKRNIVENAVRDAVLEVLTPERH-IDL 93 
                                       5566666666666666666666666666666666555455666555433333355556666665666555433.566 PP

                                       HHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  90 leelkellkd.ktsvlvGqSGvGKStLinallp 121
                                       le +k++ ++  ++v+vG  G GK+t i +l++
  gi|242398400|ref|YP_002993824.1|  94 LEMIKSKEEKpFVIVFVGFNGGGKTTTIAKLAN 126
                                       67777776666799**************99986 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 2.1
                                       EEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TT CS
                       RsgA_GTPase  50 vivlnKiDlleeeeeleelkeelealgyevllvsak 85 
                                        +v+   D       +e+++e+ +++g++v++   k
  gi|242398400|ref|YP_002993824.1| 134 SVVIAASDTFRAGA-IEQVEEHAKRVGVKVIKHGYK 168
                                       56777788888888.99999*******999987655 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.27
                                       TTTHTTHHHHHHHCTTSEEEEECSTTSSHH CS
                       RsgA_GTPase  84 aktkegleelkellkdktsvlvGqSGvGKS 113
                                        +  +++++++++ k +++++vG S +G  
  gi|242398400|ref|YP_002993824.1| 202 RNLMDEMKKIARVTKPDLVIFVGDSLAGNA 231
                                       4456889999999999*******9988865 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   2.8e-05     0.012       2      49 ..     107     158 ..     106     201 .. 0.60

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.8e-05
                            AAA_28   2 ivitGgestGKTtlleaLaar....gypvvpEaareileeklakgedalpwv 49 
                                       iv++G  ++GKTt++++La+     g +vv  a  ++     ++ e++++ v
  gi|242398400|ref|YP_002993824.1| 107 IVFVGFNGGGKTTTIAKLANWlkknGLSVVIAASDTFRAGAIEQVEEHAKRV 158
                                       9******************554556999886666666655555555555544 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 ?    4.0   0.1     0.088        38       5      28 ..     115     138 ..     111     143 .. 0.86
   2 !    9.8   0.0    0.0014      0.62      94     160 ..     178     245 ..     169     256 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.088
                            CLP1_P   5 sGKSTlarlLlNyalrkgrkpvyv 28 
                                        GK+T ++ L+N++ ++g ++v+ 
  gi|242398400|ref|YP_002993824.1| 115 GGKTTTIAKLANWLKKNGLSVVIA 138
                                       5*****************999875 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0014
                            CLP1_P  94 kleenkkakasgliIntpGwvk..glgaellleliealepdvvvvldqeellnelkrdlplskvkvvkl 160
                                        +e  k+++ ++++++t G  +     ++ +++++++ +pd+v++++++   n + ++++ ++ ++vk+
  gi|242398400|ref|YP_002993824.1| 178 SIEHAKARGIDVVLVDTAGRNElnRNLMDEMKKIARVTKPDLVIFVGDSLAGNAILEQAR-QFNEAVKI 245
                                       455667889999*******7652123356678899999**********999999988888.55555554 PP

>> Fe-ADH  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.15        65      57     107 ..     108     132 ..      62     141 .. 0.65
   2 !   11.3   0.3   0.00026      0.11       6      89 ..     143     224 ..     138     226 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.15
                                       E.EEE-S---HHHHHHHHTTS-TT.--EEEEEESHHHHHHHHHHHHHTT.. CS
                            Fe-ADH  57 vfdgvepnptleeveeaaalareegadvviavGGGsviDtAKaialllanp 107
                                       vf g++                          GGG++  +AK+++ l +n+
  gi|242398400|ref|YP_002993824.1| 108 VFVGFN--------------------------GGGKTTTIAKLANWLKKNG 132
                                       333333..........................5666666666666666653 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00026
                                       EETTGGGGHHHHHTTT-..EEEEEEEHHHH.HH.THHHHHHHHHCTT-EEEE.EEE.-S---HHHHHHHHTTS-TT. CS
                            Fe-ADH   6 fgkgaleelgellkklgakralivtdkgslkksglldkvlesleeagievtvfdgv.epnptleeveeaaalareeg 81 
                                       f +ga+e+++e++k+ g+ ++ i ++ +s   + ++ + +e+ ++ gi+v+++d+  + +     ++e+ ++ar ++
  gi|242398400|ref|YP_002993824.1| 143 FRAGAIEQVEEHAKRVGV-KV-IKHGYKSD-PAAVAYDSIEHAKARGIDVVLVDTAgRNELNRNLMDEMKKIARVTK 216
                                       889**************6.44.33444433.4556677777778*******9999978888888899999******* PP

                                       --EEEEEE CS
                            Fe-ADH  82 advviavG 89 
                                       +d+vi vG
  gi|242398400|ref|YP_002993824.1| 217 PDLVIFVG 224
                                       *****888 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   7.6e-05     0.033       1      45 [.     103     147 ..     103     161 .. 0.91
   2 ?   -1.3   0.1       4.2   1.8e+03      27      54 ..     183     209 ..     169     236 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7.6e-05
                                       S-EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTT CS
                        APS_kinase   1 rgvvvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgL 45 
                                       +++v+ + G+ g GK+t   +l++ L+++g sv++   d+ R g 
  gi|242398400|ref|YP_002993824.1| 103 KPFVIVFVGFNGGGKTTTIAKLANWLKKNGLSVVIAASDTFRAGA 147
                                       589************************************999875 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 4.2
                                       HHTT--EEEEEHHHHTTTTTTT--SSHH CS
                        APS_kinase  27 vekgisvylLdGdnvRhgLnkdLgfsee 54 
                                       +++gi v+l+d    R++Ln++L  +++
  gi|242398400|ref|YP_002993824.1| 183 KARGIDVVLVDTA-GRNELNRNLMDEMK 209
                                       5566666666644.48888888854332 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1      0.46     2e+02      89     106 ..     119     136 ..      37     166 .. 0.60
   2 ?   11.2   0.0   0.00094      0.41       7      85 ..     166     250 ..     160     258 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.46
                                       ---HHHHHHHHHTT-EEE CS
                     CoA_binding_2  89 sedeeaaelaeeagirvv 106
                                       +  +++a++++++g+ vv
  gi|242398400|ref|YP_002993824.1| 119 TTIAKLANWLKKNGLSVV 136
                                       334444444444444433 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00094
                                       T--S-TTSHHHHHHHHHHHHT--EEEESSS-SEETTEES----T......T--EEEE-S-HHHHGGGHHHHHHH... CS
                     CoA_binding_2   7 GasdnpgkfgykvlryllehglpvvpVnpkeeeilgekvyaslae.d.pepvdlvdvftppeatpeivkealal... 78 
                                       G +++p+  +y  ++  +++g++vv V   ++  l ++   ++++ + ++++dlv ++  + a  +i+++a +    
  gi|242398400|ref|YP_002993824.1| 166 GYKSDPAAVAYDSIEHAKARGIDVVLVDTAGRNELNRNLMDEMKKiArVTKPDLVIFVGDSLAGNAILEQARQFnea 242
                                       78899**********************99997777777555555433489***********9999999999766333 PP

                                       .--SEEEE CS
                     CoA_binding_2  79 .gakavwl 85 
                                        ++ +v+l
  gi|242398400|ref|YP_002993824.1| 243 vKIDGVIL 250
                                       44666665 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   7.1e-05     0.031       4      42 ..     107     146 ..     104     171 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.1e-05
                                       EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH.. CS
                             KTI12   4 vvltGlPssGKstrakeLakaleeekrsvvviddeslg.i 42 
                                       +v+ G+   GK+t  ++La+ l++++ svv+  +++++ +
  gi|242398400|ref|YP_002993824.1| 107 IVFVGFNGGGKTTTIAKLANWLKKNGLSVVIAASDTFRaG 146
                                       899******************************9999852 PP

>> DUF2855  Protein of unknown function (DUF2855)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   6.5e-05     0.028     197     247 ..     172     226 ..     131     254 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6.5e-05
                           DUF2855 197 kvvsYddlesleaa.kkvvivDfagrdelleklhealkd...kgklvlsvavGst 247
                                         v+Yd++e+++a    vv+vD agr+el+++l +++k+     k  l++ vG +
  gi|242398400|ref|YP_002993824.1| 172 AAVAYDSIEHAKARgIDVVLVDTAGRNELNRNLMDEMKKiarVTKPDLVIFVGDS 226
                                       5789*****999877788********************97765556666777765 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1       1.9   8.4e+02     114     137 ..      50      78 ..      42     109 .. 0.53
   2 ?   10.9   2.8   0.00075      0.33       4      52 ..     109     151 ..     106     258 .. 0.55

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.9
                                       HHHHHHHHHTTTSEEEEE--SS-.....- CS
                          NTPase_1 114 fkeaveevLksekpvlavihrrk.....d 137
                                       +ke ++e L  +k+ +++ +r+      +
  gi|242398400|ref|YP_002993824.1|  50 LKERIKEKLVGQKVKIGTNKRNIvenavR 78 
                                       55555555555555555555554322222 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00075
                                       EE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE-------EEEEEET CS
                          NTPase_1   4 iTGppGvGKtTlvkkvlellkssgvkvgGfyteevreggrrigFkivdl 52 
                                         G  G GKtT + k+++ lk++g++v        r      g  i ++
  gi|242398400|ref|YP_002993824.1| 109 FVGFNGGGKTTTIAKLANWLKKNGLSVVIAASDTFR-----AG-AIEQV 151
                                       568899***************999988432222222.....22.23444 PP

>> ATPgrasp_N  ATP-grasp N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       4.4   1.9e+03       2      12 ..     153     163 ..     151     177 .. 0.83
   2 ?   12.0   0.1   0.00054      0.23       2      61 ..     180     249 ..     179     255 .. 0.66

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 4.4
                                       HHHHHTT-EEE CS
                        ATPgrasp_N   2 eaAkaLGikvv 12 
                                       e Ak+ G+kv+
  gi|242398400|ref|YP_002993824.1| 153 EHAKRVGVKVI 163
                                       68******996 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00054
                                       HHHHHTT-EEEEEEETTS-.....---S-TT.EEEEEEE-TTT-...H...HHHHHHHHHHHHHS--SEEE CS
                        ATPgrasp_N   2 eaAkaLGikvvlvdeedew.....apeelaelvekfipldlaqd...p...daaleavralsrerpvdGiv 61 
                                       e Aka Gi+vvlvd  +++     + +e+++ ++++   dl      +   +a+le  r++ ++ ++dG++
  gi|242398400|ref|YP_002993824.1| 180 EHAKARGIDVVLVDTAGRNelnrnLMDEMKK-IARVTKPDLVIFvgdSlagNAILEQARQFNEAVKIDGVI 249
                                       89**************766543332222333.555555554332111334469999999999999***985 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   0.00017     0.075      12     124 ..     106     207 ..      94     227 .. 0.51

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00017
                            AAA_19  12 vllvtaGpGtGKTrvlkhivallvelggvkpeeillv..aftgrAakelrerlaalgae..atTiHrlalldfddll 84 
                                       v++ ++  G GKT+++ +  ++l+++g +    ++++  +f   A ++++e  + +g++      H+    + d+  
  gi|242398400|ref|YP_002993824.1| 106 VIVFVGFNGGGKTTTIAKLANWLKKNG-L--SVVIAAsdTFRAGAIEQVEEHAKRVGVKviK---HGY---KSDPAA 173
                                       34456779***************9999.4..4455551145555789999999777776330...333...333333 PP

                            AAA_19  85 tealelleeaeeekklqeee.llivDEfqdvdelqyrLlka 124
                                          +++  ++ e+ k  ++  +++vD +   +el  +L+++
  gi|242398400|ref|YP_002993824.1| 174 ---VAY--DSIEHAKA-RGIdVVLVDTAG-RNELNRNLMDE 207
                                       ...222..12222222.222255555432.22333333333 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00013     0.058      18     127 ..     100     213 ..      84     226 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00013
                                       ..HCTS-EEEEESTTSSCHHHHHHHHHHCHCTCCCEEEEESSHHHHHCC.TSEECHHHHT-TTSSS-HHHH..HHHT CS
                              PIF1  18 lnekgklfFvtGsgGtgKtflwkallkklrsegkivlavAssGvAalllegGrtahsrfkiplekdeestc..kikr 92 
                                       ++ek+ ++ + G+ G gKt    +l + l+++g  v+  As    a  +e+    + r+++ + k+  ++   +++ 
  gi|242398400|ref|YP_002993824.1| 100 KEEKPFVIVFVGFNGGGKTTTIAKLANWLKKNGLSVVIAASDTFRAGAIEQVEEHAKRVGVKVIKHGYKSDpaAVAY 176
                                       5678899999*******************************999999999988888888888766544333247888 PP

                                       SCCCHHHHHC-SEEEEECGGG..SBHHHHHHHHHHHH CS
                              PIF1  93 gsklaellkktsliiwDEapm..verecfealdrtlr 127
                                       +s +  +   ++++++D a    ++r++++++ +++r
  gi|242398400|ref|YP_002993824.1| 177 DSIEHAKARGIDVVLVDTAGRneLNRNLMDEMKKIAR 213
                                       8888888888888888888541256777777777665 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00044      0.19       2      80 ..     115     194 ..     114     240 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00044
                    Glyco_transf_4   2 GGverhvleLaraLarrGheVtvvtpgddgpleeev..elvvrvprvplpllkrllrslaflrrlrrllkrekpDvv 76 
                                       GG  + +  La+ L ++G  V++ ++++ ++ + e+  e+ +rv+ +   +++      a + +  +++k+ ++Dvv
  gi|242398400|ref|YP_002993824.1| 115 GGKTTTIAKLANWLKKNGLSVVIAASDTFRAGAIEQveEHAKRVGVKV-IKHGYKSDPAAVAYDSIEHAKARGIDVV 190
                                       899999******************777666655555323333333322.3333344445556678888888899998 PP

                    Glyco_transf_4  77 Hahs 80 
                                        + +
  gi|242398400|ref|YP_002993824.1| 191 LVDT 194
                                       7665 PP

>> UvdE  UV-endonuclease UvdE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00021     0.092      94     171 ..      45     129 ..      28     137 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00021
                              UvdE  94 elakelglRltfH.PeqftllnSdrkevtesairdl.......ayHdklldalklaeqqdavliiHvGGkfgdkeaa 162
                                       e++ el+ R++    +q + ++ ++++++e+a+rd        + H  ll+ +k +e+ +  +i+ vG + g+k ++
  gi|242398400|ref|YP_002993824.1|  45 EVVDELKERIKEKlVGQKVKIGTNKRNIVENAVRDAvlevltpERHIDLLEMIKSKEE-KPFVIVFVGFNGGGKTTT 120
                                       5666777777654258999***************952333333469999999998888.889999***999****** PP

                              UvdE 163 lerfkenik 171
                                       ++++++ +k
  gi|242398400|ref|YP_002993824.1| 121 IAKLANWLK 129
                                       **9987665 PP

>> ZnuA  Zinc-uptake complex component A periplasmic
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.1    0.0021      0.94     183     227 ..     102     163 ..      39     176 .. 0.71
   2 ?    5.0   0.0     0.031        13     167     223 ..     155     213 ..     154     242 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0021
                                       S...............HHHHHHHHHHHHHTT-SEEEEET.TS-THHHHHHHHHHT.-EEEEE CS
                                       x...............xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx.xxxxxx RF
                              ZnuA 183 e...............aaqiaalieeikeagvkaifvep.laspklaetlaeeag.vkvatl 227
                                       e                 +ia+l++ +k++g+ ++++ + +++  ++e++ e a+ v v ++
  gi|242398400|ref|YP_002993824.1| 102 EkpfvivfvgfngggkTTTIAKLANWLKKNGLSVVIAASdTFRAGAIEQVEEHAKrVGVKVI 163
                                       345555555555558899*********************788********997743444444 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.031
                                       HHHTT-EEEEEESSSSS.HHHHHHHHHHHHHTT-SEEEEETTS-THHHHHHHHHHT..-E CS
                                       xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xx RF
                              ZnuA 167 arayglevagiagiste.aaqiaalieeikeagvkaifveplaspklaetlaeeag..vk 223
                                       a++ g++v++  g +++ aa   + ie++k++g+ +++v++  +++l ++l +e +  ++
  gi|242398400|ref|YP_002993824.1| 155 AKRVGVKVIKH-GYKSDpAAVAYDSIEHAKARGIDVVLVDTAGRNELNRNLMDEMKkiAR 213
                                       68889999976.8888877777799********************999999998743444 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 ?    6.0   0.0     0.026        12      13      78 ..     121     190 ..     106     195 .. 0.55
   2 ?    6.9   0.1     0.014         6      36      81 ..     178     223 ..     153     232 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.026
                   Glyco_trans_4_2  13 tlrlakeLakrgyeVhvitpkkgakdeleaegihvhrlkvdrkg.pleyl...kafkl..kklikkikPDvv 78 
                                         +la+ L+k+g+ V+++ +++ + +    e+++ h  +v++k+ + +y    +a ++  ++  k++++Dvv
  gi|242398400|ref|YP_002993824.1| 121 IAKLANWLKKNGLSVVIAASDTFRAG--AIEQVEEHAKRVGVKViKHGYKsdpAAVAYdsIEHAKARGIDVV 190
                                       3678999*************999643..33444444444444444333321112223322555666666666 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.014
                   Glyco_trans_4_2  36 akdeleaegihvhrlkvdrkgpleylk.af.klkklikkikPDvvhah 81 
                                       + ++ +a gi v  ++  ++g  e+ + ++ ++kk+ +  kPD+v+ +
  gi|242398400|ref|YP_002993824.1| 178 SIEHAKARGIDVVLVD--TAGRNELNRnLMdEMKKIARVTKPDLVIFV 223
                                       4566778888888888..7776666644555*************9865 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1     0.015       6.5       1      44 [.     121     164 ..     121     170 .. 0.94
   2 ?    4.1   0.0     0.084        37      75     103 ..     214     242 ..     204     259 .. 0.63

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.015
                                       HHHHHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EEEE CS
                      TPP_enzyme_M   1 iekaaellkaakrpvilvGggvarsgaseelrelaeklgiPvvt 44 
                                       i+k+a+ lk+    v+++ + + r+ga e+++e a+++g+ v+ 
  gi|242398400|ref|YP_002993824.1| 121 IAKLANWLKKNGLSVVIAASDTFRAGAIEQVEEHAKRVGVKVIK 164
                                       7899***********************************99975 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.084
                                       HHH-SEEEEES-SSSTCCCTTTTTTTTTT CS
                      TPP_enzyme_M  75 leeaDlvlalGarfddirttgsepefape 103
                                       + + Dlv+++G  +      ++ ++f++ 
  gi|242398400|ref|YP_002993824.1| 214 VTKPDLVIFVGDSLAGNAILEQARQFNEA 242
                                       56677777777666553333333355433 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00043      0.19       7      49 ..      94     138 ..      88     144 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00043
                     TrwB_AAD_bind   7 vplpkeretqh..ilivGttGsGKtqalekllrairargdraivl 49 
                                       + + k++e++   i++vG  G GKt+++ kl +++++ g  ++++
  gi|242398400|ref|YP_002993824.1|  94 LEMIKSKEEKPfvIVFVGFNGGGKTTTIAKLANWLKKNGLSVVIA 138
                                       55666666665114568**********************999986 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       5.7   2.5e+03      88     109 ..      35      56 ..       9      97 .. 0.61
   2 ?   12.7   0.5    0.0002     0.086       3      40 ..     106     142 ..     105     210 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 5.7
                            AAA_31  88 idLaeaeielvelekkeeilke 109
                                       ++L ea++ l  +++ +e++ke
  gi|242398400|ref|YP_002993824.1|  35 LELLEADVALEVVDELKERIKE 56 
                                       3333333333333333333333 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.0002
                            AAA_31   3 vIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDp 40 
                                       vI+++ + GG GKTTt  +la +l k+g  v +   D+
  gi|242398400|ref|YP_002993824.1| 106 VIVFVGFNGG-GKTTTIAKLANWLKKNGLSVVIAASDT 142
                                       6888888888.*******************99987776 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00053      0.23      14      85 ..      92     151 ..      78     227 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00053
                            AAA_16  14 salervrsgrp..elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrql 85 
                                       ++le+++s ++   +++++G  G GK++ + +l++ l+k+g  ++ +  d +              r + ++q+
  gi|242398400|ref|YP_002993824.1|  92 DLLEMIKSKEEkpFVIVFVGFNGGGKTTTIAKLANWLKKNGLSVVIAASDTF--------------RAGAIEQV 151
                                       5666666666664677899***************988888766666666666..............22222222 PP

>> Torsin  Torsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.2    0.0021       0.9      47      83 ..      98     134 ..      37     165 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0021
                                       -SS-SS-EEEEEEE-TTSSHHHHHHHHHHHHSTTGGG CS
                            Torsin  47 nekpkkpLvlsfhGwtGtGknfvaeiiaenlyrdGlr 83 
                                       + k +kp+v+ f G+ G Gk      +a+ l ++Gl 
  gi|242398400|ref|YP_002993824.1|  98 KSKEEKPFVIVFVGFNGGGKTTTIAKLANWLKKNGLS 134
                                       46889****************9999999999999985 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00094      0.41       1      83 [.     115     227 ..     114     251 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00094
                   Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvltpapapg....apeleedgvrvhrlpvprrpspladlaal............. 60 
                                       gG ++ +a la +L + G +V++ +++  ++    + e+++ +v v  ++ +++++p a +  +             
  gi|242398400|ref|YP_002993824.1| 115 GGKTTTIAKLANWLKKNGLSVVIAASDTFRAgaieQVEEHAKRVGVKVIKHGYKSDPAAVAYDSiehakargidvvl 191
                                       6778899******************6666653333444555566666677777776555422223333444444444 PP

                   Glyco_trans_4_4  61 ..............ralrrllrqrrerpdvvhahs.pt 83 
                                                       ++ +   r  +pd+v+  + ++
  gi|242398400|ref|YP_002993824.1| 192 vdtagrnelnrnlmDEMKKIA--RVTKPDLVIFVGdSL 227
                                       444444333322222223333..566777777666555 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 ?    0.9   1.0      0.82   3.6e+02      48     111 ..       7      82 ..       3      90 .. 0.61
   2 ?   10.0   0.1    0.0013      0.57       6      72 ..      89     154 ..      87     228 .. 0.53

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.82
                          ATPase_2  48 dkyviyyialreesiskldefie.........eeeekkklekalgiavpkaeleeilk...eksklvfkaiellle 111
                                       +k  ++++++ + +is++d   +         e +++ ++ + l+++++++ + + +k   +k++ v++a+ ++  
  gi|242398400|ref|YP_002993824.1|   7 EKLSLFVDKVAQTEISEKDVENAlwdlelellEADVALEVVDELKERIKEKLVGQKVKigtNKRNIVENAVRDAVL 82 
                                       5566777777777777777764466777767744444444444455555555555555555777777777766655 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0013
                          ATPase_2   6 kelkeleeilerepneiyfiY.GpegsGKtaLlkeiienledkdkyviyyialreesiskldefieee 72 
                                       + ++ le i ++e+++++ ++ G  g GKt+ + ++++ l++ +  v+  ia ++ + + + e +ee+
  gi|242398400|ref|YP_002993824.1|  89 RHIDLLEMIKSKEEKPFVIVFvGFNGGGKTTTIAKLANWLKKNGLSVV--IAASDTFRAGAIEQVEEH 154
                                       4555566665555555554444******************88776554..333333333333332322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1107  (0.0617435); expected 358.6 (0.02)
Passed bias filter:                      820  (0.045736); expected 358.6 (0.02)
Passed Vit filter:                       144  (0.00803168); 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 0.34s 00:00:01.13 Elapsed: 00:00:00.51
# Mc/sec: 1762.63
//
Query:       gi|242398401|ref|YP_002993825.1|  [L=212]
Description: Small neutral amino acid transporter [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.5e-61  206.6  15.2    2.9e-61  206.4  15.2    1.0  1  MarC        MarC family integral membrane protein
  ------ inclusion threshold ------
      0.028   14.5   0.3      0.028   14.5   0.3    2.4  2  COX4_pro_2  Bacterial aa3 type cytochrome c oxidase subunit I


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 !  206.4  15.2   3.2e-65   2.9e-61       2     203 .]       8     210 ..       7     210 .. 0.97

  Alignments for each domain:
  == domain 1  score: 206.4 bits;  conditional E-value: 3.2e-65
                              MarC   2 kaiikafvsLlaiinplgnvpvflslleevskee.rkrialkasilallillvfllfGelilklfgisidalkiaGg 77 
                                       ++++++f +L+a++np+g+vpvfls+++++++ e     a+++s+ +++ l++f+l+Ge+i+k+fg +ida+ iaGg
  gi|242398401|ref|YP_002993825.1|   8 RTFLYVFGTLFAVMNPIGAVPVFLSIIQHCKSYEgMISLAKRTSVAVFVTLTAFALLGEWIFKFFGSTIDAFAIAGG 84 
                                       678999***********************98755267899************************************* PP

                              MarC  78 illfliaidmlkakqkkekkkkseeeeseekdeiavvPLAlPliaGPgaittvlvlaseassivekvavvlaillaa 154
                                       illf +a++ml+++ ++ k +++eeee+ +  eia+vPLA+Pli+GPg+ittv++++++  s   k+av+lail+  
  gi|242398401|ref|YP_002993825.1|  85 ILLFRMALEMLSGNLSTVKISHEEEEEAVNLSEIAIVPLAIPLISGPGSITTVMIHMAKNASYLGKAAVMLAILITS 161
                                       ***************************************************************************** PP

                              MarC 155 litllilllsslilrllgktginaleRlmGllLvalavqlivdGikeil 203
                                       ++++++l++++ + ++lgk gi++++R+mGl+L+ +avql+++Gik+++
  gi|242398401|ref|YP_002993825.1| 162 FLVYVVLRSAEKVQQRLGKVGIRLITRMMGLILASMAVQLVINGIKGAF 210
                                       **********************************************986 PP

>> COX4_pro_2  Bacterial aa3 type cytochrome c oxidase subunit IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.3   3.1e-06     0.028      16      45 ..      35      64 ..      33      65 .. 0.93
   2 ?   -2.3   0.2      0.56     5e+03      34      43 ..     151     160 ..     146     163 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.1e-06
                        COX4_pro_2 16 eHekTYagFlkltkwgtlavavllvlmaif 45
                                      +H k Y+g + l+k++++av v l ++a+ 
  gi|242398401|ref|YP_002993825.1| 35 QHCKSYEGMISLAKRTSVAVFVTLTAFALL 64
                                      799************************985 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.56
                        COX4_pro_2  34 avavllvlma 43 
                                       a+++l++l +
  gi|242398401|ref|YP_002993825.1| 151 AAVMLAILIT 160
                                       4555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1070  (0.0596798); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); 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 0.32s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 1243.29
//
Query:       gi|242398402|ref|YP_002993826.1|  [L=260]
Description: ABC transporter ATP-binding protein [Thermococcus sibiricus MM 739]
Scores for complete 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  103.2   0.0    2.3e-29  102.7   0.0    1.2  1  ABC_tran      ABC transporter
    4.1e-14   53.1   0.1      9e-06   25.7   0.0    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    1.6e-06   27.7   0.0    4.2e-05   23.1   0.0    2.1  1  SMC_N         RecF/RecN/SMC N terminal domain
    3.8e-05   24.3   0.0    6.2e-05   23.6   0.0    1.3  1  AAA_23        AAA domain
    0.00012   21.7   0.0    0.00023   20.8   0.0    1.4  1  AAA_29        P-loop containing region of AAA domain
    0.00025   21.3   0.0     0.0013   19.0   0.0    2.0  1  AAA_22        AAA domain
    0.00051   19.8   0.0    0.00089   19.0   0.0    1.4  1  AAA_30        AAA domain
    0.00054   18.9   0.0    0.00087   18.2   0.0    1.4  1  DLIC          Dynein light intermediate chain (DLIC)
    0.00067   19.5   0.0        0.1   12.3   0.0    2.1  2  AAA_15        AAA ATPase domain
      0.001   19.0   0.0     0.0021   18.0   0.0    1.4  1  RsgA_GTPase   RsgA GTPase
     0.0016   18.9   0.0     0.0023   18.4   0.0    1.4  1  AAA_16        AAA ATPase domain
     0.0019   18.6   0.4     0.0073   16.7   0.4    2.0  1  AAA           ATPase family associated with various cellular 
     0.0033   17.1   0.0     0.0052   16.4   0.0    1.2  1  AAA_27        AAA domain
     0.0055   16.7   0.0     0.0086   16.0   0.0    1.3  1  ATPase_2      ATPase domain predominantly from Archaea
     0.0063   15.7   0.0      0.012   14.8   0.0    1.4  2  G-alpha       G-protein alpha subunit
     0.0065   17.0   0.0      0.012   16.2   0.0    1.5  1  AAA_18        AAA domain
     0.0069   16.1   0.0      0.013   15.2   0.0    1.5  1  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
  ------ inclusion threshold ------
       0.02   14.1   0.0      0.066   12.4   0.0    1.8  1  NB-ARC        NB-ARC domain
      0.021   14.7   0.2      0.045   13.7   0.2    1.5  1  NACHT         NACHT domain
      0.024   14.7   0.0      0.049   13.6   0.0    1.5  1  TsaE          Threonylcarbamoyl adenosine biosynthesis protei
      0.029   14.6   0.1       0.64   10.3   0.1    2.4  1  SbcCD_C       Putative exonuclease SbcCD, C subunit
       0.03   14.1   0.0       0.47   10.2   0.0    2.1  2  IstB_IS21     IstB-like ATP binding protein
      0.043   12.5   0.0       0.52    8.9   0.0    2.0  2  AAA_13        AAA domain
      0.043   14.0   0.0        0.2   11.8   0.0    1.9  2  AAA_33        AAA domain
      0.048   13.6   0.0       0.16   11.9   0.0    1.8  2  Rad17         Rad17 P-loop domain
      0.052   13.1   0.3      0.094   12.3   0.3    1.4  1  cobW          CobW/HypB/UreG, nucleotide-binding domain
      0.071   12.7   0.2       0.13   11.8   0.2    1.4  1  SRP54         SRP54-type protein, GTPase domain
      0.082   12.9   0.1       0.19   11.8   0.1    1.6  1  AAA_5         AAA domain (dynein-related subfamily)
      0.092   12.7   0.0       0.18   11.7   0.0    1.5  1  BCA_ABC_TP_C  Branched-chain amino acid ATP-binding cassette 
       0.11   12.0   0.0        1.3    8.5   0.0    2.5  3  AAA_7         P-loop containing dynein motor region
       0.11   11.5   0.0       0.18   10.9   0.0    1.2  1  T2SSE         Type II/IV secretion system protein
       0.14    9.7   0.1       0.18    9.3   0.1    1.1  1  DUF3584       Protein of unknown function (DUF3584)
       0.17   12.1   0.2       0.29   11.4   0.2    1.4  1  AAA_28        AAA domain
       0.21   11.6   0.0       0.33   10.9   0.0    1.3  1  ResIII        Type III restriction enzyme, res subunit


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.7   0.0   4.3e-32   2.3e-29       2     136 ..      18     163 ..      17     164 .. 0.93

  Alignments for each domain:
  == domain 1  score: 102.7 bits;  conditional E-value: 4.3e-32
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSB..H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..x RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpelt..v 76 
                                       +nv++kl  ++++ ++G+nGaGK+tLl+++agl+++ +G++l+ gk+  e     +r+ i+++pq  +l++++   v
  gi|242398402|ref|YP_002993826.1|  18 ENVTFKLDSDQTLLLLGPNGAGKTTLLRAVAGLHQNYKGTLLVFGKPPIE-----SRNVISYVPQSYSLNERVPltV 89 
                                       79***************************************999988877.....9**********99999874215 PP

                                       HHH..................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEEST CS
                                       xxx..................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  77 ren..................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEp 135
                                        e                   +  +e+++al+ +gl  lkd++     s+LSgGqkqrv laral++kpkllllDEp
  gi|242398402|ref|YP_002993826.1|  90 IEVvamgalykrglmhfniprNLLREATEALEFVGLGSLKDKRF----SELSGGQKQRVLLARALISKPKLLLLDEP 162
                                       5559*************999999999******************....***************************** PP

                                       T CS
                                       x RF
                          ABC_tran 136 t 136
                                        
  gi|242398402|ref|YP_002993826.1| 163 L 163
                                       7 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   1.7e-08     9e-06       3      72 ..      31      99 ..      30     110 .. 0.85
   2 !   25.4   0.1   2.1e-08   1.1e-05     234     299 ..     133     196 ..     107     197 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 1.7e-08
                            AAA_21  3 vliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvry 72
                                      +l GpNg+GK++LL+a  +l++ +  ++ l   ++++ +  +i++ + +y+ ++++ ++++e++  g  y
  gi|242398402|ref|YP_002993826.1| 31 LLLGPNGAGKTTLLRAVAGLHQ-NYKGTLLVFGKPPIESRNVISYVPQSYSLNERVPLTVIEVVAMGALY 99
                                      699******************9.88888889999999999999999999999888888888777666665 PP

  == domain 2  score: 25.4 bits;  conditional E-value: 2.1e-08
                            AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltTHSp 299
                                       ++elS G+k+   l+ al++ +   +lll+DEp + L+P++  +++ +l k++++ g   i+tTH+p
  gi|242398402|ref|YP_002993826.1| 133 FSELSGGQKQRVLLARALISKP---KLLLLDEPLSALDPSARVEVVSVLaKIKQEIGLAMIITTHDP 196
                                       7899*****9988888888877...9********************99987777778999******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 !   23.1   0.0   7.9e-08   4.2e-05      20     205 ..      22     202 ..       6     212 .. 0.69

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 7.9e-08
                                       EETTSS.EEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--.BTTCSSTTEEEEEEEEEETTEESSSSS CS
                                       xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  20 lpfsks.ftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk.skekasvkkaeveitfdnedkklkiek 94 
                                        ++++     ++GpNG+GK+ ll A+    G +++      k + l++     +++    +v   ++ +++ ++ + 
  gi|242398402|ref|YP_002993826.1|  22 FKLDSDqTLLLLGPNGAGKTTLLRAV---AGLHQN-----YKGTLLVFGkPPIESRNVISYVPQSYSLNER-VPLTV 89 
                                       444444044679*************9...564333.....5566677763333344444555555555444.68999 PP

                                       SCEEEEEEEETTSEEEEEETTEEE-H.HHHHHHHHCTT-STT...CS-HHHHHHHHHHHHHHHHCCS--SEEEECTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  95 eevsisrrvkrkgeseykingkevtk.kevsellesagiske...lLSgGektLvalaLlfAiqkvkpaplyllDei 167
                                        ev+ +  +++ g  ++ i ++  ++ +e  e++    ++ +   +LSgG+k+ v    l+A   +++  l llDe 
  gi|242398402|ref|YP_002993826.1|  90 IEVVAMGALYKRGLMHFNIPRNLLREaTEALEFVGLGSLKDKrfsELSGGQKQRV----LLARALISKPKLLLLDEP 162
                                       9999999999999999999888877645555554444444334448*****9843....4444455666799***** PP

                                       TTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHHHCCC- CS
                                       xxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxx RF
                             SMC_N 168 daaLDeknvkkvaellkekskn..aQfivislreemleka 205
                                        +aLD + + +v+++l + +++    +i+++++ + l++ 
  gi|242398402|ref|YP_002993826.1| 163 LSALDPSARVEVVSVLAKIKQEigLAMIITTHDPNPLTEI 202
                                       ***************9988777557899999998876655 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   1.2e-07   6.2e-05      11      39 ..      18      47 ..       2      54 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 1.2e-07
                            AAA_23 11 rdqeidF.skgltlItGpNGaGKTTildAi 39
                                      +++++ + s+   l+ GpNGaGKTT+l+A+
  gi|242398402|ref|YP_002993826.1| 18 ENVTFKLdSDQTLLLLGPNGAGKTTLLRAV 47
                                      5566666888999***************97 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   4.4e-07   0.00023      14      43 ..      19      48 ..      14      54 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 4.4e-07
                            AAA_29 14 ghtieidlkgatlltGpsGsGKSTllDAiq 43
                                      + t+++d +++ ll Gp+G+GK+Tll A++
  gi|242398402|ref|YP_002993826.1| 19 NVTFKLDSDQTLLLLGPNGAGKTTLLRAVA 48
                                      578889977799**************9886 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   2.5e-06    0.0013       5      99 ..      27     161 ..      23     194 .. 0.60

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.5e-06
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaee.......................erpevvfvtlpsst...sskd 55 
                                       ++ l++ G+ G+GKTtllr ++  +++++                           er+++  +++ + +   ++  
  gi|242398402|ref|YP_002993826.1|  27 DQTLLLLGPNGAGKTTLLRAVAGLHQNYKGTLLvfgkppiesrnvisyvpqsyslnERVPLTVIEVVAMGalyKRGL 103
                                       67799******************998776555599999985544444444444444222222222222222212222 PP

                            AAA_22  56 llrellralglelka..........erlsseell.ealeqalrarav...ielliiDE 99 
                                       +  ++ r+l +e+ +          + ++ +el   + ++ l ara    ++ll++DE
  gi|242398402|ref|YP_002993826.1| 104 MHFNIPRNLLREATEalefvglgslKDKRFSELSgGQKQRVLLARALiskPKLLLLDE 161
                                       2333333333333335555666666666666666666666666666666666777776 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   1.7e-06   0.00089      16      51 ..      25      60 ..      10      76 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.7e-06
                            AAA_30 16 sgdrvavltGpAGtGKttalkalreaweaaggrvig 51
                                      ++d++ +l Gp G+GKtt+l+a++ ++++ +g++++
  gi|242398402|ref|YP_002993826.1| 25 DSDQTLLLLGPNGAGKTTLLRAVAGLHQNYKGTLLV 60
                                      5677999*********************99766665 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.6e-06   0.00087      20      57 ..      22      59 ..      15     118 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.6e-06
                              DLIC 20 sklPsgksvlvlGedgsGkttliaklqGveeekkGrGl 57
                                       kl s++++l+lG +g+Gkttl+  + G+ ++ kG  l
  gi|242398402|ref|YP_002993826.1| 22 FKLDSDQTLLLLGPNGAGKTTLLRAVAGLHQNYKGTLL 59
                                      59*********************************866 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   0.00019       0.1      14      43 ..      17      47 ..      15      80 .. 0.83
   2 ?    5.2   0.0     0.027        14     322     366 ..     152     196 ..     133     198 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00019
                            AAA_15 14 lkdveidlsee.ltvliGkNnsGKSsileal 43
                                       ++v+ +l+++ + +l G+N++GK+++l+a 
  gi|242398402|ref|YP_002993826.1| 17 VENVTFKLDSDqTLLLLGPNGAGKTTLLRAV 47
                                      566666676665889*************996 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.027
                            AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSp 366
                                       +k+++ll++EP   L p+a  +++  l+++ ++     iitTH p
  gi|242398402|ref|YP_002993826.1| 152 SKPKLLLLDEPLSALDPSARVEVVSVLAKIKQEIGLAMIITTHDP 196
                                       57899*****************************99*******98 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   3.9e-06    0.0021      84     121 ..      11      49 ..       3      58 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3.9e-06
                                       TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  84 aktkegleelkellkd.ktsvlvGqSGvGKStLinallp 121
                                        ++++++e+++ +l++ +t +l+G+ G+GK+tL+ a+++
  gi|242398402|ref|YP_002993826.1|  11 YDRQKAVENVTFKLDSdQTLLLLGPNGAGKTTLLRAVAG 49 
                                       56678999******998*****************99887 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   4.3e-06    0.0023      25      66 ..      28      70 ..      11     161 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 4.3e-06
                            AAA_16 25 elvllsGesGvGKsslvrellralekd..ggiflrgkcdqlesa 66
                                      + +ll G+ G GK++l+r+++  l ++  g +++ gk    +++
  gi|242398402|ref|YP_002993826.1| 28 QTLLLLGPNGAGKTTLLRAVA-GLHQNykGTLLVFGKPPIESRN 70
                                      689*****************9.5666633444477776666444 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.4   1.4e-05    0.0073       1      21 [.      30      50 ..      30     202 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.4e-05
                                      EEEESSTTSSHHHHHHHHHHH CS
                               AAA  1 vllyGppGtGKTllakavake 21
                                      +ll Gp G GKT+l +ava  
  gi|242398402|ref|YP_002993826.1| 30 LLLLGPNGAGKTTLLRAVAGL 50
                                      69****************975 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   9.8e-06    0.0052      18      49 ..      19      50 ..      14      55 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 9.8e-06
                            AAA_27 18 sldfsaeeadlhliyGpNEAGKstalrAisdl 49
                                      +++f+ ++++  l++GpN AGK+t+lrA+  l
  gi|242398402|ref|YP_002993826.1| 19 NVTFKLDSDQTLLLLGPNGAGKTTLLRAVAGL 50
                                      5678888889999***************9866 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.6e-05    0.0086       1      47 [.      10      54 ..      10      74 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.6e-05
                          ATPase_2  1 FfdRekelkeleeilerepneiyfiYGpegsGKtaLlkeiienledk 47
                                      ++dR+k+++++   l++  ++ +++ Gp g GKt+Ll+ ++  ++++
  gi|242398402|ref|YP_002993826.1| 10 YYDRQKAVENVTFKLDS--DQTLLLLGPNGAGKTTLLRAVAGLHQNY 54
                                      58*********999999..8889999************999887654 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   2.3e-05     0.012       7      49 ..      11      53 ..       5      75 .. 0.87
   2 ?   -2.3   0.0       3.6   1.9e+03     133     162 ..     218     248 ..     126     254 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.3e-05
                                      XXXXXXXXXXXXXE..EEEEEEEESTTSSHHHHHHHHHHHCS- CS
                           G-alpha  7 idkslkaerkarkkkrevkllllGqseSGKsTilkqlkllykk 49
                                       d++   e+ ++k +++ +llllG ++ GK+T+l+ +  l+++
  gi|242398402|ref|YP_002993826.1| 11 YDRQKAVENVTFKLDSDQTLLLLGPNGAGKTTLLRAVAGLHQN 53
                                      688888889999999999******************9999975 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.6
                                       HHHHHCCSHHHHHHHCCG.CCTT--TTHHHH CS
                           G-alpha 133 dikaLwndpgiqelyerr.nkiklednaeyF 162
                                       + +++  d++i ++y ++ + ik+   +  F
  gi|242398402|ref|YP_002993826.1| 218 SPEEVLRDEIITKVYGSQsKAIKVGKRMYCF 248
                                       4455666777777777443666665555555 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   2.2e-05     0.012       2      43 ..      31      86 ..      30     115 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.2e-05
                            AAA_18  2 lltGtpGvGKttlakeLskrl.gf.............gvnlrdvakenglllevdp 43
                                      ll G+ G+GKttl ++++ ++ ++             ++n++++++++++l e+ p
  gi|242398402|ref|YP_002993826.1| 31 LLLGPNGAGKTTLLRAVAGLHqNYkgtllvfgkppieSRNVISYVPQSYSLNERVP 86
                                      689****************99777*********************99998887766 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   2.5e-05     0.013       3      32 ..      29      58 ..      27      92 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.5e-05
                         PduV-EutP  3 killiGkvgsGKttLtqalkgeelkYkktq 32
                                       +ll+G+ g+GKttL +a+ g + +Yk t 
  gi|242398402|ref|YP_002993826.1| 29 TLLLLGPNGAGKTTLLRAVAGLHQNYKGTL 58
                                      689***********************9985 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00013     0.066       2      87 ..      14     123 ..      13     205 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00013
                                       HHHHHHHHHHHHCTTTSCSEEEEEEESTTSSHHHHHHHHCCSHCCCCCCBTEEEEE..................... CS
                            NB-ARC   2 eksvekviekLlekdelqslvvalvGmgGvGKttlakqilnksdevegrFdsvawv..................... 57 
                                       +k ve+v  kL+   + q   + l G  G GKttl++ +       ++++ +   v                     
  gi|242398402|ref|YP_002993826.1|  14 QKAVENVTFKLD---SDQ--TLLLLGPNGAGKTTLLRAVAGL----HQNYKGTLLVfgkppiesrnvisyvpqsysl 81 
                                       677888888888...334..6899************998766....4555555555555566666666666666666 PP

                                       ............EEESXXHHHHHHHXXHHHHHCCCTTSSSS- CS
                            NB-ARC  58 ............vvsktdkseeiletilkeLslseddleeke 87 
                                                    ++  +k   +  +i ++L ++  +  e+ 
  gi|242398402|ref|YP_002993826.1|  82 nervpltvievvAMGALYKRGLMHFNIPRNLLREATEALEFV 123
                                       666666666555555555555555555555555555555555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2   8.5e-05     0.045       2      22 ..      29      49 ..      28      63 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8.5e-05
                                      CEEEEC-TTTCHHHHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqklal 22
                                      +++l G++G GKTtLl+ +a 
  gi|242398402|ref|YP_002993826.1| 29 TLLLLGPNGAGKTTLLRAVAG 49
                                      789**************9985 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   9.2e-05     0.049       6      40 ..      16      48 ..      11      55 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.2e-05
                                      HHHHHHHHHHHCHTEEEEEEESTTSSHHHHHHHHH CS
                              TsaE  6 etealgkklakalgdvilLeGdLGaGKTtlvrgla 40
                                      ++e++  kl +   +++lL G+ GaGKTtl r++a
  gi|242398402|ref|YP_002993826.1| 16 AVENVTFKLDS--DQTLLLLGPNGAGKTTLLRAVA 48
                                      44555555554..778****************987 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 ?   10.3   0.1    0.0012      0.64      28      89 ..     131     179 ..     124     180 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0012
                           SbcCD_C  28 rssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                       +++++lSGG+kq    + la   +al+s+       ++l++LDE  s lD+  + +++++l+
  gi|242398402|ref|YP_002993826.1| 131 KRFSELSGGQKQR---VLLA---RALISK-------PKLLLLDEPLSALDPSARVEVVSVLA 179
                                       6778888888843...3333...334444.......89*************99998888775 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 ?   10.2   0.0    0.0009      0.47      44      68 ..      24      48 ..      11      61 .. 0.84
   2 ?    1.6   0.0      0.38     2e+02     104     148 ..     149     194 ..     130     206 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0009
                         IstB_IS21 44 iekkenivllGpsGvGKshlaialg 68
                                      +++ + ++llGp G+GK+ l  a++
  gi|242398402|ref|YP_002993826.1| 24 LDSDQTLLLLGPNGAGKTTLLRAVA 48
                                      578899************9988865 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.38
                         IstB_IS21 104 krllkvdllilDdlgllpldqaeaellfeviekryerr..siiitsn 148
                                       + + k++ll+lD+  l  ld  ++ ++  v++k  +    ++iit+ 
  gi|242398402|ref|YP_002993826.1| 149 ALISKPKLLLLDE-PLSALDPSARVEVVSVLAKIKQEIglAMIITTH 194
                                       4467899*****9.589999999999999999877663236777775 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0   0.00099      0.52      21      41 ..      32      52 ..      25      67 .. 0.86
   2 ?    1.4   0.0      0.18        96     524     570 ..     151     195 ..     144     223 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00099
                            AAA_13 21 iYGwNGaGKTtLSrllrslel 41
                                      + G NGaGKTtL r+ + l +
  gi|242398402|ref|YP_002993826.1| 32 LLGPNGAGKTTLLRAVAGLHQ 52
                                      669***********9999855 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.18
                            AAA_13 524 igkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHn 570
                                       i+k k   +D P S LD  +   v+s + +    ++    ++i TH 
  gi|242398402|ref|YP_002993826.1| 151 ISKPKLLLLDEPLSALDPSARVEVVSVLAKIK--QEIGLAMIITTHD 195
                                       67899999**********99999999988875..3333467888886 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00038       0.2       3      21 ..      31      49 ..      30      89 .. 0.87
   2 ?   -0.4   0.0       2.2   1.2e+03      68     115 ..     152     227 ..     129     243 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00038
                            AAA_33  3 llvGlpGsGKstlaerllk 21
                                      ll G++G+GK+tl++ ++ 
  gi|242398402|ref|YP_002993826.1| 31 LLLGPNGAGKTTLLRAVAG 49
                                      688************9864 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 2.2
                            AAA_33  68 sagrnvildat..nlsrrerarflklarrlgvp..........................vrivvvetdeetlkeRl 115
                                       s+ + ++ld +   l++++r ++++++ +++ +                           +++++ ++ee+l++ +
  gi|242398402|ref|YP_002993826.1| 152 SKPKLLLLDEPlsALDPSARVEVVSVLAKIKQEiglamiitthdpnplteigdkimllnKELIAFGSPEEVLRDEI 227
                                       5555555555533344555555555544443333333444444444444444444444455666666666666655 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0    0.0003      0.16      40      68 ..      22      50 ..       3      59 .. 0.73
   2 ?   -1.3   0.0       3.3   1.7e+03      35     162 ..     145     181 ..     131     198 .. 0.48

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0003
                             Rad17 40 LesrkkriLLisGPsGCgkstvvkvLske 68
                                       +    + LL+ GP G gk+t ++ ++  
  gi|242398402|ref|YP_002993826.1| 22 FKLDSDQTLLLLGPNGAGKTTLLRAVAGL 50
                                      333445899**************988765 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 3.3
                             Rad17  35 lkadvLesrkkriLLisGPsGCgkstvvkvLskelgiklrewlnpvslkepdnqksdfkgltekesrflsqiesfke 111
                                       l a  L s++k                                                                  
  gi|242398402|ref|YP_002993826.1| 145 LLARALISKPK------------------------------------------------------------------ 155
                                       44555555433.................................................................. PP

                             Rad17 112 leLkdakylklqklGddlrtdkklilvedlPnkfyrdsdalrevirkylrs 162
                                                              l+l+++  +    ++    ev+    ++
  gi|242398402|ref|YP_002993826.1| 156 -----------------------LLLLDEPLSALDPSA--RVEVVSVLAKI 181
                                       .......................333333222222221..12333333333 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   0.3   0.00018     0.094       3      26 ..      30      53 ..      28      61 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00018
                                      EEEEESTTCCHHHHHHHHHCT--S CS
                              cobW  3 tvltGflGsGKTtLlnhllenrag 26
                                      ++l G+ G+GKTtLl+++   +++
  gi|242398402|ref|YP_002993826.1| 30 LLLLGPNGAGKTTLLRAVAGLHQN 53
                                      6789************99844444 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   0.00025      0.13       3      28 ..      29      54 ..      27      62 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00025
                                      EEEEEESTTSSHHHHHHHHHHHHHHT CS
                             SRP54  3 villvGlqGaGKTttlaKLaallkke 28
                                       +ll+G++GaGKTt l  +a l ++ 
  gi|242398402|ref|YP_002993826.1| 29 TLLLLGPNGAGKTTLLRAVAGLHQNY 54
                                      689************99999777665 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00035      0.19       2      24 ..      30      53 ..      29      72 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00035
                                      EEEE--SSSSHHHHHHHGGGGB.S CS
                             AAA_5  2 vlLvGppGtgKselaerlaaal.n 24
                                      +lL+Gp G gK++l + +a +  n
  gi|242398402|ref|YP_002993826.1| 30 LLLLGPNGAGKTTLLRAVAGLHqN 53
                                      89**************99988743 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 ?   11.7   0.0   0.00035      0.18       1      15 [.     212     226 ..     212     227 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00035
                      BCA_ABC_TP_C   1 rvIAeGtPaEvrndP 15 
                                       ++IA G+P+Ev +d+
  gi|242398402|ref|YP_002993826.1| 212 ELIAFGSPEEVLRDE 226
                                       58***********97 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0    0.0025       1.3      30      53 ..      24      47 ..      12      63 .. 0.82
   2 ?   -1.1   0.0       2.2   1.2e+03     135     172 ..      78     115 ..      62     117 .. 0.78
   3 ?   -0.4   0.0       1.3   6.9e+02      98     111 ..     241     254 ..     229     259 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0025
                             AAA_7 30 lknkkpvllvGptGtGKtviikdl 53
                                      l++++ +ll Gp G GKt++++ +
  gi|242398402|ref|YP_002993826.1| 24 LDSDQTLLLLGPNGAGKTTLLRAV 47
                                      5678899************99875 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.2
                             AAA_7 135 wYdrkklefkeikdvqlvaamgppgggrneitpRllrh 172
                                        Y++++    ++++v+ ++a  + g  +++i+  llr 
  gi|242398402|ref|YP_002993826.1|  78 SYSLNERVPLTVIEVVAMGALYKRGLMHFNIPRNLLRE 115
                                       57777777788999999999999999999999888885 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1.3
                             AAA_7  98 ggkklvvFvDDlnm 111
                                        gk++ +F+ D+++
  gi|242398402|ref|YP_002993826.1| 241 VGKRMYCFIGDVHL 254
                                       79*********986 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   0.00033      0.18     115     156 ..      14      54 ..       3      67 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00033
                             T2SSE 115 kekiaevlrkavrerglilvsGgTgsGKttllyallkeinks 156
                                       ++++++v  k   + +++l+ G+ g GKttll a+    +++
  gi|242398402|ref|YP_002993826.1|  14 QKAVENVTFKL-DSDQTLLLLGPNGAGKTTLLRAVAGLHQNY 54 
                                       45555554444.788999**************9987766655 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   0.00033      0.18      13      37 ..      23      47 ..      17      48 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00033
                           DUF3584 13 eldldghtnieGtNaaGKTtLlrLi 37
                                      +ld d    + G N+aGKTtLlr +
  gi|242398402|ref|YP_002993826.1| 23 KLDSDQTLLLLGPNGAGKTTLLRAV 47
                                      68888888999************75 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   0.00055      0.29       3      21 ..      31      51 ..      29      63 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00055
                            AAA_28  3 vitGgestGKTtlleaLa..a 21
                                       ++G+ ++GKTtll+a a   
  gi|242398402|ref|YP_002993826.1| 31 LLLGPNGAGKTTLLRAVAglH 51
                                      589*************99442 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00062      0.33       4      60 ..       9      60 ..       6      85 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00062
                                      E-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEE CS
                            ResIII  4 lreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflfl 60
                                      +++  ++a+en+  kl+   d+ +l+  + G+GKT + +++++ l++++k   +l++
  gi|242398402|ref|YP_002993826.1|  9 IYYDRQKAVENVTFKLD--SDQTLLLLGPNGAGKTTL-LRAVAGLHQNYK--GTLLV 60
                                      6677899******9995..999*************65.666777777755..55555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); 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: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.45
# Mc/sec: 1745.27
//
Query:       gi|242398403|ref|YP_002993827.1|  [L=273]
Description: zinc ABC transporter permease [Thermococcus sibiricus MM 739]
Scores for complete 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   96.8  33.9    1.9e-27   96.4  33.9    1.0  1  ABC-3     ABC 3 transport family
     0.0012   17.9  33.2     0.0012   17.9  33.2    1.5  2  FecCD     FecCD transport family


Domain annotation for each model (and alignments):
>> ABC-3  ABC 3 transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.4  33.9   2.1e-31   1.9e-27       3     251 ..       4     266 ..       3     271 .. 0.92

  Alignments for each domain:
  == domain 1  score: 96.4 bits;  conditional E-value: 2.1e-31
                             ABC-3   3 eflqrallasilvslacallgsfvvlrrqsllgdalsHaalpGvalayllgvn......lllgailvgliaavalel 73 
                                       e+l+rall++i+vs+  ++l+ ++ +r+ ++l  a  H+ l G +l+++lg+       +l+ a+++++++   +++
  gi|242398403|ref|YP_002993827.1|   4 EYLFRALLGGIMVSILLGMLSPLINMRGLAFLTHATFHSLLFGAVLGMILGLIfensslILWVALVITIFVVASIAF 80 
                                       789***********************************************999888888888888888888888888 PP

                             ABC-3  74 lkrktklkedtaigivlsvflalglvlvslikk.........skvdldsyLfGniltisqedliliaiieavvllll 141
                                       l++k  +++dtaigi++s++ ++ ++++ +  k          ++++ syL G++  i+ +dl+ ++   a+++ ++
  gi|242398403|ref|YP_002993827.1|  81 LEEK-GFSSDTAIGIIASFIAGFTVLAFGILYKvmatrpyfaLSQSIVSYLTGELFLITINDLLFLVLGGALIFFVM 156
                                       8876.699**********87666666555544444456889999********************************* PP

                             ABC-3 142 llfwkelllitfdeelAkveglsvkllkllllalialavvvalqavGviLvialliiPaatArrltrslesllivAi 218
                                       llf++++l ++fd e  ++   + kl+  ll ++++++ ++++++vG+i +  + ++P+a+A++l+++l+++l ++ 
  gi|242398403|ref|YP_002993827.1| 157 LLFYRDFLYVSFDAEGLESYSGNAKLYLTLLYIIVGATGALIVRTVGLITLQVIAVLPGAIALMLSNDLRKILGISL 233
                                       ***************************************************************************** PP

                             ABC-3 219 llglvsvvaGlllSyyldlatGavivlvatllf 251
                                       +l l   ++ ++l y  +++++++ ++++ +++
  gi|242398403|ref|YP_002993827.1| 234 ALTLSIQILSIILAYLTNIPPSGIATIMLGFVY 266
                                       ***********************9999987765 PP

>> FecCD  FecCD transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1      0.13   1.2e+03     132     152 ..       8      28 ..       6      43 .. 0.70
   2 !   17.9  33.2   1.4e-07    0.0012      82     305 ..      46     266 ..      39     273 .] 0.85

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.13
                             FecCD 132 kliLaGiavsallsaltslll 152
                                       + +L Gi+vs+ll+ l+ l+ 
  gi|242398403|ref|YP_002993827.1|   8 RALLGGIMVSILLGMLSPLIN 28 
                                       557778888877776666554 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 1.4e-07
                             FecCD  82 gaalgavlalllllgslslfalplaaflgallalllvlllarkrkgasplkliLaGiavsallsaltsllllllnee 158
                                       ga+lg++l+l++     ++  ++++a++  +++++ + +l +k+ +++++  i+a ++ ++ + a+  l +++++  
  gi|242398403|ref|YP_002993827.1|  46 GAVLGMILGLIF----ENSSLILWVALVITIFVVASIAFLEEKGFSSDTAIGIIASFIAGFTVLAFGILYKVMATRP 118
                                       455555555554....566668888888889999999999999999999999**************99999998443 PP

                             FecCD 159 ...alesilfwllGslsgaswskvllllvllllllllllllarkldllalgdetAkslGvnvervrllllllvallt 232
                                           ++si+ +l+G l  ++++++l+l++  +l+++++ll++r++  +++++e  +s   n + +  ll+++v +  
  gi|242398403|ref|YP_002993827.1| 119 yfaLSQSIVSYLTGELFLITINDLLFLVLGGALIFFVMLLFYRDFLYVSFDAEGLESYSGNAKLYLTLLYIIVGATG 195
                                       344899*********************************************************************** PP

                             FecCD 233 avavalvGpigFvGL.ivPhiarllvgadhrkllplsallGallllladllarlllsptelpvgivtaliGapf 305
                                       a++v  vG i++  + + P  + l++++d rk+l +s  l+  + +l+ +la l   ++  p gi t ++G ++
  gi|242398403|ref|YP_002993827.1| 196 ALIVRTVGLITLQVIaVLPGAIALMLSNDLRKILGISLALTLSIQILSIILAYLT--NIP-PSGIATIMLGFVY 266
                                       ***********95552558888889999*********999998888888877665..333.7788888888665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       960  (0.0535445); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); 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):               2  [number of targets reported over threshold]
# CPU time: 0.69u 0.35s 00:00:01.04 Elapsed: 00:00:00.54
# Mc/sec: 1533.97
//
Query:       gi|242398404|ref|YP_002993828.1|  [L=224]
Description: Ribonuclease HII [Thermococcus sibiricus MM 739]
Scores for complete 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-52  176.3   0.0    7.6e-52  176.0   0.0    1.1  1  RNase_HII  Ribonuclease HII
     0.0081   15.6   0.0      0.015   14.7   0.0    1.4  1  DUF4003    Protein of unknown function (DUF4003)


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 !  176.0   0.0   8.5e-56   7.6e-52       2     197 ..       5     200 ..       4     201 .. 0.89

  Alignments for each domain:
  == domain 1  score: 176.0 bits;  conditional E-value: 8.5e-56
                                       EEEEE-TT-SBS-EEEEEEEECGHHHHHHHCTTGTTGTTS-HHHHHHHHHHHHSEEEEEEE-HHHHH.HHTTTS-HH CS
                         RNase_HII   2 GiDEaGrGpvlGplvvaavavekereeelkklgvkDSKkLskqkreeLaklikkkiekrklvaeeikyaseneinln 78 
                                       GiDEaGrGpv+Gplv+aav++++ ++e++++lgvkDSKkLs++kreeL+++i + +    +     +  +++e + n
  gi|242398404|ref|YP_002993828.1|   5 GIDEAGRGPVVGPLVIAAVVIDESKIEKFEALGVKDSKKLSPKKREELFEKIIELVDDYFILELSPEDIDKREGTMN 81 
                                       9****************************************************777654333333333667777778 PP

                                       HHHHHHHHHHHHHHHHTCEECCECCCE--SS.HHHHHHHHHHHHC..CEEEEETTGGGT-HHHHHHHHHHHHHHHHH CS
                         RNase_HII  79 eikaaltlaviklleklgvkvdeilvdgvtt.peslkkkleqiik..ikvtvekkadekyllvaaASiiAkverdee 152
                                       + +++++++v   l+ l++k+d +++d+ +  +e++   +++ ++   k+++e+kad+ky+ vaaASi+Akv+rd  
  gi|242398404|ref|YP_002993828.1|  82 DFEVENFAKV---LNSLKIKPDLVYIDAADVnEERFGIVVREKLSfyPKIIAEHKADSKYIPVAAASILAKVTRDKA 155
                                       8887777665...6778899*******9998888889999998777789**************************** PP

                                       HHHHHHHCSH.--TTSSTTSHHHHHHHHHHHHH..S--TTB-TTSHH CS
                         RNase_HII 153 lellkrkpgtldkgsGyasdektrallkkgats..klpdivrlsfkt 197
                                       +e+lk+ +g  ++gsGy+sd+ tr++l+++ ++    p +vr+s+kt
  gi|242398404|ref|YP_002993828.1| 156 IERLKEIYG--NIGSGYPSDPITRKFLEEYYKEhgSFPPVVRRSWKT 200
                                       *******98..*********************99999********98 PP

>> DUF4003  Protein of unknown function (DUF4003)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.7e-06     0.015      50     129 ..      92     168 ..      78     171 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.7e-06
                           DUF4003  50 fSnfrgnnrlilaallalneedpeeaiqevlkiyekLkeegFkkssylyltAyiilkasekeeydekiqrtkeiyke 126
                                        ++++ +  l+ + + ++nee     ++e l+ y k + e+   s+y +++A +il    k ++d+ i+r keiy +
  gi|242398404|ref|YP_002993828.1|  92 LNSLKIKPDLVYIDAADVNEERFGIVVREKLSFYPKIIAEHKADSKYIPVAAASIL---AKVTRDKAIERLKEIYGN 165
                                       555666666666777777777777789999*************************6...7999************98 PP

                           DUF4003 127 mKk 129
                                       + +
  gi|242398404|ref|YP_002993828.1| 166 IGS 168
                                       755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       934  (0.0520944); expected 358.6 (0.02)
Passed bias filter:                      580  (0.0323498); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 1587.44
//
Query:       gi|242398405|ref|YP_002993829.1|  [L=524]
Description: membrane-bound dolichyl-phosphate-mannose-protein mannosyltransferase [Thermococcus sibiricus MM 739]
Scores for complete 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   22.3   9.2    0.00013   22.3   9.2    2.4  3  PMT_2     Dolichyl-phosphate-mannose-protein mannosyltransfer
     0.0035   17.1   6.6     0.0035   17.1   6.6    2.4  2  GT87      Glycosyltransferase family 87
     0.0063   16.1   1.7     0.0063   16.1   1.7    2.7  3  PMT_4TMC  C-terminal four TMM region of protein-O-mannosyltra
  ------ inclusion threshold ------
       0.65    9.5  24.4      0.023   14.3  12.1    3.1  2  PMT       Dolichyl-phosphate-mannose-protein mannosyltransfer


Domain annotation for each model (and alignments):
>> PMT_2  Dolichyl-phosphate-mannose-protein mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       2.7   1.2e+04     146     153 ..      18      25 ..      10      39 .. 0.51
   2 !   22.3   9.2   2.8e-08   0.00013       2     151 ..     207     351 ..     206     359 .. 0.71
   3 ?   -0.2   0.3      0.22     1e+03      74     109 ..     411     445 ..     393     453 .. 0.68

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 2.7
                             PMT_2 146 lllalllf 153
                                       +l+al++ 
  gi|242398405|ref|YP_002993829.1|  18 ALVALIIL 25 
                                       22222222 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 2.8e-08
                             PMT_2   2 hPPliawllalftklfgfselairlv....salagvltilllyllarrlfgkraallaalllavvplfvalsalftp 74 
                                       hP l   ++ l++ +  ++    rl+     +++ +l++l+ y++ar ++   a+++a ++ a+ pl++a+s+++ +
  gi|242398405|ref|YP_002993829.1| 207 HPFLGKDIIMLGMLIE-DKPIFWRLPglieHVIINILVLLATYRIARSYL---ASFIALVFSAFDPLLYATSLTGML 279
                                       6777777777777774.444444444011156677777777888888876...59********************** PP

                             PMT_2  75 daplvllwalalylllraleknklkywllagvlfGlgflsKytaallliaall.yllis.arrilkekkpylallla 149
                                       d+   ++++l++yll+   ek     +  +g+++Gl+  +K + a+ ++ +l+  l  + + ++l ++ ++l ++ +
  gi|242398405|ref|YP_002993829.1| 280 DIHVAFFTTLFMYLLIS--EK-----YNSSGISIGLAAATKLNGAFSYPIILIkTLKSKiELKKLFTSLFLLPVTGF 349
                                       ***********999885..33.....5579*******************6666555555544455555555555555 PP

                             PMT_2 150 ll 151
                                       l+
  gi|242398405|ref|YP_002993829.1| 350 LI 351
                                       55 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.22
                             PMT_2  74 pdaplvllwalalylllraleknklkywllagvlfG 109
                                       +d +l+l +a +++++  a+ ++k k ++ +g+++ 
  gi|242398405|ref|YP_002993829.1| 411 TDPILMLSMAVFIFAIPYAAIRRK-KLLIPFGIFWS 445
                                       466666666666666666666666.67777777765 PP

>> GT87  Glycosyltransferase family 87
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   6.6   7.9e-07    0.0035      29     122 ..     239     325 ..     231     438 .. 0.75
   2 ?   -0.2   1.8      0.15   6.9e+02     118     162 ..     427     472 ..     415     509 .. 0.65

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 7.9e-07
                              GT87  29 lnlaalllalrlllrrlgralasavalalllaalalepv.lstlgfGqinllllllvlldllllrrrrpllaGlliG 104
                                       +n+++ll a+++++r +       +a +++l++ a+ p+ + t  +G  ++ +++   l++ ll +++   +G+ iG
  gi|242398405|ref|YP_002993829.1| 239 INILVLL-ATYRIARSY-------LASFIALVFSAFDPLlYATSLTGMLDIHVAFFTTLFMYLLISEKYNSSGISIG 307
                                       4555555.455555553.......556666789******999***********************998889****** PP

                              GT87 105 laaaiKltPalfllylll 122
                                       laaa Kl +a+   + l+
  gi|242398405|ref|YP_002993829.1| 308 LAAATKLNGAFSYPIILI 325
                                       ********9887776666 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.15
                              GT87 118 lylllrrrwralaaa.aatalvltalpllllppssleyfletlfdt 162
                                        y ++rr+   +  + + +++++ +l +ll +  +++++ + l  +
  gi|242398405|ref|YP_002993829.1| 427 PYAAIRRKKLLIPFGiFWSTIAFYGLQWLLGGKTQFSFYATPLVPA 472
                                       3666666655555555666777778888888888888888844444 PP

>> PMT_4TMC  C-terminal four TMM region of protein-O-mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0      0.95   4.2e+03     130     145 ..      16      31 ..      11      46 .. 0.55
   2 ?    0.7   0.7     0.073   3.3e+02     156     186 ..     246     276 ..     226     287 .. 0.80
   3 !   16.1   1.7   1.4e-06    0.0063      19      81 ..     379     433 ..     372     467 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.95
                          PMT_4TMC 130 lfailllaalldfllk 145
                                       +fa+++l +l  f+++
  gi|242398405|ref|YP_002993829.1|  16 YFALVALIILGTFWYS 31 
                                       4444444444444443 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.073
                          PMT_4TMC 156 lvklivvvvllvlviavFiffspltyGlpgt 186
                                       ++++i+   l++++++vF  f pl y++++t
  gi|242398405|ref|YP_002993829.1| 246 ATYRIARSYLASFIALVFSAFDPLLYATSLT 276
                                       4567777788899999**********99876 PP

  == domain 3  score: 16.1 bits;  conditional E-value: 1.4e-06
                          PMT_4TMC  19 lteshpyaSepyeWplllrgisywtkneekkqiyllGNpvlwwlstiallvfvllllalllrr 81 
                                        ++shp +S  +eW + lr+ ++ ++      i+++  p+l+ +  +++++    + + ++rr
  gi|242398405|ref|YP_002993829.1| 379 YKGSHPANSPFWEWFISLRPFAFHYNP----DIFAVTDPILMLSMAVFIFA----IPYAAIRR 433
                                       5678*********************96....79*******98877766663....33344444 PP

>> PMT  Dolichyl-phosphate-mannose-protein mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3  12.1     5e-06     0.023      94     194 ..     237     325 ..     223     355 .. 0.88
   2 ?   -0.6   4.1      0.17   7.8e+02     114     177 ..     415     479 ..     407     518 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5e-06
                               PMT  94 slivplvyltllelgfskltallaallvllenslitlsryilldspLlfftllsmyclvkferkapfsrswwlwlll 170
                                       + i +lv l ++++ +s l++ +a ++ +++++l++ s   +ld+  +fft+l my+l+  +            +  
  gi|242398405|ref|YP_002993829.1| 237 VIINILVLLATYRIARSYLASFIALVFSAFDPLLYATSLTGMLDIHVAFFTTLFMYLLISEK------------YNS 301
                                       67889*****************************************************9986............557 PP

                               PMT 171 tgvalglavsvKwvglftvllvgl 194
                                        g+++gla  +K +g+f +  +++
  gi|242398405|ref|YP_002993829.1| 302 SGISIGLAAATKLNGAFSYPIILI 325
                                       8***************99955554 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.17
                               PMT 114 allaallvllenslitlsryilldspLlfftllsmyclvkfe.rkapfsrswwlwllltgvalgl 177
                                        +l+++ +++   + +++r  ll ++ +f+ + ++y l +    k++fs  +   + +  v+lg+
  gi|242398405|ref|YP_002993829.1| 415 LMLSMAVFIFAIPYAAIRRKKLLIPFGIFWSTIAFYGLQWLLgGKTQFSFYATPLVPAGAVTLGV 479
                                       589999999999999*********************99998887788998888888888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (524 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       690  (0.0384851); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); 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: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.45
# Mc/sec: 3523.66
//
Query:       gi|242398406|ref|YP_002993830.1|  [L=378]
Description: methyltransferase [Thermococcus sibiricus MM 739]
Scores for complete 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   45.6   0.0    1.4e-11   44.2   0.0    1.7  2  Methyltransf_15  RNA cap guanine-N2 methyltransferase
    2.9e-06   27.9   0.0    1.5e-05   25.6   0.0    2.2  3  Methyltransf_25  Methyltransferase domain
    3.4e-06   27.0   0.1    8.8e-06   25.7   0.1    1.6  2  Methyltransf_18  Methyltransferase domain
    0.00012   21.9   0.0    0.00022   21.0   0.0    1.4  1  Methyltransf_31  Methyltransferase domain
    0.00012   21.6   0.1    0.00021   20.8   0.1    1.3  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    0.00062   20.4   0.0     0.0023   18.5   0.0    2.0  2  Methyltransf_11  Methyltransferase domain
     0.0011   18.5   0.0     0.0021   17.6   0.0    1.3  1  MTS              Methyltransferase small domain
     0.0025   17.6   0.0      0.004   16.9   0.0    1.4  1  Met_10           Met-10+ like-protein
     0.0031   17.2   0.0     0.0055   16.4   0.0    1.3  1  UPF0020          Putative RNA methylase family UPF0020
     0.0084   15.8   0.0      0.014   15.1   0.0    1.2  1  CmcI             Cephalosporin hydroxylase
  ------ inclusion threshold ------
      0.073   13.4   0.1        0.2   12.0   0.0    1.8  2  AdoMet_MTase     Predicted AdoMet-dependent methyltransferase


Domain annotation for each model (and alignments):
>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   0.0   8.7e-15   1.4e-11       4      78 ..      80     151 ..      78     192 .. 0.84
   2 ?   -4.0   0.0       6.1   9.9e+03      44      57 ..     208     221 ..     206     231 .. 0.77

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 8.7e-15
                   Methyltransf_15   4 ilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklklekikvdlvflS 78 
                                       i D+ +G G + i fa++ ++ +a++i+++kl  a++Nae Y v+dkit+++gd ++   k  +++i  d++f  
  gi|242398406|ref|YP_002993830.1|  80 IADVSCGIGIQLIFFAKYADRAYAVDIDEKKLFYATKNAEKYRVKDKITFIHGDSLS---KNVVDRIDADVIFSD 151
                                       77****************************************************765...445566666777744 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 6.1
                   Methyltransf_15  44 vYgvsdkitlvlgd 57 
                                       +Ygv +++t+  g 
  gi|242398406|ref|YP_002993830.1| 208 LYGVLNRLTFYFGP 221
                                       69999999888775 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       4.9     8e+03      31      50 ..      31      47 ..      28      63 .. 0.70
   2 !   25.6   0.0   9.5e-09   1.5e-05       1      70 [.      80     150 ..      80     167 .. 0.86
   3 ?   -2.0   0.0       3.8   6.2e+03      63      93 ..     263     293 ..     242     295 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 4.9
                                      HHHHHHHHHHHHHTTTTEEE CS
                   Methyltransf_25 31 eemleaareraeeeglnvef 50
                                      +e +e+ar+r+++++   +f
  gi|242398406|ref|YP_002993830.1| 31 DEIIEIARARIKAKN---KF 47
                                      678999999997654...44 PP

  == domain 2  score: 25.6 bits;  conditional E-value: 9.5e-09
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTT.TEEEEEE CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedg.sfDlvvs 70 
                                       + d+ cG G  ++ +ak     + ++vDi+e+ l +a ++ae+ ++  +++f++gd  + +  d+   D+++s
  gi|242398406|ref|YP_002993830.1|  80 IADVSCGIGIQLIFFAKYA--DRAYAVDIDEKKLFYATKNAEKYRVkdKITFIHGDSLSKNVVDRiDADVIFS 150
                                       78**************996..9********************999999********97766544437777776 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 3.8
                                       TTEEEEEEEST.GGGSSHHHHHHHHHHHHHHE CS
                   Methyltransf_25  63 gsfDlvvssga.lhhlsdedlekalkeiarvL 93 
                                       +s+D+  ++++ +h ++ +++  +++e +r L
  gi|242398406|ref|YP_002993830.1| 263 QSVDYADLINElFHEVD-QNIWMLIREKRRTL 293
                                       57777777777444455.77888888888877 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.1   5.4e-09   8.8e-06      15      84 ..      77     144 ..      70     149 .. 0.85
   2 ?   -3.4   0.0         5   8.1e+03      48      78 ..     290     320 ..     268     326 .. 0.71

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 5.4e-09
                   Methyltransf_18  15 gsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGleklkeeevd 84 
                                        +++aD+ +  g+  i+ +  + a++++a+Di e+ l  a +n+ek++++dki+++ +d l+k   + +d
  gi|242398406|ref|YP_002993830.1|  77 PESIADVSCGIGIQLIFFA--KYADRAYAVDIDEKKLFYATKNAEKYRVKDKITFIHGDSLSKNVVDRID 144
                                       46899****9999888887..7999************************************987655455 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 5
                   Methyltransf_18  48 egplekakeniekagledkievrlsdGlekl 78 
                                       +  l++++e+i++  ++ +  vr   G++++
  gi|242398406|ref|YP_002993830.1| 290 RRTLATSEEEIKSDYFKRRYIVRGILGFHPV 320
                                       4567777777777777777777766666666 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   1.4e-07   0.00022       6      81 ..      79     151 ..      76     194 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.4e-07
                   Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdieeleklledekfDlilsn 81 
                                       ++ D+ CG G  ++ +a+ +    + + +Di+e+ + +A++na+k  ++  ++F +gd  +++  + +   D+i+s+
  gi|242398406|ref|YP_002993830.1|  79 SIADVSCGIGIQLIFFAKYA---DRAYAVDIDEKKLFYATKNAEKYRVKdKITFIHGDSLSKNV-VDRIDADVIFSD 151
                                       688*******9999999542...3589**********************9*********99662.555778999998 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.1   1.3e-07   0.00021     162     231 ..      77     149 ..      66     151 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.3e-07
                              PrmA 162 geevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklev.a...lseellkeekadviv 231
                                        e++ Dv +G Gi  i  ak  a++++avDiDe  +  a +Nae+ +v++k++  +   ls++++++  advi+
  gi|242398406|ref|YP_002993830.1|  77 PESIADVSCGIGIQLIFFAKY-ADRAYAVDIDEKKLFYATKNAEKYRVKDKITFiHgdsLSKNVVDRIDADVIF 149
                                       47899***********99997.789*************************997632333566677778888886 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.4e-06    0.0023       2      59 ..      82     141 ..      81     152 .. 0.84
   2 ?   -1.9   0.0       3.3   5.4e+03      62      62 ..     265     265 ..     244     295 .. 0.52

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.4e-06
                                       EET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-T CS
                   Methyltransf_11   2 dvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl..kvefvvadaeklpfed 59 
                                       dv cG G+ +  +ak++ r ++vD++++ l +a ++a++ ++  k++f+++d  + ++ d
  gi|242398406|ref|YP_002993830.1|  82 DVSCGIGIQLIFFAKYADRAYAVDIDEKKLFYATKNAEKYRVkdKITFIHGDSLSKNVVD 141
                                       99****************************999999999999999*****9987655444 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.3
                                       E CS
                   Methyltransf_11  62 f 62 
                                       +
  gi|242398406|ref|YP_002993830.1| 265 V 265
                                       2 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.3e-06    0.0021      33     105 ..      78     152 ..      62     155 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.3e-06
                                       SEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTTTSTTS..-EEEEEE-- CS
                               MTS  33 gkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..vevvasdvleeveek..kfdlivsNP 105
                                       ++++D+ cG+G+  + +ak  ++    +vd+d + l  a++n+e+ +++  +++++ d l++   +  + d+i s P
  gi|242398406|ref|YP_002993830.1|  78 ESIADVSCGIGIQLIFFAKYADR--AYAVDIDEKKLFYATKNAEKYRVKdkITFIHGDSLSKNVVDriDADVIFSDP 152
                                       579********999999998888..79*********************99999999999887554401455666655 PP

>> Met_10  Met-10+ like-protein
   #    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     101     161 ..      77     135 ..      39     197 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.5e-06
                                       T-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GG CS
                            Met_10 101 gevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpileDgr 161
                                        e + dv  GiG   i  aky++    +a+d++ +   y ++n +  +v+++++ i +D+ 
  gi|242398406|ref|YP_002993830.1|  77 PESIADVSCGIGIQLIFFAKYADR--AYAVDIDEKKLFYATKNAEKYRVKDKITFIHGDSL 135
                                       47899***************7665..5********************************74 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   3.3e-06    0.0055      78     129 ..     100     152 ..      73     155 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.3e-06
                                       -EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--.STTS---EEEE-- CS
                           UPF0020  78 klygsDldrrvvqgareNaekagvgdliefsqadaakLr.lkegevdvivtnp 129
                                       + y++D+d++ +  a +Naek++v+d+i+f   d  + +  ++ + dvi ++p
  gi|242398406|ref|YP_002993830.1| 100 RAYAVDIDEKKLFYATKNAEKYRVKDKITFIHGDSLSKNvVDRIDADVIFSDP 152
                                       489*****************************998755544555777777776 PP

>> CmcI  Cephalosporin hydroxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   8.3e-06     0.014      31     105 ..      75     145 ..      52     151 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 8.3e-06
                              CmcI  31 lkPdliietGiahGGsalfsasllallkskrkvlaididirek..nrqaieahplasrieliegssvdpeiveqvks 105
                                       + P+ i ++    G  ++f+a+  + +       a+did ++     ++ e+++++++i++i+g+s++ ++v+++++
  gi|242398406|ref|YP_002993830.1|  75 VNPESIADVSCGIGIQLIFFAKYADRA------YAVDIDEKKLfyATKNAEKYRVKDKITFIHGDSLSKNVVDRIDA 145
                                       678888888888888889998877766......899999998633566778899*******************9975 PP

>> AdoMet_MTase  Predicted AdoMet-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00012       0.2      58     100 ..      76     118 ..      52     129 .. 0.77
   2 ?   -3.0   0.0       5.8   9.4e+03      28      38 ..     250     260 ..     241     272 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00012
                      AdoMet_MTase  58 ketsfvdvgcgngllvyvlaaegykgygidlrkrklwelypae 100
                                       ++ s++dv cg g+ +  +a    + y +d+  +kl+      
  gi|242398406|ref|YP_002993830.1|  76 NPESIADVSCGIGIQLIFFAKYADRAYAVDIDEKKLFYATKNA 118
                                       5889**********9999*****************98554444 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 5.8
                      AdoMet_MTase  28 estdplkfvfe 38 
                                        +  p+k+++e
  gi|242398406|ref|YP_002993830.1| 250 WCETPKKYLYE 260
                                       45679999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); 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: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 2403.51
//
Query:       gi|242398407|ref|YP_002993831.1|  [L=80]
Description: hypothetical protein TSIB_0416 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 529.12
//
Query:       gi|242398408|ref|YP_002993832.1|  [L=601]
Description: Glucosamine-fructose-6-phosphate aminotransferase [Thermococcus sibiricus MM 739]
Scores for complete 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-54  181.3   1.8    7.9e-30  103.4   1.6    2.3  2  SIS         SIS domain
    1.3e-21   77.2   0.0      3e-21   76.0   0.0    1.6  1  GATase_6    Glutamine amidotransferase domain
    8.2e-20   70.9   0.0    1.9e-19   69.8   0.0    1.6  1  GATase_7    Glutamine amidotransferase domain
  ------ inclusion threshold ------
      0.028   14.5   0.3       0.31   11.1   0.0    2.8  2  bact-PGI_C  Bacterial phospho-glucose isomerase C-terminal SI
       0.04   13.9   1.8       0.66   10.0   0.1    3.0  3  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 !  103.4   1.6   2.2e-33   7.9e-30       2     131 .]     283     412 ..     282     412 .. 0.98
   2 !   75.9   0.0   6.8e-25   2.5e-21       2     130 ..     456     583 ..     455     584 .. 0.90

  Alignments for each domain:
  == domain 1  score: 103.4 bits;  conditional E-value: 2.2e-33
                                       HCTSSEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHHH CS
                               SIS   2 LakakriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaaelake 78 
                                       +a+ ++++v+++Gtsy+++  +++ l+++ ++vv ve+ase++++  + +d + lvi+i++sget+d++aa++lak+
  gi|242398408|ref|YP_002993832.1| 283 IANYEKVFVVAMGTSYHAGIAAKYFLQRLVNKVVLVEEASEFRYEFEDIVDGNSLVIAITQSGETADTLAAIKLAKR 359
                                       78889************************************************************************ PP

                                       TTSEEEEEESSTTSHHHHHSSEEEEEEEECHCSSSHCHHHHHHHHHHHHHHHH CS
                               SIS  79 rgakiiaITdskgsplareadlalyinaepetlvastksltaqlaaldalava 131
                                       +gak++++ +  gs + r +dl+ly++a+pe++va+tk++t+ql++l +la+a
  gi|242398408|ref|YP_002993832.1| 360 KGAKVLSVVNVVGSMATRLSDLVLYTHAGPEIGVAATKTYTTQLTVLAMLAIA 412
                                       **************************************************985 PP

  == domain 2  score: 75.9 bits;  conditional E-value: 6.8e-25
                                       HCTSSEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHH.HHH CS
                               SIS   2 LakakriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaae.lak 77 
                                       L ++k  +++G+G s a+a+e+alkl+ei++i++e+ +a+elkhg+lal++++ +v++i ++g t+d+  ++  +++
  gi|242398408|ref|YP_002993832.1| 456 LVNKKDFFYIGRGVSVATALEGALKLKEISYIHAEGLSAGELKHGPLALVEDGVPVVAIVPTGKTFDKMVSNIqEVN 532
                                       8899***************************************************************9988888*** PP

                                       HTTSEEEEEESSTTSHHHHHSSEEEEEEEECHCSSSHCHHHHHHHHHHHHHHH CS
                               SIS  78 ergakiiaITdskgsplareadlalyinaepetlvastksltaqlaaldalav 130
                                       +r++ +i++ d++   l + + + l ++  +e l + ++ +++ql+a++++++
  gi|242398408|ref|YP_002993832.1| 533 ARKGLVISLGDNE--ELEKVSQVFLKMPRIDELLSPVVYIVPLQLLAYYLAVL 583
                                       *********9665..566666445666666666***************99986 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.0   0.0   8.4e-25     3e-21      13     133 ..      65     192 ..      52     193 .. 0.85

  Alignments for each domain:
  == domain 1  score: 76.0 bits;  conditional E-value: 8.4e-25
                          GATase_6  13 evalaHvRlaivglaeeegaqPfpsedgrlllvhNGeiynykelreelpalkglafrsrsDtevllall.eelG... 85 
                                       + +++H+R+a++g +++  a+P +  +g++++vhNG i+ny elre+l+   g++f+s++Dtev+++l+ eel    
  gi|242398408|ref|YP_002993832.1|  65 RRGIGHTRWATHGIPNDINAHPHTDCSGKIAIVHNGIIENYIELREKLEG-SGHEFKSDTDTEVIAHLIeEELKssk 140
                                       568************99999******************************.****************9984555666 PP

                          GATase_6  86 ......eevlerlrGmfafaiwdk.rentlilardrlgvkplyyavdesglafas 133
                                              ++l +l+G fa  i+   ++++l ++r+   ++pl+ +v ++ +  as
  gi|242398408|ref|YP_002993832.1| 141 lfedalRRALLQLKGSFALGIIYTdDKEHLYFVRN---ESPLVLGVGNGEMFAAS 192
                                       773444555559*******9998889999999955...59999998777776666 PP

>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.8   0.0   5.3e-23   1.9e-19      12     122 ..      83     198 ..      70     199 .. 0.88

  Alignments for each domain:
  == domain 1  score: 69.8 bits;  conditional E-value: 5.3e-23
                          GATase_7  12 gaQPmvssedgrlvivfnGeiyNykelreeLeakghrfrtksDtevllallea.........ewgeealerlnGmfA 79 
                                       +a P + + +g+++iv+nG i Ny elre+Le +gh+f++++Dtev+++l+e+         + +++al +l+G+fA
  gi|242398408|ref|YP_002993832.1|  83 NAHPHT-DCSGKIAIVHNGIIENYIELREKLEGSGHEFKSDTDTEVIAHLIEEelkssklfeDALRRALLQLKGSFA 158
                                       567777.5789***********************************************9999999999********* PP

                          GATase_7  80 faiw.deeekrlllaRDrlGikPLyygedkgdallfaSelkall 122
                                       + i+ ++++++l+ +R+   + PL +g  +g +++ aS + a+l
  gi|242398408|ref|YP_002993832.1| 159 LGIIyTDDKEHLYFVRN---ESPLVLGVGNG-EMFAASDIPAFL 198
                                       *7651677779******...7********85.9******99986 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 ?   -0.8   0.1       0.4   1.4e+03      74      74 ..     339     339 ..     274     386 .. 0.48
   2 ?   11.1   0.0   8.7e-05      0.31       2     141 ..     446     590 ..     445     596 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.4
                                       E CS
                        bact-PGI_C  74 v 74 
                                       +
  gi|242398408|ref|YP_002993832.1| 339 I 339
                                       1 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 8.7e-05
                                       G-HHHHHHHHHTTSEEEEE-..TT-THHHHHHHHHHHHTT----B---.SSHHHHHHHTTSS-GGGGTTEEEEEESS CS
                        bact-PGI_C   2 knpakqlAlelagklpviygssellevaArRfknqlnenAKipafagvlpeanhneivgleaeeelkkrlrlvllrd 78 
                                       +n+ k lA+el++k   +y   ++  + A   + +l+e++ i+a      e++h  ++++e   ++ + +++v  ++
  gi|242398408|ref|YP_002993832.1| 446 ENKIKALAEELVNKKDFFYIGRGVSVATALEGALKLKEISYIHAEGLSAGELKHGPLALVE---DGVPVVAIVPTGK 519
                                       6899999****99888888768888888999999999*******999999*******9993...4444555554446 PP

                                       HH.............HHHHHHHHTTTS.SEEEEE---SSSH..HHHHHHHHHHHHHHHHHHHHHCT---S- CS
                        bact-PGI_C  79 eeeh.....prvkkraeivkelaeerg.vrvtevkaegesp..lerlaslillgDfvSvylAllrgvDPtp 141
                                       + ++     ++v++r  +v +l  ++   +v++v ++      l   +  i+ + + ++ylA+lrg DP +
  gi|242398408|ref|YP_002993832.1| 520 TFDKmvsniQEVNARKGLVISLGDNEElEKVSQVFLKMPRIdeLLSPVVYIVPLQLLAYYLAVLRGNDPDK 590
                                       66556666788888888888888777767888888876554113333334455799*************76 PP

>> SIS_2  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0       0.1   3.6e+02      23      59 ..     274     313 ..     251     323 .. 0.67
   2 ?   10.0   0.1   0.00018      0.66     105     137 ..     336     368 ..     324     369 .. 0.87
   3 ?   -0.9   0.0      0.42   1.5e+03      26      65 ..     450     489 ..     444     504 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.1
                                       HHHHHHHHHHHTT--EEEEESG...GGHHHHHHTSSSTT- CS
                             SIS_2  23 kaaeliadslenggkvlvfGsG...hSaalaeelaaragg 59 
                                       k ++ +a+ ++n +kv+v   G   h+ ++a+++  r+++
  gi|242398408|ref|YP_002993832.1| 274 KTIDKVAEEIANYEKVFVVAMGtsyHAGIAAKYFLQRLVN 313
                                       3456677778888888877776445777888888888775 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00018
                                       -EEEEE-SS--SHHHHHHHHHHHHHT-EEEEEE CS
                             SIS_2 105 DvLlviSnsGnnavvveaaeaakergmkviAlt 137
                                        + + i +sG+ a  ++a++ ak++g+kv  ++
  gi|242398408|ref|YP_002993832.1| 336 SLVIAITQSGETADTLAAIKLAKRKGAKVLSVV 368
                                       456789***********************9886 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.42
                                       HHHHHHHHTT--EEEEESGGGHHHHHHTSSSTT-BTTEEE CS
                             SIS_2  26 eliadslenggkvlvfGsGhSaalaeelaaragglaefer 65 
                                       +++a+ l n++ ++  G G S a a e a ++  +  +++
  gi|242398408|ref|YP_002993832.1| 450 KALAEELVNKKDFFYIGRGVSVATALEGALKLKEISYIHA 489
                                       6788899999999999*****9999998887776666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (601 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       726  (0.0404931); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); 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: 0.69u 0.30s 00:00:00.99 Elapsed: 00:00:00.48
# Mc/sec: 3784.18
//
Query:       gi|242398409|ref|YP_002993833.1|  [L=951]
Description: Oligosaccharyl transferase STT3 subunit superfamily [Thermococcus sibiricus MM 739]
Scores for complete 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-60  200.8   0.1    1.5e-59  199.7   0.1    1.6  1  OST_P2       Oligosaccharyltransferase Peripheral 2 domain
    3.9e-38  129.6   2.2    9.5e-38  128.4   2.2    1.7  1  OST_IS       Oligosaccharyltransferase Insert domain
    3.7e-05   24.0  10.8    3.7e-05   24.0  10.8    3.4  3  PMT_2        Dolichyl-phosphate-mannose-protein mannosyltrans
  ------ inclusion threshold ------
        3.7    7.2  15.1      0.036   13.8   2.5    2.8  3  Tetraspanin  Tetraspanin family


Domain annotation for each model (and alignments):
>> OST_P2  Oligosaccharyltransferase Peripheral 2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.7   0.1   3.4e-63   1.5e-59       1     132 []     810     941 ..     810     941 .. 1.00

  Alignments for each domain:
  == domain 1  score: 199.7 bits;  conditional E-value: 3.4e-63
                                       EEE-EE-S--EETTEE-BTTBSS-TT-EEEEEEEEEESS-E.EEEEEEEEEEEEEEE-SSSSTT-TT--EEEEEEEE CS
                            OST_P2   1 GPvGvltdapkvnGkivnPskilkeGqsGelelkaafrkdy.tvdlylratviylvrknGkdiddkdaalePhmdii 76 
                                       GPvG+lt+apk+nG++v+P++il++GqsGelelka+fr+dy ++dlylratviylvr++G+++dd++aa+ePhmdii
  gi|242398409|ref|YP_002993833.1| 810 GPVGALTEAPKLNGNLVSPIRILNDGQSGELELKAGFRRDYsKMDLYLRATVIYLVRTQGENRDDPKAAFEPHMDII 886
                                       9**************************************************************************** PP

                                       EEEEEEEEEEE-SEEEEEEEEEE--TTCHHHHHHHHHHHHGGGEEEEEEEEEEEEE CS
                            OST_P2  77 tyvkvaeglkvkegentikaqaslPedvissyieelkkkyGdkvvvrgirvePvfi 132
                                       +y+kva gl+++++e ++k+q+s+Pe vi++yie+l+ +yGdkv vrgirvePvfi
  gi|242398409|ref|YP_002993833.1| 887 HYEKVAGGLSTTNKELYFKGQVSFPE-VIQPYIEKLNGEYGDKVEVRGIRVEPVFI 941
                                       **************************.****************************8 PP

>> OST_IS  Oligosaccharyltransferase Insert domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.4   2.2   2.1e-41   9.5e-38       1      83 []     587     671 ..     587     671 .. 0.99

  Alignments for each domain:
  == domain 1  score: 128.4 bits;  conditional E-value: 2.1e-41
                                       S------EEEEEB..ESSEEEETTTTEEEEE.SSSSEEEEE...TTEEEE-SEEEETTT--EEE--SE--EEEEEES CS
                            OST_IS   1 eRdnvttllpldk.vaenkYlnaYakleldv.enegkkvvviviGnqqgePlqsiflpsgevikGsGsFPYvvyvtp 75 
                                       eRdn++++lp+d+ ++en+Y+++Ya++++++ e+egkk++viv+GnqqgeP+q+i++++gevi+GsG+FPYvvy+++
  gi|242398409|ref|YP_002993833.1| 587 ERDNRGMILPFDQkIGENSYYSRYAGIQFHIiEQEGKKIGVIVAGNQQGEPVQTINMQTGEVIPGSGNFPYVVYAFS 663
                                       8***********99****************99********************************************* PP

                                       SEEEEEEG CS
                            OST_IS  76 tyavlaYY 83 
                                       +yav++YY
  gi|242398409|ref|YP_002993833.1| 664 NYAVAVYY 671
                                       *******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 !   24.0  10.8   8.4e-09   3.7e-05       7     111 ..      97     204 ..      90     265 .. 0.81
   2 ?   -1.5   0.9      0.59   2.6e+03     138     138 ..     247     247 ..     214     326 .. 0.59
   3 ?   -0.3   7.2      0.25   1.1e+03       9      71 ..     383     445 ..     376     475 .. 0.70

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 8.4e-09
                             PMT_2   7 awllalftklfgf.selairlvsalagvltilllyllarrlfgkraallaalllavvplfvalsa..lftpdaplvl 80 
                                       + ll  f++++g   + ++ +++ ++g+ +i++ y+l r+l + +a+++aal ++++    + ++  + + d p+++
  gi|242398409|ref|YP_002993833.1|  97 PALLYRFLSVLGLeAIEVFKMWPPIVGFFSIIGAYFLGRKLHSDWAGIWAALVMMFSVAHWTRTFsgNARGDGPFLM 173
                                       556666788889779999**************************************887777777556667****** PP

                             PMT_2  81 lwalalylllraleknklkywllagvlfGlg 111
                                       + + a+++++ +le n++k  +++g lf+++
  gi|242398409|ref|YP_002993833.1| 174 FFLYAVLFMFYYLEINEIKRKAVFGSLFVIS 204
                                       **************99988887777666542 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.59
                             PMT_2 138 k 138
                                       k
  gi|242398409|ref|YP_002993833.1| 247 K 247
                                       0 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.25
                             PMT_2   9 llalftklfgfselairlvsalagvltilllyllarrlfgkraallaalllavvplfvalsal 71 
                                       + +++ +l  ++  a +l+  +++ l+++l++  +r lf ++ a+l ++ + v  lf+++ a+
  gi|242398409|ref|YP_002993833.1| 383 IFRFLKALSQNKVDAKNLFLLVFYGLSVYLMWTAVRFLFLASGAVLLTFGIFVGELFGIVEAM 445
                                       6677778878888899999999****************9988887776655554445555553 PP

>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   0.0       2.4   1.1e+04      39      67 ..      11      39 ..       5      43 .. 0.65
   2 ?   -2.5   5.1      0.75   3.4e+03       7     129 ..     196     361 ..     195     367 .. 0.53
   3 ?   13.8   2.5     8e-06     0.036      10     138 ..     372     512 ..     369     514 .. 0.70

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 2.4
                                      ..............XXXXXXXXXXXXXXX CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Tetraspanin 39 lsesaedpailaillivvGvllfllgflG 67
                                      +++s +++++ +i + ++  +++l++++G
  gi|242398409|ref|YP_002993833.1| 11 KEKSISSFDFSKIRVYILPLTVILIAIIG 39
                                      45566666666667777777777777776 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.75
                                       XXXXXXXXXXXXXXXX......XXXXXX..............XXX.....................XXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxx......xxxxxx..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Tetraspanin   7 ffnllfwligivllav......Gvwlrl..............khaeaalacllsesaedpailaillivvGvllfll 63 
                                       +f  lf++ g+++l+v      G++++l              k +      ++ ++   p++lail      +  +l
  gi|242398409|ref|YP_002993833.1| 196 VFGSLFVISGVLMLSVwngspfGLMVLLgfaslyavgtfifgKVE----DVKKFAKEFYPSYLAIL-----LIGYAL 263
                                       677889999999999988888855554455555544444433111....11222223344444222.....233344 PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--HHH.................................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................................. RF
                       Tetraspanin  64 gflGcigalkenkcllltfsllllvlfllelaagilgfvfsdk.................................. 106
                                       +  G++ +    ++   +f+ l l+ ++++ +     + +sdk                                  
  gi|242398409|ref|YP_002993833.1| 264 TSSGIVKVGGHIRFAFEVFLGLALLTLIMLYGGKY--LNYSDKthrfgvvavvvllgftgaylyvgpklfslmsgay 338
                                       55555555555555555555555555554444333..3344444466666666666666666666666666666666 PP

                                       ........HHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                       Tetraspanin 107 argkvseiinnaievkyrddldl 129
                                       +  +v+e +++  +++++d  ++
  gi|242398409|ref|YP_002993833.1| 339 QSTQVYETVQELAKTTWEDVKRY 361
                                       66666666666666666666655 PP

  == domain 3  score: 13.8 bits;  conditional E-value: 8e-06
                                       XXXXXXXXXXXXXX.XXXXX......XXX.....................XXXXXXXXXXXXX.....XXXXXXXXX CS
                                       xxxxxxxxxxxxxx.xxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxx RF
                       Tetraspanin  10 llfwligivllavG.vwlrl......khaeaalacllsesaedpailaillivvGvllfllgf.....lGcigalke 74 
                                       +l+ l+gi+++++  + + l       +++  l  +  + +   ++++ l+++ G++l+ +g+     +G++ a++e
  gi|242398409|ref|YP_002993833.1| 372 FLLSLLGIAIVIFRfLKA-LsqnkvdAKNLFLLVFYGLSVYLMWTAVRFLFLASGAVLLTFGIfvgelFGIVEAMQE 447
                                       788899999999963333.246666533333334444555666666666677777766666542122278******* PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXX--HHH.........HHHHHHHHHHHHHHHHHH.THHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
                       Tetraspanin  75 nkcllltfsllllvlfllelaagilgfvfsdkargkv.seiinnaievkyrddldlkkc.qnllds 138
                                       +    +++++ll++lf+   ++g+ +  +s k  g++ + ++++++ + +r++ + +++ ++++d+
  gi|242398409|ref|YP_002993833.1| 448 KVSTKALYATLLILLFIPIPIVGANTTYNSAKVSGEAvTPSWEETL-KWLRESTNEYDTaTSWWDY 512
                                       ************************6666666645444388899999.7788888888888899987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (951 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       794  (0.0442858); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.86u 0.31s 00:00:01.17 Elapsed: 00:00:00.51
# Mc/sec: 5593.55
//
Query:       gi|242398410|ref|YP_002993834.1|  [L=128]
Description: 50S ribosomal protein L7Ae [Thermococcus sibiricus MM 739]
Scores for 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-31  107.6   0.3    2.5e-31  107.3   0.3    1.1  1  Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 famil
    0.00053   19.8   0.1    0.00079   19.3   0.1    1.3  1  PELOTA_1        PELOTA RNA binding domain
  ------ inclusion threshold ------
      0.032   14.7   0.1      0.037   14.5   0.1    1.3  1  eRF1_3          eRF1 domain 3


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 !  107.3   0.3   4.2e-35   2.5e-31       2      94 ..      23     115 ..      22     116 .. 0.95

  Alignments for each domain:
  == domain 1  score: 107.3 bits;  conditional E-value: 4.2e-35
                                       HHHHHHHHHHHHTEEEESHHHHHHHHHTTTESEEEEETTSSSGGHHHHHHHHHHHTTEEEEEESCHHHHHHHTTSSS CS
                    Ribosomal_L7Ae   2 aieevlkkakkagklvlGlkevtkalergeaklvilAedvepeekkkllealckekevpyvkvkskkeLGelvgkkr 78 
                                       ++ e+++ a+++gk+++G++e+tka+erg+aklv++Aedv+pee++++l+ lc+eke+py++v+skkeLG+++g ++
  gi|242398410|ref|YP_002993834.1|  23 KALEAVEIARDTGKVRKGTNETTKAVERGQAKLVVIAEDVDPEEIVAHLPPLCEEKEIPYIYVSSKKELGAAAGIEV 99 
                                       56789999********************************************************************* PP

                                       ECSEEEEEESTTTHHH CS
                    Ribosomal_L7Ae  79 pvsalaikdegdskdl 94 
                                       p++++ai+++g+ ++l
  gi|242398410|ref|YP_002993834.1| 100 PSASVAIIEPGKGREL 115
                                       *********9987665 PP

>> PELOTA_1  PELOTA RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1   1.3e-07   0.00079      17      70 ..      32      87 ..      16      98 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.3e-07
                          PELOTA_1 17 edinliKPgigEaTRvlLRRvPekvlvrdeee..pdlahlllLakekgvpveevpd 70
                                      +d+  ++ g  E+T+++ R + + v+++++ +  + +ahl  L++ek++p+  v++
  gi|242398410|ref|YP_002993834.1| 32 RDTGKVRKGTNETTKAVERGQAKLVVIAEDVDpeEIVAHLPPLCEEKEIPYIYVSS 87
                                      68899999********************988833559************9887755 PP

>> eRF1_3  eRF1 domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   6.2e-06     0.037      14      53 ..      29      68 ..      16     127 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.2e-06
                                      HHHCTCSSEEESHHHHHHHHHTT-EEEEEEEHCHHTSSSH CS
                            eRF1_3 14 elakdtgkavYGveevlkalemgAvetLLvseelersrdt 53
                                      e+a+dtgk+  G +e+ ka+e g  + +++ e+++ ++ +
  gi|242398410|ref|YP_002993834.1| 29 EIARDTGKVRKGTNETTKAVERGQAKLVVIAEDVDPEEIV 68
                                      7999*****************************9988755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 888.44
//
Query:       gi|242398411|ref|YP_002993835.1|  [L=70]
Description: 30S ribosomal protein S28e [Thermococcus sibiricus MM 739]
Scores for complete 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  101.5   4.8      2e-29  101.4   4.8    1.0  1  Ribosomal_S28e  Ribosomal protein S28e


Domain annotation for each model (and alignments):
>> Ribosomal_S28e  Ribosomal protein S28e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.4   4.8   1.1e-33     2e-29       2      64 .]       4      66 ..       3      66 .. 0.97

  Alignments for each domain:
  == domain 1  score: 101.4 bits;  conditional E-value: 1.1e-33
                                      --EEEEEEEEEE---SSSSEEEEEEEE-S-SS-S-EEEEEEES---TT-EEEES--S--TT-- CS
                    Ribosomal_S28e  2 eaklAeVikvlgrtGsrGevtqVrvellegkdkgriiiRnVkGPvreGDiLtLlEterEArrL 64
                                      e ++AeVi+++grtG++GevtqV+v++leg dkgr+i Rn+kGPvr GDi++L+EterEAr++
  gi|242398411|ref|YP_002993835.1|  4 EGYPAEVIEIVGRTGVTGEVTQVKVRVLEGMDKGRVIRRNIKGPVRLGDIVILRETEREAREI 66
                                      6799*********************************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      186  (0.0103743); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 502.44
//
Query:       gi|242398412|ref|YP_002993836.1|  [L=67]
Description: 50S ribosomal protein L24e [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-24   86.4   5.2    1.2e-24   86.3   5.2    1.0  1  Ribosomal_L24e   Ribosomal protein L24e
    7.5e-05   22.6   3.4    0.00011   22.1   3.4    1.2  1  zf-FCS           MYM-type Zinc finger with FCS sequence motif
    0.00013   22.0   4.5    0.00021   21.3   4.5    1.3  1  YHS              YHS domain
    0.00054   20.2   3.3     0.0011   19.2   3.3    1.6  1  Arc_trans_TRASH  Archaeal TRASH domain
    0.00093   19.5   0.5    0.00096   19.5   0.5    1.1  1  DUF3268          zinc-finger-containing domain
  ------ inclusion threshold ------
      0.034   13.6   0.1      0.068   12.6   0.1    1.5  1  zf-ribbon_3      zinc-ribbon domain


Domain annotation for each model (and alignments):
>> Ribosomal_L24e  Ribosomal protein L24e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.3   5.2   3.9e-28   1.2e-24       2      59 ..       3      60 ..       2      67 .] 0.93

  Alignments for each domain:
  == domain 1  score: 86.3 bits;  conditional E-value: 3.9e-28
                                      XX-B-TTT-SB--SS--EEEE-TTS-EEEESSHHHHHHHHTT--GGGSTTSTTT-XXX CS
                    Ribosomal_L24e  2 ktekCsFsgykiyPGhGkrfvrnDgkvfrFlssKceklfkqkrnPrklkWTkayRrah 59
                                      +++ Cs++g++ +PG+Gk++vrnDg+v++F+s+Kcek+f + rnPrklkWTka+ +a+
  gi|242398412|ref|YP_002993836.1|  3 RWNVCSYCGKEFEPGTGKMYVRNDGRVYFFCSRKCEKYFFMGRNPRKLKWTKAFEEAK 60
                                      6789*************************************************98776 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 !   22.1   3.4   3.6e-08   0.00011       6      37 ..       7      37 ..       5      41 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 3.6e-08
                            zf-FCS  6 CwfCkkyikgkpeftyvlendgvvgqFCStsC 37
                                      C++C+k+++ ++    ++ ndg v+ FCS+ C
  gi|242398412|ref|YP_002993836.1|  7 CSYCGKEFEPGT-GKMYVRNDGRVYFFCSRKC 37
                                      ********8888.578***************9 PP

>> YHS  YHS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   4.5   7.1e-08   0.00021       6      37 ..      10      41 ..       9      44 .. 0.96

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 7.1e-08
                               YHS  6 cgmkvdkekaeekseYkGkeYyFcSegCkdkF 37
                                      cg+  ++++ + +++ +G+ Y+FcS +C+  F
  gi|242398412|ref|YP_002993836.1| 10 CGKEFEPGTGKMYVRNDGRVYFFCSRKCEKYF 41
                                      9***************************9988 PP

>> Arc_trans_TRASH  Archaeal TRASH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   3.3   3.8e-07    0.0011       1      33 [.       7      41 ..       7      43 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 3.8e-07
                   Arc_trans_TRASH  1 CDYCGkeiv.geP.ivyklknkvYyvCCktCksel 33
                                      C YCGke   g+  + ++   +vY++C   C++ +
  gi|242398412|ref|YP_002993836.1|  7 CSYCGKEFEpGTGkMYVRNDGRVYFFCSRKCEKYF 41
                                      99*****96333314456677**********9866 PP

>> DUF3268  zinc-finger-containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.5   3.2e-07   0.00096       3      59 ..       5      60 ..       3      67 .] 0.76

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 3.2e-07
                           DUF3268  3 trCpyCGekvilvsaseiYkerskgkllylC.pkCdayvgvhkgtkiplGtlAnaelr 59
                                      ++C+yCG++    +  ++Y  r+ g++++ C +kC+ y  + ++ ++ + t A +e +
  gi|242398412|ref|YP_002993836.1|  5 NVCSYCGKEFEPGT-GKMY-VRNDGRVYFFCsRKCEKYFFMGRNPRKLKWTKAFEEAK 60
                                      58******998765.5789.899999999**99*****98888877766666544443 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   2.3e-05     0.068      15      25 ..       3      13 ..       2      14 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.3e-05
                       zf-ribbon_3 15 ddnvCpyCGtk 25
                                      ++nvC yCG++
  gi|242398412|ref|YP_002993836.1|  3 RWNVCSYCGKE 13
                                      79*******86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); 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: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 527.56
//
Query:       gi|242398413|ref|YP_002993837.1|  [L=489]
Description: DnaG-related protein, containing Toprim domain [Thermococcus sibiricus MM 739]
Scores for complete 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-14   52.1   0.6    2.7e-13   50.2   0.4    2.1  2  Toprim_4       Toprim domain
    3.2e-06   27.5   0.0    8.8e-06   26.1   0.0    1.8  1  Toprim_2       Toprim-like
    0.00069   19.8   0.4    0.00069   19.8   0.4    3.0  3  Toprim         Toprim domain
  ------ inclusion threshold ------
      0.043   13.5   1.1       0.12   12.1   1.1    1.7  1  OxoGdeHyase_C  2-oxoglutarate dehydrogenase C-terminal


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 ?   -1.8   0.0      0.99   4.4e+03      25      44 ..     134     153 ..     132     170 .. 0.76
   2 !   50.2   0.4     6e-17   2.7e-13       2      76 ..     223     306 ..     222     321 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.99
                          Toprim_4  25 avlggalspldgirpeklkt 44 
                                       a+l  al++ d i+p++ ++
  gi|242398413|ref|YP_002993837.1| 134 AILAAALETIDRIGPSEARI 153
                                       67889999999999998888 PP

  == domain 2  score: 50.2 bits;  conditional E-value: 6e-17
                          Toprim_4   2 eiiiVEgyaDvlalekagiknvvavlggalspldgirpeklkt.enlve....aekkvkevilaldgDa.....eGe 68 
                                        iiiVEg+aDvl+l k gikn++av g+++ p+  i+++k ++ +++++    +e ++ke++++ d D+     eG+
  gi|242398413|ref|YP_002993837.1| 223 SIIIVEGRADVLNLLKHGIKNAIAVEGTSI-PETIIKLSKERIvTAFTDgdrgGELILKELLQVADIDYvarapEGK 298
                                       69****************************.******999999999999********************99999999 PP

                          Toprim_4  69 ataerlae 76 
                                       ++ e  ++
  gi|242398413|ref|YP_002993837.1| 299 EVEELTKK 306
                                       99988877 PP

>> Toprim_2  Toprim-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0     2e-09   8.8e-06       1      86 [.     225     300 ..     225     304 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 2e-09
                          Toprim_2   1 vvfEgaiDalSlaqlgikektnvvalgGtalteaalkllerypekkvvla.lDnDkaGrkaakrlaellreagvrek 76 
                                       +++Eg  D+l l+++gik   n++a+ Gt+++e+ +kl +++    +v a +D D+ G+   k+l +++      + 
  gi|242398413|ref|YP_002993837.1| 225 IIVEGRADVLNLLKHGIK---NAIAVEGTSIPETIIKLSKER----IVTAfTDGDRGGELILKELLQVADI----DY 290
                                       69***************9...********9999999988877....55554**********9999988842....34 PP

                          Toprim_2  77 irelpegkDw 86 
                                       +++ pegk +
  gi|242398413|ref|YP_002993837.1| 291 VARAPEGKEV 300
                                       5556666665 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.2      0.67     3e+03      34      34 ..     157     157 ..      71     205 .. 0.55
   2 !   19.8   0.4   1.5e-07   0.00069       2      93 ..     224     293 ..     223     303 .. 0.84
   3 ?   -1.3   1.1      0.56   2.5e+03      44      62 ..     356     381 ..     296     388 .. 0.62

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.67
                                       E CS
                            Toprim  34 d 34 
                                        
  gi|242398413|ref|YP_002993837.1| 157 R 157
                                       1 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 1.5e-07
                                       EEEESSHHHHHHHHHTHTSTEEEEEEESSSSEEEHSTTEEEEEECTTTHHHHHHHHHHHHHHSEEEEE.CSSSHHHH CS
                            Toprim   2 lvivEgpsdaktiakalgsgfqavtaslGhildletefkpvyeeiedkkkvlkalkelakradeiila.tDpDreGe 77 
                                       ++ivEg +d+ ++ k    g ++++a+ G+ +  +                   +k ++   ++i+ a tD+Dr Ge
  gi|242398413|ref|YP_002993837.1| 224 IIIVEGRADVLNLLKH---GIKNAIAVEGTSIPETI------------------IKLSK---ERIVTAfTDGDRGGE 276
                                       89**************...9************9998..................77666...5666666******** PP

                                       HHHHHHHHHHT.HHHTT CS
                            Toprim  78 aiawellevlk.ellen 93 
                                        i +ell+v++ +++ +
  gi|242398413|ref|YP_002993837.1| 277 LILKELLQVADiDYVAR 293
                                       ********998665555 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.56
                                       E.......ECTTTHHHHHHHHHHHHH CS
                            Toprim  44 e.......eiedkkkvlkalkelakr 62 
                                       e       ei++k+ +++++k + ++
  gi|242398413|ref|YP_002993837.1| 356 EsktevqeEIHEKEPKIEEVKVEVEK 381
                                       02333446888888888888777655 PP

>> OxoGdeHyase_C  2-oxoglutarate dehydrogenase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.1   2.7e-05      0.12      15      78 ..     307     365 ..     298     377 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.7e-05
                     OxoGdeHyase_C  15 rvledeeeealkepekvkrvvlcsGkvyydLlkerekkekekdvaivriEqlyPfpfeelkeel 78 
                                       ++++  +++    +e+v   ++  Gk +y+L+kere+k     + i ++E++     +e++ee+
  gi|242398413|ref|YP_002993837.1| 307 EIIKSLRSK--VPAEQVINELFAKGKSFYELMKEREQK---PPTPIEKVEEVPMESKTEVQEEI 365
                                       555555553..5688999999***************76...56999999997555556677766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (489 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1273  (0.0710023); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.69u 0.27s 00:00:00.96 Elapsed: 00:00:00.49
# Mc/sec: 3012.13
//
Query:       gi|242398414|ref|YP_002993838.1|  [L=126]
Description: DnaG-related small protein [Thermococcus sibiricus MM 739]
Scores for complete 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-06   26.5   0.2    1.3e-05   25.3   0.2    1.7  1  Toprim        Toprim domain
    0.00066   20.1   0.1     0.0014   19.1   0.1    1.6  1  Toprim_4      Toprim domain
     0.0064   16.9   0.0      0.009   16.4   0.0    1.2  1  Toprim_2      Toprim-like
  ------ inclusion threshold ------
      0.082   13.3   0.0        0.1   13.0   0.0    1.2  1  Toprim_3      Toprim domain
       0.14   11.4   0.2        7.1    5.8   0.1    2.0  2  CPSF_A        CPSF A subunit region
        1.5    8.9   4.4        2.6    8.2   0.2    2.6  3  Exonuc_VII_S  Exonuclease VII small subunit


Domain annotation for each model (and alignments):
>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.2   4.5e-09   1.3e-05      53      90 ..      51      88 ..       9     103 .. 0.75

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 4.5e-09
                                      HHHHHHHHHHHSEEEEECSSSHHHHHHHHHHHHHHTHH CS
                            Toprim 53 lkalkelakradeiilatDpDreGeaiawellevlkel 90
                                      l++++  a+ ++ i+++tD Dr Ge +a++l ++l+ +
  gi|242398414|ref|YP_002993838.1| 51 LAEIALTASHYHDIMILTDFDRKGEDLAKKLTQYLEGY 88
                                      34488889************************998833 PP

>> Toprim_4  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.1   4.7e-07    0.0014       3      84 ..      22      91 ..      20      96 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 4.7e-07
                          Toprim_4  3 iiiVEgyaDvlalekagiknvvavlggalspldgirpeklktenlveaekkvkevilaldgDaeGeataerlaelllee 81
                                      +i+VEg  D +al k g+++ +  l  ++ pl++i+++  ++            +++++d D  Ge  a++l + l+  
  gi|242398414|ref|YP_002993838.1| 22 VILVEGMRDEVALRKLGVETEIIKLS-RF-PLAEIALTASHY----------HDIMILTDFDRKGEDLAKKLTQYLEGY 88
                                      89**************9998887665.89.99****999999..........9********************966444 PP

                          Toprim_4 82 gvk 84
                                      + +
  gi|242398414|ref|YP_002993838.1| 89 KCR 91
                                      444 PP

>> Toprim_2  Toprim-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0     3e-06     0.009       1      77 [.      23      94 ..      23     109 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3e-06
                          Toprim_2  1 vvfEgaiDalSlaqlgikektnvvalgGtalteaalkllerypekkvvlalDnDkaGrkaakrlaellreagvreki 77
                                      +++Eg+ D  +l +lg +  t+ +  ++  ++ a + l +++    +++ +D D++G++ ak+l + l+  ++r+  
  gi|242398414|ref|YP_002993838.1| 23 ILVEGMRDEVALRKLGVE--TEII-KLSR-FPLAEIALTASHY-HDIMILTDFDRKGEDLAKKLTQYLEGYKCRVDT 94
                                      699**************8..4555.5555.5666666666663.45********************99766644433 PP

>> Toprim_3  Toprim domain
   #    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       2      69 ..      22      87 ..      21     109 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.4e-05
                          Toprim_3  2 liivEGietaLsileartgaaviAllsaanlkaiawpe.rgkrvviaaDnDaandGreaaeklaerlea 69
                                      +i+vEG+ +  ++++  +++ +i l s   l++ia++  ++ +++i+ D D +  G+  a+kl++ le+
  gi|242398414|ref|YP_002993838.1| 22 VILVEGMRDEVALRKLGVETEIIKL-SRFPLAEIALTAsHYHDIMILTDFDRK--GEDLAKKLTQYLEG 87
                                      6889999999999767777766655.5555677998866**************..********998875 PP

>> CPSF_A  CPSF A subunit region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0    0.0086        26      90     148 ..      10      69 ..       5      73 .. 0.82
   2 ?    5.8   0.1    0.0024       7.1      58      92 ..      76     111 ..      70     113 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.0086
                                       ES----EEEETTEEEE.E-SSEEEEEEE-TTS-EEEEEEEE-SS-EEEEEEETTEEEEEE CS
                            CPSF_A  90 kgavtalaefqGrllv.gvgqkvrvydlgedktLlrkafldtqlyvvslkvlgnriivgD 148
                                       ++ +  l ef+G +lv g+   v +++lg ++++++ +++  + +++++++  +++i+ D
  gi|242398414|ref|YP_002993838.1|  10 EQLIDKLREFNGVILVeGMRDEVALRKLGVETEIIKLSRFPLAEIALTASHYHDIMILTD 69 
                                       56677899*****6555***************9999999966668888888888888777 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0024
                                       SS--E..EEEEEEEEEE-SS--EEEEEEEEEEEES- CS
                            CPSF_A  58 dpaars.GrilvfeiievpetnrkLklvhkeevkga 92 
                                       d+a++   ++  ++ + + +t+r+Lk+++k+++kg+
  gi|242398414|ref|YP_002993838.1|  76 DLAKKLtQYLEGYKCRVDTNTRRELKKIAKKDIKGI 111
                                       555554555555666666789*************95 PP

>> Exonuc_VII_S  Exonuclease VII small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.2   0.00088       2.6       1      16 [.       2      17 ..       2      20 .. 0.91
   2 ?    2.0   0.1     0.076   2.3e+02      31      50 ..      73      92 ..      72      94 .. 0.84
   3 ?   -2.8   0.1       2.3   6.7e+03       7      13 ..      99     105 ..      97     112 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00088
                      Exonuc_VII_S  1 FEealaeLeeIvekLE 16
                                      + e++++Le++++kL 
  gi|242398414|ref|YP_002993838.1|  2 YAENYKRLEQLIDKLR 17
                                      88************96 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.076
                      Exonuc_VII_S 31 eGvkLlkeCekkLdeaeqkv 50
                                      +G+ L+k++ + L+  + +v
  gi|242398414|ref|YP_002993838.1| 73 KGEDLAKKLTQYLEGYKCRV 92
                                      7999*********9887666 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 2.3
                      Exonuc_VII_S   7 eLeeIve 13 
                                       eL++I++
  gi|242398414|ref|YP_002993838.1|  99 ELKKIAK 105
                                       5555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       872  (0.0486363); expected 358.6 (0.02)
Passed bias filter:                      676  (0.0377043); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 796.34
//
Query:       gi|242398415|ref|YP_002993839.1|  [L=267]
Description: transcriptional regulator [Thermococcus sibiricus MM 739]
Scores for complete 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   65.6   0.0    5.1e-18   64.7   0.0    1.5  1  TrmB            Sugar-specific transcriptional regulator TrmB
    1.4e-05   24.5   0.1    1.9e-05   24.0   0.1    1.2  1  Regulator_TrmB  Archaeal transcriptional regulator TrmB


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.7   0.0   5.7e-22   5.1e-18       1      68 []      13      81 ..      13      81 .. 0.98

  Alignments for each domain:
  == domain 1  score: 64.7 bits;  conditional E-value: 5.7e-22
                                      HH.HCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE--HH CS
                              TrmB  1 Lq.klGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYravdpe 68
                                      Lq ++ L+ yEa++Y+aL+  g +t  e+a+ ++vp ++ Y+vLrsLe+kG+   ++g+ ++Yr+v+p+
  gi|242398415|ref|YP_002993839.1| 13 LQeHFELNLYEARAYVALVGFGVLTPAELASVSEVPAPRTYDVLRSLEKKGFALSQPGKANKYRPVHPK 81
                                      7889**************************************************************995 PP

>> Regulator_TrmB  Archaeal transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.1   2.1e-09   1.9e-05       1     134 [.     128     266 ..     128     267 .] 0.87

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 2.1e-09
                                       -EEEESSHHHHHHHHHHHHHH-SSEEEEEE-GGGHHHHHHHHHHHHHTT-EEEEEESS......----GGGSSSSEE CS
                    Regulator_TrmB   1 avwvvksretvierieelIesAenelivslpselLeelreeliaaaergvtVllliyp......dedleeldleeva 71 
                                       +vw+v+++++   + +e++e  e+e++++ +      l+ e+ aa+++g +  +l+ +      +  +    ++   
  gi|242398415|ref|YP_002993839.1| 128 RVWIVRGIRNSTLKTQEMLEGVEKEILLADNGYVAANLDTEITAAVDKGAKAKILVLKqilprlETSKIMDYYKAGK 204
                                       59***************************999999***********************9*88854444555566778 PP

                                       EEEE-S---S.EEEEETTTEEEEE-SSS-.EEEE--HHHHHHHHHHHHHH........HHH-EE CS
                    Regulator_TrmB  72 tevrvrrsgapllvivDrkrgvvaprevl.rdkeeeyaiifkekelihvlshyFlttlWktsev 134
                                        e+++ ++++  ++i D++  +   ++++ r  + e+ +++k+ +++ ++   F+++ Wk+++ 
  gi|242398415|ref|YP_002993839.1| 205 LELKTLDKIELPMLICDEEVFFAL-EDLAaRYFNYETQVWVKDFRVVELFKSKFNEY-WKKGKK 266
                                       999*******66799998765555.5555599999*********************9.**9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1205  (0.0672095); expected 358.6 (0.02)
Passed bias filter:                      733  (0.0408835); 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: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 1746.88
//
Query:       gi|242398416|ref|YP_002993840.1|  [L=70]
Description: hypothetical protein TSIB_0425 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
       0.01   15.7   0.1      0.012   15.5   0.1    1.1  1  TrmB        Sugar-specific transcriptional regulator TrmB
      0.032   14.0   0.3      0.041   13.7   0.3    1.1  1  HTH_IclR    IclR helix-turn-helix domain
      0.078   12.8   0.0       0.08   12.8   0.0    1.1  1  DUF742      Protein of unknown function (DUF742)
       0.11   12.4   0.5       0.92    9.4   0.5    2.0  1  HTH_5       Bacterial regulatory protein, arsR family
       0.13   12.7   0.3       0.16   12.3   0.3    1.4  1  FaeA        FaeA-like protein
       0.15   12.3   2.0       0.22   11.8   2.0    1.5  1  TFIIE_beta  TFIIE beta subunit core domain


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.1     4e-06     0.012      16      58 ..       8      50 ..       6      65 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4e-06
                                      HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB 16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                       +++ +++ta+eia+e+++  ++  + L +L+  G +e  ++ 
  gi|242398416|ref|YP_002993840.1|  8 DVVRTKEKTAEEIAHETKITLAQTKRLLLRLLAQGKIESLEKD 50
                                      578999******************************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 ?   13.7   0.3   1.4e-05     0.041       8      48 ..       6      44 ..       4      48 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.4e-05
                                      HHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          HTH_IclR  8 iLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyv 48
                                      iLd +++     t  e+A++t ++ + + RlL  L  +G +
  gi|242398416|ref|YP_002993840.1|  6 ILDVVRTKEK--TAEEIAHETKITLAQTKRLLLRLLAQGKI 44
                                      7777777777..59*********************999965 PP

>> DUF742  Protein of unknown function (DUF742)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.7e-05      0.08      44      87 ..       2      46 ..       1      60 [. 0.91

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.7e-05
                            DUF742 44 ehrailrLcre.plsVaelaAelklPvgvvrvLlsdLldaglltv 87
                                      +h++il+ +r+  ++  e+a e+k+ ++ ++ Ll  Ll++g++++
  gi|242398416|ref|YP_002993840.1|  2 KHEKILDVVRTkEKTAEEIAHETKITLAQTKRLLLRLLAQGKIES 46
                                      5899******97788889************************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 ?    9.4   0.5   0.00031      0.92       6      36 ..       5      35 ..       4      46 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00031
                                      HHHHHHTTSSEEHHHHHHHHTS-HHHHHHHH CS
                             HTH_5  6 kILklLaegelcvcelaeelglsqstvShHL 36
                                      kIL  ++ +e+++ e+a e++++ + + + L
  gi|242398416|ref|YP_002993840.1|  5 KILDVVRTKEKTAEEIAHETKITLAQTKRLL 35
                                      79*******************9866665555 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.3   5.5e-05      0.16      13      47 ..      11      46 ..       1      59 [. 0.75

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.5e-05
                                      S----H.HHHHHHHTS-HHHHHHHHHHHHHHSSEEE CS
                              FaeA 13 kapckT.reiAdalglsaYQaRyYLeqLekegkikr 47
                                      ++  kT  eiA  + ++  Q +  L  L ++gki+ 
  gi|242398416|ref|YP_002993840.1| 11 RTKEKTaEEIAHETKITLAQTKRLLLRLLAQGKIES 46
                                      344455168*************************84 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 ?   11.8   2.0   7.4e-05      0.22      18      56 ..      14      52 ..       1      70 [] 0.72

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.4e-05
                        TFIIE_beta 18 plsleeIlsylslqldlsdknwllleaLknnpkiey...Dpk 56
                                       ++ eeI+ ++++   l ++++lll++L +  kie    D+k
  gi|242398416|ref|YP_002993840.1| 14 EKTAEEIAHETKI--TLAQTKRLLLRLLAQ-GKIESlekDGK 52
                                      6899*********..888999999999975.56766544554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       902  (0.0503096); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 457.69
//
Query:       gi|242398417|ref|YP_002993841.1|  [L=108]
Description: Sjogren's syndrome/scleroderma autoantigen 1 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.6e-14   51.6   0.5    1.2e-13   51.0   0.5    1.3  1  Auto_anti-p27    Sjogren's syndrome/scleroderma autoantigen 1
    0.00021   21.2   0.7      0.023   14.7   0.1    2.2  2  DNA_ligase_ZBD   NAD-dependent DNA ligase C4 zinc finger doma
    0.00072   19.5   0.6     0.0011   18.9   0.6    1.2  1  DZR              Double zinc ribbon
    0.00099   18.4   1.5      0.071   12.5   0.1    2.2  2  zf-ribbon_3      zinc-ribbon domain
     0.0064   16.2   1.1        3.7    7.4   0.0    2.5  2  zinc_ribbon_5    zinc-ribbon domain
     0.0099   16.2   0.4      0.016   15.5   0.4    1.4  1  GAT              GAT domain
  ------ inclusion threshold ------
      0.012   15.5   2.2       0.17   11.8   0.3    2.2  2  Nudix_N_2        Nudix N-terminal
      0.015   15.3   0.3      0.024   14.6   0.3    1.3  1  zinc-ribbons_6   zinc-ribbons
      0.039   13.9   3.0        2.4    8.2   0.7    2.3  2  Ogr_Delta        Ogr/Delta-like zinc finger
      0.043   14.1   1.3       0.46   10.8   0.0    2.1  2  zf-LITAF-like    LITAF-like zinc ribbon domain
      0.073   13.2   0.0        6.4    7.0   0.0    2.3  2  zf-Mss51         Zinc-finger of mitochondrial splicing suppre
       0.08   12.6   5.0       0.34   10.6   5.0    1.9  1  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
      0.099   13.1   1.3       0.15   12.5   1.3    1.3  1  DUF3837          Domain of unknown function (DUF3837)
        0.1   12.8   3.0        2.1    8.5   3.5    2.1  2  NOB1_Zn_bind     Nin one binding (NOB1) Zn-ribbon like
       0.12   12.7   0.5        3.4    8.1   0.0    2.2  2  Lar_restr_allev  Restriction alleviation protein Lar
       0.14   12.0   3.8        1.3    8.9   3.8    2.3  1  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger
       0.14   12.0   4.9       0.63    9.8   5.0    2.0  1  zinc_ribbon_2    zinc-ribbon domain
       0.21   12.1   1.3        9.8    6.8   1.3    2.6  1  Zn_ribbon_recom  Recombinase zinc beta ribbon domain
       0.36   11.0   4.0        1.1    9.5   0.3    2.2  2  Zn-ribbon_8      Zinc ribbon domain
       0.48   11.1   5.1          2    9.2   0.3    2.3  2  zf-ISL3          zinc-finger of transposase IS204/IS1001/IS10
       0.57    9.7   3.3        2.5    7.7   3.3    2.1  2  TF_Zn_Ribbon     TFIIB zinc-binding
        1.1    9.3   5.6        9.4    6.3   0.3    2.2  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
        1.3    8.4   6.0        8.1    5.9   0.1    2.6  3  zf-TFIIB         Transcription factor zinc-finger


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 !   51.0   0.5   1.5e-16   1.2e-13       3      40 .]      12      47 ..      10      47 .. 0.91

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 1.5e-16
                     Auto_anti-p27  3 mgelLlkGwtMLaetCpvCgvPLmrdrkggkvyCvaCd 40
                                      +  lLl G++ML+ +Cp+Cg+PL++   +gk++C++C+
  gi|242398417|ref|YP_002993841.1| 12 ITPLLLSGAKMLDRHCPQCGSPLFKL--NGKIFCPVCE 47
                                      5679*********************8..4899*****6 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 !   14.7   0.1   2.9e-05     0.023       1      12 [.      26      37 ..      26      41 .. 0.85
   2 ?    5.1   0.1      0.03        23       2       6 ..      43      47 ..      42      54 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.9e-05
                    DNA_ligase_ZBD  1 hCPvCGsavvRe 12
                                      hCP CGs++ + 
  gi|242398417|ref|YP_002993841.1| 26 HCPQCGSPLFKL 37
                                      9*******9775 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.03
                    DNA_ligase_ZBD  2 CPvCG 6 
                                      CPvC 
  gi|242398417|ref|YP_002993841.1| 43 CPVCE 47
                                      ****6 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.6   1.4e-06    0.0011      12      38 ..      24      50 ..      20      55 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.4e-06
                               DZR 12 arfCseCgtklkavaaedrCpsCgekv 38
                                      +r C++Cg++l + + +++Cp C++  
  gi|242398417|ref|YP_002993841.1| 24 DRHCPQCGSPLFKLNGKIFCPVCEHRK 50
                                      589*******999999*******9875 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.1   9.1e-05     0.071       3      11 ..      25      33 ..      23      36 .. 0.71
   2 ?    4.9   0.1     0.022        18       2      10 ..      40      48 ..      39      55 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.1e-05
                       zf-ribbon_3  3 vrCPnCGap 11
                                      ++CP+CG+p
  gi|242398417|ref|YP_002993841.1| 25 RHCPQCGSP 33
                                      477777775 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.022
                       zf-ribbon_3  2 tvrCPnCGa 10
                                      +++CP C +
  gi|242398417|ref|YP_002993841.1| 40 KIFCPVCEH 48
                                      567888855 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0    0.0047       3.7       4      14 ..      26      37 ..      23      39 .. 0.80
   2 !    7.2   0.2    0.0054       4.2       3      20 ..      41      58 ..      40      62 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0047
                     zinc_ribbon_5  4 rCpdCdt.kFkl 14
                                       Cp+C++  Fkl
  gi|242398417|ref|YP_002993841.1| 26 HCPQCGSpLFKL 37
                                      6*****945887 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0054
                     zinc_ribbon_5  3 irCpdCdtkFklvdsklK 20
                                      i Cp C+   kl  s+lK
  gi|242398417|ref|YP_002993841.1| 41 IFCPVCEHRKKLRKSELK 58
                                      77**************99 PP

>> GAT  GAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.4   2.1e-05     0.016      34      76 ..      62     104 ..      55     105 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.1e-05
                               GAT  34 kamqpriqklieetadeedllaelLqlNDeLnnvlerYerlkk 76 
                                       +++ +++  l+++++d+ d l++ L++ D + ++le+Y+r +k
  gi|242398417|ref|YP_002993841.1|  62 ESLIEKLNMLANTLPDDIDELKKYLEVMDMIITLLEKYKRREK 104
                                       566689999******************************9765 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.3   0.00022      0.17       1      10 [.      25      34 ..      25      37 .. 0.90
   2 ?    3.5   0.1      0.09        70       2      11 ..      42      51 ..      41      56 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00022
                                      -B-TTT--B- CS
                         Nudix_N_2  1 kFCsqCGtpv 10
                                      ++C+qCG+p+
  gi|242398417|ref|YP_002993841.1| 25 RHCPQCGSPL 34
                                      89******97 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.09
                                      B-TTT--B-E CS
                         Nudix_N_2  2 FCsqCGtpve 11
                                      FC+ C ++ +
  gi|242398417|ref|YP_002993841.1| 42 FCPVCEHRKK 51
                                      8999977755 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.3     3e-05     0.024       2      27 ..      26      51 ..      24      60 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3e-05
                                      --SSS-S--EE-SSEEE-TTT--EEE CS
                    zinc-ribbons_6  2 kCpeCqqelekrgeqyhCeaCqedlk 27
                                      +Cp+C ++l k + +++C  C+++ k
  gi|242398417|ref|YP_002993841.1| 26 HCPQCGSPLFKLNGKIFCPVCEHRKK 51
                                      79999999999999999999998655 PP

>> Ogr_Delta  Ogr/Delta-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.7    0.0031       2.4       1       8 [.      26      33 ..      26      36 .. 0.90
   2 ?    5.8   0.1     0.017        13       2      15 ..      43      56 ..      42      58 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0031
                         Ogr_Delta  1 rCPhCgap 8 
                                      +CP+Cg+p
  gi|242398417|ref|YP_002993841.1| 26 HCPQCGSP 33
                                      8*****98 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.017
                         Ogr_Delta  2 CPhCgapaaartsr 15
                                      CP C+++   r+s+
  gi|242398417|ref|YP_002993841.1| 43 CPVCEHRKKLRKSE 56
                                      *******9999986 PP

>> zf-LITAF-like  LITAF-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00058      0.46      44      66 ..      12      34 ..       8      38 .. 0.88
   2 ?    2.4   0.3      0.24   1.9e+02       6      14 ..      41      49 ..      38      65 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00058
                     zf-LITAF-like 44 liPfcvdslkdvehyCpnCgall 66
                                      + P+++++ k  + +Cp+Cg+ l
  gi|242398417|ref|YP_002993841.1| 12 ITPLLLSGAKMLDRHCPQCGSPL 34
                                      469****************9876 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.24
                     zf-LITAF-like  6 vdCpaCqqr 14
                                      + Cp C++r
  gi|242398417|ref|YP_002993841.1| 41 IFCPVCEHR 49
                                      778888876 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0    0.0082       6.4      15      27 ..      23      35 ..       7      39 .. 0.86
   2 ?    4.5   0.0     0.047        37       1      10 [.      42      51 ..      42      87 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0082
                          zf-Mss51 15 vdfeCpdCGipty 27
                                       d  Cp+CG p +
  gi|242398417|ref|YP_002993841.1| 23 LDRHCPQCGSPLF 35
                                      5678******975 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.047
                          zf-Mss51  1 lCPvpkhkqt 10
                                      +CPv++h+++
  gi|242398417|ref|YP_002993841.1| 42 FCPVCEHRKK 51
                                      5****99987 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 ?   10.6   5.0   0.00044      0.34       4      30 ..      25      49 ..      24      50 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00044
                     zf-NADH-PPase  4 rFCgrCGaptepaeggwarvCpaCgle 30
                                      r C++CG+p  +  g  +  Cp C ++
  gi|242398417|ref|YP_002993841.1| 25 RHCPQCGSPLFKLNG--KIFCPVCEHR 49
                                      89*********9999..9999999987 PP

>> DUF3837  Domain of unknown function (DUF3837)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.3   0.00019      0.15      38      89 ..      58     108 .]      53     108 .] 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00019
                           DUF3837  38 lglpeieekeeleelkekleeelkkvspkdekekklikllkdYepdeevdeq 89 
                                        g+ e + +e+l+ l + l ++++++++  e    +i ll++Y++ e+++e+
  gi|242398417|ref|YP_002993841.1|  58 KGV-EESLIEKLNMLANTLPDDIDELKKYLEVMDMIITLLEKYKRREKTNET 108
                                       566.557789999999*********************************995 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 ?    4.8   0.3     0.042        32      21      32 ..      22      33 ..      17      38 .. 0.80
   2 ?    8.5   3.5    0.0027       2.1      11      39 ..      27      57 ..      25      74 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.042
                      NOB1_Zn_bind 21 mtkkFCpkCGnk 32
                                      m  + Cp+CG++
  gi|242398417|ref|YP_002993841.1| 22 MLDRHCPQCGSP 33
                                      66789*****86 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0027
                      NOB1_Zn_bind 11 ChaCfkvt.kdmtkkFCpkCGn.ktLkrvav 39
                                      C  C +   k + k FCp C + k L++ ++
  gi|242398417|ref|YP_002993841.1| 27 CPQCGSPLfKLNGKIFCPVCEHrKKLRKSEL 57
                                      8888886526699********9889998765 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 ?    2.7   0.3      0.21   1.7e+02       5      12 ..      26      33 ..      25      38 .. 0.84
   2 ?    8.1   0.0    0.0044       3.4       6      23 ..      43      60 ..      42      90 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.21
                   Lar_restr_allev  5 pCPfCggr 12
                                       CP Cg++
  gi|242398417|ref|YP_002993841.1| 26 HCPQCGSP 33
                                      59999986 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0044
                   Lar_restr_allev  6 CPfCggravlersqrvva 23
                                      CP C +r++l +s+++  
  gi|242398417|ref|YP_002993841.1| 43 CPVCEHRKKLRKSELKGV 60
                                      ************998765 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 ?    8.9   3.8    0.0016       1.3       2      17 ..      25      40 ..      24      55 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0016
                                      EE-SSS--EEEEEE-S CS
                    zf-C4_Topoisom  2 ekCPkCggdLvlkrgk 17
                                      + CP+Cg++L + +gk
  gi|242398417|ref|YP_002993841.1| 25 RHCPQCGSPLFKLNGK 40
                                      78********987766 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   5.0   0.00081      0.63       2      19 ..      27      46 ..      26      52 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00081
                     zinc_ribbon_2  2 CpnCGael.q.dnakFCpyC 19
                                      Cp+CG +l + ++  FCp C
  gi|242398417|ref|YP_002993841.1| 27 CPQCGSPLfKlNGKIFCPVC 46
                                      *********989******99 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 ?    6.8   1.3     0.013       9.8       2      14 ..      37      49 ..      26      67 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.013
                   Zn_ribbon_recom  2 LsGllrCgeCGsp 14
                                      L G+++C  C ++
  gi|242398417|ref|YP_002993841.1| 37 LNGKIFCPVCEHR 49
                                      6789999999887 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.3    0.0014       1.1      26      36 ..      24      34 ..      12      38 .. 0.76
   2 ?    3.1   0.2      0.13     1e+02      28      34 ..      41      48 ..      35      55 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0014
                       Zn-ribbon_8 26 ltaCPeCgsev 36
                                      + +CP+Cgs++
  gi|242398417|ref|YP_002993841.1| 24 DRHCPQCGSPL 34
                                      345*****987 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.13
                       Zn-ribbon_8 28 a.CPeCgs 34
                                        CP C +
  gi|242398417|ref|YP_002993841.1| 41 IfCPVCEH 48
                                      449*9987 PP

>> zf-ISL3  zinc-finger of transposase IS204/IS1001/IS1096/IS1165
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.3    0.0025         2       3      18 ..      25      40 ..      24      41 .. 0.84
   2 ?    4.4   0.8     0.077        60       3      13 ..      41      51 ..      39      65 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0025
                           zf-ISL3  3 hrCPnCgsktvvkhgk 18
                                      ++CP+Cgs+  + +gk
  gi|242398417|ref|YP_002993841.1| 25 RHCPQCGSPLFKLNGK 40
                                      58******98888875 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.077
                           zf-ISL3  3 hrCPnCgsktv 13
                                      + CP C  +++
  gi|242398417|ref|YP_002993841.1| 41 IFCPVCEHRKK 51
                                      68*****9954 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   3.3    0.0032       2.5       3      26 ..      27      47 ..      25      49 .. 0.87
   2 ?    3.1   0.4     0.085        66       2       9 ..      42      49 ..      41      53 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0032
                                      ETTTTCEECHEETSTTCEEESSSS CS
                      TF_Zn_Ribbon  3 CPnCgstnlveDpergelvCtdCG 26
                                      CP Cgs+ + ++   g ++C+ C+
  gi|242398417|ref|YP_002993841.1| 27 CPQCGSPLFKLN---GKIFCPVCE 47
                                      *******87776...99******6 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.085
                                      EETTTTCE CS
                      TF_Zn_Ribbon  2 kCPnCgst 9 
                                       CP+C ++
  gi|242398417|ref|YP_002993841.1| 42 FCPVCEHR 49
                                      59***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 ?    5.9   0.7     0.016        13      19      26 ..      25      32 ..       4      39 .. 0.82
   2 ?    6.3   0.3     0.012       9.4      18      30 ..      40      53 ..      35      60 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.016
                     Zn_Tnp_IS1595 19 fvCPhCgs 26
                                      ++CP Cgs
  gi|242398417|ref|YP_002993841.1| 25 RHCPQCGS 32
                                      78*****7 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.012
                     Zn_Tnp_IS1595 18 gfvCPhCgsr.kay 30
                                      +  CP C++r k++
  gi|242398417|ref|YP_002993841.1| 40 KIFCPVCEHRkKLR 53
                                      355*****996654 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.2     0.014        11       1       9 [.      26      34 ..      25      38 .. 0.78
   2 ?    5.9   0.1      0.01       8.1       2      18 ..      43      61 ..      42      62 .. 0.83
   3 ?   -2.9   0.1       5.7   4.4e+03      31      40 ..      78      87 ..      78      87 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.014
                          zf-TFIIB  1 kCPkCqdel 9 
                                      +CP C+++l
  gi|242398417|ref|YP_002993841.1| 26 HCPQCGSPL 34
                                      688888876 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.01
                          zf-TFIIB  2 CPkCqd..eleeserggve 18
                                      CP+C +   l++se+ gve
  gi|242398417|ref|YP_002993841.1| 43 CPVCEHrkKLRKSELKGVE 61
                                      ****764469999999987 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 5.7
                          zf-TFIIB 31 drgeleklle 40
                                      d +el+k le
  gi|242398417|ref|YP_002993841.1| 78 DIDELKKYLE 87
                                      6789999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1000  (0.0557756); expected 358.6 (0.02)
Passed bias filter:                      600  (0.0334653); expected 358.6 (0.02)
Passed Vit filter:                       113  (0.00630264); 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: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 708.46
//
Query:       gi|242398418|ref|YP_002993842.1|  [L=245]
Description: Arginase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-19   70.2   0.0    5.3e-19   68.8   0.0    1.5  1  Arginase  Arginase family
  ------ inclusion threshold ------
      0.055   13.5   0.3        1.1    9.3   0.0    2.7  3  DUF3791   Protein of unknown function (DUF3791)


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 !   68.8   0.0   5.9e-23   5.3e-19      89     262 ..      57     228 ..      38     242 .. 0.85

  Alignments for each domain:
  == domain 1  score: 68.8 bits;  conditional E-value: 5.9e-23
                                       EESSGGGHHHHHHHHHHHHSTTEEEEEESSS----SSCTTTBSSSTTSHHHHHHHHTSECGCEEEEEEE-STCSH.. CS
                          Arginase  89 lGGDHsialgilralaekygkplgvihfDAHaDlrtpetegsgnshGtpfrraaeegllkpkklvqiGirsvdne.. 163
                                       + GDH  ++g+l+ ++ +     ++i +DAH+Dl +++     ++hG+++++ +ee+++++ ++v   +  ++ e  
  gi|242398418|ref|YP_002993842.1|  57 IIGDHLATYGVLKRVKTR-----SLISIDAHTDLMHDY-----LDHGSWLAYTLEEKIIERASIVGPVLMIPTTErt 123
                                       55**********999865.....7**************.....89**************988877544444444455 PP

                                       ...........HHHHHHHTTSEEEEHHHHHHHHHHHHHHHHHHHHTCTTSEEEEEEEGGGBBTTTSTSSSS-BSS-B CS
                          Arginase 164 ...........eyelakelgirvitmreidelglkavveeilervgaeedpvylSfDiDvlDpavaPGtGtpepgGl 229
                                                       ++++  +  ++ ++  ++++++e i++++g   + vyl++D+Dvl+p++    +  ++g l
  gi|242398418|ref|YP_002993842.1| 124 slwtrrvkifpALPRSRRVKGSWKAYKSLKTSSIEKIIEDIKKYLG---KDVYLTVDLDVLSPEYKI--SRFQHGEL 195
                                       8899988766655556889999***********************7...57**************85..5******* PP

                                       -HHHHHHHHHHHHCHSEEEEEEEE-B-GGGSST CS
                          Arginase 230 tlrellallrelaeklnlvgaDvvEvnPaldte 262
                                       +l+ell++++e++++ n++g+D++Ev+++   +
  gi|242398418|ref|YP_002993842.1| 196 SLSELLDIINEIKKNFNIIGCDIAEVSDKIKRS 228
                                       ***************************997763 PP

>> DUF3791  Protein of unknown function (DUF3791)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1     0.056     5e+02      21      35 ..      22      37 ..      19      39 .. 0.88
   2 ?    9.3   0.0   0.00013       1.1      37      57 ..     148     168 ..     146     170 .. 0.90
   3 ?   -2.3   0.0      0.54   4.8e+03       7      16 ..     204     213 ..     200     230 .. 0.61

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.056
                           DUF3791 21 vykllkksgvl.dyli 35
                                      +++llk++ ++ d++i
  gi|242398418|ref|YP_002993842.1| 22 ALELLKRNRIIeDFVI 37
                                      789********99986 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00013
                           DUF3791  37 cYevlHtqSkeyivedideyl 57 
                                        Y  l t S+e i+edi +yl
  gi|242398418|ref|YP_002993842.1| 148 AYKSLKTSSIEKIIEDIKKYL 168
                                       6999***************98 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 0.54
                           DUF3791   7 Ieeyarklgl 16 
                                       I+e ++ +++
  gi|242398418|ref|YP_002993842.1| 204 INEIKKNFNI 213
                                       4444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 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:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1652.27
//
Query:       gi|242398419|ref|YP_002993843.1|  [L=406]
Description: Bifunctional D-arabino 3-hexulose-6-phosphate formaldehyde lyase/phosphohexuloisomerase [Thermococcus sibiricus MM 739]
Scores for complete 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-27   94.9   6.4    6.6e-27   94.6   5.3    1.7  2  OMPdecase       Orotidine 5'-phosphate decarboxylase / HUMPS 
    4.2e-21   75.2   0.0    1.1e-20   73.8   0.0    1.7  1  SIS             SIS domain
    5.5e-09   36.2   5.4    2.4e-07   30.9   0.2    3.0  3  SIS_2           SIS domain
    1.1e-06   28.4   3.3      9e-05   22.1   0.3    2.3  2  HMGL-like       HMGL-like
    1.3e-06   27.9   1.1    3.4e-06   26.5   1.1    1.8  1  TMP-TENI        Thiamine monophosphate synthase
    1.7e-06   27.5   0.4    3.2e-06   26.6   0.4    1.4  1  ThiG            Thiazole biosynthesis protein ThiG
    1.3e-05   24.5   1.7      3e-05   23.3   1.7    1.7  1  NanE            Putative N-acetylmannosamine-6-phosphate epim
    1.4e-05   24.7   0.9     0.0001   21.8   0.4    2.1  2  His_biosynth    Histidine biosynthesis protein
    2.8e-05   23.4   0.4    0.00014   21.2   0.4    2.1  1  DUF561          Protein of unknown function (DUF561)
    0.00019   21.0   3.9      0.018   14.5   0.2    2.9  3  PEP_mutase      Phosphoenolpyruvate phosphomutase
    0.00026   20.3   0.4    0.00066   18.9   0.4    1.8  1  IGPS            Indole-3-glycerol phosphate synthase
     0.0015   17.9   3.4     0.0033   16.8   1.9    2.2  2  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
  ------ inclusion threshold ------
      0.022   13.9   2.1       0.12   11.4   2.1    2.1  1  Dus             Dihydrouridine synthase (Dus)
      0.045   12.6   3.3        3.7    6.3   1.1    3.0  3  Trp_syntA       Tryptophan synthase alpha chain
      0.052   13.3   6.8       0.13   12.0   0.1    3.0  3  QRPTase_C       Quinolinate phosphoribosyl transferase, C-ter
       0.07   12.5   0.1       0.27   10.6   0.1    2.1  2  AP_endonuc_2    Xylose isomerase-like TIM barrel
       0.21   10.5   6.1        2.2    7.2   6.2    2.4  1  IMPDH           IMP dehydrogenase / GMP reductase domain


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 !   94.6   5.3   6.2e-30   6.6e-27       3     225 .]       3     203 ..       1     203 [. 0.95
   2 ?   -2.8   0.0       3.6   3.8e+03     136     156 ..     303     324 ..     288     341 .. 0.57

  Alignments for each domain:
  == domain 1  score: 94.6 bits;  conditional E-value: 6.2e-30
                                       EEEEE-SSSHHHHHHHHHHHGG.GSSEEEEEHHHHHHHTHH.HHTHHHHHHHHHT..SEEEEEEEE-S-HHHHHHHH CS
                         OMPdecase   3 LclalDvatarelleladkvgp.sivvlKthydlvegwgfegtgaklaalarkhg..flifeDrKfaDIGntvekqa 76 
                                       L++alDv++ + ++++a+kv    + +l+++++l++++g      ++++l+++++   +i++D+K++D G+ + ++a
  gi|242398419|ref|YP_002993843.1|   3 LQVALDVTDIEHAISIAEKVARgGAHWLEVGTPLIKKEG-----IRAVELMKRRFpdRKIVADLKTMDTGALEVEMA 74 
                                       9**************************************.....**********999******************** PP

                                       HSTCHHHHTTESEEEEEGTGHHHHHHHHHHHHHHTTS.EEEEEESTSSGGHHHHHH..H..SHHHHHHHHHHHHHHH CS
                         OMPdecase  77 tagsarikewadivtvhavaGkasvkalaeaaekwgnrgllilaqmsskgnlmlqe..k..gytqacveaarehkae 149
                                             + ++ad+v + +va+++++k ++++a+k+g    ++ + +  k++ ++++  +  g+ + +v+   +++  
  gi|242398419|ref|YP_002993843.1|  75 ------ARHGADVVSILGVADDKTIKDAVTVAKKYG--IRVMADLIGVKDKVKRAKelEnmGVNYILVHTGIDEQ-- 141
                                       ......69***************************9..999***************8636999999999999999.. PP

                                       TTESEEECCCHTHHHHHHTTCSCEEEHHHTTEEEEECTTCCGGGHHHHHHHTTCSEEEESHHHHTSSSHHHHHHHH CS
                         OMPdecase 150 dfvmGfvaqetlnateedaddfihltpgigleqggdgkgqqyntpekligiagadiiivGRgIlkagdpveeaery 225
                                              aq + +      +d+ ++++ +++   ++++g++ +t++k+i+ aga iiivG +I+ka+dp++ ++r+
  gi|242398419|ref|YP_002993843.1| 142 -------AQGRNP-----LEDLEKVVKAVKI-PVAVAGGLNLETIPKVIE-AGATIIIVGGAITKAKDPENITRRI 203
                                       .......566656.....5799********9.*****************9.99*****************988875 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.6
                                       HHHHHHHHHHHHHH.TTESEEE CS
                         OMPdecase 136 tqacveaarehkae.dfvmGfv 156
                                       t  +v+aa+ +k++  +v+G+ 
  gi|242398419|ref|YP_002993843.1| 303 TRTIVDAAEIAKNQgGKVVGIT 324
                                       3334444443333334444444 PP

>> SIS  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.8   0.0     1e-23   1.1e-20       3     110 ..     246     347 ..     244     362 .. 0.91

  Alignments for each domain:
  == domain 1  score: 73.8 bits;  conditional E-value: 1e-23
                                       CTSSEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHHHT CS
                               SIS   3 akakriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaaelaker 79 
                                       + a++i+++GaG+s+ ++k +a+ l+++ ++v++v ++ +      +  +e+dl+i+is sget+  v+aae ak++
  gi|242398419|ref|YP_002993843.1| 246 IGANKIFIYGAGRSGLVGKAFAMRLMHLDFNVYVVGETIT------PAFEEGDLLIAISGSGETRTIVDAAEIAKNQ 316
                                       5699**********************************99......8899*************************** PP

                                       TSEEEEEESSTTSHHHHHSSEEEEEEEECHC CS
                               SIS  80 gakiiaITdskgsplareadlalyinaepet 110
                                       g+k+++IT+ k+s+l + +d++++i+   ++
  gi|242398419|ref|YP_002993843.1| 317 GGKVVGITSYKNSTLGKLSDVVVEIPGRTKA 347
                                       *************************988776 PP

>> SIS_2  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1       7.5     8e+03     121     135 ..      95     109 ..      89     109 .. 0.84
   2 !    7.3   0.2    0.0044       4.6       6      59 ..     222     272 ..     208     284 .. 0.72
   3 !   30.9   0.2   2.3e-10   2.4e-07      98     138 .]     287     325 ..     274     325 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 7.5
                                       HHHHHHHHHT-EEEE CS
                             SIS_2 121 eaaeaakergmkviA 135
                                       +a+  ak+ g++v A
  gi|242398419|ref|YP_002993843.1|  95 DAVTVAKKYGIRVMA 109
                                       688999999999987 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0044
                                       HHHHHHHHHHHSHHHHHHHHHHHHHHHHTT--EEEEESGGGHHHHHHTSSSTT- CS
                             SIS_2   6 vteilerivetqaeaiekaaeliadslenggkvlvfGsGhSaalaeelaaragg 59 
                                       +t++++++  + + ++e+ ++ ++d++   +k++++G+G S +  + +a r+  
  gi|242398419|ref|YP_002993843.1| 222 ITDHIKTV--ATSLKLEQ-VRGMVDAMIGANKIFIYGAGRSGLVGKAFAMRLMH 272
                                       33333333..23334444.4668999*****************99999999875 PP

  == domain 3  score: 30.9 bits;  conditional E-value: 2.3e-10
                                       HTT--TT-EEEEE-SS--SHHHHHHHHHHHHHT-EEEEEE- CS
                             SIS_2  98 lvrlkpgDvLlviSnsGnnavvveaaeaakergmkviAlts 138
                                          +++gD+L+ iS sG+   +v+aae ak++g kv+++ts
  gi|242398419|ref|YP_002993843.1| 287 A--FEEGDLLIAISGSGETRTIVDAAEIAKNQGGKVVGITS 325
                                       4..89***********************************8 PP

>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.2    0.0028       2.9      17     114 ..       7     103 ..       3     113 .. 0.72
   2 !   22.1   0.3   8.6e-08     9e-05      19     147 ..     111     237 ..     102     268 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0028
                                       SS---HHHHHHHHHHHHHHT-SEE--TSGGGT.THHHHHHHS---TT-B..--EE-SSHH.HHHHHHH....TT-SE CS
                         HMGL-like  17 kaalsveeklaiakaLdeagvdeiEvgfpaaseddfevvraiakavkkarilalvrarek.dikaavealkgagakr 92 
                                        +  ++e+ + ia++ ++ g + +Evg p   ++ + +v+  ++  ++ +i+a ++  +   +++ ++     ga++
  gi|242398419|ref|YP_002993843.1|   7 LDVTDIEHAISIAEKVARGGAHWLEVGTPLIKKEGIRAVELMKRRFPDRKIVADLKTMDTgALEVEMA--ARHGADV 81 
                                       566789999**************************************999777665544413333333..4477777 PP

                                       EEEEEES-HHHHHHHHSSTHHH CS
                         HMGL-like  93 vhvfiatselhlkaklkkdree 114
                                       v +   + +  +k  + + +++
  gi|242398419|ref|YP_002993843.1|  82 VSILGVADDKTIKDAVTVAKKY 103
                                       7777766665555555555555 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 8.6e-08
                                       ---HHHHHHHHHHHHHHT-SEE--..TS..GGGT.THHHHHHHS---TT-B..--EE-SSHHHHHHHHH....TT-S CS
                         HMGL-like  19 alsveeklaiakaLdeagvdeiEv..gf..paaseddfevvraiakavkkarilalvrarekdikaavealkgagak 91 
                                        + v++k++ ak+L+++gv++i v  g+   a + +++e++++++kavk++ + +   ++ + i + +e    aga+
  gi|242398419|ref|YP_002993843.1| 111 LIGVKDKVKRAKELENMGVNYILVhtGIdeQAQGRNPLEDLEKVVKAVKIP-VAVAGGLNLETIPKVIE----AGAT 182
                                       567899****************99885522688999*************99.9999*************....**** PP

                                       EEEEEEES-HHHHHHHHSSTHHHH..HHHHHHHHHHHHHTT-ETTT-BTTTBS--HHH CS
                         HMGL-like  92 rvhvfiatselhlkaklkkdreev..akkaeeavkaarslgkdvelsledasrtdlef 147
                                       ++ v  a+++     ++ + + +   a+ ++ +vk +++++++++  ++     +le+
  gi|242398419|ref|YP_002993843.1| 183 IIIVGGAITKAKDPENITRRILDLfwAEYMQTIVKVIQDITDHIKTVAT---SLKLEQ 237
                                       **********999888888776652268899999999999999664433...333333 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   1.1   3.2e-09   3.4e-06     106     181 .]     118     190 ..      70     190 .. 0.84

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 3.2e-09
                          TMP-TENI 106 leeaeeaealgadYigvGpifpTdtKkda.eplgleglkelaealeiPvvaiGGitlenvaevleagadgvavvsai 181
                                        + a+e+e++g++Yi v    +T   ++a     le l+++++a++iPv + GG++le++++v+eaga  + v  ai
  gi|242398419|ref|YP_002993843.1| 118 VKRAKELENMGVNYILV----HTGIDEQAqGRNPLEDLEKVVKAVKIPVAVAGGLNLETIPKVIEAGATIIIVGGAI 190
                                       44599999999999986....77788888678889**********************************99987765 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.4     3e-09   3.2e-06     121     218 ..     102     201 ..      85     214 .. 0.84

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 3e-09
                                       HTT-EEEEE...E-S-HHHHHHHHHTT-SEBEEBSSSTTS----S-HHHHHHHHHH-SS-BEEES---SHHHHHHHH CS
                              ThiG 121 keGFevlpY...vsdDlvlarrleevGcaavmPlaapiGsglGllnkealkiiieeakvPvivDAGigspsdaaqam 194
                                       k G  v++    v+d +  a+ le++G++ ++  +     ++G +  e l+ +++ +k+Pv v  G+   + + +++
  gi|242398419|ref|YP_002993843.1| 102 KYGIRVMADligVKDKVKRAKELENMGVNYILVHTGIDEQAQGRNPLEDLEKVVKAVKIPVAVAGGLNL-ETIPKVI 177
                                       5566666531115677788***************99999************************999976.6799*** PP

                                       HTT-SEEEESHHHHTSSSHHHHHH CS
                              ThiG 195 elGadavllntavaeakdpvamAr 218
                                       e Ga+ +++  a+++akdp ++ r
  gi|242398419|ref|YP_002993843.1| 178 EAGATIIIVGGAITKAKDPENITR 201
                                       *******************98765 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 !   23.3   1.7   2.9e-08     3e-05      38     180 ..      47     194 ..      17     206 .. 0.76

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 2.9e-08
                                       E-B---TTS---BS.-SHH....HHHHHHTTT-SEEEEE--SS--T--HHHHHHHHHHH--EEEEE-SSHHH....H CS
                              NanE  38 ivkrdlpdsevrit.atlk....dideLaaagadiialDatdrerpvtieelikkikekyqllmaDistlee....g 105
                                       ++kr +pd ++     t++    +++  a +gad++++ +   ++  ti++ +   k+ +  +maD+  + +    +
  gi|242398419|ref|YP_002993843.1|  47 LMKRRFPDRKIVADlKTMDtgalEVEMAARHGADVVSILGVADDK--TIKDAVTVAKKYGIRVMADLIGVKDkvkrA 121
                                       567777776654431233222227999999********9998876..6788898899999******87776611113 PP

                                       HHHHHTT-SEEE-TTTTSSTTS-.SS--HHHHHHHHHTT--EEEES---SHHHHHHHHTT--SEEEE-HHHH-HH CS
                              NanE 106 lvakklGvdivGttlsGytkeeekaepDfalvkalseaglkviaeGrintPekakkaieiGvdavvvGsaitrle 180
                                       +  +++Gv+++     G  ++++  +p  +l k +++ ++ v + G +n  e   k+ie G++ ++vG+ait+ +
  gi|242398419|ref|YP_002993843.1| 122 KELENMGVNYILV-HTGIDEQAQGRNPLEDLEKVVKAVKIPVAVAGGLNL-ETIPKVIEAGATIIIVGGAITKAK 194
                                       4456679998853.468777777788888888889999*********996.77889****************954 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0      0.46   4.9e+02      88     133 ..      19      67 ..      12      85 .. 0.74
   2 !   21.8   0.4   9.9e-08    0.0001      28     108 ..     114     193 ..      92     210 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.46
                                       HHHHHHCT-SEEEESHHHHH-THH..HHHHHHHHCGGGEEEEEEEEE.C CS
                      His_biosynth  88 veelleagadkviigtaavknpel..ikelaekfgsqkivvaiDarr.g 133
                                       +e++ + ga+ + +gt  +k+  +  ++ + ++f++ kiv+ + + + g
  gi|242398419|ref|YP_002993843.1|  19 AEKVARGGAHWLEVGTPLIKKEGIraVELMKRRFPDRKIVADLKTMDtG 67 
                                       5677788899999999999886544499999999999999998877643 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 9.9e-08
                                       TTSHHHHHHHHHHHT-SEEEEE.EHHHHCTTHHHHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESH CS
                      His_biosynth  28 agdpvelakryeeegadelhvv.DldaakegreanldlveeiaeevfipvqvGGGIrsledveelleagadkviigt 103
                                        +d v+ ak++e+ g++++ v   +d  ++gr+   d +e+++++v+ipv v GG + le++ +++eaga  +i+g 
  gi|242398419|ref|YP_002993843.1| 114 VKDKVKRAKELENMGVNYILVHtGIDEQAQGRNPLED-LEKVVKAVKIPVAVAGGLN-LETIPKVIEAGATIIIVGG 188
                                       6788999999999999998875257777666666555.5999999999999999986.6779999999999999998 PP

                                       HHHH- CS
                      His_biosynth 104 aavkn 108
                                       a  k 
  gi|242398419|ref|YP_002993843.1| 189 AITKA 193
                                       85533 PP

>> DUF561  Protein of unknown function (DUF561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.4   1.3e-07   0.00014     129     230 ..     112     203 ..     104     216 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.3e-07
                            DUF561 129 LkleeqvkLakkLeslgvdliqteGkitsiskakkvndliekslstlastyeiskkvslPvicasGlsdvtvplals 205
                                       + ++++vk ak+Le++gv++i    +i + ++ ++           l    +++k+v++Pv  a Gl+  t+p  ++
  gi|242398419|ref|YP_002993843.1| 112 IGVKDKVKRAKELENMGVNYILVHTGIDEQAQGRNP----------LEDLEKVVKAVKIPVAVAGGLNLETIPKVIE 178
                                       567889999999999999999888777666643333..........344457899********************** PP

                            DUF561 206 lgasGiGigsavsklndeeemvall 230
                                       +ga  i +g a++k +d e++   +
  gi|242398419|ref|YP_002993843.1| 179 AGATIIIVGGAITKAKDPENITRRI 203
                                       *****************99998766 PP

>> PEP_mutase  Phosphoenolpyruvate phosphomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.2   1.7e-05     0.018     164     223 ..      73     138 ..      62     145 .. 0.76
   2 !    6.8   0.1    0.0037       3.9     177     226 ..     144     193 ..     141     201 .. 0.87
   3 ?   -1.0   0.0      0.91   9.6e+02     161     202 ..     239     282 ..     223     329 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.7e-05
                        PEP_mutase 164 aYaeAGAdgvfvpglqkdaeiaelvaav.dvplnvvp.l...kgt.lsvaelaelGvarislgnhl 223
                                       + a  GAd+v + g+ +d++i++ v+   +  + v++ l   k++    +el+++Gv+ i +++ +
  gi|242398419|ref|YP_002993843.1|  73 MAARHGADVVSILGVADDKTIKDAVTVAkKYGIRVMAdLigvKDKvKRAKELENMGVNYILVHTGI 138
                                       56789****************98887774544555553333433348899**********998876 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0037
                        PEP_mutase 177 glqkdaeiaelvaavdvplnvvplkgtlsvaelaelGvarislgnhllra 226
                                       g++  ++++++v+av++p+ v  + +  ++ ++ e+G+++i++g ++ +a
  gi|242398419|ref|YP_002993843.1| 144 GRNPLEDLEKVVKAVKIPVAVAGGLNLETIPKVIEAGATIIIVGGAITKA 193
                                       55667889**************97666899**************998776 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.91
                        PEP_mutase 161 RaraYaeAGAdgvfvpglqkdaei.aelvaav.dvplnvvplkg 202
                                       R+++ a  GA+ +f+ g+ +   + ++++ ++ ++  nv + ++
  gi|242398419|ref|YP_002993843.1| 239 RGMVDAMIGANKIFIYGAGRSGLVgKAFAMRLmHLDFNVYVVGE 282
                                       56666667999999999888888645666666567777776333 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.4   6.3e-07   0.00066     122     253 ..      69     202 ..      13     203 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 6.3e-07
                                       HHHHHHHHCT-SEEEEECCCS-HHHHHHHHHHHCCTT-EEEEEES.SHHHHHHHHHTT-SEEEEESEETTTTEE-.. CS
                              IGPS 122 yqieearalgadaiLLivkvledeeleelaeaakslglevLvEvh.deeeleralklgakiiGvNnRnLktlevd.. 195
                                        ++e a ++gad++  i+ v +d+++++ +++ak++g+ v+ +    ++ ++ra +l+   +GvN    +t  +d  
  gi|242398419|ref|YP_002993843.1|  69 LEVEMAARHGADVVS-ILGVADDKTIKDAVTVAKKYGIRVMADLIgVKDKVKRAKELEN--MGVNYILVHT-GIDeq 141
                                       678999******986.67899****************9999886514667999999986..7999765554.44411 PP

                                       ...CHHHHHHCHCC-TTSEEEEESSS-SHHHHHHHCCTT-SEEEESHHHHC-TTHHHHHHH CS
                              IGPS 196 ...lntteeLaklvpkdvllvaeSGiktredveklkeegvnafLvGeslmrqedvekaire 253
                                           n  e+L k+v++  + va  G  + e++ k+ e+g+  ++vG ++++++d e+ +r+
  gi|242398419|ref|YP_002993843.1| 142 aqgRNPLEDLEKVVKAVKIPVAVAGGLNLETIPKVIEAGATIIIVGGAITKAKDPENITRR 202
                                       11145568899999999*************************************9998876 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 !   16.8   1.9   3.1e-06    0.0033     138     197 ..     136     190 ..      65     191 .. 0.65
   2 ?   -0.8   0.0      0.81   8.5e+02      86     120 ..     207     241 ..     202     277 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.1e-06
                                       TT-SS----CCHHHHHHHHHHHHHHHT---EEEEESS--TTTCHHHHHHT--EEEESHHH CS
                    Ribul_P_3_epim 138 PgfgGQkFipevlekikkvrklidekeldlkievDGGvkldnieqiaeagadvlVagsav 197
                                        g + Q+   + le ++kv k+++     + + v GG++l++i +++eaga ++++g a+
  gi|242398419|ref|YP_002993843.1| 136 TGIDEQAQGRNPLEDLEKVVKAVK-----IPVAVAGGLNLETIPKVIEAGATIIIVGGAI 190
                                       455555555555666666555555.....799*************************997 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.81
                                       EE-ST-TTHHHHHHHHHHTTSEEEEEE-TT--GGG CS
                    Ribul_P_3_epim  86 vHaEalehlkrtiqeikeaGakaglvlnpatplea 120
                                       + aE ++++ ++iq+i ++ +++  +l+ +    +
  gi|242398419|ref|YP_002993843.1| 207 FWAEYMQTIVKVIQDITDHIKTVATSLKLEQVRGM 241
                                       56777788888888888877777777776554444 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   2.1   0.00012      0.12     116     215 ..      92     189 ..      90     245 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00012
                                       HHHCCSSS-EEEEEESESS.TTTC.HHHHHHHHHHCT-SEEEEESSECCCTT-CG--CHHHHHHHHH-SS-EEEESS CS
                               Dus 116 avvkaveiPvtvkirigid.deeenalelakiveaaGaqaltvHgRtraqnyegtadweaIkevkqavsipviaNGd 191
                                       ++++av +     ir+  d    +++++ ak +e+ G++ + vH    +q  +g+  +e+ ++v +av+ipv + G+
  gi|242398419|ref|YP_002993843.1|  92 TIKDAVTVAKKYGIRVMADlIGVKDKVKRAKELENMGVNYILVHTGIDEQ-AQGRNPLEDLEKVVKAVKIPVAVAGG 167
                                       5566666666677777777878899*******************987665.56799999****************99 PP

                                       --SHHHHHHHHHHH--SEEEESCH CS
                               Dus 192 IkdaedaqaileetGadgvmigrg 215
                                         ++e + +++e  Ga  +++g +
  gi|242398419|ref|YP_002993843.1| 168 L-NLETIPKVIEA-GATIIIVGGA 189
                                       6.46777777666.6666666654 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.017        18      16      46 ..       5      35 ..       1      38 [. 0.88
   2 ?    0.4   0.0      0.22   2.3e+02     120     166 ..      57     103 ..      45     127 .. 0.78
   3 ?    6.3   1.1    0.0035       3.7     135     232 ..      99     193 ..      90     204 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.017
                                      EETTSS-HHHHHHHHHHHHHCT-SSEEEE-- CS
                         Trp_syntA 16 vtagdpdleqsleilkalekagadviElGlp 46
                                      v+++  d+e+ ++i ++++++ga  +E+G p
  gi|242398419|ref|YP_002993843.1|  5 VALDVTDIEHAISIAEKVARGGAHWLEVGTP 35
                                      56677899*********************99 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.22
                                       EETTSBCCCHHHH.HHHHHHTT-EEEEEE-TTS-HHHHHHHHHH--S- CS
                         Trp_syntA 120 ivpDlPleeaeel.veaakkkglelvflvapttsderlkevveqaegf 166
                                       iv+Dl + +   l ve+a ++g ++v+++   ++d+++k  v  a+ +
  gi|242398419|ref|YP_002993843.1|  57 IVADLKTMDTGALeVEMAARHGADVVSILGV-ADDKTIKDAVTVAKKY 103
                                       7888888888777457888999999999988.8888888887777666 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.0035
                                       HHHHTT-EEEE.EE-TTS-HHHHHHHHHH--S-EEEESTTC-SSTTSSB-TTHHHHHHHHHHCTSS-EEEESSS-SH CS
                         Trp_syntA 135 aakkkglelvf.lvapttsderlkevveqaegfvYvvsraGvTgaenavaaevdelverlkkltavPvavGFGistk 210
                                       +akk+g++++  l+    + +r ke+ +   g  Y++  +G+  ++++  + +++ +e++ k+ + Pvav  G++ +
  gi|242398419|ref|YP_002993843.1|  99 VAKKYGIRVMAdLIGVKDKVKRAKELENM--GVNYILVHTGID-EQAQGRNPLED-LEKVVKAVKIPVAVAGGLNLE 171
                                       55666665543255565555666666544..444556667774.34455566665.566666666******998765 PP

                                       HHHHHHH.TT-SEEEE-HHHHHH CS
                         Trp_syntA 211 eqvkqva.kvadGvivGSalvkk 232
                                        ++ +v+ ++a  +ivG a+ k+
  gi|242398419|ref|YP_002993843.1| 172 -TIPKVIeAGATIIIVGGAITKA 193
                                       .55555559*********99775 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 ?    3.0   0.8     0.071        75      92     154 ..      70     134 ..      40     144 .. 0.74
   2 ?   12.0   0.1   0.00012      0.13     116     162 ..     153     194 ..     139     200 .. 0.81
   3 ?   -0.4   0.0      0.82   8.7e+02     106     144 ..     204     241 ..     202     251 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.071
                                       HHHHHHHHT-SEEE.EES--HHHHHHHHHHHHHHSTTSEEEEESS-.-TTTHHHHHCTT-SEEEE CS
                         QRPTase_C  92 eleevleaeadiim.LDnfsveelkkaveelkeknkrvlievSGgv.tlenveeyaksgvdvisv 154
                                       e+e ++  +ad++  L   + +++k+av++ k+  +rv+    G   + +  +e+ ++gv++i v
  gi|242398419|ref|YP_002993843.1|  70 EVEMAARHGADVVSiLGVADDKTIKDAVTVAKKYGIRVMADLIGVKdKVKRAKELENMGVNYILV 134
                                       677788888999972555677999*****999999999988887431346778888888888866 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00012
                                       HHHHHHHHHSTTSEEEEESS--TTTHHHHHCTT-SEEEECHHCHTB- CS
                         QRPTase_C 116 kaveelkeknkrvlievSGgvtlenveeyaksgvdvisvgalthsvk 162
                                       k+v+     + ++ + v+Gg++le++ ++ + g ++i vg +++++k
  gi|242398419|ref|YP_002993843.1| 153 KVVK-----AVKIPVAVAGGLNLETIPKVIEAGATIIIVGGAITKAK 194
                                       3333.....4458899***********************99888775 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.82
                                       EES--HHHHHHHHHHHHHHSTTSEEEEESS--TTTHHHH CS
                         QRPTase_C 106 LDnfsveelkkaveelkeknkrvlievSGgvtlenveey 144
                                       LD f +e ++++v++++ +  ++++ v+ +++le+v+ +
  gi|242398419|ref|YP_002993843.1| 204 LDLFWAEYMQTIVKVIQDITDHIKT-VATSLKLEQVRGM 241
                                       7888999999999999999887776.5557777777655 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 ?   10.6   0.1   0.00026      0.27      13     114 ..      72     159 ..      64     233 .. 0.77
   2 ?   -3.5   0.0       5.4   5.6e+03      69      88 ..     303     322 ..     276     326 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00026
                                       EEECCTCSHHHHC....HHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCSHHHHHHHHHHHHHHHHHH... CS
                      AP_endonuc_2  13 Elfgrdlvpvsel....sdeelrelrkaldelglriaslslftrfgypdederearreesvdalkraielaaaL... 82 
                                       E++ r + +v++     +d+++++    ++++g+r            +      a+    +  +k+ +++a++L   
  gi|242398419|ref|YP_002993843.1|  72 EMAARHGADVVSIlgvaDDKTIKDAVTVAKKYGIR------------VM-----AD----LIGVKDKVKRAKELenm 127
                                       44444444444444444555578888899999999............33.....45....77777777777777666 PP

                                       TBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHH CS
                      AP_endonuc_2  83 GapllvlhpGtagagpkgseeeawerlaesln 114
                                       G+ ++ +h+G++ + +++++ e++e+++++++
  gi|242398419|ref|YP_002993843.1| 128 GVNYILVHTGIDEQAQGRNPLEDLEKVVKAVK 159
                                       **********9999999999999999999876 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 5.4
                                       HHHHHHHHHHHHHHTBSEEE CS
                      AP_endonuc_2  69 vdalkraielaaaLGapllv 88 
                                        + + +a+e+a+  G++++ 
  gi|242398419|ref|YP_002993843.1| 303 TRTIVDAAEIAKNQGGKVVG 322
                                       44555666666666666654 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   6.2    0.0021       2.2      82     173 ..      51     187 ..       9     194 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0021
                                       S............................................TTSXBXTTSXB-EEEEE-SSTTHHHHHHHHHH CS
                                       x............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH  82 s............................................pnaakdekgrllvgaavgvkedalervkalve 114
                                                                                      ++ ++ g  +++  +gvk d+ +r+k+l +
  gi|242398419|ref|YP_002993843.1|  51 RfpdrkivadlktmdtgalevemaarhgadvvsilgvaddktikdAVTVAKKYGIRVMADLIGVK-DKVKRAKELEN 126
                                       45555555555555555555555555566666666666655553222223334444555568888.799******** PP

                                       TT-SEEEEE-STSSSH...HHHHHHHHHHHHTTTSEE.EEEEE-SHHHHHHHHHTT-SEEEE- CS
                                       xxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 115 agvdvlvvdsahghse...kvleavkeikkkveevev.iaGnvataegakaLieagadavkvG 173
                                        gv+ ++v +   +++   + le ++++ k+v+ + v +aG + + e + ++ieaga ++ vG
  gi|242398419|ref|YP_002993843.1| 127 MGVNYILVHTGIDEQAqgrNPLEDLEKVVKAVK-IPVaVAGGL-NLETIPKVIEAGATIIIVG 187
                                       ********9975555500055555666555553.333257765.6788999********9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       795  (0.0443416); expected 358.6 (0.02)
Passed bias filter:                      578  (0.0322383); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.71u 0.28s 00:00:00.99 Elapsed: 00:00:00.47
# Mc/sec: 2610.74
//
Query:       gi|242398420|ref|YP_002993844.1|  [L=251]
Description: hypothetical protein TSIB_0429 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.013   15.8   0.0      0.025   14.9   0.0    1.3  1  FtsZ_C    FtsZ family, C-terminal domain


Domain annotation for each model (and alignments):
>> FtsZ_C  FtsZ family, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   1.4e-06     0.025      40      89 ..     197     245 ..     191     248 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.4e-06
                                       EEEEEE-TT--HHHHHHHHHHHHHHS-TTSEEEEEEEE-TT--SEEEEEE CS
                            FtsZ_C  40 lvnitggsdltlkEveevaetireevdeeanvivGavideeledeirvtv 89 
                                       l+ni  g+++ l+++ ++ ++ +++++e  ++i+G +++e l+d+i +  
  gi|242398420|ref|YP_002993844.1| 197 LINILVGENVPLSDAHRILSNFQKFLKE-KDIIWGIKMEEGLNDHIEILS 245
                                       9**********************99975.69***************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); 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: 00:00:00.46
# Mc/sec: 1624.98
//
Query:       gi|242398421|ref|YP_002993845.1|  [L=219]
Description: Hydrolase, HAD superfamily [Thermococcus sibiricus MM 739]
Scores for 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-28  100.7   0.0    1.3e-28  100.3   0.0    1.1  1  HAD_2           Haloacid dehalogenase-like hydrolase
    9.3e-19   68.6   0.0    1.5e-13   51.5   0.0    2.1  2  Hydrolase       haloacid dehalogenase-like hydrolase
    7.7e-08   32.3   0.0    1.2e-07   31.6   0.0    1.3  1  Hydrolase_like  HAD-hyrolase-like
    4.6e-06   27.2   0.0    7.4e-06   26.5   0.0    1.5  1  HAD             haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.016   15.3   0.0      0.099   12.8   0.0    2.1  1  Hydrolase_6     Haloacid dehalogenase-like hydrolase
      0.072   12.8   0.1        1.7    8.3   0.0    2.2  2  Hydrolase_3     haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.3   0.0   4.2e-32   1.3e-28       1     177 [.       4     184 ..       4     185 .. 0.84

  Alignments for each domain:
  == domain 1  score: 100.3 bits;  conditional E-value: 4.2e-32
                             HAD_2   1 iiFDlDgTlldteeliiqafnelleey..gls.elseeelrkliglslrellrklgeseeeee..kieellrkynee 72 
                                       + FD+DgTll +++li+  + +++++   +++ +  +  lr l ++s r+  ++  + +   e   i++ ++   + 
  gi|242398421|ref|YP_002993845.1|   4 VFFDIDGTLLTEKPLIMLLLPQVYDKLskKFGiSKGDARLRFLREISERKNTYEWHDWDFFFEsfGIDFKYENLIK- 79 
                                       57**************988888887764456668888999999999998888888775543334433333333332. PP

                             HAD_2  73 kkk..kevkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekkKPdpeviekalek 147
                                         +  ++++++++v+ +Le+L+ +gyklg++Ts+  e ++ kl+  ++++yFdv+vt edv+  KPdp++++ a+ek
  gi|242398421|ref|YP_002993845.1|  80 --TypHKIQVFPDVIPTLEWLRGEGYKLGVITSGP-EYQRLKLRIAKLDRYFDVVVTREDVKTVKPDPKIFLYACEK 153
                                       ..23457**************************96.689999999999***************************** PP

                             HAD_2 148 lklkkeeviyvGDsp.tDieaakkagikvia 177
                                        +++++e i++GD   +D+ + +++g+  i+
  gi|242398421|ref|YP_002993845.1| 154 VGVEPKESIMIGDDLnQDVYGPRNVGMLPIW 184
                                       **************99**********98877 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   5.8e-06     0.017       1      26 [.       1      26 [.       1      57 [. 0.81
   2 !   51.5   0.0     5e-17   1.5e-13     115     204 ..      83     173 ..      67     179 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 5.8e-06
                                      SSEEEEESBTTTBCHHHHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  1 iktvvfDkdGTLttgepsvedvivsa 26
                                      +k+v+fD+dGTL+t +p ++ +++++
  gi|242398421|ref|YP_002993845.1|  1 MKAVFFDIDGTLLTEKPLIMLLLPQV 26
                                      79**************8887776666 PP

  == domain 2  score: 51.5 bits;  conditional E-value: 5e-17
                                       HTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT.GGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 115 dplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlG.ddyfdaviasdietvakpspegkvaaireLqgkp 190
                                       ++++v+p++  ++++L+  g++++++t++ +  ++  ++ +  d+yfd+v+++++++  kp+p+++++a+++ +++p
  gi|242398421|ref|YP_002993845.1|  83 HKIQVFPDVIPTLEWLRGEGYKLGVITSGPE-YQRLKLRIAKlDRYFDVVVTREDVKTVKPDPKIFLYACEKVGVEP 158
                                       6788***********************6654.3333444455589******************************** PP

                                       GGEEEEESSHH.HHH CS
                                       xxxxxxxxxxx.xxx RF
                         Hydrolase 191 eevamVGDgvn.Daa 204
                                       +e +m+GD +n D+ 
  gi|242398421|ref|YP_002993845.1| 159 KESIMIGDDLNqDVY 173
                                       ***********9975 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.0   4.1e-11   1.2e-07       4      50 ..     141     187 ..     139     208 .. 0.90

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 4.1e-11
                                       TTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESS CS
                    Hydrolase_like   4 KPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVlt 50 
                                       KP p ++ +a e++g++p+e++miGD+l++D+ g +n+G+  + + +
  gi|242398421|ref|YP_002993845.1| 141 KPDPKIFLYACEKVGVEPKESIMIGDDLNQDVYGPRNVGMLPIWINR 187
                                       9**************************************98887765 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   2.5e-09   7.4e-06       1     114 [.       4     115 ..       4     169 .. 0.73

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 2.5e-09
                               HAD   1 alfDfDgTLldgdslelllrfllrrgaprlwralreklllalfrellrldraglaelleallaglseelaaelerfv 77 
                                       ++fD+DgTLl++ +l++ll   +  + ++ +   +  ++l ++re++++++    + ++ +++++  +++ e     
  gi|242398421|ref|YP_002993845.1|   4 VFFDIDGTLLTEKPLIMLLLPQVYDKLSKKFGISKGDARLRFLREISERKNTYEWHDWDFFFESFGIDFKYENLIKT 80 
                                       79***********************************************6666666666666666644432222222 PP

                               HAD  78 aevirpk.....lldpgalellaahraaGdrvvvvSgglrpl 114
                                                   ++ p++   l++ r +G+++ v+++g+++ 
  gi|242398421|ref|YP_002993845.1|  81 ------YphkiqVF-PDVIPTLEWLRGEGYKLGVITSGPEYQ 115
                                       ......12233357.***********************9875 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   3.3e-05     0.099       1      63 [.       4     137 ..       4     141 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.3e-05
                                       EEEESTTTSE................................................................... CS
                       Hydrolase_6   1 flfDidGvLw................................................................... 10 
                                       ++fDidG+L+                                                                   
  gi|242398421|ref|YP_002993845.1|   4 VFFDIDGTLLtekplimlllpqvydklskkfgiskgdarlrflreiserkntyewhdwdfffesfgidfkyenlikt 80 
                                       68999999999999999999999999999999999999999999999999999999999999999999999999999 PP

                                       ..ETTEE-TTHHHHHHHHHHTT-EEEEEE---SS-H.HHHHHHH.HHTT----GGGE CS
                       Hydrolase_6  11 ..rgdkaipgaaealnalraagkpvvllTNnsskse.eeyakkl.eklgvditeeqv 63 
                                         ++ +++p +  +l++lr +g+++ ++T +   ++ + +++kl + ++v +t+e+v
  gi|242398421|ref|YP_002993845.1|  81 ypHKIQVFPDVIPTLEWLRGEGYKLGVITSGPEYQRlKLRIAKLdRYFDVVVTREDV 137
                                       9999**************************987766144677775557777777776 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0   0.00057       1.7       1      13 [.       4      16 ..       4      33 .. 0.86
   2 ?    2.4   0.0     0.036   1.1e+02     195     214 ..     150     169 ..     146     172 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00057
                                      EEEEIIIIIS-TT CS
                       Hydrolase_3  1 ialDlDGTLlnsd 13
                                      +++D+DGTLl+++
  gi|242398421|ref|YP_002993845.1|  4 VFFDIDGTLLTEK 16
                                      79********987 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.036
                                       HHHHCT--GGGEEEEESSGG CS
                       Hydrolase_3 195 lakelnisleeviafGDgeN 214
                                        +++ +++++e i +GD+ N
  gi|242398421|ref|YP_002993845.1| 150 ACEKVGVEPKESIMIGDDLN 169
                                       6899**************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); 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: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1548.73
//
Query:       gi|242398422|ref|YP_002993846.1|  [L=59]
Description: hypothetical protein TSIB_0431 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 372.71
//
Query:       gi|242398423|ref|YP_002993847.1|  [L=269]
Description: hypothetical protein TSIB_0432 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-67  226.8   0.0    4.6e-65  220.0   0.0    2.0  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 !  220.0   0.0   2.6e-69   4.6e-65       4     294 ..       5     260 ..       2     261 .. 0.86

  Alignments for each domain:
  == domain 1  score: 220.0 bits;  conditional E-value: 2.6e-69
                           DUF4392   4 liardpggrgikkllkkgellkaaeslshak.......ksvlItTGFpvhpahsppeEtDGplGAialaraLqalgk 73 
                                       li++d  gr i k++ + +++k  + l +ak       ++vlI+T Fp++p +  ++EtDGp+GA+al ra+++lg 
  gi|242398423|ref|YP_002993847.1|   5 LINTDIYGRDILKVYLE-YREKNFNFLEKAKnlfienlDNVLIVTCFPIPPMQ--IAETDGPPGAVALYRAIERLGG 78 
                                       56666666666555432.333344444444455566669*************9..9********************* PP

                           DUF4392  74 kvvivtdelnekiveaaveqgvlktevpllelqdrsaeaaivfltkdgdkkeaeaeelleklkpdhliaiErpGraa 150
                                       ++ i+t e+ ++    a++                    +i+f++k + ++          +  ++li++E pGra+
  gi|242398423|ref|YP_002993847.1|  79 RAEILTCEKISS----ALRG------------------FKINFAKKPRVNQ----------Y--SLLISVETPGRAK 121
                                       ******965544....4444..................3556666765555..........4..8************ PP

                           DUF4392 151 dGnyynmrgeniselvaplddlfeaakeigiptigiGDgGNElGmGkvkeavkkhvpngekiacavaadflivagvS 227
                                       dG+yy+m g  i+   +p+d+lf +ake g+ptigiGDgGNE+GmG+++e vkk+v+ g+ki + v++d li + vS
  gi|242398423|ref|YP_002993847.1| 122 DGKYYSMSGLEIE--MSPFDELFFQAKELGVPTIGIGDGGNEIGMGNIAEIVKKYVKFGDKITSIVKVDELILSAVS 196
                                       ************9..58************************************************************ PP

                           DUF4392 228 NWggyalaaalallsskevsllpsvekeeevlealveagvvdGvtgeremsVDgleleehaeilkeL 294
                                       NWg+y+l+a ++l  +k  +ll + ++ e+vl+alv++gv+dGv +++++sVDg++le h+++l+ L
  gi|242398423|ref|YP_002993847.1| 197 NWGAYGLIAQASLEVGK--NLLRDWDE-EKVLRALVSEGVIDGVIKKPQLSVDGIPLEVHKRFLNLL 260
                                       *****************..9****996.9***********************************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); 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 0.25s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1837.04
//
Query:       gi|242398424|ref|YP_002993848.1|  [L=207]
Description: Metal-dependent phosphohydrolase, HD superfamily [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-18   66.2   2.5    3.1e-18   66.2   1.1    1.8  2  HD        HD domain
  ------ inclusion threshold ------
      0.055   13.5   0.0       0.15   12.1   0.0    1.7  1  DUF5330   Family of unknown function (DUF5330)


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 !   66.2   1.1   3.4e-22   3.1e-18       2     121 ..      38     138 ..      37     139 .. 0.95
   2 ?   -2.2   0.0      0.52   4.7e+03      84      84 ..     175     175 ..     146     200 .. 0.55

  Alignments for each domain:
  == domain 1  score: 66.2 bits;  conditional E-value: 3.4e-22
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHHHHHHH. CS
                                HD   2 leHsleVaklarrlaedlgeeedrellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevekrlgld. 77 
                                       + H  +V +l+  +++ +g  +d e+l laa lHD++ +++          +++ ++H+k+ga+i+ +++ +l+++ 
  gi|242398424|ref|YP_002993848.1|  38 FSHVKRVFNLCMHIGKAEG--ADLEVLALAAFLHDVARPLED---------KGIVEDHAKEGAKIAYRFLTSLKYSk 103
                                       79*****************..*******************44.........588899****************999* PP

                                       HHHHHHHHHTTCCHHHHHHHHHHHHCCTSCHHHHHHHHHHHHHH CS
                                HD  78 ledvaklirehheswegkkrprglaerqlslearivklaDrlaa 121
                                       +++v+++i++h++s +         + + +lea+i+++aD+l+a
  gi|242398424|ref|YP_002993848.1| 104 VDEVVHAIEAHRFSRP---------PDPRTLEAKILSDADKLDA 138
                                       ***************9.........56***************98 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.52
                                       H CS
                                HD  84 l 84 
                                       l
  gi|242398424|ref|YP_002993848.1| 175 L 175
                                       1 PP

>> DUF5330  Family of unknown function (DUF5330)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   1.6e-05      0.15      42      57 ..      83      98 ..      79     104 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.6e-05
                           DUF5330 42 eRAreGAriayellde 57
                                        A+eGA+iay +l++
  gi|242398424|ref|YP_002993848.1| 83 DHAKEGAKIAYRFLTS 98
                                      67************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       589  (0.0328518); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1482.36
//
Query:       gi|242398425|ref|YP_002993849.1|  [L=169]
Description: RNA-binding protein, containing KH domain [Thermococcus sibiricus MM 739]
Scores for complete 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   0.4    4.1e-09   36.4   0.4    1.7  1  KH_5           NusA-like KH domain
    4.6e-07   29.6   3.2    5.6e-07   29.3   1.8    1.9  2  KH_2           KH domain
    7.3e-06   25.7   0.4    1.4e-05   24.8   0.4    1.5  1  KH_1           KH domain
    0.00014   21.7   0.3    0.00042   20.1   0.1    1.8  2  Ribosomal_S7e  Ribosomal protein S7e
  ------ inclusion threshold ------
      0.014   15.2   1.0      0.047   13.6   0.4    2.1  2  KH_4           KH domain


Domain annotation for each model (and alignments):
>> KH_5  NusA-like KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.4   1.1e-12   4.1e-09       1      69 []      57     124 ..      57     124 .. 0.89

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 1.1e-12
                              KH_5   1 aGertkvaVkshnpnvdpvGaivgkkGsrikavsseLkgekidvvewseD.....laefianalsPaevlsVki 69 
                                       aG++++++V ++n     v  ++gk+G++ik +++eL g++++v+e  e      ++++++++l+Pa v  V++
  gi|242398425|ref|YP_002993849.1|  57 AGDLVVIMVGEGN-----VPLVIGKGGKNIKLLMREL-GKRVRVIEGLEIkgtdeIKKLATDLLYPASVFGVNV 124
                                       699**********.....*******************.******98644333334**************99986 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   1.8   1.6e-10   5.6e-07      18      67 ..      49     101 ..      29     111 .. 0.81
   2 ?   -2.2   0.0         1   3.7e+03      53      68 ..     151     166 ..     149     168 .. 0.66

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 1.6e-10
                                       EEEEC..CS.CEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTCEE CS
                              KH_2  18 veIer..ta.nrviiviresqpgivIGkgGsnikkigkelrkdieklegkkVk 67 
                                       ve ++  +a + v+i++ e++  +vIGkgG+nik +  el+k+++++eg ++k
  gi|242398425|ref|YP_002993849.1|  49 VEFKKavEAgDLVVIMVGEGNVPLVIGKGGKNIKLLMRELGKRVRVIEGLEIK 101
                                       55554444447799**********************************98887 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1
                                       HHHHHHHHHHTTCEEE CS
                              KH_2  53 elrkdieklegkkVkl 68 
                                       +l+ ++ k+ g++Vk+
  gi|242398425|ref|YP_002993849.1| 151 TLEDILSKIIGSDVKI 166
                                       4555666666888887 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.4     4e-09   1.4e-05       8      58 ..      67     107 ..      60     115 .. 0.79

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 4e-09
                                       GGHHHHHHTGGGHHHHHHHHHHT-EEEEESSTT...T.-EEEEEESHHHHH CS
                              KH_1   8 sslvgriIGkgGsnIkeIreetgakIkvpksedegsderevtisGspeave 58 
                                          v+++IGkgG+nIk +++e g +++v+ +         ++i+G+ e ++
  gi|242398425|ref|YP_002993849.1|  67 EGNVPLVIGKGGKNIKLLMRELGKRVRVI-EG--------LEIKGTDE-IK 107
                                       55699***************88*****99.43........88888777.44 PP

>> Ribosomal_S7e  Ribosomal protein S7e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.43   1.6e+03      17     180 ..      36      51 ..      21      63 .. 0.61
   2 !   20.1   0.1   1.2e-07   0.00042     122     182 ..     109     168 ..     103     169 .] 0.93

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.43
                                       HHHHHHHHHHHTSSCHHHHTT--ECEEEEEEETSSCEEEEEEEEHHHHHHTTTCHHHHHHHHHHHC.SSEEEEEEE- CS
                     Ribosomal_S7e  17 vaqalldleanssdlkaelrelqissakevevkkkkkaivifvpvpllkafqkiqqrlvreLeKkfsgkhvvfvaqR 93 
                                       +                                                                            
  gi|242398425|ref|YP_002993849.1|  36 I---------------------------------------------------------------------------- 36 
                                       2............................................................................ PP

                                       ----SSCG.TTSTSS--TTSSHHHHHHHHHHHHCTTS-EEEEEEEE-SSS-EEEEEEEESCTCCCHHHHHHHHHHHH CS
                     Ribosomal_S7e  94 rilkkptrrskkkqkrprsrtltaVhdaiLedlvyPseivGkrirvrldgskllkvfLdkkdqnnveekldtfsavy 170
                                                                                                                  +y
  gi|242398425|ref|YP_002993849.1|  37 ------------------------------------------------------------------------SRMLY 41 
                                       ........................................................................33455 PP

                                       HHHHS-BEEE CS
                     Ribosomal_S7e 171 kkLtgkdvvF 180
                                       k L + dv+F
  gi|242398425|ref|YP_002993849.1|  42 KLLGDADVEF 51 
                                       5555555555 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 1.2e-07
                                       HHHHHCTTS-EEEEEEEE-SSS-EEEEEEEESCTCCCHHHHHHHHHHHHHHHHS-BEEEEE CS
                     Ribosomal_S7e 122 iLedlvyPseivGkrirvrldgskllkvfLdkkdqnnveekldtfsavykkLtgkdvvFef 182
                                       +  dl+yP+ + G  + +   g+  +kv+  ++dq+++  k +t++++  k+ g dv+ +f
  gi|242398425|ref|YP_002993849.1| 109 LATDLLYPASVFGVNVVYAPSGQ-YYKVLVIRRDQQKLPAKHETLEDILSKIIGSDVKISF 168
                                       568*************9999886.9********************************9988 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.4   1.3e-05     0.047       8      52 ..      40      82 ..      34      94 .. 0.79
   2 ?   -1.1   0.0      0.48   1.7e+03       2      15 ..     150     163 ..     149     168 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.3e-05
                              KH_4  8 lkalvddpeevevteeeeeeeveielnvegedlGrvIGkrGrtld 52
                                      l +l+   ++ve +    e ++ + + v + ++ +vIGk G++++
  gi|242398425|ref|YP_002993849.1| 40 LYKLLG-DADVEFKKA-VEAGDLVVIMVGEGNVPLVIGKGGKNIK 82
                                      555553.446666665.56789999999**************997 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.48
                              KH_4   2 elvedilkalvddp 15 
                                       e +edil++++ + 
  gi|242398425|ref|YP_002993849.1| 150 ETLEDILSKIIGSD 163
                                       67899999998643 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); 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: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1112.40
//
Query:       gi|242398426|ref|YP_002993850.1|  [L=438]
Description: Aspartyl-tRNA synthetase [Thermococcus sibiricus MM 739]
Scores for 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-93  311.9   2.0    4.8e-93  311.7   2.0    1.0  1  tRNA-synt_2      tRNA synthetases class II (D, K and N)
    2.1e-13   50.0   0.1    4.1e-13   49.1   0.1    1.5  1  tRNA_anti-codon  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 !  311.7   2.0   5.4e-97   4.8e-93       3     313 ..     118     432 ..     116     433 .. 0.95

  Alignments for each domain:
  == domain 1  score: 311.7 bits;  conditional E-value: 5.4e-97
                                       CHHHHTHHHHCCSHHHHHHHHHHHHHHHHHHHHHHHTT-EE----SEESS--SSSS--EEEEETTT.TEEE-E-S-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2   3 elrlknryldlrtekvskvlrlrstvtkavrkyleengfieietPiLsksdteegarlFkvksrekekeffaLtqsp 79 
                                       ++rl+nr++dlr++++ +++++rs+  +avr++++++gf+ei+tP ++ ++te+g +lF +k  ek  + f L+qsp
  gi|242398426|ref|YP_002993850.1| 118 DTRLDNRFMDLRRPEIMAIFKIRSSTFRAVRDFFHNEGFVEIHTPKIIATATEGGTELFPMKYFEK--DAF-LAQSP 191
                                       79***********************************************************44444..555.***** PP

                                       HHHHHHHHHCTHSEEEEEEEEE--S--BTTB-S-CEEEEEEEEET-SCHH.HHHHHHHHHHHHHHHHHHCSCCCCCH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2  80 qlylellivagidrvfqiaraFRaEdsrtdrhlaEFtqieaemsfieeed.imqvleelikslvkevlessakdief 155
                                       qly+++++++g+drvf+ia+ FRaE+++t+rhl+E ++i+ em+fie+ed +m++le+li++ v+ v e+++k++++
  gi|242398426|ref|YP_002993850.1| 192 QLYKQIMMASGLDRVFEIAPIFRAEEHNTTRHLNEAWSIDGEMAFIEDEDeVMKLLEHLITYAVNYVRENNEKELQT 268
                                       *******************************************************************8888777655 PP

                                       TTTTTSEE-SSS-EEEEHHHHHHHHHTS......-SS--HHHHHHHHH....HS--SEEEEEEEBGGGSTTCBBBST CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 156 virrnskdlkkpfkrltykeaieklnei......gkdldkaderalvk....keknepvfvtdfPaelkpFyarkee 222
                                           + +++k pf+r+ty+ea+e+l++       g+d+d++ e++l +    + + + +f++++P++ kpFy  + +
  gi|242398426|ref|YP_002993850.1| 269 LGF-ELEEPKLPFRRVTYTEALEILRDLgkeiswGEDIDTEGEKLLGQyikeNYDEDLYFIYQYPSSAKPFYIMRYD 344
                                       554.46799****************9999999**9*********9998777688899******************** PP

                                       TSTTBBSEEEEEETTEEEEEEEEB--SHHHHHHHHHHCCHHSSSGGGGHHHHHHHHCT--SEEEEEEEHHHHHHHHC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 223 ddkkltesyDllingvElvgGslRiedpeeleeklkskgldeeaeekfswylealeyGapphgGlglGldRlvmlll 299
                                       +++++++s+Dl ++g+E+++G +R++++e+l++++ ++gl+    e+f++yl+a++yG+pphgG+glG +Rl+  +l
  gi|242398426|ref|YP_002993850.1| 345 NKPEISRSFDLEYRGIEITSGGQREHRYEKLKAQIAEQGLN---VESFDFYLKAFRYGMPPHGGFGLGAERLIKQML 418
                                       *****************************************...********************************* PP

                                       T-SSGGGCSSS-XX CS
                                       xxxxxxxxxxxxxx RF
                       tRNA-synt_2 300 gsesIrdviaFPkl 313
                                       ++ +Ir+v++FP+ 
  gi|242398426|ref|YP_002993850.1| 419 NLGNIREVMLFPRD 432
                                       ************96 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.1   0.1   4.5e-17   4.1e-13       2      75 ..      20      97 ..      19      98 .. 0.94

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 4.5e-17
                                      EEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEET....HHHHHHHTTS-TTSEEEEEEEEEECTTS..SEEEEEEEEE CS
                   tRNA_anti-codon  2 tvaGrvtsisdrsggkvifidlrDgtgriqvvlfr....eeatklaenlkeGdvvrvtGrvkrrpgg..elelkveeie 74
                                      +vaG+v+ +  ++ g++ f+ +rD++g++qv++ +    ee+++l  +l ++dvv v+G v+++p+    +el+ e+i 
  gi|242398426|ref|YP_002993850.1| 20 RVAGWVHEV--KDLGGIKFLWIRDREGIVQVTAPKkkvsEEVFNLIPSLHNEDVVSVEGIVNFTPKArlGFELIPEKII 96
                                      79*******..*****************************************************777677999999986 PP

                                      E CS
                   tRNA_anti-codon 75 l 75
                                      l
  gi|242398426|ref|YP_002993850.1| 97 L 97
                                      6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (438 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 2734.92
//
Query:       gi|242398427|ref|YP_002993851.1|  [L=723]
Description: hypothetical protein TSIB_0436 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.044   14.0   0.1          3    8.2   0.0    2.9  2  CARDB     CARDB
       0.15   12.3   0.0        4.8    7.4   0.0    2.7  2  DUF4115   Domain of unknown function (DUF4115)
       0.17   12.1   0.0       0.28   11.4   0.0    1.3  1  DUF4381   Domain of unknown function (DUF4381)
       0.23   10.2   5.2      0.038   12.8   0.4    2.2  3  BatD      Oxygen tolerance


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 ?    8.2   0.0   0.00066         3       2      43 ..     364     405 ..     363     446 .. 0.85
   2 ?    2.5   0.0     0.038   1.7e+02       9      66 ..     492     555 ..     479     591 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00066
                                       --EEE.EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEE CS
                             CARDB   2 pDLtvtntlnpseafvgeentitvtvkNqGtaasgatkvaly 43 
                                       ++L+++  +n ++   +e++ + v v+N G +a+ a +v+l 
  gi|242398427|ref|YP_002993851.1| 364 ANLMINFRINSDKILINEDLVVMVDVENRGRGAAIAANVELK 405
                                       5789999999999********************988888775 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.038
                                       EEC-SEEETTSEEEEEEEEEE-SSS-EEEE....EEEEEETTEEE..EEEEESEE-CTEEEEEE CS
                             CARDB   9 tlnpseafvgeentitvtvkNqGtaasgat....kvalyldgelv..gtvtvpsLaagesttvs 66 
                                       t++    +++++ ++++t++ +G++  +++    +++l++ ++l   ++ +v  ++age++t +
  gi|242398427|ref|YP_002993851.1| 492 TWSTYVHTQEKTAKLKFTISAEGKDPKYEFiknaTLQLIIPDTLDgeTKLYVGDIKAGETKTLE 555
                                       5666667788999999999999998876542222677888888886667778999999999865 PP

>> DUF4115  Domain of unknown function (DUF4115)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0    0.0011       4.8      11      43 ..      74     108 ..      66     110 .. 0.80
   2 ?    1.5   0.0     0.075   3.4e+02      19      37 ..     539     558 ..     535     569 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0011
                           DUF4115  11 veVrdadGkvlfegtlkaGetkev.sgk.ppltlt 43 
                                       ++V+++dG+v+ +++l  G ++ v +++ + ++++
  gi|242398427|ref|YP_002993851.1|  74 IKVYAKDGSVVASKVLPTGYSLPVpDNQnTLFSVR 108
                                       89*******************99955553335665 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.075
                           DUF4115  19 kvlfegtlkaGetkev.sgk 37 
                                       ++l+ g  kaGetk++ s++
  gi|242398427|ref|YP_002993851.1| 539 TKLYVGDIKAGETKTLeSDE 558
                                       5789999*********4444 PP

>> DUF4381  Domain of unknown function (DUF4381)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   6.3e-05      0.28      11      59 ..     643     692 ..     634     708 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.3e-05
                           DUF4381  11 pvswwPpapG..wwlllaalllllllvlalwllrrrkrnrreAlreLaalr 59 
                                       +vs+ Pp  G  ww ++a+l++l+ +vl++ ++   k++  +Al+eL + +
  gi|242398427|ref|YP_002993851.1| 643 SVSYLPPETGvnWWPIIAILFILVSAVLGYNYVG-LKAKYDKALKELGRKK 692
                                       6899999988889****66666888888887775.5555899***998766 PP

>> BatD  Oxygen tolerance
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.2      0.84   3.8e+03     107     153 ..     155     196 ..     141     202 .. 0.52
   2 ?   12.8   0.4   8.6e-06     0.038     337     379 ..     431     476 ..     352     529 .. 0.67
   3 ?   -3.2   0.0      0.59   2.7e+03     401     458 ..     630     688 ..     601     694 .. 0.41

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 0.84
                              BatD 107 pitikVlkseasqsssaisdedlflraevskksvYvqeqvlvtlkly 153
                                       +i++kV++     + ++++d ++ l  e  + +++++    v +kl 
  gi|242398427|ref|YP_002993851.1| 155 AIKVKVTN-----TYENKADVQITLPYETVTATIFEGDYYAVPYKLT 196
                                       45555522.....2333333334444455555555555555555555 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 8.6e-06
                              BatD 337 teeyalvPrkaGkytipaiefsyFDta...tkkyetatlpeitikV 379
                                       t+ y+l +++ G+y+i ++++sy++++   t++   +++++++++V
  gi|242398427|ref|YP_002993851.1| 431 TIIYILRATEIGTYEIGPVNVSYYNPNdelTDSPSSMSSNQLKVTV 476
                                       6779999*******************84445666777777777777 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 0.59
                              BatD 401 eevkllgkdirfikgeaslkkkgsff......lfwlllllplllf...vvllllwrkrrrenadvaa 458
                                       e+  +l++ +++i+   s+      +      + w +++++++l+   +   ++  k++  +a ++ 
  gi|242398427|ref|YP_002993851.1| 630 ESKVELAEALKNIS--VSY------LppetgvNWWPIIAILFILVsavLGYNYVGLKAKYDKALKEL 688
                                       22233333344333..112......122222244433333333321113455555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (723 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); 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:                         4  (0.000223102); expected 0.2 (1e-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 0.30s 00:00:00.97 Elapsed: 00:00:00.46
# Mc/sec: 4691.19
//
Query:       gi|242398428|ref|YP_002993852.1|  [L=118]
Description: Peptidyl-tRNA hydrolase [Thermococcus sibiricus MM 739]
Scores for complete 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  148.2   0.0    1.3e-43  148.0   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 !  148.0   0.0   7.1e-48   1.3e-43       1     116 [.       4     117 ..       4     118 .] 0.98

  Alignments for each domain:
  == domain 1  score: 148.0 bits;  conditional E-value: 7.1e-48
                                       EEEEEEEESSSSS-HHHHHHHHHHHHHHHHHHHHHH.CHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHHHHHTT-S CS
                              PTH2   1 lkmvlvvrkDLkmskGkiaaqcahAavalvkkllkesnekellkeWeeegqkkivlkveseeeLlelaakakalglp 77 
                                       +k+v++vr+DLk+skGk+a+q+ah+av ++ k+ ke ++ e++k W +egqkk+v+k+ese+eL el+a+a++lg+p
  gi|242398428|ref|YP_002993852.1|   4 YKQVMIVRSDLKLSKGKLAVQVAHGAVTAAFKAYKE-KP-EWFKGWFNEGQKKVVVKAESERELFELKAEAEKLGIP 78 
                                       79*********************************9.88.8************************************ PP

                                       EEEEEETSSSSSSTTCEEEEEEEEEEHHHHHHHHTTSEB CS
                              PTH2  78 aalirDagrtqiepgtkTvlaigPapksivdkvtgkLkl 116
                                       ++lirDag t+i+pgt T+laigP+p++iv+k+tg+Lkl
  gi|242398428|ref|YP_002993852.1|  79 NSLIRDAGLTEIPPGTITCLAIGPGPEEIVNKITGNLKL 117
                                       **************************************9 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:                      424  (0.0236488); 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: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 818.22
//
Query:       gi|242398429|ref|YP_002993853.1|  [L=422]
Description: Probable tRNA pseudouridine synthase D [Thermococcus sibiricus MM 739]
Scores for complete 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-135  452.4   0.0   1.7e-135  452.1   0.0    1.0  1  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 !  452.1   0.0  9.3e-140  1.7e-135       7     416 .]      12     418 ..       8     418 .. 0.96

  Alignments for each domain:
  == domain 1  score: 452.1 bits;  conditional E-value: 9.3e-140
                              TruD   7 yvtdtegigGrlrespeDFiVeEieefsgeeeadegeylvlrvekrnwdtldlvrelaralgisrkrvgfaGtKDkr 83 
                                       y+++++gigG+++++peDFiV+E+     ++  ++++ l++ ++k+nw+t+ +++e+a+++gi+ k+vgfaGtKD++
  gi|242398429|ref|YP_002993853.1|  12 YLSSSKGIGGKIKSKPEDFIVREV---IPRSVFRSDQCLIYLIKKQNWETMAAIKEIAKRIGIDYKNVGFAGTKDRH 85 
                                       99**********************...555577899***************************************** PP

                              TruD  84 AvTtQlisirkvepee....lealeikdvelevvgrarrklrlGdLaGNkFeirvrdvaeeeeaakraeeileelee 156
                                       A+T Q+isi   + e+    +++l+i++++l+ vgr  ++l+lG L+GN+F+i++r++++ e a +r+++il+el+ 
  gi|242398429|ref|YP_002993853.1|  86 AITYQYISICSENLESikesIASLNIEGISLKFVGRG-KPLKLGMLIGNHFQIILRGLEDPERALERTKKILKELKL 161
                                       ********9665544411226667***********86.9******************98888999************ PP

                              TruD 157 kggvPNyfGvQRFGsrrpvthlvGkaivkgdleeAvelyvgkpfeeesedtreareavaetgdleealeelpkslry 233
                                       kgg+PNyfG QRFG+rr ++h+vGk ++kgd+e+A+ +++g+ + +++ d  ear+ + +tgd+e+alee+p+ lry
  gi|242398429|ref|YP_002993853.1| 162 KGGFPNYFGSQRFGERRVINHEVGKLLLKGDFEGAALKFLGEYTGDMTGD--EARKDFLKTGDVEKALEEFPNFLRY 236
                                       ********************************************999999..89**999****************** PP

                              TruD 234 ErallkrLaekpkdykkAlealpknLqrlFvhAyqSylFNrvlseRlerglpldepveGDvvifaeerlpdtdrlql 310
                                       Era+l +++e ++++kkA+++lp+++ r+F+h+yqSylFN++ls+R+e+gl+l+e++ GD+v++ ++ lp ++++ +
  gi|242398429|ref|YP_002993853.1| 237 ERAMLYKYRE-TRSWKKAFAVLPRPIVRIFIHSYQSYLFNKALSRRIEEGLSLNEALSGDIVCQVKKGLPIRNKTFK 312
                                       **********.****************************************************************** PP

                              TruD 311 vteknveevkrliergrafvtaplvGtetelaegevgeierevleeegleledFklpklpelsskGtrRaillrved 387
                                       vte++ + v++ ++rg+a+vt+p++G  ++la+g +g+iere+l+eeg++l+ Fk+++lp l+ +G rR++l++++ 
  gi|242398429|ref|YP_002993853.1| 313 VTERSLKFVNERVKRGEAMVTGPVFGFASRLADGPMGKIEREILDEEGIDLNGFKMKQLPILAEAGGRRELLIKPRG 389
                                       ***************************************************************************** PP

                              TruD 388 lelsaeedeltleFsLpkGsYATvvlrEi 416
                                       ++++ +e++l+++F+LpkG YAT+v+rEi
  gi|242398429|ref|YP_002993853.1| 390 FKYKSSEEGLIFRFFLPKGVYATSVMREI 418
                                       ****************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); 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 0.31s 00:00:00.94 Elapsed: 00:00:00.54
# Mc/sec: 2369.99
//
Query:       gi|242398430|ref|YP_002993854.1|  [L=234]
Description: Phosphoglycolate phosphatase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-30  106.2   0.1    7.2e-19   68.5   0.0    2.1  2  Hydrolase_3      haloacid dehalogenase-like hydrolase
      9e-12   45.7   0.1    1.1e-06   29.1   0.0    3.0  3  Hydrolase        haloacid dehalogenase-like hydrolase
    0.00019   21.0   0.0    0.00056   19.5   0.0    1.9  1  S6PP             Sucrose-6F-phosphate phosphohydrolase
     0.0015   18.6   0.0     0.0029   17.7   0.0    1.6  1  HAD_2            Haloacid dehalogenase-like hydrolase
     0.0036   17.4   0.0     0.0078   16.3   0.0    1.5  1  Hydrolase_6      Haloacid dehalogenase-like hydrolase
     0.0041   17.6   0.2        4.6    7.6   0.0    2.8  3  HAD              haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.044   12.9   0.0       0.15   11.2   0.0    1.8  2  Trehalose_PPase  Trehalose-phosphatase
       0.05   13.5   0.0       0.11   12.5   0.0    1.4  1  DUF3889          Protein of unknown function (DUF3889)


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 !   36.1   0.1   2.6e-12   5.8e-09       1      73 [.       5      78 ..       5      87 .. 0.94
   2 !   68.5   0.0   3.2e-22   7.2e-19     170     250 ..     137     217 ..      95     222 .. 0.89

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 2.6e-12
                                      EEEEIIIIIS-TTS---HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEEEEGGGTEE.ECTTTEE CS
                       Hydrolase_3  1 ialDlDGTLlnsdkkisektkeaikklkekgikvviATGRslravlpvleelgldlpvialNGali.ddekgki 73
                                      i +D+DGT+   + +++e+++eai+ +++ gi v++ TG+s  ++      +g + p+ia  G++i d+++++i
  gi|242398430|ref|YP_002993854.1|  5 ISIDIDGTITYPNRRLQENAVEAIRLAENLGIPVMLVTGNSACFAYAATILIGTTGPFIAEDGGVIgDKSNNRI 78
                                      679***************************************************************87777766 PP

  == domain 2  score: 68.5 bits;  conditional E-value: 3.2e-22
                                       EEEEESTTEEEEEETT-SHHHHHHHHHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE--G CS
                       Hydrolase_3 170 titssskgyleimpkgvsKgtalkklakelnisleeviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtksn 246
                                        i   s++ + + +++v+Kg+++++ +++l+i++e+v+++GDgeND+  ++++g+ vA+++a e +k  Ad+vt++ 
  gi|242398430|ref|YP_002993854.1| 137 LIAVDSGYAIHVKQPHVNKGEGIRNACQKLGITPEQVAHIGDGENDLDAFKVVGYRVAVAQAPEVLKREADHVTTKP 213
                                       466678899*****************************************************************998 PP

                                       GGTH CS
                       Hydrolase_3 247 nedG 250
                                         dG
  gi|242398430|ref|YP_002993854.1| 214 YGDG 217
                                       8877 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   0.00011      0.24       1      32 [.       2      32 ..       2      35 .. 0.87
   2 !    6.1   0.0    0.0055        12     121     156 ..      22      57 ..      17      77 .. 0.81
   3 !   29.1   0.0   4.9e-10   1.1e-06     169     210 .]     149     190 ..      91     190 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00011
                                      SSEEEEESBTTTBCHHHHHHHHHHHHCHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  1 iktvvfDkdGTLttgepsvedvivsaalalaa 32
                                      ik++ +D+dGT+t  ++++ +  v+a + la+
  gi|242398430|ref|YP_002993854.1|  2 IKAISIDIDGTITYPNRRLQENAVEA-IRLAE 32
                                      89******************999999.66665 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0055
                                       TTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 121 peaaeavasLkaagievvlltgdnpetaeraanqlG 156
                                       + a+ea++     gi+v l+tg++  +a +a   +G
  gi|242398430|ref|YP_002993854.1|  22 ENAVEAIRLAENLGIPVMLVTGNSACFAYAATILIG 57 
                                       6788999999999***********999997777777 PP

  == domain 3  score: 29.1 bits;  conditional E-value: 4.9e-10
                                       ESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 169 etvakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                       +     + eg + a+++L++ pe+va++GDg nD+ a++ +g
  gi|242398430|ref|YP_002993854.1| 149 KQPHVNKGEGIRNACQKLGITPEQVAHIGDGENDLDAFKVVG 190
                                       22444599*****************************99876 PP

>> S6PP  Sucrose-6F-phosphate phosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   2.5e-07   0.00056     152     240 ..     141     224 ..       2     231 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 2.5e-07
                                       ETTTEEEEEETT-SHHHHHHHHHHHHT--GGGEEEEE-SGGGHHHHTSSSEEEE-TT--HHHHHHHHHH--TTE..E CS
                              S6PP 152 ssgkdlDvlPkraskgeAlryLakkleleleqilvcGdsgnDeellignvlgVvVgnaqeellqwllenakeneriy 228
                                        sg ++ v   + +kge +r  ++kl++ +eq+   Gd +nD + ++   + V V+ a e  l+ ++++   ++   
  gi|242398430|ref|YP_002993854.1| 141 DSGYAIHVKQPHVNKGEGIRNACQKLGITPEQVAHIGDGENDLDAFKVVGYRVAVAQAPEV-LKREADHVTTKP--- 213
                                       45556666667789********************************999999999998776.443333333322... PP

                                       E-SS-THHHHHH CS
                              S6PP 229 laeercaaGile 240
                                             a+Gi+ 
  gi|242398430|ref|YP_002993854.1| 214 -YGDGGAEGIIH 224
                                       .33445555555 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   1.3e-06    0.0029     138     177 ..     156     195 ..     126     196 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.3e-06
                             HAD_2 138 peviekaleklklkkeeviyvGDsptDieaakkagikvia 177
                                        e i++a++kl++++e+v  +GD  +D+ a k +g +v++
  gi|242398430|ref|YP_002993854.1| 156 GEGIRNACQKLGITPEQVAHIGDGENDLDAFKVVGYRVAV 195
                                       5799****************************99999875 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   3.5e-06    0.0078       3      41 ..       7      46 ..       5      54 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.5e-06
                                      EESTTTSEE.TTEE-TTHHHHHHHHHHTT-EEEEEE---S CS
                       Hydrolase_6  3 fDidGvLwr.gdkaipgaaealnalraagkpvvllTNnss 41
                                      +DidG++   ++++ ++a+ea++  ++ g+pv+l+T ns 
  gi|242398430|ref|YP_002993854.1|  7 IDIDGTITYpNRRLQENAVEAIRLAENLGIPVMLVTGNSA 46
                                      8******8647788999*******************9986 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.5   3.3e+03       4      10 ..       8      14 ..       6      18 .. 0.87
   2 !    7.6   0.0     0.002       4.6      86     119 ..      20      53 ..      11      80 .. 0.83
   3 !    7.0   0.0    0.0032       7.1     144     188 .]     149     187 ..     122     187 .. 0.65

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.5
                               HAD  4 DfDgTLl 10
                                      D+DgT++
  gi|242398430|ref|YP_002993854.1|  8 DIDGTIT 14
                                      9****98 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.002
                               HAD  86 ldpgalellaahraaGdrvvvvSgglrplvepll 119
                                       l++ a+e+++ +   G++v +v+g+   ++ +  
  gi|242398430|ref|YP_002993854.1|  20 LQENAVEAIRLAENLGIPVMLVTGNSACFAYAAT 53 
                                       6789******999************988887655 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0032
                               HAD 144 legkpvrgegkvaalrewlaaegegidleevvayGDspsDlpllr 188
                                        ++++ +g      +r   a ++ gi++e v  +GD+++Dl +++
  gi|242398430|ref|YP_002993854.1| 149 KQPHVNKG----EGIRN--ACQKLGITPEQVAHIGDGENDLDAFK 187
                                       44556666....55555..566699999*************9875 PP

>> Trehalose_PPase  Trehalose-phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.39   8.7e+02       3      47 ..       8      46 ..       7      57 .. 0.65
   2 ?   11.2   0.0   6.8e-05      0.15     154     205 ..     145     193 ..     130     215 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.39
                                      ETBTTTB---SSGGG--B-TTHHHHHHHHHTTS-..EEEE-SS-H CS
                   Trehalose_PPase  3 DydGTlspivedpdaavpssellslLkkLasdpknvvaivSGrsl 47
                                      D+dGT++   +     ++++++++++ +La+++ + v++v+G s 
  gi|242398430|ref|YP_002993854.1|  8 DIDGTITYPNR-----RLQENAVEAI-RLAENLGIPVMLVTGNSA 46
                                      77777766555.....4444444444.477777777888877775 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 6.8e-05
                                       EEEEE-S---HHHHHHHHHHTS--------EEEEEE-SSTTHHHHTTS-TT. CS
                   Trehalose_PPase 154 vvevrpqgvsKGkaverlleslgsadseddfvlciGDdrtDedmFsvlrktk 205
                                        + v++  v+KG+ ++   ++lg +   ++ v  iGD   D d+F+v+  + 
  gi|242398430|ref|YP_002993854.1| 145 AIHVKQPHVNKGEGIRNACQKLGIT---PEQVAHIGDGENDLDAFKVVGYRV 193
                                       689********************98...99999**************98765 PP

>> DUF3889  Protein of unknown function (DUF3889)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   4.7e-05      0.11      29      51 ..      90     112 ..      87     115 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.7e-05
                                       HHHHHHT-TT-EE---EEEEEEE CS
                           DUF3889  29 vketkkkYpgaevvdyqyvGrtk 51 
                                       ++e+kk+Yp+ae++d+ + G++ 
  gi|242398430|ref|YP_002993854.1|  90 WSELKKRYPNAEMSDTMKYGERR 112
                                       89*****************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); 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: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 1553.74
//
Query:       gi|242398431|ref|YP_002993855.1|  [L=250]
Description: Orotidine 5'-phosphate decarboxylase [Thermococcus sibiricus MM 739]
Scores for complete 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-26   91.0   0.0    9.3e-26   90.8   0.0    1.1  1  OMPdecase       Orotidine 5'-phosphate decarboxylase / HUMPS 
      0.003   18.1   0.0       0.31   11.6   0.0    2.5  2  Peptidase_S66C  LD-carboxypeptidase C-terminal domain


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 !   90.8   0.0     1e-29   9.3e-26       4     224 ..      18     239 ..      15     240 .. 0.80

  Alignments for each domain:
  == domain 1  score: 90.8 bits;  conditional E-value: 1e-29
                                       EEEE-SSSH..........HHHHHHHHHHGGGSSEEEEEHHHHHHHTHH...HHTHHHHHHHHHT.SEEEEEEEE-S CS
                         OMPdecase   4 clalDvata..........relleladkvgpsivvlKthydlvegwgfe..gtgaklaalarkhg.flifeDrKfaD 67 
                                       +++lD +            +   +++ +  + ++ +K++++++e+ g +  ++++++++l++++  ++i++D+K++D
  gi|242398431|ref|YP_002993855.1|  18 VVGLDSDIDkipkrfkdilEFNEHIVHETADLVCAYKINIAFYEKLGWKgyKVMEETIELIKQKTnVPIILDAKRGD 94 
                                       5555555555555553333333489999999*******************************9988*********** PP

                                       -HHHHHHHHHSTCHHHHTTESEEEEEGTGHHHHHHHHHHHHHHTTS.EEEEEESTSSGGHHHHHHHSHHHHHHHHHH CS
                         OMPdecase  68 IGntvekqatagsarikewadivtvhavaGkasvkalaeaaekwgnrgllilaqmsskgnlmlqekgytqacveaar 144
                                       IGnt++++a+  ++  k+++d vtv++++G +++ +++++       + +il  +s+k + + +   ++  ++e  +
  gi|242398431|ref|YP_002993855.1|  95 IGNTAKAYAE--AYFEKLKVDSVTVNPYMGRDAIIPFLKKG------HAFILLLTSNKSANEIEV-PVYSRVLELSK 162
                                       *********9..566***********************965......6799*******9999998.56666666666 PP

                                       HHHHH.TTESEEECCCHTH....HHHHHTTCSCEEEHHHTTEEEEECTTCCGGGHHHHHHHTTCSEEEESHHHHTSS CS
                         OMPdecase 145 ehkae.dfvmGfvaqetln....ateedaddfihltpgigleqggdgkgqqyntpekligiagadiiivGRgIlkag 216
                                       e + +  + +G+v+++t++     ++++  ++  l pgig+ qgg+++ ++     +l+g  +  +++v+R+I+ a+
  gi|242398431|ref|YP_002993855.1| 163 ELELAyPKKVGIVVGATKEefieGISKKSGHLSWLIPGIGA-QGGNPEILR-----DLKG--KDVMVNVSRAIIFAE 231
                                       6665567789*******99976633333689999******8.555444333.....3433..245689********* PP

                                       SHHHHHHH CS
                         OMPdecase 217 dpveeaer 224
                                       d ++ ae+
  gi|242398431|ref|YP_002993855.1| 232 DIKKSAEK 239
                                       *****998 PP

>> Peptidase_S66C  LD-carboxypeptidase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.0   0.0    0.0075        68      78     108 ..      63      93 ..       7     102 .. 0.82
   2 !   11.6   0.0   3.5e-05      0.31       6      48 ..     205     245 ..     203     248 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.0075
                                       ..---HHHHHHHHHT-GGGTTS-EEEEESES CS
                    Peptidase_S66C  78 ekeeykealeevlaeiledlkiPvlynldiG 108
                                         ++ ++++ee+++ i +++++P++ + + G
  gi|242398431|ref|YP_002993855.1|  63 LGWKGYKVMEETIELIKQKTNVPIILDAKRG 93 
                                       56677889999999999********998776 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 3.5e-05
                                       EEEHHHHHCCTTSTTS---TT..EEEEEE--TTHHHHHHHHHH CS
                    Peptidase_S66C   6 GGnlsvlasllgtpylpekdlkgkILflEdvsespyridrmLt 48 
                                       GGn ++l +l g + ++  ++ ++I+f Ed+++s+++++ +L 
  gi|242398431|ref|YP_002993855.1| 205 GGNPEILRDLKGKDVMV--NVSRAIIFAEDIKKSAEKFKDLLD 245
                                       9***************9..899*********999999998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       624  (0.0348039); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1566.69
//
Query:       gi|242398432|ref|YP_002993856.1|  [L=309]
Description: Dihydroorotate dehydrogenase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.9e-71  238.7   0.3    9.1e-71  238.5   0.3    1.0  1  DHO_dh        Dihydroorotate dehydrogenase
    0.00054   19.1   1.4     0.0054   15.9   1.4    2.0  1  Dus           Dihydrouridine synthase (Dus)
    0.00082   18.7   0.5       0.15   11.3   0.0    2.7  3  Oxidored_FMN  NADH:flavin oxidoreductase / NADH oxidase famil
    0.00095   18.3   3.0     0.0018   17.4   3.0    1.4  1  IMPDH         IMP dehydrogenase / GMP reductase domain
     0.0029   17.0   3.0     0.0076   15.7   0.7    1.9  2  NMO           Nitronate monooxygenase
  ------ inclusion threshold ------
      0.037   13.5   0.8        1.1    8.7   0.1    2.2  2  PcrB          PcrB family
      0.044   13.2   0.0       0.17   11.3   0.0    1.8  2  His_biosynth  Histidine biosynthesis protein
      0.085   12.0   0.2       0.83    8.8   0.0    2.1  2  DUF561        Protein of unknown function (DUF561)
       0.11   11.8   0.5       0.28   10.5   0.1    1.8  2  TMP-TENI      Thiamine monophosphate synthase
        0.8    8.7   7.8        9.6    5.1   6.4    2.5  2  FMN_dh        FMN-dependent dehydrogenase


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 !  238.5   0.3   5.1e-74   9.1e-71       2     295 .]       5     286 ..       4     286 .. 0.91

  Alignments for each domain:
  == domain 1  score: 238.5 bits;  conditional E-value: 5.1e-74
                                       G-EEETTEEESSSEEE-TTSSTTSSSHHHHHCTT.SSEEEEEEE-SS-B--S-S--EEEETTCTEEEE---S-BS-H CS
                            DHO_dh   2 latkvlglkfknpiglAaGfdkegeeilkllklg.fgaieigsvtpkpqeGnpkPrvfrlkedrsvlNslGlnneGl 77 
                                       l+ +v+g+kf+npi+lA+G  ++g e+  +l+++ +gai++++vt+kp+eGnp Pr+++ + +  v+Ns+Gl+n+G+
  gi|242398432|ref|YP_002993856.1|   5 LSIDVFGIKFRNPIILASGPVGFGFELMPYLDFSnIGAITLKTVTLKPREGNPPPRLVDSHGG--VINSIGLQNPGI 79 
                                       67789**********************************************************..************ PP

                                       HHHHHHHHHHHHHHHCC.CEEEEEEE-TTSS.HHHHHHHHHHHHGGGESEEEEES-SCTCCTSCCCGCHHHHHHHHH CS
                            DHO_dh  78 davlekllkrrkeqeekkelginlskakktenavddyvevvrkigpfadilelNvSsPntpglrdlqekeelkaill 154
                                       +  +e++++r+ke ++ +++g   s+a+ + ++ + + e + ki++  +i+e+N+S+Pn++g+r  +e+ +l+++++
  gi|242398432|ref|YP_002993856.1|  80 EGFVEEIAPRLKELKT-IKIG---SIAGFSMDEWEILGEEMDKIKE-IKIIEINLSCPNVKGKRRWAEDAKLTEKVV 151
                                       ***********99775.4444...5666663445556666666655.58**************************** PP

                                       HHHHHHHSSEEEEEE-SSSSHHHHHHHHHHHH.HHTECEEEE...BSEE--CTTCCGCCCCTTSSEEEEEGGGHHHH CS
                            DHO_dh 155 kvvkevskvpvlvKlaPdltdeekkdiadvll.elkldgiivtNttvqrlaidlkseknvkanktGGlsGkalkdia 230
                                       k v++ + +p+++KlaPd+td++++++++v + +++l+    +N   q ++id+++  ++ + ktGGl+G+a+k+i 
  gi|242398432|ref|YP_002993856.1| 152 KIVRKLTGKPIIAKLAPDVTDIVEIAKTAVDAgADGLTI---GN-GAQAMRIDVETGLPILKLKTGGLGGPAVKPIT 224
                                       **********************99888887776666655...55.567788************************** PP

                                       HHHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGTCHHHHHHHHHHHHH CS
                            DHO_dh 231 lkvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfegpkiakkikkeleelL 295
                                       l+ + + ++ l+  +piIg+GGi+  +Da+e+++aGAsl+ ++ta+   +p + ++i+++++++L
  gi|242398432|ref|YP_002993856.1| 225 LAKVFKTREALD--VPIIGIGGIMNWQDAIEYAMAGASLLGLGTAV-MVDPEAPVRIIEGIKAFL 286
                                       ************..*******************************9.89************9876 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   1.4     3e-06    0.0054      79     201 ..     121     254 ..     114     276 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3e-06
                                       T-SCEEEEESSTTEEETTEEEGGGGGGSHHHHHHHHHHHHCCSSS-EEEEEESESSTTTC.HHHHHHHHHHCT-SEE CS
                               Dus  79 gadeIdlNvGCPskkvtrggaGaaLlrkpdlvaqivkavvkaveiPvtvkirigiddeeenalelakiveaaGaqal 155
                                       + ++I++N+ CP  k +r+     + ++++l +++vk v+k ++ P+ +k          +++e+ak++ +aGa+ l
  gi|242398432|ref|YP_002993856.1| 121 EIKIIEINLSCPNVKGKRR-----WAEDAKLTEKVVKIVRKLTGKPIIAKLAPD----VTDIVEIAKTAVDAGADGL 188
                                       5789********9999997.....78*********************9997654....55799************** PP

                                       EEESS..................ECCCTT-C..G--CHHHHHHHHH-SS-EEEESS--SHHHHHHH CS
                               Dus 156 tvHgR..................traqnyeg..tadweaIkevkqavsipviaNGdIkdaedaqai 201
                                       t+                     t   +  +  ++ ++++ + ++a+ +p+i+ G+I +++da + 
  gi|242398432|ref|YP_002993856.1| 189 TIGNGaqamridvetglpilklkTGGLGGPAvkPITLAKVFKTREALDVPIIGIGGIMNWQDAIEY 254
                                       **6556788899999999998776655555577999999999999999999999999999998764 PP

>> Oxidored_FMN  NADH:flavin oxidoreductase / NADH oxidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       0.3   5.4e+02     247     297 ..     116     164 ..     100     166 .. 0.65
   2 ?    3.9   0.1     0.015        27     151     171 ..     170     190 ..     165     195 .. 0.87
   3 !   11.3   0.0   8.6e-05      0.15     285     339 ..     229     282 ..     218     284 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.3
                                       HCHCCEEEEEEETT-SSSSSTTS-TTTTHHHCCTTHHHHHHCCCHSSEEEE CS
                      Oxidored_FMN 247 lkelekrlkdgkklalvhaaeprkrgagsvrteqekntefvkevwkkplit 297
                                       ++++++  ++  +l+  +++  ++r+a   + + ek +++v+++  kp+i+
  gi|242398432|ref|YP_002993856.1| 116 MDKIKEIKIIEINLSCPNVKG-KRRWAEDAKLT-EKVVKIVRKLTGKPIIA 164
                                       444444444444556666666.44555555555.588999******99996 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.015
                                       HHHHHHHHHHHHHTT-SEEEE CS
                      Oxidored_FMN 151 iqefveAAkraieAgfDgVei 171
                                       +++ ve Ak a++Ag+Dg  i
  gi|242398432|ref|YP_002993856.1| 170 VTDIVEIAKTAVDAGADGLTI 190
                                       6778999***********987 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 8.6e-05
                                       HHHCCCHSSEEEE-SS--SHHHHHHHHHTTS-SEEEESTHHHH-TTHHHHHHCCT CS
                      Oxidored_FMN 285 efvkevwkkplitvgriadeekaaeivaegeadLvamgRefladpdlveklkkgl 339
                                        + +e  ++p+i++g+i + + +a+  a   a L ++g ++++dp+ + ++ +g+
  gi|242398432|ref|YP_002993856.1| 229 FKTREALDVPIIGIGGIMNWQ-DAIEYAMAGASLLGLGTAVMVDPEAPVRIIEGI 282
                                       5789999*************9.9999999*********************99887 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   3.0   9.9e-07    0.0018     131     250 ..     149     279 ..     142     287 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 9.9e-07
                                       HHHHHHHHHHHHTTTSEEEEEEE-S.HHHHHHHHHTT-SEEEE-SS-STTBH...H.....H.HHCSB---HHHHH. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx...x.....x.xxxxxxxxxxxxx. RF
                             IMPDH 131 kvleavkeikkkveeveviaGnvat.aegakaLieagadavkvGiGpGsiCt...t.....r.vvagvGvpqltAv. 196
                                       kv++ v+++  k   +  +a +v++  e ak+ ++agad++ +G G+ ++ +   t     +    g+G p +  + 
  gi|242398432|ref|YP_002993856.1| 149 KVVKIVRKLTGKP-IIAKLAPDVTDiVEIAKTAVDAGADGLTIGNGAQAMRIdveTglpilKlKTGGLGGPAVKPIt 224
                                       4444444444443.377777888773467888899999999999999888762221111112145689***998762 PP

                                       .HHHHHHHCTCT-EEEEES---SHHHHHHHHHTT-SEEEESCCCTTBTTSSSEEE CS
                                       .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 197 .aevaeaakkagvpviaDGGikysgdivkAlaaGadavmlGsllagteEspgevi 250
                                        a+v ++ +  +vp+i  GGi + +d +    aGa+ + lG  +    E+p ++i
  gi|242398432|ref|YP_002993856.1| 225 lAKVFKTREALDVPIIGIGGIMNWQDAIEYAMAGASLLGLGTAVMVDPEAPVRII 279
                                       26888999999***************9999999**********999999998776 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1       0.1   1.8e+02      51     106 ..     148     199 ..     139     209 .. 0.69
   2 !   15.7   0.7   4.2e-06    0.0076     168     235 ..     213     278 ..     209     293 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.1
                               NMO  51 akeirkvkaltdkPfgvnlflpkkdaadraekykkeleeaalelnieegvrfyrkv 106
                                       +k ++ v++lt kP+ + l  +  d  ++   +k  +   a +l i  g +   ++
  gi|242398432|ref|YP_002993856.1| 148 EKVVKIVRKLTGKPIIAKLAPDVTDIVEI---AKTAVDAGADGLTIGNGAQ-AMRI 199
                                       45678899999999988775555554444...6666666677777777766.5555 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 4.2e-06
                               NMO 168 GGhqGtpevgdkglfaLvpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqigtrfLltkesdakd 235
                                       GG  G p+v+   ++a v + ++a+d+P+i  GGi++ ++      +GAs   +gt+ ++  e++++ 
  gi|242398432|ref|YP_002993856.1| 213 GGLGG-PAVK-PITLAKVFKTREALDVPIIGIGGIMNWQDAIEYAMAGASLLGLGTAVMVDPEAPVRI 278
                                       66666.4443.33445556779****************998888889*************99998865 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.1   0.00061       1.1       8      42 ..     162     197 ..     152     211 .. 0.83
   2 ?    3.4   0.0     0.025        45     177     221 ..     234     278 ..     203     284 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00061
                                       EEEEE-TTSS-CHHHHHHHHCTT-SEEEEE.CSTCH CS
                              PcrB   8 hltklDPeeenpdEiveiviesgtDavmig.Gsqsv 42 
                                        + kl P+ + + Ei++++++ g+D++ ig G+q  
  gi|242398432|ref|YP_002993856.1| 162 IIAKLAPDVTDIVEIAKTAVDAGADGLTIGnGAQAM 197
                                       589**************************9455544 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.025
                                       HHSSSEEEEESS--SHHHHHHHHCC.SSEEEE-CHHHHHHHCHHHH CS
                              PcrB 177 klekarlivGGGirsaEkAkevvea.ADvivvGnvveekderkida 221
                                        l +  +i  GGi +  +A e++ a A  +  G++v  ++e  ++ 
  gi|242398432|ref|YP_002993856.1| 234 AL-DVPIIGIGGIMNWQDAIEYAMAgASLLGLGTAVMVDPEAPVRI 278
                                       22.233555699*************9999999**999988766654 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.63   1.1e+03      23      48 ..     165     190 ..     149     192 .. 0.71
   2 ?   11.3   0.0   9.3e-05      0.17      59     116 ..     222     279 ..     215     287 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.63
                                       CEEEETTSHHHHHHHHHHHT-SEEEE CS
                      His_biosynth  23 qelryagdpvelakryeeegadelhv 48 
                                       +   +  d+ve+ak   ++gad l++
  gi|242398432|ref|YP_002993856.1| 165 KLAPDVTDIVEIAKTAVDAGADGLTI 190
                                       55667889999999999999988765 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 9.3e-05
                                       HHHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHH CS
                      His_biosynth  59 eanldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavknpelikela 116
                                       ++ l+ v +++e++++p+   GGI + +d+ e+  aga+ + +gta++ +pe   +++
  gi|242398432|ref|YP_002993856.1| 222 PITLAKVFKTREALDVPIIGIGGIMNWQDAIEYAMAGASLLGLGTAVMVDPEAPVRII 279
                                       5667778899**************************************9999766655 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   0.1      0.12   2.1e+02      51      89 ..     149     192 ..     116     205 .. 0.68
   2 ?    8.8   0.0   0.00046      0.83     174     235 ..     224     284 ..     214     292 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.12
                            DUF561  51 klvkkvksvsniPiCvs.aveakllle....avkaGadlveiGn 89 
                                       k+vk v++ +  Pi    a +   ++e    av aGad + iGn
  gi|242398432|ref|YP_002993856.1| 149 KVVKIVRKLTGKPIIAKlAPDVTDIVEiaktAVDAGADGLTIGN 192
                                       56666666666665442122222222211126788888888887 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00046
                            DUF561 174 tlastyeiskkvslPvicasGlsdvtvplals.lgasGiGigsavsklndeeemvallseikk 235
                                       tla +++  +++++P+i   G+ +    + ++ +gas +G+g av    d e+ v +++ ik+
  gi|242398432|ref|YP_002993856.1| 224 TLAKVFKTREALDVPIIGIGGIMNWQDAIEYAmAGASLLGLGTAVM--VDPEAPVRIIEGIKA 284
                                       99*********************998888765269********995..455556666666655 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.1     2e+03      67      80 ..     178     191 ..     143     199 .. 0.60
   2 ?   10.5   0.1   0.00016      0.28     135     172 ..     221     259 ..     217     268 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.1
                          TMP-TENI  67 dlalavgadgvHlg 80 
                                       + a ++gadg+ +g
  gi|242398432|ref|YP_002993856.1| 178 KTAVDAGADGLTIG 191
                                       22333444444444 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00016
                          TMP-TENI 135 eplgleglkelaealeiPvvaiGGi.tlenvaevleaga 172
                                       +p+ l+++ +++eal +P++ iGGi + +++ e + aga
  gi|242398432|ref|YP_002993856.1| 221 KPITLAKVFKTREALDVPIIGIGGImNWQDAIEYAMAGA 259
                                       8999********************834555555555555 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0     0.067   1.2e+02      46      65 ..       3      22 ..       1      32 [. 0.85
   2 ?    5.1   6.4    0.0054       9.6     200     304 ..     143     269 ..     113     274 .. 0.72

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.067
                                      -B--EEETTEEESSSEEE-- CS
                            FMN_dh 46 vdlsttllGqklslPvliaP 65
                                      vdls++++G k++ P+++a+
  gi|242398432|ref|YP_002993856.1|  3 VDLSIDVFGIKFRNPIILAS 22
                                      79***************984 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0054
                                       -TC--HHHHHHHHHHHSSEEEEEEE-SHHH....HHHHHHTTESEEEE--GGGTSSTT.---HHHCH.........H CS
                            FMN_dh 200 dpsltwddikwlreqtklplvvKGvltaed....akraveaGvdgivvSNHGGRqldg.apatidvL.........p 262
                                       d++lt + +k +r+ t  p++ K   ++ d    ak av+aG+dg+ + N G+  ++  + + + +L         p
  gi|242398432|ref|YP_002993856.1| 143 DAKLTEKVVKIVRKLTGKPIIAKLAPDVTDiveiAKTAVDAGADGLTIGN-GAQAMRIdVETGLPILklktgglggP 218
                                       688999999**************87665554444899***********99.55554431334455554455555553 PP

                                       HH.....HHHH......SS-EEEESS--SHHHHHHHHHTT-SEEEESHHHH CS
                            FMN_dh 263 ei.....veavgg....rievlvDgGirrGsDvlkAlalGAdavllGRpfl 304
                                       ++     ++  +     +++++  gGi++ +D++     GA++ +lG +++
  gi|242398432|ref|YP_002993856.1| 219 AVkpitlAKVFKTrealDVPIIGIGGIMNWQDAIEYAMAGASLLGLGTAVM 269
                                       333334322222222347999999999999999999999999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.59u 0.36s 00:00:00.95 Elapsed: 00:00:00.53
# Mc/sec: 1755.43
//
Query:       gi|242398433|ref|YP_002993857.1|  [L=235]
Description: dihydroorotate dehydrogenase electron transfer subunit [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-12   46.5   3.3    3.9e-12   45.8   3.3    1.4  1  DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydr
    6.3e-05   23.3   0.0     0.0001   22.6   0.0    1.3  1  FAD_binding_6    Oxidoreductase FAD-binding domain
  ------ inclusion threshold ------
      0.094   12.7   1.8       0.25   11.4   1.8    1.6  1  Fer2_3           2Fe-2S iron-sulfur cluster binding domain
       0.28   11.8   1.0         16    6.2   0.0    2.3  2  NAD_binding_1    Oxidoreductase NAD-binding domain
       0.33   10.9   3.1       0.29   11.1   0.9    1.9  2  Fer2             2Fe-2S iron-sulfur cluster binding domain


Domain annotation for each model (and alignments):
>> DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydroorotate dehydrogenase B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   3.3   1.1e-15   3.9e-12       1      41 [.     194     230 ..     194     231 .. 0.95

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 1.1e-15
                                       ----SSSSSSS-TTEEEETTCTT.CEEETTTT-CEEECCCB CS
                   DHODB_Fe-S_bind   1 eerMaCGvGaClgCvvktkggdggeykrvCkdGPvFdadev 41 
                                       e++M+CG+G C +C+vktk+g     k vCk+GP F+ +e+
  gi|242398433|ref|YP_002993857.1| 194 EAMMGCGIGTCKSCAVKTKKG----VKLVCKNGPLFRKEEI 230
                                       789***************997....9***********9998 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 !   22.6   0.0   2.9e-08    0.0001       6      96 ..       7      90 ..       3      92 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 2.9e-08
                                      EEEECCTTEEEEEEEESTTTS-----TT-EEEEEECETTCCEEEEEE.BSSTTECCEEEEEEE--TT-HHHHHHHCS-T CS
                     FAD_binding_6  6 ekeevsedtrifrfklpsekqklglpvGqhvflrlkikgeaviRsYtpissenekGelellvkvypgGkmsqaLdelki 84
                                      +++++s+d   f+fkl  + +  +  +Gq+v+l+++ ++    ++++++s +n   el l +k++  G+++  + + +i
  gi|242398433|ref|YP_002993857.1|  7 KEKKISKDYGFFTFKLYGDLE--NPEAGQFVMLKAS-DEPILAKPFSIYSYKNR--ELTLFIKRV--GRLTGKIFSSPI 78
                                      4578*************8888..7889********9.888899****9999887..58889*988..************ PP

                                      T-EEEEEEEE-S CS
                     FAD_binding_6 85 gdtleikGPlGk 96
                                      g++  i+GP+G+
  gi|242398433|ref|YP_002993857.1| 79 GEMFYIRGPHGN 90
                                      ***********7 PP

>> Fer2_3  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.8     7e-05      0.25      22      73 ..     150     220 ..     138     223 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7e-05
                            Fer2_3  22 eveaeeedtvldaLlkikeev...................dptlafrasCregiCGscavainGkptlaCt 73 
                                        +e e+e+tv+d+L+ +++e                      +l   + C+ g C scav+    ++l+C+
  gi|242398433|ref|YP_002993857.1| 150 IIEEESEKTVVDVLKDVYSEEigilacgpvpmlknlpatsYVSLEAMMGCGIGTCKSCAVKTKKGVKLVCK 220
                                       578889999999999999988899999999999999986667777789**********************8 PP

>> NAD_binding_1  Oxidoreductase NAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.5     0.016        57       1      12 [.     104     115 ..     104     158 .. 0.75
   2 ?    6.2   0.0    0.0046        16      82     105 ..     156     183 ..     135     186 .. 0.69

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.016
                                       EEEEGGGGHHHH CS
                     NAD_binding_1   1 miagGtGiaPvr 12 
                                       +++gG+G+aP+ 
  gi|242398433|ref|YP_002993857.1| 104 LVGGGSGVAPLN 115
                                       79********75 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0046
                                       HHHHHH....HSSTTEEEEEECSHHHHH CS
                     NAD_binding_1  82 leells....lkkeethvyvCGppgMik 105
                                        +++++    + +ee  ++ CGp +M k
  gi|242398433|ref|YP_002993857.1| 156 EKTVVDvlkdVYSEEIGILACGPVPMLK 183
                                       33333355556679999*********87 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 ?   -1.1   0.1      0.51   1.8e+03       5      25 ..     146     165 ..     142     177 .. 0.56
   2 ?   11.1   0.9     8e-05      0.29      30      50 ..     194     214 ..     187     229 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.51
                                       TEEEEEEEETTTHBHHHHHHH CS
                              Fer2   5 gkevevevadgettlldaaee 25 
                                       +k+  +e++ ++t + d++++
  gi|242398433|ref|YP_002993857.1| 146 QKNLIIEEESEKT-VVDVLKD 165
                                       5666777666666.7777774 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 8e-05
                                       TSTTSSSSSSSSTTEEEEEES CS
                              Fer2  30 dipysCggggCgtClvevleg 50 
                                       +  ++Cg g+C +C+v+ ++g
  gi|242398433|ref|YP_002993857.1| 194 EAMMGCGIGTCKSCAVKTKKG 214
                                       56689***********98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1523.25
//
Query:       gi|242398434|ref|YP_002993858.1|  [L=421]
Description: Dihydroorotase, multifunctional complex type [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-34  120.0   0.1    1.7e-34  119.7   0.1    1.1  1  Amidohydro_1  Amidohydrolase family
    8.5e-15   55.2   0.0    3.4e-06   26.8   0.1    2.3  2  Amidohydro_3  Amidohydrolase family
    4.2e-12   46.2   0.0    6.4e-12   45.6   0.0    1.3  1  DHOase        Dihydro-orotase-like
  ------ inclusion threshold ------
      0.048   13.8   0.1       0.13   12.5   0.1    1.7  1  SspH          Small acid-soluble spore protein H 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 !  119.7   0.1   3.8e-38   1.7e-34       1     344 []      46     414 ..      46     414 .. 0.80

  Alignments for each domain:
  == domain 1  score: 119.7 bits;  conditional E-value: 3.8e-38
                                       EEEE-EEEEEEECETTECSSSGHHHHHSTTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTH.....HHHHHHHHHHT CS
                      Amidohydro_1   1 ivlPGlIDaHvHleqsllrgatledwlvppetaaealesgiktalksGtttvadmgattst.....giealleaaee 72 
                                       +v+PGlID+H H++             +p+ + +e++esg k+a+ +G+ttva m++t++       ie +++ a+e
  gi|242398434|ref|YP_002993858.1|  46 LVIPGLIDMHAHFR-------------EPGYEHRETIESGSKAAIHGGVTTVAVMPNTNPAldsprIIEHVKQRAHE 109
                                       59***********9.............******************************99889777777777777777 PP

                                       SSSEEEEEEESSEGGSGCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHHHHHHHHHHHHHTTEEE CS
                      Amidohydro_1  73 lplglrilggkvsldrgsaetskasreklkagaaetikgkadgvvkvalapheapafsdeelkealkeakkrdlpva 149
                                       +  gl  +++   ++         + +k  + +    k  a+ v  +a+ + + +  s     ea+k a++ ++p+a
  gi|242398434|ref|YP_002993858.1| 110 V--GLIDIFPTSAIT---------EGRKGNKLV--NFKSLASHV--IAFSDDGTTPQSFKIFLEAAKFARAVGKPIA 171
                                       5..655555533333.........333333332..112222222..56777777777777999************** PP

                                       EEE..TSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEE....HH..HHHHHHHHHHHHCEE.. CS
                      Amidohydro_1 150 iHa..letkgevedaeaafgetiehgthlevaeslglldeiklilahgvhlt....pt..eaellkerlkeagva.. 216
                                        Ha   e++g  +++e +f ++    ++ + aes++++++i +++ +g h++     t  ++e+  +++k+  ++  
  gi|242398434|ref|YP_002993858.1| 172 DHAeiKELSGG-SMREGQFSKRYGVSGIPDIAESIAVARDIEVARYTGAHIHiqhlSTkaSVEI-LKNAKKRTIPvt 246
                                       ****5555555.6***************************************766522645555.455566666688 PP

                                       ......HHHHHHHH...............SEHHHHHHHHHHHHTSCEEEEEECT........TSSCCGGHHHHHHHH CS
                      Amidohydro_1 217 ......hcpfsnsi...............lrsgrealrkaldeGvkvglgtDga........asgnslnlleelrla 264
                                             h+ f+++                 +++ eal k l +G++ +++tD+a          + s+ +   ++ +
  gi|242398434|ref|YP_002993858.1| 247 gevthhHLLFTDEDlkdrspfkkvnpplpTQEDQEALVKGLIDGTIDIIVTDHApyskeeksTDIESAPF---GISG 320
                                       9999997777766679****************************************99888855556656...4444 PP

                                       HHHHHHCCTT.TTHCHCHHHHHHHHHTHHHHHHTT-TTTSSSS-TTSB--EEEECCCT..............CGGGT CS
                      Amidohydro_1 265 lklqrgllye.deegglslkealrmaTingAkalglddkvGsievGkdADlvvvdldi..............laafv 326
                                       +++  ++l    e++ +s   +l+++T+++Ak+++l    G +++G+  D+v+vd+++              +++f 
  gi|242398434|ref|YP_002993858.1| 321 IETLLSSLFLiAEMYEISFVSLLEKVTWKPAKIFNLG-LRGDFAPGYVGDIVIVDPNKrwkvteksllskgkNTPFL 396
                                       43334434444479**********************7.******************33455577889999******* PP

                                       TTCTSEEEEEEEETTEEE CS
                      Amidohydro_1 327 glkkdgnvkkvivkGklv 344
                                       + + +g v  +i++Gk+v
  gi|242398434|ref|YP_002993858.1| 397 NRTLPGVVELTIKNGKIV 414
                                       ****************98 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.1   7.6e-10   3.4e-06       3      47 ..      40      84 ..      38      93 .. 0.81
   2 !   26.0   0.0   1.3e-09   5.8e-06     407     473 .]     336     415 ..     328     415 .. 0.95

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 7.6e-10
                      Amidohydro_3  3 iDakGrlvlPGFvDsHtHlagggvnlrllrlpdarvtslegvlta 47
                                      iDa+ +lv+PG++D+H+H  + g++ r++  +++++    gv+t+
  gi|242398434|ref|YP_002993858.1| 40 IDAEDKLVIPGLIDMHAHFREPGYEHRETIESGSKAAIHGGVTTV 84
                                      9**********************9997777666555555555555 PP

  == domain 2  score: 26.0 bits;  conditional E-value: 1.3e-09
                      Amidohydro_3 407 elsleealalyTrgpAkalgledrkGtLevGadADlvvld.adpldvdppelaear.............vrltvvdG 469
                                       e+s+  +l  +T +pAk+++l  r G  ++G+ +D+v+ d +++ +v+++ l +++             v+lt+++G
  gi|242398434|ref|YP_002993858.1| 336 EISFVSLLEKVTWKPAKIFNLGLR-GDFAPGYVGDIVIVDpNKRWKVTEKSLLSKGkntpflnrtlpgvVELTIKNG 411
                                       6788889999*************9.***************999***********99********************* PP

                      Amidohydro_3 470 rvvy 473
                                       ++vy
  gi|242398434|ref|YP_002993858.1| 412 KIVY 415
                                       ***9 PP

>> DHOase  Dihydro-orotase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   0.0   1.4e-15   6.4e-12       2     141 ..      45     230 ..      44     231 .. 0.90

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 1.4e-15
                            DHOase   2 rllvpglidlavhlrelsgeakeliet...........tvaaygvtfkaP........................aai 43 
                                       +l++pglid++ h re++ e +e+ie            tva +++t++a                          ai
  gi|242398434|ref|YP_002993858.1|  45 KLVIPGLIDMHAHFREPGYEHRETIESgskaaihggvtTVAVMPNTNPALdspriiehvkqrahevglidifptSAI 121
                                       89**********************************************98777988888888888888888888666 PP

                            DHOase  44 tveddsee..........afiltddtvyvtiqllefeglkk.aeLdqalkaiaeDDevtnqsavqdfelarfyGvqL 109
                                       t + +++             +++dd+   ++  +  e+ k   ++++ + ++ae  e+ ++++++++ ++++yG  +
  gi|242398434|ref|YP_002993858.1| 122 TEGRKGNKlvnfkslashVIAFSDDGTTPQSFKIFLEAAKFaRAVGKPIADHAEIKEL-SGGSMREGQFSKRYG--V 195
                                       6666666678788777768899******************9899************99.57889**********..7 PP

                            DHOase 110 kG...vCeaekivydvLlakaagcgfyvsiiytke 141
                                        G     e+  +++d+ +a+ +g++ ++ +++tk 
  gi|242398434|ref|YP_002993858.1| 196 SGipdIAESIAVARDIEVARYTGAHIHIQHLSTKA 230
                                       7777799*************************996 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 ?   12.5   0.1   2.8e-05      0.13       9      54 ..     205     246 ..     201     247 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.8e-05
                              SspH   9 IlnskemieVtYngkpVwIehvdeenetAtVhfldnpeeeqeVpvn 54 
                                       I+  ++     Y g  ++I+h++    +A V+ l ++ +++++pv+
  gi|242398434|ref|YP_002993858.1| 205 IAVARDIEVARYTGAHIHIQHLS---TKASVEIL-KNAKKRTIPVT 246
                                       55555544447***********7...99******.99999999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); 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 0.29s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 2524.58
//
Query:       gi|242398435|ref|YP_002993859.1|  [L=150]
Description: Aspartate carbamoyltransferase regulatory chain [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-31  108.2   5.7    1.9e-31  108.2   5.7    1.6  2  PyrI      Aspartate carbamoyltransferase regulatory chain, al
    7.1e-20   70.6   6.0    1.2e-19   69.9   6.0    1.4  1  PyrI_C    Aspartate carbamoyltransferase regulatory chain, me
  ------ inclusion threshold ------
      0.018   15.0   0.4      0.031   14.3   0.4    1.4  1  PriA_CRR  PriA DNA helicase Cys-rich region (CRR) domain
      0.039   14.4   0.1      0.068   13.6   0.1    1.5  1  zf-C2HE   C2HE / C2H2 / C2HC zinc-binding finger
      0.064   13.1   0.1      0.088   12.6   0.1    1.3  1  RD3       RD3 protein


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 !  108.2   5.7   5.2e-35   1.9e-31       1      94 []       4      94 ..       4      94 .. 0.96
   2 ?   -2.4   0.1       1.7   6.1e+03      80      88 ..     109     117 ..      98     127 .. 0.58

  Alignments for each domain:
  == domain 1  score: 108.2 bits;  conditional E-value: 5.2e-35
                                      X-----SCEEEEEEEETT-HHHHHHHCT--T...TS-EEEEEEEEETTTEEEEEEEEET----HHHHHHHCCC-TT-EE CS
                              PyrI  1 lkvkkienGiViDHIkagkalkvlklLkldklkseekvaiiknvkskklgkKdiikiegkelseeeldklaliapnati 79
                                      lkv++i++G+ViDHI++gk+lkvl++L+l + +++  + +++nvks+klg+Kdiik+egk l+e+e++k+aliap+at+
  gi|242398435|ref|YP_002993859.1|  4 LKVSAINKGTVIDHIPSGKGLKVLEILNLPE-DNT--ILVAINVKSQKLGRKDIIKVEGKILNEDEVNKIALIAPTATV 79
                                      69****************************6.555..****************************************** PP

                                      EEEETTEEEEEE--. CS
                              PyrI 80 niIkdgevveKkkve 94
                                      niI   evveK++ve
  gi|242398435|ref|YP_002993859.1| 80 NIIDKWEVVEKRNVE 94
                                      ************985 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.7
                                       EEEETTEEE CS
                              PyrI  80 niIkdgevv 88 
                                       n+I ++e v
  gi|242398435|ref|YP_002993859.1| 109 NCITNYEEV 117
                                       566666433 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 !   69.9   6.0   3.4e-23   1.2e-19       1      47 [.      98     144 ..      98     145 .. 0.96

  Alignments for each domain:
  == domain 1  score: 69.9 bits;  conditional E-value: 3.4e-23
                                       EEESSS--S-TTBGGGTTS-.-EEEEEETTTTEEEETTT--EEEHHH CS
                            PyrI_C   1 eiegvlkCpNpnCItnnepveskFkvedkekvklkCkYCekeiseee 47 
                                       ei g++kC NpnCItn e+v++kFkv++k+++klkC+YCe++++e+ 
  gi|242398435|ref|YP_002993859.1|  98 EIVGIIKCANPNCITNYEEVKPKFKVISKKPLKLKCHYCERTMEENM 144
                                       699****************************************9986 PP

>> PriA_CRR  PriA DNA helicase Cys-rich region (CRR) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.4   8.7e-06     0.031      13      26 ..     127     140 ..     126     140 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 8.7e-06
                          PriA_CRR  13 srnrLrCHyCgyte 26 
                                       ++ +L+CHyC +t+
  gi|242398435|ref|YP_002993859.1| 127 KPLKLKCHYCERTM 140
                                       5668******9885 PP

>> zf-C2HE  C2HE / C2H2 / C2HC zinc-binding finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   1.9e-05     0.068      36      52 ..     129     145 ..      83     146 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.9e-05
                           zf-C2HE  36 tpLkCtrCganfgnkfp 52 
                                        +LkC++C++++  +++
  gi|242398435|ref|YP_002993859.1| 129 LKLKCHYCERTMEENMV 145
                                       4689**********997 PP

>> RD3  RD3 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   2.5e-05     0.088      85     128 ..      72     115 ..      51     118 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.5e-05
                               RD3  85 kikPsecgkvisrfrevlaenevevkeivelfksvlkevleerk 128
                                        i P  + ++i+++  v + n + ++eiv ++k++  +++++ +
  gi|242398435|ref|YP_002993859.1|  72 LIAPTATVNIIDKWEVVEKRNVEVPDEIVGIIKCANPNCITNYE 115
                                       699********************************999998866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); 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 0.30s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 907.59
//
Query:       gi|242398436|ref|YP_002993860.1|  [L=306]
Description: Aspartate carbamoyltransferase [Thermococcus sibiricus MM 739]
Scores for complete 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-50  170.8   0.0    3.1e-50  170.0   0.0    1.4  1  OTCace_N      Aspartate/ornithine carbamoyltransferase, carba
    7.1e-31  107.4   0.0    1.1e-30  106.8   0.0    1.3  1  OTCace        Aspartate/ornithine carbamoyltransferase, Asp/O
     0.0023   18.0   0.0     0.0057   16.7   0.0    1.6  2  Shikimate_DH  Shikimate / quinate 5-dehydrogenase


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 !  170.0   0.0   5.2e-54   3.1e-50       2     147 ..       5     145 ..       4     146 .. 0.95

  Alignments for each domain:
  == domain 1  score: 170.0 bits;  conditional E-value: 5.2e-54
                                       -BSSGGGS-HHHHHHHHHHHHHHHHHHHTTT-STTTTT-EEEEEESS--HHHHHHHHHHHHHTTSEEEEEESTTTSC CS
                          OTCace_N   2 hllsledlskeeieelldlaaelkekvkkekkekllkgktlallFeepStRTrvSfevAakrlGgkvlslseaediq 78 
                                       +++s++d+ keeie++l++a++l+++ +++k  +++kgk+la+lF+epStRTr+Sfe+A++rlGg+v+ + ea    
  gi|242398436|ref|YP_002993860.1|   5 DVISINDFGKEEIEYVLKTAKRLENELNERKILQYAKGKILATLFFEPSTRTRFSFESAMHRLGGSVIGFAEA---S 78 
                                       789********************************************************************77...4 PP

                                       TTTGGSTTSSCHHHHHHHHHHHTSEEEEEES..SHHHHHHHHHHHSSEEEEEEETSSB-HHHHHHHHHHHH CS
                          OTCace_N  79 lssvskgrkEsleDtarvlsryvdaiviRhp..gaeeleelakyasvpviNagdgdgeHPtQaLaDlltir 147
                                       +ssv+kg  Esl Dt+r++++y+d+iviRhp  ga  ++  a+ a++pviNagdg+++HPtQ+L+Dl+ti+
  gi|242398436|ref|YP_002993860.1|  79 SSSVKKG--ESLMDTIRTVEKYADVIVIRHPreGA--ARLAAEIAEIPVINAGDGANQHPTQTLLDLYTIK 145
                                       6889999..**********************6555..88889999************************97 PP

>> OTCace  Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.8   0.0   1.9e-34   1.1e-30       3     154 ..     154     298 ..     152     301 .. 0.96

  Alignments for each domain:
  == domain 1  score: 106.8 bits;  conditional E-value: 1.9e-34
                                       .EEEEESS.TTSHHHHHHHHHHHHCT-EEEEES-TTSSH-HHHHHHHHHHHHHHT-EEEEESSCHHHHTT-SEEEE- CS
                            OTCace   3 lkiafvGd.kknnvanslikllarlgmdvvlvaPkglepdkevleeakknakksggsititedleeavkgaDvvytd 78 
                                       lkia++Gd k++++++sl+k+l+ +++++++vaP+gle+  +++ee++++      +it t+dle+++ ++D++yt+
  gi|242398436|ref|YP_002993860.1| 154 LKIALLGDlKYGRTVHSLAKALSYYDVKLYFVAPQGLEMPRHIVEEISDK-----LEITETNDLESVIPEVDILYTT 225
                                       89*************************************99*99999886.....68******************** PP

                                       -SSETTCCGGHH...HHHHHHCC.CSB-HHHHHHS-TT-EEEE-S---BTTTB-HHHHTSTTBHHHHHHHHHHHHHH CS
                            OTCace  79 vwvsmgeekere...erlkklkd.yqvteellklakkdaivlHcLPakrgeEvtdeVfdsprsvvfeqaeNrlhtik 151
                                       +++     ker+   ++++k+k+ y+v+ +ll++ak+ ++++H+LP  r +E++ eV++ + s++f+q+  ++ +++
  gi|242398436|ref|YP_002993860.1| 226 RIQ-----KERFpdpAEYNKIKGsYRVDLKLLERAKETLKIMHPLP--RVDEISYEVDKTQYSAYFRQVWSGVPVRM 295
                                       ***.....8888888999999999**********************..***************************** PP

                                       HHH CS
                            OTCace 152 All 154
                                       All
  gi|242398436|ref|YP_002993860.1| 296 ALL 298
                                       **9 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       1.6   9.8e+03      35      56 ..      97     118 ..      85     123 .. 0.61
   2 !   16.7   0.0   9.6e-07    0.0057       4      83 ..     145     226 ..     143     246 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.6
                                       T-CEEEEEESSHHHHHHHHHHH CS
                      Shikimate_DH  35 gvkkvvvaNRtlerakelaeel 56 
                                       ++ +v+v+   +e a++la e+
  gi|242398436|ref|YP_002993860.1|  97 KYADVIVIRHPREGAARLAAEI 118
                                       3445555555556666666655 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 9.6e-07
                                       HHHHS..TT-EEEEES-...SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-S CS
                      Shikimate_DH   4 kkkleslkekkvlliGa...GemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaead 77 
                                       kk+++++++ k+ l+G    G++ + +ak+L+   vk  +va   le  ++++ee++++ +e+++ ++l++++ e+d
  gi|242398436|ref|YP_002993860.1| 145 KKEFGRIDRLKIALLGDlkyGRTVHSLAKALSYYDVKLYFVAPQGLEMPRHIVEEISDK-LEITETNDLESVIPEVD 220
                                       7889999999******65559999999*****************************777.***************** PP

                                       EEEE-S CS
                      Shikimate_DH  78 vvisat 83 
                                       ++ +  
  gi|242398436|ref|YP_002993860.1| 221 ILYTTR 226
                                       *98865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); 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 0.26s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 1981.81
//
Query:       gi|242398437|ref|YP_002993861.1|  [L=189]
Description: Orotate phosphoribosyltransferase [Thermococcus sibiricus MM 739]
Scores for complete 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-24   84.5   1.2      7e-24   84.1   1.2    1.1  1  Pribosyltran  Phosphoribosyl transferase domain
    0.00094   18.7   0.0     0.0014   18.1   0.0    1.2  1  UPRTase       Uracil phosphoribosyltransferase
  ------ inclusion threshold ------
      0.082   12.5   0.0       0.12   12.0   0.0    1.3  1  DUF2529       Domain of unknown function (DUF2529)


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 !   84.1   1.2   1.2e-27     7e-24       5     132 ..      45     163 ..      41     172 .. 0.95

  Alignments for each domain:
  == domain 1  score: 84.1 bits;  conditional E-value: 1.2e-27
                                       TTT---EEEEEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........EE CS
                      Pribosyltran   5 llenpaildavarlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdesrl 81 
                                       l +np++l+ +a+l++ +++e+  + d ++g++ g+vp+a  la   + pl +vrk+k++ +++ ++          
  gi|242398437|ref|YP_002993861.1|  45 LITNPKALRLIASLMKIKIDEFALEYDKIAGPELGAVPIAVSLALVTDKPLLIVRKKKKEYGTGRQI---------E 112
                                       55789**************************************************************.........7 PP

                                       ----TTSEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE-HHHHHH CS
                      Pribosyltran  82 ledpagkkVliVDDildtGgTllaalelLkekgpeevriavlvdkpateee 132
                                        e ++g++Vl+V+D+ +tGg++l+a+++L+e+g+++v+i+v+vd+ ++++e
  gi|242398437|ref|YP_002993861.1| 113 GEVKKGERVLLVEDVTTTGGSVLRAAKALEEEGAKIVGIMVVVDREEGAKE 163
                                       899*******************************************99987 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   2.3e-07    0.0014     119     172 ..     115     167 ..      92     180 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.3e-07
                           UPRTase 119 i.aertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvlaseegvkrlaee 172
                                       + + ++vll++ v  TGgs+  a + L e+g+  + + ++ v+  eeg+k+++ +
  gi|242398437|ref|YP_002993861.1| 115 VkKGERVLLVEDVTTTGGSVLRAAKALEEEGA--KIVGIMVVVDREEGAKEALGK 167
                                       445678***********************887..466677788899999988765 PP

>> DUF2529  Domain of unknown function (DUF2529)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0     2e-05      0.12      72     119 ..     112     160 ..      83     175 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2e-05
                                       T----TT-EEEEEES-S--.HHHHHHHHHHHHHT--EEEEESS---T.. CS
                           DUF2529  72 ekeltetDrvllfsresnd.kealklakkleekgievvavsskvkeeda 119
                                       e e+++  rvll+ + +++  ++l++ak+lee+g+++v+++  v++e+ 
  gi|242398437|ref|YP_002993861.1| 112 EGEVKKGERVLLVEDVTTTgGSVLRAAKALEEEGAKIVGIMVVVDREEG 160
                                       3389999******99877626899****************999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1420.37
//
Query:       gi|242398438|ref|YP_002993862.1|  [L=92]
Description: hypothetical protein TSIB_0447 [Thermococcus sibiricus MM 739]
Scores for complete 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-05   22.4   0.2    0.00011   22.1   0.2    1.2  1  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0012   19.2   0.0     0.0015   18.9   0.0    1.2  1  Rrf2            Transcriptional regulator
     0.0013   18.5   0.1     0.0023   17.7   0.1    1.4  1  HTH_IclR        IclR helix-turn-helix domain
     0.0069   16.4   0.0     0.0086   16.1   0.0    1.2  1  HTH_20          Helix-turn-helix domain
  ------ inclusion threshold ------
      0.038   14.2   0.1      0.063   13.5   0.1    1.3  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      0.042   13.8   0.2      0.077   12.9   0.2    1.4  1  MarR            MarR family
      0.057   13.5   0.0      0.083   13.0   0.0    1.2  1  FeoC            FeoC like transcriptional regulator
      0.084   12.6   0.0      0.097   12.4   0.0    1.1  1  AphA_like       Putative AphA-like transcriptional regulator
       0.12   12.4   0.0       0.16   12.0   0.0    1.3  1  HTH_Crp_2       Crp-like helix-turn-helix domain


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.2   5.3e-08   0.00011      13      62 ..      30      80 ..      20      87 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 5.3e-08
                                      HCHHHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEE CS
                              TrmB 13 vYlaLl.klgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklY 62
                                      +Y+ L+ k+   + ++++eel+ p +   ++L+ Le+ GlVe+  g+ k +
  gi|242398438|ref|YP_002993862.1| 30 IYKLLVtKKRATSLQKLSEELETPMPWLLRMLKTLESEGLVEIFYGNEKAM 80
                                      7999**666666689****************************99996654 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   7.3e-07    0.0015      22      62 ..      37      77 ..      22      87 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 7.3e-07
                                      TCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT- CS
                              Rrf2 22 eeepvsseeiaerqnispsylekilakLrkaglvksvrGkg 62
                                      +++  s+++++e+ +++ + l ++l++L+ +glv+   G++
  gi|242398438|ref|YP_002993862.1| 37 KKRATSLQKLSEELETPMPWLLRMLKTLESEGLVEIFYGNE 77
                                      445599*****************************999986 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   1.2e-06    0.0023      14      49 ..      36      71 ..      30      71 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.2e-06
                                      TTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR 14 eapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                      +  ++ +l+ l++++  p +   R+L+tL+ +G+ve
  gi|242398438|ref|YP_002993862.1| 36 TKKRATSLQKLSEELETPMPWLLRMLKTLESEGLVE 71
                                      5567789****************************7 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   4.3e-06    0.0086      15      55 ..      30      71 ..      18      72 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.3e-06
                                      HHHHH.STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                            HTH_20 15 ilraL.araegltaselaerldlskntlsyHLrvLeeagLve 55
                                      i+++L + +++ ++  l e+l++++  l + L++Le+ gLve
  gi|242398438|ref|YP_002993862.1| 30 IYKLLvTKKRATSLQKLSEELETPMPWLLRMLKTLESEGLVE 71
                                      5566688999*******************************8 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 ?   13.5   0.1   3.1e-05     0.063      12      53 ..      29      71 ..      28      75 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.1e-05
                                      HHHHHHH.HHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                    Fe_dep_repress 12 tIYtlse.ekkvvktkdlaerLnvspssVsemlkkLekdGyve 53
                                      +IY+l   +k   + ++l+e+L+   +    mlk Le++G+ve
  gi|242398438|ref|YP_002993862.1| 29 VIYKLLVtKKRATSLQKLSEELETPMPWLLRMLKTLESEGLVE 71
                                      7999999777788899**************************8 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   3.8e-05     0.077      16      48 ..      39      71 ..      33      72 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.8e-05
                                      TTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR 16 gplsvseLakklgvskstvtrvldrLekkGlie 48
                                       + s+++L + l++  + + r+l++Le +Gl+e
  gi|242398438|ref|YP_002993862.1| 39 RATSLQKLSEELETPMPWLLRMLKTLESEGLVE 71
                                      578999*************************97 PP

>> FeoC  FeoC like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   4.2e-05     0.083       8      45 ..      34      71 ..      29      75 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.2e-05
                              FeoC  8 yleergrvslkeLsrhfkaspealeamLeqwvrkGrve 45
                                      ++ +++  sl++Ls ++++ +  l  mL +++  G ve
  gi|242398438|ref|YP_002993862.1| 34 LVTKKRATSLQKLSEELETPMPWLLRMLKTLESEGLVE 71
                                      46778888**************************9987 PP

>> AphA_like  Putative AphA-like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   4.9e-05     0.097       6      68 ..      10      76 ..       5      86 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.9e-05
                         AphA_like  6 ltpkeavrLvvLGlieraplrysel.....agavrhlvsriagPsldLlgsslellreeGLveavdGe 68
                                      +  k+ +   vLG+++r+ + y+ l     a++ ++l + +  P   Ll   l  l  eGLve   G+
  gi|242398438|ref|YP_002993862.1| 10 IRIKDNITFGVLGMVARKNVIYKLLvtkkrATSLQKLSEELETPMPWLLR-MLKTLESEGLVEIFYGN 76
                                      56799*************99997654444488999999999999888775.5999*******988554 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 ?   12.0   0.0   7.9e-05      0.16      23      67 ..      42      90 ..      23      91 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.9e-05
                                      HHHHHHHHTTSSHHHHHHHHHHHHHTTSEE..ET.EE.EEES-HHHHHH CS
                         HTH_Crp_2 23 tqeelAsmlGltretvsrilseLkreglis..rg.rr.irildleaLra 67
                                      + + l++ l +    + r+l+ L+ egl++   g  + ++    + L++
  gi|242398438|ref|YP_002993862.1| 42 SLQKLSEELETPMPWLLRMLKTLESEGLVEifYGnEKaMIMVKAKTLED 90
                                      55778888999999999*************8545234688888877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 610.96
//
Query:       gi|242398439|ref|YP_002993863.1|  [L=419]
Description: 23S rRNA (Uracil-5-)-methyltransferase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-23   82.2   0.3    6.6e-21   74.7   0.1    2.5  2  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
    3.4e-08   33.5   0.1    6.5e-08   32.6   0.1    1.4  1  Met_10           Met-10+ like-protein
    9.8e-08   31.7   0.0    1.8e-07   30.9   0.0    1.4  1  MTS              Methyltransferase small domain
      6e-05   23.7   0.0    0.00022   21.8   0.0    2.0  1  Methyltransf_25  Methyltransferase domain
    0.00014   21.7   0.0    0.00032   20.5   0.0    1.6  1  Methyltransf_31  Methyltransferase domain
    0.00017   21.1   0.0    0.00027   20.4   0.0    1.3  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    0.00082   19.0   0.0     0.0016   18.0   0.0    1.5  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
      0.001   18.7   0.0      0.002   17.8   0.0    1.4  1  Cons_hypoth95    Conserved hypothetical protein 95
     0.0034   17.2   0.0     0.0094   15.8   0.0    1.8  1  Methyltransf_23  Methyltransferase domain
  ------ inclusion threshold ------
       0.01   15.2   0.0      0.017   14.6   0.0    1.3  1  TehB             Tellurite resistance protein TehB


Domain annotation for each model (and alignments):
>> 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 ?   -2.7   0.0       1.2   2.2e+03       2      39 ..      81     115 ..      80     120 .. 0.65
   2 !   74.7   0.1   3.7e-24   6.6e-21     169     350 ..     246     409 ..     235     416 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.2
                   tRNA_U5-meth_tr   2 yeaqleekksrlkkllaefeapelevfespe.ehyrlra 39 
                                       ye+ql+ k+++l++ll+     ++ev  sp+   yr r 
  gi|242398439|ref|YP_002993863.1|  81 YEEQLKFKEQKLSELLE----MNVEVLPSPKiYDYRNRI 115
                                       78888888888888775....456666666523466665 PP

  == domain 2  score: 74.7 bits;  conditional E-value: 3.7e-24
                   tRNA_U5-meth_tr 169 elvyrqvensftqPnaavnekmleWalevtqeskgdllelycGnGnfslalarnfekvlateiakssveaaqyniaa 245
                                       +++y    nsf q n+  + ++++ + + ++ +k  +l+ly G G f + lar+  kv   e+   +ve+a  n   
  gi|242398439|ref|YP_002993863.1| 246 DVTYLIHPNSFFQTNSYQAVNLVKKVGDFVEGEK--VLDLYSGVGTFGIYLARRGFKVEGIEVNPFAVEMANRNARI 320
                                       57888999******************99998765..8**************************************99 PP

                   tRNA_U5-meth_tr 246 nkidnvqiirlsaeeltealkkkrefrrlkgidlksyafetifvdPPraGldketvk.lvkk.yerilyiscnPetl 320
                                       n+++          e+   + + re r      l  y  +t++vdPPraGl ++ +k l+k+  e ++y+scnP+t+
  gi|242398439|ref|YP_002993863.1| 321 NEVNA---------EFK--VGEDREVRD-----LGVY--DTLIVDPPRAGLHPKLIKkLLKDpPETLVYVSCNPRTF 379
                                       99863.........554..556777764.....4444..79***********9988536666257899********* PP

                   tRNA_U5-meth_tr 321 kenleelsethrverlalfdqfpythhles 350
                                        enl++l+e + +e++  +d fp+t+h+e 
  gi|242398439|ref|YP_002993863.1| 380 SENLKKLKEGYAIEEIVALDMFPHTPHIEI 409
                                       ****************************96 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.1   3.6e-11   6.5e-08      98     155 ..     274     329 ..     255     360 .. 0.82

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 3.6e-11
                                       --TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEE CS
                            Met_10  98 veegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkp 155
                                       + ege V+d++ G+G f i +a+  ++ +v +i++nP +v++ ++n + N+v+   k+
  gi|242398439|ref|YP_002993863.1| 274 FVEGEKVLDLYSGVGTFGIYLAR--RGFKVEGIEVNPFAVEMANRNARINEVNAEFKV 329
                                       679********************..9**************************998843 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.0   9.8e-11   1.8e-07      31     129 ..     276     369 ..     250     371 .. 0.86

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 9.8e-11
                                       TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEEEEE---S CS
                               MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekkfdlivsNPPf 107
                                       + +kvlDl +G+G  g+ la++  +  v+ ++v+  A+e+a++n++ n++++e+   +  e  + + +d+++  PP 
  gi|242398439|ref|YP_002993863.1| 276 EGEKVLDLYSGVGTFGIYLARRGFK--VEGIEVNPFAVEMANRNARINEVNAEFKVGEDREVRDLGVYDTLIVDPP- 349
                                       5689*****************8877..9**************************999999999999**********. PP

                                       TTTCHCHHHHHHHHHHHHHHHE CS
                               MTS 108 hagkatelavaeeliaeAkeaL 129
                                       +ag +   +++++l+++ +e L
  gi|242398439|ref|YP_002993863.1| 350 RAGLH--PKLIKKLLKDPPETL 369
                                       66666..677777777766655 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   1.2e-07   0.00022       1      58 [.     280     335 ..     280     362 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.2e-07
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGB CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedl 58 
                                       vLdl  G G++ ++la+r+   kv g+++++ ++e a+++a+ +++n+ef +g+ +++
  gi|242398439|ref|YP_002993863.1| 280 VLDLYSGVGTFGIYLARRG--FKVEGIEVNPFAVEMANRNARINEVNAEFKVGEDREV 335
                                       8*****************5..*********************9*******99876554 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   1.8e-07   0.00032       4      79 ..     277     345 ..     275     403 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.8e-07
                   Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlil 79 
                                       g +vlDl +G G++++ la + g+  +v Gi+ +++a+e A+ na+ +++ n+eF++g+  e   l     +D ++
  gi|242398439|ref|YP_002993863.1| 277 GEKVLDLYSGVGTFGIYLA-RRGF--KVEGIEVNPFAVEMANRNARINEV-NAEFKVGEDREVRDL---GVYDTLI 345
                                       679****************.4454..677*******************99.8****9986665543...4455555 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   1.5e-07   0.00027     161     222 ..     276     336 ..     263     347 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.5e-07
                              PrmA 161 egeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseell 222
                                       ege+vlD+  G G   i  a+ g  kv ++ +++ Av++a++Na++N+v+a+++v   +e+ 
  gi|242398439|ref|YP_002993863.1| 276 EGEKVLDLYSGVGTFGIYLARRGF-KVEGIEVNPFAVEMANRNARINEVNAEFKVGEDREVR 336
                                       6899*****************997.69**************************996655554 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   9.1e-07    0.0016       3      50 ..     279     326 ..     277     354 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 9.1e-07
                   Methyltransf_15   3 vilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdk 50 
                                        +lDl+sG G   i +a+ + kv +ie+n+  +++a++Na++ +v+ +
  gi|242398439|ref|YP_002993863.1| 279 KVLDLYSGVGTFGIYLARRGFKVEGIEVNPFAVEMANRNARINEVNAE 326
                                       79*****************99*********************999865 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   1.1e-06     0.002      39     136 ..     271     361 ..     261     392 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.1e-06
                                       C...HCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS- CS
                     Cons_hypoth95  39 e...iegarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkke 112
                                           +eg++vLDl++G G+ g+  + Rg  k+  +e ++ av++ ++n +  +++   ae+k  + ++++ l    +
  gi|242398439|ref|YP_002993863.1| 271 VgdfVEGEKVLDLYSGVGTFGIYLARRG-FKVEGIEVNPFAVEMANRNARINEVN---AEFKVGEDREVRDL----G 339
                                       3444899***************988777.67999**************9888866...56666666666666....6 PP

                                       EEEEEEE--SSSTTCH.HHHHHHH CS
                     Cons_hypoth95 113 efdivflDPPyakellieevlell 136
                                       ++d   +DPP a      +++++l
  gi|242398439|ref|YP_002993863.1| 340 VYDTLIVDPPRAGL-H-PKLIKKL 361
                                       8999*****95543.2.5555554 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   5.2e-06    0.0094      22      62 ..     276     322 ..     257     412 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5.2e-06
                   Methyltransf_23  22 aggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae......k 62 
                                       +g +vLd+  G+G++  +l+++gf+v+g++ +p ave+a       +
  gi|242398439|ref|YP_002993863.1| 276 EGEKVLDLYSGVGTFGIYLARRGFKVEGIEVNPFAVEMANrnarinE 322
                                       5679*********************************9976554431 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   9.4e-06     0.017      21      77 ..     267     323 ..     249     342 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 9.4e-06
                                       HHHHHCCCS-S-EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHTT- CS
                              TehB  21 evveavkivkpgkvldlgcgqgrnslylsllgydvtawdknensiafleeikekenl 77 
                                        v++  + v+  kvldl  g g   +yl+  g++v+ ++ n  ++++ ++ + ++++
  gi|242398439|ref|YP_002993863.1| 267 LVKKVGDFVEGEKVLDLYSGVGTFGIYLARRGFKVEGIEVNPFAVEMANRNARINEV 323
                                       355566778999*****************************9999988887766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (419 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      575  (0.0320709); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.47
# Mc/sec: 2668.37
//
Query:       gi|242398440|ref|YP_002993864.1|  [L=141]
Description: HTH-type transcriptional regulator lrpA [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-14   53.1   1.0    3.4e-14   52.4   1.0    1.4  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    5.4e-14   51.5   0.4    8.8e-14   50.8   0.4    1.4  1  HTH_24          Winged helix-turn-helix DNA-binding
    1.1e-12   47.8   0.0    1.8e-12   47.1   0.0    1.4  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
    6.5e-08   32.4   0.2    1.1e-07   31.7   0.2    1.4  1  HTH_11          HTH domain
    5.8e-06   26.3   0.0    1.2e-05   25.3   0.0    1.5  1  HTH_20          Helix-turn-helix domain
    1.2e-05   25.0   0.0    2.2e-05   24.1   0.0    1.4  1  HTH_IclR        IclR helix-turn-helix domain
      2e-05   24.0   0.3    5.6e-05   22.6   0.3    1.8  1  Sigma70_r4      Sigma-70, region 4
    2.2e-05   24.2   0.1    2.9e-05   23.8   0.1    1.3  1  HxlR            HxlR-like helix-turn-helix
    9.2e-05   22.3   0.1    0.00029   20.7   0.1    1.7  2  MarR_2          MarR family
    0.00018   21.1   0.3    0.00034   20.3   0.2    1.5  1  HTH_DeoR        DeoR-like helix-turn-helix domain
    0.00041   20.0   0.1     0.0014   18.3   0.1    1.8  1  Sigma70_r4_2    Sigma-70, region 4
    0.00044   20.2   0.0    0.00081   19.4   0.0    1.4  1  HTH_Mga         M protein trans-acting positive regulator (MG
    0.00068   19.7   0.1     0.0011   19.1   0.1    1.3  1  HTH_28          Helix-turn-helix domain
    0.00073   19.4   0.0     0.0023   17.8   0.1    1.8  2  MarR            MarR family
     0.0014   18.3   0.1     0.0022   17.7   0.1    1.3  1  HTH_23          Homeodomain-like domain
     0.0017   18.2   0.0     0.0028   17.5   0.0    1.4  1  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0019   17.9   0.0     0.0046   16.7   0.0    1.6  1  HTH_10          HTH DNA binding domain
     0.0026   18.1   0.1     0.0046   17.3   0.1    1.3  1  FaeA            FaeA-like protein
     0.0033   17.3   0.0     0.0084   16.0   0.0    1.7  1  HTH_36          Helix-turn-helix domain
      0.004   16.5   0.1     0.0074   15.7   0.1    1.3  1  HTH_Tnp_ISL3    Helix-turn-helix domain of transposase family
     0.0059   16.9   0.0      0.018   15.3   0.0    1.7  1  Rrf2            Transcriptional regulator
     0.0086   15.9   0.0      0.014   15.2   0.0    1.4  1  HTH_5           Bacterial regulatory protein, arsR family
  ------ inclusion threshold ------
      0.011   15.3   0.0      0.027   14.1   0.0    1.8  1  HTH_50          Helix-turn-helix domain
      0.011   16.1   0.1      0.018   15.4   0.1    1.4  1  DUF2805         Protein of unknown function (DUF2805)
      0.012   15.7   0.0      0.019   15.1   0.0    1.3  1  HTH_9           RNA polymerase III subunit RPC82 helix-turn-h
      0.012   16.0   0.1      0.019   15.4   0.1    1.4  1  HTH_27          Winged helix DNA-binding domain
      0.015   14.9   0.1      0.026   14.1   0.1    1.4  1  GerE            Bacterial regulatory proteins, luxR family
      0.015   15.2   0.4      0.037   14.0   0.2    1.8  2  HTH_Crp_2       Crp-like helix-turn-helix domain
      0.018   14.8   0.0      0.031   14.1   0.0    1.5  1  LexA_DNA_bind   LexA DNA binding domain
      0.021   14.9   0.0      0.036   14.1   0.0    1.3  1  HTH_29          Winged helix-turn helix
      0.021   15.4   0.0      0.071   13.7   0.0    1.7  2  Mga             Mga helix-turn-helix domain
      0.023   14.6   0.0      0.048   13.6   0.0    1.6  1  HTH_12          Ribonuclease R winged-helix domain
       0.03   14.3   0.0      0.055   13.4   0.0    1.4  1  HTH_1           Bacterial regulatory helix-turn-helix protein
      0.039   14.2   0.0      0.068   13.4   0.0    1.4  1  DUF2774         Protein of unknown function (DUF2774)
      0.044   13.8   0.0      0.074   13.1   0.0    1.3  1  NapD            NapD protein
      0.046   13.4   0.1      0.079   12.6   0.1    1.4  1  GntR            Bacterial regulatory proteins, gntR family
      0.065   12.9   0.0       0.12   12.1   0.0    1.4  1  DUF4423         Domain of unknown function (DUF4423)
      0.081   12.8   0.0       0.16   11.8   0.0    1.5  1  P22_Cro         DNA-binding transcriptional regulator Cro
      0.086   12.8   0.0       0.15   12.1   0.0    1.4  1  RWP-RK          RWP-RK domain
       0.12   11.7   0.2       0.21   11.0   0.0    1.4  1  RepL            Firmicute plasmid replication protein (RepL)
       0.13   12.5   0.0       0.24   11.6   0.0    1.4  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
       0.16   11.8   0.0       0.46   10.3   0.0    1.8  1  HTH_30          PucR C-terminal helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.4   1.0   7.9e-17   3.4e-14       1      42 []       2      43 ..       2      43 .. 0.98

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 7.9e-17
                     HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrLe 42
                                      LDe Dr I+e L +daR++++e+A+++G+Se++v++Rvr Le
  gi|242398440|ref|YP_002993864.1|  2 LDERDRIIIEMLTRDARTPFTEIAKALGISETAVRKRVRSLE 43
                                      8**************************************998 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.8   0.4   2.1e-16   8.8e-14       1      48 []       2      49 ..       2      49 .. 0.98

  Alignments for each domain:
  == domain 1  score: 50.8 bits;  conditional E-value: 2.1e-16
                            HTH_24  1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      lde dr I+e L +++r++ +e+A++lg+S ++v++r++ Lee+G++k
  gi|242398440|ref|YP_002993864.1|  2 LDERDRIIIEMLTRDARTPFTEIAKALGISETAVRKRVRSLEEKGILK 49
                                      79********************************************86 PP

>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.1   0.0   4.2e-15   1.8e-12       3      75 .]      70     139 ..      64     139 .. 0.91

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 4.2e-15
                                       EEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEEE CS
                    AsnC_trans_reg   3 vslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivlet 75 
                                       v ++   pe l e++ +l+e++ V+e+y  +Gd+ +++++++rd  +l +++++k+++++gv+++   i+le+
  gi|242398440|ref|YP_002993864.1|  70 VDTT---PERLFEVASKLKEFEFVRELYLSSGDHMIMAEIWARDGGDLADIMSNKIGKIDGVTKVCPAIILER 139
                                       4455...45599**********************************************************985 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.2   2.6e-10   1.1e-07       5      54 ..       9      62 ..       5      63 .. 0.89

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 2.6e-10
                            HTH_11  5 ilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg....vpIesepgr.GY 54
                                      i+e+L   +   +  e+A+ L++S+++vr+++++Lee+g    + I  +p++ GY
  gi|242398440|ref|YP_002993864.1|  9 IIEML-TRDARTPFTEIAKALGISETAVRKRVRSLEEKGilkqYTIRVDPQKlGY 62
                                      77888.55555999************************************99999 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   2.7e-08   1.2e-05      15      57 ..       9      51 ..       2      54 .. 0.92

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 2.7e-08
                                      HHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                            HTH_20 15 ilraLaraegltaselaerldlskntlsyHLrvLeeagLvevv 57
                                      i  +L+r++   ++e+a++l++s + +++++r Lee g++++ 
  gi|242398440|ref|YP_002993864.1|  9 IIEMLTRDARTPFTEIAKALGISETAVRKRVRSLEEKGILKQY 51
                                      8899***********************************9876 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   5.3e-08   2.2e-05       8      50 ..       9      50 ..       8      51 .. 0.96

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 5.3e-08
                                      HHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR  8 iLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      i+++l++ ++   ++e+A+++g++ ++v+  +++L+e G+++q
  gi|242398440|ref|YP_002993864.1|  9 IIEMLTRDART-PFTEIAKALGISETAVRKRVRSLEEKGILKQ 50
                                      78999999998.9****************************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 !   22.6   0.3   1.3e-07   5.6e-05       5      42 ..       2      40 ..       1      49 [. 0.89

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.3e-07
                                      S-HHHHHHHHHHH.TTT--HHHHHHHHTS-HHHHHHHHH CS
                        Sigma70_r4  5 Lpererevlelrf.geglTleEIgerlgiSrerVrqiek 42
                                      L+er+r ++e+   +   ++ EI++ lgiS+ +Vr + +
  gi|242398440|ref|YP_002993864.1|  2 LDERDRIIIEMLTrDARTPFTEIAKALGISETAVRKRVR 40
                                      99*********9999999************998888765 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.1   6.8e-08   2.9e-05      10      66 ..       8      65 ..       1      88 [. 0.83

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 6.8e-08
                                      HHHHHTT..S-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE- CS
                              HxlR 10 ilvellk..gkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYslt 66
                                      i++e+l+   +  f+e+++al +is+    +r r Le++g++++ ++   P+k  Y+l 
  gi|242398440|ref|YP_002993864.1|  8 IIIEMLTrdARTPFTEIAKAL-GISETAVRKRVRSLEEKGILKQYTIRVDPQKLGYNLV 65
                                      44444441255569*******.9*********************************985 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.1   6.7e-07   0.00029      10      52 ..       8      49 ..       5      57 .. 0.84
   2 ?   -1.9   0.0       7.5   3.2e+03       6      22 ..      98     114 ..      95     117 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 6.7e-07
                                      HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                            MarR_2 10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                                      ++ +   r+ r    +e+a++lg+s  av ++++ L+++G + 
  gi|242398440|ref|YP_002993864.1|  8 IIIEMLTRDAR-TPFTEIAKALGISETAVRKRVRSLEEKGILK 49
                                      55566666665.699*************************875 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 7.5
                                       HHHHHHHHHHCTTTSEE CS
                            MarR_2   6 aqarvLaaLgrrpgrdl 22 
                                        +++++a++ +r+g+dl
  gi|242398440|ref|YP_002993864.1|  98 GDHMIMAEIWARDGGDL 114
                                       57889999999999765 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.2   8.1e-07   0.00034       1      45 [.       5      49 ..       5      52 .. 0.95

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 8.1e-07
                          HTH_DeoR  1 RieqilellkqqgklsveelvellgvSeaTiRRDLneLeeqgllt 45
                                      R+  i+e+l ++     +e++  lg+Se+ +R+  + Lee+g+l+
  gi|242398440|ref|YP_002993864.1|  5 RDRIIIEMLTRDARTPFTEIAKALGISETAVRKRVRSLEEKGILK 49
                                      7889**************************************986 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1   3.3e-06    0.0014      11      47 ..       2      39 ..       1      41 [. 0.81

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.3e-06
                                      S-HHHHHHHHHHHTS.---HHHHHHHHT--HHHHHHHH CS
                      Sigma70_r4_2 11 Lperqreifllryle.glsykEIAellgisegtVksrl 47
                                      L er+r i+++   +   +  EIA+ lgise++V++r+
  gi|242398440|ref|YP_002993864.1|  2 LDERDRIIIEMLTRDaRTPFTEIAKALGISETAVRKRV 39
                                      788889999875444156899**************997 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 !   19.4   0.0   1.9e-06   0.00081       5      45 ..       4      43 ..       3      50 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.9e-06
                           HTH_Mga  5 krklkLlelLteneksltldelakeLglseltlqsdiseLn 45
                                      +r+  ++e Lt  + +++ +e+ak+Lg+se +++++++ L 
  gi|242398440|ref|YP_002993864.1|  4 ERDRIIIEMLTR-DARTPFTEIAKALGISETAVRKRVRSLE 43
                                      57889*******.***********************99886 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.1   2.5e-06    0.0011       4      41 ..       7      47 ..       4      52 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 2.5e-06
                            HTH_28  4 eiiklla.aGh..svreaArelgisrrtvyrWikryeegGi 41
                                      +ii +++ +    + +e+A++lgis++ v++ ++ +ee Gi
  gi|242398440|ref|YP_002993864.1|  7 RIIIEMLtRDArtPFTEIAKALGISETAVRKRVRSLEEKGI 47
                                      566666644323699***********************998 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   5.3e-06    0.0023      18      50 ..      19      51 ..       9      56 .. 0.85
   2 ?   -2.0   0.0       8.4   3.6e+03       2      22 ..      96     116 ..      95     120 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 5.3e-06
                                      EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR 18 lsvseLakklgvskstvtrvldrLekkGlieRs 50
                                         +e+ak+lg+s ++v + ++ Le+kG ++ +
  gi|242398440|ref|YP_002993864.1| 19 TPFTEIAKALGISETAVRKRVRSLEEKGILKQY 51
                                      5689************************98765 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 8.4
                                       -HHHHHHHHHHHHSTTEEHHH CS
                              MarR   2 tltqfviLrilyeqgplsvse 22 
                                       +   ++i++ ++ +++  +++
  gi|242398440|ref|YP_002993864.1|  96 SSGDHMIMAEIWARDGGDLAD 116
                                       667788899998887655555 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   5.2e-06    0.0022      10      46 ..       9      47 ..       1      49 [. 0.76

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 5.2e-06
                            HTH_23 10 illllae..GlsvreIAreLgvsrrTvyrwlkryreeGl 46
                                      i+ +l +  + + +eIA++Lg+s+  v++ ++  +e+G+
  gi|242398440|ref|YP_002993864.1|  9 IIEMLTRdaRTPFTEIAKALGISETAVRKRVRSLEEKGI 47
                                      44444445788999**************88888788985 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   6.7e-06    0.0028      25      55 ..      21      51 ..      10      68 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 6.7e-06
                                      HCHHCCCTTSSCHCHHHHHHHHHHCTSEEEE CS
                              TrmB 25 adeiaeelgvprskvYevLrsLedkGlVere 55
                                       +eia++lg++++ v + +rsLe+kG+ +  
  gi|242398440|ref|YP_002993864.1| 21 FTEIAKALGISETAVRKRVRSLEEKGILKQY 51
                                      479***********************98765 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.1e-05    0.0046      24      50 ..      19      45 ..      15      47 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.1e-05
                            HTH_10 24 vtlkeLAkelGIskstlsehLrkaesk 50
                                      +   e+Ak+lGIs++++ +++r+ e+k
  gi|242398440|ref|YP_002993864.1| 19 TPFTEIAKALGISETAVRKRVRSLEEK 45
                                      55689******************9998 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   1.1e-05    0.0046       5      51 ..       9      54 ..       5      56 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.1e-05
                                      HHHHHHH.S----HHHHHHHHTS-HHHHHHHHHHHHHHSSEEEE--S CS
                              FaeA  5 IleylnsikapckTreiAdalglsaYQaRyYLeqLekegkikrspvr 51
                                      I+e l++  a    +eiA+alg+s   +R     Le +g +k+  +r
  gi|242398440|ref|YP_002993864.1|  9 IIEMLTR-DARTPFTEIAKALGISETAVRKRVRSLEEKGILKQYTIR 54
                                      7888888.8888889**************************987776 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0     2e-05    0.0084      29      55 .]      22      48 ..      17      48 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2e-05
                            HTH_36 29 etlakrlglsknTvsraikeLeqlGyi 55
                                        +ak+lg+s+  v++ +++Le++G++
  gi|242398440|ref|YP_002993864.1| 22 TEIAKALGISETAVRKRVRSLEEKGIL 48
                                      57***********************97 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   1.7e-05    0.0074      21      50 ..      10      41 ..       8      42 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.7e-05
                      HTH_Tnp_ISL3 21 lellles..rsvkavArqlgvSwtTVwrildr 50
                                      +e+l+++   +++++A+ lg+S+t V+ ++++
  gi|242398440|ref|YP_002993864.1| 10 IEMLTRDarTPFTEIAKALGISETAVRKRVRS 41
                                      5666666678****************998875 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   4.3e-05     0.018      20      56 ..      13      49 ..       7      52 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.3e-05
                                      SSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2 20 eeeeepvsseeiaerqnispsylekilakLrkaglvk 56
                                        ++     +eia+  +is++ ++k ++ L+++g++k
  gi|242398440|ref|YP_002993864.1| 13 LTRDARTPFTEIAKALGISETAVRKRVRSLEEKGILK 49
                                      3344447899************************997 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   3.4e-05     0.014       6      46 ..       8      49 ..       3      50 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.4e-05
                                      HHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  6 kILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                       I+ +L +   + ++e+a++lg+s+ +v+   + L+e G+++
  gi|242398440|ref|YP_002993864.1|  8 IIIEMLTRdARTPFTEIAKALGISETAVRKRVRSLEEKGILK 49
                                      57888888566789*************************985 PP

>> HTH_50  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   6.2e-05     0.027      28      45 ..      23      40 ..       1      43 [. 0.86

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.2e-05
                            HTH_50 28 klAkrLGvShtaianklr 45
                                       +Ak+LG+S ta+ +++r
  gi|242398440|ref|YP_002993864.1| 23 EIAKALGISETAVRKRVR 40
                                      58**************98 PP

>> DUF2805  Protein of unknown function (DUF2805)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.1   4.1e-05     0.018       3      33 ..       9      40 ..       6      58 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 4.1e-05
                           DUF2805  3 iiemAweD.RtpFeaIeeqfglsekeviklMr 33
                                      iiem   D RtpF  I++  g+se  v k  r
  gi|242398440|ref|YP_002993864.1|  9 IIEMLTRDaRTPFTEIAKALGISETAVRKRVR 40
                                      678865554*****************988766 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 ?   15.1   0.0   4.4e-05     0.019      11      51 ..       2      42 ..       1      48 [. 0.90

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.4e-05
                                      STTHHHHHHHHHHHHSSBEHHHHHHHHSSTHHHHHHHHHHH CS
                             HTH_9 11 FGevvakVvetLlrkgrltlrelvkktkLsldqVkksLvvL 51
                                      ++e+ + ++e+L r +r + +e++k++++s + V+k + +L
  gi|242398440|ref|YP_002993864.1|  2 LDERDRIIIEMLTRDARTPFTEIAKALGISETAVRKRVRSL 42
                                      5677789****************************987666 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 ?   15.4   0.1   4.6e-05     0.019       4      49 ..       5      49 ..       2      60 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 4.6e-05
                            HTH_27  4 qqalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLve 49
                                       ++++++ +  r++r   ++++++l ++ +++ + ++ L+ekG ++
  gi|242398440|ref|YP_002993864.1|  5 RDRIIIEMLT-RDARTPFTEIAKALGISETAVRKRVRSLEEKGILK 49
                                      6778888888.9999999*************************884 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1     6e-05     0.026       3      44 ..       2      45 ..       1      45 [. 0.82

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6e-05
                                      S-HHHHHHHHHHCTTS-H..HHHHHHHTS-HHHHHHHHHHHHHH CS
                              GerE  3 LskRErevLrllaeGksn..keIAeelniSekTVkvhksnimkK 44
                                      L++R r + ++l+    +  +eIA++l+iSe+ V+  ++++ +K
  gi|242398440|ref|YP_002993864.1|  2 LDERDRIIIEMLTRDARTpfTEIAKALGISETAVRKRVRSLEEK 45
                                      778888888888888765448*************9999888666 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 ?   14.0   0.2   8.8e-05     0.037      25      65 ..      22      60 ..       2      61 .. 0.86
   2 ?   -1.9   0.0       8.1   3.4e+03      33      47 ..      72      86 ..      70      93 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 8.8e-05
                                      HHHHHHTTSSHHHHHHHHHHHHHTTSEEETEEEEES-HHHH CS
                         HTH_Crp_2 25 eelAsmlGltretvsrilseLkreglisrgrririldleaL 65
                                      +e+A  lG++   v +  + L+++g++++ + ir+ d+++L
  gi|242398440|ref|YP_002993864.1| 22 TEIAKALGISETAVRKRVRSLEEKGILKQYT-IRV-DPQKL 60
                                      69**************************876.776.66665 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 8.1
                                      SSHHHHHHHHHHHHH CS
                         HTH_Crp_2 33 ltretvsrilseLkr 47
                                      +t+e +  + s+Lk+
  gi|242398440|ref|YP_002993864.1| 72 TTPERLFEVASKLKE 86
                                      899999999999986 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   7.2e-05     0.031      29      57 ..      22      49 ..       2      58 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7.2e-05
                                      HHHHHHHTS-.HHHHHHHHHHHHHTTSEE CS
                     LexA_DNA_bind 29 reiaralglkSpsaveehLkaLerKGyie 57
                                       eia+alg++   av ++ + Le KG+++
  gi|242398440|ref|YP_002993864.1| 22 TEIAKALGIS-ETAVRKRVRSLEEKGILK 49
                                      69*******7.99*************986 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   8.4e-05     0.036      17      41 ..      23      47 ..      19      59 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8.4e-05
                            HTH_29 17 qiAkllglsrrtvyrwlkrfeegGl 41
                                      +iAk+lg+s++ v++ ++  ee+G+
  gi|242398440|ref|YP_002993864.1| 23 EIAKALGISETAVRKRVRSLEEKGI 47
                                      8***********************7 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   0.00017     0.071      21      66 ..       9      56 ..       4      65 .. 0.84
   2 ?   -1.3   0.0       8.1   3.5e+03      34      44 ..      87      97 ..      77     101 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00017
                                      HHHHHHHHSEEEHHHHHHHCT--HHHHHHHHHHHHH..HCHCCT-EEE CS
                               Mga 21 llkflfeeeevsieelaqelyiSestlkrkikelnk..lLkefdlelt 66
                                      +++ l  ++++ ++e+a+ l iSe+ + + ++ l++   Lk++ +++ 
  gi|242398440|ref|YP_002993864.1|  9 IIEMLTRDARTPFTEIAKALGISETAVRKRVRSLEEkgILKQYTIRVD 56
                                      567777999***********************9987447999999883 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 8.1
                                      HHHHHHCT--H CS
                               Mga 34 eelaqelyiSe 44
                                       e+ +ely+S+
  gi|242398440|ref|YP_002993864.1| 87 FEFVRELYLSS 97
                                      47888999997 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 ?   13.6   0.0   0.00011     0.048      30      50 ..      30      50 ..      20      67 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00011
                            HTH_12 30 igeravRyrLrkleergltrr 50
                                      i+e avR r r+lee+g+ ++
  gi|242398440|ref|YP_002993864.1| 30 ISETAVRKRVRSLEEKGILKQ 50
                                      89***************7765 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   0.00013     0.055      16      39 ..      21      44 ..      17      46 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00013
                                      HHHHHHHHTS-HHHHHHHHHHHHH CS
                             HTH_1 16 ftrAAeeLglsqpavsrqikrLEe 39
                                      ft+ A++Lg+s  av +++++LEe
  gi|242398440|ref|YP_002993864.1| 21 FTEIAKALGISETAVRKRVRSLEE 44
                                      6777*******************8 PP

>> DUF2774  Protein of unknown function (DUF2774)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   0.00016     0.068       6      38 ..      10      43 ..       5      52 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00016
                           DUF2774  6 vhfl.hesgknFveIAkkldirakdvaklwveve 38
                                      + +l +++   F eIAk+l+i+ + v k + + e
  gi|242398440|ref|YP_002993864.1| 10 IEMLtRDARTPFTEIAKALGISETAVRKRVRSLE 43
                                      66899*****************999998777665 PP

>> NapD  NapD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00017     0.074       8      68 ..      70     132 ..      65     135 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00017
                              NapD   8 Vqarperlaavkaalaalpgv.EvhasdeegklVvviEaesedeladtiea.iealpgVlsas 68 
                                       V + perl +v+ +l++++ v E++ s+++  +   i a + ++lad++++ i +++gV  + 
  gi|242398440|ref|YP_002993864.1|  70 VDTTPERLFEVASKLKEFEFVrELYLSSGDHMIMAEIWARDGGDLADIMSNkIGKIDGVTKVC 132
                                       7899***************998***************************877*******9885 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   0.00019     0.079      28      54 ..      22      48 ..       5      51 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00019
                                      HHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                              GntR 28 reLaaefgVsrttvReALrrLeaeglv 54
                                       e+a+++g+s t vR+  r Le++g++
  gi|242398440|ref|YP_002993864.1| 22 TEIAKALGISETAVRKRVRSLEEKGIL 48
                                      69***********************98 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00027      0.12      35      70 ..      17      50 ..       8      60 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00027
                           DUF4423 35 fkadpeelakrlrpkisaeevekalefLlklgllkk 70
                                      ++    e+ak+l+  is+  v+k ++ L++ g+lk+
  gi|242398440|ref|YP_002993864.1| 17 ARTPFTEIAKALG--ISETAVRKRVRSLEEKGILKQ 50
                                      4466789******..*******************98 PP

>> P22_Cro  DNA-binding transcriptional regulator Cro
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00038      0.16      14      31 ..      23      40 ..      21      56 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00038
                                      HHHHHHTS-HHHHHHHHT CS
                           P22_Cro 14 kvAkalgvtksAVsqWge 31
                                       +Akalg+++ AV+++  
  gi|242398440|ref|YP_002993864.1| 23 EIAKALGISETAVRKRVR 40
                                      79************9944 PP

>> RWP-RK  RWP-RK domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00034      0.15      10      36 ..      16      42 ..       7      50 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00034
                            RWP-RK 10 yFslplkeAAksLgvskttLKricRel 36
                                          p +e Ak+Lg+s+t+++++ R l
  gi|242398440|ref|YP_002993864.1| 16 DARTPFTEIAKALGISETAVRKRVRSL 42
                                      55678999**************99943 PP

>> RepL  Firmicute plasmid replication protein (RepL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0    0.0005      0.21      80     115 ..      23      55 ..       8      61 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0005
                              RepL  80 elaeetgislktvsetlkileeanilkkkanGvlvi 115
                                       e+a++ gis   v++ ++ lee +ilk+ +   + +
  gi|242398440|ref|YP_002993864.1|  23 EIAKALGISETAVRKRVRSLEEKGILKQYT---IRV 55 
                                       89*************************988...555 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00056      0.24      26      53 ..      22      49 ..      16      52 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00056
                                      HHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                    Fe_dep_repress 26 kdlaerLnvspssVsemlkkLekdGyve 53
                                      +++a++L++s   V + ++ Le++G ++
  gi|242398440|ref|YP_002993864.1| 22 TEIAKALGISETAVRKRVRSLEEKGILK 49
                                      79***********************875 PP

>> HTH_30  PucR C-terminal helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0    0.0011      0.46      16      38 ..      22      44 ..       9      45 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0011
                                      HHHHHHHTS-HHHHHHHHHHHHH CS
                            HTH_30 16 satAkaLhvHrnTlryRLrriee 38
                                      ++ AkaL+++   +r+R+r +ee
  gi|242398440|ref|YP_002993864.1| 22 TEIAKALGISETAVRKRVRSLEE 44
                                      789****************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        97  (0.00541023); 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: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 988.06
//
Query:       gi|242398441|ref|YP_002993865.1|  [L=374]
Description: NapA-type sodium/hydrogen antiporter [Thermococcus sibiricus MM 739]
Scores for complete 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  234.7  41.3    1.7e-69  234.4  41.3    1.0  1  Na_H_Exchanger  Sodium/hydrogen exchanger family


Domain annotation for each model (and alignments):
>> Na_H_Exchanger  Sodium/hydrogen exchanger family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  234.4  41.3   9.6e-74   1.7e-69       4     377 ..      10     370 ..       5     374 .] 0.94

  Alignments for each domain:
  == domain 1  score: 234.4 bits;  conditional E-value: 9.6e-74
                                       HHHHHHHHHHHHHHTTSXHHHHHHHHHHHHTTTTTS.....HHHCHCCHHHHCHHCCHHHHCTCGCCTGCCTHHHHH CS
                    Na_H_Exchanger   4 lillallvgllarrlklpeivgliiaGlllGpsglgliepseedlevlselglilllFlaGleldlrelrknlksil 80 
                                       +++ a l+g+++++l++p+++g+i+ Gl++G+++      + e++ ++s+lg+ lllFlaG+e dl e+++++k+++
  gi|242398441|ref|YP_002993865.1|  10 MLAMAKLLGWVFEKLNQPVVLGQILGGLMIGLFVES----N-EIIREFSNLGVLLLLFLAGIESDLTEFKRVGKPSI 81 
                                       44558888889**********************999....7.*********************************** PP

                                       HHHHHHHHHHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC.CCCTSTCCCCCCHHHHHHHHHHHCCC CS
                    Na_H_Exchanger  81 llallgvlitvvliGlllylllilgiplleallfgailsatdpvvvlailkeegrvperlgtlllgesvlnDavavv 157
                                        +a +gv++++v+ G+l+++   + ++++eall+gai+++t++ +++++l e++++++  gt++l+++v++D+++++
  gi|242398441|ref|YP_002993865.1|  82 SVAGVGVIFAFVF-GFLVAY---PFVDFHEALLYGAIMTPTSVSITVRVLMELRKLRSTEGTTILAAAVVDDVLGIL 154
                                       *************.*****7...667*************************************************** PP

                                       CCHHHHHHTXXXXXTSSSTSXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS..CTHHHHHHHHHHHHHHHHHHHHHT CS
                    Na_H_Exchanger 158 llavllalakeeaggetslllllliflvvavgglllglvigwllrlitrft..dddrelevllvlllallaallael 232
                                       ll+v+++l+   + g +++++++ i++ v +++ ++  + ++l++++ +++   d +e+ + ++++++++ a+ ae+
  gi|242398441|ref|YP_002993865.1| 155 LLTVIISLL---REGSIDYITIFEILVEVSGFLAVFLYFGPVLAEKAFKRIshIDLPESTTSFAIIFLIIFAYMAEH 228
                                       *********...99999999999999999999999999999999999999999999********************* PP

                                       SXXXHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHSXHHHHHXXHHHHHHHHHHHHHHHTHHHH CS
                    Na_H_Exchanger 233 lgvsgilgaflaGlvlseyefsnklseklesfreglfnplfFvlvGlsldlkvlnnhlsvlilvllilvaillgril 309
                                       l + +ilga l+Gl++++++++++++  ++ +++++f+plfFv vG+ + ++ +   +  ++++l +l+ai +++il
  gi|242398441|ref|YP_002993865.1| 229 LNLASILGAYLVGLTIGQTSYRKQVENHISILGYSIFIPLFFVEVGMRIEISYIL--HASFFAILYTLAAI-ISKIL 302
                                       ******************************************************4..55555555566665.8**** PP

                                       HHHHHTTTXSSXHHHHHHCCCCSS.BHHHHHHHHHHHHHHXHHHHTTSSTTTCSTSXHHHHHHHHHHH CS
                    Na_H_Exchanger 310 avflllrllglslrealiigfgglqrgavalalaalgpalgllarelyallivvvlftvlvqGlslkp 377
                                       +  + ++l g++l+++l ig+g+++r+ v la++ ++ ++g++  e ++++i +v+ t+++ +  lk+
  gi|242398441|ref|YP_002993865.1| 303 GCGAGAYLAGFDLKSSLRIGIGMIPRLGVELAMLTIALSSGVIGPEGLTIAISMVFATTILTPPLLKW 370
                                       ************************************************************66666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2366.88
//
Query:       gi|242398442|ref|YP_002993866.1|  [L=380]
Description: NapA-type sodium/hydrogen antiporter [Thermococcus sibiricus MM 739]
Scores for 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-72  241.9  39.0    1.1e-71  241.7  39.0    1.0  1  Na_H_Exchanger  Sodium/hydrogen exchanger family


Domain annotation for each model (and alignments):
>> Na_H_Exchanger  Sodium/hydrogen exchanger family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  241.7  39.0   5.9e-76   1.1e-71       2     379 ..       9     377 ..       7     379 .. 0.93

  Alignments for each domain:
  == domain 1  score: 241.7 bits;  conditional E-value: 5.9e-76
                                       HHHHHHHHHHHHHHHHTTSXHHHHHHHHHHHHTTTTTS.....HHHCHCCHHHHCHHCCHHHHCTCGCCTGCCTHHH CS
                    Na_H_Exchanger   2 vllillallvgllarrlklpeivgliiaGlllGpsglgliepseedlevlselglilllFlaGleldlrelrknlks 78 
                                       v+li+ a l+g++a++ k+p  +g++i G+l+Gps+l++++ s e ++++se+g++lllFlaGle+d +e+++++ +
  gi|242398442|ref|YP_002993866.1|   9 VILIV-AKLFGYIATKAKMPGALGQLIGGMLIGPSILNIVSYS-EGVHLISEIGVVLLLFLAGLETDVEEFKRVGVP 83 
                                       44455.8888888*****************************9.********************************* PP

                                       HHHHHHHHHHHHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC.CCCTSTCCCCCCHHHHHHHHHHHC CS
                    Na_H_Exchanger  79 illlallgvlitvvliGlllylllilgiplleallfgailsatdpvvvlailkeegrvperlgtlllgesvlnDava 155
                                       ++l+al+gv+i++v+ G++l+   ++g++ +eal++g+il+at+++++++il e+++++++ gt +l+ +v++D+++
  gi|242398442|ref|YP_002993866.1|  84 SFLIALGGVAIPFVM-GYFLSE--WFGYERTEALFLGGILTATSVGLTVSILMEMKKLRTKEGTAILAGAVVDDILG 157
                                       ***************.*****8..9**************************************************** PP

                                       CCCCHHHHHHTX.XXXXTSSSTSXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCTHHHHHHHHHHHHHHHHHHHHH CS
                    Na_H_Exchanger 156 vvllavllalak.eeaggetslllllliflvvavgglllglvigwllrlitrftdddrelevllvlllallaallae 231
                                       ++ll+ l+a++  +++  e   +l++ ++++++v  l+++ +++ +l+l +r   d +e+ ++++l++ l+ a++ae
  gi|242398442|ref|YP_002993866.1| 158 IILLTTLIAMYRkGHVYIEDVGILIGEVAVFFVVSWLVGKPIVKEFLSLSERI--DLPETLTAFALAITLIFAYIAE 232
                                       ***********966666666666666777777777778889999999999999..********************** PP

                                       TSXXXHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHSXHHHHHXXHHHHHHHHHHHHHHHTHHH CS
                    Na_H_Exchanger 232 llgvsgilgaflaGlvlseyefsnklseklesfreglfnplfFvlvGlsldlkvlnnhlsvlilvllilvaillgri 308
                                        + + gi ga laG++++++++++++s ++  + ++lf+p+f v +G+++d++++   l+  ++++l  v+ ++g+i
  gi|242398442|ref|YP_002993866.1| 233 QFRIAGITGAYLAGVLIAQTDEAKRISNRMITVSYSLFVPVFLVGIGIKTDISII---LHAGTFAILYSVIAIIGKI 306
                                       *****************************999***********************...5666666665555559*** PP

                                       HHHHHHTTTXSSXHHHHHHCCCCSS.BHHHHHHHHHHHHHHXHHHHTTSSTTTCSTSXHHHHHHHHHHHHH CS
                    Na_H_Exchanger 309 lavflllrllglslrealiigfgglqrgavalalaalgpalgllarelyallivvvlftvlvqGlslkpll 379
                                       ++  + + l ++  +eal +g+g+++r +val++a+++ ++++ ++  +++ +++v++t+++ +  lk+++
  gi|242398442|ref|YP_002993866.1| 307 VGCGVGALLARFKPKEALRVGIGMIPRMEVALIMANVALTENVFDKGIFSIPVTMVIITTIITPPLLKWIF 377
                                       *************************************************************8888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       690  (0.0384851); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2536.21
//
Query:       gi|242398443|ref|YP_002993867.1|  [L=185]
Description: hypothetical protein TSIB_0452 [Thermococcus sibiricus MM 739]
Scores for complete 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-27   93.4   5.1    1.6e-12   47.6   0.1    2.3  2  CBS              CBS domain
      0.009   16.0   0.0        1.4    8.9   0.0    2.2  2  Acetyltransf_10  Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
       0.11   13.2   0.3        1.2   10.0   0.0    2.3  2  PulA_N1          Pullulanase N1-terminal 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 !   47.6   0.1   2.7e-16   1.6e-12       4      54 ..      51     100 ..      43     102 .. 0.94
   2 !   47.1   1.5   3.9e-16   2.3e-12       1      55 [.     126     180 ..     126     181 .. 0.97

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 2.7e-16
                                       HSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                               CBS   4 imtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54 
                                       +m +d++tv+p+++l  +++++++++ s++ VVd++g+l+G +t++Dll++
  gi|242398443|ref|YP_002993867.1|  51 VMDKDFLTVHPQDPLTHLIRKFTSEETSAI-VVDDEGRLLGFITMKDLLQF 100
                                       5*********************988899**.******************98 PP

  == domain 2  score: 47.1 bits;  conditional E-value: 3.9e-16
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                       V+dim ++++t++ +++l+ a++lm+e+g ++lPV+d+++k++G++   D++r++
  gi|242398443|ref|YP_002993867.1| 126 VEDIMVTKPITIHIEDNLGHAIKLMIETGKHHLPVIDDEKKVHGLLEVNDIIRLI 180
                                       89***************************88*********************987 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0   0.00023       1.4      20      50 ..      66      96 ..      37     114 .. 0.78
   2 !    5.2   0.0    0.0032        19      20      51 ..     145     176 ..     128     184 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00023
                   Acetyltransf_10 20 ealrerieegealllvaeeggkivGvielrd 50
                                       +l ++++++e+  +v++++g+++G+i+++d
  gi|242398443|ref|YP_002993867.1| 66 THLIRKFTSEETSAIVVDDEGRLLGFITMKD 96
                                      344455569******************9987 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0032
                   Acetyltransf_10  20 ealrerieegealllvaeeggkivGvielrdg 51 
                                       +a++ +ie+g+++l v ++++k+ G +e+ d 
  gi|242398443|ref|YP_002993867.1| 145 HAIKLMIETGKHHLPVIDDEKKVHGLLEVNDI 176
                                       5788899*******************998775 PP

>> PulA_N1  Pullulanase N1-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00019       1.2      32      67 ..      22      57 ..       6      69 .. 0.79
   2 ?    1.0   0.1      0.12   7.4e+02      43      85 .]     140     178 ..     113     178 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00019
                                      SSEEEEEEEEEEEEESSEEEEEEE-SS---TTS--E CS
                           PulA_N1 32 edekieLeikekeeleeevkYvckleeelelgkeyl 67
                                      +++k +L +++keel +++ Y+ k++ ++ ++k+ l
  gi|242398443|ref|YP_002993867.1| 22 TGKKRHLMLQRKEELSHNIRYISKVPVKIVMDKDFL 57
                                      46788999**********************999865 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.12
                                       EEEESSEEEEEEE-SS---TTS--..EEE-TTS-EEEEEE-GGGG CS
                           PulA_N1  43 keeleeevkYvckleeelelgkey..lildehgnktdLqigaViR 85 
                                       + +l++++k        +e gk +  +i de++ +  L++  +iR
  gi|242398443|ref|YP_002993867.1| 140 EDNLGHAIKLM------IETGKHHlpVIDDEKKVHGLLEVNDIIR 178
                                       44444444433......3344444223555555666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1340.77
//
Query:       gi|242398444|ref|YP_002993868.1|  [L=484]
Description: Oxidoreductase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.2e-17   61.8   0.4    1.2e-05   24.7   0.0    3.2  3  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    1.4e-09   38.0   0.3    6.7e-06   25.9   0.1    2.3  2  DAO            FAD dependent oxidoreductase
    1.5e-08   34.2   0.6    0.00027   20.1   0.0    2.4  2  GIDA           Glucose inhibited division protein A
    9.2e-08   31.2   0.1    8.2e-06   24.8   0.1    2.2  2  HI0933_like    HI0933-like protein
    1.1e-07   31.4   0.1    3.3e-07   29.8   0.1    1.8  2  Thi4           Thi4 family
    1.6e-06   27.5   1.5    1.1e-05   24.8   0.2    2.6  3  FAD_binding_2  FAD binding domain
    1.7e-05   25.0   0.0    0.00024   21.3   0.0    2.8  3  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    2.5e-05   23.5   0.3    0.00015   21.0   0.2    1.9  2  Lycopene_cycl  Lycopene cyclase protein
    7.4e-05   23.2   0.4       0.35   11.5   0.1    2.8  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    0.00077   18.8   1.2      0.003   16.9   0.1    2.3  3  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    0.00081   18.7   0.1     0.0046   16.3   0.0    2.1  2  FAD_binding_3  FAD binding domain
  ------ inclusion threshold ------
      0.019   14.4   0.3       0.41    9.9   0.2    2.1  2  FAD_oxidored   FAD dependent oxidoreductase
      0.043   13.8   0.0       0.12   12.4   0.0    1.7  2  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 !   24.7   0.0   8.6e-09   1.2e-05       1      42 [.       7      49 ..       7      61 .. 0.86
   2 !   20.0   0.0   2.3e-07   0.00032     162     260 ..     134     231 ..     128     240 .. 0.82
   3 !   13.6   0.0   2.2e-05      0.03     255     294 .]     414     450 ..     393     450 .. 0.79

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 8.6e-09
                                      CSEEEE--SHHHHHHHHHHHH.HTS-EEEEETTHCHHHCSHHH CS
                                      xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaq.agakvtlvelegtclnggcll 42
                                      +dvv+iG+GpAGl  a +la+ + +kv++++++g +  + c++
  gi|242398444|ref|YP_002993868.1|  7 FDVVIIGAGPAGLFSAYELAEkSDLKVAVIDEGGDIESRVCPM 49
                                      69*******************67*******9777776666666 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 2.3e-07
                                       HHHT-E.EEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCE..EEESEEEE-S CS
                                       xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxx RF
                       Pyr_redox_2 162 aklgke.vtlveardrllraldkelsaaleealekeGvevklgtsvkeidgngeklevvledgee..idadlvvvav 235
                                       a++g++ ++++++  ++ + + k + + ++++le +G+++ l t+v+e+++ +    vv +  ++  i+a++++va 
  gi|242398444|ref|YP_002993868.1| 134 AQAGVKfIPIIQR--HIGSDHTKGVIKSIKDYLESKGIKFILWTKVEEFRKGEV---VVRKGVDVftIKARYIIVAP 205
                                       6677777778877..78899******************************9998...6666666677********** PP

                                       -EEES-HHCS..HCCT-EEEETTEEE- CS
                                       xxxxxxxxxx..xxxxxxxxxxxxxxx RF
                       Pyr_redox_2 236 Gvrpstelle..eklglelderggivv 260
                                       G+     + +  +k+gl+  ++g i v
  gi|242398444|ref|YP_002993868.1| 206 GRGGAEWFHDvaQKIGLKS-SHGPIDV 231
                                       **99987766778888887.6666655 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 2.2e-05
                                       TTEEE--TTSBESSTTEEE-GGGCTECCSS--HHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 255 rggivvdeflrtnvpgiyaiGDvaggkggpelaqaAvqqG 294
                                       + +++v+  l+t++++i+a+GD a   g  + +++A ++G
  gi|242398444|ref|YP_002993868.1| 414 AMQVEVNNLLETTIENIFAAGDGA---GLSRDIVNAAATG 450
                                       55899*******************...8888888877665 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.1   4.8e-09   6.7e-06       1      30 [.       8      40 ..       8      45 .. 0.90
   2 !   10.1   0.0   0.00032      0.44     141     268 ..     149     271 ..      89     305 .. 0.61

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 4.8e-09
                                      EEEEECTSHHHHHHHHHHHHTT...EEEEESSS CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg...Vtllekgd 30
                                      dvviiG+G +Gl+ AyeLa++    V++++ g 
  gi|242398444|ref|YP_002993868.1|  8 DVVIIGAGPAGLFSAYELAEKSdlkVAVIDEGG 40
                                      9******************996799*****985 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00032
                                       EEEEHHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEE.E..EEEEEEE--GGGHHHH.HTT.CT CS
                               DAO 141 gqvdpakltaalaraaealGveilegtevtgleeedgkvwgverttpgen.d..aadavVnaaGawsdll.gll.ke 212
                                       g  ++  +++++ + +e++G+++++ t+v+++++    +  v  + +g   +  +a+++++a G +  ++   + ++
  gi|242398444|ref|YP_002993868.1| 149 GSDHTKGVIKSIKDYLESKGIKFILWTKVEEFRK----GEVV--VRKGVDvFtiKARYIIVAPGRGGAEWfHDVaQK 219
                                       445777889999999*****************54....3333..22255433345678******7766443333222 PP

                                       T.....TSEE.EEEEEEEEEEEECCTHSTGSGCSEEEEE..EEETTTTEEEEEETTSEEE.EEES CS
                               DAO 213 l.....dlpi.spvrgqvlvlkplseklvspaailpvpe..tdddgrgvyvtprkdgrvl.vGgt 268
                                       +     + pi ++vr +v ++            i+      ++d+++++y   + d+ v+ ++++
  gi|242398444|ref|YP_002993868.1| 220 IglkssHGPIdVGVRVEVPAI------------IMEQITkiNHDPKFHIYTETY-DDFVRtFCAN 271
                                       223222233334444444222............222222345555555555554.3444423544 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.2     6e-05     0.083       1      40 [.       8      47 ..       8      75 .. 0.81
   2 !   20.1   0.0     2e-07   0.00027     317     383 ..     381     456 ..     356     461 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6e-05
                                      CEEEE-SSHHHHHHHHHHH.HTT--EEEEES-GGGTT--SS CS
                              GIDA  1 dviViGgGhAGceAAlaaa.rlGakvlLithkldtiaelsC 40
                                      dv++iG+G AG+  A+++a ++ +kv+ i  + ++i + +C
  gi|242398444|ref|YP_002993868.1|  8 DVVIIGAGPAGLFSAYELAeKSDLKVAVI-DEGGDIESRVC 47
                                      79***************984578999998.44444555444 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 2e-07
                                       HHTTSTT-TT--EEE--EEEEEEEE-GGGB-T.TSBBS.......SSBTEEE-CGGGTB.-SHHHHHHHHHHHHHH CS
                              GIDA 317 vlrsipGLenaeivrpGyaieydyvdprqlln.tLetk.......kvkgLflAGqinGt.eGYeEaaaqGllAGin 383
                                       v + i+GLe+++ v pG+a + + + +++++   ++++       +++++f+AG+  G     + aaa+GllA++ 
  gi|242398444|ref|YP_002993868.1| 381 VTNIIEGLEKLDRVIPGVASDHTLLYAPEIKYyAMQVEvnnlletTIENIFAAGDGAGLsRDIVNAAATGLLAARG 456
                                       455689999999999999999999999888866666642233333699***********66699*********975 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.1   5.9e-09   8.2e-06       1      35 [.       7      42 ..       7      47 .. 0.87
   2 ?    4.3   0.0      0.01        14     106     186 ..     151     223 ..     146     245 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 5.9e-09
                                      -SEEEE--SHHHHHHHHHH.HHTT--EEEE-SSSSS CS
                       HI0933_like  1 kdviviGgGaAGlmaAisa.akrgkrVlllekakkl 35
                                      +dv++iG+G+AGl+ A ++ +k + +V++++++  +
  gi|242398444|ref|YP_002993868.1|  7 FDVVIIGAGPAGLFSAYELaEKSDLKVAVIDEGGDI 42
                                      59**************998578899******99776 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.01
                                       .-CHHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----SS-GGGT--SHHHHHHHH CS
                       HI0933_like 106 dkaedivdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGGlSiPklGstgkgyklaeq 182
                                       d+ + +++ ++  l+++g+k+ l t+v++++k  + ++r  + +  +++a+++++A      P  G  +  +++a++
  gi|242398444|ref|YP_002993868.1| 151 DHTKGVIKSIKDYLESKGIKFILWTKVEEFRK-GEVVVRKGV-DVFTIKARYIIVA------PGRGGAEWFHDVAQK 219
                                       567889999*********************55.455566666.899**********......777888888888888 PP

                                       TT-- CS
                       HI0933_like 183 fght 186
                                        g++
  gi|242398444|ref|YP_002993868.1| 220 IGLK 223
                                       7775 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.1   2.4e-10   3.3e-07      18      49 ..       7      38 ..       2      42 .. 0.93
   2 ?   -2.7   0.0         2   2.8e+03     149     170 ..     188     209 ..     167     226 .. 0.67

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 2.4e-10
                                      EEEEEE--SHHHHHHHHHHHHCTTS-EEEEES CS
                              Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailer 49
                                       Dvvi+GaG++GL +ay la+k dlkva++++
  gi|242398444|ref|YP_002993868.1|  7 FDVVIIGAGPAGLFSAYELAEKSDLKVAVIDE 38
                                      6****************************975 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2
                                       SS.-B-EEEEEEEEEE--GSSS CS
                              Thi4 149 qscvDPlvirakvvvdatGhdg 170
                                       +  vD  +i+a+ ++ a G  g
  gi|242398444|ref|YP_002993868.1| 188 RKGVDVFTIKARYIIVAPGRGG 209
                                       4568888999998888888754 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.2   7.8e-09   1.1e-05       1      33 [.       8      41 ..       8      46 .. 0.89
   2 ?   -0.8   0.0      0.44     6e+02     177     215 ..     185     221 ..     148     231 .. 0.72
   3 ?   -0.3   0.1      0.32   4.4e+02     376     403 ..     417     438 ..     402     450 .. 0.74

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 7.8e-09
                                      SEEEE--SHHHHHHHHHHHHTTT.-EEEEESSSG CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGl.kvavvekeqe 33
                                      Dv++iG+G AGL +A+e+ae+   kvav++ ++ 
  gi|242398444|ref|YP_002993868.1|  8 DVVIIGAGPAGLFSAYELAEKSDlKVAVIDEGGD 41
                                      9*******************6666*****99875 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.44
                                       EEEEETTTTCEEEEEESEEEE-----GG..........G CS
                     FAD_binding_2 177 avvenpesgrevrirakavvlatgGfgrallkellgaaa 215
                                       +vv+  ++   ++i+a+ +++a g  g+++++ ++++++
  gi|242398444|ref|YP_002993868.1| 185 VVVR--KGVDVFTIKARYIIVAPGRGGAEWFHDVAQKIG 221
                                       5666..7888889*********99999888877766655 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.32
                                       EEBETTSBESTTEEESSBTEEE-STCEE CS
                     FAD_binding_2 376 vetdengrvldadgqpipGLYAaGevaa 403
                                       ve++  +++      +i++ +AaG  a+
  gi|242398444|ref|YP_002993868.1| 417 VEVNNLLET------TIENIFAAGDGAG 438
                                       556666666......*********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 !   21.3   0.0   1.7e-07   0.00024       1      31 [.      11      42 ..      11      58 .. 0.92
   2 ?   -1.2   0.0       1.9   2.6e+03      28      52 ..      81     102 ..      78     109 .. 0.71
   3 ?   -1.3   0.0         2   2.7e+03      28      54 ..     217     244 ..     209     258 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.7e-07
                                      EE--SHHHHHHHHHHHCC.TEEEEEE-SSSSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLaka.gfdvlllekrdrl 31
                                      I+GaG +Gl  Ay+La++ +++v +++ + ++
  gi|242398444|ref|YP_002993868.1| 11 IIGAGPAGLFSAYELAEKsDLKVAVIDEGGDI 42
                                      9***************987********98664 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.9
                                       SSSSSGGG-EECETTCEECTS---E CS
                     NAD_binding_8  28 rdrlGGraasyevpgvrvdygahif 52 
                                       r+++GG+++  ++++   +y ++ +
  gi|242398444|ref|YP_002993868.1|  81 RPDIGGDLTKLTRDE---NYSWQLI 102
                                       789999999988875...4555555 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 2
                                       SSSSSGGG-EECET.TCEECTS---EEE CS
                     NAD_binding_8  28 rdrlGGraasyevp.gvrvdygahifhg 54 
                                       ++++G +++   ++ gvrv+++a i+ +
  gi|242398444|ref|YP_002993868.1| 217 AQKIGLKSSHGPIDvGVRVEVPAIIMEQ 244
                                       5678888888877657899988888765 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.2   1.1e-07   0.00015       1      36 [.       8      42 ..       8      47 .. 0.93
   2 ?    0.1   0.0      0.24   3.3e+02     111     157 ..     176     227 ..     159     253 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.1e-07
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieaspsl 36
                                      Dvv+iGaGpAgl  A +l ++k +lkv +i+ + ++
  gi|242398444|ref|YP_002993868.1|  8 DVVIIGAGPAGLFSAYEL-AEKSDLKVAVIDEGGDI 42
                                      9*****************.999********988765 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.24
                     Lycopene_cycl 111 sveeeeageslvvleggr.kirarlvvdarglaslk....karrlglQtfyG 157
                                       +vee  +ge++v    ++ +i+ar +++a g + ++     a+++gl   +G
  gi|242398444|ref|YP_002993868.1| 176 KVEEFRKGEVVVRKGVDVfTIKARYIIVAPGRGGAEwfhdVAQKIGLKSSHG 227
                                       4555555555555555559**********99665556666666666666666 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0    0.0015       2.1       2      34 ..       9      42 ..       8      50 .. 0.84
   2 !   11.5   0.1   0.00025      0.35      43      71 ..     157     185 ..     146     193 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0015
                                      EEEECSSHHHHHHHHHHHHTT.SEEEEEESSSSS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelg.kkVtvversdkl 34
                                      vv++G+G  gl  A +lae    kV v++ +  +
  gi|242398444|ref|YP_002993868.1|  9 VVIIGAGPAGLFSAYELAEKSdLKVAVIDEGGDI 42
                                      8****************9966379*999987766 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00025
                                       HHHHHHHHHHTTEEEECSEEEEEEEEETT CS
                         Pyr_redox  43 skilqeklekngievllntkveeiegsed 71 
                                        k ++++le +gi+++l tkvee+++ e 
  gi|242398444|ref|YP_002993868.1| 157 IKSIKDYLESKGIKFILWTKVEEFRKGEV 185
                                       57799*******************97664 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   2.2e-06     0.003       1      30 [.      10      39 ..      10      45 .. 0.89
   2 ?   -0.4   0.0      0.38   5.3e+02     102     134 ..     175     207 ..     152     214 .. 0.66
   3 ?   -3.1   0.0       2.6   3.6e+03     292     305 .]     421     434 ..     396     434 .. 0.62

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.2e-06
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkg 30
                                      +IiGaGPaGl +a+el ++   ++ +++ g
  gi|242398444|ref|YP_002993868.1| 10 VIIGAGPAGLFSAYELAEKSDLKVAVIDEG 39
                                      7***************9998889****987 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.38
                       Pyr_redox_3 102 eeVesvkkedegfevetsketyeAkkviiAtGe 134
                                       ++Ve+  k +   +   +  t++A+++i+A G+
  gi|242398444|ref|YP_002993868.1| 175 TKVEEFRKGEVVVRKGVDVFTIKARYIIVAPGR 207
                                       455544444333333334448999999999985 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 2.6
                       Pyr_redox_3 292 eteetnvpglflaG 305
                                       +  et+++++f aG
  gi|242398444|ref|YP_002993868.1| 421 NLLETTIENIFAAG 434
                                       45688899999998 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   3.3e-06    0.0046       2      23 ..       7      28 ..       6      40 .. 0.86
   2 ?   -0.5   0.0      0.41   5.7e+02     150     167 ..     193     210 ..     175     269 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.3e-06
                                      EEEEEE--SHHHHHHHHHHHHT CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLsea 23
                                       dV+I+GaGpaGl +a +L+e+
  gi|242398444|ref|YP_002993868.1|  7 FDVVIIGAGPAGLFSAYELAEK 28
                                      69*****************986 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.41
                                       EEEEEEEEEEE--GTT-H CS
                     FAD_binding_3 150 eetvrakYlvGaDGgrSt 167
                                         t++a+Y++ a G  ++
  gi|242398444|ref|YP_002993868.1| 193 VFTIKARYIIVAPGRGGA 210
                                       369*******99998764 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.2    0.0003      0.41       1      32 [.       8      40 ..       8      42 .. 0.88
   2 ?    2.7   0.0     0.047        65      82     164 ..     141     226 ..      78     323 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0003
                      FAD_oxidored  1 DvvVvGGgpaGvaAAia.AaraGakvlLveerg 32
                                      Dvv++G+gpaG+  A+  A +++ kv++++e g
  gi|242398444|ref|YP_002993868.1|  8 DVVIIGAGPAGLFSAYElAEKSDLKVAVIDEGG 40
                                      9**************984678899**9999865 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.047
                      FAD_oxidored  82 n........tfepevakavleemlaeagvtvllntrlvevekegkriesvtveske.grktirAkvfiDATgdGdla 149
                                                + + + + + +++ l+ +g++ +l+t+++e +k      +v+v +k     ti+A+++i A g G   
  gi|242398444|ref|YP_002993868.1| 141 IpiiqrhigSDHTKGVIKSIKDYLESKGIKFILWTKVEEFRKG-----EVVV-RKGvDVFTIKARYIIVAPGRGGAE 211
                                       044445444333344445567888999************9986.....4777.46656999******9999998766 PP

                      FAD_oxidored 150 alaGvpyrvGresre 164
                                        + +v  ++G +s++
  gi|242398444|ref|YP_002993868.1| 212 WFHDVAQKIGLKSSH 226
                                       666666666666655 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   8.3e-05      0.12       1      36 [.      10      41 ..      10      51 .. 0.86
   2 ?   -3.6   0.0         7   9.6e+03     144     154 ..     103     113 ..      90     114 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.3e-05
                     NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsep 36
                                      +i+GaGp+Gl  + +L+++    s+l++ ++d+ + 
  gi|242398444|ref|YP_002993868.1| 10 VIIGAGPAGLFSAYELAEK----SDLKVAVIDEGGD 41
                                      7*****************9....59******98655 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 7
                     NAD_binding_9 144 laadaVvLAlG 154
                                       +++d+V+L+ G
  gi|242398444|ref|YP_002993868.1| 103 WEVDQVFLTHG 113
                                       7899***9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (484 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.66u 0.33s 00:00:00.99 Elapsed: 00:00:00.51
# Mc/sec: 2848.64
//
Query:       gi|242398445|ref|YP_002993869.1|  [L=302]
Description: ATPase, PP-loop superfamily [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.6e-10   40.3   0.0    4.5e-10   39.6   0.0    1.3  1  ATP_bind_3     PP-loop family
    5.6e-08   32.6   0.0    1.7e-07   31.0   0.0    1.8  1  ThiI           Thiamine biosynthesis protein (ThiI)
    4.2e-07   29.7   0.0    2.9e-06   26.9   0.0    2.2  2  QueC           Queuosine biosynthesis protein QueC
    5.2e-07   28.8   0.1      1e-06   27.8   0.1    1.6  1  tRNA_Me_trans  tRNA methyl transferase
    0.00063   18.9   0.0     0.0013   17.9   0.0    1.5  2  NAD_synthase   NAD synthase
    0.00073   19.6   0.0     0.0013   18.8   0.0    1.4  1  PAPS_reduct    Phosphoadenosine phosphosulfate reductase fami
  ------ inclusion threshold ------
      0.019   14.5   2.0      0.019   14.5   2.0    2.7  3  RecR           RecR protein
      0.037   13.7   0.0      0.071   12.7   0.0    1.4  1  DUF1241        Protein of unknown function (DUF1241)
      0.075   12.7   0.0       0.11   12.1   0.0    1.2  1  Asn_synthase   Asparagine synthase
       0.73   10.2   7.8       0.11   12.9   1.4    2.5  2  Transp_Tc5_C   Tc5 transposase C-terminal domain
       0.91    9.9   9.5       0.97    9.8   1.3    3.3  3  C1_2           C1 domain


Domain annotation for each model (and alignments):
>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   0.0   2.8e-13   4.5e-10       1     165 [.      49     217 ..      49     223 .. 0.83

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 2.8e-13
                                       EEEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE--H........H CS
                        ATP_bind_3   1 kvlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvkelckklnikleiekvdv........a 69 
                                       kvlv +SgG DS +  ++l+kl    g ++ ++h++ g+   s++ +e+ k+ c+ ++++l++ +v+          
  gi|242398445|ref|YP_002993869.1|  49 KVLVVISGGKDSAVTAYVLKKL----GYDVECLHINLGIGGYSEKSEEYAKKQCELMGVPLYVVRVREllgagigeV 121
                                       58999***************99....559**************************************9999988764 PP

                                       HCTTSTCCCHHHHHHHHHHHHCHHCCT.CEEE---BHHHHHHHHHHHHCCT--C.CHHH-S-SEEEETTCCEE-CCC CS
                        ATP_bind_3  70 kkkgknleeaARelRYevlkealkkegievlllAhhadDqaEtfllrlargsgl.aglagikeaseiasirlvRPlL 145
                                       +++         ++RY ++++ +  +g+ v++++h+ dD a  ++ +l + +    + +g     e + ++ + Pl+
  gi|242398445|ref|YP_002993869.1| 122 RTRRPACSYCGLTKRY-IFNKFAYDNGFGVIATGHNLDDEASFIFSNLMNWNTEyLAKQGPVLPGEGTFVKKIKPLY 197
                                       5556677777888999.68999999*****************99999987444313334433333334478889999 PP

                                       T--HHHHHHHHHHTT---B- CS
                        ATP_bind_3 146 kvskeeleeylkekkikwve 165
                                        ++  e+ +y+   +++++ 
  gi|242398445|ref|YP_002993869.1| 198 GLTEREVVAYALAVGLEYII 217
                                       99999999999999988876 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.0     1e-10   1.7e-07       3     131 ..      47     170 ..      45     242 .. 0.76

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 1e-10
                              ThiI   3 qgkvlaLlSgGiDSpVaaylllkRGcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdfkev.... 75 
                                       ++kvl+++SgG DS V+ay+l k G  v+++h++  +g      ek e+ a++  e  +   v l+vv  +e+    
  gi|242398445|ref|YP_002993869.1|  47 SEKVLVVISGGKDSAVTAYVLKKLGYDVECLHIN--LGI-GGYSEKSEEYAKKQCELMG---VPLYVVRVRELlgag 117
                                       89*******************************5..333.3456677777777777765...777777777662222 PP

                              ThiI  76 lkeilekvkekltivllkrkmlriAekvaeeegakalvtGesLgqVaSqtleNlrv 131
                                       + e++++ ++ + + l kr ++   +k a  +g   + tG +L   aS  ++Nl  
  gi|242398445|ref|YP_002993869.1| 118 IGEVRTRRPACSYCGLTKRYIF---NKFAYDNGFGVIATGHNLDDEASFIFSNLMN 170
                                       6788888899999999998755...78999******************99999864 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0   1.8e-09   2.9e-06       1      62 [.      49     111 ..      49     120 .. 0.88
   2 ?   -0.4   0.0      0.43     7e+02     147     176 ..     185     214 ..     138     221 .. 0.62

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 1.8e-09
                                       EEEEE--SSHHHHHHHHHHHHH-SEEEEEEEESS-T..TSHHHHHHHHHHHHT--.-EEEEE-G CS
                              QueC   1 kavvllSGGlDSttvlalakkegkevealtfdYgqr..hkkeleaakkiakelgveehkildld 62 
                                       k++v++SGG DS++ +++ kk g+ ve+l+++ g     +k  e+akk ++ +gv    ++ ++
  gi|242398445|ref|YP_002993869.1|  49 KVLVVISGGKDSAVTAYVLKKLGYDVECLHINLGIGgySEKSEEYAKKQCELMGV-PLYVVRVR 111
                                       689*****************************987755888899**********9.87777765 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.43
                                       HHTS--EEE-TTTT--HHHHHHHHHHTTHH CS
                              QueC 147 gedkkieieaPlidlsKaeivklgkelgvp 176
                                       ge++ ++   Pl+ l+ +e+v+ +  +g++
  gi|242398445|ref|YP_002993869.1| 185 GEGTFVKKIKPLYGLTEREVVAYALAVGLE 214
                                       355666667799999999999888888754 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.1   6.4e-10     1e-06       2      72 ..      49     112 ..      48     160 .. 0.89

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 6.4e-10
                     tRNA_Me_trans   2 kvvvalSgGVDSsvaaallkeqgyevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdfek 72 
                                       kv+v +SgG DS+v+a++lk+ gy+v+ ++++l            +e+  ++a++ +e +g+pl+vv +++
  gi|242398445|ref|YP_002993869.1|  49 KVLVVISGGKDSAVTAYVLKKLGYDVECLHINLGIG-------GYSEKSEEYAKKQCELMGVPLYVVRVRE 112
                                       8****************************9998766.......3455667899999*******99998775 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   7.8e-07    0.0013       5      85 ..      34     114 ..      26     156 .. 0.82
   2 ?   -2.6   0.0       1.5   2.4e+03     148     178 ..     193     222 ..     188     242 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 7.8e-07
                                       HHHHHHHHHHHCTTSEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE--- CS
                      NAD_synthase   5 lvdflkeyvkkagakgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievktidi 81 
                                       +++ + +y   + +++v++ +SGG DS+++a++ +k+  + + l + l     se++ e a++ +e +g+   ++ +
  gi|242398445|ref|YP_002993869.1|  34 VKKTIDKYKLLKASEKVLVVISGGKDSAVTAYVLKKLGYDVECLHINLGIGGYSEKSEEYAKKQCELMGVPLYVVRV 110
                                       3344444444456799******************9998899999999998888999999999999999999888888 PP

                                       HHHH CS
                      NAD_synthase  82 kpiv 85 
                                       ++ +
  gi|242398445|ref|YP_002993869.1| 111 RELL 114
                                       7765 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.5
                                       BETTTTS-HHHHHHHHHHTT--HHHHCS--B CS
                      NAD_synthase 148 lapiaellKtevkeLakelnvPervlkkpPs 178
                                       ++p+++l+ +ev + a +++  e +++  P 
  gi|242398445|ref|YP_002993869.1| 193 IKPLYGLTEREVVAYALAVGL-EYIINECPH 222
                                       789999999998877766664.455555555 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0     8e-07    0.0013       2     155 ..      50     215 ..      49     217 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 8e-07
                                       EEEE--SSCTCHHHHHHHHHHCTTHEEEEEE-ST..B-HHHHHHHHHHHHHTT-EEEEEE-SCHHHHHHHHHH-S-T CS
                       PAPS_reduct   2 lvvsvsgGkdslVllhLalkafkpvpvvfvdtgh..efpetiefvdeleeryglrlkvyepeeevaekinaekhgss 76 
                                       + v +sgGkds+V+   + k  ++v+ ++++ g     ++  e+ ++  e +g+ l v++ +e   ++i + +   +
  gi|242398445|ref|YP_002993869.1|  50 VLVVISGGKDSAVTAYVLKKLGYDVECLHINLGIggYSEKSEEYAKKQCELMGVPLYVVRVRELLGAGIGEVRT--R 124
                                       57899**************************986225677889999999999************9999999993..2 PP

                                       HHHC...HHHHHHTHHHHHHHHHCTTECEEE----CCCTTTTTTSSSEEECTTT-S............CEEE-CCCT CS
                       PAPS_reduct  77 lyee...aaeriaKveplkkaLekldedalltGaRrdesksraklpiveidedfek............slrvfPlln 138
                                          +    ++ ++K +  +k   ++++ ++ tG   d+++s    ++++ +++  +            + ++ Pl  
  gi|242398445|ref|YP_002993869.1| 125 ---RpacSYCGLTKRYIFNKFAYDNGFGVIATGHNLDDEASFIFSNLMNWNTEYLAkqgpvlpgegtfVKKIKPLYG 198
                                       ...234479****************************9997655555444444333459********777888**** PP

                                       --HHHHHHHHHHCT--B CS
                       PAPS_reduct 139 Wteedvwqyilrenipy 155
                                        te++v +y+l+ +++y
  gi|242398445|ref|YP_002993869.1| 199 LTEREVVAYALAVGLEY 215
                                       **********9999887 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.3       2.3   3.8e+03      31      36 ..       3       8 ..       2       9 .. 0.58
   2 ?    0.5   0.0      0.29   4.6e+02       8      23 ..     117     132 ..     111     136 .. 0.67
   3 ?   14.5   2.0   1.2e-05     0.019      16      35 ..     269     288 ..     266     288 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.3
                                      -CCCCS CS
                              RecR 31 CaICsd 36
                                      C++C +
  gi|242398445|ref|YP_002993869.1|  3 CRFCEN 8 
                                      666654 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.29
                                       HHHHHHHH-EE-TTT- CS
                              RecR   8 aLqeakekvrhCsrCg 23 
                                        + e++++   Cs Cg
  gi|242398445|ref|YP_002993869.1| 117 GIGEVRTRRPACSYCG 132
                                       5666666767788776 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 1.2e-05
                                       -EE-TTT--EESSSS-CCCC CS
                              RecR  16 vrhCsrCgnlteedlCaICs 35 
                                       ++ C++Cg  + ++ C++C+
  gi|242398445|ref|YP_002993869.1| 269 LKKCKICGMPSQDEKCSFCR 288
                                       799****************6 PP

>> DUF1241  Protein of unknown function (DUF1241)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   4.4e-05     0.071       4      69 ..     204     270 ..     201     284 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.4e-05
                           DUF1241   4 vaslvlqvllrpvldklekkdvaaaqtLraalskaekesPgltqdlvkgllkkkels.vnlneslLr 69 
                                       v++ +l v l+ ++++  +   a++ + ++ l+k+e++ Pg   ++vkg l+kk+l   +l+e  L+
  gi|242398445|ref|YP_002993869.1| 204 VVAYALAVGLEYIINECPHARGATTIEYKEILNKMEEKRPGTKINFVKGYLRKKHLFeAELEEIELK 270
                                       6777888888889999988888889999************************998744777777665 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0     7e-05      0.11      14      83 ..      44     112 ..      36     124 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7e-05
                      Asn_synthase  14 lradvpvGalLSGGlDSSliaalaarqsksplktFsigfeekgsdea..kyakevaehlgtehtelvlteee 83 
                                       l+a  +v +++SGG DS++ a+++++    ++ + +i +   g++e   +yak+ +e +g++   +v+ ++e
  gi|242398445|ref|YP_002993869.1|  44 LKASEKVLVVISGGKDSAVTAYVLKKLGY-DVECLHINLGIGGYSEKseEYAKKQCELMGVPL--YVVRVRE 112
                                       688999********************985.*********556666642269999999999995..5555555 PP

>> Transp_Tc5_C  Tc5 transposase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   1.4   6.6e-05      0.11      29      56 ..       2      27 ..       1      32 [. 0.91
   2 ?   -0.1   0.6      0.74   1.2e+03      26      49 ..     268     290 ..     256     294 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.6e-05
                      Transp_Tc5_C 29 dCkiegCselafikCarCkellCFdHfv 56
                                      +C +  C++ a+ik  + k++lC +Hf+
  gi|242398445|ref|YP_002993869.1|  2 KCRF--CENRAYIKLHYPKMYLCSNHFI 27
                                      5777..*********************8 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.74
                      Transp_Tc5_C  26 tsedCkiegCselaf.ikCarCkel 49 
                                       + ++Cki  C+  +   kC++C+ +
  gi|242398445|ref|YP_002993869.1| 268 ELKKCKI--CGMPSQdEKCSFCRFW 290
                                       4567777..4443322589999765 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.8      0.26   4.2e+02      20      36 ..       2      23 ..       1      27 [. 0.70
   2 ?    1.8   0.0      0.19   3.2e+02      14      30 ..     121     140 ..     104     145 .. 0.70
   3 ?    9.8   1.3   0.00059      0.97      14      40 ..     265     289 ..     254     290 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.26
                              C1_2 20 nCsaCgrk..idgff...YsCs 36
                                      +C+ C++   i+  +   Y Cs
  gi|242398445|ref|YP_002993869.1|  2 KCRFCENRayIKLHYpkmYLCS 23
                                      8*****9977433334568886 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.19
                              C1_2  14 dssesfnCsaCgrk...idg 30 
                                        +  +  Cs Cg +   i++
  gi|242398445|ref|YP_002993869.1| 121 VRTRRPACSYCGLTkryIFN 140
                                       5666678*****99555444 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.00059
                              C1_2  14 dssesfnCsaCgrkidgffYsCseCdf 40 
                                       ++ e ++C++Cg +++++  +Cs C+f
  gi|242398445|ref|YP_002993869.1| 265 EEIELKKCKICGMPSQDE--KCSFCRF 289
                                       455679********9998..9*99*98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       780  (0.0435049); expected 358.6 (0.02)
Passed bias filter:                      583  (0.0325172); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.52
# Mc/sec: 1734.03
//
Query:       gi|242398446|ref|YP_002993870.1|  [L=659]
Description: 4-alpha-glucanotransferase [Thermococcus sibiricus MM 739]
Scores for complete 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-75  252.8   0.2    1.1e-74  251.5   0.2    1.6  1  DUF1926          Domain of unknown function (DUF1926)
    5.3e-59  200.0   6.7    2.3e-58  198.0   2.1    2.8  2  Glyco_hydro_57   Glycosyl hydrolase family 57
    5.1e-35  119.6   0.9      1e-34  118.6   0.9    1.5  1  DUF1925          Domain of unknown function (DUF1925)
    5.5e-06   26.0   0.0    0.00041   19.8   0.0    2.2  2  Glyco_hydro_38N  Glycosyl hydrolases family 38 N-terminal dom
  ------ inclusion threshold ------
      0.019   14.8   0.0       0.14   11.9   0.0    2.0  2  HGD-D            2-hydroxyglutaryl-CoA dehydratase, D-compone
       0.12   12.9   0.1       0.36   11.3   0.1    1.8  2  CoA_binding_2    CoA binding domain


Domain annotation for each model (and alignments):
>> DUF1926  Domain of unknown function (DUF1926)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  251.5   0.2   3.8e-78   1.1e-74       1     279 [.     392     656 ..     392     657 .. 0.94

  Alignments for each domain:
  == domain 1  score: 251.5 bits;  conditional E-value: 3.8e-78
                           DUF1926   1 DfdlDgreEvlleseklvavlkpaqGGsliElddrkkefNllntLtRrpEaYHekileaeeeneeeeegiasihelv 77 
                                       D+d+Dgr+E++le+++++a lkp++GGs++El++++k++N+ ++L Rr+E+YHe  ++a   +ee+++g+asihel 
  gi|242398446|ref|YP_002993870.1| 392 DIDFDGRKEIMLENDNFIATLKPHYGGSIFELSSKRKAVNYNDVLPRRWEHYHEVPEAA-VPEEENKDGVASIHELG 467
                                       9******************************************************9999.88888899********* PP

                           DUF1926  78 kkkdeelkkeLvyDwyerkslvDhfldeeltlesfvqgelkeegDFanqpyeiekkkvevvlkrdGgvy...kkeit 151
                                       k++ ee+k+eL+yDw  r++l+Dhf+++e tl++++  ++ e+gDF+nqpye+  + ++v l r+Gg+y   k ++t
  gi|242398446|ref|YP_002993870.1| 468 KAIPEEIKRELAYDWQLRAILQDHFIKPEETLDNYRLVKYHEFGDFVNQPYEYILRGNKVKLWRNGGIYakeKIPAT 544
                                       **********************************************************************9999*** PP

                           DUF1926 152 lrKeytleekseleveyeltneskeiellfavElNlallaleaddrylllndkklgeeleleevkefeleDevlkkk 228
                                       ++Ke++l+e+ ++  +y+++ e++  ++lf+vElNla+++++++ +             e+ + kefe++D++  ++
  gi|242398446|ref|YP_002993870.1| 545 VEKEIELNEE-GFVAHYRVSLEKPF-KILFGVELNLAVHSVMETPG-------------EF-DEKEFEVNDPYGLGR 605
                                       *******777.*********99766.****************3333.............33.5599*********** PP

                           DUF1926 229 lelelsepaelwafPveTVSqsekgfelvyQgvavvllwpvdlkekeewkl 279
                                       +++e++++a++w+fP++T+Sqse+g++ ++Qgv+++ll+p++ + k+++k+
  gi|242398446|ref|YP_002993870.1| 606 VKIETDKQAKIWKFPIKTLSQSEAGWDFIQQGVSYTLLFPIEKEIKFKIKF 656
                                       ************************************999999777766554 PP

>> Glyco_hydro_57  Glycosyl hydrolase family 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.0   2.1   7.6e-62   2.3e-58      70     325 .]      23     268 ..       7     268 .. 0.92
   2 ?   -1.1   0.2      0.28   8.4e+02     234     301 ..     477     548 ..     473     558 .. 0.66

  Alignments for each domain:
  == domain 1  score: 198.0 bits;  conditional E-value: 7.6e-62
                                       HHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHT.TT-HHHHHHHHHHCTSEEEEEE-TT-B-GGG CS
                    Glyco_hydro_57  70 ylpateellelieeglerctelkldlavlfnlaisgplleqiqkwlnkevlelfrelqesgqvElltspyyHpllpl 146
                                       +++a+++ + ++ e+le+++ +k      +n ++sgplle+i+++ ++++++l+++l+++gq+E+++ ++y+p+l+ 
  gi|242398446|ref|YP_002993870.1|  23 FEEAYNNSYRPFMEILEEFPMMK------VNAHFSGPLLEWIEEN-KPDYIDLLKSLVKNGQLEIVVAGFYEPVLAA 92 
                                       55566666666666666666999......****************.******************************* PP

                                       -S-HHHHHHHHHHHHHHHHHHHSS--SBEE-GGG-B--SHHHHHHHTT--EEEE-C------------TTS-EE-TT CS
                    Glyco_hydro_57 147 lpdsedieaqvkkarelyeeyfgqePrgfwlpElavspeileilaelGfeylftdelaeiledkskespyrpyllkn 223
                                       +p+ ed +aq+++ +e+ ++ +g e++g+wl+E++++pe++++l+elG+ey+++d++++++++ ske++++py++++
  gi|242398446|ref|YP_002993870.1|  93 IPK-EDRIAQIEMLKEYARK-LGFEAKGVWLTERVWQPELVKSLKELGIEYVVVDDYHFMSAGLSKEELFWPYYTED 167
                                       ***.***************9.******************************************************** PP

                                       S...-EEEE--CHH-TTTSGGG-............TTSB...........-TT---TTT--BB-TT-S---H.HHHH CS
                    Glyco_hydro_57 224 gg..iavffRdreLsddigFryseqypleavddfinwlkkvkka.ksevvtialdgEnwghypetgkkeFle.klye 296
                                       gg  + vf++d++L+++i+Fr         v+++i++l+++ ++ +s+v++++ dgE++g +p t+++++++ +l +
  gi|242398446|ref|YP_002993870.1| 168 GGeiVTVFPIDEKLRYLIPFR--------PVEKVIEYLEGLVDNnPSKVAVFHDDGEKFGVWPGTHEWVYEKgWLRK 236
                                       ********************9........9*********887778*************************9999999 PP

                                       ...HHHHHHHHHHHHHHHHHHHHSS-EEEEEE CS
                    Glyco_hydro_57 297 ...eleenglielvtpsefikklkpkgliklp 325
                                          e+ +n+ i+l+t++e++ k++p+gl++lp
  gi|242398446|ref|YP_002993870.1| 237 ffdEITSNEKINLMTYTEYLGKFTPRGLVYLP 268
                                       444555555*******************9997 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.28
                                       HH-TTTSGGG-............TTSB...............-TT---TTT--BB-TT-S---H.HHHHHHHHH CS
                    Glyco_hydro_57 234 eLsddigFryseqypleavddfinwlkkvkka.....ksevvtialdgEnwghypetgkkeFle.klyeeleen 301
                                       eL +d+ +r   q  +  ++++++ ++ vk        ++ +++ l+g + + +++ g+  + + k + ++e++
  gi|242398446|ref|YP_002993870.1| 477 ELAYDWQLRAILQDHFIKPEETLDNYRLVKYHefgdfVNQPYEYILRGNKVKLWRNGGI--YAKeKIPATVEKE 548
                                       55555555555444445555555555533222457778899999999999999999998..4444888887775 PP

>> DUF1925  Domain of unknown function (DUF1925)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.6   0.9   3.5e-38     1e-34       1      79 [.     311     383 ..     311     384 .. 0.96

  Alignments for each domain:
  == domain 1  score: 118.6 bits;  conditional E-value: 3.5e-38
                           DUF1925   1 GiwknFlvkYeesnemhkrmlevskklkklaskkeaeealeallraqandaYWhGlFGGiYlphLRravyenlikae 77 
                                       GiwknF+ kY+esn mhkrml++sk ++++      +ea++++l+aq+ndaYWhG+FGG+YlphLRr v+en+ika+
  gi|242398446|ref|YP_002993870.1| 311 GIWKNFFFKYPESNFMHKRMLMISKAVREN------PEARHYILKAQCNDAYWHGVFGGVYLPHLRRTVWENIIKAQ 381
                                       9************************98888......899************************************98 PP

                           DUF1925  78 al 79 
                                       ++
  gi|242398446|ref|YP_002993870.1| 382 SY 383
                                       75 PP

>> Glyco_hydro_38N  Glycosyl hydrolases family 38 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   1.4e-07   0.00041      25     123 ..      26     123 ..      16     208 .. 0.74
   2 !    4.0   0.0    0.0093        28      39      99 ..     319     379 ..     315     408 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.4e-07
                                       TCHHHHHHHHHHHHHSTT--E.EES-CHHHHHHHCCS-CCCHHHHHHHHHCTSEEECTT-SS-B-SSSS-HHHHHHH CS
                   Glyco_hydro_38N  25 kvqrilssvlellerdpdrkF.ilseaslferwweeapeekkelvkklvaegrlevvgGgwvenDealpsgeslirq 100
                                         +++++  +e le+ p +k  ++ +  l+e+++e++p+   +l+k+lv++g+le+v +g+ e+  a++  e+ i q
  gi|242398446|ref|YP_002993870.1|  26 AYNNSYRPFMEILEEFPMMKVnAHFSGPLLEWIEENKPDYI-DLLKSLVKNGQLEIVVAGFYEPVLAAIPKEDRIAQ 101
                                       55677777788888888888734445556666666666555.555******************************** PP

                                       HHCCCHHHHCCH--EESEEEESS CS
                   Glyco_hydro_38N 101 lleGqrflkeefgvrpkvaWliD 123
                                       +   ++ + +++g + k +Wl  
  gi|242398446|ref|YP_002993870.1| 102 IEMLKE-YARKLGFEAKGVWLTE 123
                                       977666.6778999999999875 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.0093
                                       HSTT--EEES-CHHHHHHHCCS-CCCHHHHHHHHHCTSEEECTT-SS-B-SSSS-HHHHHH CS
                   Glyco_hydro_38N  39 rdpdrkFilseaslferwweeapeekkelvkklvaegrlevvgGgwvenDealpsgeslir 99 
                                       ++p+ +F++  + ++++  +e+pe +  ++k   ++  ++ v Gg   +    + +e++i+
  gi|242398446|ref|YP_002993870.1| 319 KYPESNFMHKRMLMISKAVRENPEARHYILKAQCNDAYWHGVFGGVYLPHLRRTVWENIIK 379
                                       79*************************************9999998888888888888776 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 ?   11.9   0.0   4.7e-05      0.14     160     272 ..      94     213 ..      73     216 .. 0.76
   2 ?    0.0   0.0      0.19   5.7e+02     153     190 ..     275     310 ..     256     342 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.7e-05
                                       -HHHHHHHHHHHHHHHHHHT..STS-EEEEEES---TT--HHHHHHHHT.T-EEEEEESTTTHHHHS-........S CS
                             HGD-D 160 gkeeatealeelleeleersk.seriRllltGipvellaaklmkaleaglgavvvnndacypsrlvry........v 227
                                       +ke+ ++ +e +l+e  +  k   +++ ++  + v+ +  +l k l++ +  +vv++d+ ++s++ ++        +
  gi|242398446|ref|YP_002993870.1|  94 PKEDRIAQIE-MLKEYAR--KlGFEAKGVWLTERVWQP--ELVKSLKELGIEYVVVDDYHFMSAGLSKeelfwpyyT 165
                                       7788888888.6767777..222556677999999999..9*******988999************44579999995 PP

                                       SHHH......HHHHHHHHHT--TTSS-HHHHHHHHHHHHHTT-SEEEEEE CS
                             HGD-D 228 gdvgq.....plealasgyykcpvspkerrlewirdlideykvdgvifqt 272
                                       +d+g+     p+++ + +y+ +p +p e+ +e+++ l+d++  ++++f+ 
  gi|242398446|ref|YP_002993870.1| 166 EDGGEivtvfPIDEKL-RYL-IPFRPVEKVIEYLEGLVDNNPSKVAVFHD 213
                                       5555511111555656.666.56569*****************9999996 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.19
                                       HHHHTT.S.-HHHHHHHHHHHHHHHHHHT.STS-EEEEEE CS
                             HGD-D 153 lakvvf.l.gkeeatealeelleeleerskseriRllltG 190
                                       +  ++  + + + ++e++e+l +e +     e++R+++ G
  gi|242398446|ref|YP_002993870.1| 275 MSEWSLpAkQAKLFVEFAEQLKKEGKF----EKYRVFVRG 310
                                       444444444444455555544444444....9****9887 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00012      0.36      69     106 ..     102     142 ..      90     146 .. 0.83
   2 ?   -3.2   0.0       3.9   1.2e+04      55      82 ..     180     207 ..     172     212 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00012
                                       GGGHHHHHHH...--SEEEE-TT---HHHHHHHHHTT-EEE CS
                     CoA_binding_2  69 peivkealal...gakavwlqpgsedeeaaelaeeagirvv 106
                                        e++ke +++   +ak+vwl + ++++e+++ ++e gi++v
  gi|242398446|ref|YP_002993870.1| 102 IEMLKEYARKlgfEAKGVWLTERVWQPELVKSLKELGIEYV 142
                                       56677775554445************************987 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3.9
                                       T--EEEE-S-HHHHGGGHHHHHHH--SE CS
                     CoA_binding_2  55 pvdlvdvftppeatpeivkealalgaka 82 
                                       ++  +  f+p e++ e+++ +++ ++  
  gi|242398446|ref|YP_002993870.1| 180 KLRYLIPFRPVEKVIEYLEGLVDNNPSK 207
                                       5556677888899988888887776544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (659 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       587  (0.0327403); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); 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: 0.70u 0.30s 00:00:01.00 Elapsed: 00:00:01.05
# Mc/sec: 1893.41
//
Query:       gi|242398447|ref|YP_002993871.1|  [L=206]
Description: phosphatidate cytidylyltransferase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0078   15.9   0.0      0.028   14.2   0.0    1.9  2  Gly-zipper_YMGG  YMGG-like Gly-zipper
  ------ inclusion threshold ------
       0.23   11.5   0.1       0.39   10.7   0.1    1.3  1  MHC2-interact    CLIP, MHC2 interacting


Domain annotation for each model (and alignments):
>> Gly-zipper_YMGG  YMGG-like Gly-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.8   0.2    0.0052        47      26      43 ..     112     129 ..      97     132 .. 0.45
   2 !   14.2   0.0   3.1e-06     0.028       5      39 ..     113     177 ..     109     177 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.0052
                                       XXXXXXXXXXXXXXXXXX CS
                   Gly-zipper_YMGG  26 gkGAaiGAaaGalaGgai 43 
                                       + GA+  A+ G +  ++i
  gi|242398447|ref|YP_002993871.1| 112 AIGAITVATLGDAIAAII 129
                                       333333333333333333 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 3.1e-06
                                       XXXXXXXXXXXXXXXXXX....XXXXXX.............................XXXXXXXXXXX CS
                   Gly-zipper_YMGG   5 rGAaiGAaaGAvvGaliG....sgggkG.............................AaiGAaaGala 39 
                                        GA + A +G ++ a+iG    ++                                 A+iGA aG la
  gi|242398447|ref|YP_002993871.1| 113 IGAITVATLGDAIAAIIGkpfgKH---RfkngksiegslayfltaflillvlidlphALIGALAGMLA 177
                                       466666889999999999765533...1333588999****************************997 PP

>> MHC2-interact  CLIP, MHC2 interacting
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   4.3e-05      0.39      24      54 ..       5      35 ..       2      38 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 4.3e-05
                     MHC2-interact 24 rsslkralkvaglsiLvalLiAGQavTaYfv 54
                                      ++  ++al ++gl++    L+ GQ vT+ fv
  gi|242398447|ref|YP_002993871.1|  5 SEVKRKALHLTGLTVPLLYLLFGQKVTIGFV 35
                                      55678999********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       871  (0.0485805); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1356.13
//
Query:       gi|242398448|ref|YP_002993872.1|  [L=230]
Description: Hydrolase, HAD superfamily [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-23   83.5   0.4    2.9e-23   82.9   0.0    1.5  2  HAD_2            Haloacid dehalogenase-like hydrolase
    1.4e-12   48.4   0.0    3.6e-12   47.0   0.0    1.7  1  Hydrolase        haloacid dehalogenase-like hydrolase
    2.2e-11   43.7   0.0    4.9e-11   42.5   0.0    1.6  2  Hydrolase_like   HAD-hyrolase-like
    9.4e-08   32.7   0.1    1.7e-07   31.8   0.0    1.5  2  HAD              haloacid dehalogenase-like hydrolase
    0.00028   20.8   0.1      0.037   13.9   0.0    2.7  2  NT5C             5' nucleotidase, deoxy (Pyrimidine), cytosol
    0.00049   20.2   0.0     0.0023   18.0   0.0    2.1  3  Hydrolase_6      Haloacid dehalogenase-like hydrolase
     0.0012   18.5   1.5     0.0023   17.5   0.0    2.4  3  PGP_phosphatase  Mitochondrial PGP phosphatase
  ------ inclusion threshold ------
      0.022   14.5   0.7       0.23   11.2   0.7    2.3  1  NIF              NLI interacting factor-like phosphatase
      0.027   13.9   0.1       0.06   12.7   0.1    1.6  2  Put_Phosphatase  Putative Phosphatase
      0.053   13.1   0.0       0.54    9.8   0.0    2.3  2  Acid_phosphat_B  HAD superfamily, subfamily IIIB (Acid phosph
       0.11   12.3   0.2       0.21   11.5   0.2    1.4  1  RACo_linker      RACo linker region


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 !   82.9   0.0   1.8e-26   2.9e-23       1     178 []       3     195 ..       3     195 .. 0.87
   2 ?   -3.0   0.1         4   6.5e+03      81      94 ..     212     225 ..     201     229 .. 0.68

  Alignments for each domain:
  == domain 1  score: 82.9 bits;  conditional E-value: 1.8e-26
                             HAD_2   1 iiFDlDgTlldteeliiqafnelleey...............glselseeelrkliglslrellrklgeseeeee.. 60 
                                       ++ DlD+Tl +t e+   ++ +ll +                     ++e+ r+l  l+l+el+ ++ e+  ++   
  gi|242398448|ref|YP_002993872.1|   3 VLVDLDDTLCNTWEAARWSVLRLLPHLirkgkfkallyiltqR--YKELEQSRELHLLNLDELVGNFMERVYKSTse 77 
                                       678*********************999************8662..44445555555555555655555544433333 PP

                             HAD_2  61 .kieellrkyneekkkkevkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekkKP 136
                                        +++e+++ + +     ++++y++++++L+ Lke g k+ ++T++s+e +++kle+l++++yFd  ++s +++ +K 
  gi|242398448|ref|YP_002993872.1|  78 kDLKEMFELVDTTFFS-NLRVYPDAIDFLKGLKEIGAKIVLITDSSSEWQRKKLEHLNLKNYFDSLIISGETGYSK- 152
                                       4888888999999999.**********************************************************9. PP

                             HAD_2 137 dpeviekaleklklkkeeviy.vGDsp.tDieaakkagikviav 178
                                         e+++ +l k  + ke+ iy vGD   tD+ ++k++g ++i v
  gi|242398448|ref|YP_002993872.1| 153 -LEPYNFMLAKRMFPKEREIYvVGDRDdTDMRGGKEIGATTILV 195
                                       .***************9999989*****************9986 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4
                             HAD_2  81 ydgvkelLeeLkea 94 
                                       ++++ke+Le +k++
  gi|242398448|ref|YP_002993872.1| 212 VKDLKEALEVIKHE 225
                                       56777777777665 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.0   0.0   2.2e-15   3.6e-12      60     210 .]      52     189 ..       1     189 [. 0.70

  Alignments for each domain:
  == domain 1  score: 47.0 bits;  conditional E-value: 2.2e-15
                                       HHHETTTEHHHHTHHHHHHHHHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  60 fatfigrgayaigkpewltaldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagie 136
                                        ++       + +  e++            ++   +   +  l++  +l + t+  +l+v+p+a ++++ Lk+ g +
  gi|242398448|ref|YP_002993872.1|  52 SRE-----LHLLNLDELVGNF---------MERVYKSTSEKDLKEMFELVDTTFFSNLRVYPDAIDFLKGLKEIGAK 114
                                       333.....3333333333333.........4455555555555555668899999999******************* PP

                                       EEEEESSEHHHHHHHHHHTT.GGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHH.HHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                         Hydrolase 137 vvlltgdnpetaeraanqlG.ddyfdaviasdietvakpspegkvaaireLqgkpeevamVGDgvn.DaaalaaAg 210
                                       +vl+t +++e +++ +++l+ ++yfd  i s +++ +k +p  +  a r +  k +e+ +VGD+   D+ ++++ g
  gi|242398448|ref|YP_002993872.1| 115 IVLITDSSSEWQRKKLEHLNlKNYFDSLIISGETGYSKLEPYNFMLAKRMF-PKEREIYVVGDRDDtDMRGGKEIG 189
                                       ***************************************************.88889*******999999999876 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       5.3   8.7e+03      40      51 ..     110     121 ..     108     140 .. 0.69
   2 !   42.5   0.0     3e-14   4.9e-11       5      75 .]     153     218 ..     149     218 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 5.3
                                       HCT-EEEEESSS CS
                    Hydrolase_like  40 naGwksvLVltG 51 
                                       ++G+k vL++  
  gi|242398448|ref|YP_002993872.1| 110 EIGAKIVLITDS 121
                                       567777776543 PP

  == domain 2  score: 42.5 bits;  conditional E-value: 3e-14
                                       TSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESSSSS-TTTHHHHHHHHT---SEEES- CS
                    Hydrolase_like   5 PepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVltGvtrpedleepehkptyvaddlaea 75 
                                        ep  +  a + +  + +e++++GDr +tD++g++++G++++LV++G ++       + +++y+++dl+ea
  gi|242398448|ref|YP_002993872.1| 153 LEPYNFMLAKRMF-PKEREIYVVGDRDDTDMRGGKEIGATTILVRRGYFKSLM----PKHADYIVKDLKEA 218
                                       5555555555555.45789******************************9933....4689*******997 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.0   1.1e-10   1.7e-07       1     180 [.       3     177 ..       3     183 .. 0.67
   2 ?   -2.7   0.0       4.1   6.7e+03      88     101 ..     216     230 .]     198     230 .] 0.66

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 1.1e-10
                               HAD   1 alfDfDgTLldg.dsle....lllrfllrrgaprlwralreklllalfrellrldraglaelleallagls.eelaa 71 
                                       +l D+D TL ++ + +      ll +l+r+g  +++  ++ + ++ l ++  +l  + l+el+ +++++ +    ++
  gi|242398448|ref|YP_002993872.1|   3 VLVDLDDTLCNTwEAARwsvlRLLPHLIRKGKFKALLYILTQRYKEL-EQSRELHLLNLDELVGNFMERVYkSTSEK 78 
                                       689********954444555544444444444444333333333333.33333333356788888999988899999 PP

                               HAD  72 elerfvaevirpk....lldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelgl 144
                                       +l+++++ v ++       +p+a ++l+  ++ G ++v+++ + +++ + +l++l+    l +      +++    +
  gi|242398448|ref|YP_002993872.1|  79 DLKEMFELVDTTFfsnlRVYPDAIDFLKGLKEIGAKIVLITDSSSEWQRKKLEHLN----LKN------YFDSL--I 143
                                       99999977777776665367********999*************************....999......77777..3 PP

                               HAD 145 egkpvrgegkvaalre...wlaaegegidleevvayGDs 180
                                       + + +      ++l+    +la++  + ++e ++++GD 
  gi|242398448|ref|YP_002993872.1| 144 ISGETGY----SKLEPynfMLAKRMFPKERE-IYVVGDR 177
                                       3333333....44444333555666666554.7888885 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4.1
                               HAD  88 pgalella.ahraaG 101
                                        +ale+++ +h+++G
  gi|242398448|ref|YP_002993872.1| 216 KEALEVIKhEHKKRG 230
                                       588888887777765 PP

>> NT5C  5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.024        39       2      19 ..       1      18 [.       1      25 [. 0.86
   2 !   13.9   0.0   2.3e-05     0.037      46      94 ..      73     124 ..      35     141 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.024
                              NT5C  2 sivlvDlDgvladlygkm 19
                                      ++vlvDlD+ l++++++ 
  gi|242398448|ref|YP_002993872.1|  1 MLVLVDLDDTLCNTWEAA 18
                                      679**********99875 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 2.3e-05
                              NT5C  46 kPeqreslyrf..ltepglFadlepipgarevLeeladeg.rlvvitaallq 94 
                                       k   ++ l +   l    +F++l+  p+a + L+ l ++g ++v+it +   
  gi|242398448|ref|YP_002993872.1|  73 KSTSEKDLKEMfeLVDTTFFSNLRVYPDAIDFLKGLKEIGaKIVLITDSSSE 124
                                       444444444332677899**********************9******98766 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       2.6   4.3e+03       3      29 ..       5      32 ..       3      61 .. 0.49
   2 !   18.0   0.0   1.4e-06    0.0023       8      91 ..      90     179 ..      87     185 .. 0.78
   3 ?   -2.7   0.0       4.1   6.7e+03      13      31 ..     209     227 ..     206     228 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.6
                                      EESTTTSEETTEE.-TTHHHHHHHHHHT CS
                       Hydrolase_6  3 fDidGvLwrgdka.ipgaaealnalraa 29
                                      +D+d +L +  +a    + ++l  l ++
  gi|242398448|ref|YP_002993872.1|  5 VDLDDTLCNTWEAaRWSVLRLLPHLIRK 32
                                      5666666554443122333333333333 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 1.4e-06
                                       TSEETTEE-TTHHHHHHHHHHTT-EEEEEE---SS-HHHHHHHH.HHTT--...--GGGEEEHHHHHHHHHHHH..S CS
                       Hydrolase_6   8 vLwrgdkaipgaaealnalraagkpvvllTNnsskseeeyakkl.eklgvd...iteeqvvtsataaaeylkkr..k 78 
                                       ++  + +++p a ++l+ l++ g ++vl+T +ss+ +++ +++l  k  +d   i+ e  ++  ++   +l+kr   
  gi|242398448|ref|YP_002993872.1|  90 TFFSNLRVYPDAIDFLKGLKEIGAKIVLITDSSSEWQRKKLEHLnLKNYFDsliISGETGYSKLEPYNFMLAKRmfP 166
                                       56677789**************************9999888888544555565566677777777777777777555 PP

                                       XXXEEEEESXHHH CS
                       Hydrolase_6  79 adkkvlvigeegl 91 
                                       +++ ++v+g  ++
  gi|242398448|ref|YP_002993872.1| 167 KEREIYVVGDRDD 179
                                       5889999998765 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 4.1
                                       TEE-TTHHHHHHHHHHTT- CS
                       Hydrolase_6  13 dkaipgaaealnalraagk 31 
                                       d +++  +eal++++ ++k
  gi|242398448|ref|YP_002993872.1| 209 DYIVKDLKEALEVIKHEHK 227
                                       6677778889988888776 PP

>> PGP_phosphatase  Mitochondrial PGP phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.4   2.2e+03      44      57 ..       3      16 ..       2      24 .. 0.78
   2 !   17.5   0.0   1.4e-06    0.0023     124     166 ..     156     198 ..      94     200 .. 0.87
   3 ?   -2.3   0.1       1.8     3e+03     106     116 ..     218     228 ..     203     229 .. 0.60

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.4
                   PGP_phosphatase 44 vvlDKDnclaapke 57
                                      v++D D++l++  e
  gi|242398448|ref|YP_002993872.1|  3 VLVDLDDTLCNTWE 16
                                      789*******8765 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 1.4e-06
                   PGP_phosphatase 124 leyfkerkvveeadeiavvgDRllTdvllanmmGslgvwlrdg 166
                                       ++++ ++++  +  ei vvgDR  Td+  ++++G++++++r+g
  gi|242398448|ref|YP_002993872.1| 156 YNFMLAKRMFPKEREIYVVGDRDDTDMRGGKEIGATTILVRRG 198
                                       56667777888999*************************9987 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 1.8
                   PGP_phosphatase 106 gipVlrhkekK 116
                                        ++V++h++kK
  gi|242398448|ref|YP_002993872.1| 218 ALEVIKHEHKK 228
                                       26777777776 PP

>> NIF  NLI interacting factor-like phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.7   0.00014      0.23      40     131 ..      57     139 ..       1     162 [. 0.48

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00014
                               NIF  40 defLkelsklyevvifTasseeyaeavidildpekkllshrlyrescvkkkgeyvKdLsllgrdlsrvvivDdspds 116
                                          L+el+ ++   ++ ++se+  +++ + +d++    + r+y ++      +++K L+ +g    ++v++ ds+ +
  gi|242398448|ref|YP_002993872.1|  57 LLNLDELVGNFMERVYKSTSEKDLKEMFELVDTTFF-SNLRVYPDAI-----DFLKGLKEIG---AKIVLITDSSSE 124
                                       444444444444444444444444444444444432.3333444444.....3344444332...234444444444 PP

                               NIF 117 felqpengipiksff 131
                                       +++++ ++++ k++f
  gi|242398448|ref|YP_002993872.1| 125 WQRKKLEHLNLKNYF 139
                                       444444444444444 PP

>> Put_Phosphatase  Putative Phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.4   2.3e+03       2      14 ..       2      14 ..       1      49 [. 0.67
   2 ?   12.7   0.1   3.7e-05      0.06      41     119 ..      63     143 ..      41     157 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.4
                   Put_Phosphatase  2 lvvfDFDktiide 14
                                      lv++D D t+ + 
  gi|242398448|ref|YP_002993872.1|  2 LVLVDLDDTLCNT 14
                                      7889999998874 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 3.7e-05
                   Put_Phosphatase  41 lwnelmdrvlkelheqg.vseadikkv..lrsiplspglvelikslakkkleldliiiSDaNsffieeileaagled 114
                                       l  ++m+rv k   e++ +++ ++ ++  + ++ + p  ++ +k l  k+ +  +++i D+ s    + le+++l++
  gi|242398448|ref|YP_002993872.1|  63 LVGNFMERVYKSTSEKDlKEMFELVDTtfFSNLRVYPDAIDFLKGL--KEIGAKIVLITDSSSEWQRKKLEHLNLKN 137
                                       55689******9999986777777554226899*************..6789************************* PP

                   Put_Phosphatase 115 lFse.i 119
                                       +F++ i
  gi|242398448|ref|YP_002993872.1| 138 YFDSlI 143
                                       **9844 PP

>> Acid_phosphat_B  HAD superfamily, subfamily IIIB (Acid phosphatase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.21   3.3e+02      75      89 ..       2      16 ..       1      36 [. 0.82
   2 ?    9.8   0.0   0.00033      0.54     118     174 ..      98     152 ..      93     199 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.21
                                      EEEE--BTTTEEHHH CS
                   Acid_phosphat_B 75 avvfDiDeTvLsnsp 89
                                       v +D+D+T+ ++ +
  gi|242398448|ref|YP_002993872.1|  2 LVLVDLDDTLCNTWE 16
                                      5899*****988766 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00033
                                       ECCHHHHHHHHHHTTEEEEEEEEEECCCHHHHHHHHHHCT-TTBSCCEEECCSTTC- CS
                   Acid_phosphat_B 118 ipgalelikkvverGvkiffvsgRseeqkaaTvenLkkagfssweklilkgkkdkqk 174
                                        p a++++k ++e G ki+++++ s e + + +e L  +++ +   li+ g+++ +k
  gi|242398448|ref|YP_002993872.1|  98 YPDAIDFLKGLKEIGAKIVLITDSSSEWQRKKLEHLNLKNYFD--SLIISGETGYSK 152
                                       58899**********************8888899888888544..677777776555 PP

>> RACo_linker  RACo linker region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   0.00013      0.21      34      68 ..       7      40 ..       4      59 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00013
                       RACo_linker 34 LkeaLekqwdleidlsvLrkLpevLrkgnwkVtva 68
                                      L + L + w+  ++ svLr Lp+++rkg++k  + 
  gi|242398448|ref|YP_002993872.1|  7 LDDTLCNTWE-AARWSVLRLLPHLIRKGKFKALLY 40
                                      6677888885.899****************97655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       685  (0.0382063); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        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 0.30s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 1472.76
//
Query:       gi|242398449|ref|YP_002993873.1|  [L=73]
Description: hypothetical protein TSIB_0458 [Thermococcus sibiricus MM 739]
Scores for complete 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   55.9   7.8    2.5e-15   55.9   7.8    1.6  2  DUF131    Protein of unknown function DUF131


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 ?   -0.7   0.3     0.064   1.1e+03      26      31 ..       4       9 ..       2      19 .. 0.56
   2 !   55.9   7.8   1.4e-19   2.5e-15      14      60 ..      20      65 ..       8      67 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.064
                            DUF131 26 GVvliG 31
                                      G+++iG
  gi|242398449|ref|YP_002993873.1|  4 GLIFIG 9 
                                      555555 PP

  == domain 2  score: 55.9 bits;  conditional E-value: 1.4e-19
                            DUF131 14 eaekeesrvkgGGVvliGPIPIiFGsdkrlaktaiiLaIilmillli 60
                                      +a+++e++v+ GGV++iGPIPI+FG+++  + +a+iLa++lm+l+++
  gi|242398449|ref|YP_002993873.1| 20 SASSGETNVESGGVIMIGPIPIVFGTNRG-VTLAMILAVLLMVLWIV 65
                                      78999*********************976.5689***********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       952  (0.0530983); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 508.25
//
Query:       gi|242398450|ref|YP_002993874.1|  [L=392]
Description: Na+/H+ antiporter [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-53  182.3  46.2    1.5e-53  181.9  46.2    1.0  1  Na_H_Exchanger  Sodium/hydrogen exchanger family
  ------ inclusion threshold ------
      0.095   11.6  27.1      0.033   13.1  11.8    3.7  3  Cons_hypoth698  Conserved hypothetical protein 698
        2.4    8.3   8.4        8.6    6.5   0.4    3.5  3  Ldr_toxin       Toxin Ldr, type I toxin-antitoxin system


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 !  181.9  46.2   2.6e-57   1.5e-53       3     377 ..       9     379 ..       7     387 .. 0.86

  Alignments for each domain:
  == domain 1  score: 181.9 bits;  conditional E-value: 2.6e-57
                                       HHHHHHHHHHHHHHHTTSXHHHHHHHHHHHHTTTTTS.....HHHCHCCHHHHCHHCCHHHHCTCGCCTGCCTHHHH CS
                    Na_H_Exchanger   3 llillallvgllarrlklpeivgliiaGlllGpsglgliepseedlevlselglilllFlaGleldlrelrknlksi 79 
                                       +l++la  + +l+++  +++i++ i++G++lGp++l+++ ps e l+vlse+gl + ++++Gl  +++++ +n+ ++
  gi|242398450|ref|YP_002993874.1|   9 ILLVLAKSLEWLFEKKEIHPIIAHILTGMILGPFFLNVVVPS-EPLKVLSEFGLLMMMLYMGLTSNFSSIASNKSKA 84 
                                       344446666668*****************************9.********************************** PP

                                       HHHHHHHHHHHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC.CCCTSTCCCCCCHHHHHHHHHHHCC CS
                    Na_H_Exchanger  80 lllallgvlitvvliGlllylllilgiplleallfgailsatdpvvvlailkeegrvperlgtlllgesvlnDavav 156
                                       +l+a lgv+++++l G+l+ +   +g  l++a+++g+ l  t + v++ +l  + r++++l ++l+g++  +D++av
  gi|242398450|ref|YP_002993874.1|  85 ILVAALGVIFSFIL-GFLTVY--AFGKGLAAAIFVGVTLGNTAIEVTSGVL-LKARIRKELSSILMGAAFADDIMAV 157
                                       **************.**9997..799*************************.************************* PP

                                       CCCHHHHHHTXXXXXTSSSTSXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS..CTHHHHHHHHHHHHHHHHHHHHH CS
                    Na_H_Exchanger 157 vllavllalakeeaggetslllllliflvvavgglllglvigwllrlitrft..dddrelevllvlllallaallae 231
                                        l+ ++ a+ k    ge + + l++ ++ +++++ ++ lv  +++++ +rf    ++ ++++ ++++l +++a++ae
  gi|242398450|ref|YP_002993874.1| 158 YLIGIITAMTK----GELAFSPLVVLTIKIVLFITAVLLVSEYIFKRSSRFYsiLRNLNIFFTFTIVLTFFLAMIAE 230
                                       *********84....44444455555555555555555555555555555554449999999999999********* PP

                                       TSXXXHHHHHHHHHHHHHHHHHHTT...HHHH..........HHHHHHHHHHHHHHHHHHHHSXHHHHHXXHHHHHH CS
                    Na_H_Exchanger 232 llgvsgilgaflaGlvlseyefsnk...lsek..........lesfreglfnplfFvlvGlsldlkvlnnhlsvlil 295
                                        +g++ i+ga laGl++s+ +++ +   +  +          l  + + +f+plfF++vGl +++++    +  + l
  gi|242398450|ref|YP_002993874.1| 231 RVGLHQIIGAYLAGLTISRLRERRDplvI--SkiklneligdLQVVLTEFFIPLFFIYVGLMFNPSLN---ELSIVL 302
                                       ******************88888888643..33586566666666666****************6666...666667 PP

                                       HHHHHHHHHTHHHHHHHHHTTTXSSXHHHHHHCCCCSS.BHHHHHHHHHHHHHHXHHHHTTSSTTTCSTSXHHHHHH CS
                    Na_H_Exchanger 296 vllilvaillgrilavflllrllglslrealiigfgglqrgavalalaalgpalgllarelyallivvvlftvlvqG 372
                                       + l+++a ++g++l+  l  +l+++++++a+++g+g+ +rg++ la++ +g  +gl+++ l+a++++v ++t +   
  gi|242398450|ref|YP_002993874.1| 303 IGLLYLAAVIGKFLGCGLGMKLFKFDWKSAALVGIGMGGRGSLELAILKFGIEEGLIDQSLFAAVVIVSMLTAV--- 376
                                       7777777779**************************************************************99... PP

                                       HHHHH CS
                    Na_H_Exchanger 373 lslkp 377
                                         ++p
  gi|242398450|ref|YP_002993874.1| 377 --TTP 379
                                       ..444 PP

>> Cons_hypoth698  Conserved hypothetical protein 698
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1  11.8   5.5e-06     0.033       9     142 ..      10     139 ..       3     167 .. 0.78
   2 ?    1.7  14.7     0.016        94     149     273 ..      86     212 ..      84     245 .. 0.63
   3 ?    6.5   0.6   0.00055       3.3      85     137 ..     301     355 ..     285     388 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.5e-06
                    Cons_hypoth698   9 iavlalllakvellfaklsalllAillGillgnflklqeqlkaGvafskkklLrlgivllGfrltlsdiakvGlkgv 85 
                                       + vla+ l+   +  +++ +++  il G++lg+f+      ++ +++ +++ L +    +G++ ++s ia+  +k++
  gi|242398450|ref|YP_002993874.1|  10 LLVLAKSLEWL-FEKKEIHPIIAHILTGMILGPFFLNVVVPSEPLKVLSEFGLLMMMLYMGLTSNFSSIASNKSKAI 85 
                                       33444444443.577889999999*********99999999999********************************* PP

                    Cons_hypoth698  86 lldiivlistfllvlllgakllkldkklalLvaaGssiCGasAilavepv.ikareee 142
                                       l+ ++ +i++f+l +l +  +++   + a+ v++     G  Ai  ++ v +kar  +
  gi|242398450|ref|YP_002993874.1|  86 LVAALGVIFSFILGFLTV-YAFGKGLAAAIFVGVTL---GNTAIEVTSGVlLKARIRK 139
                                       **************9999.89999999999888864...6777777766523566555 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.016
                    Cons_hypoth698 149 vivllgtvamllyPalatllsltdeefgvfaGasvhevaqVvaagelvseeaak..iAvivKltRvll.lapvvlll 222
                                        +++lg+++ +++ +l  ++  +  ++++f+G+++ ++a  v +g l+++   k     i  +   ++  +++v l+
  gi|242398450|ref|YP_002993874.1|  86 LVAALGVIFSFILGFLTVYAFGKGLAAAIFVGVTLGNTAIEVTSGVLLKARIRKelS-SIL-MGAAFAdDIMAVYLI 160
                                       5899******************************************99998887642.333.222222122233333 PP

                    Cons_hypoth698 223 slllakreeesetkeakitiPwFvlgFlvvallntlvllp..selvsalktls 273
                                       +++ a ++ e   +    ++   +++F+ ++ll + ++++  s + s+l++l 
  gi|242398450|ref|YP_002993874.1| 161 GIITAMTKGELAFSP-LVVLTIKIVLFITAVLLVSEYIFKrsSRFYSILRNLN 212
                                       333344444334444.5566666777777777777666666644444444443 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.00055
                    Cons_hypoth698  85 vlldiivlistf..llvlllgakllkldkklalLvaaGssiCGasAilavepvik 137
                                       vl+ ++ l++++  +l + lg+kl+k+d k a+Lv++G +  G+   ++++  i+
  gi|242398450|ref|YP_002993874.1| 301 VLIGLLYLAAVIgkFLGCGLGMKLFKFDWKSAALVGIGMGGRGSLELAILKFGIE 355
                                       5555555554442257888999****************98666655555555554 PP

>> Ldr_toxin  Toxin Ldr, type I toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.4    0.0014       8.6      17      29 ..      28      40 ..      26      42 .. 0.92
   2 ?   -2.0   0.1      0.67     4e+03       9      22 ..     105     118 ..     104     120 .. 0.76
   3 ?    4.8   0.5     0.005        30       7      26 ..     147     166 ..     145     171 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0014
                                      HHHHHHHHHHHHH CS
                         Ldr_toxin 17 PvlAGIlaaaIVn 29
                                      P++A Il+ +I +
  gi|242398450|ref|YP_002993874.1| 28 PIIAHILTGMILG 40
                                      9**********87 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.67
                                       HHHHHHHHHHHHHH CS
                         Ldr_toxin   9 aFWHDLAAPvlAGI 22 
                                       aF   LAA +  G+
  gi|242398450|ref|YP_002993874.1| 105 AFGKGLAAAIFVGV 118
                                       56667999998886 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.005
                                       HHHHHHHHHHHHHHHHHHHH CS
                         Ldr_toxin   7 aMaFWHDLAAPvlAGIlaaa 26 
                                       + aF  D+ A  l GI++a+
  gi|242398450|ref|YP_002993874.1| 147 GAAFADDIMAVYLIGIITAM 166
                                       779999*************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1069  (0.0596241); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.45
# Mc/sec: 2631.42
//
Query:       gi|242398451|ref|YP_002993875.1|  [L=389]
Description: L-tyrosine decarboxylase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.2e-34  117.1   0.0    2.6e-33  115.3   0.0    1.7  1  Pyridoxal_deC    Pyridoxal-dependent decarboxylase conserved 
    4.3e-11   42.4   0.0    1.6e-09   37.2   0.0    2.0  2  Aminotran_5      Aminotransferase class-V
    7.6e-09   35.3   0.3    4.9e-08   32.7   0.0    1.9  2  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    0.00015   21.1   0.0    0.00029   20.2   0.0    1.4  1  Beta_elim_lyase  Beta-eliminating lyase
    0.00052   18.8   0.0      0.067   11.9   0.0    2.3  2  SepSecS          O-phosphoseryl-tRNA(Sec) selenium transferas
  ------ inclusion threshold ------
      0.011   15.0   0.0      0.019   14.2   0.0    1.3  1  Aminotran_1_2    Aminotransferase class I and II


Domain annotation for each model (and alignments):
>> Pyridoxal_deC  Pyridoxal-dependent decarboxylase conserved domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.3   0.0   8.7e-37   2.6e-33      78     373 ..      70     337 ..       6     339 .. 0.90

  Alignments for each domain:
  == domain 1  score: 115.3 bits;  conditional E-value: 8.7e-37
                                       HHHHHHHHHHHHHHTT--GGGTCCT-EEEEESSHHHHHHHHHHHHHHHHHHHHHHHTTTS.HHHHHCCEEEEEETTS CS
                     Pyridoxal_deC  78 televvvldwlaellglpeeflekegggvlqvgssestllallAartkvikemkekgkelkeaeildklvlytsdqa 154
                                        e+e   +++l+ell+l        + g + +g++e++ la+ A+r+     + + +          k+ l   + a
  gi|242398451|ref|YP_002993875.1|  70 KEIEEEAVQMLGELLHLK------RAYGNIVSGGTEANVLAVRAFRN-----VSNVE----------KPELILPESA 125
                                       689999999999999998......36788899999**9999877764.....44444..........6677888899 PP

                                       -HHHHHHHHHHT-EEEEE--BTTTBB-HHHHHHHHHHHHCTT.EEEEEEEEBS-TTT-BB--HHHHHHHHHHCT-EE CS
                     Pyridoxal_deC 155 hssvekaalvlgvklrvipldengklrgaalekaieedkekGlipffvvatlGttvlgaFddlkelgdicekydlwl 231
                                       h s  ka+ +l+vkl    l+ ++++ +++ e +i ++     ++  +v ++Gtt+lg  dd+  l di   y+++l
  gi|242398451|ref|YP_002993875.1| 126 HFSFLKASDLLKVKLVWADLNRDYSVNVKDVESKITDN-----TI-GIVGIAGTTGLGVVDDIPALSDIAVDYGIPL 196
                                       ******************************99999764.....44.6889*************************** PP

                                       EEE-TTGGGGGGSGGGGG.......GGTTGGGESEEEEECCCCTS--SS-EEEEESSCCGCHHHH-EEECCCT.TTT CS
                     Pyridoxal_deC 232 HvDAAyaGsaficpeirh.......llkgieradSitvnphKlllvlldcsalivkdkealqqalqleaeYLeheds 301
                                       H+DAA++G  f+ p+ +        +++++  ++Sit+ phK++++++ ++ +++++k+ +   + + a YL     
  gi|242398451|ref|YP_002993875.1| 197 HIDAAFGG--FVIPFAKAlgyelpdFDFKLKGVQSITIDPHKMGMAPIPAGGIVFRKKKYMDAIN-VLAPYLA---- 266
                                       ********..*****99999999999******************************999876655.8888**9.... PP

                                       TTSEECCCGSSSSSG.HHTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTEEECSTTBSSEEEEE CS
                     Pyridoxal_deC 302 dvaadlgtkaiplsr.rvrilklwfvlralGveglqnqirksvelakyleklirkderfeivaevelglVcFr 373
                                            + + +i   r   +++ +w +++ lG eg++n++++ +e+a  ++++i++  r  ++ e+ l  V+F 
  gi|242398451|ref|YP_002993875.1| 267 --GGKIFQATITGTRlGANAIAVWALFKHLGFEGYKNVVKEAMENALWFAEQIKRLDRVYLIREPMLNIVSFG 337
                                       ..5789999999999999*****************************************************95 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.2   0.0   5.5e-13   1.6e-09      42     177 ..      70     201 ..      44     215 .. 0.87
   2 ?    3.4   0.0      0.01        31     250     321 ..     276     343 ..     218     377 .. 0.81

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 5.5e-13
                                       HHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC.-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEE CS
                       Aminotran_5  42 tkaveearekvaelinaeseeeiiftsGtteainlvalslars.lkpgdeivvteaehhanlvpwqelakrtgakvk 117
                                       +++ eea + + el++ + ++  i +sG+tea+ l+++++++    ++ e ++ e+ h + l    ++++  ++k++
  gi|242398451|ref|YP_002993875.1|  70 KEIEEEAVQMLGELLHLKRAYGNI-VSGGTEANVLAVRAFRNVsNVEKPELILPESAHFSFL----KASDLLKVKLV 141
                                       456677777778888888766555.7**************9999999***************....6666678**** PP

                                       EEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-T CS
                       Aminotran_5 118 vipldeegeldldelekllnektklvaithvsnvtGtiqpveeigklakkkgalvlvDaa 177
                                       ++ l+++ +++++++e++++++t  +   +  + +G++++++++ ++a ++g+ +++Daa
  gi|242398451|ref|YP_002993875.1| 142 WADLNRDYSVNVKDVESKITDNTIGIVGIAGTTGLGVVDDIPALSDIAVDYGIPLHIDAA 201
                                       ***********************9999999*****************************8 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.01
                                       .SS--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-CTCBSEEEEEETTCSH CS
                       Aminotran_5 250 aGTpnvagiiglgaaleyleeigleaiekhekelaeyllerlkslpgvrlygpdkaerrasivsfnfkgvha 321
                                        GT   a++i++ a +++l   g++++ k++ e a +  e++k l+ v+l+     e   +ivsf  k+++ 
  gi|242398451|ref|YP_002993875.1| 276 TGTRLGANAIAVWALFKHLGFEGYKNVVKEAMENALWFAEQIKRLDRVYLIR----EPMLNIVSFGSKRLKK 343
                                       489999999****************************************977....5667777776655543 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.0   1.6e-11   4.9e-08      41     146 ..      91     201 ..      69     204 .. 0.86
   2 ?    0.5   0.1       0.1     3e+02     231     299 ..     314     381 ..     300     388 .. 0.67

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 1.6e-11
                                       EEEESSHHHHHHHHHHH.TTTT..TT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSSB-GGGCGGG--TTEEE CS
                   DegT_DnrJ_EryC1  41 aiavssGtaAlhlaLra.lgvg..pgdeVIvpsltFvatanavlelgakpvfvDvdpdtynidpaaieaaitertka 114
                                          vs Gt+A+ la ra  +v+  ++ e+I p    ++  +a   l  k v +D +  +y ++++++e++it +t +
  gi|242398451|ref|YP_002993875.1|  91 GNIVSGGTEANVLAVRAfRNVSnvEKPELILPESAHFSFLKASDLLKVKLVWADLN-RDYSVNVKDVESKITDNTIG 166
                                       456999***********845555679*****************************9.89****************66 PP

                                       EE...EB-GGGB---HHHHHHHHHHCT-EEEEE-T CS
                   DegT_DnrJ_EryC1 115 Il...pVhlyGqvadmdalkaiaakhglkvieDaA 146
                                       I+       +G v d++al +ia ++g+++  DaA
  gi|242398451|ref|YP_002993875.1| 167 IVgiaGTTGLGVVDDIPALSDIAVDYGIPLHIDAA 201
                                       66111456678899********************9 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.1
                                       HHHHCTHHHHHHHHHHHHHHHH...HHHHTCCCCEESCGGTTSSSEEESCEEEEEHCCHHHCHHHHHHHHHH CS
                   DegT_DnrJ_EryC1 231 laqLerldelvarRreiaelyk...eeLaelegtaelttpketkkhawhlyavlveeeaevkrdelvealke 299
                                        +q++rld++   R+ ++++ +   ++L+++e +++++        + h+  +++    +vkr++l+++lk+
  gi|242398451|ref|YP_002993875.1| 314 AEQIKRLDRVYLIREPMLNIVSfgsKRLKKIEAELKARGWG----ISAHRGYIRIVMMPHVKREHLMNFLKD 381
                                       57888999988888877777651115666666544444444....44555555555554589******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 !   20.2   0.0   9.8e-08   0.00029      52     241 ..      93     278 ..      57     363 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 9.8e-08
                                       EES-HHHHHHHHH....HHH--TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTTTBE-HHHHHHHS--S-TT CS
                   Beta_elim_lyase  52 fvpqGtaAnsill....killqrgeevivtepahihfdetgaiaelagvklrdlknkeaGkmdlekleaaikevgah 124
                                        v  Gt An +++    ++  + ++e i+ e ah+ f  +  +     vkl+ ++ +++  ++++++e++i++    
  gi|242398451|ref|YP_002993875.1|  93 IVSGGTEANVLAVrafrNVSNVEKPELILPESAHFSFLKASDLL---KVKLVWADLNRDYSVNVKDVESKITD---- 162
                                       4677999***9996665444578899999999*99998776664...45555555555569***********9.... PP

                                       S-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETT...HHHHHHHHTS-CHHHH...TTSSEEEEE CS
                   Beta_elim_lyase 125 eekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgAR...fanaakslgeivkemf...syvDsvtms 195
                                        + i+++ ++ T+    G    ++ + ++++ia +ygiplh+D+A    ++  ak+lg ++ +     ++v s+t+ 
  gi|242398451|ref|YP_002993875.1| 163 -NTIGIVGIAGTTGL--GV---VDDIPALSDIAVDYGIPLHIDAAFggfVIPFAKALGYELPDFDfklKGVQSITID 233
                                       .589*********98..65...5999******************94332455569999988887556699******* PP

                                       SSSTT--SS..-EEEEE-HH....HHHHHHHHHHHHT-.--SSTHHHHH CS
                   Beta_elim_lyase 196 lkKdllanv..Ggvlafrddeledylaerveqrkylgg.glrqagvlaa 241
                                         K ++a++  Gg+++ +++    y++    ++ yl+g ++ qa + + 
  gi|242398451|ref|YP_002993875.1| 234 PHKMGMAPIpaGGIVFRKKK----YMDAINVLAPYLAGgKIFQATITGT 278
                                       *******9944566666666....6665555666665414456665555 PP

>> SepSecS  O-phosphoseryl-tRNA(Sec) selenium transferase, SepSecS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   2.3e-05     0.067     103     195 ..     118     203 ..      71     207 .. 0.76
   2 !    4.7   0.0    0.0035        10     266     296 ..     292     322 ..     276     342 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.3e-05
                                       CCEEEEEETCHHHHHHHCTT-EEEEE-EEECTTEEEEHHHHHHHHHHCCTCCCEEEEEECSSTTTTB----HHHHHH CS
                           SepSecS 103 kviwvridekSslkavelaGleialvekvlegDelitdvedveeiiekkreevilavlstlsffaprspDdvkeiak 179
                                       + i +  ++ S lka  l  l++ lv   l++D+  ++v+dve++i+    ++i +v    ++  + + Dd+++++ 
  gi|242398451|ref|YP_002993875.1| 118 ELILPESAHFSFLKASDL--LKVKLVWADLNRDY-SVNVKDVESKITD---NTIGIVGIAGTTGLG-VVDDIPALSD 187
                                       567777788888888776..68888999999998.5899999999988...444444333344445.5566****** PP

                                       HHHCCT--EEEEGCCC CS
                           SepSecS 180 iCaeydvPhlvNgAYa 195
                                       i  +y++P+ + +A++
  gi|242398451|ref|YP_002993875.1| 188 IAVDYGIPLHIDAAFG 203
                                       **************97 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0035
                                       HHCCHHHCCHHHHHHHHHHHHHHHHHHHHHH CS
                           SepSecS 266 lllGskaykkllkeqkesfkllreklkklae 296
                                         lG ++yk+++ke +e      e++k+l++
  gi|242398451|ref|YP_002993875.1| 292 KHLGFEGYKNVVKEAMENALWFAEQIKRLDR 322
                                       679*************************996 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 ?   14.2   0.0   6.2e-06     0.019      43     196 ..      66     208 ..      30     222 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6.2e-06
                                       TTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHH..HTTT-EEEEEESS-THHHHHHHHTTSEE CS
                     Aminotran_1_2  43 idglpeleealakflgrseklklkreaavvvgsGagaliealifllk..lnpgdeilvpdptyasyknilrlsggev 117
                                        +g++e ee+  + lg  e l lkr    +v++G+ a+  a+ ++ +  +  + e ++p+  + s+ ++  l ++++
  gi|242398451|ref|YP_002993875.1|  66 HRGSKEIEEEAVQMLG--ELLHLKRAYGNIVSGGTEANVLAVRAFRNvsNVEKPELILPESAHFSFLKASDLLKVKL 140
                                       5799************..9*******88888888888877776665444667788********************** PP

                                       EEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCB CS
                     Aminotran_1_2 118 vryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfv 194
                                       v   l+   d++++++++e ++++       t +i+        G+v + + l ++   a  y++ l +D a++gfv
  gi|242398451|ref|YP_002993875.1| 141 VWADLN--RDYSVNVKDVESKITD------NTIGIVGIAGTTGLGVVDDIPALSDI---AVDYGIPLHIDAAFGGFV 206
                                       ****99..***************9......45566655556789999999999999...*****************9 PP

                                       SS CS
                     Aminotran_1_2 195 fg 196
                                         
  gi|242398451|ref|YP_002993875.1| 207 IP 208
                                       75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); 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: 0.65u 0.30s 00:00:00.95 Elapsed: 00:00:00.49
# Mc/sec: 2375.99
//
Query:       gi|242398452|ref|YP_002993876.1|  [L=63]
Description: hypothetical protein TSIB_0461 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.076   13.2   0.1      0.078   13.1   0.1    1.2  1  DUF1492   Protein of unknown function (DUF1492)


Domain annotation for each model (and alignments):
>> DUF1492  Protein of unknown function (DUF1492)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   4.4e-06     0.078      22      56 ..       2      36 ..       1      56 [. 0.93

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.4e-06
                           DUF1492 22 dvyveLvvakediekktaeaikkklelqrlidkle 56
                                      ++y e++ + e i+ +t e++++ + l++l+++l 
  gi|242398452|ref|YP_002993876.1|  2 NIYSEVIKMYEVINLSTGEIVRRGKVLEKLLQNLP 36
                                      59****************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); 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: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 424.86
//
Query:       gi|242398453|ref|YP_002993877.1|  [L=446]
Description: Phosphomethylpyrimidine kinase [Thermococcus sibiricus MM 739]
Scores for complete 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-94  314.5   1.1    5.4e-94  314.2   1.1    1.1  1  Phos_pyr_kin  Phosphomethylpyrimidine kinase
      1e-59  200.8   0.0    2.7e-59  199.5   0.0    1.7  2  ThiP_synth    Thiamine-phosphate synthase
    1.1e-13   51.2   0.3    4.1e-13   49.3   0.2    1.9  2  PfkB          pfkB family carbohydrate kinase
      0.002   17.6   2.6      0.007   15.8   2.5    1.8  1  HK            Hydroxyethylthiazole kinase family


Domain annotation for each model (and alignments):
>> Phos_pyr_kin  Phosphomethylpyrimidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  314.2   1.1   1.2e-97   5.4e-94       1     246 []      12     255 ..      12     255 .. 0.99

  Alignments for each domain:
  == domain 1  score: 314.2 bits;  conditional E-value: 1.2e-97
                                       ETTSSSHHHHHHHHHHHTTEEEEEEEEEEEEEETTCEEEEEE--HHHHHHHHHHHHHTS--SEEEE-S--SHHHHHH CS
                      Phos_pyr_kin   1 DssGGAGiqADlktfsalgvygmsvitaltaqntkgvkevhplpaelveaqleavledvkvdavKiGmlasaeiiev 77 
                                       Ds+GGAGi+ADlktfsa+gv+g+ +it++taqnt++v++++++++e+v++q+eav+ed++vda+K+Gml++a+ii++
  gi|242398453|ref|YP_002993877.1|  12 DSGGGAGIEADLKTFSAFGVHGLVAITSVTAQNTQEVRAIYDISPEVVAKQIEAVVEDIGVDAAKTGMLSNAKIIKA 88 
                                       9**************************************************************************** PP

                                       HHHHHHHTTSSEEEE---SSCTSSSBSSHHHHHHHHHHTGGG-SEEE-BHHHHHHHHT---SSHHHHHHHHHHHHH. CS
                      Phos_pyr_kin  78 vaeklkkykvpvVlDPVmvaksgselleeeavealkeeLlplatvitPNlpEaeaLlgekikteedmkeaakkllk. 153
                                       va+++kky++p+V+DPVm+aksg++ll+e+a+eal e+++plat++tPN  Eae+L+g+ki+ +ed+k+aak +++ 
  gi|242398453|ref|YP_002993877.1|  89 VAKTVKKYEFPLVVDPVMIAKSGAPLLREDAMEALIEKIIPLATLVTPNKSEAEKLSGMKIEGLEDAKKAAKIIVEe 165
                                       ****************************************************************************9 PP

                                       TT-SEEEEEEGGS-SSSEEEEEEEETSSEEEEEEEE----S--BTHHHHHHHHHHHHHHCTSSHHHHHHHHHHHHHH CS
                      Phos_pyr_kin 154 lgakaVlikGghlegeeavvtdvlydgeeveeleaerietknthGtGCtlssaiaaelakgesleeAvkkAkeyvte 230
                                       lgak  ++kGghl+ +eav  dvly +e+++e++a+ ++   thGtGC++s+ai+a+lakg++leeAv+ Ake++t 
  gi|242398453|ref|YP_002993877.1| 166 LGAKGAIVKGGHLSLSEAV--DVLYFNEKFREYRAPFVK-GCTHGTGCSFSAAITANLAKGKKLEEAVRIAKEFITM 239
                                       *************777777..******************.************************************* PP

                                       HHHCG-BSTSSS-B-- CS
                      Phos_pyr_kin 231 aikealelgkgagpvn 246
                                        i ++ ++g+g+ pvn
  gi|242398453|ref|YP_002993877.1| 240 GIYYGPRIGHGHCPVN 255
                                       **************97 PP

>> ThiP_synth  Thiamine-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       0.7   3.1e+03      77     107 ..      44      77 ..      27     105 .. 0.56
   2 !  199.5   0.0   5.9e-63   2.7e-59       2     164 ..     273     442 ..     272     443 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.7
                                       C-TT--EEEEEE--...HHHHHHHCCTTSEEEE- CS
                        ThiP_synth  77 fdpevraainiryd...ekilealeelglkvvef 107
                                       + +evra  +i+ +   ++i++ +e+ g++++++
  gi|242398453|ref|YP_002993877.1|  44 NTQEVRAIYDISPEvvaKQIEAVVEDIGVDAAKT 77 
                                       4455555555554333355555555555555544 PP

  == domain 2  score: 199.5 bits;  conditional E-value: 5.9e-63
                                       HHHHHHHHHCC--.GCC--TT-B-EEEE-S..T--SGGGEEEETT-EEE-TSSEEE-S-EEETS-CHHHHHHHHHHC CS
                        ThiP_synth   2 leralelleeeeefakliPevgsNiayalp..dAksieDvaavpGRIvrvkgrvkvvgepefgasshvarvllaamk 76 
                                       l +al++l++++++++  Pevg+N+ yalp  +A+s eDva+v+GRIv++++++k+vg +efgas+h+ r++l++m+
  gi|242398453|ref|YP_002993877.1| 273 LGNALKELMSIDNLYEHAPEVGMNFIYALPklYARSKEDVAGVKGRIVKFGNKIKPVGWVEFGASDHLTRAILTFME 349
                                       678************************************************************************** PP

                                       C-TT--EEEEEE--HHHHHHHCCTTSEEEE--CCCS-CCC....T-HHHHHHHHHHHCC.S-ECEEEE--BCTB--E CS
                        ThiP_synth  77 fdpevraainirydekilealeelglkvvefdreeepeev....gstmewgvaeaieel.evpdviydeGgvGkEpm 148
                                       f+pevr+a+n++y+e++++++++lglkv+ +dr+eepee+    g+t++wgv++aie+  + pd+iy+ G++GkEpm
  gi|242398453|ref|YP_002993877.1| 350 FFPEVRSALNLKYSEELIKKASSLGLKVSFYDRREEPEEIkakeGGTIPWGVKTAIERInDKPDIIYHLGDWGKEPM 426
                                       ***********************************************************989*************** PP

                                       EEEEESSHHHHHHHHH CS
                        ThiP_synth 149 iyvlgkdaeevvekvl 164
                                       + ++g+++e v++k++
  gi|242398453|ref|YP_002993877.1| 427 LLIFGENPEIVLRKLK 442
                                       *************986 PP

>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.3   0.2   9.2e-17   4.1e-13     160     283 ..      98     234 ..      79     236 .. 0.75
   2 ?   -2.9   0.0       0.7   3.2e+03      64      87 ..     362     385 ..     361     392 .. 0.82

  Alignments for each domain:
  == domain 1  score: 49.3 bits;  conditional E-value: 9.2e-17
                                       E...EEEEECESSSHH......HHHHHHHHHCTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTSSEEEEEE CS
                              PfkB 160 t...fdpnlldplgaq......fkeallellaladllkpneeElealtgekledieealaalhklkakgaktvvvtl 227
                                       +   +dp++ +++ga       +   ++++++la+l++pn +E+e+l+g+k+e  e+a++a++         +v  l
  gi|242398453|ref|YP_002993877.1|  98 FplvVDPVMIAKSGAPllredaMEALIEKIIPLATLVTPNKSEAEKLSGMKIEGLEDAKKAAKI--------IVEEL 166
                                       445567777777777676667667889999**********************999999999876........66666 PP

                                       GGGEEEEEE..............TTEEEEEEE.SSSS-SBGTTHHHHHHHHHHHHHHTTHHHHHHHHHHH CS
                              PfkB 228 GkeGalvve..............kdgelkvpavpkvkvvDttGAGDsfvggflaallegksleealrfan 283
                                       G++Ga+v+               +++  +  a p vk   t G+G sf ++++a+l++gk+leea+r+a 
  gi|242398453|ref|YP_002993877.1| 167 GAKGAIVKGghlslseavdvlyfNEKFREYRA-PFVK-GCTHGTGCSFSAAITANLAKGKKLEEAVRIAK 234
                                       66666666666666666667776444444444.5444.56***************************996 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.7
                                       HHHHHHHHHHHTTEEETTEEEESS CS
                              PfkB  64 fGeflleelkkegvdtdyvkided 87 
                                       ++e+l+++ ++ g++++++ + e+
  gi|242398453|ref|YP_002993877.1| 362 YSEELIKKASSLGLKVSFYDRREE 385
                                       78999999*********9998776 PP

>> HK  Hydroxyethylthiazole kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   2.5   1.6e-06     0.007      57     202 ..      77     224 ..      55     240 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.6e-06
                                       -TT--HHHHHHHHHHHHHHHHTT--EEEE-TT...BTTBHHHHHHHHHHHHHS--..SEEEEEHHHHHHHHTSSCCS CS
                                HK  57 iGtleekaiealkaAvksakevnrPvvlDPVg...vgAtelRrelalellkevkl..avikGNasEilslaglelkv 128
                                       +G l++  ++++ka +k+ k+ + P+v+DPV    +gA  lR++ ++ l+++  +   ++  N+sE  +l+g++  +
  gi|242398453|ref|YP_002993877.1|  77 TGMLSN--AKIIKAVAKTVKKYEFPLVVDPVMiakSGAPLLREDAMEALIEKIIPlaTLVTPNKSEAEKLSGMK--I 149
                                       688888..89999999***************622358999**********876532267999*********986..5 PP

                                       CSS.SSSS-SHHHHHHHHHHHHHHTSE....EEEESSSEEEEESSEEEEEE-S-G.GGGGSTTHHHHHHHHHHHHHT CS
                                HK 129 kGv.DskeaataavaavqkvAqklrvv....vvvtGevDvvsdgkkvyklknGte.llgkitasGCllgsvvaafla 199
                                        G+ D+k+aa+    +v+++  k  +v      ++ +vDv+   +k  + +   + + g   ++GC+++++++a la
  gi|242398453|ref|YP_002993877.1| 150 EGLeDAKKAAK---IIVEELGAKGAIVkgghLSLSEAVDVLYFNEKFREYRA--PfVKGCTHGTGCSFSAAITANLA 221
                                       67724444444...34444444433221111445555555544444333322..22445566899999999988887 PP

                                       TBS CS
                                HK 200 vkk 202
                                         k
  gi|242398453|ref|YP_002993877.1| 222 KGK 224
                                       543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); 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: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 2892.19
//
Query:       gi|242398454|ref|YP_002993878.1|  [L=161]
Description: ThiW protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.7e-43  146.0  13.5    9.7e-43  145.8  13.5    1.0  1  ThiW          Thiamine-precursor transporter protein (ThiW)
    1.3e-05   25.3  22.8    5.8e-05   23.3  22.8    1.9  1  ECF_trnsprt   ECF transporter, substrate-specific component
    7.7e-05   22.3  12.9    0.00013   21.5  12.9    1.4  1  5TM-5TMR_LYT  5TMR of 5TMR-LYT
  ------ inclusion threshold ------
       0.15   12.2   3.1        0.3   11.2   0.8    2.5  2  ArAE_1        Aromatic acid exporter family member 1
        3.9    7.6   8.6       0.52   10.5   0.8    2.6  3  DUF4229       Protein of unknown function (DUF4229)


Domain annotation for each model (and alignments):
>> ThiW  Thiamine-precursor transporter protein (ThiW)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.8  13.5   2.7e-46   9.7e-43       1     149 [.      10     156 ..      10     157 .. 0.94

  Alignments for each domain:
  == domain 1  score: 145.8 bits;  conditional E-value: 2.7e-46
                              ThiW   1 lallavlialgvvlssllsipvgvakvaPvqhvvNvvaavllGPwyalavalvisliRnllgtgtllalpGsiiGal 77 
                                       la++ +++algv+l+++ s+pvg++kvaP+qh++Nv+++vllGPw+a  +al i+++R+ lg+gt++++pG+i+Ga+
  gi|242398454|ref|YP_002993878.1|  10 LAYVGIFTALGVILGTI-SFPVGPTKVAPFQHFINVITGVLLGPWWASLTALFIGTLRMSLGVGTIFSIPGGIPGAF 85 
                                       7899*************.*********************************************************** PP

                              ThiW  78 lagllyrltrklllaalgEvlGtgiiGallaypvaklllgkeaallvlvisFilstliGsviallvlkalek 149
                                        +gl+y+++++  +aa+ E+l t++iG++l+ ++   l++ ++ ++ ++++F+ stl+G+++++l+lkal++
  gi|242398454|ref|YP_002993878.1|  86 TVGLMYKIVKN-DWAAFSEPLATVFIGGTLSSLLFGPLINIQKGVVWFWVAFAPSTLVGTTLGFLILKALRR 156
                                       *********99.68899***********97666666666888889999**********************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 !   23.3  22.8   1.6e-08   5.8e-05       2     120 ..       9     150 ..       8     157 .. 0.67

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 1.6e-08
                                       HHHHHHHHHHHHHHHHHHHEEE.STS...EEESHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHCHT-SSTTHHHH.. CS
                       ECF_trnsprt   2 klvitglliAisivlsllgyiplpni...kitiihipvllggllfGpikGailgiitsvlkailtggtgalssfv.. 73 
                                       kl+ +g+++A+ ++l+    i +p+     + + h++ ++ g+l+Gp+++ + ++++ +l++ l g ++++s+++  
  gi|242398454|ref|YP_002993878.1|   9 KLAYVGIFTALGVILG---TISFPVGptkVAPFQHFINVITGVLLGPWWASLTALFIGTLRMSL-GVGTIFSIPGgi 81 
                                       89**************...888885577459*********************************.566556554444 PP

                                       ..................HHHHHHHHCHHHHHHHHHHCCCHTTHHHH.............................. CS
                       ECF_trnsprt  74 ..................piaflsriligliagllykkgkkknlkei.............................. 102
                                                                                     +                              
  gi|242398454|ref|YP_002993878.1|  82 pgaftvglmykivkndwaA---------------------------Fseplatvfiggtlssllfgpliniqkgvvw 131
                                       4444444444444444330...........................3444444444444444444444444444334 PP

                                       .HHHHHHHHCCCCCHHHHH CS
                       ECF_trnsprt 103 .vvsfilagvlgtivatll 120
                                        +v+f+ ++++gt +++l+
  gi|242398454|ref|YP_002993878.1| 132 fWVAFAPSTLVGTTLGFLI 150
                                       4788888888888777776 PP

>> 5TM-5TMR_LYT  5TMR of 5TMR-LYT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5  12.9   3.6e-08   0.00013      14     161 ..       5     149 ..       1     157 [. 0.75

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 3.6e-08
                      5TM-5TMR_LYT  14 tlksklllglifglfsilgtytgieie.gaiantRaigvvvaGllgGplvGliagliaglhRyllgGftalacgist 89 
                                       t+ +kl+++ if+++++++   ++++    +a + +   v+ G+l Gp+++ +++l +g +R++lg  + ++ +   
  gi|242398454|ref|YP_002993878.1|   5 TRTQKLAYVGIFTALGVILGTISFPVGpTKVAPFQHFINVITGVLLGPWWASLTALFIGTLRMSLGV-GTIFSIPGG 80 
                                       778999********************7559*********************************8876.999999*** PP

                      5TM-5TMR_LYT  90 ilagllaGlihrklkrrrkkltvlvalligllveilqmllilllakpfdqalalvktialPmilvnslgtal 161
                                       i  ++ +Gl+++ +k+++    + + l++ +++ +l  ll+  l++ ++  + +    a P +lv ++  +l
  gi|242398454|ref|YP_002993878.1|  81 IPGAFTVGLMYKIVKNDW--AAFSEPLATVFIGGTLSSLLFGPLINIQKGVVWFWVAFA-PSTLVGTTLGFL 149
                                       ***************954..445555555555555555665555544444444433333.444444333333 PP

>> ArAE_1  Aromatic acid exporter family member 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.8   8.5e-05       0.3      38      90 ..      28      80 ..       1     123 [. 0.78
   2 ?   -3.6   0.1         3   1.1e+04      59      66 ..     141     148 ..     131     154 .. 0.50

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 8.5e-05
                            ArAE_1 38 lsiqptkkrslrtalerllasvlaliiavvffellGykpiviglvlllfiplt 90
                                      + + ptk   ++ +++ + +++l+   a + ++++G   +++g+  ++ ip  
  gi|242398454|ref|YP_002993878.1| 28 FPVGPTKVAPFQHFINVITGVLLGPWWASLTALFIGTLRMSLGVGTIFSIPGG 80
                                      56899*********************************************954 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 3
                            ArAE_1  59 vlaliiav 66 
                                       ++++ +++
  gi|242398454|ref|YP_002993878.1| 141 LVGTTLGF 148
                                       22333222 PP

>> DUF4229  Protein of unknown function (DUF4229)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   1.2      0.17     6e+02      23      41 ..      44      62 ..      10      71 .. 0.68
   2 ?   -0.1   0.1      0.28     1e+03       9      29 ..      59      81 ..      54      90 .. 0.73
   3 ?   10.5   0.8   0.00014      0.52      10      55 ..     108     156 ..     106     158 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.17
                           DUF4229 23 rliglpvpllvaallAlvv 41
                                      ++ g+ ++ ++a l Al +
  gi|242398454|ref|YP_002993878.1| 44 VITGVLLGPWWASLTALFI 62
                                      3333336667777777776 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.28
                           DUF4229  9 aLfvvltavillvarliglp..v 29
                                      aLf++++   l+v+ ++ +p  +
  gi|242398454|ref|YP_002993878.1| 59 ALFIGTLRMSLGVGTIFSIPggI 81
                                      68888888888888888777443 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.00014
                           DUF4229  10 Lfvvltavillvarliglp...vpllvaallAlvvalplSmvllkklRd 55 
                                       +f++ t+  ll++ li ++   v ++va+  + +v   l++++lk lR+
  gi|242398454|ref|YP_002993878.1| 108 VFIGGTLSSLLFGPLINIQkgvVWFWVAFAPSTLVGTTLGFLILKALRR 156
                                       5788888889999999999998888888889*****************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1066.91
//
Query:       gi|242398455|ref|YP_002993879.1|  [L=197]
Description: Thiamine-phosphate pyrophosphorylase [Thermococcus sibiricus MM 739]
Scores for complete 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-61  204.4   0.2      1e-60  204.2   0.2    1.1  1  TMP-TENI      Thiamine monophosphate synthase
    4.7e-08   32.8   0.7    5.7e-08   32.5   0.7    1.1  1  NMO           Nitronate monooxygenase
    0.00013   21.2   0.1    0.00018   20.7   0.1    1.2  1  NanE          Putative N-acetylmannosamine-6-phosphate epimer
    0.00036   19.9   0.1     0.0006   19.2   0.1    1.3  1  ThiG          Thiazole biosynthesis protein ThiG
    0.00098   18.6   2.1      0.016   14.7   0.6    2.2  2  His_biosynth  Histidine biosynthesis protein
     0.0025   17.0   0.2     0.0067   15.6   0.2    1.7  2  DUF561        Protein of unknown function (DUF561)
  ------ inclusion threshold ------
      0.011   14.9   0.4      0.032   13.4   0.1    1.8  2  IGPS          Indole-3-glycerol phosphate synthase
      0.023   14.5   0.1      0.061   13.1   0.0    1.8  2  QRPTase_C     Quinolinate phosphoribosyl transferase, C-termi


Domain annotation for each model (and alignments):
>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  204.2   0.2   4.6e-64     1e-60       4     181 .]       2     175 ..       1     175 [. 0.98

  Alignments for each domain:
  == domain 1  score: 204.2 bits;  conditional E-value: 4.6e-64
                          TMP-TENI   4 vtdskldkneellevveealkggvtlvqlRekeldarellelaeklaalcrkygvpliindrvdlalavgadgvHlg 80 
                                       +td++l+   + +e v+eal+gg+t +qlR k++ + e+++  +++++l+++y++  +++dr+d+ala +adgv lg
  gi|242398455|ref|YP_002993879.1|   2 ITDRRLK---SEIESVREALEGGATSIQLRIKNAPTGEMIKIGKEIRELTKEYDALYFVDDRLDVALATDADGVQLG 75 
                                       7776666...8899*************************************************************** PP

                          TMP-TENI  81 qddlpvaearellgpdliiGlSvhsleeaeeaealgadYigvGpifpTdtKkdaeplgleglkelaealeiPvvaiG 157
                                        +d+p++ a+e +gp+liiG+Sv+sleea++ae++gadY+g+G++fpT+tK d +++gleglk+++e+++iPvvaiG
  gi|242398455|ref|YP_002993879.1|  76 PEDMPISLAKE-IGPNLIIGASVYSLEEALKAEKEGADYLGAGSVFPTPTKRDVKVIGLEGLKRIVESVKIPVVAIG 151
                                       *********99.99*************************************************************** PP

                          TMP-TENI 158 Gitlenvaevleagadgvavvsai 181
                                       Gi+++n+ +vl++g+dg+a++sai
  gi|242398455|ref|YP_002993879.1| 152 GINHKNARDVLKTGVDGIAIISAI 175
                                       ***********************8 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   0.7   2.6e-11   5.7e-08      47     240 ..       4     190 ..       1     196 [. 0.80

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 2.6e-11
                               NMO  47 aDrlakeirkvkaltdk.Pfgvnlflpkkdaadraekykkeleeaalelnieegvrfyrkvevvldekvevvsfgfg 122
                                         rl+ ei+ v+++ +     + l+++++ +++   k  ke+ e  +e+  ++ v    +++v l + ++ v +g +
  gi|242398455|ref|YP_002993879.1|   4 DRRLKSEIESVREALEGgATSIQLRIKNAPTGEM-IKIGKEIRELTKEYDALYFVD--DRLDVALATDADGVQLGPE 77 
                                       5579999999999999878899999999999998.778888999999999999999..9999999999998877654 PP

                               NMO 123 lpteevvarlkeag..vvliptissvkearkvearGaDalivqGpeaGGhqGtpevgdkglfaL..vpqvldavdiP 195
                                           +++   ke g  +++  ++ s +ea k+e+ GaD l      aG   +tp + d++ + L  ++++++ v+iP
  gi|242398455|ref|YP_002993879.1|  78 ---DMPISLAKEIGpnLIIGASVYSLEEALKAEKEGADYL-----GAGSVFPTPTKRDVKVIGLegLKRIVESVKIP 146
                                       ...5556555665511555566779*************98.....578889988888866666633689******** PP

                               NMO 196 viAaGGiidrrgvaaaLalGAsgvqigtrfLltkesdakdahkkk 240
                                       v+A GGi+ +++   +L  G  g++i ++ +++++ +      +k
  gi|242398455|ref|YP_002993879.1| 147 VVAIGGIN-HKNARDVLKTGVDGIAIISAIMGAEDVKRATEEMRK 190
                                       ******97.678899*****************9997655544444 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 !   20.7   0.1   8.2e-08   0.00018      93     183 ..      91     182 ..      61     190 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 8.2e-08
                                       -EEEEE-SSHHHHHHHHHTT-SEEE-TTTTSSTTS-..SS--HHHHHHHHHT.T--EEEES---SHHHHHHHHTT-- CS
                              NanE  93 qllmaDistleeglvakklGvdivGttlsGytkeeek.aepDfalvkalsea.glkviaeGrintPekakkaieiGv 167
                                       +++ a + +lee+l a+k G+d++G+     t ++++ +   ++ +k ++e+ ++ v+a G in  ++a++++++Gv
  gi|242398455|ref|YP_002993879.1|  91 LIIGASVYSLEEALKAEKEGADYLGAGSVFPTPTKRDvKVIGLEGLKRIVESvKIPVVAIGGINH-KNARDVLKTGV 166
                                       56668899*****************9866666666656777788788887653899*******97.78********* PP

                                       SEEEE-HHHH-HHHHH CS
                              NanE 168 davvvGsaitrleeia 183
                                       d + + sai   e++ 
  gi|242398455|ref|YP_002993879.1| 167 DGIAIISAIMGAEDVK 182
                                       *********9887764 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   2.7e-07    0.0006     165     224 ..     134     192 ..     113     194 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 2.7e-07
                                       HHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSHHHHHHHHHHHH CS
                              ThiG 165 ealkiiieeakvPvivDAGigspsdaaqamelGadavllntavaeakdpvamArafklav 224
                                       e lk i+e++k+Pv+   Gi + ++a  +++ G+d++ + +a+  a+d  +  + +++ +
  gi|242398455|ref|YP_002993879.1| 134 EGLKRIVESVKIPVVAIGGINH-KNARDVLKTGVDGIAIISAIMGAEDVKRATEEMRKII 192
                                       56899***********999975.789**********************999888888766 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.022        50     168     223 ..      66     120 ..      41     125 .. 0.86
   2 !   14.7   0.6   6.9e-06     0.016      63     109 ..     134     179 ..     124     194 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.022
                                       ETTTTTTSS---HHHHHHHHHHHSSEEEEESS--SHHHHHHHHHTTCSEEEESHHH CS
                      His_biosynth 168 didrdGtlsGpdleltkelaeavkipviasGGvgsledlkelksegvdavivgsal 223
                                         d+dG++ Gp+     +la+++  ++i++  v sle+  ++++eg+d + +gs++
  gi|242398455|ref|YP_002993879.1|  66 ATDADGVQLGPEDMP-ISLAKEIGPNLIIGASVYSLEEALKAEKEGADYLGAGSVF 120
                                       558999999997544.4899999999999999999999999999999999999988 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 6.9e-06
                                       HHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-T CS
                      His_biosynth  63 dlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavknp 109
                                       + +++i+e+v+ipv   GGI++ + ++++l+ g+d + i +a +   
  gi|242398455|ref|YP_002993879.1| 134 EGLKRIVESVKIPVVAIGGINHKN-ARDVLKTGVDGIAIISAIMGAE 179
                                       556788888888888888888888.8888888888887777655444 PP

>> DUF561  Protein of unknown function (DUF561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.77   1.7e+03     211     224 ..      38      51 ..      21      70 .. 0.56
   2 !   15.6   0.2     3e-06    0.0067     179     236 ..     137     194 ..     126     197 .] 0.86

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.77
                            DUF561 211 iGigsavsklndee 224
                                       i ig+ +++l++e 
  gi|242398455|ref|YP_002993879.1|  38 IKIGKEIRELTKEY 51 
                                       33444444443333 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 3e-06
                            DUF561 179 yeiskkvslPvicasGlsdvtvplalslgasGiGigsavsklndeeemvallseikka 236
                                         i+++v++Pv++  G+++  +   l+ g  Gi i sa+   +d +   + +++i++ 
  gi|242398455|ref|YP_002993879.1| 137 KRIVESVKIPVVAIGGINHKNARDVLKTGVDGIAIISAIMGAEDVKRATEEMRKIIEE 194
                                       5799***********************************9999887777776666654 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.37   8.4e+02      37      78 ..      14      52 ..       3      54 .. 0.67
   2 ?   13.4   0.1   1.4e-05     0.032     199     253 ..     136     187 ..     125     188 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.37
                                      HHHHCHCHTTS-EEEEEE-SEETTTEESBSS--HHHHHHHHT CS
                              IGPS 37 faeaLresekklaliaEvKkaSPskgliredfdpaeiAkkye 78
                                        eaL+     +++ + +K   P+ ++i+   ++ e+ k+y+
  gi|242398455|ref|YP_002993879.1| 14 VREALEG--GATSIQLRIKN-APTGEMIKIGKEIRELTKEYD 52
                                      4444444..44444455665.599999999999999999997 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 1.4e-05
                                       HHHHCHCC-TTSEEEEESSS-SHHHHHHHCCTT-SEEEESHHHHC-TTHHHHHHH CS
                              IGPS 199 teeLaklvpkdvllvaeSGiktredveklkeegvnafLvGeslmrqedvekaire 253
                                        ++++++v+  + +va  Gi+ +++++++ ++gv+++ + +++m +edv++a++e
  gi|242398455|ref|YP_002993879.1| 136 LKRIVESVK--IPVVAIGGIN-HKNARDVLKTGVDGIAIISAIMGAEDVKRATEE 187
                                       445555554..8999****97.678999999********************9987 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 ?   -2.0   0.0       1.2   2.7e+03      91     122 ..      12      45 ..       9      63 .. 0.63
   2 ?   13.1   0.0   2.7e-05     0.061      83     162 ..      93     179 ..      62     182 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.2
                                       HHHHHHHHHT-SEEEE..ES--HHHHHHHHHHHH CS
                         QRPTase_C  91 eeleevleaeadiimL..Dnfsveelkkaveelk 122
                                       e ++e+le +a  i+L   n  + e+ k+ +e++
  gi|242398455|ref|YP_002993879.1|  12 ESVREALEGGATSIQLriKNAPTGEMIKIGKEIR 45 
                                       6677777777777766223444455555555554 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 2.7e-05
                                       EEEEESSHHHHHHHHHHT-SEEEEES--HHHHHHHHHHHHHHSTT.......SEEEEESS--TTTHHHHHCTT-SEE CS
                         QRPTase_C  83 ievevesleeleevleaeadiimLDnfsveelkkaveelkeknkr.......vlievSGgvtlenveeyaksgvdvi 152
                                       i   v+slee+ ++ +++ad      + ++ +k+ v+++     +       + + + Gg++ +n +++ k+gvd i
  gi|242398455|ref|YP_002993879.1|  93 IGASVYSLEEALKAEKEGADYLGAGSVFPTPTKRDVKVIGLEGLKrivesvkIPVVAIGGINHKNARDVLKTGVDGI 169
                                       5666788888888888888888888876666666666664444333555555788899******************* PP

                                       EECHHCHTB- CS
                         QRPTase_C 153 svgalthsvk 162
                                       ++ +++ +++
  gi|242398455|ref|YP_002993879.1| 170 AIISAIMGAE 179
                                       9988887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); 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: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 1178.54
//
Query:       gi|242398456|ref|YP_002993880.1|  [L=268]
Description: Hydroxyethylthiazole kinase [Thermococcus sibiricus MM 739]
Scores for complete 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-86  288.5   0.3    4.2e-86  288.3   0.3    1.0  1  HK            Hydroxyethylthiazole kinase family
    3.9e-09   36.4   0.3      5e-09   36.0   0.3    1.1  1  Carb_kinase   Carbohydrate kinase
    1.2e-06   28.2   0.6    1.6e-06   27.7   0.6    1.2  1  Phos_pyr_kin  Phosphomethylpyrimidine kinase
  ------ inclusion threshold ------
       0.13   12.5   0.0       0.25   11.6   0.0    1.4  1  DUF3392       Protein of unknown function (DUF3392)


Domain annotation for each model (and alignments):
>> HK  Hydroxyethylthiazole kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  288.3   0.3   9.5e-90   4.2e-86       1     246 []      10     255 ..      10     255 .. 0.98

  Alignments for each domain:
  == domain 1  score: 288.3 bits;  conditional E-value: 9.5e-90
                                       HHHHHHH--EEEEE--TTTHHHHHHHHHHHT-EEEE--STTTHHHHHHTSSEEEEE-TT--HHHHHHHHHHHHHHHH CS
                                HK   1 lkklreksPlvhhiTNkVaqnfsANvllAlgaSPimseaeeEvselakianaLllNiGtleekaiealkaAvksake 77 
                                       l+klr+k+Pl+h+iTN+V++n +AN llA+gaSP+m++a eE++e+  +a+aL++NiGtl+e++i  + +Av+ ake
  gi|242398456|ref|YP_002993880.1|  10 LEKLRKKRPLIHNITNYVVMNTTANALLAIGASPVMAHAIEELEEMIGLADALVINIGTLDEHKIYSMLKAVEIAKE 86 
                                       689************************************************************************** PP

                                       TT--EEEE-TTBTTBHHHHHHHHHHHHHS--SEEEEEHHHHHHHHTSSCCSCSSSSSS-SHH.HHHHHHHHHHHHTS CS
                                HK  78 vnrPvvlDPVgvgAtelRrelalellkevklavikGNasEilslaglelkvkGvDskeaata.avaavqkvAqklrv 153
                                       +++Pv+lDPVg+gAt+lR++++l+ll+ + ++v++GN +Ei++l+g+++k++GvDs   +++ a ++++++A+++++
  gi|242398456|ref|YP_002993880.1|  87 LRKPVILDPVGAGATKLRTKTSLKLLELGSISVVRGNFGEIAALLGEHGKTRGVDSATYDENiAKTIAKEAAREFNT 163
                                       **************************************************************559************ PP

                                       EEEEESSSEEEEESSEEEEEE-S-GGGGGSTTHHHHHHHHHHHHHTTBSSHHHHHHHHHHHHHHHH.HHHHHHHTTH CS
                                HK 154 vvvvtGevDvvsdgkkvyklknGtellgkitasGCllgsvvaaflavkkdkllaaveavllykvAgkeaaarsegsg 230
                                       vv+vtG vD+v dg++vy + nGt++lg++t++GC+ +s+++aflav+k +l a++++++++++A+++a+++ + +g
  gi|242398456|ref|YP_002993880.1| 164 VVAVTGPVDYVGDGRRVYGVANGTPMLGRVTGTGCMVTSIIGAFLAVEK-PLRATIAGLTTFEIAAEKAVEEASYPG 239
                                       **********************************************975.79999********************** PP

                                       HHHHHHHHHHHH--HH CS
                                HK 231 sFqvelldalsqltee 246
                                       +F+v+l d l+++  e
  gi|242398456|ref|YP_002993880.1| 240 TFHVKLYDWLYRIDVE 255
                                       ***********99765 PP

>> Carb_kinase  Carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   0.3   1.1e-12     5e-09      36     232 ..      32     239 ..      18     250 .. 0.82

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 1.1e-12
                                       TTTCCCCTTTTTCEECCTTHTTTS...--SSS-SEEEE-TT-SSSHCHHH...HCHHHCCCCS-EEEE...GGGGGS CS
                       Carb_kinase  36 eaiavlksylpevivhplledeqakileklerldavviGpGLgrdekikk...lleevlekdeplviD...AdgLnl 106
                                       +a a l      v++h ++     +  e    +da+vi  G   + ki     ++e + e ++p+++D   A++ +l
  gi|242398456|ref|YP_002993880.1|  32 TANALLAIGASPVMAHAIE-----ELEEMIGLADALVINIGTLDEHKIYSmlkAVEIAKELRKPVILDpvgAGATKL 103
                                       3444444445556666666.....3445677889999999955554443323399999999*******998899999 PP

                                       GGGG....TTTTSSEEEE--HHHHHHHCTTTCH.........HCCSHHHHHHHHHHHHTTEEEEESTTSEEEECTTE CS
                       Carb_kinase 107 laqkne.lserkaeviLTPhkkEfkrLlkaivk.........keddrlelarelaqklnavvllkgekdvivspege 173
                                       +++ +  l e  +  +   + +E + Ll+  +k          e+   ++a+e+a++ n+vv + g +d + + +  
  gi|242398456|ref|YP_002993880.1| 104 RTKTSLkLLELGSISVVRGNFGEIAALLGEHGKtrgvdsatyDENIAKTIAKEAAREFNTVVAVTGPVDYVGD-GRR 179
                                       999888888999999***********************99987888899*********************999.99* PP

                                       EEEE----GGG.-STTHHHHHHHHHHHHHHCTSSHHHHHHHHHHHHHHHHHHHCCCT-T.S CS
                       Carb_kinase 174 vlinstgssal.akGGsGDvLaGligalLaqneasyeaaiaaawlhgaasdeaaekkgv.g 232
                                       v+ + +g+++l ++ G+G   + +iga+La+++ ++ a ia+      a+++a e++++ g
  gi|242398456|ref|YP_002993880.1| 180 VYGVANGTPMLgRVTGTGCMVTSIIGAFLAVEK-PLRATIAGLTTFEIAAEKAVEEASYpG 239
                                       ********987589******************9.9***************99999988755 PP

>> Phos_pyr_kin  Phosphomethylpyrimidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.6   3.7e-10   1.6e-06      26     223 ..      23     220 ..      20     243 .. 0.67

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 3.7e-10
                                       EEEEEEEETTCEEEEEE--HHHHHHHHHHHHHTS...--SEEEE-S--SHHHHHHHHHHH..HHTTSSEEEE---SS CS
                      Phos_pyr_kin  26 italtaqntkgvkevhplpaelveaqleavledv...kvdavKiGmlasaeiievvaekl..kkykvpvVlDPVmva 97 
                                       it  +++nt++   +    + ++++ +e + e +   +  ++ iG l +++i +++ ++   k+ + pv+lDPV + 
  gi|242398456|ref|YP_002993880.1|  23 ITNYVVMNTTANALLAIGASPVMAHAIEELEEMIglaDALVINIGTLDEHKIYSMLKAVEiaKELRKPVILDPVGA- 98 
                                       5556666655544433333333333333333333100556899***********9965433355667******965. PP

                                       CTSSSBSSHHHHHHHHHHTGGG-SEEE-BHHHHHHHHT---SSHH.HHHHHHHHHHHTT-SEEEEEEGGS.-SSSEE CS
                      Phos_pyr_kin  98 ksgselleeeavealkeeLlplatvitPNlpEaeaLlgekiktee.dmkeaakkllklgakaVlikGghl.egeeav 172
                                        + ++l +++ +++l+   l   +v+  N+ E++aLlge+ kt   d  +  ++++k+ ak        +   +   
  gi|242398456|ref|YP_002993880.1|  99 -GATKLRTKTSLKLLE---LGSISVVRGNFGEIAALLGEHGKTRGvDSATYDENIAKTIAKEAAREFNTVvAVTGP- 170
                                       .344555555555555...7999***************66664333555555555555444444222222111233. PP

                                       EEEEEETSSEEEEEEEE----S--BTHHHHHHHHHHHHHHCTSSHHHHHHH CS
                      Phos_pyr_kin 173 vtdvlydgeeveeleaerietknthGtGCtlssaiaaelakgesleeAvkk 223
                                        +d++ dg +v+ + +      +  GtGC + s i a la +++l+ +++ 
  gi|242398456|ref|YP_002993880.1| 171 -VDYVGDGRRVYGVANGTPMLGRVTGTGCMVTSIIGAFLAVEKPLRATIAG 220
                                       .499***************************************99998865 PP

>> DUF3392  Protein of unknown function (DUF3392)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   5.5e-05      0.25      39      90 ..       9      60 ..       4      73 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.5e-05
                           DUF3392 39 llkrllsslkfvlrvlvfvllcafGyGllivlltPllakaLaqleslllalv 90
                                      +l++l ++++++  ++ +v++++   +ll + ++P++a+a+++le+++ ++ 
  gi|242398456|ref|YP_002993880.1|  9 ALEKLRKKRPLIHNITNYVVMNTTANALLAIGASPVMAHAIEELEEMIGLAD 60
                                      566677788899999*****************************98875543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.52
# Mc/sec: 1564.45
//
Query:       gi|242398457|ref|YP_002993881.1|  [L=217]
Description: Transcriptional activator, [Thermococcus sibiricus MM 739]
Scores for 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-47  162.7   3.5    1.1e-47  162.5   3.5    1.0  1  TENA_THI-4  TENA/THI-4/PQQC family


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 !  162.5   3.5   6.4e-52   1.1e-47       2     209 ..       9     211 ..       8     212 .. 0.96

  Alignments for each domain:
  == domain 1  score: 162.5 bits;  conditional E-value: 6.4e-52
                                       HHCHHHHHHHHCSHHHHHHHTT-S-HHHHHHHHHHHHHHHHHHHHHHHHHHHC-SSHHHHHHHHHHHHHHHHCHHHH CS
                        TENA_THI-4   2 aqlrpiwkeyinHpFvkalakGtlpreqfqayviqdylylknfvrvlaiilskssdlevrrelesrivdhdgeeiel 78 
                                       ++++ iw ++ nHpFv+ l++Gtlp e+f++yv+qdy+yl+   r+l ii+sks d++ +r++ + +++ +++e+ +
  gi|242398457|ref|YP_002993881.1|   9 QKADYIWHRILNHPFVIELYQGTLPIEKFKFYVLQDYNYLVGLTRTLTIIASKS-DFDLMRKILKLAQEEASTELVN 84 
                                       78899*********************************************9985.899999**************** PP

                                       HHHHHHHTT-HHHHHCTTT--HHHHHHHHHHHHHHCHS-HHHHHHHHHHHHHHHHHHHHHHCCHHHS-TSCHHHHHH CS
                        TENA_THI-4  79 hlrlaealGlsreelsktkpspatkayvrylldlarrgslaeavaallpclfvyqeiaerlkeklralegpeyyewv 155
                                       ++rl e+lGl+ e+  k++psp+++ay +++  +a  g+  e +a  +pc ++y eia++  ++l+ +e++ y  w+
  gi|242398457|ref|YP_002993881.1|  85 YERLLEELGLTIEDAIKEEPSPTNYAYMNFMNLTAFLGTPYEGLATIMPCFWSYMEIARHHEKLLETNENSLYVNWA 161
                                       ***************************************************************************** PP

                                       HHHCSHHHHHHHHHHHHHHHHHHHTSHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                        TENA_THI-4 156 keyaseefraaveeakrllerllakvsdeqleelqeiflkalefetsfltmald 209
                                       + y+s+e+ + ve     l++ll+k+++ +  +l+++f++a+++e++f++ma++
  gi|242398457|ref|YP_002993881.1| 162 EVYLSKEYIELVEN----LKELLDKTNNTEFHRLESVFERASKYEYMFWDMAYK 211
                                       *********99999....667777888889**********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       753  (0.041999); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1379.55
//
Query:       gi|242398458|ref|YP_002993882.1|  [L=426]
Description: probable hydroxymethylpyrimidine transporter CytX [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.1e-46  158.0  27.4    3.9e-46  157.7  27.4    1.1  1  Transp_cyt_pur  Permease for cytosine/purines, uracil, thiami
  ------ inclusion threshold ------
       0.21   10.6   2.1       0.28   10.2   0.2    1.8  2  US30            Family of unknown function


Domain annotation for each model (and alignments):
>> Transp_cyt_pur  Permease for cytosine/purines, uracil, thiamine, allantoin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.7  27.4   4.3e-50   3.9e-46       1     416 [.       9     387 ..       9     408 .. 0.87

  Alignments for each domain:
  == domain 1  score: 157.7 bits;  conditional E-value: 4.3e-50
                    Transp_cyt_pur   1 pvpeeeRtwktlnlfsiWlganlnintwvigalglalgLnwwqsvlviivgnligaifvallglaGakyGlpfpils 77 
                                       pv+++++t ++  l++iW+ga ++i+ +  gal+ +  L+++ ++lviivg l+g +++ l++l G ++ lp+++ls
  gi|242398458|ref|YP_002993882.1|   9 PVEKSKKTFTLITLLAIWFGAGISIAEFWAGALL-TPALSLGMAILVIIVGHLLGNAIMGLIALEGEETSLPTMVLS 84 
                                       8*******************************99.5559************************************** PP

                    Transp_cyt_pur  78 RasfGirgsllplllrvviaivwfgvqawiGsealllmlgkifgkwleiggailgtsltelvtffifwvvslvivll 154
                                       Ras Gi+gs+lp++l  +  i+w+++  ++G++a++  + k fg            ++  +v ++  +v+ ++  + 
  gi|242398458|ref|YP_002993882.1|  85 RASLGIKGSILPSILNYLQLIGWTAIMLIVGANAMNA-VSKTFG----------FEGYPLWVLLL--GVLVTLWTYI 148
                                       **********************************976.677778..........66788999877..577889999* PP

                    Transp_cyt_pur 155 gvskirkffviaallvpvaafgfliwalvkaegGpvldkavklgkse.lflsavagvlagfatlilnapDFtryakt 230
                                       g+++ +k+++iaall+ +++  +   +l+k  ++++l k++     e   + a+ +v+a + +++++++D++r+ak+
  gi|242398458|ref|YP_002993882.1| 149 GPKNWEKLEKIAALLLLALSLWLTYVTLKKFPLSDLLTKPGTG---EiGAMLALDLVIAMPLSWAPLIADYSRFAKN 222
                                       ********************99999999999998888866444...33234567777777777777777******** PP

                    Transp_cyt_pur 231 kkssvkiqlvavpllftlllligilvaaaakaayganawspldilakfdetagvllililvalaqlgvnisanllsa 307
                                       k+s+ ++  +++++ ++l++++g+l   a    +  ++ +++          g+ ++++l+     +++ ++ ++sa
  gi|242398458|ref|YP_002993882.1| 223 KNSAFWGTYLGYFISSSLFYFVGALTNMAIGEGDPIEIVAAY----------GIGIPAMLIITFSTVTTTFLDVYSA 289
                                       ********************9987765544444333333333..........7779********************* PP

                    Transp_cyt_pur 308 gldlaallPkkinikrgsliaavialvivpwkllssssklftaflsllavflspvagviiadyfvvrrgylklaaly 384
                                       + + +++ P k+  k ++l++ +++++ +++  +++ ++    fl l+++++ + a+++i dyf v++gy +++al+
  gi|242398458|ref|YP_002993882.1| 290 AITYKNISP-KADAKKQVLFVGALGVILALVFPMEQYES----FLLLIGGAFVSLAAIMITDYFLVKKGY-NAEALF 360
                                       *********.*********************99999999....99************************8.678999 PP

                    Transp_cyt_pur 385 trrrgsaYwyrkgvNwravaayivGiaaglvg 416
                                       +  +++++    g+N +a++++ +G +  +++
  gi|242398458|ref|YP_002993882.1| 361 D--ENGPFA---GYNSKAIIIWSIGFIFYMGL 387
                                       9..9****9...*************9877655 PP

>> US30  Family of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.2   3.1e-05      0.28     138     182 ..       6      51 ..       1      62 [. 0.83
   2 ?   -0.7   0.1     0.064   5.7e+02     137     178 ..      76     118 ..      70     124 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 3.1e-05
                              US30 138 evppatrtsstygvlsafvvwigsglnii.wwtgivllaadalglg 182
                                       e+ p  ++  t+ +++ + +w g+g+ i  +w+g +l  a +lg+ 
  gi|242398458|ref|YP_002993882.1|   6 EIKPVEKSKKTFTLITLLAIWFGAGISIAeFWAGALLTPALSLGMA 51 
                                       899999*********************97589**998877666653 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.064
                              US30 137 aevppatrtsstygvlsafvvwigsglniiwwtgivlla.ada 178
                                       + +p    + ++ g+  +++  i + l++i wt i+l+  a+a
  gi|242398458|ref|YP_002993882.1|  76 TSLPTMVLSRASLGIKGSILPSILNYLQLIGWTAIMLIVgANA 118
                                       556666666777888888888899999********98752555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       871  (0.0485805); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 2749.62
//
Query:       gi|242398459|ref|YP_002993883.1|  [L=338]
Description: N2, N2-dimethylguanosine tRNA methyltransferase [Thermococcus sibiricus MM 739]
Scores for 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  103.6   0.0    1.3e-28  100.1   0.0    2.1  1  UPF0020          Putative RNA methylase family UPF0020
    1.9e-14   54.0   0.0    4.7e-14   52.7   0.0    1.7  2  THUMP            THUMP domain
    4.1e-10   39.6   0.0    6.1e-10   39.1   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
      3e-08   33.6   0.0    9.9e-06   25.4   0.0    2.2  2  N6_N4_Mtase      DNA methylase
    7.1e-08   33.1   0.0    1.5e-07   32.0   0.0    1.6  1  Methyltransf_25  Methyltransferase domain
    8.9e-08   32.0   0.0    1.5e-07   31.2   0.0    1.4  1  Cons_hypoth95    Conserved hypothetical protein 95
    1.6e-06   27.8   0.0    2.6e-06   27.1   0.0    1.3  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
    1.9e-06   27.4   0.0    2.9e-06   26.8   0.0    1.2  1  N6_Mtase         N-6 DNA Methylase
    8.2e-05   23.2   0.0    0.00015   22.3   0.0    1.5  1  Methyltransf_11  Methyltransferase domain
    0.00021   20.8   0.0       0.02   14.3   0.0    2.1  2  AviRa            RRNA methyltransferase AviRa
     0.0017   17.9   0.0     0.0026   17.3   0.0    1.3  1  MTS              Methyltransferase small domain
  ------ inclusion threshold ------
       0.03   14.1   0.0       0.21   11.4   0.0    2.1  2  Methyltransf_23  Methyltransferase domain
      0.045   13.2   0.0      0.085   12.3   0.0    1.4  1  Methyltransf_4   Putative methyltransferase
      0.046   13.5   0.0       0.08   12.8   0.0    1.4  1  N6-adenineMlase  Probable N6-adenine methyltransferase
       0.06   14.1   0.0       0.12   13.2   0.0    1.5  1  Methyltransf_12  Methyltransferase domain
       0.11   11.9   0.0       0.16   11.3   0.0    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm


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 !  100.1   0.0   1.1e-31   1.3e-28       3     194 ..     165     330 ..     163     332 .. 0.91

  Alignments for each domain:
  == domain 1  score: 100.1 bits;  conditional E-value: 1.1e-31
                                       SS-SS---SS-HHHHHHHHHHTT--TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH--E CS
                           UPF0020   3 yRefngpapLketLAaalvrlagwkpgepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelkl 79 
                                       +R+f++p +L ++LA+a+++la++k++   lDP+ G+G+ilIEa+llg +++                         
  gi|242398459|ref|YP_002993883.1| 165 RRPFFKPIALPPRLARAMINLARAKKE--VLDPFMGTGGILIEAGLLGLKVY------------------------- 214
                                       8*********************99875..8********************99......................... PP

                                       EEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--..STTS---EEEE----------HHHH.HHHHHHHHHHHH CS
                           UPF0020  80 ygsDldrrvvqgareNaekagvgdliefsqadaakLr..lkegevdvivtnpPYGerlgskkal.ekLYseflrelk 153
                                        g+Dl + +v+ga++N+e++g+++ + +++ da+kL    +++e+++ivt+pPYG + +  +++ e+LY++ l+++ 
  gi|242398459|ref|YP_002993883.1| 215 -GVDLRKDMVDGAKQNLEHYGIKNYV-LKKGDATKLGklFPDKEFEAIVTDPPYGTSATLGGKVrEELYEKALESIY 289
                                       .*********************9987.6788*****9877888*********************9************ PP

                                       HH-TT..-EEEEEESSHHHHHCC---..ESEEEEEEETTEEEE CS
                           UPF0020 154 rvlrgggrlvlltsenkalekaleer..alrkvkeknvklgll 194
                                       +vl+g   l ++++++ + ek++e+   ++ +++ ++v+ +l+
  gi|242398459|ref|YP_002993883.1| 290 EVLDG--HLSIAFPTSFEAEKVAERIgfEVLEKYYQRVHSSLD 330
                                       *****..****************99855555666677777765 PP

>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.7   0.0   4.2e-17   4.7e-14      48     143 ..      49     149 ..       6     150 .. 0.84
   2 ?   -2.5   0.0       4.4     5e+03      67      78 ..     280     291 ..     274     326 .. 0.60

  Alignments for each domain:
  == domain 1  score: 52.7 bits;  conditional E-value: 4.2e-17
                                       T.....TECEEEEE.....EEEEESSHHHHHHHHHHHHHHHHHHCT-EEEEEEEESSSTSSSHHHHHHHHHHHHHHC CS
                             THUMP  48 r.....giqrvipv.....cevceadledileaakeivkkkfeeeketFaVrvkrrgkhfeftsreinrevGkaive 114
                                             +++r+ ++     +   +++le+++ +a+++ + +f+++  +F+V  + + ++  ++  +++re+G++iv+
  gi|242398459|ref|YP_002993883.1|  49 NesafsYLKRLGMAheygnLLFSGESLEELYLKAENLEWGNFIAG--SFKVDRETMLNC-RYNVENLERELGAIIVR 122
                                       233335666666666676778899*********************..************.***************** PP

                                       CTT-EE-SSS-SEEEEEEEETTEEEEEEE CS
                             THUMP 115 ktglkVdlenPdivvrveiikdkayisid 143
                                       ++  kV+l++Pd++vrv++ + k++++i+
  gi|242398459|ref|YP_002993883.1| 123 QGF-KVNLTSPDTLVRVYCGQ-KLWVGIR 149
                                       **9.***************99.7999998 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.4
                                       HHHHHHHHHHHH CS
                             THUMP  67 ileaakeivkkk 78 
                                       ++e+a e +++ 
  gi|242398459|ref|YP_002993883.1| 280 LYEKALESIYEV 291
                                       444444444433 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1   0.0   5.4e-13   6.1e-10       4     100 ..     189     291 ..     186     328 .. 0.83

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 5.4e-13
                   Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlils 80 
                                       +++vlD+  GtG +++e+  +lg   +v+G+D  ++++  A++n+++ g++n+ +++gd+++l kl+ d+ f  i++
  gi|242398459|ref|YP_002993883.1| 189 KKEVLDPFMGTGGILIEAG-LLG--LKVYGVDLRKDMVDGAKQNLEHYGIKNYVLKKGDATKLGKLFPDKEFEAIVT 262
                                       689***************9.765..79*************************************99*********** PP

                   Methyltransf_31  81 n......evl...naladpdkileeierv 100
                                       +      ++l         +k+le+i +v
  gi|242398459|ref|YP_002993883.1| 263 DppygtsATLggkVREELYEKALESIYEV 291
                                       96666553335554444445555555554 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0   8.8e-09   9.9e-06     162     229 ..     158     226 ..      75     228 .. 0.82
   2 !    6.4   0.0    0.0056       6.3       3      39 ..     259     292 ..     257     323 .. 0.76

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 8.8e-09
                                       TTS-CHH...----SS---HHHHHHHHHHHS-TT-EEEETT-TTTHHHHHHHHTT-EEEEEESSHHHHHHH CS
                       N6_N4_Mtase 162 kkskgdt...kkkHpaqkPvallerlIklstkkgdivlDpFaGSGtTavaakelgrkfiGieieeeyvela 229
                                        ++++++   + k p+  P  l++ +I+l   k   vlDpF+G+G ++++a  lg k +G++  +  v+ a
  gi|242398459|ref|YP_002993883.1| 158 FEKRKADrrpFFK-PIALPPRLARAMINLARAKK-EVLDPFMGTGGILIEAGLLGLKVYGVDLRKDMVDGA 226
                                       4444444233333.78889999999998876665.59**************************99988765 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0056
                                       EEEE--SSSSSCS.....GCCGCCHHHHHHHHHHHHH CS
                       N6_N4_Mtase   3 livtdpPYntgkdyendeqyeeedsyeeyleflekvl 39 
                                        ivtdpPY+t+           e+ ye+ le +++vl
  gi|242398459|ref|YP_002993883.1| 259 AIVTDPPYGTSAT---LGGKVREELYEKALESIYEVL 292
                                       69*********99...444444455555555555555 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   0.0   1.3e-10   1.5e-07       1      93 [.     192     292 ..     192     294 .. 0.83

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 1.3e-10
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBS..SSTTTEEEEEE.... CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlp..fedgsfDlvvs.... 70 
                                       vLd   GtG +++++    g  kv+gvD+ ++m++ a++++e+ g+ n  + +gda++l   f+d++f ++v     
  gi|242398459|ref|YP_002993883.1| 192 VLDPFMGTGGILIEAGLL-G-LKVYGVDLRKDMVDGAKQNLEHYGIkNYVLKKGDATKLGklFPDKEFEAIVTdppy 266
                                       89999*********9977.5.**********************9999************7779********986665 PP

                                       ..ESTGGG.SSHHHHHHHHHHHHHHE CS
                   Methyltransf_25  71 ..sgalhh.lsdedlekalkeiarvL 93 
                                         s +l   + +e +ekal+ i++vL
  gi|242398459|ref|YP_002993883.1| 267 gtSATLGGkVREELYEKALESIYEVL 292
                                       53222444466666677777777776 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.0   1.4e-10   1.5e-07      41     129 ..     188     272 ..     179     321 .. 0.84

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 1.4e-10
                                       CC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEE CS
                     Cons_hypoth95  41 egarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdiv 117
                                        +++vLD f G+G++ +EA   g  k++ v+  k +v   k+nle+ ++++   +lk+ ++ +l kl   ++ef+ +
  gi|242398459|ref|YP_002993883.1| 188 AKKEVLDPFMGTGGILIEAGLLG-LKVYGVDLRKDMVDGAKQNLEHYGIKN--YVLKKGDATKLGKL-FPDKEFEAI 260
                                       6789***************9999.6899********************998..77777777888788.47789**** PP

                                       EE--SSSTTCH. CS
                     Cons_hypoth95 118 flDPPyakelli 129
                                         DPPy +++++
  gi|242398459|ref|YP_002993883.1| 261 VTDPPYGTSATL 272
                                       ******999774 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 !   27.1   0.0   2.3e-09   2.6e-06       3      82 ..     191     267 ..     189     274 .. 0.92

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 2.3e-09
                   Methyltransf_15   3 vilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklklekikvdlvflSp 79 
                                        +lD+f G+GG  i+  l + kv++++  ++ +  a++N e Yg+++ + l++gd ++l + +  ++   + +++ p
  gi|242398459|ref|YP_002993883.1| 191 EVLDPFMGTGGILIEAGLLGLKVYGVDLRKDMVDGAKQNLEHYGIKNYV-LKKGDATKLGKLFPDKEF--EAIVTDP 264
                                       68*******************************************9987.689***999998887777..9999999 PP

                   Methyltransf_15  80 PwG 82 
                                       P G
  gi|242398459|ref|YP_002993883.1| 265 PYG 267
                                       998 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.0   2.6e-09   2.9e-06      31     138 ..     175     269 ..     158     286 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 2.6e-09
                          N6_Mtase  31 PrevsklivellepksgesvyDpacGsggllvqaekvlkeedgktkelsiyGqeknettyrLakmNlllhgieykkv 107
                                       P  + + +++l+  k++  v+Dp +G+gg+l++a             l++yG+++ +  +  ak Nl   gi++  v
  gi|242398459|ref|YP_002993883.1| 175 PPRLARAMINLARAKKE--VLDPFMGTGGILIEAGL---------LGLKVYGVDLRKDMVDGAKQNLEHYGIKNY-V 239
                                       56677888888877776..9************9976.........479*************************99.7 PP

                          N6_Mtase 108 kirlgdtlekpkfekdkkfdvvvaNppfnqk 138
                                        ++ + t   + f  dk+f+++v+ pp++++
  gi|242398459|ref|YP_002993883.1| 240 LKKGDATKLGKLFP-DKEFEAIVTDPPYGTS 269
                                       77788888889999.*************987 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   1.3e-07   0.00015       5      66 ..     197     261 ..     193     293 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.3e-07
                                       -TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTS..S-TT-EEEEE CS
                   Methyltransf_11   5 cGtGrlaealakrgarvvgvDlskemlklakekaseegl.kvefvvadaeklp..fednsfDlvv 66 
                                       +GtG ++ +    g +v+gvDl k m++ ak++ +  g+ +  + ++da+kl   f+d+ f ++v
  gi|242398459|ref|YP_002993883.1| 197 MGTGGILIEAGLLGLKVYGVDLRKDMVDGAKQNLEHYGIkNYVLKKGDATKLGklFPDKEFEAIV 261
                                       68888888888899************************998889********558*******998 PP

>> AviRa  RRNA methyltransferase AviRa
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.014        16      42     100 ..     181     231 ..     161     252 .. 0.78
   2 !   14.3   0.0   1.8e-05      0.02     164     217 ..     254     308 ..     231     321 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.014
                             AviRa  42 alellekkeegapltlyDpCCGgayLltvlgllhgkkikkvlasDvdeevlelakkNLs 100
                                       a+  l ++++    ++ Dp  G++ +l   gll      kv++ D  +++++ ak+NL+
  gi|242398459|ref|YP_002993883.1| 181 AMINLARAKK----EVLDPFMGTGGILIEAGLLGL----KVYGVDLRKDMVDGAKQNLE 231
                                       4444433333....688999999999999999874....79****************97 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 1.8e-05
                             AviRa 164 ekevdivitDlPYGelvswqge.seepvkqlleslaavldpeesvvaviadkkkk 217
                                        ke + ++tD PYG  ++  g+ +ee  ++ les+++vld + s+   ++ + +k
  gi|242398459|ref|YP_002993883.1| 254 DKEFEAIVTDPPYGTSATLGGKvREELYEKALESIYEVLDGHLSIAFPTSFEAEK 308
                                       345899****************889999***********9998887665554444 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   2.3e-06    0.0026      31     138 ..     188     299 ..     178     335 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.3e-06
                                       TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTT...TSTTS-EEEEEE CS
                               MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvle...eveekkfdlivs 103
                                       ++++vlD   G+G + +++      ++v  vd  +  ++ ak+nle+ +++   + + d+++    +++k+f++iv+
  gi|242398459|ref|YP_002993883.1| 188 AKKEVLDPFMGTGGILIEAGLLG--LKVYGVDLRKDMVDGAKQNLEHYGIKnYVLKKGDATKlgkLFPDKEFEAIVT 262
                                       67789999999997777776655..559***********************866666676651115669******** PP

                                       ---STTTCHCHHHHHHHHHHHHHHHEEE..EEEEEEE CS
                               MTS 104 NPPfhagkatelavaeeliaeAkeaLke..gGeLliV 138
                                        PP+ ++     +v eel ++A e   e  +G+L i 
  gi|242398459|ref|YP_002993883.1| 263 DPPYGTSATLGGKVREELYEKALESIYEvlDGHLSIA 299
                                       ********************99887654335666665 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   0.00019      0.21      19      62 ..     184     236 ..     163     264 .. 0.74
   2 ?   -0.4   0.0      0.83   9.3e+02     135     164 ..     289     319 ..     271     320 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00019
                   Methyltransf_23  19 k.lraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae........k 62 
                                       +  ra+++vLd   GtG  l ++   g +v+gvDl+  +v+ a+        k
  gi|242398459|ref|YP_002993883.1| 184 NlARAKKEVLDPFMGTGGILIEAGLLGLKVYGVDLRKDMVDGAKqnlehygiK 236
                                       235999***********99**9*******************997766666552 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.83
                   Methyltransf_23 135 ylvpagrhi..sffsarslkelleeaGlevve 164
                                       y+v + +h+   f ++ + ++ +e+ G+ev+e
  gi|242398459|ref|YP_002993883.1| 289 YEVLD-GHLsiAFPTSFEAEKVAERIGFEVLE 319
                                       56666.66656788888899999******987 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   7.6e-05     0.085      28      77 ..     213     261 ..     197     265 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.6e-05
                                       EEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCCHHHHCS-TTSEEEEE CS
                    Methyltransf_4  28 flGiEirvkvvakvlkkiealelkNlrilrgdalkvllelledgslekif 77 
                                       + G+++r+++v+ + ++ e++++kN  + +gda + l +l++d+++e i+
  gi|242398459|ref|YP_002993883.1| 213 VYGVDLRKDMVDGAKQNLEHYGIKNYVLKKGDA-TKLGKLFPDKEFEAIV 261
                                       679******************************.99*********99986 PP

>> N6-adenineMlase  Probable N6-adenine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   7.1e-05      0.08      85     153 ..     251     334 ..     224     338 .] 0.67

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.1e-05
                   N6-adenineMlase  85 l..kgkfdviviDPPF.........lseeclkklaktaklllk...klilctgevmeelekllgvkkt.kfepehen 146
                                       l  +++f+ iv+DPP+         + ee+ +k+ + +  +l    ++ + t+   e++++++g++   k++ + ++
  gi|242398459|ref|YP_002993883.1| 251 LfpDKEFEAIVTDPPYgtsatlggkVREELYEKALESIYEVLDghlSIAFPTSFEAEKVAERIGFEVLeKYYQRVHS 327
                                       256899***********999999997777777665555555557766777787777779999987776566666555 PP

                   N6-adenineMlase 147 klsnefr 153
                                       +l + f+
  gi|242398459|ref|YP_002993883.1| 328 SLDRYFY 334
                                       5666555 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0    0.0001      0.12       6      71 ..     198     261 ..     197     293 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.0001
                   Methyltransf_12   6 GtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvv 71 
                                       GtG +l +      +++++gvD+ +++++ ak+ l +++ +n    + +a+ l++l++ + f ++v
  gi|242398459|ref|YP_002993883.1| 198 GTGGILIEAGLL--GLKVYGVDLRKDMVDGAKQNLEHYGIKNYVLKKGDATKLGKLFPDKEFEAIV 261
                                       677777766666..9****************************************99999999998 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00014      0.16     157     213 ..     184     239 ..     179     263 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00014
                              PrmA 157 klvkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveakl 213
                                       +l ++++evlD   G+G + i a +Lg  kv++vD+ +  v+ ak+N+e  ++++ +
  gi|242398459|ref|YP_002993883.1| 184 NLARAKKEVLDPFMGTGGILIEAGLLGL-KVYGVDLRKDMVDGAKQNLEHYGIKNYV 239
                                       5678999****767766666999***97.69******************99998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 2049.41
//
Query:       gi|242398460|ref|YP_002993884.1|  [L=246]
Description: ATPase, PP-loop superfamily [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0073   16.0   0.2     0.0073   16.0   0.2    3.8  4  SHOCT          Short C-terminal domain
  ------ inclusion threshold ------
      0.035   14.5   0.7       0.39   11.1   0.1    2.4  2  CM_2           Chorismate mutase type II
       0.19   10.5   0.0       0.25   10.1   0.0    1.2  1  tRNA_Me_trans  tRNA methyl transferase


Domain annotation for each model (and alignments):
>> SHOCT  Short C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.2   1.2e-06    0.0073      11      27 ..      25      41 ..      24      41 .. 0.89
   2 ?   -0.0   0.2      0.13     8e+02      18      24 ..      48      54 ..      48      56 .. 0.87
   3 ?    1.1   0.0     0.061   3.7e+02       1      11 [.     186     196 ..     186     198 .. 0.89
   4 ?   -0.6   0.2       0.2   1.2e+03       9      17 ..     226     233 ..     221     234 .. 0.56

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.2e-06
                             SHOCT 11 arGeIteEEFeakKakL 27
                                       rGeI+eE +e+ Ka +
  gi|242398460|ref|YP_002993884.1| 25 VRGEISEETYERLKALI 41
                                      59************965 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.13
                             SHOCT 18 EEFeakK 24
                                      EEFe+ K
  gi|242398460|ref|YP_002993884.1| 48 EEFERSK 54
                                      9***977 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.061
                             SHOCT   1 daLekLkeLya 11 
                                       +a++ L ++ya
  gi|242398460|ref|YP_002993884.1| 186 EAIKVLGKRYA 196
                                       699*******9 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 0.2
                             SHOCT   9 LyarGeIte 17 
                                       L+ +G+I++
  gi|242398460|ref|YP_002993884.1| 226 LR-AGAIDK 233
                                       44.566665 PP

>> CM_2  Chorismate mutase type II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1     0.075   4.5e+02      36      65 ..       9      40 ..       3      49 .. 0.71
   2 ?   11.1   0.1   6.6e-05      0.39      13      68 ..     189     245 ..     184     246 .] 0.84

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.075
                                      SS-HHHHHHHHHHHHH..HHS-HHHHHHHHHH CS
                              CM_2 36 vydpeReaevlerlee..galdeeaierifre 65
                                      +  + R ++ le le+  g+++ee++er+   
  gi|242398460|ref|YP_002993884.1|  9 FIKTYRLQQSLEALERvrGEISEETYERLKAL 40
                                      45556777777777776668999999998555 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 6.6e-05
                                       HHHHHHHHHHHHHHHHHHHCTS.GSS-HHHHHHHHHHHHHHHS-HHHHHHHHHHHHH CS
                              CM_2  13 eLLaeRaelakevgeyKkeegl.pvydpeReaevlerleegaldeeaierifreiis 68 
                                       + L +R +l       K++++  p++     + vl++l++ga+d+e +++++++i++
  gi|242398460|ref|YP_002993884.1| 189 KVLGKRYALGFGCSLWKSAAKTtPILKRFGIQRVLRELRAGAIDKEIAKALIKDILR 245
                                       667777777777777887666669999999************************986 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   4.2e-05      0.25       2      39 ..      58      95 ..      57     121 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 4.2e-05
                     tRNA_Me_trans  2 kvvvalSgGVDSsvaaallkeqgyevigvflklweeed 39
                                      k++ a+S G DS+ ++++lk +g++v+ v++kl + +d
  gi|242398460|ref|YP_002993884.1| 58 KIALAFSMGSDSTASLLILKWAGFDVVPVMVKLPQMND 95
                                      8999**************************99877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      580  (0.0323498); 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: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1521.96
//
Query:       gi|242398461|ref|YP_002993885.1|  [L=253]
Description: competence damage-inducible protein A [Thermococcus sibiricus MM 739]
Scores for 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-35  119.4   0.0    1.5e-34  118.8   0.0    1.3  1  MoCF_biosynth  Probable molybdopterin binding domain
  ------ inclusion threshold ------
      0.088   12.6   0.8       0.18   11.6   0.4    1.8  2  ScsC_N         Copper resistance protein ScsC N-terminal doma
       0.13   12.3   0.1       0.37   10.8   0.0    1.7  1  B12-binding    B12 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 !  118.8   0.0   2.5e-38   1.5e-34       1     142 [.       6     178 ..       6     180 .. 0.95

  Alignments for each domain:
  == domain 1  score: 118.8 bits;  conditional E-value: 2.5e-38
                                       EEEEE-HHHHTTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTS.SEEEEESS-SSSTT--HHH CS
                     MoCF_biosynth   1 avitvGdellsgkieDtngpllaellkelgvevskytvvpDdeeeikeallaaleea.dviittGGtGptpdDvtpe 76 
                                       ++it+Gdell+g+++D+n++++a++l+e g+ v+++t+v+Dd eeik  +++ l+++ +v+++ GG+Gpt+dDvt  
  gi|242398461|ref|YP_002993885.1|   6 EIITIGDELLTGNTVDSNSAFIAQKLTEKGYWVRRITTVGDDVEEIKTVVREVLSREpEVLVIAGGLGPTHDDVTML 82 
                                       59************************************************66666666******************* PP

                                       HHHHHHSEE-HHHHHHHHHHHHHHCC...............................TTSHGGGGGGE.EETTEEEE CS
                     MoCF_biosynth  77 alaklfekelegfeeafrrvslkpgk...............................pvgvapgailsravgktiig 122
                                       a+a++++ ele+ e +++r++ ++ +                                vg apga l  + +++i++
  gi|242398461|ref|YP_002993885.1|  83 AVARALNLELELREDILKRIEEFYLElykkgfvddpkinearkkmayiprgveilnnTVGAAPGAFLIYK-NTKIFV 158
                                       ***********************988**************************************999865.667*** PP

                                       E-SSHHHHHHHHHHHHHGGH CS
                     MoCF_biosynth 123 LPGspkavkealeeillpal 142
                                       LPG p+++k+++e+ ++p l
  gi|242398461|ref|YP_002993885.1| 159 LPGMPREMKAMFENEVSPKL 178
                                       ***************99987 PP

>> ScsC_N  Copper resistance protein ScsC N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.4   3.1e-05      0.18       3      21 ..      49      67 ..      47      69 .. 0.92
   2 ?   -2.7   0.0      0.91   5.5e+03      20      26 ..     202     208 ..     201     211 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.1e-05
                            ScsC_N  3 aaiekivrdYLleNPEiLv 21
                                      ++i+++vr+ L   PE+Lv
  gi|242398461|ref|YP_002993885.1| 49 EEIKTVVREVLSREPEVLV 67
                                      89****************7 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.91
                            ScsC_N  20 LvEAlqa 26 
                                       LvEAl+ 
  gi|242398461|ref|YP_002993885.1| 202 LVEALNR 208
                                       9999986 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   6.3e-05      0.37      61      97 ..      44      80 ..      20      88 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 6.3e-05
                       B12-binding 61 ltsqleavkelvellkrirprvkvvvGGahpsldpee 97
                                      ++  +e++k +v+++ ++ p+v v++GG +p+ d   
  gi|242398461|ref|YP_002993885.1| 44 VGDDVEEIKTVVREVLSREPEVLVIAGGLGPTHDDVT 80
                                      66778899999***88999***********9988655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      577  (0.0321825); 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: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 1497.64
//
Query:       gi|242398462|ref|YP_002993886.1|  [L=485]
Description: Pyruvate kinase (PYK) [Thermococcus sibiricus MM 739]
Scores for complete 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-117  392.4   8.7   2.1e-117  391.9   8.7    1.2  1  PK         Pyruvate kinase, barrel domain
    1.1e-23   83.6   0.1    1.1e-21   77.3   0.0    3.1  3  PK_C       Pyruvate kinase, alpha/beta domain
    0.00069   18.7   0.8     0.0019   17.2   0.3    1.9  2  IMPDH      IMP dehydrogenase / GMP reductase domain
     0.0019   17.4   0.1     0.0073   15.5   0.0    1.9  2  HpcH_HpaI  HpcH/HpaI aldolase/citrate lyase family
  ------ inclusion threshold ------
      0.029   14.6   0.6        1.2    9.4   0.1    3.3  3  DUF3006    Protein of unknown function (DUF3006)
       0.14   12.2   0.2       0.76    9.8   0.0    2.3  2  Paz_1      PAZ domain


Domain annotation for each model (and alignments):
>> PK  Pyruvate kinase, barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  391.9   8.7  7.2e-121  2.1e-117       2     341 ..      16     349 ..      15     355 .. 0.97

  Alignments for each domain:
  == domain 1  score: 391.9 bits;  conditional E-value: 7.2e-121
                                       --SEEEEEESCCCTSHHHHHHHHHHTEEEEEEETTSS-HHHHHHHHHHHHHHHHTTTTS-EEEEE---S-EBB--BT CS
                                PK   2 rrtkivctlGPasesvekleklieaGlnvvrlnfshGsheehqerienvreaekklgkkvaillDtkGpeirtgllk 78 
                                       ++tki++t+GPas+++ ++ek+i+aG+ v+r+nfshG+ eeh+++ie +r++++kl+k vail D+ G ++r+g++k
  gi|242398462|ref|YP_002993886.1|  16 HKTKIIATIGPASRHAGTIEKMIKAGMSVARINFSHGTLEEHTKTIELIRKTAEKLEKIVAILGDLPGVKMRVGKIK 92 
                                       59*************************************************************************** PP

                                       TCSSSEEE-TTSEEEEE-SCTCTTTBBTTEEEBS-TTHHHHS-TTEEEEETTTTEEEEEEEEETTEEEEEEESS-EE CS
                                PK  79 dgkkdielkegdklkvsldeklkeegdeelialdyknivkdvevGktilvdDGllslkvlevdeekeleveventgv 155
                                       +  ++i+lk+gdk+ +++ +    egde +i +++k+  k v+ G++i++ DG + l+v+ev e++ +e+ v n+g+
  gi|242398462|ref|YP_002993886.1|  93 G--DSITLKKGDKVVLTTRDV---EGDETTIPVEFKDFPKLVSKGDVIYLSDGYIMLRVEEVRENE-VECVVVNGGT 163
                                       9..57**********998765...45789*********************************9988.********** PP

                                       E-SS-BEE-TTS---S-SS-HHHHHHHHHHHHCT-SEEEETTE-SHHHHHHHHHHHTCCCTTSEEEEEE-SCHHHHT CS
                                PK 156 lgskkgvnlpgtkvdlpalsekDkadlrfgvkqgvdliaasfvrkasDvkevrevleeegkeikiiakienqegven 232
                                       l s+kg+n+p ++++++a++ +D + ++f+++qg+d i +sfv +  Dv +v++ le+++ +  iiakie+ ++v+n
  gi|242398462|ref|YP_002993886.1| 164 LFSHKGINIPKANLPIEAITPRDFEIIEFAIEQGIDAIGLSFVGSVYDVLKVKSFLEKKKGNNFIIAKIERPDAVRN 240
                                       ************************************************************999************** PP

                                       HHHHHHHSSEEEEEHHHHHHHSTCCCHHHHHHHHHHHHHHHT--EEEESSTTGGGGTSSS--HHHHHHHHHHHHHT- CS
                                PK 233 ldeileasDgimvarGDlGieipaekvllvqkklikkcnlagkpvitatqmlesmiknPrptraevsDvanavlDGt 309
                                       +deil+a+DgimvarGDlG+e+p ek++++qk+likk+nla kpvitatqml sm+++  p raev+Dvana+lDGt
  gi|242398462|ref|YP_002993886.1| 241 FDEILNAADGIMVARGDLGVEMPIEKLPIMQKQLIKKANLAAKPVITATQMLVSMTTERIPKRAEVTDVANAILDGT 317
                                       ***************************************************************************** PP

                                       SEEEESHHHHTSS-HHHHHHHHHHHHHHHHHT CS
                                PK 310 DavmLsgetakGkyPveavkamaevaleaeka 341
                                       DavmLs eta GkyPve+v++ma++a+++e+ 
  gi|242398462|ref|YP_002993886.1| 318 DAVMLSEETAIGKYPVESVEMMAKIAKTTEEY 349
                                       ****************************9975 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 ?    2.4   0.2     0.057   1.7e+02      88     106 ..      95     113 ..      42     118 .. 0.63
   2 ?   -2.2   0.0       1.6   4.7e+03      39      63 ..     177     212 ..     146     258 .. 0.59
   3 !   77.3   0.0   3.5e-25   1.1e-21       1     116 [.     373     481 ..     373     482 .. 0.94

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.057
                                       TTSS-STSEEEEEE-SSSS CS
                              PK_C  88 aglvkkgdevvvtaGtpkg 106
                                       +  +kkgd+vv+t+ + +g
  gi|242398462|ref|YP_002993886.1|  95 SITLKKGDKVVLTTRDVEG 113
                                       3357*********998877 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.6
                                       SEEEEEESHHHH...........HHHHHHCTTEEHH CS
                              PK_C  39 vpiiavtpnelt...........arqlalyrGvypv 63 
                                       +pi a+tp++ +           a  l++++ vy v
  gi|242398462|ref|YP_002993886.1| 177 LPIEAITPRDFEiiefaieqgidAIGLSFVGSVYDV 212
                                       555555554433333333333334444444444444 PP

  == domain 3  score: 77.3 bits;  conditional E-value: 3.5e-25
                                       HHHHHHHHHHHHHHT-SEEEEE-SSSHHHHHHHHT-TSSEEEEEESHHHHHHHHHHCTTEEHHH.HHHHH...TTSH CS
                              PK_C   1 eaiakaaveaaeelgakaIvvltesGetArliskyrpkvpiiavtpneltarqlalyrGvypvlvekaktaestdel 77 
                                       eai++++++a   +++k+I+++t++G t+rlis+++pk +i+a+++ne+++++la++ Gvyp+ +e     e+++e 
  gi|242398462|ref|YP_002993886.1| 373 EAITQSVIDALCAIDIKYILTPTRTGLTPRLISRFKPKQWILAFSNNERVCNSLAFSYGVYPFCME-----EEFNE- 443
                                       79*************************************************************875.....34555. PP

                                       HHHHHHHHHHTTSS-STSEEEEEE-SSSS..SS--EEEE CS
                              PK_C  78 lreavkvakeaglvkkgdevvvtaGtpkgesgttNtlrV 116
                                        ++++  +k  g+vk++d+v +t G p+g++  tNt+r+
  gi|242398462|ref|YP_002993886.1| 444 -KDMIMLVKGLGIVKEDDTVLLTEGKPIGKTIGTNTIRI 481
                                       .577878899****************************9 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.3   6.5e-07    0.0019      91     188 ..      16     114 ..       4     163 .. 0.80
   2 ?   -1.3   0.0      0.29   8.7e+02     220     238 ..     307     325 ..     304     372 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 6.5e-07
                                       SXB-EEEEE-SSTTHHHHHHHHHHTT-SEEEEE-STSSSHHHHHHHHHHHHHTTTSEEEEEEE-SHHHHHH.HHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx RF
                             IMPDH  91 grllvgaavgvkedalervkalveagvdvlvvdsahghsekvleavkeikkkveeveviaGnvataegaka.Lieag 166
                                       ++  + a++g  + +   ++++++ag+ v  ++ +hg  e+ +++++ i+k++e++e i+  + +  g+k  + +  
  gi|242398462|ref|YP_002993886.1|  16 HKTKIIATIGPASRHAGTIEKMIKAGMSVARINFSHGTLEEHTKTIELIRKTAEKLEKIVAILGDLPGVKMrVGKIK 92 
                                       56677899*********************************************999999888888777765144667 PP

                                       -SEEEE-SS-STTBHHHHHCSB CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 167 adavkvGiGpGsiCttrvvagv 188
                                        d +    G   + ttr v g 
  gi|242398462|ref|YP_002993886.1|  93 GDSITLKKGDKVVLTTRDVEGD 114
                                       7777777777777777777775 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.29
                                       HHHHHHHHTT-SEEEESCC CS
                                       xxxxxxxxxxxxxxxxxxx RF
                             IMPDH 220 gdivkAlaaGadavmlGsl 238
                                        d++ A+  G+davml + 
  gi|242398462|ref|YP_002993886.1| 307 TDVANAILDGTDAVMLSEE 325
                                       799999999*****99765 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 !   15.5   0.0   2.4e-06    0.0073      79     158 ..     191     262 ..     180     292 .. 0.80
   2 ?   -2.2   0.0      0.63   1.9e+03     141     179 ..     336     374 ..     332     391 .. 0.60

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.4e-06
                                       G.HHHTTSSEEEESS--SHHHHHHHHHHTSHTTTS---HCCC-EEEEEE-SHHHHHTHHHHH.TSTTEEEEEE-HHH CS
                         HpcH_HpaI  79 e.vldlgaqvvlvPkvetaeealevvsalrepekgirganketrllaqiEsaegvknaeeIa.avegldgvflGaeD 153
                                       e ++++g++++ + +v +  ++l+v+s l++ +       ++  ++a iE  ++v n +eI+ a++g   ++++  D
  gi|242398462|ref|YP_002993886.1| 191 EfAIEQGIDAIGLSFVGSVYDVLKVKSFLEKKK-------GNNFIIAKIERPDAVRNFDEILnAADG---IMVARGD 257
                                       357889999999999999999999999999999.......9999*****************966655...5556666 PP

                                       HHHHT CS
                         HpcH_HpaI 154 lsadl 158
                                       l +++
  gi|242398462|ref|YP_002993886.1| 258 LGVEM 262
                                       66666 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.63
                                       STTEEEEEE-HHHHHHHTT-TTSTTSHHHHHHHHHHHHT CS
                         HpcH_HpaI 141 vegldgvflGaeDlsadlgtkrspegtevldarerilta 179
                                       ve ++ ++  +e +  +lg++r     ++l  r+ i  a
  gi|242398462|ref|YP_002993886.1| 336 VEMMAKIAKTTEEYRESLGHSRLRAWIDLLPKRSTIKEA 374
                                       455555666677777777777777777777444444444 PP

>> DUF3006  Protein of unknown function (DUF3006)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.1   0.00041       1.2       8      52 ..     101     149 ..     100     157 .. 0.75
   2 ?    0.0   0.0      0.34     1e+03      20      32 ..     168     181 ..     153     186 .. 0.78
   3 ?    0.5   0.0      0.24     7e+02      19      54 ..     290     328 ..     285     336 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00041
                           DUF3006   8 gdlAVleled....getidiprsdLpegakeGdvLeieddeieldpeet 52 
                                       gd +Vl ++d    ++ti ++ +d+p+ +  Gdv+ ++d+ i l+ ee 
  gi|242398462|ref|YP_002993886.1| 101 GDKVVLTTRDvegdETTIPVEFKDFPKLVSKGDVIYLSDGYIMLRVEEV 149
                                       56778877777632333669999***************77788877775 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.34
                           DUF3006  20 t.idiprsdLpega 32 
                                       + i+ip+ +Lp +a
  gi|242398462|ref|YP_002993886.1| 168 KgINIPKANLPIEA 181
                                       4499*******875 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.24
                           DUF3006  19 et.idiprsdLpegakeGdvLeie.dd.eieldpeetek 54 
                                       ++ +    +++p+ a+  dv +   d+ + ++  eet+ 
  gi|242398462|ref|YP_002993886.1| 290 QMlVSMTTERIPKRAEVTDVANAIlDGtDAVMLSEETAI 328
                                       5545678899**********9999888779999999986 PP

>> Paz_1  PAZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00025      0.76      19      50 ..     198     234 ..     189     247 .. 0.78
   2 ?   -2.1   0.0       1.3   3.9e+03      54      71 ..     355     372 ..     335     381 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00025
                                       EEETT----EEEEEEEESG.....GSTTHHHHHHHHH CS
                             Paz_1  19 vkpigidfvgrvqdvfkak.....ekgeeffrlcmer 50 
                                       +  ig+ fvg v dv+k k     +kg++f+   +er
  gi|242398462|ref|YP_002993886.1| 198 IDAIGLSFVGSVYDVLKVKsflekKKGNNFIIAKIER 234
                                       5689***********9975333226888888777777 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.3
                                       HHHHHHHHHHHHSHHHHH CS
                             Paz_1  54 ksskkaweellknrelre 71 
                                       +s  +aw +ll +r   +
  gi|242398462|ref|YP_002993886.1| 355 HSRLRAWIDLLPKRSTIK 372
                                       566788888887775443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (485 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.67u 0.32s 00:00:00.99 Elapsed: 00:00:00.52
# Mc/sec: 2790.21
//
Query:       gi|242398463|ref|YP_002993887.1|  [L=66]
Description: hypothetical protein TSIB_0472 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.31s 00:00:00.77 Elapsed: 00:00:00.50
# Mc/sec: 396.79
//
Query:       gi|242398464|ref|YP_002993888.1|  [L=55]
Description: hypothetical protein TSIB_0473 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.033   14.6   0.0      0.038   14.4   0.0    1.0  1  DUF4199   Protein of unknown function (DUF4199)
      0.038   14.0   0.0      0.043   13.8   0.0    1.1  1  PGA2      Protein trafficking PGA2
      0.067   12.9   0.1      0.068   12.9   0.1    1.0  1  OFeT_1    Ferrous iron uptake permease, iron-lead transporter
      0.096   13.0   0.0        0.1   13.0   0.0    1.1  1  ERGIC_N   Endoplasmic Reticulum-Golgi Intermediate Compartmen


Domain annotation for each model (and alignments):
>> DUF4199  Protein of unknown function (DUF4199)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   8.4e-06     0.038      77     115 ..      12      49 ..      11      54 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 8.4e-06
                           DUF4199  77 slvagllsavfqyiyfnfidpdfienyiaeilekleeak 115
                                       +++++++s++f y++++++  ++  +y+++ +e+l+e++
  gi|242398464|ref|YP_002993888.1|  12 TFIGSIISVIFGYLLIRVF-TTWYSRYLEKKEEELKEKE 49 
                                       69**************988.999*******999988654 PP

>> PGA2  Protein trafficking PGA2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   9.6e-06     0.043      14      52 ..      11      49 ..       5      53 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 9.6e-06
                              PGA2 14 kdwi.rlvlivggYlllRPYleklfkklqekqrekeeeke 52
                                      k +i  ++ +++gYll+R +   +  +  ek++e+ +eke
  gi|242398464|ref|YP_002993888.1| 11 KTFIgSIISVIFGYLLIRVFT-TWYSRYLEKKEEELKEKE 49
                                      566634788999******885.566666777777666665 PP

>> OFeT_1  Ferrous iron uptake permease, iron-lead transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   1.5e-05     0.068      69     103 ..      14      48 ..       7      55 .] 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.5e-05
                            OFeT_1  69 vaavilfyfGyrllrsarryfkgikkkkkeeeeeg 103
                                       ++++i + fGy l+r     + +  +kk+ee +e+
  gi|242398464|ref|YP_002993888.1|  14 IGSIISVIFGYLLIRVFTTWYSRYLEKKEEELKEK 48 
                                       789*************9999999988887875543 PP

>> ERGIC_N  Endoplasmic Reticulum-Golgi Intermediate Compartment (ERGIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.2e-05       0.1      14      49 ..       8      43 ..       3      53 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.2e-05
                                      X.XXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXX-E CS
                           ERGIC_N 14 ltqktlsGgiislvcillilfLllselteylttevk 49
                                      +t kt+ G+iis++   l++ ++++ +++yl+++ +
  gi|242398464|ref|YP_002993888.1|  8 ITDKTFIGSIISVIFGYLLIRVFTTWYSRYLEKKEE 43
                                      5679**************************977643 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       871  (0.0485805); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.31s 00:00:00.75 Elapsed: 00:00:00.49
# Mc/sec: 339.15
//
Query:       gi|242398465|ref|YP_002993889.1|  [L=50]
Description: hypothetical protein TSIB_0474 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       814  (0.0454013); expected 358.6 (0.02)
Passed bias filter:                      591  (0.0329634); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 323.46
//
Query:       gi|242398466|ref|YP_002993890.1|  [L=350]
Description: Pyruvate formate lyase activating like protein [Thermococcus sibiricus MM 739]
Scores for complete 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-16   59.8   0.1    9.2e-15   55.4   0.0    2.7  3  Radical_SAM  Radical SAM superfamily
    1.1e-08   35.5   0.0    2.5e-08   34.3   0.0    1.6  1  Fer4_12      4Fe-4S single cluster domain
    2.8e-07   30.7   0.7    5.2e-07   29.8   0.0    1.8  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 ?   -0.1   0.1      0.18   1.1e+03     108     143 ..      25      71 ..       5      75 .. 0.53
   2 !   55.4   0.0   1.5e-18   9.2e-15       2     156 ..     137     284 ..     136     295 .. 0.86
   3 ?    0.3   0.0      0.14   8.1e+02     121     144 ..     324     346 ..     286     350 .] 0.72

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.18
                                       EEBSSSHH...........HHHHHHTCTSHHHHHHHHHHHHHHTTSE CS
                                       xxxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 108 gleaadde...........kvlklmnrghtfeevlealeklreagik 143
                                       ++ ++ ++            +++ +   + +e  +e++e+lr++++k
  gi|242398466|ref|YP_002993890.1|  25 SILSGEERpnffytnrvevNFKEDTDLEELWEIHKEGMERLRKNNLK 71 
                                       44444444444444444444455555556667777777777776665 PP

  == domain 2  score: 55.4 bits;  conditional E-value: 1.5e-18
                                       EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgi 78 
                                       +++ gCn+rC+fC+++   +++++g + s+ + ++++  + +  g+k+v l+ggep+ +  f+ + +r+++     i
  gi|242398466|ref|YP_002993890.1| 137 IFFSGCNFRCVFCQNWDI-SQHRVGLMYSPKDMAAKIAVA-YAEGAKNVNLVGGEPTPNLLFILESLRYVRV---PI 208
                                       6899************98.777777777777777777777.5667*****************9999999997...9* PP

                                       EEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  79 ritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGe 155
                                        +   +n ++  e+ +++l+   vd +  + + ++de+ lk+   ++ +e + +++ +++++   +  +r++++pG 
  gi|242398466|ref|YP_002993890.1| 209 PVIWNSNMYMS-EKSMALLDG-VVDLYLADFKWGNDEDALKYSSAPKYWEITTRNFLLAKKHYKAEFLIRHLLIPGH 283
                                       **********7.777777777.66*******************988****************7777*********97 PP

                                       S CS
                                       x RF
                       Radical_SAM 156 n 156
                                        
  gi|242398466|ref|YP_002993890.1| 284 L 284
                                       5 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.14
                                       HTCTSHHHHHHHHHHHHHHTTSET CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 121 mnrghtfeevlealeklreagikr 144
                                         r+ t++e l+a ++ +e g+k+
  gi|242398466|ref|YP_002993890.1| 324 D-RRLTNDEMLKAAQLVKEFGLKN 346
                                       2.7789999999999999999985 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.0   4.3e-12   2.5e-08       8      99 ..     135     222 ..     128     234 .. 0.87

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 4.3e-12
                           Fer4_12   8 lslfvsgCnlsCkgCfnketwsfksgkeft.kelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeek 83 
                                       +++f+sgCn++C +C n ++ + + g  ++ k+++++i   +  e  + + l+GGEP    n   +le +++v+   
  gi|242398466|ref|YP_002993890.1| 135 YTIFFSGCNFRCVFCQNWDISQHRVGLMYSpKDMAAKIA-VAYAEGAKNVNLVGGEPTP--NLLFILESLRYVRVPI 208
                                       799**************************8466666665.5558999************..9999999999999888 PP

                           Fer4_12  84 pekdiwlytgytleel 99 
                                       p  +iw ++ y+ e+ 
  gi|242398466|ref|YP_002993890.1| 209 P--VIWNSNMYMSEKS 222
                                       8..9****99988765 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 ?   -3.9   1.0       2.5   1.5e+04       7      13 ..      95     101 ..      91     118 .. 0.62
   2 !   29.8   0.0   8.8e-11   5.2e-07       3      75 ..     137     205 ..     135     228 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 2.5
                           Fer4_14   7 gCnlsCk 13 
                                        C+++C 
  gi|242398466|ref|YP_002993890.1|  95 LCEFKCH 101
                                       5888887 PP

  == domain 2  score: 29.8 bits;  conditional E-value: 8.8e-11
                           Fer4_14   3 vrlsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlk 75 
                                       + +sgCn+ C++C n +  + ++g  ++ +++ + +  + ++   ++++ l+GGeP    n   +l+ +++++
  gi|242398466|ref|YP_002993890.1| 137 IFFSGCNFRCVFCQNWDISQHRVGLMYSPKDMAAKI--AVAYAEGAKNVNLVGGEPT--PNLLFILESLRYVR 205
                                       446*********************************..4444444577********8..35544444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 2399.07
//
Query:       gi|242398467|ref|YP_002993891.1|  [L=621]
Description: Tungsten-containing formaldehyde:ferredoxin oxidoreductase (FOR) [Thermococcus sibiricus MM 739]
Scores for complete 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-108  362.0   0.2   4.5e-108  361.7   0.2    1.1  1  AFOR_C    Aldehyde ferredoxin oxidoreductase, domains 2 & 3
    6.7e-76  254.6   1.3    9.3e-76  254.1   1.3    1.2  1  AFOR_N    Aldehyde ferredoxin oxidoreductase, N-terminal doma


Domain annotation for each model (and alignments):
>> AFOR_C  Aldehyde ferredoxin oxidoreductase, domains 2 & 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  361.7   0.2    5e-112  4.5e-108       2     382 .]     218     607 ..     217     607 .. 0.93

  Alignments for each domain:
  == domain 1  score: 361.7 bits;  conditional E-value: 5e-112
                                       HHHHHHHHHHHSH.HHHHHHHH-GGGHHHHHHHTT---BTTTTBS--TTGGGGSHHHHHHHTEEEE.E-TT-SS--E CS
                            AFOR_C   2 lgkkiqkeiksspqvtaelrkyGTaelvnianetgalptknfqegtfekaekisgealeekylvknegCfsCpiaCg 78 
                                       l +++++ i +sp  +  +++ GT++ ++++ne++alpt+nf++g+fe a++i+g ++e  ++vk++gC +C++ Cg
  gi|242398467|ref|YP_002993891.1| 218 LSQEAYNAILNSP-GYPFWHRQGTMAALEWTNENSALPTRNFSDGSFEFARSIDGFTMEG-MKVKQRGCPYCNMPCG 292
                                       67889999999**.677*******************************9**********9.*****99********* PP

                                       EEEE......ETEE---HHHHHHHTGGGT---HHHHHHHHHHHHHHTB-HHHHHHHHHHHHHHHHTTSS-HHHHTS- CS
                            AFOR_C  79 revkveegkkvkvegpeyetlaalGsnlgiddleailklnelcdelGlDtisaGntiafamelyekGllkkedtdgl 155
                                       ++v   +g++   +  +ye++a+lGsnlg  +l+++  ln+++de+GlDtis+G  i+ +me+ ekGl+k+e+    
  gi|242398467|ref|YP_002993891.1| 293 NVVLDADGQE---SELDYENVALLGSNLGLGKLNEVSVLNRIADEMGLDTISLGVSISYVMEAKEKGLIKDENA--- 363
                                       ***9888775...667******************************************************9775... PP

                                       ---TT-THHHHHHHHHHHTT-T.THHHHTT-HHHHHHCTT-GGG--EETTEE--SS-GGG-HHHHHHHHH-TTSS-S CS
                            AFOR_C 156 elefgdaeallellekiAkreg.igdllAeGvkrlaeklgaeelamhvkGlelpaydprgakgmalaYatsnrGacH 231
                                         efgd +++ +l  +iA+r+g +g+l AeGvk ++eklga+++amhvkGle++ y++   ++malaY ts  Ga+H
  gi|242398467|ref|YP_002993891.1| 364 -PEFGDFKKAKQLALDIAYRRGeLGNLAAEGVKGMSEKLGAKDFAMHVKGLEVSGYNCFIYPAMALAYGTSAIGAHH 439
                                       .89************************************************************************** PP

                                       GGG-THHHH............S---TT....--.HHHHHHHHHHHH.HHHHHHHHT--GGGG-HHH......HHHHH CS
                            AFOR_C 232 lrayliale............ekvdpl....et.egkaelvkwfqd.ltalvdslglCkftseaeerldlelyakll 290
                                        +a++ia+e            +    +    ++  +ka+ v+  q+ +  l+++l++C++++ +e+ l+l+ y+kl+
  gi|242398467|ref|YP_002993891.1| 440 KEAWVIAWEigtapiegekaqK----VeykiSYdPEKAAKVIELQRlRGGLFEMLTACRLPW-VEVGLSLDYYPKLI 511
                                       *********9999999865532....333335534888888888886889************.899*********** PP

                                       HHHHT----HHHHHHHHHHHHHHHHHHHHHHT--...HHHS---HHHHHS---SSTTTT---...-HHHHHHHHHHH CS
                            AFOR_C 291 savtGidvteeellkaGeRiynleRlfnlreGlt...rkddtlperlleeplkegpakgkvl.edeleemldeyYel 363
                                       +a+tG+++t+++l+ka++R+y l R++++re+ +   r+ d  per+++e lk+gp kg++l +++++ +l+eyY+l
  gi|242398467|ref|YP_002993891.1| 512 EAITGVKYTWDDLYKAADRVYALMRAYWVREYNSnwsREMDYPPERWFKEGLKSGPYKGQHLdKEKYDVLLNEYYKL 588
                                       *******************************866666789*********************97888*********** PP

                                       HT--TTS---HHHHHHCT- CS
                            AFOR_C 364 rGWdetGvPtketlkrLgL 382
                                       r Wde+G+P+ketlk+LgL
  gi|242398467|ref|YP_002993891.1| 589 RSWDERGIPKKETLKDLGL 607
                                       ******************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 !  254.1   1.3     1e-79   9.3e-76       1     198 []       6     204 ..       6     204 .. 0.97

  Alignments for each domain:
  == domain 1  score: 254.1 bits;  conditional E-value: 1e-79
                                       SEEEEEETTTTEEEEEE--HHHHHHH-SCHHHHHHHHHHHS-TTS-TTSTTS-EEEEE-TTTTSSSTTB-EEEEEEE CS
                            AFOR_N   1 gkilrvdLstgkieveelpeelaekylGgrglaakllldevppgvdplspenplvfatGpltgtpapgsgrlvvvak 77 
                                       g+ilrvdL+++k++v+e++ee+a++++Ggrglaa++l++e+ ++vdpl+p+n+l+fa Gp++g p p+ g++v++ak
  gi|242398467|ref|YP_002993891.1|   6 GRILRVDLTNNKVWVQEYSEEVAKNFIGGRGLAAWILWNEA-KNVDPLGPDNKLIFASGPFNGLPTPSGGKMVIAAK 81 
                                       69*************************************97.78********************************* PP

                                       -TTTSSEEEEEEETCHHHHHHHCT-SEEEEES--SS-EEEEEETTEEEEEE-TTTTTS-HHHHHHHHHHHHTSEEE. CS
                            AFOR_N  78 sPltgtlgesnaGgrfgaelkraGydaivieGkaekpvylvieddkveiedaedlwgldtyettealkeelgdkva. 153
                                       sP tg++g+ n G  +  +l++aGyda+v+eGka+kpvy++iedd+v+i +ae lwg++t+et+++lke +g++v  
  gi|242398467|ref|YP_002993891.1|  82 SPITGGYGDGNLGTMATVHLRKAGYDALVVEGKAKKPVYIYIEDDNVSILSAEGLWGKTTFETEKELKEVHGKNVGv 158
                                       *********************************************************************99995555 PP

                                       .EE-HHHHTT-TTB-E.EETTEEE-SSSHHHHHHHTTEEEEEEE-- CS
                            AFOR_N 154 .viGpaGenlvrfAsisvddgraagrgGlGavmgsKnlkaivvrgt 198
                                        +iGp Genlv++A+++ ++graagr G+GavmgsK+lka+vv+gt
  gi|242398467|ref|YP_002993891.1| 159 lSIGPGGENLVKYAVVISQEGRAAGRPGMGAVMGSKKLKAVVVKGT 204
                                       5***************777*************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (621 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); 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: 0.69u 0.34s 00:00:01.03 Elapsed: 00:00:00.53
# Mc/sec: 3498.37
//
Query:       gi|242398468|ref|YP_002993892.1|  [L=67]
Description: hypothetical protein TSIB_0477 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score 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   0.7      0.015   15.0   0.7    1.1  1  DUF2512   Protein of unknown function (DUF2512)
      0.018   15.0   4.3        0.9    9.6   0.9    2.1  2  FixQ      Cbb3-type cytochrome oxidase component FixQ
      0.064   12.9   1.3      0.067   12.8   1.3    1.0  1  DUF4131   Domain of unknown function (DUF4131)
      0.069   12.8   2.1      0.071   12.8   2.1    1.1  1  Orai-1    Mediator of CRAC channel activity
       0.25   11.4   1.2       0.29   11.2   1.2    1.0  1  Vma12     Endoplasmic reticulum-based factor for assembly of 
          1    8.9   5.0        3.4    7.3   1.9    2.0  2  SLC3A2_N  Solute carrier family 3 member 2 N-terminus


Domain annotation for each model (and alignments):
>> DUF2512  Protein of unknown function (DUF2512)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.7   4.9e-06     0.015      67     111 ..      19      63 ..       7      67 .] 0.92

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.9e-06
                           DUF2512  67 glafvvvWlltavlldnsvsiaiasllsAlvislfEiffHrYlek 111
                                       +++f+++W+l+ + ++n  ++a   ++ +l++ ++ +++H ++ +
  gi|242398468|ref|YP_002993892.1|  19 LVTFFLLWILVLCWVQNPKTTAKEPFIITLSFVVLTFIYHVWVYS 63 
                                       679*************************************98865 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 ?    7.0   0.1    0.0019       5.5      12      34 ..      16      38 ..      13      42 .. 0.66
   2 ?    9.6   0.9    0.0003       0.9      12      35 ..      44      67 .]      43      67 .] 0.91

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0019
                              FixQ 12 swgllflvllfygvviyafrpgn 34
                                      ++ l+ ++ll + v+ ++ +p+ 
  gi|242398468|ref|YP_002993892.1| 16 TLILVTFFLLWILVLCWVQNPKT 38
                                      56677777777777777777665 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0003
                              FixQ 12 swgllflvllfygvviyafrpgnr 35
                                      ++ +l +v+l  ++ ++++  ++r
  gi|242398468|ref|YP_002993892.1| 44 FIITLSFVVLTFIYHVWVYSRKRR 67
                                      57899**************99986 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   1.3   2.2e-05     0.067       4      53 ..      13      64 ..      10      67 .] 0.63

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.2e-05
                           DUF4131  4 plalvllalllllllllllllrr..rprrrvllllllllllallgfalrapq 53
                                      +l+ ++l++++ll +l l++ ++   + +  +++ l + +l +++ ++ + +
  gi|242398468|ref|YP_002993892.1| 13 SLKTLILVTFFLLWILVLCWVQNpkTTAKEPFIITLSFVVLTFIYHVWVYSR 64
                                      5666677777777777666655465555555777777777777777776655 PP

>> Orai-1  Mediator of CRAC channel activity
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   2.1   2.4e-05     0.071     120     162 ..      20      62 ..       7      67 .] 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.4e-05
                            Orai-1 120 illFLvevallswvkFlavssaaalvvtailvpvlilfvvfav 162
                                       + +FL+ + +l+wv+  +++++  +++t+  v+ + ++ v ++
  gi|242398468|ref|YP_002993892.1|  20 VTFFLLWILVLCWVQNPKTTAKEPFIITLSFVVLTFIYHVWVY 62 
                                       889************9988877777766666665555555544 PP

>> Vma12  Endoplasmic reticulum-based factor for assembly of V-ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.2   9.6e-05      0.29      87     131 ..      18      65 ..      13      67 .] 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 9.6e-05
                             Vma12  87 vvavffavwialrsartp...slpvrvllslvvallVgvAEvvvyaky 131
                                       ++++ff +wi++  ++++   + +  ++++l + +l+++  v+vy+++
  gi|242398468|ref|YP_002993892.1|  18 ILVTFFLLWILVLCWVQNpktTAKEPFIITLSFVVLTFIYHVWVYSRK 65 
                                       789*******9999988887755556899999999**********986 PP

>> SLC3A2_N  Solute carrier family 3 member 2 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   1.9    0.0011       3.4      32      51 ..      13      32 ..      10      35 .. 0.87
   2 ?    3.0   0.1     0.025        75      24      46 ..      39      61 ..      36      63 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0011
                          SLC3A2_N 32 rvRwlllilfwlvwlgmLvg 51
                                      +++ l+l++f+l+w+++L +
  gi|242398468|ref|YP_002993892.1| 13 SLKTLILVTFFLLWILVLCW 32
                                      577899**********9976 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.025
                          SLC3A2_N 24 landPfWvrvRwlllilfwlvwl 46
                                       a++Pf + +  ++l + + vw+
  gi|242398468|ref|YP_002993892.1| 39 TAKEPFIITLSFVVLTFIYHVWV 61
                                      5999*************9*9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       894  (0.0498633); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 432.78
//
Query:       gi|242398469|ref|YP_002993893.1|  [L=45]
Description: hypothetical protein TSIB_0478 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); 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: 0.43u 0.31s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 283.82
//
Query:       gi|242398470|ref|YP_002993894.1|  [L=76]
Description: molybdopterin converting factor, subunit 1 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-06   28.9   0.0    1.5e-06   28.7   0.0    1.1  1  ThiS      ThiS family
  ------ inclusion threshold ------
      0.014   15.2   0.0      0.029   14.2   0.0    1.5  2  Ub-Mut7C  Mut7-C ubiquitin


Domain annotation for each model (and alignments):
>> ThiS  ThiS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.0   1.7e-10   1.5e-06       3      77 .]       6      76 .]       4      76 .] 0.89

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 1.7e-10
                                      ETTCCHHHHT..CEEEEESSTSBHHHHHHHHHHHTCHHGTTTTEEEEETTEEEGCCTTTSB--TTCEEEEEESTTC- CS
                              ThiS  3 lfaelrelag..eeelelaegstvaelleaLgerypelalerrvavavNgeivprlwldtelkdgDevailppVaGG 77
                                      l +    la+  e e+ l+ ++t  e+l+++  ry+e       ++ +Ng+ ++    ++++ ++De+ ++p+ +GG
  gi|242398470|ref|YP_002993894.1|  6 LMGAFAHLAKarELEVKLEGPKTANEILREVIPRYDEF---HDKIIFINGKPAKG---EAIVEENDEIKVMPVLSGG 76
                                      5666666666678999*******************877...88999*********...******************9 PP

>> Ub-Mut7C  Mut7-C ubiquitin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.37   3.3e+03      20      34 ..      14      28 ..       5      38 .. 0.59
   2 ?   14.2   0.0   3.2e-06     0.029      51      76 ..      47      72 ..      44      75 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.37
                          Ub-Mut7C 20 rreralavafdeaat 34
                                      ++ r+l+v+ ++  t
  gi|242398470|ref|YP_002993894.1| 14 AKARELEVKLEGPKT 28
                                      445555555555544 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 3.2e-06
                          Ub-Mut7C 51 lilvnGesvgfshiledGdrvavypv 76
                                      +i +nG++++ ++i+e+ d ++v+pv
  gi|242398470|ref|YP_002993894.1| 47 IIFINGKPAKGEAIVEENDEIKVMPV 72
                                      689**********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 554.53
//
Query:       gi|242398471|ref|YP_002993895.1|  [L=216]
Description: Glycosyltransferase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-40  137.6   0.0    4.3e-40  137.3   0.0    1.1  1  Glycos_transf_2  Glycosyl transferase family 2
      1e-12   48.5   0.0    1.2e-12   48.2   0.0    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    3.4e-10   39.9   0.0    6.1e-10   39.0   0.0    1.4  2  Glyco_tranf_2_2  Glycosyltransferase like family 2
    5.8e-06   26.7   0.0      1e-05   25.9   0.0    1.4  1  Glyco_tranf_2_4  Glycosyl transferase family 2
     0.0045   16.5   0.0     0.0065   16.0   0.0    1.3  1  Glyco_transf_21  Glycosyl transferase family 21
  ------ inclusion threshold ------
       0.03   13.9   0.0      0.069   12.7   0.0    1.6  1  DUF374           Domain of unknown function (DUF374)
      0.046   13.4   0.0      0.065   12.9   0.0    1.2  1  Glyco_tranf_2_5  Glycosyltransferase like family


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.3   0.0   1.7e-43   4.3e-40       1     168 [.       8     162 ..       8     164 .. 0.97

  Alignments for each domain:
  == domain 1  score: 137.3 bits;  conditional E-value: 1.7e-43
                                       EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglra 77 
                                       s++ip+yNe+  + ++l  + +      +eiivvDDgS+D+t+e+++++     + +vir++en+Gk++a+n+g+++
  gi|242398471|ref|YP_002993895.1|   8 SIIIPAYNEAGRIGNVLSKIPDF----ADEIIVVDDGSKDNTAEVAKKY-----GAKVIRLKENQGKGAAMNTGMKE 75 
                                       8*****************88888....**********************.....9********************** PP

                                       --SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTTC CS
                   Glycos_transf_2  78 atgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnlsfe 154
                                       atgd+i+f+DaD +++p+ + kl++++ +d+ad v+g+r  + +++++  r       + l +   + +l++n+ + 
  gi|242398471|ref|YP_002993895.1|  76 ATGDIIVFIDADGQHNPEEITKLLKPILQDEADFVIGSRLIKVQGKRPLIRK----VSNFLSTSLIRLKLGINVKDT 148
                                       ****************************************999999999998....579****************** PP

                                       STCCCEEEEHHHHH CS
                   Glycos_transf_2 155 igsaallrrealee 168
                                        +++++l+re l e
  gi|242398471|ref|YP_002993895.1| 149 QSGFRALKREFLPE 162
                                       **********9866 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 !   48.2   0.0   4.8e-16   1.2e-12       4     127 ..       7     117 ..       4     160 .. 0.87

  Alignments for each domain:
  == domain 1  score: 48.2 bits;  conditional E-value: 4.8e-16
                   Glyco_tranf_2_3   4 lavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksraln 80 
                                       +++++p++ne+ ++g+vl  +      ++e++vv+d+s++ t+eva+     +++   +v++ ++n   +gk  a+n
  gi|242398471|ref|YP_002993895.1|   7 ISIIIPAYNEAGRIGNVLSKIPD---FADEIIVVDDGSKDNTAEVAKK----YGA---KVIRLKEN---QGKGAAMN 70 
                                       89***************998887...69****************9986....766...57766564...5789999* PP

                   Glyco_tranf_2_3  81 ealravksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfll 127
                                        +++ +++d+++++D+D    P+ + +ll  +l++++++v ++++ +
  gi|242398471|ref|YP_002993895.1|  71 TGMKEATGDIIVFIDADGQHNPEEITKLLKPILQDEADFVIGSRLIK 117
                                       ********************************9999**999888776 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 !   39.0   0.0   2.4e-13   6.1e-10       1     105 [.       8     101 ..       8     120 .. 0.88
   2 ?   -3.4   0.0       2.1   5.3e+03     195     233 ..     174     211 ..     171     214 .. 0.73

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 2.4e-13
                   Glyco_tranf_2_2   1 svviplraseerhyieervlqkakyydeeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarNrGa 77 
                                       s++ip +++ +r  i + + ++  +     e+ivvddgS ++++e+ ++  ++  +   +++     +++aa N G+
  gi|242398471|ref|YP_002993895.1|   8 SIIIPAYNEAGR--IGNVLSKIPDF---ADEIIVVDDGSKDNTAEVAKKYGAKVIRLK-ENQ-----GKGAAMNTGM 73 
                                       799*********..99999999998...7789*************9999887766655.555.....9********* PP

                   Glyco_tranf_2_2  78 skaesdlvlFlDaDcfissDkfekilkl 105
                                       ++a +d+++F+DaD    ++++ k+lk 
  gi|242398471|ref|YP_002993895.1|  74 KEATGDIIVFIDADGQHNPEEITKLLKP 101
                                       ************************9994 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.1
                   Glyco_tranf_2_2 195 lllRlakaikslekmpvellykarakslsnykGfrrfle 233
                                       ll++  k+   +++ pve  y  +++ ++ ++   rfl+
  gi|242398471|ref|YP_002993895.1| 174 LLIKAVKKGARVKEVPVERIYGIETGHFR-FEDVIRFLK 211
                                       66666666677778888888888888888.887777776 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 !   25.9   0.0   4.1e-09     1e-05       1      81 [.      14      87 ..      14      93 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 4.1e-09
                   Glyco_tranf_2_4  1 rneadiLpeflahhlalgfdrilvydndstDgtrailkelpevkllhvdksyederrqvellkallaryaeadwvlvvD 79
                                      +nea +++++l  + ++ +d+i+v+d++s+D+t+++ k++  +k+++ +++      + +++++ +++ a +d ++++D
  gi|242398471|ref|YP_002993895.1| 14 YNEAGRIGNVLSKIPDF-ADEIIVVDDGSKDNTAEVAKKY-GAKVIRLKENQG----KGAAMNTGMKE-ATGDIIVFID 85
                                      69***************.******************9995.778888887665....45667766666.4899999999 PP

                   Glyco_tranf_2_4 80 aD 81
                                      aD
  gi|242398471|ref|YP_002993895.1| 86 AD 87
                                      99 PP

>> Glyco_transf_21  Glycosyl transferase family 21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   2.5e-06    0.0065      18      66 ..      65     113 ..      57     157 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.5e-06
                   Glyco_transf_21  18 KvnnllqaleaakydllvisDsdvrvkpdyLeellaaledpkvglVtsl 66 
                                       K  ++++++++a  d++v+ D+d   +p+ +++ll+++ ++++ +V + 
  gi|242398471|ref|YP_002993895.1|  65 KGAAMNTGMKEATGDIIVFIDADGQHNPEEITKLLKPILQDEADFVIGS 113
                                       778999**********************************999999874 PP

>> DUF374  Domain of unknown function (DUF374)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.7e-05     0.069      22      68 ..      46      92 ..      39      93 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.7e-05
                            DUF374 22 arvlerlGiktirGSsskggaealremlralkegesvaitpDgPrGP 68
                                      a+v++++G k+ir   ++g+ +a+   +++   +  v i +Dg + P
  gi|242398471|ref|YP_002993895.1| 46 AEVAKKYGAKVIRLKENQGKGAAMNTGMKEATGDIIVFIDADGQHNP 92
                                      899****************************9**********97766 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 ?   12.9   0.0   2.5e-05     0.065      23      77 ..      47     100 ..      41     134 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.5e-05
                   Glyco_tranf_2_5  23 evpegyeveiiairnaksiaeaynkalsasdakykvYlhqDvliinkdfikdlle 77 
                                       ev ++y + +i++++++   +a n +++++   + v+++ D    n++ i++ll+
  gi|242398471|ref|YP_002993895.1|  47 EVAKKYGAKVIRLKENQGKGAAMNTGMKEATGDIIVFIDADGQH-NPEEITKLLK 100
                                       7889999*********************************9764.4444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1323.96
//
Query:       gi|242398472|ref|YP_002993896.1|  [L=217]
Description: zinc-dependent protease [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.8e-50  170.6   1.1    9.1e-49  166.1   1.1    2.0  1  Peptidase_M54  Peptidase family M54
     0.0006   19.7   0.0    0.00084   19.2   0.0    1.4  1  Peptidase_M10  Matrixin
     0.0068   15.1   0.9      0.012   14.2   0.9    1.3  1  Metallopep     Putative peptidase family
  ------ inclusion threshold ------
      0.011   16.3   0.7      0.035   14.6   0.1    2.1  3  Reprolysin_3   Metallo-peptidase family M12B Reprolysin-like
      0.011   15.9   0.0      0.036   14.2   0.0    1.8  2  Reprolysin_5   Metallo-peptidase family M12
      0.018   14.0   0.1      0.027   13.4   0.1    1.2  1  Peptidase_M66  Peptidase M66
       0.02   14.5   0.1      0.088   12.4   0.0    1.9  2  Reprolysin_4   Metallo-peptidase family M12B Reprolysin-like
      0.045   13.6   0.0      0.073   13.0   0.0    1.4  1  Reprolysin_2   Metallo-peptidase family M12B Reprolysin-like
      0.048   12.9   0.0      0.085   12.1   0.0    1.3  1  DUF4953        Met-zincin


Domain annotation for each model (and alignments):
>> Peptidase_M54  Peptidase family M54
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.1   1.1   4.6e-52   9.1e-49       1     194 []       1     210 [.       1     210 [. 0.88

  Alignments for each domain:
  == domain 1  score: 166.1 bits;  conditional E-value: 4.6e-52
                                       -EEEEEESSS--T...THHHHHHHHHHHHHHHH-S-E.EEEEE----..........GGGEETTTTEEEHHHHHHHH CS
                     Peptidase_M54   1 mekiavvyvggkefewllfevvDrverflsdvglevkivyagrikLPpgllirveteegavkmyrleavveallgkL 77 
                                       me + +v v+++  e l+  v+ rv+ ++++ +l++++vy g   L pg l+ ++te+g vk y+le v e l  kL
  gi|242398472|ref|YP_002993896.1|   1 MELVGFVHVSNTFNERLIARVYKRVNAYFKSKNLPIRLVYLGELELGPGYLVNIQTENGNVKGYPLEGVTELLHAKL 77 
                                       88899999999999*********************************************************999998 PP

                                       HT--S--...............S...EE........EEEESS-EE-TT-S-BSEEE-SSSSEEEEE-T--.....SH CS
                     Peptidase_M54  78 kemkddv.............ndD...sitkifgittlplgsrdqyidiykkvlGievsiGnyavlalsikefytedk 138
                                        + ++++             +++   ++ kifgi  +p+ sr+ y+d y+k+lGi+ +  + +v++lsik+f  +d+
  gi|242398472|ref|YP_002993896.1|  78 IHTQEEImekrktreeknenKNNnvsKMNKIFGILNFPIVSRNPYLDFYEKFLGIQQDFHELKVMVLSIKPFEDNDE 154
                                       654333211111111111113331225779*********************************************** PP

                                       HHHHHHHHHHHHHHHHHHTT----S-TSTTS--SSHHHHHHS-SS--HHHHHHHHH CS
                     Peptidase_M54 139 eLflervvkevlhelGhlyGLshCkedCvmnfsndlkdvDrkapkyCksCleklkr 194
                                       ++f +r +k++lhe+Gh +GL hC+edCvmn+++ + ++D++  ++C++C  +lkr
  gi|242398472|ref|YP_002993896.1| 155 KVFEKRLFKGILHEVGHAFGLNHCQEDCVMNPPKVIGEWDLRRDDFCERCFVELKR 210
                                       *****************************************************997 PP

>> Peptidase_M10  Matrixin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   4.2e-07   0.00084     106     149 ..     158     199 ..      57     202 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 4.2e-07
                                       SEEHHHHHHHHHHHHTTBESXSSTTSTTSSSCTXTTTXSSXHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M10 106 gvslflVaaHEiGHalGLeHssdkdalmyplykeekkvrlskdD 149
                                       +  lf   +HE+GHa GL+H  ++d +m p      + +l +dD
  gi|242398472|ref|YP_002993896.1| 158 EKRLFKGILHEVGHAFGLNHC-QEDCVMNPPKV-IGEWDLRRDD 199
                                       456888899***********5.56779998653.4566677776 PP

>> Metallopep  Putative peptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.9   6.1e-06     0.012     318     336 ..     165     184 ..     164     187 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6.1e-06
                        Metallopep 318 flHEiGHllglpHqed.Gvm 336
                                       +lHE+GH++gl H+++  vm
  gi|242398472|ref|YP_002993896.1| 165 ILHEVGHAFGLNHCQEdCVM 184
                                       69***********8664888 PP

>> Reprolysin_3  Metallo-peptidase family M12B Reprolysin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.7   3.3e+03       4      23 ..      18      38 ..      16      47 .. 0.82
   2 ?   -2.5   0.1       3.4   6.8e+03      36      48 ..      91     103 ..      70     110 .. 0.49
   3 ?   14.6   0.1   1.7e-05     0.035     110     123 ..     164     177 ..     133     178 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.7
                      Reprolysin_3  4 iaalvnranqiye.rdlgirl 23
                                      ia + +r+n+ ++ ++l irl
  gi|242398472|ref|YP_002993896.1| 18 IARVYKRVNAYFKsKNLPIRL 38
                                      667789999999988888886 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.4
                      Reprolysin_3  36 dpytkkdateald 48 
                                        ++ +++++ +++
  gi|242398472|ref|YP_002993896.1|  91 REEKNENKNNNVS 103
                                       2222223344443 PP

  == domain 3  score: 14.6 bits;  conditional E-value: 1.7e-05
                      Reprolysin_3 110 tvaHEiGHnfganH 123
                                        + HE+GH fg+nH
  gi|242398472|ref|YP_002993896.1| 164 GILHEVGHAFGLNH 177
                                       578*********** PP

>> Reprolysin_5  Metallo-peptidase family M12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.1   2.2e+03      27      52 ..      16      40 ..       8      51 .. 0.78
   2 ?   14.2   0.0   1.8e-05     0.036     143     160 ..     162     182 ..     126     202 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.1
                      Reprolysin_5 27 anivnlvnrasnvyeresnislglan 52
                                      + i+ + +r+ n+y+++ n+ ++l+ 
  gi|242398472|ref|YP_002993896.1| 16 RLIARVYKRV-NAYFKSKNLPIRLVY 40
                                      5677788899.999999998888875 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 1.8e-05
                      Reprolysin_5 143 vqvvaHElGHnfGavH...Dc 160
                                       ++ + HE+GH+fG +H   Dc
  gi|242398472|ref|YP_002993896.1| 162 FKGILHEVGHAFGLNHcqeDC 182
                                       66689***********55555 PP

>> Peptidase_M66  Peptidase M66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   1.3e-05     0.027     191     209 ..     160     178 ..     155     185 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.3e-05
                     Peptidase_M66 191 tltgefiHEqGHalGLpHy 209
                                       +l +  +HE+GHa+GL+H 
  gi|242398472|ref|YP_002993896.1| 160 RLFKGILHEVGHAFGLNHC 178
                                       5566678***********4 PP

>> Reprolysin_4  Metallo-peptidase family M12B Reprolysin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.48   9.6e+02      12      41 ..      81     110 ..      74     116 .. 0.77
   2 ?   12.4   0.0   4.4e-05     0.088     139     155 ..     165     181 ..     154     189 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.48
                      Reprolysin_4  12 dpeyvaelgsvdevraainalvtvlnevYg 41 
                                       + e +++ ++ +e + + n+ v  +n+++g
  gi|242398472|ref|YP_002993896.1|  81 QEEIMEKRKTREEKNENKNNNVSKMNKIFG 110
                                       555666668888889999999999999987 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 4.4e-05
                      Reprolysin_4 139 fAHEiGHtfGaaHdlsd 155
                                       + HE+GH fG++H  +d
  gi|242398472|ref|YP_002993896.1| 165 ILHEVGHAFGLNHCQED 181
                                       67***********7664 PP

>> Reprolysin_2  Metallo-peptidase family M12B Reprolysin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   3.7e-05     0.073     123     144 ..     159     180 ..     127     204 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.7e-05
                      Reprolysin_2 123 tkeidvvaHEvGHaFGatHdnd 144
                                       ++  + + HEvGHaFG +H ++
  gi|242398472|ref|YP_002993896.1| 159 KRLFKGILHEVGHAFGLNHCQE 180
                                       44555588***********654 PP

>> DUF4953  Met-zincin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   4.3e-05     0.085       4      29 ..     152     177 ..     150     179 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.3e-05
                           DUF4953   4 fpdelmgallrfvvaHEvGhtLGLrh 29 
                                        ++++++++l   + HEvGh++GL+h
  gi|242398472|ref|YP_002993896.1| 152 NDEKVFEKRLFKGILHEVGHAFGLNH 177
                                       5788899999999************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1138  (0.0634726); expected 358.6 (0.02)
Passed bias filter:                      617  (0.0344135); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1547.52
//
Query:       gi|242398473|ref|YP_002993897.1|  [L=281]
Description: hypothetical protein TSIB_0482 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.6e-07   29.8   0.7       0.27   11.0   0.0    4.8  5  Prenyltrans    Prenyltransferase and squalene oxidase repeat
  ------ inclusion threshold ------
      0.015   13.9   0.0       0.27    9.7   0.0    2.1  2  Ribophorin_II  Oligosaccharyltransferase subunit Ribophorin I


Domain annotation for each model (and alignments):
>> Prenyltrans  Prenyltransferase and squalene oxidase repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.0   0.00082       7.4       4      21 ..      12      29 ..       9      29 .. 0.90
   2 ?   -0.2   0.1     0.098   8.8e+02      34      44 .]      80      90 ..      76      90 .. 0.84
   3 ?   -1.4   0.1      0.22     2e+03       2      12 ..     150     160 ..     149     160 .. 0.87
   4 !    6.0   0.0    0.0011        10      17      44 .]     203     231 ..     198     231 .. 0.91
   5 !   11.0   0.0     3e-05      0.27       5      25 ..     239     259 ..     236     275 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.00082
                                      HHHHHHHHHHSHTTS-BB CS
                       Prenyltrans  4 ekavefLlscQnedGGwg 21
                                      ++++ +++ + +edGG++
  gi|242398473|ref|YP_002993897.1| 12 REILKYIEERRHEDGGYC 29
                                      6899************86 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.098
                                      HHHHHHHHHCT CS
                       Prenyltrans 34 ywalaaLallG 44
                                       +a+ +La+lG
  gi|242398473|ref|YP_002993897.1| 80 SMAIEGLAILG 90
                                      589******98 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.22
                                       HHHHHHHHHHH CS
                       Prenyltrans   2 dvekavefLls 12 
                                        +ek+ ef++s
  gi|242398473|ref|YP_002993897.1| 150 EKEKIKEFIES 160
                                       58*******87 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.0011
                                       TS-BBSSTTS.SBBHHHHHHHHHHHHHCT CS
                       Prenyltrans  17 dGGwggrpgs.esdtyytywalaaLallG 44 
                                        GG+ + p s ++ +  t++al +L+llG
  gi|242398473|ref|YP_002993897.1| 203 YGGFTEVPYSlPPYLEPTFYALRGLKLLG 231
                                       69*********99**************98 PP

  == domain 5  score: 11.0 bits;  conditional E-value: 3e-05
                                       HHHHHHHHHSHTTS-BBSSTT CS
                       Prenyltrans   5 kavefLlscQnedGGwggrpg 25 
                                       + ++f++  Qn+ GG++ + +
  gi|242398473|ref|YP_002993897.1| 239 EHINFIRALQNPNGGFRRSLE 259
                                       5589************87766 PP

>> Ribophorin_II  Oligosaccharyltransferase subunit Ribophorin II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0     3e-05      0.27     115     240 ..      36     162 ..      30     165 .. 0.79
   2 ?    4.5   0.0    0.0012        11      14      93 ..     139     231 ..     129     249 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 3e-05
                     Ribophorin_II 115 dasveelyyavsslkllklkidka.kvlkalkallkkDdsleslgyalniaseldqskevkkavskledlveqadev 190
                                       ++++++ yyav+   ll++k+ ++ k++  l   lk  + + ++++a++  + l   k+++k  + l+ ++e++d +
  gi|242398473|ref|YP_002993897.1|  36 ETNINDTYYAVKIYDLLGMKVPEQeKTIGFLYDSLKPQQAVVAVSMAIEGLAILGA-KDLAK--DGLSLVFEKYDPL 109
                                       57899*****************999**************************99954.45544..4566789999999 PP

                     Ribophorin_II 191 dgkylqfeggLst..TalvvrGilklakavkk.kpaiteeqvvkLanyllsrk 240
                                       +gk+    gg +   Ta+ +++++ ++ a+k  + +i++e++ k+ +++ s +
  gi|242398473|ref|YP_002993897.1| 110 QGKFAVGLGGSEEfgTATPLEATYWMLRALKAtNHKISPEEKEKIKEFIESFR 162
                                       99998544444422388888888888888765478888888888877776655 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0012
                     Ribophorin_II  14 aktsssylsasdrsrlkevfesgess..sdle.....eayyalaglevlgekvskea....Ckfvvkllsssk...l 76 
                                        k++++ +s ++++++ke +es ++    +l+      +y+a+  l++l+ k++k++    C+ v   + ++    +
  gi|242398473|ref|YP_002993897.1| 139 LKATNHKISPEEKEKIKEFIESFRKGdgYGLKqatttMTYQAIYSLNSLDYKIPKTShfhrCE-VYGGFTEVPyslP 214
                                       455566699999999998888433333344444445578999999999999999999899985.4444444431234 PP

                     Ribophorin_II  77 ssleslfyalsankalk 93 
                                         le  fyal+  k+l+
  gi|242398473|ref|YP_002993897.1| 215 PYLEPTFYALRGLKLLG 231
                                       56778888888777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); 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: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1748.48
//
Query:       gi|242398474|ref|YP_002993898.1|  [L=128]
Description: crcB like protein [Thermococcus sibiricus MM 739]
Scores for complete 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   83.7   7.8    1.1e-23   83.3   7.8    1.0  1  CRCB             CrcB-like protein, Camphor Resistance (CrcB)
      0.004   17.2   3.1      0.014   15.4   3.1    2.0  1  Phage_holin_3_3  LydA holin phage, holin superfamily III


Domain annotation for each model (and alignments):
>> CRCB  CrcB-like protein, Camphor Resistance (CrcB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.3   7.8   1.2e-27   1.1e-23       2      94 ..      13     122 ..      12     123 .. 0.91

  Alignments for each domain:
  == domain 1  score: 83.3 bits;  conditional E-value: 1.2e-27
                                       HHHHHHHHHHHHHHHH.HHHHBE...BHHHHHHHHHHHHHHHHHHH..............HHTTTHHHHHS-SHHHH CS
                              CRCB   2 lvalggalGallRyllssllnkr...plgtlavNvlGsfllgllla..............llttGflGglTTfStfv 61 
                                       +v++gg+lGa++Ry +++ll      p+gtl+vN ++sfllg+l++              +++tGf+Ggl+TfStf+
  gi|242398474|ref|YP_002993898.1|  13 AVGVGGMLGAIMRYSIAGLLPVYkdfPVGTLLVNSIASFLLGYLYGlvffgyevspnwrvFFGTGFCGGLSTFSTFS 89 
                                       799*************777655499999******************887777777777777**************** PP

                                       HHHHHHHHHT-HHHHHHHHHHHHHHHHHHHHHH CS
                              CRCB  62 lelvslleegellaallyvllsvvlgllavvlg 94 
                                       +e++sll+e+e++ all++ +++++++ +v+lg
  gi|242398474|ref|YP_002993898.1|  90 YETFSLLREREHFLALLNISANIIITVSLVFLG 122
                                       *******9999****************999988 PP

>> Phage_holin_3_3  LydA holin phage, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   3.1   1.6e-06     0.014       3      63 ..      14      75 ..      10      86 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.6e-06
                   Phage_holin_3_3  3 iivlAllGGlvsylmrakkg.rrrfsikellleivvSgfvGllvfllceelglsqlltlaia 63
                                      ++v ++lG +++y +       + f++  ll+  ++S + G+l +l+ + +++s+++++++ 
  gi|242398474|ref|YP_002993898.1| 14 VGVGGMLGAIMRYSIAGLLPvYKDFPVGTLLVNSIASFLLGYLYGLVFFGYEVSPNWRVFFG 75
                                      555566666666666666668999**********************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 866.36
//
Query:       gi|242398475|ref|YP_002993899.1|  [L=126]
Description: hypothetical protein TSIB_0484 [Thermococcus sibiricus MM 739]
Scores for complete 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-38  130.9   0.2    3.8e-38  129.7   0.1    1.6  2  DUF190    Uncharacterized ACR, COG1993


Domain annotation for each model (and alignments):
>> DUF190  Uncharacterized ACR, COG1993
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.7   0.1   2.1e-42   3.8e-38       2      96 ..      11     105 ..      10     106 .. 0.98
   2 !    2.9   0.0    0.0078   1.4e+02      62      77 ..     103     118 ..     102     122 .. 0.90

  Alignments for each domain:
  == domain 1  score: 129.7 bits;  conditional E-value: 2.1e-42
                                       EEEEEEETT-EETTEEHHHHHHHHHHHTT-S--EEEE-S---------------------EEEEEEEE-HHHHHHHH CS
                            DUF190   2 lLrIyigesdrlegkplyeaivelareeglagatvlrGieGfgassrihtakllelsedlPvvieivdteekieafl 78 
                                       +++Iyige+d+++g+ply+aive++re+glagatv+rGi Gfg++sr+h++++l+ls+dlP++ie vd+   ie+ +
  gi|242398475|ref|YP_002993899.1|  11 RMTIYIGENDTWHGRPLYKAIVEKLREMGLAGATVYRGIYGFGKKSRVHSSDVLRLSTDLPIIIETVDRGHMIERAI 87 
                                       689************************************************************************** PP

                                       HHHHT----SEEEEEEEE CS
                            DUF190  79 pelkelvkeglvtlekve 96 
                                       +e+k+++k+g++t+e+v 
  gi|242398475|ref|YP_002993899.1|  88 NEIKPMIKDGMITVEPVI 105
                                       ***************995 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.0078
                                       EEEEEEEE-HHHHHHH CS
                            DUF190  62 Pvvieivdteekieaf 77 
                                       Pv++++v t+e++++f
  gi|242398475|ref|YP_002993899.1| 103 PVIVVWVGTKEEMKKF 118
                                       9************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 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:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 874.24
//
Query:       gi|242398476|ref|YP_002993900.1|  [L=191]
Description: hypothetical protein TSIB_0485 [Thermococcus sibiricus MM 739]
Scores for complete 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-32  111.8   0.3    2.5e-32  111.5   0.3    1.1  1  DUF835    Protein of unknown function (DUF835)


Domain annotation for each model (and alignments):
>> DUF835  Protein of unknown function (DUF835)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.5   0.3   1.4e-36   2.5e-32       9     136 .]      67     186 ..      62     186 .. 0.95

  Alignments for each domain:
  == domain 1  score: 111.5 bits;  conditional E-value: 1.4e-36
                            DUF835   9 keilsdlvkegvkvlaitRenpkkirekvkienvkviwltkveeentvsPtnlekltetivkflkeaekgvvliDgl 85 
                                        +++++l k ++k++ i+R++     + +++   + +w++k+e+en+v+Pt lek+++ + k ++ ++    + Dg+
  gi|242398476|ref|YP_002993900.1|  67 DYLIANLLK-DKKLVGIVRNH-----HLFEKHDFPCLWISKIEKENSVRPTHLEKILHWVTKTITHDH--GLIFDGV 135
                                       578899999.5*********7.....5789999***********************************..6999*** PP

                            DUF835  86 eyLvlengFesvlkflltlkDavllkngtlilvidkealeekelalLkref 136
                                       eyL+lengFe ++kfll+lkD +ll++++l+lv+d++++ee++l+lL ref
  gi|242398476|ref|YP_002993900.1| 136 EYLILENGFEPTFKFLLNLKDHILLRDSILVLVVDERTFEERQLSLLYREF 186
                                       **************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.52
# Mc/sec: 1096.86
//
Query:       gi|242398477|ref|YP_002993901.1|  [L=409]
Description: Phosphopantothenoylcysteine synthetase/decarboxylase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      4e-58  196.3   3.4    2.8e-56  190.3   0.8    2.2  2  DFP           DNA / pantothenate metabolism flavoprotein
    2.5e-40  137.8   5.0      4e-39  133.9   2.5    2.2  2  Flavoprotein  Flavoprotein
     0.0014   19.1   1.2       0.33   11.3   0.0    3.3  2  Radical_SAM   Radical SAM superfamily
  ------ inclusion threshold ------
      0.053   13.3   0.1        8.1    6.2   0.0    3.2  3  MutL_C        MutL C terminal dimerisation domain
      0.069   13.6   0.3          3    8.3   0.0    3.0  3  DUF5099       Domain of unknown function (DUF5099)
      0.069   13.8   6.5       0.43   11.3   0.2    3.6  4  PTS_IIB       PTS system, Lactose/Cellobiose specific IIB sub
       0.12   11.7   0.3         19    4.6   0.0    2.2  2  SBP_bac_3     Bacterial extracellular solute-binding proteins
       0.22   12.0   4.0        0.5   10.9   0.4    2.6  2  Usp           Universal stress protein family


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 !    6.5   0.1     0.003       6.7      33      57 ..      39      63 ..      36     110 .. 0.67
   2 !  190.3   0.8   1.2e-59   2.8e-56       1     185 [.     197     378 ..     197     379 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.003
                                      HHHHHHHHHTT-EEEEEE-S-SS-- CS
                               DFP 33 yalAeaaaarGaeVtlvsgpvslet 57
                                      ++lA+++++ GaeV+ v +p++ + 
  gi|242398477|ref|YP_002993901.1| 39 VKLARELIRHGAEVHAVMSPSAQKI 63
                                      689****************965332 PP

  == domain 2  score: 190.3 bits;  conditional E-value: 1.2e-59
                                       TTT-EEEEEES-EEEECCTTEEEEE----HHHHHHHHHHHHTT-EEEEEE-S-SS---TT-.EEEE--SHHHHHHHH CS
                               DFP   1 legkkvlvtaGpTrEaiDpVRfisNrSSGkmGyalAeaaaarGaeVtlvsgpvsletpegv.evvkvesaeemleav 76 
                                       l+gk+vlvtaG+TrE+iDp+Rfi+NrSSGkmG+alAe+a  rGaeVtl+  + s+  p+ v + v+ve++eemle +
  gi|242398477|ref|YP_002993901.1| 197 LAGKRVLVTAGATREYIDPIRFITNRSSGKMGVALAEEAEFRGAEVTLIRTKGSV--PSFVeNQVEVETVEEMLEVI 271
                                       689***********************************************99654..5556479************* PP

                                       HHHHTT-..SEEEE---S--EEES-------------..----EEE---HHHHHHHC-S.S-EEEEEEE-SS....- CS
                               DFP  77 eealkea..divimaAAvaDyrpkeaaeeKikkeeeeeeltleleknpdilaelaekkkkkqllvGFaaete....e 147
                                       e++l+++  divi aAAv+D+r+k++ + Kik    ++ ltlele++p+i+ ++ ++ +++ +lvGF+aet     e
  gi|242398477|ref|YP_002993901.1| 272 ENELNSKkyDIVILAAAVSDFRIKDKVSVKIKS---GKALTLELEPTPKIIDRV-KELQPDVFLVGFKAETGlsedE 344
                                       *99955455**********************96...568***************.56668889*******955688* PP

                                       HHHHHHHHHHHTT-SEEEEEEGGGTTGGG-SS-EEEEE CS
                               DFP 148 llenareklerkgldlivaNdvskeeagfgsdenevtl 185
                                       l+e ar+++er g d++vaN+++    +fgs+ene++l
  gi|242398477|ref|YP_002993901.1| 345 LIEAARKQIERAGSDIVVANTLK----AFGSEENEAIL 378
                                       **********************9....59*****9987 PP

>> Flavoprotein  Flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.9   2.5   1.8e-42     4e-39       1     158 []      23     192 ..      23     192 .. 0.95
   2 ?    4.2   0.0     0.014        32      18      73 ..     230     288 ..     223     292 .. 0.74

  Alignments for each domain:
  == domain 1  score: 133.9 bits;  conditional E-value: 1.8e-42
                                       EEEEEEE-SSCGGGCHHHHHHHHHHTTEEEEEEESCHHHHCCHHGGS...........TCSSHHHHHH....CTTES CS
                      Flavoprotein   1 kkillgiTGsvaaikalellekLkkegievqvvltkaAkkfiskeklklaa.......redpilhiel....rrwad 66 
                                       kki+l+i Gs+aa++ ++l ++L+++g+ev+ v++++A+k+i++  +++a+       +++ ++h+el    ++++d
  gi|242398477|ref|YP_002993901.1|  23 KKIVLAIPGSIAAVECVKLARELIRHGAEVHAVMSPSAQKIIHPYAMEFATgnpvvteITGFVEHVELagehENKVD 99 
                                       79*****************************************9999998899****999********887777*** PP

                                       EEEEEEEEHHHHHHHHTT--SSHHHHHH.HTHCCTTEEEEE.--HHCCTCSTCHHHHHHH.HT.............. CS
                      Flavoprotein  67 llviaPasantlakianGiadnlltlil.ratakkpiliaPamnpamyenpqtlknlekl.eegvtvikPsegdigk 141
                                       l++++Pa+ant++kia+Gi d+++t+++  a a++pi+iaPam+  mye+p++++n+ekl + gv++i+    ++gk
  gi|242398477|ref|YP_002993901.1| 100 LVLVCPATANTISKIACGIDDTPVTTVVtTAFAHTPIMIAPAMHFTMYEHPIVKENIEKLkKLGVEFIGSR-FEEGK 175
                                       *************************9995559****************************66********9.8999* PP

                                       ..GHHHHHHHHHHCHHT CS
                      Flavoprotein 142 gkmaeieeivgkildkl 158
                                       +k+a++eeiv  +++kl
  gi|242398477|ref|YP_002993901.1| 176 AKVASVEEIVYHVIKKL 192
                                       **********9998875 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.014
                                       HHHHHHHHTTEEEEEEESCHHHHCCHHGGS......TCSSHHHHHH.CTTESEEEEEEE CS
                      Flavoprotein  18 ellekLkkegievqvvltkaAkkfiskeklklaa..redpilhiel.rrwadllviaPa 73 
                                        l e+ + +g+ev+++ tk +   + ++++++++  +  ++ ++el ++++d+++ a a
  gi|242398477|ref|YP_002993901.1| 230 ALAEEAEFRGAEVTLIRTKGSVPSFVENQVEVETveEMLEVIENELnSKKYDIVILAAA 288
                                       566666779**********9987666665666663356667777777789999998865 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   0.00015      0.33      63     143 ..      84     165 ..      30     171 .. 0.80
   2 ?    4.4   0.5      0.02        44      23      98 ..     173     268 ..     168     400 .. 0.51

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00015
                                       HHHHHHHHHHTCCCTEEEEEEECSSCHG.HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx RF
                       Radical_SAM  63 fvellerlaklavpgiritvetngtlpd.eeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealekl 137
                                       fve +e + +  ++++ +++++++t  +  +++  +++ +v++v  ++ a ++ ++   m+  +++   v+e++ekl
  gi|242398477|ref|YP_002993901.1|  84 FVEHVELAGEH-ENKVDLVLVCPATANTiSKIACGIDDTPVTTVVTTAFAHTPIMIAPAMHfTMYEHPIVKENIEKL 159
                                       44444444444.489***********9999*********************************************** PP

                                       HHTTSE CS
                                       xxxxxx RF
                       Radical_SAM 138 reagik 143
                                       +++g++
  gi|242398477|ref|YP_002993901.1| 160 KKLGVE 165
                                       ***987 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.02
                                       HHHHHHHHHHHHHHHH.HHHH.HHTTSEEEEEESSTGGGS..................................... CS
                                       xxxxxxxxxxxxxxxx.xxxx.xxxxxxxxxxxxxxxxxx..................................... RF
                       Radical_SAM  23 egrgrslsveeileev.kelk.aekgvkevilgggeplly..................................... 60 
                                       eg++++ sveei+ +v k+l+ ++  +k v+++ g    y                                     
  gi|242398477|ref|YP_002993901.1| 173 EGKAKVASVEEIVYHViKKLHrKDLAGKRVLVTAGATREYidpirfitnrssgkmgvalaeeaefrgaevtlirtkg 249
                                       56777778888888774555443333555555543333332222222222222222222222222222222222222 PP

                                       ...........TTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHH CS
                                       ...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  61 ...........pdfvellerlaklavpgiritvetngtlpdeeklerll 98 
                                                                                 e +e++l
  gi|242398477|ref|YP_002993901.1| 250 svpsfvenqveV------------------------------ETVEEML 268
                                       222222222221..............................2222222 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 ?    0.4   0.0      0.22   4.9e+02      92     121 ..      25      54 ..      20      72 .. 0.77
   2 ?    6.2   0.0    0.0036       8.1      59      96 ..     142     181 ..     128     186 .. 0.82
   3 ?    2.1   0.0     0.068   1.5e+02      95     133 ..     250     284 ..     226     298 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.22
                                       EEEEEECCCTTTSHHHHHHHHHHHHCCCSS CS
                            MutL_C  92 ivravPallrqqnleelirelleelaekgk 121
                                       iv a+P  +   +  +l rel+ + ae + 
  gi|242398477|ref|YP_002993901.1|  25 IVLAIPGSIAAVECVKLARELIRHGAEVHA 54 
                                       67899999999***********99999886 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0036
                                       EE--HHHHHHHHHCHHHHHHCT-EEEE..-STTEEEEEEE CS
                            MutL_C  59 lelspeeaalleehkeeLaklGfelee..fgpnslivrav 96 
                                       ++++  e  +++e+ e+L+klG+e+    f++++++v +v
  gi|242398477|ref|YP_002993901.1| 142 MHFTMYEHPIVKENIEKLKKLGVEFIGsrFEEGKAKVASV 181
                                       6777788889***************866688888887765 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.068
                                       EEECCCTTTSHHHHHHHHHHHHCCCSS-H-HCCHHHHHH CS
                            MutL_C  95 avPallrqqnleelirelleelaekgkesleekleella 133
                                       +vP+++++q + e+++e+le ++++     ++k  +++ 
  gi|242398477|ref|YP_002993901.1| 250 SVPSFVENQVEVETVEEMLEVIENEL----NSKKYDIVI 284
                                       79*****************9988765....344555555 PP

>> DUF5099  Domain of unknown function (DUF5099)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.39   8.6e+02      21      65 ..      61     106 ..      51     111 .. 0.70
   2 ?    0.2   0.1      0.44   9.9e+02      14      48 ..     150     184 ..     142     198 .. 0.72
   3 ?    8.3   0.0    0.0014         3      37      74 ..     260     297 ..     230     303 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.39
                           DUF5099  21 kklkkkygikivkligekkdkvlikeeidf.enksvlpdlvilcnd 65 
                                       +k+ + y +++ +     ++    +e++++  +++++ dlv+ c  
  gi|242398477|ref|YP_002993901.1|  61 QKIIHPYAMEFATGNPVVTEITGFVEHVELaGEHENKVDLVLVCPA 106
                                       5556666666555555555666677888887799999*****9965 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.44
                           DUF5099  14 evskeeikklkkkygikivkl.igekkdkvlikeei 48 
                                        + ke+i+klkk  g++++ +  +e k kv  +eei
  gi|242398477|ref|YP_002993901.1| 150 PIVKENIEKLKK-LGVEFIGSrFEEGKAKVASVEEI 184
                                       788999999998.99998866245667777777766 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0014
                           DUF5099  37 ekkdkvlikeeidfenksvlpdlvilcndklvFklksp 74 
                                       e ++  ++ e i+ e +s+++d+vil   +  F++k+ 
  gi|242398477|ref|YP_002993901.1| 260 EVETVEEMLEVIENELNSKKYDIVILAAAVSDFRIKDK 297
                                       333333455666668899***************99876 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 ?    2.7   0.0     0.092   2.1e+02      36      77 ..      86     125 ..      71     137 .. 0.61
   2 ?   -2.8   0.0       4.7   1.1e+04      20      34 ..     156     169 ..     151     197 .. 0.65
   3 ?   11.3   0.2   0.00019      0.43      26      74 ..     256     304 ..     233     318 .. 0.83
   4 ?    1.1   0.1      0.29   6.4e+02      15      66 ..     345     391 ..     336     408 .. 0.64

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.092
                                       EE.GGGHHHHHHT-SEEEEEESSGGCTHHHHTTSEEEEECTTH CS
                           PTS_IIB  36 gv.eleaeeiaddaDlvllapqvrvkdlarfagkpvavinikd 77 
                                       +  el a e ++++Dlvl+ p ++   +++ a   ++ ++++ 
  gi|242398477|ref|YP_002993901.1|  86 EHvEL-AGEHENKVDLVLVCPATAN-TISKIAC-GIDDTPVTT 125
                                       44344.4455666********9993.4333332.244444444 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.7
                                       HHHHHHHCTEEEEET CS
                           PTS_IIB  20 lekaakelgieaege 34 
                                       +ek +k+lg+e +g+
  gi|242398477|ref|YP_002993901.1| 156 IEK-LKKLGVEFIGS 169
                                       544.56777776655 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.00019
                                       HCTEEEEETTEE..GGGHHHHHHT-SEEEEEESSGGCTHHHHTTSEEEEEC CS
                           PTS_IIB  26 elgieaegeagv..eleaeeiaddaDlvllapqvrvkdlarfagkpvavin 74 
                                       e+++e+e +++    +e+e +++++D+v+la+ v   d+  + ++ v++ +
  gi|242398477|ref|YP_002993901.1| 256 ENQVEVETVEEMleVIENELNSKKYDIVILAAAVS--DFRIKDKVSVKIKS 304
                                       5568888888888899****************999..77766664455554 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 0.29
                                       HHHHHHHHHHHHCTEEEEETTEEGGGHHHHHHT-SEEEEEESSGGCTHHHHT CS
                           PTS_IIB  15 maaeklekaakelgieaegeagveleaeeiaddaDlvllapqvrvkdlarfa 66 
                                       ++ e+ +k  + +g +++++++ ++  +e+     ++l++++++ k+l r +
  gi|242398477|ref|YP_002993901.1| 345 LI-EAARKQIERAGSDIVVANTLKAFGSEE---NEAILVGKDFT-KKLPRMN 391
                                       55.677777788888888888883333333...35788888888.5665555 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 ?    4.6   0.0    0.0085        19     105     122 ..     194     211 ..     180     224 .. 0.81
   2 ?    4.4   0.1    0.0094        21      37      74 ..     258     295 ..     229     302 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0085
                                       CGCGTTSEEEEETTSHHH CS
                                       xxxxxxxxxxxxxxxxxx RF
                         SBP_bac_3 105 ladLkgkkvgvqagstae 122
                                        +dL+gk+v v+ag t e
  gi|242398477|ref|YP_002993901.1| 194 RKDLAGKRVLVTAGATRE 211
                                       46************9988 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0094
                                       T-EEEEEE-SGGGHHHHHHTTSSSEEESSEB--HHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SBP_bac_3  37 gvkvefvpvswdelipalksgkvDiaiaaititpeRee 74 
                                       +v+ve v+   + + ++l+s+k+Di+i a ++++ R +
  gi|242398477|ref|YP_002993901.1| 258 QVEVETVEEMLEVIENELNSKKYDIVILAAAVSDFRIK 295
                                       45666665556667789*********999999888865 PP

>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.2      0.15   3.4e+02       3      36 ..      23      55 ..      22     115 .. 0.78
   2 ?   10.9   0.4   0.00022       0.5      23     119 ..     232     342 ..     223     369 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.15
                                      SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEE CS
                               Usp  3 krIlVavDgseeskkAlewAlelakargaelill 36
                                      k+I++a+ gs ++ + ++ A el ++ gae++++
  gi|242398477|ref|YP_002993901.1| 23 KKIVLAIPGSIAAVECVKLARELIRH-GAEVHAV 55
                                      79999999999999999999888776.8997665 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00022
                                       HHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH..............HHHHHHCTTCEEEEE CS
                               Usp  23 lelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada..............akaaaeaggvkvevv 85 
                                       +e+a+ rgae++l++   + +s  + + + e+ ee le  e el  ++               k++   ++++ +  
  gi|242398477|ref|YP_002993901.1| 232 AEEAEFRGAEVTLIRTKGSVPSFVENQVEVETVEEMLEVIENELNSKKydivilaaavsdfrIKDKVSVKIKSGKAL 308
                                       5578889***********************************999999**************9999999******** PP

                                       EEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTT CS
                               Usp  86 veegdpaeeilevaeeedadliVvGsrgrsglsr 119
                                       ++e +p ++i++ ++e+++d  +vG + ++gls+
  gi|242398477|ref|YP_002993901.1| 309 TLELEPTPKIIDRVKELQPDVFLVGFKAETGLSE 342
                                       ****************************999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       940  (0.052429); expected 358.6 (0.02)
Passed bias filter:                      677  (0.0377601); 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: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.45
# Mc/sec: 2704.97
//
Query:       gi|242398478|ref|YP_002993902.1|  [L=270]
Description: Small-conductance mechanosensitive channel [Thermococcus sibiricus MM 739]
Scores for 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-50  171.2   0.2      2e-50  171.2   0.2    1.3  2  MS_channel       Mechanosensitive ion channel
    0.00029   20.8   5.3    0.00029   20.8   5.3    2.5  3  TM_helix         Conserved TM helix
  ------ inclusion threshold ------
       0.36   10.2   3.6       0.53    9.6   3.6    1.2  1  TssN             Type VI secretion system, TssN
       0.42   10.5   4.9          4    7.4   0.0    3.2  3  Bacillus_PapR    Bacillus PapR protein


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 ?   -5.3   1.7         4   1.8e+04       3      15 ..      19      31 ..      17      38 .. 0.55
   2 !  171.2   0.2   4.4e-54     2e-50       4     206 .]      60     256 ..      57     256 .. 0.97

  Alignments for each domain:
  == domain 1  score: -5.3 bits;  conditional E-value: 4
                                      HHHHHHHHHHHHH CS
                        MS_channel  3 ilkiliivvgili 15
                                      i+++l+++vg+++
  gi|242398478|ref|YP_002993902.1| 19 ITAVLVLIVGFIV 31
                                      4445555555554 PP

  == domain 2  score: 171.2 bits;  conditional E-value: 4.4e-54
                                       HHHHHHHHHHHHHHHTTT--SCCHHHHH.HHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESSSEEEEEEEE CS
                        MS_channel   4 lkiliivvgilivlsllgvnvsallavl.GalglalglalkdlisnlvaGiillfekpfkiGDlveigdieGtVedi 79 
                                       l+ l++v +il++   lgv+v++++ +l +++gl lg++++d++ nl+aG+ l + +pf+ GD+v+i++ +G+Ve +
  gi|242398478|ref|YP_002993902.1|  60 LSALLYVAVILLAVRALGVEVGSVVLGLsAVIGLILGFGMQDTLTNLAAGVWLAALRPFEKGDVVTIAGQTGKVEAV 136
                                       677999**************999988773679********************************************* PP

                                       -SSEEEEEETTSEEEEEEHHHHHTS-EEESSS.SSEEEEEEEEEE-TTS-...HHHHHHHHHHHHHH-TTB-TTS-E CS
                        MS_channel  80 glrttkirtfdgrivtiPnsslvtsnieNlsresgtrrikvsigvtyssdvkklekvleelkealkekpevlkdkel 156
                                       g  +t + t+d+ ++tiPn+ ++ + i+N++r ++trr+ v++gv+y++d   l+k+++  +e +k++p++l+d+e+
  gi|242398478|ref|YP_002993902.1| 137 GVMSTELLTPDNVLITIPNKLVWGNVITNYTR-MPTRRVSVDVGVAYGTD---LDKAVKLAMELMKNHPKLLNDPEP 209
                                       ********************************.*****************...************************ PP

                                       EEEEEEE-SSSEEEEEEEEEET...TTHHHHHHHHHHHHHHHHHHHT--- CS
                        MS_channel 157 lvvldefgdsslnfevrvfvktvvpeeylsvqseinlrikkileeegiei 206
                                        v+++ +gdss+n+++r+++kt   e++++v+ ++++ i +   +egiei
  gi|242398478|ref|YP_002993902.1| 210 SVIITGLGDSSINLQLRAWTKT---EDHWAVKVDLTKGIYELYMKEGIEI 256
                                       **********************...***********************97 PP

>> TM_helix  Conserved TM helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   5.3   6.4e-08   0.00029      16      47 ..      17      48 ..      16      51 .. 0.95
   2 ?   -0.9   0.3      0.38   1.7e+03      11      18 ..      57      64 ..      48      73 .. 0.50
   3 ?   -2.5   0.1       1.1   5.1e+03      25      31 ..      90      96 ..      87     109 .. 0.60

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 6.4e-08
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTS CS
                          TM_helix 16 nLvgAilILlvGwiiAkfvsrlvtkllaktgi 47
                                      +++ A+l+L+vG+i+Ak++    +k l+kt++
  gi|242398478|ref|YP_002993902.1| 17 QIITAVLVLIVGFIVAKIIVASFKKGLKKTKL 48
                                      8****************************986 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.38
                                      HTTHSHHH CS
                          TM_helix 11 lsflPnLv 18
                                      + fl  L+
  gi|242398478|ref|YP_002993902.1| 57 ARFLSALL 64
                                      33333344 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 1.1
                                      HHHHHHH CS
                          TM_helix 25 lvGwiiA 31
                                      ++G+i++
  gi|242398478|ref|YP_002993902.1| 90 VIGLILG 96
                                      4444443 PP

>> TssN  Type VI secretion system, TssN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   3.6   0.00012      0.53      63     118 ..      18      76 ..      11     106 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00012
                              TssN  63 illqilylllGilhlylllkkffkelkekk...ilfeilltlivillglvlfvlvfnll 118
                                       i++ +l+l++G++ + +++ +f+k lk++k   +++e+l  ++++ll +++ +l +  l
  gi|242398478|ref|YP_002993902.1|  18 IITAVLVLIVGFIVAKIIVASFKKGLKKTKlsgLVIEFLARFLSALLYVAVILLAVRAL 76 
                                       789999**********************9977778888888888888777777766655 PP

>> Bacillus_PapR  Bacillus PapR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   1.2     0.053   2.4e+02       4      22 ..      59      78 ..      56      82 .. 0.78
   2 ?    7.4   0.0    0.0009         4      15      44 ..      90     119 ..      80     120 .. 0.88
   3 ?    0.9   0.0     0.094   4.2e+02      16      28 ..     178     190 ..     173     195 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.053
                     Bacillus_PapR  4 FLaCsL.vavamLaGvaFGv 22
                                      FL   L vav +La  a Gv
  gi|242398478|ref|YP_002993902.1| 59 FLSALLyVAVILLAVRALGV 78
                                      66554449*******9*998 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0009
                     Bacillus_PapR  15 LaGvaFGvGqDqaLtnqqeevqLasDLPFe 44 
                                       + G   G G    Ltn    v La+  PFe
  gi|242398478|ref|YP_002993902.1|  90 VIGLILGFGMQDTLTNLAAGVWLAALRPFE 119
                                       468899***99******************9 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.094
                     Bacillus_PapR  16 aGvaFGvGqDqaL 28 
                                        Gva+G   D+a+
  gi|242398478|ref|YP_002993902.1| 178 VGVAYGTDLDKAV 190
                                       6*****9999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       881  (0.0491383); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 1688.60
//
Query:       gi|242398479|ref|YP_002993903.1|  [L=275]
Description: Translation initiation factor eIF-2B, delta subunit [Thermococcus sibiricus MM 739]
Scores for complete 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-52  176.4   0.0    2.2e-51  174.8   0.0    1.8  1  IF-2B           Initiation factor 2 subunit family
  ------ inclusion threshold ------
      0.018   14.3   0.0       0.11   11.6   0.0    1.9  2  Regulator_TrmB  Archaeal transcriptional regulator TrmB


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 !  174.8   0.0   2.4e-55   2.2e-51      19     282 .]      32     271 ..      17     271 .. 0.90

  Alignments for each domain:
  == domain 1  score: 174.8 bits;  conditional E-value: 2.4e-55
                                       HHHHCCCSTHHHHHHHHHHHHHHHHTSSTS-HHHHHHHHHHHHHHHCCTTTSSHHHHHHHHHHHHHHHHHHHHHHHH CS
                             IF-2B  19 vikdaktskvaeLkeelrkaidlLkkarPtavslgnairrllkeiselksssdvkeakksliekikelikeieeade 95 
                                       +++ a+  +++e+ + l++ + ++ + +Pt+ sl n +r++              +  + +  k++e+i+  eea++
  gi|242398479|ref|YP_002993903.1|  32 YARLAEILEGEEFLNGLKDLGVEILNVNPTMASLYNLVRFIPI-----------IDNPEFVAAKANEFIRLSEEAKR 97 
                                       44555566799****************************9988...........346788999************** PP

                                       HHHHHHHTTC-TTEEEEEES--SHHHHHHHHHHHTTEEEEEEEEEXTTTTHHHTHHHHHHHTTXEEEEEEGGGHHHH CS
                             IF-2B  96 kigdiaaelikdgdtilTicnsktvlevlraaakekkkfkVivvEsrPrlqGrltakeLvqagipvtlitdsavayv 172
                                        ig+i++eli ++++i+T+++s+tvle+l++a++++k fkVi  Es P+ +G  +ak+L++ +ip+ +itd+ ++ +
  gi|242398479|ref|YP_002993903.1|  98 EIGNIGSELIDQNEIIITHSYSSTVLEILKKAKEKGKAFKVIISESGPDYEGLFFAKKLEEFEIPFEVITDAQLGLF 174
                                       ***************************************************************************** PP

                                       HHCTESEEEEEXSEEETTSEEEEETTHHHHHHHHHHTTXEEEEEXXGGGBESTSSSGGGSSXXBEXTHHHHEETTEE CS
                             IF-2B 173 mseevdkvivGAdrilenGaiankiGTsslAvlAkefnipvlvvaeslkfservqldedifieerdpeellnitger 249
                                        ++  + ++vGAd+i+++G ++nk+GT+ lA++++   ip++v+ae++k++++++ ++           ++ i+ + 
  gi|242398479|ref|YP_002993903.1| 175 AKN-ATLALVGADNITKDGYVFNKAGTYLLALACNDNGIPFYVAAETFKIHPEARAED-----------IKIIERKF 239
                                       999.*************************************************66555...........44455544 PP

                                       SSTTTEEEEEBSEEEEEGGGXSEEEETTEEEXC CS
                             IF-2B 250 iaeeelkvvnpafDvtPpelItliITevGvlpp 282
                                       +++  + ++n++fD tP ++I +iITe+G+l p
  gi|242398479|ref|YP_002993903.1| 240 KRD-HIIIRNYLFDATPWKYIRGIITELGILVP 271
                                       434.788**********************9865 PP

>> Regulator_TrmB  Archaeal transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0     0.022     2e+02      65     121 ..      60     117 ..      56     122 .. 0.87
   2 ?   11.6   0.0   1.2e-05      0.11      36     113 ..     120     197 ..     109     201 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.022
                                       GSSSSEEEEEE-S---S..EEEEETTTEEEEE-SSS-EEEE--HHHHHHHHHHHHHH. CS
                    Regulator_TrmB  65 ldleevatevrvrrsga.pllvivDrkrgvvaprevlrdkeeeyaiifkekelihvls 121
                                       +++++ ++ vr++  ++ p++v++ +++ +  ++e++r+  +  + +++++e+i + s
  gi|242398479|ref|YP_002993903.1|  60 PTMASLYNLVRFIPIIDnPEFVAAKANEFIRLSEEAKREIGNIGSELIDQNEIIITHS 117
                                       667788899************************9999999999999999999997655 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 1.2e-05
                                       HHHHHHHHHHHHTT-EEEEEESS----GGGSSSSEEEEEE-S---S.EEEEETTTEEEEE-SSS-....EEEE--HH CS
                    Regulator_TrmB  36 eelreeliaaaergvtVllliypdedleeldleevatevrvrrsgapllvivDrkrgvvaprevl....rdkeeeya 108
                                       +++ e l++a+e+g +  ++i++    + +d+e+ + + ++ +   p+ vi+D++ g++a++++l     d+ ++ +
  gi|242398479|ref|YP_002993903.1| 120 STVLEILKKAKEKGKAFKVIISE----SGPDYEGLFFAKKLEEFEIPFEVITDAQLGLFAKNATLalvgADNITKDG 192
                                       57788899999999999999999....88899******************************999999999999999 PP

                                       HHHHH CS
                    Regulator_TrmB 109 iifke 113
                                       ++f++
  gi|242398479|ref|YP_002993903.1| 193 YVFNK 197
                                       99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.46
# Mc/sec: 1805.29
//
Query:       gi|242398480|ref|YP_002993904.1|  [L=227]
Description: TBP-interacting protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-36  124.9   0.7    1.8e-36  124.2   0.7    1.3  1  TBPIP_N     TBP-interacting protein N-terminus
    0.00038   20.0   0.2    0.00038   20.0   0.2    1.8  2  zf_UBZ      Ubiquitin-Binding Zinc Finger
      0.001   18.6   0.0     0.0029   17.2   0.0    1.7  1  zf_C2H2_13  Zinc finger domain
  ------ inclusion threshold ------
       0.07   13.0   0.0       0.17   11.8   0.0    1.6  1  GSAP-16     gamma-Secretase-activating protein C-term


Domain annotation for each model (and alignments):
>> TBPIP_N  TBP-interacting protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.2   0.7     4e-40   1.8e-36       1     100 []       3     102 ..       3     102 .. 0.99

  Alignments for each domain:
  == domain 1  score: 124.2 bits;  conditional E-value: 4e-40
                                       HHTS-HHHHHHHHHHTT-TTEEEEEETTEEEEEETTT--EEEEEE-SSHHHHHHHS.S---SSEEEEEES-TT-EEE CS
                           TBPIP_N   1 yeelsekikkvytkvrtlddyhweiedslitgihkksnlklvidvakskeeadklaqkkevnnlmvvvvpdkevfyv 77 
                                       y+el+ ++k+vy+k+r lddyhw+i +++i g h+ks+l + i v  ske+a+kl+++k+  ++ + v+p++++fy+
  gi|242398480|ref|YP_002993904.1|   3 YSELNADVKRVYAKIRALDDYHWHIYEDTIIGHHRKSELPIRISVVGSKEKAEKLSEQKNGPGIDIAVIPNNNTFYI 79 
                                       89*************************************************************************** PP

                                       ETTEEEEEGGGHHHHHHHHHHTE CS
                           TBPIP_N  78 kngafvlalkylkatladisdhi 100
                                       kng f+l+ ++lkatl di+dhi
  gi|242398480|ref|YP_002993904.1|  80 KNGVFILSERFLKATLMDINDHI 102
                                       **********************8 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -5.0   1.8         4   1.8e+04      21      24 ..      21      24 ..      21      24 .. 0.89
   2 !   20.0   0.2   8.4e-08   0.00038       3      21 ..     149     167 ..     147     167 .. 0.93

  Alignments for each domain:
  == domain 1  score: -5.0 bits;  conditional E-value: 4
                            zf_UBZ 21 eDwH 24
                                      +D+H
  gi|242398480|ref|YP_002993904.1| 21 DDYH 24
                                      6*** PP

  == domain 2  score: 20.0 bits;  conditional E-value: 8.4e-08
                            zf_UBZ   3 ylCerCgkeipeselqEHe 21 
                                       y Ce+Cgk+i +++++EH+
  gi|242398480|ref|YP_002993904.1| 149 YKCEKCGKYIDIESVPEHL 167
                                       99****************5 PP

>> zf_C2H2_13  Zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   6.5e-07    0.0029      18      39 ..     149     170 ..     138     172 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 6.5e-07
                        zf_C2H2_13  18 RvCnkCGkPisleaivdHLenh 39 
                                         C+kCGk i +e++ +HL +h
  gi|242398480|ref|YP_002993904.1| 149 YKCEKCGKYIDIESVPEHLAKH 170
                                       55*****************998 PP

>> GSAP-16  gamma-Secretase-activating protein C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.8e-05      0.17      77      99 ..      78     100 ..      71     102 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.8e-05
                           GSAP-16  77 Yidngvleltedvvkkllkdldd 99 
                                       Yi+ngv++l+e+++k+ l d++d
  gi|242398480|ref|YP_002993904.1|  78 YIKNGVFILSERFLKATLMDIND 100
                                       ********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); 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: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1447.55
//
Query:       gi|242398481|ref|YP_002993905.1|  [L=625]
Description: Threonyl-tRNA synthetase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-55  186.0   0.4      3e-55  186.0   0.4    2.1  2  tRNA-Thr_ED      Archaea-specific editing domain of threonyl-
    1.1e-24   86.4   4.8    2.8e-24   85.1   3.4    2.3  2  HGTP_anticodon   Anticodon binding domain
    7.9e-19   68.3   0.2    1.8e-18   67.2   0.2    1.6  1  tRNA-synt_2b     tRNA synthetase class II core domain (G, H, 
  ------ inclusion threshold ------
      0.015   14.8   0.2      0.015   14.8   0.2    1.8  2  HGTP_anticodon2  Anticodon binding domain of tRNAs
        0.1   12.3   0.3       0.37   10.5   0.0    2.0  2  Sigma54_DBD      Sigma-54, DNA binding domain
        0.6    9.4   2.8          1    8.7   0.3    2.1  2  TIM              Triosephosphate isomerase
       0.66   10.7   5.4        5.9    7.7   0.0    3.4  2  Ku_C             Ku70/Ku80 C-terminal arm


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 !  186.0   0.4   1.2e-58     3e-55       1     137 []       1     139 [.       1     139 [. 0.99
   2 ?   -1.9   0.1       1.2   3.1e+03      39      65 ..     576     602 ..     550     607 .. 0.73

  Alignments for each domain:
  == domain 1  score: 186.0 bits;  conditional E-value: 1.2e-58
                                       -EEEEEEEEEEEEEEEEESSSS-...SS---EEEESSEEEEEEE-BTT--H...HHHHHHHHHHHHHHHHHT-SEEE CS
                       tRNA-Thr_ED   1 mrlLlihadeleyeakkkalkeae..eeeekegrleealvvFiavEkeDeeekekvvekavkeikkvakkvkakkvv 75 
                                       mr+Llih+d+leye+k+kalk++e  +e++k+grl+e+l vF++vEk De+++e++v+kavkei++v+++vk+++++
  gi|242398481|ref|YP_002993905.1|   1 MRILLIHSDYLEYEVKDKALKKPEeiSENQKKGRLDEVLAVFMSVEKVDEQNPEEIVKKAVKEIEEVVSQVKTNNIF 77 
                                       9**********************9898999*********************************************** PP

                                       EEE-STS-SSB--HHHHHHHHHHHHHHHHTT.-EEEE--SSEEEEEEEEE--STTSEEEEE- CS
                       tRNA-Thr_ED  76 lypyaHLssslaspevakeilkkleeklkekglevkraPFGwykefeisckGhpLaelsrei 137
                                       +yp+aHLss+l+sp+va +ilk++e++lk+kg++v raPFG+yk+f++sckGhpLaelsr+i
  gi|242398481|ref|YP_002993905.1|  78 VYPFAHLSSELGSPDVALRILKEIENELKNKGYNVRRAPFGYYKAFKLSCKGHPLAELSRTI 139
                                       ************************************************************97 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.2
                                       EEEE-BTT--H...HHHHHHHHHHHHH CS
                       tRNA-Thr_ED  39 vFiavEkeDeeekekvvekavkeikkv 65 
                                       v +   +eD+++ e  ve ++kei++ 
  gi|242398481|ref|YP_002993905.1| 576 VITVRKREDNKQYEIQVEDLIKEIRQK 602
                                       444445678888888899999999875 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.83   2.1e+03      17      32 ..      97     112 ..      88     114 .. 0.84
   2 !   85.1   3.4   1.1e-27   2.8e-24       1      93 [.     512     601 ..     512     602 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.83
                                       HHHHHHHHHHTTTSEE CS
                    HGTP_anticodon  17 yakklaeeLraagirv 32 
                                         k++ +eL+++g++v
  gi|242398481|ref|YP_002993905.1|  97 ILKEIENELKNKGYNV 112
                                       568999*******987 PP

  == domain 2  score: 85.1 bits;  conditional E-value: 1.1e-27
                                       SEEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTC CS
                    HGTP_anticodon   1 qvvviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtr 77 
                                       qv +ip++e   ++++ya  +a +L+ a ir+++dd+ne+++kkirea++ +ip+++vvGe+e + g++tvr+r++ 
  gi|242398481|ref|YP_002993905.1| 512 QVRIIPVSE---KYLDYALYIAGKLEGAKIRADVDDRNERLNKKIREAEKEWIPYIIVVGENEKRMGVITVRKREDN 585
                                       89*******...9***************************************************99*********** PP

                                       EEEEEETTHHHHHHHH CS
                    HGTP_anticodon  78 eqervsldelveklke 93 
                                       +q+++++++l++++++
  gi|242398481|ref|YP_002993905.1| 586 KQYEIQVEDLIKEIRQ 601
                                       **************97 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 !   67.2   0.2   6.9e-22   1.8e-18       7     178 ..     287     491 ..     282     492 .. 0.84

  Alignments for each domain:
  == domain 1  score: 67.2 bits;  conditional E-value: 6.9e-22
                                       TSEEEEE-SSSHHHHHHHHHHHEEEBGGSSEEEEEEEEE.EBTTTS.TBCTTTB-SEEEEEEEEEEES.GGGHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx.xxxxxxxxxxxxxxxxxxxxx.xxxxxxxx RF
                      tRNA-synt_2b   7 ndreyiLkPtneetfvelirdevlrskrLPlklyqiqtk.yRdEks.dsrGLlRvreFhqkdgyvfha.easlddsl 80 
                                        d+++ L+  ++ +   + +d ++  ++LPl++y++++  +R+Ek+ +++GL R+r F++ d + + +  +++ +++
  gi|242398481|ref|YP_002993905.1| 287 GDKRFFLRFAACFGQFLIKKDATISYRHLPLRMYELTRYsFRREKRgELSGLRRLRAFTMPDMHTVAKnLQQAMEEF 363
                                       4688899999999999999999555566*******99855******99******************9966999**** PP

                                       HHHHHHHHHHHHHTT.SC....EEEEEE....GTTSC..........................BTTSEEEEEEEEET CS
                                       xxxxxxxxxxxxxxxxxx....xxxxxx....xxxxx..........................xxxxxxxxxxxxxx RF
                      tRNA-synt_2b  81 rdlikaisriferlglef....raiiel....msaks..........................adykdkkefeavse 123
                                       ++  k+  ++++ +gl         i+     +   +                          +    k ef+ v++
  gi|242398481|ref|YP_002993905.1| 364 KKQYKLSMEVLKGVGLTPedyeV-AIRFtedfW---NenkdfivdlagiigkpvliemwkqrfFYFILKFEFNFVDN 436
                                       ***************95435542.222222233...14457889999999999999999998444467899999999 PP

                                       TTSEEEEEEEEEEEETHHHHHTTEEEECTTSSEEEEEEEEEE.EE.HHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx.xxxxxxxxxxx RF
                      tRNA-synt_2b 124 sltkgieigtiqklgtrlserlgatvldennreksvimicaa.ig.veRllsaileq 178
                                        l+k+  ++t+q +  + s+r+g+t+ de+++ek + +++ +  g +eR++ aile+
  gi|242398481|ref|YP_002993905.1| 437 -LDKAAALSTVQID-VENSQRFGITYYDEEGQEKYPLLLHCSpSGaIERVMYAILEK 491
                                       .*************.99*************************9999*********97 PP

>> HGTP_anticodon2  Anticodon binding domain of tRNAs
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.2      0.64   1.6e+03     162     188 ..      49      73 ..      14      81 .. 0.56
   2 ?   14.8   0.2   5.8e-06     0.015      12     102 ..     517     602 ..     510     607 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.64
                   HGTP_anticodon2 162 kksnkrekveqddAqeaaaelvkslln 188
                                         +n +e+v++  A ++ +e+v+++ +
  gi|242398481|ref|YP_002993905.1|  49 DEQNPEEIVKK--AVKEIEEVVSQVKT 73 
                                       44444444444..44444444444443 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 5.8e-06
                   HGTP_anticodon2  12 sfdksiLrtsgvellqeLWahnIsAdlaldasksleelvskarddgvswiviikqqnkskskekplkvkslekkedv 88 
                                        +++++L +  + +  +L   +I+Ad+  d  + l+  +++a+++ + +i+++ +  ++k++   + v++ e ++ +
  gi|242398481|ref|YP_002993905.1| 517 PVSEKYL-DYALYIAGKLEGAKIRADV-DDRNERLNKKIREAEKEWIPYIIVVGE--NEKRM-GVITVRKREDNKQY 588
                                       5677777.778889999999*******.444436666666666666667777777..34555.89************ PP

                   HGTP_anticodon2  89 dldldelvswlkqe 102
                                       ++++++l++ ++q 
  gi|242398481|ref|YP_002993905.1| 589 EIQVEDLIKEIRQK 602
                                       *******9987776 PP

>> Sigma54_DBD  Sigma-54, DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.2       1.1   2.8e+03      90     118 ..      46      73 ..      38      78 .. 0.66
   2 ?   10.5   0.0   0.00014      0.37      24      55 ..     480     511 ..     476     519 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.1
                                       XCSSTSSBHHTHHHHCCTHHHHHHCTS-T CS
                       Sigma54_DBD  90 ssvsseeggeasaeaikalikklieaEdk 118
                                       ++v++++ +e  ++a+k  i++++ + + 
  gi|242398481|ref|YP_002993905.1|  46 EKVDEQNPEEIVKKAVK-EIEEVVSQVKT 73 
                                       46777777777788887.67777776555 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00014
                                       HHHHHHHHHHHHHHHHHHXSSXXXXXXXHHHH CS
                       Sigma54_DBD  24 tllkvaeeiverQkdflekgeealrpltlrev 55 
                                        + +v+ +i+e+Q++ ++kg++ + pl l+ +
  gi|242398481|ref|YP_002993905.1| 480 AIERVMYAILEKQAKIMKKGKKPMYPLWLSPI 511
                                       589************************99877 PP

>> TIM  Triosephosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.2      0.13   3.3e+02     113     160 ..      31      78 ..       7     111 .. 0.79
   2 ?    8.7   0.3   0.00039         1      94     153 ..     538     602 ..     532     610 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.13
                                       HHTT-EEEEEE---HHHHHTT.HHHHHHHHHHHHTTTS-CCCGGCEEE CS
                               TIM 113 lksglkpilCvGEtleereagkteevvkeqlkeilkkldeealknvvi 160
                                       +k  l  +l v  ++e+ ++++ ee+vk+ +kei + +++ +++n+++
  gi|242398481|ref|YP_002993905.1|  31 KKGRLDEVLAVFMSVEKVDEQNPEEIVKKAVKEIEEVVSQVKTNNIFV 78 
                                       455677777888888888888889999999998888888887777765 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00039
                                       HHHHST--HHHHHHHHHHHHHTT-EEEEEE---HHH.....HHTT.HHHHHHHHHHHHTTTS-CC CS
                               TIM  94 rrqlfkEtdelvakKvkaalksglkpilCvGEtlee.....reagkteevvkeqlkeilkkldee 153
                                        r+ + + +e ++kK++ a k+ +  i+ vGE+++       ++++ ++  + q+++++k+++++
  gi|242398481|ref|YP_002993905.1| 538 IRADVDDRNERLNKKIREAEKEWIPYIIVVGENEKRmgvitVRKREDNKQYEIQVEDLIKEIRQK 602
                                       58889999*************************99866666455556666677777777777665 PP

>> Ku_C  Ku70/Ku80 C-terminal arm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   3.0      0.25   6.4e+02      30      71 ..      12      62 ..       4      76 .. 0.57
   2 ?    7.7   0.0    0.0023       5.9      35      64 ..     344     373 ..     330     386 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.25
                                      ..---SS--HHHHHHHHH-.....HHHHHHHHHHHHH.........HHHHH CS
                              Ku_C 30 e.eledktlpkyeaidkra.gslleewkelfeleeedke.......kkkek 71
                                      e e +dk l+k+e+i++++ +  l+e+   f+  e+  e       kk+ k
  gi|242398481|ref|YP_002993905.1| 12 EyEVKDKALKKPEEISENQkKGRLDEVLAVFMSVEKVDEqnpeeivKKAVK 62
                                      457777777777777777766677777777776665554445333333332 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0023
                                       S--HHHHHHHHH-....HHHHHHHHHHHHH CS
                              Ku_C  35 ktlpkyeaidkragslleewkelfeleeed 64 
                                        t+p+   ++k++++++ee+k++++l  e 
  gi|242398481|ref|YP_002993905.1| 344 FTMPDMHTVAKNLQQAMEEFKKQYKLSMEV 373
                                       599*********************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (625 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1149  (0.0640861); expected 358.6 (0.02)
Passed bias filter:                      774  (0.0431703); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); 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: 0.78u 0.33s 00:00:01.11 Elapsed: 00:00:00.51
# Mc/sec: 3709.31
//
Query:       gi|242398482|ref|YP_002993906.1|  [L=46]
Description: hypothetical protein TSIB_0491 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       131  (0.0073066); expected 358.6 (0.02)
Passed bias filter:                      115  (0.00641419); 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: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 335.30
//
Query:       gi|242398483|ref|YP_002993907.1|  [L=199]
Description: RNA-binding protein, containing S1 domain [Thermococcus sibiricus MM 739]
Scores for complete 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   36.6   0.0    5.8e-09   35.6   0.0    1.6  1  ECR1_N         Exosome complex exonuclease RRP4 N-terminal re
    1.7e-08   35.0   1.2    3.1e-06   27.7   0.2    2.4  2  EXOSC1         Exosome component EXOSC1/CSL4
    1.3e-05   25.5   0.3       0.12   12.8   0.1    2.4  2  S1             S1 RNA binding domain
     0.0077   16.1   0.1      0.015   15.2   0.1    1.4  1  Prok-RING_1    Prokaryotic RING finger family 1
  ------ inclusion threshold ------
       0.04   14.7   0.1      0.062   14.1   0.1    1.3  1  PCB_OB         Penicillin-binding protein OB-like domain
      0.049   13.8   1.6      0.081   13.1   1.6    1.3  1  Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (
      0.054   13.5   0.3      0.089   12.8   0.3    1.2  1  DZR            Double zinc ribbon
      0.058   13.4   0.2      0.058   13.4   0.2    1.9  1  Zn_Tnp_IS1595  Transposase zinc-ribbon domain
        0.2   11.7   1.3       0.41   10.7   1.3    1.7  1  HypA           Hydrogenase/urease nickel incorporation, metal
       0.23   11.4   1.6        0.6   10.1   1.6    1.8  1  DUF1610        Domain of unknown function (DUF1610)


Domain annotation for each model (and alignments):
>> ECR1_N  Exosome complex exonuclease RRP4 N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   0.0   3.2e-12   5.8e-09       1      37 [.      14      50 ..      14      51 .. 0.96

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 3.2e-12
                                      EE-TT-EEEETTTSEE-TTEEEETTEEEESSSEEEEE CS
                            ECR1_N  1 iVtPGevlttdeefmrGhGTYvrggtiyAsvaGtvev 37
                                      +V+PG+ l+  eef++G+G+ +++g++yA+ +G v++
  gi|242398483|ref|YP_002993907.1| 14 LVLPGDYLGVIEEFLPGEGVIEENGELYAARMGRVKI 50
                                      69*********************************97 PP

>> EXOSC1  Exosome component EXOSC1/CSL4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.2   1.7e-09   3.1e-06       1      50 [.      68     124 ..      68     127 .. 0.92
   2 !    7.1   0.1    0.0045       8.1      92     107 ..     124     139 ..     122     141 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 1.7e-09
                                       -S-TT-EEEEEEEEEESSEEEEEEEEECTB.......SBCCCEEECCCTTSS--STS CS
                            EXOSC1   1 lPkegdvVLarvtrlrkkqalveilsvege.......nnvlsdsgvgangegavkei 50 
                                       lP++gd+V+arv +++ + a+ve+l +eg+          l+  +v+++++g+v+++
  gi|242398483|ref|YP_002993907.1|  68 LPQVGDIVIARVLEVKSQAAIVELLKIEGRkgyreiaTSKLAGIHVSQVKDGYVESM 124
                                       8****************************9999888878889999999999999986 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0045
                                       GGCTEECTTEEEEEEE CS
                            EXOSC1  92 viemfrpGDIvraqvi 107
                                       +   f+ GDIvra+v+
  gi|242398483|ref|YP_002993907.1| 124 MNSEFKIGDIVRAKVL 139
                                       6678*********997 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0   0.00029      0.51       2      30 ..      69      96 ..      68     106 .. 0.93
   2 !   12.8   0.1   6.6e-05      0.12      32      65 ..     111     143 ..     107     151 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00029
                                      STTTCEEEEEEEEEETTEEEEEETTTEEE CS
                                S1  2 pekgevveGeVtsvtkgGafVelgngveg 30
                                      p++g++v + V +v   +a+Vel+ ++eg
  gi|242398483|ref|YP_002993907.1| 69 PQVGDIVIARVLEVKSQAAIVELL-KIEG 96
                                      799*********************.8887 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 6.6e-05
                                       EEGGGSSSSCEESCHHHCEETTEEEEEEEEEEET CS
                                S1  32 vpaselsrdarvedpdevlkvGdevkvkvlkvdk 65 
                                       +++s++++   ve+ + ++k+Gd v++kvl  +k
  gi|242398483|ref|YP_002993907.1| 111 IHVSQVKDG-YVESMNSEFKIGDIVRAKVLTNNK 143
                                       9******99.9******************97655 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 !   15.2   0.1   8.6e-06     0.015       6      30 ..     161     185 ..     158     190 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 8.6e-06
                       Prok-RING_1   6 kCpvCgkelkeedDiVvCpeCgtpy 30 
                                        C+ C+  l  +  + vCp+Cg + 
  gi|242398483|ref|YP_002993907.1| 161 LCSSCKVSLVRKGNALVCPKCGRSE 185
                                       6*********************875 PP

>> PCB_OB  Penicillin-binding protein OB-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   3.5e-05     0.062      25     100 ..      65     141 ..      46     155 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.5e-05
                                       CCTSSTCTTEEEEEEEEEETTEEEEEE..TTS-EEEEEGGGGTTTGCCTTTS-B---CCCHCCC--TTEEEEEEE-T CS
                            PCB_OB  25 lkklpdsgelrpAvVlsvseksarvgl..rdgetgtipleglkwarkvlsdkkqgkapksasdvlkpGdvvlvrkee 99 
                                       + +lp++g+++ A Vl+v+ ++a v+l   +g++g  ++++ k a   +s+  ++  ++s++  +k Gd+v+ +  +
  gi|242398483|ref|YP_002993907.1|  65 VPPLPQVGDIVIARVLEVKSQAAIVELlkIEGRKGYREIATSKLAGIHVSQV-KDGYVESMNSEFKIGDIVRAKVLT 140
                                       5678899*******************96635566655555555555544444.456799*************99887 PP

                                       T CS
                            PCB_OB 100 d 100
                                       +
  gi|242398483|ref|YP_002993907.1| 141 N 141
                                       5 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   1.6   4.5e-05     0.081      18      40 .]     162     182 ..     159     182 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.5e-05
                     Auto_anti-p27  18 CpvCgvPLmrdrkggkvyCvaCd 40 
                                       C+ C+v L+r  kg+ ++C+ C+
  gi|242398483|ref|YP_002993907.1| 162 CSSCKVSLVR--KGNALVCPKCG 182
                                       **********..789*******6 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.3     5e-05     0.089      14      38 ..     161     185 ..     155     190 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5e-05
                               DZR  14 fCseCgtklkavaaedrCpsCgekv 38 
                                        Cs C+ +l +  ++ +Cp+Cg++ 
  gi|242398483|ref|YP_002993907.1| 161 LCSSCKVSLVRKGNALVCPKCGRSE 185
                                       7999999999999999999999875 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 ?   13.4   0.2   3.2e-05     0.058      16      35 ..     173     194 ..     167     197 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.2e-05
                     Zn_Tnp_IS1595  16 pngfvCPhCgsrkayrikt..r 35 
                                       +n  vCP+Cg +++++++t  r
  gi|242398483|ref|YP_002993907.1| 173 GNALVCPKCGRSESRKLSTyyR 194
                                       6789******99***9999554 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.3   0.00023      0.41      69      97 ..     158     186 ..      81     192 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00023
                                       -EEEETTTS-EEECHHHHHS-TTTSSS-E CS
                              HypA  69 vkvrCreCgkefeleekalrCpkCgsadv 97 
                                       + + C++C+ +   + +al CpkCg+++ 
  gi|242398483|ref|YP_002993907.1| 158 IYALCSSCKVSLVRKGNALVCPKCGRSES 186
                                       4578*****8887666689******9865 PP

>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   1.6   0.00033       0.6       1      23 [.     162     182 ..     162     183 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00033
                           DUF1610   1 CtSCGaelaprEravvFpCPNCG 23 
                                       C+SC + l+  ++a    CP+CG
  gi|242398483|ref|YP_002993907.1| 162 CSSCKVSLVRKGNAL--VCPKCG 182
                                       9********999765..6****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1225.05
//
Query:       gi|242398484|ref|YP_002993908.1|  [L=209]
Description: hypothetical protein TSIB_0493 [Thermococcus sibiricus MM 739]
Scores for complete 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-43  146.0   4.9      1e-42  145.9   4.9    1.0  1  DUF2067   Uncharacterized protein conserved in archaea (DUF20
  ------ inclusion threshold ------
      0.069   12.9   0.3       0.16   11.7   0.3    1.6  1  DUF2102   Uncharacterized protein conserved in archaea (DUF21
      0.076   12.8   0.3       0.25   11.1   0.1    1.8  2  P2_N      Viral coat protein P2 N-terminal domain
      0.095   12.5   0.1        5.3    6.9   0.1    2.4  2  KH_1      KH domain
       0.11   13.0   4.5       0.31   11.6   0.1    3.1  3  YusW      YusW-like protein
       0.29   11.4   0.1       0.29   11.4   0.1    2.5  4  DUF3970   Protein of unknown function (DUF3970)


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 !  145.9   4.9   3.3e-46     1e-42       1     185 [.       9     195 ..       9     196 .. 0.98

  Alignments for each domain:
  == domain 1  score: 145.9 bits;  conditional E-value: 3.3e-46
                           DUF2067   1 iklndeeeleeflekise.kiksaeevkievegnrllievyGtekeikdiirrikellre...klkkekrglfkysl 73 
                                       i+++d+ e ee+++++++ +++++++v+++++  +l+i+++Gt++ei++++++++e++ +   +l+++++g+++y +
  gi|242398484|ref|YP_002993908.1|   9 IHVKDDLEKEELMKELQKiELPAFIYVHGKLN--SLKINIQGTKDEIREAMEKVREIHYRvrsRLYPDRKGFYQYNV 83 
                                       6899**************************77..*************************99**************** PP

                           DUF2067  74 sdllreagapvppdvLvdaLkllGykaelreenvlktnapleevvelaerlseiykelrfknlskaakrvvavvsvl 150
                                       +d++reag+ ++++ L ++L+llG  a l+ ++ l ++ ++ e+v l+++l e++++++ ++ ++++++v+a +sv 
  gi|242398484|ref|YP_002993908.1|  84 NDIFREAGVSISIPTLTKTLELLGEHADLK-GDKLISSLSWGEIVNLVKKLGEVLTDISLQT-TRQIREVIAPISVT 158
                                       ******************************.*******************************.9************* PP

                           DUF2067 151 tgldpdevieellekGlLe..eeegkivlrkewkkal 185
                                         +dp+ev+e +++ G+ e  e+++k++l+k++++a 
  gi|242398484|ref|YP_002993908.1| 159 LNIDPQEVLELAVDFGVAEykEDKFKYELVKNKEQAM 195
                                       *****************9999*************996 PP

>> DUF2102  Uncharacterized protein conserved in archaea (DUF2102)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.3   5.4e-05      0.16       2      66 ..       7      78 ..       6      85 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.4e-05
                           DUF2102  2 vvieseaevtpselvrkvyeleedvti....ketCfGllvegeeeevekvveevrkld...pnkifvkeRgf 66
                                      +vi+ ++++ ++el+++++++e +  i    k +   ++++g+++e+++++e+vr+++   +++++  ++gf
  gi|242398484|ref|YP_002993908.1|  7 IVIHVKDDLEKEELMKELQKIELPAFIyvhgKLNSLKINIQGTKDEIREAMEKVREIHyrvRSRLYPDRKGF 78
                                      7888899999999*****99999844433448899999*****************98622234556555555 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 ?   -1.4   0.0      0.61   1.8e+03      84     114 ..      19      49 ..       5      57 .. 0.72
   2 ?   11.1   0.1   8.4e-05      0.25       8      51 ..     119     162 ..     116     171 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.61
                              P2_N  84 isaktkagqrlgaLvTsaidnltleveiaaa 114
                                         +k++++++l a+  + ++  +l+++i+++
  gi|242398484|ref|YP_002993908.1|  19 ELMKELQKIELPAFIYVHGKLNSLKINIQGT 49 
                                       4567777777777777777777788888773 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 8.4e-05
                              P2_N   8 envvagetatlklpiGptYekIvLelggtakaqItrirvklNgk 51 
                                       ++  +ge ++l  ++G ++++I L+++    + I  i+v+lN +
  gi|242398484|ref|YP_002993908.1| 119 SSLSWGEIVNLVKKLGEVLTDISLQTTRQIREVIAPISVTLNID 162
                                       67789*************************************66 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1    0.0018       5.3      23      66 .]      22      62 ..      17      62 .. 0.75
   2 ?    3.2   0.0     0.026        77      21      37 ..      82      98 ..      80     113 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0018
                                      HHHHHHH.T-EEEEESSTT...T.-EEEEEESHHHHHHHHHHHHH CS
                              KH_1 23 keIreet.gakIkvpksedegsderevtisGspeavekAkeliee 66
                                      ke+++ +  a I v  ++    ++  + i+G+++ + +A+e+++e
  gi|242398484|ref|YP_002993908.1| 22 KELQKIElPAFIYVH-GK---LNSLKINIQGTKDEIREAMEKVRE 62
                                      666666666777766.33...36779*****9999******9975 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.026
                                      HHHHHHHHHT-EEEEES CS
                              KH_1 21 nIkeIreetgakIkvpk 37
                                      n+++I +e g++I +p 
  gi|242398484|ref|YP_002993908.1| 82 NVNDIFREAGVSISIPT 98
                                      8999***99*****994 PP

>> YusW  YusW-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1      0.33   9.9e+02      44      70 ..      31      57 ..       9      67 .. 0.74
   2 ?   11.6   0.1    0.0001      0.31      45      87 ..     130     173 ..     127     177 .. 0.90
   3 ?    2.8   0.6     0.058   1.7e+02       4      28 ..     168     194 ..     166     208 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.33
                              YusW 44 AleelealLseLsvdsetsedevisqv 70
                                      A+ ++   L++L+++ +  +de+ ++ 
  gi|242398484|ref|YP_002993908.1| 31 AFIYVHGKLNSLKINIQGTKDEIREAM 57
                                      555667777888888777777777665 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.0001
                              YusW  45 leelealLseLsvdsetsedevisqvlsalnld.edveefelev 87 
                                       +++l ++L+++s+++++++ evi  +   ln+d ++v e+ +++
  gi|242398484|ref|YP_002993908.1| 130 VKKLGEVLTDISLQTTRQIREVIAPISVTLNIDpQEVLELAVDF 173
                                       678999***************************88888887765 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.058
                              YusW   4 eLdveyed..edeyeveYekekdetea 28 
                                       eL v+++    +e +++Ye+ k++++a
  gi|242398484|ref|YP_002993908.1| 168 ELAVDFGVaeYKEDKFKYELVKNKEQA 194
                                       66677654448889999**99999776 PP

>> DUF3970  Protein of unknown function (DUF3970)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.2       2.8   8.4e+03      14      22 ..      18      26 ..      14      30 .. 0.62
   2 ?   11.4   0.1   9.8e-05      0.29       3      26 ..      43      67 ..      41      73 .. 0.91
   3 ?   -2.9   0.0       2.8   8.2e+03      12      21 ..     125     134 ..     124     141 .. 0.83
   4 ?   -2.6   0.4       2.3   6.8e+03      40      52 ..     184     196 ..     176     201 .. 0.66

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.8
                           DUF3970 14 eeflkslek 22
                                      ee++k+l+k
  gi|242398484|ref|YP_002993908.1| 18 EELMKELQK 26
                                      556666554 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 9.8e-05
                           DUF3970  3 rvRlaGkqeEieeflkslek.nyev 26
                                      ++ ++G+++Ei e+++++ + +y v
  gi|242398484|ref|YP_002993908.1| 43 KINIQGTKDEIREAMEKVREiHYRV 67
                                      7899***************999987 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 2.8
                           DUF3970  12 Eieeflksle 21 
                                       Ei++++k+l 
  gi|242398484|ref|YP_002993908.1| 125 EIVNLVKKLG 134
                                       8999999985 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 2.3
                           DUF3970  40 KYkysKdvrvYle 52 
                                       KY+  K+  + +e
  gi|242398484|ref|YP_002993908.1| 184 KYELVKNKEQAME 196
                                       7777777665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1178  (0.0657036); expected 358.6 (0.02)
Passed bias filter:                      766  (0.0427241); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
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 0.29s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1288.97
//
Query:       gi|242398485|ref|YP_002993909.1|  [L=95]
Description: DNA-directed RNA polymerase subunit L [Thermococcus sibiricus MM 739]
Scores for complete 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   72.0   0.1      3e-20   71.8   0.1    1.1  1  RNA_pol_L_2   RNA polymerase Rpb3/Rpb11 dimerisation domain
    3.7e-10   39.1   0.0    6.1e-10   38.4   0.0    1.4  1  RNA_pol_L     RNA polymerase Rpb3/Rpb11 dimerisation domain
  ------ inclusion threshold ------
      0.018   15.2   0.0      0.027   14.6   0.0    1.4  1  Cadherin_pro  Cadherin prodomain like


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 !   71.8   0.1     5e-24     3e-20       2      72 ..      13      85 ..      12      88 .. 0.93

  Alignments for each domain:
  == domain 1  score: 71.8 bits;  conditional E-value: 5e-24
                                      EEEEEES--HHHHHHHHHHHTTSTTEEEEEEECSST..TTSEEEEEEEESTSS-HHHHHHHHHHHHHHHHHHH CS
                       RNA_pol_L_2  2 ltfeingEDhTLgnlLrhlllknpsVefagYkipHP..lepkmnlriqtkssnnpleaLkkalkdlldicdel 72
                                      l+f + gEDhT++nlL + l++n++V+fa+Y+i+HP  +  k  +ri t+++++p +aL++a++++ d  +++
  gi|242398485|ref|YP_002993909.1| 13 LEFYLVGEDHTFANLLSETLHENKHVTFAAYTIEHPvlMARKPRFRISTDGKITPEKALEEAAQKIFDRAKDV 85
                                      68999*******************************7666*************************99988776 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 !   38.4   0.0     1e-13   6.1e-10       1      65 [.      14      78 ..      14      82 .. 0.92

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 1e-13
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         RNA_pol_L  1 efllrgvdhtlgNaLRrillsevpgvaiea.....pvvkvntdkdklilevetdgslkPeealkeAlkiL 65
                                      ef l g+dht++N L  +l+ e+  v ++a     pv        k  +++ tdg ++Pe+al+eA++++
  gi|242398485|ref|YP_002993909.1| 14 EFYLVGEDHTFANLLSETLH-ENKHVTFAAytiehPV----LMARKPRFRISTDGKITPEKALEEAAQKI 78
                                      7999****************.*********9999988....6777789*******************987 PP

>> Cadherin_pro  Cadherin prodomain like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   4.5e-06     0.027      29      68 ..      39      77 ..      19      85 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.5e-06
                                      --B--SS---EEEE---SEEEEETTTEEEEES--S-SSS- CS
                      Cadherin_pro 29 kfedCkgnkkiqyessdpdFkveeDGtvyakrevklssek 68
                                      +f+  + ++ +      p+F++++DG ++ +++++ +++k
  gi|242398485|ref|YP_002993909.1| 39 TFAAYTIEHPVL-MARKPRFRISTDGKITPEKALEEAAQK 77
                                      555554444444.67899****************998874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 665.56
//
Query:       gi|242398486|ref|YP_002993910.1|  [L=129]
Description: hypothetical protein TSIB_0495 [Thermococcus sibiricus MM 739]
Scores for 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-46  155.2   0.0      1e-45  155.0   0.0    1.0  1  Ribonucleas_3_2  Ribonuclease III
  ------ inclusion threshold ------
       0.17   12.2   0.0        0.3   11.4   0.0    1.3  1  NdhM             Cyanobacterial and plastid NDH-1 subunit M


Domain annotation for each model (and alignments):
>> Ribonucleas_3_2  Ribonuclease III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.0   0.0   1.1e-49     1e-45       1     118 [.      11     128 ..      11     129 .] 0.99

  Alignments for each domain:
  == domain 1  score: 155.0 bits;  conditional E-value: 1.1e-49
                                       HHHHHHHHHHHHHHHHHHHHHHHTS-------HHHHHHHHHHTTGGGCS-.CGGCCGHHHHHHHHHHHHHHTTSS-H CS
                   Ribonucleas_3_2   1 kglaklGdslinllvslaltellGkPtGervPnaslaialelaglskllkprvdkhakGdiaeallayaWlkgkisi 77 
                                       k+l+++Gdsl+n+++slal+ +lG P   rvPnasl+i le agl + ++pr+dkh+kGdiaea++ayaW++g++si
  gi|242398486|ref|YP_002993910.1|  11 KNLSRFGDSLVNFIFSLALSRYLGYPNAGRVPNASLTIGLEKAGLLHCVPPRTDKHGKGDIAEAIIAYAWFEGEMSI 87 
                                       89*************************************************************************** PP

                                       HHHHHHHHCT--GGGG-TTTHHHHHHHHHHHHHHHHHHHHH CS
                   Ribonucleas_3_2  78 eeaveilkknlddevldfsrkkeaigkalaklleeiserle 118
                                       +eav+il+kn+++++++ srkke ig+a+ +ll++i erl 
  gi|242398486|ref|YP_002993910.1|  88 DEAVDILSKNFSSDITHPSRKKEVIGNAFGELLKIIKERLA 128
                                       ***************************************96 PP

>> NdhM  Cyanobacterial and plastid NDH-1 subunit M
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   3.3e-05       0.3      60     102 ..       5      47 ..       2      52 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.3e-05
                              NdhM  60 gedlteynlrriGsdlehfirkllqkGeisynlesrvlnysmG 102
                                        +d+t+ nl r G +l +fi +l  +  + y    rv n s+ 
  gi|242398486|ref|YP_002993910.1|   5 SKDFTDKNLSRFGDSLVNFIFSLALSRYLGYPNAGRVPNASLT 47 
                                       5899***********************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 945.99
//
Query:       gi|242398487|ref|YP_002993911.1|  [L=268]
Description: AP endonuclease [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.9e-18   64.3   0.0    1.2e-17   64.0   0.0    1.1  1  AP_endonuc_2   Xylose isomerase-like TIM barrel
     0.0084   16.3   0.0      0.014   15.6   0.0    1.4  1  MukF_C         MukF C-terminal domain
  ------ inclusion threshold ------
      0.046   14.0   0.0      0.071   13.4   0.0    1.4  1  Uricase        Uricase
       0.09   13.3   0.0       0.18   12.3   0.0    1.4  1  CoA_binding_2  CoA binding domain
       0.13   12.2   0.1       0.47   10.5   0.1    1.9  1  Hjc            Archaeal holliday junction resolvase (hjc)


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 !   64.0   0.0   3.4e-21   1.2e-17       8     210 .]      29     228 ..      22     228 .. 0.90

  Alignments for each domain:
  == domain 1  score: 64.0 bits;  conditional E-value: 3.4e-21
                                       T-SEEEEECCTCSHHHHC..HHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCS.HHHHHHHHHHHHHHHHH CS
                      AP_endonuc_2   8 GfdgvElfgrdlvpvsel..sdeelrelrkaldelglriaslslftrfgypdederear.reesvdalkraielaaa 81 
                                        +d+v++f++ l  +++    +++lr + +al+  g++   ++++t  +      r+     ++++ +k  i+ a +
  gi|242398487|ref|YP_002993911.1|  29 DYDFVQIFPHALGLIKNGqvVEKGLRSIENALKGVGVK-YTIRMPTSVNL-----RDNTyYSRHFNVAKAVIDVAIK 99 
                                       59**************99********************.45555555544.....444455556************* PP

                                       HTBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSEEEEE--TTTTSSSTCHHHHHHHHHHTTTTEEE CS
                      AP_endonuc_2  82 LGapllvlhpGtagagpkgseeeawerlaeslneladyaekegvklalEtlagsgvelgdeelarlldavdspnvgv 158
                                       LGa+++v+++G         +  ++++ +e+l++la++ae  g+k+alE++ +       ++++++++ ++ +n+g+
  gi|242398487|ref|YP_002993911.1| 100 LGAKIVVMQSG---------RTGRLDLEIEALQQLAEMAENFGIKIALENTYSV------KDTLYVVESINKENLGF 161
                                       *********99.........99****************************9877......69*************** PP

                                       EEEHHHHHHH....TTTHHHHHHHHHGGEEEEEE.EESS...........TTTTSSTTEESTTSSSS CS
                      AP_endonuc_2 159 clDtgHllia....eedvddalraladrikhvHikDakg...........dlgagrdrhvpigeGei 210
                                       +lD gH+++     e+ + + ++   +++ ++ i+D++g              + +d h+++geG i
  gi|242398487|ref|YP_002993911.1| 162 ALDLGHAFLSaqgdENKFLEDVKLGTEKTIILMIHDNFGkffpkvdpidaLAYGVGDLHLMPGEGKI 228
                                       ***********999999999999999***********************877788889*******87 PP

>> MukF_C  MukF C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   3.9e-06     0.014      50     128 ..      26     102 ..      21     136 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.9e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                            MukF_C  50 alrdeevtGelPeeleyeeleeieeqlaerieealavykekgkpldlaevlrdylakyPksqhfdvarllvdqavrl 126
                                       +++d + +   P++l   +  ++ e+  ++ie+al+    k  ++ + + ++   ++y  s+hf+va+ ++d a++l
  gi|242398487|ref|YP_002993911.1|  26 KIKDYDFVQIFPHALGLIKNGQVVEKGLRSIENALKGVGVK-YTIRMPTSVNLRDNTY-YSRHFNVAKAVIDVAIKL 100
                                       56677777777777777777777777777777777766544.3444444444333445.589*************** PP

                                       XX CS
                            MukF_C 127 Gv 128
                                       G 
  gi|242398487|ref|YP_002993911.1| 101 GA 102
                                       *6 PP

>> Uricase  Uricase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0     2e-05     0.071      43      86 ..     135     172 ..      71     188 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2e-05
                                       HHH-STTT---CCHHHHHHHHHHHHH--SSHH.HHHHHHHHHHHC CS
                           Uricase  43 yfagdnsdvvasdSvkntvYkmakkhgvespe.Falllakhflek 86 
                                        +a +n     + Svk t+Y++ +    +++  Fal l++ fl++
  gi|242398487|ref|YP_002993911.1| 135 KIALEN-----TYSVKDTLYVVESI--NKENLgFALDLGHAFLSA 172
                                       456677.....************99..334447**********86 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   5.1e-05      0.18      67     111 ..      89     142 ..      83     146 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.1e-05
                                       HHGGGHHHHHHH--SEEEE-TT.........---HHHHHHHHHTT-EEE.ES-H CS
                     CoA_binding_2  67 atpeivkealalgakavwlqpg.........sedeeaaelaeeagirvvgdrCi 111
                                       ++ ++++ a++lgak v++q+g         +  +++ae+ae+ gi++  ++ +
  gi|242398487|ref|YP_002993911.1|  89 VAKAVIDVAIKLGAKIVVMQSGrtgrldleiEALQQLAEMAENFGIKIALENTY 142
                                       677899999********************9999999*********998766665 PP

>> Hjc  Archaeal holliday junction resolvase (hjc)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00013      0.47      30      81 ..      93     142 ..      52     153 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00013
                                       S-SEEEEETTEEEEEEEEEESSSEEEEEHHHHHHHHHHHHHHTCEEEEEEEE CS
                               Hjc  30 lpDviAirgdvvlviEvKsskkeriylkkeqvekllefarkaggelllavkl 81 
                                       + Dv Ai+ +  +v+ + s +  r+ l+ e +++l+e+a+++g++  l   +
  gi|242398487|ref|YP_002993911.1|  93 VIDV-AIKLGAKIVV-MQSGRTGRLDLEIEALQQLAEMAENFGIKIALENTY 142
                                       4453.5555544444.45556569999*****************98876555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1858.51
//
Query:       gi|242398488|ref|YP_002993912.1|  [L=335]
Description: protease [Thermococcus sibiricus MM 739]
Scores for complete 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-39  134.7   0.4    4.1e-39  134.0   0.1    1.5  2  Peptidase_S49  Peptidase family S49
      4e-09   36.6   0.0    7.3e-09   35.8   0.0    1.4  1  CLP_protease   Clp protease
      3e-06   26.5   0.0    3.9e-06   26.1   0.0    1.2  1  SDH_sah        Serine dehydrogenase proteinase
     0.0017   17.8   0.6      0.016   14.5   0.3    2.2  2  ECH_1          Enoyl-CoA hydratase/isomerase
  ------ inclusion threshold ------
      0.018   15.3   0.3       0.11   12.7   0.0    2.3  3  Imm7           Immunity protein 7
        0.1   13.5   0.2       0.17   12.7   0.2    1.3  1  DUF4482        Domain of unknown function (DUF4482)
       0.11   12.7   2.2       0.15   12.2   0.2    2.3  3  DUF3896        Protein of unknown function (DUF3896)
       0.15   11.6   0.1       0.31   10.6   0.1    1.5  1  L6_membrane    L6 membrane protein
       0.17   10.2   0.4       0.24    9.7   0.4    1.2  1  DUF5312        Family of unknown function (DUF5312)


Domain annotation for each model (and alignments):
>> Peptidase_S49  Peptidase family S49
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       2.5   5.1e+03      61      88 ..      43      70 ..      20      78 .. 0.56
   2 !  134.0   0.1   2.1e-42   4.1e-39       3     153 ..     150     299 ..     148     300 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.5
                                      EEEEEESSTTCCCCCTTSS--HHHHHHH CS
                     Peptidase_S49 61 evqvvkaGeyksavslrrelteeereil 88
                                      +v+vv+ G+ k++ s      +++ e l
  gi|242398488|ref|YP_002993912.1| 43 NVTVVYNGTVKEVESNATIALQAKIEEL 70
                                      5566666666666544444444444444 PP

  == domain 2  score: 134.0 bits;  conditional E-value: 2.1e-42
                                       HHTT--EEEEEEEEEETHHHHHHTTSSEEEE-TT-EEE---EEEEEEE-HHHHHHTT-EEEEEESSTTCCCCCTTSS CS
                     Peptidase_S49   3 kkakkPvvasaenvaaSggYylasaadkivanpstivgsiGvitqllnlenlldklgvevqvvkaGeyksavslrre 79 
                                       ++ +kP+va+ +++aaSggY++a+aadki+a+p + vgsiGv   + +le+ +++ gv+v+v+k+G+yk+++   r+
  gi|242398488|ref|YP_002993912.1| 150 LSYEKPIVAYTGGMAASGGYLIACAADKIIADPLAEVGSIGVLYVHYDLEQNYAQNGVKVNVFKTGKYKDTGAEWRD 226
                                       6779************************************************************************* PP

                                       --HHHHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHCHHCCHEEEHHHHHHTTSSSEETSHHHHHHHHHHHCHC CS
                     Peptidase_S49  80 lteeereilqrlldetyqqFvqtVaknRnlsveqvdkiAegrvltgqqAlklgLvdelgtvddavaeleelakv 153
                                       lteeere+++++++  +++F+q+V ++Rnl+ + + k  +grv+++++ +k  Lvd +g +d +++ lee  +v
  gi|242398488|ref|YP_002993912.1| 227 LTEEEREMIKNEVNTYFEYFLQVVGEGRNLDLNTTRKYGDGRVWFASE-VKGTLVDDTGDLDFTISALEEILNV 299
                                       **********************************************99.6789*************99997776 PP

>> CLP_protease  Clp protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8   0.0   3.6e-12   7.3e-09      18      98 ..      95     177 ..      78     186 .. 0.88

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 3.6e-12
                                       EEEEES-BSHHHHHHHHHHHHHHHHH-SSS-EEEEEEE--B-HHHHHHHHHHHHHS..SS-EEEEEEEEEETHHHHH CS
                      CLP_protease  18 iiflgseiddevankiiaqLllLeaedpdkdillyinspGGsvtaglaIydtmqyi..kpdvsticlGlaaSmgsll 92 
                                       i+ + ++id++ a ++i+++  + + d++  ++l i+spGG v   ++Iy  ++ +  + +++ +  G+aaS g l+
  gi|242398488|ref|YP_002993912.1|  95 ILPVVGPIDETAAFDVISKIREIRNDDNIGGVVLWIESPGGYVGPVITIYKELKKLsyEKPIVAYTGGMAASGGYLI 171
                                       566889***********************************************98855566778888********** PP

                                       HHTS-T CS
                      CLP_protease  93 laagek 98 
                                       ++a++k
  gi|242398488|ref|YP_002993912.1| 172 ACAADK 177
                                       ****98 PP

>> SDH_sah  Serine dehydrogenase proteinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0     2e-09   3.9e-06      64     156 ..      93     190 ..      59     255 .. 0.78

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 2e-09
                           SDH_sah  64 flGipiykfitiedseevlrairltpkdkpid...liihtpGGlvlaatqiakalkehkaktrviv..phyamsGGt 135
                                       +  +p+   i+   + +v+  ir   +d  i    l i +pGG v     i k lk+   +  ++      a sGG 
  gi|242398488|ref|YP_002993912.1|  93 IAILPVVGPIDETAAFDVISKIREIRNDDNIGgvvLWIESPGGYVGPVITIYKELKKLSYEKPIVAytGGMAASGGY 169
                                       55556666666666667777777777777664322889******************98877665541156889**** PP

                           SDH_sah 136 lialaadeiildenavlGpvd 156
                                       lia aad+ii d+ a +G + 
  gi|242398488|ref|YP_002993912.1| 170 LIACAADKIIADPLAEVGSIG 190
                                       **************9999764 PP

>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0     0.098     2e+02      20      46 ..     102     128 ..      89     136 .. 0.87
   2 !   14.5   0.3   8.3e-06     0.016      86     120 ..     151     185 ..     134     193 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.098
                                       E-HHHHHHHHHHHHHHHHSTTECEEEE CS
                             ECH_1  20 lsaelltEliqalekleddksvravvL 46 
                                       ++++  +++i  + ++++d ++++vvL
  gi|242398488|ref|YP_002993912.1| 102 IDETAAFDVISKIREIRNDDNIGGVVL 128
                                       677888999999**************9 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 8.3e-06
                                       HSSSEEEEEE-SEEETHHHHHHHHSSEEEEETTTE CS
                             ECH_1  86 tvpkpviaavnGaaigGGlelalacDiviaadnas 120
                                       + +kp++a   G a+ GG ++a a+D +ia+  a+
  gi|242398488|ref|YP_002993912.1| 151 SYEKPIVAYTGGMAASGGYLIACAADKIIADPLAE 185
                                       5799**************************97776 PP

>> Imm7  Immunity protein 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.2   2.4e+03      88     118 ..      26      57 ..      23      69 .. 0.72
   2 ?   -1.8   0.0       1.8   3.6e+03      20      36 ..      60      76 ..      41      95 .. 0.58
   3 ?   12.7   0.0   5.8e-05      0.11      83     115 ..     186     219 ..     176     224 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.2
                              Imm7  88 llyvrdde.dkenenefrvfvlarGevtered 118
                                       lly++++e +k  ++   v v+  G+v+e+e 
  gi|242398488|ref|YP_002993912.1|  26 LLYINNNElQKAIQERGNVTVVYNGTVKEVES 57 
                                       68888555145667777899999999988765 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.8
                              Imm7 20 eallesivkeieskide 36
                                      +  l+  ++e++++++ 
  gi|242398488|ref|YP_002993912.1| 60 TIALQAKIEELQKELEY 76
                                      33344444444444443 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 5.8e-05
                              Imm7  83 pGsyGllyvr.ddedkenenefrvfvlarGevte 115
                                        Gs G+lyv+ d e++  +n ++v v++ G+ ++
  gi|242398488|ref|YP_002993912.1| 186 VGSIGVLYVHyDLEQNYAQNGVKVNVFKTGKYKD 219
                                       59********899999999***********9876 PP

>> DUF4482  Domain of unknown function (DUF4482)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   8.8e-05      0.17      20      62 ..      43      87 ..      30      95 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.8e-05
                           DUF4482 20 eLldrfdrERkewesqwke.lqkkieeLqkevklrrk.inmnera 62
                                      +    ++   ke+es+  + lq kieeLqke+++ ++   +n ++
  gi|242398488|ref|YP_002993912.1| 43 NVTVVYNGTVKEVESNATIaLQAKIEELQKELEYIKGqLRTNRTE 87
                                      555556666799999987559************777623333333 PP

>> DUF3896  Protein of unknown function (DUF3896)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       3.4   6.7e+03      23      27 ..      65      69 ..      45      82 .. 0.47
   2 ?   12.2   0.2   7.5e-05      0.15      30      52 ..     227     250 ..     223     254 .. 0.91
   3 ?   -3.8   0.0       7.9   1.6e+04      42      52 ..     290     300 ..     286     303 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 3.4
                           DUF3896 23 kklss 27
                                       k+++
  gi|242398488|ref|YP_002993912.1| 65 AKIEE 69
                                      33333 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 7.5e-05
                           DUF3896  30 lskkereqlkleidny.eyilnlv 52 
                                       l++ ere +k e++ y ey l +v
  gi|242398488|ref|YP_002993912.1| 227 LTEEEREMIKNEVNTYfEYFLQVV 250
                                       899***********987*****99 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 7.9
                           DUF3896  42 idnyeyilnlv 52 
                                       i   e iln+ 
  gi|242398488|ref|YP_002993912.1| 290 ISALEEILNVK 300
                                       66778899985 PP

>> L6_membrane  L6 membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00016      0.31       8      41 ..       7      40 ..       2      52 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00016
                       L6_membrane  8 kclGlsLlplallsivaNilllfpngkteylkee 41
                                      k+l+++L  l+ l+i+ N+ll++ n + +++ +e
  gi|242398488|ref|YP_002993912.1|  7 KYLSFILTLLLALAIIGNVLLYINNNELQKAIQE 40
                                      7899********************9998884433 PP

>> DUF5312  Family of unknown function (DUF5312)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.4   0.00012      0.24     444     532 ..      32     122 ..      24     124 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00012
                           DUF5312 444 akleerlspeGeiGkrfakvkke..kvatlkkkrklealmkeieseakeliksaqealkslekiLsgilsgskksry 518
                                       ++l++++ ++G++ + ++   ke  + at+  ++k+e l ke e    +l ++  e +++ ++iL  +   ++++++
  gi|242398488|ref|YP_002993912.1|  32 NELQKAIQERGNVTVVYNGTVKEveSNATIALQAKIEELQKELEYIKGQLRTNRTEKANVTIAILPVVGPIDETAAF 108
                                       579999***********98877655899************************************************* PP

                           DUF5312 519 dtlsNlsslqgrdn 532
                                       d++s + +++  dn
  gi|242398488|ref|YP_002993912.1| 109 DVISKIREIRNDDN 122
                                       *********98887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1543  (0.0860617); expected 358.6 (0.02)
Passed bias filter:                     1132  (0.0631379); expected 358.6 (0.02)
Passed Vit filter:                       127  (0.0070835); 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: 0.73u 0.35s 00:00:01.08 Elapsed: 00:00:00.53
# Mc/sec: 1902.44
//
Query:       gi|242398489|ref|YP_002993913.1|  [L=167]
Description: hypothetical protein TSIB_0498 [Thermococcus sibiricus MM 739]
Scores for complete 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-63  210.9   3.3    9.4e-63  210.7   3.3    1.0  1  Ph1570    Ph1570 protein


Domain annotation for each model (and alignments):
>> Ph1570  Ph1570 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.7   3.3   5.2e-67   9.4e-63       1     154 [.      11     165 ..      11     166 .. 0.98

  Alignments for each domain:
  == domain 1  score: 210.7 bits;  conditional E-value: 5.2e-67
                            Ph1570   1 mlceeklevfengfkddkfnleievygkdarklllalirelylpeygeeyvypfecakefwgiyldasevkgeeael 77 
                                       m cee+l++fengf+d+kfnl+ie+ygk+ar++lla+i+ely+p yg eyvypfecakefwg+y+++se+  e+ +l
  gi|242398489|ref|YP_002993913.1|  11 MKCEEHLNIFENGFEDGKFNLKIEYYGKNARRILLAVIFELYSPIYGTEYVYPFECAKEFWGVYMESSEIVPENLDL 87 
                                       78*************************************************************************** PP

                            Ph1570  78 kplkflsesvksklekvleeidapievkelielekaevaklkdgllvlgknfllde.kgrlfvfnkpsvrelilkyi 153
                                       +  kf+++++ +k +  l+ei+ p e+k  +++e +e++k kdgllv+g+nfl+d  k  lfvfnkp+ rel++ky+
  gi|242398489|ref|YP_002993913.1|  88 SRPKFITRALIDKAKSLLNEIEVPEEIKRSLDIETSEIYKFKDGLLVIGRNFLIDGgKKILFVFNKPHARELLIKYL 164
                                       ******************************************************964788****************9 PP

                            Ph1570 154 k 154
                                       +
  gi|242398489|ref|YP_002993913.1| 165 G 165
                                       6 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:                      431  (0.0240393); 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: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 997.18
//
Query:       gi|242398490|ref|YP_002993914.1|  [L=329]
Description: hypothetical protein TSIB_0499 [Thermococcus sibiricus MM 739]
Scores for complete 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  132.0  30.9    3.1e-38  131.7  30.9    1.0  1  AI-2E_transport  AI-2E family transporter


Domain annotation for each model (and alignments):
>> AI-2E_transport  AI-2E family transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.7  30.9   1.7e-42   3.1e-38       4     326 ..       9     322 ..       6     323 .. 0.93

  Alignments for each domain:
  == domain 1  score: 131.7 bits;  conditional E-value: 1.7e-42
                   AI-2E_transport   4 ilvllllllalypfiselllplliAlvlayllnpvvkfL.kkrgvkrvlavllvlllllvllvllvlllvplliaql 79 
                                       + v +++l+++++ + +l+  +++Al +ay+l+p  ++L +k g + + +v+  +++ll++ ++++++l       +
  gi|242398490|ref|YP_002993914.1|   9 FVVSIIILFVVWKTVEPLITSIIFALTVAYILHPAHTRLaQKIGSRESAIVFSAIMSLLLVGFIFGVALW------F 79 
                                       6678888888888888***********************8888888888888888888888888888888......9 PP

                   AI-2E_transport  80 tqlvkslpayidslqnilnelpslleelenliqalkqslskilsnilssilnsllsllasllglilslvlvllllff 156
                                       ++++ sl +yi++ ++++ +l+  l+        + +s++  ++++ +++ ++lls++ s+++l+l++++++++++ 
  gi|242398490|ref|YP_002993914.1|  80 RDVTGSLVNYINESLEWFISLD--LPPD------IAKSATILFERVSEKLSEYLLSYTLSIPKLLLQAIIFIVVFYG 148
                                       *********************9..5555......679**************************************** PP

                   AI-2E_transport 157 llldgeklrqgilkllpervrervkailrelektlsgylrgqvlvaliigvlvfigllilgvpy...alllailvgl 230
                                       +l + + l   +++llpe++r+   ++++++ +tl ++lr+ + +++  g+++  g++++ v     ++  +i+  +
  gi|242398490|ref|YP_002993914.1| 149 ILIHSHSLSAELYSLLPEERRDLGIELIEKARDTLNAILRTWLMLSVSKGIILTLGFYVFRVADlsgSIAAGIVCVV 225
                                       ************************************************************99874435788888889 PP

                   AI-2E_transport 231 anliPyiGavivlipiaiialltgg.ikevlivlivvllvqliegnilePklmgkrlglhplvillsllaggklfGl 306
                                       + l+P+iG+++v+++ ai++l+ g+ ++ ++++++++ll++   + +++Pkl+ ++++++ ++ l+ +++g++ fG+
  gi|242398490|ref|YP_002993914.1| 226 LELLPVIGGWLVWLVGAIYLLTQGQiFAGIMFAIYGALLISPGPDITIRPKLVAEGAKMNSALALIGIFGGIMAFGI 302
                                       99***********************9999999********************************************* PP

                   AI-2E_transport 307 vGlilavpltavikaileay 326
                                        G+ +++++++++ ++le++
  gi|242398490|ref|YP_002993914.1| 303 KGIVIGPVALGLLLTLLEEW 322
                                       ****************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1077  (0.0600703); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); 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):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 2398.58
//
Query:       gi|242398491|ref|YP_002993915.1|  [L=70]
Description: hypothetical protein TSIB_0500 [Thermococcus sibiricus MM 739]
Scores for complete 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   22.0   3.8    0.00015   21.8   3.8    1.1  1  DUF4870   Domain of unknown function (DUF4870)
  ------ inclusion threshold ------
       0.86    9.9   3.7       0.68   10.2   0.8    2.1  2  DUF4112   Domain of unknown function (DUF4112)


Domain annotation for each model (and alignments):
>> DUF4870  Domain of unknown function (DUF4870)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   3.8   1.7e-08   0.00015      51     105 ..       4      56 ..       1      60 [. 0.88

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.7e-08
                           DUF4870  51 qislliysiilivlsllvligflllllllllllnlvlviiaaikanegeeyrypl 105
                                       +i++l ++ii i++  + ++g+  +l  l+ l+ l++ i ++ ka++ge+y++p+
  gi|242398491|ref|YP_002993915.1|   4 TITFLAITIIDIIFGAIPFFGW--ILGSLVTLVGLIFWIPGMAKAYQGEYYKFPI 56 
                                       5777777888888888899999..******************************8 PP

>> DUF4112  Domain of unknown function (DUF4112)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.8   7.5e-05      0.68      65      88 ..       5      28 ..       1      32 [. 0.84
   2 ?    0.9   0.2     0.061   5.4e+02      27      41 ..      33      47 ..      26      67 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 7.5e-05
                           DUF4112 65 lrmlvnialDlliglvPvvGdlfd 88
                                      + +l+  ++D+++g++P+ G ++ 
  gi|242398491|ref|YP_002993915.1|  5 ITFLAITIIDIIFGAIPFFGWILG 28
                                      56788899************9975 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.061
                           DUF4112 27 ldpiigliPvvGdvi 41
                                      l ++i +iP++ +++
  gi|242398491|ref|YP_002993915.1| 33 LVGLIFWIPGMAKAY 47
                                      455666666654443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 448.44
//
Query:       gi|242398492|ref|YP_002993916.1|  [L=80]
Description: Fe2+ transport protein, [Thermococcus sibiricus MM 739]
Scores for complete 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   73.3   2.2    1.5e-20   73.2   2.2    1.0  1  FeoA      FeoA domain
  ------ inclusion threshold ------
       0.16   11.7   0.0       0.17   11.6   0.0    1.0  1  DUF2931   Protein of unknown function (DUF2931)


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 !   73.2   2.2   1.7e-24   1.5e-20       1      74 []       7      78 ..       7      78 .. 0.97

  Alignments for each domain:
  == domain 1  score: 73.2 bits;  conditional E-value: 1.7e-24
                                      EEGGG--TT-EEEEEEE-TT.SSHHHHHHHHT--TT-EEEEEEE-TTS-SEEEEETTEEEEE-HHHHTTEEEEE CS
                              FeoA  1 vpLsdlkeGergeiarisdedpellrrLremGlvpGarievvarapfggplvvrvgdtrvaLgreeAqaIlVea 74
                                      v+Ls++ eGerg++++++   +++++rL+ mG+ pG++i v+ +a f gp+++++g tr+aLgr++A++I+V++
  gi|242398492|ref|YP_002993916.1|  7 VRLSQMREGERGTVVNVQGG-HRVRQRLLGMGIAPGTKIVVI-KAGFSGPYIIALGSTRLALGRGIAERIIVRR 78
                                      68***************876.9********************.99***************************96 PP

>> DUF2931  Protein of unknown function (DUF2931)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   1.9e-05      0.17     124     173 ..      22      78 ..       8      80 .] 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.9e-05
                           DUF2931 124 kkrsgdkdyrdniilGLaPgGkvkvwLtgag.......vgndielakgiaeeifddk 173
                                       + ++g++++++ + +G+aPg k++v   g          ++++ l++giae+i ++ 
  gi|242398492|ref|YP_002993916.1|  22 NVQGGHRVRQRLLGMGIAPGTKIVVIKAGFSgpyiialGSTRLALGRGIAERIIVRR 78 
                                       5567777999999**********99988866899***99999***********9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       293  (0.0163422); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.50
# Mc/sec: 477.36
//
Query:       gi|242398493|ref|YP_002993917.1|  [L=681]
Description: FeoB ferrous iron transport protein B - like protein [Thermococcus sibiricus MM 739]
Scores for complete 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-63  211.7   3.3    1.4e-62  209.8   1.1    2.2  2  FeoB_N        Ferrous iron transport protein B
    8.2e-42  142.0  16.1    1.7e-26   92.7   4.3    2.8  2  Gate          Nucleoside recognition
    2.1e-18   65.7   0.4    9.3e-18   63.7   0.4    2.3  1  FeoB_C        Ferrous iron transport protein B C terminus
    2.4e-18   66.3   1.1    3.8e-18   65.6   0.2    1.8  2  MMR_HSR1      50S ribosome-binding GTPase
    3.7e-16   59.5   0.5    6.9e-16   58.6   0.5    1.5  1  FeoB_Cyto     FeoB cytosolic helical domain
    2.2e-07   31.0   0.3    0.00091   19.2   0.1    2.4  2  RsgA_GTPase   RsgA GTPase
    3.9e-06   26.4   0.5    1.2e-05   24.8   0.1    1.9  2  SRPRB         Signal recognition particle receptor beta subun
    0.00031   20.5   0.5      0.001   18.8   0.2    2.1  2  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
     0.0011   18.5   0.6      0.011   15.3   0.2    2.4  2  GTP_EFTU      Elongation factor Tu GTP binding domain
     0.0037   16.9   0.0      0.011   15.3   0.0    1.8  1  Ras           Ras family
  ------ inclusion threshold ------
       0.01   15.6   0.1      0.092   12.5   0.1    2.4  1  ATP_bind_1    Conserved hypothetical ATP binding protein
      0.069   13.2   0.9       0.85    9.7   0.1    2.5  2  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain


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 !  209.8   1.1   9.4e-66   1.4e-62       2     155 ..      20     174 ..      19     175 .. 0.98
   2 ?    1.6   0.0      0.12   1.8e+02      97     153 ..     221     279 ..     210     282 .. 0.79

  Alignments for each domain:
  == domain 1  score: 209.8 bits;  conditional E-value: 9.4e-66
                                       EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHHHHHHHHHHCTS CS
                            FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYslsayseeekvardflleee 78 
                                        +al+GnpnvGktt+fnaltg +q+vgNwpGvtvekkeg lk+++ke+ +vDlPG+Ysl+a s++e +ar+fll  +
  gi|242398493|ref|YP_002993917.1|  20 VIALAGNPNVGKTTIFNALTGLRQHVGNWPGVTVEKKEGILKYHNKEFLVVDLPGTYSLTANSIDELIARNFLLGGN 96 
                                       59*************************************************************************** PP

                                       SSEEEEEEEGGGHHHHHHHHHHHHHTT.SSEEEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTTTBTHHHHHH CS
                            FeoB_N  79 pdvvvnvvdatnlernLyLtlqllelg.vpvvlalnmideaekkgieidlkkLsekLgvpvvktsakkkegieellk 154
                                       ++vvv++vd+++l rnL+Lt++++e+g ++v++aln+id a+k+gi+ d+kk+++ +gvpv++++ak++egieel++
  gi|242398493|ref|YP_002993917.1|  97 ANVVVDIVDSSSLMRNLFLTMEIFEMGiKNVIIALNKIDIAKKRGISFDVKKMEKVIGVPVIPMNAKNGEGIEELKA 173
                                       ***************************557899******************************************97 PP

                                       H CS
                            FeoB_N 155 a 155
                                        
  gi|242398493|ref|YP_002993917.1| 174 M 174
                                       6 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.12
                                       HHHHHHHTTSSEE.EEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTTTBT.HHHHH CS
                            FeoB_N  97 Ltlqllelgvpvv.lalnmideaekkgieidlkkLsekLgvpvvktsakkkeg.ieell 153
                                       L ++ll  +++v+ l+ln +   + ++i i++++L++  + p   ++a++k + i++l+
  gi|242398493|ref|YP_002993917.1| 221 LAIKLLTRDQEVIkLVLNYLGSKKMDEILIHISELEKYYKHPLDIVIANQKYEfIDKLM 279
                                       5566777776666589**********************999997777766643166665 PP

>> Gate  Nucleoside recognition
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.4   4.0   9.1e-18   1.4e-14       2     111 ..     369     463 ..     368     464 .. 0.96
   2 !   92.7   4.3   1.2e-29   1.7e-26       1     111 [.     530     651 ..     530     652 .. 0.98

  Alignments for each domain:
  == domain 1  score: 54.4 bits;  conditional E-value: 9.1e-18
                              Gate   2 lkagpiillasiliwflssssllgrigkllepvfaplgqeldwkatvslltgfaakevvvgtlgtlytsalgellqg 78 
                                       l ++p+++l+++ +++l++s++++r++ ++e +++ +g  l++k+++++++ f+   ++v+++++++         +
  gi|242398493|ref|YP_002993917.1| 369 LSFFPLVFLLFVAMSILEDSGYMARAATVMERIMRIFG--LPGKSFIPMVLAFG---CNVPAIMSTR---------T 431
                                       6789**********************************..**************...*********9.........* PP

                              Gate  79 fdtpksalafllfvllytpcvatlavivrelgs 111
                                        +++++++ ++l++ l  pc a+++vi   +g+
  gi|242398493|ref|YP_002993917.1| 432 LEDERDRILTMLVNPLV-PCSARMVVITFLAGA 463
                                       ****************5.9*******9988876 PP

  == domain 2  score: 92.7 bits;  conditional E-value: 1.2e-29
                              Gate   1 llkagpiillasiliwflss........ssllgrigkllepvfaplgqeldwkatvslltgfaakevvvgtlgtly. 68 
                                       l+kag++il++si iw+lss         s+++++g+++ep+   +g  ldwka+vsl++g++ake v++t g++y 
  gi|242398493|ref|YP_002993917.1| 530 LRKAGTVILFGSIAIWYLSSypqaigsgLSYAEKLGRVFEPFTMLMG--LDWKAAVSLIFGIIAKENVIATYGVIYg 604
                                       689********************************************..**************************** PP

                              Gate  69 ....tsalgellqgfdtpksalafllfvllytpcvatlavivrelgs 111
                                           ++al  l + + t  +a+++ l+++ly+pc+at+++i+ e g 
  gi|242398493|ref|YP_002993917.1| 605 igenEEALIMLMRAAMTSLQAFVLALVTTLYIPCIATIGAIRAEGGN 651
                                       ***999999999********************************996 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 !   63.7   0.4   6.2e-21   9.3e-18       2      53 .]     474     525 ..     473     525 .. 0.96

  Alignments for each domain:
  == domain 1  score: 63.7 bits;  conditional E-value: 6.2e-21
                            FeoB_C   2 fslYllgilvallvalllkktt.lkgepspfvmELPpYrlPslknvliktweR 53 
                                       +++Y++++++all+al+l k + +kge+ pfvmELP+Y +Ps+k  li++weR
  gi|242398493|ref|YP_002993917.1| 474 VGVYAISLFLALLSALILGK-FvIKGEENPFVMELPEYAIPSWKIALIHSWER 525
                                       799*****************.77*****************************9 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.6   0.2   2.5e-21   3.8e-18       2     114 .]      21     133 ..      20     133 .. 0.84
   2 ?   -3.3   0.0       6.2   9.2e+03      65     101 ..     234     256 ..     221     275 .. 0.48

  Alignments for each domain:
  == domain 1  score: 65.6 bits;  conditional E-value: 2.5e-21
                                       EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSS..HHHHHHHHHHHHHHHHCT CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGlie..gaseekglgkaflaleea 76 
                                       +a++G+pNvGK+t++naltg + +v+++pg+T + +eg +k+++ke+ +vD+pG ++   +s ++ ++++fl   +a
  gi|242398493|ref|YP_002993917.1|  21 IALAGNPNVGKTTIFNALTGLRQHVGNWPGVTVEKKEGILKYHNKEFLVVDLPGTYSltANSIDELIARNFLLGGNA 97 
                                       89****************************************************986657788889******9999* PP

                                       SEEEEEEETTTTCSHH..HHHHHHHHHHHTTSEEEEEEES CS
                          MMR_HSR1  77 dlillvvdaseeklkp..ldeeleelleeakkplilvlnk 114
                                       ++++ +vd+s + +++  l  e+ e+     k++i++lnk
  gi|242398493|ref|YP_002993917.1|  98 NVVVDIVDSS-SLMRNlfLTMEIFEMG---IKNVIIALNK 133
                                       ********77.4333311334455554...3778888887 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 6.2
                                       HHHHHHHHHHCTSEEEEEEETTTTCSHHHHHHHHHHH CS
                          MMR_HSR1  65 glgkaflaleeadlillvvdaseeklkpldeeleell 101
                                       +l  ++l  +++d il+ ++              el 
  gi|242398493|ref|YP_002993917.1| 234 KLVLNYLGSKKMDEILIHIS--------------ELE 256
                                       33334444444443333332..............222 PP

>> FeoB_Cyto  FeoB cytosolic helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.6   0.5   4.6e-19   6.9e-16       1      90 [.     192     283 ..     192     284 .. 0.92

  Alignments for each domain:
  == domain 1  score: 58.6 bits;  conditional E-value: 4.6e-19
                         FeoB_Cyto   1 YgeeiEkaiekleellkesnlkaklppRwlAlklLegDeelleelked..pelraeveearkeleaelgedledvIv 75 
                                       Y+e iE++i  ++ +l+e+ l++ ++ RwlA+klL +D+e+++ + ++   +  +e+   ++ele+ +++ l+ vI+
  gi|242398493|ref|YP_002993917.1| 192 YDEPIEREIGHISGILNETPLAQCYNVRWLAIKLLTRDQEVIKLVLNYlgSKKMDEILIHISELEKYYKHPLDIVIA 268
                                       9******************************************999854446677777778999999********** PP

                         FeoB_Cyto  76 darykfiegilrevv 90 
                                       +++y+fi++++ + v
  gi|242398493|ref|YP_002993917.1| 269 NQKYEFIDKLMHQFV 283
                                       ***********9987 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0   0.00058      0.87      91     124 ..       8      42 ..       2      75 .. 0.81
   2 !   19.2   0.1   6.1e-07   0.00091      42      99 ..     119     177 ..      97     180 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00058
                                       HHHHHHCTT..SEEEEECSTTSSHHHHHHHHCTT-- CS
                       RsgA_GTPase  91 eelkellkd..ktsvlvGqSGvGKStLinallpele 124
                                       ++++++ k+  k+++l+G+  vGK+t+ nal++  +
  gi|242398493|ref|YP_002993917.1|   8 KDISKNKKQglKVIALAGNPNVGKTTIFNALTGL-R 42 
                                       55555555547999*****************985.3 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 6.1e-07
                                       HHHTT-.EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTT CS
                       RsgA_GTPase  42 aeekgi.epvivlnKiDlleeeeeleelkeelealgyevllvsaktkegleelkellkd 99 
                                       + e gi +++i+lnKiD+++++    ++k+  + +g++v+ ++ak++eg+eelk+++++
  gi|242398493|ref|YP_002993917.1| 119 IFEMGIkNVIIALNKIDIAKKRGISFDVKKMEKVIGVPVIPMNAKNGEGIEELKAMISE 177
                                       34556657999************677788888889*******************99875 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 !   24.8   0.1   8.1e-09   1.2e-05       5     115 ..      20     136 ..      16     154 .. 0.80
   2 ?   -1.2   0.1      0.78   1.2e+03      96     123 ..     246     273 ..     242     277 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 8.1e-09
                                       EEEEE-STTSSHHHHHHHHHHS....S---B---SS-EEETTG...GGTT-SEEEETT-GCCSHHHHHHHHHHG... CS
                             SRPRB   5 avllvGlsdsGKTslftrLttd....svkktvtSqessaalkvksekgskltliDfPGheklrqklleklkaks... 74 
                                        + l+G  + GKT++f+ Lt         + vt  +++  lk+   +++++ ++D+PG  +l  + +++l+a++   
  gi|242398493|ref|YP_002993917.1|  20 VIALAGNPNVGKTTIFNALTGLrqhvGNWPGVTVEKKEGILKY---HNKEFLVVDLPGTYSLTANSIDELIARNfll 93 
                                       5779***************976443334456666677778888...999****************999999988222 PP

                                       ..GEEEEEEEEETTS-HHHHHHHHHHHHHHHHHHHHHTT---E CS
                             SRPRB  75 ..slkglvfvvDStidpkevkevAEllyeilliteklkdavdi 115
                                         ++  +v +vDS+   +++  + E +   + +++++ +++di
  gi|242398493|ref|YP_002993917.1|  94 ggNANVVVDIVDSSSLMRNLFLTMEIFEMGIKNVIIALNKIDI 136
                                       2235569999**********99999998777777777788776 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.78
                                       HHHHHHHHHHHHHHTT---EEEEEE-TT CS
                             SRPRB  96 AEllyeilliteklkdavdiliACnKqe 123
                                        E l++i    +  k  +di+iA +K e
  gi|242398493|ref|YP_002993917.1| 246 DEILIHISELEKYYKHPLDIVIANQKYE 273
                                       68888888888888*********99987 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.2   6.9e-07     0.001       2     142 ..      19     176 ..      18     177 .. 0.72
   2 ?   -3.4   0.0         5   7.5e+03      74      95 ..     287     308 ..     281     310 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 6.9e-07
                         PduV-EutP   2 kkilliGkvgsGKttLtqalkg........eelkYkkt.qaiefsde...viDtPGeylenrklysalivtsa.... 62 
                                       k i l G+ ++GKtt+ +al+g          ++ +k    ++++++   v+D PG y    +    li+  +    
  gi|242398493|ref|YP_002993917.1|  19 KVIALAGNPNVGKTTIFNALTGlrqhvgnwPGVTVEKKeGILKYHNKeflVVDLPGTYSLTANSIDELIARNFllgg 95 
                                       5678999*************99877777773344444404444444333369*******999999999875543333 PP

                         PduV-EutP  63 eadvia.lvqdateeesvf.ppgfasvfnkeviGiitkidlaedeeniea.veelLksaGaekifevsavekegiee 136
                                       +a+v++ +v +++ ++++f + ++ ++  k+vi  + kid+a ++  i+  v+++ k  G+  ++ ++a + egiee
  gi|242398493|ref|YP_002993917.1|  96 NANVVVdIVDSSSLMRNLFlTMEIFEMGIKNVIIALNKIDIA-KKRGISFdVKKMEKVIGV-PVIPMNAKNGEGIEE 170
                                       88876526666666777663678899999*************.566666515666666777.57799********** PP

                         PduV-EutP 137 llkyle 142
                                       l+++++
  gi|242398493|ref|YP_002993917.1| 171 LKAMIS 176
                                       *99986 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 5
                         PduV-EutP  74 teeesvfppgfasvfnkeviGi 95 
                                        e +++f++ + +++++++ Gi
  gi|242398493|ref|YP_002993917.1| 287 GEVHETFSDYIDKILTHPLYGI 308
                                       5667899*********999998 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 ?    0.4   0.0      0.27   4.1e+02       6      24 ..      21      39 ..      18      47 .. 0.84
   2 !   15.3   0.2   7.5e-06     0.011      53     191 ..      50     178 ..      45     181 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.27
                                      EEEEESTTSSHHHHHHHHH CS
                          GTP_EFTU  6 igiighvDhGKtTLtdrLl 24
                                      i+++g  + GKtT+  +L+
  gi|242398493|ref|YP_002993917.1| 21 IALAGNPNVGKTTIFNALT 39
                                      6788999*******99997 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 7.5e-06
                                       TSCSSCEEEEEETTCSSEEEEEEEESSSGGGHHHHHHHHHT-SE.....EEEEEETTTB.STHHHHHHHHHHHHTTT CS
                          GTP_EFTU  53 giTiksaaisleketkkylinliDtPGHvdFskevirglrvlDg.....avlvvdaveG.vepqteevlrlalkegv 123
                                       g+T++ +   l+  ++++++ ++D PG  + + + i  l + ++     a +vvd+v+    ++   +   + ++g+
  gi|242398493|ref|YP_002993917.1|  50 GVTVEKKEGILK--YHNKEFLVVDLPGTYSLTANSIDELIARNFllggnANVVVDIVDSsSLMRNLFLTMEIFEMGI 124
                                       677777777777..999***********999999888765555411112679***9988333444556667889999 PP

                                       E.EEEEEESCGST.HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHHH CS
                          GTP_EFTU 124 p.iivfiNKmDrl.kaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvktllealvel 191
                                       + +i+++NK+D + k  ++  v+++++ +                 vpv+++ a++geg+++l  ++ e+
  gi|242398493|ref|YP_002993917.1| 125 KnVIIALNKIDIAkKRGISFDVKKMEKVI----------------GVPVIPMNAKNGEGIEELKAMISEM 178
                                       99***********6667888888888666................3899999999999999998888765 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   7.6e-06     0.011       3     156 ..      22     175 ..      19     180 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 7.6e-06
                                       EEEESTTSSHHHHHHHHHHSSCSSSCTTTSSEEEEEEEEEETTEEEEEEEEEETTSGGGHH......HHHHHHTTES CS
                               Ras   3 vlvGdsavGKtslllrfvkdkFkeeyesTigvdfytkeievdgkevkleiwDTAGqeefks......lrelyyrdae 73 
                                        l G+ +vGKt++ +  +  + +    + + v++++  +++++ke  + + D  G    ++      ++++++ +++
  gi|242398493|ref|YP_002993917.1|  22 ALAGNPNVGKTTIFNALTGLRQHVGNWPGVTVEKKEGILKYHNKE--FLVVDLPGTYSLTAnsidelIARNFLLGGN 96 
                                       467899999999999999888888888888788888877777775..446676666544321111113444444555 PP

                                       EEEEEEETTBHHHHHTHHHHHHHHHHHSTTTSEEEEEEETTTGGGG-SS-HHHHHHHHHHHTSEEEEEBTTTTCTHH CS
                               Ras  74 gillvyditsresfenvkkwveeikrvaeenvpivLvGnKvDleekravsteegeelakelglkfletSAktnenve 150
                                       +  +v di +++s+ +   ++ ei ++  +nv  ++  nK+D+++kr +s++ ++++ k +g++ + + Ak+ e++e
  gi|242398493|ref|YP_002993917.1|  97 AN-VVVDIVDSSSLMRNLFLTMEIFEMGIKNV--IIALNKIDIAKKRGISFD-VKKMEKVIGVPVIPMNAKNGEGIE 169
                                       54.5669******9999999999999988755..5555************97.588********************9 PP

                                       HHHHHH CS
                               Ras 151 eafeel 156
                                       e+  ++
  gi|242398493|ref|YP_002993917.1| 170 ELKAMI 175
                                       975554 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 ?   12.5   0.1   6.2e-05     0.092      83     186 ..      56     155 ..      28     192 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.2e-05
                        ATP_bind_1  83 deeleke.eddyllfDtPGQielfthseslakiveeLes.efalvvvyLvDsqrltdptkfisgllsalsamlrlel 157
                                       +e + k+ ++++l++D PG   l   s +   i +++     a vvv +vDs       +++ +l++++ +  +   
  gi|242398493|ref|YP_002993917.1|  56 KEGILKYhNKEFLVVDLPGTYSLTANSIDEL-IARNFLLgGNANVVVDIVDSS------SLMRNLFLTMEIFEMGIK 125
                                       44455775789********999988887777.555555536666667777765......567776666666655556 PP

                        ATP_bind_1 158 PhvvvlnkfDllkek.lekeleffedveal 186
                                         +++lnk+D++k++   ++++ +e v  +
  gi|242398493|ref|YP_002993917.1| 126 NVIIALNKIDIAKKRgISFDVKKMEKVIGV 155
                                       78899******9988989999999876544 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 ?    9.7   0.1   0.00057      0.85      57     100 ..     126     175 ..     121     179 .. 0.75
   2 ?    1.0   0.1      0.28   4.2e+02      64      99 ..     244     281 ..     233     285 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00057
                      MMR_HSR1_Xtn  57 pclyvlNKiDlisle....eldelare..pnsvviSaekelnldeLkeki 100
                                       +++++lNKiD +++     +++++++     ++++ a+++ +++eLk +i
  gi|242398493|ref|YP_002993917.1| 126 NVIIALNKIDIAKKRgisfDVKKMEKVigVPVIPMNAKNGEGIEELKAMI 175
                                       5799*******76652222345555534458999*************998 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.28
                      MMR_HSR1_Xtn  64 KiDl..isleeldelarepnsvviSaekelnldeLkek 99 
                                       K+D+  i+++el++ +++p  +vi+ +k   +d+L+++
  gi|242398493|ref|YP_002993917.1| 244 KMDEilIHISELEKYYKHPLDIVIANQKYEFIDKLMHQ 281
                                       8887668999*********9999999999999999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (681 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       918  (0.051202); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); 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: 0.72u 0.32s 00:00:01.04 Elapsed: 00:00:00.48
# Mc/sec: 4294.22
//
Query:       gi|242398494|ref|YP_002993918.1|  [L=79]
Description: LexA-related DNA-binding protein [Thermococcus sibiricus MM 739]
Scores for 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   22.5   0.1     0.0001   22.3   0.1    1.2  1  FeoC            FeoC like transcriptional regulator
    0.00011   22.0   0.1    0.00014   21.7   0.1    1.1  1  TrmB            Sugar-specific transcriptional regulator TrmB
    0.00044   20.0   0.1    0.00055   19.7   0.1    1.1  1  DUF4423         Domain of unknown function (DUF4423)
     0.0009   19.1   0.3     0.0011   18.8   0.3    1.1  1  HTH_11          HTH domain
     0.0011   19.1   0.1     0.0014   18.7   0.1    1.1  1  DUF2250         Uncharacterized protein conserved in archaea 
     0.0011   18.5   0.3     0.0016   18.0   0.3    1.3  1  HTH_24          Winged helix-turn-helix DNA-binding
     0.0015   18.4   0.0     0.0018   18.1   0.0    1.1  1  MarR_2          MarR family
     0.0019   18.0   0.2      0.003   17.4   0.2    1.3  1  HTH_5           Bacterial regulatory protein, arsR family
     0.0028   17.7   0.5     0.0048   17.0   0.5    1.3  1  Sigma70_r3      Sigma-70 region 3
     0.0048   16.7   0.0     0.0058   16.4   0.0    1.1  1  HTH_IclR        IclR helix-turn-helix domain
     0.0072   15.8   0.3      0.012   15.1   0.3    1.4  1  Sigma70_r4      Sigma-70, region 4
     0.0094   16.0   0.0      0.012   15.7   0.0    1.1  1  HTH_20          Helix-turn-helix domain
  ------ inclusion threshold ------
      0.011   15.8   1.5      0.063   13.4   0.6    2.1  2  Exonuc_VII_S    Exonuclease VII small subunit
      0.012   15.3   0.1      0.019   14.6   0.1    1.3  1  Sigma70_r4_2    Sigma-70, region 4
      0.015   15.2   0.0      0.023   14.6   0.0    1.2  1  HTH_36          Helix-turn-helix domain
      0.021   14.6   0.1      0.025   14.3   0.1    1.1  1  PheRS_DBD1      PheRS DNA binding domain 1
      0.022   15.1   0.0      0.027   14.8   0.0    1.1  1  Rrf2            Transcriptional regulator
      0.033   14.1   0.1      0.073   13.0   0.1    1.6  1  FhuF_C          FhuF 2Fe-2S C-terminal domain
      0.037   14.2   0.0      0.047   13.8   0.0    1.1  1  HTH_28          Helix-turn-helix domain
      0.043   13.7   0.1      0.059   13.3   0.1    1.2  1  MarR            MarR family
      0.043   14.5   0.1      0.063   13.9   0.1    1.2  1  RPA_C           Replication protein A C terminal
      0.045   13.9   0.0      0.052   13.7   0.0    1.2  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
      0.053   13.6   0.0      0.074   13.2   0.0    1.2  1  HTH_9           RNA polymerase III subunit RPC82 helix-turn-h
      0.072   13.1   0.1      0.092   12.7   0.1    1.2  1  HTH_Crp_2       Crp-like helix-turn-helix domain
      0.073   12.5   0.0      0.073   12.5   0.0    1.1  1  RepL            Firmicute plasmid replication protein (RepL)
      0.074   12.4   0.1      0.089   12.2   0.1    1.3  1  RNA_pol_Rpc34   RNA polymerase Rpc34 subunit
      0.094   12.1   0.0       0.18   11.2   0.0    1.4  2  HTH_Tnp_ISL3    Helix-turn-helix domain of transposase family
       0.17   11.9   0.1       0.17   11.9   0.1    1.2  1  DUF4211         Domain of unknown function (DUF4211)


Domain annotation for each model (and alignments):
>> FeoC  FeoC like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.1   1.6e-07    0.0001      17      61 ..      18      58 ..       3      76 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.6e-07
                              FeoC 17 lkeLsrhfkaspealeamLeqwvrkGrvekvaataccsgsCkkCg 61
                                       ke++ ++++s e +e+++ +++  G vek + +     sC +C 
  gi|242398494|ref|YP_002993918.1| 18 SKEIAERLEMSVEEVEGIIKILESLGYVEKIEIGE----SCGSCP 58
                                      48******************************955....555554 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.1   2.1e-07   0.00014      16      57 ..       9      50 ..       8      64 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 2.1e-07
                                      HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESS CS
                              TrmB 16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekg 57
                                       L+k+g  t +eiae+l+ +   v  +++ Le+ G+Ve+++ 
  gi|242398494|ref|YP_002993918.1|  9 ELIKEGVRTSKEIAERLEMSVEEVEGIIKILESLGYVEKIEI 50
                                      699************************************984 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.1   8.6e-07   0.00055      32      74 ..      11      51 ..       7      53 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 8.6e-07
                           DUF4423 32 lkdfkadpeelakrlrpkisaeevekalefLlklgllkkdedg 74
                                      +k++ ++ +e+a+rl   +s+eeve ++++L++lg ++k e g
  gi|242398494|ref|YP_002993918.1| 11 IKEGVRTSKEIAERLE--MSVEEVEGIIKILESLGYVEKIEIG 51
                                      56777899********..********************98765 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.3   1.7e-06    0.0011       4      44 ..       6      46 ..       3      51 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.7e-06
                            HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg..v 44
                                      ++lel+  ++g  +++e+Ae+L++S   v   Ik+Le+lg   
  gi|242398494|ref|YP_002993918.1|  6 DVLELI--KEGVRTSKEIAERLEMSVEEVEGIIKILESLGyvE 46
                                      566666..44558***************************443 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 !   18.7   0.1   2.1e-06    0.0014      21      56 ..      14      49 ..       4      53 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.1e-06
                           DUF2250 21 nvdYaksiakeleipleevrellkkLeelGLlerve 56
                                      +v  +k ia++le+++eev+ ++k Le+lG +e+ e
  gi|242398494|ref|YP_002993918.1| 14 GVRTSKEIAERLEMSVEEVEGIIKILESLGYVEKIE 49
                                      67779****************************976 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.3   2.5e-06    0.0016      11      48 .]       9      46 ..       7      46 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.5e-06
                            HTH_24 11 lLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      +L k++  + +e+Aerl +S+  v   +k Le+ G+++
  gi|242398494|ref|YP_002993918.1|  9 ELIKEGVRTSKEIAERLEMSVEEVEGIIKILESLGYVE 46
                                      577888899***************************96 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   2.8e-06    0.0018      11      53 ..       8      47 ..       6      52 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.8e-06
                                      HHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                            MarR_2 11 LaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53
                                      L  +  + +   t +e+a+rl +s   v  i+k L++ G+ve+
  gi|242398494|ref|YP_002993918.1|  8 LELIKEGVR---TSKEIAERLEMSVEEVEGIIKILESLGYVEK 47
                                      555544443...99***************************97 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.2   4.6e-06     0.003       7      47 .]       7      47 ..       6      47 .. 0.95

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.6e-06
                                      HHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5  7 ILklLaegelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                      +L l  eg +++ e+ae l++s   v    k+L+ +G+Vek
  gi|242398494|ref|YP_002993918.1|  7 VLELIKEGVRTSKEIAERLEMSVEEVEGIIKILESLGYVEK 47
                                      6889999********************************97 PP

>> Sigma70_r3  Sigma-70 region 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.5   7.5e-06    0.0048      22      43 ..      17      38 ..      16      42 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 7.5e-06
                                      XHHHHHHHHTXXHHHHHHHHHH CS
                        Sigma70_r3 22 tpeEiAeeLglseekVrevlea 43
                                      t  EiAe+L++s+e+V+ ++++
  gi|242398494|ref|YP_002993918.1| 17 TSKEIAERLEMSVEEVEGIIKI 38
                                      678**************99875 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0     9e-06    0.0058       7      50 ..       6      47 ..       3      49 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 9e-06
                                      HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR  7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      ++L+++ e+ +    +e+A+r+ ++   v ++++ L+ lGyve+
  gi|242398494|ref|YP_002993918.1|  6 DVLELIKEGVRT--SKEIAERLEMSVEEVEGIIKILESLGYVEK 47
                                      799********6..9***************************97 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.3   1.9e-05     0.012      11      39 ..       6      34 ..       3      38 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.9e-05
                                      HHHHHHHTTT--HHHHHHHHTS-HHHHHH CS
                        Sigma70_r4 11 evlelrfgeglTleEIgerlgiSrerVrq 39
                                      +vlel  +  +T +EI+erl +S e V  
  gi|242398494|ref|YP_002993918.1|  6 DVLELIKEGVRTSKEIAERLEMSVEEVEG 34
                                      699**********************9965 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.8e-05     0.012      15      59 ..       7      50 ..       6      52 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.8e-05
                                      HHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECT CS
                            HTH_20 15 ilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvre 59
                                      +l ++  ++ +t +e+aerl++s  ++   +++Le+ g+ve  + 
  gi|242398494|ref|YP_002993918.1|  7 VLELI-KEGVRTSKEIAERLEMSVEEVEGIIKILESLGYVEKIEI 50
                                      67777.8999******************************98765 PP

>> Exonuc_VII_S  Exonuclease VII small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.6   9.8e-05     0.063      22      49 ..       4      31 ..       3      33 .. 0.88
   2 ?    2.8   0.2       0.2   1.3e+02       2      17 ..      26      41 ..      26      43 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.8e-05
                      Exonuc_VII_S 22 LeeslklyeeGvkLlkeCekkLdeaeqk 49
                                      L++ l+l +eGv+ +ke  ++L+   ++
  gi|242398494|ref|YP_002993918.1|  4 LDDVLELIKEGVRTSKEIAERLEMSVEE 31
                                      9*********************976555 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.2
                      Exonuc_VII_S  2 EealaeLeeIvekLEs 17
                                      E +++e e I++ LEs
  gi|242398494|ref|YP_002993918.1| 26 EMSVEEVEGIIKILES 41
                                      66899*********97 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1     3e-05     0.019      18      43 ..       7      32 ..       5      34 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3e-05
                                      HHHHHHTS---HHHHHHHHT--HHHH CS
                      Sigma70_r4_2 18 ifllryleglsykEIAellgisegtV 43
                                      +++l+ +   + kEIAe+l++s+  V
  gi|242398494|ref|YP_002993918.1|  7 VLELIKEGVRTSKEIAERLEMSVEEV 32
                                      8999999999************9877 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   3.6e-05     0.023      29      55 .]      19      45 ..      17      45 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.6e-05
                            HTH_36 29 etlakrlglsknTvsraikeLeqlGyi 55
                                      + +a+rl++s++ v  +ik Le lGy+
  gi|242398494|ref|YP_002993918.1| 19 KEIAERLEMSVEEVEGIIKILESLGYV 45
                                      67************************6 PP

>> PheRS_DBD1  PheRS DNA binding domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   3.9e-05     0.025      13      48 ..      11      45 ..       3      53 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.9e-05
                        PheRS_DBD1 13 Lekkgev.dslelAaelgvdHqkvVGavKSLqalgel 48
                                      +  k++v +s e+A++l+++ + v G++K L++lg +
  gi|242398494|ref|YP_002993918.1| 11 I--KEGVrTSKEIAERLEMSVEEVEGIIKILESLGYV 45
                                      3..577779*************************944 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   4.2e-05     0.027      25      58 ..      15      48 ..       7      57 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.2e-05
                                      -B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              Rrf2 25 pvsseeiaerqnispsylekilakLrkaglvksv 58
                                        +s+eiaer ++s + +e i++ L+  g+v+ +
  gi|242398494|ref|YP_002993918.1| 15 VRTSKEIAERLEMSVEEVEGIIKILESLGYVEKI 48
                                      469****************************865 PP

>> FhuF_C  FhuF 2Fe-2S C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   0.00011     0.073      11      21 .]      49      59 ..      47      59 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00011
                            FhuF_C 11 pggeyCgsCPL 21
                                      + ge CgsCPL
  gi|242398494|ref|YP_002993918.1| 49 EIGESCGSCPL 59
                                      5699******8 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   7.4e-05     0.047       5      40 ..       7      43 ..       6      48 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.4e-05
                            HTH_28  5 iikllaaGh.svreaArelgisrrtvyrWikryeegG 40
                                      +++l+++G+ + +e+A++l +s + v + ik +e+ G
  gi|242398494|ref|YP_002993918.1|  7 VLELIKEGVrTSKEIAERLEMSVEEVEGIIKILESLG 43
                                      6788899*99*********************999987 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   9.2e-05     0.059      19      49 ..      17      47 ..       7      52 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.2e-05
                                      EHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              MarR 19 svseLakklgvskstvtrvldrLekkGlieR 49
                                      + +e+a++l++s   v  +++ Le  G++e+
  gi|242398494|ref|YP_002993918.1| 17 TSKEIAERLEMSVEEVEGIIKILESLGYVEK 47
                                      557**************************98 PP

>> RPA_C  Replication protein A C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   9.8e-05     0.063      66      97 ..      13      45 ..       4      45 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9.8e-05
                                      TTEEH.HHHHHHSTSXHHHHHHHHHHHHHTTSE CS
                             RPA_C 66 eGvhv.deiaqklrlsvndvkqavdeLsneGii 97
                                      eGv   +eia++l++sv++v+ +++ L++ G++
  gi|242398494|ref|YP_002993918.1| 13 EGVRTsKEIAERLEMSVEEVEGIIKILESLGYV 45
                                      57765269*********************9986 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   8.2e-05     0.052      20      54 ..      17      51 ..      12      72 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8.2e-05
                    B-block_TFIIIC 20 tqsdLakeskqdprslfyrlksLekkgLIvkqsii 54
                                      t++++a  ++++++ + +++k Le+ g+++k++i 
  gi|242398494|ref|YP_002993918.1| 17 TSKEIAERLEMSVEEVEGIIKILESLGYVEKIEIG 51
                                      5677889999**********************994 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   0.00012     0.074      22      45 ..      10      33 ..       7      45 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00012
                                      HHHHSSBEHHHHHHHHSSTHHHHH CS
                             HTH_9 22 LlrkgrltlrelvkktkLsldqVk 45
                                      L+++g +t++e+++++++s  +V 
  gi|242398494|ref|YP_002993918.1| 10 LIKEGVRTSKEIAERLEMSVEEVE 33
                                      9*******************9997 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 ?   12.7   0.1   0.00014     0.092      23      53 ..      17      47 ..       9      53 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00014
                                      HHHHHHHHTTSSHHHHHHHHHHHHHTTSEEE CS
                         HTH_Crp_2 23 tqeelAsmlGltretvsrilseLkreglisr 53
                                      t +e+A++l ++ e v  i++ L+  g++++
  gi|242398494|ref|YP_002993918.1| 17 TSKEIAERLEMSVEEVEGIIKILESLGYVEK 47
                                      678*************************983 PP

>> RepL  Firmicute plasmid replication protein (RepL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00011     0.073      75     111 ..      15      51 ..       4      73 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
                              RepL  75 iatnRelaeetgislktvsetlkileeanilkkkanG 111
                                       + t++e+ae+ ++s++ v   +kile  +++ k+  G
  gi|242398494|ref|YP_002993918.1|  15 VRTSKEIAERLEMSVEEVEGIIKILESLGYVEKIEIG 51 
                                       679**************************99998766 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 ?   12.2   0.1   0.00014     0.089     105     135 ..      18      48 ..       7      63 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00014
                                       HHHHHHTTGXXHHHHHHHHHHHHHTTXXEEE CS
                     RNA_pol_Rpc34 105 srtiksklnLhksvvkkcLksLeskkyiksv 135
                                       s++i ++l +  ++v+ ++k+Les +y+ ++
  gi|242398494|ref|YP_002993918.1|  18 SKEIAERLEMSVEEVEGIIKILESLGYVEKI 48 
                                       799************************9875 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00028      0.18      20      49 ..       7      37 ..       5      39 .. 0.94
   2 ?   -2.7   0.0       6.1   3.9e+03      20      33 ..      50      62 ..      49      63 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00028
                      HTH_Tnp_ISL3 20 ilellles.rsvkavArqlgvSwtTVwrild 49
                                      +lel +e+ r+ k++A++l  S   V+ i++
  gi|242398494|ref|YP_002993918.1|  7 VLELIKEGvRTSKEIAERLEMSVEEVEGIIK 37
                                      8999************************986 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 6.1
                      HTH_Tnp_ISL3 20 ilelllesrsvkav 33
                                      i e++ ++ + k +
  gi|242398494|ref|YP_002993918.1| 50 IGESCGSC-PLKKI 62
                                      78999999.88866 PP

>> DUF4211  Domain of unknown function (DUF4211)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00027      0.17     114     142 ..      46      78 ..       3      79 .] 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00027
                           DUF4211 114 e....ekkCdAcnrskhpatysvrlsGkpYnkk 142
                                       e    +++C +c ++k ++   ++++G+ Y+ k
  gi|242398494|ref|YP_002993918.1|  46 EkieiGESCGSCPLKKICPGSCIVFKGNIYQMK 78 
                                       04445689**********************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1046  (0.0583412); expected 358.6 (0.02)
Passed bias filter:                      806  (0.0449551); expected 358.6 (0.02)
Passed Vit filter:                       106  (0.00591221); 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 0.33s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 477.89
//
Query:       gi|242398495|ref|YP_002993919.1|  [L=413]
Description: NDP-sugar synthase [Thermococcus sibiricus MM 739]
Scores for complete 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-47  160.2   0.0    8.8e-47  159.8   0.0    1.2  1  NTP_transferase  Nucleotidyl transferase
    2.2e-12   46.2   4.8    1.5e-05   24.5   0.2    2.7  2  Hexapep          Bacterial transferase hexapeptide (six repea
      5e-10   40.0   0.0    7.8e-10   39.3   0.0    1.3  1  NTP_transf_3     MobA-like NTP transferase domain
  ------ inclusion threshold ------
      0.015   15.1   0.0      0.025   14.3   0.0    1.3  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
          2    8.2   7.2         14    5.5   2.6    3.3  2  Hexapep_2        Hexapeptide repeat of succinyl-transferase


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.8   0.0   2.5e-50   8.8e-47       1     246 [.       2     233 ..       2     235 .. 0.95

  Alignments for each domain:
  == domain 1  score: 159.8 bits;  conditional E-value: 2.5e-50
                                       EEEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHH.TT-SEEEEEEETTTHHHHHHHHTTS.GGGTSEE CS
                   NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlan.sgieeiivvltqehsflveeqlkeg.skfgvev 75 
                                       kavILaGG GtRL+PL++t++k+++pvlg  + +q+ l++l + s+i+e ++ + ++ + +++e ++++ s++  ++
  gi|242398495|ref|YP_002993919.1|   2 KAVILAGGFGTRLRPLSSTRPKPMIPVLGR-PNLQYILENLQKiSEIDE-VILSVHYMRGEIREFIEDKmSDYPKDI 76 
                                       79****************************.************9*****.99999999999999998762455589* PP

                                       EEEEESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEE CS
                   NTP_transferase  76 lialepegkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGvie 152
                                        ++  p++ +t +A++ +++++ de+     lv+ gD++++ ++ee++k +++++a  ++t+++++v ++++yGv+ 
  gi|242398495|ref|YP_002993919.1|  77 RFINDPMPLETGGALKNVEDVVSDEF-----LVIYGDVFTNFNFEELIKAHKANDA--LITVALTKVYDPEKYGVVV 146
                                       ***********************988.....9************************..******************* PP

                                       ECTTSBEEEEECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-E CS
                   NTP_transferase 153 adeegrverfvEKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyW 229
                                       +deeg++ +f+EKP ++k s+l+++GiY+ n+e+l ++     +  ++  +  ++lpk +++g ++ +++ + + yW
  gi|242398495|ref|YP_002993919.1| 147 TDEEGKIVDFEEKPLRPK-SNLIDAGIYMVNKEILNEI-----PKGKEIYFEREVLPKFVAQGLAHGYMMPRNN-YW 216
                                       ******************.*******************.....789999*****************99999887.9* PP

                                       EEXSSHHHHHHHHHHHH CS
                   NTP_transferase 230 sDvGtldslleanekla 246
                                        D+Gt+++++ a++ ++
  gi|242398495|ref|YP_002993919.1| 217 VDLGTPEDFFYAHQLIL 233
                                       ***********998776 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.2   4.2e-09   1.5e-05       8      35 ..     261     288 ..     247     293 .. 0.91
   2 !   22.8   1.0   1.5e-08   5.3e-05       2      35 ..     313     346 ..     312     347 .. 0.91

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 4.2e-09
                                       EEE-TTEEEETTEEE-TTEEEETTEEEE CS
                           Hexapep   8 vlIgpfaviggnVkIGdnvkIgagvvig 35 
                                       v+I+++++ig++VkI  +++Ig+++v+ 
  gi|242398495|ref|YP_002993919.1| 261 VYIDSGVKIGHGVKIKAYTYIGPNTVVE 288
                                       89************************95 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 1.5e-08
                                       EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                       +++G++v++g+++++ +n+++Gd++kI  + vi 
  gi|242398495|ref|YP_002993919.1| 313 SILGEGVVVGKNVILKENAVVGDYAKIYDNLVIY 346
                                       689************************9998885 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 !   39.3   0.0   2.2e-13   7.8e-10       1     122 [.       3     133 ..       3     171 .. 0.82

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 2.2e-13
                                       EEEEEESS-TTTT.....TTHHHHCCCCCCHHHHHHHHHCTT..-CEEEEECSH..CHHHHHHTTC......TS-EE CS
                      NTP_transf_3   1 aviLAGGrSsRmg.....gdKallplggkpllervldalraa.gvdevvvvggd..eevlaalarl......gvrvv 63 
                                       aviLAGG ++R+      ++K+++p+ g+p l+++l++l++  ++dev++++ +   e+++ ++++      ++r++
  gi|242398495|ref|YP_002993919.1|   3 AVILAGGFGTRLRplsstRPKPMIPVLGRPNLQYILENLQKIsEIDEVILSVHYmrGEIREFIEDKmsdypkDIRFI 79 
                                       79**********7554335***********************66********9976567776655555445579999 PP

                                       E-TTSS-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEE CS
                      NTP_transf_3  64 ededpgkgplaslaaalraaadadavlvlacDmPlltpelverllaaaaasgadvvvpt 122
                                       +d+ p   ++++l+   + +  +d +lv+ +D+  +t    e+l++a++a++a ++v+ 
  gi|242398495|ref|YP_002993919.1|  80 NDPMP-LETGGALKNVEDVV--SDEFLVIYGDV--FTNFNFEELIKAHKANDALITVAL 133
                                       99976.56677777777765..799*******9..477778888888887777776664 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 ?   14.3   0.0     7e-06     0.025       2      62 ..       2      64 ..       1      79 [. 0.86

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7e-06
                                      EEEEECTTSSCTT-...SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHHHH CS
                              IspD  2 vvvipAAGsGkRmk...aglpKqflelkgqtllehtvdallaskavdkivvvvseddteefeql 62
                                       +vi A G+G+R++   + +pK  + + g++ l+  ++ l++ +++d++++ v+  + +e++++
  gi|242398495|ref|YP_002993919.1|  2 KAVILAGGFGTRLRplsSTRPKPMIPVLGRPNLQYILENLQKISEIDEVILSVHYMR-GEIREF 64
                                      69**********7533389*********************************99877.555555 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.2     0.023        83      15      30 ..     262     279 ..     259     288 .. 0.81
   2 ?    5.5   2.6    0.0039        14       5      32 ..     316     333 ..     311     346 .. 0.48

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.023
                                       EE..SEEE-TT-EE-TT- CS
                         Hexapep_2  15 gi..GvslGdncvvgaGv 30 
                                       +i  Gv++G ++++ a  
  gi|242398495|ref|YP_002993919.1| 262 YIdsGVKIGHGVKIKAYT 279
                                       6777999**999998855 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0039
                                       -TT-EE-TT-EESEEE-TT-EE-TT-EE CS
                         Hexapep_2   5 GdnCliGanagiGvslGdncvvgaGvvi 32 
                                       G+          Gv +G+n+++  + v+
  gi|242398495|ref|YP_002993919.1| 316 GE----------GVVVGKNVILKENAVV 333
                                       33..........3333333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 2488.33
//
Query:       gi|242398496|ref|YP_002993920.1|  [L=266]
Description: hypothetical protein TSIB_0505 [Thermococcus sibiricus MM 739]
Scores for complete 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-23   80.8   0.0    8.8e-23   80.1   0.0    1.3  1  DisA_N    DisA bacterial checkpoint controller nucleotide-bin
  ------ inclusion threshold ------
       0.23   11.4   0.6       0.99    9.5   0.1    2.2  2  UIM       Ubiquitin interaction motif


Domain annotation for each model (and alignments):
>> DisA_N  DisA bacterial checkpoint controller nucleotide-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.1   0.0   9.8e-27   8.8e-23       3     119 .]     133     257 ..     131     257 .. 0.83

  Alignments for each domain:
  == domain 1  score: 80.1 bits;  conditional E-value: 9.8e-27
                                       HHHHHHHHT--EEEEEESSSC........C.CTTCCTSEEEEEE--HHHHHHHTSTTSTTCSSEEEE.ETTEEEEEE CS
                            DisA_N   3 aveelskkkiGaliviereee........l.keiietgvkldaevskellkeifekksplhDGAvii.rdgrivaag 69 
                                       ++e++++k +G+++vi+++++        + + +    +++ ++ ++e++ke+     + +DGA++i ++gr+++ag
  gi|242398496|ref|YP_002993920.1| 133 SLEGREGKPVGTIFVIGDTRNvirhsyqmVpNPFKGYKINILDRSTREIIKEF-----AFLDGAFVInKSGRVLCAG 204
                                       68999****************655555442123333445666999********.....*********88******** PP

                                       EEE--.TT..-TTS.ST-SHHHHHHHHHHHHSSSEEEEE-TTTS-EEEEETTEE CS
                            DisA_N  70 viLpl.se..nkel.kelGtRHraAlgiseetdalvivVSeetgkislakdgkl 119
                                       ++L++  +    ++ ++lG+RH aA+gis+ t+a++i+VSe+ g ++++k+gk+
  gi|242398496|ref|YP_002993920.1| 205 RYLDIdLKktAVRIpSGLGSRHLAAAGISKLTKAIAITVSES-GVVRVFKNGKI 257
                                       ****975545445656*************************9.*********85 PP

>> UIM  Ubiquitin interaction motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.17   1.5e+03       6      12 ..      11      17 ..      10      17 .. 0.89
   2 ?    9.5   0.1   0.00011      0.99       4      15 ..     124     135 ..     124     136 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.17
                               UIM  6 LqrAlal 12
                                      L++A++l
  gi|242398496|ref|YP_002993920.1| 11 LKKAIEL 17
                                      89***98 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00011
                               UIM   4 edLqrAlalSlq 15 
                                       e L++A++lSl+
  gi|242398496|ref|YP_002993920.1| 124 EVLELAIELSLE 135
                                       789********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); 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 0.28s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1648.81
//
Query:       gi|242398497|ref|YP_002993921.1|  [L=177]
Description: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.2e-29  101.0   0.1    6.6e-29  100.7   0.1    1.1  1  Flavoprotein    Flavoprotein
  ------ inclusion threshold ------
      0.038   13.0   0.0      0.055   12.5   0.0    1.1  1  Lipoprotein_18  NlpB/DapX lipoprotein


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 !  100.7   0.1   7.4e-33   6.6e-29       1     125 [.       1     156 [.       1     165 [. 0.89

  Alignments for each domain:
  == domain 1  score: 100.7 bits;  conditional E-value: 7.4e-33
                                       EEEEEEE-SSCGGGCHHHHHHHHHHTTEEEEEEESCHHHHCCHHG.GS....TCSSHHHHHHCT.......TESEEE CS
                      Flavoprotein   1 kkillgiTGsvaaikalellekLkkegievqvvltkaAkkfiske.klklaaredpilhielrr.......wadllv 69 
                                       +k++++iTG+++ai++++l+e L++ g+ev  +++ ++ k+++ e  ++++    +  + +l+        ++d+++
  gi|242398497|ref|YP_002993921.1|   1 MKVVVAITGASGAIYGIRLIEVLRSLGHEVVSIASGTGLKVVQYElGIEFEP---DFHEKDLSApiasgsyKFDAVI 74 
                                       79*****************************************998444433...4444444334555555****** PP

                                       EEEEEHHHHHHHHTT--SSHH..............................HHHHHTHCCTTEEEEE.--HHCCTCS CS
                      Flavoprotein  70 iaPasantlakianGiadnll..............................tlilratakkpiliaPamnpamyenp 116
                                       +aP+s++tl++ianG+adnl+                              ++++   ++++++++P ++pa+y +p
  gi|242398497|ref|YP_002993921.1|  75 VAPCSMKTLSAIANGFADNLItrtadvalkerrklvlliretplnlihiqnMSKV---TQAGAIVMP-ASPAFYPQP 147
                                       *********************************************9999999999...99*******.********* PP

                                       TCHHHHHHH CS
                      Flavoprotein 117 qtlknlekl 125
                                       ++l+++ ++
  gi|242398497|ref|YP_002993921.1| 148 KSLDDMINF 156
                                       ******999 PP

>> Lipoprotein_18  NlpB/DapX lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   6.2e-06     0.055     231     282 ..      18      70 ..      17      74 .. 0.96

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.2e-06
                                       HHHHHHHHTTEEEEEEETTTTEEEEEEXXXXHHHHHHHTSXX..XXXXSEEEEE CS
                    Lipoprotein_18 231 rLplvLpklgfevedrdrsqGlyevkYkepssgfWsslgake..ldlkegeYrl 282
                                       rL +vL++lg ev++  + +Gl  v+Y e + +f  ++ +k+   ++++g+Y++
  gi|242398497|ref|YP_002993921.1|  18 RLIEVLRSLGHEVVSIASGTGLKVVQY-ELGIEFEPDFHEKDlsAPIASGSYKF 70 
                                       899************************.7*************9999******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1264.10
//
Query:       gi|242398498|ref|YP_002993922.1|  [L=160]
Description: transcription regulator, Lrp/AsnC family [Thermococcus sibiricus MM 739]
Scores for complete 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-15   55.3   1.2    3.4e-15   55.3   1.2    1.7  2  HTH_24           Winged helix-turn-helix DNA-binding
    8.2e-12   44.8   0.8    1.4e-11   44.0   0.8    1.4  1  HTH_AsnC-type    AsnC-type helix-turn-helix domain
    1.2e-06   28.5   0.1    1.9e-06   27.8   0.1    1.3  1  HTH_20           Helix-turn-helix domain
    1.3e-05   25.1   0.0    2.4e-05   24.3   0.0    1.4  1  NapD             NapD protein
    1.4e-05   24.8   0.1    3.1e-05   23.7   0.1    1.6  1  HTH_5            Bacterial regulatory protein, arsR family
    4.8e-05   23.1   0.0    9.1e-05   22.2   0.0    1.4  1  HTH_IclR         IclR helix-turn-helix domain
    0.00016   22.1   0.1    0.00031   21.2   0.1    1.4  1  HTH_27           Winged helix DNA-binding domain
     0.0005   19.9   0.0    0.00083   19.2   0.0    1.4  1  TrmB             Sugar-specific transcriptional regulator Trm
    0.00061   19.6   0.0     0.0013   18.6   0.0    1.4  1  MarR_2           MarR family
    0.00068   19.1   0.4     0.0012   18.3   0.4    1.5  1  Sigma70_r4       Sigma-70, region 4
    0.00089   19.2   0.5     0.0016   18.3   0.5    1.4  1  HTH_11           HTH domain
     0.0017   18.2   0.4     0.0032   17.4   0.4    1.4  1  MarR             MarR family
     0.0031   17.9   0.0     0.0057   17.0   0.0    1.4  1  Penicillinase_R  Penicillinase repressor
     0.0094   15.7   0.1      0.026   14.3   0.1    1.8  1  HTH_23           Homeodomain-like domain
  ------ inclusion threshold ------
      0.013   15.3   0.7      0.074   12.8   0.1    2.2  2  HTH_38           Helix-turn-helix domain
      0.022   14.5   0.4      0.038   13.7   0.4    1.4  1  HTH_DeoR         DeoR-like helix-turn-helix domain
      0.023   14.5   0.9      0.092   12.6   0.2    2.3  3  RuvB_C           RuvB C-terminal winged helix domain
      0.053   13.4   0.1       0.36   10.7   0.1    2.1  2  DAHP_snth_FXD    DAHP synthase ferredoxin-like domain
       0.08   12.8   0.0       0.13   12.1   0.0    1.4  1  DUF742           Protein of unknown function (DUF742)
       0.12   13.4   0.1         28    5.8   0.0    2.9  4  AMP-binding_C    AMP-binding enzyme C-terminal domain
        2.3    8.3   4.7       0.88    9.7   0.3    2.4  3  Cullin_Nedd8     Cullin protein neddylation 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 !   55.3   1.2     4e-18   3.4e-15       1      48 []       4      51 ..       4      51 .. 0.98
   2 ?   -2.6   0.1       5.1   4.3e+03       6      15 ..     120     129 ..     117     129 .. 0.79

  Alignments for each domain:
  == domain 1  score: 55.3 bits;  conditional E-value: 4e-18
                            HTH_24  1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      ld++dr+IL+lL++++r++++e +erl+ + st++ r+k+L+e G+I+
  gi|242398498|ref|YP_002993922.1|  4 LDDLDREILKLLREDARLTISEMSERLNKPESTIHFRIKKLIERGVIE 51
                                      79*********************************************7 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 5.1
                            HTH_24   6 rkILelLqkn 15 
                                        ++L+++++n
  gi|242398498|ref|YP_002993922.1| 120 EELLKCIEEN 129
                                       5789999998 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.0   0.8   1.7e-14   1.4e-11       1      41 [.       4      44 ..       4      45 .. 0.99

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 1.7e-14
                     HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrL 41
                                      LD++Dr IL++L+edaR++ +e++er++  est++ R+++L
  gi|242398498|ref|YP_002993922.1|  4 LDDLDREILKLLREDARLTISEMSERLNKPESTIHFRIKKL 44
                                      8***************************************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 !   27.8   0.1   2.3e-09   1.9e-06      11      57 ..       7      53 ..       2      55 .. 0.92

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 2.3e-09
                                      HHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                            HTH_20 11 vRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevv 57
                                        r+il++L++++ lt se  erl  + +t+++++++L e g +e+ 
  gi|242398498|ref|YP_002993922.1|  7 LDREILKLLREDARLTISEMSERLNKPESTIHFRIKKLIERGVIERY 53
                                      5699****************************************985 PP

>> NapD  NapD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   2.8e-08   2.4e-05      14      72 ..      85     144 ..      80     146 .. 0.94

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 2.8e-08
                              NapD  14 rlaavkaalaalpgvEvhasdeegklVvviEaesedeladtiea.iealpgVlsaslvyh 72 
                                        l+ v+++la lp+v + +++ee++++  + a+s++el++ ie+ i+++p V ++s +y 
  gi|242398498|ref|YP_002993922.1|  85 YLEYVSRNLAMLPNVLLVGKTEEERIIALVGADSKEELLKCIEEnIKSIPSVKNVSVHYI 144
                                       68899*************************************988*************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 !   23.7   0.1   3.6e-08   3.1e-05       5      46 ..       9      51 ..       7      52 .. 0.95

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 3.6e-08
                                      HHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  5 lkILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      ++ILklL+e   l+++e +e l++++st+    kkL e G++e
  gi|242398498|ref|YP_002993922.1|  9 REILKLLREdARLTISEMSERLNKPESTIHFRIKKLIERGVIE 51
                                      59*******888****************************997 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   1.1e-07   9.1e-05       8      50 ..      11      52 ..      10      53 .. 0.95

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.1e-07
                                      HHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR  8 iLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      iL++l+e ++ lt+se+++r+  p St h  ++ L+e+G +e+
  gi|242398498|ref|YP_002993922.1| 11 ILKLLREDAR-LTISEMSERLNKPESTIHFRIKKLIERGVIER 52
                                      9999999999.9***************************9986 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.1   3.6e-07   0.00031       4      50 ..       7      52 ..       4      54 .. 0.94

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 3.6e-07
                            HTH_27  4 qqalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLver 50
                                      +++ +L l+r +++r ++++ ++rln   s+i+  +kkL+e+G++er
  gi|242398498|ref|YP_002993922.1|  7 LDREILKLLR-EDARLTISEMSERLNKPESTIHFRIKKLIERGVIER 52
                                      68899*****.**********************************86 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   9.7e-07   0.00083      16      54 ..      13      52 ..       4      63 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 9.7e-07
                                      HHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEE CS
                              TrmB 16 aLl.klgpatadeiaeelgvprskvYevLrsLedkGlVer 54
                                      +Ll +  ++t++e +e+l+ p+s++   +++L+++G++er
  gi|242398498|ref|YP_002993922.1| 13 KLLrEDARLTISEMSERLNKPESTIHFRIKKLIERGVIER 52
                                      45559999******************************98 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.5e-06    0.0013      13      53 ..      14      52 ..       5      54 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.5e-06
                                      HHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                            MarR_2 13 aLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53
                                       L r++  +lt++e  +rl+ + s+++ ++k+L ++G +er
  gi|242398498|ref|YP_002993922.1| 14 LL-REDA-RLTISEMSERLNKPESTIHFRIKKLIERGVIER 52
                                      44.4444.3*******************************9 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.4   1.4e-06    0.0012       5      46 ..       4      46 ..       1      47 [. 0.93

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.4e-06
                                      S-HHHHHHHHHHH.TTT--HHHHHHHHTS-HHHHHHHHHHHHH CS
                        Sigma70_r4  5 Lpererevlelrf.geglTleEIgerlgiSrerVrqiekrAlr 46
                                      L++ +re+l+l + +  lT +E +erl+ ++++++ ++k+ ++
  gi|242398498|ref|YP_002993922.1|  4 LDDLDREILKLLReDARLTISEMSERLNKPESTIHFRIKKLIE 46
                                      8999*******999*********************99999776 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.5   1.9e-06    0.0016       3      44 ..       9      49 ..       8      60 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.9e-06
                            HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                      + il+lL +++  ++++e++e+Ln  ++t++ +Ik+L e gv
  gi|242398498|ref|YP_002993922.1|  9 REILKLL-REDARLTISEMSERLNKPESTIHFRIKKLIERGV 49
                                      579****.66666*************************9993 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.4   3.7e-06    0.0032       8      51 ..      11      54 ..       9      56 .. 0.96

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.7e-06
                                      HHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                              MarR  8 iLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRsk 51
                                      iL +l+e   l++se+ ++l+   st+   +++L+++G ieR+ 
  gi|242398498|ref|YP_002993922.1| 11 ILKLLREDARLTISEMSERLNKPESTIHFRIKKLIERGVIERYT 54
                                      899***************************************86 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   6.7e-06    0.0057       3      55 ..       6      54 ..       4      62 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 6.7e-06
                                      -S-SHHHHHHHHHS-EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEE CS
                   Penicillinase_R  3 elEaevmeilwekgeatvkevveeleeekelaysTVktllrrLvkKgllsrek 55
                                      +l++e++++l+e  ++t++e  e+l+++    +sT++  +++L ++g+++r++
  gi|242398498|ref|YP_002993922.1|  6 DLDREILKLLREDARLTISEMSERLNKP----ESTIHFRIKKLIERGVIERYT 54
                                      6889************************....*****************9975 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.1   3.1e-05     0.026       9      44 ..      10      47 ..       9      53 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.1e-05
                            HTH_23  9 rillllae..GlsvreIAreLgvsrrTvy.rwlkryree 44
                                      +il+ll+e  +l+++e +++L+ +++T+  r++k   e 
  gi|242398498|ref|YP_002993922.1| 10 EILKLLREdaRLTISEMSERLNKPESTIHfRIKKLI-ER 47
                                      69*****99********************9999975.45 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   8.6e-05     0.074       5      38 ..       4      38 ..       3      44 .. 0.79
   2 ?    0.2   0.0      0.77   6.6e+02       9      27 ..      46      67 ..      43      67 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.6e-05
                            HTH_38  5 LsleeReeIerlla.eGlslreIArrLgrspsTIs 38
                                      L   +Re +  l++ + l+++e+  rL++  sTI+
  gi|242398498|ref|YP_002993922.1|  4 LDDLDREILKLLREdARLTISEMSERLNKPESTIH 38
                                      666788666666643559****************5 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.77
                            HTH_38  9 eReeIerl.laeGlslr..eIA 27
                                      eR +Ier  +  G+s r  eIA
  gi|242398498|ref|YP_002993922.1| 46 ERGVIERYtIVLGKSARpnEIA 67
                                      8999999866788888877776 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 ?   13.7   0.4   4.5e-05     0.038       4      46 ..      10      52 ..       8      54 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.5e-05
                          HTH_DeoR  4 qilellkqqgklsveelvellgvSeaTiRRDLneLeeqglltR 46
                                      +il+ll+++  l++ e +e+l+  e Ti   +++L e g+++R
  gi|242398498|ref|YP_002993922.1| 10 EILKLLREDARLTISEMSERLNKPESTIHFRIKKLIERGVIER 52
                                      8***************************999999999999998 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 ?   12.6   0.2   0.00011     0.092       4      56 ..       4      52 ..       3      54 .. 0.91
   2 ?   -1.5   0.0       2.8   2.4e+03      53      66 ..     101     114 ..      96     120 .. 0.80
   3 ?   -2.2   0.0       4.7     4e+03      10      19 ..     121     130 ..     113     146 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00011
                                      --HHHHHHHHHHHHT.TT--B-HHHHHHHTT--HHHHHHTTHHHHHHTTSEEE CS
                            RuvB_C  4 LdeldikyLkllkekfkggpvglktlaailgeeketiedviEPyLlkeglIer 56
                                      Ld+ld+++Lkll    ++  + ++ +++ l+ +++ti   i   L+++g Ier
  gi|242398498|ref|YP_002993922.1|  4 LDDLDREILKLLR---EDARLTISEMSERLNKPESTIHFRIK-KLIERGVIER 52
                                      899*********9...79*******************99985.6888888887 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.8
                                       SEEEETTEEEE-HH CS
                            RuvB_C  53 lIertsrGRilTkk 66 
                                       l+ +t+  Ri+   
  gi|242398498|ref|YP_002993922.1| 101 LVGKTEEERIIALV 114
                                       78899999999755 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 4.7
                                       HHHHHHHHT. CS
                            RuvB_C  10 kyLkllkekf 19 
                                       ++Lk++ e+ 
  gi|242398498|ref|YP_002993922.1| 121 ELLKCIEENI 130
                                       5566666553 PP

>> DAHP_snth_FXD  DAHP synthase ferredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       1.2     1e+03       3      23 ..      55      75 ..      54      76 .. 0.88
   2 ?   10.7   0.1   0.00042      0.36      32      62 ..     104     139 ..      98     141 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.2
                     DAHP_snth_FXD  3 ivmkkgateeqieevieriee 23
                                      iv+ k+a +++i  v+ ++e+
  gi|242398498|ref|YP_002993922.1| 55 IVLGKSARPNEIAFVVLELEK 75
                                      8999********999988875 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00042
                     DAHP_snth_FXD  32 kGeertViGviGdtsk.....ldkeqlealpgVekV 62 
                                       k ee+ +i+++G +sk      ++e+++++p V++V
  gi|242398498|ref|YP_002993922.1| 104 KTEEERIIALVGADSKeellkCIEENIKSIPSVKNV 139
                                       568999******988844443468*********998 PP

>> DUF742  Protein of unknown function (DUF742)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00015      0.13      43      98 ..       6      63 ..       1      72 [. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00015
                            DUF742 43 pehrailrLcre..plsVaelaAelklPvgvvrvLlsdLldaglltvrapvtdraaeq 98
                                      +  r+il+L re  +l++ e++ +l+ P ++++  +  L++ g ++ ++ v  ++a+ 
  gi|242398498|ref|YP_002993922.1|  6 DLDREILKLLREdaRLTISEMSERLNKPESTIHFRIKKLIERGVIERYTIVLGKSARP 63
                                      55799******9999******************************9988887766555 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0      0.32   2.7e+02      46      71 ..      49      75 ..      29      79 .. 0.72
   2 ?    2.2   0.0      0.43   3.7e+02      55      70 ..      58      74 ..      49      99 .. 0.64
   3 ?    5.8   0.0     0.033        28      17      61 ..     101     137 ..      96     149 .. 0.69
   4 ?    5.7   0.0     0.034        29       2      31 ..     126     155 ..     125     158 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.32
                                      HHHHHHHHT-TTTS-SEEEE-.S---B CS
                     AMP-binding_C 46 Lkahvrkelgpyavpkkvvfv.delpk 71
                                      ++++ +  lg+ a+p+++ fv  el+k
  gi|242398498|ref|YP_002993922.1| 49 VIERYTIVLGKSARPNEIAFVvLELEK 75
                                      555555578999999999977346655 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.43
                                      -TTTS-SEEEE-.S--- CS
                     AMP-binding_C 55 gpyavpkkvvfv.delp 70
                                      g+ a+p+++ fv  el+
  gi|242398498|ref|YP_002993922.1| 58 GKSARPNEIAFVvLELE 74
                                      55555555554423333 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.033
                                       EE-----TTS---EEEEEE------HHHHHHHHHHHHT-TTTS-S CS
                     AMP-binding_C  17 VvGvpdevkGealvafVvlkdgsealeeeLkahvrkelgpyavpk 61 
                                        vG+++e   e+++a+V    +s   +eeL + +++++ ++   k
  gi|242398498|ref|YP_002993922.1| 101 LVGKTEE---ERIIALVGA--DS---KEELLKCIEENIKSIPSVK 137
                                       5899999...999999998..43...4899998888888874333 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.034
                                       HHHHHHSSTTEEEEEEE-----TTS---EE CS
                     AMP-binding_C   2 vEsalvshpaVaeaaVvGvpdevkGealva 31 
                                       +E+ + s p V+++ V+ ++d +kGe +++
  gi|242398498|ref|YP_002993922.1| 126 IEENIKSIPSVKNVSVHYIKDFKKGEEIKG 155
                                       89***************9999999998876 PP

>> Cullin_Nedd8  Cullin protein neddylation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.3     0.001      0.88      29      59 ..      22      52 ..      11      54 .. 0.92
   2 ?   -0.6   0.1       1.6   1.4e+03      45      60 ..      75      92 ..      72      93 .. 0.85
   3 ?   -2.1   0.1         5   4.2e+03      44      50 ..     122     128 ..     118     149 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.001
                      Cullin_Nedd8 29 vieqlskrftpsiadikkrIesLiekeYleR 59
                                      +i+++s+r +   + i  rI++Lie++ +eR
  gi|242398498|ref|YP_002993922.1| 22 TISEMSERLNKPESTIHFRIKKLIERGVIER 52
                                      6888999999999*****************9 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.6
                      Cullin_Nedd8 45 kkrIesLiek..eYleRd 60
                                      k +Ie+ ++k  eY++R+
  gi|242398498|ref|YP_002993922.1| 75 KPVIEDFLDKylEYVSRN 92
                                      568999999999999996 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 5
                      Cullin_Nedd8  44 ikkrIes 50 
                                         k+Ie+
  gi|242398498|ref|YP_002993922.1| 122 LLKCIEE 128
                                       4566664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       870  (0.0485247); expected 358.6 (0.02)
Passed bias filter:                      681  (0.0379832); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1114.35
//
Query:       gi|242398499|ref|YP_002993923.1|  [L=172]
Description: Adenylate cyclase, class 2 [Thermococcus sibiricus MM 739]
Scores for complete 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-26   91.6   3.3    6.1e-26   91.4   3.3    1.0  1  CYTH          CYTH domain
  ------ inclusion threshold ------
       0.11   12.6   0.1        0.2   11.8   0.1    1.3  1  Glyoxalase_5  Hydroxyphenylpyruvate dioxygenase, HPPD, N-term


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 !   91.4   3.3   6.8e-30   6.1e-26       3     179 .]       2     159 ..       1     159 [. 0.93

  Alignments for each domain:
  == domain 1  score: 91.4 bits;  conditional E-value: 6.8e-30
                                       EEEEEEEE-HHHHHHHHHHHHHCTCEEEEEEEEEEEEEE-TTTHHHHTTEEEEEEEETTTEEE.EEEEEECSSST.. CS
                              CYTH   3 EvEvKflvsaaeyedlelrlaelrakeettveqrdtYydtpdrdlartdeaLRiRraegdgee.ltlKgpgvdge.. 76 
                                       EvEvKf+v   +++++e +++ l+a+  + + q+d Y+d p  dl      LRiR   + +++ l +K+ +++++  
  gi|242398499|ref|YP_002993923.1|   2 EVEVKFKV---DFNEIEGKIKALGATFIGEEVQEDLYFDLPLPDL------LRIRHIVNLNKViLGYKEIKDEKNee 69 
                                       9*******...78888888************************99......****888999999*******777677 PP

                                       EEEEEEEECCCEEECCCCHHHHHHHHHHHTT-EEEEEEEEEEEEEEETTEEEEEEEETTTTEEEEEEEEEESSHHHH CS
                              CYTH  77 reevegevsreEyeeplsdaaeaaelldglglepvasvkklRrkyklegvevalDaveflegeevEiElevedeeev 153
                                         e+e+ v+         d+++++e+l++lg+++ + vkk+Rr+ykl++++++l+ ve+l g++++iE+ +++ +e 
  gi|242398499|ref|YP_002993923.1|  70 FDEIEVGVE---------DFNKMKEILERLGFKEDVWVKKYRRVYKLGNITFELNTVEGL-GDFLDIEVISDNVNE- 135
                                       777777777.........******************************************.***********9999. PP

                                       HHHHHHHHHHHHHTTEEGGGBSCSHH CS
                              CYTH 154 keaaekllallrelglssaskirrsy 179
                                         a e +++++ +lgl++++ + r y
  gi|242398499|ref|YP_002993923.1| 136 --AKERIWEVAGKLGLKEKDIESRLY 159
                                       ..7888899***********999988 PP

>> Glyoxalase_5  Hydroxyphenylpyruvate dioxygenase, HPPD, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   2.2e-05       0.2       9      57 ..      69     116 ..      66     122 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.2e-05
                      Glyoxalase_5   9 GfefvefaapeaealeelfeklGftavarhrskdvtlyrqGginfilne 57 
                                        f+ +e + ++ ++++e++e+lGf++ +   +k  ++y+ G+i+f ln+
  gi|242398499|ref|YP_002993923.1|  69 EFDEIEVGVEDFNKMKEILERLGFKEDVW-VKKYRRVYKLGNITFELNT 116
                                       58899*******************97543.3455578********9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 1296.26
//
Query:       gi|242398500|ref|YP_002993924.1|  [L=397]
Description: GTPase, containing TGS domain [Thermococcus sibiricus MM 739]
Scores for complete 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-35  120.7   0.0    7.4e-35  119.9   0.0    1.4  1  MMR_HSR1_C     GTPase of unknown function C-terminal
    4.2e-20   71.9   0.0    4.2e-19   68.7   0.0    2.3  2  MMR_HSR1       50S ribosome-binding GTPase
      6e-13   48.6   0.0    1.6e-12   47.3   0.0    1.8  1  TGS            TGS domain
    4.3e-10   39.3   0.1    6.5e-07   29.0   0.0    2.4  2  FeoB_N         Ferrous iron transport protein B
  ------ inclusion threshold ------
      0.015   15.3   0.0      0.034   14.1   0.0    1.6  1  MMR_HSR1_Xtn   C-terminal region of MMR_HSR1 domain
      0.016   14.8   0.1      0.088   12.4   0.0    2.1  2  PrpR_N         Propionate catabolism activator
      0.019   14.9   0.1      0.084   12.8   0.0    2.0  2  RsgA_GTPase    RsgA GTPase
      0.075   13.2   0.0        1.3    9.3   0.0    2.4  2  YchF-GTPase_C  Protein of unknown function (DUF933)


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 !  119.9   0.0   3.3e-38   7.4e-35       1     112 []     220     327 ..     220     327 .. 0.97

  Alignments for each domain:
  == domain 1  score: 119.9 bits;  conditional E-value: 3.3e-38
                        MMR_HSR1_C   1 alNKaDlpaadenieklkekypkdk.kvvpvsAaaElaLrkaakqglikYepgdedfeikedklkeldekqkkaLek 76 
                                       a+NKaD  a+de ie++ ++ +k+  +v+p+sAaaEl Lrkaa++g+i+Y+pg++df++ +     l+ekqk+ L+ 
  gi|242398500|ref|YP_002993924.1| 220 AANKADA-ASDEDIERIIKEGKKRGyTVIPTSAAAELTLRKAANAGYIDYIPGAKDFKVIKP----LNEKQKHGLDL 291
                                       89*****.***********98865589********************************998....*********** PP

                        MMR_HSR1_C  77 irdlvlkrygsTGVqealnaavfelldlivVYPVed 112
                                       ir+ vl+r+gsTGVqe++n+a+f++l+l++VYPVed
  gi|242398500|ref|YP_002993924.1| 292 IREKVLDRFGSTGVQEVINRAIFDILQLVPVYPVED 327
                                       **********************************97 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.7   0.0   1.9e-22   4.2e-19       1      97 [.       2     131 ..       2     153 .. 0.77
   2 ?    0.4   0.0      0.29   6.5e+02      79     114 .]     185     223 ..     159     223 .. 0.63

  Alignments for each domain:
  == domain 1  score: 68.7 bits;  conditional E-value: 1.9e-22
                                       EEEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEE...ETTEE........................EEE CS
                          MMR_HSR1   1 evaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvk...lkgke........................iel 50 
                                       ev+ivG+pNvGKSt++ a t   ++++++p+tT+d n g      +   +                        i++
  gi|242398500|ref|YP_002993924.1|   2 EVGIVGKPNVGKSTFFAAATLVDVQIANYPFTTIDANIGVSYataV---HpckeigcvpnpqnyeyrngvslipIKM 75 
                                       69*************************************6653331...1355556666666677777777777*** PP

                                       EECGGCSSHHHHHHHHHHHHHHHHC.TSEEEEEEETT.........TTCSHHHHHHH CS
                          MMR_HSR1  51 vDtpGliegaseekglgkaflalee.adlillvvdas.........eeklkpldeel 97 
                                       +D++Gl+ ga+e++glg++fl+  + a+++++++d++         + ++++  e++
  gi|242398500|ref|YP_002993924.1|  76 IDVAGLVPGAHERRGLGNKFLDDLRmASALIHIIDVTgktdvegqpT-EYHDPVEDI 131
                                       *****999**************99978********887666655532.233333444 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.29
                                       EEEEEETTTTCSHHHHHHHHHHHHH...TTSEEEEEEES CS
                          MMR_HSR1  79 illvvdaseeklkpldeeleellee...akkplilvlnk 114
                                       +l+ v++s++  k  d++l ++ +e    +kpli+++nk
  gi|242398500|ref|YP_002993924.1| 185 ALHKVELSDDPTKWSDNDLFNFVRElrkINKPLIIAANK 223
                                       4444554433333355666666555555899****9998 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.3   0.0   7.1e-16   1.6e-12      13      59 ..     345     393 ..     330     394 .. 0.91

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 7.1e-16
                                       EETTB-HHHHHHHHSTTHHHHEEEEEECS..EEEETTSBB-SSEEEEEE CS
                               TGS  13 lprgatveDfAykIhrslakkfiyAlVnG..qrvgldhvLedgdvveIv 59 
                                       +++gat++D+Ayk+h++l+k+f+yA   +  +r g d++L+ +d+++Iv
  gi|242398500|ref|YP_002993924.1| 345 MKKGATPRDLAYKVHTDLGKSFLYAVNAKthRRIGEDYELQYNDIIKIV 393
                                       89****************************9*****************9 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.0   2.9e-10   6.5e-07       2      41 ..       2      41 ..       1      52 [. 0.91
   2 !    8.0   0.0   0.00085       1.9      97     148 ..     206     256 ..     200     263 .. 0.82

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 2.9e-10
                                      EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEE CS
                            FeoB_N  2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegk 41
                                      +v +vG+pnvGk+t+f a t ++ +++N+p +t++ + g 
  gi|242398500|ref|YP_002993924.1|  2 EVGIVGKPNVGKSTFFAAATLVDVQIANYPFTTIDANIGV 41
                                      6889*******************************98876 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00085
                                       HHHHHHHTTSSEEEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTTTBT CS
                            FeoB_N  97 LtlqllelgvpvvlalnmideaekkgieidlkkLsekLgvpvvktsakkkeg 148
                                       ++ +l  +++p+++a n+ d+a+++ ie  +k+  +k g  v++tsa+ +  
  gi|242398500|ref|YP_002993924.1| 206 FVRELRKINKPLIIAANKADAASDEDIERIIKE-GKKRGYTVIPTSAAAELT 256
                                       6778999*******************9977776.455699999999987655 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 ?   14.1   0.0   1.5e-05     0.034      41      94 ..     199     258 ..     180     265 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.5e-05
                      MMR_HSR1_Xtn  41 tvDdlidvieg.nrvYipclyvlNKiDlisleeldelare.....pnsvviSaekelnld 94 
                                       + +dl +++ +  +  +p +++ NK+D++s+e+++++ +e       ++++Sa+ el l 
  gi|242398500|ref|YP_002993924.1| 199 SDNDLFNFVRElRKINKPLIIAANKADAASDEDIERIIKEgkkrgYTVIPTSAAAELTLR 258
                                       5678888887735578999******************99766766689999999998875 PP

>> PrpR_N  Propionate catabolism activator
   #    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      74     106 ..       3      36 ..       2      55 .. 0.77
   2 ?   12.4   0.0   3.9e-05     0.088      42     123 ..     164     247 ..     159     266 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.48
                            PrpR_N  74 ialvgfeniikglkt.lselldldieiytinsee 106
                                       +++vg +n+ k++    + l+d++i  y++++ +
  gi|242398500|ref|YP_002993924.1|   3 VGIVGKPNVGKSTFFaAATLVDVQIANYPFTTID 36 
                                       7999999987776651455569999999999876 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 3.9e-05
                            PrpR_N  42 lrkhvsvPVveikvsgyDilralkqakklge..kialvgfeniikglktlselldldieiytinseeeaeaavkelk 116
                                       l+k++  ++  i vs+ D+l+al +++   +  k       n++++l+++++ l +  +     s e++e+++ke k
  gi|242398500|ref|YP_002993924.1| 164 LSKAIAEQLTGIGVSEEDVLQALHKVELSDDptKWSDNDLFNFVRELRKINKPLIIAANKADAASDEDIERIIKEGK 240
                                       667777777889*************999886235666666789********************************** PP

                            PrpR_N 117 aegvevv 123
                                       ++g++v+
  gi|242398500|ref|YP_002993924.1| 241 KRGYTVI 247
                                       *****98 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.72   1.6e+03     104     116 ..       5      17 ..       3      26 .. 0.85
   2 ?   12.8   0.0   3.8e-05     0.084      30      89 ..     198     256 ..     189     263 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.72
                                       EECSTTSSHHHHH CS
                       RsgA_GTPase 104 lvGqSGvGKStLi 116
                                       +vG+  vGKSt+ 
  gi|242398500|ref|YP_002993924.1|   5 IVGKPNVGKSTFF 17 
                                       689999*****86 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 3.8e-05
                                       --HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTT CS
                       RsgA_GTPase  30 lslnlldrfLvlaeekgiepvivlnKiDlleeeeeleelkeelealgyevllvsaktkeg 89 
                                        s n l  f+ ++ + + +++i+ nK+D +++e+ +e++ +e ++ gy+v+ +sa  + +
  gi|242398500|ref|YP_002993924.1| 198 WSDNDLFNFVRELRKINKPLIIAANKADAASDED-IERIIKEGKKRGYTVIPTSAAAELT 256
                                       56667777788888888899**************.******************9986655 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 ?    9.3   0.0   0.00058       1.3      15      42 ..     343     370 ..     335     376 .. 0.86
   2 ?    1.5   0.1      0.16   3.5e+02      61      81 ..     372     392 ..     369     394 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00058
                     YchF-GTPase_C  15 WtikkgttapqaAgviHsDfekgFirae 42 
                                       + +kkg+t  + A ++H+D+ k F+ a 
  gi|242398500|ref|YP_002993924.1| 343 FLMKKGATPRDLAYKVHTDLGKSFLYAV 370
                                       56899*******************9885 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.16
                     YchF-GTPase_C  61 agklrlegkdyvvqdgDiilf 81 
                                       a++ r+ g dy +q +Dii +
  gi|242398500|ref|YP_002993924.1| 372 AKTHRRIGEDYELQYNDIIKI 392
                                       5667899***********976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      588  (0.032796); 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: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2644.45
//
Query:       gi|242398501|ref|YP_002993925.1|  [L=360]
Description: leucyl aminopeptidase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-11   44.0   0.6    9.6e-11   41.1   0.2    2.4  2  Peptidase_M29  Thermophilic metalloprotease (M29)


Domain annotation for each model (and alignments):
>> Peptidase_M29  Thermophilic metalloprotease (M29)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0     0.017     3e+02      11      98 ..      18     106 ..      15     132 .. 0.73
   2 !   41.1   0.2   5.3e-15   9.6e-11     185     352 ..     151     327 ..     145     357 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.017
                                       HHH.HTTT---TT-EEEEEE.ETT-HHHHHHHHHHHHHTT-SEEEEEEE-HHHHHHHHHHS-TT-TT---HHHHHHH CS
                     Peptidase_M29  11 llv.kvglnlqkgqevvina.evealelarlvaeeaykagakkvvvewsdeeltkerlknaseeqleevpeweaekl 85 
                                       ++v k  l+++ g+e++i + + e  e    ++++a k +a++ +v +++ + t  + + a  e++++ p++ ++  
  gi|242398501|ref|YP_002993925.1|  18 VIVmKDVLSVEDGEEILIITnPGEVFEISLSLFNAAKKFKARPTIV-VQETKGTLDYAERAVIEAIKSEPDIVISIS 93 
                                       5543677888888877665515567788888888888888888888.777777888888888888888888887777 PP

                                       HHHHHTT-EEEEE CS
                     Peptidase_M29  86 eelveegaarlsi 98 
                                       e+ + + a  ++i
  gi|242398501|ref|YP_002993925.1|  94 EQKLGKDAHGINI 106
                                       7777666665554 PP

  == domain 2  score: 41.1 bits;  conditional E-value: 5.3e-15
                                       HHHHHHHHHHHHHHHHHTT-SEEEEE.ETTEEEEEEE-TTB--EESS---SSS----SBSS---EEE-EEEEEEEEE CS
                     Peptidase_M29 185 WeehnaelekrakyLnelkfkeLhyksspgtdLtvglaeghiWiggaektkkgiefvaNiPteevftaPdkrgvnGv 261
                                       + +  +e++ ++k+Ln+   ke+h+++++gtdL v++ ++++ ++ +++  ++     NiP +evf++P   + +Gv
  gi|242398501|ref|YP_002993925.1| 151 YAKLRDEVTIISKILNH--GKEIHITTEKGTDLMVDI-RNRKPLKDDGDF-RKAGSGGNIPAGEVFISPTVGKSEGV 223
                                       6677888888999***9..9*****************.666666666664.5777789******************* PP

                                       EE-SS-EEETTEEE...BS-EEEEETTEEEEEE-SB-HHHHHHHT.............TSSSGGGSEEEEE---TTS CS
                     Peptidase_M29 262 vratkPlsysGnli...egirltFedGkvveakAekGeevLkkll.............etDegarrLGEvALvpnds 322
                                       ++++  l ++G+ i   + +++ +e+G   +++  +  + L+k +             e  +++ +LGEv ++ n  
  gi|242398501|ref|YP_002993925.1| 224 IVFDGTLGLGGENIipeKPVKVYVENGFLSRIEGGEAAKKLEKAIkdaekmaieigklEEAKNSWHLGEVGIGLNP- 299
                                       **********9888666679999999999999766666666666533333333333335567889*********98. PP

                                       HHHHHT-----HHHHHT..TS-EEEEE---GG CS
                     Peptidase_M29 323 pisqsgilfyntLfDen..ascHlAlGaaype 352
                                         +q   +  + L De+   ++H+A+Ga y +
  gi|242398501|ref|YP_002993925.1| 300 -KAQ---MSGKLLEDEKirKTIHIAIGANYDN 327
                                       .344...7889999****9*********9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2287.43
//
Query:       gi|242398502|ref|YP_002993926.1|  [L=76]
Description: snRNP Sm-like protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-20   71.2   0.1    4.5e-20   71.1   0.1    1.0  1  LSM       LSM domain
  ------ inclusion threshold ------
      0.014   15.5   0.0      0.015   15.5   0.0    1.1  1  SM-ATX    Ataxin 2 SM domain


Domain annotation for each model (and alignments):
>> LSM  LSM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.1   0.1   5.1e-24   4.5e-20       2      67 .]       8      72 ..       7      72 .. 0.96

  Alignments for each domain:
  == domain 1  score: 71.1 bits;  conditional E-value: 5.1e-24
                                      HHHHTTTSEEEEEETTSEEEEEEEEEEETTSEEEEEEEEEEETTETEEEEEEEEEEEGGGEEEEEE CS
                               LSM  2 flkklinkkvtvelkngrelrGtLkgfDqfmNlvLedveetlkdkkekrklglvliRGnnivlisl 67
                                       ++k+++k+v+v+lk g e+rG+L+g+D ++N+vL d++ + +++  k+++g+++iRG+n++ is+
  gi|242398502|ref|YP_002993926.1|  8 VIHKSLDKEVLVILKRGAEYRGKLIGYDIHLNVVLADAQLIENGE-PKKSYGKIVIRGDNVLAISP 72
                                      5799**************************************999.****************9986 PP

>> SM-ATX  Ataxin 2 SM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.0   1.6e-06     0.015      13      59 ..      14      56 ..       2      73 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.6e-06
                                      TSEEEEEETTS-EEEEEEEEE-T..T--EEEEEEEETTS........ CS
                            SM-ATX 13 GkevevtvknGevyeGifstvslekdfsvvLkmarkvkkansksssp 59
                                       kev v +k G+ y+G + +++    ++vvL  a+++++  ++++++
  gi|242398502|ref|YP_002993926.1| 14 DKEVLVILKRGAEYRGKLIGYDI--HLNVVLADAQLIEN--GEPKKS 56
                                      57999******************..**************..333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       245  (0.013665); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 487.20
//
Query:       gi|242398503|ref|YP_002993927.1|  [L=70]
Description: 50S ribosomal protein L37e [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       155  (0.00864521); expected 358.6 (0.02)
Passed bias filter:                      147  (0.00819901); 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: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 486.92
//
Query:       gi|242398504|ref|YP_002993928.1|  [L=335]
Description: hypothetical protein TSIB_0513 [Thermococcus sibiricus MM 739]
Scores for complete 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   28.3   0.0      3e-05   23.9   0.0    2.0  1  NMT1_2     NMT1-like family
     0.0016   17.9   0.0      0.095   12.1   0.0    2.3  1  SBP_bac_3  Bacterial extracellular solute-binding proteins, f
     0.0073   16.6   0.4       0.47   10.8   0.1    2.7  3  DUF5603    Domain of unknown function (DUF5603)
  ------ inclusion threshold ------
      0.037   14.0   0.0       0.19   11.6   0.0    1.9  2  NMT1       NMT1/THI5 like
       0.13   11.9   0.0       0.36   10.5   0.0    1.7  1  GntR       Bacterial regulatory proteins, gntR family
       0.18   11.1   0.1        1.2    8.4   0.1    2.3  2  DUF3834    Protein of unknown function (DUF3834)
       0.21   11.1   0.0       0.83    9.2   0.0    1.9  2  OpuAC      Substrate binding domain of ABC-type glycine betai


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 !   23.9   0.0   1.2e-08     3e-05      39     243 ..     101     278 ..      70     285 .. 0.73

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 1.2e-08
                            NMT1_2  39 lekqaswaelrdkllagelDaahv.ltpapllidlGiggakadmkvlaslnlnGqaitlsnklkdkkvsdakalkdl 114
                                       ++   s+ el ++l  g++D+a   l  ++l + l++     ++k++a     G ++++++           +l   
  gi|242398504|ref|YP_002993928.1| 101 VVVYDSALELTNALSLGKVDLACSpLITQVLFALLTK-----NLKIAAGCGFGGGGVVVRE-----------NL--- 158
                                       5555555555555555555555554444444444444.....5555555555555555543...........22... PP

                            NMT1_2 115 vakkkaskplkiavtfpgsthdlllrywLaaaGldpeadvklvvvpp.pqmvanlkagtidgfcvgePwnaqavaeg 190
                                             +k++ki+  ++ st +++l+ +L++++l     v++v  +  +++v+++ +g+id++   eP+ + +  e+
  gi|242398504|ref|YP_002993928.1| 159 ------KKGIKIGS-SELSTMETMLKLFLEKHNLIG--RVQVVYFKKpEEIVKAFLKGEIDALSIWEPYLSEL--EK 224
                                       ......2689***9.9*****************987..788888765499*******************6665..78 PP

                            NMT1_2 191 iGvtaltsqelwkdhPekvlgvredfveknpntaralvkalleAtkwlda.kke 243
                                       +G++     + +   P++ lgv+ +f+  n+++  ++++   e t+ l++ ++e
  gi|242398504|ref|YP_002993928.1| 225 LGFKTYRYVQTFGLYPCCTLGVNYEFLRLNKELFYKFIESYKENTEKLEQrREE 278
                                       888877777777779******************999999999988888864433 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 !   12.1   0.0   3.7e-05     0.095      40     165 ..      99     221 ..      89     236 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.7e-05
                                       EEEEE-.SGGGHHHHHHTTSSSEEESSEB--HHH....HTTEEEESESEEEEEEEEEEETTSHGTCCHSSCGCGTTS CS
                                       xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SBP_bac_3  40 vefvpv.swdelipalksgkvDiaiaaititpeR....eekvdFsqpyfsagqvllvrkkdaskissiksladLkgk 111
                                       v +v + s  el +al  gkvD+a++++ it+       +++         g +++vr++       +k     kg 
  gi|242398504|ref|YP_002993928.1|  99 VRVVVYdSALELTNALSLGKVDLACSPL-ITQVLfallTKNLKIAAGCGFGGGGVVVREN-------LK-----KGI 162
                                       4455555666677777777777777776.4433322225666666666667777777732.......55.....677 PP

                                       EEEEETTSHHHHHHHHHHHC.....TSEEEEESSHHHHHHHHHTTSSSEEEEEHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SBP_bac_3 112 kvgvqagstaeellkeelkk.....gaeivefdtleealqaLkngrvdavvadspvlay 165
                                       k+g +  st e++lk  l+k      +++v+f+  ee ++a  +g++da+   +p l +
  gi|242398504|ref|YP_002993928.1| 163 KIGSSELSTMETMLKLFLEKhnligRVQVVYFKKPEEIVKAFLKGEIDALSIWEPYLSE 221
                                       8**********9988755557898999999*******************9888887765 PP

>> DUF5603  Domain of unknown function (DUF5603)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.043   1.1e+02      24     100 ..      37     120 ..      24     123 .. 0.73
   2 !   10.8   0.1   0.00018      0.47      69     103 ..     179     213 ..     152     215 .. 0.85
   3 ?   -2.7   0.0         3   7.6e+03      27      38 ..     265     274 ..     239     286 .. 0.47

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.043
                                       -EE-TTHHHH...HHCTSSSEEEES..SSEEEE--SHH.....HHHHHHHHHHHHHHTTSSE..EEEESSHHHHHHH CS
                           DUF5603  24 veedkekeeklkdeelgkiafvlvgkneksykiygsle.....eqkkvskvldklslegkie..lvyygekeealrd 93 
                                        +e+ e++ k+    lgk ++ +   +e  + i g+l             +l+  +legk++  +v y    e  + 
  gi|242398504|ref|YP_002993928.1|  37 AIESLERDRKILRRGLGKKTYRVWIVEEAPFPIEGTLRlgllkALEYPHALLSAKDLEGKYDvrVVVYDSALELTNA 113
                                       577788888888888998888777778888999988752111123334578999999**997335888888888888 PP

                                       HHTTS-S CS
                           DUF5603  94 lekgkid 100
                                       l+ gk+d
  gi|242398504|ref|YP_002993928.1| 114 LSLGKVD 120
                                       8888887 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00018
                                       HHHHHHHTTSSEEEEESSHHHHHHHHHTTS-SEEE CS
                           DUF5603  69 vldklslegkielvyygekeealrdlekgkidylf 103
                                        l+k +l g++++vy+ + ee  + + kg+id l 
  gi|242398504|ref|YP_002993928.1| 179 FLEKHNLIGRVQVVYFKKPEEIVKAFLKGEIDALS 213
                                       5899****************************875 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 3
                                       -TTHHHH...HH CS
                           DUF5603  27 dkekeeklkdee 38 
                                        ke+ ekl  e+
  gi|242398504|ref|YP_002993928.1| 265 YKENTEKL--EQ 274
                                       23333332..22 PP

>> NMT1  NMT1/THI5 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.35   8.9e+02      22      51 ..      98     127 ..      90     142 .. 0.77
   2 ?   11.6   0.0   7.5e-05      0.19      92     211 ..     160     274 ..     157     279 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.35
                                       EEEEE--SSTTHHHHHHHCTS-SEEEE-HH CS
                              NMT1  22 dVeivepadpsdatelvasgkadfgvsyqe 51 
                                       dV++v +    + t+++  gk+d+++s  +
  gi|242398504|ref|YP_002993928.1|  98 DVRVVVYDSALELTNALSLGKVDLACSPLI 127
                                       677777777778888888899999888755 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 7.5e-05
                                       TTSEEEE-S-TTHHHHHHHHHHHTT--GGG-EEEE-.TT-HHH.HHHCTSSSEEECEETTTHHHHHHHTT--EE.EE CS
                              NMT1  92 kGkrigyvgspfekallkallakdggdpsdvtlvnvggtslak.alltgkvDaaiggyenwegvelesegkelr.if 166
                                       kG +ig ++ +  +++lk +l+k+++    v++v  +  + +  a+l+g++Da       we +  e+e+   + + 
  gi|242398504|ref|YP_002993928.1| 160 KGIKIGSSELSTMETMLKLFLEKHNL-IGRVQVVYFKKPEEIVkAFLKGEIDALS----IWEPYLSELEKLGFKtYR 231
                                       688999999999*************9.88899988887766555********998....455555555555333055 PP

                                       -GGGTT-----SEEEEEEHHHHHH-HHHHHHHHHHHHHHHHHHHH CS
                              NMT1 167 aladlgvpdyyslvlitnekllkenpelvkkFlrAlkkGyeyala 211
                                       +++ +g   y   +l +n ++l+ n+el+ kF++ +k+ +e + +
  gi|242398504|ref|YP_002993928.1| 232 YVQTFGL--YPCCTLGVNYEFLRLNKELFYKFIESYKENTEKLEQ 274
                                       6777776..8888999******************99988776655 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00014      0.36      34      57 ..      27      50 ..      25      53 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00014
                                      HTS-HHHHHHHHHHHHHTTSEEEE CS
                              GntR 34 fgVsrttvReALrrLeaeglverr 57
                                      ++ sr+t+ eA+  Le++  + rr
  gi|242398504|ref|YP_002993928.1| 27 LNYSRSTIAEAIESLERDRKILRR 50
                                      678***************999987 PP

>> DUF3834  Protein of unknown function (DUF3834)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.25   6.4e+02      95     146 ..      99     146 ..      90     175 .. 0.68
   2 ?    8.4   0.1   0.00045       1.2      83     174 ..     175     279 ..     152     296 .. 0.64

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.25
                           DUF3834  95 aevvyaddpeevlkllnegevdsavvaselkkgeafedllkklgvyvpGsCg 146
                                         vv +d   e+ ++l  g+vd  +  s+l +  +f+ l k  ++ ++  Cg
  gi|242398504|ref|YP_002993928.1|  99 VRVVVYDSALELTNALSLGKVD--LACSPLITQVLFALLTK--NLKIAAGCG 146
                                       4577778999999999999994..55567777777776666..444444566 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00045
                           DUF3834  83 llrilldlkki..kaevvyaddpeevlkllnegevdsavva....sel.kkgeafedllkklgvyvpGsCgaavk.. 150
                                       +l++ l+++++  + +vvy  +pee++k+  +ge+d+  +     sel k g     +++  g+y    C   v+  
  gi|242398504|ref|YP_002993928.1| 175 MLKLFLEKHNLigRVQVVYFKKPEEIVKAFLKGEIDALSIWepylSELeKLGFKTYRYVQTFGLYPC--CTLGVNye 249
                                       6677777777645789*******************99776521112221234444455555555533..54444311 PP

                           DUF3834 151 .....en.eeefidaYeeGIelikedpeea 174
                                            ++ + +fi+ Y+e  e+++++ eea
  gi|242398504|ref|YP_002993928.1| 250 flrlnKElFYKFIESYKENTEKLEQRREEA 279
                                       111112334566777777777776666666 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 ?   -1.2   0.0      0.49   1.2e+03      29      55 ..      97     123 ..      90     149 .. 0.78
   2 ?    9.2   0.0   0.00032      0.83      12      64 ..     168     221 ..     160     280 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.49
                                       EEEEEEEEESHHHHHHHHHTTSSSEEE CS
                             OpuAC  29 ykveltnlgstavlfaalasGdiDvyp 55 
                                       y+v+++  +s   l +al+ G++D+++
  gi|242398504|ref|YP_002993928.1|  97 YDVRVVVYDSALELTNALSLGKVDLAC 123
                                       566666677766689999999999987 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00032
                                       HHHHHHHHHHHHHHHTTE..EEEEEEEESHHHHHHHHHTTSSSEEEEEEHHHHHH CS
                             OpuAC  12 eqevlaeilkqllekkGy..kveltnlgstavlfaalasGdiDvypeewtgtaye 64 
                                       e   +  +lk +lek+++   v+++ + + + +++a  +G+iD++   w + ++e
  gi|242398504|ref|YP_002993928.1| 168 ELSTMETMLKLFLEKHNLigRVQVVYFKKPEEIVKAFLKGEIDALS-IWEPYLSE 221
                                       555678899*******7669**************************.****9843 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1026  (0.0572257); expected 358.6 (0.02)
Passed bias filter:                      793  (0.04423); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.48
# Mc/sec: 2091.34
//
Query:       gi|242398505|ref|YP_002993929.1|  [L=454]
Description: Sodium-driven multidrug efflux pump protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-71  239.4  25.8    4.3e-38  130.5  10.7    3.1  4  MatE             MatE
    1.8e-09   36.8  23.2    2.4e-07   29.7  11.3    3.1  3  MurJ             Lipid II flippase MurJ
    2.4e-06   27.7   7.8    2.4e-06   27.7   7.8    4.2  4  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai
    9.9e-06   25.0   9.9    1.7e-05   24.2   2.6    3.0  3  Polysacc_synt_3  Polysaccharide biosynthesis protein
  ------ inclusion threshold ------
      0.018   15.2   0.6      0.018   15.2   0.6    5.1  5  VirB3            Type IV secretory pathway, VirB3-like protei


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 !  130.5  10.7   1.2e-41   4.3e-38       1     160 [.      15     174 ..      15     175 .. 1.00
   2 ?   -0.9   0.2      0.32   1.1e+03      78      91 ..     197     210 ..     188     230 .. 0.61
   3 !  122.9   7.0   2.7e-39   9.5e-36       1     161 []     239     405 ..     239     405 .. 0.99
   4 ?   -4.0   0.5       2.8   9.9e+03      75      93 ..     424     442 ..     416     444 .. 0.65

  Alignments for each domain:
  == domain 1  score: 130.5 bits;  conditional E-value: 1.2e-41
                              MatE   1 PialenllesllslidtllvgrlgskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqgli 77 
                                       P++l+n+ ++l++l+d+++vg+lgs a+A+v+++ +++++++ +++++st++ +lv++++Gak+ ++a++al q+++
  gi|242398505|ref|YP_002993929.1|  15 PAILANIGQTLVNLVDMVMVGQLGSLAIASVGLGGQFSWFMMPLMFAISTGTLALVARFVGAKDIDMAEKALEQSVY 91 
                                       9**************************************************************************** PP

                              MatE  78 lllllsliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislislll 154
                                       l++++s++++l++++f ++ l++++++e+v++++  y+r+ +l++p++++++++ ++lrgag+tk+p+ ++l+++  
  gi|242398505|ref|YP_002993929.1|  92 LAFFMSIPVMLFGIFFGDDALKIMGASEDVIKIGYSYIRMFFLFYPVNFMSFAAFSALRGAGDTKTPMKLTLLTNGA 168
                                       ***************************************************************************** PP

                              MatE 155 niplny 160
                                       n++lny
  gi|242398505|ref|YP_002993929.1| 169 NVLLNY 174
                                       *****9 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.32
                              MatE  78 lllllsliiallvl 91 
                                       l++l+++i+ l+++
  gi|242398505|ref|YP_002993929.1| 197 LSILIAFIVGLVLF 210
                                       44444444444433 PP

  == domain 3  score: 122.9 bits;  conditional E-value: 2.7e-39
                              MatE   1 PialenllesllslidtllvgrlgskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqgli 77 
                                       P+ +e +++s+++++ +++v r+g+ alAa++++l++ s+ +++++g+++a+++lvgq+lG++n+++a+++++ +l+
  gi|242398505|ref|YP_002993929.1| 239 PATVERVIFSFYNFLYISIVTRFGTIALAAHQVGLRVESIAYMPAFGFNVAASALVGQSLGEENPEKAEKVVYEALK 315
                                       899************************************************************************** PP

                              MatE  78 lllllsliiallvllfseqilslftqdee.....vlelakrylrililgipalalqlvlsgilrgagktkvplyisl 149
                                       ++ +++ i+a+++++f+++++  f ++ +     vl la+ yl i+++++++l+ ++vlsg lrgag+tk p+y+++
  gi|242398505|ref|YP_002993929.1| 316 MVSVFMGIMAIILVVFPKYLVMPFVTKSDpnyaeVLRLASIYLIIVGISEIPLGWTFVLSGSLRGAGDTKSPMYVTA 392
                                       *************************999999********************************************** PP

                              MatE 150 isl.llniplnyl 161
                                       is  l++i+ +y+
  gi|242398505|ref|YP_002993929.1| 393 ISKlLFRIIPSYI 405
                                       ***9*****9997 PP

  == domain 4  score: -4.0 bits;  conditional E-value: 2.8
                              MatE  75 glilllllsliiallvllf 93 
                                       + +l++ l  +++++ ++f
  gi|242398505|ref|YP_002993929.1| 424 AAWLAMTLETFTTAAFFWF 442
                                       5566666666666666666 PP

>> MurJ  Lipid II flippase MurJ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7  11.3   6.6e-11   2.4e-07     198     405 ..       7     215 ..       1     261 [. 0.77
   2 !   11.3   3.1   2.7e-05     0.096      47     153 ..     301     416 ..     277     435 .. 0.69
   3 ?    1.7   0.4     0.021        75     349     402 ..     382     446 ..     366     453 .. 0.73

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 6.6e-11
                              MurJ 198 kkflklllptllgvsvsqlnllvdtalAsflaegsvsilayadri..lqlPlglfgvsistvlLPrlSrsakekded 272
                                       +++ +l+ p++l++  + l  lvd+++   l + +++ +  +     +++Pl +   +ist  L+ ++r + +kd d
  gi|242398505|ref|YP_002993929.1|   7 RRLWALAWPAILANIGQTLVNLVDMVMVGQLGSLAIASVGLGGQFswFMMPL-M--FAISTGTLALVARFVGAKDID 80 
                                       6777888888888888888888888777776666666665554331133343.3..4677888999*********** PP

                              MurJ 273 evrdllsqairltllllipvsfgllvlskpivsllferGnFseedveatae.vLaayalgLipyalvklllrvfYA. 347
                                        +++ l+q++ l ++++ipv  + +++++ +++++        edv ++++  ++++    ++y ++ +  ++f A 
  gi|242398505|ref|YP_002993929.1|  81 MAEKALEQSVYLAFFMSIPVMLFGIFFGDDALKIMG-----ASEDVIKIGYsYIRMFF---LFYPVNFMSFAAFSAl 149
                                       **********************************97.....34455544441455653...4555555555555552 PP

                              MurJ 348 ..redtktPvkislislvlnills......llllpplgvvglalatslsaliglvllyvllrkrlk 405
                                          +dtktP+k++l++   n+ll+       ++lp+l+vvg ala++ls li +++ +vl  k + 
  gi|242398505|ref|YP_002993929.1| 150 rgAGDTKTPMKLTLLTNGANVLLNyglifgNFGLPRLEVVGAALASGLSILIAFIVGLVLFLKGAL 215
                                       1157********************9988777889*********************99988777554 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 2.7e-05
                              MurJ  47 kdeekaaefvrkvltllilvlllvtligilaapllirllatgf...deetlelavsllril....lpylllvslsav 116
                                       ++ eka+++v + l +++++++++++i ++++++l++ + t++    +e l+la+  l i+    +p  +   ls+ 
  gi|242398505|ref|YP_002993929.1| 301 ENPEKAEKVVYEALKMVSVFMGIMAIILVVFPKYLVMPFVTKSdpnYAEVLRLASIYLIIVgiseIPLGWTFVLSGS 377
                                       6899*************************************995555566666666655554444566666666666 PP

                              MurJ 117 fgavLnarkkFfapafsPvllNv..svIltllllanklg 153
                                       + +   ++    + a+s +l+ +  s Il+ +++ + ++
  gi|242398505|ref|YP_002993929.1| 378 LRGAGDTKSPMYVTAISKLLFRIipSYILGFGFSFWMIH 416
                                       666666666666666666666664556666666666666 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.021
                              MurJ 349 edtktPvkislislvlnills...........llllpplgvvglalatslsaliglvllyvllrk 402
                                       +dtk+P++++ is  l  ++            ++ +  +gvv+  la +l     +++++++ ++
  gi|242398505|ref|YP_002993929.1| 382 GDTKSPMYVTAISKLLFRIIPsyilgfgfsfwMIHIEGMGVVAAWLAMTLETFTTAAFFWFIFKR 446
                                       79999999999986554433335555666577777778888888888888888888888888776 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 ?   -3.7   4.7       3.3   1.2e+04      90     119 ..      36      62 ..       7     108 .. 0.54
   2 !   27.7   7.8   6.7e-10   2.4e-06       2      86 ..     129     228 ..     128     275 .. 0.75
   3 ?   -1.2   0.5      0.53   1.9e+03      97     110 ..     317     330 ..     306     343 .. 0.55
   4 !   14.6   3.4   6.9e-06     0.025       1      80 [.     357     446 ..     357     453 .. 0.70

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 3.3
                   Polysacc_synt_C  90 rllkpllaalvmgivvylllllllglllla 119
                                       +l  +++a++++g+    + +++++l +  
  gi|242398505|ref|YP_002993929.1|  36 QLGSLAIASVGLGGQ---FSWFMMPLMFAI 62 
                                       334444444444444...222222222211 PP

  == domain 2  score: 27.7 bits;  conditional E-value: 6.7e-10
                   Polysacc_synt_C   2 LailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllli......plfgivGaaiatvlallvvavl 72 
                                       ++++ l  ++ ++s    s L g g +k+++k ++++  ++++ln+ li      p++ +vGaa+a+ l+ l+++++
  gi|242398505|ref|YP_002993929.1| 129 IRMFFLFYPVNFMSFAAFSALRGAGDTKTPMKLTLLTNGANVLLNYGLIfgnfglPRLEVVGAALASGLSILIAFIV 205
                                       57788888999999999********************************97777777777**************999 PP

                   Polysacc_synt_C  73 nlyalrr.llgikl........e 86 
                                        l++  +  l +++        e
  gi|242398505|ref|YP_002993929.1| 206 GLVLFLKgALILRFrpsfkpdwE 228
                                       96554442555555544444443 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.53
                   Polysacc_synt_C  97 aalvmgivvyllll 110
                                       ++++mgi++++l+ 
  gi|242398505|ref|YP_002993929.1| 317 VSVFMGIMAIILVV 330
                                       34444444332222 PP

  == domain 4  score: 14.6 bits;  conditional E-value: 6.9e-06
                   Polysacc_synt_C   1 vLailalsiiflslstvlssiLqglgrqkialkalvigal.........vklilnllli..plfgivGaaiatvlal 66 
                                       +L i+ +s i+l+++ vls+ L g g +k ++++++i+ l         + +++++++i    +g+v a +a++l  
  gi|242398505|ref|YP_002993929.1| 357 YLIIVGISEIPLGWTFVLSGSLRGAGDTKSPMYVTAISKLlfriipsyiLGFGFSFWMIhiEGMGVVAAWLAMTLET 433
                                       5889999****************************999776555555555555555555323345566666666666 PP

                   Polysacc_synt_C  67 lvvavlnlyalrrl 80 
                                       +++a++ ++ + ++
  gi|242398505|ref|YP_002993929.1| 434 FTTAAFFWF-IFKR 446
                                       666666554.4444 PP

>> Polysacc_synt_3  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.0   0.2    0.0066        24     176     283 ..       8     115 ..       2     119 .. 0.74
   2 !   24.2   2.6   4.8e-09   1.7e-05     142     281 ..     199     337 ..     186     344 .. 0.86
   3 ?   -0.9   0.0      0.21   7.6e+02      78     101 ..     344     367 ..     339     370 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.0066
                   Polysacc_synt_3 176 elfsfglklllsnllnylarnldnlliGkvlssaaLGlYsvakrlaslpvaeitsviakVlfPalSrlq..ddkkkl 250
                                       +l +  + ++l+n+ ++l++ +d +++G++ +s a++ +  + +++ +++  +  +i++ ++  ++r+   +d +  
  gi|242398505|ref|YP_002993929.1|   8 RLWALAWPAILANIGQTLVNLVDMVMVGQL-GSLAIASVGLGGQFSWFMM-PLMFAISTGTLALVARFVgaKDIDMA 82 
                                       677888999999***************985.6666777777777654433.44455566666666665411566788 PP

                   Polysacc_synt_3 251 relylkvlrlialivlPiavglavvaellvkvl 283
                                       ++++++++ l  ++++P++ + +++ + ++k++
  gi|242398505|ref|YP_002993929.1|  83 EKALEQSVYLAFFMSIPVMLFGIFFGDDALKIM 115
                                       8899999999999999**999999998887765 PP

  == domain 2  score: 24.2 bits;  conditional E-value: 4.8e-09
                   Polysacc_synt_3 142 LvigtllssllslvllwlaskwrprlkfslkslkelfsfglklllsnllnylarnldnlliGkvlssaaLGlYsvak 218
                                       ++i  ++  l+ ++   l++++rp++k +++++k+++++g+ ++++ ++  +++ l+  ++ + +++ aL+  +v+ 
  gi|242398505|ref|YP_002993929.1| 199 ILIAFIVG-LVLFLKGALILRFRPSFKPDWEVIKRILRIGVPATVERVIFSFYNFLYISIVTR-FGTIALAAHQVGL 273
                                       55555554.445555677899********************************9999999876.799********** PP

                   Polysacc_synt_3 219 rlasl.pvaeitsviakVlfPalSrlqddkkklrelylkvlrlialivlPiavglavvaellvk 281
                                       r+ s+ ++  +   +a+ ++   S   ++++k +++++++l+++++++  +a++l+v+ ++lv 
  gi|242398505|ref|YP_002993929.1| 274 RVESIaYMPAFGFNVAASALVGQSLGEENPEKAEKVVYEALKMVSVFMGIMAIILVVFPKYLVM 337
                                       **98636789999999999999**************************9999999999999886 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.21
                   Polysacc_synt_3  78 qpelvtvlrvlalvlilsglssvq 101
                                       +p+ ++vlr++++ li+ g+s ++
  gi|242398505|ref|YP_002993929.1| 344 DPNYAEVLRLASIYLIIVGISEIP 367
                                       588899*************99886 PP

>> VirB3  Type IV secretory pathway, VirB3-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   1.0       0.1   3.6e+02      36      64 ..      54      82 ..      29      87 .. 0.65
   2 ?   -2.0   0.2       1.2   4.4e+03      15      28 ..      95     108 ..      90     145 .. 0.67
   3 ?    1.2   0.9      0.12   4.2e+02      16      51 ..     181     215 ..     179     221 .. 0.60
   4 ?   15.2   0.6   5.1e-06     0.018      30      68 ..     316     352 ..     279     357 .. 0.82
   5 ?    3.1   1.4     0.032   1.2e+02      27      73 ..     400     445 ..     385     453 .. 0.68

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.1
                             VirB3 36 vglslwillllvplhlvlrliakrDpqmf 64
                                      +   l++++   +l lv+r++ ++D +m 
  gi|242398505|ref|YP_002993929.1| 54 FMMPLMFAISTGTLALVARFVGAKDIDMA 82
                                      33334444456688999999999999886 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.2
                             VirB3  15 llGvplelvllnll 28 
                                       ++ +p++l+ + ++
  gi|242398505|ref|YP_002993929.1|  95 FMSIPVMLFGIFFG 108
                                       66666666666554 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.12
                             VirB3  16 lGvplelvllnllvsvilflvglslwillllvplhl 51 
                                       +G+p+  v+ ++l+s++ +l+++ + ++ l++   l
  gi|242398505|ref|YP_002993929.1| 181 FGLPRLEVVGAALASGLSILIAFIVGLV-LFLKGAL 215
                                       5777777777777777777755544444.4444444 PP

  == domain 4  score: 15.2 bits;  conditional E-value: 5.1e-06
                             VirB3  30 svilflvglslwillllvplhlvlrliakrDpqmfrvll 68 
                                       +v +  + + ++i+l+++p +lv+ +++k+Dp+  +vl 
  gi|242398505|ref|YP_002993929.1| 316 MVSV--FMGIMAIILVVFPKYLVMPFVTKSDPNYAEVLR 352
                                       3333..55889999999*******************994 PP

  == domain 5  score: 3.1 bits;  conditional E-value: 0.032
                             VirB3  27 llvsvilflvglslwillllvplhlvlrliakrDpqmfrvlllrlkt 73 
                                       ++ s il + g+s+w++ +  + +++++l+   +      ++  + +
  gi|242398505|ref|YP_002993929.1| 400 IIPSYILGF-GFSFWMIHIEGMGVVAAWLAMTLETFTTAAFFWFIFK 445
                                       444445555.999**99999999999999877666655555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       675  (0.0376485); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.51
# Mc/sec: 2692.30
//
Query:       gi|242398506|ref|YP_002993930.1|  [L=391]
Description: N(2),N(2)-dimethylguanosine tRNA methyltransferase [Thermococcus sibiricus MM 739]
Scores for complete 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-117  390.5   0.0   1.1e-116  390.1   0.0    1.0  1  TRM            N2,N2-dimethylguanosine tRNA methyltransferase
  ------ inclusion threshold ------
      0.023   14.5   0.0      0.046   13.5   0.0    1.5  1  Met_10         Met-10+ like-protein
      0.075   12.7   0.0       0.15   11.7   0.0    1.4  1  Cons_hypoth95  Conserved hypothetical protein 95


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 !  390.1   0.0  1.9e-120  1.1e-116      15     372 ..      34     384 ..      21     388 .. 0.91

  Alignments for each domain:
  == domain 1  score: 390.1 bits;  conditional E-value: 1.9e-120
                                       -TT--SS--GGGHHHHHHHHHH...HHHHHHHH-S-EEEEESS-TTSHHHHHHHHH-S-EEEEEEE-S-HHHHHHHH CS
                               TRM  15 skkeeVFYNPvqefnRDlsvlvirqlellkkklgekikvldaLsasGlRaiRfalEvpgvkevlaNDisekAvelik 91 
                                       + +++VFYNP+++ nRDlsvlv   l++l++k     kvldaLsa+G+R+iR+alE ++++e+++NDi++ A eli 
  gi|242398506|ref|YP_002993930.1|  34 Y-DAPVFYNPIMALNRDLSVLV---LKALGSK-----KVLDALSATGVRGIRYALE-TEAEEAWLNDINPSAFELII 100
                                       3.47******************...8888999.....8******************.88999*************** PP

                                       HHHHHTT--..............GGEEEE-S-HHHHHC--SS-EEEEEE--SS--GGGHHHHHHHEEEEEEEEEEE- CS
                               TRM  92 eNvklneve..............eivvineddAnvllaekkkrfdviDlDPfGspapfldsavqsvkekglLlvTaT 154
                                       +N + n  e                + + ++dAn+l++ek ++fd+iDlDPfGsp++fldsa++svk+kg +++TaT
  gi|242398506|ref|YP_002993930.1| 101 KNLENNFGEkpileremaiitreRKIIATNKDANLLMTEKFRYFDFIDLDPFGSPMEFLDSALRSVKRKGTIAITAT 177
                                       **55443334555566667777534555555********************************************** PP

                                       -HHHHTTSSHHHHHHHHSSB---STTHHHHHHHHHHHHHHHHHHTTTEEEEEEEEEEETTEEEEEEEEEE-HHHHHH CS
                               TRM 155 DtavLaGaspekclrkYgavalkselcHEvalRillkavareaakYekavepllslsadfYvrvfvkvktgaakvkk 231
                                       Dta+L+Ga+ ++c+r+Y++ +l+ elcHE++lRil+++var+aakY+  +++l+++++d+Y+r+f+++k+ga++++k
  gi|242398506|ref|YP_002993930.1| 178 DTAPLCGAHSKACVRRYNSIPLRGELCHESGLRILIGTVARYAAKYDLGIKVLVAYYKDHYFRAFLQLKDGAKEGDK 254
                                       ***************************************************************************** PP

                                       HHTTEEEEEEETTT--EEEE--GGG--SB-TTT-SBEEEEEEEE-S-S--HHHHHHHHHHHCT..-TTS-HHHHHHH CS
                               TRM 232 vleklglvlhCsgClseekvkglakfkaecehcgaklhlaGPlwlgplkdkefveevleeaekekeeelkkrvkklL 308
                                       +l +lg+v++       ++++g ++   e+ ++ +kl++ GPlwlgplkd++f+e+++ + e+  e + kk+v+++L
  gi|242398506|ref|YP_002993930.1| 255 SLMNLGYVYF-------DTKNGKFE--IEKRFLPSKLNAFGPLWLGPLKDQKFIEKMILKSEE-CELAQKKKVLNFL 321
                                       **********.......67777666..79*****************************99999.58888******** PP

                                       HHHHHHHS--SS-EEHHHHHHHHT-SS---HHHHHHH....TT-EE-TTSTTEEE-SS-HHHHH CS
                               TRM 309 klikeElldaplyydlsqlasvlklsvpplkkvvsalkelgfevsrtHakpkaikTnapleavv 372
                                       +++ +E ld+p++yd+++la++ +l+v++l+++ + l+e g++vsrtH++p+aikT+ap+e+ +
  gi|242398506|ref|YP_002993930.1| 322 NTLLKE-LDEPFFYDTHALARRNSLEVRKLSEIGAILQEKGYKVSRTHFSPTAIKTDAPFEEAL 384
                                       ******.****************************************************99765 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   7.7e-06     0.046     101     171 ..      60     145 ..      36     174 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.7e-06
                                       T-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCE....EEEES-GGG---TT-EE... CS
                            Met_10 101 gevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvv....kpileDgrevireqlad... 170
                                        + V+d +   G   i  a  ++a++ + +d+nP++++++ +n++ N  ek +     +i +  r++i +++     
  gi|242398506|ref|YP_002993930.1|  60 SKKVLDALSATGVRGIRYALETEAEEAWLNDINPSAFELIIKNLENNFGEKPIlereMAIITRERKIIATNKDAnll 136
                                       568999999999999*99*99*************************9877766111123444444444433333244 PP

                                       ........E CS
                            Met_10 171 ........r 171
                                                
  gi|242398506|ref|YP_002993930.1| 137 mtekfryfD 145
                                       444443332 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   2.5e-05      0.15      39     142 ..      57     172 ..      45     181 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.5e-05
                                       CHCC-EEEETT-TTSHHHHH.HHHTT-SEEEEEES-HHHHHHHHHHHCCCT--T...........TTEEEEES-HHH CS
                     Cons_hypoth95  39 eiegarvLDlfaGsGalglE.AlSRgakkavlvekdkeavkilkenleelklee...........etaelkedalea 103
                                       ++  ++vLD  + +G+ g+  Al  +a++a l + +++a++++ +nle+   e+           + ++++ ++++a
  gi|242398506|ref|YP_002993930.1|  57 ALGSKKVLDALSATGVRGIRyALETEAEEAWLNDINPSAFELIIKNLENNFGEKpileremaiitRERKIIATNKDA 133
                                       467889*************669*************************975444457777666666445556666666 PP

                                       HCTS--SS-EEEEEEE--SSSTTCH.HHHHHHHHHTT-E CS
                     Cons_hypoth95 104 llklakkkeefdivflDPPyakellieevlelleekkll 142
                                        l  ++k ++fd++ lDP     +++  +l+++++k+ +
  gi|242398506|ref|YP_002993930.1| 134 NLLMTEKFRYFDFIDLDPFGSPMEFLDSALRSVKRKGTI 172
                                       6666789999*******8444445577888888777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); 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 0.26s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2721.26
//
Query:       gi|242398507|ref|YP_002993931.1|  [L=87]
Description: 50S ribosomal protein L35Ae [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-19   69.0   0.2    4.3e-19   68.5   0.2    1.3  1  Ribosomal_L35Ae  Ribosomal protein L35Ae
    2.9e-08   33.8   0.1    0.00032   20.9   0.1    2.1  2  RimM             RimM N-terminal domain


Domain annotation for each model (and alignments):
>> Ribosomal_L35Ae  Ribosomal protein L35Ae
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.5   0.2   4.8e-23   4.3e-19       2      94 ..       2      86 ..       1      87 [] 0.94

  Alignments for each domain:
  == domain 1  score: 68.5 bits;  conditional E-value: 4.8e-23
                                      EEEEEEEEEE--SSSSS-EEEEEEESS--SHHHHHCCTT-EE..EEE-......TTT-EEEEEEEEECTTTTEEEEEET CS
                   Ribosomal_L35Ae  2 yvkavflgykrgkrnqrentaLlkiegvkskeeaefylGkrvayvykakkkkkgskvrviwGkvtrahGnsgvvrakFk 80
                                       +k+++l+y r+k+ q++n++++k  g++ske+a+  +Gk+v   +k+       + + + Gk+tr+hG +g v+a Fk
  gi|242398507|ref|YP_002993931.1|  2 IMKGIVLSYMRSKEYQHNNHMIIKPLGIESKEQAATLIGKKVL--WKS------PSGKLLVGKITRTHGIRGEVKAIFK 72
                                      68****************************************6..566......6799********************* PP

                                      T--SSS-TT-EEEE CS
                   Ribosomal_L35Ae 81 knLppkaigarvrv 94
                                      k Lp++aig  v++
  gi|242398507|ref|YP_002993931.1| 73 KALPGQAIGGYVEI 86
                                      *********99986 PP

>> RimM  RimM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0   3.7e-05      0.34      52      79 ..      17      44 ..       5      47 .. 0.84
   2 !   20.9   0.1   3.5e-08   0.00032       2      18 ..      54      70 ..      53      78 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.7e-05
                                      EETTEEEEEETT--SHHHHHTTTT-EEE CS
                              RimM 52 vhkkgvivklegvddrdaAealkgaelf 79
                                       h+++ i+k  g+++ ++A  l g +++
  gi|242398507|ref|YP_002993931.1| 17 QHNNHMIIKPLGIESKEQAATLIGKKVL 44
                                      4699********************9986 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 3.5e-08
                                      EEEEEEEETTTTEEEEE CS
                              RimM  2 vGkIvgahGlkGevkVk 18
                                      vGkI+++hG++Gevk  
  gi|242398507|ref|YP_002993931.1| 54 VGKITRTHGIRGEVKAI 70
                                      9*************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       240  (0.0133861); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.28s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 609.19
//
Query:       gi|242398508|ref|YP_002993932.1|  [L=176]
Description: Flavin reductase-related oxidoreductase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-20   73.1   0.0    3.2e-20   72.8   0.0    1.1  1  Flavin_Reduct  Flavin reductase like domain


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 !   72.8   0.0   1.8e-24   3.2e-20       6     139 ..       8     138 ..       4     149 .. 0.87

  Alignments for each domain:
  == domain 1  score: 72.8 bits;  conditional E-value: 1.8e-24
                                       EE-EEEEE.EETTEEEEEEESSEEEEETTTTEEEEEEETTSHHHHHHHHHSEEEEEEEBCCGHHHHHHTCS...SCC CS
                     Flavin_Reduct   6 qpvavvttsvpptsplgatlssftslsldPplvafslrlpsstadalkeagefvinllsesqealadafsqksgprt 82 
                                          +++++  ++++ + + + + t ls +P +v++s+++ ++t+d +k+ +efvi++ s +   l d + ++  +++
  gi|242398508|ref|YP_002993932.1|   8 MRTFLIVS-GQGEEVNIMAADWLTYLSTKPIIVGVSINPHRYTHDLIKKYKEFVISIPSIEI--LKDVLIAGR-KSG 80 
                                       55677887.8899999*****************************************99844..333333333.367 PP

                                       CCCCCCCCCEEECT.CCCSEEETTCSEEEEEEEEEEECCTTEEEEEEEEEEEEESTTE CS
                     Flavin_Reduct  83 ddksifagltwees.ptgapallgalasleCqvvgsvelgdhelfigeVvavkvgdda 139
                                        dk++   +t+ +s + + p +++ala+leC+v++++++g  + f++eVv++  +++a
  gi|242398508|ref|YP_002993932.1|  81 PDKLKHMSITLLPSkRIQTPSIKEALANLECKVIDERNYGNYTFFVAEVVDYTQKEEA 138
                                       7999999999999988999********************************9888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1386.95
//
Query:       gi|242398509|ref|YP_002993933.1|  [L=44]
Description: hypothetical protein TSIB_0518, partial [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00053   20.0   0.2    0.00056   19.9   0.2    1.0  1  Ribonuc_L-PSP  Endoribonuclease L-PSP


Domain annotation for each model (and alignments):
>> Ribonuc_L-PSP  Endoribonuclease L-PSP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.2   3.1e-08   0.00056      58      86 ..      16      44 .]       8      44 .] 0.92

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 3.1e-08
                                      HTT--GGGEEEEEEEESSGGGHHHHHHHH CS
                     Ribonuc_L-PSP 58 aagaslsdvVkvtvFladiedfaevnevy 86
                                      + ga++++v kv+v+l di +f ++n++y
  gi|242398509|ref|YP_002993933.1| 16 TTGATVDSVTKVNVYLDDIYNFGKFNKIY 44
                                      689************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); 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: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 319.80
//
Query:       gi|242398510|ref|YP_002993934.1|  [L=213]
Description: hypothetical protein TSIB_0519 [Thermococcus sibiricus MM 739]
Scores for complete 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-49  168.0   1.2    2.5e-49  167.9   1.2    1.0  1  DUF257    Pyrococcus protein of unknown function, DUF257


Domain annotation for each model (and alignments):
>> DUF257  Pyrococcus protein of unknown function, DUF257
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.9   1.2   1.4e-53   2.5e-49       2     202 ..       7     208 ..       6     211 .. 0.97

  Alignments for each domain:
  == domain 1  score: 167.9 bits;  conditional E-value: 1.4e-53
                            DUF257   2 lletlrpGetvLiEyssssvpevllyliakyskeknvPllvdDvlDtllivlkhlkllGldvpe.esikviKigGtk 77 
                                        l++++ GetvLiEyss + p + + ++++ +kek+   +vdD+lDtl++++ +l+l+G +++  ++ kviK gG  
  gi|242398510|ref|YP_002993934.1|   7 ILDNIQLGETVLIEYSSKVAPILFFSELVDWAKEKGYSAVVDDILDTLYLYKVQLELVGANMSFlNDLKVIKFGGRF 83 
                                       799************************************************************99************ PP

                            DUF257  78 evgnvvkkidfdkdpsiylskykravekvsve.etvinlvlglerllllldnrrdlyklvksikkylgnknRkafyl 153
                                       +vg++  +++ ++ p+i  +kyk  +  ++ e +tv+n+vlg e+++ll++ + d+ +l+++  +++g+k R+a+y+
  gi|242398510|ref|YP_002993934.1|  84 NVGQIFGRLHIER-PEIREQKYKEFFGPLLEEgKTVVNPVLGFEKIFLLQESKADILNLMNETLSFVGEKPRIALYF 159
                                       *************.*****************96666***************************************** PP

                            DUF257 154 inrnllesikPellplLEeiassvieiesekealivrilKslnldivgt 202
                                       in ++les+ Pe lpl+Ee as++++++ e +   + ++Ks+n +++g 
  gi|242398510|ref|YP_002993934.1| 160 INSDVLESTAPEALPLFEELASTILKVDIEGKLYKFSVVKSVNNNLLGL 208
                                       ********************************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       269  (0.0150036); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1624.46
//
Query:       gi|242398511|ref|YP_002993935.1|  [L=179]
Description: Small heat shock protein [Thermococcus sibiricus MM 739]
Scores for complete 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   73.5   0.8    1.8e-20   73.0   0.8    1.2  1  HSP20       Hsp20/alpha crystallin family
    2.2e-13   49.5   0.1    3.9e-13   48.8   0.1    1.4  1  ArsA_HSP20  HSP20-like domain found in ArsA
     0.0069   17.4   0.0       0.01   16.8   0.0    1.2  1  CS          CS domain
  ------ inclusion threshold ------
      0.028   14.8   0.1      0.049   14.0   0.1    1.3  1  PIH1_CS     PIH1 CS-like domain
      0.052   13.6   0.0       0.51   10.4   0.1    2.0  2  GvpH        GvpH


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 !   73.0   0.8   4.9e-24   1.8e-20       1      96 [.      74     170 ..      74     178 .. 0.92

  Alignments for each domain:
  == domain 1  score: 73.0 bits;  conditional E-value: 4.9e-24
                                       E--SSEEEEEEEEE-TT--CCCEEEEEETTEEEEEEE--....---TT----SS---EEEEEE--STTB-TTT-EEE CS
                             HSP20   1 dikeeeeefevkldvpglkkeelkvkvednrvlvkgehe..eeeedekglikerssrkFsrkftLPenvdadkvkas 75 
                                       di ++ eef +++++pg+kke++kv v ++ v ++++ +  +e e+e  ++ er ++ ++r+++LPe+v ++k ka+
  gi|242398511|ref|YP_002993935.1|  74 DIFDTGEEFVITAELPGVKKEDIKVRVLEDAVYIEAQVKreQELEEEGAIRIERYYSGYRRAIRLPEEVIPEKAKAK 150
                                       578899******************************9887688888889999************************* PP

                                       EETTEEEEEEEBSS--..--- CS
                             HSP20  76 lkdGvLtvtvpkkepekkkke 96 
                                       +++GvL++ vpkk+p kk +e
  gi|242398511|ref|YP_002993935.1| 151 YNNGVLEIRVPKKHPTKK-EE 170
                                       ***************977.44 PP

>> ArsA_HSP20  HSP20-like domain found in ArsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.8   0.1   1.1e-16   3.9e-13       2      62 ..      80     159 ..      79     160 .. 0.98

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 1.1e-16
                        ArsA_HSP20   2 deyvlkldLPfvdkeeidlsrsgdeLtIkig....................nfrRqitLPsvlarkevtsAkfedgv 58 
                                        e+v++++LP+v+ke+i+++  +d   I+++                     +rR i LP+ +  +++ +Ak+++gv
  gi|242398511|ref|YP_002993935.1|  80 EEFVITAELPGVKKEDIKVRVLEDAVYIEAQvkreqeleeegairieryysGYRRAIRLPEEVIPEKA-KAKYNNGV 155
                                       689***************************************************************99.******** PP

                        ArsA_HSP20  59 LeIr 62 
                                       LeIr
  gi|242398511|ref|YP_002993935.1| 156 LEIR 159
                                       ***7 PP

>> CS  CS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   2.8e-06      0.01       8      76 .]      78     162 ..      75     162 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.8e-06
                                       ETTEEEEEEE-TTCTTTTTCEEEEEETTEEEEEE.TS.CEEEEECE.................BSS-BETTTEEEEE CS
                                CS   8 tldeVvvtiyvkkvnikkkdvkvefkerslkvki.gk.eklliege.................LfgpIdpeesswti 65 
                                       t +e v+t ++++v  kk+d+kv+  e+ ++++   k e++l e+e                 L +++ pe+++ + 
  gi|242398511|ref|YP_002993935.1|  78 TGEEFVITAELPGV--KKEDIKVRVLEDAVYIEAqVKrEQEL-EEEgairieryysgyrrairLPEEVIPEKAKAKY 151
                                       5678899******9..*************7777764545554.44568****************************9 PP

                                       ETTEEEEEEEB CS
                                CS  66 eskkveitLkK 76 
                                        +  +ei + K
  gi|242398511|ref|YP_002993935.1| 152 NNGVLEIRVPK 162
                                       99999998766 PP

>> PIH1_CS  PIH1 CS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   1.4e-05     0.049      31      87 ..      80     153 ..      77     161 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.4e-05
                           PIH1_CS  31 kelaieielPllksikevklrvgerrlel..................eskk.akyfLslkLpYpvdedkveAkFvk 87 
                                       +e++i+ elP++   +++k+rv e+ + +                  e      y+  ++Lp +v  +k++Ak+++
  gi|242398511|ref|YP_002993935.1|  80 EEFVITAELPGV-KKEDIKVRVLEDAVYIeaqvkreqeleeegairiER-YySGYRRAIRLPEEVIPEKAKAKYNN 153
                                       689*********.6799************************99997543.2589********************96 PP

>> GvpH  GvpH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00014      0.51      98     125 ..      77     104 ..      73     118 .. 0.83
   2 ?    0.9   0.0      0.11   4.1e+02     155     171 ..     152     168 ..     142     172 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00014
                              GvpH  98 ddsdelvvvadlpGvtdedvdvaletde 125
                                       d ++e+v+ a+lpGv  ed+ v +  d 
  gi|242398511|ref|YP_002993935.1|  77 DTGEEFVITAELPGVKKEDIKVRVLEDA 104
                                       6799***************999886454 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.11
                              GvpH 155 rnqvlelrlarsedsdg 171
                                       +n vle+r+ + +++  
  gi|242398511|ref|YP_002993935.1| 152 NNGVLEIRVPKKHPTKK 168
                                       799******99999854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1121.90
//
Query:       gi|242398512|ref|YP_002993936.1|  [L=810]
Description: CDC48/VCP like protein, AAA superfamily [Thermococcus sibiricus MM 739]
Scores for complete 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  339.3   0.0    6.6e-51  172.2   0.0    2.7  2  AAA              ATPase family associated with various cellul
    3.5e-36  123.2   0.5    7.3e-35  119.0   1.6    2.6  2  CDC48_N          Cell division protein 48 (CDC48), N-terminal
    6.8e-34  115.4   3.9    1.4e-17   63.2   0.2    3.0  2  AAA_lid_3        AAA+ lid domain
    1.8e-16   60.7   0.0    1.6e-08   34.9   0.0    3.3  2  AAA_2            AAA domain (Cdc48 subfamily)
    3.7e-16   59.3   0.2    3.1e-07   30.3   0.0    3.5  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    1.5e-15   58.0   2.0    1.9e-06   28.4   0.0    4.2  4  AAA_16           AAA ATPase domain
    1.3e-13   50.5   0.7    4.8e-13   48.7   0.3    2.2  1  CDC48_2          Cell division protein 48 (CDC48), domain 2
    6.3e-12   45.9   6.2      0.001   19.3   0.0    5.3  4  AAA_22           AAA domain
    6.6e-12   45.6   0.0    1.8e-05   24.7   0.0    3.0  3  AAA_14           AAA domain
    1.6e-11   44.4   2.6    0.00042   20.3   0.1    4.5  2  AAA_5            AAA domain (dynein-related subfamily)
    4.2e-11   42.6   0.1    0.00029   20.1   0.0    3.2  3  TIP49            TIP49 P-loop domain
    9.8e-11   42.0   0.0    0.00041   20.5   0.0    2.7  2  AAA_33           AAA domain
    3.5e-09   36.5   0.6    0.00049   20.0   0.0    3.1  2  Vps4_C           Vps4 C terminal oligomerisation domain
    2.5e-08   34.5   0.0      0.014   15.9   0.0    3.1  2  AAA_18           AAA domain
    4.8e-08   32.9   0.1     0.0095   15.7   0.1    2.6  2  IstB_IS21        IstB-like ATP binding protein
    6.2e-08   33.0   0.0      0.018   15.4   0.0    2.6  2  RNA_helicase     RNA helicase
    9.7e-08   31.9   0.1      0.038   13.7   0.0    3.7  3  Sigma54_activat  Sigma-54 interaction domain
      1e-07   31.9   0.0     0.0097   15.6   0.0    2.5  2  AAA_24           AAA domain
    1.2e-07   31.8   0.0     0.0047   16.8   0.0    3.4  3  Bac_DnaA         Bacterial dnaA  protein
    5.2e-07   29.2   0.6      0.032   13.6   0.1    2.6  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    1.1e-06   29.0   0.0      0.035   14.4   0.0    3.0  2  AAA_28           AAA domain
    1.7e-06   27.4   0.0      0.028   13.6   0.0    2.4  2  DUF815           Protein of unknown function (DUF815)
    2.1e-06   27.7   0.1          1    9.3   0.0    4.3  4  NACHT            NACHT domain
    5.7e-06   26.0   0.0      0.095   12.2   0.0    2.6  2  AAA_7            P-loop containing dynein motor region
    6.3e-06   25.9   5.0       0.14   11.8   1.6    4.4  3  AAA_25           AAA domain
    8.4e-06   26.3   0.0       0.18   12.3   0.0    2.9  2  ABC_tran         ABC transporter
    1.5e-05   25.0   4.4      0.012   15.5   0.0    3.9  4  ATPase_2         ATPase domain predominantly from Archaea
    1.7e-05   24.8   0.0       0.14   12.2   0.0    2.7  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
    3.6e-05   23.3   1.3       0.36   10.3   0.0    3.2  3  PhoH             PhoH-like protein
    6.4e-05   22.8   0.0       0.56   10.1   0.0    2.7  2  AAA_3            ATPase family associated with various cellul
    7.1e-05   22.3   5.7       0.21   10.9   0.0    4.2  5  ATPase           KaiC
    7.9e-05   22.0   0.0      0.097   11.9   0.0    2.3  2  DUF2075          Uncharacterized conserved protein (DUF2075)
    8.6e-05   21.8   0.1        0.4    9.7   0.0    2.3  2  Parvo_NS1        Parvovirus non-structural protein NS1
    0.00013   21.3   2.8        0.3   10.3   0.0    3.4  3  Zeta_toxin       Zeta toxin
    0.00036   20.3   0.4        1.2    8.9   0.0    3.1  2  AAA_30           AAA domain
    0.00041   20.2   0.3       0.79    9.5   0.0    2.7  2  AAA_11           AAA domain
    0.00046   20.6   0.4        3.2    8.2   0.0    3.9  3  AAA_17           AAA domain
    0.00065   19.0   0.0       0.75    8.9   0.0    2.6  2  NB-ARC           NB-ARC domain
     0.0028   18.0   2.8        3.2    8.1   0.1    3.3  3  AAA_19           AAA domain
     0.0045   16.9   3.5        8.3    6.3   0.0    4.7  4  NTPase_1         NTPase
  ------ inclusion threshold ------
      0.012   14.7   0.0        5.1    6.1   0.0    2.6  2  T2SSE            Type II/IV secretion system protein
      0.017   15.2   0.0        6.7    6.8   0.0    2.6  2  Sigma54_activ_2  Sigma-54 interaction domain
      0.021   14.6   0.7        5.9    6.6   0.0    3.1  3  Cytidylate_kin   Cytidylate kinase
      0.022   14.4   0.0        1.5    8.4   0.0    3.0  3  Zot              Zonular occludens toxin (Zot)
      0.024   14.7   0.0        8.6    6.3   0.0    2.7  2  ResIII           Type III restriction enzyme, res subunit
      0.029   14.4   0.3        9.3    6.4   0.0    2.9  2  DUF1905          Domain of unknown function (DUF1905)
      0.041   12.8   0.0        7.2    5.4   0.0    2.7  3  AFG1_ATPase      AFG1-like ATPase
      0.044   13.4   0.0        3.4    7.3   0.0    2.4  2  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
      0.065   12.6   2.4         15    4.9   0.0    3.6  3  IPT              Isopentenyl transferase
      0.065   13.0   0.0        2.2    7.9   0.0    2.2  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.091   12.9   1.8         13    5.8   0.0    3.8  3  SKI              Shikimate kinase
       0.11   12.3   0.0         24    4.8   0.0    2.5  2  AAA_29           P-loop containing region of AAA domain
       0.17   11.0   0.0         23    4.0   0.0    2.6  2  DAP3             Mitochondrial ribosomal death-associated pro
        2.9    8.4   4.8         48    4.5   2.7    3.7  2  RuvA_C           RuvA, 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 !  172.2   0.0     2e-53   6.6e-51       1     131 [.     219     348 ..     219     349 .. 0.98
   2 !  164.4   0.0   5.1e-51   1.7e-48       1     131 [.     555     684 ..     555     685 .. 0.97

  Alignments for each domain:
  == domain 1  score: 172.2 bits;  conditional E-value: 2e-53
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTC CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgs 77 
                                       vllyGppGtGKTllakava+e++++f+ i+g+e++sky gese+++re+fke +e+a psi+fiDEida+a++r + 
  gi|242398512|ref|YP_002993936.1| 219 VLLYGPPGTGKTLLAKAVANEANAHFIAINGPEIMSKYYGESEERLREVFKESEENA-PSIIFIDEIDAIAPKRGEV 294
                                       79*****************************************************99.****************999 PP

                                       CCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  78 eseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                       + e+e+rvv+qLlt +dg+k++ +kvivigatnrpd ldpal+r gRfdr+iei+
  gi|242398512|ref|YP_002993936.1| 295 TGEVEKRVVAQLLTLMDGLKSR-GKVIVIGATNRPDALDPALRRpGRFDREIEIG 348
                                       *********************6.77***************************996 PP

  == domain 2  score: 164.4 bits;  conditional E-value: 5.1e-51
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTC CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgs 77 
                                       +llyGppGtGKTllakava+e++++f+ i g+e+lsk+vgesek+ire+f++a++ a p+++fiDEida+a++r ++
  gi|242398512|ref|YP_002993936.1| 555 ILLYGPPGTGKTLLAKAVATESEANFIGIRGPEVLSKWVGESEKNIREIFRKARQAA-PTVIFIDEIDAIAPRRGSD 630
                                       69******************************************************9.****************999 PP

                                       CCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  78 eseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                        +++++r++nqLlte+dg +++ s v+vi+atnrpd ldpallr gRfdr+i ++
  gi|242398512|ref|YP_002993936.1| 631 VNRVTDRLINQLLTEMDGIEEN-SGVVVIAATNRPDILDPALLRpGRFDRIILVP 684
                                       9********************7.55**************************9886 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 !  119.0   1.6   2.2e-37   7.3e-35       1      85 []       8      92 ..       8      92 .. 0.98
   2 ?   -1.2   0.0       7.1   2.4e+03      20      64 ..     204     249 ..     204     250 .. 0.60

  Alignments for each domain:
  == domain 1  score: 119.0 bits;  conditional E-value: 2.2e-37
                                      CEEEECCSS-CSSTTEEEE-HHHHHHHTS-TTSEEEEECCCCEEEEEEEBSTTSTTTTEEEE-HHHHHHHT--TTEEEE CS
                           CDC48_N  1 rLrVaeapqedvgrgivridpedmeelglepgdvveiegkrkTvaivwpaepedegkgiIrmdgvtRknagvsiGdkVt 79
                                      +L+Va a+q+dvgrgivr+d+++m+++g+++gd+vei g+++T+a+vwpa+pedeg +iIrmdg +Rknagv++Gd+Vt
  gi|242398512|ref|YP_002993936.1|  8 KLKVASAYQRDVGRGIVRVDRNAMRKIGVQTGDIVEIIGTKNTAAVVWPAYPEDEGLEIIRMDGTIRKNAGVGLGDEVT 86
                                      69*************************************999************************************* PP

                                      EEEE-- CS
                           CDC48_N 80 Vrkaev 85
                                      +rkaev
  gi|242398512|ref|YP_002993936.1| 87 IRKAEV 92
                                      ***985 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 7.1
                                       -HHHHHHHTS-TTSEEEEEC...CCCEE.EEEEEBSTTSTTTTEEEE-H CS
                           CDC48_N  20 dpedmeelglepgdvveieg...krkTv.aivwpaepedegkgiIrmdg 64 
                                       +pe++e+lg+ep + v + g   + kT  a+++++e    +   I+++g
  gi|242398512|ref|YP_002993936.1| 204 HPEVFEKLGIEPPKGVLLYGppgTGKTLlAKAVANEA---NAHFIAING 249
                                       58999******99999887641133333344444433...356666665 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.2   0.6   1.2e-16   3.8e-14       3      42 ..     434     472 ..     431     494 .. 0.87
   2 !   63.2   0.2   4.2e-20   1.4e-17       1      45 []     707     768 ..     707     768 .. 0.84

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 1.2e-16
                         AAA_lid_3   3 dlkeLAerTeGySGADlaalcreAallAlrrgikeitmed 42 
                                        l+eLAe+T+G++GADlaal reAa++Alrr i+e ++ d
  gi|242398512|ref|YP_002993936.1| 434 LLEELAEKTHGFVGADLAALAREAAMAALRRLIEE-GKID 472
                                       589****************************9987.2233 PP

  == domain 2  score: 63.2 bits;  conditional E-value: 4.2e-20
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrr................gik..eitmedfee 45 
                                       dv+l+eLA+rTeGy+GAD++a++reAa++++rr                  +  ++tm+dfee
  gi|242398512|ref|YP_002993936.1| 707 DVNLEELAKRTEGYTGADIEAVVREAAFNTMRRaisegiikpgtrasdiR-ErvKVTMRDFEE 768
                                       9********************************77777777777777431.234699999987 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.0   4.8e-11   1.6e-08       6     105 ..     219     312 ..     215     319 .. 0.91
   2 !   21.7   0.0   5.4e-07   0.00018       6      92 ..     555     633 ..     550     656 .. 0.81

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 4.8e-11
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKi 80 
                                       +ll gp g+Gkt+laka+a+  ++    ++i ++  e++     + + ++++  ++  ++ ee+   i+++DEid i
  gi|242398512|ref|YP_002993936.1| 219 VLLYGPPGTGKTLLAKAVANEANA----HFIAINGPEIMS----KYYGESEERLREVFKESEENApsIIFIDEIDAI 287
                                       6889******************96....************....********************9************ PP

                                       ---.---------HHHHHHHHHHHH- CS
                             AAA_2  81 hpk.essgadvSregVqrdLLqileg 105
                                       +pk ++ + +v +  V+  LL +++g
  gi|242398512|ref|YP_002993936.1| 288 APKrGEVTGEVEK-RVVAQLLTLMDG 312
                                       **97777777766.577789999997 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 5.4e-07
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKi 80 
                                       ill gp g+Gkt+laka+a   ++    ++i +   e+l     + + ++++  ++   +a +    ++++DEid i
  gi|242398512|ref|YP_002993936.1| 555 ILLYGPPGTGKTLLAKAVATESEA----NFIGIRGPEVLS----KWVGESEKNIREIFRKARQAAptVIFIDEIDAI 623
                                       8999***************99985....************....77777777777887777777799********** PP

                                       ------------ CS
                             AAA_2  81 hpkessgadvSr 92 
                                       +p  + g+dv r
  gi|242398512|ref|YP_002993936.1| 624 AP--RRGSDVNR 633
                                       **..55555544 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.0   9.3e-10   3.1e-07      33     104 ..     216     295 ..     192     343 .. 0.77
   2 !   24.8   0.0   4.4e-08   1.5e-05      35      97 ..     554     624 ..     516     631 .. 0.82

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 9.3e-10
                            RuvB_N  33 ldhvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihrlsrave 101
                                          vllyGpPG Gkt lak +a+e ++++ +  gP +      e +  l  ++++ ee+   ++fidei  ++++  
  gi|242398512|ref|YP_002993936.1| 216 PKGVLLYGPPGTGKTLLAKAVANEANAHFIAINGPEImskyygESEERLREVFKESEENapSIIFIDEIDAIAPKRG 292
                                       5679*******************************984333333445688888777665337********9999887 PP

                            RuvB_N 102 evl 104
                                       ev 
  gi|242398512|ref|YP_002993936.1| 293 EVT 295
                                       775 PP

  == domain 2  score: 24.8 bits;  conditional E-value: 4.4e-08
                            RuvB_N  35 hvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihrls 97 
                                        +llyGpPG Gkt lak +a+e ++++    gP +      e ++++  ++ + ++    v+fidei  ++
  gi|242398512|ref|YP_002993936.1| 554 GILLYGPPGTGKTLLAKAVATESEANFIGIRGPEVlskwvgESEKNIREIFRKARQAapTVIFIDEIDAIA 624
                                       69*************************999999653433345678999999887765337******98775 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0   5.6e-09   1.9e-06      24     140 ..     216     321 ..     205     332 .. 0.75
   2 ?    0.3   0.4       2.4     8e+02      98     152 ..     391     459 ..     359     483 .. 0.44
   3 !   18.5   0.0   6.2e-06     0.002      24      51 ..     552     579 ..     542     597 .. 0.82
   4 ?    6.3   0.0     0.034        11     123     149 ..     600     625 ..     595     658 .. 0.70

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 5.6e-09
                            AAA_16  24 pelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrek 100
                                       p  vll+G++G+GK+ l+++++++++++   f++ +  +  ++  y    + l r e++++ +++   a    + ++
  gi|242398512|ref|YP_002993936.1| 216 PKGVLLYGPPGTGKTLLAKAVANEANAH---FIAINGPEI-MSKYYGESEERL-R-EVFKESEEN---APSIIFIDE 283
                                       589*******************977755...888888888.333343355555.4.555544444...455566666 PP

                            AAA_16 101 leealaavpelagaeasrllellkrllallsrderplvlv 140
                                       +++ +   +e++g+ ++r+ ++l  l++ l+++++  v+v
  gi|242398512|ref|YP_002993936.1| 284 IDAIAPKRGEVTGEVEKRVVAQLLTLMDGLKSRGK--VIV 321
                                       7777779999999999***********99999888..443 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 2.4
                            AAA_16  98 rekleealaavpelagaea..................srllellkrllallsrderplvlvlDdlqwadeasl 152
                                       r++ e+al  + +la++e+                  +rl +ll + l  +++  +   +  D +  a+ea +
  gi|242398512|ref|YP_002993936.1| 391 RDAAERALYKIEDLADKEEiirrairdiddklyeevkHRLIDLLLEEL--AEK-TH-GFVGADLAALAREAAM 459
                                       222222222222222222222222222222333222233333333333..332.33.2333344444444444 PP

  == domain 3  score: 18.5 bits;  conditional E-value: 6.2e-06
                            AAA_16  24 pelvllsGesGvGKsslvrellralekd 51 
                                       p  +ll+G++G+GK+ l+++++++ e++
  gi|242398512|ref|YP_002993936.1| 552 PKGILLYGPPGTGKTLLAKAVATESEAN 579
                                       5889******************988777 PP

  == domain 4  score: 6.3 bits;  conditional E-value: 0.034
                            AAA_16 123 lkrllallsrderplvlvlDdlqwade 149
                                       ++++++++++ + p+v+++D+++ + +
  gi|242398512|ref|YP_002993936.1| 600 IREIFRKARQ-AAPTVIFIDEIDAIAP 625
                                       6788899999.999*********5443 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 !   48.7   0.3   1.5e-15   4.8e-13       2      63 ..     108     169 ..     107     170 .. 0.93

  Alignments for each domain:
  == domain 1  score: 48.7 bits;  conditional E-value: 1.5e-15
                                       .SCCCCHHHHCCCTTEEE-TTEEEEECCTCCCEEEEEEEECCCCSCEEECTSCCEEESTTCC CS
                           CDC48_2   2 idgdemaylkrqFlgrpvtkGdlvvfefkgqeiklvVvstePkgpvgitetTeielgtkpve 63 
                                       +  d+++ l +++ grpv+ Gd++++ ++gqe+++vV+ t+P+g+v ite Te ++++k v+
  gi|242398512|ref|YP_002993936.1| 108 FGHDFVDWLHSRLVGRPVVRGDYIRIGVLGQELTFVVTATTPSGVVQITEFTEFTVSEKTVK 169
                                       6678888899**********************************************999876 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   3.1e-06     0.001       8      48 ..     219     250 ..     214     274 .. 0.69
   2 ?    5.2   0.0     0.074        24      76     132 ..     262     326 ..     251     331 .. 0.70
   3 ?   -0.1   0.6       3.2     1e+03      39     116 ..     393     466 ..     375     495 .. 0.72
   4 !   17.0   0.3   1.6e-05    0.0053       8      59 ..     555     606 ..     550     667 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 3.1e-06
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlp 48 
                                       ++++G++GtGKT+l++ ++++++++         ++ ++ p
  gi|242398512|ref|YP_002993936.1| 219 VLLYGPPGTGKTLLAKAVANEANAH---------FIAINGP 250
                                       689******************9544.........4433333 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.074
                            AAA_22  76 eellealeqalraravielliiDEaqhlr..s........eealeeLrsllnlsrkgvqliLvGtpe 132
                                       e+l+e + + +++ a  +++ iDE++ +   +        ++++ +L +l++  ++  ++i++G ++
  gi|242398512|ref|YP_002993936.1| 262 ERLREVFKE-SEENAP-SIIFIDEIDAIApkRgevtgeveKRVVAQLLTLMDGLKSRGKVIVIGATN 326
                                       333333333.333444.7**********887245667788999999999999878888999999876 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 3.2
                            AAA_22  39 rpevvfvtlpsstsskdllrellralglelkaerlsseellealeqalraravielliiDEaqhlrseealeeLrsl 115
                                        +e +++++  + + +++ r+  r+++++l +    +++l+++l + l ++   +++  D a    +e+a+  Lr+l
  gi|242398512|ref|YP_002993936.1| 393 AAERALYKIEDLADKEEIIRRAIRDIDDKLYE--EVKHRLIDLLLEELAEKTH-GFVGADLAALA-REAAMAALRRL 465
                                       45555777777778888888888888888888..8888888888888888777.77777766666.66666666665 PP

                            AAA_22 116 l 116
                                        
  gi|242398512|ref|YP_002993936.1| 466 I 466
                                       4 PP

  == domain 4  score: 17.0 bits;  conditional E-value: 1.6e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevv.fvtlpsstsskdllre 59 
                                       ++++G++GtGKT+l++ ++ +  e++++  ++pev+ +    s+++ ++++r+
  gi|242398512|ref|YP_002993936.1| 555 ILLYGPPGTGKTLLAKAVATES-EANFIGIRGPEVLsKWVGESEKNIREIFRK 606
                                       89*****************997.334444477777754444444466666655 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   5.5e-08   1.8e-05       5     101 ..     219     325 ..     216     342 .. 0.82
   2 ?   -1.3   0.1       6.1     2e+03      28      66 ..     405     444 ..     395     496 .. 0.70
   3 !   16.9   0.0   1.4e-05    0.0047       5      76 ..     555     623 ..     552     664 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 5.5e-08
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe.kllelileklkeekktylflDEiqev.... 76 
                                       +++ G+  +GKT l+k +++e      +++ in  +   k + ++e +l e+++e+  e+  +++f+DEi  +    
  gi|242398512|ref|YP_002993936.1| 219 VLLYGPPGTGKTLLAKAVANEAN---AHFIAINGPEIMSKYYGESEeRLREVFKESE-ENAPSIIFIDEIDAIapkr 291
                                       7899***************9888...********99999887765536777777764.4599**********99999 PP

                            AAA_14  77 ........pewekalkslvd.egknldvivtGSn 101
                                               +++   l  l+d  +++++viv G  
  gi|242398512|ref|YP_002993936.1| 292 gevtgeveKRVVAQLLTLMDgLKSRGKVIVIGAT 325
                                       9999888888888888888853357888888865 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 6.1
                            AAA_14  28 vkkesilyinldderdkkladpe.kllelileklkeekkt 66 
                                       ++ke+i+  ++ d +dk +++ + +l++l+le+l e+ + 
  gi|242398512|ref|YP_002993936.1| 405 ADKEEIIRRAIRDIDDKLYEEVKhRLIDLLLEELAEKTHG 444
                                       5788888888888888776654447888888875443444 PP

  == domain 3  score: 16.9 bits;  conditional E-value: 1.4e-05
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev 76 
                                       +++ G+  +GKT l+k ++ e+     +++ i   +   k   ++ek++++i++k+++   t++f+DEi  +
  gi|242398512|ref|YP_002993936.1| 555 ILLYGPPGTGKTLLAKAVATESE---ANFIGIRGPEVLSKWVGESEKNIREIFRKARQAAPTVIFIDEIDAI 623
                                       7899***************9988...99999999999888888777777777777556699********987 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.1   1.3e-06   0.00042       1     136 [.     218     337 ..     218     338 .. 0.66
   2 !   18.5   0.6   4.5e-06    0.0015       2     135 ..     555     672 ..     554     675 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.3e-06
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------.G-SEEEEESGGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar.egeilvlDEver 76 
                                       +vlL GppGtgK+ la+ +a   n+ +  +++++ +++     + +           +++++ +  ++i+++DE++ 
  gi|242398512|ref|YP_002993936.1| 218 GVLLYGPPGTGKTLLAKAVANEANAHFIAINGPEIMSKYYGESEER--------LREVFKESEEnAPSIIFIDEIDA 286
                                       59******************************99777643222222........23333333334889999999998 PP

                                       --HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHHT CS
                             AAA_5  77 aesevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalrs 136
                                       + ++  ++     e+r   ++++ +l++  +     ++ vi+++n++d     l+palr+
  gi|242398512|ref|YP_002993936.1| 287 IAPKRGEVT-GEVEKRV--VAQLLTLMDGLKS--RGKVIVIGATNRPD----ALDPALRR 337
                                       887544444.2223333..3355555544442..22288888888888....77888775 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 4.5e-06
                                       EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGGG CS
                             AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEver 76 
                                       +lL GppGtgK+ la+ +a   ++++  + +++      ++ ++    g+ +    ++ r+ar   + ++++DE++ 
  gi|242398512|ref|YP_002993936.1| 555 ILLYGPPGTGKTLLAKAVATESEANFIGIRGPE------VLSKWV---GESEKNIREIFRKARqaAPTVIFIDEIDA 622
                                       89****************999999998888887......666666...55555558888888878899********* PP

                                       --HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHH CS
                             AAA_5  77 aesevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalr 135
                                       + +   + ++++ ++   +l      + +++      + via++n++d     l+pal+
  gi|242398512|ref|YP_002993936.1| 623 IAPRRGSDVNRVTDRLINQLLTEMDGIEENS-----GVVVIAATNRPD----ILDPALL 672
                                       ***9999999999988777655555554444.....399******999....6666665 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   8.8e-07   0.00029      51     103 ..     217     268 ..     211     286 .. 0.86
   2 ?   -2.8   0.0       8.6   2.8e+03      20      48 ..     439     471 ..     402     472 .. 0.68
   3 !   18.7   0.0   2.5e-06   0.00082      51     106 ..     553     607 ..     547     623 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 8.8e-07
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXX CS
                             TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte.vltqal 103
                                       ++vLl Gp+gtGkt la a+++e +   +f+a++g e+ s     +e  l + +
  gi|242398512|ref|YP_002993936.1| 217 KGVLLYGPPGTGKTLLAKAVANEAN--AHFIAINGPEIMSKYYGESEeRLREVF 268
                                       89********************977..89**********987766541455555 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 8.6
                                       XXXXXXXXXX...XXXXXXX.XXXXXXXXXXXX CS
                             TIP49  20 ekeeeglvGq...kkareaa.gvivelikekkl 48 
                                        ++++g+vG      areaa + + +li+e+k+
  gi|242398512|ref|YP_002993936.1| 439 AEKTHGFVGAdlaALAREAAmAALRRLIEEGKI 471
                                       345567777522134677652456678887776 PP

  == domain 3  score: 18.7 bits;  conditional E-value: 2.5e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXX CS
                             TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkktev.ltqalrks 106
                                       +++Ll Gp+gtGkt la a++ e  ++  f+ + g ev s  v  +e  + + +rk+
  gi|242398512|ref|YP_002993936.1| 553 KGILLYGPPGTGKTLLAKAVATE--SEANFIGIRGPEVLSKWVGESEKnIREIFRKA 607
                                       89*******************98..5689**************99985378889987 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   1.2e-06   0.00041       2      80 ..     219     327 ..     219     352 .. 0.78
   2 !   18.7   0.0   4.5e-06    0.0015       2      80 ..     555     663 ..     555     743 .. 0.70

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.2e-06
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt............................dy 48 
                                       vll G+pG+GK+ la+ ++++    ++ ++ ++++++++g+ +++++                              
  gi|242398512|ref|YP_002993936.1| 219 VLLYGPPGTGKTLLAKAVANEANahFIAINGPEIMSKYYGESEERLRevfkeseenapsiifideidaiapkrgeVT 295
                                       7899***************99889999************98888777777777777778888888888877776544 PP

                            AAA_33  49 trvldrlyqilnelarkalsagrnvildatnl 80 
                                        +v++r+ ++l  l +   s+g+ +++ atn+
  gi|242398512|ref|YP_002993936.1| 296 GEVEKRVVAQLLTLMDGLKSRGKVIVIGATNR 327
                                       45777777777777776667777777777765 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 4.5e-06
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt............................dy 48 
                                       +ll G+pG+GK+ la+ ++ +    ++ ++ ++++++ +g+ +++++                            d 
  gi|242398512|ref|YP_002993936.1| 555 ILLYGPPGTGKTLLAKAVATESEanFIGIRGPEVLSKWVGESEKNIReifrkarqaaptvifideidaiaprrgsDV 631
                                       6789***************999999999*****88888887777666677777777777888888888777777788 PP

                            AAA_33  49 trvldrlyqilnelarkalsagrnvildatnl 80 
                                       +rv+drl+++l    +   +  + v++ atn+
  gi|242398512|ref|YP_002993936.1| 632 NRVTDRLINQLLTEMDGIEENSGVVVIAATNR 663
                                       88888888887777766666666677777743 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 !   13.5   0.0   0.00016     0.054       9      44 ..     468     503 ..     466     511 .. 0.89
   2 !   20.0   0.0   1.5e-06   0.00049      22      54 ..     753     786 ..     748     792 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00016
                            Vps4_C   9 pgaiemtwmdipsdkllePpvtlkDflkalkkarpt 44 
                                       +g+i    + ip++ l e +vt++Df +alk + p+
  gi|242398512|ref|YP_002993936.1| 468 EGKIDFEAESIPKEVLEELKVTRRDFYEALKMVEPS 503
                                       5778888899**9999999*************9998 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 1.5e-06
                            Vps4_C  22 dklleP.pvtlkDflkalkkarptVskeDLekhe 54 
                                       +++ e+ +vt++Df++a+kk+ p+Vs+e +e ++
  gi|242398512|ref|YP_002993936.1| 753 SDIRERvKVTMRDFEEAMKKVGPSVSEETMEYYK 786
                                       56667779********************999887 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   7.9e-05     0.026       1      35 [.     219     271 ..     219     327 .. 0.61
   2 !   15.9   0.0   4.3e-05     0.014       1      78 [.     555     657 ..     555     671 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 7.9e-05
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf..................gvnlrdvaken 35 
                                       +ll G+pG+GKt lak+++++ +                    ++lr+v+ke+
  gi|242398512|ref|YP_002993936.1| 219 VLLYGPPGTGKTLLAKAVANEANAhfiaingpeimskyygesEERLREVFKES 271
                                       799***************99864456777777666666666644444444444 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 4.3e-05
                            AAA_18   1 IlltGtpGvGKttlakeLskrl..gf.......................gvnlrdvakenglllevdpe...aldes 49 
                                       Ill G+pG+GKt lak+++ +   +f                        ++ r+ a+     +e d+      ++ 
  gi|242398512|ref|YP_002993936.1| 555 ILLYGPPGTGKTLLAKAVATESeaNFigirgpevlskwvgeseknireiFRKARQAAPTVIFIDEIDAIaprRGSDV 631
                                       99****************65532245888888888888888744444444444444444444444444466655555 PP

                            AAA_18  50 krldedkldklldaleenssaleegknlv 78 
                                       +r+ +   ++ll++++++    e+ +++v
  gi|242398512|ref|YP_002993936.1| 632 NRVTDRLINQLLTEMDGIE---ENSGVVV 657
                                       5666666666666666653...3444445 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   0.1   2.9e-05    0.0095      48      73 ..     217     242 ..     210     249 .. 0.86
   2 !   14.3   0.0   7.7e-05     0.025      48      71 ..     553     576 ..     547     621 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.9e-05
                         IstB_IS21  48 enivllGpsGvGKshlaialgveavr 73 
                                       ++++l Gp+G+GK+ la a++ ea +
  gi|242398512|ref|YP_002993936.1| 217 KGVLLYGPPGTGKTLLAKAVANEANA 242
                                       6899*****************99966 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 7.7e-05
                         IstB_IS21  48 enivllGpsGvGKshlaialgvea 71 
                                       ++i+l Gp+G+GK+ la a+++e 
  gi|242398512|ref|YP_002993936.1| 553 KGILLYGPPGTGKTLLAKAVATES 576
                                       6799***************99875 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   7.3e-05     0.024       1      34 [.     219     252 ..     219     287 .. 0.80
   2 !   15.4   0.0   5.4e-05     0.018       1     106 [.     555     662 ..     555     663 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 7.3e-05
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsv 34 
                                       ++lyGp+g+GK++lak +a++   ++  ++ +++
  gi|242398512|ref|YP_002993936.1| 219 VLLYGPPGTGKTLLAKAVANEANAHFIAINGPEI 252
                                       689***************9999988844443433 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 5.4e-05
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl......klkkkdsvys.rnpeddfwdgYt..gqevvvidDfgqvkdeenps 68 
                                       i+lyGp+g+GK++lak +a++ + ++      +   +++v    ++  +++ + +   ++v+ id++ ++  +   +
  gi|242398512|ref|YP_002993936.1| 555 ILLYGPPGTGKTLLAKAVATESEANFigirgpE-VLSKWVGEsEKNIREIFRKARqaAPTVIFIDEIDAIAPRRGSD 630
                                       789**************9999998887777642.3334444434444455544443567788888888887662222 PP

                      RNA_helicase  69 dlaelirlvsstpyplnmasleekgtlftSkvvivtsN 106
                                             rl+  +++ ++m+ +ee     + +vvi+ +N
  gi|242398512|ref|YP_002993936.1| 631 VNRVTDRLI--NQLLTEMDGIEEN----SGVVVIAATN 662
                                       333333333..4567777777776....5666777776 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   0.00011     0.038      23      61 ..     217     252 ..     203     293 .. 0.85
   2 !   10.0   0.0    0.0016      0.53      23      47 ..     553     577 ..     539     584 .. 0.85
   3 ?    3.2   0.0      0.19        62      90     143 ..     608     663 ..     598     681 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00011
                                       S-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS CS
                   Sigma54_activat  23 lsvlitGesGtGKellaraiheaskrkekpfvavncaai 61 
                                         vl+ G  GtGK+lla+a+ ++   ++++f+a+n  +i
  gi|242398512|ref|YP_002993936.1| 217 KGVLLYGPPGTGKTLLAKAVANE---ANAHFIAINGPEI 252
                                       679****************9765...5688999997766 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0016
                                       S-EEEECSTTSSHHHHHHHHHHHST CS
                   Sigma54_activat  23 lsvlitGesGtGKellaraiheask 47 
                                         +l+ G  GtGK+lla+a+ ++s+
  gi|242398512|ref|YP_002993936.1| 553 KGILLYGPPGTGKTLLAKAVATESE 577
                                       679****************998876 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.19
                                       HHTTTSEEEEETGGGS-HHHHHHHHHHHHHSEEESBTSSS..EEE--EEEEEEESS CS
                   Sigma54_activat  90 ekadgGtlfLDeigelplelQekLlrvlqegevervGssk..eikvdvriiaatne 143
                                       ++a   ++f+Dei  + ++  + + rv ++   + + + +  e +  v +iaatn+
  gi|242398512|ref|YP_002993936.1| 608 RQAAPTVIFIDEIDAIAPRRGSDVNRVTDRLINQLLTEMDgiEENSGVVVIAATNR 663
                                       5788899*************999999998877777777653356778999999997 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   2.9e-05    0.0097       5      77 ..     219     287 ..     216     300 .. 0.77
   2 !   13.5   0.0   0.00013     0.043       5      28 ..     555     580 ..     552     636 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.9e-05
                            AAA_24   5 iliyGpsgiGKTtlakel..gpkplfidtekGlksldadkfpdieswedfldevvelaaeladyktlviDtidel 77 
                                       +l+yGp+g+GKT lak    + ++ fi +++   ++  + +   es e +++ ++e +++ +  ++++iD id +
  gi|242398512|ref|YP_002993936.1| 219 VLLYGPPGTGKTLLAKAVanEANAHFIAING--PEIMSKYYG--ESEERLREVFKESEENAP--SIIFIDEIDAI 287
                                       89***************99888888888877..333333333..377888888888877777..88999988876 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.00013
                            AAA_24   5 iliyGpsgiGKTtlakel..gpkplf 28 
                                       il+yGp+g+GKT lak    + ++ f
  gi|242398512|ref|YP_002993936.1| 555 ILLYGPPGTGKTLLAKAVatESEANF 580
                                       89*************99855444444 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.4e-05    0.0047      37     200 ..     219     386 ..     213     406 .. 0.74
   2 ?   -0.5   0.1       2.7   9.1e+02     159     193 ..     446     485 ..     424     501 .. 0.76
   3 !   10.2   0.0    0.0015      0.51      37     142 ..     555     665 ..     544     719 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.4e-05
                                       EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHHHTT-.SEEEEE-GGGGTT- CS
                          Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkkaeefkeklrkv.DvLliDDiqflagk 112
                                       +++yg+ G Gkt L ka++ne+ ++      + +++ e +++     +++  e fke+  ++  ++ iD+i  +a k
  gi|242398512|ref|YP_002993936.1| 219 VLLYGPPGTGKTLLAKAVANEANAH-----FIAINGPEIMSKYYGESEERLREVFKESEENApSIIFIDEIDAIAPK 290
                                       79****************9987665.....56688999999999999999999****9886527899*******999 PP

                                       H.........HHHHHHHHHHHHHHTTT-EEEEEESS-TTT-SS--HHHHHHHHSSEEEE-----HHHHHHHHHHHHH CS
                          Bac_DnaA 113 e.........ktqeelfhtfnalleegkqvvlssDrsPkeleeledrlrsrfeaGlvvdieppdletrlailkkkie 180
                                                 ++  +l+++++ l   gk +v+ +   P +l+    r   rf++   ++i  pd++ r +il+ + +
  gi|242398512|ref|YP_002993936.1| 291 RgevtgevekRVVAQLLTLMDGLKSRGKVIVIGATNRPDALDPAL-RRPGRFDRE--IEIGVPDKQGRKEILQIHTR 364
                                       62222211113445788888999999************9987654.335788875..56667999999999987666 PP

                                       HTT--..--TTHHHHHHHH--S CS
                          Bac_DnaA 181 aekle..vpeevlefiaervtd 200
                                          +e   ++e ++ + +++++
  gi|242398512|ref|YP_002993936.1| 365 GMPIEpdFRKEEVKKVLKELKQ 386
                                       5555555555555555555555 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 2.7
                                       EEEE-----HHHHHHHHHHHHHHTT--.....--TTHHHH CS
                          Bac_DnaA 159 lvvdieppdletrlailkkkieaekle.....vpeevlef 193
                                       + +d+    +e ++a l++ ie+ k++     +p+evle 
  gi|242398512|ref|YP_002993936.1| 446 VGADLAALAREAAMAALRRLIEEGKIDfeaesIPKEVLEE 485
                                       5567888889999999999999999987777788888764 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.0015
                                       EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHHHT.T-SEEEEE-GGGGTT- CS
                          Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkkaeefkeklr.kvDvLliDDiqflagk 112
                                       +++yg+ G Gkt L ka++ e ++n+       + + e l++ v   +++  e f++  + +  v+ iD+i  +a +
  gi|242398512|ref|YP_002993936.1| 555 ILLYGPPGTGKTLLAKAVATESEANFIG-----IRGPEVLSKWVGESEKNIREIFRKARQaAPTVIFIDEIDAIAPR 626
                                       79****************9987777655.....56888888999888888888888776624568889999999876 PP

                                       HHHH..HHHHHHHHHHH.......TTT-EEEEEESS-TT CS
                          Bac_DnaA 113 ektq..eelfhtfnall.......eegkqvvlssDrsPk 142
                                        +++       ++n+ll       e++  vv+++   P 
  gi|242398512|ref|YP_002993936.1| 627 RGSDvnRVTDRLINQLLtemdgieENSGVVVIAATNRPD 665
                                       543311322233333331111111444555666666665 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   0.00014     0.048      25      43 ..     219     237 ..     215     242 .. 0.91
   2 !   13.6   0.1   9.8e-05     0.032      25      43 ..     555     573 ..     544     578 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00014
                      Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                       +ll+GppG+GKt+lak+++
  gi|242398512|ref|YP_002993936.1| 219 VLLYGPPGTGKTLLAKAVA 237
                                       89*************9875 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 9.8e-05
                      Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                       +ll+GppG+GKt+lak+++
  gi|242398512|ref|YP_002993936.1| 555 ILLYGPPGTGKTLLAKAVA 573
                                       89*************9875 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0    0.0001     0.035       2      44 ..     219     266 ..     218     297 .. 0.71
   2 !   11.3   0.0   0.00088      0.29       2      30 ..     555     588 ..     554     622 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 0.0001
                            AAA_28   2 ivitGgestGKTtlleaLaar.gypvv....pEaareileeklakged 44 
                                       + + G+++tGKT l++a a++ +   +    pE++ +++ e  ++ ++
  gi|242398512|ref|YP_002993936.1| 219 VLLYGPPGTGKTLLAKAVANEaNAHFIaingPEIMSKYYGESEERLRE 266
                                       6799***************65544433113677777666655555444 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00088
                            AAA_28   2 ivitGgestGKTtlleaLaar...gypvv..pEa 30 
                                       i + G+++tGKT l++a a +   ++  +  pE+
  gi|242398512|ref|YP_002993936.1| 555 ILLYGPPGTGKTLLAKAVATEseaNFIGIrgPEV 588
                                       7899***************554333222234444 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0   0.00044      0.15      52      84 ..     215     247 ..     205     288 .. 0.71
   2 !   13.6   0.0   8.5e-05     0.028      21     115 ..     511     619 ..     495     667 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00044
                            DUF815  52 pannvLLwGarGtGKSslvkallneyaeegLrl 84 
                                       p + vLL+G  GtGK  l ka+ ne++++ +++
  gi|242398512|ref|YP_002993936.1| 215 PPKGVLLYGPPGTGKTLLAKAVANEANAHFIAI 247
                                       56789********************99988665 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 8.5e-05
                            DUF815  21 evdevklddLvgidkqkealvente.......qfleg..lpannvLLwGarGtGKSslvkallneyaeeg..Lrlie 86 
                                       e+ +v+++d+ g+++ k++l e +e       +f++   +p + +LL+G  GtGK  l ka+ +e +++   +r  e
  gi|242398512|ref|YP_002993936.1| 511 EIPNVRWNDIGGLEEVKQQLREAVEwplkypeAFMAMgiNPPKGILLYGPPGTGKTLLAKAVATESEANFigIRGPE 587
                                       56778999999999999999888753332222565432367899*******************99988764567677 PP

                            DUF815  87 vekedlkelpklvell.r..erperfilfvDD 115
                                       v  + + e +k ++++ r  +++   ++f+D 
  gi|242398512|ref|YP_002993936.1| 588 VLSKWVGESEKNIREIfRkaRQAAPTVIFIDE 619
                                       77666655544333331311223346777775 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0     0.003         1       3      24 ..     219     240 ..     217     244 .. 0.89
   2 ?    1.2   0.0       0.9     3e+02      60     115 ..     255     312 ..     250     359 .. 0.70
   3 !    8.7   0.0    0.0047       1.6       3      23 ..     555     575 ..     553     580 .. 0.89
   4 ?    2.5   0.0      0.36   1.2e+02      62     115 ..     593     645 ..     585     673 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.003
                                       EEEEC-TTTCHHHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklalaw 24 
                                       v+l G++G GKT L++ +a ++
  gi|242398512|ref|YP_002993936.1| 219 VLLYGPPGTGKTLLAKAVANEA 240
                                       799**************99876 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.9
                                       CCCTS--SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH.............HHHHHCT CS
                             NACHT  60 sqlpepaapvsevwavllelperlLlilDglDelvtdlgq....kekqpvrtlLselirk 115
                                       + + e++++ +ev+++  e++ ++ +i D +D ++ + g+      +++v   L +l+ +
  gi|242398512|ref|YP_002993936.1| 255 KYYGESEERLREVFKESEENAPSIIFI-DEIDAIAPKRGEvtgeV-EKRVVAQLLTLMDG 312
                                       567788999999999999999999985.*****999999998844.44444444477766 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0047
                                       EEEEC-TTTCHHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                       ++l G++G GKT L++ +a++
  gi|242398512|ref|YP_002993936.1| 555 ILLYGPPGTGKTLLAKAVATE 575
                                       7899************99986 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.36
                                       CTS--SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH.........HHHHHCT CS
                             NACHT  62 lpepaapvsevwavllelperlLlilDglDelvtdlgqkekqpvrtlLselirk 115
                                         e++++++e +   ++++  +++ +D +D ++   g + ++ +++l+++l+++
  gi|242398512|ref|YP_002993936.1| 593 VGESEKNIRE-IFRKARQAAPTVIFIDEIDAIAPRRGSDVNRVTDRLINQLLTE 645
                                       5677777888.44446777888899*********99999999999999999987 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     0.095      31      60 ..     214     242 ..     206     256 .. 0.82
   2 !   10.8   0.0   0.00077      0.26      25      58 ..     544     577 ..     540     584 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00029
                             AAA_7  31 knkkpvllvGptGtGKtviikdllkkldke 60 
                                       +  k vll+Gp GtGKt+++k + ++ +  
  gi|242398512|ref|YP_002993936.1| 214 EPPKGVLLYGPPGTGKTLLAKAVANEAN-A 242
                                       55688*****************999887.3 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00077
                             AAA_7  25 llelllknkkpvllvGptGtGKtviikdllkkld 58 
                                       ++ + ++  k +ll+Gp GtGKt+++k + ++ +
  gi|242398512|ref|YP_002993936.1| 544 FMAMGINPPKGILLYGPPGTGKTLLAKAVATESE 577
                                       66677777899***************99776655 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0045       1.5      36      52 ..     219     235 ..     213     240 .. 0.87
   2 ?    0.5   0.0       1.1   3.7e+02     129     176 ..     263     310 ..     252     325 .. 0.76
   3 !   11.8   1.6   0.00041      0.14      36     148 ..     555     658 ..     541     658 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0045
                            AAA_25  36 allaGapgtGKttlald 52 
                                       +ll+G+pgtGKt la  
  gi|242398512|ref|YP_002993936.1| 219 VLLYGPPGTGKTLLAKA 235
                                       69***********9965 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1.1
                            AAA_25 129 dvdaleaaieevegvrlvviDplsralggdensnsdv.galvealeria 176
                                        ++++ ++ ee + +  + iD ++++ +   +   +v +++v++l  + 
  gi|242398512|ref|YP_002993936.1| 263 RLREVFKESEE-NAPSIIFIDEIDAIAPKRGEVTGEVeKRVVAQLLTLM 310
                                       45566677777.56***********999977777776688888886664 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 0.00041
                            AAA_25  36 allaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgealrddarllvldlagve 112
                                       +ll+G+pgtGKt la  +a +  +  ++ g++ pe    ++   E +  e+ r++r++  ++       ++d     
  gi|242398512|ref|YP_002993936.1| 555 ILLYGPPGTGKTLLAKAVATE--SEANFIGIRGPEVLSKWVGESEKNIREIFRKARQAAPTV------IFIDE---- 619
                                       69**********998655544..556788876677777777777666656655555444443......33321.... PP

                            AAA_25 113 slpLfakdrggtl...ltadvdaleaaieeveg.vrlvvi 148
                                        ++ +a++rg+ +   +++ +++l  +++ +e+  ++vvi
  gi|242398512|ref|YP_002993936.1| 620 -IDAIAPRRGSDVnrvTDRLINQLLTEMDGIEEnSGVVVI 658
                                       .222222222222223677777777777777665666665 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0    0.0014      0.47       6      66 ..     211     269 ..     210     411 .. 0.82
   2 !   12.3   0.0   0.00056      0.18       6      73 ..     547     613 ..     544     662 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0014
                                       EEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   6 lklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpq 66 
                                       l +++ + v + G+ G+GK+ L+k++a++ +     i ++g ++ ++   +++++++ +++
  gi|242398512|ref|YP_002993936.1| 211 LGIEPPKGVLLYGPPGTGKTLLAKAVANEANA--HFIAINGPEIMSKYYGESEERLREVFK 269
                                       5678888899*****************99864..566667766666555555555555554 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00056
                                       EEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
                          ABC_tran   6 lklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpe 73 
                                       + +++ + + + G+ G+GK+ L+k++a +++  +  i ++g ++ ++   +++k+i+ ++ +  q  p+
  gi|242398512|ref|YP_002993936.1| 547 MGINPPKGILLYGPPGTGKTLLAKAVATESE--ANFIGIRGPEVLSKWVGESEKNIREIFRKaRQAAPT 613
                                       6678888899*****************9986..678888999999988889999998888884444454 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   3.7e-05     0.012      16     122 ..     212     322 ..     205     325 .. 0.63
   2 ?   -1.7   0.9       6.8   2.3e+03      63     119 ..     375     428 ..     366     444 .. 0.58
   3 !    7.8   0.0    0.0082       2.7      21      45 ..     553     577 ..     542     642 .. 0.83
   4 ?   -0.4   0.0       2.6   8.7e+02     110     131 ..     600     624 ..     584     662 .. 0.59

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.7e-05
                          ATPase_2  16 erepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefie.......eeeekkklekal... 82 
                                         ep + +++YGp g GKt L k ++++ +     ++  i+  e+ ++++ e+ e       e              
  gi|242398512|ref|YP_002993936.1| 212 GIEPPKGVLLYGPPGTGKTLLAKAVANEANA----HFIAINGPEIMSKYYGESEErlrevfkE----------Seen 274
                                       557777899**********999999999844....3445555556556665553333332211..........1122 PP

                          ATPase_2  83 .........giavpkaeleeilkeksklvfkaielllekikkkgkkiii 122
                                                 +a+  +++ e+  e  k v +++  l++ +k +gk i+i
  gi|242398512|ref|YP_002993936.1| 275 apsiifideIDAIAPKRG-EVTGEVEKRVVAQLLTLMDGLKSRGKVIVI 322
                                       222233443334444444.566788889999999999999999997666 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 6.8
                          ATPase_2  63 skldefieeeeekkklekalgiavpkaeleeilkeksklvfkaielllekikkkgkk 119
                                       +++++ ++e ++++++++a+  a+ k e    l +k + + +ai ++ +k+ ++ k 
  gi|242398512|ref|YP_002993936.1| 375 EEVKKVLKELKQDDRFRDAAERALYKIED---LADKEEIIRRAIRDIDDKLYEEVKH 428
                                       34445555666666666666555555333...3456666666666666666665554 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0082
                          ATPase_2  21 eiyfiYGpegsGKtaLlkeiienle 45 
                                       + +++YGp g GKt L k +++++e
  gi|242398512|ref|YP_002993936.1| 553 KGILLYGPPGTGKTLLAKAVATESE 577
                                       55899************99998874 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 2.6
                          ATPase_2 110 lekikkkgkk...iiiiiDelqkli 131
                                       +++i +k+++    +i+iDe+  + 
  gi|242398512|ref|YP_002993936.1| 600 IREIFRKARQaapTVIFIDEIDAIA 624
                                       3444455555555899999998776 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   0.00042      0.14      19      59 ..     216     256 ..     188     267 .. 0.75
   2 !    9.7   0.0    0.0024      0.79      21      45 ..     549     578 ..     517     587 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00042
                                       TEEEEEEESTTSSHHHHHHHHHHHTT--..----TTTTSEEEE CS
                              TsaE  19 gdvilLeGdLGaGKTtlvrglakalgve..evkSPTFtlveeY 59 
                                        + +lL+G+ G+GKT l++++a++ + +  +++ P   ++++Y
  gi|242398512|ref|YP_002993936.1| 216 PKGVLLYGPPGTGKTLLAKAVANEANAHfiAINGP--EIMSKY 256
                                       3459*******************998877777777..455555 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0024
                                       E.....EEEEESTTSSHHHHHHHHHHHTT- CS
                              TsaE  21 v.....ilLeGdLGaGKTtlvrglakalgv 45 
                                       +     ilL+G+ G+GKT l++++a + + 
  gi|242398512|ref|YP_002993936.1| 549 InppkgILLYGPPGTGKTLLAKAVATESEA 578
                                       0344449*****************987665 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0    0.0011      0.36      22      43 ..     219     240 ..     211     246 .. 0.86
   2 !   10.1   0.1    0.0012       0.4      22      42 ..     555     575 ..     542     580 .. 0.84
   3 ?   -2.2   0.0       7.1   2.4e+03      66      97 ..     749     780 ..     737     801 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0011
                                       EEEE--TTSSTTHHHHHHHHHH CS
                              PhoH  22 vfaiGpaGtGKtylavalavea 43 
                                       v   Gp GtGKt+la a+a ea
  gi|242398512|ref|YP_002993936.1| 219 VLLYGPPGTGKTLLAKAVANEA 240
                                       6789************999765 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0012
                                       EEEE--TTSSTTHHHHHHHHH CS
                              PhoH  22 vfaiGpaGtGKtylavalave 42 
                                       +   Gp GtGKt+la a+a e
  gi|242398512|ref|YP_002993936.1| 555 ILLYGPPGTGKTLLAKAVATE 575
                                       5678************99976 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 7.1
                                       -SS---------TTTHHHHHHHTTTS-TTCHH CS
                              PhoH  66 GflpgdleekvdpylrplydaLkdllgaekve 97 
                                       G    d++e+v++ +r + +a+k++  + + e
  gi|242398512|ref|YP_002993936.1| 749 GTRASDIRERVKVTMRDFEEAMKKVGPSVSEE 780
                                       56678999999999999999999875332222 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0    0.0017      0.56       2      30 ..     219     247 ..     218     293 .. 0.88
   2 !   10.0   0.0    0.0017      0.58       2      37 ..     555     589 ..     554     669 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0017
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkri 30 
                                       vll g PG++ktll+ka+a+  +++f  i
  gi|242398512|ref|YP_002993936.1| 219 VLLYGPPGTGKTLLAKAVANEANAHFIAI 247
                                       7999*****************99999766 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0017
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftpdll 37 
                                       +ll g PG++ktll+ka+a+  +++f  i+  p++l
  gi|242398512|ref|YP_002993936.1| 555 ILLYGPPGTGKTLLAKAVATESEANFIGIR-GPEVL 589
                                       7999*****************999998776.45555 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0    0.0013      0.42      14      37 ..     211     234 ..     191     243 .. 0.87
   2 ?   -1.8   0.0       4.9   1.6e+03     108     153 ..     261     312 ..     239     323 .. 0.66
   3 ?   -2.8   0.1       9.9   3.3e+03     119     147 ..     392     418 ..     354     466 .. 0.56
   4 !   10.9   0.0   0.00064      0.21      13      41 ..     546     574 ..     520     585 .. 0.83
   5 ?    0.4   0.0         1   3.4e+02     109     148 ..     598     639 ..     587     653 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0013
                            ATPase  14 gGipegrvvlitGepGtGKtifal 37 
                                        Gi   + vl++G pGtGKt++a+
  gi|242398512|ref|YP_002993936.1| 211 LGIEPPKGVLLYGPPGTGKTLLAK 234
                                       578888899*************97 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.9
                            ATPase 108 ieelaeaikeika...krvviDsitgl...ayeekeavaReilrqlvrvlkk 153
                                        e+l+e+ ke ++   + + iD i+++     e + +v ++ + ql++ + +
  gi|242398512|ref|YP_002993936.1| 261 EERLREVFKESEEnapSIIFIDEIDAIapkRGEVTGEVEKRVVAQLLTLMDG 312
                                       4566666666555444778889988883212333444556666777766655 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 9.9
                            ATPase 119 kakrvviDsitglayeekeavaReilrql 147
                                        a    + +i+ l   +ke+ +R+ +r +
  gi|242398512|ref|YP_002993936.1| 392 DAAERALYKIEDL--ADKEEIIRRAIRDI 418
                                       3333333333333..33333333333332 PP

  == domain 4  score: 10.9 bits;  conditional E-value: 0.00064
                            ATPase  13 kgGipegrvvlitGepGtGKtifalqFli 41 
                                         Gi   + +l++G pGtGKt++a+  + 
  gi|242398512|ref|YP_002993936.1| 546 AMGINPPKGILLYGPPGTGKTLLAKAVAT 574
                                       468888899**************987655 PP

  == domain 5  score: 0.4 bits;  conditional E-value: 1
                            ATPase 109 eelaeaikeika...krvviDsitglayeekeavaReilrqlv 148
                                       ++++e+ ++ ++   + + iD i+++a +  ++v R + ++l+
  gi|242398512|ref|YP_002993936.1| 598 KNIREIFRKARQaapTVIFIDEIDAIAPRRGSDVNRVT-DRLI 639
                                       44555544444334488888888888555555555543.3333 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     0.097       4      65 ..     219     273 ..     216     302 .. 0.70
   2 !    7.9   0.0    0.0047       1.5       4      25 ..     555     576 ..     552     619 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00029
                           DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvl.vlrealakkeekkkkkeafe 65 
                                       vl  G +GtGKt+++ ++++e+       +a+++  N+p+++ +++ + +++  ++ +ke+ e
  gi|242398512|ref|YP_002993936.1| 219 VLLYGPPGTGKTLLAKAVANEA-------NAHFIAINGPEIMsKYYGESEERL-REVFKESEE 273
                                       6789****************99.......788888888886625555555555.444444333 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0047
                           DUF2075   4 vlVtGvaGtGKtvvllnllael 25 
                                       +l  G +GtGKt+++ ++++e 
  gi|242398512|ref|YP_002993936.1| 555 ILLYGPPGTGKTLLAKAVATES 576
                                       6789***********9999987 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 !    9.7   0.0    0.0012       0.4     117     136 ..     219     238 ..     213     245 .. 0.90
   2 !    9.6   0.0    0.0013      0.43     117     136 ..     555     574 ..     543     578 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0012
                         Parvo_NS1 117 vwfyGpantGktnlaeaIak 136
                                       v++yGp+ tGkt la+a a+
  gi|242398512|ref|YP_002993936.1| 219 VLLYGPPGTGKTLLAKAVAN 238
                                       89***************997 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0013
                         Parvo_NS1 117 vwfyGpantGktnlaeaIak 136
                                       +++yGp+ tGkt la+a a+
  gi|242398512|ref|YP_002993936.1| 555 ILLYGPPGTGKTLLAKAVAT 574
                                       89***************997 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0   0.00091       0.3      14      51 ..     214     249 ..     206     266 .. 0.88
   2 !    9.4   0.0    0.0018       0.6      16      49 ..     552     583 ..     544     588 .. 0.87
   3 ?   -2.2   0.1       6.3   2.1e+03      55      90 ..     760     795 ..     756     800 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00091
                        Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnvvrldp 51 
                                       e Pk +ll G pG GK+ la+++++e   +  ++ +++
  gi|242398512|ref|YP_002993936.1| 214 EPPKGVLLYGPPGTGKTLLAKAVANEA--NAHFIAING 249
                                       56999*********************8..788888776 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0018
                        Zeta_toxin  16 PklillgGqpGAGKselaellkdelerqgnvvrl 49 
                                       Pk ill G pG GK+ la+++++e   + n++ +
  gi|242398512|ref|YP_002993936.1| 552 PKGILLYGPPGTGKTLLAKAVATES--EANFIGI 583
                                       999********************98..6777765 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 6.3
                        Zeta_toxin  55 RelhPeyeeilkadpkkaseltqkdaselvekllqe 90 
                                       +   +++ee++k+   ++se t +  +++ e+ +++
  gi|242398512|ref|YP_002993936.1| 760 KVTMRDFEEAMKKVGPSVSEETMEYYKRIEEMFIKK 795
                                       556788999999999999999999999988888776 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0    0.0035       1.2      21      43 ..     219     241 ..     206     251 .. 0.83
   2 !    8.0   0.2    0.0063       2.1      22      44 ..     556     578 ..     543     637 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0035
                            AAA_30  21 avltGpAGtGKttalkalreawe 43 
                                       ++l Gp+GtGKt + ka+++ ++
  gi|242398512|ref|YP_002993936.1| 219 VLLYGPPGTGKTLLAKAVANEAN 241
                                       6789************9977555 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0063
                            AAA_30  22 vltGpAGtGKttalkalreawea 44 
                                       +l Gp+GtGKt + ka++   ea
  gi|242398512|ref|YP_002993936.1| 556 LLYGPPGTGKTLLAKAVATESEA 578
                                       688**********9999876555 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0    0.0024      0.79      19      42 ..     218     241 ..     196     285 .. 0.75
   2 !    7.9   0.0    0.0073       2.4      19      38 ..     554     573 ..     533     614 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0024
                            AAA_11  19 itliqGPPGtgKTktivellsqll 42 
                                        +l+ GPPGtgKT    ++ ++++
  gi|242398512|ref|YP_002993936.1| 218 GVLLYGPPGTGKTLLAKAVANEAN 241
                                       5799*********88888888776 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0073
                            AAA_11  19 itliqGPPGtgKTktivell 38 
                                         l+ GPPGtgKT    ++ 
  gi|242398512|ref|YP_002993936.1| 554 GILLYGPPGTGKTLLAKAVA 573
                                       5699*********6555544 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0096       3.2       1      25 [.     222     246 ..     222     296 .. 0.76
   2 ?    0.5   0.3       2.2   7.5e+02      47      74 ..     416     445 ..     388     490 .. 0.68
   3 ?    6.8   0.0     0.026       8.5       1      48 [.     558     606 ..     558     652 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0096
                                       EE-TTSSHHHHHHHHHHHHTEEEEE CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthls 25 
                                       +G+PG GK+ +++ ++ + + +++ 
  gi|242398512|ref|YP_002993936.1| 222 YGPPGTGKTLLAKAVANEANAHFIA 246
                                       7************999998766553 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 2.2
                                       C....TSHHHHHHHHHHHHHHHHHHHHHSSEE CS
                            AAA_17  47 r....klpleekkelqkeaaekiaeeakkkgv 74 
                                       r    kl++e+k++l +++ e++ae+  ++g+
  gi|242398512|ref|YP_002993936.1| 416 RdiddKLYEEVKHRLIDLLLEELAEK--THGF 445
                                       22224677777777777777777775..3444 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.026
                                       EE-TTSSHHHHHHHHHHHH..TEEEEEHHHHHHHHHHTTTSHSSHHHHCT CS
                            AAA_17   1 lGgPGsGKgtqceklveky..gfthlsaGdllreeakrgglakardemrk 48 
                                       +G+PG GK+ +++ ++ +   +f  +   ++l + + +++ ++ r+ +rk
  gi|242398512|ref|YP_002993936.1| 558 YGPPGTGKTLLAKAVATESeaNFIGIRGPEVLSKWVGESE-KNIREIFRK 606
                                       7***********9998765225555555555555544444.345555555 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0    0.0023      0.75      22      43 ..     218     239 ..     204     246 .. 0.79
   2 !    7.0   0.0    0.0087       2.9      23      44 ..     555     576 ..     549     585 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0023
                                       EEEEEESTTSSHHHHHHHHCCS CS
                            NB-ARC  22 vvalvGmgGvGKttlakqilnk 43 
                                        v l+G +G GKt lak + n+
  gi|242398512|ref|YP_002993936.1| 218 GVLLYGPPGTGKTLLAKAVANE 239
                                       4889***************998 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0087
                                       EEEEESTTSSHHHHHHHHCCSH CS
                            NB-ARC  23 valvGmgGvGKttlakqilnks 44 
                                       + l+G +G GKt lak +  +s
  gi|242398512|ref|YP_002993936.1| 555 ILLYGPPGTGKTLLAKAVATES 576
                                       679*************998874 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    0.0095       3.2      11      33 ..     217     239 ..     213     275 .. 0.81
   2 ?   -1.4   0.0       8.2   2.7e+03      95     125 ..     268     298 ..     251     323 .. 0.70
   3 ?    7.8   0.2     0.011       3.8      11      32 ..     553     574 ..     545     622 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0095
                            AAA_19  11 kvllvtaGpGtGKTrvlkhival 33 
                                       k +l+ ++pGtGKT + k++ ++
  gi|242398512|ref|YP_002993936.1| 217 KGVLLYGPPGTGKTLLAKAVANE 239
                                       56899*********988776655 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 8.2
                            AAA_19  95 eeekklqeeellivDEfqdvdelqyrLlkal 125
                                        +e++ ++  ++++DE+  + +   ++  ++
  gi|242398512|ref|YP_002993936.1| 268 FKESEENAPSIIFIDEIDAIAPKRGEVTGEV 298
                                       3444444556999999998887666655555 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.011
                            AAA_19  11 kvllvtaGpGtGKTrvlkhiva 32 
                                       k +l+ ++pGtGKT + k++ +
  gi|242398512|ref|YP_002993936.1| 553 KGILLYGPPGTGKTLLAKAVAT 574
                                       66899*********88776654 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.027       9.1       2      32 ..     219     249 ..     218     265 .. 0.84
   2 ?   -0.5   0.1         3   9.9e+02      82     104 ..     261     284 ..     248     300 .. 0.74
   3 ?    6.3   0.0     0.025       8.3       2      38 ..     555     588 ..     554     592 .. 0.76
   4 ?    0.1   0.0       1.9   6.4e+02      81     104 ..     596     620 ..     591     623 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.027
                                       EEEE--TTSSHHHHHHHHHHHH...GGGEEE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgG 32 
                                       v++ GppG+GKt l k v+++ + + + ++G
  gi|242398512|ref|YP_002993936.1| 219 VLLYGPPGTGKTLLAKAVANEANAHFIAING 249
                                       6788**************9998766555555 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 3
                                       HHHHHHHHHHHH.HHH-EEEE--- CS
                          NTPase_1  82 eelalealrkal.seadviviDEi 104
                                       ee   e+++++  + + +i iDEi
  gi|242398512|ref|YP_002993936.1| 261 EERLREVFKESEeNAPSIIFIDEI 284
                                       55556667666635566******9 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.025
                                       EEEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgGfyteev 38 
                                       +++ GppG+GKt l k v+ +    + +  G+  +ev
  gi|242398512|ref|YP_002993936.1| 555 ILLYGPPGTGKTLLAKAVATES---EANFIGIRGPEV 588
                                       6788*******99999988776...556667766666 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 1.9
                                       HHHHHHHHHHHHH.HHH-EEEE--- CS
                          NTPase_1  81 feelalealrkal.seadviviDEi 104
                                        e+ + e++rka    + vi iDEi
  gi|242398512|ref|YP_002993936.1| 596 SEKNIREIFRKARqAAPTVIFIDEI 620
                                       577778889998844555******9 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 ?    5.8   0.0     0.019       6.4     130     156 ..     217     243 ..     190     251 .. 0.87
   2 ?    6.1   0.0     0.015       5.1     116     152 ..     539     575 ..     395     583 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.019
                             T2SSE 130 glilvsGgTgsGKttllyallkeinks 156
                                       + +l+ G+ g+GKt l+ a+ +e n++
  gi|242398512|ref|YP_002993936.1| 217 KGVLLYGPPGTGKTLLAKAVANEANAH 243
                                       558999****************99987 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.015
                             T2SSE 116 ekiaevlrkavrerglilvsGgTgsGKttllyallke 152
                                       +  +++++  ++  + il+ G+ g+GKt l+ a+ +e
  gi|242398512|ref|YP_002993936.1| 539 KYPEAFMAMGINPPKGILLYGPPGTGKTLLAKAVATE 575
                                       4456666777777889**************9998776 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 ?    6.8   0.0      0.02       6.7      24      46 ..     219     241 ..     213     290 .. 0.81
   2 ?    5.5   0.0      0.05        17      24      47 ..     555     578 ..     550     633 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.02
                                       EEEEEETT--HHHHHHCC--TTS CS
                   Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsg 46 
                                       v+l G++G+gk+l A++ ++++ 
  gi|242398512|ref|YP_002993936.1| 219 VLLYGPPGTGKTLLAKAVANEAN 241
                                       9****************998764 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.05
                                       EEEEEETT--HHHHHHCC--TTS- CS
                   Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgp 47 
                                       ++l G++G+gk+l A++ + +s+ 
  gi|242398512|ref|YP_002993936.1| 555 ILLYGPPGTGKTLLAKAVATESEA 578
                                       799**************9988775 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0     0.018       5.9       4      27 ..     222     245 ..     219     249 .. 0.90
   2 ?   -1.9   0.1         7   2.3e+03      70     116 ..     362     411 ..     352     425 .. 0.67
   3 ?    4.8   0.0      0.06        20       3      27 ..     557     581 ..     555     583 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.018
                                       E-STTSSHHHHHHHHHHHHT-EEE CS
                    Cytidylate_kin   4 DGPagsGKssvaralaeklglkyl 27 
                                        GP g+GK  +a+a+a++ +++++
  gi|242398512|ref|YP_002993936.1| 222 YGPPGTGKTLLAKAVANEANAHFI 245
                                       6*******************9997 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 7
                                       EETTEE-TTGGGSHHHHHHHHHHTTSHHHHHHHHH...HHHTT-BSSBEE CS
                    Cytidylate_kin  70 llngedveeelrsdevekavSavaaipavRailvk...klrelvkkarvv 116
                                          g+ +e + r++ev+k+  ++ +  ++R++  +   k+ +l++k++++
  gi|242398512|ref|YP_002993936.1| 362 HTRGMPIEPDFRKEEVKKVLKELKQDDRFRDAAERalyKIEDLADKEEII 411
                                       56677788888888888888888888888866554111444455555555 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.06
                                       EE-STTSSHHHHHHHHHHHHT-EEE CS
                    Cytidylate_kin   3 iDGPagsGKssvaralaeklglkyl 27 
                                       + GP g+GK  +a+a+a++ +++++
  gi|242398512|ref|YP_002993936.1| 557 LYGPPGTGKTLLAKAVATESEANFI 581
                                       67****************9998876 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0    0.0045       1.5       4      62 ..     220     283 ..     219     304 .. 0.83
   2 ?    1.4   0.0      0.64   2.1e+02       4      60 ..     556     617 ..     555     625 .. 0.52
   3 ?    0.1   0.0       1.6   5.2e+02      65     102 ..     596     633 ..     586     688 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0045
                               Zot   4 lvtGapGsgKts..gavkkdllpalk..egRkiitnidGlrlerieqvlgekvs.tarliridn 62 
                                       l +G+pG+gKt+  +av ++++      +g +i+ +  G   er++ v++e  + ++ +i+id+
  gi|242398512|ref|YP_002993936.1| 220 LLYGPPGTGKTLlaKAVANEANAHFIaiNGPEIMSKYYGESEERLREVFKESEEnAPSIIFIDE 283
                                       679********733679998888444357**********************9999999***993 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.64
                               Zot   4 lvtGapGsgKtsga..vkkdllpalk..egRkiitnidGlrlerieqvlgekvs.tarliri 60 
                                       l +G+pG+gKt+ a  v  +         g ++  +  G   ++i+ +++++ + ++ +i+i
  gi|242398512|ref|YP_002993936.1| 556 LLYGPPGTGKTLLAkaVATESEANFIgiRGPEVLSKWVGESEKNIREIFRKARQaAPTVIFI 617
                                       56899999999865113332222111223555555555555555555555555544455555 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 1.6
                               Zot  65 gaetlkefakwatidkgallviDEcqeifpvrakegrk 102
                                       +++ + e++  a+ +   +++iDE   i p r   ++ 
  gi|242398512|ref|YP_002993936.1| 596 SEKNIREIFRKARQAAPTVIFIDEIDAIAPRRGSDVNR 633
                                       55666677777776788999****99998887665444 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0     0.026       8.6      21      50 ..     200     242 ..     186     293 .. 0.73
   2 ?    5.4   0.0     0.051        17      21      46 ..     532     574 ..     498     620 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.026
                                       ...............TTSEEEEEESTTSTHHHHHHHHHHHH-S CS
                            ResIII  21 s.............krdkrglikmaTGtGKTlvaaklierllk 50 
                                                     +  k +l+  + GtGKTl+a +++ +   
  gi|242398512|ref|YP_002993936.1| 200 LplkhpevfeklgiEPPKGVLLYGPPGTGKTLLAKAVANEANA 242
                                       344455555555558899999***********99877776654 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.051
                                       ...................TTSEEEEEESTTSTHHHHHHHHHH CS
                            ResIII  21 s.................krdkrglikmaTGtGKTlvaaklie 46 
                                       +                 +  k +l+  + GtGKTl+a +++ 
  gi|242398512|ref|YP_002993936.1| 532 EavewplkypeafmamgiNPPKGILLYGPPGTGKTLLAKAVAT 574
                                       3555555556666667778889999***********9955554 PP

>> DUF1905  Domain of unknown function (DUF1905)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1     0.081        27      56      80 ..      20      44 ..       5      45 .. 0.85
   2 ?    6.4   0.0     0.028       9.3      52      80 ..      59      87 ..      47      88 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.081
                                      T-EEEEE-HHHHHHHT--TTSEEEE CS
                           DUF1905 56 ggyiLpvkaavrkaigkeaGdtvtv 80
                                      g+ i+ v+++ +++ig++ Gd v++
  gi|242398512|ref|YP_002993936.1| 20 GRGIVRVDRNAMRKIGVQTGDIVEI 44
                                      88899*****************986 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.028
                                      ESSTT-EEEEE-HHHHHHHT--TTSEEEE CS
                           DUF1905 52 pmgkggyiLpvkaavrkaigkeaGdtvtv 80
                                      p+++g  i+ ++ ++rk +g+  Gd+vt+
  gi|242398512|ref|YP_002993936.1| 59 PEDEGLEIIRMDGTIRKNAGVGLGDEVTI 87
                                      5566888999*****************98 PP

>> AFG1_ATPase  AFG1-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.022       7.2      59      79 ..     213     233 ..     187     246 .. 0.86
   2 ?    4.0   0.0     0.057        19      60      79 ..     550     569 ..     524     577 .. 0.90
   3 ?   -3.1   0.0       8.2   2.7e+03     157     198 ..     653     697 ..     631     732 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.022
                       AFG1_ATPase  59 vepvrglYlwGgvGrGKtylm 79 
                                        ep++g+ l+G+ G GKt l 
  gi|242398512|ref|YP_002993936.1| 213 IEPPKGVLLYGPPGTGKTLLA 233
                                       58****************986 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.057
                       AFG1_ATPase  60 epvrglYlwGgvGrGKtylm 79 
                                       +p++g+ l+G+ G GKt l 
  gi|242398512|ref|YP_002993936.1| 550 NPPKGILLYGPPGTGKTLLA 569
                                       79***************985 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 8.2
                       AFG1_ATPase 157 rgvtlvaTSNia....PedLykdglqrqrFLpaIdlleshlevlev 198
                                        gv+++a  N++    P  L ++++ r    pa d ++ +le+ +v
  gi|242398512|ref|YP_002993936.1| 653 SGVVVIAATNRPdildPALLRPGRFDRIILVPAPD-VKARLEIFKV 697
                                       58999999997433335555555555555555544.4555555555 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 ?    7.3   0.0      0.01       3.4      18      67 ..     220     275 ..     217     326 .. 0.76
   2 ?    3.4   0.0      0.15        51      18      65 ..     556     609 ..     550     666 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.01
                                       EEEESTTSSHHHHHHHHHHHSSTS.....S.EEEEEEESEEHHHHHHHHHHCHHSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx.....x.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  18 lipgafgvGktvisqslskqsnsd.....d.aiiyvgiGergnevaevleefpegt 67 
                                       l+ g  g+Gkt +++++++++n++        i     Ge ++ ++ev++e +e+ 
  gi|242398512|ref|YP_002993936.1| 220 LLYGPPGTGKTLLAKAVANEANAHfiainGpEIMSKYYGESEERLREVFKESEENA 275
                                       678999***************99966665236666679**********99999943 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.15
                                       EEEESTTSSHHHHHHHHHHHSSTS.....S.EEEEEEESEEHHHHHHHHHHCHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx.....x.xxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  18 lipgafgvGktvisqslskqsnsd.....d.aiiyvgiGergnevaevleefpe 65 
                                       l+ g  g+Gkt ++++++ +s+++        +    +Ge +++++e++++ ++
  gi|242398512|ref|YP_002993936.1| 556 LLYGPPGTGKTLLAKAVATESEANfigirGpEVLSKWVGESEKNIREIFRKARQ 609
                                       688999**************9777555542355555688888888888777665 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.044        15       5      32 ..     220     247 ..     217     249 .. 0.90
   2 ?    1.2   0.1      0.61     2e+02     103     158 ..     381     440 ..     379     446 .. 0.73
   3 ?    3.4   0.0      0.12        41       5      29 ..     556     580 ..     553     584 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.044
                               IPT   5 lifGatttGKtaeaiklaketgapvivl 32 
                                       l++G+ +tGKt  a ++a+e  a  i++
  gi|242398512|ref|YP_002993936.1| 220 LLYGPPGTGKTLLAKAVANEANAHFIAI 247
                                       89*****************999888775 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.61
                               IPT 103 lkrmakdeywnadf.ewevkrlrlpdedvflakakkRvrqmlrpeeegas...lldElae 158
                                       lk++ +d ++++   ++  k+  l+d++  + +a++ + + l  e +++    ll+Elae
  gi|242398512|ref|YP_002993936.1| 381 LKELKQDDRFRDAAeRALYKIEDLADKEEIIRRAIRDIDDKLYEEVKHRLidlLLEELAE 440
                                       77888877776555155667888******************9987776531124666665 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.12
                               IPT   5 lifGatttGKtaeaiklaketgapv 29 
                                       l++G+ +tGKt  a ++a e  a  
  gi|242398512|ref|YP_002993936.1| 556 LLYGPPGTGKTLLAKAVATESEANF 580
                                       89****************9887665 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 ?    2.7   0.0      0.27        91       5      71 ..     223     284 ..     219     291 .. 0.60
   2 ?    7.9   0.0    0.0067       2.2       4      71 ..     558     620 ..     555     625 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.27
                   Viral_helicase1   5 GvpGcGKStlirkllrts..liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                       G pG GK+ l + ++++   + + +n p  e+ ++   +++ +  + +++ ++++       i+++DE+
  gi|242398512|ref|YP_002993936.1| 223 GPPGTGKTLLAKAVANEAnaHFIAINGP--EIMSKYYGESEERLREVFKESEENA-----PSIIFIDEI 284
                                       78**************966333333333..4444444444444444444433333.....358888886 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0067
                   Viral_helicase1   4 hGvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                        G pG GK+ l + ++ +s  ++  +r   e+l++++ +++++  + ++++ +a+       ++++DE+
  gi|242398512|ref|YP_002993936.1| 558 YGPPGTGKTLLAKAVATESeANFIGIRG-PEVLSKWVGESEKNIREIFRKARQAAPT-----VIFIDEI 620
                                       588*************999*99999999.********99999999999999988754.....8999997 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.041        13       1      23 [.     225     247 ..     225     275 .. 0.75
   2 ?   -1.2   0.2       5.8   1.9e+03     102     137 ..     390     429 ..     368     440 .. 0.51
   3 ?    3.8   0.0      0.17        57       1      23 [.     561     583 ..     561     611 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.041
                                       TTSSHHHHHHHHHHHHTSEEEEH CS
                               SKI   1 mGaGKstvGkllAkklglefiDl 23 
                                       +G+GK+ ++k++A++ + +fi +
  gi|242398512|ref|YP_002993936.1| 225 PGTGKTLLAKAVANEANAHFIAI 247
                                       69******************965 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 5.8
                                       HHHTTSSGGGCSCHH...HHHHHHHHH.HHHHHHCCSSCE CS
                               SKI 102 lkadkeRPllqeksk...eeelleela.ereplyeeaadv 137
                                        ++  eR+l++ ++    ee  ++ ++   ++lyee++++
  gi|242398512|ref|YP_002993936.1| 390 FRDAAERALYKIEDLadkEEIIRRAIRdIDDKLYEEVKHR 429
                                       2222335555554442222223455555555556555555 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.17
                                       TTSSHHHHHHHHHHHHTSEEEEH CS
                               SKI   1 mGaGKstvGkllAkklglefiDl 23 
                                       +G+GK+ ++k++A + + +fi +
  gi|242398512|ref|YP_002993936.1| 561 PGTGKTLLAKAVATESEANFIGI 583
                                       69****************99965 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     0.073        24      21      39 ..     216     233 ..     206     238 .. 0.76
   2 ?    4.6   0.0     0.081        27      21      42 ..     552     572 ..     543     574 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.073
                            AAA_29  21 lkgatlltGpsGsGKSTll 39 
                                       +kg +ll Gp G+GK+ l 
  gi|242398512|ref|YP_002993936.1| 216 PKG-VLLYGPPGTGKTLLA 233
                                       356.9**********8765 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.081
                            AAA_29  21 lkgatlltGpsGsGKSTllDAi 42 
                                       +kg +ll Gp G+GK+ l  A+
  gi|242398512|ref|YP_002993936.1| 552 PKG-ILLYGPPGTGKTLLAKAV 572
                                       456.9**********8776555 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 ?    4.0   0.0      0.07        23      23      56 ..     216     248 ..     208     258 .. 0.76
   2 ?    4.0   0.0     0.073        24      25      55 ..     554     583 ..     548     606 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.07
                                       --EEEEE-SSSSSTTTTHHHHHHHGGGS--EEEE CS
                              DAP3  23 vkrlvltGekgsGKSvlLlqalayAlekgwvvlh 56 
                                        k ++l+G +g+GK++ L++a+a  +++ ++ ++
  gi|242398512|ref|YP_002993936.1| 216 PKGVLLYGPPGTGKTL-LAKAVANEANAHFIAIN 248
                                       56689*********86.67777766666666555 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.073
                                       EEEEE-SSSSSTTTTHHHHHHHGGGS--EEE CS
                              DAP3  25 rlvltGekgsGKSvlLlqalayAlekgwvvl 55 
                                        ++l+G +g+GK++ L++a+a   e++++ +
  gi|242398512|ref|YP_002993936.1| 554 GILLYGPPGTGKTL-LAKAVATESEANFIGI 583
                                       578*********85.7777777666666655 PP

>> RuvA_C  RuvA, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   2.7      0.15        48      19      46 ..     393     418 ..     372     419 .. 0.70
   2 ?   -0.1   0.0       4.1   1.4e+03      32      42 ..     722     732 ..     715     736 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.15
                                       HHHHHHHHHHC-TTS-HHHHHHHHHCCT CS
                            RuvA_C  19 eaekAvakvlanpgasveelIraALklL 46 
                                        ae+A+ k+  ++ a+ ee+Ir A++ +
  gi|242398512|ref|YP_002993936.1| 393 AAERALYKI--EDLADKEEIIRRAIRDI 418
                                       355666666..66677********9975 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 4.1
                                       TS-HHHHHHHH CS
                            RuvA_C  32 gasveelIraA 42 
                                       ga++e+++r+A
  gi|242398512|ref|YP_002993936.1| 722 GADIEAVVREA 732
                                       67777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (810 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1050  (0.0585643); expected 358.6 (0.02)
Passed bias filter:                      848  (0.0472977); expected 358.6 (0.02)
Passed Vit filter:                       123  (0.00686039); expected 17.9 (0.001)
Passed Fwd filter:                        54  (0.00301188); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              54  [number of targets reported over threshold]
# CPU time: 1.01u 0.37s 00:00:01.38 Elapsed: 00:00:00.54
# Mc/sec: 4541.56
//
Query:       gi|242398513|ref|YP_002993937.1|  [L=170]
Description: Intracellular protease 1 [Thermococcus sibiricus MM 739]
Scores for complete 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-57  194.3   0.0    1.3e-57  194.2   0.0    1.0  1  DJ-1_PfpI   DJ-1/PfpI family
    0.00046   19.8   0.0    0.00069   19.3   0.0    1.2  1  Catalase_C  C-terminal domain found in long catalases
    0.00053   19.8   0.0    0.00064   19.5   0.0    1.3  1  GATase      Glutamine amidotransferase class-I
  ------ inclusion threshold ------
      0.044   13.4   0.0      0.056   13.0   0.0    1.3  1  GATase_3    CobB/CobQ-like glutamine amidotransferase domain
      0.096   12.8   0.2        1.4    9.1   0.0    2.2  2  SH3_12      Xrn1 SH3-like domain
       0.16   11.8   0.0       0.21   11.4   0.0    1.3  1  SNO         SNO glutamine amidotransferase family


Domain annotation for each model (and alignments):
>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  194.2   0.0   4.4e-61   1.3e-57       1     164 [.       5     167 ..       5     168 .. 0.99

  Alignments for each domain:
  == domain 1  score: 194.2 bits;  conditional E-value: 4.4e-61
                                       EEEEEEEETTBEHHHHHHHHHHHHHTTEEEEEEESSTSEEEETTSEEEE-SEEGGGCTCCG-SEEEE--BHHHHHHH CS
                         DJ-1_PfpI   1 kkvlvlladgvedvElivpvdvlkragikvdvvsvdkeevkgsrGlkvtvdaslddvkaaeyDalvlpGGragperl 77 
                                       +kvl+l+ad++ed+El++p+ ++k++g++v ++s +k++++g++ ++v vd ++d+v+++e+DalvlpGGra pe +
  gi|242398513|ref|YP_002993937.1|   5 MKVLFLTADTFEDLELFYPLYRMKEEGHEVYIASNKKGTIVGKHNYSVNVDLVFDEVNPDEFDALVLPGGRA-PEIV 80 
                                       69**********************************************************************.**** PP

                                       HTSHHHHHHHHHHHHTT-EEEEETTTHHHHHHTTTTTTSEE--SGGGHHHHHHTTSEE-SSSEEEETTEEEESSGGG CS
                         DJ-1_PfpI  78 renekvvelvkefaekgklvaaICagpqlLaaagvlkgrrvTsypavkdklekagakyvdkrvvvdgnlvTsrgpga 154
                                       r  +k+ve++k+++e+gk+va+IC+gpq+L++a vlkgr+ T++ ++kd+l +aga+y+dk+vvvdgn+v+sr+pg+
  gi|242398513|ref|YP_002993937.1|  81 RIYPKAVEIAKKMFEAGKPVASICHGPQILISARVLKGRKGTCVVTIKDDLINAGAEYIDKEVVVDGNWVSSRHPGD 157
                                       ***************************************************************************** PP

                                       HHHHHHHHHH CS
                         DJ-1_PfpI 155 aiefalelle 164
                                       ++++++e+++
  gi|242398513|ref|YP_002993937.1| 158 LYAWMREFVK 167
                                       *******997 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 !   19.3   0.0   2.3e-07   0.00069      30     127 ..      38     125 ..      28     140 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 2.3e-07
                        Catalase_C  30 egvdvtvvaeklgsaegvnrTYstadaveFDaivvadgaeslfsakataasslfpagrplqllldayrhgKpigalG 106
                                       ++ + t+v+++   + +v+  +   +  eFDa+v+ +g    +            +++++++ +++++ gKp++ + 
  gi|242398513|ref|YP_002993937.1|  38 SNKKGTIVGKHN-YSVNVDLVFDEVNPDEFDALVLPGGRAPEI---------VRIYPKAVEIAKKMFEAGKPVASIC 104
                                       556678999888.78889999*****************44433.........3568899****************** PP

                        Catalase_C 107 sgaealkaagisaeepGVyva 127
                                       +g ++l +a + + ++G  v 
  gi|242398513|ref|YP_002993937.1| 105 HGPQILISARVLKGRKGTCVV 125
                                       ********9999988886554 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   2.1e-07   0.00064      22      87 ..      50     113 ..      27     146 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 2.1e-07
                                       -EEEEEETTSHHHHHHHTHHSTSEEEEEEE..SSCTT.TTTHHHHHHHHCTSTS-EEEETHHHHHHHHH CS
                            GATase  22 vkvevvpidasaeeilellknpdgilvsgG..pgspg.vegkieaikearenkiPiLGICLGmQllaie 87 
                                       ++v+v+ +  +      + +++d+++++gG  p  +  + +++e++k+++e+++P+  IC G Q+l+ +
  gi|242398513|ref|YP_002993937.1|  50 YSVNVDLVFDEV-----NPDEFDALVLPGGraPEIVRiYPKAVEIAKKMFEAGKPVASICHGPQILISA 113
                                       444444444222.....24589******9955555559***************************9865 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.9e-05     0.056      35      90 ..      60     112 ..      16     128 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.9e-05
                          GATase_3  35 eslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqmLGe 90 
                                       e  +++ d+++lpGg+  +    + ++ ++++++    eag+pv  iC G q+L +
  gi|242398513|ref|YP_002993937.1|  60 EVNPDEFDALVLPGGRAPEIVRIYPKAVEIAKKMF---EAGKPVASICHGPQILIS 112
                                       3333779*********9999999999977777665...589************965 PP

>> SH3_12  Xrn1 SH3-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0   0.00047       1.4      24      41 ..      41      60 ..      32      67 .. 0.80
   2 ?    1.6   0.0       0.1     3e+02      22      57 ..     118     163 ..     109     168 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00047
                            SH3_12 24 rGtVVg..rsdtlleVlfDe 41
                                      +Gt+Vg  + +  ++++fDe
  gi|242398513|ref|YP_002993937.1| 41 KGTIVGkhNYSVNVDLVFDE 60
                                      8*****553347789****8 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.1
                            SH3_12  22 GlrGtVVg........rsdtlle..VlfDeeflsgtdlggrcskmr 57 
                                       G +Gt V         +  ++++  V+ D   +s  + g+  + mr
  gi|242398513|ref|YP_002993937.1| 118 GRKGTCVVtikddlinAGAEYIDkeVVVDGNWVSSRHPGDLYAWMR 163
                                       6777766667666665223444344999999999777777666666 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   6.9e-05      0.21      30      85 ..      62     115 ..      32     129 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.9e-05
                                       GGCC-SEEEE-SS-HHHHHHHHHHTT-HHHHHHHHHTT.--EEEETHH.HHHHCCEE CS
                               SNO  30 dlaevdaliiPGGestamskliertglyedllefvknsekvvlGtCaG.lillskel 85 
                                       + +e dal++PGG +  + ++  +     ++ +++ ++ k+v   C G  il+s+++
  gi|242398513|ref|YP_002993937.1|  62 NPDEFDALVLPGGRAPEIVRIYPKAV---EIAKKMFEAGKPVASICHGpQILISARV 115
                                       55789****************99987...6777778888999999999557777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.33s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1044.83
//
Query:       gi|242398514|ref|YP_002993938.1|  [L=141]
Description: RNA-binding protein, CRS1/YhbY family [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.3e-13   50.9   0.1    1.3e-13   50.9   0.1    1.5  2  CRS1_YhbY  CRS1 / YhbY (CRM) domain
     0.0074   16.2   0.4        1.9    8.5   0.0    2.4  2  HTH_Crp_2  Crp-like helix-turn-helix domain
  ------ inclusion threshold ------
       0.17   11.5   7.0        1.3    8.6   7.0    1.9  1  PTRF_SDPR  PTRF/SDPR family


Domain annotation for each model (and alignments):
>> CRS1_YhbY  CRS1 / YhbY (CRM) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.9   0.1   2.2e-17   1.3e-13       1      84 []       8      95 ..       8      95 .. 0.92
   2 ?   -2.9   0.1       1.4   8.3e+03      42      46 ..     110     114 ..     102     130 .. 0.52

  Alignments for each domain:
  == domain 1  score: 50.9 bits;  conditional E-value: 2.2e-17
                         CRS1_YhbY  1 LtekelrrLrhlairlkpkvkiGkaGvtkevvdeiheklkteelvkvkc.....egppalnmkrmaeiLeektgglviq 74
                                      L+ k +r+ r++  +++pk  +G++G+ ++v+ ei  +lk+  + kv++        ++ +++ +ae+++e t++++i+
  gi|242398514|ref|YP_002993938.1|  8 LPGKVRRAIRAKYYDIEPKAWVGRKGLEESVISEIATQLKKDGILKVEIrkgafT-STNMDRESIAEKVAELTDSELID 85
                                      68899********************************************987753.34455889*************** PP

                         CRS1_YhbY 75 rsgtsivLYR 84
                                      ++g+ ++L+R
  gi|242398514|ref|YP_002993938.1| 86 VRGKRFILFR 95
                                      *********9 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.4
                         CRS1_YhbY  42 eelvk 46 
                                       +e+ k
  gi|242398514|ref|YP_002993938.1| 110 KEVSK 114
                                       33322 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 !    7.3   0.1   0.00075       4.5      33      63 ..      34      67 ..      31      68 .. 0.75
   2 !    8.5   0.0   0.00032       1.9      32      58 ..      65      93 ..      62     103 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00075
                                      SSHHHHHHHHHHHHHTTSEE..ETEE.EEES-HH CS
                         HTH_Crp_2 33 ltretvsrilseLkreglis..rgrr.irildle 63
                                      l  + +s i ++Lk++g+++   +++ ++ ++++
  gi|242398514|ref|YP_002993938.1| 34 LEESVISEIATQLKKDGILKveIRKGaFTSTNMD 67
                                      5567899************964354557777765 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00032
                                      TSSHHHHHHHHHHHHHTTSEE.ETEE.EE CS
                         HTH_Crp_2 32 GltretvsrilseLkreglis.rgrr.ir 58
                                      ++ re++    +eL +  li+ rg+r i 
  gi|242398514|ref|YP_002993938.1| 65 NMDRESIAEKVAELTDSELIDvRGKRfIL 93
                                      799******************77777554 PP

>> PTRF_SDPR  PTRF/SDPR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   7.0   0.00022       1.3     158     215 ..      35     119 ..      29     140 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00022
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...........................XXXXXXXXXXXXXX CS
                         PTRF_SDPR 158 eeeaeesraerlkrsslkkvdslKkaFskenlektr...........................qniekkvnklgtki 207
                                       ee++ +  a++lk+ ++ kv+  K aF+  n+++                             +  ek ++kl+ k 
  gi|242398514|ref|YP_002993938.1|  35 EESVISEIATQLKKDGILKVEIRKGAFTSTNMDRESiaekvaeltdselidvrgkrfilfrprEGWEKYLKKLKLKE 111
                                       566677789*******************6666643333444444444444444444444444477777777777777 PP

                                       XXXXXXXX CS
                         PTRF_SDPR 208 vtpErrek 215
                                       v++Erre 
  gi|242398514|ref|YP_002993938.1| 112 VSKERREE 119
                                       77777754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       842  (0.046963); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 926.11
//
Query:       gi|242398515|ref|YP_002993939.1|  [L=150]
Description: 30S ribosomal protein S19e [Thermococcus sibiricus MM 739]
Scores for complete 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-57  190.9   0.0    8.5e-57  190.7   0.0    1.0  1  Ribosomal_S19e  Ribosomal protein S19e
    0.00019   21.0   0.2    0.00055   19.5   0.0    1.8  2  GntR            Bacterial regulatory proteins, gntR family
  ------ inclusion threshold ------
      0.027   12.9   0.0      0.035   12.5   0.0    1.1  1  DUF505          Protein of unknown function (DUF505)
      0.032   14.2   0.0      0.046   13.7   0.0    1.2  1  HTH_45          Winged helix-turn-helix
      0.034   14.1   0.0       0.11   12.5   0.0    1.9  2  HTH_12          Ribonuclease R winged-helix domain


Domain annotation for each model (and alignments):
>> Ribosomal_S19e  Ribosomal protein S19e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.7   0.0   2.4e-60   8.5e-57       1     136 [.       3     138 ..       3     139 .. 0.98

  Alignments for each domain:
  == domain 1  score: 190.7 bits;  conditional E-value: 2.4e-60
                                       TSSSHHHHHHHHHS--S---S-SSS-SSSS-SS-S-SS-SSTTTHHHHHHHHHHHTS--TTSGGGGS----SS-SSS CS
                    Ribosomal_S19e   1 tvkdVpaeelikalaeeLkksgklevPewadlvKtgsakelapededWfyvRaAsilRkvylrgpvGverlrkvYGg 77 
                                       tv+dVp + l++++a++Lk+  ++++Pew+ +vKtg +ke+ p+++dW+y+R+As+ Rkvy++gpvG+erlr+ YGg
  gi|242398515|ref|YP_002993939.1|   3 TVYDVPGDLLVERVAQKLKEFPEIKPPEWTLFVKTGRHKERVPDQDDWWYYRVASVFRKVYVDGPVGIERLRTWYGG 79 
                                       79*************************************************************************** PP

                                       -------THHHHHHHHHTTSSS--SSS---SS-HHHHHTHHHHH--SS--S--XXXXXX CS
                    Ribosomal_S19e  78 kkrrgvrpshfvkasgsvirkilqqLeklglvkkekkkgrrltkkGqrlldriaeevak 136
                                       +k+rg++p+hf k+sgs++rk+lqqLe++gl++k  ++gr++t+kG+++ld+ a++++k
  gi|242398515|ref|YP_002993939.1|  80 RKNRGHAPEHFYKGSGSIVRKALQQLEAAGLITKIPGEGRVVTPKGRSFLDKAATDLKK 138
                                       ********************************9999******************99876 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1      0.99   3.6e+03       2      11 ..      13      22 ..      12      22 .. 0.78
   2 !   19.5   0.0   1.5e-07   0.00055      34      64 .]      91     121 ..      89     121 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.99
                                      HHHHHHHHHH CS
                              GntR  2 yeqvyerLre 11
                                       e+v+++L+e
  gi|242398515|ref|YP_002993939.1| 13 VERVAQKLKE 22
                                      6899999985 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 1.5e-07
                                       HTS-HHHHHHHHHHHHHTTSEEEETTCEEEE CS
                              GntR  34 fgVsrttvReALrrLeaeglverrqgrGtfV 64 
                                       ++ s + vR+AL++Lea+gl++  +g+G +V
  gi|242398515|ref|YP_002993939.1|  91 YKGSGSIVRKALQQLEAAGLITKIPGEGRVV 121
                                       6778899********************9776 PP

>> DUF505  Protein of unknown function (DUF505)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   9.9e-06     0.035     500     546 ..      97     144 ..      87     147 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.9e-06
                            DUF505 500 evrealeklearglvevlpdgnvvlTeaGel.ikrAlsgvpeglgnpv 546
                                        vr+al++lea gl+  +p ++ v+T  G   +++A    +++l++++
  gi|242398515|ref|YP_002993939.1|  97 IVRKALQQLEAAGLITKIPGEGRVVTPKGRSfLDKAATDLKKELEEAI 144
                                       599**************************8548999999999988876 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.3e-05     0.046      35      69 ..      97     132 ..      94     140 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.3e-05
                            HTH_45  35 llnkYLdmLvekglikk.skekYvlTekGlellekl 69 
                                       +++k L++L   gli+k  +e  v+T kG+ +l+k 
  gi|242398515|ref|YP_002993939.1|  97 IVRKALQQLEAAGLITKiPGEGRVVTPKGRSFLDKA 132
                                       57889**********8879**************986 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   3.1e-05      0.11      35      65 ..      98     128 ..      89     129 .. 0.89
   2 ?   -2.5   0.0       1.5   5.3e+03      20      30 ..     133     144 ..     131     146 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.1e-05
                            HTH_12  35 vRyrLrkleergltrrvgyagreltEkGlee 65 
                                       vR  L+ le  gl+ +    gr +t kG + 
  gi|242398515|ref|YP_002993939.1|  98 VRKALQQLEAAGLITKIPGEGRVVTPKGRSF 128
                                       9**************************9875 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.5
                            HTH_12  20 aeeLkkr.gydi 30 
                                       a++Lkk  +++i
  gi|242398515|ref|YP_002993939.1| 133 ATDLKKElEEAI 144
                                       778888877777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); 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: 0.51u 0.34s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 877.51
//
Query:       gi|242398516|ref|YP_002993940.1|  [L=112]
Description: DNA-binding protein PH1060 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.4e-25   88.9  18.0    2.7e-25   88.8  18.0    1.0  1  dsDNA_bind   Double-stranded DNA-binding domain
  ------ inclusion threshold ------
      0.054   13.5  12.2      0.035   14.1  10.4    1.5  1  Lipase_chap  Proteobacterial lipase chaperone protein
       0.16   12.4   4.8       0.12   12.9   2.4    1.9  2  PP2C_C       Protein serine/threonine phosphatase 2C, C-termi
        3.8    7.6  16.0        1.6    8.8   1.3    2.1  2  GvpG         Gas vesicle protein G


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 !   88.8  18.0   6.1e-29   2.7e-25       1     107 [.       8     111 ..       8     112 .] 0.90

  Alignments for each domain:
  == domain 1  score: 88.8 bits;  conditional E-value: 6.1e-29
                                       XXXXXXXXXXXXXXXXXXXX...XXXX--SS..S--SSHHHHTTS--HHHHHHHHHHTTT-HHHHHHHHHHHHHHHH CS
                        dsDNA_bind   1 irkarlaelqaqagsssgsggaseqqeqqqeaseeeakqaiLsqiLepeAreRLsrirlvkperaeavenrLiqlaq 77 
                                       ir+++l elq++  ++++    +e+++ +qe + e++ qai++qiL++eAreRL+r++lv+pe a++ve  L+ql+q
  gi|242398516|ref|YP_002993940.1|   8 IRRKKLLELQKKLAEQKR----AEEEQIRQEMELEAQLQAIMKQILTSEARERLTRVKLVRPELARQVELILVQLYQ 80 
                                       9**********9987665....3455555566799****************************************** PP

                                       --SS-----HHHHHHHHHHHS-.--XXXXX. CS
                        dsDNA_bind  78 sGqlrskvteeqLkeLLeqvae.kkketkiv 107
                                        Gq+++++t+e+Lk++L q++  ++ke +i+
  gi|242398516|ref|YP_002993940.1|  81 AGQITERITDEKLKRILAQIDArTRKEFRIK 111
                                       *********************9777778886 PP

>> Lipase_chap  Proteobacterial lipase chaperone protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1  10.4   7.7e-06     0.035      80     142 ..       9      72 ..       3      83 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7.7e-06
                       Lipase_chap  80 kqqrlaalraqlPeslrearraqqrseelaarlaelkkqg.aseqqrrqaraalvgpeaaqRla 142
                                       ++++l +l+++l e+ r++ ++ ++++el+a+l+++ kq   se+ +r  r++lv pe a++++
  gi|242398516|ref|YP_002993940.1|   9 RRKKLLELQKKLAEQKRAEEEQIRQEMELEAQLQAIMKQIlTSEARERLTRVKLVRPELARQVE 72 
                                       6788899*****************************999989999999************9987 PP

>> PP2C_C  Protein serine/threonine phosphatase 2C, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   2.4   2.6e-05      0.12      14      54 ..      27      67 ..      22      74 .. 0.80
   2 ?   -1.2   0.0      0.63   2.8e+03      23      32 ..      88      97 ..      72     108 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.6e-05
                            PP2C_C 14 seeavkkEkeldekleervkeiiekeekkeeldlekvlkvL 54
                                      +ee +++E+el+++l++ +k+i+ +e ++  + ++ v  +L
  gi|242398516|ref|YP_002993940.1| 27 EEEQIRQEMELEAQLQAIMKQILTSEARERLTRVKLVRPEL 67
                                      689*********************66666666555555555 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.63
                            PP2C_C 23 eldekleerv 32
                                        dekl++ +
  gi|242398516|ref|YP_002993940.1| 88 ITDEKLKRIL 97
                                      3334443333 PP

>> GvpG  Gas vesicle protein G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   9.3     0.013        57      34      70 ..      10      46 ..       2      58 .. 0.82
   2 ?    8.8   1.3   0.00036       1.6      21      71 ..      51     106 ..      44     109 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.013
                              GvpG 34 rkeLaaLqqeLdaGeIdeeeFdrrEeelLdrLealer 70
                                      rk+L++Lq++L + +  eee  r+E el  +L+a+ +
  gi|242398516|ref|YP_002993940.1| 10 RKKLLELQKKLAEQKRAEEEQIRQEMELEAQLQAIMK 46
                                      699******************************9987 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00036
                              GvpG  21 eraeeqlddqenlrkeLaa.....LqqeLdaGeIdeeeFdrrEeelLdrLealerl 71 
                                        +a+e l   + +r eLa+     L q  +aG+I+e   d++  ++L +++a +r 
  gi|242398516|ref|YP_002993940.1|  51 SEARERLTRVKLVRPELARqveliLVQLYQAGQITERITDEKLKRILAQIDARTRK 106
                                       4566667777777777765444446777899********************98764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2430  (0.135535); expected 358.6 (0.02)
Passed bias filter:                      669  (0.0373138); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 664.30
//
Query:       gi|242398517|ref|YP_002993941.1|  [L=104]
Description: hypothetical protein TSIB_0526 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       865  (0.0482459); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); 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: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 660.26
//
Query:       gi|242398518|ref|YP_002993942.1|  [L=299]
Description: Transcription initiation factor IIB [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.4e-43  144.5   0.8    1.4e-20   73.1   0.0    2.4  2  TFIIB            Transcription factor TFIIB repeat
    6.7e-19   67.1   1.0    1.1e-18   66.5   1.0    1.3  1  TF_Zn_Ribbon     TFIIB zinc-binding
    6.2e-05   22.4   1.1     0.0055   16.2   0.4    3.6  4  Sigma70_r4       Sigma-70, region 4
    0.00049   19.7   1.0    0.00082   19.0   1.0    1.4  1  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI
     0.0005   19.7   0.6    0.00079   19.1   0.6    1.3  1  A2L_zn_ribbon    A2L zinc ribbon domain
    0.00094   19.4   1.1     0.0017   18.6   1.1    1.4  1  Prim_Zn_Ribbon   Zinc-binding domain of primase-helicase
     0.0017   18.1   0.8       0.22   11.4   0.3    3.5  3  HTH_AsnC-type    AsnC-type helix-turn-helix domain
     0.0021   17.4   0.1       0.28   10.6   0.1    3.4  4  HTH_Tnp_ISL3     Helix-turn-helix domain of transposase famil
     0.0025   17.8   0.0     0.0044   17.1   0.0    1.6  1  RB_B             Retinoblastoma-associated protein B domain
     0.0084   15.6   0.0       0.68    9.5   0.0    3.0  3  GerE             Bacterial regulatory proteins, luxR family
      0.009   15.4   3.0      0.091   12.2   3.0    2.1  1  zf-ribbon_3      zinc-ribbon domain
     0.0097   15.9   0.1        9.4    6.3   0.0    3.8  4  HTH_29           Winged helix-turn helix
  ------ inclusion threshold ------
       0.01   15.6   0.0        4.8    6.9   0.0    2.2  2  Cyclin_N         Cyclin, N-terminal domain
      0.013   15.4   0.2        2.4    8.2   0.0    2.6  2  HTH_11           HTH domain
      0.024   14.8   0.3      0.045   13.9   0.3    1.4  1  DUF2318          Predicted membrane protein (DUF2318)
      0.025   14.9   0.2      0.062   13.7   0.2    1.7  1  Lar_restr_allev  Restriction alleviation protein Lar
      0.036   14.7   0.0      0.078   13.7   0.0    1.5  1  FYDLN_acid       Protein of unknown function (FYDLN_acid)
      0.047   13.6   0.1       0.09   12.7   0.1    1.4  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
      0.073   13.5   0.0         17    5.9   0.0    3.0  3  HARE-HTH         HB1, ASXL, restriction endonuclease HTH doma
       0.11   12.3   3.4        4.7    7.1   0.1    3.8  4  HTH_23           Homeodomain-like domain
       0.17   12.4   0.0       0.33   11.5   0.0    1.5  1  RPA_interact_C   Replication protein A interacting C-terminal
       0.21   11.6   0.9        0.5   10.4   0.9    1.7  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
       0.26   11.5   1.6       0.53   10.5   1.6    1.5  1  Auto_anti-p27    Sjogren's syndrome/scleroderma autoantigen 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 !   69.9   0.2   1.8e-22   1.4e-19       3      71 .]     118     186 ..     116     186 .. 0.97
   2 !   73.1   0.0   1.8e-23   1.4e-20       1      71 []     212     282 ..     212     282 .. 0.98

  Alignments for each domain:
  == domain 1  score: 69.9 bits;  conditional E-value: 1.8e-22
                                       HHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                             TFIIB   3 rfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                       r+ ++l+Lp+ V+++A  l++ a++++++ Grs ++++AAc+y Acr+ +  rt+ ei+++++V +k+i
  gi|242398518|ref|YP_002993942.1| 118 RLGARLNLPKHVEEEAARLYRDAVKKGLIRGRSIESVIAACVYAACRLLKIPRTLDEIADMAKVDKKEI 186
                                       77899**************************************************************98 PP

  == domain 2  score: 73.1 bits;  conditional E-value: 1.8e-23
                                       HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                             TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                       +++fad+l+L+e  +++A el+++++++++++G+spag++AA+lyiA ++e++krtq+e+++ ++V+e+t+
  gi|242398518|ref|YP_002993942.1| 212 VNKFADELGLSERTRRRAIELLDQVYNMGLTSGKSPAGLVAAALYIAGLLEGEKRTQREVAEAARVTEVTV 282
                                       689******************************************************************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 !   66.5   1.0   1.4e-21   1.1e-18       2      43 .]       6      47 ..       5      47 .. 0.98

  Alignments for each domain:
  == domain 1  score: 66.5 bits;  conditional E-value: 1.4e-21
                                      EETTTTCEECHEETSTTCEEESSSSBEEEECCCCCCCHHHHH CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGlVlednsidegpewref 43
                                      +CP+Cgs+++v+Dperge++C +CG V+++n+id gpewr+f
  gi|242398518|ref|YP_002993942.1|  6 VCPVCGSDKFVYDPERGEIICANCGFVIQENIIDMGPEWRAF 47
                                      8***************************************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 ?   -3.1   0.0       7.7     6e+03      23      33 ..     116     126 ..     115     127 .. 0.79
   2 ?    1.7   0.0      0.24   1.9e+02      20      31 ..     169     180 ..     164     183 .. 0.87
   3 ?   -1.2   0.0         2   1.5e+03      27      40 ..     216     228 ..     216     237 .. 0.64
   4 !   16.2   0.4     7e-06    0.0055      18      48 ..     263     293 ..     254     294 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 7.7
                                       HHHHHHHHTS- CS
                        Sigma70_r4  23 leEIgerlgiS 33 
                                       l  +g+rl+++
  gi|242398518|ref|YP_002993942.1| 116 LDRLGARLNLP 126
                                       56789999997 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.24
                                       T--HHHHHHHHT CS
                        Sigma70_r4  20 glTleEIgerlg 31 
                                       ++Tl EI+++  
  gi|242398518|ref|YP_002993942.1| 169 PRTLDEIADMAK 180
                                       68******9965 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 2
                                       HHHHTS-HHHHHHH CS
                        Sigma70_r4  27 gerlgiSrerVrqi 40 
                                       +++lg+S+ r r++
  gi|242398518|ref|YP_002993942.1| 216 ADELGLSE-RTRRR 228
                                       67888885.44554 PP

  == domain 4  score: 16.2 bits;  conditional E-value: 7e-06
                                       TTT--HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                        Sigma70_r4  18 geglTleEIgerlgiSrerVrqiekrAlrkL 48 
                                       ge++T+ E++e   +++ +Vr + k+ ++kL
  gi|242398518|ref|YP_002993942.1| 263 GEKRTQREVAEAARVTEVTVRNRYKEMVEKL 293
                                       899************************9998 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   1.0     1e-06   0.00082       1      32 []       1      34 [.       1      34 [. 0.87

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1e-06
                           zf-RRN7  1 wekgppCgvCgc.rsftl.ddGfyyCrrChtqeg 32
                                      ++k+ +C+vCg+ + ++  + G  +C +C+ +++
  gi|242398518|ref|YP_002993942.1|  1 MTKHRVCPVCGSdKFVYDpERGEIICANCGFVIQ 34
                                      57889*******9766666************987 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 !   19.1   0.6     1e-06   0.00079       3      30 ..       4      32 ..       2      34 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1e-06
                     A2L_zn_ribbon  3 lkvCsvCggngiln.seqgylvCieCgas 30
                                       +vC vCg+++ ++  e+g+ +C +Cg++
  gi|242398518|ref|YP_002993942.1|  4 HRVCPVCGSDKFVYdPERGEIICANCGFV 32
                                      68*************************98 PP

>> Prim_Zn_Ribbon  Zinc-binding domain of primase-helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   1.1   2.2e-06    0.0017       2      33 ..       3      30 ..       2      36 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.2e-06
                                      EEE--TTTT-TTTEEETT....S-EEETTTTB CS
                    Prim_Zn_Ribbon  2 khspCPvCGGrDrFrfddkdgrGtwfCrqCgg 33
                                      kh  CPvCG +D+F +d    rG  +C  C g
  gi|242398518|ref|YP_002993942.1|  3 KHRVCPVCG-SDKFVYDP--ERGEIICANC-G 30
                                      8899****8.6****998..89********.5 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.94   7.3e+02      18      31 ..     188     201 ..     187     203 .. 0.89
   2 ?    2.0   0.0      0.24   1.9e+02      24      36 ..     216     228 ..     212     233 .. 0.79
   3 !   11.4   0.3   0.00028      0.22      17      41 ..     265     289 ..     258     290 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.94
                     HTH_AsnC-type  18 isyaeLAervGlSe 31 
                                       +s++ +A+ ++l++
  gi|242398518|ref|YP_002993942.1| 188 RSFRFIARNLNLTP 201
                                       69999*******97 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.24
                     HTH_AsnC-type  24 AervGlSestvlr 36 
                                       A+++GlSe t +r
  gi|242398518|ref|YP_002993942.1| 216 ADELGLSERTRRR 228
                                       99******98655 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.00028
                     HTH_AsnC-type  17 RisyaeLAervGlSestvlrRvrrL 41 
                                       +++ +e+Ae+  ++e tv++R++ +
  gi|242398518|ref|YP_002993942.1| 265 KRTQREVAEAARVTEVTVRNRYKEM 289
                                       6899******************987 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.24   1.9e+02      18      46 ..     160     188 ..     157     194 .. 0.87
   2 ?    0.9   0.0      0.38     3e+02      28      41 ..     188     201 ..     184     204 .. 0.85
   3 ?   -1.5   0.0       2.2   1.7e+03      34      43 ..     216     225 ..     214     232 .. 0.84
   4 !   10.6   0.1   0.00036      0.28      19      49 ..     256     287 ..     252     290 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.24
                      HTH_Tnp_ISL3  18 ayilelllesrsvkavArqlgvSwtTVwr 46 
                                       +++ +ll+  r+  ++A++  v+ + + r
  gi|242398518|ref|YP_002993942.1| 160 YAACRLLKIPRTLDEIADMAKVDKKEIGR 188
                                       789999***************99999887 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.38
                      HTH_Tnp_ISL3  28 rsvkavArqlgvSw 41 
                                       rs++ +Ar l++++
  gi|242398518|ref|YP_002993942.1| 188 RSFRFIARNLNLTP 201
                                       59*********987 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 2.2
                      HTH_Tnp_ISL3  34 ArqlgvSwtT 43 
                                       A++lg+S++T
  gi|242398518|ref|YP_002993942.1| 216 ADELGLSERT 225
                                       8899999988 PP

  == domain 4  score: 10.6 bits;  conditional E-value: 0.00036
                      HTH_Tnp_ISL3  19 yilellles.rsvkavArqlgvSwtTVwrild 49 
                                       yi+ ll    r+ ++vA+  +v++ TV+++++
  gi|242398518|ref|YP_002993942.1| 256 YIAGLLEGEkRTQREVAEAARVTEVTVRNRYK 287
                                       78888888899******************997 PP

>> RB_B  Retinoblastoma-associated protein B domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   5.6e-06    0.0044      10      88 ..     109     185 ..      87     239 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 5.6e-06
                              RB_B  10 yklaavrlrdLcerLklsselrekiwtlfehvlveetellkdRhlDqillcavYvvakvtkeelsFkeiikaYrkqp 86 
                                       +  a + l +L +rL+l ++++e++  l + ++   + l++ R ++ ++ ++vY+ +++ k  +++ ei ++ +  +
  gi|242398518|ref|YP_002993942.1| 109 LAFALSELDRLGARLNLPKHVEEEAARLYRDAVK--KGLIRGRSIESVIAACVYAACRLLKIPRTLDEIADMAKVDK 183
                                       667889999999************9999999885..68*******************************98877655 PP

                              RB_B  87 qa 88 
                                       ++
  gi|242398518|ref|YP_002993942.1| 184 KE 185
                                       55 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       1.4   1.1e+03      17      32 ..     187     202 ..     185     205 .. 0.83
   2 ?    1.7   0.0      0.24   1.9e+02      23      33 ..     215     225 ..     211     226 .. 0.87
   3 !    9.5   0.0   0.00088      0.68      19      48 ..     267     296 ..     257     296 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.4
                                       TS-HHHHHHHHTS-HH CS
                              GerE  17 GksnkeIAeelniSek 32 
                                       G s   IA++ln+ +k
  gi|242398518|ref|YP_002993942.1| 187 GRSFRFIARNLNLTPK 202
                                       666777******9986 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.24
                                       HHHHHTS-HHH CS
                              GerE  23 IAeelniSekT 33 
                                        A+el++Se+T
  gi|242398518|ref|YP_002993942.1| 215 FADELGLSERT 225
                                       69********9 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.00088
                                       -HHHHHHHHTS-HHHHHHHHHHHHHHHT-S CS
                              GerE  19 snkeIAeelniSekTVkvhksnimkKLnvk 48 
                                       +  e+Ae+  + e TV++  +++ +KL++k
  gi|242398518|ref|YP_002993942.1| 267 TQREVAEAARVTEVTVRNRYKEMVEKLGLK 296
                                       5689***********************975 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   3.0   0.00012     0.091       2      26 .]       4      33 ..       3      33 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00012
                       zf-ribbon_3  2 tvrCPnCGa.p.l...ssddnvCpyCGtkl 26
                                      ++ CP CG+ + +   + + ++C++CG ++
  gi|242398518|ref|YP_002993942.1|  4 HRVCPVCGSdKfVydpERGEIICANCGFVI 33
                                      678*****9987666689*********986 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       4.5   3.5e+03       5      13 ..      64      72 ..      63      75 .. 0.86
   2 ?   -1.5   0.0       3.5   2.7e+03      16      28 ..     191     203 ..     187     205 .. 0.78
   3 ?    6.3   0.0     0.012       9.4      19      38 ..     216     235 ..     211     236 .. 0.88
   4 ?    4.3   0.1     0.051        39       5      31 ..     257     284 ..     254     297 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 4.5
                            HTH_29  5 llllaeGvs 13
                                      +ll+++G+s
  gi|242398518|ref|YP_002993942.1| 64 ILLHDKGLS 72
                                      79*****98 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.5
                            HTH_29  16 sqiAkllglsrrt 28 
                                       + iA++l+l++++
  gi|242398518|ref|YP_002993942.1| 191 RFIARNLNLTPKK 203
                                       679*****99986 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.012
                            HTH_29  19 Akllglsrrtvyrwlkrfee 38 
                                       A  lgls+rt +r++++ ++
  gi|242398518|ref|YP_002993942.1| 216 ADELGLSERTRRRAIELLDQ 235
                                       889*************9876 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.051
                            HTH_29   5 llllaeGvs.tvsqiAkllglsrrtvyr 31 
                                       ++ l eG++ t +++A++ ++++ tv++
  gi|242398518|ref|YP_002993942.1| 257 IAGLLEGEKrTQREVAEAARVTEVTVRN 284
                                       6678899999999999999999999975 PP

>> Cyclin_N  Cyclin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0    0.0062       4.8      55     122 ..     133     197 ..     106     200 .. 0.75
   2 ?    6.4   0.0    0.0093       7.2      36     102 ..     210     278 ..     203     296 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0062
                                       HHHHHHHHHHHS---CCCHHHHHHHHHHHHHHHHSSS---HHHHHHHTTTSS-HHHHHHHHHHHHHHT CS
                          Cyclin_N  55 avnyldRflskksvpkdklqlvgatcLllAaKveeisppkledlvyitdeafteeeilemErliLetL 122
                                       a++++   ++k  ++ + ++ v a+c++ A+++ +i p +l++++ +++  ++++ei +  r i + L
  gi|242398518|ref|YP_002993942.1| 133 AARLYRDAVKKGLIRGRSIESVIAACVYAACRLLKI-PRTLDEIADMAK--VDKKEIGRSFRFIARNL 197
                                       556666666666677778999************999.999999998866..77777777666666665 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0093
                                       HHHHHHHHHTT--TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHHHHHSSS..---HHHHHHHT CS
                          Cyclin_N  36 dwlvevaekfkltpetlflavnyldRflskksvpkdklqlvgatcLllAaKveeis..ppkledlvyit 102
                                       d++ + a ++ l+++t   a+++ld+++    ++ +    ++a++L++A+ +e  +    ++ + + +t
  gi|242398518|ref|YP_002993942.1| 210 DYVNKFADELGLSERTRRRAIELLDQVYNMGLTSGKSPAGLVAAALYIAGLLEGEKrtQREVAEAARVT 278
                                       778888999999*****************99999999999*********98853321244555555554 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0    0.0031       2.4      19      40 ..     213     234 ..     212     242 .. 0.91
   2 ?    4.5   0.0     0.044        34      13      43 ..     264     294 ..     254     299 .] 0.77

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0031
                            HTH_11  19 eeLAeeLnvSrrtvrrdIkaLe 40 
                                       ++ A+eL++S+rt rr I+ L 
  gi|242398518|ref|YP_002993942.1| 213 NKFADELGLSERTRRRAIELLD 234
                                       578***************9995 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.044
                            HTH_11  13 rgpisgeeLAeeLnvSrrtvrrdIkaL.eelg 43 
                                       ++  +  e Ae   v++ tvr++ k++ e+lg
  gi|242398518|ref|YP_002993942.1| 264 EK-RTQREVAEAARVTEVTVRNRYKEMvEKLG 294
                                       43.6888999999*********9999877776 PP

>> DUF2318  Predicted membrane protein (DUF2318)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.3   5.7e-05     0.045      36      67 ..       6      39 ..       2      43 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.7e-05
                           DUF2318 36 aCevCekkgYv..qegeelvCknCgvrfaldsig 67
                                      +C vC+++++v   e  e++C nCg +++ + i+
  gi|242398518|ref|YP_002993942.1|  6 VCPVCGSDKFVydPERGEIICANCGFVIQENIID 39
                                      7****7776664478899********99988776 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 ?   13.7   0.2   7.9e-05     0.062       4      36 ..       5      31 ..       2      57 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.9e-05
                   Lar_restr_allev  4 kpCPfCggravlersqrvvaeigqcvyCadCga 36
                                        CP Cg+++ +   +r+       ++Ca+Cg 
  gi|242398518|ref|YP_002993942.1|  5 RVCPVCGSDKFVYDPERG------EIICANCGF 31
                                      67*******999998888......59******9 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 ?   13.7   0.0    0.0001     0.078      10      54 ..       5      51 ..       2      79 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.0001
                        FYDLN_acid 10 riCpscga.kF.YDLnkdPivcpkcgeefepeevlksraaaaeaeea 54
                                      r+Cp cg+ kF YD ++  i+c +cg +++ + +    + +a ++++
  gi|242398518|ref|YP_002993942.1|  5 RVCPVCGSdKFvYDPERGEIICANCGFVIQENIIDMGPEWRAFDASQ 51
                                      9*****955999****************9998873333333333333 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   0.00012      0.09      30      57 ..       6      34 ..       5      38 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00012
                    OrfB_Zn_ribbon 30 tCseCgsknke.alsgrtfkCpnCgfead 57
                                       C++Cgs +   ++++ +  C nCgf+++
  gi|242398518|ref|YP_002993942.1|  6 VCPVCGSDKFVyDPERGEIICANCGFVIQ 34
                                      6******998889*************975 PP

>> HARE-HTH  HB1, ASXL, restriction endonuclease HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0      0.13     1e+02      25      53 ..     138     164 ..     131     172 .. 0.83
   2 ?   -0.4   0.0         2   1.6e+03      29      62 ..     177     208 ..     164     211 .. 0.76
   3 ?    5.9   0.0     0.022        17      22      49 ..     231     256 ..     228     265 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.13
                                       HHHHHHTTS-..GGHHGCHHH.HHHHHHH CS
                          HARE-HTH  25 ekiqekglikltgktpeatlaaqlytdik 53 
                                       + +++kgli   g++ e  +aa+ y+ ++
  gi|242398518|ref|YP_002993942.1| 138 RDAVKKGLIR--GRSIESVIAACVYAACR 164
                                       67899*****..*************9986 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 2
                                       HHTTS-..GGHHGCHHH.HHHHHHH..HSTTEEES CS
                          HARE-HTH  29 ekglikltgktpeatlaaqlytdik.gddslFvkv 62 
                                       ++  ++  +k+  ++ +  ++++++  +++lFvk 
  gi|242398518|ref|YP_002993942.1| 177 DMAKVD--KKEIGRSFR-FIARNLNlTPKKLFVKP 208
                                       444455..777778888.89999999999999996 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.022
                                       HHHHHHHHHTTS-..GGHHGCHHH.HHH CS
                          HARE-HTH  22 eIwekiqekglikltgktpeatlaaqly 49 
                                       e+++++  +gl +  gk+p   +aa+ly
  gi|242398518|ref|YP_002993942.1| 231 ELLDQVYNMGLTS--GKSPAGLVAAALY 256
                                       8999999******..************9 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.2       5.1     4e+03      36      40 ..      91      95 ..      86     107 .. 0.50
   2 ?   -2.4   0.0       6.1   4.7e+03      17      30 ..     187     200 ..     174     202 .. 0.60
   3 ?    3.6   0.0     0.077        60       3      14 ..     222     233 ..     214     245 .. 0.59
   4 ?    7.1   0.1     0.006       4.7      17      39 ..     265     287 ..     251     296 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 5.1
                            HTH_23 36 rwlkr 40
                                      r +k+
  gi|242398518|ref|YP_002993942.1| 91 RLRKW 95
                                      44443 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 6.1
                            HTH_23  17 GlsvreIAreLgvs 30 
                                       G s r IAr L+ +
  gi|242398518|ref|YP_002993942.1| 187 GRSFRFIARNLNLT 200
                                       55555577877766 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.077
                            HTH_23   3 sereRlrillll 14 
                                       ser R r++ ll
  gi|242398518|ref|YP_002993942.1| 222 SERTRRRAIELL 233
                                       444555555555 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.006
                            HTH_23  17 GlsvreIAreLgvsrrTvyrwlk 39 
                                       + ++re+A++  v++ Tv++  k
  gi|242398518|ref|YP_002993942.1| 265 KRTQREVAEAARVTEVTVRNRYK 287
                                       789****************5544 PP

>> RPA_interact_C  Replication protein A interacting C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00042      0.33       1      27 [.       6      35 ..       6      82 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00042
                    RPA_interact_C  1 lCPvCkkrklkets..evifCe.Cglrlet 27
                                      +CPvC ++k+  +     i+C+ Cg+ ++ 
  gi|242398518|ref|YP_002993942.1|  6 VCPVCGSDKFVYDPerGEIICAnCGFVIQE 35
                                      6******99988543477***99***9987 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.9   0.00064       0.5      18      44 ..       4      30 ..       2      32 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00064
                     Zn_Tnp_IS1595 18 gfvCPhCgsr.kayriktrglfqCkeCr 44
                                      ++vCP Cgs+  +y  ++ g   C+ C+
  gi|242398518|ref|YP_002993942.1|  4 HRVCPVCGSDkFVYDPER-GEIICANCG 30
                                      689*******66777775.999999997 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.6   0.00068      0.53      17      40 .]       6      30 ..       3      30 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00068
                     Auto_anti-p27 17 tCpvC.gvPLmrdrkggkvyCvaCd 40
                                      +CpvC +   + d+++g+++C++C+
  gi|242398518|ref|YP_002993942.1|  6 VCPVCgSDKFVYDPERGEIICANCG 30
                                      7****66667777799********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       759  (0.0423336); expected 358.6 (0.02)
Passed bias filter:                      670  (0.0373696); expected 358.6 (0.02)
Passed Vit filter:                       115  (0.00641419); 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: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1989.01
//
Query:       gi|242398519|ref|YP_002993943.1|  [L=340]
Description: Flap structure-specific endonuclease [Thermococcus sibiricus MM 739]
Scores for 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  102.8   0.0    2.3e-29  101.6   0.0    1.7  1  XPG_I       XPG I-region
    2.9e-23   82.3   0.0      6e-23   81.2   0.0    1.5  1  XPG_N       XPG N-terminal domain
     0.0076   16.1   0.3      0.013   15.3   0.3    1.3  1  Pep3_Vps18  Pep3/Vps18/deep orange family
  ------ inclusion threshold ------
       0.26   11.5   1.6        0.8   10.0   1.0    2.2  1  TPR_2       Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> XPG_I  XPG I-region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.6   0.0     5e-33   2.3e-29       2      94 .]     141     236 ..     140     236 .. 0.94

  Alignments for each domain:
  == domain 1  score: 101.6 bits;  conditional E-value: 5e-33
                                       HHT--EEE-SS-HHHHHHHHHHTTSSSEEE-SSSHHHHTT-SEEEESTT..ECECTT....EEECEEEEEEHHHHHH CS
                             XPG_I   2 lmgipyvvApgEAEAqcayLqkkglvdaviseDsDlllFGapkvlrnls.kkkskkk..kekekkkvevidlekvlk 75 
                                       lmgip+v+Ap+E+EAq+ay+++kg+v+a +s+D+D+llFG+pk++rnl+ ++k+k    + + ++k+e i le+vlk
  gi|242398519|ref|YP_002993943.1| 141 LMGIPWVQAPSEGEAQAAYMASKGDVWASASQDYDSLLFGTPKLVRNLTiTGKRKLPgkDVYIEVKPELILLEDVLK 217
                                       8***********************************************975555554879999************** PP

                                       HHT--HHHHHHHHHHHCET CS
                             XPG_I  76 elgltreqlidlaillgcD 94 
                                       el+ltre+li+lail+g+D
  gi|242398519|ref|YP_002993943.1| 218 ELKLTREKLIELAILVGTD 236
                                       ******************9 PP

>> XPG_N  XPG N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.2   0.0   1.3e-26     6e-23      17     101 .]      12     101 ..       6     101 .. 0.96

  Alignments for each domain:
  == domain 1  score: 81.2 bits;  conditional E-value: 1.3e-26
                                       EEEEGGGGTTEEEEEEHHHHHHHHHHHSE.ETTEE-BS.....-HHHHHHHHHHHHHHHTTEEEEEEE--S--GGGH CS
                             XPG_N  17 rsvsiealegkklaiDaslwlyrfliavreqlgnalen.....tshlmglfsrllrlldfgikPifVFdgkapdlkk 88 
                                       +++++e+l+g+k+aiDa   +y+fl ++r+++g+ l+      tshl glf+r++ l++ gikP +VFdgk+p++kk
  gi|242398519|ref|YP_002993943.1|  12 KELELENLNGRKVAIDAFNAIYQFLSTIRQKDGTPLMDskgriTSHLSGLFYRTINLMEAGIKPAYVFDGKPPEFKK 88 
                                       6789********************************9999************************************* PP

                                       HHHHHHHHHHHHH CS
                             XPG_N  89 eelekrserrqea 101
                                       +elekr e r+ea
  gi|242398519|ref|YP_002993943.1|  89 KELEKRAETREEA 101
                                       ********99985 PP

>> Pep3_Vps18  Pep3/Vps18/deep orange family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.3   2.9e-06     0.013     107     148 ..      98     139 ..      94     140 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.9e-06
                                       ESHHHHHHHHH-XXXXXXXXXXXX.XXXXXXXXXXXXXXXXX CS
                        Pep3_Vps18 107 rdEdrdvWklylekgkFdeAlklaknpaqrdqVltaqadalf 148
                                       r+E+ + W++ l +g+ +eA+k+a+++++++++l++ a++l+
  gi|242398519|ref|YP_002993943.1|  98 REEALEKWEIALARGELEEAKKYAQRASKINEILIEDAKKLL 139
                                       6788888*******************************9987 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   1.0   0.00018       0.8      10      31 ..     107     128 ..     106     129 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00018
                             TPR_2  10 ayyklgdyeeAleafekAleld 31 
                                       +++++g++eeA+++ ++A +++
  gi|242398519|ref|YP_002993943.1| 107 IALARGELEEAKKYAQRASKIN 128
                                       67899*************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       666  (0.0371465); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); 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):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 2161.75
//
Query:       gi|242398520|ref|YP_002993944.1|  [L=465]
Description: Acetyl-CoA synthetase I (ACSI, ADP-forming), subunit alpha [Thermococcus sibiricus MM 739]
Scores for complete 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-55  186.3   0.6    1.7e-54  183.3   0.2    2.5  3  Succ_CoA_lig    Succinyl-CoA ligase like flavodoxin domain
    3.4e-21   75.9   0.6    1.5e-19   70.6   0.1    2.4  2  CoA_binding_2   CoA binding domain
    1.6e-14   54.4   2.4    2.7e-14   53.6   1.1    2.1  2  CoA_binding     CoA binding domain
  ------ inclusion threshold ------
      0.064   12.5   0.0       0.11   11.7   0.0    1.3  1  DUF4849         Putative glycoside hydrolase Family 18, chiti
       0.44   11.0   3.2       0.36   11.3   0.8    2.1  2  Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domai


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 !  183.3   0.2   4.9e-58   1.7e-54       1     138 []     159     296 ..     159     296 .. 0.99
   2 ?   -0.8   0.0      0.33   1.2e+03       3      27 ..     306     330 ..     304     333 .. 0.88
   3 ?   -1.4   0.0      0.53   1.9e+03      75      94 ..     405     424 ..     370     430 .. 0.68

  Alignments for each domain:
  == domain 1  score: 183.3 bits;  conditional E-value: 4.9e-58
                      Succ_CoA_lig   1 pGkialisqSGalalalldwaasrglgfskvvslGneadvdvadlleylaedpetkvillylEsirdgrkflsaarr 77 
                                       pGk+al+sqSGal++al+ w+  +++g+s vvs+Gn++d+d ad+ley+++d++t +il+y+E+++dgrkf+++a+r
  gi|242398520|ref|YP_002993944.1| 159 PGKLALVSQSGALGIALMGWTILEKVGLSAVVSIGNKSDLDDADMLEYFENDENTGAILIYMEGVKDGRKFMETAKR 235
                                       79*************************************************************************** PP

                      Succ_CoA_lig  78 aarkkpvvvlksGrseagaraaashtgalagsdavvdaafrqaGvlrvdsleelfdaaell 138
                                       ++ kkp++++k+Grse+ga+aaashtg+lag d +++aaf+q+Gvlr+ ++ e fd a++l
  gi|242398520|ref|YP_002993944.1| 236 VSMKKPIIIIKAGRSERGAKAAASHTGSLAGADSIYTAAFKQSGVLRALTIGEAFDWARTL 296
                                       *********************************************************9986 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.33
                      Succ_CoA_lig   3 kialisqSGalalalldwaasrglg 27 
                                       ++ +i+  G+++++  d+a++++l+
  gi|242398520|ref|YP_002993944.1| 306 NVVIITNGGGIGVMATDAAEEEDLK 330
                                       68899**************999876 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.53
                      Succ_CoA_lig  75 arraarkkpvvvlksGrsea 94 
                                        ++  rkkp+vv  +G  ea
  gi|242398520|ref|YP_002993944.1| 405 YEASGRKKPLVVAIVGGIEA 424
                                       45566779999988886555 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.6   0.1   4.1e-23   1.5e-19       1     114 [.      13     142 ..      13     144 .. 0.91
   2 ?    3.2   0.0     0.033   1.2e+02      71     105 ..     404     438 ..     365     442 .. 0.78

  Alignments for each domain:
  == domain 1  score: 70.6 bits;  conditional E-value: 4.1e-23
                                       --EEEET--S-TTSHHHHHHHHHHH...HT--EEEESSS-SEETTEE....S----T....T--EEEE-S-HHHHGG CS
                     CoA_binding_2   1 rtiaVvGasdnpgkfgykvlrylle...hglpvvpVnpkeeeilgek....vyaslaedpepvdlvdvftppeatpe 70 
                                       r++aVvGas +pgk gy ++++l e   +g ++++Vn k++ei+       vy+s+ + p +vd+++v++p++ + +
  gi|242398520|ref|YP_002993944.1|  13 RSVAVVGASGKPGKIGYAIMKNLIEygyEG-KIYAVNVKGGEIEVSGrkfkVYESILDVPDEVDMAVVVVPAKFVSQ 88 
                                       79***********************66555.8********88876434477******758***************** PP

                                       GHHHHHHH--SEEEE-TT..........---HHHHHHHHHTT-EEE.ES-HHHH CS
                     CoA_binding_2  71 ivkealalgakavwlqpg..........sedeeaaelaeeagirvvgdrCilve 114
                                       +v+e++++g+k++ + ++           ++e+++e a+++g+r++g++  +++
  gi|242398520|ref|YP_002993944.1|  89 VVEECGKKGVKVLPIISSgfgelgeegkKVEEQLVETAHKYGMRILGPNIFGIV 142
                                       *************999999*****************************977776 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.033
                                       GHHHHHHH--SEEEE-TT---HHHHHHHHHTT-EE CS
                     CoA_binding_2  71 ivkealalgakavwlqpgsedeeaaelaeeagirv 105
                                        +++ +++++ +v +  g+e +ea++l++e+gi+ 
  gi|242398520|ref|YP_002993944.1| 404 EYEASGRKKPLVVAIVGGIEAKEAIDLLNERGIPA 438
                                       233334446999999****************9975 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.6   1.1   7.5e-18   2.7e-14       2      96 .]      11     107 ..      10     107 .. 0.92
   2 ?   -2.4   0.0       2.3   8.2e+03      70      87 ..     419     436 ..     401     447 .. 0.63

  Alignments for each domain:
  == domain 1  score: 53.6 bits;  conditional E-value: 7.5e-18
                                       TTEEEEEETTTSHHHHHH.HHHHHHHHECEE.EEEEC-TTTTTCEET..TEEEESCHHHHHHHCTTTEEEEES-HHH CS
                       CoA_binding   2 kdtkviviGagglgiagl.yhfkeklkygik.avfgvnprkvgtevl..glpvyksvdeleektevdvavitvPaes 74 
                                       k+ +v+v+Ga+g+ ++++   +k+ ++yg + +++ vn + +  ev+    +vy+s+ +++++  vd+av++vPa++
  gi|242398520|ref|YP_002993944.1|  11 KPRSVAVVGASGKPGKIGyAIMKNLIEYGYEgKIYAVNVKGGEIEVSgrKFKVYESILDVPDE--VDMAVVVVPAKF 85 
                                       6789**************999*******************555666666799***********..************ PP

                                       HHHHHHHHHHTT-SEEEEESST CS
                       CoA_binding  75 aqeavdelveagikgiviiteg 96 
                                       + ++v+e+ ++g+k+  ii++g
  gi|242398520|ref|YP_002993944.1|  86 VSQVVEECGKKGVKVLPIISSG 107
                                       ***************9999876 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.3
                                       S-HHHHHHHHHHHHHTT- CS
                       CoA_binding  70 vPaesaqeavdelveagi 87 
                                       v   +a+ea+d l e gi
  gi|242398520|ref|YP_002993944.1| 419 VGGIEAKEAIDLLNERGI 436
                                       333344455544444444 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 ?   11.7   0.0   3.1e-05      0.11      49     100 ..      59     106 ..      33     132 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.1e-05
                           DUF4849  49 vpssqaqslsalPDSvDfvsltnpeelseaeleeikkvkeKGtkvlysisfs 100
                                         ++  +s+ ++PD vD+ +++ p++   +  ee     +KG+kvl  is s
  gi|242398520|ref|YP_002993944.1|  59 RKFKVYESILDVPDEVDMAVVVVPAKFVSQVVEEC---GKKGVKVLPIIS-S 106
                                       5578889*****************88888777765...57****997665.3 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 ?   11.3   0.8    0.0001      0.36       2      93 ..      15     100 ..      14     105 .. 0.86
   2 ?   -3.4   0.1       3.5   1.2e+04       2      21 ..     416     433 ..     416     435 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0001
                                       EEEETTTSHHHHHHHHHHHC.TSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEEGGGGGCTT-SEEEE-SCHH CS
                    Semialdhyde_dh   2 vaivGatGyvGqellrlLee.hpevelvvllsssrsaGkklaeavkaleegkdlkvedvdeeelkevdivflalpag 77 
                                       va+vGa+G  G+    ++++   +  +  +++ +  +G +++        g+++kv +   +  +evd+++  +pa+
  gi|242398520|ref|YP_002993944.1|  15 VAVVGASGKPGKIGYAIMKNlIEYGYEGKIYAVNV-KGGEIEVS------GRKFKVYESILDVPDEVDMAVVVVPAK 84 
                                       9*******************766667777777777.89999888......668888886777779************ PP

                                       HHHHHHHHHHHTTSEE CS
                    Semialdhyde_dh  78 vskelapklaeagvkv 93 
                                         +++++++ ++gvkv
  gi|242398520|ref|YP_002993944.1|  85 FVSQVVEECGKKGVKV 100
                                       **************98 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 3.5
                                       EEEETTTSHHHHHHHHHHHC CS
                    Semialdhyde_dh   2 vaivGatGyvGqellrlLee 21 
                                       vaivG  G   +e + lL+e
  gi|242398520|ref|YP_002993944.1| 416 VAIVG--GIEAKEAIDLLNE 433
                                       89999..9999999999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (465 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); 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: 0.59u 0.25s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 3113.56
//
Query:       gi|242398521|ref|YP_002993945.1|  [L=1214]
Description: Reverse gyrase [Thermococcus sibiricus MM 739]
Scores for complete 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-82  277.6   4.2    1.6e-80  271.1   4.2    2.3  1  Topoisom_bac    DNA topoisomerase
    1.4e-26   92.7   0.3    1.1e-25   89.9   0.0    2.6  2  Toprim          Toprim domain
    2.5e-12   46.9   0.1    1.3e-11   44.6   0.0    2.3  1  DEAD            DEAD/DEAH box helicase
    8.1e-11   42.3   1.8    2.3e-05   24.7   0.0    4.8  4  Helicase_C      Helicase conserved C-terminal domain
    9.8e-09   34.5   1.9    1.5e-08   33.9   0.2    2.2  2  zf_Rg           Reverse gyrase zinc finger
      7e-08   32.6   2.9    2.9e-07   30.7   0.8    2.7  2  ResIII          Type III restriction enzyme, res subunit
    0.00027   21.0   0.5    0.00027   21.0   0.5    2.2  2  Zn-ribbon_8     Zinc ribbon domain
     0.0015   18.5   1.7      0.036   14.1   0.0    2.9  3  HypA            Hydrogenase/urease nickel incorporation, meta
     0.0023   17.3   0.1     0.0051   16.2   0.1    1.6  1  DctP            Bacterial extracellular solute-binding protei
  ------ inclusion threshold ------
      0.022   14.7   4.4      0.031   14.2   0.2    2.6  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
       0.13   12.3   4.8       0.43   10.6   0.3    2.3  2  DZR             Double zinc ribbon
       0.15   11.8   2.5       0.16   11.6   0.1    2.2  2  TackOD1         Thaumarchaeal output domain 1
       0.35   10.6   9.4       0.23   11.2   5.3    2.2  2  Rubredoxin_2    Rubredoxin metal binding domain
        1.9    8.6   6.2        6.9    6.7   0.4    2.3  2  zinc-ribbons_6  zinc-ribbons
        3.3    7.9   4.6       0.54   10.5   0.1    2.0  1  NOB1_Zn_bind    Nin one binding (NOB1) Zn-ribbon like
        3.8    8.1   6.8        4.1    8.0   0.1    2.8  2  zf-C4pol        C4-type zinc-finger of DNA polymerase delta
        5.8    7.1   8.5        3.3    7.9   0.2    3.1  3  UPF0547         Uncharacterised protein family UPF0547


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 !  271.1   4.2   1.5e-83   1.6e-80       2     412 ..     818    1202 ..     817    1203 .. 0.87

  Alignments for each domain:
  == domain 1  score: 271.1 bits;  conditional E-value: 1.5e-83
                      Topoisom_bac    2 inenlvdaaeaRrelDwliGinlsrlltkklkgkkvlsaGRVqtptLaliveRereienFvpeeyweveatlkke 76  
                                        ine  v+a+ +Rr+ D++iG++ls+ l++ ++++  lsaGRVqtp+L++i++R++e   Fv  e   v++tl   
  gi|242398521|ref|YP_002993945.1|  818 INEGRVNAQIVRRIEDRWIGFELSQKLWE-VFENPYLSAGRVQTPVLSWIIQRYKE---FVESEINFVQLTL--- 885 
                                        79999***********************8.8889*******************987...6555555555443... PP

                      Topoisom_bac   77 kkekekkkkkkkerikdkeeaeaileklkk..keakvesvekkekkkppplpfdtttLqkeasrklglsakktls 149 
                                                         +++   +le++k+  +e++ve+v  +ek+ +p  p++t+t++++asr l++s + t++
  gi|242398521|ref|YP_002993945.1|  886 -----------------ENDLSVVLEDVKDgvEEVVVEDVHLEEKEINPLPPYTTDTMLQDASRFLKFSTDYTMR 943 
                                        .................3344445555544322689***********6655************************ PP

                      Topoisom_bac  150 iaqkLYekaglitYpRTdstrlseeaelkailealakkygkeylefaekllkktkkksvvknkkveaHeAIrPte 224 
                                        +aq+L+e  gl tY RTdst++s+   ++ ++e+++++ g+ey+         ++k+    +++ + He+IrPt+
  gi|242398521|ref|YP_002993945.1|  944 LAQDLFEV-GLLTYIRTDSTHVSNVG-IEVAKEYITDEIGEEYFV--------PRKW----GEE-GTHECIRPTR 1003
                                        *******5.*****************.9*********98887777........4545....444.89******** PP

                      Topoisom_bac  225 elpklkels...............ddekklYelIvrrflaslmkdakyeettvkleveeeefkasgk.tilekGf 283 
                                         +++  +l                +d+ +lY+++++rf+ s+mk+ k+   +++++++  + +++g  +il +G+
  gi|242398521|ref|YP_002993945.1| 1004 PIDT-GRLMqllrdgvitlargltRDHFRLYDMVFKRFMTSQMKATKVLYEKATIDARIAKAEVEGYvEILYEGW 1077
                                        *995.344446689999999999988888*************************999888888888626899*** PP

                      Topoisom_bac  284 kkvykeekkeeeeeelpelkegeevkvkeveleekkTkppkryteasLikamekagiGtpaTraeiieklvergY 358 
                                        +k+ +   k+     lp+l++g+++kvke  +++ k  + + ++++++i++m++++iG+p+T+a+i+++l++r Y
  gi|242398521|ref|YP_002993945.1| 1078 TKLRNLPLKK-----LPKLEKGQKIKVKE--TKKWKAPKVPLFSQGDIIALMKEHKIGRPSTYAKIVKTLLDRHY 1145
                                        ***9865554.....9***********99..77778888899********************************* PP

                      Topoisom_bac  359 verkk..kslvptelGkalvell.ekfkdlvspelTaeleekLdeIaegkadakevl 412 
                                        v + k  k+lvptelG+++++ l +k+kdlvs+e T++lee +  I+e k+d++evl
  gi|242398521|ref|YP_002993945.1| 1146 VIETKgrKKLVPTELGTKVYHYLiTKYKDLVSEERTKQLEELMGLIEEDKIDYQEVL 1202
                                        *99844799**************9999****************************98 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       1.9   2.1e+03      44      59 ..     246     272 ..     169     297 .. 0.65
   2 !   89.9   0.0     1e-28   1.1e-25       2     103 .]     642     803 ..     641     803 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.9
                                       E...........ECTTTHHHHHHHHHH CS
                            Toprim  44 e...........eiedkkkvlkalkel 59 
                                       +           +++dk+++lk+l+++
  gi|242398521|ref|YP_002993945.1| 246 KlkklmakylngNRKDKNEQLKELNKQ 272
                                       033333344467666666666665443 PP

  == domain 2  score: 89.9 bits;  conditional E-value: 1e-28
                                       EEEESSHHHHHHHHHTHT..................STEEEEEEESSSSEEEHS................TTEEEEE CS
                            Toprim   2 lvivEgpsdaktiakalg..................sgfqavtaslGhildlet................efkpvye 44 
                                       l+ivE+p++a+tia+++g                  +  ++++as Gh++dl t                 f p+y+
  gi|242398521|ref|YP_002993945.1| 642 LMIVESPNKARTIANFFGhpskrrigdlvayevsigELMLTILASGGHMFDLITndnyhgvlikekegklYFIPIYD 718
                                       9****************************************************************999998888888 PP

                                       ...........................ECTTTHHHHHHHHHHHHHHSEEEEECSSSHHHHHHHHHHHHHHTHHHTTT CS
                            Toprim  45 ...........................eiedkkkvlkalkelakradeiilatDpDreGeaiawellevlkellenk 94 
                                                                   ++d  +++ka++e+a+++dei++ tDpD+eGe+iaw++++vl ++++  
  gi|242398521|ref|YP_002993945.1| 719 tlkrcrecghqfvdweskgvcprcgsnDVRDVLENVKAMREIAQEVDEILIGTDPDTEGEKIAWDIRNVLSPYTPT- 794
                                       88899999999999999999******************************************************99. PP

                                       EEEEEESSS CS
                            Toprim  95 igrvefsei 103
                                       i+r+ef+e+
  gi|242398521|ref|YP_002993945.1| 795 IKRIEFHEV 803
                                       *******96 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.6   0.0   1.3e-14   1.3e-11       3     140 ..      88     222 ..      86     241 .. 0.79

  Alignments for each domain:
  == domain 1  score: 44.6 bits;  conditional E-value: 1.3e-14
                                       HHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   3 iQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvl 79 
                                        Q+  ++ +++g+++ + a+TG+GK+   ++  +   y    k g+k  i+ Pt+ L+ qt++++k+f +++++ v+
  gi|242398521|ref|YP_002993945.1|  88 AQKTWVKRLVKGKSFSIIAPTGMGKSVFGAFMSIY--Y---AKYGKKSYIILPTTPLVTQTIKRVKTFAENTGIDVN 159
                                       69999999******************987777773..3...49999************************9888888 PP

                                       EE.ET....TSSHHHHHHHHHTT.CSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHH CS
                                       xx.xx....xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  80 li.ig....gvaardqlskldng.vdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsd 140
                                       l  ++    ++++++ ++k++ g  di+++  + l++ ++   ++ +++ f+ +D +d +l+   s+
  gi|242398521|ref|YP_002993945.1| 160 LAyYHgnmkKKEKEEMIQKIQTGdFDILITSGQYLARNFD--LIKDKKFDFIFVDDVDAFLKA--SK 222
                                       442552222444555555556558******9999998774..445788999*******99987..44 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 !   24.7   0.0   2.2e-08   2.3e-05      21      73 ..     139     190 ..     117     196 .. 0.77
   2 ?    3.0   0.3      0.12   1.3e+02       6      71 ..     214     293 ..     210     305 .. 0.67
   3 !    6.9   0.0    0.0072       7.6      14      85 ..     348     421 ..     337     443 .. 0.64
   4 ?    2.1   0.0      0.23   2.5e+02      96     109 ..     550     563 ..     541     564 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 2.2e-08
                                       EEESSHHHHHHHHHHHHHT..TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEES CS
                        Helicase_C  21 ifvntidrlekvklllekk..gikvavlhgelpqnereeileqfnkgesdvLiat 73 
                                       ++++ti+r+   k + e+   +++ a++hg+++++e+ee++++ + g++d+Li++
  gi|242398521|ref|YP_002993945.1| 139 LVTQTIKRV---KTFAENTgiDVNLAYYHGNMKKKEKEEMIQKIQTGDFDILITS 190
                                       334445555...888777777899****************************986 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.12
                                       HHHHHHHTTTTSEEEEEESSHH.HHHH.HHHHHHHTTSTEEEESTTSTHHHHH............HHHHHHH.TTSS CS
                        Helicase_C   6 llellkleeeggkilifvntid.rlek.vklllekkgikvavlhgelpqnere............eileqfn.kges 67 
                                       + ++lk +++ +++li + + + +++k  ++++  k++ + +l+g+ + ++ +            + +++f+ k+++
  gi|242398521|ref|YP_002993945.1| 214 VDAFLKASKNIDRSLILLGFNEeMIQKaWEIIK-LKKLMAKYLNGNRKDKNEQlkelnkqiniieKEIREFKdKNKI 289
                                       556777778888888888888867777777774.45699999***65555554477777777777777777744444 PP

                                       SEEE CS
                        Helicase_C  68 dvLi 71 
                                        vLi
  gi|242398521|ref|YP_002993945.1| 290 GVLI 293
                                       4553 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0072
                                       TTTSEEEEEESSHH...HHHH.HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGG....GTSSSTS CS
                        Helicase_C  14 eeggkilifvntid...rlek.vklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdv....aerGidi 82 
                                       + g   lifv+  +    +e+ +++l +  g+kv      l +  +++ l++f +ge+d+L+        + rG+di
  gi|242398521|ref|YP_002993945.1| 348 VLGPGGLIFVPIDQgiaYAERlTNYL-QDLGFKVE-----LISARNKKGLQRFENGEVDYLVGVATyygsIVRGLDI 418
                                       44555566666666322222234444.33367774.....444578899**********99666555566779**** PP

                                       TTE CS
                        Helicase_C  83 pkv 85 
                                       p +
  gi|242398521|ref|YP_002993945.1| 419 PHL 421
                                       954 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.23
                                       SHHHHHHHHTTSSS CS
                        Helicase_C  96 nvtsyiqriGRtgR 109
                                       +v++yiq+ GRt R
  gi|242398521|ref|YP_002993945.1| 550 DVRTYIQATGRTSR 563
                                       6899********99 PP

>> zf_Rg  Reverse gyrase zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.2   1.4e-11   1.5e-08       3      37 ..       2      38 ..       1      48 [. 0.87
   2 ?   -1.9   0.1       2.2   2.3e+03       8      14 ..     737     743 ..     735     755 .. 0.78

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 1.4e-11
                             zf_Rg  3 kavfeklCPNCgGdisdeRlekGLpCkrClPke..gd 37
                                      ka+++  CPNC+ +isdeRl k  pC+ Cl +e   d
  gi|242398521|ref|YP_002993945.1|  2 KAIYKGMCPNCEDKISDERLYKKHPCEICLEDEitSD 38
                                      89****************************9986555 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.2
                             zf_Rg   8 klCPNCg 14 
                                         CP Cg
  gi|242398521|ref|YP_002993945.1| 737 GVCPRCG 743
                                       5799998 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   0.8   2.7e-10   2.9e-07      21     141 ..      86     214 ..      53     255 .. 0.79
   2 ?    0.4   0.0      0.55   5.8e+02       5      35 ..     269     300 ..     263     302 .. 0.78

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 2.7e-10
                                       ............TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG....... CS
                            ResIII  21 s..........krdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseayke... 84 
                                                   + k + i ++TG+GK++  a +  +++k gk  k  ++ p++ l+ qt++++k f++++  +   
  gi|242398521|ref|YP_002993945.1|  86 WsaqktwvkrlVKGKSFSIIAPTGMGKSVFGAFMSIYYAKYGK--KSYIILPTTPLVTQTIKRVKTFAENTGIDvnl 160
                                       044444444445778899**********999888888888555..9***********************99877888 PP

                                       .....GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETG CS
                            ResIII  85 .....igkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEa 141
                                            ++kk+++++ ++ ++++ + +il+t+ q l ++        +  ++++fd+i++D +
  gi|242398521|ref|YP_002993945.1| 161 ayyhgNMKKKEKEEMIQ-KIQTGDFDILITSGQYLARNF-------DLIKDKKFDFIFVDDV 214
                                       88765555555555555.99*******************.......8889999999999975 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.55
                                       -HHHHHHHHHHT......TTSEEE.EEESTTS CS
                            ResIII   5 reyQeeaienlleklkskrdkrgl.ikmaTGt 35 
                                        + Q+++ie+ + ++k+k++  +l i+ aTG+
  gi|242398521|ref|YP_002993945.1| 269 LNKQINIIEKEIREFKDKNKIGVLiIASATGS 300
                                       57899999999999996555555558999997 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   1.0       4.1   4.3e+03      29      34 ..       9      14 ..       4      31 .. 0.68
   2 !   21.0   0.5   2.6e-07   0.00027       7      38 ..     722     749 ..     715     751 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 4.1
                       Zn-ribbon_8 29 CPeCgs 34
                                      CP+C  
  gi|242398521|ref|YP_002993945.1|  9 CPNCED 14
                                      676653 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 2.6e-07
                       Zn-ribbon_8   7 rCeeCghefevlqsisdapltaCPeCgs.evrr 38 
                                       rC+eCgh+f  + s     + +CP+Cgs +vr 
  gi|242398521|ref|YP_002993945.1| 722 RCRECGHQFVDWES-----KGVCPRCGSnDVRD 749
                                       6***********96.....567******88875 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 ?    2.0   0.4      0.19     2e+02      70      98 ..       6      36 ..       2      42 .. 0.81
   2 ?   -3.2   0.0       7.8   8.3e+03      38      58 ..     232     252 ..     230     258 .. 0.82
   3 !   14.1   0.0   3.4e-05     0.036      70      98 ..     720     748 ..     669     755 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.19
                                      EEEETTTS-EEECHH.H.HHS-TTTSSS-EE CS
                              HypA 70 kvrCreCgkefelee.k.alrCpkCgsadve 98
                                      k +C +C+ +++ e+ + +  C+ C + +++
  gi|242398521|ref|YP_002993945.1|  6 KGMCPNCEDKISDERlYkKHPCEICLEDEIT 36
                                      568*********887645789****887765 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 7.8
                                       T--HHHHHHHHHHHHCC.TTT CS
                              HypA  38 gvepeaLefafellaegtvle 58 
                                       g ++e+++ a+e+++ +++++
  gi|242398521|ref|YP_002993945.1| 232 GFNEEMIQKAWEIIKLKKLMA 252
                                       568999*******99888765 PP

  == domain 3  score: 14.1 bits;  conditional E-value: 3.4e-05
                                       EEEETTTS-EEECHHHHHS-TTTSSS-EE CS
                              HypA  70 kvrCreCgkefeleekalrCpkCgsadve 98 
                                         rCreCg++f   e++  Cp+Cgs+dv+
  gi|242398521|ref|YP_002993945.1| 720 LKRCRECGHQFVDWESKGVCPRCGSNDVR 748
                                       569********95555578******9986 PP

>> DctP  Bacterial extracellular solute-binding protein, family 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   4.8e-06    0.0051       8      83 ..     136     212 ..     130     272 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.8e-06
                                       TSHHHHHHHHHHHHHHHHTTTSEEEEEEETTTTTTHH.HHHHHHHTTSSSEEEEEGGGGTTTSGGGGGGGSTTTSCS CS
                              DctP   8 gspkhkaaekfaklveektnGkvkievypssqLggde.eviealknGtvdivatssakleglvpeigvldlPFlfed 83 
                                       ++p  +++ k  k+++e t+ +v +  y+ ++ ++++ e+i+++++G++di++ts  +l+  ++ i+  ++ F+f d
  gi|242398521|ref|YP_002993945.1| 136 TTPLVTQTIKRVKTFAENTGIDVNLAYYHGNMKKKEKeEMIQKIQTGDFDILITSGQYLARNFDLIKDKKFDFIFVD 212
                                       566666776777899999***********9988888779********************999998888888888844 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.6      0.46   4.8e+02      31      53 ..       9      31 ..       7      39 .. 0.86
   2 ?   14.2   0.2   2.9e-05     0.031      23      60 ..     715     750 ..     704     754 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.46
                    OrfB_Zn_ribbon 31 CseCgsknkealsgrtfkCpnCg 53
                                      C++C  k ++++  +++ C+ C 
  gi|242398521|ref|YP_002993945.1|  9 CPNCEDKISDERLYKKHPCEICL 31
                                      *********99999999999886 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 2.9e-05
                    OrfB_Zn_ribbon  23 npayTSktCseCgsknkealsgrtfkCpnCgfeadrDv 60 
                                         + T k+C eCg++  +   + + +Cp+Cg    rDv
  gi|242398521|ref|YP_002993945.1| 715 PIYDTLKRCRECGHQFVD--WESKGVCPRCGSNDVRDV 750
                                       445599************..999*************98 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.6     0.093        99      30      44 ..       8      22 ..       2      37 .. 0.67
   2 ?   10.6   0.3   0.00041      0.43      12      36 ..     720     744 ..     714     749 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.093
                               DZR 30 rCpsCgekvdpearf 44
                                      +Cp+C+ k++ e  +
  gi|242398521|ref|YP_002993945.1|  8 MCPNCEDKISDERLY 22
                                      788887777666544 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00041
                               DZR  12 arfCseCgtklkavaaedrCpsCge 36 
                                        + C eCg++    +++ +Cp+Cg+
  gi|242398521|ref|YP_002993945.1| 720 LKRCRECGHQFVDWESKGVCPRCGS 744
                                       5679999999888888999999987 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.6       1.7   1.7e+03      87     133 ..       6      16 ..       2      38 .. 0.63
   2 ?   11.6   0.1   0.00015      0.16      70     173 ..     717     747 ..     692     758 .. 0.62

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.7
                           TackOD1  87 revCpkCkSidieeqelihhftCgnvgpeeeflkegkleCpkCktkL 133
                                       + +Cp+C+                                     k+
  gi|242398521|ref|YP_002993945.1|   6 KGMCPNCED------------------------------------KI 16 
                                       445555554....................................33 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00015
                           TackOD1  70 vdrirlCpsCksghlnvrevCpkCkSidieeqelihhftCgnvgpeeeflkegkleCpkCktkLrhiGvDYdrplev 146
                                       +d+++                                                                        
  gi|242398521|ref|YP_002993945.1| 717 YDTLKR----------------------------------------------------------------------- 722
                                       455555....................................................................... PP

                           TackOD1 147 ykCnsCkslfsepevkarClsCekese 173
                                         C++C++ f++ e k +C +C+++  
  gi|242398521|ref|YP_002993945.1| 723 --CRECGHQFVDWESKGVCPRCGSNDV 747
                                       ..5555555555555555555555443 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.38     4e+02      15      21 ..       7      13 ..       4      14 .. 0.85
   2 ?   11.2   5.3   0.00022      0.23       2      22 ..     722     744 ..     722     746 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.38
                      Rubredoxin_2 15 GrCpsCg 21
                                      G Cp+C 
  gi|242398521|ref|YP_002993945.1|  7 GMCPNCE 13
                                      89****6 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00022
                      Rubredoxin_2   2 vCsqCGfesakwf..GrCpsCgs 22 
                                       +C++CG+++  w   G Cp Cgs
  gi|242398521|ref|YP_002993945.1| 722 RCRECGHQFVDWEskGVCPRCGS 744
                                       8***********777******97 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   1.0     0.041        43       2      25 ..       8      33 ..       7      40 .. 0.79
   2 ?    6.7   0.4    0.0065       6.9       2      24 ..     722     744 ..     717     755 .. 0.62

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.041
                                      --SSS-S--EE-S..SEEE-TTT--E CS
                    zinc-ribbons_6  2 kCpeCqqelekrg..eqyhCeaCqed 25
                                       Cp+C+ +++ +   ++  Ce C ed
  gi|242398521|ref|YP_002993945.1|  8 MCPNCEDKISDERlyKKHPCEICLED 33
                                      5********9555468889**99774 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0065
                                       --SSS-S--EE-SSEEE-TTT-- CS
                    zinc-ribbons_6   2 kCpeCqqelekrgeqyhCeaCqe 24 
                                        C+eC ++ +  +++  C  C +
  gi|242398521|ref|YP_002993945.1| 722 RCRECGHQFVDWESKGVCPRCGS 744
                                       35555555553333555555554 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 ?   10.5   0.1   0.00051      0.54       9      41 ..     721     754 ..     716     765 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00051
                      NOB1_Zn_bind   9 lrChaCfkvtkd.mtkkFCpkCGnktLkrvavsv 41 
                                        rC+ C + + d  +k  Cp+CG++ ++ v   v
  gi|242398521|ref|YP_002993945.1| 721 KRCRECGHQFVDwESKGVCPRCGSNDVRDVLENV 754
                                       79****99887769**********9988776555 PP

>> zf-C4pol  C4-type zinc-finger of DNA polymerase delta
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.1       0.1   1.1e+02       1      34 [.       9      50 ..       9      60 .. 0.78
   2 ?    8.0   0.1    0.0038       4.1       1      41 [.     723     767 ..     723     769 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.1
                          zf-C4pol  1 ClvCkeklk......kalCkkCrsdkqes..llkllsrlkel 34
                                      C +C++k++      k+ C+ C +d+ +s  +++l+s ++e 
  gi|242398521|ref|YP_002993945.1|  9 CPNCEDKISderlykKHPCEICLEDEITSdtYFDLISGIREG 50
                                      999**7777777888999****99988888899999887765 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0038
                          zf-C4pol   1 ClvCkeklk....kalCkkCrsdkqesllkllsrlkelekklnel 41 
                                       C  C++++     k +C +C s++ + +l+ ++ ++e+ ++++e+
  gi|242398521|ref|YP_002993945.1| 723 CRECGHQFVdwesKGVCPRCGSNDVRDVLENVKAMREIAQEVDEI 767
                                       88999655466679******9999999*********999998775 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.2      0.22   2.3e+02       3      11 ..       9      17 ..       8      17 .. 0.90
   2 ?    7.9   0.2    0.0031       3.3      15      25 ..     721     731 ..     720     732 .. 0.89
   3 ?    0.6   0.4      0.58   6.1e+02       2       7 ..     738     743 ..     737     745 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.22
                           UPF0547  3 CPeCeakvP 11
                                      CP Ce k++
  gi|242398521|ref|YP_002993945.1|  9 CPNCEDKIS 17
                                      *****9996 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0031
                           UPF0547  15 qfCphCGyvFq 25 
                                       ++C++CG+ F 
  gi|242398521|ref|YP_002993945.1| 721 KRCRECGHQFV 731
                                       78*******96 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.58
                           UPF0547   2 vCPeCe 7  
                                       vCP+C 
  gi|242398521|ref|YP_002993945.1| 738 VCPRCG 743
                                       588875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1416  (0.0789782); expected 358.6 (0.02)
Passed bias filter:                      855  (0.0476881); expected 358.6 (0.02)
Passed Vit filter:                       124  (0.00691617); 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):              17  [number of targets reported over threshold]
# CPU time: 1.08u 0.40s 00:00:01.48 Elapsed: 00:00:00.57
# Mc/sec: 6390.26
//
Query:       gi|242398522|ref|YP_002993946.1|  [L=182]
Description: zinc finger SWIM domain protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-06   28.2   0.3      2e-06   27.3   0.3    1.5  1  SWIM      SWIM zinc finger


Domain annotation for each model (and alignments):
>> SWIM  SWIM zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.3   1.1e-10     2e-06      12      38 ..      49      71 ..      41      73 .. 0.84

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 1.1e-10
                              SWIM 12 lnkatCsCpefqkngipCkHalAvlla 38
                                       n + C+Cp     g  CkH++A+l+a
  gi|242398522|ref|YP_002993946.1| 49 KNSNKCTCP----QGKDCKHVAAALSA 71
                                      5699*****....************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       694  (0.0387082); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); 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 0.33s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 1103.67
//
Query:       gi|242398523|ref|YP_002993947.1|  [L=597]
Description: Probable translation initiation factor IF-2 [Thermococcus sibiricus MM 739]
Scores for complete 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    5.9e-31  107.5   0.0    2.6  2  GTP_EFTU     Elongation factor Tu GTP binding domain
    3.2e-31  107.1   0.5    1.2e-30  105.2   0.5    2.1  1  GTP_EFTU_D4  Elongation factor Tu domain 4
    5.5e-23   81.1   3.8    5.5e-23   81.1   3.8    2.1  2  IF-2         Translation-initiation factor 2
    4.1e-14   52.7  10.4      6e-13   49.0   0.1    3.7  5  GTP_EFTU_D2  Elongation factor Tu domain 2
    1.1e-08   35.1   0.5    5.8e-08   32.8   0.0    2.5  2  MMR_HSR1     50S ribosome-binding GTPase
    0.00075   19.7   0.0     0.0043   17.3   0.0    2.3  1  Roc          Ras of Complex, Roc, domain of DAPkinase
     0.0072   16.1   0.0       0.02   14.7   0.0    1.8  1  ATP_bind_1   Conserved hypothetical ATP binding protein
  ------ inclusion threshold ------
      0.014   15.0   0.0      0.043   13.4   0.0    1.8  1  Ras          Ras family
      0.044   13.8   0.0       0.81    9.7   0.0    2.6  2  Dynamin_N    Dynamin family
       0.29   11.6   1.4       0.63   10.5   0.4    2.1  2  Na_Ca_ex_C   C-terminal extension of sodium/calcium exchanger


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 !  107.5   0.0   3.3e-34   5.9e-31       5     189 ..       8     214 ..       4     219 .. 0.76
   2 ?   -1.7   0.1         1   1.8e+03     107     144 ..     334     375 ..     324     463 .. 0.65

  Alignments for each domain:
  == domain 1  score: 107.5 bits;  conditional E-value: 3.3e-34
                                       EEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHH...HHHST...HCHSHHHHHHTSCSSCEEEEEETTCSSEEEEEE CS
                          GTP_EFTU   5 nigiighvDhGKtTLtdrLlyktgaiskkgeka...eeerv...lDtlkeErergiTiksaaisleketkkylinli 75 
                                        i+++ghvDhGKt+L+dr+  ++ a +++g  +   ++  +   +D  k+     ++     i+l        + +i
  gi|242398523|ref|YP_002993947.1|   8 IIAVLGHVDHGKTSLLDRIRNTHVAEKEAGGITqhiGA--TevpIDVVKQLAGPLLSLWKGEIKLP------GLLFI 76 
                                       689****************9766666665544422321..12335555555555555555555555......9**** PP

                                       EESSSGGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGST...........HHHHHH CS
                          GTP_EFTU  76 DtPGHvdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrl...........kaelke 141
                                       DtPGH+ F++   rg + +D+a+l++d++eG +pqt e +++++k+++p++v+ NK+Dr+             ++k+
  gi|242398523|ref|YP_002993947.1|  77 DTPGHEAFTSLRARGGSLADLAILIIDVNEGFQPQTLESIEILRKYKTPFVVAANKIDRIkgwkvvenepfLVNIKK 153
                                       **************************************************************999998888666666 PP

                                       HHHHHHHHHHHH..............HHHHHHHHHTTT.........TTEEEEEEBTTTTBTHHHHHHHHH CS
                          GTP_EFTU 142 iveevkqklsrk..............eeklekygekge.........kevpvvfgSalkgegvktllealv 189
                                       + + ++q+l++k                         +         ke  ++++Sa+ g gv +ll  + 
  gi|242398523|ref|YP_002993947.1| 154 QDQRAQQDLETKlweligkfyelgfqV----------NrfdrvkdfrKELAIIPISAKYGIGVPELLVLIS 214
                                       666666666555666655555444331..........355555666679****************998775 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1
                                       STHHHHHHHHHHHHTTTE..EEEEEESCGST..HHHHHHHHH CS
                          GTP_EFTU 107 vepqteevlrlalkegvp..iivfiNKmDrl..kaelkeive 144
                                        +   +e+l++++++ +    + +i K+D +   + l++  +
  gi|242398523|ref|YP_002993947.1| 334 LKRARREILEQIKSVIIStdKVGVIVKADTIgsLEALSKELH 375
                                       555566777777777666667777777777744222222222 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 !  105.2   0.5   6.6e-34   1.2e-30       2      86 .]     467     553 ..     466     553 .. 0.95

  Alignments for each domain:
  == domain 1  score: 105.2 bits;  conditional E-value: 6.6e-34
                                       -CEEEEEEE..EEEETCCCEEEEEEEEEEEEETT-EEEETTE.EEEEEEEEEETTEEESEEETT-EEEEEEESS-TT CS
                       GTP_EFTU_D4   2 Pgkikilpg..vvfrrsdpaivGvevlgGvikpgvklikedGrevGeilqiqdkgkkleeakaGqevaisiegkivG 76 
                                       Pg ik+ p+  +vfrrs+paivG+evl+G+ikpg++lik++G +vG+i++i++k++ l+eak+G++va++ieg+ivG
  gi|242398523|ref|YP_002993947.1| 467 PGVIKLFPDerYVFRRSHPAIVGIEVLEGRIKPGYPLIKQNGDKVGVIKSIKSKEDFLQEAKKGDQVAVAIEGAIVG 543
                                       777888875449***************************************************************** PP

                                       TS--TT-EEE CS
                       GTP_EFTU_D4  77 rqikegdily 86 
                                       r+i+ g+ily
  gi|242398523|ref|YP_002993947.1| 544 RHIHPGEILY 553
                                       *********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 !   81.1   3.8   3.1e-26   5.5e-23      10     105 .]     350     446 ..     339     446 .. 0.87
   2 ?   -1.9   0.1       2.1   3.7e+03      31      59 ..     521     551 ..     507     563 .. 0.66

  Alignments for each domain:
  == domain 1  score: 81.1 bits;  conditional E-value: 3.1e-26
                                       SCSSCCEEEEEESSHHHHHHHHHHHHCTT.SSTEEEECEEEESSB-HHHHHHHHH.ST.....EEEEEESSSCTHHH CS
                              IF-2  10 eegkelnviikaDvqGsleAlkeaLekleseevkvkvihsgvGaitesDvelasa.sn.....aiiigFnvkvskka 80 
                                        ++++++vi+kaD+ GsleAl++ L++      ++++ +++vG+i+++Dv+ a + ++     +++igFnvkv+++a
  gi|242398523|ref|YP_002993947.1| 350 ISTDKVGVIVKADTIGSLEALSKELHEK-----NIPIRKADVGNISKTDVMEALSvKEeepfyGVVIGFNVKVNEDA 421
                                       24499*********************98.....5*******************7742256888************** PP

                                       HHCCCCCTSEEEEESSHHHHHHHHH CS
                              IF-2  81 kklaekegvkirlynvIYkliddvk 105
                                       +++a+ +++ ++ +n+IYkli+d++
  gi|242398523|ref|YP_002993947.1| 422 EEVAKAKNIPLFVNNIIYKLIEDYE 446
                                       **********************985 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.1
                                       HHHHHCTT..SSTEEEECEEEESS.B-HHHH CS
                              IF-2  31 keaLekles.eevkvkvihsgvGa.itesDv 59 
                                       +++L++ ++ ++v v +  + vG  i+  ++
  gi|242398523|ref|YP_002993947.1| 521 EDFLQEAKKgDQVAVAIEGAIVGRhIHPGEI 551
                                       4678888778999999888888854555555 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 ?   -3.7   0.0         9   1.6e+04      17      41 ..      24      49 ..      24      56 .. 0.65
   2 !   49.0   0.1   3.3e-16     6e-13       1      73 [.     247     325 ..     247     326 .. 0.92
   3 ?   -0.8   0.0       1.2   2.1e+03      49      65 ..     350     366 ..     330     372 .. 0.71
   4 ?   -2.6   0.0       4.2   7.5e+03      44      60 ..     401     417 ..     377     422 .. 0.62
   5 !    8.5   0.5    0.0014       2.6       3      74 .]     487     553 ..     486     553 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 9
                                      EEEEEECTCTTSEE...EEEEEEEEEEE CS
                       GTP_EFTU_D2 17 devrilgndtskke...ivtrissletf 41
                                      d++r+   ++ +ke   i+  i+++e++
  gi|242398523|ref|YP_002993947.1| 24 DRIRN--THVAEKEaggITQHIGATEVP 49
                                      56677..555556566677777777765 PP

  == domain 2  score: 49.0 bits;  conditional E-value: 3.3e-16
                                       EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEE...........ETTSEEEEEEEESSCCSG CS
                       GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededea...........vaganaGvivaikgleda 66 
                                       Gt++++++y+Gtl+k+d+++++g+d+    ivt+i++l+++ +++de            ++ a aG+++a+++le+a
  gi|242398523|ref|YP_002993947.1| 247 GTTIDVIIYDGTLRKDDTIVVGGKDK---AIVTKIRALLKP-KPLDEIrdprykfdhvnEVSASAGIKIAAPDLEEA 319
                                       9********************66543...6***********.7799999***************************8 PP

                                       SSTTCEE CS
                       GTP_EFTU_D2  67 iivGdtl 73 
                                        ++G+++
  gi|242398523|ref|YP_002993947.1| 320 -LAGSPV 325
                                       .999875 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 1.2
                                       ETTSEEEEEEEESSCCS CS
                       GTP_EFTU_D2  49 vaganaGvivaikgled 65 
                                       +  + +Gviv+++ + +
  gi|242398523|ref|YP_002993947.1| 350 ISTDKVGVIVKADTIGS 366
                                       66788999999887765 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 4.2
                                       EESEEETTSEEEEEEEE CS
                       GTP_EFTU_D2  44 dedeavaganaGvivai 60 
                                       +e+e+  g+++G++v++
  gi|242398523|ref|YP_002993947.1| 401 KEEEPFYGVVIGFNVKV 417
                                       34555778888888776 PP

  == domain 5  score: 8.5 bits;  conditional E-value: 0.0014
                                       EEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEEE CS
                       GTP_EFTU_D2   3 valgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtlt 74 
                                       ++++ v +G +k+G  +    +  + k  v+ i+s+   +  ++ea +g+++ v + +  +  +i  G++l+
  gi|242398523|ref|YP_002993947.1| 487 IVGIEVLEGRIKPGYPLIK--Q-NGDK--VGVIKSIKSKEDFLQEAKKGDQVAVAIEGAIVGRHIHPGEILY 553
                                       6778899999999999886..4.4455..8**************************9998888888888875 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.0   3.2e-11   5.8e-08       2     114 .]       9     132 ..       8     132 .. 0.80
   2 ?   -0.9   0.3      0.94   1.7e+03      70      70 ..     378     378 ..     319     465 .. 0.56

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 3.2e-11
                                       EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETT.EE.................EEEEECGGCSSHH CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkg.ke.................ielvDtpGliega 60 
                                       +a++G+   GK++L+ ++ ++++  ++  g T++i   +v ++  k+                 + ++DtpG  e  
  gi|242398523|ref|YP_002993947.1|   9 IAVLGHVDHGKTSLLDRIRNTHVAEKEAGGITQHIGATEVPIDVvKQlagpllslwkgeiklpgLLFIDTPG-HE-- 82 
                                       89******************999999999******99998866422255666666666677777********.44.. PP

                                       HHHHHHHHHHHHHHC.TSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                          MMR_HSR1  61 seekglgkaflalee.adlillvvdaseeklkpldeeleelleeakkplilvlnk 114
                                            ++   ++  + adl++l++d++ e+++p+  e  e+l++ k p+++++nk
  gi|242398523|ref|YP_002993947.1|  83 --A--FTSLRARGGSlADLAILIIDVN-EGFQPQTLESIEILRKYKTPFVVAANK 132
                                       ..2..222222222348********88.88**********************998 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.94
                                       H CS
                          MMR_HSR1  70 f 70 
                                        
  gi|242398523|ref|YP_002993947.1| 378 N 378
                                       1 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 !   17.3   0.0   2.4e-06    0.0043       2     119 ..       9     134 ..       8     135 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.4e-06
                                       EEEESSTTSSHHHHHHCHCT-CCC-EEE....TTTTEEEEEEECG.GSGGCT...TBTTTTCEEEEEEEE-SGGCTT CS
                               Roc   2 vvlvGdsgvGKtsllkrfvedkfsekek....stigvdfltkevt.kikgve...ndkkvkkvklniWDtaGqerfr 70 
                                       + ++G    GKtsll+r+ + ++ eke     + ig++ +  +v+ ++ g      + ++k   l + Dt G+e f 
  gi|242398523|ref|YP_002993947.1|   9 IAVLGHVDHGKTSLLDRIRNTHVAEKEAggitQHIGATEVPIDVVkQLAGPLlslWKGEIKLPGLLFIDTPGHEAFT 85 
                                       6789*******************999862211444444433333212222221112233444456788********* PP

                                       TT-HHHHCTSCEEEEEEEGHHHHCHHHHHHHHHHHCS.SS-EEEEEE-TT CS
                               Roc  71 slhplylreaalailvydsrssenlkeWlkelkkvag.kspvilvgnkiD 119
                                       sl+    + a+lail++d ++  +  + l++++  ++ k+p+++ +nkiD
  gi|242398523|ref|YP_002993947.1|  86 SLRARGGSLADLAILIIDVNEGFQ-PQTLESIEILRKyKTPFVVAANKID 134
                                       ******************765544.355788887766477999999***9 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 !   14.7   0.0   1.1e-05      0.02      94     214 ..      74     176 ..      44     208 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.1e-05
                        ATP_bind_1  94 llfDtPGQielfthseslakiveeLesefalvvvyLvDsqrltdptkfisgllsalsamlrlelPhvvvlnkfDllk 170
                                       l +DtPG   +  +++ +         + a  ++ ++D++       f  ++l ++ ++ ++++P+vv+ nk+D +k
  gi|242398523|ref|YP_002993947.1|  74 LFIDTPGHEAFTSLRARGG--------SLADLAILIIDVNEG-----FQPQTLESIEILRKYKTPFVVAANKIDRIK 137
                                       5567777666666666666........555566777776654.....4455566679******************99 PP

                        ATP_bind_1 171 eklekeleffedvealslllekeeekykklaeaiaelleefalv 214
                                              +++e+   l ++++++++++++l+ ++ el+ +f++ 
  gi|242398523|ref|YP_002993947.1| 138 -----GWKVVENEPFLVNIKKQDQRAQQDLETKLWELIGKFYEL 176
                                       .....8999999999999999999**************999976 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.4e-05     0.043       3     118 ..      10     137 ..       8     165 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.4e-05
                                       EEEESTTSSHHHHHHHHHHSSCSSSCTTTSSEEEEEEEEEET.............TEEEEE...EEEEETTSGGGHH CS
                               Ras   3 vlvGdsavGKtslllrfvkdkFkeeyesTigvdfytkeievd.............gkevkl...eiwDTAGqeefks 63 
                                        ++G    GKtsll r  + +  e+    i      +e+ +d             + e+kl      DT G e f+s
  gi|242398523|ref|YP_002993947.1|  10 AVLGHVDHGKTSLLDRIRNTHVAEKEAGGITQHIGATEVPIDvvkqlagpllslwKGEIKLpglLFIDTPGHEAFTS 86 
                                       6899999999999999999999999888887777778888888888999999999667765221578********** PP

                                       HHHHHHTTESEEEEEEETTBHHHHHTHHHHHHHHHHHSTTTSEEEEEEETTTGGG CS
                               Ras  64 lrelyyrdaegillvyditsresfenvkkwveeikrvaeenvpivLvGnKvDlee 118
                                       lr    + a+ ++l+ d+++   f+  +    ei r+ +  +p+v+ +nK+D  +
  gi|242398523|ref|YP_002993947.1|  87 LRARGGSLADLAILIIDVNE--GFQPQTLESIEILRKYK--TPFVVAANKIDRIK 137
                                       ***************99975..55544433345666655..699999***99765 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00045      0.81       1      34 [.       9      42 ..       9      48 .. 0.91
   2 ?    0.7   0.0      0.27   4.9e+02      93     111 ..      63      81 ..      46      89 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00045
                                      EEEEEBTTTTHHHHHHHHHTS--S---SSS---S CS
                         Dynamin_N  1 iavvGsqSsGKSSvlnaLlgedilprgpnptTrr 34
                                      iav+G++ +GK+S+l+ +   ++  ++++ +T+ 
  gi|242398523|ref|YP_002993947.1|  9 IAVLGHVDHGKTSLLDRIRNTHVAEKEAGGITQH 42
                                      89****************9999999999888875 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.27
                                       EEEEETTS-SEEEEE---B CS
                         Dynamin_N  93 lkilsllvkgltlvDlPGl 111
                                       l + +++ +gl ++D+PG 
  gi|242398523|ref|YP_002993947.1|  63 LWKGEIKLPGLLFIDTPGH 81 
                                       5566788899********6 PP

>> Na_Ca_ex_C  C-terminal extension of sodium/calcium exchanger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0         9   1.6e+04      52      69 ..     329     346 ..     308     349 .. 0.65
   2 ?   10.5   0.4   0.00035      0.63      28      90 ..     525     587 ..     503     591 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 9
                        Na_Ca_ex_C  52 eeakdleesrkevirilk 69 
                                       +++++l+ +r+e+++ +k
  gi|242398523|ref|YP_002993947.1| 329 RDEEELKRARREILEQIK 346
                                       445555566666555444 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00035
                        Na_Ca_ex_C  28 eleekeegvellldgklveeaeeseeakdleesrkevirilkelkqkyPdkdleqleelanye 90 
                                       ++++k ++v + ++g +v ++ +  e+  ++ s++++ir++kel+    d+d+e l++ a+ +
  gi|242398523|ref|YP_002993947.1| 525 QEAKKGDQVAVAIEGAIVGRHIHPGEILYVDISKDDAIRLVKELRDMLDDTDIEALKNTAKVK 587
                                       334455667778889999999889999999***************************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (597 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.81u 0.33s 00:00:01.14 Elapsed: 00:00:00.56
# Mc/sec: 3187.83
//
Query:       gi|242398524|ref|YP_002993948.1|  [L=203]
Description: ATPase, PP-loop superfamily [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-05   24.2   0.0    5.4e-05   23.0   0.0    1.5  2  Asn_synthase     Asparagine synthase
    6.8e-05   22.5   0.0    9.4e-05   22.0   0.0    1.3  1  QueC             Queuosine biosynthesis protein QueC
     0.0024   16.7   0.0     0.0039   16.0   0.0    1.4  1  tRNA_Me_trans    tRNA methyl transferase
     0.0084   15.7   0.0      0.023   14.3   0.0    1.9  1  ThiI             Thiamine biosynthesis protein (ThiI)
     0.0093   15.7   0.1      0.062   13.1   0.1    2.0  1  ATP_bind_3       PP-loop family
  ------ inclusion threshold ------
      0.027   14.0   0.0      0.043   13.3   0.0    1.5  1  Diphthami_syn_2  Diphthamide synthase


Domain annotation for each model (and alignments):
>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   1.8e-08   5.4e-05      25      86 ..       8      65 ..       2      77 .. 0.85
   2 ?   -2.4   0.0      0.99     3e+03     227     245 ..      99     117 ..      75     117 .. 0.70

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 1.8e-08
                      Asn_synthase 25 SGGlDSSliaalaarqsksplktFsigfeekgsdeakyakevaehlgtehtelvlteeelld 86
                                      SGG DSSl a++++r    ++k +++ f     d  kya+e+a+ lg eh e+++  + +l+
  gi|242398524|ref|YP_002993948.1|  8 SGGKDSSLAAYILKRLGY-EVKLVTVNF--GVLDSWKYARETAQSLGFEH-EVRFLDRKILE 65
                                      ***************986.9********..999****************7.66665555554 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.99
                      Asn_synthase 227 DrasmahglEaRvPflDhr 245
                                       +r+s     + RvP+lD+r
  gi|242398524|ref|YP_002993948.1|  99 ERISDGTRRDDRVPLLDQR 117
                                       5666666667799999986 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   3.2e-08   9.4e-05       5      70 ..       6      70 ..       2      93 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 3.2e-08
                                      E--SSHHHHHHHHHHHHH-SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-E..EEEE-GGGGGGSCG CS
                              QueC  5 llSGGlDSttvlalakkegkevealtfdYgqrhkkeleaakkiakelgveeh..kildldllkelggs 70
                                      l SGG DS+ ++++ k+ g+ev+++t+++g   +   ++a++ a++lg  eh  + ld ++l++ ++ 
  gi|242398524|ref|YP_002993948.1|  6 LYSGGKDSSLAAYILKRLGYEVKLVTVNFGVLDS--WKYARETAQSLGF-EHevRFLDRKILEKATEM 70
                                      78****************************8644..5667777777776.440145676777666655 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.3e-06    0.0039       2      33 ..       2      33 ..       1      62 [. 0.85

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.3e-06
                     tRNA_Me_trans  2 kvvvalSgGVDSsvaaallkeqgyevigvflk 33
                                      +v  + SgG DSs+aa++lk+ gyev+ v+++
  gi|242398524|ref|YP_002993948.1|  2 EVYHLYSGGKDSSLAAYILKRLGYEVKLVTVN 33
                                      577788********************999876 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   7.6e-06     0.023       6      36 ..       3      33 ..       1     162 [. 0.79

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7.6e-06
                              ThiI  6 vlaLlSgGiDSpVaaylllkRGcrvvlvhlk 36
                                      v  L SgG DS  aay+l + G +v+lv+++
  gi|242398524|ref|YP_002993948.1|  3 VYHLYSGGKDSSLAAYILKRLGYEVKLVTVN 33
                                      66799**********************9985 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.1   2.1e-05     0.062       6     154 ..       7     144 ..       5     154 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.1e-05
                                       --SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE--H...HHCTTSTCCCH CS
                        ATP_bind_3   6 vSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvkelckklnikleiekvdv...akkkgknleea 79 
                                       +SgG DS +  ++l++l    g ++ +++v++g+ ++ k  +e+ ++l  ++++++   k+     +   ++n  ++
  gi|242398524|ref|YP_002993948.1|   7 YSGGKDSSLAAYILKRL----GYEVKLVTVNFGVLDSWKYARETAQSLGFEHEVRFLDRKILEkatEMCIKDNHPNN 79 
                                       6********99999999....5599****************************999888777644333346677777 PP

                                       HHHHHHHH.HHHCHHCCT.CEEE---BHHHHHHHHHHHHCCT--CCHHH-S-SEEEETTCCEE-CCCT--HHHHHH CS
                        ATP_bind_3  80 ARelRYev.lkealkkegievlllAhhadDqaEtfllrlargsglaglagikeaseiasirlvRPlLkvskeelee 154
                                       A ++  e+ l+e+++ e++e +  +  +dD +  +  r +r+            + + +++++RPlL +  ++++e
  gi|242398524|ref|YP_002993948.1|  80 AIQFIHEMaLEEIARCEDVERISDGTRRDDRVPLLDQRKTRS-----------LEDRFNVQYIRPLLGLGYKTIRE 144
                                       766666543888888999999999999999886655444442...........23345677777777776666666 PP

>> Diphthami_syn_2  Diphthamide synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.5e-05     0.043       1      33 [.       1      33 [.       1      75 [. 0.82

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.5e-05
                   Diphthami_syn_2  1 mkvavlysGGkDsilaLykalke.sevesLvsvi 33
                                      m v  lysGGkDs la y   +  +ev+ Lv+v 
  gi|242398524|ref|YP_002993948.1|  1 MEVYHLYSGGKDSSLAAYILKRLgYEVK-LVTVN 33
                                      67888************97665557776.56655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       562  (0.0313459); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.63u 0.34s 00:00:00.97 Elapsed: 00:00:00.55
# Mc/sec: 1105.20
//
Query:       gi|242398525|ref|YP_002993949.1|  [L=576]
Description: Glutamyl-tRNA synthetase [Thermococcus sibiricus MM 739]
Scores for complete 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-82  276.9   0.0    2.4e-82  276.4   0.0    1.2  1  tRNA-synt_1c    tRNA synthetases class I (E and Q), catalytic
      1e-30  106.9   0.0    2.1e-30  105.9   0.0    1.6  1  tRNA-synt_1c_C  tRNA synthetases class I (E and Q), anti-codo


Domain annotation for each model (and alignments):
>> tRNA-synt_1c  tRNA synthetases class I (E and Q), catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  276.4   0.0   2.6e-86   2.4e-82       1     312 [.     102     408 ..     102     410 .. 0.96

  Alignments for each domain:
  == domain 1  score: 276.4 bits;  conditional E-value: 2.6e-86
                                       S-EEEE---SSSS-BHHHHHHHHHHHHHHHHTT-EEEEEE--SSCCC--HH..HHHHHHHHHHHTT---SSEEEEGG CS
                      tRNA-synt_1c   1 kVrtRfaPePtGyLHiGhakaallnylfAknnnGkfilRieDTdperekee..aeesiledlkwlgikwdekptyqs 75 
                                       kV+tRfaP+P G  H+G+a+aa+l++ +A+ ++GkfilR++DTdp+ + +e  + + i+edlkwlg++  +++ ++s
  gi|242398525|ref|YP_002993949.1| 102 KVVTRFAPNPDGAFHLGNARAAILSHEYARIYDGKFILRFDDTDPKVKRPEpiFYDWIIEDLKWLGFQI-DEIHHAS 177
                                       79******************************************98666554489**************.66***** PP

                                       GGHHHHHHHHHHHHHTTSEEEE-STHHHHHHHHCCSSHSS-TTTTS-HHHHHHHHHHHHHTTHSTTTS-EEEESSBT CS
                      tRNA-synt_1c  76 drfdelkkyaeeLikkGkAYvcectkeeleeereeqeklgskerdrydeenlklfeeemkkgkaegekavvRlkide 152
                                       dr++++++yae+L++ GkAYvc c++ e +++r e   + +++r+ + e +lk + ++m +g++++++avvR+k d 
  gi|242398525|ref|YP_002993949.1| 178 DRLEIYYSYAEKLLEMGKAYVCTCNPAEYKKLRDE--GKPCPHRELPPEVQLKEW-KKMLSGEYKEGEAVVRIKTDL 251
                                       *********************************99..9*****************.89******************* PP

                                       TSS.GGGSSTEEEEEEESGGGSBTTTBTSTSEEE-HHHHHHHHHHHTT-SEEEEEGGGGCCHHHHHHHHHHTT-S.- CS
                      tRNA-synt_1c 153 ess.vefrDlvrgriklepqeihdlvivksdiyPtYdfavvidDaleeithvlrteefldntpkyiwllealglevp 228
                                       +++  ++rD  + ri  +p   h+++++k+++ P Y+fa ++dD+  ++th++r++e+ +n+ ++  ++++lg+e p
  gi|242398525|ref|YP_002993949.1| 252 RHPnPAVRDWPALRIIDDP--NHPRTGNKYRVWPLYNFASAVDDHELGVTHIFRGQEHAENETRQRYMYDYLGWEYP 326
                                       ***9**********99999..8*****************************************************88 PP

                                       EEEEEE--EEETTSB-SHHHHHHHHHTTSSSSTT-TTSCBHHHHHHCTB-HHHHHHHHHHHCCCSSS.EEEEHHHHH CS
                      tRNA-synt_1c 229 pfiheylrlnlekkklSKRklsllvdekqvkewddlreallnflrrlGwtpekerelftreeliksfdlnresksle 305
                                       + +h   rl +e+  lSK k    v+e ++ +wdd+r+ ++++lrr+G++pe+++el+ + +l ks+ +++++++l+
  gi|242398525|ref|YP_002993949.1| 327 ETVH-HGRLSIEGVILSKSKTRKGVEEGKYLGWDDPRLGTIRALRRRGIQPEAIKELIIEVGLKKSD-TTISWDNLA 401
                                       8887.589**********************************************************9.********* PP

                                       HHHHHHH CS
                      tRNA-synt_1c 306 afdrkkL 312
                                       a++r  +
  gi|242398525|ref|YP_002993949.1| 402 AINRRLI 408
                                       *998765 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 !  105.9   0.0   2.4e-34   2.1e-30       1     174 []     412     562 ..     412     562 .. 0.90

  Alignments for each domain:
  == domain 1  score: 105.9 bits;  conditional E-value: 2.4e-34
                    tRNA-synt_1c_C   1 ApRymaVldpvkvtienlpegkeeelevplhpknpelgtrkvpfs..keiyiereDakrlkpgeevrLkelynikve 75 
                                       A+Ry++V dp+ ++i +++  +e  +evplhp++ e+g rk++f+  k +y++r+D++ lk  e vrLk+l+n+k+ 
  gi|242398525|ref|YP_002993949.1| 412 ANRYFFVADPIPMEIRGYN--EEFIAEVPLHPDHLERGVRKLKFTpeKPVYVSRDDLELLKSSEYVRLKDLFNVKIL 486
                                       89**************998..589*********************5558**************************** PP

                    tRNA-synt_1c_C  76 evekdesgevtelkleydgesleearkkkg.iihWvsaeeaveaevrlYdrLfkeeededfllnpdslkvl.eegla 150
                                       ev+        ++ +e+d+ ++e+ar+++  +ihWv++    ++                ++l p++++ + ++gl+
  gi|242398525|ref|YP_002993949.1| 487 EVS------EERIAAEFDSIEYEKARENRWrMIHWVPE--GKPC----------------EVLVPEGDELIvKNGLL 539
                                       *94......2346689999999999************6..5666................667777776666***** PP

                    tRNA-synt_1c_C 151 epalanlkkgdivQfeRiGyfrvd 174
                                       e + anlk++divQfeR+G++r+d
  gi|242398525|ref|YP_002993949.1| 540 EMD-ANLKVNDIVQFERFGFVRID 562
                                       **9.678***************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (576 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); 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: 0.70u 0.36s 00:00:01.06 Elapsed: 00:00:00.54
# Mc/sec: 3225.29
//
Query:       gi|242398526|ref|YP_002993950.1|  [L=164]
Description: Nucleoside diphosphate kinase [Thermococcus sibiricus MM 739]
Scores for 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-58  194.7   0.0      7e-58  194.4   0.0    1.0  1  NDK       Nucleoside diphosphate kinase


Domain annotation for each model (and alignments):
>> NDK  Nucleoside diphosphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  194.4   0.0   3.9e-62     7e-58       1     134 [.      13     149 ..      13     150 .. 0.99

  Alignments for each domain:
  == domain 1  score: 194.4 bits;  conditional E-value: 3.9e-62
                                       EEEEEEE-HHHHHTT-HHHHHHHHHHHT-EEEEEEEECE-HHHHHHHTGGGTTSTTHHHHHHHHTSSEEEEEEEEST CS
                               NDK   1 ertlvliKPdavkrgligeiisrleekglkivalkmlrlteeqaeehYaehkgkpffeelvefmtsgpvvalvlege 77 
                                       ertlv+iKPdav rglig+iisr+e+kglki+++km+++++e+ae+hY+ehkgkpffe l++++t++p v++vleg+
  gi|242398526|ref|YP_002993950.1|  13 ERTLVIIKPDAVVRGLIGKIISRFEKKGLKIIGMKMIHIDRELAEKHYEEHKGKPFFEPLIDYITKAPSVVMVLEGR 89 
                                       89*************************************************************************** PP

                                       THHHHHHHHH--SSTTTSSTTSHHHHH-SSSTT...-SEEE-SSHHHHHHHHHHHSTGGG CS
                               NDK  78 daiekvreliGatnpaeaapgtiRadfgvslge...NlvHgSdseesaereiklfFkeee 134
                                        ai +vr+++Gat+p++a+pgtiR+d+g+++g+   N++H+Sdsee+a+rei+l+Fk+ee
  gi|242398526|ref|YP_002993950.1|  90 CAIGVVRKMCGATDPKDAEPGTIRGDYGLDVGDaiyNVIHASDSEETAKREIALYFKDEE 149
                                       *******************************88899*********************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.54
# Mc/sec: 921.06
//
Query:       gi|242398527|ref|YP_002993951.1|  [L=416]
Description: peptidase U34, dipeptidase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-11   43.7   1.9    1.1e-10   41.1   0.7    2.1  2  Peptidase_C69  Peptidase family C69
    0.00028   20.7   0.0    0.00048   19.9   0.0    1.6  1  AAT            Acyl-coenzyme A:6-aminopenicillanic acid acyl-


Domain annotation for each model (and alignments):
>> Peptidase_C69  Peptidase family C69
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   0.7   1.2e-14   1.1e-10      80     197 ..      74     191 ..       2     235 .. 0.64
   2 !    1.9   0.0    0.0096        86     332     397 ..     287     351 ..     231     356 .. 0.71

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 1.2e-14
                     Peptidase_C69  80 eagineanvamsatetittnervlgadPlvskggigeedlitlvLpyiksARegvkrlgdlleeyGt.....ye... 148
                                       e g+ne n a+ +t         + ++  + + gi   d+i l L++ k+A+e+++ + +++e+yG+     ye   
  gi|242398527|ref|YP_002993951.1|  74 EMGVNEFNLAIGNTA--------VFTKEKIPERGILGMDMIRLALERTKTAKEAMEFIINIIESYGQggngsYEhkm 142
                                       455565555555543........3333445577888899**************************862222254555 PP

                     Peptidase_C69 149 ..sngvafsDkneiWylEtigGhhWvAvRvPddayvvaaNqlrid.efdlnd 197
                                         sn+++++D++e W lEt +G++WvA++v  +++  ++N l i+ ++dl +
  gi|242398527|ref|YP_002993951.1| 143 lySNSFIVADPKEAWVLET-AGKNWVAKKV--ESVYSISNALTIEdDWDLVS 191
                                       5569**************9.589******9..45555678888851466544 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.0096
                     Peptidase_C69 332 irgvqwlafgs.asfavlvPfytnvektpayyr.dtteevttdnlyWlnrliavlvdseydateedve 397
                                        +g++w++  s + ++ + P++ +   tp  +    t++++ ++ +W ++    + +++y++++++ +
  gi|242398527|ref|YP_002993951.1| 287 GKGMHWFTGTSlPCLSIFKPIFFE---TPLELGeRPTNKYNPKSYWWCMERFHRVFQTNYREYIREFS 351
                                       567888765441557888888875...4444431667889999******************9998765 PP

>> AAT  Acyl-coenzyme A:6-aminopenicillanic acid acyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   5.4e-08   0.00048       2      99 ..      12     132 ..      11     258 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 5.4e-08
                                       SSSE..EEEEEEEE-S-S--EEEEE--S..................SS--EEEE.SSSS-SEEEEEETTS-EEEE-T CS
                               AAT   2 ngkdgkllgrNeDldpetlsnrflvvased................sgfaslgy.agslpGrtdGiNeaGLavtinl 61 
                                       +++++ l+++N D dp+ ++ + ++  ++                 + +a++   +  ++G ++G+Ne  La++++ 
  gi|242398527|ref|YP_002993951.1|  12 TRDNTMLFAKNSDRDPNEAQILEVIPRQKHeeesvkltyvefpqvkETYAVILSrPWWIWGAEMGVNEFNLAIGNTA 88 
                                       566777*******99999998887755544568***********9999*99988799999***************88 PP

                                       TS-TTT-.--------HHHHHHH.--SHHHHHHTHHHH.....T CS
                               AAT  62 lslkklr.akGfprafitRllLekcesveeAvellkei.....p 99 
                                       +  k++   +G+  +  +Rl Le++++ +eA+e++  i      
  gi|242398527|ref|YP_002993951.1|  89 VFTKEKIpERGILGMDMIRLALERTKTAKEAMEFIINIiesygQ 132
                                       88777652689**********************98776455550 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       775  (0.0432261); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); 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: 0.61u 0.34s 00:00:00.95 Elapsed: 00:00:00.50
# Mc/sec: 2493.31
//
Query:       gi|242398528|ref|YP_002993952.1|  [L=158]
Description: small multidrug export protein [Thermococcus sibiricus MM 739]
Scores for complete 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-29  103.3   4.7    1.6e-29  103.0   4.7    1.1  1  Sm_multidrug_ex  Putative small multi-drug export protein


Domain annotation for each model (and alignments):
>> Sm_multidrug_ex  Putative small multi-drug export protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.0   4.7   8.8e-34   1.6e-29       1     121 []      20     146 ..      20     146 .. 0.88

  Alignments for each domain:
  == domain 1  score: 103.0 bits;  conditional E-value: 8.8e-34
                   Sm_multidrug_ex   1 Elrgaiplgillgldpllallvsvlgn.llp..vplillflrkllellkkkkl..lkklfekleekaekksekie.k 71 
                                       E r+ai++gi  g+++  +l+++ +g  ll+  +pl+l ++++++  l+++ l  +++l+ k++e+++kk++ +  k
  gi|242398528|ref|YP_002993952.1|  20 EGRYAIVYGIGRGYPISSTLIMASIGVvLLSltLPLLLPLIDWVMLKLENTFLgdVARLYLKYVERVRKKAHPYVeK 96 
                                       78************************965541145555559999886666655899*************9888854* PP

                   Sm_multidrug_ex  72 ygflGLllFvaiPLpgTGawtGsliasllglkkkkallaillGvliaglI 121
                                       +gflGL++FvaiPLpgTG+wtGsl+a+++g+kk+k++la+++G l++++I
  gi|242398528|ref|YP_002993952.1|  97 WGFLGLVVFVAIPLPGTGVWTGSLAAYIFGIKKRKTILALIIGGLLSIMI 146
                                       **********************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.35s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 902.50
//
Query:       gi|242398529|ref|YP_002993953.1|  [L=442]
Description: zinc-dependent protease, TldD/PmbA family [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.2e-48  165.5   1.4    2.7e-48  165.2   1.4    1.1  1  PmbA_TldD   Putative modulator of DNA gyrase
  ------ inclusion threshold ------
       0.12   12.5   0.1       0.32   11.2   0.1    1.7  1  PFO_beta_C  Pyruvate ferredoxin oxidoreductase beta subunit C


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 !  165.2   1.4     3e-52   2.7e-48       2     279 .]      21     304 ..      20     304 .. 0.81

  Alignments for each domain:
  == domain 1  score: 165.2 bits;  conditional E-value: 3e-52
                                       EEEEEEEEEEEEEEEETTEEEEEEEEEEEEEEEEEEETTEEEEEE...ESSHHHHHHHHHHHHHHCCS---TT-... CS
                         PmbA_TldD   2 aevrleesestsvrfengevetnsssedsglgvrvikggrlgfastldtsdealeeaveraveiaklapedpea... 75 
                                       + v ++e ++++vrf+n+e++ +++++++ + + v +++rl++++ + ++++++e++++  +++ k  + ++++   
  gi|242398529|ref|YP_002993953.1|  21 VVVLAHEQNRRQVRFANNEITVAKNWHTQKVELFVEYQKRLASTTLTALDENTIEKTLQMLMKSVKNLAAKEDYygi 97 
                                       568899****************************999******664444445999****999999999999988887 PP

                                       .......GGS-HHHHHHHHHHHHHH.CHCST.......TEEEEE.EEEEE......EEE.EEEEEEETTSEEEEEEE CS
                         PmbA_TldD  76 .......eevsaeekielleelekalrsadp.......kiensk.garisgvsaslsaskeeklianSeGldveqtr 137
                                              +        ++ e +++a+ + d+         +n++ + +++ v + l +++ + ++ +++G++++++ 
  gi|242398529|ref|YP_002993953.1|  98 aegpfkyK--------DIPETFDEAIVKLDKpndyvevA-INAAlEEGAKRVAGVLYTEHNKLYLTTNNGVEAFDEG 165
                                       65333331........33444445555555555555532.22223445555556677775777777788******** PP

                                       EEEEEEEEEEE...STCSETEEEEEEEE.SSHHHS..SSHHHHHHHHHHCTTT-B---SEEEEEEE-HHHHHHHHHG CS
                         PmbA_TldD 138 trvslslsvia.d.dggsgdgmgggsgy.edleeedleeiaeeaaekalasleakplppgkypVvlspeavgsllhe 211
                                       t +++s+ +   d ++      g g+++ + l+e+d+e+++++a e a+ + ++ + ++g+++Vv++p a+++ll++
  gi|242398529|ref|YP_002993953.1| 166 TGIEISVRAFIgDeES------GHGTNSvRILKEFDPESAGRKAGEIAKLATNPIQGEAGTFEVVFDPLAFANLLSY 236
                                       ***********55333......335555455666999***************************************7 PP

                                       HHHHHTBHHHHHTT--TTTT-TTSB-S-TT--EEEETT-......-SB-TTSBB---EEEEETTEE--- CS
                         PmbA_TldD 212 avghaleadavlegrSflkdklGekvaselltivddpts.gglgsypfDdEGvptqrtvlIenGvLkny 279
                                       +   +++a av +g Sfl +klG+kva+e++ti d ++  +++g++ fDdEGvpt++t++IenG Lk+y
  gi|242398529|ref|YP_002993953.1| 237 MS-FMTSAFAVEAGFSFLVGKLGQKVANENVTIKDIGNMpNAYGTRKFDDEGVPTRETTIIENGELKTY 304
                                       55.6**************77******************99****************************9 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 ?   11.2   0.1   3.5e-05      0.32      11      57 ..     109     152 ..     102     160 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.5e-05
                                       XXXXX-EEEGGGST---EE.HHHHHHHHT-----EEEEEEEETTS--H CS
                        PFO_beta_C  11 dwYkervykleedgyDpsd.lekAlekalewgdkiplGifYkeekpty 57 
                                       + ++e ++kl++    p+d +e A++ ale g k + G++Y e+ + y
  gi|242398529|ref|YP_002993953.1| 109 ETFDEAIVKLDK----PNDyVEVAINAALEEGAKRVAGVLYTEHNKLY 152
                                       568999999998....44536789******************888777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (442 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 2872.98
//
Query:       gi|242398530|ref|YP_002993954.1|  [L=474]
Description: zinc-dependent protease, TldD/PmbA family [Thermococcus sibiricus MM 739]
Scores for complete 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  189.0   0.0    2.4e-55  188.4   0.0    1.3  1  PmbA_TldD    Putative modulator of DNA gyrase
  ------ inclusion threshold ------
       0.13   12.2   0.1        4.5    7.2   0.0    2.3  2  Autophagy_N  Autophagocytosis associated protein (Atg3), N-te


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 !  188.4   0.0   2.7e-59   2.4e-55       1     279 []      21     327 ..      21     327 .. 0.85

  Alignments for each domain:
  == domain 1  score: 188.4 bits;  conditional E-value: 2.7e-59
                                       EEEEEEEEEEEEEEEEETTEEEEEEEEEEEEEEEEEEETTEEEEEE...ESSHHHHHHHHHHHHHHCCS---TT-.. CS
                         PmbA_TldD   1 eaevrleesestsvrfengevetnsssedsglgvrvikggrlgfastldtsdealeeaveraveiaklapedpea.. 75 
                                       +ae+r+ee+++t++ + ng+ e ++   d+g+g+rv+++g +gfast+ +++e++ eav++av++ak a++  ++  
  gi|242398530|ref|YP_002993954.1|  21 YAEARFEEKNGTEIVMKNGNPEGLGILADRGIGIRVLVEGGMGFASTNVLTKESVSEAVKKAVKLAKAAAKIRNKpi 97 
                                       89********************************************9988889*************99999999999 PP

                                       ....................GGS-HHHHHHHHHHHHHH.CHCSTTEEEEEEEEEE......EEE.EEEEEEETTSEE CS
                         PmbA_TldD  76 ....................eevsaeekielleelekalrsadpkienskgarisgvsaslsaskeeklianSeGld 132
                                                           +++saeek ++l+ +e+++++           +   +  ++ +   +k+++n+eG++
  gi|242398530|ref|YP_002993954.1|  98 qfseetfhqvsyevkmkkdfRDISAEEKMNYLKLIEEKVKETGV--------TTPMRFLRYGDFMWHKIFMNNEGAF 166
                                       *******9999999999999999999999999999976554444........222223344444567********** PP

                                       EEEEEEEEEEEEEEEE..S..TCS....ETEEEEEEEE.........SSHHHS..SSHHHHHHHHHHCTTT-B---S CS
                         PmbA_TldD 133 veqtrtrvslslsvia.dd..ggs....gdgmgggsgy.........edleeedleeiaeeaaekalasleakplpp 193
                                       v +  +rvs+ ++ ++ ++  +++    +   +  sg          +     ++ +  ++a +k+++    +++p 
  gi|242398530|ref|YP_002993954.1| 167 VASFIPRVSVTYNLVVfEEgqMEQapfvQ---RAFSGGleliekdqpW-----EWAAKDAKALQKLIKEG--QKPPE 233
                                       ****************9953533354332...3333333334333333.....45558888888888888..999** PP

                                       EEEEEEE-HHHHHHHHHGHHHHHTBHHHHH......TT--TTTT.-TTSB-S-TT--EEEETT-......-SB-TTS CS
                         PmbA_TldD 194 gkypVvlspeavgsllheavghaleadavl......egrSflkd.klGekvaselltivddpts.gglgsypfDdEG 262
                                       gk +Vv+spe++g  +he+vgh+ e+d++       +g Sf k+ +lGe+++sel+t+++dpt  +++g+y +DdEG
  gi|242398530|ref|YP_002993954.1| 234 GKVDVVISPEVAGIAVHESVGHPYELDRIMgreaaqAGESFVKPeMLGERIGSELVTVIEDPTVpNSWGFYLYDDEG 310
                                       ********************************99999*****9977*****************99************ PP

                                       BB---EEEEETTEE--- CS
                         PmbA_TldD 263 vptqrtvlIenGvLkny 279
                                       v++++++lI+nG+ + +
  gi|242398530|ref|YP_002993954.1| 311 VKARPRYLIKNGIINEF 327
                                       *************9876 PP

>> Autophagy_N  Autophagocytosis associated protein (Atg3), N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0    0.0005       4.5      19      43 ..     134     158 ..     120     160 .. 0.87
   2 ?    2.4   0.0     0.016   1.4e+02      23      57 ..     184     222 ..     176     230 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0005
                                       XXXXXXXXXXXXXXXXXXXXXXXXX CS
                       Autophagy_N  19 SkFretGvitpeeFvaAGDyLvhkf 43 
                                        k +etGv tp  F   GD++ hk+
  gi|242398530|ref|YP_002993954.1| 134 EKVKETGVTTPMRFLRYGDFMWHKI 158
                                       4679*****************9985 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.016
                                       XXXXXXXXXXXX....XXXXXXXXXXXXXXXXXXXXXXX CS
                       Autophagy_N  23 etGvitpeeFva....AGDyLvhkfptWsWasaeeskrk 57 
                                       e+G++    Fv+     G  L++k + W+Wa+++ +  +
  gi|242398530|ref|YP_002993954.1| 184 EEGQMEQAPFVQrafsGGLELIEKDQPWEWAAKDAKALQ 222
                                       567777777775433257789**********88766544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (474 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       647  (0.0360868); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); 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: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.51
# Mc/sec: 2811.48
//
Query:       gi|242398531|ref|YP_002993955.1|  [L=612]
Description: hypothetical protein TSIB_0540 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-07   31.0   1.0      3e-07   30.2   0.1    1.9  3  ABC_transp_aux  ABC-type uncharacterized transport system
    5.1e-06   26.8   0.0    1.1e-05   25.8   0.0    1.6  1  ThuA            Trehalose utilisation
      0.001   19.5   0.0     0.0024   18.3   0.0    1.7  1  DUF4350         Domain of unknown function (DUF4350)
  ------ inclusion threshold ------
      0.034   13.6   0.0      0.075   12.5   0.0    1.5  1  GATase1_like    Putative glutamine amidotransferase
      0.045   13.1   0.0      0.076   12.4   0.0    1.3  1  DUF4159         Domain of unknown function (DUF4159)
      0.094   13.5   0.2        1.7    9.5   0.0    3.0  3  Big_7           Bacterial Ig domain


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 ?   -2.8   0.1       1.2   3.5e+03      23      58 ..     188     223 ..     179     258 .. 0.61
   2 ?   -3.4   0.0       1.8   5.3e+03     166     189 ..     251     275 ..     215     295 .. 0.66
   3 !   30.2   0.1     1e-10     3e-07     167     264 ..     399     487 ..     336     490 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.2
                    ABC_transp_aux  23 leepvtikvylsenlalppelkalekevkdlLeeya 58 
                                       l+e vt+ +y++++l+ +  +   +++ k+l  ey 
  gi|242398531|ref|YP_002993955.1| 188 LDENVTFLIYVDGQLFKNETILMKANSSKELSYEYT 223
                                       466777777777776522333333555555555553 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.8
                    ABC_transp_aux 166 e.adfleeleenYnveevdldsedi 189
                                       +  d++++l   Y+++ v+  +   
  gi|242398531|ref|YP_002993955.1| 251 HpMDIMSRLTTFYDIRYVTYLKPLL 275
                                       3366777777777777776665544 PP

  == domain 3  score: 30.2 bits;  conditional E-value: 1e-10
                    ABC_transp_aux 167 adfleeleenY....nveevdldsedilpedidvlviakptkdlseeelykldqflmnGgkllvfldpvaeeqdsls 239
                                       +++++++e++     +v++ +l+ e+   + ++vl+i +p++d+++ee ++++++++nGg ll+  d +a ++    
  gi|242398531|ref|YP_002993955.1| 399 QKLITKMEDELgwmvDVNNEKLTPETL--SYYNVLIITNPRSDITDEEAQAIKEWVENGGGLLITGDWYAFVY---- 469
                                       344444444333333666666664444..68***************************************877.... PP

                    ABC_transp_aux 240 epsaaprtsnLedllaeyGvrinpg 264
                                                 L+++ +e+G+r+n++
  gi|242398531|ref|YP_002993955.1| 470 -------YRSLNKVTEEFGIRFNDD 487
                                       .......3679***********997 PP

>> ThuA  Trehalose utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   3.7e-09   1.1e-05       1      84 [.     382     460 ..     382     578 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 3.7e-09
                                       EEEEEE-..-.SHHHH-...HHHHHH-HHHT-EEEEETTS.G--HHHHHT-SEEEEE-G..GS-HHHHHH.HHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThuA   1 rVLvfsgtagerhdsieaaieaieklgkengfevdatedaavfteenLaqydvvvflstegevldaaqeaalqryve 77 
                                       rVLv s     +h + ++  ++i k+  e g  vd+ +++  +t e+L+ y+v++  +   ++ d++++a ++++ve
  gi|242398531|ref|YP_002993955.1| 382 RVLVDSS--HGQHYNDQRLQKLITKMEDELGWMVDVNNEK--LTPETLSYYNVLIITNPRSDITDEEAQA-IKEWVE 453
                                       6888887..44899999999****************9886..9***************987888888887.****** PP

                                       TT-EEEE CS
                                       xxxxxxx RF
                              ThuA  78 aGgGfvg 84 
                                       +GgG++ 
  gi|242398531|ref|YP_002993955.1| 454 NGGGLLI 460
                                       ****986 PP

>> DUF4350  Domain of unknown function (DUF4350)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0     8e-07    0.0024      35      68 ..     428     461 ..     390     462 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 8e-07
                           DUF4350  35 dgtllvvapdlrlteeelaallewvarGntlvla 68 
                                        ++l++++p+  +t+ee++a+ ewv++G+ l+++
  gi|242398531|ref|YP_002993955.1| 428 YNVLIITNPRSDITDEEAQAIKEWVENGGGLLIT 461
                                       56899*****99*****************99875 PP

>> GATase1_like  Putative glutamine amidotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.5e-05     0.075      89     119 ..     437     467 ..     425     475 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.5e-05
                      GATase1_like  89 esksvPnrlkllkdyvaeGggllmvGGylsf 119
                                       +s+++ +  + +k++v++Gggll+ G +++f
  gi|242398531|ref|YP_002993955.1| 437 RSDITDEEAQAIKEWVENGGGLLITGDWYAF 467
                                       688899999*******************999 PP

>> DUF4159  Domain of unknown function (DUF4159)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   2.5e-05     0.076       9      85 ..     389     460 ..     379     481 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.5e-05
                                       .----.-STTHHHHHHHHHHHHSSS-B-SS-EEE-TT-TTGGG-SEEEEEESS------HHHHHHHHHHHTT-EEEE CS
                           DUF4159   9 ggdwdadspaglrnLskflnertslevpeepagvdlsddeLfeyPllYltghgnvkfssaeakaLraYlrkGGfLli 85 
                                       +g+ ++d  + l++L++ +++++   v+ + +++++++  L+ y +l +t +    ++++ea+a+++++++GG Lli
  gi|242398531|ref|YP_002993955.1| 389 HGQHYND--QRLQKLITKMEDELGWMVDVNNEKLTPET--LSYYNVLIITNP-RSDITDEEAQAIKEWVENGGGLLI 460
                                       5666655..88999999999999999888888877766..999999977765.5699***************88877 PP

>> Big_7  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.3      0.75   2.2e+03      47      59 ..      68      80 ..      44      88 .. 0.61
   2 ?    9.5   0.0   0.00057       1.7      14      70 .]     171     234 ..     165     234 .. 0.78
   3 ?   -2.5   0.0         3   9.1e+03       9      25 ..     520     536 ..     512     536 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.75
                                      E-SSSEEEEEE-- CS
                             Big_7 47 dtsapysltwttt 59
                                      d+ + y+++wt +
  gi|242398531|ref|YP_002993955.1| 68 DNWNEYTINWTNK 80
                                      3337899999874 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00057
                                       EBTSEEEEEEEEE-SS-E..EEEEE..EETTEE.......EEEE-SSSEEEEEE--...SEEEEEEE CS
                             Big_7  14 vsggtvtisasAsddggv..skVef..yvdgtl.g.....lgtdtsapysltwtttaltagthtltV 70 
                                       + +++++i++  +++  +  ++V+f  yvdg+l +     + +++s   s+++t +  t gth++++
  gi|242398531|ref|YP_002993955.1| 171 FRNQPFKIKVILQNN-KIldENVTFliYVDGQLfKnetilMKANSSKELSYEYTLQ--TLGTHQIKA 234
                                       556677777777777.555688999889****9889***98888888999999987..679**9986 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 3
                                       -TT--EBTSEEEEEEEE CS
                             Big_7   9 angatvsggtvtisasA 25 
                                       +++ +++g+t+++s++A
  gi|242398531|ref|YP_002993955.1| 520 SSQLYYNGDTLDVSGNA 536
                                       55567779999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (612 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); 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: 0.71u 0.32s 00:00:01.03 Elapsed: 00:00:00.54
# Mc/sec: 3433.75
//
Query:       gi|242398532|ref|YP_002993956.1|  [L=171]
Description: Cobalamin adenosyltransferase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.5e-50  169.7   0.0    6.2e-50  169.5   0.0    1.0  1  Cob_adeno_trans  Cobalamin adenosyltransferase
  ------ inclusion threshold ------
      0.025   14.5   1.5      0.033   14.1   1.5    1.4  1  Phage_Mu_Gam     Bacteriophage Mu Gam like protein
      0.029   14.3   0.0      0.039   13.9   0.0    1.3  1  DUF2621          Protein of unknown function (DUF2621)


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 !  169.5   0.0     1e-53   6.2e-50       1     164 []       3     160 ..       3     160 .. 0.95

  Alignments for each domain:
  == domain 1  score: 169.5 bits;  conditional E-value: 1e-53
                                       XXXXXXXXXXXXXXXX.XXXTTHHHHHHHHHHHHHHHHHHHHHHHCTTTTHHHHHHHHHHHHHHHHHHHHHHT.-BT CS
                   Cob_adeno_trans   1 iyTrtGDkGtTslvggervsKddprveayGtvDelnsaiglarallaeeeeelkeaLeeiqneLfdlgaelatpekk 77 
                                       i+T+tGDkGtT++++ger+ K +p++ea Gt+Del+s++g a++++   ++elke Le+iq eL +l+ae+a+   k
  gi|242398532|ref|YP_002993956.1|   3 ITTKTGDKGTTGIFTGERIVKFSPIIEANGTIDELSSFLGEAKHYV---DDELKEILEKIQVELYSLMAEIAS---K 73 
                                       89*****************************************777...678*******************94...5 PP

                                       CCG-S--HHHHHHHHHHHHHHHHHS--EESEEES-SSHHHHHHHHHHHHHHHHHHHHHHHHHHS..HHHHHHHHHHH CS
                   Cob_adeno_trans  78 kekkkiteeeveelekeideleaelpplksfilpggspaaaalhvaRtvcRraERavvelaeee.veeevlkylNRL 153
                                        e+kk+ e+e+++le+ i ++e++++ l+ f++pg++ a+a+l+v+R+v+RraER+v ++  e  + e++lkylNRL
  gi|242398532|ref|YP_002993956.1|  74 GEYKKVGEKEISHLEELIRKFEEDVK-LEGFVIPGSTLASAKLDVCRAVARRAERKVSKVVLEYgIAEDALKYLNRL 149
                                       788899*999*************999.99*******************************9877999********** PP

                                       HHHHHHHHHHH CS
                   Cob_adeno_trans 154 SDlLfvlarvv 164
                                       SDlLfv+ar++
  gi|242398532|ref|YP_002993956.1| 150 SDLLFVMARYI 160
                                       *********85 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 ?   14.1   1.5   5.6e-06     0.033       6      62 ..      29      99 ..      25     168 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.6e-06
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHH..............HHHHHHHHHHHHHHHHCTH CS
                      Phage_Mu_Gam  6 walrkiaelkreleeieaeaneeiaaikekleaelepl..............kkeieylesllkqYaeank 62
                                      +a ++i el+  l e+++ +++e ++i ek + el++l              +kei++le+l++++ e  k
  gi|242398532|ref|YP_002993956.1| 29 EANGTIDELSSFLGEAKHYVDDELKEILEKIQVELYSLmaeiaskgeykkvgEKEISHLEELIRKFEEDVK 99
                                      6778999**********************************************************988776 PP

>> DUF2621  Protein of unknown function (DUF2621)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   6.5e-06     0.039      23     111 ..      14     105 ..      10     136 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.5e-06
                           DUF2621  23 GffmfrkflkrlpkedGkseldwqeeyiektrhlwtdeekelleelvspvpelfrdvakekiagkigela...leek 96 
                                       G f   + +k  p  + + ++d    ++ +++h  +de ke+le++   + +l+ ++a +    k+ge     lee 
  gi|242398532|ref|YP_002993956.1|  14 GIFTGERIVKFSPIIEANGTIDELSSFLGEAKHYVDDELKEILEKIQVELYSLMAEIASKGEYKKVGEKEishLEEL 90 
                                       66777788888999999999****************************************99999998651126777 PP

                           DUF2621  97 akeitedliikGyil 111
                                        ++ +ed+ ++G+++
  gi|242398532|ref|YP_002993956.1|  91 IRKFEEDVKLEGFVI 105
                                       888999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       799  (0.0445647); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1065.64
//
Query:       gi|242398533|ref|YP_002993957.1|  [L=231]
Description: Aspartate racemase [Thermococcus sibiricus MM 739]
Scores for complete 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-67  225.9   0.0    6.2e-67  225.7   0.0    1.0  1  Asp_Glu_race     Asp/Glu/Hydantoin racemase
  ------ inclusion threshold ------
      0.064   12.6   0.0       0.13   11.7   0.0    1.4  1  Pantoate_transf  Ketopantoate hydroxymethyltransferase


Domain annotation for each model (and alignments):
>> Asp_Glu_race  Asp/Glu/Hydantoin racemase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  225.7   0.0   6.9e-71   6.2e-67       1     223 [.      11     224 ..      11     225 .. 0.96

  Alignments for each domain:
  == domain 1  score: 225.7 bits;  conditional E-value: 6.9e-71
                                       EEECSCCCCHHHHHHHHHHBTTSSGGGS..EEEEE-CCS-TCHHHHHCH.T..THHHHHHHHHHHHCTTESEEEE-- CS
                      Asp_Glu_race   1 IGgmgpeatlsvlrklveatpaesdqehlplivlndsaipdrteaieeesgddpvlklleaakkLekagadaiviaC 77 
                                       +Ggmgp at+++ r++v++tpa++dq+h+++i++n+s++pdrt++i  ++g+dp+++ll++a+kLek gad+i+++C
  gi|242398533|ref|YP_002993957.1|  11 LGGMGPLATVDLFRRIVMKTPAKKDQDHPRIIIYNNSKVPDRTAYI-LGRGKDPLPELLDSARKLEKWGADFIIMPC 86 
                                       7*********************************************.456888************************ PP

                                       CHHHHHHHHHHHH-SSEEEECHHHHHHHHHHHSS-EEEEEE-HHHHHCTHHHHHHHHHGT.EEE....T-CCCHHCC CS
                      Asp_Glu_race  78 nTahavadelqkkikiPvlgiveataealkatgvkkvglLgTrgtlksglyqkeleanqgievvvpseelqssvnqa 154
                                       nTah +a+++qk+i+iP+++++e++ae++k+ g+kk glL+T+gt+k  +y+++l + +gie+ vp+e++q+ ++ a
  gi|242398533|ref|YP_002993957.1|  87 NTAHFFAEDIQKAINIPLINMIEEAAEHIKNLGLKKAGLLATEGTVKGLVYHRALLK-RGIEIAVPNEKDQKALMDA 162
                                       *********************************************************.6****************** PP

                                       HCHHHHTT-TTSHHHHHHHHHHHHHHTTT-SEEEE-STTHHHHHHHHHHCC-TT.SEEEEHHHHHHHHH CS
                      Asp_Glu_race 155 iyeelkaGevteearrailkllerlaergadaviLGCTelplllekaealekeksvpvidptdilaret 223
                                       iye +kaG+++   r+++l++ ++l e+ +d++i GCTe +++l ++     + +vp+idp+d++a+++
  gi|242398533|ref|YP_002993957.1| 163 IYEGIKAGNLEWG-RQKMLEVAKKL-EKRCDGLIAGCTEVSVALRQE-----DFEVPFIDPMDVIAEKA 224
                                       **********999.99999999955.9****************9999.....459***********987 PP

>> Pantoate_transf  Ketopantoate hydroxymethyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   1.4e-05      0.13     154     200 ..      58     105 ..      52     111 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.4e-05
                   Pantoate_transf 154 gkteeeaeklledakaleeaGafalvlEavpae.lakeiteklsiptI 200
                                       g+ ++   +ll++a++le+ Ga  +++ + +a+  a+ i+++++ip I
  gi|242398533|ref|YP_002993957.1|  58 GRGKDPLPELLDSARKLEKWGADFIIMPCNTAHfFAEDIQKAINIPLI 105
                                       777788889*******************9877637***********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.66
# Mc/sec: 1048.83
//
Query:       gi|242398534|ref|YP_002993958.1|  [L=47]
Description: hypothetical protein TSIB_0543 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.044   13.7   0.6      0.066   13.2   0.6    1.3  1  Gram_pos_anchor  LPXTG cell wall anchor motif


Domain annotation for each model (and alignments):
>> Gram_pos_anchor  LPXTG cell wall anchor motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.6   3.7e-06     0.066      20      39 ..      25      44 ..      20      45 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.7e-06
                                      XXXXXXXXXXXXXXXXXXXX CS
                   Gram_pos_anchor 20 ltaaGllallggllLlvkrR 39
                                      l +++ la+++g+l ++kr+
  gi|242398534|ref|YP_002993958.1| 25 LIILAMLAIALGMLYYFKRK 44
                                      55666666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       740  (0.0412739); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.50
# Mc/sec: 280.77
//
Query:       gi|242398535|ref|YP_002993959.1|  [L=313]
Description: exonuclease-like protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-32  112.5   0.2    6.7e-32  110.8   0.0    1.9  3  RNase_H_2        RNase_H superfamily
    4.4e-06   26.5   0.0      1e-05   25.3   0.0    1.6  2  DNA_pol_B_exo2   Predicted 3'-5' exonuclease related to the e
    1.8e-05   24.0   0.2    2.9e-05   23.4   0.2    1.2  1  DNA_pol_B_exo1   DNA polymerase family B, exonuclease domain
     0.0043   17.6   0.0       0.01   16.4   0.0    1.7  1  HHH_5            Helix-hairpin-helix domain
  ------ inclusion threshold ------
       0.05   13.4   0.0       0.12   12.2   0.0    1.6  1  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
       0.12   12.4   0.0       0.15   12.1   0.0    1.2  1  PTS_2-RNA        RNA 2'-phosphotransferase, Tpt1 / KptA famil
       0.17   12.2   0.0       0.31   11.3   0.0    1.4  1  Cdd1             Pathogenicity locus


Domain annotation for each model (and alignments):
>> RNase_H_2  RNase_H superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.4   3.7e+03      72     117 ..      11      33 ..       4      56 .. 0.54
   2 ?   -2.2   0.0       1.4   3.5e+03      38      71 ..      91     125 ..      79     127 .. 0.58
   3 !  110.8   0.0   2.6e-35   6.7e-32       2     165 ..     144     307 ..     143     308 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.4
                         RNase_H_2  72 pflkrlfkkykldeeefrhiDLlkelrkkklesysLksvekelgie 117
                                       + lkr+f                       +e y+ k +e+++ ++
  gi|242398535|ref|YP_002993959.1|  11 KELKRRF-----------------------MEKYGEKPLEEAFPVR 33 
                                       4444444.......................4444444444444333 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.4
                         RNase_H_2  38 aeepeeekailelflellekk..kalvtfngksFDv 71 
                                       +++p+ e+++++++  lle++  +++v + g++F +
  gi|242398535|ref|YP_002993959.1|  91 MKHPRFENEASRIL-RLLEERriHEIVEYIGRRFKM 125
                                       45556666666644.333333247788888888865 PP

  == domain 3  score: 110.8 bits;  conditional E-value: 2.6e-35
                         RNase_H_2   2 ffDiEttGlspkknliyliGvldvdekeiekltqllaeepeeekailelflellekkkalvtfngksFDvpflkrlf 78 
                                        +DiEt Gl      i+liG  ++ ++e++ ++q++a++ +ee++i ++fl+ +++k+al+tfng++FDvpf+++++
  gi|242398535|ref|YP_002993959.1| 144 VVDIETLGLFN--CPIILIGTGEFRGNEFI-VKQYFARNLREEESIIRMFLDAVREKEALITFNGRRFDVPFIQERL 217
                                       68*******99..66**************9.********************************************** PP

                         RNase_H_2  79 kkyklde.eefrhiDLlkelrkkkl..esysLksveke.lgierreedlsGsqavklyqeylrtgdeellekilaYN 151
                                       + y ++e  e++ +D++   r  ++     +L+++e++ lgier+ +d++ + ++ +y  yl+tg+ +l  +i+++N
  gi|242398535|ref|YP_002993959.1| 218 QHYGIEEkLELPNYDIYLFSRGLVVgvPDHRLQTLERYlLGIERE-DDVPSALIPDFYYYYLKTGKAALAIPIIKHN 293
                                       ******98888******9999988888555********7777777.9****************************** PP

                         RNase_H_2 152 edDvralatlyekl 165
                                         D++++a+l++ l
  gi|242398535|ref|YP_002993959.1| 294 ALDIITTARLFDML 307
                                       **********9876 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 ?   -3.1   0.0         2   5.2e+03     139     158 ..      99     118 ..      84     125 .. 0.56
   2 !   25.3   0.0     4e-09     1e-05      25      78 ..     170     223 ..     152     231 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2
                    DNA_pol_B_exo2 139 dGskVaelyqegklkeireY 158
                                       ++s++ +l +e +++ei eY
  gi|242398535|ref|YP_002993959.1|  99 EASRILRLLEERRIHEIVEY 118
                                       34444444555555555555 PP

  == domain 2  score: 25.3 bits;  conditional E-value: 4e-09
                    DNA_pol_B_exo2  25 fkvksl.geeessekelikkffegvekkkpqlVsfngrgfDlpvleyralkhgvs 78 
                                       f vk+   ++  +e+++i+ f+++v++k+  l++fngr fD+p ++ r   +g++
  gi|242398535|ref|YP_002993959.1| 170 FIVKQYfARNLREEESIIRMFLDAVREKE-ALITFNGRRFDVPFIQERLQHYGIE 223
                                       4444442556677999*********9998.8***************998888886 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 !   23.4   0.2   1.1e-08   2.9e-05     234     279 ..     179     222 ..     162     233 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1.1e-08
                                       EESSHHHHHHHHHHHHHHH--SEEEESSTTTTHHHHHHHHHHHCCT CS
                    DNA_pol_B_exo1 234 efdsEkelLqaflefikqydPdvitgYNidnFDlpYilnRakelyk 279
                                       + ++E  +++ fl+ ++++  + ++++N+  FD+p+i++R++++ +
  gi|242398535|ref|YP_002993959.1| 179 NLREEESIIRMFLDAVREK--EALITFNGRRFDVPFIQERLQHYGI 222
                                       5679***************..*********************8776 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   4.1e-06      0.01       7      31 ..      68      92 ..      61     117 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 4.1e-06
                                      STT--HHHHHHHHTTT--SHHHHHH CS
                             HHH_5  7 vsGiGpktAlallsaGiesvedlaa 31
                                      ++G+Gp+t ++l + G++++ dl++
  gi|242398535|ref|YP_002993959.1| 68 LPGVGPRTEMKLKERGYSTLKDLMK 92
                                      7**********************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 ?   12.2   0.0   4.7e-05      0.12       8      31 ..      70      93 ..      66     102 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.7e-05
                   DNA_pol_lambd_f  8 GVGpktAkkwyakGirtledlrak 31
                                      GVGp+t  k+ ++G+ tl+dl ++
  gi|242398535|ref|YP_002993959.1| 70 GVGPRTEMKLKERGYSTLKDLMKH 93
                                      9********************993 PP

>> PTS_2-RNA  RNA 2'-phosphotransferase, Tpt1 / KptA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0     6e-05      0.15      21      70 ..      75     140 ..      67     225 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6e-05
                         PTS_2-RNA  21 egLkiredGyvkvedlLelpklkslk......vtleeikevVesndKqRFelvel...........e 70 
                                       +++k++e Gy  ++dl+++p++++        +++++i+e+Ve    +RF++ ++           e
  gi|242398535|ref|YP_002993959.1|  75 TEMKLKERGYSTLKDLMKHPRFENEAsrilrlLEERRIHEIVEY-IGRRFKMSHPlilhcaafhdlE 140
                                       6799******************986667777778999*****98.4578987655455555555550 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00012      0.31       5      36 ..      62      93 ..      58     109 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00012
                              Cdd1  5 lkelqdiPniGkalaedlvelGirsveelkge 36
                                      l++l  +P++G+++ ++l e G++++++l ++
  gi|242398535|ref|YP_002993959.1| 62 LSSLSLLPGVGPRTEMKLKERGYSTLKDLMKH 93
                                      678999***********************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.60u 0.34s 00:00:00.94 Elapsed: 00:00:00.52
# Mc/sec: 1801.77
//
Query:       gi|242398536|ref|YP_002993960.1|  [L=194]
Description: hypothetical protein TSIB_0545 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       892  (0.0497518); expected 358.6 (0.02)
Passed bias filter:                      716  (0.0399353); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.31s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 1144.39
//
Query:       gi|242398537|ref|YP_002993961.1|  [L=203]
Description: hypothetical protein TSIB_0547 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.1e-38  130.1   0.0    9.4e-38  129.7   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 !  129.7   0.0   5.2e-42   9.4e-38       4     212 ..       5     185 ..       2     186 .. 0.92

  Alignments for each domain:
  == domain 1  score: 129.7 bits;  conditional E-value: 5.2e-42
                                       HHHHHHH....HHHHHCCHC-GGGHHHHHHHHC-SSEEEEEEES-EEEEE............EESSTT-STT-EEEE CS
                              TYW3   4 akiLeeLsvpdtdkspkGsvDekirelideinsledlvTtSSCsGRvsvflegrksaeaeeeaaksggkkgggkwlf 80 
                                       ++ L+ L     ++ ++++vD +i++l+ +ins ++++TtSSCsGR+ v+            +++  g k  ++wl+
  gi|242398537|ref|YP_002993961.1|   5 RESLKIL----INAIKENKVDDDIIDLLFLINSINGVYTTSSCSGRMGVI------------EEPGIGVKPLARWLL 65 
                                       5555555....678999*********************************............45555556889**** PP

                                       EESS---HHHHHHHHCS--..............SSEEEEEEE--EEEEEESSHHHHHHHHHHHHHCT-TT-EEEEEC CS
                              TYW3  81 vsHdpvkeeellaelfgleeeegsaksseseeeerlilfkfePmILHvlcrslesAqkllsaAleaGfreSGivslk 157
                                       ++H+pv+ ee+ ++l++ +              ++ i +k++P+I+Hv ++s+e A+k+++++l++Gf+++  + l+
  gi|242398537|ref|YP_002993961.1|  66 KEHRPVTFEEVKESLKNAQ--------------NGIIFLKVQPPIFHVVAESMEIAKKIHEIGLASGFKYTTFKALN 128
                                       **********999999997..............79****************************************** PP

                                       TTEEEEEEE---EEEEEEE..STS---HHHHHHHHHHHHHHHHHHHHHHHHHHHHC- CS
                              TYW3 158 kkkvivairsglklevpig..kellvseeylkllvklanerfeenkkrierfeealk 212
                                       k++++v+i  ++ l vp+g  ++ l+s+eyl++ vkl n+++e+ k+r+ r+ee++k
  gi|242398537|ref|YP_002993961.1| 129 KGRMLVEINGTEYLTVPLGmdGKTLISDEYLEFSVKLGNKMLERSKSRLPRLEENFK 185
                                       ********************855*******************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       726  (0.0404931); expected 358.6 (0.02)
Passed bias filter:                      591  (0.0329634); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 1563.82
//
Query:       gi|242398538|ref|YP_002993962.1|  [L=322]
Description: Translation initiation factor eIF-2B, delta subunit [Thermococcus sibiricus MM 739]
Scores for complete 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-89  299.4   0.4    2.6e-89  299.2   0.4    1.0  1  IF-2B     Initiation factor 2 subunit family
  ------ inclusion threshold ------
      0.041   14.1   0.5       0.69   10.2   0.0    2.4  2  BtrH_N    Butirosin biosynthesis protein H, N-terminal


Domain annotation for each model (and alignments):
>> IF-2B  Initiation factor 2 subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  299.2   0.4   2.9e-93   2.6e-89       1     282 []      18     299 ..      18     299 .. 0.98

  Alignments for each domain:
  == domain 1  score: 299.2 bits;  conditional E-value: 2.9e-93
                                       SS-SHHHHHHHHHHHHHHHHHHCCCSTHHHHHHHHHHHHHHHHTSSTS-HHHHHHHHHHHH.HHHCCTTTSSHHHHH CS
                             IF-2B   1 kvrGspaiaiaalevllevikdaktskvaeLkeelrkaidlLkkarPtavslgnairrllk.eiselksssdvkeak 76 
                                       ++rG+ +ia++a+ +l++ ++++k+++++eL++e ++a++lL  +rPtavsl na+r+++  + ++++  ++++e k
  gi|242398538|ref|YP_002993962.1|  18 EIRGAGKIARSAALALQIQAEKSKAQTADELWNETKEAARLLYHTRPTAVSLPNALRYVTYrAKAAYSGGASLEELK 94 
                                       589********************************************************996567788999****** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHTTC-TTEEEEEES--SHHHHHHHHHHHTTEEEEEEEEEXTTTTHHHTHHHH CS
                             IF-2B  77 ksliekikelikeieeadekigdiaaelikdgdtilTicnsktvlevlraaakekkkfkVivvEsrPrlqGrltake 153
                                         +++ +ke+i++ e+a + i++++a++i+dgd+i+T+c+sk++++v+r a++++k++kViv+E+rPr qG+ltake
  gi|242398538|ref|YP_002993962.1|  95 FVIMNSAKEFIHNSENAVKRIAEFGAKRIEDGDIIMTHCHSKAAIGVMRRAWEDGKDIKVIVTETRPRYQGKLTAKE 171
                                       ***************************************************************************** PP

                                       HHHTTXEEEEEEGGGHHHHHHCTESEEEEEXSEEETTSEEEEETTHHHHHHHHHHTTXEEEEEXXGGGBESTSSSGG CS
                             IF-2B 154 LvqagipvtlitdsavayvmseevdkvivGAdrilenGaiankiGTsslAvlAkefnipvlvvaeslkfservqlde 230
                                       L++agipv +++d a+++ m++  dkv+ GAd+i++nGa++nk+GT+ lA+ Ake+++ v+ +ae++kf++++ l++
  gi|242398538|ref|YP_002993962.1| 172 LAEAGIPVIYVVDGAARHYMKM-TDKVVMGADSITANGAVINKVGTALLALTAKEHRVWVMIAAETYKFHPETLLGQ 247
                                       **********************.****************************************************** PP

                                       GSSXXBEXTHHHHEETTEESSTTTEEEEEBSEEEEEGGGXSEEEETTEEEXC CS
                             IF-2B 231 difieerdpeellnitgeriaeeelkvvnpafDvtPpelItliITevGvlpp 282
                                        + ieerdp e++++++ ++ ++++ v npafDvtPpe+I++iITe+ v+pp
  gi|242398538|ref|YP_002993962.1| 248 LVEIEERDPYEVVPKEELETWPKNIVVKNPAFDVTPPEYIDVIITEKSVIPP 299
                                       ***********************************************99987 PP

>> BtrH_N  Butirosin biosynthesis protein H, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1     0.029   2.6e+02      51      85 ..      22      55 ..      11      85 .. 0.77
   2 ?   10.2   0.0   7.7e-05      0.69      63     119 ..     150     206 ..      77     213 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.029
                            BtrH_N 51 kpgdlekrlakrlglkvevketkdpeeawkalkee 85
                                      + g++ +++a  l+++ e ++ ++++e+w++ ke+
  gi|242398538|ref|YP_002993962.1| 22 A-GKIARSAALALQIQAEKSKAQTADELWNETKEA 55
                                      3.6799999999*****************987764 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 7.7e-05
                            BtrH_N  63 lglkvevketkdpeeawkalkeeLdaGrpvivqvdvyyLpYlpkesrlhfnaHnvvv 119
                                        ++kv v et+   +++ + ke  +aG+pvi  vd +   Y++   ++ ++a  + +
  gi|242398538|ref|YP_002993962.1| 150 KDIKVIVTETRPRYQGKLTAKELAEAGIPVIYVVDGAARHYMKMTDKVVMGADSITA 206
                                       578999999999999999999999*******************88888888776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       702  (0.0391544); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); 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: 0.65u 0.28s 00:00:00.93 Elapsed: 00:00:00.51
# Mc/sec: 1912.22
//
Query:       gi|242398539|ref|YP_002993963.1|  [L=417]
Description: aspartate aminotransferase [Thermococcus sibiricus MM 739]
Scores for complete 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-40  139.5   0.0    1.7e-40  139.3   0.0    1.0  1  Aminotran_1_2   Aminotransferase class I and II
    1.1e-15   57.4   0.0    1.6e-15   56.9   0.0    1.1  1  Aminotran_MocR  Alanine-glyoxylate amino-transferase
  ------ inclusion threshold ------
       0.14   12.7   0.2        2.7    8.6   0.0    2.6  2  MerR-DNA-bind   MerR, DNA binding


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 !  139.3   0.0   2.8e-44   1.7e-40      19     363 .]      63     407 ..      44     407 .. 0.91

  Alignments for each domain:
  == domain 1  score: 139.3 bits;  conditional E-value: 2.8e-44
                                       HHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-E CS
                     Aminotran_1_2  19 tlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgde 95 
                                        ++e+ k+  +  +   ++ +yg+++g   l+ ala+++++++++++ +   +  +sG++++++++ +++ +npgd 
  gi|242398539|ref|YP_002993963.1|  63 IIEEITKEVLK--EHAAQALQYGTTKGFTPLRLALAEWMRKRYEIPISKV-DIMITSGSQQALDLIGRVF-INPGDI 135
                                       45555555555..7778899******************************.*******************.****** PP

                                       EEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEE.ESS-TTT--B--HHHHH CS
                     Aminotran_1_2  96 ilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilv.esphNPtGtvatleele 171
                                       ++v  pty    +++++++ e+v++pl+   d ++ ++ lee+l+e+ ++ k++kv+++  + +NP G+ ++++  +
  gi|242398539|ref|YP_002993963.1| 136 VVVEGPTYLATLQAFKYYDPELVQIPLD---DEGMRVDLLEEKLEELEKEGKRVKVVYTiPTFQNPAGVTMSEKRRK 209
                                       **************************77...7799**********************853899************** PP

                                       HHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHHHHHHHH CS
                     Aminotran_1_2 172 klldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilgnaavvsqlrklsr 248
                                        ll+la +y ++++ D  Y+++ +  +   + +   +e+  +l +g++sK + ++G+R+G+i+g +++++ l+++++
  gi|242398539|ref|YP_002993963.1| 210 RLLELASQYDFIIVEDNPYGELRYSGEHIKP-IKAWDEGGRVLYLGTFSKIL-APGFRIGWIAGEPHFIRKLEIAKQ 284
                                       ************************9887667.6666666678********98.6******************99999 PP

                                       HHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS...TEEEECCSCSSEEEEEETHH.CHHH CS
                     Aminotran_1_2 249 pfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLael...glkvlasqsgmflltdlsae.take 319
                                       ++     +  q ++ + ++  +l   ++   ++ ++ +r+ + ++L+e    g+k++++++gmf+++ l+++ + k+
  gi|242398539|ref|YP_002993963.1| 285 SIDLctNTFSQVIAWKYVEGGHLD-AHIPRIVDFYKPKRDAMLKALEEFmpeGVKWTKPEGGMFVWVTLPESiDTKA 360
                                       876655999999999999999975.5********************999************************99** PP

                                       HHHHHHHTCTEEEEEGGGGTS....TTEEEEECTTS-HHHHHHHHHHH CS
                     Aminotran_1_2 320 lskkLleevgvyvtpgtsftv....pgrlRitvAglteeeleelveal 363
                                       +++k + + gv+ +pg+ f +    ++  R+++  ++ee+++e +++l
  gi|242398539|ref|YP_002993963.1| 361 MFEKAVSK-GVAYVPGEAFFAyrdvKNAMRLNFTYVSEEKIREGIKRL 407
                                       ********.*********9999***999*****9*********99986 PP

>> Aminotran_MocR  Alanine-glyoxylate amino-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.9   0.0   2.6e-19   1.6e-15     128     410 ..     137     412 ..     129     416 .. 0.84

  Alignments for each domain:
  == domain 1  score: 56.9 bits;  conditional E-value: 2.6e-19
                                       EEEES--HHHHHHHHHHT-EEEEEEEETTEE-HHHH....HHHHHC-TTEEEEEE-SSS-TTT-----HHHHHHHHT CS
                    Aminotran_MocR 128 lvtvpGydrhfllleelGielltvdlqddGpdvdav....eklvaedasvkGilavpkysnptGetiseevarrlaa 200
                                       +v  p y   +   + +  el+ ++l+d+G  vd +    e+l  e   vk ++++p++ np+G t+se++ +rl  
  gi|242398539|ref|YP_002993963.1| 137 VVEGPTYLATLQAFKYYDPELVQIPLDDEGMRVDLLeeklEELEKEGKRVKVVYTIPTFQNPAGVTMSEKRRKRLLE 213
                                       56667777777777788889***********99965111167888999***************************99 PP

                                       ---SSTT-EEEEE-TTSS-BS.SSSS----HHHHHHHHT-TTSEEEEEESTTTS-TTSS-EEEEE-HHHHHHHHHHH CS
                    Aminotran_MocR 201 lkaaapdfrifaddayavhdlvaeedkdanivalardaGhpdrafvlastskitfaGaGvafvassedniawlkkyl 277
                                       l  +  df i  d+ y        +++ + i  +  +     r + l + ski   G  ++ +a  ++ i+ l+   
  gi|242398539|ref|YP_002993963.1| 214 LA-SQYDFIIVEDNPYGELRY--SGEHIKPI-KAWDE---GGRVLYLGTFSKILAPGFRIGWIAGEPHFIRKLEIAK 283
                                       95.678**********86555..44444433.33334...4599****************************99877 PP

                                       HHC-S---HHHHHHHHHHHHHSTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTSSEEE---SBSS-EEEEESSS-H CS
                    Aminotran_MocR 278 GlqsiGpdkveqlrhvkflkdyeGlealmrdhaeliapkfeavlevleaelggaevatwteprGGyfisldtldgva 354
                                           +  + + q+   k++++   l a++ +  ++ +pk +a+l++le+ +       wt+p+GG f+ +   +++ 
  gi|242398539|ref|YP_002993963.1| 284 QSIDLCTNTFSQVIAWKYVEGG-HLDAHIPRIVDFYKPKRDAMLKALEEFMPE--GVKWTKPEGGMFVWVTLPESID 357
                                       7777899*******99998775.59**********************998864..368***********99999986 PP

                                       HH.HHHHHHHCTEE---TTTTSSTT--SSS-EEEE--SSS-HHHHHHHHHHHHHHHH CS
                    Aminotran_MocR 355 kr.vvklaeeaGvsltaaGatypaGedpkdrnirlaptlppleevetamdvvatcvk 410
                                        + + + a   Gv+  +  a +   +d k++ +rl  t  + e++++ ++ +a  +k
  gi|242398539|ref|YP_002993963.1| 358 TKaMFEKAVSKGVAYVPGEAFFA-YRDVKNA-MRLNFTYVSEEKIREGIKRLAEAIK 412
                                       54167899999****99777665.5899885.9**************9999998776 PP

>> MerR-DNA-bind  MerR, DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0   0.00045       2.7      11      28 ..      25      42 ..      23      50 .. 0.87
   2 ?    0.9   0.1      0.12   6.9e+02      38      50 ..     169     181 ..     159     187 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00045
                                      HHTT--HHHHHHHHHHHH CS
                     MerR-DNA-bind 11 rrlGFsLdeIrelLalyd 28
                                      ++lG+  +eIrelL l +
  gi|242398539|ref|YP_002993963.1| 25 KALGMKASEIRELLKLVE 42
                                      89************9865 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.12
                                       HHHHHHHHHHHHH CS
                     MerR-DNA-bind  38 rallarklaelee 50 
                                        +ll++kl+ele+
  gi|242398539|ref|YP_002993963.1| 169 VDLLEEKLEELEK 181
                                       3689999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       808  (0.0450667); expected 358.6 (0.02)
Passed bias filter:                      695  (0.038764); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.67u 0.30s 00:00:00.97 Elapsed: 00:00:00.49
# Mc/sec: 2560.98
//
Query:       gi|242398540|ref|YP_002993964.1|  [L=242]
Description: transcription regulator, containing DNA-binding HTH domain [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.9e-10   39.6   0.1      2e-09   37.3   0.0    2.1  2  HTH_19          Helix-turn-helix domain
    6.2e-08   32.6   0.0    1.5e-07   31.3   0.0    1.7  1  HTH_3           Helix-turn-helix
    3.5e-07   30.5   0.0    7.4e-07   29.4   0.0    1.5  1  HTH_31          Helix-turn-helix domain
  ------ inclusion threshold ------
      0.092   12.3   0.1       0.24   11.0   0.1    1.8  1  HTH_24          Winged helix-turn-helix DNA-binding
       0.12   12.4   0.0       0.29   11.3   0.0    1.7  1  MqsA_antitoxin  Antitoxin component of bacterial toxin-antito
       0.13   12.7   0.0          1    9.8   0.0    2.3  3  HTH_26          Cro/C1-type HTH DNA-binding domain


Domain annotation for each model (and alignments):
>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.0   6.6e-13     2e-09       4      52 ..      27      75 ..      24      84 .. 0.92
   2 ?   -0.7   0.0       0.5   1.5e+03      42      63 ..     140     161 ..     104     162 .. 0.59

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 6.6e-13
                            HTH_19  4 LkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaeal 52
                                       ++ Re +g++q el+++lg+s s is +E+g+++ p+a++++k++eal
  gi|242398540|ref|YP_002993964.1| 27 MRKWREIFGISQTELSSELGVSSSVISDYEGGRRKSPGASTIRKFVEAL 75
                                      6899****************************999*******9999986 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.5
                            HTH_19  42 aelllkiaealgidleyllqge 63 
                                       + ++ +i  +l+++ e++l+++
  gi|242398540|ref|YP_002993964.1| 140 YTVIDSIQAILEMSSEEFLKLY 161
                                       3333667777777777777766 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.0   5.1e-11   1.5e-07       2      48 ..      28      75 ..      27      76 .. 0.96

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 5.1e-11
                                      HHHHHHTTHHHHHHHHHHTSSHHHHHHHHTT.SSCSBHHHHHHHHHHH CS
                             HTH_3  2 kelRkqlglsqeeLAeklGvsrstisriEnG.ernPsletlkklakaL 48
                                      +++R+  g+sq+eL+ +lGvs s is++E G + +P  +t+ k  +aL
  gi|242398540|ref|YP_002993964.1| 28 RKWREIFGISQTELSSELGVSSSVISDYEGGrRKSPGASTIRKFVEAL 75
                                      899*****************************999********99997 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   2.5e-10   7.4e-07       3      54 ..      24      75 ..      24      81 .. 0.93

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 2.5e-10
                            HTH_31  3 GalLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaral 54
                                      G + r +Re  G+sq+e+   lgvs s +s++E Grr  p  ++++++++al
  gi|242398540|ref|YP_002993964.1| 24 GKTMRKWREIFGISQTELSSELGVSSSVISDYEGGRRKSPGASTIRKFVEAL 75
                                      66789999999************************************99996 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   8.1e-05      0.24      17      36 ..      35      54 ..      35      55 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 8.1e-05
                            HTH_24 17 risqreLAerlglSpstvnr 36
                                      +isq+eL+ +lg+S+s ++ 
  gi|242398540|ref|YP_002993964.1| 35 GISQTELSSELGVSSSVISD 54
                                      79**************9886 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 ?   11.3   0.0   9.6e-05      0.29      64     112 ..      17      65 ..       1      79 [. 0.74

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 9.6e-05
                    MqsA_antitoxin  64 vnaelvdpafiarvrkkleldqreaaeifGgGvnafsryekGkvrppla 112
                                       +  ++  ++++++ r+ ++++q e+++ +G+     s ye G+ ++p a
  gi|242398540|ref|YP_002993964.1|  17 ITLSSDPGKTMRKWREIFGISQTELSSELGVSSSVISDYEGGRRKSPGA 65 
                                       33333345778899****************************9998754 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00034         1      10      50 ..      35      75 ..      27      76 .. 0.91
   2 ?   -0.9   0.0      0.78   2.3e+03      50      61 ..     111     122 ..     109     124 .. 0.80
   3 ?   -2.5   0.0       2.5   7.5e+03      41      58 ..     141     158 ..     131     160 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00034
                            HTH_26 10 gitkseLargtgisaatlsrlvkgkpervsldtLdkiCdaL 50
                                      gi+++eL+  +g+s++ +s +  g+ +++ ++t+ k+ +aL
  gi|242398540|ref|YP_002993964.1| 35 GISQTELSSELGVSSSVISDYEGGRRKSPGASTIRKFVEAL 75
                                      79**********************99999999999887766 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.78
                            HTH_26  50 LgctpgDLleye 61 
                                       + +t+ DLle +
  gi|242398540|ref|YP_002993964.1| 111 FPVTIKDLLEAI 122
                                       6689*****986 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 2.5
                            HTH_26  41 dtLdkiCdaLgctpgDLl 58 
                                       +++d i ++L+++ ++ l
  gi|242398540|ref|YP_002993964.1| 141 TVIDSIQAILEMSSEEFL 158
                                       678888888888877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); 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: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 1654.24
//
Query:       gi|242398541|ref|YP_002993965.1|  [L=265]
Description: hypothetical protein TSIB_0551 [Thermococcus sibiricus MM 739]
Scores for complete 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-76  254.3   1.0    5.9e-76  253.9   1.0    1.1  1  PPS_PS    Phosphopantothenate/pantothenate synthetase
  ------ inclusion threshold ------
       0.23   10.4   2.0       0.23   10.4   0.3    1.7  2  Dsl1_N    Retrograde transport protein Dsl1 N terminal


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 !  253.9   1.0   6.5e-80   5.9e-76       1     175 [.      69     244 ..      69     245 .. 0.97

  Alignments for each domain:
  == domain 1  score: 253.9 bits;  conditional E-value: 6.5e-80
                            PPS_PS   1 lllakkpvisvNGNtaaLvaeeiveLaealgaklevNlfyrteeRvekiaellkeag.aeevlgleedaripelese 76 
                                       lllak+pv+svNGN+aaLv++e +eLa+al+akle+NlfyrteeRv++ia+ lk+ +   e+lg++  ++ip+lese
  gi|242398541|ref|YP_002993965.1|  69 LLLAKHPVVSVNGNVAALVPKETMELAKALDAKLEINLFYRTEERVKAIADELKKYDpNVELLGINPTKKIPNLESE 145
                                       79****************************************************98725689*************** PP

                            PPS_PS  77 RakvskeGiysaDvvlvplEDGDRaeaLvkmgKkviaiDLNPlsRtartatitivdnvvRalpnlteavkelkkksk 153
                                       R+kv++eGi +aDvv+vplEDGDR+eaLv+mgK vi+iDLNPlsR+ar+a+itivdn+vRa p++te ++e+kk s+
  gi|242398541|ref|YP_002993965.1| 146 RGKVDEEGIWKADVVVVPLEDGDRTEALVAMGKFVITIDLNPLSRSARMADITIVDNIVRAYPRMTELAREMKKLSR 222
                                       ***************************************************************************** PP

                            PPS_PS 154 eeleeivkefdnkkvlkealke 175
                                       eele+i++e+dn ++l+e+l +
  gi|242398541|ref|YP_002993965.1| 223 EELEKIISEYDNGQILSETLLH 244
                                       *****************99865 PP

>> Dsl1_N  Retrograde transport protein Dsl1 N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1     0.092   8.2e+02      14      69 ..      74     131 ..      63     134 .. 0.66
   2 ?   10.4   0.3   2.5e-05      0.23     274     319 ..     213     258 ..     202     262 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.092
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXX CS
                            Dsl1_N  14 dplllkeksekskeekldleeilkketqLskeL..hdlnkLktissLikefktnlell 69 
                                        p++  + +  +   k+ +e  ++ +++L+ +L  ++ ++ k i++ +k++  n+ell
  gi|242398541|ref|YP_002993965.1|  74 HPVVSVNGNVAALVPKETMELAKALDAKLEINLfyRTEERVKAIADELKKYDPNVELL 131
                                       5555555555554444455555566777777764356678999999999999999987 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 2.5e-05
                                       XXXXXXXXXXXXXXXXXXXXXX.X..XXXXXXXXXXXXXXXXX..XXX CS
                            Dsl1_N 274 lstEllklvksnaseiledens.sl.keqvlkindkLkkLsekkkssw 319
                                       l+ E+ kl +++ ++i+++ ++ ++ +e++l+in++LkkLs++  ++w
  gi|242398541|ref|YP_002993965.1| 213 LAREMKKLSREELEKIISEYDNgQIlSETLLHINSRLKKLSQE--GIW 258
                                       788999******99999876552455***************99..666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1071  (0.0597356); expected 358.6 (0.02)
Passed bias filter:                      819  (0.0456802); 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: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 1698.01
//
Query:       gi|242398542|ref|YP_002993966.1|  [L=153]
Description: hypothetical protein TSIB_0552 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      0.008   16.6   0.0      0.016   15.6   0.0    1.5  1  DUF3837   Domain of unknown function (DUF3837)
  ------ inclusion threshold ------
      0.075   13.8   0.0       0.14   12.9   0.0    1.4  1  DUF4359   Domain of unknown function (DUF4359)


Domain annotation for each model (and alignments):
>> DUF3837  Domain of unknown function (DUF3837)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.8e-06     0.016      19      56 ..      58      94 ..      52     105 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.8e-06
                           DUF3837 19 ailtgnyElayalGllakllglpeieekeeleelkekl 56
                                       +++ + E++ a+G++ k ++l  ++e+++ +elk+k+
  gi|242398542|ref|YP_002993966.1| 58 QHMIKDAEIFVAIGIVGKFTSL-VVREIKTAQELKKKI 94
                                      68********************.99***********98 PP

>> DUF4359  Domain of unknown function (DUF4359)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.6e-05      0.14      50      97 ..      28      77 ..      20      80 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.6e-05
                           DUF4359 50 sakpqikelieestqrqNfilfSiyttelslks..psykfetlGafgkfy 97
                                      +++ +i ++iee  +++Nfil S y  +   +   +++ f ++G++gkf 
  gi|242398542|ref|YP_002993966.1| 28 QTERAILKIIEERLNSNNFILPSEYGLKPTQHMikDAEIFVAIGIVGKFT 77
                                      5778999******************9887654476777888******996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       660  (0.0368119); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 979.51
//
Query:       gi|242398543|ref|YP_002993967.1|  [L=159]
Description: hypothetical protein TSIB_0553 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.016   14.9   0.3       0.11   12.1   0.0    2.1  2  DUF4547   Domain of unknown function (DUF4547)


Domain annotation for each model (and alignments):
>> DUF4547  Domain of unknown function (DUF4547)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   6.2e-06      0.11      57     112 ..      31      86 ..      16      90 .. 0.90
   2 ?    1.1   0.1     0.014   2.6e+02      89     120 ..      88     118 ..      85     134 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.2e-06
                           DUF4547  57 ilysyvievliclhtrvleklpdlvrslptlasvlrrkvknkrirvvwesileeyg 112
                                       + y+ +i v + +    le+ p lvr++   a +lr k k  +   + +s++eey 
  gi|242398543|ref|YP_002993967.1|  31 VTYADLIAVGMVFTKVFLEQDPILVRNIGNAAKMLRLKRKRGEPVNILDSLVEEYR 86 
                                       67999999999999999***********************99999999****9985 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.014
                           DUF4547  89 svlrrkvknkrirvvwesileeyglqegdita 120
                                        +lr+  k+ ++r v   ++e   l +g i a
  gi|242398543|ref|YP_002993967.1|  88 QILRKSSKDENVRKVVIDVIE-ILLDDGHIEA 118
                                       589999******999888876.4466666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       861  (0.0480228); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); 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: 0.60u 0.34s 00:00:00.94 Elapsed: 00:00:00.55
# Mc/sec: 862.99
//
Query:       gi|242398544|ref|YP_002993968.1|  [L=130]
Description: hypothetical protein TSIB_0554 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.08   12.2   0.0      0.097   11.9   0.0    1.1  1  Meth_synt_2  Cobalamin-independent synthase, Catalytic domain


Domain annotation for each model (and alignments):
>> Meth_synt_2  Cobalamin-independent synthase, Catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   5.4e-06     0.097      96     171 ..       8      85 ..       4      94 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.4e-06
                                       EE-SS---SS-SSTHHHHHHTTS-SS-..BEEEEE-HHHHHHTSEE-TTS-HHHHHHHHHHHHHHHHHHHHHTT-SE CS
                       Meth_synt_2  96 iivgdvsrpaamtvkesalaqsltdkp..vkglltGpvtilnwsfvrddvdraeaaaqialalrdevkdLeaaGikv 170
                                       iiv  v+  + +++  +   q++ +++  + +l +G +++++ +++r +   ++++ ++ la   ev  L +aGi  
  gi|242398544|ref|YP_002993968.1|   8 IIVWYVMESKTLRYIIAENIQITRRNNidLIELPNGASSVISSGRIRTNARTEDVLIELCLAGVGEVVLLREAGIDR 84 
                                       5666667777777777777777777775678999****************************************976 PP

                                       E CS
                       Meth_synt_2 171 i 171
                                       i
  gi|242398544|ref|YP_002993968.1|  85 I 85 
                                       6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 760.25
//
Query:       gi|242398545|ref|YP_002993969.1|  [L=803]
Description: hypothetical protein TSIB_0555 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-13   51.3  34.0     0.0025   17.9   0.8    6.8  6  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
    4.1e-10   39.0  92.9    6.6e-06   25.1  33.4    4.7  5  AAA_13           AAA domain
    1.4e-09   37.6   1.0    1.4e-09   37.6   1.0   11.4  8  Rad50_zn_hook    Rad50 zinc hook motif
    1.6e-08   34.7  13.8    1.6e-08   34.7  13.8    3.2  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
      6e-08   32.8  74.1    0.00023   21.2   6.7    8.4  8  DUF1664          Protein of unknown function (DUF1664)
    6.7e-08   32.6  25.3    6.7e-08   32.6  25.3    4.2  1  AAA_15           AAA ATPase domain
    2.1e-07   31.1   0.0    5.3e-07   29.8   0.0    1.7  1  SbcCD_C          Putative exonuclease SbcCD, C subunit
    2.3e-07   31.1  46.7     0.0074   16.7   0.7    9.0  6  NPV_P10          Nucleopolyhedrovirus P10 protein
    7.2e-07   28.4 115.5     0.0078   15.1  20.0    5.3  6  Spc7             Spc7 kinetochore protein
    1.2e-05   24.8  56.6     0.0085   15.5  10.4    4.5  4  DUF4407          Domain of unknown function (DUF4407)
    3.4e-05   23.0 112.0     0.0028   16.6  40.5    3.7  3  DUF812           Protein of unknown function (DUF812)
     0.0001   21.8   9.2     0.0001   21.8   9.2    5.0  5  CorA             CorA-like Mg2+ transporter protein
    0.00013   22.0  78.6     0.0051   16.8  14.7    6.4  6  Laminin_II       Laminin Domain II
    0.00018   19.7  11.8    0.00018   19.7  11.8    3.6  3  Prominin         Prominin
    0.00031   20.9  11.6    0.00031   20.9  11.6    8.6  8  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
     0.0006   19.5  27.0     0.0006   19.5  27.0    6.5  4  YkyA             Putative cell-wall binding lipoprotein
     0.0025   15.4  86.0     0.0018   15.9  26.3    3.1  3  DUF3584          Protein of unknown function (DUF3584)
     0.0027   17.6  11.9     0.0027   17.6  11.9    7.6  7  Sec8_exocyst     Sec8 exocyst complex component specific doma
     0.0034   17.9  12.2     0.0034   17.9  12.2    8.8  7  DUF16            Protein of unknown function DUF16
     0.0039   17.5 100.2       0.46   10.7  25.4    6.4  5  ATG16            Autophagy protein 16 (ATG16)
     0.0043   16.8  14.3     0.0043   16.8  14.3    6.0  5  DUF713           Protein of unknown function (DUF713)
     0.0045   16.9  69.4      0.036   14.0   8.3    7.6  7  Sec34            Sec34-like family
     0.0045   16.5   6.8       0.22   10.9   0.2    3.6  4  Mce4_CUP1        Cholesterol uptake porter CUP1 of Mce4, puta
     0.0049   16.9 113.3      0.072   13.2  12.4    8.4  6  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
     0.0071   16.4 135.6       0.42   10.6  31.9    6.7  4  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
     0.0079   15.8   8.1     0.0079   15.8   8.1    8.6  9  Fzo_mitofusin    fzo-like conserved region
     0.0082   15.5 128.2       0.24   10.7  27.0    6.5  6  GAS              Growth-arrest specific micro-tubule binding
     0.0083   14.7   9.2      0.071   11.6   0.1    3.3  4  FUSC             Fusaric acid resistance protein family
  ------ inclusion threshold ------
      0.011   15.5   3.4      0.011   15.5   3.4    5.3  3  DUF3287          Protein of unknown function (DUF3287)
      0.016   15.7  80.0       0.16   12.5  14.3    8.7  5  Syntaxin-6_N     Syntaxin 6, N-terminal
       0.02   15.1   2.8       0.02   15.1   2.8    6.8  7  OrfB_IS605       Probable transposase
      0.022   14.3  68.5      0.031   13.8   9.2    4.3  4  Exonuc_VII_L     Exonuclease VII, large subunit
      0.026   14.7  82.2      0.044   14.0   8.0    6.1  6  Fib_alpha        Fibrinogen alpha/beta chain family
      0.031   14.5  41.3       0.12   12.6   2.0    8.2  7  DUF948           Bacterial protein of unknown function (DUF94
      0.036   14.4  77.2       0.17   12.3   2.2    8.4  8  Syntaxin_2       Syntaxin-like protein
       0.06   13.8  47.9        2.7    8.5   4.2    6.7  7  T3SSipB          Type III cell invasion protein SipB
      0.086   13.4 138.8          2    9.0  23.1    7.7  5  APG6_N           Apg6 coiled-coil region
      0.091   12.6  44.4       0.24   11.2   1.6    6.7  7  MCPsignal        Methyl-accepting chemotaxis protein (MCP) si
       0.11   12.7  29.3      0.098   12.9   1.5    8.3  7  WXG100           Proteins of 100 residues with WXG
       0.12   12.7  96.2        2.2    8.7   9.0   10.7 11  BLOC1_2          Biogenesis of lysosome-related organelles co
       0.16   12.4  39.7       0.13   12.6   2.6    9.5  8  LPP              Lipoprotein leucine-zipper
       0.16   11.8  82.8       0.39   10.5   3.5    7.4  7  SKA1             Spindle and kinetochore-associated protein 1
        0.2   11.4   1.4       0.63    9.8   0.2    2.5  2  PRT_C            Plant phosphoribosyltransferase C-terminal
       0.29    9.3 112.2       0.97    7.5  23.2    4.4  3  EzrA             Septation ring formation regulator, EzrA
       0.38   10.8  23.8        2.1    8.4   0.2    6.7  6  PilJ             Type IV pili methyl-accepting chemotaxis tra
       0.69    9.4  77.8      0.067   12.7  14.5    5.3  4  MscS_porin       Mechanosensitive ion channel porin domain
       0.75    9.0  80.5      0.069   12.4  27.0    3.5  3  ALIX_LYPXL_bnd   ALIX V-shaped domain binding to HIV
       0.83   10.1  11.0        1.8    9.0   4.6    4.0  3  DASH_Hsk3        DASH complex subunit Hsk3 like
        1.6    7.3   5.0         15    4.1   5.0    2.7  1  TLV_coat         ENV polyprotein (coat polyprotein)
        1.7    8.7  77.7          1    9.5   6.3    9.3  8  COG2             COG (conserved oligomeric Golgi) complex com
        1.8    8.9 113.3      0.023   15.0  10.4    6.9  7  Uso1_p115_C      Uso1 / p115 like vesicle tethering protein, 
        2.2    7.3  13.3       0.86    8.6   0.5    4.3  4  Filo_VP35        Filoviridae VP35
        2.3    8.7  98.0         31    4.9  18.3    5.5  4  Fez1             Fez1
        2.5    6.8  97.9      0.076   11.8  20.1    6.7  4  Tektin           Tektin family
        2.8    7.0  76.5       0.78    8.8   8.0    6.8  6  APG17            Autophagy protein Apg17
        3.9    7.5 140.8      0.081   12.9   5.4   11.8 12  Prefoldin_2      Prefoldin subunit
        4.5    7.0 114.0      0.013   15.2  30.8    6.5  6  DUF4201          Domain of unknown function (DUF4201)
        4.5    7.6  95.2       0.64   10.3  18.6    8.9  7  DUF5082          Domain of unknown function (DUF5082)
        5.1    7.3  66.2        2.7    8.2   1.5    7.9  8  COG5             Golgi transport complex subunit 5
        6.1    6.5  83.5      0.015   15.1  22.5    4.8  4  Laminin_I        Laminin Domain I
        8.3    4.6 115.3       0.68    8.2  48.0    2.7  2  MAD              Mitotic checkpoint protein
        9.4    6.4  15.6        3.1    8.0   2.4    5.4  6  MbeD_MobD        MbeD/MobD like


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 !   17.9   0.8   8.5e-06    0.0025      37      99 ..     107     171 ..      97     172 .. 0.87
   2 !   11.2   2.1   0.00097      0.28      16      84 ..     181     262 ..     177     276 .. 0.75
   3 !    8.8   0.1    0.0052       1.5      12      98 ..     278     371 ..     271     380 .. 0.69
   4 !   16.6   3.3   2.1e-05    0.0062      28     115 ..     409     505 ..     400     507 .. 0.66
   5 ?    6.8   0.1     0.022       6.5      18      67 ..     473     518 ..     472     526 .. 0.49
   6 !   12.0   1.8   0.00056      0.16      24     130 ..     542     659 ..     518     668 .. 0.63

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 8.5e-06
                      Baculo_PEP_C  37 atlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq...dtlrneLtnlnsiltnLls 99 
                                       ++ ++++e+++ +++ +lks   e++++l++ +++L++++++l+   ++l+++L +++ +l++L++
  gi|242398545|ref|YP_002993969.1| 107 EQVKNELEKEIAEIEGKLKS-KYEQRDKLKQEIQELNRQIKELKqklKSLSQQLSAIERELNELNA 171
                                       67889999999999999999.5668889***************978888999**********9986 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00097
                      Baculo_PEP_C  16 ldLtnvLnairlqnvqilaqlatllda...ietqLnalsedlksllaeldt.........rldtlltnLtdalnalq 80 
                                       l+Lt+++++irl + qi  +l+++l++    +++L++l+ ++++ ++ l++         +l+t  ++L++ ln+++
  gi|242398545|ref|YP_002993969.1| 181 LELTKIIESIRLVQEQI-KKLEEDLNEskkAKEKLKELEGEIRK-IPLLEEyikqfnkfkELNTKKEQLEKDLNKIS 255
                                       8****************.99999988612156789999999998.55555556677778888888888888888887 PP

                      Baculo_PEP_C  81 ...dtlr 84 
                                          ++ +
  gi|242398545|ref|YP_002993969.1| 256 airEEAN 262
                                       5555444 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0052
                      Baculo_PEP_C  12 gnqfldLtnvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldt....rldtlltnLtdalnalq...d 81 
                                       g +f+++ + L+ i   +++i++ + +++++i++  ++l++ ++++l+ l +    + ++ l++L++  ++l+    
  gi|242398545|ref|YP_002993969.1| 278 GEEFIEVPTDLSEIEKSTTTISTLVRSTVAQIKKDTEELEKLISEALKFLPEptieAKEKKLKELKEEEKRLEnivS 354
                                       55778888888888888888888888888888888888877777777777666555444555555555555554546 PP

                      Baculo_PEP_C  82 tlrneLtnlnsiltnLl 98 
                                        lr+eL  +   +++L 
  gi|242398545|ref|YP_002993969.1| 355 GLRKELGEVSGRINDLR 371
                                       66777777777777765 PP

  == domain 4  score: 16.6 bits;  conditional E-value: 2.1e-05
                      Baculo_PEP_C  28 qnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq......dtlrneLtnlnsi....l 94 
                                       ++ +i+ q+ + +++ e+q  +++e+++++++   +r+++l +++++   +l+      + + +eL+nl+++    +
  gi|242398545|ref|YP_002993969.1| 409 LE-EIVKQIRREIEEAENQKRTIKEEIERVSKINVERIEQLQKEIEEMKEKLAkhytelEGIITELNNLENDirpkI 484
                                       43.45699999999999999999999999776555566665555555555555444566666677777776522225 PP

                      Baculo_PEP_C  95 tnLlssvtNinstLnnllqal 115
                                       +++ s++  i++ Ln l++ +
  gi|242398545|ref|YP_002993969.1| 485 SEIESEIKEIEERLNELIEEI 505
                                       677888888888888887766 PP

  == domain 5  score: 6.8 bits;  conditional E-value: 0.022
                      Baculo_PEP_C  18 LtnvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldtrldt 67 
                                       L+n+ n+ir    +i +++++ +++ie++Ln+l e++ +  ++ +++l++
  gi|242398545|ref|YP_002993969.1| 473 LNNLENDIRP---KI-SEIESEIKEIEERLNELIEEIGEKPEDPENELKE 518
                                       4444445532...23.3445555555555555555555544444444444 PP

  == domain 6  score: 12.0 bits;  conditional E-value: 0.00056
                      Baculo_PEP_C  24 airlqnvqilaqlatlldaietqLnalsedlksllaeldt.......rldtlltnLtdalnalq......dtlrneL 87 
                                       +i+  + ++  +l++ + ++++++++l  d ++  +++++       +++++ t+L+++ ++l+      ++++ e+
  gi|242398545|ref|YP_002993969.1| 542 DIKEAQEKL-RKLENKKHELQEEIKKLGYDKQH-HEKVRKeheellrKFESTKTELEEKTKSLEknlkdlTEVEAEI 616
                                       555555555.55555555555555555443222.2222223344444455555555555554443333334788899 PP

                      Baculo_PEP_C  88 tnlnsiltnLlssvtNinstLnnllqalnnldlgalsqeleda 130
                                       + l+ + +nL +++  i++ Ln l     +++ ++++  l+++
  gi|242398545|ref|YP_002993969.1| 617 KELEEKRNNLKAELDKIKKLLNDLERIRRAYHRDGVQRLLRQK 659
                                       9999999999999999988888886666666777776666655 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8  12.6   0.00048      0.14     413     480 ..     105     172 ..      57     190 .. 0.61
   2 ?    5.2  20.2     0.023       6.6     281     471 ..     193     378 ..     177     389 .. 0.52
   3 !   20.4  34.3   5.8e-07   0.00017     253     478 ..     379     596 ..     372     600 .. 0.74
   4 !   25.1  33.4   2.3e-08   6.6e-06     283     469 ..     443     639 ..     431     644 .. 0.85
   5 !   17.1  10.5   5.8e-06    0.0017     374     571 ..     581     772 ..     573     776 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00048
                            AAA_13 413 eykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeeinkeLkafGlgeleLkfe 480
                                        +++ +++lek+i + e +lk ++++  kl++ei+eL +q+++ k+  + + ++L+a+ ++  eL++ 
  gi|242398545|ref|YP_002993969.1| 105 YFEQVKNELEKEIAEIEGKLKSKYEQRDKLKQEIQELNRQIKELKQKLKSLSQQLSAIERELNELNAK 172
                                       34444555555555555555555555555555555555555555555555555555552222222222 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.023
                            AAA_13 281 feekqerLekliekveskkselleklkavsde..asensafeedkeelkaeaealeeqLkg...lqraleaKrkepf 352
                                       ++e++++Le+++++ +++k++l+e   ++ +    +e+++ +++ +el++++e+le+ L++   ++++ ++  k   
  gi|242398545|ref|YP_002993969.1| 193 VQEQIKKLEEDLNESKKAKEKLKELEGEIRKIplLEEYIKQFNKFKELNTKKEQLEKDLNKisaIREEANKAMKSCK 269
                                       56677777777777766665554443333333333445566777777777777777777662212233333333333 PP

                            AAA_13 353 ksvelesvkakiesikklvaeineliakhNekvanleeekeeakkklelhlveeleseldeykkkykklekaiekle 429
                                         ve+ +v ++  ++  +++ei+++ +     v +  ++ ++ +++le+ + e l +            e +ie  e
  gi|242398545|ref|YP_002993969.1| 270 VYVEYIEVGEEFIEVPTDLSEIEKSTTTISTLVRSTVAQIKKDTEELEKLISEAL-K---------FLPEPTIEAKE 336
                                       3556666666665455555555555544444444444444444444444222211.1.........12245555566 PP

                            AAA_13 430 kelkeeeaelkkleeeikeLekqlrdekpaaeeinkeLkafG 471
                                       k+lke ++e k le+ ++ L+k+l ++   ++++ k L   G
  gi|242398545|ref|YP_002993969.1| 337 KKLKELKEEEKRLENIVSGLRKELGEVSGRINDLRKALDMLG 378
                                       666666666666666666666666666666666666655555 PP

  == domain 3  score: 20.4 bits;  conditional E-value: 5.8e-07
                            AAA_13 253 assdtCpFCgqplpaerkaaLeahFddefeekqerLekliekveskkselleklkavsde.asensafeedkeelka 328
                                       + s+ Cp C+ +l+ e + + +   ++    ++++Le++++++ ++++e+ ++  ++ +e ++  ++  e +e+l++
  gi|242398545|ref|YP_002993969.1| 379 E-SEACPVCKTKLTPEHRDRVKHEMEE----EIKSLEEIVKQIRREIEEAENQKRTIKEEiERVSKINVERIEQLQK 450
                                       4.499**************99976666....6666888888888888666555544444434444556777999999 PP

                            AAA_13 329 eaealeeqLkglqraleaKrkepfksvelesvkakiesikklvaeineliakhNekvanleeekeeakkklelhlve 405
                                       e+e+++e+L + + +le  ++e+ +    +++ +ki++i+++++ei+e   + Ne ++++ e+ e+ +++l+  +  
  gi|242398545|ref|YP_002993969.1| 451 EIEEMKEKLAKHYTELEGIITELNN--LENDIRPKISEIESEIKEIEE---RLNELIEEIGEKPEDPENELKELR-- 520
                                       99999999*9999999999999988..235666666666666666654...567777777777777777666633.. PP

                            AAA_13 406 eleseldeyk...kkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeeinkeLkafGlgeleLk 478
                                       + ++e+d++k   + y+kl ++i++++++l++ e+++ +l+eeik L    + +++  +e +++L++f  ++ eL+
  gi|242398545|ref|YP_002993969.1| 521 KKKEEYDRLKpiaDRYEKLLEDIKEAQEKLRKLENKKHELQEEIKKLGYDKQHHEKVRKEHEELLRKFESTKTELE 596
                                       3355555555555999999999*************************99999999999999999999955555555 PP

  == domain 4  score: 25.1 bits;  conditional E-value: 2.3e-08
                            AAA_13 283 ekqerLekliekveskkselleklkavsde.asensafeedkeelkaeaealeeqLkglqraleaKrkepfksve.l 357
                                       e +e+L+k ie++++k ++  ++l+ +++e +++++  + +++e+++e++++ee+L++l +++ +K ++p ++++ l
  gi|242398545|ref|YP_002993969.1| 443 ERIEQLQKEIEEMKEKLAKHYTELEGIITElNNLENDIRPKISEIESEIKEIEERLNELIEEIGEKPEDPENELKeL 519
                                       44889999999999999999999999998657777889999*******************************88746 PP

                            AAA_13 358 esvkaki...esikklvaeineliakhNekvanleeekeeakkklelhlv.....eeleseldeykkkykklekaie 426
                                        + k++    + i +  +++ e i++  ek  +le++k e+++++++        e++++e +e+ +k++++++++e
  gi|242398545|ref|YP_002993969.1| 520 RKKKEEYdrlKPIADRYEKLLEDIKEAQEKLRKLENKKHELQEEIKKLGYdkqhhEKVRKEHEELLRKFESTKTELE 596
                                       77776665556788999999999********************9998655555558888888888899999999999 PP

                            AAA_13 427 klekelkeeeaelkkleeeikeLekqlrdekpaaeeinkeLka 469
                                       + +k+l+++ ++l ++e+eikeLe++ ++ k   ++i k+L++
  gi|242398545|ref|YP_002993969.1| 597 EKTKSLEKNLKDLTEVEAEIKELEEKRNNLKAELDKIKKLLND 639
                                       99999999999999*************************9986 PP

  == domain 5  score: 17.1 bits;  conditional E-value: 5.8e-06
                            AAA_13 374 ineliakhNekvanleeekeeakkklelhlveeleseldeykkkykklekaieklekelkeeeaelkkleee.ikeL 449
                                        +el +k+  + ++lee++++++k+l+   + e+e+e++e+++k ++l++++ k +k l++ e+  +++  + ++ L
  gi|242398545|ref|YP_002993969.1| 581 HEELLRKFESTKTELEEKTKSLEKNLKD--LTEVEAEIKELEEKRNNLKAELDKIKKLLNDLERIRRAYHRDgVQRL 655
                                       3333344444444444444444444443..33344444444444444444444444444443333333322212222 PP

                            AAA_13 450 ekqlrdekpaaeeinkeLkafGlgeleLkfeee..kkgYri..vrkggsqaaetLSeGEktaIaflYFlkslkedds 522
                                          lr  +++a  i ++ + + ++++++++++    + + i  v++  + +  tLS GEk a+a+   l+    + s
  gi|242398545|ref|YP_002993969.1| 656 ---LR--QKIAPIISELATGY-IENFNMDITDIylSEDFDItvVKNSVEVPISTLSGGEKVAVALALRLAIAR-ALS 725
                                       ...22..23333344444556.888888888767755555500555567788**************9998887.333 PP

                            AAA_13 523 eigkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnl 571
                                       +     iv++D P   LD +     +  ++  ++++  + Q+ i TH+ 
  gi|242398545|ref|YP_002993969.1| 726 K--SLSIVIMDEPTTHLDEERRKDLVEILDRFFKSEGAIPQVVIVTHHP 772
                                       3..469*****************999988888779999*********85 PP

>> Rad50_zn_hook  Rad50 zinc hook motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   1.1      0.25        73       1      17 [.     134     150 ..     134     154 .. 0.91
   2 ?   -1.3   0.1         7     2e+03       1      16 [.     169     184 ..     169     188 .. 0.86
   3 ?   -0.3   1.9       3.3   9.6e+02       4      19 ..     331     346 ..     329     348 .. 0.86
   4 !   37.6   1.0   4.9e-12   1.4e-09       3      50 ..     365     411 ..     363     413 .. 0.96
   5 ?    0.2   0.7       2.3   6.7e+02       5      17 ..     445     457 ..     440     463 .. 0.55
   6 ?    0.2   0.8       2.4     7e+02       2      15 ..     488     501 ..     484     508 .. 0.72
   7 ?   -1.4   0.4       7.6   2.2e+03      40      51 ..     594     605 ..     585     611 .. 0.79
   8 ?   -0.2   0.6       3.2   9.4e+02       2      17 ..     613     628 ..     612     632 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.25
                                       HHHHHHHHHHHHHHHTT CS
                     Rad50_zn_hook   1 lhqeteelnkkieelke 17 
                                       l+qe+ eln+ i+elk+
  gi|242398545|ref|YP_002993969.1| 134 LKQEIQELNRQIKELKQ 150
                                       799************98 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 7
                                       HHHHHHHHHHHHHHHT CS
                     Rad50_zn_hook   1 lhqeteelnkkieelk 16 
                                       l+++++++n+ ++el+
  gi|242398545|ref|YP_002993969.1| 169 LNAKEKRYNELMLELT 184
                                       6899999*99999997 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 3.3
                                       HHHHHHHHHHHHTT-S CS
                     Rad50_zn_hook   4 eteelnkkieelkeak 19 
                                       ++e  +kk++elke++
  gi|242398545|ref|YP_002993969.1| 331 TIEAKEKKLKELKEEE 346
                                       688889********98 PP

  == domain 4  score: 37.6 bits;  conditional E-value: 4.9e-12
                                       HHHHHHHHHHHHHTT-SEE-TTT--EE-HHHHHHHHHHHHHHHHHHH. CS
                     Rad50_zn_hook   3 qeteelnkkieelkeakgcCPlCgReldeehrseLikelqsklerlpe 50 
                                       +++++l+k++++l e++  CP+C+ +l++ehr ++  e+++++++l+e
  gi|242398545|ref|YP_002993969.1| 365 GRINDLRKALDMLGESE-ACPVCKTKLTPEHRDRVKHEMEEEIKSLEE 411
                                       68999************.****************************98 PP

  == domain 5  score: 0.2 bits;  conditional E-value: 2.3
                                       HHHHHHHHHHHTT CS
                     Rad50_zn_hook   5 teelnkkieelke 17 
                                       +e+l+k iee ke
  gi|242398545|ref|YP_002993969.1| 445 IEQLQKEIEEMKE 457
                                       3444444444443 PP

  == domain 6  score: 0.2 bits;  conditional E-value: 2.4
                                       HHHHHHHHHHHHHH CS
                     Rad50_zn_hook   2 hqeteelnkkieel 15 
                                       ++e++e++++++el
  gi|242398545|ref|YP_002993969.1| 488 ESEIKEIEERLNEL 501
                                       67777777777776 PP

  == domain 7  score: -1.4 bits;  conditional E-value: 7.6
                                       HHHHHHHHHH.. CS
                     Rad50_zn_hook  40 elqsklerlpee 51 
                                       el++k+++l+++
  gi|242398545|ref|YP_002993969.1| 594 ELEEKTKSLEKN 605
                                       777888888775 PP

  == domain 8  score: -0.2 bits;  conditional E-value: 3.2
                                       HHHHHHHHHHHHHHTT CS
                     Rad50_zn_hook   2 hqeteelnkkieelke 17 
                                       ++e++el++k ++lk 
  gi|242398545|ref|YP_002993969.1| 613 EAEIKELEEKRNNLKA 628
                                       6889999999999885 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   2.4       4.4   1.3e+03     171     208 ..     179     216 ..      91     290 .. 0.55
   2 !   34.7  13.8   5.6e-11   1.6e-08     108     301 ..     531     774 ..     395     775 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 4.4
                            AAA_21 171 ifadyfgfakekrllqrlvrslklveielsdlgegeel 208
                                       +  ++ +  + +rl+q+ +++l ++ +e  + +e+ ++
  gi|242398545|ref|YP_002993969.1| 179 LMLELTKIIESIRLVQEQIKKLEEDLNESKKAKEKLKE 216
                                       33333333333333333333333333333333332222 PP

  == domain 2  score: 34.7 bits;  conditional E-value: 5.6e-11
                            AAA_21 108 edvfnpeargirggvsvfslkelsvsepndlqfgkaltditsrawsllllldglrke....rigllnifadyfgfak 180
                                       + ++ +e+  +++ +  ++l+ l+ ++ + ++ +k l +++ ++++ ++++++l+ +    +  l +  +++ +  k
  gi|242398545|ref|YP_002993969.1| 531 PIADRYEKLLEDIKEAQEKLRKLENKKHELQEEIKKLGYDKQHHEKVRKEHEELLRKfestKTELEEKTKSLEKNLK 607
                                       44444455555555555555555555555555555555555555555555555555555554444444444444444 PP

                            AAA_21 181 ekrllqrlvrslklveielsdlgegeeliasvderlrer...................................... 219
                                        ++ ++  +++l + +++l ++++++++     er+r++                                      
  gi|242398545|ref|YP_002993969.1| 608 DLTEVEAEIKELEEKRNNLKAELDKIKKLLNDLERIRRAyhrdgvqrllrqkiapiiselatgyienfnmditdiyl 684
                                       44444444444444444444444444444444444444444446666666666666666666666666666666666 PP

                            AAA_21 220 ..gvvflengdgqelparelSdGtkrll..alltallralkkg.sllliDEpEngLHPkllrrllell.....kels 286
                                         ++ + + ++  e+p++ lS G k +   al +a++ral+k+ s+++ DEp ++L+ ++ + l+e+l     +e +
  gi|242398545|ref|YP_002993969.1| 685 seDFDITVVKNSVEVPISTLSGGEKVAValALRLAIARALSKSlSIVIMDEPTTHLDEERRKDLVEILdrffkSEGA 761
                                       66*************************7346667777777777**********************888877755555 PP

                            AAA_21 287 rngaQviltTHSpll 301
                                           Qv+++TH p+l
  gi|242398545|ref|YP_002993969.1| 762 --IPQVVIVTHHPEL 774
                                       ..5**********97 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   6.7   8.1e-07   0.00023      51     123 ..     100     172 ..      91     173 .. 0.93
   2 ?    2.5   1.1       0.5   1.4e+02      74     107 ..     182     215 ..     173     226 .. 0.49
   3 ?    3.7   1.9      0.21        62      55     113 ..     238     298 ..     226     310 .. 0.60
   4 ?    7.9   0.7      0.01       2.9      41     114 ..     304     378 ..     300     383 .. 0.89
   5 ?    6.3   3.8     0.033       9.6      70     108 ..     401     439 ..     385     444 .. 0.75
   6 !   14.0   3.8   0.00013     0.039      49     109 ..     444     504 ..     440     522 .. 0.89
   7 ?    2.9   1.9      0.37   1.1e+02      65     106 ..     526     567 ..     503     573 .. 0.64
   8 !   11.3   6.0   0.00092      0.27      44     114 ..     575     641 ..     570     646 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 8.1e-07
                           DUF1664  51 eqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerieek 123
                                        +v    +++k++L+++i++++ kl++  e   ++k+e++e++++++e++++++s+++  + +e +l+++++k
  gi|242398545|ref|YP_002993969.1| 100 REVIYYFEQVKNELEKEIAEIEGKLKSKYEQRDKLKQEIQELNRQIKELKQKLKSLSQQLSAIERELNELNAK 172
                                       5666777899***********************************************************9876 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.5
                           DUF1664  74 kldeqkeiskeikeevtevredlseigedvesvk 107
                                       +l + +e ++ ++e++++++edl+e ++  e++k
  gi|242398545|ref|YP_002993969.1| 182 ELTKIIESIRLVQEQIKKLEEDLNESKKAKEKLK 215
                                       4445555555555555555555554444333333 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.21
                           DUF1664  55 eslaatkrhLssridrvdkkldeqkeiskeikeevt..evredlseigedvesvkeavegl 113
                                       ++l++ k++L+++++++ +  +e +++ k+ k  v+  ev e+  e+ +d++++++  +++
  gi|242398545|ref|YP_002993969.1| 238 KELNTKKEQLEKDLNKISAIREEANKAMKSCKVYVEyiEVGEEFIEVPTDLSEIEKSTTTI 298
                                       5788999999999999888888877777766655541133333444444444444443333 PP

  == domain 4  score: 7.9 bits;  conditional E-value: 0.01
                           DUF1664  41 davesvskqleqvseslaatkrhLss.ridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegle 114
                                       + v+++ k+ e++ + ++++ + L +  i+  +kkl+e ke  k +++ v+ +r++l e++  ++ +++a   l+
  gi|242398545|ref|YP_002993969.1| 304 STVAQIKKDTEELEKLISEALKFLPEpTIEAKEKKLKELKEEEKRLENIVSGLRKELGEVSGRINDLRKALDMLG 378
                                       57889999999999999999999965379999********************************99999988776 PP

  == domain 5  score: 6.3 bits;  conditional E-value: 0.033
                           DUF1664  70 rvdkkldeqkeiskeikeevtevredlseigedvesvke 108
                                       ++++++++ +ei k+i++e++e++++ ++i+e++e v++
  gi|242398545|ref|YP_002993969.1| 401 EMEEEIKSLEEIVKQIRREIEEAENQKRTIKEEIERVSK 439
                                       466777777888888888888888888888888888765 PP

  == domain 6  score: 14.0 bits;  conditional E-value: 0.00013
                           DUF1664  49 qleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkea 109
                                       ++eq+++++++ k++L+++  +++  + e +++ ++i+ +++e++++++ei+e ++++ e 
  gi|242398545|ref|YP_002993969.1| 444 RIEQLQKEIEEMKEKLAKHYTELEGIITELNNLENDIRPKISEIESEIKEIEERLNELIEE 504
                                       699************************************************9998876554 PP

  == domain 7  score: 2.9 bits;  conditional E-value: 0.37
                           DUF1664  65 ssridrvdkkldeqkeiskeikeevtevredlseigedvesv 106
                                        +r++ + ++ ++  e +ke +e++ +++++ +e++e+++++
  gi|242398545|ref|YP_002993969.1| 526 YDRLKPIADRYEKLLEDIKEAQEKLRKLENKKHELQEEIKKL 567
                                       456666666666666666666666666666666666666554 PP

  == domain 8  score: 11.3 bits;  conditional E-value: 0.00092
                           DUF1664  44 esvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegle 114
                                       e+v k+ e++  + ++tk +L+++ ++++k+l++ +e+     +e++e++e+ ++++ +++++k++ ++le
  gi|242398545|ref|YP_002993969.1| 575 EKVRKEHEELLRKFESTKTELEEKTKSLEKNLKDLTEVE----AEIKELEEKRNNLKAELDKIKKLLNDLE 641
                                       78999999999**************99999999988765....5667899999999999999999999987 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6  25.3   2.3e-10   6.7e-08     132     367 ..     513     773 ..     485     774 .. 0.76

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 2.3e-10
                            AAA_15 132 sdekisvekkkskkelpkekeeklekekeelkidkedlkklikkleeslkkeeelknvlksaiiklllisakRnvsd 208
                                        +e +++ k       +ke+++ l+   + +++  ed+k+  +kl++  +k+ el++ +k++ ++ +  +++R+  +
  gi|242398545|ref|YP_002993969.1| 513 ENELKELRK-------KKEEYDRLKPIADRYEKLLEDIKEAQEKLRKLENKKHELQEEIKKLGYDKQHHEKVRKEHE 582
                                       112222222.......2222222233333344444555555555555555555899999999999999999999999 PP

                            AAA_15 209 edsekkssllgklkekileealqekl.........eeelteklkeiqeklkeidkklaeelk............... 261
                                       e+  k +s++++l ek+++  l++ l         ++el+ek ++++ +l++i+k l++ +                
  gi|242398545|ref|YP_002993969.1| 583 ELLRKFESTKTELEEKTKS--LEKNLkdlteveaeIKELEEKRNNLKAELDKIKKLLNDLERirrayhrdgvqrllr 657
                                       9999999999999998877..455556789999999999999999999999999999887779**********9999 PP

                            AAA_15 262 kilkkkidkikkfnykgkkneeieik...........ddeelplnknGsGvqrllllillileaekkdekeeknvil 327
                                       +++ ++i+++  + + +++   ++i            + +e+p++  + G + ++ l+l ++ a+     +++  i+
  gi|242398545|ref|YP_002993969.1| 658 QKIAPIISELATGYIENFNMDITDIYlsedfditvvkNSVEVPISTLSGGEKVAVALALRLAIARAL---SKSLSIV 731
                                       88888888887777777777777776889999999********************************...99***** PP

                            AAA_15 328 liEEPEahLHpqaqkvlikllkelandnkt..QviitTHSph 367
                                       +++EP +hL  +  k l++ l +  +++    Qv+i TH p 
  gi|242398545|ref|YP_002993969.1| 732 IMDEPTTHLDEERRKDLVEILDRFFKSEGAipQVVIVTHHPE 773
                                       ****************************99*********885 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 !   29.8   0.0   1.8e-09   5.3e-07      25      89 ..     696     753 ..     678     754 .. 0.87

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 1.8e-09
                           SbcCD_C  25 elsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                       +++  ++tlSGGek ++++lal +a+a ++s+      +l++v++DE    lDee+++ l+e+l+
  gi|242398545|ref|YP_002993969.1| 696 SVEVPISTLSGGEK-VAVALALRLAIARALSK------SLSIVIMDEPTTHLDEERRKDLVEILD 753
                                       4667899*******.99999999999999999......6**********************9986 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   3.4    0.0009      0.26      11      60 ..     136     168 ..     108     190 .. 0.53
   2 ?    2.9   4.0      0.52   1.5e+02      11      51 ..     188     221 ..     180     273 .. 0.68
   3 ?    1.8   0.3       1.2   3.5e+02       7      62 ..     300     353 ..     286     381 .. 0.62
   4 !   10.8   5.6    0.0018      0.53       4      73 ..     411     484 ..     408     529 .. 0.87
   5 ?    3.6   0.1      0.31        91       9      36 ..     539     566 ..     536     579 .. 0.85
   6 !   16.7   0.7   2.6e-05    0.0074      21      66 ..     593     638 ..     583     648 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0009
                           NPV_P10  11 adikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkven 60 
                                       ++i++++ +++                  l++kL ++s+qL ++e ++++
  gi|242398545|ref|YP_002993969.1| 136 QEIQELNRQIKE-----------------LKQKLKSLSQQLSAIERELNE 168
                                       223333333333.................333333333333333333332 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.52
                           NPV_P10  11 adikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqL 51 
                                       + i+        +q+q+++++e+l++ ++ +ekL ++  ++
  gi|242398545|ref|YP_002993969.1| 188 ESIR-------LVQEQIKKLEEDLNESKKAKEKLKELEGEI 221
                                       4444.......456666666666666665666655554443 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 1.2
                           NPV_P10   7 lvIradikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaelet...kvenIq 62 
                                       +++r+ ++++++  + l++ + +  + lp+       ++a  ++L+el++    +enI 
  gi|242398545|ref|YP_002993969.1| 300 TLVRSTVAQIKKDTEELEKLISEALKFLPEP-----TIEAKEKKLKELKEeekRLENIV 353
                                       6667777777777777777776666666552.....24444444444444222233332 PP

  == domain 4  score: 10.8 bits;  conditional E-value: 0.0018
                           NPV_P10   4 niLlvIradikavddkVdalqqqvddvqe.nlpdvtelnekLdaqsaqLaeletkvenIqdiLn...pdevPdl 73 
                                        i  +Ir +i++ +++   +++++++v++ n++ +++l+++++++ ++La+  t++e I   Ln   +d+ P++
  gi|242398545|ref|YP_002993969.1| 411 EIVKQIRREIEEAENQKRTIKEEIERVSKiNVERIEQLQKEIEEMKEKLAKHYTELEGIITELNnleNDIRPKI 484
                                       6899*********************998769999************9999999988888777774443445554 PP

  == domain 5  score: 3.6 bits;  conditional E-value: 0.31
                           NPV_P10   9 IradikavddkVdalqqqvddvqenlpd 36 
                                        ++dik+ ++k+  l+++ +++qe++++
  gi|242398545|ref|YP_002993969.1| 539 LLEDIKEAQEKLRKLENKKHELQEEIKK 566
                                       5789999999999999999999988876 PP

  == domain 6  score: 16.7 bits;  conditional E-value: 2.6e-05
                           NPV_P10  21 dalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdiLn 66 
                                       + l+++ +++++nl+d+te+++++ ++ ++ ++l++++++I+++Ln
  gi|242398545|ref|YP_002993969.1| 593 TELEEKTKSLEKNLKDLTEVEAEIKELEEKRNNLKAELDKIKKLLN 638
                                       5899999**************************************9 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4  28.2    0.0061       1.8     155     257 ..     110     211 ..      88     218 .. 0.31
   2 ?    1.4  20.8      0.42   1.2e+02     138     282 ..     177     320 ..     172     333 .. 0.84
   3 !   15.1  20.0   2.7e-05    0.0078     149     275 ..     333     459 ..     321     461 .. 0.86
   4 !   14.3  25.5   4.7e-05     0.014     149     278 ..     400     526 ..     389     533 .. 0.58
   5 !   14.6  25.9   3.8e-05     0.011     137     262 ..     452     576 ..     444     582 .. 0.80
   6 !   14.1  25.0   5.6e-05     0.016     153     260 ..     534     640 ..     526     655 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0061
                              Spc7 155 kelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelk...aeieekkkelaelqeq 228
                                       k++Lek+ +e++  l++  e++++l++e+++l+++ +el++    +L++l ++l++++   +e+++k+k+++el  +
  gi|242398545|ref|YP_002993969.1| 110 KNELEKEIAEIEGKLKSKYEQRDKLKQEIQELNRQIKELKQ----KLKSLSQQLSAIErelNELNAKEKRYNELMLE 182
                                       22222222222222222222222333333333333333222....22222222222220002222233333333333 PP

                              Spc7 229 leeleekieelkeqkseleeeiaeaervl 257
                                       l+++ e+i  ++eq+++lee+++e+++ +
  gi|242398545|ref|YP_002993969.1| 183 LTKIIESIRLVQEQIKKLEEDLNESKKAK 211
                                       33333333333333333333333333333 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.42
                              Spc7 138 egLkegleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesid.keeLeelreelaelka 213
                                       ++L+ +l++++e+++  +e+++k ee l+e + + +e+ +ele e++k+   +e +++ +  +eL++ +e+l++  +
  gi|242398545|ref|YP_002993969.1| 177 NELMLELTKIIESIRLVQEQIKKLEEDLNESK-KAKEKLKELEGEIRKIPLLEEYIKQFNkFKELNTKKEQLEKDLN 252
                                       67888888888888888888888888888865.5678888888888888888888888885799************* PP

                              Spc7 214 eieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrlkeevkaleelt 282
                                       +i++ ++e ++  +  +   e i e+ e+  e+ ++++e e+ +       +s v ++k+  ++le+l 
  gi|242398545|ref|YP_002993969.1| 253 KISAIREEANKAMKSCKVYVEYI-EVGEEFIEVPTDLSEIEKSTTTISTLVRSTVAQIKKDTEELEKLI 320
                                       ********999999999999999.566888999999999999999999999999999999999999875 PP

  == domain 3  score: 15.1 bits;  conditional E-value: 2.7e-05
                              Spc7 149 egleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelael 225
                                       e+ e+  ++L+++e+ l++++  l++e  e++ ++++l++a + l +++   + +++ + +  +   +e ++e+++l
  gi|242398545|ref|YP_002993969.1| 333 EAKEKKLKELKEEEKRLENIVSGLRKELGEVSGRINDLRKALDMLGESEACPVCKTKLTPEHRDRVKHEMEEEIKSL 409
                                       55567778899999999999999999999999999999998888888777777777777777777777777****** PP

                              Spc7 226 qeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrlkeev 275
                                       +e +++++ +iee+++qk++++eei++  ++  e+ +  ++e++++ke++
  gi|242398545|ref|YP_002993969.1| 410 EEIVKQIRREIEEAENQKRTIKEEIERVSKINVERIEQLQKEIEEMKEKL 459
                                       ***********************************************997 PP

  == domain 4  score: 14.3 bits;  conditional E-value: 4.7e-05
                              Spc7 149 egleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelael 225
                                        ++ee+ + Le+  +++ +  +e e++k +++ee+e+  + + e  +  ++e+ee++e+la++ +e+e      +el
  gi|242398545|ref|YP_002993969.1| 400 HEMEEEIKSLEEIVKQIRREIEEAENQKRTIKEEIERVSKINVERIEQLQKEIEEMKEKLAKHYTELEGII---TEL 473
                                       45555555555555555555555555555555555555554333333335555555555555555555333...344 PP

                              Spc7 226 qeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrlkeevkal 278
                                       ++  ++++ ki+e++++++e+ee+++e  + + e+ +  e+e+++l+++ ++ 
  gi|242398545|ref|YP_002993969.1| 474 NNLENDIRPKISEIESEIKEIEERLNELIEEIGEKPEDPENELKELRKKKEEY 526
                                       44444556678888888888888888887777777777777777776665544 PP

  == domain 5  score: 14.6 bits;  conditional E-value: 3.8e-05
                              Spc7 137 legLkegleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelka 213
                                       +e++ke+l +++++le   ++L++ e+ +     e+e+e +e+ee+l++l e+  e  +  ++eL+elr++ +e + 
  gi|242398545|ref|YP_002993969.1| 452 IEEMKEKLAKHYTELEGIITELNNLENDIRPKISEIESEIKEIEERLNELIEEIGEKPEDPENELKELRKKKEEYD- 527
                                       5777888888888888888888888888888888888888888888888888888877788********9988876. PP

                              Spc7 214 eieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckg 262
                                        ++   +++++l e+++e +ek+ +l+++k+el+eei++    ++ +++
  gi|242398545|ref|YP_002993969.1| 528 RLKPIADRYEKLLEDIKEAQEKLRKLENKKHELQEEIKKLGYDKQHHEK 576
                                       577799999***************************9987666655554 PP

  == domain 6  score: 14.1 bits;  conditional E-value: 5.6e-05
                              Spc7 153 edkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeql 229
                                       + +e+L ++ +e++e l +le++k el+ee++kl   ++ +e++ ke  eel +++++ k+e+eek k l++  ++l
  gi|242398545|ref|YP_002993969.1| 534 DRYEKLLEDIKEAQEKLRKLENKKHELQEEIKKLGYDKQHHEKVRKEH-EELLRKFESTKTELEEKTKSLEKNLKDL 609
                                       5578899999**************************999999988776.7777789********************* PP

                              Spc7 230 eeleekieelkeqkseleeeiaeaervleec 260
                                       +e+e++i+el+e++++l++e+ + +++l+  
  gi|242398545|ref|YP_002993969.1| 610 TEVEAEIKELEEKRNNLKAELDKIKKLLNDL 640
                                       *********************9999988765 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1  16.0   0.00031      0.09     107     237 ..     108     262 ..     101     269 .. 0.68
   2 !   11.4   7.6   0.00051      0.15     121     234 ..     333     467 ..     292     476 .. 0.72
   3 !   15.5  10.4   2.9e-05    0.0085     108     233 ..     440     571 ..     438     590 .. 0.65
   4 ?    5.5   4.4     0.032       9.2     115     161 ..     594     642 ..     574     653 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00031
                           DUF4407 107 eIdaelaeeqqeeakelkeqlaaa..ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtk.......... 171
                                        ++ el++e +e + +lk+++++   l++e++el++qi++l++++++++++l+a ++e+++    +k          
  gi|242398545|ref|YP_002993969.1| 108 QVKNELEKEIAEIEGKLKSKYEQRdkLKQEIQELNRQIKELKQKLKSLSQQLSAIERELNELNAKEKrynelmlelt 184
                                       4555666666666666666666657799***********99999999999999999999955555558988888888 PP

                           DUF4407 172 .........gtgttgvaGkgpaakekkaqldaaqaelaelkakld........atarlaalraelaeleaerakera 231
                                                ++++++ + +  + k++k++l++++ e+ +              +  ++++l++++++le++++k+ a
  gi|242398545|ref|YP_002993969.1| 185 kiiesirlvQEQIKKLEEDLNESKKAKEKLKELEGEIRK-----IplleeyikQFNKFKELNTKKEQLEKDLNKISA 256
                                       887766666666666666666666666666666666655.....033333444667777777777777777666666 PP

                           DUF4407 232 asqaaa 237
                                         ++a+
  gi|242398545|ref|YP_002993969.1| 257 IREEAN 262
                                       555554 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00051
                           DUF4407 121 kelkeqlaaaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtk..........gtgttgvaGkgpaake 187
                                       ++ +++l+ +l++e ++le+ ++ l++e+ + + r+++lr++++   + +             +   ++  +++ k+
  gi|242398545|ref|YP_002993969.1| 333 EAKEKKLK-ELKEEEKRLENIVSGLRKELGEVSGRINDLRKALDMLGESEAcpvcktkltpEHRDRVKHEMEEEIKS 408
                                       33333322.48888888888888888888888888888888888444433356666556664444455556666666 PP

                           DUF4407 188 kkaqldaaqaelaelkakld............atarlaalraelaeleaerakeraasq 234
                                        ++  +++++e++e++++ +            + +r+++l++e++e+++++ak  ++ +
  gi|242398545|ref|YP_002993969.1| 409 LEEIVKQIRREIEEAENQKRtikeeiervskiNVERIEQLQKEIEEMKEKLAKHYTELE 467
                                       8888889999998888886689999999999999**********999999998777665 PP

  == domain 3  score: 15.5 bits;  conditional E-value: 2.9e-05
                           DUF4407 108 Idaelaeeqqeeakelkeqlaaa......ltaelaeleaqia....alqaeidaaearldalraeaqkeldgtk... 171
                                       I+ e +e+ q+e++e ke+la++        +el++le++i+    ++++ei++ e+rl++l +e  ++    +   
  gi|242398545|ref|YP_002993969.1| 440 INVERIEQLQKEIEEMKEKLAKHytelegIITELNNLENDIRpkisEIESEIKEIEERLNELIEEIGEK----Pedp 512
                                       666666777777777777777777776675566666666666333355555555555555555555544....4444 PP

                           DUF4407 172 gtgttgvaGkgpaakekkaqldaaqaelaelkakldatarlaalraelaeleaerakeraas 233
                                        ++ +  + k +++++ k  +d++++ l+++k+    +++l +l++++ el++e++k   ++
  gi|242398545|ref|YP_002993969.1| 513 ENELKELRKKKEEYDRLKPIADRYEKLLEDIKEA---QEKLRKLENKKHELQEEIKKLGYDK 571
                                       88899999**********************9998...6666666666666666665543333 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.032
                           DUF4407 115 eqqeeakelkeqlaaa......ltaelaeleaqiaalqaeidaaearldalra 161
                                       e +e++k+l++    +       +ae++ele+++++l+ae+d+ ++ l++l++
  gi|242398545|ref|YP_002993969.1| 594 ELEEKTKSLEK----NlkdlteVEAEIKELEEKRNNLKAELDKIKKLLNDLER 642
                                       22333333333....24444779999999999999999999999999998876 PP

>> DUF812  Protein of unknown function (DUF812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6  40.5   9.7e-06    0.0028     296     468 ..      93     271 ..      43     321 .. 0.76
   2 ?    3.7  49.7      0.08        23     238     486 ..     308     571 ..     279     579 .. 0.66
   3 !   10.5  36.6   0.00067      0.19     331     489 ..     483     650 ..     472     657 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 9.7e-06
                            DUF812 296 tkgsrfthaeklqftke..ela.kkaeteeelkkkreeeleelqeqieeleskieeleeeikklessikqveeelee 369
                                       +k+ +f ++    f++   el+ + ae e  lk k e+  ++l+++i+el+++i+el++++k+l+++++ +e el+e
  gi|242398545|ref|YP_002993969.1|  93 EKAWQFMREVIYYFEQVknELEkEIAEIEGKLKSKYEQR-DKLKQEIQELNRQIKELKQKLKSLSQQLSAIERELNE 168
                                       333344444333333333323323445555566666655.9************************************ PP

                            DUF812 370 ekeeneelekevklkkktlellpdaeeniekLqalveasaqrlvelak.qWekhRvplieeyrel...kesksekek 442
                                       ++++ ++ ++ +   +k++e +   +e+i+kL++++++s++   +l++ + e +++pl+eey +     ++ ++k++
  gi|242398545|ref|YP_002993969.1| 169 LNAKEKRYNELMLELTKIIESIRLVQEQIKKLEEDLNESKKAKEKLKElEGEIRKIPLLEEYIKQfnkFKELNTKKE 245
                                       ***************************************99999998734466779*****9764111356788999 PP

                            DUF812 443 eaerkleeikklrekmkevaeelrqk 468
                                       + e+ l++i ++re+  ++ + ++  
  gi|242398545|ref|YP_002993969.1| 246 QLEKDLNKISAIREEANKAMKSCKVY 271
                                       9****************999998865 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.08
                            DUF812 238 eeeykkrkkeklqkrlaeqlrkaalkseeae.ssasksksdlaellsefseksetdslktkgsrfthaeklqftke. 312
                                       + +   ++ ekl +++ + l +   + +e++ ++ +++++ l++++s +++                        e 
  gi|242398545|ref|YP_002993969.1| 308 QIKKDTEELEKLISEALKFLPEPTIEAKEKKlKELKEEEKRLENIVSGLRK------------------------El 360
                                       222222334444444555555555555555555555555555555555522........................12 PP

                            DUF812 313 .................................ela..kkaeteeelkkkreeeleelqeqieeleskieeleeeik 354
                                                                        + +   k+e eee+ k  ee +++++++iee+e++  +++eei+
  gi|242398545|ref|YP_002993969.1| 361 gevsgrindlrkaldmlgeseacpvcktkltpeH-RdrVKHEMEEEI-KSLEEIVKQIRREIEEAENQKRTIKEEIE 435
                                       2222222222222222222335555544443322.144555556665.5566688999999**************99 PP

                            DUF812 355 kles.sikqveeeleeekeeneelekevklkkktlellpdaeen....iekLqalveasaqrlvelakqWekhRvpl 426
                                       ++++ +++++e+  +e +e +e+l+k +   + ++  l++ e+     i++ ++++++ ++rl el ++  ++ +  
  gi|242398545|ref|YP_002993969.1| 436 RVSKiNVERIEQLQKEIEEMKEKLAKHYTELEGIITELNNLENDirpkISEIESEIKEIEERLNELIEEIGEKPEDP 512
                                       9865488999999999999999999999999999999999887622225799********************99999 PP

                            DUF812 427 ieeyrelkesksekekeaerkleeikklrekmkevaeelrqkeellkqLvaeleklpkdv 486
                                        +e++el+++k+e  ++ +   ++ +kl e +ke++e+lr+ e++  +L++e++kl  d+
  gi|242398545|ref|YP_002993969.1| 513 ENELKELRKKKEE-YDRLKPIADRYEKLLEDIKEAQEKLRKLENKKHELQEEIKKLGYDK 571
                                       9999999887655.5678888888888889999999999999999999999988887665 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.00067
                            DUF812 331 eleelqeqieeleskieeleeeikklessikqveeeleeekeeneelekevklkkktlellpdaeeniekLqalvea 407
                                       +++e++++i+e+e++++el eei +  ++ +   +el+++kee  +l+   +  +k+le +++a+e ++kL++   +
  gi|242398545|ref|YP_002993969.1| 483 KISEIESEIKEIEERLNELIEEIGEKPEDPENELKELRKKKEEYDRLKPIADRYEKLLEDIKEAQEKLRKLENKKHE 559
                                       455666666666666666666665555555555666666666666666666677777777788***********999 PP

                            DUF812 408 saqrlvela...kqWekhR...vplieeyrelkesksekekeaerkleeikklrekmkevaee...lrqkeellkqL 475
                                        ++++++l+   +  ek R   + l++++++ k++ +ek+k+ e+ l+++ ++++++ke++e+   l+ + +++k+L
  gi|242398545|ref|YP_002993969.1| 560 LQEEIKKLGydkQHHEKVRkehEELLRKFESTKTELEEKTKSLEKNLKDLTEVEAEIKELEEKrnnLKAELDKIKKL 636
                                       99999999644356677662225799999999999999999999999999999999999998544478888999999 PP

                            DUF812 476 vaeleklpkdvsRs 489
                                       +++le++ +  +R 
  gi|242398545|ref|YP_002993969.1| 637 LNDLERIRRAYHRD 650
                                       99999999999985 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   9.2   3.5e-07    0.0001     113     223 ..      96     205 ..      63     213 .. 0.89
   2 ?   -2.4   0.0       8.1   2.3e+03     178     213 ..     238     273 ..     221     282 .. 0.56
   3 ?    1.9   0.9       0.4   1.1e+02     134     216 ..     288     375 ..     274     380 .. 0.61
   4 !   12.3  16.6   0.00027     0.078      86     220 ..     404     555 ..     400     563 .. 0.86
   5 ?   -0.1   5.9       1.6   4.7e+02     122     179 ..     587     649 ..     580     691 .. 0.49

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 3.5e-07
                              CorA 113 yrlldeivdrlfellekleeeldeledel..edstkkeilrelaqlrrrlvklrralapnrevlkrllakaddklld 187
                                       +++++e++ +++++  +le+e+ e+e  l  + ++++++ +e+ +l r++ +l++ l+ + + l + ++ ++ ++l+
  gi|242398545|ref|YP_002993969.1|  96 WQFMREVIYYFEQVKNELEKEIAEIEGKLksKYEQRDKLKQEIQELNRQIKELKQKLKSLSQQL-SAIE-RELNELN 170
                                       57899999999999****************777777778889999*******************.7777.4666666 PP

                              CorA 188 dedkeylrdlldelerllemlealrerleslqdtys 223
                                       +++ +++++l+ el++++e +  ++e++ +l + ++
  gi|242398545|ref|YP_002993969.1| 171 AKE-KRYNELMLELTKIIESIRLVQEQIKKLEEDLN 205
                                       665.69************************998776 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 8.1
                              CorA 178 lakaddkllddedkeylrdlldelerllemlealre 213
                                       ++ + +k+  ++d + ++ +++e++++++  +++ e
  gi|242398545|ref|YP_002993969.1| 238 KELNTKKEQLEKDLNKISAIREEANKAMKSCKVYVE 273
                                       332222222233335566666666666666666655 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.4
                              CorA 134 ldeledeledstkkeilrelaqlrrrlvklrralapnrevlk....rllakaddkllddedkeylrdlldeler... 203
                                       l e+e+   + ++   ++++aq++++  +l++ +++  + l     + ++k++++l +  ++++l+++ + l++   
  gi|242398545|ref|YP_002993969.1| 288 LSEIEKST-TTISTLVRSTVAQIKKDTEELEKLISEALKFLPeptiEAKEKKLKELKE--EEKRLENIVSGLRKelg 361
                                       55566665.6666677778888888888888888888888876633333322222222..22456665555555555 PP

                              CorA 204 .llemlealrerle 216
                                        ++  ++ lr+ l+
  gi|242398545|ref|YP_002993969.1| 362 eVSGRINDLRKALD 375
                                       56666666666665 PP

  == domain 4  score: 12.3 bits;  conditional E-value: 0.00027
                              CorA  86 eplealdevikrlkdeggkpkspgellyrlldeivdrlfellekleeeldeledel.............edstkkei 149
                                       e++++l+e++k++++e ++ ++ ++ + + ++++ + + e +e+l +e++e  + l              ++ +++i
  gi|242398545|ref|YP_002993969.1| 404 EEIKSLEEIVKQIRREIEEAENQKRTIKEEIERVSKINVERIEQLQKEIEEMKEKLakhytelegiiteLNNLENDI 480
                                       78999*********9999***************************************98888888888888888888 PP

                              CorA 150 lrelaqlrrrlvklrralapnrevlkrlla..kaddkllddedkey..lrdlldelerllemlealrerleslqd 220
                                       + ++++++ ++ ++++ l+++ e + +  +   ++ k+l ++++ey  l+ + d+ e+lle+++  +e+l++l +
  gi|242398545|ref|YP_002993969.1| 481 RPKISEIESEIKEIEERLNELIEEIGEKPEdpENELKELRKKKEEYdrLKPIADRYEKLLEDIKEAQEKLRKLEN 555
                                       888888888888888888888888886666775555555555555566***********************9987 PP

  == domain 5  score: -0.1 bits;  conditional E-value: 1.6
                              CorA 122 rlfellekleeeldeledel.....edstkkeilrelaqlrrrlvklrralapnrevlkrlla 179
                                       +++ +  +lee+++ le++l      + + ke+ ++  +l+ +l k+++ l++++++  ++++
  gi|242398545|ref|YP_002993969.1| 587 KFESTKTELEEKTKSLEKNLkdlteVEAEIKELEEKRNNLKAELDKIKKLLNDLERIRRAYHR 649
                                       555566666666666666666555433333333333344555555555555555555422222 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2  13.0     0.002      0.57      16      97 ..     107     192 ..      90     200 .. 0.79
   2 ?    3.6  10.6      0.22        64      16     112 ..     173     271 ..     166     275 .. 0.67
   3 ?    7.3   2.3     0.015       4.3      15     104 ..     277     372 ..     272     375 .. 0.83
   4 ?    3.3  11.5      0.27        78       7      95 ..     401     494 ..     389     499 .. 0.65
   5 !    9.0   3.4    0.0046       1.3      18      78 ..     444     501 ..     439     522 .. 0.60
   6 !   16.8  14.7   1.7e-05    0.0051       5     100 ..     543     638 ..     539     640 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.002
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH.......H CS
                        Laminin_II  16 leqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeasss....l 88 
                                       ++++++l++++ +++ kl++  ++ ++ +++++++n++i++ +++ k L +++  ++  l+el+ +e+  +     l
  gi|242398545|ref|YP_002993969.1| 107 EQVKNELEKEIAEIEGKLKSKYEQRDKLKQEIQELNRQIKELKQKLKSLSQQLSAIERELNELNAKEKRYNElmleL 183
                                       57788888888888889888888889999999999999999999999999999999999999999988877766666 PP

                                       HHHHHHHHH CS
                        Laminin_II  89 sdniseike 97 
                                        + i+ i+ 
  gi|242398545|ref|YP_002993969.1| 184 TKIIESIRL 192
                                       666666664 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.22
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXX--TTTTT...GGGHHHHHHHHHH.. CS
                        Laminin_II  16 leqlaplsqnlentkeklseinrsveetnekvk...dankairdArrsvkkLeklapqL...ldklkelkqleeass 86 
                                       ++  ++l  +l ++ e++  +++++++ +e+++   +a++ +++ + +++k+   +++    ++k+kel++++e+  
  gi|242398545|ref|YP_002993969.1| 173 EKRYNELMLELTKIIESIRLVQEQIKKLEEDLNeskKAKEKLKELEGEIRKIPL-LEEYikqFNKFKELNTKKEQ-- 246
                                       567788999999999999999999999999998443444556666666666532.33330224555555555555.. PP

                                       .HHHHHHHHHHHHHHHHHHHHT---E CS
                        Laminin_II  87 slsdniseikelIaqARkaAnkikvs 112
                                        l +++++i ++ + A ka  + kv 
  gi|242398545|ref|YP_002993969.1| 247 -LEKDLNKISAIREEANKAMKSCKVY 271
                                       .8888888887777777777777775 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.015
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXX.--TTTTTGGGHHHHHHHHHH..... CS
                        Laminin_II  15 vleqlaplsqnlentkeklseinrsveetnekvk.dankairdArrsvkkL.eklapqLldklkelkqleeasss.. 87 
                                       v e   ++ ++l++++++  +i + v+ t +++k d  +  ++ +++ k L e +++  ++klkelk+ e+  ++  
  gi|242398545|ref|YP_002993969.1| 277 VGEEFIEVPTDLSEIEKSTTTISTLVRSTVAQIKkDTEELEKLISEALKFLpEPTIEAKEKKLKELKEEEKRLENiv 353
                                       66667788899999999999999999999999986777888999999999955588999999999999999988888 PP

                                       ..HHHHHHHHHHHHHHHHH CS
                        Laminin_II  88 ..lsdniseikelIaqARk 104
                                         l +++ e+   I+  Rk
  gi|242398545|ref|YP_002993969.1| 354 sgLRKELGEVSGRINDLRK 372
                                       8888888888877777776 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.27
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHH CS
                        Laminin_II   7 eanetakevleqlaplsqnlentkeklseinrsveetne....kvkdankairdArrsvkkLeklapqLldklkelk 79 
                                       e +e +k+ +e+++++  ++e+ +++  +i++++e++ +     +++++k i++ +++  k   +++ ++  l++l+
  gi|242398545|ref|YP_002993969.1| 401 EMEEEIKSLEEIVKQIRREIEEAENQKRTIKEEIERVSKinveRIEQLQKEIEEMKEKLAKHYTELEGIITELNNLE 477
                                       67788888899999999999999999999998887776521113445555555555555555555566666655555 PP

                                       HHHHH....HHHHHHHH CS
                        Laminin_II  80 qleeasss.lsdnisei 95 
                                       +   ++ s +  +i+ei
  gi|242398545|ref|YP_002993969.1| 478 NDIRPKISeIESEIKEI 494
                                       55555444455555555 PP

  == domain 5  score: 9.0 bits;  conditional E-value: 0.0046
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHH CS
                        Laminin_II  18 qlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkel 78 
                                        +++l++++e++kekl +  +++e +   + ++n+  +d r +++++e ++ +++++l+el
  gi|242398545|ref|YP_002993969.1| 444 RIEQLQKEIEEMKEKLAKHYTELEGI---ITELNNLENDIRPKISEIESEIKEIEERLNEL 501
                                       45678888888888777766664444...34444445555555555555555555555544 PP

  == domain 6  score: 16.8 bits;  conditional E-value: 1.7e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHH CS
                        Laminin_II   5 aaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkql 81 
                                       ++ea+e++ + ++++++l+++++++  + ++ ++  +e +e+++++  +  + +++ k Lek++ +L +   e+k+l
  gi|242398545|ref|YP_002993969.1| 543 IKEAQEKLRKLENKKHELQEEIKKLGYDKQHHEKVRKEHEELLRKFESTKTELEEKTKSLEKNLKDLTEVEAEIKEL 619
                                       89**********************9777666666656688899999999999*****************999***** PP

                                       HHH...HHHHHHHHHHHHH CS
                        Laminin_II  82 eeassslsdniseikelIa 100
                                       ee++++l++++++ik+l +
  gi|242398545|ref|YP_002993969.1| 620 EEKRNNLKAELDKIKKLLN 638
                                       ****************976 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2  23.1    0.0009      0.26     194     410 ..      97     318 ..      90     326 .. 0.73
   2 !   19.7  11.8   6.2e-07   0.00018     248     409 ..     332     499 ..     320     506 .. 0.86
   3 ?    1.5  13.5      0.19        54     241     706 ..     536     642 ..     510     682 .. 0.45

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0009
                          Prominin 194 qhidhvlvqnyeelekhvsddLddagkhlgldla..dtlesnvlpaLaelerllenlkeakeqLeqvnklekeLrks 268
                                       q +++v+ + +e++++++++++ +++ +l ++ +  d+l++++ +   ++++l ++lk+ ++qL+++++ ++eL  +
  gi|242398545|ref|YP_002993969.1|  97 QFMREVIYY-FEQVKNELEKEIAEIEGKLKSKYEqrDKLKQEIQELNRQIKELKQKLKSLSQQLSAIERELNELNAK 172
                                       567889999.*******************99876226799998888899*************************999 PP

                          Prominin 269 gsqLrdglrgvkrdlnqa..lsnlCqs.eeCskilssleiekldtskcldqlpnvdevlealeevletnlss.ivke 341
                                        +++++ + +  + ++++  +++++++ ee  + +++++ +  +++ +++++p ++e++++ ++  e n+++ + ++
  gi|242398545|ref|YP_002993969.1| 173 EKRYNELMLELTKIIESIrlVQEQIKKlEEDLNESKKAKEKLKELEGEIRKIPLLEEYIKQFNKFKELNTKKeQLEK 249
                                       9998888777777777542155567733333333333333356788888****************888876425667 PP

                          Prominin 342 glarlneipekvknqtaevvpdlkkalakgreqikklakkip.realdavisdle.nterssktfddvvek 410
                                       +l+++ +i+e +++ +++   ++  +  + +e++ ++ +++   e+  ++is+l  +t  ++k+ ++++ek
  gi|242398545|ref|YP_002993969.1| 250 DLNKISAIREEANKAMKSC--KVYVEYIEVGEEFIEVPTDLSeIEKSTTTISTLVrSTVAQIKKDTEELEK 318
                                       7777777777777777654..23333344566777777777554555666666666888888888888877 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 6.2e-07
                          Prominin 248 lkeakeqLeqvnklekeLrksgsqLrdglrgvkrdlnqalsn...lCqseeCskilssleiekldtskcl..dqlpn 319
                                       +++ +++L+++++ ek+L    s Lr+ l +v  ++n++ +    l +se C   +++l+ e+ d  k    +++++
  gi|242398545|ref|YP_002993969.1| 332 IEAKEKKLKELKEEEKRLENIVSGLRKELGEVSGRINDLRKAldmLGESEACPVCKTKLTPEHRDRVKHEmeEEIKS 408
                                       5667899********************999998877776665311444799*999999999999987776799**** PP

                          Prominin 320 vdevlealeevle..tnlssivkeglarlneipekvknqtaevvpdlkkalakgreqikklakkiprealdavisdl 394
                                       ++e++++++  +e  +n ++++ke+++r+ +i+    +q+++ ++++k++lak  ++++ + +++ ++  +++  ++
  gi|242398545|ref|YP_002993969.1| 409 LEEIVKQIRREIEeaENQKRTIKEEIERVSKINVERIEQLQKEIEEMKEKLAKHYTELEGIITEL-NNLENDIRPKI 484
                                       ********8766522578899********************************************.99999999999 PP

                          Prominin 395 enterssktfddvve 409
                                       +++e+++k+ ++ ++
  gi|242398545|ref|YP_002993969.1| 485 SEIESEIKEIEERLN 499
                                       999999999888766 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.19
                          Prominin 241 lerllenlkeakeqLeqvnklekeLrksgsqLrdglrgvkrdlnqalsnlCqseeCskilssleiekldtskcldql 317
                                        e+lle++kea+e+L+++++ + eL+++ ++L                                             
  gi|242398545|ref|YP_002993969.1| 536 YEKLLEDIKEAQEKLRKLENKKHELQEEIKKL--------------------------------------------- 567
                                       34444444444444444444444444444444............................................. PP

                          Prominin 318 pnvdevlealeevletnlssivkeglarlneipekvknqtaevvpdlkkalakgreqikklakkiprealdavisdl 394
                                                                                                                    
  gi|242398545|ref|YP_002993969.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                          Prominin 395 enterssktfddvvekyekyrwliglivcsllllivvililgLlcGilGlsrtatptdrgcskntGasfLlvgvgls 471
                                                                                                                    
  gi|242398545|ref|YP_002993969.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                          Prominin 472 FlffsllmlvvlltFlvGlnvyklvCeplesneLfrvlDtpgllpeldLsrllskklkknltisevikaCkanesif 548
                                                                                                                    
  gi|242398545|ref|YP_002993969.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                          Prominin 549 kvLrlnnlydieellnikklteeiqkelenlkvdlsnlelLteeerkdLeklresglskihsslyleqlckkltkvn 625
                                                                                                                    
  gi|242398545|ref|YP_002993969.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                          Prominin 626 letlaekleelanelsngk..knlkqslkneaqdlraiqqelvlplessvkklkksvkklde..........ensdl 690
                                                            k+ ++++++e ++l +  + + ++le+++k+l+k++k+l e          + ++l
  gi|242398545|ref|YP_002993969.1| 568 ------------------GydKQHHEKVRKEHEELLRKFESTKTELEEKTKSLEKNLKDLTEveaeikeleeKRNNL 626
                                       ..................13334444444444443333333344444444444444444444444222222233333 PP

                          Prominin 691 qesikkllaaveraen 706
                                       +++++k+ + ++++e 
  gi|242398545|ref|YP_002993969.1| 627 KAELDKIKKLLNDLER 642
                                       3333333333333333 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 !   20.9  11.6   1.1e-06   0.00031      14     101 ..      72     163 ..      58     169 .. 0.80
   2 ?    1.4  10.7       1.2   3.6e+02      36      99 ..     157     223 ..     155     227 .. 0.65
   3 ?    7.3   3.2     0.019       5.5      25      94 ..     231     299 ..     222     309 .. 0.52
   4 ?    2.7   5.2      0.51   1.5e+02      44     101 ..     305     364 ..     300     374 .. 0.70
   5 !   11.3  14.4     0.001       0.3      23     100 ..     398     476 ..     388     481 .. 0.88
   6 ?    4.4   1.2      0.14        42      77     106 ..     478     507 ..     472     509 .. 0.77
   7 ?    7.2  18.6      0.02       5.7      15     104 ..     516     609 ..     509     613 .. 0.83
   8 ?    5.0   2.9     0.099        29      30      55 ..     615     640 ..     610     659 .. 0.66

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.1e-06
                                       HHHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT....S-TCCCCCCCHHHHHHHHHH CS
                      Seryl_tRNA_N  14 vkeklkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkk....edaeeliaevkelkeelkal 86 
                                       ++++ +kR+e    +  l +l+++++ ++  +  + + +Nel keI+++  k     e++++l++e++el+ ++k+l
  gi|242398545|ref|YP_002993969.1|  72 LDQAPAKRKEVIGRLLGLEKLEKAWQFMREVIYYFEQVKNELEKEIAEIEGKLkskyEQRDKLKQEIQELNRQIKEL 148
                                       556667888888888888888888888888888888888888888887665545559******************** PP

                                       HHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  87 eaelkeleaelekll 101
                                       +++lk l+++l ++ 
  gi|242398545|ref|YP_002993969.1| 149 KQKLKSLSQQLSAIE 163
                                       **********99875 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHH...HHHHHHHHHHH CS
                      Seryl_tRNA_N  36 ekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkalea...elkeleaelek 99 
                                       ++  +++ el+el+a+ ++ ++ + ++ k  e +  + +++k+l e+l++ ++   +lkele e+ k
  gi|242398545|ref|YP_002993969.1| 157 QQLSAIERELNELNAKEKRYNELMLELTKIIESIRLVQEQIKKLEEDLNESKKakeKLKELEGEIRK 223
                                       5566777888888888888888888888877777777777777777766554411155555555544 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.019
                                       CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  25 kadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkele 94 
                                        +++ ++ el++k+++l+++l+++ a r e++k+++++k    +  e+ +e  e+ ++l+++e+  ++++
  gi|242398545|ref|YP_002993969.1| 231 IKQFNKFKELNTKKEQLEKDLNKISAIREEANKAMKSCKVYV-EYIEVGEEFIEVPTDLSEIEKSTTTIS 299
                                       344555555555555555555555555555555555555543.444455555555555555555555444 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.51
                                       HHHHHHHHHHHHHHHCCCCCCTT..S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  44 eleelqaerNelskeIgkakkkk..edaeeliaevkelkeelkaleaelkeleaelekll 101
                                       ++ ++++   el k I++a k      +e+  ++ kelkee k+le+ ++ l++el ++ 
  gi|242398545|ref|YP_002993969.1| 305 TVAQIKKDTEELEKLISEALKFLpePTIEAKEKKLKELKEEEKRLENIVSGLRKELGEVS 364
                                       566777777777888887777666667777777777777777777777777777776654 PP

  == domain 5  score: 11.3 bits;  conditional E-value: 0.001
                                       CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT.S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  23 edkadvdelleldekrrelqveleelqaerNelskeIgkakkkk.edaeeliaevkelkeelkaleaelkeleaele 98 
                                       + ++  +e+ +l+e  ++++ e+ee+ +++ ++ +eI++ +k + e +e+l +e++e+ke+l++  +el+ + +el+
  gi|242398545|ref|YP_002993969.1| 398 VKHEMEEEIKSLEEIVKQIRREIEEAENQKRTIKEEIERVSKINvERIEQLQKEIEEMKEKLAKHYTELEGIITELN 474
                                       455666899**********************************9999999999999999999999999999988888 PP

                                       HH CS
                      Seryl_tRNA_N  99 kl 100
                                       +l
  gi|242398545|ref|YP_002993969.1| 475 NL 476
                                       76 PP

  == domain 6  score: 4.4 bits;  conditional E-value: 0.14
                                       HHHHHHHHHHHHHHHHHHHHHHHHHCTS-- CS
                      Seryl_tRNA_N  77 kelkeelkaleaelkeleaeleklllaiPN 106
                                       +++  +++++e e ke+e++l++l+ +i+ 
  gi|242398545|ref|YP_002993969.1| 478 NDIRPKISEIESEIKEIEERLNELIEEIGE 507
                                       566778888899999999999988888875 PP

  == domain 7  score: 7.2 bits;  conditional E-value: 0.02
                                       HHHHCCCT....CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHH CS
                      Seryl_tRNA_N  15 keklkkRg....edkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkale 87 
                                        + l+k++    + k   d++ +l e  +e+q +l +l +++ el++eI+k+  +k+  e++++e +el  +++ ++
  gi|242398545|ref|YP_002993969.1| 516 LKELRKKKeeydRLKPIADRYEKLLEDIKEAQEKLRKLENKKHELQEEIKKLGYDKQHHEKVRKEHEELLRKFESTK 592
                                       4445555433336677888999999999****************************9******************99 PP

                                       HHHHHHHHHHHHHHCTS CS
                      Seryl_tRNA_N  88 aelkeleaeleklllai 104
                                       +el+e ++ lek l  +
  gi|242398545|ref|YP_002993969.1| 593 TELEEKTKSLEKNLKDL 609
                                       99999999999988765 PP

  == domain 8  score: 5.0 bits;  conditional E-value: 0.099
                                       HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  30 elleldekrrelqveleelqaerNel 55 
                                       e+ el+ekr +l++el+++++  N l
  gi|242398545|ref|YP_002993969.1| 615 EIKELEEKRNNLKAELDKIKKLLNDL 640
                                       45556666666666666666555544 PP

>> YkyA  Putative cell-wall binding lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   6.3      0.11        31      18     118 ..     279     375 ..     269     380 .. 0.64
   2 ?    0.9  17.2       1.1   3.1e+02      45     118 ..     391     467 ..     388     472 .. 0.59
   3 ?    2.1   8.6      0.48   1.4e+02      31      95 ..     474     537 ..     469     544 .. 0.61
   4 !   19.5  27.0   2.1e-06    0.0006      18     113 ..     541     640 ..     534     650 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.11
                              YkyA  18 kefeeqqekLtelekkeqelyeeiielgmdefdkikklsdealenveeReellekekesieeakeefekikeeieei 94 
                                       +ef e    L+e ek  + +     +l  +   +ikk  +e+ ++++e  + l +    ie+ +++++++kee + +
  gi|242398545|ref|YP_002993969.1| 279 EEFIEVPTDLSEIEKSTTTIS----TLVRSTVAQIKKDTEELEKLISEALKFLPE--PTIEAKEKKLKELKEEEKRL 349
                                       667777777777776655443....334455666888888888888888888877..67777777777777775555 PP

                              YkyA  95 e..deelkkeaeelieameeryeayd 118
                                       e   + l+ke+ e+   +++  +a d
  gi|242398545|ref|YP_002993969.1| 350 EniVSGLRKELGEVSGRINDLRKALD 375
                                       41134577777776666666665555 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 1.1
                              YkyA  45 gmdefdkikklsdealenveeReellekekesieeakeefekikeeieei...edeelkkeaeelieameeryeayd 118
                                       + ++ d++k + +e ++++ee  +++  e e  e+ k  +++  e +++i     e+l+ke+ee++e++ + y+  +
  gi|242398545|ref|YP_002993969.1| 391 TPEHRDRVKHEMEEEIKSLEEIVKQIRREIEEAENQKRTIKEEIERVSKInveRIEQLQKEIEEMKEKLAKHYTELE 467
                                       55666777777777777777766666665444444444444444444444554456778888888888877777665 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.48
                              YkyA  31 ekkeqelyeeiielgmdefdkikklsdealenveeReellekekesieeakeefekikeeieeie 95 
                                        + e+++  +i e   +e ++i++  +e++e + e+ e  e+e + + + kee++ +k++ + +e
  gi|242398545|ref|YP_002993969.1| 474 NNLENDIRPKISEI-ESEIKEIEERLNELIEEIGEKPEDPENELKELRKKKEEYDRLKPIADRYE 537
                                       44444444444432.34566677777777777777777777777777777777777777776663 PP

  == domain 4  score: 19.5 bits;  conditional E-value: 2.1e-06
                              YkyA  18 kefeeqqekLtelekkeqelyeeiielgmde..fdkikklsdealenveeReellekekesieeakeefekikeeie 92 
                                       ++++e+qekL +le+k++el eei +lg d+   +k+ k+ +e+l   e  +++le+  +s+e+  + ++++++ei+
  gi|242398545|ref|YP_002993969.1| 541 EDIKEAQEKLRKLENKKHELQEEIKKLGYDKqhHEKVRKEHEELLRKFESTKTELEEKTKSLEKNLKDLTEVEAEIK 617
                                       789*********************999877655999***************************************** PP

                              YkyA  93 eiede..elkkeaeelieameer 113
                                       e+e++  +lk e+++ ++ +++ 
  gi|242398545|ref|YP_002993969.1| 618 ELEEKrnNLKAELDKIKKLLNDL 640
                                       **665447888888888877764 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1  25.4    0.0028      0.82     266     412 ..     108     263 ..      64     275 .. 0.39
   2 !   15.9  26.3   6.1e-06    0.0018     225     484 ..     266     526 ..     256     531 .. 0.86
   3 ?    1.6  22.6      0.13        38     226     342 ..     535     651 ..     517     666 .. 0.47

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0028
                           DUF3584 266 llkgelkadeerlaekqeevqeakaelkqqlrtledelkeaidelnqelsaakaklaakeselealeeqkkkyed.. 340
                                        +k el++++ +++ k++   e+  +lkq++++l+ +    i+el+q+l+ ++++l+a+e+el++l++++k+y++  
  gi|242398545|ref|YP_002993969.1| 108 QVKNELEKEIAEIEGKLKSKYEQRDKLKQEIQELNRQ----IKELKQKLKSLSQQLSAIERELNELNAKEKRYNElm 180
                                       3333333333333333333333333333333322222....223334444444444444444444444444443311 PP

                           DUF3584 341 ....adieklkadldqlpsirselee...leeeldaltekhqdvq..ekydrrkqkike..eleeeleklkerleai 406
                                           + ie+ +  ++q+ +++++l+e   ++e+l+ l+++++++   e+y ++  k ke   ++e+lek  ++  ai
  gi|242398545|ref|YP_002993969.1| 181 leltKIIESIRLVQEQIKKLEEDLNEskkAKEKLKELEGEIRKIPllEEYIKQFNKFKElnTKKEQLEKDLNKISAI 257
                                       11112233333334444444433332111223333334444433211333333333322102222233333333333 PP

                           DUF3584 407 reekdr 412
                                       ree+++
  gi|242398545|ref|YP_002993969.1| 258 REEANK 263
                                       333333 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 6.1e-06
                           DUF3584 225 qdveeWiediqalaaiekvrpeieklqeefeqleslelr.Lsllkgelkadeerlaekqe....evqeakaelkqql 296
                                       +  + ++e i+  +++ +v  +++++++ + ++ +l+ + ++ +k+++++ e+ ++e ++     + eak+++ ++l
  gi|242398545|ref|YP_002993969.1| 266 KSCKVYVEYIEVGEEFIEVPTDLSEIEKSTTTISTLVRStVAQIKKDTEELEKLISEALKflpePTIEAKEKKLKEL 342
                                       556778888899999999999*************998752789999999999999998752221567888999999* PP

                           DUF3584 297 rtledelkeaidelnqelsaakaklaakeselealeeqkkkyedadieklkadldqlpsirseleeleeeldaltek 373
                                       +++e+ l++ ++ l++el + ++ ++  ++ l+ l e++       + k k   ++ + +++e+ee  ++l+ + ++
  gi|242398545|ref|YP_002993969.1| 343 KEEEKRLENIVSGLRKELGEVSGRINDLRKALDMLGESE----ACPVCKTKLTPEHRDRVKHEMEEEIKSLEEIVKQ 415
                                       ***********************************9985....57999***************************** PP

                           DUF3584 374 hqdvqekydrrkqkikeeleeeleklkerleaireekdrlkaaieealealesqlrkqleaqkeelneeekelesrl 450
                                       ++   e+ +++k  ikee e++++ + er e+++ e ++ k++  +++ +le     +l++ +++++ +  e+es++
  gi|242398545|ref|YP_002993969.1| 416 IRREIEEAENQKRTIKEEIERVSKINVERIEQLQKEIEEMKEKLAKHYTELEGIIT-ELNNLENDIRPKISEIESEI 491
                                       9998899999*******************99999999999***********99988.99999999999999999999 PP

                           DUF3584 451 selklrldsatate.Eeleqieeadealekaqeel 484
                                       +e + rl++ + +  E+ e+ e++ ++l+k +ee+
  gi|242398545|ref|YP_002993969.1| 492 KEIEERLNELIEEIgEKPEDPENELKELRKKKEEY 526
                                       99999999987764155566666667777777766 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.13
                           DUF3584 226 dveeWiediqala.aiekvrpeieklqeefeqleslelrLsllkgelkadeerlaekqeevqeakaelkqqlrtled 301
                                       + e+++edi+  + ++ k +++ ++lqee+++l    ++   + +e ++  ++ ++ ++e +e+ ++l+++l+ l+ 
  gi|242398545|ref|YP_002993969.1| 535 RYEKLLEDIKEAQeKLRKLENKKHELQEEIKKLGYDKQHHEKVRKEHEELLRKFESTKTELEEKTKSLEKNLKDLT- 610
                                       3344444444332134444444444444444444444444444444444444444444444444444444444433. PP

                           DUF3584 302 elkeaidelnqelsaakaklaakeselealeeqkkkyedad 342
                                       e++ +i+el+++ +++ka+l+++++ l+ le+ +++y  ++
  gi|242398545|ref|YP_002993969.1| 611 EVEAEIKELEEKRNNLKAELDKIKKLLNDLERIRRAYHRDG 651
                                       23344444444444555555555555555555555555555 PP

>> Sec8_exocyst  Sec8 exocyst complex component specific domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6  11.9   9.4e-06    0.0027      52     141 ..     109     199 ..      97     200 .. 0.79
   2 ?    4.6   4.0     0.093        27      75     141 ..     184     249 ..     182     250 .. 0.76
   3 ?   -1.2   6.3         6   1.7e+03      80     127 ..     305     357 ..     233     372 .. 0.70
   4 ?    3.4   8.1      0.22        63      39     131 ..     403     496 ..     393     508 .. 0.79
   5 ?    1.3   0.2      0.97   2.8e+02      80     121 ..     483     528 ..     478     532 .. 0.76
   6 ?    4.9   1.4     0.078        23      73     108 ..     535     573 ..     523     583 .. 0.78
   7 ?    0.6   6.4       1.6   4.6e+02      74     135 ..     581     636 ..     571     648 .. 0.54

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 9.4e-06
                      Sec8_exocyst  52 ieeaLqevvnehhqaFnssiasYskilssiqesqekvselKesleeakkklstkkkeLkelnarsakyke.vieiLd 127
                                       ++++L++ + e   +  s      k+ + iqe +++++elK++l++  ++ls+ + eL+elna+ ++y+e ++e+ +
  gi|242398545|ref|YP_002993969.1| 109 VKNELEKEIAEIEGKLKSKYEQRDKLKQEIQELNRQIKELKQKLKSLSQQLSAIERELNELNAKEKRYNElMLELTK 185
                                       4444444444444444555555688999****************************************995677778 PP

                      Sec8_exocyst 128 aieelkkvpdkieq 141
                                        ie ++ v ++i +
  gi|242398545|ref|YP_002993969.1| 186 IIESIRLVQEQIKK 199
                                       8999*999999986 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.093
                      Sec8_exocyst  75 skilssiqesqekvselKesleeakkklstkkkeLkelnarsakykevieiLdaieelkkvpdkieq 141
                                       +ki++si   qe++++l e+l+e+kk+ ++k keL+    +   ++e i+  ++ +el++  +++e+
  gi|242398545|ref|YP_002993969.1| 184 TKIIESIRLVQEQIKKLEEDLNESKKA-KEKLKELEGEIRKIPLLEEYIKQFNKFKELNTKKEQLEK 249
                                       58999*******************986.344444554455555578888888888888888888775 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 6
                      Sec8_exocyst  80 siqesqekvselKesleeakk.....klstkkkeLkelnarsakykevieiLd 127
                                       ++++ +++++el + ++ea k      +++k+k+Lkel+++ ++++++++ L 
  gi|242398545|ref|YP_002993969.1| 305 TVAQIKKDTEELEKLISEALKflpepTIEAKEKKLKELKEEEKRLENIVSGLR 357
                                       44455555555555555554422222467788888888888888888887775 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.22
                      Sec8_exocyst  39 ahrlkefkqlkkqieeaLqevvnehhqaFnssiasYski.lssiqesqekvselKesleeakkklstkkkeLkelna 114
                                        +++k+++++ kqi ++++e+ n+ + +  + i   ski ++ i++ q++++e+Ke+l++  ++l+    eL++l++
  gi|242398545|ref|YP_002993969.1| 403 EEEIKSLEEIVKQIRREIEEAENQ-KRTIKEEIERVSKInVERIEQLQKEIEEMKEKLAKHYTELEGIITELNNLEN 478
                                       568899999999999999997666.567899999999996799**********************999999999988 PP

                      Sec8_exocyst 115 rsa.kykevieiLdaiee 131
                                       + + k +e+ + +++iee
  gi|242398545|ref|YP_002993969.1| 479 DIRpKISEIESEIKEIEE 496
                                       765245555555555554 PP

  == domain 5  score: 1.3 bits;  conditional E-value: 0.97
                      Sec8_exocyst  80 siqesqekvselKesleeakkklstk....kkeLkelnarsakyke 121
                                       +i+e +++++e+ e+l+e  +++++k    ++eLkel ++  +y++
  gi|242398545|ref|YP_002993969.1| 483 KISEIESEIKEIEERLNELIEEIGEKpedpENELKELRKKKEEYDR 528
                                       6888889999999999999999966522226789999999988876 PP

  == domain 6  score: 4.9 bits;  conditional E-value: 0.078
                      Sec8_exocyst  73 sYskilssiqesqekvsel...Kesleeakkklstkkke 108
                                        Y+k+l+ i+e+qek+++l   K++l+e  kkl+++k++
  gi|242398545|ref|YP_002993969.1| 535 RYEKLLEDIKEAQEKLRKLenkKHELQEEIKKLGYDKQH 573
                                       69************9988844467777777777777766 PP

  == domain 7  score: 0.6 bits;  conditional E-value: 1.6
                      Sec8_exocyst  74 YskilssiqesqekvselKesleeakkklstkkkeLkelnarsakykevieiLdaieelkkv 135
                                       ++++l+++++ +++++e  +sle+  k+l++ ++e+kel+++  ++k        ++++kk+
  gi|242398545|ref|YP_002993969.1| 581 HEELLRKFESTKTELEEKTKSLEKNLKDLTEVEAEIKELEEKRNNLKAE------LDKIKKL 636
                                       5556666666666666666666666666666666666665554444332......2222222 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9  12.2   1.2e-05    0.0034      25      88 ..     106     169 ..     103     179 .. 0.91
   2 ?    2.8   5.9      0.55   1.6e+02      36      78 ..     169     211 ..     163     223 .. 0.41
   3 ?   -0.4  14.7       5.6   1.6e+03       8      98 ..     219     312 ..     212     382 .. 0.73
   4 ?   -0.7  13.3       7.1   2.1e+03      47      98 ..     403     458 ..     386     478 .. 0.40
   5 ?    0.9   6.7       2.2   6.5e+02      24      62 ..     472     510 ..     449     527 .. 0.57
   6 ?    3.9   9.4      0.26        76      29      83 ..     522     579 ..     513     592 .. 0.76
   7 ?    3.5   9.9      0.34        98      31      87 ..     580     639 ..     570     660 .. 0.65

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.2e-05
                                       HHHB-..BHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHH CS
                             DUF16  25 lnefkdsnkqrLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetleli 88 
                                       +++ k++ ++++ +ie k++++ eq +kl+q++++++ +ikelk++ k  +++l ++++ l+ +
  gi|242398545|ref|YP_002993969.1| 106 FEQVKNELEKEIAEIEGKLKSKYEQRDKLKQEIQELNRQIKELKQKLKSLSQQLSAIERELNEL 169
                                       78899999*********************************************99998888754 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.55
                                       HHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.. CS
                             DUF16  36 Lkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeel 78 
                                       L+  e++ + l  ++ k+ + ++  +e+ik+l+++ +  +++ 
  gi|242398545|ref|YP_002993969.1| 169 LNAKEKRYNELMLELTKIIESIRLVQEQIKKLEEDLNESKKAK 211
                                       3333333444444444444444444444444444433333322 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 5.6
                                       XXXXX.X.XTTB-BHHHHHHB-....BHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHH..HHHHHHH.... CS
                             DUF16   8 eivKkiPvkteYVTrkqlnefkds..nkqrLkkieakvdklgeqinkleqkvekqgekikelkv..eqkaqgeelnk 80 
                                          +kiP  +eY+  kq+n+fk+    k++L+k  +k+++  e+ nk  +  +   e i+  ++  e+ +   e++k
  gi|242398545|ref|YP_002993969.1| 219 GEIRKIPLLEEYI--KQFNKFKELntKKEQLEKDLNKISAIREEANKAMKSCKVYVEYIEVGEEfiEVPTDLSEIEK 293
                                       456778*9****8..9******8644577899999999988888887777777777766544431144445555665 PP

                                       ...HHHHHH.HHHHHHHHH CS
                             DUF16  81 vdetlelil.etLqkinkR 98 
                                          t+  ++  t+++i+k 
  gi|242398545|ref|YP_002993969.1| 294 STTTISTLVrSTVAQIKKD 312
                                       5555543331455555554 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 7.1
                                       .HHHHHHHHHHHHHHHHHHHHHHHHHHHHH............HHHHHHHHHHHHHHH CS
                             DUF16  47 geqinkleqkvekqgekikelkveqkaqgeeln.....kvdetleliletLqkinkR 98 
                                       +e+i+ le++v++   +i+e +++  + +ee++     +  e +e + + +++++++
  gi|242398545|ref|YP_002993969.1| 403 EEEIKSLEEIVKQIRREIEEAENQKRTIKEEIErvskiN-VERIEQLQKEIEEMKEK 458
                                       334444444444444444444444444444444222110.11222222222222222 PP

  == domain 5  score: 0.9 bits;  conditional E-value: 2.2
                                       HHHHB-..BHHHHHHHHHHHH...HHHHHHHHHHHHHHH CS
                             DUF16  24 qlnefkdsnkqrLkkieakvdklgeqinkleqkvekqge 62 
                                       +ln+  ++   ++ +ie +++  +e++n+l +++ ++ e
  gi|242398545|ref|YP_002993969.1| 472 ELNNLENDIRPKISEIESEIKEIEERLNELIEEIGEKPE 510
                                       566666666666777777777666666666666544433 PP

  == domain 6  score: 3.9 bits;  conditional E-value: 0.26
                                       -..BHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......... CS
                             DUF16  29 kdsnkqrLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeeln...kvde 83 
                                       k++   rLk i ++ +kl e i++ ++k +k+++k +el++e+k+ g + +   kv +
  gi|242398545|ref|YP_002993969.1| 522 KKEEYDRLKPIADRYEKLLEDIKEAQEKLRKLENKKHELQEEIKKLGYDKQhheKVRK 579
                                       455778999***********************************99987764444443 PP

  == domain 7  score: 3.5 bits;  conditional E-value: 0.34
                                       .BHHHHHHHHHHHH...HHHHHHHHHHHHHHH...HHHHHHHHHHHHHH.......HHHH CS
                             DUF16  31 snkqrLkkieakvdklgeqinkleqkvekqge...kikelkveqkaqgeelnkvdetlel 87 
                                       + ++ L+k+e + + l+e+ + le++ + ++e   +ikel+++ +  ++el+k+++ l+ 
  gi|242398545|ref|YP_002993969.1| 580 EHEELLRKFESTKTELEEKTKSLEKNLKDLTEveaEIKELEEKRNNLKAELDKIKKLLND 639
                                       455556777776666677766666666554332226777777777777777777666654 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  25.4    0.0016      0.46      77     179 ..     111     216 ..     107     236 .. 0.92
   2 !    8.4   7.3     0.008       2.3      20     161 ..     226     375 ..     220     380 .. 0.63
   3 ?    3.1  16.4      0.34        98      69     149 ..     399     483 ..     379     518 .. 0.64
   4 ?    5.1  10.4      0.08        23      88     145 ..     514     570 ..     499     578 .. 0.85
   5 !    8.4  14.5    0.0079       2.3      83     150 ..     574     641 ..     569     650 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0016
                             ATG16  77 qsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklv 153
                                       ++le+++a++   l+  y +r +l+q ++eln ++++l++klk+ +++l ++e+e ++l+ k k+ +e + e++k +
  gi|242398545|ref|YP_002993969.1| 111 NELEKEIAEIEGKLKSKYEQRDKLKQEIQELNRQIKELKQKLKSLSQQLSAIERELNELNAKEKRYNELMLELTKII 187
                                       6899************************************************************************* PP

                             ATG16 154 q...dlqDElsaLqlqlnqaEeklrklek 179
                                       +    +q+ +  L+  ln   ++++kl++
  gi|242398545|ref|YP_002993969.1| 188 EsirLVQEQIKKLEEDLNESKKAKEKLKE 216
                                       96667899999999999988888777765 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.008
                             ATG16  20 liqaynrLldrtsaleaenaklekaaasakssksskksakekeasasq.................snskqsakiqsl 79 
                                       l + y + +++ ++l++++++lek  ++ ++         ++ea+++                  + +++ ++i+++
  gi|242398545|ref|YP_002993969.1| 226 LLEEYIKQFNKFKELNTKKEQLEKDLNKISA--------IREEANKAMksckvyveyievgeefiEVPTDLSEIEKS 294
                                       6677888899999999999999888776654........22222222222344555666667777777777777777 PP

                             ATG16  80 eqklaql.reelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqd 155
                                       ++++++l r+ +a+  k  +el++ + e+ + l   e +++++e++l+el++e ++le  ++ +++el e    ++d
  gi|242398545|ref|YP_002993969.1| 295 TTTISTLvRSTVAQIKKDTEELEKLISEALKFLP--EPTIEAKEKKLKELKEEEKRLENIVSGLRKELGEVSGRIND 369
                                       7777765466666666666666666554444333..23566666777777777777777777777777777777777 PP

                             ATG16 156 lqDEls 161
                                       l+ +l+
  gi|242398545|ref|YP_002993969.1| 370 LRKALD 375
                                       776665 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.34
                             ATG16  69 nskqsakiqsleqklaqlreelaelyksrgelaqrlleln....eelqkleeklkedeerlaeleaeraaletklkd 141
                                       + + +++i+sle+ ++q+r e +e+  ++ + ++ + +++    e +++l+++++e++e+la+  +e + + t+l++
  gi|242398545|ref|YP_002993969.1| 399 KHEMEEEIKSLEEIVKQIRREIEEAENQKRTIKEEIERVSkinvERIEQLQKEIEEMKEKLAKHYTELEGIITELNN 475
                                       45677888888888888888888887777777766666552223356666666666666666666666666666666 PP

                             ATG16 142 reeelrek 149
                                       +e+ +r k
  gi|242398545|ref|YP_002993969.1| 476 LENDIRPK 483
                                       66666655 PP

  == domain 4  score: 5.1 bits;  conditional E-value: 0.08
                             ATG16  88 eelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreee 145
                                       +el+el k+++e  +rl+   +  +kl e +ke +e+l++le+++ +l++++k++   
  gi|242398545|ref|YP_002993969.1| 514 NELKELRKKKEE-YDRLKPIADRYEKLLEDIKEAQEKLRKLENKKHELQEEIKKLGYD 570
                                       688898666655.68*************************************997655 PP

  == domain 5  score: 8.4 bits;  conditional E-value: 0.0079
                             ATG16  83 laqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelreke 150
                                         ++r+e +el+++ + +++ l e++++l+k  + l+e e++++ele++r++l+ +l++ ++ l+++e
  gi|242398545|ref|YP_002993969.1| 574 HEKVRKEHEELLRKFESTKTELEEKTKSLEKNLKDLTEVEAEIKELEEKRNNLKAELDKIKKLLNDLE 641
                                       55666666666666666666666666666666666666666666666666666666666666666555 PP

>> DUF713  Protein of unknown function (DUF713)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   6.2     0.027       7.8      41     108 ..     100     166 ..      90     169 .. 0.71
   2 ?   -1.0   4.7       4.2   1.2e+03      64     106 ..     280     321 ..     238     379 .. 0.61
   3 !   16.8  14.3   1.5e-05    0.0043      22     153 ..     398     524 ..     397     533 .. 0.91
   4 ?    2.5   2.1      0.37   1.1e+02      46      83 ..     531     567 ..     516     572 .. 0.87
   5 ?    2.0  11.8      0.53   1.5e+02      37     107 ..     543     608 ..     535     667 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.027
                            DUF713  41 repivklknrfsdfeeeikksdkeekklekedleelqselsnLakkvlsaynkLeeafeklkelsekf 108
                                       re i  + +   ++e+ei++++ +  k + e++++l++e+++L++++ ++ +kL+   ++l+ ++++ 
  gi|242398545|ref|YP_002993969.1| 100 REVIYYFEQVKNELEKEIAEIEGK-LKSKYEQRDKLKQEIQELNRQIKELKQKLKSLSQQLSAIEREL 166
                                       444444444445556666666633.3335589************************999999998876 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 4.2
                            DUF713  64 eekklekedleelqselsnLakkvlsaynkLeeafeklkelse 106
                                       e+ ++   dl+e+++ ++ ++  v s+  +++++ e+l++l +
  gi|242398545|ref|YP_002993969.1| 280 EFIEVPT-DLSEIEKSTTTISTLVRSTVAQIKKDTEELEKLIS 321
                                       4444443.55555555555555555555555555555555543 PP

  == domain 3  score: 16.8 bits;  conditional E-value: 1.5e-05
                            DUF713  22 lklrFeekEqewsdwlkklrepivklknrfsdfeeeikksdkeekklekedleelqselsnLakkvlsaynkLeeaf 98 
                                       +k+  ee+ ++ ++ +k++r++i ++ n+  +++eei++ +    k++ e  e+lq+e++++++k+ + y +Le   
  gi|242398545|ref|YP_002993969.1| 398 VKHEMEEEIKSLEEIVKQIRREIEEAENQKRTIKEEIERVS----KINVERIEQLQKEIEEMKEKLAKHYTELEGII 470
                                       6888999999***************************9999....889999************************** PP

                            DUF713  99 eklkelsekfedkiFlkvLqksisdvatklleilevldeleldk.ekleelrelfs 153
                                       ++l++l+++   k  +  + ++i ++ + l+e++e++ e  +d+ ++l+elr++ +
  gi|242398545|ref|YP_002993969.1| 471 TELNNLENDIRPK--ISEIESEIKEIEERLNELIEEIGEKPEDPeNELKELRKKKE 524
                                       **********999..599*******************9999888678888887654 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.37
                            DUF713  46 klknrfsdfeeeikksdkeekklekedleelqselsnL 83 
                                        +  r++++ e+ik+ +++ +kle+ +++elq+e+++L
  gi|242398545|ref|YP_002993969.1| 531 PIADRYEKLLEDIKEAQEKLRKLEN-KKHELQEEIKKL 567
                                       56789999999******99999998.9999****9998 PP

  == domain 5  score: 2.0 bits;  conditional E-value: 0.53
                            DUF713  37 lkklrepivklknrfsdfeeeikksdkeekklekedleelqselsnLakkvlsaynkLeeafeklkelsek 107
                                       +k+ +e++ kl n+ ++++eeikk       ++k+++e++++e ++L +k  s+  +Lee+ ++l++  ++
  gi|242398545|ref|YP_002993969.1| 543 IKEAQEKLRKLENKKHELQEEIKKLG-----YDKQHHEKVRKEHEELLRKFESTKTELEEKTKSLEKNLKD 608
                                       67778888899999999999998888.....6677788899999999999999999999998888764433 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   8.3   0.00012     0.036       4      66 ..     123     185 ..     120     189 .. 0.93
   2 ?    4.4  12.6      0.11        32       2     141 ..     166     308 ..     166     315 .. 0.81
   3 ?    2.6   0.1       0.4   1.2e+02       5      52 ..     332     379 ..     329     383 .. 0.87
   4 !    7.9   7.8    0.0093       2.7      13      87 ..     400     479 ..     391     499 .. 0.76
   5 ?   -1.2   0.0       5.9   1.7e+03      33      52 ..     484     503 ..     478     510 .. 0.46
   6 !   11.6   5.7   0.00064      0.19       3      74 ..     517     591 ..     515     594 .. 0.84
   7 ?    6.2   6.3      0.03       8.7       9      79 ..     578     645 ..     575     667 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 0.00012
                             Sec34   4 qLeskeeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeiee 66 
                                       +L+sk e+ d+l ++++e+++q++el++k ks s++ s+++++ ++l +++kr++el  e+++
  gi|242398545|ref|YP_002993969.1| 123 KLKSKYEQRDKLKQEIQELNRQIKELKQKLKSLSQQLSAIERELNELNAKEKRYNELMLELTK 185
                                       7999****************************************************9877765 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.11
                             Sec34   2 ldqLeskeeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrlee..laeeieekLkyFeeldp 76 
                                       l++L++ke++++el+ +++++ e+++ ++e+ k+ +e+ ++ ++a e+l e + ++++  l ee  ++ + F+el++
  gi|242398545|ref|YP_002993969.1| 166 LNELNAKEKRYNELMLELTKIIESIRLVQEQIKKLEEDLNESKKAKEKLKELEGEIRKipLLEEYIKQFNKFKELNT 242
                                       579999********************************999999999998777666652246777778999999999 PP

                             Sec34  77 itrkLnspgss.lvksesFlemLkklDeclefleehpefkeaetYlirfkqcltrAltliknyvvn 141
                                        +++L++   +    +e+  + +k+    +e++e  +ef e  t l+  ++  t   tl+++ v +
  gi|242398545|ref|YP_002993969.1| 243 KKEQLEKDLNKiSAIREEANKAMKSCKVYVEYIEVGEEFIEVPTDLSEIEKSTTTISTLVRSTVAQ 308
                                       999999888886677888888889999999999998888888887777777777777777776655 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.4
                             Sec34   5 LeskeeecdelleqtdealeqLeeleekfksvsektsslheaceqlle 52 
                                       +e+ke++++el e+ +++++ ++ l+++  +vs + ++l++a + l e
  gi|242398545|ref|YP_002993969.1| 332 IEAKEKKLKELKEEEKRLENIVSGLRKELGEVSGRINDLRKALDMLGE 379
                                       678899999999999999999999999999999999999999887765 PP

  == domain 4  score: 7.9 bits;  conditional E-value: 0.0093
                             Sec34  13 delleqtdealeqLeeleekfksvsektsslheaceql....leeqkrleelaeeieekL.kyFeeldpitrkLnsp 84 
                                       +e+ e++++++e +++++ + ++ +++ ++++e+ e++    +e  ++l++  ee++ekL k+++el+ i ++Ln+ 
  gi|242398545|ref|YP_002993969.1| 400 HEMEEEIKSLEEIVKQIRREIEEAENQKRTIKEEIERVskinVERIEQLQKEIEEMKEKLaKHYTELEGIITELNNL 476
                                       567788888888888899999999999999999888882222344556666666667787569************97 PP

                             Sec34  85 gss 87 
                                       + +
  gi|242398545|ref|YP_002993969.1| 477 END 479
                                       766 PP

  == domain 5  score: -1.2 bits;  conditional E-value: 5.9
                             Sec34  33 fksvsektsslheaceqlle 52 
                                        ++++++ ++++e+ ++l+e
  gi|242398545|ref|YP_002993969.1| 484 ISEIESEIKEIEERLNELIE 503
                                       33334444444444444333 PP

  == domain 6  score: 11.6 bits;  conditional E-value: 0.00064
                             Sec34   3 dqLeskeeecdel...leqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLkyFeel 74 
                                       ++L++k+ee+d+l    ++ +++le+++e +ek ++ ++k ++l+e+ ++l  ++++ e++ +e ee L+ Fe+ 
  gi|242398545|ref|YP_002993969.1| 517 KELRKKKEEYDRLkpiADRYEKLLEDIKEAQEKLRKLENKKHELQEEIKKLGYDKQHHEKVRKEHEELLRKFEST 591
                                       67777777777652216788889999999999********************************99999999976 PP

  == domain 7  score: 6.2 bits;  conditional E-value: 0.03
                             Sec34   9 eeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLkyFeeldpitr 79 
                                       ++e +ell++ ++++++Lee +++ ++  ++ ++++++ ++l e++++l+   ++i++ L+   +l++i r
  gi|242398545|ref|YP_002993969.1| 578 RKEHEELLRKFESTKTELEEKTKSLEKNLKDLTEVEAEIKELEEKRNNLKAELDKIKKLLN---DLERIRR 645
                                       5677788888888888888888887777777777777777777777777777777777664...4444444 PP

>> Mce4_CUP1  Cholesterol uptake porter CUP1 of Mce4, putative
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.3     0.021         6      35      98 ..     143     206 ..     137     214 .. 0.92
   2 ?   -0.1   0.0       1.7     5e+02      39      67 ..     233     260 ..     227     318 .. 0.83
   3 ?   -2.0   0.0       6.8     2e+03     126     149 ..     450     473 ..     406     502 .. 0.54
   4 !   10.9   0.2   0.00076      0.22      31     122 ..     537     627 ..     532     645 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.021
                         Mce4_CUP1  35 esltdlnevLdelNprlpqlredireladladvYadaapdlldaLdnavttsrTiveqqaeLda 98 
                                       +++++l + L+ l ++l  ++++++el++  + Y++   +l +++++++  ++ i++ +++L++
  gi|242398545|ref|YP_002993969.1| 143 RQIKELKQKLKSLSQQLSAIERELNELNAKEKRYNELMLELTKIIESIRLVQEQIKKLEEDLNE 206
                                       68999*******************************************9999999999888875 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.7
                         Mce4_CUP1  39 dlnevLdelNprlpqlredireladladv 67 
                                       ++n+ ++elN++ +ql++d++++ ++ + 
  gi|242398545|ref|YP_002993969.1| 233 QFNK-FKELNTKKEQLEKDLNKISAIREE 260
                                       5554.589999999999999998887665 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 6.8
                         Mce4_CUP1 126 adlrptlelLakYspeltCllrnl 149
                                       ++ +++ e Lak+  el  ++++l
  gi|242398545|ref|YP_002993969.1| 450 KEIEEMKEKLAKHYTELEGIITEL 473
                                       333333333333333333333333 PP

  == domain 4  score: 10.9 bits;  conditional E-value: 0.00076
                         Mce4_CUP1  31 erlGesltdlnevLdelNprlpqlredireladladvYadaapdlldaLdnavttsrTiveqqaeLdalllaavgls 107
                                       e+l e +++++e L++l+++  +l+e+i++l   ++  +++ ++  + L+++  t++ ++e+ ++L++ l +++++ 
  gi|242398545|ref|YP_002993969.1| 537 EKLLEDIKEAQEKLRKLENKKHELQEEIKKLGYDKQHHEKVRKEHEELLRKFESTKTELEEKTKSLEKNLKDLTEVE 613
                                       56668899******************************************************************997 PP

                         Mce4_CUP1 108 ntgadllerngdnLi 122
                                        + ++ le+ ++nL 
  gi|242398545|ref|YP_002993969.1| 614 AEIKE-LEEKRNNLK 627
                                       76655.566666665 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2  12.4   0.00025     0.072      67     127 ..     100     160 ..      87     162 .. 0.87
   2 ?    2.5   7.4      0.48   1.4e+02      34      85 ..     165     216 ..     160     223 .. 0.69
   3 ?    5.5   2.4     0.057        16      48      88 ..     229     269 ..     226     296 .. 0.87
   4 ?    3.9   4.0      0.18        52      79     117 ..     334     372 ..     300     379 .. 0.70
   5 !   11.9  18.0   0.00061      0.18      11     116 ..     400     502 ..     393     504 .. 0.76
   6 ?    4.7  30.0       0.1        30       7     117 ..     513     628 ..     507     643 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00025
                        TPR_MLP1_2  67 nelkaeiaelkaeaesakaeleeseesweeqkeelekelselekriedlneqNklLhdQlE 127
                                        e+    +++k+e+e+  ae+e + +s  eq+++l++e++el+++i++l+++ k L +Ql 
  gi|242398545|ref|YP_002993969.1| 100 REVIYYFEQVKNELEKEIAEIEGKLKSKYEQRDKLKQEIQELNRQIKELKQKLKSLSQQLS 160
                                       5566667999*************************************************96 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.48
                        TPR_MLP1_2  34 qaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesaka 85 
                                       + +++++ +++Y + +++  + +++++ + e++++l+++++e k++ e++k+
  gi|242398545|ref|YP_002993969.1| 165 ELNELNAKEKRYNELMLELTKIIESIRLVQEQIKKLEEDLNESKKAKEKLKE 216
                                       4456677777777777777777777777777777777777777777776664 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.057
                        TPR_MLP1_2  48 elvkhaedvkelqalreelnelkaeiaelkaeaesakaele 88 
                                       e +k+ +  kel++ +e+l++  ++i+ +++ea++a ++++
  gi|242398545|ref|YP_002993969.1| 229 EYIKQFNKFKELNTKKEQLEKDLNKISAIREEANKAMKSCK 269
                                       7889999999***********************99998876 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.18
                        TPR_MLP1_2  79 eaesakaeleeseesweeqkeelekelselekriedlne 117
                                       + e+  +el+e+e+ +e+  + l+kel e+  ri+dl +
  gi|242398545|ref|YP_002993969.1| 334 AKEKKLKELKEEEKRLENIVSGLRKELGEVSGRINDLRK 372
                                       345555788999999999999999999999999999987 PP

  == domain 5  score: 11.9 bits;  conditional E-value: 0.00061
                        TPR_MLP1_2  11 kslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhae.dvkelqalreelnelkaeiaelkaeaesakae 86 
                                       ++++ee++++e+ ++++++++e+ +++ ++ ++    e+   ++ +v+ +++l +e++e+k+++a+  +e+e   +e
  gi|242398545|ref|YP_002993969.1| 400 HEMEEEIKSLEEIVKQIRREIEEAENQKRTIKE----EIERVSKiNVERIEQLQKEIEEMKEKLAKHYTELEGIITE 472
                                       345555555555555555555555555555555....444444327888899999********************** PP

                        TPR_MLP1_2  87 leeseesweeqkeelekelselekriedln 116
                                       l++ e+ +  + +e+e+e++e+e+r+++l 
  gi|242398545|ref|YP_002993969.1| 473 LNNLENDIRPKISEIESEIKEIEERLNELI 502
                                       ****************************96 PP

  == domain 6  score: 4.7 bits;  conditional E-value: 0.1
                        TPR_MLP1_2   7 eeeikslkeekeeaeaklqklqedlekqaeiakeaqqk...Yerelvkhaedvkelqalreelnelkaeiaelkaea 80 
                                       e+e+k+l+++kee+++ l+ + +  ek  e  keaq+k    e+   +  e++k+l   ++ ++++++e +el  + 
  gi|242398545|ref|YP_002993969.1| 513 ENELKELRKKKEEYDR-LKPIADRYEKLLEDIKEAQEKlrkLENKKHELQEEIKKLGYDKQHHEKVRKEHEELLRKF 588
                                       5677777777777753.444444444444444444444000444555556888888888****************** PP

                        TPR_MLP1_2  81 esakaeleeseesweeqkeel...ekelselekriedlne 117
                                       es+k+elee+++s+e+  + l   e e++ele+++++l++
  gi|242398545|ref|YP_002993969.1| 589 ESTKTELEEKTKSLEKNLKDLtevEAEIKELEEKRNNLKA 628
                                       ***************9987663337799999999999876 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 !   10.6  31.9    0.0015      0.42      27     133 ..     111     219 ..     105     223 .. 0.85
   2 ?    1.8  19.2      0.75   2.2e+02      22     138 ..     193     316 ..     190     318 .. 0.81
   3 ?    6.2  31.8     0.033       9.6      14     137 ..     401     525 ..     393     527 .. 0.81
   4 !    9.7  30.3    0.0027      0.79       6     103 ..     544     644 ..     541     654 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0015
                    CENP-F_leu_zip  27 enLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLekelqkkqervseLesln 103
                                       ++Le+e+ ++e ++ +   + ++ k+e+++l+ +i+el+++l+ l+++L+a+ +e +eL+ + +  +e + eL ++ 
  gi|242398545|ref|YP_002993969.1| 111 NELEKEIAEIEGKLKSKYEQRDKLKQEIQELNRQIKELKQKLKSLSQQLSAIERELNELNAKEKRYNELMLELTKII 187
                                       47**************************************************************************9 PP

                    CENP-F_leu_zip 104 ssle...nlleekEqekvqmkeeskaaveeLqt 133
                                       +s++   ++++++E++  ++++++k++++eL+ 
  gi|242398545|ref|YP_002993969.1| 188 ESIRlvqEQIKKLEED-LNESKKAKEKLKELEG 219
                                       9975332778888876.4445555666666665 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.75
                    CENP-F_leu_zip  22 LkdkvenLerelemseenqekvi.leaEtsk....aevetlkeeieelaeelreleldLvalrsekeeLekelqkkq 93 
                                       +++++++Le +l++s++ +ek++ le E  k    +e  +  ++ +el+++ ++le dL++++  +ee +k ++  +
  gi|242398545|ref|YP_002993969.1| 193 VQEQIKKLEEDLNESKKAKEKLKeLEGEIRKipllEEYIKQFNKFKELNTKKEQLEKDLNKISAIREEANKAMKSCK 269
                                       799*****************995388888883333344445568899****************************99 PP

                    CENP-F_leu_zip  94 ervseLeslnssle..nlleekEqekvqmkeeskaaveeLqtqlkel 138
                                         v+  e  ++ +e    l+e E+    ++    ++v +++++ +el
  gi|242398545|ref|YP_002993969.1| 270 VYVEYIEVGEEFIEvpTDLSEIEKSTTTISTLVRSTVAQIKKDTEEL 316
                                       99999998776554227788888888888888888888888888887 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.033
                    CENP-F_leu_zip  14 eserkadsLkdkvenLerelemseenqekvileaEt.sk...aevetlkeeieelaeelreleldLvalrsekeeLe 86 
                                       e+e++  sL++ v+++ re+e++e+++  ++ e E  sk   + +e+l++eiee++e+l +  ++L+ +  e ++Le
  gi|242398545|ref|YP_002993969.1| 401 EMEEEIKSLEEIVKQIRREIEEAENQKRTIKEEIERvSKinvERIEQLQKEIEEMKEKLAKHYTELEGIITELNNLE 477
                                       67788889999999999999999999999999998634522245666999999999999999999999999999999 PP

                    CENP-F_leu_zip  87 kelqkkqervseLeslnsslenlleekEqekvqmkeeskaaveeLqtqlke 137
                                       ++++    ++se es   ++e+ l+e+ +e  +  e+ +++++eL++ ++e
  gi|242398545|ref|YP_002993969.1| 478 NDIRP---KISEIESEIKEIEERLNELIEEIGEKPEDPENELKELRKKKEE 525
                                       88765...6888888888888888888888888888888888888888776 PP

  == domain 4  score: 9.7 bits;  conditional E-value: 0.0027
                    CENP-F_leu_zip   6 lhvlekLKeserkadsLkdkvenLerelemse...enqekvileaEtskaevetlkeeieelaeelreleldLvalr 79 
                                       ++++ekL++ e k+  L++ +++L  +++  e   ++ e++ +  E+ k e+e+  + +e+  + l+e e+++++l 
  gi|242398545|ref|YP_002993969.1| 544 KEAQEKLRKLENKKHELQEEIKKLGYDKQHHEkvrKEHEELLRKFESTKTELEEKTKSLEKNLKDLTEVEAEIKELE 620
                                       6789********************87765554222799****************99999999999************ PP

                    CENP-F_leu_zip  80 sekeeLekelqkkqervseLesln 103
                                       + +++L+ el k ++  ++Le+++
  gi|242398545|ref|YP_002993969.1| 621 EKRNNLKAELDKIKKLLNDLERIR 644
                                       *********************986 PP

>> Fzo_mitofusin  fzo-like conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   7.7    0.0051       1.5      90     154 ..     108     168 ..      95     178 .. 0.59
   2 ?    3.7   3.7      0.14        41     116     154 ..     185     223 ..     167     232 .. 0.83
   3 ?   -0.2   0.5       2.2   6.3e+02     115     146 ..     238     262 ..     227     274 .. 0.57
   4 ?    0.1   1.5       1.7     5e+02     104     150 ..     307     351 ..     288     365 .. 0.43
   5 ?   -0.0   0.2       1.9   5.6e+02      96     118 ..     339     361 ..     324     381 .. 0.56
   6 ?    1.7   9.8      0.58   1.7e+02      99     152 ..     409     466 ..     388     472 .. 0.57
   7 ?    1.3   4.8      0.77   2.2e+02     106     157 ..     448     496 ..     445     529 .. 0.55
   8 ?    1.8   3.2      0.53   1.5e+02     117     154 ..     529     566 ..     517     570 .. 0.82
   9 !   15.8   8.1   2.7e-05    0.0079      93     157 ..     571     635 ..     567     637 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0051
                     Fzo_mitofusin  90 ncshqvqqelsstfarlcqqvdetekeleeeikelekeiekleevqkkakllrnkaslleseLek 154
                                       ++++ +++e+++   +l+++ + ++++l++ei+el+++i++l+   +k+k l ++ s +e+eL++
  gi|242398545|ref|YP_002993969.1| 108 QVKNELEKEIAEIEGKLKSKYE-QRDKLKQEIQELNRQIKELK---QKLKSLSQQLSAIERELNE 168
                                       2333344444444444444433.34567777777777776654...4666666666666666665 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.14
                     Fzo_mitofusin 116 eleeeikelekeiekleevqkkakllrnkaslleseLek 154
                                       ++ e+i+ ++++i+klee  +++k+ ++k ++le e++k
  gi|242398545|ref|YP_002993969.1| 185 KIIESIRLVQEQIKKLEEDLNESKKAKEKLKELEGEIRK 223
                                       5667899999***********************999876 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 2.2
                     Fzo_mitofusin 115 keleeeikelekeiekleevqkkakllrnkas 146
                                       kel+++ ++lek+++k+ ++ ++       a+
  gi|242398545|ref|YP_002993969.1| 238 KELNTKKEQLEKDLNKISAIREE-------AN 262
                                       34455555555555555544444.......33 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 1.7
                     Fzo_mitofusin 104 arlcqqvdetekeleeeikelekeie..kleevqkkakllrnkaslles 150
                                       a+++++    ++ele+ i+e  k +   ++e+ +kk+k l+++ ++le+
  gi|242398545|ref|YP_002993969.1| 307 AQIKKD----TEELEKLISEALKFLPepTIEAKEKKLKELKEEEKRLEN 351
                                       222222....222222222222222111344445555555554444444 PP

  == domain 5  score: -0.0 bits;  conditional E-value: 1.9
                     Fzo_mitofusin  96 qqelsstfarlcqqvdetekele 118
                                        +el++  +rl++ v   +kel 
  gi|242398545|ref|YP_002993969.1| 339 LKELKEEEKRLENIVSGLRKELG 361
                                       34555555555555555555543 PP

  == domain 6  score: 1.7 bits;  conditional E-value: 0.58
                     Fzo_mitofusin  99 lsstfarlcq...qvdetekeleeeikelek.eiekleevqkkakllrnkaslleseL 152
                                       l++ ++++++   + ++++++++eei++++k ++e++e++qk+ + +++k  +  +eL
  gi|242398545|ref|YP_002993969.1| 409 LEEIVKQIRReieEAENQKRTIKEEIERVSKiNVERIEQLQKEIEEMKEKLAKHYTEL 466
                                       2333333333000344455667777777655467777777777777777766655555 PP

  == domain 7  score: 1.3 bits;  conditional E-value: 0.77
                     Fzo_mitofusin 106 lcqqvdetekeleeeikelekeiekleevqkkakllrnkaslleseLekfee 157
                                       l+++++e++++l ++ +ele  i++l+++++    +r k s++ese+++ ee
  gi|242398545|ref|YP_002993969.1| 448 LQKEIEEMKEKLAKHYTELEGIITELNNLEND---IRPKISEIESEIKEIEE 496
                                       44444444444444444444444444444332...33444444444443332 PP

  == domain 8  score: 1.8 bits;  conditional E-value: 0.53
                     Fzo_mitofusin 117 leeeikelekeiekleevqkkakllrnkaslleseLek 154
                                       l+   ++ ek +e ++e+q+k+++l nk ++l++e++k
  gi|242398545|ref|YP_002993969.1| 529 LKPIADRYEKLLEDIKEAQEKLRKLENKKHELQEEIKK 566
                                       55556778888999999***************999986 PP

  == domain 9  score: 15.8 bits;  conditional E-value: 2.7e-05
                     Fzo_mitofusin  93 hqvqqelsstfarlcqqvdetekeleeeikelekeiekleevqkkakllrnkaslleseLekfee 157
                                       +q ++++ + +++l ++ + t++elee++k+lek+++ l ev+ + k l +k ++l++eL+k ++
  gi|242398545|ref|YP_002993969.1| 571 KQHHEKVRKEHEELLRKFESTKTELEEKTKSLEKNLKDLTEVEAEIKELEEKRNNLKAELDKIKK 635
                                       5667778889999***********************************************99875 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0  30.8    0.0014      0.39      29     131 ..     111     213 ..      89     220 .. 0.75
   2 ?    3.8  13.3      0.11        31      54     170 ..     205     325 ..     204     327 .. 0.88
   3 ?    3.2   1.6      0.17        48      44      82 ..     334     372 ..     329     383 .. 0.49
   4 !    8.6  21.1    0.0037       1.1      30     139 ..     401     508 ..     396     516 .. 0.84
   5 !   10.7  27.0   0.00082      0.24      28     141 ..     484     600 ..     482     600 .. 0.90
   6 !    8.6  12.7    0.0037       1.1      27      86 ..     587     646 ..     585     650 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0014
                               GAS  29 kslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlk 105
                                       ++l +ei+e++ k +++  + ++++qe ++l+ ++k+++++++ L +ql   e++ ++l++ ++r++el  el+++ 
  gi|242398545|ref|YP_002993969.1| 111 NELEKEIAEIEGKLKSKYEQRDKLKQEIQELNRQIKELKQKLKSLSQQLSAIERELNELNAKEKRYNELMLELTKII 187
                                       56777888888888888888888888888888888888888888888888888888888888888888888888888 PP

                               GAS 106 wehevleqrfekvekerdelykkfea 131
                                       ++ + ++++++k+e++ +e +k  e+
  gi|242398545|ref|YP_002993969.1| 188 ESIRLVQEQIKKLEEDLNESKKAKEK 213
                                       88888888888888877776665544 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.11
                               GAS  54 qenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkw..ehevleqrfekvekerdelykk 128
                                       +e k+ ke+Lk++e e+ +    l++y k+++++k+l+++ ++lek l++++   e  ++ ++  kv  e+ e+ ++
  gi|242398545|ref|YP_002993969.1| 205 NESKKAKEKLKELEGEIRKIP-LLEEYIKQFNKFKELNTKKEQLEKDLNKISAirEEANKAMKSCKVYVEYIEVGEE 280
                                       5889999*******9999985.79999999999****99999999999998862255667777888999******** PP

                               GAS 129 feaa...iqevqqktglknllLekklkalqeelEkkeaqleevla 170
                                       f ++   + e+ + t   ++l+   +++++++ E+ e+ ++e+l+
  gi|242398545|ref|YP_002993969.1| 281 FIEVptdLSEIEKSTTTISTLVRSTVAQIKKDTEELEKLISEALK 325
                                       *99988899999**************************9999885 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.17
                               GAS  44 rnekelseisqenkrlkepLkkaeeeveeLrkqlknyek 82 
                                       ++ek+l+e+++e krl+  +  +++e+ e   ++++ +k
  gi|242398545|ref|YP_002993969.1| 334 AKEKKLKELKEEEKRLENIVSGLRKELGEVSGRINDLRK 372
                                       444555555555555555555444444444443333333 PP

  == domain 4  score: 8.6 bits;  conditional E-value: 0.0037
                               GAS  30 slKeeieelkkkeernekelseisqenkrlkepLkkaee.eveeLrkqlknyekdkqslknlkarlkelekelkdlk 105
                                       ++ eei+ l++  ++ ++e++e++++++ +ke+++++ + +ve+ ++  k+ e+ k++l+   ++++ele  +++l 
  gi|242398545|ref|YP_002993969.1| 401 EMEEEIKSLEEIVKQIRREIEEAENQKRTIKEEIERVSKiNVERIEQLQKEIEEMKEKLA---KHYTELEGIITELN 474
                                       6889******************************99866256666666667777666655...57777777777777 PP

                               GAS 106 wehevleqrfekvekerdelykkfeaaiqevqqk 139
                                          +  + +++++e+e++e++++ ++ i+e+ +k
  gi|242398545|ref|YP_002993969.1| 475 NLENDIRPKISEIESEIKEIEERLNELIEEIGEK 508
                                       77788999*********************99877 PP

  == domain 5  score: 10.7 bits;  conditional E-value: 0.00082
                               GAS  28 IkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdl 104
                                       I +  +ei+e++++ ++   e+ e  ++ ++  ++L+k +ee ++L+  + +yek  +++k+++++l++le++ ++l
  gi|242398545|ref|YP_002993969.1| 484 ISEIESEIKEIEERLNELIEEIGEKPEDPENELKELRKKKEEYDRLKPIADRYEKLLEDIKEAQEKLRKLENKKHEL 560
                                       777788888888888888888888888888888888888899999999***************************** PP

                               GAS 105 kwehevl...eqrfekvekerdelykkfeaaiqevqqktg 141
                                       ++e + l   +q+ ekv ke +el +kfe++  e+ +kt+
  gi|242398545|ref|YP_002993969.1| 561 QEEIKKLgydKQHHEKVRKEHEELLRKFESTKTELEEKTK 600
                                       *****997778*********************99999985 PP

  == domain 6  score: 8.6 bits;  conditional E-value: 0.0037
                               GAS  27 lIkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqs 86 
                                       + +s K e+ee+ k  e+n k+l e+++e k+l+e+ +++++e+++ +k l++ e+ + +
  gi|242398545|ref|YP_002993969.1| 587 KFESTKTELEEKTKSLEKNLKDLTEVEAEIKELEEKRNNLKAELDKIKKLLNDLERIRRA 646
                                       567889999999999999999999999999999999999999999999999988887765 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.1   0.00024     0.071     213     319 ..     137     242 ..     115     276 .. 0.71
   2 ?    1.4   0.1      0.31        89     242     324 ..     395     476 ..     294     489 .. 0.46
   3 ?    5.4   1.3     0.019       5.4     188     331 ..     397     571 ..     368     593 .. 0.60
   4 ?    2.5   2.4      0.14        41     237     331 ..     545     639 ..     495     669 .. 0.49

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00024
                              FUSC 213 rirararalrrllsrmlallallsslarllarlraeeaaavpelaallaelaaleaaaaaealeaalaalrarlral 289
                                       +i++ +r++++l +++ +l+++ls+++r+l++l+a+e++      +l+ el ++   ++    +++++ l+++l++ 
  gi|242398545|ref|YP_002993969.1| 137 EIQELNRQIKELKQKLKSLSQQLSAIERELNELNAKEKRY----NELMLELTKI--IESIRLVQEQIKKLEEDLNES 207
                                       5667789999999999999999999999999999988877....4555555553..335667788888888888887 PP

                              FUSC 290 rrale.....adadtaalllarlaellaelaqlla 319
                                       ++a e     +   ++  ll++   ++ ++ +l++
  gi|242398545|ref|YP_002993969.1| 208 KKAKEklkelEGEIRKIPLLEEYIKQFNKFKELNT 242
                                       77777444444444444444444444444444444 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.31
                              FUSC 242 larlraeeaaavpelaallaelaaleaaaaaealeaalaalrarlralrrale.adadtaalllarlaellaelaql 317
                                         r+++e +++ ++l+++++++++  + + ae ++  +++  +r+ +++ ++  + +   +++ + la +  el  +
  gi|242398545|ref|YP_002993969.1| 395 RDRVKHEMEEEIKSLEEIVKQIRR--EIEEAENQKRTIKEEIERVSKINVERIeQLQKEIEEMKEKLAKHYTELEGI 469
                                       122222222222224444444444..222233333333333333322222222344444455555555555555555 PP

                              FUSC 318 laslral 324
                                        ++l++l
  gi|242398545|ref|YP_002993969.1| 470 ITELNNL 476
                                       5555555 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.019
                              FUSC 188 aararlaadilalealrsqaayesprirararalrrllsrmlal.lallsslarllarlraeeaaavpelaallael 263
                                       +  +++ ++i  le+ ++q + e ++  ++ r +++   r+  + + ++  l+++ ++++++ a++  el+ ++ el
  gi|242398545|ref|YP_002993969.1| 397 RVKHEMEEEIKSLEEIVKQIRREIEEAENQKRTIKEEIERVSKInVERIEQLQKEIEEMKEKLAKHYTELEGIITEL 473
                                       45566666666777777777777777777777777766666665356777777777777777777777777777777 PP

                              FUSC 264 aal............eaaaaaealeaalaalrarlralrrale..........adadtaalllarlaellaelaqll 318
                                        +l            +     +++e++l++l +++ +  +++e          ++ d+   ++ r   ll++  +++
  gi|242398545|ref|YP_002993969.1| 474 NNLendirpkiseieS---EIKEIEERLNELIEEIGEKPEDPEnelkelrkkkEEYDRLKPIADRYEKLLEDIKEAQ 547
                                       7777777776664331...3444444444444444444444444555555554455555666666666666666666 PP

                              FUSC 319 aslraleaaiaa...........a 331
                                       ++lr+le+   +           +
  gi|242398545|ref|YP_002993969.1| 548 EKLRKLENKKHElqeeikklgydK 571
                                       666666665554433433366652 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.14
                              FUSC 237 slarllarlraeeaaavpelaallaelaal.eaaaaaealeaalaalrarlralrraleadadtaalllarlaella 312
                                       + ++ l+ l  ++++ +       +e+++l  +++ +e+ +++ ++l +++++++++le       +   +l   l+
  gi|242398545|ref|YP_002993969.1| 545 EAQEKLRKLENKKHELQ-------EEIKKLgYDKQHHEKVRKEHEELLRKFESTKTELE-------EKTKSLEKNLK 607
                                       11111111111111111.......11111121112233333333333333333333333.......55555555555 PP

                              FUSC 313 elaqllaslraleaaiaa.............a 331
                                       +l+++ a++++le+ + +             +
  gi|242398545|ref|YP_002993969.1| 608 DLTEVEAEIKELEEKRNNlkaeldkikkllnD 639
                                       55555555555555555544444444444443 PP

>> DUF3287  Protein of unknown function (DUF3287)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   3.4   3.8e-05     0.011      51     108 ..     125     182 ..     106     197 .. 0.89
   2 ?   -1.7   4.5       7.4   2.2e+03      64     113 ..     394     440 ..     387     450 .. 0.77
   3 ?   -1.4   0.1       6.2   1.8e+03      73      95 ..     479     501 ..     449     520 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.8e-05
                           DUF3287  51 eealdfidkvvekHrrlcderqklgkkrqtleaRiarveRklreleseprdWeeleld 108
                                       ++ ++  dk++++ + l+ + ++l++k+++l + + ++eR+l el+++ + + el l+
  gi|242398545|ref|YP_002993969.1| 125 KSKYEQRDKLKQEIQELNRQIKELKQKLKSLSQQLSAIERELNELNAKEKRYNELMLE 182
                                       6789999****************************************99999998776 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 7.4
                           DUF3287  64 HrrlcderqklgkkrqtleaRiarveRklreleseprdWeeleldevari 113
                                       Hr +   ++++   +++le  + ++ R++ e e + r  ++ e+++v +i
  gi|242398545|ref|YP_002993969.1| 394 HRDRV--KHEMEEEIKSLEEIVKQIRREIEEAENQKRT-IKEEIERVSKI 440
                                       55544..56889999***************88877665.66677777776 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 6.2
                           DUF3287  73 klgkkrqtleaRiarveRklrel 95 
                                        ++ k+  +e  i ++e +l el
  gi|242398545|ref|YP_002993969.1| 479 DIRPKISEIESEIKEIEERLNEL 501
                                       44445555555555555444444 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 ?   12.5  14.3   0.00057      0.16       3      98 ..     106     200 ..     105     224 .. 0.90
   2 ?    1.4   1.0       1.7   4.9e+02      52      94 ..     209     260 ..     200     273 .. 0.50
   3 ?    4.1   6.2      0.23        68       7      95 ..     258     360 ..     245     363 .. 0.64
   4 ?    5.0   9.4      0.13        37       7      62 ..     557     611 ..     534     614 .. 0.68
   5 ?    7.9   1.4     0.016       4.6      36      63 ..     616     643 ..     610     659 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00057
                      Syntaxin-6_N   3 FfevkeeVqkslnkaeslyrrw.erlledtssstseeldetrteLrkalrsiewdledLeetvriveknpskfkide 78 
                                       F +vk+e +k++ ++e+ +++  e+ +++ + ++ +el+++ +eL+++l+s++++l+ +e+  + +++++++++   
  gi|242398545|ref|YP_002993969.1| 106 FEQVKNELEKEIAEIEGKLKSKyEQ-RDKLK-QEIQELNRQIKELKQKLKSLSQQLSAIERELNELNAKEKRYNELM 180
                                       789*************988776155.44433.4599********************************9999**999 PP

                      Syntaxin-6_N  79 kelsrrrafveevreevkem 98 
                                        el++  + ++ v+e++k++
  gi|242398545|ref|YP_002993969.1| 181 LELTKIIESIRLVQEQIKKL 200
                                       *****************987 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 1.7
                      Syntaxin-6_N  52 siewdledLeetvriv...ek.....npsk.fkidekelsrrrafveevree 94 
                                       +++++l++Le  +r +   e+     n+ k  + ++++l++  + ++++ree
  gi|242398545|ref|YP_002993969.1| 209 KAKEKLKELEGEIRKIpllEEyikqfNKFKeLNTKKEQLEKDLNKISAIREE 260
                                       4555555555555322111112222233333555555555555555555554 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.23
                      Syntaxin-6_N   7 keeVqkslnkaeslyrrw....erlledtss.s.tseeldetrteLrkalrsiewdledLeetv.........rive 68 
                                       +ee +k++++++  y ++    e+  e++++ s  +++    +t +r+++ +i++d e+Le+ +          ++e
  gi|242398545|ref|YP_002993969.1| 258 REEANKAMKSCKV-YVEYievgEEFIEVPTDlSeIEKSTTTISTLVRSTVAQIKKDTEELEKLIsealkflpePTIE 333
                                       5555555555443.3333244445555544442356666677788899****************5555444444667 PP

                      Syntaxin-6_N  69 knpskfkidekelsrrrafveevreev 95 
                                       ++++k k  ++e +r +++v+ +r+e+
  gi|242398545|ref|YP_002993969.1| 334 AKEKKLKELKEEEKRLENIVSGLRKEL 360
                                       777776666666666667777666665 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.13
                      Syntaxin-6_N   7 keeVqkslnkaeslyrrwerlledtssstseeldetrteLrkalrsiewdledLee 62 
                                       k+e q++++k+    +  e+++++ ++    ++++t+teL+++ +s+e++l+dL e
  gi|242398545|ref|YP_002993969.1| 557 KHELQEEIKKLGYDKQHHEKVRKEHEE-LLRKFESTKTELEEKTKSLEKNLKDLTE 611
                                       344555555555544555554444333.68999********************987 PP

  == domain 5  score: 7.9 bits;  conditional E-value: 0.016
                      Syntaxin-6_N  36 seeldetrteLrkalrsiewdledLeet 63 
                                        +el+e r++L+++l++i++ l+dLe+ 
  gi|242398545|ref|YP_002993969.1| 616 IKELEEKRNNLKAELDKIKKLLNDLERI 643
                                       589**********************985 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   4.5       0.7     2e+02      49      95 ..     109     152 ..      94     173 .. 0.66
   2 ?    0.1   0.7         3   8.7e+02      45      82 ..     151     188 ..     142     193 .. 0.73
   3 ?   -0.5   0.8       4.7   1.4e+03      39      59 ..     203     223 ..     185     256 .. 0.63
   4 ?    1.0   0.1       1.6   4.7e+02      44      89 ..     307     358 ..     293     367 .. 0.70
   5 ?   -0.0   1.8       3.4   9.8e+02      63     105 ..     412     465 ..     391     475 .. 0.47
   6 ?    0.9   4.8       1.8   5.2e+02      39      84 ..     539     584 ..     528     595 .. 0.75
   7 ?   15.1   2.8     7e-05      0.02      41     117 ..     597     673 ..     583     676 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.7
                        OrfB_IS605  49 dykylakeiaelqsklkksknykkasrklarlhrkrsrrrkhllhkl 95 
                                        + +l+keiae++ klk +    +++ kl+   ++++r++k+l +kl
  gi|242398545|ref|YP_002993969.1| 109 VKNELEKEIAEIEGKLKSK---YEQRDKLKQEIQELNRQIKELKQKL 152
                                       5667788888888777766...3555555555555555555554444 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 3
                        OrfB_IS605  45 rlksdykylakeiaelqsklkksknykkasrklarlhr 82 
                                       +lks  ++l+   +el  + +k+k+y +   +l+++ +
  gi|242398545|ref|YP_002993969.1| 151 KLKSLSQQLSAIERELNELNAKEKRYNELMLELTKIIE 188
                                       56777777777788888888888888888888877765 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 4.7
                        OrfB_IS605  39 flykgrrlksdykylakeiae 59 
                                        l++++++k+++k+l+ ei++
  gi|242398545|ref|YP_002993969.1| 203 DLNESKKAKEKLKELEGEIRK 223
                                       345555555555555555554 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 1.6
                        OrfB_IS605  44 rrlksdykylakeiaelqsklkkskn......ykkasrklarlhrkrsrrrk 89 
                                       +++k+d ++l+k i e  ++l++ ++       k+ +++++rl + +s  rk
  gi|242398545|ref|YP_002993969.1| 307 AQIKKDTEELEKLISEALKFLPEPTIeakekkLKELKEEEKRLENIVSGLRK 358
                                       5788888999999999888888887655555466666666666666655555 PP

  == domain 5  score: -0.0 bits;  conditional E-value: 3.4
                        OrfB_IS605  63 klkkskn...........ykkasrklarlhrkrsrrrkhllhklathliktlke 105
                                       ++k+ ++            k+  ++++++  +r ++++  ++++  +l+k++ e
  gi|242398545|ref|YP_002993969.1| 412 IVKQIRReieeaenqkrtIKEEIERVSKINVERIEQLQKEIEEMKEKLAKHYTE 465
                                       333333222222222111234444444444444455555555555566665555 PP

  == domain 6  score: 0.9 bits;  conditional E-value: 1.8
                        OrfB_IS605  39 flykgrrlksdykylakeiaelqsklkksknykkasrklarlhrkr 84 
                                        l + +++++++++l++++ elq  +kk +  k+  +k+++ h+++
  gi|242398545|ref|YP_002993969.1| 539 LLEDIKEAQEKLRKLENKKHELQEEIKKLGYDKQHHEKVRKEHEEL 584
                                       6778899999999999999999999999875444455666666554 PP

  == domain 7  score: 15.1 bits;  conditional E-value: 7e-05
                        OrfB_IS605  41 ykgrrlksdykylakeiaelqsklkksknykkasrklarlhrkrsrrrkhllhklathliktlkevgvetLnvgnmk 117
                                        k ++l +++k l++  ae+  + +k +n k+   k+++l + + r+r+ +++  +++l+++  +  +++L  g+  
  gi|242398545|ref|YP_002993969.1| 597 EKTKSLEKNLKDLTEVEAEIKELEEKRNNLKAELDKIKKLLNDLERIRRAYHRDGVQRLLRQKIAPIISELATGYIE 673
                                       45599*******************************************************************99976 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 ?   11.3  17.4   0.00065      0.19     140     258 ..     108     223 ..      90     228 .. 0.65
   2 ?    4.5   3.9     0.076        22     155     222 ..     300     368 ..     226     415 .. 0.47
   3 ?   13.8   9.2   0.00011     0.031     136     253 ..     410     530 ..     407     544 .. 0.78
   4 ?    1.4  16.4      0.64   1.9e+02     165     259 ..     547     636 ..     528     666 .. 0.42

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00065
                      Exonuc_VII_L 140 pdkaeleeqleelerrlekaikrlleekkqrleklasrlkspeellerkrqrldeleerleralkkq...lkkkrer 213
                                       ++k+ele++++e+e         +l++k ++ +kl++++++ ++++++ +q+l++l+++l++ ++++   l++k++r
  gi|242398545|ref|YP_002993969.1| 108 QVKNELEKEIAEIEG--------KLKSKYEQRDKLKQEIQELNRQIKELKQKLKSLSQQLSA-IERElneLNAKEKR 175
                                       233344444444444........555555555666666666666666666666666666666.44442336666666 PP

                      Exonuc_VII_L 214 leelkerl.k..ekleekkerlkklkerlelleekkerleeleeklea 258
                                       ++el  +l k  e+++  +e++kkl+e l++ +++ke+l+ele ++++
  gi|242398545|ref|YP_002993969.1| 176 YNELMLELtKiiESIRLVQEQIKKLEEDLNESKKAKEKLKELEGEIRK 223
                                       6666666644888999999999***999**999999999999988765 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.076
                      Exonuc_VII_L 155 rlekaikrlleekkqrlekl.asrlk.speellerkrqrldeleerleralkkqlkkkrerleelkerlk 222
                                        l +++  ++++  ++lekl +++lk  pe  +e+k+++l+el+e+ +r l++ ++  r++l e++ r++
  gi|242398545|ref|YP_002993969.1| 300 TLVRSTVAQIKKDTEELEKLiSEALKfLPEPTIEAKEKKLKELKEEEKR-LENIVSGLRKELGEVSGRIN 368
                                       1222222233444444444433444445555666666666665555555.55555555555555553332 PP

  == domain 3  score: 13.8 bits;  conditional E-value: 0.00011
                      Exonuc_VII_L 136 elvvpdkaeleeqleelerrlekaikrlleekkqrleklasrlkspeellerkrqrldeleerleralkkq....lk 208
                                       e +v+++++  e+ e+++r ++++i+r  + + +r+e+l++++++ +e+l+++  +l+ + ++l++ l++     ++
  gi|242398545|ref|YP_002993969.1| 410 EEIVKQIRREIEEAENQKRTIKEEIERVSKINVERIEQLQKEIEEMKEKLAKHYTELEGIITELNN-LENDirpkIS 485
                                       5677777777889999999****************************************9998888.4444455588 PP

                      Exonuc_VII_L 209 kkrerleelkerlkekleekkerlkklkerlelleekkerleele 253
                                       + +++++e++erl+e +ee  e+ ++ +++l++l++kke++++l+
  gi|242398545|ref|YP_002993969.1| 486 EIESEIKEIEERLNELIEEIGEKPEDPENELKELRKKKEEYDRLK 530
                                       999999999999976666666666666677777777777666554 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 0.64
                      Exonuc_VII_L 165 eekkqrleklasrlkspeellerkrqrldeleerleralkkqlkkkrerleelkerl.k..ekleekkerlkklker 238
                                       +ek ++le+ +++l++  ++l  ++q+ ++++++ e+ l +++++ +++lee +++l k  ++l+       +++++
  gi|242398545|ref|YP_002993969.1| 547 QEKLRKLENKKHELQEEIKKLGYDKQHHEKVRKEHEE-LLRKFESTKTELEEKTKSLeKnlKDLT-------EVEAE 615
                                       2222233333344444444555555555555444444.444444444444444433322222222.......22222 PP

                      Exonuc_VII_L 239 lelleekkerleeleekleal 259
                                       +++leek+++l++  +k+++l
  gi|242398545|ref|YP_002993969.1| 616 IKELEEKRNNLKAELDKIKKL 636
                                       222333333333222222221 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 ?   14.0   8.0   0.00015     0.044      78     130 ..     105     157 ..      67     161 .. 0.90
   2 ?    1.9  13.6      0.78   2.3e+02      36     138 ..     158     270 ..     153     275 .. 0.44
   3 ?    6.3   0.3     0.035        10      28     109 ..     290     372 ..     276     391 .. 0.46
   4 ?   10.6  15.8    0.0017      0.49      29     129 ..     398     495 ..     393     507 .. 0.54
   5 ?   10.3   7.9    0.0021       0.6      22     124 ..     469     570 ..     468     576 .. 0.90
   6 ?    3.7  15.6      0.22        64      32     128 ..     538     640 ..     527     646 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 0.00015
                                       HHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  78 vikksskeleeeilrlketidaqesnirvLqnvlesneqkiqkLeqdidqker 130
                                       +++++++ele+ei++++ +++++ ++  +L++ +++++++i++L+q+ +++ +
  gi|242398545|ref|YP_002993969.1| 105 YFEQVKNELEKEIAEIEGKLKSKYEQRDKLKQEIQELNRQIKELKQKLKSLSQ 157
                                       789********************************************998876 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.78
                                       HHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH.............HHHHHHHHHHHHHHCCCHHHHHHHC CS
                         Fib_alpha  36 dlekleneleeisnstkeaeelvkeikdslrekqkskkd.............ndnvikksskeleeeilrlketida 99 
                                       +l+ +e+el+e++ ++k  +el+ e+++++++    +++              ++ +k+++ e++ +i  l+e i +
  gi|242398545|ref|YP_002993969.1| 158 QLSAIERELNELNAKEKRYNELMLELTKIIESIRLVQEQikkleedlneskkAKEKLKELEGEIR-KIPLLEEYI-K 232
                                       55555555555555555555554444333332222222111122222111112335666666666.666667766.5 PP

                                       CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSB-EE CS
                         Fib_alpha 100 qesnirvLqnvlesneqkiqkLeqdidqkerkCkepCkd 138
                                       q+++ ++L +  e++e++++k+ ++i +  +k  ++Ck+
  gi|242398545|ref|YP_002993969.1| 233 QFNKFKELNTKKEQLEKDLNKI-SAIREEANKAMKSCKV 270
                                       6666666655555555555554.2444444445555555 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.035
                                       CCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHCCCHHHHHHHCCHHH CS
                         Fib_alpha  28 kyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdn.dnvikksskeleeeilrlketidaqesn 103
                                       + ek++++  + +++++++i++ t+e e+l++e  + l e   ++k++  + +k+ +k+le+ ++ l++++ +   +
  gi|242398545|ref|YP_002993969.1| 290 EIEKSTTTISTLVRSTVAQIKKDTEELEKLISEALKFLPEPTIEAKEKkLKELKEEEKRLENIVSGLRKELGEVSGR 366
                                       33333322222334444444444444444444444444333333332223334444444443334444444444444 PP

                                       HHHHHH CS
                         Fib_alpha 104 irvLqn 109
                                       i+ L++
  gi|242398545|ref|YP_002993969.1| 367 INDLRK 372
                                       444444 PP

  == domain 4  score: 10.6 bits;  conditional E-value: 0.0017
                                       CCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHH CS
                         Fib_alpha  29 yekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnir 105
                                       +++++++++++le+ +++i+++ +eae+  ++ik+ +++  k +    + i++++ke+ee  ++l +  ++ e  i 
  gi|242398545|ref|YP_002993969.1| 398 VKHEMEEEIKSLEEIVKQIRREIEEAENQKRTIKEEIERVSKINV---ERIEQLQKEIEEMKEKLAKHYTELEGIIT 471
                                       556666666666666666666666666666666666555444443...44555555555444444444444445555 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 106 vLqnvlesneqkiqkLeqdidqke 129
                                       +L n+ ++ + ki+++e++i++ e
  gi|242398545|ref|YP_002993969.1| 472 ELNNLENDIRPKISEIESEIKEIE 495
                                       555555555555555555544333 PP

  == domain 5  score: 10.3 bits;  conditional E-value: 0.0021
                                       HHHCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHH CS
                         Fib_alpha  22 lqdlllkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketid 98 
                                       + + l++ e+d++ +++++e+e++ei+++ +e  e + e  +  +++ k+ +++++ + +++   + ++++l e i+
  gi|242398545|ref|YP_002993969.1| 469 IITELNNLENDIRPKISEIESEIKEIEERLNELIEEIGEKPEDPENELKELRKKKEEYDRLKPIAD-RYEKLLEDIK 544
                                       5678999*********************99998888888888888888888889999****99999.********** PP

                                       CCHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  99 aqesnirvLqnvlesneqkiqkLeqd 124
                                       +  +++r+L n  ++++++i+kL  d
  gi|242398545|ref|YP_002993969.1| 545 EAQEKLRKLENKKHELQEEIKKLGYD 570
                                       **********************9765 PP

  == domain 6  score: 3.7 bits;  conditional E-value: 0.22
                                       CCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHCCCHHHHHHH...CCHH CS
                         Fib_alpha  32 dvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnv...ikksskeleeeilrlketid...aqes 102
                                       ++ +d+++ +++l++++n+++e +e +k++    ++++k  k+++++   +++ ++elee+   l+++++   + e 
  gi|242398545|ref|YP_002993969.1| 538 KLLEDIKEAQEKLRKLENKKHELQEEIKKLGYDKQHHEKVRKEHEELlrkFESTKTELEEKTKSLEKNLKdltEVEA 614
                                       56788999999999999999999999999987777777777777555000455567888888888887642213447 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 103 nirvLqnvlesneqkiqkLeqdidqk 128
                                       +i++L +  ++++ ++ k+++  + +
  gi|242398545|ref|YP_002993969.1| 615 EIKELEEKRNNLKAELDKIKKLLNDL 640
                                       88888777777777777777665554 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 ?   12.6   2.0   0.00042      0.12      23      85 ..     133     191 ..     131     202 .. 0.84
   2 ?    0.9   0.1       1.9   5.4e+02      33      51 ..     188     206 ..     172     236 .. 0.44
   3 ?   -0.7   1.0       6.2   1.8e+03      28      46 ..     237     255 ..     197     301 .. 0.63
   4 ?   12.0   0.4   0.00065      0.19      28      77 ..     445     494 ..     439     502 .. 0.88
   5 ?    3.2   0.1      0.37   1.1e+02      29      71 ..     485     527 ..     478     569 .. 0.57
   6 ?    3.5   4.3      0.29        85      22      88 ..     551     620 ..     536     628 .. 0.79
   7 ?    4.2   1.9      0.19        54      21      76 ..     585     639 ..     575     649 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00042
                            DUF948  23 klkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvs 85 
                                       klk+ ++e++++i+el+++++++++++ ++ ++ ne    +n k ++ ++l+ ++ ++ es++
  gi|242398545|ref|YP_002993969.1| 133 KLKQEIQELNRQIKELKQKLKSLSQQLSAIERELNE----LNAKEKRYNELMLELTKIIESIR 191
                                       789999*********************999999999....78888888887777777766664 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 1.9
                            DUF948  33 atieelekqvdpilkeved 51 
                                       ++i+ +++q++++ +++++
  gi|242398545|ref|YP_002993969.1| 188 ESIRLVQEQIKKLEEDLNE 206
                                       2222222333333222222 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 6.2
                            DUF948  28 ldeaaatieelekqvdpil 46 
                                       ++e+++  e+lek++++i+
  gi|242398545|ref|YP_002993969.1| 237 FKELNTKKEQLEKDLNKIS 255
                                       3444444444444444333 PP

  == domain 4  score: 12.0 bits;  conditional E-value: 0.00065
                            DUF948  28 ldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteav 77 
                                       ++++++ iee+++++ +  +e+e+++++ n+l +d++ k+ ++++ ++++
  gi|242398545|ref|YP_002993969.1| 445 IEQLQKEIEEMKEKLAKHYTELEGIITELNNLENDIRPKISEIESEIKEI 494
                                       7899***********************************99998755554 PP

  == domain 5  score: 3.2 bits;  conditional E-value: 0.37
                            DUF948  29 deaaatieelekqvdpilkevedllakvnelledvneklekvd 71 
                                       +e+++ i+e+e++++++++e+ +  +  ++ l+++++k e+ d
  gi|242398545|ref|YP_002993969.1| 485 SEIESEIKEIEERLNELIEEIGEKPEDPENELKELRKKKEEYD 527
                                       5555666666666666666655555544444444444444333 PP

  == domain 6  score: 3.5 bits;  conditional E-value: 0.29
                            DUF948  22 lklkktldeaaatieele...kqvdpilkevedllakvnelledvneklekvdplteavadlgesvseln 88 
                                       +kl++   e+++ i++l+   ++ +++ ke e+ll+k + +  +++ek++++++  + + ++ + ++el+
  gi|242398545|ref|YP_002993969.1| 551 RKLENKKHELQEEIKKLGydkQHHEKVRKEHEELLRKFESTKTELEEKTKSLEKNLKDLTEVEAEIKELE 620
                                       4555555566666666667777888899999999999999999999999999999999999999988885 PP

  == domain 7  score: 4.2 bits;  conditional E-value: 0.19
                            DUF948  21 llklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdpltea 76 
                                       l+k ++t +e+++  ++lek+++ ++ eve+ +++ +e  ++++ +l+k+++l + 
  gi|242398545|ref|YP_002993969.1| 585 LRKFESTKTELEEKTKSLEKNLKDLT-EVEAEIKELEEKRNNLKAELDKIKKLLND 639
                                       44555555566666666665555543.34444444444444455566666655554 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   8.1     0.027       7.8      15      60 ..     113     159 ..     100     180 .. 0.52
   2 ?    4.9  14.5      0.12        34       2      98 ..     149     249 ..     148     252 .. 0.69
   3 ?    3.1   1.1      0.42   1.2e+02      15      57 ..     227     269 ..     214     276 .. 0.70
   4 ?   11.5   3.5     0.001       0.3       4      95 ..     287     418 ..     275     424 .. 0.67
   5 ?   12.3   2.2   0.00059      0.17       2      97 ..     357     456 ..     356     468 .. 0.71
   6 ?    4.4  12.4      0.17        50      12      98 ..     470     562 ..     440     565 .. 0.56
   7 ?    7.3  12.1     0.021         6      20      99 ..     517     601 ..     513     603 .. 0.69
   8 ?    6.7   5.8     0.033       9.6       3      75 ..     583     660 ..     581     671 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.027
                        Syntaxin_2  15 leklvkqLgtk.kdteelreklhelieeinelikktnellkklsqld 60 
                                       lek +  ++ k k   e r+kl++ i+e+n+ ik+ +++lk+lsq  
  gi|242398545|ref|YP_002993969.1| 113 LEKEIAEIEGKlKSKYEQRDKLKQEIQELNRQIKELKQKLKSLSQQL 159
                                       44555555554433444455555555555555555555555555432 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.12
                        Syntaxin_2   2 ssnlqkinsnvstleklvkqLgtk.kdteelreklhelieeinelikktnellkklsqldnsssds...qqklqkek 74 
                                       +++l+++++++s +e+ ++ L+ k k   el  +l ++ie+i+ + +++++l ++l++ ++ +++       + k  
  gi|242398545|ref|YP_002993969.1| 149 KQKLKSLSQQLSAIERELNELNAKeKRYNELMLELTKIIESIRLVQEQIKKLEEDLNESKKAKEKLkelEGEIRKIP 225
                                       57899*******************54689999777777777666666666666666665555543344466666667 PP

                        Syntaxin_2  75 LkkdfkealqeFqkiqrqyaekek 98 
                                       L +++ +  ++F+++  + ++ ek
  gi|242398545|ref|YP_002993969.1| 226 LLEEYIKQFNKFKELNTKKEQLEK 249
                                       777777777777777776666666 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.42
                        Syntaxin_2  15 leklvkqLgtkkdteelreklhelieeinelikktnellkkls 57 
                                       le+++kq ++ k+    +e+l++  ++i+ + ++ n+ +k+++
  gi|242398545|ref|YP_002993969.1| 227 LEEYIKQFNKFKELNTKKEQLEKDLNKISAIREEANKAMKSCK 269
                                       6777777777777666677777777777777777777776655 PP

  == domain 4  score: 11.5 bits;  conditional E-value: 0.001
                        Syntaxin_2   4 nlqkinsnvstleklvkqLgtk..kdteelr.............................eklhelieeinelikkt 49 
                                        l++i ++++t+  lv++   +  kdteel                              +          +l + +
  gi|242398545|ref|YP_002993969.1| 287 DLSEIEKSTTTISTLVRSTVAQikKDTEELEklisealkflpeptieakekklkelkeeeK----------RLENIV 353
                                       5677777777777777774443447888888888888888888888888844444444442..........444444 PP

                        Syntaxin_2  50 nellkklsqldnsssds................qqkl...qkekLkkdfkealqeFqkiqrqyae 95 
                                       + l k+l +++   +d                 + kl    +++ k++++e ++++++i++q+++
  gi|242398545|ref|YP_002993969.1| 354 SGLRKELGEVSGRINDLrkaldmlgeseacpvcKTKLtpeHRDRVKHEMEEEIKSLEEIVKQIRR 418
                                       44444444433333333334444444566779977776889*********************986 PP

  == domain 5  score: 12.3 bits;  conditional E-value: 0.00059
                        Syntaxin_2   2 ssnlqkinsnvstleklvkqLgtkkd........teelrekl.helieeinelikktnellkklsqldnsssdsqqk 69 
                                        ++l ++++ ++ l+k ++ Lg +          t+e r+++ he+ eei+ l + +++  +++++ +n+     ++
  gi|242398545|ref|YP_002993969.1| 357 RKELGEVSGRINDLRKALDMLGESEAcpvcktklTPEHRDRVkHEMEEEIKSLEEIVKQIRREIEEAENQ-----KR 428
                                       5788899999**************6655555566888888876666666666666666666666666664.....46 PP

                        Syntaxin_2  70 lqkekLkkdfkealqeFqkiqrqyaeke 97 
                                       ++ke + +  k  +++ +++q++++e +
  gi|242398545|ref|YP_002993969.1| 429 TIKEEIERVSKINVERIEQLQKEIEEMK 456
                                       6777777777777777777777776654 PP

  == domain 6  score: 4.4 bits;  conditional E-value: 0.17
                        Syntaxin_2  12 vstleklvkqLgtk.....kdteelreklhelieeinelikktnellkklsqldnsssds.......qqkl..qkek 74 
                                       +++l++l +++  k      + +e+ e+l+elieei e  ++ ++ lk+l +       +       +  +    ek
  gi|242398545|ref|YP_002993969.1| 470 ITELNNLENDIRPKiseieSEIKEIEERLNELIEEIGEKPEDPENELKELRK-------KkeeydrlKP-IadRYEK 538
                                       2333333333322222222235555566666666666666666666666665.......0444444433.34788** PP

                        Syntaxin_2  75 LkkdfkealqeFqkiqrqyaekek 98 
                                       L +d+kea +++ k+ ++  e + 
  gi|242398545|ref|YP_002993969.1| 539 LLEDIKEAQEKLRKLENKKHELQE 562
                                       ************999888777665 PP

  == domain 7  score: 7.3 bits;  conditional E-value: 0.021
                        Syntaxin_2  20 kqLgtkkdteelreklhelieeinelikktnellkklsqldnsssds.....qqklqkekLkkdfkealqeFqkiqr 91 
                                       k L +kk+  +  + + +  e++ e ik+ +e+l+kl++ ++ ++ +       k  +ek +k+ +e+l++F+++  
  gi|242398545|ref|YP_002993969.1| 517 KELRKKKEEYDRLKPIADRYEKLLEDIKEAQEKLRKLENKKHELQEEikklgYDKQHHEKVRKEHEELLRKFESTKT 593
                                       555555554444455566666666666666666666666666665555555555559******************** PP

                        Syntaxin_2  92 qyaekekq 99 
                                       + +ek+k+
  gi|242398545|ref|YP_002993969.1| 594 ELEEKTKS 601
                                       *****996 PP

  == domain 8  score: 6.7 bits;  conditional E-value: 0.033
                        Syntaxin_2   3 snlqkinsnvstleklvkqLgtk.kdteelreklhelieeinel...ikktnellkklsqldnsssds.qqklqkek 74 
                                       + l k+ s  ++le+++k+L+++ kd +e+  +++el e+ n+l   + k+++ll++l+++ +  + +  q+l ++k
  gi|242398545|ref|YP_002993969.1| 583 ELLRKFESTKTELEEKTKSLEKNlKDLTEVEAEIKELEEKRNNLkaeLDKIKKLLNDLERIRRAYHRDgVQRLLRQK 659
                                       57889999999************99*999998887777776666222678899999999998877655777777777 PP

                        Syntaxin_2  75 L 75 
                                       +
  gi|242398545|ref|YP_002993969.1| 660 I 660
                                       6 PP

>> T3SSipB  Type III cell invasion protein SipB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   4.2    0.0092       2.7      50     106 ..     112     165 ..      89     181 .. 0.59
   2 ?    6.9   5.6     0.028         8      52     142 ..     173     266 ..     157     275 .. 0.82
   3 ?    3.6   0.3      0.29        85      21      93 ..     289     363 ..     284     391 .. 0.61
   4 ?    3.9   1.1      0.23        67      37      90 ..     405     459 ..     393     466 .. 0.68
   5 ?    3.8   0.4      0.25        73      34     101 ..     449     515 ..     441     528 .. 0.64
   6 ?    6.9   8.8     0.027       7.9      53     134 ..     527     607 ..     519     630 .. 0.71
   7 ?    4.3   3.0      0.17        50      38      93 ..     578     633 ..     571     653 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0092
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---------CHHHH CS
                           T3SSipB  50 talseakgatddleaaiekadqaksaadaatkkvdeaqkrlkeLaPdePekakleaa 106
                                       ++ +e +++  +l+ + e+ d++k+++++++++++e +++lk+L   + +  ++e++
  gi|242398545|ref|YP_002993969.1| 112 ELEKEIAEIEGKLKSKYEQRDKLKQEIQELNRQIKELKQKLKSL---SQQLSAIERE 165
                                       44455666666666666666666666666666666666666666...3333333333 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.028
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...HHTT---------CHHHHHHHHH..HHHHHHHHHHHH CS
                           T3SSipB  52 lseakgatddleaaiekadqaksaadaatkkvdeaqk...rlkeLaPdePekakleaaeqQagaaadalqadealqK 125
                                        +  +++  +l++ ie +  ++ +++++++ ++e +k   +lkeL+ +  +   le+  +Q ++ ++   ++e+l+K
  gi|242398545|ref|YP_002993969.1| 173 EKRYNELMLELTKIIESIRLVQEQIKKLEEDLNESKKakeKLKELEGEIRKIPLLEEYIKQFNKFKELNTKKEQLEK 249
                                       455667777899999999999********99998766666*****77666677788899999978************ PP

                                       HHHHHHHHHHHHHHHHH CS
                           T3SSipB 126 kldaasklsekakakek 142
                                        l+  s+++e+a +  k
  gi|242398545|ref|YP_002993969.1| 250 DLNKISAIREEANKAMK 266
                                       **********9976655 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.29
                                       HHHHHHHHHHHHHHHHTTTTT----STHHHHHHHHHHH..HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT- CS
                           T3SSipB  21 sqLenrlaawkamskaqqeaasklSdelqtalseakga..tddleaaiekadqaksaadaatkkvdeaqkrlkeL 93 
                                       s++e+  ++     ++++++ +k  +el++++sea +      +ea+ +k++++k + + +++ v+   k l e+
  gi|242398545|ref|YP_002993969.1| 289 SEIEKSTTTISTLVRSTVAQIKKDTEELEKLISEALKFlpEPTIEAKEKKLKELKEEEKRLENIVSGLRKELGEV 363
                                       555555555555555666666666666666666665541133456666666666666666666666666666555 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.23
                                       TTTTT----STHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHH CS
                           T3SSipB  37 qqeaasklSdelqtalseakgatddleaaiekadqak.saadaatkkvdeaqkrl 90 
                                       + + ++++ +++++ ++ea++ ++ +++ ie++ +++   +++++k ++e +++l
  gi|242398545|ref|YP_002993969.1| 405 EIKSLEEIVKQIRREIEEAENQKRTIKEEIERVSKINvERIEQLQKEIEEMKEKL 459
                                       4455666777777777777777777777777777766245777777777777776 PP

  == domain 5  score: 3.8 bits;  conditional E-value: 0.25
                                       HHHTTTTT----STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--------- CS
                           T3SSipB  34 skaqqeaasklSdelqtalseakgatddleaaiekadqaksaadaatkkvdeaqkrlkeLaPdePeka 101
                                       +k  +e+++kl ++  ++ +   ++ +  ++   k+ +++s++++ +++++e  + + e  P++Pe  
  gi|242398545|ref|YP_002993969.1| 449 QKEIEEMKEKLAKHYTELEGIITELNNLENDIRPKISEIESEIKEIEERLNELIEEIGEK-PEDPENE 515
                                       444444555555555555555555555555556678888999999999999999988887.9999753 PP

  == domain 6  score: 6.9 bits;  conditional E-value: 0.027
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---------CHHHHHHHHH..HHHHHHHHHHHHHHHH CS
                           T3SSipB  53 seakgatddleaaiekadqaksaadaatkkvdeaqkrlkeLaPdePekakleaaeqQagaaadalqadealqKklda 129
                                       +  k ++d +e+  e +++a+ +  ++++k  e q+ +k+L  d+  + k++++++ +  + ++++ +   +K+ + 
  gi|242398545|ref|YP_002993969.1| 527 DRLKPIADRYEKLLEDIKEAQEKLRKLENKKHELQEEIKKLGYDKQHHEKVRKEHEELLRKFESTKTEL-EEKTKSL 602
                                       556678899999999999999999999999999999999999999999999999999988855554433.2333333 PP

                                       HHHHH CS
                           T3SSipB 130 askls 134
                                        + l+
  gi|242398545|ref|YP_002993969.1| 603 EKNLK 607
                                       33333 PP

  == domain 7  score: 4.3 bits;  conditional E-value: 0.17
                                       TTTT----STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT- CS
                           T3SSipB  38 qeaasklSdelqtalseakgatddleaaiekadqaksaadaatkkvdeaqkrlkeL 93 
                                       +++ ++l  +++    e ++ t+ le+  + + +++++++++++k ++ ++ l+++
  gi|242398545|ref|YP_002993969.1| 578 RKEHEELLRKFESTKTELEEKTKSLEKNLKDLTEVEAEIKELEEKRNNLKAELDKI 633
                                       55667788889999999999999999999999999999999999999988877766 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0  23.1    0.0067         2      12     118 ..      90     189 ..      85     199 .. 0.74
   2 ?    2.7  15.4      0.58   1.7e+02      29      95 ..     194     262 ..     176     269 .. 0.73
   3 ?    5.4   9.7     0.087        25      19      98 ..     307     381 ..     258     384 .. 0.78
   4 ?    5.4  28.1     0.085        25      32     118 ..     516     601 ..     498     603 .. 0.78
   5 ?    8.1  18.8     0.013       3.7      22     104 ..     575     650 ..     569     660 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0067
                            APG6_N  12 eeldkqleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaale 88 
                                       e+l+k  + +++ +  +e+  ++l+ke  e e    +l++  e+ +kl++e +el +++kel+++ ++l ++l+a+e
  gi|242398545|ref|YP_002993969.1|  90 EKLEKAWQFMREVIYYFEQVKNELEKEIAEIE---GKLKSKYEQRDKLKQEIQELNRQIKELKQKLKSLSQQLSAIE 163
                                       56666666666666677777788888876665...688888888888999999999999999999999999999999 PP

                            APG6_N  89 eelealeeeeerfwreynelqlelleleee 118
                                       +el++l+++e+r    ynel lel++  e 
  gi|242398545|ref|YP_002993969.1| 164 RELNELNAKEKR----YNELMLELTKIIES 189
                                       999999999976....46666666665555 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.58
                            APG6_N  29 eeflkklkkekkeeekqdeeleeleeelek..lekeeeelleeLkelekereeleaelaaleeeleale 95 
                                       +e  kkl+++ +e++k +e+l+ele e++k  l +e  + +++ kel +++e+le++l+++++  e+ +
  gi|242398545|ref|YP_002993969.1| 194 QEQIKKLEEDLNESKKAKEKLKELEGEIRKipLLEEYIKQFNKFKELNTKKEQLEKDLNKISAIREEAN 262
                                       33344444444444445679**********88999999*********************9998777655 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.087
                            APG6_N  19 eqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeeleale 95 
                                       +q +k+ +++e+  ++  k        +  +e+ e++l++l++ee++l++    l ke  e+   +++l++ l+ l 
  gi|242398545|ref|YP_002993969.1| 307 AQIKKDTEELEKLISEALKFL-----PEPTIEAKEKKLKELKEEEKRLENIVSGLRKELGEVSGRINDLRKALDMLG 378
                                       333444444444443333332.....45679999999*************************999999999999988 PP

                            APG6_N  96 eee 98 
                                       e e
  gi|242398545|ref|YP_002993969.1| 379 ESE 381
                                       877 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.085
                            APG6_N  32 lkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaal...eeelealeeeeerfwrey 105
                                       lk+l+k+k+e     + l+ + +++ekl ++ +e++e+L++le+++ el++e+++l   ++ +e++ +e e+ +r++
  gi|242398545|ref|YP_002993969.1| 516 LKELRKKKEE----YDRLKPIADRYEKLLEDIKEAQEKLRKLENKKHELQEEIKKLgydKQHHEKVRKEHEELLRKF 588
                                       6777777555....4599999999*******************************9444566666777777777777 PP

                            APG6_N 106 nelqlelleleee 118
                                        + ++el+e+ + 
  gi|242398545|ref|YP_002993969.1| 589 ESTKTELEEKTKS 601
                                       7777777776654 PP

  == domain 5  score: 8.1 bits;  conditional E-value: 0.013
                            APG6_N  22 ekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeee 98 
                                       ek r++ ee l+k++++k       +elee  ++lek  k+  e ++e+kele++r +l+ael ++++ l++le+  
  gi|242398545|ref|YP_002993969.1| 575 EKVRKEHEELLRKFESTK-------TELEEKTKSLEKNLKDLTEVEAEIKELEEKRNNLKAELDKIKKLLNDLERIR 644
                                       445555566666666663.......3455556666666666666666777777777777777777777777777666 PP

                            APG6_N  99 erfwre 104
                                       +++ r+
  gi|242398545|ref|YP_002993969.1| 645 RAYHRD 650
                                       666655 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 ?    7.4   2.8     0.012       3.5      87     156 ..     109     178 ..      99     194 .. 0.86
   2 ?    2.5   0.2      0.38   1.1e+02      97     140 ..     182     224 ..     171     236 .. 0.80
   3 ?    6.4   2.2     0.025       7.1      78     154 ..     238     312 ..     234     329 .. 0.78
   4 ?    0.7   0.1       1.4   4.1e+02      96     161 ..     307     370 ..     302     380 .. 0.39
   5 ?    4.5   6.5     0.094        27      98     162 ..     398     467 ..     393     477 .. 0.57
   6 ?    4.1   0.3      0.12        36      78     153 ..     474     549 ..     467     569 .. 0.69
   7 ?   11.2   1.6   0.00083      0.24      77     162 ..     550     634 ..     546     645 .. 0.56

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.012
                                       HHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  87 aakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsa 156
                                         +e+e+ i+ei+ + ++  e  ++ +q+++e   +++e +++lk+++++ + ++ +++e++a  +   +
  gi|242398545|ref|YP_002993969.1| 109 VKNELEKEIAEIEGKLKSKYEQRDKLKQEIQELNRQIKELKQKLKSLSQQLSAIERELNELNAKEKRYNE 178
                                       56899999****************************************************9987766555 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.38
                                       .............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHH CS
                         MCPsignal  97 eiqkeindsvesleetrqrveegselveetgealkeiveavaev 140
                                       e++k   +s++ ++e  ++ ee +++ ++++e+lke+  ++ ++
  gi|242398545|ref|YP_002993969.1| 182 ELTKI-IESIRLVQEQIKKLEEDLNESKKAKEKLKELEGEIRKI 224
                                       55443.4688999999999***************9999999887 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.025
                                       HHHHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  78 rkLAersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeq 154
                                       ++L ++  q  k+++++  +i +e n++++s +  ++ +e+g e +e   ++l+ei ++++ +++lv+   a  ++ 
  gi|242398545|ref|YP_002993969.1| 238 KELNTKKEQLEKDLNKI-SAIREEANKAMKSCKVYVEYIEVGEEFIEV-PTDLSEIEKSTTTISTLVRSTVAQIKKD 312
                                       56667777777777775.59**********************999975.678************9998655444443 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 1.4
                                       ..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  96 ieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasieev 161
                                       ++i+k++++  + ++e+ +   e   ++e  +++lke+ e+ ++++++v+ + +   e s  i++ 
  gi|242398545|ref|YP_002993969.1| 307 AQIKKDTEELEKLISEALKFLPE--PTIEAKEKKLKELKEEEKRLENIVSGLRKELGEVSGRINDL 370
                                       34444444444444443333322..22333344444444444444444444444443333333333 PP

  == domain 5  score: 4.5 bits;  conditional E-value: 0.094
                                       ............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHH.....HHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  98 iqkeindsvesleetrqrveegselveetgealkeiveavaev.....adlvqeiaaaseeqsasieevn 162
                                       +++e+++ ++slee ++++    e++e+ ++++ke  e+v+++     ++l +ei    e++++  +e  
  gi|242398545|ref|YP_002993969.1| 398 VKHEMEEEIKSLEEIVKQIRREIEEAENQKRTIKEEIERVSKInveriEQLQKEIEEMKEKLAKHYTELE 467
                                       5677777777777777777777777777766666666655554100004444555555555555555554 PP

  == domain 6  score: 4.1 bits;  conditional E-value: 0.12
                                       HHHHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  78 rkLAersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaasee 153
                                        +L +    +  eie+ i+ei++  n+ +e + e  +  e+ +++ ++ +e+  ++   +++ ++l+++i+ a e+
  gi|242398545|ref|YP_002993969.1| 474 NNLENDIRPKISEIESEIKEIEERLNELIEEIGEKPEDPENELKELRKKKEEYDRLKPIADRYEKLLEDIKEAQEK 549
                                       5566666667789999999999999999999999999999999998888876555555555555555555555444 PP

  == domain 7  score: 11.2 bits;  conditional E-value: 0.00083
                                       HHHHHHHHHHHHHHHHHHH....................HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  77 VrkLAersaqaakeieali......ieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqei 147
                                        rkL ++  +  +ei++l       +++ ke ++ ++ +e+t+++ ee ++  e+  ++l e+ ++++e+++  +++
  gi|242398545|ref|YP_002993969.1| 550 LRKLENKKHELQEEIKKLGydkqhhEKVRKEHEELLRKFESTKTELEEKTKSLEKNLKDLTEVEAEIKELEEKRNNL 626
                                       68888888888888888761111114555555555556666666666665555655555555555555555555555 PP

                                       HHHHHHHHHHHHHHH CS
                         MCPsignal 148 aaaseeqsasieevn 162
                                       +a        ++++ 
  gi|242398545|ref|YP_002993969.1| 627 KA-------ELDKIK 634
                                       54.......444444 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 ?   12.9   1.5   0.00034     0.098      24      83 ..     107     168 ..      90     171 .. 0.78
   2 ?   -0.7   0.0       5.9   1.7e+03      14      38 ..     340     364 ..     333     378 .. 0.72
   3 ?    2.5   0.1       0.6   1.7e+02       3      37 ..     389     423 ..     387     437 .. 0.79
   4 ?    3.8   0.1      0.23        66      49      79 ..     448     478 ..     442     482 .. 0.74
   5 ?   -1.0   0.0       7.4   2.1e+03      14      34 ..     485     502 ..     478     508 .. 0.44
   6 ?    6.4   0.2     0.036        11      11      85 ..     541     613 ..     525     614 .. 0.72
   7 ?    1.9   0.0      0.93   2.7e+02       8      37 ..     611     640 ..     607     643 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00034
                                       HHHHHHHHHHHHHCGCGCTHH..HCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  24 edelqrlkaevdalqsgWsGa..aadafqaefeewkqaaqklvdaLeeisealkqaanafed 83 
                                       e++ ++l++e+++++++ + +   +d+ ++e++e+++++++l+++L+++s++l ++ +++ +
  gi|242398545|ref|YP_002993969.1| 107 EQVKNELEKEIAEIEGKLKSKyeQRDKLKQEIQELNRQIKELKQKLKSLSQQLSAIERELNE 168
                                       56666777777777776664322788999*************************99988765 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 5.9
                                       HHHHHHHHHHHHHHHHHHHHHHHCG CS
                            WXG100  14 arfqkqaeeledelqrlkaevdalq 38 
                                       +++++++++le++++ l++e+ +++
  gi|242398545|ref|YP_002993969.1| 340 KELKEEEKRLENIVSGLRKELGEVS 364
                                       5666777777777777777776653 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.6
                                       CSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                            WXG100   3 kvdpeelrqaaarfqkqaeeledelqrlkaevdal 37 
                                       k +pe  + +  ++ ++ ++le++++++++e+++ 
  gi|242398545|ref|YP_002993969.1| 389 KLTPEHRDRVKHEMEEEIKSLEEIVKQIRREIEEA 423
                                       56777777788888888889999999999888876 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.23
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  49 fqaefeewkqaaqklvdaLeeisealkqaan 79 
                                        q+e+ee+k++++k +++Le+i  +l++  n
  gi|242398545|ref|YP_002993969.1| 448 LQKEIEEMKEKLAKHYTELEGIITELNNLEN 478
                                       4677788888888888888888888877665 PP

  == domain 5  score: -1.0 bits;  conditional E-value: 7.4
                                       HHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  14 arfqkqaeeledelqrlkaev 34 
                                       +++ ++ +e+e++l++l   +
  gi|242398545|ref|YP_002993969.1| 485 SEIESEIKEIEERLNEL---I 502
                                       33333344444444433...3 PP

  == domain 6  score: 6.4 bits;  conditional E-value: 0.036
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHCGCGCTHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  11 qaaarfqkqaeeledelqrlkaevdalqsgWsGaaadafqaefeewkqaaqklvdaLeeisealkqaanafedaD 85 
                                       + ++++q++  +le+   +l+ e+++l  g+  +  ++ ++e ee+ ++++  +++Lee +++l+++ + +++++
  gi|242398545|ref|YP_002993969.1| 541 EDIKEAQEKLRKLENKKHELQEEIKKL--GYDKQHHEKVRKEHEELLRKFESTKTELEEKTKSLEKNLKDLTEVE 613
                                       444444444444444444444444444..8999999999999999999999999999999999999888888776 PP

  == domain 7  score: 1.9 bits;  conditional E-value: 0.93
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                            WXG100   8 elrqaaarfqkqaeeledelqrlkaevdal 37 
                                       e+++ ++++ +++++l++el+++k+ +++l
  gi|242398545|ref|YP_002993969.1| 611 EVEAEIKELEEKRNNLKAELDKIKKLLNDL 640
                                       566777777777777777777777777666 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 ?   -0.7   0.1       6.4   1.8e+03      55      95 ..      77     117 ..      67     118 .. 0.77
   2 ?    7.5  11.6     0.017       4.8      41      94 ..     119     165 ..      90     172 .. 0.56
   3 ?    7.6   6.9     0.017       4.8      34      86 ..     150     202 ..     149     206 .. 0.82
   4 ?    1.7   5.3       1.1   3.2e+02      39      77 ..     186     224 ..     173     238 .. 0.53
   5 ?    4.6   1.8      0.13        39      48      74 ..     235     261 ..     221     270 .. 0.80
   6 ?    4.6   0.4      0.14        39      35      82 ..     273     321 ..     267     323 .. 0.87
   7 ?    2.0   0.2      0.88   2.5e+02      36      64 ..     346     374 ..     330     381 .. 0.43
   8 ?    8.7   9.0    0.0075       2.2      29      89 ..     399     457 ..     393     463 .. 0.80
   9 ?    6.4   5.2     0.039        11      23      77 ..     450     501 ..     441     507 .. 0.56
  10 ?    1.5  11.4       1.3   3.7e+02      33      95 ..     533     606 ..     516     607 .. 0.65
  11 ?    7.6   8.0     0.017       4.8      42      84 ..     584     626 ..     570     647 .. 0.57

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 6.4
                           BLOC1_2  55 ekyeelqpylqqidqiekqvteLeeavseLDeyskeLEakf 95 
                                       +k +e+   l  ++++ek  + + e+++  ++   eLE+ +
  gi|242398545|ref|YP_002993969.1|  77 AKRKEVIGRLLGLEKLEKAWQFMREVIYYFEQVKNELEKEI 117
                                       55666666666789999999999999999999999999865 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.017
                           BLOC1_2  41 dvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeLEak 94 
                                       ++         kl++kye+ ++++q+i+++++q++eL++  + L +  +++E  
  gi|242398545|ref|YP_002993969.1| 119 EIE-------GKLKSKYEQRDKLKQEIQELNRQIKELKQKLKSLSQQLSAIERE 165
                                       222.......34555555555555555555555555555555555555555543 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.017
                           BLOC1_2  34 ekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDe 86 
                                       +k k+l+++++ +e++l++ln+k++  ++++ ++ +i ++++  +e +++L+e
  gi|242398545|ref|YP_002993969.1| 150 QKLKSLSQQLSAIERELNELNAKEKRYNELMLELTKIIESIRLVQEQIKKLEE 202
                                       57788888888999999999999988888888888888888888888888876 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 1.1
                           BLOC1_2  39 lkdvaaslekkleklnekyeelqpylqqidqiekqvteL 77 
                                       + +++  ++++++kl+e  +e ++ +++++++e +++++
  gi|242398545|ref|YP_002993969.1| 186 IIESIRLVQEQIKKLEEDLNESKKAKEKLKELEGEIRKI 224
                                       334444445556666666666666666666666666553 PP

  == domain 5  score: 4.6 bits;  conditional E-value: 0.13
                           BLOC1_2  48 kkleklnekyeelqpylqqidqiekqv 74 
                                       +k+++ln k+e+l++ l++i +i ++ 
  gi|242398545|ref|YP_002993969.1| 235 NKFKELNTKKEQLEKDLNKISAIREEA 261
                                       357899999999999999999998875 PP

  == domain 6  score: 4.6 bits;  conditional E-value: 0.14
                           BLOC1_2  35 kykklkdvaaslekkleklnekyeelqpylq.qidqiekqvteLeeavs 82 
                                       +y ++ ++  ++ ++l+++++   +++ +++  + qi+k+++eLe+++s
  gi|242398545|ref|YP_002993969.1| 273 EYIEVGEEFIEVPTDLSEIEKSTTTISTLVRsTVAQIKKDTEELEKLIS 321
                                       7999999999999999999999999999875279***********9987 PP

  == domain 7  score: 2.0 bits;  conditional E-value: 0.88
                           BLOC1_2  36 ykklkdvaaslekkleklnekyeelqpyl 64 
                                        k l++++++l+k+l +++ + + l++ l
  gi|242398545|ref|YP_002993969.1| 346 EKRLENIVSGLRKELGEVSGRINDLRKAL 374
                                       23333444444444444444333333333 PP

  == domain 8  score: 8.7 bits;  conditional E-value: 0.0075
                           BLOC1_2  29 NeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeysk 89 
                                        ++++e++k+l+++++++++++e+ ++++ ++++ ++++ +i+  v+++e++ +e++e+  
  gi|242398545|ref|YP_002993969.1| 399 KHEMEEEIKSLEEIVKQIRREIEEAENQKRTIKEEIERVSKIN--VERIEQLQKEIEEMKE 457
                                       578899************************************6..4555555555555444 PP

  == domain 9  score: 6.4 bits;  conditional E-value: 0.039
                           BLOC1_2  23 klLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteL 77 
                                       k +e++ e+ +++y++l+ ++ +l++  ++++    ++++  ++i++ie++++eL
  gi|242398545|ref|YP_002993969.1| 450 KEIEEMKEKLAKHYTELEGIITELNNLENDIRP---KISEIESEIKEIEERLNEL 501
                                       345566666666666666666666666666655...4444455555666666555 PP

  == domain 10  score: 1.5 bits;  conditional E-value: 1.3
                           BLOC1_2  33 sekykklkdvaaslekkleklnekyeelqpylqqi...........dqiekqvteLeeavseLDeyskeLEakf 95 
                                       + +y+kl + ++++++kl kl++k++elq+ ++++           ++ e+ ++++e++  eL+e +k+LE+++
  gi|242398545|ref|YP_002993969.1| 533 ADRYEKLLEDIKEAQEKLRKLENKKHELQEEIKKLgydkqhhekvrKEHEELLRKFESTKTELEEKTKSLEKNL 606
                                       56788888888888888888888888888888877444333322222334445566777777777777777665 PP

  == domain 11  score: 7.6 bits;  conditional E-value: 0.017
                           BLOC1_2  42 vaaslekkleklnekyeelqpylqqidqiekqvteLeeavseL 84 
                                        + ++e++  +l+ek ++l+++l+ + ++e++++eLee  + L
  gi|242398545|ref|YP_002993969.1| 584 LLRKFESTKTELEEKTKSLEKNLKDLTEVEAEIKELEEKRNNL 626
                                       4455555555566666666666666666666666666543332 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   2.6   0.00046      0.13       3      36 ..     132     165 ..     130     178 .. 0.81
   2 ?    3.3   0.3      0.37   1.1e+02       9      35 ..     190     216 ..     182     217 .. 0.81
   3 ?    4.5   0.2      0.16        47      10      39 ..     238     263 ..     234     266 .. 0.75
   4 ?    0.1   0.0       3.8   1.1e+03       5      30 ..     349     374 ..     336     380 .. 0.73
   5 ?    6.5   0.6     0.039        11       5      39 ..     402     436 ..     400     439 .. 0.92
   6 ?    1.8   0.4       1.1   3.3e+02      11      32 ..     447     461 ..     437     505 .. 0.58
   7 ?   -0.4   0.1       5.3   1.5e+03       8      31 ..     542     565 ..     534     575 .. 0.56
   8 ?    2.8   0.2      0.54   1.6e+02       3      28 ..     610     635 ..     598     644 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00046
                               LPP   3 deLssqVsqLkskvdqlssdvnsakaaaqaakeE 36 
                                       d+L +++++L++++++l+++++s+++++ a+  E
  gi|242398545|ref|YP_002993969.1| 132 DKLKQEIQELNRQIKELKQKLKSLSQQLSAIERE 165
                                       7888888999999999998888888888887766 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.37
                               LPP   9 VsqLkskvdqlssdvnsakaaaqaake 35 
                                       +   ++++++l++d+n++k+a ++ ke
  gi|242398545|ref|YP_002993969.1| 190 IRLVQEQIKKLEEDLNESKKAKEKLKE 216
                                       556689*************99988776 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.16
                               LPP  10 sqLkskvdqlssdvnsakaaaqaakeEAaR 39 
                                       ++L++k +ql++d+n+++a    ++eEA+ 
  gi|242398545|ref|YP_002993969.1| 238 KELNTKKEQLEKDLNKISA----IREEANK 263
                                       689**********998764....5555554 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 3.8
                               LPP   5 LssqVsqLkskvdqlssdvnsakaaa 30 
                                       L + Vs L ++  ++s  +n++++a+
  gi|242398545|ref|YP_002993969.1| 349 LENIVSGLRKELGEVSGRINDLRKAL 374
                                       55567777777777777777777765 PP

  == domain 5  score: 6.5 bits;  conditional E-value: 0.039
                               LPP   5 LssqVsqLkskvdqlssdvnsakaaaqaakeEAaR 39 
                                       + +++++L++ v+q+  ++++a+++  ++keE +R
  gi|242398545|ref|YP_002993969.1| 402 MEEEIKSLEEIVKQIRREIEEAENQKRTIKEEIER 436
                                       66899***************************888 PP

  == domain 6  score: 1.8 bits;  conditional E-value: 1.1
                               LPP  11 qLkskvdqlssdvnsakaaaqa 32 
                                       qL+++++++++++       ++
  gi|242398545|ref|YP_002993969.1| 447 QLQKEIEEMKEKL-------AK 461
                                       3333333333332.......22 PP

  == domain 7  score: -0.4 bits;  conditional E-value: 5.3
                               LPP   8 qVsqLkskvdqlssdvnsakaaaq 31 
                                       ++++ ++k  +l+++  +++++++
  gi|242398545|ref|YP_002993969.1| 542 DIKEAQEKLRKLENKKHELQEEIK 565
                                       555555555555555555444444 PP

  == domain 8  score: 2.8 bits;  conditional E-value: 0.54
                               LPP   3 deLssqVsqLkskvdqlssdvnsaka 28 
                                       +e+ +++++L++k ++l+++++++k+
  gi|242398545|ref|YP_002993969.1| 610 TEVEAEIKELEEKRNNLKAELDKIKK 635
                                       56677888888888888888887775 PP

>> SKA1  Spindle and kinetochore-associated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   7.7    0.0064       1.9       9      91 ..      87     169 ..      81     180 .. 0.76
   2 ?    4.7  11.2     0.079        23      15      96 ..     174     253 ..     163     286 .. 0.65
   3 ?    1.7   2.3      0.67   1.9e+02      34      69 ..     290     325 ..     277     369 .. 0.48
   4 ?    1.5   0.3      0.77   2.2e+02      21      64 ..     335     378 ..     329     400 .. 0.75
   5 ?    8.5   9.2    0.0057       1.6      20      80 ..     394     455 ..     381     467 .. 0.83
   6 ?    4.2  12.9      0.11        32      20     122 ..     479     582 ..     464     597 .. 0.73
   7 ?   10.5   3.5    0.0013      0.39      19      67 ..     603     650 ..     587     666 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0064
                                       ...............XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.....XXXXXXXXXXXXXXXX CS
                              SKA1   9 vslrainqdpallkedlskieaevsaleellnklkkelqeeeeaikklkkeieaslkqqeklqhlkenlpshlpkkt 85 
                                       + l ++++  + ++e++  +e+  ++le+ +++++  l+++ e+ +klk+ei++  +q ++l++ ++ l ++l   +
  gi|242398545|ref|YP_002993969.1|  87 LGLEKLEKAWQFMREVIYYFEQVKNELEKEIAEIEGKLKSKYEQRDKLKQEIQELNRQIKELKQKLKSLSQQLSAIE 163
                                       55666677777888888899999999999999999999999999999999999999888888887777777776555 PP

                                       XXXXXX CS
                              SKA1  86 aassae 91 
                                       ++ ++ 
  gi|242398545|ref|YP_002993969.1| 164 RELNEL 169
                                       554444 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.079
                                       .........XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.....XXXXXXXXXXXXXXXXXXXXXX CS
                              SKA1  15 nqdpallkedlskieaevsaleellnklkkelqeeeeaikklkkeieaslkqqeklqhlkenlpshlpkktaassae 91 
                                       +++++l    l ki ++++ ++e+++kl++ l+e ++a++klk e+e  +++   l+   ++ +++ + +t++++ e
  gi|242398545|ref|YP_002993969.1| 174 KRYNEL-MLELTKIIESIRLVQEQIKKLEEDLNESKKAKEKLK-ELEGEIRKIPLLEEYIKQFNKFKELNTKKEQLE 248
                                       445555.778999999***************************.999999555556666666665544344333333 PP

                                       XXXXX CS
                              SKA1  92 eskss 96 
                                       +  ++
  gi|242398545|ref|YP_002993969.1| 249 KDLNK 253
                                       33222 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.67
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..... CS
                              SKA1  34 aleellnklkkelqeeeeaikklkkeieaslkqqek 69 
                                       ++e++   + + +++   +ikk ++e+e+ + +  k
  gi|242398545|ref|YP_002993969.1| 290 EIEKSTTTISTLVRSTVAQIKKDTEELEKLISEALK 325
                                       333333333333333333333333333333322222 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 0.77
                                       ...XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              SKA1  21 lkedlskieaevsaleellnklkkelqeeeeaikklkkeieasl 64 
                                        +++l+++++e + le+ ++ l+kel e +  i++l+k +++  
  gi|242398545|ref|YP_002993969.1| 335 KEKKLKELKEEEKRLENIVSGLRKELGEVSGRINDLRKALDMLG 378
                                       57788899999999999999999999998888888887776655 PP

  == domain 5  score: 8.5 bits;  conditional E-value: 0.0057
                                       ....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX......XXXXXXXXXXX CS
                              SKA1  20 llkedlskieaevsaleellnklkkelqeeeeaikklkkeieaslkqqek.lqhlkenlpsh 80 
                                           +  ++e+e+++lee ++++++e++e e+++ ++k+eie+  k + + +++l++++ + 
  gi|242398545|ref|YP_002993969.1| 394 HRDRVKHEMEEEIKSLEEIVKQIRREIEEAENQKRTIKEEIERVSKINVErIEQLQKEIEEM 455
                                       5555667899***********************************99988899999988654 PP

  == domain 6  score: 4.2 bits;  conditional E-value: 0.11
                                       ....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.....XXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              SKA1  20 llkedlskieaevsaleellnklkkelqeeeeaikklkkeieaslkqqeklqhlkenlpshlpkktaassaeeskss 96 
                                         ++++s+ie+e++++ee ln+l +e+ e+ e  ++  ke+ ++ ++  +l+ +++ + + l++ ++a+++ ++ ++
  gi|242398545|ref|YP_002993969.1| 479 DIRPKISEIESEIKEIEERLNELIEEIGEKPEDPENELKELRKKKEEYDRLKPIADRYEKLLEDIKEAQEKLRKLEN 555
                                       34789**********************999888777777******99999************998888877666666 PP

                                       XXXXXXXXXXXXX...XXXXXXXXXXXXX CS
                              SKA1  97 speeeeeteskke...keeeaekakkpkk 122
                                       +++e +e+ +  +   ++++ ek +k+++
  gi|242398545|ref|YP_002993969.1| 556 KKHELQEEIK--KlgyDKQHHEKVRKEHE 582
                                       5554443222..22454455555444444 PP

  == domain 7  score: 10.5 bits;  conditional E-value: 0.0013
                                       .....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX... CS
                              SKA1  19 allkedlskieaevsaleellnklkkelqeeeeaikklkkeieaslkqq 67 
                                       +   +dl ++eae+++lee+ n+lk+el++ ++++++l+  i + ++++
  gi|242398545|ref|YP_002993969.1| 603 EKNLKDLTEVEAEIKELEEKRNNLKAELDKIKKLLNDLE-RIRRAYHRD 650
                                       33458999******************************9.888877665 PP

>> PRT_C  Plant phosphoribosyltransferase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.2    0.0022      0.63      28      88 ..     489     553 ..     468     569 .. 0.73
   2 ?   -1.6   0.1       7.1   2.1e+03      25      80 ..     611     669 ..     599     671 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0022
                             PRT_C  28 lklskadsvnpdeLdEEFDsfPssrdldvvrmR.....YdrlRsvagrvqtvlGdvAtqgErlqal 88 
                                         ++++++ +++eL EE  + P   + ++  +R     Ydrl+ +a+r  ++l d+    E+l+ l
  gi|242398545|ref|YP_002993969.1| 489 SEIKEIEE-RLNELIEEIGEKPEDPENELKELRkkkeeYDRLKPIADRYEKLLEDIKEAQEKLRKL 553
                                       44555543.57899999999995555444333333555*******************999999876 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 7.1
                             PRT_C  25 hmdlklskadsvnpdeLdEEFDsfP.ssrdldvvrmRYdr...lRsvagrvqtvlGdvAt 80 
                                        +++ ++++++ ++++L+ E D++    +dl+ +r  Y r    R + +++  ++ ++At
  gi|242398545|ref|YP_002993969.1| 611 EVEAEIKELEE-KRNNLKAELDKIKkLLNDLERIRRAYHRdgvQRLLRQKIAPIISELAT 669
                                       55666666665.567899999999977899999999998855457778888888888876 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  12.3    0.0054       1.6     356     433 ..      92     169 ..      88     170 .. 0.66
   2 ?    0.9  68.1      0.34        97      64     408 ..     147     504 ..     146     530 .. 0.60
   3 ?    7.5  23.2    0.0034      0.97      95     208 ..     535     642 ..     532     673 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0054
                                       HHHHHHHHHHHHS-SS---STTGGGTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSS CS
                              EzrA 356 lekdyeeleekleekkvaYSelqeeleeleekleeieekqeeileslkslrkdEkrAreqldeikkelkeikrkiek 432
                                       lek  + ++e +   +++  el++e+ e+e kl+   e+ +++++++++l ++ k+ +++l+ ++++l+ i+r++++
  gi|242398545|ref|YP_002993969.1|  92 LEKAWQFMREVIYYFEQVKNELEKEIAEIEGKLKSKYEQRDKLKQEIQELNRQIKELKQKLKSLSQQLSAIERELNE 168
                                       44444555555555555566777777777777777777777777777777777777777777777777777777776 PP

                                       - CS
                              EzrA 433 s 433
                                        
  gi|242398545|ref|YP_002993969.1| 169 L 169
                                       5 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.34
                                       HHHHHHHHHHHHHTHHHHHT-GGGT--S-SHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHHHH CS
                              EzrA  64 ewkkkwdeiktkklpeieellfeaeelldkykfkkakkklaeleeeldeveekikkileelkelteseeknreeiek 140
                                       e+k+k + +++ +l +ie +l+e++  ++++++++++ +l+++ e +  v+e+ikk+ e+l+e ++ +ek +e   +
  gi|242398545|ref|YP_002993969.1| 147 ELKQKLKSLSQ-QLSAIERELNELN--AKEKRYNELMLELTKIIESIRLVQEQIKKLEEDLNESKKAKEKLKELEGE 220
                                       56666666666.7777777777776..67777777778888888888888888888887777766555555554444 PP

                                       HHHHHHHHHHT--TTTTHHHHH...HHHHHHHHHHH-------------....---HHHHHHHHHHHHHHHHHHHHH CS
                              EzrA 141 lkekYrelrkkllanrfsygea...leelekqleniekefsefeelten....gdyveakeilkkleeeideleevi 210
                                       +++    l +++ ++ ++++e    +e+lek+l++i    +e ++++++     +y+e+ e   ++ ++++e+e+ +
  gi|242398545|ref|YP_002993969.1| 221 IRKI--PLLEEYIKQFNKFKELntkKEQLEKDLNKISAIREEANKAMKSckvyVEYIEVGEEFIEVPTDLSEIEKST 295
                                       4432..12334444444443331116778888888888888888888873333467788888888888888888888 PP

                                       HHHHHHHTTTTTTSHHHHHHHHHHHHHSTTS--SGGGSSSSSHHHHHHHHHHHHHHHHTT--..HHHHHHHHHHHHH CS
                              EzrA 211 eeiPelleelkkelpkqleelkegykemkeegYaleelniekeieelekkieeilerlkele..ledveeelktiee 285
                                        +i +l++ +  +++k  eel++ + e      ++     e +ie+ ekk++e+ e+ k+le  +   ++el +++ 
  gi|242398545|ref|YP_002993969.1| 296 TTISTLVRSTVAQIKKDTEELEKLISE----ALKFLP---EPTIEAKEKKLKELKEEEKRLEniVSGLRKELGEVSG 365
                                       888888888888888888887655544....344444...4556666666666666666664445667777777777 PP

                                       HHHHHHHHHH..HHHHHHHHHTTTS.........SSSSHHHHT--HHHHTTGGG-TTTS-GGGSSTTTSTTHHHHH. CS
                              EzrA 286 eidsLyddle..kEveAkkeveknl.........kelkeklehlekqnkelkeeldrlkqsYeLseeeleklrele. 350
                                       +i++L + l+   E eA   ++++l         +e++e+++ le+++k++++e+++ +++ +  +ee+e++ +++ 
  gi|242398545|ref|YP_002993969.1| 366 RINDLRKALDmlGESEACPVCKTKLtpehrdrvkHEMEEEIKSLEEIVKQIRREIEEAENQKRTIKEEIERVSKINv 442
                                       77777665442257777666665532222222225777778888888888888888877777666778888777774 PP

                                       HHHHHHHHHHHHHHHHHS-SS---STTGGGTHHHHH....HHHHHHHHHHHHHHHHHHHHHH CS
                              EzrA 351 kelkelekdyeeleekleekkvaYSelqeeleelee....kleeieekqeeileslkslrkd 408
                                       +++++l+k++ee++ekl+++ +    +  el++le+    k++eie++ +ei+e l++l ++
  gi|242398545|ref|YP_002993969.1| 443 ERIEQLQKEIEEMKEKLAKHYTELEGIITELNNLENdirpKISEIESEIKEIEERLNELIEE 504
                                       55777777777777777766554444444444444311125566666666666666666543 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0034
                                       HHHHTTHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHHHHHHHHHHHHHHT--TTTTHHHHHHHHHHHHHH CS
                              EzrA  95 kfkkakkklaeleeeldeveekikkileelkelteseeknreeieklkekYrelrkkllanrfsygealeelekqle 171
                                       ++ k+ ++++e++e+l ++e+k ++++ee+k+l   ++    + ek++++ +el +k+++++ +++e +++lek+l+
  gi|242398545|ref|YP_002993969.1| 535 RYEKLLEDIKEAQEKLRKLENKKHELQEEIKKLGYDKQ----HHEKVRKEHEELLRKFESTKTELEEKTKSLEKNLK 607
                                       67788888999999999999999999999999865443....33566777777777777777777777777777777 PP

                                       HH----------------HHHHHHHHHHHHHHHHHHH CS
                              EzrA 172 niekefsefeeltengdyveakeilkkleeeidelee 208
                                       ++ +  +e++el e+ + ++a+  l+k+++ +++le+
  gi|242398545|ref|YP_002993969.1| 608 DLTEVEAEIKELEEKRNNLKAE--LDKIKKLLNDLER 642
                                       7777777777777777766664..5666666666655 PP

>> PilJ  Type IV pili methyl-accepting chemotaxis transducer N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   3.5      0.16        45      36      73 ..     144     181 ..      95     221 .. 0.58
   2 ?    0.1   0.0       2.8     8e+02      50      58 ..     331     339 ..     291     383 .. 0.50
   3 ?    0.4   0.1       2.1   6.2e+02      75     102 ..     391     427 ..     347     440 .. 0.58
   4 ?    0.2   0.2       2.6   7.4e+02      77     103 ..     402     428 ..     388     466 .. 0.46
   5 ?    8.4   0.2    0.0071       2.1      38     105 ..     478     550 ..     457     563 .. 0.77
   6 ?    5.8   0.7     0.045        13      35      93 ..     586     642 ..     572     663 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.16
                              PilJ  36 gaydaaearaqlretiaqfdrtlaalrlgdpapgllvp 73 
                                       ++ +  ++ ++l++++++++r l++l+ +++ ++ l  
  gi|242398545|ref|YP_002993969.1| 144 QIKELKQKLKSLSQQLSAIERELNELNAKEKRYNELML 181
                                       22333444444555555555555555555444444433 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 2.8
                              PilJ  50 tiaqfdrtl 58 
                                       ti++ ++ l
  gi|242398545|ref|YP_002993969.1| 331 TIEAKEKKL 339
                                       222222333 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 2.1
                              PilJ  75 e.........avraqleaveqlWqelkkpaeaalaqq 102
                                       +         ++ ++++++e+  ++ ++ +e a +q+
  gi|242398545|ref|YP_002993969.1| 391 TpehrdrvkhEMEEEIKSLEEIVKQIRREIEEAENQK 427
                                       1344564444556666666666666666664444443 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 2.6
                              PilJ  77 vraqleaveqlWqelkkpaeaalaqqd 103
                                       + ++++++e+  ++ ++ +e a +q+ 
  gi|242398545|ref|YP_002993969.1| 402 MEEEIKSLEEIVKQIRREIEEAENQKR 428
                                       333333333333333333322222221 PP

  == domain 5  score: 8.4 bits;  conditional E-value: 0.0071
                              PilJ  38 ydaaearaqlretiaqfdrtlaalrlgdpapgllvpae.....avraqleaveqlWqelkkpaeaalaqqdda 105
                                        d+  + +++++ i++++++l++l +   + +  + +e     + +++++++ +  ++++k +e +  +q+++
  gi|242398545|ref|YP_002993969.1| 478 NDIRPKISEIESEIKEIEERLNELIEEIGEKPEDPENElkelrKKKEEYDRLKPIADRYEKLLEDIKEAQEKL 550
                                       466677789999************9995555555555579899999999999999999999997766666654 PP

  == domain 6  score: 5.8 bits;  conditional E-value: 0.045
                              PilJ  35 agaydaaearaqlretiaqfdrtlaalrlgdpapgllvpae.avraqleaveqlWqelkk 93 
                                             ++ +++l+e+ + ++++l+ l++ +++   l  +  + +a+l+++ +l + l++
  gi|242398545|ref|YP_002993969.1| 586 RKF---ESTKTELEEKTKSLEKNLKDLTEVEAEIKELEEKRnNLKAELDKIKKLLNDLER 642
                                       344...788899999999999999999999888877777778899999888888777665 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 ?   12.7  14.5   0.00023     0.067      80     159 ..     110     184 ..      67     194 .. 0.82
   2 ?    2.3   9.7      0.36     1e+02      16     187 ..     198     375 ..     195     380 .. 0.63
   3 ?    8.1  12.3    0.0061       1.8      36     139 ..     403     501 ..     399     523 .. 0.59
   4 ?   -1.4  19.4       4.7   1.4e+03      27     132 ..     538     640 ..     511     658 .. 0.39

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00023
                        MscS_porin  80 leeLeqrllqtssqlqelqeqlaqlnsqlvelqtrperaqqqltearqrlqeirnrLnstaaagealsqaqrtalqa 156
                                        +eLe+++++ + +l +  eq+ +l+++++el+ ++ ++ q+l + +q+l++i+++Ln++     +  + + + l  
  gi|242398545|ref|YP_002993969.1| 110 KNELEKEIAEIEGKLKSKYEQRDKLKQEIQELNRQIKELKQKLKSLSQQLSAIERELNEL-----NAKEKRYNELML 181
                                       689*******************************************************99.....666666666666 PP

                        MscS_porin 157 ela 159
                                       el 
  gi|242398545|ref|YP_002993969.1| 182 ELT 184
                                       655 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.36
                        MscS_porin  16 kallqdLeqalnl...LdkidkskkkaeelqkaiddaPkelrelqqeleal...qkkkeeaskeilaklsleeLeqr 86 
                                       k+l +dL+++ +    L++ +    k+  l++ i+++  + +el+ + e+l    +k ++  +e  +++++     +
  gi|242398545|ref|YP_002993969.1| 198 KKLEEDLNESKKAkekLKELEGEIRKIPLLEEYIKQFN-KFKELNTKKEQLekdLNKISAIREEANKAMKSCKVYVE 273
                                       44444444333330003333333344444555555554.23344444443322256667777778888888888888 PP

                        MscS_porin  87 llqtssqlqelqeqlaqlnsqlvelqtrperaqqqltearqrlqei.rnrLnstaaagealsqaqrtalqaelaale 162
                                       ++++ ++  e+ ++l++++++ ++++t      +q+ +  ++l+++ + +L+ +++++ +  + +   l+ e++ le
  gi|242398545|ref|YP_002993969.1| 274 YIEVGEEFIEVPTDLSEIEKSTTTISTLVRSTVAQIKKDTEELEKLiSEALKFLPEPTIEAKEKKLKELKEEEKRLE 350
                                       88888888888888888888888888888888888888888888864556677755555888888888888888888 PP

                        MscS_porin 163 aqieeleqellsnnnrqeLlklqrd 187
                                       + ++ l++el   + r++ l++ +d
  gi|242398545|ref|YP_002993969.1| 351 NIVSGLRKELGEVSGRINDLRKALD 375
                                       8888888888887777776666655 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0061
                        MscS_porin  36 kkkaeelqkaiddaPkelrelqqelealqkkkeeaskeilaklsleeLeqrllqtssqlqelqeqlaqlnsqlvelq 112
                                       +++++ l++ +++  +e++e++++  +   k+e +   +++   +e+L++++++ +++l++  ++l  + ++l++l+
  gi|242398545|ref|YP_002993969.1| 403 EEEIKSLEEIVKQIRREIEEAENQKRTI--KEEIERVSKINVERIEQLQKEIEEMKEKLAKHYTELEGIITELNNLE 477
                                       4555555555555555555555555555..44444445555566667777777777777766666666655555555 PP

                        MscS_porin 113 trperaqqqltearqrlqeirnrLnst 139
                                          + ++ +++e   +++ei+ rLn++
  gi|242398545|ref|YP_002993969.1| 478 ---NDIRPKISEIESEIKEIEERLNEL 501
                                       ...566777777777777777777655 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 4.7
                        MscS_porin  27 nlLdkidkskkkaeelqkaiddaPkelrelqqeleal.qkkkeeaskeilaklsleeLeqrllqtssqlqelqeqla 102
                                       +lL++i++ ++k+++l+ +  + ++e+++l  + +   +  ke++   +  + + +eLe +       l+++ ++l+
  gi|242398545|ref|YP_002993969.1| 538 KLLEDIKEAQEKLRKLENKKHELQEEIKKLGYDKQHHeKVRKEHEELLRKFESTKTELEEK----TKSLEKNLKDLT 610
                                       2444444444444444444444444444444443333333333333333333333333333....222222223333 PP

                        MscS_porin 103 qlnsqlvelqtrperaqqqltearqrlqei 132
                                       + ++++ el+   + + ++l + ++ l+++
  gi|242398545|ref|YP_002993969.1| 611 EVEAEIKELEEKRNNLKAELDKIKKLLNDL 640
                                       333333333333333333333333333333 PP

>> ALIX_LYPXL_bnd  ALIX V-shaped domain binding to HIV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3  25.7      0.29        85     106     262 ..     100     266 ..      90     281 .. 0.57
   2 ?    7.5  20.7    0.0075       2.2      28     265 ..     239     474 ..     235     476 .. 0.67
   3 ?   12.4  27.0   0.00024     0.069      73     268 ..     455     644 ..     453     650 .. 0.58

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.29
                    ALIX_LYPXL_bnd 106 kedlelLsgpeeeleaalp.......ssssaaa...sesveeqirklrsllekldelkaereqllkdlkekaendDi 172
                                       +e +   ++ ++ele+ +        s+ ++ +   +++ +e  r++++l +kl++l ++   ++++l+e  +++  
  gi|242398545|ref|YP_002993969.1| 100 REVIYYFEQVKNELEKEIAeiegklkSKYEQ-RdklKQEIQELNRQIKELKQKLKSLSQQLSAIERELNELNAKEKR 175
                                       4555555555555555544333433122222.123355555555577777788888888888888888887777777 PP

                    ALIX_LYPXL_bnd 173 tpklltekkrdiaanefealfeeelekydplqeqleqslakqeellkeiq......eaneefeqskksdseqsqrqr 243
                                        ++l++e+++   + e   l +e+++k++++ ++ +++++k +el  ei+      e  ++f++ k+ +    ++q 
  gi|242398545|ref|YP_002993969.1| 176 YNELMLELTK---IIESIRLVQEQIKKLEEDLNESKKAKEKLKELEGEIRkiplleEYIKQFNKFKELNT--KKEQL 247
                                       8888888888...444568888888888888888888888888888888733333322333333333333..23344 PP

                    ALIX_LYPXL_bnd 244 eevlqkleaaydkykelks 262
                                       e+ l+k++a  ++ ++ ++
  gi|242398545|ref|YP_002993969.1| 248 EKDLNKISAIREEANKAMK 266
                                       4444444444444333333 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0075
                    ALIX_LYPXL_bnd  28 dlqelkerneeiLdeieklLdeEesedeklrakygtrWtrqpSseltaelraelqkyreileeAsesDkivrqklqe 104
                                       +l+++ke+ e+ L++i++ ++eE+++  k  + y ++       e+ +e+ +   ++ ei ++ +   + vr+++++
  gi|242398545|ref|YP_002993969.1| 239 ELNTKKEQLEKDLNKISA-IREEANKAMKSCKVYVEYI------EVGEEFIEVPTDLSEIEKSTTTISTLVRSTVAQ 308
                                       555555555555555543.4555555555555555533......3477888888889999999999999******** PP

                    ALIX_LYPXL_bnd 105 nkedlelLsgpeeeleaalp....ssssaaasesveeqirklrsllekldelkaereqllkdlkekaendDi..... 172
                                       +k+d e+L++  +e  ++lp    +++++ + ++ +e+ ++l+++++ l +   e   +++dl+   ++ D+     
  gi|242398545|ref|YP_002993969.1| 309 IKKDTEELEKLISEALKFLPeptiEAKEK-KLKELKEEEKRLENIVSGLRKELGEVSGRINDLR---KALDMlgese 381
                                       ********998899999999444322222.2345555555666666666666666666666665...3444422222 PP

                    ALIX_LYPXL_bnd 173 .....tpklltekkrdiaanefealfeeelekydplqeqleqslakqeellkeiqeaneefeqskksdseqsqrqre 244
                                            ++kl  e ++       ++ +eee++ ++++++q+  ++++ e+  ++i+e  e+ ++   ++ eq q++ e
  gi|242398545|ref|YP_002993969.1| 382 acpvcKTKLTPEHRD-----RVKHEMEEEIKSLEEIVKQIRREIEEAENQKRTIKEEIERVSKINVERIEQLQKEIE 453
                                       222223344444444.....223447899999999999999999999999999999999999999999999999999 PP

                    ALIX_LYPXL_bnd 245 evlqkleaaydkykelksnle 265
                                       e+ +kl++ y++ + ++++l+
  gi|242398545|ref|YP_002993969.1| 454 EMKEKLAKHYTELEGIITELN 474
                                       999999999999999988886 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 0.00024
                    ALIX_LYPXL_bnd  73 ltaelraelqkyreileeAsesDkivrqklqenkedlelLsgpeeeleaalpssssaaasesveeqirklrsllekl 149
                                         ++l ++  ++++i++e ++ ++++r k+ e+++++++++   +el + + ++     +e+ e+++++lr+  e+ 
  gi|242398545|ref|YP_002993969.1| 455 MKEKLAKHYTELEGIITELNNLENDIRPKISEIESEIKEIEERLNELIEEIGEK-----PEDPENELKELRKKKEEY 526
                                       5689999*********************************88878888887732.....456777777777666666 PP

                    ALIX_LYPXL_bnd 150 delkaereqllkdlkekaendDitpklltekkr................diaanefealfeeelekydplqeqleqs 210
                                       d+lk   ++ +k l++ +e++    kl ++k +                +       +  ee l+k+++ +++le++
  gi|242398545|ref|YP_002993969.1| 527 DRLKPIADRYEKLLEDIKEAQEKLRKLENKKHElqeeikklgydkqhheK-----VRKEHEELLRKFESTKTELEEK 598
                                       66666555555555554455533355444444444444455543222111.....1111223333555555555555 PP

                    ALIX_LYPXL_bnd 211 lakqeellkeiqeaneefeqskksdseqsqrqreevlqkleaaydkykelksnleegl 268
                                        ++ e+ lk+++e+ +e+++  ++             ++l+a  dk+k+l ++le  +
  gi|242398545|ref|YP_002993969.1| 599 TKSLEKNLKDLTEVEAEIKELEEK------------RNNLKAELDKIKKLLNDLERIR 644
                                       555555555555555555544444............4444444444444444444433 PP

>> DASH_Hsk3  DASH complex subunit Hsk3 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   4.6    0.0063       1.8       7      36 ..     134     163 ..     130     171 .. 0.79
   2 ?    0.7   0.0       2.4   7.1e+02      10      25 ..     444     459 ..     442     461 .. 0.86
   3 ?    0.8   0.1       2.2   6.4e+02       7      23 ..     595     611 ..     592     612 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0063
                         DASH_Hsk3   7 LasqLaqLqaNLadteellevtseQaesir 36 
                                       L +++++L+++++++++ l+  s+Q+++i+
  gi|242398545|ref|YP_002993969.1| 134 LKQEIQELNRQIKELKQKLKSLSQQLSAIE 163
                                       788888888888888888888888888875 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 2.4
                         DASH_Hsk3  10 qLaqLqaNLadteell 25 
                                       +++qLq+ +++++e l
  gi|242398545|ref|YP_002993969.1| 444 RIEQLQKEIEEMKEKL 459
                                       789*********9987 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 2.2
                         DASH_Hsk3   7 LasqLaqLqaNLadtee 23 
                                       L ++ ++L +NL+d++e
  gi|242398545|ref|YP_002993969.1| 595 LEEKTKSLEKNLKDLTE 611
                                       788899********986 PP

>> TLV_coat  ENV polyprotein (coat polyprotein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   5.0     0.052        15     432     532 ..     133     231 ..     125     234 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.052
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTGGGTSHHHHHTS--------HHHHHHHHHHHHHHHHHHH CS
                          TLV_coat 432 alekDvqaleesIskleksltslaevvlQNRRGLDlLfleeGGlCaALkEeCCFyadksgivrdsiakLqerleqrq 508
                                       +l++ +q+l+  I++l+++l sl++      R L  L ++e      + E      +  ++v+++i+kL e+l++++
  gi|242398545|ref|YP_002993969.1| 133 KLKQEIQELNRQIKELKQKLKSLSQQLSAIERELNELNAKEKRYNELMLELTKII-ESIRLVQEQIKKLEEDLNESK 208
                                       6889999999999999999999999999999999999999998877777777665.999****************** PP

                                       HHHH-XXXX.XXXXXXXXXXXXXX CS
                          TLV_coat 509 rllednqlwfegllglspwlttll 532
                                       ++ e+ +   eg   + p l + +
  gi|242398545|ref|YP_002993969.1| 209 KAKEKLKEL-EGEIRKIPLLEEYI 231
                                       **9999886.99988888887776 PP

>> COG2  COG (conserved oligomeric Golgi) complex component, COG2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   8.7     0.014         4      50     128 ..     109     189 ..      90     190 .. 0.86
   2 ?    5.3   4.9     0.067        19      64     128 ..     169     233 ..     167     241 .. 0.79
   3 ?    9.5   6.3    0.0035         1      22     108 ..     241     325 ..     227     353 .. 0.76
   4 ?    0.1   0.1       2.7   7.9e+02      66      94 ..     341     369 ..     334     381 .. 0.42
   5 ?    1.8   4.4      0.83   2.4e+02      66     104 ..     401     435 ..     396     447 .. 0.57
   6 ?    7.6   1.0     0.013       3.7      78     111 ..     445     478 ..     433     480 .. 0.85
   7 ?    6.5   4.1     0.028       8.1      64     119 ..     466     529 ..     464     557 .. 0.44
   8 ?   -0.1  13.7       3.1     9e+02      71     129 ..     574     640 ..     528     644 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.014
                              COG2  50 vnedyad.FvslSghLvglqeeleevesplaaarkkvesvreklsereeeveskleeakeleekr.ellklllklde 124
                                       v ++++    ++ g+L++  e+ ++++++++++ ++++++++kl+  ++++++  +e +el++k+ ++ +l+l+l++
  gi|242398545|ref|YP_002993969.1| 109 VKNELEKeIAEIEGKLKSKYEQRDKLKQEIQELNRQIKELKQKLKSLSQQLSAIERELNELNAKEkRYNELMLELTK 185
                                       555555556788899******************************************99998766588899998888 PP

                              COG2 125 vvek 128
                                        +e+
  gi|242398545|ref|YP_002993969.1| 186 IIES 189
                                       7765 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.067
                              COG2  64 Lvglqeeleevesplaaarkkvesvreklsereeeveskleeakeleekrellklllkldevvek 128
                                       L   +++ +e+  +l+++ + ++ v+e++++ ee++++  +++++l+e +  ++ + +l+e +++
  gi|242398545|ref|YP_002993969.1| 169 LNAKEKRYNELMLELTKIIESIRLVQEQIKKLEEDLNESKKAKEKLKELEGEIRKIPLLEEYIKQ 233
                                       66668889999****************************99999999988555554444444444 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.0035
                              COG2  22 lrhgvpLeslrrdLeaylkllekellelvnedyadFvslSghLvglqeeleevesplaaarkkvesvreklsereee 98 
                                       + ++ +Le+  + + a+ ++ +k++ ++  + y ++++++++ + + ++l+e+e++ +++ + v+s+++++++  ee
  gi|242398545|ref|YP_002993969.1| 241 NTKKEQLEKDLNKISAIREEANKAMKSC--KVYVEYIEVGEEFIEVPTDLSEIEKSTTTISTLVRSTVAQIKKDTEE 315
                                       4444445555555555666777777776..67999****************************************** PP

                              COG2  99 veskleeake 108
                                       +e+ ++ea +
  gi|242398545|ref|YP_002993969.1| 316 LEKLISEALK 325
                                       *****99865 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 2.7
                              COG2  66 glqeeleevesplaaarkkvesvreklse 94 
                                        l+ee +++e  ++ +rk++ +v   +++
  gi|242398545|ref|YP_002993969.1| 341 ELKEEEKRLENIVSGLRKELGEVSGRIND 369
                                       33333333333333333333333333332 PP

  == domain 5  score: 1.8 bits;  conditional E-value: 0.83
                              COG2  66 glqeeleevesplaaarkkvesvreklsereeeveskle 104
                                        ++ee++ +e  ++++r+++e+++++    +ee+    e
  gi|242398545|ref|YP_002993969.1| 401 EMEEEIKSLEEIVKQIRREIEEAENQKRTIKEEI----E 435
                                       4666666666666666666665555444444333....3 PP

  == domain 6  score: 7.6 bits;  conditional E-value: 0.013
                              COG2  78 laaarkkvesvreklsereeeveskleeakelee 111
                                       +++++k++e+++ekl+++ +e+e+ + e ++le+
  gi|242398545|ref|YP_002993969.1| 445 IEQLQKEIEEMKEKLAKHYTELEGIITELNNLEN 478
                                       68999**********************9999886 PP

  == domain 7  score: 6.5 bits;  conditional E-value: 0.028
                              COG2  64 Lvglqeeleevesplaaarkkvesvreklsereeeveskleea........keleekrellkll 119
                                       L g+ +el+++e ++    +++es +++++er +e+ +++ e+        kel++k+e  ++l
  gi|242398545|ref|YP_002993969.1| 466 LEGIITELNNLENDIRPKISEIESEIKEIEERLNELIEEIGEKpedpenelKELRKKKEEYDRL 529
                                       5566666666555555555555555555555544444444443110010014444444333333 PP

  == domain 8  score: -0.1 bits;  conditional E-value: 3.1
                              COG2  71 leevesplaaarkkvesvreklsereeeveskleeakeleekr........ellklllkldevvekl 129
                                        e+v+++ +++ +k+es++ +l+e+ + +e++l++ +e+e++         +l   l k++++++ l
  gi|242398545|ref|YP_002993969.1| 574 HEKVRKEHEELLRKFESTKTELEEKTKSLEKNLKDLTEVEAEIkeleekrnNLKAELDKIKKLLNDL 640
                                       4677777888888888888888888888888888887777776433333344444455555555555 PP

>> Uso1_p115_C  Uso1 / p115 like vesicle tethering protein, C terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4  21.2      0.15        45       7      91 ..     107     185 ..     105     203 .. 0.75
   2 ?   10.3   4.7    0.0023      0.66       3      72 ..     288     364 ..     286     382 .. 0.87
   3 ?   15.0  10.4   8.1e-05     0.023       2      83 ..     338     435 ..     337     437 .. 0.89
   4 ?    6.0  12.1     0.049        14      16      83 ..     398     467 ..     395     480 .. 0.75
   5 ?    5.0   9.6       0.1        29       4      84 ..     446     518 ..     438     529 .. 0.48
   6 ?    3.0  26.5      0.42   1.2e+02       3     108 ..     484     611 ..     482     611 .. 0.90
   7 ?    7.2  23.5     0.021       6.1       1      99 [.     548     647 ..     548     651 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.15
                       Uso1_p115_C   7 eseaaslkdeneklkaelqslskalesleqkeakkaaesqakeleaenkklekeleklraelkeekekekekqkEld 83 
                                       e+ +++l++e ++ + +l+s+ ++  +l+q+   ++ + q kel+++ k+l+++l +++ el+e + kek     ++
  gi|242398545|ref|YP_002993969.1| 107 EQVKNELEKEIAEIEGKLKSKYEQRDKLKQE--IQELNRQIKELKQKLKSLSQQLSAIERELNELNAKEK----RYN 177
                                       5556778888888888888888888888888..7777778888888888888899999888888777775....789 PP

                       Uso1_p115_C  84 DLLlllgD 91 
                                       +L+l l+ 
  gi|242398545|ref|YP_002993969.1| 178 ELMLELTK 185
                                       99987775 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0023
                       Uso1_p115_C   3 aseleseaaslkdeneklkaelqslskalesleqk.......eakkaaesqakeleaenkklekeleklraelkeek 72 
                                       +se+e+++++++++ +++ a++++ +++le+l ++       +  +a e++ kel++e k+le+ +  lr+el e  
  gi|242398545|ref|YP_002993969.1| 288 LSEIEKSTTTISTLVRSTVAQIKKDTEELEKLISEalkflpePTIEAKEKKLKELKEEEKRLENIVSGLRKELGEVS 364
                                       689*****************************9999999*98888999999*************8888888887655 PP

  == domain 3  score: 15.0 bits;  conditional E-value: 8.1e-05
                       Uso1_p115_C   2 kaseleseaaslkdeneklkaelqslskalesleqk................eakkaaesqakeleaenkklekele 62 
                                       k++el++e + l++  + l +el++ s ++++l+++                   ++ + +++e+e+e+k+le+ ++
  gi|242398545|ref|YP_002993969.1| 338 KLKELKEEEKRLENIVSGLRKELGEVSGRINDLRKAldmlgeseacpvcktkLTPEHRDRVKHEMEEEIKSLEEIVK 414
                                       889********************************************886543445567789*************** PP

                       Uso1_p115_C  63 klraelkeekekekekqkEld 83 
                                       ++r e++e++++++  ++E++
  gi|242398545|ref|YP_002993969.1| 415 QIRREIEEAENQKRTIKEEIE 435
                                       ********9988876588876 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.049
                       Uso1_p115_C  16 eneklkaelqslskalesleqkeakkaaesqakeleaenkklek....eleklraelkeekekekekqkEld 83 
                                       ++ +++ e++sl++ +++ +++   ++ae+q++++++e+++++k    ++e+l++e++e kek  +  +El+
  gi|242398545|ref|YP_002993969.1| 398 VKHEMEEEIKSLEEIVKQIRRE--IEEAENQKRTIKEEIERVSKinveRIEQLQKEIEEMKEKLAKHYTELE 467
                                       5678888888888888888888..888888888888888888888887888888888888888765566666 PP

  == domain 5  score: 5.0 bits;  conditional E-value: 0.1
                       Uso1_p115_C   4 seleseaaslkdeneklkaelqslskalesleqkeakkaaesqakeleaenkklekeleklraelkeekekekekqk 80 
                                       ++l++e +++k+  +k+ +el+   ++l++le+      ++ + +e+e+e+k+ e++l +l +e+ e  e+    ++
  gi|242398545|ref|YP_002993969.1| 446 EQLQKEIEEMKEKLAKHYTELEGIITELNNLEND-----IRPKISEIESEIKEIEERLNELIEEIGEKPEDP---EN 514
                                       3344444444444444444444444444444444.....666666666666666665555555555444433...33 PP

                       Uso1_p115_C  81 EldD 84 
                                       El +
  gi|242398545|ref|YP_002993969.1| 515 ELKE 518
                                       3333 PP

  == domain 6  score: 3.0 bits;  conditional E-value: 0.42
                       Uso1_p115_C   3 aseleseaaslkdeneklkaelqslskalesleqk.eakkaaesqakeleaenkklekeleklraelkeekekekek 78 
                                        se+ese +++++  ++l  e++++ +  e++ ++  +kk+   + k + ++ +kl +++++++++l++ ++k+ e 
  gi|242398545|ref|YP_002993969.1| 484 ISEIESEIKEIEERLNELIEEIGEKPEDPENELKElRKKKEEYDRLKPIADRYEKLLEDIKEAQEKLRKLENKKHEL 560
                                       5899999999999999999999999888887777778888889999999999999999***********99999877 PP

                       Uso1_p115_C  79 .................qkEldDLLlll....gDleeKvekykarLkelGe 108
                                                        +kE ++LL  +    + leeK +++++ Lk+l+e
  gi|242398545|ref|YP_002993969.1| 561 qeeikklgydkqhhekvRKEHEELLRKFestkTELEEKTKSLEKNLKDLTE 611
                                       899**********************998776689**************997 PP

  == domain 7  score: 7.2 bits;  conditional E-value: 0.021
                       Uso1_p115_C   1 ekaseleseaaslkdeneklkaelqslskalesleqkeakkaaesqakeleaenkklek...eleklraelkeekek 74 
                                       ek+++le+++ +l++e +kl  + q  +k  ++ e+   + + es ++ele++ k+lek   +l +++ae+ke +ek
  gi|242398545|ref|YP_002993969.1| 548 EKLRKLENKKHELQEEIKKLGYDKQHHEKVRKEHEEL--LRKFESTKTELEEKTKSLEKnlkDLTEVEAEIKELEEK 622
                                       5899*******************99999999999999..9999999************9777777889999999999 PP

                       Uso1_p115_C  75 ekekqkEldDLLlllgDleeKveky 99 
                                        ++ ++Eld    ll Dle  +  y
  gi|242398545|ref|YP_002993969.1| 623 RNNLKAELDKIKKLLNDLERIRRAY 647
                                       9988**************9877777 PP

>> Filo_VP35  Filoviridae VP35
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.5     0.003      0.86      69     130 ..     110     172 ..      77     216 .. 0.80
   2 ?   -1.9   0.1       4.6   1.3e+03      84     126 ..     407     454 ..     396     468 .. 0.46
   3 ?    2.7   0.2      0.18        53      71     101 ..     472     502 ..     457     510 .. 0.64
   4 ?    2.2   0.2      0.26        75      85     118 ..     587     620 ..     578     641 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.003
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHH.HHHHHHHHHHHHHHHXXX CS
                         Filo_VP35  69 krtladllivvnrqiidiestlseletrvtelerqlheikpvld.maktlealskvlaemlak 130
                                       k+ l + +  ++ ++ +      +l++ ++el+rq++e+k  l+ +++ l+a+++ l e+ ak
  gi|242398545|ref|YP_002993969.1| 110 KNELEKEIAEIEGKLKSKYEQRDKLKQEIQELNRQIKELKQKLKsLSQQLSAIERELNELNAK 172
                                       56666666666666665555678899************9987764899***********9998 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.6
                                       HHHHHHHHHHHHHHHHHHHHHH....HCHHHHHHH.HHHHHHHHHHHH CS
                         Filo_VP35  84 idiestlseletrvtelerqlh....eikpvldma.ktlealskvlae 126
                                        + e  + ++ + ++e e+q +    ei+ v ++    +e l+k + e
  gi|242398545|ref|YP_002993969.1| 407 KSLEEIVKQIRREIEEAENQKRtikeEIERVSKINvERIEQLQKEIEE 454
                                       333333444444444444443311112223333321234444444444 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.18
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Filo_VP35  71 tladllivvnrqiidiestlseletrvtele 101
                                        l +l   ++ +i++ies + e+e+r++el 
  gi|242398545|ref|YP_002993969.1| 472 ELNNLENDIRPKISEIESEIKEIEERLNELI 502
                                       4555556666666666666666666666654 PP

  == domain 4  score: 2.2 bits;  conditional E-value: 0.26
                                       HHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHH CS
                         Filo_VP35  85 diestlseletrvtelerqlheikpvldmaktle 118
                                       + est +ele++ ++le++l++++ v    k le
  gi|242398545|ref|YP_002993969.1| 587 KFESTKTELEEKTKSLEKNLKDLTEVEAEIKELE 620
                                       569999**************99998876666655 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3  30.7      0.71   2.1e+02      11     148 ..     116     255 ..      64     267 .. 0.61
   2 ?   -0.8  25.8       6.1   1.8e+03      38     160 ..     307     432 ..     210     439 .. 0.73
   3 ?    4.9  18.3      0.11        31      45     177 ..     443     571 ..     436     573 .. 0.69
   4 ?    0.9  21.5       1.8   5.3e+02      40     142 ..     543     645 ..     541     668 .. 0.47

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.71
                              Fez1  11 EislLKqQLkdsqaevtqklseivalkaqlrelrakleekeeeikeleeslee...ktlelevcenelqrkkseael 84 
                                       Ei+ +   Lk    +  +  +ei +l  q++el++kl++  ++++ +e +l+e   k++  +++  el +  ++  l
  gi|242398545|ref|YP_002993969.1| 116 EIAEIEGKLKSKYEQRDKLKQEIQELNRQIKELKQKLKSLSQQLSAIERELNElnaKEKRYNELMLELTKIIESIRL 192
                                       45555555554443333444566667777777777777777666666655443111444455555566666666677 PP

                              Fez1  85 lrekvekleeelkelreelselsleeeeaalesdeakaqrqeaeeleelkreverlraeLkeer 148
                                       ++e+++klee+l+e +++ ++l++ e e   +    ++  ++ ++ +el+ + e+l++ L++  
  gi|242398545|ref|YP_002993969.1| 193 VQEQIKKLEEDLNESKKAKEKLKELEGEI-RKIPLLEEYIKQFNKFKELNTKKEQLEKDLNKIS 255
                                       77777777777777666555544333332.2222333333444555666666666666655544 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 6.1
                              Fez1  38 aqlrelrakleekeeeikel..eesleektlelevcenelqrkkseaellrekvekleeelkelreelselsleeee 112
                                       aq++  +++le+  +e+ ++  e ++e k+++l+++++e +r ++ ++ lr+++++++  +++lr++l +l ++e+ 
  gi|242398545|ref|YP_002993969.1| 307 AQIKKDTEELEKLISEALKFlpEPTIEAKEKKLKELKEEEKRLENIVSGLRKELGEVSGRINDLRKALDMLGESEAC 383
                                       4555555555555444444323556788888899999999999***********************99998887777 PP

                              Fez1 113 aalesdeakaqrqe.aeeleelkreverlraeLkeerqkkeeqassFeq 160
                                        +++++ + ++r++ ++e+ee+ +++e++ ++++ e ++ e+q+ + ++
  gi|242398545|ref|YP_002993969.1| 384 PVCKTKLTPEHRDRvKHEMEEEIKSLEEIVKQIRREIEEAENQKRTIKE 432
                                       6655555444444433344444444444555555555554544444433 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.11
                              Fez1  45 akleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelselsleeeeaa.lesdea 120
                                       +++e+ ++ei+e++e+l ++ +ele +  el++ +   + +r k++++e+e+ke+ e+l+el +e  e+     +e 
  gi|242398545|ref|YP_002993969.1| 443 ERIEQLQKEIEEMKEKLAKHYTELEGIITELNNLE---NDIRPKISEIESEIKEIEERLNELIEEIGEKPeDPENEL 516
                                       56788888899999999988888888888887664...557888999999999999999997766544432445566 PP

                              Fez1 121 kaqrqeaeeleelkreverlraeLkeerqkkeeqassFeqERrtWqeeKekVirYqk 177
                                       k+ r+++ee ++lk   +r ++ L+  ++++e+   + e+ ++  qee  k + Y k
  gi|242398545|ref|YP_002993969.1| 517 KELRKKKEEYDRLKPIADRYEKLLEDIKEAQEKL-RKLENKKHELQEEIKK-LGYDK 571
                                       6777777777777777777766666665554444.6667777777666544.55555 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 1.8
                              Fez1  40 lrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelselsleeeeaale 116
                                       ++e+++kl++ e++ +el+e++++   +  + ++e  rk+ ++ellr k e++++el+e  ++l+++ ++ +e ++e
  gi|242398545|ref|YP_002993969.1| 543 IKEAQEKLRKLENKKHELQEEIKKLGYD--KQHHEKVRKE-HEELLR-KFESTKTELEEKTKSLEKNLKDLTEVEAE 615
                                       7888888888888888888877554443..3333322222.122222.23333333333333333333323333333 PP

                              Fez1 117 sdeakaqrqe....aeeleelkreverlra 142
                                        +e +++r++     +++++l +++er+r+
  gi|242398545|ref|YP_002993969.1| 616 IKELEEKRNNlkaeLDKIKKLLNDLERIRR 645
                                       333333332211113344444444444443 PP

>> Tektin  Tektin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8  20.1   0.00026     0.076     240     356 ..     104     220 ..      92     223 .. 0.82
   2 ?    4.4  21.2     0.045        13     143     356 ..     234     436 ..     226     439 .. 0.83
   3 ?    3.3  21.1     0.095        28     248     362 ..     447     565 ..     435     568 .. 0.63
   4 ?   -0.8  12.2       1.7   4.9e+02      36      94 ..     576     637 ..     569     651 .. 0.42

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00026
                            Tektin 240 aqaeavnealrkrieetedaknkleeqlkkvleeiaeleknieeLekairdkeaplklaqtRlenRtq..RpnvElc 314
                                         +e+v ++l+k i+e+e   +   eq++k+++ei+el+++i+eL++++++ +++l   +  l++ +   +  +El+
  gi|242398545|ref|YP_002993969.1| 104 YYFEQVKNELEKEIAEIEGKLKSKYEQRDKLKQEIQELNRQIKELKQKLKSLSQQLSAIERELNELNAkeKRYNELM 180
                                       56789999999999999999999999999999999999999999999999999999999999998876224457888 PP

                            Tektin 315 rDeaqyrLveEvkeleetieaLkeklaeaeaslkaLertrle 356
                                        +    +++e ++ ++e+i++L+e l+e++++ ++L++ + e
  gi|242398545|ref|YP_002993969.1| 181 LE--LTKIIESIRLVQEQIKKLEEDLNESKKAKEKLKELEGE 220
                                       88..45899999999999999999999999999888876655 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.045
                            Tektin 143 eeqlrllraakhkLekdlsdKkeAleiDeeclslkntsanisykpgaerlpetsstpeeWekftkdnieraekerqa 219
                                       +++ ++l++ k++Lekdl +K +A++ +e +  +k+ +  ++y +  e++ e   +p++  ++ k++ + +   r++
  gi|242398545|ref|YP_002993969.1| 234 FNKFKELNTKKEQLEKDL-NKISAIR-EEANKAMKSCKVYVEYIEVGEEFIE---VPTDLSEIEKSTTTISTLVRST 305
                                       456778888889999998.6888887.4555556665555555444444444...5888888888899999999999 PP

                            Tektin 220 sakLreaidsilkqtandlraqaeavnealrkrieetedaknkleeqlkkvleeiaeleknieeLekaird..keap 294
                                        a+++++++++ k +++ l+   e + ea +k+++e+++  + le+  + +++e+ e+   i++L+ka++    +++
  gi|242398545|ref|YP_002993969.1| 306 VAQIKKDTEELEKLISEALKFLPEPTIEAKEKKLKELKEEEKRLENIVSGLRKELGEVSGRINDLRKALDMlgESEA 382
                                       999********9********************************************************985226889 PP

                            Tektin 295 lklaqtRlenRtqRpnvElcrDeaqyrLveEvkeleetieaLkeklaeaeaslkaLertrle 356
                                         +++t+l            rD +++++ eE+k lee +++ +++++eae++ + ++++  +
  gi|242398545|ref|YP_002993969.1| 383 CPVCKTKLTP--------EHRDRVKHEMEEEIKSLEEIVKQIRREIEEAENQKRTIKEEIER 436
                                       99******98........568*******************************9998887655 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.095
                            Tektin 248 alrkrieetedaknkleeqlkkvleeiaelekni....eeLekairdkeaplklaqtRlenRtqRpnvElcrDeaqy 320
                                       +l+k iee+++   k  ++l+ + +e+++le++i    +e+e++i++ e+ l      + ++ + p++El +   ++
  gi|242398545|ref|YP_002993969.1| 447 QLQKEIEEMKEKLAKHYTELEGIITELNNLENDIrpkiSEIESEIKEIEERLNELIEEIGEKPEDPENELKELRKKK 523
                                       34444444444444444444444444444444321111344444444444444444445566667777777777777 PP

                            Tektin 321 rLveEvkeleetieaLkeklaeaeaslkaLertrleleedia 362
                                       + ++ +k + +  e+L e ++ea+++l++Le++++el+e+i+
  gi|242398545|ref|YP_002993969.1| 524 EEYDRLKPIADRYEKLLEDIKEAQEKLRKLENKKHELQEEIK 565
                                       7777788899999***************************97 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 1.7
                            Tektin  36 ktkktqadsnkrLeeRiediefwkeeLekeleelke...eieaLeeekrrlekalealeepl 94 
                                       k++k++++  +++e   +++e   + Lek+l++l+e   ei++Lee +++l+ +l+++++ l
  gi|242398545|ref|YP_002993969.1| 576 KVRKEHEELLRKFESTKTELEEKTKSLEKNLKDLTEveaEIKELEEKRNNLKAELDKIKKLL 637
                                       33333333333333333344444444444333332222244444444444444444444333 PP

>> APG17  Autophagy protein Apg17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   2.5     0.094        27     268     322 ..      92     143 ..      87     150 .. 0.58
   2 ?    8.8   8.0    0.0027      0.78     239     331 ..     147     235 ..     144     238 .. 0.81
   3 ?    0.4   8.1      0.93   2.7e+02     244     330 ..     237     326 ..     227     363 .. 0.67
   4 ?    2.1   1.3      0.29        83     233     285 ..     309     366 ..     303     404 .. 0.68
   5 ?    6.7  11.6     0.012       3.4     222     321 ..     391     488 ..     368     489 .. 0.69
   6 ?    1.4  20.0      0.49   1.4e+02     121     289 ..     484     647 ..     483     659 .. 0.69

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.094
                                       HHHHHHHHHHHHHHHH....HHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHH CS
                             APG17 268 iekllsalkkaleeleevgkklpeylaifkaeeeflerweeekekieekleelee 322
                                       +ek+++ +++++  +e+v+++l++ +a   ++e  l+ + e+++k++++++el+ 
  gi|242398545|ref|YP_002993969.1|  92 LEKAWQFMREVIYYFEQVKNELEKEIA---EIEGKLKSKYEQRDKLKQEIQELNR 143
                                       566666666666666666666666666...5555555555555555555555543 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0027
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHHHHHH...HHHHHHH CS
                             APG17 239 eledVvkelqerleemekakkllsekkeeiekllsalkkaleeleevgkklpeylaifkaeeeflerweeekekiee 315
                                       el++ +k+l ++l+++e++ ++l++k++++++l+ +l+k++e ++ v++++++  +   + +e  +  +e+ +++e 
  gi|242398545|ref|YP_002993969.1| 147 ELKQKLKSLSQQLSAIERELNELNAKEKRYNELMLELTKIIESIRLVQEQIKKLEE---DLNESKKA-KEKLKELEG 219
                                       777778999999*********************************77776666666...33333333.666888999 PP

                                       HHHHHHHHHHHHHHHH CS
                             APG17 316 kleeleeLrefYegFl 331
                                       +++++  L+e+ ++F 
  gi|242398545|ref|YP_002993969.1| 220 EIRKIPLLEEYIKQFN 235
                                       9999999999999886 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.93
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHHHHHHHHHH....HHHHHHHH CS
                             APG17 244 vkelqerleemekakkllsekkeeiekllsalkkaleeleevgk...klpeylaifkaeeeflerw.eeekekieek 316
                                       +kel+++ e++ek+ + +s+ +ee++k++++ k  +e +e vg+   ++p  l+ ++++++ +++   ++ ++i+++
  gi|242398545|ref|YP_002993969.1| 237 FKELNTKKEQLEKDLNKISAIREEANKAMKSCKVYVEYIE-VGEefiEVPTDLSEIEKSTTTISTLvRSTVAQIKKD 312
                                       4778888888888888888888888888888877777777.533255666667766667677766557788888888 PP

                                       HHHHHHHHHHHHHH CS
                             APG17 317 leeleeLrefYegF 330
                                       +eele+L++   +F
  gi|242398545|ref|YP_002993969.1| 313 TEELEKLISEALKF 326
                                       88888887665555 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.29
                                       HHHHHHHHHHHHHHHHHHHHHH.....HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.. CS
                             APG17 233 lekDaaeledVvkelqerleem.....ekakkllsekkeeiekllsalkkaleeleev 285
                                       ++kD++ele+ + e  + l e      ek+ k+l+e+++++e+++s l+k l e++  
  gi|242398545|ref|YP_002993969.1| 309 IKKDTEELEKLISEALKFLPEPtieakEKKLKELKEEEKRLENIVSGLRKELGEVSGR 366
                                       6788888888777766655555555567777777777777777777777777666543 PP

  == domain 5  score: 6.7 bits;  conditional E-value: 0.012
                                       -CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHH....HHHHHHHHHH CS
                             APG17 222 seeereelleVlekDaaeledVvkelqerleemekakkllsekkeeiekll.salkkaleeleevgkklpeylaifk 297
                                       ++e r+   + +e+  + le++vk+++ ++ee e++k +++e+ e++ k++ + + ++ +e+ee+++kl+++ +   
  gi|242398545|ref|YP_002993969.1| 391 TPEHRDRVKHEMEEEIKSLEEIVKQIRREIEEAENQKRTIKEEIERVSKINvERIEQLQKEIEEMKEKLAKHYT--- 464
                                       55555555556666667788888888888888888888888888888887624455666678888888888888... PP

                                       HHHHHHHH...HHHHHHHHHHHHH CS
                             APG17 298 aeeeflerweeekekieekleele 321
                                       + e ++++ ++ +++i  k++e+e
  gi|242398545|ref|YP_002993969.1| 465 ELEGIITELNNLENDIRPKISEIE 488
                                       777777777777777777777765 PP

  == domain 6  score: 1.4 bits;  conditional E-value: 0.49
                                       TTHHHHHHHHHHHHHHHHHHHHHTTHH..HHHHHHHHHHH..........-------..STCCHHHHHHHHHHHHHH CS
                             APG17 121 veelkealkesidelqaaqkkldssllefdtdlrelkkel..........sksksks..essslipellkeleslee 185
                                       ++e+++++ke+ ++l+++ +++ ++ +  +++l+el+k+           +  +  +  e  +  +e l++le+  +
  gi|242398545|ref|YP_002993969.1| 484 ISEIESEIKEIEERLNELIEEIGEKPEDPENELKELRKKKeeydrlkpiaDRYE--KllEDIKEAQEKLRKLENKKH 558
                                       678888888888888888888888888888888888887754444444321111..123444555555555555555 PP

                                       HHHHHHHHHHHHHHHHHHH................S-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHH CS
                             APG17 186 emAslLesLtnHfDqcvkAvkltegggalrraaaelseeereelleVlekDaaeledVvkelqerleem...ekakk 259
                                       e+ + ++ L   +D+  +                    +e+eell+  e  ++ele+  k+l+++l+++   e++ k
  gi|242398545|ref|YP_002993969.1| 559 ELQEEIKKLG--YDKQHHE----------------KVRKEHEELLRKFESTKTELEEKTKSLEKNLKDLtevEAEIK 617
                                       5555555553..4443222................234678899999999999999999999999988888899999 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHH....HH CS
                             APG17 260 llsekkeeiekllsalkkaleeleevgkkl 289
                                       +l+ek++++++ l+++kk+l++le +++++
  gi|242398545|ref|YP_002993969.1| 618 ELEEKRNNLKAELDKIKKLLNDLERIRRAY 647
                                       999999999999999999999999886655 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9  11.6     0.043        12      61     104 ..     107     150 ..     102     151 .. 0.91
   2 ?    5.9   9.4     0.043        12      62      96 ..     136     170 ..     132     178 .. 0.56
   3 ?   12.9   5.4   0.00028     0.081       6      47 ..     182     224 ..     177     227 .. 0.85
   4 ?    7.2   9.3     0.016       4.6       7      98 ..     230     322 ..     225     327 .. 0.75
   5 ?    5.9   1.6     0.041        12      60      99 ..     335     374 ..     329     380 .. 0.69
   6 ?    3.8   8.8      0.19        54      56      96 ..     398     438 ..     397     445 .. 0.83
   7 ?    1.1   8.9       1.3   3.8e+02      73     102 ..     429     462 ..     424     468 .. 0.48
   8 ?    5.5   3.8     0.056        16      69     101 ..     443     475 ..     442     476 .. 0.77
   9 ?    9.4   2.2    0.0033      0.95      59     102 ..     465     508 ..     463     512 .. 0.89
  10 ?    2.8   4.2      0.39   1.1e+02      61     102 ..     513     553 ..     509     554 .. 0.84
  11 ?    2.0  11.5      0.67   1.9e+02       2      36 ..     545     579 ..     520     580 .. 0.71
  12 ?   -1.2  29.7       6.5   1.9e+03       2     101 ..     545     639 ..     544     641 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.043
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCTS CS
                       Prefoldin_2  61 eevkeeLeerketlekeiktlekqleklekeleelkeelqkklq 104
                                       e+vk+eLe++++++e ++k+  +q +kl++e++el  +++++ q
  gi|242398545|ref|YP_002993969.1| 107 EQVKNELEKEIAEIEGKLKSKYEQRDKLKQEIQELNRQIKELKQ 150
                                       78999******************************999998766 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.043
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  62 evkeeLeerketlekeiktlekqleklekeleelk 96 
                                       + ++eL+ ++++l++++k+l++ql+ +e+el+el 
  gi|242398545|ref|YP_002993969.1| 136 QEIQELNRQIKELKQKLKSLSQQLSAIERELNELN 170
                                       44455555555555555555555555555555554 PP

  == domain 3  score: 12.9 bits;  conditional E-value: 0.00028
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-TT.--E CS
                       Prefoldin_2   6 kfqqlqqqlqqlaqqikqletqlkelelvleelellded.tkv 47 
                                       +++++ + ++ +++qik+le++l+e+++++e l++l+ + +k+
  gi|242398545|ref|YP_002993969.1| 182 ELTKIIESIRLVQEQIKKLEEDLNESKKAKEKLKELEGEiRKI 224
                                       6677788999**************************9876665 PP

  == domain 4  score: 7.2 bits;  conditional E-value: 0.016
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-TT--EE...EEETTEEEEE-HHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2   7 fqqlqqqlqqlaqqikqletqlkelelvleelelldedtkvy...klvGdvlvkqdkeevkeeLeerketlekeikt 80 
                                       + +  ++ ++l ++++qle++l+++  + ee +++ ++ kvy     vG+ +++++ +  ++e e++  t+++ +++
  gi|242398545|ref|YP_002993969.1| 230 YIKQFNKFKELNTKKEQLEKDLNKISAIREEANKAMKSCKVYveyIEVGEEFIEVPTD--LSEIEKSTTTISTLVRS 304
                                       555556667777777777777777777777777777776665111689*****98777..78899999999999999 PP

                                       HHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  81 lekqleklekeleelkee 98 
                                          q++k  +ele+l +e
  gi|242398545|ref|YP_002993969.1| 305 TVAQIKKDTEELEKLISE 322
                                       999999999999998765 PP

  == domain 5  score: 5.9 bits;  conditional E-value: 0.041
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  60 keevkeeLeerketlekeiktlekqleklekeleelkeel 99 
                                       ke+ ++eL+e++++le  ++ l k+l ++  ++++l++ l
  gi|242398545|ref|YP_002993969.1| 335 KEKKLKELKEEEKRLENIVSGLRKELGEVSGRINDLRKAL 374
                                       4555667777777777777777777777777777777766 PP

  == domain 6  score: 3.8 bits;  conditional E-value: 0.19
                                       EEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  56 vkqdkeevkeeLeerketlekeiktlekqleklekeleelk 96 
                                       vk++ ee ++ Lee  +++  ei++ e+q++++++e+e + 
  gi|242398545|ref|YP_002993969.1| 398 VKHEMEEEIKSLEEIVKQIRREIEEAENQKRTIKEEIERVS 438
                                       68888899999999999999999999999999999988765 PP

  == domain 7  score: 1.1 bits;  conditional E-value: 1.3
                                       HHHHHHHHHHH....HHHHHHHHHHHHHHHHHCC CS
                       Prefoldin_2  73 tlekeiktlek....qleklekeleelkeelqkk 102
                                       t+++ei++++k    ++e+l+ke+ee+ke+l k 
  gi|242398545|ref|YP_002993969.1| 429 TIKEEIERVSKinveRIEQLQKEIEEMKEKLAKH 462
                                       4444444443322225666666666666666553 PP

  == domain 8  score: 5.5 bits;  conditional E-value: 0.056
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                       Prefoldin_2  69 erketlekeiktlekqleklekeleelkeelqk 101
                                       er+e+l+kei++++++l k+ +ele + +el++
  gi|242398545|ref|YP_002993969.1| 443 ERIEQLQKEIEEMKEKLAKHYTELEGIITELNN 475
                                       578888888888888888888888888887775 PP

  == domain 9  score: 9.4 bits;  conditional E-value: 0.0033
                                       -HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC CS
                       Prefoldin_2  59 dkeevkeeLeerketlekeiktlekqleklekeleelkeelqkk 102
                                       ++e +++eL++ ++++  +i+++e++++++e++l+el ee+ +k
  gi|242398545|ref|YP_002993969.1| 465 ELEGIITELNNLENDIRPKISEIESEIKEIEERLNELIEEIGEK 508
                                       567789999999**************************998765 PP

  == domain 10  score: 2.8 bits;  conditional E-value: 0.39
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC CS
                       Prefoldin_2  61 eevkeeLeerketlekeiktlekqleklekeleelkeelqkk 102
                                       e+ ++eL ++ke+++ ++k + +++ekl ++++e +e+l+k+
  gi|242398545|ref|YP_002993969.1| 513 ENELKELRKKKEEYD-RLKPIADRYEKLLEDIKEAQEKLRKL 553
                                       555678888888875.89*********************985 PP

  == domain 11  score: 2.0 bits;  conditional E-value: 0.67
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2   2 elinkfqqlqqqlqqlaqqikqletqlkelelvle 36 
                                       e ++k+++l+++ ++l+++ik+l  +++++e+v +
  gi|242398545|ref|YP_002993969.1| 545 EAQEKLRKLENKKHELQEEIKKLGYDKQHHEKVRK 579
                                       34666667777777777777777777777776666 PP

  == domain 12  score: -1.2 bits;  conditional E-value: 6.5
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-TT--EEEEETTEEEEE-HHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2   2 elinkfqqlqqqlqqlaqqikqletqlkelelvleelelldedtkvyklvGdvlvkqdkeevkeeLeerketlekei 78 
                                       e ++k+++l+++ ++l+++ik+l  +++++e+v +e e+l      +++  ++ ++++ ++++++L++ + ++e+ei
  gi|242398545|ref|YP_002993969.1| 545 EAQEKLRKLENKKHELQEEIKKLGYDKQHHEKVRKEHEELLRK---FES-TKTELEEKTKSLEKNLKD-LTEVEAEI 616
                                       5689************************************999...444.444555566666666654.556899** PP

                                       HHHHHHHHHHHHHHHHHHHHHHC CS
                       Prefoldin_2  79 ktlekqleklekeleelkeelqk 101
                                       k+le++  +l++el+++k+ l+ 
  gi|242398545|ref|YP_002993969.1| 617 KELEEKRNNLKAELDKIKKLLND 639
                                       ******************98875 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   8.6     0.017       4.9     100     176 ..      89     160 ..      79     161 .. 0.68
   2 ?   15.2  30.8   4.6e-05     0.013      50     172 ..     130     255 ..     125     258 .. 0.88
   3 ?   -1.7  14.0       7.2   2.1e+03      89     172 ..     335     424 ..     290     429 .. 0.61
   4 ?   -0.8  15.3       3.7   1.1e+03      93     175 ..     399     480 ..     385     481 .. 0.86
   5 ?    6.2  24.6     0.026       7.5      56     176 ..     443     565 ..     439     568 .. 0.77
   6 ?    4.5  22.0     0.088        25      57     139 ..     552     634 ..     552     654 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.017
                           DUF4201 100 lkekeerlaklrkelykvklerdklrkqneklkqqggllrvPaLlkDYdktkekveekrksvkkLrrkvkilemrlk 176
                                       l+++e+  + +r+ +y  ++ ++ l+k+ ++++ ++   ++++  +  dk k++++e+  ++k+L++k+k+l+++l+
  gi|242398545|ref|YP_002993969.1|  89 LEKLEKAWQFMREVIYYFEQVKNELEKEIAEIEGKLKS-KYEQ--R--DKLKQEIQELNRQIKELKQKLKSLSQQLS 160
                                       55666666667777777777777777777777777766.5544..2..67777777777777777777777777765 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 4.6e-05
                           DUF4201  50 enqalnkkIeernkeLkrlkkkttktvhalthlkeklhmlese...lselkkelkekeerlaklrkelykvklerdk 123
                                       +  +l+++I+e n ++k+lk+k ++ +++l+ +   l++l+++   ++el  el ++ e ++ +++++ k++++ + 
  gi|242398545|ref|YP_002993969.1| 130 QRDKLKQEIQELNRQIKELKQKLKSLSQQLSAIERELNELNAKekrYNELMLELTKIIESIRLVQEQIKKLEEDLNE 206
                                       56689999999999999999999999999999999888666552226777778888999999999************ PP

                           DUF4201 124 lrkqneklkqqggllrvPaLlkDYdktkekveekrksvkkLrrkvkile 172
                                        +k +eklk+  g++r+  Ll++Y+k+ +k +e+  + ++L++ +++++
  gi|242398545|ref|YP_002993969.1| 207 SKKAKEKLKELEGEIRKIPLLEEYIKQFNKFKELNTKKEQLEKDLNKIS 255
                                       *******************************************998875 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 7.2
                           DUF4201  89 leselselkkelkekeerlaklrkelykvklerdklrkqneklkq.qggllrvPaLlkDYdktk.....ekveekrk 159
                                        e++l+elk+e k++e+    lrkel +v  + + lrk  + l + + + +++++L+ +  +++     e+++++++
  gi|242398545|ref|YP_002993969.1| 335 KEKKLKELKEEEKRLENIVSGLRKELGEVSGRINDLRKALDMLGEsEACPVCKTKLTPEHRDRVkhemeEEIKSLEE 411
                                       45566666666666666666666666666666666666666664313455666666665544440001145555555 PP

                           DUF4201 160 svkkLrrkvkile 172
                                        vk++rr+++++e
  gi|242398545|ref|YP_002993969.1| 412 IVKQIRREIEEAE 424
                                       6666666666555 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 3.7
                           DUF4201  93 lselkkelkekeerlaklrkelykvklerdklrkqneklkqqggllrvPaLlkDYdktkekveekrksvkkLrrkvk 169
                                        +e+++e+k++ee  +++r+e++++++++  ++++ e++++ + + r ++L k+ ++ kek+++   +++ + ++++
  gi|242398545|ref|YP_002993969.1| 399 KHEMEEEIKSLEEIVKQIRREIEEAENQKRTIKEEIERVSKINVE-RIEQLQKEIEEMKEKLAKHYTELEGIITELN 474
                                       578999999999999999999999999999999999999999999.9999999999999999988888887777777 PP

                           DUF4201 170 ilemrl 175
                                       +le+ +
  gi|242398545|ref|YP_002993969.1| 475 NLENDI 480
                                       777665 PP

  == domain 5  score: 6.2 bits;  conditional E-value: 0.026
                           DUF4201  56 kkIeernkeLkrlkkkttktvhalthlkeklhmleselselkkelk.ekeerlaklrkelykvklerdklrkqnekl 131
                                       ++Ie  +ke++++k+k +k+  +l+ +   l+ le+  + + +e++ e++e +++l + +++  ++ +  +++ ++l
  gi|242398545|ref|YP_002993969.1| 443 ERIEQLQKEIEEMKEKLAKHYTELEGIITELNNLENDIRPKISEIEsEIKEIEERLNELIEEIGEKPEDPENELKEL 519
                                       88999999999999999999999988888888888877777777652344445567777777778888888899999 PP

                           DUF4201 132 kqqggllrv.PaLlkDYdktkekveekrksvkkLrrkvkilemrlk 176
                                       +++++++++   +   Y+k  e+++e +++++kL+ k  +l++ +k
  gi|242398545|ref|YP_002993969.1| 520 RKKKEEYDRlKPIADRYEKLLEDIKEAQEKLRKLENKKHELQEEIK 565
                                       9999988752334445999999999999999999998888888887 PP

  == domain 6  score: 4.5 bits;  conditional E-value: 0.088
                           DUF4201  57 kIeernkeLkrlkkkttktvhalthlkeklhmleselselkkelkekeerlaklrkelykvklerdklrkqneklkq 133
                                       k+e++++eL++  kk +++ +  + +++   +l ++++  k+el+ek++ l+k  k l++v++e + l++++++lk+
  gi|242398545|ref|YP_002993969.1| 552 KLENKKHELQEEIKKLGYDKQHHEKVRKEHEELLRKFESTKTELEEKTKSLEKNLKDLTEVEAEIKELEEKRNNLKA 628
                                       89*************************************************99999999999999999999999999 PP

                           DUF4201 134 qggllr 139
                                       ++  ++
  gi|242398545|ref|YP_002993969.1| 629 ELDKIK 634
                                       877643 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   2.8    0.0037       1.1      80     122 ..     100     142 ..      79     143 .. 0.89
   2 ?    7.1  10.1     0.021       6.1      66     122 ..     115     170 ..     110     171 .. 0.69
   3 ?    2.6   3.5      0.52   1.5e+02      15      43 ..     193     221 ..     182     232 .. 0.82
   4 ?    4.2   5.4      0.17        48      25     111 ..     236     327 ..     226     343 .. 0.77
   5 ?    2.1   0.1      0.78   2.2e+02      85     121 ..     341     377 ..     329     379 .. 0.67
   6 ?    1.0  22.6       1.7   4.9e+02      14     118 ..     401     505 ..     393     523 .. 0.71
   7 ?   10.3  18.6    0.0022      0.64      13     122 ..     537     641 ..     518     642 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0037
                           DUF5082  80 qtyvdkldelidaieeEIerLenqiseaqgvldtlqsqlnslk 122
                                       ++++   ++++ ++e+EI ++e ++++++   d+l++++++l+
  gi|242398545|ref|YP_002993969.1| 100 REVIYYFEQVKNELEKEIAEIEGKLKSKYEQRDKLKQEIQELN 142
                                       55666679*********************************97 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.021
                           DUF5082  66 nnydgirsnlessyqtyvdkldelidaieeEIerLenqiseaqgvldtlqsqlnslk 122
                                       ++  +i+ +l+s+y++  dkl++ i+++++ I++L+++++++++ l+ ++++ln+l+
  gi|242398545|ref|YP_002993969.1| 115 KEIAEIEGKLKSKYEQ-RDKLKQEIQELNRQIKELKQKLKSLSQQLSAIERELNELN 170
                                       4555566677777766.5777777777777777777777777777777777777775 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.52
                           DUF5082  15 lrseiaaleekIerLkeaktklsdekesl 43 
                                        +++i++lee++ + k+ak+kl++ + ++
  gi|242398545|ref|YP_002993969.1| 193 VQEQIKKLEEDLNESKKAKEKLKELEGEI 221
                                       68899999999999999999999887766 PP

  == domain 4  score: 4.2 bits;  conditional E-value: 0.17
                           DUF5082  25 kIerLkeaktklsdekeslkqkkkklekplnsse.....sWkGkeennydgirsnlessyqtyvdkldelidaieeE 96 
                                       k ++L + k++l++  +++++ +++ +k   s +        G+e  ++ +++s++e+s++t+ + +++++++i+++
  gi|242398545|ref|YP_002993969.1| 236 KFKELNTKKEQLEKDLNKISAIREEANKAMKSCKvyveyIEVGEEFIEVPTDLSEIEKSTTTISTLVRSTVAQIKKD 312
                                       556777777777777777777777777766666644422223555566677788*********************** PP

                           DUF5082  97 IerLenqiseaqgvl 111
                                       +e+Le+ isea ++l
  gi|242398545|ref|YP_002993969.1| 313 TEELEKLISEALKFL 327
                                       *********997765 PP

  == domain 5  score: 2.1 bits;  conditional E-value: 0.78
                           DUF5082  85 kldelidaieeEIerLenqiseaqgvldtlqsqlnsl 121
                                       +l+e ++++e+ ++ L++++ e +g ++ l ++l++l
  gi|242398545|ref|YP_002993969.1| 341 ELKEEEKRLENIVSGLRKELGEVSGRINDLRKALDML 377
                                       4455556667777777777777777777777777766 PP

  == domain 6  score: 1.0 bits;  conditional E-value: 1.7
                           DUF5082  14 elrseiaaleekIerLkeaktklsdekeslkqkkkklekplnssesWkGkeennydgirsnlessyqtyvdkldeli 90 
                                       e+++ei++lee ++  ++  ++ + +k ++k++++ ++k+ ++  +   ke ++ ++++++ +++ + ++++l +l+
  gi|242398545|ref|YP_002993969.1| 401 EMEEEIKSLEEIVKQIRREIEEAENQKRTIKEEIERVSKINVERIEQLQKEIEEMKEKLAKHYTELEGIITELNNLE 477
                                       56667777777777777777777777777777777777777777666666667777777777777777777777777 PP

                           DUF5082  91 daieeEIerLenqiseaqgvldtlqsql 118
                                         i  +I+++e++i+e +  l+ l +++
  gi|242398545|ref|YP_002993969.1| 478 NDIRPKISEIESEIKEIEERLNELIEEI 505
                                       7777777777777777777777766555 PP

  == domain 7  score: 10.3 bits;  conditional E-value: 0.0022
                           DUF5082  13 aelrseiaaleekIerLkeaktklsdekeslkqkkkklekplnssesWkGkeennydgirsnlessyqtyvdkldel 89 
                                       ++l ++i+  +ek+++L+  k +l++e ++l  +k+  ek   ++e++  k    +++   +le++++  +++l++l
  gi|242398545|ref|YP_002993969.1| 537 EKLLEDIKEAQEKLRKLENKKHELQEEIKKLGYDKQHHEKVRKEHEELLRK----FESTKTELEEKTKSLEKNLKDL 609
                                       455566777777777777777777777777777777777777777666654....4445558888888889999988 PP

                           DUF5082  90 idaieeEIerLenqiseaqgvldtlqsqlnslk 122
                                         ++e EI++Le+++++++  ld++++ ln+l+
  gi|242398545|ref|YP_002993969.1| 610 T-EVEAEIKELEEKRNNLKAELDKIKKLLNDLE 641
                                       5.69***************************96 PP

>> COG5  Golgi transport complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   9.3     0.021       6.2      40     128 ..     104     192 ..      97     195 .. 0.87
   2 ?   -0.0   1.5       3.2   9.1e+02      34      83 ..     206     253 ..     191     265 .. 0.50
   3 ?    6.4   1.2     0.032       9.3      37     120 ..     293     378 ..     286     390 .. 0.70
   4 ?    8.2   1.5    0.0093       2.7      42     114 ..     367     439 ..     363     442 .. 0.90
   5 ?    3.4   6.5      0.28        80      43     112 ..     410     476 ..     396     481 .. 0.60
   6 ?    3.8   6.4      0.21        60      31     104 ..     430     507 ..     422     525 .. 0.58
   7 ?    1.3   5.0       1.3   3.6e+02      35     112 ..     484     560 ..     471     567 .. 0.43
   8 ?    6.5  13.1      0.03       8.6      30     116 ..     552     640 ..     527     649 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.021
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-TTHHHHHHHHHHHHHHHHHHHHH CS
                              COG5  40 ydiqeldkrlrqlitsnhleLlehlskskslssvlselksslesLsasyerlkskvlepyeeaeklqsalkrlhqtl 116
                                       y  ++++++l+++i + + +L ++ +++ +l++  +el+ ++++L++ ++ l+++++    e+++l+++ kr  + +
  gi|242398545|ref|YP_002993969.1| 104 YYFEQVKNELEKEIAEIEGKLKSKYEQRDKLKQEIQELNRQIKELKQKLKSLSQQLSAIERELNELNAKEKRYNELM 180
                                       66789*****************************************************9999999999999877766 PP

                                       HHHHHHHHHHHH CS
                              COG5 117 dLlrralrflhl 128
                                         l +++  ++l
  gi|242398545|ref|YP_002993969.1| 181 LELTKIIESIRL 192
                                       666666666655 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 3.2
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              COG5  34 plkrlnydiqeldkrlrqlitsnhleLlehlskskslssvlselkssles 83 
                                       + k+ ++ ++el+ ++r++     +e +++++k k+l+   ++l++ l++
  gi|242398545|ref|YP_002993969.1| 206 ESKKAKEKLKELEGEIRKIPLL--EEYIKQFNKFKELNTKKEQLEKDLNK 253
                                       2344444455555555444332..23455555555555555555555554 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.032
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXX.XXXXXXXXXXXXXXXXXXXX-TTHHHHHHHHHHHHHHHH CS
                              COG5  37 rlnydiqeldkrlrqlitsnhleLlehlsksks.lss.vlselksslesLsasyerlkskvlepyeeaeklqsalkr 111
                                       + +  i+ l +    +i++  +eL + +s+ ++ l + + +  +++l++L++  +rl++ v+   +e+ +++ +++ 
  gi|242398545|ref|YP_002993969.1| 293 KSTTTISTLVRSTVAQIKKDTEELEKLISEALKfLPEpTIEAKEKKLKELKEEEKRLENIVSGLRKELGEVSGRIND 369
                                       55555555666666666666666666666655523345667778888888888888888888888888888888888 PP

                                       HHHHHHHHH CS
                              COG5 112 lhqtldLlr 120
                                       l+++ld+l 
  gi|242398545|ref|YP_002993969.1| 370 LRKALDMLG 378
                                       888888875 PP

  == domain 4  score: 8.2 bits;  conditional E-value: 0.0093
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-TTHHHHHHHHHHHHHHHHHHH CS
                              COG5  42 iqeldkrlrqlitsnhleLlehlskskslssvlselksslesLsasyerlkskvlepyeeaeklqsalkrlhq 114
                                       i++l+k l+ l  s++ ++ +   + ++ + v +e++++++sL++ ++++++++ e  ++ ++ +++++r+ +
  gi|242398545|ref|YP_002993969.1| 367 INDLRKALDMLGESEACPVCKTKLTPEHRDRVKHEMEEEIKSLEEIVKQIRREIEEAENQKRTIKEEIERVSK 439
                                       788999999999999999999999999999**************************99999999999999876 PP

  == domain 5  score: 3.4 bits;  conditional E-value: 0.28
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXX-TTHHHHHHHHHHHHHHHHH CS
                              COG5  43 qeldkrlrqlitsnhleLlehlskskslssvlselk.sslesLsasyerlkskvlepyeeaeklqsalkrl 112
                                       +e+ k++r++i + +    ++ +++k++ + +s+++ +++e+L++ +e +k+k+ + y+e+e   ++l++l
  gi|242398545|ref|YP_002993969.1| 410 EEIVKQIRREIEEAE----NQKRTIKEEIERVSKINvERIEQLQKEIEEMKEKLAKHYTELEGIITELNNL 476
                                       444444444444443....4455555555534444325777888888888888888888877777777776 PP

  == domain 6  score: 3.8 bits;  conditional E-value: 0.21
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXXXXXXXXXX-TTHHHHHHHH CS
                              COG5  31 lstplkrlnydiqeldkrlrqlitsnhleLlehlsk....skslssvlselksslesLsasyerlkskvlepyeeae 103
                                       ++ +++r++    e  ++l+++i + +++L +h ++    +++l+++ ++++++++++++ ++ +++ + e +ee+ 
  gi|242398545|ref|YP_002993969.1| 430 IKEEIERVSKINVERIEQLQKEIEEMKEKLAKHYTElegiITELNNLENDIRPKISEIESEIKEIEERLNELIEEIG 506
                                       44555555444444444555555555555555554422224566667777777777777777777777666666665 PP

                                       H CS
                              COG5 104 k 104
                                       +
  gi|242398545|ref|YP_002993969.1| 507 E 507
                                       4 PP

  == domain 7  score: 1.3 bits;  conditional E-value: 1.3
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXX......XXXXXXXXXXXX-TTHHHHHHHHH CS
                              COG5  35 lkrlnydiqeldkrlrqlitsnhleLlehlskskslss.vlselkss......lesLsasyerlkskvlepyeeaek 104
                                       ++ +++ i+e++        ++ +eL+e++ ++ +  +  l+el+++      l+ +   ye+l +++ e  e+++k
  gi|242398545|ref|YP_002993969.1| 484 ISEIESEIKEIE--------ERLNELIEEIGEKPEDPEnELKELRKKkeeydrLKPIADRYEKLLEDIKEAQEKLRK 552
                                       333333333333........333334444433333333344444332111111445556666666666666666666 PP

                                       HHHHHHHH CS
                              COG5 105 lqsalkrl 112
                                       l+++   l
  gi|242398545|ref|YP_002993969.1| 553 LENKKHEL 560
                                       66655555 PP

  == domain 8  score: 6.5 bits;  conditional E-value: 0.03
                                       XXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXX-TTHHHHHHHH CS
                              COG5  30 dlstplkrlnydiqel..dkrlrqlitsnhleLlehlskskslss.vlselksslesLsasyerlkskvlepyeeae 103
                                        l+ +   l++ i++l  dk+ +++++++h+eLl ++++ k++ +  +++l+++l++L++    +k ++ e+ ++++
  gi|242398545|ref|YP_002993969.1| 552 KLENKKHELQEEIKKLgyDKQHHEKVRKEHEELLRKFESTKTELEeKTKSLEKNLKDLTEVEAEIK-ELEEKRNNLK 627
                                       4455555566666665447999***************988776666************99888886.4677777777 PP

                                       HHHHHHHHHHHHH CS
                              COG5 104 klqsalkrlhqtl 116
                                           ++k+l + l
  gi|242398545|ref|YP_002993969.1| 628 AELDKIKKLLNDL 640
                                       7666666665544 PP

>> Laminin_I  Laminin Domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1  22.5     5e-05     0.015       9     151 ..      94     246 ..      86     276 .. 0.72
   2 ?    4.1   1.1      0.11        33       7      66 ..     299     356 ..     289     380 .. 0.69
   3 ?   -0.5  27.1       2.8   8.1e+02      82     239 ..     404     565 ..     393     566 .. 0.81
   4 ?   -1.0  19.4         4   1.2e+03     112     195 ..     542     622 ..     534     647 .. 0.54

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5e-05
                         Laminin_I   9 galeapykinanledltkeLqek....lskesakkskieilekelesLaqeteeLqkkatqvlakaqkvnaesertl 81 
                                        a++ ++++ +  e+ ++eL++     + k ++k ++ + l++e+++L+ +++eL +k++  +++ + +++e ++ +
  gi|242398545|ref|YP_002993969.1|  94 KAWQFMREVIYYFEQVKNELEKEiaeiEGKLKSKYEQRDKLKQEIQELNRQIKELKQKLKSLSQQLSAIERELNELN 170
                                       56666666666666666666543111155666777777777788888888888888888888888777777666655 PP

                         Laminin_I  82 ...nnakeLaekikkladnikeilekvatlne..neealpssklseelaeaqr..lLeelrsRdftkqleeaeaelk 151
                                          ++ +eL  +  k++++i  + e++++l+e  ne++ +++kl+e   e+ +  lLee  +++f+k +e ++++ +
  gi|242398545|ref|YP_002993969.1| 171 akeKRYNELMLELTKIIESIRLVQEQIKKLEEdlNESKKAKEKLKELEGEIRKipLLEEY-IKQFNKFKELNTKKEQ 246
                                       21155678999999999999999*******9999******************95559997.8999888888876544 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.11
                         Laminin_I   7 ltgaleapykinanledltkeLqeklskesakkskieilekelesLaqeteeLqkkatqv 66 
                                       +t++  ++ +i    e+l+k ++e l+    ++  ie +ek+l++L++e ++L + +   
  gi|242398545|ref|YP_002993969.1| 299 STLVRSTVAQIKKDTEELEKLISEALKF--LPEPTIEAKEKKLKELKEEEKRLENIVSGL 356
                                       3555555666666666666666655555..466678888999999999999997765555 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 2.8
                         Laminin_I  82 nnakeLaekikkladnikeilekvatlneneealpssklseelaeaqrlLeelrsRdftkqleeaeaelkaAqkLLs 158
                                       +++k+L+e +k+++++i+e+ ++  t+ e+ e +++ + ++  ++ q+ +ee++++ + k+ +e e    + ++L +
  gi|242398545|ref|YP_002993969.1| 404 EEIKSLEEIVKQIRREIEEAENQKRTIKEEIERVSKINVER-IEQLQKEIEEMKEK-LAKHYTELEGIITELNNLEN 478
                                       5899*************************888888777665.45566666777443.79999999999********* PP

                         Laminin_I 159 rvqtllqklqeenkaLkealrdsLaeyeakLsDlrelleeAaaktrdanrln...lanqanlr...eiekkkeevse 229
                                        ++ +++++  e k ++e l++ ++e  +k +D ++ l+e   k  + +rl     + ++ l+   e+++k  ++++
  gi|242398545|ref|YP_002993969.1| 479 DIRPKISEIESEIKEIEERLNELIEEIGEKPEDPENELKELRKKKEEYDRLKpiaDRYEKLLEdikEAQEKLRKLEN 555
                                       ****************************************9999999999872223445555522267777778888 PP

                         Laminin_I 230 eknqleetlk 239
                                       +k +l+e +k
  gi|242398545|ref|YP_002993969.1| 556 KKHELQEEIK 565
                                       8888888887 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 4
                         Laminin_I 112 eealpssklseelaeaqrlLeelrsRdftkqleeaeaelkaAqkLLsrvqtllqklqeenkaLkealrdsLaeyeak 188
                                       + + +++kl +  ++   l ee+  + ++  ++  e++ k+ ++LL + ++   +l e++k+L+++  ++L e ea+
  gi|242398545|ref|YP_002993969.1| 542 DIKEAQEKLRKLENKKHELQEEI--KKLGYDKQHHEKVRKEHEELLRKFESTKTELEEKTKSLEKN-LKDLTEVEAE 615
                                       34444455544444444455555..55666666666666666666666666666666666666555.4446666666 PP

                         Laminin_I 189 LsDlrel 195
                                        + l+e 
  gi|242398545|ref|YP_002993969.1| 616 IKELEEK 622
                                       6555553 PP

>> MAD  Mitotic checkpoint protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2  48.0    0.0024      0.68      69     334 ..      94     374 ..      68     381 .. 0.73
   2 ?    0.7  59.6      0.43   1.3e+02      23     242 ..     400     635 ..     387     645 .. 0.56

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0024
                               MAD  69 ealreqiElarlkkknlealnkkekekesklaearevisalknelaelkrqiekqelelsekeseleelqerldllk 145
                                       +a + + E+    ++ +++l+k+  e e kl++  e  ++lk+e++el+rqi++ +++l++ +++l +++++l++l+
  gi|242398545|ref|YP_002993969.1|  94 KAWQFMREVIYYFEQVKNELEKEIAEIEGKLKSKYEQRDKLKQEIQELNRQIKELKQKLKSLSQQLSAIERELNELN 170
                                       4444455555566688899999999999999999******************************************* PP

                               MAD 146 kklseleqliqqlekkqkelaeaeqrikeLefeiqsqeddslivknskselaripelekeler......lreenkkl 216
                                       +k + +++l+ +l k  ++    +++ik Le  +++ ++ ++ +k+ + e+ +ip le+ +++      l+ + ++l
  gi|242398545|ref|YP_002993969.1| 171 AKEKRYNELMLELTKIIESIRLVQEQIKKLEEDLNESKKAKEKLKELEGEIRKIPLLEEYIKQfnkfkeLNTKKEQL 247
                                       *******************************************************9998766511111133444555 PP

                               MAD 217 nelkenkelLkEevedlkk..kLe.reEkareelvkLelekekleqeLksWeklaqdtgLnlrsP.....ealsrki 285
                                       ++  + ++ ++Ee++   k  k +  + ++ ee +++  +++ +e+      +l  +t  ++++      + +s+ +
  gi|242398545|ref|YP_002993969.1| 248 EKDLNKISAIREEANKAMKscKVYvEYIEVGEEFIEVPTDLSEIEKSTTTISTLVRSTVAQIKKDteeleKLISEAL 324
                                       55555566677776654431233312345677888888888888888777777777777766654211113456667 PP

                               MAD 286 eqLqqeeivlkeek.sslesslkqlekaqreleqelaqllkkiedlkkkr 334
                                       ++L +  i  ke+k ++l+++ k+le+ ++ l++el ++ ++i+dl+k +
  gi|242398545|ref|YP_002993969.1| 325 KFLPEPTIEAKEKKlKELKEEEKRLENIVSGLRKELGEVSGRINDLRKAL 374
                                       77777777777776346777888888888888888888888888887765 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.43
                               MAD  23 lehkrarielekkasalkrqleeesdrnqelqkrikllekreeekeealreqiElarlk.kknlealnkkekekesk 98 
                                        e +++   le+ +++ +r++ee  ++++ ++++i+++ k   e+ e+l+++iE+ + k  k  ++l+    e ++ 
  gi|242398545|ref|YP_002993969.1| 400 HEMEEEIKSLEEIVKQIRREIEEAENQKRTIKEEIERVSKINVERIEQLQKEIEEMKEKlAKHYTELEGIITELNNL 476
                                       45555666666666666666666666666666666666666666666666666655533134444455555555555 PP

                               MAD  99 laearevisalknelaelkrqiekqelelsek....eseleelqerldllkk...klseleqliqqlekkqkelaea 168
                                       ++++r  is+++ e++e ++ +++   e+ ek    e+el+el+++++++++    +  +e+l ++ +++q++l + 
  gi|242398545|ref|YP_002993969.1| 477 ENDIRPKISEIESEIKEIEERLNELIEEIGEKpedpENELKELRKKKEEYDRlkpIADRYEKLLEDIKEAQEKLRKL 553
                                       55555444444444444444433333333222111134444444444333321113444555555555555555555 PP

                               MAD 169 eqrikeLefeiqs...qeddslivknskselar.i....pelekelerlreenkklnelkenkelLkEevedlkkkL 237
                                       e++  eL+ ei++    ++  + v++ ++el+r +     ele++ + l+++ k l e++ +++ L+E+ ++lk+ L
  gi|242398545|ref|YP_002993969.1| 554 ENKKHELQEEIKKlgyDKQHHEKVRKEHEELLRkFestkTELEEKTKSLEKNLKDLTEVEAEIKELEEKRNNLKAEL 630
                                       55555555555555544444555555555553312222378999999999999999999999999999999999999 PP

                               MAD 238 ereEk 242
                                       ++  k
  gi|242398545|ref|YP_002993969.1| 631 DKIKK 635
                                       99766 PP

>> MbeD_MobD  MbeD/MobD like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   2.4     0.011       3.1      16      70 .]     125     157 ..     100     178 .. 0.55
   2 ?   -1.1   0.0       7.1   2.1e+03      22      61 ..     338     377 ..     332     380 .. 0.64
   3 ?   -0.4   0.3       4.6   1.3e+03      48      66 ..     442     460 ..     401     465 .. 0.63
   4 ?    1.3   0.1       1.3   3.7e+02      12      53 ..     445     486 ..     441     502 .. 0.67
   5 ?   -0.5   0.2       4.6   1.3e+03      26      61 ..     577     609 ..     534     621 .. 0.65
   6 ?    0.8   0.0       1.9   5.6e+02       6      21 ..     634     649 ..     628     652 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.011
                         MbeD_MobD  16 QqdYeqrlqeWesafaelqrmfeltqrenaaLseqvtgLsqQVesLseqvrRlsr 70 
                                         +Yeqr +                      L++ +++L +Q+++L ++++ ls+
  gi|242398545|ref|YP_002993969.1| 125 KSKYEQRDK----------------------LKQEIQELNRQIKELKQKLKSLSQ 157
                                       333333333......................555555555555555555544443 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 7.1
                         MbeD_MobD  22 rlqeWesafaelqrmfeltqrenaaLseqvtgLsqQVesL 61 
                                       +l+e ++  + l ++++  ++e++  s ++++L +  + L
  gi|242398545|ref|YP_002993969.1| 338 KLKELKEEEKRLENIVSGLRKELGEVSGRINDLRKALDML 377
                                       5555555555566666667777777777777777766665 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 4.6
                         MbeD_MobD  48 seqvtgLsqQVesLseqvr 66 
                                        e++++L + +e++ e+++
  gi|242398545|ref|YP_002993969.1| 442 VERIEQLQKEIEEMKEKLA 460
                                       4677777777777766665 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 1.3
                         MbeD_MobD  12 lEqLQqdYeqrlqeWesafaelqrm.feltqrenaaLseqvtg 53 
                                       +EqLQ++ e  +++    ++el  +  el + en  ++ ++ +
  gi|242398545|ref|YP_002993969.1| 445 IEQLQKEIEEMKEKLAKHYTELEGIiTELNNLEN-DIRPKISE 486
                                       6999999999999999999998865145555555.55555555 PP

  == domain 5  score: -0.5 bits;  conditional E-value: 4.6
                         MbeD_MobD  26 WesafaelqrmfeltqrenaaLseqvtgLsqQVesL 61 
                                           ++el r fe t+ e+   +e+ + L +  ++L
  gi|242398545|ref|YP_002993969.1| 577 VRKEHEELLRKFESTKTEL---EEKTKSLEKNLKDL 609
                                       3445555555565555543...55555555555555 PP

  == domain 6  score: 0.8 bits;  conditional E-value: 1.9
                         MbeD_MobD   6 kqLLsAlEqLQqdYeq 21 
                                       k+LL+ lE + ++Y++
  gi|242398545|ref|YP_002993969.1| 634 KKLLNDLERIRRAYHR 649
                                       68************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (803 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      4331  (0.241564); expected 358.6 (0.02)
Passed bias filter:                     1222  (0.0681577); expected 358.6 (0.02)
Passed Vit filter:                       533  (0.0297284); expected 17.9 (0.001)
Passed Fwd filter:                       412  (0.0229795); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              62  [number of targets reported over threshold]
# CPU time: 7.41u 0.38s 00:00:07.79 Elapsed: 00:00:01.37
# Mc/sec: 1776.12
//
Query:       gi|242398546|ref|YP_002993970.1|  [L=384]
Description: DNA double-strand break repair Mre11 nuclease [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-13   51.6   0.2    6.7e-13   49.6   0.0    2.1  3  Metallophos    Calcineurin-like phosphoesterase
    8.2e-12   45.6   0.0    1.4e-11   44.8   0.0    1.4  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
  ------ inclusion threshold ------
      0.072   13.4   0.0       0.56   10.5   0.0    2.1  2  TetR_C_24      Tetracyclin repressor-like, C-terminal 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 !   49.6   0.0   1.1e-16   6.7e-13       1     203 [.       1     189 [.       1     190 [. 0.69
   2 ?   -1.6   0.0      0.53   3.2e+03     112     140 ..     220     253 ..     195     288 .. 0.61
   3 ?   -2.1   0.0      0.79   4.7e+03      35      64 ..     282     314 ..     253     333 .. 0.64

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 1.1e-16
                                       EEEEEEESBTB........TTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHH....TS CS
                       Metallophos   1 lrilvigDlHl........algggqlddllkllddllreekpdlvllaGDlvdrgdlekellellaalvky....pi 65 
                                       +ri++i+D+Hl        ++++  ++++++++++ ++e ++d++++aGD++d   ++ + l+  ++ ++     +i
  gi|242398546|ref|YP_002993970.1|   1 MRIAHIADTHLgyrqynleERENDIYEAFNEAVEKMIEE-RVDVFVHAGDFFDSPRPPIKALYVAKEGIRKlrehNI 76 
                                       89*************999999999999999999999888.**************977775555544444447888** PP

                                       EEEEEC-TTSCHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTE.........EEEEEEESECEEE.THHHH CS
                       Metallophos  66 pvylllGNHegfeeellnkygylgifsepwrsdaevfnnlplaslgsgs.........lkvlllhGgspel.lvsld 132
                                       ++ ++lG H++ + +  +++                   lp+ ++g+ +         + +  l+G   +l  ++l+
  gi|242398546|ref|YP_002993970.1|  77 KILTVLGEHDTPRRKAMPPQML---------------LDLPILGIGKVQkvvlngvafFGISNLKGRRVDLlKEELS 138
                                       **********322233333333...............4455555555523321111111233333332111222244 PP

                                       HHHHHHHSCHHHHCCHHHHHHHHHHTTCSEEEEEESSESSCSSSCSCCHHHHHHHHHHTTESEEEEESSSS CS
                       Metallophos 133 klgslnleleapepgdewlkdlekrekadwvivlgHsplyrgsgylfgdealedllkkygvdlvisGHtHv 203
                                       k+++l +e                       ++++H  +  +  +  g  +le +    ++ ++ +GH+H 
  gi|242398546|ref|YP_002993970.1| 139 KVDHLAKE-------------------YNKSVLIAHQAIK-KFLPFEGAYELEMVDLPREISYYAFGHIHS 189
                                       44444433...................4556888888888.888899999***9999999**********6 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.53
                                       TTE..EEEEEEESECEEE....THHHHHHHHHHHS CS
                       Metallophos 112 sgs..lkvlllhGgspel....lvsldklgslnle 140
                                       +    ++++ l+G+ pe+    l+s+ ++  +++ 
  gi|242398546|ref|YP_002993970.1| 220 K-GkgFYIVDLDGDLPEIhkidLESIRPQFEVSYT 253
                                       2.236788888888777753333333333333333 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.79
                                       SEEEEESTSSSSSHHHHHHHHHHHHHHHH...T CS
                       Metallophos  35 dlvllaGDlvdrgdlekellellaalvky...p 64 
                                         + + GD++   +l +++ e l++lv+y   +
  gi|242398546|ref|YP_002993970.1| 282 LKINVQGDIIRKAELIEKIREILEKLVPYrilR 314
                                       344555888888877777888888888875551 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 !   44.8   0.0   2.4e-15   1.4e-11       1     155 [.       1     215 [.       1     232 [. 0.71

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 2.4e-15
                     Metallophos_2   1 MklaiiSDlH.............snldaleavlealkevgvdaiihaGDl.eeeep.........evleellela.p 53 
                                       M++a+i+D+H             + ++a ++++e++ e++vd  +haGD+     p         e +++l+e + +
  gi|242398546|ref|YP_002993970.1|   1 MRIAHIADTHlgyrqynleerenDIYEAFNEAVEKMIEERVDVFVHAGDFfDSPRPpikalyvakEGIRKLREHNiK 77 
                                       9*******************999999999999*****************76444445666655546777777777** PP

                     Metallophos_2  54 vlaVrGNnD........................eevveedvlreaaelgtdlpeeaelel..............age 92 
                                       +l+V G +D                        +      vl+  a++g +  + ++++l               ++
  gi|242398546|ref|YP_002993970.1|  78 ILTVLGEHDtprrkamppqmlldlpilgigkvqK-----VVLNGVAFFGISNLKGRRVDLlkeelskvdhlakeYNK 149
                                       *********9999999988888888875544440.....44444444444443333333322222212222222333 PP

                     Metallophos_2  93 kvlliHgdpl.......gvkdalaellkeaeegsdvvvcGHtHvpevekeggvlvvnPGsvgeprdgdpe 155
                                       +vl+ H+  +       +++ ++ +l +e      ++++GH+H ++ve  g  ++ + Gs +  r+++  
  gi|242398546|ref|YP_002993970.1| 150 SVLIAHQAIKkflpfegAYELEMVDLPRE----ISYYAFGHIHSRTVESFGRSYLAYSGSTEIMRKSEIS 215
                                       48888887449887766666666666666....55*************************9998776654 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 ?    0.0   0.0      0.16   9.8e+02      35      69 ..      17      52 ..       7      64 .. 0.59
   2 ?   10.5   0.0   9.4e-05      0.56       4      55 ..     296     347 ..     293     350 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.16
                                      GS-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTSB.- CS
                         TetR_C_24 35 aLspehreeiralrreyerllrdlieeGvaagef.e 69
                                      +L++ + + + a  +++e+++++ ++  v ag+f +
  gi|242398546|ref|YP_002993970.1| 17 NLEERENDIYEAFNEAVEKMIEERVDVFVHAGDFfD 52
                                      444444555555555556666666666666666655 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 9.4e-05
                                       HHHHHHHHHHHHHHHHHHTHHHHHHHHHHGGGS-HHHHHHHHHHHHHHHHHH CS
                         TetR_C_24   4 paerLralvrahveviaeereeaavllrelraLspehreeiralrreyerll 55 
                                         e++r++++++v + + + + +++ ++   +L+p + +ei +lrr + + l
  gi|242398546|ref|YP_002993970.1| 296 LIEKIREILEKLVPYRILRYDIHFIGTNVPTNLTPNNIKEIGDLRRLFVEYL 347
                                       57********************************************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       702  (0.0391544); expected 358.6 (0.02)
Passed bias filter:                      614  (0.0342462); 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: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 2487.34
//
Query:       gi|242398547|ref|YP_002993971.1|  [L=210]
Description: hypothetical protein TSIB_0557 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0045   17.5  11.1     0.0049   17.4   7.6    2.5  2  AF0941-like  AF0941-like
  ------ inclusion threshold ------
      0.025   14.7   0.7       0.13   12.4   0.2    2.4  3  Swi5         Swi5
      0.069   13.2   0.3       0.16   12.0   0.1    1.8  2  DUF1043      Protein of unknown function (DUF1043)
      0.091   12.5   0.3        2.9    7.6   0.0    2.2  2  LUD_dom      LUD domain
       0.19   11.7   2.0       0.75    9.8   0.8    2.1  2  Laminin_II   Laminin Domain II
        2.1    8.8   7.9        2.1    8.8   3.1    3.1  3  V-SNARE      Vesicle transport v-SNARE protein N-terminus


Domain annotation for each model (and alignments):
>> AF0941-like  AF0941-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   7.6   1.6e-06    0.0049      23      96 ..      27      99 ..       5     135 .. 0.67
   2 ?   -1.8   4.3       1.5   4.4e+03      54      68 ..     146     160 ..      73     210 .] 0.52

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.6e-06
                                      -GGGHHHHT-HHHHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHCTT----- CS
                       AF0941-like 23 iekvldelldkeeieelfrsdvedvleklkagdieeeeakknlklLkvyvvsqLdehykrvlelledkekkiek 96
                                       e+ +  ll +e i+ +f++d ++++ ++k+g i  +ea + lk L   +   L++   +  elle+ e + +k
  gi|242398547|ref|YP_002993971.1| 27 LEEIVPSLLTEEGIARMFKKDKDQIIIDYKKGLISRKEALQQLKELEDIA-EDLKKYVFEARELLEKLEIETQK 99
                                      3444455556******************************9999887543.44555555555555555554444 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.5
                                       TSS-HHHHHHHHHHH CS
                       AF0941-like  54 gdieeeeakknlklL 68 
                                        + + +e +++l+ +
  gi|242398547|ref|YP_002993971.1| 146 PEFQRDEYEDALDAI 160
                                       233333333333333 PP

>> Swi5  Swi5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.4   4.3e+03       5      21 ..      13      29 ..       9      46 .. 0.62
   2 ?   12.4   0.2   4.2e-05      0.13       3      49 ..      67     110 ..      65     117 .. 0.90
   3 ?   -1.1   0.0      0.69   2.1e+03      12      29 ..     150     167 ..     145     203 .. 0.62

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.4
                                      HHHHHHHHHHHHHHHHH CS
                              Swi5  5 ikeleeqleelekelae 21
                                      ++e+++q++++   l+e
  gi|242398547|ref|YP_002993971.1| 13 LEEMNAQIRRTSRGLEE 29
                                      44445555554444444 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 4.2e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHH CS
                              Swi5   3 aeikeleeqleelekelaelkeelkekkdpeetvkrhIklLheYNEi 49 
                                       +++kele+  e l+k + e++e l+   + e + ++ I +L+e+NE 
  gi|242398547|ref|YP_002993971.1|  67 QQLKELEDIAEDLKKYVFEARELLE---KLEIETQKMIIKLREFNEF 110
                                       789999*999*************99...599***************6 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.69
                                       HHHHHHHHHHHHHHHHHH CS
                              Swi5  12 leelekelaelkeelkek 29 
                                        +e+e++l+++ke l+e 
  gi|242398547|ref|YP_002993971.1| 150 RDEYEDALDAIKEFLEEY 167
                                       566777777777766653 PP

>> DUF1043  Protein of unknown function (DUF1043)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       2.2   6.5e+03      58      90 ..      13      45 ..      12      50 .. 0.59
   2 ?   12.0   0.1   5.4e-05      0.16      32      74 ..      64     106 ..      54     137 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.2
                           DUF1043 58 LetlaedyqkLyqhlaksseeLlpeleeqelfq 90
                                      Le+++ + ++  + l++   +Ll+e+  +++f+
  gi|242398547|ref|YP_002993971.1| 13 LEEMNAQIRRTSRGLEEIVPSLLTEEGIARMFK 45
                                      556666666666666666666666655555555 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 5.4e-05
                           DUF1043  32 elekakaeleeqkqeledHfaqsaelLetlaedyqkLyqhlak 74 
                                       e  ++ +ele+  ++l+++  +++elLe+l+ ++qk+  +l +
  gi|242398547|ref|YP_002993971.1|  64 EALQQLKELEDIAEDLKKYVFEARELLEKLEIETQKMIIKLRE 106
                                       44455679****************************9877765 PP

>> LUD_dom  LUD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.2     0.024        73      44      79 ..      33      66 ..       5      92 .. 0.69
   2 ?    7.6   0.0   0.00098       2.9      21      60 ..     153     191 ..     148     202 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.024
                           LUD_dom 44 tdlgeiglapalhsgreevldlfeekl.....treareelr 79
                                        l e g+a ++++++ +++  ++++l     +        
  gi|242398547|ref|YP_002993971.1| 33 SLLTEEGIARMFKKDKDQIIIDYKKGLisrkeA-------L 66
                                      345899999****************99654441.......2 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00098
                           LUD_dom  21 aeealelilellkeksvvseggstdlgeiglapalhsgre 60 
                                        e+al++i+e l+e+ +++ + + +l+e ++ + lh++  
  gi|242398547|ref|YP_002993971.1| 153 YEDALDAIKEFLEEYYSGVIVAQPRLKESII-EFLHRNGV 191
                                       59****************************9.88888765 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.13     4e+02      18      39 ..      12      33 ..       4      49 .. 0.68
   2 ?    9.8   0.8   0.00025      0.75      35      80 ..      64     109 ..      38     132 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.13
                                      XXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II 18 qlaplsqnlentkeklseinrs 39
                                       l+++++++ +t+  l+ei  s
  gi|242398547|ref|YP_002993971.1| 12 ELEEMNAQIRRTSRGLEEIVPS 33
                                      5667777777777766666544 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00025
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHH CS
                        Laminin_II  35 einrsveetnekvkdankairdArrsvkkLeklapqLldklkelkq 80 
                                       e+ ++++e ++ ++d++k + +Ar+   kLe + ++++ kl+e ++
  gi|242398547|ref|YP_002993971.1|  64 EALQQLKELEDIAEDLKKYVFEARELLEKLEIETQKMIIKLREFNE 109
                                       5557788899999999999999************999999999876 PP

>> V-SNARE  Vesicle transport v-SNARE protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.35   1.1e+03      18      37 ..      13      30 ..       4      31 .. 0.75
   2 ?    8.8   3.1   0.00069       2.1      24      51 ..      73     100 ..      40     107 .. 0.82
   3 ?   -1.3   0.0         1     3e+03      54      67 ..     148     161 ..     122     168 .. 0.56

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.35
                           V-SNARE 18 lageerkaalreiekkldea 37
                                      l  ee +a++r+  + l+e+
  gi|242398547|ref|YP_002993971.1| 13 L--EEMNAQIRRTSRGLEEI 30
                                      3..88899999999999985 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00069
                           V-SNARE  24 kaalreiekkldeaeelldqMelEvrnl 51 
                                            +++k++ ea+ell+++e+E++ +
  gi|242398547|ref|YP_002993971.1|  73 EDIAEDLKKYVFEARELLEKLEIETQKM 100
                                       455677899999*************976 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1
                           V-SNARE  54 serasykaklreyk 67 
                                        +r++y   l  +k
  gi|242398547|ref|YP_002993971.1| 148 FQRDEYEDALDAIK 161
                                       44445544444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1644  (0.091695); expected 358.6 (0.02)
Passed bias filter:                      950  (0.0529868); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 1429.19
//
Query:       gi|242398548|ref|YP_002993972.1|  [L=532]
Description: ATPase [Thermococcus sibiricus MM 739]
Scores for complete 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-38  132.6   2.2    5.2e-38  131.4   0.3    2.1  2  DUF87            Helicase HerA, central domain
      6e-13   48.2   0.1      5e-09   35.3   0.1    2.1  2  DUF853           Bacterial protein of unknown function (DUF85
      7e-07   29.3   3.1    7.7e-07   29.2   1.1    2.1  2  HAS-barrel       HAS barrel domain
    3.8e-05   22.8   0.2     0.0041   16.1   0.0    2.2  2  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
    7.9e-05   21.7   0.1     0.0056   15.6   0.1    2.5  2  AAA_10           AAA-like domain
     0.0053   17.2   0.0       0.06   13.8   0.0    2.6  2  AAA              ATPase family associated with various cellul
     0.0089   14.4   0.1        0.9    7.8   0.0    2.2  2  GCP5-Mod21       gamma-Tubulin ring complex non-core subunit 
  ------ inclusion threshold ------
      0.011   15.8   0.1       0.31   11.0   0.0    2.4  2  ResIII           Type III restriction enzyme, res subunit
      0.014   15.0   0.0      0.042   13.5   0.0    1.8  1  Zot              Zonular occludens toxin (Zot)
      0.017   15.4   0.0        2.1    8.6   0.0    2.8  2  AAA_22           AAA domain
      0.021   14.2   0.0       0.27   10.6   0.0    2.3  2  FtsK_SpoIIIE     FtsK/SpoIIIE family
      0.066   12.0   0.0        0.1   11.3   0.0    1.4  1  T4SS-DNA_transf  Type IV secretory system Conjugative DNA tra
       0.17   12.0   0.0        1.1    9.3   0.0    2.2  2  Torsin           Torsin


Domain annotation for each model (and alignments):
>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.4   0.3   3.8e-41   5.2e-38       2     227 .]     144     360 ..     143     360 .. 0.90
   2 ?    0.5   0.1      0.38   5.3e+02     126     191 ..     430     524 ..     406     531 .. 0.55

  Alignments for each domain:
  == domain 1  score: 131.4 bits;  conditional E-value: 3.8e-41
                             DUF87   2 eiGrllsgsevpvyldlnklvtrHlAilgsTGsGKSntvavLleellekkgatililDpHGEYgkal....ekllse 74 
                                        iG+l+++ +v+v l +  + +rHlAil++TG+GKS+t++vLleel+ +kgat+++lDpH +Y+ ++     k++ +
  gi|242398548|ref|YP_002993972.1| 144 FIGHLITRPRVKVQLTIRGF-RRHLAILAQTGAGKSYTAGVLLEELY-DKGATVIVLDPHADYVFISqskdGKRILP 218
                                       69***************555.**************************.***********************9***** PP

                             DUF87  75 kvkvitpspsa.........kdkelkinpwsldpeelldlleeddkpaaavqrsvleealdqakakeekeklssdep 142
                                       +v+v+++++s+          +++++i++++l+p+e++++ ++  ++++ + ++++++a++++k +e+ ++++++++
  gi|242398548|ref|YP_002993972.1| 219 RVDVFRTRESTgrytkedigHMETFEIKFSDLSPDEIFTITGI--RDEWLNIQKAVRDAVKELK-NEKPGRYTVEDL 292
                                       *******9999********************************..999999999*********9.699999****99 PP

                             DUF87 143 veklleelkkekeelrklknqaiarlldkledllrkggsfsnsstdliallleklekegkitiidlsgvdelaqqlv 219
                                       ++k    l+       +++++   r ++ +e+l+  + +  + +t +++ll     k+++i+++dlsg+++ +++++
  gi|242398548|ref|YP_002993972.1| 293 INK----LE-------SMDSNDSLRAIKYIEKLKGLKVFG-EVTTPIENLL-----KPQHISVMDLSGLSDHVADYI 352
                                       993....33.......555566666666777777666666.6667777777.....********************* PP

                             DUF87 220 vsvilrri 227
                                       +  il ++
  gi|242398548|ref|YP_002993972.1| 353 AYKILSEV 360
                                       ****9875 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.38
                             DUF87 126 dqaka......keekeklssdepveklleelk.......................kekeelrklknqaiarlldkle 173
                                       +q+        +++  ++s+++  e ll++l                        ++k+++  ++ ++  rl+++l+
  gi|242398548|ref|YP_002993972.1| 430 SQIIMrmtnpeDQKAVRASAEQVSEDLLNDLPglnvgeavivgemtkmpvmvkirERKTKEGGADIDIVTRLSEALK 506
                                       33333332233333333444444444444444777777777777777777777755555777777777777777777 PP

                             DUF87 174 dllrkggsfsnsstdlia 191
                                       + +++++s+++   + i+
  gi|242398548|ref|YP_002993972.1| 507 EAKEYEESKDEIIREEIK 524
                                       777777776333333333 PP

>> DUF853  Bacterial protein of unknown function (DUF853)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   8.9e-05      0.12      11      67 ..     154     210 ..     147     229 .. 0.86
   2 !   35.3   0.1   3.6e-12     5e-09     182     362 ..     305     471 ..     268     487 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 8.9e-05
                            DUF853  11 qelalalklanrhGliaGatGtGktvtLqvlaeslseaGvpvfladvkGdLsgiaka 67 
                                        +++l+++   rh  i   tG+Gk  t  vl e+l + G +v++ d   d   i+++
  gi|242398548|ref|YP_002993972.1| 154 VKVQLTIRGFRRHLAILAQTGAGKSYTAGVLLEELYDKGATVIVLDPHADYVFISQS 210
                                       56788888899***********************************99999888775 PP

  == domain 2  score: 35.3 bits;  conditional E-value: 3.6e-12
                            DUF853 182 qreLltLeqqGaekffGePaLdledllrtdadGrGvislLaadkllqsPklyatfLlWllseLfeeLPevGdldkPk 258
                                       +r++  +e+  + k+fGe +  +e+ll+ +      is+++ + l  + + y ++   +lse++ +  e G    P 
  gi|242398548|ref|YP_002993972.1| 305 LRAIKYIEKLKGLKVFGEVTTPIENLLKPQ-----HISVMDLSGLSDHVADYIAYK--ILSEVYYQ-REHGKYKYPV 373
                                       577777788888899*************99.....8*********99999999985..7*****88.69******** PP

                            DUF853 259 lvfffdeahLLfndapkallekveqvvrL.irskGvGvyfvtqnPldlPdtvLaqLGnrvqhalraftpkdqkavka 334
                                       +v+  +eah +  +  ++l +++ + +    r  Gv + + tq P+ + ++vL+q  +++   +r   p+dqkav+a
  gi|242398548|ref|YP_002993972.1| 374 FVL-VEEAHRFIPKKENTLSKRIAKRIAAeGRKFGVFLILLTQRPQKIDQDVLSQCNSQI--IMRMTNPEDQKAVRA 447
                                       998.69*****************876654167778888899**************98866..79************* PP

                            DUF853 335 aadtfranpefdveeaiteLgvGealvs 362
                                       +a+ + +    d+ + +  L+vGea++ 
  gi|242398548|ref|YP_002993972.1| 448 SAEQVSE----DLLNDLPGLNVGEAVIV 471
                                       **98865....78888999******984 PP

>> HAS-barrel  HAS barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   1.1   5.6e-10   7.7e-07       1      90 [.      14     110 ..      14     111 .. 0.81
   2 ?   -2.3   0.0       3.8   5.2e+03      51      56 ..     290     295 ..     257     324 .. 0.52

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 5.6e-10
                        HAS-barrel   1 iGevigestssslifrvegskdvkvGeyVeielp.......dgeivlGmvtdirrgn..selsndlalvlsleelee 68 
                                       iG+v+ge+t s+++f++e +k + +++yV+++          +  vlG+++ i +++    + + +   + l+++e 
  gi|242398548|ref|YP_002993972.1|  14 IGVVVGETTHSEFYFAIEDTKTPQIWDYVVVRSKevvdgteKDVLVLGQIVAITSYSpgLSEYTPYPVAEKLKDAEI 90 
                                       8*******************************99****9999999**********9966444555555666666666 PP

                        HAS-barrel  69 angddevalatedtgvkvlGev 90 
                                        ++ +++ +++ +   +v+G+v
  gi|242398548|ref|YP_002993972.1|  91 IEPRNFAQVKVLGF--TVGGKV 110
                                       66666666666644..666666 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.8
                        HAS-barrel  51 selsnd 56 
                                       ++l n 
  gi|242398548|ref|YP_002993972.1| 290 EDLINK 295
                                       222223 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 !   16.1   0.0     3e-06    0.0041      11      56 ..     160     205 ..     154     217 .. 0.87
   2 ?    4.4   0.0      0.01        14     262     313 ..     397     440 ..     393     457 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3e-06
                     TrwB_AAD_bind  11 keretqhilivGttGsGKtqalekllrairargdraivlDltGafv 56 
                                        +  ++h++i+  tG+GK+ ++  ll+++  +g ++ivlD++ ++v
  gi|242398548|ref|YP_002993972.1| 160 IRGFRRHLAILAQTGAGKSYTAGVLLEELYDKGATVIVLDPHADYV 205
                                       555689************************************9987 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.01
                     TrwB_AAD_bind 262 ksllaegRkfGgavvlglqsiaqlrevYGedaaqsilslvntklilrvsdae 313
                                       k+++aegRkfG+ ++l  q  +++         q +ls +n+++i+r+++ e
  gi|242398548|ref|YP_002993972.1| 397 KRIAAEGRKFGVFLILLTQRPQKID--------QDVLSQCNSQIIMRMTNPE 440
                                       57889***************99996........4566666666666666544 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   4.1e-06    0.0056      23     166 ..     166     313 ..     157     324 .. 0.76
   2 ?    3.1   0.0     0.026        36     259     305 ..     393     438 ..     371     447 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.1e-06
                            AAA_10  23 asliiGdlGnGKSvlakllvlyisllggkaliiDpkkerekfketlpeiakkinvvtLdseeenegvL..dPlvllk 97 
                                       + +i+ ++G+GKS++a +l   +   g  ++++Dp ++ + f  + +  ++ + +v++ + +e  g    + +  ++
  gi|242398548|ref|YP_002993972.1| 166 HLAILAQTGAGKSYTAGVLLEELYDKGATVIVLDPHAD-YVFISQSKDGKRILPRVDVFRTRESTGRYtkEDIGHME 241
                                       78999*********************************.88888887766666667765555555543114455555 PP

                            AAA_10  98 ..eekeaeslaedilelllgvkkkesekkaalseaveavle.gkq.rgllavieelrkedekvareiarhles 166
                                         e k +     +i+  ++g++++  + ++a+++av++ ++ ++    ++++i++l++ d++++  + +++e+
  gi|242398548|ref|YP_002993972.1| 242 tfEIKFSDLSPDEIF-TITGIRDEWLNIQKAVRDAVKELKNeKPGrYTVEDLINKLESMDSNDSLRAIKYIEK 313
                                       333334444444555.479******************99853333378999******9999998888777766 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.026
                            AAA_10 259 kkllkelvRiGRsynaavylvtqsadDvlkeelknniglklaFretd 305
                                       k++ k +   GR++  +++l tq ++ ++++ l++  + +++ r t+
  gi|242398548|ref|YP_002993972.1| 393 KRIAKRIAAEGRKFGVFLILLTQRPQKIDQDVLSQCNS-QIIMRMTN 438
                                       6788899999****************999887665444.33445455 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         1   1.4e+03       7      26 ..     173     195 ..     168     219 .. 0.74
   2 !   13.8   0.0   4.4e-05      0.06      57     129 ..     368     433 ..     334     436 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1
                                       TTSSHHHHHHHHHHHH...THEE CS
                               AAA   7 pGtGKTllakavakel...gvef 26 
                                        G GK+++a  + +el   g+++
  gi|242398548|ref|YP_002993972.1| 173 TGAGKSYTAGVLLEELydkGATV 195
                                       699********999984432443 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 4.4e-05
                                       S..TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSSEEEE CS
                               AAA  57 a..kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRfdrkie 129
                                       +   p+ ++++E++++++++       e+++ + + + +  + +k + v++i+ t+rp+k+d+ +l + ++++i 
  gi|242398548|ref|YP_002993972.1| 368 KykYPVFVLVEEAHRFIPKK-------ENTLSKRIAKRIAAEGRKFG-VFLILLTQRPQKIDQDVL-SQCNSQII 433
                                       3545799*************.......66666677777766666555.9*****************.99998875 PP

>> GCP5-Mod21  gamma-Tubulin ring complex non-core subunit mod21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0   0.00066       0.9     445     505 ..     232     292 ..     221     296 .. 0.92
   2 !    4.3   0.0    0.0075        10     197     254 ..     370     429 ..     356     445 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00066
                        GCP5-Mod21 445 lidskvarsdnyqlkagefsLeLsyelqsfsdrFeslekafeEakkeLseKkfskfvyghl 505
                                         ++++   +++++k  + s +  +++    d++ +++ka  +a keL++ k +++ + +l
  gi|242398548|ref|YP_002993972.1| 232 YTKEDIGHMETFEIKFSDLSPDEIFTITGIRDEWLNIQKAVRDAVKELKNEKPGRYTVEDL 292
                                       56899999*************************************************9987 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0075
                        GCP5-Mod21 197 qsfifskveevldlvP.kldtlseeieesillelkdfGkelevlnqvase.kqcrflksd 254
                                       +  +f  vee  + +P k +tls+ i + i  e   fG  l +l q  ++  q+ + +++
  gi|242398548|ref|YP_002993972.1| 370 KYPVFVLVEEAHRFIPkKENTLSKRIAKRIAAEGRKFGVFLILLTQRPQKiDQDVLSQCN 429
                                       4557899*********77789*****************9999998654431445455555 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 ?   11.0   0.0   0.00022      0.31      25      60 ..     165     198 ..     149     217 .. 0.82
   2 ?    2.2   0.0      0.12   1.6e+02     127     148 ..     363     387 ..     272     437 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00022
                                       SEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEE CS
                            ResIII  25 krglikmaTGtGKTlvaaklierllkkgkeekflfl 60 
                                       +++ i + TG+GK+++a  l e+l+ kg    +++l
  gi|242398548|ref|YP_002993972.1| 165 RHLAILAQTGAGKSYTAGVLLEELYDKGA--TVIVL 198
                                       45669999******************987..66666 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.12
                                       HHHTTT-S...EEEEETGGGTTS.T CS
                            ResIII 127 ellrdrfd...viiiDEaHrlgakk 148
                                       + ++++++   ++++ EaHr+  kk
  gi|242398548|ref|YP_002993972.1| 363 QREHGKYKypvFVLVEEAHRFIPKK 387
                                       22222222345899******99863 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   3.1e-05     0.042      83     139 ..     374     429 ..     356     438 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.1e-05
                               Zot  83 llviDEcqeifpvrakegrkdpevi.naftehRhlgwDivlltqdiskihkevralae 139
                                       ++++ E++++ p++ + +   + +     +e R++g  ++lltq + ki+++v   ++
  gi|242398548|ref|YP_002993972.1| 374 FVLVEEAHRFIPKKENTLS--KRIAkRIAAEGRKFGVFLILLTQRPQKIDQDVLSQCN 429
                                       99***********999744..34444667899*******************9976665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0    0.0015       2.1       5      45 ..     164     207 ..     161     241 .. 0.72
   2 ?    3.5   0.0     0.057        78      89     126 ..     368     411 ..     354     440 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0015
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaee.....erpevvfv 45 
                                       +++l++ +++G+GK++++  lle+l    k ++     +++++vf+
  gi|242398548|ref|YP_002993972.1| 164 RRHLAILAQTGAGKSYTAGVLLEELY--DKGATvivldPHADYVFI 207
                                       6899**************99999982..222224555555555554 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.057
                            AAA_22  89 rav.ielliiDEaqhlrseealeeL.rsllnl.....srkgvqli 126
                                       +++ +++++++Ea++++ ++  ++L +++++      +++gv li
  gi|242398548|ref|YP_002993972.1| 368 KYKyPVFVLVEEAHRFI-PKKENTLsKRIAKRiaaegRKFGVFLI 411
                                       3336789********94.555555533333323443344444444 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.22     3e+02      36      59 ..     161     184 ..     143     188 .. 0.73
   2 ?   10.6   0.0    0.0002      0.27     210     242 ..     386     418 ..     368     454 .. 0.66

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.22
                                       GGS-.SEEEE--TTSSHHHHHHHH CS
                      FtsK_SpoIIIE  36 kkmashllvaGatgsGKStalntL 59 
                                       ++   hl ++  tg GKS +  +L
  gi|242398548|ref|YP_002993972.1| 161 RGFRRHLAILAQTGAGKSYTAGVL 184
                                       44448*************876555 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0002
                                       HH....HHHHHHHHHHHCGGGTEEEEEEES--- CS
                      FtsK_SpoIIIE 210 kdssvlvedaivRlarkgraaglHlllatqrls 242
                                       k+++ l + +++R+a+ gr+ g++l+l tqr++
  gi|242398548|ref|YP_002993972.1| 386 KKENTLSKRIAKRIAAEGRKFGVFLILLTQRPQ 418
                                       444555666666666666666666666666654 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 ?   11.3   0.0   7.6e-05       0.1      40      83 ..     160     205 ..     128     325 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 7.6e-05
                   T4SS-DNA_transf  40 tdGdf.ehvlvvAptrsgK..gvgvviPnllkwkqsiVvlDpkgEla 83 
                                         G f  h  + A t++gK  ++gv +  l  ++ +++vlDp ++ +
  gi|242398548|ref|YP_002993972.1| 160 IRG-FrRHLAILAQTGAGKsyTAGVLLEELYDKGATVIVLDPHADYV 205
                                       334.5689***********66699******************99965 PP

>> Torsin  Torsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00083       1.1      57      83 ..     168     194 ..     157     208 .. 0.89
   2 ?   -1.1   0.0       1.4   1.9e+03      49      84 ..     332     367 ..     314     402 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00083
                                       EEEE-TTSSHHHHHHHHHHHHSTTGGG CS
                            Torsin  57 sfhGwtGtGknfvaeiiaenlyrdGlr 83 
                                       ++  +tG+Gk++ a ++ e+ly +G  
  gi|242398548|ref|YP_002993972.1| 168 AILAQTGAGKSYTAGVLLEELYDKGAT 194
                                       55679*******************975 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.4
                                       S-SS-EEEEEEE-TTSSHHHHHHHHHHHHSTTGGGS CS
                            Torsin  49 kpkkpLvlsfhGwtGtGknfvaeiiaenlyrdGlrs 84 
                                       kp+   v+ + G +    +++a  i  ++y +  + 
  gi|242398548|ref|YP_002993972.1| 332 KPQHISVMDLSGLSDHVADYIAYKILSEVYYQREHG 367
                                       566666777888888888888888888887655444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (532 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       986  (0.0549947); expected 358.6 (0.02)
Passed bias filter:                      739  (0.0412181); 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: 0.69u 0.31s 00:00:01.00 Elapsed: 00:00:00.46
# Mc/sec: 3486.34
//
Query:       gi|242398549|ref|YP_002993973.1|  [L=438]
Description: hypothetical protein TSIB_0559 [Thermococcus sibiricus MM 739]
Scores for complete 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-19   68.7   0.1      1e-18   68.0   0.1    1.4  1  NurA           NurA domain
  ------ inclusion threshold ------
       0.16   12.3   0.7        9.1    6.6   0.1    2.4  2  Syntaxin-18_N  SNARE-complex protein Syntaxin-18 N-terminus


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 !   68.0   0.1   1.1e-22     1e-18       2     242 .]      60     406 ..      59     406 .. 0.83

  Alignments for each domain:
  == domain 1  score: 68.0 bits;  conditional E-value: 1.1e-22
                                       EEEEEEEEEEEEEETTCEEEEEEEEEEECCEEECCCEEEECEBTCCHHEEEEEHHHHHHHHHHHHHHHHHHHCGGCC CS
                              NurA   2 rvaAvDGSngvvrlsggilyilsayavvgggkerleealslasvdsispsdelerrirllmetlElklgallleekg 78 
                                       +v+A+D+S+   rl +g+l++++++  + +gk+++ e ++++++ + s  ++  ++i++ me lE+kl+ ++ + + 
  gi|242398549|ref|YP_002993973.1|  60 NVLAIDSSYQMERLKNGGLFYVVRAL-GLNGKNEHRELEADFDYTEGSAHEV-TSIIQRKMEYLEIKLARKAISDGF 134
                                       89**********99999999999999.7777777777778888887676666.************************ PP

                                       SCEEEEECSHHCCCH....HHHHHHHHHHHHHHHHHHHHHTT-....TTCEEEEESS-SCTCCHCCC.......... CS
                              NurA  79 edllllDGsligslv....efdelheeleyeeylyslsrllea....glnlvgvaKsfrskellnll.......... 137
                                       ++++l+DGsl+g +     e+   ++ +  ++y++++++l++     ++ ++g++K + sk +   l          
  gi|242398549|ref|YP_002993973.1| 135 NGVVLIDGSLYGRIShliiESPLSNDREFFIKYYQEVMKLFKLakenNVLVIGISKESGSKFFRDFLikqiitlpev 211
                                       ************9999999999999****************999999****************************** PP

                                       ...............................................S--HHHHCCHHCCHCH---STTS-HHHHTT CS
                              NurA 138 .........................................letlligesisDiallgallrkpgytspllkilrek 173
                                                                                   ++ + + +D +l++a + +pgyt+pll + ++ 
  gi|242398549|ref|YP_002993973.1| 212 rgevsdeeakklistsldrkreafeyvkqlklkysniglleEILKELTTPRPDYQLIEASITEPGYTVPLLLGPSSR 288
                                       ************************888888888777777442233344455677777777777************99 PP

                                       .................................-HCCHHHHHH-EEEEEEES..................STTTTEE CS
                              NurA 174 .................................pllrealidkeiyfaYvrl..................egggsil 199
                                                                                          +                  ++ +s+l
  gi|242398549|ref|YP_002993973.1| 289 wvrrikqiemdpigylktqfpilsnnedflkyaK-----------------VvlnrlkelpaivsfhvlpDKRDSPL 348
                                       ****************777555555555555542.................3333455555555555555******* PP

                                       EEEHHHHHH.C..............CHHHHHHHHHH..TTB-SSSBCC.HHHHHHHHCC CS
                              NurA 200 rleipaevs.t..............akdedvlsllasqrlsisGYprp.LalAhelaki 242
                                       r+++pa++  +              + + +vls +a + + +  Y ++ L+++++++k+
  gi|242398549|ref|YP_002993973.1| 349 RIDVPAFCIgSstkfqdvgwpepidEDISEVLSIVA-TGYGGLDYHNIwLWKVDREVKF 406
                                       ******9876689********988888888888888.555555555558*******996 PP

>> Syntaxin-18_N  SNARE-complex protein Syntaxin-18 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1     0.001       9.1      17      66 ..     210     259 ..     195     272 .. 0.86
   2 ?    3.5   0.0    0.0094        84      39      59 ..     312     332 ..     304     338 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.001
                     Syntaxin-18_N  17 sssskseekeakkrkkkrlkkskekdeFikeAkeilkhItkLrkfLleir 66 
                                       + +++ +++eakk  +++l +++e  e++k+ k  +++I  L+++L+e  
  gi|242398549|ref|YP_002993973.1| 210 EVRGEVSDEEAKKLISTSLDRKREAFEYVKQLKLKYSNIGLLEEILKELT 259
                                       456788899999**********************************9975 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.0094
                     Syntaxin-18_N  39 kekdeFikeAkeilkhItkLr 59 
                                       +++++F+k Ak +l+ +++L 
  gi|242398549|ref|YP_002993973.1| 312 SNNEDFLKYAKVVLNRLKELP 332
                                       6789*************9995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (438 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 2755.69
//
Query:       gi|242398550|ref|YP_002993974.1|  [L=87]
Description: hypothetical protein TSIB_0560 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.024   13.5   0.2      0.024   13.5   0.2    1.1  1  DUF917    Protein of unknown function (DUF917)
       0.11   12.5   0.0       0.13   12.2   0.0    1.1  1  EVE       EVE domain


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 ?   13.5   0.2   2.6e-06     0.024       6      36 ..      13      43 ..       8      71 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.6e-06
                                      HHHHHHHTTTT-SS-HHHHHHHHTT-SBTT- CS
                            DUF917  6 latGaavLGtGGGGspysgylllrqaleegk 36
                                       + G a++G GGGG+ + g   ++ a+e g+
  gi|242398550|ref|YP_002993974.1| 13 AVLGGAFFGGGGGGDLKLGLKHAKLAIELGE 43
                                      578******************9999998764 PP

>> EVE  EVE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.5e-05      0.13      99     144 ..      46      84 ..      32      85 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.5e-05
                                       EEEEEEEEEEHHHHTTHGTCTTSHHHHCCT-SEEEE-HHHHHHHHH CS
                               EVE  99 pvkklkrplslkelkaepelegmkllrkgrlsvrpvteedwelile 144
                                       + k+l ++l++ ++k+  +++g  +      ++r+++eed++li+ 
  gi|242398550|ref|YP_002993974.1|  46 F-KPLIPKLKFITNKK--KWSGHLM----GKAMREIPEEDYNLIEG 84 
                                       3.68899999999999..6788888....999************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       243  (0.0135535); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.34s 00:00:00.87 Elapsed: 00:00:00.54
# Mc/sec: 484.64
//
Query:       gi|242398551|ref|YP_002993975.1|  [L=224]
Description: hydantoin racemase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-14   54.3   0.2    6.7e-14   52.3   0.2    1.7  1  Asp_Glu_race     Asp/Glu/Hydantoin racemase
    3.9e-08   33.0   2.3    3.9e-05   23.2   0.1    2.1  2  Pantoate_transf  Ketopantoate hydroxymethyltransferase
      1e-05   25.3   0.2     0.0033   17.1   0.0    2.2  2  Amdase           Arylmalonate decarboxylase
    1.5e-05   24.5   0.1    4.1e-05   23.1   0.1    1.6  1  AroM             AroM protein
    0.00047   19.7   0.1        0.4   10.1   0.0    2.1  2  Peripla_BP_1     Periplasmic binding proteins and sugar bindi
     0.0012   19.2   0.2        1.6    9.1   0.0    2.1  2  HAD              haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.039   13.6   0.2        2.3    7.8   0.0    2.2  2  Peripla_BP_6     Periplasmic binding protein
       0.18   12.2   0.6         18    5.8   0.0    2.4  2  Nitro_FeMo-Co    Dinitrogenase iron-molybdenum cofactor


Domain annotation for each model (and alignments):
>> Asp_Glu_race  Asp/Glu/Hydantoin racemase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.3   0.2     3e-17   6.7e-14      41     216 ..      43     203 ..      28     207 .. 0.80

  Alignments for each domain:
  == domain 1  score: 52.3 bits;  conditional E-value: 3e-17
                                       TCHHHH.HCH.T..THHHHHHHHHHHHCTTESEEEE--CHHHHHHHHHHHH-SSEEEECHHHHHHHHHHHSS-EEEE CS
                      Asp_Glu_race  41 drteai.eeesgddpvlklleaakkLekagadaiviaCnTahavadelqkkikiPvlgiveataealkatgvkkvgl 116
                                       d ++ i +e++++++ +k+l+ ak++e+ g+dai+i C     +++e +k +++Pv+g +  +a al+   ++k+g+
  gi|242398551|ref|YP_002993975.1|  43 DQPKGIyDEKTEEEAKPKILRLAKEFENEGVDAIIISCAAD-PAVEEARKLVSVPVIG-AGSSASALALAYARKIGV 117
                                       55555523334444455**********************99.****************.99999999999******* PP

                                       EE-HHHHHCTHHHHHHHHHGT.EEE....T-CCCHHCCHCHHHHTT-TTSHHHHHHHHHHHHHHTTT-SEEEE-STT CS
                      Asp_Glu_race 117 LgTrgtlksglyqkeleanqgievvvpseelqssvnqaiyeelkaGevteearrailkllerlaergadaviLGCTe 193
                                       L   ++ + +++++ l ++  i      e++ + v      ++  + +t+  r++ +++ +rl+e+g++a++LGCT 
  gi|242398551|ref|YP_002993975.1| 118 LN-LTEETPRVIKEVLGDK-LI-----AEDHPEGV------SNTLDLMTDWGRKEAINAARRLKEKGVEAIVLGCTG 181
                                       *8.6666666777776663.45.....33333344......46677888888888888888899************* PP

                                       HHHHHHHHHHCC-TT.SEEEEHH CS
                      Asp_Glu_race 194 lplllekaealekeksvpvidpt 216
                                       ++++   a+ leke ++pvidp+
  gi|242398551|ref|YP_002993975.1| 182 MSTI-MIAPILEKEVGIPVIDPV 203
                                       **88.7777899999******96 PP

>> Pantoate_transf  Ketopantoate hydroxymethyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.1   1.7e-08   3.9e-05     155     231 ..      53     129 ..      44     140 .. 0.78
   2 !    9.7   0.4   0.00023      0.51     161     207 ..     158     209 ..     151     213 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1.7e-08
                   Pantoate_transf 155 kteeeaeklledakaleeaGafalvlEavpaelakeiteklsiptIGIGAGaacdGqvlvlhDllglt..ekfkpkf 229
                                        +ee++ k+l+ ak++e+ G+ a+++ +   +  +e  + +s+p+I  GAG++ ++  l +   +g+   ++++p+ 
  gi|242398551|ref|YP_002993975.1|  53 TEEEAKPKILRLAKEFENEGVDAIIISCAADPAVEEARKLVSVPVI--GAGSSASALALAYARKIGVLnlTEETPRV 127
                                       3566778**************************************9..67777777777777666665223445666 PP

                   Pantoate_transf 230 vk 231
                                       +k
  gi|242398551|ref|YP_002993975.1| 128 IK 129
                                       65 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00023
                   Pantoate_transf 161 eklledakaleeaGafalvlEavpae...lakeiteklsiptI..GIGAGaa 207
                                       ++ ++ a++l+e G+ a+vl ++  +   +a  + +++ ip+I   I+AGa 
  gi|242398551|ref|YP_002993975.1| 158 KEAINAARRLKEKGVEAIVLGCTGMStimIAPILEKEVGIPVIdpVIAAGAV 209
                                       677899***************987643338999**********777899875 PP

>> Amdase  Arylmalonate decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.0    0.0028       6.3     158     208 ..      69     119 ..      51     128 .. 0.68
   2 !   17.1   0.0   1.5e-06    0.0033     158     200 ..     168     211 ..     146     221 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0028
                            Amdase 158 aapeadallisCGGLrtldvvreledelglpvv...ssalAGlwdavrlaglda 208
                                       +++ +da++isC      ++v+e ++ + +pv+   ssa A + + +r++g  +
  gi|242398551|ref|YP_002993975.1|  69 ENEGVDAIIISCAAD---PAVEEARKLVSVPVIgagSSASALALAYARKIGVLN 119
                                       57889*******765...555566666777777554788888888888777655 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 1.5e-06
                            Amdase 158 aapeadallisCGGLrtldvvreledelglpvvssal.AGlwda 200
                                       +++ ++a+++ C G++t+ +   le+e+g+pv+     AG+  +
  gi|242398551|ref|YP_002993975.1| 168 KEKGVEAIVLGCTGMSTIMIAPILEKEVGIPVIDPVIaAGAVTL 211
                                       46789****************************87641465544 PP

>> AroM  AroM protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.1   1.8e-08   4.1e-05      68     207 ..      54     203 ..      51     211 .. 0.70

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1.8e-08
                              AroM  68 kekveprlqaaiakleeegvdlilllcTgefpelea.kapliepqrileslvaalvk..kkqlgvivPleeqaeqae 141
                                       +e+ +p++ +  +++e+egvd+i++ c  + p++e+ ++++  p     s  +al+    +++gv+  +ee  + ++
  gi|242398551|ref|YP_002993975.1|  54 EEEAKPKILRLAKEFENEGVDAIIISCAAD-PAVEEaRKLVSVPVIGAGSSASALALayARKIGVLNLTEETPRVIK 129
                                       5677888999999**************996.333332555555554444444444433378*****98888877777 PP

                              AroM 142 kkweelak.....evvvavaspygse..eelaeaarelaeqgadlivldciGYteem.kaavaealgkpVllar 207
                                       +   +        e v  + + + ++  +e  +aar+l+e+g++ ivl c G +  m + ++++++g+pV+ + 
  gi|242398551|ref|YP_002993975.1| 130 EVLGDKLIaedhpEGVSNTLDLMTDWgrKEAINAARRLKEKGVEAIVLGCTGMSTIMiAPILEKEVGIPVIDPV 203
                                       6665433333433445555555544345777789*******************98883568999******9774 PP

>> Peripla_BP_1  Periplasmic binding proteins and sugar binding domain of LacI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0   0.00069       1.5      41      88 ..      57     103 ..      47     144 .. 0.82
   2 !   10.1   0.0   0.00018       0.4      38      84 ..     153     201 ..     112     213 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00069
                                       SHHHHHHHHHHHHHTT-SEEEEE-S-GGHHHHHHHHHH.T-EEEEESS- CS
                      Peripla_BP_1  41 eeedlakaidllkakgidgliiatsdtsfdditakaes.gipvialeda 88 
                                        ++++++ ++  +++g+d++ii  +++   ++ +  +   +pvi ++  
  gi|242398551|ref|YP_002993975.1|  57 AKPKILRLAKEFENEGVDAIIISCAADP--AVEEARKLvSVPVIGAGSS 103
                                       567788999999**********866665..6666666667799988765 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00018
                                       E-SSHHHHHHHHHHHHHTT-SEEEEE-S-GGHHHHHH.HHHH.T-EEEE CS
                      Peripla_BP_1  38 aageeedlakaidllkakgidgliiatsdtsfddita.kaes.gipvia 84 
                                        + + +++ +a++ lk+kg+++++++  + s   i    +++ gipvi 
  gi|242398551|ref|YP_002993975.1| 153 TDWGRKEAINAARRLKEKGVEAIVLGCTGMSTIMIAPiLEKEvGIPVID 201
                                       344455556****************977777444443134445799985 PP

>> HAD  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   0.00073       1.6      68     160 ..      40     130 ..      15     149 .. 0.66
   2 !    8.6   0.0     0.001       2.3      88     130 ..     158     206 ..     137     221 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00073
                               HAD  68 elaaelerfvaevirpklldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevdd...rltge 141
                                       +++++ + +++e+ ++   +p++l+l ++   +G+  +++S++ +p ve+  +++    v++      +    +   
  gi|242398551|ref|YP_002993975.1|  40 CIEDQPKGIYDEKTEEE-AKPKILRLAKEFENEGVDAIIISCAADPAVEEARKLVS-VPVIGAGSSASAlalAY--- 111
                                       44555555554444444.55666777776669******************997666.66666633333333222... PP

                               HAD 142 lglegkpvrgegkvaalre 160
                                       ++ +g +   e+++++++e
  gi|242398551|ref|YP_002993975.1| 112 ARKIGVLNLTEETPRVIKE 130
                                       2346666666666666666 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.001
                               HAD  88 pgalellaahraaGdrvvvv..Sgglrplvepll.aelg...adevlat 130
                                        +a  + ++ +++G++ +v+  +g   +++ p+l +e+g   +d v+a 
  gi|242398551|ref|YP_002993975.1| 158 KEAINAARRLKEKGVEAIVLgcTGMSTIMIAPILeKEVGipvIDPVIAA 206
                                       56677777777********877999*********88***9999999987 PP

>> Peripla_BP_6  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.016        36      53      86 ..      81     110 ..      58     127 .. 0.71
   2 ?    7.8   0.0     0.001       2.3      55     100 ..     158     203 ..     153     213 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.016
                                       SHHHHHHHHHHHHHCT--SEEEE-BSHHHHHHHH CS
                      Peripla_BP_6  53 dpdraaeaarrlvdqdgvdalvgplssavaaava 86 
                                        +d a+e ar+lv+      ++g+ ssa a+a+a
  gi|242398551|ref|YP_002993975.1|  81 AADPAVEEARKLVS----VPVIGAGSSASALALA 110
                                       46778888888888....4566766666555553 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.001
                                       HHHHHHHHHHHHCT--SEEEE-BSHHHHHHHHHHHHH.HT-EEEESS CS
                      Peripla_BP_6  55 draaeaarrlvdqdgvdalvgplssavaaavaevlak.dgvpvigpa 100
                                       ++a++aarrl++ +gv a+v + +   +  +a++l+k  g+pvi p+
  gi|242398551|ref|YP_002993975.1| 158 KEAINAARRLKE-KGVEAIVLGCTGMSTIMIAPILEKeVGIPVIDPV 203
                                       57999*******.*****9999988889999****995689999965 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 ?    4.7   0.1     0.017        38      35      74 ..      53      92 ..      38     113 .. 0.72
   2 ?    5.8   0.0    0.0079        18      39      64 ..     156     181 ..     111     188 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.017
                                      CCCTSSCSSTHHHHHHHHTT-SEEEESSSCHHHHHHHCTT CS
                     Nitro_FeMo-Co 35 aadaegggggklaqllaeegvdvvivgkiGpralakleaa 74
                                        ++++ +  +la+  ++egvd++i +    +a+++ ++ 
  gi|242398551|ref|YP_002993975.1| 53 TEEEAKPKILRLAKEFENEGVDAIIISCAADPAVEEARKL 92
                                      556667788899999**********998888888777666 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0079
                                       SSCSSTHHHHHHHHTT-SEEEESSSC CS
                     Nitro_FeMo-Co  39 egggggklaqllaeegvdvvivgkiG 64 
                                       + ++ +++a++l+e+gv++++ g  G
  gi|242398551|ref|YP_002993975.1| 156 GRKEAINAARRLKEKGVEAIVLGCTG 181
                                       45778889999999999999877555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.59u 0.34s 00:00:00.93 Elapsed: 00:00:00.51
# Mc/sec: 1325.42
//
Query:       gi|242398552|ref|YP_002993976.1|  [L=119]
Description: Uncharacterized HTH-type transcriptional regulator, partial [Thermococcus sibiricus MM 739]
Scores for complete 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   26.5   0.0    5.9e-06   26.2   0.0    1.2  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
     0.0046   16.8   0.1      0.007   16.2   0.1    1.3  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
  ------ inclusion threshold ------
      0.021   14.4   0.1      0.038   13.6   0.1    1.5  1  HTH_24          Winged helix-turn-helix DNA-binding


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 !   26.2   0.0   9.9e-10   5.9e-06       1      60 [.      48     108 ..      48     114 .. 0.92

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 9.9e-10
                                       EEEEE-GGG.TTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTT CS
                    AsnC_trans_reg   1 vlvslepgh.peqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklas 60 
                                       vl++l+p+  +eq+ +f+++l e++   e+y + Gdyd+l+    +d+ +l++ ++e ++ 
  gi|242398552|ref|YP_002993976.1|  48 VLIKLKPEIpKEQIIQFKKKLMEHEHTFEVYEIWGDYDILVGTFGEDISDLRKSVVEIIQG 108
                                       799***777*******************************************999998775 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 !   16.2   0.1   1.2e-06     0.007      18      37 ..       1      20 [.       1      25 [. 0.85

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.2e-06
                     HTH_AsnC-type 18 isyaeLAervGlSestvlrR 37
                                      +s ae+++r+GlS s+v+ R
  gi|242398552|ref|YP_002993976.1|  1 MSDAEIGRRIGLSKSAVRWR 20
                                      6889*************755 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 ?   13.6   0.1   6.3e-06     0.038      19      45 ..       2      28 ..       1      30 [. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.3e-06
                            HTH_24 19 sqreLAerlglSpstvnrrlkrLeeeG 45
                                      s +e+ +r+glS+s+v++r  +L++ G
  gi|242398552|ref|YP_002993976.1|  2 SDAEIGRRIGLSKSAVRWRRINLQKRG 28
                                      668***************966666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 792.76
//
Query:       gi|242398553|ref|YP_002993977.1|  [L=108]
Description: DNA-directed RNA polymerase subunit m [Thermococcus sibiricus MM 739]
Scores for complete 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-22   77.3  14.2    1.8e-21   75.7   3.1    3.1  3  TFIIS_C          Transcription factor S-II (TFIIS)
    2.2e-14   53.0  13.1      1e-12   47.7   2.3    3.1  3  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
    8.1e-07   28.5  10.6    0.00097   18.6   1.8    2.8  2  TF_Zn_Ribbon     TFIIB zinc-binding
    1.5e-06   28.1  12.5     0.0034   17.3   2.2    3.2  3  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
    5.6e-06   26.2   6.5     0.0014   18.5   0.3    2.7  2  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
    1.2e-05   24.8  14.9       0.09   12.5   0.1    4.2  4  zinc_ribbon_2    zinc-ribbon domain
    2.4e-05   24.2   3.2      0.086   12.8   0.2    3.2  3  PhnA_Zn_Ribbon   PhnA Zinc-Ribbon
    4.3e-05   23.4   6.2      0.047   13.7   6.3    2.6  1  DZR              Double zinc ribbon
    0.00014   21.5   8.6      0.029   14.1   1.8    3.9  3  A2L_zn_ribbon    A2L zinc ribbon domain
    0.00015   21.4   0.0    0.00015   21.4   0.0    3.9  4  Baculo_LEF5_C    Baculoviridae late expression factor 5 C-ter
    0.00026   20.8  12.3       0.47   10.4   0.2    4.3  3  zinc_ribbon_4    zinc-ribbon domain
    0.00062   19.1  17.7      0.072   12.5   4.9    4.0  3  zf-ribbon_3      zinc-ribbon domain
     0.0011   18.5  12.8        1.6    8.4   0.8    4.2  4  zf_C2H2_10       C2H2 type zinc-finger
     0.0014   18.9   9.4      0.014   15.6   1.0    2.9  2  IBR              IBR domain, a half RING-finger domain
     0.0081   16.5   8.0       0.42   11.0   0.6    2.6  2  Lar_restr_allev  Restriction alleviation protein Lar
     0.0081   16.3  14.0        2.8    8.2   2.7    4.0  3  zinc_ribbon_13   Nucleic-acid-binding protein containing Zn-r
  ------ inclusion threshold ------
       0.01   15.8   2.4       0.51   10.4   0.1    2.5  2  Elf1             Transcription elongation factor Elf1 like
      0.016   15.2   6.4       0.45   10.6   3.1    2.8  2  HypA             Hydrogenase/urease nickel incorporation, met
      0.022   14.9   3.6      0.022   14.9   3.6    2.8  3  Auto_anti-p27    Sjogren's syndrome/scleroderma autoantigen 1
      0.028   14.3   9.0        6.4    6.8   0.1    4.0  4  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
      0.033   13.9   7.8       0.41   10.4   0.3    3.0  2  Ribosomal_S27e   Ribosomal protein S27
       0.06   13.0  10.7        2.1    8.0   0.1    4.1  4  zf_UBZ           Ubiquitin-Binding Zinc Finger
      0.071   13.4   6.0          1    9.7   6.0    2.4  1  Rpr2             RNAse P Rpr2/Rpp21/SNM1 subunit domain
      0.078   13.1   8.5          2    8.6   1.5    2.6  2  DUF2387          Probable metal-binding protein (DUF2387)
      0.078   13.1  11.7        4.3    7.5   0.2    3.6  3  zf-Mss51         Zinc-finger of mitochondrial splicing suppre
      0.088   12.9  13.9        1.8    8.7   2.7    4.0  3  zf-ACC           Acetyl-coA carboxylase zinc finger domain
      0.098   12.5   3.8        0.4   10.6   0.1    2.2  2  eIF-5_eIF-2B     Domain found in IF2B/IF5
       0.11   12.4   0.1       0.11   12.4   0.1    2.7  3  Cys_rich_CPCC    Cysteine-rich CPCC
       0.11   12.4  17.6        3.6    7.6   2.5    4.1  2  Nudix_N_2        Nudix N-terminal
       0.12   12.5  16.7        4.6    7.4   0.4    4.3  4  UPF0547          Uncharacterised protein family UPF0547
       0.14   12.1   5.8        1.1    9.3   0.2    2.6  2  zinc-ribbons_6   zinc-ribbons
       0.15   11.8  20.2       0.38   10.5   0.1    4.1  4  Rubredoxin_2     Rubredoxin metal binding domain
       0.18   11.6   1.8        3.3    7.5   0.3    2.1  2  CK_II_beta       Casein kinase II regulatory subunit
       0.22   12.1   4.4         10    6.8   4.4    2.7  1  RPA_interact_C   Replication protein A interacting C-terminal
        0.3   11.2   9.3        1.3    9.2   0.8    3.1  2  Ribosomal_L37ae  Ribosomal L37ae protein family
       0.34   11.0  18.4         10    6.3   0.8    4.3  3  Zn-ribbon_8      Zinc ribbon domain
       0.39    9.2   3.8       0.26    9.8   0.6    1.9  2  Terminase_GpA    Phage terminase large subunit (GpA)
       0.44   10.3  13.0        7.5    6.3   2.5    3.5  3  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
       0.46   10.1   3.9        1.9    8.1   0.4    2.1  2  DpnI             Dam-replacing family
       0.49   10.2  13.7       0.41   10.4   2.4    3.7  2  zinc_ribbon_10   Predicted integral membrane zinc-ribbon meta
       0.61    9.5  13.1          1    8.8   1.4    3.1  2  zf-TFIIB         Transcription factor zinc-finger
       0.68    9.6  15.6        6.4    6.5   0.2    4.1  4  zf-tcix          Putative treble-clef, zinc-finger, Zn-bindin
       0.88    9.6  12.1        2.1    8.4   1.4    3.9  4  CpXC             CpXC protein
        1.9    9.0  13.4         14    6.3   0.2    4.1  4  zf-H2C2_2        Zinc-finger double domain
        2.1    8.1  12.3        4.2    7.1   3.9    3.6  3  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
        2.8    8.0  12.0         10    6.2   0.2    4.0  4  ADK_lid          Adenylate kinase, active site lid
        2.9    7.8  16.6        3.1    7.8   5.5    3.1  2  DUF3797          Domain of unknown function (DUF3797)
        3.1    8.6  11.6        6.1    7.7   3.4    3.1  2  zinc_ribbon_15   zinc-ribbon family
        3.3    7.7   9.6       0.85    9.6   1.1    2.6  2  C1_1             Phorbol esters/diacylglycerol binding domain
        3.7    6.7   5.7        2.3    7.4   0.4    2.3  2  Baculo_ME53      Baculoviridae ME53
        3.8    7.6  18.1        2.5    8.2   0.6    4.1  4  DUF1610          Domain of unknown function (DUF1610)
        5.6    7.0  11.5        1.3    9.1   1.9    3.0  3  Ogr_Delta        Ogr/Delta-like zinc finger
        5.7    7.0   9.4        2.7    8.0   1.0    3.0  3  Prok-RING_1      Prokaryotic RING finger family 1
          6    6.9  15.5        4.5    7.3   1.0    3.6  3  Zn_ribbon_SprT   SprT-like zinc ribbon domain
          6    7.1  16.3        6.7    7.0   4.5    3.7  3  NOB1_Zn_bind     Nin one binding (NOB1) Zn-ribbon like
        6.4    6.6  16.2        5.7    6.8   3.0    3.3  2  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger
        7.4    7.3  14.5        7.2    7.4   0.1    4.0  4  zf-ISL3          zinc-finger of transposase IS204/IS1001/IS10
        8.4    6.8   7.2        2.2    8.6   0.7    2.4  2  DUF3268          zinc-finger-containing domain


Domain annotation for each model (and alignments):
>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.3      0.11        33       2       8 ..       3       9 ..       2      11 .. 0.84
   2 ?    4.4   0.2      0.11        34      29      36 ..      20      27 ..      17      29 .. 0.72
   3 !   75.7   3.1   5.9e-24   1.8e-21       1      39 []      67     105 ..      67     105 .. 0.98

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.11
                           TFIIS_C 2 kCpkCgs 8
                                      CpkCg+
  gi|242398553|ref|YP_002993977.1| 3 FCPKCGN 9
                                     5****97 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.11
                           TFIIS_C 29 ykCtkCgh 36
                                      ++C kCg+
  gi|242398553|ref|YP_002993977.1| 20 FVCRKCGY 27
                                      67777776 PP

  == domain 3  score: 75.7 bits;  conditional E-value: 5.9e-24
                           TFIIS_C   1 akCpkCgsreayffqlQtRsaDEpmtvfykCtkCghrWr 39 
                                       ++CpkCg++eay+++lQtR++DEp+t+fy+CtkCg++Wr
  gi|242398553|ref|YP_002993977.1|  67 ITCPKCGNDEAYWWELQTRAGDEPSTIFYRCTKCGYTWR 105
                                       68************************************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 !   47.7   2.3   3.3e-15     1e-12       1      34 [.       1      32 [.       1      34 [. 0.93
   2 ?    5.2   0.8     0.062        19       4       9 ..      69      74 ..      67      74 .. 0.96
   3 ?    6.7   0.1     0.021       6.4      16      29 ..      88     102 ..      82     104 .. 0.79

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 3.3e-15
                                      EEBESTTTSBEEEEECSCCCEEEESSSS-EEESS CS
                    RNA_POL_M_15KD  1 lkFCpkCgNlLlpkedkegknfeCrqCgYeepad 34
                                      +kFCpkCgN +lp++++ +  f Cr+CgYeep d
  gi|242398553|ref|YP_002993977.1|  1 MKFCPKCGNIMLPDKKRGV--FVCRKCGYEEPLD 32
                                      9*************99999..67*********87 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.062
                                      ESTTTS CS
                    RNA_POL_M_15KD  4 CpkCgN 9 
                                      CpkCgN
  gi|242398553|ref|YP_002993977.1| 69 CPKCGN 74
                                      *****9 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.021
                                       CSCCCE.EEESSSS- CS
                    RNA_POL_M_15KD  16 dkegkn.feCrqCgY 29 
                                       d+  ++ + C +CgY
  gi|242398553|ref|YP_002993977.1|  88 DEPSTIfYRCTKCGY 102
                                       555667899****** PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   1.8   3.1e-06   0.00097       3      27 ..       4      27 ..       3      31 .. 0.90
   2 !   13.7   1.8    0.0001     0.032       2      27 ..      68     102 ..      67     104 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 3.1e-06
                                      ETTTTCEECHEETSTTCEEESSSSB CS
                      TF_Zn_Ribbon  3 CPnCgstnlveDpergelvCtdCGl 27
                                      CP+Cg+  ++ D +rg +vC +CG+
  gi|242398553|ref|YP_002993977.1|  4 CPKCGNI-MLPDKKRGVFVCRKCGY 27
                                      *****86.59**************7 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 0.0001
                                       EETTTTCEE.C.......HEE.TSTTCEEESSSSB CS
                      TF_Zn_Ribbon   2 kCPnCgstn.l.......veD.pergelvCtdCGl 27 
                                       +CP+Cg+++ +         D p++  ++Ct+CG+
  gi|242398553|ref|YP_002993977.1|  68 TCPKCGNDEaYwwelqtrAGDePSTIFYRCTKCGY 102
                                       8******997799999885555888888******7 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   4.8    0.0013       0.4      21      45 ..       4      27 ..       2      28 .. 0.87
   2 !   12.1   0.0   0.00048      0.15      18      38 ..      15      39 ..       9      40 .. 0.79
   3 !   17.3   2.2   1.1e-05    0.0034      19      46 .]      67     103 ..      63     103 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0013
                     Zn_Tnp_IS1595 21 CPhCgsrkayriktrglfqCkeCrk 45
                                      CP+Cg+  +   k+ g+f C++C++
  gi|242398553|ref|YP_002993977.1|  4 CPKCGNIMLPDKKR-GVFVCRKCGY 27
                                      *****998888886.********98 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00048
                     Zn_Tnp_IS1595 18 g....fvCPhCgsrkayriktrglf 38
                                      +    fvC +Cg++++  ++t+ ++
  gi|242398553|ref|YP_002993977.1| 15 KkrgvFVCRKCGYEEPLDLETASKY 39
                                      444569**********999998777 PP

  == domain 3  score: 17.3 bits;  conditional E-value: 1.1e-05
                     Zn_Tnp_IS1595  19 fvCPhCgsrkay..rikt.......rglfqCkeCrkq 46 
                                        +CP+Cg+++ay  +++t          ++C +C+++
  gi|242398553|ref|YP_002993977.1|  67 ITCPKCGNDEAYwwELQTragdepsTIFYRCTKCGYT 103
                                       68*******66522666699****99********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 !   18.5   0.3   4.6e-06    0.0014      30      56 ..       3      29 ..       2      37 .. 0.88
   2 !    9.8   1.4    0.0023      0.71      29      56 ..      67     104 ..      38     105 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 4.6e-06
                    OrfB_Zn_ribbon 30 tCseCgsknkealsgrtfkCpnCgfea 56
                                       C++Cg ++ +++++ +f+C++Cg+e 
  gi|242398553|ref|YP_002993977.1|  3 FCPKCGNIMLPDKKRGVFVCRKCGYEE 29
                                      5**********9************985 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0023
                    OrfB_Zn_ribbon  29 ktCseCgsknke..........alsgrtfkCpnCgfea 56 
                                        tC++Cg    +          ++s+  ++C++Cg+++
  gi|242398553|ref|YP_002993977.1|  67 ITCPKCGNDEAYwwelqtragdEPSTIFYRCTKCGYTW 104
                                       59******999999999888877888889******987 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.1   0.00029      0.09      14      20 ..       2       8 ..       1      17 [. 0.77
   2 ?    5.8   0.4     0.038        12       2       8 ..      22      28 ..      18      28 .. 0.58
   3 !    9.0   0.1    0.0038       1.2       2       7 ..      69      74 ..      60      75 .. 0.67
   4 ?    6.1   0.7      0.03       9.2       1       7 [.      96     102 ..      94     103 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00029
                     zinc_ribbon_2 14 kFCpyCG 20
                                      kFCp+CG
  gi|242398553|ref|YP_002993977.1|  2 KFCPKCG 8 
                                      6777777 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.038
                     zinc_ribbon_2  2 CpnCGae 8 
                                      C +CG+e
  gi|242398553|ref|YP_002993977.1| 22 CRKCGYE 28
                                      5555543 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0038
                     zinc_ribbon_2  2 CpnCGa 7 
                                      Cp+CG+
  gi|242398553|ref|YP_002993977.1| 69 CPKCGN 74
                                      555555 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.03
                     zinc_ribbon_2   1 fCpnCGa 7  
                                       +C++CG+
  gi|242398553|ref|YP_002993977.1|  96 RCTKCGY 102
                                       5777775 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.2      0.38   1.2e+02      22      26 ..       4       8 ..       3      10 .. 0.68
   2 !    7.9   0.0    0.0099       3.1      17      28 ..      17      28 ..      12      28 .. 0.90
   3 !   12.8   0.2   0.00028     0.086       4      29 ..      68     104 ..      61     105 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.38
                    PhnA_Zn_Ribbon 22 CpeCa 26
                                      Cp+C+
  gi|242398553|ref|YP_002993977.1|  4 CPKCG 8 
                                      66665 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0099
                    PhnA_Zn_Ribbon 17 gallvCpeCahE 28
                                      + ++vC +C++E
  gi|242398553|ref|YP_002993977.1| 17 RGVFVCRKCGYE 28
                                      579*******98 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 0.00028
                    PhnA_Zn_Ribbon   4 kCplCaSeytY...........edgallvCpeCahEw 29 
                                        Cp+C+ +++Y             +  + C +C++ w
  gi|242398553|ref|YP_002993977.1|  68 TCPKCGNDEAYwwelqtragdePSTIFYRCTKCGYTW 104
                                       5********************999999*******988 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   6.3   0.00015     0.047       1      37 [.       4      75 ..       4     106 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00015
                               DZR  1 CpqCgeelppdar....fCseCgtk..lkavaa.............................edrCpsCgek 37
                                      Cp+Cg+ + pd++    +C +Cg +  l+ ++a                             +++Cp+Cg +
  gi|242398553|ref|YP_002993977.1|  4 CPKCGNIMLPDKKrgvfVCRKCGYEepLDLETAskykitqkikhdredipvieqdvatlpkvKITCPKCGND 75
                                      ******966666668889*****8877444444679999***********************999***9976 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 !   14.1   1.8   9.2e-05     0.029       5      33 .]       3      31 ..       2      31 .. 0.93
   2 ?    5.0   0.0     0.065        20      24      29 ..      69      74 ..      66      87 .. 0.65
   3 ?    3.0   0.1      0.28        87      24      29 ..      97     102 ..      94     104 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 9.2e-05
                     A2L_zn_ribbon  5 vCsvCggngilnseqgylvCieCgasfpy 33
                                       C +Cg+ ++  +++g  vC +Cg+++p+
  gi|242398553|ref|YP_002993977.1|  3 FCPKCGNIMLPDKKRGVFVCRKCGYEEPL 31
                                      5999**********************995 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.065
                     A2L_zn_ribbon 24 CieCga 29
                                      C++Cg+
  gi|242398553|ref|YP_002993977.1| 69 CPKCGN 74
                                      666655 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.28
                     A2L_zn_ribbon  24 CieCga 29 
                                       C +Cg+
  gi|242398553|ref|YP_002993977.1|  97 CTKCGY 102
                                       777777 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 ?    0.5   0.3       1.5   4.8e+02      35      41 ..       2       8 ..       1       9 [. 0.83
   2 ?    2.8   0.5      0.32        97      36      41 ..      21      26 ..      19      27 .. 0.84
   3 ?   -0.1   0.3       2.5   7.7e+02      36      41 ..      68      73 ..      65      74 .. 0.85
   4 !   21.4   0.0   4.8e-07   0.00015      21      41 ..      81     101 ..      75     102 .. 0.95

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 1.5
                     Baculo_LEF5_C 35 ryCskCg 41
                                      + C kCg
  gi|242398553|ref|YP_002993977.1|  2 KFCPKCG 8 
                                      68****9 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.32
                     Baculo_LEF5_C 36 yCskCg 41
                                      +C+kCg
  gi|242398553|ref|YP_002993977.1| 21 VCRKCG 26
                                      7****9 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 2.5
                     Baculo_LEF5_C 36 yCskCg 41
                                      +C kCg
  gi|242398553|ref|YP_002993977.1| 68 TCPKCG 73
                                      6****9 PP

  == domain 4  score: 21.4 bits;  conditional E-value: 4.8e-07
                     Baculo_LEF5_C  21 EiQnRagDEivsfvryCskCg 41 
                                       E Q+RagDE   +   C kCg
  gi|242398553|ref|YP_002993977.1|  81 ELQTRAGDEPSTIFYRCTKCG 101
                                       99******************9 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   2.9      0.52   1.6e+02      28      34 ..       4      10 ..       4      28 .. 0.64
   2 !    9.9   0.1    0.0022      0.67      24      33 ..      65      74 ..      60      75 .. 0.81
   3 !   10.4   0.2    0.0015      0.47      27      36 .]      96     105 ..      89     105 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.52
                     zinc_ribbon_4 28 CskCghv 34
                                      C+kCg++
  gi|242398553|ref|YP_002993977.1|  4 CPKCGNI 10
                                      6666654 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0022
                     zinc_ribbon_4 24 vkvrCskCgh 33
                                      vk++C+kCg+
  gi|242398553|ref|YP_002993977.1| 65 VKITCPKCGN 74
                                      7888888886 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.0015
                     zinc_ribbon_4  27 rCskCghvFr 36 
                                       rC+kCg ++r
  gi|242398553|ref|YP_002993977.1|  96 RCTKCGYTWR 105
                                       9********7 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   4.9   0.00023     0.072       2      24 ..       1      27 [.       1      28 [. 0.78
   2 !    9.6   0.4     0.002      0.61       3      10 ..      67      74 ..      65      75 .. 0.66
   3 ?    2.9   0.4      0.25        79      19      24 ..      97     102 ..      94     103 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00023
                       zf-ribbon_3  2 tvrCPnCGa.pl...ssddnvCpyCGt 24
                                      +++CP+CG+  l   + ++ vC +CG+
  gi|242398553|ref|YP_002993977.1|  1 MKFCPKCGNiMLpdkKRGVFVCRKCGY 27
                                      89*******54744455888*****98 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.002
                       zf-ribbon_3  3 vrCPnCGa 10
                                      ++CP+CG+
  gi|242398553|ref|YP_002993977.1| 67 ITCPKCGN 74
                                      66777775 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.25
                       zf-ribbon_3  19 CpyCGt 24 
                                       C++CG+
  gi|242398553|ref|YP_002993977.1|  97 CTKCGY 102
                                       888886 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 !    8.4   0.8    0.0051       1.6       5      14 ..       4      14 ..       2      15 .. 0.80
   2 ?    6.9   0.0     0.015       4.5       3      15 ..      20      33 ..      19      36 .. 0.81
   3 ?    6.6   0.4     0.018       5.4       4       9 ..      68      73 ..      66      76 .. 0.82
   4 ?    2.9   0.1      0.27        83       4      11 ..      96     103 ..      94     104 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0051
                        zf_C2H2_10  5 CPKCqek.lPD 14
                                      CPKC+ + lPD
  gi|242398553|ref|YP_002993977.1|  4 CPKCGNImLPD 14
                                      ****8863787 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.015
                        zf_C2H2_10  3 fsCPKCqeklP.Di 15
                                      f C KC++  P D+
  gi|242398553|ref|YP_002993977.1| 20 FVCRKCGYEEPlDL 33
                                      89******999555 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.018
                        zf_C2H2_10  4 sCPKCq 9 
                                       CPKC+
  gi|242398553|ref|YP_002993977.1| 68 TCPKCG 73
                                      7****8 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.27
                        zf_C2H2_10   4 sCPKCqek 11 
                                        C KC++ 
  gi|242398553|ref|YP_002993977.1|  96 RCTKCGYT 103
                                       6*****95 PP

>> IBR  IBR domain, a half RING-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   1.0   4.6e-05     0.014      19      47 ..       2      28 ..       1      29 [. 0.92
   2 ?    6.4   1.9     0.033        10      18      47 ..      66     103 ..      34     104 .. 0.59

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.6e-05
                               IBR 19 kwCprpdCeaiieksegcksvtCskCgfe 47
                                      k Cp  +C++i+ ++++ +   C+kCg+e
  gi|242398553|ref|YP_002993977.1|  2 KFCP--KCGNIMLPDKKRGVFVCRKCGYE 28
                                      79**..***********99999*****97 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.033
                               IBR  18 lkwCprpdCe..aii..eksegcks......vtCskCgfe 47 
                                       ++ Cp  +C+   ++  e +   ++       +C+kCg+ 
  gi|242398553|ref|YP_002993977.1|  66 KITCP--KCGndEAYwwELQTRAGDepstifYRCTKCGYT 103
                                       67788..777442223333333111345555668888875 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 !    8.7   1.6    0.0071       2.2       4      37 ..       2      34 ..       1      52 [. 0.64
   2 !   11.0   0.6    0.0014      0.42       5      36 ..      68     102 ..      65     108 .] 0.78

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0071
                   Lar_restr_allev  4 kpCPfCggravlersqrvvaeigqcvyCadCga......s 37
                                      k CP Cg+     +  r+      ++ C +Cg+       
  gi|242398553|ref|YP_002993977.1|  2 KFCPKCGNIMLPDKK-RG------VFVCRKCGYeepldlE 34
                                      669***987665555.33......578*****95443331 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.0014
                   Lar_restr_allev   5 pCPfCggravlersqrvvaeigq...cvyCadCga 36 
                                        CP Cg+++ +  + +++a+ ++   +  C++Cg+
  gi|242398553|ref|YP_002993977.1|  68 TCPKCGNDEAYWWELQTRAGDEPstiFYRCTKCGY 102
                                       5*****99987666666666666779999*****9 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 ?    2.6   0.4      0.51   1.6e+02       2       7 ..       4       9 ..       3      16 .. 0.83
   2 ?    7.6   0.2     0.013       4.1      36      51 ..      20      35 ..      12      43 .. 0.74
   3 !    8.2   2.7     0.009       2.8       1      44 [.      68     103 ..      68     104 .. 0.67

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.51
                    zinc_ribbon_13 2 CpKCgn 7
                                     CpKCgn
  gi|242398553|ref|YP_002993977.1| 4 CPKCGN 9
                                     ****98 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.013
                    zinc_ribbon_13 36 vsCknCgYtelYkaet 51
                                        C++CgY e  + et
  gi|242398553|ref|YP_002993977.1| 20 FVCRKCGYEEPLDLET 35
                                      57******99666555 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.009
                    zinc_ribbon_13   1 kCpKCgnteaevkevaatGs.glskifdvqnkkfitvsCknCgYt 44 
                                       +CpKCgn+ea   e+++  +   s          i+  C++CgYt
  gi|242398553|ref|YP_002993977.1|  68 TCPKCGNDEAYWWELQTRAGdEPST---------IFYRCTKCGYT 103
                                       5999999999999998754403333.........34467777776 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.5     0.066        20      42      54 ..      16      28 ..       3      54 .. 0.59
   2 ?   10.4   0.1    0.0016      0.51      18      53 ..      63     102 ..      44     106 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.066
                              Elf1 42 kiaevsCkvCges 54
                                      k+++  C++Cg +
  gi|242398553|ref|YP_002993977.1| 16 KRGVFVCRKCGYE 28
                                      4555555555543 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0016
                              Elf1  18 lptkFdCpfCnheksvevkldkkek....iaevsCkvCge 53 
                                        + k +Cp C+++++   +l+++ +    +   +C++Cg 
  gi|242398553|ref|YP_002993977.1|  63 PKVKITCPKCGNDEAYWWELQTRAGdepsTIFYRCTKCGY 102
                                       456789*************999999888888889****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 ?    8.5   0.8    0.0062       1.9      72     107 ..       3      41 ..       1      45 [. 0.72
   2 ?   10.6   3.1    0.0015      0.45      68      96 ..      17      76 ..      14     104 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0062
                                       EETTTS-EEECHHH..HHS-TTTSSS.-EEEEESSSEEE CS
                              HypA  72 rCreCgkefeleek..alrCpkCgsa.dveivsGeellv 107
                                        C +Cg+ +  ++k   + C kCg +  +++ + +  ++
  gi|242398553|ref|YP_002993977.1|   3 FCPKCGNIMLPDKKrgVFVCRKCGYEePLDLETASKYKI 41 
                                       5999*99998776447889****9763566666666555 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0015
                                      --EEEETTTS-EEECHHHHH...............................S-TTTSSS- CS
                              HypA 68 pvkvrCreCgkefeleekal...............................rCpkCgsad 96
                                      + ++ Cr+Cg+e  l+ +++                               +CpkCg+ +
  gi|242398553|ref|YP_002993977.1| 17 RGVFVCRKCGYEEPLDLETAskykitqkikhdredipvieqdvatlpkvkiTCPKCGNDE 76
                                      67899*****999877531135688999****************************9876 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 ?   14.9   3.6   7.1e-05     0.022      18      40 .]       4      26 ..       2      26 .. 0.94
   2 ?    4.1   0.1      0.17        53      34      40 .]      67      73 ..      53      74 .. 0.72
   3 ?   -1.3   0.3       8.5   2.6e+03      18      22 ..      97     101 ..      95     103 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 7.1e-05
                     Auto_anti-p27 18 CpvCgvPLmrdrkggkvyCvaCd 40
                                      Cp+Cg +++ d+k+g  +C  C+
  gi|242398553|ref|YP_002993977.1|  4 CPKCGNIMLPDKKRGVFVCRKCG 26
                                      **********************6 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.17
                     Auto_anti-p27 34 vyCvaCd 40
                                      + C+ C+
  gi|242398553|ref|YP_002993977.1| 67 ITCPKCG 73
                                      5555553 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 8.5
                     Auto_anti-p27  18 CpvCg 22 
                                       C +Cg
  gi|242398553|ref|YP_002993977.1|  97 CTKCG 101
                                       77786 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 ?    3.8   0.1      0.18        56      27      32 ..       3       8 ..       2      13 .. 0.70
   2 ?    1.1   0.4       1.2   3.8e+02      14      18 ..      22      26 ..      21      27 .. 0.72
   3 ?    5.7   0.0     0.046        14      26      34 ..      67      75 ..      60      77 .. 0.76
   4 ?    6.8   0.1     0.021       6.4       3      18 ..      86     101 ..      84     103 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.18
                           DUF35_N 27 vCphCg 32
                                      +Cp+Cg
  gi|242398553|ref|YP_002993977.1|  3 FCPKCG 8 
                                      577776 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 1.2
                           DUF35_N 14 CpdCG 18
                                      C++CG
  gi|242398553|ref|YP_002993977.1| 22 CRKCG 26
                                      88887 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.046
                           DUF35_N 26 avCphCgsd 34
                                        Cp+Cg d
  gi|242398553|ref|YP_002993977.1| 67 ITCPKCGND 75
                                      679999976 PP

  == domain 4  score: 6.8 bits;  conditional E-value: 0.021
                           DUF35_N   3 aaaegrLvgqrCpdCG 18 
                                       a++e+  ++ rC++CG
  gi|242398553|ref|YP_002993977.1|  86 AGDEPSTIFYRCTKCG 101
                                       6778888899*****9 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.3    0.0013      0.41      10      52 ..       4      47 ..       2      50 .. 0.86
   2 ?    4.8   2.1     0.076        24       6      17 ..      65      76 ..      64     104 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0013
                                      -TTTS-EEEEESS-SS-EEESSST..CEEEEECSSSEEESSCEEE CS
                    Ribosomal_S27e 10 CpdCenetvvFshaatvvkCisCg..kvLvePtGGkaklkaqile 52
                                      Cp+C+n+    ++   v  C +Cg  ++L   t  k k++++i+ 
  gi|242398553|ref|YP_002993977.1|  4 CPKCGNIM-LPDKKRGVFVCRKCGyeEPLDLETASKYKITQKIKH 47
                                      ******96.57999999******9556899999999999999986 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.076
                                      EEEE-TTTS-EE CS
                    Ribosomal_S27e  6 ldvkCpdCenet 17
                                      +++ Cp+C+n  
  gi|242398553|ref|YP_002993977.1| 65 VKITCPKCGNDE 76
                                      5899****9965 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.1    0.0068       2.1       3      16 ..       2      15 ..       1      17 [. 0.83
   2 ?    2.6   0.1      0.33     1e+02       3       9 ..      20      26 ..      18      34 .. 0.84
   3 ?    5.3   0.1     0.049        15       3       9 ..      67      73 ..      65      83 .. 0.88
   4 ?    1.8   0.6      0.59   1.8e+02       3       9 ..      95     101 ..      94     103 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0068
                            zf_UBZ  3 ylCerCgkeipese 16
                                       +C++Cg  +++++
  gi|242398553|ref|YP_002993977.1|  2 KFCPKCGNIMLPDK 15
                                      59******999886 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.33
                            zf_UBZ  3 ylCerCg 9 
                                      ++C +Cg
  gi|242398553|ref|YP_002993977.1| 20 FVCRKCG 26
                                      89****9 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.049
                            zf_UBZ  3 ylCerCg 9 
                                      ++C++Cg
  gi|242398553|ref|YP_002993977.1| 67 ITCPKCG 73
                                      79****9 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.59
                            zf_UBZ   3 ylCerCg 9  
                                       y C +Cg
  gi|242398553|ref|YP_002993977.1|  95 YRCTKCG 101
                                       89****8 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 ?    9.7   6.0    0.0033         1      46      89 ..       2     100 ..       1     101 [. 0.68

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0033
                                       TB-TTT--B--CTTTEEEEE............E-SSS-E...................................... CS
                              Rpr2  46 tvCkkCgsvlipgvtcsvrv............enkskkkkkkkkka............................... 79 
                                       ++C kCg++++p  +  v v            e +sk k  +   +                               
  gi|242398553|ref|YP_002993977.1|   2 KFCPKCGNIMLPDKKRGVFVcrkcgyeepldlETASKYKITQ---Kikhdredipvieqdvatlpkvkitcpkcgnd 75 
                                       79******************8888887777773333332222...02346678999999999998666666666666 PP

                                       .................EEEEETTT CS
                              Rpr2  80 ...............dvlvvtClaC 89 
                                                       ++ ++C++C
  gi|242398553|ref|YP_002993977.1|  76 eaywwelqtragdepSTIFYRCTKC 100
                                       6666666666666665556666666 PP

>> DUF2387  Probable metal-binding protein (DUF2387)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.9    0.0091       2.8      11      62 ..       4      50 ..       2      63 .. 0.75
   2 ?    8.6   1.5    0.0064         2      10      39 ..      68     103 ..      65     106 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0091
                           DUF2387 11 CPrCsemDkirmweedeveyrECvsCgftdelsekgqsvakelktrvnkdee 62
                                      CP+C +     m  + ++ +  C +Cg+ + l+ + ++ + ++++++ +d+e
  gi|242398553|ref|YP_002993977.1|  4 CPKCGNI----MLPDKKRGVFVCRKCGYEEPLDLE-TASKYKITQKIKHDRE 50
                                      8888863....66777788999********99998.5556666667766654 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0064
                           DUF2387  10 vCPrCsemDkirmwe.....ede..veyrECvsCgft 39 
                                        CP+C + D+  +we      de  + +  C++Cg+t
  gi|242398553|ref|YP_002993977.1|  68 TCPKCGN-DEAYWWElqtraGDEpsTIFYRCTKCGYT 103
                                       6****96.6666666222222222355678******8 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 ?    4.1   2.4      0.16        49       2      24 ..       4      27 ..       3      30 .. 0.76
   2 ?    7.5   0.2     0.014       4.3      11      23 ..      61      73 ..      41      81 .. 0.82
   3 ?    7.3   2.9     0.017       5.1       2      25 ..      69     103 ..      69     105 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.16
                          zf-Mss51  2 CPvpkhkqt.apkhvdfeCpdCGi 24
                                      CP + + +  ++k+  f C +CG+
  gi|242398553|ref|YP_002993977.1|  4 CPKCGNIMLpDKKRGVFVCRKCGY 27
                                      8888655445678889******97 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.014
                          zf-Mss51 11 apkhvdfeCpdCG 23
                                      +  +v+++Cp+CG
  gi|242398553|ref|YP_002993977.1| 61 TLPKVKITCPKCG 73
                                      55689*******9 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.017
                          zf-Mss51   2 CPvpkhkqt...........apkhvdfeCpdCGip 25 
                                       CP + ++++           +p+ + + C +CG+ 
  gi|242398553|ref|YP_002993977.1|  69 CPKCGNDEAywwelqtragdEPSTIFYRCTKCGYT 103
                                       999998888999999999999************85 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   2.7    0.0057       1.8       4      26 .]       4      25 ..       4      25 .. 0.87
   2 ?    5.2   0.8     0.073        22       2       8 ..      67      73 ..      67      74 .. 0.73
   3 ?    2.6   0.1      0.46   1.4e+02       3       8 ..      96     101 ..      94     103 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0057
                            zf-ACC  4 CpsCgemlykkeLernlyVCPkC 26
                                      Cp+Cg++++  +  r  +VC+kC
  gi|242398553|ref|YP_002993977.1|  4 CPKCGNIMLP-DKKRGVFVCRKC 25
                                      ********95.557999999999 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.073
                            zf-ACC  2 tKCpsCg 8 
                                      + Cp+Cg
  gi|242398553|ref|YP_002993977.1| 67 ITCPKCG 73
                                      5689988 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.46
                            zf-ACC   3 KCpsCg 8  
                                       +C++Cg
  gi|242398553|ref|YP_002993977.1|  96 RCTKCG 101
                                       799998 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 ?    3.2   0.6      0.25        78      90     116 ..       4      27 ..       2      28 .. 0.65
   2 ?   10.6   0.1    0.0013       0.4      88     116 ..      67     102 ..      32     103 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.25
                                       TSSSTSTCEEECCSSSCEEEEESSSTC CS
                      eIF-5_eIF-2B  90 CkeCkspetelekeerllvlkCkaCga 116
                                       C++C++    l  ++r  v+ C++Cg 
  gi|242398553|ref|YP_002993977.1|   4 CPKCGNIM--LPDKKRG-VFVCRKCGY 27 
                                       99998764..3333443.478****96 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0013
                                       TSTSSSTSTCEEECC.......SSSCEEEEESSSTC CS
                      eIF-5_eIF-2B  88 VlCkeCkspetelek.......eerllvlkCkaCga 116
                                       ++C++C++ e            e ++++ +C++Cg 
  gi|242398553|ref|YP_002993977.1|  67 ITCPKCGNDEAYWWElqtragdEPSTIFYRCTKCGY 102
                                       89******99754333337776788999******96 PP

>> Cys_rich_CPCC  Cysteine-rich CPCC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00034      0.11       3      29 ..       4      30 ..       2      45 .. 0.80
   2 ?   -0.5   0.1       3.6   1.1e+03       2       8 ..      68      74 ..      67      81 .. 0.84
   3 ?    0.0   0.4       2.5   7.6e+02       1       9 [.      95     103 ..      95     106 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00034
                     Cys_rich_CPCC  3 CpcCgyltleeeegsydiCpvCfWedD 29
                                      Cp Cg ++l++++  + +C  C +e+ 
  gi|242398553|ref|YP_002993977.1|  4 CPKCGNIMLPDKKRGVFVCRKCGYEEP 30
                                      *********99986666*****99974 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 3.6
                     Cys_rich_CPCC  2 qCpcCgy 8 
                                      +Cp Cg 
  gi|242398553|ref|YP_002993977.1| 68 TCPKCGN 74
                                      7999996 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 2.5
                     Cys_rich_CPCC   1 yqCpcCgyl 9  
                                       y+C  Cgy+
  gi|242398553|ref|YP_002993977.1|  95 YRCTKCGYT 103
                                       68*****96 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   7.3     0.059        18       1      30 [.       2      27 ..       2      28 .. 0.75
   2 ?    7.6   2.5     0.012       3.6       3      31 ..      69     103 ..      68     104 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.059
                                      -B-TTT--B-EEE--TT-SS-EEEETTTTE CS
                         Nudix_N_2  1 kFCsqCGtpvelripdgDnreRlvCpaCgt 30
                                      kFC++CG+     + ++ +r  +vC +Cg+
  gi|242398553|ref|YP_002993977.1|  2 KFCPKCGNI---ML-PDKKRGVFVCRKCGY 27
                                      8******97...34.355667788888886 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.012
                                       -TTT--B-E....EE--TT-SS-E..EEETTTTEE CS
                         Nudix_N_2   3 CsqCGtpve....lripdgDnreR..lvCpaCgti 31 
                                       C++CG+  +    l++ +gD+     ++C++Cg++
  gi|242398553|ref|YP_002993977.1|  69 CPKCGNDEAywweLQTRAGDEPSTifYRCTKCGYT 103
                                       999*998444555999999997643389****985 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.4     0.015       4.6      14      21 ..       1       8 [.       1       9 [. 0.92
   2 ?    5.5   0.4     0.059        18      16      23 ..      21      28 ..      19      28 .. 0.89
   3 ?    3.6   0.2      0.23        71       3      21 ..      69      73 ..      66      75 .. 0.64
   4 ?    5.8   0.5     0.047        14      16      24 ..      96     104 ..      95     105 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.015
                           UPF0547 14 aqfCphCG 21
                                      ++fCp CG
  gi|242398553|ref|YP_002993977.1|  1 MKFCPKCG 8 
                                      79*****9 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.059
                           UPF0547 16 fCphCGyv 23
                                      +C+ CGy+
  gi|242398553|ref|YP_002993977.1| 21 VCRKCGYE 28
                                      6******7 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.23
                           UPF0547  3 CPeCeakvPvaaqfCphCG 21
                                      CP               CG
  gi|242398553|ref|YP_002993977.1| 69 CPK--------------CG 73
                                      555..............55 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.047
                           UPF0547  16 fCphCGyvF 24 
                                       +C  CGy +
  gi|242398553|ref|YP_002993977.1|  96 RCTKCGYTW 104
                                       5999***99 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.2    0.0036       1.1       3      24 ..       4      27 ..       2      41 .. 0.79
   2 ?    4.3   1.4      0.13        40       2      23 ..      68     101 ..      67     105 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0036
                                      -SSS-S--E..E-SSEEE-TTT-- CS
                    zinc-ribbons_6  3 CpeCqqele..krgeqyhCeaCqe 24
                                      Cp+C + +   k+   + C++C  
  gi|242398553|ref|YP_002993977.1|  4 CPKCGNIMLpdKKRGVFVCRKCGY 27
                                      999*99999644447899999975 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.13
                                       --SSS-S--E.E-S...........SEEE-TTT- CS
                    zinc-ribbons_6   2 kCpeCqqele.krg...........eqyhCeaCq 23 
                                       +Cp+C +    + +             y+C +C 
  gi|242398553|ref|YP_002993977.1|  68 TCPKCGNDEAyWWElqtragdepstIFYRCTKCG 101
                                       7999988766566656666666665556666664 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.7      0.94   2.9e+02      17      21 ..       4       8 ..       3       9 .. 0.78
   2 ?   10.5   0.1    0.0012      0.38       1      11 [.      20      30 ..      20      31 .. 0.89
   3 ?    3.8   0.6      0.15        47       3      13 ..      69      79 ..      68      80 .. 0.71
   4 ?    8.0   2.0    0.0078       2.4       1       9 [.      95     103 ..      95     107 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.94
                      Rubredoxin_2 17 CpsCg 21
                                      Cp Cg
  gi|242398553|ref|YP_002993977.1|  4 CPKCG 8 
                                      88887 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0012
                      Rubredoxin_2  1 YvCsqCGfesa 11
                                      +vC++CG+e +
  gi|242398553|ref|YP_002993977.1| 20 FVCRKCGYEEP 30
                                      8*******975 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.15
                      Rubredoxin_2  3 CsqCGfesakw 13
                                      C +CG++ a w
  gi|242398553|ref|YP_002993977.1| 69 CPKCGNDEAYW 79
                                      77888877777 PP

  == domain 4  score: 8.0 bits;  conditional E-value: 0.0078
                      Rubredoxin_2   1 YvCsqCGfe 9  
                                       Y+C +CG++
  gi|242398553|ref|YP_002993977.1|  95 YRCTKCGYT 103
                                       9*******8 PP

>> CK_II_beta  Casein kinase II regulatory subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1      0.12        37     127     141 ..       3      17 ..       1      23 [. 0.85
   2 ?    7.5   0.3     0.011       3.3      97     132 ..      39      73 ..      19      88 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.12
                        CK_II_beta 127 yCpkCedvYspkssr 141
                                       +CpkC ++  p+++r
  gi|242398553|ref|YP_002993977.1|   3 FCPKCGNIMLPDKKR 17 
                                       9*******9998854 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.011
                        CK_II_beta  97 fgrCprvlCekqkvLPvGlsdkpgektvklyCpkCe 132
                                       +    ++  ++ + +Pv  +d+ +  +vk+ CpkC 
  gi|242398553|ref|YP_002993977.1|  39 YKITQKIK-HDREDIPVIEQDVATLPKVKITCPKCG 73 
                                       55555544.445668********************6 PP

>> RPA_interact_C  Replication protein A interacting C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   4.4     0.033        10       1      46 [.       3      64 ..       3     104 .. 0.54

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.033
                    RPA_interact_C  1 lCPvCkkrklkets.evifCe.Cglrlet..............seesltleelkrrlaetve 46
                                      +CP C +  l  ++  v +C+ Cg +                 ++++ ++  +++ +a+  +
  gi|242398553|ref|YP_002993977.1|  3 FCPKCGNIMLPDKKrGVFVCRkCGYEEPLdletaskykitqkiKHDREDIPVIEQDVATLPK 64
                                      6*********999879999*99*954333223355555555443444455555555555444 PP

>> Ribosomal_L37ae  Ribosomal L37ae protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.8    0.0041       1.3      36      59 ..       4      27 ..       1      50 [. 0.92
   2 ?    4.2   2.1      0.15        45      32      63 ..      65     106 ..      55     107 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0041
                                      ESSSSSSEEEEEETTEEEETTTTE CS
                   Ribosomal_L37ae 36 CpfcgktkvkRkavgiwkCkkcgk 59
                                      Cp+cg+  +  k  g++ C+kcg+
  gi|242398553|ref|YP_002993977.1|  4 CPKCGNIMLPDKKRGVFVCRKCGY 27
                                      **********************97 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.15
                                       S-BEESSSSSSEEEEE..........ETTEEEETTTTEEEE- CS
                   Ribosomal_L37ae  32 akytCpfcgktkvkRk..........avgiwkCkkcgktvaG 63 
                                        k tCp+cg+++  ++          ++  ++C+kcg+t+ G
  gi|242398553|ref|YP_002993977.1|  65 VKITCPKCGNDEAYWWelqtragdepSTIFYRCTKCGYTWRG 106
                                       567888888887665511111111112335678888887765 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1      0.13        41      29      34 ..       4       9 ..       1      13 [. 0.78
   2 ?    2.7   6.9      0.46   1.4e+02      25      34 ..      57      74 ..      19      77 .. 0.55
   3 ?    6.3   0.8     0.034        10       6      13 ..      95     102 ..      94     105 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.13
                       Zn-ribbon_8 29 CPeCgs 34
                                      CP+Cg 
  gi|242398553|ref|YP_002993977.1|  4 CPKCGN 9 
                                      999995 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.46
                       Zn-ribbon_8 25 p........ltaCPeCgs 34
                                               +++CP+Cg 
  gi|242398553|ref|YP_002993977.1| 57 QdvatlpkvKITCPKCGN 74
                                      044444454677999997 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.034
                       Zn-ribbon_8   6 YrCeeCgh 13 
                                       YrC++Cg 
  gi|242398553|ref|YP_002993977.1|  95 YRCTKCGY 102
                                       9******6 PP

>> Terminase_GpA  Phage terminase large subunit (GpA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1      0.59   1.8e+02     230     244 ..       4      18 ..       2      51 .. 0.67
   2 ?    9.8   0.6   0.00084      0.26     199     237 ..      67     104 ..      60     107 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.59
                     Terminase_GpA 230 Cphcgslieehhkra 244
                                       Cp+cg ++ +++kr 
  gi|242398553|ref|YP_002993977.1|   4 CPKCGNIMLPDKKRG 18 
                                       666666665555554 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00084
                     Terminase_GpA 199 vpCphCgelqelsferlkwpegeaeekaryvCphcgsli 237
                                       + Cp+Cg+     + +l+  +g+++++  y C +cg  +
  gi|242398553|ref|YP_002993977.1|  67 ITCPKCGNDEA-YWWELQTRAGDEPSTIFYRCTKCGYTW 104
                                       78*****9755.56678999999*************887 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 ?    6.3   2.5     0.024       7.5       3      25 ..       4      27 ..       3      28 .. 0.87
   2 ?    4.0   0.1      0.13        40      14      24 ..      63      73 ..      56      74 .. 0.73
   3 ?    5.8   0.5     0.036        11      19      25 ..      96     102 ..      93     103 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.024
                                      -SSS--B--.--SSS----SSS-- CS
                    DNA_RNApol_7kD  3 CgeCgaevs.lkkgdpiRCkeCGh 25
                                      C +Cg+ +  +kk+ +  C++CG+
  gi|242398553|ref|YP_002993977.1|  4 CPKCGNIMLpDKKRGVFVCRKCGY 27
                                      88999887779999999******8 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.13
                                      SSS----SSS- CS
                    DNA_RNApol_7kD 14 kgdpiRCkeCG 24
                                      ++  i C +CG
  gi|242398553|ref|YP_002993977.1| 63 PKVKITCPKCG 73
                                      556799****9 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.036
                                       --SSS-- CS
                    DNA_RNApol_7kD  19 RCkeCGh 25 
                                       RC++CG+
  gi|242398553|ref|YP_002993977.1|  96 RCTKCGY 102
                                       9999997 PP

>> DpnI  Dam-replacing family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.4     0.006       1.9      33      77 ..       3      46 ..       1      53 [. 0.77
   2 ?    3.5   0.2      0.16        49      31      53 ..      66      88 ..      59     105 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.006
                                      --TTT--SS-EE--------EEE-TTT-..-EEEEEEEES.S--SEEE CS
                              DpnI 33 yCpkCgskklsefennkpvaDfyCesck..eefeLkskks.klskkiv 77
                                      +CpkCg+ +l     +k+   f C++c   e  +L + ++ k+++ki+
  gi|242398553|ref|YP_002993977.1|  3 FCPKCGNIMLP----DKKRGVFVCRKCGyeEPLDLETASKyKITQKIK 46
                                      9******9776....5566679*****754678887766668888886 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.16
                                      H---TTT--SS-EE--------E CS
                              DpnI 31 nlyCpkCgskklsefennkpvaD 53
                                      ++ CpkCg+ +   +e  +++ D
  gi|242398553|ref|YP_002993977.1| 66 KITCPKCGNDEAYWWELQTRAGD 88
                                      578*****997555554444444 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 ?    1.5   3.7       0.8   2.5e+02      40      51 ..      15      26 ..       3      29 .. 0.65
   2 ?   10.4   2.4    0.0013      0.41      20      52 ..      64     102 ..      56     104 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.8
                    zinc_ribbon_10 40 leevkyrCpkCg 51
                                      +++  ++C kCg
  gi|242398553|ref|YP_002993977.1| 15 KKRGVFVCRKCG 26
                                      455578888887 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0013
                    zinc_ribbon_10  20 ryalICskChshnGlap......keeleevkyrCpkCga 52 
                                        +++ C+kC +   +         +e++++ yrC kCg 
  gi|242398553|ref|YP_002993977.1|  64 KVKITCPKCGNDEAYWWelqtraGDEPSTIFYRCTKCGY 102
                                       56899999998887654455567899***********97 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   1.4    0.0033         1       2      26 ..       4      26 ..       3      26 .. 0.92
   2 ?    4.4   4.5     0.076        24       2      26 ..      69     101 ..      68     104 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0033
                          zf-TFIIB  2 CPkCqdeleeserggveidyCpqCr 26
                                      CPkC++ + + +++g  +++C +C+
  gi|242398553|ref|YP_002993977.1|  4 CPKCGNIMLPDKKRG--VFVCRKCG 26
                                      *********999999..89999996 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.076
                          zf-TFIIB   2 CPkCqd.ele....eser...ggveidyCpqCr 26 
                                       CPkC++ e      +++        +++C++C+
  gi|242398553|ref|YP_002993977.1|  69 CPKCGNdEAYwwelQTRAgdePSTIFYRCTKCG 101
                                       ****87366677553433654557778899997 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 ?    6.5   0.2     0.021       6.4      11      18 ..       2       9 ..       1      11 [. 0.83
   2 ?    4.4   0.3      0.09        28       7      18 ..      16      27 ..      13      30 .. 0.87
   3 ?    5.3   0.3     0.047        15      12      17 ..      68      73 ..      60      75 .. 0.81
   4 ?    2.5   0.5      0.36   1.1e+02      12      17 ..      96     101 ..      95     103 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.021
                           zf-tcix 11 rkCpkCGt 18
                                      + CpkCG 
  gi|242398553|ref|YP_002993977.1|  2 KFCPKCGN 9 
                                      77*****6 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.09
                           zf-tcix  7 lRGvrkCpkCGt 18
                                      +RGv  C kCG 
  gi|242398553|ref|YP_002993977.1| 16 KRGVFVCRKCGY 27
                                      69*********6 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.047
                           zf-tcix 12 kCpkCG 17
                                       CpkCG
  gi|242398553|ref|YP_002993977.1| 68 TCPKCG 73
                                      5***** PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.36
                           zf-tcix  12 kCpkCG 17 
                                       +C+kCG
  gi|242398553|ref|YP_002993977.1|  96 RCTKCG 101
                                       5****9 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.2      0.69   2.1e+02      40      46 ..       4      10 ..       1      17 [. 0.74
   2 ?    4.3   0.1      0.12        39      37      53 ..      19      35 ..      12      44 .. 0.81
   3 ?    8.4   1.4    0.0066       2.1      24      48 ..      53      77 ..      21      95 .. 0.69
   4 ?    1.6   0.3      0.87   2.7e+02      38      46 ..      95     103 ..      89     106 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.69
                              CpXC 40 CpkCgat 46
                                      CpkCg+ 
  gi|242398553|ref|YP_002993977.1|  4 CPKCGNI 10
                                      8888875 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.12
                              CpXC 37 eatCpkCgatakleapl 53
                                       ++C kCg++  l+ ++
  gi|242398553|ref|YP_002993977.1| 19 VFVCRKCGYEEPLDLET 35
                                      589*****999887665 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0066
                              CpXC 24 pelkeklldgslfeatCpkCgatak 48
                                      p +++++ +    ++tCpkCg++ +
  gi|242398553|ref|YP_002993977.1| 53 PVIEQDVATLPKVKITCPKCGNDEA 77
                                      5667777777778999999998765 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 0.87
                              CpXC  38 atCpkCgat 46 
                                       ++C kCg+t
  gi|242398553|ref|YP_002993977.1|  95 YRCTKCGYT 103
                                       79*****97 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.7       2.2   6.7e+02      17      21 ..       4       8 ..       2       9 .. 0.84
   2 ?    3.4   0.3      0.39   1.2e+02      14      22 ..      17      27 ..      13      28 .. 0.75
   3 ?    5.3   0.0     0.097        30      15      21 ..      67      73 ..      45      75 .. 0.85
   4 ?    6.3   0.2     0.045        14      14      23 ..      94     103 ..      87     103 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 2.2
                         zf-H2C2_2 17 CplCd 21
                                      Cp+C+
  gi|242398553|ref|YP_002993977.1|  4 CPKCG 8 
                                      99996 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.39
                         zf-H2C2_2 14 p..yeCplCdk 22
                                      +  + C +C++
  gi|242398553|ref|YP_002993977.1| 17 RgvFVCRKCGY 27
                                      34599****98 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.097
                         zf-H2C2_2 15 yeCplCd 21
                                       +Cp+C+
  gi|242398553|ref|YP_002993977.1| 67 ITCPKCG 73
                                      79****7 PP

  == domain 4  score: 6.3 bits;  conditional E-value: 0.045
                         zf-H2C2_2  14 pyeCplCdka 23 
                                       +y C +C+++
  gi|242398553|ref|YP_002993977.1|  94 FYRCTKCGYT 103
                                       39******96 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   3.9     0.013       4.2       4      30 ..       2      28 ..       1      29 [. 0.79
   2 ?    3.6   0.1      0.17        54      24      28 ..      69      73 ..      66      76 .. 0.67
   3 ?    0.8   0.1       1.3   3.9e+02      23      29 ..      96     102 ..      95     103 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.013
                     zf-NADH-PPase  4 rFCgrCGaptepaeggwarvCpaCgle 30
                                      +FC++CG  + p +     vC  Cg+e
  gi|242398553|ref|YP_002993977.1|  2 KFCPKCGNIMLPDKKRGVFVCRKCGYE 28
                                      6******98888888777777777776 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.17
                     zf-NADH-PPase 24 CpaCg 28
                                      Cp Cg
  gi|242398553|ref|YP_002993977.1| 69 CPKCG 73
                                      55555 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 1.3
                     zf-NADH-PPase  23 vCpaCgl 29 
                                       +C  Cg+
  gi|242398553|ref|YP_002993977.1|  96 RCTKCGY 102
                                       7999996 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 ?    4.0   0.1      0.16        51       4      10 ..       4      10 ..       2      11 .. 0.82
   2 ?    2.7   0.1       0.4   1.2e+02       3       8 ..      21      26 ..      20      28 .. 0.83
   3 ?    6.2   0.2     0.032        10      18      28 ..      63      73 ..      54      75 .. 0.73
   4 ?    0.9   0.3       1.5   4.8e+02       4       9 ..      97     102 ..      95     105 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.16
                                      -TTT--E CS
                           ADK_lid  4 CpkCGrs 10
                                      CpkCG +
  gi|242398553|ref|YP_002993977.1|  4 CPKCGNI 10
                                      9999975 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.4
                                      E-TTT- CS
                           ADK_lid  3 vCpkCG 8 
                                      vC+kCG
  gi|242398553|ref|YP_002993977.1| 21 VCRKCG 26
                                      899998 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.032
                                      -SSTTB-TTT- CS
                           ADK_lid 18 PkveglCDkCG 28
                                      Pkv+  C kCG
  gi|242398553|ref|YP_002993977.1| 63 PKVKITCPKCG 73
                                      77777777776 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 1.5
                                       -TTT-- CS
                           ADK_lid   4 CpkCGr 9  
                                       C kCG 
  gi|242398553|ref|YP_002993977.1|  97 CTKCGY 102
                                       888885 PP

>> DUF3797  Domain of unknown function (DUF3797)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   3.3      0.12        37      16      23 ..       4      11 ..       2      28 .. 0.86
   2 ?    7.8   5.5      0.01       3.1      13      46 ..      66     102 ..      55     104 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.12
                           DUF3797 16 CPeCgNnk 23
                                      CP+CgN+ 
  gi|242398553|ref|YP_002993977.1|  4 CPKCGNIM 11
                                      ******86 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.01
                           DUF3797  13 YvqCPeCgNnkvlNsegkviieddt...fyreCkCgf 46 
                                        + CP+CgN+     e + +  d+    fyr  kCg+
  gi|242398553|ref|YP_002993977.1|  66 KITCPKCGNDEAYWWELQTRAGDEPstiFYRCTKCGY 102
                                       579*******999999999776652245999999987 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   1.1      0.51   1.6e+02      79      86 .]       1       8 [.       1       8 [. 0.88
   2 ?    7.7   3.4      0.02       6.1      33      73 ..      15      74 ..       9     106 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.51
                    zinc_ribbon_15 79 fkyCpkCg 86
                                      +k+CpkCg
  gi|242398553|ref|YP_002993977.1|  1 MKFCPKCG 8 
                                      58*****9 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.02
                    zinc_ribbon_15 33 kkkpylacskCkslleaskelgkeiekkesse...................kkeCknCgk 73
                                      kk+ +++c+kC++  + + e+ ++ + +++++                   k +C++Cg+
  gi|242398553|ref|YP_002993977.1| 15 KKRGVFVCRKCGYEEPLDLETASKYKITQKIKhdredipvieqdvatlpkvKITCPKCGN 74
                                      557788999999988888888777777777777899999999999999999888888886 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   1.1    0.0027      0.85      12      36 ..       2      27 ..       1      28 [. 0.90
   2 ?    2.3   1.8       0.5   1.6e+02      25      37 ..      91     103 ..      61     104 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0027
                                      -B-TTT-SB--S.SSS-EEEETTT-- CS
                              C1_1 12 tfCkhCgeflwg.kekqglkCswCkl 36
                                      +fC +Cg+++   k +  + C+ C++
  gi|242398553|ref|YP_002993977.1|  2 KFCPKCGNIMLPdKKRGVFVCRKCGY 27
                                      79********88799999******97 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.5
                                       SS-EEEETTT--E CS
                              C1_1  25 ekqglkCswCkll 37 
                                       ++  ++C+ C+++
  gi|242398553|ref|YP_002993977.1|  91 STIFYRCTKCGYT 103
                                       5567999999985 PP

>> Baculo_ME53  Baculoviridae ME53
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.4    0.0074       2.3     269     304 ..       3      39 ..       1      49 [. 0.76
   2 ?    1.8   0.7      0.36   1.1e+02     284     293 ..      93     103 ..      52     107 .. 0.62

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0074
                       Baculo_ME53 269 ycklckktkly...tknPvlscskcGftnvyyfteysky 304
                                       +c  c    ++    k+ v+ c kcG+ ++  +   sky
  gi|242398553|ref|YP_002993977.1|   3 FCPKCG--NIMlpdKKRGVFVCRKCGYEEPLDLETASKY 39 
                                       455555..676678899**********999877766666 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.36
                       Baculo_ME53 284 vls.cskcGft 293
                                       +++ c+kcG+t
  gi|242398553|ref|YP_002993977.1|  93 IFYrCTKCGYT 103
                                       33337777776 PP

>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   2.4     0.047        15      19      24 .]       4       9 ..       3       9 .. 0.90
   2 ?    2.5   0.1      0.46   1.4e+02      16      23 ..      19      26 ..      12      27 .. 0.88
   3 ?    8.2   0.6     0.008       2.5      18      24 .]      68      74 ..      65      74 .. 0.83
   4 ?    0.5   0.1         2   6.1e+02      15      23 ..      92     101 ..      86     102 .. 0.60

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.047
                           DUF1610 19 CPNCGE 24
                                      CP+CG+
  gi|242398553|ref|YP_002993977.1|  4 CPKCGN 9 
                                      *****7 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.46
                           DUF1610 16 vFpCPNCG 23
                                      vF C +CG
  gi|242398553|ref|YP_002993977.1| 19 VFVCRKCG 26
                                      7******9 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.008
                           DUF1610 18 pCPNCGE 24
                                       CP+CG+
  gi|242398553|ref|YP_002993977.1| 68 TCPKCGN 74
                                      6*****7 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 2
                           DUF1610  15 vvFp.CPNCG 23 
                                       ++F+ C +CG
  gi|242398553|ref|YP_002993977.1|  92 TIFYrCTKCG 101
                                       5555466666 PP

>> Ogr_Delta  Ogr/Delta-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.2      0.16        51       2       9 ..       4      11 ..       3      19 .. 0.87
   2 ?   -1.2   0.1       6.9   2.1e+03      23      35 ..      17      27 ..      11      28 .. 0.65
   3 ?    9.1   1.9    0.0041       1.3       1      38 [.      68     105 ..      68     108 .] 0.87

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.16
                         Ogr_Delta  2 CPhCgapa 9 
                                      CP+Cg+ +
  gi|242398553|ref|YP_002993977.1|  4 CPKCGNIM 11
                                      *****866 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 6.9
                         Ogr_Delta 23 eryyqCsnfeCga 35
                                      + +++C+   Cg+
  gi|242398553|ref|YP_002993977.1| 17 RGVFVCRK--CGY 27
                                      55678887..776 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0041
                         Ogr_Delta   1 rCPhCgapaaartsrnlskdvre...ryyqCsnfeCgatfv 38 
                                       +CP+Cg+  a +   ++ + + e   ++y C+   Cg+t +
  gi|242398553|ref|YP_002993977.1|  68 TCPKCGNDEAYWWELQTRA-GDEpstIFYRCTK--CGYTWR 105
                                       6******999999999888.888899******9..**9976 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   1.0    0.0089       2.7       6      27 ..       3      26 ..       1      28 [. 0.86
   2 ?    3.0   0.3      0.31        95      21      27 ..      67      73 ..      64      76 .. 0.77
   3 ?   -0.5   0.1       3.8   1.2e+03      23      27 ..      97     101 ..      94     105 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0089
                       Prok-RING_1  6 kCpvCgkelkee..dDiVvCpeCg 27
                                       Cp Cg+ + ++    + vC +Cg
  gi|242398553|ref|YP_002993977.1|  3 FCPKCGNIMLPDkkRGVFVCRKCG 26
                                      6******998775578*******9 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.31
                       Prok-RING_1 21 VvCpeCg 27
                                      ++Cp+Cg
  gi|242398553|ref|YP_002993977.1| 67 ITCPKCG 73
                                      4688888 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 3.8
                       Prok-RING_1  23 CpeCg 27 
                                       C++Cg
  gi|242398553|ref|YP_002993977.1|  97 CTKCG 101
                                       66666 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 ?    3.9   3.0      0.17        52       7      31 ..       4      26 ..       3      29 .. 0.78
   2 ?    2.5   0.1      0.46   1.4e+02       7      12 ..      69      74 ..      67      77 .. 0.80
   3 ?    7.3   1.0     0.014       4.5       5      14 ..      95     102 ..      91     105 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.17
                    Zn_ribbon_SprT  7 CtgCgreythhlsirrhnYrCrrCk 31
                                      C+ Cg        ++r    Cr+C+
  gi|242398553|ref|YP_002993977.1|  4 CPKCG--NIMLPDKKRGVFVCRKCG 26
                                      99999..4777777777789****7 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.46
                    Zn_ribbon_SprT  7 CtgCgr 12
                                      C+ Cg+
  gi|242398553|ref|YP_002993977.1| 69 CPKCGN 74
                                      999984 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.014
                    Zn_ribbon_SprT   5 YrCtgCgrey 14 
                                       YrCt Cg  y
  gi|242398553|ref|YP_002993977.1|  95 YRCTKCG--Y 102
                                       9999999..3 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   4.5     0.022       6.7      24      34 ..       2      12 ..       1      49 [. 0.84
   2 ?    5.7   0.3     0.052        16      23      32 ..      66      75 ..      59      86 .. 0.85
   3 ?    0.1   0.4         3   9.3e+02       9      30 ..      95     101 ..      88     105 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.022
                      NOB1_Zn_bind 24 kFCpkCGnktL 34
                                      kFCpkCGn +L
  gi|242398553|ref|YP_002993977.1|  2 KFCPKCGNIML 12
                                      7*******887 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.052
                      NOB1_Zn_bind 23 kkFCpkCGnk 32
                                      k  CpkCGn+
  gi|242398553|ref|YP_002993977.1| 66 KITCPKCGND 75
                                      566*****97 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 3
                      NOB1_Zn_bind   9 lrChaCfkvtkdmtkkFCpkCG 30 
                                       +rC+ C               G
  gi|242398553|ref|YP_002993977.1|  95 YRCTKC---------------G 101
                                       455555...............4 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   3.0     0.018       5.7       4      22 ..       4      21 ..       2      32 .. 0.76
   2 ?    3.7   5.4      0.18        55       2      10 ..      67      75 ..      66     104 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.018
                                      -SSS--EEEEEE-SSSEEE CS
                    zf-C4_Topoisom  4 CPkCggdLvlkrgkkGkFv 22
                                      CPkCg+ + l  +k+G Fv
  gi|242398553|ref|YP_002993977.1|  4 CPKCGNIM-LPDKKRGVFV 21
                                      ****9655.5677777887 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.18
                                      EE-SSS--E CS
                    zf-C4_Topoisom  2 ekCPkCggd 10
                                      ++CPkCg+d
  gi|242398553|ref|YP_002993977.1| 67 ITCPKCGND 75
                                      69*****75 PP

>> zf-ISL3  zinc-finger of transposase IS204/IS1001/IS1096/IS1165
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.4      0.12        37       4      15 ..       3      16 ..       2      19 .. 0.69
   2 ?    2.5   0.6       0.8   2.5e+02       4      11 ..      21      28 ..      18      50 .. 0.69
   3 ?    7.4   0.1     0.023       7.2       3      12 ..      67      76 ..      66      81 .. 0.84
   4 ?    0.2   0.3       3.9   1.2e+03       4      10 ..      96     102 ..      95     107 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.12
                           zf-ISL3  4 rCPnCgsk..tvvk 15
                                       CP+Cg+   +++k
  gi|242398553|ref|YP_002993977.1|  3 FCPKCGNImlPDKK 16
                                      6*****97444455 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.8
                           zf-ISL3  4 rCPnCgsk 11
                                      +C++Cg  
  gi|242398553|ref|YP_002993977.1| 21 VCRKCGYE 28
                                      79999976 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.023
                           zf-ISL3  3 hrCPnCgskt 12
                                      ++CP+Cg+  
  gi|242398553|ref|YP_002993977.1| 67 ITCPKCGNDE 76
                                      79*****975 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 3.9
                           zf-ISL3   4 rCPnCgs 10 
                                       rC +Cg 
  gi|242398553|ref|YP_002993977.1|  96 RCTKCGY 102
                                       6888885 PP

>> DUF3268  zinc-finger-containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   1.0       1.3   3.9e+02      27      37 ..      16      26 ..       1      35 [. 0.66
   2 ?    8.6   0.7     0.007       2.2       3      37 ..      67     101 ..      65     106 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 1.3
                           DUF3268 27 gkllylCpkCd 37
                                      ++ +++C+kC+
  gi|242398553|ref|YP_002993977.1| 16 KRGVFVCRKCG 26
                                      33466777775 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.007
                           DUF3268   3 trCpyCGekvilvsaseiYkerskgkllylCpkCd 37 
                                       ++Cp CG+  ++  + +   + +  +++y C+kC+
  gi|242398553|ref|YP_002993977.1|  67 ITCPKCGNDEAYWWELQTRAGDEPSTIFYRCTKCG 101
                                       68********9999999999**************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                       128  (0.00713927); expected 17.9 (0.001)
Passed Fwd filter:                        86  (0.0047967); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              58  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 644.87
//
Query:       gi|242398554|ref|YP_002993978.1|  [L=60]
Description: hypothetical protein TSIB_0564 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       756  (0.0421663); expected 358.6 (0.02)
Passed bias filter:                      560  (0.0312343); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 397.51
//
Query:       gi|242398555|ref|YP_002993979.1|  [L=249]
Description: DNA polymerase sliding clamp [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-19   69.5   0.1    6.1e-17   61.5   0.0    2.1  2  PCNA_N    Proliferating cell nuclear antigen, N-terminal doma
    1.6e-09   38.0   0.0    7.6e-09   35.8   0.0    2.1  3  PCNA_C    Proliferating cell nuclear antigen, C-terminal doma
      2e-08   33.6   0.0    5.5e-06   25.7   0.0    2.0  2  Rad1      Repair protein Rad1/Rec1/Rad17
     0.0021   17.6   0.0     0.0041   16.6   0.0    1.8  1  Rad9      Rad9
  ------ inclusion threshold ------
       0.13   11.6   0.0       0.22   10.9   0.0    1.3  1  DUF4901   Domain of unknown function (DUF4901)


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 !   61.5   0.0   1.7e-20   6.1e-17       2     109 ..       3     109 ..       2     125 .. 0.86
   2 !    6.0   0.0    0.0025         9      11      93 ..     136     222 ..     129     235 .. 0.83

  Alignments for each domain:
  == domain 1  score: 61.5 bits;  conditional E-value: 1.7e-20
                                       EEEEESSHHHHHHHHHHHTTTCSEEEEEEETTEEEEEEE-TTSSEEEEEEEEGGGSSEEEESS-EEEEEEHHHHHHH CS
                            PCNA_N   2 learleqasllkklleaikdlvneanfdcddsGislqalDsshvaLvslelrsegfekyrCDrnlalgvnlnslski 78 
                                       +e+ ++ a  +  l+++  +l++ea+f++ ++G+s++a+D s+v L  l+l ++ f+ky  D + ++gvn+  + k+
  gi|242398555|ref|YP_002993979.1|   3 FEIVFDGAKEFADLIDTASNLIDEAAFKIAEEGMSMRAMDPSRVVLLDLNLPASIFSKYDIDGEETVGVNMDHFKKV 79 
                                       6777888888999**************************************************************** PP

                                       HTTSTTTSEEEEEEETTSSEEEEEEEECTSS CS
                            PCNA_N  79 lkcannedsvtlkaedeadtlalvfesekkd 109
                                       lk ++ +d+++l+   e++ l +++e + k 
  gi|242398555|ref|YP_002993979.1|  80 LKRGKGKDILVLRKG-EENFLEITLEGTAKR 109
                                       ***********9864.456677777766554 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0025
                                       HHHHHH.HHHTT..TCSE.EEEEEETTEEEEEEE-TTSSEEEEEEEEGGGSSEEEESS-EEEEEEHHHHHHHHTTST CS
                            PCNA_N  11 llkkll.eaikd..lvne.anfdcddsGislqalDsshvaLvslelrsegfekyrCDrnlalgvnlnslskilkcan 83 
                                       +l  +l ea+kd  lv++ + f ++++ + ++a  +++   ++l+l++eg  +   + +      ++ l+ + k  +
  gi|242398555|ref|YP_002993979.1| 136 ILGEVLkEAVKDasLVSDsIKFIAKENEFIMKAEGETQEVEIKLTLEDEGLLDLNVEEETKSAYGVSYLADMAKGIG 212
                                       5555554677775556542689999********999999999****************9999999999******999 PP

                                       TTSEEEEEEE CS
                            PCNA_N  84 nedsvtlkae 93 
                                       + d v+l+  
  gi|242398555|ref|YP_002993979.1| 213 KADEVVLRFG 222
                                       9999999865 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 ?   -1.7   0.0      0.83     3e+03      15      45 ..      10      40 ..       5      42 .. 0.84
   2 ?   -3.1   0.0       2.3   8.1e+03      65      82 ..      95     112 ..      91     115 .. 0.84
   3 !   35.8   0.0   2.1e-12   7.6e-09      21     127 ..     144     245 ..     127     246 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.83
                                      HHHHHHHHHHHTTT-SEEEEEEETTEEEEEE CS
                            PCNA_C 15 ssefaricrdlsqlsdsvvisvtkegvkfsa 45
                                      + efa ++   s+l d+   +++ eg+  +a
  gi|242398555|ref|YP_002993979.1| 10 AKEFADLIDTASNLIDEAAFKIAEEGMSMRA 40
                                      7899999999999999999999999988776 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.3
                                       GGGCBEEEESS-EEEEEE CS
                            PCNA_C  65 eeeavklelkepvtltfa 82 
                                       ee++ ++ l+ + + tf 
  gi|242398555|ref|YP_002993979.1|  95 EENFLEITLEGTAKRTFR 112
                                       789999999999999996 PP

  == domain 3  score: 35.8 bits;  conditional E-value: 2.1e-12
                                       HHHHHTTT-SEEEEEEETTEEEEEEEETTEEEEEEE--BEESSSGGGCBEEEESS-EEEEEEHHHHHHHGGGGGC-S CS
                            PCNA_C  21 icrdlsqlsdsvvisvtkegvkfsasGdiGsasivlkqvkdvdkeeeavklelkepvtltfalkYlaeftkatsLse 97 
                                        ++d s +sds+   +  +    +a+G+  + +i+l       ++e    l+++e  +  +++ Yla+++k+   ++
  gi|242398555|ref|YP_002993979.1| 144 AVKDASLVSDSIKFIAKENEFIMKAEGETQEVEIKLT-----LEDEGLLDLNVEEETKSAYGVSYLADMAKGIGKAD 215
                                       68999999***99999889999999999877765553.....4578999**************************** PP

                                       EEEEEEETTSEEEEEEEETTCEEEEEEE-B CS
                            PCNA_C  98 rvtlslssevPlvveykikdvgllayllak 127
                                       +v l++ +e+Pl ++y i+d g l++lla+
  gi|242398555|ref|YP_002993979.1| 216 EVVLRFGNEMPLQMDYPIRDEGRLTFLLAP 245
                                       ****************************98 PP

>> Rad1  Repair protein Rad1/Rec1/Rad17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1   0.0    0.0014         5       8      63 ..       9      66 ..       3      96 .. 0.80
   2 !   25.7   0.0   1.5e-09   5.5e-06     154     263 ..     119     221 ..      90     227 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0014
                              Rad1  8 nvseLatlLksia.fkdkalvqissdGlkfi.vednrvlqaqafldkalFtsYtfena 63
                                       ++e+a+l+++ + + d+a  +i ++G+++   + +rv+   + l+ ++F++Y ++ +
  gi|242398555|ref|YP_002993979.1|  9 GAKEFADLIDTASnLIDEAAFKIAEEGMSMRaMDPSRVVLLDLNLPASIFSKYDIDGE 66
                                      567777887766515568***********9625889******************9544 PP

  == domain 2  score: 25.7 bits;  conditional E-value: 1.5e-09
                              Rad1 154 edldleldrqevvlkvilkselLhsalteLdatskklkilassekkapvfalsakgelgssevefpneksvlekfev 230
                                       e+l+l+l +   ++  ++ +e+L++a+++ + +s+++k++a++    + f ++a+ge++++e++++ e + l  ++v
  gi|242398555|ref|YP_002993979.1| 119 EELELDLPELPFTVRAVILGEVLKEAVKDASLVSDSIKFIAKE----NEFIMKAEGETQEVEIKLTLEDEGLLDLNV 191
                                       6788888899999999*************************99....58**************************** PP

                              Rad1 231 sslsessessYkfallkkaakalalssKvslrm 263
                                          +e+++  Y +++l+ +ak +  +  v lr 
  gi|242398555|ref|YP_002993979.1| 192 E--EETKSA-YGVSYLADMAKGIGKADEVVLRF 221
                                       *..555555.*************9999999996 PP

>> Rad9  Rad9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.2e-06    0.0041       2      69 ..      14      79 ..      13     201 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.2e-06
                              Rad9  2 aralqclsrigdelyleisedglelrtvnssrSayalvtlkksfFdkyekevseqirckilvKsvlsv 69
                                      a ++ ++s + de  ++i e+g+++r+++ sr     ++l  s+F+ky+ + +e++ + +    + +v
  gi|242398555|ref|YP_002993979.1| 14 ADLIDTASNLIDEAAFKIAEEGMSMRAMDPSRVVLLDLNLPASIFSKYDIDGEETVGVNM--DHFKKV 79
                                      6678999*****************************************877777766554..333333 PP

>> DUF4901  Domain of unknown function (DUF4901)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0     6e-05      0.22      18      82 ..     151     210 ..     144     238 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 6e-05
                           DUF4901  18 vednegvdekerlliWedkadeearieitldletgeliklridkekddaisgsekaiesaeqake 82 
                                       v d + + +ke+ +i    + e +++ei l le + l++l++++e   a   s      a+ ak 
  gi|242398555|ref|YP_002993979.1| 151 VSDSIKFIAKENEFIMKA-EGETQEVEIKLTLEDEGLLDLNVEEETKSAYGVSYL----ADMAKG 210
                                       678888999999999865.567889********************9888776632....344444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:01.11
# Mc/sec: 675.69
//
Query:       gi|242398556|ref|YP_002993980.1|  [L=189]
Description: hypothetical protein TSIB_0566 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0081   16.7   0.4      0.014   15.9   0.4    1.6  1  Mga       Mga helix-turn-helix domain


Domain annotation for each model (and alignments):
>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.4   8.1e-07     0.014      24      86 ..      42     107 ..       9     108 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 8.1e-07
                                       HHHHHSEEEHHHHHHHCT--HHHHHHHHHH..HHHHCH.CCT-EEETTCCEEES-HHHHHHHHHHH CS
                               Mga  24 flfeeeevsieelaqelyiSestlkrkike..lnklLk.efdleltkknlklrGdEeqiRyfyael 86 
                                          e+ +   ee+ q+ly+Se  +  k+++  ++ +L+  +d+ ++ +++ l+GdE++i +++a +
  gi|242398556|ref|YP_002993980.1|  42 IKAESSKERGEEIEQQLYLSELGIAEKLAReiIRARLHkIVDMAVEGRPFNLVGDEKKIFSIIATF 107
                                       44567778899*************99998766999**9668******************9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       977  (0.0544927); expected 358.6 (0.02)
Passed bias filter:                      603  (0.0336327); 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: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1196.08
//
Query:       gi|242398557|ref|YP_002993981.1|  [L=627]
Description: formate dehydrogenase [Thermococcus sibiricus MM 739]
Scores for complete 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-45  154.2   0.0    6.4e-44  150.6   0.0    2.0  1  Molybdopterin    Molybdopterin oxidoreductase
    1.5e-19   70.1   0.0    3.1e-19   69.0   0.0    1.5  1  Molydop_binding  Molydopterin dinucleotide binding domain
    1.5e-05   24.9   0.0    3.2e-05   23.8   0.0    1.6  1  Molybdop_Fe4S4   Molybdopterin oxidoreductase Fe4S4 domain
  ------ inclusion threshold ------
      0.087   12.6   0.0       0.32   10.8   0.0    2.1  1  MEDS             MEDS: MEthanogen/methylotroph, DcmR Sensory 


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 !  150.6   0.0   1.4e-47   6.4e-44       1     414 [.      50     422 ..      50     438 .. 0.84

  Alignments for each domain:
  == domain 1  score: 150.6 bits;  conditional E-value: 1.4e-47
                                       B--S-EEECTTTTTSEEEE--HHHHHHHHHHHHHHHHHHCSGGGEEEEEBTSSCSHHHHHHHHHHHHHTT-EEE-BE CS
                     Molybdopterin   1 RlkyPmvRkqargeGkFvrvsWdeAleliaaslkytikkygpdrvagfssgplmsmeslaslkkllsllggknlsfy 77 
                                       Rlk+P+vR  +  + +F++  W+eA +++aa+l +ti+k+g+++v ++   +   ++++a   +l+  l  ++l + 
  gi|242398557|ref|YP_002993981.1|  50 RLKTPLVR--EDLREDFKETGWKEAINFVAARLSETIQKHGSESVLVYNYAGDRGVVNYAFPLRLFHYLNASMLDY- 123
                                       9*******..555799*******************************66666666*****9999999999976655. PP

                                       ECCGGGTTHHHH..CHHCCCCCTTTS-SS-CCGGGG-SEEEEESS-HHHHSHHHHHHHHHHHHTTC-EEEEECSSB- CS
                     Molybdopterin  78 dwyadlppasaq..qtigsdsrsnyessnpledlensdliilwGsNvreerpilnarirkaalkkkakvivigprya 152
                                          +d   ++ +         ++  + + + edl n +li+ wG N+ ++       ++ a +++ ++  v++  ++
  gi|242398557|ref|YP_002993981.1| 124 -GICDR-AGQEAlrD------VYGTAVGMDPEDLKNQKLIVYWGVNPFWTNLHG---FMLAKRYG-LEKWVVDVVKT 188
                                       .34444.23332221......33334455566******************9999...77777885.999999***** PP

                                       HCGGGCSEEEEEHTTTHHHHHHHHHHHHHHCCCCTCHHHHHHEECHHHCCCCCCCEECCSHHHHHHCCHHHHHHHHH CS
                     Molybdopterin 153 ellkfadewlaikpgtdaalalamghvilqelkvdkeflrkytygkeetdmpllvtleeetgkkkevvariarelar 229
                                       e++k+  +   i+p+td+ +al+ + vi++++ +d ef++k  yg+e++ ++l+    + ++k++++  +++ e+a 
  gi|242398557|ref|YP_002993981.1| 189 ETAKKSEKFFQIRPNTDVLFALGVARVIVESNIYDREFVEKNVYGFEKFVEYLSTIDLDFVAKETGIQGEKIEEFAF 265
                                       *9*************************************************************************** PP

                                       HHHHHTSSEEEEECHHHHTSTTHHHHHHHHHHHHHHCTHCSSTTCEEEEESSCTTHHHCHHHHTCCTTCCCCCCCTT CS
                     Molybdopterin 230 naaktagksmiivGaglnhrqdgdaiyravinLallvgnvgqpgGgwahlnGqlilagaaekvgalpvllsvkslke 306
                                       ++a+++g   i +G gl++++ g +++ra++ L  lvg        ++ +   +++ +  ++   l           
  gi|242398557|ref|YP_002993981.1| 266 EYAEKKG--VIHIGYGLQRSFMGGEAVRAIAILPTLVGHK------FGFIYDMKTIDKSYAEGEFL----------- 323
                                       *******..7777**********************98744......33333345777766666666........... PP

                                       HHHHHCCCTTTCSTSS--ECGGCHHHHHHTTSSSEEEEESH.HHHHSTTSCCCHCHHHCSSEEE.EEESCSSHHHHT CS
                     Molybdopterin 307 ekikfaaeqpgnlgnfprnlfversnllkssgkkvlyllgnnpevdhadenevekalekldlvv.vldgrltstaly 382
                                                      ++r+  ++ ++ ++++++k+ly+ + np  + +++n++ ka  k d++v v d++lt+taly
  gi|242398557|ref|YP_002993981.1| 324 -----------RTRPVKRIPQMKLAEFIENGDIKFLYIYNANPLASLPNQNRLRKAIMKNDVFVvVHDIFLTDTALY 389
                                       ...........4444444444555678899****************************8887651669999****** PP

                                       SSEEEEBE-CCGSEEEEE-TTSEEEE.EEESSS CS
                     Molybdopterin 383 aDiiLPaatwyEkedlytndegrfqh.lkqavs 414
                                       a+++LPa+t++E+ d+  +  +r     +++++
  gi|242398557|ref|YP_002993981.1| 390 AHVVLPASTFFERLDIADSYYHRYVAlNEPVTQ 422
                                       ***************999888887776666655 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.0   0.0     7e-23   3.1e-19      25     110 ..     536     620 ..     522     621 .. 0.90

  Alignments for each domain:
  == domain 1  score: 69.0 bits;  conditional E-value: 7e-23
                                       HCSSS-EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEESSB-TTEEEEESSHCC.....S-GHCTS.--SCST CS
                   Molydop_binding  25 akpepevveinpedAaalGikdGdlVevesrrGsvevrakvtervrpGvvfmpfgwweagekggnaNalt.ddatdp 100
                                       +  +p ++ i+p+dA ++Gikd+d+Vev++++G ++ rakv+e+v+ G v+++ ++w     g n+N lt d+ +++
  gi|242398557|ref|YP_002993981.1| 536 NIIDP-YLHISPQDADERGIKDNDEVEVFNEYGNIKTRAKVSEDVPSGIVVLYKAFWP-KLLGWNVNFLTtDETVEK 610
                                       44455.***************************************************9.999********9999999 PP

                                       TT--CSTT-E CS
                   Molydop_binding 101 lsgtpefksv 110
                                       +  + +++s+
  gi|242398557|ref|YP_002993981.1| 611 YGNGSAYHST 620
                                       9999999987 PP

>> Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0     7e-09   3.2e-05      11      50 ..       4      42 ..       2      47 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 7e-09
                                      BTT--EEEEEEETTEEEEEEE-TTSTTTTT---HHHHTCH CS
                    Molybdop_Fe4S4 11 CgvgCglevhvkdgkivkvegdpdhpvnegrlCvKGrtll 50
                                      C   C++  + k g + +v+g+p+hp+++g lC+KG+ l 
  gi|242398557|ref|YP_002993981.1|  4 CYDTCSIISELKEG-VLRVKGNPSHPITRGFLCPKGALLS 42
                                      77778886666666.55*******************9775 PP

>> MEDS  MEDS: MEthanogen/methylotroph, DcmR Sensory domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   7.2e-05      0.32      18      77 ..     432     489 ..     391     500 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 7.2e-05
                              MEDS  18 vpfikaglargekvlyvasastldelrealrkagldvdaalesgqleildaeety.lrggg 77 
                                        + ++++l+ + ++ly   +s++d +r+ l+k+gl  ++++e+g +++ + e++y +++g+
  gi|242398557|ref|YP_002993981.1| 432 TRLLAKALDIKNPCLY---ESDEDVIRKILEKNGLSFEELKERGFVKVEEKERFYnTPSGK 489
                                       567889999999***9...689**********************99*********544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (627 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.31s 00:00:00.97 Elapsed: 00:00:00.50
# Mc/sec: 3798.62
//
Query:       gi|242398558|ref|YP_002993982.1|  [L=110]
Description: hypothetical protein TSIB_0568 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00078   19.6   0.0      0.001   19.2   0.0    1.2  1  FeS_assembly_P  Iron-sulfur cluster assembly protein


Domain annotation for each model (and alignments):
>> FeS_assembly_P  Iron-sulfur cluster assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   5.6e-08     0.001       3      43 ..      20      60 ..      18      77 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 5.6e-08
                                      HHHHHHTT-B-TTTSSBCCCCT---EEEE-T-EEEEEE--S CS
                    FeS_assembly_P  3 avlaaLrtVtDPelgvdlvslglvreidieggkVsvditlt 43
                                      +vl+ L+tV+DP +  +++++gl+ + ++e++k  + +++ 
  gi|242398558|ref|YP_002993982.1| 20 DVLEELSTVIDPISTMNILDAGLLAGFNVEEDKLELWLAVE 60
                                      89*******************************99888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 801.08
//
Query:       gi|242398559|ref|YP_002993983.1|  [L=123]
Description: hypothetical protein TSIB_0569 [Thermococcus sibiricus MM 739]
Scores for complete 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   36.3   0.0    6.9e-09   35.7   0.0    1.2  1  FeS_assembly_P  Iron-sulfur cluster assembly protein
     0.0035   16.9   0.8       0.24   10.9   0.2    2.1  2  UPF0128         Uncharacterised protein family (UPF0128)
  ------ inclusion threshold ------
      0.011   15.8   0.2      0.015   15.3   0.2    1.4  1  E2F_TDP         E2F/DP family winged-helix DNA-binding domain
      0.065   12.4   0.0      0.091   11.9   0.0    1.1  1  TTL             Tubulin-tyrosine ligase family
       0.11   12.6   0.0         10    6.2   0.0    2.7  2  DUF4911         Domain of unknown function (DUF4911)


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 !   35.7   0.0   1.9e-12   6.9e-09       3      61 ..      24      84 ..      23      93 .. 0.86

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 1.9e-12
                                      HHHHHHTT-B-TTTSSBCCCCT---EEEE-T..-EEEEEE--SSTT-TTHHHHHHHHHHHH CS
                    FeS_assembly_P  3 avlaaLrtVtDPelgvdlvslglvreidieg..gkVsvditltypacslaeairadaeaal 61
                                      +v + L++V+DPe+ +++v+ glv+++++eg    V + +   +p c++  a+++ +++ +
  gi|242398559|ref|YP_002993983.1| 24 RVVEELKKVKDPETELNIVEEGLVYGVTVEGkkAMVWLLLVKSTPSCHFCQALAMNVQKRI 84
                                      68889**************************5555555666688******99999999876 PP

>> UPF0128  Uncharacterised protein family (UPF0128)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.2   6.7e-05      0.24     145     170 ..       8      33 ..       3      63 .. 0.85
   2 !    5.0   0.0    0.0043        15     157     179 ..      79     101 ..      64     108 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 6.7e-05
                           UPF0128 145 eeskPlpyeelPpvarrflreakkve 170
                                       +e  P+  +e+Pp +rr+++e kkv+
  gi|242398559|ref|YP_002993983.1|   8 KEKAPVGTKEFPPEVRRVVEELKKVK 33 
                                       5678999*****************97 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0043
                           UPF0128 157 pvarrflreakkvekdmGfGrla 179
                                       +v +r++r++ +v k+ GfG + 
  gi|242398559|ref|YP_002993983.1|  79 NVQKRIVRDIINVLKESGFGIVQ 101
                                       6889****************774 PP

>> E2F_TDP  E2F/DP family winged-helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.2   4.2e-06     0.015      11      54 ..      24      93 ..       1     104 [. 0.83

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.2e-06
                           E2F_TDP 11 kfvellkesakgtlslneaakeLv..........................dkkdekvkkRRiYDilNVLe 54
                                      ++ve lk+ ++ +++ln + + Lv                          +  +++v+kR + Di+NVL+
  gi|242398559|ref|YP_002993983.1| 24 RVVEELKKVKDPETELNIVEEGLVygvtvegkkamvwlllvkstpschfcQALAMNVQKRIVRDIINVLK 93
                                      566666666666788888888888999999999999999**********9999****************6 PP

>> TTL  Tubulin-tyrosine ligase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.5e-05     0.091     249     283 ..      56      90 ..      47      98 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.5e-05
                                       XXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXX CS
                               TTL 249 nlkpwLlEvNasPdlksttkldaelkeeliddvln 283
                                       +  +wLl v ++P+++  ++l +++ +++++d++n
  gi|242398559|ref|YP_002993983.1|  56 KAMVWLLLVKSTPSCHFCQALAMNVQKRIVRDIIN 90 
                                       5679******************************9 PP

>> DUF4911  Domain of unknown function (DUF4911)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.023        81      39      55 ..      15      31 ..      14      32 .. 0.90
   2 ?    6.2   0.0    0.0028        10      18      42 ..      43      67 ..      42      69 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.023
                           DUF4911 39 tpdtkeellelLesLkk 55
                                      t+++ +e+++++e+Lkk
  gi|242398559|ref|YP_002993983.1| 15 TKEFPPEVRRVVEELKK 31
                                      78899**********96 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0028
                           DUF4911 18 ydgLavvttvdkkkGlvrirttpdt 42
                                      ++gL++  tv++kk++v++   ++t
  gi|242398559|ref|YP_002993983.1| 43 EEGLVYGVTVEGKKAMVWLLLVKST 67
                                      69****************9876665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       760  (0.0423894); expected 358.6 (0.02)
Passed bias filter:                      626  (0.0349155); 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: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 872.17
//
Query:       gi|242398560|ref|YP_002993984.1|  [L=278]
Description: Aldose reductase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-63  214.7   0.0    7.9e-62  209.1   0.0    2.0  1  Aldo_ket_red  Aldo/keto reductase family
  ------ inclusion threshold ------
      0.051   13.8   0.1       0.11   12.8   0.1    1.5  1  AP2           AP2 domain


Domain annotation for each model (and alignments):
>> Aldo_ket_red  Aldo/keto reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  209.1   0.0   8.9e-66   7.9e-62       2     288 ..      21     273 ..      20     278 .] 0.98

  Alignments for each domain:
  == domain 1  score: 209.1 bits;  conditional E-value: 8.9e-66
                                       EEEE-SSS-ST....TS-HHHHHHHHHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH-TTTGGG-EEEEEE--SSS CS
                      Aldo_ket_red   2 lglGtwqlgsk...eeiskeealellrraleaGinffDtAevYgkgqseellGealkksrkkreeviiatKvdlrda 75 
                                       +g+Gtw +g++   ++  +ee++++lr+ le G+n++DtAe+Y  g+seel+Gea+k+  ++re+++i++K+     
  gi|242398560|ref|YP_002993984.1|  21 IGMGTWGVGGRetpDYSRDEESIDALRYGLELGMNLIDTAEFYASGHSEELVGEAIKE--FEREDIFIVSKI----- 90 
                                       9*********************************************************..************..... PP

                                       TTSSSS-HHHHHHHHHHHHHHHT-S-EEEEEE-S--TTS-.HHHHHHHHHHHHHTTSEEEEEEES--HHHHHHH.HH CS
                      Aldo_ket_red  76 eiksglskeniresleeslkrLgtdyvDllllHrpdpslpsieevldaleelvkeGkiraiGvSnfsveqleka.kk 151
                                        +++++  e+  ++ ++s krLgt y+Dl+llH+p+ +  +i ++l ale+lv+eG+ir+iGvSnf+ e l+k  + 
  gi|242398560|ref|YP_002993984.1|  91 -WPVHFGYESAKRAARASAKRLGT-YIDLYLLHWPTDNFGRIKDTLHALEDLVDEGLIRYIGVSNFDLELLKKSqEV 165
                                       .**********************6.*************************************************999 PP

                                       TTT--EEEEE-B-BTT.-HHHHTTHHHHHHHTT-EEEEBSTTGGGTTGTTTSS---SSSCCC-------TS-HHHHH CS
                      Aldo_ket_red 152 kkkvkivavqveynll.releeegllelckkkgvpliaysplggGlltgkyqseedkedkeprkdlkrdertsknld 227
                                        +k++i ++qv+y+l  r+ e++glle+++ ++v l+ay+pl +G+l                              
  gi|242398560|ref|YP_002993984.1| 166 MRKYEIMVNQVKYSLKdRRPEHSGLLEYMRRENVTLMAYTPLEKGSLA----------------------------- 213
                                       9**********************************************9............................. PP

                                       HHHHHHHHHHHTT--HHHHHHHHHTTSTT-SEEEE--SSHHHHHHHHGGGG----HHHHHH CS
                      Aldo_ket_red 228 aaeelselakehgvslaqlalryalsqpavgivipgasnieqlednldalelklseeevae 288
                                       +++ lse++ ++g++ aq+al++++ ++ ++++ip+a+n  ++++n++a+ ++lsee++++
  gi|242398560|ref|YP_002993984.1| 214 KNRCLSEIGIKYGKTAAQIALNWLI-WKENVVAIPKATNKYHIKENFGAMGWRLSEEDYEA 273
                                       6899*********************.9*******************************986 PP

>> AP2  AP2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   1.2e-05      0.11      29      51 ..      89     111 ..      80     114 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.2e-05
                               AP2  29 rfsvgkyGfeeAkraAiaarkkl 51 
                                       ++++ ++G+e AkraA a +k+l
  gi|242398560|ref|YP_002993984.1|  89 KIWPVHFGYESAKRAARASAKRL 111
                                       68999************999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); 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 0.26s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1965.75
//
Query:       gi|242398561|ref|YP_002993985.1|  [L=79]
Description: hypothetical protein TSIB_0571 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.7e-06   27.1   3.9    3.3e-06   26.8   3.9    1.0  1  Lys_export  Lysine exporter LysO


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 !   26.8   3.9   1.8e-10   3.3e-06       3      75 ..       6      75 ..       4      77 .. 0.84

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 1.8e-10
                        Lys_export  3 aliaGillGllllleaelleeelseylLylLlflvGislgsskelleklkklnlkllllplatilgsllggll 75
                                       l+aG+l+G+ll+ +a++ +++ ++++L+lL+f+ Gi+ g+ +  ++++ kl l  ++++ +tilgsl+++ll
  gi|242398561|ref|YP_002993985.1|  6 PLLAGVLTGYLLKNKAKISMDKPMTVALLLLIFFMGIEAGRVE--INAF-KLLLYSIVFASFTILGSLFVALL 75
                                      689*************************************994..3343.55566667778999999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.30s 00:00:00.71 Elapsed: 00:00:00.47
# Mc/sec: 506.95
//
Query:       gi|242398562|ref|YP_002993986.1|  [L=195]
Description: hypothetical protein TSIB_0572 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-58  197.9  16.3    1.3e-58  197.7  16.3    1.0  1  Lys_export  Lysine exporter LysO


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 !  197.7  16.3   7.4e-63   1.3e-58       2     189 ..       9     191 ..       5     192 .. 0.96

  Alignments for each domain:
  == domain 1  score: 197.7 bits;  conditional E-value: 7.4e-63
                        Lys_export   2 laliaGillGllllleaelleeelseylLylLlflvGislgsskelleklkklnlkllllplatilgsllggllaal 78 
                                       ++l++G+l+G ++ +++     ++ e++LylL+f++G+++g+sk l e+l+kl++ +lllp+ati+gsl+gg++a++
  gi|242398562|ref|YP_002993986.1|   9 VTLVLGMLVGKTTTFDF----GNFYEFMLYLLIFIIGVDIGKSKGLGEELRKLGKMALLLPVATIIGSLIGGFFASM 81 
                                       56788888888777665....799***************************************************** PP

                        Lys_export  79 llglslkeslavasGfGwYSLsgilitelkgaelGtiallanllREllalllipllakrfgklaaisvaGatsmDtt 155
                                       ll++slk +l +a+GfGwYSL+g+l++  +++ +G+i++lanl RE+l+++++p+ +kr++k   i ++Gat+mDtt
  gi|242398562|ref|YP_002993986.1|  82 LLDVSLKWGLGIAAGFGWYSLTGPLLAA-YSPIYGVIGFLANLTREILTIIFYPIAIKRIPKEVGIVMGGATTMDTT 157
                                       **************************77.8*********************************************** PP

                        Lys_export 156 LPiitkssgkevvvlaivhGvilsllvPilvslf 189
                                       LPii+k+ g+e+++la+vhG+il+ ++P+l++l+
  gi|242398562|ref|YP_002993986.1| 158 LPIIAKFGGTEITLLAFVHGFILTAIAPFLIPLI 191
                                       ********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); 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: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1275.02
//
Query:       gi|242398563|ref|YP_002993987.1|  [L=110]
Description: 50S ribosomal protein L44E [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-26   92.3   5.8    3.1e-26   91.7   5.8    1.3  1  Ribosomal_L44   Ribosomal protein L44
    0.00039   20.8   5.0     0.0018   18.6   2.2    2.3  2  Ribosomal_L33   Ribosomal protein L33
     0.0066   16.5   2.5       0.69   10.1   0.4    2.3  2  Zn-ribbon_8     Zinc ribbon domain
     0.0067   16.3   2.1        2.1    8.3   0.1    2.3  2  Nudix_N_2       Nudix N-terminal
  ------ inclusion threshold ------
       0.02   15.0   1.8      0.088   13.0   0.3    2.1  2  NOB1_Zn_bind    Nin one binding (NOB1) Zn-ribbon like
      0.028   14.4   0.6        0.2   11.7   0.6    1.9  2  HypA            Hydrogenase/urease nickel incorporation, meta
      0.043   14.3   4.7        4.1    8.0   0.2    2.5  2  zf-H2C2_2       Zinc-finger double domain
      0.083   12.9   3.5        1.2    9.2   0.4    2.2  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
       0.14   12.4   3.7        0.3   11.4   0.5    2.0  2  zf-LITAF-like   LITAF-like zinc ribbon domain
       0.15   11.9   0.6        4.3    7.2   0.0    2.2  2  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal
       0.16   11.4   1.8          6    6.4   0.2    2.2  2  zf-ribbon_3     zinc-ribbon domain


Domain annotation for each model (and alignments):
>> Ribosomal_L44  Ribosomal protein L44
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.7   5.8   1.9e-29   3.1e-26       1      76 []      34     110 .]      34     110 .] 0.98

  Alignments for each domain:
  == domain 1  score: 91.7 bits;  conditional E-value: 1.9e-29
                                       EEEEEEEEE-------SSSHHHHHHHH.H-SSSGGGGS----.--SSBB--EEEEETTT--EEE--.--BBS--EEE CS
                     Ribosomal_L44   1 kHtehkveqykkgkdselaqgkRrydrkqsgygGqtkpvfkkkaKttKKivlrleCteCkkkrlka.lkRakkfelv 76 
                                       kHt hkve++kk+ +sel++g+Rr++r  +gy G ++p + +++K+ KK++lr++CteC+k++++  ++R+kkfelv
  gi|242398563|ref|YP_002993987.1|  34 KHTVHKVERVKKRPRSELSAGQRRFRRILKGYKGFPRPNPAGREKPVKKLDLRYRCTECGKAHTRGqGFRVKKFELV 110
                                       8****************************************************************879*******96 PP

>> Ribosomal_L33  Ribosomal protein L33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   2.2   1.1e-06    0.0018      30      44 ..      25      39 ..      17      42 .. 0.90
   2 ?    2.6   0.0      0.11   1.8e+02       6      12 ..      88      94 ..      82     107 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.1e-06
                                      EEEEETTTTEEEEEE CS
                     Ribosomal_L33 30 lkKYcprcrkhtlhk 44
                                      ++ Ycp+c+kht+hk
  gi|242398563|ref|YP_002993987.1| 25 IRTYCPFCKKHTVHK 39
                                      677***********9 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.11
                                      EET.... CS
                     Ribosomal_L33  6 eCtecks 12
                                      +Ctec++
  gi|242398563|ref|YP_002993987.1| 88 RCTECGK 94
                                      6****98 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.1    0.0068        11      27      39 ..      27      40 ..      17      40 .. 0.76
   2 !   10.1   0.4   0.00042      0.69       6      19 ..      87     100 ..      86     108 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0068
                       Zn-ribbon_8 27 taCPeCgs.evrrv 39
                                      t CP C++ +v++v
  gi|242398563|ref|YP_002993987.1| 27 TYCPFCKKhTVHKV 40
                                      45******999886 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00042
                       Zn-ribbon_8   6 YrCeeCghefevlq 19 
                                       YrC+eCg+ +++ q
  gi|242398563|ref|YP_002993987.1|  87 YRCTECGKAHTRGQ 100
                                       *******9887655 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.3    0.0024       3.8       2      22 ..      28      48 ..      27      49 .. 0.94
   2 !    8.3   0.1    0.0013       2.1      21      32 ..      85      96 ..      73      96 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0024
                                      B-TTT--B-EEE--TT-SS-E CS
                         Nudix_N_2  2 FCsqCGtpvelripdgDnreR 22
                                      +C+ C + + ++++   +r+R
  gi|242398563|ref|YP_002993987.1| 28 YCPFCKKHTVHKVERVKKRPR 48
                                      9*************9999999 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0013
                                      -EEEETTTTEEE CS
                         Nudix_N_2 21 eRlvCpaCgtih 32
                                       R++C+ Cg  h
  gi|242398563|ref|YP_002993987.1| 85 LRYRCTECGKAH 96
                                      69******9866 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 ?   13.0   0.3   5.4e-05     0.088      19      61 ..      22      64 ..      17      76 .. 0.66
   2 ?    1.7   0.1      0.18   2.9e+02      10      32 ..      88      95 ..      79     107 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.4e-05
                      NOB1_Zn_bind 19 kdmtkkFCpkCGnktLkrvavsvdengelklhlkknfqlnlrG 61
                                      +++ + +Cp C ++t+++v+ + ++  +     +++f+  l+G
  gi|242398563|ref|YP_002993987.1| 22 PKQIRTYCPFCKKHTVHKVERVKKRPRSELSAGQRRFRRILKG 64
                                      567899*************987776644333444444444444 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.18
                      NOB1_Zn_bind 10 rChaCfkvtkdmtkkFCpkCGnk 32
                                      r               C +CG++
  gi|242398563|ref|YP_002993987.1| 88 R---------------CTECGKA 95
                                      3...............6666653 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   0.2     0.045        74      85      99 ..      24      39 ..      10      45 .. 0.71
   2 ?   11.7   0.6   0.00012       0.2      69     111 ..      25     108 ..      20     109 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.045
                                      H.HHS-TTTSSS-EEE CS
                              HypA 85 k.alrCpkCgsadvei 99
                                      + ++ Cp C+++ v+ 
  gi|242398563|ref|YP_002993987.1| 24 QiRTYCPFCKKHTVHK 39
                                      2345799999988765 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00012
                                       -EEEETTTS-EEECHHHHH............................................S-TTTSSS-EEEEE CS
                              HypA  69 vkvrCreCgkefeleekal............................................rCpkCgsadveivs 101
                                       ++++C  C+k++ ++ +++                                            rC +Cg+a+   ++
  gi|242398563|ref|YP_002993987.1|  25 IRTYCPFCKKHTVHKVERVkkrprselsagqrrfrrilkgykgfprpnpagrekpvkkldlryRCTECGKAH---TR 98 
                                       667788888766644421234677778888888888888888888888888888888888888*******86...68 PP

                                       SSSEEEEEEE CS
                              HypA 102 Geellvksie 111
                                       G++++vk++e
  gi|242398563|ref|YP_002993987.1|  99 GQGFRVKKFE 108
                                       9*****9998 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 ?    7.8   0.6    0.0029       4.7      16      26 .]      28      38 ..      17      38 .. 0.81
   2 ?    8.0   0.2    0.0025       4.1      11      24 ..      80      96 ..      76      98 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0029
                         zf-H2C2_2 16 eCplCdkaFkt 26
                                       Cp+C+k +++
  gi|242398563|ref|YP_002993987.1| 28 YCPFCKKHTVH 38
                                      6******9876 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0025
                         zf-H2C2_2 11 gek...pyeCplCdkaF 24
                                      ++k   +y C +C+ka 
  gi|242398563|ref|YP_002993987.1| 80 VKKldlRYRCTECGKAH 96
                                      45533359*******85 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.4   0.00071       1.2      19      36 ..      26      44 ..      17      60 .. 0.75
   2 ?    4.6   0.2     0.019        31      37      45 ..      86      94 ..      75      96 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00071
                     Zn_Tnp_IS1595 19 fv.CPhCgsrkayriktrg 36
                                      ++ CP+C++ +++++++ +
  gi|242398563|ref|YP_002993987.1| 26 RTyCPFCKKHTVHKVERVK 44
                                      445******9999999833 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.019
                     Zn_Tnp_IS1595 37 lfqCkeCrk 45
                                      +++C eC+k
  gi|242398563|ref|YP_002993987.1| 86 RYRCTECGK 94
                                      799999987 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 ?   11.4   0.5   0.00019       0.3       4      23 ..      25      44 ..      22      49 .. 0.85
   2 ?    2.0   0.1      0.15   2.5e+02      54      64 ..      84      94 ..      81      98 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00019
                     zf-LITAF-like  4 tqvdCpaCqqrvvTsveyks 23
                                       +++Cp+C++++v +ve+ +
  gi|242398563|ref|YP_002993987.1| 25 IRTYCPFCKKHTVHKVERVK 44
                                      6789*********9999875 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.15
                     zf-LITAF-like 54 dvehyCpnCga 64
                                      d +++C++Cg+
  gi|242398563|ref|YP_002993987.1| 84 DLRYRCTECGK 94
                                      67788999987 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 ?    3.2   0.1     0.045        73      40      52 ..      22      34 ..      15      36 .. 0.79
   2 ?    7.2   0.0    0.0026       4.3      41      52 ..      83      94 ..      74      96 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.045
                    zinc_ribbon_10 40 leevkyrCpkCga 52
                                      +++++ +Cp+C+ 
  gi|242398563|ref|YP_002993987.1| 22 PKQIRTYCPFCKK 34
                                      6778889****85 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0026
                    zinc_ribbon_10 41 eevkyrCpkCga 52
                                       +++yrC +Cg 
  gi|242398563|ref|YP_002993987.1| 83 LDLRYRCTECGK 94
                                      5789******96 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.2    0.0037         6       3      11 ..      27      35 ..      26      38 .. 0.82
   2 ?    4.3   0.1     0.018        29       3      13 ..      87      97 ..      86     101 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0037
                       zf-ribbon_3  3 vrCPnCGap 11
                                      ++CP C+++
  gi|242398563|ref|YP_002993987.1| 27 TYCPFCKKH 35
                                      58****985 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.018
                       zf-ribbon_3  3 vrCPnCGa.pls 13
                                      +rC +CG+ + +
  gi|242398563|ref|YP_002993987.1| 87 YRCTECGKaH-T 97
                                      5899999877.4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.50
# Mc/sec: 664.99
//
Query:       gi|242398564|ref|YP_002993988.1|  [L=65]
Description: 30S ribosomal protein S27e [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-24   85.3   0.9    1.9e-24   85.1   0.9    1.0  1  Ribosomal_S27e  Ribosomal protein S27
     0.0018   17.6   1.2        0.1   12.0   0.1    2.1  2  zf-RanBP        Zn-finger in Ran binding protein and others
     0.0028   17.1   0.4     0.0036   16.8   0.4    1.2  1  TF_Zn_Ribbon    TFIIB zinc-binding
     0.0061   16.6   0.1     0.0069   16.4   0.1    1.1  1  HypA            Hydrogenase/urease nickel incorporation, meta
  ------ inclusion threshold ------
      0.043   13.8   0.2       0.06   13.4   0.2    1.2  1  zinc_ribbon_6   Zinc-ribbon
       0.06   13.5   0.2      0.097   12.8   0.2    1.3  1  Zn-ribbon_8     Zinc ribbon domain
      0.061   13.0   0.4      0.082   12.6   0.4    1.2  1  TackOD1         Thaumarchaeal output domain 1
       0.11   12.6   0.1        3.4    7.8   0.0    2.1  2  zf-BED          BED zinc finger
       0.36   10.7   1.9        4.5    7.2   0.1    2.1  3  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 !   85.1   0.9   9.5e-28   1.9e-24       1      54 [.      11      64 ..      11      65 .] 0.98

  Alignments for each domain:
  == domain 1  score: 85.1 bits;  conditional E-value: 9.5e-28
                                      -S--EEEEE-TTTS-EEEEESS-SS-EEESSSTCEEEEECSSSEEESSCEEEEE CS
                    Ribosomal_S27e  1 prskFldvkCpdCenetvvFshaatvvkCisCgkvLvePtGGkaklkaqilerl 54
                                      p+skFl+vkC dC+ne++vFs +at v C+ Cg++LveP GG++ +ka++le+l
  gi|242398564|ref|YP_002993988.1| 11 PKSKFLRVKCIDCGNEQIVFSNPATKVRCLVCGSTLVEPAGGRGIIKAKVLEVL 64
                                      89*************************************************997 PP

>> zf-RanBP  Zn-finger in Ran binding protein and others
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.7   0.1    0.0096        19      18      27 ..      17      26 ..      16      27 .. 0.84
   2 !   12.0   0.1   5.1e-05       0.1      13      26 ..      31      44 ..      30      45 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0096
                                      SSB-TTT--B CS
                          zf-RanBP 18 stkCvaCqap 27
                                      ++kC+ C+++
  gi|242398564|ref|YP_002993988.1| 17 RVKCIDCGNE 26
                                      789****985 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 5.1e-05
                                      EEESSSSB-TTT-- CS
                          zf-RanBP 13 qNfawstkCvaCqa 26
                                      +N+a++++C+ C++
  gi|242398564|ref|YP_002993988.1| 31 SNPATKVRCLVCGS 44
                                      7***********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 !   16.8   0.4   1.8e-06    0.0036       2      29 ..      19      46 ..      18      58 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.8e-06
                                      EETTTTCEECHEETSTTCEEESSSSBEE CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGlVl 29
                                      kC +Cg++++v+ +  + ++C  CG+ l
  gi|242398564|ref|YP_002993988.1| 19 KCIDCGNEQIVFSNPATKVRCLVCGSTL 46
                                      8************************865 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   3.5e-06    0.0069      69     105 ..      16      55 ..       8      62 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.5e-06
                                       -EEEETTTS-EEECHH..H.HHS-TTTSSS-EEEEESSSE CS
                              HypA  69 vkvrCreCgkefelee..k.alrCpkCgsadveivsGeel 105
                                       ++v+C +Cg+e  + +  + ++rC  Cgs+ ve  +G+++
  gi|242398564|ref|YP_002993988.1|  16 LRVKCIDCGNEQIVFSnpAtKVRCLVCGSTLVEPAGGRGI 55 
                                       689******9987544243688************999986 PP

>> zinc_ribbon_6  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2     3e-05      0.06      22      55 ..      10      44 ..       2      45 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3e-05
                     zinc_ribbon_6 22 eyknkkvkilCnDCekksevkfh.vlglkCkeCgS 55
                                        k+k  ++ C DC++++ v       ++C  CgS
  gi|242398564|ref|YP_002993988.1| 10 MPKSKFLRVKCIDCGNEQIVFSNpATKVRCLVCGS 44
                                      4567899*********9996554166789999998 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   4.9e-05     0.097       7      36 ..      19      46 ..      16      48 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.9e-05
                       Zn-ribbon_8  7 rCeeCghefevlqsisdaplta.CPeCgsev 36
                                      +C +Cg+e  v+   s ++ ++ C  Cgs++
  gi|242398564|ref|YP_002993988.1| 19 KCIDCGNEQIVF---SNPATKVrCLVCGSTL 46
                                      8*****555444...46667777******65 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.4   4.1e-05     0.082     147     171 ..      18      45 ..      12      50 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.1e-05
                           TackOD1 147 ykCnsCks...lfsepevkarClsCeke 171
                                       +kC +C++   +fs+p++k+rCl C+++
  gi|242398564|ref|YP_002993988.1|  18 VKCIDCGNeqiVFSNPATKVRCLVCGST 45 
                                       578888654448*************986 PP

>> zf-BED  BED zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1     0.048        95      16      25 ..      17      26 ..       8      27 .. 0.83
   2 ?    7.8   0.0    0.0017       3.4      14      26 ..      34      46 ..      29      54 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.048
                                      --EETTTTEE CS
                            zf-BED 16 kavCryCgki 25
                                      +++C+ Cg++
  gi|242398564|ref|YP_002993988.1| 17 RVKCIDCGNE 26
                                      89*****985 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0017
                                      SS--EETTTTEE- CS
                            zf-BED 14 eqkavCryCgkil 26
                                       +k++C  Cg +l
  gi|242398564|ref|YP_002993988.1| 34 ATKVRCLVCGSTL 46
                                      69********987 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1    0.0036       7.2      28      37 ..      17      26 ..      13      28 .. 0.79
   2 ?    7.2   0.1    0.0023       4.5       2      13 ..      19      30 ..      18      36 .. 0.76
   3 ?    3.0   0.2     0.048        96      27      36 ..      35      44 ..      31      46 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0036
                           TFIIS_C 28 fykCtkCghr 37
                                       +kC++Cg++
  gi|242398564|ref|YP_002993988.1| 17 RVKCIDCGNE 26
                                      6899999985 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0023
                           TFIIS_C  2 kCpkCgsreayf 13
                                      kC  Cg+++++f
  gi|242398564|ref|YP_002993988.1| 19 KCIDCGNEQIVF 30
                                      788888888777 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.048
                           TFIIS_C 27 vfykCtkCgh 36
                                      + ++C+ Cg 
  gi|242398564|ref|YP_002993988.1| 35 TKVRCLVCGS 44
                                      5688999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); 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: 0.41u 0.30s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 427.77
//
Query:       gi|242398565|ref|YP_002993989.1|  [L=278]
Description: Translation initiation factor 2 subunit alpha [Thermococcus sibiricus MM 739]
Scores for complete 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   85.2   0.3      1e-23   83.6   0.1    1.8  2  EIF_2_alpha  Eukaryotic translation initiation factor 2 alpha
    7.3e-14   51.9   0.1    1.8e-13   50.6   0.1    1.7  1  S1           S1 RNA binding domain


Domain annotation for each model (and alignments):
>> EIF_2_alpha  Eukaryotic translation initiation factor 2 alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.26   2.3e+03      72      85 ..      54      67 ..      43      95 .. 0.72
   2 !   83.6   0.1   1.2e-27     1e-23       2     116 .]     125     236 ..     124     236 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.26
                                      HHHHHHHHHHHST. CS
                       EIF_2_alpha 72 veaIkeaLkageea 85
                                      v +I++ Lk+g++ 
  gi|242398565|ref|YP_002993989.1| 54 VRNIRDYLKEGQKI 67
                                      66788888876663 PP

  == domain 2  score: 83.6 bits;  conditional E-value: 1.2e-27
                                       HHCTHHHHTTTTS-HHHHH.HHHHSTTHHHHHTTS-TTTHHHHHHCTHHHHHHT-EEEEEEEEEEE-STTHHHHHHH CS
                       EIF_2_alpha   2 yeevgwklyekyghaydaF.klaitdeevldkleipeeveeaLveiikkklkpqkvkiradieltcftkdGveaIke 77 
                                       ++ev  +l+e+yg++y aF ++a ++ e+++ l ip+e+  +L eiik  +++++v+i a++e+t  t++Gve Ike
  gi|242398565|ref|YP_002993989.1| 125 WKEVWIPLEEEYGEVYAAFeDVAQNGIEIIKGL-IPDEWLPVLEEIIKSYVEIPTVTIDAEFEITVPTPNGVEVIKE 200
                                       689999*************99***********8.******************************************* PP

                                       HHHHHST.S..TTSSSEEEEEEEESSSSEEEEEEEES.. CS
                       EIF_2_alpha  78 aLkageeasneeeveeeeevkikliapPeYvltvetldk 116
                                       aL ++++ +nee   + ++vk ++ ++P+Y+++++++d+
  gi|242398565|ref|YP_002993989.1| 201 ALIKARDTANEE---KGVDVKFSYLGAPRYRIDITAPDY 236
                                       ***999977777...89*******************997 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.6   0.1   2.1e-17   1.8e-13       2      75 .]      12      86 ..      12      86 .. 0.98

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 2.1e-17
                                      STTTCEEEEEEEEEETTEEEEEET..TTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEEETTTTEEEEEEC CS
                                S1  2 pekgevveGeVtsvtkgGafVelg..ngvegfvpaselsrdarvedpdevlkvGdevkvkvlkvdkdrrriilsik 75
                                      pe+ge v ++V+++ ++Gaf  l+   g +gf ++se++    v+++ + lk+G+++ +kv++vd +++ i+ls+k
  gi|242398565|ref|YP_002993989.1| 12 PEEGEFVVATVKDIHNYGAFLSLDeyPGKDGFMHISEVAPT-FVRNIRDYLKEGQKIVAKVIRVDPTKGHIDLSLK 86
                                      799**********************99*************9.********************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       676  (0.0377043); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); 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: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1769.28
//
Query:       gi|242398566|ref|YP_002993990.1|  [L=59]
Description: Ribosome biogenesis protein Nop10 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-26   91.6   4.0    2.5e-26   91.4   4.0    1.0  1  Nop10p           Nucleolar RNA-binding protein, Nop10p family
    9.1e-05   21.9   0.7    0.00011   21.6   0.7    1.2  1  RecR             RecR protein
    0.00053   18.0   0.2    0.00053   18.0   0.2    1.0  1  PolC_DP2         DNA polymerase II large subunit DP2
     0.0024   17.5   0.9       0.43   10.3   0.2    2.2  2  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
  ------ inclusion threshold ------
      0.012   15.6   1.1      0.018   15.0   1.1    1.3  1  DZR              Double zinc ribbon
       0.02   14.7   4.2        1.3    8.9   0.3    2.3  2  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger
       0.02   14.7   0.5      0.044   13.7   0.5    1.6  1  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
      0.021   14.4   0.8      0.021   14.4   0.8    2.5  3  zf-tcix          Putative treble-clef, zinc-finger, Zn-bindin
      0.027   14.7   1.7        0.1   12.9   1.7    1.8  2  zf-nanos         Nanos RNA binding domain
      0.029   14.4   1.1      0.036   14.2   1.1    1.2  1  DUF1272          Protein of unknown function (DUF1272)
      0.034   13.5   5.9       0.38   10.2   5.9    2.1  1  zf-ribbon_3      zinc-ribbon domain
      0.035   12.9   1.0      0.042   12.6   1.0    1.1  1  NRDD             Anaerobic ribonucleoside-triphosphate reduct
      0.055   13.5   1.3        9.1    6.4   0.1    2.2  2  DNA_ligase_ZBD   NAD-dependent DNA ligase C4 zinc finger doma
      0.087   12.8   2.5        2.8    7.9   0.2    2.4  2  Nudix_N_2        Nudix N-terminal
        0.1   13.0   6.2        1.9    8.9   0.3    2.2  2  Lar_restr_allev  Restriction alleviation protein Lar
       0.11   12.8   2.6       0.65   10.3   1.7    2.2  2  Ribosomal_L32p   Ribosomal L32p protein family
       0.13   12.9   4.6        2.3    9.0   0.2    2.2  2  zf-ISL3          zinc-finger of transposase IS204/IS1001/IS10
       0.22   11.6   4.3        1.4    9.0   0.2    2.1  2  CpXC             CpXC protein
       0.26   11.4   5.8        1.3    9.2   0.6    2.2  2  Zn-ribbon_8      Zinc ribbon domain
       0.27   11.2   2.6        5.2    7.1   0.1    2.1  2  Cys_rich_CPXG    Cysteine-rich CPXCG
       0.39   10.7   3.9        4.3    7.4   0.3    2.3  2  zf_CopZ          Zinc binding domain
       0.47   10.5   4.3        7.7    6.6   0.2    2.2  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
       0.55   10.0   8.0        1.8    8.4   1.7    2.2  2  zinc_ribbon_2    zinc-ribbon domain
       0.97    9.0   6.0         13    5.4   6.0    2.1  2  TF_Zn_Ribbon     TFIIB zinc-binding
          1    9.2   6.3        1.2    9.0   0.2    2.4  2  Cys_rich_KTR     Cysteine-rich KTR
        1.5    9.4   7.8        3.8    8.0   0.5    2.3  2  Zn-C2H2_12       Autophagy receptor zinc finger-C2H2 domain
        1.6    8.8   9.0         12    6.0   5.9    2.2  2  YhfH             YhfH-like protein
        1.7    8.7   4.9        9.3    6.3   0.4    2.2  2  Ogr_Delta        Ogr/Delta-like zinc finger
        2.5    7.7   7.8        5.1    6.7   1.9    2.4  2  zf_C2H2_10       C2H2 type zinc-finger
        5.6    7.0  10.7        6.3    6.9   3.4    2.2  2  DUF1610          Domain of unknown function (DUF1610)


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 !   91.4   4.0   4.3e-29   2.5e-26       1      51 [.       1      51 [.       1      52 [. 0.98

  Alignments for each domain:
  == domain 1  score: 91.4 bits;  conditional E-value: 4.3e-29
                                      .----EE-TTT--EESSSB-TTT-SB-B-SS--S--TT-TTCHHHHHCHHH CS
                            Nop10p  1 mksylrkcgkcrvYTLkkvcpecggptksahPaRFSPdDkyskyRralKkr 51
                                      m+++++kc+kc++YTLk++cp cg++tk ahP++FSP+D+y++yRr+lKk+
  gi|242398566|ref|YP_002993990.1|  1 MRFKIKKCPKCGEYTLKETCPLCGEKTKLAHPPKFSPEDPYGEYRRRLKKE 51
                                      9************************************************97 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.7   1.9e-07   0.00011      14      35 ..       3      24 ..       1      27 [. 0.90

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.9e-07
                                      HH-EE-TTT--EESSSS-CCCC CS
                              RecR 14 ekvrhCsrCgnlteedlCaICs 35
                                       k++ C++Cg +t ++ C+ C 
  gi|242398566|ref|YP_002993990.1|  3 FKIKKCPKCGEYTLKETCPLCG 24
                                      58*******************6 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 !   18.0   0.2   8.9e-07   0.00053     616     643 ..       3      30 ..       1      54 [. 0.85

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 8.9e-07
                          PolC_DP2 616 iarrkCkkCgketlearCeeCgekteek 643
                                       ++ +kC+kCg+ tl+ +C+ Cgekt+  
  gi|242398566|ref|YP_002993990.1|   3 FKIKKCPKCGEYTLKETCPLCGEKTKLA 30 
                                       56789********************974 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 ?    6.1   0.0     0.015       8.9       6      29 ..       8      13 ..       5      18 .. 0.63
   2 !   10.3   0.2   0.00073      0.43       6      17 ..      20      31 ..      20      31 .. 0.94

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.015
                     zf-NADH-PPase  6 CgrCGaptepaeggwarvCpaCgl 29
                                      C++CG                  +
  gi|242398566|ref|YP_002993990.1|  8 CPKCG------------------E 13
                                      55555..................4 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00073
                     zf-NADH-PPase  6 CgrCGaptepae 17
                                      C+ CG +t++a+
  gi|242398566|ref|YP_002993990.1| 20 CPLCGEKTKLAH 31
                                      *********987 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   1.1     3e-05     0.018      13      41 ..       6      30 ..       3      37 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3e-05
                               DZR 13 rfCseCgtk.lkavaaedrCpsCgekvdpe 41
                                      + C++Cg+  lk     ++Cp Cgek+++ 
  gi|242398566|ref|YP_002993990.1|  6 KKCPKCGEYtLK-----ETCPLCGEKTKLA 30
                                      569999998454.....9999999998765 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 ?    8.9   0.3    0.0021       1.3       2       9 ..       6      13 ..       5      16 .. 0.84
   2 ?    7.2   0.3    0.0069       4.2       2      10 ..      18      26 ..      17      30 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0021
                                      EE-SSS-- CS
                    zf-C4_Topoisom  2 ekCPkCgg 9 
                                      +kCPkCg+
  gi|242398566|ref|YP_002993990.1|  6 KKCPKCGE 13
                                      69****95 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0069
                                      EE-SSS--E CS
                    zf-C4_Topoisom  2 ekCPkCggd 10
                                      e+CP Cg++
  gi|242398566|ref|YP_002993990.1| 18 ETCPLCGEK 26
                                      89*****75 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 ?   13.7   0.5   7.4e-05     0.044       8      33 ..       2      25 ..       2      29 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.4e-05
                           DUF35_N  8 rLvgqrCpdCGtvqfPPravCphCgs 33
                                      r+ + +Cp+CG +       Cp Cg 
  gi|242398566|ref|YP_002993990.1|  2 RFKIKKCPKCGEYTL--KETCPLCGE 25
                                      78999********96..899999986 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 ?   14.4   0.8   3.6e-05     0.021      10      19 ..       5      14 ..       2      15 .. 0.89
   2 ?    2.4   0.3       0.2   1.2e+02      12      17 ..      19      24 ..      16      27 .. 0.86
   3 ?   -2.0   0.2       4.7   2.8e+03      10      12 ..      48      50 ..      45      59 .] 0.52

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.6e-05
                           zf-tcix 10 vrkCpkCGty 19
                                      ++kCpkCG y
  gi|242398566|ref|YP_002993990.1|  5 IKKCPKCGEY 14
                                      9*******77 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.2
                           zf-tcix 12 kCpkCG 17
                                       Cp CG
  gi|242398566|ref|YP_002993990.1| 19 TCPLCG 24
                                      5****9 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 4.7
                           zf-tcix 10 vrk 12
                                      ++k
  gi|242398566|ref|YP_002993990.1| 48 LKK 50
                                      443 PP

>> zf-nanos  Nanos RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.2       1.5   9.2e+02      35      41 ..       7      13 ..       3      17 .. 0.80
   2 ?   12.9   1.7   0.00017       0.1      33      53 ..      17      37 ..       7      38 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.5
                          zf-nanos 35 vCpiCga 41
                                      +Cp Cg 
  gi|242398566|ref|YP_002993990.1|  7 KCPKCGE 13
                                      6999985 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00017
                          zf-nanos 33 kyvCpiCgatgdkAHttkycp 53
                                      k +Cp+Cg + + AH  k+ p
  gi|242398566|ref|YP_002993990.1| 17 KETCPLCGEKTKLAHPPKFSP 37
                                      458*************99987 PP

>> DUF1272  Protein of unknown function (DUF1272)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   1.1     6e-05     0.036      32      48 ..       8      24 ..       2      34 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6e-05
                           DUF1272 32 CaeCaeevlenvCPncg 48
                                      C +C e +l+++CP cg
  gi|242398566|ref|YP_002993990.1|  8 CPKCGEYTLKETCPLCG 24
                                      ****************8 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   5.9   0.00063      0.38       3      25 ..       6      26 ..       5      27 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00063
                       zf-ribbon_3  3 vrCPnCGaplssddnvCpyCGtk 25
                                      ++CP+CG+   +   +Cp CG+k
  gi|242398566|ref|YP_002993990.1|  6 KKCPKCGEY--TLKETCPLCGEK 26
                                      68******5..566789999976 PP

>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   1.0     7e-05     0.042     506     529 ..       4      27 ..       1      33 [. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7e-05
                                       -EEEETT.--EESSSB-TTT--BE CS
                              NRDD 506 kidvCnecgykgeiekCpkCgsee 529
                                       ki+ C++cg   ++e+Cp Cg++ 
  gi|242398566|ref|YP_002993990.1|   4 KIKKCPKCGEYTLKETCPLCGEKT 27 
                                       7899******999999*****665 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 ?    6.4   0.1     0.016       9.3       1       7 [.       7      13 ..       7      18 .. 0.83
   2 ?    6.4   0.1     0.015       9.1       1       8 [.      19      26 ..      19      30 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.016
                    DNA_ligase_ZBD  1 hCPvCGs 7 
                                      +CP CG 
  gi|242398566|ref|YP_002993990.1|  7 KCPKCGE 13
                                      6*****6 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.015
                    DNA_ligase_ZBD  1 hCPvCGsa 8 
                                      +CP CG +
  gi|242398566|ref|YP_002993990.1| 19 TCPLCGEK 26
                                      7*****87 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.2     0.041        24       3       8 ..       8      13 ..       6      18 .. 0.79
   2 ?    7.9   0.2    0.0047       2.8       3      16 ..      20      33 ..      20      48 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.041
                                      -TTT-- CS
                         Nudix_N_2  3 CsqCGt 8 
                                      C++CG+
  gi|242398566|ref|YP_002993990.1|  8 CPKCGE 13
                                      888886 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0047
                                      -TTT--B-EEE--T CS
                         Nudix_N_2  3 CsqCGtpvelripd 16
                                      C+ CG++++l+ p+
  gi|242398566|ref|YP_002993990.1| 20 CPLCGEKTKLAHPP 33
                                      *********99885 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   1.0     0.008       4.8       3      11 ..       5      13 ..       4      19 .. 0.81
   2 ?    8.9   0.3    0.0032       1.9       5      19 ..      19      33 ..      15      44 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.008
                   Lar_restr_allev  3 LkpCPfCgg 11
                                      +k CP Cg+
  gi|242398566|ref|YP_002993990.1|  5 IKKCPKCGE 13
                                      89******8 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0032
                   Lar_restr_allev  5 pCPfCggravlersq 19
                                       CP Cg++ +l + +
  gi|242398566|ref|YP_002993990.1| 19 TCPLCGEKTKLAHPP 33
                                      6*******9998755 PP

>> Ribosomal_L32p  Ribosomal L32p protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   1.7    0.0011      0.65      26      46 ..       5      24 ..       1      27 [. 0.80
   2 ?    3.2   0.3      0.19   1.1e+02      28      39 ..      19      31 ..      17      32 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0011
                                      EEEETTTCCEECTTC-BTTTT CS
                    Ribosomal_L32p 26 lvecpncgelklpHrvcpscG 46
                                      + +cp+cge++l    cp cG
  gi|242398566|ref|YP_002993990.1|  5 IKKCPKCGEYTLK-ETCPLCG 24
                                      789********96.5677776 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.19
                                      EETTTC.CEECTT CS
                    Ribosomal_L32p 28 ecpncg.elklpH 39
                                      +cp cg ++kl+H
  gi|242398566|ref|YP_002993990.1| 19 TCPLCGeKTKLAH 31
                                      7*****6677777 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 ?    6.5   0.4     0.023        14       4      13 ..       7      16 ..       5      18 .. 0.84
   2 ?    9.0   0.2    0.0038       2.3       4      13 ..      19      28 ..      16      52 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.023
                           zf-ISL3  4 rCPnCgsktv 13
                                      +CP+Cg+ t+
  gi|242398566|ref|YP_002993990.1|  7 KCPKCGEYTL 16
                                      6*****9875 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0038
                           zf-ISL3  4 rCPnCgsktv 13
                                      +CP Cg+kt+
  gi|242398566|ref|YP_002993990.1| 19 TCPLCGEKTK 28
                                      8*******87 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.6     0.048        29      39      46 ..       7      14 ..       2      18 .. 0.70
   2 ?    9.0   0.2    0.0023       1.4      38      52 ..      18      32 ..      15      44 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.048
                              CpXC 39 tCpkCgat 46
                                      +CpkCg+ 
  gi|242398566|ref|YP_002993990.1|  7 KCPKCGEY 14
                                      68888875 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0023
                              CpXC 38 atCpkCgatakleap 52
                                       tCp Cg+++kl +p
  gi|242398566|ref|YP_002993990.1| 18 ETCPLCGEKTKLAHP 32
                                      589999999999998 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.6    0.0022       1.3      27      37 ..       6      17 ..       1      19 [. 0.75
   2 ?    3.9   6.1     0.098        59       7      35 ..       7      26 ..       7      30 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0022
                       Zn-ribbon_8 27 taCPeCgs.evr 37
                                      ++CP+Cg+ +++
  gi|242398566|ref|YP_002993990.1|  6 KKCPKCGEyTLK 17
                                      45*****97775 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.098
                       Zn-ribbon_8  7 rCeeCghefevlqsisdapltaCPeCgse 35
                                      +C +Cg e++ l       +++CP Cg++
  gi|242398566|ref|YP_002993990.1|  7 KCPKCG-EYT-L-------KETCPLCGEK 26
                                      566677.444.1.......2348888875 PP

>> Cys_rich_CPXG  Cysteine-rich CPXCG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.2     0.065        39       2       9 ..       7      14 ..       6      16 .. 0.86
   2 ?    7.1   0.1    0.0086       5.2       2      12 ..      19      29 ..      19      31 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.065
                     Cys_rich_CPXG  2 qCPyCgee 9 
                                      +CP Cge 
  gi|242398566|ref|YP_002993990.1|  7 KCPKCGEY 14
                                      6*****96 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0086
                     Cys_rich_CPXG  2 qCPyCgeeiev 12
                                      +CP Cge++++
  gi|242398566|ref|YP_002993990.1| 19 TCPLCGEKTKL 29
                                      5******9875 PP

>> zf_CopZ  Zinc binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.3     0.052        31       2       9 ..       6      13 ..       5      15 .. 0.87
   2 ?    7.4   0.3    0.0072       4.3       1      12 [.      17      28 ..      17      32 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.052
                                      -B-TTT-- CS
                           zf_CopZ  2 kkCPvCgk 9 
                                      kkCP+Cg+
  gi|242398566|ref|YP_002993990.1|  6 KKCPKCGE 13
                                      79****97 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0072
                                      X-B-TTT--B-E CS
                           zf_CopZ  1 kkkCPvCgkkGk 12
                                      k++CP Cg+k k
  gi|242398566|ref|YP_002993990.1| 17 KETCPLCGEKTK 28
                                      579******976 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.5     0.015       8.7      20      26 ..       7      13 ..       1      18 [. 0.73
   2 ?    6.6   0.2     0.013       7.7      20      28 ..      19      28 ..      14      48 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.015
                     Zn_Tnp_IS1595 20 vCPhCgs 26
                                       CP+Cg 
  gi|242398566|ref|YP_002993990.1|  7 KCPKCGE 13
                                      4****95 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.013
                     Zn_Tnp_IS1595 20 vCPhCgsr.k 28
                                      +CP Cg + k
  gi|242398566|ref|YP_002993990.1| 19 TCPLCGEKtK 28
                                      8*****6643 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   1.7     0.003       1.8       1       7 [.       7      13 ..       6      14 .. 0.68
   2 ?    5.4   0.5     0.027        16       2       8 ..      20      26 ..      18      28 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.003
                     zinc_ribbon_2  1 fCpnCGa 7 
                                      +Cp+CG+
  gi|242398566|ref|YP_002993990.1|  7 KCPKCGE 13
                                      5777774 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.027
                     zinc_ribbon_2  2 CpnCGae 8 
                                      Cp CG++
  gi|242398566|ref|YP_002993990.1| 20 CPLCGEK 26
                                      6666654 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   6.0     0.021        13       2      28 ..       7      26 ..       6      30 .. 0.77
   2 ?    4.9   0.5     0.031        18       2       9 ..      19      26 ..      18      34 .. 0.62

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.021
                                      EETTTTCEECHEETSTTCEEESSSSBE CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGlV 28
                                      kCP+Cg ++ + +      +C+ CG+ 
  gi|242398566|ref|YP_002993990.1|  7 KCPKCGEYT-LKE------TCPLCGEK 26
                                      8*****764.444......79999975 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.031
                                      EETTTTCE CS
                      TF_Zn_Ribbon  2 kCPnCgst 9 
                                      +CP Cg +
  gi|242398566|ref|YP_002993990.1| 19 TCPLCGEK 26
                                      45555554 PP

>> Cys_rich_KTR  Cysteine-rich KTR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.3     0.075        45      30      37 ..       8      15 ..       6      19 .. 0.69
   2 ?    9.0   0.2     0.002       1.2       5      15 ..      19      29 ..      18      34 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.075
                      Cys_rich_KTR 30 CPKCkqet 37
                                      CPKC + t
  gi|242398566|ref|YP_002993990.1|  8 CPKCGEYT 15
                                      77776555 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.002
                      Cys_rich_KTR  5 lcPvCgnkTRl 15
                                      +cP+Cg kT+l
  gi|242398566|ref|YP_002993990.1| 19 TCPLCGEKTKL 29
                                      5********86 PP

>> Zn-C2H2_12  Autophagy receptor zinc finger-C2H2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   1.6     0.062        37       1       9 [.       6      14 ..       6      14 .. 0.92
   2 ?    8.0   0.5    0.0064       3.8       2       8 ..      19      25 ..      18      26 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.062
                        Zn-C2H2_12  1 KeCPlCseq 9 
                                      K+CP C+e+
  gi|242398566|ref|YP_002993990.1|  6 KKCPKCGEY 14
                                      9******96 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0064
                        Zn-C2H2_12  2 eCPlCse 8 
                                      +CPlC+e
  gi|242398566|ref|YP_002993990.1| 19 TCPLCGE 25
                                      7****98 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   5.9     0.019        12      14      25 ..       6      18 ..       2      20 .. 0.80
   2 ?    4.5   0.5     0.058        35      15      22 ..      19      26 ..      15      30 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.019
                              YhfH 14 KkCteCGke.ieE 25
                                      KkC++CG+  ++E
  gi|242398566|ref|YP_002993990.1|  6 KKCPKCGEYtLKE 18
                                      9******975666 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.058
                              YhfH 15 kCteCGke 22
                                      +C+ CG++
  gi|242398566|ref|YP_002993990.1| 19 TCPLCGEK 26
                                      7*****97 PP

>> Ogr_Delta  Ogr/Delta-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.5     0.053        32       1       7 [.       7      13 ..       7      15 .. 0.87
   2 ?    6.3   0.4     0.016       9.3       1       8 [.      19      26 ..      19      32 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.053
                         Ogr_Delta  1 rCPhCga 7 
                                      +CP+Cg+
  gi|242398566|ref|YP_002993990.1|  7 KCPKCGE 13
                                      6****96 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.016
                         Ogr_Delta  1 rCPhCgap 8 
                                      +CP+Cg++
  gi|242398566|ref|YP_002993990.1| 19 TCPLCGEK 26
                                      6*****97 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 ?    6.7   1.9    0.0086       5.1       5      10 ..       8      13 ..       6      15 .. 0.88
   2 ?    4.0   0.4     0.062        37       4      11 ..      19      26 ..      17      27 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0086
                        zf_C2H2_10  5 CPKCqe 10
                                      CPKC+e
  gi|242398566|ref|YP_002993990.1|  8 CPKCGE 13
                                      ****98 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.062
                        zf_C2H2_10  4 sCPKCqek 11
                                       CP C+ek
  gi|242398566|ref|YP_002993990.1| 19 TCPLCGEK 26
                                      6*****97 PP

>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   3.4     0.011       6.3      19      24 .]       8      13 ..       7      13 .. 0.94
   2 ?    4.8   0.7     0.048        29      19      24 .]      20      25 ..      19      25 .. 0.92

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.011
                           DUF1610 19 CPNCGE 24
                                      CP+CGE
  gi|242398566|ref|YP_002993990.1|  8 CPKCGE 13
                                      *****9 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.048
                           DUF1610 19 CPNCGE 24
                                      CP CGE
  gi|242398566|ref|YP_002993990.1| 20 CPLCGE 25
                                      *****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                       112  (0.00624686); expected 17.9 (0.001)
Passed Fwd filter:                        32  (0.00178482); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              30  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.46
# Mc/sec: 387.87
//
Query:       gi|242398567|ref|YP_002993991.1|  [L=261]
Description: 3-isopropylmalate dehydratase [Thermococcus sibiricus MM 739]
Scores for complete 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-48  164.8   0.0    3.1e-48  164.6   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 !  164.6   0.0   1.7e-52   3.1e-48       1     212 [.      19     236 ..      19     237 .. 0.91

  Alignments for each domain:
  == domain 1  score: 164.6 bits;  conditional E-value: 1.7e-52
                                       EEEESSCGGGHHHHHHHHHHHHTTEEEEEEEEHCCHSBCCCC.SEEEEETT..EEE-SEEE.EEE..TTT.SEEEEE CS
                              PAC2   1 LilGfpgiGnVgqlavdlLiesleaekvgeidsdyllpfvgprpvvlveeg..relepprl.yak..dsgsrdllvl 72 
                                       +i+G+pgiG+Vg+la+d+Li++l+a+k++e++s+  +      ++v+v+++  ++l+ +++ y+k  d++ rdl+++
  gi|242398567|ref|YP_002993991.1|  19 FIEGLPGIGLVGKLAADHLIQELKAKKFAELYSPR-FM-----HQVIVKKDstVDLMRNEFyYWKspDKEHRDLIIV 89 
                                       69*********************************.99.....99******9*********666686666******* PP

                                       EE...E-HSCHHH..HHHHHHHHHHHHTTESEEEEEEEEEESS-ES..TTS-.EEEEEESSHHHHHHHH.......C CS
                              PAC2  73 qg...repilqye..efakalldwaeelgvkevvvLggldageradvphtrpekvtgaatdeelleele.......e 137
                                       +g   + p   y   e++ ++ld++e++g + ++++gg+   e+    + +p kv + +td e  e+++       e
  gi|242398567|ref|YP_002993991.1|  90 TGdtqVPPTDSYGhfEVVGKMLDFVEQFGTRDIITMGGYQVPEL----DGEP-KVLASFTDLETKEKYKelpvvirE 161
                                       **885444444449**************************8777....4688.9**************636655544 PP

                                       T-CEEEEHHHHHHHHHHHHTT-EEEEEEEEEECCC--HHHHHHHHHHHHHHHT---HCHHHHHHHHHHHHHHHHH CS
                              PAC2 138 seyggivgitglLlsaakergipavgllaevphylpdPkaaaalleflskllglevdtedLeedaeeleeqleel 212
                                        e+g ivg++glLl+ +k rg+++v++l+e+ +y++d kaa+a+l++++k+l+le+d++ L+e+a+e ee l+++
  gi|242398567|ref|YP_002993991.1| 162 DEGGAIVGAAGLLLGIGKLRGMKGVCFLGESLGYIVDAKAAKAVLSVVAKVLNLEIDMSALDERAKETEEILKKV 236
                                       4**********************************************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1182  (0.0659267); expected 358.6 (0.02)
Passed bias filter:                      848  (0.0472977); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1768.29
//
Query:       gi|242398568|ref|YP_002993992.1|  [L=421]
Description: Phosphohydrolase, PHP family [Thermococcus sibiricus MM 739]
Scores for complete 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   25.0   0.0    2.7e-05   23.8   0.0    1.6  1  PHP_C          PHP-associated
     0.0031   17.8   0.1     0.0071   16.7   0.0    1.5  1  PHP            PHP domain
     0.0071   15.8   0.1      0.014   14.9   0.1    1.5  1  TF_Zn_Ribbon   TFIIB zinc-binding
  ------ inclusion threshold ------
      0.014   15.1   0.3      0.031   14.0   0.1    1.6  2  HAUS4          HAUS augmin-like complex subunit 4
       0.11   12.4   1.3       0.29   11.1   1.3    1.8  1  zinc_ribbon_4  zinc-ribbon domain


Domain annotation for each model (and alignments):
>> PHP_C  PHP-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   7.4e-09   2.7e-05       6      53 ..     176     225 ..     173     227 .. 0.93

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 7.4e-09
                             PHP_C   6 rArrfAeklglpgtgGSDAH..rleeVGrayTefeepiatpdelleaire 53 
                                       +A+++ ++++l  + +SDAH  ++  +Gr ++ fe + at++e+ +ai +
  gi|242398568|ref|YP_002993992.1| 176 MADKIKAHHNLVYLSNSDAHspQPHRLGREFNRFEVEDATFEEIKKAILK 225
                                       7999****************666789**********************97 PP

>> PHP  PHP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0     2e-06    0.0071       1      94 [.       6     154 ..       6     223 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2e-06
                                       EEEE--CCC.--.S-H..HHHHHHHHHCT-SEEEEEEEEBTT......HHHHHHHHHHHHTTTTSEEEEEEE..... CS
                                       xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               PHP   1 dlHvHteys.lldgalsieelvkkakelglkaiaiTDhgnlf......gyvefykaakkkykagikpiiGleayvad 70 
                                       dlH+H+ ys +++  ++   l++ ak +gl  ++  D  n        +y + + +  + + +gik ++ +e   ++
  gi|242398568|ref|YP_002993992.1|   6 DLHIHSRYSkAVSKLMTFPILAENAKLKGLGIVGTGDILNPKwegellKYSQKVDEG-TYEIKGIKFLLTAE---VE 78 
                                       89********99899999999999999999999999999999999666666666666.23338999999999...33 PP

                                       .............E....EHHHH...................................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxx...................................................... RF
                               PHP  71 dsekerpshltllaknqeGyknl...................................................... 93 
                                       d+  +r +hl++   n e +++l                                                      
  gi|242398568|ref|YP_002993992.1|  79 DN--KRVHHLLI-FPNIETVRELrerlkhyskdvesegrphlslnaseiadlsnefdvligpshaftpwtalykeyn 152
                                       32..34444444.4476666666666555555555555555555555555555556666666666666555555544 PP

                                       .H CS
                                       .x RF
                               PHP  94 .l 94 
                                        +
  gi|242398568|ref|YP_002993992.1| 153 sI 154
                                       42 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   3.9e-06     0.014       3      36 ..     249     282 ..     247     287 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.9e-06
                                       ETTTTCEECHEETSTTCEEESSSSBEEEECCCCC CS
                      TF_Zn_Ribbon   3 CPnCgstnlveDpergelvCtdCGlVlednside 36 
                                       C  C +++ +eD++r   +C+ CG V+     d 
  gi|242398568|ref|YP_002993992.1| 249 CSRCYTKYRLEDAKRLGWRCELCGGVIKKGVHDR 282
                                       99************************98877765 PP

>> HAUS4  HAUS augmin-like complex subunit 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       1.8   6.4e+03     174     190 ..      95     111 ..      91     128 .. 0.53
   2 ?   14.0   0.1   8.6e-06     0.031     140     212 ..     149     219 ..     145     222 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.8
                             HAUS4 174 lrkirekLeealeeeea 190
                                        r++re+L+  ++  e+
  gi|242398568|ref|YP_002993992.1|  95 VRELRERLKHYSKDVES 111
                                       34444444433333333 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 8.6e-06
                             HAUS4 140 keyleakCeamllKlrvlelellldtYtkekvaalrkirekLeealeeeeaelqkaeerLrsYeilgkeFeel 212
                                       key   k    + K+  lel l  d+Y ++k++a++++  +L++  ++++ + ++  +  +++e+ +  Fee+
  gi|242398568|ref|YP_002993992.1| 149 KEYNSIKEAYGNYKIHFLELGLSADSYMADKIKAHHNLV-YLSNS-DAHSPQPHRLGREFNRFEVEDATFEEI 219
                                       6777778888899***********************995.56554.445556678888899999999999998 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.3   8.2e-05      0.29       3      33 ..     247     273 ..     246     276 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 8.2e-05
                     zinc_ribbon_4   3 itCpsCkakyeiddeklpakgvkvrCskCgh 33 
                                       + C +C +ky+++d+    k+   rC  Cg 
  gi|242398568|ref|YP_002993992.1| 247 TACSRCYTKYRLEDA----KRLGWRCELCGG 273
                                       57************6....555566666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       700  (0.0390429); expected 358.6 (0.02)
Passed bias filter:                      662  (0.0369234); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2809.23
//
Query:       gi|242398569|ref|YP_002993993.1|  [L=328]
Description: galactose-1-phosphate uridylyltransferase [Thermococcus sibiricus MM 739]
Scores for complete 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-25   90.5   0.4    1.8e-24   87.2   0.1    2.5  2  GalP_UDP_transf  Galactose-1-phosphate uridyl transferase, N-
    7.1e-18   64.9   0.0    1.1e-17   64.2   0.0    1.2  1  GalP_UDP_tr_C    Galactose-1-phosphate uridyl transferase, C-
    2.9e-06   27.9   0.0      0.013   16.3   0.0    2.3  2  HIT              HIT domain
    8.2e-06   24.9   0.1    1.5e-05   24.0   0.0    1.4  2  DUF4921          Domain of unknown function (DUF4921)
    6.8e-05   23.3   0.2    0.00046   20.6   0.0    2.0  2  DcpS_C           Scavenger mRNA decapping enzyme C-term bindi
     0.0092   15.3   0.2       0.02   14.2   0.0    1.7  2  DUF4931          Domain of unknown function (DUF4931)


Domain annotation for each model (and alignments):
>> GalP_UDP_transf  Galactose-1-phosphate uridyl transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.2   0.1   5.9e-28   1.8e-24      12     184 .]       4     153 ..       1     153 [. 0.90
   2 ?   -2.2   0.0       1.6   4.8e+03     113     147 ..     208     242 ..     207     255 .. 0.74

  Alignments for each domain:
  == domain 1  score: 87.2 bits;  conditional E-value: 5.9e-28
                   GalP_UDP_transf  12 shrrfnpltgewvlvsphrtkrpwqgqqekiskdtlpekDklkcyLcPgnsrangefnpky.kstfvftndFpalse 87 
                                       +++r+npltg+w++vs+ r++rpw     ++       k    c++cPg +++       y  ++    n+Fp +s 
  gi|242398569|ref|YP_002993993.1|   4 RELRYNPLTGQWIMVSAVRKNRPW-----RP-------K--NFCPFCPGGEETG------YgWEVLLLPNRFPMFSF 60 
                                       789*********************.....33.......3..46*****987753......4455689********** PP

                   GalP_UDP_transf  88 dsnyikteaiaknilfkaepayGrceviifsskhel.tladlspkdikavvaaWqektaelkakeypkcvlifENkG 163
                                       ++++++      +  +k++ a G+c vi+  ++h l  l +ls +++++vv+ W++ t+elk++ +++++ if NkG
  gi|242398569|ref|YP_002993993.1|  61 NAPKPES-----KGFYKKARALGQCSVIVETPEHGLkDLEELSIEQMTKVVQLWKQITEELKNNPHIAYLSIFRNKG 132
                                       **99988.....348*******************9526999************************************ PP

                   GalP_UDP_transf 164 aamgvsnphPHgqiwaeehlp 184
                                       +++gvs++hPHgq++a +++p
  gi|242398569|ref|YP_002993993.1| 133 EEIGVSLTHPHGQLYALPFIP 153
                                       *****************9998 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.6
                   GalP_UDP_transf 113 eviifsskheltladlspkdikavvaaWqektael 147
                                       ev i+  +h + l +l++++i + ++  +  t +l
  gi|242398569|ref|YP_002993993.1| 208 EVHIYPKRHIQWLTQLTQAEILNLADILRVTTGTL 242
                                       67777788888899999999988888766555555 PP

>> GalP_UDP_tr_C  Galactose-1-phosphate uridyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.2   0.0   3.8e-21   1.1e-17       7     160 ..     165     316 ..     159     322 .. 0.85

  Alignments for each domain:
  == domain 1  score: 64.2 bits;  conditional E-value: 3.8e-21
                                       HHHHHH.SS-HHHHHHHHHHHH-TTEEEE-SSEEEE--TT--STT-EEEEESS--SSGGG--HHHHHHHHHHHHHHH CS
                     GalP_UDP_tr_C   7 kYfagsngsillhdyvqmelaekervvelkdsflavvpylakWPfevlllrkaevkslaeladeekedlaailkkla 83 
                                       +Y     ++ l+   +  el+ k  ++e +d f+   p++a WPfev + +k++++ l++l+++e  +la il+  +
  gi|242398569|ref|YP_002993993.1| 165 RYYNRF-KKCLFCKILDEELKGKRLIYENND-FILFLPFFANWPFEVHIYPKRHIQWLTQLTQAEILNLADILRVTT 239
                                       555554.677777788899999999999999.********************************************* PP

                                       HHHHHHCTS---EEEEEE---SCCCTTTT--EEEEE--BCSSTTEB----THHHHT-E.EESS-HHHHHHHHH.CS- CS
                     GalP_UDP_tr_C  84 rkydnlfetsfeysmGlhqaplnaeednswlHaHfevpllrsatvrkieVGlelLper.lrdllaEqaaerlrnals 159
                                          + lfe +++y m ++qap+++e +   lH+ f+ pllr++   k+  G e+ +     d ++E +a +l+na +
  gi|242398569|ref|YP_002993993.1| 240 GTLNSLFERQMPYVMTVYQAPFKGECPFYHLHIEFY-PLLREKDKLKYAAGIEMGTWDfTYDGIPEENARKLKNACK 315
                                       ***********************9987555555555.6889999899999****87541679999999999998876 PP

                                       S CS
                     GalP_UDP_tr_C 160 e 160
                                       +
  gi|242398569|ref|YP_002993993.1| 316 K 316
                                       5 PP

>> HIT  HIT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0   0.00063       1.9      33      89 ..      87     143 ..      74     144 .. 0.91
   2 !   16.3   0.0   4.2e-06     0.013       6      67 ..     186     247 ..     182     273 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00063
                                       ESSTGCSGGGCCHHHHHHHHHHHHHHHHHHHTCTTCCCEEEEEEESGGGT-SSSS-E CS
                               HIT  33 pkkhlselhdlteeelakllsavkkvakalqkkfknkglrvvinngahagqsvahlH 89 
                                       p   l++l++l+ e ++k++++ k++ ++l+++ +   l ++ n+g++ g s  h H
  gi|242398569|ref|YP_002993993.1|  87 PEHGLKDLEELSIEQMTKVVQLWKQITEELKNNPHIAYLSIFRNKGEEIGVSLTHPH 143
                                       44579999*************************9999*************9999988 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 4.2e-06
                                       CCEEEE-SSEEEEE-SS-SSSSEEEEEESSTGCSGGGCCHHHHHHHHHHHHHHHHHHHTCTT CS
                               HIT   6 stvvyeddlvlafldidpkapghlLvipkkhlselhdlteeelakllsavkkvakalqkkfk 67 
                                       ++++ye++++++fl  ++ +p  + + pk+h++ l++lt++e+ +l  + +    +l+  f+
  gi|242398569|ref|YP_002993993.1| 186 KRLIYENNDFILFLPFFANWPFEVHIYPKRHIQWLTQLTQAEILNLADILRVTTGTLNSLFE 247
                                       678************************************99998888887777777776664 PP

>> DUF4921  Domain of unknown function (DUF4921)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.3       1.1   3.3e+03       9      29 ..       8      28 ..       7      31 .. 0.85
   2 !   24.0   0.0     5e-09   1.5e-05     195     330 ..      97     236 ..      86     244 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.1
                           DUF4921  9 vnPftGtevWtvpgrgnrPls 29
                                       nP+tG  +   + r nrP +
  gi|242398569|ref|YP_002993993.1|  8 YNPLTGQWIMVSAVRKNRPWR 28
                                      69****999999999999976 PP

  == domain 2  score: 24.0 bits;  conditional E-value: 5e-09
                           DUF4921 195 lsveeheafiaftvdalkdlykrnryvrYvavfqnWLkpaGasfdhlhkqlvaiDergvqaeaeiarlrenPnlyne 271
                                       ls+e+ ++++++    +++  k+n+++ Y ++f+n  +  G s+ h h ql a+  + ++ + ++++ r+  n +++
  gi|242398569|ref|YP_002993993.1|  97 LSIEQMTKVVQLWK-QITEELKNNPHIAYLSIFRNKGEEIGVSLTHPHGQLYALPFIPLKVRLKMENSRRYYNRFKK 172
                                       55555555555543.45556699**************************************************9999 PP

                           DUF4921 272 lavdyaakhnl....viaendhavafagfGhryp.tlevysksatkePweqseeevravsdlvh 330
                                       +      +++l    +i en+  + f  f   +p  +++y k + +   + +++e+ +++d++ 
  gi|242398569|ref|YP_002993993.1| 173 CLFCKILDEELkgkrLIYENNDFILFLPFFANWPfEVHIYPKRHIQWLTQLTQAEILNLADILR 236
                                       86544444443333388999999999999999995699****999999999**********986 PP

>> DcpS_C  Scavenger mRNA decapping enzyme C-term binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.31   9.2e+02      39      76 ..      82     119 ..      72     143 .. 0.71
   2 !   20.6   0.0   1.5e-07   0.00046       1      97 [.     172     272 ..     172     285 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.31
                                       EEESS---SGGG--TTTTTHHHHHHHHHHHHHHHTT-T CS
                            DcpS_C  39 vipkrdikslrdLtkehlpllkemrekakkvieekyne 76 
                                       vi++   + l+dL++  ++ + ++++  k++ ee +n+
  gi|242398569|ref|YP_002993993.1|  82 VIVETPEHGLKDLEELSIEQMTKVVQLWKQITEELKNN 119
                                       66666666677887778888888888888887776655 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 1.5e-07
                                       T-HHHHHHTTSS.-B-EEEE-SSEEEEE-SS-SSSEEEEEEESS---SGGG--TTTTTHHHHHHHHHHHHHHHTT-T CS
                            DcpS_C   1 kwvfnilakgke.pervvyedekfvvlkDikpkaklhllvipkrdikslrdLtkehlpllkemrekakkvieekyne 76 
                                       k++f+++ +++   +r++ye+++f+++    +  ++ + + pkr+i+ l++Lt++++  l+++ ++    +++ +++
  gi|242398569|ref|YP_002993993.1| 172 KCLFCKILDEELkGKRLIYENNDFILFLPFFANWPFEVHIYPKRHIQWLTQLTQAEILNLADILRVTTGTLNSLFER 248
                                       699***99999868999*************************************************99999999966 PP

                                       ...-EEEEE--SCCCT--S-S--E CS
                            DcpS_C  77 ...vdaeelrvgvhyqPsvyhlHl 97 
                                          +     ++ ++ +  +yhlH+
  gi|242398569|ref|YP_002993993.1| 249 qmpYVMTVYQAPFKGECPFYHLHI 272
                                       444444445555666669999998 PP

>> DUF4931  Domain of unknown function (DUF4931)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       1.2   3.5e+03      18      29 ..      31      42 ..      23      59 .. 0.65
   2 !   14.2   0.0   6.8e-06      0.02      54     125 ..      81     153 ..      71     196 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.2
                           DUF4931 18 tacPfcdreklt 29
                                      + cPfc   + t
  gi|242398569|ref|YP_002993993.1| 31 NFCPFCPGGEET 42
                                      569999765544 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 6.8e-06
                           DUF4931  54 tvlietde.ceedistyseehlrellrfgvkhwlelekseeyksvllfknhGPlsGGsikhahmqivGlkeld 125
                                        v++et e   +d+ + s e + +++++  +   el+++ +   + +f+n G   G s+ h+h q+  l  + 
  gi|242398569|ref|YP_002993993.1|  81 SVIVETPEhGLKDLEELSIEQMTKVVQLWKQITEELKNNPHIAYLSIFRNKGEEIGVSLTHPHGQLYALPFIP 153
                                       5788886515789***************999999*******999*********************98876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       826  (0.0460706); expected 358.6 (0.02)
Passed bias filter:                      713  (0.039768); 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: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 2095.00
//
Query:       gi|242398570|ref|YP_002993994.1|  [L=423]
Description: Beta-glucan glucohydrolase [Thermococcus sibiricus MM 739]
Scores for 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-88  296.8  13.9    3.7e-87  292.6  13.9    2.0  1  Glyco_hydro_1   Glycosyl hydrolase family 1
  ------ inclusion threshold ------
      0.018   14.6   1.7      0.055   13.0   0.8    2.1  2  Glyco_hydro_cc  Glycosyl hydrolase catalytic core
      0.023   13.9   0.5       0.48    9.5   0.0    2.4  3  Glyco_hydro_10  Glycosyl hydrolase family 10


Domain annotation for each model (and alignments):
>> Glyco_hydro_1  Glycosyl hydrolase family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  292.6  13.9   6.1e-91   3.7e-87       4     452 ..       6     409 ..       4     410 .. 0.91

  Alignments for each domain:
  == domain 1  score: 292.6 bits;  conditional E-value: 6.1e-91
                                       GS-TT-EEEEE--HHHHH--TTSTT---BHHHHHHHHGGGSTTS---SSTT-HHHHHHHHHHHHHHTT-SEEEEE-- CS
                     Glyco_hydro_1   4 tfpedFlwgaataayqiEGawnedGkgesiwDtftetpgkvlegsngdvacdsYhrykeDvallkelgvkayrfSis 80 
                                        fp+ Fl+g+at+++qiEG  +        w  + e+ gk  ++s    ac++++ ykeD++l++ lg + yrfSi 
  gi|242398570|ref|YP_002993994.1|   6 VFPKSFLFGTATSSHQIEGNNKW-----NDWW-YYEQIGKLPYKSG--KACNHWELYKEDISLMHSLGYDGYRFSIE 74 
                                       6******************7543.....3354.5666678777665..59*************************** PP

                                       HHHHSTTSTT---HHHHHHHHHHHHHHHHTT-EEEEEEESS--BHHHHHH-GGG-SHHHHHHHHHHHHHHHHHTTT- CS
                     Glyco_hydro_1  81 WpRilPkGegeinekGlayYerLidelleagieplvTlyHwdlPqaLqdeGgwenrsiidafkeyaevvfkrfgdkv 157
                                       W+Ri+Pk  +ei+e+ l+ Y ++i+ l ++gi+p vTl+H+  P ++++ Gg+++++  +++++y e+v   ++d v
  gi|242398570|ref|YP_002993994.1|  75 WSRIFPKE-NEIDENALNRYLEIIELLVKSGITPNVTLHHFTSPIWFMQRGGFAKEENLKYWEQYVETVAGILKD-V 149
                                       *******7.9*****************************************************************.* PP

                                       -EEEEEE-HHHHHHHHHTSS-STT-S-TTTHHHHHHHHHHHHHHHHHHHHHHHTTT-EEEEEEEEEEEEESSSSHHH CS
                     Glyco_hydro_1 158 klwlTfnEpnvvallgyltgefaPgkkdleaayeaaHnlllaharavklykevaqkgkigivlnlslaeplseseed 234
                                       kl++TfnEp+v +++gylt+ ++P +k+  +a+++a nll+aha a++   +     k+giv n+  + ++s  e+d
  gi|242398570|ref|YP_002993994.1| 150 KLVATFNEPMVYVMMGYLTAYWPPFVKSPFKAFKVAANLLKAHALAYEILSS---RLKVGIVKNIPIMLAASYMERD 223
                                       **********************************************998876...569******************* PP

                                       HHHHHHHHHHHTHHHHHHHHHSS--HHHHHHHGGG..S----HHHHHHHTT--SEEEEEEEEEEEEEE--...-STT CS
                     Glyco_hydro_1 235 keaaeraleflngwfldpvvkGdYpeemkellrergalpeiteedkellkgkadflglnyYtsrlvknkeseeasls 311
                                       k+aae+a+++ n  fld++  G+    + ++        ++ e+        +df+g+nyYt + vk + ++ + + 
  gi|242398570|ref|YP_002993994.1| 224 KKAAEKADNLFNWNFLDAIWSGKLKGVLSTY--------TVPES-------DVDFIGVNYYTASEVKYSWNPIKFFF 285
                                       **********************987766554........34444.......579*********99999885555555 PP

                                       ---SSGGGGG-SBSS-B-SSSS-B-HHHHHHHHHHHHHTS----EEEEE----EE-BSSSHHH--HHHHHHHHHHHH CS
                     Glyco_hydro_1 312 kteekkleeevdpslpktdigwiiepeglrkllellkkeYqklpiyiteNGlgakdeieegkveDdkRidYlkehln 388
                                       +++ + l+e+      kt++gw ++peg++k ++ + ++Y+ +p+yiteNG+++ d        D+ R +++ +hl+
  gi|242398570|ref|YP_002993994.1| 286 EAKLADLSER------KTQMGWSVYPEGIYKAITAV-SRYE-KPMYITENGIATLD--------DEWRKEFVVQHLQ 346
                                       5544444444......5******************9.89*9.9*********8655........99*********** PP

                                       HHHHHHHTT--EEEEEEE-SB----GGGTTSEE--SEEEETTTTTEEEE-HHHHHHHHHHH-SS CS
                     Glyco_hydro_1 389 evkkaiedgvdlkgYvawsllDnfewaegyskrfGlvyvdrnetleRtpkkSakwykeviekng 452
                                        v+kai++g+d++gY+ ws++Dn+ew eg++ rfGl+ +d ++t eR+p++Sa+ y e+++k++
  gi|242398570|ref|YP_002993994.1| 347 YVQKAIDEGYDVRGYFYWSFMDNYEWKEGFEPRFGLIEID-YKTYERKPRESAYVYGEIAQKKE 409
                                       ****************************************.9******************9986 PP

>> Glyco_hydro_cc  Glycosyl hydrolase catalytic core
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.16   9.3e+02      92     110 ..     133     153 ..     126     175 .. 0.62
   2 ?   13.0   0.8   9.2e-06     0.055     154     215 ..     309     369 ..     301     377 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.16
                    Glyco_hydro_cc  92 klwkqliqplr.e.kgvklvs 110
                                       k+w+q++++++   k+vklv+
  gi|242398570|ref|YP_002993994.1| 133 KYWEQYVETVAgIlKDVKLVA 153
                                       555555555553235555544 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 9.2e-06
                    Glyco_hydro_cc 154 kehieelheaynkpiWvTEfalqsesgdasqeetkeflnevlawldsqeyVeryawfgfrse 215
                                        + i+ + ++y+kp+++TE ++   +++  +e + + l+ v + +d+  +V  y++ +f+++
  gi|242398570|ref|YP_002993994.1| 309 YKAITAV-SRYEKPMYITENGIATLDDEWRKEFVVQHLQYVQKAIDEGYDVRGYFYWSFMDN 369
                                       5667777.99***********988888888888999999999999999********996655 PP

>> Glyco_hydro_10  Glycosyl hydrolase family 10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0      0.75   4.5e+03       6      25 ..       7      26 ..       6      30 .. 0.81
   2 ?    1.9   0.1     0.017        99      83     131 ..     113     159 ..     108     197 .. 0.75
   3 ?    9.5   0.0     8e-05      0.48     215     293 ..     305     379 ..     297     401 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 0.75
                                      HHHTTEEEEEESCHGHHCTT CS
                    Glyco_hydro_10  6 akakfkvgtavsaseleges 25
                                      + ++f +gta+s++++eg++
  gi|242398570|ref|YP_002993994.1|  7 FPKSFLFGTATSSHQIEGNN 26
                                      567899******99999874 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.017
                                       SSS--HHHHTSCCCHHHHHHHHHHHHHHHHHHHHTTTTESEEEEEES-B CS
                    Glyco_hydro_10  83 hsqlPdwvkkengskaeeallkrlenhiktvverykgkiyawDVVNEav 131
                                       h   P w+ ++    a+e+ lk  e++++tv++ +k+ ++     NE +
  gi|242398570|ref|YP_002993994.1| 113 HFTSPIWFMQRG-GFAKEENLKYWEQYVETVAGILKD-VKLVATFNEPM 159
                                       457899*99983.3444468999*********99995.77777777776 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 8e-05
                                       HHHHHHHHHHHHTTTSEEEEEEEEEECETTSSHHHHHHHHHHHHHHHHHHHHHCTTTEEEEEESSSBGGGSTTHHHS CS
                    Glyco_hydro_10 215 iseieaalkklaalglevaitELDirvkkssseeealeaqakrykelvkallevkekitgvtvWgvtDkysWlsglk 291
                                       ++ i +a++++++    ++itE  i++ ++++++e   +  + +++ ++  +     + g   W ++D+y W +g+ 
  gi|242398570|ref|YP_002993994.1| 305 PEGIYKAITAVSRYEKPMYITENGIATLDDEWRKEFVVQHLQYVQKAIDEGY----DVRGYFYWSFMDNYEWKEGFE 377
                                       67889999*******************9888755555555555555555444....566***************976 PP

                                       TT CS
                    Glyco_hydro_10 292 kk 293
                                       ++
  gi|242398570|ref|YP_002993994.1| 378 PR 379
                                       65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2722.51
//
Query:       gi|242398571|ref|YP_002993995.1|  [L=427]
Description: transporter [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-56  191.8  24.9    3.1e-49  167.8  21.0    2.0  2  MFS_1         Major Facilitator Superfamily
    1.4e-09   37.3  21.3    2.8e-08   33.0  18.9    2.4  2  Sugar_tr      Sugar (and other) transporter
    5.5e-05   22.2  22.3     0.0024   16.8   0.4    4.4  4  MFS_1_like    MFS_1 like family
  ------ inclusion threshold ------
      0.019   13.6  20.8       0.45    9.1  10.5    3.2  4  ATG22         Vacuole effluxer Atg22 like
       0.25    9.6  24.6      0.093   11.0   1.7    3.8  4  OATP          Organic Anion Transporter Polypeptide (OATP) fa
        9.2    5.7   9.2        1.2    8.7   0.3    2.9  2  E1-E2_ATPase  E1-E2 ATPase


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 !  167.8  21.0   1.1e-52   3.1e-49       6     313 ..       3     315 ..       1     323 [. 0.83
   2 !   28.4   2.6   2.5e-10   7.5e-07      83     182 ..     304     409 ..     290     426 .. 0.73

  Alignments for each domain:
  == domain 1  score: 167.8 bits;  conditional E-value: 1.1e-52
                             MFS_1   6 flsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalglllllf 81 
                                       ++ +++ ++l p++   ++ ++gi+++++gl+ t++ +++a+ ++++G+lsd  G r+ +l++g+ll  + ++l ++
  gi|242398571|ref|YP_002993995.1|   3 AFLMADQNLLPPNYQ-QIMAEFGITETQMGLVSTIFVATSALITIVWGFLSDI-GQRKkLLVIGVLLGEIPCFLTAY 77 
                                       6778999999****9.7889********************************6.87777************777777 PP

                             MFS_1  82 asslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyila 158
                                       +++++ ll++r+l+G+g g+++p+g++liad+f +e+rgr+++++ ++f++G+++g++++gl++   +Wr +f+i+a
  gi|242398571|ref|YP_002993995.1|  78 VQNYYQLLAMRFLTGIGIGSIIPIGYSLIADMFEEEKRGRGYAYIETAFGFGTLFGMIVAGLIT---SWRPPFIIAA 151
                                       79999***********************************************************...********** PP

                             MFS_1 159 ivsllafvlfllllpeepperkrkspkeee.........kgtgpaplvpawkallkdpvlwillialllfffgfsgl 226
                                       +  ++++ l  +++++e+p+ + + +ke++           + ++++++  k+l+++  ++ ++i  +++++ + ++
  gi|242398571|ref|YP_002993995.1| 152 VPNFILAPL--FYIVAEEPR-RGEGEKELKkvlekgyeyTYRLNKEVIK--KSLKTRTNIL-IFIQGIIGTVPWGII 222
                                       ******885..444444444.4444555545788888665555555555..8999999997.8888888889***** PP

                             MFS_1 227 ltllplylqevlglsglllaglllallalvgailallagrlsdr......lgrrrrlllallllllaalglallavt 297
                                       +++l +++  ++g+    +a+++l l++l ++i++ll+g+  d        gr +++ la++l+++aa+g+++ +++
  gi|242398571|ref|YP_002993995.1| 223 MYWLVSFFIVTRGME-KSTATFVLLLVGLSTVIGSLLGGFAGDYfearekGGRAIITGLAIFLGMIAAIGMIIYPLP 298
                                       ***************.7999999999999999999999999999555555555666777777777777777777777 PP

                             MFS_1 298 .ssavllllvlvliGfg 313
                                        + +++++++l++++f 
  gi|242398571|ref|YP_002993995.1| 299 sELTLIHWIGLMIYSFV 315
                                       45555555577777763 PP

  == domain 2  score: 28.4 bits;  conditional E-value: 2.5e-10
                             MFS_1  83 sslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg......... 149
                                       +++  l++ + vl  +  + + p++ a+++++  +e+rg ++gl+++  ++G + gpl+gg+l++ l          
  gi|242398571|ref|YP_002993995.1| 304 IHWIgLMIYSFVLIQFV-SYAGPNVRAIVSQVNLPEDRGTVFGLFNILDNVGKATGPLFGGFLIETLRsagysdala 379
                                       44554666666666666.8*********************************************8877799999777 PP

                             MFS_1 150 Wravfyilaivsllafvlfllllpeepperkrk 182
                                       ++++ +i a++ + ++    ++l+ +++ ++  
  gi|242398571|ref|YP_002993995.1| 380 YEYTLLIGALFWIPCAA---VWLWIRKSYPEDR 409
                                       77777777777777766...5555555544443 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0  18.9   9.5e-12   2.8e-08      44     370 ..      26     326 ..       2     344 .. 0.73
   2 ?    0.7   7.8      0.06   1.8e+02      47     213 ..     240     414 ..     212     425 .. 0.65

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 9.5e-12
                                       ...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHH CS
                          Sugar_tr  44 ssvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlas 120
                                       +++++gl+  if++ +++  ++ g+l+d+  Rkk l+i+++l  i  +l+a  +   ++++l+++R+l+Gig+G + 
  gi|242398571|ref|YP_002993995.1|  26 TETQMGLVSTIFVATSALITIVWGFLSDIGQRKKLLVIGVLLGEIPCFLTAYVQ---NYYQLLAMRFLTGIGIGSII 99 
                                       6789**************************************************...9******************* PP

                                       HHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHGGGS---HHH CS
                          Sugar_tr 121 vlvPmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllilllflPESPry 197
                                        +   +i+ +  +++Rg+   + ++a  fG l++ i+      +++   wr ++ +++vp  +l+ l++ + E Pr 
  gi|242398571|ref|YP_002993995.1| 100 PIGYSLIADMFEEEKRGRGYAYIETAFGFGTLFGMIVAG---LITS---WRPPFIIAAVPNFILAPLFYIVAEEPR- 169
                                       *********************************988764...4566...999*********999999999999887. PP

                                       HHHTT-HH.HHHHHHHHHHHCHHHHHHHHHHHHHHHHHHH.....HTTHHHHSH...HHHHHHHHHHHHHHTTHHHH CS
                          Sugar_tr 198 lvekgkee.eakevlaklrgeedadrelaeekdsleaeqeeekaswkellssktvrqrlligvvlqifqqltGinai 273
                                          +g+ e e k+vl+k     + +      k+ ++++          l+++      + i + +q +   + + +i
  gi|242398571|ref|YP_002993995.1| 170 ---RGEGEkELKKVLEK-----GYEYTYRLNKEVIKKS----------LKTR------TNILIFIQGIIGTVPWGII 222
                                       ...44434366777777.....2222222222223333..........2223......3355555555555555578 PP

                                       HHHTTTHH.HHSS-THH..HHHHHHHHHHHHHHHHHHHHHHHHS-SHH....HHHHHHHHHHHHHHHHH..HHHHTT CS
                          Sugar_tr 274 myysptif.enlglsks..llvtiivgvvnfvatfvaiflvdrfGRRt....llllGaagmaicfvilgivalllva 343
                                       my   ++f  + g++ks    v ++vg  +++ ++ + f  d+f  R+      ++G+a+ + + + +g++ ++l++
  gi|242398571|ref|YP_002993995.1| 223 MYWLVSFFiVTRGMEKStaTFVLLLVGLSTVIGSLLGGFAGDYFEAREkggrAIITGLAIFLGMIAAIGMIIYPLPS 299
                                       88888877346788888443333444444455555554666666444212226888999999999999999999999 PP

                                       SS......CHHHHHHHHHHHHHHHTTTTHH CS
                          Sugar_tr 344 ks...kaasivaivfialfialfalgwgpv 370
                                       +     +++ ++  f+++ ++ +a   gp 
  gi|242398571|ref|YP_002993995.1| 300 ELtliHWIGLMIYSFVLIQFVSYA---GPN 326
                                       986666666666666666555555...555 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.06
                                       HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHH....HHHH..HHHHHHHHHHHHH-TTTT.....SS-TGGGGGHHHH CS
                          Sugar_tr  47 lsglivsiflvGaiiGslfagllgdrfGRkk....slli..aavlfvigavlqaaakgk.....nsvevlivgRvlv 112
                                       + ++++ ++ +  +iGsl++g++gd+f  +     ++++  a++l +i+a+ +++ +        ++  l++  +++
  gi|242398571|ref|YP_002993995.1| 240 TATFVLLLVGLSTVIGSLLGGFAGDYFEAREkggrAIITglAIFLGMIAAIGMIIYPLPseltlIHWIGLMIYSFVL 316
                                       33444444555577888888888888854432222344423666668888888887754555555666666666666 PP

                                       HHHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHGG CS
                          Sugar_tr 113 GigvGlasvlvPmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllilll 189
                                         +v  a   v   +s +  ++ Rg++ +l++    +G   +  fg +l +t  + g+   l+ ++    ll+ +l+
  gi|242398571|ref|YP_002993995.1| 317 IQFVSYAGPNVRAIVSQVNLPEDRGTVFGLFNILDNVGKATGPLFGGFLIETLRSAGYSDALAYEYT---LLIGALF 390
                                       6667777777777788888888888888888888888888888888888666665676666666653...5577777 PP

                                       GS---HHHHHHTT-HHHHHHHHHH CS
                          Sugar_tr 190 flPESPrylvekgkeeeakevlak 213
                                       ++P    +l +++ + e++ ++++
  gi|242398571|ref|YP_002993995.1| 391 WIPCAAVWLWIRKSYPEDRDMVKE 414
                                       777777888777777776666655 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 !   16.8   0.4   7.9e-07    0.0024      20      74 ..      14      67 ..       4      74 .. 0.81
   2 !   14.7   2.9   3.4e-06      0.01     291     376 ..      59     143 ..      58     150 .. 0.93
   3 !    4.6   1.4    0.0042        13     348     380 ..     237     269 ..     207     271 .. 0.71
   4 ?    1.4   0.0     0.038   1.1e+02     347     376 ..     340     368 ..     327     376 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 7.9e-07
                        MFS_1_like 20 PYltiylkskglkaseigiitlilpltsilsppiwgvlaDrfgkrkkvvilslll 74
                                      P  +  + + g++  + g++++i  +ts l   +wg+l+D  g+rkk++++++ll
  gi|242398571|ref|YP_002993995.1| 14 PNYQQIMAEFGITETQMGLVSTIFVATSALITIVWGFLSDI-GQRKKLLVIGVLL 67
                                      5566679999******************************6.6666666666655 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 3.4e-06
                        MFS_1_like 291 klliiallayilrfllyaiienawlvlpievLhgisfgllwaaaveyvskiapksleatgqgllsglyfglGralGs 367
                                       kll+i++l+  +  +l a+++n   +l + +L gi +g +  ++ + +++++ ++ +++g + ++++ fg+G+ +G 
  gi|242398571|ref|YP_002993995.1|  59 KLLVIGVLLGEIPCFLTAYVQNYYQLLAMRFLTGIGIGSIIPIGYSLIADMFEEEKRGRGYAYIETA-FGFGTLFGM 134
                                       7999999999999*************************************************88877.********* PP

                        MFS_1_like 368 liGGllwdl 376
                                       +++Gl+  +
  gi|242398571|ref|YP_002993995.1| 135 IVAGLITSW 143
                                       ****98655 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.0042
                        MFS_1_like 348 atgqgllsglyfglGralGsliGGllwdlksai 380
                                        +  + ++ l +gl + +Gsl+GG+  d+++a+
  gi|242398571|ref|YP_002993995.1| 237 EKSTATFVLLLVGLSTVIGSLLGGFAGDYFEAR 269
                                       344567788999*************98888775 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 0.038
                        MFS_1_like 347 eatgqgllsglyfglGralGsliGGllwdl 376
                                       ++t+ gl+++l   +G+a G l+GG+l+++
  gi|242398571|ref|YP_002993995.1| 340 RGTVFGLFNIL-DNVGKATGPLFGGFLIET 368
                                       67888888888.679************964 PP

>> ATG22  Vacuole effluxer Atg22 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   1.3    0.0002      0.61      75     137 ..      32      91 ..      16     120 .. 0.78
   2 ?   -1.2   0.0       0.2   5.9e+02     430     470 ..     130     166 ..      89     176 .. 0.72
   3 ?    9.1  10.5   0.00015      0.45     298     444 ..     219     369 ..     147     398 .. 0.76
   4 ?    0.7   0.1     0.054   1.6e+02     224     256 ..     377     409 ..     368     423 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0002
                             ATG22  75 ytfslsvllqavvvislsglADygnyrknlLlafaligslstilfllvtpkkYllgavlyivs 137
                                       +++ + v++ a++ i+ + l+D+g+ rk+lL++ +l+g + ++l + v  ++Y+ + ++  + 
  gi|242398571|ref|YP_002993995.1|  32 LVSTIFVATSALITIVWGFLSDIGQ-RKKLLVIGVLLGEIPCFLTAYV--QNYYQLLAMRFLT 91 
                                       577899*****************97.88999999******99998886..3454444444444 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.2
                             ATG22 430 svigplivglItDrtgnirsafvflavLlvvplpllllvdv 470
                                        ++g+++ glIt    + r++f++ av  ++  pl+++v  
  gi|242398571|ref|YP_002993995.1| 130 TLFGMIVAGLIT----SWRPPFIIAAVPNFILAPLFYIVAE 166
                                       456777777775....6788888877755555555555554 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.00015
                             ATG22 298 iatvsstavlfaktelkmstaklillsivaviaavlGaflwplvsrrlnlktkktllaiivlfeliplyGllGiilg 374
                                          +++  v f+  + +m++++ + + +++ +++v+G++l  +   +++++ k    +i  l++++ + + +G+i  
  gi|242398571|ref|YP_002993995.1| 219 WGIIMYWLVSFFIVTRGMEKSTATFVLLLVGLSTVIGSLLGGFAGDYFEAREKGGRAIITGLAIFLGMIAAIGMIIY 295
                                       4457788889999999***********************************99877788888888888888888888 PP

                             ATG22 375 kiGlkqpwEfyvlavvyglvlgglssys....RslfseLiPrGkEaaFFsLyaitdkgssvigplivglItDrt 444
                                        ++ +     ++  ++y++vl  + sy+    R++ s++  + +  + F+L++i+d  +   gpl  g +++  
  gi|242398571|ref|YP_002993995.1| 296 PLPSELTLIHWIGLMIYSFVLIQFVSYAgpnvRAIVSQVNLPEDRGTVFGLFNILDNVGKATGPLFGGFLIETL 369
                                       88888888888888888888888888866666*******6666667779****************999888765 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.054
                             ATG22 224 tfslrlalllvGlwWliftipaalllkkrpgpp 256
                                         ++ ++ll+ +l W+ ++ +++++ k+ p ++
  gi|242398571|ref|YP_002993995.1| 377 ALAYEYTLLIGALFWIPCAAVWLWIRKSYPEDR 409
                                       5678899****************9999888554 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 ?   10.2   0.7   5.5e-05      0.17      25      86 ..      17      78 ..       6      86 .. 0.92
   2 ?   11.0   1.7   3.1e-05     0.093     136     193 ..      85     142 ..      77     144 .. 0.90
   3 ?    2.5   3.5     0.011        34     285     383 ..     194     295 ..     164     299 .. 0.71
   4 ?   -2.7   0.1      0.45   1.4e+03     343     359 ..     354     370 ..     340     396 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 5.5e-05
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP 25 ttiEkrFklpsstsgliassneignillilfvsYfggrghrPrwigigallmalgslllalP 86
                                      ++i  +F+++ +++gl+++++  +++l++++ +++ + g+r +++ ig+ll  + ++l+a  
  gi|242398571|ref|YP_002993995.1| 17 QQIMAEFGITETQMGLVSTIFVATSALITIVWGFLSDIGQRKKLLVIGVLLGEIPCFLTAYV 78
                                      678889****************************************************9875 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 3.1e-05
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP 136 flaqlllGiGatpiytlGisYidDnvkkknsplylgilyalrilGpalGfllGslllk 193
                                       ++  +l GiG   i+++G+s i D  ++++     +++ ++  +G  +G ++++l+++
  gi|242398571|ref|YP_002993995.1|  85 LAMRFLTGIGIGSIIPIGYSLIADMFEEEKRGRGYAYIETAFGFGTLFGMIVAGLITS 142
                                       45579************************************************99876 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.011
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP 285 kalkrllknpifllvilssvfeillvaGfitFlpkylEtqFslsaseAnlltGvvvipgaalGillgGllvkklkls 361
                                       +++k+ lk ++ +l+ +++++  + +  ++ +l  +  +  ++++s+A++++ + v ++ ++G llgG+    ++ +
  gi|242398571|ref|YP_002993995.1| 194 EVIKKSLKTRTNILIFIQGIIGTVPWGIIMYWLVSFFIVTRGMEKSTATFVLLL-VGLSTVIGSLLGGFAGDYFEAR 269
                                       578888999999999999999999999999999999999999999999987633.3335556666666666655555 PP

                                       xxx....xxxxxxxxxxxxxxxxxxx RF
                              OATP 362 akk....laklvlvvsllslllllll 383
                                        k+    +  l+++++++++++++++
  gi|242398571|ref|YP_002993995.1| 270 EKGgraiITGLAIFLGMIAAIGMIIY 295
                                       55521116666666666666666665 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 0.45
                                       xxxxxxxxxxxxxxxxx RF
                              OATP 343 gaalGillgGllvkklk 359
                                       g a+G l+gG+l++ l+
  gi|242398571|ref|YP_002993995.1| 354 GKATGPLFGGFLIETLR 370
                                       45566666777666655 PP

>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.3   0.00039       1.2     120     168 ..      31      79 ..      14      90 .. 0.85
   2 ?   -0.6   3.1      0.28   8.2e+02      98     143 ..     193     239 ..     177     311 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00039
                                       HHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHHHHHS-TTHHHHHH CS
                      E1-E2_ATPase 120 kvlvpvvlliallvflialllgkslaeallralallvaaiPcaLplavp 168
                                       + ++++ ++ ++l+ +++ +l +  ++  l ++++l++ iPc L + v 
  gi|242398571|ref|YP_002993995.1|  31 GLVSTIFVATSALITIVWGFLSDIGQRKKLLVIGVLLGEIPCFLTAYVQ 79 
                                       56788899999999999999999999******************99876 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.28
                                       STTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-ST.TTSS CS
                      E1-E2_ATPase  98 arlveeakskktplqkkldklgkvlvpvvlliallvfliall.lgks 143
                                        ++++++ +++t++  +++ +++++ + +++  l+ f+i    ++ks
  gi|242398571|ref|YP_002993995.1| 193 KEVIKKSLKTRTNILIFIQGIIGTVPWGIIMYWLVSFFIVTRgMEKS 239
                                       55566666666666666666666655444444444444432202222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1006  (0.0561102); expected 358.6 (0.02)
Passed bias filter:                      560  (0.0312343); 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):               6  [number of targets reported over threshold]
# CPU time: 0.75u 0.31s 00:00:01.06 Elapsed: 00:00:00.48
# Mc/sec: 2682.17
//
Query:       gi|242398572|ref|YP_002993996.1|  [L=364]
Description: Alpha-galactosidase [Thermococcus sibiricus MM 739]
Scores for complete 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  152.4   0.0    3.3e-44  151.4   0.0    1.5  1  Glyco_hydro_57   Glycosyl hydrolase family 57
     0.0038   17.1   0.0     0.0059   16.5   0.0    1.3  1  Polysacc_deac_1  Polysaccharide deacetylase


Domain annotation for each model (and alignments):
>> Glyco_hydro_57  Glycosyl hydrolase family 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.4   0.0   3.7e-48   3.3e-44      67     317 ..      25     287 ..       3     294 .. 0.93

  Alignments for each domain:
  == domain 1  score: 151.4 bits;  conditional E-value: 3.7e-48
                                       HHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHT.TT-HHHHHHHHHHCTSEEEEEE-TT-B- CS
                    Glyco_hydro_57  67 kksylpateellelieeglerctelkldlavlfnlaisgplleqiqkwlnkevlelfrelqesgqvElltspyyHpl 143
                                       +k y+p+++ l++          e++      f l+++g++le    +l++e+++l++e +e g +E+l+++y+H++
  gi|242398572|ref|YP_002993996.1|  25 EKAYFPVISKLIKA---------EIP------FGLNVTGYTLE----ILPNEIISLIKEGIEVGLIEILGTSYTHAI 82 
                                       56666666666666.........677......***********....99**************************** PP

                                       GGG-S-HHHHHHHHHHHHHHHHHHHSS--SBEE-GGG-B--SHHHHHHHTT--EEEE-C-----------.....-T CS
                    Glyco_hydro_57 144 lpllpdsedieaqvkkarelyeeyfgqePrgfwlpElavspeileilaelGfeylftdelaeiledkske.....sp 215
                                       lpllp   ++eaqv+k++e+ e+++  +P+gfwlpEla++p i++il+++ +eylf+d++a++l++++++     +p
  gi|242398572|ref|YP_002993996.1|  83 LPLLPL-NRVEAQVQKDKEVKEKILDTSPKGFWLPELAYDPLIPAILKDNSYEYLFADGEAMLLSNHLNSairhiKP 158
                                       ******.*************************************************************99******* PP

                                       TS-EE-TTS.......-EEEE--CHH-TTTSGGG-........................................TT CS
                    Glyco_hydro_57 216 yrpyllkngg......iavffRdreLsddigFrys............................eqypleavddfinw 258
                                       ++p l+++++      +++f+  reL+ ++ + +s                            + +pl+ +++++ w
  gi|242398572|ref|YP_002993996.1| 159 LYPHLIRAQRgegfvyLNYFLGIRELKRAVKLAFSgkvaleavkeidavpvwvainttimlgiGNFPLMNPKKAASW 235
                                       ********999****************************************************9************* PP

                                       SB..........-TT---TTT--BB-TT-S---HHHHHHHHHHHHHHHHHHHHHHHHHS CS
                    Glyco_hydro_57 259 lkkvkkaksevvtialdgEnwghypetgkkeFleklyeeleenglielvtpsefikklk 317
                                       +k+    k+e++++++d+E++g++  +g k  +  l   l+      +++pse   k+ 
  gi|242398572|ref|YP_002993996.1| 236 IKE----KDEILLYGTDIEFLGYRDIAGYKMNIDSLLMLLDHLN-DTVCLPSEL--KHS 287
                                       **7....9********************9999999999888888.888888887..555 PP

>> Polysacc_deac_1  Polysaccharide deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   6.6e-07    0.0059      36     123 ..      43     135 ..      24     136 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.6e-07
                                       EEEE-HHHHCH-....HHHHHHHHHTT.EEEEE--SS--EGGGSHHHHHHHHHHHHHHHHHHHHS----EEE-GGGE CS
                   Polysacc_deac_1  36 tffvigglvedy....pdevremaasG.veignHtinhsnlkrlseeevrreierakdalrkalgreprlfryPygs 107
                                        + v+g + e +     ++++e  + G +ei   +++h  l  l  ++v++++++ k++ +k+l   p+ f  P ++
  gi|242398572|ref|YP_002993996.1|  43 GLNVTGYTLEILpneiISLIKEGIEVGlIEILGTSYTHAILPLLPLNRVEAQVQKDKEVKEKILDTSPKGFWLPELA 119
                                       44444444444411115556666666666666788****************************************** PP

                                       E-HHHHHHHHHTT.EE CS
                   Polysacc_deac_1 108 asatvlevarelgfay 123
                                       ++  + +++++  ++y
  gi|242398572|ref|YP_002993996.1| 120 YDPLIPAILKDNSYEY 135
                                       *****99999988877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2324.53
//
Query:       gi|242398573|ref|YP_002993997.1|  [L=349]
Description: Galactokinase [Thermococcus sibiricus MM 739]
Scores for complete 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-15   55.6   2.0    2.5e-14   53.3   0.0    2.2  2  GHMP_kinases_N   GHMP kinases N terminal domain
    2.5e-14   52.5   0.2    7.1e-14   51.1   0.0    1.9  2  GalKase_gal_bdg  Galactokinase galactose-binding signature
    1.4e-13   51.0   0.1    2.6e-13   50.1   0.1    1.5  1  GHMP_kinases_C   GHMP kinases C terminal


Domain annotation for each model (and alignments):
>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.3   0.0   4.1e-18   2.5e-14       4      65 ..      92     156 ..      90     157 .. 0.92
   2 ?    1.0   0.8     0.084     5e+02      10      21 ..     301     312 ..     295     313 .. 0.86

  Alignments for each domain:
  == domain 1  score: 53.3 bits;  conditional E-value: 4.1e-18
                                       EEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHH..HH.HHHHHHHHHHHHHHHHHSHHHHHHHHS CS
                    GHMP_kinases_N   4 ikseiPvgaGLGSSAAlavalvaAllallglsl..ee.aklaleaerlaqggngsggDvaasvyG 65 
                                       +++++P+gaGL+SSA++ +a++a l+++++l l  ++ a +a+eae++++g+ +++ D++a+++G
  gi|242398573|ref|YP_002993997.1|  92 VYGNLPLGAGLSSSASFELAALAFLNRAYDLYLppRDmALMAQEAENKFVGVPCGILDQFAITFG 156
                                       799**************************977776335999*********9*************9 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.084
                                       TTSSSCHHHHHH CS
                    GHMP_kinases_N  10 vgaGLGSSAAla 21 
                                       +gaG+G+SA + 
  gi|242398573|ref|YP_002993997.1| 301 TGAGFGGSAIAL 312
                                       59*******776 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 !   51.1   0.0   1.2e-17   7.1e-14      14      45 ..       4      35 ..       2      39 .. 0.92
   2 ?   -2.4   0.1      0.59   3.5e+03       2      14 ..     150     162 ..     149     163 .. 0.77

  Alignments for each domain:
  == domain 1  score: 51.1 bits;  conditional E-value: 1.2e-17
                                      EEEEEEEEEE--S-TTTT-EEEEEEEEEEEEE CS
                   GalKase_gal_bdg 14 asAPGRvnLiGEHtDYngGfVlpmAieqdiyi 45
                                      +++PGRvnLiGEHtDY  G+ +pmA+++ +++
  gi|242398573|ref|YP_002993997.1|  4 VQSPGRVNLIGEHTDYTLGYAMPMAVNLYTVL 35
                                      689**************************997 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.59
                                       HHHHHHS---EEE CS
                   GalKase_gal_bdg   2 eFqktFgkepfva 14 
                                       +F+ tFgk ++v+
  gi|242398573|ref|YP_002993997.1| 150 QFAITFGKRDHVI 162
                                       68899**998665 PP

>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.1   0.1   4.4e-17   2.6e-13       2      83 ..     250     329 ..     249     331 .. 0.91

  Alignments for each domain:
  == domain 1  score: 50.1 bits;  conditional E-value: 4.4e-17
                    GHMP_kinases_C   2 lealergdlellgellnlsqrs.elkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkdeaeqvar 77 
                                       + al++gd+ ++ge+l++ +r+      +g++++el+  ++++ elGa+ga+l+GaG+G++ +al+ ++++a++  +
  gi|242398573|ref|YP_002993997.1| 250 RRALRKGDIIEVGEILTRAHRDiAR--NYGVSCEELDFFVNKAIELGAYGARLTGAGFGGSAIALV-EEEKAKEFGE 323
                                       5799*****************9966..8**************************************.9999988877 PP

                    GHMP_kinases_C  78 alreef 83 
                                        + +e+
  gi|242398573|ref|YP_002993997.1| 324 VILKEY 329
                                       776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2515.92
//
Query:       gi|242398574|ref|YP_002993998.1|  [L=311]
Description: Thiamine monophosphate kinase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-15   57.8   0.0      2e-15   57.2   0.0    1.3  1  AIRS      AIR synthase related protein, N-terminal domain
    7.5e-07   29.4   0.1      1e-06   29.0   0.1    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 !   57.2   0.0   2.3e-19     2e-15       1      93 [.      23     132 ..      23     133 .. 0.90

  Alignments for each domain:
  == domain 1  score: 57.2 bits;  conditional E-value: 2.3e-19
                                       SSSE........EEEEEEEEE.EECCTCCCC........HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC......HH CS
                              AIRS   1 dDaa........vvvttdshnrpvlvepvhf........iGakavavnlsDlaamGArPlalllslalp......wl 55 
                                       dDa+        +vvt d     +lv  ++         +G k+ ++n+sD+aamGA+P+++l s+ +p       l
  gi|242398574|ref|YP_002993998.1|  23 DDAGaikwknewLVVTND-----MLVRTTDVpdimtpeqVGFKVFTMNVSDVAAMGATPIGFLFSIGVPrdferdYL 94 
                                       788866666666588888.....88877777777888999************************************* PP

                                       HHHHHHHHHHHHHTT-EEEEEEEEEESSEEEEEEEEEE CS
                              AIRS  56 eevvrglaeaaeelgvplvgGdtsfsneptisvtavGl 93 
                                       e++ rg+a+a e + +p+++ dt++  +++i   avG 
  gi|242398574|ref|YP_002993998.1|  95 EGISRGIARASEFYRTPIISADTNEACDLIIDGIAVGK 132
                                       *************************98899*9999996 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 !   29.0   0.1   1.1e-10     1e-06       1     153 [.     143     291 ..     143     294 .. 0.79

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 1.1e-10
                                       STTEEEEEEETSSCTCCHHHHHHHCHHHCTSHTTTSEHHHHHHH.HHHHHHHHHHHHHHTTECEEEE--TTHHHHHH CS
                            AIRS_C   1 kpGdvliltgslGlggagtslkrkileeeglddsavqlgdvlle.ptliyvkralaalkglvkaahDvTgGGLlgal 76 
                                       k Gd++ +tg +G   ag +++   + + g+  ++v l + lle + +i++ + l      ++aa D+++ G +  l
  gi|242398574|ref|YP_002993998.1| 143 KIGDLVCVTGDIGRALAG-LKVYFRNLKIGERTRKV-LYEKLLEpKARIKEGQVLSK---YANAAIDISD-GMSKEL 213
                                       579********9999999.88888888877653333.44444440345555555555...8*********.8***** PP

                                       HHHHHTTTEEEEEECGTHHHHHHHH........HHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEE CS
                            AIRS_C  77 aemapasgvgaeidldkvpifdele........splemllsensGrllvavppeeadavlaileeeglpeaavIGev 145
                                       + +a+ s+v++ i+++k+pi++e+         +p+e++l+  ++  l++  pee+   l++l+     ++avIG+v
  gi|242398574|ref|YP_002993998.1| 214 HLIAEMSKVKIIINAEKLPIREEVFevaellglDPIEVALASGEEFELIFTIPEEH---LDQLD---F-DFAVIGRV 283
                                       **********************9987888888888888888888888888888888...67777...5.8******* PP

                                       EESSSEEE CS
                            AIRS_C 146 takeelsv 153
                                       +++e++++
  gi|242398574|ref|YP_002993998.1| 284 EKGEGVYL 291
                                       ***98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2287.96
//
Query:       gi|242398575|ref|YP_002993999.1|  [L=38]
Description: hypothetical protein TSIB_0585 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       862  (0.0480785); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); 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 0.31s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 236.38
//
Query:       gi|242398576|ref|YP_002994000.1|  [L=48]
Description: hypothetical protein TSIB_0586 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.081   13.3   0.0      0.081   13.3   0.0    1.1  1  EHN       Epoxide hydrolase N terminus


Domain annotation for each model (and alignments):
>> EHN  Epoxide hydrolase N terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   4.5e-06     0.081      42      66 ..      20      44 ..       4      47 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.5e-06
                               EHN 42 kdelkelldyWkeeydWraeearln 66
                                      +d  ++++d W+ e++W+++++ l 
  gi|242398576|ref|YP_002994000.1| 20 EDDYTNIKDFWRMEFSWKRKQDFLG 44
                                      467899***************9885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 299.43
//
Query:       gi|242398577|ref|YP_002994001.1|  [L=221]
Description: transcription regulator, containing DNA-binding HTH domain [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-22   78.6   0.1    3.5e-22   78.0   0.1    1.3  1  HTH_10          HTH DNA binding domain
    7.1e-08   31.9   0.0    1.5e-07   30.9   0.0    1.5  1  HTH_24          Winged helix-turn-helix DNA-binding
    1.1e-05   24.8   0.1    2.1e-05   23.9   0.1    1.4  1  Sigma70_r4      Sigma-70, region 4
    0.00025   20.8   0.0    0.00062   19.6   0.0    1.6  1  HTH_5           Bacterial regulatory protein, arsR family
    0.00052   19.8   0.0    0.00081   19.2   0.0    1.3  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    0.00094   18.8   0.1     0.0022   17.6   0.1    1.6  1  Sigma70_r4_2    Sigma-70, region 4
      0.001   18.9   0.0     0.0022   17.8   0.0    1.5  1  MarR_2          MarR family
     0.0026   17.7   0.0     0.0057   16.7   0.0    1.6  1  HTH_Mga         M protein trans-acting positive regulator (MG
     0.0028   17.2   0.0     0.0051   16.3   0.0    1.4  1  GerE            Bacterial regulatory proteins, luxR family
     0.0076   16.2   0.1      0.022   14.7   0.0    1.8  1  HTH_11          HTH domain
     0.0081   16.1   0.1      0.016   15.2   0.1    1.4  1  HTH_Crp_2       Crp-like helix-turn-helix domain
     0.0086   16.2   0.0      0.025   14.8   0.0    1.7  1  HTH_17          Helix-turn-helix domain
     0.0094   16.1   0.0      0.027   14.7   0.0    1.8  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
  ------ inclusion threshold ------
      0.025   14.4   0.0      0.046   13.5   0.0    1.4  1  HTH_23          Homeodomain-like domain
      0.026   14.3   0.0      0.054   13.3   0.0    1.5  1  HTH_IclR        IclR helix-turn-helix domain
      0.034   13.9   0.5       0.11   12.3   0.5    1.9  1  LexA_DNA_bind   LexA DNA binding domain
      0.041   14.0   0.0      0.091   12.9   0.0    1.5  1  Sigma70_r3      Sigma-70 region 3
      0.055   13.6   0.0      0.094   12.9   0.0    1.3  1  HTH_28          Helix-turn-helix domain
      0.074   13.1   0.0       0.16   12.1   0.0    1.5  1  HTH_3           Helix-turn-helix
       0.12   12.8   0.4       0.36   11.3   0.1    1.9  2  HTH_40          Helix-turn-helix domain
       0.13   12.2   0.0       0.27   11.2   0.0    1.6  1  MarR            MarR family


Domain annotation for each model (and alignments):
>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.0   0.1   4.1e-25   3.5e-22       1      53 []     165     217 ..     165     217 .. 0.98

  Alignments for each domain:
  == domain 1  score: 78.0 bits;  conditional E-value: 4.1e-25
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaesklie 53 
                                       LT kqle+l lAy++GYFd PRr+tl+eLA+ l++s+st++ehLrka++k++e
  gi|242398577|ref|YP_002994001.1| 165 LTGKQLETLLLAYKSGYFDDPRRITLRELAEMLNLSPSTVKEHLRKAQRKIFE 217
                                       8**************************************************85 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.0   1.7e-10   1.5e-07      15      43 ..     184     213 ..     182     214 .. 0.90

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 1.7e-10
                            HTH_24  15 npr.isqreLAerlglSpstvnrrlkrLee 43 
                                       +pr i+ reLAe+l+lSpstv+++l++ ++
  gi|242398577|ref|YP_002994001.1| 184 DPRrITLRELAEMLNLSPSTVKEHLRKAQR 213
                                       7777**********************9765 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.1   2.5e-08   2.1e-05       2      48 ..     162     215 ..     162     217 .. 0.92

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 2.5e-08
                                       HHHS-HHHHHHHHHHH.......TTT--HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                        Sigma70_r4   2 LasLpererevlelrf.......geglTleEIgerlgiSrerVrqiekrAlrkL 48 
                                       L++L+ ++ e l l +        +  Tl E++e+l++S ++V+ ++++A rk+
  gi|242398577|ref|YP_002994001.1| 162 LSKLTGKQLETLLLAYksgyfddPRRITLRELAEMLNLSPSTVKEHLRKAQRKI 215
                                       789999999999999999999877888***********************9986 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   7.3e-07   0.00062      18      38 ..     190     210 ..     186     210 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 7.3e-07
                                       HHHHHHHHTS-HHHHHHHHHH CS
                             HTH_5  18 vcelaeelglsqstvShHLkk 38 
                                         elae+l+ls+stv +HL+k
  gi|242398577|ref|YP_002994001.1| 190 LRELAEMLNLSPSTVKEHLRK 210
                                       679****************97 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   9.5e-07   0.00081      17      40 ..     187     210 ..     183     212 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 9.5e-07
                     HTH_AsnC-type  17 RisyaeLAervGlSestvlrRvrr 40 
                                       Ri+ +eLAe+++lS+stv + +r+
  gi|242398577|ref|YP_002994001.1| 187 RITLRELAEMLNLSPSTVKEHLRK 210
                                       99****************987765 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   2.6e-06    0.0022      29      53 ..     190     214 ..     188     215 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.6e-06
                                       HHHHHHHHT--HHHHHHHHHHHHHH CS
                      Sigma70_r4_2  29 ykEIAellgisegtVksrlsRArkk 53 
                                        +E Ae+l++s++tVk +l++A +k
  gi|242398577|ref|YP_002994001.1| 190 LRELAEMLNLSPSTVKEHLRKAQRK 214
                                       589******************9666 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   2.6e-06    0.0022      18      47 ..     184     213 ..     178     214 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.6e-06
                                       TTSEEEHHHHHHHHTSSHHHHHHHHHHHHH CS
                            MarR_2  18 pgrdltvgelarrlglsksavsrilkrLva 47 
                                       ++r++t +ela+ l+ls+s+v  +l+++++
  gi|242398577|ref|YP_002994001.1| 184 DPRRITLRELAEMLNLSPSTVKEHLRKAQR 213
                                       6789***********************987 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 !   16.7   0.0   6.7e-06    0.0057      18      52 ..     185     220 ..     181     221 .] 0.85

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 6.7e-06
                           HTH_Mga  18 eksltldelakeLglseltlqsdiseLnel.Fpeel 52 
                                        +++tl ela+ L+ls +t+++ +++ +   F+e +
  gi|242398577|ref|YP_002994001.1| 185 PRRITLRELAEMLNLSPSTVKEHLRKAQRKiFEELI 220
                                       689********************9998876677665 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0     6e-06    0.0051      21      45 ..     191     215 ..     188     216 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 6e-06
                                       HHHHHHHTS-HHHHHHHHHHHHHHH CS
                              GerE  21 keIAeelniSekTVkvhksnimkKL 45 
                                        e Ae ln+S+ TVk h++ +++K+
  gi|242398577|ref|YP_002994001.1| 191 RELAEMLNLSPSTVKEHLRKAQRKI 215
                                       688*********************7 PP

>> HTH_11  HTH 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     0.022      15      39 ..     186     211 ..     182     217 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.6e-05
                            HTH_11  15 p.isgeeLAeeLnvSrrtvrrdIkaL 39 
                                         i+  eLAe Ln+S +tv  ++++ 
  gi|242398577|ref|YP_002994001.1| 186 RrITLRELAEMLNLSPSTVKEHLRKA 211
                                       449****************9998775 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 !   15.2   0.1   1.8e-05     0.016      19      47 ..     185     213 ..     169     214 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.8e-05
                                       EEEHHHHHHHHHTTSSHHHHHHHHHHHHH CS
                         HTH_Crp_2  19 elpltqeelAsmlGltretvsrilseLkr 47 
                                         ++t +elA+ml+l+++tv   l++ +r
  gi|242398577|ref|YP_002994001.1| 185 PRRITLRELAEMLNLSPSTVKEHLRKAQR 213
                                       457999****************9998776 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   2.9e-05     0.025       3      24 ..     189     210 ..     188     217 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.9e-05
                            HTH_17   3 tveEaAelLgvsrstvyrlirr 24 
                                       t  E+Ae+L++s+stv + +r+
  gi|242398577|ref|YP_002994001.1| 189 TLRELAEMLNLSPSTVKEHLRK 210
                                       899**************98763 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 !   14.7   0.0   3.2e-05     0.027      24      45 ..     189     210 ..     183     214 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.2e-05
                                       -HHHHHHHHTS-HHHHHHHHHH CS
                    Fe_dep_repress  24 ktkdlaerLnvspssVsemlkk 45 
                                       +  +lae Ln sps+V e l+k
  gi|242398577|ref|YP_002994001.1| 189 TLRELAEMLNLSPSTVKEHLRK 210
                                       5679****************99 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   5.4e-05     0.046      16      39 ..     184     210 ..     169     214 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.4e-05
                            HTH_23  16 e..GlsvreIAreLgvsrrTvy.rwlk 39 
                                       +  +++ re A++L+ s++Tv  + +k
  gi|242398577|ref|YP_002994001.1| 184 DprRITLRELAEMLNLSPSTVKeHLRK 210
                                       26699****************944444 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   6.3e-05     0.054      16      39 ..     185     208 ..     183     210 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.3e-05
                                       BSS-BHHHHHHHHTS-HHHHHHHH CS
                          HTH_IclR  16 pqeltlselArrtglpkStvhRlL 39 
                                       p++ tl+elA+ + l++Stv  +L
  gi|242398577|ref|YP_002994001.1| 185 PRRITLRELAEMLNLSPSTVKEHL 208
                                       7889****************8877 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   0.5   0.00012      0.11      27      53 ..     189     214 ..     162     218 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00012
                                       -HHHHHHHHTS-.HHHHHHHHHHHHHT CS
                     LexA_DNA_bind  27 sireiaralglkSpsaveehLkaLerK 53 
                                       + re+a+ l+l+ ps+v+ehL++ +rK
  gi|242398577|ref|YP_002994001.1| 189 TLRELAEMLNLS-PSTVKEHLRKAQRK 214
                                       78*********7.*********99998 PP

>> Sigma70_r3  Sigma-70 region 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00011     0.091      22      46 ..     189     213 ..     185     217 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
                                       XHHHHHHHHTXXHHHHHHHHHHHXX CS
                        Sigma70_r3  22 tpeEiAeeLglseekVrevleaare 46 
                                       t  E+Ae L+ls++ V+e l+ a++
  gi|242398577|ref|YP_002994001.1| 189 TLRELAEMLNLSPSTVKEHLRKAQR 213
                                       678******************9987 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00011     0.094      14      36 ..     189     211 ..     172     215 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
                            HTH_28  14 svreaArelgisrrtvyrWikry 36 
                                       + re+A+ l++s++tv+  +++ 
  gi|242398577|ref|YP_002994001.1| 189 TLRELAEMLNLSPSTVKEHLRKA 211
                                       89**************9999986 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00018      0.16       9      26 ..     187     204 ..     184     206 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00018
                                       THHHHHHHHHHTSSHHHH CS
                             HTH_3   9 glsqeeLAeklGvsrsti 26 
                                        ++++eLAe+l++s+st+
  gi|242398577|ref|YP_002994001.1| 187 RITLRELAEMLNLSPSTV 204
                                       589**************8 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       9.4     8e+03       9      21 ..      51      63 ..      44      71 .. 0.61
   2 ?   11.3   0.1   0.00043      0.36      13      39 ..     188     214 ..     186     220 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 9.4
                            HTH_40  9 leeglsieeIAke 21
                                      ++e l+ eeI k+
  gi|242398577|ref|YP_002994001.1| 51 FKEDLKAEEIVKK 63
                                      3444555555443 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00043
                            HTH_40  13 lsieeIAkerglkesTIegHLaeliee 39 
                                        ++ e A+  +l++sT+ +HL ++ ++
  gi|242398577|ref|YP_002994001.1| 188 ITLRELAEMLNLSPSTVKEHLRKAQRK 214
                                       5899*****************998776 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00032      0.27      17      40 ..     187     210 ..     165     214 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00032
                                       TEEHHHHHHHHTS-HHHHHHHHHH CS
                              MarR  17 plsvseLakklgvskstvtrvldr 40 
                                        +++ eLa++l++s+stv + l++
  gi|242398577|ref|YP_002994001.1| 187 RITLRELAEMLNLSPSTVKEHLRK 210
                                       58999*************998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      513  (0.0286129); expected 358.6 (0.02)
Passed Vit filter:                       106  (0.00591221); 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: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1409.99
//
Query:       gi|242398578|ref|YP_002994002.1|  [L=89]
Description: hypothetical protein TSIB_0588 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00034   20.4   0.3    0.00071   19.4   0.1    1.6  2  RHH_4     Ribbon-helix-helix domain
  ------ inclusion threshold ------
      0.036   14.0   6.9      0.041   13.8   1.1    2.6  3  RHH_1     Ribbon-helix-helix protein, copG family
       0.05   13.7   0.5      0.065   13.3   0.4    1.3  1  MetOD2    Metanogen output domain 2


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 !   19.4   0.1   1.2e-07   0.00071      11      57 ..       4      53 ..       1      56 [. 0.82
   2 ?   -1.7   0.0      0.46   2.8e+03      35      49 ..      70      83 ..      67      87 .. 0.68

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.2e-07
                                      EEEEEEEEHHHHHHHHHHHHHTT--HHHHHHHH.HHH...HSS.THHHHH CS
                             RHH_4 11 hrTSirLEpafWdaLeeiArregltvnaLiaeidadr...rgeanLasal 57
                                       +TSi + ++ W +L++ A++e+  +++L++ei +++   + e +L  ++
  gi|242398578|ref|YP_002994002.1|  4 IKTSIYIDAELWWELKKDAAEEKKDLSKLLEEIISEElllGVEDSLRGMI 53
                                      68*******************************66666655555555555 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.46
                                      -HHHHHHHH.HHHHS CS
                             RHH_4 35 tvnaLiaeidadrrg 49
                                      +v++L+  + +d+r+
  gi|242398578|ref|YP_002994002.1| 70 SVSELVRAM-RDERE 83
                                      688888888.55544 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 ?   13.8   1.1   6.8e-06     0.041       2      37 ..       6      41 ..       5      43 .. 0.96
   2 ?   -2.3   0.0      0.83   4.9e+03      31      38 ..      51      58 ..      48      59 .. 0.63
   3 ?    3.2   0.1     0.015        89      24      32 ..      70      78 ..      67      84 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.8e-06
                                      EEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHH CS
                             RHH_1  2 vsirldeellerLdelarrrgrSrSelIReAlreyl 37
                                      +si++d+el  +L + a+++++  S l++e + e l
  gi|242398578|ref|YP_002994002.1|  6 TSIYIDAELWWELKKDAAEEKKDLSKLLEEIISEEL 41
                                      79******************************9987 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.83
                                      HHHHHHHH CS
                             RHH_1 31 eAlreyle 38
                                       ++re+ e
  gi|242398578|ref|YP_002994002.1| 51 GMIREFEE 58
                                      56777665 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.015
                                      SHHHHHHHH CS
                             RHH_1 24 SrSelIReA 32
                                      S+Sel+R++
  gi|242398578|ref|YP_002994002.1| 70 SVSELVRAM 78
                                      888888875 PP

>> MetOD2  Metanogen output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.4   1.1e-05     0.065      27      73 ..      17      63 ..       6      77 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.1e-05
                            MetOD2 27 rLaks.vevnkrllslLsqtydidddkaevseeieaalknlekkleaq 73
                                      +L k  +e +k l +lL+++  ++   + v++ ++ +++++e+k+e++
  gi|242398578|ref|YP_002994002.1| 17 ELKKDaAEEKKDLSKLLEEIISEELL-LGVEDSLRGMIREFEEKIEFE 63
                                      455541566677999*********66.99*****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       762  (0.042501); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 598.11
//
Query:       gi|242398579|ref|YP_002994003.1|  [L=150]
Description: PilT protein domain protein [Thermococcus sibiricus MM 739]
Scores for complete 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   41.8   1.5      2e-10   41.2   1.5    1.3  1  PIN       PIN domain
  ------ inclusion threshold ------
      0.052   13.7   0.0      0.094   12.9   0.0    1.5  1  PPR_2     PPR repeat family
       0.21   11.2   4.2        4.8    6.8   0.1    2.7  3  Arm_3     Atypical Arm repeat


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 !   41.2   1.5   3.4e-14     2e-10       1     120 [.       6     140 ..       6     142 .. 0.92

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 3.4e-14
                                       EEE-HHHHHHHHTTSHHHHHHHHHHHTS....SEEEEEHHHHHHHHHHHHS...........SCHCHHHHHHHHHHH CS
                               PIN   1 ivlDTsvliallrgeekaeaarklleel....eelvtsalvlaEllyvlar...........rkskrekaaelvell 62 
                                       ++lD++++i+ + +e+++e++ kl+ ++     +l +s   + E+l vl +            ++ r +   +++++
  gi|242398579|ref|YP_002994003.1|   6 VYLDSNAIIKRYVKEKNSEEIIKLYRKAyngeVKLSFSLWNIGEVLGVLDKarrlerldiesYELVRARFLSETLRM 82 
                                       69****************************878888888888*****************887777777777888888 PP

                                       HHHHTSEEEEBCHHHHHHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHHHHH CS
                               PIN  63 lllsalkilpidaeiaeeaaeialkygllpnDaliaAtAkehgikliatfDedfrrva 120
                                        +l  l+++p+ a+i+e+ +++++ky +  +Dal +   k+ + + ++t D+++++va
  gi|242398579|ref|YP_002994003.1|  83 KQLGILRLIPVHASILEKSWQLIEKYHIYQADALQILSSKRINVDEFYTGDKRLNEVA 140
                                       8899999999**********************************************97 PP

>> PPR_2  PPR repeat family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.6e-05     0.094       7      28 ..      11      32 ..      10      43 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.6e-05
                             PPR_2  7 NtlIsglckkgkveeAfklfne 28
                                      N++I+ ++k++++ee +kl+ +
  gi|242398579|ref|YP_002994003.1| 11 NAIIKRYVKEKNSEEIIKLYRK 32
                                      9******************975 PP

>> Arm_3  Atypical Arm repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.3     0.003        18      26      45 ..       5      24 ..       3      30 .. 0.84
   2 ?   -1.3   0.1      0.28   1.7e+03      25      33 ..      27      35 ..      22      35 .. 0.73
   3 ?    6.8   0.1   0.00081       4.8      26      39 ..      96     109 ..      94     120 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.003
                             Arm_3 26 eIYkkAlkIiekYFseeeee 45
                                       +Y  + +Ii +Y  e + e
  gi|242398579|ref|YP_002994003.1|  5 TVYLDSNAIIKRYVKEKNSE 24
                                      79999*********999553 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.28
                             Arm_3 25 eeIYkkAlk 33
                                       + Y+kA++
  gi|242398579|ref|YP_002994003.1| 27 IKLYRKAYN 35
                                      567999997 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.00081
                             Arm_3  26 eIYkkAlkIiekYF 39 
                                        I +k++++iekY+
  gi|242398579|ref|YP_002994003.1|  96 SILEKSWQLIEKYH 109
                                       589**********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1001.01
//
Query:       gi|242398580|ref|YP_002994004.1|  [L=283]
Description: ABC-type multidrug transport system [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.9e-27   94.1   0.0    1.6e-26   93.5   0.0    1.3  1  ABC_tran         ABC transporter
    3.2e-14   53.4   0.3    3.3e-10   40.3   0.0    2.2  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
      9e-05   23.1   0.2    0.00031   21.3   0.0    1.8  2  AAA_23           AAA domain
    9.8e-05   23.0   1.3     0.0013   19.5   0.6    2.5  2  DUF4162          Domain of unknown function (DUF4162)
    0.00026   20.8   0.2        0.2   11.3   0.6    2.2  2  AAA_15           AAA ATPase domain
     0.0016   18.9   0.3     0.0091   16.4   0.3    2.1  1  AAA              ATPase family associated with various cellul
  ------ inclusion threshold ------
       0.02   14.6   0.1      0.061   13.0   0.0    1.7  2  AAA_30           AAA domain
      0.023   14.6   0.1      0.037   13.9   0.1    1.2  1  dNK              Deoxynucleoside kinase
       0.03   14.0   0.1      0.052   13.2   0.1    1.3  1  SRP54            SRP54-type protein, GTPase domain
      0.039   13.9   0.0      0.057   13.3   0.0    1.4  1  Rad17            Rad17 P-loop domain
      0.048   13.6   0.0      0.089   12.7   0.0    1.4  1  RsgA_GTPase      RsgA GTPase
      0.069   12.8   0.2        0.8    9.3   0.1    2.4  2  Thymidylate_kin  Thymidylate kinase
       0.12   11.6   0.0        2.7    7.2   0.0    2.1  2  Zeta_toxin       Zeta toxin
       0.17   10.5   0.0        3.2    6.3   0.0    2.1  2  AAA_13           AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.5   0.0   1.2e-29   1.6e-26       2     136 ..      20     157 ..      19     158 .. 0.97

  Alignments for each domain:
  == domain 1  score: 93.5 bits;  conditional E-value: 1.2e-29
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       +n+s++++ege+++++G+nGaGK+t +k+l +  k+  Ge+++ gkdl++   + + ++igv ++ p + ++lt+ e
  gi|242398580|ref|YP_002994004.1|  20 ENLSFEVEEGEIYGFLGPNGAGKTTTVKILVKIIKDYTGEVKVFGKDLRK-WGKDYYNKIGVSFEFPAVYSKLTALE 95 
                                       79************************************************.99999********************* PP

                                       H........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       n        ++  ++ ++l+ +gl++ +++ v    + +S+G+k+++ larall +p++++lDEp 
  gi|242398580|ref|YP_002994004.1|  96 NlqffasfyKKHLDPMNVLKMVGLDKEANQLV----AGFSKGMKKKLDLARALLPDPEVFFLDEPL 157
                                       *****999888888************999999....*****************************6 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.2   0.00013      0.17       2      30 ..      32      54 ..      31      88 .. 0.78
   2 !   40.3   0.0   2.6e-13   3.3e-10     213     301 ..     125     191 ..      63     193 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00013
                            AAA_21  2 nvliGpNgsGKSnLLdaldllarldrdve 30
                                       ++ GpNg+GK++  ++l       + ++
  gi|242398580|ref|YP_002994004.1| 32 YGFLGPNGAGKTTTVKIL------VKIIK 54
                                      5789************99......44444 PP

  == domain 2  score: 40.3 bits;  conditional E-value: 2.6e-13
                            AAA_21 213 derlrergvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrng 289
                                       ++                   ++ +S G+k+ l l+ all ++    ++++DEp  gL+P+  r++ +ll e ++ng
  gi|242398580|ref|YP_002994004.1| 125 QL-------------------VAGFSKGMKKKLDLARALLPDP---EVFFLDEPLEGLDPASARKIKDLLLEMRENG 179
                                       33...................3456***************999...9***********************99999** PP

                            AAA_21 290 aQviltTHSpll 301
                                         ++ltTH+ ++
  gi|242398580|ref|YP_002994004.1| 180 KTIFLTTHNMYV 191
                                       *********987 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   2.4e-07   0.00031       2      36 ..       4      46 ..       4      50 .. 0.83
   2 ?   -2.6   0.0       5.2   6.7e+03     124     137 ..     244     257 ..     210     275 .. 0.57

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 2.4e-07
                            AAA_23  2 Lkienfrsf....rdqe.idF...skgltlItGpNGaGKTTil 36
                                      ++++n+r++    r++e + F   +  ++ + GpNGaGKTT +
  gi|242398580|ref|YP_002994004.1|  4 IEVKNVRKYygdvRGVEnLSFeveEGEIYGFLGPNGAGKTTTV 46
                                      789*******99955444777778779**************76 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 5.2
                            AAA_23 124 llgskkiilnlilf 137
                                       ++g++++ l++i+ 
  gi|242398580|ref|YP_002994004.1| 244 NIGQNEKFLKIIQE 257
                                       33333333333322 PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.53   6.7e+02       3      21 ..     213     234 ..     212     247 .. 0.74
   2 !   19.5   0.6   9.8e-07    0.0013      49      81 .]     247     278 ..     239     278 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.53
                                       HHHHHTTS-SSEEEEE...--- CS
                           DUF4162   3 leeiKrsygknrieve...ada 21 
                                       ++e+K ++gk+ ++ve   ++ 
  gi|242398580|ref|YP_002994004.1| 213 PSELKVKMGKRLVRVEyvaNGG 234
                                       78*************9875333 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 9.8e-07
                                       -------------EEEEEEEE---HHHHHHHHH CS
                           DUF4162  49 aanellkaltsgveirsFeeeePsLndIFiekv 81 
                                       ++++ lk + +  e+r+++ eeP+L++IF++++
  gi|242398580|ref|YP_002994004.1| 247 QNEKFLKII-QEHEVRRINTEEPTLEEIFLKVT 278
                                       566777777.999*****************986 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.6   0.00015       0.2      25      75 ..      31      77 ..       4     140 .. 0.70
   2 !    7.5   0.0    0.0023       2.9     323     368 ..     147     191 ..     127     192 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00015
                            AAA_15 25 ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifenisesk 75
                                      +  + G+N++GK++ +++l ++++        ++k+  +dl+++ +++ +k
  gi|242398580|ref|YP_002994004.1| 31 IYGFLGPNGAGKTTTVKILVKIIKDY----TGEVKVFGKDLRKWGKDYYNK 77
                                      67799**************9999954....456677777777775444443 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0023
                            AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSphi 368
                                       ++ +++++EP   L p   + + +ll+e+ +++k  +++tTH+ ++
  gi|242398580|ref|YP_002994004.1| 147 DPEVFFLDEPLEGLDPASARKIKDLLLEMRENGK-TIFLTTHNMYV 191
                                       567899999999999******************9.9*******987 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.3   7.1e-06    0.0091       3      66 ..      34     155 ..      32     201 .. 0.59

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 7.1e-06
                                       EESSTTSSHHHHHHHHHHHHTHE..EEEEETTTCSSS........................................ CS
                               AAA   3 lyGppGtGKTllakavakelgve..fleisgsellsk........................................ 37 
                                       + Gp G GKT+++k ++k ++ +   +++ g++l+ k                                        
  gi|242398580|ref|YP_002994004.1|  34 FLGPNGAGKTTTVKILVKIIKDYtgEVKVFGKDLR-Kwgkdyynkigvsfefpavyskltalenlqffasfykkhld 109
                                       78*****************9744222333333443.32334444444444444444445555555555555555555 PP

                                       ................STTHHHHHHHHHHHHHHHTS.TSEEEEEET CS
                               AAA  38 ................yvgesekkirelfkeakeka.kpsilfiDE 66 
                                                       +v   +k +++ ++ a++   +p ++f+DE
  gi|242398580|ref|YP_002994004.1| 110 pmnvlkmvgldkeanqLVAGFSKGMKKKLDLARALLpDPEVFFLDE 155
                                       5566665543333333555555555555555555558888888888 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   4.7e-05     0.061      22      52 ..      33      63 ..      25      69 .. 0.83
   2 ?   -1.6   0.0       1.4   1.8e+03      44      77 ..     177     210 ..     165     261 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.7e-05
                            AAA_30 22 vltGpAGtGKttalkalreaweaaggrvigl 52
                                         Gp G+GKtt++k l++++++  g+v ++
  gi|242398580|ref|YP_002994004.1| 33 GFLGPNGAGKTTTVKILVKIIKDYTGEVKVF 63
                                      5679******************997777765 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.4
                            AAA_30  44 aaggrviglAptgkaAkvLaeelgieastiakll 77 
                                       ++g+++++ +++  +A++L + +g+  +   +l+
  gi|242398580|ref|YP_002994004.1| 177 ENGKTIFLTTHNMYVADELCDRVGFIVDGAVRLV 210
                                       4566777777777777777777776555444444 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   2.9e-05     0.037       5      74 ..      36     113 ..      34     132 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.9e-05
                                       ESTTSSHHHHHHHHHC....CST.CEEEE-HHHHCCSSSSHHHHHHHHSHHHHH..HHH.HHHHHHHHHHHHHCHHS CS
                               dNK   5 GnIgaGKstlvklLsk....klg.vkvfeEpvdkwtnvqknlLekfYkdpsrws..fal.qtyvllsrlkqqleala 73 
                                       G+ gaGK+t vk+L k     +g vkvf     kw ++  n +   ++ p+ +s  +al + ++++s++k++l++++
  gi|242398580|ref|YP_002994004.1|  36 GPNGAGKTTTVKILVKiikdYTGeVKVFGKDLRKWGKDYYNKIGVSFEFPAVYSklTALeNLQFFASFYKKHLDPMN 112
                                       7779*****888776511115557999*99*****99999*********9999844345256899999999999875 PP

                                       S CS
                               dNK  74 t 74 
                                        
  gi|242398580|ref|YP_002994004.1| 113 V 113
                                       4 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1     4e-05     0.052       6      38 ..      34      66 ..      30      71 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4e-05
                                      EEESTTSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                             SRP54  6 lvGlqGaGKTttlaKLaallkkegkkvllvaaD 38
                                      ++G++GaGKTtt+  L +++k+   +v +   D
  gi|242398580|ref|YP_002994004.1| 34 FLGPNGAGKTTTVKILVKIIKDYTGEVKVFGKD 66
                                      89***************9999987777776666 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   4.4e-05     0.057      47      69 ..      31      53 ..      17     123 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.4e-05
                             Rad17 47 iLLisGPsGCgkstvvkvLskel 69
                                      i    GP G gk+t+vk+L k+ 
  gi|242398580|ref|YP_002994004.1| 31 IYGFLGPNGAGKTTTVKILVKII 53
                                      66678***************986 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   6.9e-05     0.089      87     131 ..      16      61 ..       4      66 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.9e-05
                                       HTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S--- CS
                       RsgA_GTPase  87 kegleelkellkd.ktsvlvGqSGvGKStLinallpelelktgevs 131
                                        +g+e+l+ ++++ ++  ++G+ G+GK+t ++ l+   +  tgev+
  gi|242398580|ref|YP_002994004.1|  16 VRGVENLSFEVEEgEIYGFLGPNGAGKTTTVKILVKIIKDYTGEVK 61 
                                       46899999999998********************999999999886 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1   0.00063       0.8       3      23 ..      36      56 ..      34      66 .. 0.86
   2 ?    0.5   0.0      0.32   4.2e+02      39      62 ..     165     191 ..     132     201 .. 0.56

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00063
                                      ESTTSSHHHHHHHHHHHHHHT CS
                   Thymidylate_kin  3 GlDGaGKttqaellkerlkee 23
                                      G +GaGKtt +++l++ +k+ 
  gi|242398580|ref|YP_002994004.1| 36 GPNGAGKTTTVKILVKIIKDY 56
                                      899*************99875 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.32
                                       HHHHHHHHH...TCS---HHHHHHHHH CS
                   Thymidylate_kin  39 Gekirelll...keeeleeqteallfa 62 
                                       ++ki++lll   ++ +   +t +++++
  gi|242398580|ref|YP_002994004.1| 165 ARKIKDLLLemrENGKTIFLTTHNMYV 191
                                       444444444433333333444455554 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0    0.0021       2.7      23      58 ..      36      71 ..      28      95 .. 0.88
   2 ?    2.1   0.0     0.079     1e+02      94     122 ..     197     223 ..     186     233 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0021
                        Zeta_toxin 23 GqpGAGKselaellkdelerqgnvvrldpDdlRelh 58
                                      G  GAGK+++ + l + ++ + + v++ + dlR+  
  gi|242398580|ref|YP_002994004.1| 36 GPNGAGKTTTVKILVKIIKDYTGEVKVFGKDLRKWG 71
                                      678***************999999999999999865 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.079
                        Zeta_toxin  94 ngyniivegtlrspdvvkklaealkkaGY 122
                                        ++ +iv+g+ r  d++++l+ ++ k  +
  gi|242398580|ref|YP_002994004.1| 197 DRVGFIVDGAVRLVDNPSELKVKMGK--R 223
                                       5899*************998877766..4 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0    0.0025       3.2      23      39 ..      36      52 ..      27     114 .. 0.81
   2 ?    2.2   0.0     0.042        54     551     576 ..     168     194 ..     145     200 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0025
                            AAA_13 23 GwNGaGKTtLSrllrsl 39
                                      G NGaGKTt  ++l ++
  gi|242398580|ref|YP_002994004.1| 36 GPNGAGKTTTVKILVKI 52
                                      78*******99998775 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.042
                            AAA_13 551 iksrll.kkkkakQlfiLTHnleffke 576
                                       ik+ ll  +++ k +f+ THn++   e
  gi|242398580|ref|YP_002994004.1| 168 IKDLLLeMRENGKTIFLTTHNMYVADE 194
                                       555555567999**********98666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1746.65
//
Query:       gi|242398581|ref|YP_002994005.1|  [L=233]
Description: hypothetical protein TSIB_0591 [Thermococcus sibiricus MM 739]
Scores for 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   23.9  16.4      2e-05   23.9  16.4    1.6  2  ABC2_membrane_3  ABC-2 family transporter protein
  ------ inclusion threshold ------
       0.03   14.3  10.6      0.071   13.1  10.6    1.8  1  ABC2_membrane_4  ABC-2 family transporter protein
      0.045   13.7   1.0       0.15   11.9   1.0    1.9  1  DUF2721          Protein of unknown function (DUF2721)


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 ?   -1.9   0.2      0.23   1.4e+03     159     179 ..      14      34 ..       9      37 .. 0.60
   2 !   23.9  16.4   3.3e-09     2e-05     158     339 ..      39     212 ..      33     220 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.23
                   ABC2_membrane_3 159 vasflvgliliilifitasfi 179
                                       v s++++++++i + ++++ +
  gi|242398581|ref|YP_002994005.1|  14 VRSYVYPVYILIGLAYGLMLM 34 
                                       566777766666665555533 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 3.3e-09
                   ABC2_membrane_3 158 nvasflvg.liliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilllafglgi 233
                                       ++  ++v+ ++l+ + +++++f+ ++i  Ek+ +++  + v+++   +y+l+k l + +++++ ++li+++      
  gi|242398581|ref|YP_002994005.1|  39 QYLPTMVPiFLLFEPGLVGFMFVGTEIFAEKKDGAIGALAVTPIEWRSYILAKTLLLSVLSIIGAILIMAIGTR--- 112
                                       566677886777888999*****************************************************776... PP

                   ABC2_membrane_3 234 pfgnlglllllfllfglayialgyllsslfknsetaqilifivilllsgffgglfpledlpsalkwifsiiPffapg 310
                                       + ++l ++++ ++l +++y+ lg  +s+  ++ ++ ++ i+ v++ +s++ ++ +    l s + ++++ iP++   
  gi|242398581|ref|YP_002994005.1| 113 SLNGLPYVIVGVFLVSIVYTLLGIGISAKYHDLDDYFVPIMGVLV-ISLLPFVHY-HGYLTSEIWKVLYAIPSYPGL 187
                                       789**************************8888887554444444.333333333.223334466688888888766 PP

                   ABC2_membrane_3 311 lgllrlitgdplweil.lsliilalfavvy 339
                                       +++ + ++     ei   ++++ a+  +v+
  gi|242398581|ref|YP_002994005.1| 188 YFF-KAPFE----EISrDAMTWSAVALIVW 212
                                       666.44442....33333344444444444 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 ?   13.1  10.6   1.2e-05     0.071      30     146 ..      24     136 ..       7     183 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.2e-05
                   ABC2_membrane_4  30 llyfnllgktgldpaefyslsvfgftlllllplilgi.iasylifrEeqndtlknLltiPvsrtklllaKlivllll 105
                                       l+  ++    +++p+++    ++++ +ll+ p ++g  + ++ if E++++ +  L + P++ ++++laK ++l +l
  gi|242398581|ref|YP_002994005.1|  24 LIGLAYGLMLMVFPEQYLPT-MVPI-FLLFEPGLVGFmFVGTEIFAEKKDGAIGALAVTPIEWRSYILAKTLLLSVL 98 
                                       55555544555666666553.3332.45667777776588999******************************9999 PP

                   ABC2_membrane_4 106 svllmlvtflitvlfallsgfvgfsvklvlellkkclelgl 146
                                       s++  ++ ++  + +  l g + + v+ +l +++ +++lg+
  gi|242398581|ref|YP_002994005.1|  99 SIIGAILIMA--IGTRSLNGLPYVIVGVFLVSIV-YTLLGI 136
                                       9866554332..2233333433333333333333.222222 PP

>> DUF2721  Protein of unknown function (DUF2721)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   1.0   2.5e-05      0.15      56     116 ..      82     139 ..      67     141 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.5e-05
                           DUF2721  56 lrrRarlirrailllvlsallvvlvvlllflsallsldlsllaailfvlalllllvslllf 116
                                       +++R+ ++ + +ll vls++ ++l+++   ++  + + l  +++ +f+++++ +l+++ ++
  gi|242398581|ref|YP_002994005.1|  82 IEWRSYILAKTLLLSVLSIIGAILIMA---IGTRSLNGLPYVIVGVFLVSIVYTLLGIGIS 139
                                       567888888888888887776665554...33345679***************99998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       754  (0.0420548); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); 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):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.34s 00:00:00.93 Elapsed: 00:00:00.55
# Mc/sec: 1280.42
//
Query:       gi|242398582|ref|YP_002994006.1|  [L=234]
Description: permease [Thermococcus sibiricus MM 739]
Scores for complete 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   31.1  16.8    1.3e-07   31.1  16.8    1.4  1  ABC2_membrane_3  ABC-2 family transporter protein
    3.4e-05   23.9  16.1    0.00011   22.2  15.9    1.9  1  ABC2_membrane_4  ABC-2 family transporter protein
  ------ inclusion threshold ------
      0.093   12.0  18.2      0.073   12.3  12.3    2.2  2  ABC2_membrane_2  ABC-2 family transporter protein
       0.31   11.0   2.5       0.39   10.7   1.3    1.8  2  DUF3290          Protein of unknown function (DUF3290)


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 !   31.1  16.8   2.9e-11   1.3e-07     162     338 ..      51     228 ..      37     229 .. 0.78

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 2.9e-11
                   ABC2_membrane_3 162 flvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilll.afglgipfgn 237
                                       +l+ l+++++ +i +++  ++++ Eke ++++ + v ++s  ++++ +++++ +  ++ +++   + a+   ++ ++
  gi|242398582|ref|YP_002994006.1|  51 ILALLVMVFIPMILGMIPGFMMADEKEDKTIQALQVIPISSEAFLTYRLTWTSITTAVLTVISPKIlAIE--FSQKG 125
                                       233355555555566667779***********************************99999998762555..77778 PP

                   ABC2_membrane_3 238 lglllllfllfglayialgyllssl.fknsetaqilifivilllsgffgglfpledlpsalkwifsiiPffapglgl 313
                                       +++l +lf++  ++y  l++++s   ++  +   +l ++++l++++ +++++   +l+  +++++ ++P++++ +++
  gi|242398582|ref|YP_002994006.1| 126 FLALGVLFVFEVWIYGLLITVFSESrMQALTVSKVLGWFLMLPPLIKLVVVW--RNLSMDWSKFTAFLPTYWLYKVF 200
                                       8777788888899999999999877577777788999999999999999998..88998899*************** PP

                   ABC2_membrane_3 314 lrlitgd.plwe..illsliilalfavv 338
                                         ++ +d + ++  i+ +l++l+ ++++
  gi|242398582|ref|YP_002994006.1| 201 EGIPLNDySDFPiaIGVHLVWLVPLVLL 228
                                       ***9777333334466888888755554 PP

>> ABC2_membrane_4  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2  15.9   2.4e-08   0.00011       9     161 ..      18     158 ..      12     182 .. 0.69

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 2.4e-08
                   ABC2_membrane_4   9 lkrskivwllvlaallvpllallyfnllgktgldpaefyslsvfgftlllllplilgiiasylifrEeqndtlknLl 85 
                                       l+r  +++ +v+++l v ll++ yf+  ++ g+    +y    + + +++++p+ilg+i ++++ +E++++t+  L 
  gi|242398582|ref|YP_002994006.1|  18 LRRDPMLLYSVTMIL-VLLLIVRYFK--DRIGV----YYP--ILALLVMVFIPMILGMIPGFMMADEKEDKTIQALQ 85 
                                       445555554444444.4355555554..33333....444..456668899************************** PP

                   ABC2_membrane_4  86 tiPvsrtklllaKlivllllsvllmlvtflitvlfallsgfvgfsvklvlellkkclelgllvffavlpiialvll 161
                                       +iP+s+ ++l   l+ + +++++l++++  i ++     gf ++   +vl+++  ++   l+++f  + + al++ 
  gi|242398582|ref|YP_002994006.1|  86 VIPISSEAFLTYRLTWTSITTAVLTVISPKILAIEFSQKGFLAL---GVLFVFEVWIYGLLITVFSESRMQALTVS 158
                                       *********************99999988776665555555555...56666666665555555555555555544 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 ?    3.2   0.3      0.01        45       2      36 ..       9      43 ..       8      50 .. 0.84
   2 ?   12.3  12.3   1.6e-05     0.073      79     278 ..      54     227 ..      45     233 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.01
                   ABC2_membrane_2  2 aiakkEfrdlvrsrrfl.lltvllplidvalaylkd 36
                                      ai+k +++ l+r++++l  +t++l+l+ ++++y+kd
  gi|242398582|ref|YP_002994006.1|  9 AIYKTDLKLLRRDPMLLySVTMILVLL-LIVRYFKD 43
                                      69999*********9862577888888.99999987 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 1.6e-05
                   ABC2_membrane_2  79 timavlipviaalfgadaiagEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvllalaiilalgiv 155
                                       +++ v+ip+i  ++   + a+Eke++T+ +l   P+s  + l+  +   ++    +av+++++        ++l i+
  gi|242398582|ref|YP_002994006.1|  54 LLVMVFIPMILGMIPGFMMADEKEDKTIQALQVIPISSEAFLTYRLTWTSIT---TAVLTVIS-------PKILAIE 120
                                       67889******999999***********************999999988888...77777777.......999**** PP

                   ABC2_membrane_2 156 laledllllvvasvlllllvvflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavpqeindf 232
                                       ++ + +l l v++v+ + +      gll+ +++ s+ +a++++ +l  +l++   i l  v  +l++         +
  gi|242398582|ref|YP_002994006.1| 121 FSQKGFLALGVLFVFEVWI-----YGLLITVFSESRMQALTVSKVLGWFLMLPPLIKLVVVWRNLSMDWS------K 186
                                       **************77774.....59*****************999999988777766666666664433......5 PP

                   ABC2_membrane_2 233 lsllsptsayntllneilagsdlnalgstatnllilllllavllvl 278
                                       ++ + pt +   +++ i+ ++     +s++  ++ + l+ +v+lvl
  gi|242398582|ref|YP_002994006.1| 187 FTAFLPTYWLYKVFEGIPLND-----YSDFPIAIGVHLVWLVPLVL 227
                                       555666666666666666666.....55555555555555555555 PP

>> DUF3290  Protein of unknown function (DUF3290)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.3   8.8e-05      0.39      22      85 ..      25      87 ..      21     112 .. 0.84
   2 ?   -3.2   0.0       1.7   7.4e+03      17      41 ..     208     232 ..     204     233 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 8.8e-05
                           DUF3290 22 lilvlllllivvlilylrnrldtkyRdLsiilllllllllgiqysdyqqsqsassqssqmvsfi 85
                                      l  v ++l++++++ y+++r+   y  L++++++++ ++lg+ +  ++   ++++++ q++++i
  gi|242398582|ref|YP_002994006.1| 25 LYSVTMILVLLLIVRYFKDRIGVYYPILALLVMVFIPMILGM-IPGFMMADEKEDKTIQALQVI 87
                                      55677788888999****************999999999997.667777777777777777776 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.7
                           DUF3290  17 llryililvlllllivvlilylrnr 41 
                                       +    + + + l+ +v l+l +r+r
  gi|242398582|ref|YP_002994006.1| 208 YSDFPIAIGVHLVWLVPLVLLFRKR 232
                                       5555556666666666677777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       791  (0.0441185); 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:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1498.00
//
Query:       gi|242398583|ref|YP_002994007.1|  [L=51]
Description: hypothetical protein TSIB_0593 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-15   57.1   1.6    1.8e-15   57.1   1.6    1.0  1  DUF104    Protein of unknown function DUF104


Domain annotation for each model (and alignments):
>> DUF104  Protein of unknown function DUF104
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.1   1.6     1e-19   1.8e-15       1      37 [.       5      41 ..       5      50 .. 0.91

  Alignments for each domain:
  == domain 1  score: 57.1 bits;  conditional E-value: 1e-19
                            DUF104  1 MskvIeavYEnGvLKPLekvdLkEGeevkikIeeake 37
                                      Ms++Ie++YE+GvLKPL+k+ +k+Ge++ ++I+++ +
  gi|242398583|ref|YP_002994007.1|  5 MSEIIEVIYEKGVLKPLKKLPFKDGEKLIVEIRKRDK 41
                                      9********************************9443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.31s 00:00:00.76 Elapsed: 00:00:00.50
# Mc/sec: 304.46
//
Query:       gi|242398584|ref|YP_002994008.1|  [L=65]
Description: hypothetical protein TSIB_0594 [Thermococcus sibiricus MM 739]
Scores for complete 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   21.3   0.2    0.00034   21.1   0.2    1.1  1  PIN           PIN domain
  ------ inclusion threshold ------
      0.015   15.3   1.5      0.053   13.5   1.5    1.7  1  SRP_TPR_like  Putative TPR-like repeat


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 !   21.1   0.2   3.8e-08   0.00034       6      48 ..       6      52 ..       3      64 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 3.8e-08
                                      HHHHHHHTTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHS....S CS
                               PIN  6 svliallrgeekaeaarklleeleelvtsalvlaEllyvlar....r 48
                                      +v++++l   e++++ark+le+ e+ +t++++l+E++++ +r     
  gi|242398584|ref|YP_002994008.1|  6 NVIVSYLLYTERTKEARKILEQEEAFATTINTLEEAMFIGMRlifeE 52
                                      9************************************9998855541 PP

>> SRP_TPR_like  Putative TPR-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   1.5   5.9e-06     0.053      24      63 ..      12      64 ..       3      65 .] 0.81

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.9e-06
                      SRP_TPR_like 24 liklekyeeaLkllkkgs.............alsedvrfEkaYvlYklkkykk 63
                                      l+  e+ +ea k+l++++              +   ++fE+ Y  Yklkk+kk
  gi|242398584|ref|YP_002994008.1| 12 LLYTERTKEARKILEQEEafattintleeamFIGMRLIFEEHYGDYKLKKLKK 64
                                      67778888888888888888888887777667778899*************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 413.06
//
Query:       gi|242398585|ref|YP_002994009.1|  [L=42]
Description: nucleic acid-binding protein, containing PIN domain, partial [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-10   41.8   0.0    1.4e-10   41.7   0.0    1.0  1  PIN       PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.7   0.0   7.9e-15   1.4e-10      85     121 ..       1      37 [.       1      38 [. 0.96

  Alignments for each domain:
  == domain 1  score: 41.7 bits;  conditional E-value: 7.9e-15
                                       HHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHHHHHH CS
                               PIN  85 alkygllpnDaliaAtAkehgikliatfDedfrrvak 121
                                       +++y+llpnDali+  +k+hgi++iatfD+df++v++
  gi|242398585|ref|YP_002994009.1|   1 MERYSLLPNDALIVLACKAHGINKIATFDSDFENVEF 37 
                                       689*******************************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       209  (0.0116571); expected 358.6 (0.02)
Passed bias filter:                      201  (0.0112109); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.44
# Mc/sec: 287.59
//
Query:       gi|242398586|ref|YP_002994010.1|  [L=361]
Description: Act-like pyruvate formate-lyase activating enzyme related protein [Thermococcus sibiricus MM 739]
Scores for complete 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   80.3   0.7    3.8e-21   76.2   0.1    2.7  3  Radical_SAM     Radical SAM superfamily
      1e-07   32.3   0.1    2.3e-07   31.2   0.1    1.5  1  Fer4_12         4Fe-4S single cluster domain
     0.0049   17.0   0.2     0.0049   17.0   0.2    1.9  2  DiS_P_DiS       Bacterial Peptidase A24 N-terminal domain
     0.0083   16.1   0.4        1.8    8.6   0.0    2.6  2  ADK_lid         Adenylate kinase, active site lid
  ------ inclusion threshold ------
      0.026   14.3   1.5       0.41   10.5   0.1    2.6  2  zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
       0.03   14.3   2.7      0.037   14.1   0.1    2.3  2  DZR             Double zinc ribbon
      0.039   13.6   3.6       0.59    9.8   0.3    2.7  2  zf_C2H2_13      Zinc finger domain
       0.22   11.7   0.1       0.22   11.7   0.1    1.8  2  Fer4_14         4Fe-4S single cluster domain
       0.22   11.0   0.2       0.22   11.0   0.2    2.8  3  zf-ribbon_3     zinc-ribbon domain
        4.5    7.1  15.2       0.34   10.7   1.0    3.0  3  zinc_ribbon_2   zinc-ribbon domain
        4.7    7.2  11.9        1.7    8.7   0.7    3.2  3  zf-dskA_traR    Prokaryotic dksA/traR C4-type 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 !   76.2   0.1   2.3e-24   3.8e-21       4     166 ..      92     247 ..      90     248 .. 0.92
   2 ?    0.6   0.0      0.41   6.7e+02     124     155 ..     277     309 ..     259     311 .. 0.77
   3 ?   -0.7   0.1      0.99   1.6e+03       8      18 ..     335     345 ..     335     357 .. 0.79

  Alignments for each domain:
  == domain 1  score: 76.2 bits;  conditional E-value: 2.3e-24
                                       ESEESS--TTTSCCTT...HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCT CS
                                       xxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   4 trgCnlrCsfCarpet...vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpg 77 
                                       t gCn+ C++C+++e     ++ ++ ++ + e i++++k ++    ++ +  +  ep+ +++fv ++ +lak+  +g
  gi|242398586|ref|YP_002994010.1|  92 TVGCNMHCIHCQNWEIsqsNETFPYLENATSEAIVRLAKHYA----CESIAYTYNEPTIWYEFVLETSKLAKE--AG 162
                                       68**************999999999999999******99999....***************************..7* PP

                                       EEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET.EEEEEEEBT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                       Radical_SAM  78 iritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikr.vvdrivglp 153
                                       +++ ++tng+   ee  ++l+++  d ++++++a+ de + +++ + +++e  +++  ++++  +   v  +++++p
  gi|242398586|ref|YP_002994010.1| 163 LKNILVTNGYIN-EEPFRALAPYI-DAMNIDIKAFRDE-FYRKISKVPGVEPSKRTAIIAKKE-FGIhVELTYLIIP 235
                                       ***********8.**********9.*************.777777999999999999988887.4444********* PP

                                       TTSHHHHHHHHHH CS
                                       xxxxxxxxxxxxx RF
                       Radical_SAM 154 Gendeeleellel 166
                                         nd+e ee+  +
  gi|242398586|ref|YP_002994010.1| 236 TLNDSE-EEISAF 247
                                       *****9.887766 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.41
                                       TSHHHHHHHHHHHHHHTTSET.EEEEEEEBTTT CS
                                       xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                       Radical_SAM 124 ghtfeevlealeklreagikr.vvdrivglpGe 155
                                       +  +e + +a ++++e g+k   v +++g+ Ge
  gi|242398586|ref|YP_002994010.1| 277 PTPVETIEKAYRIAKEEGLKFvYVGNVPGHNGE 309
                                       566788999999999999997666777777776 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.99
                                       SS--TTTSCCT CS
                                       xxxxxxxxxxx RF
                       Radical_SAM   8 nlrCsfCarpe 18 
                                       n++C +C  p 
  gi|242398586|ref|YP_002994010.1| 335 NGKCEYCGEPI 345
                                       789****9985 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 !   31.2   0.1   1.4e-10   2.3e-07       6     100 ..      86     178 ..      81     202 .. 0.82

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 1.4e-10
                           Fer4_12   6 vrlslfvsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkk.esiegltllGGEPllpenaeallelvkevke 81 
                                       + +s+ + gCn++C  C n e+ + ++  ++ +++  e+i +l+k +  e + ++  EP     +e +le  k  ke
  gi|242398586|ref|YP_002994010.1|  86 CAFSIGTVGCNMHCIHCQNWEISQSNETFPYLENATSEAIVRLAKhYACESIAYTYNEPTI--WYEFVLETSKLAKE 160
                                       55677788***********************866666665555551666************..8899********** PP

                           Fer4_12  82 ekpekdiwlytgytleels 100
                                       +++ k+i++++gy++ee  
  gi|242398586|ref|YP_002994010.1| 161 AGL-KNILVTNGYINEEPF 178
                                       **9.8**********9864 PP

>> DiS_P_DiS  Bacterial Peptidase A24 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.5       6.6   1.1e+04      28      35 ..      97     104 ..      92     108 .. 0.76
   2 !   17.0   0.2     3e-06    0.0049      28      64 ..     311     347 ..     303     351 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 6.6
                         DiS_P_DiS  28 SrCpkCgh 35 
                                        +C +C++
  gi|242398586|ref|YP_002994010.1|  97 MHCIHCQN 104
                                       57888875 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 3e-06
                         DiS_P_DiS  28 SrCpkCghklkwleliPvlSylllrgrCraCkakisl 64 
                                         CpkCg++l ++    +  y +  g+C++C+++i++
  gi|242398586|ref|YP_002994010.1| 311 TYCPKCGKPLIVRWGFTIEEYHIKNGKCEYCGEPIPI 347
                                       57*********************************87 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0    0.0011       1.8      23      34 ..     312     323 ..     302     324 .. 0.91
   2 ?    4.8   0.2     0.017        28      20      30 ..     334     344 ..     330     346 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0011
                                       B-TTT--.-B-- CS
                           ADK_lid  23 lCDkCGepLvqR 34 
                                        C kCG pL++R
  gi|242398586|ref|YP_002994010.1| 312 YCPKCGKPLIVR 323
                                       6*********99 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.017
                                       STTB-TTT--. CS
                           ADK_lid  20 veglCDkCGep 30 
                                       ++g+C  CGep
  gi|242398586|ref|YP_002994010.1| 334 KNGKCEYCGEP 344
                                       58********8 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00025      0.41       3      14 ..     312     323 ..     311     326 .. 0.88
   2 ?    2.1   0.3      0.11   1.7e+02       2      11 ..     336     345 ..     335     354 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00025
                                       E-SSS--EEEEE CS
                    zf-C4_Topoisom   3 kCPkCggdLvlk 14 
                                        CPkCg++L+++
  gi|242398586|ref|YP_002994010.1| 312 YCPKCGKPLIVR 323
                                       6*********98 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.11
                                       EE-SSS--EE CS
                    zf-C4_Topoisom   2 ekCPkCggdL 11 
                                       +kC+ Cg+++
  gi|242398586|ref|YP_002994010.1| 336 GKCEYCGEPI 345
                                       79*****986 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.5       1.4   2.3e+03      30      36 ..      98     104 ..      80     114 .. 0.72
   2 ?   14.1   0.1   2.2e-05     0.037      12      39 ..     310     346 ..     303     350 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.4
                               DZR  30 rCpsCge 36 
                                       +C +C+ 
  gi|242398586|ref|YP_002994010.1|  98 HCIHCQN 104
                                       5666654 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 2.2e-05
                               DZR  12 arfCseCgtklkavaa.........edrCpsCgekvd 39 
                                         +C++Cg++l              + +C  Cge+++
  gi|242398586|ref|YP_002994010.1| 310 YTYCPKCGKPLIVRWGftieeyhikNGKCEYCGEPIP 346
                                       5699999999984444999999999999999999865 PP

>> zf_C2H2_13  Zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.3   0.00036      0.59      14      28 ..     307     321 ..     302     324 .. 0.85
   2 ?    3.9   0.3     0.026        42      20      28 ..     338     346 ..     330     348 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00036
                        zf_C2H2_13  14 nlnYRvCnkCGkPis 28 
                                       n +Y  C kCGkP+ 
  gi|242398586|ref|YP_002994010.1| 307 NGEYTYCPKCGKPLI 321
                                       568999*******96 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.026
                        zf_C2H2_13  20 CnkCGkPis 28 
                                       C+ CG Pi 
  gi|242398586|ref|YP_002994010.1| 338 CEYCGEPIP 346
                                       *******95 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   0.2       6.6   1.1e+04       5      16 ..      30      48 ..      28      67 .. 0.57
   2 ?   11.7   0.1   0.00013      0.22       6      91 ..      93     173 ..      89     193 .. 0.67

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 6.6
                           Fer4_14  5 lsgCnlsCk.......gCd 16
                                         C+l+C         C 
  gi|242398586|ref|YP_002994010.1| 30 CHLCPLNCIisegqrgSCK 48
                                      5568888876666665555 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00013
                           Fer4_14   6 sgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekk 82 
                                        gCn++C  C n e  +s+ + p+ e+  ++ +  l k++   + +  t  eP ++   + +l+  k  ke +  k+
  gi|242398586|ref|YP_002994010.1|  93 VGCNMHCIHCQNWEISQSNETFPYLENATSEAIVRLAKHYA-CESIAYTYNEPTIW--YEFVLETSKLAKEAG-LKN 165
                                       69**********99999999999988888887766655555.55588888888766..344444444444444.344 PP

                           Fer4_14  83 iwletngtl 91 
                                       i + tng +
  gi|242398586|ref|YP_002994010.1| 166 ILV-TNGYI 173
                                       443.44444 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.7       2.8   4.6e+03      17      23 ..      97     103 ..      96     104 .. 0.75
   2 ?   11.0   0.2   0.00014      0.22       2      12 ..     310     320 ..     309     323 .. 0.80
   3 ?    3.5   0.7      0.03        49      18      26 .]     337     345 ..     336     345 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.8
                       zf-ribbon_3  17 nvCpyCG 23 
                                       ++C +C+
  gi|242398586|ref|YP_002994010.1|  97 MHCIHCQ 103
                                       5899996 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00014
                       zf-ribbon_3   2 tvrCPnCGapl 12 
                                       +++CP+CG+pl
  gi|242398586|ref|YP_002994010.1| 310 YTYCPKCGKPL 320
                                       67999999964 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.03
                       zf-ribbon_3  18 vCpyCGtkl 26 
                                       +C yCG+++
  gi|242398586|ref|YP_002994010.1| 337 KCEYCGEPI 345
                                       599999876 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       5.1   8.4e+03       2       5 ..      99     102 ..      98     104 .. 0.61
   2 ?   10.7   1.0   0.00021      0.34      14      23 .]     311     320 ..     308     320 .. 0.73
   3 ?    6.2   0.9    0.0054       8.8      16      23 .]     338     345 ..     334     346 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 5.1
                     zinc_ribbon_2   2 CpnC 5  
                                       C +C
  gi|242398586|ref|YP_002994010.1|  99 CIHC 102
                                       6666 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00021
                     zinc_ribbon_2  14 kFCpyCGtpl 23 
                                       ++Cp+CG pl
  gi|242398586|ref|YP_002994010.1| 311 TYCPKCGKPL 320
                                       6777777775 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.0054
                     zinc_ribbon_2  16 CpyCGtpl 23 
                                       C+yCG+p+
  gi|242398586|ref|YP_002994010.1| 338 CEYCGEPI 345
                                       89999885 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 ?   -0.2   0.2       0.6   9.7e+02      26      31 ..      98     103 ..      97     104 .. 0.86
   2 ?    4.6   0.6     0.019        31       1      12 [.     308     319 ..     308     320 .. 0.89
   3 ?    8.7   0.7     0.001       1.7       4      14 ..     336     346 ..     330     347 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.6
                      zf-dskA_traR  26 lCveCq 31 
                                       +C+ Cq
  gi|242398586|ref|YP_002994010.1|  98 HCIHCQ 103
                                       7****9 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.019
                      zf-dskA_traR   1 giygsCeeCGEp 12 
                                       g y +C +CG+p
  gi|242398586|ref|YP_002994010.1| 308 GEYTYCPKCGKP 319
                                       67999*****97 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.001
                      zf-dskA_traR   4 gsCeeCGEpIp 14 
                                       g+Ce CGEpIp
  gi|242398586|ref|YP_002994010.1| 336 GKCEYCGEPIP 346
                                       56********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 2138.91
//
Query:       gi|242398587|ref|YP_002994011.1|  [L=274]
Description: hypothetical protein TSIB_0597 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0014   19.2   0.1      0.041   14.5   0.0    2.2  2  FlgT_N         Flagellar assembly protein T, N-terminal domai
  ------ inclusion threshold ------
      0.044   13.9   2.0        1.9    8.6   0.2    2.4  2  Lipase_GDSL_3  GDSL-like Lipase/Acylhydrolase family
       0.17   12.6   1.1       0.64   10.8   0.1    2.1  2  RraB           Regulator of ribonuclease activity B


Domain annotation for each model (and alignments):
>> FlgT_N  Flagellar assembly protein T, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.044   2.6e+02      14      57 ..      15      58 ..      11      67 .. 0.76
   2 !   14.5   0.0   6.8e-06     0.041      19      54 ..     164     200 ..     160     212 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.044
                            FlgT_N 14 nddiAreqAredAlkqAllyagaqvgsisslqqllegsltetqf 57
                                      nd+ A e+A e+ +k   +  +++v++i +++ l + +  +++ 
  gi|242398587|ref|YP_002994011.1| 15 NDKKALERAVEEIVKSLKNEDTLKVENIRAEEILENPDDDMLKY 58
                                      67777778888888999999999999999888877776665555 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 6.8e-06
                            FlgT_N  19 reqAredAlkqAllyagaqvg.sisslqqllegslte 54 
                                       +++A+ed+lk+A  y ga+++  +s++q+  +g+l  
  gi|242398587|ref|YP_002994011.1| 164 DQKAIEDVLKKAFDYEGAKINkIVSKVQEEKNGKLRI 200
                                       468******************6666777777776654 PP

>> Lipase_GDSL_3  GDSL-like Lipase/Acylhydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.2   0.00031       1.9     113     157 ..      13      57 ..       2      66 .. 0.86
   2 ?    4.7   0.1    0.0048        29      98     150 ..     157     209 ..      91     215 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00031
                     Lipase_GDSL_3 113 lekeveaknkaleelvkklkkekekklylisskellgkdeeatvd 157
                                       l + ++a ++a+ee+vk+lk+e++ k+  i ++e+l++  ++++ 
  gi|242398587|ref|YP_002994011.1|  13 LSNDKKALERAVEEIVKSLKNEDTLKVENIRAEEILENPDDDMLK 57 
                                       566788999***************************998888765 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0048
                     Lipase_GDSL_3  98 lvedlsttkglvdeklekeveaknkaleelvkklkkekekklylisskellgk 150
                                       +ve     ++ ++  l+k+   + + ++++v k+++ek+ kl +++++el+++
  gi|242398587|ref|YP_002994011.1| 157 VVEVFGEDQKAIEDVLKKAFDYEGAKINKIVSKVQEEKNGKLRILAAAELISS 209
                                       566666677788888888888899999999*******************9986 PP

>> RraB  Regulator of ribonuclease activity B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1      0.25   1.5e+03      43      73 ..      37      67 ..       4      84 .. 0.55
   2 ?   10.8   0.1   0.00011      0.64      20      90 ..     148     224 ..     143     227 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.25
                              RraB 43 leklgyevedaeedeedgeevycldlskems 73
                                      l+ ++++ e++ e+++d+  +y   ++ + +
  gi|242398587|ref|YP_002994011.1| 37 LKVENIRAEEILENPDDDMLKYSMMVEADLE 67
                                      3333444444444445544555555555544 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00011
                              RraB  20 kpreiehhfyfedeedlekfaeeleklgyevedaeede......edgeevycldlskemsldaeeIdaiteeleela 90 
                                       + rei + f+ e + + +k++e++ k+ +++e a+ ++      e+++++  + +  e + + e+++++t ++  +a
  gi|242398587|ref|YP_002994011.1| 148 DDREILYRFVVEVFGEDQKAIEDVLKKAFDYEGAKINKivskvqEEKNGKLRILAAAELISSFENLFQLTGKFAPVA 224
                                       5799********************************999*99998889**********************9998877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       879  (0.0490267); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); 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):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2086.37
//
Query:       gi|242398588|ref|YP_002994012.1|  [L=518]
Description: hypothetical protein TSIB_0598 [Thermococcus sibiricus MM 739]
Scores for 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-09   36.0   0.1      7e-09   36.0   0.1    2.0  3  S_layer_C  S-layer like family, C-terminal region


Domain annotation for each model (and alignments):
>> S_layer_C  S-layer like family, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0      0.39   6.9e+03     105     122 ..      89     106 ..      55     113 .. 0.75
   2 ?   -2.8   0.0      0.28   5.1e+03      57      87 ..     285     316 ..     268     331 .. 0.66
   3 !   36.0   0.1   3.9e-13     7e-09     132     220 .]     421     515 ..     397     515 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 0.39
                         S_layer_C 105 vgekvkvlsadvkaekik 122
                                       + +++ ++ ++vka++ +
  gi|242398588|ref|YP_002994012.1|  89 FQDSITSTEVEVKAKDTH 106
                                       556777777777777654 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.28
                         S_layer_C  57 lalkykgdkladikdkdkvd.ianyaklkfdD 87 
                                       l   y +  ++++ ++ + d i+n+++++  D
  gi|242398588|ref|YP_002994012.1| 285 LESDYGVTGVTNVTKELEKDkIENFVHMRIGD 316
                                       55556666666666665555577777766666 PP

  == domain 3  score: 36.0 bits;  conditional E-value: 3.9e-13
                         S_layer_C 132 taPivvLD.tEveldsvdknLiLvGGPvvNkvtkeLedk...lkvaityeednksaatiavienaan..gndvlvvA 202
                                       + P   +D tE ++ +  k++ ++GG v+Nkv ++Le+     kva  +e+  ++ +   ++e  +n  +n v++vA
  gi|242398588|ref|YP_002994012.1| 421 AVPDYEVDlTEFNVAENTKDVYIIGGWVSNKVWAQLEEVfgeEKVAEWKEDVMDEDGYALIVEPLPNdpDNYVIIVA 497
                                       455555554677999999*******************986446788777888888999999999999899******* PP

                         S_layer_C 203 GsDRegTkaAalaliekl 220
                                       G D  +T++A+ +li+ +
  gi|242398588|ref|YP_002994012.1| 498 GQDYMKTAEAVDELIDLI 515
                                       ***************875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (518 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       633  (0.0353059); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); 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: 0.66u 0.33s 00:00:00.99 Elapsed: 00:00:00.52
# Mc/sec: 2999.61
//
Query:       gi|242398589|ref|YP_002994013.1|  [L=587]
Description: oxidative cyclase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.5e-26   93.1   0.1    1.8e-25   90.3   0.0    2.3  2  Radical_SAM  Radical SAM superfamily
    4.7e-05   23.6   0.0    0.00043   20.5   0.0    2.4  2  HHH_3        Helix-hairpin-helix motif


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.3   0.0     2e-29   1.8e-25       1     167 []     210     409 ..     210     409 .. 0.97
   2 ?   -0.4   0.0      0.15   1.4e+03      47     101 ..     424     474 ..     413     498 .. 0.71

  Alignments for each domain:
  == domain 1  score: 90.3 bits;  conditional E-value: 2e-29
                                       EEEESEESS-.....-TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEE.............SSTGGG CS
                                       xxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............xxxxxx RF
                       Radical_SAM   1 vvvtrgCnlr.....CsfCarpetvrregrgrslsveeileevkelkaekgvkevilg.............ggepll 59 
                                       ++ +rgC+ +     CsfC+ p    r+++ +++++e+i++ev++l ++ gvk++ +g             +  p+ 
  gi|242398589|ref|YP_002994013.1| 210 IESQRGCPKAagiggCSFCTEPV---RYKTIEDRPIEDIVKEVEIL-YNLGVKHFRIGrqscifsymakpdSRVPIP 282
                                       5789*****99***********9...9*******************.8***************************** PP

                                       STTHHHHHHHHHHTC........CCTEEEEEEECSSCHGHHHHHHHHHTT..-SEEEEEEBSSSHHHHHHHHTCTSH CS
                                       xxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  60 ypdfvellerlakla........vpgiritvetngtlpdeeklerllelg..vdrvslgleaaddekvlklmnrght 126
                                       +p+ +e+l++ ++          v++ + ++++n+++ + +++++l e+g   ++v++gle+ad++ v +l+n + t
  gi|242398589|ref|YP_002994013.1| 283 NPEAIEKLFKGIRAVapkiktlhVDNANPAIIANYPKESIRIAKALIEYGtpGNVVAFGLETADPK-VARLNNLNST 358
                                       ***********9999***************************************************.******99** PP

                                       HHHHHHHHHHHHHTTSET..........EEEEEEEBTTTSHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 127 feevlealeklreagikr..........vvdrivglpGendeeleellell 167
                                       +ee++ea+++l+++g kr           +++++glpGe+++++e ++e+l
  gi|242398589|ref|YP_002994013.1| 359 PEETYEAVKILNKVGAKRgyngmplllpGINILFGLPGETKKTYELTYEFL 409
                                       ***************9999999999999*******************9996 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.15
                                       SEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  47 vkevilgggepllypdfvellerlaklavpgiritvetngtlpdeeklerllelg 101
                                       +++v+++ g+pl + ++  ++e+ +kl     +  + + +  +   +l+rl++ g
  gi|242398589|ref|YP_002994013.1| 424 IRQVVVFPGTPLWNMREKIKTEKHKKL---IHHYKYKIRHEID-YPMLKRLVPVG 474
                                       899999999999998888777777777...5555555555554.55555555555 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.17   1.5e+03      39      59 ..     178     198 ..     173     202 .. 0.87
   2 !   20.5   0.0   4.8e-08   0.00043       5      48 ..     532     571 ..     531     574 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.17
                             HHH_3  39 pfksreeLlkvkglgpktfeq 59 
                                       +f+s  eL +   lg++ + q
  gi|242398589|ref|YP_002994013.1| 178 RFRSYSELRDYALLGAEVVKQ 198
                                       69*************999888 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 4.8e-08
                             HHH_3   5 gvdiNtAsaeeLqklpGlgpklAknIvayReknGpfksreeLlk 48 
                                       ++++N  s + L +lpGlg+k++ +I+a R    pf++ e +lk
  gi|242398589|ref|YP_002994013.1| 532 PINVNRESSKVLGYLPGLGKKKIIKILAQR----PFENKEKFLK 571
                                       59****************************....******9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (587 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); 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: 0.67u 0.29s 00:00:00.96 Elapsed: 00:00:00.50
# Mc/sec: 3517.47
//
Query:       gi|242398590|ref|YP_002994014.1|  [L=182]
Description: Rubrerythrin-related protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.8e-14   52.9   4.9    4.8e-14   52.9   4.9    1.9  2  Rubrerythrin  Rubrerythrin
    0.00066   19.8   1.1       0.04   14.0   0.0    2.3  2  DUF1877       Domain of unknown function (DUF1877)
     0.0061   16.8   0.4        2.8    8.2   0.0    2.6  2  Coat_F        Coat F domain
  ------ inclusion threshold ------
      0.018   15.2   1.9        1.3    9.3   0.4    2.1  2  Ferritin_2    Ferritin-like domain
      0.021   14.5   1.8       0.06   13.0   0.1    2.3  3  DUF3231       Protein of unknown function (DUF3231)
      0.031   13.9   0.0      0.066   12.8   0.0    1.6  2  Ndc80_HEC     HEC/Ndc80p family
      0.095   12.5   0.4      0.095   12.5   0.4    2.2  3  DUF2202       Uncharacterized protein domain (DUF2202)
       0.27   11.3   1.8       0.63   10.1   0.7    2.3  2  SapB_1        Saposin-like type B, region 1
       0.59    9.8   0.1       0.59    9.8   0.1    2.9  3  Rpn9_C        Rpn9 C-terminal helix
        1.6    8.9   5.0         11    6.3   0.2    2.9  3  HSR           HSR 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 ?    2.9   0.4     0.076   1.4e+02     101     137 .]      13      49 ..       2      49 .. 0.72
   2 !   52.9   4.9   2.7e-17   4.8e-14       9     137 .]      37     170 ..      29     170 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.076
                                       HHHHHHHHHTTSHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Rubrerythrin 101 rfyeelaekegneeakklfkklaeaEkkHeerlrkll 137
                                        ++++++e   +  +k+l+ +++++E k +e++ +l+
  gi|242398590|ref|YP_002994014.1|  13 SKFKQILEAISKLGTKELLVYWMDQEVKEAEMYHRLY 49 
                                       3455566666666778999999999999999999986 PP

  == domain 2  score: 52.9 bits;  conditional E-value: 2.7e-17
                                       HHHHHHHHHHH.HHHCHH.TT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSBBS-------TT...GG CS
                      Rubrerythrin   9 gEssarrlYke.laekak.egypqiaelFeelAeeEreHakilnklleklepelelevkekvreyaeakpkf...lt 80 
                                        E ++ ++Y   +a   + +  +++++lF+++  +  eHa+ l kl++ ++p++e++  +    ++e  +k    l+
  gi|242398590|ref|YP_002994014.1|  37 QEVKEAEMYHRlYAISSEvNWDEKVSKLFLDMYNDCLEHAETLLKLYRTMYPDEEVIKVDLPALEVELSEKRlrdLV 113
                                       56555555554044455566789********************************4444444444444444311156 PP

                                       HHHHHHHHHHHHHHHHHCHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Rubrerythrin  81 taknLeeaiegayaeeeemyrfyeelaekegneeakklfkklaeaEkkHeerlrkll 137
                                       ++  L+e++e  +  e+ ++ +ye la+++++ee+k ++k+lae E++H+erlr l+
  gi|242398590|ref|YP_002994014.1| 114 YQGRLQEILEYLMGTEKIAHDVYEYLAKQTTDEEVKAILKWLAEIENGHYERLRSLY 170
                                       777999************************************************997 PP

>> DUF1877  Domain of unknown function (DUF1877)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.4     0.018        32      92     127 ..      13      48 ..       6      92 .. 0.77
   2 !   14.0   0.0   2.2e-05      0.04      69     107 ..     124     161 ..     108     173 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.018
                           DUF1877  92 eqVkevaeaLaeldfeelrerfdaeeleeaeiYpni 127
                                       ++ k++ ea+++l  +el      +e++eae Y+++
  gi|242398590|ref|YP_002994014.1|  13 SKFKQILEAISKLGTKELLVYWMDQEVKEAEMYHRL 48 
                                       56799****************************983 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 2.2e-05
                           DUF1877  69 vvlGgeelgeedegygparlltpeqVkevaeaLaeldfe 107
                                        ++G e++  +d+ ++ a+ +t e+Vk++ ++Lae++  
  gi|242398590|ref|YP_002994014.1| 124 YLMGTEKIA-HDVYEYLAKQTTDEEVKAILKWLAEIENG 161
                                       689*****8.*************************9865 PP

>> Coat_F  Coat F domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1   0.0    0.0072        13      30      53 ..      59      82 ..      47      85 .. 0.86
   2 !    8.2   0.0    0.0016       2.8       3      39 ..     119     155 ..     118     168 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0072
                            Coat_F 30 pelRqtlkqilneeiemqeelfnl 53
                                      + + + + ++ n+++e++e l +l
  gi|242398590|ref|YP_002994014.1| 59 EKVSKLFLDMYNDCLEHAETLLKL 82
                                      567789999********9998765 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0016
                            Coat_F   3 kdiandlLsteKsaarnyataitEasnpelRqtlkqi 39 
                                       ++i++ l+ teK a + y   + +++++e++++lk +
  gi|242398590|ref|YP_002994014.1| 119 QEILEYLMGTEKIAHDVYEYLAKQTTDEEVKAILKWL 155
                                       799****************************999754 PP

>> Ferritin_2  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0      0.01        18       6      60 ..      31      82 ..      26     108 .. 0.83
   2 ?    9.3   0.4    0.0007       1.3       4      61 ..     120     170 ..     117     180 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.01
                        Ferritin_2  6 LnfAlnlEyleaafYtaalegaslddkalldaevrevaeeiakheeaHveflkaa 60
                                      L + +  E  ea+ Y++  +   ++++ + d++v +++ +++++  +H+e+l + 
  gi|242398590|ref|YP_002994014.1| 31 LVYWMDQEVKEAEMYHRLYA---ISSEVNWDEKVSKLFLDMYNDCLEHAETLLKL 82
                                      55666679999****99998...344899********************999665 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0007
                        Ferritin_2   4 diLnfAlnlEyleaafYtaalegaslddkalldaevrevaeeiakheeaHveflkaal 61 
                                       +iL++ +  E ++ + Y++ ++       ++ d+ev+++++ +a+ e +H+e l++  
  gi|242398590|ref|YP_002994014.1| 120 EILEYLMGTEKIAHDVYEYLAK-------QTTDEEVKAILKWLAEIENGHYERLRSLY 170
                                       7999999999999999999997.......67999*****************9999875 PP

>> DUF3231  Protein of unknown function (DUF3231)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1      0.38   6.8e+02      34      61 ..       2      29 ..       1      33 [. 0.84
   2 ?   -1.4   0.0      0.87   1.6e+03      43      62 ..      57      76 ..      19      83 .. 0.60
   3 ?   13.0   0.1   3.3e-05      0.06      27      68 ..     128     169 ..     118     173 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.38
                           DUF3231 34 litgFlqvaedkeikelleralelsnkh 61
                                      +++ F  + e+ + k++le  ++l++k+
  gi|242398590|ref|YP_002994014.1|  2 MHQRFKTKEEKSKFKQILEAISKLGTKE 29
                                      6788888899999999999999998886 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.87
                           DUF3231 43 edkeikelleralelsnkhi 62
                                       d+++++l+    + + +h 
  gi|242398590|ref|YP_002994014.1| 57 WDEKVSKLFLDMYNDCLEHA 76
                                      35556666555555555554 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 3.3e-05
                           DUF3231  27 anslgialitgFlqvaedkeikelleralelsnkhikelkel 68 
                                       ++ ++  ++++ ++++ d+e+k++l+   e+ n h ++l +l
  gi|242398590|ref|YP_002994014.1| 128 TEKIAHDVYEYLAKQTTDEEVKAILKWLAEIENGHYERLRSL 169
                                       46788899*****************************99987 PP

>> Ndc80_HEC  HEC/Ndc80p family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       3.2   5.7e+03     115     129 ..      47      61 ..      44      67 .. 0.69
   2 ?   12.8   0.0   3.7e-05     0.066      26      86 ..     103     163 ..      85     174 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 3.2
                         Ndc80_HEC 115 qlaAvgtphtwptll 129
                                       +l+A++++ +w + +
  gi|242398590|ref|YP_002994014.1|  47 RLYAISSEVNWDEKV 61 
                                       577777777776654 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 3.7e-05
                         Ndc80_HEC  26 erDprplrdksfqseliqellefLk.ennfehsisaktlksPsqkdfssifkfLykrldpsy 86 
                                       e   ++lrd  +q +l qe+le+L  +++  h + +   k+ +  ++  i+k+L +  + +y
  gi|242398590|ref|YP_002994014.1| 103 ELSEKRLRDLVYQGRL-QEILEYLMgTEKIAHDVYEYLAKQTTDEEVKAILKWLAEIENGHY 163
                                       5567899999999887.57778876155666***********************87655555 PP

>> DUF2202  Uncharacterized protein domain (DUF2202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.2      0.64   1.1e+03     112     151 ..      11      51 ..       4      62 .. 0.49
   2 ?   -0.1   0.6       0.4   7.2e+02      16      48 ..      42      82 ..      27     112 .. 0.56
   3 ?   12.5   0.4   5.3e-05     0.095       3      51 ..     120     172 ..     118     182 .] 0.78

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.64
                           DUF2202 112 dnkdikevYenllkGsrnhlRsfvrkleer.gkeYepqyis 151
                                       +++  k++ e + k   + l  ++ + e +  + Y+  y  
  gi|242398590|ref|YP_002994014.1|  11 EKSKFKQILEAISKLGTKELLVYWMDQEVKeAEMYHRLYAI 51 
                                       55555555555555444444444444433202334444444 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.4
                           DUF2202 16 rDvYlelYdr.....wk...lqiflniakseqthtdavksl 48
                                       ++Y +lY       w+    ++fl++ +   +h +++ +l
  gi|242398590|ref|YP_002994014.1| 42 AEMYHRLYAIssevnWDekvSKLFLDMYNDCLEHAETLLKL 82
                                      35666666431111132111345555555555555554444 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 5.3e-05
                           DUF2202   3 dsllymreeeklarDvYlelYdrwk....lqiflniakseqthtdavksllek 51 
                                       + l y+   ek+a+DvY+ l +++      +i + +a+ e+ h + ++sl   
  gi|242398590|ref|YP_002994014.1| 120 EILEYLMGTEKIAHDVYEYLAKQTTdeevKAILKWLAEIENGHYERLRSLYAE 172
                                       678899999*********998776422225689999*********99999765 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 ?   -2.4   0.0       2.8     5e+03      25      31 ..     120     126 ..     119     127 .. 0.80
   2 ?   10.1   0.7   0.00035      0.63       7      31 ..     129     153 ..     129     153 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.8
                                       HHHHHHH CS
                            SapB_1  25 eIieaLe 31 
                                       eI+e+L 
  gi|242398590|ref|YP_002994014.1| 120 EILEYLM 126
                                       8999996 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00035
                                       HHHHHHHHHHH-SS--HHHHHHHHH CS
                            SapB_1   7 efvVkeveklLkdNkTeeeIieaLe 31 
                                       e++ ++v+++L +++T ee+++ L+
  gi|242398590|ref|YP_002994014.1| 129 EKIAHDVYEYLAKQTTDEEVKAILK 153
                                       6899*****************9985 PP

>> Rpn9_C  Rpn9 C-terminal helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.5      0.48   8.6e+02      11      21 ..      28      39 ..      20      41 .. 0.68
   2 ?    9.8   0.1   0.00033      0.59      15      24 ..      55      64 ..      55      68 .. 0.94
   3 ?   -3.1   0.0       3.4     6e+03      18      23 ..     145     150 ..     145     151 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.48
                                      HHHHHHH.HHHH CS
                            Rpn9_C 11 KdrLVeW.deqV 21
                                      K+ LV W d++V
  gi|242398590|ref|YP_002994014.1| 28 KELLVYWmDQEV 39
                                      556777866666 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00033
                                      HHHHHHHHHH CS
                            Rpn9_C 15 VeWdeqVtkL 24
                                      V+Wde V+kL
  gi|242398590|ref|YP_002994014.1| 55 VNWDEKVSKL 64
                                      9********9 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 3.4
                                       HHHHHH CS
                            Rpn9_C  18 deqVtk 23 
                                       de+V++
  gi|242398590|ref|YP_002994014.1| 145 DEEVKA 150
                                       89**86 PP

>> HSR  HSR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.2     0.063   1.1e+02      39      85 ..      13      59 ..       9      65 .. 0.89
   2 ?    0.6   0.0      0.35   6.3e+02      39      59 ..      67      87 ..      62      96 .. 0.91
   3 ?    6.3   0.2     0.006        11      34      95 ..     111     172 ..      91     176 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.063
                               HSR 39 kmykesleacrnlvpvqkvvYnvLseLektfslsllealfsevnlke 85
                                       ++k++lea ++l   +  vY + +e+++ +  + l a+ sevn +e
  gi|242398590|ref|YP_002994014.1| 13 SKFKQILEAISKLGTKELLVYWMDQEVKEAEMYHRLYAISSEVNWDE 59
                                      57999999999999999999*99999999999999999999999765 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.35
                               HSR 39 kmykesleacrnlvpvqkvvY 59
                                      +my+++le+ ++l ++ + +Y
  gi|242398590|ref|YP_002994014.1| 67 DMYNDCLEHAETLLKLYRTMY 87
                                      69*******999999999999 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.006
                               HSR  34 slitekmykesleacrnlvpvqkvvYnvLseLektfslsllealfsevnlkeYpdLkeilks 95 
                                       +l+ + +++e+le    ++++ + vY+ L +  ++++ + +     e+   +Y +L++++ +
  gi|242398590|ref|YP_002994014.1| 111 DLVYQGRLQEILEYLMGTEKIAHDVYEYLAKQTTDEEVKAILKWLAEIENGHYERLRSLYAE 172
                                       56777778888888888888888888888776666665554444467788899999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1202  (0.0670422); expected 358.6 (0.02)
Passed bias filter:                      658  (0.0367003); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 1070.76
//
Query:       gi|242398591|ref|YP_002994015.1|  [L=179]
Description: rubrerythrin-related protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.3e-09   37.3   9.9    4.1e-09   36.9   9.9    1.1  1  Rubrerythrin  Rubrerythrin
  ------ inclusion threshold ------
      0.031   14.6   0.6      0.031   14.6   0.6    2.0  2  DUF5638       Family of unknown function (DUF5638)
      0.034   14.1   5.7       0.11   12.4   5.6    2.0  1  Ferritin      Ferritin-like domain
      0.095   12.2   0.3       0.26   10.8   0.2    1.8  1  DNA_gyraseB   DNA gyrase B
       0.16   12.3   1.8       0.35   11.2   0.3    2.1  2  DUF2383       Domain of unknown function (DUF2383)
       0.48   10.2   1.9        1.1    9.0   0.1    2.5  3  DUF4535       Domain of unknown function (DUF4535)
       0.57   10.4   7.3        6.2    7.0   7.3    2.3  1  W2            eIF4-gamma/eIF5/eIF2-epsilon


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 !   36.9   9.9   1.6e-12   4.1e-09       1     134 [.      26     164 ..      26     167 .. 0.87

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 1.6e-12
                                       HHHHHHHHHHHHHHHHHHHHHHCHH..TT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH..B.SSBBS----- CS
                      Rubrerythrin   1 eiLekAiagEssarrlYkelaekak..egypqiaelFeelAeeEreHakilnklleklepele.levkekvreyaea 74 
                                       e+L++ i++E ++ ++Y  l+e  k    +++i ++F +l +e  eHa++l ++++k++p++e + v+   ++ + +
  gi|242398591|ref|YP_002994015.1|  26 ELLSYKIKAEVEEAEVYYRLYELSKemIWNEEIPKIFYQLYQENLEHAEKLLEFYKKIFPGKEpVPVDLPSIKPVLT 102
                                       7999******99888888888877734468*********************************99888888888777 PP

                                       --TTGGHHH..HHHHHHHHHHHHHHCHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHHHHH CS
                      Rubrerythrin  75 kpkflttak..nLeeaiegayaeeeemyrfyeelaekegneeakklfkklaeaEkkHeerlr 134
                                       +++ + + +   Le++ie+ +++e+ + +  e +   ++n+e+++l ++la+ E++ ++rl+
  gi|242398591|ref|YP_002994015.1| 103 EETLKDFLEkaRLEHLIEILMKNEKMAKEICEYVSTTAENPEVRELAQWLAKREEERYNRLK 164
                                       666666554447889****************************************9999887 PP

>> DUF5638  Family of unknown function (DUF5638)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.6   1.2e-05     0.031       5      68 ..       8      71 ..       5      76 .. 0.85
   2 ?   -1.5   0.1       1.2     3e+03       7      33 ..     108     132 ..     102     138 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.2e-05
                                      HHHHHHHHHHHHHHHT------HHHHHHHHHHHHHHHHHHHT--SHHHHHHHHH.HHHHHHHHHH CS
                           DUF5638  5 lekrLseCdeklsalfedkelsekikkqlqeiktyYnesftkakkektkeeive.eYeelvllls 68
                                      + + L++C ekl ++  ++ ls+kik++++e + yY+  ++ +k+ + +eei +  Y+ +  +l+
  gi|242398591|ref|YP_002994015.1|  8 VSRILQKCLEKLPQMTPGELLSYKIKAEVEEAEVYYRL-YELSKEMIWNEEIPKiFYQLYQENLE 71
                                      66789******************************976.899***99999998734666666665 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHHHT------HHHHHHH CS
                           DUF5638   7 krLseCdeklsalfedkelsekikkql 33 
                                       + L++    l++l e   ++ek++k++
  gi|242398591|ref|YP_002994015.1| 108 DFLEKAR--LEHLIEILMKNEKMAKEI 132
                                       4444443..666666666666666666 PP

>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   5.6   4.4e-05      0.11      32     132 ..      57     163 ..      25     172 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.4e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHT..TS.....SHHHHHH...C-SSSS.CS.SHHHHHHHHHHHHHHHHHHHH CS
                          Ferritin  32 glaeffdeqaeeerehadklaerilal..Ggtpv.ltraelee...ieapke.fg.sveevleaalehekkvteslr 100
                                       ++ + f++ ++e +eha+kl+e+ +++  G +pv ++  ++++   +e+ k+  +   +e+l ++l   +k  +++ 
  gi|242398591|ref|YP_002994015.1|  57 EIPKIFYQLYQENLEHAEKLLEFYKKIfpGKEPVpVDLPSIKPvltEETLKDfLEkARLEHLIEILMKNEKMAKEIC 133
                                       56689******************988755776651333344444444444445333556666666666666777777 PP

                                       HHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHH CS
                          Ferritin 101 elielaeeegDpatadfledfleeqeehewel 132
                                       e +  ++e   p  +++++++ + +ee  + l
  gi|242398591|ref|YP_002994015.1| 134 EYVSTTAE--NPEVRELAQWLAKREEERYNRL 163
                                       77777776..5*************99987776 PP

>> DNA_gyraseB  DNA gyrase B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2    0.0001      0.26     120     165 ..      98     143 ..      97     152 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0001
                       DNA_gyraseB 120 KekLgnsevksivekvvseeleafleenkeeakkilekaveaakar 165
                                       K +L+ +  k ++ek+  e+l ++l++n++ ak+i+e +   a++ 
  gi|242398591|ref|YP_002994015.1|  98 KPVLTEETLKDFLEKARLEHLIEILMKNEKMAKEICEYVSTTAENP 143
                                       67899999*****************************999888765 PP

>> DUF2383  Domain of unknown function (DUF2383)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1      0.51   1.3e+03      20      52 ..      46      78 ..      36      84 .. 0.81
   2 ?   11.2   0.3   0.00014      0.35       6      51 ..     119     164 ..     114     175 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.51
                                      HHHHHHT--SHHHHHHHHHHHHHHHHHHHHHHH CS
                           DUF2383 20 ykeaaekvkdpqlktlleriaeereeaaeeLqs 52
                                      y+  +e + ++++ +++ +  +e  e+ae+L +
  gi|242398591|ref|YP_002994015.1| 46 YELSKEMIWNEEIPKIFYQLYQENLEHAEKLLE 78
                                      777888888889999999999999999998876 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00014
                                       HHHHHHHHHHHHHHHHHHHHT--SHHHHHHHHHHHHHHHHHHHHHH CS
                           DUF2383   6 LndLietlkdgeegykeaaekvkdpqlktlleriaeereeaaeeLq 51 
                                       ++ L++++k+++e+++ + + +++p++++l++  a+  ee+  +L+
  gi|242398591|ref|YP_002994015.1| 119 IEILMKNEKMAKEICEYVSTTAENPEVRELAQWLAKREEERYNRLK 164
                                       5568999**************************9999999888886 PP

>> DUF4535  Domain of unknown function (DUF4535)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1   0.00044       1.1      20      44 ..      57      82 ..      54      82 .. 0.94
   2 ?   -2.5   0.0       1.7   4.5e+03      33      42 ..     104     113 ..      93     114 .. 0.60
   3 ?   -3.3   0.1       3.1   7.9e+03      33      43 ..     164     174 ..     162     174 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00044
                           DUF4535 20 eVPnv.kklaakglekakeleeaykK 44
                                      e+P +  +l+++ le a++l+e ykK
  gi|242398591|ref|YP_002994015.1| 57 EIPKIfYQLYQENLEHAEKLLEFYKK 82
                                      79999999*****************9 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.7
                           DUF4535  33 ekakeleeay 42 
                                       e +k+++e+ 
  gi|242398591|ref|YP_002994015.1| 104 ETLKDFLEKA 113
                                       5667777765 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 3.1
                           DUF4535  33 ekakeleeayk 43 
                                       +++k+l  a++
  gi|242398591|ref|YP_002994015.1| 164 KIIKKLSAAKR 174
                                       67788777766 PP

>> W2  eIF4-gamma/eIF5/eIF2-epsilon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   7.3    0.0024       6.2      16      75 ..      51     158 ..      10     160 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0024
                                W2  16 keellkllakilkaLYdeDileEeailkWgek..........................................ksk 50 
                                       +    + ++ki+ +LY+e +   e +l++++k                                             
  gi|242398591|ref|YP_002994015.1|  51 EMIWNEEIPKIFYQLYQENLEHAEKLLEFYKKifpgkepvpvdlpsikpvlteetlkdflekarlehlieilmkN-- 125
                                       33378889************************9999888888888888777666665555544444444443321.. PP

                                W2  51 aekg......kkkvrkkae............pfvewLeeaeee 75 
                                          +      +       e            ++ +wL+  eee
  gi|242398591|ref|YP_002994015.1| 126 ---EkmakeiC-------EyvsttaenpevrELAQWLAKREEE 158
                                       ...01122231.......2333333344444888888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1217  (0.0678789); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1221.01
//
Query:       gi|242398592|ref|YP_002994016.1|  [L=273]
Description: Probable dimethyladenosine transferase [Thermococcus sibiricus MM 739]
Scores for complete 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-57  192.8   0.4    6.8e-57  192.5   0.4    1.1  1  RrnaAD           Ribosomal RNA adenine dimethylase
    9.2e-08   32.7   0.0      2e-07   31.6   0.0    1.6  1  Methyltransf_25  Methyltransferase domain
    6.3e-06   26.8   0.0    1.6e-05   25.5   0.0    1.7  1  Methyltransf_11  Methyltransferase domain
    3.7e-05   23.3   0.0    8.9e-05   22.1   0.0    1.6  2  MTS              Methyltransferase small domain
     0.0015   18.3   0.0     0.0025   17.6   0.0    1.4  1  Methyltransf_31  Methyltransferase domain
     0.0025   17.0   0.1      0.016   14.3   0.0    2.1  2  DREV             DREV methyltransferase
  ------ inclusion threshold ------
      0.026   14.4   0.0      0.039   13.8   0.0    1.4  1  Methyltransf_23  Methyltransferase domain
      0.043   13.6   0.1      0.086   12.7   0.1    1.4  1  PRMT5            PRMT5 arginine-N-methyltransferase
      0.077   12.5   0.0       0.14   11.6   0.0    1.4  1  Methyltransf_4   Putative methyltransferase
       0.08   12.7   0.0       0.17   11.6   0.0    1.5  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
       0.13   11.9   0.0       0.26   11.0   0.0    1.5  1  UPF0020          Putative RNA methylase family UPF0020


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 !  192.5   0.4   4.1e-60   6.8e-57       3     231 ..      15     226 ..      13     266 .. 0.94

  Alignments for each domain:
  == domain 1  score: 192.5 bits;  conditional E-value: 4.1e-60
                                       CCXXGCG--EE--HHHHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTTTCCCEE CS
                            RrnaAD   3 klrksygqnflknkkvineIldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkklskdeklk 79 
                                       k ++++gqnfl+   vi++ ++ ++++++ t+leigpG G+lT eLakra +v ++E+d+r++++l+k+ +  ++++
  gi|242398592|ref|YP_002994016.1|  15 KPNSDLGQNFLIVGDVIKREVERAEIKNSETILEIGPGLGVLTDELAKRAGKVYAIEKDSRIIEILKKEYN-WSNVE 90 
                                       6799****************************************************************777.9**** PP

                                       EE-S-CCGHHHHHHHCTTTCCCCEEEEEEE--TTTHHHHHHHHHHGGGGCEEEEEEEEEHHHHHHHH--TTSTT-SH CS
                            RrnaAD  80 vvhqDflkfetpeevtekdsihqeflvvanlPyeistqlvkqlleesrfglvkmllwlqkefarrllarpgskkrsr 156
                                       +++ D+lk ++pe+           +vv+nlPy+is+++ ++ll+ + f  ++++l+ q efa+r++a+pg+k++sr
  gi|242398592|ref|YP_002994016.1|  91 IMQGDALKIKFPEFN----------KVVSNLPYQISSPITFKLLK-YDF--ERAVLIYQLEFAQRMVAKPGDKNYSR 154
                                       *************55..........9******************6.888..9************************* PP

                                       HHHHHHHHEEEEEEEEC-GGCECS--SSSEEEEEEEE-SS-S--S-HHHHHHHHHHHHCTTTSBCCCHCCCTSTC CS
                            RrnaAD 157 lsvlreaftdvklvakveksifsPppkvdsalvelerkdedlpqkdlkkyesvvrkllnrkrktlstslksllpg 231
                                       lsv+++a ++v lv+ +++ +f P+pkvdsa++ +e+k++d   ++++  e +v++l+  +rk  s++lk  +++
  gi|242398592|ref|YP_002994016.1| 155 LSVMVQAKVNVDLVERIGRGAFYPKPKVDSAVIVMEPKPKD---EQIELNENLVKALFQHRRKLASKALKDSYHM 226
                                       ****************************************9...5888999*****************9988876 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.0   1.2e-10     2e-07       1      72 [.      46     111 ..      46     130 .. 0.88

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 1.2e-10
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEEES CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvssg 72 
                                       +L++G G G lt +lakr   +kv++++ +++ +e+ +++++   + nve++qgda +++f++  f+ vvs+ 
  gi|242398592|ref|YP_002994016.1|  46 ILEIGPGLGVLTDELAKRA--GKVYAIEKDSRIIEILKKEYN---WsNVEIMQGDALKIKFPE--FNKVVSNL 111
                                       8*****************7..9*******************4...449**************8..99999953 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   9.8e-09   1.6e-05       1      67 [.      47     109 ..      47     117 .. 0.93

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 9.8e-09
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEE CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvs 67 
                                       L++G G G l+ +lakr+++v++++ + + +++ k++++ ++  ve++++da k++f++  f  vvs
  gi|242398592|ref|YP_002994016.1|  47 LEIGPGLGVLTDELAKRAGKVYAIEKDSRIIEILKKEYNWSN--VEIMQGDALKIKFPE--FNKVVS 109
                                       89**************************************98..9************99..666666 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   5.4e-08   8.9e-05      31     115 ..      42     121 ..      18     165 .. 0.87
   2 ?   -1.9   0.0       1.3   2.1e+03      56      81 ..     196     221 ..     180     251 .. 0.56

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 5.4e-08
                                       TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEEEEE---S CS
                               MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekkfdlivsNPPf 107
                                        s+++l +G G Gvl+ +lak+  +  v ++++d r +e+ k+ ++ ++  ve+++ d+l+     +f+ +vsN P+
  gi|242398592|ref|YP_002994016.1|  42 NSETILEIGPGLGVLTDELAKRAGK--VYAIEKDSRIIEILKKEYNWSN--VEIMQGDALKIKF-PEFNKVVSNLPY 113
                                       5778*****************9999..9**************9988777..699******9888.8*********99 PP

                                       TTTCHCHH CS
                               MTS 108 hagkatel 115
                                       + ++ ++ 
  gi|242398592|ref|YP_002994016.1| 114 QISSPITF 121
                                       87766555 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.3
                                       .EEEEEESBHHHHHHHHHHHHHTTGC CS
                               MTS  56 aevtlvdvdarAlesakenleankle 81 
                                        +++l ++  +Al   ++ l++++l+
  gi|242398592|ref|YP_002994016.1| 196 EQIELNENLVKALFQHRRKLASKALK 221
                                       23444455555555555555554444 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.6e-06    0.0025       3      83 ..      42     112 ..      40     158 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.6e-06
                   Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlil 79 
                                       +  ++l++G G G lt ela+++   ++v+ i+ + + ie  +++    + +nve  qgd+ +++  + +  f+ ++
  gi|242398592|ref|YP_002994016.1|  42 NSETILEIGPGLGVLTDELAKRA---GKVYAIEKDSRIIEILKKE---YNWSNVEIMQGDALKIK--FPE--FNKVV 108
                                       6679****************886...57*************9995...5688************9..885..***** PP

                   Methyltransf_31  80 snev 83 
                                       sn +
  gi|242398592|ref|YP_002994016.1| 109 SNLP 112
                                       9944 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0     1e-05     0.016      89     138 ..      37      85 ..       3     109 .. 0.77
   2 ?    0.0   0.0      0.22   3.6e+02     116     155 ..     128     168 ..     115     171 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1e-05
                              DREV  89 pasdqedkklldlGaGdGeitkrvaptfeevyatelsetmrdrlkkkkyn 138
                                        a  ++++++l++G G G +t  +a+   +vya e  +++++ lkk +yn
  gi|242398592|ref|YP_002994016.1|  37 RAEIKNSETILEIGPGLGVLTDELAKRAGKVYAIEKDSRIIEILKK-EYN 85 
                                       333456789*******************************998875.565 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.22
                              DREV 116 fee...vyatelsetmrdrlkkkkynvlsalelqetdvkldli 155
                                       fe+   +y  e +++m  +   k+y  ls++  +  +v+ dl+
  gi|242398592|ref|YP_002994016.1| 128 FERavlIYQLEFAQRMVAKPGDKNYSRLSVMVQA--KVNVDLV 168
                                       4445569999****************99988655..6777776 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.4e-05     0.039       9      62 ..      31      98 ..      22     168 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.4e-05
                   Methyltransf_23  9 lsdklerllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae................k 62
                                      +++++er+    + +  +L+iG+G G l+++l+++  +v++++ +++ +ei++                k
  gi|242398592|ref|YP_002994016.1| 31 IKREVERAE--IKNSETILEIGPGLGVLTDELAKRAGKVYAIEKDSRIIEILKkeynwsnveimqgdalK 98
                                      456666665..79999*******************99********9999999866655555444444442 PP

>> PRMT5  PRMT5 arginine-N-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   5.3e-05     0.086      64     136 ..      42     103 ..      25     113 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.3e-05
                                       -EEEEEEES-TTSHHHHHHHHHHHHHCCCEEEEEEEES-HHHHHHHHHHHHHHTTCCGCEEEES-CCCCCHCC CS
                             PRMT5  64 kklvilvvGaGRGplvdralkaleetkvtkvkivavEKnpnavvtLqkkvneekWeekveviksdmrelkaee 136
                                       ++ +il +G G G l d+    ++    +  k++a+EK ++ + +L+k+    +W ++ve+++ d  ++k +e
  gi|242398592|ref|YP_002994016.1|  42 NSETILEIGPGLGVLTDEL---AK----RAGKVYAIEKDSRIIEILKKE---YNW-SNVEIMQGDALKIKFPE 103
                                       3556777777777777653...33....3459**************888...67*.99******988887765 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   8.4e-05      0.14       3      63 ..      44      99 ..      42     112 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.4e-05
                                      EEEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCCH CS
                    Methyltransf_4  3 pvvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgdalkv 63
                                       ++leiG G G ++ +lAk+  ++   +iE+ +++++ + k   +++ +N++i++gdalk+
  gi|242398592|ref|YP_002994016.1| 44 ETILEIGPGLGVLTDELAKRAGKV--YAIEKDSRIIEILKK---EYNWSNVEIMQGDALKI 99
                                      5789***************98865..689999988876544...6799**********775 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0    0.0001      0.17      67     132 ..      36      95 ..      19     104 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0001
                                       HHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES- CS
                              PCMT  67 ellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgD 132
                                       e  e+k+ + +Le+G G G lt    +l ++ g+v +ie+  +++e  k++    + +nv ++ gD
  gi|242398592|ref|YP_002994016.1|  36 ERAEIKNSETILEIGPGLGVLTD---ELAKRAGKVYAIEKDSRIIEILKKEY---NWSNVEIMQGD 95 
                                       55679999***********9986...5667888999*******999888654...45566777766 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00016      0.26      73     133 ..      61     115 ..      30     121 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00016
                                       HHHH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE------ CS
                           UPF0020  73 araelklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnpPYGe 133
                                       a++  k+y++++d+r+++  ++   +++++  +e+ q da k++    e++ +v+n+PY +
  gi|242398592|ref|YP_002994016.1|  61 AKRAGKVYAIEKDSRIIEILKK---EYNWS-NVEIMQGDALKIK--FPEFNKVVSNLPYQI 115
                                       445567999*******999875...56665.5789999**9999..5579*********76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); 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:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1839.48
//
Query:       gi|242398593|ref|YP_002994017.1|  [L=213]
Description: RNA-binding protein [Thermococcus sibiricus MM 739]
Scores for complete 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-68  229.6   0.6    3.1e-68  229.3   0.6    1.1  1  DUF655    Protein of unknown function (DUF655)
    7.8e-05   22.9   0.0    0.00015   21.9   0.0    1.5  1  HHH_6     Helix-hairpin-helix motif
     0.0032   17.7   0.0     0.0072   16.6   0.0    1.6  1  HHH_3     Helix-hairpin-helix motif
  ------ inclusion threshold ------
      0.079   12.8   0.2       0.23   11.3   0.1    1.8  2  UBA_3     Fungal ubiquitin-associated 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 !  229.3   0.6   6.8e-72   3.1e-68       2     180 ..      29     205 ..      28     206 .. 0.97

  Alignments for each domain:
  == domain 1  score: 229.3 bits;  conditional E-value: 6.8e-72
                                       --EEEEEEEETT--TT--S-GGG-.--EEEEEETTT--EEEEEE-TT----TT-EEE-SSS--SSEEEEEEE--GGG CS
                            DUF655   2 eeeaivLDylpeGypddkhrehrd.kpvvqalgereltLlelvplkevdilkldevaigkgksdkivkikreisyed 77 
                                       ee+a+vLDylp+Gy d +h+++r+ +p++q++ge+ +tLle++p++  d+   ++v igkg++dk+  i+++++y++
  gi|242398593|ref|YP_002994017.1|  29 EEYAYVLDYLPTGYLDLEHQNFREkRPIAQVVGEKAFTLLEVIPKT--DLMLYERVFIGKGERDKVLMISKKLNYDN 103
                                       89******************999626*****************986..68899************************ PP

                                       S-HHHHHHHHHHHHHHHHTTHHHHHHHH-----B-SSSBGGGGSTT--HHHHHHHHHHHHHS---SHHHHHHHSTT- CS
                            DUF655  78 LtdvaraeLpdvvekivkekEdrfveffneaepitiRlHaLelLpgvgkklarkileeRerrrFesFedvkkrvkgl 154
                                       Lt++a+aeLp+++e+ivk++E+rfv+ffn a pit RlH+LelLpg+gkk++++ileeR+r +F+sF+d+k+rvkgl
  gi|242398593|ref|YP_002994017.1| 104 LTPTAKAELPYILEEIVKNNEERFVKFFNLAPPITNRLHSLELLPGIGKKHMWDILEERQREPFKSFDDLKHRVKGL 180
                                       ***************************************************************************** PP

                                       --HHHHHHHHHHHHHH-TTSS--SS- CS
                            DUF655 155 kdpaeilverileEiedktekYylFv 180
                                        dp++++++ril+E+e+k ++Y+lFv
  gi|242398593|ref|YP_002994017.1| 181 ADPVKMIAKRILDELENK-DRYRLFV 205
                                       *****************9.99****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 !   21.9   0.0   3.4e-08   0.00015      29      74 ..     144     195 ..     140     210 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 3.4e-08
                             HHH_6  29 LaaikglgeaaaerivaeRekegpfksledlarrvds.......lnkrqleaL 74 
                                       L+ + g+g++ + +i++eR+ ++pfks++dl +rv+        + kr l+ L
  gi|242398593|ref|YP_002994017.1| 144 LELLPGIGKKHMWDILEERQ-REPFKSFDDLKHRVKGladpvkmIAKRILDEL 195
                                       777889*************9.8*************965444444444444444 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.6e-06    0.0072      14      52 ..     142     180 ..     138     184 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.6e-06
                             HHH_3  14 eeLqklpGlgpklAknIvayReknGpfksreeLl.kvkgl 52 
                                         L+ lpG+g+k    I++ R ++ pfks+++L+ +vkgl
  gi|242398593|ref|YP_002994017.1| 142 HSLELLPGIGKKHMWDILEER-QREPFKSFDDLKhRVKGL 180
                                       67999****************.888*********899998 PP

>> UBA_3  Fungal ubiquitin-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   5.2e-05      0.23      22      55 .]      88     121 ..      82     121 .. 0.94
   2 ?   -1.8   0.0      0.64   2.9e+03      45      53 ..     187     195 ..     176     197 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.2e-05
                                       -HHHHHHHHHHS--SS--SS--HHHHHHHHHHT- CS
                             UBA_3  22 ekdkvievLkrLgiksldpednetankileELLk 55 
                                       e+dkv  + k+L++ +l p  +++   ileE+ k
  gi|242398593|ref|YP_002994017.1|  88 ERDKVLMISKKLNYDNLTPTAKAELPYILEEIVK 121
                                       8******************************876 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.64
                                       HHHHHHHHH CS
                             UBA_3  45 tankileEL 53 
                                        a +il+EL
  gi|242398593|ref|YP_002994017.1| 187 IAKRILDEL 195
                                       578999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.52
# Mc/sec: 1237.01
//
Query:       gi|242398594|ref|YP_002994018.1|  [L=120]
Description: DNA-directed RNA polymerase, subunit F [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.8e-07   29.9   2.7    9.1e-07   29.2   2.7    1.3  1  RNA_pol_Rpb4  RNA polymerase Rpb4


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 !   29.2   2.7   5.1e-11   9.1e-07       2     123 .]      12     119 ..       5     119 .. 0.83

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 5.1e-11
                                       E-HHHHHHHHHHHHHHHHCHHHHHTCCCCCHHSHCHTCHHCHHHHHHHHHHHCTHHTTSSHHHHHHHHHHHTTST.. CS
                      RNA_pol_Rpb4   2 LsnsEvllvlkeeleerknkdkkeseddkisekeevkgnlnkilkktleyltnkfsrlkneekfnelvellksfe.. 76 
                                       +s  E++++l ++ ee  +k             e+ ++   ++ + +le+ ++ fs+l  +++++el+e+l      
  gi|242398594|ref|YP_002994018.1|  12 ISIPEAKELLLKRKEEG-AK-------------ENPEEPIFYEARISLEHAER-FSKLS-ADQAKELREKLIGLFew 72 
                                       66677777777444444.33.............34456777788888999999.****9.99999999999854449 PP

                                       STHHHHHHHHHCSTSSHHHHHHHSTTGTTTSTSHHHHHHHHHHHHHT CS
                      RNA_pol_Rpb4  77 LtkaEklqlvnlkPesavelktlieeleerfedeqleeiLdelkeve 123
                                       L++  + ++++++P++  ++k +++++e   + e+ e+iL++l +++
  gi|242398594|ref|YP_002994018.1|  73 LDERTATKIIDIMPKDYFDIKIVFAKEEHIPTKEEAEKILEILDKYR 119
                                       ********************************************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       775  (0.0432261); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); 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: 766.64
//
Query:       gi|242398595|ref|YP_002994019.1|  [L=100]
Description: 50S ribosomal protein L21e [Thermococcus sibiricus MM 739]
Scores for complete 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-33  112.6   0.7    7.1e-33  112.5   0.7    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 !  112.5   0.7   3.9e-37   7.1e-33       2     100 ..       6     100 .]       5     100 .] 0.98

  Alignments for each domain:
  == domain 1  score: 112.5 bits;  conditional E-value: 3.9e-37
                                       --S-STTTT-TTTTS--GGG-SS--SHHHH----TT-EEEE---TT--SS---GGGTT-EEEE..EEEETTEEEEEE CS
                    Ribosomal_L21e   2 knskglrrgtrklfskkfrkkgvpplstylreykkGdkVdikidpsvqkgmphkryhGktgrvynvtkravgvivnk 78 
                                       ++ +  rr+tr ++sk++r+kg+p l+++l+e++ G+kV+i+i+ps+qkgmp +r+hGktg+v  ++kr+ ++iv+ 
  gi|242398595|ref|YP_002994019.1|   6 QKAHTIRRKTRGKLSKSPRRKGLPALTKFLQEFETGQKVHIVIEPSYQKGMPDPRFHGKTGTV--IGKRGDAYIVQL 80 
                                       678999*********************************************************..************ PP

                                       EETTE..EEEEEE-GGGEEE-- CS
                    Ribosomal_L21e  79 kvggkileKriivriehlkksk 100
                                        +g+k   K+ ++++ hl+++k
  gi|242398595|ref|YP_002994019.1|  81 ADGDK--VKTFFIHPVHLRPQK 100
                                       *****..*************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); 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 0.32s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 625.77
//
Query:       gi|242398596|ref|YP_002994020.1|  [L=390]
Description: RNA-binding protein, containing THUMP domain [Thermococcus sibiricus MM 739]
Scores for 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-13   48.5   0.5    9.2e-13   48.5   0.5    2.8  3  THUMP     THUMP domain
  ------ inclusion threshold ------
       0.11   13.1   0.3       0.39   11.3   0.1    2.0  2  P-II      Nitrogen regulatory protein P-II


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 !   48.5   0.5     1e-16   9.2e-13      56     143 ..      58     164 ..      27     165 .. 0.93
   2 ?    2.6   0.1     0.015   1.3e+02      82     108 ..     225     249 ..     215     252 .. 0.79
   3 ?   -1.6   0.2      0.28   2.5e+03      38      55 ..     296     312 ..     268     346 .. 0.54

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 1e-16
                                       E..EEEEESSHHHHHHHHHHHHHHHHHHCT-..EEEEEEEESSSTS...............SSHHHHHHHHHHHHHH CS
                             THUMP  56 v..cevceadledileaakeivkkkfeeeke..tFaVrvkrrgkhf...............eftsreinrevGkaiv 113
                                       +  ce ce  ++++  +a++  +k  + + e  tF V++++++  +               e ++re+nre+Gk++ 
  gi|242398596|ref|YP_002994020.1|  58 PpkCELCEGVFKKVDHLARMCYEKASKMGLEfeTFLVGSRFPKGILekeqkimnefdlkyaEPINRELNREIGKILE 134
                                       156**************************99*************99******************************* PP

                                       CCTT-EE-SSS-SEEEEEEEETTEEEEEEE CS
                             THUMP 114 ektglkVdlenPdivvrveiikdkayisid 143
                                         +++ V+ enPd+v+++e+  ++++++i 
  gi|242398596|ref|YP_002994020.1| 135 IILQKQVNKENPDVVFIIEPYTERIELQIK 164
                                       ****************************96 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.015
                                       CT-EEEEEEEESSSTSSSHHHHHHHHH CS
                             THUMP  82 eketFaVrvkrrgkhfeftsreinrev 108
                                       +   F V+vkr+ k+ +++ +ei+ e+
  gi|242398596|ref|YP_002994020.1| 225 GR-PFVVEVKRPIKR-KINLKEIAEEI 249
                                       33.8***********.99999998887 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.28
                                       HHHHHHHHTSTTECEEEE CS
                             THUMP  38 ellkealekargiqrvip 55 
                                       e + +al++a+ i+ + p
  gi|242398596|ref|YP_002994020.1| 296 ENVVKALKRAE-IHQMTP 312
                                       22222333322.444444 PP

>> P-II  Nitrogen regulatory protein P-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.64   5.7e+03      83      97 ..     222     236 ..     217     239 .. 0.83
   2 ?   11.3   0.1   4.4e-05      0.39       5      53 ..     290     336 ..     286     348 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.64
                                       TTSEEEEEEEESEEE CS
                              P-II  83 iGDGkiFvlpveevi 97 
                                       +G G+ Fv++v++ i
  gi|242398596|ref|YP_002994020.1| 222 LGNGRPFVVEVKRPI 236
                                       6999******99765 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 4.4e-05
                                       EEGGGHHHHHHHHHHTTGGCEEEEEEEEEESTCCEEEECTTEEEEEEEE CS
                              P-II   5 irpekleevkeaLekagvkgltvtevkGrGkqkghtelyrgaeyevell 53 
                                       i  e++e+v +aL++a+++++t  +v+Gr  +   +++ r +e e el+
  gi|242398596|ref|YP_002994020.1| 290 ISREEVENVVKALKRAEIHQMTPRRVLGRRVN--LVRIRRIHEIEGELI 336
                                       567899*********************96443..456666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       751  (0.0418874); expected 358.6 (0.02)
Passed bias filter:                      604  (0.0336884); 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: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.50
# Mc/sec: 2344.50
//
Query:       gi|242398597|ref|YP_002994021.1|  [L=97]
Description: transcriptional regulator consisting of an HTH domain fused to a Zn-ribbon [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0042   16.9   0.4     0.0072   16.2   0.4    1.3  1  HTH_5           Bacterial regulatory protein, arsR family
     0.0097   15.9   0.2      0.014   15.4   0.2    1.2  1  DZR             Double zinc ribbon
  ------ inclusion threshold ------
      0.013   15.5   0.7      0.022   14.7   0.7    1.4  1  ADK_lid         Adenylate kinase, active site lid
      0.022   14.7   0.8      0.027   14.4   0.8    1.2  1  Type2_restr_D3  Type-2 restriction enzyme D3 domain
      0.038   14.2   0.1      0.045   14.0   0.1    1.1  1  UPF0122         Putative helix-turn-helix protein, YlxM / p13
      0.043   13.8   1.1       0.07   13.1   1.0    1.4  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.057   13.2   4.5       0.19   11.5   4.5    1.8  1  Rubredoxin_2    Rubredoxin metal binding domain
      0.085   13.0   2.2       0.16   12.1   2.2    1.4  1  Zn-ribbon_8     Zinc ribbon domain
      0.097   12.6   4.4        2.5    8.1   0.5    2.4  2  zinc_ribbon_4   zinc-ribbon domain
       0.96    9.4   2.8        5.8    6.9   0.4    2.2  2  HalOD2          Halobacterial output domain 2
        1.1    9.2   4.2       0.52   10.3   0.6    2.0  2  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
        1.3    8.9   3.0        2.7    7.9   0.1    2.1  2  zf-C2H2_3       zinc-finger of acetyl-transferase ESCO


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 !   16.2   0.4   4.8e-06    0.0072       4      27 ..       5      28 ..       3      29 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.8e-06
                                      HHHHHHHHTTSSEEHHHHHHHHTS CS
                             HTH_5  4 RlkILklLaegelcvcelaeelgl 27
                                      R kI+klL+e+ ++v+ela +l++
  gi|242398597|ref|YP_002994021.1|  5 RQKIIKLLEERDYSVSELALMLEI 28
                                      789****************99987 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.2   9.6e-06     0.014      12      44 ..      59      92 ..      52      92 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 9.6e-06
                               DZR 12 arfCseCgtklkavaa.edrCpsCgekvdpearf 44
                                         C++Cg   k++ + + rCp+C+++  +e rf
  gi|242398597|ref|YP_002994021.1| 59 PAQCKKCGFIFKPEIKvPGRCPKCKSEWIEEPRF 92
                                      578*******9987779********997777665 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 ?   14.7   0.7   1.5e-05     0.022       4      30 ..      62      85 ..      60      88 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.5e-05
                                      -TTT--EEETTTB--SSTTB-TTT--. CS
                           ADK_lid  4 CpkCGrsYhvvfnpPkveglCDkCGep 30
                                      C+kCG ++       kv+g C kC ++
  gi|242398597|ref|YP_002994021.1| 62 CKKCGFIFK---PEIKVPGRCPKCKSE 85
                                      *********...336*********987 PP

>> Type2_restr_D3  Type-2 restriction enzyme D3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.8   1.8e-05     0.027      13      60 ..       3      47 ..       1      53 [. 0.90

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.8e-05
                    Type2_restr_D3 13 tRRtiilkylleskkrrsleeikayLklagleEdveTIkDDiqglini 60
                                      tRR  i+k l+e     s+ e+   L++ g + + + I DDi+++ n+
  gi|242398597|ref|YP_002994021.1|  3 TRRQKIIKLLEERD--YSVSELALMLEIRG-KGSKKIILDDIKAIANV 47
                                      8*********8888..9999*******999.88999*******99996 PP

>> UPF0122  Putative helix-turn-helix protein, YlxM / p13 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1     3e-05     0.045      19      74 ..       3      60 ..       1      70 [. 0.81

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3e-05
                           UPF0122 19 TekqanylelyyadDlSlsEiAeefnv....srqavydnikrtekllekyEekLklleky 74
                                      T +q + ++l  + D+S+sE+A   ++    s++ + d ik + +++++ E k+ l++  
  gi|242398597|ref|YP_002994021.1|  3 TRRQ-KIIKLLEERDYSVSELALMLEIrgkgSKKIILDDIKAIANVVKR-EGKILLIQPA 60
                                      5555.6899**************999976667999*******9999876.7777776654 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   1.0   4.7e-05      0.07      71      96 ..      60      86 ..      53      91 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.7e-05
                                      EEETTTS-EEECHHH.HHS-TTTSSS- CS
                              HypA 71 vrCreCgkefeleek.alrCpkCgsad 96
                                      ++C++Cg  f+ e k   rCpkC+s+ 
  gi|242398597|ref|YP_002994021.1| 60 AQCKKCGFIFKPEIKvPGRCPKCKSEW 86
                                      68*********77655679*****975 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   4.5   0.00013      0.19       2      22 ..      61      84 ..      61      86 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00013
                      Rubredoxin_2  2 vCsqCGfes...akwfGrCpsCgs 22
                                      +C++CGf +   +k+ GrCp C+s
  gi|242398597|ref|YP_002994021.1| 61 QCKKCGFIFkpeIKVPGRCPKCKS 84
                                      7******973337*********96 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   2.2   0.00011      0.16       7      34 ..      61      84 ..      61      88 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00011
                       Zn-ribbon_8  7 rCeeCghefevlqsisdaplta.CPeCgs 34
                                      +C++Cg  f +  +      +  CP+C+s
  gi|242398597|ref|YP_002994021.1| 61 QCKKCGFIFKPEIK-----VPGrCPKCKS 84
                                      6*********9886.....4444****98 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.5    0.0017       2.5      26      36 .]      60      70 ..      57      70 .. 0.86
   2 ?    5.9   0.2     0.008        12      27      34 ..      78      85 ..      74      87 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0017
                     zinc_ribbon_4 26 vrCskCghvFr 36
                                      ++C+kCg +F+
  gi|242398597|ref|YP_002994021.1| 60 AQCKKCGFIFK 70
                                      69*****9995 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.008
                     zinc_ribbon_4 27 rCskCghv 34
                                      rC+kC+  
  gi|242398597|ref|YP_002994021.1| 78 RCPKCKSE 85
                                      56666655 PP

>> HalOD2  Halobacterial output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1     0.084   1.3e+02       2      10 ..      59      67 ..      58      70 .. 0.73
   2 ?    6.9   0.4    0.0039       5.8       2      12 ..      76      86 ..      75      89 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.084
                            HalOD2  2 PekCseCsl 10
                                      P +C +C++
  gi|242398597|ref|YP_002994021.1| 59 PAQCKKCGF 67
                                      778888876 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0039
                            HalOD2  2 PekCseCsldW 12
                                      P +C++C+ +W
  gi|242398597|ref|YP_002994021.1| 76 PGRCPKCKSEW 86
                                      99********* PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.2      0.67     1e+03       4       9 ..      61      66 ..      55      67 .. 0.78
   2 ?   10.3   0.6   0.00035      0.52      22      29 ..      79      86 ..      76      87 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.67
                    PhnA_Zn_Ribbon  4 kCplCa 9 
                                      +C +C+
  gi|242398597|ref|YP_002994021.1| 61 QCKKCG 66
                                      788884 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00035
                    PhnA_Zn_Ribbon 22 CpeCahEw 29
                                      Cp+C++Ew
  gi|242398597|ref|YP_002994021.1| 79 CPKCKSEW 86
                                      77777777 PP

>> zf-C2H2_3  zinc-finger of acetyl-transferase ESCO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.1    0.0018       2.7      14      25 ..      60      71 ..      55      75 .. 0.80
   2 ?    1.6   0.5      0.17   2.5e+02      15      20 ..      78      83 ..      70      88 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0018
                         zf-C2H2_3 14 sqCkeCgMvYnp 25
                                       qCk+Cg ++ p
  gi|242398597|ref|YP_002994021.1| 60 AQCKKCGFIFKP 71
                                      68*****98866 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.17
                         zf-C2H2_3 15 qCkeCg 20
                                      +C++C+
  gi|242398597|ref|YP_002994021.1| 78 RCPKCK 83
                                      5****7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       852  (0.0475208); expected 358.6 (0.02)
Passed bias filter:                      693  (0.0386525); expected 358.6 (0.02)
Passed Vit filter:                       101  (0.00563333); 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 0.33s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 580.71
//
Query:       gi|242398598|ref|YP_002994022.1|  [L=444]
Description: Glutamyl-tRNA(Gln) amidotransferase subunit D [Thermococcus sibiricus MM 739]
Scores for complete 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-60  203.0   0.0    5.6e-60  202.2   0.0    1.4  1  Asparaginase    Asparaginase, N-terminal
    2.9e-37  127.4   0.0    5.6e-37  126.4   0.0    1.5  1  Asparaginase_C  Glutaminase/Asparaginase C-terminal domain
    1.9e-18   65.5   1.3    4.3e-18   64.4   1.3    1.6  1  GatD_N          GatD N-terminal domain
  ------ inclusion threshold ------
      0.047   13.7   0.1       0.09   12.8   0.1    1.4  1  MeMO_Hyd_G      Methane monooxygenase, hydrolase gamma chain
       0.08   12.3   0.0       0.18   11.1   0.0    1.5  1  DUF1460         Protein of unknown function (DUF1460)


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 !  202.2   0.0   1.6e-63   5.6e-60       1     188 [.      99     293 ..      99     296 .. 0.97

  Alignments for each domain:
  == domain 1  score: 202.2 bits;  conditional E-value: 1.6e-63
                                       EEEEEEEESGGGEEECTTS--CCEES-HHHHHCCTTTCCCCSEEEEEEEEEE-GGG--HHHHHHHHHHHHHHCCT.- CS
                      Asparaginase   1 kvlvlatGGTiasekdesggalapalsaeellealpelekiaeleseqlanidSsnmtpadwlklaeaieealee.y 76 
                                       +v +++tGGTias+ d+++ga++ a++aeel +a+pe+ +ia+++ + l+ni S++m+p+ w+++a+++++al++  
  gi|242398598|ref|YP_002994022.1|  99 NVTIIGTGGTIASKIDYKTGAVHAAFTAEELAKAVPEIFEIANITPRLLFNIMSEDMKPEYWKRMAHEVARALNSgE 175
                                       699**********************************************************************666* PP

                                       SEEEEE--STTHHHHHHHHHHHEES.SSEEEEE--SS-TTSTT-SHHHHHHHHHHHHHCGGTTSECEEEETTE.... CS
                      Asparaginase  77 dgfVvlhGTDTlaytAsaLslmlknldkpvvltGsqrplselrsDgpeNlldAllvaasseriagvlvvfngk.... 149
                                       dg+++ hGTDT+ y+A+aLs+ml++l+kpv+++Gsqr++++++sD+++Nl+ + ++a ++  + +v++v++g+    
  gi|242398598|ref|YP_002994022.1| 176 DGVIIGHGTDTMGYSAAALSFMLRDLGKPVIFVGSQRSSDRPSSDAAMNLICSTRMAVEN--FGEVAIVMHGEtgdt 250
                                       **********************************************************87..*************** PP

                                       ...EEETTTEEE-BSSSSS-EEETTT--SEEE.ETTEEEESEE CS
                      Asparaginase 150 ...llranrvtKvhtssldaFespnlgplaev.egskvkvnke 188
                                           +r+++v+K+hts++daF+s+n  p+a++ ++++v++ +e
  gi|242398598|ref|YP_002994022.1| 251 yclAHRGTKVRKMHTSRRDAFRSINDVPIAKIwHDGRVEYLRE 293
                                       ******************************9978888888765 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 !  126.4   0.0   1.6e-40   5.6e-37       1     114 []     312     425 ..     312     425 .. 0.99

  Alignments for each domain:
  == domain 1  score: 126.4 bits;  conditional E-value: 1.6e-40
                                       -EEEEE--TT--HHHHHHHHHTT--EEEEEEBTTTB--HHHHHHHHHHHTTT-EEEEEESSSBS-----H.....HH CS
                    Asparaginase_C   1 rVvvlklhpgmdtkvlkallkkgakGvvlegtGvGnlpsallealkeakargivvvatsqcpsgsvsnseyeagkel 77 
                                       +V+++k++pg+++++++ +++kg+kG+v+egtG G++p+++++++++a+++g ++++tsqc++g+v+ ++y++g++l
  gi|242398598|ref|YP_002994022.1| 312 KVALIKVYPGITGEIIDFFVDKGYKGIVIEGTGLGHAPNEIIPTMERAVEEGAIICMTSQCLYGRVNLNVYSTGRKL 388
                                       7**************************************************************************** PP

                                       HHHTEEE-TT--HHHHHHHHHHHCTT---HHHHHHHH CS
                    Asparaginase_C  78 erlgvisaddmtpeaarikLmlllgkgldpaevrklf 114
                                        ++gvi ++dm pe+a++kLm++lg++++ +ev+k++
  gi|242398598|ref|YP_002994022.1| 389 LKAGVIPCEDMLPETAYVKLMWVLGHTQNLEEVKKMM 425
                                       ***********************************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 !   64.4   1.3   1.2e-21   4.3e-18       2      55 .]      19      76 ..      18      76 .. 0.95

  Alignments for each domain:
  == domain 1  score: 64.4 bits;  conditional E-value: 1.2e-21
                                      -TT-EEEEE-SS....-EEEEEE----TTS-SSEEEEEETTS-EEEEE-TT-.---EE CS
                            GatD_N  2 evGDlikvekkg....reyeGilmPrselsdddiivlKLdnGYNiGikieeiekiell 55
                                      ++GD+++v +k+    ++++GilmP +els+++++++KLdnGYNiG+ i++i +i++l
  gi|242398598|ref|YP_002994022.1| 19 NIGDYVEVIEKEngvaVTHRGILMPPYELSKGETLTIKLDNGYNIGVLIDQIAEIRVL 76
                                      79*****9888879999**************************************997 PP

>> MeMO_Hyd_G  Methane monooxygenase, hydrolase gamma chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   2.5e-05      0.09       7      64 ..     261     318 ..     256     321 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.5e-05
                                       HHHHHHHHHT--SHHHHHHHHHHHHHHHSSTT-S-STTTTTH.HHHHHHHHHHHHHHHH CS
                        MeMO_Hyd_G   7 rsewlakiaelktlekaaallkdfrkdhtspfrtsyeldlds.lwieakleeklavlka 64 
                                       r+    + +++ ++++   + k +    +  +r++y++  ds +w++ kleek+a++k 
  gi|242398598|ref|YP_002994022.1| 261 RKMHTSRRDAFRSINDV-PIAKIWHDGRVEYLREDYRKRSDSeVWVDDKLEEKVALIKV 318
                                       55555666666666654.344556677777789****9999659************995 PP

>> DUF1460  Protein of unknown function (DUF1460)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   5.1e-05      0.18     152     177 ..      17      42 ..       8      46 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 5.1e-05
                                       TS-TT-EEEEEEEES-EEEEEEEEEE CS
                           DUF1460 152 rlktGdiiaivtektgLdVsHvGlvi 177
                                        l+ Gd+++++ +++g+ V+H G+++
  gi|242398598|ref|YP_002994022.1|  17 GLNIGDYVEVIEKENGVAVTHRGILM 42 
                                       5788*******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (444 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); 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: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 3139.95
//
Query:       gi|242398599|ref|YP_002994023.1|  [L=629]
Description: Glutamyl-tRNA(Gln) amidotransferase subunit E [Thermococcus sibiricus MM 739]
Scores for complete 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-65  219.8   0.0    8.5e-65  218.9   0.0    1.6  1  GatB_N          GatB/GatE catalytic domain
    2.8e-26   92.2   8.5    2.8e-26   92.2   8.5    2.6  3  GatB_Yqey       GatB domain
    9.8e-17   61.0   2.2    2.2e-16   59.8   0.2    2.7  3  GAD             GAD domain
    6.9e-09   35.9   1.3    2.7e-08   34.0   1.3    2.2  1  YqeY            Yqey-like protein
     0.0064   17.0   0.8        6.8    7.3   0.0    3.6  3  DUF4473         Domain of unknown function (DUF4473)
  ------ inclusion threshold ------
       0.13   11.6   2.9      0.099   12.0   0.5    2.1  3  DUF1133         Protein of unknown function (DUF1133)
       0.14   12.1   3.1        1.3    9.0   0.5    3.4  3  DUF1967         Domain of unknown function (DUF1967)
       0.14   11.9   0.3        5.3    6.8   0.0    2.3  2  RNase_Zc3h12a   Zc3h12a-like Ribonuclease NYN domain
        0.2   11.6   1.8        1.4    8.8   0.9    2.7  3  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
        0.3   11.3   2.5         29    4.9   0.0    3.7  4  KicB            MukF winged-helix 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 !  218.9   0.0   4.7e-68   8.5e-65       2     271 ..      13     444 ..      12     446 .. 0.96

  Alignments for each domain:
  == domain 1  score: 218.9 bits;  conditional E-value: 4.7e-68
                                       EEEEEEEEEB--SB-SSSSSBSSSSCE.........S.TTSS--TTTTTS........................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx.........x.xxxxxxxxxxxx........................... RF
                            GatB_N   2 viGlEiHaqlktksKlFssasteeege.........e.pnsevsevdlal........................... 41 
                                       ++GlEiH ql+tk KlFs+++++ +++         + + se++e+d a+                           
  gi|242398599|ref|YP_002994023.1|  13 KVGLEIHRQLDTK-KLFSAVPSQLHDNvdftferrlRpTMSELGEIDQAAleefkrgrafvyegnykytdlvyvdee 88 
                                       89*********96.****99977333355666777744899*******99************************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+ +++ea+++a++++  ln+   +e++f+RK+++++++ +g+Q+t+    ++ ++G++++   +v+i +i+l
  gi|242398599|ref|YP_002994023.1|  89 P---PHmPDEEALKVALQITYLLNAIPVDEVHFMRKIVIDGSNVSGFQRTA----IVgMNGKVDTpWGSVGIPTICL 158
                                       8...99889******************************************....666******9899********* PP

                                       EE---EEEEEETTEEEEETTSTT-EEEEEEE-STB-SHHHHHHHHHHHHHHHHHHTSB--SGGGTTEEEEEEEEECT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            GatB_N 116 EeDaaksvheekeeslvdlnRaGvpLiEivtepdlrspeearavveklrellralgvsdgnmeeGslRcDvNvSvre 192
                                       EeDa++ +++ +++ +++l+R+G+pLiEi+t+pd+++pe+a+ v++ +++ lra++++++++  G++R+D+NvS++ 
  gi|242398599|ref|YP_002994023.1| 159 EEDACRIIEQGERKAIYRLDRLGIPLIEIATTPDIHHPEQAKIVAKFIGDALRATRKVKRGL--GTIRQDLNVSIKG 233
                                       *********9999*************************************************..************4 PP

                                       SETTSSS.--EEEEEE-SHHHHHHHHHHHHHHHHHHH........................................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................................ RF
                            GatB_N 193 eekgeeegtrvEiKnlnslksiekaieyeierqiell........................................ 229
                                              g+r+EiK++++l++i  +ie e++rq++ll                                        
  gi|242398599|ref|YP_002994023.1| 234 -------GARIEIKGVQELDMIPVIIEREVQRQLNLLkikeelqkrgvkeedlkeefydvtdifsgtgskiiartlk 303
                                       .......59******************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                            GatB_N 230 ............................................................................. 229
                                                                                                                    
  gi|242398599|ref|YP_002994023.1| 304 kggkilaiklpkfrgligfeiqpgrrlgtemadrakkyvkgifhidelpnygisqeevdkvverlnlgefdafvlva 380
                                       ***************************************************************************** PP

                                       .........................-EEEEEETTTTEEEEECC--.--...-EEE-TTS--EE--HHH CS
                                       .........................xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                            GatB_N 230 .........................qeTrkfdedkgetvslRske.eaedYryfpepdlppleiseel 271
                                                                +eTr++ +d g+t+++R+ + +a   r++pe+d+pp+ +seel
  gi|242398599|ref|YP_002994023.1| 381 aeeeiakkalreilqrareaisgvpEETRRALPD-GNTQYMRPLPgKA---RMYPETDIPPIFMSEEL 444
                                       **********************************.**********555...************99986 PP

>> GatB_Yqey  GatB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.21   3.7e+02      42      69 ..     370     397 ..     350     412 .. 0.71
   2 ?   -3.5   0.1       4.9   8.7e+03      61      84 ..     444     468 ..     440     478 .. 0.55
   3 !   92.2   8.5   1.5e-29   2.8e-26       2     148 .]     485     624 ..     484     624 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.21
                                       HHHHHHHHHHHHTTSSGHHHHHHHHHHH CS
                         GatB_Yqey  42 peqlaellkliaegkIskkiakevleel 69 
                                         ++  ++   ae++I+kk+ +e+l+  
  gi|242398599|ref|YP_002994023.1| 370 LGEFDAFVLVAAEEEIAKKALREILQRA 397
                                       5566677777788888888888888765 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 4.9
                                       HHHHHHHHHHHH.TXXHHHHHHHCT CS
                         GatB_Yqey  61 iakevleellee.gkspeeiieekg 84 
                                         ke+le l e  + +++  ++e++
  gi|242398599|ref|YP_002994023.1| 444 LKKEILENLPEYpQAKVNRYVKEYK 468
                                       4455555555555555555555554 PP

  == domain 3  score: 92.2 bits;  conditional E-value: 1.5e-29
                                       HHHHHHHHSS.HHHHHHHHHTCHHHHHHHHTXXTTCSSTTHHHHHHHHHHHHTTSSGHHHHHHHHHHHHHH.TXXHH CS
                         GatB_Yqey   2 ffeevvkegadaklaanwllnellgelnkegleieelkltpeqlaellkliaegkIskkiakevleellee.gkspe 77 
                                       +fee+++ g ++ ++a+ +l+ +l+ l+ke ++ ++  +t+ ++++ +kl++e+kI+k++ +e+++el+ + +k++ 
  gi|242398599|ref|YP_002994023.1| 485 LFEELIAMGIKP-SLAASILVVVLKGLKKE-VSTDN--ITETHIKDAFKLLHENKIAKEALEEIFKELALHpEKTAL 557
                                       799**9999555.55566777788888887.67777..*******************************999***** PP

                                       HHHHHCTXXXXXXSSXHHHHHHHHHHTXHHHHHHHTTXXTTSTHHHHHHHHHTTSSXSXHHHHHHHHHHHS CS
                         GatB_Yqey  78 eiieekgLkqisdeeeleklveeviaenpkavedyksgkekalkflvGqvMkktkGkadpklvnellkekL 148
                                       ++ eekgL+ +s+ +e+ek++ee+++en   ++ +k++ + a+++l+G+ M k++Gkad+klvn+l+++k+
  gi|242398599|ref|YP_002994023.1| 558 QVAEEKGLTLLSE-GEVEKIIEEIVREN---IDVVKEKGMGAMGMLMGRAMAKLRGKADGKLVNQLVRKKI 624
                                       ************8.**************...*************************************997 PP

>> GAD  GAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.8   0.2   1.2e-19   2.2e-16       2      95 .]     299     390 ..     298     390 .. 0.97
   2 ?   -1.5   0.1       1.6   2.9e+03      61      80 ..     568     587 ..     539     595 .. 0.81
   3 ?   -2.4   0.1       3.1   5.6e+03      43      50 ..     602     609 ..     571     628 .. 0.46

  Alignments for each domain:
  == domain 1  score: 59.8 bits;  conditional E-value: 1.2e-19
                                       HHHHHSTEEEEEEEETTG-TTTSHHHHHHHHHHHHHTTHSHCEEEEESSGGEETTTCCC.S-HHHHHHHHHHCT--T CS
                               GAD   2 sealksggsvkalrvpggaaklsrkeideleefakelgakglawikvegegltgpiakf.lteeevkklleavgaee 77 
                                       + +lk+gg++ a+++p+ +++l++ ei++++++++e++++++ +  v+g +++++++ + +++eev k++e+++  e
  gi|242398599|ref|YP_002994023.1| 299 ARTLKKGGKILAIKLPK-FRGLIGFEIQPGRRLGTEMADRAKKY--VKGIFHIDELPNYgISQEEVDKVVERLNLGE 372
                                       6789*************.8*************************..99***************************** PP

                                       TEEEEEEEEEHHHHHHHH CS
                               GAD  78 gDillfvAdkkktvnkal 95 
                                        D++++vA ++++++kal
  gi|242398599|ref|YP_002994023.1| 373 FDAFVLVAAEEEIAKKAL 390
                                       ****************97 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.6
                                       S-HHHHHHHHHHCT--TTEE CS
                               GAD  61 lteeevkklleavgaeegDi 80 
                                       l+e ev+k++e +  e+ D+
  gi|242398599|ref|YP_002994023.1| 568 LSEGEVEKIIEEIVRENIDV 587
                                       68888888888877776666 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 3.1
                                       CEEEEESS CS
                               GAD  43 lawikveg 50 
                                       +a +k++g
  gi|242398599|ref|YP_002994023.1| 602 RAMAKLRG 609
                                       33333333 PP

>> YqeY  Yqey-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   1.3   1.5e-11   2.7e-08      91     142 ..     568     623 ..     504     624 .. 0.86

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 1.5e-11
                                       --HHHHHHHHHHHHHH....TT--BGGGHHHHHHHHHHHHTTTS-HHHHHHHHHHH CS
                              YqeY  91 lseeeiealvkeaiae....vgaesmkdmGkvmkalkpkvkGkaDgkkvsalvkek 142
                                       lse e+e++++e++ e    v++++m +mG +m+ +++k++GkaDgk v++lv++k
  gi|242398599|ref|YP_002994023.1| 568 LSEGEVEKIIEEIVREnidvVKEKGMGAMGMLMGRAMAKLRGKADGKLVNQLVRKK 623
                                       666666666666555422227999*****************************997 PP

>> DUF4473  Domain of unknown function (DUF4473)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       2.9   5.3e+03       7      19 ..     265     277 ..     263     279 .. 0.87
   2 !    7.3   0.0    0.0038       6.8       9      70 ..     349     411 ..     347     414 .. 0.84
   3 ?    5.7   0.2     0.012        21       4      43 ..     482     522 ..     480     549 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.9
                           DUF4473   7 akaeLvaaGlsek 19 
                                       +k+eL++ G++e+
  gi|242398599|ref|YP_002994023.1| 265 IKEELQKRGVKEE 277
                                       799******9985 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0038
                           DUF4473   9 aeLvaaGlsekaadglv...kiaekfksefakakgdkeaakkafeklkaevdafiktqseeDqaa 70 
                                       +eL   G+s++ +d++v   +++e   + f  ++  +e akka+ ++++ + + i  ++ee ++a
  gi|242398599|ref|YP_002994023.1| 349 DELPNYGISQEEVDKVVerlNLGEF--DAFVLVAAEEEIAKKALREILQRAREAISGVPEETRRA 411
                                       689999**********933345655..778888**********************9999986665 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.012
                           DUF4473   4 aeeakaeLvaaGlsekaadglvkiaek.fksefakakgdke 43 
                                       ++e  +eL+a+G+++  a+ ++ +  k  k+e ++ +  + 
  gi|242398599|ref|YP_002994023.1| 482 RDELFEELIAMGIKPSLAASILVVVLKgLKKEVSTDNITET 522
                                       68999**************9987766645555555544444 PP

>> DUF1133  Protein of unknown function (DUF1133)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       2.5   4.4e+03     115     142 ..     244     271 ..     205     276 .. 0.74
   2 ?   -3.5   0.0       3.2   5.8e+03      51      70 ..     381     400 ..     375     406 .. 0.74
   3 ?   12.0   0.5   5.5e-05     0.099      50     157 ..     514     625 ..     509     629 .] 0.70

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.5
                           DUF1133 115 ysglisvlvdryelrgkskrkmaeelna 142
                                          +i v+ +r   r    +k+ eel++
  gi|242398599|ref|YP_002994023.1| 244 ELDMIPVIIEREVQRQLNLLKIKEELQK 271
                                       4467888889988888888888888886 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3.2
                           DUF1133  51 askkltktavnealrrlkka 70 
                                       a + ++k a+ e+l+r + a
  gi|242398599|ref|YP_002994023.1| 381 AEEEIAKKALREILQRAREA 400
                                       56789999999999998765 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 5.5e-05
                           DUF1133  50 laskkltktavnealrrlkkagiekpeleaflreilnskqksglafcsdee.alkidrvisevlve.ysglisvlvd 124
                                       ++++ +t t +++a++ l+   i k  le +++e+    +k+ l    ++  +l  ++ + +++ e  +  i+v+++
  gi|242398599|ref|YP_002994023.1| 514 VSTDNITETHIKDAFKLLHENKIAKEALEEIFKELALHPEKTALQVAEEKGlTLLSEGEVEKIIEEiVRENIDVVKE 590
                                       67789*************************************99876554323444666666666656666777776 PP

                           DUF1133 125 ryelr.gk.skrkmaeelnakhpewslstcerrid 157
                                       +  +  g+   r ma++  ++  +   +  +++i+
  gi|242398599|ref|YP_002994023.1| 591 KGMGAmGMlMGRAMAKLRGKADGKLVNQLVRKKIQ 625
                                       65443133134566666666666666666666665 PP

>> DUF1967  Domain of unknown function (DUF1967)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.5   0.00075       1.3      37      59 ..     256     278 ..     253     279 .. 0.92
   2 ?    0.3   0.0      0.38   6.9e+02      11      34 ..     353     376 ..     346     381 .. 0.80
   3 ?   -0.5   0.0      0.66   1.2e+03      43      56 ..     482     495 ..     458     498 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00075
                                       HHHHHHHTTHHHHHHTTT--TT- CS
                           DUF1967  37 farrLkklGvedaLrkaGakeGd 59 
                                        +r+L+ l + ++L+k+G+ke d
  gi|242398599|ref|YP_002994023.1| 256 VQRQLNLLKIKEELQKRGVKEED 278
                                       69*******************98 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.38
                                       EEEEE-HHHHHHHTTEEE-TGGGH CS
                           DUF1967  11 vfvVeGekierlvkqtnfeneeav 34 
                                        + ++ e+++++v++ n+ + +a+
  gi|242398599|ref|YP_002994023.1| 353 NYGISQEEVDKVVERLNLGEFDAF 376
                                       48999************9988876 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.66
                                       HTTHHHHHHTTT-- CS
                           DUF1967  43 klGvedaLrkaGak 56 
                                       + ++ ++L ++G+k
  gi|242398599|ref|YP_002994023.1| 482 RDELFEELIAMGIK 495
                                       33455666666666 PP

>> RNase_Zc3h12a  Zc3h12a-like Ribonuclease NYN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0     0.003       5.3       3      13 ..     120     130 ..     118     158 .. 0.83
   2 ?    2.9   0.1     0.047        85      43     129 ..     504     591 ..     499     596 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.003
                     RNase_Zc3h12a   3 rtivIDGsnVa 13 
                                       r ivIDGsnV+
  gi|242398599|ref|YP_002994023.1| 120 RKIVIDGSNVS 130
                                       99********9 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.047
                     RNase_Zc3h12a  43 tvfvpkfrkealkkekvsdkea...leeLekenlivltpskyldgkksvsyddrlilelAeekdGvivsndnyrdll 116
                                       +v+++ ++ke  +++++++ ++   ++ L+++++ + + ++ +  k+   + ++++l++Aeek   ++s  + + ++
  gi|242398599|ref|YP_002994023.1| 504 VVVLKGLKKEV-STDNITETHIkdaFKLLHENKIAKEALEEIF--KELALHPEKTALQVAEEKGLTLLSEGEVEKII 577
                                       55666665555.6666666554111444444444433333333..47777899************************ PP

                     RNase_Zc3h12a 117 sen.kelkdiveer 129
                                       +e   e +d+v+e+
  gi|242398599|ref|YP_002994023.1| 578 EEIvRENIDVVKEK 591
                                       99659999999986 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 ?   -1.1   0.0       0.9   1.6e+03      55     108 ..     271     324 ..     240     345 .. 0.71
   2 ?   -1.1   0.0      0.95   1.7e+03      97     146 ..     501     521 ..     486     537 .. 0.60
   3 ?    8.8   0.9    0.0008       1.4      77     136 ..     536     605 ..     507     607 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.9
                                       TTEEEES-HHHHHTT--EEEE---HHHHHHHHHHHCCC--TT-EEEE---SEET CS
                    NAD_Gly3P_dh_N  55 enlvattdlaealkgadiivlvvPsqalrevlkklkgllkkkailvsliKGiee 108
                                       +  v ++dl+e   +++ i+    s++++++lkk  ++l+ k +    + G+e 
  gi|242398599|ref|YP_002994023.1| 271 KRGVKEEDLKEEFYDVTDIFSGTGSKIIARTLKKGGKILAIKLPKFRGLIGFEI 324
                                       344567899999999999999999999999999988887766666655556555 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.95
                                       -EEEE---SEET.TTEEHHHHHHHHH-S--EEEEESS--HHHHHTT--EE CS
                    NAD_Gly3P_dh_N  97 ailvsliKGieegtlkllsevieeelkeekvavlsGpslAeEvakgkpta 146
                                        ilv ++KG+++                             Ev  +++t+
  gi|242398599|ref|YP_002994023.1| 501 SILVVVLKGLKK-----------------------------EVSTDNITE 521
                                       456666667633.............................333333333 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0008
                                       --HHHHHHHHHHHCCC--TT-EEEE---SE....ET.TTEEHHHHHHHHH-S--......EEEEESS--H CS
                    NAD_Gly3P_dh_N  77 vPsqalrevlkklkgllkkkailvsliKGi....eegtlkllsevieeelkeek......vavlsGpslA 136
                                       + ++al+e++k+l+ + +k a  v   KG+    e +  k+++e+++e+++  k      +++l+G  +A
  gi|242398599|ref|YP_002994023.1| 536 IAKEALEEIFKELALHPEKTALQVAEEKGLtllsEGEVEKIIEEIVRENIDVVKekgmgaMGMLMGRAMA 605
                                       77899*************************9997778889999999999887666788889999998887 PP

>> KicB  MukF winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.016        29      91     110 ..     167     186 ..     164     189 .. 0.87
   2 ?    1.0   0.0      0.26   4.6e+02      37      71 ..     266     300 ..     255     304 .. 0.81
   3 ?   -3.1   0.0       4.8   8.5e+03      51      76 ..     373     401 ..     356     404 .. 0.55
   4 ?    2.4   0.0     0.097   1.7e+02      31      59 ..     505     533 ..     492     545 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.016
                                       SSSTTSEEEEE-HHHHHHHH CS
                              KicB  91 eltegesiyrltplgigitd 110
                                       e+ e ++iyrl +lgi +++
  gi|242398599|ref|YP_002994023.1| 167 EQGERKAIYRLDRLGIPLIE 186
                                       678999**********8876 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.26
                                       HHT--SSSEEHHHHHHHHHHHHHHTT--STTHHHH CS
                              KicB  37 neerldeelseaelvdafrlvskafeqseetlavr 71 
                                       +ee ++  ++e +l++ f+ v++ f  +   +  r
  gi|242398599|ref|YP_002994023.1| 266 KEELQKRGVKEEDLKEEFYDVTDIFSGTGSKIIAR 300
                                       5666777899***************9888777766 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 4.8
                                       HHHHHHHHHHTT--STT...HHHHHHHHH CS
                              KicB  51 vdafrlvskafeqseet...lavrannai 76 
                                        daf lv+ + e ++++   + +ra +ai
  gi|242398599|ref|YP_002994023.1| 373 FDAFVLVAAEEEIAKKAlreILQRAREAI 401
                                       47777776655555443111567777777 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.097
                                       HHHHHHHHT--SSSEEHHHHHHHHHHHHH CS
                              KicB  31 laiavlneerldeelseaelvdafrlvsk 59 
                                       + ++ l++e ++++++e++++daf+l+ +
  gi|242398599|ref|YP_002994023.1| 505 VVLKGLKKEVSTDNITETHIKDAFKLLHE 533
                                       45677899999*************98764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (629 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       923  (0.0514808); expected 358.6 (0.02)
Passed bias filter:                      600  (0.0334653); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.70u 0.29s 00:00:00.99 Elapsed: 00:00:00.45
# Mc/sec: 4225.10
//
Query:       gi|242398600|ref|YP_002994024.1|  [L=207]
Description: hypothetical protein TSIB_0610 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score 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   12.3   2.7       0.11   11.8   2.7    1.1  1  ABC2_membrane_2  ABC-2 family transporter protein
       0.98    9.6   5.4        3.5    7.8   0.2    2.6  3  YtpI             YtpI-like 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 ?   11.8   2.7   1.2e-05      0.11     118     175 ..     135     193 ..     134     197 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.2e-05
                   ABC2_membrane_2 118 eillgKfigglaigla.iavallatvllalaiilalgivlaledllllvvasvlllllv 175
                                       +i+ gK+   ++  l+ +a+ +  ++l+++a  la+++v+++++l ++v++++++++++
  gi|242398600|ref|YP_002994024.1| 135 KIVEGKLTKKSTFELVlTAIEVALGLLTFVAGYLAFENVIDISQLSNIVAFVLFFIFAL 193
                                       7999*************************************************988865 PP

>> YtpI  YtpI-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1      0.63   5.6e+03      16      34 ..      12      30 ..       8      41 .. 0.75
   2 ?    7.8   0.2   0.00039       3.5      52      80 ..     142     170 ..     136     176 .. 0.89
   3 ?    3.8   0.2     0.007        62      56      79 ..     178     202 ..     173     205 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.63
                              YtpI 16 vkafrtkdplekkllsaka 34
                                      +k++++k ++ekk   ak 
  gi|242398600|ref|YP_002994024.1| 12 RKSRKEKPEREKKTKPAKK 30
                                      5778888888888877775 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00039
                              YtpI  52 llestvalvvgavflvlGlanlfaGiray 80 
                                         +st++lv  a+ ++lGl  ++aG+ a+
  gi|242398600|ref|YP_002994024.1| 142 TKKSTFELVLTAIEVALGLLTFVAGYLAF 170
                                       5789*********************9876 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.007
                              YtpI  56 tvalvvgav.flvlGlanlfaGira 79 
                                       +++ +v++v f +++l ++  G+r+
  gi|242398600|ref|YP_002994024.1| 178 QLSNIVAFVlFFIFALQSIKKGYRK 202
                                       5566666542899**********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1472  (0.0821016); expected 358.6 (0.02)
Passed bias filter:                      750  (0.0418317); 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: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 1316.80
//
Query:       gi|242398601|ref|YP_002994025.1|  [L=216]
Description: hypothetical protein TSIB_0611 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score 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   11.8   0.5      0.078   11.3   0.5    1.2  1  DUF2070   Predicted membrane protein (DUF2070)


Domain annotation for each model (and alignments):
>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.5   4.3e-06     0.078     124     179 ..     124     179 ..     111     191 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.3e-06
                           DUF2070 124 desllkavlpaliqpllailllvlyfspesfllllllslifalavylfivvvdrpl 179
                                        +++++  +++++++l + +++ l+f+ +s+  +ll+s+++a++v+l+  ++d+p+
  gi|242398601|ref|YP_002994025.1| 124 PKKHKRFPVVTFLISLGIGAVAPLFFEAKSYWDYLLSSILIAALVLLVTLLIDYPF 179
                                       56788899999999999999999*******************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.52
# Mc/sec: 1260.02
//
Query:       gi|242398602|ref|YP_002994026.1|  [L=407]
Description: 3-hydroxy-3-methylglutaryl-coenzyme A reductase [Thermococcus sibiricus MM 739]
Scores for complete 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-138  461.9   2.0   1.6e-138  461.7   2.0    1.0  1  HMG-CoA_red  Hydroxymethylglutaryl-coenzyme A reductase


Domain annotation for each model (and alignments):
>> HMG-CoA_red  Hydroxymethylglutaryl-coenzyme A reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  461.7   2.0  9.1e-143  1.6e-138       2     367 .]      31     407 .]      30     407 .] 0.99

  Alignments for each domain:
  == domain 1  score: 461.7 bits;  conditional E-value: 9.1e-143
                                       HHHHHHHHHHS-HHHHHHHTT----.HHHHHHHSSS---------EEEEEEEETTE....EEEEEE---STTHHHHH CS
                       HMG-CoA_red   2 veeRrklleelteeeleelkeesld.eevadkmiEnviGyvqlPlGvagpllingk....eylvPmAteEgslvAsa 73 
                                        e Rrk+le+  + +l++++++s+d ++v++k+iEn+iG+vq+P+Gvagpl+ing+    e+++P+At+Eg+lvAs+
  gi|242398602|ref|YP_002994026.1|  31 TEVRRKALEKRFNISLKNIGHYSIDpSQVIGKNIENMIGAVQIPMGVAGPLKINGEyakgEFYIPLATTEGALVASV 107
                                       689************************************************************************** PP

                                       HHHHHHHHHTT-B.EEEE----EEEEEEEE.--S-HHHHHHHHHTHHHHHHHHHHCSHH.CCT-EEEEEEEEE-SSE CS
                       HMG-CoA_red  74 srgakainesgGvkttvlkdgmtraqvvllesvedaaelkkwiekkeeleelanaaest.srggglkdievvlagrl 149
                                       +rg++ ++++gGvkttv++d+mtra+++ ++++++a+e+ +w+  +e+le l+++a s+ +r+g+l+++++++ g++
  gi|242398602|ref|YP_002994026.1| 108 NRGCSTLTAAGGVKTTVIDDKMTRAPLLKCPDARRAREVAQWV--EENLEYLQEKAVSKvTRHGKLRRVKPHIIGNN 182
                                       *******************************************..9******99888878***************** PP

                                       EEEEEEEE-TTC--HHHHHHHHHHHHHHHHHHHTSEEEEEEE-S--GGGEEEEEEEEEHHHH..-SSTTHHHHHHHH CS
                       HMG-CoA_red 150 vvlrlkvdtgDAmGaNmvnkateaaaelieeefgeeellsilsNlctdkkasainaiegrgksvvaeatigeevvek 226
                                       ++lr++++tgDAmG+Nmv++a e+++++iee+f + ++l++++Nlc dkk++a+n+i+grgk+v+aea++++e+ve+
  gi|242398602|ref|YP_002994026.1| 183 LYLRFEFETGDAMGMNMVTIASEEIMKVIEEHFADVKYLALSGNLCVDKKPNAMNFINGRGKTVIAEAVVPREIVER 259
                                       ***************************************************************************** PP

                                       HHHHHHHHHH-HHHH....HHHHHHH.......HHHHHHHHHHTT--HHHHHHHHHHHTTSEEETTTEEEEEEEEE. CS
                       HMG-CoA_red 227 ilkasaealvdlnra.n.igtankGiggfnahaaNgiaAvflAtGqDlaaveesshaiaaleevedgdlygsvtlPs 301
                                        lk+++e ++++n + n +g+a++G+ gfnah+ N++ A+flAtGqD a++ e+sh+i++ e +++gdly+s+t+Ps
  gi|242398602|ref|YP_002994026.1| 260 KLKTTPELIAEVNYRkNlVGSAQAGSYGFNAHFGNIVGAIFLATGQDEAQITEGSHGITLAEVTPEGDLYISITMPS 336
                                       ***************************************************************************** PP

                                       ----SBSHHHHH-HHHHHHHHTT---HH........HHHHHHHHHHHHHHHHHHHHHT-----HHHHHHHH CS
                       HMG-CoA_red 302 leVGtvGGgtklppqaellkllgvkgak.....nakeLaeiiaavgLAqelsalrALaaeglqkgHmklhr 367
                                       le+GtvGGgt++p+q+e+l+++gv+g +     nak++aei+a+++LA+els+l+A+aa++l+k+H++l+r
  gi|242398602|ref|YP_002994026.1| 337 LEIGTVGGGTRVPTQREALSIMGVAGGGnppgtNAKKFAEIVASAVLAGELSLLAAIAAKHLAKAHKELGR 407
                                       ********************************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       693  (0.0386525); expected 358.6 (0.02)
Passed bias filter:                      579  (0.032294); 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: 0.68u 0.30s 00:00:00.98 Elapsed: 00:00:00.51
# Mc/sec: 2400.49
//
Query:       gi|242398603|ref|YP_002994027.1|  [L=252]
Description: Cell division inhibitor minD like protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.4e-18   67.2   0.0    2.3e-18   66.5   0.0    1.4  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    3.6e-13   49.8   0.0    7.1e-13   48.8   0.0    1.4  1  AAA_31       AAA domain
    1.2e-08   34.7   0.0    4.6e-07   29.6   0.0    2.2  1  ParA         NUBPL iron-transfer P-loop NTPase
    2.1e-07   30.7   0.0    2.4e-05   23.9   0.0    2.6  2  CBP_BcsQ     Cellulose biosynthesis protein BcsQ
    5.7e-06   26.0   0.3      0.068   12.6   0.0    2.1  2  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
    1.7e-05   24.2   0.1    2.8e-05   23.5   0.1    1.6  1  ArsA_ATPase  Anion-transporting ATPase
    0.00032   20.4   0.1    0.00055   19.6   0.1    1.3  1  SRP54        SRP54-type protein, GTPase domain
    0.00032   20.3   0.2       0.38   10.3   0.1    2.3  2  GTP_EFTU     Elongation factor Tu GTP binding domain
     0.0041   16.6   0.0     0.0062   16.0   0.0    1.3  1  KTI12        Chromatin associated protein KTI12
     0.0099   15.7   1.4      0.045   13.6   0.1    2.1  2  AAA_26       AAA domain
  ------ inclusion threshold ------
      0.016   15.1   0.0      0.025   14.5   0.0    1.3  1  APS_kinase   Adenylylsulphate kinase
       0.02   14.2   0.0      0.098   11.9   0.0    1.9  2  Zeta_toxin   Zeta toxin
      0.024   14.4   0.0      0.039   13.7   0.0    1.3  1  PRK          Phosphoribulokinase / Uridine kinase family
      0.026   13.8   0.4      0.084   12.1   0.0    1.8  2  DUF1611      Domain of unknown function (DUF1611_C) P-loop do
       0.22   10.6   0.2       0.43    9.6   0.2    1.4  1  T2SSE        Type II/IV secretion system protein


Domain annotation for each model (and alignments):
>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.5   0.0     2e-21   2.3e-18       1     128 []       3     221 ..       3     221 .. 0.88

  Alignments for each domain:
  == domain 1  score: 66.5 bits;  conditional E-value: 2e-21
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH....................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................... RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep....................... 54 
                                       ++i+ + GG+GKTt++anL +++ ++ +r+l++D D   +nl   + len   +                       
  gi|242398603|ref|YP_002994027.1|   3 VIIVTGRGGAGKTTTTANLSVYFGQKDYRTLAIDGDLFLPNLGFHFALENVSYTlhsilknpdvdpewaiykhekta 79 
                                       689***************************************98666666666688899999*************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|242398603|ref|YP_002994027.1|  80 vnvmpgstrlqdvvgispkrlreivelmkykfpvlfldsptgipfdtlptfevadyqiivveverspihsfeamven 156
                                       **************************************************************988866655554443 PP

                                       CCHCCCHHHHHHCHCHHHH......EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHHTS- CS
                                       xxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  55 dlkrllellealgkkkall....lkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeavaeapargep 127
                                        + + l++                + +gvvln+v ++     ++  +ee++q  g+pv+g+ip+de+v+e+++ g p
  gi|242398603|ref|YP_002994027.1| 157 EINK-LRM----------IgeeyGLKIGVVLNKVMES--GDIIEHIVEEIEQNVGLPVIGIIPFDENVPESINVGIP 220
                                       3333.222..........24444567********999..888888999999999*****************998887 PP

                                       H CS
                                       x RF
                              CbiA 128 v 128
                                       +
  gi|242398603|ref|YP_002994027.1| 221 I 221
                                       6 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.8   0.0     6e-16   7.1e-13       6     163 ..       5     156 ..       2     168 .. 0.87

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 6e-16
                            AAA_31   6 ianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQa.nattglgiekneiektlyevli.eeknikeaiiktkven 80 
                                       i+  +GG GKTTt+ nl++ + ++++++L +D D    n+ +++    ++++ tl+++l   +++ + ai+k++ + 
  gi|242398603|ref|YP_002994027.1|   5 IVTGRGGAGKTTTTANLSVYFGQKDYRTLAIDGDLFLpNLGFHFA--LENVSYTLHSILKnPDVDPEWAIYKHEKTA 79 
                                       66779*****************************86427777665..688999*****965999**********999 PP

                            AAA_31  81 ldlipssidLaeaeielvelekkeeilkellekvkdeYDyiiiDcpPsLglltenaLvasdsviipvqaeayaleGl 157
                                       ++++p+s+ L+++    v+++   ++l+e++e +k ++ + ++D p  +   t   + ++d+ ii+v+ e   ++ +
  gi|242398603|ref|YP_002994027.1|  80 VNVMPGSTRLQDV----VGISP--KRLREIVELMKYKFPVLFLDSPTGIPFDTLPTFEVADYQIIVVEVERSPIHSF 150
                                       9*********986....45555..5678*******************************************999999 PP

                            AAA_31 158 eqllkt 163
                                       e+++++
  gi|242398603|ref|YP_002994027.1| 151 EAMVEN 156
                                       999853 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 !   29.6   0.0   3.8e-10   4.6e-07       6     239 ..       3     235 ..       2     241 .. 0.71

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 3.8e-10
                              ParA   6 iavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgvee.........ekpeqsekkliPvea.kg 72 
                                       ++++ g+GG GK+t+++nl++ + +k++++  +D D++ p++   + +e+         ++p      + P  a ++
  gi|242398603|ref|YP_002994027.1|   3 VIIVTGRGGAGKTTTTANLSVYFGQKDYRTLAIDGDLFLPNLGFHFALENvsytlhsilKNPD-----VDPEWAiYK 74 
                                       57899******************************************9996555543333333.....444443444 PP

                              ParA  73 ikvmSigflle.sedeavvwrGpmkskaikqllkdvewgelDyLiiDlPPGtgDeqltvaqklplagaviVt...tp 145
                                        +   ++++   ++ + vv  +p+  + i +l+k   + +  +L++D P G    +l  ++  + + +++V    +p
  gi|242398603|ref|YP_002994027.1|  75 HEKTAVNVMPGsTRLQDVVGISPKRLREIVELMK---Y-KFPVLFLDSPTGIPFDTLPTFEVADYQ-IIVVEverSP 146
                                       4444444443312345788888877777777665...4.4789********999999999988754.4444311245 PP

                              ParA 146 qevaladvkkaiemfkkvkvkv...lGvveNmsgfvcpkcgekteifgkgggeklaeelgvpllgeipldpeireas 219
                                        +   a v+ +i+ ++ +  +    +Gvv N       k  e+ +i  ++ +e++ +++g+p++g ip+d+++ e++
  gi|242398603|ref|YP_002994027.1| 147 IHSFEAMVENEINKLRMIGEEYglkIGVVLN-------KVMESGDII-EHIVEEIEQNVGLPVIGIIPFDENVPESI 215
                                       4555556666666555554443111455554.......444445555.5678999********************** PP

                              ParA 220 degkplvlkepeseaakale 239
                                       + g p++  +p+s+aa a+ 
  gi|242398603|ref|YP_002994027.1| 216 NVGIPILGYKPKSDAALAFY 235
                                       *******9999999887775 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0     2e-08   2.4e-05       1     149 [.       1     144 [.       1     152 [. 0.78
   2 ?    3.6   0.0     0.033        39     196     224 ..     204     232 ..     182     244 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 2e-08
                          CBP_BcsQ   1 mkvlalqGvRGGvGttsllaaLawalhelgesvlviDlsp.dnlLrlhFnvdieqregwaraeldgapwrqaaleya 76 
                                       m+v+ ++G RGG+G+t+ +a L+  + + +++ l+iD       L +hF ++  + +     +  + + + a+++  
  gi|242398603|ref|YP_002994027.1|   1 MPVIIVTG-RGGAGKTTTTANLSVYFGQKDYRTLAIDGDLfLPNLGFHFALENVSYTLHSILKNPDVDPEWAIYKHE 76 
                                       99999999.***************************95431344788888874443333333334444455555554 PP

                          CBP_BcsQ  77 p.gldllPfGelnveekenlqqlaekaeallaalkelkeqyrwillDlpagasaltrellaladlvllvvepda 149
                                       +  ++++P G+++ ++   +     ++++l + ++ +k+++  ++lD p+g    t  + ++ad ++ vve + 
  gi|242398603|ref|YP_002994027.1|  77 KtAVNVMP-GSTRLQDVVGI-----SPKRLREIVELMKYKFPVLFLDSPTGIPFDTLPTFEVADYQIIVVEVER 144
                                       41567777.99988888755.....6788999999999*******************************99875 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.033
                          CBP_BcsQ 196 vihrDealaEalaakqPlgeyrpdslaae 224
                                       +i  De ++E++ +  P+  y+p+s aa 
  gi|242398603|ref|YP_002994027.1| 204 IIPFDENVPESINVGIPILGYKPKSDAAL 232
                                       5777*********************9985 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 !   11.5   0.0   0.00012      0.14       3      34 ..       4      35 ..       2      40 .. 0.85
   2 !   12.6   0.0   5.7e-05     0.068     140     239 ..     132     236 ..     125     247 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00012
                         Fer4_NifH  3 iaiyGkGGiGksttsqnlsaalaemgkkvliv 34
                                      i + G+GG Gk+tt++nls  + ++  + l +
  gi|242398603|ref|YP_002994027.1|  4 IIVTGRGGAGKTTTTANLSVYFGQKDYRTLAI 35
                                      6789***************9999888887766 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 5.7e-05
                         Fer4_NifH 140 kaqevyivtsgelmalyaann.iakgiekyaksgg...vrlgGliinsrkvddereliekfaee....lgtkvlevv 208
                                        a++ +iv++ e   +++    + + i+k +  g+   +++ G++ n  kv +  ++ie+++ee    +g++v+ ++
  gi|242398603|ref|YP_002994027.1| 132 VADYQIIVVEVERSPIHSFEAmVENEINKLRMIGEeygLKI-GVVLN--KVMESGDIIEHIVEEieqnVGLPVIGII 205
                                       67888888888888777654413455666555544311555.89999..57887777777665411117899***** PP

                         Fer4_NifH 209 Prdeivrkaelrkktvieyapeseqakeyre 239
                                       P de+v ++      +  y+p+s+ a  + e
  gi|242398603|ref|YP_002994027.1| 206 PFDENVPESINVGIPILGYKPKSDAALAFYE 236
                                       ******9887777778888888887766665 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.1   2.3e-08   2.8e-05       2      84 ..       2      83 ..       1     197 [. 0.79

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 2.3e-08
                                      EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-ST.TTHHHHHHTS--BSS-EEETSSEEEEE--HHHHHHHHHCC CS
                       ArsA_ATPase  2 kvilvgGKGGVGKttvsaatavklsekgkkvllistDP.AhslsDsfdqklgkeptkvkeNLsavEidpeveleeakqe 79
                                       vi+v+G+GG GKtt  a ++v+  +k++++l i  D   ++l   f   l++    ++  L   ++dpe ++++ ++ 
  gi|242398603|ref|YP_002994027.1|  2 PVIIVTGRGGAGKTTTTANLSVYFGQKDYRTLAIDGDLfLPNLGFHFA--LENVSYTLHSILKNPDVDPEWAIYKHEKT 78
                                      689*****************************9998842456654443..34555556666666666666666666666 PP

                                      HHGGG CS
                       ArsA_ATPase 80 vqkee 84
                                      + + +
  gi|242398603|ref|YP_002994027.1| 79 AVNVM 83
                                      55555 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1   4.6e-07   0.00055       3      40 ..       3      40 ..       1      43 [. 0.94

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 4.6e-07
                                      EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTS CS
                             SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvllvaaDtf 40
                                      vi++ G  GaGKTtt+a L+ ++ ++ +++l +  D f
  gi|242398603|ref|YP_002994027.1|  3 VIIVTGRGGAGKTTTTANLSVYFGQKDYRTLAIDGDLF 40
                                      899***************************99999988 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 !    8.0   0.0    0.0015       1.8       6      35 ..       4      33 ..       1      45 [. 0.83
   2 !   10.3   0.1   0.00032      0.38      88     150 ..     127     197 ..     102     239 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0015
                                      EEEEESTTSSHHHHHHHHHHHTTSSCHHHH CS
                          GTP_EFTU  6 igiighvDhGKtTLtdrLlyktgaiskkge 35
                                      i++ g   +GKtT+t +L  + g+ + ++ 
  gi|242398603|ref|YP_002994027.1|  4 IIVTGRGGAGKTTTTANLSVYFGQKDYRTL 33
                                      77889999*************999887665 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00032
                                       HHHHHT-SEEEEEEETTTB........STHHHHHHHHHHHHTTTEEEEEEESCGSTHHHHHHHHHHHHHHH CS
                          GTP_EFTU  88 irglrvlDgavlvvdaveG........vepqteevlrlalkegvpiivfiNKmDrlkaelkeiveevkqkl 150
                                         + +v+D+ ++vv++++         ve+  +++  +  ++g++i v++NK+ + ++ +++ivee++q++
  gi|242398603|ref|YP_002994027.1| 127 LPTFEVADYQIIVVEVERSpihsfeamVENEINKLRMIGEEYGLKIGVVLNKVMESGDIIEHIVEEIEQNV 197
                                       556789***********8888888888999999999999****************************9987 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   5.2e-06    0.0062       1      40 [.       1      40 [.       1      56 [. 0.92

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 5.2e-06
                                      E.EEEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHH CS
                             KTI12  1 MpLvvltGlPssGKstrakeLakaleeekrsvvviddesl 40
                                      Mp +++tG   +GK+t +++L+ ++ +++++   id + +
  gi|242398603|ref|YP_002994027.1|  1 MPVIIVTGRGGAGKTTTTANLSVYFGQKDYRTLAIDGDLF 40
                                      *****************************99999987765 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.28   3.4e+02       4      31 ..       4      31 ..       2      33 .. 0.79
   2 !   13.6   0.1   3.7e-05     0.045     160     193 ..     172     210 ..     147     213 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.28
                            AAA_26  4 fvtgtdtgvGKTvvslgLvralkrkgvk 31
                                      ++++ + g+GKT++++ L  ++ +k+++
  gi|242398603|ref|YP_002994027.1|  4 IIVTGRGGAGKTTTTANLSVYFGQKDYR 31
                                      566777899******9998888777765 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 3.7e-05
                            AAA_26 160 lGvilNkvrnp.....envetlekksgipvlGvvPylpd 193
                                       +Gv+lNkv +        ve++e++ g+pv+G++P +++
  gi|242398603|ref|YP_002994027.1| 172 IGVVLNKVMESgdiieHIVEEIEQNVGLPVIGIIPFDEN 210
                                       6******988865654499****************9986 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   2.1e-05     0.025       4      40 ..       3      39 ..       1      52 [. 0.90

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.1e-05
                                      EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHH CS
                        APS_kinase  4 vvwltGlsgsGKstianalekkLvekgisvylLdGdn 40
                                      v+ +tG  g+GK+t + +l+ +  +k +++  +dGd 
  gi|242398603|ref|YP_002994027.1|  3 VIIVTGRGGAGKTTTTANLSVYFGQKDYRTLAIDGDL 39
                                      7899*******************************96 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   8.2e-05     0.098      18      54 ..       3      40 ..       2      43 .. 0.88
   2 ?   -0.5   0.0      0.52   6.2e+02      94     119 ..     170     195 ..     135     201 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.2e-05
                        Zeta_toxin 18 lillgGqpGAGKselaellkdele.rqgnvvrldpDdl 54
                                      +i++ G  GAGK+++ + l  +++ ++ + + +d+D +
  gi|242398603|ref|YP_002994027.1|  3 VIIVTGRGGAGKTTTTANLSVYFGqKDYRTLAIDGDLF 40
                                      689****************9999877788899999976 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.52
                        Zeta_toxin  94 ngyniivegtlrspdvvkklaealkk 119
                                        ++ +++   ++s d +++++e++++
  gi|242398603|ref|YP_002994027.1| 170 LKIGVVLNKVMESGDIIEHIVEEIEQ 195
                                       58899999999999999999988765 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   3.3e-05     0.039       1      38 [.       3      40 ..       3      51 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.3e-05
                               PRK  1 vIgvagsSGaGkttvarklekifgrekvkaaeiegdsf 38
                                      vI v+g  GaGktt++++l   fg++  ++  i+gd f
  gi|242398603|ref|YP_002994027.1|  3 VIIVTGRGGAGKTTTTANLSVYFGQKDYRTLAIDGDLF 40
                                      799*********************99999888888766 PP

>> DUF1611  Domain of unknown function (DUF1611_C) P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1       0.6   7.1e+02      14      37 ..       3      25 ..       1      35 [. 0.70
   2 ?   12.1   0.0     7e-05     0.084     117     192 ..     133     205 ..     119     211 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.6
                           DUF1611 14 rvlvvGTdcavGKrttaleleeal 37
                                      +++v G +  +GK tt+ +l   +
  gi|242398603|ref|YP_002994027.1|  3 VIIVTGRGG-AGKTTTTANLSVYF 25
                                      566666654.6******9997655 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 7e-05
                           DUF1611 117 PdalvLchrpgrkhirglpeialppleeeieliealaakkkvvgislNtknlseeeakealeeleeelglpvvdpv 192
                                       +d+ +++ + +r+ i+ ++ +  +++++   + e++  k   +g+ lN+   s + +++++ee+e+++glpv  ++
  gi|242398603|ref|YP_002994027.1| 133 ADYQIIVVEVERSPIHSFEAMVENEINKLRMIGEEYGLK---IGVVLNKVMESGDIIEHIVEEIEQNVGLPVIGII 205
                                       68889999999999***9997777777766666665554...7**********999****************9876 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 ?    9.6   0.2   0.00036      0.43     131     159 ..       3      31 ..       2      37 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00036
                             T2SSE 131 lilvsGgTgsGKttllyallkeinksder 159
                                       +i+v+G  g GKtt++  l  ++ ++d r
  gi|242398603|ref|YP_002994027.1|   3 VIIVTGRGGAGKTTTTANLSVYFGQKDYR 31 
                                       59*************98887777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      565  (0.0315132); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); 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: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 1658.60
//
Query:       gi|242398604|ref|YP_002994028.1|  [L=82]
Description: RNA-binding protein, containing TRAM domain [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-15   55.3   2.3      6e-15   55.0   2.3    1.1  1  TRAM      TRAM domain
     0.0085   15.8   0.6      0.047   13.4   0.2    2.2  2  Hexapep   Bacterial transferase hexapeptide (six repeats)
  ------ inclusion threshold ------
       0.11   12.4   0.1        7.2    6.5   0.0    2.0  2  DUF5035   Domain of unknown function (DUF5035)
       0.12   12.5   0.0       0.14   12.3   0.0    1.3  1  Sec-ASP3  Accessory Sec secretory system ASP3


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 !   55.0   2.3   1.3e-18     6e-15       2      62 .]      25      81 ..      24      81 .. 0.97

  Alignments for each domain:
  == domain 1  score: 55.0 bits;  conditional E-value: 1.3e-18
                                      XXXXXEEEEEEEEE-.TTSEEEEEET.TEEEEETT--T..TEEEEEEEEEE-SSEEEEEEE CS
                              TRAM  2 syvGstqeVlveglsksegegiGrtdngkvvfvpgdlpgIGdfVeVkItkvkrqyLrGell 62
                                      ++vG+ + V++e l+ + g+gi+r++ g+vvfvp+++   Gd+Ve+ I  vk ++++Gel+
  gi|242398604|ref|YP_002994028.1| 25 VKVGERYKVKIEALG-KGGDGIARIK-GFVVFVPNTKV--GDEVEIVINSVKQKFAFGELI 81
                                      68*************.**********.*********99..*******************85 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.11   4.9e+02      18      25 ..      23      30 ..      22      37 .. 0.80
   2 !   13.4   0.2   1.1e-05     0.047       9      28 ..      47      66 ..      32      71 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.11
                                      TTEEE-TT CS
                           Hexapep 18 gnVkIGdn 25
                                      ++Vk+G++
  gi|242398604|ref|YP_002994028.1| 23 PPVKVGER 30
                                      78999975 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 1.1e-05
                                      EE-TTEEEETTEEE-TTEEE CS
                           Hexapep  9 lIgpfaviggnVkIGdnvkI 28
                                       I  f+v+ +n+k+Gd v I
  gi|242398604|ref|YP_002994028.1| 47 RIKGFVVFVPNTKVGDEVEI 66
                                      5777**************98 PP

>> DUF5035  Domain of unknown function (DUF5035)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0    0.0016       7.2      26      58 ..      10      42 ..       2      54 .. 0.75
   2 ?    4.4   0.0    0.0068        30      38      51 ..      55      68 ..      51      72 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0016
                           DUF5035 26 skeedyankmeelPalkvgdevevlllldGnGa 58
                                      + ++   ++  +lP++kvg++ +v +   G G 
  gi|242398604|ref|YP_002994028.1| 10 VGKRKMDRRAPKLPPVKVGERYKVKIEALGKGG 42
                                      555566678889********9999988777765 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0068
                           DUF5035 38 lPalkvgdevevll 51
                                      +P  kvgdeve+++
  gi|242398604|ref|YP_002994028.1| 55 VPNTKVGDEVEIVI 68
                                      7999*******986 PP

>> Sec-ASP3  Accessory Sec secretory system ASP3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   3.1e-05      0.14      39      62 ..      14      37 ..       9      79 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.1e-05
                          Sec-ASP3 39 qsqriepsLPllkegeeYklevna 62
                                      +++r+ p+LP +k ge+Yk++++a
  gi|242398604|ref|YP_002994028.1| 14 KMDRRAPKLPPVKVGERYKVKIEA 37
                                      57899****************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 578.39
//
Query:       gi|242398605|ref|YP_002994029.1|  [L=352]
Description: Probable L-threonine 3-dehydrogenase [Thermococcus sibiricus MM 739]
Scores for complete 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  124.9   2.5    1.6e-36  124.5   1.6    1.6  2  ADH_N         Alcohol dehydrogenase GroES-like domain
    2.1e-31  108.6   0.0    4.7e-31  107.5   0.0    1.6  1  ADH_zinc_N    Zinc-binding dehydrogenase
    3.1e-10   39.9   0.1      5e-10   39.2   0.1    1.3  1  Glu_dehyd_C   Glucose dehydrogenase C-terminus
    1.5e-09   39.0   0.0    2.9e-09   38.1   0.0    1.5  1  ADH_zinc_N_2  Zinc-binding dehydrogenase
  ------ inclusion threshold ------
      0.011   15.6   0.0      0.023   14.6   0.0    1.6  1  ADH_N_2       N-terminal domain of oxidoreductase
      0.071   12.4   2.1       0.16   11.2   2.1    1.6  1  AlaDh_PNT_C   Alanine dehydrogenase/PNT, C-terminal domain
      0.097   12.6   0.4        1.3    8.9   0.0    2.5  2  UPF0146       Uncharacterised protein family (UPF0146)


Domain annotation for each model (and alignments):
>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.5   1.6   6.1e-40   1.6e-36       2     108 ..      35     143 ..      34     144 .. 0.97
   2 ?   -3.4   0.0       3.5     9e+03      54      64 ..     215     225 ..     207     229 .. 0.81

  Alignments for each domain:
  == domain 1  score: 124.5 bits;  conditional E-value: 6.1e-40
                                       TEEEEEEEEEEE-HHHHHHHTTS..TTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE-SSSHHHHTT CS
                             ADH_N   2 gevlikvkaagiCgsDlhilkgg..kelevklplilGHEivGeveevgpevkklkvGdrVvvepliscgeCaaCkeg 76 
                                       gevlikv a++iCg+Dlhi++ +  ++++ k+p+i+GHE++Gev+evgp+v++lk+Gd + +e +i cgeC++C++g
  gi|242398605|ref|YP_002994029.1|  35 GEVLIKVLATSICGTDLHIYEWNewAQSRIKPPQIMGHEVAGEVVEVGPGVHNLKIGDYISAETHIVCGECYQCRTG 111
                                       89*******************99888999************************************************ PP

                                       -GGG-TTBEETTTSS-SSSBSEEEECGGGEEE CS
                             ADH_N  77 eenlCeeakllgvsldGgfaeyvvvpekklvk 108
                                       ++++C++ k++gv+ dG faey +vp+++++k
  gi|242398605|ref|YP_002994029.1| 112 NYHVCQNTKIFGVDSDGVFAEYAIVPAQNAWK 143
                                       **************************999875 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 3.5
                                       -TT-EEEE-SE CS
                             ADH_N  54 kvGdrVvvepl 64 
                                       kvG  Vv++p+
  gi|242398605|ref|YP_002994029.1| 215 KVGADVVINPM 225
                                       89999999986 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.5   0.0   1.8e-34   4.7e-31       1     129 [.     183     313 ..     183     314 .. 0.96

  Alignments for each domain:
  == domain 1  score: 107.5 bits;  conditional E-value: 1.8e-34
                                       HHHHHHHHHHHHTT-.EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCSHHHHHHHH CS
                        ADH_zinc_N   1 gvGlaavqlAkalGa.eviavdsseeklelakklGadevinykeadlverikeltggegvdvvfecvGsgatleaal 76 
                                       ++Gl+++ +Aka+Ga  vi+  +se ++ lakk Gad+vin+ e+d+v ++k+lt+g+gvdv +e++G++++le+ l
  gi|242398605|ref|YP_002994029.1| 183 PLGLLGITVAKASGAsLVIVSEPSEFRRNLAKKVGADVVINPMEEDVVREVKDLTNGNGVDVFLEFSGAPRALEQGL 259
                                       79****************************************444******************************** PP

                                       HCEEEEEEEEECSCTSSEEEEEHHHHH.HTT-EEEEE-SSCHHHHHHHHHHHHH CS
                        ADH_zinc_N  77 kllkpgGrlvvvGggkgeeefdlrnll.lkeksilGsllgslreefkealdlla 129
                                       ++++p Gr+ + G++ +e +fd++nl+ +k + i G+++ +l+++++++ +ll+
  gi|242398605|ref|YP_002994029.1| 260 QAVTPAGRVSLLGLFPKEVTFDINNLViFKALEIHGITGRHLWQTWYTVSNLLK 313
                                       **************999999*****766*******************9998875 PP

>> Glu_dehyd_C  Glucose dehydrogenase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2   0.1     2e-13     5e-10      29     200 ..     171     338 ..     153     350 .. 0.75

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 2e-13
                       Glu_dehyd_C  29 wepesalvlGaGslGLLalalleaeerglervyvlgrrdrpdptidlveelGatYvds..retpvdeipeas..eem 101
                                          +++l++GaG+lGLL +++ +a  +g + v ++   +  + + +l +++Ga  v +  +e+ v e+ + +  + +
  gi|242398605|ref|YP_002994029.1| 171 VASKTVLITGAGPLGLLGITVAKA--SGASLV-IVS--EPSEFRRNLAKKVGADVVINpmEEDVVREVKDLTngNGV 242
                                       56789*************887775..566533.333..46678899*******877432256778888876522689 PP

                       Glu_dehyd_C 102 dlvvEaTGsakhafeaiealapnGvaaLlGvpedsevevdggelhrelvleNkalvGsvNanrrhfeaavdtLaalp 178
                                       d+ +E  G+++++ + ++a+ p+G + LlG+  ++ v +d+++l    + +   + G +  +  +   +v++L +  
  gi|242398605|ref|YP_002994029.1| 243 DVFLEFSGAPRALEQGLQAVTPAGRVSLLGLFPKE-VTFDINNLV---IFKALEIHGITGRHLWQTWYTVSNLLKSG 315
                                       ******************************97554.666665553...44455566666667666667788888888 PP

                       Glu_dehyd_C 179 eslldelvtkvv.dldeleeAfe 200
                                       +  ld ++t+++ ++d++eeAfe
  gi|242398605|ref|YP_002994029.1| 316 KLNLDPVITHKYkGFDKFEEAFE 338
                                       88899999998735899999998 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   0.0   1.1e-12   2.9e-09       2     132 ..     217     349 ..     216     350 .. 0.78

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 1.1e-12
                                       T-SEEEETTSTTHH....HHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE--.--..S-EEE-CHHHCTTT-E CS
                      ADH_zinc_N_2   2 GAdevidyrtedfe....aatggegvDvvldtvggealleaslkvlpggGrlvsig.gpp.lsaallkpakkrkgrs 72 
                                       GAd vi+  +ed++    + t+g+gvDv l+  g + +le+ l+++ + Gr+  +g  p  ++++++          
  gi|242398605|ref|YP_002994029.1| 217 GADVVINPMEEDVVrevkDLTNGNGVDVFLEFSGAPRALEQGLQAVTPAGRVSLLGlFPKeVTFDINN------LVI 287
                                       9*****9999999999*99***************99999*******666**98877433233333333......344 PP

                                       EEE--GGG...-.-HHHHHHHHHHHHHHH..----EEEEEE.GGGHHHHHHHHHSS--SSEEE CS
                      ADH_zinc_N_2  73 vkyeflfsmkasaqadileelaalieeGk..lrpvvdrvfp.leeaaeAhrylesgrarGKiV 132
                                       +k+  +  ++ ++  ++  ++ +l+++Gk  l pv+++ ++ +++  eA++++++g+ +GK+V
  gi|242398605|ref|YP_002994029.1| 288 FKALEIHGITGRHLWQTWYTVSNLLKSGKlnLDPVITHKYKgFDKFEEAFELMRAGK-TGKVV 349
                                       444444433333567779***********5556****99655************998.59998 PP

>> ADH_N_2  N-terminal domain of oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   9.2e-06     0.023      18      75 ..      22      79 ..       3     101 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 9.2e-06
                           ADH_N_2 18 feleeeelpelkdGevlvralylSv...DPymRgrmndaksyvepvelgdvmrggavgeVv 75
                                       el+e+++p++k+Gevl+++l  S+   D  +  + + a+s ++p    + m  ++ geVv
  gi|242398605|ref|YP_002994029.1| 22 AELVEVDVPNPKEGEVLIKVLATSIcgtDLHIYEWNEWAQSRIKP---PQIMGHEVAGEVV 79
                                      499****************99998733355555555555555553...3333333334444 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 ?   11.2   2.1   6.3e-05      0.16      16      76 ..     164     221 ..     157     262 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6.3e-05
                                       EEETTCEETCB---EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH.TTTCECE CS
                       AlaDh_PNT_C  16 kgtlaGgvpgvepakvlviGgGvaGlqAiatakglgakVtvlDvrparleqles.lgakfve 76 
                                        ++laG v      +vl+ G+G  Gl  i +ak+ ga+ +++   ++ +++l + +ga  v 
  gi|242398605|ref|YP_002994029.1| 164 DTVLAGSVA---SKTVLITGAGPLGLLGITVAKASGASLVIVSEPSEFRRNLAKkVGAD-VV 221
                                       578999999...999***********************999988888888887768877.43 PP

>> UPF0146  Uncharacterised protein family (UPF0146)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.16     4e+02      12      35 ..      73      97 ..      64     114 .. 0.75
   2 ?    8.9   0.0   0.00052       1.3      89     117 ..     211     237 ..     189     248 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.16
                                      S-SSEEEEET-TT-.-HHHHHHHHH CS
                           UPF0146 12 nargkvvEvGiGrk.ldvaealakr 35
                                      +  g vvEvG G + l++ ++++  
  gi|242398605|ref|YP_002994029.1| 73 EVAGEVVEVGPGVHnLKIGDYISAE 97
                                      56789******97526788887765 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00052
                                       HHHHHHT-EEEEE-BTTB-----TT-EEE CS
                           UPF0146  89 dvakkvgAaliikpLlgedvvvekelklv 117
                                       ++akkvgA+++i+p+ ++ v  e++  l+
  gi|242398605|ref|YP_002994029.1| 211 NLAKKVGADVVINPMEEDVV-REVK-DLT 237
                                       589***********987764.3333.344 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.61u 0.34s 00:00:00.95 Elapsed: 00:00:00.55
# Mc/sec: 1941.27
//
Query:       gi|242398606|ref|YP_002994030.1|  [L=503]
Description: Phenylalanyl-tRNA synthetase alpha chain [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-82  277.1   0.0    1.7e-82  276.6   0.0    1.2  1  tRNA-synt_2d     tRNA synthetases class II core domain (F)
    5.6e-05   22.7   0.0      0.064   12.7   0.0    2.4  2  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
     0.0013   17.9   0.0       0.38    9.8   0.0    2.5  2  tRNA-synt_2      tRNA synthetases class II (D, K and N)
  ------ inclusion threshold ------
      0.017   15.0  10.6        2.3    8.1   5.5    3.5  2  TFIIE_alpha      TFIIE alpha subunit
      0.088   12.7   5.0       0.82    9.6   0.3    3.8  4  TrmB             Sugar-specific transcriptional regulator Trm
       0.66   10.2   4.1       0.92    9.7   0.1    2.6  3  DUF2582          Winged helix-turn-helix domain (DUF2582)


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 !  276.6   0.0   5.7e-86   1.7e-82       2     244 ..     226     498 ..     225     499 .. 0.98

  Alignments for each domain:
  == domain 1  score: 276.6 bits;  conditional E-value: 5.7e-86
                                       .-TSSCTSCTSHSB-SHHHHHHHHHHHHHHCTTCEESS.TTSEEEHHHHTSTTTSTTTSHHHCHTTSEBTCTSSS-. CS
                      tRNA-synt_2d   2 idvtlpgkrieagklhpltkvleeikeiflelgfeeve.gpevesefynfdaLnvpqdhpaRdmqdtFylkkpeka. 76 
                                       +++++p kr+++gk++p++++l++i++ ++e+gf e++ ++ +e++f+nfdaL++pq+hpaRd++dt+ lk p+   
  gi|242398606|ref|YP_002994030.1| 226 FNIHAPVKRLYPGKKQPYRTFLDKIRRKLIEMGFIEMTvESLIETQFWNFDALFQPQNHPARDWTDTYQLKYPKYGf 302
                                       699***********************************9*******************************999999* PP

                                       ................................ECESEEE-SSTHHHHHHHH.TTS-SSEEEEEEEEEEBSST-SSSB CS
                      tRNA-synt_2d  77 ................................veekllLRthttavqirtl.ekkkppikiisigrvfRrdavDath 120
                                                                       ++  l+ R+h+ta+++r+l +  ++p k+++i+rvfR d +D+th
  gi|242398606|ref|YP_002994030.1| 303 lpdetlvervkashehgwitgsrgwgykwdprTAMLLMPRAHATALSARQLgKGVQIPGKYFAIQRVFRPDVLDRTH 379
                                       ******************************988888999************9999********************** PP

                                       -SEEEEEEEEEEETT--HHHHHHHHHHHHHHHCTSTEEEEEEECEETTEEEEEEEEEEECCSSSSEEEEEEEEEE-H CS
                      tRNA-synt_2d 121 laeFhqveglvvdenvsladlkgvleellkklfgaevkvrfrpsyfpftePsaevdvylvekkkkwlEllgaGmvrp 197
                                       l+eF+qv+g+vv+e +++++l+g+l+ ++ ++ ga+ kv+f p+y+pftePs+++++y+  ++ +w+E++gaG++r+
  gi|242398606|ref|YP_002994030.1| 380 LIEFNQVDGFVVGETLTFKHLLGILKRFAVEIAGAK-KVKFLPDYYPFTEPSVQMSAYH--EELGWVEFGGAGVFRE 453
                                       ************************************.**********************..**************** PP

                                       HHHHHTT-.TTSEEEEEEEEHHHHHHHHHT-SSGHHHHTT.HHHHGG CS
                      tRNA-synt_2d 198 evleavgideevsgfafGlGveRlamlkygieDiRelvendlrflrq 244
                                       e+++++gi  +v+++a+G+G++Rlam+k+gi+DiR+l++ dl++lr+
  gi|242398606|ref|YP_002994030.1| 454 EMTKPLGI--DVPVIAWGIGIDRLAMFKLGIDDIRYLFSYDLKWLRE 498
                                       ********..**********************************997 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 !    7.4   0.0   0.00092       2.7       6      45 ..     231     270 ..     228     287 .. 0.88
   2 !   12.7   0.0   2.2e-05     0.064      97     209 ..     361     467 ..     351     471 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00092
                   tRNA_synthFbeta   6 PkapttegelnkeqklrrklrdllagaGlnEvitysfvse 45 
                                       P   + +g++++ + + +k+r+ l+++G+ E+   s++  
  gi|242398606|ref|YP_002994030.1| 231 PVKRLYPGKKQPYRTFLDKIRRKLIEMGFIEMTVESLIET 270
                                       777788999***********************99999876 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 2.2e-05
                   tRNA_synthFbeta  97 vrlFEigkvflkd.seeelpeeerhlaivltgkreeeswsekaravdfydlkgivealleslgi.ekvefepaehpa 171
                                        + F i++vf++d  + +   e +++ + ++g++             f +l gi+++++ ++   +kv+f p+ +p+
  gi|242398606|ref|YP_002994030.1| 361 GKYFAIQRVFRPDvLDRTHLIEFNQVDGFVVGET-----------LTFKHLLGILKRFAVEIAGaKKVKFLPDYYPF 426
                                       688**********999999***************...........*************9888777************ PP

                   tRNA_synthFbeta 172 lhpgrsAeikvdgk...evGvlGelhpevleafdlkqrvyv 209
                                        +p  +++ + ++    e G +G +  e+ + ++++ +v++
  gi|242398606|ref|YP_002994030.1| 427 TEPSVQMSAYHEELgwvEFGGAGVFREEMTKPLGIDVPVIA 467
                                       ***9888776644233499999******9999999999876 PP

>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0   0.00013      0.38      80     119 ..     352     387 ..     346     417 .. 0.83
   2 !    5.4   0.0    0.0028       8.4     287     308 ..     468     489 ..     460     494 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00013
                                       HHHHHHHHHCTHSEEEEEEEEE--S--BTTB-S-CEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2  80 qlylellivagidrvfqiaraFRaEdsrtdrhlaEFtqie 119
                                       ql + + i++   ++f i r+FR   ++ ++ + EF q++
  gi|242398606|ref|YP_002994030.1| 352 QLGKGVQIPG---KYFAIQRVFRPDVLDRTHLI-EFNQVD 387
                                       5556666666...***************77766.*****9 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0028
                                       EEEEHHHHHHHHCT-SSGGGCS CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 287 lglGldRlvmlllgsesIrdvi 308
                                       +g+G+dRl m+ lg ++Ir + 
  gi|242398606|ref|YP_002994030.1| 468 WGIGIDRLAMFKLGIDDIRYLF 489
                                       79****************9775 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1    0.0049        15      29      63 ..      21      55 ..       6      69 .. 0.86
   2 ?    8.1   5.5   0.00076       2.3      17     101 ..      77     165 ..      70     168 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0049
                                      BHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEE CS
                       TFIIE_alpha 29 teedlakelkidlnelrklLnrLyearlvkykrrr 63
                                      + ++l ke+++d+  + +++  L++++l+k + ++
  gi|242398606|ref|YP_002994030.1| 21 SFDELVKETGLDQVAVMRAILWLQSKGLAKLHEKQ 55
                                      5599**************************99765 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00076
                                       HHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEE......TTTEEEEEEEEEECCCHCCCHHH CS
                       TFIIE_alpha  17 lvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrd......eekswykyywrinyeklvdvvkr 87 
                                        +l+ L+ekg+vt edl + l+    elr+++  L++++ + ++++ d       ek+ +  +     + +++v+ +
  gi|242398606|ref|YP_002994030.1|  77 RALKLLVEKGKVTLEDLREVLS--EDELRPIIGILRKEGWATVRKEDDvltlelTEKGKEALTKERPIDIALKVLAE 151
                                       5799***************987..779******************99998887778888888777777888888888 PP

                                       HHHHHHHHHHHHHC CS
                       TFIIE_alpha  88 kleevvkkLeekle 101
                                       k e  ++++ee l+
  gi|242398606|ref|YP_002994030.1| 152 KREVEAREIEELLS 165
                                       88888888887766 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.3   0.00028      0.82       6      64 ..       3      61 ..       1      64 [. 0.90
   2 ?    1.4   0.0       0.1     3e+02      10      32 ..      75      97 ..      70     120 .. 0.84
   3 ?   -0.2   0.2      0.31   9.3e+02      16      34 ..     148     166 ..     145     177 .. 0.67
   4 ?   -0.5   0.0       0.4   1.2e+03      43      55 ..     251     263 ..     244     274 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00028
                                      HHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE CS
                              TrmB  6 LseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYra 64
                                      Ls  E  + ++L +l++a+ de+ +e+g+++  v +++  L +kGl +  ++++++ + 
  gi|242398606|ref|YP_002994030.1|  3 LSYQEKVTLIKLRELKKASFDELVKETGLDQVAVMRAILWLQSKGLAKLHEKQKRVVKI 61
                                      7778888999999***********************************99998887765 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.1
                                      CCCHCHHHHHHCCCHHCHHCCCT CS
                              TrmB 10 EakvYlaLlklgpatadeiaeel 32
                                      E ++ + L+++g+ t +++ e l
  gi|242398606|ref|YP_002994030.1| 75 ERRALKLLVEKGKVTLEDLREVL 97
                                      56788889999999999998865 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.31
                                       HHHHHCCCHHCHHCCCTTS CS
                              TrmB  16 aLlklgpatadeiaeelgv 34 
                                       +L ++ + +a+ei e l +
  gi|242398606|ref|YP_002994030.1| 148 VLAEKREVEAREIEELLSL 166
                                       6667778888888776654 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 0.4
                                       HHHHHHCTSEEEE CS
                              TrmB  43 LrsLedkGlVere 55 
                                        r+L+++G++e  
  gi|242398606|ref|YP_002994030.1| 251 RRKLIEMGFIEMT 263
                                       589*******976 PP

>> DUF2582  Winged helix-turn-helix domain (DUF2582)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1   0.00031      0.92      17      47 ..      14      44 ..      12      59 .. 0.86
   2 ?    1.0   0.1      0.16   4.7e+02      15      61 ..      80     124 ..      69     128 .. 0.81
   3 ?   -3.2   0.1       3.2   9.5e+03      17      36 ..     149     168 ..     147     175 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00031
                                      HCCSSSEEHHHHHHHCT-SCHHHHHHHHHHH CS
                           DUF2582 17 LnengeislkelkrktglsdkelalAiGWLa 47
                                      L e +++s+ el ++tgl++  ++ Ai WL 
  gi|242398606|ref|YP_002994030.1| 14 LRELKKASFDELVKETGLDQVAVMRAILWLQ 44
                                      78889************************96 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.16
                                       HHHCCSSSEEHHHHHHHCT-SCHHHHHHHHHHHCTTSEEEEEETTEE CS
                           DUF2582  15 hlLnengeislkelkrktglsdkelalAiGWLaREdKivierkekel 61 
                                       +lL e+g+++l++l+  + ls++el   iG L +E+   ++++++ l
  gi|242398606|ref|YP_002994030.1|  80 KLLVEKGKVTLEDLR--EVLSEDELRPIIGILRKEGWATVRKEDDVL 124
                                       678899999999997..468899999999999999888888777665 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 3.2
                                       HCCSSSEEHHHHHHHCT-SC CS
                           DUF2582  17 Lnengeislkelkrktglsd 36 
                                       L e++e+ + e+++  +l++
  gi|242398606|ref|YP_002994030.1| 149 LAEKREVEAREIEELLSLKE 168
                                       66666666666665555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (503 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       652  (0.0363657); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.70u 0.31s 00:00:01.01 Elapsed: 00:00:00.53
# Mc/sec: 2861.24
//
Query:       gi|242398607|ref|YP_002994031.1|  [L=560]
Description: Phenylalanyl-tRNA synthetase beta chain [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.8e-47  159.9   0.1    1.1e-46  159.0   0.0    1.5  2  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
    2.4e-14   53.4   0.8    2.9e-13   49.9   0.4    2.6  2  B5               tRNA synthetase B5 domain
    7.6e-14   51.8   0.0    1.4e-13   50.9   0.0    1.3  1  B3_4             B3/4 domain
    2.2e-08   34.2   0.3    1.7e-06   28.1   0.0    3.5  3  PhetRS_B1        Phe-tRNA synthetase beta subunit B1 domain
    5.4e-05   22.8   0.0    0.00016   21.2   0.0    1.9  1  tRNA-synt_2d     tRNA synthetases class II core domain (F)


Domain annotation for each model (and alignments):
>> tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       1.7   6.1e+03     145     174 ..     303     336 ..     302     339 .. 0.62
   2 !  159.0   0.0   3.1e-50   1.1e-46       1     213 [.     352     550 ..     352     551 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 1.7
                   tRNA_synthFbeta 145 dlkgivealleslgi.ek...vefepaehpalhp 174
                                       d+k ++e+++ ++ + ++   +++ +  +  +hp
  gi|242398607|ref|YP_002994031.1| 303 DIKDLLERMMYEVDFvDRrvkLRYPAFRNDIMHP 336
                                       7899999999999884223333333455555555 PP

  == domain 2  score: 159.0 bits;  conditional E-value: 3.1e-50
                   tRNA_synthFbeta   1 IpstlPkapttegelnkeqklrrklrdllagaGlnEvitysfvseke.ldklleddderkavelanPlsedqsvlRt 76 
                                       I++  P+ +++++  ++  ++++++rdl++g+Gl+Ev+t+++++++  +dk+  + +e++ ve++nP+s+  s+lR+
  gi|242398607|ref|YP_002994031.1| 352 IEPEEPELAVQGK-GDDFVDFENAIRDLMVGFGLQEVMTFNLTNREAqFDKM--NIPEEDIVEIENPISQKWSALRR 425
                                       5666777777777.78999************************976516666..679******************** PP

                   tRNA_synthFbeta  77 sLlpglLevlarNlargnedvrlFEigkvflkd.seeelpeeerhlaivltgkreeeswsekaravdfydlkgivea 152
                                        Llp+l+e l++N + + +  r+FE+gk  l d s e++   e++l +++++++           v f ++k+i+++
  gi|242398607|ref|YP_002994031.1| 426 WLLPSLMEFLSQNTHEEYP-QRIFEVGKATLIDeSRETKTISESKLVVAIAHPK-----------VTFTEAKEILDS 490
                                       *******************.*************999999***************...........************ PP

                   tRNA_synthFbeta 153 lleslgiekvefepaehpalhpgrsAeikvdgkevGvlGelhpevleafdlkqrvyvfEld 213
                                       +l++lg  ++++++ e+ ++ pgr+ ei v+gk+vG++Ge+hp+vle+++++ +v++fE+ 
  gi|242398607|ref|YP_002994031.1| 491 VLRHLGA-EYTIREIEYGSFIPGRAGEIIVEGKKVGIIGEIHPQVLENWGVEMPVAAFEIF 550
                                       *******.***************************************************96 PP

>> B5  tRNA synthetase B5 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.16   5.9e+02       4      32 ..       7      52 ..       4     137 .. 0.75
   2 !   49.9   0.4     8e-17   2.9e-13       2      67 .]     285     349 ..     284     349 .. 0.96

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.16
                                      EHHHHHHHHTS---HHHHHHHHHHTT-E.................. CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxx.................x RF
                                B5  4 rvekinkllGidlseeeiikiLkrlgce.................r 32
                                      +   +++l+G +++ +e ++++   +ce                  
  gi|242398607|ref|YP_002994031.1|  7 AKHDLERLVGKEFTVDEWEDLFLYAKCElddiwehegkiyfkadaK 52
                                      5677899999999999999999999998666555555555444440 PP

  == domain 2  score: 49.9 bits;  conditional E-value: 8e-17
                                       EEEHHHHHHHHTS---HHHHHHHHHHTT-E.EESSTTCEEEE--TT-TT--SHHHHHHHHHHHH-G CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                                B5   2 slrvekinkllGidlseeeiikiLkrlgceriekdkdlllVtvPswRsDlereeDliEEvaRlyGY 67 
                                       ++++++i++l+G++l++++i+++L+r+ +e+    +  ++   P++R+D+ ++ D+ E+v+++yGY
  gi|242398607|ref|YP_002994031.1| 285 EVDLNYIKRLAGVELTDKDIKDLLERMMYEV-DFVDRRVKLRYPAFRNDIMHPRDVLEDVLIAYGY 349
                                       6899**************************8.888888***************************9 PP

>> B3_4  B3/4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.9   0.0   3.8e-17   1.4e-13      35     133 ..     119     245 ..     101     258 .. 0.92

  Alignments for each domain:
  == domain 1  score: 50.9 bits;  conditional E-value: 3.8e-17
                                       --HHHHHHHHHHHHHT-.....-EEEEEGGGTBTEEE.EEE--TTEEEEBTTS-EEEE-T................. CS
                              B3_4  35 innvVDitNyvmlelgq.....PlhafDldkiqgdiv.vrlakegeklvtldgkerelde................. 88 
                                       ++ ++ ++++v l lg+     ++++fD+dk+++++  ++  +++ k+++l+  ere+++                 
  gi|242398607|ref|YP_002994031.1| 119 LKQIIQLQEKVALTLGRkrkevAIGTFDFDKLSPPFYyKAVEPQKIKFIPLN-CEREMSAdeileehekgkeyghli 194
                                       57899*******************************9888899999******.667776667*************** PP

                                       ....TSEEEETEEEEE.EETTTEEBT.TTB--TT--EEEEEEEE--HHHHH CS
                              B3_4  89 ....edlviadsekpv.slagvmgge.eskvsedTknvfleaaafdpvsir 133
                                            +++ +dse++v s+++v+++e + kv+e+Tk++f+ +++++ ++i 
  gi|242398607|ref|YP_002994031.1| 195 kgrpYYPLLVDSEGNVlSMPPVINSEtHGKVTEETKSIFIDITGWNLETIM 245
                                       *************************85679***************988875 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 !   28.1   0.0   4.9e-10   1.7e-06       1      78 [.       1      70 [.       1      74 [. 0.93
   2 ?    1.5   0.1     0.097   3.5e+02       7      36 ..     287     316 ..     284     335 .. 0.80
   3 ?   -1.8   0.0       1.1   3.8e+03      22      34 ..     373     385 ..     370     417 .. 0.64

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 4.9e-10
                         PhetRS_B1  1 MPtisvkkeaLfkalgkelteeeledllfefGlElDeiveeeekkkadkkseeviykidi.pAnryDLLcleglaralk 78
                                      MP   v k++L +++gke+t +e edl+     ElD+i e e          + ++k d    nr+DL ++eg+ar ++
  gi|242398607|ref|YP_002994031.1|  1 MPKFDVAKHDLERLVGKEFTVDEWEDLFLYAKCELDDIWEHEG---------KIYFKADAkDTNRPDLWSAEGIARQVR 70
                                      9***************************************999.........89999996369************9876 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.097
                         PhetRS_B1   7 kkeaLfkalgkelteeeledllfefGlElD 36 
                                       + +++ ++ g elt++ ++dll +   E+D
  gi|242398607|ref|YP_002994031.1| 287 DLNYIKRLAGVELTDKDIKDLLERMMYEVD 316
                                       567778888999999999999988877777 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 1.1
                         PhetRS_B1  22 eeledllfefGlE 34 
                                       + + dl++ fGl 
  gi|242398607|ref|YP_002994031.1| 373 NAIRDLMVGFGLQ 385
                                       5688999999983 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 !   21.2   0.0   4.5e-08   0.00016      13     214 ..     362     547 ..     330     551 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 4.5e-08
                                       HSB-SHHHHHHHHHHHHHHCTTCEESSTTSEEEHHHHTSTTTSTTTSHHHCHTTSEBTCTSSS-ECESEEE-SSTHH CS
                      tRNA-synt_2d  13 agklhpltkvleeikeiflelgfeevegpevesefynfdaLnvpqdhpaRdmqdtFylkkpekaveekllLRthtta 89 
                                       +gk + + ++ + i+++++ +g +ev   ++ +    fd +n+p++       d   +++p +  ++   LR    +
  gi|242398607|ref|YP_002994031.1| 362 QGKGDDFVDFENAIRDLMVGFGLQEVMTFNLTNREAQFDKMNIPEE-------DIVEIENPIS--QKWSALRRWLLP 429
                                       56666677788999999********999999999999*****9986.......5556666666..667899999999 PP

                                       HHHHHH...TTS-SSEEEEEEEEEEBSST-SSSB-SEEEEEEEEEEETT--HHHHHHHHHHHHHHHCTSTEEEEEEE CS
                      tRNA-synt_2d  90 vqirtl...ekkkppikiisigrvfRrdavDathlaeFhqveglvvdenvsladlkgvleellkklfgaevkvrfrp 163
                                         +  l   ++++ p++i+ +g++   d+   t++++  ++   ++  +v++++ k +l+++l++l gae ++r + 
  gi|242398607|ref|YP_002994031.1| 430 SLMEFLsqnTHEEYPQRIFEVGKATLIDESRETKTISESKLVVAIAHPKVTFTEAKEILDSVLRHL-GAEYTIR-EI 504
                                       99999987677789****************************************************.**97776.45 PP

                                       CEETTEEEEEEEEEEECCSSSSEEEEEEEEEE-HHHHHHTT-.TTSEEEEE CS
                      tRNA-synt_2d 164 syfpftePsaevdvylvekkkkwlEllgaGmvrpevleavgideevsgfaf 214
                                       +y  f  P+   ++ +   ++k   ++  G ++p+vle+ g+  e++++af
  gi|242398607|ref|YP_002994031.1| 505 EYGSF-IPGRAGEIIV---EGKK--VGIIGEIHPQVLENWGV--EMPVAAF 547
                                       56666.6999999999...4444..455688***********..9999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (560 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); 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:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 4240.97
//
Query:       gi|242398608|ref|YP_002994032.1|  [L=266]
Description: tRNA pseudouridine synthase A [Thermococcus sibiricus MM 739]
Scores for complete 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-23   81.5   0.0    6.6e-17   61.9   0.0    2.1  2  PseudoU_synth_1  tRNA pseudouridine synthase


Domain annotation for each model (and alignments):
>> PseudoU_synth_1  tRNA pseudouridine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0     2e-07    0.0037       4      75 ..       8      76 ..       6     103 .. 0.78
   2 !   61.9   0.0   3.7e-21   6.6e-17       2     108 .]     128     227 ..     127     227 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2e-07
                   PseudoU_synth_1  4 elvGthdfgsfckqkqekkntvrtileaaieevsgeekellvvtvkgsgFldhqVRamvgvl.favgqgklsp 75
                                      +++Gt+++g f  q+q++ +tv   l   ++++    +++ ++++kg++++d++V a+++v+ f   + +l++
  gi|242398608|ref|YP_002994032.1|  8 AYDGTKFYG-F--QRQPDLRTVEGELIKVLKKLGII-EDVKEANFKGASRTDRGVSALGNVIaFNTAKPELAE 76
                                      69*******.*..88889888888888888877777.4677********************966655555544 PP

  == domain 2  score: 61.9 bits;  conditional E-value: 3.7e-21
                   PseudoU_synth_1   2 akelvGthdfgsfckqkqekkntvrtileaaieevsgeekellvvtvkgsgFldhqVRamvgvlfavgqgklspedv 78 
                                       a++++G+hdf++f ++ +e +++vr+i ++++      ++  +vv+++g++Fl+ + R+++ +l ++g g ls  dv
  gi|242398608|ref|YP_002994032.1| 128 AEAFLGRHDFSNF-ARLEEFRKPVREINRIDVF----SRGRIIVVEIEGKSFLWEMTRRIITALKLCGLGVLSIGDV 199
                                       789**********.5666669************....77889*********************************** PP

                   PseudoU_synth_1  79 kellnakkrkkiavetapavglvlfhvrYd 108
                                       + +l+ k +kk   + ap++ lvl++v Y+
  gi|242398608|ref|YP_002994032.1| 200 ELMLKEKVDKK--LPPAPPENLVLWEVGYE 227
                                       *******9876..**************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); 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: 0.53u 0.33s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1595.45
//
Query:       gi|242398609|ref|YP_002994033.1|  [L=456]
Description: DNA/RNA repair helicase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-17   64.4   0.0    5.8e-17   62.2   0.0    2.2  2  ResIII         Type III restriction enzyme, res subunit
      1e-12   48.4   0.1    4.2e-12   46.4   0.1    2.1  1  Helicase_C     Helicase conserved C-terminal domain
    2.4e-05   24.2   0.3    0.00022   21.0   0.1    2.7  2  DEAD           DEAD/DEAH box helicase
    7.7e-05   22.5   0.0    0.00031   20.5   0.0    2.1  2  SWI2_SNF2      SWI2/SNF2 ATPase
  ------ inclusion threshold ------
      0.011   14.9   0.8      0.019   14.1   0.1    1.7  2  ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
      0.012   14.9   0.0      0.021   14.1   0.0    1.4  1  DUF2075        Uncharacterized conserved protein (DUF2075)


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 !   62.2   0.0     2e-20   5.8e-17       1     169 [.      96     235 ..      96     237 .. 0.90
   2 ?   -2.0   0.0         1   3.1e+03      33      59 ..     390     417 ..     357     452 .. 0.74

  Alignments for each domain:
  == domain 1  score: 62.2 bits;  conditional E-value: 2e-20
                                       --EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGG CS
                            ResIII   1 klelreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkf 77 
                                       k++lr+yQ++ +++ l      + + g+++++ G+GKT++ ++li++l        +l++v++k+ll q+ ++++++
  gi|242398609|ref|YP_002994033.1|  96 KYQLRKYQQKTLKKAL------KTNMGVLALPVGSGKTIIGLRLIYELNL-----STLIIVHTKELLYQWADNIREV 161
                                       5799*******99998......5678************************.....5********************* PP

                                       TGG....GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.TTTHHHH CS
                            ResIII  78 lseaykeigkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakkswreil 154
                                       l  +       + gd++        ++ ++v+ iq+l ++         ++l++ + v+++DE+Hr++a++++ e+ 
  gi|242398609|ref|YP_002994033.1| 162 LGIE-----PGLVGDNNWD------ERPVTVAMIQTLLSRG-------VDKLQKPYAVLLFDECHRTSAAEKFYELG 220
                                       *965.....4566776666......79************99.......678888889************99999987 PP

                                       HT---SEEEEEESS- CS
                            ResIII 155 ekfkeavllglTATp 169
                                        ++ +++++gl+ATp
  gi|242398609|ref|YP_002994033.1| 221 ISLTQKLRFGLSATP 235
                                       77888*********9 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1
                                       TTSTHHHHH.HHHHHHH-S.....-EEE CS
                            ResIII  33 TGtGKTlva.aklierllkkgkeekflf 59 
                                        G GK+ ++ +++i r l+ ++++++++
  gi|242398609|ref|YP_002994033.1| 390 AGGGKSDIMtIQTIGRALRPKGRSHAVI 417
                                       5677777776777766666555544443 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 !   46.4   0.1   1.4e-15   4.2e-12       4     109 ..     305     408 ..     302     410 .. 0.88

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 1.4e-15
                                       HHHHHHH.HHTTTTSEEEEEESSHHHHHH.HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTS CS
                        Helicase_C   4 eallell.kleeeggkilifvntidrlek.vklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaer 78 
                                       +a++++  kl ++g+++li v++i++ +  ++++ +kkgik+  l +  ++ +r ei+e+f++ge++vLi+t  + +
  gi|242398609|ref|YP_002994033.1| 305 KAIVRIAyKLAKQGHRVLIDVKRIEHGNVlIEMF-KKKGIKAEFLSS--QSPNRWEIFEKFKNGEINVLIST-LLKE 377
                                       55666645899**************664447888.6779********..7889*****************98.78** PP

                                       SSTSTTESEEEESSSSSSHHHHHHHHTTSSS CS
                        Helicase_C  79 GidipkvnlVinfdlprnvtsyiqriGRtgR 109
                                       G+dip+++ +i  +  ++    iq iGR+ R
  gi|242398609|ref|YP_002994033.1| 378 GVDIPEISAIILAGGGKSDIMTIQTIGRALR 408
                                       *****************************99 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.1   7.4e-08   0.00022       2     136 ..     101     213 ..     100     239 .. 0.68
   2 ?   -2.7   0.0       1.4   4.2e+03      23      52 ..     390     417 ..     383     419 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 7.4e-08
                                       HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   2 diQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrv 78 
                                       ++Q+++++ +l+ +  ++a ++GsGKT + l  ++ +        +  +li++ t+eL  q ++n+++++  i  + 
  gi|242398609|ref|YP_002994033.1| 101 KYQQKTLKKALKTNMGVLALPVGSGKTIIGLRLIY-E-------LNLSTLIIVHTKELLYQWADNIREVLG-I--EP 166
                                       68*************************99666665.3.......45789******************9998.2..23 PP

                                       EEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  79 lliiggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldq 136
                                          + g++  d++ +    v ++ +  +r +d l+      +   +l +DE++r +  
  gi|242398609|ref|YP_002994033.1| 167 G--LVGDNNWDERPVT---VAMIQTLLSRGVDKLQ------KPYAVLLFDECHRTSAA 213
                                       2..2255555555555...4444444444444332......33466667777776654 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.4
                                       TTSSHHHHHHHHHHHHHHHSTTSTS-EEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  23 TGsGKTlaflipvlqivyetkgktgpkali 52 
                                        G GK+ ++ i  + + ++   k +  a+i
  gi|242398609|ref|YP_002994033.1| 390 AGGGKSDIMTIQTIGRALR--PKGRSHAVI 417
                                       5999999999999987775..555555666 PP

>> SWI2_SNF2  SWI2/SNF2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0     1e-07   0.00031      18     205 ..     113     291 ..      96     309 .. 0.72
   2 ?   -2.3   0.0      0.94   2.8e+03      28      71 ..     391     433 ..     389     454 .. 0.62

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1e-07
                         SWI2_SNF2  18 rkgGviWHtqGSGKsltmvflakklleeelknpkvvvvtDRkdLdkQlsktfakageekpkqaesrkeLkellekes 94 
                                       ++ Gv+    GSGK++  + l  +l          ++++  k+L  Q +++++++   +p        L+   + ++
  gi|242398609|ref|YP_002994033.1| 113 TNMGVLALPVGSGKTIIGLRLIYELNL------STLIIVHTKELLYQWADNIREVLGIEP-------GLVGDNNWDE 176
                                       567777777888888777666655555......345555667888888888887766665.......4555555668 PP

                         SWI2_SNF2  95 ekiifttiqKfeeeekeklevlsereniivlvDEaHRsqygelakklrkalpnaafigFTGTPilk...kdkktkev 168
                                       + + +++iq + ++    +++l++    ++l+DE+HR+   e   +l   l +  ++g+  TP  +   ++ k + +
  gi|242398609|ref|YP_002994033.1| 177 RPVTVAMIQTLLSR---GVDKLQKPY-AVLLFDECHRTSAAEKFYELGISLTQKLRFGLSATPWRRirgEELKIEGI 249
                                       89999999999763...356666655.899*********************************88755566778889 PP

                         SWI2_SNF2 169 FgeyidkYtikeaveDgavvp.....ilYesrlaklelkeee 205
                                        g +i + + ++ ++ +   +     i+Yes +  l+ + +e
  gi|242398609|ref|YP_002994033.1| 250 VGPIIYEIKAEDLIKEKFLAKprfmiIEYESSMPPLAERYKE 291
                                       999999999999999988877777778888888887776665 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.94
                         SWI2_SNF2  28 GSGKsltmvflakklleeelknpkvvvvtDRkdLdkQlsktfak 71 
                                       G GKs  m++ +   +  + k     v++D kd d  l+++f +
  gi|242398609|ref|YP_002994033.1| 391 GGGKSDIMTIQTIGRAL-RPKGRSHAVIVDVKDDDPLLFTHFIE 433
                                       88999877765433333.44555556667777766666666654 PP

>> ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1      0.65     2e+03     185     224 ..      69     112 ..      64     115 .. 0.63
   2 ?   14.1   0.1   6.5e-06     0.019      89     156 ..     350     414 ..     289     425 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.65
                     ERCC3_RAD25_C 185 lvdqGYafkvitele..el..eeeeelaystkeeqkellqkvla 224
                                       l  +GY  ++i e e  ++  + + + +y+ ++ q++ l+k+l+
  gi|242398609|ref|YP_002994033.1|  69 LNSKGYRVRIIDEREieGIeiNATWNEKYQLRKYQQKTLKKALK 112
                                       55689999999765532332144456777777777777777765 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 6.5e-06
                     ERCC3_RAD25_C  89 tseaerlkilqkfkknpkvntiflskvgDtsiDlPeanvliqisshfgsrrqeaqrlGriLrakkksn 156
                                        ++ +r +i++kfk+  ++n +++s +  + +D+Pe + +i  +    s     q +Gr Lr+k +s+
  gi|242398609|ref|YP_002994033.1| 350 SQSPNRWEIFEKFKNG-EIN-VLISTLLKEGVDIPEISAIIL-AGGGKSDIMTIQTIGRALRPKGRSH 414
                                       46678********987.566.679**************9995.6667889999***********9864 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0     7e-06     0.021      11     105 ..     123     215 ..     121     226 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7e-06
                           DUF2075  11 GtGKtvvllnllael.....eddeeertavylsvNhplvlvlrealakkeekkkkkeafeklssfinnlsefkkaee 82 
                                       G+GKt+++l+l++el          ++       N ++vl ++  l +++      ++     ++i++l    ++  
  gi|242398609|ref|YP_002994033.1| 123 GSGKTIIGLRLIYELnlstlIIVHTKELLYQWADNIREVLGIEPGLVGDN----NWDERPVTVAMIQTLL---SRGV 192
                                       9**************66433222233333334567788888888888877....5666666777788877...7777 PP

                           DUF2075  83 kkeepkedvvivDEAhrlltksd 105
                                       +k +++  v+++DE hr    ++
  gi|242398609|ref|YP_002994033.1| 193 DKLQKPYAVLLFDECHRTSAAEK 215
                                       999**************877554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (456 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.42
# Mc/sec: 3222.04
//
Query:       gi|242398610|ref|YP_002994034.1|  [L=422]
Description: 3-octaprenyl-4-hydroxybenzoate decarboxylyase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-94  317.7   0.2    1.3e-94  317.3   0.2    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 !  317.3   0.2   7.4e-99   1.3e-94       7     406 .]      10     387 ..       7     387 .. 0.92

  Alignments for each domain:
  == domain 1  score: 317.3 bits;  conditional E-value: 7.4e-99
                                       TTSEEEEESEB-TBTHHHHHHHHHHHHT--EEEEEEBTTB.TT-EEEE-TTS-HCHHHHHHTS-GHHHHHHHHHHHH CS
                              UbiD   7 agelvrikeevdpelEiaeiarrvleeggpallFenvkgkgskfpvltnlfgtrervalalglssleeileklaell 83 
                                       ++e++ i+e+v+ ++Ei++ + + +    + +lF++v  +  +++v +n+ +tr+r+a+ lg++  eei++ + +++
  gi|242398610|ref|YP_002994034.1|  10 QDEVILIEEPVSKKFEISHYILQYK---DRPILFKDV--D--GWEVTSNVWSTRDRIAKYLGIK-KEEITHFMMNAM 78 
                                       678999*****************98...779******..4..5*******************86.5*********** PP

                                       HS..----EE--GCG-GGGSEEECCCCC--HHHS---BSSTTSSS-EEECEEEEEE-TTTT-EEEEEEEEEEEETTE CS
                              UbiD  84 epkppippkvvesekapcqeevvlegddvdLskLPvltlwpgDgGpyitlglvitrdpetgkrnlgiyRmqvldknk 160
                                       ++  p p   ve  ka + e+      d++L++LP+++++p+DgGpy+t+++ i++d +++  nl+++R +v d+++
  gi|242398610|ref|YP_002994034.1|  79 DN--PKPYISVE--KAGFFENS---TRDFSLKELPIPQYFPKDGGPYFTSAIYIAKD-DNDFVNLSYHRTMVRDEKS 147
                                       *7..45666774..46667566...589****************************9.7799*************** PP

                                       EEE--TTTHCHHHHHHHHHHCCT--EEEEEEES--HHHHHHCTS--TTT-TCHHHHHHHH....TS--EEEE-SSSS CS
                              UbiD 161 lglhwqihkggaehlrkakkkggeplpvavaiGvdPaltlaAvaplPeglsElefaGalr....gepvelvkcetvd 233
                                       + +++++++  a+ +++  +  ge+l+v +++G +  ++laA+++ P+g+sEl++a+ ++    g+ +e+v++  ++
  gi|242398610|ref|YP_002994034.1| 148 ATVRLVPRHLYAM-WKEKVEH-GEELDVRIIVGNPIHILLAAATSPPYGVSELNIASSMSemafGKALEVVNV--NG 220
                                       9999997766333.3333333.69***********************************99999*******66..78 PP

                                       SEEETT-SEEEEEEEECCEEEECTTTC-TTSCEEC--CCEEEEEEEEEEE-TT-EEEE-SSSCCSHHHHCHHHHHHH CS
                              UbiD 234 levpadAEivleGeidpgetapEGPfgdhtGyysevrdefpvfkVtaithRkdpiypttvvgkppeedallgkalea 310
                                       ++vpa++E+v+e  i p e+ +EGPf+d+tG+y+ vr+ +pv+  ++++h ++pi+++++     e+ +l+g++ e+
  gi|242398610|ref|YP_002994034.1| 221 IPVPAESEFVFEAKILP-ELDKEGPFVDITGTYDIVRE-QPVVVFEKMYHVDKPIFHALFSSGY-EHYMLMGLPKEP 294
                                       *****************.69*************99988.6*****************9955555.************ PP

                                       HHHHHHHCCSTTEEEEEE-GGGTTTCEEEEECHHHTCCHHHHHHHHHHCCTTGGC-SEEEEEEETTS-TTSHHHHHH CS
                              UbiD 311 lflpllkkqvpevkdvhlpeeggfhllavvsikkrypghakkvmealwalkqqlsltKlvivvDedvdvrdlkevlw 387
                                        +++ +k+ vp+v+ v+l+e g+++l+av+si k+++g+ k+++ a+++ ++  sl K+v vvDed++++d +ev+w
  gi|242398610|ref|YP_002994034.1| 295 QIYKSVKQVVPKVHGVRLTEGGCMWLHAVISITKQHEGDGKNAILAAFTGHP--SL-KHVAVVDEDINIYDDREVEW 368
                                       ************************************************9999..99.******************** PP

                                       HHHHC--CCCCEEEECCCE CS
                              UbiD 388 aiatrvdpdrDlviiegtr 406
                                       aiatr+++d+Dl++i++tr
  gi|242398610|ref|YP_002994034.1| 369 AIATRFQADKDLIVIPKTR 387
                                       ***************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2798.20
//
Query:       gi|242398611|ref|YP_002994035.1|  [L=260]
Description: Pyrroline-5-carboxylate reductase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-36  125.0   0.2    2.5e-36  124.1   0.2    1.5  1  P5CR_dimer       Pyrroline-5-carboxylate reductase dimerisati
    7.8e-22   77.7   2.0    1.7e-21   76.6   2.0    1.6  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    2.3e-12   47.4   0.4    9.4e-12   45.4   0.3    1.9  2  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
    4.1e-11   42.7   0.3    6.1e-11   42.2   0.3    1.3  1  IlvN             Acetohydroxy acid isomeroreductase, NADPH-bi
    5.9e-10   39.0   0.8      2e-09   37.3   0.8    1.9  1  ApbA             Ketopantoate reductase PanE/ApbA
    2.3e-08   34.1   4.3    6.5e-06   26.2   4.3    2.3  1  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
    1.1e-07   31.3   0.1    1.9e-07   30.6   0.1    1.4  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
    5.4e-07   29.8   0.4      9e-07   29.1   0.4    1.5  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
    4.9e-06   25.7   0.1    9.4e-06   24.8   0.1    1.4  1  PDH              Prephenate dehydrogenase
    1.6e-05   24.9   0.5    3.8e-05   23.8   0.5    1.6  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
    3.2e-05   23.9   0.5    3.2e-05   23.9   0.5    2.5  2  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
    6.7e-05   23.4   0.6    0.00012   22.5   0.6    1.5  1  CoA_binding_2    CoA binding domain
    8.6e-05   22.2   0.8     0.0016   18.0   0.1    2.4  2  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
    0.00013   21.5   0.0    0.00019   21.0   0.0    1.2  1  Epimerase        NAD dependent epimerase/dehydratase family
    0.00017   21.6   0.4    0.00033   20.6   0.4    1.6  1  NAD_binding_10   NAD(P)H-binding
    0.00047   20.4   1.3     0.0025   18.0   0.9    2.2  2  TrkA_N           TrkA-N domain
     0.0007   19.5   1.4     0.0016   18.3   1.4    1.6  1  Rossmann-like    Rossmann-like domain
    0.00076   19.0   4.7      0.012   15.1   2.5    2.6  3  adh_short        short chain dehydrogenase
    0.00083   19.7   0.2     0.0018   18.7   0.2    1.5  1  UDPG_MGDP_dh_C   UDP-glucose/GDP-mannose dehydrogenase family
     0.0033   17.2   0.3       0.13   12.1   0.1    2.3  2  QRPTase_C        Quinolinate phosphoribosyl transferase, C-te
      0.004   16.8   0.6     0.0058   16.2   0.6    1.5  1  NmrA             NmrA-like family
     0.0044   17.3   1.0       0.01   16.1   1.0    1.6  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
     0.0049   17.0   0.1     0.0083   16.2   0.1    1.5  1  POR              Pyruvate ferredoxin/flavodoxin oxidoreductas
      0.007   15.8   1.7      0.028   13.8   1.7    1.9  2  ThiF             ThiF family
     0.0078   15.6   0.0      0.013   14.9   0.0    1.3  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
      0.008   15.4   1.6      0.013   14.8   1.2    1.5  1  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
  ------ inclusion threshold ------
      0.011   16.3   3.7      0.015   15.9   1.3    2.3  2  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
      0.015   14.9   0.6      0.033   13.8   0.3    1.6  2  DAO              FAD dependent oxidoreductase
      0.016   15.4   0.6      0.046   14.0   0.6    1.8  1  NAD_binding_8    NAD(P)-binding Rossmann-like domain
      0.016   15.1   1.1      0.032   14.1   0.9    1.7  1  UPF0146          Uncharacterised protein family (UPF0146)
      0.019   15.4   1.2      0.055   13.9   0.9    1.9  2  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
       0.02   15.5   0.2      0.043   14.5   0.2    1.6  1  PglD_N           PglD N-terminal domain
      0.022   14.3   0.9      0.069   12.7   0.8    1.8  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
      0.025   15.2   1.7      0.066   13.9   1.2    2.1  1  CoA_binding      CoA binding domain
       0.03   15.1   1.2      0.037   14.8   0.2    1.7  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
      0.031   13.4   0.0      0.048   12.8   0.0    1.3  1  RmlD_sub_bind    RmlD substrate binding domain
      0.041   14.3   1.1      0.089   13.2   1.1    1.6  1  NAD_binding_7    Putative NAD(P)-binding
      0.089   12.1   0.1       0.19   11.0   0.1    1.5  2  Amino_oxidase    Flavin containing amine oxidoreductase
      0.094   12.9   0.2       0.39   10.9   0.2    2.1  1  UPF0180          Uncharacterised protein family (UPF0180)
        0.1   11.9   1.3       0.19   11.0   1.3    1.5  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
        0.1   13.1   0.0       0.22   12.0   0.0    1.6  1  XdhC_C           XdhC Rossmann domain
       0.12   11.4   1.3       0.17   10.9   1.3    1.5  1  GIDA             Glucose inhibited division protein A
       0.14   12.2   1.4       0.53   10.4   1.4    1.9  1  Ldh_1_N          lactate/malate dehydrogenase, NAD binding do


Domain annotation for each model (and alignments):
>> P5CR_dimer  Pyrroline-5-carboxylate reductase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.1   0.2   5.9e-39   2.5e-36       1     101 [.     151     253 ..     151     255 .. 0.98

  Alignments for each domain:
  == domain 1  score: 124.1 bits;  conditional E-value: 5.9e-39
                                       CCHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHHHHCHS..HHHHHHHH--TTSHHHH CS
                        P5CR_dimer   1 EkqldavtalsGsgpAyvflliealadagvklGlsreeArelaaqtvaGaaklllese..paelrdkvtspgGtTia 75 
                                       E+++da+t+lsGsgpAy  +++eal+ +g k Gl+r++Ar  aaqt++G+akllle++  pa++r++vt+pgGtTi 
  gi|242398611|ref|YP_002994035.1| 151 EEYMDAITGLSGSGPAYASVFLEALIYSGLKVGLPRDIARLAAAQTLLGTAKLLLETDfhPAQVREMVTTPGGTTID 227
                                       899**************************************************9988899***************** PP

                                       HHHHHHHTTHHHHHHHHHHHHHHHHH CS
                        P5CR_dimer  76 glkeleegglraavieaveaaakrsk 101
                                       g+ ele++++r+a+++aveaa+k+sk
  gi|242398611|ref|YP_002994035.1| 228 GIFELEDSRFRTAIMKAVEAATKKSK 253
                                       ************************97 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.6   2.0     4e-24   1.7e-21       1      97 []       2      91 ..       2      91 .. 0.95

  Alignments for each domain:
  == domain 1  score: 76.6 bits;  conditional E-value: 4e-24
                                      EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHHHH CS
                     F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedveevls 79
                                      +i++iGaG +g+a+a+ l+++g   +e+v a++r+ +k+  + e++gv+v+  dn+ aae+ad+v+lavkp++v++vl+
  gi|242398611|ref|YP_002994035.1|  2 RIAVIGAGTIGSAVAKALAEEG---YEVV-ATRRKTSKV-MWLEDYGVEVSN-DNKAAAEKADIVILAVKPNKVKKVLE 74
                                      79********************...****.977777777.7889********.************************** PP

                                      HCGHHHHTTSEEEEESSS CS
                     F420_oxidored 80 elakdalkgklvisvlag 97
                                      e+ k a +gk++is +ag
  gi|242398611|ref|YP_002994035.1| 75 EV-KPAVEGKILISFAAG 91
                                      **.999*********997 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 !   45.4   0.3   2.3e-14   9.4e-12       1      88 [.       2      87 ..       2      95 .. 0.94
   2 ?   -1.1   0.0       4.4   1.8e+03     136     154 ..     130     148 ..     129     150 .. 0.88

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 2.3e-14
                                      EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHSHCCC CS
                     NAD_binding_2  1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdeviegllea 79
                                      +i++iG G++Gs  a+ l+++gy+v++  r+++kv  l + g+++ ++ +++++++d+vi+ vk  ++v++v+e++++a
  gi|242398611|ref|YP_002994035.1|  2 RIAVIGAGTIGSAVAKALAEEGYEVVATRRKTSKVMWLEDYGVEVSNDNKAAAEKADIVILAVKP-NKVKKVLEEVKPA 79
                                      59*************************************************************86.88*******9998 PP

                                      --TT-EEEE CS
                     NAD_binding_2 80 lkkgdilid 88
                                      + +g+ili 
  gi|242398611|ref|YP_002994035.1| 80 V-EGKILIS 87
                                      7.6888886 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 4.4
                                       HHHHHHHHHHHHHHEEEEE CS
                     NAD_binding_2 136 eeafervkpvleaigakvt 154
                                       +e++e v+ ++ a+g+++ 
  gi|242398611|ref|YP_002994035.1| 130 KEEIELVERIFGAFGKCIR 148
                                       78999***********985 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 !   42.2   0.3   1.5e-13   6.1e-11       6     101 ..       2      96 ..       1     113 [. 0.88

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 1.5e-13
                                       -EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEH.HHHHHT-SEEEE-S-HHHHHHHHHHHT CS
                              IlvN   6 kiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltv.aeavkkadvvmiliPDelqkevyeeei 81 
                                       +iaviG G+ G a a+ l + g +vv + r++s +v   ++ g+ev +  + a++kad+v++ +  +  k+v+ ee+
  gi|242398611|ref|YP_002994035.1|   2 RIAVIGAGTIGSAVAKALAEEGYEVVATRRKTS-KVMWLEDYGVEVSNDnKAAAEKADIVILAVKPNKVKKVL-EEV 76 
                                       69***********************98888887.778889******8761567899****9999878888899.89* PP

                                       GGG--TT-EEEESSSHHHHT CS
                              IlvN  82 epnlkegkalafahGfnihf 101
                                       +p ++ +  ++fa G++++f
  gi|242398611|ref|YP_002994035.1|  77 KPAVEGKILISFAAGLSLNF 96 
                                       ****************9988 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.8   4.7e-12     2e-09       1     105 [.       3      92 ..       3     132 .. 0.80

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 4.7e-12
                                       EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHCEEEEETTCEEEEEECEEECCHSCCCCS-ESEEEE-S CS
                              ApbA   1 iailGaGaiGsllaakLakagadvtlilrsr.rlealkknGlrltseggeeilrppealsaeekselepidlvivtv 76 
                                       ia++GaG iGs +a  La+ g++v+   r+  +++ l++ G++++ ++         +++ae      ++d+vi++v
  gi|242398611|ref|YP_002994035.1|   3 IAVIGAGTIGSAVAKALAEEGYEVVATRRKTsKVMWLEDYGVEVSNDN---------KAAAE------KADIVILAV 64 
                                       89***************************9977776666666666655.........44444......89******* PP

                                       SGGGHHHHHHHHGGGECTCEEEEEESSSS CS
                              ApbA  77 KayqteealeeikplldpntvvlllqNGl 105
                                       K   ++++lee+kp+++ + + +++  Gl
  gi|242398611|ref|YP_002994035.1|  65 KPNKVKKVLEEVKPAVEGK-ILISFAAGL 92 
                                       *****************98.666666555 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 !   26.2   4.3   1.6e-08   6.5e-06       2     115 ..       3     101 ..       2     120 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 1.6e-08
                                       EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHHSSBTTTBTT----TTEEEES-HHHHHTT--EEEE--- CS
                    NAD_Gly3P_dh_N   2 iavlGaGswGtalAkvlaenghevrlwvreeelieeineehenvkyLpgiklpenlvattdlaealkgadiivlvvP 78 
                                       iav+GaG  G+a+Ak+lae+g ev+   r+             v  L++      +++++d ++a+++adi++l+v 
  gi|242398611|ref|YP_002994035.1|   3 IAVIGAGTIGSAVAKALAEEGYEVVATRRKTSK----------VMWLED----YGVEVSNDNKAAAEKADIVILAVK 65 
                                       9********************988865554433..........345554....578999****************** PP

                                       HHHHHHHHHHHCCC--TT-EEEE---SEET.TTEEHH CS
                    NAD_Gly3P_dh_N  79 sqalrevlkklkgllkkkailvsliKGieegtlklls 115
                                        + +++vl+++k+ + + +il+s + G++ + lk+l+
  gi|242398611|ref|YP_002994035.1|  66 PNKVKKVLEEVKPAV-EGKILISFAAGLSLNFLKRLT 101
                                       *************99.7899********887777765 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 !   30.6   0.1   4.5e-10   1.9e-07      38     103 ..       2      68 ..       1      91 [. 0.91

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 4.5e-10
                                       EEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEEC.SHHHHHHH-SEEEE-S--ST CS
                      2-Hacid_dh_C  38 tvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelv.sleellaesDivslhlpltp 103
                                       ++++iG+G IG+avak l++ g +v+a+ r+ +k    e++gve+  + +++ +++Div+l++  ++
  gi|242398611|ref|YP_002994035.1|   2 RIAVIGAGTIGSAVAKALAEEGYEVVATRRKTSKVMWLEDYGVEVSnDNKAAAEKADIVILAVKPNK 68 
                                       789****************************9999999*****8776999999********998776 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.4   2.1e-09     9e-07       1      87 [.       1      76 [.       1     120 [. 0.85

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 2.1e-09
                                      EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEBSSHHHHHHH-SEEEE-S-HHH CS
                            DapB_N  1 ikvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglgklgvavtddleevlekadvliDFTtpea 79
                                      +++av+Ga G++G++v+ka+ e e++e+va   +++         +++ l+  gv+v++d ++++ekad++i   +p+ 
  gi|242398611|ref|YP_002994035.1|  1 MRIAVIGA-GTIGSAVAKALAE-EGYEVVATRRKTS---------KVMWLEDYGVEVSNDNKAAAEKADIVILAVKPNK 68
                                      89*****9.************9.******9977776.........77888999*********************99999 PP

                                      HHHHHHHH CS
                            DapB_N 80 vlenlkla 87
                                      v+++l+ +
  gi|242398611|ref|YP_002994035.1| 69 VKKVLEEV 76
                                      99988765 PP

>> PDH  Prephenate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.1   2.2e-08   9.4e-06       1      75 [.      15      86 ..      15     100 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 2.2e-08
                                      HHHHHHHTT--SEEEEE-SSHHHHHHHHHTTSSSEEES-GGGGCCGSEEEE-S-GGGHHHHHHHHHHHS-TT-EE CS
                               PDH  1 laralrrkgfkvtvigydideekaeaalelglvdeatddieavkeadivvlavPvevilevlkelaphlkedali 75
                                      +a+al ++g    v+ + ++++k    ++ g++  +++  +a+++adiv+lav ++++++vl+e++p+++ + li
  gi|242398611|ref|YP_002994035.1| 15 VAKALAEEG--YEVVATRRKTSKVMWLEDYGVEVSNDN-KAAAEKADIVILAVKPNKVKKVLEEVKPAVEGKILI 86
                                      689999999..555666666666666678999999999.59**************************99988776 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.5   9.2e-08   3.8e-05      14      87 ..       2      68 ..       1      86 [. 0.80

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 9.2e-08
                                      EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SSSSS CS
                      Shikimate_DH 14 kvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisatasee 87
                                      ++ +iGaG +++ vak+L+++g++ vv + R  +++  l e+++         ++ k++ ++ad+vi a++ ++
  gi|242398611|ref|YP_002994035.1|  2 RIAVIGAGTIGSAVAKALAEEGYE-VVATRRKTSKVMWL-EDYGV-----EVSNDNKAAAEKADIVILAVKPNK 68
                                      789********************9.77777888888877.56633.....3567888999********987655 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 !   23.9   0.5   7.7e-08   3.2e-05       2      34 ..       3      35 ..       2      42 .. 0.91
   2 ?    3.2   0.2      0.17        70      67     122 ..      44      97 ..      42     108 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 7.7e-08
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHH CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseea 34
                                      +aviGaGt+G+ +a+++a++g+eVv + +++++
  gi|242398611|ref|YP_002994035.1|  3 IAVIGAGTIGSAVAKALAEEGYEVVATRRKTSK 35
                                      9************************99988765 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.17
                                       EEEES-HHHHH.C-SEEEE-S-SSHHHHHHHHHHHHCCS-TTSEEEE--SSS-HHHH CS
                           3HCDH_N  67 isfttdleeav.dadlviEavvEnlelKrkvfaelekiakpdailasnTSslsisel 122
                                       +++++d ++a+ +ad+vi av  n ++K kv++e++ ++ +  il+s + +ls++ l
  gi|242398611|ref|YP_002994035.1|  44 VEVSNDNKAAAeKADIVILAVKPN-KVK-KVLEEVKPAV-EGKILISFAAGLSLNFL 97 
                                       567888888888999999999766.444.5888988887.66677777777777666 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.6   2.9e-07   0.00012       2     103 ..       2     105 ..       1     117 [. 0.78

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 2.9e-07
                                       -EEEET--S-TTSHHHHHHHHHHHHT--EEEESSS-SEETTEE....S----T........T--EEEE-S-HHHHGG CS
                     CoA_binding_2   2 tiaVvGasdnpgkfgykvlryllehglpvvpVnpkeeeilgek....vyaslaed....pepvdlvdvftppeatpe 70 
                                       +iaV+G     g  g  v++ l e+g++vv+   k +++   +    +   +++d     e+ d+v ++++p+++ +
  gi|242398611|ref|YP_002994035.1|   2 RIAVIG----AGTIGSAVAKALAEEGYEVVATRRKTSKVMWLEdygvE---VSNDnkaaAEKADIVILAVKPNKVKK 71 
                                       699***....7889**********************999997734432...2222245689**************** PP

                                       GHHHH.HHH--SEEEE-TT---HHHHHHHHHTT- CS
                     CoA_binding_2  71 ivkea.lalgakavwlqpgsedeeaaelaeeagi 103
                                       +++e+  a++ k ++ +++  +  +++++  a+i
  gi|242398611|ref|YP_002994035.1|  72 VLEEVkPAVEGKILISFAAGLSLNFLKRLTGAKI 105
                                       *****44557777777777777777777766665 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 !   18.0   0.1   3.9e-06    0.0016       1      39 [.       1      39 [.       1      46 [. 0.91
   2 ?    2.5   0.1      0.23        96      64      87 ..      44      66 ..      36      82 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3.9e-06
                                      SEEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHH CS
                    UDPG_MGDP_dh_N  1 mkisviGlGYvGlvtaavlaeighevigvDideekvdkl 39
                                      m+i+viG+G +G   a +lae g ev+     ++kv  l
  gi|242398611|ref|YP_002994035.1|  1 MRIAVIGAGTIGSAVAKALAEEGYEVVATRRKTSKVMWL 39
                                      89*************************999998888655 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.23
                                      EEEES-HHHHHHC-SEEEE----- CS
                    UDPG_MGDP_dh_N 64 lsfttdvekaveeadvifiaVgTP 87
                                      ++ ++d + a+e+ad++++aV  P
  gi|242398611|ref|YP_002994035.1| 44 VEVSNDNKAAAEKADIVILAVK-P 66
                                      6778899999**********96.4 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   4.5e-07   0.00019       2      43 ..       4      44 ..       3      83 .. 0.70

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 4.5e-07
                                      EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC CS
                         Epimerase  2 lVtGatGfiGsalvkallekgyevigldrlssasntarledl 43
                                       V+Ga G iGsa++kal+e+gyev++  r++s+  + ++  +
  gi|242398611|ref|YP_002994035.1|  4 AVIGA-GTIGSAVAKALAEEGYEVVATRRKTSKVMWLEDYGV 44
                                      57776.************************888876654433 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.4   7.8e-07   0.00033       3      73 ..       8      69 ..       7     134 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 7.8e-07
                                      TSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCC CS
                    NAD_binding_10  3 tGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsalggggk 73
                                       G +G++++k l+++ g+ev+a  R+++k+  le+  g+     +v  ++d ++a + ad+V+ a+ +++ 
  gi|242398611|ref|YP_002994035.1|  8 AGTIGSAVAKALAEE-GYEVVATRRKTSKVMWLED-YGV-----EV--SNDNKAAAEKADIVILAVKPNKV 69
                                      79**********999.5*************98874.333.....33..4567799999*******987765 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.9     6e-06    0.0025       1      47 [.       3      49 ..       3      72 .. 0.84
   2 ?    1.1   0.1       1.1   4.7e+02      21      41 ..      56      76 ..      41      85 .. 0.58

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 6e-06
                                      EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTTSEEEES CS
                            TrkA_N  1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreeglevvvg 47
                                      i++iG+G++G+++a+ L e g+ +vv+  ++ ++v  l++ g+ev + 
  gi|242398611|ref|YP_002994035.1|  3 IAVIGAGTIGSAVAKALAEeGY-EVVATRRKTSKVMWLEDYGVEVSND 49
                                      79*****************777.5999999999999999999887654 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 1.1
                                      TEEEEEEESSHHHHHHHHHTT CS
                            TrkA_N 21 gkdvvvidkdeerveelreeg 41
                                      + d+v+   ++++v+++ ee 
  gi|242398611|ref|YP_002994035.1| 56 KADIVILAVKPNKVKKVLEEV 76
                                      134555555555555555555 PP

>> Rossmann-like  Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   1.4   3.7e-06    0.0016      12     113 ..       2      98 ..       1     108 [. 0.72

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.7e-06
                     Rossmann-like  12 svGiisaGrvGtalgaaleraghvvvgisaisaasreraerrlPdvpvl.evedvaaraellllavPdaelpglvkg 87 
                                        + +i+aG +G+a+++al+  g+ vv+     ++s+    +   +v+v  + +  a++a++++lav   ++ +++++
  gi|242398611|ref|YP_002994035.1|   2 RIAVIGAGTIGSAVAKALAEEGYEVVATRR--KTSKVMWLEDY-GVEVSnDNKAAAEKADIVILAVKPNKVKKVLEE 75 
                                       5789********************998654..45554443333.33443034567899****************999 PP

                     Rossmann-like  88 laatgavraGtivahtsganGveila 113
                                       +  +    +G+i++  ++   ++ l+
  gi|242398611|ref|YP_002994035.1|  76 VKPA---VEGKILISFAAGLSLNFLK 98 
                                       9766...5677776666655555555 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   2.5   2.8e-05     0.012       4      43 ..       4      41 ..       2      77 .. 0.68
   2 ?    3.9   0.2     0.079        33      20      83 ..      52     117 ..      43     139 .. 0.74
   3 ?   -1.9   0.0       4.6   1.9e+03      29      48 ..     205     225 ..     176     255 .. 0.51

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.8e-05
                                      EEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHH CS
                         adh_short  4 lvtGassGIGraiakelakeGakvvvvdrseekleevake 43
                                       v+Ga+  IG a+ak+la+eG++vv++ r+ +k+  +++ 
  gi|242398611|ref|YP_002994035.1|  4 AVIGAG-TIGSAVAKALAEEGYEVVATRRKTSKV-MWLED 41
                                      677877.9******************99999887.44444 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.079
                                       HHHTT-EEEEEESCHHHHHHHHHHHHHT.TSEEEEEE-TTTSHHHHHHHH.HHHHHHHSSESEEEE CS
                         adh_short  20 lakeGakvvvvdrseekleevakelkee.gakalaiqvDvtdreevealv.ekavkklgkldvLvn 83 
                                        a+e a++v+++ +++k+++v++e+k + + k+l+  +   + + +++l  +k+v  + ++ vLv+
  gi|242398611|ref|YP_002994035.1|  52 AAAEKADIVILAVKPNKVKKVLEEVKPAvEGKILISFAAGLSLNFLKRLTgAKIVRAMSNIAVLVK 117
                                       57888999999999*********9999976665554444445666666553567777777777775 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 4.6
                                       E.EESCHHHHHHHHHHHHHTT CS
                         adh_short  29 v.vdrseekleevakelkeeg 48 
                                       + +d ++++++e+++  + + 
  gi|242398611|ref|YP_002994035.1| 205 LeTDFHPAQVREMVTTPGGTT 225
                                       334444444444444444333 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 !   18.7   0.2   4.3e-06    0.0018      22      96 ..      15      85 ..      11      90 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 4.3e-06
                                      HHHHHHHCTSEEEEE-SSTHHCCCCHHGGBTCCEEES-CHHHHTT-SEEEE-S--GGGGGS-HHHHHHCCSS-EE CS
                    UDPG_MGDP_dh_C 22 iieeLleegaevkiyDPkvkeeaveaeleekgvevvdsleealkgadaiviltehdefkeldlaklkelmkpavv 96
                                      +++ L+eeg+ev++   k+++    +   ++gvev ++ + a+++ad+++++++ ++ k++ l+++k  ++ +++
  gi|242398611|ref|YP_002994035.1| 15 VAKALAEEGYEVVATRRKTSKVMWLE---DYGVEVSNDNKAAAEKADIVILAVKPNKVKKV-LEEVKPAVEGKIL 85
                                      7899*********9999999877666...79*****************************5.7888877776665 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 ?    3.7   0.0      0.12        49       6      39 ..      13      46 ..       9      48 .. 0.86
   2 !   12.1   0.1    0.0003      0.13      88     149 ..      47     105 ..      43     118 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.12
                                      HHHHHHHHCTSSEEEE-S---TTTHHHHHHHHHH CS
                         QRPTase_C  6 armveaaksakvrildTRkttPglrllekyAvli 39
                                      +++++a++++   +++TR+ t  + +le y v +
  gi|242398611|ref|YP_002994035.1| 13 SAVAKALAEEGYEVVATRRKTSKVMWLEDYGVEV 46
                                      567788888999******************9976 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.0003
                                       SSHHHHHHHHHHT-SEEEEES--HHHHHHHHHHH.HHHSTTSEEEEESS--TTTHHHHHCTT- CS
                         QRPTase_C  88 esleeleevleaeadiimLDnfsveelkkaveel.keknkrvlievSGgvtlenveeyaksgv 149
                                       +++   +++++++adi+ L  ++++++kk++ee+  + ++++li+ + g++l+ ++ +   ++
  gi|242398611|ref|YP_002994035.1|  47 SND---NKAAAEKADIVIL-AVKPNKVKKVLEEVkPAVEGKILISFAAGLSLNFLKRLTGAKI 105
                                       444...45778899****9.79************5567888************9999887764 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.6   1.4e-05    0.0058       1      50 [.       3      49 ..       3     135 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.4e-05
                                      EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEEES CS
                              NmrA  1 IlviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelvkg 50
                                      I+viGa G +G++v++al+++g++v a  R+t++     l++ Gve+ ++
  gi|242398611|ref|YP_002994035.1|  3 IAVIGA-GTIGSAVAKALAEEGYEVVATRRKTSKV--MWLEDYGVEVSND 49
                                      899997.********************99988654..5688888887533 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   1.0   2.5e-05      0.01       1      65 [.       3      75 ..       3      96 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.5e-05
                                      EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH..............TTTCEEEEE--TTTHHHHHHH CS
                   Sacchrp_dh_NADP  1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaaka..............lgvrfeaialdaenyeavLaa 65
                                      + +iGaG +G+ava+ la+++      +va+r k++  ++   +               + ++ + a+ ++++++vL++
  gi|242398611|ref|YP_002994035.1|  3 IAVIGAGTIGSAVAKALAEEGYE----VVATRRKTS--KVMWLEdygvevsndnkaaaEKADIVILAVKPNKVKKVLEE 75
                                      689****************9854....555555555..33322233566666666666666666666666666666666 PP

>> POR  Pyruvate ferredoxin/flavodoxin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1     2e-05    0.0083       4      85 ..       7      87 ..       6     126 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2e-05
                                      THHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEES.SHHHHHHHGGGEEEE.. CS
                               POR  4 GvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllval.daetlsehldglkpg.. 79
                                      G+ t+g   aka+a++Gy+v+a+r   s+ +     + v +s++   ++ + ++ad+++    ++ ++++l+++kp   
  gi|242398611|ref|YP_002994035.1|  7 GAGTIGSAVAKALAEEGYEVVATRRKTSKVMWLE-DYGVEVSNDN--KAAA-EKADIVILAvKPNKVKKVLEEVKPAve 81
                                      899**********************999888766.6789999993..5555.79**99877366***********9877 PP

                                      EEEEEE CS
                               POR 80 giiiyn 85
                                      g i++ 
  gi|242398611|ref|YP_002994035.1| 82 GKILIS 87
                                      888775 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   1.7   6.7e-05     0.028      20      42 ..       2      24 ..       1      81 [. 0.86
   2 ?    0.1   0.0         1   4.2e+02     101     128 ..      48      75 ..      24      97 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.7e-05
                                      EEEEE--SHHHHHHHHHHHHHTT CS
                                      xxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF 20 kvllvGaGglGsellknLalsGv 42
                                      +++++GaG++Gs ++k+La  G 
  gi|242398611|ref|YP_002994035.1|  2 RIAVIGAGTIGSAVAKALAEEGY 24
                                      89*****************8775 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1
                                       CS-HHHHTT-SEEEEESSSHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF 101 tvleellesvDlVvdalDniearrlvnr 128
                                       + ++   e++D+V++a+   ++++ + +
  gi|242398611|ref|YP_002994035.1|  48 NDNKAAAEKADIVILAVKPNKVKKVLEE 75 
                                       3467889999****99987777776655 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 !   14.9   0.0   3.1e-05     0.013       5      76 ..       7      78 ..       6      81 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.1e-05
                                      TTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--T....T-HHHHHHHHHHHT- CS
                     GDP_Man_Dehyd  5 iaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDl....tDssslerllaevqp 76
                                      +aG iGs +a+ L e+gyev+ + r++s++    +e    +   +++++    k+D+       ++++++l+ev+p
  gi|242398611|ref|YP_002994035.1|  7 GAGTIGSAVAKALAEEGYEVVATRRKTSKV--MWLEDYGVEV--SNDNKAAAEKADIvilaVKPNKVKKVLEEVKP 78
                                      79******************9987777664..4555544322..33445555555552222234556666666655 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   1.2     3e-05     0.013     144     201 ..       2      62 ..       1      95 [. 0.73

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3e-05
                                       EEEEES-SHHHHHHHHHHHHHT-E.EEEEESSSSSS..TTS-HHHHHHHHHHHHHTTEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 144 rivvvGgGyiGvElAaalaklgke.vtlveardrll..raldkelsaaleealekeGvevk 201
                                       ri+v+G+G iG+ +A ala+ g+e v      ++++  + ++ e+s+  ++a ek ++ + 
  gi|242398611|ref|YP_002994035.1|   2 RIAVIGAGTIGSAVAKALAEEGYEvVATRRKTSKVMwlEDYGVEVSNDNKAAAEKADIVIL 62 
                                       6899999999999999999999994444555667778888888888888888777777665 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.9   1.3   3.6e-05     0.015       1      30 [.       2      31 ..       2      62 .. 0.87
   2 ?   -0.7   0.0       5.4   2.3e+03      27      58 ..     105     136 ..      94     138 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3.6e-05
                                      EEEEECSSHHHHHHHHHHHHTTSEEEEEES CS
                         Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvver 30
                                      +++v+G+G+ig  +A+alae g +V    r
  gi|242398611|ref|YP_002994035.1|  2 RIAVIGAGTIGSAVAKALAEEGYEVVATRR 31
                                      79********************99976555 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 5.4
                                       EEESSSSSSTTSSHHHHHHHHHHHHHTTEEEE CS
                         Pyr_redox  27 vversdkllrllDeeaskilqeklekngievl 58 
                                       +v +++++  l  e + +++++ l k+ ie++
  gi|242398611|ref|YP_002994035.1| 105 IVRAMSNIAVLVKESFTAYTTDDLDKEEIELV 136
                                       55556666666677778888888888888875 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.3   7.8e-05     0.033       2      24 ..       3      27 ..       2      35 .. 0.88
   2 ?   -2.1   0.0       5.3   2.2e+03     195     213 ..      84     100 ..      37     140 .. 0.49

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.8e-05
                                      EEEECTSHHHHHHHHHHHHTT..EE CS
                               DAO  2 vviiGGGiiGlstAyeLarrg..Vt 24
                                      +++iG+G iG+++A +La++g  V+
  gi|242398611|ref|YP_002994035.1|  3 IAVIGAGTIGSAVAKALAEEGyeVV 27
                                      9******************998754 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 5.3
                                       E.EEE--GGGHHHHHTTCTT CS
                               DAO 195 a.vVnaaGawsdllgllkel 213
                                         +  aaG+  ++l   k+l
  gi|242398611|ref|YP_002994035.1|  84 IlISFAAGLSLNFL---KRL 100
                                       14556666666666...444 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.6   0.00011     0.046       1      23 [.       5      27 ..       5      31 .. 0.96

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 0.00011
                                      EE--SHHHHHHHHHHHCCTEEEE CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvl 23
                                      ++GaG  G++ A +La++g++v+
  gi|242398611|ref|YP_002994035.1|  5 VIGAGTIGSAVAKALAEEGYEVV 27
                                      8********************96 PP

>> UPF0146  Uncharacterised protein family (UPF0146)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.9   7.7e-05     0.032      16     101 ..       2      87 ..       1     123 [. 0.87

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7.7e-05
                                       EEEEET-TT-.-HHHHHHHHHS-EEEEE-SS-S....STTEE---SSS--HHHHTTEEEEEEES--TTSHHHHHHHH CS
                           UPF0146  16 kvvEvGiGrk.ldvaealakrgvdlvatDikekkakegvrivrDDvtdPnleiYkgadliYslRpPaelqsaildva 91 
                                       +++ +G+G+   +va+ala+ g ++vat  k +k+   ++ +  +v + n +  + ad++     P+ +++ + +v 
  gi|242398611|ref|YP_002994035.1|   2 RIAVIGAGTIgSAVAKALAEEGYEVVATRRKTSKVM-WLEDYGVEVSNDNKAAAEKADIVILAVKPNKVKKVLEEVK 77 
                                       8999****86379***************99998665.567788899************9988888999********* PP

                                       HHHT-EEEEE CS
                           UPF0146  92 kkvgAaliik 101
                                        +v+ +++i 
  gi|242398611|ref|YP_002994035.1|  78 PAVEGKILIS 87 
                                       ***9999986 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.9   0.00013     0.055       1      98 [.       2      90 ..       2     106 .. 0.76
   2 ?   -1.3   0.0       6.6   2.8e+03      48      73 ..     117     142 ..      72     150 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00013
                                      EEEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEEGGGGGCTT-SEEEE-SCHHHH CS
                    Semialdhyde_dh  1 kvaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavkaleegkdlkvedvdeeelkevdivflalpagvs 79
                                      ++a++G  G +G+++++ L+e+       +++++r + +k+  +     e   ++v++ ++++ +++div+la+  +  
  gi|242398611|ref|YP_002994035.1|  2 RIAVIG-AGTIGSAVAKALAEEG----YEVVATRR-KTSKVMWL-----EDYGVEVSNDNKAAAEKADIVILAVKPNKV 69
                                      69****.8************954....33344555.34444444.....234567777678999*********999999 PP

                                      HHHHHHH..HHTTSEEEESSS CS
                    Semialdhyde_dh 80 kelapkl..aeagvkviDlss 98
                                      k++ +++  a +g ++i+ ++
  gi|242398611|ref|YP_002994035.1| 70 KKVLEEVkpAVEGKILISFAA 90
                                      999988867778888888876 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 6.6
                                       GTTTECEBEEEGGGGGCTT-SEEEE- CS
                    Semialdhyde_dh  48 leegkdlkvedvdeeelkevdivfla 73 
                                        e+ + ++ +d d+ee++ v+ +f a
  gi|242398611|ref|YP_002994035.1| 117 KESFTAYTTDDLDKEEIELVERIFGA 142
                                       34455555566666666666666655 PP

>> PglD_N  PglD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.2    0.0001     0.043       1      72 [.       2      71 ..       2      76 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 0.0001
                            PglD_N  1 kivIiGaGGhgkvvadiieangeyeiigflDdnkkte.vegypvlgkaiellkslseeeyevvi.AIGnnkvRk 72
                                      +i++iGaG  g  va+ +  +g ye+++   +++k   +e+y v     ++ ++  +e+ ++vi A+  nkv+k
  gi|242398611|ref|YP_002994035.1|  2 RIAVIGAGTIGSAVAKALAEEG-YEVVATRRKTSKVMwLEDYGVEV---SNDNKAAAEKADIVIlAVKPNKVKK 71
                                      69********************.**999887777643244554443...3333444455555544999999987 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 ?   12.7   0.8   0.00017     0.069       5      30 ..      10      35 ..       6      90 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00017
                                      SHHHHHHHHHHHTT-EEEEEESSGGH CS
                      adh_short_C2  5 gIGraiAkalaeeGaevvltdlneea 30
                                       IG a+AkalaeeG+evv+t ++ ++
  gi|242398611|ref|YP_002994035.1| 10 TIGSAVAKALAEEGYEVVATRRKTSK 35
                                      6*******************998876 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   1.2   0.00016     0.066       5      84 ..       2      78 ..       1      91 [. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00016
                                      EEEEETTTSHHHHHHHHHHHHHHECEEEEEEC-TTTTTCEETTEEEESCHHHHHHHCTTTEEEEES-HHHHHHHHHHHH CS
                       CoA_binding  5 kviviGagglgiaglyhfkeklkygikavfgvnprkvgtevlglpvyksvdeleektevdvavitvPaesaqeavdelv 83
                                      +++viGag  g+a++   +e+ +y+++a    + + +  e  g++v ++ + + ek  +d+ +++v +++++++ +e+ 
  gi|242398611|ref|YP_002994035.1|  2 RIAVIGAGTIGSAVAKALAEE-GYEVVATRRKTSKVMWLEDYGVEVSNDNKAAAEK--ADIVILAVKPNKVKKVLEEVK 77
                                      799*******99998777776.77777777777777889999**************..*************99988864 PP

                                      H CS
                       CoA_binding 84 e 84
                                       
  gi|242398611|ref|YP_002994035.1| 78 P 78
                                      4 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.2   8.9e-05     0.037       1      76 [.       1      70 [.       1      81 [. 0.78

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 8.9e-05
                                      EEEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHH.HHHTTHEEESSHHHHHTCTTESEEEE-S-GGGHH CS
                      GFO_IDH_MocA  1 lrvaiiGaGkigskhlrplnesqrleevvalldpdaeraeav.aesfgveaysdleelladpeidavivatpngthe 76
                                      +r+a+iGaG igs  +++l e+  ++evva    + + ++ +  e +gve+ +d ++ ++  ++d+vi a+ +++ +
  gi|242398611|ref|YP_002994035.1|  1 MRIAVIGAGTIGSAVAKALAEE--GYEVVAT---RRKTSKVMwLEDYGVEVSNDNKAAAE--KADIVILAVKPNKVK 70
                                      69**************888888..8888843...33333333479*****8888888888..99******9997644 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00011     0.048       1      34 [.       1      56 [.       1      90 [. 0.70

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00011
                                      EEEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT.......................T CS
                     RmlD_sub_bind  1 mkilvtGanGqlGseLakqlaeeglevlaltre.......................e 34
                                      m+i v+Ga G +Gs++ak+laeeg+ev+a+ r+                       +
  gi|242398611|ref|YP_002994035.1|  1 MRIAVIGA-GTIGSAVAKALAEEGYEVVATRRKtskvmwledygvevsndnkaaaeK 56
                                      89999997.99*******************999777777666655555444444443 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   1.1   0.00021     0.089       9      78 ..       2      73 ..       1      90 [. 0.72

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00021
                     NAD_binding_7  9 kvlvvGgGevAarkvrklleagakvtvvapevkeeleelvklaeeel......ekdlegadlviaatddrelneri 78
                                      ++ v+G+G+++   ++ l+e+g +v+    +    +++ + l++  +      ++  e+ad+vi a++ +++++ +
  gi|242398611|ref|YP_002994035.1|  2 RIAVIGAGTIGSAVAKALAEEGYEVVATRRK----TSKVMWLEDYGVevsndnKAAAEKADIVILAVKPNKVKKVL 73
                                      689******************9988766666....444444444333222211555889********998887755 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00045      0.19     210     267 ..      13      73 ..       6      94 .. 0.84
   2 ?   -3.2   0.0       9.3   3.9e+03     335     370 ..     211     246 ..     191     252 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00045
                                       HHHHHHHHHTTTTEEEETSEEEEEEEE.ETTCEEEEETTSTEE.EESEEEE-S-HHHHH..S CS
                     Amino_oxidase 210 sqlpealaeelrgldirlntrVkeikr.egdgvtvtledgevv.eaDaVvvTvplgvlk..a 267
                                       s++++alae ++   + ++++ +++ + e+ gv v   +     +aD V+++v ++ +k   
  gi|242398611|ref|YP_002994035.1|  13 SAVAKALAE-EGYEVVATRRKTSKVMWlEDYGVEVSNDNKAAAeKADIVILAVKPNKVKkvL 73 
                                       68999****.999**************9999999976555555***************9443 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 9.3
                                       TTEEEEEEEEEC.HHHHHHHTTS-HHHHHHHHHHHHH CS
                     Amino_oxidase 335 pgkglvllvyvg.gdaaneleslsdeelvqavlrdLr 370
                                       p ++   +v+++ g+ ++ +  l d+    a+++ ++
  gi|242398611|ref|YP_002994035.1| 211 PAQVR-EMVTTPgGTTIDGIFELEDSRFRTAIMKAVE 246
                                       33344.5666666777777777777777777777766 PP

>> UPF0180  Uncharacterised protein family (UPF0180)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.2   0.00095      0.39      10      29 ..      13      32 ..      12      93 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00095
                           UPF0180 10 snvkeaLrekGYeVvdlete 29
                                      s v++aL+e+GYeVv  + +
  gi|242398611|ref|YP_002994035.1| 13 SAVAKALAEEGYEVVATRRK 32
                                      5799***********99863 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 ?   11.0   1.3   0.00045      0.19      30     100 ..       2      65 ..       1      89 [. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00045
                                       EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHCHHHHHHHHHHHH-SEEEE--- CS
                       AlaDh_PNT_C  30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvevlksqeellaeavkeadvvigtvl 100
                                       ++ viG+G+ G + +++ ++ g +V+++  ++++   le++g +   v + +    + a+++ad+vi +v+
  gi|242398611|ref|YP_002994035.1|   2 RIAVIGAGTIGSAVAKALAEEGYEVVATRRKTSKVMWLEDYGVE---VSNDN----KAAAEKADIVILAVK 65 
                                       689*************************************9999...32222....345678899998874 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00052      0.22       2      63 ..       4      75 ..       3      91 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00052
                                      EEE--STTHHHHHHHHHHHTEEEEEEES-GGGG...........-GGG-TT-SE-EEEE--S-HHHHHHHHHH CS
                            XdhC_C  2 vifGaghvaqalarlaaalgfrvtvvdpreefa...........tkerfpeadetavvvlthdhklDaealea 63
                                      +++Gag ++ a+a+ +a+ g++v+  + +++             + ++ ++a+++ +v+l  +++  +++le+
  gi|242398611|ref|YP_002994035.1|  4 AVIGAGTIGSAVAKALAEEGYEVVATRRKTSKVmwledygvevsN-DNKAAAEKADIVILAVKPNKVKKVLEE 75
                                      79*********************9998888433577777777642.333334446666666666666666665 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   1.3   0.00042      0.17       2      38 ..       3      39 ..       2     140 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00042
                                      EEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT-- CS
                              GIDA  2 viViGgGhAGceAAlaaarlGakvlLithkldtiael 38
                                      + ViG+G  G++ A a+a+ G++v+    k++++++l
  gi|242398611|ref|YP_002994035.1|  3 IAVIGAGTIGSAVAKALAEEGYEVVATRRKTSKVMWL 39
                                      78***********************999999988765 PP

>> Ldh_1_N  lactate/malate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   1.4    0.0013      0.53       1      26 [.       1      25 [.       1      71 [. 0.77

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0013
                                      EEEEEETTTSHHHHHHHHHHHHTTSS CS
                           Ldh_1_N  1 vkvavvGaaGgiGqslalllankkla 26
                                      +++av+Ga G+iG+++a +la++++ 
  gi|242398611|ref|YP_002994035.1|  1 MRIAVIGA-GTIGSAVAKALAEEGYE 25
                                      69******.***********998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       874  (0.0487478); expected 358.6 (0.02)
Passed bias filter:                      692  (0.0385967); expected 358.6 (0.02)
Passed Vit filter:                       107  (0.00596798); expected 17.9 (0.001)
Passed Fwd filter:                        43  (0.00239835); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              43  [number of targets reported over threshold]
# CPU time: 0.66u 0.32s 00:00:00.98 Elapsed: 00:00:00.48
# Mc/sec: 1612.27
//
Query:       gi|242398612|ref|YP_002994036.1|  [L=425]
Description: Serine hydroxymethyltransferase [Thermococcus sibiricus MM 739]
Scores for 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-77  261.4   0.0    1.3e-77  261.1   0.0    1.0  1  SHMT             Serine hydroxymethyltransferase
    4.2e-11   42.6   0.0    6.7e-11   42.0   0.0    1.2  1  Aminotran_1_2    Aminotransferase class I and II
    4.7e-08   32.4   0.2    7.1e-08   31.8   0.2    1.3  1  Aminotran_5      Aminotransferase class-V
    1.5e-07   31.0   0.0    3.3e-07   29.9   0.0    1.5  1  Beta_elim_lyase  Beta-eliminating lyase
    0.00086   18.4   0.0     0.0037   16.3   0.0    1.8  2  SelA             L-seryl-tRNA selenium transferase
    0.00086   17.9   0.0     0.0038   15.8   0.0    1.9  2  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
  ------ inclusion threshold ------
      0.015   14.6   0.1      0.022   14.1   0.1    1.3  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
      0.034   14.1   0.0       0.08   12.8   0.0    1.6  2  Lactamase_B_3    Beta-lactamase superfamily domain
      0.048   13.8   0.1       0.12   12.5   0.1    1.6  1  CheD             CheD chemotactic sensory transduction


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 !  261.1   0.0   6.6e-81   1.3e-77       7     399 .]       9     386 ..       4     386 .. 0.92

  Alignments for each domain:
  == domain 1  score: 261.1 bits;  conditional E-value: 6.6e-81
                                       HHHHHHHHHHHHHHHSEE-STT-----HHHHHHHTSGGGG----EETTEESSST-HHHHHHHHHHHHHHHHHCT-ST CS
                              SHMT   7 evaeiikkekerqkeeieliasenftskavlealGsvltnkyaeGyPGkryyGGcefvdeveelaqdrakelfkldp 83 
                                       +v e ++  ++ ++++i+liasen+ts++ + a+ s +  kyaeG+P +ryy Gc++vdeve +  d   +lf+ d 
  gi|242398612|ref|YP_002994036.1|   9 KVLEFVEGHEKWRSSTINLIASENVTSPSTVRAIASGFMHKYAEGWPKQRYYQGCKYVDEVELIGVDLFCKLFRSD- 84 
                                       6777888878888999************************************************************. PP

                                       TTEEEE---SSHHHHHHHHHHHHT-TT-EEEEESCTTTSTGGGT-BTSS-B-SHHHHHSEEEEE-B-TTTSSB-HHH CS
                              SHMT  84 akwgvnvqplsGsqanlavytallepgdrilgldladGGhlthGakveskkisassklfesveykvdketglidyde 160
                                          +++++p sG++an+a +  l e gd+ + l+ ++GGh++h                e+ ++  d+++  id ++
  gi|242398612|ref|YP_002994036.1|  85 ---FADLRPISGTNANQAAFFGLTEAGDKAIVLHTSHGGHISHMPFGAA-----GMRGLEVHTWPFDNDEFNIDVEK 153
                                       ...****************************************654444.....444567777777889******** PP

                                       HHHHHHHH--SEEEEE-SST-S---HHHHHHHHHHTT-EEEEE-GGGHHHHHTTSS--GCC.TSSEEEEESSSTT-S CS
                              SHMT 161 lekkakefkPklivaGtsaysrlidyarlreiadevgayllvdmahiaGlvaagvipsPfe.yadvvtttthktlrG 236
                                         +  +e  Pk++v G s ++     + l  +a+evga+++ d ah+ Gl+ +g + +P++  adv+t+ thkt+ G
  gi|242398612|ref|YP_002994036.1| 154 AAQMIRELEPKIVVFGGSLFPFPHPVKELAPVAKEVGAFVMYDAAHVLGLIGGGQFQDPLReGADVITSSTHKTFPG 230
                                       ***********************************************************96269************* PP

                                       -S-EEEEEC-SEEEEETTTEEEEHHHHHHHHHHHTTTT-SS--HHHHHHHHHHHHHCTSHHHHHHHHHHHHHHHHHH CS
                              SHMT 237 prgglillrkgvksvdktgkevleelekkinsavfPglqGGPlnhviaakavalkealepefkvyqkqvlknakala 313
                                       p+gg+il++           + l e + k++ a+fPg+    + h +a+k v+  e le   k+y++qv+knakala
  gi|242398612|ref|YP_002994036.1| 231 PQGGVILYK-----------D-LGEATAKLQWAIFPGVLSNHHLHHMAGKVVTAAEMLEF-GKAYAEQVVKNAKALA 294
                                       *********...........3.5577899**********************998776653.49************** PP

                                       HHHHHTT-EEGG...GS-SSSEEEEEGGG.GTS-HHHHHHHHHHTTEE-EEE--TTS..STTTT-SEEEEESHHHHH CS
                              SHMT 314 ealkekgyklvs...gGtdnhlvlvdlre.kgldGkraekvlekvnitankntvPgd..ksalvtsGlrlGtpalts 384
                                       ea+ e+g+k++    g t +h v+vd++e ++  G  a  +le++ i  nkn +P d  ++   +sGlr+G   +t+
  gi|242398612|ref|YP_002994036.1| 295 EAMAEEGFKVIGedkGYTKSHQVIVDVSElHEAGGGWAAPLLEEAGIILNKNLLPWDplEKVNAPSGLRIGVQEMTR 371
                                       ***********7322459*********9835677889999*****************999999************** PP

                                       TT--HHHHHHHHHHH CS
                              SHMT 385 rgfkeedlekvakfi 399
                                        g+ e+d++++a+f+
  gi|242398612|ref|YP_002994036.1| 372 VGMMEDDMKEIARFM 386
                                       ************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 !   42.0   0.0   3.3e-14   6.7e-11      74     332 ..      91     343 ..      81     374 .. 0.81

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 3.3e-14
                                       ESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHH.....HHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCT CS
                     Aminotran_1_2  74 gsGagaliealifllklnpgdeilvpdptyasykn.....ilrlsggevvryplyseedfhldlealeealkeapeg 145
                                       +sG++a+++a++ l++  +gd+ +v   +++ ++      ++ ++g+ev+++p  + ++f++d+e+  + ++e+   
  gi|242398612|ref|YP_002994036.1|  91 ISGTNANQAAFFGLTE--AGDKAIVLHTSHGGHIShmpfgAAGMRGLEVHTWP-FDNDEFNIDVEKAAQMIREL--- 161
                                       6899999888888887..***************97444446789999999999.669****************7... PP

                                       TETEEEEEEESS-TTT--B--HHH.HHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSS CS
                     Aminotran_1_2 146 nkktkvilvesphNPtGtvatlee.leklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsK 221
                                         ++k++++       G++++ ++ +++l+ +ak+ +++++ D a+  +  g  ++      + e+ + +i++s  K
  gi|242398612|ref|YP_002994036.1| 162 --EPKIVVFG------GSLFPFPHpVKELAPVAKEVGAFVMYDAAHVLGLIGGGQF---QDPLREGAD-VITSSTHK 226
                                       ..88*****7......7888877659999999********************8777...668888877.88999999 PP

                                       TT.SSGGG-EEEEEEEH...HHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Aminotran_1_2 222 af.GlaGeRvGyilgna...avvsqlrklsrpflsssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLae 294
                                        f G  G   G il+++   a ++ +  +  ++ls  +l +++ +++ +a++  ++ ++ ++++ k++k l +++ae
  gi|242398612|ref|YP_002994036.1| 227 TFpGPQG---GVILYKDlgeATAKLQWAIFPGVLSNHHLHHMAGKVVTAAEML-EFGKAYAEQVVKNAKALAEAMAE 299
                                       99899**...*****999976666667777888889*************9976.6********************** PP

                                       STEEEECCSCSSEEEEEETHHCHHHHHHH.......HHHTCTEEE CS
                     Aminotran_1_2 295 lglkvlasqsgmflltdlsaetakelskk.......Lleevgvyv 332
                                        g+kv++++ g+   + +     +el ++       Llee g+++
  gi|242398612|ref|YP_002994036.1| 300 EGFKVIGEDKGYTKSHQVIVD-VSELHEAgggwaapLLEEAGIIL 343
                                       ********9998633333222.24444445555556666666655 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.2   3.5e-11   7.1e-08      70     218 ..      93     242 ..      91     316 .. 0.82

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 3.5e-11
                                       HHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGT..HHHHHHHHHHTEEEEEEEBETT.SCBEGGGHHHH--.TTEEE CS
                       Aminotran_5  70 tteainlvalslarslkpgdeivvteaehhanl..vpwqelakrtgakvkvipldee.geldldeleklln.ektkl 142
                                       +t+a++++  +l    ++gd+++v ++ h + +  +p  ++   +g++v+ +p+d++  ++d++++++ ++  ++k+
  gi|242398612|ref|YP_002994036.1|  93 GTNANQAAFFGL---TEAGDKAIVLHTSHGGHIshMPFGAAG-MRGLEVHTWPFDNDeFNIDVEKAAQMIReLEPKI 165
                                       7889999999*9...899999999888775554226888887.67********9865169**********8468999 PP

                                       EEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTT....TS---HHHHTESEEEEETTT.TTSSTT-EEEEEE CS
                       Aminotran_5 143 vaithvsnvtGtiqpveeigklakkkgalvlvDaaqavg....hipidvkklgvDflafsghK.llgPtGiGvlyvr 214
                                       v +    +     +pv+e++ +ak++ga+v+ Daa  +g     +  d  + g+D++++s+hK + gP+G Gv+  +
  gi|242398612|ref|YP_002994036.1| 166 VVFG--GSLFPFPHPVKELAPVAKEVGAFVMYDAAHVLGliggGQFQDPLREGADVITSSTHKtFPGPQG-GVILYK 239
                                       9875..689999***********************9886222245579999************999****.555555 PP

                                       HHHH CS
                       Aminotran_5 215 kell 218
                                       + l 
  gi|242398612|ref|YP_002994036.1| 240 D-LG 242
                                       5.44 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.0   1.7e-10   3.3e-07      54     242 ..      91     337 ..      74     401 .. 0.79

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 1.7e-10
                                       S-HHHHHHHHHHHH--TTEEEEEETT-HH.HHSST.THHHHCC--EEEEE-..EBTTTBE-HHHHHHHS--S-TTS- CS
                   Beta_elim_lyase  54 pqGtaAnsillkillqrgeevivtepahi.hfdet.gaiaelagvklrdlk..nkeaGkmdlekleaaikevgahee 126
                                        +Gt An+ ++  l++ g++ iv +++h+ h      ++a + g ++++ +  n+e  ++d+ek +++i+e      
  gi|242398612|ref|YP_002994036.1|  91 ISGTNANQAAFFGLTEAGDKAIVLHTSHGgHISHMpFGAAGMRGLEVHTWPfdNDE-FNIDVEKAAQMIRE--L--- 161
                                       59*****************9999999664234333445556666666655511666.9*************..2... PP

                                       EEEEEEEESSBTTTTTB---HHH.HHHHHHHHHHCT-EEEEEETTHHHHHHHHTS-CHHHHTTSSEEEEESSSTT-- CS
                   Beta_elim_lyase 127 kiklisltvTnntagGqvvslee.lrevaaiakkygiplhlDgARfanaakslgeivkemfsyvDsvtmslkKdlla 202
                                       ++k++       + gG   +  + ++e+a +ak+ g  +++D+A ++      g+    + +++D++t s  K    
  gi|242398612|ref|YP_002994036.1| 162 EPKIV-------VFGGSLFPFPHpVKELAPVAKEVGAFVMYDAAHVLGLI-GGGQFQDPLREGADVITSSTHKTFPG 230
                                       34444.......4699999975449*********************9876.555555566689************** PP

                                       SS-EEEEE-HH........................................HHHHHHHHHHHHT---SSTHHHHH.. CS
                   Beta_elim_lyase 203 nvGgvlafrddel....................................edylaerveqrkylggglrqagvlaa.. 241
                                       + Ggv++ +d ++                                    + y ++ v+ +k+l++ + + g+++   
  gi|242398612|ref|YP_002994036.1| 231 PQGGVILYKDLGEataklqwaifpgvlsnhhlhhmagkvvtaaemlefgKAYAEQVVKNAKALAEAMAEEGFKVIge 307
                                       **********9999**********************************************************99875 PP

                                       .............................. CS
                   Beta_elim_lyase 242 .............................l 242
                                                                    +
  gi|242398612|ref|YP_002994036.1| 308 dkgytkshqvivdvselheagggwaapllE 337
                                       555555555555555555444444444442 PP

>> SelA  L-seryl-tRNA selenium transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.9e-06    0.0037     172     226 ..     184     239 ..     176     250 .. 0.79
   2 ?   -1.1   0.0      0.36   7.1e+02      83     115 ..     312     343 ..     308     345 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.9e-06
                                       -EEEEEES-B-S-GGG.GT-----BHHHHHHTT-SEEEEETTSTT-SSS-EEEEE- CS
                              SelA 172 pvleDlGsGllvdlse.yglskePtvqealaeGvdlvsfsGDkllGgpqaGiivGk 226
                                       pv +++G+ ++ d ++  gl    ++q+ l+eG+d+++ s  k + gpq G+i+ k
  gi|242398612|ref|YP_002994036.1| 184 PVAKEVGAFVMYDAAHvLGLIGGGQFQDPLREGADVITSSTHKTFPGPQGGVILYK 239
                                       4555556666666544268999999****************************965 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.36
                                       HBTSEEEEETTSGTEETTTEEHHHHHHHHTBEE CS
                              SelA  83 aagkeviisrGeLveiGGsfriPdvmkkaGvkL 115
                                       ++ ++vi+   eL e GG +  P ++++aG+ L
  gi|242398612|ref|YP_002994036.1| 312 TKSHQVIVDVSELHEAGGGWAAP-LLEEAGIIL 343
                                       567899*************9998.688888877 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 !   15.8   0.0   1.9e-06    0.0038      75     221 ..      92     246 ..      78     280 .. 0.75
   2 ?    0.5   0.0     0.086   1.7e+02     271     320 ..     246     291 ..     239     305 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.9e-06
                                       SHHHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHH.TTCEEEE..EST....TSHHHHHHHCCT.TEEEEEE CS
                   Cys_Met_Meta_PP  75 sGmaAiaaailallkaGdeivvsddlYggtqrllkkvlkk.lgievkf..vdt....sdleelekaike.ntklvyl 143
                                       sG+ A +aa++ l +aGd+ +v ++ +gg  + +   +    g+ev+   +d      d+e+ +++i+e + k+v +
  gi|242398612|ref|YP_002994036.1|  92 SGTNANQAAFFGLTEAGDKAIVLHTSHGGHISHMPFGAAGmRGLEVHTwpFDNdefnIDVEKAAQMIRElEPKIVVF 168
                                       9****************************999888766553456665511455323234566666777788999988 PP

                                       ESS-TTTT----HHHHHHHHHHTT-EEEEEGTTT.....HTTTS-GGGGT-SEEEEETTTTTTCSSS--EEEEEESS CS
                   Cys_Met_Meta_PP 144 EtptnpllkvvDiekiaklakkagvlvvvDntfa.....spllqrplklgaDivvhSaTKylgGhsdvvaGvivvkg 215
                                            p+   + ++++a +ak++g+ v+ D++ +      + +q pl+ gaD+++ S+ K   G +   +Gvi+ k+
  gi|242398612|ref|YP_002994036.1| 169 GGSLFPFP--HPVKELAPVAKEVGAFVMYDAAHVlgligGGQFQDPLREGADVITSSTHKTFPGPQ---GGVILYKD 240
                                       76666665..5689****************9865112115689****************9988876...67777666 PP

                                       CHHHHH CS
                   Cys_Met_Meta_PP 216 keelkk 221
                                         e + 
  gi|242398612|ref|YP_002994036.1| 241 LGEATA 246
                                       444444 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.086
                                       TTEEEEE-TT.STTSTTHHHHHHHSSSG-SEEEEEESSHHHHHHHHHHC-S CS
                   Cys_Met_Meta_PP 271 pkvekvyYpg.lpshpqhelakkqlkgaggvlsFelkseeekakkfvdnlk 320
                                        k ++  +pg l++h+ h++a k ++ a  +l F         +++v+n k
  gi|242398612|ref|YP_002994036.1| 246 AKLQWAIFPGvLSNHHLHHMAGKVVTAA-EMLEFGKAYA----EQVVKNAK 291
                                       5789999999456677788888888877.9999976554....34444444 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   1.1e-05     0.022      88     185 ..     138     238 ..      91     282 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.1e-05
                                       EEE-B-TTTSSB-GGGCGGG--TTEEEEEE..B-GGGB---HHHHHHHHHHCT-EEEEE-TT-TT-EETT...EECC CS
                   DegT_DnrJ_EryC1  88 vfvDvdpdtynidpaaieaaitertkaIlp..VhlyGqvadmdalkaiaakhglkvieDaAhAlGatykg...kkvG 159
                                            d d +nid++++++ i e    I++    l+  +  +++l  +a++ g  v+ DaAh lG    g    ++ 
  gi|242398612|ref|YP_002994036.1| 138 HTWPFDNDEFNIDVEKAAQMIRELEPKIVVfgGSLFPFPHPVKELAPVAKEVGAFVMYDAAHVLGLIGGGqfqDPLR 214
                                       44556889***************99555541258899999*************************887774443555 PP

                                       CSSSEEEEE-BTTSSS-SSS-EEEEE CS
                   DegT_DnrJ_EryC1 160 algdaavfSFyptKnlttGeGGavvt 185
                                       + +d+ + S +  K++    GG+++ 
  gi|242398612|ref|YP_002994036.1| 215 EGADVITSSTH--KTFPGPQGGVILY 238
                                       55555555544..4555555555555 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 ?   12.8   0.0     4e-05      0.08      86     160 ..      89     167 ..      60     168 .. 0.86
   2 ?   -2.9   0.0       2.8   5.6e+03      49      59 ..     264     287 ..     256     330 .. 0.45

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4e-05
                     Lactamase_B_3  86 davggsergenngflleq..dgltiyhlGhlahelsseelke.lgrvDvvltPvgg.pltlgqeealelakrLkpkl 158
                                       ++  g++ ++   f l++  d+  ++h  h++h  +++  ++ +  ++v   P +  ++ ++ e+a++++++L+pk+
  gi|242398612|ref|YP_002994036.1|  89 RPISGTNANQAAFFGLTEagDKAIVLHTSHGGHISHMPFGAAgMRGLEVHTWPFDNdEFNIDVEKAAQMIRELEPKI 165
                                       5667788888899999996668889999999999888877552668*********989******************* PP

                     Lactamase_B_3 159 vl 160
                                       v+
  gi|242398612|ref|YP_002994036.1| 166 VV 167
                                       98 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.8
                     Lactamase_B_3  49 Hahletlkql.............a 59 
                                       H++ + + ++              
  gi|242398612|ref|YP_002994036.1| 264 HMAGKVVTAAemlefgkayaeqvV 287
                                       444444443333333332222221 PP

>> CheD  CheD chemotactic sensory transduction
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   5.8e-05      0.12      40     101 ..     264     322 ..     258     325 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.8e-05
                                       G-EEEEEE----S.....---SS-HHHHHHHHHHHHHHHTT--EEEEEE-SSS-EEEEEETT CS
                              CheD  40 rleaklaGGAqmfafessksdvlniGerNveavkelLkeegipivaedvggnygRtvlfdpa 101
                                       ++  k++  A+m++f +      +   +N++a+ e+++eeg++++ ed g +++ +v++d++
  gi|242398612|ref|YP_002994036.1| 264 HMAGKVVTAAEMLEFGK--A-YAEQVVKNAKALAEAMAEEGFKVIGEDKGYTKSHQVIVDVS 322
                                       56678888899999844..2.3333369******************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       760  (0.0423894); expected 358.6 (0.02)
Passed bias filter:                      698  (0.0389313); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.42
# Mc/sec: 3023.41
//
Query:       gi|242398613|ref|YP_002994037.1|  [L=255]
Description: NAD-dependent deacetylase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      4e-58  196.2   0.0    4.8e-58  196.0   0.0    1.1  1  SIR2           Sir2 family
     0.0044   17.1   0.4      0.012   15.7   0.4    1.6  1  Zn-ribbon_8    Zinc ribbon domain
     0.0054   16.5   0.0      0.011   15.5   0.0    1.5  1  TPP_enzyme_M   Thiamine pyrophosphate enzyme, central domain
  ------ inclusion threshold ------
      0.063   13.2   2.4        2.4    8.1   1.3    2.5  2  A1_Propeptide  A1 Propeptide


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 !  196.0   0.0   1.1e-61   4.8e-58       1     177 []      20     198 ..      20     198 .. 0.96

  Alignments for each domain:
  == domain 1  score: 196.0 bits;  conditional E-value: 1.1e-61
                                       -GGGGGGGT---SSSTTSHHHHSCHHHHSSHHHHHHHHHHHHHHHHHHHHHHHCCTSS--HHHHHHHHHHHTTCEEE CS
                              SIR2   1 GAGiStesGipdfRskeGlyaklakeelaspealfskkllveevfyniarellaeeaepnaaHkalkklekkgkllr 77 
                                       GAG+S+esGip+fR++ Gl+++++ ee+a+pea+++++ lv++ fy++++++++  a+pn+aH al++lek+g l++
  gi|242398613|ref|YP_002994037.1|  20 GAGVSAESGIPTFRDRGGLWENYRIEEVATPEAFRKDPNLVWS-FYKMRMKIMK-GAKPNNAHLALAELEKMGILKA 94 
                                       9******************************************.****999999.5********************* PP

                                       EEES-SSSHHHHTT-SSEEETTEEEEEEEETTTSBEEE...CCGGHCHHHCCTT.B-TTTCCBEEEEE--CTSB-S. CS
                              SIR2  78 liTQNiDgLekkaGskkvvelHGslakakcvkcekkld...keelqeeieaekvpecekcgkllkpdvvfFGealp. 150
                                       +iTQNiD+L+++aG++++velHG++ ++kc++c++ ++     +l++ ++++++p+c++c +ll+pdvv+FGe lp 
  gi|242398613|ref|YP_002994037.1|  95 VITQNIDNLHREAGNQHIVELHGNIYRVKCTRCDYMENlleSGKLEDFLKEKNLPKCPECASLLRPDVVWFGEPLPq 171
                                       *********************************98765111668889999**************************9 PP

                                       HHHHHHHHHHHH-SEEEEES--STSTT CS
                              SIR2 151 dklkkliekveeadlllviGtSlkVap 177
                                       ++l+k+++ +e+ad+ lv+GtS++V p
  gi|242398613|ref|YP_002994037.1| 172 EALQKAFKLAERADVCLVVGTSAQVFP 198
                                       9************************87 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.4   2.7e-06     0.012       3      35 ..     119     157 ..     119     160 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.7e-06
                       Zn-ribbon_8   3 iYeYrCeeCghefe......vlqsis.dapltaCPeCgse 35 
                                       iY  +C++C+   e      +l  +  +++l++CPeC s 
  gi|242398613|ref|YP_002994037.1| 119 IYRVKCTRCD-YMEnllesgKLEDFLkEKNLPKCPECASL 157
                                       89********.7777888887777776777999****885 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   2.5e-06     0.011      65     137 .]     171     242 ..     152     242 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.5e-06
                                       GGSCHHHHHHHHH-SEEEEES-SSSTCCCTTTTT.TTTTT-.EEEEEESSCCCCTTCC--SEEEECTHHHHHHHH CS
                      TPP_enzyme_M  65 lhgskaanealeeaDlvlalGarfddirttgsep.efapea.kiihididpaeigknyqvdlaivgdvketleaL 137
                                         + ++a +++e+aD++l++G+  +  + +++ p  ++ ++  +i+i+++++ i     +d+ i g+++e++++L
  gi|242398613|ref|YP_002994037.1| 171 QEALQKAFKLAERADVCLVVGTSAQV-FPAAYVPyIVKDNGgSVIEINTKESGITP--IADVFIRGKAGEVMQSL 242
                                       55677888999**********99877.66778886666666788888877666665..579********999986 PP

>> A1_Propeptide  A1 Propeptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.013        56      15      26 ..      31      43 ..      31      45 .. 0.89
   2 ?    8.1   1.3   0.00054       2.4      14      28 ..     131     145 ..     131     146 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.013
                                      HHHH.TT-HHHHH CS
                     A1_Propeptide 15 tLrE.kglLeeFL 26
                                      t+r+ +gl+e+++
  gi|242398613|ref|YP_002994037.1| 31 TFRDrGGLWENYR 43
                                      78999*******8 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00054
                                       HHHHHTT-HHHHHHH CS
                     A1_Propeptide  14 etLrEkglLeeFLke 28 
                                       e+L E g+Le+FLke
  gi|242398613|ref|YP_002994037.1| 131 ENLLESGKLEDFLKE 145
                                       68999*********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      570  (0.0317921); 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: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1913.03
//
Query:       gi|242398614|ref|YP_002994038.1|  [L=131]
Description: hypothetical protein TSIB_0624 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-18   65.2   0.3      5e-17   61.6   0.1    2.5  2  DUF3783   Domain of unknown function (DUF3783)
  ------ inclusion threshold ------
      0.027   14.4   0.0      0.028   14.4   0.0    1.1  1  SPX       SPX domain
       0.11   12.6   0.9        9.1    6.5   0.1    3.1  3  SepRS_C   O-phosphoseryl-tRNA synthetase C-terminal domain


Domain annotation for each model (and alignments):
>> DUF3783  Domain of unknown function (DUF3783)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0     0.067     4e+02       2      25 ..       1      27 [.       1      41 [. 0.74
   2 !   61.6   0.1   8.4e-21     5e-17       1      56 []      56     111 ..      56     111 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.067
                           DUF3783  2 mlvfsgfssee...ldklldalkkagl 25
                                      m++  gf  ee   l+++l+++k  g+
  gi|242398614|ref|YP_002994038.1|  1 MILVIGFEKEEffkLKNILSEFKIYGV 27
                                      677789999996666666666665555 PP

  == domain 2  score: 61.6 bits;  conditional E-value: 8.4e-21
                           DUF3783   1 emlvfsgfsseeldklldalkkaglpiplkAvlTptNinWtlkeLleElekEheym 56 
                                       ++++++g+++e ++++++ +k  g+p+ ++A++Tpt+++W+l++Ll El +E ey+
  gi|242398614|ref|YP_002994038.1|  56 KFILMHGIPNEKVKEVMKRIKLLGIPDVIFATTTPTSLTWKLEDLLNELIREDEYF 111
                                       69*****************************************************8 PP

>> SPX  SPX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   4.6e-06     0.028     181     203 ..      92     127 ..      47     131 .] 0.79

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.6e-06
                               SPX 181 r.............aekeFferLdseLnkvetFyka 203
                                       +             +e+e+f+ L +e +k +tFy +
  gi|242398614|ref|YP_002994038.1|  92 SltwkledllneliREDEYFRKLKEEKQKMNTFYLK 127
                                       244555566667779*******************86 PP

>> SepRS_C  O-phosphoseryl-tRNA synthetase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.023   1.4e+02      10      14 ..      24      28 ..      23      41 .. 0.88
   2 ?    6.5   0.1    0.0015       9.1      12      24 ..      62      73 ..      61      74 .. 0.91
   3 ?   -0.6   0.1      0.25   1.5e+03      10      15 ..      77      82 ..      76      83 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.023
                                      EEEEE CS
                           SepRS_C 10 IlGvP 14
                                      I+GvP
  gi|242398614|ref|YP_002994038.1| 24 IYGVP 28
                                      9**** PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0015
                                      EEES-TTTCCHHH CS
                           SepRS_C 12 GvPdtekwkeare 24
                                      G+P +ek+ke+++
  gi|242398614|ref|YP_002994038.1| 62 GIP-NEKVKEVMK 73
                                      9**.******986 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.25
                                      EEEEES CS
                           SepRS_C 10 IlGvPd 15
                                       lG+Pd
  gi|242398614|ref|YP_002994038.1| 77 LLGIPD 82
                                      59***6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1024  (0.0571142); expected 358.6 (0.02)
Passed bias filter:                      607  (0.0338558); 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: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 793.00
//
Query:       gi|242398615|ref|YP_002994039.1|  [L=239]
Description: Hydrolase, HAD superfamily [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.5e-33  113.8   0.0    1.5e-32  113.2   0.0    1.3  1  HAD_2            Haloacid dehalogenase-like hydrolase
    5.7e-20   72.5   0.1    8.2e-19   68.7   0.1    2.1  1  Hydrolase        haloacid dehalogenase-like hydrolase
    4.9e-17   61.8   0.0    9.5e-17   60.8   0.0    1.4  1  Hydrolase_like   HAD-hyrolase-like
    1.8e-08   35.0   0.1    2.6e-08   34.5   0.1    1.2  1  HAD              haloacid dehalogenase-like hydrolase
    0.00064   19.4   0.0     0.0011   18.6   0.0    1.4  1  PGP_phosphatase  Mitochondrial PGP phosphatase
  ------ inclusion threshold ------
      0.064   13.0   0.0       0.91    9.2   0.0    2.4  3  Hydrolase_3      haloacid dehalogenase-like hydrolase
      0.082   12.6   0.1       0.52   10.0   0.0    2.3  2  PNK3P            Polynucleotide kinase 3 phosphatase


Domain annotation for each model (and alignments):
>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.2   0.0   5.7e-36   1.5e-32       1     177 [.       5     193 ..       5     194 .. 0.87

  Alignments for each domain:
  == domain 1  score: 113.2 bits;  conditional E-value: 5.7e-36
                             HAD_2   1 iiFDlDgTlldteeliiqafnelleey.........glselseeelrkliglslrellrklgeseeeeekieellrk 68 
                                       i FDlD+Tl+dt+ l   a +++++++         +    ++ el   +g +    +++l  + + + + + +   
  gi|242398615|ref|YP_002994039.1|   5 IFFDLDDTLVDTSRLAELARKNAIDNMiqhglpvdfETAYNELLELIAEYGSNFPHHFDYLLRRLDLKYNPKWVAAG 81 
                                       67**********************99999999885533344555666777777777788887777777755555555 PP

                             HAD_2  69 yneekkk..kevkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekkKPdpeviek 143
                                       + + +++   +++ +++++++L +L+e+gy+lgi+T+++  +++ek+ +l+i+++F+ +v+s+  + kKP+p++++k
  gi|242398615|ref|YP_002994039.1|  82 VIAYHNTkfAHLREVKNARKALIKLREMGYRLGIITDGNPIKQWEKVLRLDIDDFFEYVVVSDFEGVKKPHPKIYQK 158
                                       55555554558****************************************************************** PP

                             HAD_2 144 aleklklkkeeviyvGDsp.tDieaakkagikvia 177
                                       al+ +++k+ee+++vGD   +Di +ak++g+++++
  gi|242398615|ref|YP_002994039.1| 159 ALKIFGVKAEEAVMVGDRLySDIFGAKRVGMHTVW 193
                                       *********************************99 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.7   0.1   3.2e-22   8.2e-19       2     210 .]       3     188 ..       2     188 .. 0.77

  Alignments for each domain:
  == domain 1  score: 68.7 bits;  conditional E-value: 3.2e-22
                                       SEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETTTEHHHHTHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase   2 ktvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakarsgaltgfatfigrgayaigkpewlt 78 
                                       ++++fD+d TL++++ ++ ++ +++      a+    +h +   +  a++++ + +++++       +      +l+
  gi|242398615|ref|YP_002994039.1|   3 EVIFFDLDDTLVDTS-RLAELARKN------AIDNMIQHGLPVDFETAYNELLELIAEYGS-----NFPHHFDYLLR 67 
                                       78**********888.777888888......333335566666666666666666666666.....55555555666 PP

                                       HHHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  79 aldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanql 155
                                       +l               +     +  + +    t    l+  + a++a+ +L+++g++++++t +np  +++   +l
  gi|242398615|ref|YP_002994039.1|  68 RL-------------DLKYNPKWVAAGVIAYHNTKFAHLREVKNARKALIKLREMGYRLGIITDGNPIKQWEKVLRL 131
                                       66.............444444444433444444444555677889**************************777778 PP

                                       T.GGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHH.HHHHHHHTT CS
                                       x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                         Hydrolase 156 G.ddyfdaviasdietvakpspegkvaaireLqgkpeevamVGDgvn.DaaalaaAg 210
                                       + dd+f+ v+ sd e+v+kp+p+++++a++ +++k ee +mVGD++  D+ +++++g
  gi|242398615|ref|YP_002994039.1| 132 DiDDFFEYVVVSDFEGVKKPHPKIYQKALKIFGVKAEEAVMVGDRLYsDIFGAKRVG 188
                                       888999****************************************99999998876 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.8   0.0   3.7e-20   9.5e-17       3      75 .]     149     220 ..     148     220 .. 0.96

  Alignments for each domain:
  == domain 1  score: 60.8 bits;  conditional E-value: 3.7e-20
                                       STTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESSSSS-TTTHHHHHHHHT---SEEES- CS
                    Hydrolase_like   3 gKPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVltGvtrpedleepehkptyvaddlaea 75 
                                        KP+p +y  al+ +g++ ee +m+GDrl++Di gA+++G+++v  + G++++ +le  e ++++ +ddl e+
  gi|242398615|ref|YP_002994039.1| 149 KKPHPKIYQKALKIFGVKAEEAVMVGDRLYSDIFGAKRVGMHTVWFRYGKYANRELE-YEQHADFKIDDLLEL 220
                                       6******************************************************88.888999999**9985 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   0.1     1e-11   2.6e-08       1     160 [.       5     167 ..       5     181 .. 0.80

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 1e-11
                               HAD   1 alfDfDgTLldgdsle......lllrfllrrgaprlwralreklllalfrellrldraglaelleallaglseelaa 71 
                                       ++fD+D TL+d++ l       +++  ++++g p +++++  +ll+ + +e+++++  +++ ll++l   ++++  a
  gi|242398615|ref|YP_002994039.1|   5 IFFDLDDTLVDTSRLAelarknAIDN-MIQHGLPVDFETAYNELLELI-AEYGSNFPHHFDYLLRRLDLKYNPKWVA 79 
                                       79**********88888999955555.***************999999.999***9****************99999 PP

                               HAD  72 elerfvaevirpklldp..galellaahraaGdrvvvvSgg.lrplvepllaelgadevlatelevdd..rltgelg 143
                                           ++ ++ + + l++   a+++l + r+ G+r+ +++ g +   +e +l +l+    ++  +e++   ++ g  +
  gi|242398615|ref|YP_002994039.1|  80 AGVIAY-HNTKFAHLREvkNARKALIKLREMGYRLGIITDGnPIKQWEKVL-RLD----IDDFFEYVVvsDFEGVKK 150
                                       999999.33443335567899999999************775899999999.888....666566555558888877 PP

                               HAD 144 legkpvrgegkvaalre 160
                                       +++k+  ++ k+  +++
  gi|242398615|ref|YP_002994039.1| 151 PHPKIYQKALKIFGVKA 167
                                       77777777777766666 PP

>> PGP_phosphatase  Mitochondrial PGP phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   4.3e-07    0.0011     120     166 ..     156     197 ..     127     199 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 4.3e-07
                   PGP_phosphatase 120 aeevleyfkerkvveeadeiavvgDRllTdvllanmmGslgvwlrdg 166
                                        +  l+ f       +a+e ++vgDRl  d+  a+++G  +vw+r g
  gi|242398615|ref|YP_002994039.1| 156 YQKALKIFGV-----KAEEAVMVGDRLYSDIFGAKRVGMHTVWFRYG 197
                                       4555555544.....499*************************9876 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   0.00036      0.91       1      34 [.       5      38 ..       5      57 .. 0.91
   2 ?    0.9   0.0      0.13   3.2e+02      19      55 ..      98     134 ..      93     149 .. 0.82
   3 ?   -3.0   0.0       1.9     5e+03     193     211 ..     157     175 ..     152     177 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00036
                                      EEEEIIIIIS-TTS---HHHHHHHHHHHHTTSEE CS
                       Hydrolase_3  1 ialDlDGTLlnsdkkisektkeaikklkekgikv 34
                                      i++DlD+TL++     +   k+ai +++++g  v
  gi|242398615|ref|YP_002994039.1|  5 IFFDLDDTLVDTSRLAELARKNAIDNMIQHGLPV 38
                                      89************9*************999877 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.13
                                       HHHHHHHHHHHTTSEEEEE-.SS-HHHHHHHHHHCCCC CS
                       Hydrolase_3  19 ktkeaikklkekgikvviAT.GRslravlpvleelgld 55 
                                       ++++a+ kl+e g+ + i T G+++++ ++vl+ l++d
  gi|242398615|ref|YP_002994039.1|  98 NARKALIKLREMGYRLGIITdGNPIKQWEKVLR-LDID 134
                                       6789************88776999999999998.7766 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 1.9
                                       HHHHHHCT--GGGEEEEES CS
                       Hydrolase_3 193 kklakelnisleeviafGD 211
                                       +k +k ++++ ee + +GD
  gi|242398615|ref|YP_002994039.1| 157 QKALKIFGVKAEEAVMVGD 175
                                       5667888889999999998 PP

>> PNK3P  Polynucleotide kinase 3 phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0    0.0002      0.52       2      24 ..       4      26 ..       3      55 .. 0.73
   2 ?    0.1   0.0      0.22   5.7e+02      93     105 ..     146     158 ..      89     217 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0002
                             PNK3P  2 iaaFDlDstliktksgkefakda 24
                                      +++FDlD+tl+ t+  +e a+++
  gi|242398615|ref|YP_002994039.1|  4 VIFFDLDDTLVDTSRLAELARKN 26
                                      899***********977777643 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.22
                             PNK3P  93 dkyRKPetGmwee 105
                                       + ++KP++ ++++
  gi|242398615|ref|YP_002994039.1| 146 EGVKKPHPKIYQK 158
                                       3344444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); 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: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 1632.23
//
Query:       gi|242398616|ref|YP_002994040.1|  [L=187]
Description: hypothetical protein TSIB_0626 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-20   73.5   0.1    3.1e-20   72.7   0.1    1.4  1  ASCH           ASCH domain
  ------ inclusion threshold ------
       0.08   13.4   0.2       0.15   12.5   0.2    1.6  1  Ribosomal_L26  Ribosomal proteins L26 eukaryotic, L24P archae
       0.11   13.1   0.7        0.4   11.3   0.1    2.0  2  DUF5600        Domain of unknown function (DUF5600)
       0.14   12.5   0.7       0.17   12.1   0.7    1.2  1  Abi_2          Abi-like protein


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 !   72.7   0.1     7e-24   3.1e-20       3     107 .]      10     109 ..       8     109 .. 0.95

  Alignments for each domain:
  == domain 1  score: 72.7 bits;  conditional E-value: 7e-24
                                       E-TTHHHHHHTTS--EEEESSTTTGGGT-CEEEEEECCCCTSEEEEEEEEEEEEEEHHHHHHHHHCHCC--.-HCHH CS
                              ASCH   3 fhqelaslivsGkKtaeirvwdeelpkvrgdllilaalkptgralgivevtkvevkpfeevteehalkege.sleew 78 
                                       +++ ++s+i++GkKt +ir++++e   ++ + +++ a++p++  ++++++t++++k+++e+t e+a k+g+ +l e+
  gi|242398616|ref|YP_002994040.1|  10 IDNVYKSKILKGKKTSTIRFGNYE---AKPGSEVYLAITPSDSVIAKIKITDIKKKRVKELTLEDARKDGFkELNEL 83 
                                       5788********************...5558999999**************************************** PP

                                       HHHHHCCHHHHHCCEEEEEEEEEEEEEEE CS
                              ASCH  79 revheefyeeeseeyedelvvveefelve 107
                                       ++++ ++y+ +++   d++v+++ef+++e
  gi|242398616|ref|YP_002994040.1|  84 INALNKIYGTLHG---DDEVTIIEFDVIE 109
                                       ************9...*********9975 PP

>> 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 ?   12.5   0.2   3.4e-05      0.15      46      77 ..      31      63 ..       3      68 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.4e-05
                                      xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
                     Ribosomal_L26 46 trekangttvpvgihpSkvvItklkl.Dkdrkk 77
                                      + e + g++v++ i pS  vI k+k+ D ++k+
  gi|242398616|ref|YP_002994040.1| 31 NYEAKPGSEVYLAITPSDSVIAKIKItDIKKKR 63
                                      5567789*******************6655554 PP

>> DUF5600  Domain of unknown function (DUF5600)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1     9e-05       0.4      29      94 ..      62     133 ..      49     142 .. 0.75
   2 ?   -0.3   0.0      0.35   1.6e+03      27      52 ..     158     182 ..     146     186 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 9e-05
                           DUF5600  29 kempsvfgke......kkkkeLieelpeiyekvsrkhnlplgdFPdvekfkeklkaldftkfkklkpkliea 94 
                                       k+++++  ++      k+ +eLi+ l++iy +++   ++ + +F  +ekf+e +    ++ ++  kp+ i++
  gi|242398616|ref|YP_002994040.1|  62 KRVKELTLEDarkdgfKELNELINALNKIYGTLHGDDEVTIIEFDVIEKFEEAIPLKWLKALNYRKPEEIAK 133
                                       455555555544445556789*******************************99777777777767766665 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.35
                           DUF5600  27 lrkempsvfgkekkkkeLieelpeiy 52 
                                       l++ +++ +g +k k+ L++  ++ y
  gi|242398616|ref|YP_002994040.1| 158 LKSAVRK-YGPKKVKDSLLKAYHKLY 182
                                       3333333.555666777777777766 PP

>> Abi_2  Abi-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.7   3.8e-05      0.17      31     115 ..      87     180 ..      59     187 .] 0.65

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.8e-05
                             Abi_2  31 feeilalykfDrkLrslllkaieriEialrtaiayelskedeeayldsdnfkkkkkkkkekkk.liekiekei.... 102
                                       +++i+ + + D ++  + ++ ie++E+a+  +++++l ++++e+    +++ +++ k++++ + +i++i +e     
  gi|242398616|ref|YP_002994040.1|  87 LNKIYGTLHGDDEVTIIEFDVIEKFEEAIPLKWLKALNYRKPEEIA--KLYVENDLKESADVDlIIKRIYSEGlksa 161
                                       6788889999****************************76666665..44656655554444453333333332222 PP

                             Abi_2 103 ......erskesfikhykk 115
                                             ++ k+s++k y+k
  gi|242398616|ref|YP_002994040.1| 162 vrkygpKKVKDSLLKAYHK 180
                                       2222211222335666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       815  (0.0454571); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 1078.55
//
Query:       gi|242398617|ref|YP_002994041.1|  [L=155]
Description: Transcription regulator, Lrp/AsnC family [Thermococcus sibiricus MM 739]
Scores for complete 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   69.5   0.1    2.7e-19   68.9   0.1    1.3  1  AsnC_trans_reg   Lrp/AsnC ligand binding domain
    5.6e-18   64.2   0.6    8.6e-18   63.6   0.6    1.3  1  HTH_24           Winged helix-turn-helix DNA-binding
    1.8e-16   59.6   0.0    3.2e-16   58.9   0.0    1.4  1  HTH_AsnC-type    AsnC-type helix-turn-helix domain
    7.7e-07   28.9   0.1    1.8e-06   27.8   0.1    1.5  1  TrmB             Sugar-specific transcriptional regulator Trm
    9.1e-06   25.6   0.0    1.7e-05   24.8   0.0    1.4  1  NapD             NapD protein
    1.9e-05   24.5   0.1    3.8e-05   23.5   0.1    1.5  1  HTH_11           HTH domain
    2.4e-05   24.1   0.1    3.7e-05   23.5   0.1    1.3  1  HTH_5            Bacterial regulatory protein, arsR family
    6.8e-05   22.6   0.0    0.00016   21.4   0.0    1.5  1  HTH_IclR         IclR helix-turn-helix domain
    0.00034   20.6   0.1     0.0017   18.3   0.0    2.0  2  HTH_Mga          M protein trans-acting positive regulator (M
    0.00037   20.4   0.0    0.00064   19.7   0.0    1.4  1  HTH_Crp_2        Crp-like helix-turn-helix domain
    0.00049   19.8   0.2      0.001   18.8   0.2    1.5  1  LexA_DNA_bind    LexA DNA binding domain
    0.00082   19.1   0.1     0.0021   17.8   0.0    1.7  1  HTH_23           Homeodomain-like domain
     0.0013   18.7   0.0     0.0022   18.0   0.0    1.3  1  HTH_20           Helix-turn-helix domain
     0.0018   18.4   0.2     0.0074   16.4   0.0    1.9  2  AsnC_trans_reg2  AsnC-like ligand binding domain
     0.0019   18.7   0.1     0.0036   17.8   0.1    1.5  1  HTH_27           Winged helix DNA-binding domain
     0.0029   17.7   0.0     0.0052   16.9   0.0    1.4  1  HTH_28           Helix-turn-helix domain
     0.0042   17.0   0.1     0.0081   16.1   0.1    1.5  1  MarR             MarR family
  ------ inclusion threshold ------
       0.01   16.2   0.3       0.24   11.8   0.1    2.3  2  Rrf2             Transcriptional regulator
      0.023   14.5   0.2      0.059   13.2   0.0    1.8  1  HTH_10           HTH DNA binding domain
      0.029   14.8   0.3      0.067   13.7   0.2    1.9  1  HTH_40           Helix-turn-helix domain
      0.029   14.1   0.1      0.054   13.3   0.1    1.4  1  HTH_DeoR         DeoR-like helix-turn-helix domain
       0.03   14.2   0.0      0.048   13.5   0.0    1.4  1  MarR_2           MarR family
      0.035   13.7   0.8      0.053   13.1   0.2    1.5  2  DDRGK            DDRGK domain
      0.038   14.1   0.0      0.055   13.6   0.0    1.4  1  B-block_TFIIIC   B-block binding subunit of TFIIIC
      0.041   14.1   0.1       0.09   13.0   0.1    1.6  1  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
      0.048   13.6   0.1       0.08   12.9   0.1    1.4  1  HTH_36           Helix-turn-helix domain
      0.073   13.4   0.2       0.13   12.6   0.2    1.4  1  Penicillinase_R  Penicillinase repressor
        0.1   13.2   0.2       0.29   11.7   0.1    1.8  1  Mga              Mga helix-turn-helix domain
       0.11   12.1   0.1       0.11   12.1   0.1    2.1  2  HTH_50           Helix-turn-helix domain
       0.12   12.5   0.0       0.29   11.3   0.0    1.6  1  HTH_9            RNA polymerase III subunit RPC82 helix-turn-
       0.14   12.0   0.0       0.27   11.1   0.0    1.5  1  Phage_AlpA       Prophage CP4-57 regulatory protein (AlpA)
       0.18   11.7   0.2       0.18   11.7   0.2    1.8  2  TFIIE_alpha      TFIIE alpha subunit


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 !   68.9   0.1   4.9e-22   2.7e-19       1      75 []      76     146 ..      76     146 .. 0.97

  Alignments for each domain:
  == domain 1  score: 68.9 bits;  conditional E-value: 4.9e-22
                                       EEEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEEE CS
                    AsnC_trans_reg   1 vlvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivlet 75 
                                       +l++ + g+   + +++++l ++pe+ve+y  tGdyd++lk+++r+  +l++fl++ +++++gv  t+t++vl+t
  gi|242398617|ref|YP_002994041.1|  76 ILIKARAGK---YADVAKELVKYPEIVEIYENTGDYDMILKIRTRNSTELNEFLNK-IGEIDGVVATHTMVVLKT 146
                                       689999999...*****************************************999.****************96 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.6   0.6   1.5e-20   8.6e-18       1      48 []      10      57 ..      10      57 .. 0.99

  Alignments for each domain:
  == domain 1  score: 63.6 bits;  conditional E-value: 1.5e-20
                            HTH_24  1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      ldetd++IL++Lqkn+r++ re+++r+gl  stv +r+k+L+e+G+Ik
  gi|242398617|ref|YP_002994041.1| 10 LDETDKEILKVLQKNSRTPLREISKRVGLAESTVYERIKKLKEKGVIK 57
                                      7**********************************************8 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.9   0.0   5.7e-19   3.2e-16       1      42 []      10      51 ..      10      51 .. 0.98

  Alignments for each domain:
  == domain 1  score: 58.9 bits;  conditional E-value: 5.7e-19
                     HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrLe 42
                                      LDe+D+ IL+ Lq+++R++ +e+++rvGl+estv +R+++L+
  gi|242398617|ref|YP_002994041.1| 10 LDETDKEILKVLQKNSRTPLREISKRVGLAESTVYERIKKLK 51
                                      8***************************************95 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.1   3.2e-09   1.8e-06       6      54 ..      10      58 ..      10      64 .. 0.93

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 3.2e-09
                                      HHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEE CS
                              TrmB  6 LseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVer 54
                                      L e++ ++ ++L k+ +   +ei++++g+ +s+vYe +++L++kG++++
  gi|242398617|ref|YP_002994041.1| 10 LDETDKEILKVLQKNSRTPLREISKRVGLAESTVYERIKKLKEKGVIKK 58
                                      678999999*************************************997 PP

>> NapD  NapD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   2.9e-08   1.7e-05       6      68 ..      76     139 ..      74     145 .. 0.94

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 2.9e-08
                              NapD   6 lvVqarperlaavkaalaalpg.vEvhasdeegklVvviEaesedeladtieaiealpgVlsas 68 
                                       ++++ar ++ a+v+++l + p+ vE++ ++++  +++ i + ++ el + +++i +++gV++++
  gi|242398617|ref|YP_002994041.1|  76 ILIKARAGKYADVAKELVKYPEiVEIYENTGDYDMILKIRTRNSTELNEFLNKIGEIDGVVATH 139
                                       689****************99868************************************9986 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.1   6.8e-08   3.8e-05       4      44 ..      16      59 ..      14      70 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 6.8e-08
                            HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg....v 44
                                       il+ L ++++  +  e++++ ++ ++tv+ +Ik+L+e+g    +
  gi|242398617|ref|YP_002994041.1| 16 EILKVL-QKNSRTPLREISKRVGLAESTVYERIKKLKEKGvikkF 59
                                      799***.88888****************************55554 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.1   6.5e-08   3.7e-05       2      47 .]      12      58 ..      11      58 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 6.5e-08
                                      HHHHHHHHHHTTSS.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5  2 ptRlkILklLaege.lcvcelaeelglsqstvShHLkkLreaGLVek 47
                                      +t  +ILk L++++ +   e+++ +gl +stv +  kkL+e G+++k
  gi|242398617|ref|YP_002994041.1| 12 ETDKEILKVLQKNSrTPLREISKRVGLAESTVYERIKKLKEKGVIKK 58
                                      56679*******874668**************************986 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   2.8e-07   0.00016       8      49 ..      17      57 ..      16      58 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 2.8e-07
                                      HHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR  8 iLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                      iL+ l +  +   l+e+++r gl+ Stv+  ++ L e G ++
  gi|242398617|ref|YP_002994041.1| 17 ILKVLQKNSRT-PLREISKRVGLAESTVYERIKKLKEKGVIK 57
                                      99999999997.9************************99887 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 !   18.3   0.0     3e-06    0.0017       5      54 ..      12      61 ..      11      64 .. 0.90
   2 ?   -1.0   0.0       3.4   1.9e+03      11      30 ..      73      92 ..      71      93 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3e-06
                           HTH_Mga  5 krklkLlelLteneksltldelakeLglseltlqsdiseLnel.Fpeelsi 54
                                      +++ ++l  L + +++++l e++k+ gl e+t+ ++i +L+e  ++++++i
  gi|242398617|ref|YP_002994041.1| 12 ETDKEILKVLQK-NSRTPLREISKRVGLAESTVYERIKKLKEKgVIKKFTI 61
                                      57899*******.****************************9777777766 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3.4
                           HTH_Mga 11 lelLteneksltldelakeL 30
                                      l++++  +++ ++ ++akeL
  gi|242398617|ref|YP_002994041.1| 73 LAFILIKARAGKYADVAKEL 92
                                      55555449999999999998 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   1.1e-06   0.00064      25      65 ..      30      68 ..       9      69 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.1e-06
                                      HHHHHHTTSSHHHHHHHHHHHHHTTSEEETEEEEES-HHHH CS
                         HTH_Crp_2 25 eelAsmlGltretvsrilseLkreglisrgrririldleaL 65
                                      +e++ ++Gl  +tv   +++Lk++g+i++    +i+d+eaL
  gi|242398617|ref|YP_002994041.1| 30 REISKRVGLAESTVYERIKKLKEKGVIKKF--TIIPDPEAL 68
                                      79**************************65..69*****99 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 !   18.8   0.2   1.8e-06     0.001      26      57 ..      28      57 ..       9      61 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.8e-06
                                      --HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE CS
                     LexA_DNA_bind 26 PsireiaralglkSpsaveehLkaLerKGyie 57
                                      P  rei++++gl+  s+v e+ k+L+ KG+i+
  gi|242398617|ref|YP_002994041.1| 28 P-LREISKRVGLA-ESTVYERIKKLKEKGVIK 57
                                      4.79*********.9***************97 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   3.8e-06    0.0021      16      46 ..      22      55 ..      11      57 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.8e-06
                            HTH_23 16 e...GlsvreIAreLgvsrrTvyrwlkryreeGl 46
                                      +   + + reI+++ g  ++Tvy  +k+ +e+G+
  gi|242398617|ref|YP_002994041.1| 22 QknsRTPLREISKRVGLAESTVYERIKKLKEKGV 55
                                      33457799***************77777799996 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   3.9e-06    0.0022       8      55 ..      10      57 ..       7      58 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3.9e-06
                                      S-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                            HTH_20  8 ahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLve 55
                                      ++++  +il+ L  +    + e+ +r++l+ +t++ ++++L e g ++
  gi|242398617|ref|YP_002994041.1| 10 LDETDKEILKVLQKNSRTPLREISKRVGLAESTVYERIKKLKEKGVIK 57
                                      5677789999999999999************************99986 PP

>> AsnC_trans_reg2  AsnC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1       2.3   1.3e+03      57      82 .]      26      51 ..      15      58 .. 0.75
   2 !   16.4   0.0   1.3e-05    0.0074       2      81 ..      68     147 ..      67     149 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 2.3
                   AsnC_trans_reg2 57 eevlaeiaaatgledyevLpstrefK 82
                                      ++ l+ei++++gl +  v   ++++K
  gi|242398617|ref|YP_002994041.1| 26 RTPLREISKRVGLAESTVYERIKKLK 51
                                      55678888888888777666666665 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 1.3e-05
                   AsnC_trans_reg2   2 lGfkanalvawkvpeerveevaevvaelpevtHcYeRewpynlyfmvharseeeveevlaeiaaatgledyevLpst 78 
                                       lGf+  a + +k++  ++ +va+ + ++pe+  +Ye   +y +   + +r+ +e++e+l++i +  g+  +++++ +
  gi|242398617|ref|YP_002994041.1|  68 LGFNLLAFILIKARAGKYADVAKELVKYPEIVEIYENTGDYDMILKIRTRNSTELNEFLNKIGEIDGVVATHTMVVL 144
                                       8999999999******************************************************9999877777766 PP

                   AsnC_trans_reg2  79 ref 81 
                                       ++ 
  gi|242398617|ref|YP_002994041.1| 145 KTH 147
                                       655 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   6.4e-06    0.0036       7      50 ..      16      58 ..      10      61 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 6.4e-06
                            HTH_27  7 lvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLver 50
                                       +L +++  + r  l+++++r+ +  s++ + +kkL ekG++++
  gi|242398617|ref|YP_002994041.1| 16 EILKVLQ-KNSRTPLREISKRVGLAESTVYERIKKLKEKGVIKK 58
                                      6788888.99999****************************976 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   9.2e-06    0.0052      13      41 ..      26      55 ..      15      58 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 9.2e-06
                            HTH_28 13 h.svreaArelgisrrtvyrWikryeegGi 41
                                      + + re+++++g+ ++tvy  ik++ e G+
  gi|242398617|ref|YP_002994041.1| 26 RtPLREISKRVGLAESTVYERIKKLKEKGV 55
                                      3499*********************99985 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   1.4e-05    0.0081       7      49 ..      16      58 ..      10      61 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.4e-05
                                      HHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              MarR  7 viLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieR 49
                                      +iL  l  +    + e+ k++g+  stv + +++L +kG i++
  gi|242398617|ref|YP_002994041.1| 16 EILKVLQKNSRTPLREISKRVGLAESTVYERIKKLKEKGVIKK 58
                                      6899999999999**************************9987 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00042      0.24      19      56 ..      20      57 ..      16      60 .. 0.86
   2 ?    2.2   0.0      0.41   2.3e+02       9      24 ..     136     151 ..     132     155 .] 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00042
                                      HSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2 19 keeeeepvsseeiaerqnispsylekilakLrkaglvk 56
                                        ++++   ++ei++r+++ +s +   ++kL+++g++k
  gi|242398617|ref|YP_002994041.1| 20 VLQKNSRTPLREISKRVGLAESTVYERIKKLKEKGVIK 57
                                      445556689***************************98 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.41
                                       HHHHHHHHHHHSSTCC CS
                              Rrf2   9 yalhallyLakeeeee 24 
                                       +a+h++++L++++e +
  gi|242398617|ref|YP_002994041.1| 136 VATHTMVVLKTHKETT 151
                                       89*********99876 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   0.00011     0.059      23      50 ..      26      53 ..      23      55 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00011
                            HTH_10 23 rvtlkeLAkelGIskstlsehLrkaesk 50
                                      r+ l+e++k+ G+++st++e+++k ++k
  gi|242398617|ref|YP_002994041.1| 26 RTPLREISKRVGLAESTVYERIKKLKEK 53
                                      56799******************98877 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2   0.00012     0.067      15      41 ..      29      57 ..      13     117 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00012
                            HTH_40 15 ieeIAkerglkesTIegHLaelieeg..e 41
                                      + eI+k+ gl+esT+++ + +l e+g  +
  gi|242398617|ref|YP_002994041.1| 29 LREISKRVGLAESTVYERIKKLKEKGviK 57
                                      78***********************9442 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 ?   13.3   0.1   9.6e-05     0.054       3      46 ..      15      58 ..      14      60 .. 0.96

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.6e-05
                          HTH_DeoR  3 eqilellkqqgklsveelvellgvSeaTiRRDLneLeeqglltR 46
                                      ++il+ l++     + e++ + g +e T+   +++L+e+g++++
  gi|242398617|ref|YP_002994041.1| 15 KEILKVLQKNSRTPLREISKRVGLAESTVYERIKKLKEKGVIKK 58
                                      79***************************************998 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   8.6e-05     0.048      13      53 ..      20      58 ..      10      68 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.6e-05
                                      HHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                            MarR_2 13 aLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53
                                      +L  + +     +e+ +r gl  s+v  ++k+L ++G + +
  gi|242398617|ref|YP_002994041.1| 20 VLQKNSR--TPLREISKRVGLAESTVYERIKKLKEKGVIKK 58
                                      5555555..6889************************9965 PP

>> DDRGK  DDRGK domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.2   9.4e-05     0.053     101     143 ..      14      56 ..       4      60 .. 0.91
   2 ?   -2.8   0.0       7.4   4.1e+03     129     146 ..     118     135 ..     106     149 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.4e-05
                                       HHHHHHHHHH-SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS CS
                             DDRGK 101 leefinyikekKvvlleelavkfklktqevierikeLeeqgsl 143
                                        +e+++ ++++  + l e++ + +l  + v erik+L+e+g +
  gi|242398617|ref|YP_002994041.1|  14 DKEILKVLQKNSRTPLREISKRVGLAESTVYERIKKLKEKGVI 56 
                                       578999999999****************************988 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 7.4
                                       HHHHHHHHHHHHSSS-EE CS
                             DDRGK 129 evierikeLeeqgsltGv 146
                                       +  e  + L++ g++ Gv
  gi|242398617|ref|YP_002994041.1| 118 NSTELNEFLNKIGEIDGV 135
                                       443333444445555555 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   9.8e-05     0.055      25      55 ..      33      84 ..      29     129 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.8e-05
                    B-block_TFIIIC 25 akeskqdprslfyrlksLekkgLIvkqsii.....................d 55
                                      +k ++   + ++ r+k+L++kg I+k +ii                     +
  gi|242398617|ref|YP_002994041.1| 33 SKRVGLAESTVYERIKKLKEKGVIKKFTIIpdpealgfnllafilikaragK 84
                                      55566667889******************87776666666666666655551 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   0.00016      0.09      26      52 ..      30      56 ..      15      58 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00016
                                      HHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                    Fe_dep_repress 26 kdlaerLnvspssVsemlkkLekdGyv 52
                                       ++++r + + s+V e +kkL+++G +
  gi|242398617|ref|YP_002994041.1| 30 REISKRVGLAESTVYERIKKLKEKGVI 56
                                      58**********************965 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   0.00014      0.08      29      55 .]      30      56 ..      21      56 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00014
                            HTH_36 29 etlakrlglsknTvsraikeLeqlGyi 55
                                      + ++kr gl ++Tv+  ik+L ++G i
  gi|242398617|ref|YP_002994041.1| 30 REISKRVGLAESTVYERIKKLKEKGVI 56
                                      5799********************976 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   0.00023      0.13       4      53 ..      13      58 ..      10      61 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00023
                                      S-SHHHHHHHHHS-EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EE CS
                   Penicillinase_R  4 lEaevmeilwekgeatvkevveeleeekelaysTVktllrrLvkKgllsr 53
                                       ++e++++l +++++  +e+ +++     la+sTV   +++L +Kg++++
  gi|242398617|ref|YP_002994041.1| 13 TDKEILKVLQKNSRTPLREISKRVG----LAESTVYERIKKLKEKGVIKK 58
                                      5679999999999999999877654....77****************986 PP

>> Mga  Mga 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   0.00052      0.29      20      56 ..      16      52 ..       9      62 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00052
                                      HHHHHHHHHSEEEHHHHHHHCT--HHHHHHHHHHHHH CS
                               Mga 20 qllkflfeeeevsieelaqelyiSestlkrkikelnk 56
                                      ++lk l ++ ++ + e+++++ + est++  ik+l++
  gi|242398617|ref|YP_002994041.1| 16 EILKVLQKNSRTPLREISKRVGLAESTVYERIKKLKE 52
                                      68999999***************************98 PP

>> HTH_50  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1    0.0002      0.11       2      46 ..       4      49 ..       3      51 .. 0.88
   2 ?   -2.7   0.4       8.6   4.8e+03      36      46 ..     138     148 ..     137     148 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0002
                            HTH_50  2 gsLkeyveefErelikkayek.YpStRklAkrLGvShtaianklrk 46
                                       s++ +++e+++e++k + ++  +  R + kr G+  +++  +++k
  gi|242398617|ref|YP_002994041.1|  4 ESMRGILDETDKEILKVLQKNsRTPLREISKRVGLAESTVYERIKK 49
                                      578999*********99987625779*****************998 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 8.6
                            HTH_50  36 Shtaianklrk 46 
                                       +ht ++ k +k
  gi|242398617|ref|YP_002994041.1| 138 THTMVVLKTHK 148
                                       79*99999886 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   0.0   0.00051      0.29      10      44 ..       9      43 ..       6      46 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00051
                                      CSTTHHHHHHHHHHHHSSBEHHHHHHHHSSTHHHH CS
                             HTH_9 10 hFGevvakVvetLlrkgrltlrelvkktkLsldqV 44
                                      +++e+ + + ++L +++r +lre++k+++L  + V
  gi|242398617|ref|YP_002994041.1|  9 ILDETDKEILKVLQKNSRTPLREISKRVGLAESTV 43
                                      78888899**********************99877 PP

>> Phage_AlpA  Prophage CP4-57 regulatory protein (AlpA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00048      0.27       6      26 ..      29      49 ..      28      78 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00048
                        Phage_AlpA  6 lreVeqktglsrstiYrlikd 26
                                      lre+ + +gl++st+Y+ ik+
  gi|242398617|ref|YP_002994041.1| 29 LREISKRVGLAESTVYERIKK 49
                                      689999***********9994 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   0.00033      0.18       8      58 ..       7      57 ..       4      60 .. 0.94
   2 ?   -1.1   0.1       3.1   1.8e+03      64      64 ..     100     100 ..      71     142 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00033
                                      HHCS-HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEE CS
                       TFIIE_alpha  8 rkfygeeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvk 58
                                      r++ +e  +++l+vL +++ +   +++k +++    + + + +L+e++++k
  gi|242398617|ref|YP_002994041.1|  7 RGILDETDKEILKVLQKNSRTPLREISKRVGLAESTVYERIKKLKEKGVIK 57
                                      678889999****************************************97 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 3.1
                                       E CS
                       TFIIE_alpha  64 d 64 
                                       +
  gi|242398617|ref|YP_002994041.1| 100 E 100
                                       2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       945  (0.0527079); expected 358.6 (0.02)
Passed bias filter:                      705  (0.0393218); expected 358.6 (0.02)
Passed Vit filter:                       114  (0.00635841); expected 17.9 (0.001)
Passed Fwd filter:                        32  (0.00178482); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              32  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1027.77
//
Query:       gi|242398618|ref|YP_002994042.1|  [L=387]
Description: GTPase, GTP1/OBG family, containing TGS domain [Thermococcus sibiricus MM 739]
Scores for complete 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   75.4   0.1    8.9e-21   74.1   0.0    1.7  2  MMR_HSR1        50S ribosome-binding GTPase
    5.4e-21   74.4   0.0    1.9e-20   72.7   0.0    2.0  2  TGS             TGS domain
    1.1e-18   67.2   0.2    2.3e-18   66.1   0.2    1.6  1  MMR_HSR1_Xtn    C-terminal region of MMR_HSR1 domain
    9.6e-11   41.4   0.1    9.3e-10   38.2   0.0    2.2  2  FeoB_N          Ferrous iron transport protein B
    0.00013   22.0   0.2      0.011   15.9   0.2    2.6  1  YchF-GTPase_C   Protein of unknown function (DUF933)
    0.00071   20.1   0.0      0.002   18.7   0.0    1.8  1  MMR_HSR1_C      GTPase of unknown function C-terminal
     0.0025   17.8   3.3        1.5    8.7   0.0    3.2  3  RsgA_GTPase     RsgA GTPase
  ------ inclusion threshold ------
      0.013   15.9   2.6       0.46   10.9   0.6    2.6  2  Myb_DNA-bind_4  Myb/SANT-like DNA-binding domain
      0.017   15.2   1.1       0.14   12.2   1.1    2.8  1  Dynamin_N       Dynamin family
      0.042   12.9   1.1       0.27   10.3   0.3    2.1  2  Dus             Dihydrouridine synthase (Dus)
      0.052   13.0   0.1       0.18   11.2   0.0    1.9  2  SRPRB           Signal recognition particle receptor beta sub
        0.1   13.2   1.1       0.34   11.6   1.1    1.8  1  DUF573          Protein of unknown function, DUF573
       0.15   12.2   0.0       0.33   11.1   0.0    1.4  1  MnmE_helical    MnmE 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 !   74.1   0.0   6.5e-24   8.9e-21       1     103 [.      83     186 ..      83     202 .. 0.90
   2 ?   -2.6   0.0       4.2   5.8e+03      65      77 ..     278     288 ..     263     319 .. 0.40

  Alignments for each domain:
  == domain 1  score: 74.1 bits;  conditional E-value: 6.5e-24
                                       EEEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHHHHHC.T CS
                          MMR_HSR1   1 evaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseekglgkaflalee.a 76 
                                       +v+++G pNvGKS+L++ l +    ++d+p+tT +++ g +++k+ +i+lv +pGliega  +kg+g ++l++++ a
  gi|242398618|ref|YP_002994042.1|  83 QVVLAGLPNVGKSSLLKVLADVDIDIADYPFTTVEPIPGMMNHKDVQIQLVEVPGLIEGAALGKGMGTQLLSVIRnA 159
                                       599***************************************999***************************99889 PP

                                       SEEEEEEETTTTCSHHHHHHHHHHHHH CS
                          MMR_HSR1  77 dlillvvdaseeklkpldeeleellee 103
                                       d+i++vvd+s++ +k+++  l+e+ + 
  gi|242398618|ref|YP_002994042.1| 160 DAIAIVVDLSQDPIKQMKIILKEFERA 186
                                       **********99999998888887543 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4.2
                                       HHHHHHHHHHCTS CS
                          MMR_HSR1  65 glgkaflaleead 77 
                                       +l k++ +  + +
  gi|242398618|ref|YP_002994042.1| 278 RLVKTYND--RFK 288
                                       34444443..222 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       4.2   5.8e+03      12      30 ..     237     255 ..     232     260 .. 0.78
   2 !   72.7   0.0   1.3e-23   1.9e-20       1      59 [.     314     385 ..     314     386 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 4.2
                                       EEETTB-HHHHHHHHSTTH CS
                               TGS  12 dlprgatveDfAykIhrsl 30 
                                       ++++  t eDf  ++  sl
  gi|242398618|ref|YP_002994042.1| 237 TVKEPVTLEDFSDALDDSL 255
                                       5778889999998887777 PP

  == domain 2  score: 72.7 bits;  conditional E-value: 1.3e-23
                                       EEEEE.TTSSEEE.....EETTB-HHHHHHHHSTTHHHHEEEEEECS.......EEEETTSBB-SSEEEEEE CS
                               TGS   1 irvyt.PdGkvpd.....lprgatveDfAykIhrslakkfiyAlVnG.......qrvgldhvLedgdvveIv 59 
                                       irv+t  +G+ p      l++g+ v D+A +Ih+++ak+f+yA+V+G       qrvg dhvLedgd+veI 
  gi|242398618|ref|YP_002994042.1| 314 IRVFTkSPGEDPAyppiaLKKGSKVLDVAERIHKDFAKNFKYARVWGksakfpgQRVGPDHVLEDGDIVEIH 385
                                       89***99****************************************************************6 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   0.2   1.7e-21   2.3e-18       2     104 ..     205     311 ..     204     313 .. 0.90

  Alignments for each domain:
  == domain 1  score: 66.1 bits;  conditional E-value: 1.7e-21
                      MMR_HSR1_Xtn   2 gGikitstvkltkldeetvkkilkeykihnaevliredvtvDdlidviegnrvYipclyvlNKiDl.isleeldela 77 
                                       gGi i+++ +l + d  +v+k+l+e +ih+ae++++e vt++d+ d++ ++ v+ +++++ NK D   s e+ ++l 
  gi|242398618|ref|YP_002994042.1| 205 GGIVINGQ-HLIQGDIGEVMKMLREEGIHSAEITVKEPVTLEDFSDALDDSLVWRKAIIIANKGDIpGSRENYERLV 280
                                       99999988.5677999*************************************************987778888887 PP

                      MMR_HSR1_Xtn  78 re....pnsvviSaekelnldeLkekiweeL 104
                                       ++     +++++Sa+k+ n++ Lke++++ +
  gi|242398618|ref|YP_002994042.1| 281 KTyndrFKIIPVSAKKKANIEVLKEELYQLV 311
                                       75444359********************865 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 !   38.2   0.0   6.7e-13   9.3e-10       2      58 ..      83     139 ..      82     193 .. 0.83
   2 ?    0.8   0.0      0.23   3.1e+02     136     155 ..     287     306 ..     268     307 .. 0.87

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 6.7e-13
                                       EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----S CS
                            FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiY 58 
                                       +v+l+G pnvGk++l+  l++++ +++ +p +tve   g +++k+ ++++v +PG  
  gi|242398618|ref|YP_002994042.1|  83 QVVLAGLPNVGKSSLLKVLADVDIDIADYPFTTVEPIPGMMNHKDVQIQLVEVPGLI 139
                                       699****************************************************74 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.23
                                       S-EEEEBTTTTBTHHHHHHH CS
                            FeoB_N 136 vpvvktsakkkegieellka 155
                                       ++++++sakkk +ie l+++
  gi|242398618|ref|YP_002994042.1| 287 FKIIPVSAKKKANIEVLKEE 306
                                       689************99986 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 !   15.9   0.2   7.8e-06     0.011      17      44 ..     332     359 ..     314     386 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 7.8e-06
                     YchF-GTPase_C  17 ikkgttapqaAgviHsDfekgFiraevi 44 
                                       +kkg+++ + A  iH+Df k+F  a+v 
  gi|242398618|ref|YP_002994042.1| 332 LKKGSKVLDVAERIHKDFAKNFKYARVW 359
                                       799********************99986 PP

>> 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 !   18.7   0.0   1.4e-06     0.002       2      42 ..     264     304 ..     263     317 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.4e-06
                        MMR_HSR1_C   2 lNKaDlpaadenieklkekypkdkkvvpvsAaaElaLrkaa 42 
                                       +NK D+p ++en+e+l ++y+++ k++pvsA+    ++ ++
  gi|242398618|ref|YP_002994042.1| 264 ANKGDIPGSRENYERLVKTYNDRFKIIPVSAKKKANIEVLK 304
                                       8********************888*******9887776555 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.2    0.0021       2.9     100     121 ..      82     103 ..      39     111 .. 0.78
   2 ?   -0.7   0.0      0.84   1.2e+03      15      46 ..     158     187 ..     148     257 .. 0.61
   3 !    8.7   0.0    0.0011       1.5      49      99 ..     260     309 ..     255     315 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0021
                                       SEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase 100 ktsvlvGqSGvGKStLinallp 121
                                       + +vl+G   vGKS+L+++l+ 
  gi|242398618|ref|YP_002994042.1|  82 SQVVLAGLPNVGKSSLLKVLAD 103
                                       6789**************9986 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.84
                                       S--EEEEEEESTTTT--HHHHHHHHHHHHHTT CS
                       RsgA_GTPase  15 NvdqllivvslkepelslnlldrfLvlaeekg 46 
                                       N d + ivv l+++ +++  +  +L ++e++g
  gi|242398618|ref|YP_002994042.1| 158 NADAIAIVVDLSQDPIKQMKI--ILKEFERAG 187
                                       677777777776665554333..333333333 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0011
                                       EEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTT CS
                       RsgA_GTPase  49 pvivlnKiDlleeeeeleelkeelealgyevllvsaktkegleelkellkd 99 
                                        +i+ nK D+  ++e++e+l +++++  ++++ vsak+k+++e lke+l +
  gi|242398618|ref|YP_002994042.1| 260 AIIIANKGDIPGSRENYERLVKTYNDR-FKIIPVSAKKKANIEVLKEELYQ 309
                                       68999**********9********998.*******************9976 PP

>> Myb_DNA-bind_4  Myb/SANT-like DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.1     0.011        16      41      74 ..       7      40 ..       4      45 .. 0.85
   2 ?   10.9   0.6   0.00034      0.46      46      82 ..      39      75 ..      34      83 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.011
                                      HHHHHHHC----HHHHHHHHHHHHHHHHCSSSSS CS
                    Myb_DNA-bind_4 41 aeamaergykrspeqCkeKienLkkrYkkekere 74
                                      ae +a+++ +r++  + eKi+ L+k Y ++ +++
  gi|242398618|ref|YP_002994042.1|  7 AEYLAAEEEYRQARTIPEKIRALEKMYATVPKHK 40
                                      6778888888******************998874 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00034
                                      HHC----HHHHHHHHHHHHHHHHCSSSSSS----S-- CS
                    Myb_DNA-bind_4 46 ergykrspeqCkeKienLkkrYkkekerekgsgsswp 82
                                       +g ++   q+k+Ki +L+k+++k +++ kg g s+ 
  gi|242398618|ref|YP_002994042.1| 39 HKGTEKLRLQIKRKISELRKEFEKQQSQRKGGGYSFS 75
                                      578999999******************9988887765 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.1    0.0001      0.14      45     143 ..      33     173 ..      21     183 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0001
                                       --CCS...SSEEEET-EB--CHHHHHHHHHHHHHHHTSSSS--SS................................ CS
                         Dynamin_N  45 easeravkeelkekekkledfsevreeieketekiagankgiskk................................ 89 
                                       +a+  ++k + k + +  +++se+r+e+ek++++ +g + ++s k                                
  gi|242398618|ref|YP_002994042.1|  33 YATVPKHKGTEKLRLQIKRKISELRKEFEKQQSQRKGGGYSFSVKkegasqvvlaglpnvgkssllkvladvdidia 109
                                       55555666677777888999****************99999998899****************************** PP

                                       ........-EEEEEEETTS-SEEEEE---B-SSSGTTS...HHHHHHHSTTEEEEEEEETTS-CC CS
                         Dynamin_N  90 ........villkilsllvkgltlvDlPGldsvnkrdq...elvkeyikkadiilavtsanhdls 143
                                               +i   + + ++ ++ lv +PGl++ ++  +     + + i++ad+i  v++ ++d  
  gi|242398618|ref|YP_002994042.1| 110 dypfttvePI-PGMMNHKDVQIQLVEVPGLIEGAALGKgmgTQLLSVIRNADAIAIVVDLSQDPI 173
                                       ***9987533.344556667899*********9999998888899999***********999865 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.3   0.00019      0.27     228     287 ..      10      69 ..       1      87 [. 0.82
   2 ?    0.9   0.0      0.14     2e+02     109     147 ..     275     314 ..     269     318 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00019
                                       HHHHSC------HHHHHHHHHHHHHHCHHTTCCCCCCHHHHHHHHHHHHHHTTTTCHHHH CS
                               Dus 228 avktgeaepapplaeeaeiveehlkkleeelgedkglrkirkhlawylkglkkaaelrre 287
                                        + ++e+++a ++ e+++++e+++  + +++g +k   +i +++++++k+++k++  r+ 
  gi|242398618|ref|YP_002994042.1|  10 LAAEEEYRQARTIPEKIRALEKMYATVPKHKGTEKLRLQIKRKISELRKEFEKQQSQRKG 69 
                                       456668888999**************************************9999887765 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.14
                                       HHHHHHHHHHCCSS.S-EEEEEESESSTTTC.HHHHHHHH CS
                               Dus 109 lvaqivkavvkave.iPvtvkirigiddeeenalelakiv 147
                                         +++vk+  +  + iPv++k +  i+  +e++ +l++i+
  gi|242398618|ref|YP_002994042.1| 275 NYERLVKTYNDRFKiIPVSAKKKANIEVLKEELYQLVDII 314
                                       5678999999999999**********96666666666654 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       1.2   1.6e+03      47      72 ..      30      55 ..      15      60 .. 0.70
   2 ?   11.2   0.0   0.00013      0.18       4      59 ..      82     138 ..      79     184 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.2
                                      GGTT-SEEEETT-GCCSHHHHHHHHH CS
                             SRPRB 47 kgskltliDfPGheklrqklleklka 72
                                      ++   t+    G eklr +++ k+ +
  gi|242398618|ref|YP_002994042.1| 30 EKMYATVPKHKGTEKLRLQIKRKISE 55
                                      55555555667999999999988755 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00013
                                       -EEEEE-STTSSHHHHHHHHHHS...S---B---SS-EEETTG...GGTT-SEEEETT- CS
                             SRPRB   4 pavllvGlsdsGKTslftrLttd...svkktvtSqessaalkvksekgskltliDfPGh 59 
                                        +v+l+Gl + GK sl++ L       +    t +e+     + ++k+ +++l+++PG 
  gi|242398618|ref|YP_002994042.1|  82 SQVVLAGLPNVGKSSLLKVLADVdidIADYPFTTVEPIPG--MMNHKDVQIQLVEVPGL 138
                                       579***************9997633234444455555443..4579***********95 PP

>> DUF573  Protein of unknown function, DUF573
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.1   0.00024      0.34      20      81 ..      16      77 ..       8      84 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00024
                            DUF573 20 fksktgtspk.sdldafyeavksslssdvsksqlseKlrrLkkkyrnavskikkgkdpsfkkp 81
                                      +++ +  + k + l+++y++v +   +++   q++ K+ +L+k +++ +s+ +kg + sf+ +
  gi|242398618|ref|YP_002994042.1| 16 YRQARTIPEKiRALEKMYATVPKHKGTEKLRLQIKRKISELRKEFEKQQSQ-RKGGGYSFSVK 77
                                      5555555444688999999999999999999****************9998.56666666654 PP

>> MnmE_helical  MnmE helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00024      0.33      73     131 ..      48     311 ..      33     326 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00024
                                       xxxxxxxxxxxxxxxxxxxxxxxx..................................................... RF
                      MnmE_helical  73 elkeelekllatakrgellreGik..................................................... 96 
                                       ++k+++++l +++++++  r+G                                                       
  gi|242398618|ref|YP_002994042.1|  48 QIKRKISELRKEFEKQQSQRKGGGysfsvkkegasqvvlaglpnvgkssllkvladvdidiadypfttvepipgmmn 124
                                       67777777777777777777777777777788888888888888888888888888888888888888888888888 PP

                                       ............................................................................. RF
                      MnmE_helical  97 ............................................................................. 96 
                                                                                                                    
  gi|242398618|ref|YP_002994042.1| 125 hkdvqiqlvevpgliegaalgkgmgtqllsvirnadaiaivvdlsqdpikqmkiilkeferagikinkrkpkveikr 201
                                       88888888888888888888888888888888888888888888888888888888888888888999999999999 PP

                                       ..................................................................xxxxxxx.... RF
                      MnmE_helical  97 ..................................................................Dllkeke.... 103
                                                                                                         D+  + e    
  gi|242398618|ref|YP_002994042.1| 202 mpmggivingqhliqgdigevmkmlreegihsaeitvkepvtledfsdalddslvwrkaiiiankgDIPGSREnyer 278
                                       99999999999999999999999999999999999999999999999888888888888888888865555556777 PP

                                       ....xxxxxxxxxxxxxxxxxxxxxxxxxxx.x RF
                      MnmE_helical 104 ....ekeeeevlkiSaktgegieeLeeaike.l 131
                                            +++ +++ +Sak++++ie L+e++ + +
  gi|242398618|ref|YP_002994042.1| 279 lvktYNDRFKIIPVSAKKKANIEVLKEELYQlV 311
                                       777777788888*****************8844 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1008  (0.0562218); expected 358.6 (0.02)
Passed bias filter:                      757  (0.0422221); expected 358.6 (0.02)
Passed Vit filter:                       101  (0.00563333); 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: 0.70u 0.34s 00:00:01.04 Elapsed: 00:00:00.51
# Mc/sec: 2281.24
//
Query:       gi|242398619|ref|YP_002994043.1|  [L=301]
Description: Pyruvate-formate lyase-activating enzyme [Thermococcus sibiricus MM 739]
Scores for complete 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-24   86.2   4.6    4.8e-24   85.6   2.3    2.2  2  Radical_SAM     Radical SAM superfamily
    4.1e-17   61.2   9.4    3.5e-09   36.1   1.5    2.5  2  Fer4            4Fe-4S binding domain
    2.8e-15   56.8   5.0    1.2e-13   51.5   5.0    2.8  1  Fer4_12         4Fe-4S single cluster domain
      2e-11   44.3  14.0    4.2e-11   43.3  14.0    1.6  1  Fer4_7          4Fe-4S dicluster domain
      3e-11   42.9  14.3    6.5e-07   29.2   1.9    2.3  2  Fer4_6          4Fe-4S binding domain
    3.5e-11   43.1  10.0    7.2e-11   42.1  10.0    1.5  1  Fer4_21         4Fe-4S dicluster domain
    4.6e-11   42.1  11.3    4.4e-06   26.5   3.6    2.5  2  Fer4_2          4Fe-4S binding domain
    2.9e-10   40.1  24.4      9e-08   32.1  13.8    2.2  2  Fer4_10         4Fe-4S dicluster domain
    1.1e-09   39.0  10.9    0.00015   22.6   2.6    2.5  2  Fer4_16         4Fe-4S double cluster binding domain
    1.2e-08   34.9  31.3    2.6e-08   33.9  14.0    1.9  2  Fer4_9          4Fe-4S dicluster domain
    1.8e-07   31.5   2.3     0.0041   17.5   0.0    2.4  2  Fer4_8          4Fe-4S dicluster domain
    3.1e-06   27.3  17.1     0.0002   21.6   1.9    2.6  2  Fer4_4          4Fe-4S binding domain
    1.3e-05   25.6  12.5     0.0079   16.7   3.4    2.6  2  Fer4_13         4Fe-4S single cluster domain of Ferredoxin I
    0.00021   21.4  11.0     0.0005   20.2   1.5    3.0  2  Fer4_14         4Fe-4S single cluster domain
    0.00034   21.3   7.3     0.0015   19.2   0.6    2.4  2  Fer4_15         4Fe-4S single cluster domain
    0.00058   20.6  23.9     0.0027   18.5   6.2    2.6  2  Fer4_3          4Fe-4S binding domain
     0.0011   19.4  14.9      0.093   13.3   3.4    2.4  3  Fer4_17         4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.024   14.4   2.9      0.059   13.1   2.9    1.7  1  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal
      0.031   14.5  12.7       0.15   12.3  12.7    1.9  1  Fer4_18         4Fe-4S dicluster domain
       0.38   11.6  15.1       0.16   12.8   3.1    2.5  2  Fer4_22         4Fe-4S dicluster 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 !   85.6   2.3   5.4e-27   4.8e-24       2     159 ..      24     232 ..      23     236 .. 0.95
   2 ?   -0.6   0.0       1.7   1.6e+03      26      40 ..     274     288 ..     258     299 .. 0.78

  Alignments for each domain:
  == domain 1  score: 85.6 bits;  conditional E-value: 5.4e-27
                                       EEESEESS--TTTSCCTT........................................................HHH CS
                                       xxxxxxxxxxxxxxxxxx........................................................xxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpet........................................................vrr 22 
                                       ++++gC+l C++C++pe                                                         ++ 
  gi|242398619|ref|YP_002994043.1|  24 IFMKGCPLSCWWCHNPEGvspkpelmyfefkcihchtcvkvcpenaisfdenetqqidrekctgcgvcasacptSAL 100
                                       79*************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHH.HHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxx.xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  23 egrgrslsveeileevkelk.aekg.vkevilgggepllypdfvellerlaklavpgiritvetngtlpdeeklerl 97 
                                       + +gr+++vee+l e+++    +++ +++v+++ggepl +p+f ++ +++ k+  + i++tv t+g+ p +e+l+ +
  gi|242398619|ref|YP_002994043.1| 101 RLVGRVITVEELLTEIEKDIkLYDDsGGGVTFSGGEPLSQPKFLVESLKELKK--RYIHTTVDTSGYAP-KEVLKQI 174
                                       ****************9999877788***************997777777776..8*************.******* PP

                                       HHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  98 lelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGendee 159
                                       l+   d +  +++ +d+ ++ k++  g  ++ ++e+l+ l+  g + v+ r +++pG +d +
  gi|242398619|ref|YP_002994043.1| 175 LPHT-DLFLYDIKLYDSGEHEKYT--GVPNDIIIENLKFLTGQGKE-VILRFPIIPGITDTD 232
                                       **66.*************888888..589**************999.************976 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.7
                                       HHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxx RF
                       Radical_SAM  26 grslsveeileevke 40 
                                        ++++++eil+ +ke
  gi|242398619|ref|YP_002994043.1| 274 IHHRPPDEILKWIKE 288
                                       567888888888876 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   1.3   5.7e-10   5.1e-07       6      24 .]      53      71 ..      49      71 .. 0.91
   2 !   36.1   1.5   3.9e-12   3.5e-09       2      23 ..      79     100 ..      79     101 .. 0.94

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 5.7e-10
                                      TTSSS-THHHHHSTTTEEE CS
                              Fer4  6 ekCigCGaCvevCPvgAIt 24
                                       kCi+C +Cv+vCP +AI+
  gi|242398619|ref|YP_002994043.1| 53 FKCIHCHTCVKVCPENAIS 71
                                      59***************96 PP

  == domain 2  score: 36.1 bits;  conditional E-value: 3.9e-12
                                       EEETTTSSS-THHHHHSTTTEE CS
                              Fer4   2 videekCigCGaCvevCPvgAI 23 
                                       +id ekC+gCG C+++CP+ A+
  gi|242398619|ref|YP_002994043.1|  79 QIDREKCTGCGVCASACPTSAL 100
                                       59*****************998 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 !   51.5   5.0   1.3e-16   1.2e-13       2     116 ..      16     184 ..      15     199 .. 0.88

  Alignments for each domain:
  == domain 1  score: 51.5 bits;  conditional E-value: 1.3e-16
                           Fer4_12   2 nGeGvrlslfvsgCnlsCkgCfnketwsfk............................................... 31 
                                       +G+G+r+++f++gC+lsC  C+n+e  s+k                                               
  gi|242398619|ref|YP_002994043.1|  16 DGPGIRTTIFMKGCPLSCWWCHNPEGVSPKpelmyfefkcihchtcvkvcpenaisfdenetqqidrekctgcgvca 92 
                                       7**************************99999********************************************* PP

                           Fer4_12  32 ..........sgkeft.kelleeiiedlk..kesiegltllGGEPllpenaeallelvkevkeekpekdiwlytgyt 95 
                                                  g+ +t +ell ei +d+k  ++s  g+t++GGEPl   + + l+e +ke+k++++  + + ++gy 
  gi|242398619|ref|YP_002994043.1|  93 sacptsalrlVGRVITvEELLTEIEKDIKlyDDSGGGVTFSGGEPLS--QPKFLVESLKELKKRYI-HTTVDTSGYA 166
                                       **********7777777*********9984457779***********..*****************.69******** PP

                           Fer4_12  96 leelskkekeellkeid.vlvd 116
                                        +e++k+    +l   d +l d
  gi|242398619|ref|YP_002994043.1| 167 PKEVLKQ----ILPHTDlFLYD 184
                                       ***9976....44444422334 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.3  14.0   4.7e-14   4.2e-11       1      52 []      54      99 ..      54      99 .. 0.92

  Alignments for each domain:
  == domain 1  score: 43.3 bits;  conditional E-value: 4.7e-14
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                      +Ci+C+ Cv++Cp +ai++de       e+ +id ekC+gCg+C+++CPt a
  gi|242398619|ref|YP_002994043.1| 54 KCIHCHTCVKVCPENAISFDEN------ETQQIDREKCTGCGVCASACPTSA 99
                                      7******************996......34589****************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 !   18.9   4.9   1.2e-06    0.0011       8      24 .]      54      70 ..      54      70 .. 0.97
   2 !   29.2   1.9   7.3e-10   6.5e-07       4      24 .]      80     100 ..      79     100 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.2e-06
                            Fer4_6  8 kCigCgdCvrvCPegai 24
                                      kCi+C  Cv+vCPe+ai
  gi|242398619|ref|YP_002994043.1| 54 KCIHCHTCVKVCPENAI 70
                                      8***************8 PP

  == domain 2  score: 29.2 bits;  conditional E-value: 7.3e-10
                            Fer4_6   4 idpdkCigCgdCvrvCPegai 24 
                                       id++kC+gCg C+++CP+ a+
  gi|242398619|ref|YP_002994043.1|  80 IDREKCTGCGVCASACPTSAL 100
                                       9*****************996 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1  10.0     8e-14   7.2e-11       7      53 ..      54      97 ..      51     102 .. 0.93

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 8e-14
                           Fer4_21  7 kCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPv 53
                                      kCi+C  C+++C++   +ai++d++++ ++  ++C+GC +C+s CP+
  gi|242398619|ref|YP_002994043.1| 54 KCIHCHTCVKVCPE---NAISFDENETQQIDREKCTGCGVCASACPT 97
                                      8************7...9****************************7 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.9   6.4e-07   0.00058       9      22 .]      54      67 ..      47      67 .. 0.89
   2 !   26.5   3.6   4.9e-09   4.4e-06       4      22 .]      79      97 ..      77      97 .. 0.95

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 6.4e-07
                            Fer4_2  9 rCigCgaCvsaCPa 22
                                      +Ci+C +Cv++CP+
  gi|242398619|ref|YP_002994043.1| 54 KCIHCHTCVKVCPE 67
                                      7************5 PP

  == domain 2  score: 26.5 bits;  conditional E-value: 4.9e-09
                            Fer4_2  4 vvdtdrCigCgaCvsaCPa 22
                                      ++d+++C+gCg C saCP+
  gi|242398619|ref|YP_002994043.1| 79 QIDREKCTGCGVCASACPT 97
                                      69****************7 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1  13.8     1e-10     9e-08       7      56 .]      53      96 ..      48      96 .. 0.89
   2 !   21.1   2.8   2.7e-07   0.00024       3      23 ..      79      99 ..      77     126 .. 0.76

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 1e-10
                           Fer4_10  7 dtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                       +Ci+C +Cvk+CP       +    +e+e+++++ ekCtgcg C++aCP
  gi|242398619|ref|YP_002994043.1| 53 FKCIHCHTCVKVCPE------NAISFDENETQQIDREKCTGCGVCASACP 96
                                      69*************......66666788889999**************9 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 2.7e-07
                           Fer4_10  3 vidddtCirCgkCvkaCPadl 23
                                      +id+++C++Cg C +aCP+++
  gi|242398619|ref|YP_002994043.1| 79 QIDREKCTGCGVCASACPTSA 99
                                      699***************966 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   2.6   1.7e-07   0.00015       1      27 [.      54      80 ..      54      84 .. 0.80
   2 !   21.2   1.3   4.6e-07   0.00041       1      20 [.      84     103 ..      84     126 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.7e-07
                           Fer4_16  1 rCgtCgkCaevCPtnaikekkekeiea 27
                                      +C+ C+ C++vCP+nai+ +++++ ++
  gi|242398619|ref|YP_002994043.1| 54 KCIHCHTCVKVCPENAISFDENETQQI 80
                                      5*****************996555444 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 4.6e-07
                           Fer4_16   1 rCgtCgkCaevCPtnaikek 20 
                                       +C++Cg Ca++CPt+a++  
  gi|242398619|ref|YP_002994043.1|  84 KCTGCGVCASACPTSALRLV 103
                                       5***************9976 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   9.3   3.5e-05     0.031      31      51 .]      51      70 ..      18      70 .. 0.68
   2 !   33.9  14.0   2.9e-11   2.6e-08       1      50 [.      54      99 ..      54     100 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.5e-05
                            Fer4_9 31 aseeaCigCgaCveaCpkgai 51
                                      + e +Ci+C++Cv++Cp++ai
  gi|242398619|ref|YP_002994043.1| 51 F-EFKCIHCHTCVKVCPENAI 70
                                      2.258*************987 PP

  == domain 2  score: 33.9 bits;  conditional E-value: 2.9e-11
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50
                                      kC+ C++Cv++Cp ++++ d++e+    r+    +C+gCg C+ aCp+ a
  gi|242398619|ref|YP_002994043.1| 54 KCIHCHTCVKVCPENAISFDENETQQIDRE----KCTGCGVCASACPTSA 99
                                      7****************9999988888765....7************986 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.9   0.00012      0.11      50      64 ..      54      68 ..      46      79 .. 0.78
   2 !   17.5   0.0   4.5e-06    0.0041       3      18 ..      83      98 ..      81     159 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00012
                            Fer4_8 50 sCttcgaCtevCpvg 64
                                      +C +c+ C++vCp++
  gi|242398619|ref|YP_002994043.1| 54 KCIHCHTCVKVCPEN 68
                                      577777777777765 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 4.5e-06
                            Fer4_8  3 ekCieCgaCqsaCpvl 18
                                      ekC++Cg C saCp+ 
  gi|242398619|ref|YP_002994043.1| 83 EKCTGCGVCASACPTS 98
                                      6999999999999954 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   1.6   1.1e-05    0.0094       3      16 ..      54      67 ..      53      77 .. 0.92
   2 !   21.6   1.9   2.2e-07    0.0002       2      16 ..      83      97 ..      82     104 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.1e-05
                            Fer4_4  3 rCigCgsCvaaCPq 16
                                      +Ci+C  Cv +CP 
  gi|242398619|ref|YP_002994043.1| 54 KCIHCHTCVKVCPE 67
                                      7************5 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 2.2e-07
                            Fer4_4  2 erCigCgsCvaaCPq 16
                                      e+C+gCg+C +aCP+
  gi|242398619|ref|YP_002994043.1| 83 EKCTGCGVCASACPT 97
                                      89************6 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   1.8   7.8e-05      0.07       5      19 ..      54      68 ..      52      79 .. 0.77
   2 !   16.7   3.4   8.8e-06    0.0079       1      18 [.      80      97 ..      80      98 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.8e-05
                           Fer4_13  5 tCiacgaCvelaPdv 19
                                      +Ci c++Cv+++P+ 
  gi|242398619|ref|YP_002994043.1| 54 KCIHCHTCVKVCPEN 68
                                      8************94 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 8.8e-06
                           Fer4_13  1 VDrdtCiacgaCvelaPd 18
                                      +Dr++C++cg+C++++P 
  gi|242398619|ref|YP_002994043.1| 80 IDREKCTGCGVCASACPT 97
                                      8****************6 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 !    6.8   0.6    0.0081       7.2       1      19 [.      24      40 ..      24      52 .. 0.85
   2 !   20.2   1.5   5.6e-07    0.0005      14      94 ..      87     169 ..      51     187 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0081
                           Fer4_14  1 lfvrlsgCnlsCkgCdnke 19
                                      +f+   gC+lsC +C n e
  gi|242398619|ref|YP_002994043.1| 24 IFM--KGCPLSCWWCHNPE 40
                                      577..9*********9866 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 5.6e-07
                           Fer4_14  14 gCd......nketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekkiw 84 
                                       gC        +++ +     + +eell +i kd k ++ +  g++++GGePL   + k l++ +k+lk++y  ++ +
  gi|242398619|ref|YP_002994043.1|  87 GCGvcasacPTSALRLVGRVITVEELLTEIEKDIKLYDDSGGGVTFSGGEPL--SQPKFLVESLKELKKRY--IHTT 159
                                       3333334443444777778888899998888888887777899*********..789999***********..8888 PP

                           Fer4_14  85 letngtleie 94 
                                       + t+g + +e
  gi|242398619|ref|YP_002994043.1| 160 VDTSGYAPKE 169
                                       8888877655 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 ?    5.2   1.1      0.04        36       7      20 ..      54      67 ..      52      78 .. 0.79
   2 !   19.2   0.6   1.7e-06    0.0015       3      20 ..      80      97 ..      79     111 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.04
                           Fer4_15  7 aCigcglCvaeape 20
                                      +Ci c  Cv+++pe
  gi|242398619|ref|YP_002994043.1| 54 KCIHCHTCVKVCPE 67
                                      69999999999976 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 1.7e-06
                           Fer4_15  3 vDrdaCigcglCvaeape 20
                                      +Dr++C+gcg+C+ ++p+
  gi|242398619|ref|YP_002994043.1| 80 IDREKCTGCGVCASACPT 97
                                      9***************96 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   6.2     3e-06    0.0027       1      15 []      55      69 ..      55      69 .. 0.98
   2 !   10.6   6.7     0.001      0.94       1      15 []      85      99 ..      85      99 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 3e-06
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C++C +Cv+vCP++A
  gi|242398619|ref|YP_002994043.1| 55 CIHCHTCVKVCPENA 69
                                      *************98 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.001
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      CtgCg C  +CP+ A
  gi|242398619|ref|YP_002994043.1| 85 CTGCGVCASACPTSA 99
                                      ************976 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   3.4   0.00035      0.31      45      59 ..      54      68 ..      48      71 .. 0.66
   2 !   13.3   3.4    0.0001     0.093       1      22 [.      54      77 ..      54      84 .. 0.70
   3 !   12.4   3.4    0.0002      0.18      42      58 ..      81      97 ..      70     100 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00035
                           Fer4_17 45 lCieCgeCerkCPqg 59
                                      +Ci+C+ C+++CP++
  gi|242398619|ref|YP_002994043.1| 54 KCIHCHTCVKVCPEN 68
                                      466666666666654 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.0001
                           Fer4_17  1 rCiqCgyClpeCpsyea..ydnep 22
                                      +Ci+C  C+++Cp +++   +ne 
  gi|242398619|ref|YP_002994043.1| 54 KCIHCHTCVKVCPENAIsfDENET 77
                                      699999999999988775434444 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 0.0002
                           Fer4_17 42 kaslCieCgeCerkCPq 58
                                        ++C++Cg C+++CP 
  gi|242398619|ref|YP_002994043.1| 81 DREKCTGCGVCASACPT 97
                                      56789999999999986 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 ?   13.1   2.9   6.6e-05     0.059      21      52 ..      29      60 ..      16      62 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.6e-05
                    zinc_ribbon_10 21 yalICskChshnGlapkeeleevkyrCpkCga 52
                                       +l C  Ch+  G+ pk el +++++C +C +
  gi|242398619|ref|YP_002994043.1| 29 CPLSCWWCHNPEGVSPKPELMYFEFKCIHCHT 60
                                      578899************************86 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3  12.7   0.00017      0.15      60      96 ..      54      96 ..      47     102 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00017
                           Fer4_18 60 dcidcescvkvcP...tgidirkGlqle...ciscllcidacd 96
                                      +ci+c++cvkvcP   +  d  + +q++   c  c+ c  ac 
  gi|242398619|ref|YP_002994043.1| 54 KCIHCHTCVKVCPenaISFDENETQQIDrekCTGCGVCASACP 96
                                      7************433356899999995445***********6 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   4.2     0.069        62       1      14 [.      54      67 ..      54      79 .. 0.80
   2 ?   12.8   3.1   0.00018      0.16      74      94 ..      77      97 ..      70      99 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.069
                           Fer4_22  1 rClsCgaCtlvCpt 14
                                      +C++C +C  vCp 
  gi|242398619|ref|YP_002994043.1| 54 KCIHCHTCVKVCPE 67
                                      7***********95 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00018
                           Fer4_22 74 kekfgesgCvGCgRCieacpv 94
                                      ++++++++C+GCg C +acp+
  gi|242398619|ref|YP_002994043.1| 77 TQQIDREKCTGCGVCASACPT 97
                                      578899*************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       696  (0.0388198); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 1980.77
//
Query:       gi|242398620|ref|YP_002994044.1|  [L=351]
Description: Proline racemase [Thermococcus sibiricus MM 739]
Scores for 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-120  401.7   0.0   2.4e-120  401.5   0.0    1.0  1  Pro_racemase  Proline racemase
    0.00066   19.2   0.0    0.00098   18.7   0.0    1.2  1  PhzC-PhzF     Phenazine biosynthesis-like protein
     0.0049   15.9   0.0      0.016   14.2   0.0    1.7  2  PrpF          PrpF protein


Domain annotation for each model (and alignments):
>> Pro_racemase  Proline racemase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  401.5   0.0  3.9e-124  2.4e-120       2     324 ..      26     348 ..      25     349 .. 1.00

  Alignments for each domain:
  == domain 1  score: 401.5 bits;  conditional E-value: 3.9e-124
                                       EEEEETTEEEEEEEESS---SSSSHHHHHHHHHHH.HHHHHHHHSTTTS-TT-EEEEEE--SSTTSSEEEEEEESSS CS
                      Pro_racemase   2 vdsHteGevgrvvvgGvpelpgetlaekrrlleedldalRralllePRGhdvmsgallvppkepdadlgvifletsg 78 
                                       +d+Ht+Ge+ r++ +G+p++pg+t++ekrr+l+e+ld+lR+al+ ePRGh++m+ga++++p ++dad+gvifl+++g
  gi|242398620|ref|YP_002994044.1|  26 LDTHTAGEPLRIIFSGFPKIPGKTILEKRRYLRENLDYLRTALMWEPRGHADMYGAIITEPISEDADFGVIFLHNEG 102
                                       79*************************************************************************** PP

                                       B-SSTHHHHHHHHHHHHHTTSS-SEEEECEEEEEETTEEEEEEEECTSTSEEEEEEE-S-BEEEEEEEEEEETTTEE CS
                      Pro_racemase  79 ylpmcGsntigvvtvlletGlvevqepetklsletpaGlvevtaecrdgkvervslenvpsfvyaldvevevpglGk 155
                                       y++mcG++ti++ +v++e Glve++ep t+++++ paGl+++ +++++gk+e+v ++nvpsfv  +d e+evpglG+
  gi|242398620|ref|YP_002994044.1| 103 YSTMCGHATIALGKVAVECGLVEPKEPITEIKMDSPAGLIKIYVQTQNGKAEKVYFHNVPSFVLYKDEEIEVPGLGR 179
                                       ***************************************************************************** PP

                                       EEEEEEESSSEEEEEEGGGCTS-SSCCCHHHHHHHHHHHHHHHHHHH---TTCSTTC-SEEEEEEEEEETTTTSEEE CS
                      Pro_racemase 156 vkvDiayGGnfyaiveaeklgldlekaearelveageklrealneqlkvqhpenedirevslveltgkkeraeaear 232
                                       vk+D ayGG+fya+v+ae+lgl+ +++  r+l+++g+k+++a+ ++ +++hp +ed++ ++ +++ g+++++++++r
  gi|242398620|ref|YP_002994044.1| 180 VKYDLAYGGAFYAFVNAEDLGLKCTPEYYRKLIDVGMKIKRAIIAEKEIKHPFEEDLSFLYGTIFIGPPHDKDSHSR 256
                                       ***************************************************************************** PP

                                       EEEEETTSEB-SS--HHHHHHHHHHHHHTTSS-TT-EEEEEETTS-EEEEEEEEEEEECTCEEEEEEEEE-EEEEEE CS
                      Pro_racemase 233 naviisdkkvDRSPcGtgtsArlAvlaakGklkvgeefvqesiiGseFegrveeeaevggrkaivpeisGrafitgl 309
                                       +++i++d++vDRSP+Gtg+s rlA+l+ kG++ +g+e++ esiiG++F+g+v+ee++ g  kaivpe+ G a+it+ 
  gi|242398620|ref|YP_002994044.1| 257 HVCIFADGEVDRSPTGTGVSGRLAILYEKGEIDIGDEVTIESIIGTKFTGKVVEETKYGPHKAIVPEVGGTAHITAK 333
                                       ***************************************************************************** PP

                                       EEEEE-TT-TTTT-B CS
                      Pro_racemase 310 aqllldpsDPfaeGf 324
                                       +++++dp+DP++ Gf
  gi|242398620|ref|YP_002994044.1| 334 NTFIIDPEDPLKYGF 348
                                       **************9 PP

>> PhzC-PhzF  Phenazine biosynthesis-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   1.6e-07   0.00098      65     123 ..     105     165 ..      81     180 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.6e-07
                                       S--HHHHHHHHHHHHHHCT-...S-SCEEEEEETTEEEEE.EEEEETCEECCEEEEE-SEEE CS
                         PhzC-PhzF  65 dlcGHatlasahalaekglv...asaetveletkaGilpvkslkekddgeellielkfPvik 123
                                        +cGHat+a+ ++ +e glv   +  ++++++++aG +++  ++ +++++e +   ++P + 
  gi|242398620|ref|YP_002994044.1| 105 TMCGHATIALGKVAVECGLVepkEPITEIKMDSPAGLIKI-YVQTQNGKAEKVYFHNVPSFV 165
                                       58*****************9766667899***********.588888888888888888875 PP

>> PrpF  PrpF protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   2.7e-06     0.016      89     142 ..     103     154 ..      83     158 .. 0.87
   2 ?   -1.7   0.0      0.18   1.1e+03     182     215 ..     170     204 ..     167     208 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.7e-06
                                       -S---HHHHHHHHHHHHHTT-SGGG--EEEEEEEETTTTEEEEEEEEEETTEE- CS
                              PrpF  89 tsgnCGnlsaavGpfaieaGlvaarepvtavrilnvnigklivaevpvedGqvq 142
                                       +s  CG  + a G  a+e Glv+ +ep+t++++     + li + v++++G+ +
  gi|242398620|ref|YP_002994044.1| 103 YSTMCGHATIALGKVAVECGLVEPKEPITEIKMDS--PAGLIKIYVQTQNGKAE 154
                                       6788**************************99875..46789999999999865 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.18
                                       EEEEETT.EEEEEEEEESSSEEEEEETTTTT--S- CS
                              PrpF 182 dtldvpg.gtvevtlidaaiPlvlveaeslGltGt 215
                                       ++++vpg g+v+  l   +    +v+ae lGl+ t
  gi|242398620|ref|YP_002994044.1| 170 EEIEVPGlGRVKYDLAYGGAFYAFVNAEDLGLKCT 204
                                       6789999999999999999999*********9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.52
# Mc/sec: 2016.66
//
Query:       gi|242398621|ref|YP_002994045.1|  [L=823]
Description: Pyruvate-formate lyase [Thermococcus sibiricus MM 739]
Scores for complete 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-219  729.1   0.0   6.7e-219  728.8   0.0    1.0  1  PFL-like     Pyruvate formate lyase-like
    3.8e-30  104.5   0.0    1.6e-29  102.5   0.0    2.1  2  Gly_radical  Glycine radical
  ------ inclusion threshold ------
      0.013   14.6   2.9      0.027   13.6   2.9    1.5  1  TelA         Toxic anion resistance protein (TelA)
       0.12   12.4   3.7       0.37   10.8   0.1    2.5  2  GP24_25      Tail assembly gene products 24 & 25


Domain annotation for each model (and alignments):
>> PFL-like  Pyruvate formate lyase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  728.8   0.0  1.5e-222  6.7e-219       3     647 .]      36     685 ..      28     685 .. 0.98

  Alignments for each domain:
  == domain 1  score: 728.8 bits;  conditional E-value: 1.5e-222
                                       HHHHHHHHCC.HT.TS.EEESHHHHHHHHHHHHC..TTS-HHHHHHHHHHHHHHHS-----TT-SS---SSSSTTEE CS
                          PFL-like   3 erierlkknytlyeakpslelerarllteseket..egepvdirrakalakilsnlplyIrddElIvGsqtkkprkr 77 
                                       er+ +l+k+  ++ ++ ++++erarl+te +k +  +g++++++ra+a++++l+++ l I++++lIvG++   ++++
  gi|242398621|ref|YP_002994045.1|  36 ERVANLRKES-VE-TEVKVSSERARLITEFYKSEipKGKSIPVQRALAFKYLLEHCSLPIEEGQLIVGLRGTGVKEV 110
                                       6888899999.66.556689*************766999************************************** PP

                                       E--TTTTCHHHHTTTTTCCCSSSSTEBEECHHHHHHHH.HHHHHTTTSHHHHHHHHCHHTTHHHHTSTSEE--CHGG CS
                          PFL-like  78 aifPegsirmledeldtlaereadgfeideeekkilre.ifpyWkgktvnegvfdayteetkaaresgiitvglpda 153
                                       +++Pe++++ +ed l++l++r++ ++++dee+++ +++ i+p+Wkg+ +++ +f+ +++e+ +a+e+gi+t +++++
  gi|242398621|ref|YP_002994045.1| 111 PTYPEICVHSMED-LEILNSRQNMPYKVDEETRELYKNeIIPFWKGRAMRDMIFETLPQEWIDAYEAGIWT-EFMEQ 185
                                       **********999.999******************************************************.***** PP

                                       SSCEEEE--HHHHHTCHHHHHHHHHHHHHHHHCCTTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-SH CS
                          PFL-like 154 sgrGhiipdyervlkyGldglieeikeklakldlddpeaiekaefykaviisleavieyaeryarlaeelaeqetdp 230
                                       +  Gh++++  r+++ G+ +++eeik+k+ +ld ++pe++ek e +ka+ i+ ea+  ya+rya++ e++ae+e+dp
  gi|242398621|ref|YP_002994045.1| 186 RSPGHTAGG-GRIFRMGVLDIKEEIKKKMGELDPSNPEYYEKMEELKAMDIVAEAILIYAKRYAEKLEKMAEEEKDP 261
                                       *********.******************************************************************* PP

                                       HHHHHHHHHHHHHHHTTTS--SSHHHHHHHHHHHHHHHHHHSSC.CEEE-BSHHHHTHHHHHHHHHTTSS-HHHHHH CS
                          PFL-like 231 krkaeLleiaevcgrvpskpaetfqEAiQlvwfvhlalvkesng.aamslgRldqylypyyekDleeGrlteeeaqe 306
                                       krk+eL+++ae+c+rvp+++++tf+EA+Q +wfvh+++ +e+n+ +++++gR+dq+lyp+y++DleeGrlt+e+a+e
  gi|242398621|ref|YP_002994045.1| 262 KRKKELKQMAEICKRVPAHAPRTFWEALQHYWFVHVGVTYETNPwDSFNPGRIDQHLYPFYKRDLEEGRLTREKAKE 338
                                       ***************************************************************************** PP

                                       HHHHHHHHHTTB-----HHHHCCCTTT--.--EEEEESB-TTSSB---HHHHHHHHHHHHH--SSSEEEEEE-TTS- CS
                          PFL-like 307 lidclwlklrevrklrseeyaelfagydp.fqnltvGGqnedGrdavnelsyliLealenlklpePnlsvrvskklp 382
                                       l++c+wlk++++ ++ + ++++ ++ +++ f +l++GG+++dG+d vnelsyliLe+l+++++ +Pn  v++s+k+p
  gi|242398621|ref|YP_002994045.1| 339 LLQCFWLKFNNQPAVPKVGVTAEESFTYNdFSKLNLGGLKKDGSDGVNELSYLILEVLSEMRTLQPNTAVLISNKNP 415
                                       *************************99999*********************************************** PP

                                       HHHHHHHHHHHHTTS--CEEEEHHHHHHHHHHTT--HHHHHTEEEETTTEEEECCCEES-SSEEEECHHHHHHHHTT CS
                          PFL-like 383 eeflkkaaevsrkGlgspayenddviipallnrgvsledArdyaiaGCvepqipGkeeqffaarinlakaLelalnn 459
                                       ++fl +a++v+  G+g p ++n d +i ++l++g++ledAr  +++GCve++++Gke +++++++nl+k+L ++lnn
  gi|242398621|ref|YP_002994045.1| 416 DRFLIEALKVVGPGFGEPPFFNFDGVIVKMLRQGKTLEDARTSGVSGCVETGAFGKEAYILTGYFNLPKILGITLNN 492
                                       ***************************************************************************** PP

                                       TCETTTTCB-S-----GGG--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS--HHHHHTSTTHHHHT--GGG CS
                          PFL-like 460 Grdektgkqvgpktgdvtefksyeelmeafkkqleylvklyvealniihymhdkyapepllsalvddciergkdlge 536
                                       G+d++tgk++g +tgd+++fks+eel++af kq+++++++ +++++ii+ +++ky+p p++s++++dc+++ kd++ 
  gi|242398621|ref|YP_002994045.1| 493 GIDPRTGKKIGIETGDPRNFKSFEELWNAFVKQVNHFLDIKMKGNDIIETLYAKYLPVPFMSLWIEDCVKNAKDYNG 569
                                       ***************************************************************************** PP

                                       T-SSEECEEEEEE-HHHHHHHHHHHHHHHTTSTSS-HHHHHHHHHTTTTT-HHHHHHHHH...S--TTSS-HHHHHH CS
                          PFL-like 537 gGarynfsgpqgvGlanvaDSLsAIkklVFddkkvtleeLkealaanFegeeelrqllln...aPkYGndddevDei 610
                                       gG+ryn++++q vGl ++aDSL+AIk++VFd+k + +eeL +al++n++g+e +r++l n   +Pk+Gndd++vDei
  gi|242398621|ref|YP_002994045.1| 570 GGTRYNTQYIQVVGLGTIADSLAAIKYHVFDKKTFVMEELLNALKNNWKGYEMMREILRNpekTPKFGNDDEYVDEI 646
                                       ***********************************************************9999************** PP

                                       HHHHHHHHHHHHCTSB-.T.TSCEEEEEE--TTTHHHHH CS
                          PFL-like 611 akevvetfaeevkkykn.y.rggkftaslltissnvpyg 647
                                       ak+vv+t+++ +++y+  + r++  +a +l+++ +v++g
  gi|242398621|ref|YP_002994045.1| 647 AKKVVDTVVDLIEAYPPsPvRKASKRAYFLPTTVHVYFG 685
                                       ***************99537*****************98 PP

>> Gly_radical  Glycine radical
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0         1   4.7e+03      41      89 ..     567     617 ..     538     626 .. 0.62
   2 !  102.5   0.0   3.7e-33   1.6e-29       1     106 []     701     804 ..     701     804 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1
                                       CCHHHHHH.HCC-CCCCCCHHCCCCCC.T-SECEEEEETCCCHCCCCCSCG CS
                       Gly_radical  41 avpdalgk.eeeerienlatlldgyfe.ggfhlnvnvvsretLldAqehpe 89 
                                       ++    ++ ++ +++ +l t+ d+  + + + ++ +++  e+Ll+A +++ 
  gi|242398621|ref|YP_002994045.1| 567 YNGGGTRYnTQYIQVVGLGTIADSLAAiKYHVFDKKTFVMEELLNALKNNW 617
                                       555555555556666666666666664244444666666688888888765 PP

  == domain 2  score: 102.5 bits;  conditional E-value: 3.7e-33
                                       TTSTTSHHCCHHHCHCHHCCCCCCTSECGCETTEETTECCCCHHHHHHHCC-CCCCCCHHCCCCCC.T-SECEEEEE CS
                       Gly_radical   1 lapganpmegrdkegplaslnSvakldyevaldgislnlkavpdalgkeeeerienlatlldgyfe.ggfhlnvnvv 76 
                                       +++g++p++g+d++g+ a+++Svak+d   +++g +ln+k++pd +  ++ee+i++la+l++++f+ gg+h+++nv+
  gi|242398621|ref|YP_002994045.1| 701 VSEGISPVQGMDRKGIAAVFRSVAKCDW-DKTGGALLNQKLTPDLF--DNEENIKKLAQLIRTFFRlGGHHVQFNVI 774
                                       589*************************.*****************..*****************66********** PP

                                       TCCCHCCCCCSCGGGCCEEEESSSSEEECC CS
                       Gly_radical  77 sretLldAqehpekypqltiRVsGYavnFv 106
                                       s e L++Aq++p++ ++l++RV+GY+ +Fv
  gi|242398621|ref|YP_002994045.1| 775 SAELLREAQKRPQEFQDLMVRVAGYSDYFV 804
                                       ****************************96 PP

>> TelA  Toxic anion resistance protein (TelA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   2.9     6e-06     0.027     109     181 ..     206     277 ..     202     279 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6e-06
                              TelA 109 qdellkdnaaLdqlyeknleyfkeLekyiaaGekkleeldekllpeleakaeasgdpedaqalrdleealdrl 181
                                       ++e++k + +Ld    + +e ++eL+ + +++e+ +    ++++++le+ ae+++dp++ ++l++++e+++r+
  gi|242398621|ref|YP_002994045.1| 206 KEEIKKKMGELDPSNPEYYEKMEELKAMDIVAEA-ILIYAKRYAEKLEKMAEEEKDPKRKKELKQMAEICKRV 277
                                       7899******************************.55566699***************************987 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 ?    1.2   1.2     0.078   3.5e+02      57     110 ..     213     267 ..     195     275 .. 0.69
   2 ?   10.8   0.1   8.3e-05      0.37      31      84 ..     607     658 ..     587     670 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.078
                           GP24_25  57 iaeleeddedeLvdeysdelekviakvfrliatdPkklidal.deeedPrirael 110
                                       + el+  + +  +    +++ +++a++ ++ a+   + ++++ +ee+dP+ + el
  gi|242398621|ref|YP_002994045.1| 213 MGELDPSNPEYYEKMEELKAMDIVAEAILIYAKRYAEKLEKMaEEEKDPKRKKEL 267
                                       4455555555555556789999********9998665555551667899888776 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 8.3e-05
                           GP24_25  31 veLkpLLkLgkkareavvellkefeeiaeleeddedeLvdeysdelekviakvf 84 
                                        eL + Lk   k+ e ++e+l++ e+ +++ +d  de vde ++++ + + ++ 
  gi|242398621|ref|YP_002994045.1| 607 EELLNALKNNWKGYEMMREILRNPEKTPKFGND--DEYVDEIAKKVVDTVVDLI 658
                                       366777888899****************77665..6788888888888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (823 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1212  (0.0676); expected 358.6 (0.02)
Passed bias filter:                      866  (0.0483016); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
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: 0.89u 0.33s 00:00:01.22 Elapsed: 00:00:00.51
# Mc/sec: 4832.57
//
Query:       gi|242398622|ref|YP_002994046.1|  [L=521]
Description: sodium:neurotransmitter symporter [Thermococcus sibiricus MM 739]
Scores for complete 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-53  181.4  45.9    3.3e-30  105.3  25.3    2.6  2  SNF       Sodium:neurotransmitter symporter family


Domain annotation for each model (and alignments):
>> SNF  Sodium:neurotransmitter symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.0  12.6   4.2e-27   7.6e-23       2     115 ..       8     122 ..       7     138 .. 0.94
   2 !  105.3  25.3   1.8e-34   3.3e-30     179     492 ..     144     450 ..     140     513 .. 0.87

  Alignments for each domain:
  == domain 1  score: 81.0 bits;  conditional E-value: 4.2e-27
                               SNF   2 etwskkldfilsvvGfavgLgnvWRFPYlcyknGGGafliPYlilllvaGiPlfflelalGqytreGaitvwrkic. 77 
                                       e+w+++l fi++++G +vg gn+WRFP +    GGGafliPY i+l+++ iPl+  e  +G+ t + +i  + k + 
  gi|242398622|ref|YP_002994046.1|   8 EHWGTRLGFIFAIIGAMVGSGNIWRFPRMMAMYGGGAFLIPYSIALFTVAIPLLISEGIIGRETGNSTILGFAKYAg 84 
                                       79****************************************************************99999877661 PP

                               SNF  78 PllkgiGyasivvalyvglyYnvilawalfYlfssftt 115
                                        ++  +G +++ v++ + +yY+v+ +wal Y+++ +t 
  gi|242398622|ref|YP_002994046.1|  85 KKYAWLGAWVAWVNIGIMFYYAVVNGWALAYFVKGLTG 122
                                       67999****************************99985 PP

  == domain 2  score: 105.3 bits;  conditional E-value: 1.8e-34
                               SNF 179 eltlcllvawvvvylailkGvkssgkvvyftatfPyvvllvllvrgvlLpGavkgikfyltpdlekllepkvWidaa 255
                                       + +   l++wv     +  Gvk   kv  f      + l+v+++r+v++pGa  g++++++ d +kl++++ W +a+
  gi|242398622|ref|YP_002994046.1| 144 QPLFFTLLVWVFTWYVMAVGVKRIEKVATFMVPSLILFLVVVIIRAVTMPGADVGLTYMFKFDTTKLSNAEAWLQAY 220
                                       555667899******************988877777888999*********************************** PP

                               SNF 256 tqiffslgigfGvlialasYnkfennvyrdallvslinsltsvlaglvvFsvlGfmaeeqgekisevaeeG.pgLaF 331
                                       +q+++s g g+G+ ++++sY k+++++  ++ ++++ +++  +l gl+v + +   a   g +  +v  eG  gL F
  gi|242398622|ref|YP_002994046.1| 221 SQVLWSTGAGWGIYLTYSSYLKKKDDINLNSHITGFGDTSAALLGGLAVITTVAVTAPLIGLDPFKVYAEGnVGLTF 297
                                       *************************************************************999999777737**** PP

                               SNF 332 iaypealtklplsplwsvlFFlmlillgldsqfgtvegiitavvDefkvllrrrelltlivavlaflvglllvtegG 408
                                       i  +e   k+p++   ++lF+l l +++++sq+++ ++++  vvD f v    r+   + va++ ++ g+    + G
  gi|242398622|ref|YP_002994046.1| 298 IWLTELFPKVPAGFAIGTLFYLALFFAAFTSQIAITDVFVKNVVD-FGV---PRKKAATYVAIIGLIAGIPAAIKIG 370
                                       ********************************************9.566...6777888899999999*99988877 PP

                               SNF 409 iyvltlldkyaaslsllvvvlleaiavawvyglkkflddikemlgfrpllflklcwkfvspllllvlliasivklkp 485
                                          l+  ++++  ++llv +++ ++ v+   gl+k  +  ++    + ++++ +++ +v+pl ++v+++  i++   
  gi|242398622|ref|YP_002994046.1| 371 W--LDN-QDWVWGVALLVSAVVISF-VMLKTGLEKNREVANRGSDIKIGKWWDIMIGYVAPLSIIVVMLWWIKQSID 443
                                       4..443.356666676666655443.56678999999999999*********************9999988887644 PP

                               SNF 486 ltynayv 492
                                          +++ 
  gi|242398622|ref|YP_002994046.1| 444 WYPETWW 450
                                       4444454 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (521 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       978  (0.0545485); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); 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):               1  [number of targets reported over threshold]
# CPU time: 0.68u 0.33s 00:00:01.01 Elapsed: 00:00:00.52
# Mc/sec: 3036.43
//
Query:       gi|242398623|ref|YP_002994047.1|  [L=331]
Description: Proline racemase [Thermococcus sibiricus MM 739]
Scores for 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-105  353.4   0.1   1.2e-105  353.2   0.1    1.0  1  Pro_racemase   Proline racemase
    1.9e-07   30.8   0.0    2.8e-07   30.3   0.0    1.2  1  PhzC-PhzF      Phenazine biosynthesis-like protein
    2.3e-05   24.6   0.1       0.22   11.7   0.0    2.3  2  DAP_epimerase  Diaminopimelate epimerase


Domain annotation for each model (and alignments):
>> Pro_racemase  Proline racemase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  353.2   0.1  1.9e-109  1.2e-105       1     324 [.       9     328 ..       9     329 .. 0.99

  Alignments for each domain:
  == domain 1  score: 353.2 bits;  conditional E-value: 1.9e-109
                                       EEEEEETTEEEEEEEESS---SSSSHHHHHHHHHHH.HHHHHHHHSTTTS-TT-EEEEEE--SSTTSSEEEEEEESS CS
                      Pro_racemase   1 vvdsHteGevgrvvvgGvpelpgetlaekrrlleedldalRralllePRGhdvmsgallvppkepdadlgviflets 77 
                                       vvd+HteGe++r++++G+p ++g++++ekr+++++++d++R+all ePRGh +++ga+lvp+  + ad+gvi+++t+
  gi|242398623|ref|YP_002994047.1|   9 VVDTHTEGEPTRILLSGLP-VEGNDIIEKREYFKKHYDWIRTALLWEPRGHGDQFGAVLVPS--DTADFGVIYMDTA 82 
                                       79***************98.89***************************************8..679********** PP

                                       SB-SSTHHHHHHHHHHHHHTTSS-SEEEECEEEEEETTEEEEEEEECTSTSEEEEEEE-S-BEEEEEEEEEEETTTE CS
                      Pro_racemase  78 gylpmcGsntigvvtvlletGlvevqepetklsletpaGlvevtaecrdgkvervslenvpsfvyaldvevevpglG 154
                                       gyl mcG++t+gv+t+l+e G+ve++ep t ++letpaG ve++a+ +dg v++v++  vpsf    + e++ p++ 
  gi|242398623|ref|YP_002994047.1|  83 GYLDMCGHATMGVATALIELGIVEAKEPYTIVKLETPAGPVEAKAKVEDGVVKEVTVVDVPSFH-VGEFEINYPNIE 158
                                       ***************************************************************6.5789******** PP

                                       EEEEEEEESSSEEEEEEGGGCTS-SSCCCHHHHHHHHHHHHHHHHHHH---TTCSTTC-SEEEEEEEEEETTTTSEE CS
                      Pro_racemase 155 kvkvDiayGGnfyaiveaeklgldlekaearelveageklrealneqlkvqhpenedirevslveltgkkeraeaea 231
                                       ++++D+a+GGnfy+i +a+++gl+++k+  +el+ a+ kl + +neq+kvqhp++   ++++l +lt+++er++++ 
  gi|242398623|ref|YP_002994047.1| 159 NITIDVAFGGNFYVIADARQMGLRVRKEYIKELIPAALKLIKVANEQIKVQHPRKGVQNRINLAMLTDEPEREDSDG 235
                                       ***************************************************************************** PP

                                       EEEEEETTSEB-SS--HHHHHHHHHHHHHTTSS-TT-EEEEEETTS-EEEEEEEEEEEECTCEEEEEEEEE-EEEEE CS
                      Pro_racemase 232 rnaviisdkkvDRSPcGtgtsArlAvlaakGklkvgeefvqesiiGseFegrveeeaevggrkaivpeisGrafitg 308
                                       +n+vi +++ vDRSPcGtg++ r+A+l+ kG lk+g++fv+esi+G++F+ r+++++++g++ aivpei+G a+it 
  gi|242398623|ref|YP_002994047.1| 236 KNVVIWGEGSVDRSPCGTGSASRVATLYSKGILKEGDTFVHESILGTQFKIRIVGTTKIGDYTAIVPEITGSAYITK 312
                                       ***************************************************************************** PP

                                       EEEEEE-TT-TTTT-B CS
                      Pro_racemase 309 laqllldpsDPfaeGf 324
                                       ++q ++  +DP+ +Gf
  gi|242398623|ref|YP_002994047.1| 313 ISQDIITKNDPLWKGF 328
                                       ***************9 PP

>> PhzC-PhzF  Phenazine biosynthesis-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.0   4.6e-11   2.8e-07      49     128 ..      70     151 ..      64     193 .. 0.82

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 4.6e-11
                                       TTSSEEEEEE-SSSEES--HHHHHHHHHHHHHHCT-...S-SCEEEEEETTEEEEE.EEEEETCEECCEEEEE-SEE CS
                         PhzC-PhzF  49 ekarfrlRyFTPvaEvdlcGHatlasahalaekglv...asaetveletkaGilpvkslkekddgeellielkfPvi 122
                                       ++a+f + y      +d+cGHat++ a al+e g v   +  + v+let+aG + +k +k +d+  + ++++++P +
  gi|242398623|ref|YP_002994047.1|  70 DTADFGVIYMDTAGYLDMCGHATMGVATALIELGIVeakEPYTIVKLETPAGPVEAK-AKVEDGVVKEVTVVDVPSF 145
                                       5677777777777789******************995444456789**********7.9999999999999****99 PP

                                       EEEE-H CS
                         PhzC-PhzF 123 kteevs 128
                                       +  e++
  gi|242398623|ref|YP_002994047.1| 146 HVGEFE 151
                                       876655 PP

>> DAP_epimerase  Diaminopimelate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.1   8.1e-05      0.48      60     110 ..      79     133 ..      57     141 .. 0.76
   2 !   11.7   0.0   3.6e-05      0.22      29      95 ..     207     278 ..     194     298 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 8.1e-05
                                       ETTTEEESTTHCCHHHHHHHHHCTTS-S-SE....EEEEETTEEEEEEEECTTSS CS
                     DAP_epimerase  60 nrdgseaemCGnGvrvfaaylreggletkke....vtvetlgGeleievkddgek 110
                                          +++  mCG ++  +a++l+e g+++ ke    v+ et++G++e++ k ++  
  gi|242398623|ref|YP_002994047.1|  79 MDTAGYLDMCGHATMGVATALIELGIVEAKEpytiVKLETPAGPVEAKAKVEDGV 133
                                       55678899*****88888888888888555444446779**********999874 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 3.6e-05
                                       HHHHTTTTSTT-SEEEEEE....EEETTEEEEEEEETTTEEESTTHCCHHHHHHHHHCTTS-.S-SEEEEEE CS
                     DAP_epimerase  29 aalcdreagpgadgvlfvk....psgeediklryfnrdgseaemCGnGvrvfaaylreggle.tkkevtvet 95 
                                       +    r+   +++++ + +     ++++  ++ ++  ++   + CG+G++  +a+l+++g+  + +++++e+
  gi|242398623|ref|YP_002994047.1| 207 KVQHPRKGVQNRINLAMLTdepeREDSDGKNVVIWGEGSVDRSPCGTGSASRVATLYSKGILkEGDTFVHES 278
                                       44444555556889999997663223333344477777777788****999999999999761455555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2122.36
//
Query:       gi|242398624|ref|YP_002994048.1|  [L=326]
Description: Ornithine cyclodeaminase [Thermococcus sibiricus MM 739]
Scores for 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-97  324.2   2.6    7.8e-97  324.0   2.6    1.0  1  OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin famil
    1.4e-07   31.6   0.7    2.3e-07   31.0   0.7    1.3  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
    0.00045   19.6   0.5    0.00076   18.8   0.5    1.4  1  THF_DHG_CYH_C    Tetrahydrofolate dehydrogenase/cyclohydrolas
     0.0034   17.9   1.3     0.0092   16.5   1.3    1.7  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
  ------ inclusion threshold ------
      0.028   14.4   0.1      0.061   13.3   0.1    1.5  1  DUF3939          Protein of unknown function (DUF3939)
      0.038   14.7   0.5       0.17   12.6   0.2    2.2  2  PTS_IIB          PTS system, Lactose/Cellobiose specific IIB 
       0.13   12.7   0.5        0.3   11.6   0.5    1.6  1  DUF1318          Protein of unknown function (DUF1318)


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 !  324.0   2.6  3.1e-100   7.8e-97       5     316 ..       3     316 ..       1     318 [. 0.98

  Alignments for each domain:
  == domain 1  score: 324.0 bits;  conditional E-value: 3.1e-100
                                       EE-HHHHHCCH-HCCCHHHHHHHHHHHHCC-CE----EEEEECCGTEEEEEEEEEETTTTEEEEEEEEEETTTCCCT CS
                   OCD_Mu_crystall   5 vltaveveeelllddlakaveeafrrlasgkvkkpprvalevkdsrgelevmpaylagrellgvKlvnshpenkksg 81 
                                       +lt++++++ l++ + ++ave+af ++ + k++ p r+  e+++++g l  mp+yl++ e+l++K+v  +++n+k+ 
  gi|242398624|ref|YP_002994048.1|   3 LLTRNDLKKVLSMRETIDAVEKAFLEFYHKKAEVPLRTIIEIEKHNGFLLYMPSYLKESEALAIKVVSLYAQNPKKD 79 
                                       68999************************************************************************ PP

                                       SSSEEEEEEEE-TTT--EEEEEE-HHHHHHHHHHHHHHHHHHHS-TT--EEEEE--SHHHHHHHHHHCCCS--SEEE CS
                   OCD_Mu_crystall  82 lptvtalvvLndpetGvplalmdatlltalRTaAvsavaakyLarkdasvlaiiGaGvqaetqlealkavldikevr 158
                                       lp+v a++++ndpetG plalm++t++ta+RT+A+s+va+kyLarkda+ ++iiGaGvqa+tql a+++v+di+++ 
  gi|242398624|ref|YP_002994048.1|  80 LPSVLATILINDPETGKPLALMEGTYITAMRTGAASGVATKYLARKDAKIVGIIGAGVQARTQLWAISEVRDIEKAL 156
                                       ***************************************************************************** PP

                                       EE-SSHHHHHHHHHHCCS..CTT-EEECSCHHHHTTSSEEEE----SS-SB-GGGS-TT-EEEE-S--STT--SB-H CS
                   OCD_Mu_crystall 159 iydrdeeaaekfaenlqe.fefevsackseeeavegadivvtvTaakapilkaewvkpGahinavgadapgkteLdd 234
                                       +yd+++e a+ fae++ +  ++e++ +  ++e +e+ad++v +T+ak+p++k ew+k+G+hin +g   ++ +eLd 
  gi|242398624|ref|YP_002994048.1| 157 VYDVNKERAKVFAEEMAKkIGIEINISLTAQEIAENADVLVVATTAKEPVIKGEWIKEGTHINSIGWMGKDARELDS 233
                                       ***************99978********************************************************* PP

                                       HHHHCCEEEE.SHHHHHHHCCCCHCHHHTTSSTCGGEEEEHHHHHCTSS-..-STTSEEEEE----HHHHHHHHHHH CS
                   OCD_Mu_crystall 235 dilkradifv.dseaqareeGeiqvaiekgvlaedakvaelgeviaGkkpGRtsdeeitlfdsvGlaveDvaaaklv 310
                                       + +++++++v ++e  ++e+G+i  +i++gv++e ++ ael e++aG k GR++d+eitlf+svGla+eD  +akl+
  gi|242398624|ref|YP_002994048.1| 234 ETVRKSKLVVdSKEGVLNESGDILIPIKEGVIDETHIYAELSEIVAGIKRGRENDNEITLFKSVGLAIEDAITAKLA 310
                                       **********6667789************************************************************ PP

                                       HHHHCC CS
                   OCD_Mu_crystall 311 yeraee 316
                                       ye a+e
  gi|242398624|ref|YP_002994048.1| 311 YETALE 316
                                       **9986 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.7   8.9e-11   2.3e-07       4     100 ..     119     217 ..     116     224 .. 0.82

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 8.9e-11
                                       HHHHS..TT-EEEEES-SHHHHHHHHHHHCC.T-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGC.GHHHHHHT-SE CS
                      Shikimate_DH   4 kkkleslkekkvlliGaGemaelvakhLlak.gvkkvvvaNRtlerakelaeelkgeeiealkle.elkellaeadv 78 
                                        k l + + k v +iGaG  a+  + ++++   ++k +v   + erak +aee+ ++    ++++   +e+ ++adv
  gi|242398624|ref|YP_002994048.1| 119 TKYLARKDAKIVGIIGAGVQARTQLWAISEVrDIEKALVYDVNKERAKVFAEEMAKKIGIEINISlTAQEIAENADV 195
                                       5556666677789************99998658*********************55533444444267788899*** PP

                                       EEE-SSSSS-SB-HHHHHCCHH CS
                      Shikimate_DH  79 visataseepilekeeveealk 100
                                       +++at ++ep+++ e+++e  +
  gi|242398624|ref|YP_002994048.1| 196 LVVATTAKEPVIKGEWIKEGTH 217
                                       ****************998765 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 !   18.8   0.5     3e-07   0.00076      73     140 ..     186     264 ..     160     282 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 3e-07
                                       HHHHHCCSSEEEE-SS.-TT-B-GGGS-TT-EEEE---EEC..........-TTEEE-SB-HHHHCTTSSEE--TTT CS
                     THF_DHG_CYH_C  73 laeitreadivvvavG.kpelikaemvkegavviDvGinrv..........ekgklvGDvdfeevkevasaitPvpg 138
                                        +ei ++ad++vva+  k  +ik+e++keg+ +  +G              +k+klv D +   ++e   ++ P+++
  gi|242398624|ref|YP_002994048.1| 186 AQEIAENADVLVVATTaKEPVIKGEWIKEGTHINSIGWMGKdareldsetvRKSKLVVDSKEGVLNESGDILIPIKE 262
                                       67999*******9986155699************9998877778888888888888888887777888888888888 PP

                                       SC CS
                     THF_DHG_CYH_C 139 GV 140
                                       GV
  gi|242398624|ref|YP_002994048.1| 263 GV 264
                                       87 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   1.3   3.6e-06    0.0092       2      70 ..     130     201 ..     129     206 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.6e-06
                                       EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC......-EEECECHHHHHHH-SEEEE-S- CS
                     F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg......vkvtavdneeaaeeadvvvlavk 70 
                                       +giiGaG ++++ +  +++   + ++ + + + n+e+a+ +aee+       ++++  +++e ae+adv+v+a  
  gi|242398624|ref|YP_002994048.1| 130 VGIIGAGVQARTQLWAISEVR-DIEKAL-VYDVNKERAKVFAEEMAkkigieINISL-TAQEIAENADVLVVATT 201
                                       89*********9888777764.555555.3377777777777777666667666666.9*************975 PP

>> DUF3939  Protein of unknown function (DUF3939)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   2.4e-05     0.061      72     119 ..      15      62 ..       9      74 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.4e-05
                           DUF3939  72 ivkeiDkvQkAvdqYvkeekklPlleydelrrvnlakLleekyLkelp 119
                                       + ++iD v kA  ++++++ ++Pl++  e ++ n + L   +yLke  
  gi|242398624|ref|YP_002994048.1|  15 MRETIDAVEKAFLEFYHKKAEVPLRTIIEIEKHNGFLLYMPSYLKESE 62 
                                       6689****************************************9975 PP

>> PTS_IIB  PTS system, Lactose/Cellobiose specific IIB subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.9   4.8e+03       7      18 ..     114     125 ..     111     153 .. 0.81
   2 ?   12.6   0.2   6.6e-05      0.17      21      58 ..     170     203 ..     165     228 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.9
                                       SSSHHHHHHHHH CS
                           PTS_IIB   7 gaGmatSlmaae 18 
                                       ++G+at ++a++
  gi|242398624|ref|YP_002994048.1| 114 ASGVATKYLARK 125
                                       688888888843 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 6.6e-05
                                       HHHHHHCTEEEEETTEEGGGHHHHHHT-SEEEEEESSG CS
                           PTS_IIB  21 ekaakelgieaegeagveleaeeiaddaDlvllapqvr 58 
                                       e++ak+ gie++++ ++    +eia++aD++++a+  +
  gi|242398624|ref|YP_002994048.1| 170 EEMAKKIGIEINISLTA----QEIAENADVLVVATTAK 203
                                       799********999999....999999*******9766 PP

>> DUF1318  Protein of unknown function (DUF1318)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.5   0.00012       0.3      32      91 ..     150     213 ..     118     215 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00012
                           DUF1318  32 aaearalvkaiNakRkavYt.eiAaknglsl......eevaklaaekliekaksGeyvqeanGkWvk 91 
                                       ++  +alv ++N++R++v++ e+A+k g++       +e+a+ a   +++++ +  +++   G+W+k
  gi|242398624|ref|YP_002994048.1| 150 RDIEKALVYDVNKERAKVFAeEMAKKIGIEInisltaQEIAENADVLVVATTAKEPVIK---GEWIK 213
                                       445678*************7369988887765554556666665555566666666555...66665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       723  (0.0403257); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); 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: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.49
# Mc/sec: 2009.50
//
Query:       gi|242398625|ref|YP_002994049.1|  [L=494]
Description: Sarcosine oxidase, alpha subunit [Thermococcus sibiricus MM 739]
Scores for 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-21   74.4   0.7    9.6e-14   51.3   0.3    2.3  2  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    1.6e-12   47.2   0.0    4.7e-12   45.8   0.0    1.8  1  Fer2_4         2Fe-2S iron-sulfur cluster binding domain
    5.1e-08   33.1   0.0    8.9e-08   32.4   0.0    1.4  1  SO_alpha_A3    Sarcosine oxidase A3 domain
    1.6e-07   31.1   0.2    2.2e-07   30.6   0.2    1.2  1  FAD_oxidored   FAD dependent oxidoreductase
    2.3e-06   27.5   3.6    0.00011   21.9   3.7    2.2  2  DAO            FAD dependent oxidoreductase
     0.0001   21.5   1.5     0.0033   16.6   0.9    2.7  3  FAD_binding_2  FAD binding domain
      0.003   17.8   0.6      0.014   15.7   0.2    2.2  2  NAD_binding_8  NAD(P)-binding Rossmann-like domain
      0.003   16.9   0.2     0.0057   15.9   0.2    1.5  1  Thi4           Thi4 family
  ------ inclusion threshold ------
      0.014   14.6   5.4        0.4    9.9   2.7    2.4  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
      0.037   13.1   5.1       0.34    9.9   1.3    2.7  3  GIDA           Glucose inhibited division protein A
      0.041   12.6   2.2      0.069   11.8   1.7    1.7  2  HI0933_like    HI0933-like protein
      0.073   12.3   1.3       0.11   11.8   1.3    1.2  1  FAD_binding_3  FAD binding domain
       0.14   11.2   0.4       0.44    9.5   0.5    1.7  2  Lycopene_cycl  Lycopene cyclase protein
       0.23   11.4   1.3        2.9    7.9   0.9    2.5  2  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 !   51.3   0.3   7.5e-17   9.6e-14       2     149 ..     110     257 ..     109     258 .. 0.73
   2 !   21.2   0.0   1.1e-07   0.00014     192     278 ..     266     353 ..     261     365 .. 0.83

  Alignments for each domain:
  == domain 1  score: 51.3 bits;  conditional E-value: 7.5e-17
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHH..HCHHHHHHHHHHHHHHHHHCHHHHCCCCHCCTCE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcll..skallgvaedaeiasevvkklnqgielllgeevv 76 
                                       dv++iGgG+AG+ aal+l++  + v+l+ +e+ +l+g +++  ++     +e++++++e ++k+n+++++++g+  +
  gi|242398625|ref|YP_002994049.1| 110 DVAIIGGGIAGIGAALELQE-HLTVALI-EEKGWLGGLVFVegTPQEGFEGEPKKVIKELTSKFNENVKVFKGTMNL 184
                                       8*****************99.89*****.6666666544442222222234455556699*************9999 PP

                                       EEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC..TTBEECCSECHHHHHHCCSS-T...SEEEEES CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx...xxxxxxx RF
                       Pyr_redox_2  77 kidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGv.aenvgklvrtldsaealklkllp...krivvvG 149
                                       ++  + + + + + k+++  +i +++++lAtG+  ++l  +    ++v++    ld a ++  k+     k+++vvG
  gi|242398625|ref|YP_002994049.1| 185 GVFDEGEYFLVPAVKKDQLIEIMAKRVILATGAVENILLFENNeFPGVFR----LDFALEVMNKWGVapgKKVAVVG 257
                                       9976667899999999999**************99999666441233344....45555555554444456999998 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 1.1e-07
                                       HHHHTTEEEEESCEEEEEEETTEEEE.EEETTSCEEEESEEEE-S-EEES-HHCS.HCCT-EEEETTEE..E--TTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx..xxxxxx RF
                       Pyr_redox_2 192 alekeGvevklgtsvkeidgngekle.vvledgeeidadlvvvavGvrpstelle.eklglelderggi..vvdefl 264
                                       +lek G+e  +  ++k+++g+++ +e +++ +g+++++d v+v+    p+ + ++    +l+  ++g+   v de+ 
  gi|242398625|ref|YP_002994049.1| 266 ELEKWGIEYIVVPNPKRVEGEEK-VErLIDMNGNVYEVDAVIVSDYSLPDINPITqAGGKLKF-KHGYYvpVLDEQN 340
                                       79999*****************8.777************************999655556666.6666657788888 PP

                                       BESSTTEEE-GGGC CS
                                       xxxxxxxxxxxxxx RF
                       Pyr_redox_2 265 rtnvpgiyaiGDva 278
                                       r   +giy++G  +
  gi|242398625|ref|YP_002994049.1| 341 RI-RDGIYVAGSST 353
                                       87.9*******876 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 !   45.8   0.0   3.7e-15   4.7e-12       2      81 ..      13      88 ..      12      89 .. 0.96

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 3.7e-15
                            Fer2_4  2 rpvtltfDGkevtvpeGdtvasAllangvdvprsckygrprgelcaggeCrnClVevegepnvracstpvedGlkvetq 80
                                      ++vt++f+Gk+++++eG+++  Allangv ++++  +gr+rg ++ g       V v+g++n+    t v+dG+++e+q
  gi|242398625|ref|YP_002994049.1| 13 KKVTIYFEGKPLEAYEGEKLPVALLANGVFWITTSLQGRKRGAFTFG----PLPVVVNGVKNIDGRKTLVKDGMRIERQ 87
                                      79********************************************9....56789*********************** PP

                            Fer2_4 81 t 81
                                      +
  gi|242398625|ref|YP_002994049.1| 88 N 88
                                      8 PP

>> SO_alpha_A3  Sarcosine oxidase A3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.0   6.9e-11   8.9e-08      11      84 ..     418     491 ..     411     494 .] 0.95

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 6.9e-11
                       SO_alpha_A3  11 DvtvkdielavregfesiehvKRYttlgmgtdQgklsavnaaaivaeltgkevaevgtttlRpPlapvklaala 84 
                                       Dv  + ++  v++g  +++ vKR t l+mg  Qg+    n+a +v++ tg +++++ +   RpPl  v++ al+
  gi|242398625|ref|YP_002994049.1| 418 DVNLRKVDDVVKKGITDLQIVKRLTHLAMGFCQGRFCLFNGALLVSQRTGIDMGKIDLPVARPPLKNVRVKALS 491
                                       9999*****************************************************************99986 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.2   1.7e-10   2.2e-07       1      71 [.     110     180 ..     110     222 .. 0.82

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 1.7e-10
                      FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaee.qvvtgiareflerlrq.rg 71 
                                       Dv ++GGg+aG+ AA+   ++  +v+L+ee+g+lGGl+  ++ ++ +g++ e  +v++ +  +f e+++  +g
  gi|242398625|ref|YP_002994049.1| 110 DVAIIGGGIAGIGAALE-LQEHLTVALIEEKGWLGGLVFVEG-TPQEGFEGEPkKVIKELTSKFNENVKVfKG 180
                                       9***************9.5788***************99998.677777766568999999999888876544 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   3.7   8.8e-08   0.00011       1      30 [.     110     140 ..     110     145 .. 0.87
   2 ?    3.3   0.0     0.038        49     138     203 ..     152     218 ..     140     232 .. 0.71

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 8.8e-08
                                       EEEEECTSHHHHHHHHHHHHTT.EEEEESSS CS
                               DAO   1 dvviiGGGiiGlstAyeLarrg.Vtllekgd 30 
                                       dv+iiGGGi+G+++A+eL+++  V+l+e + 
  gi|242398625|ref|YP_002994049.1| 110 DVAIIGGGIAGIGAALELQEHLtVALIEEKG 140
                                       8*****************88758*****875 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.038
                                       TTEEEE.EHHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEE..EECTEEE.EEEEEEEE--GGG CS
                               DAO 138 pdtgqv.dpakltaalaraaealGveilegtevtgleeedgkvwgve..rttpgen.daadavVnaaGaw 203
                                       p++g   +p k+++ l +++ ++ v++++gt   g+ +e g  + +   ++++  +   a+ v++a+Ga 
  gi|242398625|ref|YP_002994049.1| 152 PQEGFEgEPKKVIKELTSKFNEN-VKVFKGTMNLGVFDE-GE-YFLVpaVKKDQLIeIMAKRVILATGAV 218
                                       555555589***********999.******999997332.22.3332443333333234477******85 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.9   2.6e-06    0.0033       1      33 [.     110     141 ..     110     154 .. 0.85
   2 ?    1.7   0.0     0.083   1.1e+02     186     204 ..     202     220 ..     189     235 .. 0.80
   3 ?   -0.6   0.0      0.43   5.5e+02     384     415 ..     335     366 ..     331     368 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.6e-06
                                       SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSG CS
                     FAD_binding_2   1 DviViGsGlAGLaAAleaaeaGlkvavvekeqe 33 
                                       Dv +iG+G+AG  AAle++e+ l+va++e ++ 
  gi|242398625|ref|YP_002994049.1| 110 DVAIIGGGIAGIGAALELQEH-LTVALIEEKGW 141
                                       9*****************776.67999998765 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.083
                                       CEEEEEESEEEE-----GG CS
                     FAD_binding_2 186 revrirakavvlatgGfgr 204
                                       +  +i ak+v+latg++++
  gi|242398625|ref|YP_002994049.1| 202 QLIEIMAKRVILATGAVEN 220
                                       55689***********997 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.43
                                       ESTTEEESSBTEEE-STCEESSSSTTS--TTH CS
                     FAD_binding_2 384 vldadgqpipGLYAaGevaaggvhganrlgGn 415
                                       vld+++++ +G Y aG  ++   h an l+G 
  gi|242398625|ref|YP_002994049.1| 335 VLDEQNRIRDGIYVAGSSTGIKSHYANYLEGK 366
                                       78999999*******************99995 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.2   1.1e-05     0.014       1      35 [.     113     146 ..     113     161 .. 0.90
   2 ?   -1.3   0.0         2   2.6e+03      17      31 ..     328     342 ..     324     343 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.1e-05
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGra 35 
                                       I+G+G++G  aA +L+++ + v l+e    lGG +
  gi|242398625|ref|YP_002994049.1| 113 IIGGGIAGIGAALELQEH-LTVALIEEKGWLGGLV 146
                                       9***************98.********99999965 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2
                                       CCTEEEEEE-SSSSS CS
                     NAD_binding_8  17 kagfdvlllekrdrl 31 
                                       k+g+ v +l+ ++r+
  gi|242398625|ref|YP_002994049.1| 328 KHGYYVPVLDEQNRI 342
                                       689*********997 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.2   4.5e-06    0.0057      17      59 ..     108     148 ..      99     232 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4.5e-06
                                       EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTT CS
                              Thi4  17 esDvvivGaGssGLtaayylakkpdlkvailersvspGGGawl 59 
                                       + Dv+i+G+G +G+ aa  l ++  l va++e++  +GG +  
  gi|242398625|ref|YP_002994049.1| 108 VVDVAIIGGGIAGIGAALELQEH--LTVALIEEKGWLGGLVFV 148
                                       57******************999..********9776665554 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   2.7   0.00031       0.4       2      32 ..     113     142 ..     112     147 .. 0.83
   2 ?    5.0   0.0    0.0097        12     102     172 ..     181     258 ..     161     260 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00031
                       Pyr_redox_3   2 IiGaGPaGlaaaielkkagledylilEkgni 32 
                                       IiG+G aG++aa+el+++     li Ekg +
  gi|242398625|ref|YP_002994049.1| 113 IIGGGIAGIGAALELQEHLT-VALIEEKGWL 142
                                       9***************9877.5677777755 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0097
                       Pyr_redox_3 102 eeVesvkkedegfevetske....tyeAkkviiAtGefdkP...nklnipGeeklvkhyskvkefhkyagqkvvViG 171
                                       ++   v  e+e f v + k+    ++ Ak+vi+AtG  ++    + +++pG  +l      ++++    g+kv+V+G
  gi|242398625|ref|YP_002994049.1| 181 TMNLGVFDEGEYFLVPAVKKdqliEIMAKRVILATGAVENIllfENNEFPGVFRLDFALEVMNKWGVAPGKKVAVVG 257
                                       444555566677777666654556899*********98875222557899999888888888999888999999999 PP

                       Pyr_redox_3 172 g 172
                                        
  gi|242398625|ref|YP_002994049.1| 258 R 258
                                       5 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   1.3   0.00027      0.34       1      30 [.     110     138 ..     110     149 .. 0.83
   2 ?    3.6   0.0     0.023        29     107     152 ..     169     218 ..     152     232 .. 0.68
   3 ?   -1.4   0.0      0.74   9.5e+02     355     385 ..     343     373 ..     339     377 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00027
                                       CEEEE-SSHHHHHHHHHHHHTT--EEEEES CS
                              GIDA   1 dviViGgGhAGceAAlaaarlGakvlLith 30 
                                       dv +iGgG AG+ AAl++ +  + v+Li +
  gi|242398625|ref|YP_002994049.1| 110 DVAIIGGGIAGIGAALELQE-HLTVALIEE 138
                                       799*************9865.577777754 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.023
                                       T..STTEEEEES-EEEEEECT...TEEEEEEETTS-EEEECEEEE--TT-B CS
                              GIDA 107 n..epnleiieeeveelivee...kkvkgvvtedgetikakavviatGtfl 152
                                       +  ++n+++++++++  + +e     v +v++++  +i ak v++atG+ +
  gi|242398625|ref|YP_002994049.1| 169 SkfNENVKVFKGTMNLGVFDEgeyFLVPAVKKDQLIEIMAKRVILATGA-V 218
                                       2346788888888876656553333456788888999***********9.3 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.74
                                       SBTEEE-CGGGTB-SHHHHHHHHHHHHHHHH CS
                              GIDA 355 vkgLflAGqinGteGYeEaaaqGllAGinaa 385
                                       ++g+++AG  +G + + ++   G l ++ + 
  gi|242398625|ref|YP_002994049.1| 343 RDGIYVAGSSTGIKSHYANYLEGKLVATYIL 373
                                       789*********9988888888877777665 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   1.7   5.4e-05     0.069       2      40 ..     110     147 ..     109     189 .. 0.84
   2 ?   -1.6   0.0      0.64   8.2e+02     110     164 ..     162     217 ..     155     218 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.4e-05
                                       SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHHH CS
                       HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakklgrKil 40 
                                       dv++iGgG AG+ aA+++ ++   V+l+e++  lg  + 
  gi|242398625|ref|YP_002994049.1| 110 DVAIIGGGIAGIGAALEL-QEHLTVALIEEKGWLGGLVF 147
                                       89***************9.78899*****9988776555 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.64
                                       HHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE..TTE..EEEESEEEE---- CS
                       HI0933_like 110 divdallkelkeagvklrletevksvekeedgkfrvkt.ksee..eleadklvlAtGG 164
                                       ++++ l+++ +e +vk+   t   +v   e++ f v + k+++  e+ a++++lAtG 
  gi|242398625|ref|YP_002994049.1| 162 KVIKELTSKFNE-NVKVFKGTMNLGVFD-EGEYFLVPAvKKDQliEIMAKRVILATGA 217
                                       667777777665.577777777777744.444465555454443378899*****995 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   1.3   8.4e-05      0.11       2      33 ..     109     139 ..     108     144 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.4e-05
                                       EEEEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                     FAD_binding_3   2 tdVlIVGaGpaGlmlallLseaGvrvvlvekr 33 
                                       +dV+I+G+G aG+ +al+L+e+   v l+e  
  gi|242398625|ref|YP_002994049.1| 109 VDVAIIGGGIAGIGAALELQEH-LTVALIEEK 139
                                       79********************.999999976 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.5   0.00034      0.44       1      31 [.     110     137 ..     110     142 .. 0.92
   2 ?   -2.1   0.0       1.2   1.5e+03     160     198 ..     293     339 ..     291     363 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00034
                     Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvlie 31 
                                       Dv++iG+G Ag+  A +l   +  l v lie
  gi|242398625|ref|YP_002994049.1| 110 DVAIIGGGIAGIGAALEL---QEHLTVALIE 137
                                       9*****************...8899999997 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.2
                     Lycopene_cycl 160 vevdnppfdldkmvlMDfrveqkl......kgltF..lYalPldsdr 198
                                       + ++ +++++d +++ D+ +++        ++l+F  +Y +P+ +++
  gi|242398625|ref|YP_002994049.1| 293 IDMNGNVYEVDAVIVSDYSLPDINpitqagGKLKFkhGYYVPVLDEQ 339
                                       6788999***********94443333444544444336777766555 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.9    0.0023       2.9       1      42 [.     112     147 ..     112     155 .. 0.82
   2 ?    1.1   0.0      0.28   3.6e+02     138     155 ..     200     217 ..     162     218 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0023
                     NAD_binding_9   1 aivGaGprGlavlerLlarakkkspleitlfdpsep.gagrvw 42 
                                       ai+G+G++G+ ++ +L ++      l++ l+++++  g g v+
  gi|242398625|ref|YP_002994049.1| 112 AIIGGGIAGIGAALELQEH------LTVALIEEKGWlG-GLVF 147
                                       8***************998......6999999887744.6665 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.28
                     NAD_binding_9 138 ladgaslaadaVvLAlGh 155
                                       +++  +++a++V+LA+G 
  gi|242398625|ref|YP_002994049.1| 200 KDQLIEIMAKRVILATGA 217
                                       34446799********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (494 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.47
# Mc/sec: 3129.02
//
Query:       gi|242398626|ref|YP_002994050.1|  [L=379]
Description: Sarcosine oxidase, beta subunit [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.9e-74  250.3   0.0    4.4e-74  250.2   0.0    1.0  1  DAO              FAD dependent oxidoreductase
    1.5e-07   30.9   0.0      2e-07   30.4   0.0    1.3  1  FAD_binding_2    FAD binding domain
    1.6e-06   28.2   0.1    4.3e-06   26.9   0.1    1.8  1  NAD_binding_8    NAD(P)-binding Rossmann-like domain
    1.2e-05   25.8   2.2    2.1e-05   25.0   0.2    2.3  2  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
    3.5e-05   23.2   0.4    0.00059   19.2   0.1    2.2  2  Thi4             Thi4 family
      4e-05   23.0   0.1    7.4e-05   22.1   0.0    1.6  2  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
    0.00012   21.5   0.2    0.00019   20.8   0.2    1.3  1  FAD_binding_3    FAD binding domain
    0.00014   21.3   1.3     0.0023   17.2   0.2    2.1  2  Pyr_redox_3      Pyridine nucleotide-disulphide oxidoreductas
     0.0037   16.4   0.3     0.0062   15.6   0.3    1.3  1  Lycopene_cycl    Lycopene cyclase protein
     0.0037   17.5   3.2     0.0058   16.9   0.4    2.2  2  TrkA_N           TrkA-N domain
      0.005   15.6   0.2     0.0092   14.7   0.2    1.4  1  HI0933_like      HI0933-like protein
      0.006   16.2   0.1      0.012   15.2   0.1    1.5  1  ApbA             Ketopantoate reductase PanE/ApbA
     0.0099   16.3   0.2      0.027   14.9   0.2    1.8  1  NAD_binding_7    Putative NAD(P)-binding
  ------ inclusion threshold ------
      0.023   14.1   2.2        0.2   11.0   2.2    2.1  1  FAD_oxidored     FAD dependent oxidoreductase
      0.028   13.7   0.7        0.1   11.9   0.1    1.9  2  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
      0.042   12.9   0.4       0.35    9.9   0.0    2.1  2  GIDA             Glucose inhibited division protein A
      0.082   11.7   1.5       0.17   10.7   1.5    1.7  1  Trp_halogenase   Tryptophan halogenase
       0.14   12.1   0.1       0.28   11.2   0.1    1.5  1  NAD_binding_9    FAD-NAD(P)-binding
       0.25   11.6   0.7       0.81    9.9   0.5    1.9  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
       0.31   11.6   2.6       0.32   11.6   0.7    2.0  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent


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 !  250.2   0.0   4.9e-77   4.4e-74       1     352 []       4     348 ..       4     348 .. 0.91

  Alignments for each domain:
  == domain 1  score: 250.2 bits;  conditional E-value: 4.9e-77
                                       EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESSSSTHHSTHHHHHHHHHHHHHHHHHHHHH CS
                               DAO   1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsglrylpeaselarlslealeelreleeel 75 
                                       d+viiGGGi+G+s A+eLa+rg  Vt+lek+ ++gsg++ r +  +++++ + ++    ++++++++e++++++ee+
  gi|242398626|ref|YP_002994050.1|   4 DIVIIGGGIVGISLAHELAKRGedVTVLEKR-FIGSGSTFRCGTGIRQQFNDEAN----VQVMKRSVELWKKYSEEY 75 
                                       9******************************.9999*************985554....4***************** PP

                                       SSTTSEEEEEEEEEESSHHHHHHHHHHHHHHHHTTTTEEEEEHHHHHHHSTTST..TTSEEEEETTEEEEEHHHHHH CS
                               DAO  76 gididyrrtGllslaadeeelealdkllallleagldaelldaeevrelepalp..gllgalfypdtgqvdpaklta 150
                                       g  +++++tG+l+l ++eee  ++++++  ++++g++++l+++ee++e+ p l+  ++ +a ++p++g +dp+++t 
  gi|242398626|ref|YP_002994050.1|  76 G--FPFEQTGYLFLLYSEEEVKQFRENISIQNRFGVPTRLITPEEAKEIVPLLDtsEIIAASWNPTDGKADPFHATT 150
                                       *..99***********9999999*999999999******************95556999****************** PP

                                       HHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEE..EEE--GGGHHHH.HTT.CTTTSEEEEEEE CS
                               DAO 151 alaraaealGveilegtevtgleeedgkvwgverttp.gendaada..vVnaaGawsdll.gll.keldlpispvrg 222
                                       a+a  a++  ++ile+te++++   d+ ++ +  +t+ g+   +++  v+na++aws+l+ +++  ++++pi+p r+
  gi|242398626|ref|YP_002994050.1| 151 AFALHAQEMSAKILEYTEAKDIIIVDNEIKAI--KTNnGI---IKTgiVINATNAWSKLInAMVkLPIRIPIEPYRH 222
                                       *********************97878889999..677698...56666**********99889987779******** PP

                                       EEEEEEECCTHSTGSGCSEEEEEEEETTTTEEEEEETTSEEEEEESSEEETTCSS.TSCSHHHHHHHHHHHHHHSGG CS
                               DAO 223 qvlvlkplseklvspaailpvpetdddgrgvyvtprkdgrvlvGgtadeesgddd.pevdeedidellealrklfPq 298
                                       q + ++p+++     +ai p+  ++   ++ y+t++  g+v+ Gg + +e g+++ +++    ++e+  +l+k++P+
  gi|242398626|ref|YP_002994050.1| 223 QAIITQPIKK-----NAINPMV-ISFKYKDSYLTQTDHGGVI-GGIG-YEVGPTYdLTPAYGFLREVTTYLSKIIPA 291
                                       *******987.....5999999.89999999****9877555.6656.45555555899999*************** PP

                                       GCG..EEEEEEEEEE.ETTSSEEEEEEETEEEEEEEEECTTTHHHHHHHHHHHHHHH CS
                               DAO 299 lgd..vlrkwaGlrp.lpdglpligetpgvkglylatGhsghGltlapatGkllael 352
                                       l++  +lr+waG+++ +pd +p ig+ ++ +++y+a+G+sghG++++pa+G+++a+l
  gi|242398626|ref|YP_002994050.1| 292 LREllILRTWAGYYAkTPDSNPAIGKIEEISDYYIAAGFSGHGFMMGPAVGEMMADL 348
                                       98855669*******66*********77788************************97 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.0   2.3e-10     2e-07       1      68 [.       4      71 ..       4     210 .. 0.72

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 2.3e-10
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S-EE-TT..SSGGSTC.CHHHHHHHH CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqGgidavlspeqkkagikdspelhrtd 68
                                      D+++iG+G+ G + A+e+a++G +v+v+ek +  +g+t+ ++ gi    + e++ +  k+s+el+ ++
  gi|242398626|ref|YP_002994050.1|  4 DIVIIGGGIVGISLAHELAKRGEDVTVLEKRFIGSGSTFRCGTGIRQQFNDEANVQVMKRSVELWKKY 71
                                      99******************************9999********999888887555555555554443 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 !   26.9   0.1   4.8e-09   4.3e-06       1      28 [.       7      34 ..       7      57 .. 0.90

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 4.8e-09
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekr 28
                                      I+G+G+ G ++A++Lak+g dv++lekr
  gi|242398626|ref|YP_002994050.1|  7 IIGGGIVGISLAHELAKRGEDVTVLEKR 34
                                      9**************************8 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.2   2.3e-08   2.1e-05       2      31 ..       5      34 ..       4      66 .. 0.91
   2 ?   -0.5   0.1       2.2   1.9e+03      41      72 ..     158     188 ..     153     198 .. 0.71

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 2.3e-08
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvvers 31
                                      +v++GgG +g+ lA +la+ g +Vtv+e +
  gi|242398626|ref|YP_002994050.1|  5 IVIIGGGIVGISLAHELAKRGEDVTVLEKR 34
                                      8*************************9975 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 2.2
                                       HHHHHHHHHHHHTTEEEECSEEEEEEEEETTS CS
                         Pyr_redox  41 easkilqeklekngievllntkveeiegsedg 72 
                                       e+s+ + e+ e++ i ++ n ++++i++++  
  gi|242398626|ref|YP_002994050.1| 158 EMSAKILEYTEAKDIIIVDN-EIKAIKTNNGI 188
                                       78888888888888866655.57888877765 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   6.5e-07   0.00059      16      61 ..       1      45 [.       1      73 [. 0.87
   2 ?    2.0   0.0      0.11        99     108     143 ..     156     190 ..     138     212 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 6.5e-07
                                      TEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTS CS
                              Thi4 16 aesDvvivGaGssGLtaayylakkpdlkvailersvspGGGawlGG 61
                                      ++sD+vi+G+G  G++ a+ lak+ +  v++le++    G +   G
  gi|242398626|ref|YP_002994050.1|  1 MKSDIVIIGGGIVGISLAHELAKR-GEDVTVLEKRFIGSGSTFRCG 45
                                      579*********************.999******987666666555 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.11
                                       HTSTTEEEEESEEEEEEEEETBTEEEEEEEEEHHHH CS
                              Thi4 108 lqlanvkllnavaveDlivregegvaGvvinwtlve 143
                                        q   +k+l+ + + D+i+ + ++++ + +n  +++
  gi|242398626|ref|YP_002994050.1| 156 AQEMSAKILEYTEAKDIIIVD-NEIKAIKTNNGIIK 190
                                       344679999999999999999.67776666655544 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 !   22.1   0.0   8.3e-08   7.4e-05     144     174 ..       4      34 ..       1     120 [. 0.69
   2 ?   -2.7   0.1       2.9   2.6e+03     181     214 ..     155     187 ..     147     200 .. 0.60

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 8.3e-08
                                       EEEEES-SHHHHHHHHHHHHHT-EEEEEESS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 144 rivvvGgGyiGvElAaalaklgkevtlvear 174
                                       +iv++GgG +G+ lA +lak g++vt++e r
  gi|242398626|ref|YP_002994050.1|   4 DIVIIGGGIVGISLAHELAKRGEDVTVLEKR 34 
                                       5666666666666666666666666666653 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.9
                                       S-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 181 ldkelsaaleealekeGvevklgtsvkeidgnge 214
                                       + +e+sa + e+ e++++ ++  +++k+i+ n+ 
  gi|242398626|ref|YP_002994050.1| 155 HAQEMSAKILEYTEAKDIIIV-DNEIKAIKTNNG 187
                                       455666666666666666666.666666666654 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.2   2.1e-07   0.00019       2      33 ..       3      34 ..       2      46 .. 0.94

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.1e-07
                                      EEEEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekr 33
                                       d++I+G+G +G++la++L+++G +v+++ekr
  gi|242398626|ref|YP_002994050.1|  3 SDIVIIGGGIVGISLAHELAKRGEDVTVLEKR 34
                                      6899**************************97 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.2   2.6e-06    0.0023       1      33 [.       6      37 ..       6      43 .. 0.92
   2 ?    2.7   0.0     0.067        60      39     132 ..     107     198 ..     101     212 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.6e-06
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgnig 33
                                      +IiG+G  G++ a+el k g  d+++lEk  ig
  gi|242398626|ref|YP_002994050.1|  6 VIIGGGIVGISLAHELAKRGE-DVTVLEKRFIG 37
                                      7*******************9.8******9776 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.067
                       Pyr_redox_3  39 ypkemtfispsftsekleipdlnaiseet.spafslkeeklsrkealeYlrevaksfelpiklfeeVesvkk.edeg 113
                                       +   +++i+p++ +e + + d   i+  + +p     + k+    a   ++  a++   +i +++e +++   ++e 
  gi|242398626|ref|YP_002994050.1| 107 FGVPTRLITPEEAKEIVPLLDTSEIIAASwNP----TDGKADPFHATTAFALHAQEMSAKILEYTEAKDIIIvDNEI 179
                                       55667888888888888888887777655234....33333334444555566667777788999999988845667 PP

                       Pyr_redox_3 114 fevetsketyeAkkviiAt 132
                                         ++t+++ +++  vi At
  gi|242398626|ref|YP_002994050.1| 180 KAIKTNNGIIKTGIVINAT 198
                                       8999*******99999998 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.3   6.9e-06    0.0062       1      31 [.       4      32 ..       4      39 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 6.9e-06
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlie 31
                                      D+v+iG+G  g+slA++l  ak g  v+++e
  gi|242398626|ref|YP_002994050.1|  4 DIVIIGGGIVGISLAHEL--AKRGEDVTVLE 32
                                      9*****************..77777777775 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.4   6.5e-06    0.0058       1      29 [.       5      33 ..       5      35 .. 0.93
   2 ?    0.5   0.1      0.79   7.1e+02      18      38 ..     165     186 ..     155     200 .. 0.62

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 6.5e-06
                                      EEEES-SHHHHHHHHHHHHTTEEEEEEES CS
                            TrkA_N  1 iiiiGlGrvGrslaeeLseggkdvvvidk 29
                                      i+iiG G vG sla+eL ++g+dv+v +k
  gi|242398626|ref|YP_002994050.1|  5 IVIIGGGIVGISLAHELAKRGEDVTVLEK 33
                                      89*****************8779***998 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.79
                                       HHTT..EEEEEEESSHHHHHHHH CS
                            TrkA_N  18 segg..kdvvvidkdeerveelr 38 
                                       +     kd++++d++ +++++  
  gi|242398626|ref|YP_002994050.1| 165 EY-TeaKDIIIVDNEIKAIKTNN 186
                                       22.12468******999998754 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.2     1e-05    0.0092       2      32 ..       4      34 ..       3      47 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1e-05
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SS CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVllleka 32
                                      d+++iGgG  G+  A ++akrg++V++lek 
  gi|242398626|ref|YP_002994050.1|  4 DIVIIGGGIVGISLAHELAKRGEDVTVLEKR 34
                                      89***************************95 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   1.4e-05     0.012       1      28 [.       5      32 ..       5      58 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.4e-05
                                      EEEES-SHHHHHHHHHHHHHTHCEEEE- CS
                              ApbA  1 iailGaGaiGsllaakLakagadvtlil 28
                                      i+i+G G +G  la++Lak g+dvt++ 
  gi|242398626|ref|YP_002994050.1|  5 IVIIGGGIVGISLAHELAKRGEDVTVLE 32
                                      89***********************985 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.2     3e-05     0.027       9      40 ..       4      35 ..       2     199 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3e-05
                     NAD_binding_7  9 kvlvvGgGevAarkvrklleagakvtvvapev 40
                                       ++++GgG v+ + ++ l++ g +vtv+ +++
  gi|242398626|ref|YP_002994050.1|  4 DIVIIGGGIVGISLAHELAKRGEDVTVLEKRF 35
                                      689************************99995 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   2.2   0.00022       0.2       1      48 [.       4      50 ..       4     200 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00022
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdig 48
                                      D+v++GGg+ G+  A   a++G  v ++e+r ++G  +t   ++ + +
  gi|242398626|ref|YP_002994050.1|  4 DIVIIGGGIVGISLAHELAKRGEDVTVLEKR-FIGSGSTFRCGTGIRQ 50
                                      9**************************9985.6666566555555555 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 ?   11.9   0.1   0.00011       0.1      29      60 ..       3      34 ..       1      61 [. 0.91
   2 ?   -0.2   0.0      0.58   5.2e+02     177     208 ..     163     197 ..     144     203 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                                      -EEEEESTSHHHHHHHHHHHHTT-EEEEEESS CS
                       AlaDh_PNT_C 29 akvlviGgGvaGlqAiatakglgakVtvlDvr 60
                                      + +++iGgG++G++ ++  ++ g +Vtvl++r
  gi|242398626|ref|YP_002994050.1|  3 SDIVIIGGGIVGISLAHELAKRGEDVTVLEKR 34
                                      679************9999999*******987 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.58
                                       HHHHHHH..HC.HHHTCCHHHCTSHHHHCCEEEET CS
                       AlaDh_PNT_C 177 tlpylee..ll.adkglkkalkedealrkglvvkk 208
                                       +l+y e+  ++  d+++k++++++ ++++g+v+++
  gi|242398626|ref|YP_002994050.1| 163 ILEYTEAkdIIiVDNEIKAIKTNNGIIKTGIVINA 197
                                       44443321133467777777777778877777765 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00039      0.35       1      29 [.       4      32 ..       4      66 .. 0.88
   2 ?    1.1   0.1      0.18   1.6e+02     102     147 ..     164     197 ..     121     209 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00039
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEEE CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLit 29
                                      d+++iGgG  G+  A ++a++G +v+ + 
  gi|242398626|ref|YP_002994050.1|  4 DIVIIGGGIVGISLAHELAKRGEDVTVLE 32
                                      79**********************99873 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.18
                                       HHHHHTSTTEEEEES-EEEEEECTTEEEEEEETTS-EEEECEEEE- CS
                              GIDA 102 teklenepnleiieeeveeliveekkvkgvvtedgetikakavvia 147
                                        e+            e++++i+ ++++k+++t++g +ik+ +v+ a
  gi|242398626|ref|YP_002994050.1| 164 LEY-----------TEAKDIIIVDNEIKAIKTNNG-IIKTGIVINA 197
                                       333...........344444444444444444443.3344444444 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.5   0.00019      0.17       1      38 [.       4      38 ..       4     210 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00019
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS-- CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlveseeigt 38
                                      +ivi+GGG+ G   A  lak +    +vt++e+  ig 
  gi|242398626|ref|YP_002994050.1|  4 DIVIIGGGIVGISLAHELAKRG---EDVTVLEKRFIGS 38
                                      69******************99...58*****998874 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00031      0.28       1      43 [.       6      43 ..       6      69 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00031
                     NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsepgagrvwr 43
                                      +i+G+G+ G++++ +L++r       ++t+ +++ +g+g+ +r
  gi|242398626|ref|YP_002994050.1|  6 VIIGGGIVGISLAHELAKRG-----EDVTVLEKRFIGSGSTFR 43
                                      7*****************95.....889999999998887766 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 ?    9.9   0.5   0.00091      0.81       1      31 [.       5      32 ..       5      36 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00091
                                      EEEE--SHHHHHHHHHHHCTCCT-GEEEEEE CS
                   Sacchrp_dh_NADP  1 vliiGaGsvGqavaellarhfdvdaeitvad 31
                                      ++iiG+G vG ++a++la++++    +tv +
  gi|242398626|ref|YP_002994050.1|  5 IVIIGGGIVGISLAHELAKRGED---VTVLE 32
                                      89******************985...88876 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 ?   11.6   0.7   0.00036      0.32       2      33 ..       5      33 ..       4      57 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00036
                                      EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEE CS
                     F420_oxidored  2 igiiGaGnmgealasgllaagaqpheivvans 33
                                      i iiG+G +g +la+ l+++g   ++++v  +
  gi|242398626|ref|YP_002994050.1|  5 IVIIGGGIVGISLAHELAKRG---EDVTVLEK 33
                                      89*******************...99987654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); 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: 0.68u 0.33s 00:00:01.01 Elapsed: 00:00:00.52
# Mc/sec: 2198.63
//
Query:       gi|242398627|ref|YP_002994051.1|  [L=477]
Description: Dye-L-proDH alpha [Thermococcus sibiricus MM 739]
Scores for complete 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  133.1   7.6    1.5e-38  132.7   7.6    1.1  1  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
    3.6e-28   97.4   0.1    7.3e-28   96.4   0.1    1.5  1  Fer2_4           2Fe-2S iron-sulfur cluster binding domain
      5e-16   58.8   2.9    1.4e-13   50.8   2.9    2.3  1  Pyr_redox_3      Pyridine nucleotide-disulphide oxidoreductas
    1.9e-15   56.9  10.2    7.4e-08   31.9   1.2    3.4  3  FAD_binding_2    FAD binding domain
    5.3e-15   55.7   9.3    1.8e-12   47.3   1.5    3.2  3  FAD_oxidored     FAD dependent oxidoreductase
    6.4e-14   51.5  10.4    3.2e-09   36.0   1.3    3.2  3  HI0933_like      HI0933-like protein
    1.8e-13   50.9   8.8    2.6e-06   27.9   0.7    3.8  3  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
    2.7e-10   40.3   2.3    4.9e-05   23.5   0.1    2.6  2  NAD_binding_8    NAD(P)-binding Rossmann-like domain
    4.9e-10   39.0  16.6      3e-05   23.3   0.9    4.1  4  GIDA             Glucose inhibited division protein A
      1e-09   38.5  10.6     0.0024   17.5   0.1    4.0  4  DAO              FAD dependent oxidoreductase
    3.3e-09   36.5   4.8    0.00043   19.6   0.4    2.5  2  FAD_binding_3    FAD binding domain
    2.5e-07   30.2   3.7     0.0012   18.1   0.0    2.9  3  Thi4             Thi4 family
    1.6e-06   28.5   2.4      0.013   15.9   0.2    3.3  3  NAD_binding_7    Putative NAD(P)-binding
    2.7e-05   23.6   9.3    7.5e-05   22.1   0.2    3.1  3  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
    6.2e-05   22.2   2.8      0.024   13.7   0.3    2.4  2  Lycopene_cycl    Lycopene cyclase protein
     0.0015   18.2   4.7     0.0039   16.9   0.6    3.1  3  ApbA             Ketopantoate reductase PanE/ApbA
     0.0043   16.8   0.2      0.036   13.8   0.2    2.2  2  ELFV_dehydrog    Glutamate/Leucine/Phenylalanine/Valine dehyd
  ------ inclusion threshold ------
      0.024   14.1   0.4       0.17   11.2   0.1    2.2  2  PALP             Pyridoxal-phosphate dependent enzyme
      0.024   14.9   1.3        8.5    6.7   0.0    3.2  2  TrkA_N           TrkA-N domain
      0.033   14.2   0.0       0.06   13.4   0.0    1.4  1  Fer2_3           2Fe-2S iron-sulfur cluster binding domain
      0.049   12.8   0.1       0.27   10.3   0.0    2.0  2  K_oxygenase      L-lysine 6-monooxygenase (NADPH-requiring)
      0.054   12.8   0.0        1.8    7.7   0.0    2.9  3  Amino_oxidase    Flavin containing amine oxidoreductase
       0.14   12.0   3.9        4.1    7.3   0.5    2.5  2  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
       0.15   12.7   2.4       0.57   10.8   0.9    2.8  2  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
       0.16   10.8   4.5       0.35    9.7   0.4    2.3  2  Trp_halogenase   Tryptophan halogenase
       0.17   11.2   0.4       0.48    9.7   0.1    1.8  2  ThiF             ThiF family
       0.22   11.4   1.8       0.41   10.5   1.8    1.4  1  DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydr
       0.25   11.8   1.9        2.4    8.6   0.0    3.0  3  YdfZ             YdfZ protein
        1.9    8.4   6.3        4.2    7.3   0.1    3.4  4  NAD_binding_9    FAD-NAD(P)-binding
        6.6    6.3   7.6        6.7    6.2   1.4    3.0  3  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.7   7.6   2.5e-41   1.5e-38       2     294 .]     120     426 ..     119     426 .. 0.81

  Alignments for each domain:
  == domain 1  score: 132.7 bits;  conditional E-value: 2.5e-41
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHH..HCHHHHHHHHHHHHH.........HHHHCHHHHC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxx.........xxxxxxxxxx RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcll..skallgvaedaeias.........evvkklnqgi 67 
                                       dv+v+GgGpAG+ aa++++  gakv+l+ +e+ +l+g+ +   +k + + +++a + +         e++   + +i
  gi|242398627|ref|YP_002994051.1| 120 DVIVVGGGPAGMMAAINASDGGAKVVLL-DENPMLGGQLVKqtHKFFGKREQFAGV-RgikiadileEEL--RKRNI 192
                                       8***************************.999999999998644444444444444.36*9**9986432..33459 PP

                                       CCCHCCT.CEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BC.....TCTTC.TTBEECCSECHHHHHHCC CS
                                       xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  68 elllgee.vvkidpgkkkvklekkkegdeekiaydklvlAtGssprdl.....gipGvaenvgklvrtldsaealkl 138
                                       el+l+++ ++ + +g+ k+++  kk+++  +++ +++v+AtG+  r +     ++pGv  ++   ++tl+++ ++k 
  gi|242398627|ref|YP_002994051.1| 193 ELFLETSaIMLLQNGEDKLVVGVKKNKELIEFKGKAVVVATGAMERMIpfennDLPGV--YGAGAIQTLMNTYGVKP 267
                                       9999988455556888999997777677777777********9666664677788898..66667799999999976 PP

                                       SS-TSEEEEES-SHHHHHHHHHHHHHT-E.EEEEESSSSSSTTS-HHHHHHHHHHHHHT.TEEEEESCEEEEEEETT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 139 kllpkrivvvGgGyiGvElAaalaklgke.vtlveardrllraldkelsaaleealeke.Gvevklgtsvkeidgng 213
                                            r+++vG+G++G+ lA +l ++g++   +vea++++        + ++++a  ++ G+ + +++++ +++gn+
  gi|242398627|ref|YP_002994051.1| 268 GD---RVLIVGAGNVGLILAYQLYQAGVKvEAIVEAMPKIG-------GYFVHAAKVRRlGIPILTRHTILRAEGNE 334
                                       64...68**********************44599**99999.......788877766666***************** PP

                                       E.........EEE...EEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EE...EETTEE..E--TTSBESSTTEEE CS
                                       x.........xxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxx..xxxxxxxxxxxxxxx RF
                       Pyr_redox_2 214 e.........kle...vvledgeeidadlvvvavGvrpstelleeklglel...derggi..vvdeflrtnvpgiya 273
                                       +         + e   v+ ++++++++d + +avG+rps ell  ++g+++    e gg     d++++t+v+gi++
  gi|242398627|ref|YP_002994051.1| 335 KvekavvaqlD-EkwnVIPGTEKVFEVDVIALAVGLRPSIELL-HQVGCQIkyvPELGGHvvIRDSRMETTVKGIFV 409
                                       *9999888552.146699999999*******************.9999999777555555235699*********** PP

                                       -GGGCTECCSS--HHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 274 iGDvaggkggpelaqaAvqqG 294
                                       +GD a    g+e a++A+ +G
  gi|242398627|ref|YP_002994051.1| 410 AGDSA----GIEEATTAMLEG 426
                                       ***99....9*****999776 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 !   96.4   0.1   1.2e-30   7.3e-28       2      81 ..      17      97 ..      16      98 .. 0.97

  Alignments for each domain:
  == domain 1  score: 96.4 bits;  conditional E-value: 1.2e-30
                            Fer2_4  2 rpvtltfDGkevtvpeGdtvasAllangvdvp.rsckygrprgelcaggeCrnClVevegepnvracstpvedGlkvet 79
                                      r+vt++f+G++++++eG+t+a Al a+g+++   s k++rprg +ca+g+C+ Cl++v+g pnvr+c+t vedG+++e 
  gi|242398627|ref|YP_002994051.1| 17 REVTIYFEGNPIKAHEGETIAMALHAAGIRTYqYSTKKHRPRGLFCAIGKCSSCLMKVNGIPNVRTCITLVEDGMQIEM 95
                                      79****************************9977********************************************9 PP

                            Fer2_4 80 qt 81
                                      q+
  gi|242398627|ref|YP_002994051.1| 96 QE 97
                                      97 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.8   2.9   2.3e-16   1.4e-13       1     305 []     122     411 ..     122     411 .. 0.71

  Alignments for each domain:
  == domain 1  score: 50.8 bits;  conditional E-value: 2.3e-16
                       Pyr_redox_3   1 iIiGaGPaGlaaaielkkagledylilEkg.nignsiyrypkemtfispsftsekleipdlnaiseetspafslkee 76 
                                       i++G+GPaG+ aai++ + g  +++ l+ +  +g  + +  ++ +f+ + ++  ++  +++  i           ee
  gi|242398627|ref|YP_002994051.1| 122 IVVGGGPAGMMAAINASDGGA-KVVLLDENpMLGGQLVK--QTHKFFGKREQFAGVRGIKIADIL----------EE 185
                                       89******************9.69999988788888875..889999976444443333333333..........34 PP

                       Pyr_redox_3  77 klsrkealeYlrevaksfelpiklfeeVesvkkedegfevetsketyeAkkviiAtGefd......kPnklnipGee 147
                                       +l+++++  +l++  +   l+  +++ V  vkk++e         +++ k v++AtG ++      + +++++ G+ 
  gi|242398627|ref|YP_002994051.1| 186 ELRKRNIELFLET-SAIMLLQNGEDKLVVGVKKNKELI-------EFKGKAVVVATGAMErmipfeNNDLPGVYGAG 254
                                       4555555555544.455677778888888888887765.......578899******97522111144555555555 PP

                       Pyr_redox_3 148 klvkhyskvkefhkyagqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvke 224
                                            +  ++ +    g++v+++G++n +   A++l+++g +V+ +++  +         y + +    rl   + +
  gi|242398627|ref|YP_002994051.1| 255 ---AIQTLMNTYGVKPGDRVLIVGAGNVGLILAYQLYQAGVKVEAIVEAMPKIG-----GYFVHAAKVRRLGIPILT 323
                                       ...4555555565667*******************************9975332.....455666666665543333 PP

                       Pyr_redox_3 225 ..ekikvlfnaevke..ikekeeeykvktedgkkvevkddvvlatGykpdlsflkk..slfelded..grpvlteet 293
                                         + ++++ n++v++  + + +e+++v   ++k +ev d + la+G +p++++l++  +++++  +  g++v+ ++ 
  gi|242398627|ref|YP_002994051.1| 324 rhTILRAEGNEKVEKavVAQLDEKWNVIPGTEKVFEV-DVIALAVGLRPSIELLHQvgCQIKYVPElgGHVVIRDSR 399
                                       3377999999999984456778888887777555444.666667************77666654333389******* PP

                       Pyr_redox_3 294 eetnvpglflaG 305
                                       +et+v+g+f+aG
  gi|242398627|ref|YP_002994051.1| 400 METTVKGIFVAG 411
                                       ***********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 !   31.9   1.2   1.2e-10   7.4e-08       1      39 [.     120     158 ..     120     166 .. 0.95
   2 !   19.2   0.1   8.9e-07   0.00053     118     205 ..     155     239 ..     153     263 .. 0.76
   3 !   11.4   0.5    0.0002      0.12       2      37 ..     271     308 ..     270     344 .. 0.88

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 1.2e-10
                                       SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGG CS
                     FAD_binding_2   1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggata 39 
                                       DviV+G+G AG++AA++a++ G+kv++++  +  gg+++
  gi|242398627|ref|YP_002994051.1| 120 DVIVVGGGPAGMMAAINASDGGAKVVLLDENPMLGGQLV 158
                                       9*******************************9999875 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 8.9e-07
                                       T-SSTEEEE-.STT-......HHHHHHHHHHHHHHTCTEEEEESEEEEEEEECTT..EEEEEEEEETTTTCEEEEEE CS
                     FAD_binding_2 118 glsatartlhdaadarretlvtghallarlvesarkagvdfqerteadeLivedg..rvtGavvenpesgrevrira 192
                                       g+  + +t+   +++++ + v g +++  l e++rk++++++ +t+a  L+++++   v+G  v+  ++++  +++ 
  gi|242398627|ref|YP_002994051.1| 155 GQLVK-QTHKFFGKREQFAGVRGIKIADILEEELRKRNIELFLETSAIMLLQNGEdkLVVG--VK--KNKELIEFKG 226
                                       55555.4555455543366678999***************************544226777..57..99******** PP

                                       SEEEE-----GG. CS
                     FAD_binding_2 193 kavvlatgGfgra 205
                                       kavv+atg+++r 
  gi|242398627|ref|YP_002994051.1| 227 KAVVVATGAMERM 239
                                       ***********92 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.0002
                                       EEEE--SHHHHHHHHHHHHTTT-E.EEEESSSGGGS.G CS
                     FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkv.avvekeqefgg.a 37 
                                       v+++G+G  GL  A+++ +aG kv a+ve +++ gg  
  gi|242398627|ref|YP_002994051.1| 271 VLIVGAGNVGLILAYQLYQAGVKVeAIVEAMPKIGGyF 308
                                       9*********************9989*****9999851 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.3   1.5     3e-15   1.8e-12       1      43 [.     120     162 ..     120     179 .. 0.85
   2 ?    4.6   0.0     0.028        17      90     144 ..     180     234 ..     177     237 .. 0.83
   3 !    7.6   0.3    0.0035       2.1       2      42 ..     271     312 ..     270     366 .. 0.87

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 3e-15
                      FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglv 43 
                                       Dv+VvGGgpaG++AAi A   Gakv+L++e+++lGG+l ++  
  gi|242398627|ref|YP_002994051.1| 120 DVIVVGGGPAGMMAAINASDGGAKVVLLDENPMLGGQLVKQTH 162
                                       9*************************************99874 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.028
                      FAD_oxidored  90 kavleemlaeagvtvllntrlvevekegkriesvtveskegrktirAkvfiDATg 144
                                       + +lee l++ +++++l+t ++   ++g++   v v+++++ +++++k ++ ATg
  gi|242398627|ref|YP_002994051.1| 180 ADILEEELRKRNIELFLETSAIMLLQNGEDKLVVGVKKNKELIEFKGKAVVVATG 234
                                       568999999*****************986644555544457**********9998 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0035
                      FAD_oxidored   2 vvVvGGgpaGvaAAiaAaraGakv.lLveergvlGGlltsgl 42 
                                       v++vG+g  G++ A++  +aG kv ++ve  + +GG +  ++
  gi|242398627|ref|YP_002994051.1| 271 VLIVGAGNVGLILAYQLYQAGVKVeAIVEAMPKIGGYFVHAA 312
                                       89**********************88**********988765 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   1.3   5.4e-12   3.2e-09       2      37 ..     120     155 ..     119     161 .. 0.93
   2 !    9.9   0.1   0.00045      0.27     110     164 ..     178     235 ..     164     238 .. 0.85
   3 !   10.5   0.4    0.0003      0.18       2      36 ..     270     305 ..     269     313 .. 0.89

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 5.4e-12
                                       SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-H CS
                       HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakklgr 37 
                                       dviv+GgG+AG+maAi+a++ g++V+ll++++ lg 
  gi|242398627|ref|YP_002994051.1| 120 DVIVVGGGPAGMMAAINASDGGAKVVLLDENPMLGG 155
                                       8******************************99885 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00045
                                       HHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE..TTE..EEEESEEEE---- CS
                       HI0933_like 110 divdallkelkeagvklrletevksvekeedgkfrvkt.ksee..eleadklvlAtGG 164
                                       +i d+l++el++++++l let+   + ++ + k+ v + k++e  e++ +++v+AtG 
  gi|242398627|ref|YP_002994051.1| 178 KIADILEEELRKRNIELFLETSAIMLLQNGEDKLVVGVkKNKEliEFKGKAVVVATGA 235
                                       799*****************999999888888899988444444467899*******7 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.0003
                                       SEEEE--SHHHHHHHHHHHHTT--E.EEE-SSSSS- CS
                       HI0933_like   2 dviviGgGaAGlmaAisaakrgkrV.lllekakklg 36 
                                       +v+++G+G  Gl  A ++ ++g +V +++e+++k+g
  gi|242398627|ref|YP_002994051.1| 270 RVLIVGAGNVGLILAYQLYQAGVKVeAIVEAMPKIG 305
                                       699**********************55899999998 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   0.2   9.1e-06    0.0054       2      44 ..     121     163 ..     120     175 .. 0.85
   2 !    9.2   0.1    0.0031       1.8      39      75 ..     176     214 ..     165     220 .. 0.77
   3 !   27.9   0.7   4.3e-09   2.6e-06       1      76 [.     270     339 ..     270     346 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 9.1e-06
                                       EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHH CS
                         Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeask 44 
                                       v+vvGgG  g+++A ++++ g+kV +++ +++l  +l +++ k
  gi|242398627|ref|YP_002994051.1| 121 VIVVGGGPAGMMAAINASDGGAKVVLLDENPMLGGQLVKQTHK 163
                                       89*****************************999666555555 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0031
                                       SHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTS..EEE CS
                         Pyr_redox  39 Deeaskilqeklekngievllntkveeiegsedg..ves 75 
                                       + ++++il+e+l+k++ie+ l+t++  + ++++   v +
  gi|242398627|ref|YP_002994051.1| 176 GIKIADILEEELRKRNIELFLETSAIMLLQNGEDklVVG 214
                                       56799******************9988886665324555 PP

  == domain 3  score: 27.9 bits;  conditional E-value: 4.3e-09
                                       EEEEECSSHHHHHHHHHHHHTTSEE.EEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEE CS
                         Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkV.tvversdkllrllDeeaskilqeklekngievllntkveeiegsedgvesv 76 
                                       +v++vG+G++gl lA  l + g kV  +ve+++k+          + + k++++gi +l+ +++ + eg+e+ ve+ 
  gi|242398627|ref|YP_002994051.1| 270 RVLIVGAGNVGLILAYQLYQAGVKVeAIVEAMPKIG------GYFVHAAKVRRLGIPILTRHTILRAEGNEK-VEKA 339
                                       79***********************99*********......5556689**********************9.5544 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.1   8.2e-08   4.9e-05       1      37 [.     123     159 ..     123     175 .. 0.91
   2 !   16.0   0.3   1.8e-05     0.011       1      34 [.     273     307 ..     273     320 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 8.2e-08
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-E CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraas 37 
                                       +vG+G +G+ aA  +++ g++v+ll+ ++ lGG++  
  gi|242398627|ref|YP_002994051.1| 123 VVGGGPAGMMAAINASDGGAKVVLLDENPMLGGQLVK 159
                                       8********************************9765 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 1.8e-05
                                       EE--SHHHHHHHHHHHCCTEEEE.EE-SSSSSSGG CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvl.llekrdrlGGr 34 
                                       IvGaG  Gl +Ay L +ag++v+ ++e+ +++GG 
  gi|242398627|ref|YP_002994051.1| 273 IVGAGNVGLILAYQLYQAGVKVEaIVEAMPKIGGY 307
                                       9********************96378999999996 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.9     5e-08     3e-05       1      31 [.     120     150 ..     120     165 .. 0.85
   2 !    8.1   0.1    0.0021       1.3     102     156 ..     184     240 ..     167     262 .. 0.72
   3 !    8.0   0.7    0.0023       1.4       2      36 ..     271     305 ..     270     313 .. 0.91
   4 !    9.0   0.3    0.0011      0.67     349     386 ..     399     435 ..     392     439 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 5e-08
                                       CEEEE-SSHHHHHHHHHHHHTT--EEEEES- CS
                              GIDA   1 dviViGgGhAGceAAlaaarlGakvlLithk 31 
                                       dviV+GgG AG+ AA++a+  Gakv+L+ ++
  gi|242398627|ref|YP_002994051.1| 120 DVIVVGGGPAGMMAAINASDGGAKVVLLDEN 150
                                       8**************************9554 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0021
                                       HHHHHTSTTEEEEES-EEEEEECT...TEEEEEEETTS.-EEEECEEEE--TT-BT-EE CS
                              GIDA 102 teklenepnleiieeeveelivee...kkvkgvvtedg.etikakavviatGtflkgki 156
                                       +e+l++  n+e++ e+ + +++++   k v gv+++++  ++k kavv+atG+ ++  i
  gi|242398627|ref|YP_002994051.1| 184 EEELRK-RNIELFLETSAIMLLQNgedKLVVGVKKNKElIEFKGKAVVVATGA-MERMI 240
                                       445554.77887777666666666666778899888772579999*******9.54444 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0023
                                       EEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT CS
                              GIDA   2 viViGgGhAGceAAlaaarlGakvlLithkldtia 36 
                                       v ++G+G  G+  A+++ ++G+kv  i++ + +i+
  gi|242398627|ref|YP_002994051.1| 271 VLIVGAGNVGLILAYQLYQAGVKVEAIVEAMPKIG 305
                                       89***********************9999888887 PP

  == domain 4  score: 9.0 bits;  conditional E-value: 0.0011
                                       TSBBSSSBTEEE-CGGGTB-SHHHHHHHHHHHHHHHHH CS
                              GIDA 349 tLetkkvkgLflAGqinGteGYeEaaaqGllAGinaar 386
                                       ++et  vkg+f+AG+  G e  + a+  G +AGi aa+
  gi|242398627|ref|YP_002994051.1| 399 RMETT-VKGIFVAGDSAGIEEATTAMLEGKIAGIGAAL 435
                                       78887.**************7888888*******9997 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1     4e-06    0.0024       1      36 [.     120     156 ..     120     166 .. 0.91
   2 !    7.5   0.0    0.0045       2.7     152     203 ..     183     236 ..     172     256 .. 0.77
   3 !   15.1   1.1   2.1e-05     0.013       1      41 [.     270     312 ..     270     320 .. 0.83
   4 ?    2.3   0.1      0.17     1e+02     157     229 ..     329     397 ..     309     415 .. 0.57

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4e-06
                                       EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSG CS
                               DAO   1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiagsga 36 
                                       dv+++GGG +G+ +A  ++  g  V+ll+ ++ +g g+
  gi|242398627|ref|YP_002994051.1| 120 DVIVVGGGPAGMMAAINASDGGakVVLLDENPMLG-GQ 156
                                       8*****************88779********9998.65 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0045
                                       HHHHHHHTT-EEEESECEEEE.EE.EETCEEEEEEECT.EEE.EEEEEEEE--GGG CS
                               DAO 152 laraaealGveilegtevtgl.ee.edgkvwgverttp.gen.daadavVnaaGaw 203
                                       l ++++++ +e++++t +  l ++ ed+ v+gv  +++ + + ++ +avV+a+Ga 
  gi|242398627|ref|YP_002994051.1| 183 LEEELRKRNIELFLETSAIMLlQNgEDKLVVGV--KKNkELIeFKGKAVVVATGAM 236
                                       677899999*****9999997344455999999..4554666567799******97 PP

  == domain 3  score: 15.1 bits;  conditional E-value: 2.1e-05
                                       EEEEECTSHHHHHHHHHHHHTT...EEEEESSSSTTSSGGGSSE CS
                               DAO   1 dvviiGGGiiGlstAyeLarrg...VtllekgdiagsgaSgrns 41 
                                       +v+i+G+G +Gl  Ay+L ++g    +++e+ + +g g   +++
  gi|242398627|ref|YP_002994051.1| 270 RVLIVGAGNVGLILAYQLYQAGvkvEAIVEAMPKIG-GYFVHAA 312
                                       59*******************999779999988888.7666665 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.17
                                       HHTT-EEEESECEEEEEEEETCEEEEE.EECTEEEEEEEEEEE--GGGHH..HHHTTCTT..TSEEEEEEEEEEEEE CS
                               DAO 157 ealGveilegtevtgleeedgkvwgve.rttpgendaadavVnaaGawsd..llgllkel..dlpispvrgqvlvlk 228
                                       +a G e +e++ v  l+e     w+v   t  + ++++d + +a G+  +  ll   +++  +++ +p  g ++v++
  gi|242398627|ref|YP_002994051.1| 329 RAEGNEKVEKAVVAQLDE----KWNVIpGT--EKVFEVDVIALAVGLRPSieLL---HQVgcQIKYVPELGGHVVIR 396
                                       333334444444444533....36663422..22357899******99766344...55533346689999999983 PP

                                       E CS
                               DAO 229 p 229
                                        
  gi|242398627|ref|YP_002994051.1| 397 D 397
                                       3 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.4   7.2e-07   0.00043       1      32 [.     118     149 ..     118     152 .. 0.93
   2 !   18.0   0.4   2.2e-06    0.0013       4      32 ..     271     300 ..     269     305 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 7.2e-07
                                       EEEEEEE--SHHHHHHHHHHHHTTHHEEEEES CS
                     FAD_binding_3   1 etdVlIVGaGpaGlmlallLseaGvrvvlvek 32 
                                       e+dV++VG+GpaG+m+a   s  G +vvl++ 
  gi|242398627|ref|YP_002994051.1| 118 EADVIVVGGGPAGMMAAINASDGGAKVVLLDE 149
                                       579**************************986 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 2.2e-06
                                       EEEE--SHHHHHHHHHHHHTTHHE.EEEES CS
                     FAD_binding_3   4 VlIVGaGpaGlmlallLseaGvrv.vlvek 32 
                                       VlIVGaG +Gl+la  L +aGv+v  +ve 
  gi|242398627|ref|YP_002994051.1| 271 VLIVGAGNVGLILAYQLYQAGVKVeAIVEA 300
                                       9**********************6256665 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0     2e-06    0.0012      16      56 ..     117     156 ..     113     165 .. 0.89
   2 ?   -2.2   0.1       3.4     2e+03     103     145 ..     182     225 ..     177     239 .. 0.67
   3 !   12.1   0.1   0.00014     0.084      20      55 ..     271     306 ..     257     341 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2e-06
                                       TEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TT CS
                              Thi4  16 aesDvvivGaGssGLtaayylakkpdlkvailersvspGGG 56 
                                       +e+Dv++vG+G++G+ aa   +   + kv++l+++  +GG 
  gi|242398627|ref|YP_002994051.1| 117 IEADVIVVGGGPAGMMAAINASDG-GAKVVLLDENPMLGGQ 156
                                       699***************998877.********99888885 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.4
                                       HHHHHHTSTTEEEEESEEEEEEEEETB.TEEEEEEEEEHHHHTC CS
                              Thi4 103 llskvlqlanvkllnavaveDlivreg.egvaGvvinwtlvela 145
                                       +l + l + n+ l+  +++  l+   + + v Gv  n  l+e +
  gi|242398627|ref|YP_002994051.1| 182 ILEEELRKRNIELFLETSAIMLLQNGEdKLVVGVKKNKELIEFK 225
                                       55566666777777777776666655337778887777777754 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 0.00014
                                       EEEE--SHHHHHHHHHHHHCTTS-E.EEEESSSS--T CS
                              Thi4  20 vvivGaGssGLtaayylakkpdlkv.ailersvspGG 55 
                                       v+ivGaG  GL  ay l ++ ++kv ai+e+   +GG
  gi|242398627|ref|YP_002994051.1| 271 VLIVGAGNVGLILAYQLYQA-GVKVeAIVEAMPKIGG 306
                                       89*****************9.***9567777777776 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.1    0.0026       1.5       9      40 ..     120     151 ..     117     203 .. 0.74
   2 ?    1.3   0.0      0.79   4.7e+02      18      54 ..     213     246 ..     206     259 .. 0.83
   3 !   15.9   0.2   2.2e-05     0.013       8      40 ..     269     301 ..     267     365 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0026
                     NAD_binding_7   9 kvlvvGgGevAarkvrklleagakvtvvapev 40 
                                        v+vvGgG+ ++  + +  + gakv++++++ 
  gi|242398627|ref|YP_002994051.1| 120 DVIVVGGGPAGMMAAINASDGGAKVVLLDENP 151
                                       799************************99983 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.79
                     NAD_binding_7  18 vAarkvrklleagakvtvvapevkeeleelvklaeee 54 
                                       v+ +k + l+e++ k +vva     ++e+ + +++++
  gi|242398627|ref|YP_002994051.1| 213 VGVKKNKELIEFKGKAVVVATG---AMERMIPFENND 246
                                       899999************9998...667666666655 PP

  == domain 3  score: 15.9 bits;  conditional E-value: 2.2e-05
                     NAD_binding_7   8 kkvlvvGgGevAarkvrklleagakvtvvapev 40 
                                        +vl+vG+G+v++  +++l +ag kv  + +++
  gi|242398627|ref|YP_002994051.1| 269 DRVLIVGAGNVGLILAYQLYQAGVKVEAIVEAM 301
                                       79*************************999985 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 !   22.1   0.2   1.3e-07   7.5e-05      28      75 ..     118     165 ..     114     235 .. 0.83
   2 ?    5.3   0.7     0.017        10      24      56 ..     263     296 ..     251     339 .. 0.85
   3 ?    0.3   0.1      0.59   3.5e+02      18      47 ..     408     437 ..     363     460 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.3e-07
                                       --EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCEC CS
                       AlaDh_PNT_C  28 pakvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfv 75 
                                       +a v+v+GgG aG+ A+ +a+  gakV++lD +p    ql +  +kf+
  gi|242398627|ref|YP_002994051.1| 118 EADVIVVGGGPAGMMAAINASDGGAKVVLLDENPMLGGQLVKQTHKFF 165
                                       599******************************998888777655554 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.017
                                       TCB---.EEEEESTSHHHHHHHHHHHHTT-EEEE CS
                       AlaDh_PNT_C  24 pgvepa.kvlviGgGvaGlqAiatakglgakVtv 56 
                                        gv+p+ +vl++G+G +Gl  +    + g kV++
  gi|242398627|ref|YP_002994051.1| 263 YGVKPGdRVLIVGAGNVGLILAYQLYQAGVKVEA 296
                                       46888758***********988888888888876 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.59
                                       ETTCEETCB---EEEEESTSHHHHHHHHHH CS
                       AlaDh_PNT_C  18 tlaGgvpgvepakvlviGgGvaGlqAiata 47 
                                        +aG   g+e+a++  + g +aG+ A+ +a
  gi|242398627|ref|YP_002994051.1| 408 FVAGDSAGIEEATTAMLEGKIAGIGAALIA 437
                                       345666666666666666666666666554 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.3   3.9e-05     0.024       1      36 [.     120     153 ..     120     164 .. 0.88
   2 !    8.3   0.1    0.0017         1       2      36 ..     271     304 ..     270     330 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.9e-05
                     Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvlieaspsl 36 
                                       Dv+v+G+GpAg+  A +   +  g kvvl++  p l
  gi|242398627|ref|YP_002994051.1| 120 DVIVVGGGPAGMMAAINA--SDGGAKVVLLDENPML 153
                                       9***********999999..999*******877654 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0017
                     Lycopene_cycl   2 vvviGaGpAglslAarlteakpglkv.vlieaspsl 36 
                                       v+++GaG  gl lA +l   ++g+kv  ++ea p++
  gi|242398627|ref|YP_002994051.1| 271 VLIVGAGNVGLILAYQL--YQAGVKVeAIVEAMPKI 304
                                       89***************..88888883467887776 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1       2.1   1.3e+03       2      31 ..     122     151 ..     121     170 .. 0.85
   2 ?    1.0   0.0       0.5     3e+02      94     104 ..     197     207 ..     178     234 .. 0.74
   3 !   16.9   0.6   6.5e-06    0.0039       1      29 [.     271     299 ..     271     313 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2.1
                                       EEES-SHHHHHHHHHHHHHTHCEEEE-SCH CS
                              ApbA   2 ailGaGaiGsllaakLakagadvtlilrsr 31 
                                        ++G G  G + a + +  ga+v+l++ ++
  gi|242398627|ref|YP_002994051.1| 122 IVVGGGPAGMMAAINASDGGAKVVLLDENP 151
                                       799999999999999999*******99887 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.5
                                       TCEEEEEESSS CS
                              ApbA  94 pntvvlllqNG 104
                                       ++++++llqNG
  gi|242398627|ref|YP_002994051.1| 197 ETSAIMLLQNG 207
                                       4579******9 PP

  == domain 3  score: 16.9 bits;  conditional E-value: 6.5e-06
                                       EEEES-SHHHHHHHHHHHHHTHCEEEE-S CS
                              ApbA   1 iailGaGaiGsllaakLakagadvtlilr 29 
                                       ++i+GaG +G +la++L++ag +v  i+ 
  gi|242398627|ref|YP_002994051.1| 271 VLIVGAGNVGLILAYQLYQAGVKVEAIVE 299
                                       68**********************99875 PP

>> ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.84     5e+02      33      59 ..     119     145 ..      61     152 .. 0.71
   2 !   13.8   0.2   6.1e-05     0.036      22     165 ..     260     409 ..     249     415 .. 0.67

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.84
                                       EEEEEE--SHHHHHHHHHHHHCT-EEE CS
                     ELFV_dehydrog  33 krvaisGsGnvgsyaallltelgakvv 59 
                                       + v++ G G  g +aa  +++ gakvv
  gi|242398627|ref|YP_002994051.1| 119 ADVIVVGGGPAGMMAAINASDGGAKVV 145
                                       456666777777777777777777776 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 6.1e-05
                                       HHHTTTS-STTEEEEEE--SHHHHHHHHHHHHCT-EEEEEEESS....EEEEETTEE........-HHHHHHHHHCS CS
                     ELFV_dehydrog  22 lkklkldslegkrvaisGsGnvgsyaallltelgakvvavsDss....GviydpeGl........dieellelkeer 86 
                                       +++++ +   g rv i G Gnvg   a  l ++g kv a+++      G+ ++   +         ++++l+ + ++
  gi|242398627|ref|YP_002994051.1| 260 MNTYGVK--PGDRVLIVGAGNVGLILAYQLYQAGVKVEAIVEAMpkigGYFVHAAKVrrlgipilTRHTILRAEGNE 334
                                       4444444..6889***************************9975333366665554444444777777777776666 PP

                                       SSSTTHSHHSTSTSEEESHHSHHHHSS-SEEEE-.SSTTSB-HHHHTHTHHTT-SEEE-SSSS-B-HHHHHHHHHTT CS
                     ELFV_dehydrog  87 ksvkeykkssekkaeyieneeellelkvdilvPc.AtqneideenakalikngvklvvEgANlpttqeAkeileeag 162
                                       k  k +  + ++k ++i++ e+++  +vd++  + ++  +i+   ++ ++ +++k+v E     +  +++   + +g
  gi|242398627|ref|YP_002994051.1| 335 KVEKAVVAQLDEKWNVIPGTEKVF--EVDVIALAvGLRPSIEL--LH-QVGCQIKYVPELGGHVVIRDSRMETTVKG 406
                                       654444445556888999988887..56777777788888865..33.55666778877666666666555555555 PP

                                       -EE CS
                     ELFV_dehydrog 163 vlv 165
                                       ++v
  gi|242398627|ref|YP_002994051.1| 407 IFV 409
                                       555 PP

>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.57   3.4e+02     167     190 ..     124     147 ..     101     185 .. 0.70
   2 ?   11.2   0.1   0.00029      0.17      53     135 ..     266     355 ..     248     425 .. 0.70

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.57
                                       SSHHHHHHHHHHHHHSTT-EEEEE CS
                              PALP 167 gGgliaGiaaglkerrpdvrvigv 190
                                       +Gg  aG++a++ ++++  +v+  
  gi|242398627|ref|YP_002994051.1| 124 VGGGPAGMMAAINASDGGAKVVLL 147
                                       344466666666666665666555 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00029
                                       TTTSEEEEEBSSHHHHHHHHHHHHHT-EEEEEEETTS-H....HHHHHHHHTT-......EEEEECCHHHHHHHHHH CS
                              PALP  53 tgaktvveassGNhgralAaaaallGlkvtivvpadasp....ekvallrllGa......evvevggdydeavaaaa 119
                                       +++++v+  ++GN g+ lA+    +G+kv+  v+a  +       +a+ r+lG       ++ + +g+ + ++a++a
  gi|242398627|ref|YP_002994051.1| 266 KPGDRVLIVGAGNVGLILAYQLYQAGVKVEAIVEAMPKIggyfVHAAKVRRLGIpiltrhTILRAEGNEKVEKAVVA 342
                                       68899**************************9776655344457777777777544443333333555555555544 PP

                                       HHHHHSTTCEE--TTT CS
                              PALP 120 elaaegegaylvsqfd 135
                                       +l    e++ +++ ++
  gi|242398627|ref|YP_002994051.1| 343 QLD---EKWNVIPGTE 355
                                       444...4455555555 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0     0.014       8.5       1      32 [.     121     152 ..     121     165 .. 0.88
   2 ?    5.8   0.1     0.026        16       1      24 [.     271     294 ..     271     348 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.014
                                       EEEES-SHHHHHHHHHHHHTTEEEEEEESSHH CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdee 32 
                                       +i++G G  G+  a + s+gg +vv+ d ++ 
  gi|242398627|ref|YP_002994051.1| 121 VIVVGGGPAGMMAAINASDGGAKVVLLDENPM 152
                                       79*****************7767******985 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.026
                                       EEEES-SHHHHHHHHHHHHTT.EEE CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLsegg.kdv 24 
                                       ++i+G+G+vG  la +L ++g k v
  gi|242398627|ref|YP_002994051.1| 271 VLIVGAGNVGLILAYQLYQAGvK-V 294
                                       68***************996523.4 PP

>> Fer2_3  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0    0.0001      0.06      50      81 ..      60      92 ..       9     112 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.0001
                            Fer2_3 50 asCregiCGscavainGkp.tlaCtatikdlak 81
                                        C  g C sc +++nG p    C + ++d  +
  gi|242398627|ref|YP_002994051.1| 60 LFCAIGKCSSCLMKVNGIPnVRTCITLVEDGMQ 92
                                      67****************934589999998764 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.93   5.5e+02       4      37 ..     120     151 ..     117     172 .. 0.79
   2 ?   10.3   0.0   0.00046      0.27     131     215 ..     209     292 ..     197     303 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.93
                       K_oxygenase   4 DligiGiGpsnLsLailleevkkelkalflerqp 37 
                                       D+i +G Gp+ +  ai +++     k++ l+++p
  gi|242398627|ref|YP_002994051.1| 120 DVIVVGGGPAGMMAAINASDGG--AKVVLLDENP 151
                                       8899999998887777766655..6677776665 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00046
                       K_oxygenase 131 elltveskdaegeeeelearnlvlgvG.tepkiPevleklegkervvHsseylerkeellakkriaVvGsGqSaaei 206
                                       + l v + +++ e  e++ +++v+++G  e+ iP   ++l g      + ++l ++   + ++r+++vG+G  +  +
  gi|242398627|ref|YP_002994051.1| 209 DKLVVGV-KKNKELIEFKGKAVVVATGaMERMIPFENNDLPG-VYGAGAIQTLMNTYGVKPGDRVLIVGAGNVGLIL 283
                                       5566776.45677899***********8899***99999986.444444555666667999***********99999 PP

                       K_oxygenase 207 fedllrrqk 215
                                       +++l++   
  gi|242398627|ref|YP_002994051.1| 284 AYQLYQAGV 292
                                       999988754 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.38   2.3e+02       2      31 ..     129     158 ..     128     167 .. 0.91
   2 ?    7.7   0.0    0.0031       1.8       3      28 ..     280     306 ..     280     308 .. 0.94
   3 ?   -1.4   0.0       1.7     1e+03     399     428 ..     384     413 ..     380     423 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.38
                                       HHHHHHHHHHHTTEEEEEEESSSSSBTTS- CS
                     Amino_oxidase   2 aGLaaArqLlsaGfdVtvlEardrvGGRir 31 
                                       aG++aA   ++ G +V++l  ++ +GG + 
  gi|242398627|ref|YP_002994051.1| 129 AGMMAAINASDGGAKVVLLDENPMLGGQLV 158
                                       9**************************765 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0031
                                       HHHHHHHHHHTTEEE.EEEESSSSSBT CS
                     Amino_oxidase   3 GLaaArqLlsaGfdV.tvlEardrvGG 28 
                                       GL+ A+qL +aG++V  ++Ea + +GG
  gi|242398627|ref|YP_002994051.1| 280 GLILAYQLYQAGVKVeAIVEAMPKIGG 306
                                       9***********99956*********9 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 1.7
                                       EE.BTTHHHHHHHHHHCHHCSTTEEE.SGG CS
                     Amino_oxidase 399 syvsvgpghedydplakpegdprlffAGeh 428
                                       +yv+   gh  +++++++  ++++f+AG++
  gi|242398627|ref|YP_002994051.1| 384 KYVPELGGHVVIRDSRMETTVKGIFVAGDS 413
                                       5677777888888888888*********98 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.2     0.024        14       2      40 ..     121     159 ..     120     191 .. 0.82
   2 ?    7.3   0.5    0.0068       4.1       2      28 ..     271     297 ..     270     313 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.024
                                       EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHH CS
                           3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdiseealekale 40 
                                       v v+G G  G   a  +   g +Vvl+d ++    +  +
  gi|242398627|ref|YP_002994051.1| 121 VIVVGGGPAGMMAAINASDGGAKVVLLDENPMLGGQLVK 159
                                       78**************************99865555555 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0068
                                       EEEE--SCCHHHHHHHHHHTT-EEEEE CS
                           3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlv 28 
                                       v ++GaG +G  +a+++ +ag++V  +
  gi|242398627|ref|YP_002994051.1| 271 VLIVGAGNVGLILAYQLYQAGVKVEAI 297
                                       789*********************865 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       7.5   4.5e+03      19      48 ..     204     230 ..     198     240 .. 0.59
   2 ?   10.8   0.9   0.00095      0.57       2      31 ..     271     300 ..     270     395 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 7.5
                                       HHTTS-GGCEEEEEESSCCCHHHHHHHHC- CS
                     F420_oxidored  19 laagaqpheivvansrnpekaeelaeelgv 48 
                                       l++g  + ++vv+  ++++++ e++ ++ v
  gi|242398627|ref|YP_002994051.1| 204 LQNG--EDKLVVG-VKKNKELIEFKGKAVV 230
                                       5666..5556655.5555656666655544 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00095
                                       EEEETTSHHHHHHHHHHHHTTS-GGCEEEE CS
                     F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivva 31 
                                       + i+GaGn+g  la +l +ag++ + iv a
  gi|242398627|ref|YP_002994051.1| 271 VLIVGAGNVGLILAYQLYQAGVKVEAIVEA 300
                                       6689*****************999988865 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.4   0.00058      0.35       1      29 [.     120     145 ..     120     154 .. 0.77
   2 ?    2.5   0.3     0.087        52       1      31 [.     270     297 ..     270     316 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00058
                                       EEEEE--SHHHHHHHHHHHHHTTTSSEEE CS
                    Trp_halogenase   1 kivivGGGtaGwlaAaalakalkgklevt 29 
                                       ++++vGGG+aG +aA+  +  +   ++v 
  gi|242398627|ref|YP_002994051.1| 120 DVIVVGGGPAGMMAAINASDGG---AKVV 145
                                       699************9766554...4455 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.087
                                       EEEEE--SHHHHHHHHHHHHHTTTSSEEEEE CS
                    Trp_halogenase   1 kivivGGGtaGwlaAaalakalkgklevtlv 31 
                                       +++ivG+G  G + A  l +a+   ++v+ +
  gi|242398627|ref|YP_002994051.1| 270 RVLIVGAGNVGLILAYQLYQAG---VKVEAI 297
                                       699***************9999...555544 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1    0.0008      0.48      20      43 ..     270     293 ..     255     299 .. 0.92
   2 ?   -2.7   0.0       5.2   3.1e+03     187     209 ..     427     449 ..     380     460 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0008
                                       EEEEE--SHHHHHHHHHHHHHTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF  20 kvllvGaGglGsellknLalsGvg 43 
                                       +vl+vGaG +G +l+ +L  +Gv+
  gi|242398627|ref|YP_002994051.1| 270 RVLIVGAGNVGLILAYQLYQAGVK 293
                                       8*********************97 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.2
                                       -B-HHHHHHHHHHHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF 187 paiatttavvaglaalellklls 209
                                        + +   a++ag+a  e lk ++
  gi|242398627|ref|YP_002994051.1| 427 KIAGIGAALIAGVASPEWLKEIE 449
                                       35677789999999999998873 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 ?   10.5   1.8   0.00069      0.41       5      30 ..      61      83 ..      58      85 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00069
                                      SSSSSSS-TTEEEETTCTT.CEEETT CS
                   DHODB_Fe-S_bind  5 aCGvGaClgCvvktkggdggeykrvC 30
                                       C++G C +C +k++g     ++r+C
  gi|242398627|ref|YP_002994051.1| 61 FCAIGKCSSCLMKVNGI---PNVRTC 83
                                      5*************875...478888 PP

>> YdfZ  YdfZ protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.2       9.9   5.9e+03      16      33 ..     121     138 ..     119     143 .. 0.85
   2 ?    0.9   0.0       1.1   6.5e+02      34      59 ..     218     243 ..     189     244 .. 0.73
   3 ?    8.6   0.0     0.004       2.4      10      29 ..     265     284 ..     261     298 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 9.9
                              YdfZ  16 VMiagtgevgvikaihtd 33 
                                       V+++g g  g+++ai++ 
  gi|242398627|ref|YP_002994051.1| 121 VIVVGGGPAGMMAAINAS 138
                                       889999999****99875 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 1.1
                              YdfZ  34 gltaeqvrrekcVelegveerfaPle 59 
                                       +++  + + + +V+ +g+ er+ P+e
  gi|242398627|ref|YP_002994051.1| 218 NKELIEFKGKAVVVATGAMERMIPFE 243
                                       55555666677888899*******98 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.004
                              YdfZ  10 ittGsrVMiagtgevgvika 29 
                                       +++G rV+i+g g+vg i a
  gi|242398627|ref|YP_002994051.1| 265 VKPGDRVLIVGAGNVGLILA 284
                                       689**************987 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.1    0.0071       4.2       2      44 ..     123     160 ..     122     164 .. 0.79
   2 ?   -0.3   0.0       1.6   9.3e+02     113     154 ..     190     234 ..     174     236 .. 0.64
   3 ?    2.1   0.3       0.3   1.8e+02       2      19 ..     273     290 ..     272     306 .. 0.87
   4 ?   -2.3   0.0       6.3   3.8e+03     130     154 ..     344     368 ..     333     369 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0071
                     NAD_binding_9   2 ivGaGprGlavlerLlarakkkspleitlfdpsep.gagrvwrt 44 
                                       +vG+Gp+G++++ +  +        ++ l d++++ g g+  ++
  gi|242398627|ref|YP_002994051.1| 123 VVGGGPAGMMAAINASDG-----GAKVVLLDENPMlG-GQLVKQ 160
                                       8**********9886655.....79999999999955.666555 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.6
                     NAD_binding_9 113 egvtvevhraevvdleeradgqavlladgas...laadaVvLAlG 154
                                       +++++ + ++ +  l++ +d+  v  +++++   ++ +aVv+A+G
  gi|242398627|ref|YP_002994051.1| 190 RNIELFLETSAIMLLQNGEDKLVVGVKKNKElieFKGKAVVVATG 234
                                       45555555666666777777765555444433236889******9 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.3
                     NAD_binding_9   2 ivGaGprGlavlerLlar 19 
                                       ivGaG  Gl ++ +L + 
  gi|242398627|ref|YP_002994051.1| 273 IVGAGNVGLILAYQLYQA 290
                                       9*************9886 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 6.3
                     NAD_binding_9 130 radgqavlladgaslaadaVvLAlG 154
                                        ++++ v+  +++ +++d + LA+G
  gi|242398627|ref|YP_002994051.1| 344 LDEKWNVIPGTEKVFEVDVIALAVG 368
                                       4556677778888999*******99 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 ?    2.6   0.2      0.14        86       3      33 ..     121     151 ..     119     164 .. 0.91
   2 ?   -3.0   0.0       7.4   4.4e+03     157     180 ..     196     220 ..     191     223 .. 0.64
   3 ?    6.2   1.4     0.011       6.7       2      29 ..     270     297 ..     269     387 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.14
                                       EEEE--STTHHHHHHHHHHCTSEEEEE-S-H CS
                    UDPG_MGDP_dh_N   3 isviGlGYvGlvtaavlaeighevigvDide 33 
                                       + v+G G  G++ a+  +  g +v+++D + 
  gi|242398627|ref|YP_002994051.1| 121 VIVVGGGPAGMMAAINASDGGAKVVLLDENP 151
                                       789*************************985 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 7.4
                                       -TTSHHHHHHS.-S-EEEEESSCHH CS
                    UDPG_MGDP_dh_N 157 regsavkdlln.pdrvviGveekka 180
                                       +e sa+  l+n +d+ v+Gv+++k+
  gi|242398627|ref|YP_002994051.1| 196 LETSAIMLLQNgEDKLVVGVKKNKE 220
                                       5555555555436888899887765 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.011
                                       EEEEE--STTHHHHHHHHHHCTSEEEEE CS
                    UDPG_MGDP_dh_N   2 kisviGlGYvGlvtaavlaeighevigv 29 
                                       ++ ++G+G vGl+ a  l ++g++v  +
  gi|242398627|ref|YP_002994051.1| 270 RVLIVGAGNVGLILAYQLYQAGVKVEAI 297
                                       789*******************999665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (477 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              30  [number of targets reported over threshold]
# CPU time: 0.73u 0.32s 00:00:01.05 Elapsed: 00:00:00.48
# Mc/sec: 2992.92
//
Query:       gi|242398628|ref|YP_002994052.1|  [L=168]
Description: Dye-linked L-proline dehydrogenase gamma2 subunit [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-06   27.9   2.3    1.4e-06   27.9   2.3    2.7  3  Fer4          4Fe-4S binding domain
    1.6e-06   27.9  13.2      8e-05   22.5   0.8    2.3  2  Fer4_6        4Fe-4S binding domain
    2.4e-06   27.6  10.1    4.3e-06   26.8  10.1    1.4  1  Fer4_21       4Fe-4S dicluster domain
    4.1e-06   27.3  19.6    0.00014   22.3  10.3    1.9  2  Fer4_7        4Fe-4S dicluster domain
    3.7e-05   23.8   9.4    8.5e-05   22.6   9.5    1.6  1  Fer4_9        4Fe-4S dicluster domain
    0.00012   22.8  13.1     0.0037   18.1   4.1    2.5  2  Fer4_3        4Fe-4S binding domain
    0.00012   22.0   2.4    0.00012   22.0   2.4    2.4  2  Fer4_2        4Fe-4S binding domain
    0.00025   21.1  13.0    0.00058   19.9  13.1    1.5  1  Fer4_10       4Fe-4S dicluster domain
    0.00027   21.3   1.4     0.0099   16.3   0.0    2.3  2  Fer4_8        4Fe-4S dicluster domain
     0.0029   18.1   0.1     0.0029   18.1   0.1    2.6  2  Fer4_13       4Fe-4S single cluster domain of Ferredoxin I
     0.0037   17.6   0.6     0.0037   17.6   0.6    2.3  2  Fer4_4        4Fe-4S binding domain
      0.004   18.0  13.1       0.21   12.5   2.3    2.4  3  Fer4_16       4Fe-4S double cluster binding domain
  ------ inclusion threshold ------
      0.015   16.0   0.2      0.015   16.0   0.2    2.7  2  Fer4_15       4Fe-4S single cluster domain
        0.2   11.6   0.0       0.29   11.1   0.0    1.2  1  Phage_base_V  Type VI secretion system, phage-baseplate injec
        2.5    8.7  12.0        0.4   11.3   1.9    2.5  4  Fer4_17       4Fe-4S dicluster domain
        3.2    8.0  11.4       0.79    9.9   2.4    2.2  1  Fer4_18       4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.2       3.1   3.4e+03      16      21 ..      38      43 ..      37      45 .. 0.75
   2 !    9.1   3.2     0.001       1.1      13      23 ..      48      58 ..      46      59 .. 0.85
   3 !   27.9   2.3   1.2e-09   1.4e-06       1      22 [.      67      88 ..      67      90 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3.1
                                      HHSTTT CS
                              Fer4 16 evCPvg 21
                                        CP +
  gi|242398628|ref|YP_002994052.1| 38 PECPQE 43
                                      57**86 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.001
                                      HHHHHSTTTEE CS
                              Fer4 13 aCvevCPvgAI 23
                                       C+e+CP++A 
  gi|242398628|ref|YP_002994052.1| 48 PCAEICPTNAV 58
                                      5********95 PP

  == domain 3  score: 27.9 bits;  conditional E-value: 1.2e-09
                                      EEEETTTSSS-THHHHHSTTTE CS
                              Fer4  1 vvideekCigCGaCvevCPvgA 22
                                      +v+ +ekCigC +Cv++CP  A
  gi|242398628|ref|YP_002994052.1| 67 PVVEYEKCIGCSLCVQICPGLA 88
                                      6899***************765 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   5.7   0.00078      0.87      10      23 ..      44      57 ..      40      58 .. 0.84
   2 !   22.5   0.8   7.2e-08     8e-05       2      20 ..      67      85 ..      66      93 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00078
                            Fer4_6 10 igCgdCvrvCPega 23
                                      i C +C+ +CP++a
  gi|242398628|ref|YP_002994052.1| 44 IPCTPCAEICPTNA 57
                                      36**********98 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 7.2e-08
                            Fer4_6  2 veidpdkCigCgdCvrvCP 20
                                      +++ ++kCigC  Cv +CP
  gi|242398628|ref|YP_002994052.1| 67 PVVEYEKCIGCSLCVQICP 85
                                      7999*************** PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8  10.1   3.9e-09   4.3e-06       9      52 ..      44      85 ..      37      89 .. 0.90

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 3.9e-09
                           Fer4_21  9 igCgkCliaCedtshqaieidaktvlkvve.deCvGCnlCssvCP 52
                                      i C+ C+  C+   ++a+ +++ + l+vve ++C+GC lC+++CP
  gi|242398628|ref|YP_002994052.1| 44 IPCTPCAEICP---TNAVLMEHPNALPVVEyEKCIGCSLCVQICP 85
                                      88*********...699999999999998549************* PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3  10.3   1.3e-07   0.00014       4      49 ..      45      85 ..      39      88 .. 0.89
   2 !   17.0   1.8     6e-06    0.0068       1      23 [.      73      95 ..      73     110 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.3e-07
                            Fer4_7  4 gCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCP 49
                                       C  C++ Cp++a+ ++       ++ +++++ekC+gC  Cv+ CP
  gi|242398628|ref|YP_002994052.1| 45 PCTPCAEICPTNAVLMEHP-----NALPVVEYEKCIGCSLCVQICP 85
                                      6***************765.....4567999**************9 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 6e-06
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeee 23
                                      +CigC  Cv+ Cp  a+ +  + 
  gi|242398628|ref|YP_002994052.1| 73 KCIGCSLCVQICPGLAFFMVHYI 95
                                      7************8887776554 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   9.5   7.6e-08   8.5e-05       4      47 ..      45      85 ..      39      89 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 7.6e-08
                            Fer4_9  4 gCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCp 47
                                       C+ C e Cp+++v +++ +    ++    e+CigC  Cv++Cp
  gi|242398628|ref|YP_002994052.1| 45 PCTPCAEICPTNAVLMEHPNALPVVEY---EKCIGCSLCVQICP 85
                                      4************98888888877755...48***********9 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   1.6    0.0015       1.7       4      15 .]      46      57 ..      39      57 .. 0.93
   2 !   18.1   4.1   3.3e-06    0.0037       1      13 [.      74      86 ..      74      88 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0015
                            Fer4_3  4 CgaCvevCPvgA 15
                                      C +C e CP++A
  gi|242398628|ref|YP_002994052.1| 46 CTPCAEICPTNA 57
                                      889*******98 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 3.3e-06
                            Fer4_3  1 CtgCgaCvevCPv 13
                                      C+gC++Cv+ CP 
  gi|242398628|ref|YP_002994052.1| 74 CIGCSLCVQICPG 86
                                      ************7 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   5.6      0.11   1.2e+02       4      22 .]      35      55 ..      32      55 .. 0.78
   2 !   22.0   2.4     1e-07   0.00012       3      21 ..      67      85 ..      65      85 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.11
                            Fer4_2  4 vvdtdrCig...CgaCvsaCPa 22
                                      v+ ++ C +   C +C   CP+
  gi|242398628|ref|YP_002994052.1| 35 VAIPE-CPQeipCTPCAEICPT 55
                                      55666.777777*********7 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 1e-07
                            Fer4_2  3 vvvdtdrCigCgaCvsaCP 21
                                      +vv+ ++CigC+ Cv+ CP
  gi|242398628|ref|YP_002994052.1| 67 PVVEYEKCIGCSLCVQICP 85
                                      899***************9 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9  13.1   5.2e-07   0.00058      10      56 .]      44      85 ..      37      85 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 5.2e-07
                           Fer4_10 10 irCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      i C+ C + CP+     +a   + +++   + +ekC+gc  Cv++CP
  gi|242398628|ref|YP_002994052.1| 44 IPCTPCAEICPT-----NAVLMEHPNALPVVEYEKCIGCSLCVQICP 85
                                      78**********.....888888889999999**************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 ?    4.2   0.3     0.053        60      54      64 ..      46      56 ..      17      65 .. 0.79
   2 !   16.3   0.0   8.9e-06    0.0099       2      17 ..      71      91 ..      70     135 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.053
                            Fer4_8 54 cgaCtevCpvg 64
                                      c  C+e Cp++
  gi|242398628|ref|YP_002994052.1| 46 CTPCAEICPTN 56
                                      66677777664 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 8.9e-06
                            Fer4_8  2 lekCieCgaCqsaCp.....v 17
                                       ekCi+C++C + Cp     +
  gi|242398628|ref|YP_002994052.1| 71 YEKCIGCSLCVQICPglaffM 91
                                      589***********9554441 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 ?   -0.4   5.7       1.6   1.8e+03       7      18 ..      44      55 ..      39      56 .. 0.90
   2 !   18.1   0.1   2.6e-06    0.0029       1      18 [.      69      86 ..      69     115 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.6
                           Fer4_13  7 iacgaCvelaPd 18
                                      i c+ C+e++P 
  gi|242398628|ref|YP_002994052.1| 44 IPCTPCAEICPT 55
                                      78*********6 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 2.6e-06
                           Fer4_13  1 VDrdtCiacgaCvelaPd 18
                                      V+ ++Ci+c +Cv+++P 
  gi|242398628|ref|YP_002994052.1| 69 VEYEKCIGCSLCVQICPG 86
                                      7889*************4 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   4.4      0.82   9.1e+02       6      17 .]      39      56 ..      38      56 .. 0.83
   2 !   17.6   0.6   3.3e-06    0.0037       1      15 [.      71      85 ..      71     100 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.82
                            Fer4_4  6 gCgs......CvaaCPqg 17
                                      +C++      C  +CP++
  gi|242398628|ref|YP_002994052.1| 39 ECPQeipctpCAEICPTN 56
                                      5888888888999***86 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 3.3e-06
                            Fer4_4  1 qerCigCgsCvaaCP 15
                                      +e+CigC  Cv +CP
  gi|242398628|ref|YP_002994052.1| 71 YEKCIGCSLCVQICP 85
                                      59************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 !   12.5   2.3   0.00019      0.21       5      20 ..      46      61 ..      39      72 .. 0.84
   2 !   10.6   3.5   0.00075      0.85      50      65 ..      70      85 ..      61      86 .. 0.76
   3 !    9.8   3.3    0.0013       1.5       1      15 [.      73      87 ..      73     100 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00019
                           Fer4_16  5 CgkCaevCPtnaikek 20
                                      C+ Cae+CPtna+ ++
  gi|242398628|ref|YP_002994052.1| 46 CTPCAEICPTNAVLME 61
                                      ************8876 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00075
                           Fer4_16 50 kqeaitgCdiCqdvCP 65
                                      ++e+++gC  C+++CP
  gi|242398628|ref|YP_002994052.1| 70 EYEKCIGCSLCVQICP 85
                                      5678888888888888 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.0013
                           Fer4_16  1 rCgtCgkCaevCPtn 15
                                      +C++C  C+++CP  
  gi|242398628|ref|YP_002994052.1| 73 KCIGCSLCVQICPGL 87
                                      588888888888865 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   1.2       1.5   1.6e+03      10      21 ..      45      56 ..      39      62 .. 0.73
   2 ?   16.0   0.2   1.4e-05     0.015       2      21 ..      68      87 ..      68     106 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.5
                           Fer4_15 10 gcglCvaeapev 21
                                       c  C++ +p+ 
  gi|242398628|ref|YP_002994052.1| 45 PCTPCAEICPTN 56
                                      577787777764 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 1.4e-05
                           Fer4_15  2 vvDrdaCigcglCvaeapev 21
                                      vv+ ++Cigc lCv+ +p +
  gi|242398628|ref|YP_002994052.1| 68 VVEYEKCIGCSLCVQICPGL 87
                                      5899*************975 PP

>> Phage_base_V  Type VI secretion system, phage-baseplate injector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00026      0.29      53      81 ..     110     139 ..      92     147 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00026
                                       XXXTTXEEEEEEXXT.TTXXEEEEEEEXXS CS
                      Phage_base_V  53 apsvGEqvvllspsG.elatavvlpglysd 81 
                                       +p+vGE+v+lls  G e+ ++ v++ +  +
  gi|242398628|ref|YP_002994052.1| 110 VPKVGEEVILLSRVGeEVGKGKVVTVIPRE 139
                                       79***********99678889888877655 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   3.2       1.1   1.2e+03      49      58 ..      46      55 ..      33      58 .. 0.73
   2 ?    1.5   2.8      0.39   4.4e+02       5      17 ..      46      58 ..      39      72 .. 0.70
   3 ?   10.7   2.3   0.00052      0.58      44      57 ..      72      85 ..      61      87 .. 0.76
   4 ?   11.3   1.9   0.00035       0.4       1      14 [.      73      86 ..      73     107 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 1.1
                           Fer4_17 49 CgeCerkCPq 58
                                      C  C++ CP 
  gi|242398628|ref|YP_002994052.1| 46 CTPCAEICPT 55
                                      6666666665 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.39
                           Fer4_17  5 CgyClpeCpsyea 17
                                      C  C++ Cp+++ 
  gi|242398628|ref|YP_002994052.1| 46 CTPCAEICPTNAV 58
                                      6667777776655 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00052
                           Fer4_17 44 slCieCgeCerkCP 57
                                      ++Ci+C +C++ CP
  gi|242398628|ref|YP_002994052.1| 72 EKCIGCSLCVQICP 85
                                      66777777777777 PP

  == domain 4  score: 11.3 bits;  conditional E-value: 0.00035
                           Fer4_17  1 rCiqCgyClpeCps 14
                                      +Ci+C+ C++ Cp 
  gi|242398628|ref|YP_002994052.1| 73 KCIGCSLCVQICPG 86
                                      58999999999984 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   2.4   0.00071      0.79      57      72 ..      70      85 ..      56      88 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00071
                           Fer4_18 57 gagdcidcescvkvcP 72
                                      +  +ci c+ cv++cP
  gi|242398628|ref|YP_002994052.1| 70 EYEKCIGCSLCVQICP 85
                                      5678***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); 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):              16  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 995.80
//
Query:       gi|242398629|ref|YP_002994053.1|  [L=93]
Description: Proline dehydrogenase, delta subunit [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.9e-14   52.7   2.1    5.9e-14   52.1   2.1    1.3  1  Fer2_BFD     BFD-like [2Fe-2S] binding domain
    2.5e-13   50.1   0.0    2.9e-13   49.9   0.0    1.0  1  SO_alpha_A3  Sarcosine oxidase A3 domain


Domain annotation for each model (and alignments):
>> 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 !   52.1   2.1   6.6e-18   5.9e-14       1      51 []       8      60 ..       8      60 .. 0.98

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 6.6e-18
                          Fer2_BFD  1 iVCrCegvtegeIrdairraglttveevkrrtkagtg.Cgg..CrpaieeiLae 51
                                      i+CrC++vt +eI++ i ++g+ ++e +kr ++ g+g C+g  C p++  iLa+
  gi|242398629|ref|YP_002994053.1|  8 IICRCNEVTVEEIEALI-EQGVEDIEMIKRLLRIGMGpCQGrtCLPMVISILAR 60
                                      8****************.99********************************96 PP

>> SO_alpha_A3  Sarcosine oxidase A3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.9   0.0   3.2e-17   2.9e-13       3      83 ..       6      86 ..       4      89 .. 0.94

  Alignments for each domain:
  == domain 1  score: 49.9 bits;  conditional E-value: 3.2e-17
                       SO_alpha_A3  3 rqFvdlqnDvtvkdielavregfesiehvKRYttlgmgtdQgklsavnaaaivaeltgkevaevgtttlRpPlapvkla 81
                                       + ++  n vtv++ie  +++g e+ie +KR   +gmg+ Qg++     + i+a++tgk+++e+ +  +R P+ pv+ +
  gi|242398629|ref|YP_002994053.1|  6 EKIICRCNEVTVEEIEALIEQGVEDIEMIKRLLRIGMGPCQGRTCLPMVISILARKTGKSPDEIKLPATRIPIRPVPAG 84
                                      56688889***********************************999999****************************99 PP

                       SO_alpha_A3 82 al 83
                                      +l
  gi|242398629|ref|YP_002994053.1| 85 VL 86
                                      87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); 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 0.28s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 620.97
//
Query:       gi|242398630|ref|YP_002994054.1|  [L=387]
Description: Dye-linked L-proline dehydrogenase beta2 subunit [Thermococcus sibiricus MM 739]
Scores for complete 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-77  259.8   0.0    5.8e-77  259.6   0.0    1.0  1  DAO             FAD dependent oxidoreductase
    1.3e-09   37.7   0.0    1.9e-09   37.1   0.0    1.2  1  FAD_binding_2   FAD binding domain
    6.7e-06   25.6   3.4    0.00025   20.4   3.4    2.3  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    1.2e-05   24.8   1.6    0.00013   21.3   0.6    2.2  2  FAD_binding_3   FAD binding domain
    1.4e-05   24.0   1.0      0.026   13.2   0.5    2.3  2  HI0933_like     HI0933-like protein
    1.4e-05   24.5   0.2     0.0028   17.0   0.0    2.2  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    1.5e-05   25.5   2.9     0.0014   19.2   0.2    2.5  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
      6e-05   22.3   2.7    0.00038   19.6   0.2    2.3  2  GIDA            Glucose inhibited division protein A
    0.00011   22.4   0.1    0.00035   20.8   0.1    1.9  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    0.00043   19.6   1.3     0.0024   17.2   0.2    2.0  2  Thi4            Thi4 family
     0.0015   19.0   0.0     0.0078   16.6   0.0    2.0  1  NAD_binding_7   Putative NAD(P)-binding
     0.0032   16.9   4.9       0.05   12.9   4.9    2.2  1  FAD_oxidored    FAD dependent oxidoreductase
     0.0063   16.2   0.1      0.011   15.3   0.1    1.4  1  ApbA            Ketopantoate reductase PanE/ApbA
     0.0066   15.5   0.0     0.0089   15.1   0.0    1.2  1  Lycopene_cycl   Lycopene cyclase protein
  ------ inclusion threshold ------
       0.01   15.7   0.5      0.017   15.0   0.5    1.5  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
      0.017   15.2   1.1       0.15   12.1   0.3    2.4  2  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
      0.077   13.0   0.4       0.24   11.4   0.3    1.7  1  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
      0.098   11.5   2.2       0.14   10.9   0.8    1.8  2  Trp_halogenase  Tryptophan halogenase
       0.15   12.0   0.3       0.15   12.0   0.3    1.7  2  NAD_binding_9   FAD-NAD(P)-binding
       0.19   11.8   2.1       0.81    9.8   0.1    2.6  2  Phage_XkdX      Phage uncharacterised protein (Phage_XkdX)
       0.32   10.3   1.3        3.5    7.0   0.4    2.2  2  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
       0.34   10.2   3.1       0.33   10.2   0.7    1.9  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain


Domain annotation for each model (and alignments):
>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  259.6   0.0   7.1e-80   5.8e-77       2     352 .]       7     354 ..       6     354 .. 0.89

  Alignments for each domain:
  == domain 1  score: 259.6 bits;  conditional E-value: 7.1e-80
                                       EEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESSSSTHHSTHHHHHHHHHHHHHHHHHHHHHS CS
                               DAO   2 vviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsglrylpeaselarlslealeelreleeelg 76 
                                       vv+iGGG +G s+Ay+La+ g  V+l+ekg  +gsg++ r +  +++++ + ++     rl ++ +e++++l+eel+
  gi|242398630|ref|YP_002994054.1|   7 VVVIGGGSTGTSIAYHLAKLGvdVILVEKG-YIGSGSTFRCATGIRQQFTDEANI----RLQKYNVERWKRLSEELE 78 
                                       9*****************************.9999*************9866644....****************** PP

                                       STTSEEEEEEEEEESSHHHHHHHHHHHHHHHHTTTTEEEEEHHHHHHHSTT..STTTSEEEEETTEEEEEHHHHHHH CS
                               DAO  77 ididyrrtGllslaadeeelealdkllallleagldaelldaeevrelepa..lpgllgalfypdtgqvdpakltaa 151
                                        d+ +++tG+l+la++eee ea++++++l +++ ++++l+++ee++e+ p    +++l++ ++p++g ++p+k + a
  gi|242398630|ref|YP_002994054.1|  79 YDVNFKQTGYLFLATTEEEVEAFKQNIELHNKFYVPTKLITPEEAKEIVPLlnADEFLAGQWNPTDGKANPFKTVFA 155
                                       *****************************999999***************96444********************** PP

                                       HHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHHHH.HTT...CTTTSEEEEEEEE CS
                               DAO 152 laraaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsdll.gll...keldlpispvrgq 223
                                       +a++a++lG+ei+e+tevtg+  e++ v+gv  +t+ g++ +ad +Vnaa+aw+ ++ +++   ke  +pi+p ++q
  gi|242398630|ref|YP_002994054.1| 156 FAKKARELGAEIYEYTEVTGVIVENKEVQGV--KTNkGII-KADVIVNAANAWAPIInEMVglgKE-FIPIKPYKHQ 228
                                       ********************8788889****..7777997.5599**********99888876444.49******** PP

                                       EEEEEECCTHSTGSGCSEEEEEEEETTTTEEEEEE.TTSEEEEEESSEEETTCSS.TSCSHHHHHHHHHHHHHHSGG CS
                               DAO 224 vlvlkplseklvspaailpvpetdddgrgvyvtpr.kdgrvlvGgtadeesgddd.pevdeedidellealrklfPq 298
                                        + ++pl+e      +i p+  +   +++ yv+++ +dg+vl+G+    e+g+++  +++ + ++ +l+++ +++P+
  gi|242398630|ref|YP_002994054.1| 229 LVKTEPLKE-----GQIEPLVCPPAWNDS-YVLQDgEDGGVLCGTGI--EYGPTYdMTPTYDFLRGVLKWATRIIPA 297
                                       ******999.....466677656666666.66665277777766654..44444447******************** PP

                                       G..CGEEEEEEEEEE.ETTSSEEEEEEETEEEEEEEEECTTTHHHHHHHHHHHHHHH CS
                               DAO 299 l..gdvlrkwaGlrp.lpdglpligetpgvkglylatGhsghGltlapatGkllael 352
                                       l   ++lr+waG+++ +pd +p ig+ +  +g+y+a+G+sghG+++ap++G+++ael
  gi|242398630|ref|YP_002994054.1| 298 LkyVHILRQWAGFYAkTPDSNPAIGKINYIDGFYIAAGFSGHGFMMAPGVGEAMAEL 354
                                       87899**********66*********99999************************97 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   0.0   2.3e-12   1.9e-09       2     180 ..       7     189 ..       6     223 .. 0.76

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 2.3e-12
                                       EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S-EE-TT..SSGGSTC.CHHHHHHHHHHHHTTT-S. CS
                     FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqGgidavlspeqkkagikdspelhrtdtlkaldela. 77 
                                       v+ViG+G  G + A+ +a+ G +v++vek+   +g+t+ +  gi    + e++  + +   ++ ++ + ++l ++  
  gi|242398630|ref|YP_002994054.1|   7 VVVIGGGSTGTSIAYHLAKLGVDVILVEKGYIGSGSTFRCATGIRQQFTDEAN-IRLQKYNVERWKRLSEELEYDVn 82 
                                       9******************************9888888877777766666663.33335578888888999999888 PP

                                       -HHHHHHHHHTHHHHHHHHHHT.......T----B.CCTSSB-EEE-TT-SSTEEEE-.STT-......HHHHHHHH CS
                     FAD_binding_2  78 dqplveafveaapeavdeLeel.......gvpfsr.tedgpvdvrelGglsatartlhdaadarretlvtghallar 146
                                        ++   +f+++ +e+v+ ++++       +vp +  t   p  ++e   l +  + l++ ++++ +  ++ ++ + +
  gi|242398630|ref|YP_002994054.1|  83 FKQTGYLFLATTEEEVEAFKQNielhnkfYVPTKLiT---PEEAKEIVPLLNADEFLAGQWNPT-DGKANPFKTVFA 155
                                       8999*****************9777654444433342...222333322222234444333332.34447789999* PP

                                       HHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEE CS
                     FAD_binding_2 147 lvesarkagvdfqerteadeLivedgrvtGavve 180
                                       ++++ar++g +++e te++ +ive+++v G+  +
  gi|242398630|ref|YP_002994054.1| 156 FAKKARELGAEIYEYTEVTGVIVENKEVQGVKTN 189
                                       ******************************9655 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   3.4   3.1e-07   0.00025       2      58 ..       6     110 ..       5     232 .. 0.58

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 3.1e-07
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEE.....TTHCHHHCSHHHHCHHHHHHHHHHHHH................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxx................ RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlve.....legtclnggcllskallgvaedaeias................ 57 
                                       +vvviGgG  G++ a +la+ g++v+lve     ++ t+   + + ++   ++  +    +                
  gi|242398630|ref|YP_002994054.1|   6 EVVVIGGGSTGTSIAYHLAKLGVDVILVEkgyigSGSTFRCATGIRQQFTDEANIR----Lqkynverwkrlseele 78 
                                       58888888888888888888888888886444333333333333333333333322....23334666666666666 PP

                                       ...............................H CS
                                       ...............................x RF
                       Pyr_redox_2  58 ...............................e 58 
                                                                      +
  gi|242398630|ref|YP_002994054.1|  79 ydvnfkqtgylflatteeeveafkqnielhnK 110
                                       66666666666666666444444444444440 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.6   1.6e-07   0.00013       2      32 ..       5      35 ..       4      53 .. 0.94
   2 ?    2.3   0.0       0.1        81     112     144 ..     157     189 ..     151     201 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.6e-07
                                      EEEEEE--SHHHHHHHHHHHHTTHHEEEEES CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvek 32
                                      ++V+++G+G +G + a  L++ Gv+v+lvek
  gi|242398630|ref|YP_002994054.1|  5 AEVVVIGGGSTGTSIAYHLAKLGVDVILVEK 35
                                      79****************************9 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.1
                                       HHHHHHHTEEETCSEEEECCEECCCCCCCEEEE CS
                     FAD_binding_3 112 vehaeerglqvrfktevesleqdeegvtaevrd 144
                                       +++a+e g+++++ tev+++  ++++v+ + ++
  gi|242398630|ref|YP_002994054.1| 157 AKKARELGAEIYEYTEVTGVIVENKEVQGVKTN 189
                                       6899********************999987665 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.5   3.2e-05     0.026       2      33 ..       6      37 ..       5      78 .. 0.83
   2 !    9.1   0.0   0.00056      0.46      99     161 ..     138     201 ..     123     208 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.2e-05
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSS CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekak 33
                                      +v+viGgG  G   A ++ak g +V+l+ek+ 
  gi|242398630|ref|YP_002994054.1|  6 EVVVIGGGSTGTSIAYHLAKLGVDVILVEKGY 37
                                      79***************************984 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00056
                                       TEEEETT.-CHHH..HHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE- CS
                       HI0933_like  99 grlFpvsdkaedi..vdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlA 161
                                       g+  p++ ka++   v a+ k+++e g +++  tev++v  e++++  vkt +++ ++ad +v A
  gi|242398630|ref|YP_002994054.1| 138 GQWNPTDGKANPFktVFAFAKKARELGAEIYEYTEVTGVIVENKEVQGVKT-NKGIIKADVIVNA 201
                                       666677777765422668899******************************.9*******99977 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   3.4e-06    0.0028     167     197 ..       7      37 ..       2      91 .. 0.61
   2 !    5.7   0.1    0.0093       7.6      89     132 ..     158     202 ..     101     215 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.4e-06
                       Pyr_redox_3 167 vvViGgknSavDaAlelvrkgaeVtvvtrgs 197
                                       vvViGg+ ++  +A++l++ g +V +v +g 
  gi|242398630|ref|YP_002994054.1|   7 VVVIGGGSTGTSIAYHLAKLGVDVILVEKGY 37 
                                       5555555555555555555555555555543 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0093
                       Pyr_redox_3  89 evaksfelpiklfeeVesvkk.edegfevetsketyeAkkviiAt 132
                                       + a++   +i +++eV+ v   ++e   v+t+k+ ++A+ ++ A+
  gi|242398630|ref|YP_002994054.1| 158 KKARELGAEIYEYTEVTGVIVeNKEVQGVKTNKGIIKADVIVNAA 202
                                       44566677899*******9983566688**********9998775 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.2   1.7e-06    0.0014       2      30 ..       7      35 ..       6      63 .. 0.94
   2 ?    6.2   0.2     0.019        15      46      79 ..     156     189 ..     152     191 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.7e-06
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEES CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvver 30
                                      vvv+GgG +g   A  la+lg +V +ve 
  gi|242398630|ref|YP_002994054.1|  7 VVVIGGGSTGTSIAYHLAKLGVDVILVEK 35
                                      9**************************96 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.019
                                       HHHHHHHTTEEEECSEEEEEEEEETTSEEEEEEE CS
                         Pyr_redox  46 lqeklekngievllntkveeiegsedgvesvklk 79 
                                       +++k +++g e++  t+v+ +  ++++v++vk++
  gi|242398630|ref|YP_002994054.1| 156 FAKKARELGAEIYEYTEVTGVIVENKEVQGVKTN 189
                                       6799******************99999****986 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.2   4.7e-07   0.00038       1      29 [.       6      34 ..       6      62 .. 0.85
   2 ?    2.5   0.2     0.076        62     116     147 ..     171     201 ..     166     217 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 4.7e-07
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEEE CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLit 29
                                      +v+ViGgG  G+  A+++a+lG++v+L+ 
  gi|242398630|ref|YP_002994054.1|  6 EVVVIGGGSTGTSIAYHLAKLGVDVILVE 34
                                      59*************************93 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.076
                                       S-EEEEEECTTEEEEEEETTS-EEEECEEEE- CS
                              GIDA 116 eeveeliveekkvkgvvtedgetikakavvia 147
                                        ev+ +ive+k+v+gv+t++g +ika+++v a
  gi|242398630|ref|YP_002994054.1| 171 TEVTGVIVENKEVQGVKTNKG-IIKADVIVNA 201
                                       6899**************998.4667766655 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.1   4.2e-07   0.00035       1      31 [.       9      38 ..       9      74 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 4.2e-07
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrl 31
                                      ++G+G +G ++Ay+Lak g+dv l+ek+  +
  gi|242398630|ref|YP_002994054.1|  9 VIGGGSTGTSIAYHLAKLGVDVILVEKGY-I 38
                                      8**************************83.3 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.2   2.9e-06    0.0024      18      50 ..       5      36 ..       2      61 .. 0.88
   2 ?    1.1   0.1      0.24     2e+02     111     144 ..     163     195 ..     149     216 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.9e-06
                                      EEEEEE--SHHHHHHHHHHHHCTTS-EEEEESS CS
                              Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailers 50
                                      ++vv++G+Gs+G + ay lak  ++ v+++e+ 
  gi|242398630|ref|YP_002994054.1|  5 AEVVVIGGGSTGTSIAYHLAKL-GVDVILVEKG 36
                                      78*******************9.*******985 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.24
                                       TTEEEEESEEEEEEEEETBTEEEEEEEEEHHHHT CS
                              Thi4 111 anvkllnavaveDlivregegvaGvvinwtlvel 144
                                        ++ +++ + v  +iv + ++v+Gv +n  +++ 
  gi|242398630|ref|YP_002994054.1| 163 LGAEIYEYTEVTGVIVEN-KEVQGVKTNKGIIKA 195
                                       567778888888888887.888888888776654 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 !   16.6   0.0   9.6e-06    0.0078       7      75 ..       4      99 ..       2     184 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 9.6e-06
                     NAD_binding_7  7 gkkvlvvGgGevAarkvrklleagakvtvvapev........keele..........elvklaeeelekd......... 58
                                      + +v+v+GgG+ +++ +++l++ g +v++v +          +               +++l++ ++e++         
  gi|242398630|ref|YP_002994054.1|  4 KAEVVVIGGGSTGTSIAYHLAKLGVDVILVEKGYigsgstfrC---AtgirqqftdeANIRLQKYNVERWkrlseeley 79
                                      578***************************9997555554440...144445555564555555554444444444554 PP

                     NAD_binding_7 59 ...legadlviaatddreln 75
                                         ++++  ++ at+++e++
  gi|242398630|ref|YP_002994054.1| 80 dvnFKQTGYLFLATTEEEVE 99
                                      45555666666666655554 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   4.9   6.1e-05      0.05       1     140 [.       6     199 ..       6     204 .. 0.52

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.1e-05
                      FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaee..........qvvtgiareflerl 67 
                                       +vvV+GGg+ G+  A+  a+ G  v+Lve+  ++G  +t    + + ++ + e          +  +++ +e+   +
  gi|242398630|ref|YP_002994054.1|   6 EVVVIGGGSTGTSIAYHLAKLGVDVILVEKG-YIGSGSTFRCATGIRQQFTDEanirlqkynvERWKRLSEELEYDV 81 
                                       59**************************985.555444444433333322222344445333333333333333333 PP

                      FAD_oxidored  68 rq.rgga......rlk.krskwn...........................................tfepevakavl 93 
                                       +  ++g+      +++ +++  +                                             +p     ++
  gi|242398630|ref|YP_002994054.1|  82 NFkQTGYlflattEEEvEAF--KqnielhnkfyvptklitpeeakeivpllnadeflagqwnptdgKANPFKTVFAF 156
                                       33333334443321112222..0234444555555565555555555556666666666555444434444444444 PP

                      FAD_oxidored  94 eemlaeagvtvllntrlvevekegkriesvtveskegrktirAkvfi 140
                                        +  +e g +++  t++++v++e+k++++v+++    +  i+A+v++
  gi|242398630|ref|YP_002994054.1| 157 AKKARELGAEIYEYTEVTGVIVENKEVQGVKTN----KGIIKADVIV 199
                                       444466666666666666666666566666663....4555555555 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   1.4e-05     0.011       1      29 [.       7      35 ..       7      66 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.4e-05
                                      EEEES-SHHHHHHHHHHHHHTHCEEEE-S CS
                              ApbA  1 iailGaGaiGsllaakLakagadvtlilr 29
                                      ++++G G+ G+ +a++Lak g dv+l+ +
  gi|242398630|ref|YP_002994054.1|  7 VVVIGGGSTGTSIAYHLAKLGVDVILVEK 35
                                      689**********************9965 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.1e-05    0.0089       2      33 ..       7      36 ..       6      99 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.1e-05
                     Lycopene_cycl  2 vvviGaGpAglslAarlteakpglkvvlieas 33
                                      vvviG+G  g s+A +l  ak g+ v+l+e +
  gi|242398630|ref|YP_002994054.1|  7 VVVIGGGSTGTSIAYHL--AKLGVDVILVEKG 36
                                      9****************..**********975 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.5   2.1e-05     0.017       2      30 ..       7      35 ..       6     123 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.1e-05
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdi 30
                                      v viG G  G++ia+ +a+ g++V lv+ 
  gi|242398630|ref|YP_002994054.1|  7 VVVIGGGSTGTSIAYHLAKLGVDVILVEK 35
                                      89************************997 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.3   0.00019      0.15      11      41 ..       3      33 ..       1     113 [. 0.87
   2 ?    1.5   0.0      0.35   2.9e+02      69      92 ..     188     211 ..     169     214 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00019
                                      TT-EEEEES-SHHHHHHHHHHHCCT-CEEEE CS
                      Shikimate_DH 11 kekkvlliGaGemaelvakhLlakgvkkvvv 41
                                      ++++v++iG G +++ +a hL++ gv+ ++v
  gi|242398630|ref|YP_002994054.1|  3 SKAEVVVIGGGSTGTSIAYHLAKLGVDVILV 33
                                      5789**********************98877 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.35
                                       HHHHHHT-SEEEE-SSSSS-SB-H CS
                      Shikimate_DH  69 lkellaeadvvisataseepilek 92 
                                        ++ + +adv++ a ++  pi+++
  gi|242398630|ref|YP_002994054.1| 188 TNKGIIKADVIVNAANAWAPIINE 211
                                       4667889*************9985 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.3   0.00029      0.24       2      27 ..       7      32 ..       6      36 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00029
                                      EEEE--SHHHHHHHHHHHTTT--EEE CS
                    NAD_Gly3P_dh_N  2 iavlGaGswGtalAkvlaenghevrl 27
                                      + v+G+Gs Gt++A +la+ g +v l
  gi|242398630|ref|YP_002994054.1|  7 VVVIGGGSTGTSIAYHLAKLGVDVIL 32
                                      89*****************9999876 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.8   0.00018      0.14       2      37 ..       7      39 ..       6      49 .. 0.93
   2 ?   -1.1   0.0      0.78   6.3e+02     162     216 ..     158     211 ..     151     218 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00018
                                      EEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS- CS
                    Trp_halogenase  2 ivivGGGtaGwlaAaalakalkgklevtlveseeig 37
                                      +v++GGG+ G   A +lak +   ++v lve+  ig
  gi|242398630|ref|YP_002994054.1|  7 VVVIGGGSTGTSIAYHLAKLG---VDVILVEKGYIG 39
                                      9********************...9******99887 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.78
                                       HHHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS-EEE-SEEEE-SGGG-IIIII CS
                    Trp_halogenase 162 rvaearGvtrvegkvvevqldedgrveslrledgreveadlfiDcsGfrgllieq 216
                                       + a + G ++ e + v+ ++ e+ +v+++++++g  ++ad ++ +    + +i++
  gi|242398630|ref|YP_002994054.1| 158 KKARELGAEIYEYTEVTGVIVENKEVQGVKTNKGI-IKADVIVNAANAWAPIINE 211
                                       67888899999999999999999999999999997.9999999887666666665 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.3   0.00018      0.15       1      43 [.       8      45 ..       8      52 .. 0.91
   2 ?   -2.7   0.1       6.3   5.1e+03     121     151 ..     170     200 ..     155     202 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00018
                     NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsepgagrvwr 43
                                      +++G+G +G++++ +L++       +++ l+++  +g+g+ +r
  gi|242398630|ref|YP_002994054.1|  8 VVIGGGSTGTSIAYHLAKL-----GVDVILVEKGYIGSGSTFR 45
                                      69*****************.....5********9999888776 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 6.3
                     NAD_binding_9 121 raevvdleeradgqavlladgaslaadaVvL 151
                                        +ev+ +  ++++++ +++++  ++ad +v 
  gi|242398630|ref|YP_002994054.1| 170 YTEVTGVIVENKEVQGVKTNKGIIKADVIVN 200
                                       4688888888888888889999999998885 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 ?    9.8   0.1   0.00099      0.81      21      36 ..     112     127 ..     110     128 .. 0.92
   2 ?    0.1   0.4         1   8.2e+02      31      37 ..     169     175 ..     168     176 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00099
                        Phage_XkdX  21 aVgkgkITkeeYeeIT 36 
                                       +V+ + IT+ee +eI+
  gi|242398630|ref|YP_002994054.1| 112 YVPTKLITPEEAKEIV 127
                                       9**************8 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1
                        Phage_XkdX  31 eYeeITG 37 
                                       eY+e+TG
  gi|242398630|ref|YP_002994054.1| 169 EYTEVTG 175
                                       9*****9 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 ?    7.0   0.4    0.0043       3.5      37      66 ..       5      34 ..       2      40 .. 0.91
   2 ?    1.7   0.0      0.17   1.4e+02      50      99 ..     155     202 ..     154     206 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0043
                                      SEEEEES-SHHHHHHHHHHHHTT-EEEEES CS
                      2-Hacid_dh_C 37 ktvGiiGlGrIGqavakrlkafgmkviayd 66
                                       +v +iG G+ G+++a  l+++g++vi ++
  gi|242398630|ref|YP_002994054.1|  5 AEVVVIGGGSTGTSIAYHLAKLGVDVILVE 34
                                      6799**********************9876 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.17
                                       HHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-SEEEE-S CS
                      2-Hacid_dh_C  50 avakrlkafgmkviaydrskkkeeeeeelgvelvsleellaesDivslhl 99 
                                       a+ak+++++g++++ y         +e+++v+ v+ ++ + ++D++++++
  gi|242398630|ref|YP_002994054.1| 155 AFAKKARELGAEIYEYTEVTGVI--VENKEVQGVKTNKGIIKADVIVNAA 202
                                       5799**********999997755..56667889999999999***99876 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.7   0.00041      0.33      28      58 ..       4      34 ..       1      39 [. 0.91
   2 ?   -0.7   0.1      0.87   7.1e+02      71      99 ..     174     202 ..     151     207 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00041
                                      --EEEEESTSHHHHHHHHHHHHTT-EEEEEE CS
                       AlaDh_PNT_C 28 pakvlviGgGvaGlqAiatakglgakVtvlD 58
                                      +a+v+viGgG  G++ +   ++lg +V +++
  gi|242398630|ref|YP_002994054.1|  4 KAEVVVIGGGSTGTSIAYHLAKLGVDVILVE 34
                                      79************************99876 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.87
                                       TTCECEEHCHHHHHHHHHHHH-SEEEE-- CS
                       AlaDh_PNT_C  71 gakfvevlksqeellaeavkeadvvigtv 99 
                                        + +ve ++ q  + ++ + +adv++ ++
  gi|242398630|ref|YP_002994054.1| 174 TGVIVENKEVQGVKTNKGIIKADVIVNAA 202
                                       33335557777777777777888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.48
# Mc/sec: 2429.78
//
Query:       gi|242398631|ref|YP_002994055.1|  [L=41]
Description: hypothetical protein TSIB_0641 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       266  (0.0148363); expected 358.6 (0.02)
Passed bias filter:                      138  (0.00769703); expected 358.6 (0.02)
Passed Vit filter:                         3  (0.000167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 291.26
//
Query:       gi|242398632|ref|YP_002994056.1|  [L=491]
Description: sodium:solute symport protein [Thermococcus sibiricus MM 739]
Scores for 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-38  131.0  31.9      5e-38  131.0  31.9    1.6  2  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 ?   -4.2   1.0      0.31   5.6e+03     243     262 ..       8      27 ..       3      30 .. 0.49
   2 !  131.0  31.9   2.8e-42     5e-38       3     401 ..      36     424 ..      34     428 .. 0.88

  Alignments for each domain:
  == domain 1  score: -4.2 bits;  conditional E-value: 0.31
                               SSF 243 ivlilvligmisiilfaikl 262
                                       i++i+ ++++i +++fa+k+
  gi|242398632|ref|YP_002994056.1|   8 IIVIVYFVLIIGLGVFAKKF 27 
                                       33333344445566666665 PP

  == domain 2  score: 131.0 bits;  conditional E-value: 2.8e-42
                               SSF   3 lagrsltgfvlglslaasnisaasfvGlaGavaasGlavvllelgalllvlllllllaerlrnagalTlpdylskRf 79 
                                       +agr+l+   + +++aa+ +++ s v +   ++++G++ +++++   +++ l +l  a  + ++ ++T+p++++  +
  gi|242398632|ref|YP_002994056.1|  36 VAGRNLGLALTTVAIAAEWLGGTSTVAVGQWAFKYGISPIWYNISTSFGMFLFGLTWAALYHKMKVYTIPEMIERVY 112
                                       89***********************************************************************9888 PP

                               SSF  80 kgkrilvylsalslllvitlklsvdlvggaklielalGlnyetavlllaaltalYtviGGllAvvytdtiqavlmlv 156
                                       + +   ++ sa   +++  l  +v++ + ++l+  al ++++ta+++ ++ +++Yt+ GG+ +v +t+ +  +++ +
  gi|242398632|ref|YP_002994056.1| 113 DRRT--RLTSAAFFIIAYLLLSAVQIGAIGALFSGALRMDINTAIIIAGLGITIYTLAGGMYSVALTNFVHVFVIWI 187
                                       7777..9999999999999999******************************************************* PP

                               SSF 157 galilliivllevGgleslveklkeaapkvvdllt.pdslkllrdpltalslwlglvl....GvaglphilvRflaa 228
                                       g     ++ +++vG ++ + + l +   +++  lt +++l+ +     + s  l+++l    G++ ++  ++ ++aa
  gi|242398632|ref|YP_002994056.1| 188 GIGAAYLFYMSKVGWYDGIARALDQWVAQGAITLTsEKALDPFG---MGYSTVLAWILggitGTFAAQASVQPIFAA 261
                                       **************999999999888886644444144544444...44555556666111156667********** PP

                               SSF 229 kdakailkgvlkltivlilvligmisiilfaiklagavpkavgtevgvsniaypeLvvkllpnllaGlllavmlAai 305
                                       kd k++ ++ l    +++ + i++ si+l +i+l    +++vgt+ +   +a+p   + + +++l G+ +a ++Aai
  gi|242398632|ref|YP_002994056.1| 262 KDWKTAKRAALLTPLIVAPLGILVTSIVLATIALH---GNYVGTDTR---LAFPLALMMIPNPILSGITMAGVFAAI 332
                                       *********99877777777777777777777765...569999875...79**9999******************* PP

                               SSF 306 mstltslllsassaftkDlYkkirrkasakekelvgvsriivlvvislaillavqeeqkgvlklvelafaglasavl 382
                                        st + +ll  +++f++D+Y   +r + a + e+v+v r+ + + + ++i++a+  ++  ++++v++a+ g    v+
  gi|242398632|ref|YP_002994056.1| 333 ASTEAPILLGMATMFVRDIYHTKLRPK-ADDDEIVKVTRLGTFIAGIISIIMALAIKELPIATYVNYAMRG---SVF 405
                                       ********************9888887.7999**********************************99865...577 PP

                               SSF 383 avillalfwkrvneqGAla 401
                                        ++ la++w +   + A++
  gi|242398632|ref|YP_002994056.1| 406 ILLALAIYWAKPSPKAAII 424
                                       8999******988887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (491 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       988  (0.0551063); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.49
# Mc/sec: 3030.30
//
Query:       gi|242398633|ref|YP_002994057.1|  [L=41]
Description: hypothetical protein TSIB_0643 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       224  (0.0124937); expected 358.6 (0.02)
Passed bias filter:                      145  (0.00808746); 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: 00:00:00.45
# Mc/sec: 274.31
//
Query:       gi|242398634|ref|YP_002994058.1|  [L=51]
Description: 50S ribosomal protein L39e [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-21   75.3  14.1    2.6e-21   75.0  14.1    1.2  1  Ribosomal_L39  Ribosomal L39 protein


Domain annotation for each model (and alignments):
>> Ribosomal_L39  Ribosomal L39 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.0  14.1   1.4e-25   2.6e-21       1      42 []       9      50 ..       9      50 .. 0.99

  Alignments for each domain:
  == domain 1  score: 75.0 bits;  conditional E-value: 1.4e-25
                     Ribosomal_L39  1 kKlrLaKalkqNrpvPaWvrlktdrkvrynpkrRhWRrtkLk 42
                                      kKlrLaKa kqNr++P+Wv++kt+rkv ++pkrR WRrtkLk
  gi|242398634|ref|YP_002994058.1|  9 KKLRLAKAAKQNRRIPVWVIVKTNRKVLTHPKRRYWRRTKLK 50
                                      7****************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      208  (0.0116013); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 374.89
//
Query:       gi|242398635|ref|YP_002994059.1|  [L=86]
Description: 50S ribosomal protein L31e [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.9e-14   52.6   0.8    5.2e-14   52.2   0.8    1.0  1  Ribosomal_L31e  Ribosomal protein L31e


Domain annotation for each model (and alignments):
>> Ribosomal_L31e  Ribosomal protein L31e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.2   0.8   2.9e-18   5.2e-14       5      75 ..       5      75 ..       4      78 .. 0.95

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 2.9e-18
                    Ribosomal_L31e  5 reytInihkrihgvgfkkraprAlkeikkfamkemgtpdvridtrLnkavwakgirnvpyrirvrlsrkrn 75
                                      r y+I i k i+ v + kraprA   +k+f++++++  +v + t++n+ +w++gi+++p ++rv+++  + 
  gi|242398635|ref|YP_002994059.1|  5 RVYVIPIRKIIKIVPRWKRAPRAAHYVKEFIARHTKADEVLVGTDVNEKIWERGIEKPPSKLRVKVTIEER 75
                                      78**************************************************************9987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 589.84
//
Query:       gi|242398636|ref|YP_002994060.1|  [L=243]
Description: Translation initiation factor 6 [Thermococcus sibiricus MM 739]
Scores for complete 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  226.8   0.0    1.8e-67  226.6   0.0    1.1  1  eIF-6     eIF-6 family


Domain annotation for each model (and alignments):
>> eIF-6  eIF-6 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  226.6   0.0     1e-71   1.8e-67       1     196 [.      20     220 ..      20     221 .. 0.97

  Alignments for each domain:
  == domain 1  score: 226.6 bits;  conditional E-value: 1e-71
                                       .E-BTTB--HHHH-EE-SSEEEE-TTS-HHHHHHHHHHHT-EEEE--BTTBS-HHHH-EE-SSEEEEETT--HHHHH CS
                             eIF-6   1 rlsiegsseiGvfarltnkyalvpegveeefvkaieeeLkvevvettiagsrlvGslvvgNsngllvpstvtdeele 77 
                                       rl++e+s+++Gvf  +t+k+alv+eg++e++ ++++e+Lkv+++et+i++sr+vG+++++Ns++++vp ++ d el+
  gi|242398636|ref|YP_002994060.1|  20 RLDFENSPYLGVFGLATDKFALVREGLQEKKLNVLREVLKVPLIETSIMKSRIVGIFAAANSRAIVVPYYIWDAELD 96 
                                       789************************************************************************** PP

                                       HHHHHHH.....---EEE--SS--HHHHEEE-SSEEEE-GGGGG.GHHHHHHHHTSEEEE--BTTBS-TTTSEEE-S CS
                             eIF-6  78 klkeslk.....leverleekltAlGNvilaNDkvAlvhpdlsketveiiadvLgvevvrgtiagiktvGsaavvtn 149
                                       k+k sl+     +++e + +kltA+GN+il+NDk+Alv+ ++++e++++ +d+++vev+rg ia+++ vGs++vvtn
  gi|242398636|ref|YP_002994060.1|  97 KIKASLQengldVTIEPVLSKLTAFGNLILVNDKAALVSAKFTREEAKQFEDIFDVEVERGIIANYHAVGSVGVVTN 173
                                       ******99995555599************************************************************ PP

                                       SEEEE-TT--HHHHHHHHHHHT-SEEE--BTTTBS-GGGTEEE-SS- CS
                             eIF-6 150 kgllvhpkateeeleeleellkveveagTvNrGsklvgsglvaNdkg 196
                                       kg+l+hp+at+eele+le+l+kv++ +gT N+G+++vgs+++aN+ g
  gi|242398636|ref|YP_002994060.1| 174 KGGLIHPEATDEELEWLESLFKVDFYVGTANMGVPFVGSCMIANSFG 220
                                       ********************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.33s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1454.55
//
Query:       gi|242398637|ref|YP_002994061.1|  [L=78]
Description: 50S ribosomal protein LX [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.1e-11   42.1   0.1    1.2e-10   41.6   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 !   41.6   0.1   6.5e-15   1.2e-10      65     121 .]       2      58 ..       1      58 [. 0.94

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 6.5e-15
                                       ..............TEEEEEEEEEEESSHHHHHHHHHHHHHHHS---GGGEEEEEEE CS
                    Ribosomal_L18A  65 kvknygiwlrydsrsgthnfykeyrdlteegaveqvYselgsrhrakrssIqIekve 121
                                       +vk + +   ++   ++ +f+keyr+l+ e++ e v+s++gs+hr+kr +I Ie++e
  gi|242398637|ref|YP_002994061.1|   2 EVKIFRVKGTFEKGGKKFRFTKEYRALKPEDVRELVFSDIGSKHRVKRAKIFIESIE 58 
                                       5888888889999999**************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 561.55
//
Query:       gi|242398638|ref|YP_002994062.1|  [L=152]
Description: Prefoldin subunit alpha [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-29  102.7   4.3    1.6e-29  102.2   4.3    1.2  1  Prefoldin        Prefoldin subunit
    1.1e-06   28.6  11.1    0.00016   21.6   3.0    2.2  2  Prefoldin_2      Prefoldin subunit
    0.00052   19.9  12.1     0.0062   16.4   4.5    2.0  2  ERM              Ezrin/radixin/moesin family
    0.00081   19.4   1.8     0.0014   18.6   1.8    1.3  1  PriC             Primosomal replication protein priC
     0.0012   19.5   4.1     0.0012   19.5   4.1    2.4  2  SlyX             SlyX
     0.0013   18.9   2.5     0.0013   18.9   2.5    1.6  1  Fib_alpha        Fibrinogen alpha/beta chain family
     0.0027   18.2   0.5     0.0027   18.2   0.5    2.1  2  DUF16            Protein of unknown function DUF16
     0.0029   17.0   3.4     0.0029   17.0   3.4    1.8  2  FmiP_Thoc5       Fms-interacting protein/Thoc5
     0.0042   16.8   7.5      0.028   14.1   1.3    2.2  2  YkyA             Putative cell-wall binding lipoprotein
     0.0054   17.0   3.1      0.011   16.0   2.5    1.9  1  DUF5082          Domain of unknown function (DUF5082)
     0.0092   16.3   1.1      0.016   15.5   0.5    1.7  1  Gp-FAR-1         Nematode fatty acid retinoid binding protein
  ------ inclusion threshold ------
       0.01   16.0   5.7      0.089   13.0   1.3    2.3  2  KLRAQ            Predicted coiled-coil domain-containing prot
      0.013   15.8   2.6      0.013   15.8   2.6    2.1  2  OmpH             Outer membrane protein (OmpH-like)
      0.017   15.2   0.8      0.024   14.7   0.1    1.6  1  Prefoldin_3      Prefoldin subunit
      0.026   14.3   2.5      0.026   14.3   2.5    1.5  2  DUF724           Protein of unknown function (DUF724)
      0.026   14.5   1.5      0.044   13.8   0.2    1.9  2  DUF1664          Protein of unknown function (DUF1664)
      0.027   14.0   5.9      0.027   14.0   5.9    1.9  2  PspA_IM30        PspA/IM30 family
       0.04   14.1   3.0       0.04   14.1   3.0    1.8  2  CENP-Q           CENP-Q, a CENPA-CAD centromere complex subun
      0.046   13.9   2.0      0.046   13.9   2.0    2.1  2  Jnk-SapK_ap_N    JNK_SAPK-associated protein-1
      0.052   12.4   0.1      0.093   11.6   0.1    1.3  1  BRE              Brain and reproductive organ-expressed prote
      0.066   13.3   0.2      0.066   13.3   0.2    1.9  2  COG2             COG (conserved oligomeric Golgi) complex com
      0.067   12.6   0.2      0.094   12.1   0.2    1.2  1  TraF_2           F plasmid transfer operon, TraF, protein
      0.071   12.7  11.7       0.26   10.8   1.7    2.0  2  HAUS-augmin3     HAUS augmin-like complex subunit 3
       0.12   10.6   0.7       0.17   10.1   0.7    1.2  1  Fusion_gly       Fusion glycoprotein F0
       0.12   11.2  10.9      0.034   13.0   2.0    2.0  2  Spc7             Spc7 kinetochore protein
       0.13   12.4   8.7       0.12   12.5   0.9    2.1  2  UPF0242          Uncharacterised protein family (UPF0242) N-t
       0.13   12.6   2.5        1.2    9.6   0.4    2.7  2  FlaC_arch        Flagella accessory protein C (FlaC)
       0.14   12.9   2.9        3.3    8.4   2.4    2.2  2  FliD_N           Flagellar hook-associated protein 2 N-termin
       0.15   12.0   3.8       0.15   12.1   0.4    2.1  2  Laminin_II       Laminin Domain II
       0.18   11.8   4.0       0.57   10.2   0.7    2.1  2  Noelin-1         Neurogenesis glycoprotein
       0.18   12.2   8.6       0.09   13.2   3.1    2.1  2  Uso1_p115_C      Uso1 / p115 like vesicle tethering protein, 
        0.2   11.2   3.7       0.09   12.3   0.5    1.8  2  HAUS6_N          HAUS augmin-like complex subunit 6 N-terminu
       0.29    9.6   0.8       0.38    9.2   0.8    1.0  1  FUSC             Fusaric acid resistance protein family
       0.37   11.0   6.9        1.7    8.8   6.9    2.0  1  Uds1             Up-regulated During Septation
       0.46   10.3   3.8        1.6    8.5   0.4    2.3  2  Synaptobrevin    Synaptobrevin
       0.51    8.2   3.2       0.15    9.9   0.1    1.5  2  V_ATPase_I       V-type ATPase 116kDa subunit family
       0.58   10.3   4.5        0.2   11.9   0.9    2.0  2  PEP-utilisers_N  PEP-utilising enzyme, N-terminal
       0.59   10.3   6.4       0.39   10.8   1.5    2.1  2  DUF2730          Protein of unknown function (DUF2730)
       0.69   10.4   5.1       0.47   10.9   0.7    2.3  2  NPV_P10          Nucleopolyhedrovirus P10 protein
       0.77   10.4   6.5       0.49   11.1   0.9    2.2  2  YabA             Initiation control protein YabA
       0.82    9.9   7.7       0.27   11.5   0.8    2.3  2  Spc24            Spc24 subunit of Ndc80
       0.86    9.7  15.3        2.2    8.4   2.9    2.5  2  TolA_bind_tri    TolA binding protein trimerisation
        1.1    8.7   9.1      0.093   12.2   1.7    2.1  2  DegS             Sensor protein DegS
        1.2    8.5   5.6        0.2   11.0   0.9    1.9  2  Helo_like_N      Fungal N-terminal domain of STAND proteins
        1.3    9.4  11.5        1.4    9.3   3.9    2.8  3  Tup_N            Tup N-terminal
        1.3    9.0   3.7       0.42   10.5   0.2    1.8  2  EMP24_GP25L      emp24/gp25L/p24 family/GOLD
        1.4    9.0  12.8       0.34   11.0   4.3    2.1  2  ADIP             Afadin- and alpha -actinin-Binding
        1.8    8.7   8.2        1.4    9.1   2.0    2.1  2  CREPT            Cell-cycle alteration and expression-elevate
        1.9    8.8  11.3         16    5.9   4.1    2.9  2  BLOC1_2          Biogenesis of lysosome-related organelles co
        5.3    7.6   9.6       0.47   10.9   1.7    2.5  2  DUF4140          N-terminal domain of unknown function (DUF41
        6.3    6.9  16.1       0.29   11.2   5.2    2.4  2  DHR10            Designed helical repeat protein 10 domain
        7.4    5.2  12.1       0.15   10.8   3.3    2.0  2  Tektin           Tektin family
        7.4    7.1  18.0       0.67   10.4   4.6    2.7  2  ZapB             Cell division protein ZapB


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 !  102.2   4.3   4.8e-32   1.6e-29       2     120 .]      23     142 ..      22     142 .. 0.98

  Alignments for each domain:
  == domain 1  score: 102.2 bits;  conditional E-value: 4.8e-32
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT..-TT-EEEEEEETTEEEEEE--STTEEEEEEETTEEEEEEHHH CS
                         Prefoldin   2 keeleslqaelaqlkeaieelektletlktlkk.edegkevlvplgaglyvkaevkdtdkvlvdlGagyyvekslee 77 
                                       + +++ l+++l+ l+   +e+++++etl+ lk+ ede  e+lvp+gag+++k++v+d+++++v++Gagy++eksl++
  gi|242398638|ref|YP_002994062.1|  23 QGQAQLLAQNLELLNLGRNEFQAVKETLEGLKDvEDEKPEILVPIGAGSFLKGRVEDKNNAIVSVGAGYAIEKSLDD 99 
                                       67899************************************************************************ PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  78 Aiellkkkleelekqlekleeeleklkdqittleanlaqlyqk 120
                                       Ai++l+++++e+e+++ k +e+l +l  +++ l +++++l+q+
  gi|242398638|ref|YP_002994062.1| 100 AIAYLDERIKEYESAIAKTQEALHQLEHKLQDLAEKAQKLQQQ 142
                                       ****************************************996 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   1.2   0.00042      0.14       5      43 ..      17      55 ..      13      61 .. 0.91
   2 !   21.6   3.0   4.7e-07   0.00016      56     106 .]      93     143 ..      76     143 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00042
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-T CS
                       Prefoldin_2  5 nkfqqlqqqlqqlaqqikqletqlkelelvleelellde 43
                                       ++q lq q q laq+++ l+   +e + v+e+le l++
  gi|242398638|ref|YP_002994062.1| 17 YEYQLLQGQAQLLAQNLELLNLGRNEFQAVKETLEGLKD 55
                                      5899*******************************9987 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 4.7e-07
                                       EEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCTS-- CS
                       Prefoldin_2  56 vkqdkeevkeeLeerketlekeiktlekqleklekeleelkeelqkklqqq 106
                                       ++++++++++ L+er++++e  i++ ++ l++le +l++l e+ qk++qqq
  gi|242398638|ref|YP_002994062.1|  93 IEKSLDDAIAYLDERIKEYESAIAKTQEALHQLEHKLQDLAEKAQKLQQQQ 143
                                       6889********************************************997 PP

>> ERM  Ezrin/radixin/moesin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.8     0.005       1.7      20      75 ..       4      59 ..       1      67 [. 0.87
   2 !   16.4   4.5   1.8e-05    0.0062      10      50 ..     104     144 ..      99     147 .. 0.93

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.005
                               ERM 20 eaekaqeaLreseetaelLaekarraeeeaelLeqkaaeaeeeiqrlkesaekeee 75
                                      e+ +++e+L++   + +lL+ +a+ + ++ elL+  ++e+++ ++ l+  +  e+e
  gi|242398638|ref|YP_002994062.1|  4 EMSERNEQLERLAYEYQLLQGQAQLLAQNLELLNLGRNEFQAVKETLEGLKDVEDE 59
                                      89999*************************************99999876665555 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 1.8e-05
                               ERM  10 leerLkqlqeeaekaqeaLreseetaelLaekarraeeeae 50 
                                       l er+k++++ ++k+qeaL++ e + + Laeka+++++++ 
  gi|242398638|ref|YP_002994062.1| 104 LDERIKEYESAIAKTQEALHQLEHKLQDLAEKAQKLQQQQA 144
                                       789**********************************9875 PP

>> PriC  Primosomal replication protein priC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   1.8   4.1e-06    0.0014      60     141 ..       8     143 ..       3     149 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 4.1e-06
                                       TTT-HHHHHHHHHHHHHHHHHHHHHHHHHTTTSSSSST....................................... CS
                              PriC  60 eenraeqvaflaerlvaqieAlqrelattelrkkeakqkkksr.................................. 102
                                        +++ e+ a+  + l+ q + l + l+  +l ++e ++ k++                                   
  gi|242398638|ref|YP_002994062.1|   8 RNEQLERLAYEYQLLQGQAQLLAQNLELLNLGRNEFQAVKETLeglkdvedekpeilvpigagsflkgrvedknnai 84 
                                       34459********************************9775559********************************* PP

                                       .....................TTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHT....T- CS
                              PriC 103 .....................kkshqlyqelakhqeyerrLeemiaereqqlekaqslae 141
                                                            ++ ++ ++ +ak qe++++Le ++++  ++ +k q+ ++
  gi|242398638|ref|YP_002994062.1|  85 vsvgagyaiekslddaiayldERIKEYESAIAKTQEALHQLEHKLQDLAEKAQKLQQ-QQ 143
                                       *******************9999999999****************999877776666.33 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   3.3      0.51   1.7e+02       7      47 ..      11      50 ..       4      62 .. 0.43
   2 !   19.5   4.1   3.4e-06    0.0012      11      55 ..     100     144 ..      95     149 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.51
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT- CS
                              SlyX  7 eLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerl 47
                                      +LE +la+  ++++   + +a+  + +   + ++++++e l
  gi|242398638|ref|YP_002994062.1| 11 QLE-RLAYEYQLLQGQAQLLAQNLELLNLGRNEFQAVKETL 50
                                      333.4444444444444444444444444444444444444 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 3.4e-06
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXX CS
                              SlyX  11 klafqedtieeLndvvaeqqqqidrlqrqlrllaerlkeleessg 55 
                                        +a++++ i+e   ++a+ q+ + +l+++l+ lae+ ++l+++++
  gi|242398638|ref|YP_002994062.1| 100 AIAYLDERIKEYESAIAKTQEALHQLEHKLQDLAEKAQKLQQQQA 144
                                       79***************************************9976 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 !   18.9   2.5   3.8e-06    0.0013      80     131 ..      91     142 ..      39     144 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 3.8e-06
                                       HHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  80 kksskeleeeilrlketidaqesnirvLqnvlesneqkiqkLeqdidqkerk 131
                                         ++k+l++ i++l+e+i++ es i + q+ l+++e+k+q+L ++ ++++++
  gi|242398638|ref|YP_002994062.1|  91 YAIEKSLDDAIAYLDERIKEYESAIAKTQEALHQLEHKLQDLAEKAQKLQQQ 142
                                       567899***************************************9999875 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.5       1.8     6e+02      63      93 ..      25      51 ..       2      59 .. 0.37
   2 !   18.2   0.5   7.9e-06    0.0027       4      72 ..      75     144 ..      72     149 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 1.8
                                      HHHHHHHHHHHHHH..........HHHHHHHHHH CS
                             DUF16 63 kikelkveqkaqgeeln...kvdetleliletLq 93
                                      + + l ++       l+      + ++ + etL+
  gi|242398638|ref|YP_002994062.1| 25 QAQLLAQN-------LEllnLGRNEFQAVKETLE 51
                                      22222111.......1122122333444444444 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 7.9e-06
                                       XXXXXXXXX..X.XTTB-BHHHHHHB-..BHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHH CS
                             DUF16   4 GsfneivKk.iPvkteYVTrkqlnefkdsnkqrLkkieakvdklgeqinkleqkvekqgekikelkveqk 72 
                                       G ++  +   + v   Y   k l++     ++r+k+ e  ++k +e +++le+k + + ek ++l+++q 
  gi|242398638|ref|YP_002994062.1|  75 GRVEDKNNAiVSVGAGYAIEKSLDDAIAYLDERIKEYESAIAKTQEALHQLEHKLQDLAEKAQKLQQQQA 144
                                       55555555446678899999****9777789**********************************99885 PP

>> FmiP_Thoc5  Fms-interacting protein/Thoc5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.6       2.6   8.9e+02      30      45 ..       8      23 ..       3      56 .. 0.58
   2 !   17.0   3.4   8.6e-06    0.0029     105     154 ..      95     144 ..      94     152 .] 0.90

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 2.6
                        FmiP_Thoc5 30 khlqlqNllyEkshle 45
                                       + ql+ l yE + l+
  gi|242398638|ref|YP_002994062.1|  8 RNEQLERLAYEYQLLQ 23
                                      3444444444444444 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 8.6e-06
                        FmiP_Thoc5 105 kelaeqlkeleekkkkleqeieekkkfLssLppkLkslkkatkplqealg 154
                                       k+l++++  l e+ k+ e++i++ ++ L +L+ kL++l++++++lq++  
  gi|242398638|ref|YP_002994062.1|  95 KSLDDAIAYLDERIKEYESAIAKTQEALHQLEHKLQDLAEKAQKLQQQQA 144
                                       689999999************************************99754 PP

>> YkyA  Putative cell-wall binding lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.6     0.019       6.5      47      99 ..       6      58 ..       1      63 [. 0.79
   2 !   14.1   1.3   8.4e-05     0.028      52     103 ..      93     141 ..      81     147 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.019
                              YkyA 47 de.fdkikklsdealenveeReellekekesieeakeefekikeeieeiedeel 99
                                      +e +++++ l+ e  ++++ + +ll++  e ++  ++ef+ +ke++e ++d e 
  gi|242398638|ref|YP_002994062.1|  6 SErNEQLERLAYEY-QLLQGQAQLLAQNLELLNLGRNEFQAVKETLEGLKDVED 58
                                      44467777777774.68899999**********************999977544 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 8.4e-05
                              YkyA  52 ikklsdealenveeReellekekesieeakeefekikeeieeiedeelkkea 103
                                       i+k  d+a+++++eR ++ e+   +i +++e++ +++ +++++ ++++k + 
  gi|242398638|ref|YP_002994062.1|  93 IEKSLDDAIAYLDERIKEYES---AIAKTQEALHQLEHKLQDLAEKAQKLQQ 141
                                       777788888888888666666...8888888888888888888655544433 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   2.5   3.3e-05     0.011       7     122 ..      14     133 ..       8     134 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.3e-05
                           DUF5082   7 klqaqiaelrseiaaleekIerLkeaktklsdekeslk......qkkkklekplnssesWkGkeennydgirsnles 77 
                                       +l +++  l+++++ l + +e L   + + +++ke+l+      ++k ++  p+   + +kG+ e++ + i+s +  
  gi|242398638|ref|YP_002994062.1|  14 RLAYEYQLLQGQAQLLAQNLELLNLGRNEFQAVKETLEglkdveDEKPEILVPIGAGSFLKGRVEDKNNAIVS-VG- 88 
                                       6667777788888888888888885555555555554411111144444444454555777777766665555.43. PP

                           DUF5082  78 syqtyvdkldelidaieeEIerLenqiseaqgvldtlqsqlnslk 122
                                       +  ++++ ld++i+ ++e I+++e+ i + q  l +l+ +l++l+
  gi|242398638|ref|YP_002994062.1|  89 AGYAIEKSLDDAIAYLDERIKEYESAIAKTQEALHQLEHKLQDLA 133
                                       4447999************************************96 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 !   15.5   0.5   4.8e-05     0.016       7      80 ..      65     141 ..      59     148 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.8e-05
                          Gp-FAR-1   7 lPsevvealknltdeekaqlkevvknykgyknedellaalKkk...spaLyekaeklqaklkekvdkLspeakeFvk 80 
                                       +P    ++lk   ++  ++++ v   y+  k+ d+++a l ++   +++  +k ++   +l++k++ L ++a+++ +
  gi|242398638|ref|YP_002994062.1|  65 VPIGAGSFLKGRVEDKNNAIVSVGAGYAIEKSLDDAIAYLDERikeYESAIAKTQEALHQLEHKLQDLAEKAQKLQQ 141
                                       66666677777777888899999999************99876444788888888888999************9866 PP

>> KLRAQ  Predicted coiled-coil domain-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.2     0.074        25       2      20 ..      14      32 ..       8      59 .. 0.84
   2 ?   13.0   1.3   0.00026     0.089      29      71 ..     102     144 ..      95     152 .] 0.89

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.074
                             KLRAQ  2 klaqeYsKlraqakvLkka 20
                                      +la eY+ l+ qa++L + 
  gi|242398638|ref|YP_002994062.1| 14 RLAYEYQLLQGQAQLLAQN 32
                                      89************99765 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00026
                             KLRAQ  29 aslkeelkekeqslrkseqEvdsLtFrNkqLekrvellqeele 71 
                                       a l e +ke+e+++ k+++ +  L+ + + L+ + + lq++ +
  gi|242398638|ref|YP_002994062.1| 102 AYLDERIKEYESAIAKTQEALHQLEHKLQDLAEKAQKLQQQQA 144
                                       5699***********************************9866 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.5       0.3     1e+02      31      74 ..       8      45 ..       2      71 .. 0.43
   2 ?   15.8   2.6   3.9e-05     0.013      33      87 ..      95     143 ..      75     150 .. 0.54

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.3
                                      HHHHHHHHHHHHHHHHHHHHHHTTTS.-HHHHHH.HHHHHHHHHH CS
                              OmpH 31 lqaeleakekelqklqeelqkkakklekeekeqe.lqkkeqelqq 74
                                      ++++le+++ e+q lq + q        ++   e l+  ++e+q+
  gi|242398638|ref|YP_002994062.1|  8 RNEQLERLAYEYQLLQGQAQL------LAQNL-ElLNLGRNEFQA 45
                                      333333333333333333321......11111.123333333333 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 3.9e-05
                                       HHHHHHHHHHHHHHHHHHHHTTTS.-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              OmpH  33 aeleakekelqklqeelqkkakklekeekeqelqkkeqelqqkqqqkaqelqkkq 87 
                                       + l++  + l++ ++e++   ++   ++ +++l ++e +lq+ +++kaq+lq++q
  gi|242398638|ref|YP_002994062.1|  95 KSLDDAIAYLDERIKEYE---SA--IAKTQEALHQLEHKLQD-LAEKAQKLQQQQ 143
                                       444444444444444443...22..33444444444444444.444444444444 PP

>> Prefoldin_3  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   7.2e-05     0.024       2      99 .]      31     130 ..      30     130 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 7.2e-05
                       Prefoldin_3   2 kslyklreweaeydglkeeisalkeeddateedllriard..fegslvtekEveeilGekqgvtrskqQvvdlisrR 76 
                                       ++l+ l+   +e++++ke ++ lk+ +d + e l+ i+    ++g++ +++   + +G    +++s +  +  ++ R
  gi|242398638|ref|YP_002994062.1|  31 QNLELLNLGRNEFQAVKETLEGLKDVEDEKPEILVPIGAGsfLKGRVEDKNNAIVSVGAGYAIEKSLDDAIAYLDER 107
                                       57788889999************************998754367777777777777899999*************** PP

                       Prefoldin_3  77 iDYVkqniktlekrleaaenkla 99 
                                       i   +  i+  +  l++ e+kl+
  gi|242398638|ref|YP_002994062.1| 108 IKEYESAIAKTQEALHQLEHKLQ 130
                                       *999***************9995 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1       8.8     3e+03     142     147 ..      29      34 ..       3      60 .. 0.46
   2 ?   14.3   2.5   7.8e-05     0.026     100     148 ..      97     145 ..      94     151 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 8.8
                            DUF724 142 lerqla 147
                                       l ++l+
  gi|242398638|ref|YP_002994062.1|  29 LAQNLE 34 
                                       333333 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 7.8e-05
                            DUF724 100 lkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlal 148
                                       l d  + l e++k++e+ i++ +++ ++le+++++l +k ++l++q+a+
  gi|242398638|ref|YP_002994062.1|  97 LDDAIAYLDERIKEYESAIAKTQEALHQLEHKLQDLAEKAQKLQQQQAM 145
                                       677888999*************************************986 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1         4   1.4e+03      72      72 ..      37      37 ..       4      60 .. 0.48
   2 ?   13.8   0.2   0.00013     0.044      62     108 ..      95     141 ..      83     149 .. 0.64

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 4
                           DUF1664 72 d 72
                                      +
  gi|242398638|ref|YP_002994062.1| 37 N 37
                                      1 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 0.00013
                           DUF1664  62 rhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvke 108
                                       + L + i+ +d++++e + ++++++e +++++++l+++ e+ +++++
  gi|242398638|ref|YP_002994062.1|  95 KSLDDAIAYLDERIKEYESAIAKTQEALHQLEHKLQDLAEKAQKLQQ 141
                                       45555666666666666666666666666666666666666665554 PP

>> PspA_IM30  PspA/IM30 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   1.1       2.1   7.2e+02     120     142 ..      11      33 ..       3      60 .. 0.44
   2 ?   14.0   5.9     8e-05     0.027      94     144 ..      95     145 ..      91     146 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 2.1
                         PspA_IM30 120 qlealetkieelkakkellkare 142
                                       qle+l+  ++ l+ + +ll+ ++
  gi|242398638|ref|YP_002994062.1|  11 QLERLAYEYQLLQGQAQLLAQNL 33 
                                       22233333332222222222222 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 8e-05
                         PspA_IM30  94 kslekqaealetqlaqqrsaveqlrkqlealetkieelkakkellkareka 144
                                       ksl + ++ l++  ++ +sa+++ +++l +le k+++l +k ++l+ ++++
  gi|242398638|ref|YP_002994062.1|  95 KSLDDAIAYLDERIKEYESAIAKTQEALHQLEHKLQDLAEKAQKLQQQQAM 145
                                       678889999999999999999999999999999999999999999988765 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 ?   -1.8   1.5       9.3   3.1e+03      42      42 ..      27      27 ..       4      62 .. 0.47
   2 ?   14.1   3.0   0.00012      0.04      44      90 ..      97     144 ..      91     149 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 9.3
                            CENP-Q 42 s 42
                                      +
  gi|242398638|ref|YP_002994062.1| 27 Q 27
                                      1 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 0.00012
                            CENP-Q  44 elhslelLeaeiekeeralerdyeaLreLeknakaearerke.klkke 90 
                                       + ++++ L + i++ e a ++ +eaL++Le++ +++a++ ++ +++++
  gi|242398638|ref|YP_002994062.1|  97 LDDAIAYLDERIKEYESAIAKTQEALHQLEHKLQDLAEKAQKlQQQQA 144
                                       5678999********************************555476665 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 ?   -0.3   5.0       3.4   1.2e+03      36      85 ..      10      58 ..       4      62 .. 0.74
   2 ?   13.9   2.0   0.00014     0.046      86     127 ..     103     144 ..      91     148 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 3.4
                     Jnk-SapK_ap_N 36 ElLeslasrneeeeaeleelreeleqLeteyerekelrkraeeeleeied 85
                                      E+Le la +++  + ++++l ++le L +   +e ++ k++ e l  +ed
  gi|242398638|ref|YP_002994062.1| 10 EQLERLAYEYQLLQGQAQLLAQNLELLNL-GRNEFQAVKETLEGLKDVED 58
                                      89999999998888888888888887777.44555566666666666666 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 0.00014
                     Jnk-SapK_ap_N  86 qweeerkelqekveqleeenrelelkaknaadqlsrleekea 127
                                        ++e+ ke+++++++++e  ++le k++++a+++++l++++a
  gi|242398638|ref|YP_002994062.1| 103 YLDERIKEYESAIAKTQEALHQLEHKLQDLAEKAQKLQQQQA 144
                                       456777888888888888888888888888888888888765 PP

>> BRE  Brain and reproductive organ-expressed protein (BRE)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00027     0.093     126     161 ..       9      45 ..       3      50 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00027
                               BRE 126 akegsrlqfeystLvgeteltkedvevi.lGkkevea 161
                                       +++ +rl +ey+ L+g+++l  +++e++ lG++e++a
  gi|242398638|ref|YP_002994062.1|   9 NEQLERLAYEYQLLQGQAQLLAQNLELLnLGRNEFQA 45 
                                       45669*********************99899988765 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 ?   -0.3   0.2       3.2   1.1e+03      96     105 ..      43      52 ..       3      67 .. 0.52
   2 ?   13.3   0.2    0.0002     0.066      66     114 ..      96     144 ..      85     150 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 3.2
                              COG2  96 eeevesklee 105
                                        ++v++ le 
  gi|242398638|ref|YP_002994062.1|  43 FQAVKETLEG 52 
                                       2333333333 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.0002
                              COG2  66 glqeeleevesplaaarkkvesvreklsereeeveskleeakeleekre 114
                                       +l++++ +++  +++  + + +++e+l++ e+++++  e+a++l+++++
  gi|242398638|ref|YP_002994062.1|  96 SLDDAIAYLDERIKEYESAIAKTQEALHQLEHKLQDLAEKAQKLQQQQA 144
                                       789******************************************9985 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 ?   12.1   0.2   0.00028     0.094      13      96 ..      76     149 ..      68     152 .] 0.67

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00028
                            TraF_2  13 rreddvglllplsvgvevgdvdnlvDkiDdlsdildgleaavnaasadetqvdeaaddlnalLedlggdgylkasag 89 
                                       r ed+ + ++++++g+ ++    l D i  l+++++++e+a+++       ++ea+ +l+  L+dl++++  k++  
  gi|242398638|ref|YP_002994062.1|  76 RVEDKNNAIVSVGAGYAIEKS--LDDAIAYLDERIKEYESAIAK-------TQEALHQLEHKLQDLAEKA-QKLQQQ 142
                                       446666666665555555544..777788888888888888777.......8888888888888888888.666666 PP

                            TraF_2  90 vglavai 96 
                                        ++ + +
  gi|242398638|ref|YP_002994062.1| 143 QAMGFKV 149
                                       6565555 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 ?    7.3   2.8    0.0089         3      72     126 ..       4      58 ..       1      64 [. 0.88
   2 ?   10.8   1.7   0.00078      0.26      49     100 ..      97     142 ..      88     147 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0089
                      HAUS-augmin3  72 ileeeeesleaLeqelqeLqkekalklkrlnkLqvqaaslqqelrkleeeekeak 126
                                       +++e +e+le L+ e q Lq + +l+ ++l+ L++  ++ q ++++le  ++   
  gi|242398638|ref|YP_002994062.1|   4 EMSERNEQLERLAYEYQLLQGQAQLLAQNLELLNLGRNEFQAVKETLEGLKDVED 58 
                                       56788999************************************99998776655 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00078
                      HAUS-augmin3  49 LeeaLktiepsdlkqedvellevileeeeesleaLeqelqeLqkekalklkr 100
                                       L++a   ++      e  +++e+ +++ +e+l++Le +lq+L +  + ++++
  gi|242398638|ref|YP_002994062.1|  97 LDDAIAYLD------ERIKEYESAIAKTQEALHQLEHKLQDLAEKAQKLQQQ 142
                                       444444444......5566667777777888888888888887666655555 PP

>> Fusion_gly  Fusion glycoprotein F0
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.7   0.00051      0.17     106     155 ..      87     141 ..      83     145 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00051
                                       HHHHHHHHHHHH.....HHHHHHHHHHHHHTHHSSEEEECHCCSHCEEEEETTHH CS
                        Fusion_gly 106 itAgiAlakalk.....naeeiaklkeslektnkAveklqngvselvlavnalqd 155
                                       + Ag A+ k+l      ++e i++  ++++kt +A ++l+  ++ l+ + ++lq+
  gi|242398638|ref|YP_002994062.1|  87 VGAGYAIEKSLDdaiayLDERIKEYESAIAKTQEALHQLEHKLQDLAEKAQKLQQ 141
                                       5677777777651111245778888899999999999999999999999999997 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   1.8     0.083        28     212     251 ..       9      48 ..       3      64 .. 0.42
   2 ?   13.0   2.0    0.0001     0.034     196     243 ..      96     143 ..      78     148 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.083
                              Spc7 212 kaeieekkkelaelqeqleeleekieelkeqkseleeeia 251
                                       ++++e++  e++ lq q + l++++e l+  ++e+++  +
  gi|242398638|ref|YP_002994062.1|   9 NEQLERLAYEYQLLQGQAQLLAQNLELLNLGRNEFQAVKE 48 
                                       4444444444444444444444444444433333332222 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.0001
                              Spc7 196 idkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqk 243
                                       +  + ++ l e+++e ++ i++ ++ l +l+ +l++l+ek ++l++q 
  gi|242398638|ref|YP_002994062.1|  96 SLDDAIAYLDERIKEYESAIAKTQEALHQLEHKLQDLAEKAQKLQQQQ 143
                                       445566666677777777777777777777777777777777776654 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 ?    4.4   1.5      0.11        37     104     139 ..       4      49 ..       2      64 .. 0.69
   2 ?   12.5   0.9   0.00034      0.12     153     183 ..     103     133 ..      73     148 .. 0.57

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.11
                           UPF0242 104 eldakeeelerlkeenqqLqekleaiae..........dfeelkle 139
                                       e+++++e+lerl  e q Lq +++  a+          +f+++k  
  gi|242398638|ref|YP_002994062.1|   4 EMSERNEQLERLAYEYQLLQGQAQLLAQnlellnlgrnEFQAVKET 49 
                                       5678888888888888888888888887555555554444444444 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00034
                           UPF0242 153 eyqetieeqrsvlekrqdqieqLeskVrDln 183
                                        + e i+e  s + k q+  +qLe k +Dl+
  gi|242398638|ref|YP_002994062.1| 103 YLDERIKEYESAIAKTQEALHQLEHKLQDLA 133
                                       2334444444444444444444444444443 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1      0.81   2.7e+02      19      35 ..      39      55 ..       5      58 .. 0.81
   2 ?    9.6   0.4    0.0035       1.2       1      35 [.     107     141 ..     107     144 .. 0.95

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.81
                         FlaC_arch 19 vkkeneelsksveelke 35
                                       ++e++ +++++e lk+
  gi|242398638|ref|YP_002994062.1| 39 GRNEFQAVKETLEGLKD 55
                                      47788888888888875 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0035
                         FlaC_arch   1 ridelEnklsklsteletvkkeneelsksveelke 35 
                                       ri+e E+ + k++  l  ++ ++++l ++ ++l++
  gi|242398638|ref|YP_002994062.1| 107 RIKEYESAIAKTQEALHQLEHKLQDLAEKAQKLQQ 141
                                       89******************************998 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 ?    3.3   0.0      0.39   1.3e+02      21      75 ..      27      87 ..       5      98 .. 0.63
   2 ?    8.4   2.4    0.0099       3.3      21      59 ..     106     144 ..      91     151 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.39
                                      XXXXXXXXXXXXXHHHHHHHHHHHHHHHHHH..HHH.....XXGGGGGXEEEEECSTTTEEE CS
                            FliD_N 21 dkleqkktklewkqsayrelnsklsnlksal..sal.....sksstfsakkatssdesvvta 75
                                      + l q+ + l+  ++++++++  l+ lk+    +         +++f +  ++ +++++v++
  gi|242398638|ref|YP_002994062.1| 27 QLLAQNLELLNLGRNEFQAVKETLEGLKDVEdeK-PeilvpIGAGSFLKGRVEDKNNAIVSV 87
                                      4467777777777888888888888887722321.022343234555555556666666665 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0099
                                       XXXXXXXXXXXXXHHHHHHHHHHHHHHHHHHHHHXXGGG CS
                            FliD_N  21 dkleqkktklewkqsayrelnsklsnlksalsalsksst 59 
                                       +++++ ++ + + q+a+ +l+ kl++l +++++l+++++
  gi|242398638|ref|YP_002994062.1| 106 ERIKEYESAIAKTQEALHQLEHKLQDLAEKAQKLQQQQA 144
                                       468888999999*****************9988877554 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.2       1.1   3.8e+02      62      95 ..      20      53 ..       3      64 .. 0.51
   2 ?   12.1   0.4   0.00044      0.15      35      82 ..      96     143 ..      76     148 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 1.1
                                      XXX--TTTTTGGGHHHHHHHHHH...HHHHHHHH CS
                        Laminin_II 62 kkLeklapqLldklkelkqleeassslsdnisei 95
                                      + L+ +a+ L + l+ l+  +++ +++++ ++ +
  gi|242398638|ref|YP_002994062.1| 20 QLLQGQAQLLAQNLELLNLGRNEFQAVKETLEGL 53
                                      3344444455555555444444444444444444 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00044
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHH CS
                        Laminin_II  35 einrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqle 82 
                                       ++++ ++  +e +k++  ai+  +++  +Le+++++L +k ++l+q++
  gi|242398638|ref|YP_002994062.1|  96 SLDDAIAYLDERIKEYESAIAKTQEALHQLEHKLQDLAEKAQKLQQQQ 143
                                       566677778889999999999999999999999999999999998886 PP

>> Noelin-1  Neurogenesis glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1      0.35   1.2e+02      42      81 ..      20      58 ..       3      63 .. 0.79
   2 ?   10.2   0.7    0.0017      0.57      53      97 ..      99     143 ..      93     145 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.35
                          Noelin-1 42 rqllekvqnlsqsievldlRtsrdlqyvrktetllktles 81
                                      + l+ + q l+q++e+l+l  ++++q v++t + lk++e+
  gi|242398638|ref|YP_002994062.1| 20 QLLQGQAQLLAQNLELLNLG-RNEFQAVKETLEGLKDVED 58
                                      44667888899999999884.6789999999888888875 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0017
                          Noelin-1  53 qsievldlRtsrdlqyvrktetllktlesklkvveedrkelsaks 97 
                                       + i  ld+R ++    + kt++ l++le+kl+++ e+ ++l++++
  gi|242398638|ref|YP_002994062.1|  99 DAIAYLDERIKEYESAIAKTQEALHQLEHKLQDLAEKAQKLQQQQ 143
                                       6788999999999999********************999998865 PP

>> Uso1_p115_C  Uso1 / p115 like vesicle tethering protein, C terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.3      0.61   2.1e+02      21      73 ..       9      55 ..       3      82 .. 0.52
   2 ?   13.2   3.1   0.00026      0.09       4      38 ..     109     143 ..     106     150 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.61
                       Uso1_p115_C 21 kaelqslskalesleqk.eakkaaesqakeleaenkklek....eleklraelkeeke 73
                                      + +l+ l+ +++ l+ + +           l a+n +l +    e ++++++l+  k 
  gi|242398638|ref|YP_002994062.1|  9 NEQLERLAYEYQLLQGQaQ-----------LLAQNLELLNlgrnEFQAVKETLEGLKD 55
                                      4555555555555555522...........2222222222222233444444333333 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00026
                       Uso1_p115_C   4 seleseaaslkdeneklkaelqslskalesleqke 38 
                                       +e+es  a+ ++   +l+ +lq+l++++++l+q++
  gi|242398638|ref|YP_002994062.1| 109 KEYESAIAKTQEALHQLEHKLQDLAEKAQKLQQQQ 143
                                       799******************************93 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 ?   -0.3   0.1         2   6.6e+02     155     193 ..       7      42 ..       3      66 .. 0.58
   2 ?   12.3   0.5   0.00027      0.09     159     199 ..     107     144 ..      76     150 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 2
                           HAUS6_N 155 slrrflrekaaadrarqkyqenaqllekkerelraelee 193
                                       +++++l+++a +    q +q +aqll+++ + l+  + e
  gi|242398638|ref|YP_002994062.1|   7 ERNEQLERLAYE---YQLLQGQAQLLAQNLELLNLGRNE 42 
                                       555556555555...466666666666666555444333 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00027
                           HAUS6_N 159 flrekaaadrarqkyqenaqllekkerelraeleelqaelk 199
                                        ++e+++a   ++k qe ++ le+k ++l+++ ++lq+++ 
  gi|242398638|ref|YP_002994062.1| 107 RIKEYESA---IAKTQEALHQLEHKLQDLAEKAQKLQQQQA 144
                                       45555566...9***********************999864 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.8    0.0011      0.38     214     326 ..       5     144 ..       3     148 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0011
                              FUSC 214 irararalrrllsrmlallallsslarllarlraeeaaavpelaallaelaal........................ 266
                                       +++r+++l rl  + + l  +++ la++l+ l+  +++  ++++++l+ l+++                        
  gi|242398638|ref|YP_002994062.1|   5 MSERNEQLERLAYEYQLLQGQAQLLAQNLELLNLGRNEF-QAVKETLEGLKDVedekpeilvpigagsflkgrvedk 80 
                                       78899*************************999888877.4599999999999999********************* PP

                              FUSC 267 ........eaaaaaealeaalaalrarlralrraleadadtaalllarlaellaelaqllaslralea 326
                                               +  a ++ l++a+a l++r+++ ++a +      +++l +l + l++la+  ++l++++a
  gi|242398638|ref|YP_002994062.1|  81 nnaivsvgAGYAIEKSLDDAIAYLDERIKEYESAIA----KTQEALHQLEHKLQDLAEKAQKLQQQQA 144
                                       ****99997777889999999999999999999999....8888889999999999998888887765 PP

>> Uds1  Up-regulated During Septation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   6.9    0.0051       1.7      22     113 ..      11     144 ..       6     146 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0051
                              Uds1  22 eVeelkkelkaLeerlealrkkLaletklrdaarsLsrlyssskksak............................. 69 
                                       ++e l  e++ L+ + + l ++L+l +  r+  ++ ++   + +k+ +                             
  gi|242398638|ref|YP_002994062.1|  11 QLERLAYEYQLLQGQAQLLAQNLELLNLGRNEFQAVKETL-EGLKDVEdekpeilvpigagsflkgrvedknnaivs 86 
                                       5666666666666666666666666444443333333333.222222234455666666666666666666666666 PP

                              Uds1  70 ...............ssaarsnskssreslakaeeelaeserkvdelaselekleeraa 113
                                                      ++  +++ k+ + + ak++e+l+++e+k ++la++ +kl++++a
  gi|242398638|ref|YP_002994062.1|  87 vgagyaiekslddaiAYL-DERIKEYESAIAKTQEALHQLEHKLQDLAEKAQKLQQQQA 144
                                       666666666666664333.344555567899**********************999875 PP

>> Synaptobrevin  Synaptobrevin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.2      0.34   1.2e+02      25      51 ..       4      30 ..       2      37 .. 0.85
   2 ?    8.5   0.4    0.0049       1.6       9      46 ..     105     142 ..      97     149 .. 0.60

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.34
                                      HCHCCCCCHHHHCCCCHHHHHHHHHHH CS
                     Synaptobrevin 25 kvlergekldeLvdktenLqssaqqFk 51
                                      ++ er+e+l+ L  + + Lq +aq   
  gi|242398638|ref|YP_002994062.1|  4 EMSERNEQLERLAYEYQLLQGQAQLLA 30
                                      6889********999999999998765 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0049
                                       HHHHHCCCCHHCCHHHHCHCCCCCHHHHCCCCHHHHHH CS
                     Synaptobrevin   9 kaevdevkdimkeNidkvlergekldeLvdktenLqss 46 
                                        + ++e ++ + +  + + + + kl +L +k+++Lq++
  gi|242398638|ref|YP_002994062.1| 105 DERIKEYESAIAKTQEALHQLEHKLQDLAEKAQKLQQQ 142
                                       55555666666666666666666677777777776653 PP

>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.4       1.7   5.9e+02      67     111 ..       8      52 ..       3      64 .. 0.47
   2 ?    9.9   0.1   0.00045      0.15      42     114 ..      73     144 ..      68     151 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.7
                        V_ATPase_I  67 eekeldeleeelekleeelkelnenleklkkelnelvelkavlek 111
                                       ++++l++l  e + l+ + + l +nle l+  +ne +  k+ le 
  gi|242398638|ref|YP_002994062.1|   8 RNEQLERLAYEYQLLQGQAQLLAQNLELLNLGRNEFQAVKETLEG 52 
                                       334444444444444444444444444444444444444444444 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00045
                        V_ATPase_I  42 leeeieklekavikeeeaeesleapeekeldeleeelekleeelkelnenleklkkelnelvelkavlekake 114
                                       l+  +e++++a+++   a    e++ ++ +  l+e+++++e+ + +++e l++l+++l++l e+ + l++ ++
  gi|242398638|ref|YP_002994062.1|  73 LKGRVEDKNNAIVSVG-AGYAIEKSLDDAIAYLDERIKEYESAIAKTQEALHQLEHKLQDLAEKAQKLQQQQA 144
                                       5556666444444433.36666777777788888888888888888888888888888888888777776654 PP

>> PEP-utilisers_N  PEP-utilising enzyme, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1       4.7   1.6e+03      70      70 ..      36      36 ..       4      64 .. 0.55
   2 ?   11.9   0.9   0.00058       0.2      29      66 ..     104     142 ..      81     149 .. 0.47

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 4.7
                                      H CS
                   PEP-utilisers_N 70 l 70
                                      l
  gi|242398638|ref|YP_002994062.1| 36 L 36
                                      2 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00058
                                       HHHHHHHHHHHHHHHHHHHHHHHHHH..T-HHHHHHHHHH CS
                   PEP-utilisers_N  29 veaelerleeAlekvreelealaeka..lgeeeaaifeah 66 
                                        ++ ++ +e+A++k++e l +l++k+  l +e+a+ ++ +
  gi|242398638|ref|YP_002994062.1| 104 LDERIKEYESAIAKTQEALHQLEHKLqdL-AEKAQKLQQQ 142
                                       34555555555555555555555555532.2333333333 PP

>> DUF2730  Protein of unknown function (DUF2730)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.2      0.64   2.2e+02      45      75 ..       8      38 ..       1      58 [. 0.52
   2 ?   10.8   1.5    0.0012      0.39      37      85 ..      96     142 ..      92     145 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.64
                           DUF2730 45 ndkrlteletkvenLPtakdlekLkllladl 75
                                       +++l++l  + + L  + +l + +l+l +l
  gi|242398638|ref|YP_002994062.1|  8 RNEQLERLAYEYQLLQGQAQLLAQNLELLNL 38
                                      4445555555555555555555555555554 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0012
                           DUF2730  37 klaekveendkrlteletkvenLPtakdlekLkllladlrgelkaleae 85 
                                       +l + ++  d+r++e e+ +++  t++ l++L+ +l+dl  + ++l+++
  gi|242398638|ref|YP_002994062.1|  96 SLDDAIAYLDERIKEYESAIAK--TQEALHQLEHKLQDLAEKAQKLQQQ 142
                                       688999999***********98..9****************99999986 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.3       1.4   4.8e+02      23      55 ..      22      54 ..       4      67 .. 0.58
   2 ?   10.9   0.7    0.0014      0.47      12      48 ..     107     143 ..      93     149 .. 0.66

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 1.4
                           NPV_P10 23 lqqqvddvqenlpdvtelnekLdaqsaqLaele 55
                                      lq q + +++nl+ ++   ++++a  ++L+ l+
  gi|242398638|ref|YP_002994062.1| 22 LQGQAQLLAQNLELLNLGRNEFQAVKETLEGLK 54
                                      455555555555554444444555555544444 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0014
                           NPV_P10  12 dikavddkVdalqqqvddvqenlpdvtelnekLdaqs 48 
                                        ik+ ++ +   q+++++++++l+d+ e  +kL++q+
  gi|242398638|ref|YP_002994062.1| 107 RIKEYESAIAKTQEALHQLEHKLQDLAEKAQKLQQQQ 143
                                       4566666666666667777777777777777776665 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.5      0.68   2.3e+02      10      43 ..       5      38 ..       1      68 [. 0.46
   2 ?   11.1   0.9    0.0014      0.49       8      44 ..     106     142 ..      94     148 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.68
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YabA 10 leeleeqleelleeleelkeelaelleenaeLel 43
                                      ++e +eqle+l  e + l+ + + l ++ + L+l
  gi|242398638|ref|YP_002994062.1|  5 MSERNEQLERLAYEYQLLQGQAQLLAQNLELLNL 38
                                      4444455555555555555444433333333333 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0014
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YabA   8 dkleeleeqleelleeleelkeelaelleenaeLele 44 
                                       ++++e e+ +++++e l++l+++l++l e+ ++L+ +
  gi|242398638|ref|YP_002994062.1| 106 ERIKEYESAIAKTQEALHQLEHKLQDLAEKAQKLQQQ 142
                                       6788888888888888888888888888888888765 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   1.0      0.57   1.9e+02      12      43 ..      11      42 ..       3      85 .. 0.61
   2 ?   11.5   0.8    0.0008      0.27       9      44 ..     104     141 ..      96     150 .. 0.60

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.57
                             Spc24 12 elsdleselesleselaelkeeleeleeesee 43
                                      +l+ l  e + l+ + + l ++le l+  ++e
  gi|242398638|ref|YP_002994062.1| 11 QLERLAYEYQLLQGQAQLLAQNLELLNLGRNE 42
                                      44444445555555555555555555554444 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.0008
                             Spc24   9 iakelsdleselesleselaelkeeleeleeesee..k 44 
                                       + + +++ es++ + ++ l++l+++l++l e+ ++  +
  gi|242398638|ref|YP_002994062.1| 104 LDERIKEYESAIAKTQEALHQLEHKLQDLAEKAQKlqQ 141
                                       55566666666666666666666666666666665321 PP

>> TolA_bind_tri  TolA binding protein trimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   4.7     0.023       7.9      24      52 ..       9      37 ..       4      56 .. 0.83
   2 ?    8.4   2.9    0.0066       2.2       2      39 ..     104     141 ..      96     144 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.023
                     TolA_bind_tri 24 qqqlealqqelreLRGqiEelqyqleqle 52
                                       +qle+l  e + L+Gq + l+ +le l+
  gi|242398638|ref|YP_002994062.1|  9 NEQLERLAYEYQLLQGQAQLLAQNLELLN 37
                                      689999************99999998775 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0066
                     TolA_bind_tri   2 ledrvarLErilearsqlllelqqqlealqqelreLRG 39 
                                       l++r+++ E ++++ +++l++l  +l++l +  ++L+ 
  gi|242398638|ref|YP_002994062.1| 104 LDERIKEYESAIAKTQEALHQLEHKLQDLAEKAQKLQQ 141
                                       67899999999999999999999999999998888875 PP

>> DegS  Sensor protein DegS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.9      0.88     3e+02     105     154 ..       7      55 ..       3      58 .. 0.59
   2 ?   12.2   1.7   0.00028     0.093     109     159 .]      96     146 ..      93     146 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.88
                              DegS 105 erRdelerrLkklketierAeklvsqvgvvlnyLsgdlkqvsekledlkq 154
                                       er ++ler   +++    +A+ l+++++  ln+ +++++ v+e+le lk+
  gi|242398638|ref|YP_002994062.1|   7 ERNEQLERLAYEYQLLQGQAQLLAQNLE-LLNLGRNEFQAVKETLEGLKD 55 
                                       5556666555555555555555555444.467777777777777777665 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00028
                              DegS 109 elerrLkklketierAeklvsqvgvvlnyLsgdlkqvsekledlkqkqelg 159
                                       +l+  +  l+e i+  e+ + + + +l+ L+++l+++ ek ++l+q+q++g
  gi|242398638|ref|YP_002994062.1|  96 SLDDAIAYLDERIKEYESAIAKTQEALHQLEHKLQDLAEKAQKLQQQQAMG 146
                                       577788889999*************************************98 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 ?   -0.7   0.3       2.2   7.5e+02      42      57 ..      40      55 ..       4      65 .. 0.59
   2 ?   11.0   0.9   0.00058       0.2     145     181 ..     105     144 ..      93     149 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 2.2
                       Helo_like_N 42 keeleaLeevLesLee 57
                                      ++e +a +e Le L++
  gi|242398638|ref|YP_002994062.1| 40 RNEFQAVKETLEGLKD 55
                                      3344444444444444 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00058
                       Helo_like_N 145 aevleeykeliedtts...dLeehLedideklealtekse 181
                                        e ++ey++ i++t++   +Le++L+d+ ek ++l+++++
  gi|242398638|ref|YP_002994062.1| 105 DERIKEYESAIAKTQEalhQLEHKLQDLAEKAQKLQQQQA 144
                                       578999*****98875222679999999999999997764 PP

>> Tup_N  Tup N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.4      0.37   1.3e+02       4      48 ..      10      50 ..       8      55 .. 0.55
   2 ?    3.1   0.1      0.36   1.2e+02       4      29 ..      34      59 ..      31      62 .. 0.84
   3 ?    9.3   3.9     0.004       1.4      23      61 ..     104     142 ..      95     144 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.37
                             Tup_N  4 elLdavkqEfdalsqeasslkaqkdeyelkiqsqiqElqqirqtl 48
                                      e L+ +  E++ l+ +a+ l +   ++el ++   +E+q++++tl
  gi|242398638|ref|YP_002994062.1| 10 EQLERLAYEYQLLQGQAQLLAQ---NLEL-LNLGRNEFQAVKETL 50
                                      6667777777777776666653...3333.444455555555555 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.36
                             Tup_N  4 elLdavkqEfdalsqeasslkaqkde 29
                                      elL++ ++Ef+a+++ ++ lk  +de
  gi|242398638|ref|YP_002994062.1| 34 ELLNLGRNEFQAVKETLEGLKDVEDE 59
                                      89999999999999998888876665 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.004
                             Tup_N  23 lkaqkdeyelkiqsqiqElqqirqtlyeLeeahrkikqq 61 
                                       l+++ +eye+ i++  + l+q+ ++l +L e+ +k++qq
  gi|242398638|ref|YP_002994062.1| 104 LDERIKEYESAIAKTQEALHQLEHKLQDLAEKAQKLQQQ 142
                                       667789*****************************9987 PP

>> EMP24_GP25L  emp24/gp25L/p24 family/GOLD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.3         4   1.4e+03     108     145 ..       7      44 ..       3      52 .. 0.64
   2 ?   10.5   0.2    0.0012      0.42     108     142 ..     110     144 ..      71     149 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 4
                       EMP24_GP25L 108 akkekletleselkkleekldsikreqkylrereerlr 145
                                         +e+le l  e + l+ + + + +++++l+   ++++
  gi|242398638|ref|YP_002994062.1|   7 ERNEQLERLAYEYQLLQGQAQLLAQNLELLNLGRNEFQ 44 
                                       45667777777777777777777777777666665555 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0012
                       EMP24_GP25L 108 akkekletleselkkleekldsikreqkylreree 142
                                         ++ + ++++ l++le+kl+++ ++ + l+++++
  gi|242398638|ref|YP_002994062.1| 110 EYESAIAKTQEALHQLEHKLQDLAEKAQKLQQQQA 144
                                       33677777888888888888888888888887765 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   1.3      0.26        87      59     102 ..       9      45 ..       3      60 .. 0.50
   2 ?   11.0   4.3     0.001      0.34      72     117 ..      97     142 ..      91     145 .. 0.58

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.26
                              ADIP  59 netirkleaeierlqskierlktqleqlerelalvqakerqlek 102
                                       ne++       erl  +++ l+ q + l++ l+l++   ++ ++
  gi|242398638|ref|YP_002994062.1|   9 NEQL-------ERLAYEYQLLQGQAQLLAQNLELLNLGRNEFQA 45 
                                       4444.......444444455555554444444444444444443 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.001
                              ADIP  72 lqskierlktqleqlerelalvqakerqlekklktleqklknekee 117
                                       l  +i  l+++ +++e+ +a  q+++ qle kl++l +k+++++++
  gi|242398638|ref|YP_002994062.1|  97 LDDAIAYLDERIKEYESAIAKTQEALHQLEHKLQDLAEKAQKLQQQ 142
                                       4455556666666666666666666666666666666666555554 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 ?    3.4   0.5      0.23        78      69     116 ..       3      53 ..       1      66 [. 0.58
   2 ?    9.1   2.0    0.0042       1.4      80     111 ..     110     141 ..      91     145 .. 0.49

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.23
                             CREPT  69 aeleeRkklakmle...dfleaqkellakaeekleelkeklekvksvrkel 116
                                        e++eR++  + l+   ++l+ q +lla++ e l+  ++  + vk+  + l
  gi|242398638|ref|YP_002994062.1|   3 VEMSERNEQLERLAyeyQLLQGQAQLLAQNLELLNLGRNEFQAVKETLEGL 53 
                                       589999876666651113445555556666665555555555555555555 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0042
                             CREPT  80 mledfleaqkellakaeekleelkeklekvks 111
                                         e+ ++  +e+l++ e+kl++l ek++k+++
  gi|242398638|ref|YP_002994062.1| 110 EYESAIAKTQEALHQLEHKLQDLAEKAQKLQQ 141
                                       33344445555555555555555555555554 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.7     0.067        23      31      71 ..      14      54 ..       4      58 .. 0.87
   2 ?    5.9   4.1     0.046        16      36      68 ..     108     140 ..      94     147 .. 0.41

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.067
                           BLOC1_2 31 aasekykklkdvaaslekkleklnekyeelqpylqqidqie 71
                                      + +++y+ l+ +a+ l+++le ln   +e+q  ++ ++ ++
  gi|242398638|ref|YP_002994062.1| 14 RLAYEYQLLQGQAQLLAQNLELLNLGRNEFQAVKETLEGLK 54
                                      56899*************************99999888765 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.046
                           BLOC1_2  36 ykklkdvaaslekkleklnekyeelqpylqqid 68 
                                       +k++++++a++++ l++l+ k + l+++ q+++
  gi|242398638|ref|YP_002994062.1| 108 IKEYESAIAKTQEALHQLEHKLQDLAEKAQKLQ 140
                                       222233333333333333333333333222222 PP

>> DUF4140  N-terminal domain of unknown function (DUF4140)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   1.2       1.9   6.4e+02      68      98 .]       6      36 ..       2      60 .. 0.75
   2 ?   10.9   1.7    0.0014      0.47      60      96 ..     109     144 ..      76     145 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 1.9
                           DUF4140 68 kalraeleeledelaaledelaaaearlafl 98
                                      ++ +++le+l  e + l+ +++ + + l++l
  gi|242398638|ref|YP_002994062.1|  6 SERNEQLERLAYEYQLLQGQAQLLAQNLELL 36
                                      4556677777777777777777777766654 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0014
                           DUF4140  60 reaeeeelkalraeleeledelaaledelaaaearla 96 
                                       +e e+ ++++++++l++le +l++l ++++ ++++ a
  gi|242398638|ref|YP_002994062.1| 109 KEYES-AIAKTQEALHQLEHKLQDLAEKAQKLQQQQA 144
                                       23333.5999**********************99976 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 ?    1.2   3.1         1   3.5e+02      35      79 ..       5      49 ..       2      59 .. 0.52
   2 ?   11.2   5.2   0.00086      0.29      50      86 ..     106     142 ..      92     145 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 1
                             DHR10 35 lrsciklleeieaelakleeakkklkelrdaleekeielrelerk 79
                                      +++  ++le ++ e + l+ + + l+++ + l+  ++e + ++ +
  gi|242398638|ref|YP_002994062.1|  5 MSERNEQLERLAYEYQLLQGQAQLLAQNLELLNLGRNEFQAVKET 49
                                      444445555555555555555555555555555555555444444 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00086
                             DHR10  50 akleeakkklkelrdaleekeielrelerkeerlqrq 86 
                                       ++ +e ++ ++++++al+++e++l++l  k + lq+q
  gi|242398638|ref|YP_002994062.1| 106 ERIKEYESAIAKTQEALHQLEHKLQDLAEKAQKLQQQ 142
                                       5678888889999999999999999999999999998 PP

>> Tektin  Tektin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   1.6       1.1   3.8e+02     120     157 ..      14      51 ..       3      60 .. 0.57
   2 ?   10.8   3.3   0.00044      0.15     247     287 ..     102     142 ..      91     145 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.1
                            Tektin 120 eLlkEveliegvqellkrtleqaeeqlrllraakhkLe 157
                                        L  E +l++g  +ll + le ++   ++ +a+k++Le
  gi|242398638|ref|YP_002994062.1|  14 RLAYEYQLLQGQAQLLAQNLELLNLGRNEFQAVKETLE 51 
                                       34455555555555555555555555555555555554 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00044
                            Tektin 247 ealrkrieetedaknkleeqlkkvleeiaeleknieeLeka 287
                                       + l++ri+e+e+a  k +e l+++++++++l ++ ++L+++
  gi|242398638|ref|YP_002994062.1| 102 AYLDERIKEYESAIAKTQEALHQLEHKLQDLAEKAQKLQQQ 142
                                       56899999999999999999999999999999999999985 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   4.7      0.63   2.1e+02      19      62 ..      11      50 ..       2      62 .. 0.49
   2 ?   10.4   4.6     0.002      0.67       3      26 ..     119     142 ..     117     145 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.63
                              ZapB 19 titlLqmeieeLkeeneelkeenrele...eeneqlkeereawqerl 62
                                      ++++L  e++ L+ + + l+++ + l+    e +       a++e l
  gi|242398638|ref|YP_002994062.1| 11 QLERLAYEYQLLQGQAQLLAQNLELLNlgrNEFQ-------AVKETL 50
                                      3344444444444444444443333334443333.......333333 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.002
                              ZapB   3 lelLeqLEskiqkaidtitlLqme 26 
                                        e L+qLE k q + ++ ++Lq++
  gi|242398638|ref|YP_002994062.1| 119 QEALHQLEHKLQDLAEKAQKLQQQ 142
                                       699*******************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2241  (0.124993); expected 358.6 (0.02)
Passed bias filter:                     1240  (0.0691617); 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):              53  [number of targets reported over threshold]
# CPU time: 0.67u 0.30s 00:00:00.97 Elapsed: 00:00:00.47
# Mc/sec: 962.12
//
Query:       gi|242398639|ref|YP_002994063.1|  [L=308]
Description: UDP-glucose 4-epimerase [Thermococcus sibiricus MM 739]
Scores for complete 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-63  212.4   0.1      8e-63  212.1   0.1    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    2.4e-59  201.4   0.0    3.1e-59  201.1   0.0    1.1  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    3.8e-24   85.1   0.1    5.2e-24   84.7   0.1    1.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    6.4e-18   64.9   0.4    6.7e-17   61.6   0.4    2.2  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    7.2e-16   58.1   0.0    9.7e-16   57.7   0.0    1.1  1  RmlD_sub_bind    RmlD substrate binding domain
    6.9e-13   48.4   0.0    1.4e-09   37.5   0.0    2.4  2  NAD_binding_4    Male sterility protein
    4.6e-07   29.9   0.0    6.8e-07   29.3   0.0    1.2  1  NAD_binding_10   NAD(P)H-binding
    8.1e-05   22.9   0.1    0.00014   22.1   0.1    1.4  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
    0.00023   20.7   0.0     0.0006   19.3   0.0    1.7  1  adh_short        short chain dehydrogenase
     0.0021   17.7   0.1     0.0038   16.8   0.1    1.5  1  NmrA             NmrA-like family
     0.0059   16.8   0.3      0.015   15.6   0.1    1.8  2  TrkA_N           TrkA-N domain
  ------ inclusion threshold ------
       0.03   13.9   0.1      0.043   13.4   0.1    1.3  1  DUF1188          Protein of unknown function (DUF1188)
      0.045   13.7   0.4        1.1    9.1   0.4    2.6  1  KR               KR domain
       0.12   12.7   0.1       0.41   10.9   0.0    1.9  2  UPF0113          UPF0113 PUA 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 !  212.1   0.1   6.2e-66     8e-63       1     241 []       7     237 ..       7     237 .. 0.94

  Alignments for each domain:
  == domain 1  score: 212.1 bits;  conditional E-value: 6.2e-66
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC.EEEE--TT-HHHHHHHHHHHT-SEEEE--S--- CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl.elveldltdrsalerlfkeeqpdavihlAavgg 76 
                                       i+VtG++GfiGs+++++l +   +vi +d+l +a++ ++++   +++++d++d +++++l++  q+d+v+h Aa  +
  gi|242398639|ref|YP_002994063.1|   7 IVVTGGAGFIGSHIAEELSKD-NDVIIIDNL-YAGKIENIPPNvKFIRADIRDYKSMAELIS--QADYVFHEAALVS 79 
                                       89****************976.5********.666666555555******************..9*********999 PP

                                       HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHH CS
                         Epimerase  77 vaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklv 153
                                       v +s+e+p  + e+n+ gtln+l+a+++ +  +++f+sS++vYG++++ p +e+    + kp spY+++K+ +e ++
  gi|242398639|ref|YP_002994063.1|  80 VVESVERPLLTEEINVLGTLNVLKALSEGHG-KFIFASSAAVYGDNQNLPLKESE---KPKPLSPYGITKVSAEYYC 152
                                       999***********************97766.****************9988888...789**************** PP

                                       HHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHT CS
                         Epimerase 154 eayaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvlehvd 230
                                       + + + yg+++++lr+fn++G+r+g ++ ++vi+ +i+++l+g+ +++++gdg++ Rdf+yv+Dv++a++l++e   
  gi|242398639|ref|YP_002994063.1| 153 KVFYELYGVPTVSLRYFNVFGERQGYNQYAGVISIFINRALKGE-PLIIYGDGKQTRDFIYVKDVVKANILAAES-- 226
                                       ********************************************.******************************.. PP

                                       T-STTEEEEES CS
                         Epimerase 231 agdkgeiyniG 241
                                       ++++g+++n++
  gi|242398639|ref|YP_002994063.1| 227 SKANGKVFNVA 237
                                       778899***96 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 !  201.1   0.0   2.4e-62   3.1e-59       2     330 ..       9     297 ..       8     299 .. 0.92

  Alignments for each domain:
  == domain 1  score: 201.1 bits;  conditional E-value: 2.4e-62
                                       EETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SE CS
                     GDP_Man_Dehyd   2 iTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpde 78 
                                       +TG+aGfiGs++ae L +   +v++i+    ++++g+ie++         +n+k++++D++D +s+ +l++++  d 
  gi|242398639|ref|YP_002994063.1|   9 VTGGAGFIGSHIAEELSKD-NDVIIID----NLYAGKIENIP--------PNVKFIRADIRDYKSMAELISQA--DY 70 
                                       9**************9875.7788875....56889999984........5899*****************98..9* PP

                                       EEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHHH CS
                     GDP_Man_Dehyd  79 vynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYaa 155
                                       v++ AA   V +s+e P  t e+nvlGtl++L+a  +     + +f++aS++ vYG+ q+ p +E+ + +P sPY++
  gi|242398639|ref|YP_002994063.1|  71 VFHEAALVSVVESVERPLLTEEINVLGTLNVLKALSE----GHGKFIFASSAAVYGDNQNLPLKESEKPKPLSPYGI 143
                                       ***********************************76....3569******************************** PP

                                       HHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHHH CS
                     GDP_Man_Dehyd 156 aKlyadwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwghvkDyvea 232
                                       +K++a++ ++ ++e yg+++v+ ++fn  + r+g +     i+ ++ r+++g+ + +++G+++++Rd+ +vkD+v+a
  gi|242398639|ref|YP_002994063.1| 144 TKVSAEYYCKVFYELYGVPTVSLRYFNVFGERQGYNQYAGVISIFINRALKGE-PLIIYGDGKQTRDFIYVKDVVKA 219
                                       ***************************************************98.9999******************* PP

                                       HHHHHHCSS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--SB--B- CS
                     GDP_Man_Dehyd 233 mwlmlqqdkpedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevdlllgd 309
                                         l+ ++ k      a+g++++v +  + ++lel  +i+              +g    ++ + + rpg+ +   +d
  gi|242398639|ref|YP_002994063.1| 220 NILAAESSK------ANGKVFNVAKGERTSILELALKIIEI------------TG-SSSSIIFDKPRPGDIRHSQAD 277
                                       **9999998......79*****************9998753............22.2345667899*********** PP

                                       THHHHHHH----SS-HHHHHH CS
                     GDP_Man_Dehyd 310 askakeeLgWkpkvsfeelvr 330
                                       +s +  +Lg+kp++s++e++ 
  gi|242398639|ref|YP_002994063.1| 278 ISEIM-KLGFKPEYSLKEGLL 297
                                       ****9.9***********985 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.7   0.1   4.1e-27   5.2e-24       1     236 [.       8     231 ..       8     252 .. 0.83

  Alignments for each domain:
  == domain 1  score: 84.7 bits;  conditional E-value: 4.1e-27
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslv 77 
                                       vvtGgaGF+G+++ +eL + +   +v ++D     ++  e    nvk +i +D++d +++ e + ++d v+h a+lv
  gi|242398639|ref|YP_002994063.1|   8 VVTGGAGFIGSHIAEELSKDN---DVIIIDNLYAGKI--ENIPPNVK-FIRADIRDYKSMAELISQADYVFHEAALV 78 
                                       8***************98877...699***9999999..55556677.99**************************9 PP

                         3Beta_HSD  78 dvag.kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKala 153
                                        v   + +     ++nv GT nvl+a ++ g  ++++ Ssa v g+n+ + ++      +  ++++ ++y  +K  a
  gi|242398639|ref|YP_002994063.1|  79 SVVEsVERPLLTEEINVLGTLNVLKA-LSEGHGKFIFASSAAVYGDNQ-NLPLK-----ESEKPKPLSPYGITKVSA 148
                                       99883555666789**********98.5678899************43.33444.....445678999********* PP

                         3Beta_HSD 154 EklvlkaNgrtlknggrlyTcaLRpagiyGegdk......llvpllkqlaklglalfkigdeevlsdrvYvgNvawa 224
                                       E + +   +        + T++LR   ++Ge++       +++ ++++++k +  l+ +gd +++ d++Yv  v++a
  gi|242398639|ref|YP_002994063.1| 149 EYYCKVFYE-----LYGVPTVSLRYFNVFGERQGynqyagVISIFINRALKGE-PLIIYGDGKQTRDFIYVKDVVKA 219
                                       ***988777.....33479************8642112224566777777766.9********************** PP

                         3Beta_HSD 225 hilAaralqdpk 236
                                        ilAa   + + 
  gi|242398639|ref|YP_002994063.1| 220 NILAAESSKANG 231
                                       *****8766664 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.6   0.4   5.2e-20   6.7e-17       1     252 [.       7     260 ..       7     301 .. 0.79

  Alignments for each domain:
  == domain 1  score: 61.6 bits;  conditional E-value: 5.2e-20
                                       EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T CS
                   Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelk 77 
                                       ++vtG++G iGs++ +++ k +   +i++++    ly+ + e+   +   ++k+    + +d+rd ++++++++  +
  gi|242398639|ref|YP_002994063.1|   7 IVVTGGAGFIGSHIAEELSKDN--DVIIIDN----LYAGKIEN---IP-PNVKF----IRADIRDYKSMAELIS--Q 67 
                                       79*************9987654..5666653....44444333...12.22333....469*************..9 PP

                                       -SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEE.....GGGS.........S--SHHHH CS
                   Polysacc_synt_2  78 vdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliSt.....DKAv.........nPtnvmGa 140
                                        d+vfh AAl  V    e pl + + Nvlgt nv++a ++ g  k+++ S+     D            +P + +G+
  gi|242398639|ref|YP_002994063.1|  68 ADYVFHEAALVSVVESVERPLLTEEINVLGTLNVLKA-LSEGHGKFIFASSaavygDNQNlplkesekpKPLSPYGI 143
                                       **********988777778999999**********96.566778899888723333321122233333369999*** PP

                                       HHHHHHHHHHHGGG--SSS--EEEEEEE-EETTGT.T.....SSHHHHHHHHHTTSSEEE.S-TT-EEEEE-HHHHH CS
                   Polysacc_synt_2 141 tKrlaekllqalakeseekktkfvvvRfGNVlgSr.G.....SviplFkkqikeggpvtv.TdpemtRyfmtieeav 210
                                       tK  ae ++  + +         v  R+ NV+g r G      vi +F ++  +g+p+ +  d + tR f+ +++ v
  gi|242398639|ref|YP_002994063.1| 144 TKVSAEYYCKVFYELY---GVPTVSLRYFNVFGERqGynqyaGVISIFINRALKGEPLIIyGDGKQTRDFIYVKDVV 217
                                       **********999998...788999********8743333337**************9984699************* PP

                                       HH.HHHHHHH--SS-EEEE--.-EEEHHHHHHHH......... CS
                   Polysacc_synt_2 211 qL.vlqalalakggeifvldmGepvkivdlakalielsgleek 252
                                       +  +l a +   +g++f +  Ge ++i++la ++ie++g +++
  gi|242398639|ref|YP_002994063.1| 218 KAnILAAESSKANGKVFNVAKGERTSILELALKIIEITGSSSS 260
                                       9736677778889************************997654 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 !   57.7   0.0   7.5e-19   9.7e-16       3     235 ..       7     259 ..       5     280 .. 0.88

  Alignments for each domain:
  == domain 1  score: 57.7 bits;  conditional E-value: 7.5e-19
                                       EEEESTTSHHHHHHHHHCTTTSEEEEEE-TT...............T--TTSHHHHHHHHHHH--SEEEE------H CS
                     RmlD_sub_bind   3 ilvtGanGqlGseLakqlaeeglevlaltre...............eldltdaeavaellkeakpdvvvnaAAytav 64 
                                       i+vtG+ G +Gs++a++l++++ +v+ +++                ++d++d +++ael+++   d v + AA   v
  gi|242398639|ref|YP_002994063.1|   7 IVVTGGAGFIGSHIAEELSKDN-DVIIIDNLyagkienippnvkfiRADIRDYKSMAELISQ--ADYVFHEAALVSV 80 
                                       89*****************988.899887778999*************************99..788*********9 PP

                                       HHHHHSHHHHHHHHTHHHHHHHHHHHHCT-EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHHH... CS
                     RmlD_sub_bind  65 DkaEseeeaayavnaeavealAeaaaavgalLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqavla... 138
                                        +  + + + +++n+ ++ ++ +a ++   ++i+ S+  V+  +++ p +e+++++Pl+ YG tK+  E   +    
  gi|242398639|ref|YP_002994063.1|  81 VESVERPLLTEEINVLGTLNVLKALSEGHGKFIFASSAAVYGDNQNLPLKESEKPKPLSPYGITKVSAEYYCKVfye 157
                                       999999***************************************************************99887555 PP

                                       .H-SSEEEEEE-SEESS.....SSS-HHHHHHHHHHH-SEEEEESS..-EE--EEHHHHHHHHHHHHHHCHH.GGG- CS
                     RmlD_sub_bind 139 .agkkalivRtswvyge.....kgknfvktmlrlakereelkvvaD..qlgsPTsardlAevllqllekaaeekela 207
                                        +g  ++ +R   v+ge     +    ++ ++++a + e+l +  D  q++   +++d+ ++ + ++e +++     
  gi|242398639|ref|YP_002994063.1| 158 lYGVPTVSLRYFNVFGErqgynQYAGVISIFINRALKGEPLIIYGDgkQTRDFIYVKDVVKANILAAESSKA---NG 231
                                       67778888*******997543333456778899**********99877899999999999988777776665...68 PP

                                       EEEE---BS-EEHHHHHHHHHHHHCHTT CS
                     RmlD_sub_bind 208 gvyHlanegetswlefArailkeagads 235
                                       +v+ +a  + ts le+A +i++ +g++s
  gi|242398639|ref|YP_002994063.1| 232 KVFNVAKGERTSILELALKIIEITGSSS 259
                                       9********************9998876 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.0   0.00065      0.84       1      21 [.       9      29 ..       9      38 .. 0.86
   2 !   37.5   0.0   1.1e-12   1.4e-09      79     227 ..      59     190 ..      32     220 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00065
                                      EE-TTSHHHHHHHHHHHHHS- CS
                     NAD_binding_4  1 lTGaTGFLGkvLlekLLrttp 21
                                      +TG+ GF+G+++ e+L ++++
  gi|242398639|ref|YP_002994063.1|  9 VTGGAGFIGSHIAEELSKDND 29
                                      7**************988775 PP

  == domain 2  score: 37.5 bits;  conditional E-value: 1.1e-12
                                       HHHHHHHHH--EEEE--SS-S.STTSSE...EHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS- CS
                     NAD_binding_4  79 edlqelaeevdviihsaAtvnfdepyke...llrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvy 152
                                       +++ el+++ d ++h aA v+++e++++     ++Nv+Gt +vl+  ++++ +  +++ S+a+v+g++++       
  gi|242398639|ref|YP_002994063.1|  59 KSMAELISQADYVFHEAALVSVVESVERpllTEEINVLGTLNVLKALSEGHGK--FIFASSAAVYGDNQNL------ 127
                                       57899**********************96666789*************99999..**************64...... PP

                                       H......HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE--SSST---TTSHHHHHHHH CS
                     NAD_binding_4 153 eegekeekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitgesktGwingsdlgirgllg 227
                                                  ++++++ +    Y  +K+ aE+ ++   +  g+p+v +R  ++ ge + G+ n+   +i+ ++ 
  gi|242398639|ref|YP_002994063.1| 128 ----------PLKESEKPKPLSPYGITKVSAEYYCKVFYELYGVPTVSLRYFNVFGERQ-GY-NQYAGVISIFIN 190
                                       ..........3556666777789*************99999999999999999998544.33.333324444444 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 !   29.3   0.0   5.3e-10   6.8e-07       1     127 [.      11     148 ..      11     154 .. 0.73

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 5.3e-10
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETT..HHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES-....... CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRn..peklaeleaeeglevvegdvtdvedlaealkgadaVvsal....... 68 
                                       G+ G +G+++++el +++  +v +++ n  + k+++++  ++++ + +d+ d +++ae +++ad V+  +       
  gi|242398639|ref|YP_002994063.1|  11 GGAGFIGSHIAEELSKDN--DV-IIIDNlyAGKIENIP--PNVKFIRADIRDYKSMAELISQADYVFHEAalvsvve 82 
                                       99***************6..54.677886788999886..9**************************9995554433 PP

                                       --TCCHHHH.............HHHHHHHHHHCT--EEEEEEETTTTSG.CGCHHHHHHH.HCCHHHHHHHHHH CS
                    NAD_binding_10  69 ggggkdeeg.............aknivdaakeagvkRfvlvsaigvgde.vpgefgewnk.ellkaylaakraa 127
                                       +       +             + n+++a+ e g  +f++ s++ v+ + ++ +++e  k + l++y + k  a
  gi|242398639|ref|YP_002994063.1|  83 S-------VerpllteeinvlgTLNVLKALSE-GHGKFIFASSAAVYGDnQNLPLKESEKpKPLSPYGITKVSA 148
                                       1.......2222344445888899***99965.78899999999998540333344333324555555555555 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.1   1.1e-07   0.00014       5      74 ..      12      72 ..       7      84 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.1e-07
                                      --SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEE CS
                   Sacchrp_dh_NADP  5 GaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvv 74
                                      GaG++G+ +ae+l++ +dv    +++d   ++  ++  +   +++++i  d+ +y++ +a+l++++d v 
  gi|242398639|ref|YP_002994063.1| 12 GAGFIGSHIAEELSKDNDV----IIIDNLYAG--KIE-N-IPPNVKFIRADIRDYKS-MAELISQADYVF 72
                                      56**************987....677776666..443.2.479**************.********9885 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   4.7e-07    0.0006       1      72 [.       5      69 ..       5     120 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 4.7e-07
                                      SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHH CS
                         adh_short  1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekav 72
                                      k ++vtG+++ IG  ia+el k+  +v+++d+        a ++++   ++ +i++D++d++++ +l+++a 
  gi|242398639|ref|YP_002994063.1|  5 KLIVVTGGAGFIGSHIAEELSKD-NDVIIIDNL------YAGKIENIPPNVKFIRADIRDYKSMAELISQAD 69
                                      679*****************988.566666655......45566666677******************9985 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1     3e-06    0.0038       1      73 [.       7      76 ..       7     125 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3e-06
                                      EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT-SEEEE--- CS
                              NmrA  1 IlviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelvkgdlddkeslvealkgvdvvfsvtg 73
                                      I+v+G++G +G+++++ l k++ +v +++ ++   +++++  + v+++ +d+ d++s++e+++++d vf   +
  gi|242398639|ref|YP_002994063.1|  7 IVVTGGAGFIGSHIAEELSKDN-DV-IIIDNLYAGKIENIPPN-VKFIRADIRDYKSMAELISQADYVFHEAA 76
                                      89**************998865.44.56788888888888765.99***********************8766 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   1.2e-05     0.015       5      57 ..      12      63 ..       7      84 .. 0.79
   2 ?   -2.8   0.0       5.6   7.2e+03      74      90 ..     218     233 ..     210     250 .. 0.58

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.2e-05
                                      S-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHH CS
                            TrkA_N  5 GlGrvGrslaeeLseggkdvvvidkdeerveelreeglevvvgdatdeevLee 57
                                      G+G +G+++aeeLs+++ dv++id+  +   e    +++++ +d  d + ++e
  gi|242398639|ref|YP_002994063.1| 12 GAGFIGSHIAEELSKDN-DVIIIDNLYAGKIENIPPNVKFIRADIRDYKSMAE 63
                                      79*************99.6*****97765555566777788888777777665 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 5.6
                                       HHHHHHHHHHHHHTSSS CS
                            TrkA_N  74 eanilavllakelnpkk 90 
                                       +anila+++ k  n+k 
  gi|242398639|ref|YP_002994063.1| 218 KANILAAESSKA-NGKV 233
                                       566666666653.4333 PP

>> DUF1188  Protein of unknown function (DUF1188)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   3.3e-05     0.043      43      87 ..       4      50 ..       1      77 [. 0.70

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.3e-05
                                      .EEEEEE.S-CCCHHHHHHHHCCCEEEEEEES.SGGGGGGSSSTHHH CS
                           DUF1188 43 eknvlvi.GaYltGaaiakkLskkeevtlvDi.ephlkellekdvef 87
                                      +k ++v  Ga + G+ ia++Lsk+++v+++D  +    e ++++v+f
  gi|242398639|ref|YP_002994063.1|  4 NKLIVVTgGAGFIGSHIAEELSKDNDVIIIDNlYAGKIENIPPNVKF 50
                                      44455554689********************6233333445666666 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.4    0.0009       1.1       4      76 ..       8      69 ..       6     127 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0009
                                      EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHH CS
                                KR  4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeik 76
                                      ++tGG+G +G ++a+ l ++    ++++               ++e+   +v++++aD+ d +++++l+++++
  gi|242398639|ref|YP_002994063.1|  8 VVTGGAGFIGSHIAEELSKDND--VIIIDNL---------YAGKIENIPPNVKFIRADIRDYKSMAELISQAD 69
                                      79*************9988754..3333333.........223445555678888888888888888887776 PP

>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       3.9     5e+03      57      66 ..      26      35 ..       5      37 .. 0.57
   2 ?   10.9   0.0   0.00032      0.41       6      38 ..     204     236 ..     199     260 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3.9
                           UPF0113 57 aspgkivvkn 66
                                      ++++ i+++n
  gi|242398639|ref|YP_002994063.1| 26 KDNDVIIIDN 35
                                      3444555555 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00032
                           UPF0113   6 ekaeklFLYGrdvlkesilkitesvkenqvvvV 38 
                                        k  ++F+Y +dv+k +il  ++s+ +++v  V
  gi|242398639|ref|YP_002994063.1| 204 GKQTRDFIYVKDVVKANILAAESSKANGKVFNV 236
                                       578899****************99997776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.62u 0.38s 00:00:01.00 Elapsed: 00:00:00.54
# Mc/sec: 1715.50
//
Query:       gi|242398640|ref|YP_002994064.1|  [L=339]
Description: Adenylosuccinate synthetase [Thermococcus sibiricus MM 739]
Scores for 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-91  305.7   1.9      2e-43  148.9   0.0    3.0  3  Adenylsucc_synt  Adenylosuccinate synthetase
  ------ inclusion threshold ------
       0.07   12.1   0.0      0.092   11.7   0.0    1.1  1  CytochromB561_N  Cytochrome B561, N terminal


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 !  132.1   0.2   2.8e-42   2.5e-38       2     150 ..       5     150 ..       4     152 .. 0.95
   2 !  148.9   0.0   2.2e-47     2e-43     192     334 ..     150     290 ..     149     293 .. 0.96
   3 !   25.1   0.0   8.2e-10   7.4e-06     376     419 .]     290     333 ..     287     333 .. 0.92

  Alignments for each domain:
  == domain 1  score: 132.1 bits;  conditional E-value: 2.8e-42
                                       EEEE-SSS-S-HHHHHHHH..HTT-SEEEE-SB-TTSSEEEEETTEEEEESSS-GGGGSTT-EEEE-TTBEE-HHHH CS
                   Adenylsucc_synt   2 vvvGaqwGDEGKGkivDll..aeeadvvvRfqGGanAGHtvvvdgkkyklhllpSGilnpgvvnviGngvvvdpeal 76 
                                       +vvG qwGDEGKG i+ +l  +++ +v++R   G nAGH v+++gkky++++lp G +n++++ ++G+gv+vdpe++
  gi|242398640|ref|YP_002994064.1|   5 IVVGGQWGDEGKGSIIAYLaiHDKPEVIARGGVGTNAGHSVFINGKKYAVRQLPTGFMNENARLLVGAGVLVDPEVF 81 
                                       8******************444579**************************************************** PP

                                       HHHHTTSS-TT......TEEEETTSEE--HHHHHHHHHHHHH----------TTHHHHHHHHHTT---BGGGGG CS
                   Adenylsucc_synt  77 leEieeleakgvelskerllisdrahlvlpyhkalDkleeaakgkkkiGtTkkGiGpayadkvarrgirvgdll 150
                                       ++E+e+l++ +v   ++r+ ++ r++++ p hk+lD+ +   +g  kiGtT++G Gpa ad++ r++ +v+dl 
  gi|242398640|ref|YP_002994064.1|  82 FHELEHLKDFNV---RGRIGLDYRCTVIEPGHKELDRSNGYLHG--KIGTTGSGCGPANADRALRKAKQVKDLK 150
                                       ********9887...57**********************99776..**************************96 PP

  == domain 2  score: 148.9 bits;  conditional E-value: 2.2e-47
                                       HHHGGGEE-HHHHHHHHHHTT--EEEE--S-GGG-TTTSSTTSS-SS--SHHHHHHHTT--GGGEEEEEEEEESSEE CS
                   Adenylsucc_synt 192 erlkpyvvdtvallnealkegkkvLfEGaqgtllDidhGtYPfvTsSnttaggaltglglapkkidevlgvvKAytt 268
                                       ++l+py++d+ +++neal+egk vL+EG qg  l++ +G+YP+vTs  t+a+ +++  g++p+++d+v+ v+K++ t
  gi|242398640|ref|YP_002994064.1| 150 KELEPYLTDVAQEVNEALDEGKLVLVEGTQGFGLSLYYGSYPYVTSKDTSASAIASDVGIGPTRVDDVIVVFKSFPT 226
                                       6899************************************************************************* PP

                                       ESSSS--TTB--SHHHHHHHHHTT.-B-TTT--B-EEE-EEHHHHHHHHHHHT-SEEEEE-GGGGTT CS
                   Adenylsucc_synt 269 rvGeGpfptelkdevgeklrekGk.EfgtttgrpRrcGwlDlvllryavrvngvtelaltklDvldg 334
                                       rvG+Gpfpte+++e++e++   G  E+gt+tgr+Rr+Gw+D   +ry++r+ng+t la+t lD  d+
  gi|242398640|ref|YP_002994064.1| 227 RVGAGPFPTEMSEEEAERM---GLvEYGTVTGRRRRVGWFDFEFARYSARINGATMLAVTMLDKYDK 290
                                       ***********99999988...434**************************************8875 PP

  == domain 3  score: 25.1 bits;  conditional E-value: 8.2e-10
                                       S--TT---GGGS-HHHHHHHHHHHHHHTS-EEEEE-SSSTT-EE CS
                   Adenylsucc_synt 376 edisgvrsfedlpenakkyvefieellgvpvkiisvGpereqti 419
                                       ++  gv++f++lp++ak++++ iee +gvpv++i +Gpe e++i
  gi|242398640|ref|YP_002994064.1| 290 KEAFGVTDFNKLPQKAKDFIAEIEEKVGVPVALIKTGPELEHII 333
                                       667789*********************************99987 PP

>> CytochromB561_N  Cytochrome B561, N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0     1e-05     0.092     226     319 ..     135     243 ..     126     266 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1e-05
                   CytochromB561_N 226 wsrkraksakeirtekqLerflaevdekitesa..................fgkaspsnvagslnrSgsarstplrs 284
                                       ++++   +ak++++ k Le +l +v ++++e+                      + p   ++ + +S  a   ++ +
  gi|242398640|ref|YP_002994064.1| 135 NADRALRKAKQVKDLKELEPYLTDVAQEVNEALdegklvlvegtqgfglslYYGSYPYVTSKDTSASAIASDVGIGP 211
                                       455666788999999*************99999*************999975555666666688999999999**** PP

                   CytochromB561_N 285 vrmspgs.qkkttppkkgegdlPskmsmeeaieafe 319
                                        r+++     k+ p + g g +P  ms eea    e
  gi|242398640|ref|YP_002994064.1| 212 TRVDDVIvVFKSFPTRVGAGPFPTEMSEEEA----E 243
                                       *******6667778899************99....3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      559  (0.0311785); 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: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2249.99
//
Query:       gi|242398641|ref|YP_002994065.1|  [L=267]
Description: hypothetical protein TSIB_0651 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0074   15.9   0.3      0.015   14.8   0.3    1.5  1  DUF2268   Predicted Zn-dependent protease (DUF2268)


Domain annotation for each model (and alignments):
>> DUF2268  Predicted Zn-dependent protease (DUF2268)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.3   8.5e-07     0.015      57     177 ..     123     243 ..      71     260 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 8.5e-07
                           DUF2268  57 eneyskerlaallaHEyhHvvrlkqlekeeksiTllesivl....EGlAesfatelvge....eklapwtskldeet 125
                                        + +  ++l+ l+aHE+ H++ +    ++     l++  ++    EG A+  ++ + g+    e+ + w+++ + ++
  gi|242398641|ref|YP_002994065.1| 123 AELKWYNKLKGLIAHEFGHLIHWLLRGED--IEKLEDEQIMwiytEGFAQRIEDLISGRpwhlEE-PGWFEWCERNE 196
                                       34455679*************99888866..44455544433444*********99998333223.56666666555 PP

                           DUF2268 126 ...leellkkvikeeldlkgfsevseylyGdekakiPkllgYalGYkivkkyLek 177
                                          ++e+l++v+++e  l+ f      l+G  k    ++lgY+lGYk ++ ++e+
  gi|242398641|ref|YP_002994065.1| 197 giiKREFLRRVKENEP-LNPFFGSWYTLFG--K----QYLGYYLGYKFIR-WIEQ 243
                                       3325555555555444.4447777777888..3....5999999999874.4554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       764  (0.0426125); expected 358.6 (0.02)
Passed bias filter:                      585  (0.0326287); 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: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 1740.50
//
Query:       gi|242398642|ref|YP_002994066.1|  [L=61]
Description: Lysophospholipase, alpha/beta hydrolase superfamily [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-17   64.0   0.1    1.3e-17   63.9   0.1    1.0  1  Hydrolase_4    Serine aminopeptidase, S33
      2e-08   34.2   0.1    2.3e-08   34.0   0.1    1.0  1  Abhydrolase_1  alpha/beta hydrolase fold
    2.4e-06   28.3   0.1    2.8e-06   28.1   0.1    1.0  1  Abhydrolase_6  Alpha/beta hydrolase family
  ------ inclusion threshold ------
       0.17   11.9   0.0       0.23   11.4   0.0    1.2  1  RMMBL          Zn-dependent metallo-hydrolase RNA specificity
        0.2   11.2   0.0       0.21   11.1   0.0    1.0  1  Lipase_2       Lipase (class 2)


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 !   63.9   0.1   3.5e-21   1.3e-17       2      50 ..      10      57 ..       9      61 .] 0.93

  Alignments for each domain:
  == domain 1  score: 63.9 bits;  conditional E-value: 3.5e-21
                       Hydrolase_4  2 epkavvvlvHGlaehsgryaelaeaLaaqGfavyalDhrGhGrsegkrg 50
                                      ++k+ vvlvHGl+ehsgry +l++ L++qGfavy++D+ GhG+s g+r 
  gi|242398642|ref|YP_002994066.1| 10 PEKGWVVLVHGLGEHSGRYGKLIKMLNEQGFAVYTFDWPGHGKS-GERS 57
                                      67999***************************************.7664 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   0.1   6.3e-12   2.3e-08       1      48 [.      13      58 ..      13      60 .. 0.94

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 6.3e-12
                                      SEEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTT CS
                     Abhydrolase_1  1 pvlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapa 48
                                      +++v++hGl++ s+ + +  l++ L+++gf v+++D++G+g+S  +++
  gi|242398642|ref|YP_002994066.1| 13 GWVVLVHGLGEHSGRYGK--LIKMLNEQGFAVYTFDWPGHGKSGERSS 58
                                      68*************999..***********************88776 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.1   7.8e-10   2.8e-06       1      40 [.      15      53 ..      15      60 .. 0.83

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 7.8e-10
                                      EEEE--GC.....GCHHHHHHHHCCT.CEEEEE--TTSTS- CS
                     Abhydrolase_6  1 vlllHGagssassWlvapLaallaag.vhvlapDlpGhGrs 40
                                      v+l+HG+g +++ +    L + l+++ ++v+++D+pGhG s
  gi|242398642|ref|YP_002994066.1| 15 VVLVHGLGEHSGRYG--KLIKMLNEQgFAVYTFDWPGHGKS 53
                                      8*******9999996..8888888888999********944 PP

>> RMMBL  Zn-dependent metallo-hydrolase RNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   6.4e-05      0.23      31      60 ..      10      43 ..       6      45 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.4e-05
                             RMMBL 31 prn..vilvHGeeeatsalarllk..eeegidvf 60
                                      p++  v+lvHG  e+  ++ +l+k   e g  v+
  gi|242398642|ref|YP_002994066.1| 10 PEKgwVVLVHGLGEHSGRYGKLIKmlNEQGFAVY 43
                                      77789*****************976666666555 PP

>> Lipase_2  Lipase (class 2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   5.8e-05      0.21       4      43 ..      15      50 ..      12      60 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 5.8e-05
                          Lipase_2  4 viivhGnsdlaaeklskliqkflekgyteaelYattygdt 43
                                      v++vhG  +  ++++ kli+ + e+g++   +Y++ +   
  gi|242398642|ref|YP_002994066.1| 15 VVLVHGLGE-HSGRYGKLIKMLNEQGFA---VYTFDWPGH 50
                                      9******65.788*************86...599999544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 417.06
//
Query:       gi|242398643|ref|YP_002994067.1|  [L=107]
Description: hypothetical protein TSIB_0653 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0036   17.1   0.6     0.0036   17.1   0.6    2.9  3  LapA_dom  Lipopolysaccharide assembly protein A domain
  ------ inclusion threshold ------
      0.022   14.6   0.9      0.022   14.6   0.9    2.1  3  DUF2062   Uncharacterized protein conserved in bacteria (DUF2


Domain annotation for each model (and alignments):
>> LapA_dom  Lipopolysaccharide assembly protein A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   4.5      0.36   3.2e+03      28      28 ..      22      22 ..       5      54 .. 0.60
   2 ?    0.8   0.4      0.05   4.5e+02      18      29 ..      29      40 ..      22      66 .. 0.65
   3 !   17.1   0.6   4.1e-07    0.0036       6      49 ..      61     103 ..      59     107 .] 0.83

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.36
                          LapA_dom 28 g 28
                                      +
  gi|242398643|ref|YP_002994067.1| 22 I 22
                                      1 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.05
                          LapA_dom 18 pLsllllvafgi 29
                                      + ++l lv f+i
  gi|242398643|ref|YP_002994067.1| 29 SFYTLYLVLFLI 40
                                      555555555554 PP

  == domain 3  score: 17.1 bits;  conditional E-value: 4.1e-07
                          LapA_dom   6 Vtvnfl.faqv.elpLsllllvafgiGallgwllslwsylrlrrel 49 
                                       +++ +l +  v +lp  ++llvaf +G++++++ ++w   + r++ 
  gi|242398643|ref|YP_002994067.1|  61 IPLTYLaVENVkKLPALTVLLVAFELGLIAMYVKMVW---KIRWRT 103
                                       678888544467*************************...777764 PP

>> DUF2062  Uncharacterized protein conserved in bacteria (DUF2062)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       0.3   2.7e+03     121     131 ..      11      21 ..       5      39 .. 0.57
   2 ?   14.6   0.9   2.4e-06     0.022      42      72 ..      37      67 ..      30      72 .. 0.89
   3 ?   -0.6   0.2      0.12   1.1e+03     126     144 ..      86     104 ..      73     107 .] 0.62

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.3
                           DUF2062 121 lilglilallg 131
                                       ++l l+l+++g
  gi|242398643|ref|YP_002994067.1|  11 FVLVLVLGIAG 21 
                                       44444444443 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 2.4e-06
                           DUF2062 42 llaallalllrvnlpaavagtwisnPltlpp 72
                                      l+ + l +++r n+p++ +g+++s Plt++ 
  gi|242398643|ref|YP_002994067.1| 37 LFLITLSAIVRKNMPISTVGVLLSIPLTYLA 67
                                      56778999********************975 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.12
                           DUF2062 126 ilallgYflvlllwrlyrr 144
                                       ++ +++Y+ + + +r++ +
  gi|242398643|ref|YP_002994067.1|  86 LGLIAMYVKMVWKIRWRTQ 104
                                       4556677777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       754  (0.0420548); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 709.15
//
Query:       gi|242398644|ref|YP_002994068.1|  [L=240]
Description: hypothetical protein TSIB_0654 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       869  (0.048469); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 1452.40
//
Query:       gi|242398645|ref|YP_002994069.1|  [L=114]
Description: hypothetical protein TSIB_0655 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0051   17.3  10.0      0.019   15.5   1.2    2.5  2  YoqO      YoqO-like protein
  ------ inclusion threshold ------
       0.34   10.9   8.9       0.61   10.1   8.9    1.5  1  BCHF      2-vinyl bacteriochlorophyllide hydratase (BCHF)


Domain annotation for each model (and alignments):
>> YoqO  YoqO-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   1.7   0.00075       6.7      61      93 ..      28      60 ..      19      74 .. 0.77
   2 !   15.5   1.2   2.1e-06     0.019      13      54 ..      71     111 ..      60     113 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00075
                              YoqO 61 tlvilvllivflllkgqelidklsifqglltia 93
                                       l++  ++i+f ++ +  li k++if g+++  
  gi|242398645|ref|YP_002994069.1| 28 PLFVALATIMFPIIASYGLIVKFKIFPGVIFAT 60
                                      47788899*********************9854 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 2.1e-06
                              YoqO  13 llsvvlksflknesianiivigvlifvllYnwDelKkySkks 54 
                                        l + + +f++ +++++++  +v+ifv++Y +D++++  +ks
  gi|242398645|ref|YP_002994069.1|  71 DLLIGSLTFETVKTVSVKLS-TVIIFVVVYLFDKIRRGERKS 111
                                       4666677899*******998.88***********99888876 PP

>> BCHF  2-vinyl bacteriochlorophyllide hydratase (BCHF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   8.9   6.8e-05      0.61      26      90 ..       9      73 ..       7     105 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 6.8e-05
                              BCHF 26 flvflvslalvllylatgegfalvtvsvllktlllvlilitGaifekevfgkylfakeffweDvg 90
                                      ++vfl+sl+l+ l + +g+ ++++ +++++ ++  + +++   if  ++f + l+a + f  D+ 
  gi|242398645|ref|YP_002994069.1|  9 YFVFLISLILTGLAVFDGTPLFVALATIMFPIIASYGLIVKFKIFPGVIFATILWALSIFVRDLL 73
                                      689*******************************************************9999964 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       784  (0.043728); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 685.93
//
Query:       gi|242398646|ref|YP_002994070.1|  [L=46]
Description: hypothetical protein TSIB_0656 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      172  (0.0095934); 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 0.28s 00:00:00.72 Elapsed: 00:00:00.49
# Mc/sec: 284.95
//
Query:       gi|242398647|ref|YP_002994071.1|  [L=46]
Description: hypothetical protein TSIB_0657 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.31s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 286.62
//
Query:       gi|242398648|ref|YP_002994072.1|  [L=50]
Description: hypothetical protein TSIB_0658 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       590  (0.0329076); 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: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 339.40
//
Query:       gi|242398649|ref|YP_002994073.1|  [L=421]
Description: S-adenosyl-L-homocysteine hydrolase [Thermococcus sibiricus MM 739]
Scores for complete 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-66  223.4   0.0    7.8e-35  120.5   0.0    2.0  2  AdoHcyase      S-adenosyl-L-homocysteine hydrolase
    8.7e-51  172.2   0.2    1.7e-50  171.3   0.1    1.6  2  AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD bindi
    1.2e-07   31.3   0.1    2.9e-07   30.0   0.1    1.6  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
    1.4e-05   24.8   0.1    2.8e-05   23.8   0.1    1.5  1  IlvN           Acetohydroxy acid isomeroreductase, NADPH-bind
    0.00081   19.3   1.9       0.15   12.0   0.5    2.4  2  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
  ------ inclusion threshold ------
      0.014   14.6   0.1      0.028   13.6   0.1    1.5  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
      0.021   15.1   0.1      0.059   13.6   0.1    1.7  1  TrkA_N         TrkA-N domain
      0.057   12.7   0.4       0.13   11.6   0.4    1.6  1  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
        0.1   12.4   0.0       0.38   10.6   0.0    2.0  1  NifT           NifT/FixU protein


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 !  120.5   0.0   3.9e-38   7.8e-35       1     139 [.       6     139 ..       6     146 .. 0.96
   2 !  102.3   0.0   1.4e-32   2.7e-29     174     287 ..     141     416 ..     137     421 .] 0.98

  Alignments for each domain:
  == domain 1  score: 120.5 bits;  conditional E-value: 3.9e-38
                                       --B-S-GGGHHHHHHHHHHHHCC-HHHHHHHHHCTTT-TTTT-EEEEES--SHHHHHHHHHHHHTT-EEEEE-SSTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         AdoHcyase   1 dykvkdislaefGrkeielaekempglmalreeyaeekplkgariaGslhmtiqtavLietLvalGaevrWasCnif 77 
                                       dy+vkdi+la  G k+i+   + mp l ++r+e+++ kp+kg++ia +lh+ ++ta L+ tL+a Gaev  ++ n  
  gi|242398649|ref|YP_002994073.1|   6 DYCVKDINLAPEGEKKIDWVSRFMPVLQHIRKEFEKGKPFKGVKIAATLHLEMKTAFLLLTLKAAGAEVSTTASNPL 82 
                                       8**************************************************************************** PP

                                       T--HHHHHHHCCTTEEEE--TT--HHHHHHHHHHCHS-SSTS-S-SEEEESSSHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         AdoHcyase  78 stqdeaaaaiaeagvpvfawkgetleeywwcieqalkwaedekepnlilDdGGDltllvhkg 139
                                       stqd++ aa+a++gv+v+a++ge+  ey +++++al+      epn+i+DdG D+  +v k 
  gi|242398649|ref|YP_002994073.1|  83 STQDDVVAALAKNGVKVYAIRGESRGEYYEFMHKALDI-----EPNIIIDDGADMVSTVLKE 139
                                       ************************************66.....7***********9999883 PP

  == domain 2  score: 102.3 bits;  conditional E-value: 1.4e-32
                                       CCCHCC--EEEE-SHHHHHHHHHHHHTT---SEEEESTTSHHHCTTH.............................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............................. RF
                         AdoHcyase 174 tellkkikGvseetttGvhrLyelakkgkLlvpainvndsvtkskfD.............................. 220
                                       +el+ +i G seetttGv rL  ++k+g L++p i vnds tk  fD                              
  gi|242398649|ref|YP_002994073.1| 141 QELIPEIWGASEETTTGVIRLRAMEKDGVLKFPIIAVNDSYTKYLFDnrygtgqstwdgiirstnllvagknvvvvg 217
                                       5778899********************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                         AdoHcyase 221 ............................................................................. 220
                                                                                                                    
  gi|242398649|ref|YP_002994073.1| 218 ygwcgrgiamrarglgatvivvevdpikalearmdgflvmpmkeaakvgdifvtstgnincirgehfevmkdgvlma 294
                                       ***************************************************************************** PP

                                       .......................................................S-HHHHHHHHHHHHHHHHHHHH CS
                                       .......................................................xxxxxxxxxxxxxxxxxxxxxx RF
                         AdoHcyase 221 .......................................................hpsfvmsasftnqvlaqielfk 242
                                                                                              hp+ +m++sf+ q+ a   + +
  gi|242398649|ref|YP_002994073.1| 295 naghfdveiskpdleslaveinnprpniteyklkdgrrlyllaegrlvnlaaadgHPAEIMDMSFALQAKAAEYIKD 371
                                       ***********************************************************************999999 PP

                                       TTSSS-SSEEE--CHHHHHHHHHCCCCCT-------HHHHHCCTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         AdoHcyase 243 kekkyekkvyvlpkklDekvarlhleklgaklteltkeqaeyigv 287
                                       +++k e kvyvlp+++De va+++l+++g+++++lt+eq +y++ 
  gi|242398649|ref|YP_002994073.1| 372 NHEKLEPKVYVLPREIDEMVAKIKLKSMGIEIEQLTEEQRKYLES 416
                                       9999**************************************985 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       4.6   9.3e+03      42      59 ..      67      84 ..      66      96 .. 0.80
   2 !  171.3   0.1   8.4e-54   1.7e-50       1     161 [.     188     348 ..     188     349 .. 0.99

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 4.6
                                      HHHCT-EEEEE-S-HHHH CS
                     AdoHcyase_NAD 42 lkglGarvivtevdPica 59
                                      lk++Ga v  t  +P+++
  gi|242398649|ref|YP_002994073.1| 67 LKAAGAEVSTTASNPLST 84
                                      789999999998888765 PP

  == domain 2  score: 171.3 bits;  conditional E-value: 8.4e-54
                                       HHHHHCCCCCHHHHHHH-S--TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHHHHHCTT-EE--HHHCTT CS
                     AdoHcyase_NAD   1 nlygcreslvdgikratdvllaGkvavvaGyGdvGkGcaaslkglGarvivtevdPicalqaameGfevvtleevvk 77 
                                       n yg+ +s  dgi r+t++l+aGk++vv+GyG  G+G a   +glGa viv evdPi al a m+Gf v+ ++e++k
  gi|242398649|ref|YP_002994073.1| 188 NRYGTGQSTWDGIIRSTNLLVAGKNVVVVGYGWCGRGIAMRARGLGATVIVVEVDPIKALEARMDGFLVMPMKEAAK 264
                                       78*************************************************************************** PP

                                       T-SEEEE-SSSSSSB-HHHHCCS-TTEEEEE-SSTTTTBTHHHHHTTT-EEEEEETTEEEEE-TTS-EEEEEGGGSB CS
                     AdoHcyase_NAD  78 kadivvtttGnkdiitlehlkkmkddaivcniGhfdseidvaaleanalkkeevkpqvdrvtlkdgkkiillaeGrl 154
                                        +di+vt+tGn + i+ eh++ mkd ++++n Ghfd ei    le+ a+++++ +p++ +++lkdg+++ llaeGrl
  gi|242398649|ref|YP_002994073.1| 265 VGDIFVTSTGNINCIRGEHFEVMKDGVLMANAGHFDVEISKPDLESLAVEINNPRPNITEYKLKDGRRLYLLAEGRL 341
                                       ***************************************************************************** PP

                                       CHHHTS- CS
                     AdoHcyase_NAD 155 lnlgcat 161
                                       +nl++a 
  gi|242398649|ref|YP_002994073.1| 342 VNLAAAD 348
                                       ***9986 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.1   1.4e-10   2.9e-07      30     127 ..     204     297 ..     182     303 .. 0.88

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 1.4e-10
                                       SBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-SEEEE-S--STTTT CS
                      2-Hacid_dh_C  30 lgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelvsleellaesDivslhlpltpetr 106
                                       +   ++gk v ++G+G  G+ +a r++++g+ vi++++ + k  e++  g+ ++ ++e+ +  Di +  +     + 
  gi|242398649|ref|YP_002994073.1| 204 TNLLVAGKNVVVVGYGWCGRGIAMRARGLGATVIVVEVDPIKALEARMDGFLVMPMKEAAKVGDIFVTSTG----NI 276
                                       445689*********************************9988899999****************998765....99 PP

                                       TSBSHHHHHCSTTTEEEEESS CS
                      2-Hacid_dh_C 107 hlinaeelakmkkgailiNta 127
                                       + i  e+++ mk+g+++ N++
  gi|242398649|ref|YP_002994073.1| 277 NCIRGEHFEVMKDGVLMANAG 297
                                       9****************9987 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 !   23.8   0.1   1.4e-08   2.8e-05       2      65 ..     208     270 ..     207     304 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1.4e-08
                                       HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEE CS
                              IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvm 65 
                                       + gk+++v+GyG  G+  a+  r  g  v+v   +   ++ +A+ +gf v+ ++ea+k  d+ +
  gi|242398649|ref|YP_002994073.1| 208 VAGKNVVVVGYGWCGRGIAMRARGLGATVIVVEVDPI-KALEARMDGFLVMPMKEAAKVGDIFV 270
                                       579****************999999999999777766.6788******************9876 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.5   7.4e-05      0.15       1      38 [.     212     249 ..     212     272 .. 0.88
   2 !    6.4   0.0    0.0038       7.6      16      70 ..     343     397 ..     339     408 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.4e-05
                                       EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHH CS
                           3HCDH_N   1 kvaviGaGtmGagiaavfasagleVvlvdiseealeka 38 
                                       +v v+G G  G+gia+ +   g +V +v++++ ++ +a
  gi|242398649|ref|YP_002994073.1| 212 NVVVVGYGWCGRGIAMRARGLGATVIVVEVDPIKALEA 249
                                       699***************************98666555 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0038
                                       HHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEEE CS
                           3HCDH_N  16 avfasagleVvlvdiseealekalekieksleklvekgklkeeeveaalarisft 70 
                                       +++a+ g++  ++d+s +  +ka+e i+++ ekl+ k  +   e+++++a+i+ +
  gi|242398649|ref|YP_002994073.1| 343 NLAAADGHPAEIMDMSFALQAKAAEYIKDNHEKLEPKVYVLPREIDEMVAKIKLK 397
                                       678999********************************************99976 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   1.4e-05     0.028       2      51 ..     212     267 ..     191     329 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.4e-05
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEE......TTHCHHHCSHHHHCHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlve......legtclnggcllskallgvae 51 
                                       +vvv+G G+ G   a++++  ga v++ve      le  + ++ +++ k++++v++
  gi|242398649|ref|YP_002994073.1| 212 NVVVVGYGWCGRGIAMRARGLGATVIVVEvdpikaLEARMDGFLVMPMKEAAKVGD 267
                                       57777777777777777777777777776556555555555555555555555555 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   2.9e-05     0.059       1      44 [.     213     256 ..     213     264 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.9e-05
                                       EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTTSEE CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreeglev 44 
                                       ++++G+G  Gr +a + +  g   v+v++ d+ ++ e+r +g+ v
  gi|242398649|ref|YP_002994073.1| 213 VVVVGYGWCGRGIAMRARGlGA-TVIVVEVDPIKALEARMDGFLV 256
                                       79*****************777.6********9999999998776 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 ?   11.6   0.4   6.3e-05      0.13      26      63 ..     208     245 ..     188     305 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.3e-05
                                       B---EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHH CS
                       AlaDh_PNT_C  26 vepakvlviGgGvaGlqAiatakglgakVtvlDvrpar 63 
                                       v+  +v+v+G G  G   +  a+glga+V v++v+p +
  gi|242398649|ref|YP_002994073.1| 208 VAGKNVVVVGYGWCGRGIAMRARGLGATVIVVEVDPIK 245
                                       55678****************************99854 PP

>> NifT  NifT/FixU protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00019      0.38       8      49 ..     294     335 ..     287     341 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00019
                                       -SS-E.EEEETTTTEEEEEEEESSSSS-SSEEEETTS-EEE- CS
                              NifT   8 neeGklsvYvpKkDLEekvveeekeekwGgevtLanGwelel 49 
                                        ++G++ v + K DLE   ve ++++   +e++L++G +l+l
  gi|242398649|ref|YP_002994073.1| 294 ANAGHFDVEISKPDLESLAVEINNPRPNITEYKLKDGRRLYL 335
                                       57899***************999999659***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       740  (0.0412739); expected 358.6 (0.02)
Passed bias filter:                      676  (0.0377043); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); 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 0.27s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2955.11
//
Query:       gi|242398650|ref|YP_002994074.1|  [L=200]
Description: Cyclase-related protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.2e-25   88.0   0.0      1e-24   87.3   0.0    1.4  1  Cyclase   Putative cyclase


Domain annotation for each model (and alignments):
>> Cyclase  Putative cyclase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.3   0.0   5.7e-29     1e-24       1     134 [.      13     143 ..      13     145 .. 0.89

  Alignments for each domain:
  == domain 1  score: 87.3 bits;  conditional E-value: 5.7e-29
                           Cyclase   1 idLshplsedtpvwp.dp...................islsehtGTHlDapgHfae..ktidelpleelvgpavvld 55 
                                       idL+++lse+tpv+p dp                   + l+eh+GTH+Dap+Hf++  +tide+ple+++g+++v+d
  gi|242398650|ref|YP_002994074.1|  13 IDLTMELSEKTPVYPgDPkieikewtdvekdgyqmntLFLGEHSGTHVDAPAHFIPggRTIDEMPLEKFIGKGIVID 89 
                                       8*************6566778888999*****************************999****************** PP

                           Cyclase  56 vsakaaaedyeiitaedleaalakqgveikpgdivlirTgwskrledkekyrnpglseeaaewlaekgvkavGvDtl 132
                                       vs+     d +i +++++          ++  +ivl++Tg +   +        +lsee+a++l++ +vkavG+D+ 
  gi|242398650|ref|YP_002994074.1|  90 VSQL----DRNI-EPSEM----------LRVAEIVLFYTGGK---A-------IYLSEEGARYLIDLRVKAVGIDNS 141
                                       *886....4435.88888..........44568******964...3.......79********************97 PP

                           Cyclase 133 sv 134
                                        +
  gi|242398650|ref|YP_002994074.1| 142 TI 143
                                       65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1610.56
//
Query:       gi|242398651|ref|YP_002994075.1|  [L=397]
Description: Probable aminomethyltransferase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-97  325.6   0.0    2.4e-97  325.3   0.0    1.1  1  GCV_T     Aminomethyltransferase folate-binding domain
    1.3e-21   76.3   0.1    2.9e-21   75.2   0.1    1.6  1  GCV_T_C   Glycine cleavage T-protein C-terminal barrel domain


Domain annotation for each model (and alignments):
>> GCV_T  Aminomethyltransferase folate-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  325.3   0.0  2.7e-101   2.4e-97       2     257 .]       7     286 ..       6     286 .. 0.96

  Alignments for each domain:
  == domain 1  score: 325.3 bits;  conditional E-value: 2.7e-101
                             GCV_T   2 ydrhkalgakfvefagwemPvqYasesikaehlavreaaglfDvShmgkievsGpdaaalLqrlltndisklkpgka 78 
                                       +d+hk++ +k++efagwemP++Y  +sik+ehlavr+++g+fDvShmg++ ++G+da+++Lq+++tndis+++++++
  gi|242398651|ref|YP_002994075.1|   7 FDWHKEHAKKVEEFAGWEMPIWY--SSIKEEHLAVRNGVGIFDVSHMGEVFFKGKDALKFLQYVTTNDISRPPAISG 81 
                                       79*********************..**************************************************** PP

                             GCV_T  79 tytlllnedGgvidDlivarldedefllvvnaankekdlawlekaaek.....kdldvevedvteelallalqGPka 150
                                       ty+l+lne+G v+d+++v+++++d++++v+++++ ek++aw+++ +++     ++ld+e+e++t+++ ++++qGPka
  gi|242398651|ref|YP_002994075.1|  82 TYSLVLNERGAVKDETLVFNMGNDTYMMVCDSDAFEKLYAWFTS-IKRaieqyTELDLEIENKTYDYVMFSIQGPKA 157
                                       *****************************************655.33335559************************ PP

                             GCV_T 151 revlskllgadlselkffsfaevelaggkkvlvsRtgytGedGfeiyipa..............eeaeelweaLlea 213
                                       ++++++l+g+d+++l++f+++evel+ g+k+l+sR+gytGe+Gfe+y+++              e+a  +we++lea
  gi|242398651|ref|YP_002994075.1| 158 KDLAMELFGIDINQLWWFQAKEVELD-GIKMLLSRSGYTGENGFEVYFEDvnpyhpdeskhgkpEKALYVWEKILEA 233
                                       **************************.************************************************** PP

                             GCV_T 214 gkeegvkpaGlgArdtlRlEaglrlyghd......ldee...ttPleaglgwa 257
                                       g+++g+kpaGlgArdtlRlEag++lyg++      l+++   +tPl+a+l++a
  gi|242398651|ref|YP_002994075.1| 234 GQKYGIKPAGLGARDTLRLEAGYTLYGNEtkelqlLSTDideVTPLQANLEFA 286
                                       *****************************77777755557789*******985 PP

>> GCV_T_C  Glycine cleavage T-protein C-terminal barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.2   0.1   3.3e-25   2.9e-21       2      80 .]     310     387 ..     310     387 .. 0.96

  Alignments for each domain:
  == domain 1  score: 75.2 bits;  conditional E-value: 3.3e-25
                           GCV_T_C   2 rlvglelddgapllrggepilrdgevvGhvTSgaysptlgksialAyvkaelaklgtevevevrgkrvpaevvkkpf 78 
                                       ++v++++ d+  ++r g+++++dg+++G+vTSg+ sp lg  i+ A+vk+e+ak+g e+e+evr+++ +a  v++pf
  gi|242398651|ref|YP_002994075.1| 310 KMVHFKMVDR-GVPRAGYKVYADGKEIGEVTSGTLSPLLGIGIGVAFVKPEYAKPGVEIEIEVREQKKKALTVAPPF 385
                                       6899***844.488*************************************************************** PP

                           GCV_T_C  79 yD 80 
                                       yD
  gi|242398651|ref|YP_002994075.1| 386 YD 387
                                       *9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2466.41
//
Query:       gi|242398652|ref|YP_002994076.1|  [L=265]
Description: Universal stress protein [Thermococcus sibiricus MM 739]
Scores for complete 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  121.4   6.3    5.7e-18   65.8   0.4    2.8  2  Usp       Universal stress protein family
     0.0043   16.8   0.1      0.031   14.0   0.0    2.3  3  RQC       RQC domain


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.8   0.4   6.3e-22   5.7e-18      31     141 .]      17     118 ..       1     118 [. 0.91
   2 !   56.9   1.0   3.5e-19   3.1e-15       3     141 .]     139     263 ..     138     263 .. 0.86

  Alignments for each domain:
  == domain 1  score: 65.8 bits;  conditional E-value: 6.3e-22
                                       SEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTCEEEEEEEESSHHHHHHHHHHHTTSSEE CS
                               Usp  31 aelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggvkvevvveegdpaeeilevaeeedadli 107
                                        +l+l+h++d  a + ++ +  +  eeel   ++e          +a+g++ve  v+ g p+ ei+e+a+e+++dl+
  gi|242398652|ref|YP_002994076.1|  17 KKLYLVHIVDITATDIEAVELMKIDEEELNRIAEEI---------RAKGIDVEPMVKIGIPSLEIAEIAQENNVDLV 84 
                                       479***********************9999999988.........589***************************** PP

                                       EEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp 108 VvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                       +v s+g++ l+++llGS++++++r +++pVl+V+
  gi|242398652|ref|YP_002994076.1|  85 LVPSKGENILRQMLLGSTASNLVRATKKPVLLVK 118
                                       *********************************8 PP

  == domain 2  score: 56.9 bits;  conditional E-value: 3.5e-19
                                       SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTT CS
                               Usp   3 krIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeagg 79 
                                       kr +Va+D+se+s+k+l    ++ +    e++l+hv+d  + ++     e a+ + +e ++               +
  gi|242398652|ref|YP_002994076.1| 139 KRPIVALDFSECSEKVLNVVKKFEEL-IEEITLIHVVDYGRAEELEKNIENAKAKLEEFSRLF-------------K 201
                                       5668*************998886555.568*******98877776666665555555555544.............5 PP

                                       CEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  80 vkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                       + v+ +v+ g ++++il  a ++d ++iV+G++grs +++lllGS++e+v+r ++ pVl+V+
  gi|242398652|ref|YP_002994076.1| 202 APVKSEVLAGIASRSILGSALARDSSIIVMGKKGRSVIKDLLLGSTAERVVRDSKLPVLLVP 263
                                       79**********************************************************97 PP

>> RQC  RQC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.0       1.4   1.2e+04      59      75 ..      40      56 ..      38      61 .. 0.78
   2 !   14.0   0.0   3.5e-06     0.031       4      56 ..     144     199 ..     141     241 .. 0.79
   3 ?    0.3   0.0     0.063   5.7e+02      24      44 ..     233     253 ..     220     259 .. 0.82

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 1.4
                                      S-HHHHHHHHHHHHHTT CS
                               RQC 59 lskkewrrlirqLiaeg 75
                                      ++++e++r+++++ a+g
  gi|242398652|ref|YP_002994076.1| 40 IDEEELNRIAEEIRAKG 56
                                      67888888888888877 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 3.5e-06
                                       EEE-HHHHHHHHHHHHHTT...S-SBHHHHHHHHHT---CCCCCTTGGGSTTTTTT CS
                               RQC   4 tvDvteeaqkilscvyrtg...qrfgaghivdvLrGsktkkirqlghdklstfGig 56 
                                         D++e+++k+l++v++++   + +++ h+vd  r ++ +k  ++   kl+ f+ +
  gi|242398652|ref|YP_002994076.1| 144 ALDFSECSEKVLNVVKKFEeliEEITLIHVVDYGRAEELEKNIENAKAKLEEFSRL 199
                                       57****************64668*********************999999999755 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.063
                                       -SBHHHHHHHHHT---CCCCC CS
                               RQC  24 rfgaghivdvLrGsktkkirq 44 
                                       + g + i d+L Gs  +++ +
  gi|242398652|ref|YP_002994076.1| 233 KKGRSVIKDLLLGSTAERVVR 253
                                       567889999999*99999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1218  (0.0679346); expected 358.6 (0.02)
Passed bias filter:                      817  (0.0455686); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.50
# Mc/sec: 1591.96
//
Query:       gi|242398653|ref|YP_002994077.1|  [L=289]
Description: restriction endonuclease [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-11   44.0   0.8    9.2e-07   29.0   0.2    2.4  2  HSDR_N    Type I restriction enzyme R protein N terminus (HSD
    5.6e-11   42.4   0.0    1.1e-10   41.5   0.0    1.5  1  HSDR_N_2  Type I restriction enzyme R protein N terminus (HSD
     0.0017   18.2   0.2     0.0041   17.0   0.0    1.7  2  PDDEXK_9  PD-(D/E)XK nuclease superfamily
  ------ inclusion threshold ------
       0.11   12.4   0.0        0.2   11.5   0.0    1.4  1  SfsA      Sugar fermentation stimulation protein RE domain


Domain annotation for each model (and alignments):
>> HSDR_N  Type I restriction enzyme R protein N terminus (HSDR_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   2.8e-06     0.012       2      35 ..      24      57 ..      23      59 .. 0.92
   2 !   29.0   0.2     2e-10   9.2e-07     115     191 ..      52     123 ..      49     126 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.8e-06
                                      SSHHHHHH.HHHHHHHHTT-EE............ CS
                            HSDR_N  2 lsEaeleqelidellrelGyqvlskkdveiegrr 35
                                       +E++++q+li e++r lG++ +++ +v +e+r+
  gi|242398653|ref|YP_002994077.1| 24 KNEEAVKQHLIGEIFRTLGWDWENPREVRPEERT 57
                                      69***************************99975 PP

  == domain 2  score: 29.0 bits;  conditional E-value: 2e-10
                                       --S.SSS---EEEEEEETTEEEEEEEE--TT-HHHHHHHHTSS---.---SSSGGGGG-.....-EEEEE-SS-EEE CS
                            HSDR_N 115 tvt.gnqkrrpDivlfvnglplvviElKrpgtieeAinQikryrkeksdvsipqlfrYl.....qfgvisngketrf 185
                                       + + +++  r+D+ l    + ++++E+K+      +in +k+ r +     ++ql rY+     ++g+i+ng ++++
  gi|242398653|ref|YP_002994077.1|  52 RPEeRTEDGRADYALVLEDKVVAYVEAKN-----LGINVLKNER-A-----LRQLARYCfsrgvKYGIITNGAQWKI 117
                                       445678899********************.....4566777766.5.....89************************ PP

                                       EE--SS CS
                            HSDR_N 186 yaktkr 191
                                       ++ +++
  gi|242398653|ref|YP_002994077.1| 118 VKAFEE 123
                                       998765 PP

>> HSDR_N_2  Type I restriction enzyme R protein N terminus (HSDR_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.5   0.0   2.5e-14   1.1e-10       1     101 [.      25     125 ..      25     130 .. 0.90

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 2.5e-14
                          HSDR_N_2   1 pEEwvRqklikyLveelgypkeliavekelqlgskkkraDivvykkdkkpllivecKapsvki..seevleqlksYl 75 
                                       +EE v q+li ++ ++lg + e+  +e++ +  ++ +raD++++ +d k++  ve+K+  +++  +e++l ql++Y+
  gi|242398653|ref|YP_002994077.1|  25 NEEAVKQHLIGEIFRTLGWDWENP-REVRPEERTEDGRADYALVLED-KVVAYVEAKNLGINVlkNERALRQLARYC 99 
                                       59*****************99984.5666677799**********99.9*************99899********** PP

                          HSDR_N_2  76 ealkaeylvvtNglehivykvdkkkk 101
                                          +++y+++tNg + +++k  +++ 
  gi|242398653|ref|YP_002994077.1| 100 FSRGVKYGIITNGAQWKIVKAFEENS 125
                                       *****************999766665 PP

>> PDDEXK_9  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   9.2e-07    0.0041      21      83 ..      50     106 ..      25     125 .. 0.83
   2 ?   -2.6   0.0       1.1     5e+03      56      65 ..     242     251 ..     227     262 .. 0.49

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 9.2e-07
                          PDDEXK_9  21 evksEdetnkGriDlllkpkektkkkiyifEfKylkekesekekaeealeQikekgyaekyke 83 
                                       ev++E++t++Gr+D +l+    ++k +  +E K   +  ++  k+e al+Q+ ++  +  +k+
  gi|242398653|ref|YP_002994077.1|  50 EVRPEERTEDGRADYALV---LEDKVVAYVEAK---NLGINVLKNERALRQLARYCFSRGVKY 106
                                       79***************9...455677778***...999***************987777766 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.1
                          PDDEXK_9  56 kekesekeka 65 
                                        ek+seke++
  gi|242398653|ref|YP_002994077.1| 242 AEKASEKERN 251
                                       3333344333 PP

>> SfsA  Sugar fermentation stimulation protein RE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   4.6e-05       0.2       5      54 ..      32      81 ..      25      99 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.6e-05
                                      HHHHHHHEE...........EEES-EETTEE-SEEEE-S.SSEEEEEEEE- CS
                              SfsA  5 klveeales.glielagyeeikrevkygnsriDfllekeeeekcyvEVKsv 54
                                       l+ e+++  g+   ++ +e+++e + ++ r D++l  e++  +yvE K+ 
  gi|242398653|ref|YP_002994077.1| 32 HLIGEIFRTlGWD-WENPREVRPEERTEDGRADYALVLEDKVVAYVEAKNL 81
                                      4556666654443.335689*****************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); 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:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 2026.95
//
Query:       gi|242398654|ref|YP_002994078.1|  [L=245]
Description: hypothetical protein TSIB_0664 [Thermococcus sibiricus MM 739]
Scores for 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-37  125.8   0.0    1.6e-36  125.1   0.0    1.3  1  DUF364    Putative heavy-metal chelation
    9.3e-15   54.6   0.0    1.8e-14   53.7   0.0    1.5  1  DUF4213   Putative heavy-metal chelation


Domain annotation for each model (and alignments):
>> DUF364  Putative heavy-metal chelation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.1   0.0   1.7e-40   1.6e-36       3     134 ..     105     232 ..     103     244 .. 0.91

  Alignments for each domain:
  == domain 1  score: 125.1 bits;  conditional E-value: 1.7e-40
                            DUF364   3 ldlleikkgkkVvvVGyfapvlkklkekgaeltvlelnpnlleeeegdlpdeaaeellpeadvviitGstLvngtle 79 
                                        dl  +++ kk++v+G++ p+++ lkekg+e+ v+e+np+l+++e +  +d+ +++llpe+d+vi++Gs+L+n tl+
  gi|242398654|ref|YP_002994078.1| 105 TDL--VDDAKKIAVIGNMPPIVRSLKEKGKEIFVFERNPKLWDRETL--SDSLEYYLLPEMDAVIVSGSALINCTLD 177
                                       555..7789******************************99999875..9*************************** PP

                            DUF364  80 rllelakkaaevvlvGPsapllpevlfdyGvdviagvvvtdpdkllraiaeGggt 134
                                        ++e++kka++v+l+G +a++lpe+l+++Gv+++a+v+v+d +k+   ++ G   
  gi|242398654|ref|YP_002994078.1| 178 MIVERSKKAKKVILTGATAQVLPEFLKGSGVTHLASVKVIDVEKAILNLKMGIFR 232
                                       *********************************************9999988654 PP

>> DUF4213  Putative heavy-metal chelation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.7   0.0     2e-18   1.8e-14       2      74 .]       8      90 ..       7      90 .. 0.89

  Alignments for each domain:
  == domain 1  score: 53.7 bits;  conditional E-value: 2e-18
                           DUF4213  2 eelieaapedltVedvviGlnwtlVelsdg...gaGlAyt.......eagklvgkparelaelllswnplersvGlAai 70
                                      e+++++++ed ++ d+ +Gl +t+V+l+++    +GlA+t        + ++   +++e++    s n++er++G+A+i
  gi|242398654|ref|YP_002994078.1|  8 EKAMKKIKEDFRIVDFSFGLPYTYVVLEGPegkAIGLAMTlpedigeYKTSFKSPSLKEFIDKTDSLNIIERTLGIATI 86
                                      688999**********************85778*******88866543344688************************* PP

                           DUF4213 71 NAll 74
                                      NA++
  gi|242398654|ref|YP_002994078.1| 87 NAIS 90
                                      **85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1634.35
//
Query:       gi|242398655|ref|YP_002994079.1|  [L=261]
Description: glutamine amidotransferase, class II [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-08   34.3   0.0    3.5e-08   33.7   0.0    1.2  1  GATase_6  Glutamine amidotransferase domain
    1.8e-07   30.3   0.0    2.8e-07   29.7   0.0    1.2  1  GATase_4  Glutamine amidotransferases class-II
  ------ inclusion threshold ------
       0.19   12.0   0.0       0.51   10.6   0.0    1.7  2  APOC4     Apolipoprotein C4


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 !   33.7   0.0   5.8e-12   3.5e-08      10     111 ..      71     182 ..      56     204 .. 0.76

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 5.8e-12
                          GATase_6  10 ved....evalaHvRlaivglaeeega.qPf...psedgrlllvhNGeiynykelreelpalkglafrsrsDtevll 78 
                                        e+    +v+laH+R a++g+  +  + +P+   + e  ++++ hNG+ ++   l  +++ l++ ++++ sD++vl 
  gi|242398655|ref|YP_002994079.1|  71 LESldgfGVLLAHTRAASQGTV-NLFNaHPLvysSPEGFNFWFYHNGDLDKQI-L-IDMAGLDNEKLKDISDSYVLG 144
                                       433333359************8.55555***863344446**********994.4.4555559999**********6 PP

                          GATase_6  79 a.lleelG...eevl.erlrGmfafaiwdkrentlila 111
                                         ll++lG   ++++ +++r++++++ ++  +  l+++
  gi|242398655|ref|YP_002994079.1| 145 LyLLSSLGsfsKDMIlKKFREIVPVVRTTLNTASLFIT 182
                                       6599******988888********99888877777776 PP

>> GATase_4  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.0   4.7e-11   2.8e-07      29     113 ..      34     120 ..      27     133 .. 0.82

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 4.7e-11
                          GATase_4  29 tdahadGwGiafyegkaarvfkdpepsaesp..laelvreyp.iksknvvaHiRkatqGevklenthpFvRel.wgr 101
                                          h+dGwG+ +  + +  + k ++p  e +  + +++ + + +   +++aH R a+qG+v+l n+hp v +   g 
  gi|242398655|ref|YP_002994079.1|  34 NPYHKDGWGFVWISKDGLDYYKTSRPIFEDTkgVRKFLESLDgF--GVLLAHTRAASQGTVNLFNAHPLVYSSpEGF 108
                                       467**********************9886542266777776633..4689******************997652789 PP

                          GATase_4 102 ewifAHnGdlke 113
                                       ++ f HnGdl++
  gi|242398655|ref|YP_002994079.1| 109 NFWFYHNGDLDK 120
                                       9*********54 PP

>> APOC4  Apolipoprotein C4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       2.7   1.6e+04      23      34 ..      10      21 ..       9      28 .. 0.67
   2 ?   10.6   0.0   8.5e-05      0.51      18      56 ..     157     194 ..     148     225 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 2.7
                             APOC4 23 kvkelveplvtr 34
                                      +++e+v+ lv+ 
  gi|242398655|ref|YP_002994079.1| 10 EMREFVNALVKS 21
                                      567777777764 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 8.5e-05
                             APOC4  18 slvkskvkelveplvtrtrerwqwfwgPeafqgfvqtyy 56 
                                        ++ +k +e + p+v  t ++   f +P+ ++gfv +y 
  gi|242398655|ref|YP_002994079.1| 157 DMILKKFRE-IVPVVRTTLNTASLFITPSEIKGFVTAYM 194
                                       567789999.5599***********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 1920.14
//
Query:       gi|242398656|ref|YP_002994080.1|  [L=274]
Description: Dihydropteroate synthase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.9e-61  207.9   0.0    2.1e-61  207.7   0.0    1.0  1  Pterin_bind  Pterin binding enzyme
    0.00097   18.0   0.1     0.0013   17.5   0.1    1.1  1  CdhD         CO dehydrogenase/acetyl-CoA synthase delta subun
  ------ inclusion threshold ------
       0.13   12.3   0.3        3.1    7.9   0.0    3.0  3  DUF4974      Domain of unknown function (DUF4974)


Domain annotation for each model (and alignments):
>> Pterin_bind  Pterin binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  207.7   0.0   3.6e-65   2.1e-61       1     244 []      14     254 ..      14     254 .. 0.96

  Alignments for each domain:
  == domain 1  score: 207.7 bits;  conditional E-value: 3.6e-65
                                       EEEEETTTTTCHCCHHCTHHHHHHHHHHHHHHTT-SEEEEESS-TSTT-.-CCHHHHHHHHHHHHHHHHHHHCTSEE CS
                       Pterin_bind   1 mgilNvtpdsfsdggkfedldkalaqarkmveeGAdilDiggestrPga.ervdeeeelervvpvlealrdeadvpi 76 
                                       mg++Nv+p+sf++g++ +  d+++++a km+e+GA+ +Dig++st P   + +++eee++r v  l+ lrd++dvpi
  gi|242398656|ref|YP_002994080.1|  14 MGVINVSPESFFKGSIRQREDEIIETALKMLEDGASFIDIGAKSTAPYLeNQIPVEEEIRRAVWTLSILRDNVDVPI 90 
                                       9**********************************************98789************************* PP

                                       EEE-S-HHHHHHHHHTTSEEEEETTTTSSSTTHHHHHHHHT-EEEEESECSSTTTHCCCCCCCSSHHHHHHHHHHHH CS
                       Pterin_bind  77 siDttkaevaeaAlkagadivNdvsgeerdpkmlelvaeagaavvvmhmrgtpktmqeeegqyedvveeveaflear 153
                                       siDtt+a+vae+A+k+gadi+Nd+sg+++dpkm+e+++e+++++++ + +        ++ +  d v+ev  +l+++
  gi|242398656|ref|YP_002994080.1|  91 SIDTTNAKVAEEAIKVGADIINDISGLKGDPKMVEVAREYDVPLILCAHK-------DVK-DFSDPVHEVINALQES 159
                                       *********************************************99998.......445.889************* PP

                                       HHHHHHTT--GGGEEEETTTTS.....STTHHHHHHHHHTHHHHHHTTSSEBEEEGTTGHHHHHHHCTTCHGHHHHH CS
                       Pterin_bind 154 veaaeeaGvaperillDpgigf.....gkteehnlellrrldelrealevpvllGvSrksflgrllelgkaeeRdag 225
                                       ++ a +  +++e+i +Dp igf         e + +++++l+ l +++++p+l+GvSrksf+g+++   +++eR ag
  gi|242398656|ref|YP_002994080.1| 160 LQIAYKNNIEKEKIAIDPAIGFlrpkyPPWYEWDSKVIANLNLL-KMFGLPILVGVSRKSFIGAITGRRDPTERLAG 235
                                       **********************9865555578999*********.********************96666******* PP

                                       HHHHHHHHHHTT-SEEEES CS
                       Pterin_bind 226 taaflalaaaaGadivrVh 244
                                       ++ ++a+a+ +Ga+i+r+h
  gi|242398656|ref|YP_002994080.1| 236 SLGATAIAVWNGANIIRTH 254
                                       ******************9 PP

>> CdhD  CO dehydrogenase/acetyl-CoA synthase delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   2.3e-07    0.0013      49     160 ..      30     147 ..      14     163 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.3e-07
                                       HHHHTT-EEE....ETTEEEE--EEEEE--SSST............HHHHHHHHHHHCC--SEEEEE-SSHHHHHHH CS
                              CdhD  49 aerieevvddwakkrvgekltldaiairlistdP...........akkfakavekvakavkvplvlggsdpevlkaa 114
                                       ++r +e+ +  a k+ +   ++ +i i ++st P            +++  ++  + ++v+vp+ + + +++v ++a
  gi|242398656|ref|YP_002994080.1|  30 RQREDEIIET-ALKMLED--GASFIDIGAKSTAPylenqipveeeIRRAVWTLSILRDNVDVPISIDTTNAKVAEEA 103
                                       5666666664.6677777..8999999*************997777777777888999******************* PP

                                       HTTTCCC--EEEEE-TTTHHHHHHHHHHTT--EEEE-.SSHHHHHH CS
                              CdhD 115 levvederpllyaAtkddykeiaelaleykvpvvllsindleelke 160
                                       ++v +d    +    ++   +++e+a ey+vp++l + +d+++  +
  gi|242398656|ref|YP_002994080.1| 104 IKVGADIINDI--SGLKGDPKMVEVAREYDVPLILCAHKDVKDFSD 147
                                       ***99644443..33444479********************98765 PP

>> DUF4974  Domain of unknown function (DUF4974)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.12   7.3e+02      36      55 ..      25      46 ..      18      51 .. 0.73
   2 ?    7.9   0.0   0.00052       3.1      43      69 ..     146     174 ..     123     175 .. 0.85
   3 ?   -0.6   0.0      0.23   1.3e+03      40      59 ..     250     269 ..     247     273 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.12
                                      EEEEE..S-.-.HHHHHHHHHH CS
                           DUF4974 36 ftgtf..srnesleevLelLek 55
                                      f g++  +++e +e +L++Le 
  gi|242398656|ref|YP_002994080.1| 25 FKGSIrqREDEIIETALKMLED 46
                                      6677753556679999999985 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00052
                                       .-.HHHHHHHHHHHH--EEE..ETTEEEE CS
                           DUF4974  43 nesleevLelLektggikyk..iegnkii 69 
                                       ++++ ev+++L+++ +i yk  ie++ki 
  gi|242398656|ref|YP_002994080.1| 146 SDPVHEVINALQESLQIAYKnnIEKEKIA 174
                                       5799***************9888888886 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.23
                                       ES-.-.HHHHHHHHHHHH-- CS
                           DUF4974  40 fsrnesleevLelLektggi 59 
                                       + r+ ++ e L++++ t+ i
  gi|242398656|ref|YP_002994080.1| 250 IIRTHDVRETLDAIKITHFI 269
                                       557889999*****999755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.34s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 1598.95
//
Query:       gi|242398657|ref|YP_002994081.1|  [L=323]
Description: GHMP kinase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-08   33.8   0.0    8.7e-08   32.4   0.0    1.7  2  GHMP_kinases_C  GHMP kinases C terminal
    7.5e-08   32.5   0.1    1.6e-07   31.4   0.1    1.6  2  GHMP_kinases_N  GHMP kinases N terminal domain
  ------ inclusion threshold ------
       0.11   11.8   0.3        2.9    7.0   0.0    2.0  2  MobL            MobL relaxases


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 ?   -3.2   0.0       1.8   1.1e+04      10      17 ..     116     123 ..     101     132 .. 0.50
   2 !   32.4   0.0   1.5e-11   8.7e-08       1      83 [.     203     285 ..     203     287 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.8
                    GHMP_kinases_C  10 lellgell 17 
                                       ++llg++ 
  gi|242398657|ref|YP_002994081.1| 116 ASLLGRGN 123
                                       22333333 PP

  == domain 2  score: 32.4 bits;  conditional E-value: 1.5e-11
                    GHMP_kinases_C   1 llealergdlellgellnlsqrs....elkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkdeae 73 
                                       ll+al+++++e++g++l++ q +     ++++ g+  + ++ +le+l+e++   ++  ++++Gpt+++l+ +kd+ e
  gi|242398657|ref|YP_002994081.1| 203 LLPALKERNIEEFGKHLTEIQMLvgkhFEEYQGGEFREDVKFMLEFLKENT---YGHGQSSWGPTLYGLI-KKDDYE 275
                                       689************************8889********************...****************.777768 PP

                    GHMP_kinases_C  74 qvaralreef 83 
                                        ++r+ ++++
  gi|242398657|ref|YP_002994081.1| 276 VIKRKAQNFL 285
                                       8888877766 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 !   31.4   0.1   2.7e-11   1.6e-07       2      66 .]      76     136 ..      75     136 .. 0.95
   2 ?   -3.6   0.0       2.4   1.4e+04      38      56 ..     241     261 ..     231     262 .. 0.68

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 2.7e-11
                                       EEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHHHHHHHHHHHHHHH...HHHHHHSHHHHHHHHSS CS
                    GHMP_kinases_N   2 ivikseiPvgaGLGSSAAlavalvaAllallglsleeaklaleaerla...qggngsggDvaasvyGg 66 
                                       i +++ iP + GLGS + l++++ +Al++l+       ++ +e+erla   ++gn+sg  ++a+ yGg
  gi|242398657|ref|YP_002994081.1|  76 IDVENAIPRHVGLGSTTQLTLGVGLALAKLN-------NIRVEIERLAsllGRGNNSGAGIYAFKYGG 136
                                       6799**************************9.......899999999999999**************8 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 2.4
                                       H..HHHHHHHHHHHHHHHHHS CS
                    GHMP_kinases_N  38 e..aklaleaerlaqggngsg 56 
                                       +  ++l +  e+  ++g +s+
  gi|242398657|ref|YP_002994081.1| 241 DvkFMLEFLKENTYGHGQSSW 261
                                       345677778888887787775 PP

>> MobL  MobL relaxases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0   0.00049       2.9     253     285 ..      39      71 ..      36      80 .. 0.92
   2 ?    2.8   0.0    0.0092        55     267     335 ..     211     285 ..     206     311 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.00049
                              MobL 253 kLpkdrkkwrygsnamkearpliDelvdkylek 285
                                        +p+d+ + ++++++ k++r  iD++++++l+ 
  gi|242398657|ref|YP_002994081.1|  39 VMPHDKLEIKANEEDAKTIRFVIDKMNQEFLTG 71 
                                       69****************************975 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.0092
                              MobL 267 amkearpliDelvdkylekskkkeleellerlekeqkeykk.aYgegs.....erykdykknkleelkermgnav 335
                                       +++e+ + ++e+ +   +++++ +  e++e+++   +++k+ +Yg+g+       y   kk ++e +k++++n +
  gi|242398657|ref|YP_002994081.1| 211 NIEEFGKHLTEIQMLVGKHFEEYQGGEFREDVKFMLEFLKEnTYGHGQsswgpTLYGLIKKDDYEVIKRKAQNFL 285
                                       567777788888888888888889999*****99999987527*****999988899999999999999998843 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 2046.93
//
Query:       gi|242398658|ref|YP_002994082.1|  [L=347]
Description: hypothetical protein TSIB_0668 [Thermococcus sibiricus MM 739]
Scores for complete 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-25   87.6   0.0    8.7e-25   87.0   0.0    1.3  1  DUF835    Protein of unknown function (DUF835)
  ------ inclusion threshold ------
      0.024   14.0   8.2      0.034   13.4   8.2    1.1  1  DUF4401   Domain of unknown function (DUF4401)


Domain annotation for each model (and alignments):
>> DUF835  Protein of unknown function (DUF835)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.0   0.0   9.7e-29   8.7e-25      20     135 ..     231     343 ..     215     344 .. 0.92

  Alignments for each domain:
  == domain 1  score: 87.0 bits;  conditional E-value: 9.7e-29
                            DUF835  20 vkvlaitRenpkkirekvkienvkviwltkveeentvsPtnlekltetivkflkeaekg....vvliDgleyLvlen 92 
                                       +++la+ R+ +k        +++  + l++ve +++  Pt+l k+te+  k++kea+++    + +i+gle+L l+n
  gi|242398658|ref|YP_002994082.1| 231 YPTLAFLRN-FKP------FPGWISYLLSTVEMPKALYPTDLYKITEISTKYFKEAQQKgtkgIAIIEGLEFLKLYN 300
                                       567888888.344......58999******************************999888999************** PP

                            DUF835  93 gFesvlkflltlkDavllkngtlilvidkealeekelalLkre 135
                                       +F++v+k+l++++D + l+ngtli++++++a+++ke+a L+r 
  gi|242398658|ref|YP_002994082.1| 301 DFDAVAKMLSNVRDCATLNNGTLIVFAEESAWDKKEWATLRRI 343
                                       *****************************************97 PP

>> DUF4401  Domain of unknown function (DUF4401)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   8.2   3.8e-06     0.034      92     249 ..      12     192 ..       4     194 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.8e-06
                           DUF4401  92 lllallslalavlfpdallrfLsvlaa..allallglllsgllplaialvllllallflvlllnealklkargraal 166
                                       ++l+ l + l++l+     r +s+l++  a+++ + ++  g ++  +  +++ la +f++l ++++  +++++  +l
  gi|242398658|ref|YP_002994082.1|  12 ITLIKLLAGLLFLIAYLRTRRFSTLLIsfAWFLSIPVATFGAVDIRVENAMISLAYAFTLLAVFRL--IQEERIISL 86 
                                       566777777888888888888999999888999999999999999999999999999999998877..9999***** PP

                           DUF4401 167 leplayglllslllaglvllan........................dtltallkaasalllagvlllllWrvlisrr 219
                                        ++++ ++ l+l++ g+  +                            ++++ + a+ l ++++l+ ++   l ++ 
  gi|242398658|ref|YP_002994082.1|  87 PKSITIAVPLALAVTGVGTSLIksipdegylidgifefiaglivieSLSAYYKRNAKGLGISLALSGIM-STLYPMF 162
                                       ************999999988899999998888888888888888533333333444444444444444.4778888 PP

                           DUF4401 220 lklpklllaavllallllallslfaPglaa 249
                                       +++p+++l++ ++a l++++ ++f + +++
  gi|242398658|ref|YP_002994082.1| 163 YQKPPNMLITSIAAWLIIVPQFWFYSKIIY 192
                                       ***********************9988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 2302.85
//
Query:       gi|242398659|ref|YP_002994083.1|  [L=562]
Description: ATPase, RNase L inhibitor like protein [Thermococcus sibiricus MM 739]
Scores for complete 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  147.1   0.0    1.6e-22   80.5   0.0    2.5  2  ABC_tran       ABC transporter
    1.1e-14   55.0   5.2     0.0054   16.6   0.0    4.3  4  AAA_21         AAA domain, putative AbiEii toxin, Type IV TA 
    2.7e-14   53.1   3.7    3.3e-05   23.5   0.0    4.1  4  SMC_N          RecF/RecN/SMC N terminal domain
    3.5e-07   29.7   3.5    7.1e-07   28.8   3.5    1.5  1  Fer4           4Fe-4S binding domain
    6.2e-07   29.9   0.2      0.021   15.3   0.0    3.3  3  AAA            ATPase family associated with various cellular
    4.7e-06   26.5   0.3      0.038   13.7   0.0    3.7  4  AAA_15         AAA ATPase domain
    5.5e-06   26.9   0.1       0.11   12.9   0.0    2.7  2  AAA_16         AAA ATPase domain
      6e-06   26.3   1.5    9.7e-06   25.6   1.5    1.3  1  Fer4_21        4Fe-4S dicluster domain
    9.8e-06   25.6   0.0       0.15   12.0   0.0    2.3  2  Rad17          Rad17 P-loop domain
      4e-05   23.4   0.2      0.071   12.8   0.0    2.4  2  AAA_24         AAA domain
    4.8e-05   23.9   1.5       0.02   15.4   0.1    3.8  4  AAA_18         AAA domain
    7.9e-05   22.6   3.0    0.00015   21.7   3.0    1.5  1  Fer4_6         4Fe-4S binding domain
    0.00016   21.8   0.4    0.00029   20.9   0.4    1.4  1  Fer4_10        4Fe-4S dicluster domain
    0.00021   21.4   1.0    0.00039   20.5   1.0    1.4  1  Fer4_9         4Fe-4S dicluster domain
    0.00023   21.7   7.9      0.065   13.7   0.1    2.9  2  AAA_23         AAA domain
     0.0003   20.6   0.6       0.62    9.7   0.0    3.0  2  AAA_30         AAA domain
    0.00035   20.8   0.1       0.44   10.7   0.0    2.9  2  AAA_33         AAA domain
    0.00035   20.9   0.0        1.3    9.5   0.0    2.5  2  RNA_helicase   RNA helicase
    0.00052   20.3   0.1        1.3    9.2   0.0    2.9  2  AAA_28         AAA domain
    0.00091   19.8   2.0      0.002   18.6   2.0    1.5  1  Fer4_7         4Fe-4S dicluster domain
     0.0012   18.9   1.9     0.0025   17.8   1.9    1.5  1  Fer4_2         4Fe-4S binding domain
     0.0012   18.5   0.1        1.6    8.5   0.0    2.4  2  AAA_29         P-loop containing region of AAA domain
     0.0013   19.0   0.9       0.43   10.8   0.0    2.9  2  AAA_22         AAA domain
     0.0015   18.4   0.5       0.26   11.2   0.0    2.5  2  NACHT          NACHT domain
     0.0016   18.5   0.5        1.4    9.0   0.0    3.5  3  AAA_14         AAA domain
     0.0025   17.7   0.0       0.22   11.4   0.0    2.4  2  RsgA_GTPase    RsgA GTPase
     0.0028   17.3   1.4       0.43   10.2   0.0    2.5  2  SRP54          SRP54-type protein, GTPase domain
     0.0041   17.0   0.1        2.3    8.0   0.0    2.4  2  dNK            Deoxynucleoside kinase
     0.0049   16.1   0.1       0.68    9.1   0.0    2.5  2  NB-ARC         NB-ARC domain
      0.006   17.5   1.5      0.013   16.4   1.5    1.5  1  Fer4_16        4Fe-4S double cluster binding domain
     0.0093   15.4   0.1        3.1    7.2   0.0    2.5  2  PhoH           PhoH-like protein
  ------ inclusion threshold ------
      0.014   15.5   0.6       0.89    9.7   0.0    2.8  2  MMR_HSR1       50S ribosome-binding GTPase
      0.018   13.7   0.1        2.9    6.4   0.0    2.1  2  AAA_13         AAA domain
       0.02   14.9   1.6        1.2    9.1   0.0    3.2  3  TsaE           Threonylcarbamoyl adenosine biosynthesis prote
      0.022   15.3   0.4      0.047   14.2   0.4    1.5  1  Fer4_17        4Fe-4S dicluster domain
      0.038   13.7   0.0          4    7.1   0.0    2.3  2  VirE           Virulence-associated protein E
      0.039   14.0   0.7         13    5.7   0.0    2.7  2  AAA_5          AAA domain (dynein-related subfamily)
      0.039   13.5   0.0         11    5.5   0.0    2.4  2  AAA_7          P-loop containing dynein motor region
      0.052   13.3   0.2        5.5    6.7   0.1    2.8  3  ATP_bind_1     Conserved hypothetical ATP binding protein
      0.054   13.3   0.0       0.14   11.9   0.0    1.6  1  RNase_Zc3h12a  Zc3h12a-like Ribonuclease NYN domain
      0.071   12.9   0.0         10    5.8   0.0    2.7  2  RuvB_N         Holliday junction DNA helicase RuvB P-loop dom
      0.074   12.6   2.7        8.8    5.9   0.0    3.3  3  AAA_25         AAA domain
      0.076   11.8   0.3        0.6    8.9   0.0    2.0  2  DLIC           Dynein light intermediate chain (DLIC)
      0.083   12.2   0.6        3.4    6.9   0.0    2.4  2  ATPase         KaiC
        0.1   12.5   0.4        5.5    6.8   0.1    2.5  2  ATPase_2       ATPase domain predominantly from Archaea
       0.13   12.8   1.3       0.29   11.6   1.3    1.5  1  Fer4_8         4Fe-4S dicluster domain
       0.15   11.8   0.4        6.8    6.4   0.0    2.9  2  IstB_IS21      IstB-like ATP binding protein
       0.17   12.1   0.2         18    5.6   0.1    3.0  2  SbcCD_C        Putative exonuclease SbcCD, C subunit
        0.2   11.6   1.0        8.3    6.3   0.0    3.0  3  MobB           Molybdopterin guanine dinucleotide synthesis p
       0.27   11.6   4.1         15    5.9   0.0    3.0  3  AAA_19         AAA domain
       0.38   11.4   3.6       0.72   10.5   3.6    1.4  1  Fer4_4         4Fe-4S binding domain
       0.39   10.6   5.9        2.5    8.0   0.1    3.4  3  NTPase_1       NTPase
       0.54   11.3   5.5       0.98   10.5   5.5    1.4  1  Fer4_3         4Fe-4S binding domain
       0.82    9.7   3.2        4.1    7.4   0.0    3.0  2  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 !   64.2   0.0   5.3e-20   1.8e-17       8     136 ..      67     209 ..      66     210 .. 0.79
   2 !   80.5   0.0   4.9e-25   1.6e-22       5     137 .]     329     453 ..     325     453 .. 0.86

  Alignments for each domain:
  == domain 1  score: 64.2 bits;  conditional E-value: 5.3e-20
                                       EETTSEEEEEESTTSSHHHHHHHHTTSS--....SEEEE........EETTCEGGG..B-HHHCCHCEEEE-SS--S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxx........xxxxxxxxx..xxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   8 lkegekvaivGenGaGKStLlkllagllkp....teGei........lldgkdlke..qeleslrkeigvlpqepql 70 
                                       lkeg +v+i+G+nG+GK+t +++l+g+  p                  ++g++l++  ++l++ + +  v pq   l
  gi|242398659|ref|YP_002994083.1|  67 LKEGMVVGILGPNGTGKTTAVRILSGEILPnlcgS---NdnwdnvirMFRGNELQNyfEKLKEGNIKKVVKPQYVDL 140
                                       789*************************9975551...333344455666888888444444444444555677888 PP

                                       -TTSBHHHH........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  71 fpeltvren........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                        p++ v+ +        +++  +ek++++l+l ++ d+ +    ++LSgG+ qrva+a+a++++++++++DEp+
  gi|242398659|ref|YP_002994083.1| 141 IPKV-VKGKvrdlltraDEKGVLEKLVQELELLNILDREI----QHLSGGELQRVAIAAAMARDADFYFFDEPS 209
                                       8888.66667999986555555************999999....*****************************7 PP

  == domain 2  score: 80.5 bits;  conditional E-value: 4.9e-25
                                       EEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   5 slklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvrenes 81 
                                       s +++++e+v ivG+nG GK+t++k+lag ++p eG++             +++ ++++ pq  ++++e tv+e  s
  gi|242398659|ref|YP_002994083.1| 329 SGEIYKSEVVSIVGPNGIGKTTFVKMLAGVEEPSEGKV-------------EWELKVSYKPQYIKVDYEGTVYELLS 392
                                       56899*********************************.............7999********************66 PP

                                       HTC.........HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  82 dee.........iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       +++          +++l+ lgl++l +++v      LSgG+ qrva+a++ll++++l+llDEp+a
  gi|242398659|ref|YP_002994083.1| 393 KVDpakllsnfyKTELLNPLGLPDLYERKV----DDLSGGELQRVAIAACLLRDADLYLLDEPSA 453
                                       666333444444666777777777888888....*****************************75 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.5   0.00023     0.077       2      20 ..      73      91 ..      72     119 .. 0.84
   2 !   16.6   0.0   1.6e-05    0.0054     172     299 ..     149     241 ..     101     245 .. 0.73
   3 !   11.0   0.0   0.00081      0.27       3      22 ..     339     358 ..     337     373 .. 0.83
   4 !   14.3   0.1   8.1e-05     0.027     227     287 ..     415     476 ..     382     486 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00023
                            AAA_21  2 nvliGpNgsGKSnLLdald 20
                                       ++ GpNg+GK++  ++l+
  gi|242398659|ref|YP_002994083.1| 73 VGILGPNGTGKTTAVRILS 91
                                      689***************5 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 1.6e-05
                            AAA_21 172 fadyfgfakekrllqrlvrslklveielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrllall 248
                                       ++d+++ a+ek+ l++lv +l l +i ++                                 + +lS G ++  a++
  gi|242398659|ref|YP_002994083.1| 149 VRDLLTRADEKGVLEKLVQELELLNILDRE--------------------------------IQHLSGGELQRVAIA 193
                                       444455555555555555555555555544................................5799******99*** PP

                            AAA_21 249 tallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSp 299
                                       +a++r++   +++++DEp + L+ +   ++++ +++l+++g  v+++ H+ 
  gi|242398659|ref|YP_002994083.1| 194 AAMARDA---DFYFFDEPSSYLDIRQRLKVAKAIRKLAEEGKSVMVVEHDL 241
                                       *******...9*************888777788877666666666665555 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00081
                            AAA_21   3 vliGpNgsGKSnLLdaldll 22 
                                        ++GpNg GK+++ + l ++
  gi|242398659|ref|YP_002994083.1| 339 SIVGPNGIGKTTFVKMLAGV 358
                                       59***********9998765 PP

  == domain 4  score: 14.3 bits;  conditional E-value: 8.1e-05
                            AAA_21 227 gdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHP....kllrrllellkelsr 287
                                       +d +e+ +++lS G ++  a+++ llr++   +l+l+DEp + L+     ++ r +  l++++++
  gi|242398659|ref|YP_002994083.1| 415 PDLYERKVDDLSGGELQRVAIAACLLRDA---DLYLLDEPSAYLDVeqrlAVSRAIRHLMEKNEK 476
                                       578899999********999999999999...9*************7766444777777755554 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.067        22      26      39 ..      72      85 ..      52      92 .. 0.82
   2 !   23.5   0.0   9.8e-08   3.3e-05     126     211 ..     171     253 ..     108     260 .. 0.77
   3 !    8.9   0.1    0.0027       0.9      22      42 ..     333     353 ..     316     358 .. 0.72
   4 !   14.6   0.0     5e-05     0.017     136     205 ..     424     491 ..     383     504 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.067
                                      EEEEEESTTSSHHH CS
                                      xxxxxxxxxxxxxx RF
                             SMC_N 26 ftaivGpNGSGKsn 39
                                      +  i+GpNG GK+ 
  gi|242398659|ref|YP_002994083.1| 72 VVGILGPNGTGKTT 85
                                      5679********96 PP

  == domain 2  score: 23.5 bits;  conditional E-value: 9.8e-08
                                       HHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx RF
                             SMC_N 126 llesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislreem 201
                                       ll+  + +++ LSgGe + va+a      +++ a +y++De  + LD +++ kva+ +++  ++   ++v+ ++  +
  gi|242398659|ref|YP_002994083.1| 171 LLNILDREIQHLSGGELQRVAIAAA----MARDADFYFFDEPSSYLDIRQRLKVAKAIRKLAEEgKSVMVVEHDLAV 243
                                       33334445679*****998888655....67999*************************998885778888888777 PP

                                       CCC-SCEEEE CS
                                       xxxxxxxxxx RF
                             SMC_N 202 lekadklvgv 211
                                       l   + ++ v
  gi|242398659|ref|YP_002994083.1| 244 LDYLSDIIHV 253
                                       7776666666 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0027
                                       TTSSEEEEEESTTSSHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  22 fsksftaivGpNGSGKsnlld 42 
                                       +++++ +ivGpNG GK+ ++ 
  gi|242398659|ref|YP_002994083.1| 333 YKSEVVSIVGPNGIGKTTFVK 353
                                       4567899**********9886 PP

  == domain 4  score: 14.6 bits;  conditional E-value: 5e-05
                                       CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHHHCCC- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxx RF
                             SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn..aQfivislreemleka 205
                                        LSgGe + va+a        + a lyllDe  a LD +++ +v++ +++  ++     +v+ ++  m+   
  gi|242398659|ref|YP_002994083.1| 424 DLSGGELQRVAIAAC----LLRDADLYLLDEPSAYLDVEQRLAVSRAIRHLMEKneKTALVVEHDVLMIDYI 491
                                       69****999998766....589999***********************965443226677777776666655 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   3.5   2.1e-09   7.1e-07       2      24 .]      16      38 ..      15      38 .. 0.92

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 2.1e-09
                                      EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  2 videekCigCGaCvevCPvgAIt 24
                                      +i e  C+gCG+Cv  CP++AIt
  gi|242398659|ref|YP_002994083.1| 16 IIQEASCTGCGICVHKCPFNAIT 38
                                      788999****************7 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   6.3e-05     0.021       3      51 ..      75     134 ..      73     195 .. 0.74
   2 !   10.6   0.0    0.0017      0.57       3      20 ..     340     357 ..     338     395 .. 0.89
   3 ?   -0.7   0.0       5.3   1.8e+03      42      67 ..     463     491 ..     440     497 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 6.3e-05
                                       EESSTTSSHHHHHHHHHHHH......THE......EEEEETTTCSSSSTTHHHHHHHHHHH CS
                               AAA   3 lyGppGtGKTllakavakel......gve......fleisgsellskyvgesekkirelfk 51 
                                       + Gp GtGKT++++ +  e+      + +      +  + g el + + + +e +i++++k
  gi|242398659|ref|YP_002994083.1|  75 ILGPNGTGKTTAVRILSGEIlpnlcgS-NdnwdnvIRMFRGNELQNYFEKLKEGNIKKVVK 134
                                       67*****************65544540.233334355556666666666666777776665 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0017
                                       EESSTTSSHHHHHHHHHH CS
                               AAA   3 lyGppGtGKTllakavak 20 
                                       ++Gp G+GKT+++k +a 
  gi|242398659|ref|YP_002994083.1| 340 IVGPNGIGKTTFVKMLAG 357
                                       79*************996 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 5.3
                                       HHHHHHHHHHHHHHTS...TSEEEEEETG CS
                               AAA  42 sekkirelfkeakeka...kpsilfiDEi 67 
                                        ++ ir+l+++ ++ a   ++ +l+iD i
  gi|242398659|ref|YP_002994083.1| 463 VSRAIRHLMEKNEKTAlvvEHDVLMIDYI 491
                                       5688999999988888999999***9965 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0       0.1        34      28      43 ..      75      90 ..      66      92 .. 0.87
   2 ?    4.3   0.0      0.08        27     322     364 ..     198     239 ..      92     244 .. 0.85
   3 !   13.7   0.0   0.00011     0.038      18      43 ..     331     355 ..     317     401 .. 0.82
   4 ?   -2.1   0.0       7.1   2.4e+03     324     356 ..     443     475 ..     440     482 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.1
                            AAA_15 28 liGkNnsGKSsileal 43
                                      + G+N++GK++++++l
  gi|242398659|ref|YP_002994083.1| 75 ILGPNGTGKTTAVRIL 90
                                      77**********9998 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.08
                            AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                        + ++++++EP  +L + +   ++k++++la+++k  v++  H
  gi|242398659|ref|YP_002994083.1| 198 RDADFYFFDEPSSYLDIRQRLKVAKAIRKLAEEGK-SVMVVEH 239
                                       4679*****************************98.6776655 PP

  == domain 3  score: 13.7 bits;  conditional E-value: 0.00011
                            AAA_15  18 eidlseeltvliGkNnsGKSsileal 43 
                                       ei  se +  ++G+N++GK++++++l
  gi|242398659|ref|YP_002994083.1| 331 EIYKSE-VVSIVGPNGIGKTTFVKML 355
                                       444344.99***************99 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 7.1
                            AAA_15 324 nvilliEEPEahLHpqaqkvlikllkelandnk 356
                                        +++l++EP a+L  ++   + ++++ l ++n+
  gi|242398659|ref|YP_002994083.1| 443 ADLYLLDEPSAYLDVEQRLAVSRAIRHLMEKNE 475
                                       6899*********99999999999998888886 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   0.00098      0.33      25     107 ..      71     188 ..      60     249 .. 0.53
   2 !   12.9   0.0   0.00032      0.11      21      50 ..     329     360 ..     322     483 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00098
                            AAA_16  25 elvllsGesGvGKsslvrellralekd............ggiflrgkcdql.....esa.......ipysalaqala 77 
                                        +v + G+ G+GK++ vr l  ++  +            +   +rg+  q+     +++         y+ l+    
  gi|242398659|ref|YP_002994083.1|  71 MVVGILGPNGTGKTTAVRILSGEILPNlcgsndnwdnviR--MFRGNELQNyfeklKEGnikkvvkPQYVDLIPKVV 145
                                       567799************9999999997766777764330..24444444422211222444444433344333333 PP

                            AAA_16  78 reellrqlldeaesaeleawrekleeala..............a 107
                                       + + +r+ll++a+++ + +   + +e l+              +
  gi|242398659|ref|YP_002994083.1| 146 K-GKVRDLLTRADEKGVLEKLVQELELLNildreiqhlsggelQ 188
                                       3.444444444444444444444444444555533333334330 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00032
                            AAA_16  21 sgrp...elvllsGesGvGKsslvrellralek 50 
                                       sg+    e+v ++G+ G+GK++ v++l+  +e+
  gi|242398659|ref|YP_002994083.1| 329 SGEIyksEVVSIVGPNGIGKTTFVKMLA-GVEE 360
                                       555555599***************9998.3444 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   1.5   2.9e-08   9.7e-06      24      58 ..       4      38 ..       1      39 [. 0.88

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 2.9e-08
                           Fer4_21 24 qaieidaktvlkvv.edeCvGCnlCssvCPvedcie 58
                                      +ai id++++ +++ e +C+GC +C++ CP  ++i+
  gi|242398659|ref|YP_002994083.1|  4 EAIIIDEDKYKPIIqEASCTGCGICVHKCPF-NAIT 38
                                      79**********984679************7.8887 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   0.00044      0.15      47      73 ..      72      98 ..      56     126 .. 0.80
   2 !   11.2   0.0    0.0008      0.27      42      81 ..     332     373 ..     318     404 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00044
                             Rad17 47 iLLisGPsGCgkstvvkvLskelgikl 73
                                      ++ i GP G gk+t+v++Ls e  ++l
  gi|242398659|ref|YP_002994083.1| 72 VVGILGPNGTGKTTAVRILSGEILPNL 98
                                      55689***************9987765 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.0008
                             Rad17  42 srkkriLLisGPsGCgkstvvkvLskelgik..lrewlnpvs 81 
                                         k +++ i GP G gk+t vk+L+    ++    ew   vs
  gi|242398659|ref|YP_002994083.1| 332 IYKSEVVSIVGPNGIGKTTFVKMLAGVEEPSegKVEWELKVS 373
                                       55667899****************976655411456666666 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0052       1.7       3      22 ..      71      90 ..      69      99 .. 0.83
   2 !   12.8   0.0   0.00021     0.071       4      22 ..     337     355 ..     334     383 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0052
                            AAA_24  3 lkiliyGpsgiGKTtlakel 22
                                      + + i Gp+g+GKTt ++ l
  gi|242398659|ref|YP_002994083.1| 71 MVVGILGPNGTGKTTAVRIL 90
                                      6789***********98866 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00021
                            AAA_24   4 kiliyGpsgiGKTtlakel 22 
                                        + i+Gp+giGKTt++k+l
  gi|242398659|ref|YP_002994083.1| 337 VVSIVGPNGIGKTTFVKML 355
                                       5779*************98 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1     6e-05      0.02       1      47 [.      73     127 ..      73     180 .. 0.76
   2 ?    0.1   0.0       3.4   1.1e+03      36      90 ..     199     247 ..     164     255 .. 0.67
   3 ?    3.2   0.0      0.36   1.2e+02       3      19 ..     340     356 ..     338     380 .. 0.88
   4 ?    0.5   0.0       2.5   8.2e+02      31      82 ..     439     491 ..     416     554 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 6e-05
                            AAA_18   1 IlltGtpGvGKttlakeLskrl.gf.......gvnlrdvakenglllevdpeald 47 
                                       +++ G+ G+GKtt  + Ls +   +       ++n++ +++ n+l  ++++ +  
  gi|242398659|ref|YP_002994083.1|  73 VGILGPNGTGKTTAVRILSGEIlPNlcgsndnWDNVIRMFRGNELQNYFEKLKEG 127
                                       689***************8774333578889999999999999988887777333 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 3.4
                            AAA_18  36 glllevdpealdeskrldedkldklldaleenssaleegknlvidghlaelesea 90 
                                       +  +++++e   +s  ld+ ++ k+ +a+++ +   eegk++ +  h    +++ 
  gi|242398659|ref|YP_002994083.1| 199 DADFYFFDE---PSSYLDIRQRLKVAKAIRKLA---EEGKSVMVVEHDLAVLDYL 247
                                       444555555...789999999999999999986...4777776655555555554 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.36
                            AAA_18   3 ltGtpGvGKttlakeLs 19 
                                       + G+ G GKtt+ k L+
  gi|242398659|ref|YP_002994083.1| 340 IVGPNGIGKTTFVKMLA 356
                                       89**********99985 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 2.5
                            AAA_18  31 vakenglllevdpealdeskrldedkldklldaleenss...aleegknlvidgh 82 
                                       ++++ +l+l ++p      +++++  + ++++ l+e ++      e+++l id +
  gi|242398659|ref|YP_002994083.1| 439 LLRDADLYLLDEPS--AYLDVEQRLAVSRAIRHLMEKNEktaLVVEHDVLMIDYI 491
                                       55666666666666..333333333344455555555554544555555555544 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   3.0   4.5e-07   0.00015       2      24 .]      15      37 ..      14      37 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 4.5e-07
                            Fer4_6  2 veidpdkCigCgdCvrvCPegai 24
                                      + i++ +C+gCg Cv  CP++ai
  gi|242398659|ref|YP_002994083.1| 15 PIIQEASCTGCGICVHKCPFNAI 37
                                      7799******************8 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.4   8.7e-07   0.00029       2      24 ..      15      43 ..      14      68 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 8.7e-07
                           Fer4_10  2 vvidddtCirCgkCvkaCPadl......t 24
                                      ++i++ +C++Cg Cv  CP+++       
  gi|242398659|ref|YP_002994083.1| 15 PIIQEASCTGCGICVHKCPFNAitivnlP 43
                                      6899****************775333330 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   1.0   1.2e-06   0.00039       2      25 ..      22      45 ..       4      52 .. 0.70

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.2e-06
                            Fer4_9  2 CtgCgaCveaCpagvvvedaaerk 25
                                      CtgCg Cv++Cp+++++  + +++
  gi|242398659|ref|YP_002994083.1| 22 CTGCGICVHKCPFNAITIVNLPEE 45
                                      777777777777777766666665 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   4.5     0.013       4.4      22      39 ..      73      90 ..      67     230 .. 0.76
   2 !   13.7   0.1    0.0002     0.065      10      38 ..     320     354 ..     317     358 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.013
                            AAA_23 22 tlItGpNGaGKTTildAi 39
                                      + I GpNG+GKTT ++ +
  gi|242398659|ref|YP_002994083.1| 73 VGILGPNGTGKTTAVRIL 90
                                      679**********98755 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 0.0002
                            AAA_23  10 frdqeidF......skgltlItGpNGaGKTTildA 38 
                                       +++++++       ++ ++ I+GpNG GKTT++  
  gi|242398659|ref|YP_002994083.1| 320 YGNFKLEVesgeiyKSEVVSIVGPNGIGKTTFVKM 354
                                       55555555445555566999***********9865 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0    0.0019      0.62      16      38 ..      69      90 ..      62      97 .. 0.83
   2 !    7.6   0.0    0.0087       2.9      17      48 ..     336     365 ..     330     369 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0019
                            AAA_30 16 sgdrvavltGpAGtGKttalkal 38
                                      +g +v+ + Gp GtGKtta++ l
  gi|242398659|ref|YP_002994083.1| 69 EG-MVVGILGPNGTGKTTAVRIL 90
                                      44.69999***********9976 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0087
                            AAA_30  17 gdrvavltGpAGtGKttalkalreaweaaggr 48 
                                       +  v+ ++Gp G GKtt +k l+ + e ++g+
  gi|242398659|ref|YP_002994083.1| 336 E--VVSIVGPNGIGKTTFVKMLAGVEEPSEGK 365
                                       3..899**************999887766555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0     0.021       7.1       2      19 ..      73      90 ..      72     145 .. 0.88
   2 !   10.7   0.0    0.0013      0.44       1      20 [.     337     356 ..     337     363 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.021
                            AAA_33  2 vllvGlpGsGKstlaerl 19
                                      v + G++G+GK+t ++ l
  gi|242398659|ref|YP_002994083.1| 73 VGILGPNGTGKTTAVRIL 90
                                      6678*********99865 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0013
                            AAA_33   1 lvllvGlpGsGKstlaerll 20 
                                       +v +vG++G GK+t+++ l+
  gi|242398659|ref|YP_002994083.1| 337 VVSIVGPNGIGKTTFVKMLA 356
                                       7889************9886 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0    0.0038       1.3       3      28 ..      75     103 ..      73     129 .. 0.71
   2 !    8.8   0.0    0.0061         2       2      19 ..     339     356 ..     338     376 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0038
                      RNA_helicase   3 lyGpsgeGKStlakeLakallkkl...kl 28 
                                       + Gp+g+GK+t+++ L+ ++l +l   ++
  gi|242398659|ref|YP_002994083.1|  75 ILGPNGTGKTTAVRILSGEILPNLcgsND 103
                                       78***************999977755322 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0061
                      RNA_helicase   2 wlyGpsgeGKStlakeLa 19 
                                        ++Gp+g+GK+t++k La
  gi|242398659|ref|YP_002994083.1| 339 SIVGPNGIGKTTFVKMLA 356
                                       589************976 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0     0.004       1.3       4      20 ..      75      91 ..      72     130 .. 0.87
   2 ?    7.8   0.0     0.011       3.7       2      20 ..     338     356 ..     337     371 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.004
                            AAA_28  4 itGgestGKTtlleaLa 20
                                      i+G+ +tGKTt ++ L+
  gi|242398659|ref|YP_002994083.1| 75 ILGPNGTGKTTAVRILS 91
                                      99************998 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.011
                            AAA_28   2 ivitGgestGKTtlleaLa 20 
                                       + i+G+ + GKTt ++ La
  gi|242398659|ref|YP_002994083.1| 338 VSIVGPNGIGKTTFVKMLA 356
                                       679***************9 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   2.0   6.1e-06     0.002       1      22 [.      21      42 ..      21      58 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 6.1e-06
                            Fer4_7  1 rCigCgaCvaaCpvkaieldee 22
                                      +C+gCg Cv  Cp +ai++ + 
  gi|242398659|ref|YP_002994083.1| 21 SCTGCGICVHKCPFNAITIVNL 42
                                      5****************98754 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   1.9   7.4e-06    0.0025       3      21 ..      15      33 ..      13      34 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 7.4e-06
                            Fer4_2  3 vvvdtdrCigCgaCvsaCP 21
                                      + + +++C+gCg+Cv+ CP
  gi|242398659|ref|YP_002994083.1| 15 PIIQEASCTGCGICVHKCP 33
                                      5566789************ 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 ?    7.3   0.0     0.011       3.7      21      39 ..      68      87 ..      58      91 .. 0.81
   2 !    8.5   0.0    0.0049       1.6      21      39 ..     334     352 ..     320     361 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.011
                            AAA_29 21 lkg.atlltGpsGsGKSTll 39
                                       +g ++ + Gp+G+GK+T +
  gi|242398659|ref|YP_002994083.1| 68 KEGmVVGILGPNGTGKTTAV 87
                                      46667789*********965 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0049
                            AAA_29  21 lkgatlltGpsGsGKSTll 39 
                                        ++++ ++Gp+G GK+T++
  gi|242398659|ref|YP_002994083.1| 334 KSEVVSIVGPNGIGKTTFV 352
                                       456889***********97 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.2     0.049        16      10      24 ..      75      89 ..      68      94 .. 0.83
   2 !   10.8   0.0    0.0013      0.43       7      29 ..     337     359 ..     332     489 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.049
                            AAA_22 10 vtGesGtGKTtllrr 24
                                      + G+ GtGKTt +r 
  gi|242398659|ref|YP_002994083.1| 75 ILGPNGTGKTTAVRI 89
                                      78*********9985 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0013
                            AAA_22   7 ilvvtGesGtGKTtllrrlleql 29 
                                       ++ ++G+ G+GKTt +++l+   
  gi|242398659|ref|YP_002994083.1| 337 VVSIVGPNGIGKTTFVKMLAGVE 359
                                       6789**************98654 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1     0.066        22       3      20 ..      73      90 ..      71      97 .. 0.85
   2 !   11.2   0.0   0.00079      0.26       2      21 ..     337     356 ..     336     360 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.066
                                      EEEEC-TTTCHHHHHHHH CS
                             NACHT  3 vilqGeaGsGKTtLlqkl 20
                                      v + G++G GKTt ++ l
  gi|242398659|ref|YP_002994083.1| 73 VGILGPNGTGKTTAVRIL 90
                                      6799*********99865 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00079
                                       CEEEEC-TTTCHHHHHHHHH CS
                             NACHT   2 lvilqGeaGsGKTtLlqkla 21 
                                       +v + G++G+GKTt+++ la
  gi|242398659|ref|YP_002994083.1| 337 VVSIVGPNGIGKTTFVKMLA 356
                                       7889************9886 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.077        26       3      25 ..      71      93 ..      69     135 .. 0.79
   2 ?    0.2   0.0       2.2   7.4e+02      56      85 ..     191     220 ..     152     243 .. 0.62
   3 !    9.0   0.0    0.0042       1.4       2      25 ..     335     358 ..     334     405 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.077
                            AAA_14  3 kilvitGaRrvGKTtllkqlike 25
                                       ++ i G+  +GKTt ++ l  e
  gi|242398659|ref|YP_002994083.1| 71 MVVGILGPNGTGKTTAVRILSGE 93
                                      6899***********99877655 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 2.2
                            AAA_14  56 ileklkeekktylflDEiqevpewekalks 85 
                                         + +++++  + f+DE + + ++++ lk 
  gi|242398659|ref|YP_002994083.1| 191 AIAAAMARDADFYFFDEPSSYLDIRQRLKV 220
                                       333333346778999999888555554443 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0042
                            AAA_14   2 rkilvitGaRrvGKTtllkqlike 25 
                                       ++++ i+G+  +GKTt++k l+  
  gi|242398659|ref|YP_002994083.1| 335 SEVVSIVGPNGIGKTTFVKMLAGV 358
                                       57999*************999854 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0      0.16        53      97     122 ..      67      93 ..      60     130 .. 0.85
   2 !   11.4   0.0   0.00066      0.22      97     130 ..     333     366 ..     313     372 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.16
                                       CTT.SEEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase  97 lkd.ktsvlvGqSGvGKStLinallpe 122
                                       lk+  ++ ++G+ G GK+t +  l +e
  gi|242398659|ref|YP_002994083.1|  67 LKEgMVVGILGPNGTGKTTAVRILSGE 93 
                                       555366779**********99999887 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00066
                                       CTTSEEEEECSTTSSHHHHHHHHCTT-----S-- CS
                       RsgA_GTPase  97 lkdktsvlvGqSGvGKStLinallpelelktgev 130
                                        k++++ +vG+ G+GK+t++++l++ +e + g+v
  gi|242398659|ref|YP_002994083.1| 333 YKSEVVSIVGPNGIGKTTFVKMLAGVEEPSEGKV 366
                                       5678999****************99766665555 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.4     0.039        13       3      19 ..      72      88 ..      70      95 .. 0.82
   2 !   10.2   0.0    0.0013      0.43       2      24 ..     336     358 ..     335     367 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.039
                                      EEEEEESTTSSHHHHHH CS
                             SRP54  3 villvGlqGaGKTttla 19
                                      v+ ++G++G+GKTt++ 
  gi|242398659|ref|YP_002994083.1| 72 VVGILGPNGTGKTTAVR 88
                                      56689*********985 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0013
                                       EEEEEEESTTSSHHHHHHHHHHH CS
                             SRP54   2 nvillvGlqGaGKTttlaKLaal 24 
                                       +v+ +vG++G+GKTt +  La +
  gi|242398659|ref|YP_002994083.1| 336 EVVSIVGPNGIGKTTFVKMLAGV 358
                                       57889***********9999865 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0069       2.3       3      50 ..      75     125 ..      73     130 .. 0.87
   2 ?    6.7   0.0     0.018       5.9       2      21 ..     339     358 ..     338     407 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0069
                                       EEESTTSSHHHHHHHHHCCSTCEEEE-HHHHCCSSSS....HHHHHHHHSHH CS
                               dNK   3 veGnIgaGKstlvklLskklgvkvfeEpvdkwtnvqk....nlLekfYkdps 50 
                                       + G+ g GK+t v +Ls ++  + +  ++d+w nv +    n L++++++ +
  gi|242398659|ref|YP_002994083.1|  75 ILGPNGTGKTTAVRILSGEI-LPNLCGSNDNWDNVIRmfrgNELQNYFEKLK 125
                                       56889***************.999999*****99888888888888888765 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.018
                                       EEEESTTSSHHHHHHHHHCC CS
                               dNK   2 vveGnIgaGKstlvklLskk 21 
                                       ++ G+ g GK+t+vk+L+  
  gi|242398659|ref|YP_002994083.1| 339 SIVGPNGIGKTTFVKMLAGV 358
                                       78999************854 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.054        18      21      37 ..      71      87 ..      66     169 .. 0.87
   2 !    9.1   0.0    0.0021      0.68      19      38 ..     334     353 ..     325     368 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.054
                                      EEEEEEESTTSSHHHHH CS
                            NB-ARC 21 lvvalvGmgGvGKttla 37
                                      +vv++ G  G GKtt +
  gi|242398659|ref|YP_002994083.1| 71 MVVGILGPNGTGKTTAV 87
                                      79************954 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0021
                                       CSEEEEEEESTTSSHHHHHH CS
                            NB-ARC  19 qslvvalvGmgGvGKttlak 38 
                                       +s vv++vG  G+GKtt +k
  gi|242398659|ref|YP_002994083.1| 334 KSEVVSIVGPNGIGKTTFVK 353
                                       5679*************987 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   1.5   3.9e-05     0.013       2      18 ..      22      38 ..       8      53 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.9e-05
                           Fer4_16  2 CgtCgkCaevCPtnaik 18
                                      C++Cg C+  CP nai+
  gi|242398659|ref|YP_002994083.1| 22 CTGCGICVHKCPFNAIT 38
                                      77777777777777775 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.035        11      16      34 ..      67      85 ..      62      91 .. 0.84
   2 !    7.2   0.0    0.0093       3.1      16      49 ..     332     366 ..     325     376 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.035
                                      HHH-SEEEEE--TTSSTTH CS
                              PhoH 16 lkkndivfaiGpaGtGKty 34
                                      lk+  +v ++Gp GtGKt 
  gi|242398659|ref|YP_002994083.1| 67 LKEGMVVGILGPNGTGKTT 85
                                      667789999********95 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0093
                                       HHH-SEEEEE--TTSSTT.HHHHHHHHHHHHTTS- CS
                              PhoH  16 lkkndivfaiGpaGtGKt.ylavalavealkkkkv 49 
                                       + k+++v ++Gp G GKt ++ + ++ve  +++kv
  gi|242398659|ref|YP_002994083.1| 332 IYKSEVVSIVGPNGIGKTtFVKMLAGVEEPSEGKV 366
                                       66899************736778888888777776 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.2      0.32   1.1e+02       2      22 ..      73      93 ..      72     104 .. 0.89
   2 ?    9.7   0.0    0.0027      0.89       2      47 ..     338     387 ..     337     490 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.32
                                      EEEEESTTSSHHHHHHHHHTS CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltge 22
                                      v+i+G   +GK+t ++ l+ge
  gi|242398659|ref|YP_002994083.1| 73 VGILGPNGTGKTTAVRILSGE 93
                                      89*************999986 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0027
                                       EEEEESTTSSHHHHHHHHHT....STEEESSSTTSSSSEEEEEEEETTEE CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltg....ekaivsdkpgtTrdinegrvklkgke 47 
                                       v ivG    GK+t+++ l g    ++ +v+ +  +  ++++++v+++g+ 
  gi|242398659|ref|YP_002994083.1| 338 VSIVGPNGIGKTTFVKMLAGveepSEGKVEWELKVSYKPQYIKVDYEGTV 387
                                       78****************99654447899999999999999999977644 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1     0.024       7.8      21      37 ..      75      91 ..      73     107 .. 0.89
   2 ?    6.4   0.0    0.0088       2.9      21      58 ..     340     371 ..     335     386 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.024
                            AAA_13 21 iYGwNGaGKTtLSrllr 37
                                      i G NG+GKTt  r+l+
  gi|242398659|ref|YP_002994083.1| 75 ILGPNGTGKTTAVRILS 91
                                      679********999987 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0088
                            AAA_13  21 iYGwNGaGKTtLSrllrslelgetepkfangsieitng 58 
                                       i G NG GKTt+ ++l+ +e+       ++g++e++ +
  gi|242398659|ref|YP_002994083.1| 340 IVGPNGIGKTTFVKMLAGVEE------PSEGKVEWELK 371
                                       679***************964......34667777655 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0      0.32   1.1e+02      19      39 ..      70      90 ..      57      96 .. 0.81
   2 ?    9.1   0.0    0.0037       1.2      19      40 ..     335     356 ..     321     367 .. 0.83
   3 ?   -1.2   0.1       5.6   1.9e+03      69     115 ..     443     489 ..     434     495 .. 0.71

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.32
                                      TEEEEEEESTTSSHHHHHHHH CS
                              TsaE 19 gdvilLeGdLGaGKTtlvrgl 39
                                      g v+ + G+ G+GKTt vr l
  gi|242398659|ref|YP_002994083.1| 70 GMVVGILGPNGTGKTTAVRIL 90
                                      5678889999******99976 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0037
                                       TEEEEEEESTTSSHHHHHHHHH CS
                              TsaE  19 gdvilLeGdLGaGKTtlvrgla 40 
                                       ++v+ + G+ G GKTt+v+ la
  gi|242398659|ref|YP_002994083.1| 335 SEVVSIVGPNGIGKTTFVKMLA 356
                                       57899**************987 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 5.6
                                       EE-TT-SSTHHHHHCTTCCCCSTSCEEEEETGGGGCCCS-S-CEEEE CS
                              TsaE  69 fDlYRledeeeleelgleeyleeeavvlvEWpekleellpeedleie 115
                                       +DlY l++++   +++ + +++++   l+E  ek++ +++++ l i+
  gi|242398659|ref|YP_002994083.1| 443 ADLYLLDEPSAYLDVEQRLAVSRAIRHLMEKNEKTALVVEHDVLMID 489
                                       69999999888777777766655457888888886555555655665 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.4   0.00014     0.047      45      58 ..      21      34 ..       9      47 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 0.00014
                           Fer4_17 45 lCieCgeCerkCPq 58
                                      +C++Cg C++kCP 
  gi|242398659|ref|YP_002994083.1| 21 SCTGCGICVHKCPF 34
                                      56666666666664 PP

>> VirE  Virulence-associated protein E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0     0.012         4      47      92 ..      65     110 ..      55     136 .. 0.79
   2 ?    4.1   0.0       0.1        34      53      73 ..     336     357 ..     329     369 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.012
                              VirE  47 PgiKfDfvlvLvGkqgsgKstfleklgeewftdslksvedkdavek 92 
                                       P  K  +v+ + G+ g+gK+t +++l++e   +   s ++ d+v  
  gi|242398659|ref|YP_002994083.1|  65 PVLKEGMVVGILGPNGTGKTTAVRILSGEILPNLCGSNDNWDNVIR 110
                                       7889999*******************99988887777776665443 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.1
                              VirE  53 fvlvLvGkqgsgKstflekl.g 73 
                                       +v+ +vG+ g+gK+tf++ l g
  gi|242398659|ref|YP_002994083.1| 336 EVVSIVGPNGIGKTTFVKMLaG 357
                                       68889*************9954 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.1     0.044        15       4      20 ..      75      91 ..      73     102 .. 0.87
   2 ?    5.7   0.0     0.041        13       4      20 ..     340     356 ..     337     367 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.044
                                      EE--SSSSHHHHHHHGG CS
                             AAA_5  4 LvGppGtgKselaerla 20
                                      ++Gp GtgK++ ++ l+
  gi|242398659|ref|YP_002994083.1| 75 ILGPNGTGKTTAVRILS 91
                                      68**********99987 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.041
                                       EE--SSSSHHHHHHHGG CS
                             AAA_5   4 LvGppGtgKselaerla 20 
                                       +vGp G+gK+++++ la
  gi|242398659|ref|YP_002994083.1| 340 IVGPNGIGKTTFVKMLA 356
                                       89***********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 ?    5.5   0.0     0.032        11      30      52 ..      67      89 ..      61     136 .. 0.86
   2 ?    5.4   0.0     0.034        11      35      53 ..     337     355 ..     331     375 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.032
                             AAA_7 30 lknkkpvllvGptGtGKtviikd 52
                                      lk+++ v + Gp GtGKt+ ++ 
  gi|242398659|ref|YP_002994083.1| 67 LKEGMVVGILGPNGTGKTTAVRI 89
                                      5677778899********99875 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.034
                             AAA_7  35 pvllvGptGtGKtviikdl 53 
                                        v +vGp G GKt+ +k l
  gi|242398659|ref|YP_002994083.1| 337 VVSIVGPNGIGKTTFVKML 355
                                       5789***********9975 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 ?    3.4   0.0      0.17        57       1      17 [.      75      91 ..      75      98 .. 0.87
   2 ?   -2.2   0.0       8.8   2.9e+03      47     135 ..     214     244 ..     196     268 .. 0.52
   3 ?    6.7   0.1     0.017       5.5       1      18 [.     340     357 ..     340     367 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.17
                        ATP_bind_1  1 vvGpaGsGKttfvgals 17
                                      ++Gp G GKtt v+ ls
  gi|242398659|ref|YP_002994083.1| 75 ILGPNGTGKTTAVRILS 91
                                      68**********98776 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 8.8
                        ATP_bind_1  47 irelitledvmedlglgpngalvvaleflresldwldeelekeeddyllfDtPGQielfthseslakiveeLesefa 123
                                       ir  ++++++  +                                                          L++e++
  gi|242398659|ref|YP_002994083.1| 214 IRQRLKVAKAIRK----------------------------------------------------------LAEEGK 232
                                       4444444444444..........................................................444444 PP

                        ATP_bind_1 124 lvvvyLvDsqrl 135
                                        v+v+  D  +l
  gi|242398659|ref|YP_002994083.1| 233 SVMVVEHDLAVL 244
                                       444443333333 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.017
                        ATP_bind_1   1 vvGpaGsGKttfvgalse 18 
                                       +vGp G GKttfv+ l+ 
  gi|242398659|ref|YP_002994083.1| 340 IVGPNGIGKTTFVKMLAG 357
                                       79***********98875 PP

>> RNase_Zc3h12a  Zc3h12a-like Ribonuclease NYN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00042      0.14     111     154 ..     466     509 ..     462     510 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00042
                     RNase_Zc3h12a 111 nyrdllsenkelkdiveerllsftfvkdkfmlpddplkrkgpsl 154
                                        +r l+++n++   +ve+ +l++++  d++m+ ++ ++++g+ l
  gi|242398659|ref|YP_002994083.1| 466 AIRHLMEKNEKTALVVEHDVLMIDYISDRIMVFEGEPGKHGKAL 509
                                       67999**********************************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 ?    3.9   0.0      0.12        39      38      58 ..      75      95 ..      69     129 .. 0.89
   2 ?    5.8   0.0     0.031        10      35      54 ..     337     356 ..     316     394 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.12
                            RuvB_N 38 lyGpPGlGkttlakiiakelg 58
                                      + Gp G Gktt  +i++ e+ 
  gi|242398659|ref|YP_002994083.1| 75 ILGPNGTGKTTAVRILSGEIL 95
                                      68**************99975 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.031
                            RuvB_N  35 hvllyGpPGlGkttlakiia 54 
                                        v ++Gp G+Gktt+ k++a
  gi|242398659|ref|YP_002994083.1| 337 VVSIVGPNGIGKTTFVKMLA 356
                                       46789**********99988 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.063        21      29      50 ..      66      87 ..      61     102 .. 0.86
   2 ?   -0.6   0.1       2.5   8.3e+02      93     153 ..     192     249 ..     184     253 .. 0.66
   3 ?    5.9   0.0     0.026       8.8      31      53 ..     333     355 ..     327     375 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.063
                            AAA_25 29 llpagelallaGapgtGKttla 50
                                      +l +g ++ + G+ gtGKtt++
  gi|242398659|ref|YP_002994083.1| 66 VLKEGMVVGILGPNGTGKTTAV 87
                                      6789999999**********86 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2.5
                            AAA_25  93 vgealrddarllvldlagveslpLfakdrggtlltadvdaleaaieeveg..vrlvviDplsr 153
                                       + +a+++da+ ++ d +++     + ++r+  +++ ++++l+++ ++v     +l v+D ls 
  gi|242398659|ref|YP_002994083.1| 192 IAAAMARDADFYFFDEPSS-----YLDIRQRLKVAKAIRKLAEEGKSVMVveHDLAVLDYLSD 249
                                       4556677888888886665.....455566666888888888887776543366777776665 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.026
                            AAA_25  31 pagelallaGapgtGKttlaldl 53 
                                        + e++ ++G+ g GKtt++  l
  gi|242398659|ref|YP_002994083.1| 333 YKSEVVSIVGPNGIGKTTFVKML 355
                                       578999************98555 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.66   2.2e+02      25      47 ..      70      92 ..      60      95 .. 0.77
   2 ?    8.9   0.0    0.0018       0.6      27      55 ..     337     365 ..     328     382 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.66
                              DLIC 25 gksvlvlGedgsGkttliaklqG 47
                                      g  v +lG +g+Gktt +  l G
  gi|242398659|ref|YP_002994083.1| 70 GMVVGILGPNGTGKTTAVRILSG 92
                                      4456689*********9987766 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0018
                              DLIC  27 svlvlGedgsGkttliaklqGveeekkGr 55 
                                        v ++G +g Gktt++  l Gvee+  G+
  gi|242398659|ref|YP_002994083.1| 337 VVSIVGPNGIGKTTFVKMLAGVEEPSEGK 365
                                       57799********************9997 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1      0.18        61      17      34 ..      68      85 ..      55      88 .. 0.88
   2 ?    6.9   0.0      0.01       3.4      13      37 ..     329     353 ..     316     360 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.18
                            ATPase 17 pegrvvlitGepGtGKti 34
                                       eg vv i G  GtGKt+
  gi|242398659|ref|YP_002994083.1| 68 KEGMVVGILGPNGTGKTT 85
                                      68899************7 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.01
                            ATPase  13 kgGipegrvvlitGepGtGKtifal 37 
                                       +g i++ +vv i+G  G GKt+f++
  gi|242398659|ref|YP_002994083.1| 329 SGEIYKSEVVSIVGPNGIGKTTFVK 353
                                       478999****************986 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0      0.22        73      21      89 ..      71     144 ..      66     178 .. 0.61
   2 ?    6.8   0.1     0.017       5.5      20      42 ..     335     357 ..     328     389 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.22
                          ATPase_2  21 eiyfiYGpegsGKtaLlk....eiienledkdk.yviyyialreesiskldefieeeeekkklekalgiavpka 89 
                                       +++ i Gp g GKt+ ++    ei+ nl  +++     +  +r+ +++++ e+++e + kk ++ +  + +pk+
  gi|242398659|ref|YP_002994083.1|  71 MVVGILGPNGTGKTTAVRilsgEILPNLCGSNDnWDNVIRMFRGNELQNYFEKLKEGNIKKVVKPQYVDLIPKV 144
                                       577799********987744445666663333313333445566666666666665555555555555555555 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.017
                          ATPase_2  20 neiyfiYGpegsGKtaLlkeiie 42 
                                       +e++ i Gp g+GKt+++k ++ 
  gi|242398659|ref|YP_002994083.1| 335 SEVVSIVGPNGIGKTTFVKMLAG 357
                                       57899*************98765 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.3   0.00088      0.29       4      17 ..      21      34 ..      11      53 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00088
                            Fer4_8  4 kCieCgaCqsaCpv 17
                                      +C++Cg C ++Cp+
  gi|242398659|ref|YP_002994083.1| 21 SCTGCGICVHKCPF 34
                                      46666666666664 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.45   1.5e+02      48      61 ..      71      84 ..      59      94 .. 0.79
   2 ?    6.4   0.0      0.02       6.8      44      67 ..     332     355 ..     324     374 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.45
                         IstB_IS21 48 enivllGpsGvGKs 61
                                        + +lGp G+GK+
  gi|242398659|ref|YP_002994083.1| 71 MVVGILGPNGTGKT 84
                                      55679********9 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.02
                         IstB_IS21  44 iekkenivllGpsGvGKshlaial 67 
                                       i k+e + ++Gp G+GK+ +   l
  gi|242398659|ref|YP_002994083.1| 332 IYKSEVVSIVGPNGIGKTTFVKML 355
                                       56789999**********887666 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   0.1     0.055        18      26      51 ..     175     197 ..     166     226 .. 0.79
   2 ?    3.0   0.0      0.35   1.2e+02      27      47 ..     419     439 ..     415     469 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.055
                           SbcCD_C  26 lsrssgtlSGGekqflaylalaaala 51 
                                       l+r+++ lSGGe q    +a+aaa+a
  gi|242398659|ref|YP_002994083.1| 175 LDREIQHLSGGELQR---VAIAAAMA 197
                                       68999*******964...56666665 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.35
                           SbcCD_C  27 srssgtlSGGekqflaylala 47 
                                       +r++  lSGGe q +a  a +
  gi|242398659|ref|YP_002994083.1| 419 ERKVDDLSGGELQRVAIAACL 439
                                       678899999999877655544 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 ?    2.4   0.0      0.41   1.4e+02       1      18 [.      72      89 ..      72      97 .. 0.85
   2 ?   -1.5   0.0       6.6   2.2e+03      17      37 ..     221     241 ..     219     248 .. 0.84
   3 ?    6.3   0.0     0.025       8.3       1      20 [.     337     356 ..     337     368 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.41
                              MobB  1 vlgivgksgsGKTtLlek 18
                                      v+gi g +g+GKTt +  
  gi|242398659|ref|YP_002994083.1| 72 VVGILGPNGTGKTTAVRI 89
                                      689***********8765 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 6.6
                              MobB  17 eklipelkarglrvgtiKhah 37 
                                        k i++l+++g +v ++ h+ 
  gi|242398659|ref|YP_002994083.1| 221 AKAIRKLAEEGKSVMVVEHDL 241
                                       688999***********9986 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.025
                              MobB   1 vlgivgksgsGKTtLlekli 20 
                                       v++ivg +g GKTt+++ l 
  gi|242398659|ref|YP_002994083.1| 337 VVSIVGPNGIGKTTFVKMLA 356
                                       689*************9885 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.3     0.058        19      11      28 ..      71      88 ..      66      97 .. 0.83
   2 ?    5.9   0.0     0.046        15       9      30 ..     334     355 ..     328     367 .. 0.86
   3 ?   -1.4   0.0       7.8   2.6e+03      89     113 ..     469     493 ..     435     496 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.058
                            AAA_19 11 kvllvtaGpGtGKTrvlk 28
                                       v+ ++++ GtGKT+ ++
  gi|242398659|ref|YP_002994083.1| 71 MVVGILGPNGTGKTTAVR 88
                                      57889**********987 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.046
                            AAA_19   9 kekvllvtaGpGtGKTrvlkhi 30 
                                       k++v+ ++++ G GKT+ +k+ 
  gi|242398659|ref|YP_002994083.1| 334 KSEVVSIVGPNGIGKTTFVKML 355
                                       78999************99875 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 7.8
                            AAA_19  89 elleeaeeekklqeeellivDEfqd 113
                                       +l+e++e++  + e+++l++D ++d
  gi|242398659|ref|YP_002994083.1| 469 HLMEKNEKTALVVEHDVLMIDYISD 493
                                       3344555666666667999997776 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   3.6    0.0022      0.72       3      17 .]      21      35 ..      18      35 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0022
                            Fer4_4  3 rCigCgsCvaaCPqg 17
                                      +C+gCg Cv  CP++
  gi|242398659|ref|YP_002994083.1| 21 SCTGCGICVHKCPFN 35
                                      6************85 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1      0.15        51       2      19 ..      73      90 ..      72      97 .. 0.82
   2 ?    8.0   0.1    0.0076       2.5       2      21 ..     338     357 ..     337     367 .. 0.83
   3 ?   -0.9   0.0       4.2   1.4e+03      94     133 ..     441     483 ..     427     498 .. 0.59

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.15
                                      EEEE--TTSSHHHHHHHH CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkv 19
                                      v i Gp G+GKtT v+ +
  gi|242398659|ref|YP_002994083.1| 73 VGILGPNGTGKTTAVRIL 90
                                      5688*********99865 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0076
                                       EEEE--TTSSHHHHHHHHHH CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvle 21 
                                       v i Gp G+GKtT+vk ++ 
  gi|242398659|ref|YP_002994083.1| 338 VSIVGPNGIGKTTFVKMLAG 357
                                       6799***********98765 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 4.2
                                       HHH-EEEE---ST.TGGG-H.HHHHHHHHHHT.TTSEEEEE-- CS
                          NTPase_1  94 seadviviDEiGk.mElksk.kfkeaveevLk.sekpvlavih 133
                                       ++ad++++DE    + ++ +  +++a++++++ +ek  l+v h
  gi|242398659|ref|YP_002994083.1| 441 RDADLYLLDEPSAyLDVEQRlAVSRAIRHLMEkNEKTALVVEH 483
                                       5666666666443133322214678888888855666665555 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   5.5     0.003      0.98       1      15 []      22      36 ..      22      36 .. 0.97

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.003
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      CtgCg Cv  CP +A
  gi|242398659|ref|YP_002994083.1| 22 CTGCGICVHKCPFNA 36
                                      ************998 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0     0.012       4.1      26      48 ..      73      95 ..      70     109 .. 0.88
   2 ?    1.2   0.2         1   3.4e+02      26      43 ..     338     355 ..     335     357 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.012
                             DUF87 26 lAilgsTGsGKSntvavLleell 48
                                      ++ilg  G+GK++ v++L  e+l
  gi|242398659|ref|YP_002994083.1| 73 VGILGPNGTGKTTAVRILSGEIL 95
                                      79****************99987 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 1
                             DUF87  26 lAilgsTGsGKSntvavL 43 
                                       + i+g  G GK+++v+ L
  gi|242398659|ref|YP_002994083.1| 338 VSIVGPNGIGKTTFVKML 355
                                       5799999*********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (562 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                       112  (0.00624686); expected 17.9 (0.001)
Passed Fwd filter:                        54  (0.00301188); 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: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.51
# Mc/sec: 3344.76
//
Query:       gi|242398660|ref|YP_002994084.1|  [L=37]
Description: hypothetical protein TSIB_0670 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.49
# Mc/sec: 228.60
//
Query:       gi|242398661|ref|YP_002994085.1|  [L=894]
Description: ATP-dependent RNA helicase, [Thermococcus sibiricus MM 739]
Scores for complete 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   78.3   0.0    1.3e-21   77.2   0.0    1.6  1  DEAD        DEAD/DEAH box helicase
    8.4e-21   74.4   0.0    6.8e-20   71.5   0.0    2.3  2  Helicase_C  Helicase conserved C-terminal domain
    3.5e-15   56.5   0.0    9.6e-15   55.1   0.0    1.8  1  DUF1998     Domain of unknown function (DUF1998)
    4.5e-09   36.5   0.0    1.3e-08   35.1   0.0    1.8  1  ResIII      Type III restriction enzyme, res subunit
  ------ inclusion threshold ------
      0.077   11.8   0.0       0.13   11.0   0.0    1.3  1  Adeno_IVa2  Adenovirus IVa2 protein


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 !   77.2   0.0   3.6e-25   1.3e-21       2     174 ..      48     225 ..      47     227 .. 0.79

  Alignments for each domain:
  == domain 1  score: 77.2 bits;  conditional E-value: 3.6e-25
                                       HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHH..HHHTTT.ST CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxx.xx RF
                              DEAD   2 diQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnl..kkfkky.id 75 
                                       + Q  a++++++g++++v  +T+sGK+++f ++++++ ++   +++   l+v Ptr+L++++++++  ++f  + i+
  gi|242398661|ref|YP_002994085.1|  48 KHQVDALEALYSGENIVVTTPTASGKSEIFRLAIFDNYLS---NPQDTYLLVYPTRALINNQYEKFniENFHFFrIT 121
                                       67999******************************99986...777789***************9943333332333 PP

                                       ...SEEEEEETTSSHHHHHHHH.HTTCSEEEEEHHHHHHHH..HCTSSH..CTTEEEEEEETHHHHHHTTTHHHHHH CS
                                       ...xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx..xxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  76 ...lrvlliiggvaardqlskl.dngvdivvgtpgrlddll..stgkln..lsqvrflVlDEadrlldqgfsdfinr 144
                                           +   i++g+   ++++kl ++++++v++tp++++  +  +++  +  l+++++lV+DE + +    f+   + 
  gi|242398661|ref|YP_002994085.1| 122 ekmFS-AKILTGDVDWSERRKLiREKPRVVFTTPDMIHYNIlrNKRDYDwlLRNIKYLVVDELHIYRGV-FGTNASY 196
                                       44333.34566666666666663788*************664544444477****************98.9999999 PP

                                       HHHHSHHHCTTSTTTSEEEEEESSBSHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 145 ilnqlpqitcdgklqrqvivlSATlpkdvk 174
                                       ++++l ++ ++  ++ q+i lSATl  ++k
  gi|242398661|ref|YP_002994085.1| 197 LFKRLLKALERWGKKPQIISLSATLR-NPK 225
                                       99999888887777889********7.554 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.36   1.3e+03      16      61 ..      98     145 ..      78     151 .. 0.64
   2 !   71.5   0.0   1.9e-23   6.8e-20       7     110 ..     266     373 ..     260     374 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.36
                                       TSEEEEEESSHH.HHHHHHHHHHHT.TSTEEEESTTSTHHHHHHHHHH CS
                        Helicase_C  16 ggkilifvntid.rlekvklllekk.gikvavlhgelpqnereeileq 61 
                                         ++li  ++ + ++e++++++ ++  +++ +l+g+   +er++ +++
  gi|242398661|ref|YP_002994085.1|  98 PTRALINNQYEKfNIENFHFFRITEkMFSAKILTGDVDWSERRKLIRE 145
                                       344444444444555445555333346999999999999999998875 PP

  == domain 2  score: 71.5 bits;  conditional E-value: 1.9e-23
                                       HHHH.HHTTTTSEEEEEESSHHHHHH.HHHHHHHT.TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSS CS
                        Helicase_C   7 lell.kleeeggkilifvntidrlek.vklllekk.gikvavlhgelpqnereeileqfnkgesdvLiatdvaerGi 80 
                                        +++ +l e+g k+l+f  +++  ek +++ll++   +k++++ g+lp+n r ei ++f++g+  vL++t+++e Gi
  gi|242398661|ref|YP_002994085.1| 266 RKIVeNLAEKGIKTLVFFDSRKGTEKlMRFLLTSPaIYKTTTYKGTLPKNIRWEIEKEFKEGKLLVLLTTNALELGI 342
                                       3444556899************998877888666667**************************************** PP

                                       TSTTESEEEESSSSSS.HHHHHHHHTTSSST CS
                        Helicase_C  81 dipkvnlVinfdlprn.vtsyiqriGRtgRa 110
                                       di +++ Vin+++p + + s+iqr GR+gR 
  gi|242398661|ref|YP_002994085.1| 343 DIGDLDAVINYGIPPDgLFSLIQRFGRAGRK 373
                                       **************555*************6 PP

>> DUF1998  Domain of unknown function (DUF1998)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.1   0.0   2.7e-18   9.6e-15       1      83 []     785     867 ..     785     867 .. 0.95

  Alignments for each domain:
  == domain 1  score: 55.1 bits;  conditional E-value: 2.7e-18
                           DUF1998   1 lehalinalplflqcdesdlgteckapedep.rkrpariliydavpgGaGiaekaaelleellraalelieecdCee 76 
                                       +eh +i+++p+f  +d+++lg+++++++  p    ++ +++yd+ +gG+G+ae ++  +e+l+++ +e++++c+C+ 
  gi|242398661|ref|YP_002994085.1| 785 IEHNMIKIAPIFTYVDSRELGGYSYESFPGPlFIGKPIVFVYDGNEGGSGLAEILYTNVETLMEKSMEHLKNCNCS- 860
                                       58***********************77665598999***************************************8. PP

                           DUF1998  77 aGCpaCl 83 
                                       +GCp C+
  gi|242398661|ref|YP_002994085.1| 861 DGCPLCV 867
                                       ******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 !   35.1   0.0   3.5e-12   1.3e-08       2     170 ..      44     222 ..      43     223 .. 0.78

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 3.5e-12
                                       -EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHH.HHHHHHH-S.....-EEEEESSHHHHHHHH.....H CS
                            ResIII   2 lelreyQeeaienlleklkskrdkrglikmaTGtGKTlva.aklierllkkgkeekflflvprkslleqtl.....e 72 
                                       ++l+++Q +a+e+l         +++++  +T +GK+ +  +++ +++l++ +++  l++ p+++l++  +     e
  gi|242398661|ref|YP_002994085.1|  44 FKLYKHQVDALEALY------SGENIVVTTPTASGKSEIFrLAIFDNYLSN-PQDTYLLVYPTRALINNQYekfniE 113
                                       689999999999995......6789***************99999999987.667***********99999455555 PP

                                       HGGGGTGG....GEEEESSS-B--.........-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS. CS
                            ResIII  73 efkkflseaykeigkkvsgdkkka..kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgak 147
                                       +f  f  +++++  k+++gd + +  ++  +++ ++++tt ++++ ++  +++ + + l  +++++++DE H +++ 
  gi|242398661|ref|YP_002994085.1| 114 NFHFFRITEKMFSAKILTGDVDWSerRKLIREKPRVVFTTPDMIHYNI-LRNKRDYDWLLRNIKYLVVDELHIYRGV 189
                                       5566666666666666666555554344448999***********999.8899999999999**********99886 PP

                                       ....T..TTHHHHHT-....--SEEEEEESS-S CS
                            ResIII 148 ....k..swreilekf....keavllglTATpe 170
                                           +   ++++l+++    k+  ++ l+AT++
  gi|242398661|ref|YP_002994085.1| 190 fgtnAsyLFKRLLKALerwgKKPQIISLSATLR 222
                                       555414566666666644456699999999975 PP

>> Adeno_IVa2  Adenovirus IVa2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   3.6e-05      0.13      64     132 ..      39     105 ..      11     115 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.6e-05
                        Adeno_IVa2  64 iekldakllrddGelsslnyglqPviGviyGPtGsGksqllrnlissklisPiPetvifitPekdmipP 132
                                       ie++  kl ++  ++ +l+        v+  Pt sGks+++r  i  + +s + +t +++ P++ +i  
  gi|242398661|ref|YP_002994085.1|  39 IEEMGFKLYKH--QVDALEALYSGENIVVTTPTASGKSEIFRLAIFDNYLSNPQDTYLLVYPTRALINN 105
                                       45566666666..333333333333347899*********************************99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (894 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); 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: 0.81u 0.33s 00:00:01.14 Elapsed: 00:00:00.52
# Mc/sec: 5200.60
//
Query:       gi|242398662|ref|YP_002994086.1|  [L=131]
Description: hypothetical protein TSIB_0672 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0073   15.0   0.7     0.0085   14.8   0.7    1.2  1  GOLGA2L5  Putative golgin subfamily A member 2-like protein 5
     0.0086   16.2   2.1      0.014   15.5   2.1    1.4  1  UPF0242   Uncharacterised protein family (UPF0242) N-terminus
       0.01   16.5   1.4      0.019   15.6   0.2    1.9  2  YabA      Initiation control protein YabA
  ------ inclusion threshold ------
      0.047   13.7   1.0       0.12   12.4   1.0    1.7  1  RHH_3     Ribbon-helix-helix domain
      0.066   13.7   6.9      0.097   13.1   2.2    2.2  2  ZapB      Cell division protein ZapB


Domain annotation for each model (and alignments):
>> GOLGA2L5  Putative golgin subfamily A member 2-like protein 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.7   2.4e-06    0.0085      48     121 ..      52     127 ..      17     129 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.4e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXX...X..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          GOLGA2L5  48 svsqvqeLeaslaeLknqaavkpaeeeaqp..pagPseeeqrlqeeleqLqkekealagqlqaqvrDneqLsrlnq 121
                                           ++ Le+s+ eLk+++ +  +e ++    + g se ++ l  el+ L  e ++l+  l++++  n +L +l q
  gi|242398662|ref|YP_002994086.1|  52 PKGDLKALENSVEELKKKVGILEKEWAPLRykAYGVSEDNKLLAIELSGLLAENSQLKRFLRKKIDKNLELRKLIQ 127
                                       4567899***********9999888866635599*************************************99976 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 !   15.5   2.1   3.9e-06     0.014      74     151 ..      46     123 ..       3     130 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.9e-06
                           UPF0242  74 eaklteldeglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelkleleeqLaekqel 150
                                        ++ +e + +lk  e+++eel+++   L++e +    +     e+n+ L ++l+   +++++lk++l +++++  el
  gi|242398662|ref|YP_002994086.1|  46 SENFKEPKGDLKALENSVEELKKKVGILEKEWAPLRYKAYGVSEDNKLLAIELSGLLAENSQLKRFLRKKIDKNLEL 122
                                       23344444777888888888888888888888888888888899999999999999999999999999998877655 PP

                           UPF0242 151 l 151
                                        
  gi|242398662|ref|YP_002994086.1| 123 R 123
                                       4 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.57   2.1e+03       5      23 ..      21      39 ..      12      51 .. 0.63
   2 !   15.6   0.2   5.3e-06     0.019       4      58 ..      57     118 ..      54     128 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.57
                                      HHHHHHHHHHHHHHHHHHH CS
                              YabA  5 elfdkleeleeqleellee 23
                                      el++k++el+e+ +   e+
  gi|242398662|ref|YP_002994086.1| 21 ELLEKIAELSEHYRVPEEK 39
                                      5555555555555544444 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 5.3e-06
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHXXXXXX CS
                              YabA   4 kelfdkleeleeqleelleeleelkeelaelleenaeLele.......neklrerleeeekk 58 
                                       k l +++eel+++++ l +e + l+ + + + e+n+ L +e       n++l++ l+++ +k
  gi|242398662|ref|YP_002994086.1|  57 KALENSVEELKKKVGILEKEWAPLRYKAYGVSEDNKLLAIElsgllaeNSQLKRFLRKKIDK 118
                                       778899***********************************999999999999999655444 PP

>> RHH_3  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   1.0   3.2e-05      0.12       7      38 ..      16      47 ..      13      51 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.2e-05
                             RHH_3  7 vsidpelaekLkaLSekTrIprSklldeAiel 38
                                      v i+ el+ek  +LSe  r+p  k+l+ Ai++
  gi|242398662|ref|YP_002994086.1| 16 VEIPQELLEKIAELSEHYRVPEEKILEIAISE 47
                                      679************************99987 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.2     0.037   1.3e+02      21      45 ..      20      44 ..      16      53 .. 0.68
   2 ?   13.1   2.2   2.7e-05     0.097       6      65 ..      56     115 ..      54     124 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.037
                              ZapB 21 tlLqmeieeLkeeneelkeenrele 45
                                      ++L ++i+eL e  +  +e++ e+ 
  gi|242398662|ref|YP_002994086.1| 20 QELLEKIAELSEHYRVPEEKILEIA 44
                                      5666777777777777777666655 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 2.7e-05
                              ZapB   6 LeqLEskiqkaidtitlLqmeieeLkeeneelkeenreleeeneqlkeereawqerlkkL 65 
                                       L+ LE++++++  ++  L +e + L+ + +  +e n+ l  e++ l +e +++++ l+k 
  gi|242398662|ref|YP_002994086.1|  56 LKALENSVEELKKKVGILEKEWAPLRYKAYGVSEDNKLLAIELSGLLAENSQLKRFLRKK 115
                                       789*************************************88888888888888877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1206  (0.0672653); expected 358.6 (0.02)
Passed bias filter:                      741  (0.0413297); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.31s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 876.01
//
Query:       gi|242398663|ref|YP_002994087.1|  [L=108]
Description: hypothetical protein TSIB_0673 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0025   17.5  15.4     0.0027   17.4  15.4    1.0  1  DUF572           Family of unknown function (DUF572)
  ------ inclusion threshold ------
       0.02   15.0   1.2       0.02   15.0   1.2    1.6  2  DUF1877          Domain of unknown function (DUF1877)
      0.026   13.7   3.0      0.026   13.7   2.5    1.3  1  RP853            Uncharacterized RP853
      0.046   13.3   2.7      0.049   13.2   2.7    1.1  1  Polysacc_synt_4  Polysaccharide biosynthesis
          2    9.0  15.5          2    9.0  13.7    1.9  1  Cep57_MT_bd      Centrosome microtubule-binding domain of Cep
        2.3    8.4  14.7      0.039   14.1   5.4    2.2  2  DUF5446          Family of unknown function (DUF5446)
        3.3    6.7  11.1        3.3    6.7  11.1    1.1  1  Atg14            Vacuolar sorting 38 and autophagy-related su
        3.9    7.4   6.6          6    6.8   6.6    1.4  1  EMP24_GP25L      emp24/gp25L/p24 family/GOLD
        5.8    6.2  17.5         17    4.7  17.5    1.7  1  NBP1             Fungal Nap binding protein NBP1
          7    4.4   9.9        6.6    4.5   9.9    1.0  1  V_ATPase_I       V-type ATPase 116kDa subunit family
        7.9    7.6  13.1       0.55   11.3   2.3    2.2  2  DUF5320          Family of unknown function (DUF5320)
        9.3    6.6  12.8        2.6    8.4   4.4    2.5  2  Rx_N             Rx N-terminal domain


Domain annotation for each model (and alignments):
>> DUF572  Family of unknown function (DUF572)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4  15.4   1.8e-06    0.0027     104     189 ..      14     102 ..       4     108 .] 0.79

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.8e-06
                            DUF572 104 kaek......leeeeakreekekeeeeaedamkklEkrtkdskkemealesLeeLqelnqrqakvdfdanlelrkef 174
                                       ka k      l+e++  + ek+ ++   +  ++ lEk+ k ++k +e+  +LeeL+    ++a+ d++ +l lr++ 
  gi|242398663|ref|YP_002994087.1|  14 KALKnmdvikLIEKNLPKVEKTLQA---DREVFLLEKKKKLEEKLKEIEGELEELKVF-YQKATEDKELMLTLREKL 86 
                                       4444555544888887777777766...889*************************55.5568************** PP

                            DUF572 175 reekkereee.eedee 189
                                       ree++e+++e ee++ 
  gi|242398663|ref|YP_002994087.1|  87 REENEELKKElEEKKL 102
                                       ***9999998443433 PP

>> DUF1877  Domain of unknown function (DUF1877)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   1.2   1.3e-05      0.02      96     164 ..      11      81 ..       8      82 .. 0.71
   2 ?   -2.2   0.3       2.7     4e+03      17      31 ..      85      99 ..      83     105 .. 0.55

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.3e-05
                           DUF1877  96 evaeaLaeldfeelrerfdaeele....eaeiYpniweeeeeededleylleyfeelkeFykkaakagkavlv 164
                                       e+ +aL+++d  +l e+  ++  +      e++    e++++ +e l+++   +eelk Fy+ka ++++ +l+
  gi|242398663|ref|YP_002994087.1|  11 ETFKALKNMDVIKLIEKNLPKVEKtlqaDREVFL--LEKKKKLEEKLKEIEGELEELKVFYQKATEDKELMLT 81 
                                       5567777777777777776642210000234443..3458899************************998875 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.7
                           DUF1877 17 kllkdpedledflee 31
                                      kl++++e+l ++lee
  gi|242398663|ref|YP_002994087.1| 85 KLREENEELKKELEE 99
                                      555555555555554 PP

>> RP853  Uncharacterized RP853
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   2.5   1.7e-05     0.026     256     297 ..      16      56 ..       7      77 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.7e-05
                             RP853 256 lnnddvikleqsnidkfmktlqndkesllsqekvkkikqnik 297
                                       l+n dvikl + n+ k  ktlq d+e +l  ek kk+ +++k
  gi|242398663|ref|YP_002994087.1|  16 LKNMDVIKLIEKNLPKVEKTLQADREVFLL-EKKKKLEEKLK 56 
                                       899***********************9885.66677777666 PP

>> Polysacc_synt_4  Polysaccharide biosynthesis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   2.7   3.3e-05     0.049      30     102 ..      32     104 ..       5     107 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.3e-05
                   Polysacc_synt_4  30 lwkslnkggrlvlleeddeivekvkkefpeleayevkYktkvsdadeLlsaakkeaecrpvqnllasdckLal 102
                                       + k+l+  +++ lle+ +++ ek+k+   ele  +v Y+ ++ d++ +l+ ++k  e ++  +++ ++ kL++
  gi|242398663|ref|YP_002994087.1|  32 VEKTLQADREVFLLEKKKKLEEKLKEIEGELEELKVFYQKATEDKELMLTLREKLREENEELKKELEEKKLEI 104
                                       45788888999999**************************************994444444455556666665 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 ?    9.0  13.7    0.0013         2       9      72 ..      47     105 ..      44     106 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0013
                       Cep57_MT_bd   9 pkeaLaevlkeLedEfehlklelqelaaqynaldpslgkrkRkdLaeeleelvkrlEaKadqIy 72 
                                        k++L+e lke+e E+e+lk+ +q+  +  + +        R++L ee eel k+lE+K+  I+
  gi|242398663|ref|YP_002994087.1|  47 KKKKLEEKLKEIEGELEELKVFYQKATEDKELML-----TLREKLREENEELKKELEEKKLEIS 105
                                       57899999*****************999877776.....9*******************99887 PP

>> DUF5446  Family of unknown function (DUF5446)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   5.4   2.6e-05     0.039      17      59 ..      25      67 ..      17      80 .. 0.90
   2 ?   -1.1   2.9       1.4   2.2e+03      31      48 ..      81      98 ..      72     107 .. 0.48

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.6e-05
                           DUF5446 17 iEeeltevEkelseavneteaekeekeeerldllekElkdLvl 59
                                      iE++l +vEk l+        ek++k ee l  +e El++L++
  gi|242398663|ref|YP_002994087.1| 25 IEKNLPKVEKTLQADREVFLLEKKKKLEEKLKEIEGELEELKV 67
                                      9***************************************987 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.4
                           DUF5446 31 avneteaekeekeeerld 48
                                       ++e  +e +e+  + l+
  gi|242398663|ref|YP_002994087.1| 81 TLREKLREENEELKKELE 98
                                      444443443333333333 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 ?    6.7  11.1    0.0022       3.3      46     114 ..      33     107 ..       3     108 .] 0.77

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0022
                             Atg14  46 ekalegke......eaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklkkR 114
                                       ek l+  +      ++++le+k+k     leelk   ++  e ++++ + +++l++e+ee kk+l++++ +++ +
  gi|242398663|ref|YP_002994087.1|  33 EKTLQADRevflleKKKKLEEKLKEIEGELEELKVFYQKATEDKELMLTLREKLREENEELKKELEEKKLEISNK 107
                                       333333334444445578899999999999999999999999999999999999999999999999999888765 PP

>> EMP24_GP25L  emp24/gp25L/p24 family/GOLD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   6.6     0.004         6     103     152 ..      41      94 ..       3      97 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.004
                       EMP24_GP25L 103 d....ykdsakkekletleselkkleekldsikreqkylrereerlrdtnestn 152
                                       +    +k+ + +ekl+++e el++l+   ++  ++ +++ +  e+lr+ ne++ 
  gi|242398663|ref|YP_002994087.1|  41 EvfllEKKKKLEEKLKEIEGELEELKVFYQKATEDKELMLTLREKLREENEELK 94 
                                       03333556666****************************************876 PP

>> NBP1  Fungal Nap binding protein NBP1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7  17.5     0.011        17     154     239 ..       5      90 ..       2     108 .] 0.81

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.011
                              NBP1 154 elkydkqmleqLrrgrssnkserrvslrnnnleeDqvvlLqkkikklesklkdlekeLeitkkkLkFakeknkLles 230
                                       e+k +++  + L++    +  e++    ++ l++D+ v L  k kkle+klk+ e eLe +k   + a e ++L+  
  gi|242398663|ref|YP_002994087.1|   5 EIKIERETFKALKNMDVIKLIEKNLPKVEKTLQADREVFLLEKKKKLEEKLKEIEGELEELKVFYQKATEDKELMLT 81 
                                       88999999999999999999999988889999***999999999***************999988888888888655 PP

                              NBP1 231 lLddanids 239
                                       l ++ + ++
  gi|242398663|ref|YP_002994087.1|  82 LREKLREEN 90 
                                       544444444 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 ?    4.5   9.9    0.0044       6.6      52     131 ..      22     101 ..       1     108 [] 0.63

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0044
                        V_ATPase_I  52 avikeeeaeesleapeekeldeleeelekleeelkelnenleklkkelnelvelkavlekakefleeeeeeeeeees 128
                                       ++  e++  + +++ ++++   l e+ +klee+lke++ +le+lk  +++++e k+++ + +e l+ee+ee ++e +
  gi|242398663|ref|YP_002994087.1|  22 IKLIEKNLPKVEKTLQADREVFLLEKKKKLEEKLKEIEGELEELKVFYQKATEDKELMLTLREKLREENEELKKELE 98 
                                       333333333333333333333456778999999********************999999999999877544444343 PP

                        V_ATPase_I 129 eee 131
                                       e++
  gi|242398663|ref|YP_002994087.1|  99 EKK 101
                                       333 PP

>> DUF5320  Family of unknown function (DUF5320)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   2.3   0.00037      0.55      64      99 .]      30      65 ..       9      65 .. 0.84
   2 ?    2.1   3.3      0.27   4.1e+02      73      98 ..      74      99 ..      66     106 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00037
                           DUF5320 64 aetaeaskeeekelLeeqaeaLeeeleaikkrlkel 99
                                      ++ +++ + +++ +L e+++ Lee+l++i+ +l+el
  gi|242398663|ref|YP_002994087.1| 30 PKVEKTLQADREVFLLEKKKKLEEKLKEIEGELEEL 65
                                      567788899999*********************997 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.27
                           DUF5320 73 eekelLeeqaeaLeeeleaikkrlke 98
                                      e+kel+    e L+ee e++kk+l+e
  gi|242398663|ref|YP_002994087.1| 74 EDKELMLTLREKLREENEELKKELEE 99
                                      44555555555566666666666654 PP

>> Rx_N  Rx N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   4.4    0.0017       2.6      17      48 ..      40      76 ..       1      79 [. 0.85
   2 ?    2.2   1.9      0.15   2.2e+02      18      35 ..      81      98 ..      75     101 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0017
                              Rx_N 17 a.....kllkgvkeeleklkdeLesiqavLedaeerq 48
                                            ++ k+++e+l++++ eLe ++ + ++a e +
  gi|242398663|ref|YP_002994087.1| 40 RevfllEKKKKLEEKLKEIEGELEELKVFYQKATEDK 76
                                      2456668899**********************99865 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.15
                              Rx_N 18 kllkgvkeeleklkdeLe 35
                                      +l+++++ee e+lk+eLe
  gi|242398663|ref|YP_002994087.1| 81 TLREKLREENEELKKELE 98
                                      68999***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2390  (0.133304); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); 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):              12  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 721.63
//
Query:       gi|242398664|ref|YP_002994088.1|  [L=279]
Description: AlkA 3-methyladenine DNA glycosylase [Thermococcus sibiricus MM 739]
Scores for complete 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-15   55.1   0.0    1.3e-14   54.5   0.0    1.3  1  HhH-GPD   HhH-GPD superfamily base excision DNA repair protei


Domain annotation for each model (and alignments):
>> HhH-GPD  HhH-GPD superfamily base excision DNA repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.5   0.0   7.3e-19   1.3e-14       1     104 [.     106     247 ..     106     254 .. 0.92

  Alignments for each domain:
  == domain 1  score: 54.5 bits;  conditional E-value: 7.3e-19
                                       HHHHHHTTS-HHHHHHHHHHHHHHHS........HCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHHHH... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                           HhH-GPD   1 vsailsqqtsderanriierlferfg........fptpedladadeekLrelirelGfyrrKakyikelArilv... 66 
                                       v +i++qq+s+e+a + i +l+++ g        fptp+++++++eek+re+    +++ ++a yi++l ++++   
  gi|242398664|ref|YP_002994088.1| 106 VETIAQQQVSFEFAMQTIRNLVKLAGkklenlyiFPTPQSILNLSEEKFREA----KLG-YRAGYIRHLTKEYLegn 177
                                       679*************************************************....*99.***************** PP

                                       ....................................S-SSS--TTSHHHHHHHHHHTTSSSS.TTHHHHHHHHHH CS
                                       ....................................xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx RF
                           HhH-GPD  67 ....................................gkpdvlivvDvhvrrilkrlrsikek.ktkkkvekklee 104
                                                                           gk +v ++ D++++r++ ++++ ++k  ++k v+    e
  gi|242398664|ref|YP_002994088.1| 178 lnldleeldekeaikyltkfkgigrwsaelflayglGK-NVYPAGDLGMKRGIAKIFGKNPKeVKEKDVR----E 247
                                       ***********************************986.58*****************999833333333....3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1756.32
//
Query:       gi|242398665|ref|YP_002994089.1|  [L=95]
Description: hypothetical protein TSIB_0675 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.038   14.4   0.3      0.068   13.5   0.0    1.6  2  DUF2805   Protein of unknown function (DUF2805)
       0.11   12.2   0.0       0.13   12.0   0.0    1.1  1  DUF4423   Domain of unknown function (DUF4423)


Domain annotation for each model (and alignments):
>> DUF2805  Protein of unknown function (DUF2805)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1       1.1     1e+04      61      68 ..       3      10 ..       1      12 [. 0.55
   2 ?   13.5   0.0   7.6e-06     0.068      17      33 ..      40      56 ..      34      69 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.1
                           DUF2805 61 eevsrfks 68
                                      +e++rfk+
  gi|242398665|ref|YP_002994089.1|  3 TEIKRFKI 10
                                      45566665 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 7.6e-06
                           DUF2805 17 IeeqfglsekeviklMr 33
                                       ee+fg++ek+v ++Mr
  gi|242398665|ref|YP_002994089.1| 40 LEENFGIKEKDVKEIMR 56
                                      6899************9 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.4e-05      0.13      26      73 ..      24      69 ..      17      89 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.4e-05
                           DUF4423 26 irellplkdfkadpeelakrlrpkisaeevekalefLlklgllkkded 73
                                      ire+++  +  + ++ l++ ++  i++++v+++++fL+++g l+ +++
  gi|242398665|ref|YP_002994089.1| 24 IREIAKFSHSGPFWKFLEENFG--IKEKDVKEIMRFLEEAGELELHRS 69
                                      88888888888899999*****..*****************9986654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       708  (0.0394891); expected 358.6 (0.02)
Passed bias filter:                      582  (0.0324614); 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: 0.52u 0.34s 00:00:00.86 Elapsed: 00:00:00.53
# Mc/sec: 535.88
//
Query:       gi|242398666|ref|YP_002994090.1|  [L=451]
Description: NfeD nodulation like protein, probable membrane protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-18   67.4   1.0      1e-18   67.4   1.0    2.2  2  NfeD           NfeD-like C-terminal, partner-binding
    3.7e-11   43.3   0.2    5.6e-11   42.7   0.2    1.2  1  CLP_protease   Clp protease
     0.0011   18.0   0.1     0.0022   17.0   0.1    1.5  1  SDH_sah        Serine dehydrogenase proteinase
  ------ inclusion threshold ------
      0.043   13.4   0.1      0.074   12.6   0.1    1.3  1  Peripla_BP_4   Periplasmic binding protein domain
      0.094   12.7   0.2       0.21   11.6   0.2    1.5  1  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 ?   -3.1   0.1         3   1.1e+04       8      42 ..     246     277 ..     241     283 .. 0.45
   2 !   67.4   1.0   2.9e-22     1e-18       4      83 ..     356     437 ..     350     438 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3
                                       XXXXXXXXXS---SSS--S.S---GGTTSEEEEEE CS
                              NfeD   8 lllvllrplllkklkkkekktnaealiGkegvvle 42 
                                       ll++ ++ l+l  l+       + + +G++ +vl+
  gi|242398666|ref|YP_002994090.1| 246 LLTLGIWALVLGFLSP--G-WHVPETVGAIMIVLA 277
                                       4444444455554411..1.112245555555554 PP

  == domain 2  score: 67.4 bits;  conditional E-value: 2.9e-22
                                       XXXXXXXXXXXXXS---SSS--S.S---GGTTSEEEEEE-BS.-EEEEETTEEEEEE-.SS..B-TT-EEEEEEE-S CS
                              NfeD   4 vvsvlllvllrplllkklkkkekktnaealiGkegvvledig.tGrvkvdGeeWsarsege..iekgerVrVveveG 77 
                                       ++ +l++++++  + k+++kk++ t++e++iG  g+v+e+++ +G+++ +Ge W+ars+++  i  ge+Vr+ve+eG
  gi|242398666|ref|YP_002994090.1| 356 ALLALFFAFGMAAVIKARRKKAQ-TGKEEMIGLFGEVVEPLSpEGMIRARGELWRARSKDGksIGIGEKVRIVEMEG 431
                                       33345555555667777766565.*****************668**************8777*************** PP

                                       SSEEEE CS
                              NfeD  78 ltliVe 83 
                                       l+liV 
  gi|242398666|ref|YP_002994090.1| 432 LKLIVV 437
                                       *****6 PP

>> CLP_protease  Clp protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.7   0.2   1.5e-14   5.6e-11      43     179 ..      53     189 ..      19     192 .. 0.85

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 1.5e-14
                                       H-SSS-EEEEEEE--B-HHHHHHHHHHHHHSSS-EEEEEE...EEEETHHHHHHHTS-TTGEEEETTEEEEES-TEE CS
                      CLP_protease  43 edpdkdillyinspGGsvtaglaIydtmqyikpdvsticl...GlaaSmgslllaagekgkRfalpnarimihqPlg 116
                                        ++ + i + +++pGG  +a+  I + ++  + +v+t++    G+aaS+g+ ++++ +    ++ p + i   +P  
  gi|242398666|ref|YP_002994090.1|  53 RANANAIIILLDTPGGRADAMQNIIERIKSAEVPVITYVYppgGMAASAGTYIALGSHLI--AMAPGTSIGACRPIL 127
                                       34556899*******************************9999**************999..799************ PP

                                       EEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHHHHCSTEEEEHHHHHHHTSSSEE- CS
                      CLP_protease 117 gaqgqasdieieaeellkikerlneilakhtgqslekiekdldrdtflsaeeAveyGLidevi 179
                                       g++++ s ie   + ++   +  ++ lak++g+++  +ek ++ d  +++eeA++ G i+ + 
  gi|242398666|ref|YP_002994090.1| 128 GYSQNGSIIEAPPKVVNFYASY-IKSLAKASGRNETMVEKFITEDLAIDPEEALNSGVIEVIA 189
                                       ***9888888877776666655.56789*******************************9876 PP

>> SDH_sah  Serine dehydrogenase proteinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   6.2e-07    0.0022      93     170 ..      58     138 ..      44     176 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 6.2e-07
                           SDH_sah  93 pidliihtpGGlvlaatqiakalkehkaktrviv.p..hyamsGGtlialaadeiildenavlGpvdpqlgqypaas 166
                                        i +++ tpGG + a ++i + +k+ + ++   v p    a s Gt ial +  i + + + +G   p lg     s
  gi|242398666|ref|YP_002994090.1|  58 AIIILLDTPGGRADAMQNIIERIKSAEVPVITYVyPpgGMAASAGTYIALGSHLIAMAPGTSIGACRPILGYSQNGS 134
                                       5677889**************9998766653333242336889******************************9*** PP

                           SDH_sah 167 ilkv 170
                                       i+++
  gi|242398666|ref|YP_002994090.1| 135 IIEA 138
                                       9987 PP

>> Peripla_BP_4  Periplasmic binding protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   2.1e-05     0.074      48      89 ..      48      93 ..      28     115 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.1e-05
                                      HHHHHHTT-SEEEE--SSH....HHHHHHHHHHHHTT-EEEEESTT CS
                      Peripla_BP_4 48 iedaiakgvdgiivapvds....talapalkkakaaGIpVvafdsd 89
                                      i+ a  +++++ii+    +    +a++ +++++k+a +pV+++  +
  gi|242398666|ref|YP_002994090.1| 48 ISEAERANANAIIILLDTPggraDAMQNIIERIKSAEVPVITYVYP 93
                                      556666789999988777777889*******************887 PP

>> Peptidase_S49  Peptidase family S49
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   5.7e-05      0.21       3      40 ..      81     121 ..      79     129 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.7e-05
                                       HHTT--EEEEE...EEEEETHHHHHHTTSSEEEE-TT-EEE CS
                     Peptidase_S49   3 kkakkPvvasa...envaaSggYylasaadkivanpstivg 40 
                                       k+a+ Pv+ ++   +++aaS+g y+a ++  i ++p t++g
  gi|242398666|ref|YP_002994090.1|  81 KSAEVPVITYVyppGGMAASAGTYIALGSHLIAMAPGTSIG 121
                                       6788999999866689***********************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       877  (0.0489152); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.46
# Mc/sec: 2930.18
//
Query:       gi|242398667|ref|YP_002994091.1|  [L=268]
Description: membrane protease subunit, stomatin/prohibitin like protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.2e-38  130.4   6.4      1e-37  129.9   6.4    1.1  1  Band_7    SPFH domain / Band 7 family
    4.7e-05   23.2   1.5    0.00014   21.7   0.6    2.2  2  Band_7_1  SPFH domain-Band 7 family
  ------ inclusion threshold ------
        2.3    8.2   6.7       0.21   11.5   1.2    2.1  3  DUF4083   Domain of unknown function (DUF4083)


Domain annotation for each model (and alignments):
>> Band_7  SPFH domain / Band 7 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.9   6.4   1.7e-41     1e-37       2     178 .]      28     198 ..      27     198 .. 0.99

  Alignments for each domain:
  == domain 1  score: 129.9 bits;  conditional E-value: 1.7e-41
                            Band_7   2 iieegevgvvvrfGklsrvlepGlhfilPfgrsvtvvsvrvqtldvsvsltvptkDglpvtidvtviyrvpddapkl 78 
                                       i++e e++v++r G++++ ++pGl fi+P++++ ++v++r+q+ldv+v ++++tkD++pv+++++v++rv  d+ k+
  gi|242398667|ref|YP_002994091.1|  28 IVKEYERAVIFRLGRVVGARGPGLFFIIPIFEKAIIVDLRTQVLDVPV-QETITKDNVPVRVNAVVYFRV-VDPVKA 102
                                       799*********************************************.*********************.****** PP

                            Band_7  79 vaaveresanldnlirrvlesalrevisemtleellsnreelaeelknelneqlrkyGvevldvritdidpppevaq 155
                                       v++v    +n     +++ + +lr+vi++  l+ells+re+l+ el++ + e+ + +G+ v+ v i+d+++p+  ++
  gi|242398667|ref|YP_002994091.1| 103 VTQV----KNFIMATSQISQTTLRSVIGQAHLDELLSEREKLNRELQRIIDEATDPWGIKVTAVEIKDVELPAGMQR 175
                                       ****....********************************************************************* PP

                            Band_7 156 alaakqaaeaeaqaeiaraeaea 178
                                       a+a+ ++ae+e++a+i  +eae+
  gi|242398667|ref|YP_002994091.1| 176 AMARQAEAERERRARITLSEAER 198
                                       ********************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 ?   -2.0   0.0      0.39   2.3e+03      18      42 ..      28      52 ..      23      56 .. 0.84
   2 !   21.7   0.6   2.3e-08   0.00014     108     209 ..      93     183 ..      72     185 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.39
                          Band_7_1 18 ivregqeavfvneGqiaDvfapGty 42
                                      iv+e  +av  + G++    +pG +
  gi|242398667|ref|YP_002994091.1| 28 IVKEYERAVIFRLGRVVGARGPGLF 52
                                      8999999***9*9*99998888876 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 2.3e-08
                          Band_7_1 108 slrvvdpakllreivGtdgefdteeiseqlkslivtrlsdvlaeskipvldlaakseelaeklkealkeelaeyGle 184
                                        +rvvdp k ++++   +  + t++is       +t+l +v++++++   +l ++ e+l ++l+  ++e+ +  G++
  gi|242398667|ref|YP_002994091.1|  93 YFRVVDPVKAVTQVK--NFIMATSQIS-------QTTLRSVIGQAHL--DELLSEREKLNRELQRIIDEATDPWGIK 158
                                       555555555555442..2222233332.......3334444444443..4678999********************* PP

                          Band_7_1 185 lekleienislpeevekaldkrasm 209
                                       ++++ei++++lp  +++a+ ++a++
  gi|242398667|ref|YP_002994091.1| 159 VTAVEIKDVELPAGMQRAMARQAEA 183
                                       ********************99876 PP

>> DUF4083  Domain of unknown function (DUF4083)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.2   3.6e-05      0.21       3      26 ..       6      29 ..       4      33 .. 0.90
   2 ?   -2.6   0.1      0.93   5.6e+03      40      51 ..     137     148 ..     134     149 .. 0.81
   3 ?   -3.1   0.0       1.4   8.2e+03      22      40 ..     245     263 ..     236     266 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.6e-05
                           DUF4083  3 gdliyliivivLilllvfsftlfi 26
                                      +++i++i+++v +l+++ s + ++
  gi|242398667|ref|YP_002994091.1|  6 FEWIIYIVILVFVLGFLASAIKIV 29
                                      89****************988775 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.93
                           DUF4083  40 skeleqKLDkiI 51 
                                        ++l++ L +iI
  gi|242398667|ref|YP_002994091.1| 137 REKLNRELQRII 148
                                       678999999999 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 1.4
                           DUF4083  22 ftlfiRrvvsrsaakkkks 40 
                                       +  + R+++   +a kkk+
  gi|242398667|ref|YP_002994091.1| 245 MLKLFRSLSETAVAFKKKV 263
                                       4455677777777666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1682  (0.0938145); expected 358.6 (0.02)
Passed bias filter:                      814  (0.0454013); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.37s 00:00:01.01 Elapsed: 00:00:00.53
# Mc/sec: 1515.79
//
Query:       gi|242398668|ref|YP_002994092.1|  [L=260]
Description: Cell division inhibitor minD [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.6e-23   82.5   0.4    4.1e-23   81.8   0.4    1.3  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    1.8e-21   76.9   0.2    2.6e-21   76.3   0.2    1.2  1  AAA_31       AAA domain
    3.3e-18   66.0   2.9    9.5e-18   64.5   2.9    1.8  1  ParA         NUBPL iron-transfer P-loop NTPase
    1.7e-12   47.3   0.4    5.1e-07   29.4   0.1    2.1  2  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
    7.2e-10   38.7   0.0    1.1e-09   38.1   0.0    1.4  1  CBP_BcsQ     Cellulose biosynthesis protein BcsQ
    1.6e-09   37.5   0.7    2.8e-08   33.4   0.7    2.1  1  MipZ         ATPase MipZ
      5e-07   29.2   1.8    5.8e-07   29.0   0.3    1.8  2  ArsA_ATPase  Anion-transporting ATPase
     0.0005   19.4   0.2     0.0011   18.4   0.2    1.4  1  VirC1        VirC1 protein
     0.0006   19.7   0.6     0.0006   19.7   0.6    1.9  2  AAA_26       AAA domain
     0.0069   16.1   0.3      0.012   15.3   0.3    1.4  1  AAA_30       AAA domain
  ------ inclusion threshold ------
      0.036   13.7   0.7       0.08   12.6   0.3    1.7  2  SRP54        SRP54-type protein, GTPase domain
       0.09   12.7   0.0       0.16   11.8   0.0    1.4  1  APS_kinase   Adenylylsulphate kinase
      0.096   12.7   0.0       0.17   11.9   0.0    1.3  1  HU-DNA_bdg   DNA-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 !   81.8   0.4     3e-26   4.1e-23       1     127 [.       5     212 ..       5     213 .. 0.93

  Alignments for each domain:
  == domain 1  score: 81.8 bits;  conditional E-value: 3e-26
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH....................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................... RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep....................... 54 
                                       i++as+kGG+GKTt  an ++ala+ g++V+++DaD  + nl+++ g e    +                       
  gi|242398668|ref|YP_002994092.1|   5 IVFASGKGGTGKTTAIANVGVALAQFGKEVIVIDADITMANLSLILGMEDIPITlhdvlsgeaelsdaiyegpagvk 81 
                                       789****************************************87777776666999******************** PP

                                       ....................................................................CCHCCCHHH CS
                                       ....................................................................xxxxxxxxx RF
                              CbiA  55 ....................................................................dlkrllell 63 
                                                                                                           d  + + ++
  gi|242398668|ref|YP_002994092.1|  82 vipgglslekikkaknperlkelmreissladfilidapaglemtsitalligkelilvtnpeisaitDSLKTKLVA 158
                                       ***********************************************************999888888777767777 PP

                                       HHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHHTS- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  64 ealgkkkalllkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeavaeapargep 127
                                       e+lg       +++g vlnrv +e  ++l ke++e+++    vpvl +ip+d +v +a a g p
  gi|242398668|ref|YP_002994092.1| 159 EKLG------TLPLGAVLNRVTNE-KTELSKEDIETIL---DVPVLMIIPEDPEVKRASAYGIP 212
                                       7777......579*********99.699999******9...******************99987 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.3   0.2   1.9e-24   2.6e-21       2     154 ..       3     148 ..       2     159 .. 0.91

  Alignments for each domain:
  == domain 1  score: 76.3 bits;  conditional E-value: 1.9e-24
                            AAA_31   2 kvIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlD.pQanattglgiekneiektlyevlieeknikeaiiktk 77 
                                       + I++a  KGG GKTT   n+++ala+ gk v+++D+D + an++  lg+  ++i  tl++vl  e+++++ai++  
  gi|242398668|ref|YP_002994092.1|   3 RSIVFASGKGGTGKTTAIANVGVALAQFGKEVIVIDADiTMANLSLILGM--EDIPITLHDVLSGEAELSDAIYE-G 76 
                                       6799**********************************446899999996..78888*****************4.4 PP

                            AAA_31  78 venldlipssidLaeaeielvelekkeeilkellekvkdeYDyiiiDcpPsLglltenaLvasdsviipvqaeayal 154
                                          +++ip+ ++L +++     + k+ e+lkel++++++  D+i+iD+p  L++  ++aL++  ++i ++++e  a+
  gi|242398668|ref|YP_002994092.1|  77 PAGVKVIPGGLSLEKIK-----KAKNPERLKELMREISSLADFILIDAPAGLEMTSITALLIGKELILVTNPEISAI 148
                                       5888********99876.....56788999****************************************9987664 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 !   64.5   2.9   6.9e-21   9.5e-18       5     245 ..       4     233 ..       1     234 [. 0.84

  Alignments for each domain:
  == domain 1  score: 64.5 bits;  conditional E-value: 6.9e-21
                              ParA   5 viavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgvee.....ekpeqsekkli.Pvea..kgi 73 
                                        i+ +SgKGG GK+t  +n+ +aLa+ g++v ++DaDi+  ++  +lg+e+     +++ + e++l   ++    g+
  gi|242398668|ref|YP_002994092.1|   4 SIVFASGKGGTGKTTAIANVGVALAQFGKEVIVIDADITMANLSLILGMEDipitlHDVLSGEAELSdAIYEgpAGV 80 
                                       6899***********************************************6665533333355555345557899* PP

                              ParA  74 kvmSigfllesedeavvwrGpmkskaikqllkdvewgelDyLiiDlPPGtgDeqltvaqklplagaviVttpqeval 150
                                       kv+  g+ le+       + ++  + +k+l+++++    D+++iD P G      +++  l  ++ ++Vt p+  a+
  gi|242398668|ref|YP_002994092.1|  81 KVIPGGLSLEK------IKKAKNPERLKELMREISS-LADFILIDAPAGLE--MTSITALLIGKELILVTNPEISAI 148
                                       *********94......45567888999**999985.58********9875..445556667789************ PP

                              ParA 151 advkkaiemfkkvkvkvlGvveNmsgfvcpkcgekteifgkgggeklaeelgvpllgeipldpeireasdegkplvl 227
                                       +d  k+  +++k+ +  lG v N  +       ekte+    + e++ + l+vp+l  ip dpe+++as  g plv+
  gi|242398668|ref|YP_002994092.1| 149 TDSLKTKLVAEKLGTLPLGAVLNRVTN------EKTEL----SKEDIETILDVPVLMIIPEDPEVKRASAYGIPLVI 215
                                       ********************9985433......33333....3456667799************************* PP

                              ParA 228 kepeseaakaleeiaekv 245
                                       k+p+s+aa a++++a+k+
  gi|242398668|ref|YP_002994092.1| 216 KNPTSPAAIAYKQLAAKL 233
                                       **************9987 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 !   29.4   0.1   3.7e-10   5.1e-07       6      85 ..       9      84 ..       4      88 .. 0.87
   2 !   16.2   0.0     4e-06    0.0056     170     246 ..     160     235 ..     126     250 .. 0.79

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 3.7e-10
                         Fer4_NifH  6 yGkGGiGksttsqnlsaalaemgkkvlivGCDPkaDstrlllggkaqetvldtlrekgavedvkvedvvkkGyggvkcv 84
                                       GkGG Gk+t+++n+  ala++gk v+++  D      +l+lg   ++  l+ + + +     ++ d +++G  gvk++
  gi|242398668|ref|YP_002994092.1|  9 SGKGGTGKTTAIANVGVALAQFGKEVIVIDADITMANLSLILGMEDIPITLHDVLSGE----AELSDAIYEGPAGVKVI 83
                                      59*****************************************999987777665554....4899*********9987 PP

                         Fer4_NifH 85 e 85
                                       
  gi|242398668|ref|YP_002994092.1| 84 P 84
                                      5 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 4e-06
                         Fer4_NifH 170 ksggvrlgGliinsrkvddereliekfaee.lgtkvlevvPrdeivrkaelrkktvieyapeseqakeyrelarkil 245
                                       k g++ l G + n r +++++el ++ +e+ l+++vl ++P d +v++a++    ++  +p+s+ a  y++la k++
  gi|242398668|ref|YP_002994092.1| 160 KLGTLPL-GAVLN-RVTNEKTELSKEDIETiLDVPVLMIIPEDPEVKRASAYGIPLVIKNPTSPAAIAYKQLAAKLA 234
                                       4455555.56789.8788889998876665269********************999999**************9987 PP

                         Fer4_NifH 246 e 246
                                        
  gi|242398668|ref|YP_002994092.1| 235 G 235
                                       5 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   0.0   8.2e-13   1.1e-09       5     151 ..       6     147 ..       3     233 .. 0.84

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 8.2e-13
                          CBP_BcsQ   5 alqGvRGGvGttsllaaLawalhelgesvlviDlspd.nlLrlhFnvdieqregwaraeldgapwrqaaleyapgld 80 
                                       ++   +GG+G+t+ +a  + al + g++v+viD+      L l   ++ +   ++   +  +a++++a++e   g++
  gi|242398668|ref|YP_002994092.1|   6 VFASGKGGTGKTTAIANVGVALAQFGKEVIVIDADITmANLSLILGME-DIPITLHDVLSGEAELSDAIYEGPAGVK 81 
                                       555558**************************9864314578888888.88999*********************** PP

                          CBP_BcsQ  81 llPfGelnveekenlqqlaekaeallaalkelkeqyrwillDlpagasaltrellaladlvllvvepdanc 151
                                       ++P G l+ e+ +     a+++e+l++ ++e+++  ++il+D pag + +  ++l      +lv++p+ ++
  gi|242398668|ref|YP_002994092.1|  82 VIP-GGLSLEKIK----KAKNPERLKELMREISSLADFILIDAPAGLEMTSITALLIGKELILVTNPEISA 147
                                       ***.557777776....468899999999999999************99999999999*********9876 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.7     2e-11   2.8e-08       2     115 ..       4     127 ..       3     146 .. 0.69

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 2e-11
                                       EEEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHHHHHHHHHHHH.......HHT--...----E.E CS
                              MipZ   2 vivlgnekGGsGksttavhvavaLlkkGarvaaidldlrqrtlarylenraatae.......rkgls...Lplpe.a 67 
                                        iv++  kGG+Gk+t    v vaL++ G++v +id d+  + l+  l+      +       + +ls    + p  +
  gi|242398668|ref|YP_002994092.1|   4 SIVFASGKGGTGKTTAIANVGVALAQFGKEVIVIDADITMANLSLILGMEDIPITlhdvlsgEAELSdaiYEGPAgV 80 
                                       69***********************************9999888776544322210011101223321112334313 PP

                                       E-SSS-.HHHHTTS-HHHHHHHHHHHHHHHHHH-SEEEEE--SS--HHH CS
                              MipZ  68 lalsea.eeaeveeeeeaevaeleelvadleaeldfividtPGsdsals 115
                                        +++ + + +++++ ++ e  +l+el++++++ +dfi+id+P   +  s
  gi|242398668|ref|YP_002994092.1|  81 KVIPGGlSLEKIKKAKNPE--RLKELMREISSLADFILIDAPAGLEMTS 127
                                       3455442445677777777..*********************8766555 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.3   4.2e-10   5.8e-07       3      38 ..       5      40 ..       3      57 .. 0.91
   2 ?   -1.2   0.1      0.66     9e+02     201     201 ..     132     132 ..      87     180 .. 0.55

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 4.2e-10
                                      EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S CS
                       ArsA_ATPase  3 vilvgGKGGVGKttvsaatavklsekgkkvllistD 38
                                      +++ +GKGG GKtt+ a ++v l++ gk+v++i  D
  gi|242398668|ref|YP_002994092.1|  5 IVFASGKGGTGKTTAIANVGVALAQFGKEVIVIDAD 40
                                      799******************************988 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.66
                                       H CS
                       ArsA_ATPase 201 l 201
                                       l
  gi|242398668|ref|YP_002994092.1| 132 L 132
                                       1 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.2   7.6e-07    0.0011       4      39 ..       5      40 ..       3      46 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 7.6e-07
                             VirC1  4 itfcslkGGaGkttalmglcsalasdgkrvalfead 39
                                      i f+s kGG+Gktta+  +  ala+ gk v + +ad
  gi|242398668|ref|YP_002994092.1|  5 IVFASGKGGTGKTTAIANVGVALAQFGKEVIVIDAD 40
                                      789*******************************99 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       3.4   4.7e+03       3      25 ..       5      27 ..       3      36 .. 0.58
   2 !   19.7   0.6   4.4e-07    0.0006     127     196 ..     133     205 ..      87     207 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3.4
                            AAA_26  3 ifvtgtdtgvGKTvvslgLvral 25
                                      i+ ++   g GKT+ ++ +  al
  gi|242398668|ref|YP_002994092.1|  5 IVFASGKGGTGKTTAIANVGVAL 27
                                      55555556677777666554444 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 4.4e-07
                            AAA_26 127 lgapvilVargglgtinqllltiealrqknvrvlGvilNkvrnpe...nvetlekksgipvlGvvPylpdlea 196
                                       +g + ilV++++ ++i++ l t  ++ + +   lG +lN+v+n++     e +e+   +pvl ++P +p++++
  gi|242398668|ref|YP_002994092.1| 133 IGKELILVTNPEISAITDSLKTKLVAEKLGTLPLGAVLNRVTNEKtelSKEDIETILDVPVLMIIPEDPEVKR 205
                                       47799***********************9************999666789999999*************9876 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.3   8.7e-06     0.012      18      52 ..       3      37 ..       1      55 [. 0.87

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 8.7e-06
                            AAA_30 18 drvavltGpAGtGKttalkalreaweaaggrvigl 52
                                      + ++++ G  GtGKtta++ +  a+++ g++vi++
  gi|242398668|ref|YP_002994092.1|  3 RSIVFASGKGGTGKTTAIANVGVALAQFGKEVIVI 37
                                      568899********************99*999986 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.3   5.8e-05      0.08       4      39 ..       6      41 ..       3      45 .. 0.88
   2 ?   -2.5   0.0       2.4   3.3e+03      81      91 ..     109     119 ..      90     140 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.8e-05
                                      EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEEST CS
                             SRP54  4 illvGlqGaGKTttlaKLaallkkegkkvllvaaDt 39
                                      +   G  G+GKTt++a +   l + gk+v+++ aD+
  gi|242398668|ref|YP_002994092.1|  6 VFASGKGGTGKTTAIANVGVALAQFGKEVIVIDADI 41
                                      5556999*************************9997 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.4
                                       HTTSSEEEEEE CS
                             SRP54  81 eekidvvlvDT 91 
                                       ++ +d++l+D 
  gi|242398668|ref|YP_002994092.1| 109 SSLADFILIDA 119
                                       23345555553 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00012      0.16       4      52 ..       5      53 ..       2      56 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00012
                                      EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT--SS CS
                        APS_kinase  4 vvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdLgfs 52
                                      +v+ +G  g+GK+t   ++  +L + g++v+++d d    +L+  Lg++
  gi|242398668|ref|YP_002994092.1|  5 IVFASGKGGTGKTTAIANVGVALAQFGKEVIVIDADITMANLSLILGME 53
                                      7999********************************9999998888765 PP

>> HU-DNA_bdg  DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00013      0.17      22      56 ..     157     191 ..     142     195 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00013
                                       EE----EE-HHHHHHHHHHH-TTS-HHHHHHHHHH CS
                        HU-DNA_bdg  22 qvessgsltledIidemvkegtevrketienilnl 56 
                                         e  g+l l  +++++ +e+te++ke+ie+il++
  gi|242398668|ref|YP_002994092.1| 157 VAEKLGTLPLGAVLNRVTNEKTELSKEDIETILDV 191
                                       55677899999*********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); 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: 00:00:00.49
# Mc/sec: 1587.72
//
Query:       gi|242398669|ref|YP_002994093.1|  [L=81]
Description: hypothetical protein TSIB_0679 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.014   15.4   2.0      0.024   14.7   2.0    1.6  1  PspB         Phage shock protein B
      0.021   14.8   0.6      0.026   14.5   0.6    1.2  1  Ac76         Orf76 (Ac76)
       0.11   12.7   0.7       0.15   12.4   0.7    1.2  1  Sigma_reg_N  Sigma factor regulator N-terminal


Domain annotation for each model (and alignments):
>> PspB  Phage shock protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   2.0     4e-06     0.024       4      55 ..       3      52 ..       1      80 [. 0.74

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4e-06
                              PspB  4 flavpliifvlfVapiWLiLHYrskkkrskglsaedekrLeellekAeklee 55
                                      +++++l+if+lf + i Li+ Y s k++s+ +  ++e+r ++l ++  +l+e
  gi|242398669|ref|YP_002994093.1|  3 LFTTILVIFLLF-MNIFLIILYLSEKRSSRYVAYDEESR-STLKRRVTHLKE 52
                                      456677777777.56778888999888888887666554.566666666655 PP

>> Ac76  Orf76 (Ac76)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.6   4.3e-06     0.026      25      67 ..       2      46 ..       1      58 [. 0.72

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.3e-06
                              Ac76 25 ellltllllfvlFiil..lnvyyikteStpadlytekakkikKkr 67
                                      +l+ t+l++f+lF+ +  + +y  ++ S+    y e+++++ K+r
  gi|242398669|ref|YP_002994093.1|  2 SLFTTILVIFLLFMNIflIILYLSEKRSSRYVAYDEESRSTLKRR 46
                                      577888999998864410344556788888899999999999887 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 ?   12.4   0.7   2.5e-05      0.15      17      46 ..       4      33 ..       1      44 [. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.5e-05
                       Sigma_reg_N 17 lislivlllifvilvvtllylaekegnklr 46
                                      +++++v++l+f+ +++++lyl+ek+++++ 
  gi|242398669|ref|YP_002994093.1|  4 FTTILVIFLLFMNIFLIILYLSEKRSSRYV 33
                                      578889999999999999999999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2018  (0.112555); expected 358.6 (0.02)
Passed bias filter:                     1117  (0.0623013); expected 358.6 (0.02)
Passed Vit filter:                       115  (0.00641419); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.33s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 495.67
//
Query:       gi|242398670|ref|YP_002994094.1|  [L=503]
Description: thymidine phosphorylase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-14   53.7   0.1    3.6e-14   52.3   0.1    1.8  1  Glycos_trans_3N  Glycosyl transferase family, helical bundle 
    3.6e-14   52.2   0.1    1.3e-13   50.4   0.1    2.0  1  PYNP_C           Pyrimidine nucleoside phosphorylase C-termin
    5.3e-14   52.4   1.1    2.7e-13   50.1   1.1    2.0  1  Glycos_transf_3  Glycosyl transferase family, a/b domain
    1.6e-05   23.9   0.1    2.4e-05   23.3   0.1    1.2  1  DUF2254          Predicted membrane protein (DUF2254)
    6.5e-05   22.9   0.0    0.00013   22.0   0.0    1.4  1  Molydop_binding  Molydopterin dinucleotide binding domain
     0.0013   18.9   1.7     0.0024   18.0   0.0    2.4  3  CDC48_N          Cell division protein 48 (CDC48), N-terminal


Domain annotation for each model (and alignments):
>> Glycos_trans_3N  Glycosyl transferase family, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.3   0.1   1.2e-17   3.6e-14       2      63 .]      89     150 ..      88     150 .. 0.97

  Alignments for each domain:
  == domain 1  score: 52.3 bits;  conditional E-value: 1.2e-17
                                       HHHHHHHTT.---HHHHHHHHHHHHTTSS-HHHHHHHHHHHHHH---HHHHHHHHHHHHHHS CS
                   Glycos_trans_3N   2 diikklrdgeeLtaeeirfaihgilkgevtdaqiaAfLmAlrlkGetaeEiaalaeAmresg 63 
                                        +i+++++g++L + ei++++++i++ ++ d++i++f ++l ++G++ +Eia l++Am e g
  gi|242398670|ref|YP_002994094.1|  89 RYIRRKMNGQKLKKVEIEAIVKDIVNRKLRDIEISSFVTSLEINGLDMDEIAWLTTAMAETG 150
                                       69********************************************************9875 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 !   50.4   0.1   4.4e-17   1.3e-13       1      69 [.     424     485 ..     424     491 .. 0.95

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 4.4e-17
                                       EEEEE-HHHHHHHHHHTTTSBSSTTS---TT-EEEES--TT-EEBTTSEEEEEEESSSCHHHHHHHHHH CS
                            PYNP_C   1 yvseidareiGlaaveLGAGRakkeDpidlavGielhkklGdkVkkGeplatiYankeekleeavkklk 69 
                                       y+++id+++i+ +a+++GA       p d+++Gi+lh+k+G+kVk+ +pl+t++a++  +l++a+ +++
  gi|242398670|ref|YP_002994094.1| 424 YITRIDNKAITAIARAAGA-------PEDKGAGIMLHVKVGEKVKERDPLFTVHAESGTRLDQAIIQAR 485
                                       89*****************.......*************************************997766 PP

>> Glycos_transf_3  Glycosyl transferase family, a/b domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.1   1.1   8.9e-17   2.7e-13       2     253 .]     158     387 ..     157     387 .. 0.85

  Alignments for each domain:
  == domain 1  score: 50.1 bits;  conditional E-value: 8.9e-17
                                       TTBEEEEESS-SSSTHHHHHHHHHHHHHHTT-BEEEEE-STCTTCS-HHHHHCTST--ST--HHHHHHHHHHHSEEE CS
                   Glycos_transf_3   2 kdlvDivgTGGdgantfNiStaaaivvAaaGvkvakhgnrsvssksGsaDvLealgvnleltpeeveklleevgvgf 78 
                                       k+++D+++ GG+  n  Ni     ++vAaaG++++k + r+++s +G+aDv+e l   +  + +e+++++e+ g ++
  gi|242398670|ref|YP_002994094.1| 158 KPIMDVHSIGGVPGNKTNILV--VPIVAAAGLTIPKTSSRAITSAAGTADVVEVLA-PVTHSLDEIKRIVEKIGACL 231
                                       689*********999989955..599***************************995.799999*************9 PP

                                       EE..HHSSSSHHHHHHHHHHHHTT.-SSHHHCHHHHHT..SEEEEHHHHHHHHTCHSEEEEEEEESTTSSCCSTSHH CS
                   Glycos_transf_3  79 lf..apeyhkamkhvapvrrelgirTvfnlLGPLinparvkkqllgvyskelaeklaevlkelgveralvvhgdGld 153
                                       +   a +  +a +  +++ r+l i            p      l +++sk+ a +   vl ++++++++ v+   ++
  gi|242398670|ref|YP_002994094.1| 232 VWggALNLAPADDLTIKAERALSI-----------DP--RGLMLASIMSKKYAMGSQYVLIDIPTGEGVKVEK--VE 293
                                       962255555666667777777777...........44..3334558***************************..** PP

                                       HHHHHHHHHHHHHH.TTEEEEEEEEEGSSTSSSEEESHHHHSSHHHHHHHHTTHHTSCHHHHHHHHHHHHHHHHHHH CS
                   Glycos_transf_3 154 evsllakttvaelk.dgeiteytlepedfglkraelealeggepkenaeilkavlegkksaakrdlvllnagaalvl 229
                                       +++ lak  +   k  g+  e +++   +++++  + ale    ke++e++    egk   + ++  + +ag +l +
  gi|242398670|ref|YP_002994094.1| 294 DARSLAKDFIELGKrLGQYVETAITYGGQPIGHTVGPALEA---KEALETII---EGKGPGSLVEKATGLAGILLEM 364
                                       **************99******************9999999...66665554...5555544467777888888877 PP

                                       TTSSSSHHHHHHHHHHHHHTSHHH CS
                   Glycos_transf_3 230 agkadslkegvakaeevidsGkAl 253
                                        g +     g + a+e+++sGkA+
  gi|242398670|ref|YP_002994094.1| 365 GG-VAPAGMGKKMAKEILESGKAY 387
                                       76.999999*************96 PP

>> DUF2254  Predicted membrane protein (DUF2254)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.1   8.1e-09   2.4e-05     172     257 ..     394     484 ..     370     493 .. 0.70

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 8.1e-09
                           DUF2254 172 deeeeeeeeakdeeeseeeeatpiraersGylqaidveaLvklaeeh......dlvielevrpGdfvvkgeplakvw 242
                                        ee+  + + k+e+ +  +++++ +a++sGy+++id +a+ ++a+++      ++ i l+v++G+ v + +pl++v+
  gi|242398670|ref|YP_002994094.1| 394 IEEQGGDPNIKPEDIPIGDKTYTFVAQTSGYITRIDNKAITAIARAAgapedkGAGIMLHVKVGEKVKERDPLFTVH 470
                                       3344445555666667889999999*******************865111111679********************9 PP

                           DUF2254 243 geeddeelaeklrea 257
                                        e+   +l +++ +a
  gi|242398670|ref|YP_002994094.1| 471 AES-GTRLDQAIIQA 484
                                       988.34455555444 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   4.3e-08   0.00013      32      79 ..      17      64 ..       3      88 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 4.3e-08
                                      EEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEESSB-TTEEEEESS CS
                   Molydop_binding 32 veinpedAaalGikdGdlVevesrrGsvevrakvtervrpGvvfmpfg 79
                                      + i++edA+   +  GdlV++e+++ ++   ++++++++pG + ++  
  gi|242398670|ref|YP_002994094.1| 17 AFISEEDAKNAKLHPGDLVKIETAKRTIYGDVVISKTINPGEIGVTKD 64
                                      789***************************************988765 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 !   18.0   0.0     8e-07    0.0024      10      80 ..      10      79 ..       3      84 .. 0.83
   2 ?   -3.2   0.1       3.4     1e+04      74      84 ..     283     293 ..     279     294 .. 0.82
   3 ?   -3.6   0.0       4.6   1.4e+04      32      58 ..     423     449 ..     420     451 .. 0.59

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 8e-07
                                      -CSSTTEEEE-HHHHHHHTS-TTSEEEEEC.CCCEEEEEEEBSTTSTTTTEEEE-HHHHHHHT--TTEEEEE CS
                           CDC48_N 10 edvgrgivridpedmeelglepgdvveieg.krkTvaivwpaepedegkgiIrmdgvtRknagvsiGdkVtV 80
                                       ++gr  + i++ed ++ +l+pgd v+ie  kr+++  v+ +++   ++g I + + + +    s G+ V  
  gi|242398670|ref|YP_002994094.1| 10 IETGRFLAFISEEDAKNAKLHPGDLVKIETaKRTIYGDVVISKTI--NPGEIGVTKDILRSYTFSEGEVVNL 79
                                      5689**************************777677777777766..5899999999998888888888865 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3.4
                                       TTEEEEEEEE- CS
                           CDC48_N  74 iGdkVtVrkae 84 
                                        G+ V+V+k+e
  gi|242398670|ref|YP_002994094.1| 283 TGEGVKVEKVE 293
                                       6999****987 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 4.6
                                       TSEEEEECCCCEEEEEEEBSTTSTTTT CS
                           CDC48_N  32 gdvveiegkrkTvaivwpaepedegkg 58 
                                       g + +i +k  T+    +++ped+g g
  gi|242398670|ref|YP_002994094.1| 423 GYITRIDNKAITAIARAAGAPEDKGAG 449
                                       556667776666655555556666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (503 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); 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: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.42
# Mc/sec: 3610.57
//
Query:       gi|242398671|ref|YP_002994095.1|  [L=124]
Description: hypothetical protein TSIB_0681 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.9e-55  185.0   7.7      6e-55  184.7   7.7    1.1  1  DUF2095   Uncharacterized protein conserved in archaea (DUF20
  ------ inclusion threshold ------
       0.11   11.4   0.0       0.14   11.0   0.0    1.1  1  DUF1702   Protein of unknown function (DUF1702)


Domain annotation for each model (and alignments):
>> DUF2095  Uncharacterized protein conserved in archaea (DUF2095)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.7   7.7   6.7e-59     6e-55       2     128 ..       4     123 ..       3     124 .] 0.95

  Alignments for each domain:
  == domain 1  score: 184.7 bits;  conditional E-value: 6.7e-59
                           DUF2095   2 kkkkpvdelawqeydleefkrrfpalareleeergleidairldeeevleeeeeegkidfsgynptiidflrrcetd 78 
                                       kkk+p+de++wqeyd  ef++++p l++ele+ + + i++++ +e      eeee  +dfsgynpt+idf+rrcetd
  gi|242398671|ref|YP_002994095.1|   4 KKKRPIDEFPWQEYDKREFEEKYPNLTKELEKGPEVVIEGYKNKE------EEEE-VMDFSGYNPTVIDFIRRCETD 73 
                                       89***************************************9764......3444.78******************* PP

                           DUF2095  79 eealeiinwmeergeithemakelrvvlvkkgvrafgpkkewgwyerhgk 128
                                       eealeiinwme++gei he+akelr+ l+k gvr+fg kkewgwyerh k
  gi|242398671|ref|YP_002994095.1|  74 EEALEIINWMEDHGEIPHELAKELRIKLTKEGVRSFGSKKEWGWYERHRK 123
                                       ************************************************87 PP

>> DUF1702  Protein of unknown function (DUF1702)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   1.6e-05      0.14      19      54 ..      17      52 ..      11      63 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 1.6e-05
                           DUF1702 19 lekrgfeakdeeakerLetigktflaGyeaaieare 54
                                       +kr fe+k ++ +++Le+ ++ +++Gy+   e++e
  gi|242398671|ref|YP_002994095.1| 17 YDKREFEEKYPNLTKELEKGPEVVIEGYKNKEEEEE 52
                                      689*************************98777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       806  (0.0449551); expected 358.6 (0.02)
Passed bias filter:                      567  (0.0316247); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.48
# Mc/sec: 772.29
//
Query:       gi|242398672|ref|YP_002994096.1|  [L=154]
Description: Archaeal endonuclease, [Thermococcus sibiricus MM 739]
Scores for complete 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   75.1   0.0    6.5e-21   74.7   0.0    1.2  1  DUF123    Domain of unknown function DUF123
     0.0028   17.9   0.1     0.0063   16.8   0.1    1.7  1  GIY-YIG   GIY-YIG catalytic domain


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 !   74.7   0.0   7.2e-25   6.5e-21       2      93 ..      25     110 ..      24     111 .. 0.84

  Alignments for each domain:
  == domain 1  score: 74.7 bits;  conditional E-value: 7.2e-25
                            DUF123   2 elkkgvylYvGsalgsgglasRvkrHaslskkkekklhWhiDyLleseeaelaevvvaseerlEcalaeal.eaeap 77 
                                        lk+g+y+YvGsa++  +l+ R+ rH++++    k+ hWhiDyLl+++++ ++++++ s+ +lE++l+ +l ++   
  gi|242398672|ref|YP_002994096.1|  25 VLKRGYYVYVGSAMN--SLEGRILRHFRQK----KRFHWHIDYLLDKARI-IEAYLIPSNVKLEEDLSMTLdSQAVG 94 
                                       5899***********..89*******5554....58*********76644.4444556*************556669 PP

                            DUF123  78 vagfGasDckcesHLl 93 
                                       v+gfGasD + ++ L+
  gi|242398672|ref|YP_002994096.1|  95 VDGFGASDVSTKTNLY 110
                                       ***********99987 PP

>> GIY-YIG  GIY-YIG catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1     7e-07    0.0063      10      36 ..      27      54 ..      17      84 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 7e-07
                                      TTT--EEEEEE.SSHHHHHHHHHHHHHH CS
                           GIY-YIG 10 kenkliYvGst.knlekRlkqHnagkka 36
                                      k++ ++YvGs+ ++le+R+ +H+++kk+
  gi|242398672|ref|YP_002994096.1| 27 KRGYYVYVGSAmNSLEGRILRHFRQKKR 54
                                      466678*****99*********877754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1025.24
//
Query:       gi|242398673|ref|YP_002994097.1|  [L=255]
Description: PcrB like protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-65  220.2   0.0    2.8e-65  219.9   0.0    1.0  1  PcrB            PcrB family
    7.5e-09   35.4   0.1    3.1e-08   33.4   0.1    1.9  2  His_biosynth    Histidine biosynthesis protein
    1.3e-08   34.5   0.5    5.6e-06   25.8   0.1    2.1  2  ThiG            Thiazole biosynthesis protein ThiG
    1.7e-06   27.1   0.6    4.7e-05   22.4   0.4    2.1  2  Trp_syntA       Tryptophan synthase alpha chain
    3.7e-05   23.0   0.2     0.0067   15.6   0.1    2.2  2  NanE            Putative N-acetylmannosamine-6-phosphate epim
    5.6e-05   22.5   0.3    0.00012   21.4   0.2    1.5  2  DHO_dh          Dihydroorotate dehydrogenase
    7.3e-05   22.0   0.1     0.0011   18.1   0.1    2.1  2  Dus             Dihydrouridine synthase (Dus)
    0.00014   21.4   0.7    0.00033   20.1   0.2    1.8  2  G3P_antiterm    Glycerol-3-phosphate responsive antiterminato
    0.00016   20.8   0.2     0.0094   15.0   0.1    2.1  2  IMPDH           IMP dehydrogenase / GMP reductase domain
     0.0007   19.1   0.7      0.012   15.1   0.2    2.1  2  BtpA            BtpA family
     0.0041   16.6   2.0      0.011   15.1   0.3    2.2  2  NMO             Nitronate monooxygenase
     0.0081   15.5   0.7      0.018   14.4   0.3    1.7  2  TMP-TENI        Thiamine monophosphate synthase
  ------ inclusion threshold ------
      0.011   14.8   0.4      0.039   13.0   0.0    1.8  2  FMN_dh          FMN-dependent dehydrogenase
      0.026   13.9   0.2      0.048   13.0   0.2    1.4  1  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
      0.037   13.6   0.0       0.09   12.4   0.0    1.6  1  DAGK_cat        Diacylglycerol kinase catalytic domain
      0.039   13.5   0.0      0.042   13.4   0.0    1.3  1  OMPdecase       Orotidine 5'-phosphate decarboxylase / HUMPS 
      0.046   12.9   0.0      0.081   12.1   0.0    1.4  1  PEP_hydrolase   Phosphoenolpyruvate hydrolase-like


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 !  219.9   0.0   2.7e-68   2.8e-65       3     216 ..      15     237 ..      12     250 .. 0.91

  Alignments for each domain:
  == domain 1  score: 219.9 bits;  conditional E-value: 2.7e-68
                                       GGGTS.EEEEE-TTSS-C...HHHHHHHHCTT-SEEEEECST...CHHHHHHHHHHHHHCTSSS-EEEEESSGGG-- CS
                              PcrB   3 ileer.hltklDPeeenp...dEiveiviesgtDavmigGsq...svtldntvrllkkvsriklPivlepsnvegvv 72 
                                       + ee+ h ++lDPe   p      ++i  e g Da+m+gGs+   +  ld +v+++k++   +lP++l+p+   g++
  gi|242398673|ref|YP_002994097.1|  15 LKEEKlHFVLLDPEDVSPrlaSKLAKISEEVGVDAIMVGGSTgaeGEVLDGVVKAIKEN--SSLPVILFPGSHGGLS 89 
                                       456679********98761114556666899***********55445589*********..99************** PP

                                       TTSSEEEEEEETTBSSTTTTTHHHHHHHHHHHHHHHCTEEEEEEEEEBTTTSHHHHHTTB-.B-TTHHHHHHHHHHH CS
                              PcrB  73 ryaDalFvmsllnsanadWivgahalglkkvkklieseeilaegYlvvePdskvaavteak.vdlnkediaayalla 148
                                       +yaDa+F+msllns n+ +i ga+alg+ +vk++   +e+++++YlvveP+ ++++v++a+ +++ k++iaa+++la
  gi|242398673|ref|YP_002994097.1|  90 KYADAVFFMSLLNSRNPFFIAGAQALGAFRVKHYG--IEPIPMAYLVVEPGETAGWVSDANlIPRHKPKIAAAYALA 164
                                       ***********************************..**************************************** PP

                                       HHHTT-SEEEEE-.TTSSS-H.HHHHHHHHHHSSSEEEEESS--SHHHHHHHHCC.SSEEEE-CHHHHHH..H CS
                              PcrB 149 akllglrliYlEa.sGaledv.eevialkkklekarlivGGGirsaEkAkevvea.ADvivvGnvveekd..e 216
                                        +++g+rl+YlEa sGa+e++ +e+i+++k   +  livGGGir  E+Akevv+  AD+iv+G+++e+ +  e
  gi|242398673|ref|YP_002994097.1| 165 GQYMGMRLVYLEAgSGAPEHIpNEMIKVVKSAIDVPLIVGGGIRTYEDAKEVVQSgADIIVTGTAIEKAGslE 237
                                       ******************************************************************9887552 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.65   6.8e+02     184     199 ..      39      54 ..      10      84 .. 0.65
   2 !   33.4   0.1   2.9e-11   3.1e-08      53     107 ..     177     232 ..     150     250 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.65
                                       HHHHHHHSSEEEEESS CS
                      His_biosynth 184 kelaeavkipviasGG 199
                                        +++e+v +  i+ GG
  gi|242398673|ref|YP_002994097.1|  39 AKISEEVGVDAIMVGG 54 
                                       3344444444444444 PP

  == domain 2  score: 33.4 bits;  conditional E-value: 2.9e-11
                                       HHC.TTHHHHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH CS
                      His_biosynth  53 aak.egreanldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavk 107
                                       a + + + +  ++++ + +++++p+ vGGGIr++ed++e++++gad ++ gta  k
  gi|242398673|ref|YP_002994097.1| 177 AGSgAPEHIPNEMIKVVKSAIDVPLIVGGGIRTYEDAKEVVQSGADIIVTGTAIEK 232
                                       4432566677799*********************************9999997543 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0     0.003       3.1     136     182 ..      38      82 ..      31     101 .. 0.79
   2 !   25.8   0.1   5.3e-09   5.6e-06     164     211 ..     187     234 ..     171     249 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.003
                                       HHHHHHHTT-SEBEEBSSSTTS----S-HHHHHHHHHH-SS-BEEES CS
                              ThiG 136 larrleevGcaavmPlaapiGsglGllnkealkiiieeakvPvivDA 182
                                       la+  eevG+ a+m  ++  G ++G +   ++k i e+ ++Pvi+  
  gi|242398673|ref|YP_002994097.1|  38 LAKISEEVGVDAIMVGGST-G-AEGEVLDGVVKAIKENSSLPVILFP 82 
                                       567779********88875.4.678889999*************854 PP

  == domain 2  score: 25.8 bits;  conditional E-value: 5.3e-09
                                       HHHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSS CS
                              ThiG 164 kealkiiieeakvPvivDAGigspsdaaqamelGadavllntavaeak 211
                                       +e++k++ + ++vP+iv  Gi++ +da ++++ Gad ++  ta+ +a 
  gi|242398673|ref|YP_002994097.1| 187 NEMIKVVKSAIDVPLIVGGGIRTYEDAKEVVQSGADIIVTGTAIEKAG 234
                                       579999**************************************9997 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.043        45     131     201 ..      10      78 ..       6      85 .. 0.73
   2 !   22.4   0.4   4.5e-08   4.7e-05     187     232 ..     187     233 ..     179     254 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.043
                                       HHHHHHHHTT-EEEEEE-TTS-HHHHHHHHHH--S-.EEEESTTC-SSTTSSB-TTHHHHHHHHHHCTSS-E CS
                         Trp_syntA 131 elveaakkkglelvflvapttsderlkevveqaegf.vYvvsraGvTgaenavaaevdelverlkkltavPv 201
                                       ++ e +k++ l++v l +   s +  +++++ +e   v ++ + G Tgae +v    d +v+++k+ + +Pv
  gi|242398673|ref|YP_002994097.1|  10 YIHEKLKEEKLHFVLLDPEDVSPRLASKLAKISEEVgVDAIMVGGSTGAEGEVL---DGVVKAIKENSSLPV 78 
                                       567788888888888887777777777777776653378888899999998875...555677777777776 PP

  == domain 2  score: 22.4 bits;  conditional E-value: 4.5e-08
                                       HHHHHHHHHCTSS-EEEESSS-SHHHHHHHH.TT-SEEEE-HHHHHH CS
                         Trp_syntA 187 delverlkkltavPvavGFGistkeqvkqva.kvadGvivGSalvkk 232
                                       +e+++ +k++ +vP+ vG Gi+t e++k+v+ ++ad ++ G a+ k+
  gi|242398673|ref|YP_002994097.1| 187 NEMIKVVKSAIDVPLIVGGGIRTYEDAKEVVqSGADIIVTGTAIEKA 233
                                       579999************************999********998654 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 !    5.5   0.0    0.0083       8.7     157     191 ..      37      71 ..       8      72 .. 0.67
   2 !   15.6   0.1   6.4e-06    0.0067     136     179 ..     189     233 ..     166     246 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0083
                                       HHHHHHHTT--SEEEE-HHHH-HHHHHHHHHHHT- CS
                              NanE 157 ekakkaieiGvdavvvGsaitrleeiakkfveaik 191
                                       ++ak   e+Gvda++vG++     e+ +  v+aik
  gi|242398673|ref|YP_002994097.1|  37 KLAKISEEVGVDAIMVGGSTGAEGEVLDGVVKAIK 71 
                                       345556689*********99888888888888877 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 6.4e-06
                                       HHHHHHHT.T--EEEES---SHHHHHHHHTT--SEEEE-HHHH-H CS
                              NanE 136 lvkalsea.glkviaeGrintPekakkaieiGvdavvvGsaitrl 179
                                       ++k +++a ++ +i+ G i t e ak+++++G+d +v G+ai + 
  gi|242398673|ref|YP_002994097.1| 189 MIKVVKSAiDVPLIVGGGIRTYEDAKEVVQSGADIIVTGTAIEKA 233
                                       5555554436789****************************9875 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       2.7   2.8e+03     167     200 ..      23      57 ..       8      77 .. 0.61
   2 !   21.4   0.2   1.1e-07   0.00012     232     281 ..     188     235 ..     175     249 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.7
                                       EEE-S.SSSHHHHHHHHHHHHHHTECEEEE...BS CS
                            DHO_dh 167 vKlaP.dltdeekkdiadvllelkldgiivtNttv 200
                                       v l P d++     + a+   e ++d+i+v+ +t 
  gi|242398673|ref|YP_002994097.1|  23 VLLDPeDVSPRLASKLAKISEEVGVDAIMVGGSTG 57 
                                       55555234444444444445577777777666664 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 1.1e-07
                                       HHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGT CS
                            DHO_dh 232 kvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfegp 281
                                       ++i  +++ ++  +p+I  GGi + eDa e ++ GA ++  +ta+ ++g 
  gi|242398673|ref|YP_002994097.1| 188 EMIKVVKSAID--VPLIVGGGIRTYEDAKEVVQSGADIIVTGTAIEKAGS 235
                                       55556666666..9******************************988775 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.11   1.1e+02     196     217 ..      36      57 ..      31      80 .. 0.64
   2 !   18.1   0.1   1.1e-06    0.0011     173     218 ..     188     232 ..     179     249 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.11
                                       HHHHHHHHHH--SEEEESCHHC CS
                               Dus 196 edaqaileetGadgvmigrgal 217
                                       +++ +i ee G+d++m+g    
  gi|242398673|ref|YP_002994097.1|  36 SKLAKISEEVGVDAIMVGGSTG 57 
                                       5667777888888888885544 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 1.1e-06
                                       HHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHCC CS
                               Dus 173 eaIkevkqavsipviaNGdIkdaedaqaileetGadgvmigrgalg 218
                                       e Ik vk a+ +p+i+ G+I++ eda+++++  Gad ++ g + ++
  gi|242398673|ref|YP_002994097.1| 188 EMIKVVKSAIDVPLIVGGGIRTYEDAKEVVQS-GADIIVTGTAIEK 232
                                       679***************************98.***9999987665 PP

>> G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       3.2   3.4e+03      34      51 ..       9      26 ..       3      53 .. 0.56
   2 !   20.1   0.2   3.1e-07   0.00033     124     169 ..     182     228 ..     179     230 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 3.2
                                      HHHHHHHHTT-EEEEEGG CS
                      G3P_antiterm 34 eiveklkkagkkvfvhiD 51
                                      +++++  k++k+ fv +D
  gi|242398673|ref|YP_002994097.1|  9 SYIHEKLKEEKLHFVLLD 26
                                      555555555555555443 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 3.1e-07
                                       SGGG.HHHHCTSTTS...EEEEESS--SHHHHHHHCTT.SSEEEE-- CS
                      G3P_antiterm 124 Pglv.pkvikeikkelkipiiaGGLietkedveealkaGaiavstsn 169
                                       P  +  ++ik +k+++++p+i GG i+t ed +e++++Ga+ + t++
  gi|242398673|ref|YP_002994097.1| 182 PEHIpNEMIKVVKSAIDVPLIVGGGIRTYEDAKEVVQSGADIIVTGT 228
                                       66676799**********************************99975 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.021        23     113     149 ..      43      79 ..      29      84 .. 0.78
   2 !   15.0   0.1   8.9e-06    0.0094     133     173 ..     187     227 ..     160     239 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.021
                                       HHTT-SEEEEE-STSSSHHHHH.HHHHHHHHTTTSEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx RF
                             IMPDH 113 veagvdvlvvdsahghsekvle.avkeikkkveevevi 149
                                        e gvd+++v  + g + +vl+ +vk+ik++  ++ vi
  gi|242398673|ref|YP_002994097.1|  43 EEVGVDAIMVGGSTGAEGEVLDgVVKAIKENS-SLPVI 79 
                                       4789**************99984568888887.56665 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 8.9e-06
                                       HHHHHHHHHHTTTSE.EEEEEE-SHHHHHHHHHTT-SEEEE- CS
                                       xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 133 leavkeikkkveeve.viaGnvataegakaLieagadavkvG 173
                                        e++k +k+++ +v  +++G + t+e ak++++ gad++  G
  gi|242398673|ref|YP_002994097.1| 187 NEMIKVVKSAI-DVPlIVGGGIRTYEDAKEVVQSGADIIVTG 227
                                       57888899888.555155889999999999999999998776 PP

>> BtpA  BtpA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.08        85     161     204 ..      35      79 ..      28      93 .. 0.57
   2 !   15.1   0.2   1.1e-05     0.012     186     251 ..     184     249 ..     173     252 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.08
                              BtpA 161 esavkdtvergladavilsGkatGgevdlee.lklaketvkvkvl 204
                                       +s + +  e + +da+++ G +  +   l+  +k++ke  +++v+
  gi|242398673|ref|YP_002994097.1|  35 ASKLAKISEEVGVDAIMVGGSTGAEGEVLDGvVKAIKENSSLPVI 79 
                                       555555556666677766665433333333314445555556665 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 1.1e-05
                              BtpA 186 evdleelklaketvkvkvlvgsGvs.eenlekllsi.adGvivgtsikkdGkianaiDkervrkivel 251
                                       +   e +k++k +++v+ +vg G+  +e+++++++  ad +++gt i k G + +   k+r + i++ 
  gi|242398673|ref|YP_002994097.1| 184 HIPNEMIKVVKSAIDVPLIVGGGIRtYEDAKEVVQSgADIIVTGTAIEKAGSLEES--KKRLESIING 249
                                       5567899****************9636788887764399999*********98774..6677777765 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1      0.36   3.8e+02     148     197 ..      38      79 ..      31      90 .. 0.67
   2 !   15.1   0.3   1.1e-05     0.011     183     224 ..     188     229 ..     176     235 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.36
                               NMO 148 earkvearGaDalivqGpeaGGhqGtpevgdkglfaLvpqvldavdiPvi 197
                                        a++ e+ G Da+ v G+   G +G      + l  +v+ +++  ++Pvi
  gi|242398673|ref|YP_002994097.1|  38 LAKISEEVGVDAIMVGGST--GAEG------EVLDGVVKAIKENSSLPVI 79 
                                       5788899999999986653..3333......2244455555555556665 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 1.1e-05
                               NMO 183 aLvpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqigtr 224
                                       ++++ v++a+d+P+i  GGi + ++ + +   GA  +  gt+
  gi|242398673|ref|YP_002994097.1| 188 EMIKVVKSAIDVPLIVGGGIRTYEDAKEVVQSGADIIVTGTA 229
                                       5788899****************************9999998 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.8   1.9e+03     140     159 ..      36      55 ..      27      62 .. 0.61
   2 !   14.4   0.3   1.7e-05     0.018     135     180 ..     183     229 ..     155     230 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.8
                          TMP-TENI 140 eglkelaealeiPvvaiGGi 159
                                       ++l++++e++ +  + +GG 
  gi|242398673|ref|YP_002994097.1|  36 SKLAKISEEVGVDAIMVGGS 55 
                                       55566666666666666665 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 1.7e-05
                          TMP-TENI 135 eplgleglkelaealeiPvvaiGGitl.envaevleagadgvavvsa 180
                                       e +  e +k +++a+ +P+++ GGi++ e+++ev+++gad +   +a
  gi|242398673|ref|YP_002994097.1| 183 EHIPNEMIKVVKSAIDVPLIVGGGIRTyEDAKEVVQSGADIIVTGTA 229
                                       67778888889999999999999996537899999999998876655 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1      0.43   4.5e+02     230     259 ..      39      71 ..      34      79 .. 0.73
   2 ?   13.0   0.0   3.7e-05     0.039     206     242 ..     188     225 ..     142     228 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.43
                                       HHHHHHTTESEEEE--GGG...TSSTT---HHH CS
                            FMN_dh 230 akraveaGvdgivvSNHGG...Rqldgapatid 259
                                       ak   e+Gvd+i+v    G     ldg++ +i+
  gi|242398673|ref|YP_002994097.1|  39 AKISEEVGVDAIMVGGSTGaegEVLDGVVKAIK 71 
                                       55667899****997655433377888777775 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 3.7e-05
                                       HHHHHHHHHHSSEEEEE.EE-SHHHHHHHHHTTESEEE CS
                            FMN_dh 206 ddikwlreqtklplvvK.GvltaedakraveaGvdgiv 242
                                       + ik ++++ ++pl+v  G+ t edak++v+ G+d+iv
  gi|242398673|ref|YP_002994097.1| 188 EMIKVVKSAIDVPLIVGgGIRTYEDAKEVVQSGADIIV 225
                                       67999***********7369***************998 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 ?   13.0   0.2   4.6e-05     0.048     162     197 ..     194     230 ..     176     231 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.6e-05
                                       HHT---EEEEESS--T.TTCHHHHHHT--EEEESHHH CS
                    Ribul_P_3_epim 162 ekeldlkievDGGvkl.dnieqiaeagadvlVagsav 197
                                       ++  d+ + v GG+++ + ++++++ gad++V+g+a+
  gi|242398673|ref|YP_002994097.1| 194 KSAIDVPLIVGGGIRTyEDAKEVVQSGADIIVTGTAI 230
                                       34678899******75389****************97 PP

>> DAGK_cat  Diacylglycerol kinase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   8.5e-05      0.09      20      89 ..       9      82 ..       3      91 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.5e-05
                                      HHCHHHHHHCTCEEEEEE--..STTHHHHHHHHHHHCC-SEEEEEESHHHHHHHHHHHCT..HHCTTSEEEEEE CS
                          DAGK_cat 20 rkvrelleeagveleliete..epgdakelakeakeegvdlivvaGGDGtvsevlnglle..elatkpplgiiP 89
                                      + ++e+l+e+++++ l + e  +p  a +lak  +e gvd+i+v G  G  +evl+g+++  ++++ +p+ ++P
  gi|242398673|ref|YP_002994097.1|  9 SYIHEKLKEEKLHFVLLDPEdvSPRLASKLAKISEEVGVDAIMVGGSTGAEGEVLDGVVKaiKENSSLPVILFP 82
                                      5688999999999999999977788899999999999***********************99888889987777 PP

>> OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0     4e-05     0.042     162     224 ..     177     242 ..      32     243 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4e-05
                                       H...HHHHH.TTCSCEEEHHHTTEEEEECTTCCGGGHHHHHHHTTCSEEEESHHHHTSSSHHHHHHH CS
                         OMPdecase 162 n...ateed.addfihltpgigleqggdgkgqqyntpekligiagadiiivGRgIlkagdpveeaer 224
                                       +   a+e +  + +++++  i++    +g+g++ ++  k++ ++gadii+ G +I kag  +e  +r
  gi|242398673|ref|YP_002994097.1| 177 AgsgAPEHIpNEMIKVVKSAIDV-PLIVGGGIRTYEDAKEVVQSGADIIVTGTAIEKAGSLEESKKR 242
                                       33354445566677778888888.9999****99999999999****************99887665 PP

>> PEP_hydrolase  Phosphoenolpyruvate hydrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   7.7e-05     0.081     139     202 ..     190     252 ..     185     255 .] 0.81

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.7e-05
                     PEP_hydrolase 139 velikkAheldllttayvfneeearamaeaGadvivahlGlttggsigaktalsleeavelvqe 202
                                       ++++k A +  l+  + +++ e+a+++++ Gad+iv+   + + gs+  + ++ le+ ++ v+e
  gi|242398673|ref|YP_002994097.1| 190 IKVVKSAIDVPLIVGGGIRTYEDAKEVVQSGADIIVTGTAIEKAGSLEES-KKRLESIINGVKE 252
                                       67888888888888899999*******************99999998654.4567766666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 1967.32
//
Query:       gi|242398674|ref|YP_002994098.1|  [L=274]
Description: D-aminopeptidase [Thermococcus sibiricus MM 739]
Scores for complete 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-77  258.8   0.0    6.1e-77  258.6   0.0    1.0  1  Peptidase_M55  D-aminopeptidase
  ------ inclusion threshold ------
       0.15   11.5   0.0        0.2   11.1   0.0    1.2  1  Creatininase   Creatinine amidohydrolase


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 !  258.6   0.0   6.8e-81   6.1e-77       7     263 ..       1     259 [.       1     260 [. 0.98

  Alignments for each domain:
  == domain 1  score: 258.6 bits;  conditional E-value: 6.8e-81
                     Peptidase_M55   7 aDiEGvagvvsweqvepgeaeyerarrlmteevnaaiegalaagatevlVnDsHgsmrNllpeeLdervrlisGkpk 83 
                                       +D+EG+  vvs e++ ++++ y++ar++ te    ++e++++ag+ e++++DsHg+m Nllpe+L+e   l++G+p+
  gi|242398674|ref|YP_002994098.1|   1 MDLEGMPFVVSLEHLVEKGTLYKEARKIATEITLTVVEALHNAGFGEIVIADSHGPMVNLLPEKLPEYTYLVRGYPR 77 
                                       6**************************************************************************** PP

                     Peptidase_M55  84 plsmmegldesfdavlfvGyHaragtekgvlaHTysgsaieevrlngkevgEfglnaalagelgVPvvlvsGDdalc 160
                                       p+ m+ g  e++d++lf+GyHa+agt+ ++++HTysg+++ +++lng ev+Ef ln+++ g++++Pv+lv GD++l 
  gi|242398674|ref|YP_002994098.1|  78 PMAMVVGA-EKCDVALFLGYHAKAGTPYAIFDHTYSGANVGKLELNGIEVSEFLLNGYAVGHYDIPVILVGGDKKLL 153
                                       *******5.89**************************************************************9976 PP

                     Peptidase_M55 161 e.eakellpevetvavkeglgrfaakslspeeaeeaireavkeavekake..akplkleepvelevefkstalAdaa 234
                                       e ++k+++p++e v+ k++++r++a+s s +++++++++av +ave+ k+   kplkle pv+++++++++ +Ad+ 
  gi|242398674|ref|YP_002994098.1| 154 EeDVKRFTPWAERVTFKKAFSRYSAISPSLRRTKKDLENAVFKAVERYKNggTKPLKLEYPVKVRLTYNNSGMADVG 230
                                       5268*********************************************999************************* PP

                     Peptidase_M55 235 slvpgveridartvefeaedveellrale 263
                                       +l+p ++rid++t+efea+d+ e+++a++
  gi|242398674|ref|YP_002994098.1| 231 ELLPDARRIDGKTIEFEAKDIIEAYKAFQ 259
                                       **************************997 PP

>> Creatininase  Creatinine amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   2.3e-05       0.2      62     116 ..       6      61 ..       3      91 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2.3e-05
                      Creatininase  62 lpyGvseehlgfpGTislsp.etliavlrdileslarhGfrrivlvngHggnsaal 116
                                       +p+ vs ehl   GT++ ++ +  +++   ++e l+++Gf  iv+  +Hg  +++l
  gi|242398674|ref|YP_002994098.1|   6 MPFVVSLEHLVEKGTLYKEArKIATEITLTVVEALHNAGFGEIVIADSHGPMVNLL 61 
                                       788899999999999998662677889999********************766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); 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 0.29s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1820.07
//
Query:       gi|242398675|ref|YP_002994099.1|  [L=83]
Description: hypothetical protein TSIB_0685 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0067   16.4   0.1     0.0092   16.0   0.1    1.1  1  EFG_C     Elongation factor G C-terminus
  ------ inclusion threshold ------
      0.068   13.0   0.6      0.082   12.8   0.6    1.0  1  zf-ZPR1   ZPR1 zinc-finger domain


Domain annotation for each model (and alignments):
>> EFG_C  Elongation factor G C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1     1e-06    0.0092       6      65 ..       7      70 ..       7      75 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1e-06
                                      EEEEEEEEECCCCCCHHHHHHH.CT-EEEEEEEE....TTEEEEEEEEEGGG-TTHHHCHHHCT CS
                             EFG_C  6 ivkveievpeeyvgkvisdlss.rrGeiedmeqd...asgrviieaeiPlaeligfateLrslT 65
                                      iv+++i++p e  gk+++++ +  rG+i+d+      ++g   i++e+   +++++ t+L+ + 
  gi|242398675|ref|YP_002994099.1|  7 IVEINIKMPYEKRGKILKKILNeVRGKIKDIHFLpptNQGISEIRMEVVEENVQKLLTKLKRIV 70
                                      6899*************998777*********99998999*************9**99999876 PP

>> zf-ZPR1  ZPR1 zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.6   9.1e-06     0.082      77     149 ..       4      79 ..       2      82 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.1e-06
                           zf-ZPR1  77 tveipeleleippgtlegrlttvEGlLeqikeele.......keegdqaeredeekekieeflekleeliegeepft 146
                                       t++i e+++++p  +++g++  +  +L++++ +++       +++g ++ r +  +e+++++l+kl+++++ +e++t
  gi|242398675|ref|YP_002994099.1|   4 TMKIVEINIKMPY-EKRGKI--LKKILNEVRGKIKdihflppTNQGISEIRMEVVEENVQKLLTKLKRIVK-DEKVT 76 
                                       6899999999999.667766..6788888888888655555544888888866799**************9.77777 PP

                           zf-ZPR1 147 lil 149
                                       +++
  gi|242398675|ref|YP_002994099.1|  77 FKI 79 
                                       665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1058  (0.0590105); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 629.06
//
Query:       gi|242398676|ref|YP_002994100.1|  [L=772]
Description: ATP-dependent RNA helicase, [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.9e-29  101.1   0.0    1.7e-28   99.8   0.0    1.7  1  ERCC4          ERCC4 domain
    8.2e-27   93.8   0.8    4.1e-24   85.1   0.0    3.1  3  Helicase_C     Helicase conserved C-terminal domain
    5.8e-19   68.5   0.7    5.6e-17   62.1   0.0    3.2  3  DEAD           DEAD/DEAH box helicase
    1.6e-17   64.0   0.0    1.9e-16   60.5   0.0    2.6  2  ResIII         Type III restriction enzyme, res subunit
      2e-10   40.6   0.1    6.2e-10   39.0   0.1    1.9  1  HHH_2          Helix-hairpin-helix motif
    1.1e-05   25.9   1.6    2.4e-05   24.8   0.1    2.4  2  HHH_5          Helix-hairpin-helix domain
    0.00026   20.7   0.1    0.00077   19.2   0.1    1.9  1  HHH            Helix-hairpin-helix motif
  ------ inclusion threshold ------
      0.013   14.8   1.9      0.072   12.3   1.9    2.2  1  ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
      0.021   15.1   0.1       0.25   11.6   0.0    2.9  3  HHH_3          Helix-hairpin-helix motif
       0.13   12.6   1.8        1.1    9.7   0.4    2.7  2  MRP-S28        Mitochondrial ribosomal subunit protein


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 !   99.8   0.0   9.4e-32   1.7e-28       1     154 [.     564     681 ..     564     683 .. 0.97

  Alignments for each domain:
  == domain 1  score: 99.8 bits;  conditional E-value: 9.4e-32
                                       EEGGGCTSHHHH..HHTTTSEEEEE--SSSSE.EE...CTT...............EEEEEEEHHHHHHHHCCSHHH CS
                             ERCC4   1 iDsrelksgieeylleelgvevvietlpigdyilwrrkvkaeynleldieepceekvlverksaddlvasikdgrle 77 
                                       +Dsrelks++++  l+elg+  +++tl igdy ++   + +               v+verk a d+++si+dgrl+
  gi|242398676|ref|YP_002994100.1| 564 VDSRELKSQVPKI-LKELGAHLEVKTLDIGDY-IV---SED---------------VVVERKAANDFIQSIIDGRLF 620
                                       8************.******************.99...898...............********************* PP

                                       HHHHHHHH.H-SEEEEEEES-GGGTT................THHH.HHHHHHHHHHHHS-EEEEESSHHHHHHHHH CS
                             ERCC4  78 eqvsrlkrngykkpillvegldqykrknknsrnkqykakvrqinrktiesaLvqlqldfgvsilttesanetaewla 154
                                       +q++rlk+ +y kpi+++eg + y  +n              i++++i +aL +l +d+++++l++++a+e a++++
  gi|242398676|ref|YP_002994100.1| 621 DQARRLKE-AYLKPIIIIEG-ELYGIRN--------------IHPNAIRGALTALSVDWDIPVLFAKDAAEVANYIY 681
                                       ********.***********.7788877..............*********************************98 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.8   0.0    0.0096        17       6      60 ..      42     100 ..      36     107 .. 0.78
   2 !   85.1   0.0   2.3e-27   4.1e-24       4     110 ..     346     463 ..     343     464 .. 0.87
   3 ?   -2.9   0.1       4.8   8.6e+03      21      35 ..     494     512 ..     478     536 .. 0.45

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0096
                                       HHHHH...HHTTTTSEEEEEESSHH.HHHHHHHHHHHT...TSTEEEESTTSTHHHHHHHHH CS
                        Helicase_C   6 llell...kleeeggkilifvntid.rlekvklllekk...gikvavlhgelpqnereeile 60 
                                       l   +    l++ ggk+l+ ++t+   l++ + +l+ +   + ++ +l+ge+p ++r ei +
  gi|242398676|ref|YP_002994100.1|  42 L---IadyRLSKYGGKVLMLAPTKPlALQHRESFLKLFnipDERINTLTGEIPPEKRAEIWR 100
                                       3...24447899*************7665556665666567899*************99976 PP

  == domain 2  score: 85.1 bits;  conditional E-value: 2.3e-27
                                       HHHHHHH...HHTTTTSEEEEEESSHHHHHH.HHHHHHHTTSTEEEESTT........STHHHHHHHHHHHHTTSSS CS
                        Helicase_C   4 eallell...kleeeggkilifvntidrlek.vklllekkgikvavlhge........lpqnereeileqfnkgesd 68 
                                       ++l+el+    +++  +ki++f+n++++++k vk lle + ik++++ g+        l+q++++++l+ f +ge++
  gi|242398676|ref|YP_002994100.1| 346 DKLKELIrsqLKKKPSSKIIVFTNYRETAKKiVKELLEDH-IKAVRFVGQaskendkgLSQKKQKQVLNLFSQGEFN 421
                                       5555555554479999*************98866665555.88888888878888888******************* PP

                                       EEEESGGGTSSSTSTTESEEEESSSSSSHHHHHHHHTTSSST CS
                        Helicase_C  69 vLiatdvaerGidipkvnlVinfdlprnvtsyiqriGRtgRa 110
                                       vL+at+v+e+G+d+p+v+lVi++++  +  + iqr+GRtgR 
  gi|242398676|ref|YP_002994100.1| 422 VLVATSVGEEGLDVPEVDLVIFYEPVPSAIRSIQRKGRTGRH 463
                                       *****************************************7 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 4.8
                                       EEESSHH.HHHH...HHHH CS
                        Helicase_C  21 ifvntid.rlek...vkll 35 
                                        ++++++ +++k   ++ll
  gi|242398676|ref|YP_002994100.1| 494 SILEKVEdMVKKekqASLL 512
                                       4444444233223222222 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.1   0.0   3.1e-20   5.6e-17       5     169 ..      14     166 ..       8     173 .. 0.83
   2 ?    2.0   0.1     0.084   1.5e+02      42     104 ..     354     426 ..     297     442 .. 0.70
   3 ?    0.5   0.0      0.25   4.5e+02      48      79 ..     558     589 ..     477     624 .. 0.76

  Alignments for each domain:
  == domain 1  score: 62.1 bits;  conditional E-value: 3.1e-20
                                       HHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   5 aeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlli 81 
                                       +e+i +  ++++ lv  +TG GKTl++++ +  ++    +k g k+l+++Pt+ La q+ + + k+++  d r++ +
  gi|242398676|ref|YP_002994100.1|  14 QEVIYAKCKDKNSLVVLPTGLGKTLIAQLIADYRL----SKYGGKVLMLAPTKPLALQHRESFLKLFNIPDERINTL 86 
                                       45555556899*********************999....68999************************988788877 PP

                                       ETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHT.TTHHHHHHHHHHSHHHCTTST CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  82 iggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldq.gfsdfinrilnqlpqitcdgk 157
                                       +g+ + ++  +   ++  ++ +tp+ + + l  g+++l++v +lV+DEa+r   + g+    ++ ++q ++      
  gi|242398676|ref|YP_002994100.1|  87 TGEIPPEKRAEIW-RKSVVITATPQTIENDLVVGRITLEDVVLLVFDEAHRAVGNyGYVYIAKEYMRQAKH------ 156
                                       7777776666655.88899999*****997778*******************9998999999999999832...... PP

                                       TTSEEEEEESSB CS
                                       xxxxxxxxxxxx RF
                              DEAD 158 lqrqvivlSATl 169
                                           ++ l+A +
  gi|242398676|ref|YP_002994100.1| 157 --PVILGLTASP 166
                                       ..2266666665 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.084
                                       S..TTSTS-EEEEEESSHHHHHHHHHHHHHHTTT.ST.....SEEEEEETTSSHHHHHHHH...HTT.CSEEEEE CS
                                       x..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx.....xxxxxxxxxxxxxxxxxxx...xxx.xxxxxxx RF
                              DEAD  42 t..kgktgpkalivePtreLaeqtlnnlkkfkky.id.....lrvlliiggvaardqlskl...dng.vdivvgt 104
                                       +  k+k+  k+++ +  re a++++++l +   + ++      +++   +g ++++q+++l   ++g  +++v+t
  gi|242398676|ref|YP_002994100.1| 354 SqlKKKPSSKIIVFTNYRETAKKIVKELLEDHIKaVRfvgqaSKEN--DKGLSQKKQKQVLnlfSQGeFNVLVAT 426
                                       2557888899999999999999999988443332122222222222..224444444444422233346666666 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.25
                                       -EEEEEESSHHHHHHHHHHHHHHTTTSTSEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  48 pkalivePtreLaeqtlnnlkkfkkyidlrvl 79 
                                         ++i + +reL  q+ + lk+++ ++++++l
  gi|242398676|ref|YP_002994100.1| 558 HGIVIYVDSRELKSQVPKILKELGAHLEVKTL 589
                                       45778889999999999999999998775554 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 !   60.5   0.0   1.1e-19   1.9e-16      12     169 ..      13     166 ..       6     168 .. 0.73
   2 ?   -0.4   0.2      0.55   9.9e+02      47     122 ..     354     397 ..     278     425 .. 0.61

  Alignments for each domain:
  == domain 1  score: 60.5 bits;  conditional E-value: 1.1e-19
                                       HHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG.......G CS
                            ResIII  12 ienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseayke...i 85 
                                        ++++   k  +dk+ l++++TG GKTl+a  ++++ l+k +  k+l+l+p+k l  q +e f k+++ ++++    
  gi|242398676|ref|YP_002994100.1|  13 YQEVI-YAK-CKDKNSLVVLPTGLGKTLIAQLIADYRLSK-YGGKVLMLAPTKPLALQHRESFLKLFNIPDERintL 86 
                                       44444.222.5799*************9986666666655.556*********************999998764443 PP

                                       EEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.TTTHHH....HHT-- CS
                            ResIII  86 gkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakkswrei....lekfk 158
                                       ++++  +k+ +      ++ ++ +t q++ +d+        +   +   ++++DEaHr+ ++  +  i    +++ k
  gi|242398676|ref|YP_002994100.1|  87 TGEIPPEKRAE---IWRKSVVITATPQTIENDL-----VVGRITLEDVVLLVFDEAHRAVGNYGYVYIakeyMRQAK 155
                                       33344444433...3445555556899******.....66777777777************8788887633344448 PP

                                       -SEEEEEESS- CS
                            ResIII 159 eavllglTATp 169
                                       + v+lglTA p
  gi|242398676|ref|YP_002994100.1| 156 HPVILGLTASP 166
                                       8********98 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.55
                                       HH-S.....-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B--.......-SEEEEEHHHHHHTH..... CS
                            ResIII  47 rllkkgkeekflflvprkslleqtleefkkflseaykeigkkvsgdkkkakekdstnkkilvttiqsldadseee.. 121
                                       + lkk+                                                 ++k i++t++ +  +++ +e  
  gi|242398676|ref|YP_002994100.1| 354 SQLKKK------------------------------------------------PSSKIIVFTNYRETAKKIVKEll 382
                                       222233................................................34444455555544444433333 PP

                                       ............... CS
                            ResIII 122 ..............e 122
                                                     +
  gi|242398676|ref|YP_002994100.1| 383 edhikavrfvgqasK 397
                                       333333333333331 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   0.1   3.4e-13   6.2e-10       7      56 ..     716     765 ..     711     771 .. 0.92

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 3.4e-13
                             HHH_2   7 GIrhVGektAklLakrFksldaLkkasleeLlevddiGeeiAqsivefFe 56 
                                       G+++V +  A+ L k+F+++++  +a++ eL++v++iGe+iA++i++  +
  gi|242398676|ref|YP_002994100.1| 716 GLPNVSAVLARRLLKHFGNVERVFTAKESELIQVEGIGEKIAKEIRRVIT 765
                                       899******************************************98766 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   0.1         6   1.1e+04      46      55 ..     372     381 ..     371     381 .. 0.83
   2 !   24.8   0.1   1.3e-08   2.4e-05       5      51 ..     715     760 ..     711     764 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 6
                                       HHHHHHHHHH CS
                             HHH_5  46 ktAeriilel 55 
                                       +tA++i+ el
  gi|242398676|ref|YP_002994100.1| 372 ETAKKIVKEL 381
                                       6999999987 PP

  == domain 2  score: 24.8 bits;  conditional E-value: 1.3e-08
                                       HTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHH CS
                             HHH_5   5 lsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeri 51 
                                        +++ + +++A++ll++ ++ ve +  a + eL ++ GiG+k A+ i
  gi|242398676|ref|YP_002994100.1| 715 EGLPNVSAVLARRLLKH-FGNVERVFTAKESELIQVEGIGEKIAKEI 760
                                       578999***********.**************************998 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   4.3e-07   0.00077       3      28 ..     736     761 ..     734     763 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 4.3e-07
                                       HHHHTSSHHHHHTSTT-SHHHHHHHH CS
                               HHH   3 eglipasreeLlalPGVGpktAeaIl 28 
                                       e++++a + eL +++G+G+k A  I+
  gi|242398676|ref|YP_002994100.1| 736 ERVFTAKESELIQVEGIGEKIAKEIR 761
                                       899********************997 PP

>> ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.9     4e-05     0.072      60     154 ..     361     466 ..     337     542 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4e-05
                     ERCC3_RAD25_C  60 gDkiivfsDnvfaLkeyakklkkpyi.....yGet........seaerlkilqkfkknpkvntiflskvgDtsiDlP 123
                                       + kiivf++   + k++ k+l + +i     +G++        s+++++++l+ f +  ++n+++   vg++ +D+P
  gi|242398676|ref|YP_002994100.1| 361 SSKIIVFTNYRETAKKIVKELLEDHIkavrfVGQAskendkglSQKKQKQVLNLFSQG-EFNVLVATSVGEEGLDVP 436
                                       5667777666666666666555444422222344311111111567788999999875.89**************** PP

                     ERCC3_RAD25_C 124 eanvliqisshfgsrrqeaqrlGriLrakkk 154
                                       e   +i  +   +   +  qr Gr  r k +
  gi|242398676|ref|YP_002994100.1| 437 EVDLVIFYEPVPS-AIRSIQRKGRTGRHKPG 466
                                       ******8876555.55578999999999976 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0         2   3.6e+03      21      34 ..      33      47 ..      25      52 .. 0.69
   2 ?   -3.5   0.0       7.2   1.3e+04      19      33 ..     717     731 ..     715     731 .. 0.85
   3 ?   11.6   0.0   0.00014      0.25      10      30 ..     740     760 ..     738     766 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 2
                             HHH_3 21 Glgpkl.AknIvayR 34
                                      Glg++l A+ I +yR
  gi|242398676|ref|YP_002994100.1| 33 GLGKTLiAQLIADYR 47
                                      787654277788888 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 7.2
                             HHH_3  19 lpGlgpklAknIvay 33 
                                       lp ++++lA++++++
  gi|242398676|ref|YP_002994100.1| 717 LPNVSAVLARRLLKH 731
                                       78999*****99876 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.00014
                             HHH_3  10 tAsaeeLqklpGlgpklAknI 30 
                                       tA+++eL +++G+g+k+Ak+I
  gi|242398676|ref|YP_002994100.1| 740 TAKESELIQVEGIGEKIAKEI 760
                                       8******************99 PP

>> MRP-S28  Mitochondrial ribosomal subunit protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.4   0.00062       1.1      14      59 ..     314     359 ..     305     401 .. 0.75
   2 ?    1.0   0.0      0.31   5.5e+02       8      45 ..     674     711 ..     669     717 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00062
                           MRP-S28  14 rytsylgeehpasrkvvlevkvadLkleekqkhklklLagprynpe 59 
                                       ++t++l ++  +++ v+l v+ ++L+l++ +++klk L +++ +++
  gi|242398676|ref|YP_002994100.1| 314 KSTKELIQDPRMKKAVALLVQAKELGLDHPKLDKLKELIRSQLKKK 359
                                       566666666677899***********************99987765 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.31
                           MRP-S28   8 eaplrfrytsylgeehpasrkvvlevkvadLkleekqk 45 
                                       +++ ++ y +   e++++++ v++  + ++L l ++q+
  gi|242398676|ref|YP_002994100.1| 674 AEVANYIYLIAKREQEERKKEVAVRSEKKALTLADRQR 711
                                       67889999999999******************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (772 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1424  (0.0794244); expected 358.6 (0.02)
Passed bias filter:                      683  (0.0380947); 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):              10  [number of targets reported over threshold]
# CPU time: 0.76u 0.33s 00:00:01.09 Elapsed: 00:00:00.48
# Mc/sec: 4882.96
//
Query:       gi|242398677|ref|YP_002994101.1|  [L=118]
Description: hypothetical protein TSIB_0687 [Thermococcus sibiricus MM 739]
Scores for complete 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-26   91.3   0.0    5.1e-26   91.1   0.0    1.1  1  DUF134        Protein of unknown function  DUF134
    5.1e-09   35.5   0.1    7.4e-09   35.0   0.1    1.3  1  Sigma70_r4    Sigma-70, region 4
    1.7e-08   34.0   0.1    2.4e-08   33.5   0.1    1.3  1  Sigma70_r4_2  Sigma-70, region 4
    1.5e-05   24.6   0.0    2.4e-05   24.0   0.0    1.3  1  HTH_23        Homeodomain-like domain
    0.00015   21.7   0.2    0.00018   21.4   0.2    1.1  1  Sigma70_ECF   ECF sigma factor
    0.00052   20.3   0.0    0.00053   20.3   0.0    1.2  1  HTH_31        Helix-turn-helix domain
     0.0067   16.3   0.1     0.0084   16.0   0.1    1.2  1  HTH_1         Bacterial regulatory helix-turn-helix protein, 
  ------ inclusion threshold ------
      0.011   15.6   0.0      0.016   15.1   0.0    1.3  1  HTH_11        HTH domain
      0.013   15.2   0.0      0.023   14.4   0.0    1.4  1  HTH_38        Helix-turn-helix domain
       0.02   14.4   0.0      0.032   13.8   0.0    1.3  1  HTH_24        Winged helix-turn-helix DNA-binding
      0.021   14.9   0.0      0.038   14.0   0.0    1.4  1  HTH_3         Helix-turn-helix
      0.027   14.5   0.1      0.037   14.0   0.1    1.3  1  HTH_Crp_2     Crp-like helix-turn-helix domain
      0.054   13.2   0.0      0.071   12.9   0.0    1.2  1  HTH_Tnp_4     Helix-turn-helix of DDE superfamily endonucleas
      0.056   13.6   0.1       0.12   12.6   0.1    1.6  1  HTH_28        Helix-turn-helix domain
      0.088   12.7   0.0       0.14   12.1   0.0    1.3  1  MarR_2        MarR family
       0.18   10.8   0.0       0.21   10.5   0.0    1.1  1  TnsD          Tn7-like transposition protein D
       0.23   11.5   0.2       0.23   11.5   0.2    1.5  2  HTH_29        Winged helix-turn helix


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 !   91.1   0.0   4.9e-29   5.1e-26       4      93 ..       5      98 ..       1     104 [. 0.86

  Alignments for each domain:
  == domain 1  score: 91.1 bits;  conditional E-value: 4.9e-29
                            DUF134  4 kgrprklrdileePkvrifkPeaveetg..k..vaisldeleairlvdyedlkqeeaaklmGiskatlwrlltearkki 78
                                      +gr rk+r+i   P+vr f P   +  g  +  + +s +e+ea+rlvdye l+qeea + mG+s+ t+wr lt+arkk+
  gi|242398677|ref|YP_002994101.1|  5 RGRRRKMRFIGFIPEVRHFYPAKPP-FGppQppIFMSYEEFEALRLVDYEGLTQEEAGQRMGVSRGTVWRALTSARKKV 82
                                      89*******************9544.4434356********************************************** PP

                            DUF134 79 akalveGr.aiilkGG 93
                                      a+ lveGr  iil  G
  gi|242398677|ref|YP_002994101.1| 83 AQMLVEGReLIILAQG 98
                                      ********64444433 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.1     7e-12   7.4e-09       9      48 ..      43      82 ..      39      84 .. 0.91

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 7e-12
                                      HHHHHHHHHTTT--HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                        Sigma70_r4  9 erevlelrfgeglTleEIgerlgiSrerVrqiekrAlrkL 48
                                      e e l+l+ +eglT+eE g+r+g+Sr++V + ++ A++k+
  gi|242398677|ref|YP_002994101.1| 43 EFEALRLVDYEGLTQEEAGQRMGVSRGTVWRALTSARKKV 82
                                      557899*************************999999996 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 !   33.5   0.1   2.3e-11   2.4e-08      14      53 ..      42      81 ..      39      82 .. 0.93

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 2.3e-11
                                      HHHHHHHHHHTS---HHHHHHHHT--HHHHHHHHHHHHHH CS
                      Sigma70_r4_2 14 rqreifllryleglsykEIAellgisegtVksrlsRArkk 53
                                      ++ e++ l ++egl+++E+ +++g+s gtV ++l  Arkk
  gi|242398677|ref|YP_002994101.1| 42 EEFEALRLVDYEGLTQEEAGQRMGVSRGTVWRALTSARKK 81
                                      6789***********************************9 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   2.3e-08   2.4e-05       8      38 ..      44      75 ..      41      86 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 2.3e-08
                            HTH_23  8 lrilllla.eGlsvreIAreLgvsrrTvyrwl 38
                                      +++l+l++ eGl+++e+ +++gvsr Tv+r l
  gi|242398677|ref|YP_002994101.1| 44 FEALRLVDyEGLTQEEAGQRMGVSRGTVWRAL 75
                                      6899999999********************86 PP

>> Sigma70_ECF  ECF sigma factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.2   1.7e-07   0.00018     141     182 ..      44      85 ..      38      88 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.7e-07
                       Sigma70_ECF 141 arlvelrkleGlsveEiAeklgvskrtverrlalaRawlere 182
                                        + + l   eGl+ eE+++++gvs+ tv r l  aR+++++ 
  gi|242398677|ref|YP_002994101.1|  44 FEALRLVDYEGLTQEEAGQRMGVSRGTVWRALTSARKKVAQM 85 
                                       5566777899****************************9886 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0     5e-07   0.00053      13      40 ..      53      80 ..       5     103 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 5e-07
                            HTH_31 13 aGLsqeevAerlgvsestlsrlEqGrrg 40
                                      +GL+qee+++r gvs+ t+ r  + +r 
  gi|242398677|ref|YP_002994101.1| 53 EGLTQEEAGQRMGVSRGTVWRALTSARK 80
                                      4********************9986664 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1     8e-06    0.0084       7      47 ..      47      88 ..      41      97 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 8e-06
                                      HHHHHHHS.SHHHHHHHHTS-HHHHHHHHHHHHHHHTS-SEE CS
                             HTH_1  7 fvavaeeg.sftrAAeeLglsqpavsrqikrLEeelgvpLfe 47
                                      +  v  eg +  +A +++g+s  +v+r++ + ++ + + L+e
  gi|242398677|ref|YP_002994101.1| 47 LRLVDYEGlTQEEAGQRMGVSRGTVWRALTSARKKVAQMLVE 88
                                      5555555666679*************************9998 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   1.5e-05     0.016      13      42 ..      53      81 ..      43      95 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.5e-05
                            HTH_11 13 rgpisgeeLAeeLnvSrrtvrrdIkaLeel 42
                                      +g ++ ee  ++++vSr tv+r + + +++
  gi|242398677|ref|YP_002994101.1| 53 EG-LTQEEAGQRMGVSRGTVWRALTSARKK 81
                                      33.8899999************99877665 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   2.2e-05     0.023      18      41 ..      52      75 ..      39      76 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.2e-05
                            HTH_38 18 aeGlslreIArrLgrspsTIsREl 41
                                       eGl++ e ++r+g+s++T+ R l
  gi|242398677|ref|YP_002994101.1| 52 YEGLTQEEAGQRMGVSRGTVWRAL 75
                                      59********************87 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   0.0     3e-05     0.032      17      38 ..      54      75 ..      48      81 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3e-05
                            HTH_24 17 risqreLAerlglSpstvnrrl 38
                                      +++q e  +r g+S++tv+r l
  gi|242398677|ref|YP_002994101.1| 54 GLTQEEAGQRMGVSRGTVWRAL 75
                                      89******************98 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   3.6e-05     0.038       9      26 ..      54      71 ..      46      73 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.6e-05
                                      THHHHHHHHHHTSSHHHH CS
                             HTH_3  9 glsqeeLAeklGvsrsti 26
                                      gl+qee+ +++Gvsr t+
  gi|242398677|ref|YP_002994101.1| 54 GLTQEEAGQRMGVSRGTV 71
                                      9**************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 ?   14.0   0.1   3.5e-05     0.037      22      48 ..      55      81 ..      39      97 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.5e-05
                                      HHHHHHHHHTTSSHHHHHHHHHHHHHT CS
                         HTH_Crp_2 22 ltqeelAsmlGltretvsrilseLkre 48
                                      ltqee ++++G++r tv r+l+  +++
  gi|242398677|ref|YP_002994101.1| 55 LTQEEAGQRMGVSRGTVWRALTSARKK 81
                                      8********************987775 PP

>> HTH_Tnp_4  Helix-turn-helix of DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   6.7e-05     0.071      18      49 ..      53      84 ..      53      88 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.7e-05
                         HTH_Tnp_4 18 lnltyqdLayrFgvsestvsrifhkwvdlLae 49
                                      ++lt++  ++r gvs++tv+r  +   +  a+
  gi|242398677|ref|YP_002994101.1| 53 EGLTQEEAGQRMGVSRGTVWRALTSARKKVAQ 84
                                      589******************99887766665 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   0.00011      0.12       4      29 ..      45      71 ..      44      83 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00011
                            HTH_28  4 eiiklla.aGhsvreaArelgisrrtv 29
                                      e+++l+  +G ++ ea +++g+sr tv
  gi|242398677|ref|YP_002994101.1| 45 EALRLVDyEGLTQEEAGQRMGVSRGTV 71
                                      89999999999***************9 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00013      0.14       7      45 ..      43      78 ..      39      81 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00013
                                      HHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHH CS
                            MarR_2  7 qarvLaaLgrrpgrdltvgelarrlglsksavsrilkrL 45
                                      ++ +L  +  + g  lt+ e  +r+g+s+++v r+l  +
  gi|242398677|ref|YP_002994101.1| 43 EFEALRLVDYE-G--LTQEEAGQRMGVSRGTVWRALTSA 78
                                      55566666555.5..9****************9999766 PP

>> TnsD  Tn7-like transposition protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0    0.0002      0.21     193     228 ..      48      83 ..      42      97 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0002
                              TnsD 193 eLveeeglslkeiAkelgvdiktVlryakklgllke 228
                                       +Lv++egl+++e+ +++gv+ +tV r + +  + ++
  gi|242398677|ref|YP_002994101.1|  48 RLVDYEGLTQEEAGQRMGVSRGTVWRALTSARKKVA 83 
                                       57778*********************9987766655 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.3       9.7     1e+04      49      55 ..       4      10 ..       2      13 .. 0.54
   2 ?   11.5   0.2   0.00021      0.23       5      41 ..      47      83 ..      45      91 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 9.7
                            HTH_29 49 rsgrprn 55
                                      ++gr r+
  gi|242398677|ref|YP_002994101.1|  4 GRGRRRK 10
                                      4555554 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00021
                            HTH_29  5 llllaeGvstvsqiAkllglsrrtvyrwlkrfeegGl 41
                                      l+l++ ++ t  ++ +++g+sr tv r+l   +++ +
  gi|242398677|ref|YP_002994101.1| 47 LRLVDYEGLTQEEAGQRMGVSRGTVWRALTSARKKVA 83
                                      5556544449*****************9988877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); 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: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.61
# Mc/sec: 586.19
//
Query:       gi|242398678|ref|YP_002994102.1|  [L=52]
Description: hypothetical protein TSIB_0688 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 331.82
//
Query:       gi|242398679|ref|YP_002994103.1|  [L=63]
Description: Fe-S oxidoreductase, [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0072   16.2   0.1     0.0094   15.9   0.1    1.2  1  TBPIP     TBPIP/Hop2 winged helix 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 !   15.9   0.1   5.2e-07    0.0094      25      60 ..      18      54 ..      16      56 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5.2e-07
                             TBPIP 25 nlqkklgKtavqka.LdeLvdegkiieKeyGKqkiYl 60
                                      +l++ l+K++v  a +++L +egk+ie eyG +  Y+
  gi|242398679|ref|YP_002994103.1| 18 ALKELLKKANVDWAtVETLIEEGKLIELEYGEKRFYM 54
                                      6888999999986549***************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       725  (0.0404373); expected 358.6 (0.02)
Passed bias filter:                      567  (0.0316247); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 453.01
//
Query:       gi|242398680|ref|YP_002994104.1|  [L=295]
Description: ATPase, ParA/MinD family, containing ferredoxin domains [Thermococcus sibiricus MM 739]
Scores for complete 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   72.8   0.0    3.2e-20   72.5   0.0    1.2  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    1.1e-15   57.8   0.1    2.6e-08   33.6   0.0    3.0  2  ParA         NUBPL iron-transfer P-loop NTPase
    4.8e-11   42.0  20.1    2.5e-06   27.1   7.7    2.4  2  Fer4         4Fe-4S binding domain
    1.5e-10   41.1  13.8    1.5e-10   41.1  13.8    1.7  2  Fer4_21      4Fe-4S dicluster domain
    4.1e-08   32.9  12.6    0.00031   20.7   2.9    2.5  2  Fer4_2       4Fe-4S binding domain
    2.1e-07   31.7   7.5     0.0024   18.7   0.0    2.5  2  Fer4_16      4Fe-4S double cluster binding domain
    5.8e-07   29.6   0.0    0.00038   20.4   0.0    2.2  2  AAA_31       AAA domain
    7.9e-07   29.5   3.2     0.0063   17.0   1.1    2.3  2  Fer4_17      4Fe-4S dicluster domain
    9.2e-07   29.4  27.4      9e-06   26.2  14.1    2.0  2  Fer4_7       4Fe-4S dicluster domain
    1.3e-06   28.4  13.0    0.00067   19.7  15.0    2.3  2  Fer4_10      4Fe-4S dicluster domain
    3.9e-05   23.6   0.1      0.046   13.6   0.0    2.2  2  AAA_26       AAA domain
    0.00012   22.1  14.1     0.0016   18.6  14.7    2.1  2  Fer4_9       4Fe-4S dicluster domain
    0.00021   20.8   0.0      0.063   12.7   0.0    2.4  2  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
    0.00056   19.5   0.0        0.3   10.5   0.0    2.2  2  CBP_BcsQ     Cellulose biosynthesis protein BcsQ
    0.00098   18.4   0.0     0.0019   17.5   0.0    1.5  1  ArsA_ATPase  Anion-transporting ATPase
     0.0042   17.1  17.5      0.074   13.2   7.4    2.4  2  Fer4_6       4Fe-4S binding domain
  ------ inclusion threshold ------
       0.02   15.4  13.5       0.58   10.7   5.3    2.5  2  Fer4_13      4Fe-4S single cluster domain of Ferredoxin I
      0.036   14.5  13.5        1.1    9.7   4.9    2.3  4  Fer4_8       4Fe-4S dicluster domain
      0.038   14.7   7.5        3.1    8.6   0.2    2.8  2  Fer4_15      4Fe-4S single cluster domain
      0.041   14.4  13.5      0.088   13.4   2.0    2.4  2  Fer4_4       4Fe-4S binding domain
      0.055   13.0   0.0      0.074   12.6   0.0    1.2  1  DUF4088      Protein of unknown function (DUF4088)
       0.16   11.5   0.0       0.44   10.1   0.0    1.7  2  GTP_EFTU     Elongation factor Tu GTP binding domain
        1.4    9.8  13.5         10    7.1   3.5    2.4  4  Fer4_22      4Fe-4S dicluster domain
        1.6    9.8  21.1        2.1    9.5   6.4    2.4  2  Fer4_3       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 !   72.5   0.0   4.3e-23   3.2e-20       1     122 [.       3     263 ..       3     269 .. 0.98

  Alignments for each domain:
  == domain 1  score: 72.5 bits;  conditional E-value: 4.3e-23
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH....................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................... RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep....................... 54 
                                       iaias+kGGvGK+++aa+L+ +l++  +  ++vDaD +a+nl +l+g+e  +e+                       
  gi|242398680|ref|YP_002994104.1|   3 IAIASGKGGVGKSSVAAALIYLLKD-DYPLIAVDADADAPNLDLLFGVERWEEEkelvgakvakinsetcikcgica 78 
                                       89**********************9.*********************999999999********************* PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|242398680|ref|YP_002994104.1|  79 ercpydcikildenyvvneltcegcgvcrlvcpvngvitleevrsgvirktttkygfplisaqldvgrpnsgklvte 155
                                       ***************************************************************************** PP

                                       ...................................................CCHCCCHHHHHHCHCHHHH..EEEEE CS
                                       ...................................................xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  55 ...................................................dlkrllellealgkkkalllkiagvv 80 
                                                                                          d+kr+ +++++++++       a ++
  gi|242398680|ref|YP_002994104.1| 156 ekewakrimkekgiehmivdsaagigcqviaslggadvailvaeptpaslnDVKRVYRVVQHFREP-------AYLI 225
                                       ****************************************************************87.......**** PP

                                       EEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  81 lnrvdgeneetllkealeelkqrygvpvlgviprdeavaeap 122
                                       +n+ d +  ++ l+e+ +e+     +p++g+ip+d  ++++ 
  gi|242398680|ref|YP_002994104.1| 226 INKLDLNPGFKGLYEFAKEE----DIPIIGEIPYDRTIPRSM 263
                                       *****************998....9**********9998875 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 !   33.6   0.0   3.4e-11   2.6e-08       6      60 ..       3      56 ..       1      75 [. 0.81
   2 !   19.2   0.0   8.9e-07   0.00066     112     245 ..     169     289 ..     158     290 .. 0.85

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 3.4e-11
                              ParA  6 iavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeekpeq 60
                                      ia++SgKGGVGKS+va+ l + L k ++    +DaD   p++  l+gve+ + e+
  gi|242398680|ref|YP_002994104.1|  3 IAIASGKGGVGKSSVAAALIYLL-KDDYPLIAVDADADAPNLDLLFGVERWEEEK 56
                                      99*****************7766.678888889***************9854433 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 8.9e-07
                              ParA 112 lDyLiiDlPPGtgDeqltvaqklplagaviVttpqevaladvkkaiemfkkvkvkvlGvveNmsgfvcpkcgektei 188
                                       ++ +i+D   G g   ++ +     + a++V+ p  ++l+dvk+  +++++ + +   +++ +              
  gi|242398680|ref|YP_002994104.1| 169 IEHMIVDSAAGIGCQVIASLG--GADVAILVAEPTPASLNDVKRVYRVVQHFREPAYLIINKLDLNP---------- 233
                                       567777777777766554444..456799**************************999998876533.......... PP

                              ParA 189 fgkgggeklaeelgvpllgeipldpeireasdegkplvlkepeseaakaleeiaekv 245
                                        g +g  ++a+e ++p++geip d +i +++   kp+v++ pes+ +kal+ iae v
  gi|242398680|ref|YP_002994104.1| 234 -GFKGLYEFAKEEDIPIIGEIPYDRTIPRSMTMLKPVVEAFPESKSSKALKGIAEVV 289
                                       .33688999*******************************************99865 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   7.7   3.3e-09   2.5e-06       2      24 .]      65      87 ..      64      87 .. 0.94
   2 !   20.6   4.5   3.6e-07   0.00027       1      21 [.      93     113 ..      93     115 .. 0.94

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 3.3e-09
                                      EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  2 videekCigCGaCvevCPvgAIt 24
                                      +i+ e Ci+CG+C+e CP+++I+
  gi|242398680|ref|YP_002994104.1| 65 KINSETCIKCGICAERCPYDCIK 87
                                      79*******************96 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 3.6e-07
                                       EEEETTTSSS-THHHHHSTTT CS
                              Fer4   1 vvideekCigCGaCvevCPvg 21 
                                       +v++e  C gCG C  vCPv+
  gi|242398680|ref|YP_002994104.1|  93 YVVNELTCEGCGVCRLVCPVN 113
                                       689****************98 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1  13.8     2e-13   1.5e-10       1      58 [.      64     117 ..      64     118 .. 0.93
   2 ?   -2.1   0.0       5.9   4.4e+03      33      46 ..     171     184 ..     160     188 .. 0.64

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 2e-13
                           Fer4_21   1 AridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedcie 58 
                                       A+i++++Ci+Cg C+  C+   +++i+i ++++  v e +C GC +C  vCPv+++i+
  gi|242398680|ref|YP_002994104.1|  64 AKINSETCIKCGICAERCP---YDCIKILDENY-VVNELTCEGCGVCRLVCPVNGVIT 117
                                       89*****************...9*****98877.78899****************998 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 5.9
                           Fer4_21  33 vlkvvedeCvGCnl 46 
                                       ++ v +   +GC++
  gi|242398680|ref|YP_002994104.1| 171 HMIVDSAAGIGCQV 184
                                       45555666777765 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   2.3   4.7e-06    0.0035       3      22 .]      64      83 ..      61      83 .. 0.90
   2 !   20.7   2.9   4.1e-07   0.00031       3      21 ..      93     111 ..      91     112 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.7e-06
                            Fer4_2  3 vvvdtdrCigCgaCvsaCPa 22
                                      +++++++Ci Cg+C   CP+
  gi|242398680|ref|YP_002994104.1| 64 AKINSETCIKCGICAERCPY 83
                                      789****************5 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 4.1e-07
                            Fer4_2   3 vvvdtdrCigCgaCvsaCP 21 
                                       +vv++ +C gCg C+ +CP
  gi|242398680|ref|YP_002994104.1|  93 YVVNELTCEGCGVCRLVCP 111
                                       799**************** 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 !   12.9   5.0   0.00021      0.16       1      18 [.      70      87 ..      70      98 .. 0.82
   2 !   18.7   0.0   3.3e-06    0.0024       1      50 [.      99     168 ..      99     184 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00021
                           Fer4_16  1 rCgtCgkCaevCPtnaik 18
                                      +C++Cg Cae CP ++ik
  gi|242398680|ref|YP_002994104.1| 70 TCIKCGICAERCPYDCIK 87
                                      5***************98 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 3.3e-06
                           Fer4_16   1 rCgtCgkCaevCPt.naikekkekeiearecisy...................ntaekkdlaedeekckk 50 
                                       +C +Cg C  vCP+ ++i+ ++ ++  +r+++ +                    ++e+k++a+++ k+k 
  gi|242398680|ref|YP_002994104.1|  99 TCEGCGVCRLVCPVnGVITLEEVRSGVIRKTTTKygfplisaqldvgrpnsgkLVTEEKEWAKRIMKEKG 168
                                       5************944688776666666664433477777777888888888888888888888887774 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   5.1e-07   0.00038       4      73 ..       3      72 ..       1     100 [. 0.87
   2 !    7.4   0.0    0.0051       3.8     118     170 ..     169     221 ..     105     231 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 5.1e-07
                            AAA_31  4 IaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQa.nattglgiekneiektlyevlieeknikeai 73
                                      Iaia  KGGvGK+  + +l + l k ++  + vD+D+ a n+   +g+e+ e ek+l+ + + ++n + +i
  gi|242398680|ref|YP_002994104.1|  3 IAIASGKGGVGKSSVAAALIYLL-KDDYPLIAVDADADApNLDLLFGVERWEEEKELVGAKVAKINSETCI 72
                                      9******************8866.7899********98769999999999999999999877666666665 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0051
                            AAA_31 118 YDyiiiDcpPsLglltenaLvasdsviipvqaeayaleGleqllktieevkkk 170
                                          +i+D    +g+ ++ +L  +d  i + ++++ +l+ ++++++ ++++++ 
  gi|242398680|ref|YP_002994104.1| 169 IEHMIVDSAAGIGCQVIASLGGADVAILVAEPTPASLNDVKRVYRVVQHFREP 221
                                       556899*****************************************999875 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   1.1   8.4e-06    0.0063      40      59 ..      65      84 ..      42      85 .. 0.79
   2 !   12.4   0.0   0.00024      0.18       2      28 ..     100     128 ..      99     162 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 8.4e-06
                           Fer4_17 40 eekaslCieCgeCerkCPqg 59
                                      + + ++Ci+Cg C+++CP++
  gi|242398680|ref|YP_002994104.1| 65 KINSETCIKCGICAERCPYD 84
                                      357899************97 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00024
                           Fer4_17   2 CiqCgyClpeCpsyeaydne..pkkllra 28 
                                       C +Cg C+ +Cp +  +  e  +  ++r+
  gi|242398680|ref|YP_002994104.1| 100 CEGCGVCRLVCPVNGVITLEevRSGVIRK 128
                                       9***********98775544123345555 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   5.3   1.3e-05    0.0098      18      51 ..      51      84 ..      47      85 .. 0.80
   2 !   26.2  14.1   1.2e-08     9e-06       1      51 [.      70     113 ..      70     114 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.3e-05
                            Fer4_7 18 eldeeenekgtekveidpekClgCgaCvavCPtg 51
                                      +++ee++  g + ++i++e+C+ Cg C+++CP++
  gi|242398680|ref|YP_002994104.1| 51 RWEEEKELVGAKVAKINSETCIKCGICAERCPYD 84
                                      455555556778999*****************97 PP

  == domain 2  score: 26.2 bits;  conditional E-value: 1.2e-08
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtg 51 
                                       +Ci+Cg C++ Cp+++i++ +e        +++++ +C gCg+C  vCP++
  gi|242398680|ref|YP_002994104.1|  70 TCIKCGICAERCPYDCIKILDE-------NYVVNELTCEGCGVCRLVCPVN 113
                                       6******************887.......48999***************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 !   19.7  15.0     9e-07   0.00067       3      56 .]      65     111 ..      63     111 .. 0.87
   2 !   18.4   0.7   2.4e-06    0.0018       3      40 ..      94     128 ..      92     133 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 9e-07
                           Fer4_10   3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       +i+++tCi+Cg C + CP+     + +++ +e+ +v++    C+gcg C  +CP
  gi|242398680|ref|YP_002994104.1|  65 KINSETCIKCGICAERCPY-----DCIKILDENYVVNE--LTCEGCGVCRLVCP 111
                                       799****************.....77777777777776..99***********9 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 2.4e-06
                           Fer4_10   3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrk 40 
                                       v+++ tC +Cg C+ +CP+   + + + e+ +++++rk
  gi|242398680|ref|YP_002994104.1|  94 VVNELTCEGCGVCRLVCPV---NGVITLEEVRSGVIRK 128
                                       67889**************...5555555555555554 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0    0.0033       2.5       3      26 ..       3      26 ..       1      31 [. 0.88
   2 !   13.6   0.0   6.1e-05     0.046     123     194 ..     185     259 ..     153     262 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0033
                            AAA_26  3 ifvtgtdtgvGKTvvslgLvralk 26
                                      i +++   gvGK++v+++L++ lk
  gi|242398680|ref|YP_002994104.1|  3 IAIASGKGGVGKSSVAAALIYLLK 26
                                      77999999************9995 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 6.1e-05
                            AAA_26 123 iaknlgapv.ilVargglgtinqllltiealrqknvrvlGvilNkv.rnp..envetlekksgipvlGvvPylpdl 194
                                       ia   ga+v ilVa ++  ++n++   + ++ q+  + + +i+Nk+  np  + + ++ k   ip++G++Py++++
  gi|242398680|ref|YP_002994104.1| 185 IASLGGADVaILVAEPTPASLNDVKRVYRVV-QHFREPAYLIINKLdLNPgfKGLYEFAKEEDIPIIGEIPYDRTI 259
                                       444446776699***********99888755.557889*******84455777999999999**********9875 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   5.4   2.6e-05     0.019      30      51 .]      65      86 ..      46      86 .. 0.72
   2 !   18.6  14.7   2.1e-06    0.0016       2      49 ..      71     113 ..      70     116 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.6e-05
                            Fer4_9 30 aaseeaCigCgaCveaCpkgai 51
                                      + + e Ci+Cg C+e+Cp ++i
  gi|242398680|ref|YP_002994104.1| 65 KINSETCIKCGICAERCPYDCI 86
                                      223368************9987 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 2.1e-06
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkg 49 
                                       C++Cg C e Cp++ ++  + ++ ++        C gCg C  +Cp +
  gi|242398680|ref|YP_002994104.1|  71 CIKCGICAERCPYDCIKILDENYVVNEL-----TCEGCGVCRLVCPVN 113
                                       ****************999988888863.....5************84 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 !    6.2   0.0    0.0081         6       2      26 ..       2      27 ..       1      76 [. 0.78
   2 !   12.7   0.0   8.4e-05     0.063     177     247 ..     222     292 ..     162     295 .] 0.82

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0081
                         Fer4_NifH  2 kiai.yGkGGiGksttsqnlsaalae 26
                                      +iai  GkGG+Gks  ++ l   l++
  gi|242398680|ref|YP_002994104.1|  2 QIAIaSGKGGVGKSSVAAALIYLLKD 27
                                      677735********998887766654 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 8.4e-05
                         Fer4_NifH 177 gGliinsrkvddereliekfaeelgtkvlevvPrdeivrkaelrkktvieyapeseqakeyrelarkilen 247
                                       + liin+ + + + + + +fa+e +++++  +P d ++ ++    k v+e  pes+ +k  + +a+ ++e+
  gi|242398680|ref|YP_002994104.1| 222 AYLIINKLDLNPGFKGLYEFAKEEDIPIIGEIPYDRTIPRSMTMLKPVVEAFPESKSSKALKGIAEVVKEQ 292
                                       557888777778888899***********************************************999886 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0   0.00041       0.3       4      52 ..       3      51 ..       1      73 [. 0.73
   2 !    7.0   0.0    0.0049       3.7      98     230 ..     152     286 ..     141     289 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00041
                          CBP_BcsQ  4 lalqGvRGGvGttsllaaLawalhelgesvlviDlspdn.lLrlhFnvdi 52
                                      +a+   +GGvG++s++aaL + l+  ++  +++D+ +d   L l F v+ 
  gi|242398680|ref|YP_002994104.1|  3 IAIASGKGGVGKSSVAAALIYLLK-DDYPLIAVDADADApNLDLLFGVER 51
                                      5666669************98776.58999****9987536888888763 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0049
                          CBP_BcsQ  98 laekaeallaalkelkeqyrwillDlpagasaltrellaladlvllvvepdanchvrLhq.....qalpaaellLiN 169
                                       l ++++++++++ + ++  + +++D  ag   ++ + l  ad+ +lv+ep  ++    ++     q++ + ++l+iN
  gi|242398680|ref|YP_002994104.1| 152 LVTEEKEWAKRIMK-EKGIEHMIVDSAAGIGCQVIASLGGADVAILVAEPTPASLNDVKRvyrvvQHFREPAYLIIN 227
                                       66778888888766.46688999*********99999999*********99887543332222226799999***** PP

                          CBP_BcsQ 170 qfeaasqlqqDllqlWlqslrrllPl..vihrDealaEalaakqPlgeyrpdslaaeevktLa 230
                                       +++ +         l+   +++ +P+   i  D +++ ++ + +P+ e  p+s  ++++k +a
  gi|242398680|ref|YP_002994104.1| 228 KLDLNPGF----KGLYEFAKEEDIPIigEIPYDRTIPRSMTMLKPVVEAFPESKSSKALKGIA 286
                                       99866544....444455556667764468889999999999999999999888888877766 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   0.0   2.5e-06    0.0019       1      49 [.       1      49 [.       1      67 [. 0.73

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.5e-06
                                      -EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-ST.TTHHHHHHTS CS
                       ArsA_ATPase  1 lkvilvgGKGGVGKttvsaatavklsekgkkvllistDP.AhslsDsfdq 49
                                      +++ + +GKGGVGK++v+aa+ + l + ++  + +  D  A++l   f  
  gi|242398680|ref|YP_002994104.1|  1 MQIAIASGKGGVGKSSVAAALIY-LLKDDYPLIAVDADAdAPNLDLLFGV 49
                                      567789**************965.55666666666666336666666655 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   7.4   9.9e-05     0.074       1      24 []      63      86 ..      63      86 .. 0.91
   2 !    9.3   2.4    0.0016       1.2       4      22 ..      95     113 ..      94     116 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9.9e-05
                            Fer4_6  1 vveidpdkCigCgdCvrvCPegai 24
                                      v+ i+ + Ci Cg C+  CP++ i
  gi|242398680|ref|YP_002994104.1| 63 VAKINSETCIKCGICAERCPYDCI 86
                                      6889****************9866 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0016
                            Fer4_6   4 idpdkCigCgdCvrvCPeg 22 
                                       +++  C gCg C  vCP +
  gi|242398680|ref|YP_002994104.1|  95 VNELTCEGCGVCRLVCPVN 113
                                       78889************84 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   5.3   0.00077      0.58       1      17 [.      66      82 ..      66      87 .. 0.95
   2 ?    9.2   1.2    0.0024       1.8       1      17 [.      95     111 ..      95     114 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00077
                           Fer4_13  1 VDrdtCiacgaCvelaP 17
                                      ++ +tCi cg+C+e +P
  gi|242398680|ref|YP_002994104.1| 66 INSETCIKCGICAERCP 82
                                      789*************9 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0024
                           Fer4_13   1 VDrdtCiacgaCvelaP 17 
                                       V++ tC +cg+C+ ++P
  gi|242398680|ref|YP_002994104.1|  95 VNELTCEGCGVCRLVCP 111
                                       7888************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 ?    9.7   4.9    0.0015       1.1      48      62 ..      68      82 ..      31      88 .. 0.70
   2 ?    9.5   4.6    0.0018       1.3       3      16 ..      69      82 ..      67      98 .. 0.79
   3 ?    8.2   2.2    0.0044       3.3      50      63 ..      99     112 ..      89     115 .. 0.76
   4 ?    9.4   1.6    0.0018       1.4       5      63 ..     100     112 ..      96     167 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0015
                            Fer4_8 48 lwsCttcgaCtevCp 62
                                       ++C  cg C+e+Cp
  gi|242398680|ref|YP_002994104.1| 68 SETCIKCGICAERCP 82
                                      555555555555555 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0018
                            Fer4_8  3 ekCieCgaCqsaCp 16
                                      e Ci+Cg C + Cp
  gi|242398680|ref|YP_002994104.1| 69 ETCIKCGICAERCP 82
                                      67999999999998 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0044
                            Fer4_8  50 sCttcgaCtevCpv 63 
                                       +C +cg C+ vCpv
  gi|242398680|ref|YP_002994104.1|  99 TCEGCGVCRLVCPV 112
                                       47777777777776 PP

  == domain 4  score: 9.4 bits;  conditional E-value: 0.0018
                            Fer4_8   5 CieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpv 63 
                                       C +Cg C+  Cp                                              v
  gi|242398680|ref|YP_002994104.1| 100 CEGCGVCRLVCP----------------------------------------------V 112
                                       555555555555..............................................4 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 ?    7.9   2.3    0.0069       5.1       3      19 ..      66      82 ..      65      89 .. 0.90
   2 ?    8.6   0.2    0.0042       3.1       3      19 ..      95     111 ..      94     134 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0069
                           Fer4_15  3 vDrdaCigcglCvaeap 19
                                      ++ ++Ci cg C++++p
  gi|242398680|ref|YP_002994104.1| 66 INSETCIKCGICAERCP 82
                                      7889***********98 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0042
                           Fer4_15   3 vDrdaCigcglCvaeap 19 
                                       v++ +C+gcg+C  ++p
  gi|242398680|ref|YP_002994104.1|  95 VNELTCEGCGVCRLVCP 111
                                       66779********9996 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   4.0     0.027        20       1      16 [.      68      83 ..      68      84 .. 0.90
   2 ?   13.4   2.0   0.00012     0.088       3      17 .]      99     113 ..      97     117 .. 0.92

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.027
                            Fer4_4  1 qerCigCgsCvaaCPq 16
                                      +e+Ci Cg C   CP+
  gi|242398680|ref|YP_002994104.1| 68 SETCIKCGICAERCPY 83
                                      589*********9997 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00012
                            Fer4_4   3 rCigCgsCvaaCPqg 17 
                                       +C gCg+C+ +CP++
  gi|242398680|ref|YP_002994104.1|  99 TCEGCGVCRLVCPVN 113
                                       599**********75 PP

>> DUF4088  Protein of unknown function (DUF4088)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0    0.0001     0.074      73     125 ..     128     187 ..     117     222 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.0001
                           DUF4088  73 rqaaefGfal.avradWta...eelvkaareWaaaivkeakgdaalvealaa...qikas 125
                                       + ++++Gf l +++ d ++    +lv + +eWa+ i+ke + ++ +v++ a+   q+ as
  gi|242398680|ref|YP_002994104.1| 128 KTTTKYGFPLiSAQLDVGRpnsGKLVTEEKEWAKRIMKEKGIEHMIVDSAAGigcQVIAS 187
                                       456799997615678887622256899*********************987533377766 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       2.9   2.1e+03      14      32 ..      12      30 ..       6      57 .. 0.79
   2 ?   10.1   0.0   0.00059      0.44      86     138 ..     183     237 ..     166     274 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.9
                                      SSHHHHHHHHHHHTTSSCH CS
                          GTP_EFTU 14 hGKtTLtdrLlyktgaisk 32
                                       GK+++  +L+y ++++  
  gi|242398680|ref|YP_002994104.1| 12 VGKSSVAAALIYLLKDDYP 30
                                      5999999999998887665 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00059
                                       HHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGST..HHH CS
                          GTP_EFTU  86 evirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrl..kae 138
                                       +vi++l  +D+a+lv + +    +  ++v r+++  + p  ++iNK+D     + 
  gi|242398680|ref|YP_002994104.1| 183 QVIASLGGADVAILVAEPTPASLNDVKRVYRVVQHFREPAYLIINKLDLNpgFKG 237
                                       689999******************************************8766444 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   3.9     0.029        21      75      94 ..      64      83 ..      51      85 .. 0.81
   2 ?    5.6   3.5     0.039        29       2      23 ..      71      91 ..      70      97 .. 0.76
   3 ?    7.1   3.5     0.013        10      76      94 ..      94     112 ..      83     115 .. 0.78
   4 ?    5.6   3.3     0.038        28       2      17 ..     100     115 ..      99     132 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.029
                           Fer4_22 75 ekfgesgCvGCgRCieacpv 94
                                      +k+++++C+ Cg C e+cp 
  gi|242398680|ref|YP_002994104.1| 64 AKINSETCIKCGICAERCPY 83
                                      56788899999999999985 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.039
                           Fer4_22  2 ClsCgaCtlvCptCsCfdvede 23
                                      C++Cg C+  Cp   C+++ de
  gi|242398680|ref|YP_002994104.1| 71 CIKCGICAERCPY-DCIKILDE 91
                                      9999999999995.57766665 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.013
                           Fer4_22  76 kfgesgCvGCgRCieacpv 94 
                                        ++e +C GCg C  +cpv
  gi|242398680|ref|YP_002994104.1|  94 VVNELTCEGCGVCRLVCPV 112
                                       4578899999999999997 PP

  == domain 4  score: 5.6 bits;  conditional E-value: 0.038
                           Fer4_22   2 ClsCgaCtlvCptCsC 17 
                                       C +Cg C lvCp    
  gi|242398680|ref|YP_002994104.1| 100 CEGCGVCRLVCPVNGV 115
                                       6777777777776555 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   6.7     0.035        26       1      14 [.      71      84 ..      71      85 .. 0.94
   2 ?    9.5   6.4    0.0028       2.1       1      14 [.     100     113 ..     100     114 .. 0.94

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.035
                            Fer4_3  1 CtgCgaCvevCPvg 14
                                      C+ Cg C e CP++
  gi|242398680|ref|YP_002994104.1| 71 CIKCGICAERCPYD 84
                                      ************97 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0028
                            Fer4_3   1 CtgCgaCvevCPvg 14 
                                       C gCg C  vCPv+
  gi|242398680|ref|YP_002994104.1| 100 CEGCGVCRLVCPVN 113
                                       99**********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); 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: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 1954.10
//
Query:       gi|242398681|ref|YP_002994105.1|  [L=303]
Description: ATPase, ParA/MinD family, containing ferredoxin domains [Thermococcus sibiricus MM 739]
Scores for complete 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   69.7   0.0    5.4e-19   68.5   0.0    1.5  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    4.5e-15   55.8   1.4    3.9e-09   36.3   0.1    3.1  2  ParA         NUBPL iron-transfer P-loop NTPase
    1.5e-10   40.7  11.2    1.3e-05   25.1   1.9    2.3  2  Fer4_6       4Fe-4S binding domain
    3.3e-09   36.2  13.2    1.5e-05   24.6   2.4    2.3  2  Fer4         4Fe-4S binding domain
    9.8e-08   32.0   9.1    1.7e-07   31.3   9.1    1.3  1  Fer4_21      4Fe-4S dicluster domain
    2.9e-07   30.2   0.3     0.0054   16.2   0.1    2.2  2  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
      6e-07   29.5   7.7    1.1e-06   28.7   7.7    1.5  1  Fer4_9       4Fe-4S dicluster domain
    3.5e-05   24.3   3.2      0.087   13.4   0.6    2.4  2  Fer4_17      4Fe-4S dicluster domain
    6.3e-05   23.5  13.0     0.0003   21.3  13.5    1.8  2  Fer4_7       4Fe-4S dicluster domain
      7e-05   23.0  11.7     0.0047   17.3   1.6    2.2  2  Fer4_4       4Fe-4S binding domain
    7.5e-05   23.1   5.4       0.02   15.3   0.3    2.4  2  Fer4_8       4Fe-4S dicluster domain
    0.00011   22.1   0.4     0.0011   19.0   0.0    2.2  2  AAA_31       AAA domain
    0.00021   22.2  11.2      0.048   14.6   4.2    2.4  2  Fer4_16      4Fe-4S double cluster binding domain
    0.00023   21.1  11.5      0.021   14.9   1.4    2.3  2  Fer4_2       4Fe-4S binding domain
    0.00098   18.5   0.0     0.0018   17.6   0.0    1.5  1  MipZ         ATPase MipZ
     0.0013   18.8  14.3      0.033   14.3  15.7    2.1  2  Fer4_10      4Fe-4S dicluster domain
     0.0043   16.6   0.0       0.22   10.9   0.0    2.1  2  CBP_BcsQ     Cellulose biosynthesis protein BcsQ
     0.0054   15.9   2.0      0.088   12.0   0.2    2.4  2  ArsA_ATPase  Anion-transporting ATPase
  ------ inclusion threshold ------
      0.037   13.6   0.0        0.1   12.1   0.0    1.7  2  AAA_25       AAA domain
       0.11   12.0   0.4        1.4    8.3   0.2    2.2  2  PhoH         PhoH-like protein
       0.42   11.5   6.7        2.4    9.1   0.4    2.3  2  Fer4_22      4Fe-4S dicluster domain
       0.72   10.9  16.2        1.6    9.9   4.3    2.3  2  Fer4_3       4Fe-4S binding domain
        7.4    7.2  10.9        9.2    6.9   2.2    2.4  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 !   68.5   0.0   6.9e-22   5.4e-19       1     128 []      20     280 ..      20     280 .. 0.96

  Alignments for each domain:
  == domain 1  score: 68.5 bits;  conditional E-value: 6.9e-22
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH....................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................... RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep....................... 54 
                                       ia+ ++kGG+GK+t+a+nLa+al++  ++  l D+D++a+n+++l g e + e+                       
  gi|242398681|ref|YP_002994105.1|  20 IAVSGGKGGTGKSTVAINLAIALQD-YFNLTLADLDVEAPNDHLLLGIELQNEEpvkmfmpsfdyskctkckkcaev 95 
                                       7999*********************.*****************9888887777789********************* PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|242398681|ref|YP_002994105.1|  96 ceekaiitmkdgtpfliptlcsgcraceiicpvtgailesqklmghtyltetpygfplvtgkllegeerampivtma 172
                                       ***************************************************************************** PP

                                       ..............................................CCHCCCHHHHHHCHCHHHH..EEEEEEEEES CS
                                       ..............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  55 ..............................................dlkrllellealgkkkalllkiagvvlnrvd 85 
                                                                                     dl  +lel + + ++       a vv+nr d
  gi|242398681|ref|YP_002994105.1| 173 kkraksldrrlllvdtaagtsntvskaledsklliavteptplglhDLTLILELGRLMNIE-------AWVVINRSD 242
                                       *******************************************999999999999999999.......99*****98 PP

                                       S...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHHTS-H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  86 geneetllkealeelkqrygvpvlgviprdeavaeapargepv 128
                                              +k+ ++e+ q+y+ +++++ip++e++++++ +gep+
  gi|242398681|ref|YP_002994105.1| 243 LG-----EKKRVKEIAQKYNAEIVAEIPYSEDIVRSYIKGEPI 280
                                       87.....677777788888*********************997 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 !   36.3   0.1   5.1e-12   3.9e-09       5      67 ..      19      79 ..      17     104 .. 0.85
   2 !   16.2   0.2   7.1e-06    0.0055     142     245 ..     209     298 ..     168     299 .. 0.71

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 5.1e-12
                              ParA  5 viavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeekpeqsekkliP 67
                                       iav+ gKGG GKStva+nlA+aL+   ++  l D+D+  p+   llg+e ++ e  + +++P
  gi|242398681|ref|YP_002994105.1| 19 QIAVSGGKGGTGKSTVAINLAIALQ-DYFNLTLADLDVEAPNDHLLLGIELQNEEPVK-MFMP 79
                                      699*********************6.5799******************9987555444.4555 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 7.1e-06
                              ParA 142 VttpqevaladvkkaiemfkkvkvkvlGvveNmsgfvcpkcgekteifgkgggeklaeelgvpllgeipldpeirea 218
                                       Vt p  + l+d +  +e+ + ++++   v+            +++++ +k+ ++++a+++++++++eip +++i+++
  gi|242398681|ref|YP_002994105.1| 209 VTEPTPLGLHDLTLILELGRLMNIEAWVVI------------NRSDLGEKKRVKEIAQKYNAEIVAEIPYSEDIVRS 273
                                       555555555555555555555555444333............24455567899************************ PP

                              ParA 219 sdegkplvlkepeseaakaleeiaekv 245
                                         +g+p++l+e  s+ a++++e+ae+v
  gi|242398681|ref|YP_002994105.1| 274 YIKGEPIILSE--SKEARIFKELAERV 298
                                       ********996..88999999999987 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   1.9   1.6e-08   1.3e-05       2      24 .]      79     101 ..      78     101 .. 0.95
   2 !   20.6   2.1   4.3e-07   0.00034       6      24 .]     113     132 ..     110     132 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.6e-08
                            Fer4_6   2 veidpdkCigCgdCvrvCPegai 24 
                                       + +d++kC+ C +C+ vC e+ai
  gi|242398681|ref|YP_002994105.1|  79 PSFDYSKCTKCKKCAEVCEEKAI 101
                                       78******************998 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 4.3e-07
                            Fer4_6   6 pdkCigCgdCvrvCP.egai 24 
                                       p +C gC++C+++CP +gai
  gi|242398681|ref|YP_002994105.1| 113 PTLCSGCRACEIICPvTGAI 132
                                       779************66997 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   2.4   1.9e-08   1.5e-05       2      23 ..      80     101 ..      79     102 .. 0.93
   2 !   16.9   3.3     5e-06    0.0039       4      20 ..     112     128 ..     109     128 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1.9e-08
                                       EEETTTSSS-THHHHHSTTTEE CS
                              Fer4   2 videekCigCGaCvevCPvgAI 23 
                                        +d++kC++C++C+evC   AI
  gi|242398681|ref|YP_002994105.1|  80 SFDYSKCTKCKKCAEVCEEKAI 101
                                       68****************9999 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 5e-06
                                       ETTTSSS-THHHHHSTT CS
                              Fer4   4 deekCigCGaCvevCPv 20 
                                       ++ +C gC aC+ +CPv
  gi|242398681|ref|YP_002994105.1| 112 IPTLCSGCRACEIICPV 128
                                       789*************7 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   9.1   2.1e-10   1.7e-07       3      57 ..      81     132 ..      79     133 .. 0.88

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 2.1e-10
                           Fer4_21   3 idedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedci 57 
                                       +d +kC +C+kC+ +Ce+   +ai + ++ +  ++   C GC  C ++CPv+++i
  gi|242398681|ref|YP_002994105.1|  81 FDYSKCTKCKKCAEVCEE---KAIITMKDGTPFLIPTLCSGCRACEIICPVTGAI 132
                                       5789*************7...778777777777899****************998 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 !   12.1   0.0   0.00013     0.098       2      26 ..      19      44 ..      18      69 .. 0.87
   2 !   16.2   0.1   6.9e-06    0.0054     179     246 ..     236     300 ..     225     302 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00013
                         Fer4_NifH  2 kiaiy.GkGGiGksttsqnlsaalae 26
                                      +ia+  GkGG Gkst + nl++al++
  gi|242398681|ref|YP_002994105.1| 19 QIAVSgGKGGTGKSTVAINLAIALQD 44
                                      7777637****************986 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 6.9e-06
                         Fer4_NifH 179 liinsrkvddereliekfaeelgtkvlevvPrdeivrkaelrkktvieyapeseqakeyrelarkile 246
                                       ++in r+   e++ ++++a++ + ++++ +P +e++ ++ ++ + +i    es+ a  ++ela+++++
  gi|242398681|ref|YP_002994105.1| 236 VVIN-RSDLGEKKRVKEIAQKYNAEIVAEIPYSEDIVRSYIKGEPIILS--ESKEARIFKELAERVVN 300
                                       6888.88889999*******************************99854..445589*******9986 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   7.7   1.4e-09   1.1e-06       1      49 [.      85     130 ..      71     132 .. 0.90

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 1.4e-09
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpk.g 49 
                                       kCt+C++C e+C+ ++++  + ++   +       C gC+aC+ +Cp  g
  gi|242398681|ref|YP_002994105.1|  85 KCTKCKKCAEVCEEKAIITMKDGTPFLIPT----LCSGCRACEIICPVtG 130
                                       7*************9998888888888765....6************855 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.6   0.00011     0.087      42      58 ..      82      98 ..      57     100 .. 0.80
   2 !   11.0   0.1   0.00062      0.48       2      17 ..     116     131 ..     112     167 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00011
                           Fer4_17 42 kaslCieCgeCerkCPq 58
                                        s+C++C++C+++C +
  gi|242398681|ref|YP_002994105.1| 82 DYSKCTKCKKCAEVCEE 98
                                      6799***********86 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00062
                           Fer4_17   2 CiqCgyClpeCpsyea 17 
                                       C++C++C+  Cp   a
  gi|242398681|ref|YP_002994105.1| 116 CSGCRACEIICPVTGA 131
                                       6666666666665555 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   4.7   0.00015      0.12      28      50 ..      76      98 ..      65     100 .. 0.73
   2 !   21.3  13.5   3.8e-07    0.0003       1      50 [.      85     128 ..      85     131 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00015
                            Fer4_7 28 tekveidpekClgCgaCvavCPt 50
                                      +  + +d++kC+ C++C++vC  
  gi|242398681|ref|YP_002994105.1| 76 MFMPSFDYSKCTKCKKCAEVCEE 98
                                      45567899999999999999965 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 3.8e-07
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPt 50 
                                       +C++C++C+++C  kai + ++    g  ++ + p+ C+gC+aC+  CP+
  gi|242398681|ref|YP_002994105.1|  85 KCTKCKKCAEVCEEKAIITMKD----G--TPFLIPTLCSGCRACEIICPV 128
                                       7************999998886....4..78999***************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 !   10.7   2.9    0.0008      0.63       2      15 ..      84      97 ..      83     104 .. 0.91
   2 !   17.3   1.6     6e-06    0.0047       3      16 ..     115     128 ..     113     137 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0008
                            Fer4_4  2 erCigCgsCvaaCP 15
                                      ++C+ C++C  +C+
  gi|242398681|ref|YP_002994105.1| 84 SKCTKCKKCAEVCE 97
                                      69***********8 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 6e-06
                            Fer4_4   3 rCigCgsCvaaCPq 16 
                                        C gC++C+++CP+
  gi|242398681|ref|YP_002994105.1| 115 LCSGCRACEIICPV 128
                                       5************5 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.3   2.5e-05      0.02      48      64 ..      83      99 ..      54     100 .. 0.86
   2 !    9.7   0.7    0.0015       1.2      50      63 ..     115     128 ..     112     141 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.5e-05
                            Fer4_8 48 lwsCttcgaCtevCpvg 64
                                        +Ct c++C+evC ++
  gi|242398681|ref|YP_002994105.1| 83 YSKCTKCKKCAEVCEEK 99
                                      578***********986 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0015
                            Fer4_8  50 sCttcgaCtevCpv 63 
                                        C++c+aC+  Cpv
  gi|242398681|ref|YP_002994105.1| 115 LCSGCRACEIICPV 128
                                       68888888888886 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   1.4e-06    0.0011       4      42 ..      20      57 ..      18     115 .. 0.71
   2 ?    1.1   0.1      0.41   3.2e+02      23      54 ..     172     204 ..     166     298 .. 0.63

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.4e-06
                            AAA_31  4 IaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQa 42
                                      Ia++  KGG GK+T ++nla al  + + + l DlD  a
  gi|242398681|ref|YP_002994105.1| 20 IAVSGGKGGTGKSTVAINLAIALQDYFNLT-LADLDVEA 57
                                      9999*******************9765444.45777654 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.41
                            AAA_31  23 aaala.klgkkvLlvDlDpQanattglgiekne 54 
                                       a+  a +l+ + LlvD  + ++ t++  +e ++
  gi|242398681|ref|YP_002994105.1| 172 AKKRAkSLDRRLLLVDTAAGTSNTVSKALEDSK 204
                                       555453567788888888877777766654444 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 !   14.6   4.2   6.1e-05     0.048       1      19 [.      85     103 ..      85     109 .. 0.87
   2 !   11.4   0.6   0.00061      0.48       2      20 ..     116     135 ..     115     147 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6.1e-05
                           Fer4_16   1 rCgtCgkCaevCPtnaike 19 
                                       +C++C+kCaevC ++ai +
  gi|242398681|ref|YP_002994105.1|  85 KCTKCKKCAEVCEEKAIIT 103
                                       6***************965 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00061
                           Fer4_16   2 CgtCgkCaevCPt.naikek 20 
                                       C +C++C  +CP+ +ai e 
  gi|242398681|ref|YP_002994105.1| 116 CSGCRACEIICPVtGAILES 135
                                       89999999999964777766 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   1.4   2.7e-05     0.021       3      20 ..      79      96 ..      77      98 .. 0.91
   2 !   11.1   3.0   0.00043      0.34       6      21 ..     112     127 ..     108     128 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.7e-05
                            Fer4_2  3 vvvdtdrCigCgaCvsaC 20
                                      + +d  +C+ C++C  +C
  gi|242398681|ref|YP_002994105.1| 79 PSFDYSKCTKCKKCAEVC 96
                                      6799************** PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00043
                            Fer4_2   6 dtdrCigCgaCvsaCP 21 
                                        +  C gC+aC   CP
  gi|242398681|ref|YP_002994105.1| 112 IPTLCSGCRACEIICP 127
                                       5667*******999** 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   2.3e-06    0.0018       3      39 ..      20      55 ..      18     102 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.3e-06
                                      EEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--T CS
                              MipZ  3 ivlgnekGGsGksttavhvavaLlkkGarvaaidldl 39
                                      i ++  kGG+Gkst+a+ +a+aL +  ++ +  dld+
  gi|242398681|ref|YP_002994105.1| 20 IAVSGGKGGTGKSTVAINLAIALQDY-FNLTLADLDV 55
                                      678889*****************864.4444445554 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3  15.7   4.3e-05     0.033       3      56 .]      80     127 ..      78     127 .. 0.83
   2 !   12.6   1.8   0.00014      0.11       6      22 ..     113     129 ..     108     149 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.3e-05
                           Fer4_10   3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                        +d ++C++C+kC ++C       ++  +++++++    +  C gc aC  +CP
  gi|242398681|ref|YP_002994105.1|  80 SFDYSKCTKCKKCAEVC------EEKAIITMKDGTPFLIPTLCSGCRACEIICP 127
                                       57999************......3555566666666669**************9 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00014
                           Fer4_10   6 ddtCirCgkCvkaCPad 22 
                                       +  C +C++C   CP++
  gi|242398681|ref|YP_002994105.1| 113 PTLCSGCRACEIICPVT 129
                                       678************93 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   0.00029      0.22       3      34 ..      19      50 ..      18      75 .. 0.80
   2 ?    3.6   0.0      0.05        39     115     148 ..     180     213 ..     148     244 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00029
                          CBP_BcsQ  3 vlalqGvRGGvGttsllaaLawalhelgesvl 34
                                      ++a++G +GG+G+++++  La+al+   +  l
  gi|242398681|ref|YP_002994105.1| 19 QIAVSGGKGGTGKSTVAINLAIALQDYFNLTL 50
                                      699*********************98765554 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.05
                          CBP_BcsQ 115 qyrwillDlpagasaltrellaladlvllvvepd 148
                                       + r++l+D  ag+s++++++l+ + l ++v+ep 
  gi|242398681|ref|YP_002994105.1| 180 DRRLLLVDTAAGTSNTVSKALEDSKLLIAVTEPT 213
                                       45899*****************999999999885 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.2   0.00011     0.088       2      27 ..      19      44 ..      18      51 .. 0.84
   2 ?    3.1   0.1     0.055        43     264     290 ..     245     271 ..     231     278 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
                                      EEEEEEESTTSSHHHHHHHHHHHHHH CS
                       ArsA_ATPase  2 kvilvgGKGGVGKttvsaatavklse 27
                                      ++ + gGKGG GK+tv+  +a+ l +
  gi|242398681|ref|YP_002994105.1| 19 QIAVSGGKGGTGKSTVAINLAIALQD 44
                                      667789************99998865 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.055
                                       HHHHHHHHHHHTTTSEEEEEE--SS-S CS
                       ArsA_ATPase 264 qkkylkeieelfedlevvklplleeEv 290
                                       +kk++kei ++++   v+++p+ e+ v
  gi|242398681|ref|YP_002994105.1| 245 EKKRVKEIAQKYNAEIVAEIPYSEDIV 271
                                       89*******************988755 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00013       0.1      35      56 ..      20      41 ..      16      50 .. 0.88
   2 ?   -2.9   0.0       5.3   4.1e+03      13      38 ..     258     282 ..     246     283 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00013
                            AAA_25 35 lallaGapgtGKttlaldlala 56
                                      +a+  G +gtGK+t+a++la+a
  gi|242398681|ref|YP_002994105.1| 20 IAVSGGKGGTGKSTVAINLAIA 41
                                      67789***************87 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5.3
                            AAA_25  13 adlaapppprrwlvkgllpagelall 38 
                                       a++ a++p  +++v+ ++ +ge ++l
  gi|242398681|ref|YP_002994105.1| 258 AEIVAEIPYSEDIVRSYI-KGEPIIL 282
                                       447778888888888886.6777776 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.2    0.0018       1.4      19      43 ..      18      42 ..      13      49 .. 0.87
   2 ?    1.1   0.0      0.29   2.3e+02     102     137 ..     163     198 ..     157     201 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0018
                                      -SEEEEE--TTSSTTHHHHHHHHHH CS
                              PhoH 19 ndivfaiGpaGtGKtylavalavea 43
                                       +i +  G+ GtGK+ +a+ la+++
  gi|242398681|ref|YP_002994105.1| 18 MQIAVSGGKGGTGKSTVAINLAIAL 42
                                      5788999**************9976 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.29
                                       TTSEEEEEGGGGTT--B-SEEEEE-SGGG--HHHHH CS
                              PhoH 102 kgkievaplaymRGrTlndafvilDEAQnttkeqmk 137
                                       ++ + ++ +a  R ++l++ ++++D A  t+++  k
  gi|242398681|ref|YP_002994105.1| 163 ERAMPIVTMAKKRAKSLDRRLLLVDTAAGTSNTVSK 198
                                       566778999999***************988887655 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.4    0.0031       2.4      71      94 ..      75      98 ..      68     101 .. 0.85
   2 ?    5.0   1.2     0.057        45       2      94 ..     116     128 ..     112     138 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0031
                           Fer4_22 71 sefkekfgesgCvGCgRCieacpv 94
                                      ++f+ +f+ s+C+ C +C e+c +
  gi|242398681|ref|YP_002994105.1| 75 KMFMPSFDYSKCTKCKKCAEVCEE 98
                                      67788999999*******999986 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.057
                           Fer4_22   2 ClsCgaCtlvCptCsCfdvedetkeeskegervrvwdsClleeftkvaggenvrkekkerlrqrllhklsefkekfg 78 
                                       C +C aC ++Cp                                                                 
  gi|242398681|ref|YP_002994105.1| 116 CSGCRACEIICP----------------------------------------------------------------- 127
                                       555555555555................................................................. PP

                           Fer4_22  79 esgCvGCgRCieacpv 94 
                                                      v
  gi|242398681|ref|YP_002994105.1| 128 ---------------V 128
                                       ...............3 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   4.0     0.018        14       1      15 []      86     100 ..      86     100 .. 0.89
   2 ?    9.9   4.3     0.002       1.6       1      15 []     116     131 ..     116     131 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.018
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       Ct C  C evC ++A
  gi|242398681|ref|YP_002994105.1|  86 CTKCKKCAEVCEEKA 100
                                       ***********7766 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.002
                            Fer4_3   1 CtgCgaCvevCPv.gA 15 
                                       C gC+aC+  CPv gA
  gi|242398681|ref|YP_002994105.1| 116 CSGCRACEIICPVtGA 131
                                       99**********7577 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 ?    6.9   2.2     0.012       9.2       2      17 ..      82      97 ..      81      99 .. 0.88
   2 ?    4.9   1.6     0.048        38       6      17 ..     116     127 ..     113     137 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.012
                           Fer4_13  2 DrdtCiacgaCvelaP 17
                                      D ++C+ c++C+e++ 
  gi|242398681|ref|YP_002994105.1| 82 DYSKCTKCKKCAEVCE 97
                                      6689**********96 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.048
                           Fer4_13   6 CiacgaCvelaP 17 
                                       C++c aC  ++P
  gi|242398681|ref|YP_002994105.1| 116 CSGCRACEIICP 127
                                       ***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       782  (0.0436165); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.52
# Mc/sec: 1758.65
//
Query:       gi|242398682|ref|YP_002994106.1|  [L=142]
Description: hypothetical protein TSIB_0693 [Thermococcus sibiricus MM 739]
Scores for complete 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-32  110.5   0.0    6.3e-32  110.2   0.0    1.0  1  DUF364          Putative heavy-metal chelation
  ------ inclusion threshold ------
       0.18   11.8   0.0       0.88    9.6   0.0    1.8  2  DNA_photolyase  DNA photolyase


Domain annotation for each model (and alignments):
>> DUF364  Putative heavy-metal chelation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.2   0.0     7e-36   6.3e-32      10     131 ..      18     137 ..       9     141 .. 0.93

  Alignments for each domain:
  == domain 1  score: 110.2 bits;  conditional E-value: 7e-36
                            DUF364  10 kgkkVvvVGyfapvlkklkekgaeltvlelnpnlleeeegdlpdeaaeellpeadvviitGstLvngtlerllelak 86 
                                       + +kV+vVG++ p++++l+ +g+el+v+e+n +l++++   ++d+ +++llpe+d+vi +++ Lvngt++ l+++ak
  gi|242398682|ref|YP_002994106.1|  18 DAGKVAVVGNMPPLAEVLRGRGYELYVFERNAKLWDKDT--YSDALEYHLLPEMDAVIASATCLVNGTVNMLIDRAK 92 
                                       5789****************************9999986..7*********************************** PP

                            DUF364  87 kaaevvlvGPsapllpevlfdyGvdviagvvvtdpdkllraiaeG 131
                                       ka+  vl+GP+ +llpe+l+++ v+++a ++v+d +k+   ++ G
  gi|242398682|ref|YP_002994106.1|  93 KAKLFVLTGPTGQLLPEFLKGTRVTHLAAMKVVDFQKAILGLRLG 137
                                       **********************************99998777766 PP

>> DNA_photolyase  DNA photolyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0     0.088   7.9e+02      58      75 ..      31      48 ..      22      69 .. 0.71
   2 ?    9.6   0.0   9.8e-05      0.88      64      94 ..      91     121 ..      80     129 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.088
                                      HHHHHHHTT--EEEEESS CS
                    DNA_photolyase 58 LdeeLrelgirLvvrrgd 75
                                      L+e Lr +g +L+v++ +
  gi|242398682|ref|YP_002994106.1| 31 LAEVLRGRGYELYVFERN 48
                                      556666677777766644 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 9.8e-05
                                       HTT--EEEEESSHHHHHHHHHHHCTECEEEE CS
                    DNA_photolyase  64 elgirLvvrrgdpadvlpelakelgasavva 94 
                                       ++  +L+v++g++ + lpe++k + ++++ a
  gi|242398682|ref|YP_002994106.1|  91 AKKAKLFVLTGPTGQLLPEFLKGTRVTHLAA 121
                                       67789***********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1059.98
//
Query:       gi|242398683|ref|YP_002994107.1|  [L=362]
Description: Magnesium and cobalt transport protein CorA [Thermococcus sibiricus MM 739]
Scores for complete 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-78  264.5   1.7    1.5e-78  264.1   1.7    1.0  1  CorA      CorA-like Mg2+ transporter protein


Domain annotation for each model (and alignments):
>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  264.1   1.7   8.1e-83   1.5e-78       3     292 .]      69     358 ..      67     358 .. 0.98

  Alignments for each domain:
  == domain 1  score: 264.1 bits;  conditional E-value: 8.1e-83
                              CorA   3 gfvWldlssptee.eleeLaeelgldelaledlldseerprvedyddylllvlpsveldkseeeeeevplsillgdn 78 
                                       +++W++++  ++   +++L e lgl++l+led++++ +rp++e++ +y ++vl+ +++d   ++ e+ ++s+++g+ 
  gi|242398683|ref|YP_002994107.1|  69 TVTWINVTGLHDInLIKKLGEPLGLHPLTLEDIVNTAQRPKIEEFPGYVYMVLKMIHYDLATNQIEMEHVSLIIGES 145
                                       689*******998789999999******************************************************* PP

                              CorA  79 flitvrreplealdevikrlk..deggkpkspgellyrlldeivdrlfellekleeeldeledeledstkkeilrel 153
                                       +++++++++ +++d v++r++  + + +  ++  l y+l+d++vd++f ++e++ +++++led++  + +  il+el
  gi|242398683|ref|YP_002994107.1| 146 YVVSFQEKEGDVFDPVRERIRasKGRIRSMKADYLAYALMDAVVDNYFLVVEHIGDQIEDLEDRVLADPNPTILQEL 222
                                       *********************99999999999********************************************* PP

                              CorA 154 aqlrrrlvklrralapnrevlkrllakaddkllddedkeylrdlldelerllemlealrerleslqdtyssllserl 230
                                        +l+r+l ++r+a++p+re + +l++ ++  l+ +e k ylrdl+d++ ++++m+e+ r+ l  ++d+y s++s r+
  gi|242398683|ref|YP_002994107.1| 223 HRLKRDLLTIRKAVWPLREEIGALIK-SESALIRAETKVYLRDLYDHIIQIIDMVETFRDILGGIHDLYLSNISIRM 298
                                       *********************88998.************************************************** PP

                              CorA 231 NrvmkvLTvltaiflPlTlitGiyGmNfkglPelewsygypfvlllglmallailllfwfkr 292
                                       N++mkvLT++++if+PlT+i+G+yGmNf+++Pel+w +gy++v  +g+m+++ai+++++f++
  gi|242398683|ref|YP_002994107.1| 299 NEIMKVLTIIATIFIPLTFIVGVYGMNFEYMPELNWRWGYFSV--WGVMIVIAIGMVIYFRK 358
                                       *******************************************..***************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       715  (0.0398795); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 2615.60
//
Query:       gi|242398684|ref|YP_002994108.1|  [L=143]
Description: Pyrimidine dimer DNA glycosylase [Thermococcus sibiricus MM 739]
Scores for complete 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   18.6   0.0      0.003   17.5   0.0    1.6  1  Pyr_excise  Pyrimidine dimer DNA glycosylase


Domain annotation for each model (and alignments):
>> Pyr_excise  Pyrimidine dimer DNA glycosylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   1.7e-07     0.003       1      85 [.       1      80 [.       1     101 [. 0.81

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.7e-07
                                      X-----S-GGGS-HHHHHHHHHHTHHHHHHHHH.-GGGS---SS--SSTTTTGGGTTBHHHHHHHHHHHHHHHHHTT-- CS
                        Pyr_excise  1 MtrinleliseLpdqhLlaeyrElprinalakk.ergngkipkhftlgtGHvtfFynkleyLrkrylllieEmlkRgyn 78
                                      M+++ l +++ L  + L+a +rE    +a++ + +rg    p+ +       +  +  l+ +  + +++++E ++Rgy+
  gi|242398684|ref|YP_002994108.1|  1 MRLWSL-HPQYLDAKGLVALWREGLLAKAVLEGkTRGYTAHPQLIRF-----KKQERPLDAINVYLQAVLQEAQRRGYH 73
                                      899976.79**************999988887735555555555555.....566788999****************** PP

                                      -S--S-- CS
                        Pyr_excise 79 vneeekd 85
                                      ++ ++ d
  gi|242398684|ref|YP_002994108.1| 74 FDSSKID 80
                                      9988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 920.20
//
Query:       gi|242398685|ref|YP_002994109.1|  [L=213]
Description: SAM-dependent methyltransferase, UbiE/COQ5 family [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-18   67.2   0.0    2.3e-18   66.6   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
    1.5e-12   48.1   0.0    2.4e-12   47.4   0.0    1.3  1  Methyltransf_25  Methyltransferase domain
    5.8e-11   42.5   0.0    7.8e-11   42.1   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
    3.3e-09   36.4   0.0    4.4e-09   36.0   0.0    1.3  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    1.4e-07   32.2   0.0      3e-07   31.1   0.0    1.6  1  Methyltransf_12  Methyltransferase domain
    1.6e-05   24.8   0.0    1.9e-05   24.5   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    6.4e-05   22.9   0.0    0.00011   22.2   0.0    1.5  2  Methyltransf_8   Hypothetical methyltransferase
    8.8e-05   22.2   0.0    0.00013   21.6   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 !   66.6   0.0     1e-21   2.3e-18       2      96 .]      44     128 ..      43     128 .. 0.95

  Alignments for each domain:
  == domain 1  score: 66.6 bits;  conditional E-value: 1e-21
                                       EET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHH CS
                   Methyltransf_11   2 dvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedpe 78 
                                       ++G+GtGr+a++l       +gv++sk m ++a+ek+      +e++++ ae+lpf+d+s D  ++  ++++v+dpe
  gi|242398685|ref|YP_002994109.1|  44 EIGVGTGRFAAPLG----IKLGVEPSKGMAEIAREKG------IEVIEGVAESLPFPDESLDYLLMVTTICFVDDPE 110
                                       79************....6789***********9888......5669****************************** PP

                                       HHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  79 kalkeiaRvLkpgGllvi 96 
                                       kal+e++RvLk gG l+i
  gi|242398685|ref|YP_002994109.1| 111 KALREAYRVLKHGGALII 128
                                       ***************996 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.4   0.0   1.1e-15   2.4e-12       3      97 .]      44     124 ..      43     124 .. 0.94

  Alignments for each domain:
  == domain 1  score: 47.4 bits;  conditional E-value: 1.1e-15
                                       EET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSH CS
                   Methyltransf_25   3 dlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsd 79 
                                       ++G GtGr+++ l  +      +gv++s++m e+are+       +e+++g ae+lpf+d+s D+ +++ ++++++d
  gi|242398685|ref|YP_002994109.1|  44 EIGVGTGRFAAPLGIK------LGVEPSKGMAEIAREKG------IEVIEGVAESLPFPDESLDYLLMVTTICFVDD 108
                                       79***********877......59**************9......***********************988999985 PP

                                       HHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  80 edlekalkeiarvLkpgG 97 
                                          ekal+e++rvLk gG
  gi|242398685|ref|YP_002994109.1| 109 --PEKALREAYRVLKHGG 124
                                       ..569************9 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   0.0   3.5e-14   7.8e-11       9     162 ..      25     173 ..      17     176 .. 0.85

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 3.5e-14
                   Methyltransf_23   9 lsdklerllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiaekakkaqkdqfdeqeaaepqgkfdl 85 
                                       +  +le + + l++ g+  +iG GtG+++  l  +     gv++s  + eia+++   + + + +++ ++p+++ d+
  gi|242398685|ref|YP_002994109.1|  25 YLSELEAIRKLLPKEGEGAEIGVGTGRFAAPLGIK----LGVEPSKGMAEIAREKGIEVIEGV-AESLPFPDESLDY 96 
                                       4444555555567999999***********99887....8*************6666666666.68999******** PP

                   Methyltransf_23  86 IvlrevlehvpdppellrqiatllkpgGylllseplaslkedrllldwlylvpagrhisffsarslkelleeaGlev 162
                                         +  +++ v+dp+++lr +++ lk gG l++  ++++++  + ++ ++      r  +ffs ++l ell + G++ 
  gi|242398685|ref|YP_002994109.1|  97 LLMVTTICFVDDPEKALREAYRVLKHGGALIIGFVDRNSPIGQEYERNKEKSVFYREARFFSTDELLELLGKVGFRK 173
                                       ***************************************9888888885544444889*****************86 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   0.0     2e-12   4.4e-09      98     151 ..      75     128 ..      59     175 .. 0.89

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 2e-12
                                       STEEEEE--TTT-TTS-T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEE CS
                   Ubie_methyltran  98 inieflqanaeeLpfeddsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvv 151
                                       + ie + + ae Lpf d+s D++ +   +  v D +kaL+eayrvlk GG+l++
  gi|242398685|ref|YP_002994109.1|  75 KGIEVIEGVAESLPFPDESLDYLLMVTTICFVDDPEKALREAYRVLKHGGALII 128
                                       4799**********************************************9975 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.0   1.3e-10     3e-07       2      99 .]      44     126 ..      43     126 .. 0.86

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 1.3e-10
                   Methyltransf_12   2 eiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhh 78 
                                       eiG GtG+++++l  k      +gv++s+ + e a+ek  + +       e  a++l   d+  s D+ ++  +++ 
  gi|242398685|ref|YP_002994109.1|  44 EIGVGTGRFAAPLGIK------LGVEPSKGMAEIAREKGIEVI-------EGVAESLPFPDE--SLDYLLMVTTICF 105
                                       9***************......**********77777766655.......566666555444..99*********** PP

                   Methyltransf_12  79 lkdirevldnirklLkpgGrl 99 
                                       ++d++++l++++++Lk gG l
  gi|242398685|ref|YP_002994109.1| 106 VDDPEKALREAYRVLKHGGAL 126
                                       *******************75 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   8.5e-09   1.9e-05      54     113 ..      75     132 ..      44     184 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 8.5e-09
                   Methyltransf_31  54 dnveFeqgdieeleklledekfDlilsnevlnaladpdkileeiervlkpggilliedpr 113
                                       + +e+ +g +e+l+  + de+ D++l   +++ + dp+k+l+e+ rvlk gg+l+i  ++
  gi|242398685|ref|YP_002994109.1|  75 KGIEVIEGVAESLP--FPDESLDYLLMVTTICFVDDPEKALREAYRVLKHGGALIIGFVD 132
                                       456799999999**..***************************************98776 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   4.8e-08   0.00011      77     187 ..      43     159 ..       8     184 .. 0.72
   2 ?   -0.9   0.0      0.55   1.2e+03     161     182 ..     154     175 ..     149     197 .. 0.71

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 4.8e-08
                                       EEES-TT-HHHHH--S-..EE...EEESS-SST..TEEES-TTS-S--TT-EEEEEEES--.-SS-HHHHHHHHHHH CS
                    Methyltransf_8  77 adlGcGeakiaeavrekekvr...sfdlvavne..rvvacdlakvPledesvdvavfclsl.mgtnladflkeanrv 147
                                       a++G G  + a   + k  v+    +   a ++  +v+      +P  des d  ++  ++  +++ ++ l+ea+rv
  gi|242398685|ref|YP_002994109.1|  43 AEIGVGTGRFAAPLGIKLGVEpskGMAEIAREKgiEVIEGVAESLPFPDESLDYLLMVTTIcFVDDPEKALREAYRV 119
                                       56666666666555555555311123333444411344444588*********88777665268999********** PP

                                       EEEEEEEEEEEEGGG-S-HHHHHHHHHCTTEEEEEEE--S CS
                    Methyltransf_8 148 lkvGGllkvaevksrfesvklfaraltklGfevkskdlsn 187
                                       lk GG l +  v    + ++ ++r+ +k  f  + +  s+
  gi|242398685|ref|YP_002994109.1| 120 LKHGGALIIGFVDRNSPIGQEYERNKEKSVFYREARFFST 159
                                       *********9999888888888888888777766665555 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.55
                                       GG-S-HHHHHHHHHCTTEEEEE CS
                    Methyltransf_8 161 srfesvklfaraltklGfevks 182
                                       +rf s + +++ l k+Gf   +
  gi|242398685|ref|YP_002994109.1| 154 ARFFSTDELLELLGKVGFRKFE 175
                                       7999999999999999997543 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   5.8e-08   0.00013       4     104 ..      29     122 ..      27     132 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 5.8e-08
                              MetW   4 feliaelikpgsrvldlGcGdGellellkeekqvdgrGleldeegvaecvakGlsviqgdldkdlenfedksfdyvv 80 
                                       +e+i +l++++ +  ++G G G +   l    +++  G+e ++     + +kG++vi+g +++ l  f+d+s+dy +
  gi|242398685|ref|YP_002994109.1|  29 LEAIRKLLPKEGEGAEIGVGTGRFAAPL----GIK-LGVEPSKGMAEIAREKGIEVIEGVAES-L-PFPDESLDYLL 98 
                                       6788889999999999999999988888....443.699999988888999*******98875.4.79********* PP

                              MetW  81 lsqtlqatrnpkevldellrigrr 104
                                       +  t+  + +p++ l+e  r+ ++
  gi|242398685|ref|YP_002994109.1|  99 MVTTICFVDDPEKALREAYRVLKH 122
                                       ******************999654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1442.97
//
Query:       gi|242398686|ref|YP_002994110.1|  [L=356]
Description: Fe-S oxidoreductase, [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      7e-12   46.0   0.1    1.1e-11   45.4   0.1    1.3  1  Radical_SAM  Radical SAM superfamily
  ------ inclusion threshold ------
       0.06   13.8   0.0       0.14   12.6   0.0    1.5  2  DUF4600      Domain of unknown function (DUF4600)
       0.11   12.6   0.0       0.27   11.4   0.0    1.6  1  Hydrolase_6  Haloacid dehalogenase-like hydrolase


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 !   45.4   0.1   1.9e-15   1.1e-11       5     166 ..      63     230 ..      59     231 .. 0.89

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 1.9e-15
                                       SEESS--TTTSCCTT.....HHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEE.SSTGGGSTTHHHHHHHHHHTC CS
                                       xxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   5 rgCnlrCsfCarpet.....vrregrgrslsveeileevkelkaekg.vkevilg.ggepllypdfvellerlakla 74 
                                       + C+++C++C++++t     +rr  +  +l  +e+ ++v e+ ++   +++++++  gep+l++++ ++++ l++l 
  gi|242398686|ref|YP_002994110.1|  63 KVCTYACVYCQIGRTlrmeiERRAFYDPELVFREVSAKVNEAIERGEeIDYITFVpDGEPTLDANLGKEIDLLRQL- 138
                                       67******************999****************999655559*******99*******************. PP

                                       CCTEEEEEEECSSCHG.HHHHHHHHHTT-SEEEEEEBSSSHH...HHHHHHTCTSHHHHHHHHHHHHHHTTSET..E CS
                                       xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxx..x RF
                       Radical_SAM  75 vpgiritvetngtlpd.eeklerllelgvdrvslgleaadde...kvlklmnrghtfeevlealeklreagikr..v 145
                                         gi++++ tn  l+   ++ e ll+  +d vsl ++a+++    k+ +++ +  ++ ++le++  +r+  ++   v
  gi|242398686|ref|YP_002994110.1| 139 --GIKLAILTNSSLIWrQDVREDLLK--LDFVSLKVDAVSEAlwrKIDRPH-KSLSLGKILEGMLEFRKE-FRGklV 209
                                       ..*************65555666666..99************999999999.77999************9.888888 PP

                                       EEEEEEBTTTSHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 146 vdrivglpGendeeleellel 166
                                       + ++++   e d+e+e + ++
  gi|242398686|ref|YP_002994110.1| 210 TETMLIDNVEYDDEFERIGDF 230
                                       888888888999999987666 PP

>> DUF4600  Domain of unknown function (DUF4600)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.0         3   1.8e+04      78      88 ..      78      88 ..      77      91 .. 0.84
   2 ?   12.6   0.0   2.3e-05      0.14      34      88 ..     291     346 ..     280     353 .. 0.91

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 3
                           DUF4600 78 lrleqEsKayh 88
                                      lr+e E +a++
  gi|242398686|ref|YP_002994110.1| 78 LRMEIERRAFY 88
                                      79999999998 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 2.3e-05
                           DUF4600  34 rgnpsdrlasirvleklteeelnqllkqLekekkslenqlkdlel.rleqEsKayh 88 
                                        gn +++l si +++ + e++++++l++ + + +++e+ ++d +l  le E+K ++
  gi|242398686|ref|YP_002994110.1| 291 TGNVEEDLLSITAVHPMREDAVKEFLRKANADWNIIEKLIRDNKLiELEYEGKKFY 346
                                       5788999**********************************998548******997 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   4.4e-05      0.27      23      57 ..     132     166 ..     126     177 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.4e-05
                                       HHHHHHTT-EEEEEE---SS-HHHHHHHHHHTT-- CS
                       Hydrolase_6  23 lnalraagkpvvllTNnsskseeeyakkleklgvd 57 
                                       ++ lr+ g+++++lTN+s   ++++ ++l kl++ 
  gi|242398686|ref|YP_002994110.1| 132 IDLLRQLGIKLAILTNSSLIWRQDVREDLLKLDFV 166
                                       789**************************999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.33s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 2052.14
//
Query:       gi|242398687|ref|YP_002994111.1|  [L=203]
Description: Iron-molybdenum cofactor-binding protein [Thermococcus sibiricus MM 739]
Scores for complete 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-23   81.2   0.2    6.7e-23   80.8   0.2    1.1  1  Nitro_FeMo-Co   Dinitrogenase iron-molybdenum cofactor
  ------ inclusion threshold ------
        1.3    9.2  14.3       0.38   10.9  10.2    1.9  2  Keratin_2_head  Keratin type II head


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 !   80.8   0.2   7.4e-27   6.7e-23       2      94 ..      13     107 ..      12     108 .. 0.97

  Alignments for each domain:
  == domain 1  score: 80.8 bits;  conditional E-value: 7.4e-27
                                       TSCB-STCCC-SEEEEEEESSSCEEEEEEE.E.GCCCTSSCSSTHHHHHHHHTT-SEEEESSSCHHHHHHHCTTTSE CS
                     Nitro_FeMo-Co   2 gsrvdqhFGrapyFaiyeveegevkivenr.veeaadaegggggklaqllaeegvdvvivgkiGpralakleaagie 77 
                                       +++v + F+rap+F+i++v+e++++i e+   ++ a a+gg+g  ++q+l +egv+++i+ ++Gp+al  ++aagi+
  gi|242398687|ref|YP_002994111.1|  13 NDTVAPVFARAPAFYIADVDENGNMISEKViQNTGAMAGGGAGPMAVQTLINEGVEAIIAPQVGPNALGTIQAAGIK 89 
                                       689*********************9999999999******************************************* PP

                                       EEES.-SSBHHHHHHHHH CS
                     Nitro_FeMo-Co  78 vykg.aggtveealkevl 94 
                                        y++ ag++veea+k+v+
  gi|242398687|ref|YP_002994111.1|  90 LYQVaAGTPVEEAIKAVV 107
                                       ***99**********986 PP

>> Keratin_2_head  Keratin type II head
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1       0.1     9e+02      97     102 ..      50      55 ..      21     111 .. 0.64
   2 ?   10.9  10.2   4.2e-05      0.38      78     111 ..     148     181 ..     137     192 .. 0.57

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.1
                    Keratin_2_head  97 agggvG 102
                                       aggg+G
  gi|242398687|ref|YP_002994111.1|  50 AGGGAG 55 
                                       222222 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 4.2e-05
                    Keratin_2_head  78 gggggfglGfggGvglgfgagggvGggfGggggl 111
                                       g+g g g+G ggG g g g+g+g+Ggg G g++l
  gi|242398687|ref|YP_002994111.1| 148 GYGPGWGWGRGGGWGRGRGFGRGMGGGRGWGARL 181
                                       4455555555555555555555555555555533 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); 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: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1420.23
//
Query:       gi|242398688|ref|YP_002994112.1|  [L=68]
Description: hypothetical protein TSIB_0699 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.33s 00:00:00.83 Elapsed: 00:00:00.55
# Mc/sec: 374.67
//
Query:       gi|242398689|ref|YP_002994113.1|  [L=146]
Description: Iron-molybdenum cofactor-binding protein [Thermococcus sibiricus MM 739]
Scores for complete 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   85.5   0.1    3.1e-24   85.1   0.1    1.2  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 !   85.1   0.1   1.7e-28   3.1e-24       2      94 ..      13     106 ..      12     107 .. 0.95

  Alignments for each domain:
  == domain 1  score: 85.1 bits;  conditional E-value: 1.7e-28
                                       TSCB-STCCC-SEEEEEEESSSCEEEEEEEE.GCCCTSSCSSTHHHHHHHHTT-SEEEESSSCHHHHHHHCTTTSEE CS
                     Nitro_FeMo-Co   2 gsrvdqhFGrapyFaiyeveegevkivenrveeaadaegggggklaqllaeegvdvvivgkiGpralakleaagiev 78 
                                       ++ v+qhFGr+p+F+i++ve+ge+k v+   +++a+++ g+g ++aq+  +egv+vvi+g+ Gp+++  l+aagi++
  gi|242398689|ref|YP_002994113.1|  13 DDFVNQHFGRTPTFTIVDVENGEIKNVKIVLNPSASSPRGAGVQAAQFCINEGVEVVIAGQFGPNSAGVLQAAGIRM 89 
                                       678*****************9998888888899******************************************** PP

                                       EES.-SSBHHHHHHHHH CS
                     Nitro_FeMo-Co  79 ykg.aggtveealkevl 94 
                                       +++ a  tv+ea++ +l
  gi|242398689|ref|YP_002994113.1|  90 ISApATMTVREAVETFL 106
                                       *************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        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 0.34s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 853.45
//
Query:       gi|242398690|ref|YP_002994114.1|  [L=305]
Description: hypothetical protein TSIB_0701 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.28s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1853.08
//
Query:       gi|242398691|ref|YP_002994115.1|  [L=273]
Description: Hydrolase, metallo-beta-lactamase superfamily [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.4e-19   69.0   0.9      2e-18   67.1   0.6    1.9  2  Lactamase_B    Metallo-beta-lactamase superfamily
    5.3e-12   45.7   0.0    1.1e-11   44.7   0.0    1.5  2  Lactamase_B_2  Beta-lactamase superfamily domain
    3.8e-05   23.2   0.0    5.1e-05   22.8   0.0    1.2  1  Lactamase_B_6  Metallo-beta-lactamase superfamily domain
    0.00023   21.1   0.0    0.00041   20.3   0.0    1.4  1  Lactamase_B_3  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.1   0.6   4.4e-22     2e-18       6     123 ..      22     148 ..      19     192 .. 0.87
   2 ?    0.0   0.0      0.16   7.3e+02     164     197 .]     209     242 ..     169     242 .. 0.78

  Alignments for each domain:
  == domain 1  score: 67.1 bits;  conditional E-value: 4.4e-22
                                       SEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCC CS
                       Lactamase_B   6 vnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapal 82 
                                       ++s+l+e++g++iL+D+G+++   +    ++al + p++vd ++lTH+H+DH+Ggl+++ +a++  + ++a+ +  l
  gi|242398691|ref|YP_002994115.1|  22 GFSVLVEHKGKNILVDAGSDGKVLLHN--IKALNISPEEVDVIFLTHGHYDHTGGLEEFLKARKSSIDIYAHPDVFL 96 
                                       789********************9995..9*********************************************** PP

                                       HCHHHHHHHHHCCHH...........TTCHCGCCEEEEETTTEECCCTEEEE CS
                       Lactamase_B  83 fmeeaddaasrkgll...........lagvsadkpdvdeeeldgnaggrral 123
                                       ++ ++++ +   g++             +  ++++ +++e++++++ +rr++
  gi|242398691|ref|YP_002994115.1|  97 RRIALKPKRREIGIPfsqehlekigaNFILKEKPVRIFDEIYTSGEIERRTW 148
                                       *****99999999999999999998866666666666666666666666655 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.16
                                       TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEESS CS
                       Lactamase_B 164 lrgaevrdpsdaekyldsllklaglkaevlvpgH 197
                                       l g++ + ++ +  + d+++ +++  +e+l+pgH
  gi|242398691|ref|YP_002994115.1| 209 LVGGFHLSGAKKNILEDAVRGIRTFGVEKLYPGH 242
                                       5566666677778888999999999999999999 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 !   44.7   0.0   2.4e-15   1.1e-11       2     131 ..      33     157 ..      32     162 .. 0.66
   2 ?   -3.2   0.0       1.1     5e+03     182     200 ..     224     242 ..     213     243 .. 0.75

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 2.4e-15
                                       EEEES--TTHHHHHTCGGS--S.SS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHH.HHCCTTCGH CS
                     Lactamase_B_2   2 riLiDagpdlrqqalralqPve.lrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvl.avleanfvy 76 
                                       +iL+Dag d  +  + +l++ + l  +++++d+++lth+HyDH+ gl  + + r++++++ya+++v  + ++ + ++
  gi|242398691|ref|YP_002994115.1|  33 NILVDAGSD--G--KVLLHNIKaLNISPEEVDVIFLTHGHYDHTGGLEEFLKARKSSIDIYAHPDVFlRRIALKPKR 105
                                       9********..2..333455565788999***********************88888*****998851344444333 PP

                                       HHCHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEE CS
                     Lactamase_B_2  77 laleeepavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlrie 131
                                          + + + + h  ++g +f l++    ++++    +sg+ ++r+  +++G++i 
  gi|242398691|ref|YP_002994115.1| 106 REIGIP-FSQEHLEKIGANFILKEK--PVRIFDEIYTSGEIERRTWDRAVGYIIS 157
                                       333333.444444445566666533..3666666666666666666666666665 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.1
                                       TSHHHHCTTSSSSEEEEES CS
                     Lactamase_B_2 182 eeaveaaadlgakrlvliH 200
                                       e+av+ ++  g+++l++ H
  gi|242398691|ref|YP_002994115.1| 224 EDAVRGIRTFGVEKLYPGH 242
                                       6777777888888888777 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 !   22.8   0.0   1.1e-08   5.1e-05       2      83 ..      27     101 ..      26     139 .. 0.72

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.1e-08
                     Lactamase_B_6   2 LeldnvkiLlDvGwdeskvslesalkelekviptvdliLLshatlehlGayallyakfksklllnipvyatlpvvkL 78 
                                       +e  + +iL+D G+d++ v   + +k l+   ++vd+i L+h   +h G++      f +   ++i +ya  +v  L
  gi|242398691|ref|YP_002994115.1|  27 VEHKGKNILVDAGSDGK-VL-LHNIKALNISPEEVDVIFLTHGHYDHTGGLEE----FLKARKSSIDIYAHPDV-FL 96 
                                       6667889********97.43.46899999999******************865....555567899***96555.45 PP

                     Lactamase_B_6  79 Grvsl 83 
                                        r++l
  gi|242398691|ref|YP_002994115.1|  97 RRIAL 101
                                       66555 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   9.1e-08   0.00041       9      50 ..      24      72 ..      20      93 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 9.1e-08
                     Lactamase_B_3  9 sflletagarilvDPf.......kanlgyeppa......eeaDlvlisqaledHa 50
                                      s+l+e +g++ilvD +       +      + +      ee+D++ +++++ dH 
  gi|242398691|ref|YP_002994115.1| 24 SVLVEHKGKNILVDAGsdgkvllH------NIKalnispEEVDVIFLTHGHYDHT 72
                                      899************955544432......444455555***************5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       234  (0.0130515); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1938.21
//
Query:       gi|242398692|ref|YP_002994116.1|  [L=263]
Description: short-chain alcohol dehydrogenase [Thermococcus sibiricus MM 739]
Scores for complete 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-49  166.4   0.0    1.1e-48  165.9   0.0    1.1  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
    5.3e-35  120.6   0.0    6.4e-35  120.4   0.0    1.1  1  adh_short        short chain dehydrogenase
    2.3e-06   27.7   0.0      4e-06   26.9   0.0    1.4  1  KR               KR domain
    1.2e-05   25.3   0.0    1.6e-05   24.9   0.0    1.2  1  NAD_binding_10   NAD(P)H-binding
    0.00012   22.0   0.0    0.00025   21.0   0.0    1.4  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
     0.0041   16.5   0.1      0.039   13.3   0.1    2.0  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family
  ------ inclusion threshold ------
      0.015   15.2   0.0      0.034   14.1   0.0    1.5  1  ADH_zinc_N       Zinc-binding dehydrogenase
      0.016   15.9   0.0       0.15   12.8   0.0    2.1  2  Methyltransf_25  Methyltransferase domain
      0.017   15.7   0.0       0.19   12.4   0.0    2.2  2  Methyltransf_11  Methyltransferase domain
      0.018   15.0   0.0      0.032   14.2   0.0    1.3  1  Glyco_tran_WecB  Glycosyl transferase WecB/TagA/CpsF family
      0.031   13.4   0.1      0.047   12.8   0.1    1.2  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
      0.034   14.7   0.2       0.13   12.9   0.1    1.9  2  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
      0.047   13.3   0.0      0.073   12.6   0.0    1.2  1  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
      0.071   12.5   0.0       0.12   11.7   0.0    1.3  1  DUF1776          Fungal family of unknown function (DUF1776)
       0.11   12.3   0.1        1.3    8.7   0.0    2.3  2  QRPTase_C        Quinolinate phosphoribosyl transferase, C-te
       0.12   11.9   0.0        1.9    8.0   0.0    2.2  2  NmrA             NmrA-like family


Domain annotation for each model (and alignments):
>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.9   0.0   9.4e-52   1.1e-48       4     232 ..      18     257 ..      14     258 .. 0.92

  Alignments for each domain:
  == domain 1  score: 165.9 bits;  conditional E-value: 9.4e-52
                                       TSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSEE..EE--TTSHHHHHHHHHHHHHHHSSEEEEEE-- CS
                      adh_short_C2   4 sgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgaev..lecDVtdeeqvealveevvekfgklDilvnna 77 
                                       +gIG+++A+ la++Ga+v+l  +nee+ kk+ e+++ee + +v  + +D  ++e++e++v+e++ ++g+ D+++ + 
  gi|242398692|ref|YP_002994116.1|  18 KGIGFGVARVLARAGADVILLSRNEENlKKAREKIKEESNVDVsyIIADLMKREELEKTVKELQ-NIGEPDMFFFST 93 
                                       8**************************999999*****9999777*****************87.67********** PP

                                       ---EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC..CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHH CS
                      adh_short_C2  78 giapklkgpfletsreefdraldvnlyslfllakaalplmkeg..gsivnlssvgaervvpnynaygaaKaalealt 152
                                       g  ++  g f+e+s e+++ a++  ly +++l+ka++p+m+++  g+iv  +s + +  +pn +  ++++ ++ +l+
  gi|242398692|ref|YP_002994116.1|  94 GGPKP--GYFMEMSMEDWEGAVKLLLYPAVYLTKALVPAMEKKgfGRIVYSTSGAIKEPIPNIALSNVVRISMAGLV 168
                                       *****..*******************************988877********************************* PP

                                       HHHHHHHGGGTEEEEEEEE--BHCTGGGGSTT.........HHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGT CS
                      adh_short_C2 153 rylAvelgpkgiRvNavspgpikTlaasgikg.........fdelleelearaplgrlgtpeevaeaalfLasdeas 220
                                       r+lA+elgpkgi+vN + pg+i+T+ + ++++          +e l+e ++ +plgrlg+pee++ +++fLasd+ s
  gi|242398692|ref|YP_002994116.1| 169 RTLAKELGPKGITVNGIMPGIIRTDRMVQLAKdrakregksVEEALQEYAKPIPLGRLGEPEEIGYLVAFLASDLGS 245
                                       ************************8755554434434444456688999999************************* PP

                                       T--SEEEEESTT CS
                      adh_short_C2 221 yitGqtlvvDgG 232
                                       yi+G+ + vDgG
  gi|242398692|ref|YP_002994116.1| 246 YINGAMIPVDGG 257
                                       ***********9 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.4   0.0   5.7e-38   6.4e-35       3     193 ..      11     201 ..       9     203 .. 0.97

  Alignments for each domain:
  == domain 1  score: 120.4 bits;  conditional E-value: 5.7e-38
                                       EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT.TSEEEEEE-TTTSHHHHHHHHHHHHHHHSSE CS
                         adh_short   3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkee.gakalaiqvDvtdreevealvekavkklgkl 78 
                                       ++ t  s+GIG  +a+ la++Ga+v++++r+ee+l+++ +++kee + ++ +i +D+ +ree+e++v++  +++g+ 
  gi|242398692|ref|YP_002994116.1|  11 AFTTASSKGIGFGVARVLARAGADVILLSRNEENLKKAREKIKEEsNVDVSYIIADLMKREELEKTVKEL-QNIGEP 86 
                                       67899****************************************99**********************9.99**** PP

                                       SEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHH CS
                         adh_short  79 dvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaa 155
                                       d++   +G  ++g f e+s e+we  +++ l  ++ lt+a++pam k+  GrIv  +S a k+p ++ a        
  gi|242398692|ref|YP_002994116.1|  87 DMFFFSTGGPKPGYFMEMSMEDWEGAVKLLLYPAVYLTKALVPAMEKKGFGRIVYSTSGAIKEPIPNIALSNVVRIS 163
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHHCTH CS
                         adh_short 156 vagltrslakelaptgirvnavaPGlvdTdmakelrek 193
                                       +agl+r+lakel p+gi+vn+++PG+++Td + +l ++
  gi|242398692|ref|YP_002994116.1| 164 MAGLVRTLAKELGPKGITVNGIMPGIIRTDRMVQLAKD 201
                                       *****************************988777665 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0   3.6e-09     4e-06      10     109 ..      18     113 ..      13     148 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 3.6e-09
                                       SHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS---EEE CS
                                KR  10 GgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeeppikGvi 86 
                                        g+G  +ar la+ ga  ++llsR++++ ++++++i+  e+++++v+++ aD+ +++++e++++e+++ ++     +
  gi|242398692|ref|YP_002994116.1|  18 KGIGFGVARVLARAGAD-VILLSRNEENLKKAREKIK--EESNVDVSYIIADLMKREELEKTVKELQNIGE-PDMFF 90 
                                       699************95.7899***877777777777..7889***********************97664.35677 PP

                                       E---------TTT--HHHHHHHH CS
                                KR  87 haAgvlrdklleemtaedleqvl 109
                                        + g  + + ++em++ed+e ++
  gi|242398692|ref|YP_002994116.1|  91 FSTGGPKPGYFMEMSMEDWEGAV 113
                                       78888888888888888887665 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 !   24.9   0.0   1.4e-08   1.6e-05       6     107 ..      20     153 ..      16     174 .. 0.79

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1.4e-08
                                       HHHHHHHHHHHC-T-EEEEEETTHHHCH....HHHCTTTCEE..EE--TT-CCHHHHHHT......T-SEEEES--- CS
                    NAD_binding_10   6 vGrllvkellargghevtalvRnpekla....eleaeeglev..vegdvtdvedlaealk......gadaVvsalgg 70 
                                       +G  +++ l+++ g +v +l Rn+e l+    ++++e++++v  + +d+++ e+l++++k        d  ++++gg
  gi|242398692|ref|YP_002994116.1|  20 IGFGVARVLARA-GADVILLSRNEENLKkareKIKEESNVDVsyIIADLMKREELEKTVKelqnigEPDMFFFSTGG 95 
                                       555667777777.6*********999973333455666665533889*************88888667999999988 PP

                                       TCC......HHHH.................HHHHHHHHHHCT--EEEEEEETTTTSGCGC CS
                    NAD_binding_10  71 ggk......deeg.................aknivdaakeagvkRfvlvsaigvgdevpg 107
                                        +          +                 +k++v a++++g  R+v+ ++  +++ +p+
  gi|242398692|ref|YP_002994116.1|  96 PKPgyfmemS--MedwegavklllypavylTKALVPAMEKKGFGRIVYSTSGAIKEPIPN 153
                                       8877976540..155677899999999*********************999998876654 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 !   21.0   0.0   2.2e-07   0.00025      10      65 ..      20      78 ..      19      87 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.2e-07
                                      CHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTT...TTSS-HHHHCCCHH CS
                           3HCDH_N 10 mGagiaavfasagleVvlvdiseealekalekieksleklve...kgklkeeeveaala 65
                                      +G g+a v+a+ag +V l+ ++ee l+ka+eki+++ +  v+   +  +k+ee e++++
  gi|242398692|ref|YP_002994116.1| 20 IGFGVARVLARAGADVILLSRNEENLKKAREKIKEESNVDVSyiiADLMKREELEKTVK 78
                                      799*******************************9655443311134444555555554 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.1   3.4e-05     0.039      61     115 ..      20      75 ..       6      84 .. 0.81
   2 ?    0.8   0.0      0.22   2.5e+02      78     108 ..     189     219 ..     163     225 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.4e-05
                                       HHHHHHHHHHHHH.EEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T CS
                   Ubie_methyltran  61 lafklsdsvgekg.kvvvlDinenmLkvgekklkeegkinieflqanaeeLpfedd 115
                                       + f +++ + + g +v++l  ne+ Lk +++k+kee+ +++ ++ a+ ++ ++ ++
  gi|242398692|ref|YP_002994116.1|  20 IGFGVARVLARAGaDVILLSRNEENLKKAREKIKEESNVDVSYIIADLMKREELEK 75 
                                       556666665555558999****************************9998877654 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.22
                                       EES-HHHHHHHHHHHHHHTSSTEEEEE--TT CS
                   Ubie_methyltran  78 lDinenmLkvgekklkeegkinieflqanae 108
                                       +   + m++ +++++k+egk+  e lq  a+
  gi|242398692|ref|YP_002994116.1| 189 IIRTDRMVQLAKDRAKREGKSVEEALQEYAK 219
                                       445678*************997777776665 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0     3e-05     0.034       1      67 [.      19      94 ..      19      98 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3e-05
                                      HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH.T......TESEEEET..TTCHHHHHHHHHTTTSSEEEEEESSC CS
                        ADH_zinc_N  1 gvGlaavqlAkalGaeviavdsseeklelakk.l......Gadeviny..keadlverikeltggegvdvvfecvG 67
                                      g+G  +  +++ +Ga vi  +++ee+l++a++ +       + ++i    k+++l++ +kel + + +d  f  +G
  gi|242398692|ref|YP_002994116.1| 19 GIGFGVARVLARAGADVILLSRNEENLKKAREkIkeesnvDVSYIIADlmKREELEKTVKELQNIGEPDMFFFSTG 94
                                      899***************************9955554444444444449844478888888877447777776666 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00013      0.15       7      58 ..      21      70 ..      17      80 .. 0.78
   2 ?    0.5   0.0      0.92     1e+03      30      49 ..     192     211 ..     167     225 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00013
                                      TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHH.TTTTEEEEESBCCGB CS
                   Methyltransf_25  7 GtGrltlalakrlgkakvtgvDiseemleaareraee.eglnvefvqgdaedl 58
                                      G G +++ la++ g a+v+ +  +ee l++are+++e ++++v+++ +d+ + 
  gi|242398692|ref|YP_002994116.1| 21 GFG-VARVLARA-G-ADVILLSRNEENLKKAREKIKEeSNVDVSYIIADLMKR 70
                                      444.56677777.5.********************995556*******99654 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.92
                                       SHHHHHHHHHHHHHTTTTEE CS
                   Methyltransf_25  30 seemleaareraeeeglnve 49 
                                       +++m++ a+ ra++eg +ve
  gi|242398692|ref|YP_002994116.1| 192 TDRMVQLAKDRAKREGKSVE 211
                                       57899******999987665 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00017      0.19      10      54 ..      24      69 ..      17      79 .. 0.86
   2 ?    0.9   0.0      0.66   7.4e+02      26      44 ..     191     210 ..     165     225 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00017
                                      HHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCC CS
                   Methyltransf_11 10 laealakrgarvvgvDlskemlklakekaseegl.kvefvvadaek 54
                                      +a+ la++ga+v+ +  ++e lk a+ek++ee +  v+++ ad+ k
  gi|242398692|ref|YP_002994116.1| 24 VARVLARAGADVILLSRNEENLKKAREKIKEESNvDVSYIIADLMK 69
                                      467788999************************9999999999765 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.66
                                       S-HHHHHHHHHHCCHHT-.E CS
                   Methyltransf_11  26 lskemlklakekaseegl.k 44 
                                        +++m++lak++a++eg   
  gi|242398692|ref|YP_002994116.1| 191 RTDRMVQLAKDRAKREGKsV 210
                                       5679999***9999999732 PP

>> Glyco_tran_WecB  Glycosyl transferase WecB/TagA/CpsF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   2.9e-05     0.032      40     118 ..      28     107 ..      19     117 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.9e-05
                   Glyco_tran_WecB  40 aeeeglrvfllGgkpevlekaaerlrekypglriagthdgy.keeeeeaiieainas.kpdlllvglGapkqEkwia 114
                                       ++++g  v ll  ++e l+ka+e+++e+  ++++  + +   k+ee e+ ++++++  +pd+ + + G pk  ++++
  gi|242398692|ref|YP_002994116.1|  28 LARAGADVILLSRNEENLKKAREKIKEE-SNVDVSYIIADLmKREELEKTVKELQNIgEPDMFFFSTGGPKPGYFME 103
                                       4555899*********************.599999999997778999999999999878************999998 PP

                   Glyco_tran_WecB 115 rlke 118
                                          e
  gi|242398692|ref|YP_002994116.1| 104 MSME 107
                                       6655 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   4.2e-05     0.047      15      76 ..      24      80 ..      14      88 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.2e-05
                                      HHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT.. CS
                   Polysacc_synt_2 15 vrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleel 76
                                      v ++l++  + +ill+r+E +l + +++++e   ++  +v++  +i+d+ ++e+lek+++el
  gi|242398692|ref|YP_002994116.1| 24 VARVLARAGADVILLSRNEENLKKAREKIKE---ES--NVDVSYIIADLMKREELEKTVKEL 80
                                      45788888899***************99843...32..3466689************99965 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 ?   12.9   0.1   0.00011      0.13      10      47 ..      20      53 ..      19      87 .. 0.77
   2 ?   -1.5   0.0       3.4   3.9e+03      22      58 ..     179     213 ..     167     220 .. 0.40

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
                                      HHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC CS
                     F420_oxidored 10 mgealasgllaagaqpheivvansrnpekaeelaeelg 47
                                      +g+++a+ l++ag    ++++  srn+e +++++e+++
  gi|242398692|ref|YP_002994116.1| 20 IGFGVARVLARAG---ADVILL-SRNEENLKKAREKIK 53
                                      799**********...****66.**********99987 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.4
                                       TS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHH CS
                     F420_oxidored  22 gaqpheivvansrnpekaeelaeelgvkvtavdneea 58 
                                       g + + i+ +  r+   ++ ++++++   ++++ eea
  gi|242398692|ref|YP_002994116.1| 179 GITVNGIMPGIIRTDRMVQLAKDRAK--REGKSVEEA 213
                                       44444444333333333322222222..222233333 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   6.5e-05     0.073      11      97 ..      20     106 ..      19     119 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.5e-05
                                       THHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS--TTHHHHHHHHCHTTTEEEES-HHHHHHC-SEEEE----- CS
                    UDPG_MGDP_dh_N  11 vGlvtaavlaeighevigvDideekvdklnsgkipiyepgLeelvkkavesgrlsfttdvekaveeadvifiaVgTP 87 
                                       +G   a vla++g +vi++  +ee  +k +++  +  + + + ++++ ++ ++l+ t +  +++ e d++f + g P
  gi|242398692|ref|YP_002994116.1|  20 IGFGVARVLARAGADVILLSRNEENLKKAREKIKEESNVDVSYIIADLMKREELEKTVKELQNIGEPDMFFFSTGGP 96 
                                       6888899********************************************************************99 PP

                                       B-TTTTCB-T CS
                    UDPG_MGDP_dh_N  88 skkkgkaaDl 97 
                                            +++ +
  gi|242398692|ref|YP_002994116.1|  97 KPGYFMEMSM 106
                                       8764444445 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 ?   11.7   0.0   0.00011      0.12     108     202 ..     101     192 ..      91     216 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00011
                           DUF1776 108 ietiplsswaselnerllspiltlqallplltsrakqkakiivvnpsissslnlpfhapEalvssalsalfevLkre 184
                                       + +++++ w+ +++  l   + +++al+p +++   +    iv+++s   +  +p+ a+  +v  ++  l+++L++e
  gi|242398692|ref|YP_002994116.1| 101 FMEMSMEDWEGAVKLLLYPAVYLTKALVPAMEK---KGFGRIVYSTSGAIKEPIPNIALSNVVRISMAGLVRTLAKE 174
                                       5678899999988855555559999*******8...667777888888888899*********************** PP

                           DUF1776 185 lrphnidvtqikLGnldl 202
                                       l+p++i v  i  G++  
  gi|242398692|ref|YP_002994116.1| 175 LGPKGITVNGIMPGIIRT 192
                                       ********9999998865 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 ?    8.7   0.0    0.0012       1.3      90     132 ..      49      92 ..      25      99 .. 0.75
   2 ?    0.9   0.0      0.31   3.5e+02     122     158 ..     133     168 ..     120     174 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0012
                                       HHHHHHHHHHT-SEEEEES--HHHHHHHHHHHHHHSTT.SEEEE CS
                         QRPTase_C  90 leeleevleaeadiimLDnfsveelkkaveelkeknkr.vliev 132
                                        e+++e  ++ ++ i  D ++ eel+k+v+el+++ +  +  ++
  gi|242398692|ref|YP_002994116.1|  49 REKIKEESNVDVSYIIADLMKREELEKTVKELQNIGEPdMFFFS 92 
                                       34555555577999******************887644355555 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.31
                                       HHHSTTSEEEEESS--TTTHHHHHCTT-SEEEECHHC CS
                         QRPTase_C 122 keknkrvlievSGgvtlenveeyaksgvdvisvgalt 158
                                       k+  +r++ + SG ++ e + ++a s+v +is++ l+
  gi|242398692|ref|YP_002994116.1| 133 KKGFGRIVYSTSGAIK-EPIPNIALSNVVRISMAGLV 168
                                       4445669999999996.689***********998665 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0    0.0017       1.9      10      65 ..      20      80 ..      15      92 .. 0.90
   2 ?    1.7   0.0      0.14   1.6e+02      83     107 ..     125     149 ..     119     260 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0017
                                      HHHHHHHHHHHHT-EEEEEES-S.....-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT- CS
                              NmrA 10 qGksvvrallkaghkvralvRdt.....kselakslkeaGvelvkgdlddkeslvealkgv 65
                                      +G  v+r+l++ag +v  l R++      +e++k+ ++  v  + +dl  +e l++ +k+ 
  gi|242398692|ref|YP_002994116.1| 20 IGFGVARVLARAGADVILLSRNEenlkkAREKIKEESNVDVSYIIADLMKREELEKTVKEL 80
                                      67889******************9988778888888899999999**********999976 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.14
                                       HHHHHHHHHHS-SEEEEEE---GG. CS
                              NmrA  83 kklvdAakeaGvkhfiySslgddnd 107
                                       k+lv A  + G  +++yS+ g+ ++
  gi|242398692|ref|YP_002994116.1| 125 KALVPAMEKKGFGRIVYSTSGAIKE 149
                                       7899999999999999998887664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1087  (0.060628); expected 358.6 (0.02)
Passed bias filter:                      920  (0.0513135); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); 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: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.51
# Mc/sec: 1560.55
//
Query:       gi|242398693|ref|YP_002994117.1|  [L=59]
Description: hypothetical protein TSIB_0704 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); 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: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 429.44
//
Query:       gi|242398694|ref|YP_002994118.1|  [L=192]
Description: transcription regulator, YpuH-like family [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-35  122.4   2.8      3e-35  121.2   1.0    1.9  2  SMC_ScpB        Segregation and condensation complex subunit 
     0.0005   19.9   0.9      0.009   15.9   0.1    2.5  2  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0014   18.8   0.2       0.12   12.6   0.1    2.4  2  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
     0.0032   17.0   0.1       0.76    9.4   0.0    2.6  2  HTH_24          Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.013   15.4   0.1       0.74    9.7   0.1    2.5  2  HTH_5           Bacterial regulatory protein, arsR family
      0.015   15.8   0.3       0.58   10.7   0.1    2.5  2  HTH_27          Winged helix DNA-binding domain
      0.035   14.4   0.0        4.4    7.6   0.0    2.9  3  DUF4777         Domain of unknown function (DUF4777)
      0.047   13.6   0.2          1    9.4   0.1    2.6  2  MarR            MarR family
      0.086   12.6   0.0        1.4    8.8   0.0    2.2  2  LexA_DNA_bind   LexA DNA binding domain
       0.13   12.4   0.0          2    8.5   0.0    2.2  2  HTH_20          Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> SMC_ScpB  Segregation and condensation complex subunit ScpB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.2   1.0   1.7e-38     3e-35       2     153 ..      11     157 ..      10     164 .. 0.96
   2 ?    1.1   0.0      0.15   2.6e+02      54      78 ..     164     188 ..     161     191 .. 0.83

  Alignments for each domain:
  == domain 1  score: 121.2 bits;  conditional E-value: 1.7e-38
                          SMC_ScpB   2 iiEAiLfvageplsleeLakilels.keeveealeeLkeeyeeedrglelvev.aggyrlvtkpelaevvkklvkek 76 
                                        +E++Lfv+g+p+s++e++k+l+++  + +e+++e +++ey+e+++++e+v+v +++y +++k+e+++ v +l+++ 
  gi|242398694|ref|YP_002994118.1|  11 LVESALFVSGRPISVKEISKALGIKsLDYIEKLIELIAAEYAERNSAIEIVRVlGDKYVMQVKQEYSQRVIQLMPR- 86 
                                       79*********************9989*************************999*********************. PP

                          SMC_ScpB  77 kktrLsqaaletLaiIaykqpvtraeieeiRGvnsdsvvrtLlerglieekgrkeepgrpilYgtTekFleyfglks 153
                                         ++L + +l+tLa+Iay qp+ ++++ ++RG++++++v++Lle+gl+  +      +r+ ++gtT+kF e +g  +
  gi|242398694|ref|YP_002994118.1|  87 --PDLRTGELKTLALIAYLQPIEQSKLVNLRGSQVYEHVKRLLEMGLVYAEP----YERTKILGTTQKFAELYGFPE 157
                                       ..9************************************************9....6799***********999765 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.15
                          SMC_ScpB  54 aggyrlvtkpelaevvkklvkekkk 78 
                                       ++ ++ v+++e++++++k+ kek++
  gi|242398694|ref|YP_002994118.1| 164 KEAFKKVVHAEYSDLISKIEKEKEN 188
                                       67899999**********9999654 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1     0.083   1.5e+02      19      37 ..      19      37 ..       2      76 .. 0.75
   2 !   15.9   0.1     5e-06     0.009      29      59 ..     109     139 ..     103     148 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.083
                                      HHCCCHHCHHCCCTTSSCH CS
                              TrmB 19 klgpatadeiaeelgvprs 37
                                      +  p +++ei+++lg+   
  gi|242398694|ref|YP_002994118.1| 19 SGRPISVKEISKALGIKSL 37
                                      667889999***9999765 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 5e-06
                                       CCCTTSSCHCHHHHHHHHHHCTSEEEESSTT CS
                              TrmB  29 aeelgvprskvYevLrsLedkGlVerekgrp 59 
                                       ++ +++  s+vYe +++L+++GlV+ e+ ++
  gi|242398694|ref|YP_002994118.1| 109 SKLVNLRGSQVYEHVKRLLEMGLVYAEPYER 139
                                       56789999*****************998554 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.036        64      20      36 ..      20      36 ..      16      54 .. 0.83
   2 !   12.6   0.1   6.7e-05      0.12      29      57 ..     109     137 ..     101     139 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.036
                                      HSSB-HHHHHHHHTS-H CS
                    Fe_dep_repress 20 kkvvktkdlaerLnvsp 36
                                      + ++++k+++++L+++ 
  gi|242398694|ref|YP_002994118.1| 20 GRPISVKEISKALGIKS 36
                                      56899*********985 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 6.7e-05
                                       HHHHTS-HHHHHHHHHHHHHTTSEEEETT CS
                    Fe_dep_repress  29 aerLnvspssVsemlkkLekdGyveyeky 57 
                                       ++  n ++s V e +k+L ++G+v  e+y
  gi|242398694|ref|YP_002994118.1| 109 SKLVNLRGSQVYEHVKRLLEMGLVYAEPY 137
                                       778899*********************99 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.011        19      18      29 ..      23      34 ..      15      36 .. 0.87
   2 !    9.4   0.0   0.00043      0.76      25      47 ..     110     132 ..     109     133 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.011
                            HTH_24 18 isqreLAerlgl 29
                                      is +e++++lg+
  gi|242398694|ref|YP_002994118.1| 23 ISVKEISKALGI 34
                                      9**********9 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00043
                            HTH_24  25 erlglSpstvnrrlkrLeeeGlI 47 
                                       + ++l  s v +++krL e+Gl+
  gi|242398694|ref|YP_002994118.1| 110 KLVNLRGSQVYEHVKRLLEMGLV 132
                                       5678888999***********98 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 ?    3.1   0.0     0.049        89      11      27 ..      18      34 ..      16      36 .. 0.85
   2 ?    9.7   0.1   0.00041      0.74      25      46 ..     112     133 ..     108     134 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.049
                                      HTTSSEEHHHHHHHHTS CS
                             HTH_5 11 Laegelcvcelaeelgl 27
                                      ++ ++ +v e++++lg+
  gi|242398694|ref|YP_002994118.1| 18 VSGRPISVKEISKALGI 34
                                      5678999********98 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00041
                                       HTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  25 lglsqstvShHLkkLreaGLVe 46 
                                       ++l  s v +H k+L e+GLV+
  gi|242398694|ref|YP_002994118.1| 112 VNLRGSQVYEHVKRLLEMGLVY 133
                                       5666799**************6 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0      0.11     2e+02      17      51 ..      21      55 ..      16      62 .. 0.85
   2 ?   10.7   0.1   0.00032      0.58      28      65 ..     112     146 ..     109     148 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.11
                            HTH_27 17 rrkkladlcgrlnvedshisyslkkLtekGLvert 51
                                      r+ + ++++++l + +  +++ l +L+++++ er+
  gi|242398694|ref|YP_002994118.1| 21 RPISVKEISKALGIKSLDYIEKLIELIAAEYAERN 55
                                      5556699*************99999**99998665 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00032
                            HTH_27  28 lnvedshisyslkkLtekGLvertgdeadrrekrvrlT 65 
                                       +n+  s++ + +k+L e+GLv  +++e   r+k +  T
  gi|242398694|ref|YP_002994118.1| 112 VNLRGSQVYEHVKRLLEMGLVYAEPYE---RTKILGTT 146
                                       678889999************999988...88877777 PP

>> DUF4777  Domain of unknown function (DUF4777)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0    0.0025       4.4       6      29 ..       9      32 ..       5      37 .. 0.87
   2 ?    3.4   0.0     0.051        91      35      52 ..     114     131 ..     106     133 .. 0.83
   3 ?   -2.9   0.0       4.6   8.3e+03      27      38 ..     147     158 ..     146     160 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0025
                           DUF4777  6 galvlealkvlnrPaTldEiverv 29
                                       alv +al v +rP++++Ei++++
  gi|242398694|ref|YP_002994118.1|  9 KALVESALFVSGRPISVKEISKAL 32
                                      6889999*************9976 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.051
                           DUF4777  35 lseeelkkvVkntLeaAv 52 
                                       l  +++ ++Vk++Le++ 
  gi|242398694|ref|YP_002994118.1| 114 LRGSQVYEHVKRLLEMGL 131
                                       6678899*********96 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 4.6
                           DUF4777  27 ervaerydlsee 38 
                                       +++ae y+++e+
  gi|242398694|ref|YP_002994118.1| 147 QKFAELYGFPEN 158
                                       689999999987 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0       0.2   3.5e+02      17      30 ..      22      35 ..      19      36 .. 0.88
   2 ?    9.4   0.1   0.00056         1       5      48 ..      93     133 ..      89     138 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.2
                                      TEEHHHHHHHHTS- CS
                              MarR 17 plsvseLakklgvs 30
                                      p+sv+e+ k+lg++
  gi|242398694|ref|YP_002994118.1| 22 PISVKEISKALGIK 35
                                      89*********996 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00056
                                       HHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR   5 qfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlie 48 
                                       ++++L+++++ +p+ +s+L    ++  s v + ++rL + Gl++
  gi|242398694|ref|YP_002994118.1|  93 ELKTLALIAYLQPIEQSKLV---NLRGSQVYEHVKRLLEMGLVY 133
                                       7899*************996...688899999******999997 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 ?    8.8   0.0   0.00076       1.4      19      45 ..      16      42 ..      10      54 .. 0.80
   2 ?    1.4   0.0      0.15   2.7e+02      35      60 ..     112     136 ..     106     139 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00076
                                      HHHHSS---HHHHHHHHTS-.HHHHHH CS
                     LexA_DNA_bind 19 ieetgypPsireiaralglkSpsavee 45
                                      +   g p s++ei++alg+kS   +e+
  gi|242398694|ref|YP_002994118.1| 16 LFVSGRPISVKEISKALGIKSLDYIEK 42
                                      55678899************9877764 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.15
                                       HTS-.HHHHHHHHHHHHHTTSEE-GG CS
                     LexA_DNA_bind  35 lglkSpsaveehLkaLerKGyierdp 60 
                                       ++l+  s v eh k+L   G++  +p
  gi|242398694|ref|YP_002994118.1| 112 VNLR-GSQVYEHVKRLLEMGLVYAEP 136
                                       7888.78999******9999987655 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.21   3.7e+02      16      36 ..      13      34 ..      10      37 .. 0.82
   2 ?    8.5   0.0    0.0011         2      34      54 ..     112     132 ..      98     136 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.21
                                      HHHH.STCTTB-HHHHHHHHTS CS
                            HTH_20 16 lraL.araegltaselaerldl 36
                                      ++aL  ++++ +++e+ ++l++
  gi|242398694|ref|YP_002994118.1| 13 ESALfVSGRPISVKEISKALGI 34
                                      566667899**********987 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0011
                                       HTS-HHHHHHHHHHHHHCTTE CS
                            HTH_20  34 ldlskntlsyHLrvLeeagLv 54 
                                       + l+ ++++ H++ L e gLv
  gi|242398694|ref|YP_002994118.1| 112 VNLRGSQVYEHVKRLLEMGLV 132
                                       578999**************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       734  (0.0409393); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); 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: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1230.15
//
Query:       gi|242398695|ref|YP_002994119.1|  [L=353]
Description: replication factor A complex, RPA41 subunit [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-13   50.5   0.8    3.5e-09   36.5   0.1    2.8  3  tRNA_anti-codon  OB-fold nucleic acid binding domain
    4.1e-10   39.6   0.0    1.1e-09   38.2   0.0    1.8  2  Rep_fac-A_C      Replication factor-A C terminal domain
    0.00021   20.9   0.4    0.00053   19.6   0.4    1.6  1  DUF2240          Uncharacterized protein conserved in archaea
    0.00043   20.1   0.0     0.0023   17.7   0.0    1.9  2  CDC24_OB3        Cell division control protein 24, OB domain 
  ------ inclusion threshold ------
      0.011   15.8   0.1      0.028   14.5   0.1    1.6  1  DUF2396          Protein of unknown function (DUF2396)
      0.015   15.5   2.1       0.07   13.4   0.9    2.4  2  DUF4777          Domain of unknown function (DUF4777)
      0.027   12.3   0.0      0.037   11.9   0.0    1.1  1  DUF5521          Family of unknown function (DUF5521)
      0.046   13.5   3.4      0.069   13.0   0.2    2.1  2  SPAM             Salmonella surface presentation of antigen g
      0.062   13.2   0.3       0.14   12.0   0.3    1.6  1  Glycos_trans_3N  Glycosyl transferase family, helical bundle 
      0.099   12.9   0.5       0.25   11.6   0.5    1.7  1  Bac_DNA_binding  Bacterial DNA-binding protein
       0.12   12.4   0.4        4.5    7.4   0.0    2.9  3  DUF2250          Uncharacterized protein conserved in archaea


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 !   36.5   0.1   2.1e-12   3.5e-09       2      70 ..      75     152 ..      74     156 .. 0.94
   2 ?   -3.1   0.0       4.9   7.9e+03      48      58 ..     192     202 ..     184     206 .. 0.67
   3 !   11.8   0.0   0.00011      0.19      16      49 ..     243     288 ..     235     318 .. 0.81

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 2.1e-12
                                       EEEEEEEEEE........EEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEE.EEEEECTTSSEEEE CS
                   tRNA_anti-codon   2 tvaGrvtsis........drsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvt.Grvkrrpggelelk 69 
                                       +++Grv ++         d+s g+v+ + + D+tgr +vvl++ e +k+++++++G+v+++    v+++ +g +el+
  gi|242398695|ref|YP_002994119.1|  75 NIVGRVLRKYpvreykkkDGSQGRVAGLLIYDNTGRARVVLWDPEISKYYDDIQVGSVIKIInADVRESLRGLPELH 151
                                       699***********************************************************999999977767777 PP

                                       E CS
                   tRNA_anti-codon  70 v 70 
                                       v
  gi|242398695|ref|YP_002994119.1| 152 V 152
                                       7 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 4.9
                                       TTSEEEEEEEE CS
                   tRNA_anti-codon  48 eGdvvrvtGrv 58 
                                        +++v+++G++
  gi|242398695|ref|YP_002994119.1| 192 GEKFVEIRGTI 202
                                       46677777776 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 0.00011
                                       TTEEEEEEEETTEEEEEEEET............HHHHHHHTTS-TT CS
                   tRNA_anti-codon  16 gkvifidlrDgtgriqvvlfr............eeatklaenlkeG 49 
                                       + ++++ l+D tg i+v+lf             e  +k++e +k G
  gi|242398695|ref|YP_002994119.1| 243 ATILDFGLDDSTGYIRVTLFGddvveilgveleEISEKFKELIKMG 288
                                       56899****************8888888877765555555555555 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 ?   -2.4   0.1       2.2   3.6e+03     113     141 ..      12      38 ..       4      42 .. 0.54
   2 !   38.2   0.0   6.9e-13   1.1e-09       2      91 ..     196     281 ..     195     343 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.2
                                       EEEEE----------EEEEEEEEE--HHH CS
                       Rep_fac-A_C 113 rlrvkeesyndesrvrytvvkvepvdykk 141
                                       r+  ++++ + ++ + +++ ++++v+  +
  gi|242398695|ref|YP_002994119.1|  12 RI--RQKTGMSKEEIEHKIREIAKVNEIS 38 
                                       44..4444444445555566666666544 PP

  == domain 2  score: 38.2 bits;  conditional E-value: 6.9e-13
                                       EEEEEEEEEEETTTTEEEB--STT---B-EEE.TTTEEEETTTTEEESS--EEEEEEEEEE-SS-EEEEEEEHHHHH CS
                       Rep_fac-A_C   2 fsvkatvsfikkdnlvYkACpsedCnkKvvee.edgewrCekCdkeveepkyryilsikvsDstgqlwvtlFneaae 77 
                                       +++++t+ ++++  ++Y+ACp  +C +Kv ++ + ++w C +  +   +p    il + + Dstg ++vtlF +   
  gi|242398695|ref|YP_002994119.1| 196 VEIRGTIAKLYR-IIAYDACP--QCRRKVDHDsATDTWICIEHGEV--KPITATILDFGLDDSTGYIRVTLFGDDVV 267
                                       677788888775.689*****..******998688*****986655..89999************************ PP

                                       HHHSS-HHHHHHHC CS
                       Rep_fac-A_C  78 kllglsaeelkklk 91 
                                       ++lg++ ee+ +  
  gi|242398695|ref|YP_002994119.1| 268 EILGVELEEISEKF 281
                                       ******99997643 PP

>> DUF2240  Uncharacterized protein conserved in archaea (DUF2240)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.4   3.2e-07   0.00053      86     139 ..       5      56 ..       2      60 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 3.2e-07
                           DUF2240  86 tferildaiaastgiekkevvaeinelqeelkglvdveaaalvvakkegvdvdd 139
                                       t e+i+++i ++tg++k+e+  +i+e+ +  +  ++  aaal++a+++gv  dd
  gi|242398695|ref|YP_002994119.1|   5 TKEEIVERIRQKTGMSKEEIEHKIREIAKVNE--ISEHAAALLLAEEFGVKTDD 56 
                                       5699************************9999..****************9887 PP

>> CDC24_OB3  Cell division control protein 24, OB domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   1.4e-06    0.0023       2      67 ..      67     135 ..      66     143 .. 0.81
   2 ?   -0.1   0.0      0.39   6.3e+02     162     204 ..     215     271 ..     189     285 .. 0.61

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.4e-06
                         CDC24_OB3   2 LrekmlnvtLlGrvvai..fr.eknsek.kkmdryslrieDttGaidatlweeagklhfkrlrvGhlvll 67 
                                       L++ m ++ ++Grv +   +r +k++ +  + ++  l i D+tG  +++lw+    ++  +++vG ++ +
  gi|242398695|ref|YP_002994119.1|  67 LVPGMKGINIVGRVLRKypVReYKKK-DgSQGRVAGLLIYDNTGRARVVLWDPEISKYYDDIQVGSVIKI 135
                                       8899***********98774423333.33677777*****************988888888****99865 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.39
                         CDC24_OB3 162 efCqcsv................aevvrefeleitLdddtssaklfalctgqtaielLq 204
                                         C+++v                 ++  +  l   Ldd+t+ +++   + g   +e+L 
  gi|242398695|ref|YP_002994119.1| 215 PQCRRKVdhdsatdtwiciehgeVKPITATILDFGLDDSTGYIRV--TLFGDDVVEILG 271
                                       444444444444444444444454555666666666666555333..555555555555 PP

>> DUF2396  Protein of unknown function (DUF2396)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   1.7e-05     0.028       8      33 ..     213     238 ..     209     251 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.7e-05
                           DUF2396   8 kcPhcrqtipaltltdtylcerhGaf 33 
                                        cP+cr++++    tdt++c +hG  
  gi|242398695|ref|YP_002994119.1| 213 ACPQCRRKVDHDSATDTWICIEHGEV 238
                                       6***********************54 PP

>> DUF4777  Domain of unknown function (DUF4777)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.9   4.3e-05      0.07      20      46 ..       4      30 ..       2      33 .. 0.92
   2 ?   -0.0   0.0      0.68   1.1e+03      29      51 ..     266     288 ..     264     291 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.3e-05
                           DUF4777 20 aTldEivervaerydlseeelkkvVkn 46
                                      +T +Eiver++++++ s+ee++++++ 
  gi|242398695|ref|YP_002994119.1|  4 ITKEEIVERIRQKTGMSKEEIEHKIRE 30
                                      799********************9985 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.68
                           DUF4777  29 vaerydlseeelkkvVkntLeaA 51 
                                       v e++++++ee+ ++ k + +++
  gi|242398695|ref|YP_002994119.1| 266 VVEILGVELEEISEKFKELIKMG 288
                                       67889999999999999998887 PP

>> DUF5521  Family of unknown function (DUF5521)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.3e-05     0.037     237     340 ..      77     188 ..      72     210 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.3e-05
                           DUF5521 237 lvrilkksklryygkpdkkiiepyqtflevadssgtvsvilwnalcpewykslrvglvlllqdysvkks........ 305
                                       + r+l+k  +r y k d    +   + l + d++g   v+lw+    ++y  ++vg+v+ + +  v+ s        
  gi|242398695|ref|YP_002994119.1|  77 VGRVLRKYPVREYKKKDGS--QGRVAGLLIYDNTGRARVVLWDPEISKYYDDIQVGSVIKIINADVRESlrglpelh 151
                                       5588999999999887765..4556678899****************************999999887522222222 PP

                           DUF5521 306 ..ypfrlqplpvdpqiklistleiclnlrdpptniii 340
                                         +  rl  +p dp++  i  +e     + ++ ni  
  gi|242398695|ref|YP_002994119.1| 152 vsFRSRLIINPDDPRVEEIPPIEEVRSYNYTRKNIGE 188
                                       2266778889999999999988888888888888754 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 ?    1.2   0.4      0.18     3e+02      65      99 ..       2      36 ..       1      49 [. 0.82
   2 ?   13.0   0.2   4.2e-05     0.069      31     103 ..     271     346 ..     263     352 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.18
                              SPAM 65 allrkqaivrrqlkeLeLqlvaiqekrselqkeke 99
                                      ++  k  iv r +++ ++   +i+ k +e+ k  e
  gi|242398695|ref|YP_002994119.1|  2 TVITKEEIVERIRQKTGMSKEEIEHKIREIAKVNE 36
                                      5677899999999999**999**999999987655 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 4.2e-05
                              SPAM  31 dkeeeaieeqragLkeLLdlqrpegksldreelyallrkqaivrrqlke...LeLqlvaiqekrselqkekeelsk 103
                                         e+e+i e+ ++L ++  + r +g++l  +e+y +l +   vr  + e   L+L l a      ++++e e+++k
  gi|242398695|ref|YP_002994119.1| 271 GVELEEISEKFKELIKMGMTAREAGRKLAEDEFYHVLGREIFVRGNVVEdrfLGLILKASSWDEVDYKREIERVRK 346
                                       5689************************************999988765344555555555555555555555555 PP

>> Glycos_trans_3N  Glycosyl transferase family, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.3   8.9e-05      0.14       2      41 ..       8      47 ..       7      59 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.9e-05
                                      HHHHHHHTT.---HHHHHHHHHHHHT.TSS-HHHHHHHHHH CS
                   Glycos_trans_3N  2 diikklrdgeeLtaeeirfaihgilk.gevtdaqiaAfLmA 41
                                      +i++++r++   ++eei++ i++i+k +e+++  +aA+L A
  gi|242398695|ref|YP_002994119.1|  8 EIVERIRQKTGMSKEEIEHKIREIAKvNEISE-HAAALLLA 47
                                      7999**********************666655.67777665 PP

>> Bac_DNA_binding  Bacterial DNA-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.5   0.00016      0.25       2      30 ..       5      33 ..       4      47 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00016
                                      EHHHHHHHHHTT----HHHHHHHHHHHHH CS
                   Bac_DNA_binding  2 tkkeLieeiaektgltkkdakrvveafld 30
                                      tk+e++e+i +ktg++k++++  + ++ +
  gi|242398695|ref|YP_002994119.1|  5 TKEEIVERIRQKTGMSKEEIEHKIREIAK 33
                                      9*******************998887765 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.2      0.23   3.7e+02      28      55 ..      13      40 ..       6      57 .. 0.77
   2 ?    7.4   0.0    0.0028       4.5      29      59 ..     267     297 ..     262     303 .. 0.84
   3 ?   -2.1   0.0       2.7   4.3e+03      13      36 ..     326     349 ..     319     353 .] 0.70

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.23
                           DUF2250 28 iakeleipleevrellkkLeelGLlerv 55
                                      i +++ +++ee++++++++ ++  + + 
  gi|242398695|ref|YP_002994119.1| 13 IRQKTGMSKEEIEHKIREIAKVNEISEH 40
                                      678999**********999887655555 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0028
                           DUF2250  29 akeleipleevrellkkLeelGLlervegkt 59 
                                       ++ l ++lee++e++k+L ++G+  r  g+ 
  gi|242398695|ref|YP_002994119.1| 267 VEILGVELEEISEKFKELIKMGMTAREAGRK 297
                                       567889*****************99887765 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 2.7
                           DUF2250  13 vlkhlkkanvdYaksiakeleipl 36 
                                       +lk     +vdY + i +  +  l
  gi|242398695|ref|YP_002994119.1| 326 ILKASSWDEVDYKREIERVRKELL 349
                                       666667778999998877665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       759  (0.0423336); expected 358.6 (0.02)
Passed bias filter:                      648  (0.0361426); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.65u 0.34s 00:00:00.99 Elapsed: 00:00:00.55
# Mc/sec: 1947.38
//
Query:       gi|242398696|ref|YP_002994120.1|  [L=123]
Description: Replication factor A complex, RPA14 subunit [Thermococcus sibiricus MM 739]
Scores for complete 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   24.3   0.2    3.7e-05   24.0   0.2    1.1  1  Rep_fac-A_3      Replication factor A protein 3
    0.00024   20.9   0.0    0.00027   20.7   0.0    1.1  1  RMI2             RecQ-mediated genome instability protein 2
     0.0027   17.7   1.2     0.0054   16.8   1.2    1.4  1  BOF              Bacterial OB fold (BOF) protein
  ------ inclusion threshold ------
      0.086   12.8   2.3       0.18   11.8   2.3    1.8  1  tRNA_anti-codon  OB-fold nucleic acid binding domain


Domain annotation for each model (and alignments):
>> Rep_fac-A_3  Replication factor A protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.2   8.2e-09   3.7e-05      20     101 ..      28     110 ..       7     113 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 8.2e-09
                                       EEEEEEEEEEETTSSEEEEE-TTS-EEEEEESS--SS---SEEEEEEEE-TTS-E.EEEEEEE------HHHHHHHH CS
                       Rep_fac-A_3  20 tvrivgkvesvpsgktlilqstdggsvtvrlsedstleiskwvEvvGkvsddlgi.rldsvvefgedlDldlynklv 95 
                                        v+++gkv +v++ + +   ++ +g v ++ +e+   +++++v v+G+v ++ +i +  ++v+  ++++l+  ++++
  gi|242398696|ref|YP_002994120.1|  28 RVSLIGKVVKVDKIDYIFWLDDGTGVVAIECEENVLPKVGQVVRVIGRVIKNEEIhIYGEIVQDFDTVNLEYLEEIQ 104
                                       499*************9999999****************************99999999999999999999999999 PP

                                       HHHHHS CS
                       Rep_fac-A_3  96 qlthkf 101
                                       +l +k+
  gi|242398696|ref|YP_002994120.1| 105 ELEKKL 110
                                       998775 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 !   20.7   0.0   6.1e-08   0.00027      32     100 ..      22      82 ..       2     108 .. 0.70

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 6.1e-08
                              RMI2  32 vgreglevsrvWlQGtvvevdaskesllldDgtgvfvveglnelpktkkclkeGkYVmVvGvvqssspe 100
                                       ++ e l+vs +   G vv+vd+ +  + ldDgtgv+++e  +++       k G++V V+G v + ++ 
  gi|242398696|ref|YP_002994120.1|  22 IAPEDLRVSLI---GKVVKVDKIDYIFWLDDGTGVVAIECEENV-----LPKVGQVVRVIGRVIKNEEI 82 
                                       44555666655...*********99**********655555544.....5678********99554443 PP

>> BOF  Bacterial OB fold (BOF) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   1.2   1.2e-06    0.0054      31      97 ..      23      98 ..      13     105 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.2e-06
                                      S-SSEEEEEEEEEEEEEETT.EEEEEETTEEEEEE--GGGSTT-........---TTSEEEEEEEEEEETTEEEEE CS
                               BOF 31 aaDdasvslrGnivkriddD.eyvFrDasGeikveiddrvfngl........evqpkdkvkiqGkvDkelekaeid 97
                                      a +d  vsl G++vk  + D +++  D +G + +e +++v + +         v +++ ++i+G++ +++++++++
  gi|242398696|ref|YP_002994120.1| 23 APEDLRVSLIGKVVKVDKIDyIFWLDDGTGVVAIECEENVLPKVgqvvrvigRVIKNEEIHIYGEIVQDFDTVNLE 98
                                      567899********97665538999**************9985422233233456899999***999999988775 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   2.3     4e-05      0.18       4      62 ..      32      80 ..       8     104 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4e-05
                                      EEEEEEEEEEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEEEEEEECT CS
                   tRNA_anti-codon  4 aGrvtsisdrsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvtGrvkrrp 62
                                       G+v+++  +       + l+Dgtg + + +        +   k+G+vvrv Grv + +
  gi|242398696|ref|YP_002994120.1| 32 IGKVVKVD-KID---YIFWLDDGTGVVAIECEE------NVLPKVGQVVRVIGRVIKNE 80
                                      44444442.222...3456**************......88899***********9873 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       824  (0.0459591); expected 358.6 (0.02)
Passed bias filter:                      590  (0.0329076); 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: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 781.89
//
Query:       gi|242398697|ref|YP_002994121.1|  [L=267]
Description: RPA32 [Thermococcus sibiricus MM 739]
Scores for complete 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   34.2   2.3    3.9e-08   33.2   2.3    1.6  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
     0.0013   19.4   0.0     0.0029   18.3   0.0    1.5  1  RPA_C            Replication protein A C terminal
  ------ inclusion threshold ------
      0.025   15.3   1.2       0.16   12.7   0.5    2.1  2  KfrA_N           Plasmid replication region DNA-binding N-ter
      0.027   15.0   0.4        1.2    9.7   0.0    2.4  2  Hrs_helical      Hepatocyte growth factor-regulated tyrosine 
      0.048   13.5   0.0      0.089   12.6   0.0    1.4  1  RMI2             RecQ-mediated genome instability protein 2


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 !   33.2   2.3   1.1e-11   3.9e-08       3      74 ..      45     115 ..      43     117 .. 0.86

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 1.1e-11
                                       EEEEEEEEE.EEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEEEEEEECTTSSEEEEEEEEE CS
                   tRNA_anti-codon   3 vaGrvtsis.drsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvtGrvkrrpggelelkveeie 74 
                                       ++G v++     +   +  ++++Dgtg i v  fr ++tk+   +k+Gd+v+  G+v+++++   ++ ve ++
  gi|242398697|ref|YP_002994121.1|  45 IVGTVVREPtIAEDETYGKFQIDDGTGVIWVLGFR-DDTKFIRLVKRGDIVQLIGKVGEWRDD-KQVLVEGVT 115
                                       5666666555455567889****************.************************999.999999876 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 !   18.3   0.0     8e-07    0.0029      38      98 ..     197     256 ..     177     258 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 8e-07
                                       XXXXXXX.XSXHHHHHHHHHHHH.SXSTTTEEHHHHHHHS..TSXHHHHHHHHHHHHHTTSEE CS
                             RPA_C  38 nqaklankgltalaqqvlnlikqspeseeGvhvdeiaqkl..rlsvndvkqavdeLsneGiiY 98 
                                        + k +++g++++++ vl+++++   +   v++++i +kl  + + +++++av+ L++eG i+
  gi|242398697|ref|YP_002994121.1| 197 EETKEVKEGIEEAKKAVLEILRS---KGTAVSLKFIQRKLqeKYDPETIEEAVRALLTEGEIF 256
                                       445566689**************...5556***********9********************9 PP

>> KfrA_N  Plasmid replication region DNA-binding N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.5   4.4e-05      0.16      52     108 ..     157     213 ..     151     223 .. 0.84
   2 ?    0.9   0.0       0.2   7.3e+02       3      17 ..     240     254 ..     227     257 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.4e-05
                            KfrA_N  52 aaraa.pelPealaeallaalwqaaleeaeeelaaaraelqaaraaleaeraeaearv 108
                                       ++ a+ +++Pe+l +a+  +l++   e+  ee   +++ ++++ ++ ++  +ea+++v
  gi|242398697|ref|YP_002994121.1| 157 KVIAKnKGVPEDLLTAI-DELYAVIMEQKAEESVLEEELFEEETKEVKEGIEEAKKAV 213
                                       3333467**********.*********9999999999999999999999999997654 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.2
                            KfrA_N   3 eqviaaadallaeGe 17 
                                       e + +a++all eGe
  gi|242398697|ref|YP_002994121.1| 240 ETIEEAVRALLTEGE 254
                                       789999999999996 PP

>> Hrs_helical  Hepatocyte growth factor-regulated tyrosine kinase substrate
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00034       1.2      60      79 ..     126     145 ..     120     150 .. 0.91
   2 ?    3.0   0.2     0.041   1.5e+02      23      82 ..     155     218 ..     151     238 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00034
                       Hrs_helical  60 eyeslqdklaqikeareald 79 
                                       +ye l+dkl++ik+a+ a++
  gi|242398697|ref|YP_002994121.1| 126 RYETLRDKLNHIKNAKLAFE 145
                                       69**************9987 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.041
                       Hrs_helical  23 rGrsianDsav.qslFqkltamhsqllkriqeqeekrae.y.eslqdklaqikearea.ldalr 82 
                                       + + ia+++ v ++l + + ++ + ++++ +e+    +e + e+ ++  + i+ea++a l+ lr
  gi|242398697|ref|YP_002994121.1| 155 KAKVIAKNKGVpEDLLTAIDELYAVIMEQKAEESVLEEElFeEETKEVKEGIEEAKKAvLEILR 218
                                       6677777777745688888888888888765544332221313333333446678777345555 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 ?   12.6   0.0   2.5e-05     0.089      41     103 ..      42     109 ..      27     126 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.5e-05
                              RMI2  41 rvWlQGtvvevdaske.....sllldDgtgvfvveglnelpktkkclkeGkYVmVvGvvqssspepvl 103
                                       r+ + Gtvv+    +e     ++ +dDgtgv+ v g  + +k  + +k G+ V  +G v + +  + +
  gi|242398697|ref|YP_002994121.1|  42 RAKIVGTVVREPTIAEdetygKFQIDDGTGVIWVLGFRDDTKFIRLVKRGDIVQLIGKVGEWRDDKQV 109
                                       5556688885322222245789*****************99999*************99777665544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1393  (0.0776954); expected 358.6 (0.02)
Passed bias filter:                      796  (0.0443973); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 1734.97
//
Query:       gi|242398698|ref|YP_002994122.1|  [L=126]
Description: hypothetical protein TSIB_0710 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.065   12.9   0.0      0.089   12.5   0.0    1.1  1  Nrf1_DNA-bind  NLS-binding and DNA-binding and dimerisation d


Domain annotation for each model (and alignments):
>> Nrf1_DNA-bind  NLS-binding and DNA-binding and dimerisation domains of Nrf1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     5e-06     0.089     140     184 ..      31      74 ..      27      83 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5e-06
                     Nrf1_DNA-bind 140 emlkystgrgkpgWGkeslkpvwwPkdlpwanvrsdvrseeekkk 184
                                       +m k +t+ +++gW   ++k  ww +d+p+  +r d   +e++k 
  gi|242398698|ref|YP_002994122.1|  31 TMDKLATTLEELGWTV-TFKANWWTADIPYGLIRIDITQDEKEKI 74 
                                       688999999*****75.7999***************988877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 919.59
//
Query:       gi|242398699|ref|YP_002994123.1|  [L=279]
Description: 4-hydroxybenzoate octaprenyltransferase [Thermococcus sibiricus MM 739]
Scores for complete 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-44  150.0  11.5    8.3e-44  149.8  11.5    1.1  1  UbiA      UbiA prenyltransferase family
  ------ inclusion threshold ------
       0.17   12.3   0.2       0.17   12.3   0.2    2.8  3  TraL      TraL 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 !  149.8  11.5   9.2e-48   8.3e-44       6     245 ..      23     255 ..      15     272 .. 0.90

  Alignments for each domain:
  == domain 1  score: 149.8 bits;  conditional E-value: 9.2e-48
                              UbiA   6 lvglalaaggspdlllllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivllilgll 82 
                                       ++g+++a g+ p++++ ll++l ++l ++++n++NdyfD+eiD++  ++pnRPl++G++s++ al+++i l+ +++l
  gi|242398699|ref|YP_002994123.1|  23 ILGATVALGHLPPIKTSLLIFLVVFLECSWGNIINDYFDYEIDKI--NRPNRPLPRGALSKNIALVYGISLGGVAIL 97 
                                       45699999999999*******************************..****************************** PP

                              UbiA  83 llalllnpltallgllalllyvvYtglrlKrrtllgtvvggiafglppllgwaavtgslsllalllalavflltwai 159
                                       ++ +l+n+ +++++l a ll ++Y    lK  +++g++v+++  g+ p+ g+ av+    l+ +l al  fl+ +a 
  gi|242398699|ref|YP_002994123.1|  98 IA-YLINFEAFIFALGAYLLMYLYA-RKLKPQPFIGNLVVATLTGITPIYGAIAVGKI-GLAGYL-ALCAFLVNVAR 170
                                       **.**********************.7****************************886.544444.44449****** PP

                              UbiA 160 alandlrdregDrkagiktlpvvlGrkaarillalllavlllallllllalllllylllalllaalallraarlvrr 236
                                        +++d++d+egD++ g ktlp+v+G + +  + +++ +++++a  ll++ +  +l ++  +++ +++l+ a+ ++++
  gi|242398699|ref|YP_002994123.1| 171 EIFKDIEDIEGDKAQGAKTLPIVWGIESSSKIGVIFSVATIIA-SLLPVKAGIGLGYFPIIIVDGIILWAAYEVLKN 246
                                       *******************************855555555555.688999999999999999999999999999999 PP

                              UbiA 237 rdakkaakf 245
                                        ++k+a ++
  gi|242398699|ref|YP_002994123.1| 247 PSPKTAGRV 255
                                       999988776 PP

>> TraL  TraL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.4      0.14   1.2e+03      27      50 ..      95     118 ..      86     133 .. 0.58
   2 ?   -2.7   0.0      0.98   8.8e+03      33      33 ..     149     149 ..     128     172 .. 0.48
   3 ?   12.3   0.2   1.9e-05      0.17      15      61 ..     205     251 ..     192     256 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.14
                              TraL  27 llvvgillgqfviglvlglllvll 50 
                                        +++ +l+++  ++++lg+ l++ 
  gi|242398699|ref|YP_002994123.1|  95 AILIAYLINFEAFIFALGAYLLMY 118
                                       455566666666666666544322 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.98
                              TraL  33 l 33 
                                       +
  gi|242398699|ref|YP_002994123.1| 149 A 149
                                       1 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 1.9e-05
                              TraL  15 fwelDealvillllvvgillgqfviglvlglllvlllrklkkgrgdg 61 
                                       ++++ ++++ ll++  gi lg f i++v g++l+ +++ lk+ ++++
  gi|242398699|ref|YP_002994123.1| 205 IFSVATIIASLLPVKAGIGLGYFPIIIVDGIILWAAYEVLKNPSPKT 251
                                       7889999999*******************************987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1974.74
//
Query:       gi|242398700|ref|YP_002994124.1|  [L=356]
Description: hypothetical protein TSIB_0712 [Thermococcus sibiricus MM 739]
Scores for complete 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-41  140.5   0.0    7.5e-41  140.0   0.0    1.2  1  CLP1_P      mRNA cleavage and polyadenylation factor CLP1 P-l
    0.00086   19.2   0.1     0.0021   18.0   0.1    1.6  1  MobB        Molybdopterin guanine dinucleotide synthesis prot
     0.0014   18.0   0.7     0.0052   16.1   0.1    2.2  2  MipZ        ATPase MipZ
      0.007   15.8   0.4      0.007   15.8   0.4    1.6  2  ParA        NUBPL iron-transfer P-loop NTPase
     0.0088   16.1   0.6      0.017   15.2   0.4    1.8  1  CbiA        CobQ/CobB/MinD/ParA nucleotide binding domain
     0.0089   16.0   0.1      0.026   14.4   0.0    1.8  2  AAA_31      AAA domain
  ------ inclusion threshold ------
      0.021   14.4   0.5       0.36   10.4   0.1    2.2  2  GTP_EFTU    Elongation factor Tu GTP binding domain
      0.025   14.2   0.6        2.6    7.6   0.1    2.5  2  SRP54       SRP54-type protein, GTPase domain
      0.027   14.3   0.0      0.057   13.3   0.0    1.5  1  APS_kinase  Adenylylsulphate kinase
      0.031   14.2   2.8       0.13   12.2   2.6    2.0  1  NTPase_1    NTPase
      0.032   14.0   0.1      0.086   12.6   0.1    1.7  2  PduV-EutP   Ethanolamine utilisation - propanediol utilisatio
       0.14   11.6   1.3        1.1    8.7   0.1    2.4  2  Arf         ADP-ribosylation factor family
       0.14   12.2   1.6         15    5.7   0.1    2.4  2  MMR_HSR1    50S ribosome-binding GTPase
       0.15   11.1   0.6        0.3   10.1   0.2    1.6  2  LpxK        Tetraacyldisaccharide-1-P 4'-kinase
       0.58   10.0   1.8        2.9    7.7   1.9    1.8  2  DUF3323     Protein of unknown function N-terminus (DUF3323)


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 !  140.0   0.0   6.3e-44   7.5e-41       1     188 []      34     210 ..      34     210 .. 0.96

  Alignments for each domain:
  == domain 1  score: 140.0 bits;  conditional E-value: 6.3e-44
                            CLP1_P   1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDvGqseispPgtislalverpidveegfsldaplvyffGdtspsdnp 77 
                                       G++dsGK+Tla +L N++l++g k+ ++D DvGq+ i pPg isl + e+ +++ e+++ ++  +yf+G+ +p++  
  gi|242398700|ref|YP_002994124.1|  34 GGVDSGKTTLAVFLTNELLKNGFKVGVIDSDVGQKGILPPGLISLGFPEKVFNSLEEIKAEK--HYFVGTITPNQFF 108
                                       899******************************************************99887..79*******9999 PP

                            CLP1_P  78 slylalvkelareveekleenkkakasgliIntpGwvkglgaellleliealepdvvvvldqeellnelkrdlplsk 154
                                        +++  vk l++e+          +a++liI+t+G+++g g+el+  +ie+++p+++++l+++++l+++ r ++ +k
  gi|242398700|ref|YP_002994124.1| 109 GEMITGVKLLVNEAL--------DTADVLIIDTTGLIHGPGVELKRMKIEVIQPEIIIALQKKDELENIIRPFE-KK 176
                                       999999999999888........479************************************999999999999.9* PP

                            CLP1_P 155 vkvvklpkspgvvqrsreerrelreerireYFyg 188
                                        kv++l+ s+ ++  +reerr++r+e++r+YF++
  gi|242398700|ref|YP_002994124.1| 177 AKVFRLKISENAKLHTREERRRIRREKWRKYFEQ 210
                                       ********************************85 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 !   18.0   0.1   1.8e-06    0.0021       2      39 ..      30      67 ..      29      77 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.8e-06
                              MobB  2 lgivgksgsGKTtLleklipelkarglrvgtiKhahhg 39
                                      + i g  +sGKTtL   l +el ++g++vg+i  ++ +
  gi|242398700|ref|YP_002994124.1| 30 VMILGGVDSGKTTLAVFLTNELLKNGFKVGVIDSDVGQ 67
                                      5688999*************************887765 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   4.3e-06    0.0052      12      44 ..      38      70 ..      30     148 .. 0.80
   2 ?   -3.7   0.0       4.7   5.6e+03     206     244 ..     299     338 ..     288     347 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.3e-06
                                      SSHHHHHHHHHHHHHTTT--EEEEE--TTT-HH CS
                              MipZ 12 sGksttavhvavaLlkkGarvaaidldlrqrtl 44
                                      sGk+t av +   Llk+G++v++id d+ q+ +
  gi|242398700|ref|YP_002994124.1| 38 SGKTTLAVFLTNELLKNGFKVGVIDSDVGQKGI 70
                                      8***************************99875 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 4.7
                                       T-EEE---B--GGGTTTGGGT--GGGSSSS--S.---CHH CS
                              MipZ 206 GfrvasGlserviyrelfpsGltlldlkelgle.elnlsh 244
                                       Gf +  G+ + + +re+  + +t l +++l    el  ++
  gi|242398700|ref|YP_002994124.1| 299 GFCLGLGILKFINFREFTAQIITPLKKEDLENVvELRFGR 338
                                       6777777777788888888888877666654333555555 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 !   15.8   0.4   5.9e-06     0.007      13      42 ..      34      65 ..      23      79 .. 0.89
   2 ?   -3.0   0.0       3.3   3.9e+03     103     119 ..     117     133 ..     109     134 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5.9e-06
                              ParA 13 GGV..GKStvavnlAlaLakkglkvgllDaDi 42
                                      GGV  GK+t+av l+ +L k+g+kvg++D D+
  gi|242398700|ref|YP_002994124.1| 34 GGVdsGKTTLAVFLTNELLKNGFKVGVIDSDV 65
                                      78777**************************8 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.3
                              ParA 103 llkdvewgelDyLiiDl 119
                                       ll + + ++ D+LiiD+
  gi|242398700|ref|YP_002994124.1| 117 LLVNEALDTADVLIIDT 133
                                       55666678889999997 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 !   15.2   0.4   1.4e-05     0.017       9      38 ..      37      66 ..      30     198 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.4e-05
                                      TSSHHHHHHHHHHHHHHTT--EEEEEEEES CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  9 GvGKTtlaanLaralarrglrVllvDaDpq 38
                                      ++GKTtla+ L   l ++g++V ++D D+ 
  gi|242398700|ref|YP_002994124.1| 37 DSGKTTLAVFLTNELLKNGFKVGVIDSDVG 66
                                      68**************************97 PP

>> AAA_31  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     0.026      11      40 ..      34      65 ..      29     103 .. 0.92
   2 ?   -2.0   0.0       2.5   2.9e+03     132     146 ..     118     132 ..     109     175 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.2e-05
                            AAA_31 11 GGv..GKTTtsvnlaaalaklgkkvLlvDlDp 40
                                      GGv  GKTT +v l   l k+g kv ++D D 
  gi|242398700|ref|YP_002994124.1| 34 GGVdsGKTTLAVFLTNELLKNGFKVGVIDSDV 65
                                      776669************************95 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.5
                            AAA_31 132 ltenaLvasdsviip 146
                                       l++ aL ++d +ii 
  gi|242398700|ref|YP_002994124.1| 118 LVNEALDTADVLIID 132
                                       444555555555553 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1    0.0003      0.36       4      23 ..      28      47 ..      25      59 .. 0.82
   2 ?    2.3   0.1     0.091   1.1e+02      83     165 ..     107     212 ..     101     267 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0003
                                      EEEEEEESTTSSHHHHHHHH CS
                          GTP_EFTU  4 rnigiighvDhGKtTLtdrL 23
                                      ++++i+g vD+GKtTL   L
  gi|242398700|ref|YP_002994124.1| 28 VKVMILGGVDSGKTTLAVFL 47
                                      6899***********97555 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.091
                                       GHHHHHHH.....HHT-SEE.EEEEETTTBSTHHHHHHHHHHHHTTTE.EEEEEESCGST.........HHHHHHHH CS
                          GTP_EFTU  83 Fskevirg.....lrvlDga.vlvvdaveGvepqteevlrlalkegvp.iivfiNKmDrl.........kaelkeiv 143
                                       F  e+i+g      ++lD a vl++d +  +     e+ r+ +++  p ii+++ K D+l         ka++ +++
  gi|242398700|ref|YP_002994124.1| 107 FFGEMITGvkllvNEALDTAdVLIIDTTGLIHGPGVELKRMKIEVIQPeIIIALQKKDELeniirpfekKAKVFRLK 183
                                       55566666333333455665455666654444444444444444444479999999999977655444433333333 PP

                                       HHHHHHHHHH.............HHHHHHHHHTTT CS
                          GTP_EFTU 144 eevkqklsrk.............eeklekygekge 165
                                                +              ek++ky e+++
  gi|242398700|ref|YP_002994124.1| 184 ISE------NaklhtreerrrirREKWRKYFEQAQ 212
                                       333......23333446666666556666655554 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.1    0.0022       2.6       3      39 ..      29      65 ..      14      69 .. 0.92
   2 ?    4.5   0.0      0.02        24      82      99 ..     124     141 ..     110     182 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0022
                                      EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEEST CS
                             SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvllvaaDt 39
                                       ++++G   +GKTt +  L + l k+g kv ++  D+
  gi|242398700|ref|YP_002994124.1| 29 KVMILGGVDSGKTTLAVFLTNELLKNGFKVGVIDSDV 65
                                      689999999**********************998885 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.02
                                       TTSSEEEEEE--SSTTHH CS
                             SRP54  82 ekidvvlvDTaGrlqndk 99 
                                       + +dv+++DT+G  +   
  gi|242398700|ref|YP_002994124.1| 124 DTADVLIIDTTGLIHGPG 141
                                       578*********988654 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   4.8e-05     0.057       2      40 ..      27      65 ..      26      81 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.8e-05
                                      -EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHH CS
                        APS_kinase  2 gvvvwltGlsgsGKstianalekkLvekgisvylLdGdn 40
                                      +v v++ G   sGK+t+a+ l ++L ++g +v ++d d+
  gi|242398700|ref|YP_002994124.1| 27 PVKVMILGGVDSGKTTLAVFLTNELLKNGFKVGVIDSDV 65
                                      56678888899*************************996 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   2.6   0.00011      0.13       1     159 [.      29     186 ..      29     195 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00011
                                       EEEEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE-----.--EEEEEET.T--EEEEEETT---SSEETTEEE CS
                          NTPase_1   1 kvfiTGppGvGKtTlvkkvlellkssgvkvgGfyteevreggr.rigFkivdlasgeegiLarveakreprvgkyvv 76 
                                       kv+i G   +GKtTl   ++++l ++g+kv G++ ++v ++g    g       ++  + L + +a++++ vg ++ 
  gi|242398700|ref|YP_002994124.1|  29 KVMILGGVDSGKTTLAVFLTNELLKNGFKV-GVIDSDVGQKGIlPPGLISLGFPEKVFNSLEEIKAEKHYFVGTITP 104
                                       5889999**********************9.7777778777651667777777788888999999999999999999 PP

                                       -HHHHHHHH..HHH.HHHHHHHH-EEEE---STTGGG-HHHHHHHHHHHTTTSEEEEE--SS--SHHHHHHHT-TT- CS
                          NTPase_1  77 dvesfeela..lea.lrkalseadviviDEiGkmElkskkfkeaveevLksekpvlavihrrkdlalveeirerkdv 150
                                       + + f e++  ++  +++al +adv++iD  G +     ++k++  ev+++e  ++a  ++ + +++++ ++++  +
  gi|242398700|ref|YP_002994124.1| 105 N-QFFGEMItgVKLlVNEALDTADVLIIDTTGLIHGPGVELKRMKIEVIQPEI-IIALQKKDELENIIRPFEKK--A 177
                                       9.5666654113332567779***********999999999999889988765.44444444466777777766..6 PP

                                       EEEE--TTT CS
                          NTPase_1 151 kvfevteen 159
                                       kvf+++ ++
  gi|242398700|ref|YP_002994124.1| 178 KVFRLKISE 186
                                       666655444 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   7.2e-05     0.086       3      27 ..      29      53 ..      27      61 .. 0.92
   2 ?   -3.4   0.0       6.1   7.3e+03      57      81 ..     147     171 ..     126     177 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.2e-05
                         PduV-EutP  3 killiGkvgsGKttLtqalkgeelk 27
                                      k++++G v+sGKttL+  l++e lk
  gi|242398700|ref|YP_002994124.1| 29 KVMILGGVDSGKTTLAVFLTNELLK 53
                                      8***************999998876 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 6.1
                         PduV-EutP  57 livtsaeadvialvqdateeesvfp 81 
                                       +++  ++ ++i  +q+ +e e+++ 
  gi|242398700|ref|YP_002994124.1| 147 MKIEVIQPEIIIALQKKDELENIIR 171
                                       5555666777777777777776665 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.1   0.00093       1.1       4      37 ..      17      50 ..      15      59 .. 0.84
   2 ?    1.2   0.1      0.19   2.3e+02      72      83 ..     201     212 ..     195     249 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00093
                                      HHHGGTT.TTEEEEEEEESTTSSHHHHHHHHHHS CS
                               Arf  4 ilaklklkkkelrilllGLDnaGKtTilkklkle 37
                                      +++ ++++kk +++++lG   +GKtT+   l++e
  gi|242398700|ref|YP_002994124.1| 17 VIKVIEEVKKPVKVMILGGVDSGKTTLAVFLTNE 50
                                      677888999*********999*****98777665 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.19
                                       GGGGGGGCTTES CS
                               Arf  72 RplWknYfektd 83 
                                       R+ W++Yfe+ +
  gi|242398700|ref|YP_002994124.1| 201 REKWRKYFEQAQ 212
                                       678****99876 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1     0.013        15       1      23 [.      29      51 ..      29      64 .. 0.83
   2 ?    5.5   0.1     0.015        18      43      84 ..     123     162 ..      83     205 .. 0.62

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.013
                                      EEEEEESTTSSHHHHHHHHHTST CS
                          MMR_HSR1  1 evaivGrpNvGKStLinaltgek 23
                                      +v+i+G   +GK+tL   lt+e 
  gi|242398700|ref|YP_002994124.1| 29 KVMILGGVDSGKTTLAVFLTNEL 51
                                      699************99999873 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.015
                                       ETTEEEEEEECGGCSSHHHHHHHHHHHHHHHHCTSEEEEEEE CS
                          MMR_HSR1  43 lkgkeielvDtpGliegaseekglgkaflaleeadlillvvd 84 
                                       l+  ++ ++Dt Gli+g   + +l++   ++++ ++i+ + +
  gi|242398700|ref|YP_002994124.1| 123 LDTADVLIIDTTGLIHGP--GVELKRMKIEVIQPEIIIALQK 162
                                       445789*******99722..2233333333334444444443 PP

>> LpxK  Tetraacyldisaccharide-1-P 4'-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.2   0.00025       0.3      27      71 ..      20      61 ..      13      63 .. 0.90
   2 ?   -3.7   0.0         4   4.8e+03     237     252 ..      79      94 ..      77     110 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00025
                                      SS--B--SS-EEEEEESBSS-HSHHHHHHHHHHHTTTS..-EEEE CS
                              LpxK 27 llkserlpvpVivVGNitvGGtGKTPlvialvkllqarglkvgvl 71
                                      ++++++ pv+V++ G +    +GKT l++ l + l ++g+kvgv+
  gi|242398700|ref|YP_002994124.1| 20 VIEEVKKPVKVMILGGVD---SGKTTLAVFLTNELLKNGFKVGVI 61
                                      567788899999999997...78********************98 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 4
                                       TTHHHHHHHHHHHT-- CS
                              LpxK 237 gnPerFfktLealgle 252
                                       g Pe++f++Le+ ++e
  gi|242398700|ref|YP_002994124.1|  79 GFPEKVFNSLEEIKAE 94 
                                       7788888888887655 PP

>> DUF3323  Protein of unknown function N-terminus (DUF3323)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   1.9    0.0024       2.9      63      87 ..     188     212 ..     181     227 .. 0.88
   2 ?   -1.0   0.0       1.2   1.4e+03      10      33 ..     234     257 ..     232     265 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0024
                           DUF3323  63 eplltrkeeraaeaeawaavfaale 87 
                                        +l+tr+e+r+ ++e+w+++f++++
  gi|242398700|ref|YP_002994124.1| 188 AKLHTREERRRIRREKWRKYFEQAQ 212
                                       6899*******************98 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.2
                           DUF3323  10 lteeerealggllgrrlrpgesvr 33 
                                        t++e+e l++l+++ +++g++v+
  gi|242398700|ref|YP_002994124.1| 234 VTKKEKEMLENLFKWIIFHGRKVS 257
                                       6899**********9999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       832  (0.0464053); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); 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: 2501.11
//
Query:       gi|242398701|ref|YP_002994125.1|  [L=154]
Description: Transcriptional regulatory protein, asnC family [Thermococcus sibiricus MM 739]
Scores for complete 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   33.7   0.0    4.4e-08   32.9   0.0    1.4  1  MarR_2          MarR family
    3.5e-08   33.3   0.8    8.2e-08   32.1   0.8    1.6  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
    8.5e-08   32.1   2.8    1.4e-07   31.4   0.2    2.1  2  HTH_Crp_2       Crp-like helix-turn-helix domain
    8.2e-07   28.9   0.6    5.2e-06   26.3   0.6    2.3  1  HTH_11          HTH domain
    2.8e-06   27.3   0.1    7.9e-06   25.8   0.1    1.8  1  HTH_20          Helix-turn-helix domain
    4.4e-06   26.4   0.4    1.3e-05   24.9   0.0    1.9  2  HTH_5           Bacterial regulatory protein, arsR family
    5.4e-06   25.9   0.1    1.1e-05   24.8   0.1    1.6  1  HTH_24          Winged helix-turn-helix DNA-binding
    7.3e-06   25.8   0.5    1.6e-05   24.7   0.5    1.5  1  MarR            MarR family
     0.0001   22.0   0.1    0.00023   20.8   0.1    1.7  1  LexA_DNA_bind   LexA DNA binding domain
     0.0012   18.9   0.0     0.0026   17.9   0.0    1.5  1  HTH_34          Winged helix DNA-binding domain
     0.0014   19.0   0.2     0.0041   17.4   0.0    1.8  2  Rrf2            Transcriptional regulator
     0.0021   17.5   0.1     0.0092   15.5   0.1    2.2  1  Sigma70_r4      Sigma-70, region 4
     0.0049   16.7   0.4       0.18   11.7   0.0    2.6  3  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0098   16.0   0.1      0.025   14.7   0.1    1.7  1  TxDE            Toxoflavin-degrading enzyme
  ------ inclusion threshold ------
      0.011   16.3   0.7      0.026   15.0   0.2    2.0  2  HTH_27          Winged helix DNA-binding domain
      0.018   14.9   2.1       0.19   11.6   0.1    2.6  2  HTH_10          HTH DNA binding domain
      0.024   14.4   0.0      0.065   13.0   0.0    1.8  1  HTH_IclR        IclR helix-turn-helix domain
      0.033   13.7   0.8       0.94    9.1   0.8    2.5  1  GerE            Bacterial regulatory proteins, luxR family
      0.037   14.3   3.5      0.066   13.4   0.4    2.6  2  UPF0122         Putative helix-turn-helix protein, YlxM / p13
      0.044   13.7   1.5      0.048   13.6   0.1    1.8  2  HTH_36          Helix-turn-helix domain
      0.052   14.1   0.3       0.09   13.3   0.3    1.7  1  AAA_assoc_C     C-terminal AAA-associated domain
      0.056   13.5   2.4       0.47   10.6   0.3    2.8  2  HTH_7           Helix-turn-helix domain of resolvase
      0.058   13.3   0.4       0.11   12.5   0.1    1.6  2  AbiEii          Nucleotidyl transferase AbiEii toxin, Type IV
      0.062   12.9   0.0       0.15   11.6   0.0    1.6  1  HTH_CodY        CodY helix-turn-helix domain
      0.095   12.5   0.0       0.26   11.1   0.0    1.8  1  HTH_23          Homeodomain-like domain
       0.12   12.9   2.4       0.57   10.7   2.4    2.3  1  HTH_40          Helix-turn-helix domain
       0.13   12.4   2.9        8.1    6.7   0.0    3.1  3  Mrr_N           Mrr N-terminal domain


Domain annotation for each model (and alignments):
>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.0   6.6e-11   4.4e-08       3      55 ..       7      65 ..       5      70 .. 0.92

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 6.6e-11
                                      --HHHHHHHHHHHCTTTS.......EEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2  3 ltpaqarvLaaLgrrpgr.......dltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                      lt  q ++L  L+ ++         + t+ e+a++l ++++a+s++lk L + G++++ +
  gi|242398701|ref|YP_002994125.1|  7 LTSRQMDLLRKLYQEGKTievhtveK-TQDEIADELSITRQALSNHLKTLKELGYIRTGR 65
                                      8999***********988*9997755.******************************976 PP

>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.8   1.2e-10   8.2e-08       2      75 .]      88     153 ..      87     153 .. 0.95

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 1.2e-10
                                       EEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEEE CS
                    AsnC_trans_reg   2 lvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivlet 75 
                                        v++ep +    +++ e +++l+ ++ ++rvtGd d++++   +d   l+++l+e +asl+gv++t t++vlet
  gi|242398701|ref|YP_002994125.1|  88 FVRIEPTK---RKQVYESIRKLK-IKRIHRVTGDIDLIVE---ADKTRLDEILEE-VASLDGVRETITHVVLET 153
                                       68899888...99********99.****************...9***********.****************96 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.2   2.1e-10   1.4e-07       9      62 ..      17      73 ..       9      75 .. 0.78
   2 ?    0.7   0.2      0.81   5.4e+02      33      65 ..      94     129 ..      93     132 .. 0.70

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 2.1e-10
                                      HHHCTTTC...EEEEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETEE.EEES-H CS
                         HTH_Crp_2  9 rlaeragg...eielpltqeelAsmlGltretvsrilseLkreglisrgrr.irildl 62
                                      +l+++ g+     ++  tq+e+A+ l +tr+ +s  l+ Lk+ g+i++gr+ i ++d 
  gi|242398701|ref|YP_002994125.1| 17 KLYQE-GKtieVHTVEKTQDEIADELSITRQALSNHLKTLKELGYIRTGRGfIDLTDK 73
                                      45444.22242225788******************************99888999885 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.81
                                       SSHHHHHHHHHHHHHTTSEE.ETE.E.EEES-HHHH CS
                         HTH_Crp_2  33 ltretvsrilseLkreglis.rgr.r.irildleaL 65 
                                       + r +v   +++Lk + +++ +g  + i+  d  +L
  gi|242398701|ref|YP_002994125.1|  94 TKRKQVYESIRKLKIKRIHRvTGDiDlIVEADKTRL 129
                                       57889999999**99999996663134555555555 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.6   7.8e-09   5.2e-06      17      44 ..      33      60 ..      10      68 .. 0.80

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 7.8e-09
                            HTH_11 17 sgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                      + +e+A+eL+++r++  +++k+L+elg+
  gi|242398701|ref|YP_002994125.1| 33 TQDEIADELSITRQALSNHLKTLKELGY 60
                                      789************************5 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.1   1.2e-08   7.9e-06      25      58 ..      32      65 ..       9      67 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 1.2e-08
                                      B-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                            HTH_20 25 ltaselaerldlskntlsyHLrvLeeagLvevvr 58
                                       t  e+a++l+++++ ls+HL++L e g++++ r
  gi|242398701|ref|YP_002994125.1| 32 KTQDEIADELSITRQALSNHLKTLKELGYIRTGR 65
                                      56679*************************9865 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 ?   -2.1   0.1       5.5   3.6e+03      36      43 ..      15      22 ..      12      22 .. 0.88
   2 !   24.9   0.0     2e-08   1.3e-05      17      46 ..      33      62 ..      30      63 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 5.5
                                      HHHHHHTT CS
                             HTH_5 36 LkkLreaG 43
                                      L+kL+++G
  gi|242398701|ref|YP_002994125.1| 15 LRKLYQEG 22
                                      89999987 PP

  == domain 2  score: 24.9 bits;  conditional E-value: 2e-08
                                      EHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5 17 cvcelaeelglsqstvShHLkkLreaGLVe 46
                                      +  e+a+el +++ ++S HLk L+e+G+++
  gi|242398701|ref|YP_002994125.1| 33 TQDEIADELSITRQALSNHLKTLKELGYIR 62
                                      5679************************97 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.1   1.7e-08   1.1e-05      19      48 .]      33      62 ..      31      62 .. 0.97

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 1.7e-08
                            HTH_24 19 sqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      +q e+A++l +++++++ +lk L+e G+I+
  gi|242398701|ref|YP_002994125.1| 33 TQDEIADELSITRQALSNHLKTLKELGYIR 62
                                      89***************************7 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.5   2.5e-08   1.6e-05       1      48 [.       7      62 ..       7      63 .. 0.95

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 2.5e-08
                                      --HHHHHHHHHHHHSTT.EEHH.......HHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR  1 ltltqfviLrilyeqgp.lsvs.......eLakklgvskstvtrvldrLekkGlie 48
                                      lt  q+++Lr+ly++g  + v+       e+a+ l++++ ++++ l++L + G+i+
  gi|242398701|ref|YP_002994125.1|  7 LTSRQMDLLRKLYQEGKtIEVHtvektqdEIADELSITRQALSNHLKTLKELGYIR 62
                                      899*************977777999*****************************96 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 !   20.8   0.1   3.5e-07   0.00023       2      58 ..       5      63 ..       4      68 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 3.5e-07
                                      X---HHHHHHHHHHHH...HHHHHSS---HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE- CS
                     LexA_DNA_bind  2 kkLTerQrevldlika...sieetgypPsireiaralglkSpsaveehLkaLerKGyier 58
                                      +kLT rQ ++l+ + +    ie +    +  eia++l ++  +a  +hLk+L+  Gyi+ 
  gi|242398701|ref|YP_002994125.1|  5 SKLTSRQMDLLRKLYQegkTIEVHTVEKTQDEIADELSIT-RQALSNHLKTLKELGYIRT 63
                                      79**********99752226999*****************.9****************96 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   3.8e-06    0.0026      17      50 ..      34      67 ..      26      74 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3.8e-06
                            HTH_34 17 fvelkealeatdgnLsvhlkkLekagYievdkef 50
                                        e+ ++l++t  +Ls hlk+L++ gYi    +f
  gi|242398701|ref|YP_002994125.1| 34 QDEIADELSITRQALSNHLKTLKELGYIRTGRGF 67
                                      57899***********************977666 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   6.1e-06    0.0041      27      60 ..      33      66 ..      14      68 .. 0.91
   2 ?   -1.6   0.0       5.5   3.7e+03      63      82 ..     116     135 ..      92     136 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 6.1e-06
                                      -HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT CS
                              Rrf2 27 sseeiaerqnispsylekilakLrkaglvksvrG 60
                                      + +eia++ +i ++ l+  l++L++ g++++ rG
  gi|242398701|ref|YP_002994125.1| 33 TQDEIADELSITRQALSNHLKTLKELGYIRTGRG 66
                                      679****************************999 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 5.5
                                       TCEEESSHCCCSBHHHHHHH CS
                              Rrf2  63 GGyrLakppeeItlldvvra 82 
                                       G + L  ++++ +l ++++ 
  gi|242398701|ref|YP_002994125.1| 116 GDIDLIVEADKTRLDEILEE 135
                                       55667777777777777765 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   1.4e-05    0.0092       4      40 ..       6      51 ..       5      58 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.4e-05
                                      HS-HHHHHHHHHHH.........TTT--HHHHHHHHTS-HHHHHHH CS
                        Sigma70_r4  4 sLpererevlelrf.........geglTleEIgerlgiSrerVrqi 40
                                      +L+ r+ + l+  +           + T+ EI+++l i+r + + +
  gi|242398701|ref|YP_002994125.1|  6 KLTSRQMDLLRKLYqegktievhTVEKTQDEIADELSITRQALSNH 51
                                      79999*****99999999999997777*************876655 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   0.00027      0.18      21      54 ..      30      63 ..      27      67 .. 0.91
   2 ?    2.2   0.1      0.25   1.7e+02      36      47 ..      96     107 ..      90     111 .. 0.86
   3 ?   -2.3   0.0       6.3   4.2e+03      31      45 ..     121     135 ..     113     143 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00027
                                      CCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEE CS
                              TrmB 21 gpatadeiaeelgvprskvYevLrsLedkGlVer 54
                                       ++t deia el + r+   + L+ L++ G++++
  gi|242398701|ref|YP_002994125.1| 30 VEKTQDEIADELSITRQALSNHLKTLKELGYIRT 63
                                      57899**************************986 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.25
                                       CHCHHHHHHHHH CS
                              TrmB  36 rskvYevLrsLe 47 
                                       r +vYe++r+L+
  gi|242398701|ref|YP_002994125.1|  96 RKQVYESIRKLK 107
                                       889*******97 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 6.3
                                       CTTSSCHCHHHHHHH CS
                              TrmB  31 elgvprskvYevLrs 45 
                                       +++ ++++  e+L++
  gi|242398701|ref|YP_002994125.1| 121 IVEADKTRLDEILEE 135
                                       455556666666554 PP

>> TxDE  Toxoflavin-degrading enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   3.7e-05     0.025       3      50 ..      40      89 ..      39      96 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.7e-05
                              TxDE  3 EiglttedvksvgeqLeeigIpl..rdneeiepdaLNFlGekedgayiLL 50
                                      E ++t +  ++  ++L+e+g     r   +++ +aL FlGek+ +++i +
  gi|242398701|ref|YP_002994125.1| 40 ELSITRQALSNHLKTLKELGYIRtgRGFIDLTDKALEFLGEKKGDVFIFV 89
                                      778888888888899999986441134446799**************975 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.2   3.8e-05     0.026      18      67 ..      31      73 ..       7      74 .. 0.87
   2 ?   -1.7   0.0       6.6   4.4e+03      35      43 ..      99     107 ..      96     116 .. 0.58

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.8e-05
                            HTH_27 18 rkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdk 67
                                      +k++ ++++ l ++ ++ s+ lk L e G++ rtg      + ++ lTdk
  gi|242398701|ref|YP_002994125.1| 31 EKTQDEIADELSITRQALSNHLKTLKELGYI-RTG------RGFIDLTDK 73
                                      58889**************************.333......379999998 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 6.6
                            HTH_27  35 isyslkkLt 43 
                                       + +s++kL 
  gi|242398701|ref|YP_002994125.1|  99 VYESIRKLK 107
                                       445666653 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.24   1.6e+02       1      16 [.       7      22 ..       7      22 .. 0.88
   2 ?   11.6   0.1   0.00028      0.19      25      46 ..      33      54 ..      31      57 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.24
                            HTH_10  1 LTdkqlevlklAyemG 16
                                      LT +q+  l++ y+ G
  gi|242398701|ref|YP_002994125.1|  7 LTSRQMDLLRKLYQEG 22
                                      9*********988776 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00028
                            HTH_10 25 tlkeLAkelGIskstlsehLrk 46
                                      t +e+A+el I++++ls+hL+ 
  gi|242398701|ref|YP_002994125.1| 33 TQDEIADELSITRQALSNHLKT 54
                                      6689****************85 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   9.8e-05     0.065      22      49 ..      35      62 ..      12      64 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9.8e-05
                                      HHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR 22 selArrtglpkStvhRlLqtLvelGyve 49
                                       e+A+++ +++ + +++L+tL elGy++
  gi|242398701|ref|YP_002994125.1| 35 DEIADELSITRQALSNHLKTLKELGYIR 62
                                      59************************98 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.8    0.0014      0.94      18      41 ..      32      55 ..       5      57 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0014
                                      S-HHHHHHHHTS-HHHHHHHHHHH CS
                              GerE 18 ksnkeIAeelniSekTVkvhksni 41
                                      k+  eIA+el+i  +  ++h++ +
  gi|242398701|ref|YP_002994125.1| 32 KTQDEIADELSITRQALSNHLKTL 55
                                      6778****************9876 PP

>> UPF0122  Putative helix-turn-helix protein, YlxM / p13 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.4    0.0001     0.066      18      59 ..       7      57 ..       3      60 .. 0.69
   2 ?    0.3   0.2       1.3   8.6e+02      46      58 ..      95     107 ..      89     147 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.0001
                           UPF0122 18 LTekqanylelyyadDlSl.........sEiAeefnvsrqavydnikrtek 59
                                      LT++q++ l+  y++   +          EiA+e  ++rqa+++++k+ ++
  gi|242398701|ref|YP_002994125.1|  7 LTSRQMDLLRKLYQEGKTIevhtvektqDEIADELSITRQALSNHLKTLKE 57
                                      77777777777776654432222222226*****************99775 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.3
                           UPF0122  46 srqavydnikrte 58 
                                       +r+ vy++i++ +
  gi|242398701|ref|YP_002994125.1|  95 KRKQVYESIRKLK 107
                                       4555666665543 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   7.3e-05     0.048      27      55 .]      33      61 ..      15      61 .. 0.93
   2 ?   -2.0   0.2       5.6   3.7e+03      38      49 ..      95     106 ..      94     107 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.3e-05
                            HTH_36 27 sqetlakrlglsknTvsraikeLeqlGyi 55
                                      +q+ +a  l + ++  s+++k L +lGyi
  gi|242398701|ref|YP_002994125.1| 33 TQDEIADELSITRQALSNHLKTLKELGYI 61
                                      799*************************9 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 5.6
                            HTH_36  38 sknTvsraikeL 49 
                                       ++++v+  i++L
  gi|242398701|ref|YP_002994125.1|  95 KRKQVYESIRKL 106
                                       689999999998 PP

>> AAA_assoc_C  C-terminal AAA-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.3   0.00014      0.09       2      48 ..      36      82 ..      35     150 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00014
                       AAA_assoc_C  2 eLaeelelevddLlpiveaaelLglveveegdielTelGrkfveadi 48
                                      e+a+el+++ + L + +++++ Lg +++ +g i lT++  +f+  + 
  gi|242398701|ref|YP_002994125.1| 36 EIADELSITRQALSNHLKTLKELGYIRTGRGFIDLTDKALEFLGEKK 82
                                      69***************************************998765 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.3    0.0007      0.47       5      36 ..       6      46 ..       4      48 .. 0.72
   2 ?   -2.2   0.1       6.7   4.5e+03       2      14 ..     104     114 ..     104     115 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0007
                                      SS-HHHHGGGGSSTTTT--ST.........TTSSSS---SS CS
                             HTH_7  5 klskndinrvvkLleeGisis.........kIAkevnisRs 36
                                      kl++ +++ ++kL++eG +i          +IA+e+ i+R+
  gi|242398701|ref|YP_002994125.1|  6 KLTSRQMDLLRKLYQEGKTIEvhtvektqdEIADELSITRQ 46
                                      677779***********998533333343468888888887 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 6.7
                                       ---SS-HHHHGGG CS
                             HTH_7   2 Rpsklskndinrv 14 
                                       R++k+++  i+rv
  gi|242398701|ref|YP_002994125.1| 104 RKLKIKR--IHRV 114
                                       7888887..7877 PP

>> AbiEii  Nucleotidyl transferase AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       3.5   2.3e+03     216     216 ..      47      47 ..       8      99 .. 0.60
   2 ?   12.5   0.1   0.00016      0.11      27      60 ..     108     139 ..     102     152 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3.5
                            AbiEii 216 d 216
                                        
  gi|242398701|ref|YP_002994125.1|  47 A 47 
                                       2 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00016
                            AbiEii  27 yglipRfSeDIDlsllrgdrkellealkealeei 60 
                                       +++i+R + DIDl +    +k+ l+++ e ++ +
  gi|242398701|ref|YP_002994125.1| 108 IKRIHRVTGDIDLIV--EADKTRLDEILEEVASL 139
                                       578***********9..67777777766666554 PP

>> HTH_CodY  CodY helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00023      0.15       8      34 ..      35      61 ..      31      66 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00023
                          HTH_CodY  8 skiaDriGitrsvivnaLrkLesaGii 34
                                       +iaD++ itr  + n L+ L   G i
  gi|242398701|ref|YP_002994125.1| 35 DEIADELSITRQALSNHLKTLKELGYI 61
                                      68*******************998877 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00039      0.26      18      45 ..      32      59 ..      17      63 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00039
                            HTH_23 18 lsvreIAreLgvsrrTvyrwlkryreeG 45
                                      +++ eIA+eL ++r+ +++ lk+ +e G
  gi|242398701|ref|YP_002994125.1| 32 KTQDEIADELSITRQALSNHLKTLKELG 59
                                      7999***************999987655 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   2.4   0.00086      0.57       4      45 ..      23      63 ..      15     144 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00086
                            HTH_40  4 etlelleeglsieeIAkerglkesTIegHLaelieegeeidl 45
                                      +t+e +   ++ +eIA+e +++++   +HL  l e g+ i  
  gi|242398701|ref|YP_002994125.1| 23 KTIEVHTVEKTQDEIADELSITRQALSNHLKTLKELGY-IRT 63
                                      5777777788999**********************985.333 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.3     0.029        19      15      43 ..      25      53 ..      11      57 .. 0.81
   2 ?    6.7   0.0     0.012       8.1      59      85 ..      53      78 ..      50      80 .. 0.88
   3 ?    0.1   0.0       1.4   9.2e+02      14      36 ..     123     145 ..     118     153 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.029
                             Mrr_N 15 gsehrlkeirervaerfglseeeraellp 43
                                       ++h++++ ++++a++++++ ++++  l+
  gi|242398701|ref|YP_002994125.1| 25 IEVHTVEKTQDEIADELSITRQALSNHLK 53
                                      578999***************99988876 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.012
                             Mrr_N 59 tyLkkagllespkrgvwkiTekGrevl 85
                                      ++Lk+ g++ +  rg++ +T+k  e+l
  gi|242398701|ref|YP_002994125.1| 53 KTLKELGYIRTG-RGFIDLTDKALEFL 78
                                      789999999877.*********99987 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 1.4
                             Mrr_N  14 dgsehrlkeirervaerfglsee 36 
                                       +   +rl+ei e+va+  g+ e 
  gi|242398701|ref|YP_002994125.1| 123 EADKTRLDEILEEVASLDGVRET 145
                                       55566779999999988777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1271  (0.0708907); expected 358.6 (0.02)
Passed bias filter:                      837  (0.0466841); 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: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 1105.73
//
Query:       gi|242398702|ref|YP_002994126.1|  [L=190]
Description: Probable GTP-binding protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-17   63.4   0.0    2.8e-17   62.8   0.0    1.3  1  MMR_HSR1      50S ribosome-binding GTPase
    2.5e-11   43.4   0.5      3e-10   39.8   0.5    2.2  1  FeoB_N        Ferrous iron transport protein B
    5.2e-08   32.7   0.1    3.4e-06   26.7   0.1    2.3  2  GTP_EFTU      Elongation factor Tu GTP binding domain
    1.4e-05   25.1   2.0       0.02   14.8   0.3    2.9  2  RsgA_GTPase   RsgA GTPase
    0.00039   20.0   0.1       0.16   11.6   0.0    2.3  2  Ras           Ras family
     0.0035   16.8   0.3      0.015   14.8   0.3    2.2  1  SRPRB         Signal recognition particle receptor beta subun
      0.007   16.4   2.0      0.041   13.9   0.6    2.6  3  Dynamin_N     Dynamin family
     0.0071   15.4   0.8       0.47    9.4   0.1    2.2  2  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
     0.0076   16.5   0.7      0.065   13.5   0.0    2.5  2  Roc           Ras of Complex, Roc, domain of DAPkinase
  ------ inclusion threshold ------
      0.021   14.7   0.1      0.038   13.9   0.1    1.4  1  MobB          Molybdopterin guanine dinucleotide synthesis pr
      0.032   13.5   0.0       0.05   12.9   0.0    1.3  1  AIG1          AIG1 family
      0.039   13.7   0.6       0.44   10.3   0.1    2.3  2  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
      0.051   13.4   0.3       0.84    9.4   0.0    2.4  2  ATP_bind_1    Conserved hypothetical ATP binding protein
       0.06   13.4   0.8        0.1   12.6   0.1    1.7  2  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 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 !   62.8   0.0   2.2e-20   2.8e-17       2     114 .]       2     129 ..       1     129 [. 0.76

  Alignments for each domain:
  == domain 1  score: 62.8 bits;  conditional E-value: 2.2e-20
                                       EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGC.........SSHHHHHHHHHHH CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGl.........iegaseekglgka 69 
                                       +++vGr+NvGKStLi +ltg+ ++ +++pg Tr+++e+ ++  g   ++vD+pG+         i +++ + ++ + 
  gi|242398702|ref|YP_002994126.1|   2 IIFVGRSNVGKSTLIFRLTGKYVKRGKRPGITRKPIEIGWR--G--KTIVDMPGFgfmsgvpkyI-QEKIKTEIVQF 73 
                                       799***********************************998..5..58******65555543322.23333333333 PP

                                       HHHHHC.TSEEEEEEETT..........TTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                          MMR_HSR1  70 flalee.adlillvvdas..........eeklkpldeeleelleeakkplilvlnk 114
                                       ++++ +  + ++lv+d +          +++  p+d e+ ++l+e ++p+i+++nk
  gi|242398702|ref|YP_002994126.1|  74 IENNADkIETAVLVIDGKsaleiierweKRGEIPIDVEFFQFLQELEIPIIVAVNK 129
                                       33333348999*****66888887777633346899999****99*********98 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 !   39.8   0.5   2.4e-13     3e-10       3     127 ..       2     142 ..       1     178 [. 0.72

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 2.4e-13
                                       EEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSS..SSSSHHHHHHHHHHH.. CS
                            FeoB_N   3 valvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYsl..sayseeekvardfll.. 75 
                                       +++vG  nvGk+tl+ +ltg++ k g  pG+t +  e   +      +ivD+PG   +   +  ++ek+ ++++   
  gi|242398702|ref|YP_002994126.1|   2 IIFVGRSNVGKSTLIFRLTGKYVKRGKRPGITRKPIEIGWR----GKTIVDMPGFGFMsgVPKYIQEKIKTEIVQfi 74 
                                       789****************************9766665555....5679****986662356678999998877655 PP

                                       ...CTSSSEEEEEEEGGG....HHH.........HHHHHHHHHHTTSSEEEEEETHHHHHHTTEEE-H CS
                            FeoB_N  76 ...eeepdvvvnvvdatn....ler.........nLyLtlqllelgvpvvlalnmideaekkgieidl 127
                                           +++++ v v+d ++    +er         ++ ++  l el++p+++a+n++d++++ +++i+ 
  gi|242398702|ref|YP_002994126.1|  75 ennADKIETAVLVIDGKSaleiIERwekrgeipiDVEFFQFLQELEIPIIVAVNKMDKIKNLNLTINR 142
                                       555567788899***8653333455433443333466777799*****************99998874 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.024        31       6      27 ..       2      23 ..       1      51 [. 0.83
   2 !   26.7   0.1   2.7e-09   3.4e-06      90     192 ..      77     182 ..      70     184 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.024
                                      EEEEESTTSSHHHHHHHHHHHT CS
                          GTP_EFTU  6 igiighvDhGKtTLtdrLlykt 27
                                      i+++g  + GK+TL+ rL+ k 
  gi|242398702|ref|YP_002994126.1|  2 IIFVGRSNVGKSTLIFRLTGKY 23
                                      6789999********9998554 PP

  == domain 2  score: 26.7 bits;  conditional E-value: 2.7e-09
                                       HHHT-SEEEEEEETT...........TBSTHHHHHHHHHHHHTTTEEEEEEESCGSTHHHHHHHHHHHHHHHHHHHH CS
                          GTP_EFTU  90 glrvlDgavlvvdav...........eGvepqteevlrlalkegvpiivfiNKmDrlkaelkeiveevkqklsrkee 155
                                        + +++ avlv+d +           +G  p   e ++ ++++++piiv++NKmD++ ++l+ +++ + +k+     
  gi|242398702|ref|YP_002994126.1|  77 NADKIETAVLVIDGKsaleiierwekRGEIPIDVEFFQFLQELEIPIIVAVNKMDKI-KNLNLTINRLIEKF----- 147
                                       567788999999999777777777777788999999********************8.46777777777799..... PP

                                       HHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHHHS CS
                          GTP_EFTU 156 klekygekgekevpvvfgSalkgegvktllealvell 192
                                        l   +e+   +  +v++Sa+ g ++++l + + +++
  gi|242398702|ref|YP_002994126.1| 148 GLLGTWEDY--KDIFVPISAKFGTNIQELRKLIEKNI 182
                                       455555555..3569*************999988876 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.3   1.6e-05      0.02     102     123 ..       2      23 ..       1      56 [. 0.70
   2 !    8.4   0.1    0.0014       1.8      40     100 ..     114     181 ..     109     184 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.6e-05
                                       EEEECSTTSSHHHHHHHHCTT- CS
                       RsgA_GTPase 102 svlvGqSGvGKStLinallpel 123
                                       +++vG S vGKStLi +l+++ 
  gi|242398702|ref|YP_002994126.1|   2 IIFVGRSNVGKSTLIFRLTGKY 23 
                                       79****************9983 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0014
                                       HHHHHTT-EEEEEEE-GGG--HHH.HHHHHHHHHHHTT....SE..EEE--TTTHTTHHHHHHHCTTS CS
                       RsgA_GTPase  40 vlaeekgiepvivlnKiDlleeee.eleelkeelealg....ye..vllvsaktkegleelkellkdk 100
                                        +++e +i++++++nK+D +++ + ++++l e++  lg    y+  ++ +sak +++++el++l++++
  gi|242398702|ref|YP_002994126.1| 114 QFLQELEIPIIVAVNKMDKIKNLNlTINRLIEKFGLLGtwedYKdiFVPISAKFGTNIQELRKLIEKN 181
                                       5778999***************9986666666554444222244114456777788888888888776 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   0.00012      0.16       2      30 ..       2      30 ..       1      46 [. 0.82
   2 !    6.7   0.0    0.0039       4.9     103     160 ..     119     182 ..      65     184 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00012
                                      EEEEESTTSSHHHHHHHHHHSSCSSSCTT CS
                               Ras  2 lvlvGdsavGKtslllrfvkdkFkeeyes 30
                                      +++vG s+vGK++l++r + ++ k+ + +
  gi|242398702|ref|YP_002994126.1|  2 IIFVGRSNVGKSTLIFRLTGKYVKRGKRP 30
                                      799**************998776665555 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0039
                                       TTSEEEEEEETTTGGG......G-SS-HHHHHHHHHHHTSEEEEEBTTTTCTHHHHHHHHHHHH CS
                               Ras 103 envpivLvGnKvDlee......kravsteegeelakelglkfletSAktnenveeafeellrei 160
                                        ++pi++  nK+D  +      +r +++     + ++++  f+ +SAk  +n++e+ + + ++i
  gi|242398702|ref|YP_002994126.1| 119 LEIPIIVAVNKMDKIKnlnltiNRLIEKFGLLGTWEDYKDIFVPISAKFGTNIQELRKLIEKNI 182
                                       458999999****88778888899999998889999******************9877777766 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 !   14.8   0.3   1.1e-05     0.015       6     124 ..       2     132 ..       1     146 [. 0.76

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.1e-05
                                       EEEE-STTSSHHHHHHHHHHSS---B---SS-EEETTG...GGTT-SEEEETT...........-GCCSHHHHHHHH CS
                             SRPRB   6 vllvGlsdsGKTslftrLttdsvkktvtSqessaalkvksekgskltliDfPG...........heklrqklleklk 71 
                                       +++vG s+ GK +l+ rLt + vk+        ++ k  +     +t++D+PG           +ek+++++++ + 
  gi|242398702|ref|YP_002994126.1|   2 IIFVGRSNVGKSTLIFRLTGKYVKRGKRPG---ITRKPIEIGWRGKTIVDMPGfgfmsgvpkyiQEKIKTEIVQFIE 75 
                                       89*****************99999887654...55554444777899*****9555555555555889999998887 PP

                                       HHGG.EEEEEEEEE..TTS-H.HHHHHHHHHHHHHHHHHHHHTT---EEEEEE-TTS CS
                             SRPRB  72 akss.lkglvfvvD..Stidp.kevkevAEllyeilliteklkdavdiliACnKqel 124
                                       +++  + + v v+D  S+ +   + ++  E  +++   + +++ +++i++A nK + 
  gi|242398702|ref|YP_002994126.1|  76 NNADkIETAVLVIDgkSALEIiERWEKRGEIPIDVEFFQFLQELEIPIIVAVNKMDK 132
                                       776669999999994444443134566788888888888888999999999999885 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.6   3.2e-05     0.041       1      40 [.       2      41 ..       2      84 .. 0.80
   2 ?   -1.4   0.0       1.7   2.1e+03     139     164 ..      63      88 ..      55      98 .. 0.77
   3 ?   -3.1   0.0       5.7   7.3e+03      63      79 ..     169     185 ..     157     188 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.2e-05
                                      EEEEEBTTTTHHHHHHHHHTS--S---SSS---S-EEEEE CS
                         Dynamin_N  1 iavvGsqSsGKSSvlnaLlgedilprgpnptTrrplelql 40
                                      i++vG  + GKS+++  L+g+ +   +   +Tr+p+e+  
  gi|242398702|ref|YP_002994126.1|  2 IIFVGRSNVGKSTLIFRLTGKYVKRGKRPGITRKPIEIGW 41
                                      799*******************766555679*****9965 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.7
                                       TS-CCC-CHHHHHHHHSTTBTTEEEE CS
                         Dynamin_N 139 nhdlsnsealflarevdpkgkrtivv 164
                                       + ++++  ++f+++++d+ ++ ++v+
  gi|242398702|ref|YP_002994126.1|  63 QEKIKTEIVQFIENNADKIETAVLVI 88 
                                       55667777788888888887777776 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 5.7
                                       --CHHHHHHHHHHHHHH CS
                         Dynamin_N  63 edfsevreeieketeki 79 
                                       ++++e+r+ iek  +k+
  gi|242398702|ref|YP_002994126.1| 169 TNIQELRKLIEKNIKKS 185
                                       45666666666665554 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 !    9.4   0.1   0.00037      0.47      34      62 ..       4      32 ..       1      35 [. 0.88
   2 ?    4.4   0.0     0.012        16     166     229 ..     119     182 ..     116     188 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00037
                                      EEE-TTSSHHHHHHHHHHHHHCTT--EEE CS
                              MeaB 34 ltGvPGaGkstlvealglelrrrGkrvav 62
                                      + G   +Gkstl+ +l+ ++++rGkr ++
  gi|242398702|ref|YP_002994126.1|  4 FVGRSNVGKSTLIFRLTGKYVKRGKRPGI 32
                                      567888*******************9776 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.012
                                       HHH-SEEEEE---.HHHHHHHHHHHHHHHHHCSTTBTTB--EEEEEBCCCTBSHHHHHHHHHHHH CS
                              MeaB 166 leiaDiivvnkaD.kkeaekaarelraaleleeekekeWrpkvlktsavegeGidelvdaieehr 229
                                       lei  i++vnk D  k+ + + + l     l+ +  ++++   + +sa+ g  i+el + ie+  
  gi|242398702|ref|YP_002994126.1| 119 LEIPIIVAVNKMDkIKNLNLTINRLIEKFGLLGTW-EDYKDIFVPISAKFGTNIQELRKLIEKNI 182
                                       79999********7678888888888888877654.45777788889999999999998888765 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 !   13.5   0.0     5e-05     0.065       2      28 ..       2      28 ..       1      41 [. 0.86
   2 ?    0.8   0.1      0.42   5.3e+02     108     119 ..     120     131 ..      63     132 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5e-05
                                      EEEESSTTSSHHHHHHCHCT-CCC-EE CS
                               Roc  2 vvlvGdsgvGKtsllkrfvedkfseke 28
                                      +++vG s+vGK++l+ r++ + +++ +
  gi|242398702|ref|YP_002994126.1|  2 IIFVGRSNVGKSTLIFRLTGKYVKRGK 28
                                      89****************988877665 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.42
                                       SS-EEEEEE-TT CS
                               Roc 108 kspvilvgnkiD 119
                                       ++p+i+ +nk+D
  gi|242398702|ref|YP_002994126.1| 120 EIPIIVAVNKMD 131
                                       457777777777 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 ?   13.9   0.1     3e-05     0.038       2      32 ..       2      32 ..       1      38 [. 0.90

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3e-05
                              MobB  2 lgivgksgsGKTtLleklipelkarglrvgt 32
                                      + +vg+s+ GK tL+ +l  +  +rg r g+
  gi|242398702|ref|YP_002994126.1|  2 IIFVGRSNVGKSTLIFRLTGKYVKRGKRPGI 32
                                      789**********************998765 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   3.9e-05      0.05       3      92 ..       2      89 ..       1      99 [. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.9e-05
                                      EEEESSTTSSHHHHHHHHHTS--SS--TTTS---SS-EEEEEEETTEEEEEEE--SC.CCTTC...CHHCHHHHHHHHH CS
                              AIG1  3 ivlvGktgnGkSaTgNsilgkkaFesklsaqsvtkkcqkksrtwdgkkinViDTPgl.fdlsv...sadkiskeivrcl 77
                                      i+ vG++ +GkS+ +  + gk + + k    ++t+k+ +    w+gk+  ++D Pg  f + v    ++ki+ eiv+ +
  gi|242398702|ref|YP_002994126.1|  2 IIFVGRSNVGKSTLIFRLTGKYVKRGK--RPGITRKPIE--IGWRGKT--IVDMPGFgFMSGVpkyIQEKIKTEIVQFI 74
                                      89**************99999775555..899*999865..5799997..59****875554433369*********** PP

                                      HHCTT-ESEEEEEEE CS
                              AIG1 78 llseegihalllvls 92
                                      + +++ i+  +lv++
  gi|242398702|ref|YP_002994126.1| 75 ENNADKIETAVLVID 89
                                      *******99999987 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00034      0.44       4      30 ..       2      28 ..       1      93 [. 0.84
   2 ?    2.2   0.1      0.11   1.4e+02      84     142 ..     115     179 ..      72     180 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00034
                         PduV-EutP  4 illiGkvgsGKttLtqalkgeelkYkk 30
                                      i+++G++++GK tL  +l+g+ +k  k
  gi|242398702|ref|YP_002994126.1|  2 IIFVGRSNVGKSTLIFRLTGKYVKRGK 28
                                      89*****************98877554 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.11
                         PduV-EutP  84 fasvfnkeviGiitkidlaedee.nieaveelLksaGa....ekif.evsavekegieellkyle 142
                                       f + ++ ++i  + k+d+ ++ +  i+   e++   G     + if  +sa   ++i+el+k +e
  gi|242398702|ref|YP_002994126.1| 115 FLQELEIPIIVAVNKMDKIKNLNlTINRLIEKFGLLGTwedyKDIFvPISAKFGTNIQELRKLIE 179
                                       33444445555556666553221123333333334443322256653488888888888888776 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1      0.17   2.2e+02       2      24 ..       5      27 ..       4      32 .. 0.77
   2 ?    9.4   0.0   0.00065      0.84     152     209 ..     116     179 ..     110     185 .. 0.60

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.17
                        ATP_bind_1  2 vGpaGsGKttfvgalseilelrg 24
                                      vG   +GK+t++ +l+  + +rg
  gi|242398702|ref|YP_002994126.1|  5 VGRSNVGKSTLIFRLTGKYVKRG 27
                                      79999*******99986665555 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00065
                        ATP_bind_1 152 mlrlelPhvvvlnkfDllkeklekeleffedvealslllekee......ekykklaeaiaelle 209
                                       + +le+P +v++nk+D +k+ +      +e +  l + ++ ++       k+ ++ +++++l+e
  gi|242398702|ref|YP_002994126.1| 116 LQELEIPIIVAVNKMDKIKNLNLTINRLIEKFGLLGTWEDYKDifvpisAKFGTNIQELRKLIE 179
                                       5679*************99333333333333444444444333555555555555555555555 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 ?   -2.4   0.1       3.8   4.8e+03      18      32 ..      69      84 ..      59      99 .. 0.49
   2 ?   12.6   0.1   7.9e-05       0.1      56     100 ..     121     178 ..     108     183 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 3.8
                      MMR_HSR1_Xtn 18 etvkkilk.eykihna 32
                                      e v+ i +   ki  a
  gi|242398702|ref|YP_002994126.1| 69 EIVQFIENnADKIETA 84
                                      3333333212233333 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 7.9e-05
                      MMR_HSR1_Xtn  56 ipclyvlNKiDlisleel..delare...........pnsvviSaekelnldeLkeki 100
                                       ip ++++NK+D+i++ +l  ++l ++           +  v+iSa+ ++n++eL + i
  gi|242398702|ref|YP_002994126.1| 121 IPIIVAVNKMDKIKNLNLtiNRLIEKfgllgtwedykDIFVPISAKFGTNIQELRKLI 178
                                       799*********998776113444448899999988557889************9877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       913  (0.0509231); expected 358.6 (0.02)
Passed bias filter:                      600  (0.0334653); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 1299.90
//
Query:       gi|242398703|ref|YP_002994127.1|  [L=222]
Description: hypothetical protein TSIB_0715 [Thermococcus sibiricus MM 739]
Scores for complete 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   20.9   5.6    0.00041   20.5   5.6    1.2  1  UPF0242        Uncharacterised protein family (UPF0242) N-ter
     0.0025   18.2   6.9     0.0045   17.4   6.9    1.4  1  CENP-H         Centromere protein H (CENP-H)
     0.0053   16.1  13.5     0.0072   15.7  13.5    1.2  1  GAS            Growth-arrest specific micro-tubule binding
     0.0062   16.1   4.2      0.044   13.3   4.2    2.0  1  ANAPC4         Anaphase-promoting complex, cyclosome, subunit
  ------ inclusion threshold ------
      0.014   13.4   2.3      0.016   13.1   2.3    1.1  1  V_ATPase_I     V-type ATPase 116kDa subunit family
      0.028   14.1  11.7      0.054   13.2  11.7    1.4  1  SHE3           SWI5-dependent HO expression protein 3
      0.041   13.7  11.3        0.3   10.9   1.9    2.4  2  Phage_GP20     Phage minor structural protein GP20
      0.043   14.2   0.5      0.073   13.5   0.5    1.4  1  NAPRTase_N     Nicotinate phosphoribosyltransferase (NAPRTase
      0.062   12.6   9.8      0.045   13.1   7.8    1.7  2  Dynamitin      Dynamitin
      0.077   12.3   8.5       0.33   10.2   8.5    1.8  1  DUF3450        Protein of unknown function (DUF3450)
      0.077   12.9   6.6       0.14   12.0   6.6    1.5  1  PCRF           PCRF domain
      0.084   12.5   0.4       0.12   11.9   0.4    1.3  1  Foie-gras_1    Foie gras liver health family 1
      0.085   12.3  11.6       0.13   11.7  11.6    1.3  1  HMMR_N         Hyaluronan mediated motility receptor N-termin
       0.16   12.2  11.6       0.23   11.8  11.6    1.2  1  zf-C4H2        Zinc finger-containing protein
       0.25   11.1   3.0       0.27   11.0   1.4    1.8  1  Lectin_N       Hepatic lectin, N-terminal domain
       0.25   11.8   3.7        5.7    7.4   0.0    2.2  2  NUC            Nuclease domain
       0.27   11.2   2.9       0.45   10.5   2.3    1.7  1  Sec20          Sec20
       0.31   11.3   5.0       0.53   10.5   1.9    2.5  2  DASH_Dad1      DASH complex subunit Dad1
       0.31   11.3  14.4       0.57   10.4  14.4    1.4  1  TMF_TATA_bd    TATA element modulatory factor 1 TATA binding
       0.32   11.1   9.1        2.1    8.5   6.5    2.5  2  TolA_bind_tri  TolA binding protein trimerisation
        0.4    9.9   4.5       0.58    9.4   4.5    1.2  1  TMPIT          TMPIT-like protein
       0.41   10.8   5.7       0.85    9.8   1.4    3.3  4  YojJ           Bacterial membrane-spanning protein N-terminus
       0.43    9.6   4.5       0.58    9.2   4.5    1.3  1  eIF-4B         Plant specific eukaryotic initiation factor 4B
       0.43   10.2   3.6       0.79    9.3   3.6    1.5  1  LepB_N         LepB N-terminal domain
       0.44   10.6   6.3        7.2    6.7   6.0    2.3  1  DUF1664        Protein of unknown function (DUF1664)
       0.56    9.0  12.0       0.99    8.2  12.0    1.4  1  Spc7           Spc7 kinetochore protein
       0.57   10.2  13.3       0.96    9.5  12.9    1.5  1  DHR10          Designed helical repeat protein 10 domain
       0.65    9.8   8.2          3    7.7   8.2    2.1  1  FTA4           Kinetochore complex Fta4 of Sim4 subunit, or C
       0.78   10.4   8.8        1.2    9.8   1.7    2.8  2  SlyX           SlyX
       0.84   10.0   3.7        1.7    9.0   3.7    1.5  1  ATP-synt_E     ATP synthase E chain
          1    9.6   6.3        2.6    8.2   6.3    1.7  1  Fib_alpha      Fibrinogen alpha/beta chain family
          1    9.7  11.0        8.7    6.7   6.4    3.0  2  BLOC1_2        Biogenesis of lysosome-related organelles comp
          1    8.9   6.3        1.9    8.0   6.3    1.5  1  HAUS6_N        HAUS augmin-like complex subunit 6 N-terminus
        1.1    9.6  10.0        1.9    8.8   1.5    3.8  4  HALZ           Homeobox associated leucine zipper
        1.3    9.8   5.9         16    6.3   5.9    2.3  1  DUF2203        Uncharacterized conserved protein (DUF2203)
        1.7    8.2   7.5        2.5    7.6   6.2    1.9  2  Fzo_mitofusin  fzo-like conserved region
        1.8    8.1  12.8        1.5    8.4   8.5    2.1  2  DUF4795        Domain of unknown function (DUF4795)
        1.9    8.9  12.1        1.9    8.9   2.5    2.5  2  TSNAXIP1_N     Translin-associated factor X-interacting N-ter
        3.7    7.9   6.4        7.4    7.0   5.8    1.7  2  Ly49           Ly49-like protein, N-terminal region
        3.9    8.0  14.5         11    6.6  14.4    1.7  1  APG6_N         Apg6 coiled-coil region
        4.4    7.3   9.3        7.4    6.6   8.5    1.8  1  FlxA           FlxA-like protein
          5    7.6  14.7    2.1e+02    2.4   9.7    3.3  1  FlaC_arch      Flagella accessory protein C (FlaC)
        5.1    6.9  11.0         10    5.9  10.9    1.6  1  DUF724         Protein of unknown function (DUF724)
        7.9    6.6  11.8         12    6.0   2.4    3.6  4  Bap31_Bap29_C  Bap31/Bap29 cytoplasmic 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 !   20.5   5.6     1e-06   0.00041      83     168 ..      95     188 ..      41     202 .. 0.64

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1e-06
                           UPF0242  83 glktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelk......leleeqLaekqellq. 152
                                       +l+++ e+l +  +e + L +el++ke+ + ++keen +L ++  +  ++ ++l+        l+eqL +++ +l+ 
  gi|242398703|ref|YP_002994127.1|  95 SLREI-EQLHNIASEYNTLVKELEHKERVITEMKEENSKLLKQIDELTRELKRLQiikedfEHLKEQLIKQEGQLEm 170
                                       44443.58*********************************999999996655431111113455555555555441 PP

                           UPF0242 153 ..eyqetieeqrsvlekr 168
                                         ey + +e +r  +++ 
  gi|242398703|ref|YP_002994127.1| 171 arEYIKLLEGLRHDIDQI 188
                                       114444445555555554 PP

>> CENP-H  Centromere protein H (CENP-H)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   6.9   1.1e-05    0.0045      13      86 ..     100     179 ..      96     185 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.1e-05
                            CENP-H  13 sellklsqelrelqeeltevekenlrlkrknrelaaellelakekesek......eklkeelekleaelkksrqrwr 83 
                                       ++l ++++e+++l +el++ e+ + ++k++n +l++++ el++e ++ +      e+lke+l k e +l+ +r+ ++
  gi|242398703|ref|YP_002994127.1| 100 EQLHNIASEYNTLVKELEHKERVITEMKEENSKLLKQIDELTRELKRLQiikedfEHLKEQLIKQEGQLEMAREYIK 176
                                       45667777777777777777777777777777777777777777777777766676799999999999999998888 PP

                            CENP-H  84 vvk 86 
                                       ++ 
  gi|242398703|ref|YP_002994127.1| 177 LLE 179
                                       766 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 !   15.7  13.5   1.8e-05    0.0072      32     120 ..     106     194 ..      96     222 .] 0.84

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.8e-05
                               GAS  32 KeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkweh 108
                                        +e ++l k+ e++e+ + e+++en++l +++ ++++e+++L+   +++e+ k++l +++ +l+++ +++k l+   
  gi|242398703|ref|YP_002994127.1| 106 ASEYNTLVKELEHKERVITEMKEENSKLLKQIDELTRELKRLQIIKEDFEHLKEQLIKQEGQLEMAREYIKLLEGLR 182
                                       56889999***************************************************************998877 PP

                               GAS 109 evleqrfekvek 120
                                       +   q  + ve 
  gi|242398703|ref|YP_002994127.1| 183 HDIDQIKADVET 194
                                       777777666665 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 !   13.3   4.2   0.00011     0.044      15     105 ..     100     219 ..      92     221 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00011
                            ANAPC4  15 kelvelarkssqlqslleyinetlkeiseewkealelldrklrnledelkeeg........................ 67 
                                       ++l+++a+ + +l + le+ +++++e++ee +++l+++d+  r l+ ++  ++                        
  gi|242398703|ref|YP_002994127.1| 100 EQLHNIASEYNTLVKELEHKERVITEMKEENSKLLKQIDELTRELKRLQIIKEdfehlkeqlikqegqlemareyik 176
                                       78*****************************************9999876666678888888888888888888888 PP

                            ANAPC4  68 ......eeeksisaeLldllltGlispalkdfLvnqlgerglkk 105
                                             ++ ++i+a   ++ll G+i++a+k    ++l  rglkk
  gi|242398703|ref|YP_002994127.1| 177 lleglrHDIDQIKA-DVETLLKGYIEDAIKRIVNEELNARGLKK 219
                                       88887544444444.57888888888888888888888888887 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 ?   13.1   2.3     4e-05     0.016      12     127 ..      31     165 ..      25     213 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4e-05
                        V_ATPase_I  12 rDlnedvnafqrkfvkevrrcdemerklrfleeeieklekavikeeea...................eesleapeek 69 
                                       +D+n +v + q  f+ +++ ++++ ++ ++ +   ++++ ++i+ +++                   e ++ ++ ++
  gi|242398703|ref|YP_002994127.1|  31 TDINVEVDHDQFYFIFKIKAIENLAKTGEVQSGMFSSEKRIKIRPTDIvnvgpdviilgngkvpslrEIEQLHNIAS 107
                                       7999999999999999999999999999999999999888888888889999999**99999999865556667778 PP

                        V_ATPase_I  70 eldeleeelekleeelkelnenleklkkelnelvelkavlekakefleeeeeeeeeee 127
                                       e ++l +ele++e+ ++e++e+++kl k+  el+ + + l+ +ke +e+ +e+  ++e
  gi|242398703|ref|YP_002994127.1| 108 EYNTLVKELEHKERVITEMKEENSKLLKQIDELTRELKRLQIIKEDFEHLKEQLIKQE 165
                                       899999*************************999999888888888875533322222 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 ?   13.2  11.7   0.00013     0.054      44     138 ..      99     195 ..      95     214 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00013
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH..HHH CS
                              SHE3  44 lenlaslkhENdnLsslLkRKerrlkdlekelselkesveelklekkqlkkrlenssaseteleeelerlkv..qYd 118
                                       +e+l ++  E + L+  L+ Ker + ++ +e+s+l ++++el+ e k l++  e+ ++ +++l+++  +l++  +Y 
  gi|242398703|ref|YP_002994127.1|  99 IEQLHNIASEYNTLVKELEHKERVITEMKEENSKLLKQIDELTRELKRLQIIKEDFEHLKEQLIKQEGQLEMarEYI 175
                                       799***********************************************999999888888888777776522688 PP

                                       HHHHHHHHHHHHHHHHHHHH CS
                              SHE3 119 alvdsqkeYkehYqqeieeL 138
                                        l+++ ++  ++ + ++e+L
  gi|242398703|ref|YP_002994127.1| 176 KLLEGLRHDIDQIKADVETL 195
                                       88888888877777777776 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 ?    7.8   2.8    0.0065       2.7      18      67 ..     100     146 ..      86     149 .. 0.89
   2 ?   10.9   1.9   0.00073       0.3      20      72 ..     147     199 ..     145     220 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0065
                        Phage_GP20  18 akldeveeerdtlkeqlkdrdkqLedLkkkakdneeLqkqieelqaknkk 67 
                                       ++l ++ +e +tl ++l+ ++  + ++k++   n +L kqi+el+ ++k+
  gi|242398703|ref|YP_002994127.1| 100 EQLHNIASEYNTLVKELEHKERVITEMKEE---NSKLLKQIDELTRELKR 146
                                       5788999999*****************999...999********999886 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00073
                        Phage_GP20  20 ldeveeerdtlkeqlkdrdkqLedLkkkakdneeLqkqieelqaknkkakaey 72 
                                       l+ ++e+ + lkeql ++++qLe   +  k  e L  +i++++a++++  + y
  gi|242398703|ref|YP_002994127.1| 147 LQIIKEDFEHLKEQLIKQEGQLEMAREYIKLLEGLRHDIDQIKADVETLLKGY 199
                                       566889999999***********999999999*******99999999866655 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 ?   13.5   0.5   0.00018     0.073      34      95 ..     127     194 ..      99     204 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00018
                        NAPRTase_N  34 fkgeyaivagleevieylenlrfteeeieyLkrklpy......fkedfleyLrtfrfkpsevaveeee 95 
                                       ++ + +++++++e  + l++l++ +e+ e Lk++l        + +++++ L+ +r + +++++  e+
  gi|242398703|ref|YP_002994127.1| 127 KEENSKLLKQIDELTRELKRLQIIKEDFEHLKEQLIKqegqleMAREYIKLLEGLRHDIDQIKADVET 194
                                       46688999************************988889********************9999987765 PP

>> Dynamitin  Dynamitin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   7.8   0.00011     0.045     322     385 ..      96     161 ..      93     165 .. 0.91
   2 ?   -1.5   0.0       2.9   1.2e+03     258     275 ..     181     198 ..     167     215 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00011
                         Dynamitin 322 LrsLraLHeeAaefsqtLteleeeqkeiseelkslkelLekveeslke..nletvkkNvesleeri 385
                                       Lr +++LH+ A+e ++ ++ele++++ i+e  +++++lL++++e   e   l+++k+++e+l+e++
  gi|242398703|ref|YP_002994127.1|  96 LREIEQLHNIASEYNTLVKELEHKERVITEMKEENSKLLKQIDELTRElkRLQIIKEDFEHLKEQL 161
                                       8999***************************************98775336899*******99875 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.9
                         Dynamitin 258 qtahLDaierRlksllae 275
                                           +D+i++ +++ll+ 
  gi|242398703|ref|YP_002994127.1| 181 LRHDIDQIKADVETLLKG 198
                                       345677777777777664 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   8.5   0.00081      0.33      18     106 ..     102     200 ..      94     214 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00081
                           DUF3450  18 ldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyne...qlerlvasqeqe.......iasl 84 
                                       l+++ +e +  v++ +  ++ i+++++e ++ll+++ +l++el++l++ +e   +l++++ +qe +       i+ l
  gi|242398703|ref|YP_002994127.1| 102 LHNIASEYNTLVKELEHKERVITEMKEENSKLLKQIDELTRELKRLQIIKEdfeHLKEQLIKQEGQlemareyIKLL 178
                                       55555555666666666666677777777777777777777777766665411133333444444400000004445 PP

                           DUF3450  85 eeqieeieeierelvpllekmi 106
                                       e    +i++i+++++ ll+  i
  gi|242398703|ref|YP_002994127.1| 179 EGLRHDIDQIKADVETLLKGYI 200
                                       5555566666666666665555 PP

>> PCRF  PCRF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   6.6   0.00035      0.14       2      91 ..     106     197 ..      96     210 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00035
                                       HHHHTTTTTST.-GGGT..TTGGGSSSTTHHHHHTHHHHHHHHHHHHHTTTHHH...HT....-S-..-GGG...TH CS
                              PCRF   2 eeeleelekklsdpevw..edqekakklskelaeleeivealeeleealedleeakelleedeelaelaeee...le 73 
                                       ++e+++l k+l+++e +  e +e+ +kl k++ el++ +++l+ ++e  e+l+e  +l++++ +l e+a+e    le
  gi|242398703|ref|YP_002994127.1| 106 ASEYNTLVKELEHKERVitEMKEENSKLLKQIDELTRELKRLQIIKEDFEHLKE--QLIKQEGQL-EMAREYiklLE 179
                                       568888888887766441144555555666666666666666666666666655..555444333.36655334599 PP

                                       HHHHHHHHH..HHHHHT- CS
                              PCRF  74 elekeleeleeelkklLl 91 
                                        l+++++++++++++lL 
  gi|242398703|ref|YP_002994127.1| 180 GLRHDIDQIKADVETLLK 197
                                       9999*****999999996 PP

>> Foie-gras_1  Foie gras liver health family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.4    0.0003      0.12     160     203 ..     134     177 ..      87     179 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0003
                       Foie-gras_1 160 ekgvahskliidlLekaleeFskrkqtRlaeelsleiAeeylrl 203
                                        k++++ +  ++ L+   e+F+  k + +++e +le+A+ey++l
  gi|242398703|ref|YP_002994127.1| 134 LKQIDELTRELKRLQIIKEDFEHLKEQLIKQEGQLEMAREYIKL 177
                                       367888888888999999************************86 PP

>> HMMR_N  Hyaluronan mediated motility receptor N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7  11.6   0.00033      0.13     201     292 ..     105     195 ..      95     216 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00033
                            HMMR_N 201 skakvaqLkeklvslekekieekseteklleyieelsnvseqlekykldiaqleellkekndeiesLkssLeekeqe 277
                                         ++   L   l + e+  +e k+e+ kll++i+el  + ++l+  k+d ++l+e l +++ ++e  ++ ++  e  
  gi|242398703|ref|YP_002994127.1| 105 IASEYNTLVKELEHKERVITEMKEENSKLLKQIDELTRELKRLQIIKEDFEHLKEQLIKQEGQLEMAREYIKLLEG- 180
                                       5555555666666667888999*******************************************99998887777. PP

                            HMMR_N 278 lskqvkdlnekckll 292
                                       l + +++ ++ +++l
  gi|242398703|ref|YP_002994127.1| 181 LRHDIDQIKADVETL 195
                                       777777777777655 PP

>> zf-C4H2  Zinc finger-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8  11.6   0.00056      0.23       8     103 ..      98     192 ..      93     218 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00056
                           zf-C4H2   8 ktleleklknklakevealekeekcleeykkelelLeq...EkmaHveeLrlIhaDinal.Esvikeaeeekeksle 80 
                                       ++++l++++++  + v++le++e++++e+k+e ++L +   E +  +  L+ I++D ++l E+ ik     +e +le
  gi|242398703|ref|YP_002994127.1|  98 EIEQLHNIASEYNTLVKELEHKERVITEMKEENSKLLKqidELTRELKRLQIIKEDFEHLkEQLIK-----QEGQLE 169
                                       57899***************************9998863446667777788888888887445555.....456677 PP

                           zf-C4H2  81 kakklyeeykklkeevnelrsel 103
                                       +a++ ++ ++ l++++++++ ++
  gi|242398703|ref|YP_002994127.1| 170 MAREYIKLLEGLRHDIDQIKADV 192
                                       78888888888888888887764 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 ?   11.0   1.4   0.00067      0.27      72     125 ..      96     148 ..      88     150 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00067
                          Lectin_N  72 laeiqalssqggslsekvtsleaklekkqqdlkadhselllhvkqlvkdLrtLs 125
                                       l ei++l+  +++ +  v+ le k e+   ++k++ s+ll ++ +l+ +L+ L+
  gi|242398703|ref|YP_002994127.1|  96 LREIEQLHNIASEYNTLVKELEHK-ERVITEMKEENSKLLKQIDELTRELKRLQ 148
                                       679999**99*********99987.88899*********************995 PP

>> NUC  Nuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0     0.014       5.7      23      72 ..      25      74 ..      10      83 .. 0.87
   2 ?    3.4   2.7      0.23        94      66     128 ..     119     178 ..      99     194 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.014
                               NUC 23 efikkfdsirynaekdyFefafdykkftkkaegsrkkWtvctngeRieyk 72
                                      +++  +++i+ + ++d+F f f++k+ ++ a++   +  +++ ++Ri++ 
  gi|242398703|ref|YP_002994127.1| 25 QILGYVTDINVEVDHDQFYFIFKIKAIENLAKTGEVQSGMFSSEKRIKIR 74
                                      56777899999********************9999999999999999875 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.23
                               NUC  66 geRieykrkkkknkklesekinlteelkellekagidykkdd.lkeqiakede.kelfkellklf 128
                                        eR+ ++ k+++ k      ++  +el   l++ +i  ++ + lkeq++k++   e+ +e +kl+
  gi|242398703|ref|YP_002994127.1| 119 KERVITEMKEENSKL-----LKQIDELTRELKRLQIIKEDFEhLKEQLIKQEGqLEMAREYIKLL 178
                                       455544444333333.....555667777777778777776669*99999875345555555544 PP

>> Sec20  Sec20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   2.3    0.0011      0.45       4      63 ..     120     179 ..     117     190 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0011
                             Sec20   4 kqiTeslraisqllsqevqqSeenleeldastkslekleeeykqvedvlsrskklvkkle 63 
                                       + +  ++++ +  l +++++ +  l+ l+   ++ e+l+e++++ e+ l+++++ +k le
  gi|242398703|ref|YP_002994127.1| 120 ERVITEMKEENSKLLKQIDELTRELKRLQIIKEDFEHLKEQLIKQEGQLEMAREYIKLLE 179
                                       556667999999999******************************************997 PP

>> DASH_Dad1  DASH complex subunit Dad1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1      0.61   2.5e+02      11      33 ..      97     118 ..      95     119 .. 0.76
   2 ?   10.5   1.9    0.0013      0.53       4      45 ..     117     158 ..     116     160 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.61
                         DASH_Dad1  11 qeIaesmeevlnnlnaLNRsLEe 33 
                                       +eI + ++++ +  n+L ++LE+
  gi|242398703|ref|YP_002994127.1|  97 REIEQ-LHNIASEYNTLVKELEH 118
                                       56655.88888889999888886 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0013
                         DASH_Dad1   4 rqRdrliqeIaesmeevlnnlnaLNRsLEeviavgkeFesVa 45 
                                       + ++r+i+e  e+  ++l++++ L R+L  +  + ++Fe ++
  gi|242398703|ref|YP_002994127.1| 117 EHKERVITEMKEENSKLLKQIDELTRELKRLQIIKEDFEHLK 158
                                       679***********************************9875 PP

>> TMF_TATA_bd  TATA element modulatory factor 1 TATA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4  14.4    0.0014      0.57      20     109 ..     101     193 ..      96     198 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0014
                       TMF_TATA_bd  20 eirrlEgElaslkeelerleaerdeareeivklmkeneelkelkkeleelekeleelqe...ryetlLellGeksEe 93 
                                       +++   +E+++l +ele  e+   e++ee  kl+k+ +el+++ k+l+ +++ +e l+e   ++e  Le+  e    
  gi|242398703|ref|YP_002994127.1| 101 QLHNIASEYNTLVKELEHKERVITEMKEENSKLLKQIDELTRELKRLQIIKEDFEHLKEqliKQEGQLEMAREYIKL 177
                                       7889999********************************************9888888733467889********** PP

                       TMF_TATA_bd  94 veELraDvaDlKemyk 109
                                        e Lr D++ +K+ ++
  gi|242398703|ref|YP_002994127.1| 178 LEGLRHDIDQIKADVE 193
                                       ********99997655 PP

>> TolA_bind_tri  TolA binding protein trimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   6.5     0.005       2.1       9      55 ..     119     165 ..     110     169 .. 0.88
   2 ?    3.8   0.8      0.15        60      10      44 ..     159     195 ..     157     206 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.005
                     TolA_bind_tri   9 LErilearsqlllelqqqlealqqelreLRGqiEelqyqleqleerQ 55 
                                        Er +   ++ + +l++q+++l +el++L+   E++++  eql+++ 
  gi|242398703|ref|YP_002994127.1| 119 KERVITEMKEENSKLLKQIDELTRELKRLQIIKEDFEHLKEQLIKQE 165
                                       588888889999*******************************9996 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.15
                     TolA_bind_tri  10 Erilearsqlllelqqq....lealqqelreLRGqiEel 44 
                                       E+++++  +++le+ ++    le l++++++++ ++E l
  gi|242398703|ref|YP_002994127.1| 159 EQLIKQ--EGQLEMAREyiklLEGLRHDIDQIKADVETL 195
                                       566666..7788887765555889999999999999976 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   4.5    0.0014      0.58      11      87 ..     102     173 ..      95     205 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0014
                             TMPIT  11 fkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlkeves 87 
                                       ++++ ++ +++ ++le+ ++ ++++++e +k  k++ el+++lk+l+       +e +e+lke+l +++ +l+   +
  gi|242398703|ref|YP_002994127.1| 102 LHNIASEYNTLVKELEHKERVITEMKEENSKLLKQIDELTRELKRLQII-----KEDFEHLKEQLIKQEGQLEMARE 173
                                       3444555555566667777777777777777777777777777777765.....34455555555555555443333 PP

>> YojJ  Bacterial membrane-spanning protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       5.2   2.1e+03      42      53 ..      98     109 ..      96     114 .. 0.61
   2 ?    9.8   1.4    0.0021      0.85      24      55 ..     118     149 ..     100     154 .. 0.87
   3 ?   -0.0   0.2       2.4   9.6e+02      27      27 ..     170     170 ..     150     195 .. 0.50
   4 ?    0.2   0.0         2     8e+02      12      30 ..     179     197 ..     170     203 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 5.2
                              YojJ  42 elesirekfael 53 
                                       e+e++++ ++e 
  gi|242398703|ref|YP_002994127.1|  98 EIEQLHNIASEY 109
                                       666666666555 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0021
                              YojJ  24 eleevlkaldeedeClLcelesirekfaelet 55 
                                       + e v+++++ee++ lL +++++  ++++l+ 
  gi|242398703|ref|YP_002994127.1| 118 HKERVITEMKEENSKLLKQIDELTRELKRLQI 149
                                       45789***********************9996 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 2.4
                              YojJ  27 e 27 
                                        
  gi|242398703|ref|YP_002994127.1| 170 M 170
                                       2 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 2
                              YojJ  12 eklkeeLeqiekeleevlk 30 
                                       e l++ + qi+ ++e+ lk
  gi|242398703|ref|YP_002994127.1| 179 EGLRHDIDQIKADVETLLK 197
                                       6788889999999988765 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 ?    9.2   4.5    0.0014      0.58     332     431 ..      81     187 ..      60     205 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0014
                            eIF-4B 332 prPkvnPfGdakP...rev.lleekGkdWrkidlelehrrvdrpeteee..kllkeeieelkkelekeaa..enkes 400
                                         P v  +G+ k    re+  l++   ++  + +eleh++   +e +ee  kllk +i+el +el++ +   e+ e+
  gi|242398703|ref|YP_002994127.1|  81 VGPDVIILGNGKVpslREIeQLHNIASEYNTLVKELEHKERVITEMKEEnsKLLK-QIDELTRELKRLQIikEDFEH 156
                                       556666666666324466644777788899999*****76555554444226776.8*****999976543355566 PP

                            eIF-4B 401 qqessedqnslkelisekekdlellireldd 431
                                        +e+  +q+   e+ +e  k le l +++d 
  gi|242398703|ref|YP_002994127.1| 157 LKEQLIKQEGQLEMAREYIKLLEGLRHDIDQ 187
                                       6777777888888899999999999999885 PP

>> LepB_N  LepB N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   3.6    0.0019      0.79      75     148 ..      98     176 ..      89     213 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0019
                            LepB_N  75 eyqGlfnlkkftkgYilnykkikglfpaiaekakklkeklde..kllk..divskalkkipadlldketkkelak.y 146
                                       e++ l n+++ +   + +  +++ +++++ e+ +kl +++de  ++lk  +i+++ ++++ ++l+++e + e+a+ y
  gi|242398703|ref|YP_002994127.1|  98 EIEQLHNIASEYNTLVKELEHKERVITEMKEENSKLLKQIDEltRELKrlQIIKEDFEHLKEQLIKQEGQLEMAReY 174
                                       55555666666666677777889999***************9995554338**********************9624 PP

                            LepB_N 147 lg 148
                                       + 
  gi|242398703|ref|YP_002994127.1| 175 IK 176
                                       43 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   6.0     0.018       7.2      39     115 ..     105     180 ..     102     210 .. 0.56

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.018
                           DUF1664  39 lsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegles 115
                                       +++  +++ k+le+    +++ k++ s+ ++++d+   e k++ + ike+ ++++e+l + + ++e  +e ++ le+
  gi|242398703|ref|YP_002994127.1| 105 IASEYNTLVKELEHKERVITEMKEENSKLLKQIDELTRELKRL-QIIKEDFEHLKEQLIKQEGQLEMAREYIKLLEG 180
                                       5555566666666665555555555444444444433333333.345555555555555555555555555544443 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2  12.0    0.0024      0.99     148     240 ..     102     193 ..      96     215 .. 0.55

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0024
                              Spc7 148 legleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelae 224
                                       l ++ +++++L k+ e  +++  e++ee ++l +++++l ++ + l +i ke+ e l+e+l +++ ++e  ++ ++ 
  gi|242398703|ref|YP_002994127.1| 102 LHNIASEYNTLVKELEHKERVITEMKEENSKLLKQIDELTRELKRL-QIIKEDFEHLKEQLIKQEGQLEMAREYIKL 177
                                       4555555566666666666666666666666666666665544442.334556666666666666666655554444 PP

                              Spc7 225 lqeqleeleekieelk 240
                                       l+  + ++++  ++++
  gi|242398703|ref|YP_002994127.1| 178 LEGLRHDIDQIKADVE 193
                                       4444444444443333 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 ?    9.5  12.9    0.0024      0.96      25      99 ..      99     173 ..      96     179 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0024
                             DHR10  25 idalqvvekdlrsciklleeieaelakleeakkklkelrdaleekeielrelerkeerlqrqlenaeeklerlre 99 
                                       i+ l+++  + + ++k le  e+ + +++e+++kl ++ d+l+   ++l+ ++   e+l+ ql + e +le +re
  gi|242398703|ref|YP_002994127.1|  99 IEQLHNIASEYNTLVKELEHKERVITEMKEENSKLLKQIDELTRELKRLQIIKEDFEHLKEQLIKQEGQLEMARE 173
                                       788999999999999999999999999999999999999999999999999999999999999999999998887 PP

>> FTA4  Kinetochore complex Fta4 of Sim4 subunit, or CENP-50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   8.2    0.0074         3      93     164 ..     113     189 ..       7     214 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0074
                              FTA4  93 vnedltkeelIkeLPeswe.....veekeaeeepleallerYaelrarLielserrqqlqarlarlrklkallepfl 164
                                       v+e   ke++I+e+ e+ +      +e + e + l+  +e++++l+++Li+ + +++++++ ++ l+ l++ +++++
  gi|242398703|ref|YP_002994127.1| 113 VKELEHKERVITEMKEENSkllkqIDELTRELKRLQIIKEDFEHLKEQLIKQEGQLEMAREYIKLLEGLRHDIDQIK 189
                                       2333334666666666666666554444455555688899*******************************999984 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   1.7    0.0029       1.2      12      44 ..     116     148 ..     110     155 .. 0.89
   2 ?    4.1   0.6      0.17        70      19      45 ..     154     180 ..     149     194 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0029
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              SlyX  12 lafqedtieeLndvvaeqqqqidrlqrqlrlla 44 
                                       l + e++i e+ ++  +  +qid+l+r+l++l+
  gi|242398703|ref|YP_002994127.1| 116 LEHKERVITEMKEENSKLLKQIDELTRELKRLQ 148
                                       67899999********************99985 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.17
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              SlyX  19 ieeLndvvaeqqqqidrlqrqlrllae 45 
                                        e L +++++q+ q++  ++ ++ll+ 
  gi|242398703|ref|YP_002994127.1| 154 FEHLKEQLIKQEGQLEMAREYIKLLEG 180
                                       68999**********999999998876 PP

>> ATP-synt_E  ATP synthase E chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   3.7    0.0041       1.7      38      92 ..     109     165 ..      99     169 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0041
                        ATP-synt_E  38 keekereleaqekliekakaayakkkqakse.akslaegssakiddedp..dilvave 92 
                                       +++  +ele++e +i + k++  k  ++ +e  ++l   + ++ +d++   ++l+++e
  gi|242398703|ref|YP_002994127.1| 109 YNTLVKELEHKERVITEMKEENSKLLKQIDElTRELKRLQ-IIKEDFEHlkEQLIKQE 165
                                       5566789*********************999555555555.66566555577776665 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   6.3    0.0063       2.6      35     128 ..      97     195 ..      90     199 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0063
                                       HHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH..HHHHHCCCHHHHHHHCCHHHHHHHHH CS
                         Fib_alpha  35 kdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikkss..keleeeilrlketidaqesnirvLqn 109
                                       +++e+l+n  +e++   ke e+  + i+++ +e+ k  k+ d+++++++  + ++e+ + lke++++qe +++  ++
  gi|242398703|ref|YP_002994127.1|  97 REIEQLHNIASEYNTLVKELEHKERVITEMKEENSKLLKQIDELTRELKrlQIIKEDFEHLKEQLIKQEGQLEMARE 173
                                       57888888888888888888888888888888888888877888888874457899*************99999987 PP

                                       HH...HHHHHHHHHHHHHHHHH CS
                         Fib_alpha 110 vl...esneqkiqkLeqdidqk 128
                                        +   e ++++i +++ d++++
  gi|242398703|ref|YP_002994127.1| 174 YIkllEGLRHDIDQIKADVETL 195
                                       6511156778999999988876 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   6.4     0.021       8.7      38      80 ..     108     150 ..      99     164 .. 0.72
   2 ?    3.5   0.7      0.22        91      38      77 ..     156     195 ..     150     198 .. 0.58

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.021
                           BLOC1_2  38 klkdvaaslekkleklnekyeelqpylqqidqiekqvteLeea 80 
                                       ++++ +++le k   + e++ee +++l+qid++ +++++L+ +
  gi|242398703|ref|YP_002994127.1| 108 EYNTLVKELEHKERVITEMKEENSKLLKQIDELTRELKRLQII 150
                                       4555666666666666677779999999999999999999765 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.22
                           BLOC1_2  38 klkdvaaslekkleklnekyeelqpylqqidqiekqvteL 77 
                                        lk+++ + e +le  +e  + l+ +   idqi+++v++L
  gi|242398703|ref|YP_002994127.1| 156 HLKEQLIKQEGQLEMAREYIKLLEGLRHDIDQIKADVETL 195
                                       4455555555555555554445556666778888777777 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 ?    8.0   6.3    0.0047       1.9     152     210 ..     105     160 ..      93     216 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0047
                           HAUS6_N 152 hrvslrrflrekaaadrarqkyqenaqllekkerelraeleelqaelkaekeaakkekk 210
                                       ++ +++ +++e+++++r++++++e+ + l k++ el++el++lq  +k  +  ++ +++
  gi|242398703|ref|YP_002994127.1| 105 IASEYNTLVKELEHKERVITEMKEENSKLLKQIDELTRELKRLQI-IK--EDFEHLKEQ 160
                                       5678999999999999*********************99999665.33..222222333 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       5.6   2.3e+03      16      27 ..     104     115 ..     100     118 .. 0.69
   2 ?    8.8   1.5    0.0046       1.9      24      42 ..     126     144 ..     123     145 .. 0.89
   3 ?    0.4   0.0       1.9   7.9e+02      11      24 ..     151     161 ..     148     170 .. 0.60
   4 ?    3.1   0.0      0.28   1.1e+02      10      26 ..     181     197 ..     176     198 .. 0.67

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 5.6
                              HALZ  16 aLksdydsLkke 27 
                                       + +s+y+ L ke
  gi|242398703|ref|YP_002994127.1| 104 NIASEYNTLVKE 115
                                       567777777776 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0046
                              HALZ  24 LkkenekLkaelqeLkekl 42 
                                       +k+en kL++++ eL+  l
  gi|242398703|ref|YP_002994127.1| 126 MKEENSKLLKQIDELTREL 144
                                       699************9776 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 1.9
                              HALZ  11 KasYdaLksdydsL 24 
                                       K +++ Lk   ++L
  gi|242398703|ref|YP_002994127.1| 151 KEDFEHLK---EQL 161
                                       55566666...444 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.28
                              HALZ  10 LKasYdaLksdydsLkk 26 
                                       L+++ d+ k+d++ L+k
  gi|242398703|ref|YP_002994127.1| 181 LRHDIDQIKADVETLLK 197
                                       66666677777776665 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   5.9     0.039        16      20      80 ..     100     155 ..      90     221 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.039
                           DUF2203  20 eelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieelGvevkdle 80 
                                       e+l + ++e+++l++ele++++       +e+++e ++l ++i+el++e+++l +   d+e
  gi|242398703|ref|YP_002994127.1| 100 EQLHNIASEYNTLVKELEHKERV-----ITEMKEENSKLLKQIDELTRELKRLQIIKEDFE 155
                                       44444444444444444444444.....455666666666666666666666555544443 PP

>> Fzo_mitofusin  fzo-like conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   6.2    0.0062       2.5      95     154 ..     105     163 ..      95     176 .. 0.55
   2 ?   -0.5   0.0       1.9   7.8e+02      97     134 ..     172     210 ..     163     220 .. 0.58

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0062
                     Fzo_mitofusin  95 vqqelsstfarlcqqvdetekeleeeikelekeiekleevqkkakllrnkaslleseLek 154
                                       + +e ++ +++l+++ +++ +e++ee ++l k+i++l +  k+++++++  ++l+++L k
  gi|242398703|ref|YP_002994127.1| 105 IASEYNTLVKELEHK-ERVITEMKEENSKLLKQIDELTRELKRLQIIKEDFEHLKEQLIK 163
                                       455555555555544.33445566666666666666666666666666555555555533 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.9
                     Fzo_mitofusin  97 qelsstfarlcqqvdetekeleeeike.lekeiekleev 134
                                       +e  + ++ l++++d+ ++++e+ +k  +e  i+++ + 
  gi|242398703|ref|YP_002994127.1| 172 REYIKLLEGLRHDIDQIKADVETLLKGyIEDAIKRIVNE 210
                                       445555666777777777777666653245555555555 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   8.5    0.0036       1.5       7      68 ..     100     161 ..      91     170 .. 0.92
   2 ?    1.8   1.1      0.39   1.6e+02     106     167 ..     163     219 ..     155     222 .] 0.36

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0036
                           DUF4795   7 ellkklqeaieklqeelekleekvkelekrledkekklealkkqieelekvkadkeeveeel 68 
                                       e l+++ +++  l +ele  e   +e++++ +++ k+++ l+ ++++l+  k+d e+++e+l
  gi|242398703|ref|YP_002994127.1| 100 EQLHNIASEYNTLVKELEHKERVITEMKEENSKLLKQIDELTRELKRLQIIKEDFEHLKEQL 161
                                       457888999**********9***********************************9999987 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.39
                           DUF4795 106 eqeealkkaldtLq..eelkekldrlelepLkeqleerlkelq.kelqeamekedkedeaaglrk 167
                                       +qe +l+ a + ++  e l     r +++++k  +e  lk    ++++ ++  e  e +a gl+k
  gi|242398703|ref|YP_002994127.1| 163 KQEGQLEMAREYIKllEGL-----RHDIDQIKADVETLLKGYIeDAIK-RIVNE--ELNARGLKK 219
                                       4555554444444422222.....334444444444333322202222.11111..233444444 PP

>> TSNAXIP1_N  Translin-associated factor X-interacting N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   2.5    0.0046       1.9      70     110 ..     100     140 ..      91     141 .. 0.88
   2 ?    4.8   2.2     0.087        35      44      85 ..     147     191 ..     142     216 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0046
                        TSNAXIP1_N  70 aklktlsessdkraleleekreelralekeskalleeidkl 110
                                       ++l  ++++ +  + ele+k++ + ++++e+++ll++id+l
  gi|242398703|ref|YP_002994127.1| 100 EQLHNIASEYNTLVKELEHKERVITEMKEENSKLLKQIDEL 140
                                       677777888888999************************98 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.087
                        TSNAXIP1_N  44 LseIKkEYelyiahllesqreaqylkakl...ktlsessdkrale 85 
                                       L+ IK+++e   ++l +++ ++++ ++ +   ++l ++ d+ + +
  gi|242398703|ref|YP_002994127.1| 147 LQIIKEDFEHLKEQLIKQEGQLEMAREYIkllEGLRHDIDQIKAD 191
                                       777888888888888888888888866662233444444433333 PP

>> Ly49  Ly49-like protein, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   5.8     0.018       7.4      39      92 ..      99     152 ..      95     169 .. 0.84
   2 ?   -0.1   0.1       2.8   1.1e+03      50      72 ..     148     172 ..     144     197 .. 0.52

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.018
                                       .XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..HHHHHHHHHHHHHHHHHHH CS
                              Ly49  39 leetlnlsqnysimqndinlkeelLrnkslecsilkdlleslkreqkrlysktk 92 
                                        e+  n+ ++y+++ ++ + ke++++++  e s+l +++++l+re krl+  ++
  gi|242398703|ref|YP_002994127.1|  99 IEQLHNIASEYNTLVKELEHKERVITEMKEENSKLLKQIDELTRELKRLQIIKE 152
                                       55666****************************************999876544 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 2.8
                                       XXXXXXXX.XXXXXXXXX.XXXXX. CS
                              Ly49  50 simqndin.lkeelLrnk.slecsi 72 
                                       +i+++d + lke+l+++  +le+ +
  gi|242398703|ref|YP_002994127.1| 148 QIIKEDFEhLKEQLIKQEgQLEMAR 172
                                       6677776427777776532444433 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6  14.4     0.026        11      19      97 ..     100     171 ..      95     193 .. 0.58

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.026
                            APG6_N  19 eqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeeleale 95 
                                       eq+ +   +Y++  k+l+ +       +  + e +ee +kl k+ +el +eLk+l+  +e+ e   ++l +++ +le
  gi|242398703|ref|YP_002994127.1| 100 EQLHNIASEYNTLVKELEHK-------ERVITEMKEENSKLLKQIDELTRELKRLQIIKEDFEHLKEQLIKQEGQLE 169
                                       44444445555555555544.......22455566666666666666666666666666666666666666665555 PP

                            APG6_N  96 ee 97 
                                         
  gi|242398703|ref|YP_002994127.1| 170 MA 171
                                       43 PP

>> FlxA  FlxA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   8.5     0.018       7.4      18      82 ..      98     161 ..      92     180 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.018
                              FlxA  18 qiasLqkQiknlqkqLkelsesdeltkeekkkqqqliqaQIqqlqaQIaqlqqqqaekaqekqqs 82 
                                       +i++L +  ++++  +kel  + e   +e k+    + +QI+ l  ++++lq+ +++ +  k+q 
  gi|242398703|ref|YP_002994127.1|  98 EIEQLHNIASEYNTLVKELEHK-ERVITEMKEENSKLLKQIDELTRELKRLQIIKEDFEHLKEQL 161
                                       7899999999999999999999.7777778899999999*************9877655555554 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   9.7      0.53   2.1e+02       5      40 ..     112     147 ..     109     208 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.53
                         FlaC_arch   5 lEnklsklsteletvkkeneelsksveelkenVkdl 40 
                                       l ++l+  +  ++ +k+en++l k+++el ++ k+l
  gi|242398703|ref|YP_002994127.1| 112 LVKELEHKERVITEMKEENSKLLKQIDELTRELKRL 147
                                       5678999999999****************9999887 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9  10.9     0.024        10      92     164 ..      97     169 ..      93     203 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.024
                            DUF724  92 srlnkLlslkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlk 164
                                         +++L ++ +e++ l +e+++ e+ i+e ++e++kl ++idel ++ ++l+  ++ + + ke+  k+  +l+
  gi|242398703|ref|YP_002994127.1|  97 REIEQLHNIASEYNTLVKELEHKERVITEMKEENSKLLKQIDELTRELKRLQIIKEDFEHLKEQLIKQEGQLE 169
                                       5789999999999999999999999999999999999999999999999888766666533333333333333 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   0.3       0.1        42      23      41 ..     101     119 ..     100     133 .. 0.70
   2 ?    6.0   2.4     0.029        12       2      34 ..     108     147 ..     107     150 .. 0.82
   3 ?    3.8   3.4      0.14        58       1      23 [.     135     160 ..     135     180 .. 0.88
   4 ?    2.1   1.2      0.49     2e+02       4      20 ..     155     195 ..     152     197 .. 0.48

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.1
                     Bap31_Bap29_C  23 QaeglakEYDrLadehskl 41 
                                       Q  + a EY+ L +e +  
  gi|242398703|ref|YP_002994127.1| 101 QLHNIASEYNTLVKELEHK 119
                                       7778899999999997655 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.029
                     Bap31_Bap29_C   2 eiekLkkeLkkkk.......kDlealKkQaeglakEYDrL 34 
                                       e + L keL+ k+        +   l kQ++ l++E  rL
  gi|242398703|ref|YP_002994127.1| 108 EYNTLVKELEHKErvitemkEENSKLLKQIDELTRELKRL 147
                                       6788999999888777777788888999999999998777 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.14
                     Bap31_Bap29_C   1 keiekLkkeLkkkk...kDlealKkQ 23 
                                       k+i +L+ eLk+ +    D e lK+Q
  gi|242398703|ref|YP_002994127.1| 135 KQIDELTRELKRLQiikEDFEHLKEQ 160
                                       68999***999888888999999999 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.49
                     Bap31_Bap29_C   4 ekLkkeLkkkk........................kDleal 20 
                                       e Lk++L k++                        +D+e+l
  gi|242398703|ref|YP_002994127.1| 155 EHLKEQLIKQEgqlemareyiklleglrhdidqikADVETL 195
                                       55666666555555555455544444442222222666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2064  (0.115121); expected 358.6 (0.02)
Passed bias filter:                      858  (0.0478554); expected 358.6 (0.02)
Passed Vit filter:                       154  (0.00858944); expected 17.9 (0.001)
Passed Fwd filter:                        45  (0.0025099); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              44  [number of targets reported over threshold]
# CPU time: 0.75u 0.33s 00:00:01.08 Elapsed: 00:00:00.52
# Mc/sec: 1285.61
//
Query:       gi|242398704|ref|YP_002994128.1|  [L=59]
Description: Preprotein translocase subunit secG [Thermococcus sibiricus MM 739]
Scores for complete 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   55.9   0.4    3.6e-15   55.7   0.4    1.1  1  Sec61_beta  Sec61beta family
  ------ inclusion threshold ------
        0.1   13.1   0.3        3.8    8.0   0.2    2.1  2  DUF202      Domain of unknown function (DUF202)


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 !   55.7   0.4     4e-19   3.6e-15       1      41 []      14      54 ..      14      54 .. 0.97

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 4e-19
                                      XXXXXXXXXX----SS-B-THHHHHHHHHHHHHHHHHTSS- CS
                        Sec61_beta  1 SsaGLlryyeedapgikidPkvVlvlsvafiasVilLhila 41
                                      ++aGL+r+++ed+++iki+Pk  +++ ++fia+ ilL++++
  gi|242398704|ref|YP_002994128.1| 14 TGAGLMRFFDEDTRAIKISPKGAIAIVLIFIAIEILLNVFG 54
                                      68************************************986 PP

>> DUF202  Domain of unknown function (DUF202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.012   1.1e+02       4      11 ..       4      11 ..       2      12 .. 0.90
   2 ?    8.0   0.2   0.00042       3.8      24      58 ..      15      54 ..      14      58 .. 0.56

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.012
                            DUF202  4 lAnERTfL 11
                                      +A ERT+L
  gi|242398704|ref|YP_002994128.1|  4 MAKERTTL 11
                                      89****98 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00042
                            DUF202 24 glallrffl......tgepsalgkilglilivlgiltllvg 58
                                      g++l+rff       + +p+  + ++ li+i++ il+ ++g
  gi|242398704|ref|YP_002994128.1| 15 GAGLMRFFDedtraiKISPKG-AIAIVLIFIAIEILLNVFG 54
                                      889999998554443333333.3444555666666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 382.37
//
Query:       gi|242398705|ref|YP_002994129.1|  [L=63]
Description: hypothetical protein TSIB_0717 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 426.03
//
Query:       gi|242398706|ref|YP_002994130.1|  [L=463]
Description: transport protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.4e-49  168.9  54.6    1.4e-49  168.9  54.6    3.0  2  MFS_1       Major Facilitator Superfamily
    5.6e-10   38.7  15.4    5.6e-10   38.7  15.4    3.0  3  Sugar_tr    Sugar (and other) transporter
    5.7e-07   28.3   8.9    5.7e-07   28.3   8.9    2.3  2  MFS_3       Transmembrane secretion effector
    1.9e-06   27.0  33.0    4.9e-06   25.7   8.3    3.1  3  MFS_1_like  MFS_1 like family


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.9  54.6   3.2e-53   1.4e-49       2     352 ..      22     409 ..      21     410 .. 0.86
   2 ?   -2.4   5.6      0.39   1.8e+03     222     261 ..     423     456 ..     404     462 .. 0.38

  Alignments for each domain:
  == domain 1  score: 168.9 bits;  conditional E-value: 3.2e-53
                             MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglll 78 
                                        la fl+ +++s  ++alp  +++++ +++  +++++t y l+aa++ +p+G ++d  Gr++v+  g+l++al+++l
  gi|242398706|ref|YP_002994130.1|  22 TLASFLTPFMSSSMNIALP-SIGKEFSMNVVLLNWVATSYLLAAAIFLVPFGKIADIKGRKKVFSYGILIYALSSFL 97 
                                       6899***************.9*****************************************************777 PP

                             MFS_1  79 llfasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravf 154
                                       +++ s++  +l+ +r+lqG+g++++f +++a+++ +fp++erg+++g+ +a++ lG  lgp lgg l+++lgWr++f
  gi|242398706|ref|YP_002994130.1|  98 CAI-STSSvMLISFRILQGIGSAMIFGTAVAILTSVFPPRERGKVLGINAAAVYLGLSLGPFLGGSLTQYLGWRSIF 173
                                       775.77777******************************************************************** PP

                             MFS_1 155 yilaivsllafvlfllllpeepperkrkspkeee........................................... 188
                                       +++a+++l+ ++l+l+ l  +  e k +  k                                              
  gi|242398706|ref|YP_002994130.1| 174 IANAVLGLITIILVLWKLKGDWAEAKGE--K--Fdfigsivyslslaaimygfslipamsglwlvlvgvfmfllfvr 246
                                       **********997555553333333332..2..235779999*****999999999999999999988888888877 PP

                             MFS_1 189 .kgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlglsglllaglllallalvgailalla 264
                                        + + + p+++ + +++++  + +  ia+l++  +++++ +ll lylq   g+s    ag +l +  +v+ai+++la
  gi|242398706|ref|YP_002994130.1| 247 wEMKTKNPILD-INLFRNNITFTFSNIAALINYSATFAVAFLLSLYLQYIKGFS-PQNAGSILVAQPVVMAIFSPLA 321
                                       77777777777.77777777665677888888889999****************.7999999*************** PP

                             MFS_1 265 grlsdrlgrrrrlllallllllaalglallavt..ssavllll.vlvliGfglgfvfpsllalasdlappeeagtas 338
                                       grlsdr+ +    ++a ++++l++++l l+ +   ++++ +++ +l+l+Gfgl++++++ ++++++++ ++  g as
  gi|242398706|ref|YP_002994130.1| 322 GRLSDRVEP---GIIASAGMALTTVSLSLFTFLseKTSLEVIVaSLILLGFGLALFSSPNTNAIMSSVERRFYGVAS 395
                                       ******665...666666666666666666666443555555558888***************************** PP

                             MFS_1 339 glfntagslggalg 352
                                       +   t++  g  l+
  gi|242398706|ref|YP_002994130.1| 396 ATLATMRLTGQTLS 409
                                       ***99998887765 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.39
                             MFS_1 222 gfsglltllplylqevlglsglllaglllallalvgaila 261
                                        ++++ ++ p++       s   ++ +++all+++g++++
  gi|242398706|ref|YP_002994130.1| 423 NVQITPQYYPIF-----LTS-MKTVFIIFALLCFGGIFAS 456
                                       222233333333.....222.2233333444444444443 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.7  15.4   1.3e-13   5.6e-10      44     189 ..      49     188 ..      14     193 .. 0.90
   2 ?   -4.3   8.0       1.4   6.1e+03     323     436 ..     207     317 ..     200     322 .. 0.66
   3 ?   -8.8  19.4         4   1.8e+04     285     436 ..     297     449 ..     269     454 .. 0.70

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 1.3e-13
                                       ...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHH CS
                          Sugar_tr  44 ssvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlas 120
                                         vl+ +++ ++l+ a+i  + +g+++d+ GRkk++  +++++  +++l+a+++   s  +li  R+l Gig  ++ 
  gi|242398706|ref|YP_002994130.1|  49 NVVLLNWVATSYLLAAAIFLVPFGKIADIKGRKKVFSYGILIYALSSFLCAIST---SSVMLISFRILQGIGSAMIF 122
                                       568899************************************************...99****************** PP

                                       HHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHGG CS
                          Sugar_tr 121 vlvPmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllilll 189
                                       +++   +  + p++ Rg++ +++  a+ +G  ++ ++g  l ++ +   wr  +  ++v+ l+ +il+l
  gi|242398706|ref|YP_002994130.1| 123 GTAVAILTSVFPPRERGKVLGINAAAVYLGLSLGPFLGGSLTQYLG---WRSIFIANAVLGLITIILVL 188
                                       ************************************9999988888...************99888876 PP

  == domain 2  score: -4.3 bits;  conditional E-value: 1.4
                                       HHHHHHHHHHHHH..HHHHTTSS...CHHHHHHHHHHHHHHHTTTTHHHHHHHHHHSHTTTHHHHHHHHHHHHHHHH CS
                          Sugar_tr 323 GaagmaicfvilgivalllvakskaasivaivfialfialfalgwgpvpwvlvsElfpqsvRskalaiavavnwlan 399
                                       G++++++ ++ + + + l++a s  + +++ vf++l ++  ++   +   +l   lf +++  +++ ia+ +n  a+
  gi|242398706|ref|YP_002994130.1| 207 GSIVYSLSLAAIMYGFSLIPAMSGLWLVLVGVFMFLLFVRWEM--KTKNPILDINLFRNNITFTFSNIAALINYSAT 281
                                       5555555554444456666666534444444444444444444..3333345557999999999999********** PP

                                       HHHHHHHHHHHCHHHT-HHHHHHHHHHHHHHHHHHHH CS
                          Sugar_tr 400 flisllfpiiteaigggyvflvfaglavlfiifvfff 436
                                       f++++l    ++ i+ g++    ++++v+  +++ +f
  gi|242398706|ref|YP_002994130.1| 282 FAVAFLLSLYLQYIK-GFSPQNAGSILVAQPVVMAIF 317
                                       *****9999999999.777666666666666666665 PP

  == domain 3  score: -8.8 bits;  conditional E-value: 4
                                       S-THHHHHHHHHH..HHHHHHHHHHHHHHHHS-SHHHHHHHHHHHHHHHHHHH..HHHHTTSS...CHHHHHHHHHH CS
                          Sugar_tr 285 glsksllvtiivg..vvnfvatfvaiflvdrfGRRtllllGaagmaicfvilgivalllvakskaasivaivfialf 359
                                       g+s++ +++i+v   vv ++++  a  l+dr+   +  ++ +agma+ +v l+  + +l++k++   iva   ++ f
  gi|242398706|ref|YP_002994130.1| 297 GFSPQNAGSILVAqpVVMAIFSPLAGRLSDRV---EPGIIASAGMALTTVSLS-LFTFLSEKTSLEVIVASLILLGF 369
                                       55555455554432244444444444555544...6779999**********9.55555555445555554444444 PP

                                       .HHHHHTTTTHHHHHHHHHHSHTTTHHHHHHHHHHH.HHHHHHHHHHHHHHHHCHHH..T-HHHHHHHHHHHHHHHH CS
                          Sugar_tr 360 .ialfalgwgpvpwvlvsElfpqsvRskalaiavav.nwlanflisllfpiiteaig..ggyvflvfaglavlfiif 432
                                        +alf+ ++++   + + E    +v s++la    + + l+  ++ l+f i +++++    y+ ++ +++  +fiif
  gi|242398706|ref|YP_002994130.1| 370 gLALFS-SPNTNAIMSSVERRFYGVASATLATMRLTgQTLSMGIVMLIFAIYMGNVQitPQYYPIFLTSMKTVFIIF 445
                                       267777.99999999999999999999999887766155666789999******99988889999999999999999 PP

                                       HHHH CS
                          Sugar_tr 433 vfff 436
                                        +++
  gi|242398706|ref|YP_002994130.1| 446 ALLC 449
                                       8765 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   8.9   1.3e-10   5.7e-07      49     195 ..      55     197 ..      16     220 .. 0.86
   2 ?    1.7   3.8     0.015        67      46     135 ..     302     389 ..     260     427 .. 0.72

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 1.3e-10
                             MFS_3  49 lvqaaatLPifllsilaGalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlllaltlligiGaalndPaWq 125
                                        v  +  L   ++ ++ G +aD+  r+kv+  + l+ al+s l ++++     s ++l+ + +l giG+a+   +  
  gi|242398706|ref|YP_002994130.1|  55 WVATSYLLAAAIFLVPFGKIADIKGRKKVFSYGILIYALSSFLCAIST-----SSVMLISFRILQGIGSAMIFGTAV 126
                                       34455558889999********************99999999888875.....6899******************** PP

                             MFS_3 126 AsvgelvkrrdvpaAvaLnsvginiaRsvGPAlgGvlvaavGaalafavna.lsylalivallrwkrevrk 195
                                       A++  + + r+  +   +n+  + +  s GP lgG l   +G    f +na l  +++i++l++ k +  +
  gi|242398706|ref|YP_002994130.1| 127 AILTSVFPPRERGKVLGINAAAVYLGLSLGPFLGGSLTQYLGWRSIFIANAvLGLITIILVLWKLKGDWAE 197
                                       ***********************************************998725677889999999876555 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.015
                             MFS_3  46 mvAlvqaaatLPifllsilaGalaDnfdrRkvllavqlllalvsvlltvlaalg.llspwlllaltlligiGaaln. 120
                                       +   + +a  + + ++s laG l+D ++   +   + + +al++v l ++++l   +s  +++a+ +l+g G al  
  gi|242398706|ref|YP_002994130.1| 302 NAGSILVAQPVVMAIFSPLAGRLSDRVEPGII---ASAGMALTTVSLSLFTFLSeKTSLEVIVASLILLGFGLALFs 375
                                       55556667777788999999999999887644...444455566666666665414566678888999******861 PP

                             MFS_3 121 dPaWqAsvgelvkrr 135
                                       +P  +A+++  v+rr
  gi|242398706|ref|YP_002994130.1| 376 SPNTNAIMSS-VERR 389
                                       5666666554.4444 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   8.3   1.1e-09   4.9e-06     270     384 ..      61     174 ..      11     175 .. 0.88
   2 !   11.4   9.1   2.3e-05       0.1     186     322 ..     228     364 ..     202     379 .. 0.67
   3 !   12.2   8.3   1.3e-05     0.058      13     179 ..     279     430 ..     275     457 .. 0.66

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 1.1e-09
                        MFS_1_like 270 vvaeiplfffaeklleklGhvklliiallayilrfllyaiienawlvlpievLhgisfgllwaaaveyvskiapksl 346
                                        +a  ++++   k+ ++ G  k+   ++l+y+l  +l ai ++ ++++ + +L+gi  ++++++av     ++p++ 
  gi|242398706|ref|YP_002994130.1|  61 LLAAAIFLVPFGKIADIKGRKKVFSYGILIYALSSFLCAISTSSVMLISFRILQGIGSAMIFGTAVAILTSVFPPRE 137
                                       456667888899***************************************************************** PP

                        MFS_1_like 347 eatgqgllsglyfglGralGsliGGllwdlksaiflFr 384
                                       ++++ g+ +++   lG  lG ++GG l ++ + + +F 
  gi|242398706|ref|YP_002994130.1| 138 RGKVLGINAAAV-YLGLSLGPFLGGSLTQYLGWRSIFI 174
                                       *******98875.59999*********99999888885 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 2.3e-05
                        MFS_1_like 186 laallvisllvvlilnetekesklkvtkslqvllnilknpeviifllvalilgmswgiienF.lflYL.kelgasnt 260
                                       + +l+++ + v++ l   ++e k+k   +l+  +n+++n   ++f  +a+++  s  ++ +F l+lYL   +g+s  
  gi|242398706|ref|YP_002994130.1| 228 MSGLWLVLVGVFMFLLFVRWEMKTKNP-ILD--INLFRNNITFTFSNIAALINYSATFAVAFlLSLYLqYIKGFSPQ 301
                                       445555555555555555555555544.334..78888888888888888888888888888557888556788888 PP

                        MFS_1_like 261 llGslvalgvvaeiplfffaeklleklGhvklliiallayilrfllyaii.enawlvlpievL 322
                                        +Gs+++ + v   ++  +a +l +++    +  +++ ++++ ++l  ++ e+++l +++  L
  gi|242398706|ref|YP_002994130.1| 302 NAGSILVAQPVVMAIFSPLAGRLSDRVEPGIIASAGMALTTVSLSLFTFLsEKTSLEVIVASL 364
                                       888888888887777888888888888888888888888888888888887555444444433 PP

  == domain 3  score: 12.2 bits;  conditional E-value: 1.3e-05
                        MFS_1_like  13 aalgsllPYltiylk.skglkaseigiitlilpltsilsppiwgvlaDrfgkrkkvvilslllsavlflsllfipps 88 
                                       +a+ ++   l++yl+  kg+++++ g i+++ p++  + +p+ g l+Dr++    ++++++ l +v+++ ++f++  
  gi|242398706|ref|YP_002994130.1| 279 SATFAVAFLLSLYLQyIKGFSPQNAGSILVAQPVVMAIFSPLAGRLSDRVE-PGIIASAGMALTTVSLSLFTFLS-- 352
                                       55555555689****779*******************************97.5679999********99888888.. PP

                        MFS_1_like  89 kerqeesklevsvaqdvdaektfwilfllvvlasfflaa.ilvlldaatlkelgedrkdyGrqrlfG.svGyaifaf 163
                                           e++            e ++++l+ll +   +f+++ +++++ ++  +  g  +   +  rl G +++++i++ 
  gi|242398706|ref|YP_002994130.1| 353 ----EKTS----------LEVIVASLILLGFGLALFSSPnTNAIMSSVERRFYGVASATLATMRLTGqTLSMGIVML 415
                                       ....3333..........45566666666555555554424455555555555666666666666664566666666 PP

                        MFS_1_like 164 itGilidhysvnllp.y 179
                                       i+ i +  ++++  p y
  gi|242398706|ref|YP_002994130.1| 416 IFAIYMGNVQIT--PqY 430
                                       666666555553..332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (463 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       897  (0.0500307); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.25s 00:00:00.85 Elapsed: 00:00:00.41
# Mc/sec: 3388.10
//
Query:       gi|242398707|ref|YP_002994131.1|  [L=126]
Description: 30S ribosomal protein S6e [Thermococcus sibiricus MM 739]
Scores for complete 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-38  130.1   0.4      2e-37  127.9   0.4    1.8  1  Ribosomal_S6e  Ribosomal protein S6e


Domain annotation for each model (and alignments):
>> Ribosomal_S6e  Ribosomal protein S6e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.9   0.4   1.1e-41     2e-37       1     113 [.       4     124 ..       4     126 .] 0.89

  Alignments for each domain:
  == domain 1  score: 127.9 bits;  conditional E-value: 1.1e-41
                                       -EEEEEETTTTEEEEEE-CHHHCTTCTT-BSSEEEECCTTT........SSSTS.-EEEEEEEEETTC-BB-TTS-S CS
                     Ribosomal_S6e   1 mklnisdpatgkqklievdekklrtligkrigeevdgdalG........eelkg.yvlkitggsdkqGfpmkqgvlt 68 
                                       +kl+isd +tg +k+ie++++++ +lig rig+e++++ lG         e +g ++lkitgg+dk+Gfpm+++v++
  gi|242398707|ref|YP_002994131.1|   4 FKLVISDTKTGVAKQIEITGAEADKLIGLRIGDEIEAKELGfnlseifgSEIPGdVKLKITGGTDKDGFPMRPDVHG 80 
                                       79**********************************987662221111155554368******************** PP

                                       SSEEEEEEETTSSSS-SSSSS-EEEEEEE-SB--SSEEEEEEEEE CS
                     Ribosomal_S6e  69 pgrvrlLlskggvgyrprrkGerkrksvrGcivsadisqlnlviv 113
                                       p+rv++L+s+ g+g+rp+++Ger++k+vrG+++s +i+q+n++iv
  gi|242398707|ref|YP_002994131.1|  81 PRRVKILISR-GPGFRPQERGERRKKTVRGNTISPEIAQINVKIV 124
                                       **********.*********************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       250  (0.0139439); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); 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: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 926.93
//
Query:       gi|242398708|ref|YP_002994132.1|  [L=427]
Description: Translation initiation factor 2 subunit gamma [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-31  109.8   0.3    7.8e-31  107.1   0.3    1.9  1  GTP_EFTU        Elongation factor Tu GTP binding domain
    1.7e-31  108.3   0.2      4e-31  107.1   0.2    1.7  1  eIF2_C          Initiation factor eIF2 gamma, C terminal
    4.7e-12   46.1   2.1    1.2e-11   44.8   2.1    1.8  1  GTP_EFTU_D2     Elongation factor Tu domain 2
    2.6e-05   24.3   0.0    4.5e-05   23.5   0.0    1.4  1  MMR_HSR1        50S ribosome-binding GTPase
      5e-05   23.3   0.2     0.0009   19.2   0.0    2.2  2  RsgA_GTPase     RsgA GTPase
    0.00082   19.1   0.3       0.59    9.9   0.0    2.4  2  PduV-EutP       Ethanolamine utilisation - propanediol utilis
      0.001   17.0   0.0     0.0014   16.6   0.0    1.1  1  PolC_DP2        DNA polymerase II large subunit DP2
     0.0023   17.9   0.7     0.0046   17.0   0.7    1.4  1  Nop10p          Nucleolar RNA-binding protein, Nop10p family
     0.0031   17.1   0.4     0.0078   15.8   0.4    1.7  1  RecR            RecR protein
     0.0065   15.8   4.7      0.015   14.6   4.7    1.7  1  zf-ribbon_3     zinc-ribbon domain
  ------ inclusion threshold ------
      0.013   15.5   0.0      0.034   14.2   0.0    1.6  1  HypA            Hydrogenase/urease nickel incorporation, meta
       0.04   13.1   0.1      0.062   12.4   0.1    1.2  1  G-alpha         G-protein alpha subunit
      0.061   13.1   8.4       0.15   11.8   8.4    1.7  1  zinc_ribbon_2   zinc-ribbon domain
       0.07   13.1   0.4       0.55   10.2   0.0    2.3  2  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
        0.1   11.3   0.1       0.15   10.8   0.1    1.3  1  NRDD            Anaerobic ribonucleoside-triphosphate reducta
       0.11   12.5   0.9       0.21   11.5   0.9    1.6  1  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
       0.27   10.9   1.5        5.8    6.7   0.1    2.3  2  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
       0.28   10.8   6.7       0.33   10.6   0.3    2.3  2  zf-tcix         Putative treble-clef, zinc-finger, Zn-binding
       0.67   10.1   4.3         10    6.3   0.3    2.7  2  Zn-ribbon_8     Zinc ribbon domain


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 !  107.1   0.3   8.2e-34   7.8e-31       4     193 ..      28     216 ..      25     217 .. 0.90

  Alignments for each domain:
  == domain 1  score: 107.1 bits;  conditional E-value: 8.2e-34
                                       EEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEE................ CS
                          GTP_EFTU   4 rnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisle................ 64 
                                       +nig++ghvDhGKtTLt +L+   g+             +Dt++eE +rgiTik+  +  e                
  gi|242398708|ref|YP_002994132.1|  28 VNIGMVGHVDHGKTTLTRALT---GI------------WTDTHSEELRRGITIKIGFADAEirkcpscgkysnspkc 89 
                                       79******************9...33............479999************9999999************** PP

                                       .....TTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTB.STHHHHHHHHHHHHTTTE.EEEEEESCGS CS
                          GTP_EFTU  65 .....ketkkylinliDtPGHvdFskevirglrvlDgavlvvdaveG.vepqteevlrlalkegvp.iivfiNKmDr 134
                                            +++ ++++++iD+PGH+  + ++ +g++ +Dgavlv++a+e  ++pqt+e+l  ++ +g + ii++ NK+  
  gi|242398708|ref|YP_002994132.1|  90 pycgaETEFERRVSFIDSPGHEALMTTMLAGASLMDGAVLVIAANEPcPKPQTREHLMALQIVGNRnIIIAQNKIEL 166
                                       **99768999***********************************9879**************9999********** PP

                                       T.HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHHHSH CS
                          GTP_EFTU 135 l.kaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvktllealvellp 193
                                       + k++  e  +++k ++      ++  +++   + p++++Sal+g +++ l++a+ e +p
  gi|242398708|ref|YP_002994132.1| 167 VtKEQAIENYNQIK-EF------VKGTVAE---NAPIIPISALHGANIDVLISAIEEIIP 216
                                       *7667777777777.55......4444444...57********************99988 PP

>> eIF2_C  Initiation factor eIF2 gamma, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.1   0.2   4.3e-34     4e-31       2      86 .]     341     425 ..     340     425 .. 0.98

  Alignments for each domain:
  == domain 1  score: 107.1 bits;  conditional E-value: 4.3e-34
                                       EEEEEEEE-SBESSSSSCCC-----TTEEEEEEETTEEEEEEEEEEESSEEEEEEEEEEE-STTEEEEEEEEETTSE CS
                            eIF2_C   2 eleieyellerlvgvkeekkveklkkkEvLmlniGsastggvvtsvkkdeakvkLkkPvcaekgekialsRrvekrW 78 
                                       el++e++ller+vg++ee kve++k++EvL+ln+G+a t+g vt + kde+++kL+ P+cae ge++a+sR+v++rW
  gi|242398708|ref|YP_002994132.1| 341 ELRLEVHLLERVVGTEEELKVEPIKRREVLLLNVGTARTMGLVTGLGKDEVELKLQIPICAEPGERVAISRQVGSRW 417
                                       899************************************************************************** PP

                                       EEEEEEEE CS
                            eIF2_C  79 rLiGwGei 86 
                                       rLiG+G i
  gi|242398708|ref|YP_002994132.1| 418 RLIGYGFI 425
                                       ******76 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 !   44.8   2.1   1.3e-14   1.2e-11       1      72 [.     248     328 ..     248     330 .. 0.90

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 1.3e-14
                                       EEEEEEEEEESEEETTEEEEEEC.TCTTSEE......EEEEEEEEEEETEEESEEETTSEEEEEEEESSCCS..GSS CS
                       GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilg.ndtskke......ivtrissletfhededeavaganaGvivaikgled..aii 68 
                                       G+v++g++++G+lk+Gde++i++ ++ ++ +      i+t+i+sl++  + ++ea++g+ +Gv++++++  +  +++
  gi|242398708|ref|YP_002994132.1| 248 GGVIGGSIIQGKLKVGDEIEIRPgVPYEEHGrikyesITTEITSLQAGGKSVKEAYPGGLVGVGTKLDPFLTkgDLM 324
                                       89*********************98875555************************************9988766666 PP

                                       TTCE CS
                       GTP_EFTU_D2  69 vGdt 72 
                                       +G++
  gi|242398708|ref|YP_002994132.1| 325 AGNV 328
                                       6666 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   4.8e-08   4.5e-05       1     113 [.      29     162 ..      29     183 .. 0.68

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 4.8e-08
                                       EEEEEESTTSSHHHHHHHHHTS...TEEESSSTTSSSSEEEEEEEETTEE.......................EEEE CS
                          MMR_HSR1   1 evaivGrpNvGKStLinaltge...kaivsdkpgtTrdinegrvklkgke.......................ielv 51 
                                       +++ vG+   GK+tL +altg    +   + + g T++i ++  ++++ +                       + ++
  gi|242398708|ref|YP_002994132.1|  29 NIGMVGHVDHGKTTLTRALTGIwtdTHSEELRRGITIKIGFADAEIRKCPscgkysnspkcpycgaeteferrVSFI 105
                                       5899*****************6432344455669999999999886632234444555555556666666666**** PP

                                       ECGGCSSHHHHHHHHHHHHHHHHC.TSEEEEEEETTTTCSHHHHHHHHHHHHH.TTSEEEEEEE CS
                          MMR_HSR1  52 DtpGliegaseekglgkaflalee.adlillvvdaseeklkpldeeleellee.akkplilvln 113
                                       D pG  e       l  ++la  + +d ++lv+ a+e   kp+ +e    l+   ++++i++ n
  gi|242398708|ref|YP_002994132.1| 106 DSPG-HE------ALMTTMLAGASlMDGAVLVIAANEPCPKPQTREHLMALQIvGNRNIIIAQN 162
                                       ****.54......7888888877768*******9872233334333333322224445555544 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.22   2.1e+02     102     135 ..      30      60 ..      10      64 .. 0.67
   2 !   19.2   0.0   9.6e-07    0.0009       4      98 ..     100     212 ..      97     216 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.22
                                       EEEECSTTSSHHHHHHHHCTT-----S------- CS
                       RsgA_GTPase 102 svlvGqSGvGKStLinallpelelktgevseklg 135
                                       + +vG+   GK+tL  al++     t   se+l+
  gi|242398708|ref|YP_002994132.1|  30 IGMVGHVDHGKTTLTRALTGI---WTDTHSEELR 60 
                                       348999999********9984...4555555555 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 9.6e-07
                                       -S-EETTTT............EES--EEEEEEESTTTT--HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHH..... CS
                       RsgA_GTPase   4 Rknelvrpk............vaNvdqllivvslkepelslnlldrfLvlaeekgiepvivlnKiDlleeee..... 63 
                                       R+ ++++++            ++ +d +++v++++ep  ++++ + +++l    + +++i+ nKi+l+++e+     
  gi|242398708|ref|YP_002994132.1| 100 RRVSFIDSPghealmttmlagASLMDGAVLVIAANEPCPKPQTREHLMALQIVGNRNIIIAQNKIELVTKEQaieny 176
                                       5555666556666666677778889***********************************************88877 PP

                                       .HHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCT CS
                       RsgA_GTPase  64 .eleelkeelealgyevllvsaktkegleelkellk 98 
                                        +++e+ + + a + +++ +sa ++++++ l ++++
  gi|242398708|ref|YP_002994132.1| 177 nQIKEFVKGTVAENAPIIPISALHGANIDVLISAIE 212
                                       777777777778889999999999999988877765 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0   0.00063      0.59       4      27 ..      30      60 ..      27      89 .. 0.73
   2 !    7.2   0.1     0.004       3.8      40     142 ..     104     212 ..      94     213 .. 0.50

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00063
                         PduV-EutP  4 illiGkvgsGKttLtqalkg.......eelk 27
                                      i ++G+v+ GKttLt+al+g       eel+
  gi|242398708|ref|YP_002994132.1| 30 IGMVGHVDHGKTTLTRALTGiwtdthsEELR 60
                                      5689**************9855555555555 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.004
                         PduV-EutP  40 viDtPGeylenrklysalivtsaeadvialvqdateeesv.fppgfasvfnkeviGiitkidlaedeeniea...ve 112
                                       +iD+PG  +   ++      +   + via    + ++++     +++ v n+++i    ki+l+++e++ie+    +
  gi|242398708|ref|YP_002994132.1| 104 FIDSPGHEALMTTMLAGASLMDGAVLVIAANEPCPKPQTReHLMALQIVGNRNIIIAQNKIELVTKEQAIENynqIK 180
                                       57777754444433333333333333333333333322220111222222444444445677776666665411144 PP

                         PduV-EutP 113 elLks..aGaekifevsavekegieellkyle 142
                                       e++k   a  + i+ +sa++  +i+ l++ +e
  gi|242398708|ref|YP_002994132.1| 181 EFVKGtvAENAPIIPISALHGANIDVLISAIE 212
                                       5555411444568*************999887 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 !   16.6   0.0   1.5e-06    0.0014     615     757 ..      71     213 ..      45     216 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.5e-06
                          PolC_DP2 615 eiarrkCkkCgketlearCeeCgekteeklvCkkceeeveeekcekcekeakavkkkkidlkellekaleklgeree 691
                                       + + rkC++Cgk + + +C+ Cg++te + + + +++  +e+ +  + + a+ ++   + + +       + +e+  
  gi|242398708|ref|YP_002994132.1|  71 DAEIRKCPSCGKYSNSPKCPYCGAETEFERRVSFIDSPGHEALMTTMLAGASLMDGAVLVIAANEPCPKPQTREHL- 146
                                       55679***********************999999988877666665555555555555555444433344444433. PP

                          PolC_DP2 692 kleelkgvkgltskekipEpleK.gilRakhdvsvfkdgtvRyDmtdlplthfrpkeigvsveklre 757
                                          ++ g ++++  ++ +E + K   + + +++  f  gtv  ++  +p+++++ ++i+v ++ ++e
  gi|242398708|ref|YP_002994132.1| 147 MALQIVGNRNIIIAQNKIELVTKeQAIENYNQIKEFVKGTVAENAPIIPISALHGANIDVLISAIEE 213
                                       4445556666666666666666625678888899999999999999999999999988888877766 PP

>> Nop10p  Nucleolar RNA-binding protein, Nop10p family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.7   4.9e-06    0.0046       4      28 ..      73      97 ..      71      99 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.9e-06
                                      --EE-TTT--EESSSB-TTT-SB-B CS
                            Nop10p  4 ylrkcgkcrvYTLkkvcpecggptk 28
                                       +rkc++c++Y  + +cp+cg++t+
  gi|242398708|ref|YP_002994132.1| 73 EIRKCPSCGKYSNSPKCPYCGAETE 97
                                      69*********************96 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.4   8.3e-06    0.0078      13      35 ..      71      93 ..      66      96 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 8.3e-06
                                      HHH-EE-TTT--EESSSS-CCCC CS
                              RecR 13 kekvrhCsrCgnlteedlCaICs 35
                                        ++r C+ Cg ++ +  C+ C 
  gi|242398708|ref|YP_002994132.1| 71 DAEIRKCPSCGKYSNSPKCPYCG 93
                                      578*******************5 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   4.7   1.6e-05     0.015       3      25 ..      75      95 ..      73      96 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.6e-05
                       zf-ribbon_3  3 vrCPnCGaplssddnvCpyCGtk 25
                                      ++CP+CG+   s  ++CpyCG++
  gi|242398708|ref|YP_002994132.1| 75 RKCPSCGKY--SNSPKCPYCGAE 95
                                      58******5..59********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 ?   14.2   0.0   3.6e-05     0.034      23      95 ..      20      95 ..       9     101 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.6e-05
                                      ..EEEEEEEEEETTCT--H......HHHHHHHHHHHCC.TTTT-EEEEEEE--EE.EETTTS-EEECHHHHHS-TTTSS CS
                              HypA 23 arkvtkvkvevGelsgvep......eaLefafellaegtvlegaeLeieevpvkv.rCreCgkefeleekalrCpkCgs 94
                                       +k ++ +v++G + +v++      +aL+ +++  +++++ +g +++i   ++++ +C +Cgk  ++     +Cp Cg+
  gi|242398708|ref|YP_002994132.1| 20 KKKFKQAEVNIGMVGHVDHgkttltRALTGIWTDTHSEELRRGITIKIGFADAEIrKCPSCGKYSNSP----KCPYCGA 94
                                      356666677777776666421111156788888888888889999999999999846*****776644....8*****8 PP

                                      S CS
                              HypA 95 a 95
                                      +
  gi|242398708|ref|YP_002994132.1| 95 E 95
                                      6 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   6.6e-05     0.062      14      57 ..      16      61 ..       5      69 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.6e-05
                                      XXXXXXE....EEEEEEEESTTSSHHHHHHHHHHHCS----HHHHH CS
                           G-alpha 14 erkarkk..krevkllllGqseSGKsTilkqlkllykkgfseeela 57
                                       ++ +kk  + ev++ ++G+ + GK+T+ + l  + ++++see ++
  gi|242398708|ref|YP_002994132.1| 16 RKMVKKKfkQAEVNIGMVGHVDHGKTTLTRALTGIWTDTHSEELRR 61
                                      34444556679*****************************998444 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   8.4   0.00016      0.15       1      22 [.      76      95 ..      76      96 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00016
                     zinc_ribbon_2  1 fCpnCGaelqdnakFCpyCGtp 22
                                      +Cp+CG+    n++ CpyCG++
  gi|242398708|ref|YP_002994132.1| 76 KCPSCGKY--SNSPKCPYCGAE 95
                                      8******9..**********97 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.2      0.77   7.3e+02       4       8 ..      76      80 ..      70      82 .. 0.74
   2 ?   10.2   0.0   0.00058      0.55       3      18 ..      87     102 ..      84     130 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.77
                    PhnA_Zn_Ribbon  4 kCplC 8 
                                      kCp C
  gi|242398708|ref|YP_002994132.1| 76 KCPSC 80
                                      66666 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00058
                    PhnA_Zn_Ribbon   3 pkCplCaSeytYedga 18 
                                       pkCp C++e++ e + 
  gi|242398708|ref|YP_002994132.1|  87 PKCPYCGAETEFERRV 102
                                       9*********985443 PP

>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00016      0.15     506     537 ..      73     102 ..      15     103 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00016
                                       -EEEETT.--EESSSB-TTT--BE.EEEEEES CS
                              NRDD 506 kidvCnecgykgeiekCpkCgseeevevirRi 537
                                       +i  C++cg+     kCp+Cg   e+e  rR+
  gi|242398708|ref|YP_002994132.1|  73 EIRKCPSCGKYSNSPKCPYCGA--ETEFERRV 102
                                       6889******888888*****4..46666666 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.9   0.00023      0.21      11      34 ..      74      95 ..      73      99 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00023
                           DUF35_N 11 gqrCpdCGtvqfPPravCphCgsd 34
                                      +++Cp+CG++     + Cp+Cg+ 
  gi|242398708|ref|YP_002994132.1| 74 IRKCPSCGKYS--NSPKCPYCGAE 95
                                      689*******8..78******876 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 ?    3.0   0.1     0.089        84      22      28 ..      75      81 ..      74      83 .. 0.84
   2 ?    6.7   0.1    0.0061       5.8       6      16 ..      89      99 ..      85     101 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.089
                     zf-NADH-PPase 22 rvCpaCg 28
                                      r Cp+Cg
  gi|242398708|ref|YP_002994132.1| 75 RKCPSCG 81
                                      7899998 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0061
                     zf-NADH-PPase  6 CgrCGaptepa 16
                                      C+ CGa+te +
  gi|242398708|ref|YP_002994132.1| 89 CPYCGAETEFE 99
                                      ********976 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 ?   10.6   0.3   0.00035      0.33      10      19 ..      74      83 ..      73      86 .. 0.89
   2 ?    2.8   1.3     0.099        93      12      19 ..      88      95 ..      87      96 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00035
                           zf-tcix 10 vrkCpkCGty 19
                                      +rkCp+CG y
  gi|242398708|ref|YP_002994132.1| 74 IRKCPSCGKY 83
                                      8*******87 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.099
                           zf-tcix 12 kCpkCGty 19
                                      kCp CG++
  gi|242398708|ref|YP_002994132.1| 88 KCPYCGAE 95
                                      9*****96 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.3     0.011        10      23      34 ..      70      82 ..      64      86 .. 0.70
   2 ?    1.9   5.5      0.26   2.5e+02       7      36 ..      76      96 ..      76     102 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.011
                       Zn-ribbon_8 23 daplta.CPeCgs 34
                                       ++++  CP+Cg+
  gi|242398708|ref|YP_002994132.1| 70 ADAEIRkCPSCGK 82
                                      3455566****97 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.26
                       Zn-ribbon_8  7 rCeeCghefevlqsisdapltaCPeCgsev 36
                                      +C +Cg+  +          ++CP Cg+e+
  gi|242398708|ref|YP_002994132.1| 76 KCPSCGKYSN---------SPKCPYCGAET 96
                                      5778884443.........567****9944 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       831  (0.0463495); expected 358.6 (0.02)
Passed bias filter:                      752  (0.0419432); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2643.69
//
Query:       gi|242398709|ref|YP_002994133.1|  [L=146]
Description: nucleic acid-binding protein, containing PIN domain [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-31  109.6   0.2    1.2e-31  109.4   0.2    1.0  1  PIN_9          PIN like domain
    1.3e-06   28.7   0.0    1.8e-06   28.3   0.0    1.2  1  Fcf1           Fcf1
    0.00019   21.7   1.3      0.047   14.0   1.3    2.2  1  PIN_4          PIN domain
  ------ inclusion threshold ------
       0.02   15.4   0.7      0.061   13.8   0.7    1.7  1  PIN_12         PIN domain
      0.048   13.7   0.4      0.059   13.4   0.4    1.1  1  AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD bindi
       0.13   12.0   0.0        0.4   10.5   0.0    1.9  1  DUF5615        Domain of unknown function (DUF5615)


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 !  109.4   0.2     4e-35   1.2e-31       1     116 []      17     136 ..      17     136 .. 0.96

  Alignments for each domain:
  == domain 1  score: 109.4 bits;  conditional E-value: 4e-35
                             PIN_9   1 vilDtnaLmipvqfgvdifeelerll.gsvelvvpkavleELerlakagkgkertaakvalsLaerceiveae...e 73 
                                       vi Dtn+L+ip qfgv+i+ el+r+l  + e+ +p+ v++ELe ++++ +gk+  a+k+a++La++  ++e+    e
  gi|242398709|ref|YP_002994133.1|  17 VIPDTNFLLIPGQFGVNIVGELQRILdVNFEIAIPNVVVDELEVIERKVRGKDFMAVKMAKKLAKKFIVIEIGkfgE 93 
                                       789***********************8899************************************99999887878 PP

                             PIN_9  74 ekaDdailelakeldaavlvTnDreLkkrllekgipvilLRqk 116
                                       +  D++ile+a+++   ++ TnDr+Lkk+l+e+gipv++LRqk
  gi|242398709|ref|YP_002994133.1|  94 KPIDQQILEFASKTSNVIVCTNDRALKKKLRENGIPVVYLRQK 136
                                       88*************9**************************8 PP

>> Fcf1  Fcf1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.0     6e-10   1.8e-06       2      95 ..      41     138 ..      40     142 .. 0.85

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 6e-10
                                       HCTS-EEEEEEHHHHHHHHHCT..........-HHHHHHHTTSEEE----SS---HHHHHHHHH-BTB-TT-EEEE- CS
                              Fcf1   2 tLqakvkpliTqCviaeleklgkk........lkealkiaktferlkCnhkkptsaddClvsvvkkkknkkryivAt 70 
                                       +L  ++++ i + v++ele +++k        +k a k+ak+f + + ++  +++ d+ +++  +   + ++ iv+t
  gi|242398709|ref|YP_002994133.1|  41 ILDVNFEIAIPNVVVDELEVIERKvrgkdfmaVKMAKKLAKKFIVIEIGKFGEKPIDQQILEFAS---KTSNVIVCT 114
                                       6788899999999********98877888888888999999999999888556677778888888...47999**** PP

                                       S-HHHHHHHHTSTT--EEEEE--EE CS
                              Fcf1  71 qDkdlrrrlrkipgvPilyikrsvm 95 
                                       +D++l+++lr+  g+P++y++++++
  gi|242398709|ref|YP_002994133.1| 115 NDRALKKKLRE-NGIPVVYLRQKKI 138
                                       **********9.59******99886 PP

>> PIN_4  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   1.3   1.6e-05     0.047       2     127 ..      18     130 ..      17     134 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.6e-05
                             PIN_4   2 VlDTnvlLhdpealksf........keehdvviPitVleELdklKkgsserelarlarqanrlldellekesgrlkv 70 
                                       + DTn+lL   ++  ++        + + ++ iP +V++EL+ + ++ +    +     a+++ ++l +k    +++
  gi|242398709|ref|YP_002994133.1|  18 IPDTNFLLIPGQFGVNIvgelqrilDVNFEIAIPNVVVDELEVIERKVR--GKD---FMAVKMAKKLAKK---FIVI 86 
                                       7799999988888777788889999889999999999999998888776..222...2333333222221...2222 PP

                             PIN_4  71 qtsaeelpeeeseseknDnrIlavalelkeekpdrkvvLvskDinlrikAkalgiea 127
                                       +    +  e     +  D++Il++a +       ++v+ +++D+ l+ k + +gi++
  gi|242398709|ref|YP_002994133.1|  87 EIG--KFGE-----KPIDQQILEFASKT------SNVIVCTNDRALKKKLRENGIPV 130
                                       222..1222.....24577777776543......45778888888888887777776 PP

>> PIN_12  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.7   2.1e-05     0.061       4      81 ..      20     103 ..      17     140 .. 0.55

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.1e-05
                            PIN_12   4 DTnifldeffrlseeealkklleliesgkiklivpdivldEflknrekkiees...kklekalks......lsklks 71 
                                       DTn++l    +++ + ++ +l + ++  ++++++p++v+dE++   +k+  +     k+ k+l++      + k+++
  gi|242398709|ref|YP_002994133.1|  20 DTNFLLI-PGQFGVN-IVGELQRILDV-NFEIAIPNVVVDELEVIERKVRGKDfmaVKMAKKLAKkfivieIGKFGE 93 
                                       9999994.7777777.99999666666.6************987666665544555333322222244334444444 PP

                            PIN_12  72 akkklnekkk 81 
                                       +  +++ ++ 
  gi|242398709|ref|YP_002994133.1|  94 KPIDQQILEF 103
                                       4443333332 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.4     2e-05     0.059      59     155 ..      37     139 ..      31     144 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2e-05
                                       HHHHHCT.T-EE--HHHCTTT-SEEEE-SSSSSSB-HHHHCCS-TTEEEEE-SSTT.TTBTHHHHHTTT-EEEEEET CS
                     AdoHcyase_NAD  59 alqaame.GfevvtleevvkkadivvtttGnkdiitlehlkkmkddaivcniGhfd.seidvaaleanalkkeevkp 133
                                        lq +++  fe++  + vv++ +++      kd + +++ kk+ ++ iv +iG f  + id + le  +++ + +  
  gi|242398709|ref|YP_002994133.1|  37 ELQRILDvNFEIAIPNVVVDELEVIERKVRGKDFMAVKMAKKLAKKFIVIEIGKFGeKPIDQQILEFASKTSNVIVC 113
                                       5677776458999999999******99999*************************6156******999888888877 PP

                                       TEEEEE-....TTS-EEEEEGGGSBC CS
                     AdoHcyase_NAD 134 qvdrvtl....kdgkkiillaeGrll 155
                                         dr       ++g  ++ l + ++l
  gi|242398709|ref|YP_002994133.1| 114 TNDRALKkklrENGIPVVYLRQKKIL 139
                                       77765431111345556666665555 PP

>> DUF5615  Domain of unknown function (DUF5615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00014       0.4      13      65 ..      75     126 ..      69     136 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00014
                           DUF5615  13 lvellreaghdvlhvrelglegasDeeileyAkee.driivTkDkDFgellllg 65 
                                        +++l+++++ v+ + + g++   D++ile+A++  ++i+ T+D+   + l+ +
  gi|242398709|ref|YP_002994133.1|  75 MAKKLAKKFI-VIEIGKFGEK-PIDQQILEFASKTsNVIVCTNDRALKKKLREN 126
                                       5667777666.7777777755.57********8751667778888665555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1007.37
//
Query:       gi|242398710|ref|YP_002994134.1|  [L=1177]
Description: chromosome segregation ATPase [Thermococcus sibiricus MM 739]
Scores for 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-65  221.3  54.0      1e-63  214.7  54.0    4.1  1  SMC_N            RecF/RecN/SMC N terminal domain
      3e-32  111.4   1.0    1.3e-31  109.3   0.1    2.7  2  SMC_hinge        SMC proteins Flexible Hinge Domain
    7.9e-18   65.7   0.0    7.9e-18   65.7   0.0    7.3  2  AAA_23           AAA domain
    1.5e-13   51.3   2.2    1.3e-08   35.0   0.9    4.7  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    6.3e-12   45.9   2.4    6.3e-12   45.9   2.4    4.8  4  AAA_15           AAA ATPase domain
    2.3e-05   24.0   0.6    6.1e-05   22.7   0.1    2.0  1  AAA_29           P-loop containing region of AAA domain
    9.6e-05   21.2  30.6    9.6e-05   21.2  30.6    5.8  6  AAA_13           AAA domain
     0.0001   21.2  16.4     0.0001   21.2  16.4    9.4  7  Tektin           Tektin family
    0.00029   21.4 172.0    0.00034   21.2  27.2    9.8  9  APG6_N           Apg6 coiled-coil region
    0.00048   19.5  21.9    0.00048   19.5  21.9    8.4  8  GAS              Growth-arrest specific micro-tubule binding
    0.00072   19.8  23.0    0.00072   19.8  23.0    8.7  8  ATG16            Autophagy protein 16 (ATG16)
     0.0015   18.3  19.1     0.0015   18.3  19.1    6.0  5  Laminin_I        Laminin Domain I
     0.0019   17.6  12.8     0.0019   17.6  12.8    6.3  7  DUF4407          Domain of unknown function (DUF4407)
      0.003   17.1   7.8      0.003   17.1   7.8    7.3  7  MscS_porin       Mechanosensitive ion channel porin domain
     0.0038   16.2 156.3      0.078   11.8   9.3    8.0  9  Spc7             Spc7 kinetochore protein
     0.0042   17.3  11.5     0.0042   17.3  11.5   10.7  8  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
     0.0042   16.1 115.4      0.027   13.4  20.3    6.7  7  IFT57            Intra-flagellar transport protein 57
      0.006   16.6  90.6       0.52   10.4   3.0   10.1 11  DUF1664          Protein of unknown function (DUF1664)
     0.0089   16.1  26.0     0.0089   16.1  26.0    8.8  7  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
  ------ inclusion threshold ------
      0.015   15.6   3.3      0.015   15.6   3.3   12.9 11  ABC_tran_CTD     ABC transporter C-terminal domain
      0.022   14.8  50.0      0.041   13.9   1.2    7.9  8  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
      0.022   13.8 124.6      0.082   12.0  30.5    6.7  6  Atg14            Vacuolar sorting 38 and autophagy-related su
      0.031   14.2   0.2         22    5.0   0.0    4.0  2  Surfac_D-trimer  Lung surfactant protein D coiled-coil trimer
      0.045   13.8 140.5       0.17   12.0  20.5    8.9  8  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
        1.4    9.3 132.4       0.82   10.1  28.9    7.6  7  Fez1             Fez1
        1.7    6.7 135.1       0.79    7.8  13.4    6.3  5  EzrA             Septation ring formation regulator, EzrA
        4.5    4.6 118.5     0.0039   14.8  50.7    4.3  4  DUF3584          Protein of unknown function (DUF3584)


Domain annotation for each model (and alignments):
>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  214.7  54.0   1.5e-66     1e-63       1     218 [.       3    1149 ..       3    1151 .. 1.00

  Alignments for each domain:
  == domain 1  score: 214.7 bits;  conditional E-value: 1.5e-66
                                        EEEEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--.BTTCSST CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx RF
                             SMC_N    1 vlkrleienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk.skekasv 74  
                                        ++++le+++Fksy  +++++pfs++ftaivG+NGSGKsn+ dAilFvLG  sak++r++++ dli++ +ke+a +
  gi|242398710|ref|YP_002994134.1|    3 YVEKLEMRGFKSYGSRKIVVPFSRGFTAIVGANGSGKSNIGDAILFVLGGLSAKAMRATRIGDLIFAgTKEEAPA 77  
                                        689****************************************************************999***** PP

                                        TEEEEEEEEEETTEESSSSSSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT.............. CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............. RF
                             SMC_N   75 kkaeveitfdnedkklkiekeevsisrrvkrkgeseykingkevtkkevsellesagiske.............. 135 
                                        k aev+++f+ned+ ++i+++ev+i+rrv+ +g+s y++ngk+ +++++ ++l+ a+is++              
  gi|242398710|ref|YP_002994134.1|   78 KYAEVAMYFNNEDRGFPIDEDEVVIKRRVYPDGRSAYWLNGKRTSRSDILDVLSAAMISPDgynlvlqgditkfi 152 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|242398710|ref|YP_002994134.1|  153 kmspterrmiideisgiaeydekkkkameelkqaeenlarvdllirevktqldklekerndalryldlkekleva 227 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|242398710|ref|YP_002994134.1|  228 rttlltgevkrlqnliaesrardeeieveieringeleniaktivekektltqiereleeksedgildvtkkise 302 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|242398710|ref|YP_002994134.1|  303 vaskielakknielakkeisesqrrlakakedlknvsaeiekgkstierwkkrrenliaeiqkkekeknelilkl 377 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|242398710|ref|YP_002994134.1|  378 aeidknftiakqeldkveeelenakktqyfkeseitkiteeierikskisqqstrriilkskleelkaeinvkks 452 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|242398710|ref|YP_002994134.1|  453 elseidskiekasvrlreiekelekgqeklekivpeikklneelikaearkevhqnktleaiknanipgiygsla 527 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|242398710|ref|YP_002994134.1|  528 elirvrddtyltavevalgshadnvvvkddkvaeeaikflkrnrlgrltflplnkikprkldgvskgipvmdvie 602 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|242398710|ref|YP_002994134.1|  603 ydpqfknavafavgdtlivndmeeardvgigkvrmvtlegellersgaivggyyrprtklaintdeikmalasre 677 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|242398710|ref|YP_002994134.1|  678 kekdalesqinalkleqrglerelfelrvrksdvskdlqmlqkemdrflnedktlkeeietaenrlkelesfihq 752 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|242398710|ref|YP_002994134.1|  753 tkgdlaklsgrverlekirnklrkaldnpearelnqkireveheisklreelskvesrlenldirineeliprka 827 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|242398710|ref|YP_002994134.1|  828 dleeeiegivnrinafkasikqneedikslqaqleelqekeqavkdelkalrderdrlreeisqmreekeklrdv 902 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|242398710|ref|YP_002994134.1|  903 lqklrleanslkikmaqyesqlrekeselkhhdvkvvkeipedleklreeieqmedeirelepvnmkaiedyevv 977 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|242398710|ref|YP_002994134.1|  978 errylelkskrerleaekdsiiefineienqkrnvfmqtlnaiarnfselftklspggeaklvleneedpfsggl 1052
                                        *************************************************************************** PP

                                        ...............CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE CS
                                        ...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  136 ...............lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivi 195 
                                                       ++SgGek+L+ala++fAiq++kpap+yl+Deida+LD++nvk+va+l+ke+sk++Qfivi
  gi|242398710|ref|YP_002994134.1| 1053 dieakpagkevkrieAMSGGEKALTALAFVFAIQHFKPAPFYLFDEIDAHLDDANVKRVADLIKEASKDSQFIVI 1127
                                        *************************************************************************** PP

                                        -SSHHHCCC-SCEEEEEEEETTE CS
                                        xxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  196 slreemlekadklvgvtkvengv 218 
                                        +lr+ m+++adk++gv++ ++gv
  gi|242398710|ref|YP_002994134.1| 1128 TLRDVMMSNADKIIGVSM-RKGV 1149
                                        ******************.7666 PP

>> SMC_hinge  SMC proteins Flexible Hinge Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       5.8   3.9e+03      38      63 ..     173     200 ..     169     234 .. 0.62
   2 !  109.3   0.1     2e-34   1.3e-31       2     116 ..     520     630 ..     519     631 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 5.8
                         SMC_hinge  38 eetakkiieflkkk..nagratflpldr 63 
                                       +e+ kk++e lk++  n+ r+ +l  ++
  gi|242398710|ref|YP_002994134.1| 173 DEKKKKAMEELKQAeeNLARVDLLIREV 200
                                       6788999999999954466666665533 PP

  == domain 2  score: 109.3 bits;  conditional E-value: 2e-34
                         SMC_hinge   2 kgvlGrladlievd.egyekAveaalgnrlqalvvedeetakkiieflkkknagratflpldrikqknkadgandkn 77 
                                       +g++G la+li+v+ ++y +Ave+alg++++++vv+d+++a+++i+flk++++gr+tflpl++ik+++ +       
  gi|242398710|ref|YP_002994134.1| 520 PGIYGSLAELIRVRdDTYLTAVEVALGSHADNVVVKDDKVAEEAIKFLKRNRLGRLTFLPLNKIKPRKLDGVS---- 592
                                       79*****************************************************************777776.... PP

                         SMC_hinge  78 sgavplidlvevddelrkalryllgdtlvvdsldeAeel 116
                                        +  p++d++e+d+++++a+ +++gdtl+v++++eA+++
  gi|242398710|ref|YP_002994134.1| 593 -KGIPVMDVIEYDPQFKNAVAFAVGDTLIVNDMEEARDV 630
                                       .679********************************975 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.7   0.0   1.2e-20   7.9e-18       1     181 [.       6     223 ..       6     247 .. 0.57
   2 ?   -1.4  27.4       4.3   2.9e+03      93     199 ..     397     496 ..     384     504 .. 0.62

  Alignments for each domain:
  == domain 1  score: 65.7 bits;  conditional E-value: 1.2e-20
                            AAA_23   1 kLkienfrsf..rdqeidFskgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiesegkvkayv 75 
                                       kL++++f+s+  r+  + Fs+g+t+I+G NG+GK+ i dAi ++L+g +++  r  +  + +  ++ ++e+  ++y+
  gi|242398710|ref|YP_002994134.1|   6 KLEMRGFKSYgsRKIVVPFSRGFTAIVGANGSGKSNIGDAILFVLGGLSAKAMRATR--IGDLIFAGTKEEAPAKYA 80 
                                       79********7666678******************************7776666443..333333333444556666 PP

                            AAA_23  76 elt..fenkdgrytrsiererelskkkgkttkkaklellei..deleqfise...........llgskkiilnlilf 137
                                       e+   f+n+d++      +e e+  k  ++ ++    +l+   + + ++++            +l  + +i ++i +
  gi|242398710|ref|YP_002994134.1|  81 EVAmyFNNEDRGF---PIDEDEVVIKRRVYPDGRSAYWLNGkrTSRSDILDVlsaamispdgyNLVLQGDITKFIKM 154
                                       6664488877753...444444444444444444444444433222222222333566667888889999******* PP

                            AAA_23 138 lgqer.............feefelkdkkerleelekeleeledekkllekl.................eqekek 181
                                        + er                   ++kk+++eel+++ e l  ++ l++++                 +++kek
  gi|242398710|ref|YP_002994134.1| 155 SPTERrmiideisgiaeyD-----EKKKKAMEELKQAEENLARVDLLIREVktqldklekerndalryLDLKEK 223
                                       *****66666665554440.....44444444444444444444444444421111110003333333333333 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 4.3
                            AAA_23  93 erelskkkgkttkkaklelleideleqfisellgskkiilnlilflgqerfeefelkdkkerleelekeleeledek 169
                                       e e++   +kt+++++ e+++i+e  ++i+++  +++++ ++i+++ + ++ + e + kk++l e+  ++e+++ + 
  gi|242398710|ref|YP_002994134.1| 397 ELENA---KKTQYFKESEITKITEEIERIKSK--ISQQSTRRIILKSKLEELKAEINVKKSELSEIDSKIEKASVRL 468
                                       33333...335566666666666655555543..4445556666666666667777889999999999999999999 PP

                            AAA_23 170 kllekleqekekekeleeleeeleeilkel 199
                                       +++ek++  ++ +++le++  e++++++el
  gi|242398710|ref|YP_002994134.1| 469 REIEKEL--EKGQEKLEKIVPEIKKLNEEL 496
                                       9999884..334555555555555555544 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 !   24.8   0.0   2.5e-08   1.7e-05       1      24 [.      28      51 ..      28     132 .. 0.75
   2 !   35.0   0.9     2e-11   1.3e-08      84     296 ..     950    1128 ..     901    1128 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 2.5e-08
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllar 24
                                      +++++G+NgsGKSn+ da+ ++ +
  gi|242398710|ref|YP_002994134.1| 28 FTAIVGANGSGKSNIGDAILFVLG 51
                                      89*****************99854 PP

  == domain 2  score: 35.0 bits;  conditional E-value: 2e-11
                            AAA_21   84 eeklssvetllesgllldkrsleeedvfnpeargirggvsvfslkelsvsepndlqfgkaltditsrawslllll 158 
                                        +e + + e+  +  + ++ ++ e++ v+  ++ + ++ +   ++   s++e+++++ ++ ++ +  +++ ++ ++
  gi|242398710|ref|YP_002994134.1|  950 REEIEQMEDEIRELEPVNMKAIEDYEVVERRYLELKSKRERLEAEKDSIIEFINEIENQKRNVFMQTLNAIARNF 1024
                                        6777888888899999999999***************************************************** PP

                            AAA_21  159 dglrkerigllnifadyfgfakekrllqrlvrslklveielsdlgegeeliasvderlrergvvflengdgqelp 233 
                                         +l+  +++     a+++ +++e ++ ++l  + k+++ e+  +++                             
  gi|242398710|ref|YP_002994134.1| 1025 SELF--TKLSPGGEAKLVLENEEDPFSGGLDIEAKPAGKEVKRIEA----------------------------- 1068
                                        ****..**************************************75............................. PP

                            AAA_21  234 arelSdGtkrl..lalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltT 296 
                                           +S G k l  la++ a+    +  +++l+DE++++L+ + ++r+++l+ke+s+ ++Q+i+ T
  gi|242398710|ref|YP_002994134.1| 1069 ---MSGGEKALtaLAFVFAIQHFKPA-PFYLFDEIDAHLDDANVKRVADLIKEASK-DSQFIVIT 1128
                                        ...5*******533666666666666.*****************************.*****998 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.9   2.4   9.4e-15   6.3e-12       4     274 ..       5     367 ..       3     373 .. 0.75
   2 ?   -1.7  36.7       2.8   1.8e+03      70     278 ..     307     521 ..     293     548 .. 0.53
   3 ?   -3.2  22.9       7.6     5e+03     144     288 ..     707     862 ..     659     876 .. 0.57
   4 !    7.6  17.0    0.0041       2.7     152     363 ..     882    1128 ..     860    1128 .. 0.54

  Alignments for each domain:
  == domain 1  score: 45.9 bits;  conditional E-value: 9.4e-15
                            AAA_15   4 kkikikNFRslkd..veidlseeltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifeniseskdik 78 
                                       +k++ + F+s+ +  + +++s  +t ++G+N+sGKS+i +a+ + l   + k   ++ i +  +  ++++++ k  +
  gi|242398710|ref|YP_002994134.1|   5 EKLEMRGFKSYGSrkIVVPFSRGFTAIVGANGSGKSNIGDAILFVLGGLSAKAMRATRIGDLIFAGTKEEAPAKYAE 81 
                                       7889999999965448889***********************999999988888899999***************** PP

                            AAA_15  79 Idvef........................................................................ 83 
                                       ++++f                                                                        
  gi|242398710|ref|YP_002994134.1|  82 VAMYFnnedrgfpidedevvikrrvypdgrsaywlngkrtsrsdildvlsaamispdgynlvlqgditkfikmspte 158
                                       ***************************************************************************** PP

                            AAA_15  84 ............aekekakeyektlkskekkka..dlllkkkesdlkktikdkklklkknelsdekisvekkks... 143
                                                   +++ek+k+ +++lk+ e++ a  dll+ + +++l+k+ k+++ +l   ++ d k ++    +   
  gi|242398710|ref|YP_002994134.1| 159 rrmiideisgiaEYDEKKKKAMEELKQAEENLArvDLLIREVKTQLDKLEKERNDAL---RYLDLKEKL----Evar 228
                                       ****99999876444566665555555555555113334444444444444444433...233333222....1334 PP

                            AAA_15 144 ..........kkelpkekeeklekekeelkidkedlkklikkleeslkkeeelknvlksaiiklllisakRnvsd.e 209
                                                  ++l  e++   e+ + e++  + +l+++ k++ e+ k   +++  l++++++  l+  k+ ++  +
  gi|242398710|ref|YP_002994134.1| 229 ttlltgevkrLQNLIAESRARDEEIEVEIERINGELENIAKTIVEKEKTLTQIERELEEKSEDGILDVTKKISEVaS 305
                                       46787777666667777777777777777777888888888777777766689999999999999999999999844 PP

                            AAA_15 210 dsekkssllgklkekileealqekleeelteklkeiqeklkeidkklaeelkkilkkkidkik.kf 274
                                       + e  +++++ +k++i+e+  q +   + +e+lk++  ++++ ++++ e++kk  ++ i +i+ k+
  gi|242398710|ref|YP_002994134.1| 306 KIELAKKNIELAKKEISES--QRR-LAKAKEDLKNVSAEIEKGKSTI-ERWKKRRENLIAEIQkKE 367
                                       4444555555555555554..444.4578999999999999999999.666655555555554222 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.8
                            AAA_15  70 niseskdikIdvefaek.....ekakeyektlkskekkkadlllkkkesdlkktikdkk.lklkknelsdekisvek 140
                                        +  +k+i+++++++++      kake++k    + +k +   +++++++  ++i + +  + +knel+ +  +++k
  gi|242398710|ref|YP_002994134.1| 307 IELAKKNIELAKKEISEsqrrlAKAKEDLKNVSAEIEKGKS-TIERWKKRRENLIAEIQkKEKEKNELILKLAEIDK 382
                                       45566777777777333345444444444333333333333.33333333333333332023333444444444444 PP

                            AAA_15 141 kks.kkelpkekeeklekekeelkidkedlkklikkleeslkkee...elknvlksaiiklllisakRnvsdedsek 213
                                       +   +k+  ++ ee+le+ k++  ++ ++++k+ +++e +++k +   +   +lks++++l+   ++++++ ++ ++
  gi|242398710|ref|YP_002994134.1| 383 NFTiAKQELDKVEEELENAKKTQYFKESEITKITEEIERIKSKISqqsTRRIILKSKLEELKAEINVKKSELSEIDS 459
                                       44355557777788888888888899999999998777665444422355555566666655555555555555555 PP

                            AAA_15 214 kssllgklkekileealqekleeelteklkeiqeklkeidkklaeelk...kilkkkidkikkfnykg 278
                                       k +  +  +++i +e       e+ +ekl++i  ++k+++++l + ++    + +k ++ ik+ n++g
  gi|242398710|ref|YP_002994134.1| 460 KIEKASVRLREIEKE------LEKGQEKLEKIVPEIKKLNEELIKAEArkeVHQNKTLEAIKNANIPG 521
                                       555555555555554......77888888888888888888885555566633344444444444443 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 7.6
                            AAA_15 144 kkelpkekeeklekekeelkidkedlkklikkleeslkkeeelknvlksaiiklllisakRnvsdedsekkssllgk 220
                                       +k++ ++   +l+ke + +  ++++lk+ i++ e+ lk+       l+s+i +++ + ak +   e+ ek+++ l k
  gi|242398710|ref|YP_002994134.1| 707 RKSDVSKDLQMLQKEMDRFLNEDKTLKEEIETAENRLKE-------LESFIHQTKGDLAKLSGRVERLEKIRNKLRK 776
                                       233333333333333333333344444444433333333.......3345555555555555555555555555555 PP

                            AAA_15 221 lkekileealqekl......eeelteklkeiqeklkeidkklaeelk.......kilkkkidkikkfnykgkkneei 284
                                       ++++     l++k       + +l+e+l+++++ l+++d  ++eel        ++++ +++ i+ f++ +k+nee+
  gi|242398710|ref|YP_002994134.1| 777 ALDNPEARELNQKIreveheISKLREELSKVESRLENLDIRINEELIprkadleEEIEGIVNRINAFKASIKQNEED 853
                                       54444444444444455555889999999999999999999999999999999999999999999999999999998 PP

                            AAA_15 285 eik.....d 288
                                         +     +
  gi|242398710|ref|YP_002994134.1| 854 IKSlqaqlE 862
                                       776666441 PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.0041
                            AAA_15  152 eeklekekeelkidkedlkklikkleeslkkeeelknvlksaiiklllisakRnvsdedsekkssllgklkekil 226 
                                        ++ l +e+  +  +ke+l+++++kl+   ++ +         i+  ++ s  R+ ++e++ +  ++  +++e++ 
  gi|242398710|ref|YP_002994134.1|  882 RDRLREEISQMREEKEKLRDVLQKLRLEANSLK---------IKMAQYESQLREKESELKHHDVKVVKEIPEDLE 947 
                                        333333333333335555556655555555555.........333344444444444444444444444444442 PP

                            AAA_15  227 eealqekl...........................eeelteklkeiqeklkeidkklaeelkkilkkkidkikkf 274 
                                        +  l+e+                             +el++k ++++ + + i++ +            ++i++ 
  gi|242398710|ref|YP_002994134.1|  948 K--LREEIeqmedeirelepvnmkaiedyevverrYLELKSKRERLEAEKDSIIEFI------------NEIENQ 1008
                                        2..222223333344555566555555555555553333333333333333333333............333333 PP

                            AAA_15  275 nykgkkneeieik......................................ddeelplnknGsGvqrllllilli 311 
                                        + +++ + +  i                                        +e   ++ ++ G + l  l++  
  gi|242398710|ref|YP_002994134.1| 1009 KRNVFMQTLNAIArnfselftklspggeaklvleneedpfsggldieakpaGKEVKRIEAMSGGEKALTALAFVF 1083
                                        3333333333333333333344446666667777777777*8888888887666667777777777777776666 PP

                            AAA_15  312 leaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitT 363 
                                        +  + k     +  ++l++E++ahL   + k +++l+ke+++d+  Q i+ T
  gi|242398710|ref|YP_002994134.1| 1084 AIQHFK-----PAPFYLFDEIDAHLDDANVKRVADLIKEASKDS--QFIVIT 1128
                                        666666.....99*******************************..999866 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 !   22.7   0.1   9.2e-08   6.1e-05      16      48 ..      21      52 ..       7      58 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 9.2e-08
                            AAA_29 16 tieidlkgatlltGpsGsGKSTllDAiqalLvp 48
                                      +++++ +g+t ++G++GsGKS + DAi ++L +
  gi|242398710|ref|YP_002994134.1| 21 VVPFS-RGFTAIVGANGSGKSNIGDAILFVLGG 52
                                      56776.789********************9965 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.2       1.7   1.2e+03      21      36 ..      31      46 ..      24      57 .. 0.84
   2 ?    0.4  27.6      0.29   1.9e+02     292     461 ..     169     350 ..     147     354 .. 0.54
   3 !    6.3  35.8    0.0046       3.1     285     456 ..     339     508 ..     330     519 .. 0.80
   4 ?    2.6   3.6     0.063        42     408     476 ..     663     730 ..     655     738 .. 0.88
   5 !   21.2  30.6   1.4e-07   9.6e-05     265     470 ..     738     949 ..     735     954 .. 0.86
   6 ?    4.1   3.6     0.022        14     383     512 ..     944    1083 ..     936    1095 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.7
                            AAA_13 21 iYGwNGaGKTtLSrll 36
                                      i G+NG+GK+ +  ++
  gi|242398710|ref|YP_002994134.1| 31 IVGANGSGKSNIGDAI 46
                                      77*******9887665 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.29
                            AAA_13 292 iekveskkselleklkavsde....asensafeedkeelkaeaealeeqLkglqraleaKrkepfksvelesvkaki 364
                                       i+++++kk++++e+lk++ +     + + ++ + + ++l++e +    +L+ l+++le  r+ + +  e++++++ i
  gi|242398710|ref|YP_002994134.1| 169 IAEYDEKKKKAMEELKQAEENlarvDLLIREVKTQLDKLEKERNDALRYLD-LKEKLEVARTTLLT-GEVKRLQNLI 243
                                       445566666666666555553222222222222222222222222222222.34444444444444.4556666666 PP

                            AAA_13 365 esikklvaeineliakhNekvanleeekeeakkklelhlv..........eeleseldeykkkykklekaiekleke 431
                                        +     +ei+  i++ N   +n+++   e +k l + +            +++++++e  +k++ ++k+ie ++ke
  gi|242398710|ref|YP_002994134.1| 244 AESRARDEEIEVEIERINGELENIAKTIVEKEKTLTQIEReleeksedgiLDVTKKISEVASKIELAKKNIELAKKE 320
                                       66666666777777777766666666443333333333322223333333445555666667777777777777777 PP

                            AAA_13 432 lkeeeaelkkleeeikeLekqlrdekpaae 461
                                       ++e++++l+k++e+ k+  +++++ k ++e
  gi|242398710|ref|YP_002994134.1| 321 ISESQRRLAKAKEDLKNVSAEIEKGKSTIE 350
                                       777777777777777777777777777665 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.0046
                            AAA_13 285 qerLekliekveskkselleklkavsdeasensafeedkeelkaeaealeeqLkglqrale.aKrkepfksvelesv 360
                                        +++ek ++++e+ k++  + ++++ ++++e+++   + +e+++++   +++L++++++le aK+++ fk+ e++++
  gi|242398710|ref|YP_002994134.1| 339 SAEIEKGKSTIERWKKRRENLIAEIQKKEKEKNELILKLAEIDKNFTIAKQELDKVEEELEnAKKTQYFKESEITKI 415
                                       44455555555555555556677777778888889999**********************836999*********** PP

                            AAA_13 361 kakiesikklvaeineliakhNekvanleeekeeakkklelhlveeleseldeykkkykklekaieklekelkeeea 437
                                       +++ie+ik+++++  +      +++ + + e+ +a+ ++++++++e++s++++    ++++ek++ek +++l+++  
  gi|242398710|ref|YP_002994134.1| 416 TEEIERIKSKISQQST-----RRIILKSKLEELKAEINVKKSELSEIDSKIEKASVRLREIEKELEKGQEKLEKIVP 487
                                       *********9998654.....378888899999999999************************************** PP

                            AAA_13 438 elkkleee..ikeLekqlrde 456
                                       e+kkl+ee   +e +k++ + 
  gi|242398710|ref|YP_002994134.1| 488 EIKKLNEEliKAEARKEVHQN 508
                                       *******95334444444443 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.063
                            AAA_13 408 eseldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeeinkeLkafGlgele 476
                                         + de k ++++ ek+   le ++++ + e++ le e  eL+ + +d+ +  + + ke+ +f l+e++
  gi|242398710|ref|YP_002994134.1| 663 AINTDEIKMALASREKEKDALESQINALKLEQRGLERELFELRVRKSDVSKDLQMLQKEMDRF-LNEDK 730
                                       556678899999*************************************************99.77764 PP

  == domain 5  score: 21.2 bits;  conditional E-value: 1.4e-07
                            AAA_13 265 lpaerkaaLeahFddefeekqerLekliekveskkselleklkavsde..asensafeedkeelkaeaealeeqLkg 339
                                       + ++r ++Le+++ +  + + ++L+ ++e++e+ +++l + l+++ ++  +++ ++ e+++++l++e++++e++L++
  gi|242398710|ref|YP_002994134.1| 738 TAENRLKELESFIHQ-TKGDLAKLSGRVERLEKIRNKLRKALDNPEARelNQKIREVEHEISKLREELSKVESRLEN 813
                                       668899*****9999.67779************999999999999886457888889999***************** PP

                            AAA_13 340 lqraleaKrkepfk..svelesvkakiesikklvaeineliakhNekvanleeekeeakkklel..hlveeleseld 412
                                       l  ++++      +  + e+e + ++i+++k ++++ +e i++  ++ ++l+e+++++k++l++  ++  +l++e++
  gi|242398710|ref|YP_002994134.1| 814 LDIRINEELIPRKAdlEEEIEGIVNRINAFKASIKQNEEDIKSLQAQLEELQEKEQAVKDELKAlrDERDRLREEIS 890
                                       988888865322221123688999999***********************************972256899****** PP

                            AAA_13 413 eykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdek.paaeeinkeLkaf 470
                                       ++ ++++kl + ++kl  e++  + +++++e + +e+e +l+ +  + ++ei + L++ 
  gi|242398710|ref|YP_002994134.1| 891 QMREEKEKLRDVLQKLRLEANSLKIKMAQYESQLREKESELKHHDvKVVKEIPEDLEKL 949
                                       *******************************************9834578888888775 PP

  == domain 6  score: 4.1 bits;  conditional E-value: 0.022
                            AAA_13  383 ekvanleeekeeakkklelhlveel..eseldeykkkykklekaieklekelkeeeaelkkleeeikeLekq.lr 454 
                                        e  ++l ee e+++++++  +  ++   ++++  ++ y +l+ + e le+e++ + + ++++e++ ++   q l+
  gi|242398710|ref|YP_002994134.1|  944 EDLEKLREEIEQMEDEIRELEPVNMkaIEDYEVVERRYLELKSKRERLEAEKDSIIEFINEIENQKRNVFMQtLN 1018
                                        556778888888888988888554400455556669999999999999999999999999999999997655155 PP

                            AAA_13  455 dekpaaeeinkeLkafGlgeleLkfeee..kkgYrivrkg.gsqaa..etLSeGEk..taIaflY 512 
                                         + +  +e+ ++L+  G  +l L+ ee+    g  i  k  g++ +  e +S GEk  ta af++
  gi|242398710|ref|YP_002994134.1| 1019 AIARNFSELFTKLSPGGEAKLVLENEEDpfSGGLDIEAKPaGKEVKriEAMSGGEKalTALAFVF 1083
                                        67888999999999999999999888888877777766543444444589999999444555555 PP

>> Tektin  Tektin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   5.5       1.3   8.4e+02     318     365 ..     175     222 ..     170     224 .. 0.77
   2 ?    1.2   4.9      0.19   1.3e+02     251     305 ..     234     288 ..     224     291 .. 0.77
   3 ?   -0.5   3.6      0.59   3.9e+02      51      83 ..     467     499 ..     454     512 .. 0.43
   4 ?    0.0   9.2      0.42   2.8e+02      46      95 ..     702     751 ..     668     758 .. 0.72
   5 !   21.2  16.4   1.6e-07    0.0001     248     360 ..     759     867 ..     757     876 .. 0.92
   6 !    6.3   9.0    0.0054       3.6     246     296 ..     882     932 ..     867     938 .. 0.85
   7 !    7.9   7.6    0.0017       1.1     260     333 ..     939    1012 ..     933    1031 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.3
                            Tektin 318 aqyrLveEvkeleetieaLkeklaeaeaslkaLertrleleediavKa 365
                                        +++ +eE+k+ ee++++ +  ++e++++l++Le++r++  + +++K+
  gi|242398710|ref|YP_002994134.1| 175 KKKKAMEELKQAEENLARVDLLIREVKTQLDKLEKERNDALRYLDLKE 222
                                       555557899999999999999999999999999998887766666665 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.19
                            Tektin 251 krieetedaknkleeqlkkvleeiaeleknieeLekairdkeaplklaqtRlenR 305
                                         ++ +++   + +   ++++ ei++++ ++e++ k+i +ke+ l+  +  le++
  gi|242398710|ref|YP_002994134.1| 234 GEVKRLQNLIAESRARDEEIEVEIERINGELENIAKTIVEKEKTLTQIERELEEK 288
                                       5677778888888888888888888888888888888888888888877777765 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.59
                            Tektin  51 RiediefwkeeLekeleelkeeieaLeeekrrl 83 
                                       R+++ie+  e+ +++le+++ ei++L+ee  ++
  gi|242398710|ref|YP_002994134.1| 467 RLREIEKELEKGQEKLEKIVPEIKKLNEELIKA 499
                                       333333333333333333333333333333222 PP

  == domain 4  score: 0.0 bits;  conditional E-value: 0.42
                            Tektin  46 krLeeRiediefwkeeLekeleelkeeieaLeeekrrlekalealeeplh 95 
                                        +L+ R +d+++  ++L+ke+++  +e ++L+ee + +e+ l++le  +h
  gi|242398710|ref|YP_002994134.1| 702 FELRVRKSDVSKDLQMLQKEMDRFLNEDKTLKEEIETAENRLKELESFIH 751
                                       45777777888888888888888888888888888888888887776555 PP

  == domain 5  score: 21.2 bits;  conditional E-value: 1.6e-07
                            Tektin 248 alrkrieetedaknkleeqlkkvleeiaeleknieeLekairdkeaplklaqtRlenRtqRpnvElcrDeaqyrLve 324
                                        l+ r+e +e+++nkl++ l++   e  el+++i+e e +i +  + l  +++Rlen   R n El   +a   L e
  gi|242398710|ref|YP_002994134.1| 759 KLSGRVERLEKIRNKLRKALDN--PEARELNQKIREVEHEISKLREELSKVESRLENLDIRINEELIPRKA--DLEE 831
                                       5788****************97..5789***************************************9987..9*** PP

                            Tektin 325 EvkeleetieaLkeklaeaeaslkaLertrleleed 360
                                       E++ + + i+a k+++++ e+ +k+L+ +  el+e 
  gi|242398710|ref|YP_002994134.1| 832 EIEGIVNRINAFKASIKQNEEDIKSLQAQLEELQEK 867
                                       ********************************9864 PP

  == domain 6  score: 6.3 bits;  conditional E-value: 0.0054
                            Tektin 246 nealrkrieetedaknkleeqlkkvleeiaeleknieeLekairdkeaplk 296
                                        + lr+ i+++++ k+kl++ l+k++ e ++l+ ++++ e+++r+ke+ lk
  gi|242398710|ref|YP_002994134.1| 882 RDRLREEISQMREEKEKLRDVLQKLRLEANSLKIKMAQYESQLREKESELK 932
                                       46799******************************************9998 PP

  == domain 7  score: 7.9 bits;  conditional E-value: 0.0017
                            Tektin  260 knkleeqlkkvleeiaeleknieeLekairdkeaplklaqtR.lenRtqRpnvElcrDeaqyrLveEvkeleeti 333 
                                         +++ e+l+k++eei+++e++i+eLe   ++  +   +++ R le +++R ++E  +D    + ++E+++ ++++
  gi|242398710|ref|YP_002994134.1|  939 VKEIPEDLEKLREEIEQMEDEIRELEPVNMKAIEDYEVVERRyLELKSKRERLEAEKDSI-IEFINEIENQKRNV 1012
                                        5778899********************999999999999999789999**********76.88889988888776 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   8.6    0.0068       4.5      56     100 ..     169     213 ..     150     216 .. 0.86
   2 !   13.0  14.6   0.00017      0.11       8     101 ..     194     288 ..     193     292 .. 0.84
   3 ?    2.6  21.4      0.28   1.9e+02      39     129 ..     311     401 ..     291     404 .. 0.59
   4 ?    4.7  15.1     0.064        42      12      97 ..     378     460 ..     375     463 .. 0.82
   5 ?    4.5  17.8      0.07        46      11     103 ..     419     515 ..     419     519 .. 0.76
   6 !    8.2  14.2     0.005       3.3      46     127 ..     670     751 ..     659     757 .. 0.61
   7 !   10.4  20.2    0.0011      0.72      14     126 ..     732     861 ..     730     861 .. 0.84
   8 !   21.2  27.2   5.1e-07   0.00034      21     129 ..     829     934 ..     818     938 .. 0.88
   9 ?   -0.1  16.0       1.8   1.2e+03      33      92 ..     922     996 ..     919    1031 .. 0.49

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0068
                            APG6_N  56 leklekeeeelleeLkelekereeleaelaaleeelealeeeeer 100
                                       +++ ++++++++eeLk++e++ ++++  +++ + +l++le+e + 
  gi|242398710|ref|YP_002994134.1| 169 IAEYDEKKKKAMEELKQAEENLARVDLLIREVKTQLDKLEKERND 213
                                       788999***********************************9876 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00017
                            APG6_N   8 dlLleeldkqleqaekerdaYeeflkklkkekkeeek.qdeeleeleeeleklekeeeelleeLkelekereeleae 83 
                                       dlL+ e+++ql+++eker++ +++l+  +k ++  ++    e+++l++ +++ ++  ee + e++++  e e++++ 
  gi|242398710|ref|YP_002994134.1| 194 DLLIREVKTQLDKLEKERNDALRYLDLKEKLEVARTTlLTGEVKRLQNLIAESRARDEEIEVEIERINGELENIAKT 270
                                       89*****************9999988655555444336789999999999999999999999999999999999999 PP

                            APG6_N  84 laaleeelealeeeeerf 101
                                       + + e++l ++e+e e++
  gi|242398710|ref|YP_002994134.1| 271 IVEKEKTLTQIERELEEK 288
                                       999999999999998875 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.28
                            APG6_N  39 kkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreynelqlellel 115
                                       kk+ e  ++e+ e++++l+k +++ ++  +e+++ +++ e+ ++ +++l +e +++e+e+++ + +  e + + +  
  gi|242398710|ref|YP_002994134.1| 311 KKNIELAKKEISESQRRLAKAKEDLKNVSAEIEKGKSTIERWKKRRENLIAEIQKKEKEKNELILKLAEIDKNFTIA 387
                                       33333355566666666666666666666666666666666666666666666666666666666666666666666 PP

                            APG6_N 116 eeeldsleaqyeha 129
                                       ++eld++e ++e a
  gi|242398710|ref|YP_002994134.1| 388 KQELDKVEEELENA 401
                                       66666666665555 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.064
                            APG6_N  12 eeldkqleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaale 88 
                                        e+dk +  a++e d+ ee l++ kk++  +   ++e+ ++ ee+e+++++ ++  +    l+++ eel+ae++  +
  gi|242398710|ref|YP_002994134.1| 378 AEIDKNFTIAKQELDKVEEELENAKKTQYFK---ESEITKITEEIERIKSKISQQSTRRIILKSKLEELKAEINVKK 451
                                       6788888889999998888888888886554...4799999999999999999999999999999999999999999 PP

                            APG6_N  89 eelealeee 97 
                                       +el++++ +
  gi|242398710|ref|YP_002994134.1| 452 SELSEIDSK 460
                                       999988865 PP

  == domain 5  score: 4.5 bits;  conditional E-value: 0.07
                            APG6_N  11 leeldkqleqaekerdaYeeflkklkkekkeeek....qdeeleeleeeleklekeeeelleeLkelekereeleae 83 
                                       +e+++++++q+   r  +++ l++lk+e + +++     d+++e++  +l+++eke e+ +e+L+++  e ++l++e
  gi|242398710|ref|YP_002994134.1| 419 IERIKSKISQQSTRRIILKSKLEELKAEINVKKSelseIDSKIEKASVRLREIEKELEKGQEKLEKIVPEIKKLNEE 495
                                       67889999999999999999999999996665445666677777777778888888888888888888888888888 PP

                            APG6_N  84 laaleeelealeeeeerfwr 103
                                       l ++e+ +e  +++  + ++
  gi|242398710|ref|YP_002994134.1| 496 LIKAEARKEVHQNKTLEAIK 515
                                       88888887777777666665 PP

  == domain 6  score: 8.2 bits;  conditional E-value: 0.005
                            APG6_N  46 deeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreynelqlelleleeeldsl 122
                                       +  l++ e+e ++le++ ++l  e + le+e  el+   ++ ++ l+ l++e +rf++e + l+ e +  e++l+ l
  gi|242398710|ref|YP_002994134.1| 670 KMALASREKEKDALESQINALKLEQRGLERELFELRVRKSDVSKDLQMLQKEMDRFLNEDKTLKEEIETAENRLKEL 746
                                       34555666666666666666666666666666666666666666666666666666666666666666666666666 PP

                            APG6_N 123 eaqye 127
                                       e+ ++
  gi|242398710|ref|YP_002994134.1| 747 ESFIH 751
                                       66555 PP

  == domain 7  score: 10.4 bits;  conditional E-value: 0.0011
                            APG6_N  14 ldkqleqaekerdaYeeflkklkkekkeeek................qdeeleeleeeleklekeeeelleeLkele 74 
                                       l++++e+ae+  +++e+f ++ k +  + +                 ++ e +el+++++++e e ++l eeL ++e
  gi|242398710|ref|YP_002994134.1| 732 LKEEIETAENRLKELESFIHQTKGDLAKLSGrverlekirnklrkalDNPEARELNQKIREVEHEISKLREELSKVE 808
                                       67777777777777777777777664443336777777777788888888999************************ PP

                            APG6_N  75 kereeleaela.aleeelealeeeeerfwreynelqlelleleeeldsleaqy 126
                                       +  e+l+  ++ +l   +++leee e  +++ n+++   ++ ee+ +sl+aq+
  gi|242398710|ref|YP_002994134.1| 809 SRLENLDIRINeELIPRKADLEEEIEGIVNRINAFKASIKQNEEDIKSLQAQL 861
                                       *********96268999**********************************96 PP

  == domain 8  score: 21.2 bits;  conditional E-value: 5.1e-07
                            APG6_N  21 aekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeee 97 
                                       +e+e++   +  + +k++ k++   +e++++l+ +le+l+++e++   eLk+l +er++l++e+++ +ee+e+l + 
  gi|242398710|ref|YP_002994134.1| 829 LEEEIEGIVNRINAFKASIKQN---EEDIKSLQAQLEELQEKEQAVKDELKALRDERDRLREEISQMREEKEKLRDV 902
                                       5555555555566666665554...58************************************************** PP

                            APG6_N  98 eerfwreynelqlelleleeeldsleaqyeha 129
                                        ++   e n+l++++++ e +l+  e++++h+
  gi|242398710|ref|YP_002994134.1| 903 LQKLRLEANSLKIKMAQYESQLREKESELKHH 934
                                       ************************99999997 PP

  == domain 9  score: -0.1 bits;  conditional E-value: 1.8
                            APG6_N  33 kklkkekkeeek...............qdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeele 92 
                                       ++l+++++e ++                +ee+e+ e+e+++le    +++e  + +e+   el+++++ le+e++
  gi|242398710|ref|YP_002994134.1| 922 SQLREKESELKHhdvkvvkeipedlekLREEIEQMEDEIRELEPVNMKAIEDYEVVERRYLELKSKRERLEAEKD 996
                                       444444333333433444443333333444444444444444444444444444444444444444444444433 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   7.0       1.3   8.5e+02      86     125 ..     175     214 ..     165     231 .. 0.64
   2 ?    2.0   7.7      0.17   1.1e+02      28      84 ..     236     292 ..     229     316 .. 0.86
   3 !    8.3  32.4     0.002       1.3      28     168 ..     314     457 ..     306     457 .. 0.91
   4 !    6.0  10.2    0.0099       6.6      28      90 ..     447     509 ..     445     517 .. 0.92
   5 ?    1.9   5.1      0.19   1.2e+02      39      88 ..     670     719 ..     659     728 .. 0.40
   6 !   14.8  13.4     2e-05     0.014      26     119 ..     727     815 ..     722     834 .. 0.81
   7 !   19.5  21.9   7.2e-07   0.00048      16     103 ..     842     933 ..     828     939 .. 0.78
   8 ?    2.7  11.6       0.1        68      66     146 ..     924    1012 ..     922    1033 .. 0.53

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.3
                               GAS  86 slknlkarlkelekelkdlkwehevleqrfekvekerdel 125
                                       + k++ ++lk++e++l ++ +  + ++ +++k+eker++ 
  gi|242398710|ref|YP_002994134.1| 175 KKKKAMEELKQAEENLARVDLLIREVKTQLDKLEKERNDA 214
                                       3344555666666666666666666666666666666654 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.17
                               GAS  28 IkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdk 84 
                                       +k+l + i+e ++++e+ e e++ i+ e +++ +++ + e+ + + +++l++ ++d 
  gi|242398710|ref|YP_002994134.1| 236 VKRLQNLIAESRARDEEIEVEIERINGELENIAKTIVEKEKTLTQIERELEEKSEDG 292
                                       6899999********************************************998874 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.002
                               GAS  28 IkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqs....lknlkarlkeleke 100
                                       I+  K+ei e +++ ++++ +l+++s+e ++ k ++++ ++ +e+L +++++ ek+k++    l+++ ++ + +++e
  gi|242398710|ref|YP_002994134.1| 314 IELAKKEISESQRRLAKAKEDLKNVSAEIEKGKSTIERWKKRRENLIAEIQKKEKEKNElilkLAEIDKNFTIAKQE 390
                                       7778***************************************************9986222268899999999999 PP

                               GAS 101 lkdlkwehevleqrfekvekerdelykkfeaaiqevqqktglknllLekklkalqeelEkkeaqleev 168
                                       l ++++e e+ ++     e+e+ +++++ e+   +++q++  + ++L+ kl++l++e++ k+ +l+e+
  gi|242398710|ref|YP_002994134.1| 391 LDKVEEELENAKKTQYFKESEITKITEEIERIKSKISQQST-RRIILKSKLEELKAEINVKKSELSEI 457
                                       99999999999999888999***********9999999875.889********************986 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.0099
                               GAS  28 IkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknl 90 
                                       I+  K+e+ e++ k e+++ +l ei++e ++ +e+L+k   e+++L+++l + e  k+ ++n 
  gi|242398710|ref|YP_002994134.1| 447 INVKKSELSEIDSKIEKASVRLREIEKELEKGQEKLEKIVPEIKKLNEELIKAEARKEVHQNK 509
                                       67779************************************************9999988875 PP

  == domain 5  score: 1.9 bits;  conditional E-value: 0.19
                               GAS  39 kkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslk 88 
                                       k   ++ eke ++++++ + lk + + +e+e+ eLr +  + +kd q l+
  gi|242398710|ref|YP_002994134.1| 670 KMALASREKEKDALESQINALKLEQRGLERELFELRVRKSDVSKDLQMLQ 719
                                       33333333333333333333333333333333333333333333333333 PP

  == domain 6  score: 14.8 bits;  conditional E-value: 2e-05
                               GAS  26 elIkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelk 102
                                       +  k+lKeeie+ +++ ++ e  +++++ +  +l+  ++++e+ +++Lrk+l n e      ++l+++++e+e e++
  gi|242398710|ref|YP_002994134.1| 727 NEDKTLKEEIETAENRLKELESFIHQTKGDLAKLSGRVERLEKIRNKLRKALDNPEA-----RELNQKIREVEHEIS 798
                                       5569************************************************99876.....556666666666666 PP

                               GAS 103 dlkwehevleqrfekve 119
                                       +l++e   +e r+e++ 
  gi|242398710|ref|YP_002994134.1| 799 KLREELSKVESRLENLD 815
                                       66666666666665554 PP

  == domain 7  score: 19.5 bits;  conditional E-value: 7.2e-07
                               GAS  16 YYnditrnNLelIkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslk.... 88 
                                        +++ +++N e Iksl  ++eel++ke++ + el+++  e  rl+e++ + +ee+e+Lr  l++ + + +slk    
  gi|242398710|ref|YP_002994134.1| 842 AFKASIKQNEEDIKSLQAQLEELQEKEQAVKDELKALRDERDRLREEISQMREEKEKLRDVLQKLRLEANSLKikma 918
                                       5777889999*************************************************999876655555550000 PP

                               GAS  89 nlkarlkelekelkd 103
                                       + +++l+e e+elk+
  gi|242398710|ref|YP_002994134.1| 919 QYESQLREKESELKH 933
                                       555555555555544 PP

  == domain 8  score: 2.7 bits;  conditional E-value: 0.1
                               GAS   66 aeeeveeLrk.qlknyekdkqslknlkarlkelekelkdlk.......wehevleqrfekvekerdelykkfeaa 132 
                                        ++e+  eL++ ++k  ++  ++l++l+++++++e+e+++l+       +++ev+e r+ +++++r++l+++ ++ 
  gi|242398710|ref|YP_002994134.1|  924 LREKESELKHhDVKVVKEIPEDLEKLREEIEQMEDEIRELEpvnmkaiEDYEVVERRYLELKSKRERLEAEKDSI 998 
                                        555666666535555666667888888888888888888873332222344555555555555555555544444 PP

                               GAS  133 iqevqqktglknll 146 
                                        i+ + +  + k  +
  gi|242398710|ref|YP_002994134.1|  999 IEFINEIENQKRNV 1012
                                        44444433333333 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   6.0       2.1   1.4e+03     105     147 ..     177     219 ..     164     232 .. 0.57
   2 ?    1.1  19.6      0.58   3.9e+02      70     170 ..     301     401 ..     282     405 .. 0.64
   3 ?    5.3  21.0     0.032        21      80     192 ..     388     500 ..     377     512 .. 0.60
   4 ?    4.6  15.7      0.05        33      75     179 ..     672     776 ..     656     782 .. 0.89
   5 !    9.7  15.3    0.0014       0.9      82     178 ..     714     815 ..     710     825 .. 0.76
   6 !    9.2   3.3     0.002       1.3      98     154 ..     784     841 ..     780     848 .. 0.85
   7 !   19.8  23.0   1.1e-06   0.00072      98     180 ..     848     930 ..     842     933 .. 0.96
   8 ?    2.4  10.8      0.24   1.6e+02     110     186 ..     923    1000 ..     923    1001 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 2.1
                             ATG16 105 lelneelqkleeklkedeerlaeleaeraaletklkdreeelr 147
                                       ++++eel++ ee+l + +  ++e++++  +le++++d    l 
  gi|242398710|ref|YP_002994134.1| 177 KKAMEELKQAEENLARVDLLIREVKTQLDKLEKERNDALRYLD 219
                                       3445555555555555555555555555555555555444444 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.58
                             ATG16  70 skqsakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeel 146
                                       s+ ++ki+  ++++   ++e +e++++ ++ ++ l+++++e++k ++++++ ++r ++l ae+++ e++ +++  +l
  gi|242398710|ref|YP_002994134.1| 301 SEVASKIELAKKNIELAKKEISESQRRLAKAKEDLKNVSAEIEKGKSTIERWKKRRENLIAEIQKKEKEKNELILKL 377
                                       33444555555566666677777777777777777777777777777777777777777777777777777777777 PP

                             ATG16 147 rekeklvqdlqDElsaLqlqlnqa 170
                                       +e +k   + + El+  + +l+ a
  gi|242398710|ref|YP_002994134.1| 378 AEIDKNFTIAKQELDKVEEELENA 401
                                       777777777777777776666554 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.032
                             ATG16  80 eqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdl 156
                                       +q+l ++ eel+++ k++   ++ +++ +ee+++ ++k++++++r   l+++ ++l+ +++ ++ el e +  +++ 
  gi|242398710|ref|YP_002994134.1| 388 KQELDKVEEELENAKKTQYFKESEITKITEEIERIKSKISQQSTRRIILKSKLEELKAEINVKKSELSEIDSKIEKA 464
                                       56666666666666666666666666666666666666666666666666666666666666666666666666655 PP

                             ATG16 157 qDElsaLqlqlnqaEeklrklekENkeLveRWmkrk 192
                                          l   + +l++  ekl+k+  E k+L e ++k  
  gi|242398710|ref|YP_002994134.1| 465 SVRLREIEKELEKGQEKLEKIVPEIKKLNEELIKAE 500
                                       555555555555555555555555555544444433 PP

  == domain 4  score: 4.6 bits;  conditional E-value: 0.05
                             ATG16  75 kiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekek 151
                                        ++s e++  +l ++  +l  ++  l+  l el    ++  + l+  ++++++  +e ++l+++++  e++l+e+e 
  gi|242398710|ref|YP_002994134.1| 672 ALASREKEKDALESQINALKLEQRGLERELFELRVRKSDVSKDLQMLQKEMDRFLNEDKTLKEEIETAENRLKELES 748
                                       56777888888888888889999999999999999999999999999999*************************** PP

                             ATG16 152 lvqdlqDElsaLqlqlnqaEeklrklek 179
                                        +++ + +l+ L  +++ +E+ ++kl+k
  gi|242398710|ref|YP_002994134.1| 749 FIHQTKGDLAKLSGRVERLEKIRNKLRK 776
                                       **********************999986 PP

  == domain 5  score: 9.7 bits;  conditional E-value: 0.0014
                             ATG16  82 klaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeel.....rekeklv 153
                                        l+ l++e+   + +  +l++ + ++++ l++le+ + + +  la+l+ ++++le+ +++++++l     re+++ +
  gi|242398710|ref|YP_002994134.1| 714 DLQMLQKEMDRFLNEDKTLKEEIETAENRLKELESFIHQTKGDLAKLSGRVERLEKIRNKLRKALdnpeaRELNQKI 790
                                       56678888888888888888888888888888888888888888888888888888777776655222226777777 PP

                             ATG16 154 qdlqDElsaLqlqlnqaEeklrkle 178
                                        ++  E+s L+ +l+++E++l++l 
  gi|242398710|ref|YP_002994134.1| 791 REVEHEISKLREELSKVESRLENLD 815
                                       79999*****************986 PP

  == domain 6  score: 9.2 bits;  conditional E-value: 0.002
                             ATG16  98 gelaqrllelneelqkleeklkedeerlaeleaer.aaletklkdreeelrekeklvq 154
                                        el+q+++e++ e++kl+e+l++ e+rl++l  ++ ++l  + +d+eee+++  + ++
  gi|242398710|ref|YP_002994134.1| 784 RELNQKIREVEHEISKLREELSKVESRLENLDIRInEELIPRKADLEEEIEGIVNRIN 841
                                       5899***************************977516799999999999998766665 PP

  == domain 7  score: 19.8 bits;  conditional E-value: 1.1e-06
                             ATG16  98 gelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDElsaLqlqlnqaEekl 174
                                        ++++ +++l+++l++l+ek ++ + +l++l++er +l++++++ +ee + ++ ++q+l+ E ++L++++ q E++l
  gi|242398710|ref|YP_002994134.1| 848 KQNEEDIKSLQAQLEELQEKEQAVKDELKALRDERDRLREEISQMREEKEKLRDVLQKLRLEANSLKIKMAQYESQL 924
                                       68999************************************************************************ PP

                             ATG16 175 rklekE 180
                                       r+ e E
  gi|242398710|ref|YP_002994134.1| 925 REKESE 930
                                       *99988 PP

  == domain 8  score: 2.4 bits;  conditional E-value: 0.24
                             ATG16  110 elqkleeklke.deerlaeleaeraaletklkdreeelrekeklvqdlqDElsaLqlqlnqaEeklrklekENke 183 
                                        +l+++e++lk  d + ++e+ ++ ++l++++++ e+e+re+e ++ +  ++++  + ++  + +k+++le+E  +
  gi|242398710|ref|YP_002994134.1|  923 QLREKESELKHhDVKVVKEIPEDLEKLREEIEQMEDEIRELEPVNMKAIEDYEVVERRYLELKSKRERLEAEKDS 997 
                                        5788888888625577899*****************************************************888 PP

                             ATG16  184 Lve 186 
                                         +e
  gi|242398710|ref|YP_002994134.1|  998 IIE 1000
                                        765 PP

>> Laminin_I  Laminin Domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9  15.4     0.027        18     141     254 ..     174     287 ..     162     291 .. 0.92
   2 ?    0.8  15.2      0.49   3.2e+02      21     126 ..     293     397 ..     288     404 .. 0.91
   3 ?   -2.9  12.3       6.8   4.5e+03      48     111 ..     432     495 ..     403     519 .. 0.43
   4 !   18.3  19.1   2.2e-06    0.0015      16     167 ..     661     814 ..     652     824 .. 0.93
   5 ?    2.8  25.8      0.12        81      22     188 ..     827    1004 ..     819    1007 .. 0.61

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.027
                         Laminin_I 141 kqleeaeaelkaAqkLLsrvqtllqklqeenkaLkealrdsLa..eyeakLsDlrelleeAaaktrdanrlnlanqa 215
                                       +++++a +elk+A++ L+rv  l+ + + ++ +L+++ +d L   + ++kL+ +r  l     +++  ++l ++  a
  gi|242398710|ref|YP_002994134.1| 174 EKKKKAMEELKQAEENLARVDLLIREVKTQLDKLEKERNDALRylDLKEKLEVARTTLLTG--EVKRLQNLIAESRA 248
                                       78999********************************99999755789*******999865..5777899******* PP

                         Laminin_I 216 nlreiekkkeevseeknqleetlktardsLdaanllLqe 254
                                       + +eie   e++++e + + +t+ + +++L++ ++ L+e
  gi|242398710|ref|YP_002994134.1| 249 RDEEIEVEIERINGELENIAKTIVEKEKTLTQIERELEE 287
                                       ********************************9999976 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.49
                         Laminin_I  21 ledltkeLqeklskesakkskieilekelesLaqeteeLqkkatqvlakaqkvnaesertlnnakeLaekikkladn 97 
                                       + d tk+++e  sk++  k++ie+++ke+++ +    +  + ++ v+a+ +k +  +er  ++ ++L ++i+k +++
  gi|242398710|ref|YP_002994134.1| 293 ILDVTKKISEVASKIELAKKNIELAKKEISESQRRLAKAKEDLKNVSAEIEKGKSTIERWKKRRENLIAEIQKKEKE 369
                                       66899********************9999999999999999************************************ PP

                         Laminin_I  98 ikeilekvatlneneealpssklseelae 126
                                        +e++ k a++++ ++  ++++l++  +e
  gi|242398710|ref|YP_002994134.1| 370 KNELILKLAEIDK-NFTIAKQELDKVEEE 397
                                       ************9.899999998876555 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 6.8
                         Laminin_I  48 elesLaqeteeLqkkatqvlakaqkvnaesertlnnakeLaekikkladnikeilekvatlnen 111
                                           L++  eeL  + ++   + +++  ++e+++ +  e +++ +k +++++ i+  +++lne+
  gi|242398710|ref|YP_002994134.1| 432 RRIILKSKLEELKAEINVKKSELSEIDSKIEKASVRLREIEKELEKGQEKLEKIVPEIKKLNEE 495
                                       2222333333333344444444444444444444444444444444444444444444444442 PP

  == domain 4  score: 18.3 bits;  conditional E-value: 2.2e-06
                         Laminin_I  16 kinanledltkeLqeklskesakkskieilekelesLaqeteeLqkkatqvlakaqkvnaesertlnnakeLaekik 92 
                                       k+  n ++ +  L +++++++a +s+i+ l+ e  +L+ e  eL  +   v+++ q +++e++r ln+ k+L+e+i+
  gi|242398710|ref|YP_002994134.1| 661 KLAINTDEIKMALASREKEKDALESQINALKLEQRGLERELFELRVRKSDVSKDLQMLQKEMDRFLNEDKTLKEEIE 737
                                       6777889999******************************************************************* PP

                         Laminin_I  93 kladnikeilekvatlneneealp..ssklseelaeaqrlLeelrsRdftkqleeaeaelkaAqkLLsrvqtllqkl 167
                                         ++ +ke+ + + ++ ++  +l+  ++ l++  ++  + L    +R+++++ +e+e e  + ++ Ls+v+++l++l
  gi|242398710|ref|YP_002994134.1| 738 TAENRLKELESFIHQTKGDLAKLSgrVERLEKIRNKLRKALDNPEARELNQKIREVEHEISKLREELSKVESRLENL 814
                                       ******************9999993346999999**************************************99876 PP

  == domain 5  score: 2.8 bits;  conditional E-value: 0.12
                         Laminin_I   22 edltkeLqeklskesakkskieilekelesLaqeteeLqkkatqvlakaqkvnaesertlnnakeLaekikklad 96  
                                        +dl++e++  ++ ++a k  i+  e+ ++sL+ + eeLq+k++ v ++ + ++ e +r  ++++++ e+ +kl+d
  gi|242398710|ref|YP_002994134.1|  827 ADLEEEIEGIVNRINAFKASIKQNEEDIKSLQAQLEELQEKEQAVKDELKALRDERDRLREEISQMREEKEKLRD 901 
                                        578888888888888888888888888888888888888888888777777766666666666666666665555 PP

                         Laminin_I   97 nikei.......lekvatlne....neealpssk...lseelaeaqrlLeelrsRdftkqleeaeaelkaAqkLL 157 
                                         ++ +         k+a+++     +e++l   +    +e  +  ++l ee+   +++ + +e e + ++A + +
  gi|242398710|ref|YP_002994134.1|  902 VLQKLrleanslKIKMAQYESqlreKESELKHHDvkvVKEIPEDLEKLREEI--EQMEDEIRELEPVNMKAIEDY 974 
                                        5544411110004455555555554333333332000333333334444444..456777777777777777778 PP

                         Laminin_I  158 srvqtllqklqeenkaLkealrdsLaeyeak 188 
                                        + v+ ++ +l+ + + L ea +ds+ e+ ++
  gi|242398710|ref|YP_002994134.1|  975 EVVERRYLELKSKRERL-EAEKDSIIEFINE 1004
                                        88888888888888888.4447777777665 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2  11.6      0.14        94     115     248 ..     171     298 ..     163     306 .. 0.68
   2 ?    2.8  14.9     0.094        62     130     246 ..     252     376 ..     232     385 .. 0.70
   3 ?    0.7  19.0      0.41   2.7e+02     109     232 ..     310     432 ..     297     446 .. 0.81
   4 ?    4.4  14.1     0.031        20     118     239 ..     389     509 ..     378     519 .. 0.73
   5 ?    3.6   5.0     0.053        35     107     207 ..     668     765 ..     660     785 .. 0.36
   6 !   17.6  12.8   2.8e-06    0.0019     111     234 ..     766     897 ..     764     901 .. 0.75
   7 ?    5.4  11.2     0.015       9.9     124     230 ..     872     999 ..     866    1024 .. 0.55

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.14
                           DUF4407 115 eqqeeakelkeqlaaaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekkaq 191
                                       e+ e++k++ e+l+ ++++ la+ +  i++ ++++d++e++++++ + ++ + + +  ++tt   G+ ++ ++  a+
  gi|242398710|ref|YP_002994134.1| 171 EYDEKKKKAMEELK-QAEENLARVDLLIREVKTQLDKLEKERNDALRYLDLKEKLE-VARTTLLTGEVKRLQNLIAE 245
                                       45556666656655.58999999*********************999888655543.44455577787777776666 PP

                           DUF4407 192 ldaaqaelaelkakldatarlaalraelaeleaerakeraasqaaaaaddGllarle 248
                                         a+++e++   ++   + +l++  +++ e e+ +++++++ ++  ++ dG+l+ ++
  gi|242398710|ref|YP_002994134.1| 246 SRARDEEIEVEIER--INGELENIAKTIVEKEKTLTQIERELEE--KSEDGILDVTK 298
                                       66666666666666..6666666666666655555555555554..44466666555 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.094
                           DUF4407 130 altaelaeleaqiaalqaeidaaearldalraeaqkeldgtk...gtgttgvaGkgpaake....kkaqldaaqael 199
                                       + + e+++++ +++++ ++i ++e++l++ ++e++++ +      +++++ va k + ak+    +k+++ + q++l
  gi|242398710|ref|YP_002994134.1| 252 EIEVEIERINGELENIAKTIVEKEKTLTQIERELEEKSEDGIldvTKKISEVASKIELAKKnielAKKEISESQRRL 328
                                       24445555555555666666666666666555555444433377777777777777777778888999999999999 PP

                           DUF4407 200 aelkakld.atarlaalraelaeleaerakeraasqaaaaaddGllar 246
                                       a++k++l+  +a++++ ++++++ +++r++ +a+ q+++++++ l+ +
  gi|242398710|ref|YP_002994134.1| 329 AKAKEDLKnVSAEIEKGKSTIERWKKRRENLIAEIQKKEKEKNELILK 376
                                       999999998899999999999999999999999999999999888755 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.41
                           DUF4407 109 daelaeeqqeeakelkeqlaaaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaa 185
                                       +++ +e +++e++e +++la +++++l++  a+i++ +++i+  ++r+++l ae qk+ +  k++ + + a   +++
  gi|242398710|ref|YP_002994134.1| 310 AKKNIELAKKEISESQRRLA-KAKEDLKNVSAEIEKGKSTIERWKKRRENLIAEIQKKEKE-KNELILKLAEIDKNF 384
                                       45555555566666666655.4778888888888888888888888888888888887764.577777789999999 PP

                           DUF4407 186 kekkaqldaaqaelaelkakld.atarlaalraelaeleaerakeraa 232
                                       + +k++ld+ ++el+++k++   +++++++  +e+++++++++++ ++
  gi|242398710|ref|YP_002994134.1| 385 TIAKQELDKVEEELENAKKTQYfKESEITKITEEIERIKSKISQQSTR 432
                                       99****************9955999999******99999999988765 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.031
                           DUF4407 118 eeakelkeqlaaa......ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakek 188
                                       +e ++++e+l++a       ++e+++++++i++++++i+++++r+  l+ +++ el+     +++    k  +  e 
  gi|242398710|ref|YP_002994134.1| 389 QELDKVEEELENAkktqyfKESEITKITEEIERIKSKISQQSTRRIILKSKLE-ELKA----EIN---VKKSELSEI 457
                                       23333444444444445558899999999999999999999999988888887.4443....333...345667778 PP

                           DUF4407 189 kaqldaaqaelaelkakld.atarlaalraelaeleaerakeraasqaaaaa 239
                                       ++++++a+ +l e++++l+  +++l++   e+++l++e++k++a+++ ++++
  gi|242398710|ref|YP_002994134.1| 458 DSKIEKASVRLREIEKELEkGQEKLEKIVPEIKKLNEELIKAEARKEVHQNK 509
                                       8888888888888888887789999999999999999999999998876665 PP

  == domain 5  score: 3.6 bits;  conditional E-value: 0.053
                           DUF4407 107 eIdaelaeeqqeeakelkeqlaaaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgp 183
                                       eI+  la++ +e +++l++q++ al+ e++ le+++ +l+   +  +++l+ l++e+++ l+ +k+ + + ++  + 
  gi|242398710|ref|YP_002994134.1| 668 EIKMALASREKE-KDALESQIN-ALKLEQRGLERELFELRVRKSDVSKDLQMLQKEMDRFLNEDKTLK-EEIETAEN 741
                                       444444433332.344544444.333333334444444444444444444444444444444333211.11233333 PP

                           DUF4407 184 aakekkaqldaaqaelaelkakld 207
                                       + ke ++ + + + +la+l+++++
  gi|242398710|ref|YP_002994134.1| 742 RLKELESFIHQTKGDLAKLSGRVE 765
                                       333333333333333333333322 PP

  == domain 6  score: 17.6 bits;  conditional E-value: 2.8e-06
                           DUF4407 111 elaeeqqeeakelkeqlaaaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtk..........gtgttg 177
                                       +l++++++  k+l++  a +l+++++e e +i++l++e+++ e+rl++l    ++el + k              ++
  gi|242398710|ref|YP_002994134.1| 766 RLEKIRNKLRKALDNPEARELNQKIREVEHEISKLREELSKVESRLENLDIRINEELIPRKadleeeiegiV---NR 839
                                       67777888888888888888***************************************9977755542222...22 PP

                           DUF4407 178 vaGkgpaakekkaqldaaqaelaelkakld.atarlaalraelaeleaerakeraasq 234
                                       ++   ++ k+++++++ +qa+l+el++k +  +++l+alr+e+++l++e+++ r++++
  gi|242398710|ref|YP_002994134.1| 840 INAFKASIKQNEEDIKSLQAQLEELQEKEQaVKDELKALRDERDRLREEISQMREEKE 897
                                       4444555555677777777777777776557778888888888888888888777665 PP

  == domain 7  score: 5.4 bits;  conditional E-value: 0.015
                           DUF4407 124 keqlaaaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtk........gtgttgvaGkgpaakekkaql 192
                                       k++l+ al++e ++l+++i+++++e +++++ l++lr ea++    +          ++ + ++ + ++ ke  ++l
  gi|242398710|ref|YP_002994134.1| 872 KDELK-ALRDERDRLREEISQMREEKEKLRDVLQKLRLEANSLK-IKMaqyesqlrEKESELKHHDVKVVKEIPEDL 946
                                       22222.34455555555555555555555555555555554322.22245655555444455667777777788888 PP

                           DUF4407 193 daaqaelaelkakld...............atarlaalraelaeleaeraker 230
                                       +++++e+++++++++                + r  +l++++++leae+++++
  gi|242398710|ref|YP_002994134.1| 947 EKLREEIEQMEDEIRelepvnmkaiedyevVERRYLELKSKRERLEAEKDSII 999
                                       88888888888888888888888555555544444444444444444444433 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 ?   -0.5  10.3       1.1   7.2e+02     141     219 ..     178     255 ..     164     265 .. 0.84
   2 ?    5.9  21.4     0.012       8.2      39     198 ..     236     403 ..     233     406 .. 0.88
   3 !    7.9  15.9    0.0029       1.9      33     144 ..     392     504 ..     389     518 .. 0.73
   4 ?   -0.7   4.8       1.3   8.5e+02      95     169 ..     674     705 ..     659     737 .. 0.44
   5 !   17.1   7.8   4.6e-06     0.003      22     112 ..     726     815 ..     712     820 .. 0.90
   6 !    6.5  22.1     0.008       5.3      77     177 ..     844     936 ..     837     964 .. 0.87
   7 ?    1.0   0.4      0.38   2.5e+02      44      75 ..     937     969 ..     936    1012 .. 0.58

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.1
                        MscS_porin 141 aagealsqaqrtalqaelaaleaqieeleqellsnnnrqeLlklqrdllklriqqleqelqaLqellnekRlaeaek 217
                                       +a e+l qa+ ++ ++ l  +e ++++ ++e + n++++ L  l+ +l  +r + l  e++ Lq+l+ e R +  e 
  gi|242398710|ref|YP_002994134.1| 178 KAMEELKQAEENLARVDLLIREVKTQLDKLEKERNDALRYL-DLKEKLEVARTTLLTGEVKRLQNLIAESRARDEEI 253
                                       44559999999999999999999999999999999999866.68889999999999999999999999999988887 PP

                        MscS_porin 218 av 219
                                        v
  gi|242398710|ref|YP_002994134.1| 254 EV 255
                                       66 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.012
                        MscS_porin  39 aeelqkaiddaPkelrelqqelealqkkkeeaskeilak.lsleeLeqrllqtssq.lqelqeqlaqlnsqlvelqt 113
                                        + lq  i+++ ++ +e++ e+e+ + + e+  k+i +k  +l+++e++l++ s++  +++++++++  s++  +  
  gi|242398710|ref|YP_002994134.1| 236 VKRLQNLIAESRARDEEIEVEIERINGELENIAKTIVEKeKTLTQIERELEEKSEDgILDVTKKISEVASKIELAKK 312
                                       6789999999999999999******888888888887762689*******999877489****************** PP

                        MscS_porin 114 rperaqqqltearqrlqeirnrLnstaaage......alsqaqrtalqaelaaleaqieeleqellsnnnrqeLlkl 184
                                        +e a ++++e ++rl++   +L++ +a+ e      +  + +r  l ae +  e + +el + l+  ++  +++k+
  gi|242398710|ref|YP_002994134.1| 313 NIELAKKEISESQRRLAKAKEDLKNVSAEIEkgkstiERWKKRRENLIAEIQKKEKEKNELILKLAEIDKNFTIAKQ 389
                                       ***********************8887766666676666678999999****************************9 PP

                        MscS_porin 185 qrdllklriqqleq 198
                                       ++d  ++++++ ++
  gi|242398710|ref|YP_002994134.1| 390 ELDKVEEELENAKK 403
                                       99999999888766 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0029
                        MscS_porin  33 dkskkkaeelqkaiddaPkelrelqqeleal.qkkkeeaskeilaklsleeLeqrllqtssqlqelqeqlaqlnsql 108
                                       dk ++++e+ +k+      e+ ++++e+e+  +k ++++++ i+ k +leeL  +++  +s+l+e  +++ ++  +l
  gi|242398710|ref|YP_002994134.1| 392 DKVEEELENAKKTQYFKESEITKITEEIERIkSKISQQSTRRIILKSKLEELKAEINVKKSELSEIDSKIEKASVRL 468
                                       44555555555555555667888888888886666777888888889999999999999999999999999999999 PP

                        MscS_porin 109 velqtrperaqqqltearqrlqeirnrLnstaaage 144
                                       +e++  +e+ q++l +   ++++++ +L + +a++e
  gi|242398710|ref|YP_002994134.1| 469 REIEKELEKGQEKLEKIVPEIKKLNEELIKAEARKE 504
                                       999999999999999988888888888866655555 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 1.3
                        MscS_porin  95 qelqeqlaqlnsqlvelqtrperaqqqltearqrlqeirnrLnstaaagealsqaqrtalqaelaaleaqieele 169
                                       ++ +++                                            +  ++q +al+ e+  le ++ el+
  gi|242398710|ref|YP_002994134.1| 674 ASREKEK-------------------------------------------DALESQINALKLEQRGLERELFELR 705
                                       2222222...........................................3333333333333333333332222 PP

  == domain 5  score: 17.1 bits;  conditional E-value: 4.6e-06
                        MscS_porin  22 LeqalnlLdkidkskkkaeelqkaiddaPkelrelqqelealqkkkeeaskeilaklsleeLeqrllqtssqlqelq 98 
                                       L++   l ++i+  +++++el+  i +    l++l+ + e+l +k  ++ ++ l++   +eL+q++ +++ + ++l+
  gi|242398710|ref|YP_002994134.1| 726 LNEDKTLKEEIETAENRLKELESFIHQTKGDLAKLSGRVERL-EKIRNKLRKALDNPEARELNQKIREVEHEISKLR 801
                                       5666667799********************************.********************************** PP

                        MscS_porin  99 eqlaqlnsqlvelq 112
                                       e+l++ +s+l +l 
  gi|242398710|ref|YP_002994134.1| 802 EELSKVESRLENLD 815
                                       **********9986 PP

  == domain 6  score: 6.5 bits;  conditional E-value: 0.008
                        MscS_porin  77 klsleeLeqrllqtssqlqelqeqlaqlnsqlvelqtrperaqqqltearqrlqeirnrLnstaaagealsqaqrta 153
                                       k s+++ e  +++ ++ql+elqe+ +  +++l +l++  +r++++++++r++ +++r+ L+++          + ++
  gi|242398710|ref|YP_002994134.1| 844 KASIKQNEEDIKSLQAQLEELQEKEQAVKDELKALRDERDRLREEISQMREEKEKLRDVLQKL--------RLEANS 912
                                       6788899999*****************************************************........445678 PP

                        MscS_porin 154 lqaelaaleaqieeleqellsnnn 177
                                       l+++ a +e+q++e e el+ +++
  gi|242398710|ref|YP_002994134.1| 913 LKIKMAQYESQLREKESELKHHDV 936
                                       889999999999999999998876 PP

  == domain 7  score: 1.0 bits;  conditional E-value: 0.38
                        MscS_porin  44 kaiddaPkelrelqqeleal.qkkkeeaskeil 75 
                                       k++++ P+ l++l++e+e++ ++  e ++ +  
  gi|242398710|ref|YP_002994134.1| 937 KVVKEIPEDLEKLREEIEQMeDEIRELEPVNMK 969
                                       567888888888888888884444444444444 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1  19.6      0.11        70     152     259 ..     173     280 ..     160     289 .. 0.80
   2 ?    5.3  13.9     0.012       7.9     175     261 ..     228     318 ..     218     324 .. 0.78
   3 ?    0.2  31.8      0.42   2.8e+02     143     256 ..     256     369 ..     251     403 .. 0.46
   4 ?    1.4  29.9      0.18   1.2e+02     156     282 ..     305     426 ..     298     441 .. 0.85
   5 ?    5.4  27.6     0.011       7.1     141     268 ..     388     514 ..     387     518 .. 0.88
   6 !    6.6  14.3    0.0047       3.1     145     257 ..     677     771 ..     637     776 .. 0.50
   7 !   11.8   9.3   0.00012     0.078     164     251 ..     745     834 ..     744     836 .. 0.90
   8 !   11.4  13.3   0.00016       0.1     200     263 ..     839     902 ..     836     905 .. 0.93
   9 ?    4.9  22.3     0.016        10     144     251 ..     885     996 ..     885    1030 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.11
                              Spc7 152 eedkelLekqeeeldellpeleeekaeleeeleklqe.aaeelesid.keeLeelreelaelkaeieekkkelaelq 226
                                       +e k++ +++ ++++e l +++    e++ +l+kl++ +++ l  +d ke+Le +r +l +   e++++++ +ae +
  gi|242398710|ref|YP_002994134.1| 173 DEKKKKAMEELKQAEENLARVDLLIREVKTQLDKLEKeRNDALRYLDlKEKLEVARTTLLT--GEVKRLQNLIAESR 247
                                       455556666667777777777777778888888887746677888999**********965..678888******** PP

                              Spc7 227 eqleeleekieelkeqkseleeeiaeaervlee 259
                                       ++ ee+e +ie ++ + +++ + i e+e++l +
  gi|242398710|ref|YP_002994134.1| 248 ARDEEIEVEIERINGELENIAKTIVEKEKTLTQ 280
                                       ***********************9999998754 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.012
                              Spc7 175 ekaeleeeleklqeaaeelesid...keeLeelreelaelkaeieekkkelaelqeqleeleek.ieelkeqksele 247
                                       + + l+ e+++lq+  +e  + d   + e+e +  el+++ ++i ek+k l++ +++lee++e+ i ++++++se+ 
  gi|242398710|ref|YP_002994134.1| 228 RTTLLTGEVKRLQNLIAESRARDeeiEVEIERINGELENIAKTIVEKEKTLTQIERELEEKSEDgILDVTKKISEVA 304
                                       4556778888888866666665522367999999************************9998755999********* PP

                              Spc7 248 eeiaeaervleeck 261
                                       ++i+ a++ +e  k
  gi|242398710|ref|YP_002994134.1| 305 SKIELAKKNIELAK 318
                                       ****9999877544 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.42
                              Spc7 143 gleenlegleedkelLekqeeeldellpeleeeka.eleeeleklqeaaeelesidkeeLeelreelaelkaeieek 218
                                       ++e++  +le+ ++++ ++e+ l+++  elee+ +  + +  +k+ e a +  ++ k+++e +++e++e +  +++ 
  gi|242398710|ref|YP_002994134.1| 256 EIERINGELENIAKTIVEKEKTLTQIERELEEKSEdGILDVTKKISEVASK-IELAKKNIELAKKEISESQRRLAKA 331
                                       444444444444444444444444444444444442222222233332222.2234444444444444444444444 PP

                              Spc7 219 kkelaelqeqleeleekieelkeqkseleeeiaeaerv 256
                                       k++l+++ +++e+ +++ie  k+++++l +ei+++e+ 
  gi|242398710|ref|YP_002994134.1| 332 KEDLKNVSAEIEKGKSTIERWKKRRENLIAEIQKKEKE 369
                                       44444444444444444444444444444444444443 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 0.18
                              Spc7 156 elLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleel 232
                                       +++e  +++++ +++e++e + +l +  e+l++ ++e+e+  k  +e  +++ ++l aei++k+ke +el  +l+e+
  gi|242398710|ref|YP_002994134.1| 305 SKIELAKKNIELAKKEISESQRRLAKAKEDLKNVSAEIEK-GKSTIERWKKRRENLIAEIQKKEKEKNELILKLAEI 380
                                       5666778888889999999999999999999999999887.678899999999999999999999999999999999 PP

                              Spc7 233 eekieelkeqkseleeeiaeaervleeckgwsesevsrlkeevkaleelt 282
                                       +++++ +k++ +++eee+++a++++     ++ese+ +++ee ++++++ 
  gi|242398710|ref|YP_002994134.1| 381 DKNFTIAKQELDKVEEELENAKKTQ----YFKESEITKITEEIERIKSKI 426
                                       9999999999999999999887765....599999999999999998765 PP

  == domain 5  score: 5.4 bits;  conditional E-value: 0.011
                              Spc7 141 kegleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeiee 217
                                       k++l++  e+le+ k++   +e+e++++ +e+e+ k++++++ ++    + +le++ k+e++  ++el+e++++ie+
  gi|242398710|ref|YP_002994134.1| 388 KQELDKVEEELENAKKTQYFKESEITKITEEIERIKSKISQQSTRRIILKSKLEEL-KAEINVKKSELSEIDSKIEK 463
                                       56788888888888888889999999999999999999999999999988888885.7899**************** PP

                              Spc7 218 kkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesev 268
                                        + +l e +++le+ +ek+e++  ++++l+ee+ +ae  +e +++ + + +
  gi|242398710|ref|YP_002994134.1| 464 ASVRLREIEKELEKGQEKLEKIVPEIKKLNEELIKAEARKEVHQNKTLEAI 514
                                       *********************************999999998887776655 PP

  == domain 6  score: 6.6 bits;  conditional E-value: 0.0047
                              Spc7 145 eenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesid...keeLeelreelaelkaeieek 218
                                       e++ ++le++ + L+ ++  l++ l el+ +k+++++ l++lq++ + + + d   kee+e++ ++l+el++ i++ 
  gi|242398710|ref|YP_002994134.1| 677 EKEKDALESQINALKLEQRGLERELFELRVRKSDVSKDLQMLQKEMDRFLNEDktlKEEIETAENRLKELESFIHQT 753
                                       33334444444444444444444444444444444444444444444443333222344444444444444444444 PP

                              Spc7 219 kkelaelqeqleeleekieelkeqkseleeeiaeaervl 257
                                       k +la+l  ++e+le                     +++
  gi|242398710|ref|YP_002994134.1| 754 KGDLAKLSGRVERLE---------------------KIR 771
                                       444444444444444.....................444 PP

  == domain 7  score: 11.8 bits;  conditional E-value: 0.00012
                              Spc7 164 eldellpeleeekaeleeeleklqeaaeeles.idkeeLeelreelaelkaeieekkkelaelqeqleeleekie.e 238
                                       el+++ ++++   a+l+ ++e+l++ +++l + +d+ e +el ++++e++ ei+++++el++++++le+l+ +i+ e
  gi|242398710|ref|YP_002994134.1| 745 ELESFIHQTKGDLAKLSGRVERLEKIRNKLRKaLDNPEARELNQKIREVEHEISKLREELSKVESRLENLDIRINeE 821
                                       6888999999999************8888876599**************************************9626 PP

                              Spc7 239 lkeqkseleeeia 251
                                       l  +k++leeei+
  gi|242398710|ref|YP_002994134.1| 822 LIPRKADLEEEIE 834
                                       8999999999996 PP

  == domain 8  score: 11.4 bits;  conditional E-value: 0.00016
                              Spc7 200 eLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgw 263
                                       ++++++ ++++++++i++++++l+elqe+ +++++++++l++++++l+eei++ ++ +e+ +++
  gi|242398710|ref|YP_002994134.1| 839 RINAFKASIKQNEEDIKSLQAQLEELQEKEQAVKDELKALRDERDRLREEISQMREEKEKLRDV 902
                                       68999***********************************************999999988876 PP

  == domain 9  score: 4.9 bits;  conditional E-value: 0.016
                              Spc7 144 leenlegleedkelLekqeeel....dellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeie 216
                                       l+e++++++e+ke+L +  ++l    ++l+ ++ +++++l+e+  +l+    ++ +  +e+Le+lree+++ + ei+
  gi|242398710|ref|YP_002994134.1| 885 LREEISQMREEKEKLRDVLQKLrleaNSLKIKMAQYESQLREKESELKHHDVKVVKEIPEDLEKLREEIEQMEDEIR 961
                                       56889999999988776666553333899999999999***********999999999******************* PP

                              Spc7 217 ekkkelaelqeqleeleekieelkeqkseleeeia 251
                                       e++    +  e+ e +e +  elk+++++le+e  
  gi|242398710|ref|YP_002994134.1| 962 ELEPVNMKAIEDYEVVERRYLELKSKRERLEAEKD 996
                                       *9988888888888777777777777777776633 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 ?    3.4  12.7      0.13        85      23     107 ..     182     267 ..     158     268 .. 0.81
   2 ?    0.8   8.8      0.82   5.5e+02      29     100 ..     213     288 ..     208     291 .. 0.76
   3 ?    1.8  13.6      0.42   2.8e+02      35     100 ..     339     401 ..     333     404 .. 0.83
   4 ?   -1.3  18.6       3.9   2.6e+03      28     103 ..     423     495 ..     402     518 .. 0.68
   5 !   17.3  11.5   6.3e-06    0.0042      10      98 ..     665     751 ..     659     757 .. 0.89
   6 !    7.7   4.5    0.0059       3.9      44     101 ..     763     815 ..     753     823 .. 0.68
   7 !   10.9  20.2   0.00062      0.41       7      99 ..     836     933 ..     832     944 .. 0.88
   8 ?   -0.3   7.1       1.8   1.2e+03       3      86 ..     945    1027 ..     944    1033 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.13
                                       CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT.S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  23 edkadvdelleldekrrelqveleelqaerNelskeIgkakkkk.edaeeliaevkelkeelkaleaelkeleaele 98 
                                       e k+  + l  +d   re++++l++l +erN + +    + k + + ++ l  evk l++ +++  a+ +e+e e+e
  gi|242398710|ref|YP_002994134.1| 182 ELKQAEENLARVDLLIREVKTQLDKLEKERNDALRYLDLKEKLEvARTTLLTGEVKRLQNLIAESRARDEEIEVEIE 258
                                       3344445677788889*********************9999988888899999************************ PP

                                       HHHCTS--- CS
                      Seryl_tRNA_N  99 klllaiPNi 107
                                        +  ++ Ni
  gi|242398710|ref|YP_002994134.1| 259 RINGELENI 267
                                       *99999887 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.82
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT....S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  29 delleldekrrelqveleelqaerNelskeIgkakkkk....edaeeliaevkelkeelkaleaelkeleaelekl 100
                                       d+l  ld k +   +++  l  e ++l++ I++  +++     ++e++  e +++ + + ++e++l+++e ele++
  gi|242398710|ref|YP_002994134.1| 213 DALRYLDLKEKLEVARTTLLTGEVKRLQNLIAESRARDeeieVEIERINGELENIAKTIVEKEKTLTQIERELEEK 288
                                       6666677777777777777888888888888888888855656777777788899999999999999999999875 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.42
                                       HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  35 dekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaelekl 100
                                        ++ ++ ++++e  +++r +l +eI+k+ k+k   +eli + +e+ +++  +++el+++e+ele++
  gi|242398710|ref|YP_002994134.1| 339 SAEIEKGKSTIERWKKRRENLIAEIQKKEKEK---NELILKLAEIDKNFTIAKQELDKVEEELENA 401
                                       56666777888999999999999999888765...89*************************9975 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 3.9
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCT CS
                      Seryl_tRNA_N  28 vdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaelekllla 103
                                         ++ +  ++r  l+++leel+ae N    e +++  k   +e+   + +e+ +el++ +++l+++  e++kl  +
  gi|242398710|ref|YP_002994134.1| 423 KSKISQQSTRRIILKSKLEELKAEINVKKSELSEIDSK---IEKASVRLREIEKELEKGQEKLEKIVPEIKKLNEE 495
                                       34566666777777888888888888888888777764...55556667777777777777777776666666544 PP

  == domain 5  score: 17.3 bits;  conditional E-value: 6.3e-06
                                       -HHHHHHHHCCCT.CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHH CS
                      Seryl_tRNA_N  10 npeavkeklkkRg.edkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelka 85 
                                       n++++k +l++R+ e +a+  ++ +l  ++r l+ el el+ ++  +sk  +++ k+    ++ ++e k+lkee+++
  gi|242398710|ref|YP_002994134.1| 665 NTDEIKMALASREkEKDALESQINALKLEQRGLERELFELRVRKSDVSKDLQMLQKE---MDRFLNEDKTLKEEIET 738
                                       99**********9555555668999*****************************975...799************** PP

                                       HHHHHHHHHHHHH CS
                      Seryl_tRNA_N  86 leaelkeleaele 98 
                                       +e++lkele+ ++
  gi|242398710|ref|YP_002994134.1| 739 AENRLKELESFIH 751
                                       *******997665 PP

  == domain 6  score: 7.7 bits;  conditional E-value: 0.0059
                                       HHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  44 eleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaelekll 101
                                       ++e l + rN+l k+  +      +a el ++++e+  e+++l +el+++e++le+l 
  gi|242398710|ref|YP_002994134.1| 763 RVERLEKIRNKLRKALDN-----PEARELNQKIREVEHEISKLREELSKVESRLENLD 815
                                       566666666666555544.....46677778888888888888888888887777764 PP

  == domain 7  score: 10.9 bits;  conditional E-value: 0.00062
                                       HHH-HHHHHHHHCCCT.CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT....S-TCCCCCCCHH CS
                      Seryl_tRNA_N   7 irenpeavkeklkkRg.edkadvdelleldekrrelqveleelqaerNelskeIgkakkkk....edaeeliaevke 78 
                                       i + + a+k+++k+ + + k++ ++l el+ek ++++ el +l+ er +l +eI+++ ++k    +  ++l+ e+++
  gi|242398710|ref|YP_002994134.1| 836 IVNRINAFKASIKQNEeDIKSLQAQLEELQEKEQAVKDELKALRDERDRLREEISQMREEKeklrDVLQKLRLEANS 912
                                       566778899999888834456667899*********************************9888778899******* PP

                                       HHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  79 lkeelkaleaelkeleaelek 99 
                                       lk +++++e +l+e e+el++
  gi|242398710|ref|YP_002994134.1| 913 LKIKMAQYESQLREKESELKH 933
                                       ******************986 PP

  == domain 8  score: -0.3 bits;  conditional E-value: 1.8
                                        -HHHHHH-HHHHHHHHCCCT.CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCC CS
                      Seryl_tRNA_N    3 DiklirenpeavkeklkkRg.edkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaev 76  
                                        D+  +re++e++++ +++ + +  + ++++  ++++  el+++ e l ae+ ++ + I ++ ++k  ++  ++  
  gi|242398710|ref|YP_002994134.1|  945 DLEKLREEIEQMEDEIRELEpVNMKAIEDYEVVERRYLELKSKRERLEAEKDSIIEFINEIENQK--RNVFMQTL 1017
                                        77888888888888888777778888888888888888888888888888888888888888876..55566666 PP

                                        HHHHHHHHHH CS
                      Seryl_tRNA_N   77 kelkeelkal 86  
                                        +++  ++++l
  gi|242398710|ref|YP_002994134.1| 1018 NAIARNFSEL 1027
                                        6666665555 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       3.8   2.5e+03      97     119 ..      40      62 ..      39      92 .. 0.85
   2 ?    2.6   2.8     0.079        53     287     341 ..     170     224 ..     165     231 .. 0.77
   3 !    6.4  14.3    0.0057       3.8     246     349 ..     238     343 ..     227     344 .. 0.89
   4 !    8.3  18.4    0.0014      0.96     225     326 ..     327     431 ..     325     434 .. 0.88
   5 !    8.4  16.5    0.0014      0.95     244     345 ..     409     515 ..     405     518 .. 0.84
   6 !    9.1  15.6   0.00086      0.57     178     323 ..     670     820 ..     659     822 .. 0.76
   7 !   13.4  20.3   4.1e-05     0.027     243     352 ..     843     957 ..     826     961 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 3.8
                             IFT57  97 qGyGeevcyvLdeLadeaLkkkk 119
                                       + +G+++++vL  L  +a+ +++
  gi|242398710|ref|YP_002994134.1|  40 SNIGDAILFVLGGLSAKAMRATR 62 
                                       668***************99885 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.079
                             IFT57 287 sevkekykqlsegvseltrelaeiseelekvkqemeergssmtDgsplvkikkal 341
                                       +e  ek k++ e++++ +++la+++  +++vk+++++ +++ +D+     +k+ l
  gi|242398710|ref|YP_002994134.1| 170 AEYDEKKKKAMEELKQAEENLARVDLLIREVKTQLDKLEKERNDALRYLDLKEKL 224
                                       5667777888888888888888888888888888888888888887777777766 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0057
                             IFT57 246 qlkklhedisktlekiesrEkylnsqleellqeyreaqeelsevkekykqlse.gvseltrelaeiseelekvkqem 321
                                        l++l  +     e+ie   +++n +le+  +   e++++l+++++++++ se g+ + t++ +e+  ++e +k+++
  gi|242398710|ref|YP_002994134.1| 238 RLQNLIAESRARDEEIEVEIERINGELENIAKTIVEKEKTLTQIERELEEKSEdGILDVTKKISEVASKIELAKKNI 314
                                       5777777777888999999999**************************99886489********************* PP

                             IFT57 322 eergssmtDg.splvkikkaltklkkEik 349
                                       e  +++++++ + l k k+ l+++  Ei+
  gi|242398710|ref|YP_002994134.1| 315 ELAKKEISESqRRLAKAKEDLKNVSAEIE 343
                                       *******997478**************97 PP

  == domain 4  score: 8.3 bits;  conditional E-value: 0.0014
                             IFT57 225 hleqmkkhkksieeslpetksqlkklhedisktlekiesrEkylns...qleellqeyreaqeelsevkekykqlse 298
                                       +l + k+  k++++++++ ks +++ ++  ++ + +i+++Ek  n+   +l e  +++  a++el++v+e+++++++
  gi|242398710|ref|YP_002994134.1| 327 RLAKAKEDLKNVSAEIEKGKSTIERWKKRRENLIAEIQKKEKEKNElilKLAEIDKNFTIAKQELDKVEEELENAKK 403
                                       56677788899*******************************988822245555678******************** PP

                             IFT57 299 gvseltrelaeiseelekvkqemeergs 326
                                       +   ++ e ++i+ee+e++k+++ ++++
  gi|242398710|ref|YP_002994134.1| 404 TQYFKESEITKITEEIERIKSKISQQST 431
                                       **********************998875 PP

  == domain 5  score: 8.4 bits;  conditional E-value: 0.0014
                             IFT57 244 ksqlkklhedisktlekie...srEkylnsqleellqeyreaqeelsevkekykqlsegvseltrelaeiseelekv 317
                                       +s+++k+ e+i++  +ki+   +r  +l s+leel +e + ++ else+  k++++s ++ e ++el++ +e+lek+
  gi|242398710|ref|YP_002994134.1| 409 ESEITKITEEIERIKSKISqqsTRRIILKSKLEELKAEINVKKSELSEIDSKIEKASVRLREIEKELEKGQEKLEKI 485
                                       5788999999999999996333688899************************************************* PP

                             IFT57 318 kqemeergssm..tDgsplvkikkaltklk 345
                                         e+++ ++++  ++++  v++ k+l+ +k
  gi|242398710|ref|YP_002994134.1| 486 VPEIKKLNEELikAEARKEVHQNKTLEAIK 515
                                       *****9988863355566666666666666 PP

  == domain 6  score: 9.1 bits;  conditional E-value: 0.00086
                             IFT57 178 kkeekekekeeeiieskvdaaeWkl.EleRvlpqLkvtikadakdW...rahleqmkkhkksieeslpetksqlkkl 250
                                       k   +++eke++ +es+++a + ++  leR l +L+v+    +kd    ++++++  +  k+++e+++++++ lk+l
  gi|242398710|ref|YP_002994134.1| 670 KMALASREKEKDALESQINALKLEQrGLERELFELRVRKSDVSKDLqmlQKEMDRFLNEDKTLKEEIETAENRLKEL 746
                                       33347888999999999999988652699999999996666666651115566666666779999999999999999 PP

                             IFT57 251 hedisktlekiesrEkylnsqleellqeyreaqe..elsevkekykqlsegvseltrelaeiseelekvkqemee 323
                                       ++ i +t   + +   +++ +le+  +++r+a +  e  e+++k+++++ ++s+l++el++++ +le++  +++e
  gi|242398710|ref|YP_002994134.1| 747 ESFIHQTKGDLAKLSGRVE-RLEKIRNKLRKALDnpEARELNQKIREVEHEISKLREELSKVESRLENLDIRINE 820
                                       9999999999999999985.6899999999986622577899999999999999999999999999988777665 PP

  == domain 7  score: 13.4 bits;  conditional E-value: 4.1e-05
                             IFT57 243 tksqlkklhed...isktlekiesrEkylnsqleellqeyreaqeelsevkekykqlsegvseltrelaeiseelek 316
                                        k ++k+ +ed   ++ +le+++++E+ +  +l+ l +e   ++ee+s+++e+ ++l + +++l+ e ++++ ++ +
  gi|242398710|ref|YP_002994134.1| 843 FKASIKQNEEDiksLQAQLEELQEKEQAVKDELKALRDERDRLREEISQMREEKEKLRDVLQKLRLEANSLKIKMAQ 919
                                       44444444443111678999********************************************************* PP

                             IFT57 317 vkqemeergssm..tDgsplvkikkaltklkkEikqmd 352
                                        ++++ e++s++   D + + +i + l+kl++Ei+qm+
  gi|242398710|ref|YP_002994134.1| 920 YESQLREKESELkhHDVKVVKEIPEDLEKLREEIEQME 957
                                       *********987226889999****************8 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.6      0.64   4.2e+02      87     121 ..     174     208 ..     163     213 .. 0.50
   2 ?    4.9   3.5     0.038        25      55     118 ..     222     286 ..     216     291 .. 0.78
   3 !    9.4   2.7    0.0016         1      64     120 ..     296     352 ..     294     356 .. 0.89
   4 ?    6.0   7.1     0.018        12      65     121 ..     388     444 ..     354     446 .. 0.82
   5 !    7.4   3.7    0.0063       4.2      47     110 ..     437     496 ..     430     506 .. 0.82
   6 !   10.4   3.0   0.00078      0.52      55     122 ..     702     769 ..     685     780 .. 0.68
   7 !    8.4   1.3    0.0031         2      67     118 ..     766     819 ..     764     822 .. 0.81
   8 !    9.5   8.1    0.0014      0.95      42     116 ..     803     881 ..     799     895 .. 0.77
   9 !    8.1   9.4    0.0039       2.6      48     120 ..     831     906 ..     825     923 .. 0.63
  10 ?    4.1   6.5     0.068        45      54     121 ..     896     964 ..     889     975 .. 0.51
  11 ?    3.9   4.3     0.081        54      58     121 ..     929     992 ..     909     995 .. 0.56

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.64
                           DUF1664  87 eevtevredlseigedvesvkeaveglesklerie 121
                                       e+ +++ e+l++ +e++  v+ ++++++++l+++e
  gi|242398710|ref|YP_002994134.1| 174 EKKKKAMEELKQAEENLARVDLLIREVKTQLDKLE 208
                                       33334444444445555555555555555555444 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.038
                           DUF1664  55 eslaatkrh.Lssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskle 118
                                       e+l+ ++   L+ +++r+++ + e+ +  +ei+ e+++++++l++i + + + +++ +++e +le
  gi|242398710|ref|YP_002994134.1| 222 EKLEVARTTlLTGEVKRLQNLIAESRARDEEIEVEIERINGELENIAKTIVEKEKTLTQIERELE 286
                                       56666665525788999999999999999999999999999999999988888888888887776 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.0016
                           DUF1664  64 Lssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleri 120
                                        +++i +v +k++  k+ ++  k+e++e ++ l++ +ed+++v++ +e+ +s++er 
  gi|242398710|ref|YP_002994134.1| 296 VTKKISEVASKIELAKKNIELAKKEISESQRRLAKAKEDLKNVSAEIEKGKSTIERW 352
                                       58999**************************************99999988888775 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.018
                           DUF1664  65 ssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerie 121
                                       ++++d+v+++l++ k+++   ++e+t++ e++++i++++++ ++    l+skle+++
  gi|242398710|ref|YP_002994134.1| 388 KQELDKVEEELENAKKTQYFKESEITKITEEIERIKSKISQQSTRRIILKSKLEELK 444
                                       478999999999999999999999999999999999999999888888999998876 PP

  == domain 5  score: 7.4 bits;  conditional E-value: 0.0063
                           DUF1664  47 skqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeav 110
                                        ++le+++++++  k +Ls    ++d+k+++ +   +ei++e+++ +e+l++i  ++++++e  
  gi|242398710|ref|YP_002994134.1| 437 KSKLEELKAEINVKKSELS----EIDSKIEKASVRLREIEKELEKGQEKLEKIVPEIKKLNEEL 496
                                       5678888888888887776....68999999999999999999999999999999999988755 PP

  == domain 6  score: 10.4 bits;  conditional E-value: 0.00078
                           DUF1664  55 eslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleriee 122
                                        +l+  k + s++++ ++k++d   +  k +kee++++++ l+e+++ +++ k    +l +++er+e+
  gi|242398710|ref|YP_002994134.1| 702 FELRVRKSDVSKDLQMLQKEMDRFLNEDKTLKEEIETAENRLKELESFIHQTKGDLAKLSGRVERLEK 769
                                       56666677777777777777777777777777777777777777777777777666677666666664 PP

  == domain 7  score: 8.4 bits;  conditional E-value: 0.0031
                           DUF1664  67 ridrvdkkldeqkei..skeikeevtevredlseigedvesvkeavegleskle 118
                                       r++++ +kl +  +   ++e+++++ ev++++s+++e++++v++  e+l+ +++
  gi|242398710|ref|YP_002994134.1| 766 RLEKIRNKLRKALDNpeARELNQKIREVEHEISKLREELSKVESRLENLDIRIN 819
                                       67777777777665422568999***************************9997 PP

  == domain 8  score: 9.5 bits;  conditional E-value: 0.0014
                           DUF1664  42 avesvskqleqvs....eslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegle 114
                                        +++v ++le++     e+l   k +L+++i+ + +++++ k+ +k+ +e++++++ +l+e++e+ ++vk+  + l 
  gi|242398710|ref|YP_002994134.1| 803 ELSKVESRLENLDirinEELIPRKADLEEEIEGIVNRINAFKASIKQNEEDIKSLQAQLEELQEKEQAVKDELKALR 879
                                       55666677776654444777788999999999999999999999999999999999999999999999988887776 PP

                           DUF1664 115 sk 116
                                        +
  gi|242398710|ref|YP_002994134.1| 880 DE 881
                                       55 PP

  == domain 9  score: 8.1 bits;  conditional E-value: 0.0039
                           DUF1664  48 kqleqvseslaatkrhLss...ridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleri 120
                                       +++e + + ++a k  +++   +i++++++l+e +e  +++k+e++++r++ ++++e++++++e  e+l   l+++
  gi|242398710|ref|YP_002994134.1| 831 EEIEGIVNRINAFKASIKQneeDIKSLQAQLEELQEKEQAVKDELKALRDERDRLREEISQMREEKEKLRDVLQKL 906
                                       4555666666666655544222577777777777777777777777777777777777777776666665555544 PP

  == domain 10  score: 4.1 bits;  conditional E-value: 0.068
                           DUF1664  54 seslaatkrhLssridrvdkkldeqkeiskeikeevtevred.lseigedvesvkeaveglesklerie 121
                                       +e+l+++ ++L  + +++  k+ + +   +e ++e+++   + ++ei ed+e+++e +e++e +++++e
  gi|242398710|ref|YP_002994134.1| 896 KEKLRDVLQKLRLEANSLKIKMAQYESQLREKESELKHHDVKvVKEIPEDLEKLREEIEQMEDEIRELE 964
                                       444555555555555555555555555555555555444433134555555555555555555555554 PP

  == domain 11  score: 3.9 bits;  conditional E-value: 0.081
                           DUF1664  58 aatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerie 121
                                       ++ k+h  + ++++ + l++  e ++++++e+ e++    +  ed e v++   +l+sk er+e
  gi|242398710|ref|YP_002994134.1| 929 SELKHHDVKVVKEIPEDLEKLREEIEQMEDEIRELEPVNMKAIEDYEVVERRYLELKSKRERLE 992
                                       2333333445666666666667777777777777766555555666666666666666666666 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 ?    4.5  15.4     0.051        34       7      90 ..     295     378 ..     289     386 .. 0.88
   2 ?   -1.2  35.3       2.8   1.9e+03       1     133 [.     352     491 ..     352     500 .. 0.80
   3 !    7.0  14.3    0.0083       5.5      45     116 ..     671     742 ..     660     748 .. 0.78
   4 ?    4.9  18.4     0.038        25      32     127 ..     714     807 ..     713     820 .. 0.80
   5 ?    2.4  16.5      0.21   1.4e+02      18      93 ..     782     865 ..     758     866 .. 0.52
   6 !   16.1  26.0   1.3e-05    0.0089      22     118 ..     836     932 ..     826     942 .. 0.92
   7 ?    3.0  11.1      0.15        98      12      90 ..     939    1018 ..     931    1046 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.051
                    CENP-F_leu_zip   7 hvlekLKeserkadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrseke 83 
                                        v++k  e+ +k ++ k  +e  ++e+ +s++ + k++ +  +  ae+e+ k+ ie+ ++++++l +++++  +ek+
  gi|242398710|ref|YP_002994134.1| 295 DVTKKISEVASKIELAKKNIELAKKEISESQRRLAKAKEDLKNVSAEIEKGKSTIERWKKRRENLIAEIQKKEKEKN 371
                                       67788888999999999999999999999999999999999999999999999999999999999999999999999 PP

                    CENP-F_leu_zip  84 eLekelq 90 
                                       eL  +l 
  gi|242398710|ref|YP_002994134.1| 372 ELILKLA 378
                                       9977765 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.8
                    CENP-F_leu_zip   1 DekkklhvlekLKeserkadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLva 77 
                                       ++k+++++  + ++ e++++ L  k  +++++  +++++++kv+ e E++k++    ++ei +++ee +++++++++
  gi|242398710|ref|YP_002994134.1| 352 WKKRRENLIAEIQKKEKEKNELILKLAEIDKNFTIAKQELDKVEEELENAKKTQYFKESEITKITEEIERIKSKISQ 428
                                       8999999********************************************99888888888888888888888887 PP

                    CENP-F_leu_zip  78 lr.......sekeeLekelqkkqervseLeslnsslenlleekEqekvqmkeeskaaveeLqt 133
                                        +       s  eeL+ e++ k+++ se +s  ++ +  l+e E+e  + +e+ ++ v e+++
  gi|242398710|ref|YP_002994134.1| 429 QStrriilkSKLEELKAEINVKKSELSEIDSKIEKASVRLREIEKELEKGQEKLEKIVPEIKK 491
                                       774444444777777777777777788888888888888888888877777776666655554 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0083
                    CENP-F_leu_zip  45 leaEtskaevetlkeeieelaeelreleldLvalrsekeeLekelqkkqervseLeslnsslenlleekEqe 116
                                       +   +  +e  +l+++i+ l+ e r le +L +lr  k ++ k+lq  q++++   +   +l++ +e +E+ 
  gi|242398710|ref|YP_002994134.1| 671 MALASREKEKDALESQINALKLEQRGLERELFELRVRKSDVSKDLQMLQKEMDRFLNEDKTLKEEIETAENR 742
                                       555556678888999999999999999999999999999999999999999988888888888888887765 PP

  == domain 4  score: 4.9 bits;  conditional E-value: 0.038
                    CENP-F_leu_zip  32 elemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLekelqkkqervseLeslnsslen 108
                                       +l+m++++ ++   e  t k+e+et ++ ++el++  ++ + dL++l+   e Lek  +k ++  ++ e+++  l++
  gi|242398710|ref|YP_002994134.1| 714 DLQMLQKEMDRFLNEDKTLKEEIETAENRLKELESFIHQTKGDLAKLSGRVERLEKIRNKLRKALDNPEARE--LNQ 788
                                       899999999999999999999999999999999999999999999999888888888888888888777764..667 PP

                    CENP-F_leu_zip 109 lleekEqekvqmkeeskaa 127
                                        ++e E+e  +++ee  + 
  gi|242398710|ref|YP_002994134.1| 789 KIREVEHEISKLREELSKV 807
                                       7888888888888776543 PP

  == domain 5  score: 2.4 bits;  conditional E-value: 0.21
                    CENP-F_leu_zip  18 kadsLkdkvenLerelemseenqekvileaEtskaevet........lkeeieelaeelreleldLvalrsekeeLe 86 
                                       +a  L++k+ + e e+  + e+++kv+   E+    +++        l+eeie + ++ + +++ +++  ++ ++L+
  gi|242398710|ref|YP_002994134.1| 782 EARELNQKIREVEHEISKLREELSKVESRLENLDIRINEeliprkadLEEEIEGIVNRINAFKASIKQNEEDIKSLQ 858
                                       44455555555555555555555555555555554444444445555555555555555555555555555555555 PP

                    CENP-F_leu_zip  87 kelqkkq 93 
                                        +l++ q
  gi|242398710|ref|YP_002994134.1| 859 AQLEELQ 865
                                       5555544 PP

  == domain 6  score: 16.1 bits;  conditional E-value: 1.3e-05
                    CENP-F_leu_zip  22 LkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLekelqkkqervse 98 
                                       + +++++ ++ +++ ee+  ++  + E+ +++ +++k+e++ l+ e+ +l+ +++++r+eke+L   lqk + + ++
  gi|242398710|ref|YP_002994134.1| 836 IVNRINAFKASIKQNEEDIKSLQAQLEELQEKEQAVKDELKALRDERDRLREEISQMREEKEKLRDVLQKLRLEANS 912
                                       6799************************************************************************* PP

                    CENP-F_leu_zip  99 LeslnsslenlleekEqekv 118
                                       L+    + e++l+ekE e +
  gi|242398710|ref|YP_002994134.1| 913 LKIKMAQYESQLREKESELK 932
                                       ****************9943 PP

  == domain 7  score: 3.0 bits;  conditional E-value: 0.15
                    CENP-F_leu_zip   12 LKeserkadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeL. 85  
                                         Ke+ ++ ++L++ +e++e e+ ++e  + k+i + E       +lk++ e+l++e   +   ++++ ++k ++ 
  gi|242398710|ref|YP_002994134.1|  939 VKEIPEDLEKLREEIEQMEDEIRELEPVNMKAIEDYEVVERRYLELKSKRERLEAEKDSIIEFINEIENQKRNVf 1013
                                        566667777777777777777777777777777777777777777777777777777777777777776666542 PP

                    CENP-F_leu_zip   86 ekelq 90  
                                        ++ l+
  gi|242398710|ref|YP_002994134.1| 1014 MQTLN 1018
                                        44454 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 ?   -1.1  10.9       3.6   2.4e+03      19      62 ..     252     290 ..     218     310 .. 0.65
   2 ?    0.6   4.1       1.1     7e+02      14      57 ..     311     349 ..     296     353 .. 0.59
   3 ?    2.0  11.8      0.37   2.4e+02       7      60 ..     353     401 ..     350     404 .. 0.90
   4 ?    1.5   5.5      0.55   3.6e+02      14      57 ..     409     454 ..     402     456 .. 0.74
   5 ?    3.3  14.0      0.15        98       6      63 ..     450     502 ..     436     504 .. 0.92
   6 ?    2.0  12.9      0.38   2.5e+02       7      68 ..     677     747 ..     673     748 .. 0.84
   7 ?    8.7   5.8     0.003         2      11      62 ..     730     779 ..     719     780 .. 0.85
   8 ?   15.6   3.3   2.2e-05     0.015       9      67 ..     756     814 ..     750     816 .. 0.91
   9 ?    2.7   8.6      0.22   1.5e+02      13      56 ..     829     867 ..     819     881 .. 0.57
  10 ?   -1.4   9.8       4.4   2.9e+03       8      57 ..     880     931 ..     871     934 .. 0.80
  11 ?    4.5   9.2     0.062        41       9      56 ..     945     994 ..     939    1006 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 3.6
                      ABC_tran_CTD  19 aLEeeiaeleaeladpelysdpeklaelsaeleeleaeLeelye 62 
                                       ++E ei+ ++ el++ +     +++ e  + l+++e eLee+ e
  gi|242398710|ref|YP_002994134.1| 252 EIEVEIERINGELENIA-----KTIVEKEKTLTQIERELEEKSE 290
                                       33333333333333333.....5566666666666666666654 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 1.1
                      ABC_tran_CTD  14 eaeIeaLEeeiaeleaeladpelysdpeklaelsaeleeleaeL 57 
                                        + Ie   +ei+e + +la++      e l+ +sae+e+ ++ +
  gi|242398710|ref|YP_002994134.1| 311 KKNIELAKKEISESQRRLAKAK-----EDLKNVSAEIEKGKSTI 349
                                       3456666666666666666555.....55666666666555554 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.37
                      ABC_tran_CTD   7 qreleeleaeIeaLEeeiaeleaeladpelysdpeklaelsaeleeleaeLeel 60 
                                       +++ e+l aeI++ E+e+ el  +la+ +     + ++ + +el+++e+eLe++
  gi|242398710|ref|YP_002994134.1| 353 KKRRENLIAEIQKKEKEKNELILKLAEID-----KNFTIAKQELDKVEEELENA 401
                                       567799********************998.....6789999**********987 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 0.55
                      ABC_tran_CTD  14 eaeIeaLEeeiaeleaeladpelysdp....eklaelsaeleeleaeL 57 
                                       e+eI ++ eei+ +  ++++ +          kl el ae++  ++eL
  gi|242398710|ref|YP_002994134.1| 409 ESEITKITEEIERIKSKISQQSTR--RiilkSKLEELKAEINVKKSEL 454
                                       789999999999999999999833..2235566777777777666666 PP

  == domain 5  score: 3.3 bits;  conditional E-value: 0.15
                      ABC_tran_CTD   6 eqreleeleaeIeaLEeeiaeleaeladpelysdpeklaelsaeleeleaeLeelyer 63 
                                       ++ el e++++Ie+   ++ e+e+el++ +     ekl ++  e+++l++eL ++++r
  gi|242398710|ref|YP_002994134.1| 450 KKSELSEIDSKIEKASVRLREIEKELEKGQ-----EKLEKIVPEIKKLNEELIKAEAR 502
                                       5789***********************887.....99***************999988 PP

  == domain 6  score: 2.0 bits;  conditional E-value: 0.38
                      ABC_tran_CTD   7 qreleeleaeIeaLEeeiaeleaeladpely.sdp.eklaelsae.......leeleaeLeelyerWeeLe 68 
                                       ++e ++le++I+aL  e+  le el +  +  sd  + l+ l++e        ++l++e+e+++ r  eLe
  gi|242398710|ref|YP_002994134.1| 677 EKEKDALESQINALKLEQRGLERELFELRVRkSDVsKDLQMLQKEmdrflneDKTLKEEIETAENRLKELE 747
                                       68889*******************99999995666777888888866665556789**********99998 PP

  == domain 7  score: 8.7 bits;  conditional E-value: 0.003
                      ABC_tran_CTD  11 eeleaeIeaLEeeiaeleaeladpelysdpeklaelsaeleeleaeLeelye 62 
                                       ++l +eIe  E++++ele  + +     d +kl+   ++le+++++L ++++
  gi|242398710|ref|YP_002994134.1| 730 KTLKEEIETAENRLKELESFIHQTK--GDLAKLSGRVERLEKIRNKLRKALD 779
                                       47********************999..8889999999*******99988875 PP

  == domain 8  score: 15.6 bits;  conditional E-value: 2.2e-05
                      ABC_tran_CTD   9 eleeleaeIeaLEeeiaeleaeladpelysdpeklaelsaeleeleaeLeelyerWeeL 67 
                                        l++l  + e+LE+   +l ++l +pe  +  +k+ e+  e+ +l++eL + ++r e L
  gi|242398710|ref|YP_002994134.1| 756 DLAKLSGRVERLEKIRNKLRKALDNPEARELNQKIREVEHEISKLREELSKVESRLENL 814
                                       6899***********************66666***********************9988 PP

  == domain 9  score: 2.7 bits;  conditional E-value: 0.22
                      ABC_tran_CTD  13 leaeIeaLEeeiaeleaeladpelysdpeklaelsaeleeleae 56 
                                       le+eIe + ++i +  a + ++e  +d   ++ l+a+leel+++
  gi|242398710|ref|YP_002994134.1| 829 LEEEIEGIVNRINAFKASIKQNE--ED---IKSLQAQLEELQEK 867
                                       66666666666666666666655..33...44444444443332 PP

  == domain 10  score: -1.4 bits;  conditional E-value: 4.4
                      ABC_tran_CTD   8 releeleaeIeaLEeeiaeleaeladpelysdp..eklaelsaeleeleaeL 57 
                                        e ++l +eI ++ ee+++l + l++  l +++   k+a+   +l e e+eL
  gi|242398710|ref|YP_002994134.1| 880 DERDRLREEISQMREEKEKLRDVLQKLRLEANSlkIKMAQYESQLREKESEL 931
                                       5677899*****************9999887775566777777777777777 PP

  == domain 11  score: 4.5 bits;  conditional E-value: 0.062
                      ABC_tran_CTD   9 eleeleaeIeaLEeeiaelea.eladpelysdp.eklaelsaeleeleae 56 
                                        le+l +eIe++E ei ele   + + e y+    +  el  + e+leae
  gi|242398710|ref|YP_002994134.1| 945 DLEKLREEIEQMEDEIRELEPvNMKAIEDYEVVeRRYLELKSKRERLEAE 994
                                       5999***************9854444443322223355555555555555 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 ?   10.5   4.7   0.00071      0.47      23     128 ..     181     298 ..     177     309 .. 0.78
   2 ?    0.2   2.8       1.1   7.3e+02      40      80 ..     321     364 ..     291     426 .. 0.49
   3 ?    0.1   7.1       1.1   7.4e+02      17      86 ..     411     488 ..     358     532 .. 0.59
   4 ?    4.3   0.5     0.057        38      36     104 ..     690     753 ..     668     761 .. 0.56
   5 ?   13.9   1.2   6.2e-05     0.041      20     118 ..     741     843 ..     730     845 .. 0.74
   6 ?    5.7   5.2     0.022        15      17      91 ..     832     907 ..     818     924 .. 0.53
   7 ?    4.7   0.2     0.045        30      21      85 ..     902     962 ..     895     973 .. 0.77
   8 ?    1.7   0.2      0.37   2.4e+02      25      80 ..     931    1006 ..     922    1032 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00071
                      Baculo_PEP_C  23 nairlqnvqilaqlatlldaietqLnalsedlksllaeldt..rldtl.ltnLtdalnalq..........dtlrne 86 
                                       + ++  + ++ a +  l+ +++tqL++l+++ +++l  ld   +l+ + +t Lt  +++lq          ++++ e
  gi|242398710|ref|YP_002994134.1| 181 EELKQAEENL-ARVDLLIREVKTQLDKLEKERNDALRYLDLkeKLEVArTTLLTGEVKRLQnliaesrardEEIEVE 256
                                       5565555555.99999999**************99986654447765513445667777777777888**9****** PP

                      Baculo_PEP_C  87 LtnlnsiltnLlssvtNinstLnnllqalnnldlgalsqele 128
                                       ++ +n +l n++  +   ++tL+ +   l+   ++++ +  +
  gi|242398710|ref|YP_002994134.1| 257 IERINGELENIAKTIVEKEKTLTQIERELEEKSEDGILDVTK 298
                                       ***********************9999999888888777665 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.1
                      Baculo_PEP_C  40 ldaietqLnalsedlksllaeldt......rldtlltnLtdalnalq 80 
                                       + + +++L + +edlk+++ae+++      r     ++ ++ ++++q
  gi|242398710|ref|YP_002994134.1| 321 ISESQRRLAKAKEDLKNVSAEIEKgkstieR---WKKRRENLIAEIQ 364
                                       3444455555555555555555544442221...2222222222222 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 1.1
                      Baculo_PEP_C  17 dLtnvLnairlqnvqilaqlatlldaietqLnalsedlk...sllaeldtrldtlltnLtdalnalq......dtlr 84 
                                       ++t++ + i   +++i +q +t    ++++L++l+++++   s l+e+d+++++++ +L +  ++l+      +++ 
  gi|242398710|ref|YP_002994134.1| 411 EITKITEEIERIKSKI-SQQSTRRIILKSKLEELKAEINvkkSELSEIDSKIEKASVRLREIEKELEkgqeklEKIV 486
                                       3444444444444444.333333333444444444444311122223333333333333333333333322222222 PP

                      Baculo_PEP_C  85 ne 86 
                                        e
  gi|242398710|ref|YP_002994134.1| 487 PE 488
                                       23 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.057
                      Baculo_PEP_C  36 latlldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLtnlnsiltnLlssvtNi 104
                                       l+     +e++L +l        ++++++l+ l +++++ ln+  +tl++e+++ ++ l +L s +  +
  gi|242398710|ref|YP_002994134.1| 690 LKLEQRGLERELFELR----VRKSDVSKDLQMLQKEMDRFLNED-KTLKEEIETAENRLKELESFIHQT 753
                                       2222222222222221....112445556666666666666663.588888888888888888876555 PP

  == domain 5  score: 13.9 bits;  conditional E-value: 6.2e-05
                      Baculo_PEP_C  20 nvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldt.rldtlltnLtdalnalq...dtlrneLtnlns 92 
                                       n L+ + +   q+ ++la+l   +e+ L+++ ++l+++l + ++ +l++ + ++++ + +l     +++++L+nl+ 
  gi|242398710|ref|YP_002994134.1| 741 NRLKELESFIHQTKGDLAKLSGRVER-LEKIRNKLRKALDNPEArELNQKIREVEHEISKLReelSKVESRLENLDI 816
                                       55667777777777888888777776.88888888887777766578888888888888888666667778888888 PP

                      Baculo_PEP_C  93 ilt.nLlssvtNinstLnnllqalnnl 118
                                        ++ +L    + +++ ++++++ +n++
  gi|242398710|ref|YP_002994134.1| 817 RINeELIPRKADLEEEIEGIVNRINAF 843
                                       777347778888888888888888877 PP

  == domain 6  score: 5.7 bits;  conditional E-value: 0.022
                      Baculo_PEP_C  17 dLtnvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq...dtlrneLtnl 90 
                                       ++  ++n i + +++i  q ++++++++ qL++l+e+ ++ +++  ++l +  ++L + + ++    ++lr  L+ l
  gi|242398710|ref|YP_002994134.1| 832 EIEGIVNRINAFKASI-KQNEEDIKSLQAQLEELQEKEQA-VKDELKALRDERDRLREEISQMReekEKLRDVLQKL 906
                                       3444555555555555.55555555555555555544333.333334555555555555555555555555555555 PP

                      Baculo_PEP_C  91 n 91 
                                        
  gi|242398710|ref|YP_002994134.1| 907 R 907
                                       4 PP

  == domain 7  score: 4.7 bits;  conditional E-value: 0.045
                      Baculo_PEP_C  21 vLnairlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrn 85 
                                       vL+ +rl     ++ l+  +++ e+qL + +++lk+   ++ +++ + l++L + + +++d++r+
  gi|242398710|ref|YP_002994134.1| 902 VLQKLRLE----ANSLKIKMAQYESQLREKESELKHHDVKVVKEIPEDLEKLREEIEQMEDEIRE 962
                                       44444333....35678888899999999999999999999999999999999999999999983 PP

  == domain 8  score: 1.7 bits;  conditional E-value: 0.37
                      Baculo_PEP_C   25 irlqnvqilaqlatlldaietqLnalsedlksllaeldt....................rldtlltnLtdalnal 79  
                                        ++   v+++ ++ ++l+++ ++++++++++++l +   +                    rl++  + + + +n++
  gi|242398710|ref|YP_002994134.1|  931 LKHHDVKVVKEIPEDLEKLREEIEQMEDEIRELEPVNMKaiedyevverrylelkskreRLEAEKDSIIEFINEI 1005
                                        555666777777777777777777777777775542222344455555555544444445555555555555555 PP

                      Baculo_PEP_C   80 q 80  
                                        +
  gi|242398710|ref|YP_002994134.1| 1006 E 1006
                                        4 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 ?   -0.5  11.5      0.76   5.1e+02      29     117 ..     195     291 ..     174     294 .. 0.72
   2 ?    8.1  20.8    0.0018       1.2      22     117 ..     258     358 ..     257     380 .. 0.81
   3 ?    7.2  23.5    0.0034       2.3      38     149 ..     388     498 ..     370     518 .. 0.76
   4 ?    3.6  12.8     0.044        29      28     134 ..     670     787 ..     667     794 .. 0.86
   5 ?   12.0  30.5   0.00012     0.082      21     133 ..     794     925 ..     787     986 .. 0.80
   6 ?   -1.9   0.1       2.1   1.4e+03      22      53 ..     979    1010 ..     971    1023 .. 0.68

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.76
                             Atg14  29 erlaklksekeslkkkiekalegke........eaeqledkiknkkakleelksliadlrerlqelkdklsqlkkei 97 
                                         ++ +k++ + l+k+ ++al   +        +++ l+ ++k++++ + e +++ ++++ ++++++  l++  k i
  gi|242398710|ref|YP_002994134.1| 195 LLIREVKTQLDKLEKERNDALRYLDlkeklevaRTTLLTGEVKRLQNLIAESRARDEEIEVEIERINGELENIAKTI 271
                                       33444455555555555554444447777777778889999999999999999999999999999999999999999 PP

                             Atg14  98 eekkkklaklsdklkkRrsd 117
                                        ek k+l +  ++l ++ +d
  gi|242398710|ref|YP_002994134.1| 272 VEKEKTLTQIERELEEKSED 291
                                       99999999988888777665 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0018
                             Atg14  22 erlyelrerlaklksekeslkkkiekalegke.........eaeqledkiknkkakleelksliadlrerlqelkdk 89 
                                       er++ + e +ak+  eke   ++ie++le+k+         + ++ ++ki+  k+++e+ k++i+++++rl++ k++
  gi|242398710|ref|YP_002994134.1| 258 ERINGELENIAKTIVEKEKTLTQIERELEEKSedgildvtkKISEVASKIELAKKNIELAKKEISESQRRLAKAKED 334
                                       5888899999**********************999999999888999999999999999999999999999999999 PP

                             Atg14  90 lsqlkkeieekkkklaklsdklkkRrsd 117
                                       l++  +eie+ k ++++ ++     r+ 
  gi|242398710|ref|YP_002994134.1| 335 LKNVSAEIEKGKSTIERWKKR----REN 358
                                       999999999999999986654....333 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0034
                             Atg14  38 keslkkkiekalegke.eaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklkk 113
                                       k++l  k+e++le+ +  +  +e++i + ++ +e++ks+i++++ r   lk kl++lk+ei+ kk +l++ ++k+ k
  gi|242398710|ref|YP_002994134.1| 388 KQELD-KVEEELENAKkTQYFKESEITKITEEIERIKSKISQQSTRRIILKSKLEELKAEINVKKSELSEIDSKIEK 463
                                       33333.344444444413336788999999*********************************************99 PP

                             Atg14 114 Rrsdleslqneleerrkkqiaklqdaikrieqklss 149
                                          +l+ +++ele+ ++ +++k++ +ik+  + l +
  gi|242398710|ref|YP_002994134.1| 464 ASVRLREIEKELEKGQE-KLEKIVPEIKKLNEELIK 498
                                       9999999*****98876.589999999977766433 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.044
                             Atg14  28 rerlaklksekeslkkkie.kalegke..........eaeqledkiknkkakleelksliadlrerlqelkdklsql 93 
                                       +  la+  +ek++l+++i+  +le++           ++++ +++++ +++ +++  ++   l+e++++ + +l++l
  gi|242398710|ref|YP_002994134.1| 670 KMALASREKEKDALESQINaLKLEQRGlerelfelrvRKSDVSKDLQMLQKEMDRFLNEDKTLKEEIETAENRLKEL 746
                                       567888899*********9445666669********9999************************************* PP

                             Atg14  94 kkeieekkkklaklsdklkkRrsdleslqneleerrkkqia 134
                                        + i ++k  lakls  + +  +  ++l++ l + ++++++
  gi|242398710|ref|YP_002994134.1| 747 ESFIHQTKGDLAKLSGRVERLEKIRNKLRKALDNPEARELN 787
                                       *****************976666667777777776666665 PP

  == domain 5  score: 12.0 bits;  conditional E-value: 0.00012
                             Atg14  21 perlyelrerlaklksekeslkkkiekalegke...................eaeqledkiknkkakleelksliad 78 
                                       ++ + +lre+l k+ s+ e l  +i+++l  ++                   + +q e++ik+++a+leel+ + + 
  gi|242398710|ref|YP_002994134.1| 794 EHEISKLREELSKVESRLENLDIRINEELIPRKadleeeiegivnrinafkaSIKQNEEDIKSLQAQLEELQEKEQA 870
                                       568999********************999999999***************999999999999999999999999999 PP

                             Atg14  79 lrerlqelkdklsqlkkeieekkkklaklsdklkkRrsdleslqneleerrkkqi 133
                                        +++l+ l+d +++l++ei + +++ +kl+d l k r +++sl+ ++++++ ++ 
  gi|242398710|ref|YP_002994134.1| 871 VKDELKALRDERDRLREEISQMREEKEKLRDVLQKLRLEANSLKIKMAQYESQLR 925
                                       9999999999999999999999999999999999888888888877777765433 PP

  == domain 6  score: -1.9 bits;  conditional E-value: 2.1
                             Atg14   22 erlyelrerlaklksekeslkkkiekalegke 53  
                                        +r++el+ +  +l +ek+s+ + i++++++k+
  gi|242398710|ref|YP_002994134.1|  979 RRYLELKSKRERLEAEKDSIIEFINEIENQKR 1010
                                        46666666666777777766666666666665 PP

>> Surfac_D-trimer  Lung surfactant protein D coiled-coil trimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.034        22       7      23 ..     228     244 ..     226     248 .. 0.85
   2 ?    4.2   0.0     0.059        39       9      41 ..     758     790 ..     751     794 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.034
                                       HHHHHHHHHHHHHHHHH CS
                   Surfac_D-trimer   7 rveaLeGklqrLqnafs 23 
                                       r + L G+++rLqn ++
  gi|242398710|ref|YP_002994134.1| 228 RTTLLTGEVKRLQNLIA 244
                                       66889*********875 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.059
                                       HHHHHHHHHHHHHHHHHHHHHHTTTEEEETTEE CS
                   Surfac_D-trimer   9 eaLeGklqrLqnafsqYkKavLFPdGqsVGeKI 41 
                                         L G++ rL+ +  + +Ka   P+ +   +KI
  gi|242398710|ref|YP_002994134.1| 758 AKLSGRVERLEKIRNKLRKALDNPEARELNQKI 790
                                       679*****************9888877776666 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   8.2         5   3.3e+03      51      92 ..     175     223 ..     169     249 .. 0.54
   2 ?    1.6  25.8      0.42   2.8e+02       2     112 ..     306     419 ..     305     432 .. 0.88
   3 ?   12.0  20.5   0.00025      0.17       4     116 ..     385     497 ..     382     511 .. 0.95
   4 ?    8.6  12.4    0.0027       1.8      16     103 ..     668     759 ..     659     777 .. 0.85
   5 ?   11.7  13.0    0.0003       0.2       2     116 ..     728     844 ..     727     851 .. 0.91
   6 ?    8.0  17.6    0.0043       2.8       9     107 ..     782     881 ..     775     890 .. 0.81
   7 ?    8.9  23.3    0.0023       1.5       4     102 ..     827     932 ..     825     942 .. 0.48
   8 ?   10.7   4.9   0.00061      0.41      57     120 ..     944    1010 ..     936    1016 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 5
                        TPR_MLP1_2  51 khaedvkelqalreel.......nelkaeiaelkaeaesakaeleesee 92 
                                       k++++++el+++ e l        e+k+++ +l++e+++a   l+ +e+
  gi|242398710|ref|YP_002994134.1| 175 KKKKAMEELKQAEENLarvdlliREVKTQLDKLEKERNDALRYLDLKEK 223
                                       4566777777777777333333344444444444444444444444444 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.42
                        TPR_MLP1_2   2 elksleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelka 78 
                                       +++ ++++i+ +k+e++e++++l+k++edl++ +++ ++ +   er     ++ + e+q+  +e nel  ++ae+ +
  gi|242398710|ref|YP_002994134.1| 306 KIELAKKNIELAKKEISESQRRLAKAKEDLKNVSAEIEKGKSTIERWKKRRENLIAEIQKKEKEKNELILKLAEIDK 382
                                       567789999******************************************************************** PP

                        TPR_MLP1_2  79 eaesakaeleeseesweeqkeel...ekelselekri 112
                                       +   ak+el++ ee++e+ k++    e+e++++++ i
  gi|242398710|ref|YP_002994134.1| 383 NFTIAKQELDKVEEELENAKKTQyfkESEITKITEEI 419
                                       *****************99876312344455554444 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 0.00025
                        TPR_MLP1_2   4 ksleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaea 80 
                                       + +++e+++++ee e+a++++   +++++k +e+ ++ + k +++ +       +l++l++e+n  k+e++e+ ++ 
  gi|242398710|ref|YP_002994134.1| 385 TIAKQELDKVEEELENAKKTQYFKESEITKITEEIERIKSKISQQSTRRIILKSKLEELKAEINVKKSELSEIDSKI 461
                                       568999*********************************************************************** PP

                        TPR_MLP1_2  81 esakaeleeseesweeqkeelekelselekriedln 116
                                       e+a+  l e e+++e+ +e+lek + e++k  e+l 
  gi|242398710|ref|YP_002994134.1| 462 EKASVRLREIEKELEKGQEKLEKIVPEIKKLNEELI 497
                                       ****************************99999985 PP

  == domain 4  score: 8.6 bits;  conditional E-value: 0.0027
                        TPR_MLP1_2  16 ekeeaeaklqklqedlekqaeiakeaqqkYerel....vkhaedvkelqalreelnelkaeiaelkaeaesakaele 88 
                                       e++ a a  +k ++ le+q + +k  q+  erel    v +++ +k+lq l +e+++  +e ++lk+e e+a++ l+
  gi|242398710|ref|YP_002994134.1| 668 EIKMALASREKEKDALESQINALKLEQRGLERELfelrVRKSDVSKDLQMLQKEMDRFLNEDKTLKEEIETAENRLK 744
                                       5666667778889999*****************96666789************************************ PP

                        TPR_MLP1_2  89 eseesweeqkeelek 103
                                       e e+ ++++k  l k
  gi|242398710|ref|YP_002994134.1| 745 ELESFIHQTKGDLAK 759
                                       ******999988765 PP

  == domain 5  score: 11.7 bits;  conditional E-value: 0.0003
                        TPR_MLP1_2   2 elksleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelka 78 
                                       e k+l+eei++++++ +e+e+ + + + dl k + ++++ ++   r  + +a d  e ++l++++ e++ ei++l++
  gi|242398710|ref|YP_002994134.1| 728 EDKTLKEEIETAENRLKELESFIHQTKGDLAKLSGRVERLEK--IRNKLRKALDNPEARELNQKIREVEHEISKLRE 802
                                       5689*************************************9..777788999999********************* PP

                        TPR_MLP1_2  79 eaesakaeleeseeswee....qkeelekelselekriedln 116
                                       e+ ++++ le+    ++e    +k  le+e++ + +ri+  +
  gi|242398710|ref|YP_002994134.1| 803 ELSKVESRLENLDIRINEelipRKADLEEEIEGIVNRINAFK 844
                                       ************999888444459*************98765 PP

  == domain 6  score: 8.0 bits;  conditional E-value: 0.0043
                        TPR_MLP1_2   9 eikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedv.kelqalreelnelkaeiaelkaeaesak 84 
                                       e+ +l++++ e e +++kl+e+l k ++++++   +  +el+  ++d+ +e++ + +++n  ka i++ +++ +s++
  gi|242398710|ref|YP_002994134.1| 782 EARELNQKIREVEHEISKLREELSKVESRLENLDIRINEELIPRKADLeEEIEGIVNRINAFKASIKQNEEDIKSLQ 858
                                       7889**************************************8877772579*********************9999 PP

                        TPR_MLP1_2  85 aeleeseesweeqkeelekelse 107
                                       a+lee +e+ +  k+el+   +e
  gi|242398710|ref|YP_002994134.1| 859 AQLEELQEKEQAVKDELKALRDE 881
                                       99887766655555555443333 PP

  == domain 7  score: 8.9 bits;  conditional E-value: 0.0023
                        TPR_MLP1_2   4 ksleeeikslkeekeeaeaklqklqedlekqaeiakeaqq.......kYerelvkhaedvkelqalreelnelkaei 73 
                                       + leeei+ + +++++ +a +++ +ed+++ +++++e q+         +    +     +e++++ree ++l++ +
  gi|242398710|ref|YP_002994134.1| 827 ADLEEEIEGIVNRINAFKASIKQNEEDIKSLQAQLEELQEkeqavkdELKALRDERDRLREEISQMREEKEKLRDVL 903
                                       56666676666666666666666666666666666666660000000222222233333344444444444444444 PP

                        TPR_MLP1_2  74 aelkaeaesakaeleeseesweeqkeele 102
                                       ++l+ ea+s+k ++++ e+++ e+++el+
  gi|242398710|ref|YP_002994134.1| 904 QKLRLEANSLKIKMAQYESQLREKESELK 932
                                       44444444444444444444444444443 PP

  == domain 8  score: 10.7 bits;  conditional E-value: 0.00061
                        TPR_MLP1_2   57 kelqalreelnelkaeiaelkaeaesakaeleesee...sweeqkeelekelselekriedlneqNk 120 
                                        ++l++lree++++++ei+el+  + +a ++ e  e    ++++++e+le e++++ + i+++++q +
  gi|242398710|ref|YP_002994134.1|  944 EDLEKLREEIEQMEDEIRELEPVNMKAIEDYEVVERrylELKSKRERLEAEKDSIIEFINEIENQKR 1010
                                        689*************************99999988333578999******************9976 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   8.5      0.83   5.5e+02      72     155 ..     173     254 ..     157     261 .. 0.70
   2 ?    0.0  19.7       1.5   9.8e+02      35     144 ..     259     377 ..     251     383 .. 0.56
   3 ?    4.7  15.1     0.057        38      15     108 ..     331     431 ..     328     435 .. 0.73
   4 ?    9.9  12.6    0.0014      0.96      14      90 ..     435     511 ..     433     518 .. 0.93
   5 ?    5.6  22.5     0.029        19      26     155 ..     673     815 ..     665     850 .. 0.65
   6 ?   10.1  28.9    0.0012      0.82      33     159 ..     840     975 ..     825    1003 .. 0.55
   7 ?    5.5   9.3     0.032        21      37     132 ..     921    1019 ..     915    1035 .. 0.61

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.83
                              Fez1  72 enelqrkkseaellrekvekleeelkelreelselsleeeeaalesdeakaqrqeaeeleelkreverlraeLkeer 148
                                       +++ +++ +e +  +e++ +++  ++e++++l +l++e+++a l+  + k+ + e  +++ l+ ev+rl++ ++e r
  gi|242398710|ref|YP_002994134.1| 173 DEKKKKAMEELKQAEENLARVDLLIREVKTQLDKLEKERNDA-LRYLDLKE-KLEVARTTLLTGEVKRLQNLIAESR 247
                                       444555566667777778888888888888888866554444.44444444.44568999999*******9999999 PP

                              Fez1 149 qkkeeqa 155
                                        + ee +
  gi|242398710|ref|YP_002994134.1| 248 ARDEEIE 254
                                       9988764 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1.5
                              Fez1  35 alkaqlrelrakleekeeeikeleesleektle........levcenelqrkkseaellrekvekleeelkelreel 103
                                        + ++l ++ +++ eke++++++e +leek+++        + ++ ++++ +k++ el ++++++ ++ l++ +e+l
  gi|242398710|ref|YP_002994134.1| 259 RINGELENIAKTIVEKEKTLTQIERELEEKSEDgildvtkkISEVASKIELAKKNIELAKKEISESQRRLAKAKEDL 335
                                       45566666677777777777777777777766655554444444444444445566666666666666666666666 PP

                              Fez1 104 selsleeeeaalesdeakaqrqe.aeeleelkreverlraeL 144
                                       +++s+e e+ +++ ++ k++r++   e+++ ++e ++l  +L
  gi|242398710|ref|YP_002994134.1| 336 KNVSAEIEKGKSTIERWKKRRENlIAEIQKKEKEKNELILKL 377
                                       666666666655555555555553344555555555555554 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.057
                              Fez1  15 LKqQLkdsqaevtqklseivalkaqlrelrakleekeeeikeleesleektle.......levcenelqrkkseael 84 
                                        K+ Lk++ ae+ +  s i   k +  +l a++++ke+e +el  +l e +++       l+++e+el+++k+++  
  gi|242398710|ref|YP_002994134.1| 331 AKEDLKNVSAEIEKGKSTIERWKKRRENLIAEIQKKEKEKNELILKLAEIDKNftiakqeLDKVEEELENAKKTQYF 407
                                       58889999999988888888888888888899999998877766655555444333333388888888888888888 PP

                              Fez1  85 lrekvekleeelkelreelselsl 108
                                       ++ +++k+ ee++++++++s++s+
  gi|242398710|ref|YP_002994134.1| 408 KESEITKITEEIERIKSKISQQST 431
                                       888888888888888888887654 PP

  == domain 4  score: 9.9 bits;  conditional E-value: 0.0014
                              Fez1  14 lLKqQLkdsqaevtqklseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekve 90 
                                       +LK+ L + +ae++ k se+ ++ +++  ++ +l+e e+e+++ +e+le+   e++++++el ++++++e+ ++k+ 
  gi|242398710|ref|YP_002994134.1| 435 ILKSKLEELKAEINVKKSELSEIDSKIEKASVRLREIEKELEKGQEKLEKIVPEIKKLNEELIKAEARKEVHQNKTL 511
                                       59***************************************************************999999998764 PP

  == domain 5  score: 5.6 bits;  conditional E-value: 0.029
                              Fez1  26 vtqklseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelree 102
                                       ++++ +e  al +q+  l+ + +  e+e+ el+ + ++ +++l+ +++e++r  +e ++l+e++e++e+ lkel + 
  gi|242398710|ref|YP_002994134.1| 673 LASREKEKDALESQINALKLEQRGLERELFELRVRKSDVSKDLQMLQKEMDRFLNEDKTLKEEIETAENRLKELESF 749
                                       56666666677777777777777777777777777777777777777777777777777777777777777777666 PP

                              Fez1 103 lselsleeeeaa.............lesdeakaqrqe..........aeeleelkreverlraeLkeerqkkeeqa 155
                                       +++++ + ++ +                        +          +++++e ++e+ +lr+eL++ + + e+  
  gi|242398710|ref|YP_002994134.1| 750 IHQTKGDLAKLSgrverlekirnklR----------KaldnpearelNQKIREVEHEISKLREELSKVESRLENLD 815
                                       66655444444444433333333331..........0334444444456677777777777777776666666554 PP

  == domain 6  score: 10.1 bits;  conditional E-value: 0.0012
                              Fez1  33 ivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelselsle 109
                                       i a ka++++ ++++++ +++++el+e+ +  ++el+ + +e +r ++e + +re+ ekl + l++lr e+++l+ +
  gi|242398710|ref|YP_002994134.1| 840 INAFKASIKQNEEDIKSLQAQLEELQEKEQAVKDELKALRDERDRLREEISQMREEKEKLRDVLQKLRLEANSLKIK 916
                                       55566666666666666666666666666666666666666666665555555555555555555555555554444 PP

                              Fez1 110 eeeaa.........lesdeakaqrqeaeeleelkreverlraeLkeerqkkeeqassFe 159
                                        ++ +         l+ +++k+ ++  e+le+l++e+e+++ e++e +  + +  +++e
  gi|242398710|ref|YP_002994134.1| 917 MAQYEsqlrekeseLKHHDVKVVKEIPEDLEKLREEIEQMEDEIRELEPVNMKAIEDYE 975
                                       33333111111122344444444444777777788888777766665544444444444 PP

  == domain 7  score: 5.5 bits;  conditional E-value: 0.032
                              Fez1   37 kaqlrelrakleekeee.ikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelselslee 110 
                                         +qlre +++l++++ + +ke+ e le+  +e+e++e+e+++ +  +    e  e +e+   el+++ ++l++e+
  gi|242398710|ref|YP_002994134.1|  921 ESQLREKESELKHHDVKvVKEIPEDLEKLREEIEQMEDEIRELEPVNMKAIEDYEVVERRYLELKSKRERLEAEK 995 
                                        567777777777777552467777777777777777777777766666666667777777777766666665555 PP

                              Fez1  111 eeaalesdeakaqrqe..aeelee 132 
                                        ++ ++  +e ++q+++  +++l++
  gi|242398710|ref|YP_002994134.1|  996 DSIIEFINEIENQKRNvfMQTLNA 1019
                                        555555555555544433344444 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   6.4     0.047        31      95     154 ..     175     233 ..     150     237 .. 0.84
   2 ?    5.1  35.0    0.0079       5.3     272     442 ..     249     419 ..     235     432 .. 0.85
   3 ?    7.8  13.4    0.0012      0.79     350     442 ..     430     526 ..     420     537 .. 0.83
   4 ?    3.6  41.0     0.023        15     227     436 ..     686     909 ..     682     938 .. 0.56
   5 ?    2.4  13.0     0.051        34      79     171 ..     919    1010 ..     911    1019 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.047
                                       HHHHTTHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHHHHHHHHHHHHHHT--T CS
                              EzrA  95 kfkkakkklaeleeeldeveekikkileelkelteseeknreeieklkekYrelrkklla 154
                                       k kka+++l+++ee+l++v+  i++++++l++l  +e++   ++ +lkek +  r++ll+
  gi|242398710|ref|YP_002994134.1| 175 KKKKAMEELKQAEENLARVDLLIREVKTQLDKLE-KERNDALRYLDLKEKLEVARTTLLT 233
                                       558999**************************95.6778889999999999999999886 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0079
                                       -HHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHTTTSSSSSHHHHT--HHHHTTGGG-TTTS-GGGSSTTTSTTHH CS
                              EzrA 272 eledveeelktieeeidsLyddl.ekEveAkkeveknlkelkeklehlekqnkelkeeldrlkqsYeLseeeleklr 347
                                       + e++e e++ i+ e++++ +++ ekE+   +   +  ++ ++ +  ++k+++e+ ++++  k++ eL+++e+++  
  gi|242398710|ref|YP_002994134.1| 249 RDEEIEVEIERINGELENIAKTIvEKEKTLTQIERELEEKSEDGILDVTKKISEVASKIELAKKNIELAKKEISE-- 323
                                       5588999999********9987549999999999999999999*************************8888765.. PP

                                       HHHHHHHHHHHHHHHHHHHHS-SS---STTGGGTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              EzrA 348 elekelkelekdyeeleekleekkvaYSelqeeleeleekleeieekqeeileslkslrkdEkrAreqldeikkelk 424
                                         +++l + ++d++++  ++e++k +  + +++ e+l  ++++ e++ +e+  +l+++ k+ + A+++ld++++el+
  gi|242398710|ref|YP_002994134.1| 324 -SQRRLAKAKEDLKNVSAEIEKGKSTIERWKKRRENLIAEIQKKEKEKNELILKLAEIDKNFTIAKQELDKVEEELE 399
                                       .568999********************************************************************** PP

                                       HHHH..HSSS-SS-S-TTTH CS
                              EzrA 425 eikr..kieksnLPgiPesy 442
                                       ++k+  + ++s++  i+e++
  gi|242398710|ref|YP_002994134.1| 400 NAKKtqYFKESEITKITEEI 419
                                       99962256677777666665 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0012
                                       HHHHHHHHHHHHHHHHHHS-SS---STTGGGTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH..HHHHH CS
                              EzrA 350 ekelkelekdyeeleekleekkvaYSelqeeleeleekleeieekqeeileslkslrkdEkrAreqldei..kkelk 424
                                       +++   l++++eel+ +++ kk   Se+ +++e+++ +l eie+++e+ +e+l+++  + k+ +e+l +   +ke++
  gi|242398710|ref|YP_002994134.1| 430 STRRIILKSKLEELKAEINVKKSELSEIDSKIEKASVRLREIEKELEKGQEKLEKIVPEIKKLNEELIKAeaRKEVH 506
                                       556667899**********************************************************8651156777 PP

                                       HHH..HHSSS-SS-S-TTTH CS
                              EzrA 425 eik..rkieksnLPgiPesy 442
                                       + k    i++ n+Pgi  s 
  gi|242398710|ref|YP_002994134.1| 507 QNKtlEAIKNANIPGIYGSL 526
                                       6652257********96655 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.023
                                       HHHHHHHHHHHSTTS--SGGGS..SSSSHHHHHHHHHHHHHHHHTT-..-HHHHHHHHHHHHHHHHHHHHHHHH... CS
                              EzrA 227 qleelkegykemkeegYaleel..niekeieelekkieeilerlkel..eledveeelktieeeidsLyddlek... 296
                                       q++ lk   + +++e ++l     ++ k+++ l+k++++ l++ k+l  e+e +e+ lk++e+ i +   dl k   
  gi|242398710|ref|YP_002994134.1| 686 QINALKLEQRGLERELFELRVRksDVSKDLQMLQKEMDRFLNEDKTLkeEIETAENRLKELESFIHQTKGDLAKlsg 762
                                       55555556666666655554322256666666666666655544444335555555555555555544444433222 PP

                                       ....HHHHHHHHTT.....TSSSSSHHHHT--HHHHTTGGG-TTTS-GGGSSTTTSTTHHHHHHHHHHHHHHHHHHH CS
                              EzrA 297 ....EveAkkevek.....nlkelkeklehlekqnkelkeeldrlkqsYeLseeeleklrelekelkelekdyeele 364
                                             + +++  k     + +el++k+ ++e ++++l+eel++++   +L++ ++   +el  +  +le+++e ++
  gi|242398710|ref|YP_002994134.1| 763 rverLEKIRNKLRKaldnpEARELNQKIREVEHEISKLREELSKVES--RLENLDIRINEELIPRKADLEEEIEGIV 837
                                       22112233333333111113456677777777777777777777766..4777777777777777777777777777 PP

                                       HHHS-SS---STTGGGTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSS-SS- CS
                              EzrA 365 ekleekkvaYSelqeeleeleekleeieekqeeileslkslrkdEkrAreqldeikkelkeikrkieksnLP 436
                                       +++++ k++  + +e++++l+ +lee++ek + ++++lk+lr++  r re+++++++e ++++  ++k +L 
  gi|242398710|ref|YP_002994134.1| 838 NRINAFKASIKQNEEDIKSLQAQLEELQEKEQAVKDELKALRDERDRLREEISQMREEKEKLRDVLQKLRLE 909
                                       777777777777777777777777777777777777777777777777777777777777777777766663 PP

  == domain 5  score: 2.4 bits;  conditional E-value: 0.051
                                        HHHHT-GGGT--S-SHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHHHHHHHHHHHHHHT.. CS
                              EzrA   79 eieellfeaeelldkykfkkakkklaeleeeldeveekikkileelkelteseeknreeieklkekYrelrkk.. 151 
                                        + e++l e e  l+++++k     ++e+ e+l++++e+i+++ +e++el   + k  e +e ++ +Y el+ k  
  gi|242398710|ref|YP_002994134.1|  919 QYESQLREKESELKHHDVK----VVKEIPEDLEKLREEIEQMEDEIRELEPVNMKAIEDYEVVERRYLELKSKre 989 
                                        5555566666666665554....567889999999999*************999999999999999999965422 PP

                                        .--TTTTHHHHHHHHHHHHHH CS
                              EzrA  152 .llanrfsygealeelekqle 171 
                                         l+a+++s  e+++e+e+q  
  gi|242398710|ref|YP_002994134.1|  990 rLEAEKDSIIEFINEIENQKR 1010
                                        388999999999999999855 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.2      0.83   5.5e+02      17      31 ..      26      40 ..      25      42 .. 0.88
   2 ?   -0.2  38.0      0.19   1.3e+02     752    1013 ..     170     432 ..     164     434 .. 0.70
   3 ?    4.0   8.6     0.011       7.2     602     677 ..     441     516 ..     437     519 .. 0.95
   4 ?   14.8  50.7   5.9e-06    0.0039     221     495 ..     695     971 ..     660    1017 .. 0.69

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.83
                           DUF3584 17 dghtnieGtNaaGKT 31
                                      +g t i+G+N++GK 
  gi|242398710|ref|YP_002994134.1| 26 RGFTAIVGANGSGKS 40
                                      6889**********5 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.19
                           DUF3584  752 keleeaykreLkskdvDpetvkelkrkieeLekkieriekrreevreYraflqe.twlkvdslaeerpalkeqve 825 
                                        +e +e+ k+ ++++   +e+++++   i+e ++++++ ek+r+++++Y +   + + ++   l++e+++l+   +
  gi|242398710|ref|YP_002994134.1|  170 AEYDEKKKKAMEELKQAEENLARVDLLIREVKTQLDKLEKERNDALRYLDLKEKlEVARTTLLTGEVKRLQNLIA 244 
                                        455667777777777778889999999999999999999999999999998766245566678999999999999 PP

                           DUF3584  826 elesaaeeleqeltrliedtklerkklekerkalekqldqldenlr.klrdllsklaelkldadaeqae.....g 894 
                                        e ++  ee+e e +r++ ++++ +k + ++ k+l + + +l+e+   ++ d+ +k++e++ + + ++ +     +
  gi|242398710|ref|YP_002994134.1|  245 ESRARDEEIEVEIERINGELENIAKTIVEKEKTLTQIERELEEKSEdGILDVTKKISEVASKIELAKKNielakK 319 
                                        999999999999999999999999999999999999999999998888888888888777766666655111123 PP

                           DUF3584  895 elaerlaaleelkrkrerlsedvkkalerfkgvl..kdksgsglaetweklreeestlsdkalelddarkllpal 967 
                                        e++e  ++l  +k+ ++     v +++e+ k+ +   +k++ +l+ + +k ++e+++l  k  e+d+ + +    
  gi|242398710|ref|YP_002994134.1|  320 EISESQRRLAKAKEDLKN----VSAEIEKGKSTIerWKKRRENLIAEIQKKEKEKNELILKLAEIDKNFTI---A 387 
                                        444444444444444444....4444444455553346788888888888855555555555555555555...4 PP

                           DUF3584  968 eelldvlvpqkrqalreqvsvlgldlneFydvledfdrriksiskr 1013
                                        ++ ld   ++ ++a +    +   ++++  + +e ++ +i+++s r
  gi|242398710|ref|YP_002994134.1|  388 KQELDKVEEELENA-KKTQYFKESEITKITEEIERIKSKISQQSTR 432 
                                        44445444444443.3444577788889999999999999999975 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.011
                           DUF3584 602 eeLrerlqaleealqsaeakqkqaeeelkqlnaeleeakravaeaatalknardtlerlqnekesekdklekaiae 677
                                       eeL++++++ +++l +  +k+++a+ +l ++++ele+ ++++++   ++k+ +++l +++  ke  ++k  +ai++
  gi|242398710|ref|YP_002994134.1| 441 EELKAEINVKKSELSEIDSKIEKASVRLREIEKELEKGQEKLEKIVPEIKKLNEELIKAEARKEVHQNKTLEAIKN 516
                                       69******************************************************************99999986 PP

  == domain 4  score: 14.8 bits;  conditional E-value: 5.9e-06
                           DUF3584 221 r.lkkqdveeWiediqalaaiekvrpeieklqeefeqleslelrLsllkgelkadeerlae.......kqeevqeak 289
                                       r l+++  e  ++ ++ +++++  ++e+++  +e+++l+  ++ +    +el++ +++ +        + e+ ++  
  gi|242398710|ref|YP_002994134.1| 695 RgLERELFELRVRKSDVSKDLQMLQKEMDRFLNEDKTLKEEIETAENRLKELESFIHQTKGdlaklsgRVERLEKIR 771
                                       25666666667788888888888888888888888777544444444444444444444440000000444444455 PP

                           DUF3584 290 aelkqqlrtle.delkeaidelnqelsaakaklaakeselealeeqkkkyedadieklkadldqlpsirseleelee 365
                                       ++l++ l++ e  el+++i e++ e+s+++++l++ es+le+l+ + +   ++ i++ +   ++++ i + +++ ++
  gi|242398710|ref|YP_002994134.1| 772 NKLRKALDNPEaRELNQKIREVEHEISKLREELSKVESRLENLDIRIN---EELIPRKADLEEEIEGIVNRINAFKA 845
                                       555555544331356666666666666666666666666666655443...444555444456678999******** PP

                           DUF3584 366 eldaltekhqdvqekydrrkqkikeeleeeleklkerleaireekdrlkaaieealealesqlrkqleaqkeelnee 442
                                       +++  +e ++++q+++++++ k ++  ++el+ l+++++ +ree  +   +++e+l  + ++lr  lea+  +++ +
  gi|242398710|ref|YP_002994134.1| 846 SIKQNEEDIKSLQAQLEELQEK-EQAVKDELKALRDERDRLREEISQ-MREEKEKLRDVLQKLR--LEANSLKIKMA 918
                                       *****************99877.788999999999999*******99.5566778888889999..9999999999* PP

                           DUF3584 443 ekelesrlselklrldsatateEeleqieeadealekaqeelekaeaevealq 495
                                       ++e + r +e +l+ +++++ +E  e++e+  e++e+++ e+++ e  + ++ 
  gi|242398710|ref|YP_002994134.1| 919 QYESQLREKESELKHHDVKVVKEIPEDLEKLREEIEQMEDEIRELEPVNMKAI 971
                                       ****************************************9998876555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3258  (0.181717); expected 358.6 (0.02)
Passed bias filter:                      771  (0.043003); expected 358.6 (0.02)
Passed Vit filter:                       331  (0.0184617); expected 17.9 (0.001)
Passed Fwd filter:                       226  (0.0126053); 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: 5.78u 0.38s 00:00:06.16 Elapsed: 00:00:01.21
# Mc/sec: 2948.99
//
Query:       gi|242398711|ref|YP_002994135.1|  [L=219]
Description: segregation and condensation protein A [Thermococcus sibiricus MM 739]
Scores for complete 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   58.7   8.5      1e-10   42.0   7.2    2.4  2  SMC_ScpA       Segregation and condensation protein ScpA
    1.3e-05   24.3   0.0    2.3e-05   23.6   0.0    1.4  1  Rad21_Rec8     Conserved region of Rad21 / Rec8 like protein
      0.002   18.3   0.1       0.18   12.0   0.0    2.4  2  DUF4470        Domain of unknown function (DUF4470)
     0.0059   15.5   0.3       0.01   14.7   0.3    1.4  1  Pox_ATPase-GT  mRNA capping enzyme N-terminal, ATPase and gua
  ------ inclusion threshold ------
      0.011   15.7   0.4      0.079   12.8   0.0    2.1  2  CNDH2_C        Condensin II complex subunit CAP-H2 or CNDH2, 
      0.052   14.0   0.5      0.052   14.0   0.5    2.2  2  TFIIS_M        Transcription factor S-II (TFIIS), central dom


Domain annotation for each model (and alignments):
>> SMC_ScpA  Segregation and condensation protein ScpA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.0   7.2   3.4e-14     1e-10       1     136 [.      18     158 ..      18     164 .. 0.76
   2 !   16.9   1.4   1.5e-06    0.0045     167     238 ..     154     214 ..     117     217 .. 0.71

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 3.4e-14
                                       HHHHHHHHHTSSSSXXXXHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHSXXXXXXXXXXXXXXXXXXXX.. CS
                          SMC_ScpA   1 LiiakeldvtdvavakvtdqflayiktllnkleleesteylviastlvelKaasLlpleqveeeedeeleleelr.. 75 
                                       L++ +++d+++++++++t+++++ i+ + + l+l +s+ +++ as l+++K + Ll  ++ + ee ee  +e +r  
  gi|242398711|ref|YP_002994135.1|  18 LVTMGKVDPWNIDIVDITEKYIERIREM-QDLDLRISARAILAASILLRMKTEALLYTKEDDGEEQEE--EERIRvd 91 
                                       677899**********************.***************************999988877777..6666544 PP

                                       .XXXXXXXXXXXXXXXXXXXXX....XXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          SMC_ScpA  76 .dkLiarLleYrkykeeaklfk....eleaerl.ksfskarsdleefikeveevavkieksvfklie 136
                                        d  +  L    +y    +l++     le++   k   k+ +++ee i  v++  v+iek+v kl+e
  gi|242398711|ref|YP_002994135.1|  92 vDPYVPPLRRAERYYTLDDLIEalmdALEETEKrKPKKKKEVKIEEEIFVVDDFRVDIEKHVNKLYE 158
                                       57778777766666544443330001333333322223667899999999999******99988876 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 1.5e-06
                                       HHHH...............HHH....TS-EEGGGSSTT...--HHHHHHHHHHHHHHHHTT-EEEEESSTTS-EEE CS
                          SMC_ScpA 167 eellaqleqflqarlkevLldl....rswvdlseLladnkledkkelvgvFlAlLeLiknqavaleQeeflddLqv 238
                                       ++l             e++ +l    + ++ l eL+ d   +++k +  +Fl lL L +  +++l Qee++++++v
  gi|242398711|ref|YP_002994135.1| 154 NKLY------------EIVRELysntKDKIALWELVFD---PSPKIVARTFLYLLFLANMGKIELIQEEPFGEIFV 214
                                       3333............44444444435689999*****...*********************************98 PP

>> Rad21_Rec8  Conserved region of Rad21 / Rec8 like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   7.7e-09   2.3e-05      18      50 ..     183     215 ..     167     219 .] 0.89

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 7.7e-09
                                       HHHHHHHHHHHHHHHHTSEEEEESSTT--EEEE CS
                        Rad21_Rec8  18 keAArlFyelLvLatkgvIkvkQeaPYgdIlit 50 
                                       k +Ar+F  lL La  g+I++ Qe+P+g+I++ 
  gi|242398711|ref|YP_002994135.1| 183 KIVARTFLYLLFLANMGKIELIQEEPFGEIFVV 215
                                       779***************************986 PP

>> DUF4470  Domain of unknown function (DUF4470)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1     0.022        66      56      79 ..      46      69 ..      43      89 .. 0.82
   2 !   12.0   0.0   6.1e-05      0.18      47      78 ..     169     200 ..     151     208 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.022
                           DUF4470 56 ndneaeivaRnlllLslllepdds 79
                                       d +  i aR +l  s+ll+++++
  gi|242398711|ref|YP_002994135.1| 46 QDLDLRISARAILAASILLRMKTE 69
                                      588999*************99843 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 6.1e-05
                           DUF4470  47 ksrklditlndneaeivaRnlllLslllepdd 78 
                                       ++  l  ++ d++++ivaR++l L++l+++++
  gi|242398711|ref|YP_002994135.1| 169 DKIALWELVFDPSPKIVARTFLYLLFLANMGK 200
                                       3334444799*****************99876 PP

>> Pox_ATPase-GT  mRNA capping enzyme N-terminal, ATPase and guanylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.3   3.4e-06      0.01     157     206 ..     126     175 ..     115     202 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.4e-06
                                       STTS--EEEEEEEE--SSSS---HHHHHHHHHHHHHHHHSS-TTSEEE-- CS
                     Pox_ATPase-GT 157 dpkskpnvtlelEievlsdekldkkellkelvklfkalflsnaenifLvp 206
                                       +pk+k++v++e Ei v +d ++d ++ +++l+++++ l+ ++ ++i L +
  gi|242398711|ref|YP_002994135.1| 126 KPKKKKEVKIEEEIFVVDDFRVDIEKHVNKLYEIVRELYSNTKDKIALWE 175
                                       699*******************************************9976 PP

>> CNDH2_C  Condensin II complex subunit CAP-H2 or CNDH2, C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.6      0.25   7.5e+02      43      73 ..     107     137 ..      77     157 .. 0.59
   2 ?   12.8   0.0   2.6e-05     0.079     220     271 ..     158     208 ..     148     218 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.25
                           CNDH2_C  43 klqeflsalseklqavkeekkaekkgpafad 73 
                                        l+++++al ++l++++++k ++kk  ++++
  gi|242398711|ref|YP_002994135.1| 107 TLDDLIEALMDALEETEKRKPKKKKEVKIEE 137
                                       4444444444444444444444444444443 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 2.6e-05
                           CNDH2_C 220 riiesleekarvgetvsFaevVkgkekyevcRlflAsLqLANdgnVe.idskd 271
                                       +i+++l  +   +++ +  e+V + ++  v+R+fl +L LAN g +e i++++
  gi|242398711|ref|YP_002994135.1| 158 EIVRELYSN--TKDKIALWELVFDPSPKIVARTFLYLLFLANMGKIElIQEEP 208
                                       577777744..489999999**99999********************777665 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 ?    0.1   0.4      0.36   1.1e+03      79     109 ..      58      88 ..      33      90 .. 0.70
   2 ?   14.0   0.5   1.7e-05     0.052       6      65 ..     110     170 ..     107     176 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.36
                                       -STTTTS---TTTSS-HHHHHHHHHHHHHHH CS
                           TFIIS_M  79 ispeklvkmspeElaseelkeereklekeal 109
                                       + ++ l++m++e l   +    +e++e+e +
  gi|242398711|ref|YP_002994135.1|  58 LAASILLRMKTEALLYTKEDDGEEQEEEERI 88 
                                       4567788898888877777666666666666 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 1.7e-05
                                       HHHHHHHHHTT---...-.--THHHHHHHHHHHHHH.....HT------HHHHHHHHHHHHHS-T CS
                           TFIIS_M   6 kcrelLaealeedsseaeeeedveelaaeiEealfe.....kekkstdkkykqkvrslvfNLkdk 65 
                                         +e+L +alee ++     +  ++  ++iEe++f        +++  +k  + vr+l++N kdk
  gi|242398711|ref|YP_002994135.1| 110 DLIEALMDALEETEK----RKPKKKKEVKIEEEIFVvddfrVDIEKHVNKLYEIVRELYSNTKDK 170
                                       567889999998884....5678999999*****99988873344455678899********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1118  (0.0623571); expected 358.6 (0.02)
Passed bias filter:                      582  (0.0324614); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1412.70
//
Query:       gi|242398712|ref|YP_002994136.1|  [L=251]
Description: Archaeal inositol-1-monophosphatase/fructose-1, 6-bisphosphatase [Thermococcus sibiricus MM 739]
Scores for complete 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-31  108.6   0.0    4.5e-31  108.4   0.0    1.1  1  Inositol_P  Inositol monophosphatase family
    1.3e-05   24.7   0.0    2.2e-05   24.0   0.0    1.3  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 !  108.4   0.0     5e-35   4.5e-31       7     264 ..       6     248 ..       1     251 [] 0.84

  Alignments for each domain:
  == domain 1  score: 108.4 bits;  conditional E-value: 5e-35
                                       HHHHHHHHHHHHHHHHHTTTSEEEESTTTCCHHHHHHHHHHHHHHHHHHHHHHHHSTTSEEEHHCHHHHCCCT.SSS CS
                        Inositol_P   7 kaavelaakagevlreefsenelvieekskegeedlvtaadeaveelilealaekfpshkilgeetlakgekselte 83 
                                       ++a +la+ +   ++  f+++++    +  + + d  + +d+ +e+++le l+       i++ee +++++     e
  gi|242398712|ref|YP_002994136.1|   6 EIALNLAKDIEREIMPLFGQKKAGKFIGF-SPSGDKTKLVDKMAEDIVLEYLKPLG--VNIISEEIGSINN-----E 74 
                                       67778888888888888885555555555.789999999************99887..99***********.....6 PP

                                       SSEEEEEEEEETHHHHHHT-SG-EEEEEEEETTEEEEEEEEETTTTEEECEETTTEEEETCEEEEECTTSEGGGTEE CS
                        Inositol_P  84 dgltwivDPiDGTknFvrgipqvaVsigllvegkpvlGviaqPllgqlysaakgkGaflngeklplsrappiseall 160
                                       +++++ivDPiDG  nF++gip ++ s ++++  +p+ +++++ +++++y +  ++Ga+lnge ++++  +  +++++
  gi|242398712|ref|YP_002994136.1|  75 NEYCVIVDPIDGSFNFIHGIPVFGFSFAVFKGYEPLYAMLYEFITKNVYEGIPNEGAYLNGEMIRTRPLN--EDSIS 149
                                       66***********************************************************777776666..44444 PP

                                       EEEESSSSSSHHHHCHHHHHHHCCCCCHEEEBESSHHHHHHHHHHTSTSEEEEEC..EBHHHHHHHHHHHHHTTEEE CS
                        Inositol_P 161 vtlfavssrkdtseasllekvesavsaegvrsvgssalklaavaeGkadaylefg.rekkWDhAAGeaileeaGGvv 236
                                                +++  ++  +k+ + v+++  r +g+ a++la++a+G++d +++++  + + D+AAG +i +eaG+++
  gi|242398712|ref|YP_002994136.1| 150 ---------ISFYTRNRGAKLVEKVRRT--RVLGAIAIELAYLARGSLDGVIDIRnYVRPTDIAAGYIIAKEAGAII 215
                                       .........3344445677788889999..999*********************999******************** PP

                                       EESSSC.....SSSTTSSEEEEESCHHHHHHHH CS
                        Inositol_P 237 tdakge.....grlllargiiaanqkelaella 264
                                       td +g+      ++ ++ +iia n ++l +l++
  gi|242398712|ref|YP_002994136.1| 216 TDDEGRelkfnLNASEKLNIIAVNDEKLLKLIL 248
                                       ******775443344566888888666655554 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 !   24.0   0.0   2.5e-09   2.2e-05      57     130 ..      37     104 ..       9     111 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 2.5e-09
                            FBPase  57 tGdeqkklDvladeiliealkaseevkvlvSEEeeelivlerekegkyvvafDPlDGSSnidtnvsv.Gtifsiy 130
                                        Gd+ k +D +a++i+ e lk  +    ++SEE  ++     ++e +y+v++DP+DGS n   ++ v G  f+++
  gi|242398712|ref|YP_002994136.1|  37 SGDKTKLVDKMAEDIVLEYLKPLG--VNIISEEIGSI-----NNENEYCVIVDPIDGSFNFIHGIPVfGFSFAVF 104
                                       69******************9984..46899987654.....67899***********99877776545566666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1662.35
//
Query:       gi|242398713|ref|YP_002994137.1|  [L=268]
Description: membrane protein [Thermococcus sibiricus MM 739]
Scores for 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-87  291.7  23.4      1e-86  291.6  23.4    1.0  1  DUF63            Membrane protein of unknown function DUF63
  ------ inclusion threshold ------
       0.67   10.4   1.5        2.1    8.8   1.5    1.8  1  FeoB_associated  FeoB-associated Cys-rich membrane protein


Domain annotation for each model (and alignments):
>> DUF63  Membrane protein of unknown function DUF63
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  291.6  23.4   1.1e-90     1e-86       1     272 []       3     268 .]       3     268 .] 0.95

  Alignments for each domain:
  == domain 1  score: 291.6 bits;  conditional E-value: 1.1e-90
                             DUF63   1 iseFiykyYidpivykegYnivntltyaiiLivavyliykllkklkikidekfvlatipyvilgsslRvveDagllk 77 
                                       i e ++ky+idpi+y++gYnivntltyaiiL++a +++yk+lkkl+ik d+ f+ a+ipy+ilg++ R+++Da ++ 
  gi|242398713|ref|YP_002994137.1|   3 IYEILQKYFIDPIRYNQGYNIVNTLTYAIILGIAALVVYKVLKKLGIKYDNAFFRALIPYMILGAFGRALTDATII- 78 
                                       67899***********************************************************************. PP

                             DUF63  78 pplsyllitPliyflvflitlavlliskklekklkkdykklyaavGvvlvlvvlllLl..lteevvnlevlllvlll 152
                                        p syl++tP+iyflvf+it+ +lli++k+     +d++k++ ++G++lv   lllLl  l++ + n+ +l++++ +
  gi|242398713|ref|YP_002994137.1|  79 -PQSYLTVTPGIYFLVFMITFSSLLITHKF----FEDWRKVFLYFGWALVGGELLLLLfnLEKVQFNFDTLKYFIPF 150
                                       .****************************9....99******************9999555666778899999**** PP

                             DUF63 153 aavltalvllllrklklellsdklnlllllahllDasatfvgidllgYvEqHvvpsfLidltGtalvmyplkllvli 229
                                       a+++ ++++ll+ kl       k n +l++ah++Da++tfvg+d++gY+EqHv+p++L+d+tGta+vmy lk++vl+
  gi|242398713|ref|YP_002994137.1| 151 ATIALMTIYLLSIKLH----LVKKNSYLFYAHFYDATTTFVGVDFMGYWEQHVLPRYLMDITGTAAVMYFLKFAVLM 223
                                       *999999999998888....778899*************************************************** PP

                             DUF63 230 pvlyildkevkeeee..lrnlvklailvlGlaPgiRnllrmvlgv 272
                                        +ly+++   + e++  l++++k+++++lG+aPg+Rnllrm++gv
  gi|242398713|ref|YP_002994137.1| 224 VALYLMEYLQETESDkeLMDFIKMVMFILGFAPGTRNLLRMLMGV 268
                                       ******98766554456**************************97 PP

>> FeoB_associated  FeoB-associated Cys-rich membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   1.5   0.00024       2.1       4      23 ..      27      46 ..      24      50 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00024
                   FeoB_associated  4 IVgliiaaavafvirrlikk 23
                                      +  +ii++++a+v++++ kk
  gi|242398713|ref|YP_002994137.1| 27 LTYAIILGIAALVVYKVLKK 46
                                      5679**************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1077  (0.0600703); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); 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):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.53
# Mc/sec: 1534.68
//
Query:       gi|242398714|ref|YP_002994138.1|  [L=350]
Description: Glycerol-1-phosphate dehydrogenase NAD(P) [Thermococcus sibiricus MM 739]
Scores for complete 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-74  250.3   0.5    2.7e-74  250.0   0.5    1.1  1  Fe-ADH_2      Iron-containing alcohol dehydrogenase
      2e-27   95.9   0.3    3.7e-27   95.1   0.3    1.3  1  Fe-ADH        Iron-containing alcohol dehydrogenase
    4.3e-10   39.2   0.2    1.1e-09   37.8   0.2    1.7  1  DHQ_synthase  3-dehydroquinate synthase
  ------ inclusion threshold ------
      0.084   12.2   0.0       0.14   11.5   0.0    1.5  1  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 !  250.0   0.5   6.1e-78   2.7e-74       3     250 .]      17     272 ..      15     272 .. 0.92

  Alignments for each domain:
  == domain 1  score: 250.0 bits;  conditional E-value: 6.1e-78
                          Fe-ADH_2   3 gegaleklgellkelel.kkvllvadentkkaagekveeslkeagikvevveeveeeadleeveklvealreketdl 78 
                                       ge+  +k++++ k+l+l ++vl++++ +tk++ag+++e++lke   +v+ +    +ea++++v+k +e +r++++d 
  gi|242398714|ref|YP_002994138.1|  17 GEDLKDKVSQVAKRLKLgENVLILYGPKTKEIAGKDIEKHLKEF-FHVKNL--LIKEASMKNVQKALEIIRNENIDW 90 
                                       567778999999**99637**********************999.577744..46899******************* PP

                          Fe-ADH_2  79 vvavGgGtiiDiakyvsaklnvpyvsvpTaaSvDGfaspgaslvvdgkkrtvakaaaPlaviaDldvlaeAPrrlla 155
                                       +++vGgG+iiD+ak++s+k++vp++s+pT+aS+DG+as +as++  g+k+++ ka+ P+aviaD++++++AP r la
  gi|242398714|ref|YP_002994138.1|  91 LLGVGGGSIIDVAKLASFKADVPFISFPTTASHDGIASANASIRDLGAKTSI-KARPPVAVIADVNIIKTAPYRYLA 166
                                       ***************************************************9.9*********************** PP

                          Fe-ADH_2 156 sGvGDllgkytaladwklan........evseplaklsaamvqeaaeklvedkke..tealeellea.lalsgigis 221
                                       +GvGD+++++ta++dw+la+        e++++l+++sa+mv ++a+ +  +++e  ++++++l+++ +a+s++g+s
  gi|242398714|ref|YP_002994138.1| 167 AGVGDMVSNLTAVKDWELAHrirgeyfsEYAASLSLMSAKMVIKNADIIRLSNEEsvRKVIKALISSgVAMSIAGSS 243
                                       ********************9999999999*****************99764333235666666655359******* PP

                          Fe-ADH_2 222 rpaSGsEHliSHaldmlalkqalHGeqVG 250
                                       rpaSG+EHl+SHald++a+k+alHGeq+G
  gi|242398714|ref|YP_002994138.1| 244 RPASGAEHLFSHALDAIAPKPALHGEQCG 272
                                       ****************************9 PP

>> Fe-ADH  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.1   0.3   8.2e-31   3.7e-27       1     296 [.      11     296 ..      11     308 .. 0.82

  Alignments for each domain:
  == domain 1  score: 95.1 bits;  conditional E-value: 8.2e-31
                                       -SEEEEETTGGGGHHHHHTTT-...EEEEEEEHHHH.HH.THHHHHHHHHCTT-EEEE.EEE-S---HHHHHHHHTT CS
                            Fe-ADH   1 Ptrivfgkgaleelgellkklg.akralivtdkgslkksglldkvlesleeagievtvfdgvepnptleeveeaaal 76 
                                       P++++ g++  +++ + +k+l+  +++li+++++  +k+ + ++++++l ++ + v+  +   ++ + ++v++a+++
  gi|242398714|ref|YP_002994138.1|  11 PREVLLGEDLKDKVSQVAKRLKlGENVLILYGPK--TKEIAGKDIEKHL-KEFFHVK--NLLIKEASMKNVQKALEI 82 
                                       7889999998888888888886337*********..4677999******.3333333..5569************** PP

                                       S-TT.--EEEEEESHHHHHHHHHHHHHTT..................--EEEEESS-S-S-TT-SEEEEE.-TTSEE CS
                            Fe-ADH  77 areegadvviavGGGsviDtAKaialllanpevedylgegkakkkkalpliaiPTtaGtGsevtplavitdeeegek 153
                                       +r+e++d +++vGGGs iD+AK++++ +                   +p+i  PTta+ +  ++++a i   + g+k
  gi|242398714|ref|YP_002994138.1|  83 IRNENIDWLLGVGGGSIIDVAKLASFKAD------------------VPFISFPTTASHDGIASANASIR--DLGAK 139
                                       *****************************..................***********************..7889* PP

                                       EEE-..SS--SEEEEEHHHHHHS-HHHHHHHHHHHHHHHHHHHHHHT---TTSS.B--HHHHHHHHHHHHHHHHHH. CS
                            Fe-ADH 154 lsifdpellPdlaivDpeltltlPkrvtaatglDalahalEayvskkanplsda.laleairliaknleravadge. 228
                                       +si      P ++i D +++ t+P r++aa+++D ++        + a+ +    ++++a+ l + + + ++++++ 
  gi|242398714|ref|YP_002994138.1| 140 TSIK--ARPPVAVIADVNIIKTAPYRYLAAGVGDMVSNLTAVKDWELAHRIRGEyFSEYAASLSLMSAKMVIKNADi 214
                                       ****..889***************************99988865566666444436666666666666666666544 PP

                                       ....HHHHHHHHHHHHHHHHHHHHSS---.....HHHHHHHHHHC.CGGG..GGS-HHH...HHHHHH......... CS
                            Fe-ADH 229 ....dleareqmllastlaglafsnaglg.....avHalahalgalfgip..hglanai...llpavlrfnaeaape 291
                                           + e  ++++ a + +g+a+s ag +     a H ++hal a+   p  hg+ +++   ++++    n ++ +e
  gi|242398714|ref|YP_002994138.1| 215 irlsNEESVRKVIKALISSGVAMSIAGSSrpasgAEHLFSHALDAIAPKPalHGEQCGVgtiIMAYLHGLNWKKIRE 291
                                       433377******************9999999999***********77655689999987665677766667766666 PP

                                       .HHHH CS
                            Fe-ADH 292 rlaql 296
                                        l+++
  gi|242398714|ref|YP_002994138.1| 292 TLKRV 296
                                       66555 PP

>> DHQ_synthase  3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   0.2   2.5e-13   1.1e-09      16     245 ..      73     305 ..      64     322 .. 0.77

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 2.5e-13
                                       HHHHHHHHHHTT--TT-EEEEEESHHHHHHHHHHHHHBTT--EEEEEE-SHHHHHTTTSSSEEEEEETTEEEEEEEE CS
                      DHQ_synthase  16 lekildalleakleRksllialGGGvvgDlaGfvAatylRGvrfvqvPttllaqvDssvGgKtainlplgKNliGaf 92 
                                       ++++ +al   + e  + l+ +GGG + D+a ++   ++  v f+  Ptt  a  D    +  +i    +K  i a 
  gi|242398714|ref|YP_002994138.1|  73 MKNVQKALEIIRNENIDWLLGVGGGSIIDVAKLA--SFKADVPFISFPTT--ASHDGIASANASIRDLGAKTSIKA- 144
                                       4556666666666677899************985..69999********9..666666666777777777777754. PP

                                       ---SEEEEEGGGGGGS-HHHHHHHHHHHHH.HHHHT-HHHHHHHHHHHHHHHC...................TTTHH CS
                      DHQ_synthase  93 aqPkavlidlevLktLperelraGlaEviK.yalikdeelfelleenaeallk...................eeeee 149
                                         P av++d++++kt p r l+aG+++++   +++kd el ++++ +  +  +                    ++ee
  gi|242398714|ref|YP_002994138.1| 145 RPPVAVIADVNIIKTAPYRYLAAGVGDMVSnLTAVKDWELAHRIRGEYFSEYAaslslmsakmviknadiirLSNEE 221
                                       89*************************99526899*********999888877789999988888877666544555 PP

                                       HHHHHHHHHHHHHHHHHHHCCTTTTGGGGGGTTHHHHHHHHHHHTTTTS-HHHHHHHHHHHHHHHHHHTTSS-HHHH CS
                      DHQ_synthase 150 aleeliarsievkaevveeDekekglralLnlGHtigHaiEallgyekllHGeaVaiGmvlaaelseklgllkkeev 226
                                       +++++i++ i+    +        + r +    H ++Ha++a++     lHGe   +G ++ a+l            
  gi|242398714|ref|YP_002994138.1| 222 SVRKVIKALISSGVAM----SIAGSSRPASGAEHLFSHALDAIAPK-PALHGEQCGVGTIIMAYLHGLN-------W 286
                                       5566665555544433....3346778888889**********988.9************999987322.......4 PP

                                       HHHHHHHHHTT---STTTT CS
                      DHQ_synthase 227 erllkllkklglpvslkel 245
                                       ++++++lk++g p++  el
  gi|242398714|ref|YP_002994138.1| 287 KKIRETLKRVGAPTNAYEL 305
                                       5677777777777765544 PP

>> PFK  Phosphofructokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   3.1e-05      0.14      77     135 ..      73     127 ..      19     145 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.1e-05
                                       HHHHHHHHHHHHHHT--EEEEEESHHHHHHHHHHHHT..T....--EEEEEEETT--.-T CS
                               PFK  77 regrkkaaenlkklgidaLvviGGdgslkganklseerkglleelkivgiPkTidND.ip 135
                                        ++++ka+e +++++id L+ +GG   +++a+ l++ + +    ++++  P T + D i+
  gi|242398714|ref|YP_002994138.1|  73 MKNVQKALEIIRNENIDWLLGVGGGSIIDVAK-LASFKAD----VPFISFPTTASHDgIA 127
                                       35699*******************77777776.5544446....9********9988444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.64u 0.35s 00:00:00.99 Elapsed: 00:00:00.53
# Mc/sec: 1985.94
//
Query:       gi|242398715|ref|YP_002994139.1|  [L=142]
Description: hypothetical protein TSIB_0727 [Thermococcus sibiricus MM 739]
Scores for complete 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-40  138.1   0.3      2e-40  137.9   0.3    1.0  1  UPF0179   Uncharacterised protein family (UPF0179)


Domain annotation for each model (and alignments):
>> UPF0179  Uncharacterised protein family (UPF0179)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.9   0.3   1.1e-44     2e-40       1     138 [.       2     137 ..       2     139 .. 0.95

  Alignments for each domain:
  == domain 1  score: 137.9 bits;  conditional E-value: 1.1e-44
                           UPF0179   1 kitLigkklAkeGteFiylgeaeeCekCklkkvCln.LekgrkYrivevrekteheCavheegvvaveveeapieal 76 
                                       +itL+g+klAk+G+eFiy+g+a+ C++C+l++vC+  Le+gr+Y++v+vr+  eh+C++he++v++vev e  ie++
  gi|242398715|ref|YP_002994139.1|   2 TITLVGEKLAKPGVEFIYYGPADPCKSCRLARVCVGnLEPGRRYKVVRVRNI-EHSCPLHEGKVRVVEVIEPAIEVA 77 
                                       59*********************************99***************.************************ PP

                           UPF0179  77 ieskkavegskitleseeCdevecesyelcepeglkegekvkivevlgeieeckkg.rslkkv 138
                                       ie + a+ gski+l+  eC++   e+++l +pegl eg+ vki e+ ++ e c+++ +++++v
  gi|242398715|ref|YP_002994139.1|  78 IEPRVAIVGSKIKLSFVECND--PEKQSLTRPEGLFEGDIVKILEISDDFE-CDEKhYKVARV 137
                                       *******************98..8999999********************9.98764776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); 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: 00:00:00.43
# Mc/sec: 982.24
//
Query:       gi|242398716|ref|YP_002994140.1|  [L=333]
Description: Allophanate hydrolase, subunit 2 [Thermococcus sibiricus MM 739]
Scores for complete 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-91  306.2   0.0    2.5e-91  306.0   0.0    1.0  1  CT_A_B    Carboxyltransferase domain, subdomain A and B


Domain annotation for each model (and alignments):
>> CT_A_B  Carboxyltransferase domain, subdomain A and B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  306.0   0.0   1.4e-95   2.5e-91       1     263 [.      24     282 ..      24     283 .. 0.97

  Alignments for each domain:
  == domain 1  score: 306.0 bits;  conditional E-value: 1.4e-95
                                       GT----S-SSHHHHHHHHHHTTS-TTS-EEEEESC-EEEEESS-EEEEEEESCEEEEETTEEE-SSCEEEE-TT-EE CS
                            CT_A_B   1 lGvprsGamDrlalrlANrlvgNeegaaaLEitlggpelrfeedavvavtGadleatldgepvplwepvevkaGdvL 77 
                                       +Gvp+sG+mD++++rlAN lvgNe+++++LE++l gp+++f+++av+a+ G d+e++l+g+pv++w+++ +k+Gd+L
  gi|242398716|ref|YP_002994140.1|  24 FGVPVSGVMDEVSARLANYLVGNEDNTPLLEFVLHGPTIKFHSSAVFAIGG-DVEVKLNGQPVEAWKSYWAKRGDIL 99 
                                       6***********************************************977.9************************ PP

                                       EEEEESSECEEEEEETT-BE---BTTB-S-BTTTTBSTTTTS---TT-EEEBSSSTT--S-C.BGGCS---SSCSEE CS
                            CT_A_B  78 klgaakaGlraYLavaGgldvpevlgSrStdllaglGgleGraLkagdvLplgeaaaaaaakakeleaaapeeseee 154
                                       ++g +k+G++ Y+a+aGg++++++lgS+St+l+a++G+    +L++gd+L+lg a  + ++ ++ +++ +p++++e+
  gi|242398716|ref|YP_002994140.1| 100 EIGILKSGMYGYIAFAGGIACEPILGSCSTYLRANFGK----PLSSGDKLKLGYAILTGKEGKQLPKEFVPKYEKEN 172
                                       ************************************76....7*****************99999************ PP

                                       EEEEEE-TTGCCB-HHHHHHHHHS-EEEECEECSSEEEEESGG.SSC.S..TEEEEEE--TTEEEE-CTTEEEEE-T CS
                            CT_A_B 155 evrvvpGpqadlfteealeallssewtvsaesdRmGvrLdGeagler.ke.sellsegvvlGaiqvppdgqpivlla 229
                                       +vrv++Gpq+++ft++++e++l+se+tv++esdRmG+rL+G+ ++e+ ++ ++++++++++G+iqvp++g+pi++la
  gi|242398716|ref|YP_002994140.1| 173 TVRVILGPQEEHFTKRGIETFLTSEYTVTSESDRMGYRLEGP-KIEHsDKgADIITDAIPPGSIQVPKNGKPIIMLA 248
                                       *****************************************5.577743358************************* PP

                                       TS-SEEEEEEEEEE-GGGHHHHTT--TTSEEEEE CS
                            CT_A_B 230 DhqttGGYpkiatvisadldklaQlrpgdkvrFe 263
                                       D+qttGGY+ki++v++ d++k+aQ rpg+++rF+
  gi|242398716|ref|YP_002994140.1| 249 DRQTTGGYAKIGVVARVDIPKVAQKRPGERIRFK 282
                                       *********************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2514.86
//
Query:       gi|242398717|ref|YP_002994141.1|  [L=230]
Description: Allophanate hydrolase, subunit 1 [Thermococcus sibiricus MM 739]
Scores for complete 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-75  251.6   0.0      6e-75  251.4   0.0    1.0  1  CT_C_D    Carboxyltransferase domain, subdomain C and D


Domain annotation for each model (and alignments):
>> CT_C_D  Carboxyltransferase domain, subdomain C and D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  251.4   0.0   3.3e-79     6e-75       2     201 ..       4     201 ..       3     202 .. 0.97

  Alignments for each domain:
  == domain 1  score: 251.4 bits;  conditional E-value: 3.3e-79
                                       EEEEETTTEEEEEE-SS--HHHHHHHHHHHHHHHT..STTECEEEE-SSEEEEEESCCCCHHHHHH.HHHHHHHH.- CS
                            CT_C_D   2 rirplGdeallvefgeeisealskrvlalaaalrakalpgvvelvpayrsllvefdpealdaaellaalkalleeae 78 
                                       +++p+Gd+a+ + fg+eise+++k+v+a+a++++++  + +ve+vp+y+s+ v+++p +++++e++aalk  l++  
  gi|242398717|ref|YP_002994141.1|   4 KFKPAGDSAIAIIFGSEISEEINKKVHAVAETIEHASPEWLVEVVPTYTSVYVYYNPIKISYSEIVAALKPFLSA-- 78 
                                       789*********************************************************************998.. PP

                                       --------EEEEEEEESTTT-TTHHHHHHHHTS-HHHHHHHHHHS-EEEEEE-SSTT-EEE----GGG-----SS-- CS
                            CT_C_D  79 eeaaeesrlveipvcYdgevgpDLeevaelnglsveevirlhtaaeyrvaflGfapGfaylggldprlavpRrasPr 155
                                       e ++ee+r+v+ipv+Y+g++gpD+e+va++n+l+ +ev+++h++  yrv++lGf+pGfaylgg+++r+a+pR+++Pr
  gi|242398717|ref|YP_002994141.1|  79 EPKKEEKRIVKIPVVYGGDFGPDIEFVAQYNNLTIDEVVEIHSKPLYRVYMLGFLPGFAYLGGMNERIATPRLEKPR 155
                                       556677789******************************************************************** PP

                                       S-B-TTEEEEETTEEEEE-S-B---SEEEEEE-S-SB-TTSSSSBS CS
                            CT_C_D 156 trvpagsVgiageqtgiyplesPGGWqliGrTplplfdpdreppal 201
                                       ++vpagsVgiag+qtg y++esPGGW+liGrTpl+ fdp+++pp++
  gi|242398717|ref|YP_002994141.1| 156 LKVPAGSVGIAGRQTGWYAIESPGGWRLIGRTPLKTFDPTKSPPSI 201
                                       *****************************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        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 0.29s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1450.20
//
Query:       gi|242398718|ref|YP_002994142.1|  [L=255]
Description: LamB/YcsF family protein [Thermococcus sibiricus MM 739]
Scores for complete 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-104  348.6   0.0   2.1e-104  348.5   0.0    1.0  1  LamB_YcsF  LamB/YcsF family


Domain annotation for each model (and alignments):
>> LamB_YcsF  LamB/YcsF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  348.5   0.0  1.1e-108  2.1e-104       1     239 []       3     241 ..       3     241 .. 0.99

  Alignments for each domain:
  == domain 1  score: 348.5 bits;  conditional E-value: 1.1e-108
                                       EEEEEEE---BTTB--S-HHHHCCC-SEEEEE-SSSS--HHHHHHHHHHHHHTT-EEEEE---S-TTTTT-S----- CS
                         LamB_YcsF   1 idlnaDlGEsfgawklgdDeallplvtsaNiACGfHaGdpevmrktvelakekgVaiGAhpgypDlegFGRremels 77 
                                       idln+DlGEsfg++klg De++++++tsaNiACG+HaGdp +mrktv+lak+ +V++GAhpgypDl+gFGRr m+l+
  gi|242398718|ref|YP_002994142.1|   3 IDLNSDLGESFGRYKLGLDEEVMKYITSANIACGWHAGDPLIMRKTVKLAKDMNVEVGAHPGYPDLMGFGRRYMDLT 79 
                                       8**************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHTT----EE---HHHHHHHHH-HHHHHHHHHHHHHH-TT.TEEEETTSHHHHHHHHC CS
                         LamB_YcsF  78 peelealvlyQigaLkafakaegvklshvkpHGaLynqaakdeelaeavveavkaldpelillglagseleeaaeea 154
                                       +ee ++++lyQigaL af+kaeg++l+hvkpHGaLyn++++deel   v+e ++++d+++i++gl+ s+  e+aee+
  gi|242398718|ref|YP_002994142.1|  80 KEEARNYILYQIGALYAFVKAEGLTLQHVKPHGALYNALVRDEELTIGVLEGIADFDKNIIFVGLSMSKPLEIAEEM 156
                                       ***************************************************************************** PP

                                       T--EEEEEETTB-B-TTSSB--TTSTTSB---HHHHHHHHHHHHHTSEEEBTTSSEEE---SEEEE-SSSHHHHHCH CS
                         LamB_YcsF 155 glkvvaevfaDraYeadgslvprsqpgaviedpeevaervlklveegkvtavdgeevelkadsicvHgDtpeavela 231
                                       glkv++evfaDraY++dg+lv+r++pgavi+++ee+aerv+++v++g v++++ge+vel+ad+icvHgD+p+ave+ 
  gi|242398718|ref|YP_002994142.1| 157 GLKVAHEVFADRAYNPDGTLVSRRKPGAVIHNKEEIAERVISMVKDGGVKSINGEWVELRADTICVHGDNPKAVEIT 233
                                       ***************************************************************************** PP

                                       CCCCHHHH CS
                         LamB_YcsF 232 ravreale 239
                                       + +r++le
  gi|242398718|ref|YP_002994142.1| 234 AYLRKRLE 241
                                       ****9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); 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: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1926.93
//
Query:       gi|242398719|ref|YP_002994143.1|  [L=161]
Description: hypothetical protein TSIB_0731 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-18   67.3   0.4      2e-18   66.7   0.4    1.3  1  PIN_6           PIN domain of ribonuclease
    1.2e-05   24.8   0.2    2.4e-05   23.9   0.1    1.3  1  PIN_5           PINc domain ribonuclease
    6.2e-05   23.0   0.2    0.00012   22.1   0.2    1.5  1  Zn-ribbon_8     Zinc ribbon domain
    8.1e-05   22.6   0.0    0.00015   21.7   0.0    1.4  1  HypA            Hydrogenase/urease nickel incorporation, meta
    0.00088   18.6   3.2     0.0014   17.9   3.2    1.3  1  zf-ribbon_3     zinc-ribbon domain
     0.0019   18.1   3.8      0.038   13.9   0.4    2.2  2  Zn_ribbon_SprT  SprT-like zinc ribbon domain
      0.002   17.7   1.3     0.0052   16.4   1.3    1.7  1  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
  ------ inclusion threshold ------
      0.014   15.4   0.1      0.021   14.8   0.1    1.3  1  DZR             Double zinc ribbon
       0.02   15.1   0.4      0.038   14.1   0.4    1.5  1  NOB1_Zn_bind    Nin one binding (NOB1) Zn-ribbon like
      0.028   14.9   1.6       0.41   11.2   0.1    2.5  2  zf-C2H2         Zinc finger, C2H2 type
      0.028   14.4   0.1       0.05   13.6   0.1    1.3  1  zinc-ribbons_6  zinc-ribbons
       0.03   14.2   2.1          6    6.9   0.2    2.5  2  Nudix_N_2       Nudix N-terminal
      0.072   12.6   0.0       0.32   10.5   0.0    2.0  2  Sigma70_r4      Sigma-70, region 4
       0.12   11.9   4.0       0.58    9.7   4.0    2.0  1  TF_Zn_Ribbon    TFIIB zinc-binding
       0.13   12.3   1.5       0.25   11.3   1.5    1.5  1  ADK_lid         Adenylate kinase, active site lid
       0.14   11.9   0.8       0.26   10.9   0.8    1.5  1  Xin             Xin repeat
       0.16   11.9   1.4       0.26   11.3   1.4    1.3  1  Prok-RING_1     Prokaryotic RING finger family 1


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 !   66.7   0.4   1.9e-21     2e-18       1      89 []       2      85 ..       2      85 .. 0.92

  Alignments for each domain:
  == domain 1  score: 66.7 bits;  conditional E-value: 1.9e-21
                             PIN_6  1 lVlDagaliknslsslqnlaeklyttpeVvaEirdkkarerlellp..lelevrePspesvkkvtefakktGDlsvLSk 77
                                      l++Da+ +i++       +  + +ttp+V++E++d ++r  le l+   +++v+ Ps++s++kv+e a +tG+l  LS+
  gi|242398719|ref|YP_002994143.1|  2 LIIDAAIFIQS-------IDVEGITTPKVIEEVKDPESRLLLESLIsaGKVRVMVPSKDSIEKVKEKAIETGELGELSD 73
                                      67788877755.......778999********************99544****************************** PP

                             PIN_6 78 tDievlALtyeL 89
                                      +DievlAL+yeL
  gi|242398719|ref|YP_002994143.1| 74 ADIEVLALAYEL 85
                                      **********98 PP

>> PIN_5  PINc domain ribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.1   2.3e-08   2.4e-05     156     192 ..      72     108 ..      50     120 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 2.3e-08
                             PIN_5 156 saeDldvllLAkELdaavvssDeGikkwaeklGlrlv 192
                                       s  D++vl LA+EL +++ ++D  ++++a  lGl++ 
  gi|242398719|ref|YP_002994143.1|  72 SDADIEVLALAYELRGELFTDDYNLQNIAALLGLKFR 108
                                       889*******************************984 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.2   1.1e-07   0.00012       5      37 ..     121     148 ..     120     150 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.1e-07
                       Zn-ribbon_8   5 eYrCeeCghefevlqsisdaplta.CPeCgsevr 37 
                                        Y C  Cg++fe  q     pl   CP+Cgs+vr
  gi|242398719|ref|YP_002994143.1| 121 RYVCVGCGKKFE-TQ-----PLDNiCPDCGSKVR 148
                                       59**********.44.....35555******997 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   1.4e-07   0.00015      32      95 ..      67     146 ..      44     153 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.4e-07
                                       EEETTCT--HHHHHHHHHHHHCC.TTTT-EEE.................EEEE--EEEETTTS-EEECHHHHHS-TT CS
                              HypA  32 evGelsgvepeaLefafellaegtvlegaeLe.................ieevpvkvrCreCgkefeleekalrCpk 91 
                                       e+Gels  + e+L+ a+el   +  +++ +L+                  + ++ ++ C  Cgk+fe++  +  Cp+
  gi|242398719|ref|YP_002994143.1|  67 ELGELSDADIEVLALAYELRG-ELFTDDYNLQniaallglkfrtlkrgiKKVIKWRYVCVGCGKKFETQPLDNICPD 142
                                       57889999999*****99864.33466666666667778889999999666789*************9874567*** PP

                                       TSSS CS
                              HypA  92 Cgsa 95 
                                       Cgs+
  gi|242398719|ref|YP_002994143.1| 143 CGSK 146
                                       **95 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   3.2   1.4e-06    0.0014       4      25 ..     123     146 ..     122     147 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.4e-06
                       zf-ribbon_3   4 rCPnCGa.p.lssddnvCpyCGtk 25 
                                        C  CG+    ++ dn+Cp CG+k
  gi|242398719|ref|YP_002994143.1| 123 VCVGCGKkFeTQPLDNICPDCGSK 146
                                       5999***99*************86 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.4   3.6e-05     0.038       2      15 ..     119     132 ..     119     136 .. 0.87
   2 ?    5.3   0.2     0.018        19       7      19 ..     140     152 ..     139     158 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.6e-05
                    Zn_ribbon_SprT   2 kyvYrCtgCgreyt 15 
                                       k+ Y+C+gCg++++
  gi|242398719|ref|YP_002994143.1| 119 KWRYVCVGCGKKFE 132
                                       8*********9887 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.018
                    Zn_ribbon_SprT   7 CtgCgreythhls 19 
                                       C++Cg+++    +
  gi|242398719|ref|YP_002994143.1| 140 CPDCGSKVRLLPK 152
                                       *****66544444 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 !   16.4   1.3   4.9e-06    0.0052       1      27 [.     122     147 ..     122     154 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 4.9e-06
                                       -B-SSS--B----SSS----SSS---- CS
                    DNA_RNApol_7kD   1 YiCgeCgaevslkkgdpiRCkeCGhRi 27 
                                       Y C +Cg++++ ++ d i C +CG+++
  gi|242398719|ref|YP_002994143.1| 122 YVCVGCGKKFETQPLDNI-CPDCGSKV 147
                                       9****************9.*****987 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1     2e-05     0.021      29      49 .]     122     144 ..      95     152 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2e-05
                               DZR  29 drCpsCgek..vdpearfCpeCG 49 
                                       ++C+ Cg+k  ++p +++Cp CG
  gi|242398719|ref|YP_002994143.1| 122 YVCVGCGKKfeTQPLDNICPDCG 144
                                       55555555544555555555555 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.4   3.6e-05     0.038       1      32 [.     114     146 ..     114     152 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.6e-05
                      NOB1_Zn_bind   1 ikrvkswvlrChaCfkvtkd.mtkkFCpkCGnk 32 
                                       ik+v +w + C +C k +++    + Cp CG+k
  gi|242398719|ref|YP_002994143.1| 114 IKKVIKWRYVCVGCGKKFETqPLDNICPDCGSK 146
                                       89999*********997755278899*****96 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00039      0.41       1      13 [.     122     134 ..     122     136 .. 0.92
   2 ?    2.4   0.1      0.24   2.6e+02       3       7 ..     140     144 ..     139     150 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00039
                                       EEETTTTEEESSH CS
                           zf-C2H2   1 ykCpdCgksFkrk 13 
                                       y+C +Cgk+F ++
  gi|242398719|ref|YP_002994143.1| 122 YVCVGCGKKFETQ 134
                                       9*********997 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.24
                                       ETTTT CS
                           zf-C2H2   3 CpdCg 7  
                                       CpdCg
  gi|242398719|ref|YP_002994143.1| 140 CPDCG 144
                                       ****9 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   4.7e-05      0.05      16      42 ..     121     150 ..     109     152 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.7e-05
                                       EEE-TTT--EEEEE...EE-SSS-S---EE CS
                    zinc-ribbons_6  16 qyhCeaCqedlkke...alCpeCeqelevl 42 
                                       +y C  C ++++ +   ++Cp+C++++  l
  gi|242398719|ref|YP_002994143.1| 121 RYVCVGCGKKFETQpldNICPDCGSKVRLL 150
                                       689******9998722257******99876 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1    0.0071       7.5      20      29 ..     119     128 ..     118     129 .. 0.89
   2 ?    6.9   0.2    0.0057         6       3      12 ..     140     149 ..     138     160 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0071
                                       S-EEEETTTT CS
                         Nudix_N_2  20 reRlvCpaCg 29 
                                       ++R+vC  Cg
  gi|242398719|ref|YP_002994143.1| 119 KWRYVCVGCG 128
                                       68*******9 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0057
                                       -TTT--B-EE CS
                         Nudix_N_2   3 CsqCGtpvel 12 
                                       C+ CG++v+l
  gi|242398719|ref|YP_002994143.1| 140 CPDCGSKVRL 149
                                       *******986 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0    0.0003      0.32       2      33 ..      68     106 ..      68     119 .. 0.89
   2 ?   -0.1   0.0      0.64   6.8e+02      10      18 ..     115     126 ..     107     139 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0003
                                       HHHS-HHHHHHHHHHH.......TTT--HHHHHHHHTS- CS
                        Sigma70_r4   2 LasLpererevlelrf.......geglTleEIgerlgiS 33 
                                       L +L++ + evl l +        ++++l+ I++ lg+ 
  gi|242398719|ref|YP_002994143.1|  68 LGELSDADIEVLALAYelrgelfTDDYNLQNIAALLGLK 106
                                       7899*********************************85 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.64
                                       HHHHHHHH...T CS
                        Sigma70_r4  10 revlelrf...g 18 
                                       ++v++ r+   g
  gi|242398719|ref|YP_002994143.1| 115 KKVIKWRYvcvG 126
                                       789999996662 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   4.0   0.00055      0.58       1      29 [.     122     147 ..     122     156 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00055
                                       EEETTTTCEECHEETSTTCEEESSSSBEE CS
                      TF_Zn_Ribbon   1 ykCPnCgstnlveDpergelvCtdCGlVl 29 
                                       y+C  Cg +   +++   + +C+dCG+ +
  gi|242398719|ref|YP_002994143.1| 122 YVCVGCGKK---FETQPLDNICPDCGSKV 147
                                       79*****98...688889********976 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 ?   11.3   1.5   0.00024      0.25       1      30 [.     121     146 ..     121     149 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00024
                                       EEE-TTT--EEETTTB--SSTTB-TTT--. CS
                           ADK_lid   1 RrvCpkCGrsYhvvfnpPkveglCDkCGep 30 
                                       R vC  CG+ +      P  +++C +CG++
  gi|242398719|ref|YP_002994143.1| 121 RYVCVGCGKKFE---TQP-LDNICPDCGSK 146
                                       99**********...345.7********96 PP

>> Xin  Xin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.8   0.00025      0.26      10      16 .]     131     137 ..     131     137 .. 0.98

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00025
                               Xin  10 FETQPLD 16 
                                       FETQPLD
  gi|242398719|ref|YP_002994143.1| 131 FETQPLD 137
                                       ******9 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   1.4   0.00024      0.26       6      28 ..     123     145 ..     119     147 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00024
                       Prok-RING_1   6 kCpvCgkelkeedDiVvCpeCgt 28 
                                        C  Cgk+++ +    +Cp+Cg+
  gi|242398719|ref|YP_002994143.1| 123 VCVGCGKKFETQPLDNICPDCGS 145
                                       6**********955568****96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       850  (0.0474092); expected 358.6 (0.02)
Passed bias filter:                      697  (0.0388756); expected 358.6 (0.02)
Passed Vit filter:                       110  (0.00613531); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1173.02
//
Query:       gi|242398720|ref|YP_002994144.1|  [L=369]
Description: Archaeal ATPase [Thermococcus sibiricus MM 739]
Scores for complete 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   95.5   1.1    5.5e-27   95.2   0.3    1.6  2  ATPase_2  ATPase domain predominantly from Archaea
    3.6e-12   46.5   0.1    1.3e-09   38.2   0.0    2.7  1  AAA_14    AAA domain
      7e-06   26.4   0.0    1.6e-05   25.2   0.0    1.6  1  AAA_22    AAA domain
    3.6e-05   24.2   0.0    0.00011   22.6   0.0    1.8  1  AAA_16    AAA ATPase domain


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 !   95.2   0.3   1.2e-30   5.5e-27       2     232 ..      20     255 ..      19     256 .. 0.85
   2 ?   -2.0   0.0      0.62   2.8e+03      92     146 ..     267     316 ..     259     332 .. 0.61

  Alignments for each domain:
  == domain 1  score: 95.2 bits;  conditional E-value: 1.2e-30
                          ATPase_2   2 fdRekelkeleeilerepneiyfiYGpegsGKtaLlkeiienledkdk...yviyyialreesiskldefie...ee 72 
                                       fdRe+e++ +++ +++  ++i +i G +++GK++Llk ++++l++  +   +++ +++   + +++l + +e   ++
  gi|242398720|ref|YP_002994144.1|  20 FDREQEIEMIKNSAKE--YPITLILGIRRVGKSSLLKVVLNELKSGIYidvRKLHFDSGGWITNESLLKAFEnglNS 94 
                                       9**************9..*************************7754455566666666665555544444456444 PP

                          ATPase_2  73 eekkklekalgiavpkaeleeilk.eksklvfkaielllekikkkgkkiiiiiDelqklidlglngaellvkeLlnl 148
                                        +   +++ + + ++++++  i   + + + + +++++le+++k+  +iii +De+q+l+ +g +g ++++   +++
  gi|242398720|ref|YP_002994144.1|  95 LSHP-IKREVFQYLKRVKGVSIAGlQLNFEPEVSLSEILEALNKR-SRIIIAFDEAQYLRFYGRRGGKEFLTLVAYA 169
                                       4444.44444677777777777788999****************9.66********************999999999 PP

                          ATPase_2 149 iesltkekhlcvviclsSeglfie...rvyneselegrhky.ilvddldketalnflkegfkel.eelskedfeeiy 220
                                       +++l+   ++ +++ +s+ gl+++   + ++es+l+gr    i++ ++ ke + +fl++gf e  ++  +e++e + 
  gi|242398720|ref|YP_002994144.1| 170 YDNLP---NISFIFTGSEIGLLHDligVSDYESPLYGRIYNeITISPFSKELSIEFLRQGFVEAgIKIREEEIEHAA 243
                                       99976...799*************665668********9999**********************9999********* PP

                          ATPase_2 221 ryvGGkPkalve 232
                                       +++GG+P+ lve
  gi|242398720|ref|YP_002994144.1| 244 ELLGGIPGWLVE 255
                                       ********9987 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.62
                          ATPase_2  92 eeilkeksklvfkaielllekikkkgkkiiiiiDelqklidlglngaellvkeLl 146
                                       e+ +k  +++++k +e  l++++k+  + i+++    ++i++g++    l+ke+l
  gi|242398720|ref|YP_002994144.1| 267 ENAIKGVIRKAEKFLEGELRELEKRSPRYILVL----RAISMGFD-RWALIKEFL 316
                                       444455566666666666777777766666643....45555555.455555555 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.2   0.0   2.9e-13   1.3e-09       3     126 ..      37     215 ..      35     218 .. 0.76

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 2.9e-13
                            AAA_14   3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderd.................................... 43 
                                       +i +i G+RrvGK+ llk +++el     s +yi++ + ++                                    
  gi|242398720|ref|YP_002994144.1|  37 PITLILGIRRVGKSSLLKVVLNELK----SGIYIDVRKLHFdsggwitnesllkafenglnslshpikrevfqylkr 109
                                       7899*************99996665....999999999999889999888888888888877777777777766666 PP

                            AAA_14  44 .........kkladpekllelileklkeekktylflDEiqev........pewekalkslvdegknldvivtGSnsk 103
                                                + + +pe  l++ile l+++ + ++ +DE+q++        +e+ + + + +d+ +n+ +i+tGS  +
  gi|242398720|ref|YP_002994144.1| 110 vkgvsiaglQLNFEPEVSLSEILEALNKRSRIIIAFDEAQYLrfygrrggKEFLTLVAYAYDNLPNISFIFTGSEIG 186
                                       66655544211113334445555554446888899*****************************************9 PP

                            AAA_14 104 llskeia.....tslagrva.eielypls 126
                                       ll   i      + l gr+  ei++ p+s
  gi|242398720|ref|YP_002994144.1| 187 LLHDLIGvsdyeSPLYGRIYnEITISPFS 215
                                       99653333444377888754378888877 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   3.6e-09   1.6e-05       6     133 ..      37     187 ..      32     191 .. 0.73

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 3.6e-09
                            AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.......sskdllrellralglelka..... 70 
                                        i+++ G   +GK+ ll+ +l++l+  +++          ++ ++        + ++ll+++ + l+    +     
  gi|242398720|ref|YP_002994144.1|  37 PITLILGIRRVGKSSLLKVVLNELKSGIYI----------DVRKLHfdsggwiTNESLLKAFENGLN----Slshpi 99 
                                       5899********************544333..........333333321113344444444444444....444458 PP

                            AAA_22  71 ....................erlsseellealeqalraravielliiDEaqhlr...s...eealeeLrsllnlsrk 121
                                                            + + e  l+ + +al++r++  ++  DEaq+lr   +   +e l+ +   ++ +  
  gi|242398720|ref|YP_002994144.1| 100 krevfqylkrvkgvsiaglqLNFEPEVSLSEILEALNKRSR-IIIAFDEAQYLRfygRrggKEFLTLVAYAYD-NLP 174
                                       88888888889999****97777777778************.***********88872566777777766666.799 PP

                            AAA_22 122 gvqliLvGtp.el 133
                                       ++++i+ G + +l
  gi|242398720|ref|YP_002994144.1| 175 NISFIFTGSEiGL 187
                                       9****99987665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   2.5e-08   0.00011       5     149 ..      22     153 ..      19     175 .. 0.67

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 2.5e-08
                            AAA_16   5 ReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareel 81 
                                       Re+e+e++++  +     + +++l+ G + vGKssl++ +l++l+      ++ + ++l    ++      +++e+l
  gi|242398720|ref|YP_002994144.1|  22 REQEIEMIKNSAK-----EYPITLILGIRRVGKSSLLKVVLNELKSG----IYIDVRKL----HF-DSGGWITNESL 84 
                                       8899988877544.....449********************988876....33333333....11.23466777788 PP

                            AAA_16  82 lrqlldeaesaeleawrekleealaavpelagaea...srllellkrllallsrderplvlvlDdlqwade 149
                                       l++ ++ ++s +  + +++  + l+ v+ ++ a+          l+++l+ l +++r +++ +D++q +++
  gi|242398720|ref|YP_002994144.1|  85 LKAFENGLNS-LSHPIKREVFQYLKRVKGVSIAGLqlnFEPEVSLSEILEALNKRSR-IIIAFDEAQYLRF 153
                                       8888877555.3333333344444444444444445566677778888866667577.********98775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); 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: 0.65u 0.33s 00:00:00.98 Elapsed: 00:00:00.54
# Mc/sec: 2073.10
//
Query:       gi|242398721|ref|YP_002994145.1|  [L=148]
Description: HAD family hydrolase, a [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      1e-05   25.5   0.5      0.029   14.1   0.1    2.1  2  Hydrolase_3  haloacid dehalogenase-like hydrolase
    0.00083   19.7   0.7      0.081   13.2   0.0    2.3  2  Hydrolase    haloacid dehalogenase-like hydrolase
     0.0011   18.7   0.1     0.0062   16.3   0.1    2.0  1  NIF          NLI interacting factor-like phosphatase
  ------ inclusion threshold ------
      0.055   13.7   0.0       0.11   12.8   0.0    1.4  1  DUF3970      Protein of unknown function (DUF3970)
      0.099   13.0   0.1       0.21   12.0   0.1    1.7  1  Ras_bdg_2    Ras-binding domain of Byr2


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 !   10.2   0.0   0.00013      0.47       1      56 [.      14      67 ..      14      74 .. 0.82
   2 !   14.1   0.1   8.2e-06     0.029     204     228 ..      84     108 ..      72     134 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00013
                                      EEEEIIIIIS-TTS---HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCS CS
                       Hydrolase_3  1 ialDlDGTLlnsdkkisektkeaikklkekgikvviATGRslravlpvleelgldl 56
                                      +++Dl GTL   ++k+ +++ke ++kl+ + +++v+ +   + ++++ ++el+++ 
  gi|242398721|ref|YP_002994145.1| 14 VIFDLNGTL-GVEGKVRKNIKELLRKLS-EKYEIVVLSSDTFGTLKDEFNELDVKI 67
                                      69******9.6777899**********9.567777777788888888888888875 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 8.2e-06
                                       GGEEEEESSGGGHHHHHHSSEEEEE CS
                       Hydrolase_3 204 eeviafGDgeNDieMLeaaglgvAm 228
                                       e  i +G+g+ND+ MLe a+l++++
  gi|242398721|ref|YP_002994145.1|  84 EPYIGVGNGNNDVRMLENAELAICV 108
                                       567889*****************98 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.4   0.3    0.0054        19       2      12 ..      12      22 ..      11      35 .. 0.82
   2 !   13.2   0.0   2.3e-05     0.081     118     209 ..      27     102 ..      23     103 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0054
                                      SEEEEESBTTT CS
                                      xxxxxxxxxxx RF
                         Hydrolase  2 ktvvfDkdGTL 12
                                      ktv+fD+ GTL
  gi|242398721|ref|YP_002994145.1| 12 KTVIFDLNGTL 22
                                      9*********9 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 2.3e-05
                                       HBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTTGGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 118 kvkpeaaeavasLkaagievvlltgdnpetaeraanqlGddyfdaviasdietvakpspegkvaaireLqgkpeeva 194
                                       kv++ ++e++++L ++ +e+v+l++d   t +   n+l+             +  +  ++g +++ + L+ +p   +
  gi|242398721|ref|YP_002994145.1|  27 KVRKNIKELLRKLSEK-YEIVVLSSDTFGTLKDEFNELD-------------VKIELVKDGNEKLQKALKYEP--YI 87 
                                       699999******9966.999************9999988.............333555667777777776677..** PP

                                       EEESSHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxx RF
                         Hydrolase 195 mVGDgvnDaaalaaA 209
                                        VG g nD+ +l++A
  gi|242398721|ref|YP_002994145.1|  88 GVGNGNNDVRMLENA 102
                                       ************998 PP

>> NIF  NLI interacting factor-like phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   1.7e-06    0.0062       2      71 ..      13      64 ..      12      73 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.7e-06
                               NIF  2 tLVLDLDetLvhsklekskklkvegekvevsvlkRpgldefLkelsklyevvifTasseeyaeavidild 71
                                      t+++DL++tL                   v  ++R+  +e+L++ls++ye+v+ ++ +  + ++  ++ld
  gi|242398721|ref|YP_002994145.1| 13 TVIFDLNGTLG------------------VEGKVRKNIKELLRKLSEKYEIVVLSSDTFGTLKDEFNELD 64
                                      56666666665..................55589*********************998777776666666 PP

>> DUF3970  Protein of unknown function (DUF3970)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     3e-05      0.11       6      32 ..      24      51 ..      22      57 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3e-05
                           DUF3970  6 laGk.qeEieeflksleknyevtytSke 32
                                      ++Gk ++ i+e+l++l+++ye+   S +
  gi|242398721|ref|YP_002994145.1| 24 VEGKvRKNIKELLRKLSEKYEIVVLSSD 51
                                      89**9****************9877765 PP

>> Ras_bdg_2  Ras-binding domain of Byr2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   5.7e-05      0.21      19      68 ..      59     107 ..      28     120 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.7e-05
                         Ras_bdg_2  19 cfnaeeikrkvlkklglkekeveeydvyvlssnekeslrlLsdvELvtic 68 
                                        fn  ++k +++k  ++k +++ +y+ y+  +n ++ +r+L ++EL  ic
  gi|242398721|ref|YP_002994145.1|  59 EFNELDVKIELVKDGNEKLQKALKYEPYIGVGNGNNDVRMLENAELA-IC 107
                                       5677788999999999999**9***********************95.55 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       930  (0.0518713); expected 358.6 (0.02)
Passed bias filter:                      691  (0.0385409); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1007.05
//
Query:       gi|242398722|ref|YP_002994146.1|  [L=178]
Description: 2(4Fe-4S) ferredoxin-domain protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.9e-18   64.4   0.0    3.1e-17   62.7   0.0    1.7  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 !   62.7   0.0   1.8e-21   3.1e-17       2     132 ..       6     164 ..       5     176 .. 0.73

  Alignments for each domain:
  == domain 1  score: 62.7 bits;  conditional E-value: 1.8e-21
                                       EEEEEE-SSCGGGCH.HHHHHHHHHTTEEEEEEESCHHHHCCHHGGS....TCSSHHHHHHCT.............. CS
                      Flavoprotein   2 killgiTGsvaaika.lellekLkkegievqvvltkaAkkfiskeklklaaredpilhielrr.............. 63 
                                       +i++g++G+ + + + +++le Lk+ ++ev+v+l+ a++++++     + +   +i +  l r              
  gi|242398722|ref|YP_002994146.1|   6 RIAWGFSGAGHLLLEsVDVLEHLKD-HHEVKVFLSSAGEEVARIY--GVLE---RIGNFPLVReskqghafpscgsf 76 
                                       8***********9999********7.*****************44..3322...34444443345567777777999 PP

                                       ...TESEEEEEEEEHHHHHHHHTT--SSHH...........HHHHHT.HCCTTEEEEE.--...HHCCTCSTCHHHH CS
                      Flavoprotein  64 ...wadllviaPasantlakianGiadnll...........tlilra.takkpiliaPamn...pamyenpqtlknl 122
                                          ++d++vi Pa+ nt+aki +Giad+ll           + ++++ t++kp++   a+n    + y ++++l+++
  gi|242398722|ref|YP_002994146.1|  77 nlgKFDVFVISPATSNTVAKIRLGIADSLLsccasqalkskVPLIMVpTDSKPVVETKAPNgkvFKIYPRKVDLEHI 153
                                       999***************************66666666655222233456666655444431114566777777777 PP

                                       HHH.HT..... CS
                      Flavoprotein 123 ekl.eegvtvi 132
                                       + l eegv+++
  gi|242398722|ref|YP_002994146.1| 154 RALkEEGVVIL 164
                                       77755666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1264.15
//
Query:       gi|242398723|ref|YP_002994147.1|  [L=231]
Description: hypothetical protein TSIB_0735 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.037   13.7   0.0      0.071   12.8   0.0    1.4  1  End_N_terminal  N terminal extension of bacteriophage endosia


Domain annotation for each model (and alignments):
>> End_N_terminal  N terminal extension of bacteriophage endosialidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     4e-06     0.071      36      64 ..     175     203 ..     172     205 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4e-06
                                       SS---GGGEES-EEEE-SSTT--EEEE-B CS
                    End_N_terminal  36 ssLPDisrfknarfvyeRiaGqPLyYvse 64 
                                       s L D+++   ar ++ R+ G  LyY s+
  gi|242398723|ref|YP_002994147.1| 175 SVLEDLNKLEAARSLWYRLDGRNLYYGSK 203
                                       7899**********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1739.48
//
Query:       gi|242398724|ref|YP_002994148.1|  [L=331]
Description: hypothetical protein TSIB_0736 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       803  (0.0447878); expected 358.6 (0.02)
Passed bias filter:                      583  (0.0325172); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2169.39
//
Query:       gi|242398725|ref|YP_002994149.1|  [L=111]
Description: hypothetical protein TSIB_0737 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       596  (0.0332422); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.28s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 796.94
//
Query:       gi|242398726|ref|YP_002994150.1|  [L=138]
Description: nickel-responsive regulator [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-33  113.5   5.2    5.5e-33  113.0   5.2    1.3  1  NikR_C           NikR C terminal nickel binding domain
    4.8e-07   29.5   0.0    9.7e-07   28.5   0.0    1.6  1  RHH_1            Ribbon-helix-helix protein, copG family
  ------ inclusion threshold ------
      0.044   13.9   0.1       0.13   12.4   0.0    1.8  3  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit
      0.099   12.7   0.1        0.4   10.8   0.0    1.8  2  TFIID-31kDa      Transcription initiation factor IID, 31kD su


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 !  113.0   5.2   1.2e-36   5.5e-33       1      77 []      55     131 ..      55     131 .. 0.99

  Alignments for each domain:
  == domain 1  score: 113.0 bits;  conditional E-value: 1.2e-36
                                       EEEEEEEEETTSTTHHHHHHHHHHHHSSEEEEEEEEEESSSEEEEEEEEEE-HHHHHHHHHHHHTSTTEEEEEEEEE CS
                            NikR_C   1 vGvitivydhhqrelserltdiqheyhdliisslhvhldhdncLevivlkGeaeeikelaeklralkgVkhvkltli 77 
                                       +G+itivy+h++ ++ ++l d+qh+y ++iisslhvh+d++ncLeviv+kG+++++k++ae+l++lkgVkh+kl+++
  gi|242398726|ref|YP_002994150.1|  55 AGTITIVYNHDEADVVKELLDMQHDYVNEIISSLHVHMDEHNCLEVIVVKGKGSRVKTIAERLISLKGVKHGKLVMT 131
                                       69************************************************************************996 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 !   28.5   0.0   2.2e-10   9.7e-07       1      38 [.       5      43 ..       5      44 .. 0.95

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 2.2e-10
                                      EEEEEEEHHHHHHHHHHHHHHT.SSHHHHHHHHHHHHHH CS
                             RHH_1  1 rvsirldeellerLdelarrrg.rSrSelIReAlreyle 38
                                      r+ ++++e+lle++d + ++ g  +rSe+IR+++r+++ 
  gi|242398726|ref|YP_002994150.1|  5 RFGVSMPEDLLEKFDTIMEEKGyANRSEAIRDLVRDFIV 43
                                      789********************************9985 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 ?   12.4   0.0   2.9e-05      0.13      89     119 ..       3      34 ..       1      38 [. 0.87
   2 ?   -1.4   0.0      0.53   2.4e+03      60      60 ..      87      87 ..      53     106 .. 0.57
   3 ?   -3.0   0.0       1.7   7.4e+03       4      17 ..      89     102 ..      86     113 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.9e-05
                   HicB_lk_antitox  89 aeriNitlpervlkriDaavkaag.esRSgfl 119
                                         r+ +++pe++l++ D++++++g  +RS  +
  gi|242398726|ref|YP_002994150.1|   3 IIRFGVSMPEDLLEKFDTIMEEKGyANRSEAI 34 
                                       57999*******************669*9876 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.53
                   HicB_lk_antitox 60 s 60
                                      s
  gi|242398726|ref|YP_002994150.1| 87 S 87
                                      2 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 1.7
                   HicB_lk_antitox   4 aiekdedsaygvvv 17 
                                        +++de+++  v+v
  gi|242398726|ref|YP_002994150.1|  89 HVHMDEHNCLEVIV 102
                                       46777777777766 PP

>> TFIID-31kDa  Transcription initiation factor IID, 31kD subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.25   1.1e+03      12      38 ..      19      45 ..       9      48 .. 0.82
   2 ?   10.8   0.0   8.9e-05       0.4      24      53 ..      66      95 ..      60     126 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.25
                       TFIID-31kDa 12 hliLaslgvteyeerVvlqLldfayry 38
                                        i+++ g  + +e + + + df+ r+
  gi|242398726|ref|YP_002994150.1| 19 DTIMEEKGYANRSEAIRDLVRDFIVRH 45
                                      679999999999999999999999998 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 8.9e-05
                       TFIID-31kDa 24 eerVvlqLldfayrytssvLedAkvlaeha 53
                                      e +Vv+ Lld+ + y+ ++++  +v +++ 
  gi|242398726|ref|YP_002994150.1| 66 EADVVKELLDMQHDYVNEIISSLHVHMDEH 95
                                      679*****************9766655544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1111.77
//
Query:       gi|242398727|ref|YP_002994151.1|  [L=52]
Description: hypothetical protein TSIB_0740 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (52 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       221  (0.0123264); expected 358.6 (0.02)
Passed bias filter:                      168  (0.00937029); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 365.27
//
Query:       gi|242398728|ref|YP_002994152.1|  [L=620]
Description: calcium-binding protein [Thermococcus sibiricus MM 739]
Scores for 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  169.8   1.9      5e-50  169.0   1.9    1.4  1  DUF553          Transglutaminase-like domain
  ------ inclusion threshold ------
      0.015   15.8   0.0       0.11   13.0   0.0    2.1  1  Transglut_core  Transglutaminase-like superfamily
      0.033   13.9   0.0      0.067   12.9   0.0    1.4  1  PliI            Periplasmic lysozyme inhibitor of I-type lyso
       0.26   11.5  33.3       0.38   11.0   4.9    6.3  6  Binary_toxB     Clostridial binary toxin B/anthrax toxin PA C
       0.34   11.2   1.6       0.39   11.0   0.0    2.0  2  DndE            DNA sulphur modification protein DndE


Domain annotation for each model (and alignments):
>> DUF553  Transglutaminase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.0   1.9   1.4e-53     5e-50       2     154 .]     296     450 ..     295     450 .. 0.98

  Alignments for each domain:
  == domain 1  score: 169.0 bits;  conditional E-value: 1.4e-53
                            DUF553   2 klkklaekl.kkensketiinvlewvdenikYdyekaevvetllvlWatfftlskvdskilklietpkeilktkkgi 77 
                                       +++ +++++ +++++ + ++++lew+deni+Y+y+k +++e ++++W+t+   +++ +k+l+++++ ++++ +k gi
  gi|242398728|ref|YP_002994152.1| 296 EVSPVSKQFmEYNTTLDRAWAILEWIDENIQYNYTKLDLIEEMVYNWSTLSGHERELYKKLTRLQAANDTIYRKSGI 372
                                       67889999989999*************************************************************** PP

                            DUF553  78 CrDYaiLTaalLlnlniskvylvsvtfenskvgHaavavkidgtyfvlDqklpiikideylkkllk.kvkiitevei 153
                                       C DYaiLTaalLl++nis+vy++++++++++vgH +va+kid +yfvlDq+lp+ +i++y+ ++l+ ++ +i++v++
  gi|242398728|ref|YP_002994152.1| 373 CGDYAILTAALLLESNISPVYMLDINYKDKEVGHNTVAIKIDSEYFVLDQHLPMKPIGNYYWDSLRaEMGEIANVTF 449
                                       *************************************************************999999999******9 PP

                            DUF553 154 y 154
                                       y
  gi|242398728|ref|YP_002994152.1| 450 Y 450
                                       9 PP

>> Transglut_core  Transglutaminase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0     3e-05      0.11      11      75 ..     325     394 ..     301     423 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3e-05
                    Transglut_core  11 akdplekakaiyewvrknveys.....aprrtpgsrdaeavletgkGncedfaslfvallRalGipaRvv 75 
                                        +  ++k+  i+e v +  + s      +++ ++ + a++++  ++G c d+a l +all  + i   ++
  gi|242398728|ref|YP_002994152.1| 325 IQYNYTKLDLIEEMVYNWSTLSghereLYKKLTRLQAANDTIYRKSGICGDYAILTAALLLESNISPVYM 394
                                       3334444444444444333333543333344444444**********************99888865555 PP

>> PliI  Periplasmic lysozyme inhibitor of I-type lysozyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.9e-05     0.067      43     106 ..     428     491 ..     417     496 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.9e-05
                                       TTSSEEEEEEEEESSEEEEEEEE-SSSSSS-EEEEEEE-SSTT--EEEEEEEEETTTEEEEEEE CS
                              PliI  43 dldefvaGlvlsRdGsveevkladvngdkkkelvvlkrsaGsGsylsvdAfkitkkslkllasv 106
                                       ++ ++    +++  G + +v++  ++ d++ e +++ +   +G +++ +A+++t+k+++++ ++
  gi|242398728|ref|YP_002994152.1| 428 PIGNYYWDSLRAEMGEIANVTFYIIKLDENGEPIIYSNWIWTGKFMKKKAYTMTEKDIDFIIEL 491
                                       55566666788889********************************************999876 PP

>> Binary_toxB  Clostridial binary toxin B/anthrax toxin PA Ca-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   2.6    0.0017       6.3      29      60 ..      69     100 ..      44     109 .. 0.76
   2 ?   11.0   4.9   0.00011      0.38       1      60 [.      64     123 ..      64     132 .. 0.91
   3 ?    8.6   7.3   0.00059       2.1       2      61 ..     111     169 ..     110     176 .. 0.88
   4 ?    5.6   7.3    0.0052        18       1      59 [.     132     190 ..     132     196 .. 0.88
   5 ?   -1.1   8.8      0.62   2.2e+03       1      56 [.     178     232 ..     155     241 .. 0.60
   6 ?    1.9   0.0     0.074   2.6e+02       2      15 ..     254     267 ..     253     291 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0017
                                       TTHHHHHT---B---TT-SSTTSSSS-HHHHH CS
                       Binary_toxB  29 dklaekkgltkyvsdpnksstagDPysDlekv 60 
                                       dk+ + ++++ky +dp k+ ++ D  +D e+ 
  gi|242398728|ref|YP_002994152.1|  69 DKIIDGDEVHKYHTDPLKVDSDEDGLTDYEEL 100
                                       44555558899999999999999999999875 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00011
                                       --SSSSSS-HHHHHH-EEEESEEEEE--TTHHHHHT---B---TT-SSTTSSSS-HHHHH CS
                       Binary_toxB   1 lDsDdDgipdslEvnGYtldktllvPwvdklaekkgltkyvsdpnksstagDPysDlekv 60 
                                       +D+D+D i d  Ev  Y  d   ++  +d l++ ++l  y ++p ++ t+gD   D  +v
  gi|242398728|ref|YP_002994152.1|  64 PDTDGDKIIDGDEVHKYHTDPLKVDSDEDGLTDYEELFEYNTNPLDVDTDGDGLRDNVEV 123
                                       69**************************************************98886666 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.00059
                                       -SSSSSS-HHHHHH-EEEESEEEEE--TTHHHHHT---B---TT-SSTTSSSS-HHHHHH CS
                       Binary_toxB   2 DsDdDgipdslEvnGYtldktllvPwvdklaekkgltkyvsdpnksstagDPysDlekvs 61 
                                       D+D+Dg+ d+ Ev+    d tl +   d++ + ++++ y ++p    t+gD  +D +++ 
  gi|242398728|ref|YP_002994152.1| 111 DTDGDGLRDNVEVEKG-TDPTLEDTDGDNIVDADEVNTYFTNPLSQDTDGDGLTDYAEIF 169
                                       9************965.47777788888899999*********************99985 PP

  == domain 4  score: 5.6 bits;  conditional E-value: 0.0052
                                       --SSSSSS-HHHHHH-EEEESEEEEE--TTHHHHHT---B---TT-SSTTSSSS-HHHH CS
                       Binary_toxB   1 lDsDdDgipdslEvnGYtldktllvPwvdklaekkgltkyvsdpnksstagDPysDlek 59 
                                       +D+D+D i d  Evn Y+ +  + +   d l++  ++  y ++p+   ++gD   D ++
  gi|242398728|ref|YP_002994152.1| 132 EDTDGDNIVDADEVNTYFTNPLSQDTDGDGLTDYAEIFTYNTSPTTEDSDGDGMDDSAE 190
                                       59****************999999999999999999999*****999999998888665 PP

  == domain 5  score: -1.1 bits;  conditional E-value: 0.62
                                       --SSSSSS-HHHHHH-EEEESEEEEE--TTHHHHHT---B---TT-SSTTSSSS-H CS
                       Binary_toxB   1 lDsDdDgipdslEvnGYtldktllvPwvdklaekkgltkyvsdpnksstagDPysD 56 
                                       +DsD+Dg+ ds E++  t +  l +  +d l + ++l ky +dp +  ++ D   D
  gi|242398728|ref|YP_002994152.1| 178 EDSDGDGMDDSAELELKT-NPLLEDTDNDRLWDGEELVKYHTDPLNPDSDDDGLLD 232
                                       366666666666665222.2222233334444445899999999998888886666 PP

  == domain 6  score: 1.9 bits;  conditional E-value: 0.074
                                       -SSSSSS-HHHHHH CS
                       Binary_toxB   2 DsDdDgipdslEvn 15 
                                       DsD+D +pd +Ev+
  gi|242398728|ref|YP_002994152.1| 254 DSDGDYLPDGYEVK 267
                                       9********99985 PP

>> DndE  DNA sulphur modification protein DndE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00011      0.39      30      82 ..     315     367 ..     302     384 .. 0.90
   2 ?   -3.2   0.4       2.8     1e+04       3      19 ..     508     524 ..     508     529 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00011
                              DndE  30 iAlfrSLeegkkpdakeikddsglelnkktllGeyqdifeallkqrcqkdgle 82 
                                       +A++  + e+ +++ ++ +  + +++n++tl G+++++++ l + ++ +d ++
  gi|242398728|ref|YP_002994152.1| 315 WAILEWIDENIQYNYTKLDLIEEMVYNWSTLSGHERELYKKLTRLQAANDTIY 367
                                       9999999***********************************99777666665 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2.8
                              DndE   3 klSkeakeqLkkLkrrt 19 
                                       +l ++a++qLk++k+  
  gi|242398728|ref|YP_002994152.1| 508 RLKQNAETQLKSIKSTN 524
                                       56788999999999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (620 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.70u 0.31s 00:00:01.01 Elapsed: 00:00:00.50
# Mc/sec: 3708.35
//
Query:       gi|242398729|ref|YP_002994153.1|  [L=510]
Description: hypothetical protein TSIB_0743 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.6e-14   53.9  28.4    0.00083   19.6   0.1    8.2  7  DUF5122    Domain of unknown function (DUF5122) beta-propelle
    0.00012   22.2  11.1        2.4    8.5   0.2    5.7  6  Kelch_3    Galactose oxidase, central domain
    0.00025   20.7   6.1         38    4.1   0.0    6.1  6  RHS        RHS protein
     0.0031   18.3   6.9         10    7.1   0.1    5.6  5  WD40       WD domain, G-beta repeat
     0.0066   16.4  23.9        2.7    8.2   0.3    6.9  6  NHL        NHL repeat
  ------ inclusion threshold ------
      0.012   15.8   4.2        1.5    9.0   0.1    4.3  4  Tox-HDC    Toxin with a H, D/N and C signature
      0.023   14.6  14.7         26    5.0   0.1    6.2  6  PQQ        PQQ enzyme repeat
       0.26   11.7   6.5       0.45   11.0   6.5    1.3  1  MGC-24     Multi-glycosylated core protein 24 (MGC-24), sialo
       0.38   11.1   7.2         59    4.2   0.0    5.9  7  Kelch_6    Kelch motif
       0.73    8.0  11.8          1    7.5  11.8    1.1  1  SSP160     Special lobe-specific silk protein SSP160
        1.4    8.9  11.3        2.6    8.0  11.3    1.3  1  DUF3439    Domain of unknown function (DUF3439)
        1.5    8.9  18.1        3.1    7.8  18.1    1.5  1  Mucin      Mucin-like glycoprotein
        5.8    7.6  30.3        3.6    8.2   0.8    6.6  6  VCBS       Repeat domain in Vibrio, Colwellia, Bradyrhizobium


Domain annotation for each model (and alignments):
>> DUF5122  Domain of unknown function (DUF5122) beta-propeller
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.3    0.0042       5.7       2      31 ..      50      80 ..      49      81 .. 0.89
   2 !   13.2   0.1   5.9e-05     0.082       2      31 ..     102     132 ..     101     133 .. 0.92
   3 !   19.6   0.1     6e-07   0.00083       2      31 ..     154     184 ..     153     185 .. 0.93
   4 !   12.2   0.2   0.00012      0.17       3      32 ..     207     237 ..     206     237 .. 0.91
   5 !    7.0   0.5    0.0053       7.4       3      32 ..     259     288 ..     258     288 .. 0.93
   6 ?    2.6   0.5      0.13   1.7e+02       3      30 ..     310     341 ..     309     343 .. 0.62
   7 !    7.4   0.1     0.004       5.5       6      30 ..     368     393 ..     366     395 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0042
                           DUF5122  2 pDGKIlVaGsftsy.ngssdfalvRLnaDGs 31
                                      p+G ++VaG ++s  +g +d  ++RL+  G+
  gi|242398729|ref|YP_002994153.1| 50 PNGDVIVAGATGSFgAGKGDVWVLRLDEKGN 80
                                      8999********667***********98776 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 5.9e-05
                           DUF5122   2 pDGKIlVaGsftsy.ngssdfalvRLnaDGs 31 
                                       p+G I+VaG ++s   g +d  ++RL+ +G+
  gi|242398729|ref|YP_002994153.1| 102 PNGDIIVAGLTWSFgTGKTDAWILRLDENGN 132
                                       89**********667***************8 PP

  == domain 3  score: 19.6 bits;  conditional E-value: 6e-07
                           DUF5122   2 pDGKIlVaGsftsy.ngssdfalvRLnaDGs 31 
                                       p+G I+VaG++ s  +g +df ++RL+ +G+
  gi|242398729|ref|YP_002994153.1| 154 PNGDIIVAGYTESFgAGENDFWVLRLDENGN 184
                                       89**********667***************8 PP

  == domain 4  score: 12.2 bits;  conditional E-value: 0.00012
                           DUF5122   3 DGKIlVaGsftsy.ngssdfalvRLnaDGsl 32 
                                       D+ ++VaGs+ s  +g +d  ++RL+ +G+l
  gi|242398729|ref|YP_002994153.1| 207 DNDVIVAGSTASFgGGAQDLWILRLDENGNL 237
                                       77799******667***************97 PP

  == domain 5  score: 7.0 bits;  conditional E-value: 0.0053
                           DUF5122   3 DGKIlVaGsftsyngssdfalvRLnaDGsl 32 
                                       +G I+VaG  +  +g +d  ++RL+a G+l
  gi|242398729|ref|YP_002994153.1| 259 NGDIIVAGMAGFGAGKGDVWVLRLDAEGNL 288
                                       688********88***************97 PP

  == domain 6  score: 2.6 bits;  conditional E-value: 0.13
                           DUF5122   3 DGKIlVaGsftsy....ngssdfalvRLnaDG 30 
                                       +G I+VaG + s      + ++  ++RL+ +G
  gi|242398729|ref|YP_002994153.1| 310 NGDIIVAGATASFgtgtPDYPNAWVLRLDENG 341
                                       57899999999775544333333355666666 PP

  == domain 7  score: 7.4 bits;  conditional E-value: 0.004
                           DUF5122   6 IlVaGsft.syngssdfalvRLnaDG 30 
                                       I+VaG ++ s  g  df ++R+ +DG
  gi|242398729|ref|YP_002994153.1| 368 IIVAGITNsSGTGKDDFWVLRFPPDG 393
                                       9*******666**************9 PP

>> Kelch_3  Galactose oxidase, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.016        22       8      35 ..      57      89 ..      52      99 .. 0.69
   2 ?   -3.1   0.0       7.7   1.1e+04      24      34 ..     125     138 ..     116     147 .. 0.66
   3 !    8.5   0.2    0.0017       2.4       9      35 ..     162     193 ..     158     203 .. 0.77
   4 ?   -1.9   0.0       3.2   4.4e+03      20      34 ..     225     242 ..     211     249 .. 0.71
   5 ?    3.9   0.0      0.05        69      19      34 ..     275     293 ..     269     303 .. 0.83
   6 !    6.8   0.1    0.0059       8.2       7      33 ..     315     347 ..     313     357 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.016
                           Kelch_3  8 GGlgddgqdrl..ndvyvydldtn...tWaei..a 35
                                       G++  g  +   +dv+v+ ld     +W+++  +
  gi|242398729|ref|YP_002994153.1| 57 AGAT--GSFGAgkGDVWVLRLDEKgniKWQKTcgG 89
                                      5555..43333449*******88889999977652 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 7.7
                           Kelch_3  24 ydldtn...tWaei 34 
                                       + ld n   +W+++
  gi|242398729|ref|YP_002994153.1| 125 LRLDENgnvKWQKT 138
                                       44444444899976 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0017
                           Kelch_3   9 Glgddgqdrlndvyvydldtn...tWaei..a 35 
                                       G++ + + ++nd++v+ ld n   +W+++  +
  gi|242398729|ref|YP_002994153.1| 162 GYTESFGAGENDFWVLRLDENgnvKWQKTygG 193
                                       5664336789********99999***988664 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 3.2
                           Kelch_3  20 dvyvydldtn...tWaei 34 
                                       d++ + ld n   +W+++
  gi|242398729|ref|YP_002994153.1| 225 DLWILRLDENgnlKWQKT 242
                                       677555655555899876 PP

  == domain 5  score: 3.9 bits;  conditional E-value: 0.05
                           Kelch_3  19 ndvyvydldtn...tWaei 34 
                                       +dv+v+ ld++   +W+++
  gi|242398729|ref|YP_002994153.1| 275 GDVWVLRLDAEgnlKWQKT 293
                                       79******999999**987 PP

  == domain 6  score: 6.8 bits;  conditional E-value: 0.0059
                           Kelch_3   7 fGGlgd...dgqdrlndvyvydldtn...tWae 33 
                                       + G+++   +g++ + + +v+ ld n   +W++
  gi|242398729|ref|YP_002994153.1| 315 VAGATAsfgTGTPDYPNAWVLRLDENgnvKWQK 347
                                       56677777799************9999999996 PP

>> RHS  RHS protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.44     6e+02      17      25 ..      76      84 ..      75      87 .. 0.90
   2 ?    4.1   0.0     0.027        38      17      28 ..     128     139 ..     127     141 .. 0.89
   3 ?    4.1   0.0     0.027        38      17      28 ..     180     191 ..     179     193 .. 0.89
   4 ?    3.1   0.0     0.057        79      17      28 ..     232     243 ..     231     245 .. 0.89
   5 ?    2.2   0.0      0.11   1.5e+02      17      28 ..     283     294 ..     282     296 .. 0.89
   6 ?    3.1   0.1     0.059        81      17      28 ..     338     349 ..     337     351 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.44
                               RHS 17 DanGeivWa 25
                                      D+ G+i W+
  gi|242398729|ref|YP_002994153.1| 76 DEKGNIKWQ 84
                                      9*******8 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.027
                               RHS  17 DanGeivWaaey 28 
                                       D+nG++ W+ +y
  gi|242398729|ref|YP_002994153.1| 128 DENGNVKWQKTY 139
                                       9********888 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.027
                               RHS  17 DanGeivWaaey 28 
                                       D+nG++ W+ +y
  gi|242398729|ref|YP_002994153.1| 180 DENGNVKWQKTY 191
                                       9********888 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.057
                               RHS  17 DanGeivWaaey 28 
                                       D+nG++ W+ +y
  gi|242398729|ref|YP_002994153.1| 232 DENGNLKWQKTY 243
                                       9********888 PP

  == domain 5  score: 2.2 bits;  conditional E-value: 0.11
                               RHS  17 DanGeivWaaey 28 
                                       Da+G++ W+ +y
  gi|242398729|ref|YP_002994153.1| 283 DAEGNLKWQKTY 294
                                       9********888 PP

  == domain 6  score: 3.1 bits;  conditional E-value: 0.059
                               RHS  17 DanGeivWaaey 28 
                                       D+nG++ W+  y
  gi|242398729|ref|YP_002994153.1| 338 DENGNVKWQKAY 349
                                       9*******9766 PP

>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.1    0.0076        10       4      29 ..      32      59 ..      31      71 .. 0.86
   2 ?    2.1   0.1      0.31   4.2e+02       6      28 ..      86     110 ..      81     119 .. 0.76
   3 ?    3.7   0.0     0.096   1.3e+02       4      29 ..     136     163 ..     134     169 .. 0.79
   4 ?    2.7   0.1      0.19   2.6e+02       4      29 ..     188     215 ..     186     220 .. 0.83
   5 ?    0.3   0.0       1.1   1.5e+03       4      29 ..     240     267 ..     237     277 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0076
                                      EEEEESS.SSE.EEEEEETTSSEEEEEE CS
                              WD40  4 lrtltGH.ssv.tslafspdgawlasGs 29
                                      ++t+ G  ++v +++a+ p+g+ +++G 
  gi|242398729|ref|YP_002994153.1| 32 VKTYGGSdFDVaNAVAVAPNGDVIVAGA 59
                                      579999977899************9874 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.31
                                       EEESS.SS.EEEEEEETTSSEEEEE CS
                              WD40   6 tltGH.ss.vtslafspdgawlasG 28 
                                       t+ G  ++  +++a+ p+g+ +++G
  gi|242398729|ref|YP_002994153.1|  86 TCGGSdGDgAHAVAVAPNGDIIVAG 110
                                       555554224689999*******998 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.096
                                       EEEEESSSS..E.EEEEEETTSSEEEEEE CS
                              WD40   4 lrtltGHss..v.tslafspdgawlasGs 29 
                                       ++t+ G  +  v +++a  p+g+ +++G 
  gi|242398729|ref|YP_002994153.1| 136 QKTYGGS-FidVtSAVAIAPNGDIIVAGY 163
                                       5677777.334867999********9984 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.19
                                       EEEEESS..SSEEEEEEETTSSEEEEEE CS
                              WD40   4 lrtltGH..ssvtslafspdgawlasGs 29 
                                       ++t+ G   ++ t +a+s d++ +++Gs
  gi|242398729|ref|YP_002994153.1| 188 QKTYGGSsyDDATTVAVSEDNDVIVAGS 215
                                       56777775555899***********998 PP

  == domain 5  score: 0.3 bits;  conditional E-value: 1.1
                                       EEEEESS.SSE.EEEEEETTSSEEEEEE CS
                              WD40   4 lrtltGH.ssv.tslafspdgawlasGs 29 
                                       ++t+ G  + v +++ + ++g+ +++G+
  gi|242398729|ref|YP_002994153.1| 240 QKTYGGGdFEVaNAVVVADNGDIIVAGM 267
                                       567766644588999999*****99984 PP

>> NHL  NHL repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.5    0.0072       9.9       4      18 ..      43      57 ..      40      57 .. 0.85
   2 !    8.2   0.3    0.0019       2.7       4      18 ..      95     109 ..      93     109 .. 0.91
   3 ?    4.5   0.1     0.028        39       7      18 ..     150     161 ..     148     162 .. 0.92
   4 ?    4.0   0.2     0.043        59       5      18 ..     200     213 ..     197     213 .. 0.88
   5 ?    5.1   0.4     0.019        27       6      18 ..     253     265 ..     248     265 .. 0.84
   6 ?    0.3   0.1       0.6   8.3e+02      10      18 ..     307     316 ..     302     316 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0072
                                      EEEEEEETTTEEEEE CS
                               NHL  4 PhGvavdsnGdiyVa 18
                                      ++ vav +nGd++Va
  gi|242398729|ref|YP_002994153.1| 43 ANAVAVAPNGDVIVA 57
                                      6789**********8 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0019
                                       EEEEEEETTTEEEEE CS
                               NHL   4 PhGvavdsnGdiyVa 18 
                                       +h vav +nGdi+Va
  gi|242398729|ref|YP_002994153.1|  95 AHAVAVAPNGDIIVA 109
                                       699***********8 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.028
                                       EEEETTTEEEEE CS
                               NHL   7 vavdsnGdiyVa 18 
                                       va+ +nGdi+Va
  gi|242398729|ref|YP_002994153.1| 150 VAIAPNGDIIVA 161
                                       899********8 PP

  == domain 4  score: 4.0 bits;  conditional E-value: 0.043
                                       EEEEEETTTEEEEE CS
                               NHL   5 hGvavdsnGdiyVa 18 
                                       + vav+ ++d++Va
  gi|242398729|ref|YP_002994153.1| 200 TTVAVSEDNDVIVA 213
                                       679**********8 PP

  == domain 5  score: 5.1 bits;  conditional E-value: 0.019
                                       EEEEETTTEEEEE CS
                               NHL   6 GvavdsnGdiyVa 18 
                                        v+v +nGdi+Va
  gi|242398729|ref|YP_002994153.1| 253 AVVVADNGDIIVA 265
                                       58899*******8 PP

  == domain 6  score: 0.3 bits;  conditional E-value: 0.6
                                       E.TTTEEEEE CS
                               NHL  10 d.snGdiyVa 18 
                                       +  nGdi+Va
  gi|242398729|ref|YP_002994153.1| 307 LtENGDIIVA 316
                                       4489*****8 PP

>> Tox-HDC  Toxin with a H, D/N and C signature
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1    0.0011       1.5      23      58 ..      44      81 ..      33      91 .. 0.80
   2 ?    2.3   0.1      0.13   1.7e+02      25      57 ..      98     132 ..      88     142 .. 0.79
   3 ?    1.2   0.0      0.28   3.9e+02      24      56 ..     149     183 ..     140     193 .. 0.69
   4 ?    0.3   0.1      0.54   7.5e+02      28      59 ..     257     289 ..     242     298 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0011
                           Tox-HDC 23 ekiskkPngdivil..sGshGsnlgenwlpngkregel 58
                                      ++++  Pngd+ +   +Gs G+ +g+ w+     +g++
  gi|242398729|ref|YP_002994153.1| 44 NAVAVAPNGDVIVAgaTGSFGAGKGDVWVLRLDEKGNI 81
                                      678889****9985449************776666666 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.13
                           Tox-HDC  25 iskkPngdivi..lsGshGsnlgenwlpngkrege 57 
                                       ++  Pngdi +  l+ s G+ + + w+     +g+
  gi|242398729|ref|YP_002994153.1|  98 VAVAPNGDIIVagLTWSFGTGKTDAWILRLDENGN 132
                                       6678****988668999***999***965555554 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.28
                           Tox-HDC  24 kiskkPngdivil..sGshGsnlgenwlpngkreg 56 
                                       +++  Pngdi +   + s G+   + w+     +g
  gi|242398729|ref|YP_002994153.1| 149 AVAIAPNGDIIVAgyTESFGAGENDFWVLRLDENG 183
                                       56778****98852256778766667996554444 PP

  == domain 4  score: 0.3 bits;  conditional E-value: 0.54
                           Tox-HDC  28 kPngdivilsGs..hGsnlgenwlpngkregelr 59 
                                         ngdi + +G    G+ +g+ w+     eg+l+
  gi|242398729|ref|YP_002994153.1| 257 ADNGDIIV-AGMagFGAGKGDVWVLRLDAEGNLK 289
                                       55899855.554116778899***8777777765 PP

>> PQQ  PQQ enzyme repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       2.1   2.9e+03      20      27 ..      79      86 ..      75      92 .. 0.80
   2 ?    4.5   0.0     0.027        37      15      30 ..     127     141 ..     124     144 .. 0.86
   3 ?    5.0   0.1     0.019        26      15      31 ..     179     194 ..     177     200 .. 0.84
   4 ?    4.4   0.1     0.029        41      15      32 ..     231     247 ..     229     249 .. 0.87
   5 ?    0.2   0.0       0.6   8.3e+02      18      30 ..     284     296 ..     280     297 .. 0.80
   6 ?    4.9   0.1      0.02        28      15      32 ..     337     353 ..     335     355 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 2.1
                                      CCEEEEEE CS
                               PQQ 20 GkvlWrfk 27
                                      G+++W++ 
  gi|242398729|ref|YP_002994153.1| 79 GNIKWQKT 86
                                      99***975 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.027
                                       EETTTCCEEEEEESSS CS
                               PQQ  15 lDadTGkvlWrfktgg 30 
                                       lD ++G+v+W++  gg
  gi|242398729|ref|YP_002994153.1| 127 LD-ENGNVKWQKTYGG 141
                                       67.99******98876 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.019
                                       EETTTCCEEEEEESSSC CS
                               PQQ  15 lDadTGkvlWrfktggp 31 
                                       lD ++G+v+W++  gg 
  gi|242398729|ref|YP_002994153.1| 179 LD-ENGNVKWQKTYGGS 194
                                       67.89******998886 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.029
                                       EETTTCCEEEEEESSSCG CS
                               PQQ  15 lDadTGkvlWrfktggpv 32 
                                       lD ++G+++W++  gg +
  gi|242398729|ref|YP_002994153.1| 231 LD-ENGNLKWQKTYGGGD 247
                                       67.89******9999875 PP

  == domain 5  score: 0.2 bits;  conditional E-value: 0.6
                                       TTCCEEEEEESSS CS
                               PQQ  18 dTGkvlWrfktgg 30 
                                       + G+++W++  gg
  gi|242398729|ref|YP_002994153.1| 284 AEGNLKWQKTYGG 296
                                       569*****98775 PP

  == domain 6  score: 4.9 bits;  conditional E-value: 0.02
                                       EETTTCCEEEEEESSSCG CS
                               PQQ  15 lDadTGkvlWrfktggpv 32 
                                       lD ++G+v+W++  gg +
  gi|242398729|ref|YP_002994153.1| 337 LD-ENGNVKWQKAYGGSD 353
                                       67.89******9988866 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 ?   11.0   6.5   0.00033      0.45      34     114 ..     421     502 ..     399     505 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00033
                            MGC-24  34 csenstvedCsvvnvtelcsaaskstpkptnstaktttkpsstttstsva.tsgttnttvtptsqparkstFDaAsF 109
                                       + +++ v d +++  ++ +  ++ ++ ++ ++t++ttt++++t+t+t+++  + +t+tt   +s+     tF     
  gi|242398729|ref|YP_002994153.1| 421 SDSEARVMDSNAIVLNSKAIITKVIELETLKTTTTTTTTETTTSTATTTTsQEQATETTEEENSDICGPATFLVFVL 497
                                       33333443333333333333333333344444555555555555555555366677788888888889999999999 PP

                            MGC-24 110 iGGiv 114
                                       iGG+v
  gi|242398729|ref|YP_002994153.1| 498 IGGVV 502
                                       99998 PP

>> Kelch_6  Kelch motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.043        59       7      38 ..      47      78 ..      40      88 .. 0.78
   2 ?    0.5   0.0      0.61   8.4e+02       7      35 ..      99     127 ..      94     140 .. 0.65
   3 ?    0.3   0.0       0.7   9.6e+02      16      37 ..     159     181 ..     148     190 .. 0.70
   4 ?   -0.4   0.0       1.2   1.7e+03      17      36 ..     219     232 ..     202     246 .. 0.53
   5 ?    2.3   0.0      0.16   2.2e+02       7      41 ..     255     291 ..     250     296 .. 0.71
   6 ?   -1.9   0.0       3.5   4.8e+03      23      41 ..     322     346 ..     307     354 .. 0.62
   7 ?   -1.2   0.0       2.1   2.9e+03      11      34 ..     365     388 ..     359     390 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.043
                           Kelch_6  7 lvsvggkiYifGGytdsspylnkvwvydpetk 38
                                      +v+++g + ++G  +  +    +vwv++++ k
  gi|242398729|ref|YP_002994153.1| 47 AVAPNGDVIVAGATGSFGAGKGDVWVLRLDEK 78
                                      488999******99988999999999998754 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.61
                           Kelch_6   7 lvsvggkiYifGGytdsspylnkvwvydp 35 
                                       +v+++g i ++G     ++   + w++++
  gi|242398729|ref|YP_002994153.1|  99 AVAPNGDIIVAGLTWSFGTGKTDAWILRL 127
                                       47799999999977766555555555554 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.7
                           Kelch_6  16 ifGGytds.spylnkvwvydpet 37 
                                       i+ Gyt s +   n++wv++++ 
  gi|242398729|ref|YP_002994153.1| 159 IVAGYTESfGAGENDFWVLRLDE 181
                                       45566667788889999998874 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 1.2
                           Kelch_6  17 fGGytdsspylnkvwvydpe 36 
                                       fGG         ++w+++++
  gi|242398729|ref|YP_002994153.1| 219 FGGG------AQDLWILRLD 232
                                       3333......3455665554 PP

  == domain 5  score: 2.3 bits;  conditional E-value: 0.16
                           Kelch_6   7 lvsvggkiYifGGytdsspylnkvwvydpe...tksWe 41 
                                       +v+ +g i ++G ++  +    +vwv++++   + +W+
  gi|242398729|ref|YP_002994153.1| 255 VVADNGDIIVAGMAGF-GAGKGDVWVLRLDaegNLKWQ 291
                                       3556679****99987.788899999887644344555 PP

  == domain 6  score: -1.9 bits;  conditional E-value: 3.5
                           Kelch_6  23 s.....spylnkvwvydpetks.We 41 
                                             + +   v+++d   ++ W+
  gi|242398729|ref|YP_002994153.1| 322 FgtgtpDYPNAWVLRLDENGNVkWQ 346
                                       2444446677777777766663366 PP

  == domain 7  score: -1.2 bits;  conditional E-value: 2.1
                           Kelch_6  11 ggkiYifGGytdsspylnkvwvyd 34 
                                       ++ i ++G  + s++  +++wv++
  gi|242398729|ref|YP_002994153.1| 365 NSDIIVAGITNSSGTGKDDFWVLR 388
                                       667777777777699999999986 PP

>> SSP160  Special lobe-specific silk protein SSP160
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5  11.8   0.00075         1     647     711 ..     424     489 ..     398     503 .. 0.61

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00075
                            SSP160 647 esslaeaavilemyeaayqncvdpgsvpdeattttsstttttttttta.aptttttkaanapftyp 711
                                       e+ + ++ +i+   +a   ++++  ++   +tttt+ ttt+t+tttt+   +t tt   n+ +  p
  gi|242398729|ref|YP_002994153.1| 424 EARVMDSNAIVLNSKAIITKVIELETLKTTTTTTTTETTTSTATTTTSqEQATETTEEENSDICGP 489
                                       334455566666667777777777777766666666666655555554145666777777665555 PP

>> DUF3439  Domain of unknown function (DUF3439)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0  11.3    0.0019       2.6      15      69 ..     415     470 ..     404     477 .. 0.58

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0019
                           DUF3439  15 nskivkakssa.vdpdsakcsgsgkpvrsiicpttttttttttttmpttttlpttt 69 
                                       ns+ ++++s+a v ++ a +  s   +  +i   t  tttttttt  tt+t  ttt
  gi|242398729|ref|YP_002994153.1| 415 NSNATISDSEArVMDSNAIVLNSKAIITKVIELETLKTTTTTTTTETTTSTATTTT 470
                                       45554455555244444445555555566666666666666666666666666666 PP

>> Mucin  Mucin-like glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8  18.1    0.0023       3.1      45      73 ..     451     479 ..     412     490 .. 0.53

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0023
                             Mucin  45 ltttttttkppttttttttasttittktt 73 
                                       +ttttttt+ +tt+t+ttt+s+ + t+tt
  gi|242398729|ref|YP_002994153.1| 451 KTTTTTTTTETTTSTATTTTSQEQATETT 479
                                       22222222222222222222222222222 PP

>> VCBS  Repeat domain in Vibrio, Colwellia, Bradyrhizobium and Shewanella
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.4     0.068        94       9      49 ..      53     101 ..      51     106 .. 0.66
   2 ?    2.6   0.3      0.15   2.1e+02       4      39 ..     116     154 ..     105     161 .. 0.68
   3 ?    8.2   0.8    0.0026       3.6      11      48 ..     159     204 ..     155     207 .. 0.80
   4 ?    6.6   1.2    0.0083        11       7      50 ..     207     258 ..     206     261 .. 0.81
   5 ?    3.2   0.2     0.096   1.3e+02       9      40 ..     261     299 ..     259     312 .. 0.73
   6 ?    1.8   0.2      0.27   3.7e+02       9      47 ..     312     361 ..     308     367 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.068
                              VCBS   9 Dlvva........ndgglrvyrnngdGtftdvtktslgg.sgggtgvavg 49 
                                       D++va        + g ++v+r + +G+ +  +kt +g+ ++g+++vav+
  gi|242398729|ref|YP_002994153.1|  53 DVIVAgatgsfgaGKGDVWVLRLDEKGNIKW-QKTCGGSdGDGAHAVAVA 101
                                       67776666666545788*******9999875.556555515555566654 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.15
                              VCBS   4 gDGrlDlvvan.dgglrv.yrnngdGtftdvtkt.slgg 39 
                                       g G+ D  ++  d++ +v +  +  G+f dvt+  ++++
  gi|242398729|ref|YP_002994153.1| 116 GTGKTDAWILRlDENGNVkWQKTYGGSFIDVTSAvAIAP 154
                                       678889888866655555144445788888887524444 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0026
                              VCBS  11 vva........ndgglrvyrnngdGtftdvtktslggsgggtgvav 48 
                                       +va        +++ ++v+r + +G+ +   ++ +++++++t+vav
  gi|242398729|ref|YP_002994153.1| 159 IVAgytesfgaGENDFWVLRLDENGNVKWQKTYGGSSYDDATTVAV 204
                                       555444444437899*************99999***9*99999997 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.0083
                              VCBS   7 rlDlvva........ndgglrvyrnngdGtftdvtktslggsgggtgvavgD 50 
                                       + D++va        + + l+++r + +G+++   ++ +g+   +++v+v+D
  gi|242398729|ref|YP_002994153.1| 207 DNDVIVAgstasfggGAQDLWILRLDENGNLKWQKTYGGGDFEVANAVVVAD 258
                                       5799999777765433466*************99999999998999999999 PP

  == domain 5  score: 3.2 bits;  conditional E-value: 0.096
                              VCBS   9 Dlvva.......ndgglrvyrnngdGtftdvtktslggs 40 
                                       D++va       + g ++v+r ++ G+++   ++ ++  
  gi|242398729|ref|YP_002994153.1| 261 DIIVAgmagfgaGKGDVWVLRLDAEGNLKWQKTYGGSYL 299
                                       7888767766655788**********9998777665543 PP

  == domain 6  score: 1.8 bits;  conditional E-value: 0.27
                              VCBS   9 Dlvva...........ndgglrvyrnngdGtftdvtktslggsgggtgva 47 
                                       D++va           ++ + +v+r + +G+ +   ++ +++ + +t++a
  gi|242398729|ref|YP_002994153.1| 312 DIIVAgatasfgtgtpDYPNAWVLRLDENGNVKWQKAYGGSDLDVATAIA 361
                                       77777677766666555677999*******99988888777765555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (510 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1282  (0.0715043); expected 358.6 (0.02)
Passed bias filter:                      718  (0.0400469); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.80u 0.34s 00:00:01.14 Elapsed: 00:00:00.56
# Mc/sec: 2738.85
//
Query:       gi|242398730|ref|YP_002994154.1|  [L=419]
Description: hypothetical protein TSIB_0744 [Thermococcus sibiricus MM 739]
Scores for complete 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-103  344.0   0.0   9.9e-103  343.7   0.0    1.1  1  Nre_N     Archaeal Nre, N-terminal
    8.2e-36  122.3   0.0    1.2e-35  121.8   0.0    1.2  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 !  343.7   0.0  1.1e-106  9.9e-103       2     270 .]      25     292 ..      24     292 .. 1.00

  Alignments for each domain:
  == domain 1  score: 343.7 bits;  conditional E-value: 1.1e-106
                             Nre_N   2 cglkkcpileklravekakkkisskeleGsspPsvfVGrygYPkVsvgplvppvegdasvldspekwlglslediik 78 
                                       cgl +cp++ ++ra+ ++ +++ssk++eGs+pPs+f+Gr gYP V++gp++pp  gd++++d pe w++ ++edi++
  gi|242398730|ref|YP_002994154.1|  25 CGLAYCPVIARARATLRVRRSVSSKTIEGSTPPSIFIGRVGYPYVRIGPATPPLIGDTKIFDFPELWINHKIEDILE 101
                                       ***************************************************************************** PP

                             Nre_N  79 lrlslvrgekkvkvkkakedklleeiqelalsekpvdvevelekkpkaklkfdevlaPvGpsaeleklkvaenpkvp 155
                                       +r+sl++g k ++vkk++ dkl++e++ la+s+kpvdve+ l+k+p++ ++f+e+++P Gp+++l+++k+ +np++p
  gi|242398730|ref|YP_002994154.1| 102 YRWSLITGIKIADVKKPE-DKLIDELRLLAMSSKPVDVEIILKKPPRPFMTFNEHEPPQGPRSPLNNMKILGNPSIP 177
                                       *****************9.********************************************************** PP

                             Nre_N 156 rkveklveDtdlkAeeavveLyrsgvdvykiqrlLSvGlLGekkkrrlVPTrWsITAvddivgkelkkeikdlpeid 232
                                       r+vek++ Dtdl A eav++Ly+sgv v++iq+++S+G++G+k +rrlVPTrWsITAvd+++ ++l+keikd+++++
  gi|242398730|ref|YP_002994154.1| 178 RPVEKAHDDTDLPAFEAVTYLYESGVPVSHIQKVFSTGAFGVKGRRRLVPTRWSITAVDSMLCRNLIKEIKDYEPLN 254
                                       ***************************************************************************** PP

                             Nre_N 233 evevfsgeylgNrflviLaPgkwsfelvEawapgslwn 270
                                       e+ vf++++++N f++iL+P kws+e++Eaw+pgs+wn
  gi|242398730|ref|YP_002994154.1| 255 EILVFRYRLHDNLFIAILYPAKWSYEWMEAWWPGSTWN 292
                                       *************************************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 !  121.8   0.0   1.3e-39   1.2e-35       1     110 []     305     415 ..     305     415 .. 0.99

  Alignments for each domain:
  == domain 1  score: 121.8 bits;  conditional E-value: 1.3e-39
                             Nre_C   1 egyegrkeyseiaGaYyaarlavleaLekikrqakvivlreitpeYwaPvGvWqvReavrkalekkp.kefesleea 76 
                                       egy+gr++y+ i+G+Yya+ la+le+L++ikrqa++i+lrei+p++ +PvGvW+vRe+vr++++++p  ++++l+e+
  gi|242398730|ref|YP_002994154.1| 305 EGYHGRTTYPGIGGCYYASMLATLEYLKRIKRQATAILLREIYPGFKIPVGVWFVRESVRAMFNSPPvLKTDTLDEV 381
                                       789***************************************************************999******** PP

                             Nre_C  77 leevseklklplkkllkkskllkelkkqktLddF 110
                                       +e ++ ++kl + k+l++s ll+++k +kt+d+F
  gi|242398730|ref|YP_002994154.1| 382 MELLNMETKLGSGKWLSSSALLRRIKFTKTIDEF 415
                                       ********************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (419 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); 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 0.25s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 2749.42
//
Query:       gi|242398731|ref|YP_002994155.1|  [L=109]
Description: hypothetical protein TSIB_0745 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       818  (0.0456244); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); 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: 0.40u 0.32s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 717.61
//
Query:       gi|242398732|ref|YP_002994156.1|  [L=260]
Description: Soj like protein [Thermococcus sibiricus MM 739]
Scores for complete 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-53  179.0   2.2      1e-52  178.7   2.2    1.1  1  AAA_31       AAA domain
    4.2e-27   94.7   0.1    6.4e-27   94.1   0.1    1.3  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    9.2e-16   58.0   0.8    2.7e-15   56.5   0.8    1.7  1  ParA         NUBPL iron-transfer P-loop NTPase
    5.2e-13   48.9   0.0    1.7e-11   43.9   0.0    2.3  2  ArsA_ATPase  Anion-transporting ATPase
      1e-11   44.8   0.4    6.6e-05   22.5   0.0    2.5  3  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
    5.3e-11   42.4   0.0    2.6e-10   40.2   0.0    1.8  2  CBP_BcsQ     Cellulose biosynthesis protein BcsQ
    4.2e-10   39.4   0.1      7e-08   32.1   0.1    2.1  1  MipZ         ATPase MipZ
    4.7e-05   23.3   2.1       0.47   10.2   0.2    3.1  2  AAA_26       AAA domain
     0.0011   18.4   0.8       0.37   10.0   0.0    2.6  3  VirC1        VirC1 protein
  ------ inclusion threshold ------
      0.016   14.5   0.2       0.43    9.8   0.1    2.7  3  DUF1611      Domain of unknown function (DUF1611_C) P-loop do
       0.03   13.9   0.1       0.85    9.2   0.0    2.2  2  AAA_25       AAA domain
      0.056   13.4   0.3       0.11   12.5   0.3    1.5  1  ResIII       Type III restriction enzyme, res subunit
      0.084   12.5   0.1       0.33   10.5   0.1    2.0  2  SRP54        SRP54-type protein, GTPase domain
      0.088   12.6   0.0       0.22   11.3   0.0    1.6  1  CLP1_P       mRNA cleavage and polyadenylation factor CLP1 P-
       0.16   11.6   1.7       0.38   10.4   1.7    1.5  1  AAA_24       AAA domain


Domain annotation for each model (and alignments):
>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.7   2.2   8.4e-56     1e-52       3     177 .]       4     184 ..       2     184 .. 0.90

  Alignments for each domain:
  == domain 1  score: 178.7 bits;  conditional E-value: 8.4e-56
                            AAA_31   3 vIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanatt......glgiekneiektlyevlieeknikeai 73 
                                       +I+ianqKGGvGKTT s+nla+alak+g+ +L++D DpQ n+t+       ++ + n+i + l+e  +++++i++ai
  gi|242398732|ref|YP_002994156.1|   4 IISIANQKGGVGKTTISLNLAYALAKKGYDTLIIDTDPQFNLTFaligmdIIKRNDNNIGTLLIENAVKKTQIENAI 80 
                                       8******************************************96553222222334455566666689******** PP

                            AAA_31  74 iktkvenldlipssidLaeaeielvelekkeeilkellekvkdeYDyiiiDcpPsLglltenaLvasdsviipvqae 150
                                       i    enl+lips+++++++e  l+++  +e++lk++lek++deYD+iiiD pPsLg++++n+L asd+v+ip++  
  gi|242398732|ref|YP_002994156.1|  81 I-PIEENLSLIPSHLKVSAIERLLMTAYMREQRLKRVLEKIEDEYDFIIIDNPPSLGIFLINSLGASDYVLIPTELG 156
                                       *.446999********************************************************************* PP

                            AAA_31 151 ayaleGleqllktieevkkk.lnpklei 177
                                       ++++ G++  l+ i+e+k++ lnp+lei
  gi|242398732|ref|YP_002994156.1| 157 YFSVMGVQLTLDVIREIKSTeLNPDLEI 184
                                       ******************9889**9987 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.1   0.1   5.4e-30   6.4e-27       1     128 []       5     235 ..       5     235 .. 0.95

  Alignments for each domain:
  == domain 1  score: 94.1 bits;  conditional E-value: 5.4e-30
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH....................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................... RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep....................... 54 
                                       i+ia++kGGvGKTt+++nLa ala++g+++l +D+Dpq n+++ l g  + +++                       
  gi|242398732|ref|YP_002994156.1|   5 ISIANQKGGVGKTTISLNLAYALAKKGYDTLIIDTDPQFNLTFALIGMDIIKRNdnnigtllienavkktqienaii 81 
                                       78*****************************************85555555555688999***************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|242398732|ref|YP_002994156.1|  82 pieenlslipshlkvsaierllmtaymreqrlkrvlekiedeydfiiidnppslgiflinslgasdyvliptelgyf 158
                                       ***************************************************************************** PP

                                       ...CCHCCCHHHHHHCHCHHHH....EEEEEEEEESS...-TTCHHHHHHHHHHC.TS-EEEEEE--CCHCCCCHHT CS
                                       ...xxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  55 ...dlkrllellealgkkkall..lkiagvvlnrvdgeneetllkealeelkqry.gvpvlgviprdeavaeaparg 125
                                          +++  l ++++++ + +l+  l+i+g+v+n++  +  ++  +  l++lk+ y  +pv++++pr +av ++  +g
  gi|242398732|ref|YP_002994156.1| 159 svmGVQLTLDVIREIKST-ELNpdLEIMGIVANKFTRQ--SKVPQVRLDQLKETYpDLPVVAILPRAVAVEKSQGEG 232
                                       ****************87.56679*************9..9***********999*********************9 PP

                                       S-H CS
                                       xxx RF
                              CbiA 126 epv 128
                                       +pv
  gi|242398732|ref|YP_002994156.1| 233 KPV 235
                                       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 !   56.5   0.8   2.3e-18   2.7e-15       5     245 ..       4     255 ..       1     256 [. 0.82

  Alignments for each domain:
  == domain 1  score: 56.5 bits;  conditional E-value: 2.3e-18
                              ParA   5 viavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgvee.................ekpeqsekk 64 
                                       +i ++  KGGVGK+t++ nlA+aLakkg+++ ++D+D        l+g++                  +  +q e+ 
  gi|242398732|ref|YP_002994156.1|   4 IISIANQKGGVGKTTISLNLAYALAKKGYDTLIIDTDPQFNLTFALIGMDIikrndnnigtllienavK-KTQIENA 79 
                                       78999********************************77666667777665666778888888875532.3333668 PP

                              ParA  65 liPveakgikvmSigfllesedeavvwrGpmkskaikqllkdvewgelDyLiiDlPPGtgDeqltvaqklplagavi 141
                                       +iP+e ++++++  ++ ++   e +++ + m ++ +k++l+++e +e D++iiD PP  g   + ++++l  ++ v+
  gi|242398732|ref|YP_002994156.1|  80 IIPIE-ENLSLIPSHLKVS-AIERLLMTAYMREQRLKRVLEKIE-DEYDFIIIDNPPSLG---IFLINSLGASDYVL 150
                                       99998.5788888888887.8899999***************99.88**********998...78889998888888 PP

                              ParA 142 Vttp.qevaladvkkaiemfkkvkvkvlGvveNmsgfvcpkcgekteifgkgggeklaeelgvpllgeipldpeire 217
                                       + t     +++ v+ ++++++++k + l     + g+v +k ++++++ +    +   +  ++p+++ +p   ++ +
  gi|242398732|ref|YP_002994156.1| 151 IPTElGYFSVMGVQLTLDVIREIKSTELNPDLEIMGIVANKFTRQSKVPQVRLDQLKETYPDLPVVAILPRAVAVEK 227
                                       877625689999999999999888766665555556666666777776655555555556799************** PP

                              ParA 218 asdegkplvlkepeseaakaleeiaekv 245
                                       ++ egkp+++ +p+++++ka+ ++aekv
  gi|242398732|ref|YP_002994156.1| 228 SQGEGKPVFEFDPKNKVSKAFLQLAEKV 255
                                       *************************998 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.9   0.0   1.4e-14   1.7e-11       9     134 ..      11     133 ..       3     138 .. 0.75
   2 ?    2.5   0.0     0.057        68     256     283 ..     191     218 ..     181     223 .. 0.88

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 1.4e-14
                                       STTSSHHHHHHHHHHHHHHTTS-EEEEE-STTTHHHHHHTS--BSS-EEET.SSEEEEE--HHHHHHHHHCCHHGGG CS
                       ArsA_ATPase   9 KGGVGKttvsaatavklsekgkkvllistDPAhslsDsfdqklgkeptkvk.eNLsavEidpeveleeakqevqkee 84 
                                       KGGVGKtt+s  +a+ l++kg+++l+i tDP  +l   f   +g + +k + +N+ +  i+  v+  + +++ +  e
  gi|242398732|ref|YP_002994156.1|  11 KGGVGKTTISLNLAYALAKKGYDTLIIDTDPQFNLT--FAL-IGMDIIKRNdNNIGTLLIENAVKKTQIENAIIPIE 84 
                                       9**********************************7..655.77888887768999999999998777777776665 PP

                                       SCCHHHHHHHHHHHHHHTSSTTHHHHHHHHHHHHHHH..CSSSSEEEEESBS CS
                       ArsA_ATPase  85 eallgleeledvlaeelaslPGideilsfeellkyvk..eeeydvvvlDtaP 134
                                       e+l  +    +v a e      +   +  ++l++ ++  e+eyd +++D +P
  gi|242398732|ref|YP_002994156.1|  85 ENLSLIPSHLKVSAIERLL---MTAYMREQRLKRVLEkiEDEYDFIIIDNPP 133
                                       5544333333333333333...44555556666666566899********99 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.057
                                       HHHHHHHHHHHHHHHHHHHTTTSEEEEE CS
                       ArsA_ATPase 256 flearkkiqkkylkeieelfedlevvkl 283
                                       ++ ++ k+ + +l++++e++ dl+vv +
  gi|242398732|ref|YP_002994156.1| 191 KFTRQSKVPQVRLDQLKETYPDLPVVAI 218
                                       678889999***************9865 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 !   19.9   0.1   3.4e-07    0.0004       7      48 ..      10      51 ..       4      82 .. 0.81
   2 ?   -1.3   0.0      0.99   1.2e+03     245     269 ..      83     107 ..      52     109 .. 0.74
   3 !   22.5   0.0   5.5e-08   6.6e-05     161     247 ..     169     258 ..     144     260 .] 0.80

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 3.4e-07
                         Fer4_NifH  7 GkGGiGksttsqnlsaalaemgkkvlivGCDPkaDstrlllg 48
                                       kGG+Gk+t s nl+ ala++g   li+  DP+ + t  l+g
  gi|242398732|ref|YP_002994156.1| 10 QKGGVGKTTISLNLAYALAKKGYDTLIIDTDPQFNLTFALIG 51
                                      59*******************************999955554 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.99
                         Fer4_NifH 245 lenkklviPkplsedeLeelleefe 269
                                       +e++  +iP  l+  ++e ll++ +
  gi|242398732|ref|YP_002994156.1|  83 IEENLSLIPSHLKVSAIERLLMTAY 107
                                       3566688999999999999998765 PP

  == domain 3  score: 22.5 bits;  conditional E-value: 5.5e-08
                         Fer4_NifH 161 iakgiekyaksggvrlgGliins..rkvddereliekfaeel.gtkvlevvPrdeivrkaelrkktvieyapeseqa 234
                                       + + i+    + ++++ G++ n+  r+ +  +  ++++ e+  +++v++++Pr   v+k++ + k v+e++p+++++
  gi|242398732|ref|YP_002994156.1| 169 VIREIKSTELNPDLEIMGIVANKftRQSKVPQVRLDQLKETYpDLPVVAILPRAVAVEKSQGEGKPVFEFDPKNKVS 245
                                       55566666667779999*****522333333445778877763589******************************* PP

                         Fer4_NifH 235 keyrelarkilen 247
                                       k + +la+k+++n
  gi|242398732|ref|YP_002994156.1| 246 KAFLQLAEKVIKN 258
                                       **********987 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   0.0   2.2e-13   2.6e-10       4     131 ..       5     139 ..       1     154 [. 0.77
   2 ?    0.0   0.0       0.4   4.8e+02     166     232 ..     187     254 ..     177     256 .. 0.75

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 2.2e-13
                          CBP_BcsQ   4 lalqGvRGGvGttsllaaLawalhelgesvlviDlspdnlLrlhF.nvdieqre....g..waraeldgapwrqaal 73 
                                       + +   +GGvG+t+++  La+al + g+  l+iD+ p+  L++    +di +r+    g  +++ +++++++++a++
  gi|242398732|ref|YP_002994156.1|   5 ISIANQKGGVGKTTISLNLAYALAKKGYDTLIIDTDPQFNLTFALiGMDIIKRNdnniGtlLIENAVKKTQIENAII 81 
                                       5566679******************************976666532555543321111323567889999******* PP

                          CBP_BcsQ  74 eyapgldllPfGelnveekenlqq.laekaeallaalkelkeqyrwillDlpagasalt 131
                                        + ++l+l+P  +l+v+  e+l      ++++l++ l++++ +y++i++D p       
  gi|242398732|ref|YP_002994156.1|  82 PIEENLSLIPS-HLKVSAIERLLMtAYMREQRLKRVLEKIEDEYDFIIIDNPPSLGIFL 139
                                       **********4.6666666665443778899********************98776555 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.4
                          CBP_BcsQ 166 lLiNqfeaasqlqqDllqlWlqslrrllPl..vihrDealaEalaakqPlgeyrpdslaaeevktLanw 232
                                       +  N+f+ +s++ q  l   ++++ +l P+  ++ r  a+  +    +P+ e+ p+  ++++  +La+ 
  gi|242398732|ref|YP_002994156.1| 187 IVANKFTRQSKVPQVRLDQLKETYPDL-PVvaILPRAVAVEKSQGEGKPVFEFDPKNKVSKAFLQLAEK 254
                                       567888888888765444445555554.54346778889999999999999999999999999999976 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.1   5.8e-11     7e-08       2     125 ..       4     149 ..       3     160 .. 0.63

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 5.8e-11
                                       EEEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-.HH................HHHHHHHHHHHHHHT-- CS
                              MipZ   2 vivlgnekGGsGksttavhvavaLlkkGarvaaidldlrqr.tl................arylenraataerkgls 61 
                                       +i ++n+kGG Gk+t+++ +a aL+kkG     id d + + t+                +  +en ++ ++ ++  
  gi|242398732|ref|YP_002994156.1|   4 IISIANQKGGVGKTTISLNLAYALAKKGYDTLIIDTDPQFNlTFaligmdiikrndnnigTLLIENAVKKTQIENAI 80 
                                       6889************************9988887775432122111111111100111134577777766666666 PP

                                       ----EEE-SSS-.....HHHHTTS-HHHHHHHHHHHHHHHHHH-SEEEEE--SS--HHHHHHHHT-SEE CS
                              MipZ  62 Lplpealalsea.....eeaeveeeeeaevaeleelvadleaeldfividtPGsdsalsrlahsladtl 125
                                       +p+ e l+l  +     + +++   + ++ ++l+++++++e e+dfi+id P s       +   +d +
  gi|242398732|ref|YP_002994156.1|  81 IPIEENLSLIPShlkvsAIERLLMTAYMREQRLKRVLEKIEDEYDFIIIDNPPSLGIFLINSLGASDYV 149
                                       6666665543321100023334445667778********************987666555555555555 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.1   0.00064      0.76      10      30 ..      12      32 ..       4      36 .. 0.84
   2 !   10.2   0.2   0.00039      0.47     146     191 ..     164     222 ..      68     229 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00064
                            AAA_26 10 tgvGKTvvslgLvralkrkgv 30
                                       gvGKT++sl L++al +kg+
  gi|242398732|ref|YP_002994156.1| 12 GGVGKTTISLNLAYALAKKGY 32
                                      68**************98886 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00039
                            AAA_26 146 lltiealr.......qknvrvlGvilNkvrnpe.....nvetlekksg.ipvlGvvPyl 191
                                        lt+++ r       + +++++G+++Nk++ +      ++++l+++ + +pv++++P  
  gi|242398732|ref|YP_002994156.1| 164 QLTLDVIReikstelNPDLEIMGIVANKFTRQSkvpqvRLDQLKETYPdLPVVAILPRA 222
                                       45555555333322234789********9888445555888888886668****99976 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0   0.00031      0.37       3      40 ..       4      41 ..       1      47 [. 0.86
   2 ?   -1.1   0.0      0.77   9.2e+02      97     126 ..      75     105 ..      64     123 .. 0.72
   3 !    6.0   0.1    0.0054       6.5     100     165 ..     140     206 ..     111     231 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00031
                             VirC1  3 litfcslkGGaGkttalmglcsalasdgkrvalfeade 40
                                      +i+++  kGG Gktt  + l  ala +g    + ++d 
  gi|242398732|ref|YP_002994156.1|  4 IISIANQKGGVGKTTISLNLAYALAKKGYDTLIIDTDP 41
                                      5789999********************99888888775 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.77
                             VirC1  97 elnntii.assdllliPtmltpldidealat 126
                                       +++n+ii    +l liP+ l    i+  l t
  gi|242398732|ref|YP_002994156.1|  75 QIENAIIpIEENLSLIPSHLKVSAIERLLMT 105
                                       5555555256789999999987777776665 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.0054
                             VirC1 100 ntiiassdllliPtmltpldidealatyryvielllae.elaipvailrqrvPvrrltssqrlisdl 165
                                          + +sd++liPt l  + +     t  ++ e+  +e ++++++  +  +  +r+ ++ q ++ +l
  gi|242398732|ref|YP_002994156.1| 140 INSLGASDYVLIPTELGYFSVMGVQLTLDVIREIKSTElNPDLEIMGIVANKFTRQSKVPQVRLDQL 206
                                       4456789**********99999999999999999877754554443222222233333333333333 PP

>> DUF1611  Domain of unknown function (DUF1611_C) P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   0.00036      0.43      24     100 ..      14      90 ..       4     106 .. 0.74
   2 ?    1.9   0.0     0.097   1.2e+02     138     188 ..      79     128 ..      64     132 .. 0.74
   3 ?    0.5   0.0      0.26   3.1e+02     137     192 ..     158     219 ..     152     225 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00036
                           DUF1611  24 vGKrttaleleealeerGlkaafvaTgqtgili.agegvvldavv.vdfvaGa..veglvkkaaeeeepdlilveGQ 96 
                                       vGK t +l+l+ al ++G+++ ++ T+++  l+ a   + +d +  +d   G+  +e++vkk +  e+  +i +e  
  gi|242398732|ref|YP_002994156.1|  14 VGKTTISLNLAYALAKKGYDTLIIDTDPQFNLTfA--LIGMDIIKrNDNNIGTllIENAVKKTQI-EN-AIIPIEEN 86 
                                       8**************************98777634..4556666424555565446788888776.44.57777776 PP

                           DUF1611  97 gsLt 100
                                        sL+
  gi|242398732|ref|YP_002994156.1|  87 LSLI 90 
                                       6666 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.097
                           DUF1611 138 alppleeeieliealaakkkvvgislNtknlseeeakealeeleeelglpv 188
                                       a+ p+ee++ li +  +    +   l t+ + e+ +k+ le++e+e++  +
  gi|242398732|ref|YP_002994156.1|  79 AIIPIEENLSLIPSHLKVS-AIERLLMTAYMREQRLKRVLEKIEDEYDFII 128
                                       6777788877777777666.6667799999999999999999999998755 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.26
                           DUF1611 137 ialppleeeieliealaakk.....kvvgislNtknlseeeakealeeleeel.glpvvdpv 192
                                       +++ +++ ++++i+++++++     +++gi  N+   + +  + +l++l+e++ +lpvv ++
  gi|242398732|ref|YP_002994156.1| 158 FSVMGVQLTLDVIREIKSTElnpdlEIMGIVANKFTRQSKVPQVRLDQLKETYpDLPVVAIL 219
                                       566677778888888888888888899****9999999888889999999998889998876 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   0.00071      0.85      42      60 ..      12      31 ..       5      42 .. 0.86
   2 ?    2.4   0.0     0.084     1e+02     132     150 ..     112     131 ..      94     135 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00071
                            AAA_25 42 pgtGKttlaldlalava.tG 60
                                      +g+GKtt+ l+la+a+a +G
  gi|242398732|ref|YP_002994156.1| 12 GGVGKTTISLNLAYALAkKG 31
                                      8***************9554 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.084
                            AAA_25 132 aleaaieeveg.vrlvviDp 150
                                       +l +++e++e+ +++++iD+
  gi|242398732|ref|YP_002994156.1| 112 RLKRVLEKIEDeYDFIIIDN 131
                                       567777777777*******7 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.3   9.1e-05      0.11      33     139 ..      12     130 ..       5     132 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.1e-05
                                       TTSTHHHHHHHHHHHH-S..............-EEEEESSHHHHHHHHHHGGGGTGG........GEEEESSS-B-- CS
                            ResIII  33 TGtGKTlvaaklierllkkgkee.........kflflvprkslleqtleefkkflsea.yke...igkkvsgdkkka 96 
                                        G+GKT ++++l+++l+kkg+           +  f   + +++++  +++  +l e+ +k+   +       + ++
  gi|242398732|ref|YP_002994156.1|  12 GGVGKTTISLNLAYALAKKGYDTliidtdpqfNLTFALIGMDIIKRNDNNIGTLLIENaVKKtqiE-------NAII 81 
                                       59*****************99878888888887777777788888888877544444303333321.......2222 PP

                                       ..........-SEEEEEHHHHHHTH...........HHHTTT-SEEEEE CS
                            ResIII  97 ...kekdstnkkilvttiqsldadseee...eeeseellrdrfdviiiD 139
                                          ++ +   +++ v+ i++l      +    +   e+ +d++d+iiiD
  gi|242398732|ref|YP_002994156.1|  82 pieENLSLIPSHLKVSAIERLLMTAYMReqrLKRVLEKIEDEYDFIIID 130
                                       2222222334556666666554443222333455566677777788877 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00028      0.33      11      38 ..      13      40 ..       6      81 .. 0.89
   2 ?   -1.1   0.0         1   1.2e+03      76      90 ..     116     130 ..      85     132 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00028
                                      TSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                             SRP54 11 GaGKTttlaKLaallkkegkkvllvaaD 38
                                      G+GKTt    La  l k+g+++l++ +D
  gi|242398732|ref|YP_002994156.1| 13 GVGKTTISLNLAYALAKKGYDTLIIDTD 40
                                      9***********************9988 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1
                                       HHHHHHTTSSEEEEE CS
                             SRP54  76 vekakeekidvvlvD 90 
                                       v ++ e+++d++++D
  gi|242398732|ref|YP_002994156.1| 116 VLEKIEDEYDFIIID 130
                                       334456689999999 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00018      0.22       4      32 ..      13      41 ..      11      47 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00018
                            CLP1_P  4 dsGKSTlarlLlNyalrkgrkpvyvDlDv 32
                                       +GK+T++ +L+  +++kg+ ++++D+D+
  gi|242398732|ref|YP_002994156.1| 13 GVGKTTISLNLAYALAKKGYDTLIIDTDP 41
                                      59**************************9 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   1.7   0.00032      0.38      11      72 ..      12     130 ..      10     135 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00032
                            AAA_24  11 sgiGKTtlakel.......gpkplfidtekGlksldadkfpdie................swedfldevvel..... 59 
                                        g+GKTt+ ++l       g+++l+idt+  ++ + a  + di                 +                
  gi|242398732|ref|YP_002994156.1|  12 GGVGKTTISLNLayalakkGYDTLIIDTDPQFNLTFALIGMDIIkrndnnigtllienavK----------Ktqien 78 
                                       69***************************98866666655555445555554444333330..........033334 PP

                            AAA_24  60 .......................................aaeladyktlviD 72 
                                                                              ++ +++y+ ++iD
  gi|242398732|ref|YP_002994156.1|  79 aiipieenlslipshlkvsaierllmtaymreqrlkrvlEKIEDEYDFIIID 130
                                       4555555566667777777777777777777777777887778888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       749  (0.0417759); expected 358.6 (0.02)
Passed bias filter:                      605  (0.0337442); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 1612.95
//
Query:       gi|242398733|ref|YP_002994157.1|  [L=133]
Description: hypothetical protein TSIB_0747 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.18   12.1   8.1        2.4    8.5   1.6    2.2  2  DUF4383   Domain of unknown function (DUF4383)


Domain annotation for each model (and alignments):
>> DUF4383  Domain of unknown function (DUF4383)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.5   0.00018       3.2      60      91 ..      16      47 ..       7      60 .. 0.85
   2 ?    8.5   1.6   0.00013       2.4      44      83 ..      62     101 ..      56     123 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00018
                           DUF4383 60 vlglaaarsasgarlyllllgvvylllailgl 91
                                       ++l+a+ s++ arl + l++  ylll+ + +
  gi|242398733|ref|YP_002994157.1| 16 TTLLTAMFSDGPARLLGFLAAFGYLLLTFWSI 47
                                      4567777*********************9975 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00013
                           DUF4383  44 lfqvnllhnlvhllvGvlglaaarsasgarlyllllgvvy 83 
                                         +v +++n++  ++Gv+ ++++++   a ++ll+ g + 
  gi|242398733|ref|YP_002994157.1|  62 GVRVMFFLNIIAFVFGVVSFYMYTENVVAPIVLLGPGFII 101
                                       4678899**********************99999887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 871.41
//
Query:       gi|242398734|ref|YP_002994158.1|  [L=148]
Description: hypothetical protein TSIB_0748 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 1176.45
//
Query:       gi|242398735|ref|YP_002994159.1|  [L=57]
Description: hypothetical protein TSIB_0749 [Thermococcus sibiricus MM 739]
Scores for complete 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-06   25.6   0.0    1.3e-05   24.9   0.0    1.3  1  zf-H2C2_5       C2H2-type zinc-finger domain
    2.6e-05   24.4   0.2    3.2e-05   24.1   0.2    1.1  1  zf-Di19         Drought induced 19 protein (Di19), zinc-bindi
    0.00017   20.9   0.0    0.00019   20.7   0.0    1.0  1  Actin_micro     Putative actin-like family
    0.00019   21.0   0.0    0.00024   20.6   0.0    1.1  1  zf_C2H2_ZHX     Zinc-fingers and homeoboxes C2H2 finger domai
    0.00057   20.2   0.2    0.00096   19.5   0.2    1.4  1  zf-C2H2         Zinc finger, C2H2 type
     0.0013   19.4   0.3      0.002   18.8   0.3    1.4  1  zf-C2H2_4       C2H2-type zinc finger
     0.0016   18.7   0.1     0.0016   18.7   0.1    1.1  1  zf-C2H2_2       C2H2 type zinc-finger (2 copies)
     0.0035   16.9   0.0     0.0045   16.5   0.0    1.2  1  zf-C2H2_12      Zinc-finger C2H2-type
     0.0037   17.1   0.0     0.0046   16.8   0.0    1.2  1  zf-C2H2_9       C2H2 type zinc-finger (1 copy)
     0.0071   16.7   2.3      0.064   13.7   0.1    2.2  2  zf-H2C2_2       Zinc-finger double domain
  ------ inclusion threshold ------
      0.011   14.3   0.1      0.012   14.2   0.1    1.0  1  DUF629          Protein of unknown function (DUF629)
      0.014   15.8   0.2      0.017   15.6   0.2    1.3  1  zf-C2HE         C2HE / C2H2 / C2HC zinc-binding finger
      0.019   14.6   0.4      0.029   14.1   0.4    1.2  1  zinc_ribbon_2   zinc-ribbon domain
      0.021   14.8   0.0      0.026   14.5   0.0    1.3  1  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
      0.028   14.5   0.0      0.036   14.1   0.0    1.2  1  zf-Sec23_Sec24  Sec23/Sec24 zinc finger
      0.028   14.8   0.2      0.031   14.6   0.2    1.1  1  ARS2            Arsenite-resistance protein 2
      0.038   13.5   0.0      0.058   12.9   0.0    1.2  1  zf_C2H2_10      C2H2 type zinc-finger


Domain annotation for each model (and alignments):
>> zf-H2C2_5  C2H2-type zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   1.2e-08   1.3e-05       3      25 ..      20      42 ..      18      42 .. 0.96

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1.2e-08
                         zf-H2C2_5  3 CsqCDYstawksnLkRHlrrkHt 25
                                      C++C Y++++  +Lk+H++ kHt
  gi|242398735|ref|YP_002994159.1| 20 CPFCGYKAKSLEELKQHILEKHT 42
                                      **********************8 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 !   24.1   0.2   3.1e-08   3.2e-05       1      30 [.      16      46 ..      16      49 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 3.1e-08
                           zf-Di19  1 esftCPyCgk.eltvkeLveHvedeHrvesk 30
                                      ++f CP+Cg  + + +eL +H+ ++H+ +++
  gi|242398735|ref|YP_002994159.1| 16 QTFVCPFCGYkAKSLEELKQHILEKHTLNRE 46
                                      68*******8689*************98776 PP

>> Actin_micro  Putative actin-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   1.8e-07   0.00019     219     254 ..      11      47 ..       8      56 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.8e-07
                       Actin_micro 219 elkekkefsCkvCdvkfev.ekiseHllkkHiikehv 254
                                        +++ ++f+C  C++k ++ e++++H+l+kH+ + + 
  gi|242398735|ref|YP_002994159.1|  11 SMENGQTFVCPFCGYKAKSlEELKQHILEKHTLNRED 47 
                                       678999*************************986544 PP

>> zf_C2H2_ZHX  Zinc-fingers and homeoboxes C2H2 finger 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   0.00024       4      29 ..      17      42 ..      15      52 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.3e-07
                       zf_C2H2_ZHX  4 sFvCveCsfsakkfegLalHNarsHp 29
                                      +FvC  C++ ak+ e+L++H  + H+
  gi|242398735|ref|YP_002994159.1| 17 TFVCPFCGYKAKSLEELKQHILEKHT 42
                                      7*******************999997 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.2   9.1e-07   0.00096       1      23 []      18      41 ..      18      41 .. 0.96

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 9.1e-07
                                      EEETTTTEEESSHHHHHHHHHC.C CS
                           zf-C2H2  1 ykCpdCgksFkrksnLkrHirt.H 23
                                      ++Cp Cg++ k+ ++Lk+Hi   H
  gi|242398735|ref|YP_002994159.1| 18 FVCPFCGYKAKSLEELKQHILEkH 41
                                      89******************9988 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 !   18.8   0.3   1.9e-06     0.002       1      24 []      18      41 ..      18      41 .. 0.95

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.9e-06
                         zf-C2H2_4  1 fkCpiCgksFsskkaLlrHlkthH 24
                                      f Cp+Cg   +s ++L++H++  H
  gi|242398735|ref|YP_002994159.1| 18 FVCPFCGYKAKSLEELKQHILEKH 41
                                      89******************9988 PP

>> zf-C2H2_2  C2H2 type zinc-finger (2 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   1.5e-06    0.0016      50      74 ..      17      41 ..       2      55 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.5e-06
                         zf-C2H2_2 50 kleClyCekefkslealreHmkkkg 74
                                      ++ C +C+++ ksle+l++H+ +k+
  gi|242398735|ref|YP_002994159.1| 17 TFVCPFCGYKAKSLEELKQHILEKH 41
                                      5778888888778888888877653 PP

>> zf-C2H2_12  Zinc-finger C2H2-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   4.2e-06    0.0045      20      49 ..      15      42 ..      12      49 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4.2e-06
                        zf-C2H2_12 20 rrglvCmvCgeslaslklstikrHIrqvHP 49
                                      +++ vC  Cg      +l+++k+HI+++H 
  gi|242398735|ref|YP_002994159.1| 15 GQTFVCPFCGYKAK--SLEELKQHILEKHT 42
                                      6889******9866..579**********6 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 !   16.8   0.0   4.4e-06    0.0046       3      27 ..      19      43 ..      17      49 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 4.4e-06
                                      B-TTT--B-SSHHHHHHHHHHHTSS CS
                         zf-C2H2_9  3 lCPvCevkfnswkdlseHilsaask 27
                                      +CP C  k +s+++l +Hil++ + 
  gi|242398735|ref|YP_002994159.1| 19 VCPFCGYKAKSLEELKQHILEKHTL 43
                                      7******************988764 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 !   13.7   0.1   6.1e-05     0.064      13      26 .]      17      29 ..       3      29 .. 0.80
   2 ?    3.5   0.2      0.11   1.1e+02       2      10 ..      33      42 ..      32      56 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.1e-05
                         zf-H2C2_2 13 kpyeCplCdkaFkt 26
                                      + + Cp+C+++ k+
  gi|242398735|ref|YP_002994159.1| 17 T-FVCPFCGYKAKS 29
                                      3.99******9985 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.11
                         zf-H2C2_2  2 LrrHir.kHt 10
                                      L++Hi  kHt
  gi|242398735|ref|YP_002994159.1| 33 LKQHILeKHT 42
                                      899*994598 PP

>> DUF629  Protein of unknown function (DUF629)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   1.1e-05     0.012      55      83 ..      16      44 ..      10      49 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.1e-05
                            DUF629 55 rfWvCrtCsekfsdaeeckqHlvqeHvak 83
                                      +++vC  C  k ++ ee kqH++++H  +
  gi|242398735|ref|YP_002994159.1| 16 QTFVCPFCGYKAKSLEELKQHILEKHTLN 44
                                      579***********************865 PP

>> zf-C2HE  C2HE / C2H2 / C2HC zinc-binding finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.2   1.6e-05     0.017      37      60 ..      17      39 ..       9      49 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.6e-05
                           zf-C2HE 37 pLkCtrCganfgnkfpkLKeHLee 60
                                       + C  Cg    +++ +LK+H+ e
  gi|242398735|ref|YP_002994159.1| 17 TFVCPFCG-YKAKSLEELKQHILE 39
                                      699*****.************876 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.4   2.7e-05     0.029       6      22 ..       9      26 ..       9      26 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.7e-05
                     zinc_ribbon_2  6 GaelqdnakF.CpyCGtp 22
                                      G+  +++++F Cp CG++
  gi|242398735|ref|YP_002994159.1|  9 GRSMENGQTFvCPFCGYK 26
                                      78899***********96 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   2.5e-05     0.026      16      28 ..      15      28 ..      10      41 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.5e-05
                     Zn_Tnp_IS1595 16 pngfvCPhCgsr.k 28
                                      +++fvCP+Cg++ k
  gi|242398735|ref|YP_002994159.1| 15 GQTFVCPFCGYKaK 28
                                      466*******9864 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 ?   14.1   0.0   3.4e-05     0.036      19      32 ..      13      26 ..       6      31 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.4e-05
                    zf-Sec23_Sec24 19 fggkrwiCnfCnhk 32
                                      ++g++++C+fC+ k
  gi|242398735|ref|YP_002994159.1| 13 ENGQTFVCPFCGYK 26
                                      789********987 PP

>> ARS2  Arsenite-resistance protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.2     3e-05     0.031      65      94 ..      15      44 ..      10      53 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3e-05
                              ARS2 65 kdKwlCplsGKkFkgpEFvrKHilnKHaek 94
                                      ++ + Cp  G k k+ E +++Hil+KH   
  gi|242398735|ref|YP_002994159.1| 15 GQTFVCPFCGYKAKSLEELKQHILEKHTLN 44
                                      56799**********************754 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 ?   12.9   0.0   5.5e-05     0.058       3      24 ..      18      39 ..      17      39 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.5e-05
                        zf_C2H2_10  3 fsCPKCqeklPDiDtLQIHvMd 24
                                      f CP C++k+  +  L  H+++
  gi|242398735|ref|YP_002994159.1| 18 FVCPFCGYKAKSLEELKQHILE 39
                                      99*********99999999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       791  (0.0441185); expected 358.6 (0.02)
Passed bias filter:                      627  (0.0349713); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.34u 0.21s 00:00:00.55 Elapsed: 00:00:00.36
# Mc/sec: 474.55
//
Query:       gi|242398736|ref|YP_002994160.1|  [L=157]
Description: 6-pyruvoyl-tetrahydropterin synthase-related protein [Thermococcus sibiricus MM 739]
Scores for complete 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-28   97.2   0.1    7.8e-28   96.9   0.1    1.1  1  PTPS      6-pyruvoyl tetrahydropterin synthase
  ------ inclusion threshold ------
        0.1   12.4   0.4          3    7.6   0.3    2.1  2  MAJIN     Membrane-anchored junction protein
       0.12   12.9   0.1         23    5.7   0.1    2.3  2  P63C      P63C domain


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 !   96.9   0.1   1.3e-31   7.8e-28       2     121 ..      15     154 ..      14     156 .. 0.93

  Alignments for each domain:
  == domain 1  score: 96.9 bits;  conditional E-value: 1.3e-31
                                       EEEEEEEEEEE--T.TTTGGGGSTEEEEEEEEEEEEEC-STCTTBSS-HHHHHHHHHHHHHCTTTEEC.CCC-CCHH CS
                              PTPS   2 iskefeFdaaHrlr.khegkcrnlHGHnykvevtvegeeldetgmvvdfgelkealkeileelDhkfl.naddpele 76 
                                       i  + eFd++H+l   +e+kc ++HGH+ykv+v+v g+ l+e+gm++df++l+++    ++ lDhk+l ++d  +++
  gi|242398736|ref|YP_002994160.1|  15 IGWHKEFDSSHFLVlPYESKCLRIHGHTYKVDVEVWGK-LNENGMIFDFNHLSNL----IKLLDHKMLvSEDWVSVK 86 
                                       566789********9***********************.**************95....569******998888888 PP

                                       CCS.........................--HHHHHHHHHHHHHHHHGCCCGCEEEEEEEEETTEEEEEE CS
                              PTPS  77 ell........................spTaEnlaklifeelkerlqekevklskvrvwEtpnswaeyr 121
                                                                  + TaE +a++++e+++e+  ++++k  +v++wE p+s+ae++
  gi|242398736|ref|YP_002994160.1|  87 GDGsvvvekngkhlefprdevvilnkpNVTAELIAEWFAERIAEKA-GQNIKKIRVKIWEDPRSYAEIT 154
                                       76699********************8888*****************.*******************986 PP

>> MAJIN  Membrane-anchored junction protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.3   0.00051         3      65      88 ..      21      44 ..      15      50 .. 0.83
   2 ?    3.0   0.0     0.013        75      83     124 ..      98     140 ..      94     156 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00051
                             MAJIN 65 fatehfivfPykskWervshlkfk 88
                                      f   hf+v+Py sk  r+    +k
  gi|242398736|ref|YP_002994160.1| 21 FDSSHFLVLPYESKCLRIHGHTYK 44
                                      8899**********9999765555 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.013
                             MAJIN  83 shlkfkhgevvlvPyPfvftlyvemkwfhenls..pGkpindsP 124
                                        hl f  +evv+   P v +  +   wf+e ++  +G+ i+++ 
  gi|242398736|ref|YP_002994160.1|  98 KHLEFPRDEVVILNKPNVTAELI-AEWFAERIAekAGQNIKKIR 140
                                       59**************9976554.58999988622577777665 PP

>> P63C  P63C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1    0.0038        23       6      47 ..      10      53 ..       6      76 .. 0.75
   2 ?    5.3   0.0    0.0048        29      38      71 ..     110     143 ..      99     151 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0038
                              P63C  6 lseellkwekrFpdefy......kelyrlrgwkykpsakkkpkvvgkl 47
                                      + e+   w+k+F+++ +      ++  r++g++yk       +v+gkl
  gi|242398736|ref|YP_002994160.1| 10 ITERKIGWHKEFDSSHFlvlpyeSKCLRIHGHTYK----VDVEVWGKL 53
                                      6677788*****9998744444457899*****99....345666666 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0048
                              P63C  38 kkkpkvvgkltnelvYerLakdvleeLrklnpkk 71 
                                        +kp+v ++l+ e+  er+a+++ ++++k ++k 
  gi|242398736|ref|YP_002994160.1| 110 LNKPNVTAELIAEWFAERIAEKAGQNIKKIRVKI 143
                                       689*************************998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       596  (0.0332422); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); 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: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 1023.15
//
Query:       gi|242398737|ref|YP_002994161.1|  [L=140]
Description: DNA-binding protein, [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-23   82.0   0.1    4.2e-23   81.8   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 !   81.8   0.1   2.4e-27   4.2e-23       1     105 [.       7     118 ..       7     120 .. 0.91

  Alignments for each domain:
  == domain 1  score: 81.8 bits;  conditional E-value: 2.4e-27
                                       TEEEEEE-TTSBHHHHHHHHHHHHT-SSEEEEEEEEEEEEEE.EEECTTT......EE-S-EEEEEEEEEEEETT.. CS
                            DUF296   1 rphvlrlepGediveaieefarkrgiraacvlsaiGavsnvt.rladgee......kllgrfeilslsGtilpdg.. 68 
                                       r++++r+++G++++++++efa+k++i  +++ saiG+++n + +++++e+      +l+g +e++s+ G+++ ++  
  gi|242398737|ref|YP_002994161.1|   7 RTFLFRIPEGKEFLNSVTEFAKKHNILIGTI-SAIGTLRNPKiGYFEEETkqykviELEGTYELISAIGNLSLKDne 82 
                                       6899***************************.***********9999998988887777**************5567 PP

                                       ..EEEEEEEEETTSEEEEEEEEEE.EEEEEEEEEEEEE- CS
                            DUF296  69 ..lHlhvslagedgqvvgGhlaegplvaattvevvvaef 105
                                         +H+hvsl++e+g+++gGhl+eg  v  +++evvv+e+
  gi|242398737|ref|YP_002994161.1|  83 pfAHIHVSLGDEEGKMFGGHLVEG-EV--FVAEVVVQEL 118
                                       9*********************99.44..6888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 978.45
//
Query:       gi|242398738|ref|YP_002994162.1|  [L=264]
Description: glutamine amidotransferase [Thermococcus sibiricus MM 739]
Scores for complete 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-56  190.8   0.0      3e-56  190.6   0.0    1.0  1  Peptidase_C26  Peptidase C26
      1e-08   35.2   0.0    3.5e-08   33.5   0.0    1.8  1  GATase         Glutamine amidotransferase class-I


Domain annotation for each model (and alignments):
>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.6   0.0   3.4e-60     3e-56       3     216 .]       5     222 ..       3     222 .. 0.91

  Alignments for each domain:
  == domain 1  score: 190.6 bits;  conditional E-value: 3.4e-60
                     Peptidase_C26   3 igitaneeslkkeavqdaeesylaasyveavekagglpvllpieedeedvkaildkldgllltGgqdvePslygeep 79 
                                       igi+a+         +++++ +++ +yv+ v+++gg+pv +p+     ++ ++l+++dg++l+ g+d++P++yg + 
  gi|242398738|ref|YP_002994162.1|   5 IGIVASF-------NWETGALTINDTYVRRVKEVGGIPVAIPPL---LEIVDVLEAIDGIILPEGPDIHPKHYGDTL 71 
                                       5555555.......3577788899999999**************...78899************************* PP

                     Peptidase_C26  80 sekeeeadpeRdalelaLiraalergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhrehe..q.....saash 149
                                       sek e  d eRd++elaL++aale+++Pilgi rG q +nvalGG+lyqd++e+++  +h   +  +     s   h
  gi|242398738|ref|YP_002994162.1|  72 SEKIECLDVERDEFELALVKAALEKDLPILGIGRGAQAINVALGGSLYQDVNEIPKSIQHNWIRngKflvhpSTRVH 148
                                       *****************************************************9999988666655155567999** PP

                     Peptidase_C26 150 avkvekgsllaell.........gseeievnslHhqaikelaeelrveAvaeDgviEaieseeakafvlgvQwHPE 216
                                       +v+++++s+l e+l         g+  i+vns+Hhqaik+l+++++ +A aeDg+iEa+e+e    f++gvQw +E
  gi|242398738|ref|YP_002994162.1| 149 EVRIKQDSMLFEILkenlnleanGEAFIDVNSFHHQAIKKLGNDIKPVAYAEDGIIEAVEVEG--RFAIGVQWWAE 222
                                       **************9999988866778************************************..6*******887 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.0   3.9e-12   3.5e-08      35     174 ..      43     224 ..      20     236 .. 0.75

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 3.9e-12
                                       HHHHTHHSTSEEEEEEESS.CTT.................TTTHHHHHHHHCTSTS-EEEETHHHHHHHHHTTTEEE CS
                            GATase  35 eilellknpdgilvsgGpg.spg.................vegkieaikearenkiPiLGICLGmQllaiefgrkvv 93 
                                       ei + l+ +dgi+++ Gp  +p+                  e +++++k a+e+++PiLGI  G Q++  ++g++++
  gi|242398738|ref|YP_002994162.1|  43 EIVDVLEAIDGIILPEGPDiHPKhygdtlsekiecldverDEFELALVKAALEKDLPILGIGRGAQAINVALGGSLY 119
                                       5555578899999999997334477788888988888887889999****************************666 PP

                                       .........................EEECEEEEEEEEEEEETTT.........CGGTTTTSEEEEEEEEEEEEESGC CS
                            GATase  94 .........................kekekehhggtmrlgddet.........allyglknevierhrHryevnpke 136
                                                                       + ++ r+++d+          +l  + +  +++   H  ++++  
  gi|242398738|ref|YP_002994162.1| 120 qdvneipksiqhnwirngkflvhpsT------RVHEVRIKQDSMlfeilkenlNLEANGEAFIDVNSFHHQAIKK-- 188
                                       55556666666666665554433331......333344444333555555665444455588999999******9.. PP

                                       HHHTTEEEEEEEETTEEEEEEEEETTT.EEEESSBTTST CS
                            GATase 137 lepaglevtakseddeelmeiiekknp.fvgvQFHPEst 174
                                        + ++++ +a  ed+  ++e++e + + ++gvQ+  E+ 
  gi|242398738|ref|YP_002994162.1| 189 -LGNDIKPVAYAEDG--IIEAVEVEGRfAIGVQWWAEYL 224
                                       .***********887..999******99*****988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2009.68
//
Query:       gi|242398739|ref|YP_002994163.1|  [L=280]
Description: Radical SAM family protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.4e-15   56.5   0.1      1e-14   55.3   0.1    1.6  2  Radical_SAM  Radical SAM superfamily
      4e-06   26.7   6.4      0.011   15.5   0.0    2.3  2  DUF1848      Domain of unknown function (DUF1848)
  ------ inclusion threshold ------
      0.022   15.0   0.6      0.057   13.7   0.3    1.9  2  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 !   55.3   0.1   1.7e-18     1e-14       2     166 ..      23     187 ..      22     188 .. 0.80
   2 ?   -1.9   0.0      0.63   3.8e+03      79      97 ..     193     220 ..     192     260 .. 0.57

  Alignments for each domain:
  == domain 1  score: 55.3 bits;  conditional E-value: 1.7e-18
                                       EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC.... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.... RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla.... 74 
                                       +v+ gC ++C++C++++     +  +++ +e++l  +++  ++ +++++i ++   + yp + ++l+  +k      
  gi|242398739|ref|YP_002994163.1|  23 NVYTGCDHACVYCYITSY--IPKAFKIRIKENLLPNLERELQRFNKNFIIALSYSSDPYPTIDKDLRITRKVLelfk 97 
                                       6889************97..555555555555555554443444488888887777777666666666666556677 PP

                                       CCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHH..HHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  75 vpgiritvetngtlpdeeklerllelgvdrvslgleaadde..kvlklmnrghtfeevlealeklreagikrvvdri 149
                                         ++r+ + t   l  e  l++l++l    + +++ ++d+e    l+++   ++++e+++al+k+++ gi+ v+ ri
  gi|242398739|ref|YP_002994163.1|  98 RYNVRCLILTKSNLF-EQDLDLLKNLK-CAIGITVTTIDEEkaGLLEPN--APSPQERIKALKKAKKEGIP-VYARI 169
                                       79*************.***********.*************55555555..79******************.55555 PP

                                       .EEBTTTSHHHHHHHHHH CS
                                       .xxxxxxxxxxxxxxxxx RF
                       Radical_SAM 150 .vglpGendeeleellel 166
                                        +++p ++++e++e+le+
  gi|242398739|ref|YP_002994163.1| 170 dPIIPFYTWKEFDETLEE 187
                                       49*************997 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.63
                                       EEEEEECSSCHG.........HHHHHHH CS
                                       xxxxxxxxxxxx.........xxxxxxx RF
                       Radical_SAM  79 ritvetngtlpd.........eeklerl 97 
                                       +itv+t  ++pd         +e +++l
  gi|242398739|ref|YP_002994163.1| 193 HITVSTLKLRPDswrrmelkfPELMKKL 220
                                       5666666666666555554443333333 PP

>> DUF1848  Domain of unknown function (DUF1848)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   5.3   7.2e-05      0.43     239     264 ..      11      36 ..       6      37 .. 0.90
   2 !   15.5   0.0   1.8e-06     0.011      60     162 ..     111     206 ..      86     268 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 7.2e-05
                           DUF1848 239 rkeCgCveskDiGayntClhgCvYCY 264
                                        k C+C     + +y  C h CvYCY
  gi|242398739|ref|YP_002994163.1|  11 SKLCTCPFKYTLNVYTGCDHACVYCY 36 
                                       456*********************** PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.8e-06
                           DUF1848  60 pllkkleelkergiklyfqfTltdyeke..lepnvpsleerietfkelseklgkerviwRyDPilltekltvelhle 134
                                        + + l+ lk+ ++ + + +T  d ek+  lepn ps +eri+++k+  ++     v+ R DPi+   +       +
  gi|242398739|ref|YP_002994163.1| 111 LFEQDLDLLKNLKCAIGITVTTIDEEKAglLEPNAPSPQERIKALKKAKKEG--IPVYARIDPIIPFYT------WK 179
                                       345578888877777777766666666569****************987764..4699******96543......34 PP

                           DUF1848 135 kfeklaeelkgytekvviSfvdlykkvk 162
                                       +f++  eel+  ++++++S ++l     
  gi|242398739|ref|YP_002994163.1| 180 EFDETLEELSF-VSHITVSTLKLRPDSW 206
                                       44444444443.4455555544444444 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 ?   13.7   0.3   9.6e-06     0.057      12      58 ..      25      72 ..      17     150 .. 0.66
   2 ?   -1.5   0.0      0.45   2.7e+03      87     112 ..     172     195 ..     142     200 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 9.6e-06
                           Fer4_12 12 vsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkk.esiegltl 58
                                       +gC+++C +C+ ++      +  ++++ll ++ ++l+  ++++ + l
  gi|242398739|ref|YP_002994163.1| 25 YTGCDHACVYCYITSYIPKAFKIRIKENLLPNLERELQRfNKNFIIAL 72
                                      57***************9999999999999988888865433344433 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.45
                           Fer4_12  87 diwlytgytleelskkekeellkeid 112
                                        i  yt+  ++e ++    ++++ i 
  gi|242398739|ref|YP_002994163.1| 172 IIPFYTWKEFDETLE--ELSFVSHIT 195
                                       455566666666663..456665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); 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: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1926.86
//
Query:       gi|242398740|ref|YP_002994164.1|  [L=132]
Description: stress-inducible protein, OsmC/Ohr family [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.2e-17   61.9   0.0    7.8e-17   61.6   0.0    1.1  1  OsmC      OsmC-like protein


Domain annotation for each model (and alignments):
>> OsmC  OsmC-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.6   0.0   4.4e-21   7.8e-17       3      92 ..      27     116 ..      25     124 .. 0.89

  Alignments for each domain:
  == domain 1  score: 61.6 bits;  conditional E-value: 4.4e-21
                                       XSSB-HHHHHHHHHHHHHHHHHHHHTCCCT---SCEEEEEEEEEECCECTCEEEEEEEEEEE-SS-H..HHHHHHHH CS
                              OsmC   3 gsgpsPeelllaalasCfaitlravakkkgikledleveveaerdpegakgiteirlkvevkipgadseeklkklle 79 
                                       ++g+sP+  ll ++a+C++i++ ++++k++ ++e+l+ve+++er +e ++ +t+i+l+++++ ++  +eek+k+++e
  gi|242398740|ref|YP_002994164.1|  27 ENGISPMKTLLLSVAGCTSIDVVMILQKMREPIEGLDVEISGERRDEHPRIYTKIHLHYRIY-GD-VNEEKVKRAIE 101
                                       579***************************************999999999**********7.44.447******** PP

                                       HH.HHHSHHHHHH.C CS
                              OsmC  80 ka.ekrCpvsntl.k 92 
                                       ++ ek+C+v   l  
  gi|242398740|ref|YP_002994164.1| 102 LSqEKYCSVGAHLkL 116
                                       *********877744 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 970.70
//
Query:       gi|242398741|ref|YP_002994165.1|  [L=94]
Description: hypothetical protein TSIB_0755 [Thermococcus sibiricus MM 739]
Scores for complete 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-36  122.1   0.8    9.1e-36  122.0   0.8    1.0  1  DUF1884   Domain of unknown function (DUF1884)


Domain annotation for each model (and alignments):
>> DUF1884  Domain of unknown function (DUF1884)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.0   0.8   5.1e-40   9.1e-36       1      92 []       2      93 ..       2      93 .. 0.98

  Alignments for each domain:
  == domain 1  score: 122.0 bits;  conditional E-value: 5.1e-40
                                      HHHHHHHHHHHHHHHHHHHHTT----EEEE-HHHHHHHHHHHHHHHT------EETTEEEEE-GGGTTEEEEE-TTTTT CS
                           DUF1884  1 rgdlirilevieekineLkleGfePdiiLvGkeaieflkealkkeleeeeevtelsnlkveileeLGgDavvvDskvLG 79
                                      rg+liril+++eek+neLkl+GfePd++L+Gkea+eflk+++++e+++e+ v e+s+l ++ ++e+G+DavvvDskvLG
  gi|242398741|ref|YP_002994165.1|  2 RGELIRILGSVEEKANELKLDGFEPDVVLFGKEAYEFLKNQVNQEFGGEDSVSEISGLSIRVVDEFGKDAVVVDSKVLG 80
                                      799**************************************************************************** PP

                                      TSTT-EEEEE--- CS
                           DUF1884 80 qikkaakrikvep 92
                                      +  + akr+kv++
  gi|242398741|ref|YP_002994165.1| 81 LGLGGAKRLKVIK 93
                                      **********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 600.11
//
Query:       gi|242398742|ref|YP_002994166.1|  [L=299]
Description: ATP:dephospho-CoA triphosphoribosyl transferase [Thermococcus sibiricus MM 739]
Scores for complete 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-49  168.6   0.0    2.4e-49  168.5   0.0    1.0  1  CitG       ATP:dephospho-CoA triphosphoribosyl transferase
  ------ inclusion threshold ------
      0.075   13.3   0.9       0.19   12.0   0.2    2.0  2  FOP_dimer  FOP N terminal dimerisation domain
       0.15   11.9   0.0       0.29   11.0   0.0    1.3  1  NMT1       NMT1/THI5 like


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 !  168.5   0.0   4.1e-53   2.4e-49       3     280 ..      12     289 ..      10     290 .. 0.93

  Alignments for each domain:
  == domain 1  score: 168.5 bits;  conditional E-value: 4.1e-53
                                       XXXXXXXXXXXXXXXXXXXXXXXXX..XXXXHHHHHHHHHTTHHHHHHHH.............HH--HHHHHHHHHH CS
                              CitG   3 lavlAlllEvsatpKPGlVdrrdsgahdDmdfetFlaSaealapyfeeaaaaGlea..kalfeelrsiGelaekaml 77 
                                       +++l  llEv++ pKPG+V r++++  +D+++ +Fl   +++ +++ ea + G     ++l  e++++Gel++ka+ 
  gi|242398742|ref|YP_002994166.1|  12 AFTLGSLLEVAI-PKPGNVNRYRDF--EDLTLYHFLFANTSVIDVLFEATHRGELIreEKLQPEEAKLGELIKKAVG 85 
                                       788999****99.5***********..***********************888655889999*************** PP

                                       HH..------HHHHHHHHHHHHTTTTS-.......SHHHHHHHHHHHHHT--HHHHHHH.HHHHHH--......... CS
                              CitG  78 aa..tggvNThkGaifllgllaaaagrraaeeeeasleelveeaaevlaeltvedavaf.rairlakv......... 142
                                       ++  +++ N ++G+i l ++l +a g      +++++e  +e+++ ++++ +  d+++f +air+a++         
  gi|242398742|ref|YP_002994166.1|  86 NSkkVQNSNPNFGIITLAIPLTVAFG------WANNIELAREKVKLLISASSPYDSIDFyKAIRIANPkgvkkgvty 156
                                       **************************......5689********************************999877766 PP

                                       ...---..HHHHHH.TT--HHHHHHTS-TT-HHHHHHHHTSHHHHHHHH........HH-SSHHHHHHHHHHHHHHS CS
                              CitG 143 ...eel..kdelvekksltlgevlelsygvdgirgeaasgFpsvfeialpalrealasgadlndalvqallallael 214
                                          + +   delv+ ++++l + +e+s+g++ i +e+ +g++ ++   + +l+e  +s+  l++a+++++l++la++
  gi|242398742|ref|YP_002994166.1| 157 dvyD-DssFDELVR-DNINLKKLAEISSGRELIFKEWLNGYKLSYS-TFHRLKEL-TSSLPLEQATLKMFLEVLANH 229
                                       5542.145777777.9******************************.66689996.47799**************** PP

                                       --HHHHHHHHHHHHHHHHHHHH..........H-SHHHHHHHHHHHHHHT..---HHHHHHHHHHHHH CS
                              CitG 215 pDtnilrrgGaegaeevqeeArallaaggvaaeaglealeeldrelvern..isPGgsADllaatlfl 280
                                        Dt+i+r++G e ae v+++A+++l +        +  l+e+d+ l+e++   +PG+ AD++a++l l
  gi|242398742|ref|YP_002994166.1| 230 LDTLIIRKAGLEEAELVKKKAKEVLTE--------KLDLKEFDKILREKKdsRNPGSLADIMAISLSL 289
                                       **************************9........899**********9999************9865 PP

>> FOP_dimer  FOP N terminal dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   3.2e-05      0.19       7      37 ..     172     200 ..     167     208 .. 0.90
   2 ?   -1.9   0.0      0.69   4.1e+03      47      65 ..     245     262 ..     220     266 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.2e-05
                         FOP_dimer   7 eNLkkvlsikeGrlvaeLirefLeffeldyt 37 
                                        NLkk  +i+ Gr++  + +e+L+ ++l+y+
  gi|242398742|ref|YP_002994166.1| 172 INLKKLAEISSGREL--IFKEWLNGYKLSYS 200
                                       59***********98..58***********8 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.69
                         FOP_dimer  47 lseelddRealskeLnise 65 
                                       l  + + +e+l+++L+++e
  gi|242398742|ref|YP_002994166.1| 245 LVKK-KAKEVLTEKLDLKE 262
                                       3333.36777777777776 PP

>> NMT1  NMT1/THI5 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   4.9e-05      0.29     104     190 ..      72     152 ..      67     154 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4.9e-05
                                       HHHHHHHHHHHTT--GGG-EEEE-.TT-HHHHHHCTSSSEEECEETTTHHHHHHHTT--EEEE-GGGTT-----SEE CS
                              NMT1 104 ekallkallakdggdpsdvtlvnvggtslakalltgkvDaaiggyenwegvelesegkelrifaladlgvpdyyslv 180
                                       e+a l +l++k+ g+ ++v++   ++ ++   ++t  +  ++++ ++ + +el++e+++l i a + ++  d+y+ +
  gi|242398742|ref|YP_002994166.1|  72 EEAKLGELIKKAVGNSKKVQN---SNPNF--GIITLAIPLTVAFGWA-NNIELAREKVKLLISASSPYDSIDFYKAI 142
                                       78999**************99...45676..6788888877755555.789999*********************** PP

                                       EEEEHHHHHH CS
                              NMT1 181 litnekllke 190
                                        i+n k +k+
  gi|242398742|ref|YP_002994166.1| 143 RIANPKGVKK 152
                                       ****998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       596  (0.0332422); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 1899.40
//
Query:       gi|242398743|ref|YP_002994167.1|  [L=290]
Description: hypothetical protein TSIB_0757 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00027   20.8   2.9     0.0046   16.8   0.1    2.7  3  DUF2154   Cell wall-active antibiotics response 4TMS YvqF
  ------ inclusion threshold ------
      0.021   14.2   2.8        1.7    7.9   0.5    2.4  2  DUF4097   Putative adhesin
       0.67   10.2   3.7       0.18   12.0   0.7    1.6  2  DUF4418   Domain of unknown function (DUF4418)


Domain annotation for each model (and alignments):
>> DUF2154  Cell wall-active antibiotics response 4TMS YvqF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       1.6   9.4e+03      42      53 ..     105     116 ..     102     126 .. 0.67
   2 !   16.8   0.1   7.6e-07    0.0046      16      81 ..     204     272 ..     197     279 .. 0.81
   3 !    6.5   0.1    0.0013       7.5      92     114 .]     267     289 ..     261     289 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.6
                           DUF2154  42 ivirkliGdvki 53 
                                       i i++++ +v+i
  gi|242398743|ref|YP_002994167.1| 105 IAIENIAAKVTI 116
                                       677777777777 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 7.6e-07
                           DUF2154  16 dinissiiGdttiDLtk...avlpegetvivirkliGdvkilVPedvevsveasvifGdvkvldekeag 81 
                                       +  ++ ++Gd+++ L++   + + +  + i i  + Gd++i +Pe+v+v+ +++  + +v++ +e e+g
  gi|242398743|ref|YP_002994167.1| 204 SFIVTDFVGDMEVTLENcpeTEIDGYCSQIEIYRGSGDIDIHIPENVKVTPQIEGSLTSVTIDEEFETG 272
                                       55678899999999997333567777788**********************999999999988776665 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.0013
                           DUF2154  92 eeyeeaekkvkiivslliGdveV 114
                                       ee+e+ ek++k++v+++iG++ V
  gi|242398743|ref|YP_002994167.1| 267 EEFETGEKTLKLTVKSFIGKIVV 289
                                       78899***************966 PP

>> DUF4097  Putative adhesin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.5   0.00029       1.7      75     139 ..     119     201 ..     108     217 .. 0.73
   2 ?    5.5   0.1    0.0015       9.1     182     217 ..     232     267 ..     223     286 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00029
                           DUF4097  75 lPkkt..kledlqvkassG...dlsvek.............atklkaetlelksssGdltlsnvsaktltvksesGd 133
                                       +P +t   l++l v++s+G    ls ++              +++k+ +l+l +s++d++l+  +++++t++   Gd
  gi|242398743|ref|YP_002994167.1| 119 VPGNTinVLSNLPVEVSDGetlKLSCSEcekyengklliqvGNEVKLVSLTLRNSASDVDLKLGEVASVTLDNVVGD 195
                                       55555323346777777776333333335556667777776788999999999999999999999999999999999 PP

                           DUF4097 134 vtiegs 139
                                       ++++g+
  gi|242398743|ref|YP_002994167.1| 196 ISASGV 201
                                       999886 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0015
                           DUF4097 182 sltitassGdvdlslpeekkaavdassesGdvslpk 217
                                       +++i   sGd+d+ +pe+ k   +++ +  +v++++
  gi|242398743|ref|YP_002994167.1| 232 QIEIYRGSGDIDIHIPENVKVTPQIEGSLTSVTIDE 267
                                       688999999999999955443333333333444444 PP

>> DUF4418  Domain of unknown function (DUF4418)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   0.1       2.9   1.8e+04      43      53 ..       7      17 ..       3      20 .. 0.48
   2 ?   12.0   0.7   3.1e-05      0.18      41      80 ..      41      79 ..      36      84 .. 0.84

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 2.9
                           DUF4418 43 ivllvlgllal 53
                                      + l++lgll++
  gi|242398743|ref|YP_002994167.1|  7 LFLTFLGLLII 17
                                      44444444433 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 3.1e-05
                           DUF4418 41 vGivllvlgllalfvkkkklrrglsiavillgvlvilipt 80
                                       G++l+++gl  +++k+k++r++l++++il  vl+++ p+
  gi|242398743|ref|YP_002994167.1| 41 WGVILIIAGLY-VLIKDKTARTALAVIFILYLVLFLVTPS 79
                                      58888888888.6677777*************99999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       842  (0.046963); expected 358.6 (0.02)
Passed bias filter:                      603  (0.0336327); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 1753.12
//
Query:       gi|242398744|ref|YP_002994168.1|  [L=150]
Description: Transcription regulator, PspC family [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-19   69.9   0.4    1.2e-19   69.9   0.4    2.1  2  PspC      PspC domain
  ------ inclusion threshold ------
      0.018   14.5   0.9      0.018   14.5   0.9    1.7  2  DUF373    Domain of unknown function (DUF373)
       0.04   14.0   0.3      0.083   12.9   0.3    1.6  1  TspO_MBR  TspO/MBR family


Domain annotation for each model (and alignments):
>> PspC  PspC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.9   0.4     2e-23   1.2e-19       2      53 .]       7      63 ..       6      63 .. 0.96
   2 ?   -2.9   3.2         1   6.2e+03      33      45 ..     134     147 ..     103     149 .. 0.64

  Alignments for each domain:
  == domain 1  score: 69.9 bits;  conditional E-value: 2e-23
                              PspC  2 rLyRspdnkvlgGVcaGlAeyfgvdptlvRlifvlll.....glllYiilwiilPea 53
                                      rL Rs++nkv+ GV++G+Aey+++dpt++R++f+ll+      +l+Y++++i++Pe+
  gi|242398744|ref|YP_002994168.1|  7 RLKRSKKNKVFLGVLGGIAEYLKIDPTIIRILFILLClvepvFILAYFLMAIVMPEE 63
                                      899**********************************999999999*********96 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1
                              PspC  33 ifvlll.glllYii 45 
                                       i+++l+ +l lY++
  gi|242398744|ref|YP_002994168.1| 134 IVAVLIlVLGLYLV 147
                                       33333323335776 PP

>> DUF373  Domain of unknown function (DUF373)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1      0.21   1.2e+03     151     162 ..      32      43 ..       9      68 .. 0.52
   2 ?   14.5   0.9     3e-06     0.018     149     196 ..     102     150 .]      89     150 .] 0.90

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.21
                            DUF373 151 pelrktiLvplG 162
                                       p + ++++++l 
  gi|242398744|ref|YP_002994168.1|  32 PTIIRILFILLC 43 
                                       222222222222 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 3e-06
                            DUF373 149 kdpelrktiLvplGlllliyallll..lglpelalaiillllGlylllrG 196
                                       +d +l  + Lv+lG+lll+  l+ l  lgl + ++a+++l+lGlyl+ rG
  gi|242398744|ref|YP_002994168.1| 102 DDTKLFGIALVLLGALLLLKDLIKLpfLGL-REIVAVLILVLGLYLVARG 150
                                       5889999******************86554.689999**********998 PP

>> TspO_MBR  TspO/MBR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.3   1.4e-05     0.083      38     103 ..      44     146 ..      16     149 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.4e-05
                                       HHTTHHHHHHHHHHHHH......HHHHHH...............................HHHHHHHHHHHHTSGGC CS
                          TspO_MBR  38 vfppvWtvlyilmgvaa......ylvwka...............................lalyavqlvlnllwspl 77 
                                       +  pv ++ y+lm++++       ++ ++                               ++l+++ lvl  +  +l
  gi|242398744|ref|YP_002994168.1|  44 LVEPVFILAYFLMAIVMpeeeeeTITAEKipekvgmlaeeagekveklvkkapvvekkddTKLFGIALVLLGALLLL 120
                                       56788888888888888666654343444888888888888888889998999999999989*************** PP

                                       TTTTTSGGGHHHHHHHHHHHHHHHHH CS
                          TspO_MBR  78 ffglkspvlalvdivallglvvalil 103
                                          +k p+l+l +iva+l+lv+ l+l
  gi|242398744|ref|YP_002994168.1| 121 KDLIKLPFLGLREIVAVLILVLGLYL 146
                                       *******************9998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       943  (0.0525964); expected 358.6 (0.02)
Passed bias filter:                      598  (0.0333538); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1058.62
//
Query:       gi|242398745|ref|YP_002994169.1|  [L=76]
Description: PspC domain protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.7e-24   84.0   0.8    5.3e-24   83.8   0.8    1.0  1  PspC         PspC domain
  ------ inclusion threshold ------
      0.019   15.0   4.6      0.032   14.2   4.6    1.4  1  Potass_KdpF  F subunit of K+-transporting ATPase (Potass_KdpF


Domain annotation for each model (and alignments):
>> PspC  PspC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.8   0.8     6e-28   5.3e-24       1      53 []       3      61 ..       3      61 .. 0.96

  Alignments for each domain:
  == domain 1  score: 83.8 bits;  conditional E-value: 6e-28
                              PspC  1 krLyRspdnkvlgGVcaGlAeyfgvdptlvRlifvlll......glllYiilwiilPea 53
                                      k+LyRs++nk++ GVc+G+Aeyf+vd+tlvR++f++ll       +llY++l++++Pe+
  gi|242398745|ref|YP_002994169.1|  3 KKLYRSRKNKIIFGVCGGFAEYFNVDATLVRILFIILLiasvgtAVLLYLLLALVMPEE 61
                                      8***********************************999999888899*********96 PP

>> Potass_KdpF  F subunit of K+-transporting ATPase (Potass_KdpF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   4.6   3.6e-06     0.032       1      22 [.      37      60 ..      37      61 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.6e-06
                                      HHHHHHHHHHHH..HHHHHHHS-- CS
                       Potass_KdpF  1 illllvavaLlv..YLfyALlrPE 22
                                      i+ll+  v+ +v  YL+ AL+ PE
  gi|242398745|ref|YP_002994169.1| 37 IILLIASVGTAVllYLLLALVMPE 60
                                      57777777777777*********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       890  (0.0496402); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.33s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 475.51
//
Query:       gi|242398746|ref|YP_002994170.1|  [L=48]
Description: hypothetical protein TSIB_0760 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.52
# Mc/sec: 276.28
//
Query:       gi|242398747|ref|YP_002994171.1|  [L=59]
Description: hypothetical protein TSIB_0761 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.091   12.4   0.0      0.097   12.3   0.0    1.0  1  UPF0020   Putative RNA methylase family UPF0020


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 ?   12.3   0.0   5.4e-06     0.097      72     105 ..      20      56 ..       2      58 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.4e-06
                                       HHH...HH--EEEEES-HHHHHHHHHHHHHTT-GGGE CS
                           UPF0020  72 ear...aelklygsDldrrvvqgareNaekagvgdli 105
                                        ++   +e k++++++++++++ ar+N+ + ++g +i
  gi|242398747|ref|YP_002994171.1|  20 YKNstiPEEKIIAVNKIEKAIEIARKNLGRDTIGFEI 56 
                                       3342346777******************999988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       659  (0.0367561); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 345.93
//
Query:       gi|242398748|ref|YP_002994172.1|  [L=147]
Description: metalloprotease [Thermococcus sibiricus MM 739]
Scores for complete 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   56.9   0.0    2.1e-15   56.6   0.0    1.1  1  Prok-JAB  Prokaryotic homologs of the JAB domain
    6.7e-05   22.9   0.0    8.8e-05   22.5   0.0    1.2  1  JAB       JAB1/Mov34/MPN/PAD-1 ubiquitin protease
  ------ inclusion threshold ------
      0.048   13.7   0.0      0.068   13.2   0.0    1.3  1  DUF4329   Domain of unknown function (DUF4329)


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 !   56.6   0.0   3.4e-19   2.1e-15      11     107 ..      30     125 ..      21     135 .. 0.77

  Alignments for each domain:
  == domain 1  score: 56.6 bits;  conditional E-value: 3.4e-19
                          Prok-JAB  11 harrahpeEtcGlllgkeseseevivvplvnewsn......rfeipdpedslarlkfearerglevvgiwHSHpggs 81 
                                       ++ r++  E cG+l+g+   + e ++v+ +   +n      +fei dp ++l++l  +a++++ ++vgi+HSH + +
  gi|242398748|ref|YP_002994172.1|  30 KRAREENIEICGFLVGRD--EGEKVFVDYIVFEKNilksshEFEI-DPLETLKVLE-SAEKKNKDIVGIFHSHVNFP 102
                                       45567899*********8..344444443433444566799****.**********.******************** PP

                          Prok-JAB  82 arPSetDrrdaaalarvkalliivgd 107
                                       ++PS++D++ ++a      +++iv++
  gi|242398748|ref|YP_002994172.1| 103 PYPSQKDLKGMKAW---RNVWLIVNN 125
                                       *************8...455555554 PP

>> JAB  JAB1/Mov34/MPN/PAD-1 ubiquitin protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   1.5e-08   8.8e-05      19     110 ..      28     114 ..      14     119 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.5e-08
                                       HHHHHHHHTS--EEEEEEEESSSEEEEEEEEEEESEEEESSECEEEEEHHHHHHHHHHHHHHHCTTSEEEEEEEESS CS
                               JAB  19 halrtekeeeevmGlliGelnddttveitnvfalpfeetekdvdavsldqeylekksellkklrgrervvGWYhshp 95 
                                       + +r ++e+ e++G l+G  +++   +++  +++  ++  k+ ++ ++d  +  k  e+++k   +  +vG +hsh 
  gi|242398748|ref|YP_002994172.1|  28 ILKRAREENIEICGFLVGRDEGE---KVFVDYIVFEKNILKSSHEFEIDPLETLKVLESAEKK--NKDIVGIFHSHV 99 
                                       33344444459************...5566666666667777788999999777778887774..689********* PP

                                       SS-SS--HHHHHHHH CS
                               JAB  96 ditvwlsevdvrtqa 110
                                       ++  ++s+ d++ ++
  gi|242398748|ref|YP_002994172.1| 100 NFPPYPSQKDLKGMK 114
                                       **********98766 PP

>> DUF4329  Domain of unknown function (DUF4329)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.1e-05     0.068      13      66 ..      30     100 ..      21     125 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.1e-05
                           DUF4329  13 grSirenrEyagviltddeGk..yvateptagte..asve.akvp.............qgqtvvasyhtHgA 66 
                                       +r   en E++g+++ +deG+  +v +++  +++  +s++  +++             + +++v+ +h+H  
  gi|242398748|ref|YP_002994172.1|  30 KRAREENIEICGFLVGRDEGEkvFV-DYIVFEKNilKSSHeFEIDpletlkvlesaekKNKDIVGIFHSHVN 100
                                       566679**************99633.3333333311222232333455666777888899999*******76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); 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: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 950.01
//
Query:       gi|242398749|ref|YP_002994173.1|  [L=245]
Description: Molybdopterin-guanine dinucleotide biosynthesis protein B [Thermococcus sibiricus MM 739]
Scores for complete 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   68.9   0.3    6.6e-19   68.1   0.3    1.4  1  MobB      Molybdopterin guanine dinucleotide synthesis protei
    9.8e-08   31.5   0.3    1.8e-07   30.7   0.3    1.5  1  FeS       Putative Fe-S cluster
     0.0017   18.5   0.9        1.5    9.0   0.1    2.8  2  UPF0180   Uncharacterised protein family (UPF0180)
     0.0025   17.8   0.1     0.0046   17.0   0.1    1.4  1  AAA_14    AAA domain
     0.0074   15.8   0.2      0.016   14.7   0.0    1.6  2  KTI12     Chromatin associated protein KTI12
  ------ inclusion threshold ------
      0.022   15.2   0.6       0.12   12.8   0.1    2.1  2  AAA       ATPase family associated with various cellular acti
      0.064   12.9   0.4       0.16   11.6   0.4    1.7  1  SRP54     SRP54-type protein, GTPase domain
       0.11   12.6   0.0       0.24   11.5   0.0    1.8  1  CbiA      CobQ/CobB/MinD/ParA nucleotide binding domain
       0.11   12.3   1.0       0.19   11.5   0.1    1.9  2  AAA_26    AAA domain


Domain annotation for each model (and alignments):
>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.1   0.3   3.3e-22   6.6e-19       2     115 ..       4     111 ..       3     127 .. 0.88

  Alignments for each domain:
  == domain 1  score: 68.1 bits;  conditional E-value: 3.3e-22
                              MobB   2 lgivgksgsGKTtLleklipelkarglrvgtiKhahhgfdvdkpgkDsyrhrkAGAkevlvaskerlalikeleeae 78 
                                       +++vg+++sGKT+ +e++ +elk+rg++vg+ K  h +f  dk++ D+++++k  A+ v+v ++e  al+ +     
  gi|242398749|ref|YP_002994173.1|   4 MAFVGFKKSGKTAVVENVAKELKKRGYKVGIAKSMHVNF--DKKDSDTWKFKKI-ADYVVVRAQETDALLFDA---- 73 
                                       689******************************999766..899*******997.9*************9994.... PP

                              MobB  79 lsleellarlsevDlvlvEGfkke.alpkievlraelg 115
                                        +l+ ll+++ evD++l EGfk++ ++pki + + e +
  gi|242398749|ref|YP_002994173.1|  74 RDLNSLLSMMPEVDFLLLEGFKDAkHIPKIICAKIEDE 111
                                       57********************862579**99886644 PP

>> FeS  Putative Fe-S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.3   8.9e-11   1.8e-07       1      32 [.     161     191 ..     161     192 .. 0.97

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 8.9e-11
                               FeS   1 LPgtNCgaCGypgCmafAealvegeaqledCp 32 
                                       LP++NC+ CG+  C  +A+ +v+ge++++dC 
  gi|242398749|ref|YP_002994173.1| 161 LPNINCRMCGF-DCYKMAKLIVNGEKSVKDCS 191
                                       9**********.*******************5 PP

>> UPF0180  Uncharacterised protein family (UPF0180)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.1   0.00077       1.5      10      29 ..      19      44 ..      16      77 .. 0.68
   2 !    7.3   0.1    0.0026       5.2      50      77 .]     132     157 ..     110     157 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00077
                           UPF0180 10 snvkeaLrekGYeVvdlet......e 29
                                      +nv+++L+++GY+V   ++      +
  gi|242398749|ref|YP_002994173.1| 19 ENVAKELKKRGYKVGIAKSmhvnfdK 44
                                      79***********9766655455540 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0026
                           UPF0180  50 iedtetkapvInAsgktaeeIlqeveer 77 
                                       ie + ++ pvInA  kt+e I + vee+
  gi|242398749|ref|YP_002994173.1| 132 IE-KINGLPVINAL-KTPEKIADLVEEK 157
                                       55.5789******8.8********9986 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   2.3e-06    0.0046       4      71 ..       3      72 ..       1      76 [. 0.83

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.3e-06
                            AAA_14  4 ilvitGaRrvGKTtllkqlikell.....vkkesilyinldderdkkladpekllelileklkeekktylflD 71
                                      +++ +G +++GKT ++++++kel      v   + + +n+d+++ ++ + ++k+ +++  +++  ++  l++D
  gi|242398749|ref|YP_002994173.1|  3 AMAFVGFKKSGKTAVVENVAKELKkrgykVGIAKSMHVNFDKKDSDTWK-FKKIADYVVVRAQ--ETDALLFD 72
                                      67789****************999*****999**********9987666.6678888877642..45667776 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   7.9e-06     0.016       5      49 ..       5      48 ..       1      66 [. 0.84
   2 ?   -2.4   0.0       1.3   2.5e+03     148     174 ..     196     222 ..     194     234 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 7.9e-06
                                      EEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH.TTSSS-- CS
                             KTI12  5 vltGlPssGKstrakeLakaleeekrsvvviddeslgiekdsykd 49
                                       + G+  sGK+ +++++ak+l++++++v + ++  ++++k++  d
  gi|242398749|ref|YP_002994173.1|  5 AFVGFKKSGKTAVVENVAKELKKRGYKVGIAKSMHVNFDKKDS-D 48
                                      57899********************************999883.2 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.3
                                       S-SEEEE.TTS---HHHHHHHHHHHHT CS
                             KTI12 148 sPlftvlsaeeklpldeilkaliekkk 174
                                       +P + v+++ ++lp+++ ++ l+ek+ 
  gi|242398749|ref|YP_002994173.1| 196 KPRVMVKIDGKELPMKDWVQELVEKTI 222
                                       577788888888888888888888765 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   0.1   6.2e-05      0.12       2      73 ..       5      92 ..       4     135 .. 0.65
   2 ?    0.6   0.0      0.35   7.1e+02      25      57 ..     199     233 ..     176     242 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.2e-05
                                      EEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSS.................STTHHHHHHHHHHHHHHHTSTSEEEE CS
                               AAA  2 llyGppGtGKTllakavakelgvefleisgsellsk.................yvgesekkirelfkeakekakpsilf 63
                                       ++G +  GKT++++ vakel+ + +++  ++ +                   yv  +++++ +l+ +a+  +     +
  gi|242398749|ref|YP_002994173.1|  5 AFVGFKKSGKTAVVENVAKELKKRGYKVGIAKSMHVnfdkkdsdtwkfkkiadYVVVRAQETDALLFDARDLN-SLLSM 82
                                      68899999*************8554444444444222333455566667777777777777777777777776.44556 PP

                                      EETGGGHHHH CS
                               AAA 64 iDEidalaks 73
                                      + E+d l  +
  gi|242398749|ref|YP_002994173.1| 83 MPEVDFLLLE 92
                                      6666666555 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.35
                                       EEEEEETTTCS.SSSTTH.HHHHHHHHHHHHHHTS CS
                               AAA  25 efleisgsell.skyvge.sekkirelfkeakeka 57 
                                        +++i+g+el  +++v+e  ek i+++++++k+ +
  gi|242398749|ref|YP_002994173.1| 199 VMVKIDGKELPmKDWVQElVEKTIKGMLSAMKSYK 233
                                       36889999998677877735677777777777665 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.4   8.1e-05      0.16       4      35 ..       4      35 ..       1      39 [. 0.93

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.1e-05
                                      EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEE CS
                             SRP54  4 illvGlqGaGKTttlaKLaallkkegkkvllv 35
                                      +++vG++ +GKT  +  +a+ lkk+g+kv ++
  gi|242398749|ref|YP_002994173.1|  4 MAFVGFKKSGKTAVVENVAKELKKRGYKVGIA 35
                                      789**************************987 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 ?   11.5   0.0   0.00012      0.24      10      83 ..      12     130 ..       6     216 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00012
                                       SSHHHHHHHHHHHHHHTT--EEEEE.EEESSCCCCHHTTEB-HHHH............................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx............................... RF
                              CbiA  10 vGKTtlaanLaralarrglrVllvD.aDpqannlaileglendiep............................... 54 
                                       +GKT ++ n a+ l++rg++V   + + +          +++d ++                               
  gi|242398749|ref|YP_002994173.1|  12 SGKTAVVENVAKELKKRGYKVGIAKsMHVN--------FDKKDSDTwkfkkiadyvvvraqetdallfdardlnsll 80 
                                       7********************999943333........334444445555556677789999999999999999999 PP

                                       ...............CCHCCCHHH.HHHCHCHHHH.......EEEEEEEE CS
                                       ...............xxxxxxxxx.xxxxxxxxxx.....xxxxxxxxxx RF
                              CbiA  55 ...............dlkrllell.ealgkkkall.....lkiagvvlnr 83 
                                                      d+k + +++ +++  +++ l     + i g+++n+
  gi|242398749|ref|YP_002994173.1|  81 smmpevdflllegfkDAKHIPKIIcAKIEDEVKELndglaIGISGIIANK 130
                                       99999999999999988888888777777666666677888888888887 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   9.7e-05      0.19      11      49 ..      11      50 ..       9      99 .. 0.81
   2 ?   -2.1   0.1       1.4   2.8e+03     158     170 ..     122     134 ..     111     157 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 9.7e-05
                            AAA_26 11 gvGKTvvslgLvralkrkgvkvgyfKPiqtgiee.dedse 49
                                      ++GKT+v   +++ lk++g+kvg  K +     + d+d+ 
  gi|242398749|ref|YP_002994173.1| 11 KSGKTAVVENVAKELKKRGYKVGIAKSMHVNFDKkDSDTW 50
                                      79************************99777753244444 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.4
                            AAA_26 158 rvlGvilNkvrnp 170
                                        + G+i+Nk  ++
  gi|242398749|ref|YP_002994173.1| 122 GISGIIANKGIEK 134
                                       5778888885444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       976  (0.0544369); expected 358.6 (0.02)
Passed bias filter:                      688  (0.0383736); 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: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.50
# Mc/sec: 1467.70
//
Query:       gi|242398750|ref|YP_002994174.1|  [L=73]
Description: hypothetical protein TSIB_0764 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0051   16.9   0.2      0.007   16.5   0.2    1.3  1  DUF150_C  RimP C-terminal SH3 domain


Domain annotation for each model (and alignments):
>> DUF150_C  RimP C-terminal SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.2   3.9e-07     0.007       8      61 ..      14      66 ..      10      71 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.9e-07
                          DUF150_C  8 arflGelVkvklklpvegrkkftGkivevdeet....itlevdgkkrkkettipladi 61
                                      +++ G++V++       g + ftG+++e+dee      + +v+g+k+k  + ++++di
  gi|242398750|ref|YP_002994174.1| 14 ENWKGKKVALAV----GGDHSFTGILEEFDEEIillkNVMDVVGNKGK-SLIVKIDDI 66
                                      679999999995....5*************998333334456666444.466666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 551.29
//
Query:       gi|242398751|ref|YP_002994175.1|  [L=273]
Description: hypothetical protein TSIB_0765 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.035   14.2   0.2         36    4.5   0.0    3.8  4  DUF5338      Family of unknown function (DUF5338)
       0.04   14.0   0.1       0.58   10.3   0.1    2.3  2  S10_plectin  Plectin/S10 domain


Domain annotation for each model (and alignments):
>> DUF5338  Family of unknown function (DUF5338)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.56     5e+03      57      65 ..      31      39 ..      10      40 .. 0.73
   2 ?    4.5   0.0     0.004        36       4      37 ..      45      79 ..      42      84 .. 0.90
   3 ?    3.1   0.0     0.011     1e+02      30      49 ..      85     104 ..      80     113 .. 0.84
   4 ?    1.7   0.0      0.03   2.7e+02      42      57 ..     249     264 ..     248     265 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.56
                           DUF5338 57 isYeTFlrY 65
                                        Ye+F+ Y
  gi|242398751|ref|YP_002994175.1| 31 LGYEAFVGY 39
                                      468888777 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.004
                           DUF5338  4 aeeiakr.skakrskrrknrvaFLavrkdikealk 37
                                       eei ++ ++ ++++++   + FL+ ++ i+ al+
  gi|242398751|ref|YP_002994175.1| 45 LEEIGNTiNSIQSDEKEVIHQGFLGFKEQINHALE 79
                                      58899999999999999****************97 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.011
                           DUF5338  30 kdikealkaGyalktiwehL 49 
                                       +di++ l++Gy +  +++ L
  gi|242398751|ref|YP_002994175.1|  85 EDINRLLQEGYWMGDVLDQL 104
                                       69*********999998877 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.03
                           DUF5338  42 lktiwehLheegkiti 57 
                                       l +i+++L++eg+i i
  gi|242398751|ref|YP_002994175.1| 249 LEEIFRMLEKEGRIDI 264
                                       689**********987 PP

>> S10_plectin  Plectin/S10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   6.4e-05      0.58       9      59 ..     100     154 ..      97     158 .. 0.80
   2 ?    1.0   0.0     0.049   4.4e+02      31      74 ..     161     204 ..     155     219 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 6.4e-05
                                       HHHHCCCCSCEEEE--SS----SSS---HHHH.....HHHHHHCCCCTSEEEEEET CS
                       S10_plectin   9 iyeylfkegvlvakkdfelkkheelnvpnlqv.....ikalqSLksrgyvkeqfaW 59 
                                       + ++lf++ v+v++++   k +e++++++l+      +++ + L+s + + +qfa+
  gi|242398751|ref|YP_002994175.1| 100 VLDQLFRNDVIVVEENKA-KLKEDIDIKKLRFqfrfpYQLAKDLESIEKIAKQFAF 154
                                       7899**********9976.8899999999875333346888888888888888886 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.049
                                       SSS---HHHHHHHHHHCC.CCTSEEEEEETTEEEEEE-HHHHHHH CS
                       S10_plectin  31 eelnvpnlqvikalqSLk.srgyvkeqfaWrhyYytLtneGieyl 74 
                                        e++++ l++ k+ ++L+   +y +e ++   +Y+ L + Gi   
  gi|242398751|ref|YP_002994175.1| 161 YEIEIKELEIEKINRALHiAAKYFEEDMVM-GVYFALISRGIVAN 204
                                       577899999999999997345677777665.56888888888654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); 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 0.28s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 1892.50
//
Query:       gi|242398752|ref|YP_002994176.1|  [L=111]
Description: hypothetical protein TSIB_0766 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0016   18.2   6.6     0.0029   17.4   6.6    1.5  1  DUF5362      Family of unknown function (DUF5362)
  ------ inclusion threshold ------
      0.019   15.1   2.2      0.063   13.4   1.7    2.0  2  DUF4234      Domain of unknown function (DUF4234)
       0.02   14.8   8.0      0.023   14.6   8.0    1.1  1  DUF4013      Protein of unknown function (DUF4013)
      0.031   14.4   0.5      0.056   13.6   0.5    1.5  1  DUF2371      Uncharacterised conserved protein (DUF2371)
      0.046   13.7   0.8      0.072   13.1   0.1    1.7  2  Ac76         Orf76 (Ac76)
      0.088   12.6   0.2       0.14   12.0   0.2    1.4  1  MotA_ExbB    MotA/TolQ/ExbB proton channel family
       0.24   10.9   0.7       0.31   10.6   0.7    1.2  1  Stevor       Subtelomeric Variable Open Reading frame
       0.33   11.3   2.2        1.3    9.3   0.2    2.1  2  Sigma_reg_N  Sigma factor regulator N-terminal
        1.1    9.6   2.5          2    8.7   2.5    1.5  1  COX7C        Cytochrome c oxidase subunit VIIc
        3.3    7.9   7.4         14    5.9   4.4    2.4  2  Insulin_TMD  Insulin receptor trans-membrane segment
        9.1    4.9   6.7        2.1    7.0   2.2    1.6  2  DUF2207      Predicted membrane protein (DUF2207)


Domain annotation for each model (and alignments):
>> DUF5362  Family of unknown function (DUF5362)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   6.6   1.8e-06    0.0029       4      85 ..      11     101 ..       8     103 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.8e-06
                           DUF5362   4 islwmkilGvllii....lGaltcLsIigiiigvllIivglklfkaakaikealrskseeklke.....aleklaky 71 
                                       +++  k+ G+l +i    + +l  L++igi+ +++  i g  ++k  +++ e +++ + +k k      a+ +l   
  gi|242398752|ref|YP_002994176.1|  11 ARTLIKVGGILSVIepfvIAVLLLLTVIGILFAIPFAILGYWIYKRTEECTEFIENGEYKKAKDkllipAIIALILT 87 
                                       5667788888888644447899***********************99998888887776665551111155566666 PP

                           DUF5362  72 lkillilliielvl 85 
                                        ++ +il+++ l+l
  gi|242398752|ref|YP_002994176.1|  88 SRVGGILMLLGLIL 101
                                       77778888888887 PP

>> DUF4234  Domain of unknown function (DUF4234)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.7      0.73   1.2e+03       4      54 ..      30      39 ..      10      50 .. 0.64
   2 ?   13.4   1.7   3.9e-05     0.063      20      58 ..      51      93 ..      27     103 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.73
                           DUF4234  4 avvilLsivTlGIYslyWlykltrelnrlsgrkkttslllvflllslitcg 54
                                      a                                         +ll l ++g
  gi|242398752|ref|YP_002994176.1| 30 A-----------------------------------------VLLLLTVIG 39
                                      2.........................................333344444 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 3.9e-05
                           DUF4234 20 yWlykltrelnrlsgr...kkttslllv.flllslitcgiysi 58
                                      yW+yk+t+e  ++ ++   kk++++ll  +++  ++t+ + +i
  gi|242398752|ref|YP_002994176.1| 51 YWIYKRTEECTEFIENgeyKKAKDKLLIpAIIALILTSRVGGI 93
                                      9***************998555555555544433333333333 PP

>> DUF4013  Protein of unknown function (DUF4013)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   8.0   1.4e-05     0.023      75     166 ..       7     101 ..       1     102 [. 0.70

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.4e-05
                           DUF4013  75 slaagdsaagallvlall...glllalllvllllllfglllpvalarfartgslsaafnfkeilklikkki.gkyii 147
                                        +  + +++  +++l ++    ++++lll ++++l++  ++++++ ++ rt++  ++++ +e  k +k+k+ +  ii
  gi|242398752|ref|YP_002994176.1|   7 DVEMARTLIKVGGILSVIepfVIAVLLLLTVIGILFAIPFAILGYWIYKRTEECTEFIENGEYKK-AKDKLlIPAII 82 
                                       444444444444444444554555555566777777777888999999999999999999**999.65666899999 PP

                           DUF4013 148 alilllvigivlsllaill 166
                                       alil   +g++l+ll+++l
  gi|242398752|ref|YP_002994176.1|  83 ALILTSRVGGILMLLGLIL 101
                                       9999999999999999887 PP

>> DUF2371  Uncharacterised conserved protein (DUF2371)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.5   3.5e-05     0.056      41      88 ..      30      76 ..       8     102 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.5e-05
                           DUF2371 41 glvlllGllvllvGiamavlgywpkkaklaseekssssstaesssekl 88
                                      +++lll ++ +l  i +a+lgyw  k+ +++ ++  ++++ +++++kl
  gi|242398752|ref|YP_002994176.1| 30 AVLLLLTVIGILFAIPFAILGYWIYKR-TEECTEFIENGEYKKAKDKL 76
                                      2333444444555667899****9995.44445555555555555544 PP

>> Ac76  Orf76 (Ac76)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   4.4e-05     0.072      26      69 ..      33      78 ..      12      89 .. 0.77
   2 ?   -0.9   0.3       1.1   1.7e+03      12      31 ..      81     100 ..      75     103 .. 0.49

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.4e-05
                              Ac76 26 llltll.llfvlFiillnvy.yikteStpadlytekakkikKkrdl 69
                                      lllt++ +lf + + +l +  y +te  ++ + +++ kk k k  +
  gi|242398752|ref|YP_002994176.1| 33 LLLTVIgILFAIPFAILGYWiYKRTEECTEFIENGEYKKAKDKLLI 78
                                      5566655899998899987526689999*************99765 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.1
                              Ac76  12 vlafildkneklsellltll 31 
                                       ++a+il    +   +ll l+
  gi|242398752|ref|YP_002994176.1|  81 IIALILTSRVGGILMLLGLI 100
                                       55566555544443443333 PP

>> MotA_ExbB  MotA/TolQ/ExbB proton channel family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   8.3e-05      0.14      90     123 ..      29      62 ..       8      66 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.3e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MotA_ExbB  90 iaeALiaTalGlvvAipavlaynklkrkverlvl 123
                                       ia+ L+ T++G+++Aip+ ++  ++ +++e+ ++
  gi|242398752|ref|YP_002994176.1|  29 IAVLLLLTVIGILFAIPFAILGYWIYKRTEECTE 62 
                                       88889*************9999988888887766 PP

>> Stevor  Subtelomeric Variable Open Reading frame
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.7   0.00019      0.31     226     263 ..      17      59 ..       2      72 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00019
                            Stevor 226 asaassafepygiaalvllil.....avvliiLYiwlyrRRKn 263
                                       ++   s++ep+ ia+l+ll +     a+ + iL  w+y+R  +
  gi|242398752|ref|YP_002994176.1|  17 VGGILSVIEPFVIAVLLLLTVigilfAIPFAILGYWIYKRTEE 59 
                                       5556799********99986511111344568889****9765 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 ?    9.3   0.2   0.00083       1.3      14      50 ..      28      65 ..      22      67 .. 0.78
   2 ?    1.8   0.1      0.18   2.9e+02       5      34 ..      70      98 ..      68     110 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00083
                       Sigma_reg_N 14 rivlislivlllifvil.vvtllylaekegnklrevle 50
                                       i+++ l++++ i++ + + +l y + k++++ +e++e
  gi|242398752|ref|YP_002994176.1| 28 VIAVLLLLTVIGILFAIpFAILGYWIYKRTEECTEFIE 65
                                      5666677777777777778888888*******999987 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.18
                       Sigma_reg_N  5 kkakrksilrivlislivlllifvilvvtl 34
                                      kkak k+++  +++ +++  +   il++++
  gi|242398752|ref|YP_002994176.1| 70 KKAKDKLLIPAIIALILTSRV-GGILMLLG 98
                                      788888888766555554444.33333333 PP

>> COX7C  Cytochrome c oxidase subunit VIIc
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   2.5    0.0013         2      41      64 .]      32      55 ..      25      55 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0013
                                      HHHHHHHHHHHHHHHHHHHHHHTT CS
                             COX7C 41 vkywgflgvgFalPFlavrwQlkK 64
                                      +++ +++g+ Fa+PF++  + ++K
  gi|242398752|ref|YP_002994176.1| 32 LLLLTVIGILFAIPFAILGYWIYK 55
                                      577899***********9887766 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 ?    5.9   4.4    0.0085        14      14      37 ..      20      43 ..       3      45 .. 0.76
   2 ?    2.8   0.0     0.079   1.3e+02      17      35 ..      76      94 ..      68      97 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0085
                       Insulin_TMD 14 ivkIvigPviciillllvigavfv 37
                                      i+ ++   vi ++lll vig++f 
  gi|242398752|ref|YP_002994176.1| 20 ILSVIEPFVIAVLLLLTVIGILFA 43
                                      455555557888888999999996 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.079
                       Insulin_TMD 17 IvigPviciillllvigav 35
                                        i  +i +il + v+g++
  gi|242398752|ref|YP_002994176.1| 76 LLIPAIIALILTSRVGGIL 94
                                      6678899999999998874 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   2.2    0.0013       2.1     405     444 ..      24      63 ..       9      68 .. 0.67
   2 ?    1.1   0.0     0.081   1.3e+02     368     404 ..      65     101 ..      57     106 .. 0.53

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0013
                           DUF2207 405 lvlllvfllilllillliaiivlllfsrllgrrteeGael 444
                                       + ++++  l+ll++++++++i ++++ + +++rtee +e 
  gi|242398752|ref|YP_002994176.1|  24 IEPFVIAVLLLLTVIGILFAIPFAILGYWIYKRTEECTEF 63 
                                       3333667777777888888888888888888888887765 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.081
                           DUF2207 368 ergyfdkkgkkklkklsalglgliilglilillalll 404
                                       e+g ++k++ k l   ++++++   +g il+ll+l+l
  gi|242398752|ref|YP_002994176.1|  65 ENGEYKKAKDKLLIPAIIALILTSRVGGILMLLGLIL 101
                                       4455555555555555555555555555555554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       923  (0.0514808); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); 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: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 851.43
//
Query:       gi|242398753|ref|YP_002994177.1|  [L=329]
Description: Hydrogenase expression/formation protein HypE [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-32  113.1   2.6    3.2e-32  111.8   1.3    2.0  2  AIRS_C    AIR synthase related protein, C-terminal domain
    1.5e-17   64.1   0.5    3.2e-17   63.0   0.1    1.7  2  AIRS      AIR synthase related protein, N-terminal domain


Domain annotation for each model (and alignments):
>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0     0.094   8.4e+02     117     155 ..      86     124 ..      82     125 .. 0.67
   2 !  111.8   1.3   3.5e-36   3.2e-32       1     156 []     151     310 ..     151     310 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.094
                                       EEEEHGGHHHHHHHHHHTTCCCEEEEEEEEESSSEEEEE CS
                            AIRS_C 117 vavppeeadavlaileeeglpeaavIGevtakeelsviv 155
                                       +++p+++++++l+++ e   + a+++G  + +++++v+v
  gi|242398753|ref|YP_002994177.1|  86 ILLPENADEELLEKIMEDMHKSAERLGISIVGGHTEVTV 124
                                       344444447777776665556799999988888888876 PP

  == domain 2  score: 111.8 bits;  conditional E-value: 3.5e-36
                                       STTEEEEEEETSSCTCCHHHHHHHCHHHCTSHTTTSE.HHHHHHHH.HHHHHHHHHHHHHTTECEEEE--TTHHHHH CS
                            AIRS_C   1 kpGdvliltgslGlggagtslkrkileeeglddsavq.lgdvllep.tliyvkralaalkglvkaahDvTgGGLlga 75 
                                       kpGdv+ilt++ G+ g ++ + +   e ++   ++++ + ++ +   +   vk+al+a+k +v+a+hD T+GG+++ 
  gi|242398753|ref|YP_002994177.1| 151 KPGDVIILTKGAGIEGTSIIATENEEELKK--VFGKElVENAKRFLqKISVVKEALIAAKIGVHAMHDPTEGGIANG 225
                                       79**************99777663333333..3455534444443304444445555559***************** PP

                                       HHHHHHTTTEEEEEECGTHHHHHHHH.....HHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEEEE CS
                            AIRS_C  76 laemapasgvgaeidldkvpifdele.....splemllsensGrllvavppeeadavlaileeeglpeaavIGevta 147
                                        +ema+a+gvg++++++k+pi +e++     ++l++l   +sG ll+a+ppe+a++v++++++ g+ e+a++Ge  +
  gi|242398753|ref|YP_002994177.1| 226 FHEMADAAGVGFRVYYEKIPIAEETRklcehFQLDPLALISSGSLLIAAPPEKAEKVVEAIRRKGI-EVAIVGEFLE 301
                                       ******************************************************************.8********* PP

                                       SSSEEEEEE CS
                            AIRS_C 148 keelsvivk 156
                                       +++++vivk
  gi|242398753|ref|YP_002994177.1| 302 DNNVKVIVK 310
                                       *****9985 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 !   63.0   0.1   3.5e-21   3.2e-17       3      94 .]      36     139 ..      34     139 .. 0.81
   2 ?   -3.6   0.0         2   1.8e+04      57      71 ..     221     235 ..     209     236 .. 0.75

  Alignments for each domain:
  == domain 1  score: 63.0 bits;  conditional E-value: 3.5e-21
                                       SE........EEEEEEEEE.EECCTCCCC....HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC......HHHHHHHH CS
                              AIRS   3 aa........vvvttdshnrpvlvepvhf....iGakavavnlsDlaamGArPlalllslalp......wleevvrg 61 
                                       aa        +v+t d    p+      +    iG  av vn++D+a+ GA+P ++l+++ lp       le+++++
  gi|242398753|ref|YP_002994177.1|  36 AAaidfgdsvLVATSD----PIT-----GaekhIGFYAVNVNANDVATFGAKPKWFLVTILLPenadeeLLEKIMED 103
                                       5523333332344444....444.....355556******************************************* PP

                                       HHHHHHHTT-EEEEEEEEEESS...EEEEEEEEEEE CS
                              AIRS  62 laeaaeelgvplvgGdtsfsne...ptisvtavGlv 94 
                                       +++ ae+lg+++vgG+t+++ +   p++  t++G+v
  gi|242398753|ref|YP_002994177.1| 104 MHKSAERLGISIVGGHTEVTVGlnrPIVIGTMLGEV 139
                                       ******************9855667*********86 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 2
                                       HHHHHHHHHHHHTT- CS
                              AIRS  57 evvrglaeaaeelgv 71 
                                       ++++g++e+a+++gv
  gi|242398753|ref|YP_002994177.1| 221 GIANGFHEMADAAGV 235
                                       567778888877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       835  (0.0465726); expected 358.6 (0.02)
Passed bias filter:                      713  (0.039768); 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: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 1953.97
//
Query:       gi|242398754|ref|YP_002994178.1|  [L=501]
Description: Glycerol kinase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.8e-49  168.5   0.0    1.5e-23   83.6   0.0    2.3  2  FGGY_N       FGGY family of carbohydrate kinases, N-terminal 
      2e-33  115.8   0.0    5.4e-33  114.4   0.0    1.6  2  FGGY_C       FGGY family of carbohydrate kinases, C-terminal 
  ------ inclusion threshold ------
      0.048   13.2   0.0       0.22   11.0   0.0    1.9  2  BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family


Domain annotation for each model (and alignments):
>> FGGY_N  FGGY family of carbohydrate kinases, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.6   0.0   2.5e-27   1.5e-23       1     113 [.       3     111 ..       3     124 .. 0.94
   2 !   82.4   0.1   5.9e-27   3.5e-23     127     219 ..     151     247 ..     137     261 .. 0.93

  Alignments for each domain:
  == domain 1  score: 83.6 bits;  conditional E-value: 2.5e-27
                                       EEEEEEEESSEEEEEEEETTS-EEEEEEEE--EB-SSTT--EE-HHHHHHHHHHHHHHHHHHCT.-GCCEEEEEEEE CS
                            FGGY_N   1 lilglDcGttstkaivldekgkvvasaqaelelsspkegwaeqdpeeiwqalaeairkvleqagisekqikaIgisg 77 
                                       + l+lD+Gtt++ka++++ +g++vas ++  + ++p++gw+e+dp+e+++ +++ + k+ e++     ++ +++ ++
  gi|242398754|ref|YP_002994178.1|   3 YFLVLDVGTTNIKALAFS-QGELVASFEERPKPYYPHPGWVEEDPKEVIEIVYKLLDKAEEEL----GKPLGVALTN 74 
                                       789**************7.79999999999999**************************9999....99******** PP

                                       -SS-EEEEETTT.EESSEEE-TT--TTHHHHHHHHHT CS
                            FGGY_N  78 qreglvllDknd.kpLynailwkdrrtaeiveklkee 113
                                       qr ++vl+Dk++ +pLyn i+w+d+rt+ i+ek + +
  gi|242398754|ref|YP_002994178.1|  75 QRSSTVLWDKETgEPLYNMITWQDTRTEDIIEKFSSK 111
                                       ********************************98875 PP

  == domain 2  score: 82.4 bits;  conditional E-value: 5.9e-27
                                       SSTTSHHHHHHHHHHHSCCHHCCHC....EEEEHHHHHHHHHCT--EEEHHHHCTTTSEETTTTEE-HHHHHHTT-- CS
                            FGGY_N 127 lstgftlsklkWlkenepevfekie....kflliddyLiwrLtgqfvtdvtnasesmlfnikklewdeellailgip 199
                                         t ++ + l+Wl en+pe+ +++e     f+++d+++ w Ltg++vtd+tnas+++lf+   l+w++++++i+ ip
  gi|242398754|ref|YP_002994178.1| 151 FGTTHSSMHLRWLMENVPEAKKAMEkdsaIFGTVDSWISWNLTGKHVTDYTNASATGLFDPFYLKWSDNITKIVEIP 227
                                       56889999*****************99999*********************************************** PP

                                       GGGS-EEE-TCCEEEEEECC CS
                            FGGY_N 200 eelLPklvesseiigelkpe 219
                                       +++LP++v+    ige+k++
  gi|242398754|ref|YP_002994178.1| 228 KKILPQVVPNDTPIGEIKDY 247
                                       ****************9986 PP

>> FGGY_C  FGGY family of carbohydrate kinases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.48   2.9e+03      52      75 ..     161     185 ..     148     213 .. 0.66
   2 !  114.4   0.0     9e-37   5.4e-33       2     193 ..     273     454 ..     272     457 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.48
                            FGGY_C  52 awlldnl.glreeirdageveesla 75 
                                        wl++n  ++++++++++ ++++++
  gi|242398754|ref|YP_002994178.1| 161 RWLMENVpEAKKAMEKDSAIFGTVD 185
                                       6888888777777777766644444 PP

  == domain 2  score: 114.4 bits;  conditional E-value: 9e-37
                            FGGY_C   2 kvslGTssflll.vgtkpvisehglltpva.gedgkpeyalegsiavagslvawlldnlglreeirdageveeslae 76 
                                       k++ GT++f+ + vg+kp++ + gl+  va g ++ + y+legs+   gs+v+wl+d  gl   i+d +e+ +++  
  gi|242398754|ref|YP_002994178.1| 273 KMTNGTGTFIDInVGEKPLPGALGLYPMVAlGTKEHTLYLLEGSVITSGSAVEWLVDV-GL---IKDYSEI-STAF- 343
                                       6899***************66666666666999999********************99.88...8888888.5555. PP

                            FGGY_C  77 laaaeavadaggvvfvpafsglrapywdpdargtitglsssttlahiarAaleavalqlrailealekdsgkpldrl 153
                                             +++ ++v+f+pa+sgl +p+ +p+++gt+++++++t+ ++++   +e++a++ ++i++ +e+ s+++++r+
  gi|242398754|ref|YP_002994178.1| 344 ------AESENEVIFIPALSGLGTPHIRPNVKGTLFDITRGTKRTDLVKGMIEGIAMRCAEIIDHMESNSRIKIERI 414
                                       ......677789***************************************************************** PP

                            FGGY_C 154 avdGGgskndllmqllAdilgvpVerpktaeatalGaAil 193
                                       ++dGG+sk+d ++q  Ad+  +++ rpk+ +a a Ga +l
  gi|242398754|ref|YP_002994178.1| 415 IADGGLSKSDEFLQSVADLSSKDIMRPKYLNASAYGAYLL 454
                                       *************************************876 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 ?   -0.7   0.0      0.14   8.3e+02       4      22 ..       8      26 ..       6      84 .. 0.77
   2 ?   11.0   0.0   3.6e-05      0.22     187     266 ..     377     454 ..     375     455 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.14
                                      EE-SSEEEEEEEETTTEEE CS
                       BcrAD_BadFG  4 DgGsTttkavlmdekgevl 22
                                      D+G+T +ka  + + + v+
  gi|242398754|ref|YP_002994178.1|  8 DVGTTNIKALAFSQGELVA 26
                                      9999999999888766554 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 3.6e-05
                                       TT--HHHHHHHHHHHHHHHHHHHHHTT---SS.....EEEESGGGG-HHHHHHH.....HHHH-S-EE--GGGGGHH CS
                       BcrAD_BadFG 187 ggekaedIlaglhraialrvialisrsggvtde....vtltGGvakneaavkelrklvkenygevkininpdsiytg 259
                                       +g+k+ d ++g+ + ia+r +++i   +         ++  GG++k+  +++ + +l ++++++      p++  + 
  gi|242398754|ref|YP_002994178.1| 377 RGTKRTDLVKGMIEGIAMRCAEIIDHMESNSRIkierIIADGGLSKSDEFLQSVADLSSKDIMR------PKYLNAS 447
                                       699********************98887776556789*****************9999999999......7777788 PP

                                       HHHHHHH CS
                       BcrAD_BadFG 260 alGAalf 266
                                       a GA l+
  gi|242398754|ref|YP_002994178.1| 448 AYGAYLL 454
                                       8888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (501 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.51
# Mc/sec: 2980.39
//
Query:       gi|242398755|ref|YP_002994179.1|  [L=121]
Description: hypothetical protein TSIB_0769 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.3e-32  109.1   3.1    1.3e-31  108.4   3.1    1.3  1  DUF1667         Protein of unknown function (DUF1667)
  ------ inclusion threshold ------
      0.019   14.9   0.5      0.033   14.2   0.5    1.4  1  Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain


Domain annotation for each model (and alignments):
>> DUF1667  Protein of unknown function (DUF1667)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.4   3.1   1.5e-35   1.3e-31       3      81 ..      37     115 ..      35     116 .. 0.98

  Alignments for each domain:
  == domain 1  score: 108.4 bits;  conditional E-value: 1.5e-35
                           DUF1667   3 GeeYakkEvtnpkRivtstvkveggelplvpVktsepipkekifevmkeikkvkvkapvkigdvilknvlgtgvdvv 79 
                                       Ge+Y+ +E++npkRivtstv++ + ++p++pV+t+ep+pke+i++v++++k+v+v+apvk+g+vilknv +tgvdv+
  gi|242398755|ref|YP_002994179.1|  37 GEKYGIEEIKNPKRIVTSTVRILNAKYPRLPVRTAEPVPKERIKDVINALKEVVVEAPVKMGQVILKNVGNTGVDVI 113
                                       9**************************************************************************** PP

                           DUF1667  80 at 81 
                                       a 
  gi|242398755|ref|YP_002994179.1| 114 AE 115
                                       96 PP

>> Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.5   3.7e-06     0.033       7      31 ..       8      31 ..       3      52 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.7e-06
                                      E-SSBTT--EEEEEEETTEEEEEEE CS
                    Molybdop_Fe4S4  7 aCpyCgvgCglevhvkdgkivkveg 31
                                      +C  C  gC l+v+v+d++iv veg
  gi|242398755|ref|YP_002994179.1|  8 LCIRCPKGCMLTVTVRDDEIV-VEG 31
                                      799*****************5.444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 829.77
//
Query:       gi|242398756|ref|YP_002994180.1|  [L=418]
Description: FAD-dependent pyridine nucleotide-disulphide oxidoreductase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-31  109.0   0.2    3.3e-31  108.6   0.2    1.1  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    9.4e-12   45.3   3.6    2.3e-06   28.1   0.1    3.7  3  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    8.5e-10   37.9   5.3    1.7e-06   27.1   0.4    3.2  3  HI0933_like     HI0933-like protein
    1.2e-09   37.9   1.7    6.5e-06   25.6   0.2    2.3  2  FAD_binding_3   FAD binding domain
    4.3e-09   36.5   1.3    6.7e-07   29.4   0.3    2.5  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    7.4e-09   35.3   3.2     0.0003   20.1   1.9    2.9  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    1.7e-08   34.2   5.2    2.4e-08   33.8   0.8    2.6  3  FAD_oxidored    FAD dependent oxidoreductase
    2.1e-08   34.2   5.7    4.5e-05   23.2   0.9    3.2  3  DAO             FAD dependent oxidoreductase
    2.5e-07   30.1   7.0    2.8e-07   30.0   0.5    3.2  5  FAD_binding_2   FAD binding domain
    8.8e-07   28.4   2.5    6.6e-06   25.5   0.4    2.5  3  Thi4            Thi4 family
    1.6e-05   25.3   0.1      0.039   14.4   0.0    2.4  2  NAD_binding_7   Putative NAD(P)-binding
    2.9e-05   23.3   3.6    7.9e-05   21.9   0.5    2.7  3  GIDA            Glucose inhibited division protein A
    0.00013   22.1   0.7      0.025   14.6   0.3    2.7  3  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
    0.00016   20.9   2.4    0.00081   18.5   0.2    2.4  3  Lycopene_cycl   Lycopene cyclase protein
    0.00039   19.8   1.3     0.0036   16.7   0.2    2.4  3  Amino_oxidase   Flavin containing amine oxidoreductase
     0.0011   19.0   1.3       0.15   12.0   0.1    3.2  3  NAD_binding_9   FAD-NAD(P)-binding
     0.0016   18.7   2.9       0.63   10.3   0.1    2.9  2  TrkA_N          TrkA-N domain
     0.0017   18.0   0.3       0.46   10.1   0.0    2.4  2  ApbA            Ketopantoate reductase PanE/ApbA
      0.002   17.3   0.0        1.8    7.6   0.0    2.3  2  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
     0.0031   16.4   2.6       0.22   10.3   0.3    2.4  3  Trp_halogenase  Tryptophan halogenase
  ------ inclusion threshold ------
      0.024   14.5   0.1        6.3    6.7   0.0    2.2  2  YjeF_N          YjeF-related protein N-terminus
      0.044   13.8   0.0        3.2    7.7   0.0    2.4  2  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
      0.065   12.7   0.1          2    7.8   0.0    2.3  2  adh_short       short chain dehydrogenase
      0.081   12.8   0.1       0.38   10.6   0.0    2.1  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
        0.1   13.2   0.8         24    5.6   0.0    2.7  2  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
       0.11   11.8   0.8        1.1    8.5   0.0    2.2  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.6   0.2   4.8e-34   3.3e-31       1     293 [.       6     312 ..       6     316 .. 0.79

  Alignments for each domain:
  == domain 1  score: 108.6 bits;  conditional E-value: 4.8e-34
                                       CSEEEE--SHHHHHHHHHHHHHTS-EEEEE..TTHCHHHCSHHH....HCHHHHHHHHHHHHH.....HHHHCHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxx....xxxxxxxxxxxxxxx.....xxxxxxxxx RF
                       Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlve..legtclnggcll....skallgvaedaeias.....evvkklnqg 66 
                                       +dv+viGgGp Glaaa++la++g+ v lve  +e    +++c+     +k++ ++ +  e  +      + ++++++
  gi|242398756|ref|YP_002994180.1|   6 YDVIVIGGGPSGLAAATKLAEKGYSVGLVErkEELGGILDQCIHdgfgTKIFKKTLSGLEFSAffiqkVHSSNIETH 82 
                                       69***************************866444446777877666666666666666655588876555566666 PP

                                       CCCCHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BC.TCT..TC.TTBEECCSECHHHHHHCCSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx..xxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  67 ielllgeevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdl.gip..Gvaenvgklvrtldsaealklkl 140
                                       + ++ +   ++id++kk++     ++ +  ki+++++v A G++ r    i+  G  + +++    ++    l    
  gi|242398756|ref|YP_002994180.1|  83 LNTYVK--DMRIDKNKKEILTISPEGVK--KIKAKAIVYALGCRERHQfEIKigGTRPAGVYTAGMVQRLVNLYG-I 154
                                       666666..89999999999998887554..9************87776655553887777666444444444444.4 PP

                                       -T.SEEEEES-SHHHHHHHHHHHHHT-E.EEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEE CS
                                       xx.xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 141 lp.krivvvGgGyiGvElAaalaklgke.vtlveardrllraldkelsaaleealekeGvevklgtsvkeidgngek 215
                                       lp k+i++vGgG +G+ +A +l+  g+e + +v   +r+  +l+++++++    + + ++  + +t vkei g+++ 
  gi|242398756|ref|YP_002994180.1| 155 LPgKNILIVGGGDVGMIVARHLHLEGAEsILIVFPEERFA-GLPRNVQQC----VLDFKIPYRPRTIVKEIVGKER- 225
                                       446************************9888999999996.666666666....56679****************8. PP

                                       EE.EEETTSCE...........EEESEEEE-S-EEES-HHCSHCCT-EEEETTEE.E--TTSBESSTTEEE-GGGCT CS
                                       xx.xxxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 216 le.vvledgee...........idadlvvvavGvrpstelleeklglelderggi.vvdeflrtnvpgiyaiGDvag 279
                                       +e  +l + +e           +++d++v++vG+ p ++ l +++g e+d++ +  vv+ef +t+v+g +a+G  + 
  gi|242398756|ref|YP_002994180.1| 226 VEgAILAKVDEkwqpipgtdefYPCDTIVLSVGLIPYSRKL-KNIGAEIDPKTKGpVVNEFFETTVDGTFAVGNLV- 300
                                       7776666666667789999999****************999.*******8877766*****************999. PP

                                       ECCSS--HHHHHHH CS
                                       xxxxxxxxxxxxxx RF
                       Pyr_redox_2 280 gkggpelaqaAvqq 293
                                         ++++ +  Av++
  gi|242398756|ref|YP_002994180.1| 301 --QIFDYVDDAVES 312
                                       ..777776666655 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.1   3.3e-09   2.3e-06       2      53 ..       8      59 ..       7      66 .. 0.89
   2 ?    2.8   0.1      0.25   1.7e+02      41      73 ..      65      97 ..      58     106 .. 0.78
   3 !   13.6   0.1   0.00011     0.075       1      75 [.     159     228 ..     159     236 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 3.3e-09
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHT CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekn 53
                                      v+v+GgG +gl +A+ lae g +V +ver+++l   lD+ + + + +k+ k+
  gi|242398756|ref|YP_002994180.1|  8 VIVIGGGPSGLAAATKLAEKGYSVGLVERKEELGGILDQCIHDGFGTKIFKK 59
                                      89*************************************9998887776665 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.25
                                      HHHHHHHHHHHHTTEEEECSEEEEEEEEETTSE CS
                         Pyr_redox 41 easkilqeklekngievllntkveeiegsedgv 73
                                      e+s+ + +k+   +ie +lnt v+ ++ ++++ 
  gi|242398756|ref|YP_002994180.1| 65 EFSAFFIQKVHSSNIETHLNTYVKDMRIDKNKK 97
                                      56777888899999*********9988666543 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 0.00011
                                       EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEE CS
                         Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedgves 75 
                                       ++++vGgG++g+ +A  l+  g++  +++  ++      + + +++q+ + + +i  +  t v+ei+g+e+ ve+
  gi|242398756|ref|YP_002994180.1| 159 NILIVGGGDVGMIVARHLHLEGAESILIVFPEERF----AGLPRNVQQCVLDFKIPYRPRTIVKEIVGKER-VEG 228
                                       589***************99998776666655555....36777777777788899999999999998887.655 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.4   2.4e-09   1.7e-06       1      36 [.       6      41 ..       6      47 .. 0.95
   2 !    8.9   0.0   0.00079      0.54     100     164 ..      55     121 ..      44     126 .. 0.81
   3 ?    3.2   0.1     0.043        30       2      29 ..     159     186 ..     158     190 .. 0.89

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 2.4e-09
                                      -SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                       HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllekakklg 36
                                      +dviviGgG++Gl aA ++a++g +V l+e++++lg
  gi|242398756|ref|YP_002994180.1|  6 YDVIVIGGGPSGLAAATKLAEKGYSVGLVERKEELG 41
                                      59******************************9988 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00079
                                       EEEETT.-CHHHHHHHHHHHHHHT-EEE-S--EEEEECETTE...EEEEE.TTEEEEESEEEE---- CS
                       HI0933_like 100 rlFpvsdkaedivdallkelkeagvklrletevksvekeedg..kfrvktkseeeleadklvlAtGG 164
                                       ++F ++ +  +   ++++++++++++ +l+t vk+++ ++++  +++++ ++ ++++a+++v A+G 
  gi|242398756|ref|YP_002994180.1|  55 KIFKKTLSGLEFSAFFIQKVHSSNIETHLNTYVKDMRIDKNKkeILTISPEGVKKIKAKAIVYALGC 121
                                       77778888888888999*****************98655555005555558999**********996 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.043
                                       SEEEE--SHHHHHHHHHHHHTT--EEEE CS
                       HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlll 29 
                                       +++++GgG  G+  A +++ +g++ +l+
  gi|242398756|ref|YP_002994180.1| 159 NILIVGGGDVGMIVARHLHLEGAESILI 186
                                       689**************99999887776 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.2   9.4e-09   6.5e-06       1      35 [.       5      39 ..       5      41 .. 0.94
   2 !   11.5   0.1   0.00019      0.13       4      30 ..     160     186 ..     158     198 .. 0.93

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 9.4e-09
                                      EEEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSS CS
                     FAD_binding_3  1 etdVlIVGaGpaGlmlallLseaGvrvvlvekrst 35
                                      e+dV+++G+Gp+Gl +a+ L+e+G +v lve+ ++
  gi|242398756|ref|YP_002994180.1|  5 EYDVIVIGGGPSGLAAATKLAEKGYSVGLVERKEE 39
                                      589*****************************875 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00019
                                       EEEE--SHHHHHHHHHHHHTTHHEEEE CS
                     FAD_binding_3   4 VlIVGaGpaGlmlallLseaGvrvvlv 30 
                                       +lIVG+G +G++ a+ L+  G +++l+
  gi|242398756|ref|YP_002994180.1| 160 ILIVGGGDVGMIVARHLHLEGAESILI 186
                                       79*********************9987 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 !   29.4   0.3   9.8e-10   6.7e-07       1      37 [.      10      46 ..      10      65 .. 0.88
   2 ?    5.5   0.0      0.03        21       1      23 [.     162     185 ..     162     200 .. 0.86

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 9.8e-10
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-E CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraas 37
                                      ++G+G sGl+aA  La++g++v l+e+ + lGG +  
  gi|242398756|ref|YP_002994180.1| 10 VIGGGPSGLAAATKLAEKGYSVGLVERKEELGGILDQ 46
                                      8********************************6655 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.03
                                       EE--SHHHHHHHHHHHCCTEE.EE CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfd.vl 23 
                                       IvG+G  G+  A++L+ +g++ +l
  gi|242398756|ref|YP_002994180.1| 162 IVGGGDVGMIVARHLHLEGAEsIL 185
                                       9**************999985244 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 !   20.1   1.9   4.4e-07    0.0003     166     273 ..       7     127 ..       2     131 .. 0.59
   2 !   16.0   0.4     8e-06    0.0055      75     305 .]      58     297 ..      41     297 .. 0.67

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 4.4e-07
                       Pyr_redox_3 166 kvvViGgknSavDaAlelvrkgaeVtvvtrgseieke.....esdpsyslkpdienrle..elvke....ekikvlf 231
                                       +v+ViGg+ S+  aA++l++kg +V +v r++e+        ++ +  ++   + + le  +   +    ++i+ + 
  gi|242398756|ref|YP_002994180.1|   7 DVIVIGGGPSGLAAATKLAEKGYSVGLVERKEELGGIldqciHDGFGTKIFKKTLSGLEfsAFFIQkvhsSNIETHL 83 
                                       78899999999999999999999999999988876431111122233333333333222112222234446688888 PP

                       Pyr_redox_3 232 naevkeik..ekeeeykvktedgkkvevkddvvlatGykpdlsf 273
                                       n+ vk+++  ++++e+   +++g k  + + +v+a+G +  ++f
  gi|242398756|ref|YP_002994180.1|  84 NTYVKDMRidKNKKEILTISPEGVKKIKAKAIVYALGCRERHQF 127
                                       88887644215555555556777776777778888888777776 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 8e-06
                       Pyr_redox_3  75 eeklsrkealeYlrevaksfelpiklfeeVesvkkedegfevetsk.e...tyeAkkviiAtGefdkPnk.lnipGe 146
                                       ++ ls+ e+  ++ + ++s +++ +l++ V+++  ++++ e+ t + e   +++Ak ++ A G  ++ ++  +i G 
  gi|242398756|ref|YP_002994180.1|  58 KKTLSGLEFSAFFIQKVHSSNIETHLNTYVKDMRIDKNKKEILTISpEgvkKIKAKAIVYALGCRERHQFeIKIGGT 134
                                       556777777777777888999*********9766655444444433112459***********97666642455555 PP

                       Pyr_redox_3 147 ek.....lvkhyskvkefhkyagqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiek.eesdpsy.slkpdien 216
                                                ++++ v+ +  + g++++++Gg++ ++ +A +l  +gae  +++  +e+ +    ++++  l   i  
  gi|242398756|ref|YP_002994180.1| 135 RPagvytAGMVQRLVNLYGILPGKNILIVGGGDVGMIVARHLHLEGAESILIVFPEERFAgLPRNVQQcVLDFKIPY 211
                                       5333332567888888888899***********************99876666555444413344444234444444 PP

                       Pyr_redox_3 217 rleelvke....ekikvlfnaevkeikekeeeykvktedgkkvevkddvvlatGykpdlsflkkslfeldedgrpvl 289
                                       r +++vke    e+   ++ a + +++ek   ++   + ++++   d +vl +G  p  + lk+ + e+d +++  +
  gi|242398756|ref|YP_002994180.1| 212 RPRTIVKEivgkER---VEGAILAKVDEK---WQP-IPGTDEFYPCDTIVLSVGLIPYSRKLKNIGAEIDPKTKGPV 281
                                       55555543221032...223334444443...322.3334566666777778************9999997776666 PP

                       Pyr_redox_3 290 teeteetnvpglflaG 305
                                        +e  et+v+g f +G
  gi|242398756|ref|YP_002994180.1| 282 VNEFFETTVDGTFAVG 297
                                       66788999****9998 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.8   3.5e-11   2.4e-08       1      38 [.       7      44 ..       7      48 .. 0.96
   2 ?    0.5   0.0      0.42   2.9e+02      92     140 ..      69     116 ..      53     120 .. 0.79
   3 ?   -0.4   0.0      0.83   5.7e+02       2      28 ..     160     186 ..     159     195 .. 0.89

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 3.5e-11
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGll 38
                                      Dv+V+GGgp+G+aAA   a++G +v Lve+++ lGG l
  gi|242398756|ref|YP_002994180.1|  7 DVIVIGGGPSGLAAATKLAEKGYSVGLVERKEELGGIL 44
                                      9***********************************75 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.42
                      FAD_oxidored  92 vleemlaeagvtvllntrlvevekegkriesvtveskegrktirAkvfi 140
                                        + + ++ ++++  lnt +++++ ++++ e +t+ s eg k+i+Ak ++
  gi|242398756|ref|YP_002994180.1|  69 FFIQKVHSSNIETHLNTYVKDMRIDKNKKEILTI-SPEGVKKIKAKAIV 116
                                       455667889**********999998755555555.66789999999887 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.83
                      FAD_oxidored   2 vvVvGGgpaGvaAAiaAaraGakvlLv 28 
                                       +++vGGg  G++ A     +Ga+ +L+
  gi|242398756|ref|YP_002994180.1| 160 ILIVGGGDVGMIVARHLHLEGAESILI 186
                                       89************9999999999887 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.9   6.5e-08   4.5e-05       1      33 [.       7      41 ..       7      43 .. 0.95
   2 ?    0.1   0.0      0.69   4.7e+02     148     203 ..      66     122 ..      58     156 .. 0.67
   3 !   11.0   0.2   0.00034      0.24       2      26 ..     160     187 ..     159     195 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 6.5e-08
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiag 33
                                      dv++iGGG  Gl++A  La++g  V l+e+++++g
  gi|242398756|ref|YP_002994180.1|  7 DVIVIGGGPSGLAAATKLAEKGysVGLVERKEELG 41
                                      9******************************9988 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.69
                                       HHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEE.EEEEEEEE--GGG CS
                               DAO 148 ltaalaraaealGveilegtevtgleeedgkvwgverttp.gen.daadavVnaaGaw 203
                                       + a++ +++ +  +e +++t v++ + + +k   + + +p g +  +a+a+V a G+ 
  gi|242398756|ref|YP_002994180.1|  66 FSAFFIQKVHSSNIETHLNTYVKDMRIDKNKKEIL-TISPeGVKkIKAKAIVYALGCR 122
                                       66777788888888999999999985544332333.4455577755778899999976 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00034
                                       EEEECTSHHHHHHHHHHHHTT...EEEE CS
                               DAO   2 vviiGGGiiGlstAyeLarrg...Vtll 26 
                                       ++i+GGG +G+ +A++L  +g   ++++
  gi|242398756|ref|YP_002994180.1| 160 ILIVGGGDVGMIVARHLHLEGaesILIV 187
                                       99***************88888887776 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.5     4e-10   2.8e-07       1      36 [.       7      42 ..       7      53 .. 0.95
   2 ?   -2.3   0.0       2.5   1.7e+03     146     204 ..      69     124 ..      56     145 .. 0.66
   3 ?    2.1   0.2      0.12        80       2      32 ..     160     191 ..     159     198 .. 0.85
   4 ?   -2.4   0.0       2.7   1.9e+03     151     181 ..     204     233 ..     196     241 .. 0.80
   5 ?   -2.9   0.0         4   2.8e+03     381     402 ..     285     300 ..     277     305 .. 0.76

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 4e-10
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefgg 36
                                      DviViG+G +GLaAA+++ae+G +v +ve ++e gg
  gi|242398756|ref|YP_002994180.1|  7 DVIVIGGGPSGLAAATKLAEKGYSVGLVERKEELGG 42
                                      9*******************************9988 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.5
                                       HHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----GG CS
                     FAD_binding_2 146 rlvesarkagvdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgGfgr 204
                                        +++++ + +++ + +t+++++ +++++    +++    ++  +i+aka+v a g  +r
  gi|242398756|ref|YP_002994180.1|  69 FFIQKVHSSNIETHLNTYVKDMRIDKNKKEILTIS---PEGVKKIKAKAIVYALGCRER 124
                                       56777777777777777777777765544333333...556667778888877776666 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.12
                                       EEEE--SHHHHHHHHHHHHTTT.-EEEEESSS CS
                     FAD_binding_2   2 viViGsGlAGLaAAleaaeaGl.kvavvekeq 32 
                                       ++++G+G  G+  A  ++ +G+ ++++v  e+
  gi|242398756|ref|YP_002994180.1| 160 ILIVGGGDVGMIVARHLHLEGAeSILIVFPEE 191
                                       79********************7777776655 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 2.7
                                       HHTCTEEEEESEEEEEEEECTTEEEEEEEEE CS
                     FAD_binding_2 151 arkagvdfqerteadeLivedgrvtGavven 181
                                       +++ ++ +++rt ++e++  ++rv Ga++++
  gi|242398756|ref|YP_002994180.1| 204 VLDFKIPYRPRTIVKEIVG-KERVEGAILAK 233
                                       5666799999999999954.999***99984 PP

  == domain 5  score: -2.9 bits;  conditional E-value: 4
                                       TSBESTTEEESSBTEEE-STCE CS
                     FAD_binding_2 381 ngrvldadgqpipGLYAaGeva 402
                                        +++      +++G +A+G+  
  gi|242398756|ref|YP_002994180.1| 285 FFET------TVDGTFAVGNLV 300
                                       5555......99*******986 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.4   9.5e-09   6.6e-06      16      55 ..       4      42 ..       1      59 [. 0.92
   2 ?   -2.4   0.0       3.2   2.2e+03     171     213 ..      65     108 ..      43     115 .. 0.73
   3 ?    1.9   0.0      0.16   1.1e+02      18      39 ..     158     179 ..     141     194 .. 0.76

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 9.5e-09
                                      TEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--T CS
                              Thi4 16 aesDvvivGaGssGLtaayylakkpdlkvailersvspGG 55
                                       e Dv+++G+G+sGL+aa  la+k +  v ++er+  +GG
  gi|242398756|ref|YP_002994180.1|  4 YEYDVIVIGGGPSGLAAATKLAEK-GYSVGLVERKEELGG 42
                                      689*********************.**********99998 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.2
                                       TTTTHHHHHHHHCTTTS----.-ECB-HHHHHHHHHHHECEEET CS
                              Thi4 171 eivavvvkkikleakiekvkg.eksldaekaedaivkktrevvp 213
                                       e+ a+ ++k+++ + + +++   k +  +k  ++i+  + e v+
  gi|242398756|ref|YP_002994180.1|  65 EFSAFFIQKVHSSNIETHLNTyVKDMRIDKNKKEILTISPEGVK 108
                                       67777788887777777776525777777777777776666665 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.16
                                       EEEEEE--SHHHHHHHHHHHHC CS
                              Thi4  18 sDvvivGaGssGLtaayylakk 39 
                                        +++ivG+G  G+  a+ l  +
  gi|242398756|ref|YP_002994180.1| 158 KNILIVGGGDVGMIVARHLHLE 179
                                       6899************999766 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 !    8.8   0.0     0.003       2.1       9      42 ..       7      38 ..       1     119 [. 0.81
   2 !   14.4   0.0   5.7e-05     0.039       6      39 ..     156     190 ..     151     254 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.003
                     NAD_binding_7  9 kvlvvGgGevAarkvrklleagakvtvvapevke 42
                                       v+v+GgG+ ++  + kl+e+g  v +v  +  e
  gi|242398756|ref|YP_002994180.1|  7 DVIVIGGGPSGLAAATKLAEKGYSVGLVERK--E 38
                                      799***********************99988..3 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 5.7e-05
                     NAD_binding_7   6 kgkkvlvvGgGevAarkvrklleagak.vtvvape 39 
                                        gk++l+vGgG+v++  +r+l  +ga+ + +v pe
  gi|242398756|ref|YP_002994180.1| 156 PGKNILIVGGGDVGMIVARHLHLEGAEsILIVFPE 190
                                       589******************99998635666666 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.5   1.1e-07   7.9e-05       1      29 [.       7      37 ..       7      59 .. 0.85
   2 ?   -0.3   0.0      0.64   4.4e+02     120     150 ..      91     121 ..      64     149 .. 0.63
   3 ?    0.0   0.0      0.51   3.5e+02       2      38 ..     160     196 ..     159     202 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.1e-07
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEE..E CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi..t 29
                                      dviViGgG +G++AA ++a++G++v L+   
  gi|242398756|ref|YP_002994180.1|  7 DVIVIGGGPSGLAAATKLAEKGYSVGLVerK 37
                                      8**************************9433 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.64
                                       EEEECTTEEEEEEETTS-EEEECEEEE--TT CS
                              GIDA 120 eliveekkvkgvvtedgetikakavviatGt 150
                                       +++ ++k++  +  e  ++ikaka+v a G 
  gi|242398756|ref|YP_002994180.1|  91 RIDKNKKEILTISPEGVKKIKAKAIVYALGC 121
                                       2333346677777777777777777777776 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.51
                                       EEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT-- CS
                              GIDA   2 viViGgGhAGceAAlaaarlGakvlLithkldtiael 38 
                                       + ++GgG  G+  A ++   Ga+ +Li+   +++a l
  gi|242398756|ref|YP_002994180.1| 160 ILIVGGGDVGMIVARHLHLEGAESILIVFPEERFAGL 196
                                       789********************99997777777665 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.046        32      12      47 ..       5      39 ..       2      79 .. 0.88
   2 !   14.6   0.3   3.6e-05     0.025      10      42 ..     155     187 ..     147     192 .. 0.92
   3 ?   -2.3   0.0       5.9   4.1e+03     113     123 ..     196     206 ..     192     208 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.046
                                      T-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHH CS
                      Shikimate_DH 12 ekkvlliGaGemaelvakhLlakgvkkvvvaNRtle 47
                                      e  v++iG G  +  +a++L++kg+  v  + R  e
  gi|242398756|ref|YP_002994180.1|  5 EYDVIVIGGGPSGLAAATKLAEKGYS-VGLVERKEE 39
                                      5689********************99.888888766 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 3.6e-05
                                       .TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEE CS
                      Shikimate_DH  10 lkekkvlliGaGemaelvakhLlakgvkkvvva 42 
                                       l +k++l++G G ++  va+hL+ +g+++++++
  gi|242398756|ref|YP_002994180.1| 155 LPGKNILIVGGGDVGMIVARHLHLEGAESILIV 187
                                       5689**************************997 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 5.9
                                       SS-SB-TTGGG CS
                      Shikimate_DH 113 vPRdvepevae 123
                                       +PR+v+++v +
  gi|242398756|ref|YP_002994180.1| 196 LPRNVQQCVLD 206
                                       7*****99865 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.2   1.2e-06   0.00081       1      35 [.       7      39 ..       7      42 .. 0.93
   2 ?   -2.6   0.0       3.2   2.2e+03     107     141 ..      85     121 ..      66     135 .. 0.61
   3 ?    1.5   0.1      0.18   1.2e+02       2      20 ..     160     177 ..     159     195 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.2e-06
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieasps 35
                                      Dv+viG+Gp gl+ A +l  a++g +v+l+e  ++
  gi|242398756|ref|YP_002994180.1|  7 DVIVIGGGPSGLAAATKL--AEKGYSVGLVERKEE 39
                                      9*****************..**********97765 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.2
                     Lycopene_cycl 107 akvesveeeea.gesl.vvleggrkirarlvvdargl 141
                                         v+ ++ +++  e l +  eg +ki+a+++v a g 
  gi|242398756|ref|YP_002994180.1|  85 TYVKDMRIDKNkKEILtISPEGVKKIKAKAIVYALGC 121
                                       4455444444422333033445559999999988884 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.18
                     Lycopene_cycl   2 vvviGaGpAglslAarlte 20 
                                       ++++G+G  g+ +A +l +
  gi|242398756|ref|YP_002994180.1| 160 ILIVGGGDVGMIVARHL-H 177
                                       79*************99.2 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.2   5.2e-06    0.0036       2      28 ..      16      42 ..      15      44 .. 0.97
   2 ?    1.4   0.0      0.23   1.6e+02     224     263 ..      80     122 ..      70     136 .. 0.84
   3 ?   -3.0   0.0       4.6   3.2e+03     433     450 ..     302     319 ..     288     320 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5.2e-06
                                      HHHHHHHHHHHTTEEEEEEESSSSSBT CS
                     Amino_oxidase  2 aGLaaArqLlsaGfdVtvlEardrvGG 28
                                      +GLaaA++L+++G++V ++E ++ +GG
  gi|242398756|ref|YP_002994180.1| 16 SGLAAATKLAEKGYSVGLVERKEELGG 42
                                      9*************************9 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.23
                                       EEETSEEEEEEEEETTCEEEEETTSTEE...EESEEEE-S-HH CS
                     Amino_oxidase 224 dirlntrVkeikregdgvtvtledgevv...eaDaVvvTvplg 263
                                       + +lnt Vk+++ ++++  + + + e v   +a+a+v ++  +
  gi|242398756|ref|YP_002994180.1|  80 ETHLNTYVKDMRIDKNKKEILTISPEGVkkiKAKAIVYALGCR 122
                                       78***************99999988888889******998765 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 4.6
                                       TTTSHHHHHHHHHHHHHH CS
                     Amino_oxidase 433 ypgtvegAilSGlraAar 450
                                        +++v++A++S+  aA+ 
  gi|242398756|ref|YP_002994180.1| 302 IFDYVDDAVESAFMAAEG 319
                                       56789********99986 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.1   0.00022      0.15       2      37 ..      10      40 ..       9      47 .. 0.80
   2 ?    0.2   0.0      0.96   6.6e+02     119     154 ..      82     120 ..      66     122 .. 0.71
   3 ?    3.2   0.1      0.11        77       2      20 ..     162     180 ..     161     203 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00022
                     NAD_binding_9  2 ivGaGprGlavlerLlarakkkspleitlfdpsepg 37
                                      ++G+Gp+Gla++++L+++       ++ l++++e  
  gi|242398756|ref|YP_002994180.1| 10 VIGGGPSGLAAATKLAEKG-----YSVGLVERKEEL 40
                                      8***************994.....788888886553 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.96
                     NAD_binding_9 119 vhraevvdleeradgqavll...adgaslaadaVvLAlG 154
                                       ++++ v d++ ++++ ++l+   ++ ++++a+a+v AlG
  gi|242398756|ref|YP_002994180.1|  82 HLNTYVKDMRIDKNKKEILTispEGVKKIKAKAIVYALG 120
                                       347788888888888777665534447899999999999 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.11
                     NAD_binding_9   2 ivGaGprGlavlerLlara 20 
                                       ivG+G  G+ v+++L  + 
  gi|242398756|ref|YP_002994180.1| 162 IVGGGDVGMIVARHLHLEG 180
                                       9**************8774 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.1    0.0056       3.9       1      32 [.       8      39 ..       8      48 .. 0.91
   2 !   10.3   0.1   0.00091      0.63       1      33 [.     160     192 ..     160     204 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0056
                                      EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHH CS
                            TrkA_N  1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdee 32
                                      +i+iG G  G + a +L e g+ +v +++++ee
  gi|242398756|ref|YP_002994180.1|  8 VIVIGGGPSGLAAATKLAEkGY-SVGLVERKEE 39
                                      79*****************777.5999999886 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00091
                                       EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHH CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeer 33 
                                       i+i+G G+vG+ +a+ L+  g +  ++i   eer
  gi|242398756|ref|YP_002994180.1| 160 ILIVGGGDVGMIVARHLHLeGAE-SILIVFPEER 192
                                       79****************95555.5555555555 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.2     0.014       9.4       1      31 [.       8      38 ..       8      49 .. 0.91
   2 !   10.1   0.0   0.00067      0.46       1      32 [.     160     192 ..     160     277 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.014
                                      EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH CS
                              ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr 31
                                      + ++G G  G   a kLa++g+ v l+ r++
  gi|242398756|ref|YP_002994180.1|  8 VIVIGGGPSGLAAATKLAEKGYSVGLVERKE 38
                                      579************************9987 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00067
                                       EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.H CS
                              ApbA   1 iailGaGaiGsllaakLakagadvtlilrsr.r 32 
                                       i+i+G G +G ++a +L+  ga+ +li+  + r
  gi|242398756|ref|YP_002994180.1| 160 ILIVGGGDVGMIVARHLHLEGAESILIVFPEeR 192
                                       89*******************998888765545 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0    0.0033       2.3       3      38 ..       6      39 ..       4      42 .. 0.83
   2 !    7.6   0.0    0.0026       1.8     110     222 ..      79     187 ..      57     198 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0033
                       K_oxygenase  3 lDligiGiGpsnLsLailleevkkelkalflerqpe 38
                                      +D+i iG Gps L+ a  l+e+    ++  +er++e
  gi|242398756|ref|YP_002994180.1|  6 YDVIVIGGGPSGLAAATKLAEKG--YSVGLVERKEE 39
                                      8*************999999988..66666777665 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0026
                       K_oxygenase 110 eeqvrfgeeveevepdeeeeeelltveskdaegeeeelearnlvlgvGtepkiPevleklegkervvHsseylerke 186
                                        e  + ++ v++++ d+++ +e+lt++    eg  ++++a+++v + G++      ++   +++  v ++ + +r  
  gi|242398756|ref|YP_002994180.1|  79 IE-THLNTYVKDMRIDKNK-KEILTISP---EG-VKKIKAKAIVYALGCRERHQFEIKIGGTRPAGVYTAGMVQRLV 149
                                       33.6889999****99975.57999996...45.799***********87766555554444566666666666665 PP

                       K_oxygenase 187 e...llakkriaVvGsGqSaaeifedllrrqkkvelklv 222
                                       +    l +k+i++vG+G  +  ++++l+ + +  ++ +v
  gi|242398756|ref|YP_002994180.1| 150 NlygILPGKNILIVGGGDVGMIVARHLHLEGA-ESILIV 187
                                       5577999*************999999998765.445555 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.3   0.00032      0.22       1      34 [.       7      37 ..       7      43 .. 0.88
   2 ?   -3.5   0.0       5.1   3.5e+03      94     134 ..      57      97 ..      48     118 .. 0.58
   3 !    5.8   0.0    0.0078       5.4       1      24 [.     159     182 ..     159     192 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00032
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-S CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlvese 34
                                      +++++GGG++G  aA+ la+ +   ++v lve +
  gi|242398756|ref|YP_002994180.1|  7 DVIVIGGGPSGLAAATKLAEKG---YSVGLVERK 37
                                      699****************999...899999965 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 5.1
                                       .--EETTEEHHHHHHHHHHTT--S-HHHHH-SCHHHHHTTB CS
                    Trp_halogenase  94 igkqlegvalhhywlkarargaaeeledysleavaakakkf 134
                                       + k+l+g++++ +++++ ++   e   ++ ++ + ++++k 
  gi|242398756|ref|YP_002994180.1|  57 FKKTLSGLEFSAFFIQKVHSSNIETHLNTYVKDMRIDKNKK 97 
                                       45667778888888877666644444444444444444443 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.0078
                                       EEEEE--SHHHHHHHHHHHHHTTT CS
                    Trp_halogenase   1 kivivGGGtaGwlaAaalakalkg 24 
                                       +i+ivGGG  G ++A +l+  + +
  gi|242398756|ref|YP_002994180.1| 159 NILIVGGGDVGMIVARHLHLEGAE 182
                                       69***************9876644 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 ?    6.7   0.0    0.0091       6.3      39      66 ..      14      39 ..       8      50 .. 0.81
   2 ?    5.6   0.0     0.019        13      39      73 ..     166     202 ..     137     210 .. 0.64

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0091
                            YjeF_N 39 GgdglaaArhLaqegakVtvllleeeek 66
                                      G  glaaA  La++g++V +  +e++e+
  gi|242398756|ref|YP_002994180.1| 14 GPSGLAAATKLAEKGYSVGL--VERKEE 39
                                      889***************98..566555 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.019
                            YjeF_N  39 GgdglaaArhLaqegakVtvllleeee..kldedaer 73 
                                       G  g+++ArhL+ ega+ +++++ ee+   l++++++
  gi|242398756|ref|YP_002994180.1| 166 GDVGMIVARHLHLEGAESILIVFPEERfaGLPRNVQQ 202
                                       3349*************55533332221355555555 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 ?    7.7   0.0    0.0046       3.2       2      34 ..       8      40 ..       7      51 .. 0.89
   2 ?    3.5   0.0     0.089        62       2      35 ..     160     193 ..     159     205 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0046
                                      EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHH CS
                    NAD_Gly3P_dh_N  2 iavlGaGswGtalAkvlaenghevrlwvreeel 34
                                      + v+G+G  G a A+ lae+g +v l  r+eel
  gi|242398756|ref|YP_002994180.1|  8 VIVIGGGPSGLAAATKLAEKGYSVGLVERKEEL 40
                                      78************************9999976 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.089
                                       EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHH CS
                    NAD_Gly3P_dh_N   2 iavlGaGswGtalAkvlaenghevrlwvreeeli 35 
                                       i ++G+G  G  +A++l+ +g e  l+v+ ee +
  gi|242398756|ref|YP_002994180.1| 160 ILIVGGGDVGMIVARHLHLEGAESILIVFPEERF 193
                                       7899**************9999999998887655 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0    0.0029         2       2      41 ..       8      44 ..       7      74 .. 0.76
   2 ?    2.5   0.0      0.12        84       1      46 [.     158     202 ..     158     229 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0029
                                      EEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHH CS
                         adh_short  2 vvlvtGassGIGraiakelakeGakvvvvdrseekleeva 41
                                      v+++ G+ s  G+a a +la++G++v +v+r+ee    ++
  gi|242398756|ref|YP_002994180.1|  8 VIVIGGGPS--GLAAATKLAEKGYSVGLVERKEELG-GIL 44
                                      344444444..678999**************98754.444 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.12
                                       SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHH CS
                         adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelke 46 
                                       k +l++G++  +G  +a++l  eGa+ +++   ee+ + +  ++++
  gi|242398756|ref|YP_002994180.1| 158 KNILIVGGG-DVGMIVARHLHLEGAESILIVFPEERFAGLPRNVQQ 202
                                       679999998.59****************988888887777666665 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 ?   10.6   0.0   0.00056      0.38       2      44 ..       8      50 ..       7      96 .. 0.79
   2 ?   -0.6   0.0       1.6   1.1e+03       2      32 ..     160     190 ..     159     206 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00056
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHH CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseealekalekiek 44
                                      v viG G  G   a+ +a++g++V lv+++ee      + i++
  gi|242398756|ref|YP_002994180.1|  8 VIVIGGGPSGLAAATKLAEKGYSVGLVERKEELGGILDQCIHD 50
                                      78***************************99876555555555 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.6
                                       EEEE--SCCHHHHHHHHHHTT-EEEEE-S-H CS
                           3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdise 32 
                                       + ++G G +G  +a  +  +g e  l+   e
  gi|242398756|ref|YP_002994180.1| 160 ILIVGGGDVGMIVARHLHLEGAESILIVFPE 190
                                       679************9999999877765555 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 ?    5.4   0.1     0.041        28       3      37 ..       9      39 ..       7      48 .. 0.89
   2 ?    5.6   0.0     0.034        24       2      31 ..     160     187 ..     159     204 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.041
                                      EEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCC CS
                     F420_oxidored  3 giiGaGnmgealasgllaagaqpheivvansrnpe 37
                                       +iG+G  g a a +l+++g   +++ ++ +r++e
  gi|242398756|ref|YP_002994180.1|  9 IVIGGGPSGLAAATKLAEKG---YSVGLV-ERKEE 39
                                      589*****************...999977.88776 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.034
                                       EEEETTSHHHHHHHHHHHHTTS-GGCEEEE CS
                     F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivva 31 
                                       i i+G+G++g  +a+ l  +g  +++i+++
  gi|242398756|ref|YP_002994180.1| 160 ILIVGGGDVGMIVARHLHLEG--AESILIV 187
                                       6799*****************..7777755 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 ?    8.5   0.0    0.0016       1.1      30      68 ..       7      45 ..       2      98 .. 0.79
   2 ?    1.2   0.6      0.28   1.9e+02      23      46 ..     151     175 ..     136     188 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0016
                                      EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHH CS
                       AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleqle 68
                                       v+viGgG  Gl+A+   ++ g +V +++ +++    l+
  gi|242398756|ref|YP_002994180.1|  7 DVIVIGGGPSGLAAATKLAEKGYSVGLVERKEELGGILD 45
                                      69***************9999999999988877655555 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.28
                                       ETCB---E.EEEESTSHHHHHHHHH CS
                       AlaDh_PNT_C  23 vpgvepak.vlviGgGvaGlqAiat 46 
                                       + g+ p+k +l++GgG +G+  ++ 
  gi|242398756|ref|YP_002994180.1| 151 LYGILPGKnILIVGGGDVGMIVARH 175
                                       44555554389********977765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); 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: 0.75u 0.30s 00:00:01.05 Elapsed: 00:00:00.51
# Mc/sec: 2465.86
//
Query:       gi|242398757|ref|YP_002994181.1|  [L=579]
Description: dehydrogenase [Thermococcus sibiricus MM 739]
Scores for complete 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-65  220.3   0.0    6.7e-65  220.0   0.0    1.1  1  DAO             FAD dependent oxidoreductase
    9.3e-16   57.9   6.1    2.1e-15   56.8   6.1    1.6  1  Fer2_BFD        BFD-like [2Fe-2S] binding domain
    2.9e-10   39.9   0.2    1.5e-05   24.4   0.0    2.8  3  FAD_binding_3   FAD binding domain
    1.2e-09   37.8   0.1     0.0006   19.1   0.0    2.4  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    6.8e-08   32.7   0.0    1.5e-07   31.7   0.0    1.5  1  SO_alpha_A3     Sarcosine oxidase A3 domain
    8.5e-07   29.4   1.8      0.029   14.9   0.2    3.3  3  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    4.5e-05   23.6   0.1    0.00011   22.4   0.1    1.6  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    5.5e-05   22.4   0.1       0.16   11.0   0.0    2.3  2  FAD_binding_2   FAD binding domain
    5.6e-05   22.5   4.3      0.007   15.7   0.1    2.3  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    8.3e-05   21.5   0.7      0.075   11.7   0.0    2.2  2  HI0933_like     HI0933-like protein
    0.00014   21.2   0.1    0.00046   19.5   0.0    1.9  2  Thi4            Thi4 family
     0.0021   17.2   0.3      0.004   16.3   0.3    1.4  1  Lycopene_cycl   Lycopene cyclase protein
     0.0031   17.4   0.2       0.01   15.7   0.0    1.9  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
  ------ inclusion threshold ------
      0.011   15.1   1.8       0.29   10.4   0.1    2.4  2  FAD_oxidored    FAD dependent oxidoreductase
      0.011   16.0   0.0      0.026   14.8   0.0    1.6  1  TrkA_N          TrkA-N domain
      0.013   14.0   0.1      0.062   11.8   0.0    1.8  2  Mqo             Malate:quinone oxidoreductase (Mqo)
      0.021   15.0   0.7      0.045   14.0   0.7    1.5  1  Ndufs5          NADH:ubiquinone oxidoreductase, NDUFS5-15kDa
      0.026   14.8   0.0      0.071   13.4   0.0    1.8  1  BON             BON domain
       0.04   13.5   0.1      0.065   12.8   0.1    1.3  1  DUF1188         Protein of unknown function (DUF1188)
      0.042   12.9   0.2        1.6    7.7   0.0    2.2  2  GIDA            Glucose inhibited division protein A
       0.54    9.1   1.4         17    4.1   0.3    2.1  2  Trp_halogenase  Tryptophan halogenase


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 !  220.0   0.0   7.9e-68   6.7e-65       1     351 [.      86     456 ..      86     457 .. 0.85

  Alignments for each domain:
  == domain 1  score: 220.0 bits;  conditional E-value: 7.9e-68
                                       EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESSSSTHHSTHHHHHHHHHHHHHHHHHHHHH CS
                               DAO   1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsglrylpeaselarlslealeelreleeel 75 
                                       dvviiGGGiiG+++A+eL+r    ++llek++++++ga+ +n g++h+g++ +p+++ + +l   ++++++++++el
  gi|242398757|ref|YP_002994181.1|  86 DVVIIGGGIIGAGIARELSRYDlkIALLEKAPDVATGATKANNGMIHPGVA-PPKNTLKRKLNIKGNALYDKWADEL 161
                                       9*****************999889**************************9.77776888***************** PP

                                       SSTTSEEEEEEEEEESSHHHHHHHH...................HHHHHH...HHTTTTE.EEEEHHHHHHHSTT.S CS
                               DAO  76 gididyrrtGllslaadeeeleald...................kllall...leaglda.elldaeevrelepa.l 128
                                       g  + +rr G+l+l + +  l + +                             ++g++  ++++++ + ++ep  +
  gi|242398757|ref|YP_002994181.1| 162 G--FKFRRVGSLWLITPR-TLKKYRkylpgplytltlkyifpwlV----KikgMRNGVKGiKIIRGKTIFDMEPYvT 231
                                       *..89*********9644.46666656666666666666665552....0344348886658****99******976 PP

                                       TTTSEEEEETTEEEEEHHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGH CS
                               DAO 129 pgllgalfypdtgqvdpakltaalaraaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGaws 204
                                       ++ ++a+++p+tg+vdp++++ ala+ a+++Gvei+++tev+g+ +ed+ ++gv  +t+ g+  + ++vVnaaG+++
  gi|242398757|ref|YP_002994181.1| 232 KDAVAAVYVPSTGIVDPYEVAIALAENAQENGVEIHLKTEVVGFLKEDNSIKGV--VTDrGTFLC-KYVVNAAGIYA 305
                                       6999***************************************877888999**..777797555.99********* PP

                                       HHH.HTT..CTTTSEEEEEEEEEEEEEECCTHSTGSG.CSEEEEE.EEETTTTEEEEEETTSEEEEEESSEEETTCS CS
                               DAO 205 dll.gll..keldlpispvrgqvlvlkplseklvspa.ailpvpe.tdddgrgvyvtprkdgrvlvGgtadeesgdd 276
                                       d++ +l+  +  +  i+p++g  l++ + +  lv +    l      +   +g  + p+  g+++ G+ta+e  +++
  gi|242398757|ref|YP_002994181.1| 306 DEIaELAgaR--EYTIHPRKGVELMFHKDTGHLVNHCiSELF--YpQHPTTKGGGLNPTVHGNIMWGPTAVEVPDKE 378
                                       *884555422..479***********6655555544333333..3456666666799**9***********888888 PP

                                       STSCSHHHHHHHHHHHHHHSGGG..CGEEEEEEEEEE.ETTSSEEEEEEETEEEEEEEEECTTTHHHHHHHHHHHHH CS
                               DAO 277 dpevdeedidellealrklfPql..gdvlrkwaGlrp.lpdglpligetpgvkglylatGhsghGltlapatGklla 350
                                       d++v+ e+i+ +le+ ++++P++  + + r +aG+r+ +  ++++i ++ +vk++++++G+ ++Gl +apa++k++ 
  gi|242398757|ref|YP_002994181.1| 379 DVSVTREEIEFILEKYSTIIPEFpkDQLIRYFAGVRApTFTEDFIIRPAKWVKNFLHVAGIQSPGLASAPAIAKYAI 455
                                       88********************6536799********77899******99************************987 PP

                                       H CS
                               DAO 351 e 351
                                       e
  gi|242398757|ref|YP_002994181.1| 456 E 456
                                       6 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 !   56.8   6.1   2.4e-18   2.1e-15       1      51 []     502     554 ..     502     554 .. 0.97

  Alignments for each domain:
  == domain 1  score: 56.8 bits;  conditional E-value: 2.4e-18
                          Fer2_BFD   1 iVCrCegvtegeIrdairraglttveevkrrtkagtg.Cgg..CrpaieeiLae 51 
                                       i+C+Ce v+e eI++ai + g++tv+++krrt+ag+g C+g  C  +i+eiLa+
  gi|242398757|ref|YP_002994181.1| 502 IICTCETVSEAEIVEAI-KRGAQTVDAIKRRTRAGMGtCQGsyCTIKIAEILAR 554
                                       8****************.779*******************************96 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.1   0.00011     0.095       1      35 [.      84     118 ..      84     128 .. 0.89
   2 !   24.4   0.0   1.8e-08   1.5e-05     107     254 ..     251     393 ..     221     405 .. 0.84
   3 ?   -0.8   0.0      0.81     7e+02      92     149 ..     474     536 ..     435     543 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                                       EEEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSS CS
                     FAD_binding_3   1 etdVlIVGaGpaGlmlallLseaGvrvvlvekrst 35 
                                       e+dV+I+G+G  G+  a++Ls++  +  l+ek  +
  gi|242398757|ref|YP_002994181.1|  84 EYDVVIIGGGIIGAGIARELSRYDLKIALLEKAPD 118
                                       589*********************99***999765 PP

  == domain 2  score: 24.4 bits;  conditional E-value: 1.8e-08
                                       HHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEEEEEE--GTT-H.HHHHHTGGEEEEEEE CS
                     FAD_binding_3 107 leriLvehaeerglqvrfktevesleqdeegvtaevrdketgeeetvrakYlvGaDGgrSt.vrktlgiefegeetv 182
                                       +  +L+e+a+e g++++ ktev+++++++++++ +v+d+      t+ +kY+v a G     +++ +g     e t+
  gi|242398757|ref|YP_002994181.1| 251 VAIALAENAQENGVEIHLKTEVVGFLKEDNSIKGVVTDRG-----TFLCKYVVNAAGIYADeIAELAGA---REYTI 319
                                       56689*********************************96.....9***********987414555554...47788 PP

                                       EEEEEEEEEEEC-SCCCTTC....CEEEEECCTTEEEEEECCETEEEEEEEEECCE-GGGSCCCHHHHHHHHHHHH CS
                     FAD_binding_3 183 yeagvldvlfdadlsdivep....lvlilsaesrgvmviPlentlerfyvqvearaekeersekfteeevkarlre 254
                                        + + ++++f +d+ ++v++    l++ +++  +g  + P+     ++++  +a +  ++++  +t+ee+  +l++
  gi|242398757|ref|YP_002994181.1| 320 HPRKGVELMFHKDTGHLVNHciseLFYPQHPTTKGGGLNPTVH--GNIMWGPTAVEVPDKEDVSVTREEIEFILEK 393
                                       8899***********9****99988899999999999999999..4556777777777777778888877766655 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.81
                                       CHHCST-CEE--HHHHHHHHHHHHHHHT...EEETCSEE...EECCEECCCCCCCEEEECCTTE CS
                     FAD_binding_3  92 lesspervtvypqteleriLvehaeerg...lqvrfkte...vesleqdeegvtaevrdketge 149
                                        +ss +r++ +p++el++++ e+ +  g   ++ +   e   ve++++  ++v+a  r  ++g 
  gi|242398757|ref|YP_002994181.1| 474 KRSSIPRTEELPVEELNKMIKENSK-WGniiCTCETVSEaeiVEAIKRGAQTVDAIKRRTRAGM 536
                                       4789999999999999999999844.33333444444445578899999999999888877775 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0     7e-07    0.0006       1      39 [.      85     129 ..      45     165 .. 0.77
   2 !   16.2   0.0   5.7e-06    0.0048     184     241 ..     250     307 ..     239     327 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 7e-07
                                       CSEEEE--SHHHHHHHHHHHHHTS-EEEEE......TTHCHHHCS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxx RF
                       Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlve......legtclngg 39 
                                       +dvv+iGgG+ G   a++l+++ +k++l+e       + t  n+g
  gi|242398757|ref|YP_002994181.1|  85 YDVVIIGGGIIGAGIARELSRYDLKIALLEkapdvaTGATKANNG 129
                                       577777777777777777777777777776555554444444444 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 5.7e-06
                                       HHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S-EEES- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 184 elsaaleealekeGvevklgtsvkeidgngeklevvledgeeidadlvvvavGvrpst 241
                                       e++ al+e  +++Gve++l+t+v+ + +++++++ v +d  ++ +++vv a+G+ ++ 
  gi|242398757|ref|YP_002994181.1| 250 EVAIALAENAQENGVEIHLKTEVVGFLKEDNSIKGVVTDRGTFLCKYVVNAAGIYADE 307
                                       5666788999*********************9**88888888***********98874 PP

>> SO_alpha_A3  Sarcosine oxidase A3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.0   1.7e-10   1.5e-07       6      65 ..     503     562 ..     499     570 .. 0.90

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 1.7e-10
                       SO_alpha_A3   6 vdlqnDvtvkdielavregfesiehvKRYttlgmgtdQgklsavnaaaivaeltgkevae 65 
                                       ++  + v++++i +a++ g + ++ +KR t +gmgt Qg+   ++ a+i+a++ +  ++e
  gi|242398757|ref|YP_002994181.1| 503 ICTCETVSEAEIVEAIKRGAQTVDAIKRRTRAGMGTCQGSYCTIKIAEILARELNVPLRE 562
                                       56667799********************************************99877766 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.2   3.4e-05     0.029       2      34 ..      87     119 ..      86     127 .. 0.91
   2 !   11.8   0.1   0.00031      0.27      43      78 ..     252     287 ..     247     290 .. 0.87
   3 ?   -1.6   0.0       4.7     4e+03      41      58 ..     449     466 ..     446     470 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.4e-05
                                       EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSS CS
                         Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkl 34 
                                       vv++GgG ig   A +l+++  k+ ++e ++ +
  gi|242398757|ref|YP_002994181.1|  87 VVIIGGGIIGAGIARELSRYDLKIALLEKAPDV 119
                                       8*************************9998876 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00031
                                       HHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEEE CS
                         Pyr_redox  43 skilqeklekngievllntkveeiegsedgvesvkl 78 
                                       + +l+e+ ++ng+e++l+t+v+ + ++++ +++v++
  gi|242398757|ref|YP_002994181.1| 252 AIALAENAQENGVEIHLKTEVVGFLKEDNSIKGVVT 287
                                       5578999******************99999999987 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 4.7
                                       HHHHHHHHHHHHTTEEEE CS
                         Pyr_redox  41 easkilqeklekngievl 58 
                                       +++k+  e+l+k+g ++ 
  gi|242398757|ref|YP_002994181.1| 449 AIAKYAIEQLRKMGLKLK 466
                                       689999********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 !   22.4   0.1   1.3e-07   0.00011       1      36 [.      89     124 ..      89     138 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.3e-07
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG- CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraa 36 
                                       I+G+G+ G+ +A++L+++++++ llek++++   a+
  gi|242398757|ref|YP_002994181.1|  89 IIGGGIIGAGIARELSRYDLKIALLEKAPDVATGAT 124
                                       9****************************9864333 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0   0.00019      0.16       1      45 [.      86     130 ..      86     147 .. 0.82
   2 !    9.2   0.0   0.00066      0.57     135     180 ..     243     288 ..     213     322 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00019
                                       SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S-E CS
                     FAD_binding_2   1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqGgi 45 
                                       Dv++iG+G+ G   A e+++  lk+a++ek++ +   ++ +  g+
  gi|242398757|ref|YP_002994181.1|  86 DVVIIGGGIIGAGIARELSRYDLKIALLEKAPDVATGATKANNGM 130
                                       9******************************99877444444444 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00066
                                       ....HHHHHHHHHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEE CS
                     FAD_binding_2 135 etlvtghallarlvesarkagvdfqerteadeLivedgrvtGavve 180
                                       + +v+  +++ +l+e+a+++gv+++ +te++ ++ ed+ + G+v  
  gi|242398757|ref|YP_002994181.1| 243 TGIVDPYEVAIALAENAQENGVEIHLKTEVVGFLKEDNSIKGVVTD 288
                                       55666678999*******************************9876 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 !    7.8   0.9     0.002       1.7       1      30 [.      88     116 ..      87     127 .. 0.90
   2 !   15.7   0.1   8.1e-06     0.007      86     155 ..     254     323 ..     229     336 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.002
                       Pyr_redox_3   1 iIiGaGPaGlaaaielkkagledylilEkg 30 
                                       +IiG+G +G ++a el + +l ++  lEk+
  gi|242398757|ref|YP_002994181.1|  88 VIIGGGIIGAGIARELSRYDL-KIALLEKA 116
                                       7********************.799***98 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 8.1e-06
                       Pyr_redox_3  86 YlrevaksfelpiklfeeVesvkkedeg.fevetsketyeAkkviiAtGefdkPnklnipGeeklvkhysk 155
                                        l+e a+++ ++i+l++eV    ked++   v t+++t+ +k+v+ A+G +      +  G+ ++ +h +k
  gi|242398757|ref|YP_002994181.1| 254 ALAENAQENGVEIHLKTEVVGFLKEDNSiKGVVTDRGTFLCKYVVNAAGIYADE-IAELAGAREYTIHPRK 323
                                       56788999************99997665378*******************9764.4577887777777665 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.3    0.0014       1.2       1      36 [.      85     120 ..      85     129 .. 0.93
   2 !   11.7   0.0   8.8e-05     0.075     111     163 ..     251     302 ..     247     313 .. 0.93

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0014
                                       -SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                       HI0933_like   1 kdviviGgGaAGlmaAisaakrgkrVlllekakklg 36 
                                       +dv++iGgG  G   A ++++ + +++lleka+ ++
  gi|242398757|ref|YP_002994181.1|  85 YDVVIIGGGIIGAGIARELSRYDLKIALLEKAPDVA 120
                                       59*****************************98765 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 8.8e-05
                                       HHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE--- CS
                       HI0933_like 111 ivdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtG 163
                                       +  al ++++e+gv+++l+tev ++ ke++++  v t +++++ ++++v A G
  gi|242398757|ref|YP_002994181.1| 251 VAIALAENAQENGVEIHLKTEVVGFLKEDNSIKGVVT-DRGTFLCKYVVNAAG 302
                                       5568999************************999999.9**********9988 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   5.4e-07   0.00046      16      64 ..      83     132 ..      70     151 .. 0.82
   2 ?   -3.5   0.0       5.8   4.9e+03     126     138 ..     276     288 ..     254     291 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 5.4e-07
                                       TEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEES..SSS--TTTTTTSTTB CS
                              Thi4  16 aesDvvivGaGssGLtaayylakkpdlkvailer..svspGGGawlGGqlf 64 
                                        e Dvvi+G+G  G   a+ l++  dlk+a+le+   v+ G      G++ 
  gi|242398757|ref|YP_002994181.1|  83 GEYDVVIIGGGIIGAGIARELSRY-DLKIALLEKapDVATGATKANNGMIH 132
                                       489*********************.********944588888777778775 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 5.8
                                       EETBTEEEEEEEE CS
                              Thi4 126 vregegvaGvvin 138
                                       ++e+++++Gvv++
  gi|242398757|ref|YP_002994181.1| 276 LKEDNSIKGVVTD 288
                                       5777999999996 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.3   4.6e-06     0.004       1      38 [.      86     121 ..      86     127 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.6e-06
                     Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvlieaspsllf 38 
                                       Dvv+iG+G  g  +A +l  ++++lk+ l+e +p++  
  gi|242398757|ref|YP_002994181.1|  86 DVVIIGGGIIGAGIAREL--SRYDLKIALLEKAPDVAT 121
                                       9*****************..**************9854 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   0.0   1.2e-05      0.01       2      42 ..      87     127 ..      86     146 .. 0.89
   2 ?   -1.7   0.0       2.7   2.3e+03      57      91 ..     483     519 ..     434     535 .. 0.60

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.2e-05
                                       EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHH CS
                           3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdiseealekaleki 42 
                                       v +iG G++Gagia  + + +l++ l++ +++ ++ a+++ 
  gi|242398757|ref|YP_002994181.1|  87 VVIIGGGIIGAGIARELSRYDLKIALLEKAPDVATGATKAN 127
                                       89*****************************9999888765 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.7
                                       HHHHCCCHHCEEEES-HHHHH.C-SEEEE-.S-SSHH CS
                           3HCDH_N  57 eeeveaalarisfttdleeav.dadlviEa.vvEnle 91 
                                       e  ve++ + i+ +++  +++  ++ v Ea +vE ++
  gi|242398757|ref|YP_002994181.1| 483 ELPVEELNKMIKENSKWGNIIcTCETVSEAeIVEAIK 519
                                       5556666666666666666666777777764555554 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.4     0.042        36       1      32 [.      86     117 ..      86     121 .. 0.93
   2 ?   10.4   0.1   0.00034      0.29      83     154 ..     245     314 ..     216     322 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.042
                      FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveerg 32 
                                       Dvv++GGg+ G   A    r + k +L+e+ +
  gi|242398757|ref|YP_002994181.1|  86 DVVIIGGGIIGAGIARELSRYDLKIALLEKAP 117
                                       9**************************99865 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00034
                      FAD_oxidored  83 tfepevakavleemlaeagvtvllntrlvevekegkriesvtveskegrktirAkvfiDATg..dGdlaalaGv 154
                                       +++p  ++ +l e  +e+gv++ l+t++v+  ke++ i++v++     r t+ +k+++ A g    ++a+laG+
  gi|242398757|ref|YP_002994181.1| 245 IVDPYEVAIALAENAQENGVEIHLKTEVVGFLKEDNSIKGVVTD----RGTFLCKYVVNAAGiyADEIAELAGA 314
                                       57777778888888999******************9*******5....89999999999986213346666665 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0     3e-05     0.026       1      40 [.      87     126 ..      87     145 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3e-05
                                       EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHT CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelree 40 
                                       ++iiG G +G  +a+eLs++  ++ + +k ++++  +++ 
  gi|242398757|ref|YP_002994181.1|  87 VVIIGGGIIGAGIARELSRYDLKIALLEKAPDVATGATKA 126
                                       79*****************5546*********99887665 PP

>> Mqo  Malate:quinone oxidoreductase (Mqo)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   7.3e-05     0.062       2      48 ..      84     128 ..      83     136 .. 0.87
   2 ?   -0.6   0.0      0.43   3.7e+02     162     212 ..     231     280 ..     222     300 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.3e-05
                               Mqo   2 kvdvvliGaGimsatlgvllkelepelsievlerldkvaeessnawn 48 
                                       ++dvv+iG+Gi+ a ++  l++   +l+i++le+  +va+ +++a n
  gi|242398757|ref|YP_002994181.1|  84 EYDVVIIGGGIIGAGIARELSR--YDLKIALLEKAPDVATGATKANN 128
                                       58**************998886..5799***********99988765 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.43
                               Mqo 162 akekvaatrieeGtdvnfgaltrqllkalekkkgvelklkhevkdlkreed 212
                                       +k+ vaa ++ +   v+  +++ +l++++++ +gve++lk+ev  + +e++
  gi|242398757|ref|YP_002994181.1| 231 TKDAVAAVYVPSTGIVDPYEVAIALAENAQE-NGVEIHLKTEVVGFLKEDN 280
                                       5678888888888889999999999999955.9*********998877765 PP

>> Ndufs5  NADH:ubiquinone oxidoreductase, NDUFS5-15kDa
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.7   5.3e-05     0.045      38      89 ..      31      84 ..      19      88 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.3e-05
                                      HHHHHHSSSHHHHTTTSTT..HHHHHHHHHHHT-HHHHHHHHHHHHHHHH-TTS CS
                            Ndufs5 38 kewiecahgigktrakkec..kiefedfeecllrqktmkrlkeirkqreklike 89
                                       ew+e   +igk++    +  ki+++df e   + k  +r +  ++++ek++ e
  gi|242398757|ref|YP_002994181.1| 31 EEWVEIGLSIGKIKEVEGVvnKIKWKDFPEEKTKAKEEHRRRIFKENKEKILGE 84
                                      49***********976643339****************************9976 PP

>> BON  BON domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   8.3e-05     0.071      23      68 ..      11      56 ..       2      57 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.3e-05
                                      CCEEEEETTCEEEECEEECHHHHHHHHHHHHCCTTEEEEEEEEEEE CS
                               BON 23 dinVevenGvVtLsGtVdseaekekAveiarnvaGVkkVvnelkvr 68
                                      +++ e+++  V L G+V + +e+  +   + +++ V++Vvn++k +
  gi|242398757|ref|YP_002994181.1| 11 NLSFEIKDQIVFLYGEVEKYEEWVEIGLSIGKIKEVEGVVNKIKWK 56
                                      6778899999*********************************986 PP

>> DUF1188  Protein of unknown function (DUF1188)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   7.6e-05     0.065       6      78 ..      44     120 ..      39     132 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.6e-05
                                       TTSEEEE-SSBHHHHHHHHHHHHHHHHHHHHTT--..E...EEEEEES-CCCHHHHHHHHCCC.EEEEEEESSGGGG CS
                           DUF1188   6 etvkTikskvklvdivkeiaekKaeavleyleeee..l.eeknvlviGaYltGaaiakkLskk.eevtlvDiephlk 78 
                                       ++v+ +  k+k +d  +e +++K e  ++  +e++  +  e +v++iG  + Ga+ia++Ls++  ++ l++  p ++
  gi|242398757|ref|YP_002994181.1|  44 KEVEGVVNKIKWKDFPEEKTKAKEEHRRRIFKENKekIlGEYDVVIIGGGIIGAGIARELSRYdLKIALLEKAPDVA 120
                                       6888999999999999999999999988888765422237899*******************999****99988775 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0019       1.6       1      74 [.      86     165 ..      86     170 .. 0.66
   2 ?    3.0   0.0     0.049        42     111     153 ..     266     306 ..     250     321 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0019
                                       CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT--SSSSEEE-T......THHHHHHHHHHHT.-SHHHHHHHH CS
                              GIDA   1 dviViGgGhAGceAAlaaarlGakvlLithkldtiaelsCnpsiggi......akgllvrEidalg.gliikaadka 70 
                                       dv++iGgG  G   A +++r  +k++L+ +k  ++a+ +   + g i       k +l+r ++  g  l  k+ad+ 
  gi|242398757|ref|YP_002994181.1|  86 DVVIIGGGIIGAGIARELSRYDLKIALL-EKAPDVATGATKANNGMIhpgvapPKNTLKRKLNIKGnALYDKWADEL 161
                                       79**************************.333333333222222222334555667777777666656666677766 PP

                                       EEEE CS
                              GIDA  71 giqf 74 
                                       g +f
  gi|242398757|ref|YP_002994181.1| 162 GFKF 165
                                       6655 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.049
                                       EEEEES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT-BT CS
                              GIDA 111 leiieeeveeliveekkvkgvvtedgetikakavviatGtflk 153
                                       +++   ev   + e++++kgvvt++g+ + +k vv a+G + +
  gi|242398757|ref|YP_002994181.1| 266 IHLK-TEVVGFLKEDNSIKGVVTDRGTFL-CKYVVNAAGIYAD 306
                                       4444.4555666889********999765.8999999998765 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.3      0.02        17       1      34 [.      86     116 ..      86     126 .. 0.90
   2 ?    3.8   0.0     0.024        21     152     210 ..     247     304 ..     242     318 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.02
                                       EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-S CS
                    Trp_halogenase   1 kivivGGGtaGwlaAaalakalkgklevtlvese 34 
                                       ++vi+GGG+ G   A  l+++    l++ l+e++
  gi|242398757|ref|YP_002994181.1|  86 DVVIIGGGIIGAGIARELSRYD---LKIALLEKA 116
                                       69*****************999...999999975 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.024
                                       -HHHHHHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS-EEE-SEEEE-SGGG CS
                    Trp_halogenase 152 daalyakfLrrvaearGvtrvegkvvevqldedgrveslrledgreveadlfiDcsGfr 210
                                       d  ++a  L ++a+++Gv++   + v   l+ed++++++ ++ g+ +    ++ + G  
  gi|242398757|ref|YP_002994181.1| 247 DPYEVAIALAENAQENGVEIHLKTEVVGFLKEDNSIKGVVTDRGT-FLCKYVVNAAGIY 304
                                       556778899**********99988889999***********9998.6677888888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (579 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       624  (0.0348039); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); 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: 0.67u 0.28s 00:00:00.95 Elapsed: 00:00:00.46
# Mc/sec: 3810.97
//
Query:       gi|242398758|ref|YP_002994182.1|  [L=384]
Description: hypothetical protein TSIB_0772 [Thermococcus sibiricus MM 739]
Scores for complete 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   95.0   3.6    1.3e-13   50.9   0.2    3.0  3  CCG           Cysteine-rich domain
    3.4e-06   27.4   3.0    3.4e-06   27.4   3.0    2.5  3  Fer4_8        4Fe-4S dicluster domain
    9.9e-05   22.4  10.3      0.026   14.6   0.1    4.1  4  Fer4_10       4Fe-4S dicluster domain
    0.00011   22.7   4.3    0.00011   22.7   4.3    2.4  3  Fer4_7        4Fe-4S dicluster domain
    0.00054   20.8   5.0    0.00054   20.8   5.0    2.5  3  Fer4_16       4Fe-4S double cluster binding domain
     0.0011   19.5   5.0     0.0011   19.5   5.0    2.3  3  Fer4_17       4Fe-4S dicluster domain
     0.0085   16.2   6.9     0.0085   16.2   6.9    3.0  4  Fer4_9        4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.013   15.3   5.1      0.048   13.4   0.1    2.6  2  Fer4_20       Dihydroprymidine dehydrogenase domain II, 4Fe-4
      0.013   15.2   5.0        3.4    7.5   0.1    3.6  3  zf-CSL        CSL zinc finger
       0.15   12.1   8.2       0.32   11.0   0.2    2.9  3  Integrase_Zn  Integrase Zinc binding domain
        5.8    7.1  14.4       0.58   10.3   0.3    3.4  4  Fer4_21       4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> CCG  Cysteine-rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       1.3   2.1e+03      55      81 ..      73     100 ..      64     102 .. 0.69
   2 !   50.9   0.2   8.1e-17   1.3e-13       2      82 ..     159     237 ..     158     240 .. 0.95
   3 !   43.8   0.1   1.4e-14   2.2e-11       1      84 [.     277     364 ..     277     365 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.3
                               CCG  55 ealakrnve.taeetgadaivtacpgCl 81 
                                       + + + ++e ++e++++ +++  c+ C+
  gi|242398758|ref|YP_002994182.1|  73 FFIREGKLElNLENLEPLYMCLSCNACS 100
                                       5555555552456669999999999996 PP

  == domain 2  score: 50.9 bits;  conditional E-value: 8.1e-17
                               CCG   2 ayfdgChllraaypevrkalkkllealgveleelekesCCGagggrsgkeelaealakrnvetaeetgadaivtacp 78 
                                       +y  gC  +r +ype++k+  k+l+ lg +  +  +e+CCG ++++ g+ el+++la++++e +++ ga+++vt cp
  gi|242398758|ref|YP_002994182.1| 159 LYLRGC-TIREKYPELEKKAIKVLNSLGEDAFII-NEKCCGIPAYNIGNIELFKKLAREQAEIINSSGAEVVVTSCP 233
                                       6889**.**********************99988.9***************************************** PP

                               CCG  79 gCll 82 
                                       +C +
  gi|242398758|ref|YP_002994182.1| 234 SCAY 237
                                       **86 PP

  == domain 3  score: 43.8 bits;  conditional E-value: 1.4e-14
                               CCG   1 vayfdgChllraa..ypevrkalkkllealgveleel.ekesCCGagggrsgkee..laealakrnvetaeetgada 72 
                                       ++++ +C+l+ +    + ++++l k+ + +     ++ ++  CCG gg   ++ +  la ++a++++++++e +a+ 
  gi|242398758|ref|YP_002994182.1| 277 ITFHEPCKLAIGLnkPEILEEILSKIEGLEIKAPRRKrKETFCCGYGGSTVSRLRseLADEIARERLKELQE-EAEL 352
                                       69*****97777763445677888887777777777788999******998885556999************.6*** PP

                               CCG  73 ivtacpgCllql 84 
                                       ivtacp+C+l +
  gi|242398758|ref|YP_002994182.1| 353 IVTACPTCKLAF 364
                                       *********987 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   3.0   2.1e-09   3.4e-06       3      64 ..      39     106 ..      37     107 .. 0.79
   2 ?   -2.7   0.0       5.1   8.3e+03      14      18 ..     231     235 ..     211     256 .. 0.75
   3 ?   -0.0   0.1      0.75   1.2e+03      29      55 ..     340     361 ..     304     362 .. 0.64

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 2.1e-09
                            Fer4_8   3 ekCieC.gaCqsaCpvlrrtkkhlldargeaae.......dvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                        kC  C  +C++aCp+    +k+  ++ g+          +   e +le+ e l+ C++c+aC+e Cp +
  gi|242398758|ref|YP_002994182.1|  39 IKCALCpNMCRHACPISIVDGKETTSPTGKTRTaffiregK--LELNLENLEPLYMCLSCNACSEWCPFN 106
                                       689999779**********9999888888877779887441..3333333789***************75 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.1
                            Fer4_8  14 aCpvl 18 
                                       +Cp++
  gi|242398758|ref|YP_002994182.1| 231 SCPSC 235
                                       34443 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.75
                            Fer4_8  29 rgeaaedvqeeqvleeeealwsCttcg 55 
                                       r++ +e  qee     e ++ +C tc+
  gi|242398758|ref|YP_002994182.1| 340 RERLKE-LQEEA----ELIVTACPTCK 361
                                       333333.33333....45789999997 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.7     0.001       1.7       6      37 ..      38      68 ..      35      74 .. 0.72
   2 !   14.6   0.1   1.6e-05     0.026       8      24 ..      92     123 ..      87     165 .. 0.72
   3 ?    2.1   0.1      0.13   2.2e+02      27      51 ..     214     238 ..     190     246 .. 0.76
   4 ?    0.1   0.0      0.55   8.9e+02      38      49 ..     350     361 ..     336     369 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.001
                           Fer4_10  6 ddtCirCg.kCvkaCPadltsvgakgeaseeea 37
                                        +C  C   C+ aCP   + v++k+ +s+ ++
  gi|242398758|ref|YP_002994182.1| 38 LIKCALCPnMCRHACPI--SIVDGKETTSPTGK 68
                                      5689999868******9..66666666655555 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 1.6e-05
                           Fer4_10   8 tCirCgkCvkaCPadl...............t 24 
                                        C+ C++C + CP+++               +
  gi|242398758|ref|YP_002994182.1|  92 MCLSCNACSEWCPFNFsvadlirpikeeaiqK 123
                                       5*************885444444444333330 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.13
                           Fer4_10  27 gakgeaseeeavrkkvekCtgcgaC 51 
                                       + ++e+ +++  +++v +C+ c + 
  gi|242398758|ref|YP_002994182.1| 214 REQAEIINSSGAEVVVTSCPSCAYA 238
                                       5666777777778899999999765 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 0.55
                           Fer4_10  38 vrkkvekCtgcg 49 
                                        +  v +C++c 
  gi|242398758|ref|YP_002994182.1| 350 AELIVTACPTCK 361
                                       444577788775 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   4.3   6.7e-08   0.00011       1      51 [.      40     106 ..      39     107 .. 0.74
   2 ?   -2.4   0.0       4.8   7.8e+03      37      41 ..     231     235 ..     209     238 .. 0.68
   3 ?   -2.4   0.0       4.7   7.7e+03      46      50 ..     355     359 ..     345     367 .. 0.71

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 6.7e-08
                            Fer4_7   1 rCigC.gaCvaaCpvkaieldeeenekgtekv..............eidp.ekClgCgaCvavCPtg 51 
                                       +C  C + C  aCp + ++ +e +++ g+ ++              +++p  +Cl+C+aC + CP++
  gi|242398758|ref|YP_002994182.1|  40 KCALCpNMCRHACPISIVDGKETTSPTGKTRTaffiregklelnleNLEPlYMCLSCNACSEWCPFN 106
                                       68888679**************9999977444555555555444444443136************97 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.8
                            Fer4_7  37 kClgC 41 
                                       +C +C
  gi|242398758|ref|YP_002994182.1| 231 SCPSC 235
                                       22222 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 4.7
                            Fer4_7  46 avCPt 50 
                                       ++CPt
  gi|242398758|ref|YP_002994182.1| 355 TACPT 359
                                       34443 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 !   20.8   5.0   3.3e-07   0.00054       2      67 .]      41     106 ..      40     106 .. 0.77
   2 ?   -3.0   0.0       9.1   1.5e+04      55      60 ..     230     235 ..     210     238 .. 0.63
   3 ?   -1.8   0.0       3.8   6.2e+03      54      60 ..     354     360 ..     328     364 .. 0.61

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 3.3e-07
                           Fer4_16   2 CgtCgk.CaevCPtnaikekkekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvCPan 67 
                                       C  C + C  +CP + +++k+ ++   ++ ++   + + +l+ + e+ +  + +  C++C + CP+n
  gi|242398758|ref|YP_002994182.1|  41 CALCPNmCRHACPISIVDGKETTSPTGKTRTA-FFIREGKLELNLENLEPLYMCLSCNACSEWCPFN 106
                                       9999888*************555544444444.46666777777777777799*************9 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 9.1
                           Fer4_16  55 tgCdiC 60 
                                       t C  C
  gi|242398758|ref|YP_002994182.1| 230 TSCPSC 235
                                       445555 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 3.8
                           Fer4_16  54 itgCdiC 60 
                                       +t C +C
  gi|242398758|ref|YP_002994182.1| 354 VTACPTC 360
                                       3555555 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   5.0   6.6e-07    0.0011       1      60 [.      40     107 ..      40     108 .. 0.79
   2 ?   -2.9   0.0       6.5   1.1e+04      12      15 ..     232     235 ..     220     243 .. 0.72
   3 ?   -2.8   0.0       6.1   9.9e+03      44      50 ..     355     361 ..     332     366 .. 0.66

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 6.6e-07
                           Fer4_17   1 rCiqCg.yClpeCpsyeaydnepkkllraakl......glleeaeke.ekaslCieCgeCerkCPqgl 60 
                                       +C+ C  +C+ +Cp  +  ++e  ++  +++       g+le   ++ e    C++C+ C++ CP ++
  gi|242398758|ref|YP_002994182.1|  40 KCALCPnMCRHACPISIVDGKETTSPTGKTRTaffireGKLELNLENlEPLYMCLSCNACSEWCPFNF 107
                                       69999758**********999988888887766676765555544445899**************886 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 6.5
                           Fer4_17  12 Cpsy 15 
                                       Cps+
  gi|242398758|ref|YP_002994182.1| 232 CPSC 235
                                       4433 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 6.1
                           Fer4_17  44 slCieCg 50 
                                         C +C+
  gi|242398758|ref|YP_002994182.1| 355 TACPTCK 361
                                       4454444 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   6.9   5.2e-06    0.0085       1      48 [.      40     105 ..      40     108 .. 0.85
   2 !   10.0   2.3   0.00048      0.78       2      21 ..      93     112 ..      92     122 .. 0.79
   3 ?   -2.0   0.0       2.5   4.1e+03      35      39 ..     231     235 ..     207     239 .. 0.68
   4 ?   -1.0   0.1       1.2     2e+03      33      39 ..     346     360 ..     320     362 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5.2e-06
                            Fer4_9   1 kCtgCga.CveaCpagvvvedaaerkarlraase.................eaCigCgaCveaCpk 48 
                                       kC+ C + C +aCp  +v +++ +     +++                     C++C+aC e Cp 
  gi|242398758|ref|YP_002994182.1|  40 KCALCPNmCRHACPISIVDGKETTSPTGKTRTAFfiregklelnlenleplYMCLSCNACSEWCPF 105
                                       7****644******9999888887776655544489999************99***********96 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00048
                            Fer4_9   2 CtgCgaCveaCpagvvveda 21 
                                       C +C+aC e Cp++  v d 
  gi|242398758|ref|YP_002994182.1|  93 CLSCNACSEWCPFNFSVADL 112
                                       99999999999998877665 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 2.5
                            Fer4_9  35 aCigC 39 
                                       +C +C
  gi|242398758|ref|YP_002994182.1| 231 SCPSC 235
                                       34444 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 1.2
                            Fer4_9  33 e........eaCigC 39 
                                                +aC +C
  gi|242398758|ref|YP_002994182.1| 346 LqeeaelivTACPTC 360
                                       133445666677777 PP

>> Fer4_20  Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   1.4     0.069   1.1e+02      23      40 ..      40      56 ..      35      60 .. 0.85
   2 ?   13.4   0.1     3e-05     0.048      24      58 ..      93     125 ..      82     137 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.069
                                      T----TT-HHHHCSTT-- CS
                           Fer4_20 23 RClqCkkapcvkgCPvei 40
                                      +C  C  ++c ++CP++i
  gi|242398758|ref|YP_002994182.1| 40 KCALC-PNMCRHACPISI 56
                                      69999.678******986 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 3e-05
                                       ----TT-HHHHCSTT---HHHHHHHHHTT-HHHHH CS
                           Fer4_20  24 ClqCkkapcvkgCPveidipefikkiaegnleeaa 58 
                                       Cl+C  + c++ CP + ++ + i+ i+e+ +++ +
  gi|242398758|ref|YP_002994182.1|  93 CLSC--NACSEWCPFNFSVADLIRPIKEEAIQKGV 125
                                       9***..89*********************999876 PP

>> zf-CSL  CSL zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.2     0.015        25      40      54 ..      89     103 ..      70     108 .. 0.69
   2 ?    7.5   0.1    0.0021       3.4      39      58 ..     218     243 ..     194     244 .. 0.67
   3 ?    3.2   0.1     0.044        72      34      52 ..     343     362 ..     336     365 .. 0.62

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.015
                                       ..--EEEETTSSEEE CS
                            zf-CSL  40 gaevvvqCssCSLwi 54 
                                       +    + C++CS w 
  gi|242398758|ref|YP_002994182.1|  89 PLYMCLSCNACSEWC 103
                                       4477789*****996 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0021
                                       .........--EEEETTSSEEEEEE- CS
                            zf-CSL  39 e......gaevvvqCssCSLwikVkf 58 
                                       e         vv+ C+sC    +V++
  gi|242398758|ref|YP_002994182.1| 218 EiinssgAEVVVTSCPSCAYAYRVIY 243
                                       14556744556779****99999987 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.044
                                       HHTT....-.-EEEETTSSE CS
                            zf-CSL  34 leegaegae.vvvqCssCSL 52 
                                       l+e +e+ae +v+ C++C L
  gi|242398758|ref|YP_002994182.1| 343 LKELQEEAElIVTACPTCKL 362
                                       44444434516678****66 PP

>> Integrase_Zn  Integrase Zinc binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.5       4.2   6.9e+03      32      37 ..      95     100 ..      94     101 .. 0.83
   2 ?    5.8   0.1    0.0081        13      26      36 ..     225     235 ..     212     237 .. 0.89
   3 ?   11.0   0.2    0.0002      0.32      24      37 ..     348     361 ..     347     362 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 4.2
                      Integrase_Zn  32 sCptCq 37 
                                       sC +C+
  gi|242398758|ref|YP_002994182.1|  95 SCNACS 100
                                       8****6 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0081
                      Integrase_Zn  26 AreIVqsCptC 36 
                                       A+ +V+sCp+C
  gi|242398758|ref|YP_002994182.1| 225 AEVVVTSCPSC 235
                                       7889******* PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.0002
                      Integrase_Zn  24 kqAreIVqsCptCq 37 
                                       ++A+ IV++CptC+
  gi|242398758|ref|YP_002994182.1| 348 EEAELIVTACPTCK 361
                                       79***********6 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.6    0.0089        14       9      53 ..      39      54 ..      34      72 .. 0.64
   2 ?   10.3   0.3   0.00035      0.58      40      53 ..      92     105 ..      77     111 .. 0.89
   3 ?   -2.2   0.1         3   4.9e+03      35      45 ..     226     236 ..     215     241 .. 0.62
   4 ?   -2.6   0.1       3.8   6.1e+03      39      45 ..     355     361 ..     345     365 .. 0.59

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0089
                           Fer4_21  9 igCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPv 53
                                      i+C +C  +C+ ++                             P+
  gi|242398758|ref|YP_002994182.1| 39 IKCALCPNMCRHAC-----------------------------PI 54
                                      56666666666544.............................43 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00035
                           Fer4_21  40 eCvGCnlCssvCPv 53 
                                        C  Cn Cs+ CP 
  gi|242398758|ref|YP_002994182.1|  92 MCLSCNACSEWCPF 105
                                       5999********96 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 3
                           Fer4_21  35 kvvedeCvGCn 45 
                                       +vv  +C  C+
  gi|242398758|ref|YP_002994182.1| 226 EVVVTSCPSCA 236
                                       55555566665 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 3.8
                           Fer4_21  39 deCvGCn 45 
                                         C  C+
  gi|242398758|ref|YP_002994182.1| 355 TACPTCK 361
                                       3444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       798  (0.0445089); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2669.72
//
Query:       gi|242398759|ref|YP_002994183.1|  [L=465]
Description: Alkyldihydroxyacetonephosphate synthase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.3e-41  140.8   0.0    5.7e-41  139.5   0.0    1.7  2  FAD_binding_4  FAD binding domain
    2.9e-35  122.1   0.0    4.1e-35  121.6   0.0    1.2  1  FAD-oxidase_C  FAD linked oxidases, C-terminal domain


Domain annotation for each model (and alignments):
>> FAD_binding_4  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.5   0.0   6.4e-45   5.7e-41       1     138 [.      54     191 ..      54     192 .. 0.98
   2 ?   -2.5   0.0      0.44   3.9e+03      98     116 ..     414     431 ..     407     436 .. 0.73

  Alignments for each domain:
  == domain 1  score: 139.5 bits;  conditional E-value: 6.4e-45
                                       EEEEEEESSHHHHHHHHHHHHHCTSCEEEESSSTTEESTTC.SCCEEEEEETTS--EEEEETTTTEEEEETTSBHHH CS
                     FAD_binding_4   1 paavvrpeseeevaaalrlaneaglpvlvrGgGssllgqav.atggvvldlsrlnrileideeegtatveaGvtlgd 76 
                                       p+avv+pe+ eev++++++a+e+++p+ ++GgGs++lg+ + ++gg+++dl+r+++ +++ ee+  ++veaG+++  
  gi|242398759|ref|YP_002994183.1|  54 PDAVVWPENKEEVEEIVKIAHETSIPIYAYGGGSGVLGGTIpEKGGIIVDLKRMRS-IKLHEEDLLVEVEAGTNGYY 129
                                       89**************************************99*********99***.899999************** PP

                                       HHHHHHHHTTECSSGGGTTCGSBHHHTTTTT-EETTEEGG--HHGTEEEEEEEETTSEEEEE CS
                     FAD_binding_4  77 lvealaakglllglepgsgipgtvGGaiatnagGygsekyGlirdnvlglevvladGevvrl 138
                                       l+++l++kg++lg+ p+s+ p+tvGG+iat a G+ s+kyG i+d+vlgl+vvl+ Ge ++l
  gi|242398759|ref|YP_002994183.1| 130 LEKYLNKKGYTLGHFPQSLYPSTVGGWIATKATGQFSTKYGGIEDMVLGLDVVLPWGESIEL 191
                                       *********************************************************98876 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.44
                                       SBHHHTTTTT-EETTEEGG CS
                     FAD_binding_4  98 gtvGGaiatnagGygseky 116
                                         vGGai+   +G g+++ 
  gi|242398759|ref|YP_002994183.1| 414 LNVGGAISH-HHGIGRQRR 431
                                       569999998.677777665 PP

>> 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 !  121.6   0.0   4.6e-39   4.1e-35       2     249 ..     228     462 ..     227     463 .. 0.91

  Alignments for each domain:
  == domain 1  score: 121.6 bits;  conditional E-value: 4.6e-39
                                       -SEEEEEEEEESSHHHHHHHHHHHHHHT---SEEEEE-HHHHHHHHHTS-SSTTS-TTT-EEEEEEEEE-HHHHHHH CS
                     FAD-oxidase_C   2 pearavalvafpsfeaavkavreiaqagiipaalelmdkkaldlveatkgakkglpdeeealllvefegddeeeaee 78 
                                       pe+r+++++a +++ +a++ vr+i ++g +pa ++++d ++++      ++        + + ++ +egd   ++e+
  gi|242398759|ref|YP_002994183.1| 228 PEKRVNLSFASENLNDALDSVRRILRRGAKPAVVRIYDTIETKRHFYNFEK-----AYGKVATVMILEGDT-RTVEA 298
                                       899************************************999766555555.....466777777789999.78888 PP

                                       HHHHHHHHTTT-EEEEE..........ETGGGGGGGGHHHHHHHHHCTTEEEEEEEEEEEHHHHHHHHHHHHHHHHH CS
                     FAD-oxidase_C  79 elealveaileatgaadvlvaqdeaeaealwkaRkaalpylrdallkagvavlseDtsvPvsrladlvrdikalldk 155
                                       e +  v + +++t++++         +++++k R ++ +   + ++  gv+ ++ ++s+ +s++ +l++++ +++++
  gi|242398759|ref|YP_002994183.1| 299 EEK-IVGEEFKGTPIGE-------GPVDHWLKTRFNVKE--ASEFAPLGVVFDTIEVSINWSKATQLYNEVSKAMRS 365
                                       888.9***********9.......7788******99999..66669******************************* PP

                                       HH...EEEEEEEEEETTEEEEEEEEEEE...--TT--THHHHHHHHHHHHTT-----------------------TH CS
                     FAD-oxidase_C 156 yg...levvlfgHagdgnlhlyilfdlade.aeeeraeklvdevvdlavelgGsisgEHGvGldkkaylerekgeeg 228
                                        +   ++ ++ +H+++ ++++y++f+   + +  e ++k++d ++++++ +gG is++HG+G++++++l++e g  +
  gi|242398759|ref|YP_002994183.1| 366 VKgtlFASAHASHFYPQGVCFYFTFAGVPKgDPTEYYNKVWDATMRATLNVGGAISHHHGIGRQRREWLQEELGN-A 441
                                       *************************987773556678899*********************************98.9 PP

                                       HHHHHHHHHHH-TT--BSTT- CS
                     FAD-oxidase_C 229 lalmrriKaalDPkgiLNPgk 249
                                       ++++rriK+alD k+i+NPg+
  gi|242398759|ref|YP_002994183.1| 442 FEVLRRIKDALDEKRIMNPGN 462
                                       ********************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (465 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2920.30
//
Query:       gi|242398760|ref|YP_002994184.1|  [L=393]
Description: Aromatic aminotransferase [Thermococcus sibiricus MM 739]
Scores for complete 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-74  249.1   0.0    8.3e-74  248.9   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    1.7e-07   30.9   0.0    2.3e-07   30.4   0.0    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    4.2e-06   26.0   0.0    8.7e-06   24.9   0.0    1.4  2  Aminotran_5      Aminotransferase class-V
    0.00095   17.8   0.0     0.0017   17.0   0.0    1.3  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
     0.0034   16.7   0.0     0.0053   16.1   0.0    1.3  1  Beta_elim_lyase  Beta-eliminating lyase
  ------ inclusion threshold ------
      0.071   13.2   0.0       0.25   11.4   0.0    1.9  1  Rsbr_N           Rsbr 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 !  248.9   0.0   2.8e-77   8.3e-74       3     362 ..      32     382 ..      30     383 .. 0.96

  Alignments for each domain:
  == domain 1  score: 248.9 bits;  conditional E-value: 2.8e-77
                                       EEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHH CS
                     Aminotran_1_2   3 vinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGaga 79 
                                       +i Lg++e+++d    t++++++ +ke  +  ++l+ y+p+ g  el+ea+a+ ++r+++++ ++++++  + G+++
  gi|242398760|ref|YP_002994184.1|  32 IISLGIGEPDFD----TPEHIKEYAKE--ALDKGLTHYSPNIGVLELREAVAEKFKRDNGIEADPKTQIMITVGTNQ 102
                                       799*********....****9999999..66677888999999********************************** PP

                                       HHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEES CS
                     Aminotran_1_2  80 liealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilves 156
                                        i +  + + l   +e+l+p+p + sy +++ l+gg+ +++p+y+e++f+l++e+le+ ++       kt+ +++++
  gi|242398760|ref|YP_002994184.1| 103 QILMGLATF-LKDNEEVLIPSPMFVSYAPAVVLAGGKPIEVPTYEENEFRLTVEELEKHVTP------KTRALIINT 172
                                       ***999999.99*************************************************9......********* PP

                                       S-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTT.EEEEEESSSTTSSGGG-EEE CS
                     Aminotran_1_2 157 phNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepn.llivgslsKafGlaGeRvGy 232
                                       p+NPtG+v+ +++le+++++a ++ l++++De+Y+ fv++  + ++ +a ++   + +++++++sK f+++G+R+G+
  gi|242398760|ref|YP_002994184.1| 173 PNNPTGAVLAKKDLEEIASFAVEHDLMVLSDEVYEYFVYDGVKNYS-IASLDGMFErTITMNGFSKTFAMTGWRLGF 248
                                       ****************************************888888.9***************************** PP

                                       EEEEHHHHHHHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSSE CS
                     Aminotran_1_2 233 ilgnaavvsqlrklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgmf 307
                                       +++ ++vv+ + +++        +  q+a+a+al+d+    + +eemr+++++rr  + ++L+e gl+ ++++++++
  gi|242398760|ref|YP_002994184.1| 249 LTAPEWVVEKMVRFQMYNSTcpVTFIQYAAAKALRDERSW-KAVEEMRREYERRRNLVWKRLNEMGLPTVKPKGAFY 324
                                       ************99987777889*************9976.5*********************************** PP

                                       EEEEETHH..CHHHHHHHHHHTCTEEEEEGGGGTS..TTEEEEECTTS-HHHHHHHHHH CS
                     Aminotran_1_2 308 lltdlsae..takelskkLleevgvyvtpgtsftv..pgrlRitvAglteeeleelvea 362
                                        + +++    t  e+s+ +++e +v+++pg+ f++  +g +Ri++ ++  e+lee++++
  gi|242398760|ref|YP_002994184.1| 325 IIPRIKDTglTSREFSELMIKEAKVVLVPGSAFGKagEGYVRISY-ATGYEKLEEAMDR 382
                                       *********************************************.7778888888876 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.0   7.8e-11   2.3e-07      41     144 ..      93     203 ..      46     205 .. 0.83

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 7.8e-11
                                       EEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-.B-TTTSSB-GGGCGGG--TTEEEEE CS
                   DegT_DnrJ_EryC1  41 aiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvD.vdpdtynidpaaieaaitertkaIl 116
                                        i ++ Gt+   l+  a  +++++eV++ps  Fv+ a av+ +g kp+ v   +++ + ++++++e+ +t++t+a +
  gi|242398760|ref|YP_002994184.1|  93 QIMITVGTNQQILMGLATFLKDNEEVLIPSPMFVSYAPAVVLAGGKPIEVPtYEENEFRLTVEELEKHVTPKTRALI 169
                                       56667777776666667778899*************************997258899******************87 PP

                                       ...EB-GGGB--...-HHHHHHHHHHCT-EEEEE CS
                   DegT_DnrJ_EryC1 117 ...pVhlyGqva...dmdalkaiaakhglkvieD 144
                                          p +  G+v    d++++   a +h+l+v++D
  gi|242398760|ref|YP_002994184.1| 170 intPNNPTGAVLakkDLEEIASFAVEHDLMVLSD 203
                                       3334567787755679****************99 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   2.9e-09   8.7e-06      56     177 ..      86     205 ..      66     209 .. 0.87
   2 ?   -3.3   0.0       1.1   3.2e+03     258     299 ..     275     317 ..     263     369 .. 0.58

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 2.9e-09
                                       HT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTS.CBEGGG CS
                       Aminotran_5  56 inaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeeg.eldlde 131
                                       i+a+ + +i+ t Gt ++i + + ++   lk+ +e+++ +    +   p++ la   g  ++v + +e+  +l+++e
  gi|242398760|ref|YP_002994184.1|  86 IEADPKTQIMITVGTNQQILMGLATF---LKDNEEVLIPSPMFVSYA-PAVVLA--GGKPIEVPTYEENEfRLTVEE 156
                                       78999999********9999999988...***********9999999.999998..788888888776653899*** PP

                                       HHHH--TTEEEEEEESBETTTTEB...--HHHHHHHHHHTT-EEEEE-T CS
                       Aminotran_5 132 lekllnektklvaithvsnvtGti...qpveeigklakkkgalvlvDaa 177
                                       lek++++kt++++i+  +n tG +   +++eei++ a +++ +vl D +
  gi|242398760|ref|YP_002994184.1| 157 LEKHVTPKTRALIINTPNNPTGAVlakKDLEEIASFAVEHDLMVLSDEV 205
                                       **********************964447999***********9999976 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHH.HCHHHHHHHHHHHHHHHHHHHHHCTSTTEEE CS
                       Aminotran_5 258 iiglgaaleyl.eeigleaiekhekelaeyllerlkslpgvrl 299
                                        ++ ++al+   +   +e+++++ ++ ++ + +rl++++  ++
  gi|242398760|ref|YP_002994184.1| 275 QYAAAKALRDErSWKAVEEMRREYERRRNLVWKRLNEMGLPTV 317
                                       5555555555533344666777777777777777777766666 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 !   17.0   0.0   5.7e-07    0.0017     126     175 ..     153     205 ..     136     208 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 5.7e-07
                                       SHHHHHHHCCTTEEEEEEESS-TTTT---...-HHHHHHHHHHTT-EEEEEGT CS
                   Cys_Met_Meta_PP 126 dleelekaikentklvylEtptnpllkvv...DiekiaklakkagvlvvvDnt 175
                                        +eelek+++++t+++ + tp np+  v+   D+e+ia++a +++++v+ D +
  gi|242398760|ref|YP_002994184.1| 153 TVEELEKHVTPKTRALIINTPNNPTGAVLakkDLEEIASFAVEHDLMVLSDEV 205
                                       5799********************97774444*************99998875 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.8e-06    0.0053      90     167 ..     131     203 ..      44     204 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.8e-06
                                       HHHCC--EEEEE-EBTT..TBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EE CS
                   Beta_elim_lyase  90 iaelagvklrdlknkea..GkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygipl 164
                                       +++lag k++++++ e+    +++e+le+++++      k++++++ + nn   G v+  + l+e+a +a ++++ +
  gi|242398760|ref|YP_002994184.1| 131 AVVLAGGKPIEVPTYEEneFRLTVEELEKHVTP------KTRALIINTPNN-PTGAVLAKKDLEEIASFAVEHDLMV 200
                                       346688889999987763356789999999999......344555544444.57*********************99 PP

                                       EEE CS
                   Beta_elim_lyase 165 hlD 167
                                       + D
  gi|242398760|ref|YP_002994184.1| 201 LSD 203
                                       988 PP

>> Rsbr_N  Rsbr N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   8.2e-05      0.25       8      93 ..     181     266 ..     177     294 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8.2e-05
                                       HHHHHHHHHHHHHTTSSS-.--HHHHHHHHHHHHH.HHHH-SS.-SSTTHHHHHHHHHHHHHTT--HHHHHHHHHHH CS
                            Rsbr_N   8 llkewlkelkelrkeeslqtisdevyektskefvd.lilssveegneeleekleefaerlvqlGwpLkyltkgLqef 83 
                                       l+k+ l+e+++++ e++l+++sdevye    + v+   ++s++ g  e + +++ f++ +  +Gw L +lt    ++
  gi|242398760|ref|YP_002994184.1| 181 LAKKDLEEIASFAVEHDLMVLSDEVYEYFVYDGVKnYSIASLD-GMFERTITMNGFSKTFAMTGWRLGFLTAPEWVV 256
                                       77888999*********************99999615677777.667777899******************877777 PP

                                       HHHHHHHHHH CS
                            Rsbr_N  84 rkvvlellse 93 
                                        k+v  ++ +
  gi|242398760|ref|YP_002994184.1| 257 EKMVRFQMYN 266
                                       7776666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      570  (0.0317921); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.52
# Mc/sec: 2257.36
//
Query:       gi|242398761|ref|YP_002994185.1|  [L=533]
Description: Carbamoyl transferase, NodU family [Thermococcus sibiricus MM 739]
Scores for complete 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-63  212.1   0.0    5.5e-63  211.6   0.0    1.2  1  Carbam_trans_C  Carbamoyltransferase C-terminus
    3.3e-53  181.5   0.5    2.2e-42  146.0   0.2    2.1  2  Carbam_trans_N  Carbamoyltransferase N-terminus
    2.6e-07   30.6   0.0    4.6e-06   26.5   0.0    2.3  2  Peptidase_M22   Glycoprotease family
  ------ inclusion threshold ------
       0.06   12.8   0.0       0.28   10.7   0.0    2.0  1  Sua5_yciO_yrdC  Telomere recombination


Domain annotation for each model (and alignments):
>> Carbam_trans_C  Carbamoyltransferase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  211.6   0.0   1.2e-66   5.5e-63       2     168 ..     366     531 ..     365     533 .] 0.98

  Alignments for each domain:
  == domain 1  score: 211.6 bits;  conditional E-value: 1.2e-66
                    Carbam_trans_C   2 ellaegkvvgwfqgrmEfGpRALGnRSiladprkeemkeklnekikkResfrPfApsvleeeaeeyfeeekespyml 78 
                                       e l e+k++g+fqg mE+GpRALGnRSi+adpr++++ +kln++++ R+ f+PfAps+lee++ ey+++  ++++m+
  gi|242398761|ref|YP_002994185.1| 366 ESLIENKILGIFQGAMEYGPRALGNRSIIADPRDKRVVKKLNATLN-RDVFQPFAPSILEERIGEYLKDPYPNKFMT 441
                                       6799**************************************9988.**********************99****** PP

                    Carbam_trans_C  79 lvakvkeekreeipavtHvDgtaRvqtvkkeanpryhelleafekltgvpvllNTSfNvrgepivetpedalelflk 155
                                       + ++++e++ ++ pav+HvDgt+R+qt+ ke+npry++++++fek+tg+ ++lNTSfN++gepiv++pedal++f++
  gi|242398761|ref|YP_002994185.1| 442 MSYTATEKMIKDAPAVVHVDGTTRPQTLLKEDNPRYYNIIKRFEKETGIGAILNTSFNMHGEPIVCSPEDALKTFKT 518
                                       ***************************************************************************** PP

                    Carbam_trans_C 156 teldalvlgdllv 168
                                        +ld+lvl++++v
  gi|242398761|ref|YP_002994185.1| 519 AKLDLLVLENFIV 531
                                       **********998 PP

>> Carbam_trans_N  Carbamoyltransferase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.0   5.1e-12   2.3e-08       2      70 ..       3      66 ..       2      82 .. 0.90
   2 !  146.0   0.2   4.9e-46   2.2e-42     118     337 ..      86     310 ..      69     311 .. 0.85

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 5.1e-12
                    Carbam_trans_N  2 ilGikltlflHDgavalvddgklvaaveeErltrikrdqklpklkaidyaleeagvelsdiDqivfdei 70
                                      ilG+  +   HD++++l  +g++++av+eErl+rik+++++p+  +i  +l++   +++++D+i++ + 
  gi|242398761|ref|YP_002994185.1|  3 ILGVHDG---HDSGAVLF-KGEEIYAVNEERLNRIKKYRGFPE-LSIREVLKRGNANPEEVDVIAVAGL 66
                                      799**99...****9876.6899********************.79******************98765 PP

  == domain 2  score: 146.0 bits;  conditional E-value: 4.9e-46
                    Carbam_trans_N 118 kvdrkdvslyeHhlsHaaSaystSpFakkeklvlcldgdGdiaprllaveketelkikslvsfsesiGhlYaaatey 194
                                       k ++k+v+++eHhl+Ha Say+tS++  ke+l+l +d  Gd  + ++++++++e+   +  ++ +s+G  Ya +te 
  gi|242398761|ref|YP_002994185.1|  86 KDFKKKVLFVEHHLAHASSAYYTSGW--KEALALSIDATGDGLSSSIYLGRDGEMIRIAQSTYLDSLGDFYASITEL 160
                                       6799**********************..**********************999998889999*************** PP

                    Carbam_trans_N 195 lGfkknsdegKlmalaayGkpkeriveelyellkkagyrinl.ennieiskkkvhdffeasalrlkearekde.... 266
                                       lGf +   egK+m+laayG p  ++  ++ el    ++  nl   ++e++kk +++ff+ ++ + k+ + + +    
  gi|242398761|ref|YP_002994185.1| 161 LGFRPMRHEGKVMSLAAYGRPTYDL-SNIIELNGL-SFENNLrVVGLEATKK-LAEFFNYPLSKAKDIALQ-Mkkgk 233
                                       **********************443.455555544.8888886778888888.99***9988777766554.12344 PP

                    Carbam_trans_N 267 ..........dlaAsiqvflErlvvevlnivyeklkirnLclaGGvalNiklNsallesglFedvwvqPaanDsGsA 333
                                                 ++aAs q+ lE++v e+  +++   +  +L+ aGGva N+k+N+ l++   F d+wv+Pa++DsG A
  gi|242398761|ref|YP_002994185.1| 234 ldgeitqkaiEIAASAQTHLEKIVNELGLKLRS-YN-LKLAYAGGVAQNVKANAVLRK--HFPDLWVFPAMDDSGLA 306
                                       5666788899*************9888666555.44.57***************9987..6**************** PP

                    Carbam_trans_N 334 iGAA 337
                                        GAA
  gi|242398761|ref|YP_002994185.1| 307 FGAA 310
                                       ***9 PP

>> Peptidase_M22  Glycoprotease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0     0.055   2.5e+02      37      57 ..      44      64 ..      41      66 .. 0.93
   2 !   26.5   0.0     1e-09   4.6e-06      78     247 ..      86     291 ..      79     301 .. 0.70

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.055
                                      HHHHHHHHTSTGGGEEEEEEE CS
                     Peptidase_M22 37 ieealaeaglsledldaIavt 57
                                      i+e+l++ + ++e++d+Iav+
  gi|242398761|ref|YP_002994185.1| 44 IREVLKRGNANPEEVDVIAVA 64
                                      899****************97 PP

  == domain 2  score: 26.5 bits;  conditional E-value: 1e-09
                                       HHCT--EEEEEHHHHHHHCCHCTSECSSCEEEEE....SSSTEEEEEECT.TEEEEEEEESSSEHHHHHHHHHHHHT CS
                     Peptidase_M22  78 lalnkPlvgVnhleahalaarleekeefPvvllv....sGghtqvylvke.gryeilgetlddaagealdkvarllg 149
                                         ++k ++ V h  aha +a+++++ ++ ++l +    +G  +++yl+++ + ++i ++t  d +g+ + ++++llg
  gi|242398761|ref|YP_002994185.1|  86 KDFKKKVLFVEHHLAHASSAYYTSGWKEALALSIdatgDGLSSSIYLGRDgEMIRIAQSTYLDSLGDFYASITELLG 162
                                       56899***************98843344466666222257899*******999************************ PP

                                       ..S..SCCHHHHHHHCTC.S.......EET......TEEE.CHHH.HHHHHHHSTT..................... CS
                     Peptidase_M22 150 lpy..pggpkieklakeg.kkiefprplkg......ldfsfsGlk.tavlkeleke..................... 195
                                       +     +g k+ +la  g  +++++  +        +++  +Gl+ t+ l e+  +                     
  gi|242398761|ref|YP_002994185.1| 163 FRPmrHEG-KVMSLAAYGrPTYDLSNIIELnglsfeNNLRVVGLEaTKKLAEFF-Nyplskakdialqmkkgkldge 237
                                       98843344.666699988755665554443456666788888884133333332.2445675566666667777777 PP

                                       ....HHHHHHHHHHHHHHHHHHHHHHHHHHCTBSEEEEESGGGGXHHHHHCHCCHH CS
                     Peptidase_M22 196 ....vedlaasfqeavvdhlvekteralklpkakelvilGGvaankrLrealeeea 247
                                           + ++aas q + ++++v+ +   l++++  +l+ +GGva+n + ++ l+++ 
  gi|242398761|ref|YP_002994185.1| 238 itqkAIEIAASAQTH-LEKIVNELGLKLRSYNL-KLAYAGGVAQNVKANAVLRKHF 291
                                       776666777777775.66666666666666777.789999*999999887777554 PP

>> Sua5_yciO_yrdC  Telomere recombination
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   6.3e-05      0.28      97     155 ..     464     528 ..     388     533 .] 0.61

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 6.3e-05
                                       TTEEEEEE-SSHHHHHHHHHCTS-.....EEEEES-STTS-S-SSHHHHHHHC-.TTSECB-SS- CS
                    Sua5_yciO_yrdC  97 lktvGvrlPdtplarlLlealgep.....lvaTSanlsgepsitdaeeveeelg.eivdlildgg 155
                                       ++   +   d+p  +++++++++      +  TS n++gep++ ++e++ + ++ +++dl++  +
  gi|242398761|ref|YP_002994185.1| 464 TRPQTLLKEDNPRYYNIIKRFEKEtgigaILNTSFNMHGEPIVCSPEDALKTFKtAKLDLLVLEN 528
                                       44455555678888889998876568888**********************98515677766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (533 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); 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: 0.70u 0.31s 00:00:01.01 Elapsed: 00:00:00.50
# Mc/sec: 3213.01
//
Query:       gi|242398762|ref|YP_002994186.1|  [L=118]
Description: carbohydrate-binding protein [Thermococcus sibiricus MM 739]
Scores for 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   65.9   0.1    2.7e-18   65.5   0.1    1.2  1  Cupin_2          Cupin domain
    3.4e-12   46.4   0.1    4.1e-12   46.2   0.1    1.1  1  AraC_binding     AraC-like ligand binding domain
    5.7e-06   26.3   0.0    6.2e-06   26.2   0.0    1.1  1  MannoseP_isomer  Mannose-6-phosphate isomerase
    6.2e-05   22.6   0.0    0.00015   21.4   0.0    1.6  1  Cupin_1          Cupin
    0.00048   20.3   0.0    0.00072   19.7   0.0    1.3  1  CENP-C_C         Mif2/CENP-C like
     0.0091   15.7   0.0      0.013   15.2   0.0    1.4  1  Cupin_3          Protein of unknown function (DUF861)
  ------ inclusion threshold ------
      0.043   13.5   0.0      0.058   13.1   0.0    1.1  1  Auxin_BP         Auxin binding protein
      0.061   13.2   0.0      0.082   12.7   0.0    1.2  1  Asp_Arg_Hydrox   Aspartyl/Asparaginyl beta-hydroxylase
       0.08   13.1   0.0       0.11   12.7   0.0    1.2  1  Ectoine_synth    Ectoine synthase
        0.1   12.5   0.0       0.12   12.2   0.0    1.3  1  Cupin_7          ChrR Cupin-like domain
       0.18   11.4   0.0        0.2   11.3   0.0    1.1  1  AraC_binding_2   AraC-binding-like domain


Domain annotation for each model (and alignments):
>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.5   0.1   1.6e-21   2.7e-18       2      70 ..      36     104 ..      35     105 .. 0.97

  Alignments for each domain:
  == domain 1  score: 65.5 bits;  conditional E-value: 1.6e-21
                                       EEEEETTEEEEEECSSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEEEE-SSS-EEEEEE CS
                           Cupin_2   2 lvelppGesapshrHpgedeffyVleGegeltvdgeeveleaGdsvyfpagtpHrfrNtgdeparllvv 70 
                                       +ve++p +  p h+H+ + e+fy+++Ge++l +++ e++ ++Gd++++++ t H+++N+g++p+rl+vv
  gi|242398762|ref|YP_002994186.1|  36 IVEIKPRQRVPKHYHEKQYELFYIISGEAKLGIGEVEYDARPGDIYLVKPQTIHWVINEGEKPFRLFVV 104
                                       799***************************************************************997 PP

>> AraC_binding  AraC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.2   0.1   2.5e-15   4.1e-12      11      77 ..      40     107 ..      35     117 .. 0.94

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 2.5e-15
                                       STT-SEEEETT-.SEEEEEEEEE-EEEEETTEEEEE-TT-EEEE-TTS-EEEEE-TTSEEEEEEEEE- CS
                      AraC_binding  11 ypdhsfpphvhd.eyvihyvteGtgrlrlngrtydlgpGdlfLlppgepHdyesdsedgweyrwlyfe 77 
                                        p++++p+h h+ +y++ y+++G+++l +++ +yd++pGd+ L++p ++H    ++e+++++++++++
  gi|242398762|ref|YP_002994186.1|  40 KPRQRVPKHYHEkQYELFYIISGEAKLGIGEVEYDARPGDIYLVKPQTIHWVINEGEKPFRLFVVKLN 107
                                       58899************************************************************987 PP

>> MannoseP_isomer  Mannose-6-phosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   3.8e-09   6.2e-06      63     146 ..      32     114 ..       3     117 .. 0.88

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 3.8e-09
                   MannoseP_isomer  63 yqvkritvkPgeklslqkhhhraehWvvvkGtakvtvddevlllkenestyiplgaihrlenpGkiplelievqsGs 139
                                          +++++kP +++  + h  + e + +++G ak+ +++ ++  +  +   ++ ++ih + n G+ p++l  v+  +
  gi|242398762|ref|YP_002994186.1|  32 SYAQIVEIKPRQRVPKHYHEKQYELFYIISGEAKLGIGEVEYDARPGDIYLVKPQTIHWVINEGEKPFRLFVVKL-N 107
                                       4567899********999999**************************99999******************99987.7 PP

                   MannoseP_isomer 140 ylgeddi 146
                                       y+g+d +
  gi|242398762|ref|YP_002994186.1| 108 YFGDDSV 114
                                       9998875 PP

>> Cupin_1  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   9.2e-08   0.00015      38     114 ..      37     105 ..      23     117 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 9.2e-08
                                       EEE.TTEEEEEEEESSS-EEEEEEESEEEEEEEETTSS.EEEEEEEETTEEEEE-TT-EEEEEEESSSSEEEEEEEE CS
                           Cupin_1  38 vdlepgglllPhyhpnateiayvlqGegrvgfvvpgngnrdfhkklreGdvfvvPaglvhfqynsgdepavaivvfd 114
                                       v ++p+  ++ hyh +  e++y++ Ge+ +g+          + + r+Gd+  v +  +h+++n g e+ + ++v++
  gi|242398762|ref|YP_002994186.1|  37 VEIKPRQRVPKHYHEKQYELFYIISGEAKLGIG-------EVEYDARPGDIYLVKPQTIHWVINEG-EKPFRLFVVK 105
                                       44577777899******************7763.......355689********************.5555555555 PP

>> CENP-C_C  Mif2/CENP-C like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   4.4e-07   0.00072      16      84 ..      36     104 ..      30     105 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 4.4e-07
                                       EEEE-TCCCEEEEE--SEEEEEEEEESEEEEEETTEEEEEETT-EEEE-TT-EEEEEE-SSS-EEEEEE CS
                          CENP-C_C  16 ilkLppgaeKkkknskkatlvFyViqGrvevtvsktsfvigkgsvFqvPagneysieNklnkeaklfFv 84 
                                       i++++p +   k+  +k++  Fy+i G+ +  + + ++ + +g++++v       + N+++k  +lf v
  gi|242398762|ref|YP_002994186.1|  36 IVEIKPRQRVPKHYHEKQYELFYIISGEAKLGIGEVEYDARPGDIYLVKPQTIHWVINEGEKPFRLFVV 104
                                       789999888888888889999***************************888889999999999999976 PP

>> Cupin_3  Protein of unknown function (DUF861)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0     8e-06     0.013      24      72 ..      52     105 ..      30     108 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 8e-06
                                       SSEEEEEEEECEEEEEETTTEEEEEETTEEEEE-TTE......EECCCEEEEEEE CS
                           Cupin_3  24 eedEfcyileGevkvtpeggetvelraGDlvvlpkgl......sgtwdvsetvrK 72 
                                       ++ E++yi++Ge k+   g+ ++  r+GD+  +++ +      +g+  ++ +v K
  gi|242398762|ref|YP_002994186.1|  52 KQYELFYIISGEAKLGI-GEVEYDARPGDIYLVKPQTihwvinEGEKPFRLFVVK 105
                                       4589*************.9999*********999998787777777777777555 PP

>> Auxin_BP  Auxin binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   3.5e-05     0.058      50     108 ..      38      95 ..      32     100 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.5e-05
                                       EE-TT-B--EEEESS-.EEEEEEE--EEEEE--SSSSS--S-EEEEE-TTEEEEE-TT-- CS
                          Auxin_BP  50 tlapgsrtpihrhsce.evfvvlkgkgtlylasssskypgkpqelpifanstlsipvnda 108
                                        + p +r p h h  + e+f ++ g+  l +++   +y  +p ++ + +  t++  +n+ 
  gi|242398762|ref|YP_002994186.1|  38 EIKPRQRVPKHYHEKQyELFYIISGEAKLGIGE--VEYDARPGDIYLVKPQTIHWVINEG 95 
                                       57899********86449******999987775..689*****************99985 PP

>> Asp_Arg_Hydrox  Aspartyl/Asparaginyl beta-hydroxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0     5e-05     0.082      74     146 ..      30      98 ..      17     106 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5e-05
                                       GEEEEEEEEE-TTEEEEEE-S..-TTSEEEEEEE--TTEEEEETTEEE---TTEEEEE-TTS-EEEEE-SSS- CS
                    Asp_Arg_Hydrox  74 klgealfsvlepgshikpHrgptngrlrlhLgLvvPeeceirvggetrtweeGevllfDdsfeHevwnetdee 146
                                       ++++a +  ++p++++++H+     + ++ L  ++  e+++ +g+ ++  + G++ l+     H+v ne++++
  gi|242398762|ref|YP_002994186.1|  30 ERSYAQIVEIKPRQRVPKHYH----EKQYELFYIISGEAKLGIGEVEYDARPGDIYLVKPQTIHWVINEGEKP 98 
                                       5678999999*********98....6666777789999*******************************9886 PP

>> Ectoine_synth  Ectoine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   6.6e-05      0.11      43      99 ..      40      95 ..      32     106 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.6e-05
                                      -TT--EEEE-T.T-EEEEEEEE--EEEEETTT--EEEE-TTEEEEETTT-EEEEEESS CS
                     Ectoine_synth 43 kagtetelkYk.nHleavycieGegeveeledgevyeikpgtlYlldkhdkHllrakk 99
                                      k  +++  +Y+ + +e  y+i+Ge+++       +y+ +pg++Yl+  +  H++  + 
  gi|242398762|ref|YP_002994186.1| 40 KPRQRVPKHYHeKQYELFYIISGEAKLGIG--EVEYDARPGDIYLVKPQTIHWVINEG 95
                                      555566667751579**********99875..578************99999987554 PP

>> Cupin_7  ChrR Cupin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   7.7e-05      0.12      14      54 ..      22      63 ..      10     102 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.7e-05
                                      EEEEESSSS-EEEEEEEE-TTEE---EE-TT-.EEEEEEEEE CS
                           Cupin_7 14 pLerdgeekaratslvryapgsafsahkHpgg.eeilVLeGv 54
                                      pL + +  ++++ ++v+++p ++ ++h H++  e +++++G+
  gi|242398762|ref|YP_002994186.1| 22 PLFEGDLPERSYAQIVEIKPRQRVPKHYHEKQyELFYIISGE 63
                                      5555555668899****************9862556788887 PP

>> AraC_binding_2  AraC-binding-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00012       0.2      52      88 ..      46      86 ..      21     107 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00012
                    AraC_binding_2 52 l....ddfylvqlplsGraeveqggrevvlgpgdavvldpg 88
                                      +    +  y + +++sG+a +  g  e++++pgd  ++ p+
  gi|242398762|ref|YP_002994186.1| 46 PkhyhEKQYELFYIISGEAKLGIGEVEYDARPGDIYLVKPQ 86
                                      14445779****************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 832.23
//
Query:       gi|242398763|ref|YP_002994187.1|  [L=291]
Description: permease, auxin efflux carrier family [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.2e-14   51.7  19.2    2.2e-07   29.6   4.7    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 !   29.6   4.7   1.2e-11   2.2e-07      25     121 ..      20     115 ..       1     149 [. 0.79
   2 !   28.6   6.5   2.6e-11   4.6e-07     236     386 ..     148     287 ..     143     288 .. 0.88

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 1.2e-11
                         Mem_trans  25 iftpdqcsginrfVvlfavPllifhfisqnnpyemllrfiladvlvklivlillllgallskifkgslewtitlfsl 101
                                       i +++ +  +n++ v   + + if++++    +e l+++ l+ + v+li+++ ll+ +  +++f  + +w+  l++l
  gi|242398763|ref|YP_002994187.1|  20 IKSDKPFIYLNKIAVEALLTFYIFSSVAA-KDLEYLIEIRLVFIYVFLIIGLNLLSSYTYARFFVNDDRWKGALIIL 95 
                                       44555566799999999999*******98.67899****************************************** PP

                         Mem_trans 102 stlpNtlvlgipllkalyge 121
                                       st+pNt+ +g+p+ +   ++
  gi|242398763|ref|YP_002994187.1|  96 STYPNTVAMGFPIASLFLDD 115
                                       ************96655555 PP

  == domain 2  score: 28.6 bits;  conditional E-value: 2.6e-11
                         Mem_trans 236 limvlrklirnPntyssllglilslvsfkwnvimpkiiqksisilgdaglpmalfslGlfLalqpkkiacgnsvatf 312
                                       l+  l+k+++ P+t + ll+l ++  ++k +    + +   +++ g   +p+ l+  G+  +lq+ +i    +vatf
  gi|242398763|ref|YP_002994187.1| 148 LKDSLLKALKFPPTSANLLALAFVFLGIKLP----NALLTVMNQVGWWCIPLTLIYFGSRINLQKFEIRKLLEVATF 220
                                       567899***********************99....***************************************987 PP

                         Mem_trans 313 alavRlilgPlvmlvavlavgLrgslllvaivqaAlPqgivlfviAkeynvherelstllifgmlialpitlvy 386
                                        +++     P++ +++ l +   ++ + +++v+a++P++i   +i   y + e+e   + i+ +l+ l+i lv+
  gi|242398763|ref|YP_002994187.1| 221 RTVL-----PFIFVFLTLKAP--SDIFYAVLVEATMPPAIIGNAILAHYRLREEEGIGVTIVLTLMVLIIFLVF 287
                                       7655.....555555555444..67888***************************9999999999999888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       666  (0.0371465); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 1859.45
//
Query:       gi|242398764|ref|YP_002994188.1|  [L=212]
Description: hypothetical protein TSIB_0778 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-47  161.1   1.9    3.7e-47  160.8   1.9    1.0  1  DUF257    Pyrococcus protein of unknown function, DUF257
  ------ inclusion threshold ------
       0.06   13.6   0.2      0.087   13.0   0.2    1.2  1  DUF1229   Protein of unknown function (DUF1229)


Domain annotation for each model (and alignments):
>> DUF257  Pyrococcus protein of unknown function, DUF257
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.8   1.9   4.1e-51   3.7e-47       4     201 ..       8     205 ..       6     208 .. 0.94

  Alignments for each domain:
  == domain 1  score: 160.8 bits;  conditional E-value: 4.1e-51
                            DUF257   4 etlrpGetvLiEyssssvpevllyliakyskeknvPllvdDvlDtllivlkhlkllGldvpe.esikviKigGtkev 79 
                                       ++l++GetvL+E++s + p   l +++  sk+ +  l+++D+lDtl++++ +++l+G+d ++ ++ikv+K+gG  ev
  gi|242398764|ref|YP_002994188.1|   8 DSLKFGETVLLEHDSLMFPYKELAELTAWSKKRGYFLVIEDILDTLYTYKSQMELAGIDSKIlDNIKVLKTGGRLEV 84 
                                       689***********************************************************9************** PP

                            DUF257  80 gnvvkkidfdkdpsiylskykravekvsveetv.inlvlglerllllldnrrdlyklvksikkylgnknRkafylin 155
                                       gnv+++ ++   +    ++++   e+++   +  + +++gl++l+ll + + ++  lv+ i++y g+++R+afy+in
  gi|242398764|ref|YP_002994188.1|  85 GNVITRFQVSD-ILSLTKEFEMNYEHILSRIEHaTVPIVGLDKLFLLAESKLEILALVNTIARYAGSRKRTAFYFIN 160
                                       *******9876.777778888888888888666699***************************************** PP

                            DUF257 156 rnllesikPellplLEeiassvieiesekealivrilKslnldivg 201
                                       +++l +  P + plLEe as+vi+i++ + + +++i Ks n +++ 
  gi|242398764|ref|YP_002994188.1| 161 TDVLMNNIPYVIPLLEELASTVIKIYKDD-EKTFKIIKSTNNRLWK 205
                                       **************************998.789********99885 PP

>> DUF1229  Protein of unknown function (DUF1229)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.2   9.7e-06     0.087      29     139 .]      59     170 ..      36     170 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9.7e-06
                           DUF1229  29 flketyiGqriinsiaseklnehvdywnavkkdffvypkitigseytfwyhnvffdkhktsspiial..llyilslv 103
                                       ++ +  i  +i++ i  +k   + + +n +   f v   +++  e+ + y  ++    + + pi+ l  l  +    
  gi|242398764|ref|YP_002994188.1|  59 QMELAGIDSKILDNIKVLKTGGRLEVGNVIT-RFQVSDILSLTKEFEMNYEHILSRIEHATVPIVGLdkLFLLAESK 134
                                       3445557799*******************99.89********************9999999***9985445555678 PP

                           DUF1229 104 lfvialknslkrnhrsfryfhfyicfipylltvifw 139
                                       l ++al n++ r   s +   fy +    l+  i++
  gi|242398764|ref|YP_002994188.1| 135 LEILALVNTIARYAGSRKRTAFYFINTDVLMNNIPY 170
                                       9999********************999999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       694  (0.0387082); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1458.39
//
Query:       gi|242398765|ref|YP_002994189.1|  [L=645]
Description: hypothetical protein TSIB_0779 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00093   19.4   0.0        2.2    8.6   0.0    2.7  2  CARDB     CARDB
  ------ inclusion threshold ------
      0.049   14.1   0.4      0.096   13.1   0.4    1.4  1  MGC-24    Multi-glycosylated core protein 24 (MGC-24), sialom


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 !    8.6   0.0   0.00025       2.2      12      84 ..     348     428 ..     342     432 .. 0.83
   2 !    7.7   0.1   0.00046       4.2      10      83 ..     462     544 ..     456     555 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00025
                                       -SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE....EEEEESEE-CTEEEEEEEEEE-S....-S-CEEEE CS
                             CARDB  12 pseafvgeentitvtvkNqGtaasgatkvalyldgelv....gtvtvpsLaagesttvsftwtte....ategevtl 80 
                                       ps a + e ++ t+ +kN+G+++ + +++   l++e +       ++p+L  ge+++ ++ + ++    ++ g++++
  gi|242398765|ref|YP_002994189.1| 348 PSMALQFEPFNSTIVIKNTGDIDLKHIEIVPKLSEEFKiissYPLYIPELGVGEKIEFNVRIEPKkggfLQLGNIEI 424
                                       566666677788999**********************9995555666***************999777777788888 PP

                                       EEEE CS
                             CARDB  81 tvvv 84 
                                       +++v
  gi|242398765|ref|YP_002994189.1| 425 QANV 428
                                       8766 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00046
                                       EC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE..EEEEE........SEE-CTEEEEEEEEEE-S-S-C CS
                             CARDB  10 lnpseafvgeentitvtvkNqGtaasgatkvalyldgelv..gtvtv........psLaagesttvsftwtteateg 76 
                                       ln ++ +vg++ ++++tv N G+ + + t +    +++    +++++         sL+ +e++t s+ + ++ +eg
  gi|242398765|ref|YP_002994189.1| 462 LNSQNGTVGSSTQLNLTVVNMGNTKGPFTITIALPERSAIigENINLqgrfvyfeDSLNLKENKTYSLIFIPN-QEG 537
                                       5788999***************998666555555555555777777799999999999999999999999999.999 PP

                                       EEEEEEE CS
                             CARDB  77 evtltvv 83 
                                       e ++ + 
  gi|242398765|ref|YP_002994189.1| 538 EFEILAA 544
                                       9887655 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 ?   13.1   0.4   1.1e-05     0.096      57     118 ..     570     631 ..     545     637 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.1e-05
                            MGC-24  57 kstpkptnstaktttkpsstttstsva.tsgttnttvtptsqparkstFDaAsFiGGivLvLg 118
                                       ++  ++t++t+++t+ ++   t t+++  +   n+t+t     ++k  F +A F GG+  +L 
  gi|242398765|ref|YP_002994189.1| 570 ENFGNSTDETSTSTAPKIIKETITTTVtHTKVLNSTITVFP-IKQKLLFGGAGFTGGMAFILL 631
                                       33344444444444444333333333313333344433333.45899**********999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (645 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); 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: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 4483.92
//
Query:       gi|242398766|ref|YP_002994190.1|  [L=570]
Description: Flagella accessory protein [Thermococcus sibiricus MM 739]
Scores for complete 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-19   68.0   5.4    1.1e-09   38.3   0.0    3.3  4  T2SSF     Type II secretion system (T2SS), protein F
  ------ inclusion threshold ------
      0.091   11.4   0.0       0.15   10.7   0.0    1.2  1  TLV_coat  ENV polyprotein (coat polyprotein)


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 ?   -3.5   0.2       1.1   9.9e+03     100     120 ..      23      39 ..       7      42 .. 0.47
   2 !   38.3   0.0   1.2e-13   1.1e-09       1     123 [.      89     216 ..      89     218 .. 0.97
   3 ?   -2.6   0.1      0.58   5.2e+03     105     122 ..     277     294 ..     265     295 .. 0.48
   4 !   31.0   0.0   2.2e-11   1.9e-07       1     117 [.     338     461 ..     338     467 .. 0.71

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.1
                                       HHHHTTXXXXXXXXXXXXXXX CS
                             T2SSF 100 aallepllllvvallvllill 120
                                       + ll  ++     +++l+i++
  gi|242398766|ref|YP_002994190.1|  23 KVLLPSIAG----SIILFIVF 39 
                                       444433333....34444433 PP

  == domain 2  score: 38.3 bits;  conditional E-value: 1.2e-13
                                       HHHHHHHHHHTT--HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTS.SHHHHHC....T-TT.TS-HHHHHHHHHHH CS
                             T2SSF   1 flrqlatllsaGvplveaLellaeeaengplaeelkriarrlraGg.slseale....rtpssefpelvvqlirage 72 
                                       f++++a+l+ + v+ +e +++la+e+   p+++ +++i++ ++     ++ea++    rtps++f++++ +l  + +
  gi|242398766|ref|YP_002994190.1|  89 FVTYFAVLSTSEVGRNELIHTLAKEKVLEPISRDMEKIYHLIAKFNrGMPEAFRflvkRTPSKVFSDFLERLAYSLD 165
                                       899*******************************************7789*************************** PP

                                       HHT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXXXX CS
                             T2SSF  73 eggnLaevLerlaeyleeerelrrkllaallepllllvvallvllillail 123
                                       +g  L e+L + ++ +++++++ ++ ++  l +  +++  l++++++++ +
  gi|242398766|ref|YP_002994190.1| 166 SGVELREYLLQEQKIVMDDYQTFYEGALYDLDVFKEVYSSLIISVVFMVTF 216
                                       ***********************************************9876 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 0.58
                                       TXXXXXXXXXXXXXXXXX CS
                             T2SSF 105 pllllvvallvllillai 122
                                        ll+++ +++v+++++++
  gi|242398766|ref|YP_002994190.1| 277 ILLSIAGTAAVGILYFFV 294
                                       244444555555555444 PP

  == domain 4  score: 31.0 bits;  conditional E-value: 2.2e-11
                                       HHHHHHHHHH.TT--HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTSSHHHHHC....T-TT....TS-HHHHHHHH CS
                             T2SSF   1 flrqlatlls.aGvplveaLellaeeaengplaeelkriarrlraGgslseale....rtps...sefpelvvqlir 69 
                                       f+r+l++ l+ +Gv+++ +L++l++++ +g l++ ++++ +r++  ++  ++++    +t+s   + f++ ++  ++
  gi|242398766|ref|YP_002994190.1| 338 FMRSLSSSLAaSGVSMALVLKYLSSHD-FGSLTKDIRNLNKRISLKIDDTKSWKyfvsETGSwliDIFSDIFRKSLH 413
                                       78889888888****************.****************************986665333555555555555 PP

                                       HHHHHT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXX CS
                             T2SSF  70 ageeggnLaevLerlaeyleeerelrrkllaallepllllvvallvll 117
                                       +g     +++v++   e l + r+ r+++ a++ +++  +  a+++++
  gi|242398766|ref|YP_002994190.1| 414 LGADPDYVGKVISSNFERLLRLRRKRKQNVASFKGVIYGVTGAFAFSV 461
                                       555555555555555555555555555555555555555555555444 PP

>> TLV_coat  ENV polyprotein (coat polyprotein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   1.7e-05      0.15     498     554 ..     168     225 ..     161     233 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 1.7e-05
                                       HHHHHHHHHHHH.HHH-XXXX.XXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXX CS
                          TLV_coat 498 akLqerleqrqr.llednqlwfegllglspwlttllstilgpLlllLLiLllGPciln 554
                                        +L+e l q+q+ +++d q  +eg l  +  + ++ s+++  ++ ++ ++++GP+i  
  gi|242398766|ref|YP_002994190.1| 168 VELREYLLQEQKiVMDDYQTFYEGALYDLDVFKEVYSSLIISVVFMVTFIIIGPIITG 225
                                       68*******999446788999*******************9999***********974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (570 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       887  (0.0494729); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); 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: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.44
# Mc/sec: 3913.93
//
Query:       gi|242398767|ref|YP_002994191.1|  [L=541]
Description: type II secretion system protein [Thermococcus sibiricus MM 739]
Scores for complete 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-47  160.4   0.0    6.3e-47  159.9   0.0    1.2  1  T2SSE        Type II/IV secretion system protein
     0.0097   15.6   0.0      0.027   14.2   0.0    1.8  1  AAA_29       P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.042   14.3   0.0       0.19   12.3   0.0    2.0  2  ABC_tran     ABC transporter
      0.073   12.6   0.2        1.1    8.8   0.0    2.6  3  AAA_7        P-loop containing dynein motor region
       0.12   12.3   0.2       0.32   10.9   0.0    1.7  2  Microtub_bd  Microtubule binding
       0.16   11.7   0.0       0.39   10.5   0.0    1.6  1  DEAD         DEAD/DEAH box helicase
        2.3    8.0   5.5        0.8    9.5   0.1    3.0  4  CheR_N       CheR methyltransferase, all-alpha 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 !  159.9   0.0   2.5e-50   6.3e-47       4     245 ..     162     407 ..     159     431 .. 0.94

  Alignments for each domain:
  == domain 1  score: 159.9 bits;  conditional E-value: 2.5e-50
                             T2SSE   4 lleallddekvsdihvekper.vkvrervdgielreveelekaalerlisriaalakldiseerplqdarlpekgvr 79 
                                       +le l++d+ + dih+   e    +++  d     ++++ ++  l+  ++ +    ++  s+++p++d++lp +g r
  gi|242398767|ref|YP_002994191.1| 162 PLEVLIRDPYIEDIHILGAEYvSLIHKIFDA-LPTNIKFESNITLADYLKALSERIGRPASDKNPIVDGTLP-DGSR 236
                                       6788999**************8889888898.99999999999999999***********************.**** PP

                             T2SSE  80 lrvvllPvvag..ealviRkksakeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkein 154
                                       ++++  P v     +++iRk s+  l++ +l++ +++++++a+ l  a++  +++ v G T sGKtt+l++++ +i+
  gi|242398767|ref|YP_002994191.1| 237 INIIYSPDVSIkgSSATIRKFSTTPLSVVQLVKWNTFSAEVAAYLWLALEYGMSVFVCGETASGKTTTLNSIVPFIK 313
                                       *******87765689***********************************9************************** PP

                             T2SSE 155 ksderivtvEDpvEiqleganqvqlnak.....kakvtfadllraaLRlrPDrimvGEiRdketleilkAvnTGHlg 226
                                        +  +i t+ED+ E+ + ++   +l ++     + +vt+ dll+aaLR rP  i+vGEiR++e + + +A++TGH++
  gi|242398767|ref|YP_002994191.1| 314 PQ-SKIFTAEDTPEVVVPHPTWQRLTTRergpeESRVTLFDLLKAALRSRPNYIIVGEIRGAEGAIAFQAMQTGHPV 389
                                       *9.*************************9***99******************************************* PP

                             T2SSE 227 slsTlHansaagalerLeq 245
                                        ++T Ha++ ++ ++r   
  gi|242398767|ref|YP_002994191.1| 390 -MATFHAGDIKKMIQRFTG 407
                                       .**************9875 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   1.1e-05     0.027       1      51 [.     262     317 ..     262     321 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.1e-05
                            AAA_29   1 LkrlqlvNWgtfdghtiei....dlkg.atlltGpsGsGKSTllDAiqalLvpakk 51 
                                       L+ +qlv W tf+ +++       + g ++++ G++ sGK+T l +i   + p++k
  gi|242398767|ref|YP_002994191.1| 262 LSVVQLVKWNTFSAEVAAYlwlaLEYGmSVFVCGETASGKTTTLNSIVPFIKPQSK 317
                                       5679*********96654211112346799*************9999887777765 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.7   4.3e+03      53      86 ..      82     122 ..      60     147 .. 0.60
   2 ?   12.3   0.0   7.3e-05      0.19       6      42 ..     283     319 ..     280     349 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.7
                                       -HHHCCHCEEEE-SS.--S-TTSBHHHH..........HHHTCHH CS
                                       xxxxxxxxxxxxxxx.xxxxxxxxxxxx..........xxxxxxx RF
                          ABC_tran  53 eleslrkeigvlpqe.pqlfpeltvren..........esdeeie 86 
                                       + ++ r + + ++++  +l p +t+ en                +
  gi|242398767|ref|YP_002994191.1|  82 QNTEERVKYELVKEKiLELAPSKTIPENreefeifldqL----YN 122
                                       445666677777777777888888777755444433320....33 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 7.3e-05
                                       EEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   6 lklkegekvaivGenGaGKStLlkllagllkpteGei 42 
                                       l l+ g  v + Ge+ +GK+t l+ +    kp++   
  gi|242398767|ref|YP_002994191.1| 283 LALEYGMSVFVCGETASGKTTTLNSIVPFIKPQSKIF 319
                                       6789999*********************999987655 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 ?   -1.5   0.0      0.61   1.6e+03     126     147 ..     125     145 ..     109     153 .. 0.69
   2 ?    8.8   0.0   0.00042       1.1      24      55 ..     279     310 ..     267     321 .. 0.81
   3 ?    0.0   0.0       0.2   5.2e+02      67     112 ..     378     423 ..     375     450 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.61
                             AAA_7 126 lRqlldyggwYdrkklefkeik 147
                                       l q ++++g+++rk++++++i+
  gi|242398767|ref|YP_002994191.1| 125 L-QKINNRGFFSRKNVKITKIE 145
                                       5.55788999999998776654 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00042
                             AAA_7  24 yllelllknkkpvllvGptGtGKtviikdllk 55 
                                         l l l+ +++v+++G+t +GKt+++++++ 
  gi|242398767|ref|YP_002994191.1| 279 AYLWLALEYGMSVFVCGETASGKTTTLNSIVP 310
                                       5566789999****************999765 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.2
                             AAA_7  67 infsaqtsanqlqdiiesklekrrkgvygPpggkklvvFvDDlnmp 112
                                       i f+a+ + + ++ ++++   k+  + +   + +  v+F+D+ln+ 
  gi|242398767|ref|YP_002994191.1| 378 IAFQAMQTGHPVMATFHAGDIKKMIQRFTGHPINVPVTFIDNLNIA 423
                                       56666666677777776666677777777777777899*****986 PP

>> Microtub_bd  Microtubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       2.1   5.4e+03      31      81 ..      80     127 ..      72     133 .. 0.48
   2 ?   10.9   0.0   0.00013      0.32      69     102 ..     275     307 ..     264     322 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.1
                                       CCS-T.EEEETTT...TTTEEEE-SEEEECTTHCCCCCCCCHHHHHHHHTT CS
                       Microtub_bd  31 elesekakikfpeeekkkkkefsFdrvfeseseqeevfeeisqlvqsaldg 81 
                                       + ++ + ++k++   k+k  e    + ++++ e+ e+f    ql++ al++
  gi|242398767|ref|YP_002994191.1|  80 RIQNTEERVKYEL-VKEKILELAPSKTIPENREEFEIFL--DQLYNEALQK 127
                                       5555334555542.2333444444455555555555553..3555555555 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00013
                                       CCCHHHHHHHHTT--EEEEEEES........... CS
                       Microtub_bd  69 eeisqlvqsaldgynvcifaygqTGsGKtyTmeg 102
                                        e+++++  al +y +++f +g+T sGKt T+++
  gi|242398767|ref|YP_002994191.1| 275 AEVAAYLWLAL-EYGMSVFVCGETASGKTTTLNS 307
                                       66667776666.5999***************987 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00015      0.39      11      56 ..     285     333 ..     276     337 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00015
                                       HHTTCEEEEEESTTSSHHHH..HHHHHHHHHHHS.TTSTS-EEEEEESS CS
                                       xxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxx.xxxxxxxxxxxxxx RF
                              DEAD  11 ilgggdvlvaaeTGsGKTla..flipvlqivyet.kgktgpkalivePt 56 
                                       +  g +v+v++eT+sGKT+    ++p ++  ++  + +++p +++  Pt
  gi|242398767|ref|YP_002994191.1| 285 LEYGMSVFVCGETASGKTTTlnSIVPFIKPQSKIfTAEDTPEVVVPHPT 333
                                       347889************9855334444322222356777777776665 PP

>> CheR_N  CheR methyltransferase, all-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.2      0.65   1.7e+03       1      13 [.     111     123 ..     111     124 .. 0.89
   2 ?   -3.2   0.0       2.9   7.4e+03      41      49 ..     204     212 ..     199     214 .. 0.75
   3 ?   -3.2   0.0       2.9   7.4e+03      26      34 ..     431     439 ..     430     448 .. 0.71
   4 ?    9.5   0.1   0.00031       0.8      21      46 ..     498     523 ..     497     528 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.65
                                       HHHHHHHHHHHHT CS
                            CheR_N   1 edferlleliyer 13 
                                       e+fe +l+ +y++
  gi|242398767|ref|YP_002994191.1| 111 EEFEIFLDQLYNE 123
                                       69*********97 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2.9
                                       SSHHHHHHT CS
                            CheR_N  41 sfeeYldlL 49 
                                       ++++Yl++L
  gi|242398767|ref|YP_002994191.1| 204 TLADYLKAL 212
                                       567888877 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 2.9
                                       HHTHHHHHH CS
                            CheR_N  26 lkrRlsrRm 34 
                                       +k R  rR+
  gi|242398767|ref|YP_002994191.1| 431 VKGRFLRRI 439
                                       677777776 PP

  == domain 4  score: 9.5 bits;  conditional E-value: 0.00031
                                       STHHHHHTHHHHHHHTTT-SSSHHHH CS
                            CheR_N  21 yKrallkrRlsrRmralglksfeeYl 46 
                                       y++  l+ R+ +Rm++lg++++ + +
  gi|242398767|ref|YP_002994191.1| 498 YNELFLRARIIQRMAELGITNYWDVY 523
                                       78889****************97755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (541 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.67u 0.35s 00:00:01.02 Elapsed: 00:00:00.52
# Mc/sec: 3131.76
//
Query:       gi|242398768|ref|YP_002994192.1|  [L=225]
Description: Archaeal flagella-related protein H, ATPase [Thermococcus sibiricus MM 739]
Scores for complete 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-16   58.0   0.0    1.3e-15   57.4   0.0    1.2  1  ATPase           KaiC
     0.0018   18.2   0.4     0.0033   17.3   0.4    1.4  1  NACHT            NACHT domain
     0.0026   17.4   0.0     0.0078   15.8   0.0    1.7  1  AAA_25           AAA domain
     0.0086   15.4   0.0      0.024   13.9   0.0    1.7  2  Rad51            Rad51
  ------ inclusion threshold ------
      0.012   15.3   0.0        0.2   11.4   0.0    2.2  2  IstB_IS21        IstB-like ATP binding protein
      0.025   15.0   0.0      0.037   14.4   0.0    1.3  1  AAA_16           AAA ATPase domain
      0.069   11.8   0.0      0.071   11.7   0.0    1.1  1  GvpD             GvpD gas vesicle protein
      0.084   12.9   0.0       0.17   11.9   0.0    1.8  1  AAA_5            AAA domain (dynein-related subfamily)
       0.09   13.1   0.0       0.17   12.1   0.0    1.7  1  AAA_22           AAA domain
       0.12   12.4   0.1        0.3   11.1   0.1    1.9  1  AAA_14           AAA domain
       0.13   12.0   0.2        8.2    6.1   0.0    2.6  2  AAA_24           AAA domain
       0.16   11.7   0.1        1.1    9.0   0.0    2.0  2  Sigma54_activat  Sigma-54 interaction domain
       0.16   12.0   0.0       0.32   11.0   0.0    1.5  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro


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 !   57.4   0.0   9.7e-19   1.3e-15       9     222 ..       9     215 ..       4     222 .. 0.82

  Alignments for each domain:
  == domain 1  score: 57.4 bits;  conditional E-value: 9.7e-19
                            ATPase   9 DeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekleeegklai 85 
                                        + l gGip+g+ + i G+ GtGK+if+++ ++  +++ + ++ +v++  +  +++++++slG  +  +  + kl +
  gi|242398768|ref|YP_002994192.1|   9 HRRLGGGIPSGSLIFIEGDRGTGKSIFSQRLAYGFLKN-DIQVSYVSTQLTTPEFINQMESLGYSVIPFLTKRKLLF 84 
                                       45567*************************99988777.************************************** PP

                            ATPase  86 idasesaeesaeekdkedleelieelaeaikeikakrvviDsitgl.ayeekeavaReilrqlvrvlkklgvTailv 161
                                       + ++   +        ++   ++ ++ +  +  +   ++iDs+ ++   + +e+++R+   +l+  l+ l+   il+
  gi|242398768|ref|YP_002994192.1|  85 VSLYPLLSS------VSKRGRFLPRFLSEERLWEKDVIIIDSLPSIlPPKIDEETLRKFTEHLK-KLSALNKAIILT 154
                                       ****99876......3333444444444457888899*********777777777777666654.577888878888 PP

                            ATPase 162 sekssseeaaggygveefivdgvivLdlkeieeelvRtleivkmRg.tkhskkehpfeIte.e 222
                                       ++ +s+ ++     +ee i +  i+L++k   ++l+ +  ivk+    ++ +k++pf +++  
  gi|242398768|ref|YP_002994192.1| 155 AN-PSDLDSSVLSILEE-ITTMLIRLQVKVFGGDLKNSATIVKYNNaMGVFQKVIPFRVEPkA 215
                                       87.77777788888899.*************************97625788888888888744 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.4   2.4e-06    0.0033       2     151 ..      21     184 ..      20     194 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.4e-06
                                       CEEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC..-SEEEEEETTTTTTS-.......-HCHHHCCCCTS--SSS-C. CS
                             NACHT   2 lvilqGeaGsGKTtLlqklalawaegklpqga..fklvFflslrelsrsgna....rsladllfsqlpepaapvse. 71 
                                       l++++G+ G GK+++ q+la    +++ +  +   +l    +  +++  g +    ++ ++llf  l ++ + vs+ 
  gi|242398768|ref|YP_002994192.1|  21 LIFIEGDRGTGKSIFSQRLAYGFLKNDIQVSYvsTQLTTPEFINQMESLGYSvipfLTKRKLLFVSLYPLLSSVSKr 97 
                                       799*******************9999966654344444444444444444447788788889998888888888885 PP

                                       .CHHHHCCSCCCEE....EEEE-STT-SS-TCH.........HHHHHCTTTTT--EEEEEEECCCHHH....HCTTS CS
                             NACHT  72 .vwavllelperlL....lilDglDelvtdlgqkekqpvrtlLselirkkllpeasllltvrpralrd....leeql 139
                                         +  +   +erl+    +i+D+l  +         +++ + ++e ++k +  +  ++lt+ p+ l      +   l
  gi|242398768|ref|YP_002994192.1|  98 gRFLPRFLSEERLWekdvIIIDSLPSILPPKI---DEETLRKFTEHLKKLSALNKAIILTANPSDLDSsvlsI---L 168
                                       55555666677777999899999877765433...46788888888888888888899999999886653332...3 PP

                                       SCE......EEEE--T CS
                             NACHT 140 eea....ivlevegfs 151
                                       ee     i+l+v+ f+
  gi|242398768|ref|YP_002994192.1| 169 EEIttmlIRLQVKVFG 184
                                       3334445667776665 PP

>> AAA_25  AAA 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    0.0078      24     175 ..      10     147 ..       2     155 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5.6e-06
                            AAA_25  24 wlvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgeal... 97 
                                         ++g +p g+l+ + G++gtGK+ +   la+  ++ +          + V yvs+  +  e+ + ++ +g  +   
  gi|242398768|ref|YP_002994192.1|  10 RRLGGGIPSGSLIFIEGDRGTGKSIFSQRLAYGFLKND----------IQVSYVSTQLTTPEFINQMESLGYSVipf 76 
                                       5677888*************************999755..........58999999999989999999999888866 PP

                            AAA_25  98 rddarllvldlagveslpLfak.drggtlltadvdaleaaieevegvrlvviDplsralgg..densnsdvgalvea 171
                                         +++ll+++l      pL+++  ++g  l++++   e+++ e +  ++++iD+l ++l+   de+  ++ ++ +++
  gi|242398768|ref|YP_002994192.1|  77 LTKRKLLFVSL-----YPLLSSvSKRGRFLPRFL--SEERLWE-K--DVIIIDSLPSILPPkiDEETLRKFTEHLKK 143
                                       44677777776.....566666245555588887..4455555.4..899999999999887777766666666665 PP

                            AAA_25 172 leri 175
                                       l  +
  gi|242398768|ref|YP_002994192.1| 144 LSAL 147
                                       5555 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   1.8e-05     0.024      24      58 ..       6      40 ..       2      51 .. 0.92
   2 ?   -1.9   0.0       1.2   1.6e+03     161     184 ..     133     156 ..     130     187 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.8e-05
                                      HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHH CS
                             Rad51 24 kklDelLgGGietgsiteifGefrsGktqlchtlc 58
                                       +l + LgGGi++gs+  i G+ ++Gk+ +++ l+
  gi|242398768|ref|YP_002994192.1|  6 DELHRRLGGGIPSGSLIFIEGDRGTGKSIFSQRLA 40
                                      578899************************99997 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHHHHHH--EEEEEE CS
                             Rad51 161 klgkllrtLrkladefevavvitn 184
                                        l k+ ++L+kl+   ++ ++ +n
  gi|242398768|ref|YP_002994192.1| 133 TLRKFTEHLKKLSALNKAIILTAN 156
                                       688899999999877766666666 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00014       0.2      50      84 ..      22      56 ..      16      68 .. 0.88
   2 ?    1.6   0.0      0.15   2.1e+02      76     148 ..      80     156 ..      66     164 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00014
                         IstB_IS21 50 ivllGpsGvGKshlaialgveavraglsvlfvrve 84
                                      i + G  G+GKs ++  l++   +++++v++v+++
  gi|242398768|ref|YP_002994192.1| 22 IFIEGDRGTGKSIFSQRLAYGFLKNDIQVSYVSTQ 56
                                      6788***************************9975 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.15
                         IstB_IS21  76 lsvlfvrvedLveelkrarrdgklaralkrllkvdllilDdlgll...pldqaeaellfeviekrye.rrsiiitsn 148
                                        + lfv++  L++++++  r        +rl + d++i+D l      ++d++  +++ e ++k    +++ii+t+n
  gi|242398768|ref|YP_002994192.1|  80 RKLLFVSLYPLLSSVSKRGRFLPRFLSEERLWEKDVIIIDSLPSIlppKIDEETLRKFTEHLKKLSAlNKAIILTAN 156
                                       566677666666666655444444445578899999***99854322257777777777777776542677777777 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   2.7e-05     0.037      24     139 ..      17     153 ..       5     178 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.7e-05
                            AAA_16  24 p..elvllsGesGvGKsslvrellralekdggiflrgkcdql......esa......ipysalaqalareellrqll 86 
                                       p  +l+++ G++G+GKs   ++l+  + k+++ + +  ++        +++      ip+++  ++l + +l+  l 
  gi|242398768|ref|YP_002994192.1|  17 PsgSLIFIEGDRGTGKSIFSQRLAYGFLKNDIQVSYVSTQLTtpefinQMEslgysvIPFLTKRKLL-FVSLYPLLS 92 
                                       2449****************99999888886666443333332122444446555555555444444.445555555 PP

                            AAA_16  87 deaesaeleawrekleeala.......avpelagaea....srllellkrllallsrderplvl 139
                                       +    ++++++  +++++ +       ++++l++ ++    +  l++++++l++ls   + ++l
  gi|242398768|ref|YP_002994192.1|  93 SV---SKRGRFLPRFLSEERlwekdviIIDSLPSILPpkidEETLRKFTEHLKKLSALNKAIIL 153
                                       55...34444444444444455566664444444444555577777777777666666665555 PP

>> GvpD  GvpD gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   5.2e-05     0.071      10      55 ..      19      66 ..      15     153 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.2e-05
                              GvpD 10 GktllikGaPGtGktlftlrg.ldvlrresdvlyvstrvdd.etvsea 55
                                      G  + i+G  GtGk +f  r     l+++ +v yvst+ +  e ++++
  gi|242398768|ref|YP_002994192.1| 19 GSLIFIEGDRGTGKSIFSQRLaYGFLKNDIQVSYVSTQLTTpEFINQM 66
                                      77789*************99625789***********97642555555 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00012      0.17       2      46 ..      22      67 ..      21     168 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00012
                                      EEEE--SSSSHHHHHHHGGGGB.S--EEEEE--TT--HHHHH--B- CS
                             AAA_5  2 vlLvGppGtgKselaerlaaal.nreveyvqltrdtteedlkgrre 46
                                      +++ G+ GtgKs +++rla  + ++ +++   + ++t+ +++ ++e
  gi|242398768|ref|YP_002994192.1| 22 IFIEGDRGTGKSIFSQRLAYGFlKNDIQVSYVSTQLTTPEFINQME 67
                                      5789***************999999999999999999888888887 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00013      0.17       5      53 ..      19      60 ..      17     175 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00013
                            AAA_22  5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstss 53
                                       +++++ G  GtGK+   +rl++ + +       ++ +v++  +++t++
  gi|242398768|ref|YP_002994192.1| 19 GSLIFIEGDRGTGKSIFSQRLAYGFLK-------NDIQVSYVSTQLTTP 60
                                      57899******************9964.......555554444444443 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00022       0.3       4      40 ..      21      57 ..      18     164 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00022
                            AAA_14  4 ilvitGaRrvGKTtllkqlikellvkkesilyinldd 40
                                      +++i+G R +GK+ + ++l++  l ++ ++ y++ + 
  gi|242398768|ref|YP_002994192.1| 21 LIFIEGDRGTGKSIFSQRLAYGFLKNDIQVSYVSTQL 57
                                      789*****************99996666777776544 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0    0.0059       8.2       5      74 ..      22     121 ..      19     132 .. 0.72
   2 ?    3.6   0.1     0.033        46     109     130 ..     135     156 ..     131     205 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0059
                            AAA_24   5 iliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdieswedfldevvel...................... 59 
                                       i+i G+ g+GK+ +  +l + +l  d+  ++ s++ +        ++f++++++l                      
  gi|242398768|ref|YP_002994192.1|  22 IFIEGDRGTGKSIFSQRLAYGFLKNDIQVSYVSTQLTT-------PEFINQMESLgysvipfltkrkllfvslypll 91 
                                       6788*************988888888877776665555.......45555555555556666666666677778888 PP

                            AAA_24  60 ...............aaeladyktlviDti 74 
                                                      ++ l + ++++iD++
  gi|242398768|ref|YP_002994192.1|  92 ssvskrgrflprflsEERLWEKDVIIIDSL 121
                                       888888888888888666666788888887 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.033
                            AAA_24 109 eefrrllkklqelrknvifiah 130
                                       ++f++ lkkl++l+k +i++a 
  gi|242398768|ref|YP_002994192.1| 135 RKFTEHLKKLSALNKAIILTAN 156
                                       6899999999***99**99985 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0   0.00078       1.1      22      44 ..      19      41 ..       6      71 .. 0.77
   2 ?    0.2   0.0       0.4   5.5e+02      98     114 ..     167     183 ..     160     188 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00078
                                      SS-EEEECSTTSSHHHHHHHHHH CS
                   Sigma54_activat 22 dlsvlitGesGtGKellaraihe 44
                                       + ++i+G+ GtGK+++++ +  
  gi|242398768|ref|YP_002994192.1| 19 GSLIFIEGDRGTGKSIFSQRLAY 41
                                      56789*************98865 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.4
                                       EEETGGGS-HHHHHHHH CS
                   Sigma54_activat  98 fLDeigelplelQekLl 114
                                        L+ei+++ ++lQ+k++
  gi|242398768|ref|YP_002994192.1| 167 ILEEITTMLIRLQVKVF 183
                                       599***********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 ?   11.0   0.0   0.00023      0.32      12      44 ..      10      44 ..       4      62 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00023
                                      HHHHHCH..TEEEEEEESTTSSHHHHHHHHHHHTT CS
                              TsaE 12 kklakal..gdvilLeGdLGaGKTtlvrglakalg 44
                                      ++l+  +  g++i++eGd G+GK+ +++ la ++ 
  gi|242398768|ref|YP_002994192.1| 10 RRLGGGIpsGSLIFIEGDRGTGKSIFSQRLAYGFL 44
                                      444444455789******************98874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 1549.34
//
Query:       gi|242398769|ref|YP_002994193.1|  [L=158]
Description: FlaG flagella-related protein G [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-16   60.3   0.8    2.9e-16   60.1   0.8    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 !   60.1   0.8   1.6e-20   2.9e-16       1     162 [.      15     154 ..      15     156 .. 0.93

  Alignments for each domain:
  == domain 1  score: 60.1 bits;  conditional E-value: 1.6e-20
                                       X--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--EEEEEEEEEE-SSSSSEEEEEEE--T CS
                    Arch_flagellin   1 GfvgigtlIvfIAmVlVAAvaagvlintagflqqkaqstgeesteqvssgleitgdvgdsatngtineitiyvklna 77 
                                       ++++i+++I+fI+ +lVA + ag l   +++l++++++ g  + + ++ +++i++d+ +++  g    + +y+k n+
  gi|242398769|ref|YP_002994193.1|  15 ASSVISEIILFIVSLLVAGTIAGGLYIVTQDLADSISTRGTIIAQNLRVDFTIINDPENIPFLGGA--YVFYIK-NT 88 
                                       6799***********************************************************955..******.** PP

                                       TS--EEGGG-EEEEEESS--EE--E..................T-EE-TT-EEEEEEE--TTT---TT-EEEEEEE- CS
                    Arch_flagellin  78 Gsspidlnkttisvtddgqetlltadefgivvisdtdgsltngdevlekgekvelevnvneddgitagdevsvevvp 154
                                       Gs++  ++++ti+v++dg          +++ +s+ + +   +  +l + +++el + +        +++++++vv 
  gi|242398769|ref|YP_002994193.1|  89 GSEEFSFTSSTIIVFIDG----------NLIPPSNLTLT--PS--TLYPYDIGELRIST-----TLSSGYHKLVVVI 146
                                       ******************..........88888877654..44..789**********8.....699********** PP

                                       SSS--EEE CS
                    Arch_flagellin 155 enGastti 162
                                       enG+++++
  gi|242398769|ref|YP_002994193.1| 147 ENGKQREF 154
                                       ***99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.46
# Mc/sec: 1027.18
//
Query:       gi|242398770|ref|YP_002994194.1|  [L=274]
Description: Flagella-related protein d, [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.4e-28   97.0   0.0    1.1e-27   95.7   0.0    1.7  1  Arch_fla_DE   Archaeal flagella protein
     0.0071   16.6   0.4      0.018   15.3   0.1    1.8  2  V-SNARE_C     Snare region anchored in the vesicle membrane C
  ------ inclusion threshold ------
      0.012   15.7   1.5      0.025   14.7   1.5    1.6  1  Herpes_BLRF2  Herpesvirus BLRF2 protein
      0.017   13.3   0.6      0.026   12.7   0.6    1.3  1  COG6          Conserved oligomeric complex COG6
      0.018   15.3   1.1        2.7    8.3   0.2    2.8  2  Rx_N          Rx N-terminal domain
      0.071   13.8   0.1       0.87   10.3   0.0    2.4  3  RsbRD_N       RsbT co-antagonist protein rsbRD N-terminal dom
       0.13   11.0   3.3       0.17   10.7   3.3    1.1  1  AAA_32        AAA domain
       0.14   11.9   1.2       0.24   11.1   1.2    1.4  1  DUF1564       Protein of unknown function (DUF1564)
       0.15   12.5   1.9       0.21   12.0   0.5    2.1  2  MitMem_reg    Maintenance of mitochondrial structure and func
       0.28   10.7   1.6       0.48    9.9   1.6    1.4  1  DUF1002       Protein of unknown function (DUF1002)


Domain annotation for each model (and alignments):
>> Arch_fla_DE  Archaeal flagella protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.7   0.0   6.2e-31   1.1e-27       3      95 .]     154     246 ..     152     246 .. 0.96

  Alignments for each domain:
  == domain 1  score: 95.7 bits;  conditional E-value: 6.2e-31
                       Arch_fla_DE   3 kpyLeelpedyaaelvvleWlefLvervgvenaaealdyYeeigWiseevreeLlkylkgikledeekeelk.ksel 78 
                                       +++L++lp+d+a+++++l+Wl fL++r+gv n++++l++Y++igWiseev e+Llky++g++  ++++ ++k +++l
  gi|242398770|ref|YP_002994194.1| 154 RARLDHLPNDTASTMIALKWLGFLIDRAGVLNLENILEFYYTIGWISEEVLESLLKYANGTRP-HQREPNWKpDDKL 229
                                       679**********************************************************97.777789**9**** PP

                       Arch_fla_DE  79 tvedHvkSllyieklag 95 
                                       t++dH+ Sll+ie+l+g
  gi|242398770|ref|YP_002994194.1| 230 TIQDHLISLLFIERLRG 246
                                       ***************86 PP

>> V-SNARE_C  Snare region anchored in the vesicle membrane C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   9.9e-06     0.018      27      59 ..      49      81 ..      46      85 .. 0.92
   2 ?   -3.6   0.0         8   1.4e+04      49      59 ..     258     268 ..     254     270 .. 0.52

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 9.9e-06
                         V-SNARE_C 27 iledLhsQretLkrarsklhnvanrlgksnsiL 59
                                      +le+++sQ e+L+r  +++ +++++l  +++ L
  gi|242398770|ref|YP_002994194.1| 49 VLENYSSQAERLRRLDKRVEEIGKYLEEIRRHL 81
                                      8**************************999866 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 8
                         V-SNARE_C  49 anrlgksnsiL 59 
                                         +l+  n+iL
  gi|242398770|ref|YP_002994194.1| 258 ERELKMMNKIL 268
                                       44555555555 PP

>> Herpes_BLRF2  Herpesvirus BLRF2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   1.5   1.4e-05     0.025       3      69 ..       3      68 ..       1     100 [. 0.82

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.4e-05
                      Herpes_BLRF2  3 tvEdlaaelakLkvEN.kaLkkklkssvspkdeeLTaaekeavltstvgrlsskaakkieervrkevl 69
                                      t  ++  +l+kL+ E  + L k lk++   k   LT+++ +++++++ ++ ss+a++   +r++k v+
  gi|242398770|ref|YP_002994194.1|  3 TENEIDSKLQKLQGEVpNVLIKDLKNKLVSKIDILTPEQVDLIINKVLENYSSQAERL--RRLDKRVE 68
                                      5678999******995244667777777777789*********************874..45555554 PP

>> COG6  Conserved oligomeric complex COG6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.6   1.5e-05     0.026      33      95 ..      47     109 ..      23     113 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.5e-05
                              COG6  33 eefleefqpvaeqLkriesdveklnelcdemkkklssakeetsdlleeaeeLkeekkklelkq 95 
                                       +++le+++  ae+L+r++++ve++ +  +e++++l  +++  ++++e+ e+  e+  ++e ++
  gi|242398770|ref|YP_002994194.1|  47 NKVLENYSSQAERLRRLDKRVEEIGKYLEEIRRHLMDKTTLHKEFNEKSERVPERIPEVEHQE 109
                                       689**********************************************99998888888776 PP

>> Rx_N  Rx N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.2    0.0015       2.7       4      44 ..      44      84 ..      42     100 .. 0.85
   2 ?    4.8   0.0      0.02        35      25      43 ..     252     270 ..     231     273 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0015
                              Rx_N  4 allqkLadllaeeakllkgvkeeleklkdeLesiqavLeda 44
                                       +++k+ +  +++a++l+ +++ +e++ + Le i+  L d 
  gi|242398770|ref|YP_002994194.1| 44 LIINKVLENYSSQAERLRRLDKRVEEIGKYLEEIRRHLMDK 84
                                      5788999999999**********************999885 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.02
                              Rx_N  25 eeleklkdeLesiqavLed 43 
                                       e l++l++eL++++ +Le+
  gi|242398770|ref|YP_002994194.1| 252 EVLNSLERELKMMNKILEH 270
                                       6689************997 PP

>> RsbRD_N  RsbT co-antagonist protein rsbRD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.75   1.3e+03      18      54 ..      47      83 ..      39     114 .. 0.60
   2 ?   10.3   0.0   0.00049      0.87      58      98 ..     134     174 ..     118     177 .. 0.81
   3 ?   -2.2   0.0       3.9     7e+03      42      69 ..     201     233 ..     200     245 .. 0.60

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.75
                           RsbRD_N 18 eevlatypiesagllseaelreqlrelldallaalas 54
                                      ++vl++y+ + ++l + +   e++ + l+++   l +
  gi|242398770|ref|YP_002994194.1| 47 NKVLENYSSQAERLRRLDKRVEEIGKYLEEIRRHLMD 83
                                      5666777663333444444555555555555544333 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00049
                           RsbRD_N  58 dleseeeeelrealdelsrsRarqgftpsetasfvfaLKea 98 
                                       ++e +  +++real + ++ Rar ++ p++tas   aLK  
  gi|242398770|ref|YP_002994194.1| 134 TEEFQIPKDVREALINPTKMRARLDHLPNDTASTMIALKWL 174
                                       555566788******************************75 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 3.9
                           RsbRD_N  42 relldallaalas....eql.dleseeeeelre 69 
                                       +e+l+ ll+ ++     +++ +++ +++ ++ +
  gi|242398770|ref|YP_002994194.1| 201 EEVLESLLKYANGtrphQREpNWKPDDKLTIQD 233
                                       678888887766544433335555555555555 PP

>> AAA_32  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   3.3   9.3e-05      0.17     177     279 ..       4     115 ..       2     136 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 9.3e-05
                            AAA_32 177 rkeleekseeleeeleeilrelrelekeakeklkelerevakeaveplleelkekykdl.......ekvleyLeave 246
                                       ++e+++k ++l+ e+ ++l  +++l++++ +k++ l  e +  +++++le+  ++ ++l       e++ +yLe+++
  gi|242398770|ref|YP_002994194.1|   4 ENEIDSKLQKLQGEVPNVL--IKDLKNKLVSKIDILTPEQVDLIINKVLENYSSQAERLrrldkrvEEIGKYLEEIR 78 
                                       5789999999999999998..68999**************9999999999999888887666666678********* PP

                            AAA_32 247 edilenlelfleeeeeeeeee....kkkkedelkrYk 279
                                       ++++++++l +e +e++e+ +    + ++++ +k Y+
  gi|242398770|ref|YP_002994194.1|  79 RHLMDKTTLHKEFNEKSERVPeripEVEHQEGIKSYD 115
                                       ******9988777777766556777556666677774 PP

>> DUF1564  Protein of unknown function (DUF1564)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.2   0.00013      0.24       9      77 ..       4      76 ..       1      93 [. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00013
                           DUF1564  9 dqkiksklikkssetsslLiP...edylkklslkekkaLkkklplLlkkyqkrlssskrlgkkagki.lYqek 77
                                      +++i skl+k + e+ ++Li    ++++ k  +    +   ++  +l++y+ +  + +rl+k+++ i +Y e+
  gi|242398770|ref|YP_002994194.1|  4 ENEIDSKLQKLQGEVPNVLIKdlkNKLVSKIDILTPEQVDLIINKVLENYSSQAERLRRLDKRVEEIgKYLEE 76
                                      689*****************988889999999999999*************************9987456554 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 ?   12.0   0.5   0.00012      0.21      20      77 ..      47     107 ..      30     168 .. 0.75
   2 ?   -2.0   0.0       2.6   4.7e+03      26      42 ..     254     270 ..     242     272 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00012
                        MitMem_reg  20 stlstglnrqyyslkilqerldlikdYlkkve...egelpvnheilrnlqkllnllPhlet 77 
                                       ++++++ ++q + l+ l++r+++i +Yl+++     ++++ ++e  ++   + +++P +e+
  gi|242398770|ref|YP_002994194.1|  47 NKVLENYSSQAERLRRLDKRVEEIGKYLEEIRrhlMDKTTLHKEFNEKSERVPERIPEVEH 107
                                       678899999**********************933311233333344444444444445554 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.6
                        MitMem_reg  26 lnrqyyslkilqerldl 42 
                                       ln+ +  lk+++++l+ 
  gi|242398770|ref|YP_002994194.1| 254 LNSLERELKMMNKILEH 270
                                       67777888888888775 PP

>> DUF1002  Protein of unknown function (DUF1002)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   1.6   0.00027      0.48     139     216 ..       3      89 ..       1      93 [. 0.74

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00027
                           DUF1002 139 ttsela...ekigsekaaelvaevkeevak.eklkteeeikkiveevanelnin.....lsdeqiqqivnllkkiqk 206
                                       t +e++   +k++ e  + l++++k+++++  ++ t+e++  i+++v++++  +       d+ +++i + l++i+ 
  gi|242398770|ref|YP_002994194.1|   3 TENEIDsklQKLQGEVPNVLIKDLKNKLVSkIDILTPEQVDLIINKVLENYSSQaerlrRLDKRVEEIGKYLEEIRR 79 
                                       5566642345677788899********9985579*****************98866633235667778888777777 PP

                           DUF1002 207 ldldlkelkk 216
                                         +d ++l k
  gi|242398770|ref|YP_002994194.1|  80 HLMDKTTLHK 89 
                                       7777666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       986  (0.0549947); expected 358.6 (0.02)
Passed bias filter:                      627  (0.0349713); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 1833.73
//
Query:       gi|242398771|ref|YP_002994195.1|  [L=156]
Description: Archaeal flagella-related protein C [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-21   75.8   4.4    2.5e-21   75.8   4.4    2.9  2  FlaC_arch        Flagella accessory protein C (FlaC)
    2.1e-05   24.5   5.5      0.059   13.4   0.0    2.8  2  TolA_bind_tri    TolA binding protein trimerisation
    2.2e-05   24.3   2.3    0.00011   22.2   0.6    2.0  2  Sec34            Sec34-like family
    5.8e-05   22.3  10.7    0.00021   20.5  11.1    1.6  2  Atg14            Vacuolar sorting 38 and autophagy-related su
    0.00014   21.9   4.3    0.00039   20.4   4.4    1.7  1  Laminin_II       Laminin Domain II
    0.00033   20.2   3.5       0.23   10.9   0.7    2.3  2  DUF4349          Domain of unknown function (DUF4349)
    0.00092   17.5   5.6    0.00092   17.5   5.6    2.0  2  EzrA             Septation ring formation regulator, EzrA
     0.0012   18.7   4.4     0.0019   18.1   4.4    1.4  1  Yuri_gagarin     Yuri gagarin
     0.0014   18.9   1.0       0.27   11.6   0.5    2.6  2  LPP              Lipoprotein leucine-zipper
     0.0032   17.9  11.1       0.44   11.0   1.7    2.7  2  Snapin_Pallidin  Snapin/Pallidin
     0.0036   16.1  10.8       0.02   13.7   9.4    2.0  2  Tektin           Tektin family
     0.0036   16.9   5.6      0.046   13.3   3.4    2.1  2  MscS_porin       Mechanosensitive ion channel porin domain
     0.0046   17.7   9.2       0.33   11.7   2.4    2.5  2  DUF2203          Uncharacterized conserved protein (DUF2203)
     0.0058   16.7   9.1        0.3   11.1   2.7    2.6  3  DUF1664          Protein of unknown function (DUF1664)
     0.0058   16.1  15.7      0.012   15.1  15.7    1.4  1  HMMR_N           Hyaluronan mediated motility receptor N-term
     0.0066   15.7  13.4     0.0077   15.4  13.4    1.1  1  Tmemb_cc2        Predicted transmembrane and coiled-coil 2 pr
     0.0068   15.9  11.6       0.12   11.8   7.3    2.4  2  DUF4618          Domain of unknown function (DUF4618)
     0.0085   16.3   3.5       0.61   10.4   0.4    2.5  2  KxDL             Uncharacterized conserved protein
  ------ inclusion threshold ------
      0.011   15.8   2.0      0.016   15.3   1.8    1.3  1  Nup54            Nucleoporin complex subunit 54
      0.012   15.8   1.9        3.4    7.9   0.1    3.1  2  Clp_N            Clp amino terminal domain, pathogenicity isl
      0.013   14.8   1.4      0.027   13.8   1.2    1.5  1  Vps54_N          Vacuolar-sorting protein 54, of GARP complex
      0.014   15.0   6.6       0.48   10.0   3.5    2.1  2  PspA_IM30        PspA/IM30 family
      0.014   15.8  11.3          2    8.9   6.4    3.0  2  DUF4140          N-terminal domain of unknown function (DUF41
      0.015   15.4  17.9       0.73    9.8  13.9    2.2  2  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
      0.015   15.0  12.4      0.023   14.5   1.5    3.0  2  DivIC            Septum formation initiator
      0.015   15.3   2.9        3.7    7.7   1.1    2.7  2  Vps51            Vps51/Vps67
      0.017   14.0  13.6      0.018   13.9   2.8    2.2  2  Spc7             Spc7 kinetochore protein
      0.018   15.0   2.0      0.018   15.0   2.0    3.1  3  Prefoldin        Prefoldin subunit
      0.021   14.2   1.2      0.029   13.7   1.2    1.2  1  DUF4407          Domain of unknown function (DUF4407)
      0.022   14.7   7.8       0.43   10.5   3.4    2.3  2  NleF_casp_inhib  NleF caspase inhibitor
      0.022   14.8   3.0       0.23   11.5   2.8    2.0  3  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
      0.025   14.4   1.6       0.57   10.0   0.2    3.0  3  DASH_Dam1        DASH complex subunit Dam1
       0.03   14.2   3.4        1.6    8.6   0.0    2.3  2  Sec8_exocyst     Sec8 exocyst complex component specific doma
      0.044   13.8   0.2      0.044   13.8   0.2    3.5  3  Bap31_Bap29_C    Bap31/Bap29 cytoplasmic coiled-coil domain
      0.047   12.6  15.2       0.78    8.6  15.3    1.9  2  DUF812           Protein of unknown function (DUF812)
      0.048   14.1   2.0       0.84   10.2   0.1    2.6  2  COMP             Cartilage oligomeric matrix protein
      0.049   13.9  11.7      0.055   13.8   5.6    2.4  2  BLOC1_2          Biogenesis of lysosome-related organelles co
       0.05   14.0  18.1        2.8    8.4  14.3    2.6  2  DUF4200          Domain of unknown function (DUF4200)
      0.053   14.1   9.8        2.3    8.9   0.0    2.8  2  HIP1_clath_bdg   Clathrin-binding domain of Huntingtin-intera
       0.06   13.8   7.0       0.22   12.0   2.7    2.4  2  NPV_P10          Nucleopolyhedrovirus P10 protein
      0.061   11.7   4.7      0.086   11.2   4.7    1.2  1  Hemagglutinin    Haemagglutinin
      0.062   13.1   9.4       0.18   11.6   4.2    2.2  2  SKA2             Spindle and kinetochore-associated protein 2
       0.07   13.1   4.5       0.85    9.7   0.7    2.6  2  Bcr-Abl_Oligo    Bcr-Abl oncoprotein oligomerisation domain
      0.071   13.2   9.6        2.5    8.2   0.1    2.8  2  DUF2730          Protein of unknown function (DUF2730)
      0.072   13.3  12.5       0.24   11.6   7.8    2.2  2  Fib_alpha        Fibrinogen alpha/beta chain family
      0.072   11.4  13.3       0.19   10.0  13.3    1.6  1  MAD              Mitotic checkpoint protein
      0.084   13.5   0.6      0.084   13.5   0.6    3.1  2  DUF5344          Family of unknown function (DUF5344)
      0.084   12.9   1.8       0.72    9.9   0.0    2.6  2  Prp19            Prp19/Pso4-like
       0.11   12.9  10.6       0.37   11.2  10.7    1.8  1  Fez1             Fez1
       0.12   11.2   5.8       0.13   11.0   4.9    1.6  1  Fmp27_WPPW       RNA pol II promoter Fmp27 protein domain
       0.13   12.1   4.4        3.3    7.4   0.0    2.4  2  zf-CpG_bind_C    CpG binding protein zinc finger C terminal d
       0.13   12.5   1.6          1    9.7   1.4    2.1  2  DUF948           Bacterial protein of unknown function (DUF94
       0.14   10.1   3.7        0.5    8.3   3.5    1.6  1  Prominin         Prominin
       0.14   11.3   6.6       0.11   11.8   4.1    1.7  2  TMPIT            TMPIT-like protein
       0.18   10.8   9.4       0.28   10.1   9.2    1.5  1  Ran-binding      RanGTP-binding protein
       0.18   12.0  12.1       0.38   11.0   3.0    2.9  3  Spc24            Spc24 subunit of Ndc80
       0.19   10.6  13.7      0.067   12.1   9.9    1.7  2  CALCOCO1         Calcium binding and coiled-coil domain (CALC
       0.19   11.2   6.7       0.17   11.4   3.1    1.9  2  Allexi_40kDa     Allexivirus 40kDa protein
       0.21   11.8   8.9       0.38   11.0   6.8    2.1  2  ATG16            Autophagy protein 16 (ATG16)
       0.22   11.8   3.3        4.8    7.5   0.3    2.5  2  DUF3618          Protein of unknown function (DUF3618)
       0.25   11.4  11.6      0.032   14.3   1.8    2.7  2  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
       0.25   11.4  12.5       0.55   10.4   0.1    3.1  3  Swi5             Swi5
       0.26   11.4  10.0       0.84    9.7   5.1    2.8  3  ADIP             Afadin- and alpha -actinin-Binding
       0.26   11.1   6.2       0.22   11.4   3.4    1.8  2  LemA             LemA family
       0.27   10.5   5.5       0.21   10.8   3.3    1.7  2  HemX             HemX, putative uroporphyrinogen-III C-methyl
       0.27   11.9   8.3       0.28   11.8   1.4    2.9  2  SlyX             SlyX
        0.3   11.0   0.2        0.3   11.0   0.2    2.1  1  DUF4041          Domain of unknown function (DUF4041)
       0.32   11.0  17.0        3.5    7.7   3.2    2.9  2  FlxA             FlxA-like protein
       0.34   10.2   8.4       0.15   11.3   4.9    1.9  2  DUF3450          Protein of unknown function (DUF3450)
       0.35   10.6  13.1        1.3    8.8   0.3    2.9  3  RPW8             Arabidopsis broad-spectrum mildew resistance
       0.35   11.0  10.1       0.56   10.4   1.5    3.0  3  bZIP_1           bZIP transcription factor
        0.4   11.2  12.9        2.5    8.6  12.2    2.3  2  DUF16            Protein of unknown function DUF16
       0.43    9.7  11.6       0.98    8.5   7.1    2.0  2  DLP_helical      Dynamin-like helical domain
       0.47   11.0  17.2        2.3    8.8  11.1    2.2  2  APG6_N           Apg6 coiled-coil region
       0.47    9.8  10.7       0.17   11.3   6.5    1.9  1  Phlebovirus_NSM  Phlebovirus nonstructural protein NS-M
       0.52   10.1   4.4        6.6    6.5   0.8    2.3  2  USP8_interact    USP8 interacting
       0.52   10.3  17.3        2.5    8.1   8.9    3.4  1  Prefoldin_2      Prefoldin subunit
       0.54    9.9  10.7       0.97    9.1  10.7    1.6  1  GrpE             GrpE
       0.64   10.7  11.5        0.6   10.8   1.5    2.9  2  YabA             Initiation control protein YabA
       0.66   10.2  16.5        2.1    8.6   0.3    2.9  2  Cnn_1N           Centrosomin N-terminal motif 1
        0.7    9.9  11.5       0.48   10.5   5.3    2.3  2  DUF2205          Short coiled-coil protein
       0.74   10.5   9.7         22    5.7   0.1    3.4  3  GTP-bdg_M        GTP-binding GTPase Middle Region
       0.75    8.4  13.9       0.78    8.3   1.8    2.1  2  AAA_13           AAA domain
       0.82    9.7   6.5        8.8    6.4   4.0    2.9  2  DASH_Dad4        DASH complex subunit Dad4
       0.93    9.4   9.6       0.67    9.9   5.1    2.0  2  EMP24_GP25L      emp24/gp25L/p24 family/GOLD
          1    9.6  17.2          1    9.6  10.6    2.2  2  Med21            Subunit 21 of Mediator complex
          1    8.6   6.3        1.3    8.2   6.3    1.3  1  CorA             CorA-like Mg2+ transporter protein
        1.3    9.5  14.9       0.41   11.1   2.4    3.0  2  YgaB             YgaB-like protein
        1.4    6.7   8.2        3.7    5.3   8.4    1.5  1  V_ATPase_I       V-type ATPase 116kDa subunit family
        1.5    8.8  15.4        5.6    6.9   9.9    2.3  2  MIP-T3_C         Microtubule-binding protein MIP-T3 C-termina
        1.5    9.2   8.0       0.37   11.2   0.4    2.8  3  DASH_Dad2        DASH complex subunit Dad2
        1.7    8.7  13.9       0.48   10.5   0.4    3.7  4  DUF1192          Protein of unknown function (DUF1192)
        1.8    7.3   5.9        0.3    9.9   0.7    1.8  2  5_nucleotid      5' nucleotidase family
        1.8    9.6   8.9         23    6.1   0.9    3.2  3  DUF5320          Family of unknown function (DUF5320)
        1.9    8.7  18.2      0.063   13.5   7.9    2.6  2  XhlA             Haemolysin XhlA
          2    8.8  22.2        4.5    7.6   0.6    3.1  3  ABC_tran_CTD     ABC transporter C-terminal domain
          2    8.2  12.9         15    5.3  12.7    2.1  1  DUF724           Protein of unknown function (DUF724)
        2.2    8.9  16.0       0.16   12.6   3.2    2.2  2  Com_YlbF         Control of competence regulator ComK, YlbF/Y
        2.6    8.8   8.2        0.7   10.7   1.9    2.4  2  Occludin_ELL     Occludin homology domain
        2.7    7.1   5.8        6.1    6.0   1.6    2.3  2  ISG65-75         Invariant surface glycoprotein
        3.1    7.6   9.0         22    4.9   9.0    1.9  1  PCRF             PCRF domain
        3.3    7.8  13.2       0.12   12.5   3.0    2.7  3  DHR10            Designed helical repeat protein 10 domain
        3.6    7.2  12.8       0.28   10.8   0.9    2.9  3  Med4             Vitamin-D-receptor interacting Mediator subu
        3.6    8.2  14.1        2.6    8.7   3.5    3.1  3  BST2             Bone marrow stromal antigen 2
        3.8    7.1   8.3        1.3    8.6   1.8    2.7  3  DUF4988          Domain of unknown function
        3.8    7.5   9.1        3.4    7.7   2.1    2.6  3  DUF4446          Protein of unknown function (DUF4446)
        4.7    5.7  16.8      0.022   13.4   3.0    2.0  2  FapA             Flagellar Assembly Protein A
        4.9    7.1   8.4       0.27   11.1   0.9    2.6  2  WD40_alt         Alternative WD40 repeat motif
        5.1    7.4  15.4         25    5.2   9.0    3.3  3  DUF5082          Domain of unknown function (DUF5082)
        5.5    7.2  19.1        3.6    7.7  11.3    2.4  2  Tropomyosin_1    Tropomyosin like
        5.5    7.1  15.0         34    4.5  14.8    2.2  1  TssO             Type VI secretion system, TssO
        6.7    7.2  16.3        3.5    8.1   2.3    3.3  3  Fungal_TACC      Fungal Transforming acidic coiled-coil (TACC
        7.4    7.1  11.2         60    4.2   0.2    2.9  2  DUF4094          Domain of unknown function (DUF4094)
        8.2    6.3  14.8        5.7    6.8   8.4    2.3  2  Cauli_AT         Aphid transmission protein
        8.4    6.6  12.8         16    5.7   8.2    2.3  2  DUF1090          Protein of unknown function (DUF1090)
        8.7    6.8  20.2        3.2    8.2   6.3    2.7  2  CCDC-167         Coiled-coil domain-containing protein 167
          9    5.6  14.5         22    4.3   3.5    2.1  2  NBP1             Fungal Nap binding protein NBP1
        9.7    6.6  13.6        0.7   10.2   0.5    3.9  4  TSC22            TSC-22/dip/bun family


Domain annotation for each model (and alignments):
>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.8   4.4   1.7e-23   2.5e-21       1      54 [.      46      99 ..      46     100 .. 0.99
   2 ?    6.2   0.3     0.087        13      15      35 ..     111     131 ..     104     154 .. 0.69

  Alignments for each domain:
  == domain 1  score: 75.8 bits;  conditional E-value: 1.7e-23
                         FlaC_arch  1 ridelEnklsklsteletvkkeneelsksveelkenVkdllsLYEvVsnqvNPF 54
                                      ri+e+En+l++++++++t+k++++el++++e+l++++kd+++LYEvVs+++NPF
  gi|242398771|ref|YP_002994195.1| 46 RINEIENELPRIKVNIDTLKSQIQELRDEIEKLDKTIKDVMMLYEVVSQEINPF 99
                                      9***************************************************** PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.087
                         FlaC_arch  15 eletvkkeneelsksveelke 35 
                                       e+  +k+++e+++k++ ++  
  gi|242398771|ref|YP_002994195.1| 111 EIHELKQDLEDIRKEIAQIRG 131
                                       556666666666666666654 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 !   11.1   2.8    0.0021      0.31      25      50 ..      59      84 ..       9      97 .. 0.65
   2 !   13.4   0.0   0.00039     0.059      20      47 ..     112     139 ..     100     145 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0021
                     TolA_bind_tri 25 qqlealqqelreLRGqiEelqyqleq 50
                                       ++++l+++++eLR +iE+l   +++
  gi|242398771|ref|YP_002994195.1| 59 VNIDTLKSQIQELRDEIEKLDKTIKD 84
                                      34556666666666666655544443 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00039
                     TolA_bind_tri  20 llelqqqlealqqelreLRGqiEelqyq 47 
                                       ++el q le+ ++e++++RG++  l+y+
  gi|242398771|ref|YP_002994195.1| 112 IHELKQDLEDIRKEIAQIRGDLKLLAYH 139
                                       689******************9998886 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.6     7e-07   0.00011       6      76 ..      34     104 ..      31     107 .. 0.95
   2 ?    1.9   0.0       1.3   1.9e+02      15      39 ..     108     132 ..     104     143 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 7e-07
                             Sec34   6 eskeeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLkyFeeldp 76 
                                       ++ ee+++ ++++++e++++L  ++ + ++ +++ ++l+++ e+l +  k+++ l+e ++++++ F++ld+
  gi|242398771|ref|YP_002994195.1|  34 KEDEEKITLIMNRINEIENELPRIKVNIDTLKSQIQELRDEIEKLDKTIKDVMMLYEVVSQEINPFRDLDS 104
                                       567899999************************************************************96 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 1.3
                             Sec34  15 lleqtdealeqLeeleekfksvsek 39 
                                       ++++++e++++Le+++++  ++  +
  gi|242398771|ref|YP_002994195.1| 108 IVKEIHELKQDLEDIRKEIAQIRGD 132
                                       6788888889999988888887655 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 !   20.5  11.1   1.4e-06   0.00021      33     157 ..       6     129 ..       1     134 [. 0.76
   2 ?    3.3   0.1      0.24        37      95     120 ..     110     135 ..     105     143 .. 0.57

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.4e-06
                             Atg14  33 klksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsd 109
                                       k ksek+++++    al++ + +++  ++ k + +k+ ++ ++i +++++l ++k  +++lk++i+e + +++kl++
  gi|242398771|ref|YP_002994195.1|   6 KKKSEKDEIEQLEL-ALSEGN-TQENPKEQKEDEEKITLIMNRINEIENELPRIKVNIDTLKSQIQELRDEIEKLDK 80 
                                       45666666654333.333333.588888899999******************************************* PP

                             Atg14 110 klkkRrsdleslqneleerrk.kqiaklqdaikrieqklsslssktles 157
                                       ++k+ +   e +++e++  r  ++ + ++++i++ +q l+++++++++ 
  gi|242398771|ref|YP_002994195.1|  81 TIKDVMMLYEVVSQEINPFRDlDSENPIVKEIHELKQDLEDIRKEIAQI 129
                                       ***7777777788888777763455557777777777777777777765 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.24
                             Atg14  95 keieekkkklaklsdklkkRrsdles 120
                                       kei e k+ l+  ++++++ r dl++
  gi|242398771|ref|YP_002994195.1| 110 KEIHELKQDLEDIRKEIAQIRGDLKL 135
                                       44555555555555555555555544 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   4.4   2.6e-06   0.00039       6      96 ..      41     130 ..      34     137 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.6e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXX--TTTTTGGGHHHHH CS
                        Laminin_II   6 aeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsv...kkLeklapqLldklkelk 79 
                                       + + + ++e+++ l  +++n++ +k++++e+++++e+ ++ +kd ++  + +++++   ++L+ + + +++ ++elk
  gi|242398771|ref|YP_002994195.1|  41 TLIMNRINEIENELPRIKVNIDTLKSQIQELRDEIEKLDKTIKDVMMLYEVVSQEInpfRDLDSE-NPIVKEIHELK 116
                                       55666778899999999999999999999999999999999999999999998876222566665.55889999999 PP

                                       HHHHH...HHHHHHHHH CS
                        Laminin_II  80 qleeassslsdniseik 96 
                                       q  e    + ++i +i+
  gi|242398771|ref|YP_002994195.1| 117 QDLED---IRKEIAQIR 130
                                       99999...999999998 PP

>> DUF4349  Domain of unknown function (DUF4349)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.7    0.0015      0.23     117     147 ..      46      76 ..      31      83 .. 0.90
   2 !   10.0   0.1    0.0029      0.44     115     143 ..     109     137 ..      93     147 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0015
                           DUF4349 117 dlleiereLsevqaeieslegqlryLdnqva 147
                                        + eie+eL +++ +i+ l++q+++L+++++
  gi|242398771|ref|YP_002994195.1|  46 RINEIENELPRIKVNIDTLKSQIQELRDEIE 76 
                                       5789***********************9886 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0029
                           DUF4349 115 vedlleiereLsevqaeieslegqlryLd 143
                                       v+++ e++++L+++++ei +++g l+ L+
  gi|242398771|ref|YP_002994195.1| 109 VKEIHELKQDLEDIRKEIAQIRGDLKLLA 137
                                       899**********************9996 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   5.6     6e-06   0.00092     445     492 ..      39      86 ..      30      96 .. 0.87
   2 ?    4.2   0.3     0.067        10     101     123 ..     110     132 ..      96     139 .. 0.57

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 6e-06
                                       HSTTTSTTTHHHHHHHT-TT--HHHHHHHHHTTTTTSGGGTHHHHHHH CS
                              EzrA 445 elkeasdeieelakeLekkpinikevnkrldeardlveklyektneli 492
                                       +++ + ++i+e+++eL + ++ni++++++++e rd +ekl++++++++
  gi|242398771|ref|YP_002994195.1|  39 KITLIMNRINEIENELPRIKVNIDTLKSQIQELRDEIEKLDKTIKDVM 86 
                                       566778999*********************************999987 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.067
                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                              EzrA 101 kklaeleeeldeveekikkilee 123
                                       k++ el+++l++++++i++i+ +
  gi|242398771|ref|YP_002994195.1| 110 KEIHELKQDLEDIRKEIAQIRGD 132
                                       33444444444444444444444 PP

>> Yuri_gagarin  Yuri gagarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   4.4   1.2e-05    0.0019      53     124 ..      40     135 ..       2     153 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.2e-05
                      Yuri_gagarin  53 f........................lvanerlaceidalketlkdrdeqikqlqsmitsysdlsennrlkeeiydlk 105
                                       +                          + ++l  ei++l +t+kd   + + + + i+ + dl+ +n + +ei++lk
  gi|242398771|ref|YP_002994195.1|  40 ItlimnrineienelprikvnidtlKSQIQELRDEIEKLDKTIKDVMMLYEVVSQEINPFRDLDSENPIVKEIHELK 116
                                       1445555555555555555555544778889999999999999999999999999********************** PP

                      Yuri_gagarin 106 qknceqarkvrelaeelkg 124
                                       q   +  +++ ++  +lk 
  gi|242398771|ref|YP_002994195.1| 117 QDLEDIRKEIAQIRGDLKL 135
                                       *988888888888877775 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.5    0.0018      0.27       2      25 ..      61      84 ..      46      95 .. 0.83
   2 ?    5.2   0.0      0.18        27       7      30 ..     110     133 ..     106     138 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0018
                               LPP  2 ldeLssqVsqLkskvdqlssdvns 25
                                      +d L sq+++L +++++l + +++
  gi|242398771|ref|YP_002994195.1| 61 IDTLKSQIQELRDEIEKLDKTIKD 84
                                      788889999999999888877765 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.18
                               LPP   7 sqVsqLkskvdqlssdvnsakaaa 30 
                                       +++ +Lk++ + + +++++++ ++
  gi|242398771|ref|YP_002994195.1| 110 KEIHELKQDLEDIRKEIAQIRGDL 133
                                       566777777777777777776665 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   1.7    0.0029      0.44      34      89 ..      12      64 ..       9      65 .. 0.86
   2 !   10.8   3.5    0.0034      0.52      10      79 ..      63     133 ..      58     137 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0029
                   Snapin_Pallidin 34 eqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlqklkkRaekL 89
                                      +++++l  +L e +  ++   +++ ke  +K++ i +r++++++ l ++k  ++ L
  gi|242398771|ref|YP_002994195.1| 12 DEIEQLELALSEGNTQEN---PKEQKEDEEKITLIMNRINEIENELPRIKVNIDTL 64
                                      578888888887777666...****************************9988877 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0034
                   Snapin_Pallidin  10 llepkldeldeklkelrqs...QeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerl 79 
                                       +l+++++el++++++l ++      L e ++++ + +++l  +++  ++++++e ++ L  i+k++ ++   l
  gi|242398771|ref|YP_002994195.1|  63 TLKSQIQELRDEIEKLDKTikdVMMLYEVVSQEINPFRDLDSENP--IVKEIHELKQDLEDIRKEIAQIRGDL 133
                                       566666666665555544410045677888888888888888888..9*****************99998766 PP

>> Tektin  Tektin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   5.9    0.0011      0.16      37      97 ..      32      92 ..       3     102 .. 0.59
   2 !   13.7   9.4   0.00013      0.02     249     359 ..      43     145 ..      26     148 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0011
                            Tektin 37 tkktqadsnkrLeeRiediefwkeeLekeleelkeeieaLeeekrrlekalealeeplhia 97
                                       +k++++  + + +Ri++ie+    ++ +++ lk++i++L +e ++l+k+++++ + ++++
  gi|242398771|ref|YP_002994195.1| 32 EQKEDEEKITLIMNRINEIENELPRIKVNIDTLKSQIQELRDEIEKLDKTIKDVMMLYEVV 92
                                      3333444444455566666666666666666666666666666666666666666666654 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 0.00013
                            Tektin 249 lrkrieetedaknkleeqlkkvleeiaeleknieeLekairdkeaplklaqtRlenRtqRpnvElcrDeaqyrLveE 325
                                       + +ri+e+e+    ++ + + ++ +i+el ++ie+L k+i+d +    ++   ++     p  +l ++++   +v+E
  gi|242398771|ref|YP_002994195.1|  43 IMNRINEIENELPRIKVNIDTLKSQIQELRDEIEKLDKTIKDVMMLYEVVSQEIN-----PFRDLDSENP---IVKE 111
                                       4567777777777777777777777777777777777777777777777766554.....5667777777...**** PP

                            Tektin 326 vkeleetieaLkeklaeaeaslkaLertrlelee 359
                                       ++el++++e+ ++++a+ +  lk L  + ++l++
  gi|242398771|ref|YP_002994195.1| 112 IHELKQDLEDIRKEIAQIRGDLKLLAYHGVDLDK 145
                                       *************************999998876 PP

>> MscS_porin  Mechanosensitive ion channel porin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   3.4    0.0003     0.046     130     201 ..      12      83 ..       4      97 .. 0.64
   2 ?    4.0   0.0       0.2        30      37      63 ..     110     136 ..     100     152 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.0003
                        MscS_porin 130 qeirnrLnstaaagealsqaqrtalqaelaaleaqieeleqellsnnnrqeLlklqrdllklriqqleqelq 201
                                       +ei++   ++++++++ ++ ++   + +  ++ ++i+e e el    + ++ lk+q ++l+ +i++l++ ++
  gi|242398771|ref|YP_002994195.1|  12 DEIEQLELALSEGNTQENPKEQKEDEEKITLIMNRINEIENELPRIKVNIDTLKSQIQELRDEIEKLDKTIK 83 
                                       445542244444455666666666666666666666666666666666666666666666666666666665 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.2
                        MscS_porin  37 kkaeelqkaiddaPkelrelqqeleal 63 
                                       k++ el++ ++d  ke+++++ +l+ l
  gi|242398771|ref|YP_002994195.1| 110 KEIHELKQDLEDIRKEIAQIRGDLKLL 136
                                       677888999999999999988888766 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   2.4    0.0022      0.33      24      79 ..       9      64 ..       1      68 [. 0.89
   2 !    9.8   0.9    0.0085       1.3      12      85 ..      68     142 ..      62     150 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0022
                           DUF2203 24 alrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieelGvevkdl 79
                                      + ++e+e+le +l+e +++++ +e++e+e++++ ++++i+e+ +e+ +++v++  l
  gi|242398771|ref|YP_002994195.1|  9 SEKDEIEQLELALSEGNTQENPKEQKEDEEKITLIMNRINEIENELPRIKVNIDTL 64
                                      568999*******************************************9998665 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0085
                           DUF2203  12 Lpllkelleelralrkeleeleeeleeakaeaekse.aaeleaeleeleaeieelveeieelGvevkdleaglvD 85 
                                       +++l++ +e+l ++ k++  l+e ++++ +  +  + ++   +e++el++ +e++ +ei ++  ++k l+   vD
  gi|242398771|ref|YP_002994195.1|  68 IQELRDEIEKLDKTIKDVMMLYEVVSQEINPFRDLDsENPIVKEIHELKQDLEDIRKEIAQIRGDLKLLAYHGVD 142
                                       445555555555555555555555555444443333688888999999999999999999999888887766666 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   4.7    0.0025      0.37      73     118 ..      38      83 ..       6      87 .. 0.65
   2 !   11.1   2.7     0.002       0.3      56     115 ..      63     121 ..      62     131 .. 0.73
   3 ?    7.3   0.2      0.03       4.6      85     108 ..     108     131 ..      90     149 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0025
                           DUF1664  73 kkldeqkeiskeikeevtevredlseigedvesvkeavegleskle 118
                                       +k+   ++ ++ei++e+ +++ ++++++++++++++ +e+l+++++
  gi|242398771|ref|YP_002994195.1|  38 EKITLIMNRINEIENELPRIKVNIDTLKSQIQELRDEIEKLDKTIK 83 
                                       3444445555666666666666666666666666666666666665 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.002
                           DUF1664  56 slaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegles 115
                                       +l+++ ++L ++i+++dk++++++ + + +++e++  r+ l++ +  v++++e+ ++le 
  gi|242398771|ref|YP_002994195.1|  63 TLKSQIQELRDEIEKLDKTIKDVMMLYEVVSQEINPFRD-LDSENPIVKEIHELKQDLED 121
                                       6888899***************************99974.55555555555555555553 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.03
                           DUF1664  85 ikeevtevredlseigedvesvke 108
                                       i +e++e+++dl++i++++ +++ 
  gi|242398771|ref|YP_002994195.1| 108 IVKEIHELKQDLEDIRKEIAQIRG 131
                                       556666666666666666666654 PP

>> HMMR_N  Hyaluronan mediated motility receptor N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1  15.7   7.7e-05     0.012     200     322 ..       9     134 ..       3     137 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 7.7e-05
                            HMMR_N 200 eskakvaqLkeklvslekek..ieekseteklleyieelsnvseqlekykldiaqleellkekndeiesLkssLeek 274
                                       + k ++ qL+  l++ + ++  +e+k++ ek +  +++++++ ++l + k +i+ l++ ++e  deie+L +++++ 
  gi|242398771|ref|YP_002994195.1|   9 SEKDEIEQLELALSEGNTQEnpKEQKEDEEKITLIMNRINEIENELPRIKVNIDTLKSQIQELRDEIEKLDKTIKDV 85 
                                       568899999988876544443499**************************************************998 PP

                            HMMR_N 275 eqelskqvkdlnekckllekeke..elvreeeekeqtlsaEleelkeklk 322
                                          l++ v++  +  + l++e+   ++++e ++  + + +E+ +++  lk
  gi|242398771|ref|YP_002994195.1|  86 MM-LYEVVSQEINPFRDLDSENPivKEIHELKQDLEDIRKEIAQIRGDLK 134
                                       87.99999999999999999887112334444444555677777666665 PP

>> Tmemb_cc2  Predicted transmembrane and coiled-coil 2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4  13.4   5.1e-05    0.0077     183     297 ..      12     125 ..       1     129 [. 0.76

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 5.1e-05
                         Tmemb_cc2 183 desssssvesssadsnsnseestasasksaesesqeklekileelqeikeeqerleeelerlkeqlkk...elkllk 256
                                       de+++ +            +e +++++ ++++e++ek++ i++ ++ei++e  r++ ++++lk+q+++   e++ l 
  gi|242398771|ref|YP_002994195.1|  12 DEIEQLE---------LALSEGNTQENPKEQKEDEEKITLIMNRINEIENELPRIKVNIDTLKSQIQElrdEIEKLD 79 
                                       3333333.........23333333345667788999***************************8877444499**** PP

                         Tmemb_cc2 257 qaLqeeryryerLEeqlndlteLhq.....nEienLKqelasmeek 297
                                       ++++++ + ye   + +n   +L       +Ei +LKq+l ++   
  gi|242398771|ref|YP_002994195.1|  80 KTIKDVMMLYEVVSQEINPFRDLDSenpivKEIHELKQDLEDIRKE 125
                                       ***********************96333337**********99765 PP

>> DUF4618  Domain of unknown function (DUF4618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   7.3   0.00079      0.12     174     226 ..      33      85 ..       2      96 .. 0.78
   2 ?    5.8   0.1     0.054       8.2     191     231 ..     108     148 ..      99     151 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00079
                           DUF4618 174 lkatqeaLlqktlenqvlkkeiekfrefieeleeeipeLkaeveqLqaqaeep 226
                                       +k+ +e ++  +   +++++e+ + + +i++l+ +i+eL+ e+e+L + ++++
  gi|242398771|ref|YP_002994195.1|  33 QKEDEEKITLIMNRINEIENELPRIKVNIDTLKSQIQELRDEIEKLDKTIKDV 85 
                                       44555666666666678999999999999999999999999999999998876 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.054
                           DUF4618 191 lkkeiekfrefieeleeeipeLkaeveqLqaqaeepreviF 231
                                       + kei++ ++  e++++ei +++ +++ L+ +  +  ++i+
  gi|242398771|ref|YP_002994195.1| 108 IVKEIHELKQDLEDIRKEIAQIRGDLKLLAYHGVDLDKIIY 148
                                       45566666666666666666666666666655555555555 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.3     0.076        12      41      79 ..      38      76 ..      25      79 .. 0.67
   2 !   10.4   0.4     0.004      0.61      55      78 ..     110     133 ..      76     135 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.076
                              KxDL 41 erlaklrarfkqgtkllkevkkdLesifkkirslkakla 79
                                      e+ + + +r+++  + l ++k ++++++++i+ l+++++
  gi|242398771|ref|YP_002994195.1| 38 EKITLIMNRINEIENELPRIKVNIDTLKSQIQELRDEIE 76
                                      555555666666666666777777777777777766665 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.004
                              KxDL  55 kllkevkkdLesifkkirslkakl 78 
                                       k ++e+k+dLe i+k i +++  l
  gi|242398771|ref|YP_002994195.1| 110 KEIHELKQDLEDIRKEIAQIRGDL 133
                                       7899***************98765 PP

>> Nup54  Nucleoporin complex subunit 54
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   1.8   0.00011     0.016      39     133 ..      34     133 ..      26     139 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 0.00011
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SS---S..SHHHHH CS
                             Nup54  39 kaQqkevaqhrerlkeisdrleeleqkhqletsvrlekakkrhvelshRllrllrkleilrsrgyalda..eEeelr 113
                                       k  ++++++  +r++ei+++l  ++  +  ++ +++++++ +  +l + +  ++   e++++   + +   +E+ + 
  gi|242398771|ref|YP_002994195.1|  34 KEDEEKITLIMNRINEIENELPRIK-VNIDTLKSQIQELRDEIEKLDKTIKDVMMLYEVVSQEINPFRDldSENPIV 109
                                       4445566666677777777777777.666677789999999999999999999999998866644333244677777 PP

                                       HHHHHHHHHHS-..H..HH.HHHH CS
                             Nup54 114 arletleaqlnd..p..aqlkgrv 133
                                       +++ +l+++l+d  +  aq++g +
  gi|242398771|ref|YP_002994195.1| 110 KEIHELKQDLEDirKeiAQIRGDL 133
                                       777777777775321344555555 PP

>> Clp_N  Clp amino terminal domain, pathogenicity island component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.087        13      34      52 ..      54      72 ..      48      73 .. 0.88
   2 ?    7.9   0.1     0.022       3.4      26      53 .]     104     131 ..     102     131 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.087
                                      HHHTTSSHHHHHHHHHHHH CS
                             Clp_N 34 LkkaGvdldalrkaiekll 52
                                      L + +v++d+l+++i++l+
  gi|242398771|ref|YP_002994195.1| 54 LPRIKVNIDTLKSQIQELR 72
                                      56789************98 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.022
                                       CTSHHHHHHHHTTSSHHHHHHHHHHHHC CS
                             Clp_N  26 ddGlaarlLkkaGvdldalrkaiekllg 53 
                                       +++++ + + +++ dl+++rk+i +++g
  gi|242398771|ref|YP_002994195.1| 104 SENPIVKEIHELKQDLEDIRKEIAQIRG 131
                                       66788889999***************97 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 ?   13.8   1.2   0.00018     0.027      21     107 ..      52     138 ..      44     141 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00018
                           Vps54_N  21 kklpddelsyesiekevkklksqhdvvskklsqlilekreefvkelseveeiekelkesvvickngrraLdlakkel 97 
                                       ++lp ++++++++ +++++l+ + ++++k++++ ++  +e +++e++  +++++e +  v+++++ ++ L+ ++ke+
  gi|242398771|ref|YP_002994195.1|  52 NELPRIKVNIDTLKSQIQELRDEIEKLDKTIKD-VMMLYEVVSQEINPFRDLDSE-NPIVKEIHELKQDLEDIRKEI 126
                                       57899999********************99976.78899************9998.667789999999999999999 PP

                           Vps54_N  98 trt..sLellak 107
                                       ++   +L+lla+
  gi|242398771|ref|YP_002994195.1| 127 AQIrgDLKLLAY 138
                                       875336777775 PP

>> PspA_IM30  PspA/IM30 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   3.5    0.0032      0.48      72     131 ..      15      85 ..       2      94 .. 0.87
   2 ?    6.2   0.1     0.044       6.6      23      55 ..     103     135 ..     101     140 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0032
                         PspA_IM30  72 kkAkaALtkg...........eeeLArealaeikslekqaealetqlaqqrsaveqlrkqlealetkieel 131
                                       ++ ++AL++g           +ee +  ++ +i + e+++ + +   + ++s++++lr ++e+l++ i+++
  gi|242398771|ref|YP_002994195.1|  15 EQLELALSEGntqenpkeqkeDEEKITLIMNRINEIENELPRIKVNIDTLKSQIQELRDEIEKLDKTIKDV 85 
                                       5667899999999999999998999999999*********************************9999875 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.044
                         PspA_IM30  23 DPekileqairdmqselakarqalaqviarqkq 55 
                                       D+e  + ++i +++++l++ r+++aq+ ++ k 
  gi|242398771|ref|YP_002994195.1| 103 DSENPIVKEIHELKQDLEDIRKEIAQIRGDLKL 135
                                       666778899*****************9887665 PP

>> DUF4140  N-terminal domain of unknown function (DUF4140)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   6.4     0.013         2      53      95 ..      25      82 ..       2      97 .. 0.74
   2 ?    8.5   0.2     0.018       2.7      64      97 ..     104     135 ..      81     136 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.013
                           DUF4140 53 qvervpnreaeee...............elkalraeleeledelaaledelaaaearl 95
                                      +++++p +++e+e               el +++  +++l+ ++++l+de++ +++++
  gi|242398771|ref|YP_002994195.1| 25 NTQENPKEQKEDEekitlimnrineienELPRIKVNIDTLKSQIQELRDEIEKLDKTI 82
                                      5666777777777777888888888877566666666666666666666666666655 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.018
                           DUF4140  64 eeelkalraeleeledelaaledelaaaearlaf 97 
                                       +   + + +e++el+++l+++++e+a ++  l++
  gi|242398771|ref|YP_002994195.1| 104 S--ENPIVKEIHELKQDLEDIRKEIAQIRGDLKL 135
                                       3..4677788888888888888888887777766 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 ?    9.8  13.9    0.0048      0.73      18     100 ..       6      86 ..       1     100 [. 0.73
   2 ?    7.7   0.1     0.023       3.5      52      86 ..     110     144 ..      93     150 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0048
                    CENP-F_leu_zip  18 kadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLekelqkkqe 94 
                                       k+ s kd +e+Le  l  se n ++   e  +  +++  + + i+e+++el ++++++++l+s+ +eL  e++k  +
  gi|242398771|ref|YP_002994195.1|   6 KKKSEKDEIEQLE--LALSEGNTQENPKEQKEDEEKITLIMNRINEIENELPRIKVNIDTLKSQIQELRDEIEKLDK 80 
                                       5556689999986..66677776666666666667777788888888888888888888888888888888888888 PP

                    CENP-F_leu_zip  95 rvseLe 100
                                       ++++  
  gi|242398771|ref|YP_002994195.1|  81 TIKDVM 86 
                                       888765 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.023
                    CENP-F_leu_zip  52 aevetlkeeieelaeelreleldLvalrsekeeLe 86 
                                       +e+ +lk+ +e +++e  +++ dL+ l     +L+
  gi|242398771|ref|YP_002994195.1| 110 KEIHELKQDLEDIRKEIAQIRGDLKLLAYHGVDLD 144
                                       67888888888888888888888877766655555 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   1.5   0.00015     0.023      21      49 ..      56      84 ..      44      92 .. 0.66
   2 ?    7.5   0.1     0.023       3.5      24      50 ..     110     136 ..     108     146 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 0.00015
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHCC CS
                             DivIC 21 qlkqeiaalqaelaklkaeneeLeaevkd 49
                                      ++k +i++l+ ++++l++e+e+L++ +kd
  gi|242398771|ref|YP_002994195.1| 56 RIKVNIDTLKSQIQELRDEIEKLDKTIKD 84
                                      34556666666666666666666666665 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.023
                                       HHHHHHHHHHHHHHHHHHHHHHHHCC- CS
                             DivIC  24 qeiaalqaelaklkaeneeLeaevkdL 50 
                                       +ei++l+++l+ +++e+++    +k+L
  gi|242398771|ref|YP_002994195.1| 110 KEIHELKQDLEDIRKEIAQIRGDLKLL 136
                                       689999999999999999999999888 PP

>> Vps51  Vps51/Vps67
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   1.1     0.024       3.7      56      86 ..      50      80 ..       2      81 .. 0.87
   2 ?    6.7   0.0     0.051       7.8      20      47 ..     111     138 ..      97     139 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.024
                             Vps51 56 asdtIrkmksemdkldqklselkqaiskiae 86
                                      + +++ ++k ++d+l+++++el+++i+k+++
  gi|242398771|ref|YP_002994195.1| 50 IENELPRIKVNIDTLKSQIQELRDEIEKLDK 80
                                      5678889999999999999999999999876 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.051
                             Vps51  20 tlkellkveasllseiraldselkalVy 47 
                                        ++el++  +++++ei +   +lk l y
  gi|242398771|ref|YP_002994195.1| 111 EIHELKQDLEDIRKEIAQIRGDLKLLAY 138
                                       2456666666666777777777776665 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4  13.5    0.0029      0.44     182     280 ..      28     124 ..       2     126 .. 0.62
   2 ?   13.9   2.8   0.00012     0.018     147     225 ..      60     136 ..      60     153 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0029
                              Spc7 182 eleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervle 258
                                       e  k+q++ ee  ++  ++++e+ +el ++k++i+ +k +++el++++e+l+++i+++   ++ + +ei+  +++  
  gi|242398771|ref|YP_002994195.1|  28 ENPKEQKEDEEKITLIMNRINEIENELPRIKVNIDTLKSQIQELRDEIEKLDKTIKDVMMLYEVVSQEINPFRDLDS 104
                                       22233333333333446677777777777777777777777777777777777777777777777777775555544 PP

                              Spc7 259 eckgwsesevsrlkeevkalee 280
                                       e  +   +e+ +lk+ ++++ +
  gi|242398771|ref|YP_002994195.1| 105 E--NPIVKEIHELKQDLEDIRK 124
                                       3..3445788888888888765 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 0.00012
                              Spc7 147 nlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkela 223
                                       n+++l+++ ++L ++ e+ld+  +++   ++ +++e++  ++   e  +   +e++el+++l+++ +ei++ + +l+
  gi|242398771|ref|YP_002994195.1|  60 NIDTLKSQIQELRDEIEKLDKTIKDVMMLYEVVSQEINPFRDLDSE--NPIVKEIHELKQDLEDIRKEIAQIRGDLK 134
                                       57789999999999999999999999999*******9999996654..77799*****************9999987 PP

                              Spc7 224 el 225
                                        l
  gi|242398771|ref|YP_002994195.1| 135 LL 136
                                       66 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.2       7.1   1.1e+03      94     114 ..      34      54 ..      20      57 .. 0.65
   2 ?   15.0   2.0   0.00012     0.018      82     119 ..      57      94 ..      49      95 .. 0.88
   3 ?    5.9   0.1     0.074        11      89     111 ..     108     130 ..     103     137 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 7.1
                                       HHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  94 ekleeeleklkdqittleanl 114
                                       ++ ee+++ + ++i+++e++l
  gi|242398771|ref|YP_002994195.1|  34 KEDEEKITLIMNRINEIENEL 54 
                                       445566666666666666655 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 0.00012
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  82 lkkkleelekqlekleeeleklkdqittleanlaqlyq 119
                                       +k ++++l++q+++l +e+ekl ++i+ +++  + ++q
  gi|242398771|ref|YP_002994195.1|  57 IKVNIDTLKSQIQELRDEIEKLDKTIKDVMMLYEVVSQ 94 
                                       78899**********************99988777766 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.074
                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  89 lekqlekleeeleklkdqittle 111
                                       + k +++l+++le+++++i +++
  gi|242398771|ref|YP_002994195.1| 108 IVKEIHELKQDLEDIRKEIAQIR 130
                                       56778888888888888888775 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   1.2   0.00019     0.029     139     224 ..      11     131 ..       4     143 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00019
                           DUF4407 139 eaqiaalqaeidaaearldalraeaqkeldgtk.....gtgttgvaGkgpaakekkaqldaaqaelaelkakld... 207
                                       +++i++l+ ++++ +++ + ++++ ++e   t      ++ ++  ++   + ++ k+q+++++ e+++l+++++   
  gi|242398771|ref|YP_002994195.1|  11 KDEIEQLELALSEGNTQENPKEQKEDEEKI-TLimnriNEIENELPRIKVNIDTLKSQIQELRDEIEKLDKTIKdvm 86 
                                       455555555555555555555555554433.2344444444445666777777788888888888888888877888 PP

                           DUF4407 208 ............................atarlaalraelaelea 224
                                                                    +++l++ r+e+a+++ 
  gi|242398771|ref|YP_002994195.1|  87 mlyevvsqeinpfrdldsenpivkeiheLKQDLEDIRKEIAQIRG 131
                                       888888888888888887777666666666666666666666554 PP

>> NleF_casp_inhib  NleF caspase inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   3.4    0.0028      0.43      12      61 ..      46      91 ..      28      98 .. 0.78
   2 ?    6.4   0.1     0.053         8      35      58 ..     110     133 ..     101     148 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0028
                   NleF_casp_inhib 12 tlkdIkdklklifereiastTaeekikElsdkltklknsvlseredlYev 61
                                       +++I+++l +i    ++  T + +i+El+d+++kl + ++     lYev
  gi|242398771|ref|YP_002994195.1| 46 RINEIENELPRIK---VNIDTLKSQIQELRDEIEKLDKTIKDV-MMLYEV 91
                                      5789999999998...8889999*************9998754.346665 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.053
                   NleF_casp_inhib  35 ekikElsdkltklknsvlseredl 58 
                                       ++i+El+++l+++ +++ + r+dl
  gi|242398771|ref|YP_002994195.1| 110 KEIHELKQDLEDIRKEIAQIRGDL 133
                                       6899******************98 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 ?   10.9   1.4    0.0024      0.36      72     115 ..      40      82 ..      12      97 .. 0.56
   2 ?   11.5   2.8    0.0015      0.23      17     104 ..      49     129 ..      33     137 .. 0.40
   3 ?    3.4   0.0      0.49        74      34      57 ..     113     136 ..      96     148 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0024
                      Baculo_PEP_C  72 LtdalnalqdtlrneLtnlnsiltnLlssvtNinstLnnllqal 115
                                       +t  +n+++ +++neL  ++ ++ +L s++  +   ++ l +++
  gi|242398771|ref|YP_002994195.1|  40 ITLIMNRIN-EIENELPRIKVNIDTLKSQIQELRDEIEKLDKTI 82 
                                       444444444.3444444444444444444444444443333333 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.0015
                      Baculo_PEP_C  17 dLtnvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq.....dtlrneLt 88 
                                       ++ n L             ++  +d++++q+++l +++++l +   +++  l + +++ +n +      + + +e+ 
  gi|242398771|ref|YP_002994195.1|  49 EIENELP-----------RIKVNIDTLKSQIQELRDEIEKLDKT-IKDVMMLYEVVSQEINPFRdldseNPIVKEIH 113
                                       2223333...........33333333333333333333332222.22333333444444444333334334444444 PP

                      Baculo_PEP_C  89 nlnsiltnLlssvtNi 104
                                        l+++l ++  +++ i
  gi|242398771|ref|YP_002994195.1| 114 ELKQDLEDIRKEIAQI 129
                                       4444444444444444 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.49
                      Baculo_PEP_C  34 aqlatlldaietqLnalsedlksl 57 
                                        +l+++l++i +++ ++  dlk l
  gi|242398771|ref|YP_002994195.1| 113 HELKQDLEDIRKEIAQIRGDLKLL 136
                                       456666666666666666666554 PP

>> DASH_Dam1  DASH complex subunit Dam1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0       4.6     7e+02       3      23 ..      45      65 ..      38      67 .. 0.67
   2 ?   10.0   0.2    0.0037      0.57       2      30 ..      65      93 ..      64      98 .. 0.82
   3 ?    1.7   0.0       1.5   2.3e+02       3      22 ..     110     129 ..     108     134 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 4.6
                         DASH_Dam1  3 pafaeLaDsletLdknledLq 23
                                      ++++e++ +l  ++ n++ L+
  gi|242398771|ref|YP_002994195.1| 45 NRINEIENELPRIKVNIDTLK 65
                                      456667777777777766665 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0037
                         DASH_Dam1  2 epafaeLaDsletLdknledLqqihesLs 30
                                      + +++eL D++e+Ldk ++d   + e +s
  gi|242398771|ref|YP_002994195.1| 65 KSQIQELRDEIEKLDKTIKDVMMLYEVVS 93
                                      689**************999877777665 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 1.5
                         DASH_Dam1   3 pafaeLaDsletLdknledL 22 
                                       ++++eL+  le+++k + ++
  gi|242398771|ref|YP_002994195.1| 110 KEIHELKQDLEDIRKEIAQI 129
                                       56778888888877777665 PP

>> Sec8_exocyst  Sec8 exocyst complex component specific domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   1.4     0.085        13      84     129 ..      43      88 ..      34      97 .. 0.71
   2 ?    8.6   0.0     0.011       1.6      86     123 ..     110     147 ..      89     152 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.085
                      Sec8_exocyst  84 sqekvselKesleeakkklstkkkeLkelnarsakykevieiLdai 129
                                         ++++e+ ++l   k ++ t k++++el ++  k+++ i+    +
  gi|242398771|ref|YP_002994195.1|  43 IMNRINEIENELPRIKVNIDTLKSQIQELRDEIEKLDKTIKDVMML 88 
                                       4567778888888888888888888888888888888777765554 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.011
                      Sec8_exocyst  86 ekvselKesleeakkklstkkkeLkelnarsakykevi 123
                                       ++++elK++le+ +k++ + + +Lk l+++ + ++++i
  gi|242398771|ref|YP_002994195.1| 110 KEIHELKQDLEDIRKEIAQIRGDLKLLAYHGVDLDKII 147
                                       6899*************************999999988 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 ?   13.8   0.2   0.00029     0.044       2      30 ..      46      74 ..      45      80 .. 0.90
   2 ?    0.5   0.1       4.1   6.2e+02       4      14 ..      69      79 ..      68      86 .. 0.56
   3 ?    4.5   0.4      0.22        34       1      19 [.     110     128 ..     110     133 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00029
                     Bap31_Bap29_C  2 eiekLkkeLkkkkkDlealKkQaeglakE 30
                                       i++ ++eL + k ++++lK+Q++ l  E
  gi|242398771|ref|YP_002994195.1| 46 RINEIENELPRIKVNIDTLKSQIQELRDE 74
                                      799999*****************999766 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 4.1
                     Bap31_Bap29_C  4 ekLkkeLkkkk 14
                                      ++L++e++k +
  gi|242398771|ref|YP_002994195.1| 69 QELRDEIEKLD 79
                                      66666666544 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.22
                     Bap31_Bap29_C   1 keiekLkkeLkkkkkDlea 19 
                                       kei +Lk+ L+  +k++  
  gi|242398771|ref|YP_002994195.1| 110 KEIHELKQDLEDIRKEIAQ 128
                                       799*******998888865 PP

>> DUF812  Protein of unknown function (DUF812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6  15.3    0.0051      0.78     298     402 ..       8     103 ..       1     131 [. 0.41
   2 ?    4.0   0.2      0.12        18     330     356 ..     110     136 ..     103     150 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0051
                            DUF812 298 gsrfthaeklqftkeela....kkaeteeelkkkreeeleelqeqieeleskieeleeeikklessikqveeeleee 370
                                       +s+ ++ e+l++     a    +++e+ +e  k+ ee+++ + ++i+e+e+++ +++ +i++l+s+i+++ +e+e++
  gi|242398771|ref|YP_002994195.1|   8 KSEKDEIEQLEL-----AlsegNTQENPKEQ-KEDEEKITLIMNRINEIENELPRIKVNIDTLKSQIQELRDEIEKL 78 
                                       333333333333.....23122333333333.333344555555555555555555555555555555555555555 PP

                            DUF812 371 keeneelekevklkkktlellpdaeeniekLq 402
                                       +++ +     +++  + ++   d       L 
  gi|242398771|ref|YP_002994195.1|  79 DKTIKDVMMLYEVVSQEINPFRD-------LD 103
                                       55555555555544444444433.......33 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.12
                            DUF812 330 eeleelqeqieeleskieeleeeikkl 356
                                       +e++el++ +e+++++i++++ ++k l
  gi|242398771|ref|YP_002994195.1| 110 KEIHELKQDLEDIRKEIAQIRGDLKLL 136
                                       688899999999999999998888865 PP

>> COMP  Cartilage oligomeric matrix protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.2      0.94   1.4e+02      14      32 ..      65      76 ..      57      85 .. 0.57
   2 ?   10.2   0.1    0.0055      0.84      17      36 ..     112     131 ..     106     134 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.94
                              COMP 14 tqllkeLreelrqQvkEis 32
                                       + ++eLr+e       i+
  gi|242398771|ref|YP_002994195.1| 65 KSQIQELRDE-------IE 76
                                      3334555554.......44 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0055
                              COMP  17 lkeLreelrqQvkEisfLRn 36 
                                       + eL+ +l + +kEi+++R 
  gi|242398771|ref|YP_002994195.1| 112 IHELKQDLEDIRKEIAQIRG 131
                                       6799**************95 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   5.6   0.00036     0.055      32      90 ..      26      84 ..       9      87 .. 0.87
   2 ?    3.6   0.3      0.55        83      58      77 ..     110     129 ..     100     147 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00036
                           BLOC1_2 32 asekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyske 90
                                      ++e+ k+ k+  ++++  ++++ne ++el   + +id ++ q++eL + +++LD+ +k+
  gi|242398771|ref|YP_002994195.1| 26 TQENPKEQKEDEEKITLIMNRINEIENELPRIKVNIDTLKSQIQELRDEIEKLDKTIKD 84
                                      5666667777778888899999**9*****************************99886 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.55
                           BLOC1_2  58 eelqpylqqidqiekqvteL 77 
                                       +e+++++q +++i k+++++
  gi|242398771|ref|YP_002994195.1| 110 KEIHELKQDLEDIRKEIAQI 129
                                       34555555555555555443 PP

>> DUF4200  Domain of unknown function (DUF4200)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4  14.3     0.019       2.8      48     108 ..      20      80 ..       1      92 [. 0.74
   2 ?    6.7   0.1     0.062       9.5      80     102 ..     110     132 ..     103     146 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.019
                           DUF4200  48 lkfdkflkendakraralkkaeeerklkkekeaeikklkaeietlkseiekleekleeykk 108
                                       +  +   +en +++++ ++k+    +++ e e+e+ ++k++i+tlks+i++l +++e++ k
  gi|242398771|ref|YP_002994195.1|  20 ALSEGNTQENPKEQKEDEEKITLIMNRINEIENELPRIKVNIDTLKSQIQELRDEIEKLDK 80 
                                       2334557899999999999999999999999999999999999999999999999999865 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.062
                           DUF4200  80 aeikklkaeietlkseiekleek 102
                                       +ei++lk+++e++++ei++    
  gi|242398771|ref|YP_002994195.1| 110 KEIHELKQDLEDIRKEIAQIRGD 132
                                       89999999999999999887655 PP

>> HIP1_clath_bdg  Clathrin-binding domain of Huntingtin-interacting protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   4.2     0.053       8.1      25      89 ..      33      96 ..      18     106 .. 0.74
   2 ?    8.9   0.0     0.015       2.3      52      79 ..     110     137 ..     103     153 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.053
                    HIP1_clath_bdg 25 verekkeleeelerlkeeaerkleeqkeelekLkreleakraelarlkssLesseqsgeqlssql 89
                                       +   ++++  ++r++ e e++l   k ++++Lk+++++ r+e+++l +++++  +  e +s+++
  gi|242398771|ref|YP_002994195.1| 33 QKEDEEKITLIMNRIN-EIENELPRIKVNIDTLKSQIQELRDEIEKLDKTIKDVMMLYEVVSQEI 96
                                      4444444555555554.556777888999********************9999888777777665 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.015
                    HIP1_clath_bdg  52 eelekLkreleakraelarlkssLesse 79 
                                       +e+ +Lk++le+ r+e+a++++ L+  +
  gi|242398771|ref|YP_002994195.1| 110 KEIHELKQDLEDIRKEIAQIRGDLKLLA 137
                                       57899****************9998655 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   2.7    0.0015      0.22      17      65 ..      37      82 ..      32      98 .. 0.76
   2 ?    7.3   4.0     0.042       6.4       8      62 ..      56     113 ..      54     146 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0015
                           NPV_P10 17 ddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdiL 65
                                      ++k++ + +++++++++lp    ++ ++d +  q++el +++e+ +++ 
  gi|242398771|ref|YP_002994195.1| 37 EEKITLIMNRINEIENELPR---IKVNIDTLKSQIQELRDEIEKLDKTI 82
                                      68999999999999999998...56777777777777777777665544 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.042
                           NPV_P10   8 vIradikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaelet...kvenIq 62 
                                        I+ +i  ++++++ l ++++++++ ++dv  l e + +  +   +l++    v++I+
  gi|242398771|ref|YP_002994195.1|  56 RIKVNIDTLKSQIQELRDEIEKLDKTIKDVMMLYEVVSQEINPFRDLDSenpIVKEIH 113
                                       6888999999999999999999999999999888777666666666665555555554 PP

>> Hemagglutinin  Haemagglutinin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   4.7   0.00056     0.086     366     452 ..      33     124 ..      23     142 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00056
                                       HHHHHHHHHHHHHHHHHHHH...HTTTEEEBXSSXXTTTTHHHHHHHHHHHHHHH..HHHHHHHHHHHHHHHHHHHH CS
                     Hemagglutinin 366 kkstqeainkitkkvnslie...kenkqleavgkelnelekrieeldkkvddgfl..dvityniellvllenerild 437
                                       +k   e i  i +++n + +   + +++++++  ++ el+++ie+ldk ++d ++  +v++ +i+    l+ e+ + 
  gi|242398771|ref|YP_002994195.1|  33 QKEDEEKITLIMNRINEIENelpRIKVNIDTLKSQIQELRDEIEKLDKTIKDVMMlyEVVSQEINPFRDLDSENPIV 109
                                       66677888889999999876222457899***********************8753367777777666666666555 PP

                                       HHHHHHHHHHHHHHH CS
                     Hemagglutinin 438 fedsnvknleekvkk 452
                                        e +++k+  e ++k
  gi|242398771|ref|YP_002994195.1| 110 KEIHELKQDLEDIRK 124
                                       555555544444444 PP

>> SKA2  Spindle and kinetochore-associated protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   4.2    0.0012      0.18      34      96 ..      30      97 ..       2     107 .. 0.73
   2 ?    5.0   0.2      0.13        20      43      65 ..     108     130 ..      94     139 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0012
                              SKA2 34 pdna....eNpvkLlerlkkvkeelqaLkeqceellaekkelidkirttlvanrellqqLqasa..elp 96
                                      p+++    e    +++r++++ +el+ +k +++ l ++ +el d+i++ l ++ + + +L + +  e++
  gi|242398771|ref|YP_002994195.1| 30 PKEQkedeEKITLIMNRINEIENELPRIKVNIDTLKSQIQELRDEIEK-LDKTIKDVMMLYEVVsqEIN 97
                                      444445557889999**************************9999974.55666666666666555555 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.13
                              SKA2  43 LlerlkkvkeelqaLkeqceell 65 
                                       +++++ ++k++l+ +++++ ++ 
  gi|242398771|ref|YP_002994195.1| 108 IVKEIHELKQDLEDIRKEIAQIR 130
                                       56777777777777777776664 PP

>> Bcr-Abl_Oligo  Bcr-Abl oncoprotein oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.7    0.0056      0.85      13      51 ..      34      72 ..      22      83 .. 0.81
   2 ?    4.6   0.2      0.21        33      19      50 ..      98     129 ..      90     138 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0056
                     Bcr-Abl_Oligo 13 fPeeevPkmeLdsvedieqeLerCkaslrrLekelneek 51
                                        +ee  ++ ++ +++ie+eL r k ++  L+ +++e +
  gi|242398771|ref|YP_002994195.1| 34 KEDEEKITLIMNRINEIENELPRIKVNIDTLKSQIQELR 72
                                      5566666777899*******************9998865 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.21
                     Bcr-Abl_Oligo  19 PkmeLdsvedieqeLerCkaslrrLekelnee 50 
                                       P  +Lds + i +e+ + k++l  ++ke+++ 
  gi|242398771|ref|YP_002994195.1|  98 PFRDLDSENPIVKEIHELKQDLEDIRKEIAQI 129
                                       77788888888999999999998888888764 PP

>> DUF2730  Protein of unknown function (DUF2730)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   5.6     0.079        12      42      89 ..      40      85 ..       1     102 [. 0.66
   2 ?    8.2   0.1     0.017       2.5      63      88 ..     110     135 ..     100     144 .. 0.59

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.079
                           DUF2730 42 veendkrlteletkvenLPtakdlekLkllladlrgelkaleaevrql 89
                                      ++ + +r++e+e ++  +  ++++++Lk ++++lr e+++l+++++ +
  gi|242398771|ref|YP_002994195.1| 40 ITLIMNRINEIENELPRI--KVNIDTLKSQIQELRDEIEKLDKTIKDV 85
                                      344445555555433322..4455555555555555555555555554 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.017
                           DUF2730  63 kdlekLkllladlrgelkaleaevrq 88 
                                       k++++Lk +l+d+r e+ +++ +++ 
  gi|242398771|ref|YP_002994195.1| 110 KEIHELKQDLEDIRKEIAQIRGDLKL 135
                                       55555555555555555555544443 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 ?   11.6   7.8    0.0016      0.24      66     120 ..      30      84 ..       2      95 .. 0.61
   2 ?    4.1   0.2      0.33        49      33      53 ..     108     128 ..     100     138 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0016
                                       HHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  66 rekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnvlesneqkiqk 120
                                        ++qk+++++ ++i +  +e+e+e  r+k +id+  s+i++L++ +e++++ i++
  gi|242398771|ref|YP_002994195.1|  30 PKEQKEDEEKITLIMNRINEIENELPRIKVNIDTLKSQIQELRDEIEKLDKTIKD 84 
                                       2333333334555555666666677777777777777777777777777766665 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.33
                                       CCHHHCCCCCCCCCCCCHHHH CS
                         Fib_alpha  33 vkkdlekleneleeisnstke 53 
                                       + k++++l+++le+i+++  +
  gi|242398771|ref|YP_002994195.1| 108 IVKEIHELKQDLEDIRKEIAQ 128
                                       445555555555555554433 PP

>> MAD  Mitotic checkpoint protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0  13.3    0.0013      0.19     434     524 ..      48     137 ..       1     151 [. 0.58

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0013
                               MAD 434 adassskeevdslkkkleeLelerqrLreqkeelElele.rreLqgdy..dlkktkVlhlseNPaakakqqkkeqle 507
                                       ++    ++e+  +k ++++L+ + q+Lr+++e+l   ++    L  ++  +++ ++ l  seNP+ k  +  k++le
  gi|242398771|ref|YP_002994195.1|  48 NE---IENELPRIKVNIDTLKSQIQELRDEIEKLDKTIKdVMMLYEVVsqEINPFRDLD-SENPIVKEIHELKQDLE 120
                                       11...244555666666666666666888888888877744445444411344555554.7899999999999**** PP

                               MAD 508 kLqaEierlkellkkle 524
                                        +++Ei +++  lk l 
  gi|242398771|ref|YP_002994195.1| 121 DIRKEIAQIRGDLKLLA 137
                                       ******99999998765 PP

>> DUF5344  Family of unknown function (DUF5344)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.6   0.00055     0.084       4      30 ..      57      83 ..      54      87 .. 0.92
   2 ?    3.4   0.0      0.74   1.1e+02      41      58 ..     108     125 ..     100     136 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00055
                           DUF5344  4 IklnqaeVeqkLselktaaeelktsip 30
                                      Ik+n ++++++++el++ +e+l+++i+
  gi|242398771|ref|YP_002994195.1| 57 IKVNIDTLKSQIQELRDEIEKLDKTIK 83
                                      ***********************9987 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.74
                           DUF5344  41 vvekineleeeleellka 58 
                                        v++i+el+++le+++k 
  gi|242398771|ref|YP_002994195.1| 108 IVKEIHELKQDLEDIRKE 125
                                       567777777777776654 PP

>> Prp19  Prp19/Pso4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1       1.9   2.9e+02      11      37 ..      49      75 ..      41      78 .. 0.78
   2 ?    9.9   0.0    0.0047      0.72      19      39 ..     108     128 ..     101     129 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 1.9
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             Prp19 11 tlqnEWDalmletfelrkqleqtrqeL 37
                                       + nE   +  +  +l+ q++++r+e 
  gi|242398771|ref|YP_002994195.1| 49 EIENELPRIKVNIDTLKSQIQELRDEI 75
                                      556777777778889999999999986 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0047
                                       HHHHHHHHHHHHHHHHHHHHH CS
                             Prp19  19 lmletfelrkqleqtrqeLsq 39 
                                       +++e +el+++le +r+e +q
  gi|242398771|ref|YP_002994195.1| 108 IVKEIHELKQDLEDIRKEIAQ 128
                                       799***************987 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2  10.7    0.0024      0.37      52     147 ..      33     129 ..       1     139 [. 0.46

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0024
                              Fez1  52 eeikeleesleektle............levcenelqrkkseaellrekvekleeelkelreelselsleeeeaa.. 114
                                       +              +            ++++enel r k + ++l+ ++++l +e+++l ++++++ +  e  +  
  gi|242398771|ref|YP_002994195.1|  33 Q--------------KedeekitlimnrINEIENELPRIKVNIDTLKSQIQELRDEIEKLDKTIKDVMMLYEVVSqe 95 
                                       1..............11223333333336667777777766666666666666666666666666655433333322 PP

                              Fez1 115 ........lesdeakaqrqe...aeeleelkreverlraeLkee 147
                                               +          e    +e++elk+++e +r+e+++ 
  gi|242398771|ref|YP_002994195.1|  96 inpfrdldS----------EnpiVKEIHELKQDLEDIRKEIAQI 129
                                       222222211..........1333445555555555555554443 PP

>> Fmp27_WPPW  RNA pol II promoter Fmp27 protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   4.9   0.00088      0.13     167     244 ..      34     107 ..      30     145 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00088
                        Fmp27_WPPW 167 dpervqkelleeRleeleeqiekleekleelelksekedeelkeeieelekeikelkeklefletlledlkeseess 243
                                       + ++ + +l+ +R++e+e+++ +++ ++++l+++ ++    l++eie+l k+ik++   +e++++ ++ ++  ++++
  gi|242398771|ref|YP_002994195.1|  34 KEDEEKITLIMNRINEIENELPRIKVNIDTLKSQIQE----LRDEIEKLDKTIKDVMMLYEVVSQEINPFRDLDSEN 106
                                       55666789999********************999999....9************99999999999999888877654 PP

                        Fmp27_WPPW 244 e 244
                                        
  gi|242398771|ref|YP_002994195.1| 107 P 107
                                       4 PP

>> zf-CpG_bind_C  CpG binding protein zinc finger C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   2.2     0.049       7.4      26      79 ..      49     103 ..       8     109 .. 0.79
   2 ?    7.4   0.0     0.021       3.3      19      62 ..     106     150 ..      86     154 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.049
                     zf-CpG_bind_C  26 enkkklekirkeqeeakkklkelekklkkLeeliekakkl.slkeeeeeeedeed 79 
                                       e++++l +i+ +  ++k++++el ++ +kL++ i++   l ++ ++e +   + d
  gi|242398771|ref|YP_002994195.1|  49 EIENELPRIKVNIDTLKSQIQELRDEIEKLDKTIKDVMMLyEVVSQEINPFRDLD 103
                                       5677888999999999999999999999999999998888555555544344444 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.021
                     zf-CpG_bind_C  19 spsvaee.enkkklekirkeqeeakkklkelekklkkLeelieka 62 
                                       +p v e  e k+ le irke  +++  lk l  +  +L+++i +a
  gi|242398771|ref|YP_002994195.1| 106 NPIVKEIhELKQDLEDIRKEIAQIRGDLKLLAYHGVDLDKIIYEA 150
                                       2556665156889****************************9887 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   1.4    0.0066         1      25      84 ..      58     119 ..      34     124 .. 0.57
   2 ?    2.4   0.0       1.3   1.9e+02      34      52 ..     111     129 ..     106     143 .. 0.56

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0066
                            DUF948  25 kktldeaaatieelekqvdpilkevedllakvnelledvne..klekvdplteavadlgesv 84 
                                       k  +d ++++i+el+++++++ k ++d++   +++ +++n    l++ +p+++++++l + +
  gi|242398771|ref|YP_002994195.1|  58 KVNIDTLKSQIQELRDEIEKLDKTIKDVMMLYEVVSQEINPfrDLDSENPIVKEIHELKQDL 119
                                       33344445555555555555555555555555555556654556666667777666666665 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 1.3
                            DUF948  34 tieelekqvdpilkevedl 52 
                                        i+el+++++ i ke++++
  gi|242398771|ref|YP_002994195.1| 111 EIHELKQDLEDIRKEIAQI 129
                                       3444444444444444443 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   3.5    0.0033       0.5     232     279 ..      38      85 ..      23     131 .. 0.57

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0033
                          Prominin 232 snvlpaLaelerllenlkeakeqLeqvnklekeLrksgsqLrdglrgv 279
                                       ++++  +++++++ ++l+++k ++ ++++  +eLr + ++L + +++v
  gi|242398771|ref|YP_002994195.1|  38 EKITLIMNRINEIENELPRIKVNIDTLKSQIQELRDEIEKLDKTIKDV 85 
                                       444555555555555555555555555555555555555555555444 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   4.0    0.0051      0.77      21      86 ..      22      86 ..       2      91 .. 0.71
   2 ?   11.8   4.1    0.0007      0.11       2      86 ..      45     130 ..      26     147 .. 0.61

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0051
                             TMPIT 21 ykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlkeve 86
                                       + +++e  k q++  ++i+   +r++e++++l ++k +++   +++++el++e+++ +k++k+v 
  gi|242398771|ref|YP_002994195.1| 22 SEGNTQENPKEQKEDEEKITLIMNRINEIENELPRIKVNID-TLKSQIQELRDEIEKLDKTIKDVM 86
                                      45566777778888888888888888888888888888874.677788888888888888888764 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.0007
                             TMPIT   2 eeweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk.eeeeeeveelkeelke 77 
                                       ++++e+e+e+ +++ + +++k++++el   ++k+ k+ik     ++ ++++++ ++   + +   +e++elk++l++
  gi|242398771|ref|YP_002994195.1|  45 NRINEIENELPRIKVNIDTLKSQIQELRDEIEKLDKTIKDVMMLYEVVSQEINPFRDLDSeNPIVKEIHELKQDLED 121
                                       34455555555555555555555555555555555555555555555555555555442234445678888888888 PP

                             TMPIT  78 rkkvlkeve 86 
                                       ++k ++++ 
  gi|242398771|ref|YP_002994195.1| 122 IRKEIAQIR 130
                                       888887776 PP

>> Ran-binding  RanGTP-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   9.2    0.0019      0.28      49     140 ..      29     126 ..      12     154 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0019
                       Ran-binding  49 leklqkkLeskikiispaidLieliaarGntsLesaveLtksLkkeieelgerleeaaekeekskk......keeek 119
                                         k qk+ e+ki+ i + i+ ie    r  +++++  + +++L++eie+l++++++++   e  ++        +++
  gi|242398771|ref|YP_002994195.1|  29 NPKEQKEDEEKITLIMNRINEIENELPRIKVNIDTLKSQIQELRDEIEKLDKTIKDVMMLYEVVSQeinpfrDLDSE 105
                                       456788889***********************************************999888777678866522333 PP

                       Ran-binding 120 eelkkviedikeLLkrieeai 140
                                       + + k i+++k+ L++i ++i
  gi|242398771|ref|YP_002994195.1| 106 NPIVKEIHELKQDLEDIRKEI 126
                                       333333333333344444444 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   1.6       5.6   8.5e+02      18      43 ..      12      37 ..       2      44 .. 0.48
   2 ?   11.0   3.0    0.0025      0.38       4      46 ..      37      80 ..      34     106 .. 0.72
   3 ?    6.2   0.1     0.076        12       9      43 ..     108     142 ..     102     153 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 5.6
                             Spc24 18 selesleselaelkeeleeleeesee 43
                                      +e+e+le  l+e +++ +  e+++ e
  gi|242398771|ref|YP_002994195.1| 12 DEIEQLELALSEGNTQENPKEQKEDE 37
                                      34444444444444444444444333 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.0025
                             Spc24  4 nekfr.iakelsdleselesleselaelkeeleeleeesee.kes 46
                                      +ek++ i + ++++e+el +++ + + lk++++el +e e+ + +
  gi|242398771|ref|YP_002994195.1| 37 EEKITlIMNRINEIENELPRIKVNIDTLKSQIQELRDEIEKlD-K 80
                                      5555515678999999999999999999999999999888731.2 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.076
                             Spc24   9 iakelsdleselesleselaelkeeleeleeesee 43 
                                       i+ke+++l+++le++++e a+ +  l+ l  ++++
  gi|242398771|ref|YP_002994195.1| 108 IVKEIHELKQDLEDIRKEIAQIRGDLKLLAYHGVD 142
                                       899*****************999999888776665 PP

>> CALCOCO1  Calcium binding and coiled-coil domain (CALCOCO1) like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   4.4      0.31        48     102     156 ..       4      58 ..       1      60 [. 0.73
   2 ?   12.1   9.9   0.00044     0.067      50     147 ..      27     128 ..      16     137 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.31
                          CALCOCO1 102 kqkelerlseelaeeksalle.akeesearirELEeDiktltqralekEteLeRlk 156
                                       k k++ + ++e+ + + al+e +++e+ +  +E Ee i  + +r  e E eL R+k
  gi|242398771|ref|YP_002994195.1|   4 KFKKK-SEKDEIEQLELALSEgNTQENPKEQKEDEEKITLIMNRINEIENELPRIK 58 
                                       44433.3455666666777762456777888999********************98 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00044
                          CALCOCO1  50 qeaanrqreke.keeykrdr.eeldrerkelesrveelkeelkesrekveeleekqkelerlseelaeeksalleak 124
                                       qe  ++q+e e k     +r +e+++e   ++ +++ lk++++e+r+++e+l +  k++  l e++++e +   + +
  gi|242398771|ref|YP_002994195.1|  27 QENPKEQKEDEeKITLIMNRiNEIENELPRIKVNIDTLKSQIQELRDEIEKLDKTIKDVMMLYEVVSQEINPFRDLD 103
                                       455555555441444444442688999999999************************************99887666 PP

                          CALCOCO1 125 ees..earirELEeDiktltqrale 147
                                        e+  ++ i+EL +D + + +   +
  gi|242398771|ref|YP_002994195.1| 104 SENpiVKEIHELKQDLEDIRKEIAQ 128
                                       66533789*******9988776655 PP

>> Allexi_40kDa  Allexivirus 40kDa protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   1.2     0.093        14      84     140 ..      11      67 ..       3      70 .. 0.79
   2 ?   11.4   3.1    0.0011      0.17      55     137 ..      41     129 ..      38     135 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.093
                      Allexi_40kDa  84 rdalrtltklldklksvekklelsaetasdskllkklesietsleelhakldelsss 140
                                       +d++++l+  l + +++e+ +e+++++++ + ++++++ ie++l +++ ++d+l s+
  gi|242398771|ref|YP_002994195.1|  11 KDEIEQLELALSEGNTQENPKEQKEDEEKITLIMNRINEIENELPRIKVNIDTLKSQ 67 
                                       577777887777777777778888888888888999999999999999999998775 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.0011
                      Allexi_40kDa  55 thishdvdsiinklnpv..sllsqttlLselrdalrtltklldklksvekklelsa....etasdskllkklesiet 125
                                       t i + +++i n+l  +  ++ + +++++elrd++++l+k+++++  + + +++++    + +s++ ++k+++ +++
  gi|242398771|ref|YP_002994195.1|  41 TLIMNRINEIENELPRIkvNIDTLKSQIQELRDEIEKLDKTIKDVMMLYEVVSQEInpfrDLDSENPIVKEIHELKQ 117
                                       66666677777777655114445678899***********99987665554444440001455667789******** PP

                      Allexi_40kDa 126 sleelhakldel 137
                                       +le++ +++ ++
  gi|242398771|ref|YP_002994195.1| 118 DLEDIRKEIAQI 129
                                       ****99998665 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   6.8    0.0025      0.38      88     160 ..      24      96 ..       2     100 .. 0.74
   2 ?    0.5   0.0       3.9   5.9e+02      84      98 ..     113     127 ..     102     147 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0025
                             ATG16  88 eelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDEl 160
                                          +e  k++ e +++++  ++ + + e++l + + +++ l++++++l+++++++++++++   l + +  E+
  gi|242398771|ref|YP_002994195.1|  24 GNTQENPKEQKEDEEKITLIMNRINEIENELPRIKVNIDTLKSQIQELRDEIEKLDKTIKDVMMLYEVVSQEI 96 
                                       3445677888888888999999999999999999999999999999999999999999988888888887776 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 3.9
                             ATG16  84 aqlreelaelyksrg 98 
                                       ++l+++l++  k+ +
  gi|242398771|ref|YP_002994195.1| 113 HELKQDLEDIRKEIA 127
                                       222222222222211 PP

>> DUF3618  Protein of unknown function (DUF3618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.2      0.29        45       4      18 ..      61      75 ..      60      77 .. 0.88
   2 ?    7.5   0.3     0.032       4.8       2      18 ..     117     133 ..     116     134 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.29
                           DUF3618  4 peeIerdIertRaeL 18
                                      +++++ +I++ R+e+
  gi|242398771|ref|YP_002994195.1| 61 IDTLKSQIQELRDEI 75
                                      799*********996 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.032
                           DUF3618   2 rdpeeIerdIertRaeL 18 
                                       +d e+I+ +I++ R +L
  gi|242398771|ref|YP_002994195.1| 117 QDLEDIRKEIAQIRGDL 133
                                       689***********987 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   7.0       0.1        16      36      88 ..      31      83 ..       1     108 [. 0.63
   2 ?   14.3   1.8   0.00021     0.032       3      79 ..      47     132 ..      45     137 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.1
                        TPR_MLP1_2 36 eiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesakaele 88
                                      ++ ke ++k    ++  +e  +el +++  +++lk++i+el++e e++ ++++
  gi|242398771|ref|YP_002994195.1| 31 KEQKEDEEKITLIMNRINEIENELPRIKVNIDTLKSQIQELRDEIEKLDKTIK 83
                                      45555555555555556666666777777777777777777777777666654 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 0.00021
                        TPR_MLP1_2   3 lksleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYe.........relvkhaedvkelqalreelnelk 70 
                                       +++ e+e+ ++k +++ +++++q+l++++ek  +  k+    Ye         r l   +  vke+ +l+++l++++
  gi|242398771|ref|YP_002994195.1|  47 INEIENELPRIKVNIDTLKSQIQELRDEIEKLDKTIKDVMMLYEvvsqeinpfRDLDSENPIVKEIHELKQDLEDIR 123
                                       56777777788888888888888888888888888888777777555444455667778888999999999999999 PP

                        TPR_MLP1_2  71 aeiaelkae 79 
                                       +eia+++ +
  gi|242398771|ref|YP_002994195.1| 124 KEIAQIRGD 132
                                       999988765 PP

>> Swi5  Swi5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   4.7       7.1   1.1e+03       9      49 ..      11      50 ..       3      54 .. 0.65
   2 ?   10.4   0.1    0.0036      0.55       4      40 ..      60      96 ..      57     101 .. 0.81
   3 ?    5.5   0.1      0.11        17       3      29 ..     110     136 ..     108     153 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 7.1
                                      HHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHH.HHH CS
                              Swi5  9 eeqleelekelaelkeelkekkdpeetvkrhIklLheY.NEi 49
                                      ++++e+le +l+e + + +   + +++ +++I+l+ ++ NEi
  gi|242398771|ref|YP_002994195.1| 11 KDEIEQLELALSEGNTQENP--KEQKEDEEKITLIMNRiNEI 50
                                      45667777777777766553..46777788888864433655 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0036
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHH CS
                              Swi5  4 eikeleeqleelekelaelkeelkekkdpeetvkrhI 40
                                      +i +l++q++el++e+++l++  k+     e+v++ I
  gi|242398771|ref|YP_002994195.1| 60 NIDTLKSQIQELRDEIEKLDKTIKDVMMLYEVVSQEI 96
                                      6899***************999987666666666666 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.11
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              Swi5   3 aeikeleeqleelekelaelkeelkek 29 
                                       +ei+el++ le ++ke+a+++  lk  
  gi|242398771|ref|YP_002994195.1| 110 KEIHELKQDLEDIRKEIAQIRGDLKLL 136
                                       6899***************99998865 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   3.6       1.3   1.9e+02      73     125 ..       2      54 ..       1      59 [. 0.77
   2 ?    9.7   5.1    0.0055      0.84      74     129 ..      31      86 ..      13      93 .. 0.78
   3 ?    1.5   0.0       1.8   2.8e+02      74      93 ..     110     129 ..      98     139 .. 0.59

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 1.3
                              ADIP  73 qskierlktqleqlerelalvqakerqlekklktleqklknekeelqrlknal 125
                                       + k+++ +++ e  + elal++ +++++ k++k+ e+k+      ++  +n l
  gi|242398771|ref|YP_002994195.1|   2 KEKFKKKSEKDEIEQLELALSEGNTQENPKEQKEDEEKITLIMNRINEIENEL 54 
                                       67888889999999999999999999999999999998876666666655555 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0055
                              ADIP  74 skierlktqleqlerelalvqakerqlekklktleqklknekeelqrlknalqqik 129
                                       ++ +  +++ +   +++   ++++  ++ ++ tl+++++++++e+++l ++++++ 
  gi|242398771|ref|YP_002994195.1|  31 KEQKEDEEKITLIMNRINEIENELPRIKVNIDTLKSQIQELRDEIEKLDKTIKDVM 86 
                                       44455567778888888899999999999999999999999999999999999875 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 1.8
                              ADIP  74 skierlktqleqlerelalv 93 
                                       ++i  lk+ le+ ++e+a+ 
  gi|242398771|ref|YP_002994195.1| 110 KEIHELKQDLEDIRKEIAQI 129
                                       55555555555555555543 PP

>> LemA  LemA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   3.4    0.0014      0.22      28     111 ..       8      96 ..       3     101 .. 0.82
   2 ?    0.0   0.0       4.5   6.8e+02      82     101 ..     111     130 ..     101     134 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0014
                              LemA  28 khEketleevteaRakaaeaesveekaeaenqlssalsrllavaEnYPdLkan.....enfleLqeelegtEnriav 99 
                                       k Ek+ +e++  a ++ +++e+++e++e e++++  ++r++ + ++ P +k n     ++++eL +e+e++++ i+ 
  gi|242398771|ref|YP_002994195.1|   8 KSEKDEIEQLELALSEGNTQENPKEQKEDEEKITLIMNRINEIENELPRIKVNidtlkSQIQELRDEIEKLDKTIKD 84 
                                       678888888888889999*********************************87444446788888888888888887 PP

                              LemA 100 aRrrYneavrey 111
                                           Y    +e 
  gi|242398771|ref|YP_002994195.1|  85 VMMLYEVVSQEI 96 
                                       777776665555 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 4.5
                              LemA  82 nfleLqeelegtEnriavaR 101
                                       ++ eL+++le++ ++ia  R
  gi|242398771|ref|YP_002994195.1| 111 EIHELKQDLEDIRKEIAQIR 130
                                       57789999999999999877 PP

>> HemX  HemX, putative uroporphyrinogen-III C-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   3.3    0.0014      0.21      32     102 ..       9      81 ..       2      91 .. 0.68
   2 ?   -0.6   0.0       4.2   6.4e+02      65      88 ..     109     132 ..      88     141 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0014
                              HemX  32 eltaevaelqqqlaaleqqlaq.....veaekeqkqeleerlqqlaeklealekeleqlqkqleelqqqlskvsga 102
                                       +++ e+++l+ +l++ ++   q      ++++e+ + +++r+++ +++l + + ++++l++q++el+++++k++ +
  gi|242398771|ref|YP_002994195.1|   9 SEKDEIEQLELALSEGNT---QenpkeQKEDEEKITLIMNRINEIENELPRIKVNIDTLKSQIQELRDEIEKLDKT 81 
                                       333344444444443333...223333456667777789999999*************************998765 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 4.2
                              HemX  65 eerlqqlaeklealekeleqlqkq 88 
                                        +++++l+++le+ +ke++q   +
  gi|242398771|ref|YP_002994195.1| 109 VKEIHELKQDLEDIRKEIAQIRGD 132
                                       444555555555555555555444 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   1.4    0.0019      0.28       9      53 ..      37      81 ..      34      98 .. 0.77
   2 ?    3.3   0.1      0.87   1.3e+02      19      48 ..     112     134 ..     108     149 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0019
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXX CS
                              SlyX  9 EiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkelees 53
                                      E+k++   + i+e  +++ +    id l+ q+++l++++++l+++
  gi|242398771|ref|YP_002994195.1| 37 EEKITLIMNRINEIENELPRIKVNIDTLKSQIQELRDEIEKLDKT 81
                                      677777777788888888888888888888888888888777654 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.87
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHT-X CS
                              SlyX  19 ieeLndvvaeqqqqidrlqrqlrllaerlk 48 
                                       i        e  q+++ +++++++++  lk
  gi|242398771|ref|YP_002994195.1| 112 IH-------ELKQDLEDIRKEIAQIRGDLK 134
                                       33.......444444444444444444443 PP

>> DUF4041  Domain of unknown function (DUF4041)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.2     0.002       0.3      22      44 ..      60      82 ..      48      87 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.002
                           DUF4041 22 nietlekRIeksfeainklgktm 44
                                      ni+tl+++I+ +++ i+kl kt+
  gi|242398771|ref|YP_002994195.1| 60 NIDTLKSQIQELRDEIEKLDKTI 82
                                      9******************9986 PP

>> FlxA  FlxA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   3.2     0.023       3.5      25      69 ..      13      58 ..       7      60 .. 0.79
   2 ?    7.1   6.4     0.035       5.3      14      69 ..      63     130 ..      57     135 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.023
                              FlxA 25 QiknlqkqLkelsesdeltkeekk..kqqqliqaQIqqlqaQIaqlq 69
                                      +i++l+  L+e  ++ e +ke+k+  +++ li + I+ +++++ +++
  gi|242398771|ref|YP_002994195.1| 13 EIEQLELALSEGNTQ-ENPKEQKEdeEKITLIMNRINEIENELPRIK 58
                                      567777777776666.77777777779**************998875 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.035
                              FlxA  14 gsasqiasLqkQiknlqkqLkelsesdeltkeekk............kqqqliqaQIqqlqaQIaqlq 69 
                                       + +sqi++L+ +i++l k +k++    e   +e +            k + ++++ +++++++Iaq+ 
  gi|242398771|ref|YP_002994195.1|  63 TLKSQIQELRDEIEKLDKTIKDVMMLYEVVSQEINpfrdldsenpivKEIHELKQDLEDIRKEIAQIR 130
                                       56899999999999999999998877555455455566665666677888888888889988888875 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   4.9     0.001      0.15      37      92 ..      31      86 ..       5      99 .. 0.73
   2 ?   -0.1   0.1       3.1   4.8e+02      52      89 ..     111     127 ..     100     136 .. 0.50

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.001
                           DUF3450 37 kkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeie 92
                                      k++++ +++ + + ++++++++el +++v  + l++++++++ ei++l++ i+++ 
  gi|242398771|ref|YP_002994195.1| 31 KEQKEDEEKITLIMNRINEIENELPRIKVNIDTLKSQIQELRDEIEKLDKTIKDVM 86
                                      33333344455678999999999999999999999999999999999999999874 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 3.1
                           DUF3450  52 eyralkeeleslevyneqlerlvasqeqeiasleeqie 89 
                                       e+++lk+ le+++                     ++i+
  gi|242398771|ref|YP_002994195.1| 111 EIHELKQDLEDIR---------------------KEIA 127
                                       2222222222222.....................2222 PP

>> RPW8  Arabidopsis broad-spectrum mildew resistance protein RPW8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   1.5       2.9   4.4e+02      94     132 ..       8      46 ..       2      62 .. 0.50
   2 ?    6.7   3.9     0.036       5.5      32      75 ..      42      85 ..      31     102 .. 0.64
   3 ?    8.8   0.3    0.0083       1.3      45      72 ..     106     133 ..      99     135 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 2.9
                              RPW8  94 yrYkkklkeLekslrkfvqvelqvqqvrdikellakmke 132
                                        + k ++++Le  l +    e   +q  d+ ++   m+ 
  gi|242398771|ref|YP_002994195.1|   8 KSEKDEIEQLELALSEGNTQENPKEQKEDEEKITLIMNR 46 
                                       444444444444444444444444444444444444443 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.036
                              RPW8 32 silkrLestleritPvvkeieklnkeldrpreeieeLkklLeka 75
                                       i++r+++  +++  +  +i++l+ ++++ r+eie+L k++++ 
  gi|242398771|ref|YP_002994195.1| 42 LIMNRINEIENELPRIKVNIDTLKSQIQELRDEIEKLDKTIKDV 85
                                      45555555555555555567777777777777777777777664 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0083
                              RPW8  45 tPvvkeieklnkeldrpreeieeLkklL 72 
                                       +P+vkei +l+++l+  r+ei +++  L
  gi|242398771|ref|YP_002994195.1| 106 NPIVKEIHELKQDLEDIRKEIAQIRGDL 133
                                       8*************99999**9998776 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.7       8.4   1.3e+03      24      42 ..       7      25 ..       3      44 .. 0.63
   2 ?   10.4   1.5    0.0037      0.56      27      61 ..      46      80 ..      30      83 .. 0.82
   3 ?    5.1   0.1      0.16        24      39      61 ..     109     131 ..     100     134 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 8.4
                                      HHHHHHHHHHHHHHHHHHH CS
                            bZIP_1 24 KqaeieeLerrvkaLekeN 42
                                      K+ e +e e+   aL++ N
  gi|242398771|ref|YP_002994195.1|  7 KKSEKDEIEQLELALSEGN 25
                                      5555555555555555555 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0037
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1 27 eieeLerrvkaLekeNksLkseleelkkevekLks 61
                                      +i+e e++   ++    +Lks+++el++e+ekL +
  gi|242398771|ref|YP_002994195.1| 46 RINEIENELPRIKVNIDTLKSQIQELRDEIEKLDK 80
                                      56777778888888888899999999999998866 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.16
                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  39 ekeNksLkseleelkkevekLks 61 
                                        ke ++Lk+ le ++ke+++ + 
  gi|242398771|ref|YP_002994195.1| 109 VKEIHELKQDLEDIRKEIAQIRG 131
                                       67788899999999999988775 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6  12.2     0.017       2.5      35      93 ..      39      97 ..       2     124 .. 0.55
   2 ?    1.3   0.1       3.1   4.7e+02      62      88 ..     110     136 ..     102     146 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.017
                                      HHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHH CS
                             DUF16 35 rLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetleliletLq 93
                                      +++ i ++++  ++++ +++ +++++  +i+el+ e+++ ++ ++ v    e++ + ++
  gi|242398771|ref|YP_002994195.1| 39 KITLIMNRINEIENELPRIKVNIDTLKSQIQELRDEIEKLDKTIKDVMMLYEVVSQEIN 97
                                      34444444444444444444444444444444444444444444444444444444333 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 3.1
                                       HHHHHHHHHHHHHHH.......HHHHH CS
                             DUF16  62 ekikelkveqkaqgeelnkvdetleli 88 
                                       ++i+elk++ +  ++e+ ++   l+l+
  gi|242398771|ref|YP_002994195.1| 110 KEIHELKQDLEDIRKEIAQIRGDLKLL 136
                                       467777777777777777666666665 PP

>> DLP_helical  Dynamin-like helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   7.1    0.0065      0.98      30     114 ..       2      85 ..       1     101 [. 0.77
   2 ?    4.2   0.1      0.14        21      84     112 ..     106     134 ..      87     139 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0065
                       DLP_helical  30 kdeyeklSh...IeeLqdateekikknggelalieetkksvirdvlerqlpeaeerleelekevekleesakrieke 103
                                       k++++k S    Ie+L+ a +e  +++ ++++  +e k+     +++++++e+e++l +++ +++ l+++ +++++e
  gi|242398771|ref|YP_002994195.1|   2 KEKFKKKSEkdeIEQLELALSEGNTQENPKEQKEDEEKI----TLIMNRINEIENELPRIKVNIDTLKSQIQELRDE 74 
                                       577888874333888888887776666666344444443....357889**************************** PP

                       DLP_helical 104 laelkkeieea 114
                                       +++l k i++ 
  gi|242398771|ref|YP_002994195.1|  75 IEKLDKTIKDV 85 
                                       *******9975 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.14
                       DLP_helical  84 eelekevekleesakriekelaelkkeie 112
                                       + + ke+++l++++++i+ke+a+++ +++
  gi|242398771|ref|YP_002994195.1| 106 NPIVKEIHELKQDLEDIRKEIAQIRGDLK 134
                                       34667777777777777777777776665 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8  11.1     0.015       2.3      22     100 ..       8      84 ..       1     104 [. 0.67
   2 ?    5.9   0.4      0.12        18      64      90 ..     106     132 ..      93     145 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.015
                            APG6_N  22 ekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeee 98 
                                       ++e+d+ e+ +  l + +++e+   +e +e ee++  + +  +e ++eL +++ + + l++++++l+ e e+l++  
  gi|242398771|ref|YP_002994195.1|   8 KSEKDEIEQLELALSEGNTQEN--PKEQKEDEEKITLIMNRINEIENELPRIKVNIDTLKSQIQELRDEIEKLDKTI 82 
                                       4455555555555555555554..35667777778888888888888888888888888888888888888887765 PP

                            APG6_N  99 er 100
                                       + 
  gi|242398771|ref|YP_002994195.1|  83 KD 84 
                                       54 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.12
                            APG6_N  64 eelleeLkelekereeleaelaaleee 90 
                                       +  ++e+ el++  e++++e+a+++  
  gi|242398771|ref|YP_002994195.1| 106 NPIVKEIHELKQDLEDIRKEIAQIRGD 132
                                       445566666666666666666665544 PP

>> Phlebovirus_NSM  Phlebovirus nonstructural protein NS-M
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   6.5    0.0011      0.17     168     259 ..       5      96 ..       1     100 [. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0011
                   Phlebovirus_NSM 168 iknqvlhseieqlknelqkkRndikrgqekrdakklveesmArvkdlkeelkiltdelsqikseiqilrkkikd.fe 243
                                        k++  ++eieql+  l+    +    +e+++ ++ +   m r++++ +el  +  +++ +ks+iq lr+ i +  +
  gi|242398771|ref|YP_002994195.1|   5 FKKKSEKDEIEQLELALSEGNTQ-ENPKEQKEDEEKITLIMNRINEIENELPRIKVNIDTLKSQIQELRDEIEKlDK 80 
                                       56666778999999999988777.5666666666667789******************************9966157 PP

                   Phlebovirus_NSM 244 tvvpAllsvAllsllv 259
                                       t+ + ++   ++s   
  gi|242398771|ref|YP_002994195.1|  81 TIKDVMMLYEVVSQEI 96 
                                       8888888888888765 PP

>> USP8_interact  USP8 interacting
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.8     0.044       6.6       5      46 ..      46      87 ..      34     104 .. 0.58
   2 ?    4.8   0.1      0.15        23      11      40 ..     110     139 ..     100     148 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.044
                     USP8_interact  5 lvqkqqqkiaelkkevaeqkqqlseqkrelellkeyiralrs 46
                                       +++ ++++ ++k ++++ k+q++e ++e+e l ++i+ + +
  gi|242398771|ref|YP_002994195.1| 46 RINEIENELPRIKVNIDTLKSQIQELRDEIEKLDKTIKDVMM 87
                                      344555555555666666666666666666655555544433 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.15
                     USP8_interact  11 qkiaelkkevaeqkqqlseqkrelellkey 40 
                                       ++i+elk+++++ ++++++ + +l+ll + 
  gi|242398771|ref|YP_002994195.1| 110 KEIHELKQDLEDIRKEIAQIRGDLKLLAYH 139
                                       7899********************999875 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   8.9     0.017       2.5       5      99 ..      45     133 ..      37     137 .. 0.61

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.017
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-TT.--EEEEETTEEEEE-HHHHHHHHH.HHHHHHHHHHH CS
                       Prefoldin_2   5 nkfqqlqqqlqqlaqqikqletqlkelelvleelellded.tkvyklvGdvlvkqdkeevkeeLe.erketlekeik 79 
                                       n+ ++++++l  ++ +i++l+ q++el +   e+e+ld++ ++v+     +l+++  +e+++  + ++++ + kei 
  gi|242398771|ref|YP_002994195.1|  45 NRINEIENELPRIKVNIDTLKSQIQELRD---EIEKLDKTiKDVM-----MLYEVVSQEINPFRDlDSENPIVKEIH 113
                                       66777777777777777777777777654...4444444422232.....455555555555444133444777777 PP

                                       HHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  80 tlekqleklekeleelkeel 99 
                                       +l++ le+++ke+++++  l
  gi|242398771|ref|YP_002994195.1| 114 ELKQDLEDIRKEIAQIRGDL 133
                                       77777777777777776665 PP

>> GrpE  GrpE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1  10.7    0.0064      0.97       7     105 ..      26     122 ..       3     153 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0064
                                       CTTTHHHHCCCCCCTTCHHHCTTSCCCCCCTTTTTTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC.. CS
                              GrpE   7 eeeeedeeeeleeeleelekevkelkekllrllaefenlrkrtekekeeakkfaiekfakdLLpvlDnleralksak 83 
                                        +e+ +e++e ee+++ + ++++e++++l r + +++ l+ + ++ ++e++k  + k +kd + +++  +  ++ ++
  gi|242398771|ref|YP_002994195.1|  26 TQENPKEQKEDEEKITLIMNRINEIENELPRIKVNIDTLKSQIQELRDEIEK--LDKTIKDVMMLYEVVSQEINPFR 100
                                       33444445555667999999****************************9987..78999****************** PP

                                       HHH-HHHHHHHHHHHHHHHHHH CS
                              GrpE  84 eneeekslleGvemtlkqllki 105
                                       + ++e+++++ ++  ++ l++i
  gi|242398771|ref|YP_002994195.1| 101 DLDSENPIVKEIHELKQDLEDI 122
                                       ******9999999999999887 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   1.5    0.0039       0.6       6      47 ..      43      84 ..      38     103 .. 0.71
   2 ?    5.9   0.1      0.13        20       5      33 ..     107     135 ..     102     145 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0039
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YabA  6 lfdkleeleeqleelleeleelkeelaelleenaeLelenek 47
                                      ++++++e+e++l +++ ++++lk++++el +e ++L    + 
  gi|242398771|ref|YP_002994195.1| 43 IMNRINEIENELPRIKVNIDTLKSQIQELRDEIEKLDKTIKD 84
                                      567777788888888888888888888877777777655444 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.13
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YabA   5 elfdkleeleeqleelleeleelkeelae 33 
                                        ++++++el+++le++ +e+++++ +l+ 
  gi|242398771|ref|YP_002994195.1| 107 PIVKEIHELKQDLEDIRKEIAQIRGDLKL 135
                                       57788888888888888888888877765 PP

>> Cnn_1N  Centrosomin N-terminal motif 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3  10.4      0.29        44      35      72 ..      33      81 ..       1      85 [. 0.74
   2 ?    8.6   0.3     0.014       2.1      36      67 ..     103     134 ..      85     138 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.29
                            Cnn_1N 35 e...........eqkeellkenielkveveslqkelkekkkllreaeka 72
                                      +             ++e+++e+  +kv++ +l+ +++e++++++++ k 
  gi|242398771|ref|YP_002994195.1| 33 QkedeekitlimNRINEIENELPRIKVNIDTLKSQIQELRDEIEKLDKT 81
                                      0445556666667888899999999999999999999999999888875 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.014
                            Cnn_1N  36 eqkeellkenielkveveslqkelkekkkllr 67 
                                       ++ + ++ke  elk+++e+ +ke+ + +  l+
  gi|242398771|ref|YP_002994195.1| 103 DSENPIVKEIHELKQDLEDIRKEIAQIRGDLK 134
                                       6677789999**************99887765 PP

>> DUF2205  Short coiled-coil protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   5.3    0.0032      0.48      11      69 ..      32      91 ..      22      96 .. 0.85
   2 ?    3.1   0.5      0.64        98      21      45 ..     108     132 ..      92     139 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0032
                           DUF2205 11 eklerearerLqq.qakeLqssLqaLaervdeVkeehdKLesenrfLqqYIgdLmstskv 69
                                      e+ e e++ +L+  +++e+ + L  +   +d  k+  + L+ e + L + I d m   +v
  gi|242398771|ref|YP_002994195.1| 32 EQKEDEEKITLIMnRINEIENELPRIKVNIDTLKSQIQELRDEIEKLDKTIKDVMMLYEV 91
                                      67778888888755***************************************9976555 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.64
                           DUF2205  21 LqqqakeLqssLqaLaervdeVkee 45 
                                       + + ++eL++ L+++ + + +++ +
  gi|242398771|ref|YP_002994195.1| 108 IVKEIHELKQDLEDIRKEIAQIRGD 132
                                       6678899999999999999988866 PP

>> GTP-bdg_M  GTP-binding GTPase Middle Region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.9      0.16        25      48      76 ..      37      65 ..       6      67 .. 0.83
   2 ?    5.7   0.6      0.15        23      51      71 ..      61      81 ..      55      86 .. 0.78
   3 ?    5.7   0.1      0.15        22      54      75 ..     108     129 ..     103     138 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.16
                                      HHHHHHHHHHHHHHHHHHHHHHHHHH... CS
                         GTP-bdg_M 48 eldrrlireriaklkkeLekvkkkrelqr 76
                                      e +  li +ri+++++eL ++k + ++++
  gi|242398771|ref|YP_002994195.1| 37 EEKITLIMNRINEIENELPRIKVNIDTLK 65
                                      56667899***********9998877665 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.15
                                      HHHHHHHHHHHHHHHHHHHHH CS
                         GTP-bdg_M 51 rrlireriaklkkeLekvkkk 71
                                        +++ +i++l+ e+ek++k+
  gi|242398771|ref|YP_002994195.1| 61 IDTLKSQIQELRDEIEKLDKT 81
                                      567889999999999999886 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.15
                                       HHHHHHHHHHHHHHHHHHHH.. CS
                         GTP-bdg_M  54 ireriaklkkeLekvkkkrelq 75 
                                       i + i++lk++Le+++k+ ++ 
  gi|242398771|ref|YP_002994195.1| 108 IVKEIHELKQDLEDIRKEIAQI 129
                                       5567888888888888775554 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   9.1    0.0092       1.4     396     482 ..      11      80 ..       1     103 [. 0.40
   2 ?    8.3   1.8    0.0051      0.78     408     468 ..      65     134 ..      61     153 .. 0.57

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0092
                            AAA_13 396 kkklelhlveeleseldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeeinkeLkafGl 472
                                       k+++e+ +              ++  e + +++ ke+ke+e+++  + ++i+e+e++l  +k  ++ + +++++   
  gi|242398771|ref|YP_002994195.1|  11 KDEIEQLE--------------LALSEGNTQENPKEQKEDEEKITLIMNRINEIENELPRIKVNIDTLKSQIQEL-- 71 
                                       22222222..............22333333333344444444444444444444444444444444444433333.. PP

                            AAA_13 473 geleLkfeee 482
                                        ++e+++ ++
  gi|242398771|ref|YP_002994195.1|  72 -RDEIEKLDK 80 
                                       .222222222 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0051
                            AAA_13 408 eseldeykkkykklekaieklekelkeeeaelkkleee.........ikeLekqlrdekpaaeeinkeLk 468
                                       +s+++e+ ++++kl+k+i+++    +  ++e++  ++          i eL++ l+d+++ +++i   Lk
  gi|242398771|ref|YP_002994195.1|  65 KSQIQELRDEIEKLDKTIKDVMMLYEVVSQEINPFRDLdsenpivkeIHELKQDLEDIRKEIAQIRGDLK 134
                                       4555555555555555555555544444444443333222233333388888888888888888876665 PP

>> DASH_Dad4  DASH complex subunit Dad4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   4.0     0.058       8.8      13      51 ..      54      92 ..      27      95 .. 0.90
   2 ?    2.0   0.0       1.4   2.1e+02      18      40 ..     110     125 ..     106     135 .. 0.60

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.058
                         DASH_Dad4 13 LsRIiknvekLnesvvelnkeleeinkkNknvelvsqlw 51
                                      L RI  n++ L ++++el  e+e+  k  k+v ++ +++
  gi|242398771|ref|YP_002994195.1| 54 LPRIKVNIDTLKSQIQELRDEIEKLDKTIKDVMMLYEVV 92
                                      78999*********************9999998887765 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 1.4
                         DASH_Dad4  18 knvekLnesvvelnkeleeinkk 40 
                                       k        ++el++ le+i k+
  gi|242398771|ref|YP_002994195.1| 110 K-------EIHELKQDLEDIRKE 125
                                       4.......456666666666554 PP

>> EMP24_GP25L  emp24/gp25L/p24 family/GOLD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   5.1    0.0044      0.67      90     156 ..      16      83 ..       2      93 .. 0.72
   2 ?    2.1   0.2         1   1.6e+02     112     138 ..     104     130 ..      83     134 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0044
                       EMP24_GP25L  90 kvsfdievgseasd.ykdsakkekletleselkkleekldsikreqkylrereerlrdtnestnsrvv 156
                                       ++++ +  g+ +++ +++  ++ek++ + ++++++e+ l  ik +++ l+ + ++lrd +e++ + + 
  gi|242398771|ref|YP_002994195.1|  16 QLELALSEGNTQENpKEQKEDEEKITLIMNRINEIENELPRIKVNIDTLKSQIQELRDEIEKLDKTIK 83 
                                       44555555543333245555599999999999999999999999999999999999999999887765 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 1
                       EMP24_GP25L 112 kletleselkkleekldsikreqkylr 138
                                       + +++ +e+++l++ l++i++e+  +r
  gi|242398771|ref|YP_002994195.1| 104 SENPIVKEIHELKQDLEDIRKEIAQIR 130
                                       457888999999999999999987766 PP

>> Med21  Subunit 21 of Mediator complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6  10.6    0.0067         1      55     135 ..      16      96 ..       2     102 .. 0.84
   2 ?    4.2   0.5      0.31        47      99     125 ..     104     130 ..     101     139 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0067
                             Med21  55 eekeepepdspeefaatqrelardlilkeqqIeyLIssLPgigsseeeqeerikeLeeelreveeereekvkekeel 131
                                       + + + ++ + +e  ++q+e  +++ l + +I+ + ++LP i+++ ++ + +i+eL +e+++  +  ++++   e +
  gi|242398771|ref|YP_002994195.1|  16 QLELALSEGNTQENPKEQKEDEEKITLIMNRINEIENELPRIKVNIDTLKSQIQELRDEIEKLDKTIKDVMMLYEVV 92 
                                       4555666777888889999999******************************************9999998888877 PP

                             Med21 132 lkkv 135
                                        +++
  gi|242398771|ref|YP_002994195.1|  93 SQEI 96 
                                       7776 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.31
                             Med21  99 seeeqeerikeLeeelreveeereekv 125
                                       se+  +++i eL+++l+++++e ++ +
  gi|242398771|ref|YP_002994195.1| 104 SENPIVKEIHELKQDLEDIRKEIAQIR 130
                                       66667899************9988765 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   6.3    0.0089       1.3     125     220 ..      38     131 ..      12     141 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0089
                              CorA 125 ellekleeeldeledel.edstkkeilrelaq.lrrrlvklrralapnrevlkrllakaddkllddedkeylrdlld 199
                                       e +  +  +++e+e+el + + + + l++ +q lr ++ kl + +++ + ++ ++++++ ++  d +     + +  
  gi|242398771|ref|YP_002994195.1|  38 EKITLIMNRINEIENELpRIKVNIDTLKSQIQeLRDEIEKLDKTIKDVMMLY-EVVSQEINPFRDLDS---ENPIVK 110
                                       6678899999*******95555555555544449999*****9999999999.777767777777777...999999 PP

                              CorA 200 elerllemlealrerleslqd 220
                                       e++ l ++le +r+ + +++ 
  gi|242398771|ref|YP_002994195.1| 111 EIHELKQDLEDIRKEIAQIRG 131
                                       999999999999999988875 PP

>> YgaB  YgaB-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   2.4    0.0027      0.41      23      66 ..      44      92 ..      39     102 .. 0.76
   2 ?    6.6   0.6     0.065       9.9      30      57 ..     109     134 ..      99     138 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0027
                              YgaB 23 lerCqeiekeLlklek.....eaklesiqeeikrkkkeLkeiqkvFekQ 66
                                      ++r +eie+eL +++      +++++++++ei+++ k +k++  ++e  
  gi|242398771|ref|YP_002994195.1| 44 MNRINEIENELPRIKVnidtlKSQIQELRDEIEKLDKTIKDVMMLYEVV 92
                                      78999*****977653122226788899999999999999999888754 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.065
                              YgaB  30 ekeLlklekeaklesiqeeikrkkkeLk 57 
                                        ke+++l+    le+i++ei++ + +Lk
  gi|242398771|ref|YP_002994195.1| 109 VKEIHELK--QDLEDIRKEIAQIRGDLK 134
                                       44444444..457888888888888876 PP

>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   8.4     0.024       3.7      58     114 ..      26      83 ..       1     131 [. 0.46

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.024
                        V_ATPase_I  58 ea.eesleapeekeldeleeelekleeelkelnenleklkkelnelvelkavlekake 114
                                       ++ + ++++++e+++  + ++++++e+el +++ n ++lk++ +el ++ + l k+ +
  gi|242398771|ref|YP_002994195.1|  26 TQeNPKEQKEDEEKITLIMNRINEIENELPRIKVNIDTLKSQIQELRDEIEKLDKTIK 83 
                                       2122233334444555555666666666666666666666666555544444433322 PP

>> MIP-T3_C  Microtubule-binding protein MIP-T3 C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   9.9     0.037       5.6      78     152 ..      12      87 ..       8      91 .. 0.74
   2 ?    5.1   0.2      0.13        20     112     138 ..     105     131 ..      99     136 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.037
                          MIP-T3_C  78 dDidsMqrELemWrseyr.qqaeelaeerrateealeplkaqlaeleeaIkdqkekisnvrakilkNeakiqkllk 152
                                       d i+ ++  L     +++ ++++e++e+ ++ ++ +++++++l  ++ +I   k++i+++r +i k ++ i+ +++
  gi|242398771|ref|YP_002994195.1|  12 DEIEQLELALSEGNTQENpKEQKEDEEKITLIMNRINEIENELPRIKVNIDTLKSQIQELRDEIEKLDKTIKDVMM 87 
                                       6666666666665444440344444444566689999999999999999999999999999999999999987665 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.13
                          MIP-T3_C 112 leplkaqlaeleeaIkdqkekisnvra 138
                                        +p+ +++ el++ ++d +++i ++r 
  gi|242398771|ref|YP_002994195.1| 105 ENPIVKEIHELKQDLEDIRKEIAQIRG 131
                                       578899999999999999999999986 PP

>> DASH_Dad2  DASH complex subunit Dad2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   1.1       2.1   3.2e+02      63      89 ..      18      49 ..       4      59 .. 0.45
   2 ?   11.2   0.4    0.0025      0.37      13      60 ..      53      97 ..      43     101 .. 0.84
   3 ?   -0.3   0.0       9.4   1.4e+03      23      39 ..     114     130 ..     100     138 .. 0.62

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 2.1
                         DASH_Dad2 63 slkllqkaeeeaeeeeedeeeeeeee.........p 89
                                      +l+l    e+ +++e+ +e++e+ee+         +
  gi|242398771|ref|YP_002994195.1| 18 ELALS---EG-NTQENPKEQKEDEEKitlimnrinE 49
                                      44443...22.2222222222222223344444444 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.0025
                         DASH_Dad2 13 aLkqlrdlsdslakqleeLeeklstladgteavasVlanWqnvlrais 60
                                      +L +++   d+l++q++eL +++++l++   ++++V+  ++ v + i+
  gi|242398771|ref|YP_002994195.1| 53 ELPRIKVNIDTLKSQIQELRDEIEKLDK---TIKDVMMLYEVVSQEIN 97
                                      4777888899***************985...79999999999999987 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 9.4
                         DASH_Dad2  23 slakqleeLeeklstla 39 
                                       +l++ le + +++++++
  gi|242398771|ref|YP_002994195.1| 114 ELKQDLEDIRKEIAQIR 130
                                       45555555555555544 PP

>> DUF1192  Protein of unknown function (DUF1192)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1       7.1   1.1e+03      33      44 ..      11      22 ..       9      29 .. 0.81
   2 ?    1.0   0.1         3   4.5e+02      26      43 ..      44      61 ..      40      63 .. 0.84
   3 ?   10.5   0.4    0.0032      0.48      21      44 ..      60      83 ..      58      86 .. 0.89
   4 ?    4.7   0.9       0.2        30      22      42 ..     112     132 ..     110     136 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 7.1
                           DUF1192 33 eaEIaRleaaia 44
                                      ++EI+ le a++
  gi|242398771|ref|YP_002994195.1| 11 KDEIEQLELALS 22
                                      689**9999886 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 3
                           DUF1192 26 eerIalLeaEIaRleaai 43
                                       +rI + e E  R++  i
  gi|242398771|ref|YP_002994195.1| 44 MNRINEIENELPRIKVNI 61
                                      589********9999776 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.0032
                           DUF1192 21 SveELeerIalLeaEIaRleaaia 44
                                      +++ L+  I++L++EI++l+++i+
  gi|242398771|ref|YP_002994195.1| 60 NIDTLKSQIQELRDEIEKLDKTIK 83
                                      5888****************9997 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.2
                           DUF1192  22 veELeerIalLeaEIaRleaa 42 
                                       ++EL++  ++ ++EIa ++  
  gi|242398771|ref|YP_002994195.1| 112 IHELKQDLEDIRKEIAQIRGD 132
                                       78**************99866 PP

>> 5_nucleotid  5' nucleotidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   3.4      0.14        21     347     399 ..      31      83 ..       2      87 .. 0.50
   2 ?    9.9   0.7     0.002       0.3     330     399 ..      68     134 ..      47     141 .. 0.62

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.14
                                       HHHHHHHHHHHHHHHHHHHHHHHT.TTHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       5_nucleotid 347 eeleelekleelledelkklksseeeskekleeleedleelkkeirelreelk 399
                                       +e +e e++ +l+ +++++++ +  + k + ++l+++++el++ei++l +++k
  gi|242398771|ref|YP_002994195.1|  31 KEQKEDEEKITLIMNRINEIENELPRIKVNIDTLKSQIQELRDEIEKLDKTIK 83 
                                       33333333333333333333333323555555666666666666666655555 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.002
                                       -TTHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHHHHHT.T.THHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       5_nucleotid 330 vpELeeElevleekkekeeleelekleelledelkklksseee.skekleeleedleelkkeirelreelk 399
                                       ++EL++E+e l ++  k+ +   e   ++++  +++l+s+  +   ++ +el++dle+++kei+++r +lk
  gi|242398771|ref|YP_002994195.1|  68 IQELRDEIEKLDKTI-KDVMMLYEVVSQEINP-FRDLDSE--NpIVKEIHELKQDLEDIRKEIAQIRGDLK 134
                                       556666666555544.2222222233333333.4455555..34899999**************9998776 PP

>> DUF5320  Family of unknown function (DUF5320)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.9      0.15        23      63      98 ..      28      63 ..       4      64 .. 0.85
   2 ?    6.0   0.4      0.16        25      74      98 ..      60      84 ..      58      85 .. 0.88
   3 ?    3.5   0.0      0.97   1.5e+02      79      98 ..     109     128 ..      88     133 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.15
                           DUF5320 63 aaetaeaskeeekelLeeqaeaLeeeleaikkrlke 98
                                      ++++++++ ee+++l+ ++++ +e+el  ik ++++
  gi|242398771|ref|YP_002994195.1| 28 ENPKEQKEDEEKITLIMNRINEIENELPRIKVNIDT 63
                                      57788999999999****************988876 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.16
                           DUF5320 74 ekelLeeqaeaLeeeleaikkrlke 98
                                      +++ L++q++ L++e+e+++k +k+
  gi|242398771|ref|YP_002994195.1| 60 NIDTLKSQIQELRDEIEKLDKTIKD 84
                                      6789****************99986 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.97
                           DUF5320  79 eeqaeaLeeeleaikkrlke 98 
                                        +++  L++ le+i+k++++
  gi|242398771|ref|YP_002994195.1| 109 VKEIHELKQDLEDIRKEIAQ 128
                                       56788999999999999986 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   7.9   0.00042     0.063       3      49 ..      37      83 ..      35      86 .. 0.96
   2 ?    2.3   0.2       1.3     2e+02      22      45 ..     114     130 ..     104     137 .. 0.49

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00042
                              XhlA  3 kerlerietkldnleervdkleekaaeaeekiknleedlkklesnqk 49
                                      +e+++ i ++++++e+++ +++ + ++ +++i++l ++++kl +++k
  gi|242398771|ref|YP_002994195.1| 37 EEKITLIMNRINEIENELPRIKVNIDTLKSQIQELRDEIEKLDKTIK 83
                                      699****************************************9998 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 1.3
                              XhlA  22 kleekaaeaeekiknleedlkkle 45 
                                       +        ++ ++ + ++++++ 
  gi|242398771|ref|YP_002994195.1| 114 E-------LKQDLEDIRKEIAQIR 130
                                       3.......3333344444444443 PP

>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   9.8      0.24        36       5      57 ..       2      54 ..       1      57 [. 0.89
   2 ?    7.6   0.6      0.03       4.5      10      33 ..      61      84 ..      56      96 .. 0.75
   3 ?    4.7   0.2      0.23        35      16      32 ..     111     127 ..     101     138 .. 0.56

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.24
                      ABC_tran_CTD  5 keqreleeleaeIeaLEeeiaeleaeladpelysdpeklaelsaeleeleaeL 57
                                      ke+++ +   +eIe+LE  ++e +++ +  e  +d+ek++ ++++++e+e+eL
  gi|242398771|ref|YP_002994195.1|  2 KEKFKKKSEKDEIEQLELALSEGNTQENPKEQKEDEEKITLIMNRINEIENEL 54
                                      566666666899****************99988999***************99 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.03
                      ABC_tran_CTD 10 leeleaeIeaLEeeiaeleaelad 33
                                      +++l ++I++L  ei++l++ + d
  gi|242398771|ref|YP_002994195.1| 61 IDTLKSQIQELRDEIEKLDKTIKD 84
                                      567778888888888888777665 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.23
                      ABC_tran_CTD  16 eIeaLEeeiaeleaela 32 
                                       eI +L ++++++ +e+a
  gi|242398771|ref|YP_002994195.1| 111 EIHELKQDLEDIRKEIA 127
                                       33333333333333333 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3  12.7       0.1        15     125     179 ..      33      87 ..       3     139 .. 0.54

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.1
                            DUF724 125 krkleeeidelekkilelerqlallkekkeaadkeiarlkseaekleeeledveq 179
                                       +++ ee+i  + ++i e+e++l ++k + ++ +++i +l+ e ekl+++++dv  
  gi|242398771|ref|YP_002994195.1|  33 QKEDEEKITLIMNRINEIENELPRIKVNIDTLKSQIQELRDEIEKLDKTIKDVMM 87 
                                       3333444444444444444444444444444444444444444444444444432 PP

>> Com_YlbF  Control of competence regulator ComK, YlbF/YmcA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   5.2       1.9   2.9e+02      60      99 ..       8      50 ..       1      54 [. 0.63
   2 ?   12.6   3.2    0.0011      0.16      33      99 ..      67     129 ..      56     132 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 1.9
                                      HHHHHHHHHHHHHH...HTSHHHHHHHHHHHHHHHHHHHHHHH CS
                          Com_YlbF 60 eeekkelqelkeel...dknplvkeyleaeqelnellqevnki 99
                                      ++ek+e+++l+  l   +++++ ke +e e+++  +++++n+i
  gi|242398771|ref|YP_002994195.1|  8 KSEKDEIEQLELALsegNTQENPKEQKEDEEKITLIMNRINEI 50
                                      2333355555555555588888888888888888888888876 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.0011
                                       HHHHHHHHHHHHHHHHHHHHHTT----HHHHHHHHHHHHHHHTSHHHHHHHHHHHHHHHHHHHHHHH CS
                          Com_YlbF  33 elqklikefkklqkelqekqmkgeelkeeekkelqelkeeldknplvkeyleaeqelnellqevnki 99 
                                       ++q+l +e++kl k++ +++m +    e   +e++   +   +np+vke  e +q+l+++ +e+ +i
  gi|242398771|ref|YP_002994195.1|  67 QIQELRDEIEKLDKTIKDVMMLY----EVVSQEINPFRDLDSENPIVKEIHELKQDLEDIRKEIAQI 129
                                       67788888888888887777554....555557888888889*******************999887 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.9       3.7   5.6e+02      37      70 ..      13      51 ..       2      58 .. 0.48
   2 ?   10.7   1.9    0.0046       0.7      27      98 ..      57     128 ..      48     131 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 3.7
                      Occludin_ELL 37 kfseLe.....relkelkegskeykkieeeilqeykklk 70
                                      ++++Le      +++e ++++ke ++ +  i+++ ++++
  gi|242398771|ref|YP_002994195.1| 13 EIEQLElalseGNTQENPKEQKEDEEKITLIMNRINEIE 51
                                      444555222212333334444444444445555555554 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0046
                      Occludin_ELL  27 lhaeleevskkfseLerelkelkegskeykkieeeilqeykklkkdpeyqekkkrceyLkekLshiKklike 98 
                                       ++ ++++++++++eL++e+++l+++ k +  + e + qe + ++   +     k++++Lk+ L+ i+k i++
  gi|242398771|ref|YP_002994195.1|  57 IKVNIDTLKSQIQELRDEIEKLDKTIKDVMMLYEVVSQEINPFRDLDSENPIVKEIHELKQDLEDIRKEIAQ 128
                                       556788899999999999999999999888888888888888877455555556778899999999998875 PP

>> ISG65-75  Invariant surface glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   1.6      0.04       6.1      52     113 ..      36      97 ..      28     114 .. 0.83
   2 ?    3.1   0.1      0.31        47      51      92 ..     114     155 ..     107     156 .] 0.86

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.04
                          ISG65-75  52 adyllketkdklayienakekvdyyvekleslleeakekgtltesdaeklkkaceeAkaknk 113
                                       +++ +  + ++++ ien++ +++   + l+s ++e + + ++ ++++++++ ++e + ++++
  gi|242398771|ref|YP_002994195.1|  36 DEEKITLIMNRINEIENELPRIKVNIDTLKSQIQELRDEIEKLDKTIKDVMMLYEVVSQEIN 97 
                                       45555667789999999999999999999999999999999999999999999998888776 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.31
                          ISG65-75  51 tadyllketkdklayienakekvdyyvekleslleeakekgt 92 
                                       + +++l+++++++a+i  +++ + y+  +l +++ ea  +g+
  gi|242398771|ref|YP_002994195.1| 114 ELKQDLEDIRKEIAQIRGDLKLLAYHGVDLDKIIYEAISEGE 155
                                       457899**************************9999877765 PP

>> PCRF  PCRF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   9.0      0.14        22       4      98 ..      46     104 ..       3     149 .. 0.44

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.14
                                       HHTTTTTST.-GGGTTT..GGGSSSTTHHHHHTHHHHHHHHHHHHHTTTHHH...HT....-S-..-GGGTHHHHHH CS
                              PCRF   4 eleelekklsdpevwed..qekakklskelaeleeivealeeleealedleeakelleedeelaelaeeeleeleke 78 
                                       +++e+e++l + +v  d  ++++++l  e+++l+++++++                                     
  gi|242398771|ref|YP_002994195.1|  46 RINEIENELPRIKVNIDtlKSQIQELRDEIEKLDKTIKDVMM----------------------------------- 87 
                                       223333333222222111122333333333333332222222................................... PP

                                       HHHH..HHHHHT-..SSSTT CS
                              PCRF  79 leeleeelkklLlpkdende 98 
                                          l e +++ + p    d+
  gi|242398771|ref|YP_002994195.1|  88 ---LYEVVSQEINPFRDLDS 104
                                       ...22222222222222222 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 ?    0.4   0.7       4.2   6.4e+02      56      79 ..       4      27 ..       1      30 [. 0.70
   2 ?   12.5   3.0   0.00076      0.12      50     102 ..      31      83 ..      24      88 .. 0.91
   3 ?    0.8   0.1       3.1   4.8e+02      35      51 ..     112     128 ..     100     139 .. 0.49

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 4.2
                             DHR10 56 kkklkelrdaleekeielrelerk 79
                                      k k k+ +d++e++e  l+e +++
  gi|242398771|ref|YP_002994195.1|  4 KFKKKSEKDEIEQLELALSEGNTQ 27
                                      556777888888888887776666 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00076
                             DHR10  50 akleeakkklkelrdaleekeielrelerkeerlqrqlenaeeklerlreqae 102
                                       ++++e ++k++  +++++e e+el  ++ +++ l+ q++  ++++e+l ++ +
  gi|242398771|ref|YP_002994195.1|  31 KEQKEDEEKITLIMNRINEIENELPRIKVNIDTLKSQIQELRDEIEKLDKTIK 83 
                                       57899999****************************************99876 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 3.1
                             DHR10  35 lrsciklleeieaelak 51 
                                       ++++ + le+i +e+a+
  gi|242398771|ref|YP_002994195.1| 112 IHELKQDLEDIRKEIAQ 128
                                       33333333333333333 PP

>> Med4  Vitamin-D-receptor interacting Mediator subunit 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   1.2      0.45        69      36      60 ..      31      55 ..       8      64 .. 0.88
   2 ?   10.8   0.9    0.0018      0.28      29      50 ..      66      87 ..      61     106 .. 0.84
   3 ?    0.1   0.2       3.5   5.3e+02      30      56 ..     111     130 ..      99     146 .. 0.58

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.45
                              Med4 36 aeveslDekikeivksLkeyekeLk 60
                                      +e+++ +eki  i++ ++e+e+eL 
  gi|242398771|ref|YP_002994195.1| 31 KEQKEDEEKITLIMNRINEIENELP 55
                                      7899999999999999999999996 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0018
                              Med4 29 arilqLraeveslDekikeivk 50
                                       +i++Lr e+e+lD+ ik+++ 
  gi|242398771|ref|YP_002994195.1| 66 SQIQELRDEIEKLDKTIKDVMM 87
                                      68*****************986 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 3.5
                              Med4  30 rilqLraeveslDekikeivksLkeye 56 
                                       +i +L++  e   ++i +i       +
  gi|242398771|ref|YP_002994195.1| 111 EIHELKQDLEDIRKEIAQI-------R 130
                                       3333333333333333333.......3 PP

>> BST2  Bone marrow stromal antigen 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   3.0       5.3     8e+02      47      88 ..      14      53 ..       2      62 .. 0.64
   2 ?    8.7   3.5     0.017       2.6      50      85 ..      50      85 ..      32      91 .. 0.79
   3 ?    3.8   0.2      0.58        89      73      90 ..     110     127 ..     100     128 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 5.3
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              BST2 47 vvtLkasLekekaqsqkqqakvqelqgeikkLnqkLqdaeae 88
                                      +++L+ +L + ++q++ +  + +e +++i+ + +++++ e e
  gi|242398771|ref|YP_002994195.1| 14 IEQLELALSEGNTQENPK--EQKEDEEKITLIMNRINEIENE 53
                                      566777777777775544..4555566666666666665555 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.017
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              BST2 50 LkasLekekaqsqkqqakvqelqgeikkLnqkLqda 85
                                      +++ L + k +    ++++qel++ei+kL++ ++d 
  gi|242398771|ref|YP_002994195.1| 50 IENELPRIKVNIDTLKSQIQELRDEIEKLDKTIKDV 85
                                      55666666777777889***************9986 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.58
                                       HHHHHHHHHHHHHHHHCC CS
                              BST2  73 geikkLnqkLqdaeaeve 90 
                                       +ei++L+q L+d ++e+ 
  gi|242398771|ref|YP_002994195.1| 110 KEIHELKQDLEDIRKEIA 127
                                       7999******99999875 PP

>> DUF4988  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1       5.5   8.4e+02      23      53 ..      11      41 ..       3      47 .. 0.60
   2 ?    8.6   1.8    0.0087       1.3       3      40 ..      52      89 ..      43     114 .. 0.70
   3 ?    1.1   0.1       1.8   2.7e+02       6      29 ..     113     136 ..     108     154 .. 0.56

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 5.5
                           DUF4988 23 ndniealkklleegkviteveensdgsyvlt 53
                                      +d+ie+l+  l+eg++  + +e+++ + ++t
  gi|242398771|ref|YP_002994195.1| 11 KDEIEQLELALSEGNTQENPKEQKEDEEKIT 41
                                      4556666555566666666666666555555 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0087
                           DUF4988  3 ddvndlkdrvaaleeqvkelndniealkklleegkvit 40
                                      +++  +k  + +l++q++el d+ie+l k +++  ++ 
  gi|242398771|ref|YP_002994195.1| 52 NELPRIKVNIDTLKSQIQELRDEIEKLDKTIKDVMMLY 89
                                      55566666666677777777777766666554444444 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 1.8
                           DUF4988   6 ndlkdrvaaleeqvkelndnieal 29 
                                        +lk+  + + +++ ++  +++ l
  gi|242398771|ref|YP_002994195.1| 113 HELKQDLEDIRKEIAQIRGDLKLL 136
                                       555555555555555555555444 PP

>> DUF4446  Protein of unknown function (DUF4446)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   1.0       1.9   2.9e+02      29      74 ..       3      53 ..       1      58 [. 0.42
   2 ?    7.7   2.1     0.022       3.4      39      85 ..      46      92 ..      29     106 .. 0.77
   3 ?    3.6   0.1       0.4        60      51      76 ..     109     134 ..     102     145 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 1.9
                           DUF4446 29 kkykklmkgkdgksleellkekleeveelkeesee.......lekeieeleek 74
                                      +k+kk  ++++ ++le +l+e  ++  e  +e++e       ++++i+e+e++
  gi|242398771|ref|YP_002994195.1|  3 EKFKKKSEKDEIEQLELALSEGNTQ--ENPKEQKEdeekitlIMNRINEIENE 53
                                      4455555555555555555443222..22222222001233355555555555 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.022
                           DUF4446 39 dgksleellkekleeveelkeeseelekeieeleeklkkslqkvglv 85
                                      + +++e+ l +   ++++lk++ +el++eie+l++++k  +  +++v
  gi|242398771|ref|YP_002994195.1| 46 RINEIENELPRIKVNIDTLKSQIQELRDEIEKLDKTIKDVMMLYEVV 92
                                      56788899999999999999999999999999999998877666665 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.4
                           DUF4446  51 leeveelkeeseelekeieeleeklk 76 
                                       ++e++elk++ e+++kei++++ +lk
  gi|242398771|ref|YP_002994195.1| 109 VKEIHELKQDLEDIRKEIAQIRGDLK 134
                                       67899999999999999999987776 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0  11.7      0.21        31     348     415 ..       9      75 ..       1      98 [. 0.50
   2 ?   13.4   3.0   0.00015     0.022     336     410 ..      58     135 ..      55     150 .. 0.47

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.21
                              FapA 348 eleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeeleskkeea 415
                                       + ++e+e+l+ ++++ +  +++++ ++e +e++  + +  +++++el  ++ ++++lk+++++ ++e+
  gi|242398771|ref|YP_002994195.1|   9 SEKDEIEQLELALSEGNT-QENPKEQKEDEEKITLIMNRINEIENELPRIKVNIDTLKSQIQELRDEI 75 
                                       335555555555444444.3334444555555555555555555555555555555555555552221 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00015
                              FapA 336 keklkeleeeleeleeeleklkkkikklpklka...ekqlesekkeqlkklletkeklkeeleeleeelkelkeele 409
                                       k +++ l+ +++el++e+ekl+k+ik + +l +   ++  + + +++ + + ++  +lk++le++++e++++   l+
  gi|242398771|ref|YP_002994195.1|  58 KVNIDTLKSQIQELRDEIEKLDKTIKDVMMLYEvvsQEINPFRDLDSENPIVKEIHELKQDLEDIRKEIAQIRGDLK 134
                                       44445555555555555555555544444422211012233344455555555555555555555555555555554 PP

                              FapA 410 s 410
                                        
  gi|242398771|ref|YP_002994195.1| 135 L 135
                                       4 PP

>> WD40_alt  Alternative WD40 repeat motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1       6.7     1e+03      19      30 ..      46      57 ..      38      62 .. 0.81
   2 ?   11.1   0.9    0.0018      0.27      14      36 ..      62      84 ..      59      96 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 6.7
                          WD40_alt 19 rvseLeeEVrtL 30
                                      r+ e e+E+  +
  gi|242398771|ref|YP_002994195.1| 46 RINEIENELPRI 57
                                      89999*999766 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0018
                          WD40_alt 14 eqlkvrvseLeeEVrtLrKInkd 36
                                      + lk+++ eL +E++ L K  kd
  gi|242398771|ref|YP_002994195.1| 62 DTLKSQIQELRDEIEKLDKTIKD 84
                                      78*****************9998 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   9.0      0.16        25      88     121 ..      38      71 ..       5      85 .. 0.71
   2 ?    2.9   0.2      0.81   1.2e+02      91     118 ..      69      96 ..      67     102 .. 0.57
   3 ?    3.6   0.3      0.51        78       3      27 ..     110     134 ..     108     139 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.16
                           DUF5082  88 elidaieeEIerLenqiseaqgvldtlqsqlnsl 121
                                       e i  i++ I+++en++   + ++dtl+sq+++l
  gi|242398771|ref|YP_002994195.1|  38 EKITLIMNRINEIENELPRIKVNIDTLKSQIQEL 71 
                                       4455577777888888888888888888888777 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.81
                           DUF5082  91 daieeEIerLenqiseaqgvldtlqsql 118
                                       +++ +EIe+L ++i++  +  +  ++++
  gi|242398771|ref|YP_002994195.1|  69 QELRDEIEKLDKTIKDVMMLYEVVSQEI 96 
                                       4556666666666666555555555554 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.51
                           DUF5082   3 tkisklqaqiaelrseiaaleekIe 27 
                                       ++i +l+++ ++ r+eia++  +++
  gi|242398771|ref|YP_002994195.1| 110 KEIHELKQDLEDIRKEIAQIRGDLK 134
                                       5788888888888888888877665 PP

>> Tropomyosin_1  Tropomyosin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   7.9      0.84   1.3e+02      44      90 ..       7      55 ..       3      60 .. 0.73
   2 ?    7.7  11.3     0.024       3.6      10      97 ..      34     127 ..      32     137 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.84
                     Tropomyosin_1 44 nqqleeevekleeklkeakekaeesekkktnne..altrkiqlLEeele 90
                                       +   +e+e+le +l+e +++ + +e+k+ +     +  +i+ +E+el 
  gi|242398771|ref|YP_002994195.1|  7 KKSEKDEIEQLELALSEGNTQENPKEQKEDEEKitLIMNRINEIENELP 55
                                      4555689999999999988887777766655546566788899999885 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.024
                     Tropomyosin_1  10 eeaqekaeeleekvKeleqenlekeqeiksLtkknqqleeevekleeklkeakekaeesekk.....ktnne.altr 80 
                                        e  ek   + +++ e e+e  +   +i  L+ ++q+l +e+ekl++++k+++   e  +++     + ++e  + +
  gi|242398771|ref|YP_002994195.1|  34 KEDEEKITLIMNRINEIENELPRIKVNIDTLKSQIQELRDEIEKLDKTIKDVMMLYEVVSQEinpfrDLDSEnPIVK 110
                                       5667899999999***************************************9888766654111112333345778 PP

                     Tropomyosin_1  81 kiqlLEeeleesdkkLk 97 
                                        i+ L ++le+  k+++
  gi|242398771|ref|YP_002994195.1| 111 EIHELKQDLEDIRKEIA 127
                                       88888888887766665 PP

>> TssO  Type VI secretion system, TssO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5  14.8      0.22        34      51     147 ..      27     125 ..       2     126 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.22
                              TssO  51 kkfeekqkelkkkvdsiykkIdsLkpevnav.fleneIkkdlndikntygk..nssdeRykmyaqiakfykmlledK 124
                                       ++  ++qke ++k+  i ++I+ ++ e + + +  + +k +++++++ ++k  +  +    +y+++ + ++ + ++ 
  gi|242398771|ref|YP_002994195.1|  27 QENPKEQKEDEEKITLIMNRINEIENELPRIkVNIDTLKSQIQELRDEIEKldKTIKDVMMLYEVVSQEINPFRDL- 102
                                       333478999999************77776652677999***********885344444466788888888886665. PP

                              TssO 125 kelksvseniklfkkqLeeceig 147
                                       +    + ++i ++k++Le+++++
  gi|242398771|ref|YP_002994195.1| 103 DSENPIVKEIHELKQDLEDIRKE 125
                                       566788899**********9987 PP

>> Fungal_TACC  Fungal Transforming acidic coiled-coil (TACC) proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   3.4       4.8   7.2e+02      44      63 ..       4      23 ..       1      44 [. 0.68
   2 ?    8.1   2.3     0.023       3.5      35      63 ..      56      84 ..      32      91 .. 0.71
   3 ?    5.4   0.3      0.16        25      49      70 ..     107     128 ..      88     137 .. 0.66

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 4.8
                       Fungal_TACC 44 elenkslkqeieqLkkqlea 63
                                      + ++ks k+eieqL+  l+ 
  gi|242398771|ref|YP_002994195.1|  4 KFKKKSEKDEIEQLELALSE 23
                                      45677778888888777654 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.023
                       Fungal_TACC 35 kyqkkldklelenkslkqeieqLkkqlea 63
                                      +++ ++d l+ + ++l++eie+L+k+++ 
  gi|242398771|ref|YP_002994195.1| 56 RIKVNIDTLKSQIQELRDEIEKLDKTIKD 84
                                      45667777777777777777777777765 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.16
                       Fungal_TACC  49 slkqeieqLkkqleaerkEKqe 70 
                                          +ei++Lk+ le  rkE  +
  gi|242398771|ref|YP_002994195.1| 107 PIVKEIHELKQDLEDIRKEIAQ 128
                                       4456666666666666666444 PP

>> DUF4094  Domain of unknown function (DUF4094)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   6.9      0.51        77      38      80 ..      40      87 ..       2      89 .. 0.70
   2 ?    4.2   0.2      0.39        60      40      81 ..      91     132 ..      84     135 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.51
                           DUF4094 38 lklvsedcds.kdaesr...skdilg.evskthkaiqtLdktissLem 80
                                        l+ +  ++ +++  r   + d l+ ++++ +++i++Ldkti  + m
  gi|242398771|ref|YP_002994195.1| 40 ITLIMNRINEiENELPRikvNIDTLKsQIQELRDEIEKLDKTIKDVMM 87
                                      333444444433333335566688999999999999999**9987765 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.39
                           DUF4094  40 lvsedcds.kdaesrskdilgevskthkaiqtLdktissLeme 81 
                                       +vs++ ++ +d  s++  i++e+++ +++++ + k i+++  +
  gi|242398771|ref|YP_002994195.1|  91 VVSQEINPfRDLDSEN-PIVKEIHELKQDLEDIRKEIAQIRGD 132
                                       6889999988777775.899*****************998655 PP

>> Cauli_AT  Aphid transmission protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   8.4     0.038       5.7      99     161 ..      26      85 ..       4      87 .. 0.78
   2 ?    3.4   0.4      0.44        67     137     162 ..     105     130 ..      89     137 .. 0.62

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.038
                          Cauli_AT  99 ggedkekktklletLkeaqnrikkleeetkklaekivtekllkeevkdlderlseirdslkai 161
                                       ++e+ +++ +  e +  + nri+++e+e  +++ +i t   lk+++++l ++++++ + +k++
  gi|242398771|ref|YP_002994195.1|  26 TQENPKEQKEDEEKITLIMNRINEIENELPRIKVNIDT---LKSQIQELRDEIEKLDKTIKDV 85 
                                       3456677778888889999*************999987...6778888888888888888877 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.44
                          Cauli_AT 137 ekllkeevkdlderlseirdslkaii 162
                                       e+ + +e+ +l++ l+ ir+++ +i 
  gi|242398771|ref|YP_002994195.1| 105 ENPIVKEIHELKQDLEDIRKEIAQIR 130
                                       44444556666666666666665553 PP

>> DUF1090  Protein of unknown function (DUF1090)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   8.2       0.1        16      33     103 ..       6      77 ..       3      84 .. 0.79
   2 ?    3.1   0.1      0.66     1e+02      62      94 ..     113     146 ..     109     150 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.1
                           DUF1090  33 kahgnqkrvagLekaLkevkanCtdeklkaerqekveekeeeVaereaeLaeakekgd..kdkiakrqekLae 103
                                       k++ +++++++Le aL+e +++ ++ k ++e +ek+    + ++e e+eL   k + d  k++i++ ++ +++
  gi|242398771|ref|YP_002994195.1|   6 KKKSEKDEIEQLELALSEGNTQ-ENPKEQKEDEEKITLIMNRINEIENELPRIKVNIDtlKSQIQELRDEIEK 77 
                                       67889999**********9877.66677888899****************99888776556666666665555 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.66
                           DUF1090  62 aerqekveekeeeVaereaeLaeakekg.dkdki 94 
                                       +e ++++e+ ++e+a+ + +L+    +g d dki
  gi|242398771|ref|YP_002994195.1| 113 HELKQDLEDIRKEIAQIRGDLKLLAYHGvDLDKI 146
                                       6788999999999999999999888888777777 PP

>> CCDC-167  Coiled-coil domain-containing protein 167
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   6.3      0.59        89      14      60 ..       8      56 ..       3      60 .. 0.75
   2 ?    8.2   6.3     0.021       3.2       5      64 ..      60     125 ..      56     132 .. 0.68

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.59
                          CCDC-167 14 ascrerLeaverrlrkeelseeeResleeEe..aslkeqleenekeLks 60
                                      +s ++++e++e  l + + +e+ +e+ e+Ee  + ++++++e e+eL +
  gi|242398771|ref|YP_002994195.1|  8 KSEKDEIEQLELALSEGNTQENPKEQKEDEEkiTLIMNRINEIENELPR 56
                                      566889999999998877777666666655511679**********975 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.021
                          CCDC-167   5 eIdkleeklascrerLeaverrlrkeelseee........ResleeEeaslkeqleenekeLksLrke 64 
                                       +Id+l  +++++r+++e++++ ++++ +  e         R +l   e+ + ++++e  + L+ +rke
  gi|242398771|ref|YP_002994195.1|  60 NIDTLKSQIQELRDEIEKLDKTIKDVMMLYEVvsqeinpfR-DLD-SENPIVKEIHELKQDLEDIRKE 125
                                       79***********************9998887666666641.333.3344444556666666666555 PP

>> NBP1  Fungal Nap binding protein NBP1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   9.1      0.18        27     155     219 ..       7      69 ..       1      88 [. 0.85
   2 ?    4.3   3.5      0.14        22     159     219 ..      65     134 ..      56     138 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.18
                              NBP1 155 lkydkqmleqLrrgrssnkserrvslrnnnleeDqvvlLqkkikklesklkdlekeLeitkkkLk 219
                                       +k++k  +eqL    s+ + +++  +++++ +e +++l+ ++i+++e++l   + ++  +k +++
  gi|242398771|ref|YP_002994195.1|   7 KKSEKDEIEQLELALSEGNTQEN--PKEQKEDEEKITLIMNRINEIENELPRIKVNIDTLKSQIQ 69 
                                       6789999****999999999888..79999999******************99999998888765 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.14
                              NBP1 159 kqmleqLrrgrssnkserr.........vslrnnnleeDqvvlLqkkikklesklkdlekeLeitkkkLk 219
                                       k ++++Lr   ++  ++ +         ++  n+  + D  + + k+i++l++ l+d +ke+  ++ +Lk
  gi|242398771|ref|YP_002994195.1|  65 KSQIQELRDEIEKLDKTIKdvmmlyevvSQEINPFRDLDSENPIVKEIHELKQDLEDIRKEIAQIRGDLK 134
                                       344555555544444444455566556445667777889999*********************9999997 PP

>> TSC22  TSC-22/dip/bun family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.9      0.93   1.4e+02      22      51 ..      39      66 ..      37      70 .. 0.49
   2 ?   10.2   0.5    0.0046       0.7      16      34 ..      61      79 ..      57      80 .. 0.89
   3 ?    7.3   0.9     0.039         6      13      45 ..      72     104 ..      71     117 .. 0.83
   4 ?    1.0   0.1       3.5   5.4e+02      22      41 ..     111     130 ..     107     136 .. 0.69

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.93
                             TSC22 22 kIkeLeernseleeENslLkalaspeqleq 51
                                      kI+  ++r++e+e  N+l +  ++ ++l++
  gi|242398771|ref|YP_002994195.1| 39 KITLIMNRINEIE--NELPRIKVNIDTLKS 66
                                      5555566665554..344444455565554 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0046
                             TSC22 16 VevLkekIkeLeernsele 34
                                      +++Lk++I+eL +++++l 
  gi|242398771|ref|YP_002994195.1| 61 IDTLKSQIQELRDEIEKLD 79
                                      79*************9985 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.039
                             TSC22  13 rEeVevLkekIkeLeernseleeENslLkalas 45 
                                       r+e+e L ++Ik+ ++  + + +E + ++ l s
  gi|242398771|ref|YP_002994195.1|  72 RDEIEKLDKTIKDVMMLYEVVSQEINPFRDLDS 104
                                       9**************999999999888876655 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 3.5
                             TSC22  22 kIkeLeernseleeENslLk 41 
                                       +I eL ++ + +++E ++ +
  gi|242398771|ref|YP_002994195.1| 111 EIHELKQDLEDIRKEIAQIR 130
                                       57777777777777766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2605  (0.145295); expected 358.6 (0.02)
Passed bias filter:                     1134  (0.0632495); expected 358.6 (0.02)
Passed Vit filter:                       241  (0.0134419); expected 17.9 (0.001)
Passed Fwd filter:                       134  (0.00747392); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):             118  [number of targets reported over threshold]
# CPU time: 1.28u 0.39s 00:00:01.67 Elapsed: 00:00:00.62
# Mc/sec: 760.84
//
Query:       gi|242398772|ref|YP_002994196.1|  [L=218]
Description: flagellin [Thermococcus sibiricus MM 739]
Scores for complete 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-46  158.3   8.4    2.1e-46  158.1   8.4    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 !  158.1   8.4   1.2e-50   2.1e-46       1     161 [.      10     200 ..      10     203 .. 0.96

  Alignments for each domain:
  == domain 1  score: 158.1 bits;  conditional E-value: 1.2e-50
                                       X--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--EEEEEEEEEE-SSSSSEEEEEEE--T CS
                    Arch_flagellin   1 GfvgigtlIvfIAmVlVAAvaagvlintagflqqkaqstgeesteqvssgleitgdvgdsatngtineitiyvklna 77 
                                       G+vgigtlIvfIAmVlVAAvaa vlint+g+lqq+a++tg ++t++v+sgl+i+ +vg  +t+g i+ ++iy+ lna
  gi|242398772|ref|YP_002994196.1|  10 GAVGIGTLIVFIAMVLVAAVAAAVLINTSGYLQQRAEATGRQTTKEVASGLKIDKVVGHVGTSG-IDMLAIYISLNA 85 
                                       89********************************************************777776.99********** PP

                                       TS--EEGGG-EEEEEESS--EE--E...............................................T-EE- CS
                    Arch_flagellin  78 Gsspidlnkttisvtddgqetlltad.............................efgivvisdtdgsltngdevle 125
                                       Gs+pidl++t++ + d +++++l +                              +fgi vi+d+d+sl++++++++
  gi|242398772|ref|YP_002994196.1|  86 GSEPIDLTQTKLYLNDGNTVAVLEYGsgafnktvtnnifdnttlsgawstnvdgtHFGILVIQDADNSLSADTPTIN 162
                                       ************988888999999999************************************************** PP

                                       TT-EEEEEEE--..TTT---TT-EEEEEEE-SSS--EE CS
                    Arch_flagellin 126 kgekvelevnvn..eddgitagdevsvevvpenGastt 161
                                        g++v l+v+++    ++i++++e+ +ev+pe+Ga++ 
  gi|242398772|ref|YP_002994196.1| 163 AGDVVILTVDAKdvFGSEIPTRTEIAIEVRPEFGAPGY 200
                                       **********99986677*****************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       781  (0.0435607); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1440.57
//
Query:       gi|242398773|ref|YP_002994197.1|  [L=323]
Description: SAM-dependent methyltransferase [Thermococcus sibiricus MM 739]
Scores for complete 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   59.2   0.0    6.7e-16   58.4   0.0    1.4  1  Methyltransf_31  Methyltransferase domain
    9.3e-11   42.4   0.0    1.9e-10   41.4   0.0    1.5  1  Methyltransf_12  Methyltransferase domain
      2e-10   41.2   0.0    4.9e-10   40.0   0.0    1.7  1  Methyltransf_25  Methyltransferase domain
    3.8e-10   39.5   0.0    6.4e-10   38.8   0.0    1.3  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    5.1e-10   39.9   0.0      1e-09   38.9   0.0    1.5  1  Methyltransf_11  Methyltransferase domain
      9e-10   38.6   0.0    1.4e-09   38.0   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
    3.8e-06   26.8   0.0    5.6e-06   26.2   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
     0.0097   15.5   0.0      0.023   14.2   0.0    1.5  1  MTS              Methyltransferase small domain
     0.0097   15.2   0.0      0.014   14.7   0.0    1.2  1  Rsm22            Mitochondrial small ribosomal subunit Rsm22
  ------ inclusion threshold ------
      0.019   14.6   0.0      0.034   13.8   0.0    1.4  1  NodS             Nodulation protein S (NodS)


Domain annotation for each model (and alignments):
>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.4   0.0   3.7e-19   6.7e-16       2     124 ..     160     276 ..     159     305 .. 0.87

  Alignments for each domain:
  == domain 1  score: 58.4 bits;  conditional E-value: 3.7e-19
                   Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee.leklledekfDl 77 
                                       ++g+r+lDlGCG+    +el + +gp++e++GiD+s+  ++ A+++ ++lg d v +++ di++ ++k    +k+Dl
  gi|242398773|ref|YP_002994197.1| 160 RDGMRILDLGCGS-VSPIELGKHVGPNGEYIGIDFSPGLLSIAQQRIRELGMDWVFLRELDITNaIPK----RKYDL 231
                                       689**********.99999999******************************************9995....8**** PP

                   Methyltransf_31  78 ilsnevlnaladpdkileeiervlkpggilliedprllaelpakvee 124
                                       ++   vl +l++    + ++ +++ + g l+i +p   +e+ +++ +
  gi|242398773|ref|YP_002994197.1| 232 VIMSFVLEYLPEVHRNIIKALNLVDERGKLIIVEPF--RENFENIAA 276
                                       *******99999999999999999999999998887..455544444 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.4   0.0     1e-13   1.9e-10       1      97 [.     166     259 ..     166     261 .. 0.83

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 1e-13
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlh 77 
                                       L++GcG+ s ++      p+ ey+g+D+sp  +  a++++++ +    ++v l++ld+ +  ++ ++Dlv++s+vl+
  gi|242398773|ref|YP_002994197.1| 166 LDLGCGSVSPIELGKHVGPNGEYIGIDFSPGLLSIAQQRIRELG---MDWVFLRELDITNAIPKRKYDLVIMSFVLE 239
                                       89****777776666666*********************99999...588888899999999999************ PP

                   Methyltransf_12  78 hlkdirevldnirklLkpgG 97 
                                       +l+++++ + ++ +l+   G
  gi|242398773|ref|YP_002994197.1| 240 YLPEVHRNIIKALNLVDERG 259
                                       **887776666666666666 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   0.0   2.8e-13   4.9e-10       1      87 [.     165     250 ..     165     259 .. 0.82

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 2.8e-13
                                       EEEET-TTSHHHHHHHCTST.SSEEEEEESSHHHHHHHHHHHHHTTTTEEE.EESBCCGBSSSTTTEEEEEEESTGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlg.kakvtgvDiseemleaareraeeeglnvef.vqgdaedlpfedgsfDlvvssgalh 75 
                                       +LdlGcG+    ++l k++g +++++g+D+s+++l +a++r++e g+++ f ++ d+++   +++++Dlv++s++l+
  gi|242398773|ref|YP_002994197.1| 165 ILDLGCGS-VSPIELGKHVGpNGEYIGIDFSPGLLSIAQQRIRELGMDWVFlRELDITNAI-PKRKYDLVIMSFVLE 239
                                       8******9.5778999999669**********************99966663678997754.5779*********** PP

                                       GSSHHHHHHHHH CS
                   Methyltransf_25  76 hlsdedlekalk 87 
                                       +l++  +++++k
  gi|242398773|ref|YP_002994197.1| 240 YLPE-VHRNIIK 250
                                       *984.3444444 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   0.0   3.6e-13   6.4e-10      24     161 ..     138     273 ..     121     295 .. 0.84

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 3.6e-13
                                       HHHHHTTTHHHHHHHHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTE CS
                   Ubie_methyltran  24 ndvlslgihrlWkkfveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkini 100
                                       +  ls    +l+++ + ++ + + g ++lD+ +G+    ++l ++vg +g+ +++D+++ +L++++++++e g+  +
  gi|242398773|ref|YP_002994197.1| 138 DIRLSNPLNKLYREIIVRVGGLRDGMRILDLGCGSVS-PIELGKHVGPNGEYIGIDFSPGLLSIAQQRIRELGMDWV 213
                                       3346777899************************985.79********************************97554 PP

                                       EEEE--TTT-TTS-T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEEEEE----SHH CS
                   Ubie_methyltran 101 eflqanaeeLpfeddsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvvlefskvelpl 161
                                        fl          +  +D+v +sf l  +++ ++ + +a   +   G+l+++e  + + + 
  gi|242398773|ref|YP_002994197.1| 214 -FLRELDITNAIPKRKYDLVIMSFVLEYLPEVHRNIIKALNLVDERGKLIIVEPFRENFEN 273
                                       .777777777888999***********************************9977765554 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9   0.0   5.8e-13     1e-09       1      96 []     166     263 ..     166     263 .. 0.95

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 5.8e-13
                                       EEET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-TT-EEEEEEES-CCC- CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg..arvvgvDlskemlklakekaseegl.kvefvvadaeklpfednsfDlvvssevlhhv 74 
                                       Ld+GcG+ +  e  ++ g  ++++g+D+s+ +l +a+++++e g+ +v +++ d+++  +++ ++Dlv++s+vl+++
  gi|242398773|ref|YP_002994197.1| 166 LDLGCGSVSPIELGKHVGpnGEYIGIDFSPGLLSIAQQRIRELGMdWVFLRELDITN-AIPKRKYDLVIMSFVLEYL 241
                                       8************9999999************************998888******9.89999************** PP

                                       CCHHHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  75 edpekalkeiaRvLkpgGllvi 96 
                                       +++++ + ++  ++   G+l+i
  gi|242398773|ref|YP_002994197.1| 242 PEVHRNIIKALNLVDERGKLII 263
                                       ****999999999999999986 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   0.0   7.9e-13   1.4e-09       8     132 ..     148     273 ..     140     306 .. 0.76

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 7.9e-13
                   Methyltransf_23   8 elsdklerllpklraggrvLdiGcGtGillevlrengf..svtgvDlspeaveiae......kakkaqkdqfdeqea 76 
                                        +++ + r+++ lr g+r+Ld+GcG+ +  e+ +  g   +++g+D sp + +ia+      +           +++
  gi|242398773|ref|YP_002994197.1| 148 LYREIIVRVGG-LRDGMRILDLGCGSVSPIELGKHVGPngEYIGIDFSPGLLSIAQqrirelG-----------MDW 212
                                       56778888887.9**************999999999999999*******99999744222220...........222 PP

                   Methyltransf_23  77 ae..........pqgkfdlIvlrevlehvpdppellrqiatllkpgGylllseplaslkedrllld 132
                                        +          p++k+dl+++++vle +p +++++ ++ +l+ + G l++ ep ++      +++
  gi|242398773|ref|YP_002994197.1| 213 VFlrelditnaiPKRKYDLVIMSFVLEYLPEVHRNIIKALNLVDERGKLIIVEPFREN-----FEN 273
                                       225556666677999**************************************97753.....333 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 !   26.2   0.0   3.1e-09   5.6e-06      71     157 ..     159     243 ..     139     278 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 3.1e-09
                                       --TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGGTTGGG-SEEEEE CS
                              PCMT  71 lkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGrkGyeekaPYdaih 147
                                       l++g+r+L++G+Gs      l + vg++g  ++i+ ++ l + a++++++l+++ v +++ D ++  +++  Yd ++
  gi|242398773|ref|YP_002994197.1| 159 LRDGMRILDLGCGS-VSPIELGKHVGPNGEYIGIDFSPGLLSIAQQRIRELGMDWVFLRELDITNAIPKR-KYDLVI 233
                                       999**********9.56778999************************************99999888766.588888 PP

                                       ESSBBSS--H CS
                              PCMT 148 vgaaapeiPe 157
                                       ++   + +Pe
  gi|242398773|ref|YP_002994197.1| 234 MSFVLEYLPE 243
                                       7776655554 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   1.3e-05     0.023      33     139 ..     163     265 ..     157     290 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.3e-05
                                       SEEEEET-TTSHHHHHHHH.HTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTSTTS-EEEEEE---S CS
                               MTS  33 gkvlDlGcGaGvlgaalak.espeaevtlvdvdarAlesakenleankle.vevvasdvleeveekkfdlivsNPPf 107
                                        ++lDlGcG  v  ++l k   p+ e   +d +   l +a++ +++ +++ v +++ d++++++++k+dl+++   f
  gi|242398773|ref|YP_002994197.1| 163 MRILDLGCGS-VSPIELGKhVGPNGEYIGIDFSPGLLSIAQQRIRELGMDwVFLRELDITNAIPKRKYDLVIMS--F 236
                                       579******7.555666551578999************************8889999***************96..3 PP

                                       TTTCHCHHHHHHHHHHHHHHHEEEEEEEEEEE CS
                               MTS 108 hagkatelavaeeliaeAkeaLkegGeLliVa 139
                                         +     +v +++  +A +  +e G+L+iV 
  gi|242398773|ref|YP_002994197.1| 237 VLEYL--PEVHRNI-IKALNLVDERGKLIIVE 265
                                       33322..3344444.45778888888888875 PP

>> Rsm22  Mitochondrial small ribosomal subunit Rsm22
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   7.8e-06     0.014      61     141 ..     187     266 ..     164     282 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 7.8e-06
                             Rsm22  61 evlvidaseelleiskelaadapelkeaalrrsvirealeleeadLviisyvLleledesreklvknlWakask..i 135
                                       e++ id s  ll+i+++ +++        lr+  i++a+   + dLvi+s+vL+ l + +r+ ++k+l + +++   
  gi|242398773|ref|YP_002994197.1| 187 EYIGIDFSPGLLSIAQQRIRELGMDWVF-LRELDITNAIPKRKYDLVIMSFVLEYLPEVHRN-IIKAL-NLVDErgK 260
                                       5777888888888888888877766555.555556678888888**********99988887.57888.66665569 PP

                             Rsm22 136 lvivEe 141
                                       l+ivE+
  gi|242398773|ref|YP_002994197.1| 261 LIIVEP 266
                                       ****97 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.9e-05     0.034      46     132 ..     164     254 ..     123     272 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.9e-05
                              NodS  46 dalevGcaaGa...lterlapyckrltvvdvveeaiararervkesshiswi...vsdvqqfstdekfdlivvaevl 116
                                        +l++Gc + +   l +++ p  + +  +d  +  ++ a++r++e   + w+   + d+++   ++k+dl++++ vl
  gi|242398773|ref|YP_002994197.1| 164 RILDLGCGSVSpieLGKHVGPNGEYI-GIDFSPGLLSIAQQRIRE-LGMDWVflrELDITNAIPKRKYDLVIMSFVL 238
                                       55666665543112344444544443.478888888889999999.56777633368******************** PP

                              NodS 117 yyiedvaelraavrnl 132
                                        y+ +v +      nl
  gi|242398773|ref|YP_002994197.1| 239 EYLPEVHRNIIKALNL 254
                                       ***9997633333344 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 1893.61
//
Query:       gi|242398774|ref|YP_002994198.1|  [L=106]
Description: HTH transcription regulator [Thermococcus sibiricus MM 739]
Scores for complete 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  117.5   0.1    1.9e-34  117.3   0.1    1.0  1  DUF1495   Winged helix DNA-binding domain (DUF1495)
  ------ inclusion threshold ------
      0.011   15.6   0.2      0.026   14.4   0.0    1.7  2  HTH_5     Bacterial regulatory protein, arsR family
      0.017   14.9   0.0      0.025   14.3   0.0    1.2  1  DUF4364   Domain of unknown function (DUF4364)


Domain annotation for each model (and alignments):
>> DUF1495  Winged helix DNA-binding domain (DUF1495)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.3   0.1   3.2e-38   1.9e-34       1      89 [.       7      94 ..       7      95 .. 0.97

  Alignments for each domain:
  == domain 1  score: 117.3 bits;  conditional E-value: 3.2e-38
                           DUF1495  1 ilrslnkSkvRkkvllyLysiypeksnlqeisrrvrskpsnvkGaleGmgkrynsessLielGLveeeeeseglklYkl 79
                                      ilrsl++S++Rkk+l+yL++iyp+ ++l+ei+r vrs+psnvkGal Gmg+ryn++ssL++lGLve e  ++g+k+Ykl
  gi|242398774|ref|YP_002994198.1|  7 ILRSLHRSELRKKILFYLHEIYPSPTYLSEIARIVRSDPSNVKGALVGMGNRYNGDSSLVHLGLVE-EITQNGFKYYKL 84
                                      89***************************************************************5.899********* PP

                           DUF1495 80 teeGieivev 89
                                      te+G+++v +
  gi|242398774|ref|YP_002994198.1| 85 TEHGEKVVGF 94
                                      ******9965 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   4.3e-06     0.026       2      32 ..      15      48 ..       7      49 .. 0.95
   2 ?   -2.8   0.0         1   6.1e+03      39      46 ..      65      72 ..      64      73 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.3e-06
                                      HHHHHHHHHHTT...SSEEHHHHHHHHTS-HHHH CS
                             HTH_5  2 ptRlkILklLae...gelcvcelaeelglsqstv 32
                                      + R kIL++L e   ++++ +e+a++++  +s+v
  gi|242398774|ref|YP_002994198.1| 15 ELRKKILFYLHEiypSPTYLSEIARIVRSDPSNV 48
                                      6799**************************9998 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1
                                      HHHTTSEE CS
                             HTH_5 39 LreaGLVe 46
                                      L  +GLVe
  gi|242398774|ref|YP_002994198.1| 65 LVHLGLVE 72
                                      66789997 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   4.2e-06     0.025      42      75 ..      64      97 ..      63     104 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.2e-06
                           DUF4364 42 eLvesglieeeekenktlykiTekGketlelfen 75
                                       Lv+ gl+ee ++++ ++yk+Te G++++ ++++
  gi|242398774|ref|YP_002994198.1| 64 SLVHLGLVEEITQNGFKYYKLTEHGEKVVGFLKT 97
                                      69999************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.29s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 724.72
//
Query:       gi|242398775|ref|YP_002994199.1|  [L=51]
Description: hypothetical protein TSIB_0789 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       177  (0.00987227); expected 358.6 (0.02)
Passed bias filter:                      137  (0.00764125); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.34s 00:00:00.81 Elapsed: 00:00:00.52
# Mc/sec: 293.57
//
Query:       gi|242398776|ref|YP_002994200.1|  [L=430]
Description: SSS sodium solute transporter superfamily [Thermococcus sibiricus MM 739]
Scores for complete 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-52  176.4  31.6    1.1e-51  176.0  31.6    1.2  1  SSF       Sodium:solute symporter family


Domain annotation for each model (and alignments):
>> SSF  Sodium:solute symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.0  31.6   6.2e-56   1.1e-51      26     406 .]       5     375 ..       1     375 [. 0.89

  Alignments for each domain:
  == domain 1  score: 176.0 bits;  conditional E-value: 6.2e-56
                               SSF  26 sfvGlaGavaasGlavvllelgalllvlllllllaerlrnagalTlpdylskRfkgkrilvylsalslllvitlkls 102
                                        ++G+a  +a++Gl+++++ +   l++lll+l la+ +r +  +T+pd+l+ R+k+k  +++l+a+ +ll+++  l 
  gi|242398776|ref|YP_002994200.1|   5 FILGGASWGATYGLGGIWYGFACGLGLLLLGLTLAKPMRALALYTVPDVLEMRYKSKA-IRLLAAMLSLLALVGILG 80 
                                       579*******************************************************.999999999********* PP

                               SSF 103 vdlvggaklielalGlnyetavlllaaltalYtviGGllAvvytdtiqavlmlvgalilliivllevGgleslvekl 179
                                       +++ ++ + +e a+Gl  +++ +   ++ + Yt++ Gl Av +td iq +l  +g l+ +++ l +vGg+e l + l
  gi|242398776|ref|YP_002994200.1|  81 AQVWAASAVFE-AIGLPGTAGAVFATLIFIAYTAFSGLWAVALTDFIQIILGSIGVLVAVVLGLNKVGGFEGLRTSL 156
                                       *****999997.79******999999*********************************************998777 PP

                               SSF 180 keaapkv.vdlltpdslkllrdpltalslwlglvlGvaglphilvRflaakdakailkgvlkltivlilvligmisi 255
                                        ++ + + +   +  ++  l   l+al l + +++ + + +   +R++a +d k+++kg +++ ++l+++ ++    
  gi|242398776|ref|YP_002994200.1| 157 SAIPN-LpQAGGEYFNFMSLGISLFALTLAATVMY-TLIGQDFYQRLFASNDEKTARKGAIYSGVLLMVLSFLPALA 231
                                       66655.42222223333334445555555333333.33338899******************999988888888899 PP

                               SSF 256 ilfaiklagavpkavgtevgvsniaypeLvvkllpnllaGlllavmlAaimstltslllsassaftkDlYkkirrka 332
                                       ++ a  l    p+a++     +  a+p+L++ ++++++ ++++a++lAa+mst +sll +a s ++kDlY++++  +
  gi|242398776|ref|YP_002994200.1| 232 GMLALTLSSD-PQAIID---SPKTAVPKLIITVFGSGVGAIFVAAILAAVMSTADSLLSAATSHVVKDLYQSFIEPE 304
                                       9999999887.998875...6889***************************************************99 PP

                               SSF 333 sakekelvgvsriivlvvislaillavqeeqkgvlklvelafaglasavlavillalfwkrvneqGAlagliiG 406
                                        a++k+l+++s  +++ +++la+++a++ +  g++ l  +  ++ +s v+  +ll+++wkr++++GAl g+i+G
  gi|242398776|ref|YP_002994200.1| 305 -AEDKKLLNLSIGTTVAIGVLALVAALTIQ--GIIELLIYSYDIYTSGVFVPLLLGIYWKRATKEGALLGMIAG 375
                                       .99********************9999764..589*************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       842  (0.046963); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.75u 0.37s 00:00:01.12 Elapsed: 00:00:00.53
# Mc/sec: 2449.39
//
Query:       gi|242398777|ref|YP_002994201.1|  [L=227]
Description: hypothetical protein TSIB_0791 [Thermococcus sibiricus MM 739]
Scores for complete 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-53  179.8   0.9    6.3e-53  179.6   0.9    1.0  1  DUF257    Pyrococcus protein of unknown function, DUF257


Domain annotation for each model (and alignments):
>> DUF257  Pyrococcus protein of unknown function, DUF257
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.6   0.9   3.5e-57   6.3e-53       5     203 ..      16     213 ..      12     215 .. 0.96

  Alignments for each domain:
  == domain 1  score: 179.6 bits;  conditional E-value: 3.5e-57
                            DUF257   5 tlrpGetvLiEyssssvpevllyliakyskeknvPllvdDvlDtllivlkhlkllGldvpe.esikviKigGtkevg 80 
                                        ++pGetvL+Ey+ +s pe+llyl++    + +vP+++dD++Dt+++++++lk+lG+ ++   +++viKigG k+vg
  gi|242398777|ref|YP_002994201.1|  16 GIKPGETVLVEYTPISSPEILLYLMITKCMKRGVPVIIDDIADTFSEYITRLKILGVPTEDlLNAPVIKIGGDKNVG 92 
                                       589******************************************************998757************** PP

                            DUF257  81 nvvkkidfdkdpsiylskykravekvsveetvinlvlglerllllldnrrdlyklvksikkylgnknRkafylinrn 157
                                       +v+ +++  + +s++   y    ekv ++e v n+vlg+++l++ ld ++d + lv++i++++gn+ R a+y+inr+
  gi|242398777|ref|YP_002994201.1|  93 KVLGNVEIRR-YSLDFVAYSEVYEKVAPKEIVCNPVLGIHKLFVSLD-LQDARGLVRNIASFVGNETRFAVYFINRE 167
                                       *********9.*****************9999***********9986.778888*********************** PP

                            DUF257 158 llesikPellplLEeiassvieiesekealivrilKslnldivgtt 203
                                       +l++   e+l lLEei +sv ++e +ke   + + Ks n+di+g +
  gi|242398777|ref|YP_002994201.1| 168 ILKEKSLEILGLLEEISTSVFRWELHKEVYKLSVIKSPNPDILGSE 213
                                       ******9***********************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1354.36
//
Query:       gi|242398778|ref|YP_002994202.1|  [L=433]
Description: Enolase [Thermococcus sibiricus MM 739]
Scores for 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-128  425.8   0.4     1e-127  425.5   0.4    1.1  1  Enolase_C  Enolase, C-terminal TIM barrel domain
    3.9e-59  198.5   0.0    6.2e-59  197.9   0.0    1.3  1  Enolase_N  Enolase, N-terminal domain
    1.9e-07   30.9   0.0    2.8e-07   30.3   0.0    1.3  1  MR_MLE_C   Enolase C-terminal domain-like
    7.9e-05   21.9   0.1    0.00024   20.4   0.0    1.8  2  MAAL_C     Methylaspartate ammonia-lyase C-terminus
  ------ inclusion threshold ------
      0.066   13.1   0.0       0.17   11.8   0.0    1.7  1  DpnD-PcfM  DpnD/PcfM-like protein


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 !  425.5   0.4  2.8e-131    1e-127       2     294 ..     144     430 ..     143     432 .. 0.99

  Alignments for each domain:
  == domain 1  score: 425.5 bits;  conditional E-value: 2.8e-131
                                       -EE-EE-EEEEE-GGGSSSS--SSEEEEE-TT-SSHHHHHHHHHHHHHHHHHHHHHCC.GGGG-B-TTS-B----SS CS
                         Enolase_C   2 lvlPvPalnvinGGshagnklalqefmilPvgassfkealrlGaevyhklksvlkkkygksatnvGdeGGfaPnlqs 78 
                                       +vlPvP+ nvinGG hagn+l++qefmi+Pvga+sf+ea+++ +e+yh+lk++l +kygk a nvGdeGGfaP +++
  gi|242398778|ref|YP_002994202.1| 144 YVLPVPMSNVINGGAHAGNDLDFQEFMIMPVGAKSFREAIQMVSETYHTLKKILIEKYGKLAVNVGDEGGFAPPMKE 220
                                       89*************************************************************************** PP

                                       HHHHHHHHHHHHHHCT-TC..TBEEEEE--GGGCEETCTTEEECTTTTTT..GGCEEEHHHHHHHHHHHHHHS-EEE CS
                         Enolase_C  79 nkealdliveaiekaGykg..kvkialdvassefykekdkkydldfkeeesdkskkltseqladlykelvkkyPivs 153
                                         e ld +v+aie++Gyk   ++  aldvassefy+e+++ y + +ke         t e l dlyk+lv+ yPivs
  gi|242398778|ref|YP_002994202.1| 221 VTEPLDALVKAIEETGYKVgdEIAFALDVASSEFYEEEKNVYIVGGKE--------YTREGLIDLYKDLVSTYPIVS 289
                                       ******************8889****************9***999998........99******************* PP

                                       EES-S-TT-HHHHHHHHHHHTTTSEEEESTTTTT-HHHHHHHHHCT--SEEEE-HHHH-SHHHHHHHHHHHHHTT-E CS
                         Enolase_C 154 iedpldeddweawkklteelgdkvqivGddltvtnpkrlkeaiekkaanalllkvnqiGsltesleavklakeagyg 230
                                       iedp++e+d+e+++++t+elg+k+q+vGdd++vtn+krlk++ie +a+nalllkvnqiG+l+e+++a+ la +agyg
  gi|242398778|ref|YP_002994202.1| 290 IEDPVQEEDFEGFAMVTKELGKKIQLVGDDIFVTNVKRLKKGIEMGAGNALLLKVNQIGTLSEAIDAAYLAFRAGYG 366
                                       ***************************************************************************** PP

                                       EEEE--SC--S--HHHHHHHHCT-SEEE---S-SHHHHHHHHHHHHHHHHHGCC-EE-GGGCTT CS
                         Enolase_C 231 vvvshrsGetedttiadlavglsaGqiktGaparserlakynqllrieeelgekakyaGkkvrk 294
                                       vvvshrsGete +tiad+av+l+aGqiktGapars+r akynqllrieeel   a y Gkk+r+
  gi|242398778|ref|YP_002994202.1| 367 VVVSHRSGETEGSTIADIAVALNAGQIKTGAPARSDRNAKYNQLLRIEEELEGVAYYPGKKFRN 430
                                       *************************************************************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 !  197.9   0.0   1.7e-62   6.2e-59       1     131 []      10     138 ..      10     138 .. 0.98

  Alignments for each domain:
  == domain 1  score: 197.9 bits;  conditional E-value: 1.7e-62
                                       EEEEEEEEEE-TTS-EEEEEEEEETTC-EEEEE--B-BSSSSSS-B----SSTTSGGGT--HHHHHHHHHTHHHHHT CS
                         Enolase_N   1 IkkvkareildSrGnpTvevevttedgalgraavpsGaStgekealelrDgdkkrylgkgvekavenvnekiapali 77 
                                       I+ + areildSrGnpT+ev+v+t   a+graavpsGaStg +ealelrDg  kry+gkgv++avenvn++iap+l+
  gi|242398778|ref|YP_002994202.1|  10 ITGIFAREILDSRGNPTIEVDVYTP-VAMGRAAVPSGASTGIHEALELRDG-GKRYHGKGVKRAVENVNKIIAPELL 84 
                                       789*********************6.779*********************9.8************************ PP

                                       TSBTT-HHHHHHHHHHHH-STT-TTT-HHHHHHHHHHHHHHHHHHHTS-HHHHH CS
                         Enolase_N  78 gldvtdqeeiDkllielDgtenksklGaNailavSlAvakaaAkakelplyryl 131
                                       g+dvt q++iD +++elDg+enks+lGaNail+vSlAvakaaA+a+e+plyryl
  gi|242398778|ref|YP_002994202.1|  85 GMDVTLQRDIDMFMLELDGSENKSNLGANAILGVSLAVAKAAANALEIPLYRYL 138
                                       *****************************************************8 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 !   30.3   0.0   7.9e-11   2.8e-07      40     173 ..     238     390 ..     180     415 .. 0.75

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 7.9e-11
                                       HHTTTSTSEEEEE-TTT..S..............BHHHHHHHHHHHGG.GTESEEESSSSTTTHHHHHHHHHH...H CS
                          MR_MLE_C  40 avgpgddvdlmvDanqa..w..............dlatAirvarelee.ldllwlEEPvppeddleglaelra...r 96 
                                        v  gd++ +++D+  +  +              +++  i + + l + + +  +E+Pv+  +d eg a++++   +
  gi|242398778|ref|YP_002994202.1| 238 KV--GDEIAFALDVASSefYeeeknvyivggkeyTREGLIDLYKDLVStYPIVSIEDPVQE-EDFEGFAMVTKelgK 311
                                       34..5566777777777541444555555555559***********77799*********9.57********86422 PP

                                       HSSEEEESTTSSS.HHHHHHHHHHTSESEEEEBHHHHTSHHHHHHHHHHHHHTT-EEEEBS..CSSHHHHHHHHHHH CS
                          MR_MLE_C  97 asipiaagEslys.radfrelleagavdivqpdvsrvgGitearkvaalaeafgvpvapHs..gsgglglaaslhla 170
                                        +i+++++    + ++++++ +e ga  ++ ++v+++g ++ea++ a la  +g+ v++ +  g++  +++a + +a
  gi|242398778|ref|YP_002994202.1| 312 -KIQLVGDDIFVTnVKRLKKGIEMGAGNALLLKVNQIGTLSEAIDAAYLAFRAGYGVVVSHrsGETEGSTIADIAVA 387
                                       .9******987766************************************998888766652233566676666665 PP

                                       HTT CS
                          MR_MLE_C 171 aai 173
                                         +
  gi|242398778|ref|YP_002994202.1| 388 LNA 390
                                       554 PP

>> MAAL_C  Methylaspartate ammonia-lyase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.64   2.3e+03     195     218 ..     101     124 ..      92     131 .. 0.83
   2 !   20.4   0.0   6.7e-08   0.00024     109     219 ..     289     391 ..     275     398 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.64
                            MAAL_C 195 lGGscnetdvsarvsvhvalatrp 218
                                       l Gs n  + +a+++  v+la+  
  gi|242398778|ref|YP_002994202.1| 101 LDGSENKSNLGANAILGVSLAVAK 124
                                       5699999999**999999999764 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 6.7e-08
                            MAAL_C 109 liegPldagskeeqierlaelreklkekgikvelvaDe.WcntledirefvdaeaadlvqiktPDlGginntieavl 184
                                        ie+P+       q e ++ +    ke g k++lv D+ +  +++ +++ ++ +a++++ +k+  +G+++++i+a  
  gi|242398778|ref|YP_002994202.1| 289 SIEDPV-------QEEDFEGFAMVTKELGKKIQLVGDDiFVTNVKRLKKGIEMGAGNALLLKVNQIGTLSEAIDAAY 358
                                       344444.......444444445555667899****99846778999******************************* PP

                            MAAL_C 185 yckekgvgaylGGscnetdvsarvsvhvalatrpa 219
                                        + + g g+ +   + et+ s+ + + val   + 
  gi|242398778|ref|YP_002994202.1| 359 LAFRAGYGVVVSHRSGETEGSTIADIAVALN--AG 391
                                       *******************997666665554..44 PP

>> DpnD-PcfM  DpnD/PcfM-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   4.7e-05      0.17      11      33 ..     170     192 ..     169     199 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.7e-05
                         DpnD-PcfM  11 rvVeVeAeseeeAerlVeekYkn 33 
                                       +++ V A+s  eA+++V+e Y  
  gi|242398778|ref|YP_002994202.1| 170 MIMPVGAKSFREAIQMVSETYHT 192
                                       6788*****************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 2568.04
//
Query:       gi|242398779|ref|YP_002994203.1|  [L=43]
Description: SMC_N domain containing protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-10   41.3   0.6    1.8e-10   41.1   0.6    1.0  1  AAA_15    AAA ATPase domain
    2.5e-07   30.3   0.1    2.6e-07   30.3   0.1    1.0  1  SMC_N     RecF/RecN/SMC N terminal domain
    3.1e-06   27.9   0.2    3.5e-06   27.7   0.2    1.0  1  AAA_23    AAA domain
     0.0052   16.5   0.0     0.0056   16.4   0.0    1.1  1  AAA_29    P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.032   12.9   0.1      0.033   12.8   0.1    1.0  1  AAA_13    AAA domain
      0.032   14.0   1.4      0.041   13.7   1.4    1.1  1  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste


Domain annotation for each model (and alignments):
>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   0.6   5.9e-14   1.8e-10       1      36 [.       1      34 [.       1      36 [. 0.98

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 5.9e-14
                            AAA_15  1 MkIkkikikNFRslkdveidlseeltvliGkNnsGK 36
                                      M ++k+ ikN++s+k++e+++s+ ++vl+G+N+sGK
  gi|242398779|ref|YP_002994203.1|  1 M-LTKMLIKNYKSIKKAELEFSK-INVLVGPNGSGK 34
                                      7.99*******************.***********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 !   30.3   0.1   8.8e-11   2.6e-07       1      37 [.       1      34 [.       1      41 [. 0.92

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 8.8e-11
                                      EEEEEEEESETTEECEEEEEETTSSEEEEEESTTSSH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  1 vlkrleienFksyagktvilpfsksftaivGpNGSGK 37
                                      +l+++ i+n+ks+  k+++l+fsk ++++vGpNGSGK
  gi|242398779|ref|YP_002994203.1|  1 MLTKMLIKNYKSI--KKAELEFSK-INVLVGPNGSGK 34
                                      6899*********..79*****99.************ PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.2   1.2e-09   3.5e-06       2      32 ..       5      34 ..       4      34 .. 0.95

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 1.2e-09
                            AAA_23  2 LkienfrsfrdqeidFskgltlItGpNGaGK 32
                                      + i+n++s+++ e++Fs ++++++GpNG+GK
  gi|242398779|ref|YP_002994203.1|  5 MLIKNYKSIKKAELEFS-KINVLVGPNGSGK 34
                                      679**************.9***********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 !   16.4   0.0   1.9e-06    0.0056       1      35 [.       2      34 ..       2      37 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.9e-06
                            AAA_29  1 LkrlqlvNWgtfdghtieidlkgatlltGpsGsGK 35
                                      L+++ + N  ++++ ++e++   + +l+Gp+GsGK
  gi|242398779|ref|YP_002994203.1|  2 LTKMLIKNYKSIKKAELEFS--KINVLVGPNGSGK 34
                                      67888889999999999998..678*********9 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   1.1e-05     0.033       9      29 ..      15      34 ..       6      37 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.1e-05
                            AAA_13  9 gaeledfkriNliYGwNGaGK 29
                                      +aele f++iN++ G NG+GK
  gi|242398779|ref|YP_002994203.1| 15 KAELE-FSKINVLVGPNGSGK 34
                                      55665.**************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   1.4   1.4e-05     0.041       1      12 [.      23      34 ..      23      34 .. 0.97

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.4e-05
                            AAA_21  1 lnvliGpNgsGK 12
                                      +nvl+GpNgsGK
  gi|242398779|ref|YP_002994203.1| 23 INVLVGPNGSGK 34
                                      8**********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (43 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.50
# Mc/sec: 257.43
//
Query:       gi|242398780|ref|YP_002994204.1|  [L=178]
Description: hypothetical protein TSIB_0794 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       940  (0.052429); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1102.73
//
Query:       gi|242398781|ref|YP_002994205.1|  [L=154]
Description: hypothetical protein TSIB_0795 [Thermococcus sibiricus MM 739]
Scores for complete 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   64.6   0.2      2e-17   64.0   0.2    1.2  1  AAA_15    AAA ATPase domain
    2.1e-16   60.6   0.1    3.7e-16   59.8   0.1    1.3  1  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste


Domain annotation for each model (and alignments):
>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.0   0.2   2.2e-21     2e-17     286     368 ..      11      90 ..       2      91 .. 0.90

  Alignments for each domain:
  == domain 1  score: 64.0 bits;  conditional E-value: 2.2e-21
                            AAA_15 286 ik....ddeelplnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQ 358
                                       i      +++++l+++G G++ l+++++ ++++ k+        +++iE PE hLHp++q++l++ ++ ++++ + Q
  gi|242398781|ref|YP_002994205.1|  11 IIattpGGVDINLTDAGAGLNALFPIVTALAFYPKG-------STIFIEHPEMHLHPKLQYELAEFFLMVSKKREYQ 80 
                                       22467799****************************.......********************************** PP

                            AAA_15 359 viitTHSphi 368
                                       +ii+THS+h+
  gi|242398781|ref|YP_002994205.1|  81 LIIETHSEHL 90 
                                       *********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 !   59.8   0.1   4.2e-20   3.7e-16     226     302 ..      15      91 ..       4      91 .. 0.89

  Alignments for each domain:
  == domain 1  score: 59.8 bits;  conditional E-value: 4.2e-20
                            AAA_21 226 ngdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSpll 301
                                        ++g ++++++++ G   l++++tal+  +k  s+++i+ pE +LHPkl+ +l+e++   s+ +  Q+i+ THS +l
  gi|242398781|ref|YP_002994205.1|  15 TPGGVDINLTDAGAGLNALFPIVTALAFYPKG-STIFIEHPEMHLHPKLQYELAEFFLMVSKkREYQLIIETHSEHL 90 
                                       67999**********************99987.************************55444457*********999 PP

                            AAA_21 302 l 302
                                       l
  gi|242398781|ref|YP_002994205.1|  91 L 91 
                                       7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1198.56
//
Query:       gi|242398782|ref|YP_002994206.1|  [L=170]
Description: hypothetical protein TSIB_0796 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0056   17.2   0.3     0.0085   16.6   0.3    1.3  1  PIN       PIN domain
  ------ inclusion threshold ------
      0.025   15.1   0.9      0.029   14.8   0.9    1.2  1  PIN_12    PIN domain
        0.1   13.4   0.0       0.11   13.3   0.0    1.3  1  PIN_3     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 !   16.6   0.3   1.4e-06    0.0085       1      97 [.       4     130 ..       4     142 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.4e-06
                                       EEE-HHHHHHHH......TTSHHHHHHHHHHHTS.......SEEEEEHHHHHHHHHHHHS....SCHCHHHHHHHHH CS
                               PIN   1 ivlDTsvliall......rgeekaeaarklleel.......eelvtsalvlaEllyvlar....rkskrekaaelve 60 
                                       ivlDT+vl ++l      +g+e+++ a +++ el          v+++ +++E ++ l++     k++r   + +++
  gi|242398782|ref|YP_002994206.1|   4 IVLDTNVLRRALeeekglKGDEGTKLAYEIITELikikhedTIFVINEDTASEYYRHLEAlkkrLKQSRITPQSFKL 80 
                                       79**************************************999999**************88766667777777777 PP

                                       HHHHHHTSEEEEBCHHHHHHHHHHHHHHH.............SBHHHHHH CS
                               PIN  61 lllllsalkilpidaeiaeeaaeialkyg.............llpnDali 97 
                                       l  +l+ ++ +p+  + +e+ +e + +++              ++ Da++
  gi|242398782|ref|YP_002994206.1|  81 LSSILRKMRKVPTENHKFEIEGEAIGRKDyyllnsaktgaleFKVEDAFV 130
                                       77778888888888888888777777776666555555555555555555 PP

>> PIN_12  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.9   4.9e-06     0.029       1      87 [.       4      99 ..       4     145 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.9e-06
                            PIN_12  1 ifiDTnifld...........effrlseeealkklleliesgkiklivpdivldEflknrekkiees..kkle.kalks 65
                                      i++DTn++ +           e+ +l +e ++++l   i++++   ++++ +  E+++++e   ++   ++++ ++   
  gi|242398782|ref|YP_002994206.1|  4 IVLDTNVLRRaleeekglkgdEGTKLAYE-IITEL-IKIKHEDTIFVINEDTASEYYRHLEALKKRLkqSRITpQS--- 77
                                      89*******65555544444477777777.99999.77888899****************8776666222222222... PP

                            PIN_12 66 lsklksakkklnekkkllslke 87
                                      ++ l s  +k+ + ++++ + e
  gi|242398782|ref|YP_002994206.1| 78 FKLLSSILRKMRKVPTENHKFE 99
                                      4444444444444444333333 PP

>> PIN_3  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.8e-05      0.11       2      63 ..       4      74 ..       3     165 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.8e-05
                             PIN_3  2 vvlDtnvlldallfdsp.........aarkildal..etgaitlvvsprlldElervlarelaypqfklraad 63
                                      +vlDtnvl  al  ++          a++ i +++  ++++   v+ +++  E++r l+    +++ k+++  
  gi|242398782|ref|YP_002994206.1|  4 IVLDTNVLRRALEEEKGlkgdegtklAYEIITELIkiKHEDTIFVINEDTASEYYRHLEAL--KKRLKQSRIT 74
                                      79*******99886663666667886666666666999******************99444..5555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       706  (0.0393775); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); 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 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1244.48
//
Query:       gi|242398783|ref|YP_002994207.1|  [L=226]
Description: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase [Thermococcus sibiricus MM 739]
Scores for complete 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-101  336.5   0.0   6.2e-101  336.2   0.0    1.0  1  Fibrillarin  Fibrillarin
    0.00015   21.6   0.0     0.0002   21.2   0.0    1.2  1  PCMT         Protein-L-isoaspartate(D-aspartate) O-methyltran
     0.0019   18.0   0.0     0.0034   17.1   0.0    1.4  1  GCD14        tRNA methyltransferase complex GCD14 subunit
  ------ inclusion threshold ------
      0.028   14.5   0.0      0.042   14.0   0.0    1.4  1  FtsJ         FtsJ-like methyltransferase
       0.19   11.1   0.0       0.24   10.8   0.0    1.3  1  TehB         Tellurite resistance protein TehB


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 !  336.2   0.0  1.7e-104  6.2e-101       2     223 ..       4     224 ..       3     226 .] 0.97

  Alignments for each domain:
  == domain 1  score: 336.2 bits;  conditional E-value: 1.7e-104
                                       EEECSSTTEEEEE.TTSSEEEEEE-SSTT--SSSSEEEEETTEEEEEE-TTTSHHHHHHHTT-S--S--TTSEEEEE CS
                       Fibrillarin   2 eeheklegvyivk.ekgdarlatknlvpgekvYgEklikveeeEyRvWnpfrsKlaaailkglkelpikkgskvLYl 77 
                                       ++h k+ gvy+v  ++g++r+atknlvpg+kvYgE+++k+++eEyR+Wnp+rsKlaaail++lk++pik+g+ vLYl
  gi|242398783|ref|YP_002994207.1|   4 KKH-KFPGVYTVIeDDGSERIATKNLVPGQKVYGERIVKWKGEEYRIWNPNRSKLAAAILNDLKNFPIKPGTTVLYL 79 
                                       566.9*****998799999********************************************************** PP

                                       STTTSHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHHHTTSTTEEEEES-TTSGGGGTTTS--EEEEEEESSSTTHH CS
                       Fibrillarin  78 GaasGttvsHvsDivgeegvvyavefsprvlrelievakkRknivPileDArkPekYralvekvDvifaDvaqpdqa 154
                                       G+asGtt+sHvsDi+g eg+++++efsprvlrel+ ++++R+nivPil+DA+kPe+Yralv+kvDvif+Dvaqp+qa
  gi|242398783|ref|YP_002994207.1|  80 GIASGTTASHVSDIIGWEGKIFGIEFSPRVLRELVPLVEERRNIVPILGDATKPEEYRALVTKVDVIFEDVAQPTQA 156
                                       ***************************************************************************** PP

                                       HHHHHHHHHHEEEEEEEEEEEEHHHHHSSSSHHHHHHHHHHHHHHTTEEEEEEEE-TTTSTTEEEEEEE CS
                       Fibrillarin 155 rilaknaklflkeggyllisikarsidvtkepeevfkeeveklkeeglkvleqvklepyekdhalvvgk 223
                                       +il++nak++lk+ggy +isik+rsidvtkepeevf+e +++l+e  ++v+e ++lepyekdhal+v++
  gi|242398783|ref|YP_002994207.1| 157 KILIDNAKAYLKSGGYGMISIKSRSIDVTKEPEEVFREVEKELSEY-FEVVERISLEPYEKDHALIVVR 224
                                       **************************************99999875.******************9986 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   5.5e-08    0.0002      61     175 ..      57     179 ..      44     208 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 5.5e-08
                                       HHHHHHHHTT...--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GG CS
                              PCMT  61 mvalalelle...lkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGr 134
                                       + a++l+ l+   +k+g+ vL +G  sG  +  ++ ++g +g++ +ie ++++ +e    +++  ++n++ + gD +
  gi|242398783|ref|YP_002994207.1|  57 LAAAILNDLKnfpIKPGTTVLYLGIASGTTASHVSDIIGWEGKIFGIEFSPRVLRELVPLVEE--RRNIVPILGDAT 131
                                       5677777777788*****************************************999988875..568999999999 PP

                                       GTTGGG-...SEEEEEESSBBSS--HHHHHT....EEEEEEEEEEESB CS
                              PCMT 135 kGyeeka...PYdaihvgaaapeiPealidQ....LkeGGrlvvPvge 175
                                       k  e +a     d+i+  +a p   + lid     Lk+GG  ++ +++
  gi|242398783|ref|YP_002994207.1| 132 KPEEYRAlvtKVDVIFEDVAQPTQAKILIDNakayLKSGGYGMISIKS 179
                                       876665522267999999999999999998544558889988888873 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   9.5e-07    0.0034      35     162 ..      67     195 ..      58     212 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 9.5e-07
                             GCD14  35 kLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehelsqlvtvthrDvckeGfdeevs 111
                                       ++ +kpG+ v+  G  sg+ ++ ++  ++  G++f +ef  +  ++ +   +e+   ++v +       e + + + 
  gi|242398783|ref|YP_002994207.1|  67 NFPIKPGTTVLYLGIASGTTASHVSDIIGWEGKIFGIEFSPRVLRELVPLVEER--RNIVPILGDATKPEEY-RALV 140
                                       5679***********************************876555554444443..3455555544456677.5666 PP

                             GCD14 112 gkvDavfLDlPaPwea...iphaakalkkeg.grlCsfsPCieqvqrtceaLrel 162
                                        kvD +f D+ +P +a   i++a++ lk+ g g++   s  i+  ++  e++re 
  gi|242398783|ref|YP_002994207.1| 141 TKVDVIFEDVAQPTQAkilIDNAKAYLKSGGyGMISIKSRSIDVTKEPEEVFREV 195
                                       9*************99888899999997766356666677777666666666655 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.2e-05     0.042      14     106 ..      66     161 ..      53     210 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.2e-05
                                       HHHT-S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS.........HHHTTEEEECS-CCCSSHHHHHCH CS
                              FtsJ  14 ekfklfkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm.........aplpgvttiqgditdpetiekike 81 
                                       + f  +kpg+tv+ lg a G  +  ++  +g +gk++++   p          + + ++  i gd t+pe  +++ +
  gi|242398783|ref|YP_002994207.1|  66 KNFP-IKPGTTVLYLGIASGTTASHVSDIIGWEGKIFGIEFSPRvlrelvplvEERRNIVPILGDATKPEEYRALVT 141
                                       4555.68**********************9999********999898776555555788888***********9996 PP

                                       CHHHSSEEEEEE--S-SS-CHHHHH CS
                              FtsJ  82 alserkvdlvvsDgapdvsgvhdld 106
                                            kvd++  D+a  ++ +  +d
  gi|242398783|ref|YP_002994207.1| 142 -----KVDVIFEDVAQPTQAKILID 161
                                       .....8*********7666554444 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   6.7e-05      0.24      89     166 ..     129     209 ..      53     218 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 6.7e-05
                                       G----S-EEEEEEESSGGG...S-GGGHHHHHHHHHHTEEEEEEEEEEEEB--SSS--SS--S--B-TTHHHHHTTT CS
                              TehB  89 eaklderydfilstvvlmf...leaeripsiienmqectkvggynlivaamstddvpctvpfsftfkegelkeyykd 162
                                       +a+  e+y  +++ v ++f    ++ +   +i+n + + k ggy +i     + dv       f   e+el ey++ 
  gi|242398783|ref|YP_002994207.1| 129 DATKPEEYRALVTKVDVIFedvAQPTQAKILIDNAKAYLKSGGYGMISIKSRSIDVTKEPEEVFREVEKELSEYFEV 205
                                       5666788888888888887332356677789***************988777788888878889999999****998 PP

                                       SEEE CS
                              TehB 163 well 166
                                        e++
  gi|242398783|ref|YP_002994207.1| 206 VERI 209
                                       8776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); 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: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1732.43
//
Query:       gi|242398784|ref|YP_002994208.1|  [L=416]
Description: NOP5/NOP56 related protein [Thermococcus sibiricus MM 739]
Scores for complete 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-72  243.5   0.0    2.8e-72  242.9   0.0    1.2  1  Nop              snoRNA binding domain, fibrillarin
     0.0047   16.5   0.5     0.0047   16.5   0.5    2.4  2  Snf7             Snf7
  ------ inclusion threshold ------
        3.6    7.6   7.7          7    6.7   7.7    1.5  1  Peptidase_S49_N  Peptidase family S49 N-terminal


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 !  242.9   0.0   4.6e-76   2.8e-72       2     229 ..     140     365 ..     139     366 .. 0.94

  Alignments for each domain:
  == domain 1  score: 242.9 bits;  conditional E-value: 4.6e-76
                                       HHHHHHHHHHHHHHHHHHHTTTSTCHHHHS-SHHHHHHHHHHCCCCHCCT.HHTT.HH...HHHHHHHHHHCHHHH- CS
                               Nop   2 ldeidkeintlhkrvrewYswhFpELeslvkdnleYakvvkligneredlekkeedee...lakevimaakvtasts 75 
                                       ld+idk in l++r+rewYs hFpE++++++++ +Y+  +k+ig +r+++++++  e+    ++++  +++v  +++
  gi|242398784|ref|YP_002994208.1| 140 LDDIDKVINLLVSRLREWYSLHFPEIDEILPKHPQYVAFIKKIG-NRKNITRENL-ESfglGENKIARVLEV-KEKT 213
                                       79******************************************.6788866633.2246688999999999.777* PP

                                       SSS-S-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHCHHHHHHHHHHHHSSHHHHHCS-HHHHTT CS
                               Nop  76 mgaelseedlknikelcdrvleleelrkelleYlesrmsaiAPNlsaLvGeevaarLishaGgLtnLakmPastiqi 152
                                       mga ++++d++ i++l++++ +l++lr+e+++Y+e+ m+ +APNl+aLvG++++arLis aGgL++La mP+stiq+
  gi|242398784|ref|YP_002994208.1| 214 MGAWMDQKDITVIQNLAKEIEDLYKLRSEIEDYIERAMDDVAPNLKALVGAKLGARLISLAGGLKELALMPSSTIQV 290
                                       ***************************************************************************** PP

                                       TT-HHHHCCCHH.T---SSSCHHHCSHHHHHTS-CCCHHHHHHHHHHHHHHHHHHHHTT----SHHHHHHHHHHHHH CS
                               Nop 153 lGaekalfralk.kkntpkyGliyhselvqkatppklkkkiaRllaaKvalaaRiDafsekdgslGkklreeiekkl 228
                                       lGaekalfr+l+ + + pk+G+iy+ + ++k+ p+++++kiaR+la K+a+aaR+D f  + + + ++l++eie ++
  gi|242398784|ref|YP_002994208.1| 291 LGAEKALFRHLRsGAKPPKHGIIYQYPAINKS-PWWQRGKIARALAGKLAIAARVDYF--SGEYIAEELKNEIEIRI 364
                                       ************788***************88.*************************..5788999*******999 PP

                                       H CS
                               Nop 229 k 229
                                       k
  gi|242398784|ref|YP_002994208.1| 365 K 365
                                       8 PP

>> Snf7  Snf7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.5   7.9e-07    0.0047      81     134 ..     201     254 ..     191     260 .. 0.91
   2 ?   -7.3   6.4         3   1.8e+04      21      37 ..     379     393 ..     353     413 .. 0.49

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 7.9e-07
                                       HHHHHHHHHHHHHHHHHHHCTCCHHHHHHHHHHHHHHHHHTCHHHHHHHHHTT- CS
                              Snf7  81 kevlnamkqgakamkamnkkvdidkidklmdeiedqmekaeeisEalsrsldda 134
                                       +++++ ++   k+m a +++ di  i++l +eied  +  +ei++ ++r++dd+
  gi|242398784|ref|YP_002994208.1| 201 NKIARVLEVKEKTMGAWMDQKDITVIQNLAKEIEDLYKLRSEIEDYIERAMDDV 254
                                       66777788889****************************************997 PP

  == domain 2  score: -7.3 bits;  conditional E-value: 3
                                       HHHHHHHHHHHHHHHCT CS
                              Snf7  21 ekkikkleaelkklakk 37 
                                       ek +kk++   kk++kk
  gi|242398784|ref|YP_002994208.1| 379 EKPVKKEK--KKKFKKK 393
                                       22222211..1222222 PP

>> Peptidase_S49_N  Peptidase family S49 N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   7.7    0.0012         7      35      87 ..     356     408 ..     330     416 .] 0.59

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0012
                   Peptidase_S49_N  35 kkekgelevtkLneeykelkeeleealldeeelkaaekkekkeekeekkaekk 87 
                                        k++ e+++++++e+y +  ++ e+ + +e+++k ++k ++k+ + ++k++kk
  gi|242398784|ref|YP_002994208.1| 356 LKNEIEIRIKEIKEKYPNPPKRKEKPVKKEKKKKFKKKGKEKKFRGKEKKQKK 408
                                       36777888999999998887776666555555444444444444444444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1808  (0.100842); expected 358.6 (0.02)
Passed bias filter:                      817  (0.0455686); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
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: 0.67u 0.33s 00:00:01.00 Elapsed: 00:00:00.47
# Mc/sec: 2636.80
//
Query:       gi|242398785|ref|YP_002994209.1|  [L=350]
Description: 3-hydroxy-3-methylglutaryl CoA synthase [Thermococcus sibiricus MM 739]
Scores for complete 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-11   42.0   0.1    5.2e-10   39.4   0.0    2.4  3  ACP_syn_III_C   3-Oxoacyl-[acyl-carrier-protein (ACP)] syntha
      6e-05   22.8   1.9    0.00028   20.7   0.5    2.3  2  ACP_syn_III     3-Oxoacyl-[acyl-carrier-protein (ACP)] syntha
    0.00026   20.9   0.0    0.00043   20.2   0.0    1.3  1  HMG_CoA_synt_N  Hydroxymethylglutaryl-coenzyme A synthase N t
     0.0016   18.1   0.1      0.041   13.5   0.0    2.1  2  HMG_CoA_synt_C  Hydroxymethylglutaryl-coenzyme A synthase C t
     0.0052   16.2   0.0     0.0073   15.7   0.0    1.1  1  Thiolase_N      Thiolase, N-terminal domain
  ------ inclusion threshold ------
       0.14   11.7   1.0         14    5.2   0.7    2.5  2  ketoacyl-synt   Beta-ketoacyl synthase, N-terminal domain


Domain annotation for each model (and alignments):
>> ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       2.3   6.9e+03       1      16 [.      65      80 ..      65      81 .. 0.88
   2 ?   -1.8   0.3       1.2   3.6e+03      50      82 ..     131     163 ..     121     165 .. 0.74
   3 !   39.4   0.0   1.8e-13   5.2e-10       2      81 ..     224     303 ..     223     312 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.3
                                      HHHTT--GGG-SEEEE CS
                     ACP_syn_III_C  1 Lekagltpedidalvp 16
                                      L++a ++p +i+al++
  gi|242398785|ref|YP_002994209.1| 65 LKRARINPREIRALWF 80
                                      689999******9996 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.2
                                       GGHHHHHHHHHHHTTSS-TT-EEEEEEEETTTE CS
                     ACP_syn_III_C  50 aasiplaLdeaveegklkpgdlvllvgfGaGlt 82 
                                       +    +a++   ++ + +pgd++ +++  +G  
  gi|242398785|ref|YP_002994209.1| 131 SGMAKYAMAIGADTSQGRPGDHLEFTASAGGAA 163
                                       555556777777788889999999999988865 PP

  == domain 3  score: 39.4 bits;  conditional E-value: 1.8e-13
                                       HHTT--GGG-SEEEE-SSSHHHHHHHHHHHT--GGGB--TH..HHH-B-GGGHHHHHHHHHHHTTSS-TT-EEEEEE CS
                     ACP_syn_III_C   2 ekagltpedidalvphqanlriidavakklglpeekvvvnl..deyGntsaasiplaLdeaveegklkpgdlvllvg 76 
                                       e+ +++p+d+d+ v+hq n ++   vak lg+p+ekv+  l    +Gnt +   ++ ++  ++    kpgd++l+v+
  gi|242398785|ref|YP_002994209.1| 224 EELDYSPSDFDFAVFHQPNVKFPLTVAKILGIPKEKVLPGLlsGIIGNTYSGATLVGISAVLD--IAKPGDRILWVS 298
                                       77889*********************************99977789*****************..99********** PP

                                       EETTT CS
                     ACP_syn_III_C  77 fGaGl 81 
                                       fG G 
  gi|242398785|ref|YP_002994209.1| 299 FGSGA 303
                                       **996 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 !   20.7   0.5   9.5e-08   0.00028       2      65 ..     110     170 ..     109     181 .. 0.85
   2 ?    0.9   0.0      0.14   4.1e+02      38      58 ..     282     305 ..     268     320 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 9.5e-08
                                       EEE-GGGHHHHHHHHHHHHHHTTS-SEEEEEEEEEGGGCS-TTTHHHHTTB-EEEEEEEEEEES CS
                       ACP_syn_III   2 DlnaaCsgfvyalsvAdaliesgaakrvLvigaetlskilDwkdrstavlfGDGAgAvvlease 65 
                                       D++ aC++ + al+ A +++ sg+ak+++ iga+t      +      ++ + G++A ++++++
  gi|242398785|ref|YP_002994209.1| 110 DFEFACKAGTEALQAAIGFVGSGMAKYAMAIGADTSQG---RPGDHLEFTASAGGAAYIVGEKT 170
                                       8899*******************************444...55578888999999999999874 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.14
                                       GGCS-TT...THHHHTTB-EEEEE CS
                       ACP_syn_III  38 skilDwk...drstavlfGDGAgA 58 
                                       s +lD +   dr  +v fG GAg 
  gi|242398785|ref|YP_002994209.1| 282 SAVLDIAkpgDRILWVSFGSGAGS 305
                                       555665533389999******995 PP

>> HMG_CoA_synt_N  Hydroxymethylglutaryl-coenzyme A synthase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   1.4e-07   0.00043       3     172 ..       9     169 ..       7     171 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.4e-07
                    HMG_CoA_synt_N   3 kdvgilaleiylpaqyvdqaelekfdgveagkytiglgqtrmgfvsdredinslsltvvqkllertkldydaigrle 79 
                                       kdvgi++   y+p   +++ e+ +  gv+      g+   + +  +  ed  ++ +   ++ l+r +++   i  l 
  gi|242398785|ref|YP_002994209.1|   9 KDVGIVGYGAYVPMFRIKNEEIGRVWGVN------GFPIQEKSVNNLDEDAITIGIEAARNALKRARINPREIRALW 79 
                                       89*****************9999999997......566678899999****************************** PP

                    HMG_CoA_synt_N  80 vgtetiidksksvksvlmqlfeesgntdiegidtlnacyggtaalfnavnwiessawdgryalvvagdiaiydsgna 156
                                        gte+     k   +v+ + ++     d++  d   ac  gt+al  a+ ++ s +   +ya+ +  d +    g+ 
  gi|242398785|ref|YP_002994209.1|  80 FGTESKPYAVKPSATVIAEAIGA--TPDLDAADFEFACKAGTEALQAAIGFVGSGM--AKYAMAIGADTSQGRPGDH 152
                                       ****8555555555555555544..459************************9987..6899999999988777765 PP

                    HMG_CoA_synt_N 157 .rptggagavalligpd 172
                                          t  ag  a ++g +
  gi|242398785|ref|YP_002994209.1| 153 lEFTASAGGAAYIVGEK 169
                                       25677888888877765 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 ?    2.5   0.1     0.031        93      66      82 ..     229     245 ..     210     254 .. 0.79
   2 !   13.5   0.0   1.4e-05     0.041     143     220 ..     259     330 ..     247     340 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.031
                                       -GGG-SEEEE--SSHHH CS
                    HMG_CoA_synt_C  66 tlddfdyvifhsPfckl 82 
                                       +  dfd+ +fh P  k+
  gi|242398785|ref|YP_002994209.1| 229 SPSDFDFAVFHQPNVKF 245
                                       5579*********9985 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 1.4e-05
                                       HTGGGGHHHHHH---GGGHHHHHHHHHHHHS-HHHHTT-EEEEEEEETTTEEEEEEEEE-S--STTSHHHHHTTTTH CS
                    HMG_CoA_synt_C 143 kvkpsllvptevGnmYtaslyaalasllskvsadelagkriglfsYGsGlaaslfslrvkqdvsedsildiakvldl 219
                                       kv p l ++  +Gn Y  +  + + ++l  ++     g ri+  s+GsG  +  fsl v++  +e++ l   k++d 
  gi|242398785|ref|YP_002994209.1| 259 KVLPGL-LSGIIGNTYSGATLVGISAVLDIAK----PGDRILWVSFGSGAGSDAFSLIVQDAIEEKREL-APKTMDY 329
                                       555554.466799****999999999994443....589******************999888773332.4455554 PP

                                       H CS
                    HMG_CoA_synt_C 220 k 220
                                        
  gi|242398785|ref|YP_002994209.1| 330 V 330
                                       4 PP

>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   2.4e-06    0.0073      21     113 ..      51     143 ..      39     166 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.4e-06
                                       S-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCTTSTSCHHHHHHHHTTS-TTSEEEEEEHGGGHHHHHHHHHHH CS
                        Thiolase_N  21 lsaeeLlaealkallekagvdpeevdevivGnvlqagegqniarqaalkagipeevpavtvnkvcsSglkavalaaq 97 
                                         a  ++ ea++++l++a ++p e+  + +G+  +  + +  a  +a ++g   +  a   + +c  g +a+ +a++
  gi|242398785|ref|YP_002994209.1|  51 EDAITIGIEAARNALKRARINPREIRALWFGTESKPYAVKPSATVIAEAIGATPDLDAADFEFACKAGTEALQAAIG 127
                                       566778999******************************************************************** PP

                                       HHHTTSHSEEEEEEEE CS
                        Thiolase_N  98 siaageadvvvagGvE 113
                                        + +g a+ ++a+G+ 
  gi|242398785|ref|YP_002994209.1| 128 FVGSGMAKYAMAIGAD 143
                                       **************86 PP

>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0    0.0099        30      75     112 ..      39      77 ..      36      94 .. 0.79
   2 ?    5.2   0.7    0.0046        14     174     206 ..     114     146 ..      84     163 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0099
                                       THHHHHHHCTS-H.HHHHHHHHHHHHHHHHTS-HHTCTT CS
                     ketoacyl-synt  75 fgispreaeamdp.qqrllleaawealedagltpeeldg 112
                                       f i+++ ++++d  ++ + +eaa++al++a ++p+e++ 
  gi|242398785|ref|YP_002994209.1|  39 FPIQEKSVNNLDEdAITIGIEAARNALKRARINPREIRA 77 
                                       5677777777775256679***************99864 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0046
                                       GGGHHHHHHHHHHHHHHTTS-SEEEEEEEE--- CS
                     ketoacyl-synt 174 ACsSslvavhaavqslrsgeadvalaGGvelll 206
                                       AC ++  a++aa+  + sg a++a a G++++ 
  gi|242398785|ref|YP_002994209.1| 114 ACKAGTEALQAAIGFVGSGMAKYAMAIGADTSQ 146
                                       8999*************************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.28s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2308.13
//
Query:       gi|242398786|ref|YP_002994210.1|  [L=388]
Description: Acetyl-CoA acetyltransferase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-25   90.2   0.9      5e-25   88.3   0.9    1.8  1  Thiolase_N       Thiolase, N-terminal domain
    1.5e-09   37.5   0.5    1.5e-09   37.5   0.5    2.8  3  Thiolase_C       Thiolase, C-terminal domain
    2.9e-06   27.0   4.6    7.6e-05   22.4   2.1    2.7  3  ketoacyl-synt    Beta-ketoacyl synthase, N-terminal domain
     0.0051   16.6   0.9        2.9    7.8   0.0    2.4  2  ACP_syn_III      3-Oxoacyl-[acyl-carrier-protein (ACP)] synth
  ------ inclusion threshold ------
      0.019   15.0   1.2          2    8.5   0.0    3.3  3  Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain


Domain annotation for each model (and alignments):
>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.3   0.9   1.4e-28     5e-25       2     260 .]       8     225 ..       7     225 .. 0.88

  Alignments for each domain:
  == domain 1  score: 88.3 bits;  conditional E-value: 1.4e-28
                                       EEEEEEEE--EETTSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCT.TSTSC.HHHHHHHHTTS-TTS CS
                        Thiolase_N   2 vivsaartpigkfggslkdlsaeeLlaealkallekagvdpeevdevivGnvlqa.gegqn.iarqaalkagipeev 76 
                                       vi++   tp+g+    +  l  ++L+ eal +++e+ag+d  +vd+++vGn++++ + +q  +   +a  ag+  ++
  gi|242398786|ref|YP_002994210.1|   8 VIIGVGLTPVGE----HWRLGLRDLAVEALLNAMEDAGID--KVDSLYVGNMASGsFVEQEnLGALIADWAGL-GNI 77 
                                       788888899988....8889999***************97..6***********9955555499999999***.99* PP

                                       EEEEEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTTS-EEETCTTTTG.GSSSSEEEEEHHHHHHTEETTTT CS
                        Thiolase_N  77 pavtvnkvcsSglkavalaaqsiaageadvvvagGvEsmsnaptaestdvrsg.lklgdekakdllipdgladafne 152
                                       pav v+ +c+Sg +av ++++++++g  dvv ++GvE+m++a  +++t+  +  +  + e  +++            
  gi|242398786|ref|YP_002994210.1|  78 PAVKVEAACASGGAAVQEGVKAVMSGLEDVVAVVGVEKMTDAWPSDATRYLAYaADAEWELFHGVSFVA-------- 146
                                       *****************************************9877776655440444444455555544........ PP

                                       SEHHHHHHHHHHHHT--HHHHHHHHHHHHHHHHHHHHTTTTTTTBE-EEEEESSSEEEE-S-TTS-TT--HHHHHTS CS
                        Thiolase_N 153 ehmGltaenlakkykisReeqdefAvkshqkaaaaqkagkFkdeivPvkvkgkkgkktvdkdeairsevtaekLakl 229
                                          +l+ + + k+y+ + e+++ fAv+ h+++a++  a  Fk+ i              + ++ ++s+ +a++++  
  gi|242398786|ref|YP_002994210.1| 147 -LNALAMRLYMKEYGYTEEDLALFAVNAHTNGAKNSYAM-FKKPI--------------TVETVMKSSYVADPIKLF 207
                                       .6688999******************************9.***88..............78899************* PP

                                       -BSSSTTSS-BTTSB--BEEEEEEEEEEEHH CS
                        Thiolase_N 230 kpaFkkeGtvtAgnasqisDGaaavllmses 260
                                                    +as+i+DGaaav++++e+
  gi|242398786|ref|YP_002994210.1| 208 -------------DASPIADGAAAVIITTEE 225
                                       .............**************9985 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.3       2.1   7.6e+03     106     117 ..      82      93 ..      79      97 .. 0.80
   2 ?   -1.0   0.0      0.36   1.3e+03      25      48 ..     149     172 ..     142     180 .. 0.86
   3 !   37.5   0.5   4.2e-13   1.5e-09      20     101 ..     259     358 ..     242     386 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2.1
                                       EEEEEETTTEEE CS
                        Thiolase_C 106 vaalCigggqgv 117
                                       v a+C++gg +v
  gi|242398786|ref|YP_002994210.1|  82 VEAACASGGAAV 93 
                                       789999999875 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.36
                                       HHHHHHHHHHHT--GGGESEEEE- CS
                        Thiolase_C  25 ayaikkvlkkagltvedidlfEin 48 
                                       a a++  +k+ g t ed+ lf +n
  gi|242398786|ref|YP_002994210.1| 149 ALAMRLYMKEYGYTEEDLALFAVN 172
                                       5688889999*********99988 PP

  == domain 3  score: 37.5 bits;  conditional E-value: 4.2e-13
                                       GGGHHHHHHHHHHHHHT--GGGESEEEE--SBHHHHHHHHHHHT--G..................GGBSTT--HHHH CS
                        Thiolase_C  20 lglgPayaikkvlkkagltvedidlfEinEAFaaqaLavakaldldl..................ekvNvnGGaial 78 
                                       +  +   a++++ k ag++v did+fE+++AF+  a  ++++++  +                    +   GG  a 
  gi|242398786|ref|YP_002994210.1| 259 FLKAAKVAAERAYKMAGISVGDIDFFEVHDAFTIMAALSLESIGAVErgkgamlakegqiaidgdYPIQTLGGLKAR 335
                                       5556678999***********************99999999999988899*************998999******** PP

                                       -B-TTTHHHHHHHHHHHHHHHCT CS
                        Thiolase_C  79 GHPlGasGaRivvtllselkkeg 101
                                       GHP+Ga+G+ ++v ++ +l+ e 
  gi|242398786|ref|YP_002994210.1| 336 GHPVGATGVYQTVEAVWQLRGEA 358
                                       ****************9998653 PP

>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.9   0.1    0.0092        33      91     126 ..      28      61 ..      25      72 .. 0.75
   2 !   22.4   2.1   2.1e-08   7.6e-05     167     210 ..      78     121 ..      66     134 .. 0.90
   3 ?   -2.1   0.0      0.66   2.4e+03     234     253 .]     208     227 ..     175     227 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.0092
                                       HHHHHHHHHHHHHTS-HHTCTTGGEEEEEEESSTHH CS
                     ketoacyl-synt  91 llleaawealedagltpeeldgsrvgvfiGvgagdy 126
                                       l++ea  +a+edag+++  +d+  vg+++  +  ++
  gi|242398786|ref|YP_002994210.1|  28 LAVEALLNAMEDAGIDK--VDSLYVGNMASGSFVEQ 61 
                                       8999***********99..66666777766555555 PP

  == domain 2  score: 22.4 bits;  conditional E-value: 2.1e-08
                                       SEEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---SHHH CS
                     ketoacyl-synt 167 psvtvdtACsSslvavhaavqslrsgeadvalaGGvellltpea 210
                                       p+v v++AC+S+ +av+  v++++sg  dv+ + Gve ++ ++ 
  gi|242398786|ref|YP_002994210.1|  78 PAVKVEAACASGGAAVQEGVKAVMSGLEDVVAVVGVEKMTDAWP 121
                                       8999*********************************9998765 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.66
                                       -SB-BB-EEEEEEEEECHHH CS
                     ketoacyl-synt 234 dGfvlGEGvGavvLkrleda 253
                                       d   +++G++av++ ++e+a
  gi|242398786|ref|YP_002994210.1| 208 DASPIADGAAAVIITTEEKA 227
                                       55567999999999988876 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 !    7.1   0.2    0.0013       4.7       3      39 ..      82     118 ..      80     134 .. 0.87
   2 !    7.8   0.0    0.0008       2.9      52      68 ..     212     228 ..     191     238 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0013
                                       EE-GGGHHHHHHHHHHHHHHTTS-SEEEEEEEEEGGG CS
                       ACP_syn_III   3 lnaaCsgfvyalsvAdaliesgaakrvLvigaetlsk 39 
                                       ++aaC++  +a++   +++ sg    v v+g e++++
  gi|242398786|ref|YP_002994210.1|  82 VEAACASGGAAVQEGVKAVMSGLEDVVAVVGVEKMTD 118
                                       789*******************************987 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0008
                                       B-EEEEEEEEEEESSSS CS
                       ACP_syn_III  52 fGDGAgAvvleaseeeg 68 
                                        +DGA+Av+++++e+ +
  gi|242398786|ref|YP_002994210.1| 212 IADGAAAVIITTEEKAK 228
                                       68**********86554 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 ?   -0.2   0.2      0.27   9.8e+02      28      56 ..      31      59 ..      24     109 .. 0.58
   2 ?    8.5   0.0   0.00055         2      24      52 ..     261     289 ..     238     296 .. 0.89
   3 ?    2.8   0.0     0.031   1.1e+02      88     108 ..     336     356 ..     327     365 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.27
                                      HHHHHHHHHHT--GGGEEEEE-SS-SSHH CS
                   Ketoacyl-synt_C 28 raiekalaeagvdpedvdyveahgtgtpl 56
                                      +a+ +a+++ag+d+ d  yv   ++g+ +
  gi|242398786|ref|YP_002994210.1| 31 EALLNAMEDAGIDKVDSLYVGNMASGSFV 59
                                      66778888888887777777777666654 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00055
                                       HHHHHHHHHHHHHHT--GGGEEEEE-SS- CS
                   Ketoacyl-synt_C  24 eaqaraiekalaeagvdpedvdyveahgt 52 
                                       +a++ a e+a+++ag++  d+d  e h++
  gi|242398786|ref|YP_002994210.1| 261 KAAKVAAERAYKMAGISVGDIDFFEVHDA 289
                                       6778899********************97 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.031
                                       -B-GGGHHHHHHHHHHHHHHH CS
                   Ketoacyl-synt_C  88 GHleaAaGvaelikvvlalkh 108
                                       GH  +A Gv +++ +v +l+ 
  gi|242398786|ref|YP_002994210.1| 336 GHPVGATGVYQTVEAVWQLRG 356
                                       9***************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 2385.13
//
Query:       gi|242398787|ref|YP_002994211.1|  [L=135]
Description: nucleic-acid-binding protein containing a Zn-ribbon [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-21   75.6   0.2    3.3e-21   75.1   0.2    1.2  1  OB_aCoA_assoc   DUF35 OB-fold domain, acyl-CoA-associated
    3.8e-14   52.2   0.9    5.3e-14   51.8   0.9    1.2  1  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
     0.0013   18.4   0.4     0.0018   17.9   0.4    1.2  1  TackOD1         Thaumarchaeal output domain 1
     0.0062   16.0   2.7       0.55    9.8   0.1    2.6  2  TF_Zn_Ribbon    TFIIB zinc-binding
     0.0093   16.0   0.7      0.014   15.4   0.7    1.2  1  DZR             Double zinc ribbon
  ------ inclusion threshold ------
      0.012   15.6   0.2      0.016   15.1   0.2    1.2  1  zinc-ribbons_6  zinc-ribbons
      0.017   15.4   1.1      0.027   14.7   1.1    1.3  1  Ribosomal_L32p  Ribosomal L32p protein family
      0.033   14.2   0.8      0.064   13.3   0.3    1.7  2  HypA            Hydrogenase/urease nickel incorporation, meta
      0.065   13.2   2.0        3.7    7.6   0.2    2.4  2  Nudix_N_2       Nudix N-terminal
       0.11   12.6   6.0       0.44   10.7   6.0    2.0  1  Zn-ribbon_8     Zinc ribbon domain
       0.12   12.4   0.0       0.26   11.3   0.0    1.5  1  HTH_Crp_2       Crp-like helix-turn-helix domain
       0.13   12.0   0.1       0.13   12.0   0.1    2.4  2  zf-RRN7         Zinc-finger of RNA-polymerase I-specific TFII
       0.14   12.2   0.4       0.14   12.2   0.4    2.1  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
       0.14   12.4   0.4         21    5.4   0.0    2.3  2  zinc_ribbon_13  Nucleic-acid-binding protein containing Zn-ri
       0.27   11.2   2.8        7.2    6.6   0.8    2.4  2  zinc_ribbon_4   zinc-ribbon domain
       0.35   10.3   6.9        2.3    7.7   7.3    1.9  2  zf-ribbon_3     zinc-ribbon domain
       0.45   10.3   7.3       0.98    9.2   7.3    1.6  1  zinc_ribbon_2   zinc-ribbon domain
        0.9    9.6   3.2         20    5.4   0.3    2.9  3  XPA_N           XPA protein N-terminal
          1    9.3   3.4         18    5.3   0.1    2.3  2  TFIIS_C         Transcription factor S-II (TFIIS)
        1.6    8.5   6.3        8.8    6.2   6.3    2.1  1  Rubredoxin_2    Rubredoxin metal binding domain
        1.7    8.4   5.2        4.3    7.1   0.6    2.6  2  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain


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 !   75.1   0.2   3.8e-24   3.3e-21       3      65 .]      51     113 ..      50     113 .. 0.97

  Alignments for each domain:
  == domain 1  score: 75.1 bits;  conditional E-value: 3.8e-24
                                       EE-GG-EEEEEEEEEE-TTS-EEEEEEEEEEEE-TT...-EE-EEEEEEES..TT-B-EEE-S CS
                     OB_aCoA_assoc   3 elsgrGtvysftvvhrappgfaeeaPyvvgvVeLdegvrimarlvgvdpdevriGmrVravfr 65 
                                       ++sg+G+v+s+t+v+ +p g++ ++Py++++VeL+eg+ ++++l++vdp+e+ +Gm+V++v+r
  gi|242398787|ref|YP_002994211.1|  51 QFSGKGKVVSWTIVRNPPSGYEYYKPYPIALVELEEGPVVLTQLTDVDPEEIYFGMEVEMVTR 113
                                       579*********************************************************986 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 !   51.8   0.9   6.2e-17   5.3e-14       6      37 .]      17      48 ..      12      48 .. 0.92

  Alignments for each domain:
  == domain 1  score: 51.8 bits;  conditional E-value: 6.2e-17
                           DUF35_N  6 egrLvgqrCpdCGtvqfPPravCphCgsddle 37
                                       +rL+g++C++CG+v+fP+r++Cp Cgs + e
  gi|242398787|ref|YP_002994211.1| 17 KYRLIGGKCKNCGHVHFPKRPICPECGSQEIE 48
                                      69**************************9876 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.4   2.2e-06    0.0018      75     100 ..      24      49 ..      12      53 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.2e-06
                           TackOD1  75 lCpsCksghlnvrevCpkCkSidiee 100
                                        C++C + h+  r +Cp+C+S +ie 
  gi|242398787|ref|YP_002994211.1|  24 KCKNCGHVHFPKRPICPECGSQEIED 49 
                                       6**********************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 ?    5.7   0.5     0.012        10       2       9 ..      24      31 ..      23      34 .. 0.77
   2 !    9.8   0.1   0.00065      0.55       2      14 ..      38      49 ..      37      56 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.012
                                      EETTTTCE CS
                      TF_Zn_Ribbon  2 kCPnCgst 9 
                                      kC+nCg+ 
  gi|242398787|ref|YP_002994211.1| 24 KCKNCGHV 31
                                      79999975 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00065
                                      EETTTTCEECHEE CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveD 14
                                      +CP+Cgs + +eD
  gi|242398787|ref|YP_002994211.1| 38 ICPECGSQE-IED 49
                                      6*****988.555 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.7   1.6e-05     0.014       1      20 [.      25      44 ..      13      52 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.6e-05
                               DZR  1 CpqCgeelppdarfCseCgt 20
                                      C++Cg+ + p+   C+eCg+
  gi|242398787|ref|YP_002994211.1| 25 CKNCGHVHFPKRPICPECGS 44
                                      66666666666666666665 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.2   1.9e-05     0.016      18      41 ..      24      49 ..       9      57 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.9e-05
                                      E-TTT--.EEEEEEE-SSS-.S---E CS
                    zinc-ribbons_6 18 hCeaCqe.dlkkealCpeCe.qelev 41
                                      +C++C + ++ k ++CpeC+ qe+e 
  gi|242398787|ref|YP_002994211.1| 24 KCKNCGHvHFPKRPICPECGsQEIED 49
                                      7****998***********8245665 PP

>> Ribosomal_L32p  Ribosomal L32p protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   1.1   3.2e-05     0.027      28      47 ..      24      44 ..      12      50 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.2e-05
                                      EETTTCCEECTTC.-BTTTTB CS
                    Ribosomal_L32p 28 ecpncgelklpHr.vcpscGy 47
                                      +c+ncg+++ p+r +cp+cG 
  gi|242398787|ref|YP_002994211.1| 24 KCKNCGHVHFPKRpICPECGS 44
                                      8***********999****95 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 ?   13.3   0.3   7.5e-05     0.064      71      98 ..      23      48 ..      13      60 .. 0.81
   2 ?   -1.5   0.0         3   2.5e+03      32      50 ..      90     108 ..      83     119 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.5e-05
                                      EEETTTS-EEECHHHHHS-TTTSSS-EE CS
                              HypA 71 vrCreCgkefeleekalrCpkCgsadve 98
                                       +C++Cg+    ++    Cp+Cgs+++e
  gi|242398787|ref|YP_002994211.1| 23 GKCKNCGHVHFPKR--PICPECGSQEIE 48
                                      68*****7766663..47******9876 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3
                                       EEETTCT--HHHHHHHHHH CS
                              HypA  32 evGelsgvepeaLefafel 50 
                                        + +l+ v+pe + f +e+
  gi|242398787|ref|YP_002994211.1|  90 VLTQLTDVDPEEIYFGMEV 108
                                       5678888888888777665 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.2    0.0043       3.7      25      32 ..      25      32 ..      16      33 .. 0.89
   2 ?    4.9   0.1      0.03        25      22      29 ..      36      43 ..      34      47 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0043
                                      ETTTTEEE CS
                         Nudix_N_2 25 CpaCgtih 32
                                      C++Cg++h
  gi|242398787|ref|YP_002994211.1| 25 CKNCGHVH 32
                                      *******9 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.03
                                      EEEETTTT CS
                         Nudix_N_2 22 RlvCpaCg 29
                                      R +Cp Cg
  gi|242398787|ref|YP_002994211.1| 36 RPICPECG 43
                                      66777776 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   6.0   0.00052      0.44       7      35 ..      24      46 ..      17      49 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00052
                       Zn-ribbon_8  7 rCeeCghefevlqsisdapltaCPeCgs.e 35
                                      +C++Cgh++ +         + CPeCgs e
  gi|242398787|ref|YP_002994211.1| 24 KCKNCGHVHFPK-------RPICPECGSqE 46
                                      5*****888754.......456*****966 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 ?   11.3   0.0   0.00031      0.26      30      53 ..     103     126 ..     102     132 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00031
                                       HTTSSHHHHHHHHHHHHHTTSEEE CS
                         HTH_Crp_2  30 mlGltretvsrilseLkreglisr 53 
                                       + G+  e v+r  +e++++g+i  
  gi|242398787|ref|YP_002994211.1| 103 YFGMEVEMVTRKVREFEEDGIILY 126
                                       689******************975 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   2.0      0.31   2.7e+02      24      31 ..      25      32 ..      22      32 .. 0.88
   2 ?   12.0   0.1   0.00015      0.13       2      16 ..      34      51 ..      33      57 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.31
                           zf-RRN7 24 CrrChtqe 31
                                      C++C++++
  gi|242398787|ref|YP_002994211.1| 25 CKNCGHVH 32
                                      99999985 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00015
                           zf-RRN7  2 ekgppCgvCgc...rsft 16
                                       k+p+C++Cg+    +f+
  gi|242398787|ref|YP_002994211.1| 34 PKRPICPECGSqeiEDFQ 51
                                      589********7777776 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.9      0.71   6.1e+02      39      45 ..      24      30 ..      14      31 .. 0.80
   2 ?   12.2   0.4   0.00016      0.14      15      28 ..      33      46 ..      30      57 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.71
                     Zn_Tnp_IS1595 39 qCkeCrk 45
                                      +Ck C++
  gi|242398787|ref|YP_002994211.1| 24 KCKNCGH 30
                                      6777776 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00016
                     Zn_Tnp_IS1595 15 WpngfvCPhCgsrk 28
                                      +p +++CP Cgs++
  gi|242398787|ref|YP_002994211.1| 33 FPKRPICPECGSQE 46
                                      899********995 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 ?    5.1   0.1     0.031        26      37      46 ..      24      33 ..       7      36 .. 0.76
   2 ?    5.4   0.0     0.024        21       2      19 ..      39      56 ..      38      63 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.031
                    zinc_ribbon_13 37 sCknCgYtel 46
                                       CknCg++ +
  gi|242398787|ref|YP_002994211.1| 24 KCKNCGHVHF 33
                                      6*****9876 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.024
                    zinc_ribbon_13  2 CpKCgnteaevkevaatG 19
                                      Cp Cg++e+e  +++  G
  gi|242398787|ref|YP_002994211.1| 39 CPECGSQEIEDFQFSGKG 56
                                      ********9988887666 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.8    0.0085       7.2      27      34 ..      24      31 ..      23      33 .. 0.91
   2 ?    4.1   0.0      0.05        43       5      25 ..      39      58 ..      38      60 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0085
                     zinc_ribbon_4 27 rCskCghv 34
                                      +C++Cghv
  gi|242398787|ref|YP_002994211.1| 24 KCKNCGHV 31
                                      8******8 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.05
                     zinc_ribbon_4  5 CpsCkakyeiddeklpakgvk 25
                                      Cp+C+++ ei+d ++++kg+ 
  gi|242398787|ref|YP_002994211.1| 39 CPECGSQ-EIEDFQFSGKGKV 58
                                      ****998.7777777777765 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   7.3    0.0027       2.3       4      24 ..      24      44 ..      24      45 .. 0.90
   2 ?    7.7   0.6    0.0028       2.4       5      11 ..      39      45 ..      37      49 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0027
                       zf-ribbon_3  4 rCPnCGa.plssddnvCpyCGt 24
                                      +C nCG+ +  +  ++Cp CG+
  gi|242398787|ref|YP_002994211.1| 24 KCKNCGHvH-FPKRPICPECGS 44
                                      599****88.***********8 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0028
                       zf-ribbon_3  5 CPnCGap 11
                                      CP+CG++
  gi|242398787|ref|YP_002994211.1| 39 CPECGSQ 45
                                      7777765 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   7.3    0.0012      0.98       1      21 [.      24      44 ..      24      45 .. 0.96

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0012
                     zinc_ribbon_2  1 fCpnCGaelqdnakFCpyCGt 21
                                      +C+nCG+ + ++ + Cp+CG+
  gi|242398787|ref|YP_002994211.1| 24 KCKNCGHVHFPKRPICPECGS 44
                                      8*******************7 PP

>> XPA_N  XPA protein N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0      0.12     1e+02       9      21 ..       3      15 ..       2      17 .. 0.85
   2 ?   -0.1   0.3       1.2     1e+03       3       9 ..      24      30 ..      23      31 .. 0.83
   3 ?    5.4   0.3     0.023        20       1      11 [.      36      46 ..      36      50 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.12
                             XPA_N  9 kefldSyLldnFd 21
                                      ++ + S ++++F+
  gi|242398787|ref|YP_002994211.1|  3 RPMQVSRYWRHFK 15
                                      67889*******7 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.2
                             XPA_N  3 kCdeCgk 9 
                                      kC+ Cg+
  gi|242398787|ref|YP_002994211.1| 24 KCKNCGH 30
                                      7999985 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.023
                             XPA_N  1 apkCdeCgkef 11
                                      +p C eCg+++
  gi|242398787|ref|YP_002994211.1| 36 RPICPECGSQE 46
                                      599*****987 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.8      0.05        43      30      36 ..      24      30 ..      22      32 .. 0.80
   2 ?    5.3   0.1     0.021        18       3      11 ..      39      47 ..      38      52 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.05
                           TFIIS_C 30 kCtkCgh 36
                                      kC++Cgh
  gi|242398787|ref|YP_002994211.1| 24 KCKNCGH 30
                                      6888888 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.021
                           TFIIS_C  3 CpkCgsrea 11
                                      Cp+Cgs+e+
  gi|242398787|ref|YP_002994211.1| 39 CPECGSQEI 47
                                      *****9987 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   6.3      0.01       8.8       3      22 ..      25      44 ..      24      46 .. 0.94

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.01
                      Rubredoxin_2  3 CsqCGfesakwfGrCpsCgs 22
                                      C++CG+++      Cp+Cgs
  gi|242398787|ref|YP_002994211.1| 25 CKNCGHVHFPKRPICPECGS 44
                                      ******************97 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 ?    7.1   0.6    0.0051       4.3      24      32 .]      25      33 ..      24      33 .. 0.94
   2 ?    2.7   0.3      0.11        98      24      29 ..      39      44 ..      37      46 .. 0.61

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0051
                     zf-NADH-PPase 24 CpaCglehY 32
                                      C +Cg+ h+
  gi|242398787|ref|YP_002994211.1| 25 CKNCGHVHF 33
                                      ********9 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.11
                     zf-NADH-PPase 24 CpaCgl 29
                                      Cp Cg 
  gi|242398787|ref|YP_002994211.1| 39 CPECGS 44
                                      555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       562  (0.0313459); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 840.54
//
Query:       gi|242398788|ref|YP_002994212.1|  [L=122]
Description: hypothetical protein TSIB_0802 [Thermococcus sibiricus MM 739]
Scores for 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-16   58.2   9.4    1.2e-15   57.9   9.4    1.0  1  EamA      EamA-like transporter family
  ------ inclusion threshold ------
       0.15   12.4   1.0        0.2   11.9   1.0    1.2  1  DUF3007   Protein of unknown function (DUF3007)


Domain annotation for each model (and alignments):
>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.9   9.4   1.3e-19   1.2e-15       9     102 ..      30     121 ..      23     121 .. 0.97

  Alignments for each domain:
  == domain 1  score: 57.9 bits;  conditional E-value: 1.3e-19
                              EamA   9 laalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlafllffya 85 
                                       l+ +f +++ v+skil++++ p++++ +r++i+g++ ++ +l+ + +   +s++ w++l+l g+lg+++a ++f+ +
  gi|242398788|ref|YP_002994212.1|  30 LSGFFIGFGSVFSKILMKTITPFAINIIRLIIGGVFYFVALLYLGFPS--FSREVWAILILSGILGFTVADWMFLEG 104
                                       689***********************************9999999999..*************************** PP

                              EamA  86 lkktsasnaslitsleP 102
                                       ++++++s+asl+++ +P
  gi|242398788|ref|YP_002994212.1| 105 INYLGVSRASLLLTSSP 121
                                       ************99988 PP

>> DUF3007  Protein of unknown function (DUF3007)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   1.0   2.2e-05       0.2       1      47 [.      46      92 ..      46     105 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.2e-05
                           DUF3007  1 mrridvlaiglgvlllgglaylv.lqalGldslsagiwsqavlvlglv 47
                                      m+ i  +ai ++ l++gg+ y v l +lG++s+s  +w+ ++l   ++
  gi|242398788|ref|YP_002994212.1| 46 MKTITPFAINIIRLIIGGVFYFVaLLYLGFPSFSREVWAILILSG-IL 92
                                      66777899***********99762566***********9766643.33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 848.85
//
Query:       gi|242398789|ref|YP_002994213.1|  [L=186]
Description: N-acetyltransferase, GNAT family [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-22   80.2   0.5    1.8e-22   79.8   0.5    1.2  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    2.8e-16   59.6   0.0    4.7e-16   58.9   0.0    1.4  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    4.9e-15   55.7   0.2    8.2e-15   55.0   0.2    1.3  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    4.7e-08   32.9   0.0    7.4e-08   32.3   0.0    1.3  1  FR47             FR47-like protein
      1e-06   29.0   0.1    1.3e-06   28.7   0.1    1.2  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
    0.00017   22.2   0.2    0.00023   21.8   0.2    1.2  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
    0.00024   21.2   0.1    0.00035   20.6   0.1    1.3  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
    0.00052   20.1   0.0     0.0012   19.0   0.0    1.6  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
     0.0013   18.2   0.1     0.0017   17.9   0.1    1.3  1  Acetyltransf_15  Putative acetyl-transferase
     0.0066   16.3   0.0      0.023   14.5   0.0    1.8  2  Acetyltransf_18  Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.028   14.1   0.0      0.044   13.5   0.0    1.4  1  Acetyltransf_8   Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.8   0.5   1.1e-25   1.8e-22       3     117 .]      29     151 ..      27     151 .. 0.83

  Alignments for each domain:
  == domain 1  score: 79.8 bits;  conditional E-value: 1.1e-25
                                       HHHHHHHHHTH......HHHHHHHHHH...HHHHHHSTTCEEEEEEETTEEEEEEEEEEEET...TSTTEEEEEEEE CS
                    Acetyltransf_1   3 dlvellvesff......ppnedaseee...feesfsleaegllvaeedgeliGfisllkipd...ekggvayiesla 67 
                                       +lve++++ ++         e +s+ +    ++ +s+  +g++va++ ++++Gfi +  +++   e++ v++i++++
  gi|242398789|ref|YP_002994213.1|  29 TLVEIYMRGYEgmreygG--EGESY-AkryLRWCWSKASDGFFVAKDRDRVVGFIVCDNDWHsryENKIVGAIHEFV 102
                                       566677777666654322..22222.13556677999999************************************* PP

                                       ESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  68 VspeyrgkGlGsaLlealeerareegikkivlaveedndaairlYeklGF 117
                                       V++ y+gk++G++L++ ++e++ +   ++i+l+v e n++ai++YeklGF
  gi|242398789|ref|YP_002994213.1| 103 VDKGYQGKNVGTKLMDRCLEHLSKY-NNRIELWVGEKNKKAIEFYEKLGF 151
                                       ********************88887.6789*******************9 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.9   0.0   2.9e-19   4.7e-16      24     111 ..      57     156 ..      37     161 .. 0.87

  Alignments for each domain:
  == domain 1  score: 58.9 bits;  conditional E-value: 2.9e-19
                   Acetyltransf_10  24 eri.eegealllvaeeggkivGvielrdgs..........hisllfVdpeyrgqGigkaLleaveeeaekdgiklel 89 
                                       +++ ++ +  ++va++ +++vG+i  ++++           i+ ++Vd+ y+g+ +g++L+++++e+++k ++++el
  gi|242398789|ref|YP_002994213.1|  57 RWCwSKASDGFFVAKDRDRVVGFIVCDNDWhsryenkivgAIHEFVVDKGYQGKNVGTKLMDRCLEHLSKYNNRIEL 133
                                       556556666799************66777778888899******************************9999999** PP

                   Acetyltransf_10  90 tvnasp.yavpfYeklGFkavge 111
                                        v +++ +a++fYeklGFk+vg+
  gi|242398789|ref|YP_002994213.1| 134 WVGEKNkKAIEFYEKLGFKVVGK 156
                                       *****99*************986 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.0   0.2   5.1e-18   8.2e-15       4      75 ..      66     152 ..      63     153 .. 0.76

  Alignments for each domain:
  == domain 1  score: 55.0 bits;  conditional E-value: 5.1e-18
                                       EEEEEEETTEEEEEEEEEEES.........TCTEEEEE-GGGTTSSHHHHHHH.H.TT....SEEEEE.EEEE..TH CS
                    Acetyltransf_7   4 evfVaeddgkivGfialslld.........aeitrlaVdpeyrgkGiGraLle.a.ae....kgiile.qlel..na 62 
                                        +fVa+d +++vGfi++  ++         + i++++Vd+ y+gk +G++L++ + ++    +      +l++  ++
  gi|242398789|ref|YP_002994213.1|  66 GFFVAKDRDRVVGFIVCDNDWhsryenkivGAIHEFVVDKGYQGKNVGTKLMDrClEHlskyN---NRiELWVgeKN 139
                                       69*************98888899888777777777*****************95332243221...22345555433 PP

                                       HHHHHHHHHTTEE CS
                    Acetyltransf_7  63 ekaikfYeklGFe 75 
                                       +kai+fYeklGF+
  gi|242398789|ref|YP_002994213.1| 140 KKAIEFYEKLGFK 152
                                       4***********8 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.0   4.5e-11   7.4e-08      19      81 ..      93     156 ..      84     161 .. 0.89

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 4.5e-11
                                       -TTSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EEEEEETT-HHHHHHHHHHT-EEE.E CS
                              FR47  19 kdggelgalqvlpehrrrGlgsrlvkalakeiaergktvllvvvasNtpsirlyeklGfeki.e 81 
                                       k +g++    v++  +++  g++l     +++++ ++ + l+v+++N+++i++yeklGf++  +
  gi|242398789|ref|YP_002994213.1|  93 KIVGAIHEFVVDKGYQGKNVGTKLMDRCLEHLSKYNNRIELWVGEKNKKAIEFYEKLGFKVVgK 156
                                       445999999**************************************************98744 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.1   7.9e-10   1.3e-06       3     140 ..      18     157 ..      16     172 .. 0.82

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 7.9e-10
                    Acetyltransf_4   3 aateeDakeilaiyaeyvvntaitfeyevssveefekfleal.dsekeyvflvaesdrivGyaylg.qfkkrakdwk 77 
                                        +++ D + ++ +++ y + ++  +ey  +   ++++ l     +    +f + + dr+vG        ++r++++ 
  gi|242398789|ref|YP_002994213.1|  18 KLKRMDQETLETLVEIYMRGYEGMREYGGEGESYAKRYLRWCwSKASDGFFVAKDRDRVVGFIVCDnDWHSRYENKI 94 
                                       6778888888888888888888888988888889999999984455566777777*******999956777755554 PP

                    Acetyltransf_4  78 .aelsvylaerdnnkeglgrelidaleqvlkeqnienllaeiaspnensiqfhkalGFelvgif 140
                                        + +  +++++  + + +g +l+d + + l+++n ++++  +  +n+++i+f+++lGF++vg++
  gi|242398789|ref|YP_002994213.1|  95 vGAIHEFVVDKGYQGKNVGTKLMDRCLEHLSKYN-NRIELWVGEKNKKAIEFYEKLGFKVVGKS 157
                                       234555555799*********************9.789***********************985 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.2   1.4e-07   0.00023      34     138 .]      49     152 ..      18     152 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.4e-07
                    Acetyltransf_3  34 leeaeewlerawaeeseeegygwaivl.kdtgviGsvglrdleeedee.......aelgymlapsfwgkGyateavr 102
                                       ++ a+++l+  w   ++++g  + + + +d  v+G++ + +  ++  +       a  ++++++ ++gk ++t  + 
  gi|242398789|ref|YP_002994213.1|  49 ESYAKRYLR--WCWSKASDG--FFVAKdRDR-VVGFIVCDNDWHS--RyenkivgAIHEFVVDKGYQGKNVGTKLMD 118
                                       345666666..444445566..555331555.8****88743333..335889967777999999************ PP

                    Acetyltransf_3 103 alleyafeelglerlvavidkeNeaSirvleklGfe 138
                                        +le++ +    +r++  + ++N++ i  +eklGf+
  gi|242398789|ref|YP_002994213.1| 119 RCLEHLSKYN--NRIELWVGEKNKKAIEFYEKLGFK 152
                                       ******7666..99*********************7 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.1   2.1e-07   0.00035       4     127 ..      21     153 ..      18     154 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.1e-07
                                       EE-GGGHHHHHHHHHHHTT----H.....HHHHHHHHHHT......TSEEEEEEETTEEEEEEEEEEEEEEETTEEE CS
                    Acetyltransf_9   4 elteedldevlellkyaFqdeespl...eeireyfrklle......esrvlgaedngelvgqlallplelnvpGktl 71 
                                       ++++e l+  +e+  + ++  +++    e    y +++l       ++ +++a d +++vg + + + +++ + ++ 
  gi|242398789|ref|YP_002994213.1|  21 RMDQETLETLVEIYMRGYEGMREYGgegE---SYAKRYLRwcwskaSDGFFVAKDRDRVVGFIVC-DNDWHSRYENK 93 
                                       55566666666666666666666654332...333333333333445688999999999997654.55555555555 PP

                                       EEEEEEEEEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--....SSHHHHHTTT-EE CS
                    Acetyltransf_9  72 kaagvtgVavapehrgrgvlskLlaraleemreegqplsllfP....ssipiYrrfGyei 127
                                        ++++    v+  ++g+ v +kL++r le++ + + ++ l ++     +i++Y+++G+++
  gi|242398789|ref|YP_002994213.1|  94 IVGAIHEFVVDKGYQGKNVGTKLMDRCLEHLSKYNNRIELWVGeknkKAIEFYEKLGFKV 153
                                       579999********************************999999988779********87 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   7.2e-07    0.0012      17      61 ..      90     132 ..      67     134 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 7.2e-07
                   Acetyltransf_CG  17 YevrkegvldfthTeVpeelrGkGiAkkLvkaalddareeglkvv 61 
                                       Ye  ++ v +++  +V++ ++Gk+++ kL++++l++  + + ++ 
  gi|242398789|ref|YP_002994213.1|  90 YE--NKIVGAIHEFVVDKGYQGKNVGTKLMDRCLEHLSKYNNRIE 132
                                       32..33355788899***********************9999986 PP

>> Acetyltransf_15  Putative acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.1     1e-06    0.0017      48     138 ..      27     153 ..       2     181 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1e-06
                   Acetyltransf_15  48 Lvasvfivkkkyyslvs............................................silieknvleiYtlyv 80 
                                       L + v i    y ++ +                                            s  ++k v  i +++v
  gi|242398789|ref|YP_002994213.1|  27 LETLVEIYMRGYEGMREyggegesyakrylrwcwskasdgffvakdrdrvvgfivcdndwhSRYENKIVGAIHEFVV 103
                                       55555555555555555555555555555555555555555555555555555555555558888888889****** PP

                   Acetyltransf_15  81 sekyrgkGlakklLeeslkelkknYkvdnelllaLHlnpkDksMnisfalYyslgFrk 138
                                       ++ y+gk +  kl+ + l++l  +Y+++    + L + +k k   ++  +Y +lgF+ 
  gi|242398789|ref|YP_002994213.1| 104 DKGYQGKNVGTKLMDRCLEHL-SKYNNR----IELWVGEKNK---KAIEFYEKLGFKV 153
                                       *****************9999.779999....9999*99987...799********85 PP

>> Acetyltransf_18  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.4   2.2e+03      22      42 ..      61      81 ..      53      85 .. 0.61
   2 !   14.5   0.0   1.4e-05     0.023      63     116 ..     113     168 ..     108     182 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.4
                   Acetyltransf_18 22 kqaeqklvvveedgeivGygl 42
                                      + a+   +v ++ +++vG+ +
  gi|242398789|ref|YP_002994213.1| 61 SKASDGFFVAKDRDRVVGFIV 81
                                      444445566666667888865 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 1.4e-05
                   Acetyltransf_18  63 AeaLlkalvanaeg..kkvridvpeenkalielleklgfkevfecarmvkngeelp 116
                                         +L+++++++ ++  + + + v e+nk++ie+ eklgfk v ++ + v+  + l+
  gi|242398789|ref|YP_002994213.1| 113 GTKLMDRCLEHLSKynNRIELWVGEKNKKAIEFYEKLGFKVVGKSGIWVRMVKDLK 168
                                       5667776666555433449999********************99976666544444 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.7e-05     0.044      81     141 ..      97     155 ..      61     157 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.7e-05
                                       EEEEEESSHHHCTTTCHHHHHHHHHHHHHC.CTT--EEEE--BTT-HHHHHHHHHTT-EEEE CS
                    Acetyltransf_8  81 GiHlligeaeargkglttallralvhylfa.dprtrrvvvEPdvrNerairllekaGfekek 141
                                        iH ++ ++ + gk+++t+l+ ++++ l + ++r++  v+E   +N++ai+++ek+Gf+ ++
  gi|242398789|ref|YP_002994213.1|  97 AIHEFVVDKGYQGKNVGTKLMDRCLEHLSKyNNRIELWVGE---KNKKAIEFYEKLGFKVVG 155
                                       4899999******************9999845577777776...9*************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1086  (0.0605723); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 1123.80
//
Query:       gi|242398790|ref|YP_002994214.1|  [L=179]
Description: DNA binding helix-turn helix protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.5e-10   38.7   0.1    1.4e-09   37.9   0.1    1.4  1  HTH_3     Helix-turn-helix
    4.3e-06   26.7   0.5    8.6e-06   25.7   0.5    1.6  1  HTH_19    Helix-turn-helix domain
    0.00041   20.2   0.2     0.0009   19.1   0.2    1.6  1  DUF4428   Domain of unknown function (DUF4428)
     0.0012   19.1   0.1     0.0028   18.0   0.0    1.6  2  HTH_31    Helix-turn-helix domain
     0.0016   18.5   0.0     0.0027   17.8   0.0    1.4  1  zf-UDP    Zinc-binding RING-finger
  ------ inclusion threshold ------
       0.11   12.1   0.0        0.2   11.3   0.0    1.4  1  HTH_24    Winged helix-turn-helix DNA-binding
       0.12   12.9   0.0        0.2   12.2   0.0    1.4  1  HTH_26    Cro/C1-type HTH DNA-binding domain


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   0.1   5.3e-13   1.4e-09       1      52 [.      93     144 ..      93     146 .. 0.95

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 5.3e-13
                                       HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSEH CS
                             HTH_3   1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgvsl 52 
                                       ++e+ ++ gls eeL+ ++G+s + i+ri  Ge +P+++ +kkl+++++++l
  gi|242398790|ref|YP_002994214.1|  93 VREAIQKSGLSYEELSHMVGLSTNLIRRIAHGEYIPTIDEAKKLERYFKIKL 144
                                       589999******************************************9987 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.5   3.4e-09   8.6e-06       2      55 ..      91     143 ..      90     154 .. 0.94

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 3.4e-09
                            HTH_19   2 erLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealgid 55 
                                       +r++ea+ + gl+ eel++++g s + i+ i +g++  p++++ +k+ ++++i 
  gi|242398790|ref|YP_002994214.1|  91 DRVREAIQKSGLSYEELSHMVGLSTNLIRRIAHGEY-IPTIDEAKKLERYFKIK 143
                                       79*********************************9.***************97 PP

>> DUF4428  Domain of unknown function (DUF4428)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.2   3.5e-07    0.0009       1      34 [.      11      50 ..      11      58 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 3.5e-07
                           DUF4428  1 iCaiCgkKigllkr.lkleDg..yvCkdClkKl...sefl 34
                                      iC iCg +ig  +  +k+e     vC+ C++K+   ++++
  gi|242398790|ref|YP_002994214.1| 11 ICEICGAEIGGKGHtVKIEGAelLVCHRCYEKYgrkKPGT 50
                                      7*********98766999988756********97665554 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.1       5.3   1.3e+04      30      43 ..      50      63 ..      48      65 .. 0.65
   2 !   18.0   0.0   1.1e-06    0.0028       3      54 ..      90     140 ..      88     150 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 5.3
                            HTH_31 30 tlsrlEqGrrgrps 43
                                      t+s + +Gr++r++
  gi|242398790|ref|YP_002994214.1| 50 TWSPMPTGREPRRR 63
                                      56666688887554 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 1.1e-06
                            HTH_31   3 GalLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaral 54 
                                       ++++r++ +++GLs ee+   +g+s   ++r+  G+  +p+ +   +l r++
  gi|242398790|ref|YP_002994214.1|  90 ADRVREAIQKSGLSYEELSHMVGLSTNLIRRIAHGEY-IPTIDEAKKLERYF 140
                                       67888899999**************************.7*999988888776 PP

>> zf-UDP  Zinc-binding RING-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0     1e-06    0.0027       5      48 ..       6      47 ..       3      70 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1e-06
                            zf-UDP  5 dlngqiCqiCgddvgltedgelFvacnecafpvcrpcye.yerkd 48
                                      +++ +iC+iCg ++g + +    v ++    +vc+ cye y rk 
  gi|242398790|ref|YP_002994214.1|  6 KAKPRICEICGAEIGGKGH---TVKIEGAELLVCHRCYEkYGRKK 47
                                      56789*********97644...48999999********9555554 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   7.7e-05       0.2      13      36 ..      97     120 ..      93     121 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 7.7e-05
                            HTH_24  13 qknprisqreLAerlglSpstvnr 36 
                                        +++++s+ eL+ ++glS + ++r
  gi|242398790|ref|YP_002994214.1|  97 IQKSGLSYEELSHMVGLSTNLIRR 120
                                       4679**************998877 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   7.6e-05       0.2       2      42 ..      93     132 ..      92     146 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.6e-05
                            HTH_26   2 LrelmadrgitkseLargtgisaatlsrlvkgkpervsldt 42 
                                        re++++ g+++ eL+ ++g+s + + r+ +g+   +++d+
  gi|242398790|ref|YP_002994214.1|  93 VREAIQKSGLSYEELSHMVGLSTNLIRRIAHGE-YIPTIDE 132
                                       6999****************************9.3555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       794  (0.0442858); expected 358.6 (0.02)
Passed bias filter:                      596  (0.0332422); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); 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 0.35s 00:00:00.93 Elapsed: 00:00:00.54
# Mc/sec: 993.41
//
Query:       gi|242398791|ref|YP_002994215.1|  [L=123]
Description: hypothetical protein TSIB_0805 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-36  123.8   0.1      4e-36  123.5   0.1    1.1  1  DUF356    Protein of unknown function (DUF356)


Domain annotation for each model (and alignments):
>> DUF356  Protein of unknown function (DUF356)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.5   0.1   2.2e-40     4e-36       1     105 [.       1     105 [.       1     106 [. 0.98

  Alignments for each domain:
  == domain 1  score: 123.5 bits;  conditional E-value: 2.2e-40
                            DUF356   1 liliRadnkeKvlnalaDlerygklkiegkPriiepevadkilekvlkeelkkkvkvaalveveedatkaisklrki 77 
                                       ++liR+dn +K+l+alaDl ry++++i+gkP+ii p+++d+ +ek+++ee+kkk++++++++v+  ++kai +lr+i
  gi|242398791|ref|YP_002994215.1|   1 MVLIRTDNFDKALIALADLVRYAGMEIRGKPKIIPPALSDWAVEKIVGEEPKKKYRAHVVAQVDLPPAKAIGRLREI 77 
                                       69*************************************************************************** PP

                            DUF356  78 HPPaHvvvvseeydeyeellekleklke 105
                                       HPPaH++v++++  +++ell+ +++++ 
  gi|242398791|ref|YP_002994215.1|  78 HPPAHIIVIPPDTPVHKELLKLWGTFEV 105
                                       **********************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       293  (0.0163422); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 790.41
//
Query:       gi|242398792|ref|YP_002994216.1|  [L=38]
Description: hypothetical protein TSIB_0806, partial [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       262  (0.0146132); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 283.54
//
Query:       gi|242398793|ref|YP_002994217.1|  [L=61]
Description: hypothetical protein TSIB_0807 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       194  (0.0108205); expected 358.6 (0.02)
Passed bias filter:                      151  (0.00842211); 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: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 461.93
//
Query:       gi|242398794|ref|YP_002994218.1|  [L=40]
Description: hypothetical protein TSIB_0808 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      147  (0.00819901); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.23s 00:00:00.54 Elapsed: 00:00:00.38
# Mc/sec: 311.85
//
Query:       gi|242398795|ref|YP_002994219.1|  [L=312]
Description: ABC transporter [Thermococcus sibiricus MM 739]
Scores for complete 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-27   94.6   0.0    1.2e-26   93.9   0.0    1.4  1  ABC_tran  ABC transporter
    1.4e-11   44.8   0.3    2.3e-07   30.9   0.0    2.2  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    0.00071   19.4   0.0       0.36   10.5   0.0    2.2  2  AAA_15    AAA ATPase domain
     0.0014   19.1   0.6      0.003   18.1   0.6    1.6  1  AAA_23    AAA domain
     0.0057   16.1   0.1       0.27   10.7   0.0    2.1  2  SMC_N     RecF/RecN/SMC N terminal domain
  ------ inclusion threshold ------
      0.021   14.6   0.0      0.038   13.7   0.0    1.5  1  AAA_30    AAA domain
      0.032   13.9   0.3       0.15   11.7   0.1    2.0  2  SRP54     SRP54-type protein, GTPase domain
      0.033   14.5   0.0       0.08   13.2   0.0    1.6  1  AAA_22    AAA domain
        0.1   13.0   0.3       0.18   12.2   0.3    1.6  1  AAA       ATPase family associated with various cellular acti
       0.13   12.0   0.0       0.26   11.1   0.0    1.4  1  AAA_29    P-loop containing region of AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.9   0.0   6.7e-30   1.2e-26       4     137 .]      23     164 ..      20     164 .. 0.92

  Alignments for each domain:
  == domain 1  score: 93.9 bits;  conditional E-value: 6.7e-30
                                       EEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                          ABC_tran   4 vslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren. 79 
                                       ++lk+ +g +++++G+nGaGK+t +k+l+  l+pt Gei++ g ++ + ++ +  k++g++p+ p   +++t+ e  
  gi|242398795|ref|YP_002994219.1|  23 LDLKVPKGVVYGFLGPNGAGKTTTIKMLTAALRPTYGEIRIFGLEIPQ-KRVEIMKKVGYMPEIPIAYEDMTIVEFl 98 
                                       789*******************************************99.8888999*******************9* PP

                                       ............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       ............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  80 ............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                                   ++ e+ +++++ +g   l+ +++    ++LS Gqkqrva a al+ +p+ll+lDEpta
  gi|242398795|ref|YP_002994219.1|  99 tymgrlsglkkeKAMEQTKELMRYVGVGRLALNKI----KELSSGQKQRVAFASALIADPELLILDEPTA 164
                                       ********977666667888888888887777777....*****************************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 !   12.0   0.1   7.6e-05      0.14       3      24 ..      34      55 ..      32      92 .. 0.75
   2 !   30.9   0.0   1.3e-10   2.3e-07     234     297 ..     133     193 ..      95     198 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.6e-05
                            AAA_21  3 vliGpNgsGKSnLLdaldllar 24
                                      ++ GpNg+GK++ ++ l  + r
  gi|242398795|ref|YP_002994219.1| 34 GFLGPNGAGKTTTIKMLTAALR 55
                                      689************9965543 PP

  == domain 2  score: 30.9 bits;  conditional E-value: 1.3e-10
                            AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHP.kllrrllellkelsrngaQviltTH 297
                                       + elS+G+k+  a+++al++++    ll++DEp ++L+P  +++ + ++++++++ g  +++++H
  gi|242398795|ref|YP_002994219.1| 133 IKELSSGQKQRVAFASALIADP---ELLILDEPTANLDPlGRIEFIGKIISLAKE-GKTIFVSSH 193
                                       4589****************99...9*************9999999999999988.999****** PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0    0.0023       4.1      28      45 ..      35      52 ..      21     119 .. 0.81
   2 !   10.5   0.0    0.0002      0.36     294     364 ..     133     193 ..     100     194 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0023
                            AAA_15 28 liGkNnsGKSsilealdl 45
                                      + G+N++GK++ +++l  
  gi|242398795|ref|YP_002994219.1| 35 FLGPNGAGKTTTIKMLTA 52
                                      78*************976 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0002
                            AAA_15 294 lnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                       +++ +sG+++ + ++  +          +++ +l+++EP a+L p    ++i ++++la+++k  +++++H
  gi|242398795|ref|YP_002994219.1| 133 IKELSSGQKQRVAFASAL---------IADPELLILDEPTANLDPLGRIEFIGKIISLAKEGK-TIFVSSH 193
                                       555566666655444332.........345689*****************************9.9***999 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.6   1.7e-06     0.003      22      43 ..      33      54 ..      18     152 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.7e-06
                            AAA_23 22 tlItGpNGaGKTTildAiklaL 43
                                      + + GpNGaGKTT +  ++ aL
  gi|242398795|ref|YP_002994219.1| 33 YGFLGPNGAGKTTTIKMLTAAL 54
                                      6789*****************8 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.022        39      29      42 ..      35      48 ..      15      62 .. 0.84
   2 !   10.7   0.0   0.00015      0.27     134     213 ..     133     209 ..      68     215 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.022
                                      EEESTTSSHHHHHH CS
                                      xxxxxxxxxxxxxx RF
                             SMC_N 29 ivGpNGSGKsnlld 42
                                       +GpNG+GK+  + 
  gi|242398795|ref|YP_002994219.1| 35 FLGPNGAGKTTTIK 48
                                      57*******98765 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00015
                                       TTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HH.HHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 134 kelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDek.nvkkvaellkeksknaQfivislreemlekadklv 209
                                       +++LS G+k+ va    fA   +    l +lDe  a+LD   +++ + +++  +++   ++v s+    +ek+ + v
  gi|242398795|ref|YP_002994219.1| 133 IKELSSGQKQRVA----FASALIADPELLILDEPTANLDPLgRIEFIGKIISLAKEGKTIFVSSHIVSEVEKMCNYV 205
                                       4589999999766....556666667799**********86267888999999999999*************99999 PP

                                       EEEE CS
                                       xxxx RF
                             SMC_N 210 gvtk 213
                                       g+  
  gi|242398795|ref|YP_002994219.1| 206 GLIN 209
                                       9876 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.1e-05     0.038      23      63 ..      35      77 ..      27     164 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.1e-05
                            AAA_30 23 ltGpAGtGKttalkalreaweaa.g.grviglAptgkaAkvLa 63
                                        Gp G+GKtt++k l++a++   g  r++gl   +k  + ++
  gi|242398795|ref|YP_002994219.1| 35 FLGPNGAGKTTTIKMLTAALRPTyGeIRIFGLEIPQKRVEIMK 77
                                      679***************9998855466666666666666666 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   8.1e-05      0.15       5      26 ..      34      55 ..      31      66 .. 0.83
   2 ?   -1.0   0.0      0.62   1.1e+03     123     155 ..     106     138 ..     100     149 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 8.1e-05
                                      EEEESTTSSHHHHHHHHHHHHH CS
                             SRP54  5 llvGlqGaGKTttlaKLaallk 26
                                       ++G++GaGKTtt+  L a l+
  gi|242398795|ref|YP_002994219.1| 34 GFLGPNGAGKTTTIKMLTAALR 55
                                      589***********99988765 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.62
                                       TTBHTHHHHHHHHHHHHSSCSEEEEESTTSSSS CS
                             SRP54 123 attgqeavkqakaFkeavgitgviltklDgdak 155
                                       ++ +++a++q+k+  + vg++ + l k+ + ++
  gi|242398795|ref|YP_002994219.1| 106 GLKKEKAMEQTKELMRYVGVGRLALNKIKELSS 138
                                       566778888888888888888888888876554 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.4e-05      0.08      12      99 ..      37     161 ..      32     190 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.4e-05
                            AAA_22  12 GesGtGKTtllrrlleqldeeakaee................erpevv.fvtlpsst.sskdllrellralglelka 70 
                                       G+ G+GKTt++++l+  l   +   e                ++++++ ++ ++ +  +  ++l+ + r  gl++++
  gi|242398795|ref|YP_002994219.1|  37 GPNGAGKTTTIKMLTAALRPTYG--EirifgleipqkrveimKKVGYMpEIPIAYEDmTIVEFLTYMGRLSGLKKEK 111
                                       9***************9954333..2458888888866666555555576666655568888888888888888888 PP

                            AAA_22  71 .................erlsseell.ealeqalrarav...ielliiDE 99 
                                                        + ++ +el   + ++ + a a    +elli+DE
  gi|242398795|ref|YP_002994219.1| 112 ameqtkelmryvgvgrlALNKIKELSsGQKQRVAFASALiadPELLILDE 161
                                       54444444444444444333333333333333333333356666666666 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.3    0.0001      0.18       3      31 ..      35      63 ..      33     162 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0001
                                      EESSTTSSHHHHHHHHHHHHTHEEEEEET CS
                               AAA  3 lyGppGtGKTllakavakelgvefleisg 31
                                      + Gp G GKT+++k +   l  ++ ei  
  gi|242398795|ref|YP_002994219.1| 35 FLGPNGAGKTTTIKMLTAALRPTYGEIRI 63
                                      78***************999644433332 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 ?   11.1   0.0   0.00014      0.26      22      49 ..      29      57 ..      21      62 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00014
                            AAA_29 22 kg.atlltGpsGsGKSTllDAiqalLvpa 49
                                      kg ++ + Gp+G+GK+T +  ++a L p+
  gi|242398795|ref|YP_002994219.1| 29 KGvVYGFLGPNGAGKTTTIKMLTAALRPT 57
                                      56677799**********99888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.65u 0.34s 00:00:00.99 Elapsed: 00:00:00.54
# Mc/sec: 1739.61
//
Query:       gi|242398796|ref|YP_002994220.1|  [L=237]
Description: ABC-type transport system, permease component [Thermococcus sibiricus MM 739]
Scores for complete 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  18.0    5.1e-14   52.2  18.0    1.3  1  ABC2_membrane_2  ABC-2 family transporter protein
    0.00017   21.6  13.6    0.00017   21.6  13.6    1.9  2  ABC2_membrane_4  ABC-2 family transporter protein
  ------ inclusion threshold ------
      0.025   14.1  19.4       0.17   11.4  19.6    2.3  1  ABC2_membrane_5  ABC-2 family transporter protein
      0.057   12.5  26.5        0.1   11.7  26.5    1.5  1  ABC2_membrane_3  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.2  18.0   1.1e-17   5.1e-14      77     279 ..      36     229 ..       6     233 .. 0.70

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 1.1e-17
                   ABC2_membrane_2  77 vstimavlipviaalfgadaiagEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvll...alaiil 150
                                       +   ++v++ +i +++ +d++a E +rgT++llL kP+ ++ei++gKf +g++    + +++++ +l+    +++  
  gi|242398796|ref|YP_002994220.1|  36 INFWASVIGQLIVIIIMSDLLASEIDRGTIRLLLVKPIKKSEIVFGKFFSGITT---VSLIFGIPYLVmeiYMVLLY 109
                                       44567889999999**********************************999998...88888888888555444555 PP

                   ABC2_membrane_2 151 algivlaledllllvvasvlllllv.vflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavp 226
                                       ++g +  ++ +  +++a  +++l++  + a+++llS+++     a ++++gl++  +++ p + +   +++  +   
  gi|242398796|ref|YP_002994220.1| 110 KSGFEGFTATFDDFLYALGVTILVLgSLGAVSMLLSVILSRPLYASLASFGLVFTAQFILPQLPFF--DNPERFNL- 183
                                       5555555555556666666666655689*********************************99965..44443444. PP

                   ABC2_membrane_2 227 qeindflsllsptsayntllneilagsdlnalgstatnllilllllavllvlg 279
                                           ++  ll+ +   +t+l++    +     ++ a  +l+++ll + ++ lg
  gi|242398796|ref|YP_002994220.1| 184 --SYQIGVLLKRGFTLHTGLDTYKGDA-----TMSALFFLSVILLSLTFTLLG 229
                                       ..2233334445555555555544444.....455555555555555555555 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 !   21.6  13.6   3.7e-08   0.00017      48     159 ..      29     149 ..       1     170 [. 0.56
   2 ?   -0.8   0.5      0.29   1.3e+03      99     116 ..     210     227 ..     207     233 .. 0.57

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 3.7e-08
                   ABC2_membrane_4  48 s.lsvfgftll..lllplilgiiasylifrEeqndtlknLltiPvsrtklllaKlivllllsvllmlvtflitvlfa 121
                                          s+f ++++  ++  li++ii s l+  E + +t++ Ll+ P+++ +++++K++  + ++ l+  + +l++ +  
  gi|242398796|ref|YP_002994220.1|  29 InISQFLINFWasVIGQLIVIIIMSDLLASEIDRGTIRLLLVKPIKKSEIVFGKFFSGITTVSLIFGIPYLVMEIYM 105
                                       223567677666689999*************************************8655544444444444444444 PP

                   ABC2_membrane_4 122 llsgfvgfs.....vklvlellk.kclelgllvffavlpiialv 159
                                       +l+ ++gf+     ++ +l++l   +l+lg l ++ +l  ++l+
  gi|242398796|ref|YP_002994220.1| 106 VLLYKSGFEgftatFDDFLYALGvTILVLGSLGAVSMLLSVILS 149
                                       44444444321111344665555133355555555555444444 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.29
                   ABC2_membrane_4  99 livllllsvllmlvtfli 116
                                       +++l++lsv+l+ +tf++
  gi|242398796|ref|YP_002994220.1| 210 MSALFFLSVILLSLTFTL 227
                                       455666666555554443 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 ?   11.4  19.6   3.7e-05      0.17      36     164 ..      36     172 ..      18     227 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.7e-05
                   ABC2_membrane_5  36 vllifsilslvisiililttlsyDekskwnkylltLPvtrkeiVksKYlfvlililiailitlllliiavlikgn.. 110
                                       +++  s++  +i+ii++  +l+ +   ++ ++ll  P++++eiV  K+++++  + + + i +l++ i++++  +  
  gi|242398796|ref|YP_002994220.1|  36 INFWASVIGQLIVIIIMSDLLASEIDRGTIRLLLVKPIKKSEIVFGKFFSGITTVSLIFGIPYLVMEIYMVLLYKsg 112
                                       346677777778888889***********************************999999999888877655444437 PP

                   ABC2_membrane_5 111 .....vtisevllsiliglvialiflaivlPl.yfkfgvekgrivliiiifgiifllvai 164
                                             t++++l+++ + +++   ++a+++ l +++     + ++++ ++f + f+l+++
  gi|242398796|ref|YP_002994220.1| 113 fegftATFDDFLYALGVTILVLGSLGAVSMLLsVILSRPLYASLASFGLVFTAQFILPQL 172
                                       777676677777776665554444455544440444555666677777777777777765 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 ?   11.7  26.5   2.3e-05       0.1     158     295 ..      30     179 ..       8     231 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.3e-05
                   ABC2_membrane_3 158 nvasflvgliliilifitasfiavsi.....veEkesrikelqlvsgvsplqywlsk....ilgdflvyllqlllil 225
                                       n+ +    +++ ++++++++ i+  i     ++E  ++++ l+lv ++++++++++k    i+++ l++ +++l++ 
  gi|242398796|ref|YP_002994220.1|  30 NISQ----FLINFWASVIGQLIVIIImsdllASEIDRGTIRLLLVKPIKKSEIVFGKffsgITTVSLIFGIPYLVME 102
                                       3333....444444444444333332233349*************************44444455555555555442 PP

                   ABC2_membrane_3 226 l.l..afgl.....gipfgnlglllllfllfglayialgyllsslfknsetaqilifivilllsgffgglfpledlp 294
                                       + +  ++++       +f++++++l + +l + ++ a+++lls++ +++  a+++ f + + +  f+++  p+ d p
  gi|242398796|ref|YP_002994220.1| 103 IyMvlLYKSgfegfTATFDDFLYALGVTILVLGSLGAVSMLLSVILSRPLYASLASFGLVF-TAQFILPQLPFFDNP 178
                                       2223244448897778888********************************9987766666.555555555544444 PP

                   ABC2_membrane_3 295 s 295
                                       +
  gi|242398796|ref|YP_002994220.1| 179 E 179
                                       4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.34s 00:00:00.92 Elapsed: 00:00:00.53
# Mc/sec: 1352.70
//
Query:       gi|242398797|ref|YP_002994221.1|  [L=717]
Description: hypothetical protein TSIB_0811 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (717 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 4570.13
//
Query:       gi|242398798|ref|YP_002994222.1|  [L=561]
Description: Methylmalonyl-CoA mutase [Thermococcus sibiricus MM 739]
Scores for complete 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-243  808.2   0.1   3.1e-243  808.0   0.1    1.0  1  MM_CoA_mutase  Methylmalonyl-CoA mutase
  ------ inclusion threshold ------
        0.1   12.6   0.1       0.95    9.5   0.0    2.4  2  DUF4911        Domain of unknown function (DUF4911)
       0.33    9.4   3.2       0.49    8.9   3.2    1.2  1  LRIF1          Ligand-dependent nuclear receptor-interacting 


Domain annotation for each model (and alignments):
>> MM_CoA_mutase  Methylmalonyl-CoA mutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  808.0   0.1  5.2e-247  3.1e-243       2     513 .]      39     553 ..      38     553 .. 0.98

  Alignments for each domain:
  == domain 1  score: 808.0 bits;  conditional E-value: 5.2e-247
                     MM_CoA_mutase   2 TaegievkplYtaedl.eek.klgeslPGefPftRGvkatmyrgrpWtirqyagfstaeetnerykklLeaGqtgls 76 
                                       T +g+e+k+ Yt++dl + +   + ++PG++PftRGv+atmyrgr Wt+rqyagf+taee+n+ryk+lLe+Gqtgls
  gi|242398798|ref|YP_002994222.1|  39 TDDGFEIKRTYTPADLeHWDyLEKLNFPGQYPFTRGVYATMYRGRLWTMRQYAGFGTAEESNKRYKYLLEQGQTGLS 115
                                       89**************6333455668*************************************************** PP

                     MM_CoA_mutase  77 vafdlptlrgyDsdhpraegevGkaGvaidsledmetlldgidldkvsvsmtinaaalpllamylaaaeeqgvdlek 153
                                       vafdlpt++gyDsdhp+aegevGk+Gvaidsl+dme+l+dgi+ldkvs+smtina+a++llamy+ + ++qgv++++
  gi|242398798|ref|YP_002994222.1| 116 VAFDLPTQIGYDSDHPMAEGEVGKVGVAIDSLKDMEILFDGIPLDKVSTSMTINATAANLLAMYILVGQKQGVPQDQ 192
                                       ***************************************************************************** PP

                     MM_CoA_mutase 154 lsgtiqnDiLkellargtyiyppepslrliadiieyaakevpkfntisvsgyhireaGatavqElAftladGveYvr 230
                                       l+gt+qnD+Lke++argtyi+pp+ps+rl++dii y+a++vpk+n+is+sgyhireaGa+avqE+AftladG+eYv+
  gi|242398798|ref|YP_002994222.1| 193 LRGTVQNDVLKEYIARGTYIFPPQPSMRLTTDIIMYCAEHVPKWNSISISGYHIREAGANAVQEVAFTLADGIEYVK 269
                                       ***************************************************************************** PP

                     MM_CoA_mutase 231 alleaGldvdefaprlsFffaigsdffeeiAklRAaRrlWarivkekfgakeekslklrvhaqTsgvsltaqdpyvN 307
                                       a++++G+dvd+faprlsFff+++++f eeiAk+RAaRrlWari+kekf+ak+++s+ lr+h+qT+g++ltaq+p++N
  gi|242398798|ref|YP_002994222.1| 270 AVIARGMDVDKFAPRLSFFFNAHNNFLEEIAKFRAARRLWARIMKEKFNAKDPRSMLLRFHTQTGGSTLTAQQPENN 346
                                       ***************************************************************************** PP

                     MM_CoA_mutase 308 ilRttlealaAvlggtqslhtnsfDealalPtefsariArntqlilaeEsgvakvvDPlgGSyyvEaLTdelaekaw 384
                                       i+R++++alaAvlggtqslhtns+Deal+lPte+s+riA++tq+i+a+Esgv +++DPlgGSyy+E+LTd+++e+a+
  gi|242398798|ref|YP_002994222.1| 347 IVRVAIQALAAVLGGTQSLHTNSYDEALSLPTEKSVRIALRTQQIIAYESGVVDTIDPLGGSYYIEWLTDHIEEEAM 423
                                       ***************************************************************************** PP

                     MM_CoA_mutase 385 klfqeieeaGGmlkaiesGlvqeeiaesaarrqkaiesrkevivGvNkfrpneeekelevlkideeveerqaerlea 461
                                       k++++ie++GGm+kaie G++q+eia+sa+++qk++e++k++ivGvN+f   +e  ++e+lk+d++++++q+erl++
  gi|242398798|ref|YP_002994222.1| 424 KYIEKIEAMGGMMKAIERGYIQKEIADSAYKYQKEVEEKKRIIVGVNEFI-VDEPLDVEILKVDPSIRDKQIERLKK 499
                                       *************************************************5.555789******************** PP

                     MM_CoA_mutase 462 lraerdeaavkaaLaalgeaarse..nllaraveaaralatlGeisdaleevfg 513
                                       lr+erd+++v++aL++l++aa+se  nl+++++ea + latlGe++d+l+ev+g
  gi|242398798|ref|YP_002994222.1| 500 LRSERDNKKVEEALNELRKAAESEdmNLMPYIIEAHKHLATLGEVTDVLREVWG 553
                                       **********************889****************************8 PP

>> DUF4911  Domain of unknown function (DUF4911)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.21   1.3e+03      22      53 ..     397     429 ..     397     432 .. 0.75
   2 ?    9.5   0.0   0.00016      0.95       5      24 ..     522     541 ..     520     546 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.21
                           DUF4911  22 avvttvdkkkGlvrir.ttpdtkeellelLesL 53 
                                       +vv t+d+  G   i+  t + +ee+++ +e++
  gi|242398798|ref|YP_002994222.1| 397 GVVDTIDPLGGSYYIEwLTDHIEEEAMKYIEKI 429
                                       567777777777777536889999999999976 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00016
                           DUF4911   5 pediaflkfIlEaydgLavv 24 
                                       +ed++++ +I+Ea+ +La++
  gi|242398798|ref|YP_002994222.1| 522 SEDMNLMPYIIEAHKHLATL 541
                                       79****************97 PP

>> LRIF1  Ligand-dependent nuclear receptor-interacting factor 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   3.2   8.3e-05      0.49     702     745 ..     470     518 ..     446     521 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 8.3e-05
                             LRIF1 702 eesftddaFPvtppdldeTirDEKikrLKqlLrEr.....EAALEElRk 745
                                       +e   d+   v+ + +d  irD +i rLK+l  Er     E AL ElRk
  gi|242398798|ref|YP_002994222.1| 470 NEFIVDEPLDVEILKVDPSIRDKQIERLKKLRSERdnkkvEEALNELRK 518
                                       566678888899999*****************9996666678******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (561 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       928  (0.0517597); expected 358.6 (0.02)
Passed bias filter:                      566  (0.031569); 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: 0.64u 0.33s 00:00:00.97 Elapsed: 00:00:00.49
# Mc/sec: 3466.20
//
Query:       gi|242398799|ref|YP_002994223.1|  [L=190]
Description: phosphoglucose isomerase (PGI) [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.3e-41  141.9   0.1    1.5e-41  141.6   0.1    1.0  1  GPI         Glucose-6-phosphate isomerase (GPI)
      4e-08   32.8   0.0    8.8e-08   31.8   0.0    1.6  1  Cupin_2     Cupin domain
    0.00014   21.4   0.0    0.00019   21.1   0.0    1.2  1  Cupin_1     Cupin
  ------ inclusion threshold ------
      0.034   13.8   0.0      0.076   12.7   0.0    1.6  1  Cupin_3     Protein of unknown function (DUF861)
       0.05   13.2   0.0      0.073   12.7   0.0    1.2  1  DMSP_lyase  Dimethlysulfonioproprionate lyase


Domain annotation for each model (and alignments):
>> GPI  Glucose-6-phosphate isomerase (GPI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.6   0.1   4.2e-45   1.5e-41       2     175 ..      26     183 ..      25     189 .. 0.91

  Alignments for each domain:
  == domain 1  score: 141.6 bits;  conditional E-value: 4.2e-45
                               GPI   2 rkardlaavladeealkaltetldddvaYevsdslktaeegerlaadqliydvtvilPgkiGeEriktrGHyHkevd 78 
                                       r+ +d+++ + deea+k+++e  +d  +Yev+   + ++eg+      l +  tv+ Pgk+G+E ++t+GHyH++  
  gi|242398799|ref|YP_002994223.1|  26 RRLSDMKGYFIDEEAWKKMIED-GDPIIYEVYAIEQEEKEGD------LNFATTVLYPGKVGNEFFMTKGHYHSK-- 93 
                                       899***************9996.6889***************......***************************.. PP

                               GPI  79 rrstrPEvYevlkGealmlLekPeglkvddvivvevkartvvivPPnygHvsinigeedLvmanlvpkdagqdYdvi 155
                                          +r EvY +lkG++ mlL+ Peg    + + + +k +t+v+vPP++ H++in g+e+ +++ l+p+dag dY +i
  gi|242398799|ref|YP_002994223.1|  94 --IDRAEVYFGLKGKGGMLLQTPEG----EARWIPMKPGTIVYVPPYWAHRTINTGKEPFIFLALYPADAGHDYGTI 164
                                       ..9999*******************....************************************************ PP

                               GPI 156 akarGmaayiieegevlrkr 175
                                       a + G    +++e ++++++
  gi|242398799|ref|YP_002994223.1| 165 AEK-GFSKIVVDEKGKVVVK 183
                                       976.5555555444444433 PP

>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.0   2.5e-11   8.8e-08      13      71 .]      88     153 ..      75     153 .. 0.86

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 2.5e-11
                                       EECSSSEE..EEEEEEESEEEEEEC...TE..EEEEETTEEEEE-TT-EEEEEE-SSS-EEEEEEE CS
                           Cupin_2  13 shrHpged..effyVleGegeltvd...ge..eveleaGdsvyfpagtpHrfrNtgdeparllvvy 71 
                                        h+H+  d  e+++ l+G+g + +    ge  ++++++G +vy+p+   Hr +Ntg+ep+ +l +y
  gi|242398799|ref|YP_002994223.1|  88 GHYHSKIDraEVYFGLKGKGGMLLQtpeGEarWIPMKPGTIVYVPPYWAHRTINTGKEPFIFLALY 153
                                       5999999999*********5444443347788*****************************99865 PP

>> Cupin_1  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   5.2e-08   0.00019      49     114 ..      89     153 ..      61     173 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 5.2e-08
                                       EEE..SSS-EEEEEEESEEEEEEEETTSS.EEEEEE...EETTEEEEE-TT-EEEEEEESSSSEEEEEEEE CS
                           Cupin_1  49 hyh..pnateiayvlqGegrvgfvvpgngnrdfhkk...lreGdvfvvPaglvhfqynsgdepavaivvfd 114
                                       hyh     +e+ + l+G+g + + +p+      +++   +++G++++vP+ ++h ++n+g ++ +++ ++ 
  gi|242398799|ref|YP_002994223.1|  89 HYHskIDRAEVYFGLKGKGGMLLQTPEG-----EARwipMKPGTIVYVPPYWAHRTINTG-KEPFIFLALY 153
                                       77733456899999******88888887.....344457*********************.6666666554 PP

>> Cupin_3  Protein of unknown function (DUF861)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.1e-05     0.076      14      60 ..      85     135 ..      83     149 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.1e-05
                                       EECEEEEECESSEEEEEEEECEEEE...EETTTEE..EEEETTEEEEE-TTE CS
                           Cupin_3  14 ctpGkfrltyeedEfcyileGevkv...tpegget..velraGDlvvlpkgl 60 
                                       +t+G ++ ++++ E  + l+G+      tp +ge+  + +++G++v++p+ +
  gi|242398799|ref|YP_002994223.1|  85 MTKGHYHSKIDRAEVYFGLKGKGGMllqTP-EGEArwIPMKPGTIVYVPPYW 135
                                       799******************987633366.56665*************988 PP

>> DMSP_lyase  Dimethlysulfonioproprionate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0     2e-05     0.073     111     162 ..      91     148 ..      79     149 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2e-05
                        DMSP_lyase 111 Hhhaa.eelYlvls..ggaefr..qgeaewlsrgiGevifnepgikha.mrsaeePll 162
                                       H++ + +e+Y  l+  gg++++  +gea w++++ G +++ +p   h+ + +++eP++
  gi|242398799|ref|YP_002994223.1|  91 HSKIDrAEVYFGLKgkGGMLLQtpEGEARWIPMKPGTIVYVPPYWAHRtINTGKEPFI 148
                                       55555689999996225777763368899**************998872567799986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1186.91
//
Query:       gi|242398800|ref|YP_002994224.1|  [L=191]
Description: Metalloprotease [Thermococcus sibiricus MM 739]
Scores for complete 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-08   31.9   8.9    6.5e-06   25.6   0.4    3.2  3  Peptidase_M50  Peptidase family M50
  ------ inclusion threshold ------
      0.068   13.1   0.5        9.1    6.2   0.1    2.2  2  DUF2678        Protein of unknown function (DUF2678)


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 !    6.9   0.1   0.00037       3.3       2      26 ..      33      57 ..      32      62 .. 0.86
   2 !    3.6   0.7    0.0037        33      89     108 ..     110     129 ..     102     143 .. 0.84
   3 !   25.6   0.4   7.2e-10   6.5e-06     191     219 ..     142     170 ..     132     173 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00037
                                      XXXXXXXXXXXXXXXXXXXXXXXXX CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50  2 filllgilvvvHElGHflvAklcgv 26
                                      ++l ++   v+HE++H  vA++ g+
  gi|242398800|ref|YP_002994224.1| 33 VALGIFTAFVFHEIAHRQVARKYGY 57
                                      5677888999***********9986 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.0037
                                       XXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50  89 livlAGplanfilailvfvv 108
                                        i lAGp++n+ ++i+++++
  gi|242398800|ref|YP_002994224.1| 110 KISLAGPITNITVGIFALAL 129
                                       589**********9998876 PP

  == domain 3  score: 25.6 bits;  conditional E-value: 7.2e-10
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50 191 flqllalisvnLgilNLlPipvLDGghll 219
                                        l+++a++++ L+++NLlPip+LDG +++
  gi|242398800|ref|YP_002994224.1| 142 SLYYTAYVNFLLALFNLLPIPPLDGYKVF 170
                                       6899*********************9987 PP

>> DUF2678  Protein of unknown function (DUF2678)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1     0.001       9.1      39      75 ..      14      50 ..       5      80 .. 0.81
   2 ?    5.3   0.0     0.002        17      12      51 ..     100     139 ..      92     160 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.001
                           DUF2678 39 sllvlvtvvssfvfpslppkplniffavcillisssv 75
                                      s++vl  v ssf +  +p  +l if a++   i+   
  gi|242398800|ref|YP_002994224.1| 14 SFIVLTLVFSSFELTAIPYVALGIFTAFVFHEIAHRQ 50
                                      5566777789***************999877666555 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.002
                           DUF2678  12 sgldnrplfgetsardriinlvvggltsllvlvtvvssfv 51 
                                       +g ++r ++g+ s    i n++vg ++  l+    +s ++
  gi|242398800|ref|YP_002994224.1| 100 AGWQDREIYGKISLAGPITNITVGIFALALLTLGKISGIL 139
                                       57789********************999888777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1370.94
//
Query:       gi|242398801|ref|YP_002994225.1|  [L=59]
Description: RNA-binding protein, containing KH domain [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-06   27.1   1.5    2.7e-06   27.1   1.5    1.0  1  KH_2      KH domain
     0.0018   18.2   0.8     0.0022   17.9   0.8    1.3  1  KH_7      KH domain
  ------ inclusion threshold ------
      0.041   14.0   0.7      0.067   13.3   0.7    1.3  1  KH_5      NusA-like 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 !   27.1   1.5   4.5e-10   2.7e-06       8      61 ..       3      56 ..       1      59 [] 0.89

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 4.5e-10
                                      HHT.ECETEEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHH CS
                              KH_2  8 vei.kkagvskveIertanrviiviresqpgivIGkgGsnikkigkelrkdiekl 61
                                      +e+ ++  v+ +eIe + ++vi+ + + q  i++G gGs +++ +  l+k+ie +
  gi|242398801|ref|YP_002994225.1|  3 EELkRMLKVDILEIEYEGDKVIVYVPKDQVRIAVGSGGSAVRAAELVLGKKIE-I 56
                                      566567778999999999**********************************8.4 PP

>> KH_7  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.8   3.7e-07    0.0022      18      40 ..      10      32 ..       1      58 [. 0.64

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3.7e-07
                              KH_7 18 evkitdveFEGPelViYtknpkl 40
                                      +v i ++e+EG ++++Y+   + 
  gi|242398801|ref|YP_002994225.1| 10 KVDILEIEYEGDKVIVYVPKDQV 32
                                      4789*************965443 PP

>> KH_5  NusA-like KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.7   1.1e-05     0.067       6      44 ..      22      56 ..      19      57 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.1e-05
                              KH_5  6 kvaVkshnpnvdpvGaivgkkGsrikavsseLkgekidv 44
                                      kv+V+  +   d+v+ +vg +Gs ++a +  L g+ki++
  gi|242398801|ref|YP_002994225.1| 22 KVIVYVPK---DQVRIAVGSGGSAVRAAELVL-GKKIEI 56
                                      55666666...66*******************.****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.30s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 383.44
//
Query:       gi|242398802|ref|YP_002994226.1|  [L=153]
Description: hypothetical protein TSIB_0816 [Thermococcus sibiricus MM 739]
Scores for complete 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   47.1   0.2    4.7e-12   46.6   0.2    1.2  1  NYN            NYN domain
  ------ inclusion threshold ------
      0.026   15.0   0.1      0.035   14.6   0.1    1.1  1  CoA_binding_2  CoA binding domain


Domain annotation for each model (and alignments):
>> NYN  NYN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.6   0.2   5.2e-16   4.7e-12       2     146 ..       8     138 ..       7     139 .. 0.85

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 5.2e-16
                               NYN   2 vavfiDgenlpvpakgkevdyrklleeirskgelvraraygnwedeeqnkfqdalsstgikvkhkplkkrggsgkka 78 
                                       +++ i+g n+ ++    +++++ +l ++   g++v+ +++ n       +f + l +  i+     +        + 
  gi|242398802|ref|YP_002994226.1|   8 IGLVINGPNILLSK--FDISLEDILYALNDIGRIVVGKVVIN------YEFSSNLLKSIIDSGLESV-----MVNGR 71 
                                       67789999999944..48999*********************......6677555444443333322.....35689 PP

                               NYN  79 vDvelavdalelaydnkydtivLvsgDgDFaplveklrergkrVevllaeeastsseLisaadefisl 146
                                       vDv+ av+ ++++y+++++ + L ++D+ F plv ++++ gk V+v++ +e+++s++L++ ad+ i l
  gi|242398802|ref|YP_002994226.1|  72 VDVAVAVEGMKIIYNPRINVLALATRDAHFMPLVFEAKRMGKDVIVIA-PEKKVSEALQNIADKTIEL 138
                                       ************************************************.99*************9986 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   3.9e-06     0.035       5     106 ..      40     139 ..      38     146 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.9e-06
                                       EET--S-TTSHHHHHHHHHHHHT--EEEESSS-SEETTEES----T....T--EEEE-S-HHHHGGGHHHHHHH--S CS
                     CoA_binding_2   5 VvGasdnpgkfgykvlryllehglpvvpVnpkeeeilgekvyaslaedpepvdlvdvftppeatpeivkealalgak 81 
                                       VvG       f+  +l+ + ++gl+ v+Vn + +    ++  + +      + ++ ++t+ ++  ++v ea+++g  
  gi|242398802|ref|YP_002994226.1|  40 VVGKVVINYEFSSNLLKSIIDSGLESVMVNGRVDVAVAVEGMKIIY--NPRINVLALATRDAHFMPLVFEAKRMGKD 114
                                       88888888899999****************9986666656666666..369************************** PP

                                       EEEE-TT---HHHHHHHHHTT-EEE CS
                     CoA_binding_2  82 avwlqpgsedeeaaelaeeagirvv 106
                                       ++++ p+    ea++  +++ i+++
  gi|242398802|ref|YP_002994226.1| 115 VIVIAPEKKVSEALQNIADKTIELL 139
                                       *******888888888888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 973.13
//
Query:       gi|242398803|ref|YP_002994227.1|  [L=73]
Description: hypothetical protein TSIB_0817 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       804  (0.0448435); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.29s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 520.25
//
Query:       gi|242398804|ref|YP_002994228.1|  [L=119]
Description: hypothetical protein TSIB_0818 [Thermococcus sibiricus MM 739]
Scores for 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   46.6   0.0    2.6e-12   46.3   0.0    1.2  1  Cupin_2       Cupin domain
    5.6e-06   26.0   0.0      8e-06   25.5   0.0    1.2  1  Cupin_3       Protein of unknown function (DUF861)
    5.7e-06   26.3   0.0    8.3e-06   25.8   0.0    1.2  1  AraC_binding  AraC-like ligand binding domain
    0.00016   21.3   0.0    0.00022   20.9   0.0    1.1  1  DMSP_lyase    Dimethlysulfonioproprionate lyase
      0.002   17.8   0.0     0.0025   17.4   0.0    1.3  1  Cupin_1       Cupin


Domain annotation for each model (and alignments):
>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.3   0.0   7.1e-16   2.6e-12      12      70 ..      45     103 ..      32     104 .. 0.92

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 7.1e-16
                                       EEECSSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEEEE-SSS-EEEEEE CS
                           Cupin_2  12 pshrHpgedeffyVleGegeltvdgeeveleaGdsvyfpagtpHrfrNtgdeparllvv 70 
                                       ++ +H++  ef y++eGe+ l   + e++l+aGd++y ++gtpH+ +N ++ pa++l+ 
  gi|242398804|ref|YP_002994228.1|  45 GFSVHENFHEFAYIIEGEVILGTSSDETPLKAGDFMYNKPGTPHYTKNISNIPAKILWF 103
                                       467899999************************************************95 PP

>> Cupin_3  Protein of unknown function (DUF861)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   2.2e-09     8e-06      19      60 ..      46      86 ..      41     100 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 2.2e-09
                                      EEECESSEEEEEEEECEEEEEETTTEEEEEETTEEEEE-TTE CS
                           Cupin_3 19 frltyeedEfcyileGevkvtpeggetvelraGDlvvlpkgl 60
                                      f+++   +Ef+yi+eGev +   ++ +  l+aGD+++ ++g+
  gi|242398804|ref|YP_002994228.1| 46 FSVHENFHEFAYIIEGEVILGT-SSDETPLKAGDFMYNKPGT 86
                                      7778888***************.9****************98 PP

>> AraC_binding  AraC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   2.3e-09   8.3e-06      16      77 ..      44     106 ..      30     110 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 2.3e-09
                                       EEEETT-.SEEEEEEEEE-EEEEETTEEEEE-TT-EEEE-TTS-EEEEE-TTSEEEEEEEEE- CS
                      AraC_binding  16 fpphvhd.eyvihyvteGtgrlrlngrtydlgpGdlfLlppgepHdyesdsedgweyrwlyfe 77 
                                       ++  vh+ ++++ y++eG+++l     +  l++Gd +  +pg+pH+    s+ + +  w+ ++
  gi|242398804|ref|YP_002994228.1|  44 TGFSVHEnFHEFAYIIEGEVILGTSSDETPLKAGDFMYNKPGTPHYTKNISNIPAKILWFLLP 106
                                       455677779******************************************989999888765 PP

>> DMSP_lyase  Dimethlysulfonioproprionate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   6.1e-08   0.00022      90     156 ..      23      92 ..      18      98 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 6.1e-08
                        DMSP_lyase  90 ekrddvalGlvllaPkvrYPd...HhhaaeelYlvlsggaefrqgeaewlsrgiGevifnepgikhamrs 156
                                       +k+d++++G++ll P+ r P+     h++   ++ + +g ++    ++ ++ ++G+ ++n+pg +h+++ 
  gi|242398804|ref|YP_002994228.1|  23 FKNDQIQVGILLLNPNSRLPEtgfSVHENFHEFAYIIEGEVILGTSSDETPLKAGDFMYNKPGTPHYTKN 92 
                                       789*****************944423444333344445545555666669****************9875 PP

>> Cupin_1  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0     7e-07    0.0025      48     110 ..      46     101 ..      18     115 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 7e-07
                                       EEEESSS-EEEEEEESEEEEEEEETTSS.EEEEEEEETTEEEEE-TT-EEEEEEESSSSEEEE CS
                           Cupin_1  48 PhyhpnateiayvlqGegrvgfvvpgngnrdfhkklreGdvfvvPaglvhfqynsgdepavai 110
                                        ++h n +e ay+++Ge+ +g+ + +         l++Gd ++  +g +h+++n+ + pa ++
  gi|242398804|ref|YP_002994228.1|  46 FSVHENFHEFAYIIEGEVILGTSSDET-------PLKAGDFMYNKPGTPHYTKNISNIPAKIL 101
                                       57899**************98888885.......5********************98888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 813.28
//
Query:       gi|242398805|ref|YP_002994229.1|  [L=692]
Description: acetone carboxylase, subunit alpha [Thermococcus sibiricus MM 739]
Scores for 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-92  309.0   0.0    5.6e-92  308.1   0.0    1.5  1  Hydantoinase_A  Hydantoinase/oxoprolinase
    3.3e-46  157.2   0.0    9.2e-46  155.8   0.0    1.8  2  Hydant_A_N      Hydantoinase/oxoprolinase N-terminal region
  ------ inclusion threshold ------
       0.16   10.5   0.2         10    4.6   0.0    2.3  2  MutL            MutL protein


Domain annotation for each model (and alignments):
>> Hydantoinase_A  Hydantoinase/oxoprolinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  308.1   0.0   9.4e-96   5.6e-92       1     290 [.     203     497 ..     203     498 .. 0.99

  Alignments for each domain:
  == domain 1  score: 308.1 bits;  conditional E-value: 9.4e-96
                    Hydantoinase_A   1 rtetavvnAylspilreylesvekslekrgakarlmvmqsdGglvsadearkkpvetilSGPaaGvvgaaatsklag 77 
                                       rt+tav+nA ++p++++yl+ +ek+++  g++ +++ m s+Gg++s++  ++ p+ +++SGP aGv+g  a+++l g
  gi|242398805|ref|YP_002994229.1| 203 RTNTAVLNAFVKPKMKTYLDTLEKEIAGMGFEGTFYSMLSNGGVASFNFLKEYPIYAVESGPVAGVIGGIAIAELIG 279
                                       89*************************************************************************** PP

                    Hydantoinase_A  78 ekkvItfDmGGTstDvslikdgevevsletei......agvkvrlpaldirtvgagGgsilvvdeggklrvgpesag 148
                                       ek+vI++D G+T+t++sl+++ +++v +e+ +       g++v++p+++i++vg gG+si++ d  g+lrvgp++ g
  gi|242398805|ref|YP_002994229.1| 280 EKNVIVLDGGSTTTKASLVENLTPKVHSEYHVgrdkfnPGYPVKVPVIEIEEVGNGGTSIAWIDAVGNLRVGPQAMG 356
                                       ***************************************************************************** PP

                    Hydantoinase_A 149 adpgpacyrkGgteltvTDanlvLGrlqpedflsgpdgdqkldvelarraf.eelakelnlkveevAegilsvaven 224
                                       adpgpacy+kGg+++tvTDa+++ G ++p+++l   +g++k+ ++la + + e++a++ n +vee+Aegi+++a+en
  gi|242398805|ref|YP_002994229.1| 357 ADPGPACYGKGGDQPTVTDAYVINGLINPNYLL---GGEMKIYRDLAVKVVkEKIADHFNISVEEAAEGIIKIANEN 430
                                       *********************************...***************************************** PP

                    Hydantoinase_A 225 manavrklsvergldpkeltlvvfGGaGaqhaaalaeelgvkkvivppya.gvlsalGmalAdvree 290
                                        ana+r +sv++g+dp+e+tl++ GG+G+++a+ +a+ l+++k+++p+ + gv+sa+Gm+l d+r++
  gi|242398805|ref|YP_002994229.1| 431 AANAIRIISVQKGYDPREFTLIAHGGSGPMFAPFIAQDLEINKIVIPAIPpGVFSAWGMLLTDIRHD 497
                                       *************************************************99**************97 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 !  155.8   0.0   1.5e-49   9.2e-46       1     177 [.       4     178 ..       4     179 .. 0.97
   2 ?   -3.0   0.0      0.82   4.9e+03      32      46 ..     416     430 ..     372     454 .. 0.59

  Alignments for each domain:
  == domain 1  score: 155.8 bits;  conditional E-value: 1.5e-49
                        Hydant_A_N   1 rigIDvGGTfTDavaldekeeevavlKllstpdavaegirealeevleesiprtskidvvrmGTTvatNallerkge 77 
                                       r+g+D+GG fTD+v ++++++e+ ++K  +tp+++aeg+++ +++++ +     sk+d+v +G T+ +N ++ r g+
  gi|242398805|ref|YP_002994229.1|   4 RLGVDIGGAFTDLVGYNDETGELLWVKGETTPKNPAEGVLNTVRKSTLN----MSKVDMVLHGQTLVINSIITRSGA 76 
                                       689**************999***********************998655....89********************** PP

                        Hydant_A_N  78 rvaLittkgfrdlleigrqnrpdlfelrik..kplvlyeevvevderveadgevlkpldeeevrealkalkaagves 152
                                       +v+L+ttkg+rd+l ++r nr+d+++ r k  +p v++  +vev+er+  dg+++++l  e vr+ l++l ++gves
  gi|242398805|ref|YP_002994229.1|  77 KVGLLTTKGHRDVLILQRANRRDIYNFRYKkpEPFVPRGLTVEVRERIGGDGSIIESLHSEDVRKGLEKLLKEGVES 153
                                       *************************9999988899****************************************** PP

                        Hydant_A_N 153 iavvllhSylnpehElrvaeiarei 177
                                       i+v++l+Sy+np hE+++++i++e+
  gi|242398805|ref|YP_002994229.1| 154 ICVSFLNSYANPIHEIEAKKIIQEE 178
                                       ***********************97 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.82
                        Hydant_A_N  32 pdavaegirealeev 46 
                                        +++aegi+++ +e 
  gi|242398805|ref|YP_002994229.1| 416 VEEAAEGIIKIANEN 430
                                       455555555555544 PP

>> MutL  MutL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0    0.0034        20     249     267 ..       4      22 ..       1      46 [. 0.74
   2 ?    4.6   0.0    0.0017        10       1      19 [.     283     301 ..     283     313 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.0034
                              MutL 249 llvvDvGGaTTdvhsvaeg 267
                                        l+vD+GGa Td+  + ++
  gi|242398805|ref|YP_002994229.1|   4 RLGVDIGGAFTDLVGYNDE 22 
                                       689**********998333 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0017
                              MutL   1 ilviDiGSttTkvtlvdle 19 
                                       ++v+D GSttTk++lv++ 
  gi|242398805|ref|YP_002994229.1| 283 VIVLDGGSTTTKASLVENL 301
                                       5799************984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (692 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.67u 0.33s 00:00:01.00 Elapsed: 00:00:00.50
# Mc/sec: 4194.76
//
Query:       gi|242398806|ref|YP_002994230.1|  [L=582]
Description: acetone carboxylase, subunit beta [Thermococcus sibiricus MM 739]
Scores for 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-158  525.9   0.0     1e-157  525.7   0.0    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 !  525.7   0.0  5.9e-162    1e-157       1     516 []       7     528 ..       7     528 .. 0.96

  Alignments for each domain:
  == domain 1  score: 525.7 bits;  conditional E-value: 5.9e-162
                    Hydantoinase_B   1 DpitlevfrnrlmsiaeemgrtlqrtaiSpnikerlDfscalfdadgelvaqaphipvhlgsmseavkavlekfege 77 
                                       Dp+tle+++n l  + eem  +  rta Sp+i+e  Df+++++da+g+lvaqap++p + g +++a+++vlek+ +e
  gi|242398806|ref|YP_002994230.1|   7 DPFTLEIIKNGLVVANEEMFWAFARTAKSPVIYEVYDFAVGMTDAEGNLVAQAPGVPAFSGVLDFAAREVLEKWGDE 83 
                                       9*************************************************************************98* PP

                    Hydantoinase_B  78 lkpGDvlltNdPyaggtHlpDitvitPvfhegelvffvasraHhaDiGGitpGsmppdateifeEGlrippvklvee 154
                                       + pGDv+++N Py+ gtHl+D+t+i+P+f+++el++ v +++H++++GG++ Gs++p+atei++EGl++p+vkl+ee
  gi|242398806|ref|YP_002994230.1|  84 IYPGDVFVSNVPYNSGTHLNDVTLIMPMFYKDELIGLVLNKGHWSEVGGMAFGSWNPNATEIYQEGLQLPCVKLYEE 160
                                       ***************************************************************************** PP

                    Hydantoinase_B 155 geleedvlelllanvRtpednlgDlkAqiaanqvgerrlkelieeyGldtveaamdeildnaeravraalaelpdgt 231
                                       g+++++v++++l+n+R p+++ gD++Aq a+++v+++r+k+lie+yGl++v+ am++il+++e+ +r +l+elp+g+
  gi|242398806|ref|YP_002994230.1| 161 GKPNKSVVDIILENSRLPDYTYGDMEAQAASMRVAAKRVKNLIEKYGLENVKLAMKKILEDGEKYARFRLKELPKGE 237
                                       ***************************************************************************** PP

                    Hydantoinase_B 232 yeaedylddg.......ipikvtvtidgdeatvDftgtspqvkgniNaplavtlsaviyvlrclvdediplNeGclr 301
                                       +eaedy+d         + ++ ++ti++++++vDftg+++qv ++iN+p+ +t s+v  v+++++d++     G+++
  gi|242398806|ref|YP_002994230.1| 238 FEAEDYIDAAiagtdepLYVRAKITITDEKFIVDFTGSAEQVMSPINSPFPATVSGVREVYMAIMDPHAYPTGGFFK 314
                                       *******875466666679********************************************************** PP

                    Hydantoinase_B 302 pievklpegsllnpsepaavvggnvetsqrvvdvvlkalaqalpervaAasqgtmnnltfggvderggeffgyyeti 378
                                       p+e+++peg++++p +pa++ ++ +e +  ++d+v++ala+++p++++A++  ++ ++++gg+++++ge+f+++e+ 
  gi|242398806|ref|YP_002994230.1| 315 PLEIIAPEGTVFHPIKPAPT-STDWEGIAFATDLVWRALAPHVPDKLTAGHFLSIIATIVGGINDKTGEPFAIVEPQ 390
                                       ********************.668***************************************************** PP

                    Hydantoinase_B 379 agGaGArpgkdGasa.vhvhmtntrntdvEilErryPvlverfelrpdsg.GaGkyrGGdGvvreieflepevtvsi 453
                                        gG+GA++++dG+s+ v++  ++t + ++E+ Er++P+lver+ +++  g G+Gk+rGG Gv+r++++l++++ v+i
  gi|242398806|ref|YP_002994230.1| 391 PGGWGAGYDMDGTSClVACGDGETYIASTEVYERNFPILVERYMVNTKDGvGHGKFRGGFGVIRDYRILNSQALVTI 467
                                       *********************************************988777*******************99***** PP

                    Hydantoinase_B 454 lserrvfapwGlaGGepGargrvvl..nllvrgeeenlggkatvelkagdvlvietpGGGGyGdp 516
                                          r+ f+pw ++GG +G  ++v++  +    g+ ++++  +   +k+gd++ i+t+GGGG+Gdp
  gi|242398806|ref|YP_002994230.1| 468 QVGRHDFPPWSVDGGLSGPGNKVIIykD----GNAQEVRRISAEVFKRGDLVSIRTSGGGGWGDP 528
                                       **********************775221....33444344444699*****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (582 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.28s 00:00:00.93 Elapsed: 00:00:00.47
# Mc/sec: 3719.95
//
Query:       gi|242398807|ref|YP_002994231.1|  [L=365]
Description: Xaa-Pro aminopeptidase [Thermococcus sibiricus MM 739]
Scores for 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-66  222.4   0.3    6.8e-66  221.9   0.3    1.2  1  Peptidase_M24  Metallopeptidase family M24
      2e-17   64.1   0.0    3.7e-17   63.2   0.0    1.5  1  Creatinase_N   Creatinase/Prolidase N-terminal domain


Domain annotation for each model (and alignments):
>> Peptidase_M24  Metallopeptidase family M24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  221.9   0.3   7.5e-70   6.8e-66       3     207 ..     147     347 ..     145     349 .. 0.96

  Alignments for each domain:
  == domain 1  score: 221.9 bits;  conditional E-value: 7.5e-70
                                       HHHHHHHHHHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHTTTCEESSSSEEEEGGGGGSTTTBCSSSB--TTEEEEE CS
                     Peptidase_M24   3 irkaariasaaleavleaikpgvterelaaeieattlkrhgarglafppivasgenaavlhytpndrvlkegdlvli 79 
                                       ++kaa+i+++++ +++e   +g +erela+ ie+++  + ga++++f+pivasg+n+a +h++p++r++++gd+v++
  gi|242398807|ref|YP_002994231.1| 147 HKKAAEIVDKVFYRFIEGKLEGKSERELANRIEYMIKNEFGADDVSFEPIVASGPNGANPHHRPSHRKIRKGDVVIF 223
                                       799************876557************99778899************************************ PP

                                       EEEEEETTEEEEEEEEEECSSGSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHHHHHTTBCCGBSSCSEEE CS
                     Peptidase_M24  80 dagaeydgyasDitrTvlvGkftpeqrelyeavleaqeaaikavkpGvtlseidaaarevlesaglakffphglGHg 156
                                       d+ga+y gy+sD+trTv+vG++++e +++ye+v+eaqe+a+++v +G++++ +da+ar ++ ++g++++f h++GHg
  gi|242398807|ref|YP_002994231.1| 224 DYGAKYLGYCSDVTRTVVVGPPSEEVKKVYEIVKEAQETAVQKVAEGIPAEVVDATARGIISKYGYGEYFIHRTGHG 300
                                       ***************************************************************************** PP

                                       ESSSSSEEEEEESSSTTCSSB--TTBEEEEEEEEEEETTTEEEEEBEEEEE CS
                     Peptidase_M24 157 vGlevhdegpsvsresndgrkleeGmvftiEpgiyfapgeggvriedtvlv 207
                                       +G++vh+e p++s  ++++  l++GmvftiEpgiy  +g++gvried+v +
  gi|242398807|ref|YP_002994231.1| 301 LGIDVHEE-PYIS--PGNKKILKDGMVFTIEPGIY-LQGKFGVRIEDDVAL 347
                                       *******9.***9..788*****************.89**********976 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 !   63.2   0.0   4.1e-21   3.7e-17       1     132 []       6     138 ..       6     138 .. 0.94

  Alignments for each domain:
  == domain 1  score: 63.2 bits;  conditional E-value: 4.1e-21
                                       HHHHHHHHHHHTT-SEEEEECCHHHHHHHSS....-SSSEEEEEEESSCE.EEEEECTTHHHHHHHH.TTSEEEEES CS
                      Creatinase_N   1 RlerlralmeekgldallvtspenlrYltGfa.tetgsrglalvvtadga.lllvdalryteaaeesatveevveyd 75 
                                       R+ +++a   +kg +++lv + +n++YltGf+   t +r+++l+++++g  + + ++l++ e  e     +evv ++
  gi|242398807|ref|YP_002994231.1|   6 RIHKFQAHFGKKGFEGALVAPGSNFYYLTGFNpLGTLERLFVLILPSEGLlTAIAPRLYEKELEEFN---GEVVLWS 79 
                                       899*****************************99***************888888877777776666...******* PP

                                       T...HSSHHHHHHHHHHHHT-EEEE-TTSSBHHHHHHHHHHCTTSEEEETHHHHHHHHSC CS
                      Creatinase_N  76 d...pvealadllkellesekrvgveldaltvafyealkealpdaelvdaselieelRvv 132
                                       d   p++ +a+ +ke++++++++ ++++ ++v+ + + k  +++ +l ++s++i elR++
  gi|242398807|ref|YP_002994231.1|  80 DsenPYKIFATKIKETFKEGEKLLIDDT-MPVGVFLKAKDIFDKYSLHPISPVISELREI 138
                                       ***************************9.9****************************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); 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: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2400.90
//
Query:       gi|242398808|ref|YP_002994232.1|  [L=438]
Description: permease for cytosine/purines, uracil, thiamine, allantoin [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.7e-16   58.6  47.1    2.1e-15   56.4  47.1    1.8  1  Transp_cyt_pur  Permease for cytosine/purines, uracil, thiami


Domain annotation for each model (and alignments):
>> Transp_cyt_pur  Permease for cytosine/purines, uracil, thiamine, allantoin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.4  47.1   1.2e-19   2.1e-15       1     417 [.      19     396 ..      19     418 .. 0.80

  Alignments for each domain:
  == domain 1  score: 56.4 bits;  conditional E-value: 1.2e-19
                    Transp_cyt_pur   1 pvpeeeRtwktlnlfsiWlganlnintwvigalglalgLnwwqsvlviivgnligaifvallglaGakyGlpfpils 77 
                                       p+p e+R  ++l  + ++ g+ + +++ ++ga+++       ++ l  +v+ l+  i  a+++++G+k+Glp  +++
  gi|242398808|ref|YP_002994232.1|  19 PIPLEKRE-SWLSPAIVYAGCEFTLSVVMVGAGLVG-AFTVQKIALLLAVALLVTWIGNAINSYIGSKTGLPAGVIA 93 
                                       67777775.79999999**************99954.489999999999999************************* PP

                    Transp_cyt_pur  78 RasfG.irgsllplllrvviaivwfgvqawiGsealllmlgkifgkwleiggailgtsltelvtffi.fwvvslviv 152
                                       R sfG i  ++l +l+++++ ++w+++q+ i+++a+      +fg    i    + t+  +++ +++  ++v ++  
  gi|242398808|ref|YP_002994232.1|  94 RQSFGtIQSRILISLILIILGLGWWAIQTAIAANAFCA----GFG----ID---YTTEKLQWALMVVaLGIVFMLPA 159
                                       **********************************9975....666....44...44555555554441577888889 PP

                    Transp_cyt_pur 153 llgvskirkffviaallvpvaafgfliwalvkaeg..GpvldkavklgkselflsavagvlagfatlilnapDFtry 227
                                       +lg ++i+ +  + +++  ++ fg++i+++ k  g  G ++  +++      + +a+ +++++ +   + ++D++r 
  gi|242398808|ref|YP_002994232.1| 160 VLGYTSIKIVDYLGVPVGMLI-FGMGIYLAIKSYGveGILNWVPTETM---PISTALSTIIGVNVCQWVMISDYARV 232
                                       9999***99988888887777.8************8666666555555...789*********9999999******9 PP

                    Transp_cyt_pur 228 aktkkssvkiqlvavpllftlllligilvaaaakaayganawspldilakfdetagvllililvalaqlgvnisanl 304
                                       ak+  +++  + + v l+ ++l+l+g++      +a g+  w+  +++          + +  + +   ++++  n+
  gi|242398808|ref|YP_002994232.1| 233 AKPGWKNAILVPSLVILVGFILMLTGAI------MAVGVGSWDIIQVMVLLGYP----FWAYFLTFLAQWTTQLVNV 299
                                       9887555555555555555544444444......44555566666555655666....4444444555688899999 PP

                    Transp_cyt_pur 305 lsagldlaallPkkinikrgsliaavialvivpwkllssssklftaflsllavflspvagviiadyfvvrrgylkla 381
                                       +s++l + + +     ++ + + +  +++v +++ l +  +   +++l +++ ++ p+a+++  d++++r+ + +  
  gi|242398808|ref|YP_002994232.1| 300 YSPALAIGNTFN-VKERRKQQILTVFVGIVGIILALAGILER-YMNWLLFMSLLFPPIAAIMATDFLILRKERWNE- 373
                                       999999999999.6678888899999****************.999************************987654. PP

                    Transp_cyt_pur 382 alytrrrgsaYwyrkgvNwravaayivGiaaglvgv 417
                                                    ++g+N  a++  i+G++ g    
  gi|242398808|ref|YP_002994232.1| 374 -------------KSGWNIVATITLICGLLFGYYNQ 396
                                       .............46888888888888888876664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (438 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       918  (0.051202); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.75u 0.36s 00:00:01.10 Elapsed: 00:00:00.58
# Mc/sec: 2290.30
//
Query:       gi|242398809|ref|YP_002994233.1|  [L=50]
Description: hypothetical protein TSIB_0823 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.28s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 357.17
//
Query:       gi|242398810|ref|YP_002994234.1|  [L=174]
Description: transcriptional regulator [Thermococcus sibiricus MM 739]
Scores for 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   44.2   1.5    2.2e-11   43.2   1.5    1.6  1  HTH_24          Winged helix-turn-helix DNA-binding
    1.3e-11   44.1   3.1    2.2e-11   43.4   3.1    1.4  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    3.2e-06   27.0   1.6    7.9e-06   25.7   1.6    1.7  1  HTH_11          HTH domain
    0.00011   21.9   1.3     0.0002   21.0   1.3    1.5  1  HTH_DeoR        DeoR-like helix-turn-helix domain
    0.00021   21.0   0.2    0.00041   20.0   0.2    1.6  1  HTH_23          Homeodomain-like domain
     0.0028   17.3   0.1     0.0062   16.2   0.1    1.6  1  GntR            Bacterial regulatory proteins, gntR family
     0.0034   17.2   0.3       0.02   14.7   0.1    2.1  2  TrmB            Sugar-specific transcriptional regulator TrmB
      0.004   17.3   0.1     0.0068   16.5   0.1    1.4  1  HTH_28          Helix-turn-helix domain
     0.0047   17.0   0.0       0.69   10.0   0.1    2.3  2  HTH_20          Helix-turn-helix domain
     0.0067   16.5   0.2      0.015   15.4   0.2    1.7  1  Trp_repressor   Trp repressor protein
     0.0091   16.2   0.1      0.017   15.3   0.1    1.4  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
     0.0094   15.9   0.4      0.018   14.9   0.1    1.6  1  MarR            MarR family
  ------ inclusion threshold ------
      0.013   15.5   0.2      0.025   14.6   0.2    1.5  1  HTH_29          Winged helix-turn helix
       0.02   15.0   0.2        0.2   11.8   0.1    2.6  3  HTH_7           Helix-turn-helix domain of resolvase
      0.022   15.4   0.2        1.8    9.2   0.1    2.4  2  Mga             Mga helix-turn-helix domain
      0.024   14.5   2.1      0.025   14.4   0.8    1.7  2  TFIIE_alpha     TFIIE alpha subunit
      0.025   14.3   0.2      0.034   13.9   0.2    1.3  1  Baculo_gp41     Structural glycoprotein p40/gp41 conserved re
      0.032   13.6   0.0      0.062   12.7   0.0    1.4  1  HTH_Tnp_ISL3    Helix-turn-helix domain of transposase family
      0.054   13.2   0.0       0.11   12.2   0.0    1.6  1  Sigma70_r4_2    Sigma-70, region 4
      0.062   13.1   0.2       0.11   12.3   0.2    1.3  1  Rep_2           Plasmid replication protein
       0.08   12.6   0.1       0.24   11.1   0.0    1.8  2  DUF603          Protein of unknown function, DUF603
      0.084   12.7   0.0       0.17   11.7   0.0    1.5  1  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 !   43.2   1.5   2.6e-14   2.2e-11       1      47 [.      22      68 ..      22      69 .. 0.97

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 2.6e-14
                            HTH_24  1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      ld++d+kI++lL++++r+s + +Ae+l +S++tv+rr  rL+eeG++
  gi|242398810|ref|YP_002994234.1| 22 LDDLDIKIYQLLREDGRMSDTKIAEKLQVSITTVRRRRMRLQEEGIL 68
                                      79*******************************************97 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.4   3.1   2.6e-14   2.2e-11       1      41 [.      22      62 ..      22      63 .. 0.96

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 2.6e-14
                     HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrL 41
                                      LD++D+kI ++L+ed+R+s +++Ae++ +S +tv+rR  rL
  gi|242398810|ref|YP_002994234.1| 22 LDDLDIKIYQLLREDGRMSDTKIAEKLQVSITTVRRRRMRL 62
                                      8************************************7777 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   1.6   9.7e-09   7.9e-06       4      48 ..      28      72 ..      26      74 .. 0.90

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 9.7e-09
                            HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg.vpIes 48
                                      +i++lL +++g +s  ++Ae+L vS +tvrr+  +L+e g ++I++
  gi|242398810|ref|YP_002994234.1| 28 KIYQLL-REDGRMSDTKIAEKLQVSITTVRRRRMRLQEEGiLQIIA 72
                                      688888.88889****************************877776 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   1.3   2.5e-07    0.0002       4      44 ..      28      68 ..      26      71 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.5e-07
                          HTH_DeoR  4 qilellkqqgklsveelvellgvSeaTiRRDLneLeeqgll 44
                                      +i +ll+++g +s ++++e l+vS +T+RR    L+e+g+l
  gi|242398810|ref|YP_002994234.1| 28 KIYQLLREDGRMSDTKIAEKLQVSITTVRRRRMRLQEEGIL 68
                                      799***************************88888888876 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.2   5.1e-07   0.00041      13      46 ..      32      67 ..      27      74 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 5.1e-07
                            HTH_23 13 llae..GlsvreIAreLgvsrrTvyrwlkryreeGl 46
                                      ll+e  ++s ++IA++L vs  Tv+r + r +eeG+
  gi|242398810|ref|YP_002994234.1| 32 LLREdgRMSDTKIAEKLQVSITTVRRRRMRLQEEGI 67
                                      667779*******************99988889995 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   7.6e-06    0.0062      18      56 ..      33      70 ..      23      72 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.6e-06
                                      S-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              GntR 18 lrpGdkLPsereLaaefgVsrttvReALrrLeaeglver 56
                                      lr   ++ s  ++a+++ Vs ttvR+   rL++eg++++
  gi|242398810|ref|YP_002994234.1| 33 LREDGRM-SDTKIAEKLQVSITTVRRRRMRLQEEGILQI 70
                                      5666677.8889*************************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 !   14.7   0.1   2.5e-05      0.02       6      54 ..      22      70 ..      19      73 .. 0.91
   2 ?   -0.0   0.0         1   8.2e+02      49      65 ..     100     116 ..      82     118 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.5e-05
                                      HHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEE CS
                              TrmB  6 LseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVer 54
                                      L + ++k+Y+ L + g+++ ++iae+l v+ ++v +   +L + G+ ++
  gi|242398810|ref|YP_002994234.1| 22 LDDLDIKIYQLLREDGRMSDTKIAEKLQVSITTVRRRRMRLQEEGILQI 70
                                      6789******************************999989988887765 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1
                                       CTSEEEESSTTTEEEE- CS
                              TrmB  49 kGlVerekgrpklYrav 65 
                                       k ++ r   +p++Y+a+
  gi|242398810|ref|YP_002994234.1| 100 KEFISRAVFNPRIYEAT 116
                                       55666666678888886 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   8.4e-06    0.0068       8      41 ..      32      67 ..      27      73 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 8.4e-06
                            HTH_28  8 lla.aGh.svreaArelgisrrtvyrWikryeegGi 41
                                      ll  +G+ s + +A++l++s +tv+r + r++e+Gi
  gi|242398810|ref|YP_002994234.1| 32 LLReDGRmSDTKIAEKLQVSITTVRRRRMRLQEEGI 67
                                      455467779999***********************8 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.1   0.00085      0.69      14      54 ..      28      68 ..      22      70 .. 0.89
   2 ?    4.8   0.0     0.037        30      40      58 ..     136     155 ..     126     158 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00085
                                      HHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTE CS
                            HTH_20 14 rilraLaraegltaselaerldlskntlsyHLrvLeeagLv 54
                                      +i+++L++++ ++ + +ae l++s +t++++   L+e g++
  gi|242398810|ref|YP_002994234.1| 28 KIYQLLREDGRMSDTKIAEKLQVSITTVRRRRMRLQEEGIL 68
                                      89**************************9998888887765 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.037
                                       HHHHHH.HHHHHCTTEEEEC CS
                            HTH_20  40 tlsyHL.rvLeeagLvevvr 58 
                                        l yH+ + L+e+++ve  r
  gi|242398810|ref|YP_002994234.1| 136 KLKYHIdKFLREVDIVEIYR 155
                                       499***555666****9876 PP

>> Trp_repressor  Trp repressor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.2   1.8e-05     0.015      40      74 ..      28      63 ..      11      72 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.8e-05
                     Trp_repressor 40 qvvkeLLke..elsqreIaeelgvSiAtItRvsrsLk 74
                                      ++++ LL+e   +s ++Iae+l+vSi+t+ R +  L+
  gi|242398810|ref|YP_002994234.1| 28 KIYQ-LLREdgRMSDTKIAEKLQVSITTVRRRRMRLQ 63
                                      7888.88752269*****************9888777 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   2.1e-05     0.017      13      52 ..      29      68 ..      27      70 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.1e-05
                                      HHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                    Fe_dep_repress 13 IYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyv 52
                                      IY+l  e +  + +++ae L+vs  +V     +L+++G +
  gi|242398810|ref|YP_002994234.1| 29 IYQLLREDGRMSDTKIAEKLQVSITTVRRRRMRLQEEGIL 68
                                      9****************************99999999976 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   2.2e-05     0.018      10      47 ..      31      68 ..      26      69 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.2e-05
                                      HHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                              MarR 10 rilyeqgplsvseLakklgvskstvtrvldrLekkGli 47
                                       +l+e g +s +++a+kl+vs++tv r   rL ++G +
  gi|242398810|ref|YP_002994234.1| 31 QLLREDGRMSDTKIAEKLQVSITTVRRRRMRLQEEGIL 68
                                      579999***********************999999986 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.2   3.1e-05     0.025       7      42 ..      33      68 ..      27      79 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.1e-05
                            HTH_29  7 llaeGvstvsqiAkllglsrrtvyrwlkrfeegGla 42
                                      l ++G ++   iA+ l++s +tv+r ++r +e+G+ 
  gi|242398810|ref|YP_002994234.1| 33 LREDGRMSDTKIAEKLQVSITTVRRRRMRLQEEGIL 68
                                      44455557899***********************74 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00024       0.2      17      40 ..      33      57 ..      28      58 .. 0.93
   2 ?   -1.9   0.0       4.4   3.6e+03       4      17 ..      60      73 ..      58      74 .. 0.71
   3 ?   -1.6   0.0       3.6   2.9e+03      38      44 ..     153     159 ..     152     159 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00024
                                      STTTT.--STTTSSSS---SSSS-- CS
                             HTH_7 17 LleeG.isiskIAkevnisRsTvYR 40
                                      L+e+G +s +kIA+ +++s +Tv R
  gi|242398810|ref|YP_002994234.1| 33 LREDGrMSDTKIAEKLQVSITTVRR 57
                                      8999******************976 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.4
                                      -SS-HHHHGGGGSS CS
                             HTH_7  4 sklskndinrvvkL 17
                                        l++++i ++++L
  gi|242398810|ref|YP_002994234.1| 60 MRLQEEGILQIIAL 73
                                      56778888888887 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 3.6
                                       S--SS-- CS
                             HTH_7  38 vYRylad 44 
                                       +YR++++
  gi|242398810|ref|YP_002994234.1| 153 IYRIFPA 159
                                       8***986 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.1    0.0022       1.8      16      56 ..      24      64 ..       3      75 .. 0.85
   2 ?    4.2   0.0     0.079        64      27      68 ..      90     133 ..      67     139 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0022
                                      SHHHHHHHHHHHHSEEEHHHHHHHCT--HHHHHHHHHHHHH CS
                               Mga 16 slkyqllkflfeeeevsieelaqelyiSestlkrkikelnk 56
                                      +l++++ ++l e+ ++s +++a++l +S +t+ r   +l++
  gi|242398810|ref|YP_002994234.1| 24 DLDIKIYQLLREDGRMSDTKIAEKLQVSITTVRRRRMRLQE 64
                                      78899999999***********************9888775 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.079
                                       HHSEEEHHHHHHHCT--HHHHHHHHHHHHHHCH.CCT-EE...ETT CS
                               Mga  27 eeeevsieelaqelyiSestlkrkikelnklLk.efdlel...tkk 68 
                                       ++++v++ee+  + +iS++ ++  i e  ++   e+dl l   +++
  gi|242398810|ref|YP_002994234.1|  90 FKQNVKMEEI--KEFISRAVFNPRIYEATEYFGgEYDLLLrffESN 133
                                       5566666666..459****************999999988555555 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.8   3.1e-05     0.025       3      58 ..      14      69 ..      12      73 .. 0.91
   2 ?   -2.7   0.0       6.5   5.3e+03      24      32 ..      90      98 ..      74     105 .. 0.53

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.1e-05
                                      HHHHHHHCS-HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEE CS
                       TFIIE_alpha  3 lkevvrkfygeeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvk 58
                                      lk ++++  ++  +++ + L e+g +++  +a++l++ ++ +r+  +rL+e+++ +
  gi|242398810|ref|YP_002994234.1| 14 LKNILKGKLDDLDIKIYQLLREDGRMSDTKIAEKLQVSITTVRRRRMRLQEEGILQ 69
                                      78889999999999***********************************9998876 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 6.5
                                      CTTSEBHHH CS
                       TFIIE_alpha 24 ekgevteed 32
                                      +k +v+ e+
  gi|242398810|ref|YP_002994234.1| 90 FKQNVKMEE 98
                                      233333333 PP

>> Baculo_gp41  Structural glycoprotein p40/gp41 conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   4.2e-05     0.034      97     161 ..      40     104 ..       6     118 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.2e-05
                       Baculo_gp41  97 kkaeippniqkaveernqpkirlikdiinavvedllkgtangdyydvvLspklrtavnslkenva 161
                                         ++i++++q ++   +  ++rl ++ i +++  +l  +an  y dv ++ k + +++ +ke ++
  gi|242398810|ref|YP_002994234.1|  40 SDTKIAEKLQVSITTVRRRRMRLQEEGILQIIALILLRAANVAYADVLIKFKQNVKMEEIKEFIS 104
                                       5689********************************999********************999875 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   7.7e-05     0.062      16      47 ..      25      58 ..      23      59 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.7e-05
                      HTH_Tnp_ISL3 16 leayilellles..rsvkavArqlgvSwtTVwri 47
                                      l+ +i++ll+e+  +s + +A+ l vS tTV+r+
  gi|242398810|ref|YP_002994234.1| 25 LDIKIYQLLREDgrMSDTKIAEKLQVSITTVRRR 58
                                      677999******9*******************96 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00014      0.11      27      49 ..      39      61 ..      19      62 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00014
                                      --HHHHHHHHT--HHHHHHHHHH CS
                      Sigma70_r4_2 27 lsykEIAellgisegtVksrlsR 49
                                      +s   IAe+l +s +tV++r +R
  gi|242398810|ref|YP_002994234.1| 39 MSDTKIAEKLQVSITTVRRRRMR 61
                                      66667**************9887 PP

>> Rep_2  Plasmid replication protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   0.00013      0.11      57     112 ..      86     144 ..      79     157 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                             Rep_2  57 vilifknpktlesvkeklkdklkevi.sekveslrnaysYli..HednpeKaqYskkei 112
                                       v+++fk ++ +e++ke ++++++++   e  e   + y+ l+   e+npeK +Y +++ 
  gi|242398810|ref|YP_002994234.1|  86 VLIKFKQNVKMEEIKEFISRAVFNPRiYEATEYFGGEYDLLLrfFESNPEKLKYHIDKF 144
                                       889*******************999857888899*****997335888******99875 PP

>> DUF603  Protein of unknown function, DUF603
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0    0.0003      0.24      15      43 ..      34      62 ..      18      73 .. 0.79
   2 ?   -1.8   0.0       2.6   2.2e+03     142     159 ..     136     153 ..     131     158 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0003
                            DUF603 15 fregslsdkeiakklgvskvnvwrmrqkw 43
                                        +g +sd +ia+kl+vs   v r r + 
  gi|242398810|ref|YP_002994234.1| 34 REDGRMSDTKIAEKLQVSITTVRRRRMRL 62
                                      34699*************99998766553 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.6
                            DUF603 142 slkseldeyikecsirem 159
                                        lk  +d++++e+ i e+
  gi|242398810|ref|YP_002994234.1| 136 KLKYHIDKFLREVDIVEI 153
                                       689999999999999875 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00021      0.17      11      49 ..      31      69 ..      29      69 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00021
                                      T-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR 11 alaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                      +l +++++++ + +A+++ ++ +tv+R    L+e+G+++
  gi|242398810|ref|YP_002994234.1| 31 QLLREDGRMSDTKIAEKLQVSITTVRRRRMRLQEEGILQ 69
                                      57788999***************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       723  (0.0403257); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1049.95
//
Query:       gi|242398811|ref|YP_002994235.1|  [L=58]
Description: hypothetical protein TSIB_0825 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00028   20.4   0.1       0.45   10.1   0.0    2.2  2  TF_Zn_Ribbon     TFIIB zinc-binding
    0.00032   21.0   0.2    0.00038   20.8   0.2    1.1  1  Lar_restr_allev  Restriction alleviation protein Lar
     0.0074   16.0   2.6       0.01   15.5   0.1    2.1  2  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI
  ------ inclusion threshold ------
      0.054   12.9   0.9        8.2    6.0   0.1    2.2  2  zf-ribbon_3      zinc-ribbon domain
      0.056   13.6   1.7       0.19   11.9   1.7    1.8  1  zinc_ribbon_13   Nucleic-acid-binding protein containing Zn-r
       0.06   13.5   0.2       0.09   12.9   0.2    1.3  1  zf-piccolo       Piccolo Zn-finger
      0.063   13.4   1.2        2.4    8.4   0.0    2.1  2  Ribosomal_L37e   Ribosomal protein L37e
       0.07   13.4   4.7       0.37   11.1   4.7    2.0  1  Prim_Zn_Ribbon   Zinc-binding domain of primase-helicase
      0.087   12.8   1.0        3.8    7.5   0.2    2.2  2  Nudix_N_2        Nudix N-terminal
       0.36   11.0   4.6        5.9    7.1   0.1    2.5  2  UPF0547          Uncharacterised protein family UPF0547


Domain annotation for each model (and alignments):
>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0    0.0006       1.1       2      12 ..       7      17 ..       2      31 .. 0.69
   2 !   10.1   0.0   0.00025      0.45      21      30 ..      38      47 ..      35      57 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0006
                                      EETTTTCEECH CS
                      TF_Zn_Ribbon  2 kCPnCgstnlv 12
                                      +CP Cg+t++ 
  gi|242398811|ref|YP_002994235.1|  7 TCPLCGGTSFK 17
                                      57777777653 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00025
                                      EESSSSBEEE CS
                      TF_Zn_Ribbon 21 vCtdCGlVle 30
                                      +C++CG+V+ 
  gi|242398811|ref|YP_002994235.1| 38 ICESCGYVMM 47
                                      8*******86 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.2   2.1e-07   0.00038       5      39 ..       7      46 ..       4      56 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.1e-07
                   Lar_restr_allev  5 pCPfCggravlersqrvvaeigq......cvyCadCgastp 39
                                       CP Cgg   ++++++ ++++g+        +C+ Cg+   
  gi|242398811|ref|YP_002994235.1|  7 TCPLCGGTSFKFEDGKLDSKWGFtahkvkIAICESCGY-VM 46
                                      7*********************9**************9.33 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 !   15.5   0.1   5.8e-06      0.01       2      21 ..       3      22 ..       2      23 .. 0.89
   2 ?    0.2   0.5      0.35   6.2e+02      23      28 ..      38      43 ..      38      45 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 5.8e-06
                           zf-RRN7  2 ekgppCgvCgcrsftlddGf 21
                                      ++   C+ Cg++sf ++dG+
  gi|242398811|ref|YP_002994235.1|  3 RRQLTCPLCGGTSFKFEDGK 22
                                      67789**************7 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.35
                           zf-RRN7 23 yCrrCh 28
                                      +C +C+
  gi|242398811|ref|YP_002994235.1| 38 ICESCG 43
                                      687887 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1    0.0055       9.8      15      24 ..       4      13 ..       2      14 .. 0.76
   2 ?    6.0   0.1    0.0046       8.2      18      25 ..      38      45 ..      37      46 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0055
                       zf-ribbon_3 15 ddnvCpyCGt 24
                                      ++ +Cp CG+
  gi|242398811|ref|YP_002994235.1|  4 RQLTCPLCGG 13
                                      6778999985 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0046
                       zf-ribbon_3 18 vCpyCGtk 25
                                      +C +CG++
  gi|242398811|ref|YP_002994235.1| 38 ICESCGYV 45
                                      7*****98 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 ?   11.9   1.7   0.00011      0.19       2      50 ..       8      52 ..       7      57 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                    zinc_ribbon_13  2 CpKCgnteaevkevaatGsglskifdvqnkkfitvsCknCgYte.lYkae 50
                                      Cp Cg t+++ +      ++l+       +k  + +C++CgY+  +Yk +
  gi|242398811|ref|YP_002994235.1|  8 CPLCGGTSFKFE-----DGKLDSKWGFTAHKVKIAICESCGYVMmFYKGR 52
                                      666666665544.....477777778888999999*******86155554 PP

>> zf-piccolo  Piccolo Zn-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2     5e-05      0.09       2      39 ..       7      47 ..       6      52 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5e-05
                        zf-piccolo  2 lCplCk.telnvgs..keppnyntCteCkkqvCnlCGFnpt 39
                                      +CplC  t+ +++    ++    t  + k  +C  CG+ ++
  gi|242398811|ref|YP_002994235.1|  7 TCPLCGgTSFKFEDgkLDSKWGFTAHKVKIAICESCGYVMM 47
                                      7****99999988752445556788999*********9875 PP

>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0    0.0013       2.4      17      44 ..       6      34 ..       2      36 .. 0.80
   2 ?    6.2   0.5    0.0065        12      25      39 ..      30      44 ..      25      55 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0013
                    Ribosomal_L37e 17 ilCrrCgkrsyhvqkktC.ascGypsakl 44
                                       +C  Cg +s++++  +  ++ G+ ++k+
  gi|242398811|ref|YP_002994235.1|  6 LTCPLCGGTSFKFEDGKLdSKWGFTAHKV 34
                                      58**********99876537789988876 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0065
                    Ribosomal_L37e 25 rsyhvqkktCascGy 39
                                      ++ +v+   C scGy
  gi|242398811|ref|YP_002994235.1| 30 TAHKVKIAICESCGY 44
                                      667788889*****9 PP

>> Prim_Zn_Ribbon  Zinc-binding domain of primase-helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   4.7   0.00021      0.37       2      31 ..       4      42 ..       3      52 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00021
                                      EEE--TTTT-TTTEEETT................S-EEETTT CS
                    Prim_Zn_Ribbon  2 khspCPvCGGrDrFrfddkdgr............GtwfCrqC 31
                                      ++  CP CGG + F+f+d  g+              ++C +C
  gi|242398811|ref|YP_002994235.1|  4 RQLTCPLCGG-TSFKFED--GKldskwgftahkvKIAICESC 42
                                      6778******.67***99..4444667666666556677777 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.024        43      24      30 ..       7      13 ..       2      21 .. 0.67
   2 ?    7.5   0.2    0.0021       3.8      23      31 ..      37      45 ..      37      47 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.024
                                      EETTTTE CS
                         Nudix_N_2 24 vCpaCgt 30
                                      +Cp Cg 
  gi|242398811|ref|YP_002994235.1|  7 TCPLCGG 13
                                      5666664 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0021
                                      EEETTTTEE CS
                         Nudix_N_2 23 lvCpaCgti 31
                                      ++C++Cg++
  gi|242398811|ref|YP_002994235.1| 37 AICESCGYV 45
                                      58*****99 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   1.0     0.013        24      17      24 ..       8      16 ..       6      18 .. 0.70
   2 ?    7.1   0.1    0.0033       5.9      16      23 ..      38      45 ..      31      46 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.013
                           UPF0547 17 CphCG.yvF 24
                                      Cp+CG ++F
  gi|242398811|ref|YP_002994235.1|  8 CPLCGgTSF 16
                                      999963666 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0033
                           UPF0547 16 fCphCGyv 23
                                      +C  CGyv
  gi|242398811|ref|YP_002994235.1| 38 ICESCGYV 45
                                      8*89***8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.50
# Mc/sec: 348.92
//
Query:       gi|242398812|ref|YP_002994236.1|  [L=241]
Description: signaling protein, TraB family [Thermococcus sibiricus MM 739]
Scores for complete 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   57.7   0.5      5e-15   56.1   0.5    1.6  1  TraB      TraB family


Domain annotation for each model (and alignments):
>> TraB  TraB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.1   0.5   2.8e-19     5e-15      14     259 ..      17     234 ..      11     237 .. 0.81

  Alignments for each domain:
  == domain 1  score: 56.1 bits;  conditional E-value: 2.8e-19
                              TraB  14 LfGTiHvskksvyplspeveealeksdtvvvEldlsddtdeatqkelaklkllpdgktlsdllseelyarlqkalak 90 
                                       ++GT+Hvs+ks +++++ + +  e+++++++Eld+++     ++++  kl++ +  k  ++ l    + ++++++ +
  gi|242398812|ref|YP_002994236.1|  17 IIGTMHVSPKSRQKVREIILK--ERPNAIAIELDQQRF---YAIQSPKKLAFQEALKLGKSALLTYILMKVEEKIGE 88 
                                       89*******************..9***********777...555555555555556666777777788889999999 PP

                              TraB  91 rglplaaldkmkPwllalllslaelakkkagldpelvDrylaktakragkpvgglEtveeqlsllss.lpdeeqlea 166
                                        ++++      kP  + ++ +++ + +  +g +  l+D+++++ ++ +  +  + E+v + l+     lp + + e+
  gi|242398812|ref|YP_002994236.1|  89 -EFGM------KP--GEEMKEAIYM-SGLLGVPLYLIDEDIRIIME-KLLKAPFREKVFLFLESALVlLPIAPSREE 154
                                       .8999......**..5555555554.5668995555******8886.577889******888887555999999998 PP

                              TraB 167 leetldeleeakdlleelveaykegdlealeleaeaeeefpelkevlldeRnrrwaekiea........llkepgsv 235
                                         e++      +++++ +++              ++++ +p+l +vl++eRn+ +a+++++         lk+  +v
  gi|242398812|ref|YP_002994236.1| 155 NSEDI------TENYKIMMQ--------------QFKTRYPYLFKVLVEERNEIMARNLKKivddlkrmGLKK-PKV 210
                                       88666......788999999..............9*************************9555555322244.66* PP

                              TraB 236 fvaVGagHlaGedgvlalLkkkGy 259
                                        ++VG gH  G++ +l+  k++ +
  gi|242398812|ref|YP_002994236.1| 211 IAVVGLGHKKGIERILNSYKEQRF 234
                                       *****************9999866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       767  (0.0427799); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); 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: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1521.28
//
Query:       gi|242398813|ref|YP_002994237.1|  [L=306]
Description: Ribonuclease Z [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.4e-18   66.4   0.0    4.5e-08   32.9   0.0    2.1  2  Lactamase_B_2  Beta-lactamase superfamily domain
    5.7e-07   29.7   0.0    1.5e-06   28.3   0.0    1.8  2  Lactamase_B    Metallo-beta-lactamase superfamily
    0.00018   21.2   0.0    0.00032   20.3   0.0    1.4  1  Lactamase_B_4  tRNase Z endonuclease
  ------ inclusion threshold ------
      0.049   12.7   0.0      0.068   12.3   0.0    1.2  1  PDEase_II      cAMP phosphodiesterases class-II
      0.082   12.5   0.0       0.14   11.8   0.0    1.3  1  ThaI           Restriction endonuclease ThaI


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 !   31.6   0.0   3.1e-11   1.1e-07       8     136 ..      37     152 ..      31     155 .. 0.76
   2 !   32.9   0.0   1.3e-11   4.5e-08     132     200 ..     197     263 ..     192     264 .. 0.93

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 3.1e-11
                                       -TTHHHH.HTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCC...C--EE..EEEEEEHHHHHHCCTTCGHHH CS
                     Lactamase_B_2   8 gpdlrqq.alralqPvelrdelppidaVllthaHyDHlaglltlre...lrpkk..lplyapkgvlavleanfvyla 78 
                                       g +++ q  +        + ++ +i+ +++th H DH+ gl++l +   l++++  l +y+pk + + +++ ++  +
  gi|242398813|ref|YP_002994237.1|  37 GEGTLRQlDTT-------KLSPMKIEKIFITHFHGDHYLGLMSLIQtmtLWKRErpLYIYGPKYTFEFIQNYLKSGF 106
                                       44433331222.......345779**********************99966666457789*********99999999 PP

                                       CHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEE CS
                     Lactamase_B_2  79 leeepavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkr 136
                                       + + +++++hel  +++++++  + ei  + + h+ +          lG+++++++kr
  gi|242398813|ref|YP_002994237.1| 107 FRPSFEIHIHELG-ETRLKFK--DYEIWSFKVDHGIPA---------LGYVFKENDKR 152
                                       9999666666665.4445555..789****99999998.........99999977765 PP

  == domain 2  score: 32.9 bits;  conditional E-value: 1.3e-11
                                       CTTEEEEEESS-S---HHHHHHHCT-SEEEEE-S-SSTTHHHHHHT---STSHHHHCTTSSSSEEEEES CS
                     Lactamase_B_2 132 gggkrvyyigDtgyipeeigerlggadllllditayeddemirhmgHltpeeaveaaadlgakrlvliH 200
                                       ++g +++y+gDt++++ +i+   + adll++++t+++ +    + +H+t+eea+e a++++++ l l+H
  gi|242398813|ref|YP_002994237.1| 197 KKGVKIVYTGDTEQCE-RIKLFSERADLLIHEATYLSREDKG-DSYHSTVEEACETAKRAKVELLALFH 263
                                       57899*********99.88989999***********999977.9************************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 !   28.3   0.0   4.3e-10   1.5e-06       4      67 ..      18      76 ..      15     125 .. 0.90
   2 ?   -1.5   0.0      0.61   2.2e+03     143     153 ..     200     210 ..     198     263 .. 0.70

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 4.3e-10
                                      CSSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTH CS
                       Lactamase_B  4 dpvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglvea 67
                                      ++v ++ +  +g+ iL D G +t +++        +l p +++ +++TH+H DH+ gl+ l+++
  gi|242398813|ref|YP_002994237.1| 18 RNVPAIALKYGGEIILWDIGEGTLRQLDT-----TKLSPMKIEKIFITHFHGDHYLGLMSLIQT 76
                                      56777888899****************99.....8***********************999875 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.61
                                       CCEEEECTTTS CS
                       Lactamase_B 143 gkvlftGDall 153
                                        k+++tGD+  
  gi|242398813|ref|YP_002994237.1| 200 VKIVYTGDTEQ 210
                                       68999999865 PP

>> Lactamase_B_4  tRNase Z endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   8.9e-08   0.00032       6      61 ..      14      67 ..      12      69 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 8.9e-08
                     Lactamase_B_4  6 ptsDtsgPlllLqldskrYlfGkvgEgtQRavneqkvrlsklesiFLtgkvswssi 61
                                      pt++ + P ++L++  +  l  ++gEgt+R + + k++  k+e+iF+t+ +  +++
  gi|242398813|ref|YP_002994237.1| 14 PTKERNVPAIALKYGGEIILW-DIGEGTLRQLDTTKLSPMKIEKIFITHFH-GDHY 67
                                      788888899999999999999.**************************988.6655 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   1.9e-05     0.068      69     129 ..      42     103 ..      33     133 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.9e-05
                                       -HHHHHHHHHHTEEEEE-S---GGGTHHHH..HHGGGGGS-S.--EEEEE-HHHHHHHHHHTB CS
                         PDEase_II  69 reikktyeiknniksylItHsHLDHvsglv..inSaefykaqlkkktivGlpytInalqkhlF 129
                                       r+  +t ++  +i++ +ItH H DH  gl+  i   +  k   ++  i+G +yt + +q+ l 
  gi|242398813|ref|YP_002994237.1|  42 RQLDTTKLSPMKIEKIFITHFHGDHYLGLMslIQTMTLWKR-ERPLYIYGPKYTFEFIQNYLK 103
                                       556677888889****************9643666666665.69999*********9998875 PP

>> ThaI  Restriction endonuclease ThaI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.9e-05      0.14      70     121 ..     180     230 ..     171     255 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.9e-05
                                       EEETTEEEEEEEEESSS--S-EEE----HHHHHHHHHH----SEEEEEEE-T CS
                              ThaI  70 vklfgspisiktitgkeangvkliwtvdatkakefletykpkfdlilvhinw 121
                                       + + g+ i +  +tg+  +gvk+++t d++++++ ++ +  + dl++ +  +
  gi|242398813|ref|YP_002994237.1| 180 IEINGKLIYLEDVTGEPKKGVKIVYTGDTEQCER-IKLFSERADLLIHEATY 230
                                       5678999*********************999866.68899999999877666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2282.36
//
Query:       gi|242398814|ref|YP_002994238.1|  [L=332]
Description: hypothetical protein TSIB_0828 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); 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: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 2090.45
//
Query:       gi|242398815|ref|YP_002994239.1|  [L=319]
Description: TRP-repeat-containing protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-07   31.9   2.4    1.2e-07   31.9   2.4    3.0  3  TPR_12    Tetratricopeptide repeat
      6e-06   26.0  15.1    0.00078   19.4   0.4    4.5  4  TPR_2     Tetratricopeptide repeat
    2.2e-05   24.2   1.5    2.2e-05   24.2   1.5    1.8  2  RPN7      26S proteasome subunit RPN7
    0.00015   22.2   6.0       0.22   12.2   0.3    3.8  3  TPR_6     Tetratricopeptide repeat
    0.00021   20.8   0.2    0.00054   19.5   0.2    1.7  1  SNAP      Soluble NSF attachment protein, SNAP
    0.00025   20.7  17.3     0.0012   18.6   0.8    4.1  5  TPR_1     Tetratricopeptide repeat
    0.00033   20.1   1.2     0.0011   18.4   1.2    1.7  1  TPR_MalT  MalT-like TPR region
    0.00058   20.3  12.4      0.028   14.9   0.4    4.2  5  TPR_19    Tetratricopeptide repeat
     0.0019   18.1   5.3        1.1    9.5   0.7    3.4  2  TPR_7     Tetratricopeptide repeat
      0.006   16.9   2.4      0.067   13.5   0.1    2.9  2  TPR_20    Tetratricopeptide repeat
     0.0072   16.1   2.0       0.03   14.0   0.7    2.3  2  TPR_21    Tetratricopeptide repeat-like domain
     0.0083   16.0   0.1        1.1    9.2   0.0    2.6  2  Utp13     Utp13 specific WD40 associated domain
  ------ inclusion threshold ------
      0.012   15.3   1.7          2    8.1   1.8    2.9  2  RPW8      Arabidopsis broad-spectrum mildew resistance protei
      0.017   15.7   1.2       0.23   12.1   0.1    2.8  2  TPR_16    Tetratricopeptide repeat
      0.028   15.2   2.6        5.2    8.2   0.1    4.1  3  TPR_14    Tetratricopeptide repeat
      0.031   14.5   1.4      0.031   14.5   1.4    4.8  5  TPR_8     Tetratricopeptide repeat
      0.062   13.5   3.5        0.3   11.4   1.6    2.9  3  ANAPC3    Anaphase-promoting complex, cyclosome, subunit 3
       0.43   10.3   5.9        1.9    8.2   0.7    2.4  2  DUF2225   Uncharacterized protein conserved in bacteria (DUF2
       0.47   10.2   9.6        4.5    7.0   0.3    4.2  4  TPR_11    TPR repeat
        0.5   11.1   2.3       0.73   10.6   0.0    2.5  2  MUG113    Meiotically up-regulated gene 113
        3.1    7.8  11.1        2.9    7.9   0.6    3.8  3  TPR_10    Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1       1.1   9.1e+02      20      36 ..      26      42 ..      14      51 .. 0.74
   2 !   31.9   2.4   1.4e-10   1.2e-07       6      74 ..      84     150 ..      79     153 .. 0.92
   3 ?    0.8   0.1      0.74   6.3e+02      10      65 ..     168     219 ..     162     221 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.1
                            TPR_12 20 deAlellekaleiarrl 36
                                      + ++e l+++le+a++l
  gi|242398815|ref|YP_002994239.1| 26 ELSEEDLKEVLERAEKL 42
                                      57888999999999876 PP

  == domain 2  score: 31.9 bits;  conditional E-value: 1.4e-10
                            TPR_12   6 lnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                        ++la++++  g++++Al+l++  le  ++   ++ ++ a +++n+g ++++l +ye+Alel ++a ++
  gi|242398815|ref|YP_002994239.1|  84 KYHLADLYYLIGELEKALDLYRGLLEEETEK--GNLENIAKIYYNMGLIHEELLEYEKALELMNKAEKV 150
                                       569*************************999..89999***************************9876 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.74
                            TPR_12  10 aavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAl 65 
                                       a + +++g++ +A + l + l ++  l  +++ l a++     ++++  ++ye+Al
  gi|242398815|ref|YP_002994239.1| 168 AYITFEMGELSKAKAQLARILPQV--L--DNNRLRAQIHLVFEEIFEDKDNYEAAL 219
                                       667788899999999999998888..5..667788888888888888888888886 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.9   7.4e-05     0.063       2      29 ..      82     109 ..      81     112 .. 0.89
   2 !   19.4   0.4   9.1e-07   0.00078       1      28 [.     121     148 ..     121     153 .. 0.93
   3 ?   -1.4   0.1       4.2   3.6e+03      12      26 ..     172     186 ..     167     188 .. 0.78
   4 ?    0.1   0.3       1.4   1.2e+03      12      27 ..     210     225 ..     207     231 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.4e-05
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAle 29 
                                       e+ y l+++yy  g++e+Al++++  le
  gi|242398815|ref|YP_002994239.1|  82 EVKYHLADLYYLIGELEKALDLYRGLLE 109
                                       6779*******************97776 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 9.1e-07
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAl 28 
                                       a+++yn+Gl++++l +ye+Ale+++kA 
  gi|242398815|ref|YP_002994239.1| 121 AKIYYNMGLIHEELLEYEKALELMNKAE 148
                                       789***********************96 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 4.2
                             TPR_2  12 yklgdyeeAleafek 26 
                                       +++g++ +A++ + +
  gi|242398815|ref|YP_002994239.1| 172 FEMGELSKAKAQLAR 186
                                       678999999987766 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 1.4
                             TPR_2  12 yklgdyeeAleafekA 27 
                                       + +++ye Al+ +  A
  gi|242398815|ref|YP_002994239.1| 210 EDKDNYEAALHECLYA 225
                                       6789999999877666 PP

>> RPN7  26S proteasome subunit RPN7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.2       7.8   6.7e+03      18      41 ..      15      38 ..       4      50 .. 0.52
   2 !   24.2   1.5   2.6e-08   2.2e-05      22     142 ..      67     190 ..      61     246 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 7.8
                                      HHHHHHHHHHHTT-HHHHHHHHHH CS
                              RPN7 18 eLdaelkdakenlgkeeirrakld 41
                                      +L + l  + ++l +e+ ++  ++
  gi|242398815|ref|YP_002994239.1| 15 RLASLLYYKVDELSEEDLKEVLER 38
                                      444444444455555555554444 PP

  == domain 2  score: 24.2 bits;  conditional E-value: 2.6e-08
                                       HHHHHHHTT-HHHHHHHHHHHHHHHHHCT-HHHHHHHHHTCCCC--SHH...HHHHHHHHHHHHHHHTT-HHHHHHH CS
                              RPN7  22 elkdakenlgkeeirrakldlaehYlkigdleeAlkaysrireyctslk...hkidmllnlirvaiffndwdlvsky 95 
                                       ++++ ++   ke+  + k+ la+ Y+ ig+le+Al +y+ ++e+ t  +   +++++++n+  +  ++ +++++ + 
  gi|242398815|ref|YP_002994239.1|  67 KIEEFEKLAEKEDSFEVKYHLADLYYLIGELEKALDLYRGLLEEETEKGnleNIAKIYYNMGLIHEELLEYEKALEL 143
                                       56666777788999999************************999997661115667777777777777788888889 PP

                                       HHHHHCSSS---.HHHHHHHHHHHHHHHHHTT-HHHHHHHHCTS-GG CS
                              RPN7  96 lekakellekggdwerknrlkvyeGlallairkfkeAaellldilst 142
                                       ++ka+++l++ g++e   ++ + ++ +  ++++ ++A   l  il++
  gi|242398815|ref|YP_002994239.1| 144 MNKAEKVLDDLGKEEDVVQIGIHKAYITFEMGELSKAKAQLARILPQ 190
                                       9************9999999999999999999999888888887776 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.3   0.00026      0.22       3      29 ..      84     110 ..      82     111 .. 0.90
   2 !    9.9   0.1    0.0014       1.2       3      25 ..     124     146 ..     122     149 .. 0.92
   3 ?    0.3   0.1       1.6   1.4e+03      11      26 ..     172     187 ..     167     188 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00026
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   3 lyklalsyrklgdtdkAlealerlike 29 
                                        y+la +y+  g+ +kAl++++ l++e
  gi|242398815|ref|YP_002994239.1|  84 KYHLADLYYLIGELEKALDLYRGLLEE 110
                                       599*******88**********99986 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0014
                                       HHHHHHHHHH.HHHHHHHHHHHHH CS
                             TPR_6   3 lyklalsyrk.lgdtdkAlealer 25 
                                       +y+++l +++ l +++kAle++++
  gi|242398815|ref|YP_002994239.1| 124 YYNMGLIHEElL-EYEKALELMNK 146
                                       7*********88.********987 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 1.6
                                       HHHHHHHHHHHHHHHH CS
                             TPR_6  11 rklgdtdkAlealerl 26 
                                       +++g+ +kA++ l r+
  gi|242398815|ref|YP_002994239.1| 172 FEMGELSKAKAQLARI 187
                                       578999****999887 PP

>> SNAP  Soluble NSF attachment protein, SNAP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.2   6.3e-07   0.00054      68     195 ..      75     201 ..      65     209 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 6.3e-07
                                       TT-HHHHHHHHHHHHHHHHHT-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHH CS
                              SNAP  68 lkekdeaanayveAakcykkvspeeAvealekAieiytekgrfrraAklkkeiaelyekelgdlekAieaYekAael 144
                                       ++++d+    y  A   y   + e+A + ++   e  tekg++++ Ak++ +++ + e+   ++ekA+e  +kA ++
  gi|242398815|ref|YP_002994239.1|  75 AEKEDSFEVKYHLADLYYLIGELEKALDLYRGLLEEETEKGNLENIAKIYYNMGLIHEEL-LEYEKALELMNKAEKV 150
                                       4555555566777777778888999999999999999*****************999965.9*************** PP

                                       HHHTT-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTTSS-TTTGGGH CS
                              SNAP 145 yeqeeakalankcllkvAelsaelekyekAieiyekvakkslennllkysv 195
                                        ++ +++ +  ++ +  A +  e+++++kA +   ++  + l+nn l+  +
  gi|242398815|ref|YP_002994239.1| 151 LDDLGKEEDVVQIGIHKAYITFEMGELSKAKAQLARILPQVLDNNRLRAQI 201
                                       *********************************************988765 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       5.6   4.8e+03      21      31 ..      29      39 ..      26      41 .. 0.78
   2 !   12.2   0.8   0.00014      0.12       3      25 ..      83     105 ..      81     105 .. 0.91
   3 !   18.6   0.8   1.4e-06    0.0012       1      27 [.     121     147 ..     121     150 .. 0.89
   4 ?   -3.1   0.0       9.9   8.4e+03      12      21 ..     172     181 ..     168     182 .. 0.84
   5 ?   -1.1   0.1       2.3     2e+03      11      21 ..     209     219 ..     207     222 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 5.6
                                      HHHHHHHHHHS CS
                             TPR_1 21 leyyekALeln 31
                                      +e+ +++Le  
  gi|242398815|ref|YP_002994239.1| 29 EEDLKEVLERA 39
                                      79999999976 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00014
                                       HHHHHHHHHHHTT-HHHHHHHHH CS
                             TPR_1   3 alynlGnayfklgkydeAleyye 25 
                                       + y l+ +y+  g++++Al+ y+
  gi|242398815|ref|YP_002994239.1|  83 VKYHLADLYYLIGELEKALDLYR 105
                                       5699****************996 PP

  == domain 3  score: 18.6 bits;  conditional E-value: 1.4e-06
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekA 27 
                                       ak++yn+G+++ +l +y++Ale  +kA
  gi|242398815|ref|YP_002994239.1| 121 AKIYYNMGLIHEELLEYEKALELMNKA 147
                                       899******************975555 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 9.9
                                       HHTT-HHHHH CS
                             TPR_1  12 fklgkydeAl 21 
                                       f++g++ +A 
  gi|242398815|ref|YP_002994239.1| 172 FEMGELSKAK 181
                                       6899999995 PP

  == domain 5  score: -1.1 bits;  conditional E-value: 2.3
                                       HHHTT-HHHHH CS
                             TPR_1  11 yfklgkydeAl 21 
                                       +  + +y+ Al
  gi|242398815|ref|YP_002994239.1| 209 FEDKDNYEAAL 219
                                       66788999998 PP

>> TPR_MalT  MalT-like TPR region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   1.2   1.3e-06    0.0011      83     191 ..      84     191 ..      65     235 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.3e-06
                          TPR_MalT  83 llqqaeilvaqGrLheAletyeqalqlateqglqqlplvgfllvlladllyEwndLeeAeqhlqeGielleql.epe 158
                                        +++a+++   G+L++Al++y+  l+  +e++  +l+    ++  ++ ++ E  + e+A +  +++ ++l++l ++e
  gi|242398815|ref|YP_002994239.1|  84 KYHLADLYYLIGELEKALDLYRGLLE--EETEKGNLENIAKIYYNMGLIHEELLEYEKALELMNKAEKVLDDLgKEE 158
                                       46789999999**********99999..555555666555555667**************************96889 PP

                          TPR_MalT 159 aaldayvllarialaqGdleeAetllekaeela 191
                                         +++ +  a i++  G+l++A++ l+++  ++
  gi|242398815|ref|YP_002994239.1| 159 DVVQIGIHKAYITFEMGELSKAKAQLARILPQV 191
                                       999*********************999986543 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1       6.6   5.7e+03      45      64 ..       2      19 ..       2      20 .. 0.72
   2 !   14.9   0.4   3.3e-05     0.028      14      55 ..      71     111 ..      68     116 .. 0.89
   3 ?    2.2   0.1       0.3   2.6e+02      37      54 ..     140     157 ..     112     162 .. 0.70
   4 !   10.1   0.8     0.001      0.87       7      62 ..     137     198 ..     136     203 .. 0.66
   5 ?   -1.4   0.1       4.1   3.5e+03      14      35 ..     205     223 ..     197     233 .. 0.60

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 6.6
                            TPR_19 45 ealLdalpeedpddaryasL 64
                                      e+lL+a++e+d +  r+asL
  gi|242398815|ref|YP_002994239.1|  2 EELLKAIQEKDCK--RLASL 19
                                      6889999998855..66665 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 3.3e-05
                            TPR_19  14 leqalqedpknaearllLAeallalgqldeAealLdalpeed 55 
                                       +e+ l+e+ ++ e+++ LA++++  g+l++A +l   l+ee+
  gi|242398815|ref|YP_002994239.1|  71 FEK-LAEKEDSFEVKYHLADLYYLIGELEKALDLYRGLLEEE 111
                                       666.7899999***********************99999886 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.3
                            TPR_19  37 algqldeAealLdalpee 54 
                                       al   ++Ae++Ld+l++e
  gi|242398815|ref|YP_002994239.1| 140 ALELMNKAEKVLDDLGKE 157
                                       444567788888877776 PP

  == domain 4  score: 10.1 bits;  conditional E-value: 0.001
                            TPR_19   7 yaeAlalleq...alqedpk...naearllLAeallalgqldeAealLdalpeedpddarya 62 
                                       y+ Al+l+ +   +l++  k      + +  A + +++g+l +A+a L++++++  d+ r++
  gi|242398815|ref|YP_002994239.1| 137 YEKALELMNKaekVLDDLGKeedVVQIGIHKAYITFEMGELSKAKAQLARILPQVLDNNRLR 198
                                       556666666633344444442113333335588889****************9988866655 PP

  == domain 5  score: -1.4 bits;  conditional E-value: 4.1
                            TPR_19  14 leqalqedpknaearllLAeal 35 
                                       +e++++++ ++++a+    e+l
  gi|242398815|ref|YP_002994239.1| 205 FEEIFEDKDNYEAALH---ECL 223
                                       6666666555555444...443 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.7    0.0012       1.1       4      27 ..      86     109 ..      85     118 .. 0.84
   2 !    9.2   0.1    0.0016       1.3       2      22 ..     124     144 ..     123     158 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0012
                             TPR_7   4 nLarlysrlGdyeeAielyeqsLa 27 
                                        La+ly   G+ e+A++ly+ +L+
  gi|242398815|ref|YP_002994239.1|  86 HLADLYYLIGELEKALDLYRGLLE 109
                                       69******************9764 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0016
                             TPR_7   2 LlnLarlysrlGdyeeAiely 22 
                                       ++n++ ++++l +ye+A+el 
  gi|242398815|ref|YP_002994239.1| 124 YYNMGLIHEELLEYEKALELM 144
                                       89****************985 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.1   7.8e-05     0.067      13      52 ..      72     111 ..      64     147 .. 0.82
   2 ?    2.3   0.2      0.25   2.1e+02      14      80 ..     153     218 ..     144     228 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.8e-05
                            TPR_20  13 aalaanpddldarldlAlallaagryeeAleqLleilkrd 52 
                                       ++la++ d  + ++ lA++++  g+ e+Al++   +l+++
  gi|242398815|ref|YP_002994239.1|  72 EKLAEKEDSFEVKYHLADLYYLIGELEKALDLYRGLLEEE 111
                                       578999999*********************9877777665 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.25
                            TPR_20  14 alaanpddldarldlAlallaagryeeAleqLleilkrdrkweddaarkqllkif.ealgsqdplvak 80 
                                       +l ++ d +++ +  A   ++ g+  +A +qL +il + ++ ++ +a+ +l+  f e+ +++d+  a+
  gi|242398815|ref|YP_002994239.1| 153 DLGKEEDVVQIGIHKAYITFEMGELSKAKAQLARILPQVLDNNRLRAQIHLV--FeEIFEDKDNYEAA 218
                                       55666666777777788888899999999*******9999886666555554..41344555555555 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.46   3.9e+02      36      70 ..      14      47 ..       7      55 .. 0.78
   2 !   14.0   0.7   3.5e-05      0.03      52     149 ..     137     240 ..      91     261 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.46
                            TPR_21 36 aeeAsalYqqlqeaveakdaakakeaaeeladeyg 70
                                      ++ As lY +++e ++++d +++ e ae+l+ e +
  gi|242398815|ref|YP_002994239.1| 14 KRLASLLYYKVDE-LSEEDLKEVLERAEKLVLECK 47
                                      5679999999986.888888889999999986655 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 3.5e-05
                            TPR_21  52 akdaakakeaaeeladeyggtaYaalaaLllAkaaveagdlaaAkaqLewvleka.kdeelkalarlRLarvllaek 127
                                        ++a +++++ae++ d+ g+ +   +  + +A   +e g+l +AkaqL ++l +  +++ l+a ++l   ++  +++
  gi|242398815|ref|YP_002994239.1| 137 YEKALELMNKAEKVLDDLGKEEDVVQIGIHKAYITFEMGELSKAKAQLARILPQVlDNNRLRAQIHLVFEEIFEDKD 213
                                       44555788999999*******99****************************9987256679**************** PP

                            TPR_21 128 kydeAl.....ktLeakkeeafaalva 149
                                       +y++Al     ++L+a ++e f+++++
  gi|242398815|ref|YP_002994239.1| 214 NYEAALheclyAMLHARDTEYFDVAFD 240
                                       *****9222223456666666666665 PP

>> Utp13  Utp13 specific WD40 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0    0.0013       1.1      52     110 ..      19      77 ..       1     140 [. 0.82
   2 ?    4.7   0.0      0.03        25      33      72 ..     265     314 ..     199     317 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0013
                                       HHHHHHHC--HHHHHHHHHHHHHHHTSTTTHHHHHHHHHHHHHHS-HHHHHS---HHHH CS
                             Utp13  52 evdevlkslskeqleklLkyirdWntnartsevAqrvLnailkslsaeelleleglkel 110
                                        +   +++ls+e+l+++L+++++   + +  e+ ++v+++ l+ l+++++ e+e+l+e 
  gi|242398815|ref|YP_002994239.1|  19 LLYYKVDELSEEDLKEVLERAEKLVLECKDYELYKLVVYYFLEFLNIDKIEEFEKLAEK 77 
                                       4666789**********************************************976654 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.03
                                       HHHHHS-SS-..........-STSSSSSHHHHHHHHC--HHHHHHHHHHH CS
                             Utp13  33 lkevleseee..........eeesitgskevdevlkslskeqleklLkyi 72 
                                       +++v+e  +e           ++ + g++ev e + ++++  l  lL+++
  gi|242398815|ref|YP_002994239.1| 265 FTNVFEDMREffegvkavalYKDGKIGREEVSEYITKIDDRRLLDLLEFL 314
                                       44444333335666777888666777788******************997 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 ?    8.1   1.8    0.0023         2      66      91 ..      30      55 ..      11      86 .. 0.83
   2 ?    3.8   0.0     0.049        42      11      69 ..     217     280 ..     215     289 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0023
                              RPW8 66 eeLkklLekaekLVekcsklkrynvl 91
                                      e+Lk+ Le+aekLV +c     y+++
  gi|242398815|ref|YP_002994239.1| 30 EDLKEVLERAEKLVLECKDYELYKLV 55
                                      89***************998888876 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.049
                              RPW8  11 aalgellkaileakkks...ldfksilkrLestle..ritPvvkeieklnkeldrpreeieeLk 69 
                                       aal+e l a l a+++    + f+s ++ L +++   + ++v +++++++++++ +re +e  k
  gi|242398815|ref|YP_002994239.1| 217 AALHECLYAMLHARDTEyfdVAFDSLIDVLWQMMMedQFETVYNNMDMFTNVFEDMREFFEGVK 280
                                       6777777788877777522258999999999988523699**********99999998887665 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00027      0.23      31      62 ..      78     109 ..      68     113 .. 0.84
   2 ?    1.0   0.0       0.8   6.8e+02      38      60 ..     125     147 ..     120     153 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00027
                            TPR_16  31 PdaaeAllllgdaalrqgrlaeAaalyraalr 62 
                                        d  e  ++l+d+++  g+l++A++lyr +l+
  gi|242398815|ref|YP_002994239.1|  78 EDSFEVKYHLADLYYLIGELEKALDLYRGLLE 109
                                       3678999*********************9875 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.8
                            TPR_16  38 lllgdaalrqgrlaeAaalyraa 60 
                                       ++ g+++ ++ ++++A++l ++a
  gi|242398815|ref|YP_002994239.1| 125 YNMGLIHEELLEYEKALELMNKA 147
                                       55566666666666666665555 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.1    0.0061       5.2       2      30 ..      82     110 ..      81     118 .. 0.88
   2 ?    0.7   0.0       1.6   1.3e+03       4      29 ..     124     149 ..     121     163 .. 0.72
   3 ?    3.1   0.0      0.26   2.2e+02      12      41 ..     172     203 ..     167     205 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0061
                            TPR_14   2 eallalaeallalGdpdeAiallrralal 30 
                                       e+ + la++++  G++++A++l+r +l+ 
  gi|242398815|ref|YP_002994239.1|  82 EVKYHLADLYYLIGELEKALDLYRGLLEE 110
                                       56789*******************99985 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1.6
                            TPR_14   4 llalaeallalGdpdeAiallrrala 29 
                                       ++ ++ ++++l ++++A++l ++a +
  gi|242398815|ref|YP_002994239.1| 124 YYNMGLIHEELLEYEKALELMNKAEK 149
                                       55667777777788888888888755 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.26
                            TPR_14  12 lalGdpdeAiallrralalaPdd..aeawlll 41 
                                       ++ G++ +A a l r+l +  d+  ++a+++l
  gi|242398815|ref|YP_002994239.1| 172 FEMGELSKAKAQLARILPQVLDNnrLRAQIHL 203
                                       5789************9975544226676766 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       5.9     5e+03      19      32 ..      27      40 ..      26      42 .. 0.72
   2 ?    7.7   0.7    0.0053       4.6       2      28 ..      82     108 ..      81     111 .. 0.87
   3 ?   14.5   1.4   3.6e-05     0.031       1      28 [.     121     148 ..     121     150 .. 0.94
   4 ?    0.7   0.1      0.95   8.1e+02       7      24 ..     167     184 ..     165     188 .. 0.83
   5 ?   -1.3   0.0         4   3.5e+03      10      20 ..     208     218 ..     207     222 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 5.9
                                      HHHHHHHHHHHHHH CS
                             TPR_8 19 eAkeyyekaleldp 32
                                       ++e ++++le ++
  gi|242398815|ref|YP_002994239.1| 27 LSEEDLKEVLERAE 40
                                      57788888888776 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0053
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekal 28 
                                       e+ y+l+++y   g++e+A   y+  l
  gi|242398815|ref|YP_002994239.1|  82 EVKYHLADLYYLIGELEKALDLYRGLL 108
                                       6789***************99998665 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 3.6e-05
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekal 28 
                                       a++yyn+g+i+++l +ye+A e ++ka 
  gi|242398815|ref|YP_002994239.1| 121 AKIYYNMGLIHEELLEYEKALELMNKAE 148
                                       789***********************96 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.95
                                       HHHHHHHTT-HHHHHHHH CS
                             TPR_8   7 lgsiylklgdyeeAkeyy 24 
                                       +++i +++g++ +Ak+ +
  gi|242398815|ref|YP_002994239.1| 167 KAYITFEMGELSKAKAQL 184
                                       7899999*******9866 PP

  == domain 5  score: -1.3 bits;  conditional E-value: 4
                                       HHHHTT-HHHH CS
                             TPR_8  10 iylklgdyeeA 20 
                                       i +++ +ye+A
  gi|242398815|ref|YP_002994239.1| 208 IFEDKDNYEAA 218
                                       67899999999 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.6   0.00035       0.3      13      74 ..      72     132 ..      30     145 .. 0.86
   2 ?    1.4   0.1      0.44   3.8e+02      31      49 ..     129     147 ..     115     187 .. 0.67
   3 ?    0.7   0.1      0.71     6e+02      13      46 ..     148     184 ..     133     223 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00035
                                       HHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCTSHHHC-HHHHHHHHHHHHHTT-HHH CS
                            ANAPC3  13 erllaaetespedayllAlclylngqykrAyellrkaklnskslgcrylfAqcllkLkkyee 74 
                                       e+l   + +s e  y lA  +yl g+ ++A++l+r + ++++ +g +  +A+ ++ ++ ++e
  gi|242398815|ref|YP_002994239.1|  72 EKLA-EKEDSFEVKYHLADLYYLIGELEKALDLYRGLLEEETEKGNLENIAKIYYNMGLIHE 132
                                       5555.555555667889********************8888888999999999999988776 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.44
                                       HHHHHTT-HHHHHHHHHCT CS
                            ANAPC3  31 lclylngqykrAyellrka 49 
                                       l + ++ +y++A+el +ka
  gi|242398815|ref|YP_002994239.1| 129 LIHEELLEYEKALELMNKA 147
                                       4555555666666666666 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.71
                                       HHHH.HHH--HHHHHH....HHHHHHHTT-HHHHHHHH CS
                            ANAPC3  13 erllaaetespedayl....lAlclylngqykrAyell 46 
                                       e++l  +   +ed+      +A+  +++g+  +A   l
  gi|242398815|ref|YP_002994239.1| 148 EKVL-DDLGKEEDVVQigihKAYITFEMGELSKAKAQL 184
                                       3333.334444444332222255555555555555555 PP

>> DUF2225  Uncharacterized protein conserved in bacteria (DUF2225)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.4     0.027        23     146     178 ..      69     101 ..      47     111 .. 0.70
   2 ?    8.2   0.7    0.0022       1.9     104     177 ..     107     180 ..     100     221 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.027
                           DUF2225 146 elykeayekesfpvegideatvlYLiaeLerrl 178
                                       e +++  eke++ + +   a + YLi+eLe+ l
  gi|242398815|ref|YP_002994239.1|  69 EEFEKLAEKEDSFEVKYHLADLYYLIGELEKAL 101
                                       456666666666666666666777777776544 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0022
                           DUF2225 104 llcyelkkekkskkAklalrlAWlyrdkedeekeklflkkAlelykeayekesfpvegideatvlYLiaeLerr 177
                                       ll  e  k +  ++Ak++ +++ + +++ + ek +++++kA ++ ++  ++e+    gi +a +++ ++eL++ 
  gi|242398815|ref|YP_002994239.1| 107 LLEEETEKGNLENIAKIYYNMGLIHEELLEYEKALELMNKAEKVLDDLGKEEDVVQIGIHKAYITFEMGELSKA 180
                                       55666777888899999999999999999999999999999999999999999988899999999999999854 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.3    0.0052       4.5       2      18 ..      89     105 ..      88     109 .. 0.90
   2 ?    5.5   0.1     0.016        14      28      40 ..     121     133 ..     118     134 .. 0.85
   3 ?    1.5   0.1      0.29   2.5e+02      16      27 ..     136     147 ..     134     156 .. 0.67
   4 ?   -3.1   0.0       7.7   6.6e+03       4      13 ..     171     180 ..     169     184 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0052
                            TPR_11   2 dayyeqGkyeeAieaYk 18 
                                       d+yy  G++e+A+  Y+
  gi|242398815|ref|YP_002994239.1|  89 DLYYLIGELEKALDLYR 105
                                       89************997 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.016
                            TPR_11  28 aeayynLGlayyk 40 
                                       a +yyn+Gl++ +
  gi|242398815|ref|YP_002994239.1| 121 AKIYYNMGLIHEE 133
                                       789******9986 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.29
                            TPR_11  16 aYkkAlkldPdn 27 
                                       +Y+kAl+l ++ 
  gi|242398815|ref|YP_002994239.1| 136 EYEKALELMNKA 147
                                       688888876554 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 7.7
                            TPR_11   4 yyeqGkyeeA 13 
                                        +e G++ +A
  gi|242398815|ref|YP_002994239.1| 171 TFEMGELSKA 180
                                       5899999998 PP

>> MUG113  Meiotically up-regulated gene 113
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1       4.6     4e+03      49      50 ..      37      38 ..       5      76 .. 0.60
   2 ?   10.6   0.0   0.00085      0.73      23      74 ..     181     246 ..     161     249 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 4.6
                            MUG113 49 kd 50
                                      + 
  gi|242398815|ref|YP_002994239.1| 37 ER 38
                                      22 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00085
                            MUG113  23 kltllryyppsspnahrlErllhleLkd.krlrdekcdc..............EwFevpaeslkavi 74 
                                       k +l r  p    + +rl +++hl +++  + +d+  +               E+F+v ++sl +v+
  gi|242398815|ref|YP_002994239.1| 181 KAQLARILPQV-LDNNRLRAQIHLVFEEiFEDKDNYEAAlheclyamlhardtEYFDVAFDSLIDVL 246
                                       44555555444.58888888888888888555553333345778888888888*********99985 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.3      0.54   4.6e+02      21      36 ..      28      43 ..      26      44 .. 0.89
   2 ?    3.6   0.4     0.074        63       8      26 ..      87     105 ..      84     111 .. 0.76
   3 ?    7.9   0.6    0.0034       2.9       6      32 ..     118     144 ..     116     149 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.54
                            TPR_10 21 Aealleealairrrll 36
                                      +e++l+e+l++ ++l+
  gi|242398815|ref|YP_002994239.1| 28 SEEDLKEVLERAEKLV 43
                                      58999********986 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.074
                            TPR_10   8 LanalrqrgrydeAealle 26 
                                       La +++  g++++A++l++
  gi|242398815|ref|YP_002994239.1|  87 LADLYYLIGELEKALDLYR 105
                                       7888888888888888887 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0034
                            TPR_10   6 nNLanalrqrgrydeAealleealair 32 
                                        N+a +++++g  +e +  +e+al++ 
  gi|242398815|ref|YP_002994239.1| 118 ENIAKIYYNMGLIHEELLEYEKALELM 144
                                       588888888888888888888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1211  (0.0675442); expected 358.6 (0.02)
Passed bias filter:                      586  (0.0326845); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.48
# Mc/sec: 1990.42
//
Query:       gi|242398816|ref|YP_002994240.1|  [L=297]
Description: N-acetyltransferase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.3e-12   46.3   0.7    7.1e-12   45.6   0.1    1.8  2  Acetyltransf_1   Acetyltransferase (GNAT) family
    7.9e-12   45.2   0.1    2.4e-11   43.7   0.0    1.7  2  Acetyltransf_10  Acetyltransferase (GNAT) domain
    1.8e-10   41.1   0.1    3.6e-10   40.1   0.1    1.5  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    1.7e-06   28.1   0.0    4.5e-06   26.8   0.0    1.7  2  Acetyltransf_9   Acetyltransferase (GNAT) domain
    0.00096   19.1   0.0     0.0018   18.2   0.0    1.4  1  FR47             FR47-like protein
     0.0017   18.4   0.1      0.035   14.2   0.0    2.2  2  Acetyltransf_CG  GCN5-related N-acetyl-transferase
  ------ inclusion threshold ------
      0.035   14.2   0.0       0.11   12.7   0.0    1.9  1  Acetyltransf_4   Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   0.1   2.8e-15   7.1e-12      28     116 ..      65     154 ..      23     155 .. 0.87
   2 ?   -2.7   0.0       2.6   6.6e+03      22      46 ..     192     215 ..     168     216 .. 0.48

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 2.8e-15
                                       HHSTTCEEEEEEETTEEEEEEEEEEEET....TSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEE CS
                    Acetyltransf_1  28 fsleaegllvaeedgeliGfisllkipd....ekggvayieslaVspeyrgkGlGsaLlealeerareegikkivla 100
                                       + le    lvae dg++iG + +l+  +    e  + a+i+ l V++++rg G+G++ ++ +ee a+e+g+   +l 
  gi|242398816|ref|YP_002994240.1|  65 LLLEGQIPLVAEVDGKIIGNAEVLISEEpikgEIMKIAHIDVLEVHKNFRGEGVGREIIKFVEELAKENGC---ELV 138
                                       5555567789******************999977799**********************************...554 PP

                                       EETTEHHHHHHHHHTT CS
                    Acetyltransf_1 101 veedndaairlYeklG 116
                                       +  + + a+++Y+k+G
  gi|242398816|ref|YP_002994240.1| 139 TVTPEKSAVGFYKKVG 154
                                       557899******8899 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.6
                                       HH.HHHHHHSTTC.EEEEEEETTEEEE CS
                    Acetyltransf_1  22 ee.feesfsleae.gllvaeedgeliG 46 
                                       e+   ++   +++ ++++  + ++++G
  gi|242398816|ref|YP_002994240.1| 192 EMvAGKF---QTSyHHWFTAFKDRIAG 215
                                       2233333...33336666566667766 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.7   0.0   9.4e-15   2.4e-11      32     109 ..      71     158 ..      62     170 .. 0.91
   2 ?   -1.7   0.0      0.98   2.5e+03      21      44 ..     193     215 ..     160     220 .. 0.68

  Alignments for each domain:
  == domain 1  score: 43.7 bits;  conditional E-value: 9.4e-15
                   Acetyltransf_10  32 lllvaeeggkivGviel.rdgs..........hisllfVdpeyrgqGigkaLleaveeeaekdgikleltvnaspya 97 
                                       + lvae++gki+G +e+  +++          hi  l V++++rg G+g++++++vee a+++g +  +tv   + a
  gi|242398816|ref|YP_002994240.1|  71 IPLVAEVDGKIIGNAEVlISEEpikgeimkiaHIDVLEVHKNFRGEGVGREIIKFVEELAKENGCE-LVTVTPEKSA 146
                                       5689***********9987777899***********************************999988.********** PP

                   Acetyltransf_10  98 vpfYeklGFkav 109
                                       v+fY+k+G +++
  gi|242398816|ref|YP_002994240.1| 147 VGFYKKVGIEEI 158
                                       ********8776 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.98
                   Acetyltransf_10  21 alrerieegealllvaeeggkivG 44 
                                        ++ ++ + +++++    +++i+G
  gi|242398816|ref|YP_002994240.1| 193 MVAGKF-QTSYHHWFTAFKDRIAG 215
                                       444555.55666666666667777 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.1   0.1   1.4e-13   3.6e-10       6      73 ..      73     154 ..      61     157 .. 0.78

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 1.4e-13
                                       EEEEETTEEEEEEEEEEES..........TCTEEEEE-GGGTTSSHHHHHHHH....TT.SEEEEEEEEETHH.HHH CS
                    Acetyltransf_7   6 fVaeddgkivGfialslld..........aeitrlaVdpeyrgkGiGraLlea....ae.kgiileqlelnae.kai 66 
                                       +Vae dgki+G + + +++          a+i  l V++++rg G+Gr+++++    a+ +g++l+  ++++e  a+
  gi|242398816|ref|YP_002994240.1|  73 LVAEVDGKIIGNAEVLISEepikgeimkiAHIDVLEVHKNFRGEGVGREIIKFveelAKeNGCELV--TVTPEkSAV 147
                                       69*********9999999999996665544444477****************86544226889756..33222489* PP

                                       HHHHHTT CS
                    Acetyltransf_7  67 kfYeklG 73 
                                       +fY+k G
  gi|242398816|ref|YP_002994240.1| 148 GFYKKVG 154
                                       *****99 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.0   1.7e-09   4.5e-06      44     126 ..      72     156 ..      59     158 .. 0.93
   2 ?   -3.0   0.0       2.9   7.5e+03      12      44 ..     200     227 ..     195     238 .. 0.56

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 1.7e-09
                                       EEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEEEEEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--..SSHH CS
                    Acetyltransf_9  44 vlgaedngelvgqlallplelnvpGktlkaagvtgVavapehrgrgvlskLlaraleemreegqplsllfP..ssip 118
                                        l+ae +g+++g + +l  e  + G+++k+a +    v+ + rg+gv +++++ + e ++e+g +l++ +P  s+++
  gi|242398816|ref|YP_002994240.1|  72 PLVAEVDGKIIGNAEVLISEEPIKGEIMKIAHIDVLEVHKNFRGEGVGREIIKFVEELAKENGCELVTVTPekSAVG 148
                                       578999******************************************************************999** PP

                                       HHHTTT-E CS
                    Acetyltransf_9 119 iYrrfGye 126
                                       +Y++ G e
  gi|242398816|ref|YP_002994240.1| 149 FYKKVGIE 156
                                       ****9976 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.9
                                       HHHHHHHHHTT----H..HHHHHHHHHHTTSEE CS
                    Acetyltransf_9  12 evlellkyaFqdeespleeireyfrklleesrv 44 
                                         ++++ +aF+d+   + +     +++le++r+
  gi|242398816|ref|YP_002994240.1| 200 TSYHHWFTAFKDRIAGI-D----DKNYLESGRI 227
                                       55666667777666655.2....2344444443 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   6.9e-07    0.0018      22      82 ..     102     160 ..      97     165 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 6.9e-07
                                       SSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EEEEEETT-HHHHHHHHHHT-EEEEE CS
                              FR47  22 gelgalqvlpehrrrGlgsrlvkalakeiaergktvllvvvasNtpsirlyeklGfekiee 82 
                                         +  l+v++++r++G g+ ++k + +   e+g    lv+v+ ++ +  +y+k+G e+i +
  gi|242398816|ref|YP_002994240.1| 102 AHIDVLEVHKNFRGEGVGREIIKFVEELAKENGC--ELVTVTPEKSAVGFYKKVGIEEIIH 160
                                       567899****************988665544554..4677788999*********999854 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 ?    1.7   0.0      0.11   2.8e+02      56      75 ..      12      31 ..       2      39 .. 0.81
   2 !   14.2   0.0   1.4e-05     0.035      26      61 ..     103     138 ..      76     142 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.11
                   Acetyltransf_CG 56 eglkvvptCsyvaaylekhp 75
                                      ++  v + Cs ++++++k++
  gi|242398816|ref|YP_002994240.1| 12 TEEIVDVHCSGIERWFRKSE 31
                                      5666899*********9986 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 1.4e-05
                   Acetyltransf_CG  26 dfthTeVpeelrGkGiAkkLvkaalddareeglkvv 61 
                                       +++  eV++ +rG+G++++++k + + a+e+g   v
  gi|242398816|ref|YP_002994240.1| 103 HIDVLEVHKNFRGEGVGREIIKFVEELAKENGCELV 138
                                       44556899***********************98766 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   4.1e-05      0.11      41     133 ..      62     154 ..       4     163 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.1e-05
                    Acetyltransf_4  41 lealdsekeyvflvaesdrivGyaylg.qfkkr..akdwkaelsvylaerdnnkeglgrelidaleqvlkeqnienl 114
                                       l++l  e+++++ ++ +++i+G a +    ++      + a + v+ +++  + eg+gre+i+++e+ +ke++ e  
  gi|242398816|ref|YP_002994240.1|  62 LNYLLLEGQIPLVAEVDGKIIGNAEVLiSEEPIkgEIMKIAHIDVLEVHKNFRGEGVGREIIKFVEELAKENGCELV 138
                                       555555667776555599999999986322222213345566777767888999*******************9754 PP

                    Acetyltransf_4 115 laeiaspnensiqfhkalG 133
                                          ++ p+++++ f+k++G
  gi|242398816|ref|YP_002994240.1| 139 ---TVTPEKSAVGFYKKVG 154
                                       ...3568999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); 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: 0.57u 0.35s 00:00:00.92 Elapsed: 00:00:00.54
# Mc/sec: 1665.83
//
Query:       gi|242398817|ref|YP_002994241.1|  [L=195]
Description: Probable molybdopterin-guanine dinucleotide biosynthesis protein A [Thermococcus sibiricus MM 739]
Scores for complete 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  109.6   0.0    2.2e-31  109.4   0.0    1.1  1  NTP_transf_3     MobA-like NTP transferase domain
    2.5e-10   40.6   0.0    8.5e-10   38.9   0.0    1.8  1  CTP_transf_3     Cytidylyltransferase
    3.5e-07   30.2   0.0      4e-07   30.0   0.0    1.2  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
     0.0001   21.5   0.0    0.00015   21.0   0.0    1.2  1  CofC             Guanylyl transferase CofC like
    0.00029   20.5   0.3    0.00068   19.3   0.1    1.7  2  NTP_transferase  Nucleotidyl transferase


Domain annotation for each model (and alignments):
>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.4   0.0   6.1e-35   2.2e-31       1     143 [.       3     143 ..       3     161 .. 0.89

  Alignments for each domain:
  == domain 1  score: 109.4 bits;  conditional E-value: 6.1e-35
                                       EEEEEESS-TTTTTTHHHHCCCCCCHHHHHHHHHCTT..-CEEEEECSHCHHHHHHTTCTS-EEE-TTSS-SHHHHH CS
                      NTP_transf_3   1 aviLAGGrSsRmggdKallplggkpllervldalraa.gvdevvvvggdeevlaalarlgvrvvededpgkgplasl 76 
                                       +v+LAGG+SsR+gg+K+l++++gkpl+ ++++++  a +++e+v+v+  e+ +  +++lg +vv+d+    gp++++
  gi|242398817|ref|YP_002994241.1|   3 GVVLAGGKSSRFGGEKLLYKINGKPLILHTIERVLNAkKIEEIVIVTSKEKMK-SFEKLGFSVVVDKL-KIGPIGGV 77 
                                       79***********************************559********99886.79**********85.89****** PP

                                       HHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESSSEEEECC..EEEGGGHHHHHH CS
                      NTP_transf_3  77 aaalraaadadavlvlacDmPlltpelverllaaaaasgadvvvptyegerghpl..lfrarllsalaa 143
                                       ++a+++      v+v+a+DmPl++p++v+ +++++++s+  v+vp++++++ +pl  +++ + l+ +++
  gi|242398817|ref|YP_002994241.1|  78 YTAISHF---ADVFVVAGDMPLINPKFVDWIVEKFHESNTLVCVPKWKNGYLEPLhaAYSQDFLEMIKR 143
                                       *****97...59*******************************************65556666666554 PP

>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9   0.0   2.4e-13   8.5e-10       1     121 [.       2     114 ..       2     183 .. 0.78

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 2.4e-13
                                       EEEEEE-SSSSSSTT.GGGSEETTEEHHHHHHHHHHHTTTTSEEEEEES-HHHHHHHHHTTSEEEE--TTCSSHHHH CS
                      CTP_transf_3   1 iaIipARsgSkRlpg.KnlldlggkpliayvleaalkskafekvivaTDseeiknvakefgasvlvtrsslesdter 76 
                                       i +++A  +S+R+ g K l +++gkpli +++e++l++k++e++++ T++e++k + +++g sv+v + ++      
  gi|242398817|ref|YP_002994241.1|   2 IGVVLAGGKSSRFGGeKLLYKINGKPLILHTIERVLNAKKIEEIVIVTSKEKMKSF-EKLGFSVVVDKLKIGP-IGG 76 
                                       5789999******86599****************************9988877766.5677888876666643.345 PP

                                       HHHHHHHHTTT.TTSEEEEE-TT-TT--HHHHHHHHHHHHHSTTS CS
                      CTP_transf_3  77 flevvkaflmseneeiivnlqGdnPllqeevikkaietlkenqed 121
                                       ++ +++ f+ +     +  + Gd Pl++++ ++ ++e+  e++ +
  gi|242398817|ref|YP_002994241.1|  77 VYTAISHFA-D-----VFVVAGDMPLINPKFVDWIVEKFHESN-T 114
                                       566665554.5.....577889999999999999998888884.4 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 !   30.0   0.0   1.1e-10     4e-07       3      64 ..       3      62 ..       1     109 [. 0.90

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 1.1e-10
                                      EEEECTTSSCTT-SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHHHHHG CS
                              IspD  3 vvipAAGsGkRmkaglpKqflelkgqtllehtvdallaskavdkivvvvseddteefeqlll 64
                                       v+ A G+ +R   g +K++++++g++l+ ht++ +l+ k++++iv+v s+++++ fe+l  
  gi|242398817|ref|YP_002994241.1|  3 GVVLAGGKSSRF--GGEKLLYKINGKPLILHTIERVLNAKKIEEIVIVTSKEKMKSFEKLGF 62
                                      578888888887..5679***************************************99965 PP

>> CofC  Guanylyl transferase CofC like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   4.3e-08   0.00015      27     123 ..      26     120 ..      11     127 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 4.3e-08
                              CofC  27 kellkamlldvidalkrldvlvvsedeevleyaldelgvevvkek.ekdlntavekafeeieekeviiipsdiPlik 102
                                       k l++  +  v +a k  ++++v+ +e++  +++  lg  vv++k + +  + v  a+    +++v ++  d+Pli+
  gi|242398817|ref|YP_002994241.1|  26 KPLILHTIERVLNAKKIEEIVIVTSKEKMKSFEK--LGFSVVVDKlKIGPIGGVYTAI--SHFADVFVVAGDMPLIN 98 
                                       6677778888899988878*************99..*********4445555666653..389************** PP

                              CofC 103 kedvkdllelekr.advviaPa 123
                                        + v+ ++e+ ++   +v  P 
  gi|242398817|ref|YP_002994241.1|  99 PKFVDWIVEKFHEsNTLVCVPK 120
                                       *****99986544044555665 PP

>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1   1.9e-07   0.00068       2      63 ..       3      59 ..       2      68 .. 0.86
   2 ?   -3.0   0.0       1.2   4.2e+03     115     131 ..     133     149 ..     130     157 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.9e-07
                                      EEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHH.TT-SEEEEEEETTTHHHHHH CS
                   NTP_transferase  2 avILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlan.sgieeiivvltqehsflvee 63
                                      +v+LaGG+ +R+         kl+ + ++++li +t++r++n ++ieei++v+++e+  ++e+
  gi|242398817|ref|YP_002994241.1|  3 GVVLAGGKSSRFG------GEKLLYKINGKPLILHTIERVLNaKKIEEIVIVTSKEKMKSFEK 59
                                      799*****99985......58888889988************889***888888888877765 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.2
                                       ESTTHHHHHHHHHTHSS CS
                   NTP_transferase 115 ikdayeeavkkaiekaa 131
                                       +++++ e++k+ iek++
  gi|242398817|ref|YP_002994241.1| 133 YSQDFLEMIKRQIEKGE 149
                                       67788888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); 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: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1396.09
//
Query:       gi|242398818|ref|YP_002994242.1|  [L=373]
Description: ATP-NAD kinase [Thermococcus sibiricus MM 739]
Scores for complete 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-43  148.5   0.0    2.6e-43  148.3   0.0    1.0  1  NAD_kinase  ATP-NAD kinase
    1.9e-06   27.5   0.2    1.1e-05   25.1   0.0    2.4  3  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 !  148.3   0.0   2.9e-47   2.6e-43       3     292 .]       4     372 ..       2     372 .. 0.92

  Alignments for each domain:
  == domain 1  score: 148.3 bits;  conditional E-value: 2.9e-47
                                       EEEESSC....................GGTCSHHHHHHHHHHHCT-......EEEEECCGGCCSSSTT--HHHHTTT CS
                        NAD_kinase   3 givvnpi....................kkeaieraeevarwLldals....rvlevtveeklgeslaeaaefrsevi 55 
                                       g++vnpi                    +++a+ +a e +++ l+ ls    ++ ++t  ++lge+  +++ef + vi
  gi|242398818|ref|YP_002994242.1|   4 GLIVNPIagmggrvalkgtdgvveeaiRRGAEPIAIEFTKLFLKELShydvSIKFFTGPDGLGEDALKEFEFPYHVI 80 
                                       899999999999999999999999999999********999999866699899999********************* PP

                                       T--.................EEECCC-TTTTTSSSEEEEEE-HHHHHHHHHHHHHCT-EEEEEESSS--SS-SE..E CS
                        NAD_kinase  56 svlkkvkttd..........dtrkaleafadagvdliivvGGDGTaldvarllqkaeiPvlgvnaGvkgfltef..e 120
                                       +++k  +++             +k l +f  ++vd+i+++GGDGTa+d+++++++ + P+lg+++Gvk+f+++f  +
  gi|242398818|ref|YP_002994242.1|  81 KHRKIGEKEIlgvkipntnkEDTKTLTKFMSKDVDIIVFAGGDGTARDIYEAIDE-KKPILGIPTGVKMFSGVFatS 156
                                       *99887776699*****9998888899999************************6.********************* PP

                                       GGGHHHHHHHHHHT-SEEEEEEEEE.........................EEEEETTE...............EEEE CS
                        NAD_kinase 121 peaaaellekllegeirvekrevld.........................avimrskgee.........diadivie 163
                                       pe+aa+ll ++ +g++++ ++e+ld                         + ++ +k++          +ia+ + e
  gi|242398818|ref|YP_002994242.1| 157 PEDAARLLVEFTKGNAKLIEKEILDldenayrhdevkaqlygkclvpyveTLVQSAKEATpldeeeeleAIANTLVE 233
                                       *************************************************8666666666688888888788888877 PP

                                       EEESSEEEEEESSSSS-EE..EEEEETTEEEEEEEESEE.........................EEE-TGGGGTHHH CS
                        NAD_kinase 164 nsvlnevviirgpgstlie..lelyvdtelleadqldgl.........................ivstPtGstaysl 213
                                       +  l +  + +g gst+++    l+++++ll++d+++ +                         i++t  G+ ++++
  gi|242398818|ref|YP_002994242.1| 234 E--LEDGIYFLGAGSTIKKikDRLGINGTLLGVDIVEIKdgkaklvvkdaqekdllkyidkapkIIVTIVGGLNFLF 308
                                       7..5666777899999999889************98766778*********************************** PP

                                       HTT--EE-TT---EEEEEESESSS----EEE-TT-EEEEEE-SS--EEEEETTTEEEEE-TT-EEEEEEESSEEEEE CS
                        NAD_kinase 214 saGgplisPgvlailivpicPhslssrpiVvssssklrirvasrseallaldGseelelspgdevrvtasdkkfkli 290
                                       ++G+++ sP++l          + ++ +iVv+s+ k+r       + +++ +G++e++ +++++++v+ s+ + +++
  gi|242398818|ref|YP_002994242.1| 309 GRGNQQFSPKILS--------QIPKENIIVVASPAKVR-------RPIRVYTGEREVDEKLRGYIKVRISPWAERMV 370
                                       *************........9*************999.......9*************************999999 PP

                                       E. CS
                        NAD_kinase 291 rl 292
                                       ++
  gi|242398818|ref|YP_002994242.1| 371 KV 372
                                       85 PP

>> DAGK_cat  Diacylglycerol kinase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.26   2.3e+03       4      13 ..       5      14 ..       2      34 .. 0.66
   2 !   25.1   0.0   1.2e-09   1.1e-05      32      91 ..      92     145 ..      71     176 .. 0.77
   3 ?   -2.1   0.0       0.3   2.7e+03      41      54 ..     271     284 ..     245     303 .. 0.54

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.26
                                      EEE-TTCTTT CS
                          DAGK_cat  4 vivNpksGkg 13
                                      +ivNp +G g
  gi|242398818|ref|YP_002994242.1|  5 LIVNPIAGMG 14
                                      7778777743 PP

  == domain 2  score: 25.1 bits;  conditional E-value: 1.2e-09
                                       EEEEEE--STTHHHHHHHHHHHCC-SEEEEEESHHHHHHHHHHHCTHHCTTSEEEEEE-S CS
                          DAGK_cat  32 elelieteepgdakelakeakeegvdlivvaGGDGtvsevlnglleelatkpplgiiPlG 91 
                                        +++ +t+ ++d k+l+k +++ +vd+iv aGGDGt++ + +++ e   +kp lg iP+G
  gi|242398818|ref|YP_002994242.1|  92 GVKIPNTN-KEDTKTLTKFMSK-DVDIIVFAGGDGTARDIYEAIDE---KKPILG-IPTG 145
                                       45555665.6777888888888.7**********************...666666.5776 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.3
                                       TTHHHHHHHHHHHC CS
                          DAGK_cat  41 pgdakelakeakee 54 
                                       +g+ak ++k+a+e+
  gi|242398818|ref|YP_002994242.1| 271 DGKAKLVVKDAQEK 284
                                       55566666666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); 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: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2340.70
//
Query:       gi|242398819|ref|YP_002994243.1|  [L=507]
Description: Kef-type K+ transport systems, NAD-binding component [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.6e-13   49.3   8.1    9.8e-13   47.9   8.4    1.6  1  Ion_trans_2     Ion channel
      0.003   17.9   0.0     0.0053   17.1   0.0    1.3  1  zf-C3Hc3H       Potential DNA-binding domain
     0.0062   16.7   0.1        8.1    6.7   0.0    3.6  4  Pentapeptide_3  Pentapeptide repeats (9 copies)
  ------ inclusion threshold ------
      0.018   15.2   0.2       0.43   10.8   0.0    2.8  2  Pentapeptide_4  Pentapeptide repeats (9 copies)
      0.064   13.0   0.1       0.13   12.0   0.1    1.5  1  zf-TRM13_CCCH   CCCH zinc finger in TRM13 protein


Domain annotation for each model (and alignments):
>> Ion_trans_2  Ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.9   8.4   2.7e-16   9.8e-13       8      78 ..     433     506 ..     423     507 .] 0.83

  Alignments for each domain:
  == domain 1  score: 47.9 bits;  conditional E-value: 2.7e-16
                                       HHHHHHHHT........T---HHHHHHHHHHHHTTS----SSTT-----HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Ion_trans_2   8 ifgaviysl...eeg.wekwsfldalYfsfvtltTiGYGdivpetdagrlftivyillGlalfalflavlgkvlt 78 
                                       +f +++y+    +++ +   sfld  Yfs+vt tT+GYGd+ p++ + r+f+ +++l+G+++ a+fl+v+++ ++
  gi|242398819|ref|YP_002994243.1| 433 VFPTIFYITrsvTSFgVPLESFLDYEYFSVVTATTLGYGDLHPIGIG-RVFASIEALFGMFMWAVFLTVFARKYM 506
                                       44445555588855558899************************888.**********************99876 PP

>> zf-C3Hc3H  Potential DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.5e-06    0.0053       3      32 ..      11      40 ..       6      42 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.5e-06
                         zf-C3Hc3H  3 ekekkCkekalpltkyCvkHiledkkQalf 32
                                      e+++kCk+kal+++kyC+ H+  d+   l+
  gi|242398819|ref|YP_002994243.1| 11 ENGEKCKTKALAGSKYCSLHVPIDEGELLY 40
                                      5789*****************999876666 PP

>> Pentapeptide_3  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.0    0.0023       8.1       1      46 [.      63     106 ..      63     108 .. 0.88
   2 ?   -3.2   0.0       2.7   9.7e+03      16      25 ..     138     147 ..     125     149 .. 0.56
   3 !    4.8   0.1    0.0089        32      23      43 ..     276     297 ..     248     301 .. 0.72
   4 ?    0.0   0.1      0.27   9.6e+02      11      21 ..     317     327 ..     311     333 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0023
                    Pentapeptide_3   1 FsganFsgaadFrgatFsgaasFsnadFgsadFsgarFtgdvdFsg 46 
                                       F+g++++ a + ++ t +++  F+n+ + s   +++  + ++++ +
  gi|242398819|ref|YP_002994243.1|  63 FEGVQLYEA-NISNMTIKNPLVFKNSKIKSLIVENSDLK-GLSLFN 106
                                       9999*****.*****************999999999887.776655 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2.7
                    Pentapeptide_3  16 tFsgaasFsn 25 
                                        F++++s +n
  gi|242398819|ref|YP_002994243.1| 138 EFENSISLKN 147
                                       4444444444 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.0089
                    Pentapeptide_3  23 FsnadF.gsadFsgarFtgdvd 43 
                                       F ++ + ++  F+g+ F+gd++
  gi|242398819|ref|YP_002994243.1| 276 FIHTLIhNNLVFRGTAFYGDTT 297
                                       6666677777888888888875 PP

  == domain 4  score: 0.0 bits;  conditional E-value: 0.27
                    Pentapeptide_3  11 dFrgatFsgaa 21 
                                        ++++ F++++
  gi|242398819|ref|YP_002994243.1| 317 ILEDCSFNNPT 327
                                       56777777775 PP

>> Pentapeptide_4  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00012      0.43      18      69 ..      63     116 ..      62     150 .. 0.71
   2 ?    0.6   0.1      0.18   6.3e+02      22      34 ..     317     329 ..     315     339 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00012
                    Pentapeptide_4  18 FsearlrdcnFtecrl.snvnFdecnlsdvdfaevdlkrasFsgcnlknvnf.s 69 
                                       F+ ++l ++n+++  + +  +F++++++++ +++ dlk +s+ +++++ v + s
  gi|242398819|ref|YP_002994243.1|  63 FEGVQLYEANISNMTIkNPLVFKNSKIKSLIVENSDLKGLSLFNSEIERVILvS 116
                                       566666666666666644466777777777777777777777777776665533 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.18
                    Pentapeptide_4  22 rlrdcnFtecrls 34 
                                        l+dc+F+++ + 
  gi|242398819|ref|YP_002994243.1| 317 ILEDCSFNNPTME 329
                                       5788888887764 PP

>> zf-TRM13_CCCH  CCCH zinc finger in TRM13 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   3.7e-05      0.13      14      28 ..      16      30 ..      11      31 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.7e-05
                     zf-TRM13_CCCH 14 CkmtrkkgsryCgeH 28
                                      Ck ++ +gs+yC+ H
  gi|242398819|ref|YP_002994243.1| 16 CKTKALAGSKYCSLH 30
                                      *************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (507 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); 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: 0.69u 0.35s 00:00:01.04 Elapsed: 00:00:00.55
# Mc/sec: 2796.19
//
Query:       gi|242398820|ref|YP_002994244.1|  [L=132]
Description: Inosine-5'-monophosphate dehydrogenase related protein III [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-09   38.3   0.0    1.8e-09   37.8   0.0    1.3  1  ParBc     ParB-like nuclease domain
    0.00087   19.4   0.1     0.0014   18.7   0.1    1.5  1  ParBc_2   Putative ParB-like nuclease
  ------ inclusion threshold ------
       0.11   12.4   0.0        4.1    7.4   0.0    2.3  2  DUF3926   Protein of unknown function (DUF3926)


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 !   37.8   0.0     3e-13   1.8e-09       3      75 ..      36     103 ..      34     125 .. 0.84

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 3e-13
                             ParBc   3 vplseirpnplqprkdspekieelvasIkkkGllqPiivrktrqgryeiiaGerRlrAakrlglkevpvivle 75 
                                       +p++ + p+++q+    ++k+    ++I  +G   P+iv++++ g+y+i++G++R  A k lg ++v+ i+l 
  gi|242398820|ref|YP_002994244.1|  36 LPTDVLIPTQWQLS---EKKLLVVLQEIV-HGYDAPVIVLEHK-GKYYILDGHHRAYARKKLGFSQVESIILR 103
                                       67888888888888...677777778888.9***********8.*******************9999977764 PP

>> ParBc_2  Putative ParB-like nuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   2.4e-07    0.0014      43      89 ..      57     110 ..       7     127 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.4e-07
                                       B.......EEEE.EE-STT-EEE-S-HHHHHHHHHTT-....-EEEEEEEEE-TT CS
                           ParBc_2  43 k.......lvpv.VigpdgelYliDhHHllrallesgvggaekkvlvkvvadlsa 89 
                                                +pv V+ ++g++Y+ D+HH ++a  + g  ++ + ++++ ++d+ +
  gi|242398820|ref|YP_002994244.1|  57 LqeivhgyDAPViVLEHKGKYYILDGHHRAYARKKLGF-SQVESIILRPIRDIPT 110
                                       0444444456661556799***********99998666.6666777777766655 PP

>> DUF3926  Protein of unknown function (DUF3926)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0   0.00068       4.1       7      24 ..      42      59 ..      41      65 .. 0.88
   2 ?    2.3   0.0     0.026   1.6e+02       4      20 ..     105     122 ..     103     126 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00068
                           DUF3926  7 LPaPIQQSAkkvLNILQE 24
                                      +P+  Q S kk+L +LQE
  gi|242398820|ref|YP_002994244.1| 42 IPTQWQLSEKKLLVVLQE 59
                                      59999************9 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.026
                           DUF3926   4 leELPaPIQQSAkkv.LN 20 
                                       + ++P+ I  S kk  LN
  gi|242398820|ref|YP_002994244.1| 105 IRDIPTKIEKSTKKAkLN 122
                                       5689********995366 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 724.00
//
Query:       gi|242398821|ref|YP_002994245.1|  [L=224]
Description: Adenylate kinase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-39  135.2   0.0    2.3e-39  134.9   0.0    1.1  1  ADK              Adenylate kinase
      2e-20   73.6   0.0      3e-20   73.0   0.0    1.2  1  AAA_17           AAA domain
    1.2e-16   60.3   2.7      2e-16   59.7   2.7    1.3  1  ADK_lid          Adenylate kinase, active site lid
    6.4e-07   29.6   0.0    9.1e-07   29.1   0.0    1.2  1  AAA_33           AAA domain
    2.7e-06   28.0   0.1    6.3e-06   26.8   0.1    1.6  1  AAA_18           AAA domain
    0.00083   19.2   0.0     0.0016   18.2   0.0    1.4  1  Cytidylate_kin   Cytidylate kinase
     0.0029   17.9   0.0     0.0058   16.9   0.0    1.5  1  AAA_22           AAA domain
     0.0048   16.2   0.0      0.014   14.6   0.0    1.7  1  Zeta_toxin       Zeta toxin
  ------ inclusion threshold ------
       0.03   14.0   0.0       0.06   13.0   0.0    1.5  1  Thymidylate_kin  Thymidylate kinase
      0.037   14.5   0.0      0.055   13.9   0.0    1.4  1  AAA              ATPase family associated with various cellul
      0.044   13.7   0.0      0.064   13.2   0.0    1.3  1  NTPase_1         NTPase
      0.063   13.3   0.0       0.11   12.5   0.0    1.4  1  AAA_5            AAA domain (dynein-related subfamily)
      0.063   13.0   0.0       0.21   11.3   0.0    1.9  2  AAA_24           AAA domain
      0.065   12.8   0.0      0.097   12.2   0.0    1.3  1  CobU             Cobinamide kinase / cobinamide phosphate gua
      0.073   13.6   0.0       0.09   13.3   0.0    1.3  1  ABC_tran         ABC transporter
        0.1   13.0   0.0       0.21   12.0   0.0    1.6  1  RNA_helicase     RNA helicase
       0.11   12.2   0.0       0.16   11.7   0.0    1.3  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
       0.11   12.5   0.1       0.16   12.0   0.1    1.3  1  AAA_14           AAA domain
       0.12   12.6   0.0       0.16   12.2   0.0    1.3  1  AAA_28           AAA domain
       0.14   11.5   0.0       0.21   10.9   0.0    1.2  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
       0.17   11.6   0.0        0.3   10.8   0.0    1.4  1  AAA_29           P-loop containing region of AAA domain
       0.43   10.5   2.6        5.5    7.0   0.2    2.2  2  Prok-RING_1      Prokaryotic RING finger family 1
        1.6    8.5   5.2       0.71    9.6   0.7    2.2  2  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI


Domain annotation for each model (and alignments):
>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.9   0.0   2.9e-42   2.3e-39       1     150 [.       5     188 ..       5     189 .. 0.98

  Alignments for each domain:
  == domain 1  score: 134.9 bits;  conditional E-value: 2.9e-42
                                       EEESTTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHHCT-HHHHHHHHHHHTTSS--HHHHHHHHHHHHHCHGTTTEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               ADK   1 llGaPgaGKGtqaeklvkkyglahlstGdllRaevksgtelGkeakevmdkgelvpdevvvklvkeelekedkkkgf 77 
                                       + G+Pg+GK t ++++++ky+l  +++Gd++Rae+++g  lG+e+k++++kg+l+pd v+++lv ++l+k+  +++f
  gi|242398821|ref|YP_002994245.1|   5 IFGPPGSGKSTHSRRIIEKYNLEYIASGDIIRAEINKGNALGREMKKYIEKGDLLPDTVINTLVLSRLRKK--RENF 79 
                                       68*******************************************************************88..99** PP

                                       EEESB-SSHHHHHHHHHHHHHHTSEESEEEEEE--HHHHHHHHHT................................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................ RF
                               ADK  78 llDGfPRtveqaealeelleeekvkldlvleldvpeevlveRltg................................ 122
                                       ++DG+PRt eq  ale+ l +++++++l +++ +++e  ++R++g                                
  gi|242398821|ref|YP_002994245.1|  80 IIDGYPRTAEQVLALENFLYDHGIRIKLAIDIFISKEESITRISGrricrqcgavyhikynpskvpgkcdicggevi 156
                                       ***************************************************************************** PP

                                       ....GSHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                                       ....xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               ADK 123 ....DneetvkkRletykkqtkplidyykkkg 150
                                           D++e v++R + y ++++p+i++yk +g
  gi|242398821|ref|YP_002994245.1| 157 qredDTPEIVSRRYDIYINNMEPIIKFYKGQG 188
                                       ****************************9876 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.0   0.0   3.9e-23     3e-20       1     122 [.       6     125 ..       6     131 .. 0.89

  Alignments for each domain:
  == domain 1  score: 73.0 bits;  conditional E-value: 3.9e-23
                                       EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTS..HSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEE CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrggl..akardemrklpleekkelqkeaaekiaeeakkkgvl 75 
                                       +G+PGsGK+t ++++ eky+++++  Gd++r+e+++g++   + +++++k++l ++  +  ++  +++++  +++++
  gi|242398821|ref|YP_002994245.1|   6 FGPPGSGKSTHSRRIIEKYNLEYIASGDIIRAEINKGNAlgREMKKYIEKGDLLPDTVINTLVLSRLRKK--RENFI 80 
                                       6************************************7446889999*********************95..889** PP

                                       EEE-SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHH CS
                            AAA_17  76 vdghprikeqagfldglpkevleelkpdaiilleadpeeilerrlkd 122
                                       +dg+pr+ eq  +l+++  +  + + +++ i + +++ee + r   +
  gi|242398821|ref|YP_002994245.1|  81 IDGYPRTAEQVLALENFLYD--HGIRIKLAIDIFISKEESITRISGR 125
                                       *****************976..6777788888888888888887665 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 !   59.7   2.7   2.6e-19     2e-16       1      36 []     125     160 ..     125     160 .. 0.99

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 2.6e-19
                                       EEE-TTT--EEETTTB--SSTTB-TTT--.-B--GG CS
                           ADK_lid   1 RrvCpkCGrsYhvvfnpPkveglCDkCGepLvqRsD 36 
                                       Rr+C++CG++Yh+++np kv+g+CD CG++ +qR+D
  gi|242398821|ref|YP_002994245.1| 125 RRICRQCGAVYHIKYNPSKVPGKCDICGGEVIQRED 160
                                       9***********999********************9 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0   1.2e-09   9.1e-07       2     118 ..       3     125 ..       3     130 .. 0.78

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 1.2e-09
                            AAA_33   2 vllvGlpGsGKstlaerllkklgavllssdtlrr.rlfg..tdqqsktdytrvldrlyq.ilnelarkalsagrn.v 73 
                                       +l+ G+pGsGKst ++r+++k   + ++s +++r  + +     +  ++y++  d l +  +n l+ ++l+++r  +
  gi|242398821|ref|YP_002994245.1|   3 ILIFGPPGSGKSTHSRRIIEKYNLEYIASGDIIRaEINKgnALGREMKKYIEKGDLLPDtVINTLVLSRLRKKREnF 79 
                                       5789*******************99988877777255447744556667788666644435566666777666544* PP

                            AAA_33  74 ildatnlsrrerarflklarrlgvpvri.vvvetdeetlkeRlakR 118
                                       i+d   +++++  ++ +++ ++g ++++ +++  + e+   R+  R
  gi|242398821|ref|YP_002994245.1|  80 IIDGYPRTAEQVLALENFLYDHGIRIKLaIDIFISKEESITRISGR 125
                                       *************************965599999999999999988 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.1   8.1e-09   6.3e-06       1     114 [.       3     126 ..       3     129 .. 0.63

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 8.1e-09
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....gvnlrdvakenglllevdpealdeskrldedkldklldaleenssale 72 
                                       Il+ G+pG+GK+t ++++ ++ ++     g+++r  + +++ l  + ++ + e+  l  d    ++++l  ++  + 
  gi|242398821|ref|YP_002994245.1|   3 ILIFGPPGSGKSTHSRRIIEKYNLeyiasGDIIRAEINKGNALGREMKK-YIEKGDLLPDT---VINTLVLSR-LRK 74 
                                       99****************8884445466644444444443333333333.33333333333...333333333.366 PP

                            AAA_18  73 egknlvidghlaeleseaakdikk..........vvLtaspeelleRlekRg 114
                                       + +n +idg +   e+  a ++            + +  s+ee + R++ R+
  gi|242398821|ref|YP_002994245.1|  75 KRENFIIDGYPRTAEQVLALENFLydhgiriklaIDIFISKEESITRISGRR 126
                                       6778888888887777777777767777777777888889999998888885 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0     2e-06    0.0016       2      35 ..       4      37 ..       3      49 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2e-06
                                      EEE-STTSSHHHHHHHHHHHHT-EEEEHHHHHHH CS
                    Cytidylate_kin  2 aiDGPagsGKssvaralaeklglkyldtgalYRa 35
                                       i GP gsGKs+ +r++ ek +l+y+ +g + Ra
  gi|242398821|ref|YP_002994245.1|  4 LIFGPPGSGKSTHSRRIIEKYNLEYIASGDIIRA 37
                                      577***************************9996 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   7.4e-06    0.0058       8      34 ..       3      29 ..       1      54 [. 0.83

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 7.4e-06
                            AAA_22  8 lvvtGesGtGKTtllrrlleqldeeak 34
                                      ++++G++G+GK+t  rr+ e+++ e+ 
  gi|242398821|ref|YP_002994245.1|  3 ILIFGPPGSGKSTHSRRIIEKYNLEYI 29
                                      89******************9976554 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   1.9e-05     0.014      19     143 ..       3     125 ..       1     133 [. 0.84

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.9e-05
                        Zeta_toxin  19 illgGqpGAGKselaellkdelerqgnvvrldpDdlRelhPeyeeilkadpkkaseltqk.daselvekllqeaien 94 
                                       il+ G pG+GKs+ ++ + ++   + +++  ++D +R+ + + +++ ++  kk+ e  +    +++ + +l  + ++
  gi|242398821|ref|YP_002994245.1|   3 ILIFGPPGSGKSTHSRRIIEKY--NLEYIA-SGDIIRAEINKGNALGRE-MKKYIEKGDLlPDTVINTLVLSRLRKK 75 
                                       78899****************9..888886.89*******888886664.34444443330345667778999**** PP

                        Zeta_toxin  95 gyniivegtlrspdvvkklaealkkaGYevevvv.vavkkelSrlgvldR 143
                                       + n+i++g  r+ ++v  l + l + G ++++++ +  +ke+S++++  R
  gi|242398821|ref|YP_002994245.1|  76 RENFIIDGYPRTAEQVLALENFLYDHGIRIKLAIdIFISKEESITRISGR 125
                                       ********************************987999*******99988 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   7.6e-05      0.06       3      65 ..       7      71 ..       5      83 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.6e-05
                                      ESTTSSHHHHHHHHHHHHHHTTE....EEEESSSTTSHHHHHHHHHHHTCS---HHHHHHHHHHHH CS
                   Thymidylate_kin  3 GlDGaGKttqaellkerlkeegik...vvltrepggteiGekirelllkeeeleeqteallfaadr 65
                                      G  G+GK+t+++ + e+++ e i+   +++   ++g+ +G+ ++++++ + +l + t+ + ++ +r
  gi|242398821|ref|YP_002994245.1|  7 GPPGSGKSTHSRRIIEKYNLEYIAsgdIIRAEINKGNALGREMKKYIE-KGDLLPDTVINTLVLSR 71
                                      667****************99998886677777999************.88877777666555555 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     7e-05     0.055       1      27 [.       3      29 ..       3      72 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 7e-05
                                      EEEESSTTSSHHHHHHHHHHHHTHEEE CS
                               AAA  1 vllyGppGtGKTllakavakelgvefl 27
                                      +l++GppG GK++  + ++++ + e++
  gi|242398821|ref|YP_002994245.1|  3 ILIFGPPGSGKSTHSRRIIEKYNLEYI 29
                                      699*****************9876654 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   8.3e-05     0.064       1      49 [.       2      49 ..       2      77 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.3e-05
                                      EEEEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE-------EEEE CS
                          NTPase_1  1 kvfiTGppGvGKtTlvkkvlellkssgvkvgGfyteevreggrrigFki 49
                                      +++i GppG+GK+T  ++++e+  + ++  +G + +   ++g+  g ++
  gi|242398821|ref|YP_002994245.1|  2 NILIFGPPGSGKSTHSRRIIEKY-NLEYIASGDIIRAEINKGNALGREM 49
                                      58999*****************9.5668888877766667777777666 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 ?   12.5   0.0   0.00014      0.11       1      27 [.       2      28 ..       2      31 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00014
                                      EEEEE--SSSSHHHHHHHGGGGBS--E CS
                             AAA_5  1 dvlLvGppGtgKselaerlaaalnrev 27
                                      ++l+ GppG+gKs+ ++r+ + +n e+
  gi|242398821|ref|YP_002994245.1|  2 NILIFGPPGSGKSTHSRRIIEKYNLEY 28
                                      58999**************99988665 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00027      0.21       4      22 ..       2      20 ..       1      33 [. 0.86
   2 ?   -2.3   0.0         4   3.1e+03     107     129 ..      45      67 ..      37      84 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00027
                            AAA_24  4 kiliyGpsgiGKTtlakel 22
                                      +ili+Gp+g+GK+t  +++
  gi|242398821|ref|YP_002994245.1|  2 NILIFGPPGSGKSTHSRRI 20
                                      79************98876 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4
                            AAA_24 107 laeefrrllkklqelrknvifia 129
                                       l++e++++++k + l+++vi + 
  gi|242398821|ref|YP_002994245.1|  45 LGREMKKYIEKGDLLPDTVINTL 67 
                                       67888999999888888777554 PP

>> CobU  Cobinamide kinase / cobinamide phosphate guanyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00012     0.097       1      39 [.       3      39 ..       3      53 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00012
                              CobU  1 ilvtGgarSGKSefAeklaeeskekvvYiATaealDeem 39
                                      il+ G+  SGKS++  +++e++  ++ YiA++    +e+
  gi|242398821|ref|YP_002994245.1|  3 ILIFGPPGSGKSTHSRRIIEKY--NLEYIASGDIIRAEI 39
                                      79*****************965..778***998876665 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   0.00012      0.09      14      63 ..       3      51 ..       1     120 [. 0.72

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00012
                                      EEEEESTTSSHHHHHHHHTTSS--...SEEEEEETTCEGGGB-HHHCCHCEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 14 vaivGenGaGKStLlkllagllkp...teGeilldgkdlkeqeleslrkeigv 63
                                      + i+G+ G+GKSt  + ++++++    ++G+i  + +++++   + l +e++ 
  gi|242398821|ref|YP_002994245.1|  3 ILIFGPPGSGKSTHSRRIIEKYNLeyiASGDII-R-AEINK--GNALGREMKK 51
                                      679***************999988677788882.2.23333..3344444444 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00027      0.21       1      23 [.       3      25 ..       3      53 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00027
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakall 23
                                      i+++Gp+g GKSt +++++++  
  gi|242398821|ref|YP_002994245.1|  3 ILIFGPPGSGKSTHSRRIIEKYN 25
                                      689*************9988765 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0    0.0002      0.16       1      23 [.       3      34 ..       3      96 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0002
                   Viral_helicase1  1 ivvhGvpGcGKStlirkllrts.........l 23
                                      i++ G pG+GKSt+ r+++++           
  gi|242398821|ref|YP_002994245.1|  3 ILIFGPPGSGKSTHSRRIIEKYnleyiasgdI 34
                                      67999*************98855544444433 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00021      0.16       5      87 ..       3      98 ..       1     125 [. 0.69

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00021
                            AAA_14  5 lvitGaRrvGKTtllkqlikell...vkkesilyinldderd........kkladpe........kllelileklkeek 64
                                      ++i G+  +GK+t  +++i+++    + + +i+  ++++ +               e         +++l+l++l++ k
  gi|242398821|ref|YP_002994245.1|  3 ILIFGPPGSGKSTHSRRIIEKYNleyIASGDIIRAEINKGNAlgremkkyI-----EkgdllpdtVINTLVLSRLRK-K 75
                                      6899***************99989998888888888888666444332220.....123332322333555555544.6 PP

                            AAA_14 65 ktylflDEiqevpewekalkslv 87
                                      ++ +++D   +  e   al +++
  gi|242398821|ref|YP_002994245.1| 76 RENFIIDGYPRTAEQVLALENFL 98
                                      77799998888877777776554 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00021      0.16       1      46 [.       2      50 ..       2      86 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00021
                            AAA_28  1 kivitGgestGKTtlleaLaar.gypvv..pEaareileeklakgedal 46
                                      +i i+G++++GK+t ++++ ++ + +++   ++ r  ++++ a g+++ 
  gi|242398821|ref|YP_002994245.1|  2 NILIFGPPGSGKSTHSRRIIEKyNLEYIasGDIIRAEINKGNALGREMK 50
                                      599*************999877655555447777777777777766654 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00027      0.21      24      43 ..       2      21 ..       1      29 [. 0.91

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00027
                      Mg_chelatase 24 nlllvGppGsGKtmlakrlp 43
                                      n+l++GppGsGK+   +r+ 
  gi|242398821|ref|YP_002994245.1|  2 NILIFGPPGSGKSTHSRRII 21
                                      89************999985 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   0.00039       0.3      25      37 ..       3      15 ..       1      16 [. 0.92

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00039
                            AAA_29 25 tlltGpsGsGKST 37
                                      +l+ Gp GsGKST
  gi|242398821|ref|YP_002994245.1|  3 ILIFGPPGSGKST 15
                                      79**********9 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 ?    7.0   0.2    0.0071       5.5      22      31 ..     127     136 ..     126     139 .. 0.92
   2 ?    3.4   0.2     0.097        75       6      19 ..     147     161 ..     142     164 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0071
                       Prok-RING_1  22 vCpeCgtpyH 31 
                                       +C +Cg++yH
  gi|242398821|ref|YP_002994245.1| 127 ICRQCGAVYH 136
                                       7********* PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.097
                       Prok-RING_1   6 kCpvCgkel.keedD 19 
                                       kC +Cg e+ + edD
  gi|242398821|ref|YP_002994245.1| 147 KCDICGGEViQREDD 161
                                       9****9875155555 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 ?    9.6   0.7   0.00091      0.71      18      30 ..     122     134 ..     120     136 .. 0.86
   2 ?    0.5   0.3      0.62   4.9e+02       6      12 ..     147     153 ..     146     159 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00091
                           zf-RRN7  18 ddGfyyCrrChtq 30 
                                       + G+++Cr C+ +
  gi|242398821|ref|YP_002994245.1| 122 ISGRRICRQCGAV 134
                                       68*********87 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.62
                           zf-RRN7   6 pCgvCgc 12 
                                        C++Cg+
  gi|242398821|ref|YP_002994245.1| 147 KCDICGG 153
                                       6****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      575  (0.0320709); expected 358.6 (0.02)
Passed Vit filter:                       129  (0.00719505); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 1310.38
//
Query:       gi|242398822|ref|YP_002994246.1|  [L=149]
Description: hypothetical protein TSIB_0836 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.1e-20   71.7   0.2    4.1e-20   71.7   0.2    2.2  2  DUF2258          Uncharacterized protein conserved in archaea
     0.0022   17.6   8.9     0.0027   17.4   8.9    1.1  1  DUF4795          Domain of unknown function (DUF4795)
     0.0022   18.0   4.6      0.046   13.7   3.2    2.1  2  Laminin_II       Laminin Domain II
     0.0026   17.5   7.1     0.0045   16.7   7.1    1.4  1  SHE3             SWI5-dependent HO expression protein 3
     0.0035   17.9   5.7     0.0043   17.6   5.7    1.1  1  AAA_23           AAA domain
     0.0041   15.1   1.5     0.0047   14.9   1.5    1.0  1  V_ATPase_I       V-type ATPase 116kDa subunit family
     0.0073   16.8   0.9     0.0073   16.8   0.9    1.7  2  NPV_P10          Nucleopolyhedrovirus P10 protein
  ------ inclusion threshold ------
      0.018   15.0   0.4      0.043   13.8   0.1    1.6  2  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
      0.024   14.4   0.6      0.038   13.8   0.6    1.3  1  MCPsignal        Methyl-accepting chemotaxis protein (MCP) si
      0.033   14.7   0.7      0.058   13.9   0.7    1.4  1  T3SSipB          Type III cell invasion protein SipB
      0.045   13.8   1.3       0.16   12.0   0.1    2.2  2  UPF0147          Uncharacterised protein family (UPF0147)
      0.051   13.7   7.1      0.038   14.1   3.1    2.1  2  Uds1             Up-regulated During Septation
      0.061   13.4   3.6       0.82    9.7   2.6    2.3  2  HisKA            His Kinase A (phospho-acceptor) domain
      0.074   12.8   0.3       0.12   12.1   0.3    1.3  1  Acetyltransf_16  GNAT acetyltransferase, Mec-17
      0.081   12.8   0.9      0.081   12.8   0.9    2.0  2  DUF1706          Protein of unknown function (DUF1706)
       0.22   11.6   4.8       0.21   11.6   3.6    1.5  1  DUF1664          Protein of unknown function (DUF1664)
       0.25   11.5   5.0       0.43   10.8   5.0    1.3  1  COG5             Golgi transport complex subunit 5
        0.3   11.3  13.0       0.11   12.7   9.4    1.8  2  ATG16            Autophagy protein 16 (ATG16)
       0.31   11.8   2.4       0.31   11.8   0.9    1.7  2  FliD_N           Flagellar hook-associated protein 2 N-termin
       0.34   10.8   2.6       0.61    9.9   1.1    2.2  3  DASH_Dam1        DASH complex subunit Dam1
       0.42   10.9   9.1       0.99    9.7   9.0    1.9  1  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
       0.49   10.7   2.7       0.37   11.1   1.0    1.7  2  DUF948           Bacterial protein of unknown function (DUF94
       0.88   10.1   9.2       0.32   11.5   5.6    1.8  2  DUF16            Protein of unknown function DUF16
       0.94    9.9   5.0        5.7    7.4   5.0    2.1  1  H-kinase_dim     Signal transducing histidine kinase, homodim
        5.1    7.4  10.9         13    6.1   7.6    2.1  2  Spc24            Spc24 subunit of Ndc80


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 !   71.7   0.2   5.7e-23   4.1e-20       1      77 [.       4      74 ..       4      75 .. 0.96
   2 ?    0.7   0.3      0.84     6e+02      32      48 ..     106     122 ..      81     140 .. 0.61

  Alignments for each domain:
  == domain 1  score: 71.7 bits;  conditional E-value: 5.7e-23
                                      EEEECEEGGGHHHHHHHHHHHHTCCCCHTTSS.HHHHHHHHHHHHHHHHHHHHCCTT--TTSEEEEEEEEEEETTEE CS
                           DUF2258  1 lsTGlviaaaYAdKlRrvlfaalsklvkkkkeekkeiaraiaeLNkklYevlveklkidKldvvrirveyeveekkl 77
                                      lsTG+v+a +YA+K+R+vlfa  + ++      +++++ra+a+LN+ l+++l ++l+++K+dvvri++ ++++++++
  gi|242398822|ref|YP_002994246.1|  4 LSTGFVRANGYANKVRKVLFALTRGKIV-----PENVVRASAQLNQYLFDKL-QELNVKKEDVVRISIGFSIKSGEI 74
                                      89********************999888.....9******************.8*****************999876 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.84
                                       S.HHHHHHHHHHHHHHH CS
                           DUF2258  32 eekkeiaraiaeLNkkl 48 
                                          + i++++++L  kl
  gi|242398822|ref|YP_002994246.1| 106 RALEAIINELSNLSEKL 122
                                       44444445555544443 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   8.9   3.7e-06    0.0027      45     146 ..      44     144 ..      34     149 .] 0.87

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.7e-06
                           DUF4795  45 ealkkqieelekvkadkeeveeelaekadkeaLatkvsrdqfDeakkeLekmleellekleeqeealkkaldtLqee 121
                                       + l+++++el+ +k+d   ++   ++k++    +   +  q++ +kke e++l e++e +ee e+al+ ++++L+ +
  gi|242398822|ref|YP_002994246.1|  44 QYLFDKLQELNVKKEDVVRISIGFSIKSGEIEWN--YDSLQIEVYKKEEEEKLAEAMEEVEESERALEAIINELS-N 117
                                       67999***********99999999****987666..566************************************.9 PP

                           DUF4795 122 lkekld..rlelepLkeqleerlkelq 146
                                       l ekl     e++++ e l+++  +l+
  gi|242398822|ref|YP_002994246.1| 118 LSEKLKelSEEVSQIVETLKREHTSLK 144
                                       999998777788888888887777776 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.072        52      43      84 ..      18      59 ..       2      70 .. 0.65
   2 !   13.7   3.2   6.5e-05     0.046       3      52 ..      92     141 ..      90     146 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.072
                                      XXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH CS
                        Laminin_II 43 tnekvkdankairdArrsvkkLeklapqLldklkelkqleea 84
                                      + +++ +++++    ++ v+   +l + L+dkl+el+ ++e 
  gi|242398822|ref|YP_002994246.1| 18 VRKVLFALTRGKIVPENVVRASAQLNQYLFDKLQELNVKKED 59
                                      55555555555444455555555556679******9988876 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 6.5e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II   3 elaaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdank 52 
                                       e++aea e ++e ++ l+++ ++l+n++ekl+e+ ++v ++ e +k   +
  gi|242398822|ref|YP_002994246.1|  92 EKLAEAMEEVEESERALEAIINELSNLSEKLKELSEEVSQIVETLKREHT 141
                                       6789**********************************999999986655 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 !   16.7   7.1   6.3e-06    0.0045     141     205 ..      82     145 ..      41     148 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 6.3e-06
                                       HHHHHHHHHHSSSXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              SHE3 141 sleklklenekqleelqerissndkdidtkldsynnkkknlesieeeknkkllkkleslaseldl 205
                                       ++e +k+e+e++l e +e++ ++++++++ +++++n  ++l++++ee  + ++ +l++  + l+l
  gi|242398822|ref|YP_002994246.1|  82 QIEVYKKEEEEKLAEAMEEVEESERALEAIINELSNLSEKLKELSEEVSQIVE-TLKREHTSLKL 145
                                       7899****************************************988766555.55666666666 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   5.7   6.1e-06    0.0043     116     198 ..      26     128 ..       6     145 .. 0.41

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 6.1e-06
                            AAA_23 116 eleqfisellgskkiilnlilflgqer........feefelkdkke...................rleelekeleel 165
                                       ++ ++++e++ +  ++ln++lf + ++                                      ++e ++ke ee+
  gi|242398822|ref|YP_002994246.1|  26 TRGKIVPENVVRASAQLNQYLFDKLQElnvkkedvV---------RisigfsiksgeiewnydslQIEVYKKEEEEK 93 
                                       455666666666666666666666666333333330.........13333333333333333333333333333222 PP

                            AAA_23 166 edekk.llekl.eqekekekeleeleeeleeilke 198
                                        +e+  ++e+    ++   +el++l e+l+e+ +e
  gi|242398822|ref|YP_002994246.1|  94 LAEAMeEVEESeRALEAIINELSNLSEKLKELSEE 128
                                       22111011111112222222333333333332222 PP

>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   1.5   6.6e-06    0.0047     170     291 ..      15     140 ..       3     145 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 6.6e-06
                        V_ATPase_I 170 veaferilwralrg.....nlflrqaeieepledpetgekveksvfiiffqgeqlke.kikkicesfgaklyelpes 240
                                       +++ +++l+ ++rg     n++  +a++++ l d+ ++ +v+k+  + +  g ++k+  i+   +s++ ++y+ +e 
  gi|242398822|ref|YP_002994246.1|  15 ANKVRKVLFALTRGkivpeNVVRASAQLNQYLFDKLQELNVKKEDVVRISIGFSIKSgEIEWNYDSLQIEVYKKEE- 90 
                                       467889999999983333345566788999999999999999998888888866665389999*********9887. PP

                        V_ATPase_I 241 eeereeklkeveeriedlekvleqteealkevleeiakeleewklkvkkek 291
                                       ee+ +e+++evee+ + le ++++ + +l+e l+e+++e++++  ++k+e 
  gi|242398822|ref|YP_002994246.1|  91 EEKLAEAMEEVEESERALEAIINELS-NLSEKLKELSEEVSQIVETLKREH 140
                                       55688888999999999999987765.567778889988888888888875 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1         6   4.3e+03      39      47 ..      45      53 ..      29      63 .. 0.54
   2 !   16.8   0.9     1e-05    0.0073      23      67 ..      94     138 ..      80     143 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 6
                           NPV_P10 39 elnekLdaq 47
                                       l +kL+++
  gi|242398822|ref|YP_002994246.1| 45 YLFDKLQEL 53
                                      333344333 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 1e-05
                           NPV_P10  23 lqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdiLnp 67 
                                       l +++++v+e  + ++ + ++L ++s++L+el+++v++I ++L  
  gi|242398822|ref|YP_002994246.1|  94 LAEAMEEVEESERALEAIINELSNLSEKLKELSEEVSQIVETLKR 138
                                       6788999*********************************99984 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       3.2   2.3e+03      74      91 ..      37      54 ..      29      64 .. 0.60
   2 ?   13.8   0.1     6e-05     0.043      60     109 ..      89     137 ..      71     143 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 3.2
                      Baculo_PEP_C 74 dalnalqdtlrneLtnln 91
                                      +a ++l++ l  +L+ ln
  gi|242398822|ref|YP_002994246.1| 37 RASAQLNQYLFDKLQELN 54
                                      444555555555555444 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 6e-05
                      Baculo_PEP_C  60 eldtrldtlltnLtdalnalqdtlrneLtnlnsiltnLlssvtNinstLn 109
                                       e +++l++++++++++  al+ ++ neL nl  +l +L  +v  i +tL+
  gi|242398822|ref|YP_002994246.1|  89 EEEEKLAEAMEEVEESERALE-AIINELSNLSEKLKELSEEVSQIVETLK 137
                                       445677777777777777776.8889999999999999999999999985 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 ?   13.8   0.6   5.3e-05     0.038     111     160 ..      89     138 ..      73     145 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.3e-05
                                       HHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal 111 etrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasiee 160
                                       e +++ +e++e+vee+++al+ i ++ +++++ ++e++  ++++ ++++ 
  gi|242398822|ref|YP_002994246.1|  89 EEEEKLAEAMEEVEESERALEAIINELSNLSEKLKELSEEVSQIVETLKR 138
                                       556788999999*************************9999999998875 PP

>> T3SSipB  Type III cell invasion protein SipB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.7   8.1e-05     0.058      46      91 ..      92     137 ..      79     144 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 8.1e-05
                                       STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                           T3SSipB  46 delqtalseakgatddleaaiekadqaksaadaatkkvdeaqkrlk 91 
                                       ++l +a++e ++  ++lea i+++ ++  + +++ + v+++ + lk
  gi|242398822|ref|YP_002994246.1|  92 EKLAEAMEEVEESERALEAIINELSNLSEKLKELSEEVSQIVETLK 137
                                       7899*************************************99886 PP

>> UPF0147  Uncharacterised protein family (UPF0147)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00023      0.16       6      52 ..      16      62 ..      11      64 .. 0.90
   2 ?    0.4   0.2      0.93   6.7e+02      23      23 ..     123     123 ..      88     146 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00023
                                      HHHHHHHHHHHT-TTS-HHHHHHHHHHHHHHT-TTS-HHHHHHHHHH CS
                           UPF0147  6 kevielLeeiiedtsvPrniRraakeakekLkdekeslavraatais 52
                                      ++v ++L  +++ + vP n+ ra  + ++ L d+ ++l+v+  +++ 
  gi|242398822|ref|YP_002994246.1| 16 NKVRKVLFALTRGKIVPENVVRASAQLNQYLFDKLQELNVKKEDVVR 62
                                      6788999999******************************9888775 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.93
                                       H CS
                           UPF0147  23 r 23 
                                       +
  gi|242398822|ref|YP_002994246.1| 123 K 123
                                       2 PP

>> Uds1  Up-regulated During Septation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   3.1   5.3e-05     0.038      76     117 ..      86     127 ..      26     131 .. 0.80
   2 ?    1.8   0.1      0.35   2.5e+02      23      34 ..     133     144 ..     129     149 .] 0.86

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.3e-05
                              Uds1  76 nskssreslakaeeelaeserkvdelaselekleeraaevrr 117
                                        +k+++e+la+a+ee++eser  +++ +el +l+e++ e+ +
  gi|242398822|ref|YP_002994246.1|  86 YKKEEEEKLAEAMEEVEESERALEAIINELSNLSEKLKELSE 127
                                       46678899****************************999876 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.35
                              Uds1  23 VeelkkelkaLe 34 
                                       Ve+lk+e+++L+
  gi|242398822|ref|YP_002994246.1| 133 VETLKREHTSLK 144
                                       9********997 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   2.6    0.0011      0.82      25      62 ..      84     119 ..      80     136 .. 0.87
   2 ?    3.2   0.1      0.13        93      26      48 ..     121     140 ..     116     144 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0011
                                       HHHHC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHC CS
                             HisKA  25 eaLkregklteelkeyletiesearrldhlvedlLdls 62 
                                       e+ k+  +  e+l+e+ e +e+++r l++++++l  ls
  gi|242398822|ref|YP_002994246.1|  84 EVYKK--EEEEKLAEAMEEVEESERALEAIINELSNLS 119
                                       55555..4679***********************8887 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.13
                                       HHHC..T-HSSCHHHHHHHHHHH CS
                             HisKA  26 aLkregklteelkeyletiesea 48 
                                        Lk+   l+ee+ + +et+++e 
  gi|242398822|ref|YP_002994246.1| 121 KLKE---LSEEVSQIVETLKREH 140
                                       4566...9999999999999875 PP

>> Acetyltransf_16  GNAT acetyltransferase, Mec-17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.3   0.00017      0.12      14      62 ..      92     140 ..      79     146 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00017
                                       SHHHHHH..HTT-HHHHHEEHHEEHHHHHHHTT-SS-S--HHHHHHS-E CS
                   Acetyltransf_16  14 kllpekkrkaeeaqeklseiidelGkaSakaqglkkpiTsaeklqssdh 62 
                                       ++l+e ++++ee++++l +ii+el ++S k ++l++ + ++  + + +h
  gi|242398822|ref|YP_002994246.1|  92 EKLAEAMEEVEESERALEAIINELSNLSEKLKELSEEVSQIVETLKREH 140
                                       2445555577888************************999887666666 PP

>> DUF1706  Protein of unknown function (DUF1706)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.9   0.00011     0.081      82     125 ..      75     117 ..      66     120 .. 0.91
   2 ?    1.1   0.1      0.47   3.4e+02     104     125 ..     117     138 ..     114     146 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00011
                                       -CCGHHHHHHHHHHHCTTS-HHHHHHHHHHHHHHHHHHHHHS-H CS
                           DUF1706  82 kWnqlgelnqkfyekyqdlsleelleelkesheellalieslsd 125
                                       +Wn ++ l  ++y+k ++ +l+e+ ee++es ++l a+i++ls+
  gi|242398822|ref|YP_002994246.1|  75 EWN-YDSLQIEVYKKEEEEKLAEAMEEVEESERALEAIINELSN 117
                                       665.899**********************************997 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.47
                                       HHHHHHHHHHHHHHHHHHHS-H CS
                           DUF1706 104 elleelkesheellalieslsd 125
                                       +l e+lke  ee+ +++e+l+ 
  gi|242398822|ref|YP_002994246.1| 117 NLSEKLKELSEEVSQIVETLKR 138
                                       4555555555555555555543 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   3.6    0.0003      0.21      56     111 ..      82     137 ..      71     146 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0003
                           DUF1664  56 slaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeave 111
                                       +++  k++ ++++++  ++++e++++ ++i +e+++++e+l+e++e+v+++ e+ +
  gi|242398822|ref|YP_002994246.1|  82 QIEVYKKEEEEKLAEAMEEVEESERALEAIINELSNLSEKLKELSEEVSQIVETLK 137
                                       46677888889999999999999999999999999999999999999888877665 PP

>> COG5  Golgi transport complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   5.0   0.00059      0.43      49     110 ..      83     144 ..      79     145 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00059
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-TTHHHHHHHHHHHHHHH CS
                              COG5  49 lrqlitsnhleLlehlskskslssvlselksslesLsasyerlkskvlepyeeaeklqsalk 110
                                       ++   ++++++L e +++ ++ +  l+ +  +l++Ls+ ++ l+++v++  e ++  +++lk
  gi|242398822|ref|YP_002994246.1|  83 IEVYKKEEEEKLAEAMEEVEESERALEAIINELSNLSEKLKELSEEVSQIVETLKREHTSLK 144
                                       5566678999999***************************************9999888775 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1       1.5   1.1e+03      94     115 ..      36      57 ..      32      62 .. 0.57
   2 ?   12.7   9.4   0.00015      0.11     108     168 ..      91     148 ..      79     149 .] 0.76

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.5
                             ATG16  94 yksrgelaqrllelneelqkle 115
                                        ++ ++l+q l ++ +el +++
  gi|242398822|ref|YP_002994246.1|  36 VRASAQLNQYLFDKLQELNVKK 57 
                                       4555556666655555555555 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00015
                             ATG16 108 neelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDElsaLqlqln 168
                                       +e+l++  e+ +e e++l+++ +e ++l++klk++ ee     + v++l+ E+++L+l+++
  gi|242398822|ref|YP_002994246.1|  91 EEKLAEAMEEVEESERALEAIINELSNLSEKLKELSEE---VSQIVETLKREHTSLKLEFE 148
                                       56777777777777777777777777777776666655...5789**************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 ?   -1.7   0.0       6.7   4.8e+03      18      36 ..      40      59 ..      29      65 .. 0.58
   2 ?   11.8   0.9   0.00043      0.31      15      57 ..      85     129 ..      78     145 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 6.7
                                      XXXXX.XXXXXXXXXXXHHH CS
                            FliD_N 18 akldk.leqkktklewkqsa 36
                                      a+l++ l  k ++l+ k+++
  gi|242398822|ref|YP_002994246.1| 40 AQLNQyLFDKLQELNVKKED 59
                                      34444444555666655555 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00043
                                       XXXX.XXXXXXXXXXXXXXXHHHHHHHHHHHHHHHHHHHHHXX.G CS
                            FliD_N  15 aera.kldkleqkktklewkqsayrelnsklsnlksalsalsk.s 57 
                                       ++++ + +kl ++ +++e+   a++++ ++lsnl+++l++ls+  
  gi|242398822|ref|YP_002994246.1|  85 VYKKeEEEKLAEAMEEVEESERALEAIINELSNLSEKLKELSEeV 129
                                       455547788***************************998774322 PP

>> DASH_Dam1  DASH complex subunit Dam1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       2.7   1.9e+03      10      29 ..      48      60 ..      42      68 .. 0.51
   2 ?    9.9   1.1   0.00085      0.61       1      37 [.      94     130 ..      92     136 .. 0.87
   3 ?    5.1   0.3     0.027        20       3      24 ..     113     134 ..     111     144 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2.7
                         DASH_Dam1 10 DsletLdknledLqqihesL 29
                                      D+l++L       +  +e++
  gi|242398822|ref|YP_002994246.1| 48 DKLQEL-------NVKKEDV 60
                                      444444.......4444444 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00085
                         DASH_Dam1   1 lepafaeLaDsletLdknledLqqihesLsdfNeSFa 37 
                                       l++a++e ++s ++L++ +++L++++e+L++++e ++
  gi|242398822|ref|YP_002994246.1|  94 LAEAMEEVEESERALEAIINELSNLSEKLKELSEEVS 130
                                       5688999999999999999999999999999998765 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.027
                         DASH_Dam1   3 pafaeLaDsletLdknledLqq 24 
                                       +++++L+++l++L++ ++++ +
  gi|242398822|ref|YP_002994246.1| 113 NELSNLSEKLKELSEEVSQIVE 134
                                       5677777777777777776654 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 ?    9.7   9.0    0.0014      0.99      54     106 ..      78     131 ..      32     143 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0014
                                       HHHHHCCCCCCTT.S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCTS-- CS
                      Seryl_tRNA_N  54 elskeIgkakkkk.edaeeliaevkelkeelkaleaelkeleaeleklllaiPN 106
                                         s +I+  kk++ e+ +e ++ev+e    l+a+ +el++l+++l++l  ++  
  gi|242398822|ref|YP_002994246.1|  78 YDSLQIEVYKKEEeEKLAEAMEEVEESERALEAIINELSNLSEKLKELSEEVSQ 131
                                       555566666666656666666666666666666666666666666666554443 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       5.5   3.9e+03      51      51 ..      44      44 ..      15      63 .. 0.56
   2 ?   11.1   1.0   0.00052      0.37      27      71 ..      93     137 ..      82     144 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 5.5
                            DUF948 51 d 51
                                      +
  gi|242398822|ref|YP_002994246.1| 44 Q 44
                                      2 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00052
                            DUF948  27 tldeaaatieelekqvdpilkevedllakvnelledvneklekvd 71 
                                        l ea + +ee e+ +++i++e+ +l +k +el e+v++ +e+++
  gi|242398822|ref|YP_002994246.1|  93 KLAEAMEEVEESERALEAIINELSNLSEKLKELSEEVSQIVETLK 137
                                       567888888999999999999999999999999999999988876 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1       1.8   1.3e+03      23      39 ..      40      56 ..      12      77 .. 0.69
   2 ?   11.5   5.6   0.00045      0.32      24      87 ..      82     145 ..      76     148 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.8
                                      HHHHHB-..BHHHHHHH CS
                             DUF16 23 kqlnefkdsnkqrLkki 39
                                       qln++  +  q+L+  
  gi|242398822|ref|YP_002994246.1| 40 AQLNQYLFDKLQELNVK 56
                                      46777766666666543 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00045
                                       HHHHB-..BHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHH CS
                             DUF16  24 qlnefkdsnkqrLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetlel 87 
                                       q++ +k++ +++L +  ++v+  +  ++++ ++ +++ ek+kel++e+ +  e l++ + +l+l
  gi|242398822|ref|YP_002994246.1|  82 QIEVYKKEEEEKLAEAMEEVEESERALEAIINELSNLSEKLKELSEEVSQIVETLKREHTSLKL 145
                                       6677*********************************************999999988888876 PP

>> H-kinase_dim  Signal transducing histidine kinase, homodimeric domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   5.0    0.0079       5.7       2      62 ..      34     115 ..      33     144 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0079
                      H-kinase_dim   2 stlRVdakrlDyLlnlvGElVitkarLnqsleefr.....................fenglkasvtelksslqnlgr 57 
                                       +++R  a+   yL +   El ++k  + ++++ f                      +e++l+++ +e+++s + l+ 
  gi|242398822|ref|YP_002994246.1|  34 NVVRASAQLNQYLFDKLQELNVKKEDVVRISIGFSiksgeiewnydslqievykkeEEEKLAEAMEEVEESERALEA 110
                                       6788888888999999999999999999999999999************9999999666666666666666666666 PP

                      H-kinase_dim  58 isgeL 62 
                                       i++eL
  gi|242398822|ref|YP_002994246.1| 111 IINEL 115
                                       66666 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1      0.23   1.6e+02      25      61 ..      40      87 ..      31      91 .. 0.60
   2 ?    6.1   7.6     0.018        13       4      57 ..      92     145 ..      88     147 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.23
                             Spc24 25 selae.lkeeleeleeesee..........keserve.detllklklYr 61
                                      ++l++ l ++l+el+ ++e+          k+ e  e + + l++++Y+
  gi|242398822|ref|YP_002994246.1| 40 AQLNQyLFDKLQELNVKKEDvvrisigfsiKSGE-IEwNYDSLQIEVYK 87
                                      4444326677888888777765555555443333.45577778888886 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.018
                             Spc24   4 nekfriakelsdleselesleselaelkeeleeleeeseekeservedetllkl 57 
                                       +++ ++ +e+++ e++le++ +el++l e+l+el+ee ++  ++++ + t lkl
  gi|242398822|ref|YP_002994246.1|  92 EKLAEAMEEVEESERALEAIINELSNLSEKLKELSEEVSQIVETLKREHTSLKL 145
                                       455667788899999999999*************99988822222335555665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2861  (0.159574); expected 358.6 (0.02)
Passed bias filter:                     1197  (0.0667633); expected 358.6 (0.02)
Passed Vit filter:                       226  (0.0126053); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.47
# Mc/sec: 958.50
//
Query:       gi|242398823|ref|YP_002994247.1|  [L=174]
Description: hypothetical protein TSIB_0837 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-20   73.4   0.0    3.2e-20   73.1   0.0    1.1  1  NYN       NYN domain
  ------ inclusion threshold ------
      0.047   13.4   0.9       0.95    9.2   0.2    2.2  2  DUF460    Protein of unknown function (DUF460)


Domain annotation for each model (and alignments):
>> NYN  NYN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.1   0.0   3.6e-24   3.2e-20       2     146 ..      32     162 ..      31     163 .. 0.92

  Alignments for each domain:
  == domain 1  score: 73.1 bits;  conditional E-value: 3.6e-24
                               NYN   2 vavfiDgenlpvpakgkevdyrklleeirskgelvraraygnwedeeqnkfqdalsstgi.kvkhkplkkrggsgkk 77 
                                       +++ iDg n+    k+ +++++++ e++++ g++ +a++++n++++  +++ +a  ++g+ ++ +           +
  gi|242398823|ref|YP_002994247.1|  32 IGLIIDGPNILR--KEFGIKLENIKEALEKIGNIRVAKVVLNQYAP--QGLIEAVVNQGFePIIVA----------G 94 
                                       7899*******9..6557************************5444..79999*******999554..........8 PP

                               NYN  78 avDvelavdalelaydnkydtivLvsgDgDFaplveklrergkrVevllaeeastsseLisaadefisl 146
                                       ++Dv++a++a+el+y+ +++ i   ++D+DF p++++ +++gk+++v+++e +  s +L++aad++i +
  gi|242398823|ref|YP_002994247.1|  95 DTDVRIAIEAMELIYNSDIEVIGFATRDADFLPIINEGKRKGKETVVIGVE-PGFSVALQNAADYVIRM 162
                                       9************************************************66.89************987 PP

>> DUF460  Protein of unknown function (DUF460)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1    0.0071        64      65      85 ..      76      97 ..      62     112 .. 0.80
   2 ?    9.2   0.2   0.00011      0.95      18      44 ..     122     152 ..      96     167 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.0071
                            DUF460 65 eevieliselG.kpvivAtDvs 85
                                      + +ie++++ G +p+ivA D++
  gi|242398823|ref|YP_002994247.1| 76 QGLIEAVVNQGfEPIIVAGDTD 97
                                      6689999999978*****7754 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00011
                            DUF460  18 kief....eplkkkrkkklivGiDPGittgi 44 
                                         +f    ++ k+k k+++++G+ PG ++++
  gi|242398823|ref|YP_002994247.1| 122 DADFlpiiNEGKRKGKETVVIGVEPGFSVAL 152
                                       44444444455577799**********9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); 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 0.31s 00:00:00.82 Elapsed: 00:00:00.51
# Mc/sec: 1036.40
//
Query:       gi|242398824|ref|YP_002994248.1|  [L=187]
Description: hypothetical protein TSIB_0838 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-18   68.1   0.0    1.4e-18   67.7   0.0    1.1  1  NYN       NYN domain
     0.0031   17.0   0.0      0.046   13.3   0.0    2.4  2  DUF374    Domain of unknown function (DUF374)


Domain annotation for each model (and alignments):
>> NYN  NYN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.7   0.0   1.6e-22   1.4e-18       1     146 [.      35     166 ..      35     167 .. 0.92

  Alignments for each domain:
  == domain 1  score: 67.7 bits;  conditional E-value: 1.6e-22
                               NYN   1 rvavfiDgenlpvpakgkevdyrklleeirskgelvraraygnwedeeqnkfqdalsstgi.kvkhkplkkrggsgk 76 
                                       ++a++iDg n+    k+ +v+++ ++ ++++ g++ +a++++n++++  +++ +a++++g+ ++ +           
  gi|242398824|ref|YP_002994248.1|  35 KIALLIDGPNILR--KEFNVHLEDIVAALEELGNIRVAKVVLNQYAP--QGLIEAIANQGFePIIVA---------- 97 
                                       79***********..6568************************5444..8999********999665.......... PP

                               NYN  77 kavDvelavdalelaydnkydtivLvsgDgDFaplveklrergkrVevllaeeastsseLisaadefisl 146
                                       + + v+lav+a++ +y++++d+i L +++++F p++ k++e+gk++ ++++e +  s +L++aad++i l
  gi|242398824|ref|YP_002994248.1|  98 GETGVKLAVEAMREIYNQNIDIIALATRNAEFLPIILKAKEKGKETAIIGIE-PGFSAALKHAADYVIAL 166
                                       5688**********************************************87.89************987 PP

>> DUF374  Domain of unknown function (DUF374)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   5.1e-06     0.046      36      66 ..      14      44 ..       2      45 .. 0.90
   2 ?    0.9   0.0     0.038   3.4e+02      24      58 ..      85     119 ..      82     123 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.1e-06
                            DUF374 36 SsskggaealremlralkegesvaitpDgPr 66
                                      S +kgg++ +  + +++++g+++a+ +DgP+
  gi|242398824|ref|YP_002994248.1| 14 SITKGGVKSIGMIKQKIQRGKKIALLIDGPN 44
                                      557***************************6 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.038
                            DUF374  24 vlerlGiktirGSsskggaealremlralkegesv 58 
                                       +++  G+++i  +++ g + a+ +m +  +++ ++
  gi|242398824|ref|YP_002994248.1|  85 AIANQGFEPIIVAGETGVKLAVEAMREIYNQNIDI 119
                                       56677999999999977777777777776777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1199.15
//
Query:       gi|242398825|ref|YP_002994249.1|  [L=201]
Description: Multisubunit sodium/hydrogen antiporter, MnhE subunit [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.9e-37  125.9   0.9    1.2e-36  125.7   0.9    1.1  1  MNHE      Na+/H+ ion antiporter subunit


Domain annotation for each model (and alignments):
>> MNHE  Na+/H+ ion antiporter subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.7   0.9   6.7e-41   1.2e-36       2     146 .]      40     199 ..      39     199 .. 0.90

  Alignments for each domain:
  == domain 1  score: 125.7 bits;  conditional E-value: 6.7e-41
                              MNHE   2 lllflvWllltgs..lgelllGlllallvalllrrll........lplrrv........llrllayllvflweivka 60 
                                       +llf +W +++++  +++ll+G l  l+++ +++++l             +        +  +  yl++++++++++
  gi|242398825|ref|YP_002994249.1|  40 ILLFSFWTIISANlkAENLLIGGLATLVISSFMHEMLtedirrsgH----IlekilyisFFVIPQYLFIMAFRLIES 112
                                       89*******************************9988866666541....14445666755599************* PP

                              MNHE  61 nldVakrvlrpklpirpgivkvplrlksdlaltllansitltPGTltvdv..dedrrvlyvHvldv.edeeeearee 134
                                       n++Vak+++   ++i+pgivk++++l+s++++t+lansitltPGTlt+dv  +  + +lyvH++ v + ++e+a e+
  gi|242398825|ref|YP_002994249.1| 113 NFKVAKHAVF--MDINPGIVKIKTELHSNTGVTILANSITLTPGTLTLDVnkKLGETYLYVHWISVeALNREKAGEK 187
                                       **********..**************************************7768899*********7667******* PP

                              MNHE 135 ikgrlErrllei 146
                                       ikg++E +l++i
  gi|242398825|ref|YP_002994249.1| 188 IKGDIEGWLRKI 199
                                       *********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); 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: 0.47u 0.33s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1287.30
//
Query:       gi|242398826|ref|YP_002994250.1|  [L=91]
Description: multisubunit Na+/H+ antiporter [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.9e-14   53.2   4.6    2.9e-14   53.2   4.6    1.6  2  MrpF_PhaF  Multiple resistance and pH regulation protein F (M
  ------ inclusion threshold ------
       0.11   13.1   1.0       0.13   12.8   1.0    1.3  1  DUF1240    Protein of unknown function (DUF1240)


Domain annotation for each model (and alignments):
>> MrpF_PhaF  Multiple resistance and pH regulation protein F (MrpF / PhaF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.2      0.54   4.9e+03      13      15 ..      19      21 ..      14      32 .. 0.47
   2 !   53.2   4.6   3.2e-18   2.9e-14       1      53 []      36      88 ..      36      88 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.54
                         MrpF_PhaF 13 llv 15
                                      +++
  gi|242398826|ref|YP_002994250.1| 19 IAT 21
                                      222 PP

  == domain 2  score: 53.2 bits;  conditional E-value: 3.2e-18
                         MrpF_PhaF  1 aDRvvAlDllgtllvallallailtgrpayldvalvlAllgFvgtvafarfle 53
                                      aDR+v++++++t+lv++la++++++++ ++ld+a+vl +++ vg +++a+++e
  gi|242398826|ref|YP_002994250.1| 36 ADRIVGINTVTTKLVVILAIFGFIMEEYFFLDLAIVLLMVNAVGGLILAKYME 88
                                      7**************************************************86 PP

>> DUF1240  Protein of unknown function (DUF1240)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   1.0   1.4e-05      0.13       5      57 ..      11      61 ..       8      84 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.4e-05
                           DUF1240  5 FsskvvlllfssPlllYfsvlvvlvaitnklakvndklvkllaiiailsfvls 57
                                      F + v +l+ +s +l+Y +  ++  ++ ++++ +n  ++kl++i+ai++f++ 
  gi|242398826|ref|YP_002994250.1| 11 FGWGVLILIATSLILSYRV--LFGPTLADRIVGINTVTTKLVVILAIFGFIME 61
                                      8899999999998888875..5678899***********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       654  (0.0364772); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 650.97
//
Query:       gi|242398827|ref|YP_002994251.1|  [L=104]
Description: Multisubunit sodium/hydrogen antiporter, MnhG subunit [Thermococcus sibiricus MM 739]
Scores for complete 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   80.1   7.4    1.2e-22   79.9   7.4    1.0  1  PhaG_MnhG_YufB  Na+/H+ antiporter subunit
  ------ inclusion threshold ------
      0.038   14.3   0.0      0.049   14.0   0.0    1.1  1  TetR_C_11       Tetracyclin repressor-like, C-terminal domain


Domain annotation for each model (and alignments):
>> PhaG_MnhG_YufB  Na+/H+ antiporter subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.9   7.4   1.4e-26   1.2e-22       1      79 []       6      86 ..       6      86 .. 0.92

  Alignments for each domain:
  == domain 1  score: 79.9 bits;  conditional E-value: 1.4e-26
                    PhaG_MnhG_YufB  1 llllGalfvllgaigllrlpdvytRlhaatkadtlGlllillGlllrf.slaa..slkllliilfllltaPvaahliar 76
                                      llllG  ++++g++g+lr+pdvytRlhaatk+dt G++ il++l++     +    lk l+++++++l +P+++h+iar
  gi|242398827|ref|YP_002994251.1|  6 LLLLGESIMIFGTLGILRFPDVYTRLHAATKCDTGGAMTILMALAIASeA-SLliKLKFLVLAFLIALINPMVSHAIAR 83
                                      799*******************************************6633.33689999******************** PP

                    PhaG_MnhG_YufB 77 aay 79
                                       ay
  gi|242398827|ref|YP_002994251.1| 84 GAY 86
                                      998 PP

>> TetR_C_11  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   5.4e-06     0.049      27      85 ..      39      98 ..      25     100 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.4e-06
                         TetR_C_11 27 agallralla.eaqrdpelaealrerlleprraalravlrrAvarGelradadvelvldl 85
                                      +g +++ l+a ++++++ l   l   +l+   a +  ++  A+arG  + ++++e+v+d+
  gi|242398827|ref|YP_002994251.1| 39 TGGAMTILMAlAIASEASLLIKLKFLVLAFLIALINPMVSHAIARGAYKYGIKPEVVVDM 98
                                      334444444405566778999999999********************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 744.67
//
Query:       gi|242398828|ref|YP_002994252.1|  [L=64]
Description: hypothetical protein TSIB_0842 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-11   44.7   5.6    1.2e-11   44.6   5.6    1.0  1  DUF4040   Domain of unknown function (DUF4040)


Domain annotation for each model (and alignments):
>> DUF4040  Domain of unknown function (DUF4040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.6   5.6   6.4e-16   1.2e-11       3      65 ..       1      62 [.       1      64 [] 0.90

  Alignments for each domain:
  == domain 1  score: 44.6 bits;  conditional E-value: 6.4e-16
                           DUF4040  3 lvlaalaavlardrlaavillgvvGllvallfvllgAPDvAlTqaavveglttvllllalrrl 65
                                      ++l+++a+v  +++++av+ ++ ++l  +l+ vll+APDvAl  + vv ++++  +l+++r +
  gi|242398828|ref|YP_002994252.1|  1 MILLSIAVVEEKNLVNAVVKYAFLSLTFVLVLVLLKAPDVALSAI-VVGAIIIGAFLFTIREV 62
                                      7899*****************************************.66667777788888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1004  (0.0559987); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); 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):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.32s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 426.04
//
Query:       gi|242398829|ref|YP_002994253.1|  [L=81]
Description: Multisubunit sodium/hydrogen antiporter, subunit [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); 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 0.29s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 555.06
//
Query:       gi|242398830|ref|YP_002994254.1|  [L=138]
Description: Multisubunit sodium/hydrogen antiporter, MnhB subunit [Thermococcus sibiricus MM 739]
Scores for complete 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-27   94.4  14.7    7.4e-27   94.1  14.7    1.1  1  MnhB      Domain related to MnhB subunit of Na+/H+ antiporter
  ------ inclusion threshold ------
      0.071   13.1   0.2       0.11   12.4   0.2    1.4  1  DUF3290   Protein of unknown function (DUF3290)


Domain annotation for each model (and alignments):
>> MnhB  Domain related to MnhB subunit of Na+/H+ antiporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.1  14.7   8.2e-31   7.4e-27       1     123 [.       4     125 ..       4     126 .. 0.87

  Alignments for each domain:
  == domain 1  score: 94.1 bits;  conditional E-value: 8.2e-31
                              MnhB   1 ilrtvarllvplillvslylllrGhnsPGGGFqgGlilaaalillylafglee.lekllrvklaprileglglllav 76 
                                       i+rt+++l+ p+++++s yl++ Gh+sPGGGFq+G+ila+++ill+ ++g+++ ++ ++ ++  ++++eg++ ++ v
  gi|242398830|ref|YP_002994254.1|   4 IVRTTTKLVSPFLVVYSTYLMMYGHLSPGGGFQAGVILAVSIILLITSHGYKKvRKTFKFWE--VQLIEGVSGVFLV 78 
                                       79***************************************************666666666..46*********** PP

                              MnhB  77 ltgllglllg.fltslflelelllgeve.lgtallfdlgVylvVvggll 123
                                        +g+++ll+g f+ ++       +g+ +  g+++lf++gV+l+V+++++
  gi|242398830|ref|YP_002994254.1|  79 SLGIISLLFGgFFFNFLRGG--SFGSLLsGGIVPLFNIGVALKVGAAFT 125
                                       **********9777654323..34544459**************99875 PP

>> DUF3290  Protein of unknown function (DUF3290)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   1.3e-05      0.11      18      63 ..      35      80 ..      19      86 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.3e-05
                           DUF3290 18 lryililvlllllivvlilylrnrldtkyRdLsiilllllllllgi 63
                                      ++ ++il++ ++l++++  y + r + k+ ++ +i  ++ ++l+++
  gi|242398830|ref|YP_002994254.1| 35 FQAGVILAVSIILLITSHGYKKVRKTFKFWEVQLIEGVSGVFLVSL 80
                                      7889***********************************9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); 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: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 925.73
//
Query:       gi|242398831|ref|YP_002994255.1|  [L=97]
Description: Multisubunit sodium/hydrogen antiporter, MnhC subunit [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.4e-18   65.2   4.4    3.7e-18   65.1   4.4    1.0  1  Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase cha
  ------ inclusion threshold ------
      0.028   14.6   5.6      0.037   14.2   5.4    1.5  1  DUF4418      Domain of unknown function (DUF4418)
       0.15   11.2   4.0       0.19   10.9   4.0    1.0  1  LtrA         Bacterial low temperature requirement A protein 
       0.31   11.1   8.4       0.16   12.0   6.3    1.6  2  DUF2108      Predicted membrane protein (DUF2108)
          2    8.7   9.6       0.61   10.3   1.6    2.2  2  DUF4040      Domain of unknown function (DUF4040)
        7.7    6.1   6.9        1.2    8.7   3.3    1.4  2  SLATT_6      SMODS and SLOG-associating 2TM effector domain 6


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 !   65.1   4.4   1.2e-21   3.7e-18       3      94 ..       5      95 ..       3      97 .] 0.95

  Alignments for each domain:
  == domain 1  score: 65.1 bits;  conditional E-value: 1.2e-21
                                      HHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHHHHHHHHC.............TTSCGGHHHHHHHHHHHHHH CS
                       Oxidored_q2  3 llliallfliGlygvllrrnllkvliglelisnavnlllvlagvftegtlvitnpatefadplpqalvLtaivigaaet 81
                                      +++ ++++liG+y +++++nl+k +++++l+s ++ l++++ g+ ++g ++i  p+++++dplp +l+Lt +v+ +a+t
  gi|242398831|ref|YP_002994255.1|  5 EFTGIIIMLIGMYALMTKENLIKLVLSINLVSIGLVLFFIGTGYIEGGDVPI-LPRSTVVDPLPATLMLTTLVVDVAIT 82
                                      7899*****************************************9877777.99999********************* PP

                                      HHHHHHHHHHHHH CS
                       Oxidored_q2 82 avgLallvrlyre 94
                                      +++Lal++++ re
  gi|242398831|ref|YP_002994255.1| 83 SLALALVLKIRRE 95
                                      **********998 PP

>> DUF4418  Domain of unknown function (DUF4418)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   5.4   1.2e-05     0.037      41      86 ..       7      52 ..       2      88 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.2e-05
                           DUF4418 41 vGivllvlgllalfvkkkklrrglsiavillgvlviliptvligvC 86
                                      +Gi+++++g+ al++k++ ++ +lsi ++ +g+++++i t  i   
  gi|242398831|ref|YP_002994255.1|  7 TGIIIMLIGMYALMTKENLIKLVLSINLVSIGLVLFFIGTGYIEGG 52
                                      7*************************************99887665 PP

>> LtrA  Bacterial low temperature requirement A protein (LtrA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   4.0   6.4e-05      0.19     263     345 ..       6      87 ..       4      92 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 6.4e-05
                              LtrA 263 vagiillavglelllahpeelldlaaalllfggvalfllgllllkrvllgsvslsrlvllllllallalalvlaall 339
                                       + gii++ +g+  l+ +++ ++ +  + l+ +g++lf++g+  ++   + ++++s++v +l + ++l  ++v  a+ 
  gi|242398831|ref|YP_002994255.1|   6 FTGIIIMLIGMYALMTKENLIKLVLSINLVSIGLVLFFIGTGYIEGGDVPILPRSTVVDPLPATLMLTTLVVDVAIT 82 
                                       78*************9889899999999*****************55555555555554444333333322222222 PP

                              LtrA 340 alalla 345
                                        lal a
  gi|242398831|ref|YP_002994255.1|  83 SLAL-A 87 
                                       2222.2 PP

>> DUF2108  Predicted membrane protein (DUF2108)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   6.3   5.4e-05      0.16       6      60 ..       8      67 ..       4      77 .. 0.72
   2 ?   -1.4   0.1      0.81   2.4e+03      47      53 ..      77      83 ..      70      90 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.4e-05
                           DUF2108  6 alalaliGaigvillkkpldKlimlalleaGlillivakgYL...DVaia..vallePvs 60
                                       ++++liG  + +  ++ ++ + ++ l+  Gl+l+ +  gY+   DV i+  + +++P+ 
  gi|242398831|ref|YP_002994255.1|  8 GIIIMLIGMYALMTKENLIKLVLSINLVSIGLVLFFIGTGYIeggDVPILprSTVVDPLP 67
                                      578999997666666666666679*****************9666777654456677764 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.81
                           DUF2108 47 LDVaiav 53
                                      +DVai +
  gi|242398831|ref|YP_002994255.1| 77 VDVAITS 83
                                      5777654 PP

>> DUF4040  Domain of unknown function (DUF4040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   1.6    0.0002      0.61       1      35 [.      10      44 ..      10      47 .. 0.92
   2 ?    3.0   1.4     0.038   1.1e+02      40      50 ..      77      87 ..      67      92 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0002
                           DUF4040  1 lllvlaalaavlardrlaavillgvvGllvallfv 35
                                      ++++++++a+++ +++++ v+++ +v+++++l+f+
  gi|242398831|ref|YP_002994255.1| 10 IIMLIGMYALMTKENLIKLVLSINLVSIGLVLFFI 44
                                      57999999999999********************7 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.038
                           DUF4040 40 PDvAlTqaavv 50
                                      +DvA+T +a+ 
  gi|242398831|ref|YP_002994255.1| 77 VDVAITSLALA 87
                                      68888888665 PP

>> SLATT_6  SMODS and SLOG-associating 2TM effector domain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   3.3   0.00039       1.2      37      74 ..       6      44 ..       3      51 .. 0.87
   2 ?   -2.9   0.1       1.4   4.3e+03      38      69 ..      70      81 ..      62      91 .. 0.47

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00039
                           SLATT_6 37 lislislavGilalv.ieelstkllsalliiigiialyi 74
                                      + ++i + +G++al+  e+l + +ls+ l+ ig++ ++i
  gi|242398831|ref|YP_002994255.1|  6 FTGIIIMLIGMYALMtKENLIKLVLSINLVSIGLVLFFI 44
                                      67899********99578899************998877 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.4
                           SLATT_6 38 islislavGilalvieelstkllsalliiigi 69
                                      + l +l+v                     ++i
  gi|242398831|ref|YP_002994255.1| 70 LMLTTLVV--------------------DVAI 81
                                      33333333....................2333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       751  (0.0418874); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); 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):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 645.58
//
Query:       gi|242398832|ref|YP_002994256.1|  [L=509]
Description: Multisubunit sodium/hydrogen antiporter, MnhD subunit [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.8e-46  157.3  25.9    4.8e-46  157.3  25.9    2.1  2  Proton_antipo_M  Proton-conducting membrane transporter
    1.9e-07   30.7   3.2    1.9e-07   30.7   3.2    3.2  3  NADHdeh_related  NADH dehydrogenase I, subunit N related prot


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.3  25.9   5.4e-50   4.8e-46       1     275 [.     121     384 ..     121     402 .. 0.93
   2 ?   -1.6   0.9      0.13   1.2e+03      41      93 ..     448     499 ..     444     502 .. 0.78

  Alignments for each domain:
  == domain 1  score: 157.3 bits;  conditional E-value: 5.4e-50
                   Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskalelgln 77 
                                       + dL+  y+ +E+ +++++ L+++ k+k  + +A++k++l +ll+s i++l+i ++y  tg l++  ++++    + 
  gi|242398832|ref|YP_002994256.1| 121 SRDLFNYYIYMEIASVSSFALVAISKEK-GAKKAAFKYALFSLLASYIFILAIGIIYLKTGYLNLFLIKEN---LVF 193
                                       689*********************9777.99******************************9999999999...999 PP

                   Proton_antipo_M  78 slelllllllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirlllllavssneisqlllila 154
                                       s e++++l+l + +l++K++++plh+Wlpda+ +a +p+sall++++vka  +++i l+l +   s  ++++l++ a
  gi|242398832|ref|YP_002994256.1| 194 SKEINVALVLAFSSLILKIGVFPLHFWLPDAHSKADAPISALLSGLVVKAPTYGMILLILTFP-ISTLMQSILITTA 269
                                       99******************************************************9999999.9************ PP

                   Proton_antipo_M 155 iismllgslvalaqtdiKrllAySsishlGymlialavatqygveaaiihllthalfkallFllagsviyerektrd 231
                                       ++sm++g  +al q +  rllAy ++s++Gy+l+++++    +  aa  + ++h+lfk +lFl +g +  e   trd
  gi|242398832|ref|YP_002994256.1| 270 FLSMFFGIAMALIQKNSERLLAYHTVSQMGYVLLGIGL---LNPLAAAYYAMAHSLFKGGLFLSVGTI-AEHYGTRD 342
                                       **************************************...66679999****************666.77779999 PP

                   Proton_antipo_M 232 irayggLakkmPilalvllvlllslaGlPptagFlskfliLeaa 275
                                       ++++++   +  +l +++++l l+++G+ p+ g ++kf++ + +
  gi|242398832|ref|YP_002994256.1| 343 LEKLSY--RHSKFLMVAIVLLSLAIGGISPFVGAFGKFMLVKEI 384
                                       998885..68999*************************998765 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.13
                   Proton_antipo_M  41 ltllgsliLLlgilllynltgtlefeelskalelglnslelllllllllvgll 93 
                                       +  l+ +++ +g++++++  g  ef+   ++   ++++l++ ++ ++l++g+ 
  gi|242398832|ref|YP_002994256.1| 448 VRDLSFIFIGFGLFYVLKKLGLFEFQLSPLF-PDTVSELGREINVYMLFLGAF 499
                                       5567777788999999999998888754444.889999999999999999875 PP

>> NADHdeh_related  NADH dehydrogenase I, subunit N related protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   3.2   2.1e-11   1.9e-07      83     173 ..     116     214 ..      98     226 .. 0.82
   2 ?    0.3   4.2     0.042   3.7e+02     121     159 ..     243     281 ..     232     323 .. 0.78
   3 ?    0.5   0.6     0.037   3.3e+02     124     182 ..     316     371 ..     289     379 .. 0.76

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 2.1e-11
                   NADHdeh_related  83 lgavvtgdvfnftlflaliGianiGivaavkkefvleaafnyGlvaliatlplfggaalilastGtlsifelakl.. 157
                                       lga ++ d+fn+ +++ +  ++   +va  k++ + +aaf+y l +l+a+  +  + ++i  +tG l +f + +   
  gi|242398832|ref|YP_002994256.1| 116 LGAFISRDLFNYYIYMEIASVSSFALVAISKEKGAKKAAFKYALFSLLASYIFILAIGIIYLKTGYLNLFLIKENlv 192
                                       799******************************************************************97765544 PP

                   NADHdeh_related 158 .....agd.vlliaklllvlGv 173
                                            +++ vl ++ l+l +Gv
  gi|242398832|ref|YP_002994256.1| 193 fskeiNVAlVLAFSSLILKIGV 214
                                       4333322234455555555555 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.042
                   NADHdeh_related 121 afnyGlvaliatlplfggaalilastGtlsifelaklag 159
                                       a  yG++ li t p+ +    il +t  ls+f   ++a 
  gi|242398832|ref|YP_002994256.1| 243 APTYGMILLILTFPISTLMQSILITTAFLSMFFGIAMAL 281
                                       457****************************96555543 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.037
                   NADHdeh_related 124 yGlvaliatlplfggaalilastGtlsifelaklagdvlliaklllvlGvvGetGvaPf 182
                                       y +   +    lf + ++i+ + Gt  +  l+    + l++a +ll l + G  G++Pf
  gi|242398832|ref|YP_002994256.1| 316 YAMAHSLFKGGLFLSVGTIAEHYGTRDLEKLSYRHSKFLMVAIVLLSLAI-G--GISPF 371
                                       44444445556999999999999**9999999999887777777777665.3..57887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (509 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       828  (0.0461822); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.46
# Mc/sec: 3323.93
//
Query:       gi|242398833|ref|YP_002994257.1|  [L=135]
Description: Acetolactate synthase, small chain [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-12   47.3   0.4    1.9e-12   46.7   0.4    1.3  1  ACT       ACT domain
    7.8e-07   29.6   0.3    1.4e-06   28.8   0.3    1.4  1  ACT_4     ACT domain
    0.00081   19.3   0.1      0.002   18.1   0.1    1.6  1  ACT_6     ACT domain
     0.0058   16.4   0.0       0.01   15.6   0.0    1.4  1  ACT_7     ACT domain


Domain annotation for each model (and alignments):
>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.7   0.4   4.3e-16   1.9e-12       3      66 ..      59     124 ..      57     125 .. 0.93

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 4.3e-16
                                       EEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTT..ECEEEEEEEEEEHHHHHHHHHHHHTTC CS
                               ACT   3 lrvgvpDrPGlLarvfgaladrgiNidsieqrssedk..vagivfvvivvdeedleevlealkkle 66 
                                       +++ v+D+PG+La+++g+l+++ iNi + e  ++e    +a  ++v i + + +lee+l++lk++e
  gi|242398833|ref|YP_002994257.1|  59 IELVVKDKPGVLAKITGLLGKHRINILFSEAEEMEGIglGAIVAVVDISEIDTNLEELLKELKEIE 124
                                       8899********************************999999999999999999999999999886 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.3   3.2e-10   1.4e-06       7      79 ..      57     130 ..      53     130 .. 0.93

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 3.2e-10
                             ACT_4   7 vrleveaedrkglLaditqviseekanivsvnaktrkkdglaeikitveVkdve.hLsrviakLraipgVisVe 79 
                                       +++e++++d++g+La+it ++ ++++ni   +a++ +  gl  i   v ++ ++  L+++++ L++i++V++V+
  gi|242398833|ref|YP_002994257.1|  57 MEIELVVKDKPGVLAKITGLLGKHRINILFSEAEEMEGIGLGAIVAVVDISEIDtNLEELLKELKEIEEVMEVS 130
                                       689********************************98889999999*****99746****************95 PP

>> ACT_6  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1   4.4e-07     0.002      10      71 ..      64     129 ..      56     132 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 4.4e-07
                             ACT_6  10 pdrpGltasLtsvlaefgvnilDieqavihgrlsLgllvsgp....edalarlekaLlflakelgl 71 
                                       +d+pG++a++t++l ++++nil +e    +g  + +++  ++    + +l++l+k+L +  + +++
  gi|242398833|ref|YP_002994257.1|  64 KDKPGVLAKITGLLGKHRINILFSEAEEMEGIGLGAIVAVVDiseiDTNLEELLKELKEIEEVMEV 129
                                       7************************99999865544444444558777999999999987666655 PP

>> ACT_7  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   2.3e-06      0.01      19      41 ..      65      87 ..      58      92 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.3e-06
                                      SS--HHHHHHHHHHTTT---EEE CS
                             ACT_7 19 dvtGivaklaspLaeagIsifqi 41
                                      d +G++ak+++ L ++ I+i+++
  gi|242398833|ref|YP_002994257.1| 65 DKPGVLAKITGLLGKHRINILFS 87
                                      68*******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       753  (0.041999); 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:                         4  (0.000223102); expected 0.2 (1e-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: 866.34
//
Query:       gi|242398834|ref|YP_002994258.1|  [L=383]
Description: NapA-type sodium/hydrogen antiporter [Thermococcus sibiricus MM 739]
Scores for 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-30  104.1  37.5    8.6e-30  103.8  37.5    1.0  1  Na_H_Exchanger  Sodium/hydrogen exchanger family


Domain annotation for each model (and alignments):
>> Na_H_Exchanger  Sodium/hydrogen exchanger family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.8  37.5   4.8e-34   8.6e-30       6     374 ..      17     374 ..      12     380 .. 0.84

  Alignments for each domain:
  == domain 1  score: 103.8 bits;  conditional E-value: 4.8e-34
                                       HHHHHHHH...HHHHTTSXHHHHHHHHHHHHTTTTTS.....HHHCHCCHHHHCHHCCHHHHCTCGCCTGCCTHHHH CS
                    Na_H_Exchanger   6 llallvgl...larrlklpeivgliiaGlllGpsglgliepseedlevlselglilllFlaGleldlrelrknlksi 79 
                                       ++++l+++   +++r++ p  +g+i aGl+lG ++     p+ e l++l+e+g+++l+ +aGlel ++e+   +k++
  gi|242398834|ref|YP_002994258.1|  17 IIIALARIlaeIFERIGYPGFLGEISAGLFLGIVLTS--MPK-EELNLLAEFGIFFLMMYAGLELTPEEVHIGGKKS 90 
                                       333333333447**********************999..566.9********************************* PP

                                       HHHHHHHHHHHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC.CCCTSTCCCCCCHHHHHHHHHHHCC CS
                    Na_H_Exchanger  80 lllallgvlitvvliGlllylllilgiplleallfgailsatdpvvvlailkeegrvperlgtlllgesvlnDavav 156
                                       + l +l ++++++++  +++++       +e +++gails+ ++++vl++    +    ++ +++l+ +v+ ++ a+
  gi|242398834|ref|YP_002994258.1|  91 IPLYILTYALMTFVTLPFTNYT-----LSHENIIVGAILSVASAPIVLRLS---RFFGDDFLHVALSYAVISEIGAI 159
                                       **********999933344443.....68**********************...66667****************** PP

                                       CCCHHHHHHTX...XXXXTSSSTSXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCTHHHHHHHHHHHHHHHHHHHH CS
                    Na_H_Exchanger 157 vllavllalak...eeaggetslllllliflvvavgglllglvigwllrlitrftdddrelevllvlllallaalla 230
                                       v l++l+ +     + +g   +l++ ++++ +++++ +ll +  + l  + +r++ +++e  + lv++l+ ++all+
  gi|242398834|ref|YP_002994258.1| 160 VSLYILVNFEVshlSYIGLIMELVKDGIFLGTLFGINYLLNVKHKALIIKGLRSL-KSDEAVFGLVMVLSTSIALLS 235
                                       *********8555555666666666677777777777777777777777777775.********************* PP

                                       HTSXXXHHHHHHHHHHHHH....HHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHSXHHHHHXXHHHHHHHHHHHHHH CS
                    Na_H_Exchanger 231 ellgvsgilgaflaGlvls....eyefsnklseklesfreglfnplfFvlvGlsldlkvlnnhlsvlilvllilvai 303
                                       e++g++  +gaf++Gl+l     ++++  ++++ ++ + +g+f+p+fF+  G+++        ++  + v+  ++++
  gi|242398834|ref|YP_002994258.1| 236 EMIGLHFSIGAFVVGLLLHsdliGTKQYRRVHTIISGVTYGIFAPIFFAWRGINFE-------TEFSMEVVYFFILV 305
                                       *******************544433333335555777777****************.......55556666666666 PP

                                       HTHHHHHHHHHTTTXSSXHHHHHHCCCCSS.BHHHHHHHHHHHHHHXHHHHTTSSTTTCSTSXHHHHHHHH CS
                    Na_H_Exchanger 304 llgrilavflllrllglslrealiigfgglqrgavalalaalgpalgllarelyallivvvlftvlvqGls 374
                                        + ril ++ +++  g++ r  ++ + g ++ g + l +  +g   g+l+++lyal+ ++ ++ +++ +++
  gi|242398834|ref|YP_002994258.1| 306 YILRILLTMGFTW--GKDPRKTIVRASGVASFGVLGLLVGEIGYEYGVLSEHLYALASLASILGMFISTSI 374
                                       689**********..******************************************99999999966654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.67u 0.36s 00:00:01.03 Elapsed: 00:00:00.58
# Mc/sec: 2003.15
//
Query:       gi|242398835|ref|YP_002994259.1|  [L=158]
Description: Pyruvoyl-dependent arginine decarboxylase [Thermococcus sibiricus MM 739]
Scores for complete 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-39  134.1   0.1    4.5e-39  133.8   0.1    1.0  1  PvlArgDC  Pyruvoyl-dependent arginine decarboxylase (PvlArgDC


Domain annotation for each model (and alignments):
>> PvlArgDC  Pyruvoyl-dependent arginine decarboxylase (PvlArgDC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.8   0.1   2.5e-43   4.5e-39       1     161 [.       5     155 ..       5     156 .. 0.90

  Alignments for each domain:
  == domain 1  score: 133.8 bits;  conditional E-value: 2.5e-43
                          PvlArgDC   1 vPkkvfltkGvgeskeelasFdlALldAgIenfNLvkvSSilPpeaeivsveeglkelppGsivevvmarassnepg 77 
                                       +Pkk+ l ++++e++++l++Fd+ALl+ gI+n+NLvk SS++P+  e   ++e++k++p G ++++v+a+++s+epg
  gi|242398835|ref|YP_002994259.1|   5 TPKKAILLAASAEGSTKLNAFDNALLKMGIGNVNLVKLSSVIPAYIE--WIDELPKNIPVGMLLPTVYAHIESDEPG 79 
                                       69*********************************************..99************************** PP

                          PvlArgDC  78 rliaaavgvaipkdekkgGyiaEysgfgeseeeaeeeaeelaaemlattrglleekiietkeievaaveakvekygt 154
                                       ++i+aa+gv+i++  ++gG+i+Eysg++ ++eeae+ + ++++e++++ rg+    ++++ +  va+++  +++  +
  gi|242398835|ref|YP_002994259.1|  80 STITAALGVGISEG-NEGGLIYEYSGYC-TKEEAEKMVHKMVEEGFKV-RGW----KLKEFKAAVAEIT-VKDRPVA 148
                                       ***********876.9**********99.******************7.**9....4444444444443.4567788 PP

                          PvlArgDC 155 vlaaavf 161
                                       ++aa+v+
  gi|242398835|ref|YP_002994259.1| 149 AIAAVVM 155
                                       8888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      560  (0.0312343); 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: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1062.08
//
Query:       gi|242398836|ref|YP_002994260.1|  [L=124]
Description: S-adenosylmethionine decarboxylase proenzyme [Thermococcus sibiricus MM 739]
Scores for complete 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-42  144.3   0.1    1.6e-42  144.1   0.1    1.0  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 !  144.1   0.1   8.8e-47   1.6e-42       1     106 []      13     119 ..      13     119 .. 0.99

  Alignments for each domain:
  == domain 1  score: 144.1 bits;  conditional E-value: 8.8e-47
                                       EEEEEEES--HHHCTSHHHHHHHHHHHHHHCT-EEEEEEEEE-SSS-EEEEEEETTEEEEEEEEGGGTEEEEEEEEE CS
                         AdoMet_dc   1 hllvdlygcdpelledaelleqilteaaeaigatvlsvafhkfepeGvsvvvliaeShlsiHtwpetgyaaiDvftc 77 
                                       h+++dly+cdp++l+d e++e+ilteaae ++atv++  fhkf+p+Gvs+vv+++eSh++iHtwpe+gyaa+Dv+tc
  gi|242398836|ref|YP_002994260.1|  13 HVVLDLYECDPQILDDIERIEEILTEAAEVANATVIDKRFHKFSPQGVSGVVVVSESHIAIHTWPEHGYAAVDVYTC 89 
                                       99*************************************************************************** PP

                                       ST.HHHHHHHHHHHHHHT-SEEEEEEEEEE CS
                         AdoMet_dc  78 ge.ispekaleylieafkadrvtvdelkRG 106
                                       g+ + p+ka ey+i+++k +r t+ +l+RG
  gi|242398836|ref|YP_002994260.1|  90 GDhTMPLKASEYIIRELKCKRPTLVKLDRG 119
                                       ****************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 832.76
//
Query:       gi|242398837|ref|YP_002994261.1|  [L=284]
Description: Probable spermidine synthase [Thermococcus sibiricus MM 739]
Scores for complete 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-52  175.4   0.0      1e-51  175.0   0.0    1.1  1  Spermine_synth   Spermine/spermidine synthase domain
    3.4e-11   42.9   0.2    7.6e-11   41.7   0.2    1.7  1  Spermine_synt_N  Spermidine synthase tetramerisation domain
     0.0015   19.2   0.0      0.004   17.8   0.0    1.8  1  Methyltransf_25  Methyltransferase domain
     0.0096   15.8   0.0      0.016   15.1   0.0    1.3  1  Methyltransf_30  S-adenosyl-L-methionine-dependent methyltran
  ------ inclusion threshold ------
      0.047   14.4   0.0       0.14   12.9   0.0    1.8  2  Methyltransf_12  Methyltransferase domain


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 !  175.0   0.0   2.8e-55     1e-51       2     181 ..      57     240 ..      56     249 .. 0.94

  Alignments for each domain:
  == domain 1  score: 175.0 bits;  conditional E-value: 2.8e-55
                                       HHHHHHHHHHHHCCSSST-EEEEESSTTSHHHHHHTTSTT-SEEEEEES-HHHHHHHHHHSHHHHTT.....CGGCT CS
                    Spermine_synth   2 faykemiahvplmlhknpkevLiiGGgDGgvlrevvkhntvekitlvdiDqkvidfskkflpslais.....afnda 73 
                                        +y+e ++h ++++h+np++vL+iGGgDGg+lrev+kh++ve++ +v+iD+kv+++s+++l+   +        +++
  gi|242398837|ref|YP_002994261.1|  57 RSYHEPLVHPVMLSHPNPRKVLVIGGGDGGTLREVLKHESVENAIMVEIDEKVVEVSREYLKIDGGLlerliRGEEP 133
                                       68***********************************************************9876668888889*** PP

                                       TEEEEESTCHHHHCTCSS-EEEEEEECCSTTCSSCGCSSHHHHHHHHHTEEEEEEEEEEEEETTTCHHHHHHHHHHH CS
                    Spermine_synth  74 rvklvlgdgfkflkayekkfdvvivdsldpvgpaenlFskeffdllkkvlkedGviilqaekpelekelvinvdksg 150
                                       + kl++gdg++++k  +++fdv+ivds+dpvgpa+ lFs+ef+++ +++l+e G++i+q+ ++ l  + v  + k++
  gi|242398837|ref|YP_002994261.1| 134 KAKLIIGDGVEYMKSHKEHFDVIIVDSTDPVGPAKLLFSEEFYKNAYDALDEKGLYITQSGSVYLFTDEVLGAYKNM 210
                                       ***************************************************************************** PP

                                       HTTSSCEEEEEEEETTTSCSCEEEEEEEESS CS
                    Spermine_synth 151 kqvfalqvepsavlvPtylsgminfvveskk 181
                                       k++f  +v++++++v  y s + ++v  +++
  gi|242398837|ref|YP_002994261.1| 211 KKAFD-KVYYFTFPVIGYASPWSFLVGVKGD 240
                                       ****9.*********9999999888776665 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 !   41.7   0.2   2.1e-14   7.6e-11       3      53 .]       3      53 ..       1      53 [. 0.94

  Alignments for each domain:
  == domain 1  score: 41.7 bits;  conditional E-value: 2.1e-14
                                      EEEEEETTEEEEEEEEEEEEEEEESSSEEEEEEETTTEEEEEETTEEEEET CS
                   Spermine_synt_N  3 fteisdpglalelkVekvLyeekSeyQdieifesktfGkvLvLDgvvqltE 53
                                      f e ++ g ++ +k+ ++++e++S+yQ+ie++e++ fGk  v+Dg+vql E
  gi|242398837|ref|YP_002994261.1|  3 FVEWYPRGYGVGFKITSKILEVQSNYQKIELYETEGFGKLFVIDGTVQLVE 53
                                      667788899***************************************987 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   1.1e-06     0.004       1      75 [.      77     162 ..      77     187 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.1e-06
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHH...........TTTTEEEEESBC.CGBSSSTTTE CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraee...........eglnvefvqgda.edlpfedgsf 65 
                                       vL +G G G ++++++k+ + ++ ++v+i+e+ +e  re ++            e+++++++ gd  e ++ ++++f
  gi|242398837|ref|YP_002994261.1|  77 VLVIGGGDGGTLREVLKHESVENAIMVEIDEKVVEVSREYLKIdggllerlirgEEPKAKLIIGDGvEYMKSHKEHF 153
                                       899*************996589****************6665444444333334667********9566999***** PP

                                       EEEEEESTGG CS
                   Methyltransf_25  66 Dlvvssgalh 75 
                                       D++++  +  
  gi|242398837|ref|YP_002994261.1| 154 DVIIV-DSTD 162
                                       ***98.4444 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 !   15.1   0.0   4.3e-06     0.016       7      91 ..     109     194 ..     103     200 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.3e-06
                                       HHHHHHHTS-S-SEEEEEEETTTTEEEEEEES-HHHHHHHC-T-EEEEEE-SS-TTTSGG.GCSHHHHHHHHHHEEE CS
                   Methyltransf_30   7 akallkeyllalaglqrlelaaeevtlklligdarealkeldekadawFlDgFsPaknPe.lwseellkelarllkk 82 
                                       + ++ +eyl+   gl +  + +ee + kl+igd  e +k  +e++d++  D   P    + l+see++k+ +++l++
  gi|242398837|ref|YP_002994261.1| 109 VVEVSREYLKIDGGLLERLIRGEEPKAKLIIGDGVEYMKSHKEHFDVIIVDSTDPVGPAKlLFSEEFYKNAYDALDE 185
                                       55667888888888888889999******************************998766637*************** PP

                                       EEEEEES-- CS
                   Methyltransf_30  83 kgtlatyss 91 
                                       kg  +t s 
  gi|242398837|ref|YP_002994261.1| 186 KGLYITQSG 194
                                       ***999775 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   3.8e-05      0.14       1      71 [.      78     157 ..      78     161 .. 0.83
   2 ?   -2.4   0.0       2.3   8.1e+03      74      90 ..     202     218 ..     173     219 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.8e-05
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg..........ssf 67 
                                       L iG+G+G +lr++l++ +  + + v+i+++++e  +e l+  +++    ++ e+  +  l  g          ++f
  gi|242398837|ref|YP_002994261.1|  78 LVIGGGDGGTLREVLKHESVENAIMVEIDEKVVEVSREYLKIDGGLLERLIRGEEPKAK-LIIGdgveymkshkEHF 153
                                       569**************8888889*********99999999999888888888877753.33335789999999999 PP

                   Methyltransf_12  68 Dlvv 71 
                                       D+++
  gi|242398837|ref|YP_002994261.1| 154 DVII 157
                                       9988 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.3
                   Methyltransf_12  74 nvlhhlkdirevldnir 90 
                                       +vl + k++++++d+++
  gi|242398837|ref|YP_002994261.1| 202 EVLGAYKNMKKAFDKVY 218
                                       56666677777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1763.63
//
Query:       gi|242398838|ref|YP_002994262.1|  [L=117]
Description: HTH transcription regulator [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.2e-10   38.8   0.1    6.2e-10   38.8   0.1    1.6  2  TrmB           Sugar-specific transcriptional regulator TrmB
    4.6e-06   26.4   1.1    7.7e-06   25.7   1.1    1.4  1  HTH_5          Bacterial regulatory protein, arsR family
    5.2e-05   22.7   1.2    5.2e-05   22.7   1.2    1.7  2  HTH_24         Winged helix-turn-helix DNA-binding
    0.00056   19.9   0.2    0.00056   19.9   0.2    1.6  2  HTH_20         Helix-turn-helix domain
    0.00067   19.5   0.6    0.00095   19.1   0.6    1.3  1  HTH_11         HTH domain
     0.0022   17.7   0.5      0.004   16.9   0.2    1.6  1  DUF4423        Domain of unknown function (DUF4423)
     0.0025   17.9   2.8      0.039   14.0   0.5    2.4  2  DUF2250        Uncharacterized protein conserved in archaea (
     0.0025   17.6   0.6     0.0033   17.2   0.6    1.2  1  HxlR           HxlR-like helix-turn-helix
     0.0032   17.5   0.1     0.0092   16.1   0.1    1.6  2  Replic_Relax   Replication-relaxation
     0.0035   17.2   0.4      0.015   15.2   0.3    2.0  2  MarR           MarR family
     0.0037   17.2   0.0     0.0067   16.4   0.0    1.5  1  HTH_29         Winged helix-turn helix
     0.0041   17.1   3.2      0.013   15.5   2.3    2.2  2  HTH_Mga        M protein trans-acting positive regulator (MGA
     0.0054   16.6   3.1     0.0072   16.2   3.1    1.2  1  TFIIE_alpha    TFIIE alpha subunit
     0.0057   17.1   0.2     0.0094   16.4   0.2    1.5  1  HTH_40         Helix-turn-helix domain
      0.007   16.3   0.1      0.017   15.1   0.0    1.6  2  Dimerisation2  Dimerisation domain
  ------ inclusion threshold ------
      0.014   15.7   0.0      0.019   15.4   0.0    1.3  1  FaeA           FaeA-like protein
      0.023   14.8   0.2       0.05   13.7   0.2    1.6  1  HTH_9          RNA polymerase III subunit RPC82 helix-turn-he
      0.028   14.2   0.3       0.15   11.8   0.1    2.1  2  HTH_38         Helix-turn-helix domain
      0.032   14.1   0.0      0.058   13.3   0.0    1.5  1  MarR_2         MarR family
      0.038   13.8   0.2      0.091   12.5   0.2    1.6  1  LexA_DNA_bind  LexA DNA binding domain
      0.042   13.7   0.0      0.074   12.9   0.0    1.4  1  HTH_23         Homeodomain-like domain
      0.068   12.8   0.3       0.11   12.2   0.3    1.3  1  GntR           Bacterial regulatory proteins, gntR family
      0.071   12.5   0.0      0.071   12.5   0.0    1.2  1  RepL           Firmicute plasmid replication protein (RepL)
      0.093   12.6   0.0       0.16   11.9   0.0    1.3  1  HTH_AsnC-type  AsnC-type helix-turn-helix domain
      0.097   12.5   0.1       0.23   11.3   0.1    1.6  1  HTH_IclR       IclR helix-turn-helix domain
      0.099   12.3   0.1       0.19   11.3   0.1    1.4  1  RP-C           Replication protein C N-terminal domain
       0.11   12.9   0.1       0.19   12.1   0.1    1.4  1  Rrf2           Transcriptional regulator
       0.15   12.3   0.6       0.22   11.7   0.1    1.5  1  GST_C          Glutathione S-transferase, C-terminal domain
       0.15   12.5   0.4       0.36   11.4   0.1    1.8  1  DALR_2         DALR domain
       0.23   11.4   3.2       0.65   10.0   0.1    2.8  3  HTH_36         Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   0.1     1e-12   6.2e-10       3      68 .]      14      82 ..      12      82 .. 0.95
   2 ?   -2.1   0.2       6.2   3.7e+03       4      14 ..      96     106 ..      92     108 .. 0.68

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 1e-12
                                      HCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST....TTEEEE--HH CS
                              TrmB  3 klGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr....pklYravdpe 68
                                       + L+  E+k+Y  Ll ++++t ++ia+++g+++  v e L+ L++ Gl+er+  +     ++Yra +p+
  gi|242398838|ref|YP_002994262.1| 14 NFELTHSEIKIYSLLL-KEELTPRQIAKKVGLSERIVREKLKHLLELGLIERNLIKqgwlGYIYRAKNPK 82
                                      799**********999.899*********************************99999999*****9985 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 6.2
                                       CHHHHHCCCHC CS
                              TrmB   4 lGLseyEakvY 14 
                                       lGL e E k Y
  gi|242398838|ref|YP_002994262.1|  96 LGLLEEEYKKY 106
                                       67777777777 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   1.1   1.3e-08   7.7e-06       6      46 ..      23      63 ..      20      64 .. 0.95

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 1.3e-08
                                      HHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  6 kILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      kI +lL ++el+  ++a+++gls+ +v++ Lk L e+GL+e
  gi|242398838|ref|YP_002994262.1| 23 KIYSLLLKEELTPRQIAKKVGLSERIVREKLKHLLELGLIE 63
                                      78899**********************************97 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   1.2   8.6e-08   5.2e-05       3      48 .]      19      63 ..      17      63 .. 0.94
   2 ?   -2.3   0.0       5.7   3.4e+03      39      46 ..      64      71 ..      64      72 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 8.6e-08
                            HTH_24  3 etdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      + ++kI++lL k   ++ r++A+++glS   v++ lk L e GlI+
  gi|242398838|ref|YP_002994262.1| 19 HSEIKIYSLLLK-EELTPRQIAKKVGLSERIVREKLKHLLELGLIE 63
                                      67899**99999.9*******************************7 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 5.7
                            HTH_24 39 krLeeeGl 46
                                      ++L+++G+
  gi|242398838|ref|YP_002994262.1| 64 RNLIKQGW 71
                                      68999998 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.2   9.4e-07   0.00056      14      56 ..      23      64 ..      20      68 .. 0.96
   2 ?   -2.4   0.1       8.9   5.3e+03      47      56 ..      91     101 ..      85     102 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 9.4e-07
                                      HHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20 14 rilraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56
                                      +i+++L  +e+lt+ ++a+ ++ls   ++  L+ L e gL+e+
  gi|242398838|ref|YP_002994262.1| 23 KIYSLL-LKEELTPRQIAKKVGLSERIVREKLKHLLELGLIER 64
                                      79999*.**********************************97 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 8.9
                                       HHHH.CTTEEE CS
                            HTH_20  47 vLee.agLvev 56 
                                       ++ee  gL+e 
  gi|242398838|ref|YP_002994262.1|  91 KMEElLGLLEE 101
                                       67888888885 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.6   1.6e-06   0.00095       4      43 ..      23      60 ..      20      75 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.6e-06
                            HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg 43
                                      +i+ lLl+++  ++  ++A++ ++S+r vr  +k L elg
  gi|242398838|ref|YP_002994262.1| 23 KIYSLLLKEE--LTPRQIAKKVGLSERIVREKLKHLLELG 60
                                      7888996666..**************************99 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.2   6.6e-06     0.004      33      71 ..      30      65 ..      22      95 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 6.6e-06
                           DUF4423 33 kdfkadpeelakrlrpkisaeevekalefLlklgllkkd 71
                                      k++  +p+++ak+++  +s+  v++ l+ Ll+lgl++++
  gi|242398838|ref|YP_002994262.1| 30 KEE-LTPRQIAKKVG--LSERIVREKLKHLLELGLIERN 65
                                      444.89*********..********************98 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 !   14.0   0.5   6.6e-05     0.039      25      55 ..      35      65 ..      12      69 .. 0.87
   2 ?    4.0   0.1      0.09        54      32      61 ..      78     108 ..      72     111 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.6e-05
                           DUF2250 25 aksiakeleipleevrellkkLeelGLlerv 55
                                      +++iak++ ++   vre+lk+L elGL+er 
  gi|242398838|ref|YP_002994262.1| 35 PRQIAKKVGLSERIVREKLKHLLELGLIERN 65
                                      799**************************95 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.09
                           DUF2250  32 leipleevrellkkLee.lGLlervegktik 61 
                                        + p+e  ++++ k+ee lGLle+  +k  k
  gi|242398838|ref|YP_002994262.1|  78 AKNPKEALKSVFSKMEElLGLLEEEYKKYSK 108
                                       5677888888888888746****98777655 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.6   5.5e-06    0.0033      21      82 ..      35      95 ..      19     104 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 5.5e-06
                                      HHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHHHHHHHHHH CS
                              HxlR 21 fselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrslepvlqelkkw 82
                                        ++++++ ++s+++  ++L++L + glier+ +++      Y+  +  ++l+ v+++++++
  gi|242398838|ref|YP_002994262.1| 35 PRQIAKKV-GLSERIVREKLKHLLELGLIERNLIKQGWLGYIYRAKNPKEALKSVFSKMEEL 95
                                      56788888.89***********************************************9986 PP

>> Replic_Relax  Replication-relaxation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   1.5e-05    0.0092      10      46 ..      33      69 ..      26      81 .. 0.87
   2 ?   -0.3   0.0       1.6   9.3e+02      14      46 ..      74     106 ..      72     112 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.5e-05
                      Replic_Relax 10 lTtrqiarllfashratarrrLarLrelgllsr.lrkr 46
                                      lT rqia+    s+r  +r +L++L elgl++r l k+
  gi|242398838|ref|YP_002994262.1| 33 LTPRQIAKKVGLSERI-VREKLKHLLELGLIERnLIKQ 69
                                      899*************.****************99987 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.6
                      Replic_Relax  14 qiarllfashra.tarrrLarLrelgllsr.lrkr 46 
                                       +i+r+ ++++   ++++++ +L  lgll+  ++k 
  gi|242398838|ref|YP_002994262.1|  74 YIYRAKNPKEALkSVFSKMEEL--LGLLEEeYKKY 106
                                       5777777777667788888888..88888755443 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.3   2.5e-05     0.015      15      49 ..      30      64 ..      17      69 .. 0.87
   2 ?   -0.3   0.0       1.7     1e+03      45      53 ..      73      81 ..      65      83 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.5e-05
                                      STTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              MarR 15 qgplsvseLakklgvskstvtrvldrLekkGlieR 49
                                      +++l+  ++akk+g+s   v + l++L + GlieR
  gi|242398838|ref|YP_002994262.1| 30 KEELTPRQIAKKVGLSERIVREKLKHLLELGLIER 64
                                      578999****************************9 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.7
                                      TSEEEEEET CS
                              MarR 45 GlieRsksp 53
                                      G+i+R k+p
  gi|242398838|ref|YP_002994262.1| 73 GYIYRAKNP 81
                                      778888888 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.1e-05    0.0067       6      35 ..      27      55 ..      22      71 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.1e-05
                            HTH_29  6 lllaeGvstvsqiAkllglsrrtvyrwlkr 35
                                      lll+e++ t++qiAk +gls+r v+  lk 
  gi|242398838|ref|YP_002994262.1| 27 LLLKEEL-TPRQIAKKVGLSERIVREKLKH 55
                                      5677777.9*************99866555 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 ?    1.2   0.1      0.62   3.7e+02      11      25 ..       5      19 ..       3      23 .. 0.83
   2 !   15.5   2.3   2.2e-05     0.013       5      54 ..      19      67 ..       9      69 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.62
                           HTH_Mga 11 lelLteneksltlde 25
                                      lel+t+  k ++l++
  gi|242398838|ref|YP_002994262.1|  5 LELFTKKIKNFELTH 19
                                      899***999999986 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 2.2e-05
                           HTH_Mga  5 krklkLlelLteneksltldelakeLglseltlqsdiseLnel.Fpeelsi 54
                                      ++++k+ +lL++  ++lt   +ak+ glse+++++ + +L el ++e ++i
  gi|242398838|ref|YP_002994262.1| 19 HSEIKIYSLLLK--EELTPRQIAKKVGLSERIVREKLKHLLELgLIERNLI 67
                                      679*********..9************************998877776665 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   3.1   1.2e-05    0.0072      16     101 ..      22     104 ..       6     108 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.2e-05
                                       HHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTEEEEEEEEEECCC.HCCCHHHHHHH CS
                       TFIIE_alpha  16 vlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrdeekswykyywrinyek.lvdvvkrklee 91 
                                       ++ + +Ll k e+t  ++ak++++   ++r+ L +L e +l++    +   ++w  y +r + +k +++ v  k+ee
  gi|242398838|ref|YP_002994262.1|  22 IK-IYSLLLKEELTPRQIAKKVGLSERIVREKLKHLLELGLIERNLIK---QGWLGYIYRAKNPKeALKSVFSKMEE 94 
                                       44.4456669********************************977665...79******997654389999999999 PP

                                       HHHHHHHHHC CS
                       TFIIE_alpha  92 vvkkLeekle 101
                                       ++  Lee+ +
  gi|242398838|ref|YP_002994262.1|  95 LLGLLEEEYK 104
                                       9999998765 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.2   1.6e-05    0.0094       6      41 ..      25      61 ..      20     109 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.6e-05
                            HTH_40  6 lell.eeglsieeIAkerglkesTIegHLaelieege 41
                                      ++ll +e l++ +IAk+ gl+e  + + L +l+e g 
  gi|242398838|ref|YP_002994262.1| 25 YSLLlKEELTPRQIAKKVGLSERIVREKLKHLLELGL 61
                                      45555*********************99999999984 PP

>> Dimerisation2  Dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   2.9e-05     0.017      17      65 ..      18      65 ..      11      79 .. 0.90
   2 ?   -2.0   0.1       6.3   3.7e+03      59      67 ..      96     105 ..      94     112 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.9e-05
                     Dimerisation2 17 tAceLgvFdlLkeeeplsaeevaeelgasvkGterLldacvaLgLLere 65
                                      t +e++++ lL + e+l+ +++a+++g+s + ++  l+ +  LgL er+
  gi|242398838|ref|YP_002994262.1| 18 THSEIKIYSLLLK-EELTPRQIAKKVGLSERIVREKLKHLLELGLIERN 65
                                      7799********9.9*******************************987 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 6.3
                     Dimerisation2  59 LgLLere.kk 67 
                                       LgLLe e kk
  gi|242398838|ref|YP_002994262.1|  96 LGLLEEEyKK 105
                                       8999976322 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.0   3.1e-05     0.019      13      57 ..      30      74 ..       2      76 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.1e-05
                                      S----HHHHHHHHTS-HHHHHHHHHHHHHHSSEEEE--SSSSS-E CS
                              FaeA 13 kapckTreiAdalglsaYQaRyYLeqLekegkikrspvrrGvstl 57
                                      k   + r+iA+ +gls   +R  L+ L   g i+r  +++G  ++
  gi|242398838|ref|YP_002994262.1| 30 KEELTPRQIAKKVGLSERIVREKLKHLLELGLIERNLIKQGWLGY 74
                                      5667789*********************************97665 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2   8.4e-05      0.05      18      57 ..      24      62 ..      21      63 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8.4e-05
                                      HHHHHHHHSSBEHHHHHHHHSSTHHHHHHHHHHHHHTTSE CS
                             HTH_9 18 VvetLlrkgrltlrelvkktkLsldqVkksLvvLiqhrlV 57
                                      ++++Ll+   lt r+++kk++Ls + V+  L  L+ ++l+
  gi|242398838|ref|YP_002994262.1| 24 IYSLLLK-EELTPRQIAKKVGLSERIVREKLKHLLELGLI 62
                                      6666665.589********************999988876 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   0.1   0.00026      0.15      13      33 ..      24      45 ..      16      56 .. 0.78
   2 ?    0.1   0.0       1.2   7.1e+02       7      17 ..      61      71 ..      55      72 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00026
                            HTH_38 13 Ierl.laeGlslreIArrLgrs 33
                                      I+ l l+e l+ r+IA+++g s
  gi|242398838|ref|YP_002994262.1| 24 IYSLlLKEELTPRQIAKKVGLS 45
                                      5555379***********9977 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.2
                            HTH_38  7 leeReeIerll 17
                                      l eR+ I +++
  gi|242398838|ref|YP_002994262.1| 61 LIERNLIKQGW 71
                                      66999999987 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   9.6e-05     0.058      18      53 ..      31      64 ..      15      71 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.6e-05
                                      TTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                            MarR_2 18 pgrdltvgelarrlglsksavsrilkrLvaaGLver 53
                                      ++  lt++++a++ gls   v   lk L + GL+er
  gi|242398838|ref|YP_002994262.1| 31 EE--LTPRQIAKKVGLSERIVREKLKHLLELGLIER 64
                                      44..9******************************8 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   0.00015     0.091      28      59 ..      35      65 ..      31      68 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00015
                                      HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE-G CS
                     LexA_DNA_bind 28 ireiaralglkSpsaveehLkaLerKGyierd 59
                                       r+ia+++gl+  + v e+Lk L   G+ier+
  gi|242398838|ref|YP_002994262.1| 35 PRQIAKKVGLS-ERIVREKLKHLLELGLIERN 65
                                      59********7.9****************985 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00012     0.074      12      35 ..      27      50 ..      25      63 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00012
                            HTH_23 12 lllaeGlsvreIAreLgvsrrTvy 35
                                      lll+e l++r+IA++ g s+r v+
  gi|242398838|ref|YP_002994262.1| 27 LLLKEELTPRQIAKKVGLSERIVR 50
                                      5677789**************998 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.3   0.00018      0.11      21      57 ..      30      65 ..      20      70 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00018
                                      TSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              GntR 21 GdkLPsereLaaefgVsrttvReALrrLeaeglverr 57
                                       + L + r++a++ g s   vRe L+ L + gl+er+
  gi|242398838|ref|YP_002994262.1| 30 KEEL-TPRQIAKKVGLSERIVREKLKHLLELGLIERN 65
                                      5778.99***************************995 PP

>> RepL  Firmicute plasmid replication protein (RepL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00012     0.071      77     108 ..      34      65 ..      12     104 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00012
                              RepL  77 tnRelaeetgislktvsetlkileeanilkkk 108
                                       t R++a++ g+s + v+e lk l e +++ ++
  gi|242398838|ref|YP_002994262.1|  34 TPRQIAKKVGLSERIVREKLKHLLELGLIERN 65 
                                       89*********************999999875 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 ?   11.9   0.0   0.00026      0.16      19      41 ..      34      56 ..      30      57 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00026
                     HTH_AsnC-type 19 syaeLAervGlSestvlrRvrrL 41
                                      + +++A++vGlSe  v++ ++ L
  gi|242398838|ref|YP_002994262.1| 34 TPRQIAKKVGLSERIVREKLKHL 56
                                      5689*************999987 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 ?   11.3   0.1   0.00038      0.23      17      51 ..      31      65 ..      29      66 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00038
                                      SS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                          HTH_IclR 17 qeltlselArrtglpkStvhRlLqtLvelGyveqd 51
                                      +elt +++A++ gl+   v+  L+ L elG++e++
  gi|242398838|ref|YP_002994262.1| 31 EELTPRQIAKKVGLSERIVREKLKHLLELGLIERN 65
                                      7899*****************************97 PP

>> RP-C  Replication protein C N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00032      0.19      75     103 ..      36      64 ..      34      66 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00032
                              RP-C  75 aqLsralglsestlrrhlaaLveaGliir 103
                                       +q+++++glse+ +r+ l++L e+Gli r
  gi|242398838|ref|YP_002994262.1|  36 RQIAKKVGLSERIVREKLKHLLELGLIER 64 
                                       68999*********************976 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00031      0.19      25      56 ..      32      63 ..      22      73 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00031
                                      -B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2 25 pvsseeiaerqnispsylekilakLrkaglvk 56
                                       ++ ++ia+++++s+++++  l++L + gl++
  gi|242398838|ref|YP_002994262.1| 32 ELTPRQIAKKVGLSERIVREKLKHLLELGLIE 63
                                      38899*************************98 PP

>> GST_C  Glutathione S-transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00038      0.22       5      44 ..      66     105 ..      62     112 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00038
                                       HHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                             GST_C   5 isqilllfyvkaeekkeelvdealekvaevlsaleeelkk 44 
                                        ++ ++l y+ ++++++e+++ ++ k+ e l  leee+kk
  gi|242398838|ref|YP_002994262.1|  66 LIKQGWLGYIYRAKNPKEALKSVFSKMEELLGLLEEEYKK 105
                                       67899*********************************93 PP

>> DALR_2  DALR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00059      0.36      36      61 ..      80     105 ..      67     107 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00059
                                       HHHHHHHHHHHHHHGGGT-S-S-HHH CS
                            DALR_2  36 aaasalkallrelaevLGllqeepea 61 
                                       + ++alk+++ +++e+LGll+ee ++
  gi|242398838|ref|YP_002994262.1|  80 NPKEALKSVFSKMEELLGLLEEEYKK 105
                                       5568999**************98765 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.1       1.5   8.8e+02       2      15 ..      16      29 ..      16      30 .. 0.86
   2 ?   10.0   0.1    0.0011      0.65      30      55 .]      37      62 ..      34      62 .. 0.95
   3 ?   -0.1   0.1       1.6   9.6e+02      48      55 .]      65      72 ..      64      72 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 1.5
                            HTH_36  2 rLspsaklllgsla 15
                                      +L++s++ ++  l+
  gi|242398838|ref|YP_002994262.1| 16 ELTHSEIKIYSLLL 29
                                      69********9886 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0011
                            HTH_36 30 tlakrlglsknTvsraikeLeqlGyi 55
                                       +ak+ gls++ v+  +k L +lG+i
  gi|242398838|ref|YP_002994262.1| 37 QIAKKVGLSERIVREKLKHLLELGLI 62
                                      69**********************98 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 1.6
                            HTH_36 48 eLeqlGyi 55
                                      +L++ G++
  gi|242398838|ref|YP_002994262.1| 65 NLIKQGWL 72
                                      8******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       867  (0.0483574); expected 358.6 (0.02)
Passed bias filter:                      598  (0.0333538); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              30  [number of targets reported over threshold]
# CPU time: 0.57u 0.34s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 671.26
//
Query:       gi|242398839|ref|YP_002994263.1|  [L=267]
Description: 4-hydroxybenzoate octaprenyltransferase [Thermococcus sibiricus MM 739]
Scores for complete 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   6.7    1.8e-34  119.2   6.7    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 !  119.2   6.7     1e-38   1.8e-34       6     234 ..      22     247 ..      17     255 .. 0.87

  Alignments for each domain:
  == domain 1  score: 119.2 bits;  conditional E-value: 1e-38
                              UbiA   6 lvglalaaggspdlllllllllgtllaaaaanalNdyfDreiDadmert.pnRPlvsGrispkealifaivllilgl 81 
                                       l+g++++ ++ p  + +lll++ ++l+ ++a a+N+ fD+++D +++r+  + P++sG++s k al++++ +++lg 
  gi|242398839|ref|YP_002994263.1|  22 LLGMVISFKNNPEVFEALLLAISLILYVGYAFAINNCFDVDTDLLNPRKkHKNPVASGELSFKVALFTSLTTILLGG 98 
                                       889*********************************************95667************************ PP

                              UbiA  82 lllalllnpltallgllalllyvvYt..glrlKrrtllgtvvggiafglppllgwaavtgslsllalllalavfllt 156
                                       +l+ ++++ +++++ +   +l+++Y+  + rlK +++ + +  g++fg +p++   ++ g ls + +++al +f+++
  gi|242398839|ref|YP_002994263.1|  99 ILA-YFISKPAFVIYITMSFLATIYSapP-RLKSIPIADVFSHGLFFGALPFIYGGYFDGVLSDTEIFIALSLFVYS 173
                                       **9.**********************755.**********************999999****99999999999**** PP

                              UbiA 157 waialandlrdregDrkagiktlpvvlGrkaarillalllavlllallllllalllllylllalllaalallraarl 233
                                       +a+ l n+l+d+e+D+ka++kt+p+++G+ ++  l+    ++ ll+ l+lll ll +++ ++++l +a    r +++
  gi|242398839|ref|YP_002994263.1| 174 VAMELRNHLEDYESDQKANLKTTPIIIGKSTSEALIN---ILSLLS-LTLLLNLLYSPFGIVGILGVATRNRRISYR 246
                                       ******************************9998422...333333.234555555555555555555555555555 PP

                              UbiA 234 v 234
                                       +
  gi|242398839|ref|YP_002994263.1| 247 I 247
                                       5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       773  (0.0431145); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1624.46
//
Query:       gi|242398840|ref|YP_002994264.1|  [L=310]
Description: ABC transporter [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-22   79.7  29.1    3.7e-22   79.2  29.1    1.2  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 !   79.2  29.1   2.1e-26   3.7e-22       5     301 .]      15     293 ..       8     293 .. 0.89

  Alignments for each domain:
  == domain 1  score: 79.2 bits;  conditional E-value: 2.1e-26
                   LPG_synthase_TM   5 lalsalllalllrgvdlaalaaalrsldpwwlllalllallsvllralrWrlllrslgarislrrllrayliglfvn 81 
                                        + +++ la+l++++d+++l  al+++++ +l la+ll++l++++ a rW l+lr++  + s+ r ++a+  g+++ 
  gi|242398840|ref|YP_002994264.1|  15 AVAFLISLAYLYKSIDFNELSIALKEANYEYLFLAILLSFLTLFFAATRWYLVLRRV-QKTSFKRTIQAFVSGYYLM 90 
                                       33444555556888******************************************7.9****************** PP

                   LPG_synthase_TM  82 nvtPgalgGevvrayllkrkegvslskalasvvverlldllalvllgllallllggllaegaavllllalallllav 158
                                        ++P ++   +v++ l+      ++ +al+s+   + +++++++ +g+++l++           l+l+++al+lla+
  gi|242398840|ref|YP_002994264.1|  91 AILPPTV-SHIVKVKLVGG----DYFAALSSLAFGMAMEIVIILSFGFIFLGFTK---------LGLIGIALILLAF 153
                                       ****887.77777766666....999*********************99997655.........6788899999999 PP

                   LPG_synthase_TM 159 la......lllllllrrrlarlarvlkrlarllarfarklasakrklvlasprrlllafllslliwllealtlylll 229
                                       l+       +l++++ +  +  +++ ++l+ +++r  ++       ++++++  +l +f +sl++  +++l l l+ 
  gi|242398840|ref|YP_002994264.1| 154 LYdkvfhkTALAFFRFWETLGAKKIPEKLRDWWNRGYAGWN-----IARKNKSGFLSVFSISLVVIFIQILGLVLVG 225
                                       9999999999999999999************9997775444.....57889999*********************** PP

                   LPG_synthase_TM 230 ralgvdvslallllillaltlvgalpplPgGlGvrEaalalllallGvsaaealaaallyrlitlylllllG 301
                                       +a+ +++s+ ++l ++l++++++ l+ +P+G+G+ E++  +  ++     + a+++a+ly +i  y++ ++G
  gi|242398840|ref|YP_002994264.1| 226 KAFSLEISFKQALYAFLMSVIFASLSGIPSGIGANEFGILVGIGSS----TKAALTAFLYKFIFQYMYSIAG 293
                                       *************************************987777755....9999**************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       977  (0.0544927); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 2004.34
//
Query:       gi|242398841|ref|YP_002994265.1|  [L=378]
Description: Glycosyl transferase [Thermococcus sibiricus MM 739]
Scores for 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-46  155.5   0.1    2.4e-45  154.2   0.0    1.7  2  Glycos_transf_1  Glycosyl transferases group 1
    1.7e-36  125.6   0.6    3.4e-36  124.6   0.6    1.5  1  Glyco_trans_1_4  Glycosyl transferases group 1
    5.2e-27   94.9   0.1    2.6e-26   92.6   0.1    1.9  2  Glyco_transf_4   Glycosyltransferase Family 4
    4.2e-12   46.3   0.0    9.3e-11   42.0   0.0    2.3  2  Glyco_trans_1_2  Glycosyl transferases group 1
      1e-10   42.3   0.0      1e-09   39.0   0.0    2.1  2  Glyco_trans_4_4  Glycosyl transferase 4-like domain
      2e-07   31.0   0.8    0.00058   19.6   0.0    2.2  2  Glyco_transf_5   Starch synthase catalytic domain
    5.9e-07   29.6   0.1    1.1e-06   28.8   0.1    1.5  1  Glyco_trans_4_2  Glycosyl transferase 4-like
     0.0025   17.4   0.0     0.0056   16.3   0.0    1.5  1  Glyco_trans_4_5  Glycosyl-transferase family 4
  ------ inclusion threshold ------
      0.043   14.4   1.1      0.097   13.3   1.1    1.5  1  PIGA             PIGA (GPI anchor biosynthesis)


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 ?   -2.8   0.0         2     4e+03     110     122 ..     132     144 ..     110     163 .. 0.64
   2 !  154.2   0.0   1.2e-48   2.4e-45      10     171 ..     197     352 ..     187     353 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2
                                       HHHHHTT--EEEE CS
                   Glycos_transf_1 110 lEAmaaglpvias 122
                                        EA+ + +pv++s
  gi|242398841|ref|YP_002994265.1| 132 WEALGLTIPVFTS 144
                                       4555555555555 PP

  == domain 2  score: 154.2 bits;  conditional E-value: 1.2e-48
                                       TTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSH CS
                   Glycos_transf_1  10 gknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredl 86 
                                       g+  + k++l+v+r+ ++Kg+++l+ af ++     +++ lv++Gnge++  lk +a+ l++ ++v f g+v++++l
  gi|242398841|ref|YP_002994265.1| 197 GI--EGKVVLYVSRMAYRKGPHVLLNAFSKI-----EDATLVMVGNGEMLPFLKLQAKFLGIDEKVVFMGYVEDNKL 266
                                       33..789**********************87.....689************************************** PP

                                       HHHHHCESEEEEEESS.BSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHH CS
                   Glycos_transf_1  87 eellknadifvlpsis.EgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeelr 162
                                       +el+ +ad+fvlps + E+fGiv+lEAmaag+pv+a+ +gg++e+vk++e G+lv+p+n  al +ai+++l+d++lr
  gi|242398841|ref|YP_002994265.1| 267 PELFGIADVFVLPSVTaEAFGIVVLEAMAAGVPVVATSVGGIPEIVKENEAGILVPPGNELALRNAIQRILTDQKLR 343
                                       ***************************************************************************** PP

                                       HHHHHHHHH CS
                   Glycos_transf_1 163 erlgenark 171
                                       e +g n+r+
  gi|242398841|ref|YP_002994265.1| 344 EWYGSNGRR 352
                                       ******986 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 !  124.6   0.6   1.7e-39   3.4e-36       2     134 .]     201     339 ..     200     339 .. 0.92

  Alignments for each domain:
  == domain 1  score: 124.6 bits;  conditional E-value: 1.7e-39
                                       EEEEEES---GG.GTHHHHHHHHHHHH.HHEEEEEES---...HHHHHHHT..T-T.TEEEE---TH..HHHHHHH- CS
                   Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkkdvrlvivGdgp.rpeeleelaa..gleerveftGfved..laellaaa 73 
                                       +v+l+v+r+ + +kg ++ll+a+ ++   d++lv+vG+g+  p  l+ +a+  g++e+v+f+G+ved  l+el+  a
  gi|242398841|ref|YP_002994265.1| 201 KVVLYVSRM-AYRKGPHVLLNAFSKIE--DATLVMVGNGEmLP-FLKLQAKflGIDEKVVFMGYVEDnkLPELFGIA 273
                                       789******.667**************..67********9877.665455566************6667******** PP

                                       SEEEE--...---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHHHH- CS
                   Glyco_trans_1_4  74 dvfvaPs...egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailrLled 134
                                       dvfv+Ps   e fg+++lEamaag+pvVat+vggi+e+v  +e+g+lvppg++ al +ai+r+l+d
  gi|242398841|ref|YP_002994265.1| 274 DVFVLPSvtaEAFGIVVLEAMAAGVPVVATSVGGIPEIVkeNEAGILVPPGNELALRNAIQRILTD 339
                                       ********999****************************97799*******************997 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.6   0.1   1.3e-29   2.6e-26       1     170 []      14     182 ..      14     182 .. 0.90
   2 ?   -0.4   0.0      0.49   9.7e+02      83     102 ..     285     303 ..     275     343 .. 0.82

  Alignments for each domain:
  == domain 1  score: 92.6 bits;  conditional E-value: 1.3e-29
                    Glyco_transf_4   1 vGGverhvleLaraLarrGheVtvvtpgddgpleeev.elvvrvprvplpllkrllrslaflrrlrrllkre..kpD 74 
                                       +GGv+ h+++La  L +rGheV +vt +++   e e  e +++++++p + ++ l ++l++ ++  + l ++  ++D
  gi|242398841|ref|YP_002994265.1|  14 IGGVASHMHNLALKLKERGHEVAIVTNNWETGKESELaEKGIDLIKIPGVVSPVLDINLSYGLKSSEELNEFlhDFD 90 
                                       7***************************9999998889999999999999999999999999999999999999*** PP

                    Glyco_transf_4  75 vvHahspaalgaallalrr..rlgiplVltvHglyekrllkarlkplsrllralerrllrradrviavSeatadelr 149
                                       v+H+h++++ +a l a+++    ++ + lt H+     ++ +rl+ +  l   +    l+  +r+iavS+a+++ ++
  gi|242398841|ref|YP_002994265.1|  91 VIHSHHAFTPLA-LKAAKAgrIMNKATLLTTHSIS--FAHDSRLWEALGLTIPVFTSYLKYPHRIIAVSKAARAFVE 164
                                       ******999854.444444578*************..699999999999999999999******************* PP

                    Glyco_transf_4 150 erygvppekitVipnGvDler 170
                                       +   +  ++i +ipnGvD +r
  gi|242398841|ref|YP_002994265.1| 165 H---FTDSPISIIPNGVDDKR 182
                                       *...55689*********876 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.49
                    Glyco_transf_4  83 algaallalrrrlgiplVlt 102
                                       a+g ++l +++  g+p+V+t
  gi|242398841|ref|YP_002994265.1| 285 AFGIVVLEAMA-AGVPVVAT 303
                                       66777777776.9****999 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.17   3.4e+02      14      74 ..     130     160 ..     115     167 .. 0.57
   2 !   42.0   0.0   4.7e-14   9.3e-11       9      90 ..     284     367 ..     275     369 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.17
                   Glyco_trans_1_2  14 rlfEaaacGafaltddaegleelftpgkevilfedleelaekiryllanpeerraiaeaar 74 
                                       rl Ea++  +++ t++                               + p ++ a+++aar
  gi|242398841|ref|YP_002994265.1| 130 RLWEALGLTIPVFTSYL------------------------------KYPHRIIAVSKAAR 160
                                       55555555555555554..............................44444444444444 PP

  == domain 2  score: 42.0 bits;  conditional E-value: 4.7e-14
                   Glyco_trans_1_2   9 espnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraiaeaarervlaehty 83 
                                       e +  +++Ea+a+G+++++++  g++e++++++ +il+   ++  l  +i++ l++ ++r+  + ++r+ v++++++
  gi|242398841|ref|YP_002994265.1| 284 EAFGIVVLEAMAAGVPVVATSVGGIPEIVKENEAGILVPpgNELALRNAIQRILTDQKLREWYGSNGRRAVEEKYSW 360
                                       568899**************99*****************99999999****************************** PP

                   Glyco_trans_1_2  84 dhraeql 90 
                                       d+ + ++
  gi|242398841|ref|YP_002994265.1| 361 DKVVLKI 367
                                       *987665 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   0.0   5.2e-13     1e-09       1     144 [.      15     163 ..      15     177 .. 0.70
   2 ?    1.0   0.0      0.26   5.3e+02      84     105 ..     285     306 ..     272     353 .. 0.60

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 5.2e-13
                   Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvltpapapgap.eleedgvrvhrlp..vprrps..pladlaalralrrllrqrre 72 
                                       gG++ ++++la  L +rGheV ++t ++ +g + el e g+ ++ +p  v++  +  + + l+++  l ++l     
  gi|242398841|ref|YP_002994265.1|  15 GGVASHMHNLALKLKERGHEVAIVTNNWETGKEsELAEKGIDLIKIPgvVSPVLDinLSYGLKSSEELNEFL----H 87 
                                       8************************9998885537999******9997666666555777899999999999....* PP

                   Glyco_trans_4_4  73 rpdvvhahsptaglaarlarrrr..giplvvtlhglllrrgsga..vrrlyralerrllrradavlvvseaeaeel 144
                                        +dv+h+h+  ++la ++a+++r  +   ++t h+  +++ s+   +  l  ++    l+   ++++vs a ++ +
  gi|242398841|ref|YP_002994265.1|  88 DFDVIHSHHAFTPLALKAAKAGRimNKATLLTTHSISFAHDSRLweALGLTIPVFTSYLKYPHRIIAVSKAARAFV 163
                                       *********9999999999955444556788888654443322201222223334455555666666666555555 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.26
                   Glyco_trans_4_4  84 aglaarlarrrrgiplvvtlhg 105
                                       a ++++l ++++g+p+v t  g
  gi|242398841|ref|YP_002994265.1| 285 AFGIVVLEAMAAGVPVVATSVG 306
                                       3444455556899999999863 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 !   19.6   0.0   2.9e-07   0.00058       1      49 [.       2      48 ..       2      71 .. 0.82
   2 !    9.7   0.3   0.00032      0.64     132     187 ..      88     138 ..      74     164 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.9e-07
                    Glyco_transf_5  1 kilfvasEvaplaktGGLadvvgaLpkaLaklghdvrvilPrygaikee 49
                                      ki  v+  ++p  k GG+a +++ L+ +L+++gh+v +++ + ++ ke+
  gi|242398841|ref|YP_002994265.1|  2 KIALVSDWYYP--KIGGVASHMHNLALKLKERGHEVAIVTNNWETGKES 48
                                      67778888888..**************************9988554443 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00032
                    Glyco_transf_5 132 kpdvihahDWhtalvpallkelykerglfkkiktvftiHNlayqgrfpkdelaalg 187
                                        +dvih h    a+ p+ lk+++   g + + +t++t H++++ +    +e+  l 
  gi|242398841|ref|YP_002994265.1|  88 DFDVIHSHH---AFTPLALKAAK--AGRIMNKATLLTTHSISFAHDSRLWEALGLT 138
                                       389999986...88888899975..577888***********99766544443344 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 !   28.8   0.1   5.3e-10   1.1e-06      12     118 ..      20     129 ..       2     156 .. 0.70

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 5.3e-10
                   Glyco_trans_4_2  12 htlrlakeLakrgyeVhvitp..kkgakdeleaegihvhrlkvdrkgpleylkaf.klkklikki....kPDvvhah 81 
                                       h+ +la +L++rg+eV+++t+  ++g++ el ++gi +++++ ++ +p+ ++++   lk+  + +     +Dv+h h
  gi|242398841|ref|YP_002994265.1|  20 HMHNLALKLKERGHEVAIVTNnwETGKESELAEKGIDLIKIP-GVVSPVLDINLSyGLKSSEELNeflhDFDVIHSH 95 
                                       8999*****************55555588999*********9.8777777777532443332222112269****** PP

                   Glyco_trans_4_2  82 ya.kpygllgslaarlsgvipvvlsvwGldvlkfpkks 118
                                        a +p++l ++ a r+ + + ++l+ +    ++f+++s
  gi|242398841|ref|YP_002994265.1|  96 HAfTPLALKAAKAGRIMN-KATLLTTHS---ISFAHDS 129
                                       998999999999999998.666666662...3444444 PP

>> Glyco_trans_4_5  Glycosyl-transferase family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   2.8e-06    0.0056      18      73 ..      18      90 ..      11      99 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.8e-06
                   Glyco_trans_4_5 18 PlvlmelatlLrsvgaevvvltlskkggllkeladrgikvlea.................kaeelfklalkaD 73
                                         + +la  L++ g ev ++t++ + g ++ela++gi +++                   +eel ++  ++D
  gi|242398841|ref|YP_002994265.1| 18 ASHMHNLALKLKERGHEVAIVTNNWETGKESELAEKGIDLIKIpgvvspvldinlsyglkSSEELNEFLHDFD 90
                                      56799***********************************987666666666666666644455555555555 PP

>> PIGA  PIGA (GPI anchor biosynthesis)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   1.1   4.9e-05     0.097      51      85 ..      89     123 ..      84     128 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.9e-05
                              PIGA  51 idivhghqalstlaheailhaktlGlktvftDhsL 85 
                                        d++h+h+a++ la +a   ++ +   t+ t hs+
  gi|242398841|ref|YP_002994265.1|  89 FDVIHSHHAFTPLALKAAKAGRIMNKATLLTTHSI 123
                                       69********************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); 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:                         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 0.28s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 2401.41
//
Query:       gi|242398842|ref|YP_002994266.1|  [L=242]
Description: amidase [Thermococcus sibiricus MM 739]
Scores for complete 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-62  208.8   0.0    9.2e-62  208.6   0.0    1.0  1  Creatininase  Creatinine amidohydrolase


Domain annotation for each model (and alignments):
>> Creatininase  Creatinine amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  208.6   0.0   5.1e-66   9.2e-62       1     240 [.       9     237 ..       9     238 .. 0.90

  Alignments for each domain:
  == domain 1  score: 208.6 bits;  conditional E-value: 5.1e-66
                      Creatininase   1 eeltwpeveealkeddvailPvGstEqHGphlplgtDtliaealaervaeklgak...alvlPtlpyGvseehlgfp 74 
                                       eeltw+++e+++++ + +ilPvGs+E HG hlplgtD++++ ++++rv+ekl+ +   +l++P+++yG s     +p
  gi|242398842|ref|YP_002994266.1|   9 EELTWEDFEKIKTRVKGLILPVGSVEAHGKHLPLGTDVFAPLEISRRVEEKLKDRgidILIAPPIWYGHSFVLNVYP 85 
                                       69**************************************************866888***********955566** PP

                      Creatininase  75 GTislspetliavlrdileslarhGfrrivlvngHggnsaalkeaarelraehdaaavrvtaaekelaaalkleeaa 151
                                       GTi+++  t+++++++ile++a++Gf++++++ngHggn+++l  aa+e+ +++d+ +v        +++++++    
  gi|242398842|ref|YP_002994266.1|  86 GTINVKSGTFQKYVQEILEEFAKEGFEKVIILNGHGGNIYPLIGAAEEVVEKYDVEVV-------LINWWMDF---- 151
                                       *****************************************************66654.......33343333.... PP

                      Creatininase 152 eaaeeseeeegggHAgelEtSlmlalrpelVrmdraedpeeaklakegvstaedaeelspsGvlGdpskataekGea 228
                                        ++e s+  + +gHAge+EtS++la++pelV+m++a  ++ +++ +    ++    ++ p+Gv  +p +ataekGe+
  gi|242398842|ref|YP_002994266.1| 152 -KEEISRICSSQGHAGEDETSVILAINPELVKMEKAIGERRTRPVRI--IKKDIGLDIFPNGVNDNPHNATAEKGEE 225
                                       .45556666689***********************999998888775..7777778899****************** PP

                      Creatininase 229 lleaaveelael 240
                                       +le + e+++++
  gi|242398842|ref|YP_002994266.1| 226 ILEVVSEKITNI 237
                                       *******99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); 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: 0.61u 0.34s 00:00:00.95 Elapsed: 00:00:00.53
# Mc/sec: 1368.96
//
Query:       gi|242398843|ref|YP_002994267.1|  [L=219]
Description: hypothetical protein TSIB_0857 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0066   16.2   0.2      0.009   15.8   0.2    1.1  1  HlyIII        Haemolysin-III related
  ------ inclusion threshold ------
      0.016   15.4   1.4      0.016   15.4   1.4    2.3  2  ABC_tran_CTD  ABC transporter C-terminal domain
      0.022   15.2   0.1      0.047   14.2   0.1    1.5  1  Knl1_RWD_C    Knl1 RWD C-terminal domain
       0.22   11.4   0.3       0.36   10.7   0.3    1.3  1  EMP24_GP25L   emp24/gp25L/p24 family/GOLD
       0.31   11.2   0.8       0.46   10.6   0.1    1.6  2  DUF3347       Protein of unknown function (DUF3347)
       0.71   10.1   3.5       0.34   11.1   0.5    2.1  2  XhlA          Haemolysin XhlA
        1.7    8.8   8.6       0.55   10.3   5.3    1.8  2  DUF1192       Protein of unknown function (DUF1192)


Domain annotation for each model (and alignments):
>> HlyIII  Haemolysin-III related
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.2   3.5e-06     0.009      99     168 ..      40     109 ..      34     130 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.5e-06
                            HlyIII  99 alakapkagllylslilalgvlgiisklvplfsrpearplravlfi.llgllgvipllhlllvltqlgeaa 168
                                        l+ ++k g ly+++ ++ g++g  + l  +++ +e+ p++   +i ++ ++ +ip+l+ +++l++ +e+ 
  gi|242398843|ref|YP_002994267.1|  40 ILQRRTKTGELYIMFFVIWGFMGLTLLLYLKYKYSEILPFSLTPYIgAMMAFIIIPFLY-YFFLSKQSEPE 109
                                       55677889999********************************99945889999*****.88888666544 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 ?   15.4   1.4   6.3e-06     0.016      10      32 ..       5      27 ..       1      47 [. 0.82
   2 ?    0.4   0.2      0.32   8.1e+02      39      50 ..     141     152 ..     132     166 .. 0.57

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 6.3e-06
                      ABC_tran_CTD 10 leeleaeIeaLEeeiaeleaela 32
                                      lee+e +I +LE+ei+ +e++l 
  gi|242398843|ref|YP_002994267.1|  5 LEEIETRIKRLEAEIELIEERLK 27
                                      9*******************986 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.32
                      ABC_tran_CTD  39 dpeklaelsael 50 
                                       d+ekl+e+ ++l
  gi|242398843|ref|YP_002994267.1| 141 DHEKLKEIANRL 152
                                       455555555554 PP

>> Knl1_RWD_C  Knl1 RWD C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   1.8e-05     0.047       3      66 ..      24      88 ..      22      94 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.8e-05
                        Knl1_RWD_C  3 eeieflerWGg..klellkidvndtevkllfsssaafakfeltlslsasypsvplpftvqnkiGni 66
                                      e ++fl+r G+  k+++l+   +  e+ ++f  +  f  + l l l  +y  + lpf++   iG +
  gi|242398843|ref|YP_002994267.1| 24 ERLKFLDRVGAtsKYQILQRRTKTGELYIMFFVIWGFMGLTLLLYLKYKYSEI-LPFSLTPYIGAM 88
                                      789*******988*************************999999999999765.89***9999976 PP

>> EMP24_GP25L  emp24/gp25L/p24 family/GOLD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.3   0.00014      0.36     110     178 ..       2      70 ..       1      72 [. 0.96

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00014
                       EMP24_GP25L 110 kekletleselkkleekldsikreqkylrereerlrdtnestnsrvvwwsilqllvlvlvavlqvyyLk 178
                                       ke le++e+++k+le  ++ i++ +k+l +  ++ + ++ +  ++    +i++ ++  ++++  ++yLk
  gi|242398843|ref|YP_002994267.1|   2 KEVLEEIETRIKRLEAEIELIEERLKFLDRVGATSKYQILQRRTKTGELYIMFFVIWGFMGLTLLLYLK 70 
                                       56799**********************************************************999998 PP

>> DUF3347  Protein of unknown function (DUF3347)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1       1.4   3.6e+03     101     128 ..       3      30 ..       1      54 [. 0.58
   2 ?   10.6   0.1   0.00018      0.46      50      82 ..     121     155 ..     101     175 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.4
                           DUF3347 101 eiseelkekaekiaeskdieeqReaFkk 128
                                       e+ ee++++++ ++++ ++ e+R +F +
  gi|242398843|ref|YP_002994267.1|   3 EVLEEIETRIKRLEAEIELIEERLKFLD 30 
                                       5667777888888887777777777743 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00018
                           DUF3347  50 lke..vlesYlklkdALvaddakeakkaakkleek 82 
                                       +++  +   Y+ lk+AL ++d+++ k+ a+ l + 
  gi|242398843|ref|YP_002994267.1| 121 MARlaLNRFYIPLKEALKEEDHEKLKEIANRLLQG 155
                                       333345667*********************99875 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.5   0.00013      0.34       3      26 ..       2      25 ..       1      41 [. 0.67
   2 ?   -2.4   0.1       2.2   5.7e+03      32      38 ..     143     149 ..     137     154 .. 0.47

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00013
                              XhlA  3 kerlerietkldnleervdkleek 26
                                      ke le+iet+++ le +++ +ee+
  gi|242398843|ref|YP_002994267.1|  2 KEVLEEIETRIKRLEAEIELIEER 25
                                      666777777777777766666665 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.2
                              XhlA  32 ekiknle 38 
                                       ek+k++ 
  gi|242398843|ref|YP_002994267.1| 143 EKLKEIA 149
                                       2333333 PP

>> DUF1192  Protein of unknown function (DUF1192)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   5.3   0.00021      0.55      23      43 ..       6      26 ..       5      30 .. 0.91
   2 ?   -3.3   0.1       3.8   9.8e+03      31      37 ..     152     158 ..     146     165 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00021
                           DUF1192 23 eELeerIalLeaEIaRleaai 43
                                      eE+e+rI+ LeaEI+ +e+ +
  gi|242398843|ref|YP_002994267.1|  6 EEIETRIKRLEAEIELIEERL 26
                                      8**************999876 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.8
                           DUF1192  31 lLeaEIa 37 
                                       lL+ E+a
  gi|242398843|ref|YP_002994267.1| 152 LLQGEVA 158
                                       5777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1188  (0.0662614); expected 358.6 (0.02)
Passed bias filter:                      751  (0.0418874); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.63u 0.34s 00:00:00.97 Elapsed: 00:00:00.52
# Mc/sec: 1275.41
//
Query:       gi|242398844|ref|YP_002994268.1|  [L=272]
Description: hypothetical protein TSIB_0858 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.024   14.9   0.1      0.066   13.5   0.1    1.7  1  Mrpl_C      54S ribosomal protein L8 C-terminal domain
       0.21   11.8   1.0       0.43   10.8   0.3    1.8  3  Interferon  Interferon alpha/beta domain


Domain annotation for each model (and alignments):
>> Mrpl_C  54S ribosomal protein L8 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   7.4e-06     0.066       8      83 ..     108     181 ..     105     196 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.4e-06
                            Mrpl_C   8 gnlqrGnlKlWLlvkttladeskakayaplTlqnLkKmlkfkskeqllkeilavrkflkeeqelewdeeeekeavk 83 
                                       g +  G+ Kl Ll+k  l++ + + +++   l+n+   +++k  + l++e+  vrk+  e  e   +ee  k+a++
  gi|242398844|ref|YP_002994268.1| 108 GGYVAGEEKLKLLAKPRLEELEIELKFNIDDLENVLEEVEGKLDATLTTELSFVRKYFVEILEI--EEELIKKALE 181
                                       55667999*************************************************9986544..4666665555 PP

>> Interferon  Interferon alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.3   4.7e-05      0.43      79     125 ..     124     168 ..     116     175 .. 0.87
   2 ?   -3.3   0.0         1   9.2e+03      48      69 ..     194     216 ..     176     248 .. 0.56
   3 ?   -2.7   0.0      0.64   5.7e+03      74      86 ..     244     256 ..     206     259 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 4.7e-05
                                       HHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHCCCCCHHHHHHHHHHH CS
                        Interferon  79 lleqllsgLhqqleeLeacleeeaeeeeseleeeesrlalkkYFqri 125
                                        le+l  +L+  +++Le +lee +++ + +l++e     ++kYF +i
  gi|242398844|ref|YP_002994268.1| 124 RLEELEIELKFNIDDLENVLEEVEGKLDATLTTEL--SFVRKYFVEI 168
                                       6899***********************99998653..458****998 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1
                                       HHHHHHHHHHHHHH.HHHHCCS- CS
                        Interferon  48 keqaalvlhemlqq.ifnlFstn 69 
                                       ++  + + + +l q i++l +++
  gi|242398844|ref|YP_002994268.1| 194 EAMFVGIGKAVLAQmILSLAEEK 216
                                       44444444444433123333333 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 0.64
                                       T--HHHHHHHHHH CS
                        Interferon  74 awnetlleqllsg 86 
                                         +e +le++l++
  gi|242398844|ref|YP_002994268.1| 244 YFDEGALEDFLKE 256
                                       2334444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       814  (0.0454013); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); 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: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 1648.28
//
Query:       gi|242398845|ref|YP_002994269.1|  [L=48]
Description: Nucleic acid-binding protein, containing C2H2 zinc-finger [Thermococcus sibiricus MM 739]
Scores for complete 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   28.2   1.8    2.4e-06   27.7   1.8    1.2  1  zf-C2H2        Zinc finger, C2H2 type
    2.6e-05   24.7   1.3    3.8e-05   24.2   1.3    1.3  1  zf-C2H2_4      C2H2-type zinc finger
    0.00058   18.5   0.1    0.00058   18.5   0.1    1.0  1  DUF629         Protein of unknown function (DUF629)
     0.0025   17.0   0.0     0.0025   17.0   0.0    1.0  1  GcpE           GcpE protein
     0.0057   16.5   0.3     0.0091   15.8   0.3    1.4  1  zf-FPG_IleRS   Zinc finger found in FPG and IleRS
  ------ inclusion threshold ------
      0.012   15.9   0.1      0.018   15.3   0.1    1.3  1  zf-C2H2_jaz    Zinc-finger double-stranded RNA-binding
      0.018   14.5   0.0       0.02   14.3   0.0    1.3  1  Mu-like_Com    Mu-like prophage protein Com
      0.025   14.7   0.1      0.025   14.7   0.1    1.1  1  CxC7           CxC7 like cysteine cluster associated with KDZ
      0.027   14.6   0.0      0.038   14.2   0.0    1.3  1  zf-RING_7      C4-type zinc ribbon domain
      0.033   14.8   0.1      0.037   14.6   0.1    1.2  1  FOXP-CC        FOXP coiled-coil domain
      0.041   13.8   0.3      0.056   13.4   0.3    1.3  1  zinc_ribbon_4  zinc-ribbon domain
      0.046   13.8   0.0      0.051   13.7   0.0    1.2  1  zf-Mss51       Zinc-finger of mitochondrial splicing suppress
      0.047   14.0   0.1      0.049   14.0   0.1    1.0  1  zf-C2H2_2      C2H2 type zinc-finger (2 copies)
       0.05   13.9   0.2      0.062   13.6   0.2    1.1  1  zf-Di19        Drought induced 19 protein (Di19), zinc-bindin
      0.074   12.7   0.1        0.1   12.2   0.1    1.2  1  zf_UBZ         Ubiquitin-Binding Zinc Finger


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 !   27.7   1.8     2e-09   2.4e-06       1      23 []      18      41 ..      18      41 .. 0.98

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 2e-09
                                      EEETTTTEEESSHHHHHHHHHC.C CS
                           zf-C2H2  1 ykCpdCgksFkrksnLkrHirt.H 23
                                      +kCp Cg++Fk + +++rH ++ H
  gi|242398845|ref|YP_002994269.1| 18 FKCPRCGRVFKKSKDYTRHVNRaH 41
                                      9********************999 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 !   24.2   1.3   3.1e-08   3.8e-05       1      24 []      18      41 ..      18      41 .. 0.96

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 3.1e-08
                         zf-C2H2_4  1 fkCpiCgksFsskkaLlrHlkthH 24
                                      fkCp Cg++F+ +k++ rH+++ H
  gi|242398845|ref|YP_002994269.1| 18 FKCPRCGRVFKKSKDYTRHVNRAH 41
                                      8*******************9988 PP

>> DUF629  Protein of unknown function (DUF629)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1   4.9e-07   0.00058      43      85 ..       5      46 ..       1      48 [] 0.82

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 4.9e-07
                            DUF629 43 evlsfaeenkkWrfWvCrtCsekfsdaeeckqHlvqeHvaklk 85
                                      +++++++++k+  +++C +C ++f++++++  H+ + H + +k
  gi|242398845|ref|YP_002994269.1|  5 KAIKLMNRDKE-IVFKCPRCGRVFKKSKDYTRHVNRAHGHLFK 46
                                      56666666666.4679**********************99887 PP

>> GcpE  GcpE protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   2.1e-06    0.0025     250     291 ..       2      44 ..       1      48 [] 0.86

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.1e-06
                                       HHHHHTTS--SS-EEE.E----TTS-CHHHHHHHHHHHHCCCH CS
                              GcpE 250 eiLqalrlrkskteli.sCPsCgRtlfdlqelveeveealehl 291
                                       ++L+a++l ++  e++  CP+CgR+  + ++ +++v++a +hl
  gi|242398845|ref|YP_002994269.1|   2 AVLKAIKLMNRDKEIVfKCPRCGRVFKKSKDYTRHVNRAHGHL 44 
                                       589999998888887748*******************999988 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 !   15.8   0.3   7.6e-06    0.0091       3      16 ..      19      32 ..      18      38 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 7.6e-06
                                      B-TTT--BBEEEEC CS
                      zf-FPG_IleRS  3 pCpRCwryiervgq 16
                                      +CpRC+r++++ + 
  gi|242398845|ref|YP_002994269.1| 19 KCPRCGRVFKKSKD 32
                                      9*******998665 PP

>> zf-C2H2_jaz  Zinc-finger double-stranded RNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.1   1.5e-05     0.018       2      22 ..      18      38 ..      17      38 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.5e-05
                                      CBBTTTTBBBSSHHHHHCCTT CS
                       zf-C2H2_jaz  2 fYCvlCdKyFksenaldnHlk 22
                                      f C+ C + Fk+++++  H++
  gi|242398845|ref|YP_002994269.1| 18 FKCPRCGRVFKKSKDYTRHVN 38
                                      99*****************87 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 ?   14.3   0.0   1.7e-05      0.02      22      32 ..      15      25 ..       7      40 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.7e-05
                       Mu-like_Com 22 eltiKCPRCGt 32
                                      e+  KCPRCG 
  gi|242398845|ref|YP_002994269.1| 15 EIVFKCPRCGR 25
                                      7999******6 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 ?   14.7   0.1   2.1e-05     0.025      18      41 ..      16      38 ..       5      46 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.1e-05
                              CxC7 18 sliecsecgdifkdspvGyvGdGr 41
                                       + +c++cg++fk s   y+ +  
  gi|242398845|ref|YP_002994269.1| 16 IVFKCPRCGRVFKKS-KDYTRHVN 38
                                      5889**********9.88887755 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   3.2e-05     0.038      13      31 ..       3      25 ..       1      26 [. 0.66

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.2e-05
                                      HHHHH....CCSTB-EE-TTT-- CS
                         zf-RING_7 13 vlsel....ragdevvtCpeCGR 31
                                      vl+++    r ++ v++Cp CGR
  gi|242398845|ref|YP_002994269.1|  3 VLKAIklmnRDKEIVFKCPRCGR 25
                                      677774333333448*******9 PP

>> FOXP-CC  FOXP coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   3.1e-05     0.037      10      32 ..      21      43 ..      15      48 .] 0.90

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.1e-05
                           FOXP-CC 10 PgCekvledveeflkhlnseHal 32
                                      P C +v+++++++++h+n++H +
  gi|242398845|ref|YP_002994269.1| 21 PRCGRVFKKSKDYTRHVNRAHGH 43
                                      99*******************76 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.3   4.7e-05     0.056      21      36 .]      13      28 ..       8      28 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.7e-05
                     zinc_ribbon_4 21 akgvkvrCskCghvFr 36
                                      +k    +C++Cg vF+
  gi|242398845|ref|YP_002994269.1| 13 DKEIVFKCPRCGRVFK 28
                                      667789********96 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   4.3e-05     0.051      12      40 ..      13      41 ..       4      47 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.3e-05
                          zf-Mss51 12 pkhvdfeCpdCGiptycseehwedDyeah 40
                                       k++ f+Cp+CG +   s+   +  + ah
  gi|242398845|ref|YP_002994269.1| 13 DKEIVFKCPRCGRVFKKSKDYTRHVNRAH 41
                                      68899*******99999987666655555 PP

>> zf-C2H2_2  C2H2 type zinc-finger (2 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   4.1e-05     0.049      37      75 ..       7      43 ..       2      48 .] 0.72

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.1e-05
                         zf-C2H2_2 37 eglleylrekieekleClyCekefkslealreHmkkk.gH 75
                                       +l++  +e + +   C  C++ fk+ ++++ H++ + gH
  gi|242398845|ref|YP_002994269.1|  7 IKLMNRDKEIVFK---CPRCGRVFKKSKDYTRHVNRAhGH 43
                                      4555666665555...*****************9654266 PP

>> zf-Di19  Drought induced 19 protein (Di19), zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2   5.2e-05     0.062       3      26 ..      18      42 ..      16      47 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.2e-05
                           zf-Di19  3 ftCPyCgk.eltvkeLveHvedeHr 26
                                      f+CP Cg+   + k   +Hv+  H 
  gi|242398845|ref|YP_002994269.1| 18 FKCPRCGRvFKKSKDYTRHVNRAHG 42
                                      9*******4466789*******996 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   8.4e-05       0.1       3      16 ..      18      32 ..      17      36 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.4e-05
                            zf_UBZ  3 ylCerCgkeipes.e 16
                                      + C+rCg+ +  s +
  gi|242398845|ref|YP_002994269.1| 18 FKCPRCGRVFKKSkD 32
                                      79*******998855 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       734  (0.0409393); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); expected 358.6 (0.02)
Passed Vit filter:                       109  (0.00607954); 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 0.29s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 308.89
//
Query:       gi|242398846|ref|YP_002994270.1|  [L=341]
Description: transcription regulator, containing cell wall binding repeat 2 and DNA-binding HTH domains [Thermococcus sibiricus MM 739]
Scores for complete 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-09   36.1   0.1     0.0013   19.3   0.1    2.4  2  CW_binding_2     Putative cell wall binding repeat 2
    1.6e-06   28.0   0.0    3.5e-06   26.9   0.0    1.5  1  HTH_Crp_2        Crp-like helix-turn-helix domain
    4.5e-06   26.5   0.0      8e-06   25.7   0.0    1.4  1  MarR_2           MarR family
    7.1e-06   25.9   0.0    1.5e-05   24.8   0.0    1.5  1  MarR             MarR family
    4.7e-05   23.2   0.3    9.7e-05   22.2   0.3    1.5  1  TrmB             Sugar-specific transcriptional regulator Trm
    0.00019   20.9   0.1    0.00038   20.0   0.1    1.6  1  HTH_24           Winged helix-turn-helix DNA-binding
    0.00026   20.7   0.0    0.00044   20.0   0.0    1.4  1  HTH_IclR         IclR helix-turn-helix domain
    0.00051   20.4   0.4     0.0012   19.2   0.4    1.6  1  Penicillinase_R  Penicillinase repressor
    0.00099   19.0   0.0     0.0023   17.8   0.0    1.6  1  HTH_36           Helix-turn-helix domain
     0.0031   17.7   1.1      0.026   14.7   0.1    2.6  2  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
      0.008   15.8   0.1      0.016   14.8   0.1    1.5  1  GntR             Bacterial regulatory proteins, gntR family
     0.0096   15.2   0.0      0.044   13.1   0.0    1.8  2  Peptidase_U4     Sporulation factor SpoIIGA
  ------ inclusion threshold ------
       0.01   15.6   0.0      0.025   14.3   0.0    1.6  1  HTH_DeoR         DeoR-like helix-turn-helix domain
      0.015   14.6   0.0      0.026   13.9   0.0    1.3  1  DUF1670          Protein of unknown function (DUF1670)
      0.031   14.1   0.3      0.082   12.8   0.1    1.7  2  TFIIE_alpha      TFIIE alpha subunit
       0.12   12.9   0.1       0.25   11.8   0.1    1.6  1  HTH_27           Winged helix DNA-binding domain
       0.15   11.9   0.0        0.5   10.2   0.0    1.9  1  HTH_23           Homeodomain-like domain
       0.58    8.7   0.0       0.58    8.7   0.0    2.7  3  OPT              OPT oligopeptide transporter protein


Domain annotation for each model (and alignments):
>> CW_binding_2  Putative cell wall binding repeat 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   3.9e-05     0.039      22      71 .]      50     108 ..       7     108 .. 0.76
   2 !   19.3   0.1   1.3e-06    0.0013       1      61 [.     120     198 ..     120     206 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.9e-05
                                       THHHHHHHHHHHHHT--EEEE-.TS.SS.-.HHHHHHH......EEEES-TTTS-HHHH CS
                      CW_binding_2  22 faDALsaaalaakknaPiLLtd.kl.dtal.kalksat......vyilGGegvvsdsve 71 
                                         D +++ ++a  ++ P+L ++ ++ d++  ++l s++      ++i+G  ++vs++ve
  gi|242398846|ref|YP_002994270.1|  50 LIDYITVQPYARLLDIPVLPVNpQGlDEKTwAQLYSYVqlgwkkILIVGNSNAVSKEVE 108
                                       5788999**************8643433333444444499999999**********997 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 1.3e-06
                                       EE--SSHHHHHHHHHH.H.........EEET..THHHHHHHHHHHHHT--EEEE-.TS...SS.-HHHHHHH..... CS
                      CW_binding_2   1 RiaGaDRyeTaaaiak.a.........latg..faDALsaaalaakknaPiLLtd.kl...dtalkalksat..... 56 
                                       Ri+G+ R eTa ++a  +         +a+   +  AL+a+ +a +++ P+LLt  +     +        +     
  gi|242398846|ref|YP_002994270.1| 120 RIGGDVRTETAEKLAIhFyptgsktvvIASAldYGSALAASKFAMEYELPMLLTLeNDlseHA--------Iaglss 188
                                       9**************965999999986688877888******************642232211........122244 PP

                                       .....EEEES CS
                      CW_binding_2  57 .....vyilG 61 
                                            v+i+G
  gi|242398846|ref|YP_002994270.1| 189 lnpdlVIIVG 198
                                       4566566666 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0   3.5e-09   3.5e-06      21      55 ..     290     324 ..     274     336 .. 0.84

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 3.5e-09
                                       EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETE CS
                         HTH_Crp_2  21 pltqeelAsmlGltretvsrilseLkreglisrgr 55 
                                       ++ qe+l ++ G +r tvsri++eL++++l++r++
  gi|242398846|ref|YP_002994270.1| 290 KVKQEDLPELTGYSRPTVSRIIQELEKKQLVEREK 324
                                       579*****************************642 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0     8e-09     8e-06       7      55 ..     277     324 ..     273     327 .. 0.88

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 8e-09
                                       HHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2   7 qarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55 
                                       ++ v  aL + +g+ + + +l + +g+s+++vsri+++L+++ Lver++
  gi|242398846|ref|YP_002994270.1| 277 ERIVVKALIDQGGK-VKQEDLPELTGYSRPTVSRIIQELEKKQLVEREK 324
                                       66677788888886.9*******************************96 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   1.5e-08   1.5e-05      11      51 ..     284     324 ..     278     325 .. 0.93

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 1.5e-08
                                       HHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                              MarR  11 ilyeqgplsvseLakklgvskstvtrvldrLekkGlieRsk 51 
                                       ++++ g  ++ +L +  g s++tv+r++ +Lekk l+eR+k
  gi|242398846|ref|YP_002994270.1| 284 LIDQGGKVKQEDLPELTGYSRPTVSRIIQELEKKQLVEREK 324
                                       67888899*******************************86 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.3   9.7e-08   9.7e-05       6      60 ..     273     328 ..     273     338 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 9.7e-08
                                       HHHHCCCHCHHHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTT CS
                              TrmB   6 LseyEakvYlaLl.klgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpk 60 
                                       L+e E  v +aL+ + g+ + +++ e +g +r++v +++++Le+k lVerek  ++
  gi|242398846|ref|YP_002994270.1| 273 LTEKERIVVKALIdQGGKVKQEDLPELTGYSRPTVSRIIQELEKKQLVEREKVGKT 328
                                       567777777888877788999*******************************7654 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 !   20.0   0.1   3.8e-07   0.00038       8      48 .]     280     321 ..     273     321 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 3.8e-07
                            HTH_24   8 ILelLqknpr.isqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                                       + ++L ++++   q +L e +g S++tv+r +++Le++ l++
  gi|242398846|ref|YP_002994270.1| 280 VVKALIDQGGkVKQEDLPELTGYSRPTVSRIIQELEKKQLVE 321
                                       556777777779**************************9986 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   4.4e-07   0.00044      10      51 ..     282     323 ..     280     324 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 4.4e-07
                                       CT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                          HTH_IclR  10 dalaeapqeltlselArrtglpkStvhRlLqtLvelGyveqd 51 
                                       +al  +++ ++  +l + tg +++tv+R++q L++  +ve++
  gi|242398846|ref|YP_002994270.1| 282 KALIDQGGKVKQEDLPELTGYSRPTVSRIIQELEKKQLVERE 323
                                       57778888999999*************************986 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.4   1.2e-06    0.0012       1      61 [.     273     330 ..     273     337 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.2e-06
                                       ---S-SHHHHHHHHHS-EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEETTEEE CS
                   Penicillinase_R   1 lgelEaevmeilwekgeatvkevveeleeekelaysTVktllrrLvkKgllsrekegrafi 61 
                                       l+e E+ v ++l ++g    +   e l+e +  ++ TV  +++ L+kK+l++rek g++fi
  gi|242398846|ref|YP_002994270.1| 273 LTEKERIVVKALIDQGGKVKQ---EDLPELTGYSRPTVSRIIQELEKKQLVEREKVGKTFI 330
                                       578888899999888873333...4466666679************************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 !   17.8   0.0   2.3e-06    0.0023      27      54 ..     292     319 ..     273     320 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.3e-06
                            HTH_36  27 sqetlakrlglsknTvsraikeLeqlGy 54 
                                        qe+l +++g s+ Tvsr+i+eLe++ +
  gi|242398846|ref|YP_002994270.1| 292 KQEDLPELTGYSRPTVSRIIQELEKKQL 319
                                       689*********************9865 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.88   8.8e+02      45      54 ..     208     217 ..     200     219 .. 0.84
   2 !   14.7   0.1   2.6e-05     0.026      16      56 ..     284     324 ..     280     326 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.88
                                       HHHHTTSEEE CS
                    Fe_dep_repress  45 kLekdGyvey 54 
                                       kL+++Gy  y
  gi|242398846|ref|YP_002994270.1| 208 KLHSMGYQTY 217
                                       9******876 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 2.6e-05
                                       HHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                    Fe_dep_repress  16 lseekkvvktkdlaerLnvspssVsemlkkLekdGyveyek 56 
                                       l +++++vk+ dl e  + s ++Vs  +++Lek+ +ve ek
  gi|242398846|ref|YP_002994270.1| 284 LIDQGGKVKQEDLPELTGYSRPTVSRIIQELEKKQLVEREK 324
                                       567899*******************************9876 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1   1.7e-05     0.016      20      63 ..     287     329 ..     277     330 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.7e-05
                                       TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTCEEE CS
                              GntR  20 pGdkLPsereLaaefgVsrttvReALrrLeaeglverrqgrGtf 63 
                                        G k  ++++L +  g sr+tv + +++Le ++lver++ + tf
  gi|242398846|ref|YP_002994270.1| 287 QGGKV-KQEDLPELTGYSRPTVSRIIQELEKKQLVEREKVGKTF 329
                                       68888.9999***************************9877666 PP

>> Peptidase_U4  Sporulation factor SpoIIGA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.56   5.6e+02      29     138 ..       8      30 ..       2      53 .. 0.53
   2 !   13.1   0.0   4.4e-05     0.044     115     168 ..     233     288 ..     193     294 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.56
                      Peptidase_U4  29 kikklrlllaAllGalyvvlvlflpklesillsillkilvsllmvliafgpkslkeflkalllfylvsfllgGilfa 105
                                       + +   l++a ++G+++++lv+                                                       
  gi|242398846|ref|YP_002994270.1|   8 RFTVTTLIIALIIGSFMSILVY------------------------------------------------------- 29 
                                       4444455555555555533322....................................................... PP

                      Peptidase_U4 106 lsylllksknllvlllgalvaylllkllvkiik 138
                                                                        
  gi|242398846|ref|YP_002994270.1|  30 --------------------------------A 30 
                                       ................................2 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 4.4e-05
                      Peptidase_U4 115 n...llvlllgalvaylllkllvkiikkkkkkekeiyeveielkgkkievkallDTG 168
                                       +   + + ++ga++a++++  +v ++  kk+++++ ++ve+  ++++i vkal+D G
  gi|242398846|ref|YP_002994270.1| 233 EpspYTYSFIGAVLALAITVPVVLYW-AKKRWYSNKIPVEVLTEKERIVVKALIDQG 288
                                       05556667788888888877555555.678889999*******************88 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   2.5e-05     0.025       8      48 ..     284     324 ..     280     332 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.5e-05
                          HTH_DeoR   8 llkqqgklsveelvellgvSeaTiRRDLneLeeqglltRth 48 
                                       l+ q gk++ e+l el g+S  T+ R ++eLe++ l++R  
  gi|242398846|ref|YP_002994270.1| 284 LIDQGGKVKQEDLPELTGYSRPTVSRIIQELEKKQLVEREK 324
                                       78999********************************9965 PP

>> DUF1670  Protein of unknown function (DUF1670)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.6e-05     0.026      96     133 ..     281     318 ..     251     327 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.6e-05
                           DUF1670  96 fnEAyeqealltqsDlalllgvstrtvskqvkeyqeee 133
                                       ++   +q++ + q+Dl  l g s  tvs+ ++e+ +++
  gi|242398846|ref|YP_002994270.1| 281 VKALIDQGGKVKQEDLPELTGYSRPTVSRIIQELEKKQ 318
                                       344569****************************5543 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0         7     7e+03      65      78 ..      76      89 ..      61     111 .. 0.70
   2 ?   12.8   0.1   8.2e-05     0.082      14      59 ..     276     322 ..     267     327 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 7
                                      TTTEEEEEEEEEEC CS
                       TFIIE_alpha 65 eekswykyywriny 78
                                      +ek+w + y +++ 
  gi|242398846|ref|YP_002994270.1| 76 DEKTWAQLYSYVQL 89
                                      77888888777664 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 8.2e-05
                                       HHHHHHHHHHCT.TSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEE CS
                       TFIIE_alpha  14 eavlvldvLlek.gevteedlakelkidlnelrklLnrLyearlvky 59 
                                       +   v+++L+ + g+v+ edl ++++  ++ + +++ +L +++lv+ 
  gi|242398846|ref|YP_002994270.1| 276 KERIVVKALIDQgGKVKQEDLPELTGYSRPTVSRIIQELEKKQLVER 322
                                       444566666654279*****************************985 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00026      0.25       2      52 ..     274     324 ..     273     333 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00026
                            HTH_27   2 trqqalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertg 52 
                                       t+ +++v+  +  +++++k++dl + + ++  ++s ++ +L++k Lver++
  gi|242398846|ref|YP_002994270.1| 274 TEKERIVVKALIDQGGKVKQEDLPELTGYSRPTVSRIIQELEKKQLVEREK 324
                                       56666666666669999999***************************8765 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0    0.0005       0.5       3      44 ..     274     317 ..     273     321 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0005
                            HTH_23   3 sereRlrillllae..GlsvreIAreLgvsrrTvyrwlkryree 44 
                                       +e+eR+ +  l ++  +  +++  ++ g sr Tv+r+++  +++
  gi|242398846|ref|YP_002994270.1| 274 TEKERIVVKALIDQggKVKQEDLPELTGYSRPTVSRIIQELEKK 317
                                       688888888888889999999999999***********997555 PP

>> OPT  OPT oligopeptide transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.8      0.32   3.2e+02     454     480 ..       3      29 ..       1      31 [. 0.61
   2 ?    0.3   0.1      0.21   2.1e+02     592     608 ..     142     158 ..     138     159 .. 0.89
   3 ?    8.7   0.0   0.00059      0.58     234     273 ..     238     276 ..     234     296 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.32
                               OPT 454 lkasPraqfvaqliGtlvgavvniavl 480
                                       +++  r + ++ +i+ ++g++ +i+v+
  gi|242398846|ref|YP_002994270.1|   3 TGLKTRFTVTTLIIALIIGSFMSILVY 29 
                                       455556666666666666666666665 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.21
                               OPT 592 kynyvlaaGLiaGealm 608
                                       ++++v+a++L+ G al+
  gi|242398846|ref|YP_002994270.1| 142 SKTVVIASALDYGSALA 158
                                       6899***********97 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.00059
                               OPT 234 vnmliGavlswgiliPll..yysngwypaylpydvteilded 273
                                       ++ +iGavl+  i +P++  + ++ wy++++p    e+l+e+
  gi|242398846|ref|YP_002994270.1| 238 TYSFIGAVLALAITVPVVlyWAKKRWYSNKIP---VEVLTEK 276
                                       579*************999455679*******...6666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       697  (0.0388756); expected 358.6 (0.02)
Passed bias filter:                      585  (0.0326287); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 2381.57
//
Query:       gi|242398847|ref|YP_002994271.1|  [L=225]
Description: metal-dependent hydrolase [Thermococcus sibiricus MM 739]
Scores for complete 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  126.1   0.0    1.5e-36  125.8   0.0    1.1  1  Lactamase_B_3  Beta-lactamase superfamily domain
    7.5e-24   84.4   0.0    9.5e-24   84.0   0.0    1.1  1  Lactamase_B_2  Beta-lactamase superfamily domain
      2e-13   50.8   0.6    3.7e-13   49.9   0.6    1.7  1  Lactamase_B    Metallo-beta-lactamase superfamily
  ------ inclusion threshold ------
      0.093   12.2   0.0       0.14   11.5   0.0    1.3  1  Lactamase_B_6  Metallo-beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.8   0.0   3.3e-40   1.5e-36       1     163 []       3     190 ..       3     190 .. 0.82

  Alignments for each domain:
  == domain 1  score: 125.8 bits;  conditional E-value: 3.3e-40
                     Lactamase_B_3   1 eltwlghnsflletagarilvDPfka.nlgyeppa....eeaDlvlisqaledHahle.tlkql........aenvk 63 
                                       ++++lgh++f +e++g++il+DPf   n  +++ +    e++Dl+l+++a+ dH     +++q         ++++ 
  gi|242398847|ref|YP_002994271.1|   3 RIRFLGHAAFEIEGEGKKILIDPFLSgN-PTAAAKpedfERIDLILVTHAHGDHIGDSvKIAQRtgakivamYDIAS 78 
                                       589*********************7743.33333336679**************86551455536667777744444 PP

                     Lactamase_B_3  64 vleeges...........levggleiravatshdav.ggsergenngflleqdgltiyhlGhlahelsseelkelgr 128
                                       +l e+++           +ev+g+++ +v++ h ++ gg   g+ +g+++e +g++iyh G+++   ++e ++el  
  gi|242398847|ref|YP_002994271.1|  79 YLVEENQgittvgmnygpTEVDGVKLVQVPAWHSSSaGGYSIGNACGYIMEFEGIKIYHAGDTYVFKDMELFAELYG 155
                                       444433334444444444***************888468899*********************************** PP

                     Lactamase_B_3 129 vDvvltPvggpltlgqeealelakrLkpklvlPmh 163
                                       +Dv l+P+gg++t+g++ea ++++ L+pk+v+Pmh
  gi|242398847|ref|YP_002994271.1| 156 IDVALLPIGGHFTMGPKEATKAVEFLRPKYVIPMH 190
                                       **********************************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 !   84.0   0.0   2.1e-27   9.5e-24       2     201 .]      20     191 ..      19     191 .. 0.86

  Alignments for each domain:
  == domain 1  score: 84.0 bits;  conditional E-value: 2.1e-27
                                       EEEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHH CS
                     Lactamase_B_2   2 riLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvyla 78 
                                        iLiD++++  +  +++   +++ +++++id++l+thaH DH+ +   ++++++  ++++a  +++++l ++     
  gi|242398847|ref|YP_002994271.1|  20 KILIDPFLS--G--NPTA--AAKPEDFERIDLILVTHAHGDHIGDSVKIAQRTG--AKIVAMYDIASYLVEE----- 83 
                                       69*******..3..3443..224678*****************98877777544..7899999999999998..... PP

                                       CHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---.HHHHHHH CS
                     Lactamase_B_2  79 leeepavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyip.eeigerl 154
                                         ++ +++++ ++  +++e++  g+++  +pa h+s    +   g ++G+++e +g ++y++gDt  ++  e+ ++l
  gi|242398847|ref|YP_002994271.1|  84 --NQ-GITTVGMN-YGPTEVD--GVKLVQVPAWHSSSA-GGYSIGNACGYIMEFEGIKIYHAGDTYVFKdMELFAEL 153
                                       ..34.78899998.6789998..778888888888887.788899************************56699*** PP

                                       CT-SEEEEE-S-SSTTHHHHHHT---STSHHHHCTTSSSSEEEEESB CS
                     Lactamase_B_2 155 ggadllllditayeddemirhmgHltpeeaveaaadlgakrlvliHi 201
                                       +g+d++ll+i+         +++++ p+ea +a++ l++k ++++H+
  gi|242398847|ref|YP_002994271.1| 154 YGIDVALLPIG---------GHFTMGPKEATKAVEFLRPKYVIPMHY 191
                                       ***********.........9999999*******************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 !   49.9   0.6   8.3e-17   3.7e-13       4     140 ..       7     122 ..       4     190 .. 0.89

  Alignments for each domain:
  == domain 1  score: 49.9 bits;  conditional E-value: 8.3e-17
                                       CSSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHH CS
                       Lactamase_B   4 dpvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeap 80 
                                       +++ ++ ieg+g+ iLiD+ +s+  + aa     +  + +++d +++TH+H DHiG+  +++++t+++++a +++a 
  gi|242398847|ref|YP_002994271.1|   7 LGHAAFEIEGEGKKILIDPFLSGNPTAAA-----KPEDFERIDLILVTHAHGDHIGDSVKIAQRTGAKIVAMYDIAS 78 
                                       5667888*********************8.....8****************************************** PP

                                       CCHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEE CS
                       Lactamase_B  81 alfmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvvey 140
                                       +l +e  +                   v ++ ++++++g++++ v+  + +++g++++++
  gi|242398847|ref|YP_002994271.1|  79 YLVEENQGIT----------------TVGMNYGPTEVDGVKLVQVPAWHSSSAGGYSIGN 122
                                       9999888664................3777888888888888888888887777777765 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 ?   11.5   0.0   3.2e-05      0.14       5      55 ..      17      62 ..      12      81 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.2e-05
                     Lactamase_B_6  5 dnvkiLlDvGwdeskvslesalkelekviptvdliLLshatlehlGayall 55
                                      ++ kiL+D+  +++        +   +  +++dliL++ha  +h+G  + +
  gi|242398847|ref|YP_002994271.1| 17 EGKKILIDPFLSGNPT-----AAAKPEDFERIDLILVTHAHGDHIGDSVKI 62
                                      5679999999999732.....2333556899***************65444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1390.09
//
Query:       gi|242398848|ref|YP_002994272.1|  [L=400]
Description: Proteasome-activating nucleotidase [Thermococcus sibiricus MM 739]
Scores for complete 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-43  146.1   0.0    1.5e-42  145.2   0.0    1.5  1  AAA              ATPase family associated with various cellul
    2.1e-15   56.2   0.2    4.7e-15   55.1   0.2    1.6  1  AAA_lid_3        AAA+ lid domain
    1.6e-11   43.9   0.0      4e-11   42.7   0.0    1.6  1  Prot_ATP_ID_OB   Proteasomal ATPase OB C-terminal domain
    2.3e-07   30.9   0.1    3.6e-06   27.0   0.1    2.8  2  AAA_5            AAA domain (dynein-related subfamily)
    2.4e-07   31.3   0.2    0.00028   21.3   0.0    3.1  3  AAA_16           AAA ATPase domain
    1.1e-06   28.1   0.0      3e-06   26.8   0.0    1.7  1  Prot_ATP_OB_N    Proteasomal ATPase OB N-terminal domain
    1.3e-06   28.3   0.0    3.2e-06   27.0   0.0    1.6  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    1.7e-06   28.3   0.0    8.6e-06   26.0   0.0    2.1  2  AAA_2            AAA domain (Cdc48 subfamily)
    0.00017   21.9   0.1      0.019   15.3   0.0    2.6  2  AAA_22           AAA domain
    0.00025   20.3   0.0    0.00052   19.2   0.0    1.5  1  DUF815           Protein of unknown function (DUF815)
    0.00035   20.8   1.1    0.00084   19.6   0.0    2.2  2  AAA_28           AAA domain
    0.00073   19.9   0.0     0.0014   19.0   0.0    1.5  1  RNA_helicase     RNA helicase
     0.0013   18.2   0.0      0.077   12.3   0.0    2.6  3  ATPase           KaiC
     0.0026   17.8   0.0     0.0054   16.8   0.0    1.5  1  AAA_14           AAA domain
     0.0044   16.8   0.0     0.0087   15.8   0.0    1.5  1  IstB_IS21        IstB-like ATP binding protein
     0.0044   16.7   0.3     0.0079   15.8   0.3    1.4  1  NRBF2            Nuclear receptor-binding factor 2, autophagy
     0.0044   17.6   0.0       0.01   16.4   0.0    1.7  1  AAA_18           AAA domain
     0.0052   16.0   0.0     0.0092   15.2   0.0    1.3  1  TIP49            TIP49 P-loop domain
     0.0059   16.0   0.1      0.012   15.1   0.1    1.4  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0061   16.4   0.0      0.013   15.4   0.0    1.6  1  AAA_3            ATPase family associated with various cellul
     0.0088   16.5   0.1      0.023   15.1   0.0    1.8  1  AAA_17           AAA domain
  ------ inclusion threshold ------
      0.011   15.7   0.4        0.4   10.6   0.0    2.7  3  ATPase_2         ATPase domain predominantly from Archaea
      0.016   15.3   0.6       0.04   14.0   0.6    1.6  1  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
       0.02   14.4   0.5       0.11   12.1   0.0    2.3  3  AAA_25           AAA domain
      0.026   14.5   0.0      0.051   13.5   0.0    1.4  1  Rad17            Rad17 P-loop domain
      0.034   14.3   0.0      0.088   13.0   0.0    1.8  1  AAA_33           AAA domain
      0.035   13.2   0.0      0.061   12.4   0.0    1.3  1  Parvo_NS1        Parvovirus non-structural protein NS1
      0.051   14.1   0.0       0.19   12.3   0.0    1.9  1  ABC_tran         ABC transporter
      0.058   12.7   0.0        0.1   11.9   0.0    1.4  1  Zeta_toxin       Zeta toxin
      0.058   13.1   0.0       0.13   12.0   0.0    1.5  1  AAA_24           AAA domain
       0.06   13.3   0.0       0.22   11.4   0.0    1.9  2  NACHT            NACHT domain
      0.061   13.5   0.0       0.23   11.6   0.0    2.0  1  Sigma54_activ_2  Sigma-54 interaction domain
      0.066   13.6   0.8       0.28   11.6   0.0    2.4  2  BAG              BAG domain
      0.079   12.5   0.0       0.16   11.5   0.0    1.4  1  AAA_7            P-loop containing dynein motor region
       0.09   12.2   0.1       0.15   11.4   0.1    1.3  1  Not3             Not1 N-terminal domain, CCR4-Not complex com
      0.094   12.7   0.0       0.18   11.8   0.0    1.4  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
       0.11   12.8   1.2       0.31   11.4   1.2    1.6  1  TSNAXIP1_N       Translin-associated factor X-interacting N-t
       0.12   11.6   0.0        2.2    7.4   0.0    2.2  2  KAP_NTPase       KAP family P-loop domain
       0.41   10.6   1.4       0.78    9.7   0.3    2.1  1  LURAP            Leucine rich adaptor protein
       0.57   10.7   4.7       0.15   12.6   0.9    2.0  1  APG6_N           Apg6 coiled-coil region
          1    9.4   5.2       0.44   10.5   1.4    2.4  2  Prefoldin_2      Prefoldin subunit
        1.2    9.4   9.1       0.19   12.0   2.4    2.7  2  HALZ             Homeobox associated leucine zipper


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.2   0.0   3.4e-45   1.5e-42       1     132 []     178     311 ..     178     311 .. 0.96

  Alignments for each domain:
  == domain 1  score: 145.2 bits;  conditional E-value: 3.4e-45
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH... CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr... 74 
                                       vllyGppG+GKTl+aka+a+e++++f+++ gsel+ ky+ge+++ ++elf+ a+eka psi+fiDEida++ +r   
  gi|242398848|ref|YP_002994272.1| 178 VLLYGPPGCGKTLMAKALAHEVNATFIRVIGSELVRKYIGEGARLVSELFELAREKA-PSIVFIDEIDAIGAKRlde 253
                                       79******************************************************9.*****************98 PP

                                       TTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETTS CS
                               AAA  75 sgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieiel 132
                                       +++ ++e +r++ qLl+eldg++   ++v +i+atnrpd ldpallr gRfdr ie++l
  gi|242398848|ref|YP_002994272.1| 254 TTGGEREVNRTLMQLLAELDGFDPM-GEVKIIAATNRPDILDPALLRpGRFDRLIEVPL 311
                                       7778899999**************6.66***************************9985 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.1   0.2   1.1e-17   4.7e-15       2      44 ..     333     375 ..     332     376 .. 0.97

  Alignments for each domain:
  == domain 1  score: 55.1 bits;  conditional E-value: 1.1e-17
                         AAA_lid_3   2 vdlkeLAerTeGySGADlaalcreAallAlrrgikeitmedfe 44 
                                       vdlk +Ae+TeG SGADl+a++ eA++ A+r  ++ +t+edf 
  gi|242398848|ref|YP_002994272.1| 333 VDLKVIAEMTEGASGADLKAIVTEAGMFAIRSRREYVTQEDFL 375
                                       9****************************************96 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 !   42.7   0.0   9.3e-14     4e-11       2      57 .]      66     120 ..      66     120 .. 0.98

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 9.3e-14
                                       EEEEEE-TTSSEEEEE-TTS-EEEEEE-GGGSSST--TTEEEEEETTTTEEEEEE- CS
                    Prot_ATP_ID_OB   2 atVsEvlddteraiVktssdeevvvslagavpremLrpgDlVavdkdtgfifEkLP 57 
                                       +t+ E+ld+ +raiV+  ++  +vv++a  + re Lrpg +Va+d++t ++ E LP
  gi|242398848|ref|YP_002994272.1|  66 GTLIELLDE-DRAIVQNYNGPRFVVRIAPWIERENLRPGSRVALDQRTMAVIELLP 120
                                       7999*****.*********************************************9 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       2.4     1e+03      78     101 ..      61      84 ..      57     115 .. 0.87
   2 !   27.0   0.1   8.5e-09   3.6e-06       1     135 [.     177     298 ..     177     300 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 2.4
                                       -HHHHHHHHHHHHSSEEE..-SSS CS
                             AAA_5  78 esevlnsLlslleerrllleegge 101
                                       +++ +++L+ ll+e+r  + + ++
  gi|242398848|ref|YP_002994272.1|  61 PPAFAGTLIELLDEDRAIVQNYNG 84 
                                       5788999******99998887765 PP

  == domain 2  score: 27.0 bits;  conditional E-value: 8.5e-09
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEve 75 
                                       +vlL GppG+gK+ +a+ la+ +n+++  v +++  ++    g r +         s+l + ar   ++i+++DE++
  gi|242398848|ref|YP_002994272.1| 177 GVLLYGPPGCGKTLMAKALAHEVNATFIRVIGSELVRKYIGEGARLV---------SELFELARekAPSIVFIDEID 244
                                       59************************999999885555555555555.........8999899966789******** PP

                                       G--HHHHHHHHHHHHS.SEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHH CS
                             AAA_5  76 raesevlnsLlsllee.rrllleeggelvkaknddllerfrviatanpldrslnelspalr 135
                                        +  + l++      e +r l+  + el ++++   + ++ +ia++n++d     l+pal+
  gi|242398848|ref|YP_002994272.1| 245 AIGAKRLDETTGGEREvNRTLMQLLAELDGFDP---MGEVKIIAATNRPD----ILDPALL 298
                                       999888777755444404444444455555555...44599999999999....6666665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0       0.6   2.6e+02      69     107 ..      16      60 ..       5     131 .. 0.69
   2 !   21.3   0.0   6.5e-07   0.00028      16      51 ..     167     202 ..     162     217 .. 0.83
   3 ?    4.3   0.0      0.11        47     121     149 ..     221     253 ..     207     274 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.6
                            AAA_16  69 ysalaqalareellrqlldeaesaeleawrekleeala..........a 107
                                       y+ ++ +l + + +rql+ + ++  lea++e+le++l+          +
  gi|242398848|ref|YP_002994272.1|  16 YDDYVYYL-K-RRIRQLELQVRT--LEADKERLERELSrlrmemsrlrQ 60 
                                       55566677.5.678888877454..899999999988855554444431 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 6.5e-07
                            AAA_16  16 lervrsgrpelvllsGesGvGKsslvrellralekd 51 
                                       +e+v    p+ vll+G++G+GK+ ++++l+++++++
  gi|242398848|ref|YP_002994272.1| 167 FEKVGIEPPRGVLLYGPPGCGKTLMAKALAHEVNAT 202
                                       6666666679********************998876 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.11
                            AAA_16 121 ellkrllallsrderplvlvlDdlq.....wade 149
                                       +l+++l++l+++ + p ++++D+++     ++de
  gi|242398848|ref|YP_002994272.1| 221 RLVSELFELARE-KAPSIVFIDEIDaigakRLDE 253
                                       577888899999.778*********555554444 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 !   26.8   0.0     7e-09     3e-06       3      52 ..      66     115 ..      65     123 .. 0.84

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 7e-09
                     Prot_ATP_OB_N   3 GtflavnsqdgtadVlvggrrmrVavsPlvdaeeLrpGqeVlLnEalvvV 52 
                                       Gt++++ ++d+ +   ++g r++V ++P ++ e LrpG +V L+++ ++V
  gi|242398848|ref|YP_002994272.1|  66 GTLIELLDEDRAIVQNYNGPRFVVRIAPWIERENLRPGSRVALDQRTMAV 115
                                       788888866666666789***************************97776 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.0   7.5e-09   3.2e-06      35      96 ..     177     246 ..     169     255 .. 0.72

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 7.5e-09
                            RuvB_N  35 hvllyGpPGlGkttlakiiakelgvklkitsgPvleka.....gdlaalltnleek...dvlfideihrl 96 
                                        vllyGpPG Gkt +ak +a+e+++++    g  l ++     + l++ l +l ++    ++fidei  +
  gi|242398848|ref|YP_002994272.1| 177 GVLLYGPPGCGKTLMAKALAHEVNATFIRVIGSELVRKyigegARLVSELFELAREkapSIVFIDEIDAI 246
                                       69**********************9976666655544323221456666666654422379******876 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0     2e-08   8.6e-06       6     103 ..     178     269 ..     174     274 .. 0.83
   2 ?   -1.1   0.0       4.1   1.7e+03      30      55 ..     331     356 ..     308     391 .. 0.60

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 2e-08
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKi 80 
                                       +ll gp g+Gkt++akala   ++    ++ir+  sel      + + +     ++    a e+   iv++DEid i
  gi|242398848|ref|YP_002994272.1| 178 VLLYGPPGCGKTLMAKALAHEVNA----TFIRVIGSELVR----KYIGEGARLVSELFELAREKApsIVFIDEIDAI 246
                                       6889******************96....9*********99....66666666666666666666667********** PP

                                       ------------HHHHHHHHHHH CS
                             AAA_2  81 hpkessgadvSregVqrdLLqil 103
                                        +k+  +    + +V r L+q+l
  gi|242398848|ref|YP_002994272.1| 247 GAKRLDETTGGEREVNRTLMQLL 269
                                       **866666667789*****9998 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 4.1
                                       ....-EEEEEGGG-------THHHHH CS
                             AAA_2  30 kkekkliradaselleeeevehlvsr 55 
                                       kk +  ++a+++e + + +++ +v++
  gi|242398848|ref|YP_002994272.1| 331 KKVDLKVIAEMTEGASGADLKAIVTE 356
                                       44444455555555555555555543 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   4.3e-05     0.019       8      39 ..     178     200 ..     173     210 .. 0.84
   2 ?    4.3   0.0      0.11        46      57     108 ..     204     250 ..     200     284 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.3e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeer 39 
                                       ++++G++G+GKT+ ++ l+++          +
  gi|242398848|ref|YP_002994272.1| 178 VLLYGPPGCGKTLMAKALAHEV---------N 200
                                       689****************997.........4 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.11
                            AAA_22  57 lrellralglelkaerlsseellealeqalraravielliiDEaqhlrseea 108
                                        r + ++l ++  +   +  +l++ l + +r++a  +++ iDE++ +  ++ 
  gi|242398848|ref|YP_002994272.1| 204 IRVIGSELVRKYIG---EGARLVSELFELAREKAP-SIVFIDEIDAI-GAKR 250
                                       55566666655555...778899999999999999.*********99.4333 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   1.2e-06   0.00052      52     115 ..     174     242 ..     135     246 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.2e-06
                            DUF815  52 pannvLLwGarGtGKSslvkallneyaeegLrli..evekedlkelpklvellr...erperfilfvDD 115
                                       p + vLL+G  G+GK  + kal +e++++ +r+i  e+ ++ + e  +lv++l    +++   i+f+D 
  gi|242398848|ref|YP_002994272.1| 174 PPRGVLLYGPPGCGKTLMAKALAHEVNATFIRVIgsELVRKYIGEGARLVSELFelaREKAPSIVFIDE 242
                                       55679*****************************88899****99999998765222566778999997 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       6.6   2.8e+03     107     139 ..      80     113 ..      65     141 .. 0.67
   2 !   19.6   0.0     2e-06   0.00084       2      40 ..     178     221 ..     177     269 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 6.6
                            AAA_28 107 krydl.vfllppapeidddgeRredleereaide 139
                                       ++y+   f+++ ap+i++ + R+ +  +  + + 
  gi|242398848|ref|YP_002994272.1|  80 QNYNGpRFVVRIAPWIERENLRPGSRVALDQRTM 113
                                       5666667889999999999999875444333333 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 2e-06
                            AAA_28   2 ivitGgestGKTtlleaLa....argypvv.pEaareileekla 40 
                                       + + G++++GKT +++aLa    a+ ++v+  E +r+++ e+++
  gi|242398848|ref|YP_002994272.1| 178 VLLYGPPGCGKTLMAKALAhevnATFIRVIgSELVRKYIGEGAR 221
                                       6799***************65544499999********988774 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   3.2e-06    0.0014       1      26 [.     178     203 ..     178     242 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 3.2e-06
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl 26 
                                       ++lyGp+g+GK+++ak La+++  ++
  gi|242398848|ref|YP_002994272.1| 178 VLLYGPPGCGKTLMAKALAHEVNATF 203
                                       689**************999998655 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       9.1   3.9e+03      55      73 ..      36      54 ..      23      80 .. 0.60
   2 !   12.3   0.0   0.00018     0.077      12      38 ..     167     194 ..     164     203 .. 0.85
   3 ?    2.9   0.0      0.14        60     106     153 ..     221     271 ..     205     275 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 9.1
                            ATPase 55 tveepaedlrenakslGwd 73
                                      t+e ++e l ++ ++l ++
  gi|242398848|ref|YP_002994272.1| 36 TLEADKERLERELSRLRME 54
                                      3333333333333333333 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00018
                            ATPase  12 l.kgGipegrvvlitGepGtGKtifalq 38 
                                       + k Gi   r vl++G pG+GKt++a+ 
  gi|242398848|ref|YP_002994272.1| 167 FeKVGIEPPRGVLLYGPPGCGKTLMAKA 194
                                       55668999999**************985 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.14
                            ATPase 106 elieelaeaikeikakrvviDsitgl.ayeekeav..aReilrqlvrvlkk 153
                                        l++el e  +e+  + v iD i+++ a++ +e +   Re  r+l++ l++
  gi|242398848|ref|YP_002994272.1| 221 RLVSELFELAREKAPSIVFIDEIDAIgAKRLDETTggEREVNRTLMQLLAE 271
                                       688999999****************98766665553356666666666655 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.3e-05    0.0054       5      76 ..     178     246 ..     175     275 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.3e-05
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev 76 
                                       +++ G+  +GKT ++k l++e       ++ +   +   k + + ++l ++++e+++e+  +++f+DEi  +
  gi|242398848|ref|YP_002994272.1| 178 VLLYGPPGCGKTLMAKALAHEVN---ATFIRVIGSELVRKYIGEGARLVSELFELAREKAPSIVFIDEIDAI 246
                                       7899**************97766...555555444444444444446778888876666899*******876 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0     2e-05    0.0087      48      74 ..     176     202 ..     163     244 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2e-05
                         IstB_IS21  48 enivllGpsGvGKshlaialgveavra 74 
                                        +++l Gp+G GK+ +a al++e  ++
  gi|242398848|ref|YP_002994272.1| 176 RGVLLYGPPGCGKTLMAKALAHEVNAT 202
                                       6799*****************987555 PP

>> NRBF2  Nuclear receptor-binding factor 2, autophagy regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.3   1.8e-05    0.0079      87     123 ..      26      62 ..      11      71 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.8e-05
                             NRBF2  87 kiadLkrlvelLlaenerLrkenkqLkaekaRLqkep 123
                                       +i++L+  v +L a+ erL +e  +L+ e +RL++ p
  gi|242398848|ref|YP_002994272.1|  26 RIRQLELQVRTLEADKERLERELSRLRMEMSRLRQPP 62 
                                       799******************************9877 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   2.4e-05      0.01       1      44 [.     178     242 ..     178     294 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.4e-05
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....................gvnlrdvakenglllevdpe 44 
                                       +ll G+pG+GKt +ak+L+ + +                      + +l ++a+e+ +++ + +e
  gi|242398848|ref|YP_002994272.1| 178 VLLYGPPGCGKTLMAKALAHEVNAtfirvigselvrkyigegarlVSELFELAREKAPSIVFIDE 242
                                       799***************88864467777775555555666555555555555555555555555 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   2.2e-05    0.0092      51      91 ..     176     214 ..     161     229 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.2e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevysl 91 
                                       r+vLl Gp+g Gkt +a a+++e++    f+ + gse+ + 
  gi|242398848|ref|YP_002994272.1| 176 RGVLLYGPPGCGKTLMAKALAHEVN--ATFIRVIGSELVRK 214
                                       89**********************9..68999999998765 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   2.7e-05     0.012      25      43 ..     178     196 ..     170     202 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.7e-05
                      Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                       +ll+GppG+GKt++ak+l+
  gi|242398848|ref|YP_002994272.1| 178 VLLYGPPGCGKTLMAKALA 196
                                       89**************996 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0     3e-05     0.013       2      30 ..     178     206 ..     177     249 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3e-05
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkri 30 
                                       vll g PG +ktl++kala+ ++++f r+
  gi|242398848|ref|YP_002994272.1| 178 VLLYGPPGCGKTLMAKALAHEVNATFIRV 206
                                       7999**********************998 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   5.5e-05     0.023       1      37 [.     181     219 ..     181     262 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5.5e-05
                                       EE-TTSSHHHHHHHHHHHHTEEEEEH..HHHHHHHHHTT CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthlsa..Gdllreeakrg 37 
                                       +G+PG+GK+ +++ l+++++ t++    ++l+r+ + +g
  gi|242398848|ref|YP_002994272.1| 181 YGPPGCGKTLMAKALAHEVNATFIRVigSELVRKYIGEG 219
                                       7******************99998544366777766555 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1       3.6   1.5e+03      45      80 ..      14      46 ..       6      82 .. 0.53
   2 ?   10.6   0.0   0.00093       0.4      18      44 ..     173     199 ..     164     215 .. 0.80
   3 ?    1.8   0.0      0.44   1.9e+02      36      81 ..     222     268 ..     215     337 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 3.6
                          ATPase_2 45 edkdkyviyyialreesiskldefie..eeeekkklek 80
                                      e++d + +yy + r ++++   +++e  +    ++le+
  gi|242398848|ref|YP_002994272.1| 14 EEYD-DYVYYLKRRIRQLELQVRTLEadK----ERLER 46
                                      3444.455555555555555555545442....22222 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00093
                          ATPase_2  18 epneiyfiYGpegsGKtaLlkeiienl 44 
                                       ep + +++YGp g+GKt + k ++ + 
  gi|242398848|ref|YP_002994272.1| 173 EPPRGVLLYGPPGCGKTLMAKALAHEV 199
                                       6777789**********9999887665 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.44
                          ATPase_2  36 Llkeiienledkdkyviyyialreesiskldefie.eeeekkkleka 81 
                                       L+ e+ e  ++k   +++++++  +  ++lde+ + e e+++ l + 
  gi|242398848|ref|YP_002994272.1| 222 LVSELFELAREKAPSIVFIDEIDAIGAKRLDETTGgEREVNRTLMQL 268
                                       66677777777777777777777777777777755444444444444 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 ?   14.0   0.6   9.3e-05      0.04      55     101 ..      14      60 ..       6      81 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 9.3e-05
                    CENP-F_leu_zip  55 etlkeeieelaeelreleldLvalrsekeeLekelqkkqervseLes 101
                                       e+  + +  l+++ r+lel++ +l  +ke Le+el   + ++s L +
  gi|242398848|ref|YP_002994272.1|  14 EEYDDYVYYLKRRIRQLELQVRTLEADKERLERELSRLRMEMSRLRQ 60 
                                       55666677789999**********************99999999865 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1       2.9   1.2e+03      87     147 ..      24      89 ..      17      89 .. 0.47
   2 ?   12.1   0.0   0.00026      0.11      36      57 ..     178     199 ..     172     208 .. 0.92
   3 ?   -2.6   0.0       8.1   3.4e+03     131     160 ..     224     254 ..     220     271 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.9
                            AAA_25  87 rrRlravgeal....rddarl.lvldlagveslpLfakdrggtlltadvdaleaaieevegvrlvv 147
                                       +rR+r++  ++    +d++rl + l++ ++e  +L+++ +   +l + +d+ +a ++ ++g+r+vv
  gi|242398848|ref|YP_002994272.1|  24 KRRIRQLELQVrtleADKERLeRELSRLRMEMSRLRQPPAFAGTLIELLDEDRAIVQNYNGPRFVV 89 
                                       566666666665555333333122222223334555554333333444555556666666666665 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00026
                            AAA_25  36 allaGapgtGKttlaldlalav 57 
                                       +ll+G+pg+GKt +a  la++v
  gi|242398848|ref|YP_002994272.1| 178 VLLYGPPGCGKTLMAKALAHEV 199
                                       69****************9987 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 8.1
                            AAA_25 131 daleaaieevegvrlvviDplsralgg..den 160
                                        +l + ++e + +  v iD ++++ +   de+
  gi|242398848|ref|YP_002994272.1| 224 SELFELARE-KAPSIVFIDEIDAIGAKrlDET 254
                                       567777888.7799999999888554444555 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   0.00012     0.051      48      77 ..     178     207 ..     165     216 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00012
                             Rad17  48 LLisGPsGCgkstvvkvLskelgiklrewl 77 
                                       +L+ GP+GCgk+ + k L+ e    ++  +
  gi|242398848|ref|YP_002994272.1| 178 VLLYGPPGCGKTLMAKALAHEVNATFIRVI 207
                                       6899****************9988777665 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   0.00021     0.088       2      29 ..     178     207 ..     178     256 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00021
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avlls 29 
                                       vll G+pG+GK+  a+ l+ +    ++++ 
  gi|242398848|ref|YP_002994272.1| 178 VLLYGPPGCGKTLMAKALAHEVNatFIRVI 207
                                       7899**************988775555554 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00014     0.061     117     139 ..     178     200 ..     172     204 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00014
                         Parvo_NS1 117 vwfyGpantGktnlaeaIakavp 139
                                       v++yGp+ +Gkt +a+a+a+ v 
  gi|242398848|ref|YP_002994272.1| 178 VLLYGPPGCGKTLMAKALAHEVN 200
                                       89*****************9875 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00043      0.19       8      37 ..     172     201 ..     169     224 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00043
                                       EETTSEEEEEESTTSSHHHHHHHHTTSS-- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   8 lkegekvaivGenGaGKStLlkllagllkp 37 
                                       +++ + v + G+ G+GK+ ++k+la++++ 
  gi|242398848|ref|YP_002994272.1| 172 IEPPRGVLLYGPPGCGKTLMAKALAHEVNA 201
                                       666777899****************99876 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00024       0.1      14      57 ..     173     215 ..     165     255 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00024
                        Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnvvrldpDd.lRel 57 
                                       e P  +ll G pG+GK+ +a++l+ e+  +  ++r+ + + +R++
  gi|242398848|ref|YP_002994272.1| 173 EPPRGVLLYGPPGCGKTLMAKALAHEV--NATFIRVIGSElVRKY 215
                                       568889********************9..8888887665414665 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    0.0003      0.13       5      28 ..     178     203 ..     175     254 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0003
                            AAA_24   5 iliyGpsgiGKTtlakel..gpkplf 28 
                                       +l+yGp+g GKT +ak l  + ++ f
  gi|242398848|ref|YP_002994272.1| 178 VLLYGPPGCGKTLMAKALahEVNATF 203
                                       79**************9966555555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00052      0.22       3      24 ..     178     199 ..     176     203 .. 0.89
   2 ?   -1.9   0.0       6.6   2.8e+03      67     113 ..     221     269 ..     209     278 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00052
                                       EEEEC-TTTCHHHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklalaw 24 
                                       v+l G++G+GKT +++ la++ 
  gi|242398848|ref|YP_002994272.1| 178 VLLYGPPGCGKTLMAKALAHEV 199
                                       899***************9986 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 6.6
                                       SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH............HHHHH CS
                             NACHT  67 apvsevwavllelperlLlilDglDelvtdlgq...kekqpvrtlLseli 113
                                       + vse +++  e + ++++ +D +D + ++       ++++v++ L +l+
  gi|242398848|ref|YP_002994272.1| 221 RLVSELFELAREKAPSIVF-IDEIDAIGAKRLDettGGEREVNRTLMQLL 269
                                       5566666666666666666.477777665433334544455555555555 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   0.00054      0.23      24      47 ..     178     201 ..     173     256 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00054
                                       EEEEEETT--HHHHHHCC--TTS- CS
                   Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgp 47 
                                       v+l G++G+gk+l+A++L+++   
  gi|242398848|ref|YP_002994272.1| 178 VLLYGPPGCGKTLMAKALAHEVNA 201
                                       9*****************987544 PP

>> BAG  BAG domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.3         7     3e+03       9      37 ..      28      49 ..      14      55 .. 0.58
   2 ?   11.6   0.0   0.00065      0.28      31      52 ..     259     281 ..     212     288 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 7
                                      HHH.HHHHHHHHHHH..HHH..HHHHHHH CS
                               BAG  9 etllepeveafektvkkekeylylsElLl 37
                                      ++l e +v+++e+    +ke  +l+  L 
  gi|242398848|ref|YP_002994272.1| 28 RQL-ELQVRTLEA----DKE--RLERELS 49
                                      333.555555555....555..5554444 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00065
                                       H.HHHHHHHHHHHHHTCEESTHH CS
                               BAG  31 y.lsElLlklLlkLDsieiegde 52 
                                       + ++ +L++lL +LD+ +  g+ 
  gi|242398848|ref|YP_002994272.1| 259 ReVNRTLMQLLAELDGFDPMGEV 281
                                       3499***************9984 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 ?   11.5   0.0   0.00038      0.16      34      58 ..     176     200 ..     166     210 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00038
                             AAA_7  34 kpvllvGptGtGKtviikdllkkld 58 
                                       + vll+Gp G+GKt+++k l ++++
  gi|242398848|ref|YP_002994272.1| 176 RGVLLYGPPGCGKTLMAKALAHEVN 200
                                       679****************999988 PP

>> Not3  Not1 N-terminal domain, CCR4-Not complex component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00036      0.15     114     155 ..       9      50 ..       1      62 [. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00036
                              Not3 114 ldpkekekeearewlkdaideLneqvekleaeieklsskkkk 155
                                       ++ +e+e ++   +lk+ i++L+ qv +lea+ e+l+++ ++
  gi|242398848|ref|YP_002994272.1|   9 VKSHEEEYDDYVYYLKRRIRQLELQVRTLEADKERLERELSR 50 
                                       57889999****************************988765 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00041      0.18      21      48 ..     177     204 ..     146     232 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00041
                                       EEEEEESTTSSHHHHHHHHHHHTT---- CS
                              TsaE  21 vilLeGdLGaGKTtlvrglakalgveev 48 
                                        +lL+G+ G+GKT ++++la++++ + +
  gi|242398848|ref|YP_002994272.1| 177 GVLLYGPPGCGKTLMAKALAHEVNATFI 204
                                       39*******************9988733 PP

>> TSNAXIP1_N  Translin-associated factor X-interacting N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.2   0.00074      0.31      49      98 ..      14      60 ..      10      65 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00074
                        TSNAXIP1_N 49 kEYelyiahllesqreaqylkaklktlsessdkraleleekreelralek 98
                                      +EY++y+  l++++r+++++   ++tl++++++   el++ r e+++l++
  gi|242398848|ref|YP_002994272.1| 14 EEYDDYVYYLKRRIRQLELQ---VRTLEADKERLERELSRLRMEMSRLRQ 60
                                      7****************998...777777777777777777777888875 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0    0.0052       2.2      18      46 ..     173     201 ..     160     207 .. 0.84
   2 ?    1.2   0.0      0.42   1.8e+02     168     192 ..     229     253 ..     214     256 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0052
                        KAP_NTPase  18 atpivvgLygkWGsGKssllnkledelke 46 
                                       ++p  v Lyg+ G+GK+ + + l +e + 
  gi|242398848|ref|YP_002994272.1| 173 EPPRGVLLYGPPGCGKTLMAKALAHEVNA 201
                                       6777899******************9985 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.42
                        KAP_NTPase 168 LdalqkrlVvviDdLDrceteevlq 192
                                       L++++ + +v+iD++D +  +++ +
  gi|242398848|ref|YP_002994272.1| 229 LAREKAPSIVFIDEIDAIGAKRLDE 253
                                       44478899********998888776 PP

>> LURAP  Leucine rich adaptor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.3    0.0018      0.78       6      32 ..      33      59 ..      28      63 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0018
                             LURAP  6 krrskeselkrleeklrklklelanlr 32
                                      + r+ e++++rle  l  l++e++ lr
  gi|242398848|ref|YP_002994272.1| 33 QVRTLEADKERLERELSRLRMEMSRLR 59
                                      5677899*******************9 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.9   0.00035      0.15      48      96 ..      12      60 ..       2      63 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00035
                            APG6_N 48 eleeleeeleklekeeeelleeLkelekereeleaelaaleeelealee 96
                                       +ee ++ +  l++  ++l+ + + le+ +e+le+el+ l+ e ++l +
  gi|242398848|ref|YP_002994272.1| 12 HEEEYDDYVYYLKRRIRQLELQVRTLEADKERLERELSRLRMEMSRLRQ 60
                                      2233333344477777777777777777777777777777777776654 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.4     0.001      0.44      64      99 ..      20      55 ..      12      60 .. 0.84
   2 ?   -1.8   0.0       7.3   3.1e+03      38      50 ..      69      81 ..      65      88 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.001
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2 64 keeLeerketlekeiktlekqleklekeleelkeel 99
                                         L+ r+ +le +++tle  +e+le+el+ l+ e 
  gi|242398848|ref|YP_002994272.1| 20 VYYLKRRIRQLELQVRTLEADKERLERELSRLRMEM 55
                                      5569999**********************9999765 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 7.3
                                      HHHS-TT--EEEE CS
                       Prefoldin_2 38 lelldedtkvykl 50
                                      +ellded+ + ++
  gi|242398848|ref|YP_002994272.1| 69 IELLDEDRAIVQN 81
                                      89*****887655 PP

>> HALZ  Homeobox associated leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   2.4   0.00044      0.19       9      40 ..      22      53 ..      13      56 .. 0.89
   2 ?    0.6   0.1       1.6   6.7e+02      31      41 ..     146     156 ..     141     158 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00044
                              HALZ  9 vLKasYdaLksdydsLkkenekLkaelqeLke 40
                                      +LK++  +L +++  L++++e+L+ el +L+ 
  gi|242398848|ref|YP_002994272.1| 22 YLKRRIRQLELQVRTLEADKERLERELSRLRM 53
                                      6999999***********************96 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 1.6
                              HALZ  31 LkaelqeLkek 41 
                                       Lk++l eL+e 
  gi|242398848|ref|YP_002994272.1| 146 LKKQLVELREA 156
                                       9*******996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1051  (0.0586201); expected 358.6 (0.02)
Passed bias filter:                      918  (0.051202); expected 358.6 (0.02)
Passed Vit filter:                       225  (0.0125495); 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: 0.71u 0.36s 00:00:01.06 Elapsed: 00:00:00.48
# Mc/sec: 2530.35
//
Query:       gi|242398849|ref|YP_002994273.1|  [L=179]
Description: hypothetical protein TSIB_0863 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1389.27
//
Query:       gi|242398850|ref|YP_002994274.1|  [L=186]
Description: transcription regulator, containing CBS domains [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.1e-19   68.5   0.2    1.6e-09   38.1   0.0    2.3  2  CBS             CBS domain
    6.4e-15   55.0   0.4    1.8e-14   53.5   0.3    1.8  2  HTH_3           Helix-turn-helix
    1.1e-12   47.7   0.5    2.3e-12   46.7   0.3    1.7  2  HTH_19          Helix-turn-helix domain
    2.4e-12   47.0   0.0    3.6e-12   46.5   0.0    1.2  1  HTH_31          Helix-turn-helix domain
    4.7e-05   23.3   0.1     0.0002   21.2   0.1    1.9  2  HTH_37          Helix-turn-helix domain
    0.00011   22.5   0.0    0.00024   21.4   0.0    1.6  1  HTH_26          Cro/C1-type HTH DNA-binding domain
    0.00024   21.2   0.0    0.00057   20.0   0.0    1.5  1  MqsA_antitoxin  Antitoxin component of bacterial toxin-antito
    0.00073   19.3   0.1     0.0013   18.5   0.1    1.4  1  HTH_25          Helix-turn-helix domain
  ------ inclusion threshold ------
      0.017   15.1   0.0       0.42   10.6   0.0    2.5  2  HTH_Crp_2       Crp-like helix-turn-helix domain
      0.083   12.9   0.1        9.6    6.3   0.0    2.4  2  Put_DNA-bind_N  Putative DNA-binding protein N-terminus


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 !   38.1   0.0   8.7e-13   1.6e-09       1      54 [.      70     122 ..      70     125 .. 0.92
   2 !   28.4   0.0   9.1e-10   1.6e-06       2      53 ..     135     184 ..     134     186 .] 0.92

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 8.7e-13
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54 
                                       ++++m+++++ v+p +t+e +++lm e+++s++PV+   +k+vG +t++ l+r+
  gi|242398850|ref|YP_002994274.1|  70 AKELMSSPIIGVKPYETVEYVVKLMNEYNISQVPVIA-GNKVVGSITEKTLVRK 122
                                       589*********************************5.456*********9986 PP

  == domain 2  score: 28.4 bits;  conditional E-value: 9.1e-10
                                       HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEE.ETTTBEEEEEEHHHHHH CS
                               CBS   2 gdimtrdvvtvppdttleealelmrekgvsrlPVV.dedgklvGivtlrDllr 53 
                                        +im  +++ v++ +++e +  l++e  + ++ +V + +gk+ Gi+t++Dl++
  gi|242398850|ref|YP_002994274.1| 135 MEIMDGPFPIVNEYESIEVVKYLLEE--HPAI-IVqNREGKPEGIITRSDLFK 184
                                       589999******************66..78**.***9**************86 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.5   0.3     1e-17   1.8e-14       1      49 [.      13      61 ..      13      66 .. 0.96
   2 ?   -1.9   0.0       2.1   3.7e+03      38      51 ..      87     100 ..      86     101 .. 0.64

  Alignments for each domain:
  == domain 1  score: 53.5 bits;  conditional E-value: 1e-17
                                      HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHT CS
                             HTH_3  1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLg 49
                                      +k+ Rk+lg++qeeLA+++Gv++++i+++E G+  P+l+t  ++++aL+
  gi|242398850|ref|YP_002994274.1| 13 IKRFRKELGITQEELAQRAGVTQAYIAKLETGKVDPRLSTFNRILQALK 61
                                      89*********************************************97 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.1
                                       HHHHHHHHHHHTSE CS
                             HTH_3  38 letlkklakaLgvs 51 
                                       +e ++kl + +++s
  gi|242398850|ref|YP_002994274.1|  87 VEYVVKLMNEYNIS 100
                                       56677777777665 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.7   0.3   1.3e-15   2.3e-12       4      53 ..      13      61 ..      11      73 .. 0.96
   2 ?   -3.2   0.0       5.1   9.2e+03      46      57 ..      91     102 ..      83     109 .. 0.64

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 1.3e-15
                            HTH_19  4 LkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealg 53
                                      +k++R+elg+tqeela+r+g+++++i+++E+gk  +p  +++++i++al+
  gi|242398850|ref|YP_002994274.1| 13 IKRFRKELGITQEELAQRAGVTQAYIAKLETGKV-DPRLSTFNRILQALK 61
                                      89******************************99.*************98 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 5.1
                            HTH_19  46 lkiaealgidle 57 
                                        k+ ++++i+  
  gi|242398850|ref|YP_002994274.1|  91 VKLMNEYNISQV 102
                                       566677777655 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.5   0.0     2e-15   3.6e-12       6      54 ..      13      60 ..      11      62 .. 0.95

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 2e-15
                            HTH_31  6 LralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaral 54
                                       +++R++ G++qee+A+r+gv+++++ +lE+G+ + p++++ +++++al
  gi|242398850|ref|YP_002994274.1| 13 IKRFRKELGITQEELAQRAGVTQAYIAKLETGKVD-PRLSTFNRILQAL 60
                                      689*******************************7.************9 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.1   1.1e-07    0.0002      22      57 ..      12      47 ..      10      62 .. 0.89
   2 ?   -0.5   0.0      0.71   1.3e+03      49      66 ..      58      75 ..      54      76 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.1e-07
                                      HHHHHHHHCT--HHHHHHHHT--HHHHHHHHTT--T CS
                            HTH_37 22 aiaeliekrelsqseaaqllgiaqPkvsrllrgkls 57
                                      +i++++++++++q+e+aq+ g++q+ + +l+ gk++
  gi|242398850|ref|YP_002994274.1| 12 EIKRFRKELGITQEELAQRAGVTQAYIAKLETGKVD 47
                                      79*******************************986 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.71
                                      HHHHTT--TT--HHHHHH CS
                            HTH_37 49 srllrgklsrfsldkLln 66
                                       +l+  k srf+ + L++
  gi|242398850|ref|YP_002994274.1| 58 QALKECKKSRFTAKELMS 75
                                      679999999***999996 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   1.4e-07   0.00024       3      51 ..      14      61 ..      12      64 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.4e-07
                            HTH_26  3 relmadrgitkseLargtgisaatlsrlvkgkpervsldtLdkiCdaLg 51
                                      ++  ++ git+ eLa+++g+++a +++l +gk+  ++l+t ++i +aL+
  gi|242398850|ref|YP_002994274.1| 14 KRFRKELGITQEELAQRAGVTQAYIAKLETGKV-DPRLSTFNRILQALK 61
                                      6667888*************************6.*************96 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 !   20.0   0.0   3.2e-07   0.00057      69     115 ..       8      54 ..       3      64 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 3.2e-07
                    MqsA_antitoxin  69 vdpafiarvrkkleldqreaaeifGgGvnafsryekGkvrpplalvk 115
                                       +dp++i+r rk+l+++q+e+a+  G+     ++ e+Gkv p l++ +
  gi|242398850|ref|YP_002994274.1|   8 IDPKEIKRFRKELGITQEELAQRAGVTQAYIAKLETGKVDPRLSTFN 54 
                                       79************************99999***********99763 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1   7.5e-07    0.0013       3      36 ..      14      47 ..      12      48 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 7.5e-07
                                      HHHHHTTT--HHHHHHHSS--HHHHHHHHCT--T CS
                            HTH_25  3 raaRearglsleevaketkIrkdylealEeddfd 36
                                      ++ R+++g++ ee+a++  + ++y+ +lE +++d
  gi|242398850|ref|YP_002994274.1| 14 KRFRKELGITQEELAQRAGVTQAYIAKLETGKVD 47
                                      678***************************9875 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00023      0.42      18      37 ..      18      37 ..       7      41 .. 0.82
   2 ?    1.5   0.0      0.17   3.1e+02      36      47 ..      51      62 ..      49      64 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00023
                                      EEEEHHHHHHHHHTTSSHHH CS
                         HTH_Crp_2 18 ielpltqeelAsmlGltret 37
                                       el +tqeelA++ G+t+  
  gi|242398850|ref|YP_002994274.1| 18 KELGITQEELAQRAGVTQAY 37
                                      4799*************865 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.17
                                      HHHHHHHHHHHH CS
                         HTH_Crp_2 36 etvsrilseLkr 47
                                      +t++ril++Lk+
  gi|242398850|ref|YP_002994274.1| 51 STFNRILQALKE 62
                                      699*******97 PP

>> Put_DNA-bind_N  Putative DNA-binding protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.026        46      31      46 ..      25      40 ..      17      40 .. 0.87
   2 ?    6.3   0.0    0.0053       9.6       9      33 ..      49      73 ..      45      79 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.026
                                      HHHHHHCTS-HHHHHH CS
                    Put_DNA-bind_N 31 teLaealgvtaaqvRK 46
                                      +eLa+++gvt a + K
  gi|242398850|ref|YP_002994274.1| 25 EELAQRAGVTQAYIAK 40
                                      89*********99877 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0053
                                      HHHHHHHHHHHHHHTT--EE-HHHH CS
                    Put_DNA-bind_N  9 RLplYlryLeelkeegveriSSteL 33
                                      RL+++ r+L++lke +++r  ++eL
  gi|242398850|ref|YP_002994274.1| 49 RLSTFNRILQALKECKKSRFTAKEL 73
                                      9*************99999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       662  (0.0369234); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1204.68
//
Query:       gi|242398851|ref|YP_002994275.1|  [L=174]
Description: hypothetical protein TSIB_0865 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.17   12.5   0.2       0.64   10.6   0.0    2.0  3  FliG_N    FliG N-terminal domain
        1.3    8.7   9.8       0.85    9.2   0.2    2.9  3  Arm_3     Atypical Arm repeat


Domain annotation for each model (and alignments):
>> FliG_N  FliG N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0      0.97   8.7e+03      68      77 ..      19      28 ..       6      41 .. 0.55
   2 ?   10.6   0.0   7.1e-05      0.64      52      88 ..      88     125 ..      78     137 .. 0.89
   3 ?   -1.9   0.0      0.56   5.1e+03      42      61 ..     151     170 ..     146     173 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.97
                                      HCHHHHHHHH CS
                            FliG_N 68 seggeeyare 77
                                      +++ ee++ +
  gi|242398851|ref|YP_002994275.1| 19 FNDEEEFVAD 28
                                      4444444443 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 7.1e-05
                                       HHHHHHHHHHHCC.CCHHCHHHHHHHHHHHHHHSHHHH CS
                            FliG_N  52 aVleefleeleaq.eylseggeeyarelLekalgeeka 88 
                                       ++le++ +e+e++ e+l+++ ++y  e+L+ alge+++
  gi|242398851|ref|YP_002994275.1|  88 KILEQYFDEMESRwEDLTTDEINYFVEMLNDALGEHRV 125
                                       78999888886666*********************986 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.56
                                       HTTXXHHHHHHHHHHHHHHH CS
                            FliG_N  42 lksvskeeveaVleefleel 61 
                                       l++v  +e  +Vl+e +++l
  gi|242398851|ref|YP_002994275.1| 151 LENVVDSEDRHVLDEAVSIL 170
                                       67777778888999888776 PP

>> Arm_3  Atypical Arm repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.8       0.4   3.6e+03      39      49 ..      19      31 ..      19      34 .. 0.61
   2 ?    9.2   0.2   9.5e-05      0.85      32      47 ..      87     103 ..      86     108 .. 0.75
   3 ?    5.5   0.2    0.0014        13      10      38 ..     145     173 ..     139     174 .] 0.89

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.4
                             Arm_3 39 Fseeeee..ddee 49
                                      F++eee+  d ee
  gi|242398851|ref|YP_002994275.1| 19 FNDEEEFvaDMEE 31
                                      7888777744333 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 9.5e-05
                             Arm_3  32 lkIiekYFseeeee.dd 47 
                                       lkI+e+YF+e e   +d
  gi|242398851|ref|YP_002994275.1|  87 LKILEQYFDEMESRwED 103
                                       79********9654544 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.0014
                             Arm_3  10 agGldkIeaLQnheneeIYkkAlkIiekY 38 
                                       + Gl  +e+  ++e+  + + A+ I++kY
  gi|242398851|ref|YP_002994275.1| 145 IKGLYYLENVVDSEDRHVLDEAVSILTKY 173
                                       67889999999****************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); 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: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1090.66
//
Query:       gi|242398852|ref|YP_002994276.1|  [L=85]
Description: hypothetical protein TSIB_0866 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); 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: 0.44u 0.31s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 543.88
//
Query:       gi|242398853|ref|YP_002994277.1|  [L=251]
Description: Organic radical activating enzyme, radical SAM superfamily [Thermococcus sibiricus MM 739]
Scores for 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   56.3   0.0    6.4e-15   55.9   0.0    1.1  1  Radical_SAM  Radical SAM superfamily
    1.9e-09   37.7   0.0    4.7e-09   36.4   0.0    1.7  1  Fer4_14      4Fe-4S single cluster domain
    3.9e-09   36.9   0.0    6.2e-09   36.3   0.0    1.3  1  Fer4_12      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.9   0.0   1.1e-18   6.4e-15       2     166 ..      29     200 ..      28     201 .. 0.89

  Alignments for each domain:
  == domain 1  score: 55.9 bits;  conditional E-value: 1.1e-18
                                       EEESEESS--TTTSCCTT.................HHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGS CS
                                       xxxxxxxxxxxxxxxxxx.................xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpet.................vrregrgrslsveeileevkelkaekg.vkevilgggeplly 60 
                                       v + gC l+C++C+                     ++ e+++     ee++  +  l    g ++ +  +ggep+l+
  gi|242398853|ref|YP_002994277.1|  29 VRFAGCDLKCWWCDSANYiiaskvpkwryevepftGKFEYKPNPANFEEVVSAILHLD--TGdIHSISYTGGEPTLQ 103
                                       6789************99*************999888888888888888888888884..555************** PP

                                       TTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  61 pdfvellerlaklavpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealekl 137
                                        +    l + +++   g+++++etng +  +e +  ++ l  d+ s++++ a+ +   +   ++  ++ev e++++l
  gi|242398853|ref|YP_002994277.1| 104 TRNLSTLMKKMHE--LGFKNFLETNGSR--PERINDIAHLV-DYASVDIKDATAR-ATEDW-KNLVLKEV-ESIRIL 172
                                       9999999888888..6************..69999999988.*************.88888.65566666.****** PP

                                       HHTTSETEEEEEEEBTTTSHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 138 reagikrvvdrivglpGendeeleellel 166
                                       +++g+k ++  +v+  +  +e+++ +++l
  gi|242398853|ref|YP_002994277.1| 173 KRSGVK-TYAKLVVTQNTKEEDVKWYAKL 200
                                       ******.9********9999999988877 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 !   36.4   0.0   7.9e-13   4.7e-09       1      92 [.      27     130 ..      27     147 .. 0.83

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 7.9e-13
                           Fer4_14   1 lfvrlsgCnlsCkgCd...................nketwkselgkpqteelleqilkdlkkseikiqglvltGGeP 58 
                                       +fvr++gC l+C +Cd                    + +++ + ++ + ee++++il +l+  +i  + ++ tGGeP
  gi|242398853|ref|YP_002994277.1|  27 IFVRFAGCDLKCWWCDsanyiiaskvpkwryevepFTGKFEYKPNPANFEEVVSAIL-HLDTGDI--HSISYTGGEP 100
                                       7***************99999999877777777665555666778888899998888.6777777..88******** PP

                           Fer4_14  59 Lhyenkkellklvkrlkeeypekkiwletngtle 92 
                                           ++++l +l+k+++e +  +k  letng+  
  gi|242398853|ref|YP_002994277.1| 101 T--LQTRNLSTLMKKMHELG--FKNFLETNGSRP 130
                                       9..78*************99..999999999765 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 !   36.3   0.0     1e-12   6.2e-09       8     114 ..      27     146 ..      11     167 .. 0.77

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 1e-12
                           Fer4_12   8 lslfvsgCnlsCkgCfnketw.................sfk.sgkeftkelleeiiedlkkesiegltllGGEPllp 66 
                                       ++++++gC+l+C  C   +                   +f+ + ++ ++e    +i +l+   i  ++++GGEP l 
  gi|242398853|ref|YP_002994277.1|  27 IFVRFAGCDLKCWWCDSANYIiaskvpkwryevepftgKFEyKPNPANFEEVVSAILHLDTGDIHSISYTGGEPTL- 102
                                       6899***********9888887788888888777554444423344466666667778889999************. PP

                           Fer4_12  67 enaeallelvkevkeekpekdiwlytgytleelskkekeellkeidvl 114
                                        +++ l  l+k++ e ++ k+ ++++g+  e ++  +   l+++  v 
  gi|242398853|ref|YP_002994277.1| 103 -QTRNLSTLMKKMHELGF-KNFLETNGSRPERIN--DIAHLVDYASVD 146
                                       .*****************.79**********998..466666666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); 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: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 1463.78
//
Query:       gi|242398854|ref|YP_002994278.1|  [L=37]
Description: hypothetical protein TSIB_0868 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.44
# Mc/sec: 251.47
//
Query:       gi|242398855|ref|YP_002994279.1|  [L=813]
Description: ATPase, DUF699 family, fused to acetyltransferase domain [Thermococcus sibiricus MM 739]
Scores for complete 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-54  183.8   0.0    4.7e-54  182.9   0.0    1.5  1  Helicase_RecD    Helicase
    9.1e-49  165.9   0.0    2.2e-34  118.8   0.0    2.4  2  GNAT_acetyltr_2  GNAT acetyltransferase 2
    2.8e-34  116.9   0.0    1.3e-33  114.8   0.0    2.2  2  DUF1726          Domain of unknown function (DUF1726)
    0.00018   21.3   0.0    0.00082   19.1   0.1    2.1  2  tRNA_bind_2      Possible tRNA binding domain
  ------ inclusion threshold ------
       0.04   13.3   0.0      0.064   12.7   0.0    1.2  1  DUF92            Integral membrane protein DUF92
       0.15   12.4   0.0        6.4    7.0   0.0    3.1  3  AAA_22           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 !  182.9   0.0   1.6e-57   4.7e-54       1     177 []     286     460 ..     286     460 .. 0.94

  Alignments for each domain:
  == domain 1  score: 182.9 bits;  conditional E-value: 1.6e-57
                     Helicase_RecD   1 vltAdRGRGKSaalGlalaaliaegk...snilvtapskenvktlfeflakglealglkeeekkkkaekaelrvrkq 74 
                                       vltAdRGRGKS  +G+    l+ ++k   ++i+vtap+ env++lf+f++k+l++lg+k +  ++++  +e+ +++ 
  gi|242398855|ref|YP_002994279.1| 286 VLTADRGRGKSVSVGIGSIGLAVKSKkkrVRIVVTAPELENVQSLFRFAKKSLQKLGYKPKVIEENSLIKEIYAKGI 362
                                       79**************98887766666789******************************999999999******** PP

                     Helicase_RecD  75 rieyiapdellklkeqadllvvDEAAaiplpllkkllekfkrvvlatTvhGYEGtGrgfslkflkqlkkekkrelre 151
                                        ++y++p++  + +  ad+ v+DEAA i++p+l+k+l ++++v++++T+hGYEG+Grgfs+kflk+ ++  kre++e
  gi|242398855|ref|YP_002994279.1| 363 GLRYYPPTQGYNMN--ADVYVIDEAAGIHVPILHKYL-NKPKVIYSSTIHGYEGAGRGFSVKFLKKARN--KREFKE 434
                                       **********9975..7********************.777*************************764..558*** PP

                     Helicase_RecD 152 leleepiRyaegdplEkwlndlLlLd 177
                                       ++l+ piRy+++dp+E+wl+d+LlLd
  gi|242398855|ref|YP_002994279.1| 435 IHLSVPIRYESNDPIERWLFDVLLLD 460
                                       ************************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 !  118.8   0.0   7.4e-38   2.2e-34       3     123 ..     501     614 ..     499     618 .. 0.93
   2 !   45.7   0.0   1.7e-15   5.2e-12     174     226 ..     614     666 ..     612     667 .. 0.94

  Alignments for each domain:
  == domain 1  score: 118.8 bits;  conditional E-value: 7.4e-38
                   GNAT_acetyltr_2   3 vallvssHYknsPnDLqllsDaPahklfvLlapkkekkklpevlcvvqvalEGkiskesvknslsrgkrasGdlipw 79 
                                       v+++v +HY+n+P D++ll+DaP+h+  vL  ++       +++c+vq+a EG i k+ ++++ ++g +++G++ip+
  gi|242398855|ref|YP_002994279.1| 501 VGIYVLAHYRNKPSDVALLADAPHHEARVLRLKNG------KIVCAVQIAKEGGIPKKDIDKM-AKGYKPRGNIIPD 570
                                       789***************************99665......8****************99875.6778********* PP

                   GNAT_acetyltr_2  80 tlsqqfqdeefaslsGaRivRiAvhpelqkmGYGsralelleky 123
                                       ++ +++ ++efa+l+G R+vRiA+hp+++ mG Gsralell+ +
  gi|242398855|ref|YP_002994279.1| 571 MMVKHHYSKEFARLKGYRVVRIATHPDAMDMGLGSRALELLIYE 614
                                       ****************************************9865 PP

  == domain 2  score: 45.7 bits;  conditional E-value: 1.7e-15
                   GNAT_acetyltr_2 174 eekpekldylgvsfGltseLlkFWkragfspvylrqtaneltGEhsaimlrsl 226
                                       e++ e+ d++g +fG ++eL++FW r+gf+pv+l+ ++n ++GE++ai+++++
  gi|242398855|ref|YP_002994279.1| 614 EADKENFDWVGSGFGASEELIRFWIRNGFAPVHLSPSRNPVSGEYTAIVIKPI 666
                                       5678999*******************************************987 PP

>> DUF1726  Domain of unknown function (DUF1726)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.8   0.0   4.3e-37   1.3e-33       2      93 .]     130     222 ..     129     222 .. 0.98
   2 ?   -4.0   0.0       4.9   1.5e+04      66      81 ..     570     583 ..     553     584 .. 0.69

  Alignments for each domain:
  == domain 1  score: 114.8 bits;  conditional E-value: 4.3e-37
                           DUF1726   2 kesekvLGqtydllvldlfealtPnalgrlvetVrGGGliilllppleelkqlytdfhkklvveplt.eevkkrfnk 77 
                                       k ++ +LG+tydllvldl  +++Pn+lgr++etVrGGGli++l++p+e++k+++t fhk+lv++p+t ++vkkrfn+
  gi|242398855|ref|YP_002994279.1| 130 KYTRDILGRTYDLLVLDLSYDFSPNDLGRIIETVRGGGLIFVLANPFEKWKKMWTGFHKSLVTPPYTiDDVKKRFNR 206
                                       67999************************************************************************ PP

                           DUF1726  78 rfirklkehegilivd 93 
                                       r+irkl+e eg++i+d
  gi|242398855|ref|YP_002994279.1| 207 RLIRKLEEQEGVYILD 222
                                       *************987 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 4.9
                           DUF1726  66 plteevkkrfnkrfir 81 
                                       ++   vk+++ k f r
  gi|242398855|ref|YP_002994279.1| 570 DM--MVKHHYSKEFAR 583
                                       34..699999999876 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 ?   -3.1   0.0       1.7     5e+03       6      23 ..      36      53 ..      32      58 .. 0.80
   2 !   19.1   0.1   2.8e-07   0.00082      61     128 ..     720     786 ..     676     811 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.7
                                      HHHHHHHHHHHHHHHSS- CS
                       tRNA_bind_2  6 akdFrkRflsLLsyqFrk 23
                                      ++ F++R++ L s + +k
  gi|242398855|ref|YP_002994279.1| 36 IEGFHRRIIVLASDTMKK 53
                                      567********9988776 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 2.8e-07
                                       -HHHHHHHHHHHHS---HHHHHSSSSHHHHHHHH--SSTTTS-SSSSSSHHHHHHTT---HHHHHHHH CS
                       tRNA_bind_2  61 spfDlkRLesYannllDYhvilDllptlaklyFsgrlkeevkLsavqsaiLlaiGLQrksvddlekeL 128
                                       ++   kRLe++  ++l Y  +lD ++ + klyF +    +  L++ q  +L+   LQ+++ ++ +k +
  gi|242398855|ref|YP_002994279.1| 720 TEVQKKRLEMFVGKVLTYDTVLDAVKPIVKLYFLDGWM-KPYLDERQIHLLIYRVLQSHTWEETAKLI 786
                                       56667****************************99988.899*****************999988765 PP

>> DUF92  Integral membrane protein DUF92
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.1e-05     0.064     168     233 ..      50     128 ..      28     130 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.1e-05
                             DUF92 168 llellillltlaGllGsllDSlLGatlqasvvdkrtgkvvegegge.............kvvsGldlLdNnaVNlls 231
                                       ++++++l+++l G+ + ++ S+LG ++ ++++d+++ kv    +++             +  + +d+L  ++VN+ s
  gi|242398855|ref|YP_002994279.1|  50 TMKKATLAGILGGASAKIISSILGELVKKKLRDESEDKVEMLYATDalgpetfgrmryeEFRKHFDILAGDNVNVTS 126
                                       3344889999********************999988887766555589999*****999777889*********998 PP

                             DUF92 232 al 233
                                        +
  gi|242398855|ref|YP_002994279.1| 127 VT 128
                                       65 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0         1   3.1e+03      41      98 ..     167     222 ..     154     223 .. 0.78
   2 ?    7.0   0.0    0.0021       6.4       4     101 ..     281     386 ..     277     405 .. 0.64
   3 ?    0.9   0.0      0.18   5.2e+02       8      35 ..     406     433 ..     401     450 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1
                            AAA_22  41 evvfvtlpsstsskdllrellralglelkaerlsseellealeqalraravielliiD 98 
                                       +++fv ++  +++k++++ + + l  +  +  + ++++ ++l + l+++    + i+D
  gi|242398855|ref|YP_002994279.1| 167 GLIFVLANPFEKWKKMWTGFHKSLVTPPYTIDDVKKRFNRRLIRKLEEQEG--VYILD 222
                                       567888888889999999999999999998666666666888888888876..77777 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0021
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka.....erlss 75 
                                       ++g++v+t+  G GK++++      l   +k   +++  + vt+p++++ ++l+r   + l+  + +     e    
  gi|242398855|ref|YP_002994279.1| 281 RDGMIVLTADRGRGKSVSVGIGSIGLAVKSK---KKRVRIVVTAPELENVQSLFRFAKKSLQKLGYKpkvieE---- 350
                                       789**************98655555522211...255556888888888888888888888877776544330.... PP

                            AAA_22  76 eellealeqalrarav..........ielliiDEaq 101
                                         l++ ++      +             + +iDEa 
  gi|242398855|ref|YP_002994279.1| 351 NSLIKEIYAKGIGLRYypptqgynmnADVYVIDEAA 386
                                       223333333333333344455555577777777775 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.18
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeaka 35 
                                        +++G  G+G+ ++++ l++  +++++ 
  gi|242398855|ref|YP_002994279.1| 406 STIHGYEGAGRGFSVKFLKKARNKREFK 433
                                       589****************998877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (813 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      575  (0.0320709); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.80u 0.33s 00:00:01.13 Elapsed: 00:00:00.51
# Mc/sec: 4833.86
//
Query:       gi|242398856|ref|YP_002994280.1|  [L=153]
Description: hypothetical protein TSIB_0871 [Thermococcus sibiricus MM 739]
Scores for complete 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-41  139.9   1.0    6.3e-41  139.7   1.0    1.0  1  DUF1931        Domain of unknown function (DUF1931)
  ------ inclusion threshold ------
       0.02   14.7   0.0      0.026   14.4   0.0    1.2  1  MvaI_BcnI      MvaI/BcnI restriction endonuclease family
      0.059   13.7   0.4       0.46   10.8   0.2    2.2  2  CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) a
       0.13   11.6   0.0        0.3   10.4   0.0    1.5  2  OST3_OST6      OST3 / OST6 family, transporter family


Domain annotation for each model (and alignments):
>> DUF1931  Domain of unknown function (DUF1931)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.7   1.0   1.4e-44   6.3e-41       1     138 []      11     150 ..      11     150 .. 0.99

  Alignments for each domain:
  == domain 1  score: 139.7 bits;  conditional E-value: 1.4e-44
                                       HHHHHHHHHS----HHHHHHHHHHHHHHHHHCCCCHHHHHHHTT-SEE-GGGS---HHHHHHHHHHHTT..TS--SH CS
                           DUF1931   1 lerlfreaagLdvdkedlkrisdfVekklydLllvaeenAkangrdviepaDLPiTkglqesireFrkl..eeelel 75 
                                       l+++++++++L + k  +++++ +Ve+kl dL++va+enA +++ ++i+ ++LP+Tkg+++s++ Fr++   e +e+
  gi|242398856|ref|YP_002994280.1|  11 LQKILEKTCELALIKPRAEEMMKIVERKLTDLFEVAYENAMSERSETIKLRHLPLTKGFKNSMNLFRAVieSEGVEI 87 
                                       689******************************************************************98899*** PP

                                       HHHHHHHTTS-S-SSEE-HHHHCCHHHHHHHHHHHHHHHHHHHSTTSSS--HHHHHHHHHHHH CS
                           DUF1931  76 eeileqlaalppldlelseeleaelpeivGgLsvalArvikaidpevknpqtehieraeevld 138
                                       ++i + +++ +p++++l+eel +elp ivG+L+v+++r+ika++pe++n+++ehie+a++vld
  gi|242398856|ref|YP_002994280.1|  88 DPIRKFILRGIPVEVPLEEELVNELPIIVGTLFVLVGRIIKALHPEIRNVYPEHIEEAQKVLD 150
                                       *************************************************************98 PP

>> MvaI_BcnI  MvaI/BcnI restriction endonuclease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   5.8e-06     0.026     142     201 ..      29      90 ..       9     101 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.8e-06
                         MvaI_BcnI 142 ekLkkklksKlknlfyvkadkkkeegkeyfkYkkikilknk..sfekFlklleegkItvdfr 201
                                       e+++k +++Kl+ lf v +++ ++e++e +k   + ++k++  s++ F   +e++ + +d+ 
  gi|242398856|ref|YP_002994280.1|  29 EEMMKIVERKLTDLFEVAYENAMSERSETIKLRHLPLTKGFknSMNLFRAVIESEGVEIDPI 90 
                                       788999********************************987336789*************93 PP

>> CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) and archaeal histone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2    0.0001      0.46       4      61 ..       7      63 ..       4      66 .. 0.81
   2 ?    0.7   0.0      0.14   6.5e+02       8      22 ..     123     138 ..     122     150 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0001
                                      XHHHHHHHHHCCTTXS-B-HHHHHHHHHHHHHHHHHHHHHHHHHHCCTTSSCE-HHHH CS
                     CBFD_NFYB_HMF  4 PiarvkkImksdpdarkiakdAkeliaecveefieelaseAaeickkekrKtikaehi 61
                                      P  + +kI+ ++ + + i   A e++ ++ve  +++l + A+e +  e+++tik  h+
  gi|242398856|ref|YP_002994280.1|  7 PFPQLQKILEKTCELALIKPRAEEMM-KIVERKLTDLFEVAYENAMSERSETIKLRHL 63
                                      55566777777766666777776655.9****************************98 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.14
                                       HHHHHHCC.TTXS-B- CS
                     CBFD_NFYB_HMF   8 vkkImksd.pdarkia 22 
                                       v +I+k   p++r++ 
  gi|242398856|ref|YP_002994280.1| 123 VGRIIKALhPEIRNVY 138
                                       6788888877777764 PP

>> OST3_OST6  OST3 / OST6 family, transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.34   1.5e+03     125     150 ..      27      52 ..      12      60 .. 0.78
   2 ?   10.4   0.0   6.6e-05       0.3      99     173 ..      60     134 ..      56     142 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.34
                         OST3_OST6 125 daealakfisertgvkirikrppnys 150
                                       +ae+++k +++++   +++  +  +s
  gi|242398856|ref|YP_002994280.1|  27 RAEEMMKIVERKLTDLFEVAYENAMS 52 
                                       79999999999999888888777666 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 6.6e-05
                         OST3_OST6  99 lllfppkkgpkeskkkdtydfsrggfdaealakfisertgvkirikrppnyskiiitallvlllvlllklrrkll 173
                                       l + p +kg k+s +  +  ++++g + + + kfi + ++v+++++++   +  ii+ +l++l++ ++k  ++ +
  gi|242398856|ref|YP_002994280.1|  60 LRHLPLTKGFKNSMNLFRAVIESEGVEIDPIRKFILRGIPVEVPLEEELVNELPIIVGTLFVLVGRIIKALHPEI 134
                                       5677777777766688888899999********************************************999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); 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: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1016.63
//
Query:       gi|242398857|ref|YP_002994281.1|  [L=485]
Description: Phosphoenolpyruvate carboxylase [Thermococcus sibiricus MM 739]
Scores for complete 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-178  594.2   2.9   1.9e-178  594.0   2.9    1.0  1  PEPcase_2  Phosphoenolpyruvate carboxylase
  ------ inclusion threshold ------
      0.029   13.5   0.0      0.052   12.7   0.0    1.3  1  HpcH_HpaI  HpcH/HpaI aldolase/citrate lyase family


Domain annotation for each model (and alignments):
>> PEPcase_2  Phosphoenolpyruvate carboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  594.0   2.9  2.1e-182  1.9e-178       1     494 []      11     485 .]      11     485 .] 0.96

  Alignments for each domain:
  == domain 1  score: 594.0 bits;  conditional E-value: 2.1e-182
                                       --SEEEE--ST-.......SS--B-TTTHHHHHHHHHSS----EEEEE-SSB---TTHHHHHHHHHHC..TT--TTT CS
                         PEPcase_2   1 iprtmsTQHPDnakvPefaeeevisgedEveEAykalselgvdEvMwDfEGKevdehvvrkllseyeeffkekvlGe 77 
                                       iprtmsTQHPDn+ +P+fa+e+ + gedEv EA++a+s lgv+E+MwDfEGKevde+v++kll++y +ffk+k+lG+
  gi|242398857|ref|YP_002994281.1|  11 IPRTMSTQHPDNVYIPFFAHESSLGGEDEVLEAFYAFSVLGVQEQMWDFEGKEVDEFVIKKLLEKYGQFFKKKKLGR 87 
                                       9**************************************************************************** PP

                                       SSEEEEE---TTTS-HHHHHHHHHHHHHHHHH.HHHHH...SS-S-SEEEESS--SHHHHHHHHHHHHHHHH..... CS
                         PEPcase_2  78 dvfltlRvPnpkvEkaerkvlaetlesipnsydlaekf..eetkpifevilPmttsaeelievakyyekvvagkeel 152
                                       d+++t+RvPnp+vEkae+k+l+etlesip+s d+a+ f  ee++pifevilPmtts++e+ +v++ y++ + gk+ +
  gi|242398857|ref|YP_002994281.1|  88 DIRITPRVPNPSVEKAEAKLLLETLESIPRSADYAKLFygEEIAPIFEVILPMTTSSKEIERVYELYKRYIIGKQYK 164
                                       **************************************977************************************ PP

                                       ....HHHHH-SS---TTSSEEEEEE-SHHHHHTHHHHHHHHHHHT--SEEEEEEESHHHHHHH-HHHHHHHHHHHHH CS
                         PEPcase_2 153 eladlkvkelvgelkpesievIPLiEdkesllnideiveeyvkekklkelRvflarSDpAlnyGlisavllvkvAls 229
                                       +++d+k+ e++ge+ pe+i+vIPL+E+ke++ln++ei++ey++ k+ +++RvflarSDpA+nyGlisav++ k+Al+
  gi|242398857|ref|YP_002994281.1| 165 RVYDIKIYEWIGEFYPEEINVIPLFETKEAILNSHEILKEYLTGKNFEYQRVFLARSDPAMNYGLISAVIYDKYALF 241
                                       ***************************************************************************** PP

                                       HHHHHHHHHT-EEEEEEE-BSSGGGT---TTGHHHHHHHTTT-SEEEE-HHHHHTTHHHHHHHHHHHHHHGGG---- CS
                         PEPcase_2 230 elykleeelgvkiyPilGvGslpfRGhlspenveevleeYagvkTfTvQSafkYdyeeeevkeairkineaevkkpr 306
                                       ++ +leeel v+iyPi+GvGs+pfRGh+ penve++++eY++v+TfTvQS+fkYd + +ev++ai+k+ne+++kk+ 
  gi|242398857|ref|YP_002994281.1| 242 NIQELEEELSVPIYPIIGVGSAPFRGHFIPENVENTIKEYPNVQTFTVQSSFKYDNDPKEVIRAIEKVNERKRKKSA 318
                                       **********************************************************************9999999 PP

                                       ---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS---S-B----------EEE--HE---HHHHHHHHHHTT CS
                         PEPcase_2 307 elseeeeelllevieklseaYqekiekladvinevaklipkrRaRklhiglfgYsReieevelPRAIsftgalYsiG 383
                                        ++e     + ++ ek+ ++Y ++++ la+ i e+ak++p+rR+RklhiglfgYsR+i++  lPRAI+ft++lYs+G
  gi|242398857|ref|YP_002994281.1| 319 SVDEG----VFKILEKYEKEYTAELKLLAPYIREIAKFVPSRRKRKLHIGLFGYSRKINGEVLPRAIKFTASLYSLG 391
                                       99988....69****************************************************************** PP

                                       --GGGTTHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHTT--SSTTTTTS-HHHHHHHHHHHHHHHHHTT--HHHHHH CS
                         PEPcase_2 384 lPpellgissllelaeeelevllevykalkedlaeaarylnleksklkldeetvkkikedleiveeildlkyeeeeh 460
                                       +Ppellg+s+l   +e+++e l e y  l +dl++a++++n+++s++    +++ k+++++ i+ e        e+h
  gi|242398857|ref|YP_002994281.1| 392 VPPELLGLSTL---SEKDIEELAEYYYGLYRDLEFALKFFNPKTSQKFKFLNKIVKLQKEMGIEAE--------ERH 457
                                       ***********...99***************************77666555555577888887777........889 PP

                                       H-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTS-- CS
                         PEPcase_2 461 eeltsellkalkekkdeelkelilemaklRkflG 494
                                       ++lts++++   e      +++i+++a +R+flG
  gi|242398857|ref|YP_002994281.1| 458 QTLTSQIISGKFE------ESVIVQAADIRGFLG 485
                                       9888888875555......478***********9 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 ?   12.7   0.0   5.8e-06     0.052      88     159 ..     136     228 ..     131     233 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.8e-06
                                       EEESS--SHHHHHHHHHHTSHTTTS---...............HCCC-EEEEEE-SHHHHHTHHHHHTST......T CS
                         HpcH_HpaI  88 vlvPkvetaeealevvsalrepekgirg...............anketrllaqiEsaegvknaeeIaave......g 143
                                       v++P++++ +e++ v+++ ++   g                  + +e+ ++   E++e+++n +eI++        +
  gi|242398857|ref|YP_002994281.1| 136 VILPMTTSSKEIERVYELYKRYIIGKQYkrvydikiyewigefYPEEINVIPLFETKEAILNSHEILKEYltgknfE 212
                                       89***************99887745444889***********************************94333566667 PP

                                       EEEEEE-HHHHHHHTT CS
                         HpcH_HpaI 144 ldgvflGaeDlsadlg 159
                                        + vfl+ +D +++ g
  gi|242398857|ref|YP_002994281.1| 213 YQRVFLARSDPAMNYG 228
                                       7777777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (485 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       785  (0.0437838); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.69u 0.34s 00:00:01.03 Elapsed: 00:00:00.53
# Mc/sec: 2771.63
//
Query:       gi|242398858|ref|YP_002994282.1|  [L=501]
Description: Alpha-glucosidase [Thermococcus sibiricus MM 739]
Scores for complete 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-156  521.1   0.1   1.5e-156  520.8   0.1    1.1  1  DUF2139   Uncharacterized protein conserved in archaea (DUF21


Domain annotation for each model (and alignments):
>> DUF2139  Uncharacterized protein conserved in archaea (DUF2139)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  520.8   0.1  8.6e-161  1.5e-156       1     339 [.      41     374 ..      41     375 .. 0.99

  Alignments for each domain:
  == domain 1  score: 520.8 bits;  conditional E-value: 8.6e-161
                           DUF2139   1 lyytlafeaeahfikddsekiYrfelvGkaPtsGGDtYnaveavDdkiyfGGWvhaPavykgreekkaeisfknkYs 77 
                                       ly+tlafea+ahfi++ds+kiY+felvG++PtsGGDtYnave+vD++iyfGGWvhaPavy+g +++k++isf nkYs
  gi|242398858|ref|YP_002994282.1|  41 LYFTLAFEAQAHFIREDSKKIYEFELVGEKPTSGGDTYNAVETVDEFIYFGGWVHAPAVYEG-KNEKSTISFVNKYS 116
                                       8*************************************************************.78899********* PP

                           DUF2139  78 hvheydieekevkLlWkesihdeeeWagevseiiYdpledkLLlaraDGhanlGvyeidrktgearklsdkpalkGa 154
                                       hvh+yd+e++evkLlWk+sih++++Wagevs+iiYdp+edkLLlar+DGhanlG+ye drk+gea+ l+++p+lkGa
  gi|242398858|ref|YP_002994282.1| 117 HVHSYDTENDEVKLLWKDSIHHKTNWAGEVSDIIYDPYEDKLLLAREDGHANLGIYEADRKSGEAKCLNESPSLKGA 193
                                       ***************************************************************************** PP

                           DUF2139 155 lvldlacfdikedfkkgvegiecldliekkvvyeeledvekasvDgedvekresGavasaytrvfafvrGGilvgnP 231
                                       lv+d  +f++ ++f+ gv+++++ldli++k  +e+++   k ++Dg+++ ++  G+++say+rvfaf+rGG++vgnP
  gi|242398858|ref|YP_002994282.1| 194 LVHDAIFFGVGKNFELGVQELHVLDLITRK--WERFSIP-KSALDGHPIIRPVLGDMESAYNRVFAFTRGGVFVGNP 267
                                       ******************************..9999988.99*********************************** PP

                           DUF2139 232 veeeelrfvrllDfaetqyaplrsnalplgGGvlvafnaysealvrktneeeevvkkatntivgPsvLvYiaPpvak 308
                                       ++eee++f+rl+Df+ ++yap+r+nalp+gGG+l+a+na+++a++++ +++ + ++++tnti +Ps+L+Y++Pp++k
  gi|242398858|ref|YP_002994282.1| 268 LNEEEMKFARLFDFP-NFYAPMRVNALPIGGGLLIAYNAHHDAVYKPIDKNTKLMAEVTNTINAPSILLYVTPPMVK 343
                                       ***************.************************************************************* PP

                           DUF2139 309 ivgalGaritslekvgdkvllatnttpnler 339
                                       ivg++Garits+ek  +k+ll+tnttpn+++
  gi|242398858|ref|YP_002994282.1| 344 IVGVFGARITSIEKAFGKILLGTNTTPNTGA 374
                                       ****************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (501 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 3012.90
//
Query:       gi|242398859|ref|YP_002994283.1|  [L=90]
Description: hypothetical protein TSIB_0874 [Thermococcus sibiricus MM 739]
Scores for complete 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-31  105.9   0.4    9.9e-31  105.8   0.4    1.0  1  DUF3213   Protein of unknown function (DUF3213)


Domain annotation for each model (and alignments):
>> DUF3213  Protein of unknown function (DUF3213)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.8   0.4   5.5e-35   9.9e-31       1      83 [.       5      87 ..       5      88 .. 0.98

  Alignments for each domain:
  == domain 1  score: 105.8 bits;  conditional E-value: 5.5e-35
                                      EEE--S-TTTTTHHHHHTTTTTTTB------TTSS--EEE--B-S-SHHHHHHHT...TT-SS-------SS--XXXXX CS
                           DUF3213  1 dlkftdltpekakikqyelekdervyrvflngyakvaevvideekvnieelkkkleelkgevveekeltlqelieesls 79
                                      d+kf ++tpe+a+  qy+l  +  vyrvflngy+k +++++de+k+++ee+++ lee+k+e++ ek+lt  eli esls
  gi|242398859|ref|YP_002994283.1|  5 DFKFDNITPEEARRMQYKLAINLAVYRVFLNGYSKSGYIIFDESKLSREEILQMLEEFKPEIIREKTLTPDELIIESLS 83
                                      68***************************************************************************** PP

                                      XXXX CS
                           DUF3213 80 wnnv 83
                                      w n+
  gi|242398859|ref|YP_002994283.1| 84 WKNI 87
                                      **97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 608.63
//
Query:       gi|242398860|ref|YP_002994284.1|  [L=586]
Description: molybdenum cofactor biosynthesis protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-23   83.7   0.0    1.8e-23   83.7   0.0    2.6  2  Radical_SAM      Radical SAM superfamily
    5.5e-07   29.9   0.2    1.9e-06   28.2   0.0    2.1  2  Fer4_12          4Fe-4S single cluster domain
    1.4e-05   25.2   1.1      3e-05   24.1   0.0    2.1  2  Fer4_14          4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.077   13.0   0.1       0.54   10.3   0.1    2.3  2  PBS_linker_poly  Phycobilisome Linker polypeptide


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   1.5      0.92   4.1e+03       4      19 ..     120     135 ..     118     139 .. 0.83
   2 !   83.7   0.0     4e-27   1.8e-23       1     166 [.     142     301 ..     142     302 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.92
                                       ESEESS--TTTSCCTT CS
                                       xxxxxxxxxxxxxxxx RF
                       Radical_SAM   4 trgCnlrCsfCarpet 19 
                                       +  C+++C  C+r+++
  gi|242398860|ref|YP_002994284.1| 120 GVNCPFDCGLCPRHRS 135
                                       567**********974 PP

  == domain 2  score: 83.7 bits;  conditional E-value: 4e-27
                                       EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHH.HHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelk.aekg.vkevilgggepllypdfvellerlaklav 75 
                                       +v t+ Cnl C++C ++++   + ++++ ++e+i   ++ +k +e+  ++ v ++ggep+l++d++e+++ ++++  
  gi|242398860|ref|YP_002994284.1| 142 IVLTNRCNLSCWYCFFYHK--EGQPVYEPTLEQIRMMLRNAKsEEPIgANAVQFTGGEPSLRDDIIEIIKIAKEE-- 214
                                       6889**************6..*********************955555***************************.. PP

                                       CTEEEEEEECSSCHG..HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEE CS
                                       xxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  76 pgiritvetngtlpd..eeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdriv 150
                                          +i + t g++    +e ++r +e+gv++++l+ + ++++     +n ++ +e     +e+ r+ag++ +v + +
  gi|242398860|ref|YP_002994284.1| 215 GYDHIQFNTDGIRFAfePELVKRVREAGVNTFYLSFDGVTPK-----TNWKNHWEIP-LIFENVRKAGGPGIVLVPT 285
                                       9****************************************9.....6554444444.7899999************ PP

                                       EBTTTSHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxx RF
                       Radical_SAM 151 glpGendeeleellel 166
                                       +++++nd+e  +++++
  gi|242398860|ref|YP_002994284.1| 286 LIRNVNDHETGAIINF 301
                                       *******998777765 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 !   28.2   0.0   4.3e-10   1.9e-06       9      93 ..     142     223 ..     134     253 .. 0.82
   2 ?   -2.3   0.1       1.1   4.9e+03      78     103 ..     524     551 ..     519     568 .. 0.66

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 4.3e-10
                           Fer4_12   9 slfvsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesi......egltllGGEPllpenaeallelvkev 79 
                                       ++++++CnlsC +Cf       k+g+++ +++le+i   l + +       + + ++GGEP+l   +++++e++k  
  gi|242398860|ref|YP_002994284.1| 142 IVLTNRCNLSCWYCF----FYHKEGQPVYEPTLEQIRMMLRNAKSeepigaNAVQFTGGEPSL---RDDIIEIIKIA 211
                                       67899**********....6778899998888888777777644445678899**********...99********* PP

                           Fer4_12  80 keekpekdiwlytg 93 
                                       kee+++  ++ ++ 
  gi|242398860|ref|YP_002994284.1| 212 KEEGYD--HIQFNT 223
                                       ****95..454443 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.1
                           Fer4_12  78 evkeekpekdiwlytgytleelskk...e 103
                                       e+++ k  +  ++yt+  +++l ++   +
  gi|242398860|ref|YP_002994284.1| 524 ELYRDKT-QAQFSYTWEEWKKLHPDweyR 551
                                       5556665.467899999999998766542 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 ?   -3.0   0.7       1.8     8e+03       7      18 ..     122     133 ..     121     138 .. 0.79
   2 !   24.1   0.0   6.7e-09     3e-05       3      89 ..     143     225 ..     142     241 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.8
                           Fer4_14   7 gCnlsCkgCdnk 18 
                                        C++ C  C ++
  gi|242398860|ref|YP_002994284.1| 122 NCPFDCGLCPRH 133
                                       6********765 PP

  == domain 2  score: 24.1 bits;  conditional E-value: 6.7e-09
                           Fer4_14   3 vrlsgCnlsCkgCdnketwkselgkpqteelleqilk.dlkkseikiqglvltGGePLhyenkkellklvkrlkeey 78 
                                       v +++CnlsC  C+  ++  + + +p  e ++  +l+  ++++ i ++ + +tGGeP +    +++++++k  kee+
  gi|242398860|ref|YP_002994284.1| 143 VLTNRCNLSCWYCFFYHKEGQPVYEPTLE-QIRMMLRnAKSEEPIGANAVQFTGGEPSL---RDDIIEIIKIAKEEG 215
                                       4589**********766444444433333.33334443677788999**********84...589******999999 PP

                           Fer4_14  79 pekkiwletng 89 
                                          +i+++t g
  gi|242398860|ref|YP_002994284.1| 216 -YDHIQFNTDG 225
                                       .6679999987 PP

>> PBS_linker_poly  Phycobilisome Linker polypeptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.37   1.7e+03      72     101 ..     188     217 ..     175     220 .. 0.83
   2 ?   10.3   0.1   0.00012      0.54      37      62 ..     552     577 ..     519     581 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.37
                                       HHHHHHTSS--SSHHHHHHHHHHHHHCHHH CS
                   PBS_linker_poly  72 lafkhlLGRapesqaEiskyskilaekGle 101
                                        +  ++ G +p+ +++i++++ki +e+G++
  gi|242398860|ref|YP_002994284.1| 188 ANAVQFTGGEPSLRDDIIEIIKIAKEEGYD 217
                                       66778899999999**************97 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00012
                                       HTTSS-HHHHHHHHHCSHHHHHHHTT CS
                   PBS_linker_poly  37 kngeisvrefvralakSelYrkrfye 62 
                                       k++ +  +efv+++ kSelYrk++++
  gi|242398860|ref|YP_002994284.1| 552 KDKYVRTKEFVEKMKKSELYRKTYID 577
                                       3456899***************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (586 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); 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 0.29s 00:00:00.90 Elapsed: 00:00:00.45
# Mc/sec: 3931.26
//
Query:       gi|242398861|ref|YP_002994285.1|  [L=59]
Description: hypothetical protein TSIB_0876 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 385.84
//
Query:       gi|242398862|ref|YP_002994286.1|  [L=123]
Description: hypothetical protein TSIB_0878 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.035   14.2   0.2        1.2    9.2   0.1    2.4  2  Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
      0.069   13.5   0.5       0.15   12.4   0.5    1.8  1  TINF2_N     TERF1-interacting nuclear factor 2 N-terminus
      0.071   13.4   0.1         14    6.0   0.0    2.5  2  MecA_N      NTF2-like N-terminal transpeptidase domain


Domain annotation for each model (and alignments):
>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.029   1.7e+02      15      27 ..      18      30 ..      15      33 .. 0.88
   2 ?    9.2   0.1    0.0002       1.2      31      51 ..      69      89 ..      64      90 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.029
                                      T-HHHHHHHHHHH CS
                        Fis1_TPR_C 15 geYseArryvdal 27
                                      g+Y++A+  +d l
  gi|242398862|ref|YP_002994286.1| 18 GDYTKAKSHIDKL 30
                                      89*****999987 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0002
                                      TTS-HHHHHHHHHHHHHHHHT CS
                        Fis1_TPR_C 31 EPenrQaqsLkeliedkikke 51
                                       P+n++aq+L e  ed +++e
  gi|242398862|ref|YP_002994286.1| 69 GPNNENAQQLLESFEDILQHE 89
                                      6****************9998 PP

>> TINF2_N  TERF1-interacting nuclear factor 2 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.5   2.5e-05      0.15      93     135 ..      73     112 ..       4     115 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.5e-05
                           TINF2_N  93 klvqsLledpeerekflqeefpeeYGekfdaalekLllefLsr 135
                                       +  q+Lle+    e+ lq+ef+++Y + + +a ++Ll+ +Ls+
  gi|242398862|ref|YP_002994286.1|  73 ENAQQLLES---FEDILQHEFRDDYEKGYYTAWKELLTAYLSQ 112
                                       556666665...6778*************************97 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 ?    6.0   0.0    0.0023        14       3      29 ..       5      31 ..       3      38 .. 0.86
   2 ?    5.2   0.0     0.004        24       5      35 ..      46      76 ..      43     122 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0023
                                      HHHHHHHHHHHHTT-HHHHHCTB--BS CS
                            MecA_N  3 eeaaetFldawakgdykkaasllseqs 29
                                      e ++e Fl+a+  gdy ka s  ++ +
  gi|242398862|ref|YP_002994286.1|  5 EMRMEMFLKALMRGDYTKAKSHIDKLE 31
                                      66899**************99988755 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.004
                                      HHHHHHHHHHTT-HHHHHCTB--BSSBSS-H CS
                            MecA_N  5 aaetFldawakgdykkaasllseqskkeise 35
                                      a++ Fl+a++++d++++  +l +   +e+ +
  gi|242398862|ref|YP_002994286.1| 46 AINGFLSALKDNDTDSLIVQLIKGPNNENAQ 76
                                      7899**********99876665544344333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       814  (0.0454013); expected 358.6 (0.02)
Passed bias filter:                      618  (0.0344693); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 888.83
//
Query:       gi|242398863|ref|YP_002994287.1|  [L=194]
Description: Uracil-DNA glycosylase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-44  152.2   0.0    1.3e-44  151.9   0.0    1.1  1  UDG       Uracil DNA glycosylase superfamily


Domain annotation for each model (and alignments):
>> UDG  Uracil DNA glycosylase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.9   0.0   7.2e-49   1.3e-44       1     154 [.      32     185 ..      32     189 .. 0.94

  Alignments for each domain:
  == domain 1  score: 151.9 bits;  conditional E-value: 7.2e-49
                                       HHC-CTT-SEEEEESSTCHHHHHHSSSS.-STT--HHHHHHHCCCCCCCHHGCTEEEEESSS....SECGCTTCCCC CS
                               UDG   1 pgegppdakvvivGeaPgaeedatglpFsgragnllrkllneaglkrdleseqgvyitnvvkcrppgnrdtptsaei 77 
                                       pg g  ++kv++vGe Pg +ed++glpF+grag+ l++ll+++gl+r     ++vyitn+vkcrpp nr +pt++e+
  gi|242398863|ref|YP_002994287.1|  32 PGSGSYESKVMFVGEGPGYWEDQEGLPFVGRAGKVLDELLESIGLTR-----DKVYITNIVKCRPPNNR-DPTEEEV 102
                                       689999*****************************************.....*****************.******* PP

                                       TCCHHHHHHHHHHHHSSEEEEESHHHHHH........HHHHSCESCCCSCT......SEEEEES-SSTTTTTTTTSH CS
                               UDG  78 kacaplleeeiellkprlivllGktaakall......geklgklrgklleak.....irvlplphPsplnrnffksn 143
                                       kac+p+l+ +i+l++p++iv lG++   ++l      +e ++k++gk +ea+     i ++p++hP+ ++++     
  gi|242398863|ref|YP_002994287.1| 103 KACSPYLDMQIDLIRPKIIVPLGRHSMAYILrkfgfdPEPISKIHGKTFEARtlfgkIVIMPVYHPAVALYR----- 174
                                       *****************************98999998889***********778889***************..... PP

                                       HHHHHHHHHHH CS
                               UDG 144 pelkaeawedL 154
                                       p+lk+e  +d+
  gi|242398863|ref|YP_002994287.1| 175 PQLKEELQQDF 185
                                       77776665665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); 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: 00:00:00.46
# Mc/sec: 1278.68
//
Query:       gi|242398864|ref|YP_002994288.1|  [L=532]
Description: Na+/H+ antiporter, , NhaC family [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.6e-71  239.0  28.9    6.6e-71  239.0  28.9    2.1  2  Na_H_antiporter  Na+/H+ antiporter family
    1.6e-06   26.9  22.2    4.5e-06   25.4  10.7    2.8  3  DcuC             C4-dicarboxylate anaerobic carrier


Domain annotation for each model (and alignments):
>> Na_H_antiporter  Na+/H+ antiporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   2.2     0.045   4.1e+02     120     249 ..      22     150 ..       5     154 .. 0.69
   2 !  239.0  28.9   7.3e-75   6.6e-71       1     302 [.     156     485 ..     156     486 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.045
                   Na_H_antiporter 120 ntdvatalvvgalaglivatllela..slseidkllnrGiksmlgaili..lllAwgiggvlealgvteslvsslak 192
                                          v+ al++g ++g ++ ++++ +   ++++d ++   +    + il+   ++++++g v +     +++   +++
  gi|242398864|ref|YP_002994288.1|  22 TKRVLFALFIGVWVGALMVVGGNPIsaTVQTWDWIIGNALDDWNQKILLydFIIGAAFGLVYKSGA-ASAFARAITR 97 
                                       445667777777777777777776666666666666666666666666622366666666655555.9999999999 PP

                   Na_H_antiporter 193 gvvskgllplilflvallvafatGtswgtigIilpiavplaaklgisllalvravea 249
                                       +v+s + + ++  +++ ++ f     +g  +I++  ++p+ +k+ +s+  +++ + +
  gi|242398864|ref|YP_002994288.1|  98 RVKSSRAASVLGWVLGVAIFF---DDYGNTVIVGNSMRPITDKTRVSR-EMLAYIDD 150
                                       998888888888888888877...789999999999999999999998.55555555 PP

  == domain 2  score: 239.0 bits;  conditional E-value: 7.3e-75
                   Na_H_antiporter   1 vavfgdkssplsdtvgliagilktdlieeiaalgmlvqsipanvysifallvvglvvlllrdigamlraeaear... 74 
                                       va++ ++ss+++++vgli+   ++ +ie  + +++++++ p+++ysi+a+++v+lv+++ r++gaml+ae +ar   
  gi|242398864|ref|YP_002994288.1| 156 VATIALVSSWIGYEVGLIQDSFDSLGIEIGS-YAAWLSAWPYKLYSILAIVMVLLVAYTHRHYGAMLKAEYRARttg 231
                                       7999******************999999888.99****************************************888 PP

                   Na_H_antiporter  75 ...............eleekeltk.............lpiavliiltlskmpytgalalvaivkafivalafqntdv 123
                                                      +                      pi+ li++ l +m+ytg+++     +a  + +++ n+d 
  gi|242398864|ref|YP_002994288.1| 232 kvlrdgaqpmmatesD-------LgipmeggtihafiWPILALILVFLYGMWYTGGGS--EVYAAEGIKGVMSNADT 299
                                       8888877666555552.......044555557777889********************..556688899999***** PP

                   Na_H_antiporter 124 atalvvgalaglivatllela....slseidkllnrGiksmlgaililllAwgiggvlealgvteslvsslakgv.v 195
                                       a al+++++a+l+v ++ +l+    sl++i+k +++G+k m++a++illlAw+i+++++a+g t+++v + a g  v
  gi|242398864|ref|YP_002994288.1| 300 ALALLWAGFAMLVVVMFIILVkkqmSLEDIEKGIVQGMKQMVMANAILLLAWSIKSATDAVG-TADFVVNAAVGGgV 375
                                       **************************************************************.************** PP

                   Na_H_antiporter 196 skgllplilflvallvafatGtswgtigIilpiavplaaklgisl....lalvraveaggtlgdhlsPisdttilss 268
                                       + + +pli+fl+a++v+f+tGtswgt+g+i+p+a+pl+  lg       +a ++av+agg++gdh+sPisdtti+ss
  gi|242398864|ref|YP_002994288.1| 376 PGAIVPLIIFLSAAFVSFTTGTSWGTFGVIMPMAIPLGYTLGGGVgpilYASMGAVLAGGIFGDHCSPISDTTIMSS 452
                                       ******************************************9999999**************************** PP

                   Na_H_antiporter 269 tglnadhidhvsytqlpyallvapitailllvfG 302
                                       ++ ++dhidhv+ tqlpya +va+++a l+++f+
  gi|242398864|ref|YP_002994288.1| 453 MFSGSDHIDHVN-TQLPYAVTVAALSAFLYILFA 485
                                       ************.******************997 PP

>> DcuC  C4-dicarboxylate anaerobic carrier
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.3   4.1e-05      0.37     322     387 ..      25      92 ..      21      96 .. 0.82
   2 !   25.4  10.7     5e-10   4.5e-06     256     400 ..     259     417 ..     156     424 .. 0.74
   3 ?   -1.2   0.3     0.058   5.2e+02     163     220 ..     452     515 ..     442     518 .. 0.57

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 4.1e-05
                              DcuC 322 lgvalvvglargveviaeggmiidtilnlisnalsglsg..ivfilvmlliqallafvvpSgsglavl 387
                                       + +al +g+ +g+ ++++g  i++t++++   + ++l++  + + l   +i a++++v  Sg + a++
  gi|242398864|ref|YP_002994288.1|  25 VLFALFIGVWVGALMVVGGNPISATVQTWDWIIGNALDDwnQKILLYDFIIGAAFGLVYKSGAASAFA 92 
                                       679************************99999888998843455566667778888899999888876 PP

  == domain 2  score: 25.4 bits;  conditional E-value: 5e-10
                              DcuC 256 vlilfvlplilvllg................lafvivngewylpeiavlflamgilvefiaklnglkekeiveafve 316
                                       + i ++l lilv+l                 +++v+ n+   l+ + + f ++ +++ +i ++++++ ++i +  v+
  gi|242398864|ref|YP_002994288.1| 259 AFIWPILALILVFLYgmwytgggsevyaaegIKGVMSNADTALALLWAGFAMLVVVMFIILVKKQMSLEDIEKGIVQ 335
                                       4455666666664433555566777766666666666666666666666666665555566699************* PP

                              DcuC 317 GaaellgvalvvglargveviaeggmiidtilnlisnalsglsgivfilvmlliqallafvvpSgsglavltmplma 393
                                       G+++++++ ++  la  ++   +   + d++ n++ +   g++g+++ l+  l  a+++f+++ + g + + mp+++
  gi|242398864|ref|YP_002994288.1| 336 GMKQMVMANAILLLAWSIKSATDAVGTADFVVNAAVG--GGVPGAIVPLIIFLSAAFVSFTTGTSWGTFGVIMPMAI 410
                                       *******************999988888888887644..57899********************************* PP

                              DcuC 394 pLAdlvg 400
                                       pL+ ++g
  gi|242398864|ref|YP_002994288.1| 411 PLGYTLG 417
                                       **98876 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.058
                              DcuC 163 aillatqvgilastinPfavviAaeiAgvsia......dgivlrllvlviltlisiaflyfYak 220
                                        ++ ++  +    t  P+av +Aa  A + i+      +g+vl  l +v+l +i  + +++Y k
  gi|242398864|ref|YP_002994288.1| 452 SMFSGSDHIDHVNTQLPYAVTVAALSAFLYILfavglrNGFVLLGLGIVLLIVIHRVLSAWYGK 515
                                       5666777777778888888888888887666511111144444444444444444455555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (532 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1016  (0.056668); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.45
# Mc/sec: 3583.82
//
Query:       gi|242398865|ref|YP_002994289.1|  [L=354]
Description: Saccharopine reductase [Thermococcus sibiricus MM 739]
Scores for complete 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   97.4   0.0    2.1e-27   96.9   0.0    1.2  1  Sacchrp_dh_C     Saccharopine dehydrogenase C-terminal domain
    3.1e-15   56.6   0.0    4.5e-15   56.1   0.0    1.3  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
    2.6e-05   24.3   0.0    4.3e-05   23.6   0.0    1.4  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
    0.00013   22.2   0.0    0.00024   21.3   0.0    1.6  1  TrkA_N           TrkA-N domain
     0.0011   19.5   0.0     0.0019   18.7   0.0    1.5  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
  ------ inclusion threshold ------
      0.011   15.3   0.0       0.02   14.6   0.0    1.4  1  ApbA             Ketopantoate reductase PanE/ApbA
      0.061   13.2   0.0      0.092   12.6   0.0    1.3  1  NAD_binding_10   NAD(P)H-binding
      0.072   13.0   0.0       0.16   11.8   0.0    1.6  2  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding


Domain annotation for each model (and alignments):
>> Sacchrp_dh_C  Saccharopine dehydrogenase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.9   0.0   9.3e-31   2.1e-27       1     264 [.     117     344 ..     117     345 .. 0.79

  Alignments for each domain:
  == domain 1  score: 96.9 bits;  conditional E-value: 9.3e-31
                                       BTTTBHHHHHHHHHHHCCCHTTBECCCCCCCCCCCCECCCCESTTCEEESS-HHHHHHHCCSEEEEEETTEEEECT. CS
                      Sacchrp_dh_C   1 GldPGidhllamkaidevkakggkiesflsycgglpapeasdnplgYkfsWspegvlreltnpakvlengqvkevp. 76 
                                       G++PG++++l+ ++   +    gk ++ ++ +gglp   ++  pl Yk+ +sp  +++e+t+pa++++ng+++ v+ 
  gi|242398865|ref|YP_002994289.1| 117 GFAPGLSNILMGHIQAVL----GKLDEGVINVGGLP-KNPQ-PPLYYKVVFSPYDLIEEYTRPARIIRNGRLVRVDp 187
                                       9*********97666633....4577889*******.4444.5****************************888885 PP

                                       CCCSGCC.TCEEECCCCCEECTTECEEECTHCHHHHHHC.SCSEEEEEEEEEHHHHHHHHHHHTTT--SCECCCCCC CS
                      Sacchrp_dh_C  77 gsellkgakkpiyilpglslegypnrdslpyeelyglpeaktlfrgtlrypgfsellkslkelGllseepkeealka 153
                                       +++     +k+++i++ +++e +   d+l++  l +++ a++l+  tlr++g+ e +k lkelG+++ e+       
  gi|242398865|ref|YP_002994289.1| 188 LED-----IKQLKIRD-FEFESFV-SDGLRT-LLATIE-AENLYENTLRWKGHLEKMKVLKELGFFNPEN------- 248
                                       666.....46677754.7999885.678998.455566.8***************************995....... PP

                                       HHSTTCEHHHHHHHHCCHHCCCCTTEEEEEEEEEEEEEETTSEEEEEEE.EEEEEEEHH..SSSHHHHHHHHHHHHH CS
                      Sacchrp_dh_C 154 wlsegespldvlaalLekklalepgerDlvvlqhefgiesdgkkkekkt.stlvgydee..gssamaktvGvpaaia 227
                                               +++  +++   +++e  + D  ++++     ++g++   +  + +   de+  g ++ma+ +G+ +ai+
  gi|242398865|ref|YP_002994289.1| 249 --------IEFTMKVILPLMQFE--SDDFSIMEVYG---KSGEQ---EMrYFMY--DEAqgGFTSMARSTGYITAIT 307
                                       ........777777777778887..55556665543...44443...3324444..32235**************** PP

                                       HHHHHTTSCTSSEEEEGGGS..CHHHHHHHHHHHHHCT CS
                      Sacchrp_dh_C 228 aklildgkikkrGvvtpeelv.dpeiyeplleeLekeG 264
                                       a+l+l+ +  ++Gv++pe +  + ++ +++++e++k+ 
  gi|242398865|ref|YP_002994289.1| 308 ARLVLKYEF-EPGVIPPELFGmEDDLFDEIIKEVKKRN 344
                                       ******653.4******8888777**********9985 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 !   56.1   0.0     2e-18   4.5e-15       1     129 [.       3     112 ..       3     113 .. 0.93

  Alignments for each domain:
  == domain 1  score: 56.1 bits;  conditional E-value: 2e-18
                                       EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-S CS
                   Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnls 77 
                                       + ++GaG vG+ +a +l++  d+  e+ +ad+ske+l +la+      +++++lda++ e+ L++ +k+ dl+v ++
  gi|242398865|ref|YP_002994289.1|   3 ICVLGAGDVGRLIAYDLSK--DY--EVSIADKSKERL-KLAE----NFATTYELDASKFED-LVEFMKKFDLIVGAL 69 
                                       679***************9..56..88*********5.4443....34899**********.*************** PP

                                       SGGGHHHHHHHHHHHT-EEEESS-BCGCCSCHCCSHHHHHTHHHHHHCTSEE CS
                   Sacchrp_dh_NADP  78 ppissldvlkaCietgvhyvdtsiskeertnyalreavlklkekakeagvta 129
                                       p  ++ + lka+i+++ + vd+s+         + e+ l+l+++akeag+ +
  gi|242398865|ref|YP_002994289.1|  70 PGRFGFSTLKAAIKARRDIVDVSF---------MPEDPLELDDQAKEAGIRM 112
                                       ************************.........****************976 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   1.9e-08   4.3e-05      14      82 ..       2      68 ..       1      92 [. 0.90

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 1.9e-08
                                      EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHH.T.ET-EEEEGCGHHHHHHT-SEEEE- CS
                      Shikimate_DH 14 kvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeel.kgeeiealkleelkellaeadvvisa 82
                                      k++++GaG +++l+a  L+ k ++ v +a  + er  +lae++  ++e+ a k+e+l e ++++d+++ a
  gi|242398865|ref|YP_002994289.1|  2 KICVLGAGDVGRLIAYDLS-KDYE-VSIADKSKERL-KLAENFaTTYELDASKFEDLVEFMKKFDLIVGA 68
                                      89****************9.6666.9*********7.5888886788999*****************977 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   1.1e-07   0.00024       1      66 [.       3      65 ..       3      98 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.1e-07
                                      EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEE CS
                            TrkA_N  1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadav 66
                                      i ++G+G+vGr +a  Ls++++ v++ dk++er++ + e++++++  da++ e L e  ++k+d++
  gi|242398865|ref|YP_002994289.1|  3 ICVLGAGDVGRLIAYDLSKDYE-VSIADKSKERLKLA-ENFATTYELDASKFEDLVEF-MKKFDLI 65
                                      689****************995.**********9985.68899999999998877765.4555555 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 !   18.7   0.0   8.7e-07    0.0019       1      81 [.       2      81 ..       2      97 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 8.7e-07
                                      EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCH...HHHHHHHC-EEECE.CHHHHHHH-SEEEE-S-HHHHH CS
                     F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpeka...eelaeelgvkvtav.dneeaaeeadvvvlavkpedve 75
                                      ki+++GaG++g+ +a  l++     +e+ +a ++++e++   e +a +++ ++++  d  e +++ d +v a++ +   
  gi|242398865|ref|YP_002994289.1|  2 KICVLGAGDVGRLIAYDLSKD----YEVSIA-DKSKERLklaENFATTYELDASKFeDLVEFMKKFDLIVGALPGRFGF 75
                                      79**************99998....9***99.88888761114455555555544215677777999999888887777 PP

                                      HHHHHC CS
                     F420_oxidored 76 evlsel 81
                                      ++l+++
  gi|242398865|ref|YP_002994289.1| 76 STLKAA 81
                                      777766 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   8.8e-06      0.02       1      34 [.       3      36 ..       3      65 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 8.8e-06
                                      EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHH CS
                              ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr.rle 34
                                      i++lGaG +G+l+a+ L+k  ++v + ++s+ rl+
  gi|242398865|ref|YP_002994289.1|  3 ICVLGAGDVGRLIAYDLSK-DYEVSIADKSKeRLK 36
                                      89***************66.999999999997765 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   4.1e-05     0.092       3      73 ..       8      74 ..       7     117 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.1e-05
                                      TSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCC CS
                    NAD_binding_10  3 tGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsalggggk 73
                                       G vGrl++  l ++  +ev +   ++e+l+ l+ e+ +++ e+d+++ edl e +k  d +v al g+ +
  gi|242398865|ref|YP_002994289.1|  8 AGDVGRLIAYDLSKD--YEVSIADKSKERLK-LA-ENFATTYELDASKFEDLVEFMKKFDLIVGALPGRFG 74
                                      699*********998..8**99999999999.75.6899************************99955444 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 ?   11.8   0.0   7.2e-05      0.16       1      43 [.       2      43 ..       2      82 .. 0.86
   2 ?   -3.0   0.0       2.6   5.9e+03      18      50 ..     204     236 ..     202     256 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.2e-05
                                      EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHH CS
                           3HCDH_N  1 kvaviGaGtmGagiaavfasagleVvlvdiseealekalekie 43
                                      k+ v+GaG +G+ ia+ + s+++eV + d s+e+l+ a++ ++
  gi|242398865|ref|YP_002994289.1|  2 KICVLGAGDVGRLIAYDL-SKDYEVSIADKSKERLKLAENFAT 43
                                      689************986.689*************99887655 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.6
                                       HHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCT CS
                           3HCDH_N  18 fasagleVvlvdiseealekalekieksleklv 50 
                                       f+s gl++ l  i++e l + + + +  lek++
  gi|242398865|ref|YP_002994289.1| 204 FVSDGLRTLLATIEAENLYENTLRWKGHLEKMK 236
                                       566677777777766666666666555544443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2193.46
//
Query:       gi|242398866|ref|YP_002994290.1|  [L=263]
Description: amidinotransferase [Thermococcus sibiricus MM 739]
Scores for complete 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-29  101.0   0.0    6.5e-27   94.5   0.0    2.3  1  Amidinotransf  Amidinotransferase
     0.0056   16.8   0.2       0.52   10.5   0.0    2.9  3  UPF0180        Uncharacterised protein family (UPF0180)
  ------ inclusion threshold ------
      0.093   12.0   0.0       0.57    9.4   0.0    1.9  2  PAD_porph      Porphyromonas-type peptidyl-arginine deiminase
        0.2   11.6   0.0        6.3    6.9   0.0    2.2  2  RcsC           RcsC Alpha-Beta-Loop (ABL)


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 !   94.5   0.0   1.5e-30   6.5e-27      25     338 ..      30     259 ..      10     261 .. 0.90

  Alignments for each domain:
  == domain 1  score: 94.5 bits;  conditional E-value: 1.5e-30
                                       --HHHHHHHHHHHHHHHHTTT-EEEEHHHHHHHHCTSHHHHHHHHHHHSSTTTTITTTGGGS-S-HHHHHHHHHHHH CS
                     Amidinotransf  25 iilekaqkEHdafvqvLrekGveVlvledllaealeaeearkekldeklleselgiklgvklseeikiekleladka 101
                                       i ++ a+k+H+++v+ L+e+G+eV+ le l                                               
  gi|242398866|ref|YP_002994290.1|  30 IDVNLAKKQHKEYVKILKENGIEVIELEPL----------------------------------------------- 59 
                                       55789*************************............................................... PP

                                       H----EEE---GGGG-TTTTEEE..EBSEEEE---SSGGGHHHHHHHHHHHHHSHTSB-EEEEE-TTS--TT----G CS
                     Amidinotransf 102 tsnnsflipplpnlvFtrdwfst..igggvvlnpmaapnRrrErllaeliykkhpgvkvakvldisgkeeesktlEG 176
                                               ++ p++vF  d+ +    ++ +vl ++ +p Rr E++  +  +kk+        ++i++  +e++t+EG
  gi|242398866|ref|YP_002994290.1|  60 --------ENHPDSVFVQDTAIVgvNSNLAVLSRFGEPSRRGEEESIKEVLKKE-------GFEIKH-IKEPGTIEG 120
                                       ........89**************999999***********************3.......355663.5679***** PP

                                       GGEEEEETTEEEEEESSSS-HHHHHHHHHHHHHTTS-SEEEEEE--GGSSTS-GGGTEEEEETTEEEE-HHHH.TT- CS
                     Amidinotransf 177 GdfvvlskgvvaigvssRtdeegieelakklfyktvafkviaieipkgraimHldtvftvvdddavvclpsildaeg 253
                                       Gd++v ++g v +g s+Rt+ egi++la+ +       kv+ + i   ++i Hl   ++ + +++v + p ++d+e 
  gi|242398866|ref|YP_002994290.1| 121 GDVLVTDQGIVFVGLSQRTNTEGIKQLAQFFPNV----KVVGVPI---SKIFHLLSGINYLGNKTVAISPHVVDTE- 189
                                       ***************************9765555....5544455...56*************************9. PP

                                       ESS-HHHHHHHHTT-SS-EEEE-CS-SS-B---S-EEEETTEEEEETTGHHHHHHHHHTT-EEEEE-HTTTGGGS-- CS
                     Amidinotransf 254 vkakereavaqaLkekgleiIeigeeeqwnfggNvLelkpgvvvaydrntvtnekleeagievievpiselerGgGg 330
                                                      kg+++I+i+e+e   +++N+L l++++v+  +   +t ekl+++g++ +   +se  +G Gg
  gi|242398866|ref|YP_002994290.1| 190 -------------YFKGFKFITIPEDE--LYANNMLYLGEKKVLLPEGYPKTEEKLRREGFKPVLANVSEFWKGDGG 251
                                       .............6799**********..89********************************************** PP

                                       TTTT-EEE CS
                     Amidinotransf 331 arCmsapl 338
                                       + C   p+
  gi|242398866|ref|YP_002994290.1| 252 VTCLNLPF 259
                                       ***87776 PP

>> UPF0180  Uncharacterised protein family (UPF0180)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.028   1.3e+02      14      28 ..      44      58 ..      37      83 .. 0.74
   2 !   10.5   0.0   0.00012      0.52      11      52 ..      97     146 ..      95     168 .. 0.78
   3 ?   -1.3   0.0      0.59   2.6e+03      10      24 ..     224     238 ..     215     244 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.028
                           UPF0180 14 eaLrekGYeVvdlet 28
                                      + L+e+G eV++le 
  gi|242398866|ref|YP_002994290.1| 44 KILKENGIEVIELEP 58
                                      68***********96 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00012
                           UPF0180  11 nvkeaLrekGYeVvdleteedaqsvdaiVv.tG.......qdtnvmgied 52 
                                        +ke L+++G+e+  +++  + ++ d++V+ +G       q tn  gi++
  gi|242398866|ref|YP_002994290.1|  97 SIKEVLKKEGFEIKHIKEPGTIEGGDVLVTdQGivfvglsQRTNTEGIKQ 146
                                       79***************988899999998854466666666666666655 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.59
                           UPF0180  10 snvkeaLrekGYeVv 24 
                                        + +e Lr++G++ v
  gi|242398866|ref|YP_002994290.1| 224 PKTEEKLRREGFKPV 238
                                       5668999****9977 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 ?    3.4   0.0    0.0084        38      57     146 ..      39     133 ..      15     142 .. 0.64
   2 ?    9.4   0.0   0.00013      0.57     263     307 ..     124     167 ..     121     172 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.0084
                                       HHHHHHHC.........EEEEE---SSS-HHHHS-EEEE.ETEEEEEEE--HHHHTSSHHTTHHHHHHHHHH..TT- CS
                         PAD_porph  57 aeearell.........velveiptndlWlRDtgpifvvkkelaavdfrFnaWGgkyeeaekdnavarklae..agl 122
                                       ++e  + l         +e +e + + +++ Dt+ + v +  + av  rF + +    +  +++++++ l +   ++
  gi|242398866|ref|YP_002994290.1|  39 HKEYVKILkengievieLEPLENHPDSVFVQDTAIVGVNS--NLAVLSRFGEPS----RRGEEESIKEVLKKegFEI 109
                                       3333334456665554444455566788899998888885..345555554443....4556777777774424567 PP

                                       CEEEEEEE--GGGEEEESSSEEEE CS
                         PAD_porph 123 erveadlvlEGGsievdGeGtllt 146
                                       ++++++ + EGG + v ++G++++
  gi|242398866|ref|YP_002994290.1| 110 KHIKEPGTIEGGDVLVTDQGIVFV 133
                                       888899**************9987 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00013
                                       EEETTEEEEEE-SSTTCHHHHHHHHHHHSTTSEEEEEETTTGGGG CS
                         PAD_porph 263 livngavlvptfgdeekDekAleilqelfpdrevvgvdaralvlg 307
                                       l++++++++    + +++++ +++l++ fp+ +vvgv+++++++ 
  gi|242398866|ref|YP_002994290.1| 124 LVTDQGIVFVGLSQ-RTNTEGIKQLAQFFPNVKVVGVPISKIFHL 167
                                       67888888888888.789**********************99875 PP

>> RcsC  RcsC Alpha-Beta-Loop (ABL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.036   1.6e+02      16      44 ..      44      72 ..      36      84 .. 0.87
   2 ?    6.9   0.0    0.0014       6.3      12      43 ..      96     128 ..      95     131 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.036
                              RcsC 16 rlLsesgltvaryeeqevseddvlitDep 44
                                      ++L+e+g++v + e  e ++d v++ D+ 
  gi|242398866|ref|YP_002994290.1| 44 KILKENGIEVIELEPLENHPDSVFVQDTA 72
                                      689*********99999********9975 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0014
                              RcsC  12 eylqrlLsesgltvar.yeeqevseddvlitDe 43 
                                       e ++++L+++g+++++ +e  +++  dvl+tD+
  gi|242398866|ref|YP_002994290.1|  96 ESIKEVLKKEGFEIKHiKEPGTIEGGDVLVTDQ 128
                                       568899**********888889**********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       738  (0.0411624); expected 358.6 (0.02)
Passed bias filter:                      691  (0.0385409); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 1897.52
//
Query:       gi|242398867|ref|YP_002994291.1|  [L=304]
Description: GHMP kinase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-08   34.6   0.0    3.3e-08   33.6   0.0    1.5  1  GHMP_kinases_N  GHMP kinases N terminal domain


Domain annotation for each model (and alignments):
>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.0   1.8e-12   3.3e-08       6      66 .]      92     151 ..      87     151 .. 0.88

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 1.8e-12
                                       ESSHTTSSSCHHHHHHHHHHHHHHHHTTEHHHH..HHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
                    GHMP_kinases_N   6 seiPvgaGLGSSAAlavalvaAllallglslee..aklaleaerlaqggngsggDvaasvyGg 66 
                                        ++P g G+G SAA a+++++Al+  +     +  ++ +++a+++ ++ +g+ gDv a +yGg
  gi|242398867|ref|YP_002994291.1|  92 FDFPNGYGFGNSAAGALGTALALAFNFKE---KtfLQASQVAHKYEVLYKGGLGDVIAQFYGG 151
                                       589*******************9666632...2459**************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2112.12
//
Query:       gi|242398868|ref|YP_002994292.1|  [L=83]
Description: hypothetical protein TSIB_0884 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score 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   13.8   0.6       0.05   13.8   0.6    1.8  2  Toxin_GhoT_OrtT  Toxin GhoT_OrtT
        6.7    6.7   6.6         21    5.2   0.1    2.5  3  UCR_UQCRX_QCR9   Ubiquinol-cytochrome C reductase, UQCRX/QCR9


Domain annotation for each model (and alignments):
>> Toxin_GhoT_OrtT  Toxin GhoT_OrtT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.6   5.5e-06      0.05       3      37 ..       6      40 ..       5      50 .. 0.91
   2 ?   -1.4   0.1      0.33   2.9e+03      51      52 ..      60      61 ..      54      74 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.5e-06
                   Toxin_GhoT_OrtT  3 lilviYaiglvisvlitfflskdpslkirLLsall 37
                                      ++ ++Y++  ++ ++it fl k    +i L++a  
  gi|242398868|ref|YP_002994292.1|  6 FMNTLYLALTIVGLFITIFLNKSGRREIGLIAAGF 40
                                      799****************************9975 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.33
                   Toxin_GhoT_OrtT 51 lf 52
                                      +f
  gi|242398868|ref|YP_002994292.1| 60 IF 61
                                      44 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 ?   -1.6   0.0      0.29   2.6e+03      11      23 ..       8      20 ..       7      28 .. 0.64
   2 ?    4.6   0.9    0.0036        32       9      30 ..      30      51 ..      22      54 .. 0.83
   3 ?    5.2   0.1    0.0023        21      16      31 ..      58      73 ..      55      75 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.29
                                      HHHHHHHHHHHHH CS
                    UCR_UQCRX_QCR9 11 nstfvltifagAf 23
                                      n+ +++  ++g f
  gi|242398868|ref|YP_002994292.1|  8 NTLYLALTIVGLF 20
                                      5566666666654 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0036
                                      SSHHHHHHHHHHHHHHHHHHHH CS
                    UCR_UQCRX_QCR9  9 rrnstfvltifagAfvferafD 30
                                      rr    +++ f+g+f+f +af+
  gi|242398868|ref|YP_002994292.1| 30 RREIGLIAAGFTGGFAFLVAFE 51
                                      5666678889*******99996 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.0023
                                      HHHHHHHHHHHHHHHH CS
                    UCR_UQCRX_QCR9 16 ltifagAfvferafDs 31
                                        if+g+f+  ++f++
  gi|242398868|ref|YP_002994292.1| 58 PLIFVGGFIATVFFEY 73
                                      579*******999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); 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):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 596.96
//
Query:       gi|242398869|ref|YP_002994293.1|  [L=560]
Description: DNA ligase [Thermococcus sibiricus MM 739]
Scores for complete 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-65  219.1   0.4    7.5e-65  218.4   0.4    1.3  1  DNA_ligase_A_M   ATP dependent DNA ligase domain
    6.4e-40  137.3   0.2    1.2e-39  136.4   0.2    1.5  1  DNA_ligase_A_N   DNA ligase N terminus
    3.1e-23   82.2   0.0    1.3e-22   80.2   0.0    2.2  1  DNA_ligase_A_C   ATP dependent DNA ligase C terminal region
    6.4e-07   29.8   0.4      1e-06   29.2   0.4    1.3  1  RNA_ligase       RNA ligase
  ------ inclusion threshold ------
      0.044   14.0   0.5       0.16   12.1   0.0    2.2  3  FeS_assembly_P   Iron-sulfur cluster assembly protein
      0.072   13.1   0.0       0.28   11.2   0.0    2.0  1  DNA_ligase_OB_2  DNA ligase OB-like domain
        0.1   12.4   0.2       0.37   10.6   0.1    2.0  2  mRNA_cap_enzyme  mRNA capping enzyme, catalytic domain


Domain annotation for each model (and alignments):
>> DNA_ligase_A_M  ATP dependent DNA ligase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  218.4   0.4   2.9e-68   7.5e-65       1     204 []     225     423 ..     225     423 .. 0.98

  Alignments for each domain:
  == domain 1  score: 218.4 bits;  conditional E-value: 2.9e-68
                                       -EEEEEESCHHHHHHHTTTSEEEEEEEESSEEEEEEEETTEEEEEETTS-B-GGGCHHHHHHHHHHBSTTESEEEEE CS
                    DNA_ligase_A_M   1 pmLAeslksiekalkkleekafivEiKyDGeRaqvhkegdkvklfSRrlkditaakpelvkalkeafkkdeksvilD 77 
                                       pmLA+ + ++++al ++ ++++ +EiKyDG+R+qvhk+g+kv ++SRrl+++t++ pe+v+++kea+k++  +vi++
  gi|242398869|ref|YP_002994293.1| 225 PMLAQMAANVREALVEM-GGEAEFEIKYDGARVQVHKNGNKVLIYSRRLENVTKSIPEVVERVKEALKPE--KVIVE 298
                                       9****************.66666*********************************************97..8**** PP

                                       EEEEEEETTTTCBEHHHHHCHHHHCHCCTHHHHHHSEEEEEEEEEEEETTEEHTTSCHHHHHHHHHHHB--BTTTEE CS
                    DNA_ligase_A_M  78 GElvavdketgeilpfqklasrkkkkkkveeklkeaelclfvFDiLyldgesltdeplkeRrklLeeilkesedrve 154
                                       GElva ++etg+++pfq + +r+++k+++ee++++++l l +FDiLy+dg++++d+p+ eRrk+Le+++ +s++ ++
  gi|242398869|ref|YP_002994293.1| 299 GELVA-VEETGRPRPFQYVLRRFRRKYNIEEMIEKIPLELNLFDILYVDGQNMIDTPFMERRKVLESVV-NSNEWIK 373
                                       *****.5999***********************************************************.99999** PP

                                       E--EEEESSHHHHHHHHHHHHHTTECEEEEEETT-CC-TTCEEEEEEEEE CS
                    DNA_ligase_A_M 155 laeslevkdveeleelleeaiseglEGlvvKnpdskYepgkrsknwlKvK 204
                                        ae+l +k+ ee+e+++++a++ g+EGl++K  ds+Yepg+r+k+wlK+K
  gi|242398869|ref|YP_002994293.1| 374 SAENLITKSPEEAEAFYHKALDLGHEGLMAKRLDSTYEPGNRGKKWLKIK 423
                                       *************************************************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 !  136.4   0.2   4.8e-43   1.2e-39       2     173 .]       3     177 ..       2     177 .. 0.94

  Alignments for each domain:
  == domain 1  score: 136.4 bits;  conditional E-value: 4.8e-43
                                       CHHHHHHHHHHCC.---HHHHHHHHHHHHHTS-..SHHHHHHHHHH....SS-CCCS------HHHHHHHHHHHHT- CS
                    DNA_ligase_A_N   2 FaelaelfekieestkkrlekrailanffrkvesagpedlypalrL....llPdydgreygigesllakalaealgl 74 
                                       ++el+el++++e++t k l k++ +++f+++ve  +pe l  + +L    ++Pd+d+re+gige+ll+ka++ a+g+
  gi|242398869|ref|YP_002994293.1|   3 YKELVELYKRLEKTTLKTL-KTKFVSDFLKSVE--KPELLEVIPYLilgkVFPDWDERELGIGEKLLIKAVSMATGI 76 
                                       89***********665555.*********9998..5766666667777***************************** PP

                                       -HHHHHHHHHHHS-HHHHHHHHHCCHHHH.------BHHHHHHHHHHHHH-.STTHHHHHHHHHHHHHHHS-HHHHH CS
                    DNA_ligase_A_N  75 skkkikdalakvgDlgevaeevlskrstl.akkspltieevnelLdklaaa.gkgsedekkkilkkllkraspeEak 149
                                       ++++i++  +++gDlge ++ +l+kr++  + ++pltie v+++L k+a+a g gs+d+k k l++l+  asp+E k
  gi|242398869|ref|YP_002994293.1|  77 NSEEIENSVRDTGDLGESIALALNKRKQKsFFSQPLTIERVYNTLVKIAEAsGAGSQDRKLKYLANLFMDASPDEGK 153
                                       ********999************9999999*******************999************************* PP

                                       HHHHHHCT---SS--HHHHHHHHH CS
                    DNA_ligase_A_N 150 yliriilkdlriglsektvldala 173
                                       yl+r++l+ +r g++e++++dala
  gi|242398869|ref|YP_002994293.1| 154 YLARTVLGIMRTGVAEGLLRDALA 177
                                       **********************97 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 !   80.2   0.0   5.3e-26   1.3e-22       1      99 []     443     535 ..     443     535 .. 0.95

  Alignments for each domain:
  == domain 1  score: 80.2 bits;  conditional E-value: 5.3e-26
                                       GGGSEEEEEEEEEE..TTEEEEEEEE-SS--HHHHHHHHHHHGGGEECTTCESS---HHHHTTEEE-TT-EEEEEES CS
                    DNA_ligase_A_C   1 rgglvgslllgvyd..dgkleyvgkvgtGfsdaeleelrkklkelerkkppfaekvpeeekrdvWvePelvveVkfa 75 
                                       r+g+++s+llg+yd  +g+++ vgkvg+Gf+d++l e++k+lk+l +k++      + e      +eP++v+eV+++
  gi|242398869|ref|YP_002994293.1| 443 RSGVLSSFLLGAYDpvKGDFVPVGKVGSGFTDEDLVEFTKMLKPLIKKEHGK----EVE------LEPKVVIEVAYQ 509
                                       57899**************************************999999988....222......89********** PP

                                       EEECTSSSTT..EECT-EEEEE-TTS CS
                    DNA_ligase_A_C  76 eitasgkyka..slRfPrfkrlReDk 99 
                                       ei++s+ky++  +lRfPr++ lReDk
  gi|242398869|ref|YP_002994293.1| 510 EIQKSPKYESgfALRFPRYIALREDK 535
                                       *************************8 PP

>> RNA_ligase  RNA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.4   3.9e-10     1e-06       6     161 .]     248     423 ..     243     423 .. 0.69

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 3.9e-10
                                       EEE-SSEEEEEEEETT.EEEEETTCEBCTTTHHHHHHTHHHHHHHHHHHHH..ECCEEEEEEEES.......SS..T CS
                        RNA_ligase   6 tEKlDGtnfriylvke.vgvasRsqilpfgeekfkefkrwaaalrkklkeklaneelilyGElig......hsikyg 75 
                                       + K DG++++++++ + v + sR+ +           ++   +  +++ke l+ e++i+ GEl+       +     
  gi|242398869|ref|YP_002994293.1| 248 EIKYDGARVQVHKNGNkVLIYSRRLEN---------VTKSIPEVVERVKEALKPEKVIVEGELVAveetgrP----- 310
                                       67***********94449999999999.........33444566678888999889*********6544431..... PP

                                       TSS.........................EEEEEEEEEEE..CTTBECE--HHHH.HHHHHCCTB..EEEEE.SS... CS
                        RNA_ligase  76 glpk........................efyvFdifdir..dkeeqrylspdev.ealakglgtvpvlyegkfl... 122
                                                                   e+ +Fdi+ ++  +  +  ++++++v e + ++     ++++ + l   
  gi|242398869|ref|YP_002994293.1| 311 ---RpfqyvlrrfrrkynieemiekiplELNLFDILYVDgqNMIDTPFMERRKVlESVVNSN---EWIKSAENLitk 381
                                       ...2233344445556667778888999999*******964333666666666666666643...555444444332 PP

                                       HHHHHCCC.....HHHHTC--EEEEEESSSSBE.TTE.BSEEEEE CS
                        RNA_ligase 123 aaeellel...l.lskgnkrEGlVikpeselyk.nkg.raifKvk 161
                                         ee       + +  +   EGl  k  +++y+  ++ ++++K+k
  gi|242398869|ref|YP_002994293.1| 382 SPEE---AeafYhKALDLGHEGLMAKRLDSTYEpGNRgKKWLKIK 423
                                       2333...234333355669***************9999*****97 PP

>> FeS_assembly_P  Iron-sulfur cluster assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       5.6   1.4e+04       4      16 ..      26      38 ..      26      38 .. 0.84
   2 ?   -3.5   0.0       4.9   1.3e+04      57      73 ..     168     185 ..     166     186 .. 0.76
   3 ?   12.1   0.0   6.3e-05      0.16      28      66 ..     205     243 ..     196     249 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 5.6
                                      HHHHHTT-B-TTT CS
                    FeS_assembly_P  4 vlaaLrtVtDPel 16
                                      v + L++V  Pel
  gi|242398869|ref|YP_002994293.1| 26 VSDFLKSVEKPEL 38
                                      66889****9985 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 4.9
                                       HHHHHC..STT--EEEEE CS
                    FeS_assembly_P  57 aeaalr.alpgvevveVe 73 
                                       ae  lr al+ +++v+Ve
  gi|242398869|ref|YP_002994293.1| 168 AEGLLRdALADAFKVRVE 185
                                       567788888888888887 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 6.3e-05
                                       EEEE-T-EEEEEE--SSTT-TTHHHHHHHHHHHHC.STT CS
                    FeS_assembly_P  28 eidieggkVsvditltypacslaeairadaeaalralpg 66 
                                       +++ ++g ++v+i+++ p ++++++++a +++al  + g
  gi|242398869|ref|YP_002994293.1| 205 KLEGDEGLAKVKIQVGKPIKPMLAQMAANVREALVEMGG 243
                                       45556699**************************99988 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 ?   11.2   0.0   0.00011      0.28       2      66 .]     439     532 ..     438     532 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00011
                                       ...EEEEEEEEEEEEE....TTEE...EEE-SS--HHHHHH.................HHHTT-EEEEEEE-TTSSS CS
                   DNA_ligase_OB_2   2 GkGkykgmlGallvetk...kgkr...fkiGsGlsdaqRen.................ppkiGkiitykyqeltskg 55 
                                       G+G+ +g+l ++l       kg+     k+GsG++d++  +                 +     +i++ yqe+ ++ 
  gi|242398869|ref|YP_002994293.1| 439 GEGRRSGVLSSFLLGAYdpvKGDFvpvGKVGSGFTDEDLVEftkmlkplikkehgkevELEPKVVIEVAYQEIQKSP 515
                                       889999999999998873334553444799********99999999999998888866333334789*******988 PP

                                       S......-EEEEEEEE- CS
                   DNA_ligase_OB_2  56 v......pRfPsflrvR 66 
                                       +      +RfP++  +R
  gi|242398869|ref|YP_002994293.1| 516 KyesgfaLRFPRYIALR 532
                                       889999******99887 PP

>> mRNA_cap_enzyme  mRNA capping enzyme, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.2   3.1e+03      23      80 ..     250     302 ..     249     317 .. 0.61
   2 ?   10.6   0.1   0.00014      0.37      94     138 ..     338     382 ..     325     423 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.2
                                       EESSEEEEEEEEECTEEEEEEETTS-EEEESSST-BTTSSSSTCTSBGGSEEEEEEEE CS
                   mRNA_cap_enzyme  23 KaDGiRylmllteeeegvylidRenevyrvenlrfprekdkeklekvldetllDgElv 80 
                                       K DG R+ +  + +  +v +  R  e   v  +++p+  ++ k+    ++ ++ gElv
  gi|242398869|ref|YP_002994293.1| 250 KYDGARVQVHKNGN--KVLIYSRRLEN--VT-KSIPEVVERVKEALKPEKVIVEGELV 302
                                       56777777666666..57777776553..33.34555554444455667788888887 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00014
                                       EEEEEEEETTEEGTTSBHHHHHHHHHHHTHHHHHHHHHTTCCCCT CS
                   mRNA_cap_enzyme  94 liyDivaingvtvaeeplskRleilkkelikprneekktglletd 138
                                        ++Di+ ++g+++ ++p+ +R ++l+  + +    +  ++l++++
  gi|242398869|ref|YP_002994293.1| 338 NLFDILYVDGQNMIDTPFMERRKVLESVVNSNEWIKSAENLITKS 382
                                       58***********************99888877777766766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (560 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 3767.77
//
Query:       gi|242398870|ref|YP_002994294.1|  [L=191]
Description: Secreted endonuclease, Holliday junction resolvase-like protein protein [Thermococcus sibiricus MM 739]
Scores for complete 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-64  215.6   4.8    3.9e-64  215.3   4.8    1.0  1  Endonuc_Holl     Endonuclease related to archaeal Holliday ju
     0.0042   17.4   0.0      0.008   16.4   0.0    1.5  1  DUF4263          Domain of unknown function (DUF4263)
     0.0083   16.2   0.1      0.011   15.8   0.1    1.2  1  Peptidase_S49_N  Peptidase family S49 N-terminal


Domain annotation for each model (and alignments):
>> Endonuc_Holl  Endonuclease related to archaeal Holliday junction resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  215.3   4.8   6.6e-68   3.9e-64       1     160 [.      11     168 ..      11     169 .. 0.98

  Alignments for each domain:
  == domain 1  score: 215.3 bits;  conditional E-value: 6.6e-68
                      Endonuc_Holl   1 ilvlvilvlllkiskiqkklekkarelfeewkkeeaeeleklkeaeallkkeaevkleewkkkeekeiRedaikksk 77 
                                       +l++++++l +k+s++++++e+karelfeew+++e e+++++   e+ ++k++e ++++wk +eek+iRedaikksk
  gi|242398870|ref|YP_002994294.1|  11 VLIVLVFILWYKYSELKGQMERKARELFEEWRSKELETQKRVL--EEGIRKNYESEFKKWKLEEEKRIREDAIKKSK 85 
                                       68999******************************99999998..******************************** PP

                      Endonuc_Holl  78 svilgkvtEeliPlfpefsynpkDaRflGtPvDlvvFdGLsegeveeivfvEvKtGkssslseReravrdaieakrv 154
                                       +vi+g+vtE+liP+fp+f+ynpkD+Rf+GtPvD++vFdG+ +g++++ivfvEvKtGk++ l++Re++v+ ++e+++v
  gi|242398870|ref|YP_002994294.1|  86 AVIMGQVTEHLIPYFPDFKYNPKDVRFIGTPVDFIVFDGMTDGDIKRIVFVEVKTGKTGGLTSREKQVKVVVEKREV 162
                                       ***************************************************************************** PP

                      Endonuc_Holl 155 syevlr 160
                                       s+e+++
  gi|242398870|ref|YP_002994294.1| 163 SWEKIH 168
                                       ****98 PP

>> DUF4263  Domain of unknown function (DUF4263)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.3e-06     0.008       9      74 ..      79     162 ..      39     165 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.3e-06
                           DUF4263   9 kffeknpwll........ypiisefpikevdfk..s........Dfllidsl....ngnivlvEikkpdknlltkek 63 
                                       + ++k + ++        +p ++ f+      +  +        Df+++d+      + iv+vE k+ ++  lt ++
  gi|242398870|ref|YP_002994294.1|  79 DAIKKSKAVImgqvtehlIPYFPDFKY-----NpkDvrfigtpvDFIVFDGMtdgdIKRIVFVEVKTGKTGGLTSRE 150
                                       346666666634433333333333333.....133133334566*****9987445599***************998 PP

                           DUF4263  64 kk.gniapseel 74 
                                       k+ ++++ ++e+
  gi|242398870|ref|YP_002994294.1| 151 KQvKVVVEKREV 162
                                       886666655555 PP

>> Peptidase_S49_N  Peptidase family S49 N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   1.9e-06     0.011      12      91 ..       3      82 ..       1     103 [. 0.86

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.9e-06
                   Peptidase_S49_N 12 klvtlvvailvvvvlivalaakkkkekgelevtkLneeykelkeeleealldeeelkaaekkekkeekeekkaekkkak 90
                                      ++v ++v +l+v+v+i+  +  + k + e + ++L ee+++ + e ++++l+e  +k++e + kk + ee+k+ +++a 
  gi|242398870|ref|YP_002994294.1|  3 EMVWIIVGVLIVLVFILWYKYSELKGQMERKARELFEEWRSKELETQKRVLEEGIRKNYESEFKKWKLEEEKRIREDAI 81
                                      5788899999999999999988889999999**********************************99999998755443 PP

                   Peptidase_S49_N 91 e 91
                                      +
  gi|242398870|ref|YP_002994294.1| 82 K 82
                                      3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1493  (0.0832729); expected 358.6 (0.02)
Passed bias filter:                      834  (0.0465168); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 1296.71
//
Query:       gi|242398871|ref|YP_002994295.1|  [L=154]
Description: nucleic acid-binding protein, containing PIN domain [Thermococcus sibiricus MM 739]
Scores for complete 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-26   92.1   0.8    4.1e-26   91.9   0.8    1.1  1  PIN        PIN domain
  ------ inclusion threshold ------
      0.012   16.1   0.4      0.034   14.6   0.3    1.7  1  PIN_12     PIN domain
      0.024   14.3   0.0      0.033   13.9   0.0    1.2  1  DUF4423    Domain of unknown function (DUF4423)
        3.3    7.6   5.0        2.9    7.8   0.2    2.6  3  PKcGMP_CC  Coiled-coil N-terminus of cGMP-dependent protein k


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 !   91.9   0.8   9.2e-30   4.1e-26       1     122 []       6     148 ..       6     148 .. 0.95

  Alignments for each domain:
  == domain 1  score: 91.9 bits;  conditional E-value: 9.2e-30
                                       EEE-HHHHHHHH.TTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHS...................SCHCHHHHHH CS
                               PIN   1 ivlDTsvliall.rgeekaeaarklleeleelvtsalvlaEllyvlar...................rkskrekaae 57 
                                       +++D+svl+ l   +e+  e ++ l+e+   l+++++v++E++y+++                    ++ + + + +
  gi|242398871|ref|YP_002994295.1|   6 VFIDSSVLVGLNlGDEKAKELVKSLIERGCILIINPIVFSETAYKVMFtlalkdglkgvhdlkkhldKYAWTYGKVK 82 
                                       69*******99978888888888899999**************************************9999999999 PP

                                       HHHHHHH.HHTSEEEEBCHHHHHHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHHHHHHC CS
                               PIN  58 lvellll.lsalkilpidaeiaeeaaeialkygllpnDaliaAtAkehgikliatfDedfrrvakl 122
                                       +  +ll+  + lk++++++ei+e  a+i ++y ll+nDa+iaAt+k+ gik+iatfDedfr+v++l
  gi|242398871|ref|YP_002994295.1|  83 ESIALLIkNELLKVVEVNWEILELSAKIGEEYALLTNDAIIAATCKHFGIKKIATFDEDFRKVDFL 148
                                       9999999899*****************************************************985 PP

>> PIN_12  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.3   7.7e-06     0.034       1      54 [.       6      56 ..       6     124 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 7.7e-06
                            PIN_12  1 ifiDTnifldeffrlseeealkklleliesgkiklivpdivldEflknrekkie 54
                                      +fiD++++   +++l+ e + k+l++ + ++++ li++ iv+ E+  ++   + 
  gi|242398871|ref|YP_002994295.1|  6 VFIDSSVLV--GLNLGDE-KAKELVKSLIERGCILIINPIVFSETAYKVMFTLA 56
                                      8********..7999999.8889988888889************9877655555 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   7.3e-06     0.033      17      88 ..      43     113 ..      40     148 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 7.3e-06
                           DUF4423  17 yfssWyypvirellplkdfkadpeelakrlrp.kisaeevekalefLlklgllkkdedgkyrqtekslttsse 88 
                                       +fs+  y v+++ l+lkd+ + ++ l+k+l + + +  +v++++ +L k++llk  e  +++  e s ++++e
  gi|242398871|ref|YP_002994295.1|  43 VFSETAYKVMFT-LALKDGLKGVHDLKKHLDKyAWTYGKVKESIALLIKNELLKVVEV-NWEILELSAKIGEE 113
                                       688899999997.899***9**********9735689********************8.99988888887766 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 ?    1.7   0.1     0.055   2.4e+02       5      20 ..      18      33 ..      16      34 .. 0.80
   2 ?    7.8   0.2   0.00064       2.9      24      34 ..      64      74 ..      54      75 .. 0.84
   3 ?   -3.6   0.1       2.4   1.1e+04      23      30 ..     102     109 ..     102     110 .. 0.62

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.055
                         PKcGMP_CC  5 lKDERIRELEkrlaek 20
                                      l DE+ +EL k l e+
  gi|242398871|ref|YP_002994295.1| 18 LGDEKAKELVKSLIER 33
                                      669******9988776 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00064
                         PKcGMP_CC 24 IqELrskLDKf 34
                                      + +L+ +LDK+
  gi|242398871|ref|YP_002994295.1| 64 VHDLKKHLDKY 74
                                      789*******9 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 2.4
                         PKcGMP_CC  23 EIqELrsk 30 
                                       EI EL +k
  gi|242398871|ref|YP_002994295.1| 102 EILELSAK 109
                                       67777554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1043.41
//
Query:       gi|242398872|ref|YP_002994296.1|  [L=69]
Description: hypothetical protein TSIB_0889 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      3e-16   59.6   7.8    3.7e-16   59.3   7.8    1.1  1  DUF104      Protein of unknown function DUF104
  ------ inclusion threshold ------
      0.038   14.3   0.1      0.049   14.0   0.1    1.3  1  DUF190      Uncharacterized ACR, COG1993
       0.08   13.0   1.1       0.08   13.0   1.1    1.9  2  Smoothelin  Smoothelin cytoskeleton protein
       0.08   12.1   0.3      0.093   11.9   0.3    1.1  1  CENP-M      Centromere protein M (CENP-M)


Domain annotation for each model (and alignments):
>> DUF104  Protein of unknown function DUF104
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.3   7.8   8.4e-20   3.7e-16       2      56 ..       5      63 ..       4      66 .. 0.89

  Alignments for each domain:
  == domain 1  score: 59.3 bits;  conditional E-value: 8.4e-20
                            DUF104  2 skvIeavYEnGvLKPLekvdLkEGeevkikIeeakeilkklkgilk....eadeeelee 56
                                       +vIeavYEnGvLKPL+k++LkE+++v ikI + +e+ k l +++     ++d+++l+e
  gi|242398872|ref|YP_002994296.1|  5 MQVIEAVYENGVLKPLKKLKLKEHSKVIIKIIDEEELDKLLNSMVIekieNIDYKKLKE 63
                                      48*******************************88888888888878777888888887 PP

>> DUF190  Uncharacterized ACR, COG1993
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   1.1e-05     0.049      35      72 ..       3      40 ..       1      57 [. 0.88

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.1e-05
                                      EEEE-S---------------------EEEEEEEE-HH CS
                            DUF190 35 tvlrGieGfgassrihtakllelsedlPvvieivdtee 72
                                       v++ ie + ++++++  k l+l+e+  v+i+i+d+ee
  gi|242398872|ref|YP_002994296.1|  3 RVMQVIEAVYENGVLKPLKKLKLKEHSKVIIKIIDEEE 40
                                      58999******************************987 PP

>> Smoothelin  Smoothelin cytoskeleton protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   1.1   1.8e-05      0.08       6      29 ..      24      47 ..      21      49 .. 0.86
   2 ?   -0.9   0.1      0.39   1.7e+03      14      21 ..      50      57 ..      45      58 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.8e-05
                        Smoothelin  6 askltseeLeaIeDeevLdkmLeq 29
                                      ++k+ s+ + +I Dee+Ldk+L +
  gi|242398872|ref|YP_002994296.1| 24 KLKEHSKVIIKIIDEEELDKLLNS 47
                                      6788899999************75 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.39
                        Smoothelin 14 LeaIeDee 21
                                      +e+Ie+++
  gi|242398872|ref|YP_002994296.1| 50 IEKIENID 57
                                      77787765 PP

>> CENP-M  Centromere protein M (CENP-M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.3   2.1e-05     0.093       3      39 ..      16      52 ..      14      60 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.1e-05
                            CENP-M  3 vLrpfdKlpelntatvLLvgteeklkeqLaeaivkee 39
                                      vL+p++Kl  +++++v++  ++e+ +++L +++v e+
  gi|242398872|ref|YP_002994296.1| 16 VLKPLKKLKLKEHSKVIIKIIDEEELDKLLNSMVIEK 52
                                      9*******************************99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1056  (0.058899); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 482.07
//
Query:       gi|242398873|ref|YP_002994297.1|  [L=136]
Description: hypothetical protein TSIB_0890 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score 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   13.8   0.8        2.6    8.6   0.1    3.0  3  TcpE      TcpE family


Domain annotation for each model (and alignments):
>> TcpE  TcpE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0     0.057     1e+03      20      32 ..       6      18 ..       3      22 .. 0.59
   2 ?    1.4   0.0     0.025   4.5e+02       9      27 ..      35      53 ..      33      74 .. 0.63
   3 ?    8.6   0.1   0.00014       2.6       9      48 ..      91     132 ..      86     136 .] 0.88

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.057
                              TcpE 20 Lpfpislsqiivf 32
                                      L++pi+l++i+ f
  gi|242398873|ref|YP_002994297.1|  6 LKTPIELQEIAEF 18
                                      5556666655544 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.025
                              TcpE  9 pkkiqkikdfsLpfpisls 27
                                      p +i++ikd +L+ +++ +
  gi|242398873|ref|YP_002994297.1| 35 PSSIRQIKDKYLELRMKAE 53
                                      5677777776666555443 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.00014
                              TcpE   9 pkkiqkikd..fsLpfpislsqiivfvlvlvlllllaslipv 48 
                                       ++k++++k    +L+ +++  +i+v+vl  +l  +l+++++ 
  gi|242398873|ref|YP_002994297.1|  91 KYKLYEMKIscKELQKAVTTCKILVYVLASALATILGTIVAK 132
                                       78999988888*************************998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       784  (0.043728); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 898.74
//
Query:       gi|242398874|ref|YP_002994298.1|  [L=48]
Description: hypothetical protein TSIB_0891 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       216  (0.0120475); expected 358.6 (0.02)
Passed bias filter:                      193  (0.0107647); 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: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 334.00
//
Query:       gi|242398875|ref|YP_002994299.1|  [L=226]
Description: phosphoglycolate phosphatase [Thermococcus sibiricus MM 739]
Scores for complete 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   80.2   0.0    2.7e-22   79.7   0.0    1.2  1  HAD_2            Haloacid dehalogenase-like hydrolase
    2.7e-15   57.2   0.1    3.8e-14   53.5   0.1    2.0  1  Hydrolase        haloacid dehalogenase-like hydrolase
    3.3e-10   39.9   0.0    6.5e-10   38.9   0.0    1.5  1  Hydrolase_like   HAD-hyrolase-like
    6.9e-08   33.1   0.0    8.8e-08   32.8   0.0    1.1  1  HAD              haloacid dehalogenase-like hydrolase
     0.0016   18.1   1.6      0.061   12.9   1.6    2.3  1  Acid_phosphat_B  HAD superfamily, subfamily IIIB (Acid phosph
  ------ inclusion threshold ------
      0.094   12.3   0.0       0.13   11.9   0.0    1.3  1  DUF2229          CoA enzyme activase uncharacterised domain (


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 !   79.7   0.0     9e-26   2.7e-22       1     178 []      10     195 ..      10     195 .. 0.80

  Alignments for each domain:
  == domain 1  score: 79.7 bits;  conditional E-value: 9e-26
                             HAD_2   1 iiFDlDgTlldteel.iiqafnelleey..gls.elseeelrkliglsl.rellrklgeseeeee..kieellrkyn 70 
                                       +iFD+D Tl+  e +   + f+++++++  +l+ +++ e ++k++  +l r  +++lg++ ++e    i++   ky+
  gi|242398875|ref|YP_002994299.1|  10 LIFDVDETLVYYESYdGKEWFEKWAKREikNLEaNVDFETYKKMVKGKLpRSWVENLGVD-HVEFwkAIDRAKLKYR 85 
                                       69*******977666245667777766655556677778887777555526677888875.4444685555555555 PP

                             HAD_2  71 eekkk.kevkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsed..vekkKPdpevieka 144
                                       +   +   +k + +v ++L++ ke+g+k++ v++ s++ +e  l+ +g+++yFdv+++++     + KP+p +i+k 
  gi|242398875|ref|YP_002994299.1|  86 KWAAEqGLIKAFLDV-DVLKTFKEMGLKMAAVSNASQDCTEFVLNLFGLKRYFDVVLGKDYkyLDGAKPNPYLIKKS 161
                                       555554569999998.69****************************************997224567********** PP

                             HAD_2 145 leklklkkeeviyvGDsptDieaakkagikviav 178
                                       l+ l+++++e+++vGDs +Di aa+ ag k++ v
  gi|242398875|ref|YP_002994299.1| 162 LKALEVSPKEALVVGDSLSDILAAHGAGAKAVQV 195
                                       ******************************9865 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.5   0.1   1.3e-17   3.8e-14       1     210 []       7     189 ..       7     189 .. 0.76

  Alignments for each domain:
  == domain 1  score: 53.5 bits;  conditional E-value: 1.3e-17
                                       SSEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETTTEHHHHTHHH.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                         Hydrolase   1 iktvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakarsgaltgfatfigrgayaigkpe.. 75 
                                       ik+++fD+d TL+  e      ++                   + + ++ak +  +l+ +  f+   +  +gk    
  gi|242398875|ref|YP_002994299.1|   7 IKALIFDVDETLVYYE-----SYDGK-----------------EWFEKWAKREIKNLEANVDFETYKKMVKGKLPrs 61 
                                       899**********777.....44444.................3334455555555544444444555555543333 PP

                                       HHHHHHCHHHHHHHHHHHHHHCHHHHHH...TTHHHHHHHHHHTHHBHTTHH.HHHHHHHHTTEEEEEEESSEHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  76 wltaldippdlgaaigsaqsqgrtvall...qaralavftiadplkvkpeaa.eavasLkaagievvlltgdnpeta 148
                                       w++ l              + ++ ++++    a++    ++a++  +k  +  ++++++k++g++++ +++ ++   
  gi|242398875|ref|YP_002994299.1|  62 WVENL--------------GVDHVEFWKaidRAKLKYRKWAAEQGLIKAFLDvDVLKTFKEMGLKMAAVSNASQDCT 124
                                       66666..............2222222222224466777777778788888888************************ PP

                                       HHHHHHTT.GGGESEEEEHHCES..STTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                       xxxxxxxx.xxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 149 eraanqlG.ddyfdaviasdiet..vakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                       e ++n +G ++yfd+v+++d +    akp+p   ++ ++ L ++p+e ++VGD++ D+ a+  Ag
  gi|242398875|ref|YP_002994299.1| 125 EFVLNLFGlKRYFDVVLGKDYKYldGAKPNPYLIKKSLKALEVSPKEALVVGDSLSDILAAHGAG 189
                                       *************************************************************9987 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9   0.0   2.2e-13   6.5e-10       4      50 ..     152     197 ..     150     214 .. 0.91

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 2.2e-13
                                       TTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESS CS
                    Hydrolase_like   4 KPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVlt 50 
                                       KP+p +++  l++l++ p+e l++GD+  +Di++A++aG+k v V +
  gi|242398875|ref|YP_002994299.1| 152 KPNPYLIKKSLKALEVSPKEALVVGDS-LSDILAAHGAGAKAVQVMR 197
                                       ***************************.***************9976 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.0   2.9e-11   8.8e-08       2     187 ..      11     185 ..      10     186 .. 0.83

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 2.9e-11
                               HAD   2 lfDfDgTLldgdsle..lllrfllrrgaprl.wralreklllalfrellrldraglaelleallaglseelaaeler 75 
                                       +fD+D TL+  +s++  ++++++++r  + l +    e++++ +  +l r+  + l     +++++ + +  ++ + 
  gi|242398875|ref|YP_002994299.1|  11 IFDVDETLVYYESYDgkEWFEKWAKREIKNLeANVDFETYKKMVKGKLPRSWVENLGVDHVEFWKAIDRAKLKYRKW 87 
                                       8********************99999888863333344488888999999999999999999999999655555555 PP

                               HAD  76 fvaevirpklldpgalellaahraaGdrvvvvSgglrplvepllaelg....adevlatelevdd..rltgelgleg 146
                                       + ++   +++ld ++l+ ++   + G + + vS++ + ++e +l+++g    +d vl+      d  +l+g    ++
  gi|242398875|ref|YP_002994299.1|  88 AAEQGLIKAFLDVDVLKTFK---EMGLKMAAVSNASQDCTEFVLNLFGlkryFDVVLGK-----DykYLDGA--KPN 154
                                       5566666667777*******...************************************.....33499999..888 PP

                               HAD 147 kpvrgegkvaalrewlaaegegidleevvayGDspsDlpll 187
                                       +   +    ++l++       + +++e  ++GDs sD+ ++
  gi|242398875|ref|YP_002994299.1| 155 PYLIK----KSLKA------LEVSPKEALVVGDSLSDILAA 185
                                       88888....89999......777788899*********887 PP

>> Acid_phosphat_B  HAD superfamily, subfamily IIIB (Acid phosphatase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   1.6   2.1e-05     0.061      72     220 ..       6     196 ..       1     209 [. 0.65

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.1e-05
                                       SEEEEEE--BTTTEEHHHHHHHCHHHTCHH-T..........................TH................. CS
                   Acid_phosphat_B  72 kkdavvfDiDeTvLsnspYqkyqglgkkkfdp..........................ek................. 105
                                        ++a +fD+DeT+     Y ++++++k +  +                          e+                 
  gi|242398875|ref|YP_002994299.1|   6 MIKALIFDVDETLVYYESYDGKEWFEKWAKREiknleanvdfetykkmvkgklprswvENlgvdhvefwkaidrakl 82 
                                       4799**********999999999984444433323333444433433555555555540055555555555555555 PP

                                       .HHHHHHTTGGCCECCHHHHHHHHHHTTEEEEEEEEEECCCHHHHHHHHHHCT.....-TTBSCCEEECCSTTC--- CS
                   Acid_phosphat_B 106 .fdewvnkgeakaipgalelikkvverGvkiffvsgRseeqkaaTvenLkkag.....fssweklilkgkkdkqkks 176
                                        +++w +++   +    ++++k  +e G k+  vs+ s++  ++ v nL   +     + +++  +l g k+ +   
  gi|242398875|ref|YP_002994299.1|  83 kYRKWAAEQGLIKAFLDVDVLKTFKEMGLKMAAVSNASQD-CTEFVLNLFGLKryfdvVLGKDYKYLDGAKP-NP-- 155
                                       5888888888766666789999999999999999999998.4555666655556655544778888888887.33.. PP

                                       HHHHHHHHHHHHHHTTEEEEEEEESSGGGCHCCHHCTCCCCEEE CS
                   Acid_phosphat_B 177 vvsyKeerrqklekkGynivlniGDnlsDlngakeaeargerii 220
                                           K+ +  +++ k     l++GD+lsD+ +a  a+a++ +++
  gi|242398875|ref|YP_002994299.1| 156 YLIKKSLKALEVSPK---EALVVGDSLSDILAAHGAGAKAVQVM 196
                                       344467777777666...46789999999999888888874444 PP

>> DUF2229  CoA enzyme activase uncharacterised domain (DUF2229)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   4.4e-05      0.13     108     189 ..      35     149 ..      19     165 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.4e-05
                           DUF2229 108 eeeikllspvldledkke.....lakqlleelgiskkeikkAvekAleaqkafkeelrkkgeelle.....eleeeg 174
                                       ++eik+l+ ++d+e+ k+     l ++ +e+lg+++ e  kA+++A  +++++ +e +   +++l+     +++e  
  gi|242398875|ref|YP_002994299.1|  35 KREIKNLEANVDFETYKKmvkgkLPRSWVENLGVDHVEFWKAIDRAKLKYRKWAAE-QGLIKAFLDvdvlkTFKEM- 109
                                       778999********66664667777777789*********************9866.4444445545433322222. PP

                           DUF2229 175 kkg...........................ivllGrpYhild 189
                                         g                            v+lG+ Y  ld
  gi|242398875|ref|YP_002994299.1| 110 --GlkmaavsnasqdctefvlnlfglkryfDVVLGKDYKYLD 149
                                       ..1222344455556667777777777777777777777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1427.72
//
Query:       gi|242398876|ref|YP_002994300.1|  [L=321]
Description: Threonine dehydratase [Thermococcus sibiricus MM 739]
Scores for complete 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-83  279.9   0.0    2.8e-83  279.7   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 !  279.7   0.0   1.6e-87   2.8e-83       3     294 .]      17     305 ..      15     305 .. 0.99

  Alignments for each domain:
  == domain 1  score: 279.7 bits;  conditional E-value: 1.6e-87
                                       GCSSS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT- CS
                              PALP   3 lgigpTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaallGl 79 
                                       + i++TPl  +p ls++ +++++lKlE+++ tgSfK+Rg+ + l++l e+++++++v+assGNhg+a A+a++ l+l
  gi|242398876|ref|YP_002994300.1|  17 DYIRETPLDYSPFLSQKGNANVYLKLENFQLTGSFKIRGVFNKLLSLSEEEKKRGIVTASSGNHGAAFAYASNFLNL 93 
                                       679*******************************************99999************************** PP

                                       EEEEEEETTS-HHHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHHHTHHHHHHHHTTT CS
                              PALP  80 kvtivvpadaspekvallrllGaevvevggdydeavaaaaelaaegegaylvsqfdnptviegygtiglEileqlgg 156
                                         ++++p++asp+k++ +++++ e++++g+d+  ++  a+++a+e +++++v+++++p vi g+gtig E+ +qlg 
  gi|242398876|ref|YP_002994300.1|  94 NGIVFLPENASPAKIQDIKQYNVELRFYGNDTVKTEIFARNFAEE-QEMIYVPPYNDPKVIGGQGTIGVELEKQLG- 168
                                       *******************************9999999*******.*************************99997. PP

                                       TEEEEEEE-SSSHHHHHHHHHHHHHSTT-EEEEEEECTTCGGTTCCS..S.SS..B.SSS.CCSTCS.CGTTCCHHH CS
                              PALP 157 kpdavvvpvGgGgliaGiaaglkerrpdvrvigvepegsdalarslragrrvtvpvsdtiadglavg.spselafel 232
                                       k+dav+vpvGgGgli+Gia +lke+  dv++igv+pe+s+ ++ s++ag+ +++++++t+adg a g +  + +fel
  gi|242398876|ref|YP_002994300.1| 169 KIDAVLVPVGGGGLISGIAGYLKEKMKDVEIIGVQPENSAVMYYSIKAGKILELESKPTLADGTAGGiEKDSITFEL 245
                                       ***************************************************************************** PP

                                       HSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHHHHHHHHCCTTCEEEEEEE-B CS
                              PALP 233 ldrlvdeivtvsdeealeamrllarregivvepssaaalaalklreagelkegdrvvviltg 294
                                       ++++vd+++ +s+ee++e + l+ +++++++e ++a ++aa+ l+ea ++k++ +vv+il+g
  gi|242398876|ref|YP_002994300.1| 246 CRKYVDDFILLSEEEIAESILLMLEKHHMLIEGAAALSVAAY-LKEAPRFKGK-NVVLILSG 305
                                       ******************************************.**********.******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); 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: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 2005.96
//
Query:       gi|242398877|ref|YP_002994301.1|  [L=378]
Description: aromatic aminotransferase [Thermococcus sibiricus MM 739]
Scores for complete 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-42  143.9   0.0    8.9e-42  143.5   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    1.2e-05   24.0   0.0    1.9e-05   23.4   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    0.00017   20.7   0.0    0.00028   20.0   0.0    1.2  1  Aminotran_5      Aminotransferase class-V
    0.00026   19.9   0.0     0.0031   16.4   0.0    2.0  1  Aminotran_MocR   Alanine-glyoxylate amino-transferase
    0.00042   19.3   0.0     0.0006   18.8   0.0    1.2  1  Alliinase_C      Allinase
  ------ inclusion threshold ------
      0.069   13.1   0.0       0.17   11.8   0.0    1.6  1  DUF240           Domain of unknown function (DUF240)


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 !  143.5   0.0     3e-45   8.9e-42      39     348 ..      58     354 ..      46     367 .. 0.92

  Alignments for each domain:
  == domain 1  score: 143.5 bits;  conditional E-value: 3e-45
                                       ST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTS CS
                     Aminotran_1_2  39 eygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasyknilrlsgg 115
                                        yg  +glpel++ l  f++     ++k++ ++ ++ Ga  ++  ++  l ++ gd +++  pty +   + +  g+
  gi|242398877|ref|YP_002994301.1|  58 TYGYVEGLPELKKGLSGFYK-----NVKPD-TIFTTHGAIDANFQVFYSL-VESGDTVISIFPTYQQLYSVPESFGA 127
                                       699*****************.....89999.*******************.9************************* PP

                                       EEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTT CS
                     Aminotran_1_2 116 evvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYag 192
                                       ++  ++l++e+++  dl++l e++++      ktk+i+v+sp+NPtG++++++ l+ + ++a+  n++++ De Y g
  gi|242398877|ref|YP_002994301.1| 128 KIKLWHLHEENNWMPDLDELNELVDK------KTKLIVVNSPNNPTGALLDEKMLRGITEIAEDANAYVLNDESYRG 198
                                       **************************......********************************************* PP

                                       CBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEE.EHHHHHHHHHHHHHHTS..SHHHHHHHHHHHHH CS
                     Aminotran_1_2 193 fvfgsldavatranveeepnllivgslsKafGlaGeRvGyilg.naavvsqlrklsrpfls..ssllqaavaaalsd 266
                                       ++ +++d v+ +++++++   + ++s+sK ++l+G+R+G+i+  +++v++ l+      ++  s l  +++a a+++
  gi|242398877|ref|YP_002994301.1| 199 LYINPEDWVPSIVDISDR--AIATNSFSKPLSLTGLRLGWIATsSEEVAKELTLHRDYTTIsiSLLIEKLAALAIEH 273
                                       ****99988878888776..79*********************6667777777655554446666777777777777 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHS.TEEEECCSCSSEEEEEETHH.CHHHHHHHHHHTCTEEEEEGGGGTST CS
                     Aminotran_1_2 267 allkqseleemrqrlqkrrkelrdeLael.glkvlasqsgmflltdlsae.takelskkLleevgvyvtpgtsftvp 341
                                       a++     e + + l k+ k l + ++e   ++++++++g + + +++ e   +el+  L++e+   ++pg++f+++
  gi|242398877|ref|YP_002994301.1| 274 AEK---IYERNLKILRKNFKLLEEWIKEEpLVDWVPPKAGTVAFLRYNLEiPSEELAIRLIKEKSTFLVPGSCFGIE 347
                                       777...59******************999999******************9999*********************** PP

                                       TEEEEEC CS
                     Aminotran_1_2 342 grlRitv 348
                                       ++lRi +
  gi|242398877|ref|YP_002994301.1| 348 NHLRIGY 354
                                       *****98 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   6.5e-09   1.9e-05      79     177 ..      93     197 ..      81     217 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 6.5e-09
                                       HHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEEST...TSHHHHHHHCCTTEEEEEEESS-TTTT- CS
                   Cys_Met_Meta_PP  79 AiaaailallkaGdeivvsddlYggtqrllkkvlkklgievkfvdt...sdleelekaikentklvylEtptnpllk 152
                                       A ++++ +l+++Gd +++    Y+  +++ +++  k+++ + + +     dl+el++ ++++tkl+ + +p np+  
  gi|242398877|ref|YP_002994301.1|  93 ANFQVFYSLVESGDTVISIFPTYQQLYSVPESFGAKIKLWHLHEENnwmPDLDELNELVDKKTKLIVVNSPNNPTGA 169
                                       778999*******************999999988886665555443223899************************* PP

                                       ---...HHHHHHHHHHTT-EEEEEGTTT CS
                   Cys_Met_Meta_PP 153 vvD...iekiaklakkagvlvvvDntfa 177
                                       ++D   ++ i+++a +a++ v+ D ++ 
  gi|242398877|ref|YP_002994301.1| 170 LLDekmLRGITEIAEDANAYVLNDESYR 197
                                       *997767789999999999999988764 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   9.3e-08   0.00028      58     176 ..      78     194 ..      61     197 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 9.3e-08
                                       -STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBET..TSCBEGGGH CS
                       Aminotran_5  58 aeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkviplde..egeldldel 132
                                         + ++i  t+G+ +a+  v +sl   ++ gd+++        +l     + +  gak+k + l e  ++  dldel
  gi|242398877|ref|YP_002994301.1|  78 NVKPDTIFTTHGAIDANFQVFYSL---VESGDTVISIFPT-YQQL---YSVPESFGAKIKLWHLHEenNWMPDLDEL 147
                                       444466666777777888888888...8888877643333.3333...5778889999998877542278899**** PP

                                       HHH--TTEEEEEEESBETTTTEB--...HHHHHHHHHHTT-EEEEE- CS
                       Aminotran_5 133 ekllnektklvaithvsnvtGtiqp...veeigklakkkgalvlvDa 176
                                       ++l+++ktkl+ ++  +n tG + +   +  i+++a +++a+vl D 
  gi|242398877|ref|YP_002994301.1| 148 NELVDKKTKLIVVNSPNNPTGALLDekmLRGITEIAEDANAYVLNDE 194
                                       **********************7662336678999999999999885 PP

>> Aminotran_MocR  Alanine-glyoxylate amino-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0     1e-06    0.0031     126     272 ..     107     246 ..      35     260 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1e-06
                                       EEEEEES--HHHHHHHHHHT-EEEEEEEETTE...E-HHHHHHHHHC-TTEEEEEE-SSS-TTT-----HHHHHHHH CS
                    Aminotran_MocR 126 kllvtvpGydrhfllleelGielltvdlqddG...pdvdaveklvaedasvkGilavpkysnptGetiseevarrla 199
                                        ++   p y++ + + e++G ++    l+++    pd+d +++lv + +    +++v    nptG  + e++ r ++
  gi|242398877|ref|YP_002994301.1| 107 TVISIFPTYQQLYSVPESFGAKIKLWHLHEENnwmPDLDELNELVDKKTK---LIVVNSPNNPTGALLDEKMLRGIT 180
                                       4677789*************9998888876643449********987764...56788899*********9999999 PP

                                       T---SSTT-EEEEE-TTSS-BS.SSSS----HHHHHHHHT-TTSEEEEEESTT.TS-TTSS-EEEEE-HHHHHH CS
                    Aminotran_MocR 200 alkaaapdfrifaddayavhdlvaeedkdanivalardaGhpdrafvlastsk.itfaGaGvafvassedniaw 272
                                        +   a  + ++ d++y+   +   ed  + iv +       dra+   s sk ++++G  ++ +a+s++++a 
  gi|242398877|ref|YP_002994301.1| 181 EIAEDANAY-VLNDESYRGLYI-NPEDWVPSIVDI------SDRAIATNSFSKpLSLTGLRLGWIATSSEEVAK 246
                                       998888776.679****97655.334444455554......5899999999997899********999999875 PP

>> Alliinase_C  Allinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0     2e-07    0.0006     136     229 ..     153     260 ..     102     281 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2e-07
                                       .S-EEEEEESS-TTT---.-----.......-TT-EEEEEE-TT...-.STT..TS---S-B--SEEEEEHHHHHS- CS
                       Alliinase_C 136 peefielvtsPnnPdgll.reavv.......kgseakviyDlay...Y.WPh..ytpitskadedimLftlskltGh 198
                                       ++  + +v sPnnP g+l  e+++       ++ +a v+ D  y   Y  P+     i   +d  i   ++sk    
  gi|242398877|ref|YP_002994301.1| 153 KKTKLIVVNSPNNPTGALlDEKMLrgiteiaEDANAYVLNDESYrglYiNPEdwVPSIVDISDRAIATNSFSKPLSL 229
                                       44556689*******9862556665555655788999999998744332453323469999**************** PP

                                       GGG-EEEEEES-HHHHHHHHHHHHHHHSS-- CS
                       Alliinase_C 199 aGsrlGWalvkdkevakklveyieknsiGvs 229
                                       +G rlGW     +evak l+ +   ++i +s
  gi|242398877|ref|YP_002994301.1| 230 TGLRLGWIATSSEEVAKELTLHRDYTTISIS 260
                                       *******************998888888776 PP

>> DUF240  Domain of unknown function (DUF240)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   5.6e-05      0.17      40     100 ..     230     290 ..     216     299 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.6e-05
                            DUF240  40 kgndlntqlFskvkvkkLvsdenDlTtlAktalgdqlfdlkvdLtkSiidlelkeaekkfe 100
                                       +g  l +   s  +v k  + + D Tt+  ++l ++l +l ++  + i++ +lk ++k+f+
  gi|242398877|ref|YP_002994301.1| 230 TGLRLGWIATSSEEVAKELTLHRDYTTISISLLIEKLAALAIEHAEKIYERNLKILRKNFK 290
                                       55556666666667777777789************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); 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: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 2555.54
//
Query:       gi|242398878|ref|YP_002994302.1|  [L=243]
Description: ParB-like nuclease, [Thermococcus sibiricus MM 739]
Scores for complete 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-49  164.4   3.3    1.6e-48  163.4   3.3    1.5  1  DUF5603   Domain of unknown function (DUF5603)
    1.3e-09   38.2   0.0    3.1e-09   37.0   0.0    1.6  1  ParBc     ParB-like nuclease domain
    8.3e-05   21.6   0.0      0.073   11.9   0.1    2.4  2  DUF1015   Protein of unknown function (DUF1015)


Domain annotation for each model (and alignments):
>> DUF5603  Domain of unknown function (DUF5603)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.4   3.3   2.6e-52   1.6e-48       1     105 []     101     201 ..     101     201 .. 0.99

  Alignments for each domain:
  == domain 1  score: 163.4 bits;  conditional E-value: 2.6e-52
                                       --EEEEES-HHHHHHHHHHTT---EE-TTHHHH...HHCTSSSEEEES..SSEEEE--SHHHHHHHHHHHHHHHHTT CS
                           DUF5603   1 twypaikgdlnklleelkkeglrveedkekeeklkdeelgkiafvlvgkneksykiygsleeqkkvskvldklsleg 77 
                                       twypa+kgdlnk++e+lk egl+v edke+eek   +e+g+iaf+lvg +ek+++i+g+l+eqkkvskvld++s+eg
  gi|242398878|ref|YP_002994302.1| 101 TWYPAFKGDLNKVIERLKAEGLEVLEDKEAEEK---AERGEIAFALVG-KEKTFTIPGALNEQKKVSKVLDEMSVEG 173
                                       8********************************...************.79************************** PP

                                       SSEEEEESSHHHHHHHHHTTS-SEEEE- CS
                           DUF5603  78 kielvyygekeealrdlekgkidylflr 105
                                       +iel+yyg+ke+a++d+ekg+idy+f+r
  gi|242398878|ref|YP_002994302.1| 174 EIELIYYGLKEDAREDMEKGEIDYVFIR 201
                                       ***************************8 PP

>> ParBc  ParB-like nuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   0.0   5.2e-13   3.1e-09       3      76 ..      21      92 ..      12     101 .. 0.84

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 5.2e-13
                             ParBc  3 vplseirpnplqprkd.spekieelvasIkkkGll.qPiivrktr.qgryeiiaGerRlrAakrlglkevpvivlei 76
                                      ++l++++     p+ +  ++++e+ ++s  ++G+  +P +  k++ +++y i++G++R+  ++ lg+k+ p ++l+ 
  gi|242398878|ref|YP_002994302.1| 21 IELDKMK-----PHEQlVQKELEAFIESVTGSGVFwKPMLLAKVPgEDMYLIVDGHHRWAGLEKLGAKKAPSVILDY 92
                                      4444444.....444444889**************************************************888775 PP

>> DUF1015  Protein of unknown function (DUF1015)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.0   0.00027       1.6     201     223 ..      61      83 ..      19      94 .. 0.80
   2 !   11.9   0.1   1.2e-05     0.073     330     380 ..     174     224 ..     110     226 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00027
                           DUF1015 201 adkklyIADGHHRyatalavree 223
                                        ++ ++I DGHHR+a   +++ +
  gi|242398878|ref|YP_002994302.1|  61 GEDMYLIVDGHHRWAGLEKLGAK 83 
                                       566789*********88887754 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 1.2e-05
                           DUF1015 330 deridyvhgleeavekvdsgeagvafllnptsveelfavadagevmPrKST 380
                                       + ++ y +  e+a e++++ge ++ f+ ++ s+ee+++++++gev  +K+T
  gi|242398878|ref|YP_002994302.1| 174 EIELIYYGLKEDAREDMEKGEIDYVFIRKAPSKEEVMELVKRGEVYSPKTT 224
                                       4444577779****************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       633  (0.0353059); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1565.42
//
Query:       gi|242398879|ref|YP_002994303.1|  [L=207]
Description: Proteasome subunit beta precursor [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-51  175.0   1.1    1.5e-51  174.6   1.1    1.1  1  Proteasome  Proteasome subunit
  ------ inclusion threshold ------
        0.1   13.0   0.8        0.2   12.0   0.8    1.6  1  GNAT_like   GCN5-related N-acetyltransferase like domain


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 !  174.6   1.1   1.7e-55   1.5e-51       3     190 .]       8     187 ..       7     187 .. 0.97

  Alignments for each domain:
  == domain 1  score: 174.6 bits;  conditional E-value: 1.7e-55
                                       HS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSGT CS
                        Proteasome   3 kGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygrpi 79 
                                       kGtt+vGi +kdgvvl ad+ra+ g++++sk  v+Kif++ddh+++a aG ++D+  lvr +rae +lyr + g+++
  gi|242398879|ref|YP_002994303.1|   8 KGTTTVGIVCKDGVVLTADRRASLGNMVISKG-VTKIFQVDDHLALAGAGAVGDILSLVRALRAESKLYRAKVGKEM 83 
                                       6***************************9999.9******************************************* PP

                                       CHHHHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHHST CS
                        Proteasome  80 pverlvarvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekeyke 156
                                       +++    ++a+++++ +  ++  p+   +li+g+d  ++p+Ly+id++G ++e+k +v++Gsg e+a+++l++ey+e
  gi|242398879|ref|YP_002994303.1|  84 STK----ALATLTSNILSGRKYLPYFGWFLIGGYD--EKPSLYSIDMAGGITEDK-YVSAGSGMEFAYSILDNEYSE 153
                                       ***....999999999999999*************..459**************8.********************* PP

                                       TBSHHHHHHHHHHHHHHHHHHBTTSCSSEEEEEE CS
                        Proteasome 157 dltleeavelavkalkealerdklsgknievavi 190
                                       ++tl+ +v+la+ka+++a++rd+++g++i v++i
  gi|242398879|ref|YP_002994303.1| 154 KITLNNGVKLAIKAINAAIKRDVFTGDGIMVVTI 187
                                       *****************************99986 PP

>> GNAT_like  GCN5-related N-acetyltransferase like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.8   2.3e-05       0.2      10      30 ..      47      68 ..      42      91 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.3e-05
                         GNAT_like 10 ggaltvsgtga.gdpldglRAl 30
                                      +++l+++g+ga gd l+++RAl
  gi|242398879|ref|YP_002994303.1| 47 DDHLALAGAGAvGDILSLVRAL 68
                                      899*******9**********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       674  (0.0375927); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); 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: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1317.11
//
Query:       gi|242398880|ref|YP_002994304.1|  [L=648]
Description: Cleavage and polyadenylation specficity factor subunit like protein [Thermococcus sibiricus MM 739]
Scores for 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-31  105.6   8.4    2.9e-28   97.6   2.6    2.9  2  KH_7           KH domain
      2e-25   89.2   0.0      4e-25   88.2   0.0    1.5  1  Beta-Casp      Beta-Casp domain
    1.3e-20   73.1   0.2    5.2e-20   71.1   0.0    2.1  2  RMMBL          Zn-dependent metallo-hydrolase RNA specificity
    8.2e-09   35.2   0.0    1.5e-08   34.3   0.0    1.4  1  Lactamase_B_6  Metallo-beta-lactamase superfamily domain
    1.3e-07   31.9   1.8    1.3e-06   28.6   1.8    2.4  1  Lactamase_B    Metallo-beta-lactamase superfamily
    2.9e-06   27.0   9.7    0.00036   20.3   0.6    3.1  3  KH_2           KH domain
    0.00011   22.0   0.2       0.01   15.7   0.1    2.8  2  KH_1           KH domain
    0.00035   20.1   0.0    0.00077   19.0   0.0    1.5  1  Lactamase_B_2  Beta-lactamase superfamily domain
     0.0012   18.7   0.6     0.0046   16.8   0.1    2.3  2  KH_4           KH domain
  ------ inclusion threshold ------
      0.038   13.9   0.0       0.11   12.4   0.0    1.7  1  Lactamase_B_3  Beta-lactamase superfamily domain
      0.082   12.6   0.9        0.2   11.4   0.0    2.2  2  RPEL           RPEL repeat


Domain annotation for each model (and alignments):
>> KH_7  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.6   2.6   1.8e-31   2.9e-28       1      68 []       9      76 ..       9      76 .. 0.98
   2 !   10.2   0.3   0.00035      0.57       6      54 ..      81     132 ..      79     134 .. 0.84

  Alignments for each domain:
  == domain 1  score: 97.6 bits;  conditional E-value: 1.8e-31
                              KH_7  1 eevleelkekieeklPkevkitdveFEGPelViYtknpklfaengdlirklAkelrkRiviRpDpsvl 68
                                      ee+l+e++e i++ +P+e+ki+dveFEGPelViY+knp+ ++++g+li++lAk l+kRi +RpDp+vl
  gi|242398880|ref|YP_002994304.1|  9 EEILKEIREIINQMVPREAKISDVEFEGPELVIYVKNPEVVMQDGELIKNLAKVLKKRISVRPDPDVL 76
                                      689***************************************************************97 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00035
                              KH_7   6 elkekieeklPkevkitdveFEGP..elViYtknpklfa.engdlirklAke 54 
                                       + +e i+e +P+e++it++ F  +  e++i +k p l++ +ng+ +r++ ++
  gi|242398880|ref|YP_002994304.1|  81 KAEELIKELVPSEAEITNISFDPSvgEVIIEAKKPGLVIgKNGETLREITQK 132
                                       67889****************9655589999999998887888888888887 PP

>> Beta-Casp  Beta-Casp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.2   0.0   2.5e-28     4e-25       2     109 ..     434     556 ..     433     557 .. 0.88

  Alignments for each domain:
  == domain 1  score: 88.2 bits;  conditional E-value: 2.5e-28
                                       HHHHHHH..HCTT..TTS-S-EEEEE-HHHHHHHHHGGGGGG.........................E-SHH....H CS
                         Beta-Casp   2 qellylLeelwkekkledlklpiyldsplaskatevYkeyae.........................veakslewme 53 
                                       qe+++ Le++ +   +   ++piyld+ ++ +at+++++y+e                         v +++    e
  gi|242398880|ref|YP_002994304.1| 434 QEIMIALEDYARV--G-GFEVPIYLDG-MIWEATAIHTAYPEylsknlrnqifhegynpflneifkpVANAN----E 502
                                       9**********88..4.5679******.************99999999999999999999887765544333....3 PP

                                       HHH..HHHS-SSEEEEES-TTSSSSHHHHHHHHHTTSTTSEEEESS---TTSHHHH CS
                         Beta-Casp  54 skkeelnsskgpkvilassgmlegGrsrellkklledprntvilvgyqaegTlgrk 109
                                       +k   + +s++p++i+assgml gG+s+e++k+l++dprn++++v+yqaegTlgr+
  gi|242398880|ref|YP_002994304.1| 503 RKD--IIESEEPAIIIASSGMLVGGPSVEYFKHLAPDPRNSLVFVSYQAEGTLGRQ 556
                                       333..66789*********************************************8 PP

>> RMMBL  Zn-dependent metallo-hydrolase RNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0         2   3.3e+03      24      33 ..      17      26 ..      13      36 .. 0.52
   2 !   71.1   0.0   3.2e-23   5.2e-20       2      62 .]     576     639 ..     575     639 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2
                             RMMBL 24 elirklkprn 33
                                      e+i+++ pr 
  gi|242398880|ref|YP_002994304.1| 17 EIINQMVPRE 26
                                      5555555553 PP

  == domain 2  score: 71.1 bits;  conditional E-value: 3.2e-23
                             RMMBL   2 ipvkarieeid.fSgHadknellelirklkprn..vilvHGeeeatsalarllkeeegidvfiP 62 
                                       i ++++i++id fSgHad++el+++i++++pr+  vi vHGe++++++la+ +++++gi++ +P
  gi|242398880|ref|YP_002994304.1| 576 IQINMEIHTIDgFSGHADRRELMNYISRVRPRPerVITVHGEPQKCLDLASSIHKKFGISTRAP 639
                                       789********************************************************99887 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 !   34.3   0.0   9.3e-12   1.5e-08       1     149 [.     203     350 ..     203     366 .. 0.79

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 9.3e-12
                     Lactamase_B_6   1 lLeldnvkiLlDvGwdeskvsles.alkelek.....vi..ptvdliLLshatlehlGayallyakfksklllnipv 69 
                                       lL+ ++  +L+D+G++  ++++ +  l + e      v+    +d+i+++ha l+h G +++l+ +   +l  + p+
  gi|242398880|ref|YP_002994304.1| 203 LLQTNESFVLVDFGVNVAELNDPKkGLPHFEApeftyVLkeRLLDAIIVTHAHLDHSGLLPYLFRY---NL-FDGPI 275
                                       57777888899999887665543313444443333323354579**************77766654...44.599** PP

                     Lactamase_B_6  70 yatlpvvkLGrvslldlyaskgllgpedseeleledideafdkiktlkYsQklelkskldgltitaynaGhtlGGti 146
                                       y+t p+  L  ++  d ++ +++ g e      ++di+e+ ++ ++l Y    +++    +l +t +naGh+lG +i
  gi|242398880|ref|YP_002994304.1| 276 YTTPPTRDLMILLQKDFIEIQQSNGVEPLY--RMKDIKEVVKHTIALDYGEVRDISP---DLRLTLHNAGHVLGSAI 347
                                       *********999999999999999888776..559***************9999885...899************99 PP

                     Lactamase_B_6 147 Wki 149
                                        ++
  gi|242398880|ref|YP_002994304.1| 348 AHL 350
                                       776 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   1.8   7.7e-10   1.3e-06       7     194 ..     200     425 ..     195     427 .. 0.69

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 7.7e-10
                                       EEEEEEETTCEEEES--SCHHHHHHHH.......HHHHHTS.GGGGEEEEE-SBSSHHHHTTGGGCTT..HHCCEET CS
                       Lactamase_B   7 nsyliegdggviLiDtGtsteaaraal.......elaalgl.kpkdvdavilTHlHlDHiGglgglve..atdvpvg 73 
                                       ++ l++++++ +L+D G+  ++    +       ++   ++ k + +da+i+TH+HlDH G l++l +   +d p++
  gi|242398880|ref|YP_002994304.1| 200 SALLLQTNESFVLVDFGVNVAELNDPKkglphfeAPEFTYVlKERLLDAIIVTHAHLDHSGLLPYLFRynLFDGPIY 276
                                       56667777777777777777776666667777775555544144447*******************86225888999 PP

                                       CCEHHHHCCHCHHHHHHHHHCCHH.........TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSC..CEEEEE CS
                       Lactamase_B  74 avaeeapalfmeeaddaasrkgll.........lagvsadkpdvdeeeldgnaggrralyvtggpghgh..ghgvve 139
                                         + +   ++   +d+ +  +++          +++v++     d  e  ++ ++ r++ +  g++ g+   h++v+
  gi|242398880|ref|YP_002994304.1| 277 TTPPTRDLMILLQKDFIEIQQSNGveplyrmkdIKEVVKHTIALDYGEVRDISPDLRLTLHNAGHVLGSaiAHLHVG 353
                                       999999999999999999888888*****999744444444444444455555555555555555444422699999 PP

                                       ETTCCEEEECTTTSSHHCCCCCC..................TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEE CS
                       Lactamase_B 140 ygggkvlftGDallagetgridl.................tlrgaevrdpsdaekyldsllklaglkaevlv 194
                                       +g  ++++tGD+ +a+ ++  +                    r+ + +     +k+++++ + ++ k +vl+
  gi|242398880|ref|YP_002994304.1| 354 NGLHNIAVTGDFKFAPTRLFEPAnskfprletlimestygGSRDYQMPREEAEKKLIETIMHTIKRKGKVLI 425
                                       9*************8888877778888888888888766655666666666666666666666666666655 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.4   9.3e-05      0.15       1      69 [.      14      78 ..      14      84 .. 0.90
   2 !   20.3   0.6   2.2e-07   0.00036      10      54 ..      90     133 ..      79     134 .. 0.77
   3 ?   -2.5   0.1       2.9   4.7e+03       6      29 ..     493     516 ..     491     518 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.3e-05
                                      HHHHHHHHHT.ECETEEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTCEEEE CS
                              KH_2  1 eipeslavei.kkagvskveIertanrviiviresqpgivIGkgGsnikkigkelrkdieklegkkVkln 69
                                      ei+e +++ + ++a +s+ve     ++ ++vi++ +p +v  + G+ ik++ k l+k+i +  + +V l+
  gi|242398880|ref|YP_002994304.1| 14 EIREIINQMVpREAKISDVEF----EGPELVIYVKNPEVVM-QDGELIKNLAKVLKKRISVRPDPDVLLD 78
                                      79********9**********....8888***********9.*****************88777777665 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 2.2e-07
                                       T.ECETEEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHH CS
                              KH_2  10 i.kkagvskveIertanrviiviresqpgivIGkgGsnikkigkel 54 
                                       + ++a++ ++  +      +++i + +pg+vIGk+G+++++i++++
  gi|242398880|ref|YP_002994304.1|  90 VpSEAEITNISFDP--SVGEVIIEAKKPGLVIGKNGETLREITQKV 133
                                       45566666666644..6668999*******************9975 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 2.9
                                       HHHHTECETEEEEEEECCSCEEEE CS
                              KH_2   6 laveikkagvskveIertanrvii 29 
                                       +++ +++a  +k +Ie ++ ++ii
  gi|242398880|ref|YP_002994304.1| 493 IFKPVANANERKDIIESEEPAIII 516
                                       677778888888889888888887 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   6.1e-06      0.01       3      28 ..     107     132 ..     105     158 .. 0.89
   2 ?    3.2   0.0     0.049        80      43      60 ..     607     625 ..     594     630 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 6.1e-06
                                       EEEEGGGHHHHHHTGGGHHHHHHHHH CS
                              KH_1   3 rilvPsslvgriIGkgGsnIkeIree 28 
                                       ++++ +++ g++IGk+G++++eI ++
  gi|242398880|ref|YP_002994304.1| 107 EVIIEAKKPGLVIGKNGETLREITQK 132
                                       577888889**************994 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.049
                                       .T.-EEEEEE.SHHHHHHH CS
                              KH_1  43 sderevtisG.speavekA 60 
                                        +er++t+ G ++++ + A
  gi|242398880|ref|YP_002994304.1| 607 RPERVITVHGePQKCLDLA 625
                                       379*******777766666 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 !   19.0   0.0   4.7e-07   0.00077      30     165 ..     245     391 ..     225     414 .. 0.66

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 4.7e-07
                                       SEEEEE-SS--HHHHGGGGCCCC...C--EEEEEEEEHHHHH...HCCTTCGHHHCHTT..TTEEEEEE-TTSEEEE CS
                     Lactamase_B_2  30 pidaVllthaHyDHlaglltlre...lrpkklplyapkgvla...vleanfvylaleee..pavnvheldwgesfel 98 
                                        +da+++thaH DH   l+ l +   +     p+y ++ +++    l++ f+ +++ +   p  ++++++   ++++
  gi|242398880|ref|YP_002994304.1| 245 LLDAIIVTHAHLDHSGLLPYLFRynlFD---GPIYTTPPTRDlmiLLQKDFIEIQQSNGvePLYRMKDIKEVVKHTI 318
                                       69*************6677777755433...5899888887755545555544444433564444444443333333 PP

                                       ..........CSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---....HHHHHHHCT-SEEE CS
                     Lactamase_B_2  99 ..........gdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyip....eeigerlggadlll 161
                                                   ++l++t++ a h  g         ++ l +++g ++++ +gD ++ p    e +  ++  ++ l+
  gi|242398880|ref|YP_002994304.1| 319 aldygevrdiS-PDLRLTLHNAGHVLGS-------AIAHLHVGNGLHNIAVTGDFKFAPtrlfEPANSKFPRLETLI 387
                                       33333333324.6888888888888888.......788888889999999999999888333333345555566666 PP

                                       EE-S CS
                     Lactamase_B_2 162 ldit 165
                                       ++ t
  gi|242398880|ref|YP_002994304.1| 388 MEST 391
                                       6655 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       3.5   5.7e+03       4      23 ..      15      32 ..      12      47 .. 0.59
   2 !   16.8   0.1   2.8e-06    0.0046       3      52 ..      81     127 ..      79     130 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 3.5
                              KH_4  4 vedilkalvddpeevevtee 23
                                      +++i++++v  p e +++  
  gi|242398880|ref|YP_002994304.1| 15 IREIINQMV--PREAKISDV 32
                                      788899998..555555443 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 2.8e-06
                              KH_4   3 lvedilkalvddpeevevteeeeeeeveielnvegedlGrvIGkrGrtld 52 
                                        +e+++k+lv  p e e+t   + +  + e+ +e ++ G+vIGk+G+tl+
  gi|242398880|ref|YP_002994304.1|  81 KAEELIKELV--PSEAEITNI-SFDPSVGEVIIEAKKPGLVIGKNGETLR 127
                                       6799999999..899999986.7889999*******************96 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 ?   12.4   0.0   6.6e-05      0.11       6      50 ..     198     259 ..     195     265 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.6e-05
                     Lactamase_B_3   6 ghnsflletagarilvDPf.................kanlgyeppaeeaDlvlisqaledHa 50 
                                       g +++ll+t++  +lvD +                  ++ +y  +++  D++++++a+ dH 
  gi|242398880|ref|YP_002994304.1| 198 GRSALLLQTNESFVLVDFGvnvaelndpkkglphfeAPEFTYVLKERLLDAIIVTHAHLDHS 259
                                       8899*************99777777777766666533366666666***************7 PP

>> RPEL  RPEL repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00012       0.2       2      15 ..      63      76 ..      62      78 .. 0.89
   2 ?   -2.5   0.2         3   4.9e+03      12      17 ..      82      87 ..      81      88 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00012
                              RPEL  2 LerKLshRPtreEL 15
                                      L++++s RP+++ L
  gi|242398880|ref|YP_002994304.1| 63 LKKRISVRPDPDVL 76
                                      9**********976 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3
                              RPEL 12 reELve 17
                                      +eEL++
  gi|242398880|ref|YP_002994304.1| 82 AEELIK 87
                                      79***8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (648 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.73u 0.33s 00:00:01.06 Elapsed: 00:00:00.52
# Mc/sec: 3764.35
//
Query:       gi|242398881|ref|YP_002994305.1|  [L=443]
Description: threonine synthase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-61  208.9   0.1    1.5e-61  208.4   0.1    1.2  1  PALP           Pyridoxal-phosphate dependent enzyme
    2.3e-07   30.7   7.7    2.4e-06   27.4   4.6    2.5  2  PadR           Transcriptional regulator PadR-like family
    0.00011   22.0   0.1    0.00021   21.1   0.1    1.4  1  DUF4364        Domain of unknown function (DUF4364)
     0.0013   18.6   1.2     0.0052   16.7   0.4    2.3  2  HTH_45         Winged helix-turn-helix
     0.0019   16.7   0.4     0.0029   16.0   0.4    1.3  1  DUF505         Protein of unknown function (DUF505)
     0.0054   17.2   0.3       0.11   13.0   0.1    2.3  2  HTH_27         Winged helix DNA-binding domain
  ------ inclusion threshold ------
      0.026   14.7   0.0       0.46   10.7   0.0    2.4  2  ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthas
      0.028   14.4   0.1       0.06   13.3   0.1    1.5  1  Cdc6_C         CDC6, C terminal winged helix domain
      0.046   13.4   0.1        1.9    8.1   0.1    2.5  2  SMC_ScpB       Segregation and condensation complex subunit S
      0.067   13.2   0.2       0.12   12.5   0.2    1.3  1  Replic_Relax   Replication-relaxation
      0.088   12.7   0.0       0.19   11.6   0.0    1.6  1  HTH_5          Bacterial regulatory protein, arsR family
       0.16   11.2   0.0       0.25   10.5   0.0    1.2  1  IF-2B          Initiation factor 2 subunit family
       0.18   11.9   0.1       0.97    9.5   0.0    2.1  2  HTH_20         Helix-turn-helix 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 !  208.4   0.1   1.1e-64   1.5e-61       2     294 .]      61     353 ..      60     353 .. 0.95

  Alignments for each domain:
  == domain 1  score: 208.4 bits;  conditional E-value: 1.1e-64
                                       GGCSSS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT CS
                              PALP   2 tlgigpTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaallG 78 
                                       +l +g+TPlvr++   ++lg ++f+K+E  nptgSf dR a+  +++   + ++ + ++as+GN++++lAa+aa+++
  gi|242398881|ref|YP_002994305.1|  61 SLKEGGTPLVRAKI-GEKLGFAVFIKDETRNPTGSFRDRLATVGVSYGLSH-ANNGFIVASDGNAAASLAAYAARAN 135
                                       6789********75.89******************************8888.899********************** PP

                                       -EEEEEEETTS-HHHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHHHTHHHHHHHHTT CS
                              PALP  79 lkvtivvpadaspekvallrllGaevvevggdydeavaaaaelaaegegaylvsqfdnptviegygtiglEileqlg 155
                                        ++ +vvp+++  +k+ ++ ++Ga+++++g+++de+ ++a el +  +g y + + +n  + eg++t+++E++e+++
  gi|242398881|ref|YP_002994305.1| 136 KEAFVVVPKKVDRGKLIQMIAFGAKIIKYGDSVDECIEYASELSRL-NGLYDITPENNIIGLEGQKTLAFELWEDIN 211
                                       **********************************************.*****************************8 PP

                                       TTEEEEEEE-SSSHHHHHHHHHHHH....HSTT..-EEEEEEECTTCGGTTCCS..S.SS..B.SSS.CCSTCS..C CS
                              PALP 156 gkpdavvvpvGgGgliaGiaaglke....rrpd..vrvigvepegsdalarslragrrvtvpvsdtiadglavg..s 224
                                         p++v+ p+G+G+++  i++g+ke    +  +  +++++v++e+++++a+ +     +t ++  t a gl v+  +
  gi|242398881|ref|YP_002994305.1| 212 --PTHVIIPTGSGSNLYSIYKGFKEllevGAIEelPKLVAVQTENCSPIASEI---LGLTSKKDFTKALGLYVKdpV 283
                                       ..***********************8877333368******************...556666668999999999999 PP

                                       GTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHH.HHHHHHCCTTCEEEEEEE-B CS
                              PALP 225 pselafelldrlvdeivtvsdeealeamrllarregivvepssaaalaal.klreagelkegdrvvviltg 294
                                       + ela  +++++++++v v +ee   + ++la +eg+++e ssa+++ al kl+e g ++++d+v +++tg
  gi|242398881|ref|YP_002994305.1| 284 NKELATNAVKESGGTAVLVREEELDLGEKELA-KEGVFAEYSSAVVIPALlKLHEEGYFEKDDKVALVVTG 353
                                       99******************************.************************************98 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.047        65      26      55 ..     320     351 ..     311     364 .. 0.74
   2 !   27.4   4.6   1.7e-09   2.4e-06       1      74 [.     376     439 ..     376     440 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.047
                                       -CCTTHHHHHHHHHHHHHTTSEEEEEE-S..T CS
                              PadR  26 llelseGslYpaLkrLekeglvesewees..g 55 
                                       + e s + + paL +L +eg+ e+  + +  +
  gi|242398881|ref|YP_002994305.1| 320 FAEYSSAVVIPALLKLHEEGYFEKDDKVAlvV 351
                                       5678899999*************998876543 PP

  == domain 2  score: 27.4 bits;  conditional E-value: 1.7e-09
                                       HHHHHCCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHHH CS
                              PadR   1 iLalleeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrela 74 
                                       iL ll+ + +yGye+ ++le+       +++  +Y+  ++Le  +l+e+  ++    ++r yY+lT++G+r l+
  gi|242398881|ref|YP_002994305.1| 376 ILRLLRGRSMYGYELWENLEKP------MKYQAVYQHIRELESLELIEEAYKR----GRRTYYKLTEKGQRLLE 439
                                       899******************9......57889****************9886....7************9886 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.1   1.5e-07   0.00021      31      74 ..     398     442 ..     394     443 .] 0.94

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.5e-07
                           DUF4364  31 tnYfdlqqalseLvesglieee.ekenktlykiTekGketlelfe 74 
                                       ++Y  + q + eL++ +liee  ++  +t+yk+TekG++ le fe
  gi|242398881|ref|YP_002994305.1| 398 MKYQAVYQHIRELESLELIEEAyKRGRRTYYKLTEKGQRLLENFE 442
                                       89*******************989999***************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 ?   -1.1   0.0       1.4     2e+03      42      64 ..     334     357 ..     329     364 .. 0.80
   2 !   16.7   0.4   3.8e-06    0.0052      31      70 ..     398     442 ..     394     443 .] 0.87

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.4
                            HTH_45  42 mLvekglikk.skekYvlTekGle 64 
                                       +L e+g+ +k +k   v+T  Gl+
  gi|242398881|ref|YP_002994305.1| 334 KLHEEGYFEKdDKVALVVTGSGLK 357
                                       6888999855489999***99998 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 3.8e-06
                            HTH_45  31 LsykllnkYLdmLvekgli.....kkskekYvlTekGlelleklk 70 
                                       ++y+ + + +  L + +li     + + + Y+lTekG++lle+++
  gi|242398881|ref|YP_002994305.1| 398 MKYQAVYQHIRELESLELIeeaykRGRRTYYKLTEKGQRLLENFE 442
                                       789999*************888744478889**********9975 PP

>> DUF505  Protein of unknown function (DUF505)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.4   2.1e-06    0.0029     366     403 ..     403     440 ..     389     443 .] 0.83

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.1e-06
                            DUF505 366 lreaLysLesfeLieseveekgkevyvlTeyGekvled 403
                                       + + + +Les eLie+  ++  + +y lTe+G+++le+
  gi|242398881|ref|YP_002994305.1| 403 VYQHIRELESLELIEEAYKRGRRTYYKLTEKGQRLLEN 440
                                       5678899**********8766688999*********96 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.26   3.6e+02      33      58 ..     326     346 ..     313     352 .. 0.75
   2 !   13.0   0.1   8.2e-05      0.11      35      68 .]     403     434 ..     398     434 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.26
                            HTH_27  33 shisyslkkLtekGLvertgdeadrr 58 
                                       + ++ +l kL+e G++     e+d++
  gi|242398881|ref|YP_002994305.1| 326 AVVIPALLKLHEEGYF-----EKDDK 346
                                       44458999********.....44444 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 8.2e-05
                            HTH_27  35 isyslkkLtekGLvertgdeadrrekrvrlTdkG 68 
                                       +   +++L+  +L+e+  ++  +r++ ++lT+kG
  gi|242398881|ref|YP_002994305.1| 403 VYQHIRELESLELIEEAYKR--GRRTYYKLTEKG 434
                                       44779*********999999..***********9 PP

>> ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.35   4.8e+02      64      79 ..     144     159 ..     121     161 .. 0.85
   2 ?   10.7   0.0   0.00033      0.46      47      81 ..     322     356 ..     311     360 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.35
                                       TSS-TT-EEEEEEEET CS
                     ACP_syn_III_C  64 gklkpgdlvllvgfGa 79 
                                       +k+++g+l+ +++fGa
  gi|242398881|ref|YP_002994305.1| 144 KKVDRGKLIQMIAFGA 159
                                       6999***********8 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00033
                                       B-GGGHHHHHHHHHHHTTSS-TT-EEEEEEEETTT CS
                     ACP_syn_III_C  47 ntsaasiplaLdeaveegklkpgdlvllvgfGaGl 81 
                                         s+a ++ aL +++eeg +++ d+v+lv +G Gl
  gi|242398881|ref|YP_002994305.1| 322 EYSSAVVIPALLKLHEEGYFEKDDKVALVVTGSGL 356
                                       5689999999999*********************9 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   4.3e-05      0.06      35      76 ..     396     432 ..     392     439 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.3e-05
                                       ----HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEESS CS
                            Cdc6_C  35 dpltqrevsdllseLemlgileleksskGrregrtrkisLnv 76 
                                       +p++ + v+++++eLe+l ++e + +    r gr ++++L+ 
  gi|242398881|ref|YP_002994305.1| 396 KPMKYQAVYQHIRELESLELIEEAYK----R-GRRTYYKLTE 432
                                       69999******************999....5.8888888865 PP

>> SMC_ScpB  Segregation and condensation complex subunit ScpB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.08   1.1e+02     134     160 .]     222     247 ..     216     247 .. 0.90
   2 ?    8.1   0.1    0.0013       1.9     109     144 ..     401     433 ..     396     441 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.08
                          SMC_ScpB 134 grpilYgtTekFleyfglksleeLpkl 160
                                       g + lY++ + F e +++  +eeLpkl
  gi|242398881|ref|YP_002994305.1| 222 G-SNLYSIYKGFKELLEVGAIEELPKL 247
                                       4.789********************96 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0013
                          SMC_ScpB 109 vnsdsvvrtLlerglieekgrkeepgrpilYgtTek 144
                                       +++++++r+L + +liee+ +    gr + Y++Tek
  gi|242398881|ref|YP_002994305.1| 401 QAVYQHIRELESLELIEEAYK---RGRRTYYKLTEK 433
                                       5689***************95...59********97 PP

>> Replic_Relax  Replication-relaxation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   8.4e-05      0.12      26      69 ..     402     438 ..     389     442 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.4e-05
                      Replic_Relax  26 tarrrLarLrelgllsrlrkrvggarggsepyvYaLtpkGarll 69 
                                        +++ +++L++l+l++  +kr g+      ++ Y Lt+kG+rll
  gi|242398881|ref|YP_002994305.1| 402 AVYQHIRELESLELIEEAYKR-GR------RTYYKLTEKGQRLL 438
                                       6899999**********8888.23......347**********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 ?   11.6   0.0   0.00014      0.19       3      46 ..     372     417 ..     370     418 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00014
                                       HHHHHHHHHTTSSEEHHHHHHHHTS-HH..HHHHHHHHHHHTTSEE CS
                             HTH_5   3 tRlkILklLaegelcvcelaeelglsqs..tvShHLkkLreaGLVe 46 
                                       t+l IL+lL+ ++++  el e l+++    +v +H + L+ + L+e
  gi|242398881|ref|YP_002994305.1| 372 TKLSILRLLRGRSMYGYELWENLEKPMKyqAVYQHIRELESLELIE 417
                                       899*********************9987669**********99997 PP

>> IF-2B  Initiation factor 2 subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00018      0.25     189     270 ..     112     193 ..     109     196 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00018
                                       TTSEEEEETT..HHHHHHHHHHTTXEEEEEXXGG....GBESTSSSGGGSSXXBEXTHHHHEETTEESSTTTEEEEE CS
                             IF-2B 189 enGaiankiG..TsslAvlAkefnipvlvvaesl....kfservqldedifieerdpeellnitgeriaeeelkvvn 259
                                       +nG+i++  G   +slA  A ++n + +vv+++     k+ ++++++++i+   +  +e + +++      el  +n
  gi|242398881|ref|YP_002994305.1| 112 NNGFIVASDGnaAASLAAYAARANKEAFVVVPKKvdrgKLIQMIAFGAKIIKYGDSVDECIEYAS------ELSRLN 182
                                       799999999933468999999**********9855555999999999977744444444444444......7899** PP

                                       BSEEEEEGGGX CS
                             IF-2B 260 pafDvtPpelI 270
                                        ++D+tP+++I
  gi|242398881|ref|YP_002994305.1| 183 GLYDITPENNI 193
                                       ********999 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.6   2.1e+03      45      55 ..     232     242 ..     226     244 .. 0.83
   2 ?    9.5   0.0   0.00071      0.97      13      55 ..     374     417 ..     371     420 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.6
                                       HHHHHHCTTEE CS
                            HTH_20  45 LrvLeeagLve 55 
                                       +++L e+g++e
  gi|242398881|ref|YP_002994305.1| 232 FKELLEVGAIE 242
                                       799******98 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00071
                                       HHHHHHHSTCTTB-HHHHHHHHT..S-HHHHHHHHHHHHHCTTEE CS
                            HTH_20  13 rrilraLaraegltaselaerld..lskntlsyHLrvLeeagLve 55 
                                       + ilr+L r++ +   el e l+  ++ + +++H+r+Le+ +L+e
  gi|242398881|ref|YP_002994305.1| 374 LSILRLL-RGRSMYGYELWENLEkpMKYQAVYQHIRELESLELIE 417
                                       6788888.8888888888888863466788**************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (443 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.73u 0.34s 00:00:01.07 Elapsed: 00:00:00.58
# Mc/sec: 2315.95
//
Query:       gi|242398882|ref|YP_002994306.1|  [L=107]
Description: hypothetical protein TSIB_0899 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.54   10.9   8.2        2.6    8.7   5.9    2.1  2  Rab5ip    Rab5-interacting protein (Rab5ip)


Domain annotation for each model (and alignments):
>> Rab5ip  Rab5-interacting protein (Rab5ip)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   5.9   0.00015       2.6       9      80 ..      14      78 ..       7      79 .. 0.79
   2 ?    6.4   1.5   0.00073        13      23      50 ..      67      91 ..      62     106 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00015
                            Rab5ip  9 talllGvvaGilgLeslsGflfylllsllvsllfyalkvkgkskkyfrgalkelwteglvnglagFvLtWtl 80
                                      +++l+Gv+ Gil  +  +G +  ll++l+   +++a  vk    ++ ++  ++++   l +g+ gF+L+W  
  gi|242398882|ref|YP_002994306.1| 14 IGALAGVISGILSTQAPMGYVAGLLVYLISPKVVMA-VVK-DLPEELKN--DRVL---LRKGIWGFLLFWLY 78
                                      5789************99999999999999999986.444.44555666..4566...66789999999975 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.00073
                            Rab5ip 23 eslsGflfylllsllvsllfyalkvkgk 50
                                      ++++Gfl++ l ++l+s+ +++   +++
  gi|242398882|ref|YP_002994306.1| 67 KGIWGFLLFWLYFTLFSYNLIL---QPE 91
                                      6889999998888888887774...333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); 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: 0.53u 0.35s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 602.33
//
Query:       gi|242398883|ref|YP_002994307.1|  [L=227]
Description: Ribose-5-phosphate isomerase A [Thermococcus sibiricus MM 739]
Scores for complete 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-66  220.8   0.2    1.1e-65  220.4   0.2    1.1  1  Rib_5-P_isom_A  Ribose 5-phosphate isomerase A (phosphoribois
    2.8e-06   27.4   0.0     0.0006   19.8   0.0    2.2  2  DeoRC           DeoR C terminal sensor domain
  ------ inclusion threshold ------
      0.035   13.2   0.0      0.058   12.5   0.0    1.3  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 !  220.4   0.2   1.9e-69   1.1e-65       2     173 .]      51     221 ..      50     221 .. 0.97

  Alignments for each domain:
  == domain 1  score: 220.4 bits;  conditional E-value: 1.9e-69
                                       EEESSHHHHHHHHHTT--BE-GGCCSSEEEEEE--SEEETTS-EE--TTS-HHHHHHHHHTEEEEEEEEEGGGBESS CS
                    Rib_5-P_isom_A   2 gvptSeqteelaeelgipllsldeveeidlaiDGaDevdedlnliKGgGgallrEKivaaaakkfiviadesKlvek 78 
                                       g+ptS+q++ la e gip+++ldev+ id+a+DGaDevd++lnliKG+G+al+ EKi+++ a +fiv++desKlve 
  gi|242398883|ref|YP_002994307.1|  51 GIPTSHQSRLLALESGIPVVTLDEVDAIDIAVDGADEVDPHLNLIKGRGAALTMEKIIEYRAGTFIVLVDESKLVEY 127
                                       89*************************************************************************** PP

                                       TT.SS-EEEEE-GGGHHHHHHHHHHTTT-EEEE-TETTTTEE-B-TTS-EEEEEESSSBSSSHHHHHHHHHTSTTEE CS
                    Rib_5-P_isom_A  79 lg.kfpvPveVlpfaleavarelekllggkpelReakgkdgpvvTdngnlilDvkfeekiedpeelekelksipGVv 154
                                       lg + pvP+eV+p a++a+++ele  +++++elR++ +kdgpv+Tdngn+ilD+kf  kiedp ++e el++ipGVv
  gi|242398883|ref|YP_002994307.1| 128 LGqRVPVPIEVIPAAWRAIKEELEV-FNATAELRMGVKKDGPVITDNGNFILDAKF-IKIEDPLDMEIELNNIPGVV 202
                                       **55********************5.6*********99******************.5788**************** PP

                                       EESEE-S--SEEEEEETTC CS
                    Rib_5-P_isom_A 155 etGlFlgladkvlvgkedg 173
                                       e+G+F+++ad +lvg+++g
  gi|242398883|ref|YP_002994307.1| 203 ENGIFADIADIILVGTKEG 221
                                       ****************987 PP

>> DeoRC  DeoR C terminal sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0     1e-07    0.0006       4      41 ..       3      40 ..       1      50 [. 0.90
   2 !    5.5   0.0    0.0025        15      93     139 ..      78     124 ..      71     131 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1e-07
                             DeoRC  4 eeKrrIAkaAaeliedgdtifldaGtTtlelaraLaek 41
                                      e K+  Ak+A+++i d+++i l++G+Tt+++++ L +k
  gi|242398883|ref|YP_002994307.1|  3 ELKKLAAKEALRYIDDDMIIGLGTGSTTAYFIQMLGKK 40
                                      66999****************************99887 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0025
                             DeoRC  93 vdkaflgangidaegglttsdeeeaevkralieaarrvillaDssKf 139
                                       +d+a+ ga+ +d++ +l++   +   +++ +  +a   i+l+D+sK+
  gi|242398883|ref|YP_002994307.1|  78 IDIAVDGADEVDPHLNLIKGRGAALTMEKIIEYRAGTFIVLVDESKL 124
                                       78999999999999999999999999999999**************7 PP

>> Sugar-bind  Putative sugar-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   9.7e-06     0.058      36      74 ..       2      40 ..       1      50 [. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.7e-06
                                      HHHHHHHHHHHHHH--TTEEEEE-SSHHHHHHHHHTHHC CS
                        Sugar-bind 36 ealgraaaqllesllkdgdvvgvgwGrtlsavaealtpk 74
                                      e+l ++aa+   ++++d++++g+g+G t++ ++++l +k
  gi|242398883|ref|YP_002994307.1|  2 EELKKLAAKEALRYIDDDMIIGLGTGSTTAYFIQMLGKK 40
                                      677889999999*********************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1396.36
//
Query:       gi|242398884|ref|YP_002994308.1|  [L=403]
Description: hypothetical protein TSIB_0901 [Thermococcus sibiricus MM 739]
Scores for complete 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-44  150.3   0.8      5e-44  149.5   0.8    1.4  1  DUF553          Transglutaminase-like domain
     0.0078   16.6   0.0       0.23   11.9   0.0    2.3  1  Transglut_core  Transglutaminase-like superfamily
  ------ inclusion threshold ------
      0.062   13.5   0.2       0.13   12.5   0.2    1.4  1  Glyco_hydro_25  Glycosyl hydrolases family 25


Domain annotation for each model (and alignments):
>> DUF553  Transglutaminase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.5   0.8   8.4e-48     5e-44       2     154 .]     106     260 ..     105     260 .. 0.93

  Alignments for each domain:
  == domain 1  score: 149.5 bits;  conditional E-value: 8.4e-48
                            DUF553   2 klkklaeklkkensketiinvlewvdenikYdyekaevvetllvlWatfftlskvdskilklietpkeilktkkgiC 78 
                                       k++ la +lk+++ +e+++n+lew+++ni+Yd  ka+++ +++ + +++ t+  +    +++i+tp+e++k+ kgiC
  gi|242398884|ref|YP_002994308.1| 106 KISYLAIELKGQTIQESVWNILEWLQNNIEYDSYKASLPAPTIQI-SENGTIIGITGGEGTEIQTPYETIKKGKGIC 181
                                       68899**********************************666665.99***************************** PP

                            DUF553  79 rDYaiLTaalLlnlniskvylvsvtfenskvgHaavavkidgtyfvlDqklpiikideylkkll..k.kvkiiteve 152
                                       +DY+iLT+al+l++++s vy ++++fens++ H+++a+kid++yf+lDq+lp++++++y++k+   + +++ i++++
  gi|242398884|ref|YP_002994308.1| 182 TDYTILTLALMLEMDYSLVYAFEISFENSNTKHVTAAIKIDDEYFLLDQNLPPMDLGTYYNKWAlyReEKLLISNAT 258
                                       ************************************************************66542234778899999 PP

                            DUF553 153 iy 154
                                       +y
  gi|242398884|ref|YP_002994308.1| 259 VY 260
                                       98 PP

>> Transglut_core  Transglutaminase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   3.9e-05      0.23      13      69 ..     118     196 ..     109     229 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.9e-05
                    Transglut_core  13 dplekakaiyewvrknveys......................aprrtpgsrdaeavletgkGncedfaslfvallRa 67 
                                       + +e +  i ew+++n+ey+                      + + +++ +++ +++++gkG c+d++ l  al+  
  gi|242398884|ref|YP_002994308.1| 118 TIQESVWNILEWLQNNIEYDsykaslpaptiqisengtiigiTGGEGTEIQTPYETIKKGKGICTDYTILTLALMLE 194
                                       5556777777788877777777777766666666666655655667777777********************99866 PP

                    Transglut_core  68 lG 69 
                                       + 
  gi|242398884|ref|YP_002994308.1| 195 MD 196
                                       65 PP

>> Glyco_hydro_25  Glycosyl hydrolases family 25
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   2.2e-05      0.13      47     148 ..     279     383 ..     274     393 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.2e-05
                    Glyco_hydro_25  47 aaglkvgaYhFarpvnsstakaeadyFlsnvqkldastlplvlDvE.....ktssaekaaateeikkfldevkkqtG 118
                                       a+++k   Y F ++  +  a++ ++ Fl+n  ++ ++++  + D+          a++++ + e+ +f+d++     
  gi|242398884|ref|YP_002994308.1| 279 AEDFKNRNYDFTSANLAVMANDLMELFLENY-PNLSKDFY-ISDIDkkvhlPYGYANRSTWKLELPNFIDYYTLTFH 353
                                       56788999****999999*************.67767774.88999767665566777777888999*****77767 PP

                    Glyco_hydro_25 119 kkpviYtsksflknnllesqliaeyplWia 148
                                       ++ v Y ++ f++n    ++l++ ++lWi+
  gi|242398884|ref|YP_002994308.1| 354 REFVKYFYRRFTENPKVVKDLSEFNRLWIR 383
                                       77777**********9999998888****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       938  (0.0523175); expected 358.6 (0.02)
Passed bias filter:                      576  (0.0321267); 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):               3  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.49
# Mc/sec: 2495.47
//
Query:       gi|242398885|ref|YP_002994309.1|  [L=198]
Description: TRAP-type mannitol/chloroaromatic compound transport system, periplasmic component [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-11   44.4   0.0    2.4e-11   43.5   0.0    1.4  1  DctP      Bacterial extracellular solute-binding protein, fam


Domain annotation for each model (and alignments):
>> DctP  Bacterial extracellular solute-binding protein, family 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.5   0.0   1.3e-15   2.4e-11       6     136 ..      65     196 ..      60     197 .. 0.89

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 1.3e-15
                                       TTTSHHHHHHHHHHHHHHHHTTTSEEEEEEETTTTTTHH.HHHHHHHTTSSSEEEEEGGGGTTTSGGGGG.GGSTTT CS
                              DctP   6 aegspkhkaaekfaklveektnGkvkievypssqLggde.eviealknGtvdivatssakleglvpeigv.ldlPFl 80 
                                        +g+p ++ a++fa++ve+++nG++kievy +++Lg    e+++   nG vdi+++ s++l+  +p +++    P  
  gi|242398885|ref|YP_002994309.1|  65 LAGDPGFEIAQHFADEVEKMSNGRIKIEVYQAGELGFPVtEIVDSTANGVVDIAIFYSSYLASQDPVLALaGGKPGP 141
                                       578999999***************************8886999***************************7788999 PP

                                       SCSHHHHHH.HHHSHHHHHHHHHHHHHTEEEEEEEEEEEEEEEESSS--SSGGGGTT CS
                              DctP  81 fedeealkk.vlegevgekllkslekkglkvLafwenGfrqftsnkkpinspeDlkg 136
                                       +++  +l   v+  e    + ks+ek g+++++ +  G  ++  ++ pin++ Dl+g
  gi|242398885|ref|YP_002994309.1| 142 ISNPYELFYqVKTVE--DLIQKSFEKFGVVYIGPMIYGEPEILVSRVPINRLSDLNG 196
                                       999888775455554..7788899999******9999999999999*********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); expected 358.6 (0.02)
Passed bias filter:                      576  (0.0321267); 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: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1202.40
//
Query:       gi|242398886|ref|YP_002994310.1|  [L=177]
Description: hypothetical protein TSIB_0903 [Thermococcus sibiricus MM 739]
Scores for complete 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  100.9   0.1      9e-29  100.7   0.1    1.1  1  DctP      Bacterial extracellular solute-binding protein, fam
  ------ inclusion threshold ------
      0.011   16.2   0.2        3.9    8.0   0.0    2.4  2  DUF3106   Protein of unknown function (DUF3106)
      0.087   13.0   0.0       0.14   12.3   0.0    1.3  1  Cnn_1N    Centrosomin N-terminal motif 1


Domain annotation for each model (and alignments):
>> DctP  Bacterial extracellular solute-binding protein, family 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.7   0.1   1.5e-32     9e-29     151     285 ..       3     144 ..       1     146 [. 0.93

  Alignments for each domain:
  == domain 1  score: 100.7 bits;  conditional E-value: 1.5e-32
                                       HHHHTSEEEE-TGGGHHHHHHTTSSSEEEEE.HHHHHHTTGGGG-SEEEEEE.......EEEEEEEEEEEHHHHHHS CS
                              DctP 151 fkalGanptpipfgevytaLqtgvvDGqenp.lsniysqklyevqkyltltn.......hgyldllvlvnkktwdsL 219
                                       ++ lGa++  ++ ge+y+aLq g++DG e++ +++ y+++++ev+ky+ ++        ++   ++++vn + w++L
  gi|242398886|ref|YP_002994310.1|   3 YNTLGAQAMMMASGELYQALQLGTIDGLEWTdYTADYKMGFHEVAKYVLEPTpgvnlhsEAAVHAFLIVNPDLWNKL 79 
                                       6789**************************945555**************99777787777799************* PP

                                       -HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEGEHHHHHHHHHHHHHHHHHHHHH CS
                              DctP 220 pedlqaileeaakeatelqrklveeleeealqklkeagvevieltpedlaafrealkpvykeifek 285
                                       p+dl++i++ a +e+  +    v++l++e++qk +eag ++++l ped ++  e++ +++ e ++k
  gi|242398886|ref|YP_002994310.1|  80 PDDLKEIIKVASRESYLWGSHYVNTLNREYRQKWIEAGATLVKLPPEDNQKIIETAIQLHVE-YAK 144
                                       ***********************************************************999.665 PP

>> DUF3106  Protein of unknown function (DUF3106)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0   0.00066       3.9      20      50 ..     103     133 ..      76     138 .. 0.82
   2 ?    6.4   0.0     0.002        12      31      62 ..     136     167 ..     133     174 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00066
                           DUF3106  20 nelspeqreklleiaerykkltpeeqkrlqe 50 
                                       n+l+ e r+k++e  ++  kl+pe+ +++ e
  gi|242398886|ref|YP_002994310.1| 103 NTLNREYRQKWIEAGATLVKLPPEDNQKIIE 133
                                       7889999999999999999999999988765 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.002
                           DUF3106  31 leiaerykkltpeeqkrlqermeewakLspeq 62 
                                       ++++ +y+k +pe q+ + + ++ w++L +++
  gi|242398886|ref|YP_002994310.1| 136 IQLHVEYAKKSPEAQEYISRLVKVWRDLGHDE 167
                                       577889********************998776 PP

>> Cnn_1N  Centrosomin N-terminal motif 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.4e-05      0.14      30      72 ..     120     162 ..     114     163 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.4e-05
                            Cnn_1N  30 leklseeqkeellkenielkveveslqkelkekkkllreaeka 72 
                                       l kl++e++++++++ i+l+ve ++   e +e+  +l + +++
  gi|242398886|ref|YP_002994310.1| 120 LVKLPPEDNQKIIETAIQLHVEYAKKSPEAQEYISRLVKVWRD 162
                                       668999***************************9999998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1162.08
//
Query:       gi|242398887|ref|YP_002994311.1|  [L=145]
Description: TRAP-T family protein transporter, small (4 TMs) inner membrane subunit [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-21   76.8   7.4    1.6e-21   76.6   7.4    1.1  1  DctQ      Tripartite ATP-independent periplasmic transporters


Domain annotation for each model (and alignments):
>> DctQ  Tripartite ATP-independent periplasmic transporters, DctQ component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.6   7.4   8.7e-26   1.6e-21       1     129 [.       7     140 ..       7     143 .. 0.90

  Alignments for each domain:
  == domain 1  score: 76.6 bits;  conditional E-value: 8.7e-26
                              DctQ   1 mvllvlaqvflRyllnsslpwteelarylfvwlvflgaalalrrgshirvdllverlpprvrrlleliadllallfa 77 
                                       ++l+v+++v +Ry+ln++ + +  ++++l+  l+ lg+a++lr+g+h++vd++++++p++vr++l+++   ++ l +
  gi|242398887|ref|YP_002994311.1|   7 ITLVVVYEVSTRYFLNMADSRAIFVSVWLYGILFTLGGAYTLREGGHVSVDIVYRKVPEKVRKVLDVVDIGIVTLTG 83 
                                       689************888888999******************************************99888988888 PP

                              DctQ  78 avliwagw.levaaalfeettpvlg....lplwwvylvlpigaallalvalarllrl 129
                                       ++li  g  ++  +++ +e+ ++lg     p ww+ ++++i+++l++l+ +  +l+ 
  gi|242398887|ref|YP_002994311.1|  84 IILILVGTpIAWRSFMIREVDSSLGivfaPPIWWFKWIAVISVVLITLQTIPMMLEK 140
                                       888888888777888888888888877779*******************99888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       643  (0.0358637); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1091.94
//
Query:       gi|242398888|ref|YP_002994312.1|  [L=431]
Description: large integral membrane transport protein [Thermococcus sibiricus MM 739]
Scores for complete 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-82  275.8  48.2    6.7e-82  275.5  48.2    1.0  1  DctM      Tripartite ATP-independent periplasmic transporter,


Domain annotation for each model (and alignments):
>> DctM  Tripartite ATP-independent periplasmic transporter, DctM component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  275.5  48.2   3.7e-86   6.7e-82       1     415 [.       6     419 ..       6     420 .. 0.95

  Alignments for each domain:
  == domain 1  score: 275.5 bits;  conditional E-value: 3.7e-86
                              DctM   1 lvsllvllalgvpvaislalasllllallgelllgvpleqilaqrvveglssfallaipfFvlaGivlersGlakrl 77 
                                       ++ l+ l++l +pva++l ++s+++ +++       + + ++ q +++ +++ al+a+p+Fv++ +vle+sG+a++l
  gi|242398888|ref|YP_002994312.1|   6 FIFLFGLILLNIPVAFALFFTSIVFGLIFWGW----NGLYVTFQGIWSLMNNWALVALPLFVFMSAVLEKSGIADEL 78 
                                       6789*******************999998888....7777999********************************** PP

                              DctM  78 idlaaalvGrvrGGlakvsvvgsalfgaiSGsavAnvaavGsitipamkrsGykrefaaaviaasstlgqiiPPslg 154
                                       + + ++l+Gr+rG+la+++++ +  +ga+SG+ +A  a+++ i++p+m ++Gy+++ a++ i a++tl q++PPs +
  gi|242398888|ref|YP_002994312.1|  79 FTTFYKLLGRIRGSLAVIAIILGYTIGAMSGVIAAAIASLALIIYPLMVKHGYDKKLAIGSILAAGTLPQVVPPSFN 155
                                       ***************************************************************************** PP

                              DctM 155 livfamavlgvsigdlfaaaiipglllavglllavaiaak..kenlrs..ktkaelkrlgqalkeaipalllpliil 227
                                       +iv++  v+gvs+g+lfa+++  g ++a+++ ++v + +   k++++     k +l +  ++lk+ i +l +++ +l
  gi|242398888|ref|YP_002994312.1| 156 MIVYGS-VAGVSVGKLFAGGLGVGTVMAIVFSIYVLVWSHlnKDKVPVfeAGKISLGEKIASLKYLIGPLTIIFGVL 231
                                       ******.*********************99877665544433777776335566778888899999*********** PP

                              DctM 228 igillgiftpteagavavvyalviallvyrrltleevaaallstakttaavlfilaaagifaglltltgvplklsel 304
                                       + i+ gi+tptea++v+++++lv  ll +++lt + + +al+ t+k+t +   i+a+ ++f+ +++  g    + +l
  gi|242398888|ref|YP_002994312.1| 232 GSIFTGIATPTEASGVGAFLSLVYVLL-RGKLTKKVLDEALVVTLKVTSMACWIMAGGSAFSSVFSGIGGKKLVVDL 307
                                       **********************99999.************************************************* PP

                              DctM 305 llslsggkllfLilvnllvlvlGmfldttaaiiilvpilaPaaaklgidpihfgvvivlnlsiglitPPvGlalfva 381
                                       l+sl++ k+++Li  ++l+++lGmf+d++++i+i++pil Pa+  lg dp++ gv ++ +l ++++tPPvGl l++ 
  gi|242398888|ref|YP_002994312.1| 308 LMSLPAAKITVLIFSLALIFFLGMFVDPVSIIMIMTPILTPAVTGLGYDPLWWGVAFTSMLLVSYLTPPVGLGLYYF 384
                                       ****************************************************************************9 PP

                              DctM 382 ss.iakvsveeivkalvPflvvlvvalvlitlvpe 415
                                       ++ i +vs+++i++a++Pf+v++v+a+v+i+l p 
  gi|242398888|ref|YP_002994312.1| 385 KGaIDEVSMDDIYRAVLPFIVLQVIAIVIIILEPD 419
                                       972557*************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       842  (0.046963); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.34s 00:00:00.96 Elapsed: 00:00:00.51
# Mc/sec: 2565.32
//
Query:       gi|242398889|ref|YP_002994313.1|  [L=194]
Description: hypothetical protein TSIB_0906 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.013   16.0   0.3      0.021   15.4   0.3    1.3  1  RPA_interact_C  Replication protein A interacting C-terminal
       0.02   15.1   0.0        4.8    7.4   0.0    2.4  2  zf-RING_7       C4-type zinc ribbon domain
      0.065   12.7   1.9       0.73    9.3   0.1    2.2  2  zf-ribbon_3     zinc-ribbon domain
      0.072   13.2   0.3       0.19   11.8   0.3    1.7  1  zf-RRPl_C4      Putative ribonucleoprotein zinc-finger pf C4 
      0.074   12.8   0.2       0.13   12.0   0.2    1.4  1  SAP             SAP domain
        0.1   12.7   1.6       0.16   12.1   1.6    1.2  1  FYVE            FYVE zinc finger
       0.15   12.0   1.5       0.25   11.3   1.5    1.3  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
       0.28   10.8   0.8         28    4.4   0.2    2.5  2  RecR            RecR protein


Domain annotation for each model (and alignments):
>> RPA_interact_C  Replication protein A interacting C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.3   9.5e-06     0.021       2      26 ..     165     190 ..     164     194 .] 0.91

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 9.5e-06
                    RPA_interact_C   2 CPvCkkrklketsevifCe.Cglrle 26 
                                       CP+C  ++l+ +++v +C+ Cg+ ++
  gi|242398889|ref|YP_002994313.1| 165 CPICGAKELTWHEKVAYCDsCGFGVK 190
                                       ******************99**9876 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0    0.0095        21       6      31 ..     145     170 ..     145     170 .. 0.88
   2 ?    7.4   0.0    0.0021       4.8      21      30 ..     177     186 ..     171     186 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0095
                                       --B--CCHHHHHCCSTB-EE-TTT-- CS
                         zf-RING_7   6 hmelppqvlselragdevvtCpeCGR 31 
                                       +++++ +++++    ++  +Cp CG+
  gi|242398889|ref|YP_002994313.1| 145 FLVIDESTYKKWEESNKTDHCPICGA 170
                                       6788999999999999999*****96 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0021
                                       TB-EE-TTT- CS
                         zf-RING_7  21 devvtCpeCG 30 
                                       ++v++C++CG
  gi|242398889|ref|YP_002994313.1| 177 EKVAYCDSCG 186
                                       68*******9 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1   0.00033      0.73       2      11 ..     162     171 ..     161     174 .. 0.80
   2 ?    2.7   0.2     0.039        87       4       9 ..     181     186 ..     178     189 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00033
                       zf-ribbon_3   2 tvrCPnCGap 11 
                                       t +CP CGa+
  gi|242398889|ref|YP_002994313.1| 162 TDHCPICGAK 171
                                       6799999984 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.039
                       zf-ribbon_3   4 rCPnCG 9  
                                       +C +CG
  gi|242398889|ref|YP_002994313.1| 181 YCDSCG 186
                                       677777 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 ?   11.8   0.3   8.6e-05      0.19       3      25 ..     164     186 ..     162     192 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.6e-05
                        zf-RRPl_C4   3 kCkyClskklknlnetvyCeaCe 25 
                                       +C+ C  k+l+  ++  yC+ C 
  gi|242398889|ref|YP_002994313.1| 164 HCPICGAKELTWHEKVAYCDSCG 186
                                       7*********************5 PP

>> SAP  SAP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   5.9e-05      0.13       5      19 ..      29      43 ..      29      44 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.9e-05
                                      -HHHHHHHHHHTT-- CS
                               SAP  5 tVaeLKeeLkkrGLp 19
                                      +V+eLKe+L++++L+
  gi|242398889|ref|YP_002994313.1| 29 RVDELKEILRELNLK 43
                                      69***********97 PP

>> FYVE  FYVE zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.6   7.1e-05      0.16       2      32 ..     155     186 ..     154     190 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.1e-05
                                       ---...--SB-TTT--B-.-SSS--EE-TTT- CS
                              FYVE   2 kwkddsevkkCeiCakkF.sllrrrhhCrlCG 32 
                                       kw++ +++++C+iC +k  ++ ++  +C  CG
  gi|242398889|ref|YP_002994313.1| 155 KWEESNKTDHCPICGAKElTWHEKVAYCDSCG 186
                                       8*************87654999999******9 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   1.5   0.00011      0.25      28      54 ..     162     187 ..     150     190 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00011
                    OrfB_Zn_ribbon  28 SktCseCgsknkealsgrtfkCpnCgf 54 
                                          C+ Cg+k  +  ++++ +C++Cgf
  gi|242398889|ref|YP_002994313.1| 162 TDHCPICGAKELT-WHEKVAYCDSCGF 187
                                       568*********9.************9 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.2     0.012        28      28      34 ..     162     168 ..     159     172 .. 0.60
   2 ?    4.3   0.0     0.013        29      13      23 ..     176     186 ..     173     187 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.012
                                       SSS-CCC CS
                              RecR  28 edlCaIC 34 
                                       +d C+IC
  gi|242398889|ref|YP_002994313.1| 162 TDHCPIC 168
                                       4556666 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.013
                                       HHH-EE-TTT- CS
                              RecR  13 kekvrhCsrCg 23 
                                       +ekv +C  Cg
  gi|242398889|ref|YP_002994313.1| 176 HEKVAYCDSCG 186
                                       699*******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       772  (0.0430587); expected 358.6 (0.02)
Passed bias filter:                      608  (0.0339115); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); 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: 00:00:00.47
# Mc/sec: 1253.40
//
Query:       gi|242398890|ref|YP_002994314.1|  [L=187]
Description: Fuculose-1-phosphate aldolase [Thermococcus sibiricus MM 739]
Scores for complete 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  147.8   0.0    3.7e-43  147.6   0.0    1.0  1  Aldolase_II  Class II Aldolase and Adducin N-terminal domain


Domain annotation for each model (and alignments):
>> Aldolase_II  Class II Aldolase and Adducin N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.6   0.0   2.1e-47   3.7e-43       3     185 ..       9     180 ..       7     181 .. 0.94

  Alignments for each domain:
  == domain 1  score: 147.6 bits;  conditional E-value: 2.1e-47
                                       HHHHHHHHHHTTSSCTTBCEEEEEETSTTEEEEEBTSS-GGGHTGGGEEEEETTSCEEEECECSSSTB-TTHHHHHH CS
                       Aldolase_II   3 laeasrllarrglvegtgGniSvrvpeedsflitpsgvdfeeltaedlvvvdldsgevvegkekggkpssetplHla 79 
                                       l++ s+l ++rgl+ ++gGn+S+  +  ++++i+ +g  + elt  +++ +d++ g+ +    ++ +psse+ lH +
  gi|242398890|ref|YP_002994314.1|   9 LVKYSKLAHERGLTAAFGGNFSILFN--GKIFIKSTGSIMNELTRTQIAMMDFE-GNSL----SSIRPSSEWKLHVE 78 
                                       789999*****************955..89***********************9.****....3579********** PP

                                       HHHH-TT-SEEEEE--HHHHHHHTCCSTSCHCCSSHHHHC.HSSSEEEEES-SSTTCHHHHHHHHHHHHHS-SEEEE CS
                       Aldolase_II  80 iykarpdaravvHtHspaavalsalagkeglppltqeaaklllgdevpvipyaapgteelgealaealkedakavll 156
                                       +yk r+d+ra++H+H+p+ +++s+l+ +e+lp +t+ea+  +l +++p++p ++ g+ el++++a+ l+   +av++
  gi|242398890|ref|YP_002994314.1|  79 VYKLRKDIRAIAHLHPPYSIVVSTLL-EEELPIITPEAEV-YL-KKIPIVPFKPAGSWELARETAKYLE-AYDAVIM 151
                                       ***********************876.677*********9.54.66**********************9.668**** PP

                                       TTTEEEEEESSHHHHHHHHHHHHHHHHHH CS
                       Aldolase_II 157 rnHGlltvGetleeAvalaetleeaaeiq 185
                                       +nHG++tvG++l+eA++ +e +ee+a+++
  gi|242398890|ref|YP_002994314.1| 152 ENHGVVTVGKSLREAYYKTELVEESAKLW 180
                                       **************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); 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: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1252.09
//
Query:       gi|242398891|ref|YP_002994315.1|  [L=91]
Description: hypothetical protein TSIB_0908 [Thermococcus sibiricus MM 739]
Scores for complete 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-32  109.6   3.5    6.8e-32  109.4   3.5    1.0  1  UPF0147       Uncharacterised protein family (UPF0147)
  ------ inclusion threshold ------
        0.1   11.8   0.3       0.11   11.7   0.3    1.0  1  NTP_transf_7  Nucleotidyltransferase


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 !  109.4   3.5   7.6e-36   6.8e-32       4      81 .]      12      90 ..       9      90 .. 0.97

  Alignments for each domain:
  == domain 1  score: 109.4 bits;  conditional E-value: 7.6e-36
                                      HHHHHHHHH.HHHHT-TTS-HHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHHHHH CS
                           UPF0147  4 kikevielL.eeiiedtsvPrniRraakeakekLkdekeslavraataisiLdeisnDpnmPlhaRtliwevvskLEti 81
                                      +i+++i++L e++++dt vPrniRraa+ a+e+L+d++++++vraa+ai iL+eis+DpnmP+h+Rt iwev++ LE++
  gi|242398891|ref|YP_002994315.1| 12 RIQQIIQVLkEQVVQDTIVPRNIRRAAERAIESLMDTSKDPTVRAADAIVILEEISEDPNMPMHTRTIIWEVLGALEQV 90
                                      79*******889*****************************************************************97 PP

>> NTP_transf_7  Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.3   1.2e-05      0.11      26      89 ..       7      72 ..       3      90 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.2e-05
                      NTP_transf_7 26 PtlevklkdlvkvvrekleekgvevrdirlnGsaasyvlae.dealsykDlDlifave.lseeeel 89
                                       ++ev+++++++v++e++ ++ +  r+ir     a   l + ++  + +  D i+ +e +se+ ++
  gi|242398891|ref|YP_002994315.1|  7 SDVEVRIQQIIQVLKEQVVQDTIVPRNIRRAAERAIESLMDtSKDPTVRAADAIVILEeISEDPNM 72
                                      5799*************************9888776655540455778888877666514444343 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       822  (0.0458475); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 684.50
//
Query:       gi|242398892|ref|YP_002994316.1|  [L=179]
Description: Cob(I)alamin adenosyltransferase [Thermococcus sibiricus MM 739]
Scores for complete 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-61  205.8   0.0      6e-61  205.7   0.0    1.0  1  CobA_CobO_BtuR  ATP:corrinoid adenosyltransferase BtuR/CobO/C
  ------ inclusion threshold ------
      0.086   12.6   0.1        7.7    6.2   0.0    2.1  2  IstB_IS21       IstB-like ATP binding protein
      0.096   12.2   1.1       0.84    9.2   1.1    2.0  1  AAA_25          AAA domain
       0.16   12.5   0.7        1.1    9.8   0.1    2.6  2  PC_rep          Proteasome/cyclosome repeat


Domain annotation for each model (and alignments):
>> CobA_CobO_BtuR  ATP:corrinoid adenosyltransferase BtuR/CobO/CobP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.7   0.0   1.3e-64     6e-61       3     172 .]      12     179 .]      10     179 .] 0.97

  Alignments for each domain:
  == domain 1  score: 205.7 bits;  conditional E-value: 1.3e-64
                    CobA_CobO_BtuR   3 glihvytGdGKGKttAAlGlalRalgaglkvlvvqFlKgekesgElaalkkleielerlgkegfvkmeeeekeedaa 79 
                                       g+ih+ytG+GKGKttAAlGl lR+lg+g kv+++qFlK+ + +gE++ +++++i +e++g  +fv  +++ + e+ +
  gi|242398892|ref|YP_002994316.1|  12 GMIHIYTGNGKGKTTAALGLGLRMLGNGGKVIMIQFLKSPNVYGEQKKAQECGIVVESYGLPKFV--HKKPDPEEIK 86 
                                       9**************************************878***********************..45568899** PP

                    CobA_CobO_BtuR  80 aakealekakealaseeydlvvlDEinyalklglldeeevlellkkkpeklelvlTGrnapeelleaADlvtemkkv 156
                                        a++ale+++e ++++e+dlv+lDEi++al +g++d+e+v ++lk+k++ +e+vlTGr++peel+e+AD+vt mk+v
  gi|242398892|ref|YP_002994316.1|  87 VARKALERTREIVKNGEWDLVILDEICVALGFGMIDVEDVKAILKEKSPYTEVVLTGRYCPEELFELADYVTLMKEV 163
                                       ***************************************************************************** PP

                    CobA_CobO_BtuR 157 kHpydkgikarkGiey 172
                                       kHpy+kgi arkGiey
  gi|242398892|ref|YP_002994316.1| 164 KHPYQKGILARKGIEY 179
                                       ***************9 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1    0.0051        23      46      81 ..      10      45 ..       4      68 .. 0.79
   2 ?    6.2   0.0    0.0017       7.7      88     119 ..      83     114 ..      74     154 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0051
                         IstB_IS21 46 kkenivllGpsGvGKshlaialgveavraglsvlfv 81
                                      k   i +  + G GK+  a  lg +   +g +v+ +
  gi|242398892|ref|YP_002994316.1| 10 KLGMIHIYTGNGKGKTTAALGLGLRMLGNGGKVIMI 45
                                      55567788889***************9999988654 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0017
                         IstB_IS21  88 eelkrarrdgklaralkrllkvdllilDdlgl 119
                                       ee+k+ar+  + +r++ +  + dl+ilD++ +
  gi|242398892|ref|YP_002994316.1|  83 EEIKVARKALERTREIVKNGEWDLVILDEICV 114
                                       6789999999*******************975 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   1.1   0.00019      0.84      32     157 ..      10     118 ..       3     132 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00019
                            AAA_25  32 agelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelr..rRlravgealrddarllvl 106
                                       + + + ++   g GKtt+al l+l ++             gkV+++++  s +     +++++ g  ++  +   ++
  gi|242398892|ref|YP_002994316.1|  10 KLGMIHIYTGNGKGKTTAALGLGLRMLG-N---------GGKVIMIQFLKSPNVYGeqKKAQECGIVVESYGLPKFV 76 
                                       5555556666788************993.3.........47888888888876554114444444333333444444 PP

                            AAA_25 107 dlagveslpLfakdrggtl..ltadvdaleaaieevegvrlvviDplsralgg 157
                                       + +             +++  +  ++++ ++ ++   +++lv++D +  alg 
  gi|242398892|ref|YP_002994316.1|  77 HKKPD----------PEEIkvARKALERTREIVKN-GEWDLVILDEICVALGF 118
                                       42222..........22222234555665555555.77999999887666665 PP

>> PC_rep  Proteasome/cyclosome repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   0.00025       1.1       2      15 ..      27      40 ..      26      52 .. 0.84
   2 ?   -0.3   0.1       0.4   1.8e+03       4      11 ..     116     123 ..     115     140 .. 0.54

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00025
                                      HHHHHHHHCTTSTC CS
                            PC_rep  2 AllALGlihaGsgn 15
                                      A+l+LGl ++G+g 
  gi|242398892|ref|YP_002994316.1| 27 AALGLGLRMLGNGG 40
                                      9**********885 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.4
                                       HHHHHHCT CS
                            PC_rep   4 lALGliha 11 
                                       l+ G+i+ 
  gi|242398892|ref|YP_002994316.1| 116 LGFGMIDV 123
                                       56666653 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); 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 0.27s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1211.18
//
Query:       gi|242398893|ref|YP_002994317.1|  [L=362]
Description: D-aminopeptidase [Thermococcus sibiricus MM 739]
Scores for complete 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-117  389.9   0.9   9.8e-117  389.7   0.9    1.0  1  Peptidase_S58  Peptidase family S58


Domain annotation for each model (and alignments):
>> Peptidase_S58  Peptidase family S58
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  389.7   0.9  5.5e-121  9.8e-117       1     297 [.      19     339 ..      19     341 .. 0.97

  Alignments for each domain:
  == domain 1  score: 389.7 bits;  conditional E-value: 5.5e-121
                     Peptidase_S58   1 naitDVaGvrVghatlae........ge.vrtGvTvilpr.gnlfkekvvAavdvlnGfgkttgtdqleelglletp 67 
                                       n+i+DV+Gv+Vgh++l++        +  vrtGvT+ilp+ gn++kek+ A+v+v+nG+ k +g+ q++elg+letp
  gi|242398893|ref|YP_002994317.1|  19 NSIADVKGVKVGHVSLIKgegklipgKGpVRTGVTAILPHeGNIYKEKLLASVFVMNGYAKPIGLIQVRELGTLETP 95 
                                       99**************9999*****9556************************************************ PP

                     Peptidase_S58  68 ivLtntlsvgaaadgvvewlleeeee..eearsvvpvVaetnDgvlndiragavkeehvaealaaAaaapvaeGnvG 142
                                       i+Ltntl+vg+a+d+++e++l+++e+   ++ sv+pvV+e+nD++lndir+ +vk+eh++eal++A+a ++ eG+vG
  gi|242398893|ref|YP_002994317.1|  96 IILTNTLAVGTATDALIEYMLDQNEDigVSTGSVNPVVMECNDSYLNDIRGKHVKKEHIFEALKNAKA-DFDEGAVG 171
                                       **********************999999999***********************************66.8******* PP

                     Peptidase_S58 143 aGtGmiafglKGGiGtaSrvleegekeytvgalvqaNfggredlriagvpvgkelaeea.....kdgsiivvvatDa 214
                                       aGtGm+af++KGGiG++Sr+++ ++++yt+galv++Nfg+redl+iagvp g el++       ++gsii+v+atD+
  gi|242398893|ref|YP_002994317.1| 172 AGTGMSAFEFKGGIGSSSRIVDIEGRKYTIGALVLSNFGKREDLTIAGVPAGLELRNWPgkggeGKGSIIIVIATDV 248
                                       **********************999***************************88887779***************** PP

                     Peptidase_S58 215 pLskrqlkrlakraalGlartgsphsngsGDivlafstaekepe........evledeeldelfeaaaeaveeAiln 283
                                       pL++rql r+akr a+Glartg+++ ngsGDi++afsta+++++        +  +d+ l++lf+a+ae+veeAi+n
  gi|242398893|ref|YP_002994317.1| 249 PLTARQLYRVAKRGAIGLARTGGYAYNGSGDIIFAFSTAQRIKHyqkeiidiKSTPDDVLSPLFKATAETVEEAIIN 325
                                       ****************************************************8899********************* PP

                     Peptidase_S58 284 allaAetvtgrdgr 297
                                       +ll+A+ +tgrd++
  gi|242398893|ref|YP_002994317.1| 326 SLLQAKAMTGRDNH 339
                                       ***********988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); 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 0.31s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 2207.80
//
Query:       gi|242398894|ref|YP_002994318.1|  [L=398]
Description: Aminotransferase, class-V [Thermococcus sibiricus MM 739]
Scores for complete 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-29  101.5   0.0    7.4e-29  100.8   0.0    1.3  1  Aminotran_5      Aminotransferase class-V
    0.00059   18.5   0.0    0.00082   18.0   0.0    1.1  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
     0.0024   17.3   0.0     0.0033   16.8   0.0    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
  ------ inclusion threshold ------
      0.062   12.0   0.0        1.7    7.2   0.0    2.1  2  Aminotran_3      Aminotransferase class-III


Domain annotation for each model (and alignments):
>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.8   0.0   1.7e-32   7.4e-29       2     371 .]      16     387 ..      15     387 .. 0.87

  Alignments for each domain:
  == domain 1  score: 100.8 bits;  conditional E-value: 1.7e-32
                                       EEBTTTS----HHHHHHHHHHHHCTCCSSSSSSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHH CS
                       Aminotran_5   2 yldsaAttqkpqeVldalqeyytdynanvhrsvhhlgkeatkaveearekvaelinaeseeeiiftsGtteainlva 78 
                                       yl  a    +p ++l++ +++++ y +    +v +     ++++e++ ++ ++l+ ++  e++  t  tte++   +
  gi|242398894|ref|YP_002994318.1|  16 YLNTASAGFLPLTALKRSMDFLS-YLTDFREGVDSVDFLDKEIMENVLDEGKRLLRTKR-ENLTLTIQTTEGLRRLL 90 
                                       55555556677777888888744.777777788888888899****************7.88888999********* PP

                                       HHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTEB CS
                       Aminotran_5  79 lslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsnvtGti 155
                                       ls++   k+  +i+  ++e  +     +  a+r +++++vi+  ++g + l+++ekl++++t +++ + v+ ++G  
  gi|242398894|ref|YP_002994318.1|  91 LSIE--PKKSMNIISFDMEFPSLSCLLKSYAQRYNLELRVIKN-RNGWYYLEDMEKLVDDNTFAIIGSSVQWISGQR 164
                                       ***5..79*********************************97.899999*************************** PP

                                       --HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTT.TTSST.T-EEEEEEHHHHHTS..SS.STTS CS
                       Aminotran_5 156 qpveeigklakkkgalvlvDaaqavghipidvkklgvDflafsghK.llgPt.GiGvlyvrkellekleplllggem 230
                                         + e+ ++a+++ga+v+vDa+q +g   ++ +k gvD + ++g K ll P+ G G++yv+++l+e++ p+ +  +m
  gi|242398894|ref|YP_002994318.1| 165 MNLRELSRIAHEHGAWVIVDAVQHLGNLTLYPEKEGVDAVIAGGEKwLLNPSvGSGLMYVSNALIEEASPIAGLLNM 241
                                       ***********************************************888855************************ PP

                                       EEEEET.TEEE............EHCTTGGGS..SS--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCT CS
                       Aminotran_5 231 veevsl.eett............faeapskfe.aGTpnvagiiglgaaleyleeigleaiekhekelaeyllerlks 293
                                        + v    ++             f++  +k+  +G p+   +  l  ale ++eig+e+ie+h+++la ++++++ +
  gi|242398894|ref|YP_002994318.1| 242 KSPVGEwSSWWgmpekdpwgnfdFRNDARKLDfGGGPPYLLATTLWGALEVINEIGIEKIERHNTNLAGRIKDEILA 318
                                       999999777668999999999996666666553589***************************************** PP

                                       STTEEEES.-B-CTCBSEEEEEE..TTCSHHHHHHHHHHTTEEEEE.E-TTTHHHHHHTT.S-EEEEE--TTS-HHH CS
                       Aminotran_5 294 lpgvrlygpdkaerrasivsfnf..kgvhaedvatlLdeegIavrs.GhhcaqplmkrlalegtvRaSlyiynteee 367
                                       l+   + g  ++ ++++i+++++   + + e++ + +  egI v+  G               ++R+S ++yn+ ++
  gi|242398894|ref|YP_002994318.1| 319 LGLEII-G-GEDWEKSAIITIKTglSYEKEEEIYKRILAEGIKVSHrGALGH----------YGIRVSPHLYNEMKD 383
                                       *87766.6.4679999999999953333345555555555999987554444..........899999999999999 PP

                                       HHHH CS
                       Aminotran_5 368 vdrl 371
                                       ++ +
  gi|242398894|ref|YP_002994318.1| 384 IEIF 387
                                       9865 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   1.8e-07   0.00082      93     200 ..     100     212 ..      88     229 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.8e-07
                                       EEEEESTSSHHHHHHHHHTHHHTTCEEEEEST....TSHHHHHHHCCTTEEEEEEESS-TTTT----HHHHHHHHHH CS
                   Cys_Met_Meta_PP  93 eivvsddlYggtqrllkkvlkklgievkfvdt....sdleelekaikentklvylEtptnpllkvvDiekiaklakk 165
                                       +i++ d  + + + llk+++++ ++e +++        le++ek +++nt ++   ++  +  + + +++++++a++
  gi|242398894|ref|YP_002994318.1| 100 NIISFDMEFPSLSCLLKSYAQRYNLELRVIKNrngwYYLEDMEKLVDDNTFAIIGSSVQWISGQRMNLRELSRIAHE 176
                                       6677777777778899999999999999998833334589************************************* PP

                                       TT-EEEEEGTTTHT.TTS-GGGGT-SEEEEETTTTT CS
                   Cys_Met_Meta_PP 166 agvlvvvDntfasp.llqrplklgaDivvhSaTKyl 200
                                       +g+ v+vD++   + l   p k g+D v+  + K+l
  gi|242398894|ref|YP_002994318.1| 177 HGAWVIVDAVQHLGnLTLYPEKEGVDAVIAGGEKWL 212
                                       **********998878899****************8 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   7.4e-07    0.0033     102     150 ..     139     190 ..     129     199 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 7.4e-07
                                       GGCGGG--TTEEEEEEB-...GGGB---HHHHHHHHHHCT-EEEEE-TT-TT CS
                   DegT_DnrJ_EryC1 102 aaieaaitertkaIlpVh...lyGqvadmdalkaiaakhglkvieDaAhAlG 150
                                       +++e+++  +t aI+      + Gq +++ +l +ia++hg +vi Da + lG
  gi|242398894|ref|YP_002994318.1| 139 EDMEKLVDDNTFAIIGSSvqwISGQRMNLRELSRIAHEHGAWVIVDAVQHLG 190
                                       678999999**9*9976522357************************99998 PP

>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0   0.00038       1.7     173     235 ..     129     187 ..      91     190 .. 0.81
   2 ?    2.8   0.0    0.0085        38     346     403 ..     333     392 ..     286     395 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00038
                                       HHHHHHHHHHHHHHCHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEEE-TT CS
                       Aminotran_3 173 eeeaalleelealekkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvllivDEvq 235
                                        +++    +le++ek  +d++ A+i   +q   G  +     l++l  ++++h++ +ivD vq
  gi|242398894|ref|YP_002994318.1| 129 IKNRNGWYYLEDMEKLVDDNTFAIIGSSVQWISGQRMN----LRELSRIAHEHGAWVIVDAVQ 187
                                       344566778999******************99998775....99****************998 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.0085
                                       TEEEEEEBCCCETTCHHHHHHHHHCTEE-EEETT...TEEEE---TT--HHHHHHHHHHHH CS
                       Aminotran_3 346 lmiaielkeeaevkekeilkkakekGvlilsaGd...nvirllppliitdeeidelleilk 403
                                       ++i i +  + e ke+ei+k+ +++G+ + + G      ir+ p l  + ++i+ +le l+
  gi|242398894|ref|YP_002994318.1| 333 AIITIKTGLSYE-KEEEIYKRILAEGIKVSHRGAlghYGIRVSPHLYNEMKDIEIFLEFLV 392
                                       566666666666.4489***********98877666599***********99999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); 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: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 2603.13
//
Query:       gi|242398895|ref|YP_002994319.1|  [L=281]
Description: Endonuclease IV [Thermococcus sibiricus MM 739]
Scores for complete 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-21   75.6   0.0    4.8e-21   75.2   0.0    1.2  1  AP_endonuc_2  Xylose isomerase-like TIM barrel
    0.00028   20.3   0.2     0.0014   18.1   0.2    2.0  1  Amidohydro_1  Amidohydrolase family
  ------ inclusion threshold ------
       0.27   11.4   1.8       0.86    9.8   0.0    2.6  3  DUF5446       Family of unknown function (DUF5446)


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 !   75.2   0.0     8e-25   4.8e-21       2     209 ..      28     239 ..      27     240 .. 0.91

  Alignments for each domain:
  == domain 1  score: 75.2 bits;  conditional E-value: 8e-25
                                       HHHHHCT-SEEEEECCTCSHHHHCHHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCS.HHHHHHHHHHHHH CS
                      AP_endonuc_2   2 aaaaeaGfdgvElfgrdlvpvselsdeelrelrkaldelglriaslslftrfgypdederear.reesvdalkraie 77 
                                       ++++++G d++El +  +v+ +   +e++++++  ++++++ ++++ +++ + +  e   + + re+s++++ + +e
  gi|242398895|ref|YP_002994319.1|  28 EQVKKLGLDAMELEFVRGVNLK---PEMAKKIKYVAQKNDILLTAHAPYYINLNATE---K-AkREASKNRIIQSAE 97 
                                       799******************9...69***************************776...3.358999********* PP

                                       HHHHHTBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHHHHHHT..SEEEEE--TTTTSSSTCHHHHHHHHHHT CS
                      AP_endonuc_2  78 laaaLGapllvlhpGtagagpkgseeeawerlaeslneladyaekeg..vklalEtlagsgvelgdeelarlldavd 152
                                       + ++ G+  +v+h+G   ++ k+++   ++++ + ++++++ ++++g  v++  E + +++++    el r+ ++v+
  gi|242398895|ref|YP_002994319.1|  98 RLHEAGGWSVVFHAG---YYLKQEPSKVYDTIKSEIRDIVKTLQDKGvnVWIRPELTGKPTQFGSLNELIRISQEVE 171
                                       ***************...9*************************9999999**********99888*********** PP

                                       TTTEEEEEEHHHHHHH.......TTTHHHHHHHHHGG.......EEEEEE.EESSTTTTSSTTEESTTSSS CS
                      AP_endonuc_2 153 spnvgvclDtgHllia.......eedvddalraladr.......ikhvHikDakgdlgagrdrhvpigeGe 209
                                       +  v  ++D++H++++        e ++++l  l++          h+Hi+ ++    +g+ +h+++ e +
  gi|242398895|ref|YP_002994319.1| 172 Q--VLPAIDFAHCHARnkgkynsTEEWREMLSLLEEGlgrdalnNMHIHISGIEY-SDKGEKNHLNLQESD 239
                                       7..*************999998866666666666555777**9999****99999.788888898888765 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.2   2.3e-07    0.0014     127     217 ..      46     144 ..      24     281 .] 0.83

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.3e-07
                                       CCSHHHHHHHHHHHHHHHTTEEEEEE...TSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEE. CS
                      Amidohydro_1 127 pafsdeelkealkeakkrdlpvaiHa...letkgevedaeaafgetiehgthlevaeslglldeiklilahgvhlt. 199
                                       + +++e+ k++  +a k d+ +++Ha    +++++ ++ ++a +++     +   ae l+ ++   ++++ g +l  
  gi|242398895|ref|YP_002994319.1|  46 VNLKPEMAKKIKYVAQKNDILLTAHApyyINLNATEKAKREASKNR-----IIQSAERLHEAGGWSVVFHAGYYLKq 117
                                       5678999999999*************99999999998888888844.....5667777999***************7 PP

                                       .HH........HHHHHHHHHHHHCEEH CS
                      Amidohydro_1 200 .pt........eaellkerlkeagvah 217
                                        p+        e++ + + l+++gv+ 
  gi|242398895|ref|YP_002994319.1| 118 ePSkvydtiksEIRDIVKTLQDKGVNV 144
                                       733455557778888888888888873 PP

>> DUF5446  Family of unknown function (DUF5446)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.2      0.56   3.4e+03      32      47 ..      77      92 ..      75     101 .. 0.74
   2 ?   -1.5   0.0      0.48   2.8e+03      45      58 ..     121     134 ..     115     140 .. 0.77
   3 ?    9.8   0.0   0.00014      0.86       4      54 ..     157     207 ..     155     222 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.56
                           DUF5446 32 vneteaekeekeeerl 47
                                      +n+te+ k+e+  +r+
  gi|242398895|ref|YP_002994319.1| 77 LNATEKAKREASKNRI 92
                                      6888999998887776 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.48
                           DUF5446  45 erldllekElkdLv 58 
                                       ++ d + +E+ d+v
  gi|242398895|ref|YP_002994319.1| 121 KVYDTIKSEIRDIV 134
                                       67799999999975 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.00014
                           DUF5446   4 FvsKdsvLqlLeeiEeeltevEkelseavneteaekeekeeerldllekEl 54 
                                       F s ++ +++ +e+E+ l ++  +  +a n+ +    e++ e+l+lle+ l
  gi|242398895|ref|YP_002994319.1| 157 FGSLNELIRISQEVEQVLPAIDFAHCHARNKGKYNSTEEWREMLSLLEEGL 207
                                       66778899999*************************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.35s 00:00:00.95 Elapsed: 00:00:00.53
# Mc/sec: 1583.24
//
Query:       gi|242398896|ref|YP_002994320.1|  [L=353]
Description: hypothetical protein TSIB_0913 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00097   18.1  15.8    0.00097   18.1  15.8    3.1  3  Spc7             Spc7 kinetochore protein
      0.001   18.3  17.1      0.001   18.3  17.1    3.0  3  Atg14            Vacuolar sorting 38 and autophagy-related su
  ------ inclusion threshold ------
      0.019   15.2  13.0       0.08   13.2   0.9    4.5  3  DUF948           Bacterial protein of unknown function (DUF94
      0.023   15.0   4.5      0.023   15.0   4.5    3.1  3  MutS_II          MutS domain II
      0.054   13.3  27.8      0.087   12.7   7.2    3.8  3  Bacillus_HBL     Bacillus haemolytic enterotoxin (HBL)
      0.067   13.6   1.8      0.067   13.6   1.8    6.3  7  FlaC_arch        Flagella accessory protein C (FlaC)
       0.07   13.2  31.5       0.15   12.2   7.5    4.9  5  COG2             COG (conserved oligomeric Golgi) complex com
       0.15   12.6  20.4        9.6    6.8   4.0    5.6  6  NPV_P10          Nucleopolyhedrovirus P10 protein
       0.94    7.6  55.0       0.18   10.0  16.3    3.1  3  EzrA             Septation ring formation regulator, EzrA
          1    7.9  41.2       0.12   11.0  13.1    2.1  2  AAA_13           AAA domain
        1.7    8.3  35.5       0.27   10.9   9.4    2.9  2  Laminin_I        Laminin Domain I
        1.7    8.7  15.6        1.5    8.9   2.1    4.1  3  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
        1.9    8.2  15.1        1.1    9.0   1.1    3.7  3  SPACA9           Sperm acrosome-associated protein 9
        2.9    8.3  43.6       0.92    9.9   7.1    5.2  5  BLOC1_2          Biogenesis of lysosome-related organelles co
        2.9    7.7  40.6        0.2   11.5  10.8    3.5  4  PCRF             PCRF domain
        3.6    7.4  13.6         12    5.7   1.4    3.5  3  MCPsignal        Methyl-accepting chemotaxis protein (MCP) si
        7.1    7.0  52.0         12    6.3  15.9    4.2  3  OmpH             Outer membrane protein (OmpH-like)
        7.4    6.0  38.4    1.8e+04   -9.4  38.4    3.0  0  Exonuc_VII_L     Exonuclease VII, large subunit
          8    6.6  43.8        3.2    7.9   9.0    5.0  4  Fib_alpha        Fibrinogen alpha/beta chain family
        8.6    5.6  18.4        1.9    7.7   4.6    2.8  2  DUF4407          Domain of unknown function (DUF4407)
        8.8    6.9  43.0       0.04   14.4  12.0    4.4  4  DUF16            Protein of unknown function DUF16


Domain annotation for each model (and alignments):
>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   5.2       0.5   4.3e+02     204     306 ..       3     109 ..       1     113 [. 0.57
   2 !    8.3  18.1    0.0011      0.92     159     256 ..     110     208 ..     106     226 .. 0.75
   3 !   18.1  15.8   1.1e-06   0.00097     166     259 ..     245     338 ..     228     347 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.5
                              Spc7 204 lreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeae.......rvleeckgwsesevsrlke 273
                                       lre+l + ++  ++ kke+a+l    +e ++++e++   + +l +e++e+e       r+ +  k+ +e+ v++l++
  gi|242398896|ref|YP_002994320.1|   3 LREALHKYEEIQKRSKKEMAKLS---QEYTKRVEHMILDILKLLQELKEKEipkkvdpRLARIVKMERETYVRALQN 76 
                                       55555555554444444444443...344444444444444444444444322223336777788888888888888 PP

                              Spc7 274 evkaleeltgwkivslsgstleltyrselevsf 306
                                        v +++++ +++ +  + s l++++ ++l ++f
  gi|242398896|ref|YP_002994320.1|  77 MVGKIKDIEDVEKILPEISRLHVAHGRHLLLTF 109
                                       888888888887776666667776666666665 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0011
                              Spc7 159 ekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleek 235
                                       ek+  ++++ll++l++e+a+  +e+eklq  +e +++   +e++ +++ ++e +++++ + ++l+el+e++++lee+
  gi|242398896|ref|YP_002994320.1| 110 EKDVYKINNLLKSLSNEYANYVSEIEKLQP-KEIMAEKLLKEIQDFKKHINEEEQKLKDLVEMLSELNERKKKLEES 185
                                       566778999999999999999999999999.4455555599999999999999999999999999998888888887 PP

                              Spc7 236 ie..elkeqkseleeeiaeaerv 256
                                        e  +l+e+ ++l++ei+++e  
  gi|242398896|ref|YP_002994320.1| 186 SEfiALQENERKLKKEISREELN 208
                                       76335566667777777766543 PP

  == domain 3  score: 18.1 bits;  conditional E-value: 1.1e-06
                              Spc7 166 dellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeq 242
                                       +e+l+ lee  ++l +++++  e  ++    + ++L+el+++la ++ e++++k+e ++l + +e+l++ki++ +e+
  gi|242398896|ref|YP_002994320.1| 245 HEFLELLEEISDKLDKKYQNTIEWTRKNIPTKTQKLKELKRQLAGVEIELSRFKTEEESLHKSIEKLRQKINKKEEK 321
                                       67778888888999999999988776655667999****************************************** PP

                              Spc7 243 kseleeeiaeaervlee 259
                                       +++l+ee+++ e+ lee
  gi|242398896|ref|YP_002994320.1| 322 IKSLKEELQKIEKQLEE 338
                                       ************99997 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 ?    1.8   0.7      0.12   1.1e+02     122     156 ..      10      45 ..       2      83 .. 0.61
   2 ?    2.1  16.4       0.1        86      20     146 ..     102     223 ..      99     240 .. 0.68
   3 !   18.3  17.1   1.2e-06     0.001      31     127 ..     248     338 ..     234     341 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.12
                             Atg14 122 qneleerrkkqiaklqd.aikrieqklsslssktle 156
                                       ++e+++r kk++akl++ ++kr+e+++ ++ ++++e
  gi|242398896|ref|YP_002994320.1|  10 YEEIQKRSKKEMAKLSQeYTKRVEHMILDILKLLQE 45 
                                       567777777777777551445777774444444433 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.1
                             Atg14  20 gperlyelrerlaklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkk. 95 
                                       g++ l++  ++++k++   +sl +++  ++++ e       k++ k   +e+l ++i+d +++++e ++kl+ l + 
  gi|242398896|ref|YP_002994320.1| 102 GRHLLLTFEKDVYKINNLLKSLSNEYANYVSEIE-------KLQPKEIMAEKLLKEIQDFKKHINEEEQKLKDLVEm 171
                                       5668999999************************.......556666666666666666666666655555555432 PP

                             Atg14  96 ..eieekkkklaklsdklk....kRrsdleslqneleerrkkqiaklqdaikrieqk 146
                                         e++e+kkkl++ s+ ++    +     ++l++e++ ++ ++ +k+++  k+i+++
  gi|242398896|ref|YP_002994320.1| 172 lsELNERKKKLEESSEFIAlqenE-----RKLKKEISREELNLRSKVSKLQKPIKRM 223
                                       226788999999999999854443.....4555555555555555555555555544 PP

  == domain 3  score: 18.3 bits;  conditional E-value: 1.2e-06
                             Atg14  31 laklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklakl 107
                                       l  l + ++ l kk++  +e ++      ++i +k++kl+elk + a  + +l++ k+  ++l k+ie+ ++k+ k+
  gi|242398896|ref|YP_002994320.1| 248 LELLEEISDKLDKKYQNTIEWTR------KNIPTKTQKLKELKRQLAGVEIELSRFKTEEESLHKSIEKLRQKINKK 318
                                       55566677788888888888888......9*********************************************** PP

                             Atg14 108 sdklkkRrsdleslqnelee 127
                                        +k+k  +++l++++++lee
  gi|242398896|ref|YP_002994320.1| 319 EEKIKSLKEELQKIEKQLEE 338
                                       ******************98 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   4.8       0.4   3.4e+02      49      82 ..     144     177 ..       1     184 [. 0.73
   2 ?   -1.1   0.0       2.7   2.3e+03      28      72 ..     213     260 ..     207     272 .. 0.57
   3 ?   13.2   0.9   9.3e-05      0.08      26      85 ..     278     337 ..     269     339 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.4
                            DUF948  49 vedllakvnelledvneklekvdplteavadlge 82 
                                       +e+ll+++++  + +ne+ +k++ l+e + +l e
  gi|242398896|ref|YP_002994320.1| 144 AEKLLKEIQDFKKHINEEEQKLKDLVEMLSELNE 177
                                       3455555555555555566666666555555554 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.7
                            DUF948  28 ldeaaatieele...kqvdpilkevedllakvnelledvneklekvdp 72 
                                       ++++++ i+ ++   +++++ lk+++ +l++  e le ++e ++k+d+
  gi|242398896|ref|YP_002994320.1| 213 VSKLQKPIKRMRlpdNRAREFLKDSAYALEHPHEFLELLEEISDKLDK 260
                                       555555555555555666666777777777766644444444444443 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 9.3e-05
                            DUF948  26 ktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvs 85 
                                       + l+e++++++++e ++    +e e l + +++l + +n+k ek+++l e+++++ ++++
  gi|242398896|ref|YP_002994320.1| 278 QKLKELKRQLAGVEIELSRFKTEEESLHKSIEKLRQKINKKEEKIKSLKEELQKIEKQLE 337
                                       5689***************************************************99875 PP

>> MutS_II  MutS domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       5.6   4.8e+03      73     100 ..       5      32 ..       2      47 .. 0.76
   2 ?   15.0   4.5   2.7e-05     0.023      33     103 ..     125     200 ..     112     221 .. 0.82
   3 ?    0.4   2.2      0.88   7.5e+02      59      98 ..     301     338 ..     269     346 .. 0.54

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 5.6
                                       -EEEEESCCCCSHCCHHHHCHHHB--ST CS
                           MutS_II  73 srvgvretvefesekaserleedfsved 100
                                       + +  +e++++ s+k+  +l + + ++ 
  gi|242398896|ref|YP_002994320.1|   5 EALHKYEEIQKRSKKEMAKLSQEYTKRV 32 
                                       5566778888888888888888887765 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 2.7e-05
                                       EE-HHHHHHHHHH-ESEEEEESS-SCCCH.....HHHHHCHCTTT-EEEEESCCCCSHCCHHHHCHHHB--STTTT CS
                           MutS_II  33 edfeeleaeLsrlsPkElllpedlsesta.....eeessklrelrsrvgvretvefesekaserleedfsvedldg 103
                                       +++++ ++e+ +l+PkE+ +++ l+e +      +ee +kl++l++ ++  ++ ++++e++se ++++ ++++l++
  gi|242398896|ref|YP_002994320.1| 125 NEYANYVSEIEKLQPKEIMAEKLLKEIQDfkkhiNEEEQKLKDLVEMLSELNERKKKLEESSEFIALQENERKLKK 200
                                       45999*******************99988*9999999999999999999999999999998888877666666554 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.88
                                       CCHHHHHHCHCTTT-EEEEESCCCCSHCCHHHHCHHHB-- CS
                           MutS_II  59 staeeessklrelrsrvgvretvefesekaserleedfsv 98 
                                       ++      ++++lr++++  e+ +++++++ +++e+++++
  gi|242398896|ref|YP_002994320.1| 301 EE--SLHKSIEKLRQKINKKEEKIKSLKEELQKIEKQLEE 338
                                       22..233334444444444555555555555555555544 PP

>> Bacillus_HBL  Bacillus haemolytic enterotoxin (HBL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1       1.1   9.6e+02     113     138 ..      24      49 ..       2      83 .. 0.55
   2 ?   12.7   7.2    0.0001     0.087      57     137 ..     100     181 ..      78     224 .. 0.74
   3 ?    7.7   8.3    0.0035       2.9      97     137 ..     298     338 ..     245     349 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.1
                      Bacillus_HBL 113 eiqqnqkevkqlikeLkklklklakd 138
                                         q++ k v++ i ++ kl ++l+++
  gi|242398896|ref|YP_002994320.1|  24 LSQEYTKRVEHMILDILKLLQELKEK 49 
                                       33444455555555555555555544 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.0001
                      Bacillus_HBL  57 anakewlnevkPqliktiqdiigYstkFqsyyktlveav.dkkdkaellellekLqeeiqqnqkevkqlikeLkklk 132
                                       a+ +  l + ++ + k+++ ++  s+++++y ++++++  ++   ++ll+ +++ +++i++ +++ k+l+++L++l+
  gi|242398896|ref|YP_002994320.1| 100 AHGRHLLLTFEKDVYKINNLLKSLSNEYANYVSEIEKLQpKEIMAEKLLKEIQDFKKHINEEEQKLKDLVEMLSELN 176
                                       6777778888999999999999*************999867778999***************************997 PP

                      Bacillus_HBL 133 lklak 137
                                       ++ +k
  gi|242398896|ref|YP_002994320.1| 177 ERKKK 181
                                       65433 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0035
                      Bacillus_HBL  97 kkdkaellellekLqeeiqqnqkevkqlikeLkklklklak 137
                                       k++ ++l + +ekL+++i+++++++k+l +eL+k +++l++
  gi|242398896|ref|YP_002994320.1| 298 KTEEESLHKSIEKLRQKINKKEEKIKSLKEELQKIEKQLEE 338
                                       44566677777777777777777777777777777777665 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 ?   -1.8   0.3       5.1   4.3e+03      23      30 ..      21      28 ..       7      48 .. 0.51
   2 ?   -2.3   0.1       7.4   6.3e+03      30      34 ..      81      85 ..      63      96 .. 0.54
   3 ?    2.1   0.4       0.3   2.5e+02       5      34 ..     109     138 ..     106     149 .. 0.87
   4 ?    3.9   3.7     0.083        71       6      43 ..     135     171 ..     130     178 .. 0.87
   5 ?   -2.3   5.2       7.4   6.3e+03       3      29 ..     159     185 ..     158     224 .. 0.63
   6 ?   13.6   1.8   7.8e-05     0.067       1      38 [.     279     316 ..     279     318 .. 0.95
   7 ?    6.4   6.5     0.014        12       5      32 ..     311     338 ..     310     351 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 5.1
                         FlaC_arch 23 neelsksv 30
                                      + +ls++ 
  gi|242398896|ref|YP_002994320.1| 21 MAKLSQEY 28
                                      33333332 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 7.4
                         FlaC_arch 30 veelk 34
                                      +++++
  gi|242398896|ref|YP_002994320.1| 81 IKDIE 85
                                      33332 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.3
                         FlaC_arch   5 lEnklsklsteletvkkeneelsksveelk 34 
                                       +E+++ k+   l+++ +e  +  +++e+l+
  gi|242398896|ref|YP_002994320.1| 109 FEKDVYKINNLLKSLSNEYANYVSEIEKLQ 138
                                       799999999999999999999999999986 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.083
                         FlaC_arch   6 EnklsklsteletvkkeneelsksveelkenVkdllsL 43 
                                       E kl+  +++ e + ke+++ +k ++e +++ kdl+++
  gi|242398896|ref|YP_002994320.1| 135 E-KLQPKEIMAEKLLKEIQDFKKHINEEEQKLKDLVEM 171
                                       3.6888889999999*******************9986 PP

  == domain 5  score: -2.3 bits;  conditional E-value: 7.4
                         FlaC_arch   3 delEnklsklsteletvkkeneelsks 29 
                                       +e E+kl++l  +l+ + +  ++l++s
  gi|242398896|ref|YP_002994320.1| 159 NEEEQKLKDLVEMLSELNERKKKLEES 185
                                       555666666655444433333333333 PP

  == domain 6  score: 13.6 bits;  conditional E-value: 7.8e-05
                         FlaC_arch   1 ridelEnklsklsteletvkkeneelsksveelkenVk 38 
                                       +++el  +l  +++el+  k+e e+l ks+e+l ++++
  gi|242398896|ref|YP_002994320.1| 279 KLKELKRQLAGVEIELSRFKTEEESLHKSIEKLRQKIN 316
                                       789********************************996 PP

  == domain 7  score: 6.4 bits;  conditional E-value: 0.014
                         FlaC_arch   5 lEnklsklsteletvkkeneelsksvee 32 
                                       l +k++k + +++++k+e+++++k++ee
  gi|242398896|ref|YP_002994320.1| 311 LRQKINKKEEKIKSLKEELQKIEKQLEE 338
                                       6688889999999999999999888886 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 ?   -0.4   0.4       1.3   1.1e+03      92     116 ..      13      37 ..       2      49 .. 0.43
   2 ?    3.3   0.1     0.092        79      31      78 ..      42      91 ..      25      99 .. 0.78
   3 ?    7.4   6.1    0.0051       4.3      52     122 ..     125     188 ..     114     201 .. 0.55
   4 ?    0.8   0.3      0.55   4.7e+02      81      95 ..     209     223 ..     187     263 .. 0.47
   5 ?   12.2   7.5   0.00017      0.15      59     113 ..     282     336 ..     245     349 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.3
                              COG2  92 lsereeeveskleeakeleekrell 116
                                       +++r+++  +kl++    + + ++l
  gi|242398896|ref|YP_002994320.1|  13 IQKRSKKEMAKLSQEYTKRVEHMIL 37 
                                       3333333333333333333333444 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.092
                              COG2 31 lrrdLe..aylkllekellelvnedyadFvslSghLvglqeeleevespl 78
                                      l ++L+  ++ k+++ +l+++v ++ +++v   +++vg  +++e ve+ l
  gi|242398896|ref|YP_002994320.1| 42 LLQELKekEIPKKVDPRLARIVKMERETYVRALQNMVGKIKDIEDVEKIL 91
                                      55666511466899999*************99999999999999988755 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0051
                              COG2  52 edyadFvslSghLvglqeeleevesplaaarkkvesvreklsereeeveskleeakeleekrellklllkl 122
                                       ++ya++vs  ++L+  +          +++ k++++++++++e e+++++ +e  +el+e ++ l+   ++
  gi|242398896|ref|YP_002994320.1| 125 NEYANYVSEIEKLQPKEIMA-------EKLLKEIQDFKKHINEEEQKLKDLVEMLSELNERKKKLEESSEF 188
                                       44444444444444444444.......55556666666666666666666666666665555544443333 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 0.55
                              COG2  81 arkkvesvreklser 95 
                                       +r+kv+++++ ++++
  gi|242398896|ref|YP_002994320.1| 209 LRSKVSKLQKPIKRM 223
                                       333333333333332 PP

  == domain 5  score: 12.2 bits;  conditional E-value: 0.00017
                              COG2  59 slSghLvglqeeleevesplaaarkkvesvreklsereeeveskleeakeleekr 113
                                       +l  +L g++ el++++++ +++ k +e++r+k++++ee+++s  ee +++e++ 
  gi|242398896|ref|YP_002994320.1| 282 ELKRQLAGVEIELSRFKTEEESLHKSIEKLRQKINKKEEKIKSLKEELQKIEKQL 336
                                       677899****************************************999999764 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1     0.097        82      50      73 ..      70      94 ..       4      96 .. 0.78
   2 ?    4.5   0.2     0.057        49      20      38 ..      71      95 ..      61     142 .. 0.58
   3 ?    4.8   1.5     0.044        38      10      51 ..     148     189 ..     141     227 .. 0.75
   4 ?   -0.2   0.0       1.6   1.4e+03      15      31 ..     208     224 ..     201     241 .. 0.82
   5 ?    4.2   0.1     0.073        62      14      57 ..     252     293 ..     245     300 .. 0.74
   6 ?    6.8   4.0     0.011       9.6      31      66 ..     302     337 ..     263     347 .. 0.66

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.097
                           NPV_P10 50 qLaeletkvenIqdiLnpde.vPdl 73
                                       + +l++ v +I+di   ++ +P++
  gi|242398896|ref|YP_002994320.1| 70 YVRALQNMVGKIKDIEDVEKiLPEI 94
                                      3556666777777776665567877 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.057
                           NPV_P10 20 Vdalqqqv......ddvqenlpdvt 38
                                      V alq+ v      +dv++ lp+++
  gi|242398896|ref|YP_002994320.1| 71 VRALQNMVgkikdiEDVEKILPEIS 95
                                      5555555533333344444444444 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.044
                           NPV_P10  10 radikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqL 51 
                                       +++i++ ++ ++  +q+++d+ e l +++e ++kL++ s+ +
  gi|242398896|ref|YP_002994320.1| 148 LKEIQDFKKHINEEEQKLKDLVEMLSELNERKKKLEESSEFI 189
                                       667777778888888888888888888888888888777654 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 1.6
                           NPV_P10  15 avddkVdalqqqvddvq 31 
                                       ++ +kV+ lq+ +++++
  gi|242398896|ref|YP_002994320.1| 208 NLRSKVSKLQKPIKRMR 224
                                       57789999999998765 PP

  == domain 5  score: 4.2 bits;  conditional E-value: 0.073
                           NPV_P10  14 kavddkVda.lqqqvddvqenlpdvtelnekLdaqsaqLaeletk 57 
                                       ++++dk+d   q+ ++  ++n+p+    ++kL ++  qLa +e +
  gi|242398896|ref|YP_002994320.1| 252 EEISDKLDKkYQNTIEWTRKNIPT---KTQKLKELKRQLAGVEIE 293
                                       567778774268888888999988...458899999988877755 PP

  == domain 6  score: 6.8 bits;  conditional E-value: 0.011
                           NPV_P10  31 qenlpdvtelnekLdaqsaqLaeletkvenIqdiLn 66 
                                       ++ ++ +++l +k+++  +++++l++++++I++ L 
  gi|242398896|ref|YP_002994320.1| 302 ESLHKSIEKLRQKINKKEEKIKSLKEELQKIEKQLE 337
                                       444677888999999999999999999999988776 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.5  30.2       4.9   4.2e+03     193     396 ..      19     187 ..       3     227 .. 0.51
   2 ?   -2.2  17.0         1   8.8e+02      97     173 ..     145     223 ..     133     259 .. 0.78
   3 ?   10.0  16.3   0.00021      0.18     100     173 ..     270     343 ..     246     349 .. 0.43

  Alignments for each domain:
  == domain 1  score: -4.5 bits;  conditional E-value: 4.9
                                       HHHHHHHHHHHHHHHHHHHHHHHHHTTTT.TTSHHHHHHHHHHHHHSTTS--SGGGSSSSSHHHHHHHHHHHHHHHH CS
                              EzrA 193 keilkkleeeideleevieeiPelleelk.kelpkqleelkegykemkeegYaleelniekeieelekkieeilerl 268
                                       ke+ k  +e ++++e++i +i +ll+elk ke+pk+++   + + +m++e Y+   +n+  +i+++e ++e+il ++
  gi|242398896|ref|YP_002994320.1|  19 KEMAKLSQEYTKRVEHMILDILKLLQELKeKEIPKKVDPRLARIVKMERETYVRALQNMVGKIKDIE-DVEKILPEI 94 
                                       4555556667777777777777777776535677777777777777777777777777777777775.467777777 PP

                                       TT--HHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHTTTSSSSSHHHHT--HHHHTTGGG-TTTS-GGGSSTTT CS
                              EzrA 269 keleledveeelktiee...eidsLyddlekEveAkkeveknlkelkeklehlekqnkelkeeldrlkqsYeLseee 342
                                       ++l++ + +  l t e+   +i++L + l +E++ +    ++l+  + + e+l k++++ k+ +             
  gi|242398896|ref|YP_002994320.1|  95 SRLHVAHGRHLLLTFEKdvyKINNLLKSLSNEYANYVSEIEKLQPKEIMAEKLLKEIQDFKKHI------------- 158
                                       7777777777777776633346666666666665553333333333333333333333333333............. PP

                                       STTHHHHHHHHHHHHHHHHHHHHHHS-SS---STTGGGTHHHHHHHHHHHHHHH CS
                              EzrA 343 leklrelekelkelekdyeeleekleekkvaYSelqeeleeleekleeieekqe 396
                                                                +e+++   +l e+l el+e+ +++ee+ e
  gi|242398896|ref|YP_002994320.1| 159 -------------------------NEEEQKLKDLVEMLSELNERKKKLEESSE 187
                                       .........................33333333333333222222222222222 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1
                                       HHTTHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTT..THHHHHHHHHHHHHHHHT--TTTTHHHHHHHHHHHHHH CS
                              EzrA  97 kkakkklaeleeeldeveekikkileelkelteseek..nreeieklkekYrelrkkllanrfsygealeelekqle 171
                                        k+ k++++ ++ ++e e+k+k++ e l+el e ++k  +++e  +l+e+ r+l+k++ +++ ++ + +++l+k ++
  gi|242398896|ref|YP_002994320.1| 145 EKLLKEIQDFKKHINEEEQKLKDLVEMLSELNERKKKleESSEFIALQENERKLKKEISREELNLRSKVSKLQKPIK 221
                                       46667888888888888888888888888888877762245677788888888888888888888888888887776 PP

                                       HH CS
                              EzrA 172 ni 173
                                        +
  gi|242398896|ref|YP_002994320.1| 222 RM 223
                                       55 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00021
                                       THHHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHHHHHHHHHHHHHHT--TTTTHHHHHHHHHHHHHHHH CS
                              EzrA 100 kkklaeleeeldeveekikkileelkelteseeknreeieklkekYrelrkkllanrfsygealeelekqleni 173
                                       +k++ + +++l+e++ +++ +  el+ +++ ee  ++ iekl++k  + ++k+++ ++++++++++le+ l ++
  gi|242398896|ref|YP_002994320.1| 270 RKNIPTKTQKLKELKRQLAGVEIELSRFKTEEESLHKSIEKLRQKINKKEEKIKSLKEELQKIEKQLEESLLEL 343
                                       33333334444444444444444444444444444444444444444444444444444444444444444333 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4  20.3     0.055        47     283     460 ..      16     202 ..       2     211 .. 0.57
   2 ?   11.0  13.1   0.00014      0.12     316     405 ..     252     342 ..     208     351 .. 0.64

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.055
                            AAA_13 283 ekqerLekliekveskkselleklkavsdeasensafeedkeelkaeaealeeqLkglqraleaKrkepfksveles 359
                                       ++++++ kl +++ ++ ++++  + ++ +e +e+++ ++    l +  +  +e+   + + +  K+k++     +e+
  gi|242398896|ref|YP_002994320.1|  16 RSKKEMAKLSQEYTKRVEHMILDILKLLQELKEKEIPKKVDPRLARIVKMERETYVRALQNMVGKIKDIED---VEK 89 
                                       33444445555554444444444444444333333333332222222222222222222333344444444...222 PP

                            AAA_13 360 vkakie............sikklvaeineliakhNekvanleeekeeakkklelhlveeleseldeykkkykkleka 424
                                       + ++i+             ++k+v +in+l ++  +  an+ +e e+++ k    ++e+l +e++ +kk++++ e++
  gi|242398896|ref|YP_002994320.1|  90 ILPEISrlhvahgrhlllTFEKDVYKINNLLKSLSNEYANYVSEIEKLQPK--EIMAEKLLKEIQDFKKHINEEEQK 164
                                       222222333444444444888888888888888888888888888887755..344688899999999999999999 PP

                            AAA_13 425 ieklekelkeeeaelkkleee..ikeLekqlrdekpaa 460
                                       +++l + l+e ++++kklee     +L+++ r+ k+ +
  gi|242398896|ref|YP_002994320.1| 165 LKDLVEMLSELNERKKKLEESseFIALQENERKLKKEI 202
                                       99999999999999999988544777888877777666 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00014
                            AAA_13 316 nsafeedkeelkaeaealeeqLkglqraleaKrkepfk.svelesvkakiesikklvaeineliakhNekvanleee 391
                                       ++++++  +++++ +e +++++ +  ++l++ + +++  ++el+++k + es+ k+++++ + i+k  ek+++l+ee
  gi|242398896|ref|YP_002994320.1| 252 EEISDKLDKKYQNTIEWTRKNIPTKTQKLKELKRQLAGvEIELSRFKTEEESLHKSIEKLRQKINKKEEKIKSLKEE 328
                                       33344445666666666677777777777666556655567777777777777777777777777777777777777 PP

                            AAA_13 392 keeakkklelhlve 405
                                        ++++k+le +l+e
  gi|242398896|ref|YP_002994320.1| 329 LQKIEKQLEESLLE 342
                                       77777777776654 PP

>> Laminin_I  Laminin Domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5  14.7     0.014        12      14     172 ..      32     187 ..      22     200 .. 0.66
   2 ?   10.9   9.4   0.00032      0.27       7     107 ..     237     338 ..     233     352 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.014
                         Laminin_I  14 pykinanledltkeLqeklskesakkskieilekelesLaqeteeLqkkatqvlakaqkvnaesertlnnakeLaek 90 
                                       ++++   + +l +eL+ek+++++   +++ i + e e+ +   +++++k +   +  + + + s   + +   L   
  gi|242398896|ref|YP_002994320.1|  32 VEHMILDILKLLQELKEKEIPKKVDPRLARIVKMERETYVRALQNMVGKIKDIEDVEKILPEISRLHVAHGRHLLLT 108
                                       44555556666666666666666666666666555555555555555555554444333333333345555555555 PP

                         Laminin_I  91 ikkladnikeilekvatlneneealps.sklseelaeaqrlLeelrsRdftkqleeaeaelkaAqkLLsrvqtllqk 166
                                        +k + +i+ +l++    ne ++ +++ +kl+ +   a++lL+e+  +df+k+ +e e++lk   ++Ls+ +++ +k
  gi|242398896|ref|YP_002994320.1| 109 FEKDVYKINNLLKSL--SNEYANYVSEiEKLQPKEIMAEKLLKEI--QDFKKHINEEEQKLKDLVEMLSELNERKKK 181
                                       555555555555555..34455666654789999999********..89*************************888 PP

                         Laminin_I 167 lqeenk 172
                                       l e  +
  gi|242398896|ref|YP_002994320.1| 182 LEESSE 187
                                       877655 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00032
                         Laminin_I   7 ltgaleapykinanledltkeLqe.klskesakkskieilekelesLaqeteeLqkkatqvlakaqkvnaesertln 82 
                                       ++ ale+p++ ++ le+  ++L + + + ++ + ++i  + ++l++L+ +      ++ +   + + + + +e+  +
  gi|242398896|ref|YP_002994320.1| 237 SAYALEHPHEFLELLEEISDKLDKkYQNTIEWTRKNIPTKTQKLKELKRQLAGVEIELSRFKTEEESLHKSIEKLRQ 313
                                       68899*******99***999996516677788888888888888888888888888888888888888888888888 PP

                         Laminin_I  83 nakeLaekikkladnikeilekvat 107
                                       ++++ +ekik l+++++ i ++ ++
  gi|242398896|ref|YP_002994320.1| 314 KINKKEEKIKSLKEELQKIEKQLEE 338
                                       8888888888888888888888765 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 ?    2.4   0.2      0.18   1.5e+02      52      90 ..      85     130 ..       6     140 .. 0.61
   2 ?    3.0   3.3      0.11        94      35      98 ..     153     217 ..     113     224 .. 0.50
   3 ?    8.9   2.1    0.0017       1.5      39      95 ..     279     337 ..     247     352 .. 0.52

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.18
                      Baculo_PEP_C  52 edlksllaeldt.......rldtlltnLtdalnalqdtlrneLtnl 90 
                                       ed+++ l+e+++       +l  ++++   ++n+l ++l+ne  n 
  gi|242398896|ref|YP_002994320.1|  85 EDVEKILPEISRlhvahgrHLLLTFEKDVYKINNLLKSLSNEYANY 130
                                       3455555555554344333222222222223333333333333333 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.11
                      Baculo_PEP_C  35 qlatlldaietqLnalsedlksllaeldtrldtllt..nLtdalnalqdtlrneLtnlnsiltnLl 98 
                                       + ++ +++ e++L++l e l++ l+e +++l+++++  +L++   +l+++++ e  nl s+++ L+
  gi|242398896|ref|YP_002994320.1| 153 DFKKHINEEEQKLKDLVEMLSE-LNERKKKLEESSEfiALQENERKLKKEISREELNLRSKVSKLQ 217
                                       2233333333444444444443.3333335554432225555555555555544445666666555 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0017
                      Baculo_PEP_C  39 lldaietqLnalsedlksllaeldtrldtlltnLtdalnalq...dtlrneLtnlnsilt 95 
                                        l+++++qL  ++ +l++  +  ++ l++++++L +++n+ +   ++l++eL+ ++++l 
  gi|242398896|ref|YP_002994320.1| 279 KLKELKRQLAGVEIELSR-FKTEEESLHKSIEKLRQKINKKEekiKSLKEELQKIEKQLE 337
                                       333344444444444444.22223334444444444444433333333334444443332 PP

>> SPACA9  Sperm acrosome-associated protein 9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.4     0.081        69      58     108 ..      26      86 ..       5     101 .. 0.70
   2 ?    3.5   2.7     0.065        56      44      84 ..     122     184 ..      53     234 .. 0.53
   3 ?    9.0   1.1    0.0013       1.1       2      56 ..     282     336 ..     281     343 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.081
                            SPACA9  58 nstdrrilelfldivedLkklrkk..........leesnaerertaelLekcktLlkdend 108
                                       +   +r+ +++ldi++ L++l++k           + ++ ere+    L+++   +kd +d
  gi|242398896|ref|YP_002994320.1|  26 QEYTKRVEHMILDILKLLQELKEKeipkkvdprlARIVKMERETYVRALQNMVGKIKDIED 86 
                                       344578999************9998888888887666666777666666666555555555 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.065
                            SPACA9  44 t.........................ikqvqkylehacnnstdrrilelfldivedLkklrkklee 84 
                                       +                         +k++q++++h      + + l+ +++++++L++ +kklee
  gi|242398896|ref|YP_002994320.1| 122 SlsneyanyvseieklqpkeimaeklLKEIQDFKKHIN---EEEQKLKDLVEMLSELNERKKKLEE 184
                                       02222222222222233344444444556666665554...2334455556666666665555554 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0013
                            SPACA9   2 evkqqlkklelryklfkqqqktfisALeraresaldktepvstikqvqkylehac 56 
                                       e+k+ql ++e +  +fk    ++ + +e+ r+++ +k e ++++k+  + +e++ 
  gi|242398896|ref|YP_002994320.1| 282 ELKRQLAGVEIELSRFKTEEESLHKSIEKLRQKINKKEEKIKSLKEELQKIEKQL 336
                                       789****************************************987666666554 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 ?    3.0   1.7      0.15   1.3e+02      27      84 ..      20      81 ..      14      86 .. 0.80
   2 ?    9.5  10.2    0.0013       1.1      20      93 ..     111     184 ..     104     187 .. 0.93
   3 ?   -0.5   0.1       1.9   1.6e+03      65      65 ..     235     235 ..     196     263 .. 0.49
   4 ?    4.1   1.3     0.069        59      22      84 ..     248     311 ..     238     311 .. 0.65
   5 ?    9.9   7.1    0.0011      0.92      38      81 ..     303     347 ..     295     349 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.15
                           BLOC1_2 27 klNeaasekykklkdvaaslekkleklnekye..elqpylqqidqiekq..vteLeeavseL 84
                                      ++ + ++e  k +++++ ++ k l++l+ek+   +++p l +i ++e++  v+ L+++v ++
  gi|242398896|ref|YP_002994320.1| 20 EMAKLSQEYTKRVEHMILDILKLLQELKEKEIpkKVDPRLARIVKMEREtyVRALQNMVGKI 81
                                      5666667777789999999999999999999777999*****99998764478888888765 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0013
                           BLOC1_2  20 edyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeLEa 93 
                                       +d+  +++l ++ s++y+++ +++++l+ k    +++ +e+q ++++i++ e+++++L e+ seL+e  k+LE+
  gi|242398896|ref|YP_002994320.1| 111 KDVYKINNLLKSLSNEYANYVSEIEKLQPKEIMAEKLLKEIQDFKKHINEEEQKLKDLVEMLSELNERKKKLEE 184
                                       6788899999999***********************************************************97 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 1.9
                           BLOC1_2  65 q 65 
                                       +
  gi|242398896|ref|YP_002994320.1| 235 K 235
                                       2 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.069
                           BLOC1_2  22 yklLeklNeaasekykk.lkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseL 84 
                                       ++lLe++  +  +ky++ ++   +++ +k +kl+e++ +l+    ++ +++++ ++L + +++L
  gi|242398896|ref|YP_002994320.1| 248 LELLEEISDKLDKKYQNtIEWTRKNIPTKTQKLKELKRQLAGVEIELSRFKTEEESLHKSIEKL 311
                                       6777777777777777513444567777777777777777766666666666666666666655 PP

  == domain 5  score: 9.9 bits;  conditional E-value: 0.0011
                           BLOC1_2  38 klkdvaaslekkleklnekyeelqpylqqid.qiekqvteLeeav 81 
                                       +l +++++l++k++k +ek ++l++ lq+i+ q+e+++ eLee++
  gi|242398896|ref|YP_002994320.1| 303 SLHKSIEKLRQKINKKEEKIKSLKEELQKIEkQLEESLLELEEII 347
                                       567778888888888888888888888888536888888888886 PP

>> PCRF  PCRF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   3.3      0.15   1.3e+02      19      87 ..      16      82 ..       1      92 [. 0.58
   2 ?    1.6   0.8      0.25   2.2e+02      31      89 ..      71     130 ..      41     145 .. 0.47
   3 ?   11.5  10.8   0.00024       0.2      11      94 ..     141     228 ..     130     234 .. 0.77
   4 ?    6.2   9.8    0.0098       8.4      13      92 ..     269     342 ..     249     351 .. 0.48

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.15
                                      TTGGGSSSTTHHHHHTHHHHHHHHHHHHHTTTHHH...HT.....-S-..-GGGTHHHHHHHHHH..HHH CS
                              PCRF 19 edqekakklskelaeleeivealeeleealedleeakelle.edeelaelaeeeleelekeleeleeelk 87
                                      ++++++ kls+e++  +++ +++ ++ ++l++l+e ke+ +  d+ la++++ e e++ ++l+++  ++k
  gi|242398896|ref|YP_002994320.1| 16 RSKKEMAKLSQEYT--KRVEHMILDILKLLQELKE-KEIPKkVDPRLARIVKMERETYVRALQNMVGKIK 82
                                      23455555666553..3334445556666666666.5554346899999988887777777766655554 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.25
                                       HHHTHHHHHHHHHHHHHTTTHHH...HT.....-S-..-GGGTHHHHHHHHHH..HHHHH CS
                              PCRF  31 laeleeivealeeleealedleeakell.eedeelaelaeeeleelekeleeleeelkkl 89 
                                       +++l+++v +++++e++++ l e+++l  ++ ++l    e+++ ++++ l++l++e  + 
  gi|242398896|ref|YP_002994320.1|  71 VRALQNMVGKIKDIEDVEKILPEISRLHvAHGRHLLLTFEKDVYKINNLLKSLSNEYANY 130
                                       233444444444444444444444433311333333333444555555555555554444 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.00024
                                       ST.-GGGTTT.GGGSSSTTHHHHHTHHHHHHHHHHHHHTTTHHH...HT.......-S-..-GGGTHHHHHHHHHH. CS
                              PCRF  11 klsdpevwed.qekakklskelaeleeivealeeleealedleeakelle...edeelaelaeeeleelekeleele 83 
                                       ++ ++++ ++ q+  k++++e ++l+++ve+l+el+e++++lee +e+++   ++++l+++ + e  +l++++++l+
  gi|242398896|ref|YP_002994320.1| 141 EIMAEKLLKEiQDFKKHINEEEQKLKDLVEMLSELNERKKKLEESSEFIAlqeNERKLKKEISREELNLRSKVSKLQ 217
                                       344444444414555668899999***********************995545777898888888889********* PP

                                       .HHHHHT-..S CS
                              PCRF  84 eelkklLlpkd 94 
                                       + +k++ lp++
  gi|242398896|ref|YP_002994320.1| 218 KPIKRMRLPDN 228
                                       ***99988765 PP

  == domain 4  score: 6.2 bits;  conditional E-value: 0.0098
                                       .-GGGTTTGGGSSSTTHHHHHTHHHHHHHHHHHHHT.TTHHH...HT....-S-..-...GGGTHHHHHHHHHH..H CS
                              PCRF  13 sdpevwedqekakklskelaeleeivealeeleeal.edleeakelleedeelaela...eeeleelekeleeleee 85 
                                       +++++ ++++k+k+l+++la +e  ++++++ ee l +++e          +l++     ee++++l++el+++e++
  gi|242398896|ref|YP_002994320.1| 269 TRKNIPTKTQKLKELKRQLAGVEIELSRFKTEEESLhKSIE----------KLRQKInkkEEKIKSLKEELQKIEKQ 335
                                       22333334444444444444444444444433332202223..........33322221144477777777777777 PP

                                       HHHHT-. CS
                              PCRF  86 lkklLlp 92 
                                       l++ Ll 
  gi|242398896|ref|YP_002994320.1| 336 LEESLLE 342
                                       7777763 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 ?    5.5   0.4     0.015        13      78     142 ..      19      86 ..      14     101 .. 0.76
   2 ?    3.3   0.3     0.073        62     108     152 ..     143     187 ..     112     205 .. 0.59
   3 ?    5.7   1.4     0.014        12      98     147 ..     297     346 ..     277     350 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.015
                                       HHHHHHHHHHHHHHHHHH................HHHHHHHHHHHHHHHHHC.CHHHHHHHHHHHHHH CS
                         MCPsignal  78 rkLAersaqaakeiealiieiqkeinds..vesleetrqrveegselveetg.ealkeiveavaevad 142
                                       +++A+ s++ +k +e++i +i k  ++    e+ +++  r +  +++ +et  +al+++v ++++++d
  gi|242398896|ref|YP_002994320.1|  19 KEMAKLSQEYTKRVEHMILDILKLLQELkeKEIPKKVDPRLARIVKMERETYvRALQNMVGKIKDIED 86 
                                       689999***************99777651145668888899999999888843789999988877655 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.073
                                       ..HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal 108 sleetrqrveegselveetgealkeiveavaevadlvqeiaaase 152
                                       + e+  ++++   + ++e +++lk++ve+ +e+++  + +  +se
  gi|242398896|ref|YP_002994320.1| 143 MAEKLLKEIQDFKKHINEEEQKLKDLVEMLSELNERKKKLEESSE 187
                                       345555666666666666666666666666666665555555554 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.014
                                       ............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  98 iqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqei 147
                                        + e ++  +s+e+ rq++++  e++++ +e+l++i ++ +e   +++ei
  gi|242398896|ref|YP_002994320.1| 297 FKTEEESLHKSIEKLRQKINKKEEKIKSLKEELQKIEKQLEESLLELEEI 346
                                       45566677789999999999999999999999999998888766666665 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   3.2     0.021        18      14      58 ..      10      64 ..       2      97 .. 0.46
   2 ?    6.3  15.9     0.014        12      17      94 ..     140     220 ..     108     226 .. 0.78
   3 ?   -2.9  25.3       9.3   7.9e+03      19      93 ..     249     339 ..     190     352 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.021
                                      SHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS...........- CS
                              OmpH 14 spegk.aaqeqlekkfkklqaeleakekelqklqeelqkkakkle..........k 58
                                      ++e + + +++++k ++++ + +e +  ++ kl +el++k+   +          k
  gi|242398896|ref|YP_002994320.1| 10 YEEIQkRSKKEMAKLSQEYTKRVEHMILDILKLLQELKEKEIP-KkvdprlarivK 64
                                      3332202333555555555555555555555555565422211.133344444331 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.014
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS..-HHHHHH......HHHHHHHHHHHHHHHHHHHHHH CS
                              OmpH  17 gkaaqeqlekkfkklqaeleakekelqklqeelqkkakkl.ekeekeqe......lqkkeqelqqkqqqkaqelqkk 86 
                                        + + e+l k+++++++ ++++e++l++l+e l     +l e+++k +e      lq+ e++l+++ ++++ +l++k
  gi|242398896|ref|YP_002994320.1| 140 KEIMAEKLLKEIQDFKKHINEEEQKLKDLVEMLS----ELnERKKKLEEssefiaLQENERKLKKEISREELNLRSK 212
                                       4456677888889***************999995....333455555556888889999999999888888888888 PP

                                       HHHHHHHH CS
                              OmpH  87 qqellkpi 94 
                                         +l+kpi
  gi|242398896|ref|YP_002994320.1| 213 VSKLQKPI 220
                                       88888886 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 9.3
                                       HHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHTTTS.........-HHHHHH.....HHHHHHHHHHHHHHHH. CS
                              OmpH  19 aaqeqlekkf.kklqaeleakekelqklqeelqkkakkle........keekeqe.....lqkkeqelqqkqqqka. 80 
                                       +  e++ +k  kk+q+++e  +k++ ++ ++l++ +++l+         +++e e     ++k++q++++ +++k  
  gi|242398896|ref|YP_002994320.1| 249 ELLEEISDKLdKKYQNTIEWTRKNIPTKTQKLKELKRQLAgveielsrFKTEE-EslhksIEKLRQKINK-KEEKIk 323
                                       55555544444788888888888888888888755555424788887633333.2344456666666665.333332 PP

                                       ...HHHHHHHHHHHHH CS
                              OmpH  81 ...qelqkkqqellkp 93 
                                          +elqk +++l ++
  gi|242398896|ref|YP_002994320.1| 324 slkEELQKIEKQLEES 339
                                       4444444444444443 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   [No individual domains that satisfy reporting thresholds (although complete target did)]

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   3.2      0.36   3.1e+02      47      93 ..      10      39 ..       1      99 [. 0.39
   2 ?    7.9   9.0    0.0037       3.2      44     125 ..     106     186 ..      84     194 .. 0.80
   3 ?    5.7   3.4     0.019        16      22     123 ..     198     299 ..     190     301 .. 0.84
   4 ?    7.4  12.2    0.0054       4.6      34     119 ..     248     337 ..     239     353 .] 0.50

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.36
                                      CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHH CS
                         Fib_alpha 47 isnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrl 93
                                      +++ +k +++ + ++++ ++++ ++                    ++
  gi|242398896|ref|YP_002994320.1| 10 YEEIQKRSKKEMAKLSQEYTKRVEHMIL-----------------DI 39
                                      3333333333333333333332222221.................11 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0037
                                       CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  44 leeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnvlesneqkiqk 120
                                       l ++++   ++++l k++++ +++  ++ ++ +   + ++++l +ei+++k+ i+++e++++ L ++l++++++ +k
  gi|242398896|ref|YP_002994320.1| 106 LLTFEKDVYKINNLLKSLSNEYANYVSEIEKLQP-KEIMAEKLLKEIQDFKKHINEEEQKLKDLVEMLSELNERKKK 181
                                       5666677777788888888888777777775433.3445566666999***************************** PP

                                       HHHHH CS
                         Fib_alpha 121 Leqdi 125
                                       Le+ +
  gi|242398896|ref|YP_002994320.1| 182 LEESS 186
                                       *9865 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.019
                                       HHHCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHH CS
                         Fib_alpha  22 lqdlllkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketid 98 
                                       l++ +++ e +++ +++kl++ +++++   + a+e  k+    l++  +  +  +++  k+ k+ ++ i+  +++i 
  gi|242398896|ref|YP_002994320.1| 198 LKKEISREELNLRSKVSKLQKPIKRMRLPDNRAREFLKDSAYALEHPHEFLELLEEISDKLDKKYQNTIEWTRKNIP 274
                                       67778888889999999999999999999999999999888888888887777788888899999989999999999 PP

                                       CCHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  99 aqesnirvLqnvlesneqkiqkLeq 123
                                       ++ +++++L+  l   e ++++ ++
  gi|242398896|ref|YP_002994320.1| 275 TKTQKLKELKRQLAGVEIELSRFKT 299
                                       9999999999999988888888775 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.0054
                                       CHHHCCCCCCCCCCCCHH.HHHHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHCCCHHHHHHHCCHHHHHH CS
                         Fib_alpha  34 kkdlekleneleeisnst.keaeelvkeikdslrekqkskkdn...dnvikksskeleeeilrlketidaqesnirv 106
                                        + le++ ++l++  ++t + +++ + + +++l+e +++ ++     + +k  +++l + i++l+++i+++e++i+ 
  gi|242398896|ref|YP_002994320.1| 248 LELLEEISDKLDKKYQNTiEWTRKNIPTKTQKLKELKRQLAGVeieLSRFKTEEESLHKSIEKLRQKINKKEEKIKS 324
                                       55566666666544333313233333333333333333333321224555555666777777777777777777776 PP

                                       HHHHHHHHHHHHH CS
                         Fib_alpha 107 Lqnvlesneqkiq 119
                                       L++ l++ e++++
  gi|242398896|ref|YP_002994320.1| 325 LKEELQKIEKQLE 337
                                       6666665555443 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   5.7     0.064        55     131     247 ..     109     223 ..       4     230 .. 0.63
   2 ?    7.7   4.6    0.0023       1.9     108     165 ..     254     331 ..     243     349 .. 0.57

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.064
                           DUF4407 131 ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekkaqldaaqaelaelkakld 207
                                       +++++ ++++ +++l++e+++  +++++l+ +       +  ++++  +    + ++k ++l +   el+e k+kl+
  gi|242398896|ref|YP_002994320.1| 109 FEKDVYKINNLLKSLSNEYANYVSEIEKLQPKEIM--AEKLLKEIQDFKKHINEEEQKLKDLVEMLSELNERKKKLE 183
                                       55555555555555555555555555555544432..2122333333333333344444455555555555555555 PP

                           DUF4407 208 atarlaalraelaeleaerakeraasqaaaaaddGllarl 247
                                       +++++ al+++  +l++e+++e+ + +++ ++ +  ++r+
  gi|242398896|ref|YP_002994320.1| 184 ESSEFIALQENERKLKKEISREELNLRSKVSKLQKPIKRM 223
                                       8899999999999999999999888888887777666665 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0023
                           DUF4407 108 Idaelaeeqqeeakelkeqlaaa....................ltaelaeleaqiaalqaeidaaearldalraeaq 164
                                       I  +l++++q++++  ++++ ++                    +++e + l + i++l+++i+++e++++ l++e+q
  gi|242398896|ref|YP_002994320.1| 254 ISDKLDKKYQNTIEWTRKNIPTKtqklkelkrqlagveielsrFKTEEESLHKSIEKLRQKINKKEEKIKSLKEELQ 330
                                       44444444444444444444433333333333333445556565555555555555777777777777777766666 PP

                           DUF4407 165 k 165
                                       k
  gi|242398896|ref|YP_002994320.1| 331 K 331
                                       4 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   1.8       1.2     1e+03      46      92 ..      17      43 ..       1      87 [. 0.46
   2 ?    5.1   6.6     0.037        32      34     103 ..     111     183 ..      83     184 .. 0.81
   3 ?    0.0  13.3       1.4   1.2e+03      23      93 ..     149     217 ..     133     262 .. 0.66
   4 ?   14.4  12.0   4.7e-05      0.04      11      92 ..     271     351 ..     261     353 .] 0.76

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.2
                                      ..HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHH CS
                             DUF16 46 lgeqinkleqkvekqgekikelkveqkaqgeelnkvdetleliletL 92
                                       +++++kl q              e  ++       ++ +  il+ L
  gi|242398896|ref|YP_002994320.1| 17 SKKEMAKLSQ--------------EYTKRV------EHMILDILKLL 43
                                      2222222222..............222222......22222222222 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.037
                                       HHHHHHHHHHH...HHHHHHHHHHHH.HHHHH..HHHHHHHHHHHH.......HHHHHHHHHHHHHHHHHHHC CS
                             DUF16  34 qrLkkieakvdklgeqinkleqkvek.qgeki..kelkveqkaqgeelnkvdetleliletLqkinkRlDsie 103
                                       +++ ki++ +++l ++ ++   ++ek q ++i  ++l +e++  ++++n+ ++ l+ ++e L ++n+R  ++e
  gi|242398896|ref|YP_002994320.1| 111 KDVYKINNLLKSLSNEYANYVSEIEKlQPKEImaEKLLKEIQDFKKHINEEEQKLKDLVEMLSELNERKKKLE 183
                                       56778888888887777666666665255666225788888899999********************987776 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 1.4
                                       HHHHHB-.....BHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHH CS
                             DUF16  23 kqlnefkds...nkqrLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetleliletLq 93 
                                       k++++fk+     +q+Lk++ + ++ l+e+ +kle+  e    + +e k + +  +eeln     l++ +  Lq
  gi|242398896|ref|YP_002994320.1| 149 KEIQDFKKHineEEQKLKDLVEMLSELNERKKKLEESSEFIALQENERKLKKEISREELN-----LRSKVSKLQ 217
                                       677778877555667777777777777777777776666555444444444444455554.....333333333 PP

  == domain 4  score: 14.4 bits;  conditional E-value: 4.7e-05
                                       XX.X.XTTB-BHHHHHHB-..BHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH........HHH CS
                             DUF16  11 KkiPvkteYVTrkqlnefkdsnkqrLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeeln.kvdetle 86 
                                       K+iP+kt+    k+l+      + +L +++++ ++l ++i+kl qk++k++ekik lk+e ++ +++l+ ++ e  e
  gi|242398896|ref|YP_002994320.1| 271 KNIPTKTQK--LKELKRQLAGVEIELSRFKTEEESLHKSIEKLRQKINKKEEKIKSLKEELQKIEKQLEeSLLELEE 345
                                       556655432..244444444477888888888889*******************************99966777778 PP

                                       HHHHHH CS
                             DUF16  87 liletL 92 
                                       +i e +
  gi|242398896|ref|YP_002994320.1| 346 IIGEKI 351
                                       887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3663  (0.204306); expected 358.6 (0.02)
Passed bias filter:                      855  (0.0476881); expected 358.6 (0.02)
Passed Vit filter:                       244  (0.0136092); expected 17.9 (0.001)
Passed Fwd filter:                       158  (0.00881254); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 2.02u 0.39s 00:00:02.41 Elapsed: 00:00:00.63
# Mc/sec: 1680.03
//
Query:       gi|242398897|ref|YP_002994321.1|  [L=373]
Description: hypothetical protein TSIB_0914 [Thermococcus sibiricus MM 739]
Scores for complete 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-98  328.0  10.0    9.2e-98  327.8  10.0    1.0  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 !  327.8  10.0  5.2e-102   9.2e-98       5     320 ..       2     333 ..       1     355 [. 0.93

  Alignments for each domain:
  == domain 1  score: 327.8 bits;  conditional E-value: 5.2e-102
                            DUF373   5 lcvDrDdDlgrkagvktPvvGreavleaavklaladPeDSDvNalfgaikvydeLkaege..dvevavvtGdekvgv 79 
                                       l++DrDdD+g+kagvk+P++Gr+a+++aa kl+ladPeDSD+N+l++a+k+ydeLk++ e  d+eva++tG+++vgv
  gi|242398897|ref|YP_002994321.1|   2 LAIDRDDDFGKKAGVKGPIIGRDACVDAALKLSLADPEDSDANVLYAAVKLYDELKKRAEfdDIEVALITGHPEVGV 78 
                                       89*******************************************************77667*************** PP

                            DUF373  80 eadrkiaeqldevlskleadsaivVsDGaeDesvlpiiqsrvkvdsvkrVvVkqsrniEstyyll....kkalkdpe 152
                                       ++d ++++ql++vl++++ad++i V+DGaeDe+++pii s+v+++s kr+vVkqs++iE+tyy++    k++l+dpe
  gi|242398897|ref|YP_002994321.1|  79 KSDLELNKQLEKVLAQFPADGIIPVTDGAEDEQIFPIITSKVPIISTKRIVVKQSESIETTYYIIyrylKEILSDPE 155
                                       ***************************************************************************** PP

                            DUF373 153 lrktiLvplGlllliyallll.........lglpelalaiillllGlylllrGfgldelleelleklkesleegrit 220
                                        +k++++++G++lliy+++ l         + +++ ++++il+l+G+y+++++f+++e        l+ ++ eg i 
  gi|242398897|ref|YP_002994321.1| 156 AAKIFFGLPGMILLIYGIARLlsikyqqsvTIISSTVTGVILFLIGAYFFVKAFKVKE-------VLSHFFTEGFIQ 225
                                       ********************99*9**999755777999********************.......678999****** PP

                            DUF373 221 fvtyvvallllligiisgyislesvss...asvssglltlilafiygavewlalailtaslgkiideylkreekdia 294
                                       fv++v+al++l+ g++++y +les+     +    + l  +++f++g+ + +++a+ ++++gk+i++yl r++++i+
  gi|242398897|ref|YP_002994321.1| 226 FVSIVAALFVLFAGAVNAYLNLESIALeliGRYPGTELLGVVIFLNGINTSFVAALGVLMIGKVIHSYL-RRDHRIW 301
                                       ************************9998887777888999999**************************.778**** PP

                            DUF373 295 rllllpflvlaiglvlygasaylls......l 320
                                        +++ ++l+ a+++ +  ++ y ls      +
  gi|242398897|ref|YP_002994321.1| 302 YYISGLLLLPALWVTIDVTTLYALSivsfysM 333
                                       **********************9887544441 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       824  (0.0459591); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.49
# Mc/sec: 2275.87
//
Query:       gi|242398898|ref|YP_002994322.1|  [L=62]
Description: hypothetical protein TSIB_0915, partial [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.4e-11   42.9   0.1    3.7e-11   42.8   0.1    1.0  1  Thiamine_BP  Thiamine-binding protein
  ------ inclusion threshold ------
       0.05   13.1   0.0      0.057   12.9   0.0    1.0  1  LcrR         Type III secretion system regulator (LcrR)


Domain annotation for each model (and alignments):
>> Thiamine_BP  Thiamine-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.8   0.1   4.1e-15   3.7e-11      38      91 ..       1      55 [.       1      56 [. 0.98

  Alignments for each domain:
  == domain 1  score: 42.8 bits;  conditional E-value: 4.1e-15
                                      TEEEEEEE.HHHHHHHHHHHHHHHHCTTSSEEEEEEEEEEESSS---HHHHHHHH CS
                       Thiamine_BP 38 mgTtiege.ldevmevvkkahealfeaGakRvstvikiddrrdkeqtleeKvksv 91
                                      m T+ie+  l e ++++k+ he +f+ +akR s +i+id++r+k++ +++K+ksv
  gi|242398898|ref|YP_002994322.1|  1 MRTLIEATsLGEGFKIIKEPHELMFRVDAKRLSATIRIDNKRNKDRDMKNKFKSV 55
                                      89**************************************************998 PP

>> LcrR  Type III secretion system regulator (LcrR)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   6.4e-06     0.057      21      69 ..       6      56 ..       2      58 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.4e-06
                              LcrR 21 sksaialGyrveveGlelawrveeerv..wivllkrveqrrGlanPfaaly 69
                                      + +++  G+++  e  el++rv+++r+   i + +++++ r ++n f +++
  gi|242398898|ref|YP_002994322.1|  6 EATSLGEGFKIIKEPHELMFRVDAKRLsaTIRIDNKRNKDRDMKNKFKSVF 56
                                      67888899*****************983245666788888999**998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 417.29
//
Query:       gi|242398899|ref|YP_002994323.1|  [L=207]
Description: hypothetical protein TSIB_0916 [Thermococcus sibiricus MM 739]
Scores for complete 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-52  176.7   0.0    3.2e-52  176.5   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 !  176.5   0.0   1.8e-56   3.2e-52       2     166 .]      18     194 ..      17     194 .. 0.94

  Alignments for each domain:
  == domain 1  score: 176.5 bits;  conditional E-value: 1.8e-56
                                       HHHHHHHHHHTTSS-S-H..H---HHHHSEEEEEEEEEEE......CCECCCECEEEEEEHHHHHHHHHHHHHHT-T CS
                           AMMECR1   2 klareaieealkeekkle..eeakeelkekaglFVtlkekkg....eLRGCiGtleperpLaeevaenAlaaAfeDp 72 
                                       klar aiee+lk++k+le  +++++ l ek+g+FVtl++ +      LRGCiG+  p  pL+ + +++A+ aA+ Dp
  gi|242398899|ref|YP_002994323.1|  18 KLARTAIEEYLKNGKELEppQDTPPDLWEKMGVFVTLNRYNVppqqALRGCIGFPYPIYPLVIATIKAAIYAAVDDP 94 
                                       89***************99999999*************44335666******************************* PP

                                       TS----HHHHTTEEEEEEEE---EE--......GGG--TTT-EEEEEETTEEEEE-THHHHHTT--HHHHHHHHHHH CS
                           AMMECR1  73 RFspvtaeElpeleveVsvLtepepiv......ledlevgkhGliiekgsrsatlLPqvaveqgwdkeeflasllrK 143
                                       RF+p++ eEl+++++eVsvLt+pep++      +++++vg++Gli++kg +s++lLPqv+ e++wd+eefl++++ K
  gi|242398899|ref|YP_002994323.1|  95 RFPPLSIEELNKITIEVSVLTPPEPVEgppderPNKIKVGRDGLIVKKGIYSGLLLPQVPIEWNWDEEEFLSETCWK 171
                                       **************************4444556889***************************************** PP

                                       HTS-TTCCCSTTSEEEEE-EEEE CS
                           AMMECR1 144 aglrpdewkdseikltryevekf 166
                                       agl+pd+w d++++++r+++e+f
  gi|242398899|ref|YP_002994323.1| 172 AGLSPDCWLDEDTEVYRFTAEIF 194
                                       *******************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1511.02
//
Query:       gi|242398900|ref|YP_002994324.1|  [L=355]
Description: hypothetical protein TSIB_0917 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.30s 00:00:00.93 Elapsed: 00:00:00.53
# Mc/sec: 2014.85
//
Query:       gi|242398901|ref|YP_002994325.1|  [L=450]
Description: TRNA/rRNA cytosine-C5-methylase, NOL1/NOP2/Sun family, fused to N- terminal NusB regulator domain [Thermococcus sibiricus MM 739]
Scores for complete 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  174.6   0.0    2.8e-51  174.0   0.0    1.3  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
    5.8e-17   62.2   0.3    1.5e-16   60.8   0.3    1.7  1  NusB             NusB family
    1.2e-13   51.1   0.0    4.7e-13   49.2   0.0    2.0  2  Methyltransf_31  Methyltransferase domain
    1.2e-09   37.9   0.3    3.4e-08   33.1   0.1    2.2  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family
      3e-07   30.4   0.0    7.9e-07   29.0   0.0    1.6  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    5.2e-07   30.3   0.0    5.6e-06   27.0   0.0    2.5  2  Methyltransf_25  Methyltransferase domain
    5.4e-06   26.1   0.1    0.00044   19.8   0.0    2.7  2  MTS              Methyltransferase small domain
     0.0002   21.5   0.0    0.00041   20.5   0.0    1.5  1  FtsJ             FtsJ-like methyltransferase
    0.00081   18.6   0.2      0.002   17.3   0.0    1.7  2  Fibrillarin      Fibrillarin
     0.0014   19.1   0.0     0.0084   16.6   0.0    2.2  3  Methyltr_RsmF_N  N-terminal domain of 16S rRNA methyltransfer
     0.0043   16.5   0.1       0.01   15.3   0.1    1.7  2  Methyltransf_4   Putative methyltransferase
  ------ inclusion threshold ------
      0.049   13.2   0.0       0.12   11.9   0.0    1.8  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase


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 !  174.0   0.0   1.9e-54   2.8e-51       2     200 .]     255     449 ..     254     449 .. 0.92

  Alignments for each domain:
  == domain 1  score: 174.0 bits;  conditional E-value: 1.9e-54
                                       HHH---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC. CS
                   Methyltr_RsmB-F   2 llLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlgge 78 
                                        +L p+++e++lDl+aaPG+KT h+a+lm+n+g+++Avd + eRl+++++ +k Lgv+n+++++aD+ k++++    
  gi|242398901|ref|YP_002994325.1| 255 HVLSPEKGERVLDLAAAPGSKTFHVAQLMENTGEIIAVDYSLERLRKMETKMKILGVKNVKLVHADGMKFKDMRK-- 329
                                       689*******************************************************************66654.. PP

                                       .EEEEEEEE--CCGGGTTT-TCHHHH--HHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEES--STTTTHHHHHHHHH CS
                   Methyltr_RsmB-F  79 lfDriLlDaPCsgtgvirrdpdvklrrkekdiaqlaklqkellsaaidllkkgGvlvYsTCsvlveEneevieeaLk 155
                                        fD+i+lDaPCs+ g+ r+ p+vk+r +++ i+++ + qk+++  a + l+ +G + YsTCs+ ++Enee +++aL+
  gi|242398901|ref|YP_002994325.1| 330 -FDKIILDAPCSSSGTYRQFPEVKWRFNKEKIKKVIQVQKAMIRNAYKNLRDEGEMTYSTCSIRIDENEENVKYALE 405
                                       .**************************************************************************** PP

                                       H-TTEEEESSBST..TSTTSSECEECTSEEE-TTTTSS-SEEEEEEE CS
                   Methyltr_RsmB-F 156 kredvelvetels..epkglklgeeagtlrllPhtenkdgffiaklk 200
                                       k     lv+ ++s  e   +++ge     r + h ++ ++ffiaklk
  gi|242398901|ref|YP_002994325.1| 406 KV-GFDLVTYPFSwgERGFTEIGEM--VFRSFTHLHDCNSFFIAKLK 449
                                       98.6777766665105444555555..59****************96 PP

>> NusB  NusB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.8   0.3     1e-19   1.5e-16       5     133 ..      11     133 ..       5     134 .. 0.86

  Alignments for each domain:
  == domain 1  score: 60.8 bits;  conditional E-value: 1e-19
                                       HHHHHHHHHHHHH-S-HHHHHHHHHHHT-.........--HHHHHHHHHHHHHHHHTHHHHHHHHHHTTTT--GGGS CS
                              NusB   5 elalqalyqveinkedeeekeailqealn..klleeedldeedkafltelvkgvlrnleelDeliekllknwplerl 79 
                                       el++++l  +       ee+e ++++al+   ++   +  e+ +++++++++++ ++++++D + ++ lk+ ++e+l
  gi|242398901|ref|YP_002994325.1|  11 ELIADILSLI-------EERELSSKNALErtFKRVRGKDRERARGLAHAYIFEIEKWKRKIDFIGNSVLKGIKIEEL 80 
                                       6778888888.......5555555555553222455566778999******************************** PP

                                       -HHHHHHHHHHHHHHTTS-SSHHHHHHH.HHHHHHHHS-HHHHHHHHHHHHHHH CS
                              NusB  80 skvdraiLrlavyellylddvPakvaineavelakkygdeksakFvNgVLrkva 133
                                       ++++ ++Lr++++e+++   v +  a + +v ++k   d + akF+N+VLr v+
  gi|242398901|ref|YP_002994325.1|  81 DPYLANLLRIGIFEMKFK-GVVPAIATDSIVRAVKDKYDLSRAKFINAVLRDVE 133
                                       ******************.999999**************************985 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       2.4   3.5e+03      60      96 ..      51      86 ..      41      91 .. 0.72
   2 !   49.2   0.0   3.2e-16   4.7e-13       2     114 ..     260     396 ..     259     421 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.4
                   Methyltransf_31 60 qgdieeleklledekfDlilsnevl..naladpdkilee 96
                                      ++ i+e+ek ++ +k+D+ + n+vl    + ++d +l +
  gi|242398901|ref|YP_002994325.1| 51 HAYIFEIEK-WK-RKIDF-IGNSVLkgIKIEELDPYLAN 86
                                      678999887.88.89999.55577766666666666655 PP

  == domain 2  score: 49.2 bits;  conditional E-value: 3.2e-16
                   Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDli 78 
                                       +kg rvlDl+++ G +tf  a+++   +e++ +D+s e +++++++ + lg++nv++ ++d  +++     +kfD i
  gi|242398901|ref|YP_002994325.1| 260 EKGERVLDLAAAPGSKTFHVAQLMENTGEIIAVDYSLERLRKMETKMKILGVKNVKLVHADGMKFKDM---RKFDKI 333
                                       7899*****************99999**************************************6633...9***** PP

                   Methyltransf_31  79 lsnevl......................naladpdkileeiervlkpggilliedpr.....l 114
                                       + ++++                        +  +++ ++++ ++l+++g++  ++++      
  gi|242398901|ref|YP_002994325.1| 334 ILDAPCsssgtyrqfpevkwrfnkekikKVIQVQKAMIRNAYKNLRDEGEMTYSTCSirideN 396
                                       ***555555555555555555555555688888888999*****************9533322 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.1   2.3e-11   3.4e-08      32     112 ..     246     326 ..     242     337 .. 0.89
   2 ?    2.9   0.1     0.038        57      76     131 ..     362     425 ..     327     438 .. 0.64

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 2.3e-11
                                       HHHHHHHHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TT CS
                   Ubie_methyltran  32 hrlWkkfveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanae 108
                                        +l  ++v ++ ++ +g++vlD+a+  g  +f++++ ++++g+++ +D++ + L+  e k+k  g++n+++++a+++
  gi|242398901|ref|YP_002994325.1| 246 QDLASAYVAHVLSPEKGERVLDLAAAPGSKTFHVAQLMENTGEIIAVDYSLERLRKMETKMKILGVKNVKLVHADGM 322
                                       5666678899999***************************************************************9 PP

                                       T-TT CS
                   Ubie_methyltran 109 eLpf 112
                                       +++ 
  gi|242398901|ref|YP_002994325.1| 323 KFKD 326
                                       8653 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.038
                                       EEEES-HHHHHHHHHHHHHHTSS.....TEEEEE--TT..T-TTS-T-EEEEE..EES-GGG-S- CS
                   Ubie_methyltran  76 vvlDinenmLkvgekklkeegki.....nieflqanae..eLpfeddsfDvvt..vsfGlrnvtD 131
                                       +v+ +++ m++ + k l++eg +     +i+ +  n e  +   e+  fD+vt   s+G r +t+
  gi|242398901|ref|YP_002994325.1| 362 KVIQVQKAMIRNAYKNLRDEGEMtystcSIR-IDENEEnvKYALEKVGFDLVTypFSWGERGFTE 425
                                       4677888888888888888887766554333.233433013445667778777334566676666 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 !   29.0   0.0   5.3e-10   7.9e-07      61     150 ..     249     337 ..     236     342 .. 0.91

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 5.3e-10
                                       HHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGGTT CS
                              PCMT  61 mvalalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGrkGy 137
                                         a++   l+ +kg+rvL++ +  G +t  +a+l++++g +++++++ e  ++ + ++k l+++nv++v++DG k +
  gi|242398901|ref|YP_002994325.1| 249 ASAYVAHVLSPEKGERVLDLAAAPGSKTFHVAQLMENTGEIIAVDYSLERLRKMETKMKILGVKNVKLVHADGMK-F 324
                                       567888889999*************************************************************87.8 PP

                                       GGG-SEEEEEESS CS
                              PCMT 138 eekaPYdaihvga 150
                                       +++  +d+i++ a
  gi|242398901|ref|YP_002994325.1| 325 KDMRKFDKIILDA 337
                                       9999999998766 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.0   3.7e-09   5.6e-06       1      70 [.     265     335 ..     265     382 .. 0.90
   2 ?    0.8   0.0      0.57   8.5e+02      27      55 ..     364     391 ..     334     420 .. 0.65

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 3.7e-09
                                       EEEET-TTSHHHHHHHCTS.TSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEE CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrl.gkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvs 70 
                                       vLdl++ +G  t+++a+ + + +++++vD+s e l++++++++  g+ nv++v++d  +++   ++fD +++
  gi|242398901|ref|YP_002994325.1| 265 VLDLAAAPGSKTFHVAQLMeNTGEIIAVDYSLERLRKMETKMKILGVkNVKLVHADGMKFKDM-RKFDKIIL 335
                                       9*****************9769********************99999**********999854.59999887 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.57
                                       EESSHHHHHHHHHHHHHTTTTEEEEESBC CS
                   Methyltransf_25  27 vDiseemleaareraeeeglnvefvqgda 55 
                                       + ++++m+++a +++++eg ++++ ++++
  gi|242398901|ref|YP_002994325.1| 364 IQVQKAMIRNAYKNLRDEG-EMTYSTCSI 391
                                       5667889999999988876.555544444 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.92   1.4e+03     135     158 ..      17      40 ..      16      45 .. 0.84
   2 !   19.8   0.0   2.9e-07   0.00044      17     111 ..     247     343 ..     242     390 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.92
                                       EEEEEETTSCHHHHHHHHHS--EE CS
                               MTS 135 LliVanrklgyeslleelfgnvev 158
                                       L ++ +r+l  +++le++f++v+ 
  gi|242398901|ref|YP_002994325.1|  17 LSLIEERELSSKNALERTFKRVRG 40 
                                       66788999***********99875 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 2.9e-07
                                       -HHHHHHHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.E.EEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTT CS
                               MTS  17 DkGsklLletlpkelsgkvlDlGcGaGvlgaalakespeae.vtlvdvdarAlesakenleankle.vevvasdvle 91 
                                       D +s+  ++ l+ e+ ++vlDl++  G  + ++a+  +++  + +vd + + l+  ++ ++  +++ v++v+ d+++
  gi|242398901|ref|YP_002994325.1| 247 DLASAYVAHVLSPEKGERVLDLAAAPGSKTFHVAQLMENTGeIIAVDYSLERLRKMETKMKILGVKnVKLVHADGMK 323
                                       8999999****************************9988766*********************************** PP

                                       TSTTS-EEEEEE---STTTC CS
                               MTS  92 eveekkfdlivsNPPfhagk 111
                                         + +kfd i+   P  ++ 
  gi|242398901|ref|YP_002994325.1| 324 FKDMRKFDKIILDAPCSSSG 343
                                       ***********999865543 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   2.8e-07   0.00041      21     153 ..     261     410 ..     243     417 .. 0.68

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.8e-07
                                       TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS..HHH.TTEEEE.CS-CCCSSHHH.HHCHCHHHSSEEEEE CS
                              FtsJ  21 pgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm..apl.pgvtti.qgditdpetie.kikealserkvdlvv 92 
                                       +g++v+Dl+aaPG+ +  ++q ++++g ++avD      +++  +++++   +++   +   k+k+    rk+d ++
  gi|242398901|ref|YP_002994325.1| 261 KGERVLDLAAAPGSKTFHVAQLMENTGEIIAVDYSLErlRKMeTKMKILgVKNVKLVHADGmKFKD---MRKFDKII 334
                                       7899*******************999*******955524333455555555555443333312222...26788888 PP

                                       E--S-SS-CH.HHHHHHHH..........CCCCHHHHCCHCCCCECCCEEEECCCH...CCCHHHHHHHHH.CCEE CS
                              FtsJ  93 sDgapdvsgv.hdldeylq..........sqLllaalelalkllkpggtfvlkifr...geeteallkqlk.kfFe 153
                                        D   + sg+ ++++e++           +q  +a ++ a k l+ +g +   ++    +e+ e++ ++l+  +F+
  gi|242398901|ref|YP_002994325.1| 335 LDAPCSSSGTyRQFPEVKWrfnkekikkvIQVQKAMIRNAYKNLRDEGEMTYSTCSiriDENEENVKYALEkVGFD 410
                                       8887777777455555555777777777778888888888888888888776666665556555666664425555 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.3e-06     0.002      69     112 ..     260     303 ..     239     323 .. 0.88
   2 ?   -3.5   0.0         3   4.4e+03     155     183 ..     368     396 ..     362     402 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.3e-06
                                       -TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHHHHHHH CS
                       Fibrillarin  69 kkgskvLYlGaasGttvsHvsDivgeegvvyavefsprvlreli 112
                                       +kg++vL l aa G+   Hv+ +++++g + av++s   lr++ 
  gi|242398901|ref|YP_002994325.1| 260 EKGERVLDLAAAPGSKTFHVAQLMENTGEIIAVDYSLERLRKME 303
                                       799*********************************99988875 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3
                                       HHHHHHHHHHEEEEEEEEEEEEHHHHHSS CS
                       Fibrillarin 155 rilaknaklflkeggyllisikarsidvt 183
                                       + +++na   l+++g++  s  +  id  
  gi|242398901|ref|YP_002994325.1| 368 KAMIRNAYKNLRDEGEMTYSTCSIRIDEN 396
                                       56778888888888888877766666654 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 !   16.6   0.0   5.7e-06    0.0084       2      89 ..     160     250 ..     160     251 .. 0.86
   2 ?   -3.0   0.0       7.3   1.1e+04      32      41 ..     353     362 ..     344     383 .. 0.68
   3 ?   -1.3   0.0       2.2   3.3e+03      26      64 ..     385     424 ..     361     444 .. 0.60

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.7e-06
                                       -HHHHHHHHHHHGG.GHHHHHHHHH-----EEE--TTS..TTHHHHHHH..-SS--B-TT-TTEEES---...TTSH CS
                   Methyltr_RsmF_N   2 PeeFiekmkellge.eaeaflaaleeprkkglRvNtlKisveeleklse..efelepvpwceeGfyleeeerpgkhp 75 
                                       P+ ++e++ +llg  e  ++l + ++p+++ +RvN+lK++ ++l++  e  ++++++ p  +   +le ++  ++  
  gi|242398901|ref|YP_002994325.1| 160 PRWYVEYVIDLLGYeEGLRLLLSNNKPQRYYIRVNPLKTDIDSLSDYLEehGVRVTRTPVDDILKVLEYKTPITHLE 236
                                       566788888889886777889999*******************9998777888999999988888999988889999 PP

                                       HHHTTS-EE--TTT CS
                   Methyltr_RsmF_N  76 lheaGlyYiQEpSa 89 
                                        +++G++ iQ+ ++
  gi|242398901|ref|YP_002994325.1| 237 GYKEGYFVIQDLAS 250
                                       9*********9776 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 7.3
                                       EE--TTS..T CS
                   Methyltr_RsmF_N  32 lRvNtlKisv 41 
                                        R+N+ Ki++
  gi|242398901|ref|YP_002994325.1| 353 WRFNKEKIKK 362
                                       5888888653 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 2.2
                                       -----EEE--TTS..TTHHHHHHH.-SS--B-TT-TTEEE CS
                   Methyltr_RsmF_N  26 eprkkglRvNtlKisveeleklse.efelepvpwceeGfy 64 
                                       + ++ ++R++++  +v+   +    +  + p  w e Gf 
  gi|242398901|ref|YP_002994325.1| 385 TYSTCSIRIDENEENVKYALEKVGfDLVTYPFSWGERGFT 424
                                       4566788888888554433333333444556777777775 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       4.8   7.2e+03      21      54 ..     183     216 ..     179     230 .. 0.58
   2 !   15.3   0.1   6.9e-06      0.01       5     117 ..     265     388 ..     261     410 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 4.8
                                       HHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEE CS
                    Methyltransf_4  21 kknPdknflGiEirvkvvakvlkkiealelkNlr 54 
                                       +++P+  ++ ++  ++ ++ + +  e+++++  r
  gi|242398901|ref|YP_002994325.1| 183 NNKPQRYYIRVNPLKTDIDSLSDYLEEHGVRVTR 216
                                       5666666666666666666666666666555444 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 6.9e-06
                                       EEEET-TTSHHHHHHHH.HSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-C.....CCHHHHCS-TTSE.. CS
                    Methyltransf_4   5 vleiGcGkGeflvalAk.knPdknflGiEirvkvvakvlkkiealelkNlrilrgda.....lkvllelledgsl.. 73 
                                       vl++  + G+ + + A+ ++ + ++++++ + ++++k+  k++ l++kN+++++ d      ++ + +++ d+ +  
  gi|242398901|ref|YP_002994325.1| 265 VLDLAAAPGSKTFHVAQlMENTGEIIAVDYSLERLRKMETKMKILGVKNVKLVHADGmkfkdMRKFDKIILDAPCss 341
                                       677888888888888873466779*********************************77777777888887665411 PP

                                       EEEEEES---.-..-SGGGGGGSTTSHHHHHHHHHHEEEEEEEEEEE CS
                    Methyltransf_4  74 ekifilFPDP.w..fKkrhhKrRllqpellkelarvLkkgGvlelaT 117
                                       ++ + +FP   w  +K++ +K   +q++++ ++ + L+ +G+++  T
  gi|242398901|ref|YP_002994325.1| 342 SGTYRQFPEVkWrfNKEKIKKVIQVQKAMIRNAYKNLRDEGEMTYST 388
                                       67899999742411333333333357788888889999999888777 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0     8e-05      0.12       3      73 ..     264     336 ..     262     391 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8e-05
                   Methyltransf_15   3 vilDlfsGaGGnviqfalv...fekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklklekikvd 73 
                                        +lDl +  G ++ + a+      ++ia++++le+l  ++   ++ gv+ +++lv++d ++     k++ki  d
  gi|242398901|ref|YP_002994325.1| 264 RVLDLAAAPGSKTFHVAQLmenTGEIIAVDYSLERLRKMETKMKILGVK-NVKLVHADGMKFKDMRKFDKIILD 336
                                       68999999999999988874445589*********************96.699999999987777777776544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       726  (0.0404931); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.46
# Mc/sec: 2944.85
//
Query:       gi|242398902|ref|YP_002994326.1|  [L=1469]
Description: DNA polymerase [Thermococcus sibiricus MM 739]
Scores for complete 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-81  269.0   4.1    6.9e-81  269.0   4.1    2.2  2  PI-TkoII_IV      DNA polymerase II intein Domain IV
    1.9e-65  221.4   0.6    4.7e-28   98.1   0.1    3.4  3  DNA_pol_B        DNA polymerase family B
    2.5e-51  173.1   4.2    1.3e-32  112.5   0.3    2.8  2  Intein_splicing  Intein splicing domain
    9.1e-48  163.1   4.0    2.4e-36  125.5   0.1    3.0  3  DNA_pol_B_exo1   DNA polymerase family B, exonuclease domain
    2.1e-10   40.8   0.3     0.0001   22.5   0.1    3.4  2  LAGLIDADG_3      LAGLIDADG-like domain
    9.7e-10   38.5   0.0    2.5e-09   37.2   0.0    1.6  1  DNA_pol_B_exo2   Predicted 3'-5' exonuclease related to the e
    1.5e-06   28.3   0.1    4.8e-06   26.7   0.1    2.0  1  RNase_H_2        RNase_H superfamily
     0.0072   16.2   0.7      0.066   13.1   0.1    2.8  2  DUF2816          Protein of unknown function (DUF2816)
  ------ inclusion threshold ------
      0.023   13.4   0.0      0.044   12.4   0.0    1.4  1  DUF4455          Domain of unknown function (DUF4455)


Domain annotation for each model (and alignments):
>> PI-TkoII_IV  DNA polymerase II intein Domain IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  269.0   4.1   3.4e-84   6.9e-81       1     149 []     618     767 ..     618     767 .. 0.99
   2 ?   -3.5   0.1       3.2   6.5e+03      20     109 ..    1000    1018 ..     948    1026 .. 0.45

  Alignments for each domain:
  == domain 1  score: 269.0 bits;  conditional E-value: 3.4e-84
                                       S---------EEEHHHHHHTS-GGGCTTEEEEEESTT-TTHHHHHHHHHHHHTTSS.---TTHHHHHHHHHHCTSEE CS
                       PI-TkoII_IV   1 krlklpereevlnlvelllklpeeetadivltipvkGrknffkGmlrtlrwifgee.krirtarrylkhleklGyvk 76 
                                       k++kl+e+e ++n++el+l+lp+e+tadiv+tipvkGrknffkGmlrtlrwifgee krirt++ryl+hleklG+vk
  gi|242398902|ref|YP_002994326.1| 618 KKVKLNEKEVTINIPELILRLPDEATADIVMTIPVKGRKNFFKGMLRTLRWIFGEEsKRIRTFNRYLFHLEKLGFVK 694
                                       79*************************************************************************** PP

                                       E-SSSEEES-HHHHHHHHHHHHHHHHH-EEETTTTEEEEEGGGGCCCHCCS-HHHHTT-EEEETTS-EEESEE CS
                       PI-TkoII_IV  77 lkkrGyevldweglkkykklyeklvekvkynGnkreylvefndlrdviellpeeelkewkiGtlnGfrlesli 149
                                       l +rGyev+dweglk yk+lyeklve+++ynGnkreylv+fnd++dvi+++p++el+ewkiGtlnGfr+++++
  gi|242398902|ref|YP_002994326.1| 695 LLPRGYEVTDWEGLKIYKQLYEKLVESLRYNGNKREYLVMFNDIKDVISSFPQKELEEWKIGTLNGFRMDCIL 767
                                       ***********************************************************************96 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3.2
                                        TS-GGGCTTEEEEEESTT-TTHHHHHHHHHHHHTTSS---TTHHHHHHHHHHCTSEEE-SSSEEES-HHHHHHHH CS
                       PI-TkoII_IV   20 klpeeetadivltipvkGrknffkGmlrtlrwifgeekrirtarrylkhleklGyvklkkrGyevldweglkkyk 94  
                                        ++                                                                        k
  gi|242398902|ref|YP_002994326.1| 1000 NVK-----------------------------------------------------------------------K 1003
                                        222.......................................................................2 PP

                                        HHHHHHHHH-EEETT CS
                       PI-TkoII_IV   95 klyeklvekvkynGn 109 
                                        + ye  v ++  +Gn
  gi|242398902|ref|YP_002994326.1| 1004 REYEGYVYDLSVEGN 1018
                                        334444444444444 PP

>> DNA_pol_B  DNA polymerase family B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.9   0.0   4.5e-30   8.9e-27      14     166 ..     354     496 ..     346     497 .. 0.87
   2 !   25.8   0.0   2.1e-09   4.1e-06     164     204 ..    1032    1072 ..    1028    1098 .. 0.86
   3 !   98.1   0.1   2.4e-31   4.7e-28     230     458 ..    1239    1445 ..    1233    1446 .. 0.96

  Alignments for each domain:
  == domain 1  score: 93.9 bits;  conditional E-value: 4.5e-30
                                       HHHHHHHHHHHHTTBE-B-----.--SS.....-S----BE----EEESS-EEEEEETTHHHHHHHHTT-STTTCE- CS
                         DNA_pol_B  14 rveslLlrlakeegfilpdrtekkgkeee....gYqGatVlePkkglydkpvlvlDFaSLYPsiiqahNlcyttlva 86 
                                        ve  +lr a e++  +p+r++++ ++++    +Y G+ V eP++gl+++ ++ lDF SLYPsii+ hN+++ tl +
  gi|242398902|ref|YP_002994326.1| 354 LVEWYMLRVAYERNELAPNRPSDE-EYKRrlrtTYLGGYVKEPERGLWEN-IIYLDFRSLYPSIIVTHNVSPDTLER 428
                                       578899*************88884.333346656*************986.778*********************99 PP

                                       HCCHCCT--BTT...TEEE-TCC-EEE-TTS---HHHHHHHHHHHHHHHHHHHHHCS--HHHHHHHHHHHHHHHHHH CS
                         DNA_pol_B  87 seeeakeleaedeyleveveprlvefvkksvregllpklLkdllakRkaikkelkeekdefekalldkqQlalKvta 163
                                       +  ++ ++ + +             + + ++  g +p++L+dl++ R++ikke+k++ d+ +k++ld +Q a+K++a
  gi|242398902|ref|YP_002994326.1| 429 KGCQNYDVAPIV------------GYKFCKDFSGFIPSILEDLIETRQKIKKEMKSTIDPIKKKMLDYRQRAVKLLA 493
                                       999877766533............233356779******************************************** PP

                                       HHH CS
                         DNA_pol_B 164 Nsv 166
                                       Ns+
  gi|242398902|ref|YP_002994326.1| 494 NSI 496
                                       *96 PP

  == domain 2  score: 25.8 bits;  conditional E-value: 2.1e-09
                                        HHHHHHHTSTTSTT--HHHHHHHHHHHHHHHHHHHHHHHHT CS
                         DNA_pol_B  164 NsvYGftGvansrlpclalAasvTtiGRemLektkelvekk 204 
                                        Ns YG++G+ + r ++++ A+svT+ GR+ +e+t + +e+k
  gi|242398902|ref|YP_002994326.1| 1032 NSYYGYMGYPKARWYSKECAESVTAWGRHYIEMTIREIEEK 1072
                                        ***************************************98 PP

  == domain 3  score: 98.1 bits;  conditional E-value: 2.4e-31
                                        SSEEEEE-S-SSHHHHHHHHHHHHHHHHT.TSTTT--EEEEEEEEEEEEEETTEEEEEEEEESSTTSEEEEESSG CS
                         DNA_pol_B  230 TDSvfielkvkdveellkigkelaeevseklfkkplklefekvykkllLisKKkYaglkvektskanklliKGvd 304 
                                        TD  + ++ + d e++ k +ke+ +++++ +++  l+le+e  y +  +++KK+Ya +  e     +k+ ++G++
  gi|242398902|ref|YP_002994326.1| 1239 TDGFYATIPGADPETIKKKAKEFLNYINS-KLPGLLELEYEGFYLRGFFVTKKRYAVIDEE-----EKITTRGLE 1307
                                        9****************************.88888********************999888.....999****** PP

                                        GGSTTS-HHHHHHHHHHHHHHSSS....S-HHHHHHHHHHHHHHHHHHHHTT-S-GGGG-EEEEESS.CCCSSGC CS
                         DNA_pol_B  305 lvRrdncklvkevikkvlelllkdeteersleeglealksilkdvleeleenkvplekfvlskelskepenyksk 379 
                                        +vRrd+++++ke+  +vle +l++     s+e+++e++k+++    e++++ kvplek+++ +++++e ++yk+ 
  gi|242398902|ref|YP_002994326.1| 1308 VVRRDWSEIAKETQARVLEAILRE----GSVEKAVEIVKEVV----EAITKYKVPLEKLIIHEQITRELRDYKAV 1374
                                        ************************....9*****99999999....9***************************9 PP

                                        CSHHHHHHHHHHHHCSS---TTCEEEEEEBETSS.....SS-GGGTEEEHHHHHHCCSEB-HHHHHH.TTHHHHH CS
                         DNA_pol_B  380 nlphlevakrlkkrneeapevgdrisYvivekkkevkkknllaseraedpeyvleknlpidieyYls.qllkeva 453 
                                          ph+++akrl+++ + ++++g  isY++   +        ++s+r++  + +  ++ + d +yY++ q+l++v 
  gi|242398902|ref|YP_002994326.1| 1375 G-PHVAIAKRLAAK-GIKIKPGTIISYIVLRGS-------GKISDRVVLLTEYDPRKHKYDPDYYIEnQVLPAVL 1440
                                        9.*********999.799************996.......5999****99999999******************* PP

                                        HHHTT CS
                         DNA_pol_B  454 rllea 458 
                                        r+lea
  gi|242398902|ref|YP_002994326.1| 1441 RILEA 1445
                                        **985 PP

>> Intein_splicing  Intein splicing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.5   0.3   6.6e-36   1.3e-32       2     134 .]     504    1032 ..     503    1032 .. 0.98
   2 !   61.2   0.4   4.8e-20   9.6e-17       2     134 .]    1091    1238 ..    1090    1238 .. 0.84

  Alignments for each domain:
  == domain 1  score: 112.5 bits;  conditional E-value: 6.6e-36
                                        EECTTCEE.EEHHHHCC....................ECTTEEEEEETTTTEEEEEEEEEEEEEEEE.EEEEEEE CS
                                        xxxxxxxx.xxxxxxxx....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx RF
                   Intein_splicing    2 iledgeek.vkieelve....................kegeevlslnledlklevksvkkliklklk.elyeikl 54  
                                        i+e++e+k vki+e+++                     ++   lsln e+ + evk+v +li++k++ ++y i l
  gi|242398902|ref|YP_002994326.1|  504 IIENEEIKfVKIGEFIDrymeeqkdrvrtvdntevleVDNLFALSLNRESKESEVKKVRALIRHKYRgKVYAIGL 578 
                                        789999999**********99999999999988887666667788999999999999****************** PP

                                        TTS-EEEEETT-EEEECCTTEEEEEECCC--TT-EEEEE.................................... CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................................... RF
                   Intein_splicing   55 esgrkikaTpeHkllvvrdegivEkradeLkegdliavp.................................... 93  
                                        +sgrki +T++H+l+++r+++i E+++ e+k+gdli+vp                                    
  gi|242398902|ref|YP_002994326.1|  579 NSGRKITVTGGHSLFTIRKGEIREVSGAEIKAGDLIVVPkkvklnekevtinipelilrlpdeatadivmtipvk 653 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                   Intein_splicing   94 ........................................................................... 93  
                                                                                                                   
  gi|242398902|ref|YP_002994326.1|  654 grknffkgmlrtlrwifgeeskrirtfnrylfhleklgfvkllprgyevtdweglkiykqlyeklveslryngnk 728 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                   Intein_splicing   94 ........................................................................... 93  
                                                                                                                   
  gi|242398902|ref|YP_002994326.1|  729 reylvmfndikdvissfpqkeleewkigtlngfrmdcilkidenfgkllgyyvsegyagaqknktdgisysvkly 803 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                   Intein_splicing   94 ........................................................................... 93  
                                                                                                                   
  gi|242398902|ref|YP_002994326.1|  804 nenpnilgdmknaaerffgkvrvgkncvsiskkmayllmkclcgvtaenkrippiifnspepirwafleayfagd 878 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                   Intein_splicing   94 ........................................................................... 93  
                                                                                                                   
  gi|242398902|ref|YP_002994326.1|  879 gdvhpskrlrlstksellanqlifflnslgvssvkigfdsgvyrvyinedlqflrtsrekntyysnlipkeilee 953 
                                        *************************************************************************** PP

                                        ....................................HSCEEEEEEEEEEEEECEEEEEEEEETTT-EEEE.CTTE CS
                                        ....................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx RF
                   Intein_splicing   94 ....................................dadvvwdkvksievedeeeyVYdltvednhNFva.ngii 131 
                                                                            ++d+v+d+vk+++++++e+yVYdl+ve+n+NF++ +g++
  gi|242398902|ref|YP_002994326.1|  954 ifgrkfqrnitfekfkefvdsgkldkrkaklldfvlNGDIVLDRVKNVKKREYEGYVYDLSVEGNENFLVgFGLL 1028
                                        *********************************************************************99**** PP

                                        .EE- CS
                                        .xxx RF
                   Intein_splicing  132 .vHN 134 
                                         +HN
  gi|242398902|ref|YP_002994326.1| 1029 yAHN 1032
                                        ***9 PP

  == domain 2  score: 61.2 bits;  conditional E-value: 4.8e-20
                                        EECTTCEE.EEHHHHCC.............ECTTEEEEEETTTTEEEEEEEEEEEEEEEE.EEEEEEETTS-EEE CS
                                        xxxxxxxx.xxxxxxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx RF
                   Intein_splicing    2 iledgeek.vkieelve.............kegeevlslnledlklevksvkkliklklk.elyeiklesgrkik 61  
                                        +  +g+++ v+ie+l+e              e  e l l+ +  +l +k+v  ++++k k ++y+i +++   i 
  gi|242398902|ref|YP_002994326.1| 1091 VKRNGRVEfVPIEKLFErvdyrlgekeyciLESVEALTLD-NRGRLVWKKVPYVMRHKAKkKVYRIWITNSWYID 1164
                                        6789999999999999999997765555544444444444.455677777********999************** PP

                                        EETT-EEEECCTTEEEEEECCC--TT-EEEEEHSC..EEEEEEEEEEEEECEEEEEEEEETTT-EEEECTTEEE- CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Intein_splicing   62 aTpeHkllvvrdegivEkradeLkegdliavpdad..vvwdkvksievedeeeyVYdltvednhNFvangiivHN 134 
                                        +T +H+l+v  ++g+ E +  e++ + lia+ d+   v + k +  e+  +++yVYd++ve++h F+angi+vHN
  gi|242398902|ref|YP_002994326.1| 1165 VTEDHSLIVA-EDGLKEAKPIEIEGKSLIATKDDLsgVEYIKPRTLEEIPYDGYVYDIEVEETHRFFANGILVHN 1238
                                        **********.7999889999999999999776545578888999*****************************9 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 !   39.0   0.0   2.6e-13   5.1e-10      13     118 ..      32     129 ..      20     131 .. 0.84
   2 !  125.5   0.1   1.2e-39   2.4e-36     154     337 .]     130     280 ..     126     280 .. 0.90
   3 ?   -2.9   0.1       1.4   2.8e+03      58     117 ..    1031    1091 ..    1028    1098 .. 0.74

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 2.6e-13
                                       EE---EEEEEESSCGGHHHHHHHHHHHCCTTCCCEEEEEEEECCCCEECCTSSCCHHCEEEEEESSTCHHHHHHHHH CS
                    DNA_pol_B_exo1  13 fgfkpyfYceapdgkeleevkeelkelyeelskkvtkivkvelvlkkslygyekkpvpylkvsvsnpnelkkirkel 89 
                                        +f+py+Y+  ++++  +e+k+  +e ++++ + v+  vkve    k+++      v+++k+ +++p++++ ir+++
  gi|242398902|ref|YP_002994326.1|  32 PHFQPYIYALLSEDSAIDEIKQIKGERHGKTVRIVD-AVKVE----KKFLKKP---VKVWKLILEHPQDVPAIRNKI 100
                                       589*********999999999999999999988888.33333....5554444...44******************* PP

                                       HHCCCCCCCCSSS--HHHHHHHHCTS-TT CS
                    DNA_pol_B_exo1  90 spleeivdvyeydvdylerflidnkivgf 118
                                       +++  + d+yeyd+++  r+lidn++ ++
  gi|242398902|ref|YP_002994326.1| 101 REHPAVQDIYEYDIPFAKRYLIDNGLIPM 129
                                       ************************99886 PP

  == domain 2  score: 125.5 bits;  conditional E-value: 1.2e-39
                                       TCCS-EEEEEEEEEETEETTSEETTTT..--EEEEEEEECCTC.SS.SEEEEEEECCCTSS----EE--SSTCSTTE CS
                    DNA_pol_B_exo1 154 esepplrvlsFDIeckskkgkfpdaensedpiiqIscvldglgekepearklftlrecaseeeedfeltpkpeypgv 230
                                       e++ +l++l+FDIe+  ++g   +  +   +ii+Is++ ++ +        ++t+++++                 +
  gi|242398902|ref|YP_002994326.1| 130 EGDEELKMLAFDIETFYHEG--DEFGK--GEIIMISYADEEGA-------RVITWKNID-------------L---P 179
                                       56689**********99999..66666..**********9999.......9********.............3...5 PP

                                       EEEEESSHHHHHHHHHHHHHHH--SEEEESSTTTTHHHHHHHHHHHCCT.CCHCG.SCCSCTCEECCCCESEEEEEE CS
                    DNA_pol_B_exo1 231 kvlefdsEkelLqaflefikqydPdvitgYNidnFDlpYilnRakelyk.vklsklgrlnkggrskvseigfskqar 306
                                        v  + +E+e++++f+++ik++dPdvi++YN+dnFDlpY+ +Ra++l   +    l+r n++++ k+++ g+s    
  gi|242398902|ref|YP_002994326.1| 180 YVDVVSNEREMIKRFIQIIKEKDPDVIITYNGDNFDLPYLIKRAEKLGLrLI---LSRDNENPVPKIQRMGNS---- 249
                                       7888*****************************************7775233...34556*************.... PP

                                       CEEEETTSEEEEHHHHHHHHSSSSG-SHHHH CS
                    DNA_pol_B_exo1 307 ekvkisgrihlDlyrvvkrklklpsYkLnav 337
                                         v+i+grih+Dl++vvkr ++lp Y+L+av
  gi|242398902|ref|YP_002994326.1| 250 FAVEIKGRIHFDLFPVVKRAVNLPTYTLEAV 280
                                       *****************************98 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 1.4
                                        CEECCTSSCCHHC..EEEEEESSTCHHHHHHHHHHHCCCCCCCCSSS--HHHHHHHHCTS-T CS
                    DNA_pol_B_exo1   58 kkslygyekkpvp..ylkvsvsnpnelkkirkelspleeivdvyeydvdylerflidnkivg 117 
                                        ++s+ygy+  p+   y k   +++++  +   e+  ++ei+++++++v y   +  d  i +
  gi|242398902|ref|YP_002994326.1| 1031 HNSYYGYMGYPKArwYSKECAESVTAWGRHYIEM-TIREIEEKFGFKVLYADSVTSDTEIIV 1091
                                        6899999999988955555555555555555555.599999999999999988888887765 PP

>> LAGLIDADG_3  LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   1.8e-05     0.035       4      56 ..     773     829 ..     770     844 .. 0.82
   2 !   22.5   0.1   5.1e-08    0.0001       5      51 ..     869     911 ..     866     937 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.8e-05
                                       HHHHHHHHHHCCECCECSTTTTS....EEEEES-HHHHHHHHHHHHHCT.HSCEEEE CS
                       LAGLIDADG_3   4 aafLrGlfdaDGsvskskkkgvs....isltssskelledvqrlLlrlGIestiyek 56 
                                        + L G++ ++G++  +k+k+ +    ++l++ + ++l d+++  +r+  + ++ ++
  gi|242398902|ref|YP_002994326.1| 773 FGKLLGYYVSEGYAGAQKNKTDGisysVKLYNENPNILGDMKNAAERFFGKVRVGKN 829
                                       56799***************99999***********************665555555 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 5.1e-08
                                       HHHHHHHHHCCECCECSTTTTSEEEEES-HHHHHHHHHHHHHCT.HS CS
                       LAGLIDADG_3   5 afLrGlfdaDGsvskskkkgvsisltssskelledvqrlLlrlGIes 51 
                                       afL ++f++DG v  sk+    ++l+++s+ l++++   L+ lG+ s
  gi|242398902|ref|YP_002994326.1| 869 AFLEAYFAGDGDVHPSKR----LRLSTKSELLANQLIFFLNSLGVSS 911
                                       8****************7....9*********************977 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 !   37.2   0.0   1.2e-12   2.5e-09      11     169 ..     157     324 ..     154     338 .. 0.80

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 1.2e-12
                    DNA_pol_B_exo2  11 vvaisvvkarkdekfkvksl....geeessekelikkffegvekkkpq.lVsfngrgfDlpvleyralkhgvsapky 82 
                                       ++ is +  +    ++ k++     +  s+e+e+ik+f++++++k p  ++++ng +fDlp l  ra k g++    
  gi|242398902|ref|YP_002994326.1| 157 IIMISYADEEGARVITWKNIdlpyVDVVSNEREMIKRFIQIIKEKDPDvIITYNGDNFDLPYLIKRAEKLGLRLILS 233
                                       666777755555555555554454455668****************97368****************9999998777 PP

                    DNA_pol_B_exo2  83 fdegded..rekkwnnylsrystr.hlDLmdllseygaranakLdelakllglPGKlgvdGskVaelyqegk.lkei 155
                                        d+++     +   n++    + r h+DL  ++ +  +  +  L+ + +++    K  + ++++a+++++++ lk++
  gi|242398902|ref|YP_002994326.1| 234 RDNENPVpkIQRMGNSFAVEIKGRiHFDLFPVVKRAVNLPTYTLEAVYETVLGKHKSKLGAEEIAAIWETEEgLKKL 310
                                       7777655633444467777888889**********999999****99988877789999*********976549*** PP

                    DNA_pol_B_exo2 156 reYcetDvlnTYlv 169
                                       ++Y + D+  TY +
  gi|242398902|ref|YP_002994326.1| 311 AQYSMEDAKATYEL 324
                                       ***********965 PP

>> RNase_H_2  RNase_H superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.1   2.4e-09   4.8e-06       2     161 ..     139     324 ..     138     328 .. 0.75

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 2.4e-09
                         RNase_H_2   2 ffDiEt...tGlspkknliyliGvldvdekeiek....ltqllaeepeeekailelflellekk..kalvtfngksF 69 
                                        fDiEt   +G + +k+ i++i+++d ++ ++++       +++   +e++ i++++ +++++k  + ++t+ng +F
  gi|242398902|ref|YP_002994326.1| 139 AFDIETfyhEGDEFGKGEIIMISYADEEGARVITwkniDLPYVDVVSNEREMIKRFI-QIIKEKdpDVIITYNGDNF 214
                                       699997433455666799*******99999888845442236666667777777755.5555553377********* PP

                         RNase_H_2  70 Dvpflkrlfkkyklde........................eefrhiDLlkelrkkkl.esysLksvekelgierree 121
                                       D+p+l ++++k  l+                         + + h+DL+ +++++++   y L++v + +  + +  
  gi|242398902|ref|YP_002994326.1| 215 DLPYLIKRAEKLGLRLilsrdnenpvpkiqrmgnsfaveiKGRIHFDLFPVVKRAVNlPTYTLEAVYETVLGKHK-S 290
                                       *********6666666666667777777999998888877777*********997777888****9777666665.5 PP

                         RNase_H_2 122 dlsGsqavklyqeylrtgdeellekilaYNedDvralatl 161
                                       +l  ++++++++       ee l+k+++Y  +D  a++ l
  gi|242398902|ref|YP_002994326.1| 291 KLGAEEIAAIWE------TEEGLKKLAQYSMEDAKATYEL 324
                                       899999999986......4677888888888888888776 PP

>> DUF2816  Protein of unknown function (DUF2816)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1      0.63   1.3e+03       4      21 ..     468     485 ..     466     489 .. 0.86
   2 !   13.1   0.1   3.3e-05     0.066      37      59 ..    1095    1117 ..    1090    1120 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.63
                           DUF2816   4 eetkveyvPkerkvtDYy 21 
                                       +e k ++ P+++k+ DY 
  gi|242398902|ref|YP_002994326.1| 468 KEMKSTIDPIKKKMLDYR 485
                                       67788999*********5 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 3.3e-05
                           DUF2816   37 krieYvPveryderveYqpvers 59  
                                         r+e+vP+e+  erv+Y   e++
  gi|242398902|ref|YP_002994326.1| 1095 GRVEFVPIEKLFERVDYRLGEKE 1117
                                        58***************977765 PP

>> DUF4455  Domain of unknown function (DUF4455)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   2.2e-05     0.044     253     339 ..     444     531 ..     442     537 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.2e-05
                           DUF4455 253 lneqidelhaqflekLreeyeevwqecleeveklkkeLldlkv.cseeeaeklvneellplvgklqrkaeeelekld 328
                                       ++++   ++  +le+L e  +++++e  +++  +kk++ld++    +  a++++ +e lp++++   k+ +  e +d
  gi|242398902|ref|YP_002994326.1| 444 FCKDFSGFIPSILEDLIETRQKIKKEMKSTIDPIKKKMLDYRQrAVKLLANSILPNEWLPIIENEEIKFVKIGEFID 520
                                       7899999999********************************96666777*************************** PP

                           DUF4455 329 ksleelakete 339
                                        ++ee++ + +
  gi|242398902|ref|YP_002994326.1| 521 RYMEEQKDRVR 531
                                       ******98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1469 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.97u 0.31s 00:00:01.28 Elapsed: 00:00:00.48
# Mc/sec: 9278.25
//
Query:       gi|242398903|ref|YP_002994327.1|  [L=190]
Description: Dephospho-CoA kinase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.9e-20   73.7   0.0    2.8e-20   73.1   0.0    1.2  1  AAA_17      AAA domain
    9.9e-11   42.3   0.0    1.8e-10   41.5   0.0    1.4  1  AAA_18      AAA domain
      4e-07   30.3   0.0    4.6e-07   30.1   0.0    1.1  1  ADK         Adenylate kinase
    0.00035   20.8   0.1      0.001   19.2   0.0    1.8  2  AAA_33      AAA domain
  ------ inclusion threshold ------
      0.079   12.2   0.0       0.13   11.5   0.0    1.4  1  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 !   73.1   0.0   7.9e-24   2.8e-20       1     131 [.       6     132 ..       6     137 .. 0.82

  Alignments for each domain:
  == domain 1  score: 73.1 bits;  conditional E-value: 7.9e-24
                                       EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHH.....HHHH.HS CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrgglakardemrklpleekkelqkeaaeki.....aeea.kk 71 
                                       +G+PGsGKg ++ ++  kyg++h+s+Gd++reea r+g  ++ + m+ ++++ ++el ++a +k+     +e    +
  gi|242398903|ref|YP_002994327.1|   6 VGMPGSGKGQIV-RIFGKYGIPHVSMGDIVREEADRRGVPRTPEGMNSVSIQLRQELGDNAVAKLaipkvRELLkTH 81 
                                       7********777.*************************999999999887777777766555555222115554466 PP

                                       SEEEEEE-SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHHTTST-TS-S CS
                            AAA_17  72 kgvlvdghprikeqagfldglpkevleelkpdaiilleadpeeilerrlkdrtrgrdddn 131
                                       + v+++g  +++e + f d +p+   e++   +ii ++ +p++ +er+ k   rgr+dd 
  gi|242398903|ref|YP_002994327.1|  82 EAVIIEGVRSLDEIQAFKDAFPE---EKV---IIIAVHSSPQKRFERLSK---RGRSDDP 132
                                       779*********99999999998...466...89********99999987...6777774 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.5   0.0   4.9e-14   1.8e-10       1     129 [.       3     143 ..       3     144 .. 0.77

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 4.9e-14
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....gvnlrdvakenglllevdpealdeskrldedkldklldaleenss... 69 
                                       I++ G+pG+GK ++ +   k  g+     g+++r+ a  +g   + +    + s +l+++  d+++ +l    +   
  gi|242398903|ref|YP_002994327.1|   3 ICVVGMPGSGKGQIVRIFGKY-GIphvsmGDIVREEADRRGVPRTPEGM-NSVSIQLRQELGDNAVAKL----Aipk 73 
                                       9*****************997.678667777777777777777666666.3444444444444444444....3344 PP

                            AAA_18  70 ...aleegknlvidghlaeleseaakdikk......vvLtaspeelleRlekRgyeeakik.eneeaeil 129
                                           l  ++ ++i+g+++  e  a+kd+        + ++ sp++++eRl+kRg++++ ++  + ea+++
  gi|242398903|ref|YP_002994327.1|  74 vreLLKTHEAVIIEGVRSLDEIQAFKDAFPeekviiIAVHSSPQKRFERLSKRGRSDDPKSwSEFEARDW 143
                                       677888999******************999************************8875544577777776 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.0   1.3e-10   4.6e-07       1     123 [.       5     139 ..       5     186 .. 0.68

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 1.3e-10
                                       EEESTTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHHCT....-HHHHHHHHHHHTTSS--HHHHHHHHHHHHHCH.G CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x RF
                               ADK   1 llGaPgaGKGtqaeklvkkyglahlstGdllRaevksg....telGkeakevmdkgelvpdevvvklvkeeleke.d 72 
                                       ++G Pg+GKG q  ++  kyg++h+s Gd++R+e  +     t+ G +  ++ +  + + d+ v kl   ++++  +
  gi|242398903|ref|YP_002994327.1|   5 VVGMPGSGKG-QIVRIFGKYGIPHVSMGDIVREEADRRgvprTPEGMNSVSI-QLRQELGDNAVAKLAIPKVRELlK 79 
                                       69********.7889******************9965323226777665554.555556888888998888888877 PP

                                       TTTEEEEESB-SSHHHHHHHHHHHHHHTSEESEEEEEE--HHHHHHHHHT.............G CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............x RF
                               ADK  73 kkkgfllDGfPRtveqaealeelleeekvkldlvleldvpeevlveRltg.............D 123
                                       +++  +++G  R++++ +a+++ + eekv   +++ ++ + +   eRl++             +
  gi|242398903|ref|YP_002994327.1|  80 THEAVIIEGV-RSLDEIQAFKDAFPEEKV---IIIAVHSSPQKRFERLSKrgrsddpkswsefE 139
                                       8888999995.999999999985544433...44555555566666776666665555555550 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   2.9e-07     0.001       2     125 ..       3     133 ..       2     149 .. 0.67
   2 ?   -3.2   0.0       2.4   8.5e+03     130     143 .]     164     177 ..     161     185 .. 0.61

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 2.9e-07
                            AAA_33   2 vllvGlpGsGKstlaerllkklgavllssdtlrr.rlfgtdqqskt.........dytrvldr.lyqilnelarkal 67 
                                       + +vG+pGsGK + ++ +  k g  ++s  ++ r     ++++++           ++++ d+ + +     +r+ l
  gi|242398903|ref|YP_002994327.1|   3 ICVVGMPGSGKGQIVR-IFGKYGIPHVSMGDIVReEADRRGVPRTPegmnsvsiqLRQELGDNaVAKLAIPKVRELL 78 
                                       789***********98.577999777776554431333333332222333333334444555534444446666666 PP

                            AAA_33  68 sagrnvildatnlsrrerarflklarrlgvpvrivvvetdeetlkeRlakRaangddr 125
                                       +   +vi+  + +s +e ++f  ++++   +v i++v++++++  eRl kR ++ d +
  gi|242398903|ref|YP_002994327.1|  79 KTHEAVII-EGVRSLDEIQAFKDAFPEE--KVIIIAVHSSPQKRFERLSKRGRSDDPK 133
                                       66666666.689999***********55..589********************75433 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2.4
                            AAA_33 130 eealdrqkarferp 143
                                       e++l ++++++er+
  gi|242398903|ref|YP_002994327.1| 164 ESHLTQYRRKIERL 177
                                       55555555555553 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   3.6e-05      0.13      18     134 ..       2     117 ..       1     141 [. 0.76

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.6e-05
                        Zeta_toxin  18 lillgGqpGAGKselaellkdele...rqgnvvrldpDdlRelhPeyeeilka.dpkkaseltqkdaselvekllqe 90 
                                       +i ++G pG+GK+++ + + ++     + g++vr ++D  R+  P+  e ++    +   el ++++ +l+   + e
  gi|242398903|ref|YP_002994327.1|   2 IICVVGMPGSGKGQIVRIFGKYGIphvSMGDIVREEAD--RRGVPRTPEGMNSvSIQLRQELGDNAVAKLAIPKVRE 76 
                                       6889****************998866677777777777..7889999998887355556677788888999999999 PP

                        Zeta_toxin  91 aiengyniivegtlrspdvvkklaealkkaGYevevvvvavkke 134
                                       +++    +i+eg  rs d+++ +++a+ +   +v +++v  +++
  gi|242398903|ref|YP_002994327.1|  77 LLKTHEAVIIEGV-RSLDEIQAFKDAFPE--EKVIIIAVHSSPQ 117
                                       9999999999985.888888888888887..3555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      583  (0.0325172); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1291.18
//
Query:       gi|242398904|ref|YP_002994328.1|  [L=744]
Description: ski2-type helicase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.8e-25   88.3   0.0    1.7e-24   86.5   0.0    1.9  2  DEAD             DEAD/DEAH box helicase
    3.5e-12   46.7   0.1    7.6e-10   39.1   0.0    3.3  2  Helicase_C       Helicase conserved C-terminal domain
    7.7e-11   42.3   0.0    2.5e-10   40.6   0.0    1.9  2  ResIII           Type III restriction enzyme, res subunit
    3.2e-09   37.2   0.5    2.2e-08   34.6   0.2    2.6  2  HHH_5            Helix-hairpin-helix domain
    1.3e-05   25.2   0.2    8.6e-05   22.6   0.0    2.6  3  HHH_2            Helix-hairpin-helix motif
    0.00075   19.2   0.1       0.17   11.8   0.1    3.0  2  HHH              Helix-hairpin-helix motif
    0.00097   18.9   0.0     0.0036   17.1   0.0    1.9  1  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
  ------ inclusion threshold ------
      0.029   14.6   0.0      0.068   13.4   0.0    1.7  1  Cdd1             Pathogenicity locus


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.5   0.0   7.8e-28   1.7e-24       4     170 ..      51     203 ..      48     208 .. 0.86
   2 ?   -2.2   0.0       1.3     3e+03      98     116 ..     418     436 ..     386     446 .. 0.65

  Alignments for each domain:
  == domain 1  score: 86.5 bits;  conditional E-value: 7.8e-28
                                       HHHHHH.HHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEE CS
                                       xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   4 Qaeaip.lilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvl 79 
                                       Qa a++ ++l+g+++++a++T+sGKTl++ i ++++++    ++g k+++++P+++Lae+ ++++k + k +++r+ 
  gi|242398904|ref|YP_002994328.1|  51 QADALKtEVLKGKNLVLAIPTASGKTLVAEIVMINKIL----REGGKTVYLVPLKALAEEKYKEFKFWEK-LGIRIA 122
                                       6666651577***************************5....6899*******************87777.788887 PP

                                       EEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  80 liiggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdg 156
                                       +++g  ++++  + l  ++di+++t +++d+ll+ ++  ++++++++ DE++ l + +++ +++ il++l     d 
  gi|242398904|ref|YP_002994328.1| 123 MTTG--DYDSTEEWL-GKYDIIIATSEKFDSLLRHKSPWIKDINLVIADEIHLLGSYDRGATLEMILAHL-----DD 191
                                       5555..455677777.88***************877777*******************************.....44 PP

                                       TTTSEEEEEESSBS CS
                                       xxxxxxxxxxxxxx RF
                              DEAD 157 klqrqvivlSATlp 170
                                       k   q++ lSAT+ 
  gi|242398904|ref|YP_002994328.1| 192 K--AQILGLSATVG 203
                                       5..45*******86 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.3
                                       CSEEEEEHHHHHHHHHCTS CS
                                       xxxxxxxxxxxxxxxxxxx RF
                              DEAD  98 vdivvgtpgrlddllstgk 116
                                        ++v+g p++l+++ls++ 
  gi|242398904|ref|YP_002994328.1| 418 KRYVLGKPEKLFSMLSNEA 436
                                       4579999999999997655 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.064   1.4e+02       6      74 ..      84     145 ..      76     167 .. 0.70
   2 !   39.1   0.0   3.4e-13   7.6e-10       9     110 ..     257     396 ..     249     397 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.064
                                       HHHHHHHTTTTSEEEEEESSHHHHHH.HHHHHHHT....TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESG CS
                        Helicase_C   6 llellkleeeggkilifvntidrlek.vklllekk....gikvavlhgelpqnereeileqfnkgesdvLiatd 74 
                                       + ++l   +eggk++  v+ +  +e+  k +  k+    gi++a+ +g+      + + e    g++d++iat+
  gi|242398904|ref|YP_002994328.1|  84 INKIL---REGGKTVYLVPLKALAEEkYKEF--KFweklGIRIAMTTGDY-----DSTEEWL--GKYDIIIATS 145
                                       44444...89999999999999776554444..33334588887777754.....4444444..6667777765 PP

  == domain 2  score: 39.1 bits;  conditional E-value: 3.4e-13
                                       HHHHTTTTSEEEEEESSHHHHHHHHHH...............................HHHT....TSTEEEESTTS CS
                        Helicase_C   9 llkleeeggkilifvntidrlekvkll...............................lekk....gikvavlhgel 50 
                                            ++g+++l+fvnt++++ek  ll                               +          va +h+ l
  gi|242398904|ref|YP_002994328.1| 257 A---LKKGKQALVFVNTRRSAEKEALLlagkiqrfltkpeerklkqladgldttptnqK--LkealTKGVAFHHAGL 328
                                       3...489************9988344445555555677777776777777777765541..14456889999999** PP

                                       THHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEEESSSSSSH........HHHHHHHTTSSST CS
                        Helicase_C  51 pqnereeileqfnkgesdvLiatdvaerGidipkvnlVinfdlprnv........tsyiqriGRtgRa 110
                                          er  i ++f++g ++v+ at  ++ G+++p  +++i+    ++          +++q++GR+gR 
  gi|242398904|ref|YP_002994328.1| 329 GRTERSIIEDAFREGLIKVITATPTLSAGVNLPAYRVIIRDTKRYSNfgwvdipvLEIQQMMGRAGRP 396
                                       *********************************8888885555533223334444************5 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 !   40.6   0.0   1.1e-13   2.5e-10       5     169 ..      48     202 ..      40     204 .. 0.84
   2 ?   -3.2   0.0       3.2   7.1e+03      45      93 ..     417     471 ..     415     504 .. 0.55

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 1.1e-13
                                       -HHHHHHHHHHT......TTSEEEEEESTTSTHHHHH.HHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG CS
                            ResIII   5 reyQeeaienlleklkskrdkrglikmaTGtGKTlva.aklierllkkgkeekflflvprkslleqtleefkkflse 80 
                                       ++ Q++a++  +      + k+++++++T +GKTlva + +i ++l++g+  k++ lvp k+l e  ++efk + + 
  gi|242398904|ref|YP_002994328.1|  48 YPPQADALKTEV-----LKGKNLVLAIPTASGKTLVAeIVMINKILREGG--KTVYLVPLKALAEEKYKEFKFWEKL 117
                                       556666665544.....3467999***********************999..9******************988887 PP

                                       ....GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T...TTHHHH CS
                            ResIII  81 aykeigkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk...swreil 154
                                               ++gd ++  e+   + +i+++t +++d+ +      +++   + ++++i DE H lg+ +   + + il
  gi|242398904|ref|YP_002994328.1| 118 GI--RIAMTTGDYDST-EEWLGKYDIIIATSEKFDSLL-----RHKSPWIKDINLVIADEIHLLGSYDrgaTLEMIL 186
                                       74..445555555555.8899*****************.....78888899999***********984455899998 PP

                                       HT-.--SEEEEEESS- CS
                            ResIII 155 ekf.keavllglTATp 169
                                        ++ ++a +lgl+AT 
  gi|242398904|ref|YP_002994328.1| 187 AHLdDKAQILGLSATV 202
                                       888456999******6 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3.2
                                       HHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG.........GEEE.ESSS- CS
                            ResIII  45 ierllkkgkeekflflvprkslleqtleefkkflseayke.....igkk.vsgdk 93 
                                       ++r+   ++e+ f +l ++ s  +q l  +++f   ++ke     + ++ ++++k
  gi|242398904|ref|YP_002994328.1| 417 MKRYVLGKPEKLFSMLSNEASFRSQVLALITNFGVGNFKElvnflERTFyYHQRK 471
                                       5666666666667777777777777777777776666666444442222122222 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       3.1   6.9e+03      13      30 ..     593     609 ..     592     624 .. 0.73
   2 !   34.6   0.2   9.6e-12   2.2e-08       3      52 ..     669     718 ..     667     721 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 3.1
                                       HHHHHHHTTT--SHHHHH CS
                             HHH_5  13 ktAlallsaGiesvedla 30 
                                       ktA+ ll+  i+ v d++
  gi|242398904|ref|YP_002994328.1| 593 KTAKLLLDW-INEVNDVK 609
                                       899999999.99998874 PP

  == domain 2  score: 34.6 bits;  conditional E-value: 9.6e-12
                                       HHHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHH CS
                             HHH_5   3 eLlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAerii 52 
                                       eL++++ iG+k+A+al++aG++ ++d+++a + eL k+ GiG    e+i 
  gi|242398904|ref|YP_002994328.1| 669 ELITLPMIGRKRARALYNAGFKGIDDIVRAKASELLKVEGIGIGVIEKIY 718
                                       89****************************************88888876 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.1       7.3   1.6e+04      40      52 ..     159     171 ..     159     171 .. 0.88
   2 ?   -3.5   0.0       5.1   1.1e+04      48      62 ..     282     296 ..     281     297 .. 0.85
   3 !   22.6   0.0   3.9e-08   8.6e-05       7      56 ..     672     722 ..     666     728 .. 0.90

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 7.3
                             HHH_2  40 vddiGeeiAqsiv 52 
                                       ++di  +iA++i+
  gi|242398904|ref|YP_002994328.1| 159 IKDINLVIADEIH 171
                                       789999****997 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 5.1
                             HHH_2  48 AqsivefFeneknre 62 
                                       A +i++f+++++ r+
  gi|242398904|ref|YP_002994328.1| 282 AGKIQRFLTKPEERK 296
                                       7899******99887 PP

  == domain 3  score: 22.6 bits;  conditional E-value: 3.9e-08
                             HHH_2   7 GIrhVGektAklLakr.FksldaLkkasleeLlevddiGeeiAqsivefFe 56 
                                        ++ +G k A++L ++ Fk +d + +a++ eLl+v++iG  + ++i++ F 
  gi|242398904|ref|YP_002994328.1| 672 TLPMIGRKRARALYNAgFKGIDDIVRAKASELLKVEGIGIGVIEKIYQHFG 722
                                       5789*********9866******************************9996 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0      0.02        46      12      28 ..     669     685 ..     669     687 .. 0.88
   2 !   11.8   0.1   7.5e-05      0.17       3      29 ..     693     719 ..     691     720 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.02
                                       HHHTSTT-SHHHHHHHH CS
                               HHH  12 eLlalPGVGpktAeaIl 28 
                                       eL +lP +G+k+A+a +
  gi|242398904|ref|YP_002994328.1| 669 ELITLPMIGRKRARALY 685
                                       7899999*******986 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 7.5e-05
                                       HHHHTSSHHHHHTSTT-SHHHHHHHHH CS
                               HHH   3 eglipasreeLlalPGVGpktAeaIls 29 
                                       + ++ a   eLl+++G+G  + e+I++
  gi|242398904|ref|YP_002994328.1| 693 DDIVRAKASELLKVEGIGIGVIEKIYQ 719
                                       78999*************999999976 PP

>> DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.6e-06    0.0036       9      43 ..     676     711 ..     675     717 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.6e-06
                   DNA_pol_lambd_f   9 VGpktAkkwyakGirtledlra.krakLtreqqiGl 43 
                                       +G+k+A+ +y++G++ ++d+++ k ++L ++  iG+
  gi|242398904|ref|YP_002994328.1| 676 IGRKRARALYNAGFKGIDDIVRaKASELLKVEGIGI 711
                                       7*********************87788888777776 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0     3e-05     0.068       2      42 ..     664     704 ..     663     710 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3e-05
                              Cdd1   2 rkalkelqdiPniGkalaedlvelGirsveelkgedpeely 42 
                                       r++l el ++P iG++ a+ l++ G++ ++++ + ++ el 
  gi|242398904|ref|YP_002994328.1| 664 REELLELITLPMIGRKRARALYNAGFKGIDDIVRAKASELL 704
                                       578899****************************9999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (744 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         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: 00:00:00.50
# Mc/sec: 4438.67
//
Query:       gi|242398905|ref|YP_002994329.1|  [L=196]
Description: hypothetical protein TSIB_0922 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.11   12.1   0.4       0.17   11.5   0.4    1.2  1  DUF2027   Domain of unknown function (DUF2027)


Domain annotation for each model (and alignments):
>> DUF2027  Domain of unknown function (DUF2027)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.4   9.3e-06      0.17      52     112 ..      10      71 ..       8      80 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 9.3e-06
                           DUF2027  52 vepntkl.lleefekeelnelervavQliaykkdksfalkpavdvelridtvkfyKlhtFke 112
                                       +e n +l +++ + +++++++e+v+v +  +k+d + + ++++   +  +++kf+  + F+ 
  gi|242398905|ref|YP_002994329.1|  10 IEVNRRLfMIDAYFSKKVEKIEHVSVLIKRFKRDLPREAQNPLPSLITENEIKFFLKNVFST 71 
                                       6777776257999*****************************************99999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       663  (0.0369792); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); 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: 00:00:00.41
# Mc/sec: 1424.01
//
Query:       gi|242398906|ref|YP_002994330.1|  [L=46]
Description: ABC-type dipeptide transport system, ATPase component [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       184  (0.0102627); expected 358.6 (0.02)
Passed bias filter:                      143  (0.0079759); 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: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 303.44
//
Query:       gi|242398907|ref|YP_002994331.1|  [L=204]
Description: ABC-type dipeptide transport system, ATPase component [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.2e-21   76.9   0.1    2.8e-21   75.8   0.1    1.7  2  oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal reg
    1.6e-10   41.6   0.0    2.4e-10   41.0   0.0    1.3  1  ABC_tran   ABC transporter
    3.5e-06   27.0   0.0    4.2e-06   26.8   0.0    1.1  1  AAA_21     AAA domain, putative AbiEii toxin, Type IV TA syst
  ------ inclusion threshold ------
      0.031   12.9   0.1       0.21   10.2   0.0    1.9  2  AAA_13     AAA domain
      0.032   13.7   0.0      0.041   13.3   0.0    1.1  1  SMC_N      RecF/RecN/SMC N terminal domain


Domain annotation for each model (and alignments):
>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       3.3   1.2e+04      21      33 ..      20      32 ..      18      41 .. 0.71
   2 !   75.8   0.1   7.9e-25   2.8e-21       1      65 []     119     183 ..     119     183 .. 0.99

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3.3
                         oligo_HPY 21 Llrsvprldrekd 33
                                      +lrsv  +d+ek+
  gi|242398907|ref|YP_002994331.1| 20 ILRSVLIPDAEKR 32
                                      5788888888888 PP

  == domain 2  score: 75.8 bits;  conditional E-value: 7.9e-25
                         oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekdklekikgeapslerldeGCpFapRCpfaleeC 65 
                                       vE+g++ ++f++plHPYTk+Ll++vp +  + ++le i+g++p+l   +eGC+F+pRCp+a+e+C
  gi|242398907|ref|YP_002994331.1| 119 VEIGSVGQIFKNPLHPYTKGLLKAVPNPMVKSERLEAIPGTVPNLITPPEGCRFHPRCPYATEIC 183
                                       8**************************************************************** PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0   0.0   6.8e-14   2.4e-10      84     136 ..      16      67 ..       2      68 .. 0.85

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 6.8e-14
                                       CHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  84 eiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       ++ ++l+++ +++ ++++v++ p++LSgG+kqrv++  +++++pk+l++DEpt
  gi|242398907|ref|YP_002994331.1|  16 KAIEILRSVLIPD-AEKRVQNYPHELSGGMKQRVVIGTSIANDPKILVADEPT 67 
                                       4677888888888.66667799******************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.0   1.2e-09   4.2e-06     233     302 ..      36     103 ..       3     104 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 1.2e-09
                            AAA_21 233 parelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSplll 302
                                        ++elS G+k+   + t+++ ++   ++l+ DEp + L+  +++ +l+l++el++   a vil TH+  ++
  gi|242398907|ref|YP_002994331.1|  36 YPHELSGGMKQRVVIGTSIANDP---KILVADEPTTALDVTVQAQILDLINELKErYHATVILITHNLGVV 103
                                       57889*****9989999999988...9***********************666666***********8876 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0     0.046   1.7e+02     383     420 ..       5      42 ..       3      50 .. 0.88
   2 ?   10.2   0.0   5.9e-05      0.21     525     577 ..      56     106 ..      49     117 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.046
                            AAA_13 383 ekvanleeekeeakkklelhlveeleseldeykkkykk 420
                                       ++++n++e  ++a + l+  l+ ++e+ +++y +++++
  gi|242398907|ref|YP_002994331.1|   5 QRIKNIKEGIKKAIEILRSVLIPDAEKRVQNYPHELSG 42 
                                       57999***************************988765 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 5.9e-05
                            AAA_13 525 gkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleffkev 577
                                       +  ki v D P   LD +++  +  li++    +   + +++ THnl    e 
  gi|242398907|ref|YP_002994331.1|  56 NDPKILVADEPTTALDVTVQAQILDLINELK--ERYHATVILITHNLGVVAET 106
                                       5689*************************97..5666789999***9877665 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 ?   13.3   0.0   1.1e-05     0.041     136     216 ..      39     117 ..       8     120 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.1e-05
                                       CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHHHCCC-SCEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn..aQfivislreemlekadklvg 210
                                       +LSgG k+ v +        ++   + + De   aLD +  +++ +l++e +++  a +i i+++ +++++    vg
  gi|242398907|ref|YP_002994331.1|  39 ELSGGMKQRVVIGT----SIANDPKILVADEPTTALDVTVQAQILDLINELKERyhATVILITHNLGVVAETADRVG 111
                                       56777666444433....33344457889********************8877655999*********999999999 PP

                                       EEEEET CS
                                       xxxxxx RF
                             SMC_N 211 vtkven 216
                                       v+ +e+
  gi|242398907|ref|YP_002994331.1| 112 VMYAEK 117
                                       988554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       664  (0.037035); expected 358.6 (0.02)
Passed bias filter:                      601  (0.0335211); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 1424.52
//
Query:       gi|242398908|ref|YP_002994332.1|  [L=192]
Description: peptide ABC trsnaposrter substrate-binding protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 1328.51
//
Query:       gi|242398909|ref|YP_002994333.1|  [L=79]
Description: Transcriptional regulatory protein, asnC family [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-12   47.5   0.3    1.4e-12   47.3   0.3    1.0  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
     0.0015   18.5   0.5     0.0035   17.4   0.4    1.5  1  NapD            NapD protein


Domain annotation for each model (and alignments):
>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.3   0.3   1.6e-16   1.4e-12       1      75 []       6      77 ..       6      77 .. 0.95

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 1.6e-16
                                      EEEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEEE CS
                    AsnC_trans_reg  1 vlvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivlet 75
                                      vl+++e g+   +e+++  ++++  V+ + +vtG+yd +++  + dl +l r + + +++++gv +t+t iv et
  gi|242398909|ref|YP_002994333.1|  6 VLLTIEIGK---VERVIGDIKTISGVIKADAVTGPYDAIVELEASDLGELTRKILHDIHNIDGVIDTTTAIVVET 77
                                      677888899...9***********************************************************986 PP

>> NapD  NapD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.4   3.9e-07    0.0035       8      68 ..       8      70 ..       6      74 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.9e-07
                              NapD  8 VqarperlaavkaalaalpgvEvh.asdeegklVvviEaesedeladti.eaiealpgVlsas 68
                                        +  +++++v  +++++ gv  + a+++    +v +Ea++ +el+++i ++i++++gV++++
  gi|242398909|ref|YP_002994333.1|  8 LTIEIGKVERVIGDIKTISGVIKAdAVTGPYDAIVELEASDLGELTRKIlHDIHNIDGVIDTT 70
                                      567889999999******9995551445559************999876156********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.33s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 503.06
//
Query:       gi|242398910|ref|YP_002994334.1|  [L=105]
Description: Signal recognition particle 19 kDa protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-12   47.8   0.2    2.4e-12   47.6   0.2    1.1  1  SRP19     SRP19 protein


Domain annotation for each model (and alignments):
>> SRP19  SRP19 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.6   0.2   1.4e-16   2.4e-12       1      80 [.       8      94 ..       8     104 .. 0.78

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 1.4e-16
                                      EEECCCCBTTS-CCCT--S-CCCSBSS--HHHHHHHHHHCTSCEE.EEEEECTTSS......TTCCEEEEEC-...... CS
                             SRP19  1 viYPvYldskktrkeGRrvpkelavenPtaqeiaealkalglevv.vepeksyPrd......wanpGrVrvklkedgke 72
                                      vi+ + +d++  rk GR vpk+lav++P+++ei ea++al+l+++ +++e   Pr          +Gr+ v+ ++ +++
  gi|242398910|ref|YP_002994334.1|  8 VIWVNEIDARIPRKYGREVPKNLAVDRPSLEEILEAAQALRLNIInIDREALNPRVsaldenLRVNGRIVVESNHGKSK 86
                                      79*****************************************9999********954333322449999998533333 PP

                                      ....SS-C CS
                             SRP19 73 vnekiknk 80
                                      + + i++k
  gi|242398910|ref|YP_002994334.1| 87 TLKLITQK 94
                                      33333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 699.94
//
Query:       gi|242398911|ref|YP_002994335.1|  [L=205]
Description: Biotin synthetase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-07   31.3   0.9    6.9e-07   29.3   0.9    1.8  1  DUF257    Pyrococcus protein of unknown function, DUF257


Domain annotation for each model (and alignments):
>> DUF257  Pyrococcus protein of unknown function, DUF257
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.9   3.8e-11   6.9e-07       4     189 ..      12     201 ..       8     205 .] 0.76

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 3.8e-11
                            DUF257   4 etlrpGetvLiEysss.svpevllyliakyskeknvPllvdDvl...Dt.llivlkhlkllGldvpe...esikviK 72 
                                       +++  G+ vLiEy ss s++++l  +++    +k   +l+dD +   D  +  +l++      +  +   ++   i+
  gi|242398911|ref|YP_002994335.1|  12 KNVTLGDFVLIEYPSSySITKLLWGELVPEISQKE--VLIDDFFgigDLlFRGYLRKTPPEEYKKAMeitKNLRAIR 86 
                                       57899********7651677888888987777888..9****99433432345666664444443331136999*** PP

                            DUF257  73 ig.Gtkevgnvvkkidfdkdpsiylskykravekvsve.etv.inlvlglerllllldnrrdlyklvksikkylgnk 146
                                       ig G  +   + ++i+   ++s ++++y++a+ k+    ++v   + lg+ + + +  ++  l k +   ++ l  +
  gi|242398911|ref|YP_002994335.1|  87 IGvGRTSYTSIAEEIPITYEVSEFMKNYYNALMKLFSVsTKVeYSITLGVSQYIYFGGEKA-L-KAILFTRSTLPFE 161
                                       *978****************************99865524446899******999876553.3.3567778888899 PP

                            DUF257 147 nRkafylinrnllesikPellplLEeiassvieiesekealiv 189
                                         +++y++n+++l++ +   l+ L e a   ++i+ e++a  +
  gi|242398911|ref|YP_002994335.1| 162 DWTSIYFVNKDILDERQ---LAILRELANWRLKIKREESAYKM 201
                                       99*************99...88888888888888777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.48
# Mc/sec: 1276.80
//
Query:       gi|242398912|ref|YP_002994336.1|  [L=253]
Description: SAM-dependent methyltransferase, [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-27   96.8   0.0    9.1e-26   91.0   0.0    2.0  2  GCD14            tRNA methyltransferase complex GCD14 subunit
    1.5e-11   44.5   0.0      2e-11   44.0   0.0    1.1  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    1.2e-10   41.4   0.0    1.6e-10   41.0   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    9.4e-10   38.2   0.1    1.7e-09   37.4   0.1    1.4  1  GCD14_N          tRNA methyltransferase complex GCD14 subunit
    8.1e-07   29.7   0.0    1.5e-06   28.8   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
    1.9e-05   25.2   0.0    4.1e-05   24.2   0.0    1.6  1  Methyltransf_11  Methyltransferase domain
    0.00021   20.5   0.0    0.00031   19.9   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase
    0.00093   20.2   0.0     0.0015   19.5   0.0    1.3  1  Methyltransf_24  Methyltransferase domain
     0.0013   18.1   0.0     0.0022   17.4   0.0    1.4  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
     0.0013   18.4   0.0       0.22   11.2   0.0    2.1  2  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
      0.002   18.9   0.0     0.0054   17.5   0.0    1.7  1  Methyltransf_12  Methyltransferase domain
     0.0028   17.2   0.0      0.012   15.1   0.0    2.0  1  MTS              Methyltransferase small domain
     0.0059   15.8   0.0     0.0084   15.3   0.0    1.3  1  Methyltransf_3   O-methyltransferase
     0.0063   15.8   0.0     0.0084   15.4   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
  ------ inclusion threshold ------
      0.011   15.2   0.0       0.26   10.7   0.0    2.2  1  Methyltransf_4   Putative methyltransferase
      0.034   14.1   0.0      0.058   13.3   0.0    1.4  1  Methyltransf_18  Methyltransferase domain
      0.036   13.9   0.0       0.27   11.0   0.0    2.0  1  Methyltransf_23  Methyltransferase domain
       0.11   12.2   0.0          1    9.0   0.0    2.2  1  UPF0020          Putative RNA methylase family UPF0020
       0.11   13.5   0.3       0.35   11.9   0.1    1.8  2  PSK              Phytosulfokine precursor protein (PSK)


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 !   91.0   0.0   9.6e-29   9.1e-26      21     182 ..      74     232 ..      66     235 .. 0.93
   2 ?    4.5   0.1     0.025        23     229     246 ..     234     251 ..     231     252 .. 0.87

  Alignments for each domain:
  == domain 1  score: 91.0 bits;  conditional E-value: 9.6e-29
                             GCD14  21 tqilytaDisliimkLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehelsqlvtvt 97 
                                        qi++ +D + i+    + pG  ++e+G Gsg+l+  +a  ++P G++  +e  e+ a+ a  + +  ++s+ v ++
  gi|242398912|ref|YP_002994336.1|  74 PQIIHPKDAAQIVAFAGISPGDIIIEAGVGSGALTLFLANIIGPNGKIIGYEIREDFAKLAWRNVEWAGFSDRVEIK 150
                                       59*************************************************************************** PP

                             GCD14  98 hrDvckeGfdeevsgkvDavfLDlPaPweaiphaakalkkeggrlCsfsPCieqvqrtceaLre..lgfteietlev 172
                                        rD+  eG +e+   +vD + LDlP+P + ++ha++ l k gg l +++PCi+qv r  ++++e  ++ft  +t+e 
  gi|242398912|ref|YP_002994336.1| 151 LRDIY-EGIEED---NVDHIILDLPQPENVVEHAVQSL-KPGGFLVAYTPCINQVDRFYKKINEykKHFTRPKTIEC 222
                                       ***96.799544...58*********************.89********************9972257********* PP

                             GCD14 173 llrtyevrks 182
                                       l+r+ e++k+
  gi|242398912|ref|YP_002994336.1| 223 LVREQEIKKE 232
                                       *****99986 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.025
                             GCD14 229 lkPvselkghtgyLtfat 246
                                       ++P +++ +htgy+tf +
  gi|242398912|ref|YP_002994336.1| 234 IRPRTTMLAHTGYITFVR 251
                                       69999***********87 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 !   44.0   0.0   2.2e-14     2e-11      50     188 ..      70     208 ..      56     221 .. 0.85

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 2.2e-14
                                       EETTEEE--HHHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTC.S CS
                              PCMT  50 igynatiSaphmvalalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldle.n 125
                                       +  +  i  p+  a ++ +  +++g+ ++e G GsG lt  la+++g++g++++ e  +++++ a rn++  + + +
  gi|242398912|ref|YP_002994336.1|  70 MKRGPQIIHPKDAAQIVAFAGISPGDIIIEAGVGSGALTLFLANIIGPNGKIIGYEIREDFAKLAWRNVEWAGFSdR 146
                                       556667888999999*********************************************************98879 PP

                                       EEEEES-GGGTTGGG-SEEEEEESS.BBSS--HHHHHTEEEEEEEEEEESBSSSEEEEEEEEET CS
                              PCMT 126 vivvvgDGrkGyeekaPYdaihvga.aapeiPealidQLkeGGrlvvPvgeeeeQvlklvdkka 188
                                       v ++  D ++G ee    d i++    ++++ e  ++ Lk+GG lv+      +Qv   ++k +
  gi|242398912|ref|YP_002994336.1| 147 VEIKLRDIYEGIEEDNV-DHIILDLpQPENVVEHAVQSLKPGGFLVAYTP-CINQVDRFYKKIN 208
                                       ************99875.6666665156789**************98554.5566666666655 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0   0.0   1.6e-13   1.6e-10       4     120 ..      94     205 ..      91     239 .. 0.84

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 1.6e-13
                   Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdiee.leklledekfDli 78 
                                       g  ++++G G+G+lt+ la  +gp+++++G +i e+  +lA  n +  g++ +ve +  di e +e+    +++D i
  gi|242398912|ref|YP_002994336.1|  94 GDIIIEAGVGSGALTLFLANIIGPNGKIIGYEIREDFAKLAWRNVEWAGFSdRVEIKLRDIYEgIEE----DNVDHI 166
                                       556899********************************************99***********9994....79***9 PP

                   Methyltransf_31  79 lsnevlnaladpdkileeiervlkpggilliedprllaelp...a 120
                                       +      +l+ p+++ e + + lkpgg l++ +p+   +++   +
  gi|242398912|ref|YP_002994336.1| 167 IL-----DLPQPENVVEHAVQSLKPGGFLVAYTPC-INQVDrfyK 205
                                       99.....59**********************9999.444432222 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 !   37.4   0.1   1.8e-12   1.7e-09       5      51 .]       3      48 ..       1      48 [. 0.94

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 1.8e-12
                           GCD14_N  5 raGdrVqLtDaKgrkhtitLepGgefhthrGaieHDdlIGrpeGsVV 51
                                      + Gd++ L D++g+++ +t ++G efht+ G+i+  dlIG++ G+V+
  gi|242398912|ref|YP_002994336.1|  3 KYGDKIVLLDPRGKRYLVTIKEG-EFHTDLGIINLSDLIGKEFGVVI 48
                                      68******************987.7********************97 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.0   1.5e-09   1.5e-06       1      97 []      97     188 ..      97     188 .. 0.90

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 1.5e-09
                                       EEEET-TTSHHHHHHHCTST.SSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEEESTG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlg.kakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvssgal 74 
                                       ++++G G+G ltl la+ +g ++k++g +i e++ + a +++e +g+  +ve+   d+ +  +e + +D +++    
  gi|242398912|ref|YP_002994336.1|  97 IIEAGVGSGALTLFLANIIGpNGKIIGYEIREDFAKLAWRNVEWAGFsdRVEIKLRDIYEGIEE-DNVDHIILD--- 169
                                       789**************99669********************99999***********886544.48*****93... PP

                                       GGSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  75 hhlsdedlekalkeiarvLkpgG 97 
                                         l  ++ e++++++ + LkpgG
  gi|242398912|ref|YP_002994336.1| 170 --L--PQPENVVEHAVQSLKPGG 188
                                       ..2..46779************9 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   4.3e-08   4.1e-05       2      95 ..      99     191 ..      98     192 .. 0.93

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 4.3e-08
                                       EET-TTSHHHHHHHHTT...SEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT-EEEEEEES-CCC CS
                   Methyltransf_11   2 dvGcGtGrlaealakrg...arvvgvDlskemlklakekaseegl..kvefvvadaeklpfednsfDlvvssevlhh 73 
                                       ++G+G+G+l+  la+     ++++g ++ + + kla ++++ +g+  +ve+   d+ +  +e++ +D +++      
  gi|242398912|ref|YP_002994336.1|  99 EAGVGSGALTLFLANIIgpnGKIIGYEIREDFAKLAWRNVEWAGFsdRVEIKLRDIYE-GIEEDNVDHIILD----- 169
                                       78************6667889************************9999999999998.9*********987..... PP

                                       -CCHHHHHHHHHHHEEEEEEEE CS
                   Methyltransf_11  74 vedpekalkeiaRvLkpgGllv 95 
                                       +++pe +++ +++ LkpgG+lv
  gi|242398912|ref|YP_002994336.1| 170 LPQPENVVEHAVQSLKPGGFLV 191
                                       6******************998 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   3.3e-07   0.00031      16      87 ..      79     156 ..      74     166 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 3.3e-07
                                       HHHHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-...SEEEEE-S-HHHHHHHHCHTT...TCCCEEEE-S-CC CS
                            RrnaAD  16 kkvineIldklnleekltvleigpGkGilTeeLakra...kqvvvlElderLakllqkkls...kdeklkvvhqDfl 86 
                                       +k +++I+  + +++ + ++e g G G+lT  La+++    +   +E++e++akl   +++    + ++++  +D++
  gi|242398912|ref|YP_002994336.1|  79 PKDAAQIVAFAGISPGDIIIEAGVGSGALTLFLANIIgpnGKIIGYEIREDFAKLAWRNVEwagFSDRVEIKLRDIY 155
                                       666789********************************9999*************9999998888889999999988 PP

                                       G CS
                            RrnaAD  87 k 87 
                                       +
  gi|242398912|ref|YP_002994336.1| 156 E 156
                                       5 PP

>> Methyltransf_24  Methyltransferase 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    0.0015       1     102 [.      98     191 ..      98     192 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.6e-06
                   Methyltransf_24   1 vEiGvysGvstlwllralrrngagrlvavdhdpgaeeaaalare....aglddrvrlikadseealaslaagsiDll 73 
                                       +E Gv sG  tl+l+  +  ng+  ++  +  +   ++a+la +    ag++drv++   d  e +++ +   +D +
  gi|242398912|ref|YP_002994336.1|  98 IEAGVGSGALTLFLANIIGPNGK--IIGYEIRE---DFAKLAWRnvewAGFSDRVEIKLRDIYEGIEEDN---VDHI 166
                                       699******************96..******99...666665555888*********9999999988877...**** PP

                   Methyltransf_24  74 fiDgghaaeavledleallprlapggvvl 102
                                       ++D +    +  + +e++ + l+pgg+++
  gi|242398912|ref|YP_002994336.1| 167 ILDLP----QPENVVEHAVQSLKPGGFLV 191
                                       ***99....5555667999999***9997 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   2.3e-06    0.0022      37     165 ..      83     206 ..      68     226 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.3e-06
                                       HHHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSS.TEEEEE--TTT-TT CS
                   Ubie_methyltran  37 kfveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegki.nieflqanaeeLpf 112
                                       + +    +  +g  +++   G+g l++ l++ +g +gk+++ +i e+  k + + ++  g++ ++e    +  e  +
  gi|242398912|ref|YP_002994336.1|  83 AQIVAFAGISPGDIIIEAGVGSGALTLFLANIIGPNGKIIGYEIREDFAKLAWRNVEWAGFSdRVEIKLRDIYEGIE 159
                                       567777788899999**********************************************9778765555544333 PP

                                       S-T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEEEEE----SHHHHHH CS
                   Ubie_methyltran 113 eddsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvvlefskvelpllsqa 165
                                        +d  D       + +++  ++++++a + lkpGG lv       ++  + + 
  gi|242398912|ref|YP_002994336.1| 160 -EDNVDH-----IILDLPQPENVVEHAVQSLKPGGFLVAYTPCINQVDRFYKK 206
                                       .344444.....46689999999999999999999998765555555555555 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 !   11.2   0.0   0.00023      0.22       8      88 ..      93     171 ..      88     179 .. 0.89
   2 !    5.9   0.0    0.0096         9     119     158 ..     175     215 ..     171     244 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00023
                                       TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC..EEEEE CS
                   Methyltr_RsmB-F   8 eeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlggelfDriL 84 
                                       +++ i+++  + G+ T ++a+++ ++g+++  ++ +  +k   +n++  g      +e  +r i + + ++ +D+i+
  gi|242398912|ref|YP_002994336.1|  93 PGDIIIEAGVGSGALTLFLANIIGPNGKIIGYEIREDFAKLAWRNVEWAGFS--DRVEIKLRDIYEGIEEDNVDHII 167
                                       5789999999*****************************************9..45666777777889999****** PP

                                       EEE- CS
                   Methyltr_RsmB-F  85 lDaP 88 
                                       lD P
  gi|242398912|ref|YP_002994336.1| 168 LDLP 171
                                       **99 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0096
                                       HHHHHHCCCEEEEEEEE.EEES--STTTTHHHHHHHHHH-T CS
                   Methyltr_RsmB-F 119 ellsaaidllkkgGvlv.YsTCsvlveEneevieeaLkkre 158
                                       ++++ a+++lk+gG+lv Y+ C  +v+   + i+e  k+  
  gi|242398912|ref|YP_002994336.1| 175 NVVEHAVQSLKPGGFLVaYTPCINQVDRFYKKINEYKKHFT 215
                                       5788999********99788899999998888887765544 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   5.7e-06    0.0054       2      99 .]      99     190 ..      98     190 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 5.7e-06
                   Methyltransf_12   2 eiGcGtGsllrallekl.pdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlh 77 
                                       e G G+G+l+  l++ + p+ +++g++i +++  + + +  ++ + + ++ve++ +d+ +  +++ +D +++     
  gi|242398912|ref|YP_002994336.1|  99 EAGVGSGALTLFLANIIgPNGKIIGYEIREDFA-KLAWRNVEWAG-FSDRVEIKLRDIYEGIEEDNVDHIIL----- 168
                                       89*************99****************.99999999996.889*****999998888899999875..... PP

                   Methyltransf_12  78 hlkdirevldnirklLkpgGrl 99 
                                        l++++ v++++ + LkpgG l
  gi|242398912|ref|YP_002994336.1| 169 DLPQPENVVEHAVQSLKPGGFL 190
                                       579*****************86 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.3e-05     0.012      35     130 ..      97     185 ..      91     214 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.3e-05
                                       EEEET-TTSHHHHHHHHH.TTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTTTSTTS-EEEEEE---ST CS
                               MTS  35 vlDlGcGaGvlgaalake.speaevtlvdvdarAlesakenleankle..vevvasdvleeveekkfdlivsNPPfh 108
                                       ++  G G G+l++ la+   p+ ++  +++     ++a +n+e  +++  ve+  +d++e +ee+++d+i+   P  
  gi|242398912|ref|YP_002994336.1|  97 IIEAGVGSGALTLFLANIiGPNGKIIGYEIREDFAKLAWRNVEWAGFSdrVEIKLRDIYEGIEEDNVDHIILDLPQP 173
                                       67889***********96268889***********************999*********************876632 PP

                                       TTCHCHHHHHHHHHHHHHHHEE CS
                               MTS 109 agkatelavaeeliaeAkeaLk 130
                                                 e+++++A + Lk
  gi|242398912|ref|YP_002994336.1| 174 ----------ENVVEHAVQSLK 185
                                       ..........234455555555 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   8.9e-06    0.0084      48     112 ..      94     158 ..      64     194 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 8.9e-06
                                       --EEEEE--TTSHHHHHHHTTS-TT-EEEEEES-HHHHHHHHHHHHHTT-GGGEEEEES-HHHHH CS
                    Methyltransf_3  48 akrvleiGvftGyslLatalalPeDGkilaididreayeialkfiqkagvaekieliegdalkvL 112
                                          ++e Gv  G   L +a  + ++Gki+  +i ++ +++a + ++ ag+ +++e++  d  + +
  gi|242398912|ref|YP_002994336.1|  94 GDIIIEAGVGSGALTLFLANIIGPNGKIIGYEIREDFAKLAWRNVEWAGFSDRVEIKLRDIYEGI 158
                                       55689**************************************************9987755444 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   8.9e-06    0.0084      57     132 ..      88     167 ..      80     212 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 8.9e-06
                                       TTT--TT-EEEEES-TTSHHHHHHHHHH..--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-.GGG---.--S CS
                              CMAS  57 klelkpGmtlLdiGcGWGslvrravery..dvkvvglTlSkeqaklakkrvdeldlerkvevklld.yedlde.kvd 129
                                        +++ pG+ +++ G G G+l+   ++    + k++g  + ++ akla ++v+ ++++++ve+kl d ye ++e +vd
  gi|242398912|ref|YP_002994336.1|  88 FAGISPGDIIIEAGVGSGALTLFLANIIgpNGKIIGYEIREDFAKLAWRNVEWAGFSDRVEIKLRDiYEGIEEdNVD 164
                                       57899**************99988877622578*******************************9989999998999 PP

                                       EEE CS
                              CMAS 130 rvv 132
                                       +++
  gi|242398912|ref|YP_002994336.1| 165 HII 167
                                       986 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00027      0.26       4      49 ..      96     142 ..      93     240 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00027
                                       EEEEET-TTSHHHHHHHHH.STTSEEEEEES-HHHHHHHHHHHHHCT CS
                    Methyltransf_4   4 vvleiGcGkGeflvalAkk.nPdknflGiEirvkvvakvlkkieale 49 
                                       +++e G+G+G +++ lA+   P+ +++G Eir++  + +++++e  +
  gi|242398912|ref|YP_002994336.1|  96 IIIEAGVGSGALTLFLANIiGPNGKIIGYEIREDFAKLAWRNVEWAG 142
                                       789**************9637*************9999999988665 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   6.1e-05     0.058      12      87 ..      91     167 ..      83     169 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.1e-05
                   Methyltransf_18  12 vekgsrvaDiGtDHgylpiylvk.egkakkviasDinegplekakeniekagledkievrlsdGleklkeeevdtvv 87 
                                       +++g++++  G   g l+++l++  g   k+i  +i+e   + a +n+e ag++d++e+ l d  e ++e++vd ++
  gi|242398912|ref|YP_002994336.1|  91 ISPGDIIIEAGVGSGALTLFLANiIGPNGKIIGYEIREDFAKLAWRNVEWAGFSDRVEIKLRDIYEGIEEDNVDHII 167
                                       667788888888889999998862477889***************************************999**998 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00029      0.27      95     154 ..     170     232 ..      78     235 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00029
                   Methyltransf_23  95 vpdppellrqiatllkpgGylllseplaslkedrllldw.lylvpag...rhisffsarslkel 154
                                       +p p+ ++ ++ + lkpgG l+  +p  ++  dr ++++ +y  +     +  ++ +++++k+ 
  gi|242398912|ref|YP_002994336.1| 170 LPQPENVVEHAVQSLKPGGFLVAYTPCINQ-VDRFYKKInEYKKHFTrpkTIECLVREQEIKKE 232
                                       56799********************98874.344333322444333322266688888888775 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0    0.0011         1      76     130 ..     118     171 ..      69     186 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0011
                                       H--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE--- CS
                           UPF0020  76 elklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnpP 130
                                       + k++g ++ +   + a +N e ag +d++e++  d+ +   +e++vd i+ ++P
  gi|242398912|ref|YP_002994336.1| 118 NGKIIGYEIREDFAKLAWRNVEWAGFSDRVEIKLRDIYEGI-EEDNVDHIILDLP 171
                                       45799*****************************9998655.5668*******99 PP

>> PSK  Phytosulfokine precursor protein (PSK)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       6.1   5.8e+03      75      82 ..      47      54 ..      46      56 .. 0.81
   2 ?   11.9   0.1   0.00037      0.35      56      83 ..     218     247 ..     196     250 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 6.1
                               PSK 75 lveAHlDY 82
                                      + ++H+DY
  gi|242398912|ref|YP_002994336.1| 47 VINSHTDY 54
                                      5679**** PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00037
                               PSK  56 aeeaCe..egdeeeeClkRRtlveAHlDYI 83 
                                       ++ +C   e++ + eC++ Rt + AH+ YI
  gi|242398912|ref|YP_002994336.1| 218 KTIECLvrEQEIKKECIRPRTTMLAHTGYI 247
                                       45677655778899******9999*****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 1769.96
//
Query:       gi|242398913|ref|YP_002994337.1|  [L=250]
Description: methyltransferase [Thermococcus sibiricus MM 739]
Scores for complete 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-25   87.4   0.0    2.4e-24   85.9   0.0    1.8  2  Methyltransf_25  Methyltransferase domain
    1.6e-24   86.4   0.1    3.4e-24   85.3   0.1    1.6  1  Methyltransf_11  Methyltransferase domain
    3.8e-24   85.2   0.0    4.8e-24   84.9   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    2.5e-17   63.0   0.0    3.9e-17   62.4   0.0    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    1.3e-13   51.1   0.0      2e-13   50.5   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
    1.4e-12   48.2   0.0    2.7e-12   47.3   0.0    1.5  1  Methyltransf_12  Methyltransferase domain
    5.4e-07   29.4   0.0    9.2e-07   28.6   0.0    1.3  1  MetW             Methionine biosynthesis protein MetW
    1.7e-06   27.9   0.0    1.6e-05   24.7   0.0    2.1  1  UPF0020          Putative RNA methylase family UPF0020
    9.5e-06   25.5   0.0    1.5e-05   24.8   0.0    1.3  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    1.8e-05   23.5   0.0    2.2e-05   23.2   0.0    1.1  1  Methyltransf_29  Putative S-adenosyl-L-methionine-dependent m
    5.4e-05   22.8   0.0    8.7e-05   22.1   0.0    1.2  1  MTS              Methyltransferase small domain
    7.5e-05   22.1   0.0    9.9e-05   21.8   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
    0.00016   22.7   0.0     0.0023   18.9   0.0    2.2  2  Methyltransf_24  Methyltransferase domain
    0.00033   20.6   0.0    0.00054   19.9   0.0    1.3  1  Methyltransf_18  Methyltransferase domain
     0.0006   19.8   0.0    0.00083   19.4   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
    0.00069   19.1   0.0    0.00093   18.7   0.0    1.3  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    0.00091   18.7   0.0     0.0012   18.2   0.0    1.2  1  TehB             Tellurite resistance protein TehB
     0.0086   16.1   0.0      0.022   14.7   0.0    1.7  2  ADH_zinc_N       Zinc-binding dehydrogenase
  ------ inclusion threshold ------
      0.024   14.2   0.0      0.031   13.8   0.0    1.2  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
      0.028   13.9   0.1      0.049   13.2   0.1    1.3  1  DOT1             Histone methylation protein DOT1
      0.037   13.8   0.0      0.058   13.2   0.0    1.3  1  DUF938           Protein of unknown function (DUF938)
      0.039   13.8   0.3      0.099   12.5   0.2    1.8  1  Methyltransf_8   Hypothetical methyltransferase
      0.046   12.9   0.0      0.066   12.3   0.0    1.2  1  Methyltransf_20  Putative methyltransferase
      0.076   12.7   0.1       0.11   12.1   0.1    1.4  1  TPMT             Thiopurine S-methyltransferase (TPMT)
      0.082   12.4   0.0       0.17   11.3   0.0    1.6  1  Methyltransf_4   Putative methyltransferase
       0.15   11.5   0.2        1.3    8.4   0.1    2.2  2  CheR             CheR methyltransferase, SAM binding 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 !   85.9   0.0   3.4e-27   2.4e-24       1      97 []      40     134 ..      40     134 .. 0.95
   2 ?   -1.9   0.0       8.3   5.7e+03      20      38 ..     177     195 ..     168     205 .. 0.56

  Alignments for each domain:
  == domain 1  score: 85.9 bits;  conditional E-value: 3.4e-27
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEEEST.G CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvssga.l 74 
                                       v d++cGtG+ +  la+ + +++++gvD s+ m+e+a+++a+e+gl  + +f+ +da++l+f+d++fD+v+s  + l
  gi|242398913|ref|YP_002994337.1|  40 VFDVACGTGESACFLAETF-ECEIVGVDASPIMVEKAKKKAKERGLegKTTFILADAHKLSFPDNTFDVVISE-CtL 114
                                       78****************9.7*************************99************************5.659 PP

                                       GGSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  75 hhlsdedlekalkeiarvLkpgG 97 
                                       ++l+    e+al+e+ rv+kp+G
  gi|242398913|ref|YP_002994337.1| 115 CLLN---KEAALREMVRVVKPNG 134
                                       9987...579***********99 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 8.3
                                       TSSEEEEEESSHHHHHHHH CS
                   Methyltransf_25  20 gkakvtgvDiseemleaar 38 
                                       g  +v+ vD s+   e ++
  gi|242398913|ref|YP_002994337.1| 177 GLVDVVVVDKSHLIPEWMK 195
                                       4455666666654443333 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.3   0.1   4.9e-27   3.4e-24       2      93 ..      42     135 ..      41     138 .. 0.97

  Alignments for each domain:
  == domain 1  score: 85.3 bits;  conditional E-value: 4.9e-27
                                       EET-TTSHHHHHHHHTT.SEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT-EEEEEEES-CCC-C CS
                   Methyltransf_11   2 dvGcGtGrlaealakrg.arvvgvDlskemlklakekaseegl..kvefvvadaeklpfednsfDlvvssevlhhve 75 
                                       dv+cGtG  a+ la+++ +++vgvD s+ m++ ak+ka+e+gl  k +f+ ada+kl f+dn+fD+v+s  +l+ + 
  gi|242398913|ref|YP_002994337.1|  42 DVACGTGESACFLAETFeCEIVGVDASPIMVEKAKKKAKERGLegKTTFILADAHKLSFPDNTFDVVISECTLCLL- 117
                                       9********************************************99*****************************. PP

                                       CHHHHHHHHHHHEEEEEE CS
                   Methyltransf_11  76 dpekalkeiaRvLkpgGl 93 
                                       + e+al+e++Rv+kp+G 
  gi|242398913|ref|YP_002994337.1| 118 NKEAALREMVRVVKPNGC 135
                                       59***************6 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.9   0.0   6.9e-27   4.8e-24       2     125 ..      35     154 ..      34     200 .. 0.88

  Alignments for each domain:
  == domain 1  score: 84.9 bits;  conditional E-value: 6.9e-27
                   Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdieeleklledekfDl 77 
                                       +++ +v D++CGtGe +  lae+  +++e+vG+D s+ ++e+A+++a++ gl+   +F  +d+++l+  + d++fD+
  gi|242398913|ref|YP_002994337.1|  35 NEKSKVFDVACGTGESACFLAET--FECEIVGVDASPIMVEKAKKKAKERGLEgKTTFILADAHKLS--FPDNTFDV 107
                                       56789****************43..57****************************************..******** PP

                   Methyltransf_31  78 ilsnevlnaladpdkileeiervlkpggilliedprllaelpakveee 125
                                       ++s ++l +l +++++l+e+ rv+kp+g + i d+ + ++ p++++ +
  gi|242398913|ref|YP_002994337.1| 108 VISECTL-CLLNKEAALREMVRVVKPNGCVGIHDVAWKENTPRELKLK 154
                                       *******.677899**********************776666655544 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.4   0.0   5.7e-20   3.9e-17      42     151 ..      31     138 ..      19     151 .. 0.88

  Alignments for each domain:
  == domain 1  score: 62.4 bits;  conditional E-value: 5.7e-20
                                       H--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSS.TEEEEE--TTT-TTS-T-E CS
                   Ubie_methyltran  42 lvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegki.nieflqanaeeLpfeddsf 117
                                       l +  + +kv+Dva+Gtg+ a  l+++ +   ++v++D ++ m++ ++kk+ke+g   +  f+ a+a +L f d++f
  gi|242398913|ref|YP_002994337.1|  31 LCGINEKSKVFDVACGTGESACFLAETFE--CEIVGVDASPIMVEKAKKKAKERGLEgKTTFILADAHKLSFPDNTF 105
                                       55667889*****************9986..68***********************999****************** PP

                                       EEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEE CS
                   Ubie_methyltran 118 DvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvv 151
                                       Dvv +s     + +k+ aL+e+ rv+kp G + +
  gi|242398913|ref|YP_002994337.1| 106 DVV-ISECTLCLLNKEAALREMVRVVKPNGCVGI 138
                                       *98.56666678899***************9866 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.5   0.0   2.9e-16     2e-13      13     160 ..      28     178 ..      21     201 .. 0.73

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 2.9e-16
                   Methyltransf_23  13 lerllpklraggrvLdiGcGtG.illevlrengfsvtgvDlspeaveiae..........kakkaqkdqfdeqeaae 78 
                                       l++l +  +++++v d++cGtG + + +++++ ++++gvD+sp++ve+a+          k     +  +d+++ ++
  gi|242398913|ref|YP_002994337.1|  28 LAELCG-INEKSKVFDVACGTGeSACFLAETFECEIVGVDASPIMVEKAKkkakerglegK---TTFILADAHKLSF 100
                                       555555.78999**********445666688899***************988877775541...2333333446678 PP

                   Methyltransf_23  79 pqgkfdlIvlrevlehvpdppellrqiatllkpgGylllseplaslk.edrllldwlylvpagrhisffsarslkel 154
                                       p+++fd++++  +l+ +   +++lr + + +kp+G + +++++  +k ++ + l+ ++ +++       + + +k+l
  gi|242398913|ref|YP_002994337.1| 101 PDNTFDVVISECTLCLLN-KEAALREMVRVVKPNGCVGIHDVA--WKeNTPRELKLKLKDIE--GEEPETIEGWKRL 172
                                       ***************765.5*****************999984..42133333333444443..2233444555666 PP

                   Methyltransf_23 155 leeaGl 160
                                       +e+ Gl
  gi|242398913|ref|YP_002994337.1| 173 FEKVGL 178
                                       666655 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.3   0.0   3.9e-15   2.7e-12       2      98 ..      42     135 ..      41     136 .. 0.89

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 3.9e-15
                   Methyltransf_12   2 eiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhh 78 
                                       ++ cGtG+ +  l+e   ++e++gvD sp ++e+ak+k ++r+ +  + + l + + l+ ++ ++fD+v++ ++l+ 
  gi|242398913|ref|YP_002994337.1|  42 DVACGTGESACFLAET-FECEIVGVDASPIMVEKAKKKAKERGLEGKTTFILADAHKLS-FPDNTFDVVISECTLCL 116
                                       99*********99999.89**********************999987777777776543.4447***********99 PP

                   Methyltransf_12  79 lkdirevldnirklLkpgGr 98 
                                       l +++++l+++ +++kp+G+
  gi|242398913|ref|YP_002994337.1| 117 L-NKEAALREMVRVVKPNGC 135
                                       8.9****************8 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0   1.3e-09   9.2e-07      11     103 ..      34     131 ..      26     140 .. 0.81

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 1.3e-09
                              MetW  11 ikpgsrvldlGcGdGellellkeekqvdgrGleldeegvae....cvakGlsviqgdl..dkdlenfedksfdyvvl 81 
                                       i+++s+v+d+ cG Ge   +l+e+ + +  G++ +   v +    + ++Gl+     +  d     f+d++fd+v+ 
  gi|242398913|ref|YP_002994337.1|  34 INEKSKVFDVACGTGESACFLAETFECEIVGVDASPIMVEKakkkAKERGLEGKTTFIlaDAHKLSFPDNTFDVVIS 110
                                       889******************************998777651111567899877765422666678********999 PP

                              MetW  82 sqtlqatrnpkevldellrigr 103
                                         tl    n +  l+e++r+ +
  gi|242398913|ref|YP_002994337.1| 111 ECTLCL-LNKEAALREMVRVVK 131
                                       999975.577889******975 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   2.4e-08   1.6e-05      75     128 ..      58     111 ..      17     112 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 2.4e-08
                                       HH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE- CS
                           UPF0020  75 aelklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtn 128
                                        e +++g+D  + +v++a+++a++ g++++ +f  ada kL  +++ +dv++++
  gi|242398913|ref|YP_002994337.1|  58 FECEIVGVDASPIMVEKAKKKAKERGLEGKTTFILADAHKLSFPDNTFDVVISE 111
                                       45679*************************************9999******96 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   2.2e-08   1.5e-05      66     135 ..      29      97 ..      22     113 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 2.2e-08
                                       HHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTC.SEEEEES-GGG CS
                              PCMT  66 lellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldle.nvivvvgDGrk 135
                                        el  ++++++v +v +G+G  +  la+ ++  + +v+++ ++ +ve+ak++ k+ +le + +++ +D +k
  gi|242398913|ref|YP_002994337.1|  29 AELCGINEKSKVFDVACGTGESACFLAETFE--CEIVGVDASPIMVEKAKKKAKERGLEgKTTFILADAHK 97 
                                       678889****************9999*9986..667*********************99888888888765 PP

>> Methyltransf_29  Putative S-adenosyl-L-methionine-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   3.2e-08   2.2e-05     119     215 ..      38     136 ..      22     179 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 3.2e-08
                   Methyltransf_29 119 rtvlDvGCgv...asfgayllsrdvltlslapkDeheaqvqfaLeRgvpailavl.g.tkrlpyPsrsfdlihCsrC 190
                                        +v+Dv Cg    a f a  ++ +++ +  +p  + +a+ + a eRg+    + + + +++l++P ++fd++  s C
  gi|242398913|ref|YP_002994337.1|  38 SKVFDVACGTgesACFLAETFECEIVGVDASPIMVEKAK-KKAKERGLEGKTTFIlAdAHKLSFPDNTFDVV-ISEC 112
                                       5799****964448899999************9887777.679*****976654324268**********87.4556 PP

                   Methyltransf_29 191 ridwteedgilllevdRvlRpgGyf 215
                                        +   ++++  l e+ Rv++p+G  
  gi|242398913|ref|YP_002994337.1| 113 TLCLLNKEA-ALREMVRVVKPNGCV 136
                                       665555554.689*********965 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   1.3e-07   8.7e-05      31     103 ..      36     110 ..      24     114 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.3e-07
                                       TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTT.TSTTS-EEEEEE CS
                               MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..vevvasdvle.eveekkfdlivs 103
                                       ++ kv D++cG+G  ++ la+  +  e++ vd++   +e ak+ +++ +le  ++++  d+ +  ++++ fd+++s
  gi|242398913|ref|YP_002994337.1|  36 EKSKVFDVACGTGESACFLAETFE-CEIVGVDASPIMVEKAKKKAKERGLEgkTTFILADAHKlSFPDNTFDVVIS 110
                                       5779**********9999998665.59************************8877788887763677999***997 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   1.4e-07   9.9e-05      58     171 ..      32     145 ..      22     173 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.4e-07
                                       TT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG---...--SEE CS
                              CMAS  58 lelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedlde...kvdrv 131
                                        ++++ +++ d+ cG G+ +   +e ++ ++vg+  S    ++akk+ +e++le k++  l+d + l+     +d v
  gi|242398913|ref|YP_002994337.1|  32 CGINEKSKVFDVACGTGESACFLAETFECEIVGVDASPIMVEKAKKKAKERGLEGKTTFILADAHKLSFpdnTFDVV 108
                                       56778899******************************************************999886433589988 PP

                                       EEES-GGGTSGGGHHHHHHHHHHHS-TT-EEEEEEEEE-- CS
                              CMAS 132 vsvgafehvgkenydtffkklkkllkedGllllhtitslh 171
                                       +s   +  +     ++  +++ +++k++G + +h +  ++
  gi|242398913|ref|YP_002994337.1| 109 ISECTLCLLN---KEAALREMVRVVKPNGCVGIHDVAWKE 145
                                       8855544443...345566777777777777777776655 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   3.3e-06    0.0023       2     106 .]      44     141 ..      43     141 .. 0.92
   2 ?    1.5   0.0       0.9   6.2e+02      55      81 ..     159     190 ..     144     206 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 3.3e-06
                   Methyltransf_24   2 EiGvysGvstlwllralrrngagrlvavdhdpg.aeeaaalareaglddrvrlikadseealaslaagsiDllfiDg 77 
                                        +G   G s+++l+++++     ++v vd  p   e+a++ a+e gl+   ++i ad++++  s+ + ++D+++  +
  gi|242398913|ref|YP_002994337.1|  44 ACG--TGESACFLAETFEC----EIVGVDASPImVEKAKKKAKERGLEGKTTFILADAHKL--SFPDNTFDVVISEC 112
                                       689..9********98885....5899***99877778899999*****************..99999********* PP

                   Methyltransf_24  78 ghaaeavledleallprlapggvvlfdDi 106
                                               ++l+ + ++++p+g v ++D+
  gi|242398913|ref|YP_002994337.1| 113 TLCLLNKEAALREMVRVVKPNGCVGIHDV 141
                                       *99999999*******************6 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.9
                   Methyltransf_24  55 kadseealasla.....agsiDllfiDgghaa 81 
                                       +++ +e++++++      g +D++++D +h  
  gi|242398913|ref|YP_002994337.1| 159 EGEEPETIEGWKrlfekVGLVDVVVVDKSHLI 190
                                       555667777777777766789******99965 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   7.8e-07   0.00054      12      86 ..      34     108 ..      25     111 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 7.8e-07
                   Methyltransf_18  12 vekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGleklkeee.vdtv 86 
                                       ++++s+v D+ +  g  +++l+++  + +++ +D ++  +ekak+++++ gle k +++l+d  +   +++ +d+v
  gi|242398913|ref|YP_002994337.1|  34 INEKSKVFDVACGTGESACFLAETFEC-EIVGVDASPIMVEKAKKKAKERGLEGKTTFILADAHKLSFPDNtFDVV 108
                                       68899*****************99998.899*******************************97766666645554 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   1.2e-06   0.00083      21      87 ..      32      93 ..      22     133 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.2e-06
                   Methyltransf_32 21 akesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkrlsfael 87
                                      +  +++ +v Dv++G g  +  la     +++++vg+da+  +veka+k a++ g  ++ ++ f+ +
  gi|242398913|ref|YP_002994337.1| 32 CGINEKSKVFDVACGTGESACFLAE---TFECEIVGVDASPIMVEKAKKKAKERG--LEGKTTFILA 93
                                      56678899*****************...99***********************99..7777777655 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   1.3e-06   0.00093     159     256 ..      34     136 ..      22     177 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.3e-06
                              PrmA 159 vkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseellk....eekadviv 231
                                       ++e+++v+Dv +G+G  a   a     ++v+vD  ++ v+ ak+ a+  ++e k + +  +++ k    ++++dv++
  gi|242398913|ref|YP_002994337.1|  34 INEKSKVFDVACGTGESACFLAETFECEIVGVDASPIMVEKAKKKAKERGLEGKTTFI-LADAHKlsfpDNTFDVVI 109
                                       56788*********************************************99988654.3444433456799***** PP

                              PrmA 232 aNILaevlie..laedikklvkeggll 256
                                       +      l +   + ++ ++vk++g +
  gi|242398913|ref|YP_002994337.1| 110 SECTLCLLNKeaALREMVRVVKPNGCV 136
                                       987666665411345666777777765 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.8e-06    0.0012      22     166 ..      28     172 ..      22     188 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.8e-06
                                       HHHHCCCS-S-EEEEES-TTSHHHHHHHH.TT-EEEEEES-HHHHHHHHHHHHHTT-TTEEEE.E--GGG---.-S- CS
                              TehB  22 vveavkivkpgkvldlgcgqgrnslylsl.lgydvtawdknensiafleeikekenlknista.lydineakl.der 95 
                                       + e   i + +kv+d+ cg g  + +l+     ++  +d     ++  ++ ++   l++ +t  l d  ++++ d+ 
  gi|242398913|ref|YP_002994337.1|  28 LAELCGINEKSKVFDVACGTGESACFLAEtFECEIVGVDASPIMVEKAKKKAKERGLEGKTTFiLADAHKLSFpDNT 104
                                       55666677889****************85145677777777777777777777778988777525688999985678 PP

                                       EEEEEEESSGGGS-GGGHHHHHHHHHHTEEEEEEEEEEEEB--SSS--SS--S--B-TTHHHHHTTTSEEE CS
                              TehB  96 ydfilstvvlmfleaeripsiienmqectkvggynlivaamstddvpctvpfsftfkegelkeyykdwell 166
                                       +d ++s   l +l++e+    +++m +  k+ g   i      ++ p  + + +   ege  e  ++w++l
  gi|242398913|ref|YP_002994337.1| 105 FDVVISECTLCLLNKEA---ALREMVRVVKPNGCVGIHDVAWKENTPRELKLKLKDIEGEEPETIEGWKRL 172
                                       **************986...467788888888887777777778888888888888888887777887765 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   3.2e-05     0.022       1      87 [.      46     138 ..      46     160 .. 0.80
   2 ?   -2.9   0.0       8.9   6.1e+03      32      43 ..     175     187 ..     170     202 .. 0.51

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.2e-05
                                       HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTESEEEETTTC.HHHHHHHHHTTTSSEEEEEESSC.....SHHH CS
                        ADH_zinc_N   1 gvGlaavqlAkalGaeviavdsseeklelakklGadevinykea.dlverikeltggegvdvvfecvG.....sgat 71 
                                       g G  a+ lA  + +e+++vd s+  +e+akk   ++ +  k++  l ++ k  + ++ +dvv+          +a+
  gi|242398913|ref|YP_002994337.1|  46 GTGESACFLAETFECEIVGVDASPIMVEKAKKKAKERGLEGKTTfILADAHKLSFPDNTFDVVISECTlcllnKEAA 122
                                       6788999*************************99999999977644444444444599****985433355559*** PP

                                       HHHHHHCEEEEEEEEE CS
                        ADH_zinc_N  72 leaalkllkpgGrlvv 87 
                                       l++ ++++kp+G++ +
  gi|242398913|ref|YP_002994337.1| 123 LREMVRVVKPNGCVGI 138
                                       *************965 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 8.9
                                       HTT.ESEEEETTT CS
                        ADH_zinc_N  32 klG.adevinyke 43 
                                       k G +d+v+  k+
  gi|242398913|ref|YP_002994337.1| 175 KVGlVDVVVVDKS 187
                                       5555555555433 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   4.5e-05     0.031       3      82 ..      39     134 ..      37     160 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.5e-05
                   Methyltransf_15   3 vilDlfsGaGGnviqfalvfe.kviaieinleklacaqhNaevYgvsdkitlvlgdvfe...............lla 63 
                                        + D+ +G+G  +  +a++fe ++++++ ++  ++ a++ a+  g + k t++l+d  +               +l 
  gi|242398913|ref|YP_002994337.1|  39 KVFDVACGTGESACFLAETFEcEIVGVDASPIMVEKAKKKAKERGLEGKTTFILADAHKlsfpdntfdvvisecTLC 115
                                       689****************9548*********************************999777777777766666333 PP

                   Methyltransf_15  64 klklekikvdlvflSpPwG 82 
                                        l+ e++ +++v +  P G
  gi|242398913|ref|YP_002994337.1| 116 LLNKEAALREMVRVVKPNG 134
                                       3334444455555555555 PP

>> DOT1  Histone methylation protein DOT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1     7e-05     0.049      30     130 ..      24     119 ..      20     131 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7e-05
                                       HHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHH--SEEEEEE--HHHHHHHHHHHHHHHHHHHHTTB----EEEE CS
                              DOT1  30 flsevldkvnlkkedvFvDLGSGvGnvvlqaalevgcklsvGvEimdnaselaekqkeelkkrlklfGkklakiefi 106
                                       +++++ + + +++++   D   G G+  ++ a  ++c+  vGv+ +    e a+k+++e      l Gk +  +  +
  gi|242398913|ref|YP_002994337.1|  24 ITKDLAELCGINEKSKVFDVACGTGESACFLAETFECE-IVGVDASPIMVEKAKKKAKE----RGLEGKTTFILADA 95 
                                       567788899*****************************.99*99887777766666554....35567766665555 PP

                                       .SS-STT-HHHHHHGGG-SEEEE-- CS
                              DOT1 107 .rksFvenekveeiieeadvilvNN 130
                                        + sF +n +   +i+e+++ l N 
  gi|242398913|ref|YP_002994337.1|  96 hKLSFPDNTF-DVVISECTLCLLNK 119
                                       3667766655.55668888888885 PP

>> DUF938  Protein of unknown function (DUF938)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   8.4e-05     0.058      25      48 ..      36      59 ..      24      97 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.4e-05
                            DUF938 25 ttervLEiasGtGqHAvffApalp 48
                                      ++++v ++a GtG+ A+f+A++++
  gi|242398913|ref|YP_002994337.1| 36 EKSKVFDVACGTGESACFLAETFE 59
                                      3447****************9986 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   0.00014     0.099     109     163 ..      91     145 ..      28     174 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00014
                                       EES-TTS-S--TT-EEEEEEES---SS-HHHHHHHHHHHEEEEEEEEEEEEGGG- CS
                    Methyltransf_8 109 vacdlakvPledesvdvavfclslmgtnladflkeanrvlkvGGllkvaevksrf 163
                                       +  d  k+   d++ dv++   +l   n +  l+e+ rv+k+ G + + +v  + 
  gi|242398913|ref|YP_002994337.1|  91 ILADAHKLSFPDNTFDVVISECTLCLLNKEAALREMVRVVKPNGCVGIHDVAWKE 145
                                       567899999**********99999999999***************9999987665 PP

>> Methyltransf_20  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   9.6e-05     0.066     121     196 ..      24      96 ..      21     117 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9.6e-05
                   Methyltransf_20 121 lekaverlkaegrpvrildiaaGhGryvldalekaeervesillrdyselnveqGraliaekglediarfekgdaf 196
                                       ++k +++l   +++ ++ d+a+G G     a   ae+ + +i+  d s++ ve+ ++ ++e+gle  ++f  +da 
  gi|242398913|ref|YP_002994337.1|  24 ITKDLAELCGINEKSKVFDVACGTGES---ACFLAETFECEIVGVDASPIMVEKAKKKAKERGLEGKTTFILADAH 96 
                                       566777888889999**********85...44555555679999****************************9996 PP

>> TPMT  Thiopurine S-methyltransferase (TPMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00016      0.11      38      81 ..      37      81 ..      22     143 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00016
                                      -EEEEEET-TT-HHHHHH-BT.TEEEEEE-S-HHHHHHHHHHHTT CS
                              TPMT 38 glrvlvPlCGkaldlvwlAeq.grevvGvelselAvekffeeanl 81
                                      + +v+   CG ++ +  lAe  + e+vGv+ s++ vek+ ++a++
  gi|242398913|ref|YP_002994337.1| 37 KSKVFDVACGTGESACFLAETfECEIVGVDASPIMVEKAKKKAKE 81
                                      45778889***********97689**************8766554 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00025      0.17       3      51 ..      38      85 ..      36     109 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00025
                                      EEEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTS CS
                    Methyltransf_4  3 pvvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelk 51
                                      + v ++ cG Ge+   lA+ + +++++G++ +  +v+k+ kk+++++l+
  gi|242398913|ref|YP_002994337.1| 38 SKVFDVACGTGESACFLAETF-ECEIVGVDASPIMVEKAKKKAKERGLE 85
                                      5689**************987.9*********************99765 PP

>> CheR  CheR methyltransferase, SAM binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.1    0.0019       1.3      31      82 ..      36      77 ..      23      84 .. 0.79
   2 ?    0.4   0.0      0.54   3.7e+02     133     171 ..     101     136 ..      84     141 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0019
                                      SSEEEEEES-TTTHHHHHHHHHHHCHSTTTSSS-EEEEEEESSCHHHHHHHH CS
                              CheR 31 krvriwsagcssGeEpYslAmllketlpkaaklkvkilAtDidlkvlekAka 82
                                      ++ +++ ++c++Ge +      l+e       ++++i+++D +  ++ekAk+
  gi|242398913|ref|YP_002994337.1| 36 EKSKVFDVACGTGESA----CFLAE------TFECEIVGVDASPIMVEKAKK 77
                                      5678999999999964....44555......35689**************97 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.54
                                       GG--EEEEEE-SSGGGC-CHHHHHHHHHHHCCEEEEEEE CS
                              CheR 133 vlgklDvifcrnvliYfdeetqekvlerfaeklkpgglL 171
                                       + + +Dv+++   l+ +++   e+ l+++ + +kp+g +
  gi|242398913|ref|YP_002994337.1| 101 PDNTFDVVISECTLCLLNK---EAALREMVRVVKPNGCV 136
                                       5678999999999999875...56789999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); 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: 0.62u 0.35s 00:00:00.97 Elapsed: 00:00:00.54
# Mc/sec: 1399.52
//
Query:       gi|242398914|ref|YP_002994338.1|  [L=58]
Description: hypothetical protein TSIB_0931 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score 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   14.0   0.0      0.044   13.8   0.0    1.0  1  DUF3322          Uncharacterized protein conserved in bacteri
      0.067   13.1   0.1      0.083   12.8   0.1    1.3  1  Glycos_trans_3N  Glycosyl transferase family, helical bundle 


Domain annotation for each model (and alignments):
>> DUF3322  Uncharacterized protein conserved in bacteria N-term (DUF3322)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   4.9e-06     0.044      67     118 ..       3      54 ..       2      58 .] 0.95

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.9e-06
                           DUF3322  67 wesvnhrtlGtqelParlvlesledalrllgkekeaerfrallellaalape 118
                                       we +n+r+ G+  + + l  e  +++++l++++ e ++f+++le+++++ +e
  gi|242398914|ref|YP_002994338.1|   3 WEIKNNRYTGRLLVGSFLEKEEIDEFITLVAQTGEFKKFEHILEEIEEEEEE 54 
                                       999********************************************99887 PP

>> Glycos_trans_3N  Glycosyl transferase family, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   9.3e-06     0.083       3      29 ..      10      37 ..       8      50 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.3e-06
                                      HHHHHHTT.---HHHHHHHHHHHHT.TS CS
                   Glycos_trans_3N  3 iikklrdgeeLtaeeirfaihgilk.ge 29
                                      ++ +l+ g  L +eei ++i+ +++ ge
  gi|242398914|ref|YP_002994338.1| 10 YTGRLLVGSFLEKEEIDEFITLVAQtGE 37
                                      7889*******************98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       994  (0.0554409); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); 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: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 371.29
//
Query:       gi|242398915|ref|YP_002994339.1|  [L=45]
Description: hypothetical protein TSIB_0932 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       219  (0.0122148); expected 358.6 (0.02)
Passed bias filter:                      190  (0.0105974); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 358.76
//
Query:       gi|242398916|ref|YP_002994340.1|  [L=439]
Description: Zinc-dependent protease, TldD/PmbA family [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.6e-48  166.0   0.5    1.9e-48  165.7   0.5    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 !  165.7   0.5   1.1e-52   1.9e-48       1     279 []      21     314 ..      21     314 .. 0.84

  Alignments for each domain:
  == domain 1  score: 165.7 bits;  conditional E-value: 1.1e-52
                                       EEEEEEEEEEEEEEEEETTEEEEEEEEEEEEEEEEEEETTEEEEEE...ESS..HHHHHHHHHHHHHHCCS---TT- CS
                         PmbA_TldD   1 eaevrleesestsvrfengevetnsssedsglgvrvikggrlgfastldtsd..ealeeaveraveiaklapedpea 75 
                                       e+e++ e +++ s+++e+ e+e ++++  sg+g+rv ++g+ gf++ + ++   e+le+ v+r +++ak+++ + + 
  gi|242398916|ref|YP_002994340.1|  21 EWEIYWEIGRGSSFKIEKCELERAQRKYHSGIGLRVGYNGKQGFSYITGINHpkEELEKFVKRTIKLAKVGQVKFYG 97 
                                       69******************************************99777777999*************999888888 PP

                                       ..................GGS-HHHHHHHHHHHHHH.CHCSTTEEEEE..EEEEE......EEE.EEEEEEETTSEE CS
                         PmbA_TldD  76 ..................eevsaeekielleelekalrsadpkiensk..garisgvsaslsaskeeklianSeGld 132
                                                         +e++ ee+ ++ +e++++        + ++  + +   +s++l   + +  ianS+G++
  gi|242398916|ref|YP_002994340.1|  98 fpdkkpirkvngiydkkiAELEFEEALKVGKEISQK-------ESELRekYGTSYIFSGRLAFGVAKDGIANSNGIE 167
                                       986666666644444444444444444444444422.......22222456688889999999999999******** PP

                                       EEEEEEEEEEEEEEEE.STCSET.EEEEEEEE......SSHHHS..SSHHHHHHHHHHCTTT-B---SEEEEEEE-H CS
                         PmbA_TldD 133 veqtrtrvslslsviaddggsgd.gmgggsgy......edleeedleeiaeeaaekalasleakplppgkypVvlsp 202
                                       ++++ t +s+s+ ++      +d + g+g++y         +e++l+  +e+  + +  s +akpl + + ++vl+p
  gi|242398916|ref|YP_002994340.1| 168 ITEEGTAMSFSVYIVK-----KDgKVGSGDYYkasrilM-NFEKELDIGLEKSLQETELSYNAKPLNSFEGELVLEP 238
                                       ****************.....444566677778888752.333455557788899999999**************** PP

                                       HHHHHHHHGHHHHHTBHHHHHTT--TTTT-TTSB-S-TT--EEEETT-......-SB-TTSBB---EEEEETTEE-- CS
                         PmbA_TldD 203 eavgsllheavghaleadavlegrSflkdklGekvaselltivddpts.gglgsypfDdEGvptqrtvlIenGvLkn 278
                                        av+s+l+ ++ ++l +d+v+ +rS + + +Ge vas+ +t++dd+t  g+++sy+fD+EG p qrtvl+enG+Lkn
  gi|242398916|ref|YP_002994340.1| 239 HAVASILG-LFISNLRGDNVYHKRSKF-TTVGESVASDSFTLIDDATLeGKIASYSFDGEGNPGQRTVLVENGILKN 313
                                       ********.7778**************.57*****************99**************************** PP

                                       - CS
                         PmbA_TldD 279 y 279
                                       +
  gi|242398916|ref|YP_002994340.1| 314 F 314
                                       8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.37
# Mc/sec: 3516.45
//
Query:       gi|242398917|ref|YP_002994341.1|  [L=88]
Description: hypothetical protein TSIB_0934 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       240  (0.0133861); expected 358.6 (0.02)
Passed bias filter:                      205  (0.011434); 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 0.27s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 592.03
//
Query:       gi|242398918|ref|YP_002994342.1|  [L=455]
Description: Zinc-dependent protease, TldD/PmbA family [Thermococcus sibiricus MM 739]
Scores for complete 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  205.6   0.2    2.5e-60  204.7   0.2    1.5  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 !  204.7   0.2   1.4e-64   2.5e-60       1     279 []      21     309 ..      21     309 .. 0.92

  Alignments for each domain:
  == domain 1  score: 204.7 bits;  conditional E-value: 1.4e-64
                                       EEEEEEEEEEEEEEEEETTEEEEEEEEEEEEEEEEEEETTEEEEEE...ESSHHHHHHHHHHHHHHCCS---TT-.. CS
                         PmbA_TldD   1 eaevrleesestsvrfengevetnsssedsglgvrvikggrlgfastldtsdealeeaveraveiaklapedpea.. 75 
                                       ++e+r+++ + t +++ n+  e +ss+ + g+gvr+++ g++gf+s++d      e+a++ a++iak +p + +   
  gi|242398918|ref|YP_002994342.1|  21 YYEIRINKINATHIEIQNSHFEDVSSNVEIGIGVRAFS-GSWGFSSANDMR--RAEDAIKIAMKIAKTSPGNAKIyf 94 
                                       79***********************************6.9******88888..*************9999998889* PP

                                       ................GGS-HHHHHHHHHHHHHH.CHCSTTEEEEEEEEEE......EEE.EEEEEEETTSEEEEEE CS
                         PmbA_TldD  76 ................eevsaeekielleelekalrsadpkienskgarisgvsaslsaskeeklianSeGldveqt 136
                                                        +v+ eek ++l +l++   + d          + ++++ + +   e+l+ nS G+++++ 
  gi|242398918|ref|YP_002994342.1|  95 gdlirdeseikvqksfLDVDLEEKMTFLTSLDSL-LKGD---------ALPNRRIVYGDGIKEQLYFNSLGSEIKTL 161
                                       *****99999999999999999999999999954.2222.........4566677799******************* PP

                                       EEEEEEEEEEEE..S..TCSET.EEEEEEEESSHHHS..SSHHHHHHHHHHCTTT-B---SEEEEEEE-HHHHHHHH CS
                         PmbA_TldD 137 rtrvslslsvia.dd..ggsgd.gmgggsgyedleeedleeiaeeaaekalasleakplppgkypVvlspeavgsll 209
                                       ++r++ls+sv+a ++  +++    +gg +g+e +e++d+e  ++ ++eka+ +l+a+ +p+g+++V+ +pe +g+++
  gi|242398918|ref|YP_002994342.1| 162 TPRIRLSFSVTAkKNgdMQTYWkIFGGTTGWEIIEKIDIEHWTSFVKEKAKNLLNASLPPSGEFDVIVDPELAGVFI 238
                                       ************555344445556677888899999***************************************** PP

                                       HGHHHHHTBHHHHHTT--TTTT-TTSB-S-TT--EEEETT-......-SB-TTSBB---EEEEETTEE--- CS
                         PmbA_TldD 210 heavghaleadavlegrSflkdklGekvaselltivddpts.gglgsypfDdEGvptqrtvlIenGvLkny 279
                                       hea+gha+e+dav  g S++++klG+k+a e lt+vddpt  g++gsy +DdEGv+++r+++I+nGvL+ y
  gi|242398918|ref|YP_002994342.1| 239 HEALGHAAEGDAVKNGESIFENKLGKKIAVEELTVVDDPTLeGKFGSYLYDDEGVKSKRVEIIKNGVLNEY 309
                                       ********************88******************9***************************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (455 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); 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: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.53
# Mc/sec: 2588.18
//
Query:       gi|242398919|ref|YP_002994343.1|  [L=502]
Description: Probable glycine dehydrogenase [decarboxylating] subunit 2 [Thermococcus sibiricus MM 739]
Scores for complete 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   46.6   0.0    2.9e-09   36.3   0.0    2.1  2  GDC-P            Glycine cleavage system P-protein
    1.4e-08   34.1   0.1      3e-08   33.0   0.1    1.6  1  Aminotran_5      Aminotransferase class-V
    0.00026   20.4   0.0    0.00041   19.7   0.0    1.3  1  Beta_elim_lyase  Beta-eliminating lyase
     0.0013   18.1   0.3     0.0036   16.7   0.0    1.7  2  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
     0.0036   16.1   0.0        1.9    7.1   0.0    2.1  2  Pyridoxal_deC    Pyridoxal-dependent decarboxylase conserved 
  ------ inclusion threshold ------
       0.11   12.4   0.7        2.1    8.3   0.0    2.3  2  Flavi_DEAD       Flavivirus DEAD domain
       0.14   10.6   0.0       0.24    9.9   0.0    1.3  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme


Domain annotation for each model (and alignments):
>> GDC-P  Glycine cleavage system P-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   0.0   1.1e-12   2.9e-09      28     289 ..      36     306 ..      28     312 .. 0.78
   2 !    8.3   0.0   0.00036      0.92     332     427 ..     339     446 ..     333     449 .. 0.63

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 1.1e-12
                                       HHHS-GGGB--S---------HHHHHHHHHHHHTTB--.-EE--BTTB------HHHHHHTTT-HHHHS--S-SSGG CS
                             GDC-P  28 ekavPkeiklkkelkleapksEeellaelekiasknkv.vksfiGaGyydtilPaviqrnilenpewytaYtPYqaE 103
                                       + ++P+++ ++k+l+l++  sE e++++ +++++ n    + +   G   ++  + i+ ++ ++pe ++   PYq E
  gi|242398919|ref|YP_002994343.1|  36 DVQIPQHL-KRKNLELPE-LSEPEVVRHYTRLSQMNYGvDNGMYPLGSCTMKYNPKINEELANHPE-VAFIHPYQDE 109
                                       46899998.455666654.89*************99983566888999999999999998888888.56778****9 PP

                                       .G-HHHHHHHHHHHHHHHHHHT-SEE-S-BS-HHHHHHHHH.HHHHHH-SSS.....--EEEEETTS-HHHHHHHHH CS
                             GDC-P 104 .isqGrLeallnfqtlvadltGldianasllDegtAaaEAv.llaaraskkk.....akkvvvdkkvhpqtlevlkt 173
                                          qG L+ + +  + + ++ G+d     l   + A +E   +++ ra +       +++++v  + h  +      
  gi|242398919|ref|YP_002994343.1| 110 rTVQGALQIMWELEQWLKEIVGMDR--FTLQPAAGANGEFTgVMIIRAYHLDhgetqRNEIIVPDSAHGTN----PA 180
                                       457********************95..56778888888853244455544440001144556555555544....35 PP

                                       HHGGGT-EEEEE-GGG--S-..........S-EEEEEEEES-TTSB--.--HHHHHHHHHTT-EEEEEE-TTGGGTB CS
                             GDC-P 174 rakglgieivevdlteekvtd.......kekevagvlvqypnteGrie.dlkelvekakkkkslvvvaadllaLtll 242
                                        a   g+++ve ++ e+++ d       +++++ag+++  pnt G  e d+ e+++ +++   l+      l   l 
  gi|242398919|ref|YP_002994343.1| 181 SAAMAGFKVVEIPSNEQGMVDiaalenaVSEKTAGIMLTNPNTLGIFEeDILEIAKIVHDAGGLLYYDGANLNGILG 257
                                       6888999999999999999999999999999**************986269**********9998887666665554 PP

                                       .--HHHHT-SEE.EEE-TTTT---GGG----EEEEE-GGGGGG--S-EE CS
                             GDC-P 243 .kpPgelgaDiv.vGsaqrfGvPlgyGGPhagffAvkeklkRkiPGRlv 289
                                        + Pg++g D+v +   + f  P g GGP  g + vk++l   +P  lv
  gi|242398919|ref|YP_002994343.1| 258 kARPGDMGFDVVhINLHKTFSTPHGGGGPGSGPVGVKKHLIDYLPVPLV 306
                                       157*******994566789******************999888886665 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00036
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT.T-EE--SSBSSEEEE.E--T.TTHH..H...HHHHHHHTT.. CS
                             GDC-P 332 aalyavyhGkeglkeiarrihkkteilakelkkkleeelkkkkffdtlli.evee.kaae..k...vlkkaekeg.. 399
                                       a  y  + G++gl+e+ +    ++++la++lk + + el +k++    ++ + e+ k  +  k   v k+ ++ g  
  gi|242398919|ref|YP_002994343.1| 339 ALTYLKMMGRDGLREVGEVAVLNANYLAQKLKGTKGYELPHKELRKHEVVfSAEPmKRDTgvKtldVAKRLLDFGlh 415
                                       6789999*************************999999999887543222012221211100101122222222222 PP

                                       ...EE-EEESTTEEEEE--TT--HHHHHHHH CS
                             GDC-P 400 ...lnlrkvelktvgialdEtvtkedieall 427
                                          + +    ++++ i  +Etvtked++a +
  gi|242398919|ref|YP_002994343.1| 416 aptIYFPLIVHEALMIEPTETVTKEDLDAYV 446
                                       2245555566678888888888888888765 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.1   1.2e-11     3e-08      86     207 ..     163     282 ..     142     407 .. 0.82

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 1.2e-11
                                       TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTE.B--HHHH CS
                       Aminotran_5  86 kpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsnvtGt.iqpveei 161
                                        +++ei+v ++ h  n   + +++   g+kv+ ip +e+g +d+ +le++++ekt+ +++t + n++G+  +++ ei
  gi|242398919|ref|YP_002994343.1| 163 TQRNEIIVPDSAHGTNP--ASAAM--AGFKVVEIPSNEQGMVDIAALENAVSEKTAGIMLT-NPNTLGIfEEDILEI 234
                                       56678888888877776..44444..69*****************************9998.5788999889***** PP

                                       HHHHHHTT-EEEEE-TTTTT.TS---HHHHTESEEEEETTT.TTSSTT CS
                       Aminotran_5 162 gklakkkgalvlvDaaqavg.hipidvkklgvDflafsghK.llgPtG 207
                                       +k+++++g l+  D+a   g   +    ++g D++ +  hK +  P G
  gi|242398919|ref|YP_002994343.1| 235 AKIVHDAGGLLYYDGANLNGiLGKARPGDMGFDVVHINLHKtFSTPHG 282
                                       ****************976624689999*************7777776 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   1.6e-07   0.00041      72     169 ..     166     250 ..     112     290 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.6e-07
                                       EEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HH CS
                   Beta_elim_lyase  72 eevivtepahihfdetgaiaelagvklrdlknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsle 148
                                       +e+iv + ah+   ++ a a++ag k+++++++e+G +d+++le+a+ e      k++ i+lt+ n    G  +  e
  gi|242398919|ref|YP_002994343.1| 166 NEIIVPDSAHG---TNPASAAMAGFKVVEIPSNEQGMVDIAALENAVSE------KTAGIMLTNPNTL--G--IFEE 229
                                       56666667776...55677889**************************9......589********98..5..5689 PP

                                       HHHHHHHHHHHCT-EEEEEET CS
                   Beta_elim_lyase 149 elrevaaiakkygiplhlDgA 169
                                        + e+a+i+++ g  l +DgA
  gi|242398919|ref|YP_002994343.1| 230 DILEIAKIVHDAGGLLYYDGA 250
                                       9*******************9 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.4e-06    0.0036      58     147 ..     160     251 ..     121     284 .. 0.80
   2 ?   -1.3   0.0      0.41   1.1e+03     247     321 ..     361     434 ..     353     465 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.4e-06
                                       TTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSSB-GGGCGGG--TTEEEEEEB-..GGGB--.-HHHHH CS
                   DegT_DnrJ_EryC1  58 lgvgpgdeVIvpsltFvatanavlelgakpvfvDvdpdtynidpaaieaaitertkaIlpVh..lyGqva.dmdalk 131
                                        g ++++e+Ivp     +  ++++ +g k+v +  + ++ ++d aa+e+a+ e+t++I++ +  ++G +  d+ ++ 
  gi|242398919|ref|YP_002994343.1| 160 HGETQRNEIIVPDSAHGTNPASAAMAGFKVVEIPSN-EQGMVDIAALENAVSEKTAGIMLTNpnTLGIFEeDILEIA 235
                                       455699*********9999999999*****999877.899*******************996337788878999999 PP

                                       HHHHHCT-EEEEE-TT CS
                   DegT_DnrJ_EryC1 132 aiaakhglkvieDaAh 147
                                       +i ++ g  +  D A+
  gi|242398919|ref|YP_002994343.1| 236 KIVHDAGGLLYYDGAN 251
                                       9999999888888776 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.41
                                       HHHHHHHHHHTCCCCEESCGGTTSSSEEESCEEEEEHCCHHHCHHHHHHHHHHCCEE-B-SG.SCHGGGSCCHHHH CS
                   DegT_DnrJ_EryC1 247 iaelykeeLaelegtaelttpketkkhawhlyavlveeeaevkrdelvealkeegigtrvhy.pnplhrqpvyaer 321
                                       +a+++ ++L++ +g + ++ + ++  h ++  a  ++++  vk  +++++l + g+ + ++y p  +h+  + + +
  gi|242398919|ref|YP_002994343.1| 361 NANYLAQKLKGTKGYELPHKELRK--HEVVFSAEPMKRDTGVKTLDVAKRLLDFGLHAPTIYfPLIVHEALMIEPT 434
                                       688999999999987554444444..44444444445455588888999999998888777735555555444444 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 !    7.0   0.0   0.00083       2.1     150     207 ..     170     225 ..     155     268 .. 0.79
   2 !    7.1   0.0   0.00075       1.9     315     373 ..     331     390 ..     307     392 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.00083
                                       EETTS-HHHHHHHHHHT-EEEEE--BTTTBB-HHHHHHHHHHHHCTT.EEEEEEEEBS CS
                     Pyridoxal_deC 150 tsdqahssvekaalvlgvklrvipldengklrgaalekaieedkekGlipffvvatlG 207
                                         d ah      a+++g+k+ +ip++e+g +  aale+a+ e+ +   i +    tlG
  gi|242398919|ref|YP_002994343.1| 170 VPDSAHGTNPASAAMAGFKVVEIPSNEQGMVDIAALENAVSEKTAG--IMLTNPNTLG 225
                                       5567788888899***************************999887..6655555666 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.00075
                                       SGHHTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTEEECS.TTBSSEEEEE CS
                     Pyridoxal_deC 315 srrvrilklwfvlralGveglqnqirksvelakyleklirkderfeiva.evelglVcFr 373
                                       +   + ++    l+++G+ gl+++ +  v +a+yl+++++ ++ +e++  e     V+F+
  gi|242398919|ref|YP_002994343.1| 331 GNFTVLVRALTYLKMMGRDGLREVGEVAVLNANYLAQKLKGTKGYELPHkELRKHEVVFS 390
                                       5555667777899***********************************977788888887 PP

>> Flavi_DEAD  Flavivirus DEAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0   0.00084       2.1      88     132 ..     158     202 ..     144     214 .. 0.82
   2 ?    2.1   0.2     0.067   1.7e+02      36      87 ..     428     475 ..     425     488 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00084
                                       HHT------SEEEEETTT--SHHHHHHHHHHHHHHHTTS-EEEEE CS
                        Flavi_DEAD  88 lspvrkknyeliimDeahflDPasiaarGyletkaeegeaalill 132
                                       l + ++++ e+i+ D ah ++Pas a  G+   +  ++e  ++ +
  gi|242398919|ref|YP_002994343.1| 158 LDHGETQRNEIIVPDSAHGTNPASAAMAGFKVVEIPSNEQGMVDI 202
                                       666778899********************9877777777666655 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.067
                                       EEEEESSHHHHHHHHHHTTTS-EEE-------------SEEEEEHHHHHHHH CS
                        Flavi_DEAD  36 tlvLaPtrvvlaemeealkglevryktsavkeektgrelvdvmchatftkrl 87 
                                       +l++ Pt  v +e  +a  +       +  ke +t+ elv  + h t ++r+
  gi|242398919|ref|YP_002994343.1| 428 ALMIEPTETVTKEDLDAYVEALK----KISKEAYTTPELVKTAPHNTTVRRV 475
                                       67788999999998888765544....4455556999*********999875 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   9.3e-05      0.24     113     193 ..     188     270 ..     152     277 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 9.3e-05
                                       HHTTCEEEEESTTSHHHHHHHCCTTEEEEEEESS-TTTT----HHHHHHHHHHTT-EEEEEGTTTHTTT..S-GGGG CS
                   Cys_Met_Meta_PP 113 kklgievkfvdtsdleelekaikentklvylEtptnpllkvvDiekiaklakkagvlvvvDntfaspll..qrplkl 187
                                       k ++i ++   + d+++le+a++e+t  + l  p    +   Di +iak++++ag l+  D + + ++l   rp ++
  gi|242398919|ref|YP_002994343.1| 188 KVVEIPSNEQGMVDIAALENAVSEKTAGIMLTNPNTLGIFEEDILEIAKIVHDAGGLLYYDGANLNGILgkARPGDM 264
                                       4455666666778999******************99999****************************8844578999 PP

                                       T-SEEE CS
                   Cys_Met_Meta_PP 188 gaDivv 193
                                       g D+v 
  gi|242398919|ref|YP_002994343.1| 265 GFDVVH 270
                                       999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (502 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.67u 0.32s 00:00:00.99 Elapsed: 00:00:00.50
# Mc/sec: 3032.41
//
Query:       gi|242398920|ref|YP_002994344.1|  [L=454]
Description: Probable glycine dehydrogenase [decarboxylating] subunit 1 [Thermococcus sibiricus MM 739]
Scores for complete 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-121  406.5   0.0   1.4e-121  406.3   0.0    1.0  1  GDC-P            Glycine cleavage system P-protein
    6.2e-05   22.1   0.0     0.0001   21.4   0.0    1.4  1  Aminotran_5      Aminotransferase class-V
    0.00083   18.0   0.0     0.0014   17.3   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme


Domain annotation for each model (and alignments):
>> GDC-P  Glycine cleavage system P-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  406.3   0.0  2.4e-125  1.4e-121       2     428 ..       6     443 ..       5     445 .. 0.94

  Alignments for each domain:
  == domain 1  score: 406.3 bits;  conditional E-value: 2.4e-125
                                       HH-SS-HHHHHHHHHHHT-SSHHHHHHHHS-GGGB--S---------HHHHHHHHHHHHTTB--...-EE--BTTB- CS
                             GDC-P   2 rhigpsekdqkemLetlGlkslddliekavPkeiklkkelkleapksEeellaelekiasknkv...vksfiGaGyy 75 
                                       rh  p++ +++emL+ +G+ks+ dl+ ++vP++    ke++l+++ksE+e+  e+++i +knk    +  f+GaG+y
  gi|242398920|ref|YP_002994344.1|   6 RHYIPNSGHKEEMLREIGFKSIADLF-SDVPEDF--VKEFNLPEGKSEYEVFLEMNEILNKNKSvleMPTFLGAGAY 79 
                                       66667788999***************.9****98..899***********************984445689****** PP

                                       -----HHHHHHTTT-HHHHS--S-SSGGG-HHHHHHHHHHHHHHHHHHT-SEE-S-BS-HHHHHHHHHHHHHHH-SS CS
                             GDC-P  76 dtilPaviqrnilenpewytaYtPYqaEisqGrLeallnfqtlvadltGldianasllDegtAaaEAvllaaraskk 152
                                        +++Pa ++  ++e++e++t+YtPYqaEisqG L+al+++q+l+ +l Gl+i nas++D gtA+aEA+l++ar++ k
  gi|242398920|ref|YP_002994344.1|  80 FHYVPAHVKY-LIERSEFITSYTPYQAEISQGMLQALFEYQSLIGELVGLEIVNASMYDWGTAMAEAALMSARVTGK 155
                                       ********99.****************************************************************99 PP

                                       S--EEEEETTS-HHHHHHHHHHHGGGT-EEEEE-GGG--S-.........S-EEEEEEEES-TTSB---.-HHHHHH CS
                             GDC-P 153 kakkvvvdkkvhpqtlevlktrakglgieivevdlteekvtd......kekevagvlvqypnteGried.lkelvek 222
                                       k  k++v  ++hp+ +++l+t++ g g+ei+ v+  e++  d      k+++ ag+ +  pn++G ie+ +ke+ e 
  gi|242398920|ref|YP_002994344.1| 156 K--KFIVPGHLHPERKKILHTYTAGPGLEIEYVKWNENGQVDiedlkeKATDAAGIYLEVPNFFGLIEEqIKEIGEI 230
                                       9..*******************************99999999999999999****************8669****** PP

                                       HHHTT-EEEEEE-TTGGGTB--HHHHT-SEEEEE-TTTT---GGG----EEEEE-GG..GGGG--S-EEEEEEBTTS CS
                             GDC-P 223 akkkkslvvvaadllaLtllkpPgelgaDivvGsaqrfGvPlgyGGPhagffAvkek..lkRkiPGRlvGvskDaeg 297
                                       a+++ +l+vv +d+  L+++++PgelgaD+vvG+a  +G  l +GGP ag fAvk++    R++PGR++G++kDa+g
  gi|242398920|ref|YP_002994344.1| 231 AHESGALFVVGVDPTILGIIEAPGELGADVVVGEASFLGSALNFGGPRAGIFAVKNErrILRQMPGRVIGMTKDADG 307
                                       *******************************************************998899**************** PP

                                       -EEEEEE-CCGSHHCCHHHCS-S--S--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT.T-EE--SS CS
                             GDC-P 298 kralrlalqtREqHirRdkAtsniCtaqaLlAnlaalyavyhGkeglkeiarrihkkteilakelkkkleeelkkkk 374
                                       kra++++lqtREqHirR kAtsniC++ aL+A++aa+++  +G++gl+++ + i+k+t+++++ + + +e  +++ +
  gi|242398920|ref|YP_002994344.1| 308 KRAFVMTLQTREQHIRRAKATSNICSNEALVAVAAAIHMATLGPKGLQKLGEIILKNTKYFKERISEVAEIPFDGIN 384
                                       ******************************************************************99********* PP

                                       BSSEEEEE--T..TTHHHHHHHHHHTT..EE-EEESTT.EEEEE--TT--HHHHHHHHH CS
                             GDC-P 375 ffdtllievee..kaaekvlkkaekeg..lnlrkvelk.tvgialdEtvtkedieallk 428
                                       f d++++   +     e++lk++++ g  l+    el+ + ++a++Et+ ke i+al++
  gi|242398920|ref|YP_002994344.1| 385 FKDVVVKFEIPydVIHEELLKRNIHGGfyLKPHFPELEeSALLAVTETTRKEWIDALVT 443
                                       ***987754444355667*******99554444455554899************99976 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   1.7e-08    0.0001     112     193 ..     179     259 ..     138     380 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.7e-08
                                       HTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTE.B--HHHHHHHHHHTT-EEEEE-TTTTTTS---H CS
                       Aminotran_5 112 tgakvkvipldeegeldldelekllnektklvaithvsnvtGt.iqpveeigklakkkgalvlvDaaqavghipidv 187
                                        g+++++++ +e+g++d+++l+++ ++ + +  +  v n  G   ++++eig++a+++gal++v    +++ i    
  gi|242398920|ref|YP_002994344.1| 179 PGLEIEYVKWNENGQVDIEDLKEKATDAAGI--YLEVPNFFGLiEEQIKEIGEIAHESGALFVVGVDPTILGIIEAP 253
                                       699*********************9998875..889*******6678****************96666666555555 PP

                                       HHHTES CS
                       Aminotran_5 188 kklgvD 193
                                        +lg+D
  gi|242398920|ref|YP_002994344.1| 254 GELGAD 259
                                       555555 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 !   17.3   0.0   2.3e-07    0.0014      69     194 ..     132     263 ..     116     271 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.3e-07
                                       EEEEESSHHHHHHHHHHTTS-TTEE.EEEESTSSHHHHHHHHHTHHHTTCEEEEESTTSHHHH..HHHCCTTEEE.. CS
                   Cys_Met_Meta_PP  69 aalavssGmaAiaaailallkaGde.ivvsddlYggtqrllkkvlkklgievkfvdtsdleel..ekaikentkl.. 140
                                       +a ++  G+a  +aa+++   +G++  +v  +l+   +++l++++   g+e+++v  ++  ++  e   ++ t++  
  gi|242398920|ref|YP_002994344.1| 132 NASMYDWGTAMAEAALMSARVTGKKkFIVPGHLHPERKKILHTYTAGPGLEIEYVKWNENGQVdiEDLKEKATDAag 208
                                       5666777888888888888888865599999999999999*999999999999998765554411444444555444 PP

                                       EEEESS-TTTT----HHHHHHHHHHTT..-EEEEEGTTTHTTTS-GGGGT-SEEEE CS
                   Cys_Met_Meta_PP 141 vylEtptnpllkvvDiekiaklakkag..vlvvvDntfaspllqrplklgaDivvh 194
                                       +ylE p    l    i++i ++a++ g   +v vD t++ +++  p +lgaD+vv 
  gi|242398920|ref|YP_002994344.1| 209 IYLEVPNFFGLIEEQIKEIGEIAHESGalFVVGVDPTIL-GIIEAPGELGADVVVG 263
                                       9**************************6556668*9987.899***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 3010.71
//
Query:       gi|242398921|ref|YP_002994345.1|  [L=223]
Description: Hydrolase, HAD superfamily [Thermococcus sibiricus MM 739]
Scores for 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-10   39.5   0.0    1.1e-09   38.6   0.0    1.3  1  HAD_2        Haloacid dehalogenase-like hydrolase
     0.0022   18.4   0.1     0.0039   17.6   0.1    1.4  1  HAD          haloacid dehalogenase-like hydrolase
     0.0047   17.2   0.0      0.051   13.9   0.0    2.1  1  Hydrolase    haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.019   14.7   0.0       0.66    9.7   0.0    2.2  2  Hydrolase_3  haloacid dehalogenase-like hydrolase
      0.043   13.9   0.0         11    6.2   0.0    2.3  2  Hydrolase_6  Haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.6   0.0     3e-13   1.1e-09       3     126 ..       5     134 ..       3     138 .. 0.81

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 3e-13
                             HAD_2   3 FDlDgTlldteeliiqafnelleey....glselseeelrkl.iglslrellrklgeseeeeekieellrkyneekk 74 
                                       FD+DgTl+d+  +i +af ++l+++     +++l+ + l k  ++++     +++g++ +     +++ r++ ee  
  gi|242398921|ref|YP_002994345.1|   5 FDFDGTLIDSYSVIEEAFSRALKKHfpwlPFNSLWAKLLTKAeLHFERPRFGKYSGKTRQPAFFKTKFARTWFEERA 81 
                                       ************************97877566666666665525666666677777776666688888899999999 PP

                             HAD_2  75 kkevkpydgvkelLeeLkeagyklgivTsk..sreaveekleqlgiesyFdviv 126
                                       k   kp+d+ k+lL++L+e+g+k+   + +   + + e  l+  g+ ++Fd i+
  gi|242398921|ref|YP_002994345.1|  82 K-LSKPIDESKNLLKKLREEGHKVISFSAEdfLTGMKEYRLKVAGFYELFDDII 134
                                       9.9********************9877777556777888889999999999887 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   1.1e-06    0.0039       2     105 ..       4     105 ..       3     125 .. 0.58

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.1e-06
                               HAD   2 lfDfDgTLldgdsle..lllrfllrrgaprlwralreklllalfrellrldraglaelleallagls.eelaa.ele 74 
                                        fDfDgTL+d+ s +  ++ r  l+++ p  w   +  + + l +  l++   ++ ++  +  +    + ++   ++
  gi|242398921|ref|YP_002994345.1|   4 GFDFDGTLIDSYSVIeeAFSR-ALKKHFP--WLPFNSLWAKLLTKAELHF---ERPRFGKYSGKTRQpAFFKTkFAR 74 
                                       6**********6666553333.4444443..6666666666664444444...223333333333332222220233 PP

                               HAD  75 rfvaevirpklldp..galellaahraaGdrvv 105
                                        +++e +  kl +p  + + ll++ r++G++v+
  gi|242398921|ref|YP_002994345.1|  75 TWFEERA--KLSKPidESKNLLKKLREEGHKVI 105
                                       3442222..255577799999999999999774 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   1.4e-05     0.051       4      26 ..       3      25 ..       1     163 [. 0.72

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.4e-05
                                      EEEESBTTTBCHHHHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  4 vvfDkdGTLttgepsvedvivsa 26
                                      + fD+dGTL+++ +++e+++ +a
  gi|242398921|ref|YP_002994345.1|  3 IGFDFDGTLIDSYSVIEEAFSRA 25
                                      66****************99999 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00018      0.66       3      26 ..       5      28 ..       3      29 .. 0.93
   2 ?    2.7   0.0     0.024        86      18      35 ..      88     105 ..      81     122 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00018
                                      EEIIIIIS-TTS---HHHHHHHHH CS
                       Hydrolase_3  3 lDlDGTLlnsdkkisektkeaikk 26
                                      +D DGTL++s + i+e   +a+kk
  gi|242398921|ref|YP_002994345.1|  5 FDFDGTLIDSYSVIEEAFSRALKK 28
                                      9*********************97 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.024
                                       HHHHHHHHHHHHTTSEEE CS
                       Hydrolase_3  18 ektkeaikklkekgikvv 35 
                                       +++k+ +kkl+e+g+kv+
  gi|242398921|ref|YP_002994345.1|  88 DESKNLLKKLREEGHKVI 105
                                       7899************97 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     0.003        11       3      19 ..       5      21 ..       3      29 .. 0.87
   2 ?    5.4   0.0    0.0053        19      13      37 ..      84     108 ..      81     124 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.003
                                      EESTTTSEETTEE-TTH CS
                       Hydrolase_6  3 fDidGvLwrgdkaipga 19
                                      fD dG+L++ +++i++a
  gi|242398921|ref|YP_002994345.1|  5 FDFDGTLIDSYSVIEEA 21
                                      9*************998 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0053
                                       TEE-TTHHHHHHHHHHTT-EEEEEE CS
                       Hydrolase_6  13 dkaipgaaealnalraagkpvvllT 37 
                                       +k+i++++++l+ lr++g +v+ ++
  gi|242398921|ref|YP_002994345.1|  84 SKPIDESKNLLKKLREEGHKVISFS 108
                                       689***************9999776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); 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: 0.59u 0.34s 00:00:00.93 Elapsed: 00:00:00.54
# Mc/sec: 1237.03
//
Query:       gi|242398922|ref|YP_002994346.1|  [L=226]
Description: Metallophosphoesterase, calcineurin superfamily [Thermococcus sibiricus MM 739]
Scores for complete 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-07   31.5   0.4      1e-06   29.4   0.1    1.7  2  Metallophos    Calcineurin-like phosphoesterase
     0.0036   17.5   0.0     0.0055   16.9   0.0    1.2  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 !   29.4   0.1   1.1e-10     1e-06       4      76 ..      17     110 ..      17     130 .. 0.79
   2 ?    0.2   0.3       0.1     9e+02     160     202 ..     122     144 ..     105     151 .. 0.59

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 1.1e-10
                                       EEEESBTB..........TTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSS........HHHHHHHHHHHHHHH CS
                       Metallophos   4 lvigDlHl..........algggqlddllkllddllreekpdlvllaGDlvdrg........dlekellellaalvk 62 
                                       l+i+DlHl           + +  +d+ ++ l+ l++++    ++++GDl +          +le+ + + +++lv+
  gi|242398922|ref|YP_002994346.1|  17 LIIADLHLgyeeslaregIYLPKAFDQMITSLKSLIEKNHFKRLIINGDLKHSFvpfkrekiELET-FFNKISPLVE 92 
                                       79*********999888877778888888888888888899999999**99999999999999999.55556***** PP

                                       HTSEEEEEC-TTS.......C CS
                       Metallophos  63 ypipvylllGNHe.......g 76 
                                           v++++GNH+        
  gi|242398922|ref|YP_002994346.1|  93 ---EVMVIRGNHDvgmswikS 110
                                       ...9*********64444330 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.1
                                       CSEEEEEESSESSCSSSCSCCHHHHHHHHHHTTESEEEEESSS CS
                       Metallophos 160 adwvivlgHsplyrgsgylfgdealedllkkygvdlvisGHtH 202
                                       + w+iv+gH+ ++ g                   d  i GH+H
  gi|242398922|ref|YP_002994346.1| 122 RNWKIVHGHKLVE-G-------------------DRFIIGHEH 144
                                       5566666665544.1...................222444444 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 !   16.9   0.0   6.1e-07    0.0055       4     105 ..      17     150 ..      16     168 .. 0.54

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 6.1e-07
                     Metallophos_2   4 aiiSDlH...............snlda.leavlealkevgvdaiihaGD.......l..eeeepevleellela... 52 
                                       +ii+DlH               +++d+ +  + + +++    ++i  GD       +  e++    le++++     
  gi|242398922|ref|YP_002994346.1|  17 LIIADLHlgyeeslaregiylpKAFDQmITSLKSLIEKNHFKRLIINGDlkhsfvpFkrEKI---ELETFFNKIspl 90 
                                       689999999988888877777744443033346667777899*******5555433222222...444444433444 PP

                     Metallophos_2  53 ..pvlaVrGNnDeevveedvlreaaelgtdlp..eeaelel............agekvlliHgdpl.gvk 105
                                         +v ++rGN+D              + ++l     +ele+            +g+++ + H++p  +++
  gi|242398922|ref|YP_002994346.1|  91 veEVMVIRGNHD----------VGMSWIKSLGveILDELEIrnwkivhghklvEGDRFIIGHEHPAiRLR 150
                                       59**********..........233333333210122233300111111122234445555555445444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.34s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 1309.92
//
Query:       gi|242398923|ref|YP_002994347.1|  [L=241]
Description: hypothetical protein TSIB_0940 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-31  108.6  17.3    3.5e-31  108.2  17.3    1.2  1  PrsW-protease  PrsW family intramembrane metalloprotease
      1e-05   25.1   5.6      1e-05   25.1   5.6    2.1  2  YhfC           YhfC intramembrane metalloprotease


Domain annotation for each model (and alignments):
>> PrsW-protease  PrsW family intramembrane metalloprotease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.2  17.3     4e-35   3.5e-31       1     191 [.      40     212 ..      40     218 .. 0.85

  Alignments for each domain:
  == domain 1  score: 108.2 bits;  conditional E-value: 4e-35
                     PrsW-protease   1 eplwlllaaflwgalvavllalllntvlqallraelgkfiaeflaaflvaglvEEllKalgvllllllrrrefdepl 77 
                                       ep+++++++f++ga++++ +a++l+++l +  +     + a+++ ++lvag+vEE +K l++ + +  +  ++d+++
  gi|242398923|ref|YP_002994347.1|  40 EPKRFVIGTFILGATLSIGIAMILEAFLVQG-EFGYALLPATAFYMALVAGIVEEPAKTLAIRFPF--KAGQMDGIM 113
                                       79*****************999999998853.35566777899*******************9986..9******** PP

                     PrsW-protease  78 dGivygaavglGFavlEnllYyvqalpsaanegqlgglqllilRillsvagHalftallGiglglaksrrraarrvq 154
                                       dG+vyg+a+glGFa++En+lY +      +      g++++i+R++l +++Ha ++a++G+g+gl ++      ++q
  gi|242398923|ref|YP_002994347.1| 114 DGVVYGVAAGLGFAATENFLYGI------G-----FGVGTTIVRAFLTPFAHATWSAIVGVGYGLKAEG-----KIQ 174
                                       **********************6......3.....589***************************9933.....48* PP

                     PrsW-protease 155 illlglllavllHalwNllasl.aelllav.vgvllyvp 191
                                        + + l l++llH+lw++ a l  +   a  +  +l+++
  gi|242398923|ref|YP_002994347.1| 175 SVSGYLSLGILLHFLWDYFAFLsIAT-PAYyIFTILLIF 212
                                       *******************9983333.322222222222 PP

>> YhfC  YhfC intramembrane metalloprotease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   5.6   1.1e-09     1e-05       4     113 ..      24     136 ..      20     160 .. 0.78
   2 ?   -0.2   0.1     0.057   5.2e+02     189     212 ..     178     201 ..     170     217 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.1e-09
                              YhfC   4 llpiglvvwlrkklklslkvvglGalvFalfalvlerplhlallkqneatakalsapllfavygaLtAGlfEevgry 80 
                                       +l+i+ + +   k++ ++k +++G  +  +   +   ++ +a l q e+     +   + a y+aL+AG++Ee ++ 
  gi|242398923|ref|YP_002994347.1|  24 ALAILWYFYHEDKYEPEPKRFVIGTFILGATLSIGIAMILEAFLVQGEF---GYALLPATAFYMALVAGIVEEPAKT 97 
                                       57888888899*************7554444444445555555555555...4555777789*************** PP

                              YhfC  81 lalrfllkrksekkd......alayGlGhGGleaiLvgv 113
                                       la+rf++k  +          ++a GlG++ +e  L g 
  gi|242398923|ref|YP_002994347.1|  98 LAIRFPFKAGQMDGImdgvvyGVAAGLGFAATENFLYGI 136
                                       *******98766554778999999999***999998775 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.057
                              YhfC 189 lllllaillhaliDllaalyqagl 212
                                        +l l illh l D +a l  a  
  gi|242398923|ref|YP_002994347.1| 178 GYLSLGILLHFLWDYFAFLSIATP 201
                                       689999*******99988776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       763  (0.0425568); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); 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: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1468.18
//
Query:       gi|242398924|ref|YP_002994348.1|  [L=69]
Description: hypothetical protein TSIB_0941 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      0.005   16.5   0.7     0.0054   16.4   0.7    1.1  1  Tex_N     Tex-like protein N-terminal domain


Domain annotation for each model (and alignments):
>> Tex_N  Tex-like protein N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.7     3e-07    0.0054      41      87 ..       6      52 ..       2      64 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3e-07
                             Tex_N 41 eeqlreieerleylrelekrkeevlksieeqgklteeLkkkieaakt 87
                                      e++l e++  +ey++el+kr ee+ ++ +e+g   + L+++i++ ++
  gi|242398924|ref|YP_002994348.1|  6 EQALFEVRPYIEYYEELKKRVEEIASTTDEEGLFIKLLEEEIKKSEE 52
                                      56788899999*******************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       928  (0.0517597); expected 358.6 (0.02)
Passed bias filter:                      583  (0.0325172); 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: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 471.95
//
Query:       gi|242398925|ref|YP_002994349.1|  [L=579]
Description: Oligopeptide transporter, OPT family [Thermococcus sibiricus MM 739]
Scores for complete 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-64  216.7  53.6    7.1e-64  216.5  53.6    1.0  1  OPT       OPT oligopeptide transporter protein
  ------ inclusion threshold ------
       0.11   11.8   9.4       0.14   11.5   0.8    2.8  2  TssN      Type VI secretion system, TssN


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 !  216.5  53.6   7.9e-68   7.1e-64       1     615 [.      18     571 ..      18     572 .. 0.90

  Alignments for each domain:
  == domain 1  score: 216.5 bits;  conditional E-value: 7.9e-68
                               OPT   1 elTlRavvlGillgvlgsavnmyfglrtglvsissipaallafplgkalarilpklslnpgpftikEnvliqtmasa 77 
                                       e+T+ avvlG+l+g++++a+ +y g+  g++s  s +aa++++++++     l+k        t+ En+++qt+asa
  gi|242398925|ref|YP_002994349.1|  18 EVTPAAVVLGVLWGAFMAASFTYAGMIMGFTSGGSAIAAIVGWGILRGI---LKK-------GTVVENNIVQTVASA 84 
                                       68*********************************************85...877.......*************** PP

                               OPT  78 aatlalatglivvipalel..ygqsagfgylillslsvqllGvgfagplRkflvypeklifPsglataellkalhkp 152
                                       ++ +  ++g+i++ipal++   +q+++++y +l + ++++lG++f++plRk+++  ++l fP+g+a a++lk+  + 
  gi|242398925|ref|YP_002994349.1|  85 VNIS--VSGVIFTIPALYImgLHQEINTMYFFLATAAGAILGITFIIPLRKQMIEIDRLRFPTGTAVATILKTPGS- 158
                                       9999..***********9966667777**********************************************433. PP

                               OPT 153 egeeksrlkfflivflgsfvwglfplyl.fpalssfswltwiapknvvlanlfglgllp.ltfdwnviaayiGsgli 227
                                       +   +++ ++++  +++s+v +   l + fp+     ++ +++   +       l l + + +++ +++++ G gli
  gi|242398925|ref|YP_002994349.1| 159 G---IEKARLLFFGMIISAVIY---LIQqFPIFGLPHVIPETVDLGA------MLHLPAwINLTVALSLMVFGMGLI 223
                                       3...557777777446666665...4444888888888866666522......444434789*************** PP

                               OPT 228 vplwvavnmliGavlswgiliPllyysngwypaylpydvteildedgvldyekyigyglmllaalvallylvqfaai 304
                                       ++ + ++++l+G vls+ i+ P+  +  gw pa+++      ++  + +  ++  g+g+ l++++  l         
  gi|242398925|ref|YP_002994349.1| 224 TGRN-GLIVLAGGVLSYYIITPV-VKALGWIPADVQ---GGAVSGYVYSTMTRPLGIGMLLGGSIAGL--------- 286
                                       **76.6789999999********.8***********...888889999********************......... PP

                               OPT 305 tllivhtilkhgkdikaalksarsprteeddrhrrlmrkykdvpmwwylallvlslvigiivvealf...tqlpvwg 378
                                        +l  ++i+ + k++++a+k +                + +++p +  + +++l++v+++++ ++l    ++  ++ 
  gi|242398925|ref|YP_002994349.1| 287 -ILSLPVIAVAMKSLAQASKVK------------DKNGNNEELPIYYLVGGAILAFVLLLVTAYKLGdlgLGRSLLT 350
                                       .999***************999............33345679*******************9999988777777889 PP

                               OPT 379 lllalllafllaivsaiiaGltglnpvsgigkltqlifgallpgrpvanlvfgavvyaaaaqagdfmqDLKtGhllk 455
                                        l++++  f+ ++ +a+ +G+t+++pvsg+++++ +i  +l+  ++  ++++ga v  a++ a+d+mqDLKtGh+++
  gi|242398925|ref|YP_002994349.1| 351 ALIGVAWIFIASLLVAMSTGMTDWSPVSGLSLVSVMILLYLTHKNIPLTILMGATVGVAISGAADMMQDLKTGHMVG 427
                                       99999999999**********************************9999999************************* PP

                               OPT 456 asPraqfvaqliGtlvgavvniavlkllvkaygdictadasnaftaPqakvfaavavllvggkkglpwafllgavap 532
                                       a P  q+ + l+   +g +++  v+ l+ +ayg++     +++ +aPqa    ++ + +v g+ ++p   ++ ++++
  gi|242398925|ref|YP_002994349.1| 428 AIPSRQQKVELLTGWLGPIIALTVVGLIWNAYGIG-----NDKVPAPQAMALKSMVE-AVLGG-SVPVDKFIAGGLL 497
                                       *********************************99.....99***************.88888.7888777777888 PP

                               OPT 533 filllllkkfpkkstarklplplafavgfylppslsialligglianlwlkrrdaewakkynyvlaaGLiaGealmg 609
                                       + ll+l  + p         l++++++ +ylp  + i++ +g+++  + ++++  e+  +++  +aaGL++Gea m+
  gi|242398925|ref|YP_002994349.1| 498 GFLLSLSGV-P--------GLGVLIGLSMYLPMLYIIPYGLGCVVNEITKRKKGYEFIVEKVLPFAAGLMVGEAAMT 565
                                       888888777.4........49******************************************************** PP

                               OPT 610 viiafl 615
                                       ++ a+l
  gi|242398925|ref|YP_002994349.1| 566 LLFAVL 571
                                       *99987 PP

>> TssN  Type VI secretion system, TssN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.8   1.6e-05      0.14      27      86 ..      77     137 ..      56     155 .. 0.86
   2 ?    3.7   2.2    0.0038        34       5      52 ..     288     335 ..     285     400 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 1.6e-05
                              TssN  27 llkkkkliiyiLlaglvlalpgllgf.lknefvpygyillqilylllGilhlylllkkffk 86 
                                        ++     + i ++g+++++p+l  + l++e++ + ++l++ +  +lGi +++ l k++++
  gi|242398925|ref|YP_002994349.1|  77 IVQTVASAVNISVSGVIFTIPALYIMgLHQEINTMYFFLATAAGAILGITFIIPLRKQMIE 137
                                       5556666778889****************************************99988875 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.0038
                              TssN   5 lllpllavilllilsliakknkllkkkkliiyiLlaglvlalpgllgf 52 
                                       l lp++av +  ++ + + k k  ++ +l iy L+ g +la + ll  
  gi|242398925|ref|YP_002994349.1| 288 LSLPVIAVAMKSLAQASKVKDKNGNNEELPIYYLVGGAILAFVLLLVT 335
                                       667888888888888888888888888888888888888877655543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (579 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       779  (0.0434492); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); 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: 0.67u 0.32s 00:00:00.99 Elapsed: 00:00:00.49
# Mc/sec: 3558.09
//
Query:       gi|242398926|ref|YP_002994350.1|  [L=170]
Description: hypothetical protein TSIB_0943 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0039   17.3   1.0     0.0069   16.5   0.9    1.3  1  DUF2959        Protein of unknown function (DUF2959)
      0.005   17.0   0.3       0.21   11.8   0.0    2.2  2  LigT_PEase     LigT like Phosphoesterase
  ------ inclusion threshold ------
      0.012   15.4   0.3      0.017   14.9   0.3    1.3  1  MEDS           MEDS: MEthanogen/methylotroph, DcmR Sensory do
      0.016   14.9   0.2      0.021   14.5   0.2    1.2  1  Laminin_I      Laminin Domain I
      0.021   15.1   4.6      0.037   14.4   4.6    1.3  1  TBCA           Tubulin binding cofactor A
      0.033   13.9   0.4      0.045   13.5   0.4    1.3  1  DUF745         Protein of unknown function (DUF745)
       0.04   14.0   0.1       0.06   13.4   0.1    1.3  1  DUF1664        Protein of unknown function (DUF1664)
       0.05   14.0   0.0      0.069   13.5   0.0    1.2  1  GAF_3          GAF domain
      0.052   13.5   0.1      0.066   13.1   0.1    1.1  1  CheZ           Chemotaxis phosphatase, CheZ
      0.058   13.4   0.1      0.086   12.8   0.1    1.3  1  DUF1043        Protein of unknown function (DUF1043)
      0.074   13.3   0.2       0.17   12.2   0.2    1.6  1  DUF3618        Protein of unknown function (DUF3618)
      0.077   13.6   3.7       0.13   12.9   3.7    1.3  1  DUF4404        Domain of unknown function (DUF4404)
       0.08   12.7   5.3       0.11   12.3   5.3    1.3  1  TACC_C         Transforming acidic coiled-coil-containing pro
      0.083   12.4   0.8       0.12   11.8   0.8    1.2  1  DUF2884        Protein of unknown function (DUF2884)
      0.087   13.2   2.1       0.16   12.3   2.1    1.4  1  DUF641         Plant protein of unknown function (DUF641)
       0.11   13.0   1.6       0.28   11.6   0.3    2.0  2  Goodbye        fungal STAND N-terminal Goodbye domain
       0.12   11.9   0.2       0.17   11.4   0.2    1.4  1  Fzo_mitofusin  fzo-like conserved region
        1.5    9.1   8.3         48    4.4   0.1    4.6  5  TPR_2          Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> DUF2959  Protein of unknown function (DUF2959)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.9   6.9e-06    0.0069      13      78 ..      52     118 ..      49     134 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.9e-06
                           DUF2959  13 rdilvdrVekardsqeeakeqfksALerfkavvefdggeLekeyeklnkeyeesekaaeevr.erie 78 
                                       r+ l +   + +  +ee k+ +++AL+++++v+e ++ ++ek++ekl k +e+ e+ ae+ +  rie
  gi|242398926|ref|YP_002994350.1|  52 REELHKTAAHGKGGKEELKKSLEDALKEIEKVMEEKERDIEKAREKLGKVLEALENFAEKAQpLRIE 118
                                       6666777778888999***********************************9999988876523665 PP

>> LigT_PEase  LigT like Phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1     0.085        84      28      62 ..      47      82 ..      40      92 .. 0.83
   2 !   11.8   0.0   0.00021      0.21      46      78 ..      94     124 ..      87     129 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.085
                                      EET.SGGGSEEEEEEEEEESHHHHHHHHHHHHHHHH CS
                        LigT_PEase 28 kpv.rpfnpHiTLaflgevdeekvpellealaeias 62
                                      + + +++ +H T a+ +  +ee  + l++al+ei++
  gi|242398926|ref|YP_002994350.1| 47 RRQgEREELHKTAAHGKGGKEELKKSLEDALKEIEK 82
                                      44448999999999*999999999999999999975 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00021
                                       SHHHHHHHHHHHHHHHHTSBEEEEEEEEEEEEE CS
                        LigT_PEase  46 deekvpellealaeiasgaepfelkvdgvglfp 78 
                                        +ek+ ++leal+++a++a+p  l+++g+ +++
  gi|242398926|ref|YP_002994350.1|  94 AREKLGKVLEALENFAEKAQP--LRIEGIRVYG 124
                                       389999***************..*******997 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 ?   14.9   0.3   1.7e-05     0.017      38     139 ..      64     156 ..      44     168 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.7e-05
                              MEDS  38 stldelrealrkagldvdaalesgqleildaeetylrgggfdpermlealrralakaladgyaglrvigemtwalrs 114
                                          +el++ l++a  ++++++e++      +++  +++++ + +++leal+++++ka+    +g+rv+ge+   + +
  gi|242398926|ref|YP_002994350.1|  64 GGKEELKKSLEDALKEIEKVMEEK------ERD--IEKAREKLGKVLEALENFAEKAQPLRIEGIRVYGEVMTSFSK 132
                                       556788888888888888877777......444..7788888999*************888**********988888 PP

                              MEDS 115 paereelleyEallneliadepvta 139
                                       + er+   ++ a ++ +i++ ++ +
  gi|242398926|ref|YP_002994350.1| 133 A-ERHLNRAWSAYADGYIREGNAYL 156
                                       7.77766667777776666666655 PP

>> Laminin_I  Laminin Domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.2   2.2e-05     0.021      22      86 ..      71     135 ..      58     146 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.2e-05
                         Laminin_I  22 edltkeLqeklskesakkskieilekelesLaqeteeLqkkatqvlakaqkvnaesertlnnake 86 
                                       + l++ L+e ++  ++k+++ie + ++l ++ +  e++++ka+  + ++  v+ e+++ +++a+ 
  gi|242398926|ref|YP_002994350.1|  71 KSLEDALKEIEKVMEEKERDIEKAREKLGKVLEALENFAEKAQPLRIEGIRVYGEVMTSFSKAER 135
                                       57899999***************************************************999975 PP

>> TBCA  Tubulin binding cofactor A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   4.6   3.7e-05     0.037      20      78 ..      53     112 ..      48     119 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.7e-05
                              TBCA  20 kEleeqearleklkadgded.eydlkkqeevleetkamipdlkkrlekavekLeelleee 78 
                                       +El +  a+ +  k++ ++  e  lk+ e+v+ee ++ i++++++l k +e Le++ e++
  gi|242398926|ref|YP_002994350.1|  53 EELHKTAAHGKGGKEELKKSlEDALKEIEKVMEEKERDIEKAREKLGKVLEALENFAEKA 112
                                       344444444444444444455667777788888888888888888888888888888776 PP

>> DUF745  Protein of unknown function (DUF745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.4   4.5e-05     0.045      59     110 ..      65     116 ..      56     146 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.5e-05
                            DUF745  59 GKqqlveqleqelreaeavvqeekkslqsseanakaaakaakqaqqqlealk 110
                                       GK+ l ++le+ l+e e+v++e ++ ++++ +++  + +a ++  ++++ l+
  gi|242398926|ref|YP_002994350.1|  65 GKEELKKSLEDALKEIEKVMEEKERDIEKAREKLGKVLEALENFAEKAQPLR 116
                                       9*******************************99999998888877777665 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1     6e-05      0.06      36      78 ..      70     112 ..      69     139 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6e-05
                           DUF1664  36 krslsdavesvskqleqvseslaatkrhLssridrvdkkldeq 78 
                                       k+sl+da++++ k +e+   ++++++++L + ++ +++  ++ 
  gi|242398926|ref|YP_002994350.1|  70 KKSLEDALKEIEKVMEEKERDIEKAREKLGKVLEALENFAEKA 112
                                       89*****************************999998876665 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   6.9e-05     0.069      20      96 ..      41     124 ..      36     140 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.9e-05
                             GAF_3  20 evgalllldedgnklqvaagw..dgkpalsesldedsalarralssgevvsepsfae....edglpdraalavPLva 90 
                                         g+l+ +++++++l+ +a++  +gk+ l++sl+ + + +  +++++e  +e++ ++     ++l+  a  a PL++
  gi|242398926|ref|YP_002994350.1|  41 ALGILFRRQGEREELHKTAAHgkGGKEELKKSLEDALKEIEKVMEEKERDIEKAREKlgkvLEALENFAEKAQPLRI 117
                                       57899999*******766555589************************99996633322222445555555556666 PP

                             GAF_3  91 gr.qviG 96 
                                       +  +v+G
  gi|242398926|ref|YP_002994350.1| 118 EGiRVYG 124
                                       4455555 PP

>> CheZ  Chemotaxis phosphatase, CheZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   6.6e-05     0.066      10      88 ..      69     148 ..      65     167 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.6e-05
                                       XXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              CheZ  10 ltReLhdalrelgldekllekaaeeipdardrLeyvielTeqAAert....ldavekalpladklkeeakeleeewe 82 
                                       l ++L dal+e++   k +e+++++i+ ar++L  v+e  e+ Ae++    ++ +     +++++++  ++l+++w+
  gi|242398926|ref|YP_002994350.1|  69 LKKSLEDALKEIE---KVMEEKERDIEKAREKLGKVLEALENFAEKAqplrIEGIRVYGEVMTSFSKAERHLNRAWS 142
                                       6678888888875...66999*********************99998332244456666778888888889999998 PP

                                       XXXXXX CS
                              CheZ  83 rllere 88 
                                       + ++  
  gi|242398926|ref|YP_002994350.1| 143 AYADGY 148
                                       877655 PP

>> DUF1043  Protein of unknown function (DUF1043)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   8.7e-05     0.086       5      81 ..      31     107 ..      29     140 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.7e-05
                           DUF1043   5 lvvGiiiGalilrltnsklkkqkklekelekakaeleeqkqeledHfaqsaelLetlaedyqkLyqhlaksseeLlp 81 
                                       +vvG  +G+++l ++ +   + ++l+k+  + k   ee k+ led +++  +++e+ ++d +k  ++l k  e+L  
  gi|242398926|ref|YP_002994350.1|  31 VVVGGALGVMALGILFRRQGEREELHKTAAHGKGGKEELKKSLEDALKEIEKVMEEKERDIEKAREKLGKVLEALEN 107
                                       69**************************************************************9999999998844 PP

>> DUF3618  Protein of unknown function (DUF3618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   0.00017      0.17       8      26 ..      88     106 ..      85     116 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00017
                           DUF3618   8 erdIertRaeLaeTvdeLa 26 
                                       erdIe +R+ L+  +++L 
  gi|242398926|ref|YP_002994350.1|  88 ERDIEKAREKLGKVLEALE 106
                                       8***************996 PP

>> DUF4404  Domain of unknown function (DUF4404)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   3.7   0.00013      0.13       6      62 ..      53     110 ..      49     114 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00013
                           DUF4404   6 ekLheeLeqnesldeetralLeslaedieellaeedaaaeeee.laerlneaverFee 62 
                                       e+Lh++ ++ +  +ee +++Le++ ++ie++++e++   e++     ++ ea+e+F+e
  gi|242398926|ref|YP_002994350.1|  53 EELHKTAAHGKGGKEELKKSLEDALKEIEKVMEEKERDIEKAReKLGKVLEALENFAE 110
                                       7899999999999********************9999988866655567778888876 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 ?   12.3   5.3   0.00011      0.11      21      81 ..      49     109 ..      45     155 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00011
                            TACC_C  21 eeeiqelkkkveelkkenqemkkivaefektiaqlieekqkqkelakkeiqkvleekeqll 81 
                                       + e +el+k+ ++ k  ++e+kk +++  k i++++eek+++ e+a++++ kvle  e+ +
  gi|242398926|ref|YP_002994350.1|  49 QGEREELHKTAAHGKGGKEELKKSLEDALKEIEKVMEEKERDIEKAREKLGKVLEALENFA 109
                                       667789***********************************************98877655 PP

>> DUF2884  Protein of unknown function (DUF2884)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.8   0.00012      0.12     163     210 ..      61     107 ..      52     120 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00012
                           DUF2884 163 esegdnleafeqrmeklgekieeeveeqakalekkaealCeslkelda 210
                                        ++g   e++++++e+  ++ie+ +ee+++++ek  e+l + l++l++
  gi|242398926|ref|YP_002994350.1|  61 HGKGG-KEELKKSLEDALKEIEKVMEEKERDIEKAREKLGKVLEALEN 107
                                       44455.389******************************999998875 PP

>> DUF641  Plant protein of unknown function (DUF641)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   2.1   0.00016      0.16      76     124 ..      59     107 ..      40     111 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00016
                            DUF641  76 leaeiqeqrsllktyeitvkkleaelkakdseieeLkekLeeaeksnkk 124
                                        +     + +l k++e ++k++e+ +++k+ +ie+ +ekL ++ ++ ++
  gi|242398926|ref|YP_002994350.1|  59 AAHGKGGKEELKKSLEDALKEIEKVMEEKERDIEKAREKLGKVLEALEN 107
                                       22223336789999**************************998776655 PP

>> Goodbye  fungal STAND N-terminal Goodbye domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0       1.1   1.1e+03      50      72 ..       2      24 ..       1      27 [. 0.88
   2 ?   11.6   0.3   0.00028      0.28      24      69 ..      70     112 ..      54     115 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 1.1
                           Goodbye 50 klkealkkilspiqllggiaaqg 72
                                      k+k+ + +i+    l+gg +a++
  gi|242398926|ref|YP_002994350.1|  2 KMKKLIGNIMLTTGLIGGAIASA 24
                                      78999999999999999999985 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00028
                           Goodbye  24 lssvedllkqieaekdkfeefrekkeklkealkkilspiqllggia 69 
                                        +s+ed lk+ie+  +   e++++ ek++e l k+l+ ++++++ a
  gi|242398926|ref|YP_002994350.1|  70 KKSLEDALKEIEKVME---EKERDIEKAREKLGKVLEALENFAEKA 112
                                       4688888888888777...788999**************9998765 PP

>> Fzo_mitofusin  fzo-like conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   0.00017      0.17      93     144 ..      67     118 ..      52     146 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00017
                     Fzo_mitofusin  93 hqvqqelsstfarlcqqvdetekeleeeikelekeiekleevqkkakllrnk 144
                                       + +++ l+ +++++++  +e e+++e+  ++l k +e+le+  +ka+ lr +
  gi|242398926|ref|YP_002994350.1|  67 EELKKSLEDALKEIEKVMEEKERDIEKAREKLGKVLEALENFAEKAQPLRIE 118
                                       4556667777777777777777777777777777777777777777777655 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.69   6.9e+02       5      19 ..      40      54 ..      36      54 .. 0.85
   2 ?    0.6   0.1      0.82   8.2e+02      17      30 ..      73      86 ..      67      90 .. 0.78
   3 ?    4.4   0.1     0.048        48      13      31 ..      87     105 ..      84     108 .. 0.80
   4 ?   -1.0   0.0       2.5   2.5e+03      17      27 ..     130     140 ..     130     141 .. 0.84
   5 ?    3.6   0.1     0.086        85       1      15 [.     145     159 ..     145     162 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.69
                             TPR_2  5 ynlGlayyklgdyee 19
                                      ++lG + +++g+ ee
  gi|242398926|ref|YP_002994350.1| 40 MALGILFRRQGEREE 54
                                      589********9887 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.82
                             TPR_2 17 yeeAleafekAlel 30
                                      +e+Al+  ek+ e 
  gi|242398926|ref|YP_002994350.1| 73 LEDALKEIEKVMEE 86
                                      69999999998875 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.048
                             TPR_2  13 klgdyeeAleafekAleld 31 
                                       k  d e+A+e + k+le  
  gi|242398926|ref|YP_002994350.1|  87 KERDIEKAREKLGKVLEAL 105
                                       6678999999999999865 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 2.5
                             TPR_2  17 yeeAleafekA 27 
                                       + +A++++++A
  gi|242398926|ref|YP_002994350.1| 130 FSKAERHLNRA 140
                                       56999999998 PP

  == domain 5  score: 3.6 bits;  conditional E-value: 0.086
                             TPR_2   1 aealynlGlayyklg 15 
                                       a+++ + G+ay+++g
  gi|242398926|ref|YP_002994350.1| 145 ADGYIREGNAYLESG 159
                                       6899********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2014  (0.112332); expected 358.6 (0.02)
Passed bias filter:                     1422  (0.0793128); expected 358.6 (0.02)
Passed Vit filter:                       281  (0.0156729); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.64u 0.35s 00:00:00.99 Elapsed: 00:00:00.51
# Mc/sec: 1006.98
//
Query:       gi|242398927|ref|YP_002994351.1|  [L=295]
Description: hypothetical protein TSIB_0944 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0028   17.5   3.9     0.0052   16.7   0.0    2.7  2  DUF5627    Family of unknown function (DUF5627)
  ------ inclusion threshold ------
       0.24   11.8   1.2        1.4    9.3   0.0    2.5  3  zf-CCCH_7  Chromatin remodeling factor Mit1 C-terminal Zn fin
       0.94    7.6   9.9        1.4    7.1   9.9    1.2  1  SSP160     Special lobe-specific silk protein SSP160


Domain annotation for each model (and alignments):
>> DUF5627  Family of unknown function (DUF5627)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   2.6      0.23   1.4e+03      33      54 ..      55      76 ..      40     144 .. 0.50
   2 !   16.7   0.0   8.7e-07    0.0052      57      97 ..     207     247 ..     185     253 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.23
                           DUF5627 33 devvkltteslkkvefplsvkd 54
                                       e+++++t+s++k+ +  ++++
  gi|242398927|ref|YP_002994351.1| 55 SETTTTETTSINKADIIETIEK 76
                                      3344444444444443333322 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 8.7e-07
                           DUF5627  57 gsnlnctLlLtfdddgnctvssategytvsGtGkfvkkgek 97 
                                       ++  n+ L +tf +++++t++s ++ ++++GtGk  ++g+k
  gi|242398927|ref|YP_002994351.1| 207 QEGDNYLLTFTFTKEEQITLNSVQKVVKIQGTGKLWIRGDK 247
                                       44568899******************************998 PP

>> zf-CCCH_7  Chromatin remodeling factor Mit1 C-terminal Zn finger 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.2      0.72   4.3e+03       6      31 ..      51      76 ..      46      95 .. 0.65
   2 ?    9.3   0.0   0.00023       1.4      25      63 ..     123     161 ..     109     167 .. 0.84
   3 ?   -0.1   0.0       0.2   1.2e+03      38      56 ..     215     233 ..     191     236 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.72
                                      -HHHHHHHHHHHHHT----------- CS
                         zf-CCCH_7  6 aktlkiinlevkrkvekseyvrelek 31
                                      ++t + +      +++k++ ++ +ek
  gi|242398927|ref|YP_002994351.1| 51 SSTSSETTTTETTSINKADIIETIEK 76
                                      55666666666667777776666655 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00023
                                       -------B-----S--S-----EESS---HHHHHHHHHT CS
                         zf-CCCH_7  25 yvrelekDdpvfsykviekehrLvansvsklvldnflal 63 
                                       y +e   Dd+++   ++++++r+v +  + l ld++l+ 
  gi|242398927|ref|YP_002994351.1| 123 YSNETVWDDSIYYSALVKQNNRVVQKGEATLTLDEYLEK 161
                                       4455666*****9999********************976 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.2
                                       S--S-----EESS---HHH CS
                         zf-CCCH_7  38 ykviekehrLvansvsklv 56 
                                          + ke+++ +nsv k+v
  gi|242398927|ref|YP_002994351.1| 215 TFTFTKEEQITLNSVQKVV 233
                                       4568899999999999987 PP

>> SSP160  Special lobe-specific silk protein SSP160
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   9.9   0.00023       1.4     271     335 ..      18      83 ..       7      89 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00023
                            SSP160 271 aalealasssasanstsss.tstststttststtttnsttstnstsssnsstiagsidiaanltva 335
                                        ++ a  s  +s+ sts   +st  +  +stst++t s t+t  t+s n + i  +i+   ++  a
  gi|242398927|ref|YP_002994351.1|  18 VSVSACVSKESSTPSTSPPpASTPVTIDESTSTSSTSSETTTTETTSINKADIIETIEKVEKYEFA 83 
                                       345666677777777775426777788899999999999999999999999999998876666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1205  (0.0672095); expected 358.6 (0.02)
Passed bias filter:                      589  (0.0328518); 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: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 1752.75
//
Query:       gi|242398928|ref|YP_002994352.1|  [L=271]
Description: hypothetical protein TSIB_0945 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.027   14.5   0.5      0.094   12.8   0.2    2.1  2  DUF3601   Domain of unknown function (DUF3601)
      0.033   15.1   0.1        1.4    9.9   0.1    2.7  2  DUF4845   Domain of unknown function (DUF4845)
       0.11   12.0   0.0       0.25   10.9   0.0    1.6  1  NIR_SIR   Nitrite and sulphite reductase 4Fe-4S domain


Domain annotation for each model (and alignments):
>> DUF3601  Domain of unknown function (DUF3601)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   1.6e-05     0.094      40      70 ..      81     112 ..      62     125 .. 0.80
   2 ?   -1.6   0.0      0.48   2.9e+03      35      57 ..     166     188 ..     163     193 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.6e-05
                           DUF3601  40 yeaGfvLyis.klnekkIrLagaedeqeklia 70 
                                         +G+v yi   ++e+ ++ ++a ++++k+i 
  gi|242398928|ref|YP_002994352.1|  81 HSNGDVVYINeTIIEDFMYFSYATERNNKIIN 112
                                       578*******999****************984 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.48
                           DUF3601  35 veslkyeaGfvLyisklnekkIr 57 
                                       v+ +   +G+ +y+   n  kI+
  gi|242398928|ref|YP_002994352.1| 166 VTNFETTKGDGIYLVAFNFTKIY 188
                                       56788889999999988988887 PP

>> DUF4845  Domain of unknown function (DUF4845)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   0.00023       1.4       1      43 [.     109     151 ..     109     199 .. 0.89
   2 ?    2.2   0.0     0.055   3.3e+02      49      71 ..     239     262 ..     222     266 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00023
                           DUF4845   1 klvPvyleyysikkalkslekesglegmsvaeirsaldkrldi 43 
                                       k++  y+ +++i++ +++l++    + ++v+++r ++ kr+d 
  gi|242398928|ref|YP_002994352.1| 109 KIINSYIANMTIQEYFEKLKDRLPPNIKTVEDLRYEIFKRADL 151
                                       78889***********************************986 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.055
                           DUF4845  49 ikgedleieke.gggvvvslkYev 71 
                                       + +e+++ ++e + ++ ++ +Y++
  gi|242398928|ref|YP_002994352.1| 239 LLAENITSTREfNAKFEITPDYKR 262
                                       5589******************97 PP

>> NIR_SIR  Nitrite and sulphite reductase 4Fe-4S domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   4.1e-05      0.25     103     155 ..      78     131 ..      63     135 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 4.1e-05
                                       EEEEGG.GHHHHHHHHHHHHHHHS-CSSGGG-SHHHHHHHHHHHHHHHHHHHCC CS
                                       xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           NIR_SIR 103 gfvpee.evlevveaivevyrdhgdrknrkkeRlkylverlGvekFrekveeel 155
                                        +++ + +v+++ e+i+e ++++ ++++r+++ +  +++++++++ +ek++ +l
  gi|242398928|ref|YP_002994352.1|  78 KIIHSNgDVVYINETIIEDFMYFSYATERNNKIINSYIANMTIQEYFEKLKDRL 131
                                       44444469*****************************************99887 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:                      394  (0.0219756); 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: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.53
# Mc/sec: 1546.64
//
Query:       gi|242398929|ref|YP_002994353.1|  [L=100]
Description: AAA ATPase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.095   12.5   0.0      0.095   12.5   0.0    1.1  1  DUF4422   Domain of unknown function (DUF4422)


Domain annotation for each model (and alignments):
>> DUF4422  Domain of unknown function (DUF4422)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.3e-06     0.095     105     166 ..      35      98 ..       8     100 .] 0.70

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.3e-06
                           DUF4422 105 eeiekllkkydiilpkkrklkie.slyeqYkka.hhiedldllreiikekypeyleafekvlkk 166
                                        +i+++lk+  i l +++ + +   l++   +   + e+ +ll++ ikekype+ +++ek +kk
  gi|242398929|ref|YP_002994353.1|  35 LSIHEALKNPRITLWSPEAAAVLrYLRKTIPEFsISNEASKLLEKAIKEKYPEIWSSVEKHMKK 98 
                                       556666666666665555533331333334344466889999********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       762  (0.042501); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); 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: 0.51u 0.33s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 585.49
//
Query:       gi|242398930|ref|YP_002994354.1|  [L=249]
Description: Cobyrinic acid a,c-diamide synthase [Thermococcus sibiricus MM 739]
Scores for 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-64  214.6   0.2    2.2e-63  213.4   0.4    1.5  2  AAA_31       AAA domain
    6.6e-26   90.9   0.1    8.4e-26   90.5   0.1    1.1  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    1.1e-16   61.0   0.0    1.8e-16   60.4   0.0    1.3  1  CBP_BcsQ     Cellulose biosynthesis protein BcsQ
    1.2e-15   57.6   0.2    7.5e-15   55.1   0.2    1.9  1  ParA         NUBPL iron-transfer P-loop NTPase
    1.5e-13   50.8   0.1    9.3e-13   48.2   0.1    1.9  1  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
    7.8e-13   48.3   0.5    1.4e-11   44.2   0.2    2.3  2  MipZ         ATPase MipZ
    1.1e-06   28.1   1.6    0.00019   20.7   0.4    2.5  3  ArsA_ATPase  Anion-transporting ATPase
    0.00046   19.6   0.4     0.0022   17.3   0.2    1.9  2  VirC1        VirC1 protein
     0.0067   16.2   0.2      0.067   13.0   0.2    2.1  1  ATP_bind_1   Conserved hypothetical ATP binding protein
     0.0067   16.2   0.1      0.018   14.8   0.0    1.7  2  CLP1_P       mRNA cleavage and polyadenylation factor CLP1 P-
     0.0096   15.6   0.4        0.5   10.0   0.2    2.4  2  SRP54        SRP54-type protein, GTPase domain
  ------ inclusion threshold ------
      0.045   13.8   0.0      0.095   12.8   0.0    1.5  1  DUF1938      Domain of unknown function (DUF1938)
      0.048   12.6   0.1      0.083   11.8   0.1    1.3  1  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
      0.053   13.1   0.1       0.13   11.8   0.1    1.6  1  AAA_25       AAA domain
      0.057   12.7   0.2       0.11   11.8   0.2    1.4  1  DUF1611      Domain of unknown function (DUF1611_C) P-loop do
      0.064   13.0   0.0       0.13   11.9   0.0    1.5  1  AAA_24       AAA domain
       0.15   10.2   0.3        0.2    9.8   0.3    1.1  1  FTHFS        Formate--tetrahydrofolate ligase


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 !  213.4   0.4   2.1e-66   2.2e-63       1     175 [.       1     173 [.       1     175 [. 0.96
   2 ?   -2.3   0.0       3.5   3.7e+03      38      67 ..     183     214 ..     177     220 .. 0.55

  Alignments for each domain:
  == domain 1  score: 213.4 bits;  conditional E-value: 2.1e-66
                            AAA_31   1 gkvIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgiekneiektlyevlieeknikeaiiktk 77 
                                       + vI+ianqKGGvGK+Tt++nl+aala +gk vLlvD+DpQ+++t+glg+  +e++ t+y+v+i+e++i+e+++kt 
  gi|242398930|ref|YP_002994354.1|   1 MSVISIANQKGGVGKSTTAINLSAALALKGKNVLLVDMDPQGATTIGLGL--REATPTIYNVIIDEAEIEEVVVKTP 75 
                                       579*******************************************9997..66779******************** PP

                            AAA_31  78 venldlipssidLaeaeielvelekkeeilkellekvkdeYDyiiiDcpPsLglltenaLvasdsviipvqaeayal 154
                                       ++ l+l+ps+i L++aeiel +   +e+il+++l+k+k +YDyiiiD+pPsLg+lt+n+Lvasd+viip+qae+yal
  gi|242398930|ref|YP_002994354.1|  76 IDGLHLVPSNIALSGAEIELSSQIGREYILRNKLSKLKRNYDYIIIDTPPSLGVLTMNSLVASDEVIIPIQAEYYAL 152
                                       ***************************************************************************** PP

                            AAA_31 155 eGleqllktieevkkklnpkl 175
                                       eG++ llk i+ v+++l   l
  gi|242398930|ref|YP_002994354.1| 153 EGIALLLKAIRLVRDRLGIPL 173
                                       *************99876555 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.5
                            AAA_31  38 lDpQanattglgie.kneiektlyevli.eek 67 
                                       +D  +n++ +++ e k++  +++++++i +++
  gi|242398930|ref|YP_002994354.1| 183 FDKRTNLSKEVREEvKRTFGEKVFKTMIpRNV 214
                                       56666776666653244455666666554444 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 !   90.5   0.1   7.9e-29   8.4e-26       1     128 []       4     226 ..       4     226 .. 0.87

  Alignments for each domain:
  == domain 1  score: 90.5 bits;  conditional E-value: 7.9e-29
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH....................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................... RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep....................... 54 
                                       i+ia++kGGvGK+t+a+nL +ala +g++VllvD+Dpq+  +    gl++   +                       
  gi|242398930|ref|YP_002994354.1|   4 ISIANQKGGVGKSTTAINLSAALALKGKNVLLVDMDPQGATTI-GLGLREA--Tptiynviideaeieevvvktpid 77 
                                       78************************************88876.4444443..3348888999999*********** PP

                                       .........................................................................CCHC CS
                                       .........................................................................xxxx RF
                              CbiA  55 .........................................................................dlkr 58 
                                                                                                                 l+ 
  gi|242398930|ref|YP_002994354.1|  78 glhlvpsnialsgaeielssqigreyilrnklsklkrnydyiiidtppslgvltmnslvasdeviipiqaeyyALEG 154
                                       *************************************************************************5555 PP

                                       CCHHHHHHCHCHHHH.....EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEE.EEE--CCHCCCCHHTS-H CS
                                       xxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx RF
                              CbiA  59 llellealgkkkall...lkiagvvlnrvdgeneetllkealeelkqrygvpvlg.viprdeavaeapargepv 128
                                       +  ll+a++ +   l   l+i+g++++++d++  ++l ke  ee+k+ +g +v++ +ipr++++aeap+ g+p+
  gi|242398930|ref|YP_002994354.1| 155 IALLLKAIRLVRDRLgipLEIKGFLITMFDKR--TNLSKEVREEVKRTFGEKVFKtMIPRNVRLAEAPSYGRPI 226
                                       555556666555555667*************9..666666666665555**********************987 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.4   0.0   1.7e-19   1.8e-16       1     231 [.       1     244 [.       1     246 [. 0.86

  Alignments for each domain:
  == domain 1  score: 60.4 bits;  conditional E-value: 1.7e-19
                          CBP_BcsQ   1 mkvlalqGvRGGvGttsllaaLawalhelgesvlviDlspdnlLrlhFnvdieqregwaraeldgapwrqaaley.a 76 
                                       m+v+ +   +GGvG+++ +  L+ al   g++vl++D+ p+   ++   +  e + +  +  +d+a++++ +++  +
  gi|242398930|ref|YP_002994354.1|   1 MSVISIANQKGGVGKSTTAINLSAALALKGKNVLLVDMDPQGATTIGLGLR-EATPTIYNVIIDEAEIEEVVVKTpI 76 
                                       899999999*************************************99999.778889999**********998648 PP

                          CBP_BcsQ  77 pgldllPfGelnveekenlqqlaekaeallaalkelkeqyrwillDlpagasaltrellaladlvllvvepdanc.. 151
                                       +gl+l+P   + +  + +l++   ++  l ++l++lk++y++i++D p     lt + l  +d v+  ++++  +  
  gi|242398930|ref|YP_002994354.1|  77 DGLHLVPSNIALSGAEIELSSQIGREYILRNKLSKLKRNYDYIIIDTPPSLGVLTMNSLVASDEVIIPIQAEYYAle 153
                                       9******98777777777999999999******************************9999**********976533 PP

                          CBP_BcsQ 152 .......hvrLhqqalp...aaellLiNqfeaasqlqqDllqlWlqsl.rrllPlvihrDealaEalaakqPlgeyr 217
                                               +rL + +l    + + +Li  f+   +l +++    ++++ +++   +i r   laEa  +  P+  y+
  gi|242398930|ref|YP_002994354.1| 154 gialllkAIRLVRDRLGiplEIKGFLITMFDKRTNLSKEVREEVKRTFgEKVFKTMIPRNVRLAEAPSYGRPIFLYA 230
                                       3322222345555554322245679***************988776654889999********************** PP

                          CBP_BcsQ 218 pdslaaeevktLan 231
                                       pds  a++ ++La+
  gi|242398930|ref|YP_002994354.1| 231 PDSRGAKAYMKLAE 244
                                       **********9996 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 !   55.1   0.2   7.1e-18   7.5e-15       4     245 ..       2     246 ..       1     247 [. 0.78

  Alignments for each domain:
  == domain 1  score: 55.1 bits;  conditional E-value: 7.1e-18
                              ParA   4 kviavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeekpeqs.....ekkliPvea....k 71 
                                       +vi ++  KGGVGKSt+a+nl++aLa kg++v l+D+D  G      lg++e++p+       e+++  v +    +
  gi|242398930|ref|YP_002994354.1|   2 SVISIANQKGGVGKSTTAINLSAALALKGKNVLLVDMDPQGATTIG-LGLREATPTIYnviidEAEIEEVVVktpiD 77 
                                       58999************************************87654.566664443331223233333332223558 PP

                              ParA  72 gikvmSigfllesedeavvwrGpmksk.aikqllkdvewgelDyLiiDlPPGtgDeqltvaqklplagaviVttpqe 147
                                       g++++  ++ l+   + +   + +  + ++++ l++ +  + Dy+iiD+PP  g   lt+ + +  ++++i    + 
  gi|242398930|ref|YP_002994354.1|  78 GLHLVPSNIALS--GAEIELSSQIGREyILRNKLSKLK-RNYDYIIIDTPPSLG--VLTMNSLVASDEVIIPIQAEY 149
                                       888888888887..555656665555414455555555.679**********99..799999999999999889999 PP

                              ParA 148 valadvkkaiemfkkvkvkvlGvveNmsgfvcpkcgekteifgkgggeklaeelgvpll.geipldpeireasdegk 223
                                        al+ +   ++ ++ v+ + lG+   ++gf  +  +++t++ +k+  e++ +++g +++ + ip + +++ea   g+
  gi|242398930|ref|YP_002994354.1| 150 YALEGIALLLKAIRLVR-DRLGIPLEIKGFLITMFDKRTNL-SKEVREEVKRTFGEKVFkTMIPRNVRLAEAPSYGR 224
                                       99999887777777665.558************99999886.677888899999887662679************** PP

                              ParA 224 plvlkepeseaakaleeiaekv 245
                                       p++l +p+s+ aka++++ae+v
  gi|242398930|ref|YP_002994354.1| 225 PIFLYAPDSRGAKAYMKLAEEV 246
                                       *******************987 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 !   48.2   0.1   8.9e-16   9.3e-13       8     245 ..      10     247 ..       4     249 .] 0.82

  Alignments for each domain:
  == domain 1  score: 48.2 bits;  conditional E-value: 8.9e-16
                         Fer4_NifH   8 kGGiGksttsqnlsaalaemgkkvlivGCDPkaDstrlllggkaqetvldtlrekgavedvkvedvvkkGyggvkcv 84 
                                       kGG+Gkstt+ nlsaala +gk vl+v  DP+  +t  l    a++t+ +++ ++   e+v    vvk+   g++ v
  gi|242398930|ref|YP_002994354.1|  10 KGGVGKSTTAINLSAALALKGKNVLLVDMDPQGATTIGLGLREATPTIYNVIIDEAEIEEV----VVKTPIDGLHLV 82 
                                       9*******************************99996666678899******999987777....555666777777 PP

                         Fer4_NifH  85 esGGPepGvGCa.Grgvitaielleelgayd.dlDfvlyDvLGDvvCGGfalPiredkaqevyivtsgelmalyaan 159
                                        s    +G+       +++   l ++l+  + ++D+++ D       G +++      ++ev+i  ++e  al    
  gi|242398930|ref|YP_002994354.1|  83 PSNIALSGAEIElSSQIGREYILRNKLSKLKrNYDYIIIDTPPSL--GVLTMNSL-VASDEVIIPIQAEYYALEGIA 156
                                       776666666655134566666677888888846*******87654..55666533.46799**************** PP

                         Fer4_NifH 160 niakgiekyaksgg..vrlgGliin..srkvddereliekfaeelgtkvle.vvPrdeivrkaelrkktvieyapes 231
                                        + k+i+  + + g  +++ G +i   +++++  +e+ e+  ++ g kv++ ++Pr+  + +a    + ++ yap+s
  gi|242398930|ref|YP_002994354.1| 157 LLLKAIRLVRDRLGipLEIKGFLITmfDKRTNLSKEVREEVKRTFGEKVFKtMIPRNVRLAEAPSYGRPIFLYAPDS 233
                                       *******9999988345677865542268899999999999999*****97369*********************** PP

                         Fer4_NifH 232 eqakeyrelarkil 245
                                       + ak y +la+++ 
  gi|242398930|ref|YP_002994354.1| 234 RGAKAYMKLAEEVD 247
                                       **********9985 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   0.2   1.4e-14   1.4e-11       2     136 ..       3     152 ..       2     168 .. 0.66
   2 ?   -3.5   0.0       4.7   4.9e+03     199     227 ..     187     214 ..     181     222 .. 0.71

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 1.4e-14
                                       EEEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHHHHHHHHHHHHHHT-............-----E CS
                              MipZ   2 vivlgnekGGsGksttavhvavaLlkkGarvaaidldlrqrtlarylenraataerkgl............sLplpe 66 
                                       vi ++n+kGG Gkstta+ +  aL+ kG++v  +d+d + +t    l+ r at +  ++            + p+  
  gi|242398930|ref|YP_002994354.1|   3 VISIANQKGGVGKSTTAINLSAALALKGKNVLLVDMDPQGATT-IGLGLREATPTIYNViideaeieevvvKTPIDG 78 
                                       7999*******************************99755443.334444443333332000000000000233323 PP

                                       EE-SSS-HH...HHTTS-HHHH.HHHHHHHHHHHHHH-SEEEEE--SS--HHHHHHHHT-SEEEEEEESSHHHH CS
                              MipZ  67 alalseaee...aeveeeeeae.vaeleelvadleaeldfividtPGsdsalsrlahsladtlvtPlndsfvdf 136
                                          ++++ +   ae+e ++++     l++ +++l++++d+i+idtP s   l+  +   +d ++ P+   +  +
  gi|242398930|ref|YP_002994354.1|  79 LHLVPSNIAlsgAEIELSSQIGrEYILRNKLSKLKRNYDYIIIDTPPSLGVLTMNSLVASDEVIIPIQAEYYAL 152
                                       3333332221112333333332124689999***********************************98776655 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 4.7
                                       HHHHHHHT-EEE---B--GGGTTTGGGT- CS
                              MipZ 199 eeLskrvGfrvasGlserviyrelfpsGl 227
                                       ++Lsk v   v   + e+v ++ + p+ +
  gi|242398930|ref|YP_002994354.1| 187 TNLSKEVREEVKRTFGEKV-FKTMIPRNV 214
                                       6788888888888888875.677777665 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.4   1.8e-07   0.00019       8      39 ..       9      40 ..       1      46 [. 0.91
   2 !    5.9   0.0    0.0059       6.2     122     135 ..     113     126 ..      98     152 .. 0.79
   3 ?   -2.3   0.0       1.8   1.9e+03     256     281 ..     182     207 ..     176     211 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.8e-07
                                      ESTTSSHHHHHHHHHHHHHHTTS-EEEEE-ST CS
                       ArsA_ATPase  8 GKGGVGKttvsaatavklsekgkkvllistDP 39
                                       KGGVGK+t +  +++ l+ kgk+vll+  DP
  gi|242398930|ref|YP_002994354.1|  9 QKGGVGKSTTAINLSAALALKGKNVLLVDMDP 40
                                      59****************************** PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0059
                                       CSSSSEEEEESBSC CS
                       ArsA_ATPase 122 eeeydvvvlDtaPT 135
                                       +++yd++++Dt+P 
  gi|242398930|ref|YP_002994354.1| 113 KRNYDYIIIDTPPS 126
                                       689**********6 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 1.8
                                       HHHHHHHHHHHHHHHHHHHTTTSEEE CS
                       ArsA_ATPase 256 flearkkiqkkylkeieelfedlevv 281
                                       ++++r ++ k++ +e++ +f +++ +
  gi|242398930|ref|YP_002994354.1| 182 MFDKRTNLSKEVREEVKRTFGEKVFK 207
                                       78899999999999999999887665 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.2   2.1e-06    0.0022       1      39 [.       1      39 [.       1      45 [. 0.94
   2 ?   -0.2   0.0      0.49   5.2e+02      82     112 ..     114     144 ..     109     154 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.1e-06
                             VirC1  1 mklitfcslkGGaGkttalmglcsalasdgkrvalfead 39
                                      m +i+++  kGG Gk+t+ + l +ala +gk v l + d
  gi|242398930|ref|YP_002994354.1|  1 MSVISIANQKGGVGKSTTAINLSAALALKGKNVLLVDMD 39
                                      8899*******************************9988 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.49
                             VirC1  82 eGfdyaladtrgGsseln.ntiiassdllliP 112
                                       + +dy ++dt      l  n ++as d ++iP
  gi|242398930|ref|YP_002994354.1| 114 RNYDYIIIDTPPSLGVLTmNSLVAS-DEVIIP 144
                                       679*******988877762455555.555566 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 !   13.0   0.2   6.3e-05     0.067       6      99 ..      12     124 ..      10     137 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.3e-05
                        ATP_bind_1   6 GsGKttfvgalseilelrgrsvavvNLDP..A.........aeelpYeaavd...irelitledvmedlglgpngal 68 
                                       G+GK+t   +ls  l l+g++v +v +DP  A         a  + Y++ +d   i+e++    ++    + +n al
  gi|242398930|ref|YP_002994354.1|  12 GVGKSTTAINLSAALALKGKNVLLVDMDPqgAttiglglreATPTIYNVIIDeaeIEEVVVKTPIDGLHLVPSNIAL 88 
                                       9****************************421111111111222345555543334444444444444444444444 PP

                        ATP_bind_1  69 vvale...........flresldwldeelekeeddyllfDtP 99 
                                         a e           +lr++l +l+++      dy+++DtP
  gi|242398930|ref|YP_002994354.1|  89 SGA-EielssqigreyILRNKLSKLKRNY-----DYIIIDTP 124
                                       433.2334444333333333333333332.....77777777 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 !   14.8   0.0   1.7e-05     0.018       4      33 ..      12      41 ..      10      49 .. 0.91
   2 ?   -2.8   0.0       4.5   4.8e+03     100     111 ..     113     124 ..     102     138 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.7e-05
                            CLP1_P  4 dsGKSTlarlLlNyalrkgrkpvyvDlDvG 33
                                       +GKST a +L   ++ kg+++++vD+D+ 
  gi|242398930|ref|YP_002994354.1| 12 GVGKSTTAINLSAALALKGKNVLLVDMDPQ 41
                                      59**************************94 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.5
                            CLP1_P 100 kakasgliIntp 111
                                       k++ + +iI+tp
  gi|242398930|ref|YP_002994354.1| 113 KRNYDYIIIDTP 124
                                       556777888887 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.2   0.00048       0.5      11      39 ..      12      40 ..       3      46 .. 0.92
   2 ?    3.6   0.0     0.041        43      74      92 ..     107     124 ..      91     190 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00048
                                      TSSHHHHHHHHHHHHHHTTS-EEEEEEST CS
                             SRP54 11 GaGKTttlaKLaallkkegkkvllvaaDt 39
                                      G+GK tt+  L+a l  +gk+vllv +D 
  gi|242398930|ref|YP_002994354.1| 12 GVGKSTTAINLSAALALKGKNVLLVDMDP 40
                                      9************************9995 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.041
                                       HHHHHHHHTTSSEEEEEE- CS
                             SRP54  74 eavekakeekidvvlvDTa 92 
                                       ++++k k+ ++d++++DT 
  gi|242398930|ref|YP_002994354.1| 107 NKLSKLKR-NYDYIIIDTP 124
                                       55556555.99******95 PP

>> DUF1938  Domain of unknown function (DUF1938)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     9e-05     0.095      44      75 ..     179     211 ..     148     219 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9e-05
                                       HHHHHHHT------B--...-SHHHHHHHHHTT CS
                           DUF1938  44 lieflekrlskklevkeg.nsdysekvfkvliG 75 
                                       li  ++kr + + ev+e  +  + ekvfk++i 
  gi|242398930|ref|YP_002994354.1| 179 LITMFDKRTNLSKEVREEvKRTFGEKVFKTMIP 211
                                       88999**********9852679*********95 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   7.9e-05     0.083      39      74 ..      12      47 ..       3      53 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.9e-05
                                      TSSHHHHHHHHHHHHHCTT--EEEEEE--------- CS
                              MeaB 39 GaGkstlvealglelrrrGkrvavlavDPsspftGG 74
                                      G+Gkst+  +l + l+ +Gk v ++ +DP    t G
  gi|242398930|ref|YP_002994354.1| 12 GVGKSTTAINLSAALALKGKNVLLVDMDPQGATTIG 47
                                      9****************************9877655 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00012      0.13      41      69 ..      10      40 ..       2      50 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00012
                            AAA_25 41 apgtGKttlaldlalava.tGkpwlg.pvap 69
                                       +g+GK+t a++l++a+a +Gk++l  ++ p
  gi|242398930|ref|YP_002994354.1| 10 KGGVGKSTTAINLSAALAlKGKNVLLvDMDP 40
                                      58****************9999887765544 PP

>> DUF1611  Domain of unknown function (DUF1611_C) P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2    0.0001      0.11      24      60 ..      13      49 ..       3      54 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0001
                           DUF1611 24 vGKrttaleleealeerGlkaafvaTgqtgiliageg 60
                                      vGK tta++l +al  +G ++ +v ++++g+ ++g g
  gi|242398930|ref|YP_002994354.1| 13 VGKSTTAINLSAALALKGKNVLLVDMDPQGATTIGLG 49
                                      8*****************************9988766 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00013      0.13      11      89 ..      11     139 ..       9     154 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00013
                            AAA_24  11 sgiGKTtlakel.......gpkplfidtek.Glksldadkfpdie.swedfldevvel................... 59 
                                        g+GK+t+a +l       g+++l++d++  G+  +     +  +  ++ ++de++                     
  gi|242398930|ref|YP_002994354.1|  11 GGVGKSTTAINLsaalalkGKNVLLVDMDPqGATTIGLGLREATPtIYNVIIDEAEIEevvvktpidglhlvpsnia 87 
                                       69***************************989988875544433334555555555557788889999999999999 PP

                            AAA_24  60 ......................aaeladyktlviDtideleelclaevirqn 89 
                                                             ++ +++y+ ++iDt   l  l+++ +   +
  gi|242398930|ref|YP_002994354.1|  88 lsgaeielssqigreyilrnklSKLKRNYDYIIIDTPPSLGVLTMNSLVASD 139
                                       99999999999999999999*99999*********97777666666665555 PP

>> FTHFS  Formate--tetrahydrofolate ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.3   0.00019       0.2      59      92 ..       3      36 ..       1      49 [. 0.84

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00019
                                      EEESS--TT--SHHHHHHHHHHHHHHTT--EEEE CS
                             FTHFS 59 vtaitPtplGeGKttttigLaqalnklgkkavaa 92
                                      v +i+  + G GK+tt+i L+ al+  gk+++++
  gi|242398930|ref|YP_002994354.1|  3 VISIANQKGGVGKSTTAINLSAALALKGKNVLLV 36
                                      778999999*****************99999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.49
# Mc/sec: 1514.00
//
Query:       gi|242398931|ref|YP_002994355.1|  [L=575]
Description: Membrane-bound metal-dependent hydrolase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.3e-07   30.1   0.0    6.3e-07   29.1   0.0    1.5  1  Exo_endo_phos  Endonuclease/Exonuclease/phosphatase family
  ------ inclusion threshold ------
        2.3    7.3   7.7          4    6.5   7.7    1.4  1  Herpes_LMP1    Herpesvirus latent membrane protein 1 (LMP1)


Domain annotation for each model (and alignments):
>> Exo_endo_phos  Endonuclease/Exonuclease/phosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0     7e-11   6.3e-07       2     233 .]     355     565 ..     354     565 .. 0.64

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 7e-11
                                       EEEESTG......CHHHHTHHHHHHHHHHHHHHCTTSEEEEEEEBSCTCHHHHHHHHH.........TTCEEEEECC CS
                                       xxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxx RF
                     Exo_endo_phos   2 twNvngq......aspalgssrrsdrladlltaydaDvlgLQEvdddelsriplllal.........ggflgassts 63 
                                       ++N+  +      a++          l +ll++y +Dv++ QEv ++   +      +         +  ++++++ 
  gi|242398931|ref|YP_002994355.1| 355 SYNIHQGfapykgAFN-------GNELVKLLKTYSPDVMASQEVVGGMIGNG-----YqdvpvllsaYFGYYYEYS- 418
                                       5677777666655333.......334*****************888854333.....2334558888444444443. PP

                                       HECSSSTTSSEEEEEECSTEEEEEEEEEEETSSSSGCEEEEEEEEEEEEEEECCCHHGHHHHHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Exo_endo_phos  64 ptgggggggnggavlsrfpltslfrrtfiefndlvaalrreplaakleqlniashrdhdlvrdlqllalllqvealn 140
                                          ++  g++g+a++sr+pl  ++ r++   ++ + a     l    +                             
  gi|242398931|ref|YP_002994355.1| 419 ---PAVEGTYGVATFSRWPLEPIEERNLKSLGQARPAQKVKVLSNGFVL---------------------------- 464
                                       ...678**************99966666666666666665555555544............................ PP

                                       HHTTSEEEE...............................EEE-SSSTSGGGBSCGHHHHHHCTTTHHSSCESCETT CS
                                       xxxxxxxxx...............................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Exo_endo_phos 141 adrgapviv...............................aGDfNarpsdddsrvlrtrglalapapvglyllgggp 186
                                               +                               +GD Na  ++     l +   +++p         + p
  gi|242398931|ref|YP_002994355.1| 465 --------InvhmglypeeralqaeellemalkdpvaeiiLGDTNAELHEKAIEILLMEYYDAFP--------ERPP 525
                                       ........244444444444444444444444444444449*****7777777776666666554........5888 PP

                                       TTTTTTTTTEB-BEEEEEECHHHCCEEEEEEECCHHEECTSSCSSSB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Exo_endo_phos 187 tptyvtraggsrlDrilaspalalfrsgvlppplalvrrealtlSDH 233
                                       +++++ +     +D+i+ + + al +   ++ +        + +SDH
  gi|242398931|ref|YP_002994355.1| 526 YTFNWGNVDIENIDYIMIKRGSALKVKDYGWLLD-------VEVSDH 565
                                       8888888888888******866666666666555.......567999 PP

>> Herpes_LMP1  Herpesvirus latent membrane protein 1 (LMP1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   7.7   0.00045         4      86     169 ..     138     222 ..      87     235 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.00045
                                       XXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       Herpes_LMP1  86 lllmitll..lialwnlhgqalylgivlfifgcllvlglwiyllellwrlgatiwqllafflaffldlilliialyl 160
                                       +ll+i +l     lw+ +gq    g  ++ f +ll lg +iy   ++   g   + ll f+   f+  + ++i+ yl
  gi|242398931|ref|YP_002994355.1| 138 ILLVICILgaSYVLWKEKGQLKSPGFGIYAFAALLNLG-FIYPNAIMRYSGFETYYLLHFVGYSFVVTLAILISPYL 213
                                       34444444115679************************.69**99*9999*********9988888888888999** PP

                                       XXXXXXXXX CS
                       Herpes_LMP1 161 qqnwwtllv 169
                                         n +t l+
  gi|242398931|ref|YP_002994355.1| 214 AGNKFTPLL 222
                                       **9999554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (575 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.67u 0.28s 00:00:00.95 Elapsed: 00:00:00.48
# Mc/sec: 3569.96
//
Query:       gi|242398932|ref|YP_002994356.1|  [L=334]
Description: glyceraldehyde-3-phosphate dehydrogenase (GAPDH) [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.4e-32  110.3   0.1    9.2e-32  109.8   0.1    1.2  1  Gp_dh_C        Glyceraldehyde 3-phosphate dehydrogenase, C-te
    6.2e-15   55.4   0.7    3.6e-14   52.9   0.3    2.1  2  DapB_N         Dihydrodipicolinate reductase, N-terminus
    2.2e-05   24.7   0.5    0.00011   22.5   0.0    2.5  3  Gp_dh_N        Glyceraldehyde 3-phosphate dehydrogenase, NAD 
    8.9e-05   21.9   0.2      0.054   12.8   0.2    2.4  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
    0.00075   20.3   0.0     0.0028   18.4   0.0    1.9  2  GFO_IDH_MocA   Oxidoreductase family, NAD-binding Rossmann fo
     0.0052   17.4   0.0      0.099   13.3   0.0    2.8  2  NAD_binding_3  Homoserine dehydrogenase, NAD binding 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 !  109.8   0.1   3.1e-35   9.2e-32       1     158 []     146     296 ..     146     296 .. 0.97

  Alignments for each domain:
  == domain 1  score: 109.8 bits;  conditional E-value: 3.1e-35
                                       HHHHHHHHHHHHEEEEEEEEEEEECTTTSBSSSS--.SSTTTTSBTT.CSSEEEE-THHHHHHHHSGGGTTTEEEEE CS
                           Gp_dh_C   1 LaplakvlndkfgikkglmttvhaytndQkllDgpskkdlrraraaa.eniiptstgaakavglVlpelkgkldglA 76 
                                       L++++++++d +++  ++++++++++++         +d++r++++a +  + ++++++++v++V+p   ++++++A
  gi|242398932|ref|YP_002994356.1| 146 LTRTLNAIKDYIDY--VYAVMIRRAADP---------NDIKRGPVNAiKPSVEVPSHHGPDVQTVIP---INIETMA 208
                                       78999999999888..99**********.........9*********9999****************...9****** PP

                                       EEESSSSEEEEEEEEEESSTS-HHHHHHHHHHHHH....TTTTTTEEEEHSHHHGGGGTTGCS..SEEEEGGGCEEE CS
                           Gp_dh_C  77 vrVPtpnvsvvdlvvelekevtveevnaalkeaae....galkgilsyteeelvssDlvgdph..ssifdaketivv 147
                                       ++VPt+ ++v++++vel+k+ t+e+v+++++++++    ++++g+ s+++ +++++Dl+++++  ++i ++ke+i v
  gi|242398932|ref|YP_002994356.1| 209 FIVPTTLMHVHSVMVELKKPLTREDVIKIFENTTRvllfEKERGFDSTAQLIEFARDLHREWNnlYEIGVWKESISV 285
                                       **************************************************************999************ PP

                                       TTTEEEEEEEE CS
                           Gp_dh_C 148 eenlvkvvawy 158
                                       ++n++++++++
  gi|242398932|ref|YP_002994356.1| 286 KGNRLFYIQAV 296
                                       ********986 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.9   0.3   1.2e-17   3.6e-14       1     111 [.       3     118 ..       3     127 .. 0.87
   2 ?    0.7   0.0      0.18   5.3e+02      84     120 ..     127     164 ..     120     167 .. 0.64

  Alignments for each domain:
  == domain 1  score: 52.9 bits;  conditional E-value: 1.2e-17
                                       EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTC..STTTTTBHH........HHSSSS.--S-BEBSSHHHHHH CS
                            DapB_N   1 ikvavvGasGrmGkevvkaveeaedlelvaavdrke..selegkdag........ellglg.klgvavtddleevle 66 
                                       +kv+++G+ G++Gk+v +av++++d+elv++ ++k+  +++++k++g        +++ ++ k+g+++  +le++le
  gi|242398932|ref|YP_002994356.1|   3 VKVGINGY-GTIGKRVGYAVSKQADMELVGVAKTKPdfEAYRAKELGipvyaaspDFVPRFeKVGFEIVGTLEDLLE 78 
                                       69******.**************************99999999************6665555*************** PP

                                       H-SEEEE-S-HHHHHHHHHHHHHT.T-EEEE--SS--HHHHHHHHH CS
                            DapB_N  67 kadvliDFTtpeavlenlklalek.gvklViGTTGlseeelaelee 111
                                       k+dv++D T p ++ e+ k+++ek gvk+++     +  e+a+++e
  gi|242398932|ref|YP_002994356.1|  79 KVDVIVDAT-PGGMGEKNKALYEKaGVKAIF-----QGGEKASVAE 118
                                       *********.*********999998999998.....5555555555 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.18
                                       HHHHHHT.T-EEEE-.-SS--HHHHHHHHHHTTTSEEEE CS
                            DapB_N  84 lklalek.gvklViG.TTGlseeelaeleelakkigvvi 120
                                       ++ al k  v++V + TTGl +  l+ ++++ + + +v+
  gi|242398932|ref|YP_002994356.1| 127 YEKALGKdYVRVVSCnTTGL-TRTLNAIKDYIDYVYAVM 164
                                       44444443677776647777.556788888887777665 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 !   22.5   0.0   3.7e-08   0.00011       1      33 [.       3      35 ..       3      46 .. 0.87
   2 ?   -2.8   0.0       2.7     8e+03      87      96 ..      79      88 ..      78      91 .. 0.85
   3 ?   -2.1   0.0       1.6   4.8e+03      49      68 ..     267     288 ..     217     305 .. 0.58

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 3.7e-08
                                      CEEEEESTSHHHHHHHHHHHHHTTCEEEEEE-T CS
                           Gp_dh_N  1 vkvainGfGRIGrlvlralleekelevvaindl 33
                                      vkv+inG+G IG+ v  a+ ++ ++e+v + ++
  gi|242398932|ref|YP_002994356.1|  3 VKVGINGYGTIGKRVGYAVSKQADMELVGVAKT 35
                                      69****************************983 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.7
                                      TSSEEEE-SS CS
                           Gp_dh_N 87 gvdlVvestG 96
                                      +vd++v++t 
  gi|242398932|ref|YP_002994356.1| 79 KVDVIVDATP 88
                                      69*****995 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1.6
                                       TEC-SS-EEEE..TTEEEETTE CS
                           Gp_dh_N  49 hgrfkgeveae..eealvvngk 68 
                                       h+++++  e+   +e++ v+g+
  gi|242398932|ref|YP_002994356.1| 267 HREWNNLYEIGvwKESISVKGN 288
                                       4444333222222444555544 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   0.2   1.8e-05     0.054      38      78 ..       4      42 ..       1     111 [. 0.72

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.8e-05
                                      EEEEES-SHHHHHHHHHHH.HTT-EEEEESSSHHHHHCHHHH CS
                      2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlk.afgmkviaydrskkkeeeeeel 78
                                      +vGi G+G IG++v   ++ + +m+++++ ++k + e   ++
  gi|242398932|ref|YP_002994356.1|  4 KVGINGYGTIGKRVGYAVSkQADMELVGVAKTKPDFE---AY 42
                                      7999999999999987776689999999888866322...22 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 !   18.4   0.0   9.5e-07    0.0028       1      77 [.       3      94 ..       3     110 .. 0.84
   2 ?   -1.5   0.0       1.4   4.3e+03      49      86 ..     122     156 ..      97     161 .. 0.63

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 9.5e-07
                                      EEEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESS..................HHHHHTCT CS
                      GFO_IDH_MocA  1 lrvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysd..................leelladp 61
                                      ++v+i G+G ig++ +     +q + e+v++ ++++      a+++g+++y+                   le+ll+  
  gi|242398932|ref|YP_002994356.1|  3 VKVGINGYGTIGKRVG-YAVSKQADMELVGVAKTKPDFEAYRAKELGIPVYAAspdfvprfekvgfeivgtLEDLLE-- 78
                                      589*************.55555599******99998666666*********9999**********************.. PP

                                      TESEEEE-S-GGGHHH CS
                      GFO_IDH_MocA 62 eidavivatpngthee 77
                                      ++d+++ atp g +e+
  gi|242398932|ref|YP_002994356.1| 79 KVDVIVDATPGGMGEK 94
                                      9*****9999966554 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.4
                                       EEESSHHHHHTCTTESEEEE-S-GGGHHHHHHHHHHTT CS
                      GFO_IDH_MocA  49 eaysdleelladpeidavivatpngtheelakaaleag 86 
                                        a +++e+ l     d+v v++ n+t+   +++a++  
  gi|242398932|ref|YP_002994356.1| 122 VAQANYEKALG---KDYVRVVSCNTTGLTRTLNAIKDY 156
                                       34455665555...578888888888777666666655 PP

>> NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   3.3e-05     0.099       1      68 [.       9      88 ..       9     102 .. 0.88
   2 ?    0.7   0.0      0.26   7.8e+02      73      95 ..     289     311 ..     226     326 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.3e-05
                                      --SHHHHHHHHHHHH---SSEEEEEEEEESS.EEE-TT................HHHHHT--CB---HHHHHHHHS-EE CS
                     NAD_binding_3  1 GlGaiGsavleqlkrqqseielelvavadrd.sllskd................rkallasealtldlddliahldpdv 62
                                      G+G+iG++v  ++ +q++   +elv+va+ + + ++++                +  +    +++  l+dl++  ++dv
  gi|242398932|ref|YP_002994356.1|  9 GYGTIGKRVGYAVSKQAD---MELVGVAKTKpDFEAYRakelgipvyaaspdfvPRFEKVGFEIVGTLEDLLE--KVDV 82
                                      99***************6...8*********888888899999999999988886666777788899999999..**** PP

                                      EEE-S- CS
                     NAD_binding_3 63 vVEcas 68
                                      +V++++
  gi|242398932|ref|YP_002994356.1| 83 IVDATP 88
                                      ***986 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.26
                                       HTTHHHHHHTTEEEE-S--CGGG CS
                     NAD_binding_3  73 aelvlkaLkagkdvvtankgala 95 
                                       + ++ +a+ +  dvv  n +a+ 
  gi|242398932|ref|YP_002994356.1| 289 RLFYIQAVHQESDVVPENIDAIR 311
                                       66899999999999999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2159.04
//
Query:       gi|242398933|ref|YP_002994357.1|  [L=276]
Description: Phenazine biosynthesis protein PhzF family [Thermococcus sibiricus MM 739]
Scores for complete 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-59  201.4   0.0    2.5e-59  201.1   0.0    1.1  1  PhzC-PhzF  Phenazine biosynthesis-like protein


Domain annotation for each model (and alignments):
>> PhzC-PhzF  Phenazine biosynthesis-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  201.1   0.0   1.4e-63   2.5e-59       1     262 [.      11     257 ..      11     272 .. 0.91

  Alignments for each domain:
  == domain 1  score: 201.1 bits;  conditional E-value: 1.4e-63
                                       EEET-SSTTSSEEEEEEESTTCS-HHHHHHHHHHHTSSEEEEEE--SSTTSSEEEEEE-SSSEES--HHHHHHHHHH CS
                         PhzC-PhzF   1 vdaFtespfkGNpaaVvldadelddeelqsiAaelnlseTaFllkpsdekarfrlRyFTPvaEvdlcGHatlasaha 77 
                                       +daFt+++fkGNpaaVvld+ eld e + +iA elnlseTaF+ +   ek+ fr+R+FTP  E++lcGHat+a+ ++
  gi|242398933|ref|YP_002994357.1|  11 LDAFTNQAFKGNPAAVVLDCPELDAEIMLAIAGELNLSETAFVWP---EKKGFRVRFFTPGDEIPLCGHATVATFYL 84 
                                       69*******************************************...589************************** PP

                                       HHHHCT-S-SCEEEEEETTEEEEE.EEEEETCEECCEEEEE-SEEEEEE-HHHHHHHHHHCCTSGG-TTS-BEEEES CS
                         PhzC-PhzF  78 laekglvasaetveletkaGilpvkslkekddgeellielkfPvikteevssedlallakllklaaqkalpiavkst 154
                                       l   g++ ++ + ++ +k+G+l +  +    +++++ +  ++P     e++ e+l++++++++l      p+ + +t
  gi|242398933|ref|YP_002994357.1|  85 LWRLGMA-KEGMNKMISKVGELDIL-I----KDKKVWL-KQLPPKIIGELNIEELKSILGVKELV----GPALAMTT 150
                                       *****97.999************93.3....3334444.45666677899999999999999988....6888999* PP

                                       SSEEEEEEBSTCCHHHH----HHHHHHHCT-EEEEEEEETTTSSCCEEEEEEEEGGGTEEEESS-HHHHHHHHHHHH CS
                         PhzC-PhzF 155 glekvivplsseeavaelspdlaeeikkcpkkgvivtaaaeagskkdfhsRmFaPklGivEDpvtGsAsgaLaayls 231
                                       g+ + iv +   +++ +++p+++  ++ ++++g+i ++ ++  sk d ++R+FaP++G+ EDpvtG+Asg La+yl+
  gi|242398933|ref|YP_002994357.1| 151 GTPEGIVGIRTFNELMNIKPNMETLAEFSKENGIIGVYVYTLDSKFDAAGRFFAPAVGVPEDPVTGTASGILAGYLR 227
                                       **********************888999999********************************************** PP

                                       HCC-SSSEEEEEEEE-GGGT--EEEEEEEE. CS
                         PhzC-PhzF 232 eklnleesakikieqgqalgrsgtlevevev 262
                                          +l  + +  +eqg+al+r+g+ +v+ e+
  gi|242398933|ref|YP_002994357.1| 228 LTDKL-TKDSYIFEQGHALKREGKAYVKFEG 257
                                       **999.889999**************98874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       279  (0.0155614); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1717.77
//
Query:       gi|242398934|ref|YP_002994358.1|  [L=118]
Description: hypothetical protein TSIB_0951 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 755.01
//
Query:       gi|242398935|ref|YP_002994359.1|  [L=94]
Description: hypothetical protein TSIB_0952 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.7e-24   84.0   0.2    7.4e-24   83.7   0.2    1.2  1  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 !   83.7   0.2   4.1e-28   7.4e-24       1      76 [.       8      78 ..       8      79 .. 0.96

  Alignments for each domain:
  == domain 1  score: 83.7 bits;  conditional E-value: 4.1e-28
                                      EEEEEEES---SSS----...--TTTT-------TTIIIIIHHHHHHHHHHHHHS...SEEEE-S-GGGSEEEEEE CS
                            DUF167  1 gvilavrvkPgakkdaigleedaegrealkvrvaappvdGkANkalikfLakalgvpksdveivsGeksreKvvri 76
                                      gvil+++v+P+a +++i+  + +e+r++lkv+++appv+GkANk+++kf++k+lg    + ++++Ge+sreK ++i
  gi|242398935|ref|YP_002994359.1|  8 GVILQIYVQPKANTNEIE--GVDEWRGRLKVKIKAPPVEGKANKEVVKFFSKLLG---AEASLIKGETSREKDLLI 78
                                      699***************..8889*******************************...9999**********9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.22s 00:00:00.53 Elapsed: 00:00:00.35
# Mc/sec: 812.30
//
Query:       gi|242398936|ref|YP_002994360.1|  [L=169]
Description: hypothetical protein TSIB_0953 [Thermococcus sibiricus MM 739]
Scores for complete 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-12   46.1   0.7    6.5e-12   45.5   0.7    1.3  1  DUF402    Protein of unknown function (DUF402)


Domain annotation for each model (and alignments):
>> DUF402  Protein of unknown function (DUF402)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.5   0.7   3.6e-16   6.5e-12       2      68 .]      57     123 ..      56     123 .. 0.94

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 3.6e-16
                                       -EEEEE-TT-SEEEEEEEETTTEEEEEEEEEES--EE..E.EEE-EEEEEEESEEE......-HHHH CS
                            DUF402   2 lelwllplglwynvfhfldgdgrlqglYvDiatppevgegawktiDlyLDlvvspdgevevlDedEL 68 
                                        ++ + + g+ y + +++d +g+++g+Y+D+   ++++ + + + Dl LD+ ++p+ge  +lDe+EL
  gi|242398936|ref|YP_002994360.1|  57 KMIYFAFIGEKYDILKVYDREGNFKGIYIDVLAYTKREGDNLEMLDLFLDIFIFPNGEAFLLDEEEL 123
                                       66778889****************************96688*************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 1255.38
//
Query:       gi|242398937|ref|YP_002994361.1|  [L=570]
Description: Glycyl-tRNA synthetase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-24   86.4   1.4    7.8e-24   83.7   0.2    2.6  2  HGTP_anticodon   Anticodon binding domain
    1.3e-10   41.5   0.3    8.3e-10   38.9   0.1    2.5  2  tRNA-synt_2b     tRNA synthetase class II core domain (G, H, 
    7.6e-05   21.9   0.6       0.24   10.4   0.1    2.4  2  tRNA-synt_2      tRNA synthetases class II (D, K and N)
     0.0021   18.2   0.2        1.8    8.7   0.0    2.6  2  Zn-ribbon_8      Zinc ribbon domain
  ------ inclusion threshold ------
       0.01   15.3   0.0      0.065   12.7   0.0    2.1  1  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
      0.023   14.1   0.6       0.36   10.3   0.1    2.3  2  zf-ribbon_3      zinc-ribbon domain
      0.037   13.5   0.9       0.46    9.9   0.0    2.9  3  tRNA-synt_2d     tRNA synthetases class II core domain (F)
      0.068   12.6   0.0       0.14   11.5   0.0    1.5  1  F-actin_cap_A    F-actin capping protein alpha subunit
      0.089   12.5   1.8        5.6    6.7   0.2    2.5  2  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
       0.11   12.3   0.0         11    6.0   0.0    2.5  2  Plectin          Plectin repeat
       0.16   11.5   0.5        6.8    6.3   0.0    2.5  2  TF_Zn_Ribbon     TFIIB zinc-binding
       0.16   12.0   1.3        8.5    6.5   0.0    2.4  2  XPA_N            XPA protein N-terminal


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 ?    0.5   0.1      0.46   6.9e+02      17      49 ..     358     390 ..     347     397 .. 0.84
   2 !   83.7   0.2   5.2e-27   7.8e-24       1      93 [.     476     566 ..     476     567 .. 0.95

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.46
                                       HHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHH CS
                    HGTP_anticodon  17 yakklaeeLraagirvelddsnesigkkiread 49 
                                         kkl+  L+ + +  +l+ ++++i++k++e+ 
  gi|242398937|ref|YP_002994361.1| 358 IIKKLKISLNMKRVGPKLKGDAKRINQKLQEMT 390
                                       568899999999999999999999999999876 PP

  == domain 2  score: 83.7 bits;  conditional E-value: 5.2e-27
                                       SEEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTC CS
                    HGTP_anticodon   1 qvvviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtr 77 
                                       +v+v+pl  k+  l+  a ++ + L+++g+ ++++d+++++g++++++d++g+p++v++++++ e++tvt+rdrdtr
  gi|242398937|ref|YP_002994361.1| 476 EVAVLPLVAKEP-LTSIAYEIFRTLQKEGF-IVVYDEKDTVGRRYARYDEIGTPYCVTIDNQTPEDNTVTIRDRDTR 550
                                       59*******777.****************9.677779**************************************** PP

                                       EEEEEETTHHHHHHHH CS
                    HGTP_anticodon  78 eqervsldelveklke 93 
                                       eq+rv+++el+ekl+e
  gi|242398937|ref|YP_002994361.1| 551 EQIRVKIEELPEKLRE 566
                                       **************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 ?   -2.9   0.0       3.8   5.7e+03      55      72 ..      13      30 ..       9      71 .. 0.74
   2 !   38.9   0.1   5.6e-13   8.3e-10       9      92 ..     158     243 ..     155     455 .. 0.57

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 3.8
                                      TTTB-SEEEEEEEEEEES CS
                                      xxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b 55 GLlRvreFhqkdgyvfha 72
                                       L+R r+F +   ++++ 
  gi|242398937|ref|YP_002994361.1| 13 DLMRRRGFVWSSFEIYGG 30
                                      588999998888777764 PP

  == domain 2  score: 38.9 bits;  conditional E-value: 5.6e-13
                                       EEEEE-SSSHHHHHHHHHHHEEEB..GG.SSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEES.GGGHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx..xx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                      tRNA-synt_2b   9 reyiLkPtneetfvelirdevlrs..kr.LPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfha.easlddslr 81 
                                       ++ +L+P+  +++   ++   l++  ++ LP+ ++qi+  yR+E s  +G+lR+reF q + ++f   +++    ++
  gi|242398937|ref|YP_002994361.1| 158 KKGYLRPETAQGIFVNFKR--LNNfaRNqLPFGVFQIGKAYRNEISPRQGMLRLREFSQAEVEIFFDpKQKEHPHFE 232
                                       566899*999998777763..33333335****************9566*****************94455555666 PP

                                       HHHHHHHHHHH CS
                                       xxxxxxxxxxx RF
                      tRNA-synt_2b  82 dlikaisrife 92 
                                       ++  ++ r++ 
  gi|242398937|ref|YP_002994361.1| 233 EVKDEVLRFYP 243
                                       66666666553 PP

>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0   0.00024      0.37      24      52 ..      44      72 ..      42      84 .. 0.89
   2 !   10.4   0.1   0.00016      0.24      94     129 ..     189     226 ..     187     426 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00024
                                      HHHHHHHHHHHHHHHTT-EE----SEESS CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 24 lrstvtkavrkyleengfieietPiLsks 52
                                      ++ ++ k +r+ + ++gf+eietP ++ +
  gi|242398937|ref|YP_002994361.1| 44 IKRKIEKKIREAFIREGFFEIETPDITPE 72
                                      788999******************88765 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00016
                                       EEEEEEEE--S--BTT..B-S-CEEEEEEEEET-SCHH CS
                                       xxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2  94 vfqiaraFRaEdsrtd..rhlaEFtqieaemsfieeed 129
                                       vfqi++a+R+E s  +    l EF q e+e+ f  +++
  gi|242398937|ref|YP_002994361.1| 189 VFQIGKAYRNEISPRQgmLRLREFSQAEVEIFFDPKQK 226
                                       8**********98755115678********99876655 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.1    0.0052       7.8      24      37 ..      86      99 ..      79     102 .. 0.77
   2 !    8.7   0.0    0.0012       1.8      21      37 ..     123     139 ..     114     142 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0052
                       Zn-ribbon_8 24 apltaCPeCgsevr 37
                                      +plt+C++Cgs+ r
  gi|242398937|ref|YP_002994361.1| 86 DPLTECKKCGSRFR 99
                                      57888999998765 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0012
                       Zn-ribbon_8  21 isdapltaCPeCgsevr 37 
                                         ++ +++CPeCg+e+ 
  gi|242398937|ref|YP_002994361.1| 123 LIREHDIKCPECGGELA 139
                                       44556789*****9775 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 ?   12.7   0.0   4.3e-05     0.065      64     206 ..     152     339 ..      41     341 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.3e-05
                   tRNA_synthFbeta  64 anPlsedqsvlRtsLlpglLevlar..NlargnedvrlFEigkvflkd.seeel....................... 114
                                       + P ++ + +lR+   +g+  + +r  N+ar++  + +F igk ++++ s  ++                       
  gi|242398937|ref|YP_002994361.1| 152 IGPYKDKKGYLRPETAQGIFVNFKRlnNFARNQLPFGVFQIGKAYRNEiSPRQGmlrlrefsqaeveiffdpkqkeh 228
                                       568899999*************99777********************976666688999999999999999999999 PP

                   tRNA_synthFbeta 115 ..............peeerhlaivltgkreeeswsekaravd.fydlkgivealleslgi..ekvefep..aehpal 172
                                                     p e++   +++   + +e++++       f+   ++v+++l  +gi  +k++f++   e+ a 
  gi|242398937|ref|YP_002994361.1| 229 phfeevkdevlrfyPIENQLKNLGMIELTLDEAVKKGYVMNTfFAYYMAMVKRILLDIGIpaNKIRFRQqlPEERAH 305
                                       99999999999999888888888888888778887776665514566789999999999988889999865445555 PP

                   tRNA_synthFbeta 173 hpgrsAeikvdgkevGvlGelhpevleafdlkqr 206
                                           + +++++ ++ G++  +  +   ++dl+++
  gi|242398937|ref|YP_002994361.1| 306 YSSDTWDVEIHSERFGWIECVGIAYRGNYDLSRH 339
                                       5668999999999999999998888888888875 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1      0.11   1.7e+02      19      25 ..      91      97 ..      89     101 .. 0.81
   2 ?   10.3   0.1   0.00024      0.36      11      26 .]     123     138 ..     121     138 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.11
                       zf-ribbon_3 19 CpyCGtk 25
                                      C++CG++
  gi|242398937|ref|YP_002994361.1| 91 CKKCGSR 97
                                      8888876 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00024
                       zf-ribbon_3  11 plssddnvCpyCGtkl 26 
                                       ++++ d++Cp CG++l
  gi|242398937|ref|YP_002994361.1| 123 LIREHDIKCPECGGEL 138
                                       57889********986 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 ?    9.9   0.0   0.00031      0.46      76     129 ..     106     217 ..      39     223 .. 0.61
   2 ?   -3.2   0.0       3.2   4.7e+03     166     191 ..     304     327 ..     272     328 .. 0.61
   3 ?   -2.7   0.1       2.2   3.3e+03      11      48 ..     382     419 ..     376     425 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00031
                                       -.................................................ECESEEE-SSTHH...HHHHHH...TT CS
                      tRNA-synt_2d  76 a.................................................veekllLRthtta...vqirtl...ek 97 
                                       +                                                 +++k  LR  t     v+++ l   ++
  gi|242398937|ref|YP_002994361.1| 106 EvlgidteglsaehltqlirehdikcpecggeladvwyfnlmfetyigpyKDKKGYLRPETAQgifVNFKRLnnfAR 182
                                       25555666666666666666666666666666666666666666677777777888888888722245555588899 PP

                                       S-SSEEEEEEEEEEBSST...-SSSB-SEEEEEEE CS
                      tRNA-synt_2d  98 kkppikiisigrvfRrda...vDathlaeFhqveg 129
                                       +++p+ ++ ig+++R++    + + +l eF q+e 
  gi|242398937|ref|YP_002994361.1| 183 NQLPFGVFQIGKAYRNEIsprQGMLRLREFSQAEV 217
                                       99**************9644467778899999885 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3.2
                                       ETTEEEEEEEEEEECCSSSSEEEEEE CS
                      tRNA-synt_2d 166 fpftePsaevdvylvekkkkwlEllg 191
                                         +     +v++   ++  +w+E +g
  gi|242398937|ref|YP_002994361.1| 304 AHYSSDTWDVEIH--SERFGWIECVG 327
                                       4455555555554..48889999877 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 2.2
                                       TSHSB-SHHHHHHHHHHHHHHCTTCEESSTTSEEEHHH CS
                      tRNA-synt_2d  11 ieagklhpltkvleeikeiflelgfeevegpevesefy 48 
                                       i++  ++++++ l++i e + ++g+  ++g e+e+e +
  gi|242398937|ref|YP_002994361.1| 382 INQKLQEMTQEELKKIFEGLEKIGKVFLDGYELEKEDF 419
                                       44444445555555555555677777788888887755 PP

>> F-actin_cap_A  F-actin capping protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   9.6e-05      0.14      63     230 ..     212     399 ..     200     406 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 9.6e-05
                                       TTEEETTEEEEGGGTEEEEEETTTTEEEEEEE--S-.GGGHHHHHHHHHHHHH.HHHHH-TT-EEEEE......... CS
                     F-actin_cap_A  63 anklgeeryvdpkskksfkfdhlkqkasdvesvele.seleelrkalekalek.YvkehYpsgvasvy......... 128
                                        ++ + e ++dpk+k+  +f+ +k ++  + ++e + ++l  +  +l++a++k Yv +++    ++++         
  gi|242398937|ref|YP_002994361.1| 212 FSQAEVEIFFDPKQKEHPHFEEVKDEVLRFYPIENQlKNLGMIELTLDEAVKKgYVMNTFFAYYMAMVkrilldigi 288
                                       56778899************************9988889999999999998766999988886555556999***** PP

                                       ..............EEEETTEE.EEEEEEEEEEEEGGGTEEEEEEEEEEEESSEEEEEEEEEEEEEE-SSEEEEEEE CS
                     F-actin_cap_A 129 ..............pkeeeeek.elaiiivgnkynpsnFwnGrwrseytvdsssktleGkikvqvHYyEdGNVqlkt 190
                                                      ++ +  + +  + i ++++   +     +r +y ++ + k+  ++++v +HY E      k 
  gi|242398937|ref|YP_002994361.1| 289 pankirfrqqlpeeRAHYS--SdTWDVEIHSERFGWIECVGIAYRGNYDLSRHVKESGADLTVMIHYKEP-----KI 358
                                       *999999988864311222..2359999***********************999*************864.....44 PP

                                       EEEEEEEEE--SHHHHHHHHHHHHHH.HHHHHHHHHHHHHH CS
                     F-actin_cap_A 191 skevseslsvsseessakeivklike.aenkyqeeLnesye 230
                                        k+ + sl++++   + k  +k i++   + +qeeL++ +e
  gi|242398937|ref|YP_002994361.1| 359 IKKLKISLNMKRVGPKLKGDAKRINQkLQEMTQEELKKIFE 399
                                       44444444444333333333333332033344555555555 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 ?    4.5   0.1     0.019        28      20      26 ..      91      97 ..      85      98 .. 0.90
   2 ?    6.7   0.2    0.0038       5.6      10      24 ..     121     135 ..     118     137 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.019
                                      -SSS--- CS
                    DNA_RNApol_7kD 20 CkeCGhR 26
                                      Ck+CG+R
  gi|242398937|ref|YP_002994361.1| 91 CKKCGSR 97
                                      ******9 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0038
                                       ----SSS----SSS- CS
                    DNA_RNApol_7kD  10 vslkkgdpiRCkeCG 24 
                                       ++l+++  i+C eCG
  gi|242398937|ref|YP_002994361.1| 121 TQLIREHDIKCPECG 135
                                       56899999******9 PP

>> Plectin  Plectin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.043        64      28      38 ..     158     168 ..     158     170 .. 0.91
   2 ?    6.0   0.0    0.0074        11      21      32 ..     256     267 ..     253     270 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.043
                           Plectin  28 krGlldeetal 38 
                                       k+G+l++eta+
  gi|242398937|ref|YP_002994361.1| 158 KKGYLRPETAQ 168
                                       79*******98 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0074
                           Plectin  21 lsveeAvkrGll 32 
                                       l+++eAvk+G++
  gi|242398937|ref|YP_002994361.1| 256 LTLDEAVKKGYV 267
                                       89*********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   0.1     0.058        87       3      10 ..      91      98 ..      89     107 .. 0.75
   2 ?    6.3   0.0    0.0046       6.8       2       9 ..     130     137 ..     129     145 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.058
                                      ETTTTCEE CS
                      TF_Zn_Ribbon  3 CPnCgstn 10
                                      C++Cgs++
  gi|242398937|ref|YP_002994361.1| 91 CKKCGSRF 98
                                      88888875 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0046
                                       EETTTTCE CS
                      TF_Zn_Ribbon   2 kCPnCgst 9  
                                       kCP+Cg++
  gi|242398937|ref|YP_002994361.1| 130 KCPECGGE 137
                                       9*****97 PP

>> XPA_N  XPA protein N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.3      0.04        60       3      11 ..      90      98 ..      89     100 .. 0.88
   2 ?    6.5   0.0    0.0057       8.5       3      18 ..     130     145 ..     129     146 .. 0.94

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.04
                             XPA_N  3 kCdeCgkef 11
                                      +C++Cg++f
  gi|242398937|ref|YP_002994361.1| 90 ECKKCGSRF 98
                                      8******99 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0057
                             XPA_N   3 kCdeCgkefldSyLld 18 
                                       kC eCg e++d ++++
  gi|242398937|ref|YP_002994361.1| 130 KCPECGGELADVWYFN 145
                                       7*************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (570 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       892  (0.0497518); expected 358.6 (0.02)
Passed bias filter:                      751  (0.0418874); 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: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.45
# Mc/sec: 3769.76
//
Query:       gi|242398938|ref|YP_002994362.1|  [L=546]
Description: succinyl-CoA:3-ketoacid-CoA ligase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-36  125.7   0.0    1.6e-33  116.0   0.0    3.1  3  CoA_trans        Coenzyme A transferase
    2.4e-06   26.2   0.0    3.9e-06   25.5   0.0    1.2  1  Mal_decarbox_Al  Malonate decarboxylase, alpha subunit, trans


Domain annotation for each model (and alignments):
>> CoA_trans  Coenzyme A transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.0   0.0   1.8e-37   1.6e-33       5     217 .]      14     258 ..      10     258 .. 0.90
   2 ?   -2.2   0.0      0.26   2.3e+03      18      39 ..     320     336 ..     318     356 .. 0.69
   3 !    6.2   0.0   0.00066       5.9      96     152 ..     381     430 ..     369     508 .. 0.72

  Alignments for each domain:
  == domain 1  score: 116.0 bits;  conditional E-value: 1.8e-37
                                       HHHHCTT--TTEEEEE-SBTTBTHHHHHHHHHHHHT....TTSEEEEESTTTEECCHHHHHTTTEEEEEESCTTBBC CS
                         CoA_trans   5 aeavakeikdGmtvavGGFgligiPealiaalarsg....vkdltviiseagvlglgplllngsvkkviasyggetv 77 
                                       +eav+ +i d+++va++GF+l   Pe+li +l++++    + +  ++  +   +  g++l +  +  ++++  +++ 
  gi|242398938|ref|YP_002994362.1|  14 EEAVE-KISDNSVVAISGFNLLVAPEYLILKLYERYkqtgHPKGLFLEVNPIPTAPGRVLDK--IATELYNDPDQEF 87 
                                       89999.****************************9988888888888777766555555544..5555555555555 PP

                                       ...........EHHHHHHHHTTSSEEEEHHHHHHHHHHHHHHHTEETTEEEESTTTTSHGGTT.............. CS
                         CoA_trans  78 ...........nprfgkqflsgelefellpqgtlaerlraGgaglpelgfltntgigtlvapk.............. 129
                                                  +p+++k + ++ +e ++++ gt  + +r  + glp  g+lt++g+gt+++p+              
  gi|242398938|ref|YP_002994362.1|  88 lsgilvtypgwSPTLQKMIQENRIEGYTWSIGTASWFFREVARGLP--GVLTRVGLGTFLDPRedggylnelakkrk 162
                                       566666667978888888888889**********************..***************************** PP

                                       ..ESEEEEETTEEEEEEESSSEEEEEEECCEEETTCSEESSGGGHTTHSHHHHH......HEEEEEEEEEEEECTTS CS
                         CoA_trans 130 ..lkkvpgfgGaeyilepalkadvalikaskadeegnlvfeksagnfnkpaiae......aakvtileveeivekgk 198
                                         +++v ++ G+ey+l++a+k++vali+ ++ade gn++ ek+   ++ +++a+      +++++i++ve+i +  +
  gi|242398938|ref|YP_002994362.1| 163 rcKIEVVNIQGREYLLYQAPKPTVALIRGTTADELGNITTEKEGSFTEILNLAQaskaepNKGIVIAQVERIARYPS 239
                                       **99********************************************************9**************** PP

                                       SECCCESBTGGGHSEEEET CS
                         CoA_trans 199 ldpekvliPgvlvdavvea 217
                                       l p+ + +Pg lvd+vv+a
  gi|242398938|ref|YP_002994362.1| 240 LNPQDIKVPGPLVDYVVVA 258
                                       *****************85 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.26
                                       EEE-SBTTBTHHHHHHHHHHHH CS
                         CoA_trans  18 vavGGFgligiPealiaalars 39 
                                       v++G    igiP + +a++a  
  gi|242398938|ref|YP_002994362.1| 320 VNLG----IGIP-TEVAEIATE 336
                                       8899....9999.777777654 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.00066
                                       HHHHHHHHHHHHHHTEETTEEEESTTTTSHGGTTESEEEEETTEEEEEEESSSEEEE CS
                         CoA_trans  96 pqgtlaerlraGgaglpelgfltntgigtlvapklkkvpgfgGaeyilepalkadva 152
                                        +g+ ++ + +G ++++e+g+++++ ++     +  ++pg gG ++i +++++  +a
  gi|242398938|ref|YP_002994362.1| 381 YEGGVIDAASLGFMEVDEKGNVNPSLLP-----G--RLPGPGGFPVISYGSPRMFFA 430
                                       57999**********************9.....5..89********99999984444 PP

>> Mal_decarbox_Al  Malonate decarboxylase, alpha subunit, transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   4.3e-10   3.9e-06     137     213 ..     183     267 ..     155     279 .. 0.75

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 4.3e-10
                   Mal_decarbox_Al 137 iPnvalvaaekadreGnlytGantedtPaiveatafk....dgiviaqvneivd....klprvdiPadwvdfvvead 205
                                        P val+ +++ad+ Gn+ t ++   t  +  a a k    +giviaqv++i      +   + +P+  vd+vv a+
  gi|242398938|ref|YP_002994362.1| 183 KPTVALIRGTTADELGNITTEKEGSFTEILNLAQASKaepnKGIVIAQVERIARypslNPQDIKVPGPLVDYVVVAP 259
                                       699****************98887777665544444322338**********9877433346889************ PP

                   Mal_decarbox_Al 206 kpfaiepl 213
                                         f++++ 
  gi|242398938|ref|YP_002994362.1| 260 PEFHMQSA 267
                                       99988754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (546 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 3641.93
//
Query:       gi|242398939|ref|YP_002994363.1|  [L=218]
Description: Metallophosphoesterase, calcineurin superfamily [Thermococcus sibiricus MM 739]
Scores for complete 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    2.4e-24   86.4   0.0    1.4  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    1.8e-21   77.6   0.7    3.4e-21   76.7   0.7    1.4  1  Metallophos    Calcineurin-like phosphoesterase
    8.9e-19   67.8   0.7    1.3e-12   47.6   0.0    2.3  2  Metallophos_3  Metallophosphoesterase, calcineurin superfamil


Domain annotation for each model (and alignments):
>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.4   0.0   4.1e-28   2.4e-24       1     164 [.       1     205 [.       1     206 [. 0.76

  Alignments for each domain:
  == domain 1  score: 86.4 bits;  conditional E-value: 4.1e-28
                     Metallophos_2   1 MklaiiSDlHsnldaleavlealkevgvdaiihaGDl.....eeeepevleellela.pvlaVrGNnD........e 63 
                                       Mk+++i+D+H++ + ++++le+lk+++ d+i+ aGD+     +e++ ++l+e+++ + p++aV GN+D        e
  gi|242398939|ref|YP_002994363.1|   1 MKIIAITDIHGRANKVKEILEHLKGEEFDLILIAGDIthfggKEAAYNILKEFISFEkPFYAVMGNCDgrdtlellE 77 
                                       ************************************877666666668*******99***********777666652 PP

                     Metallophos_2  64 evveedvlreaaelgtdl.................peeaelel.....agekvlliHgdpl.........gvkdala 109
                                       e  ++  +++ ++ g  +                  e +  e+     ++ ++ l H  p          g +++ +
  gi|242398939|ref|YP_002994363.1|  78 ELNVNLHGKRIEFNGVGItgiggsnitpfstiwelSENEIWEIlvenyQDGDIVLSHAPPRntkvdktfvGTHAGSK 154
                                       22333333333333333366777777755555554344444445655566669999999879******995555555 PP

                     Metallophos_2 110 ellkeaeegsd.vvvcGHtHvp.evekeggvlvvnPGsvgeprdgdpetyaildtde 164
                                       +l+k  ee++  +v+cGH+H++ +++++g +l+vnPG ++++      +yai+d de
  gi|242398939|ref|YP_002994363.1| 155 SLRKFIEEKHPpLVICGHIHEAmGIDEIGRTLIVNPGPLSRG------HYAIIDFDE 205
                                       555555556666**********9******************9......999999887 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.7   0.7   5.7e-25   3.4e-21       1     203 [.       1     175 [.       1     176 [. 0.82

  Alignments for each domain:
  == domain 1  score: 76.7 bits;  conditional E-value: 5.7e-25
                                       EEEEEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHHTSEEEEEC-TTSCH CS
                       Metallophos   1 lrilvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrgdlekellellaalvkypipvylllGNHegf 77 
                                       ++i+ i+D+H     g+ ++++++l++l+ e + dl+l+aGD+++ g+ e    + l++++++ +p+y+++GN++  
  gi|242398939|ref|YP_002994363.1|   1 MKIIAITDIH-----GRANKVKEILEHLKGE-EFDLILIAGDITHFGGKEA-AYNILKEFISFEKPFYAVMGNCD-- 68 
                                       89********.....*************999.***************9999.66678******************.. PP

                                       HH.HHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTE.EEEEEEESECEEETHHHHHHHHHHHSCHHHHCC.HHHH CS
                       Metallophos  78 ee.ellnkygylgifsepwrsdaevfnnlplaslgsgs.lkvlllhGgspellvsldklgslnleleapepg.dewl 151
                                          + l++ ++l+ + +++r     fn++ + ++g+ + + + ++                    +e +e++ +e+l
  gi|242398939|ref|YP_002994363.1|  69 -GrDTLELLEELNVNLHGKRI---EFNGVGITGIGGSNiTPFSTI--------------------WELSENEiWEIL 121
                                       .22555555555555555544...477777777666655444444....................444443346677 PP

                                       HHHHHHTTCSEEEEEESSESS......CSSSCSCCHHHHHHHHHHTTESEEEEESSSS CS
                       Metallophos 152 kdlekrekadwvivlgHsply......rgsgylfgdealedllkkygvdlvisGHtHv 203
                                        +    +  d +ivl+H p+       +  g + g+++l+++ +++ + lvi+GH+H+
  gi|242398939|ref|YP_002994363.1| 122 VE----NYQDGDIVLSHAPPRntkvdkTFVGTHAGSKSLRKFIEEKHPPLVICGHIHE 175
                                       77....999************************************************7 PP

>> Metallophos_3  Metallophosphoesterase, calcineurin superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   1.4e-07   0.00081       7      53 ..       2      48 ..       1      83 [. 0.93
   2 !   47.6   0.0   2.2e-16   1.3e-12     176     251 ..     129     207 ..     109     213 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.4e-07
                                      EEEEEE--TT-GGGHHHHHHHHHHH--SEEEEES-----HHHHHHHH CS
                     Metallophos_3  7 kvlaisdlkgevellerlveviedkdpDllvlvGdlvkaeakadeye 53
                                      k++ai+d++g+ + +++++e ++  + Dl+++ Gd+ + ++k+  y+
  gi|242398939|ref|YP_002994363.1|  2 KIIAITDIHGRANKVKEILEHLKGEEFDLILIAGDITHFGGKEAAYN 48
                                      9*************************************999999997 PP

  == domain 2  score: 47.6 bits;  conditional E-value: 2.2e-16
                                       EEEEESS--S-SSTBTTBS..---S-HHHHHHHHHH--SEEEE-SS--EE..EEETTEEEEE--BGGGTEEEEEETT CS
                     Metallophos_3 176 kvlllatpPigelvadkgl..kekgsevvaelvktlnPevvvvghavkeh..eelgktlvvnPGaleeGdfavvdle 248
                                        ++l + pP  + ++dk +   ++gs+ + +++ + +P +v++gh + +   +e+g+tl+vnPG l+ G++a++d +
  gi|242398939|ref|YP_002994363.1| 129 DIVLSHAPP-RNTKVDKTFvgTHAGSKSLRKFIEEKHPPLVICGHIHEAMgiDEIGRTLIVNPGPLSRGHYAIIDFD 204
                                       578888899.566666665348*************************99999***********************99 PP

                                       TTE CS
                     Metallophos_3 249 ekk 251
                                       e++
  gi|242398939|ref|YP_002994363.1| 205 ENE 207
                                       876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 1542.90
//
Query:       gi|242398940|ref|YP_002994364.1|  [L=109]
Description: hypothetical protein TSIB_0957 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.039   14.1   0.0      0.062   13.4   0.0    1.3  1  PFO_beta_C  Pyruvate ferredoxin oxidoreductase beta subunit C
      0.085   13.1   0.0      0.091   13.0   0.0    1.1  1  DUF4263     Domain of unknown function (DUF4263)
       0.13   11.5   0.0       0.15   11.3   0.0    1.1  1  MKT1_C      Temperature dependent protein affecting M2 dsRNA 


Domain annotation for each model (and alignments):
>> 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 ?   13.4   0.0     1e-05     0.062      14      47 ..      47      80 ..      37      80 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1e-05
                                      XX-EEEGGGST---.EEHHHHHHHHT-----EEEE CS
                        PFO_beta_C 14 kervykleedgyDp.sdlekAlekalewgdkiplG 47
                                      +e vy+l+e+ ++p s++++Ale+++ew +++  G
  gi|242398940|ref|YP_002994364.1| 47 NEEVYYLDES-FEPvSNFKEALEQVFEWFERYING 80
                                      689******7.887367************998766 PP

>> DUF4263  Domain of unknown function (DUF4263)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.5e-05     0.091      35      99 ..      28      89 ..       2     107 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.5e-05
                           DUF4263 35 Dfllidsl.ngnivlvEikkpdknlltkekkkgniapseelsgaisQikkylllldknkek.geela 99
                                        + +d++ +  + + +ik+   ++l   +++   +p + +++a++Q+ +++ +  + ++  +++  
  gi|242398940|ref|YP_002994364.1| 28 ECPCKDDSiYPAVLIYDIKNEEVYYLD--ESF---EPVSNFKEALEQVFEWFERYINGEKPlMKRSP 89
                                      4567777778999*************7..444...99***************765533333355444 PP

>> MKT1_C  Temperature dependent protein affecting M2 dsRNA replication
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   2.5e-05      0.15     178     237 ..      45     107 ..      42     109 .] 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.5e-05
                            MKT1_C 178 akedalellkkvfpnvedlkedlerafefwdavyalvkelsee...kliskellkefekadew 237
                                        k+++++ l++ f+ v ++ke le+ fe+++  +++ k l +    k+  ke++++f +a + 
  gi|242398940|ref|YP_002994364.1|  45 IKNEEVYYLDESFEPVSNFKEALEQVFEWFERYINGEKPLMKRspkKSAPKEVIHRFMEAIKS 107
                                       688999999***************************999988778777799999999988665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.50
# Mc/sec: 651.84
//
Query:       gi|242398941|ref|YP_002994365.1|  [L=340]
Description: Probable deoxyhypusine synthase [Thermococcus sibiricus MM 739]
Scores for complete 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-115  383.8   0.0   5.8e-115  383.5   0.0    1.1  1  DS        Deoxyhypusine synthase
  ------ inclusion threshold ------
      0.098   13.3   0.1       0.25   12.0   0.1    1.6  1  BLI1      BLOC-1 interactor 1


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 !  383.5   0.0  6.4e-119  5.8e-115       2     286 ..      38     335 ..      37     337 .. 0.95

  Alignments for each domain:
  == domain 1  score: 383.5 bits;  conditional E-value: 6.4e-119
                                DS   2 llesyekigfqatslgeaidilnkm....rkdekctiflgltsnlissGlreiiadlvkeklvdvivtTaggieeDl 74 
                                       +++ ye+igfqat+lg+ai+i++k+     k e++ +flg+tsn++ssGlreiia+lvk+k vdvivtTagg+eeD+
  gi|242398941|ref|YP_002994365.1|  38 VIDYYERIGFQATHLGKAIEIWKKVeakrAKGEEVRVFLGYTSNIVSSGLREIIAYLVKHKKVDVIVTTAGGVEEDF 114
                                       7899*********************888778899******************************************* PP

                                DS  75 ikalgkktylgdfelddeeLrekginRignllvpnenyckfedwvreildkleeeqk....vwspselikelGkein 147
                                       ikal++ ++lg++++dd+++rekginRign++vpn++y +fe+++ +++++l+e ++     ++ se+i++lGk+++
  gi|242398941|ref|YP_002994365.1| 115 IKALKP-FILGEWSVDDAKMREKGINRIGNIFVPNDRYIEFEKHMIPFFERLLEIEReekrALTASEIIYKLGKYMD 190
                                       ******.*********************************************99544343355************** PP

                                DS 148 ......deeSilywAykndipvfcpaltDgslGdqlllfhs.vkekkklkldivkDirelndialkakktgaiilGG 217
                                             +e+SilywAykndip+fcpaltDgs+Gd +l+f +  + +++l++di++Di +ln++a++ak+t+ iilGG
  gi|242398941|ref|YP_002994365.1| 191 eklgkeKEKSILYWAYKNDIPIFCPALTDGSFGD-MLYFFKeERGDRELIIDIANDIVKLNNLAITAKETASIILGG 266
                                       99999889**************************.6666651569999***************************** PP

                                DS 218 GvpKhhilnanlmrngadyavyittaqefdGslsgatldEavSwgkikaeaksvkvyaDaTivlPLlva 286
                                       + pKh i+nanl+r g+dya+yitta ++dGslsga ++E+vSwgkika+a+ v+++aDaT+v+P+lv 
  gi|242398941|ref|YP_002994365.1| 267 SFPKHAIINANLFRGGTDYAIYITTAVPWDGSLSGAPPSEGVSWGKIKAKADYVEIWADATLVFPILVW 335
                                       *******************************************************************96 PP

>> BLI1  BLOC-1 interactor 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   2.8e-05      0.25      71     108 ..      29      66 ..       7      68 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.8e-05
                              BLI1  71 lkkleelekkveyyeklldeleefqdelevktkleknr 108
                                       l+ + +le+ ++yye++  + + + + +e+ +k+e +r
  gi|242398941|ref|YP_002994365.1|  29 LEDVSSLEEVIDYYERIGFQATHLGKAIEIWKKVEAKR 66 
                                       78899******************************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        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 0.30s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 2032.64
//
Query:       gi|242398942|ref|YP_002994366.1|  [L=446]
Description: DEXX-box atpase [Thermococcus sibiricus MM 739]
Scores for complete 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  107.0   0.3    3.9e-29  102.2   0.3    2.4  1  ATPase_2      ATPase domain predominantly from Archaea
    4.6e-30  104.0   0.7    1.2e-29  102.7   0.7    1.7  1  DUF234        Archaea bacterial proteins of unknown function
    6.3e-10   39.2   0.0    1.2e-09   38.2   0.0    1.4  1  AAA_14        AAA domain
    2.1e-05   24.9   0.0    6.7e-05   23.3   0.0    1.8  2  AAA_16        AAA ATPase domain
    0.00013   21.8   0.0    0.00029   20.6   0.0    1.6  1  MarR_2        MarR family
    0.00046   20.5   0.1      0.012   15.9   0.1    2.8  2  AAA_22        AAA domain
     0.0012   19.0   0.1     0.0048   17.0   0.0    1.9  2  DUF4143       Domain of unknown function (DUF4143)
     0.0068   16.8   0.0      0.028   14.8   0.0    2.0  2  AAA           ATPase family associated with various cellular 
  ------ inclusion threshold ------
      0.012   15.5   0.0      0.043   13.7   0.0    1.9  2  TrmB          Sugar-specific transcriptional regulator TrmB
      0.055   12.7   0.0      0.097   11.8   0.0    1.4  1  NB-ARC        NB-ARC domain
      0.076   12.9   0.0       0.18   11.7   0.0    1.6  1  HTH_5         Bacterial regulatory protein, arsR family
       0.12   11.8   0.1        4.6    6.6   0.0    2.5  3  TniB          Bacterial TniB protein
       0.16   12.4   0.0        0.8   10.1   0.0    2.0  1  RNA_helicase  RNA helicase


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 !  102.2   0.3   2.8e-32   3.9e-29       1     233 []       4     195 ..       4     195 .. 0.94

  Alignments for each domain:
  == domain 1  score: 102.2 bits;  conditional E-value: 2.8e-32
                          ATPase_2   1 FfdRekelkeleeilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkk 77 
                                       F++R +elk ++e l+++  e ++iYG++++GKt+L+ e++         ++yy a++++++ +++e+      +++
  gi|242398942|ref|YP_002994366.1|   4 FVNRTEELKAIKERLSSDGFELIVIYGRRRVGKTRLVLEAVRDF-----PHVYYLAVEGDNLRHFKET------AER 69 
                                       9****************************************888.....78**************999......332 PP

                          ATPase_2  78 lekalgiavpkaeleeilkeksklvfkaielllekikkkgkkiiiiiDelqklidlglngaellvkeLlnliesltk 154
                                       +       +p+  +        ++v + +e+ll ++++k    iiiiDe+++li    n++  +++ ++++i+ ++ 
  gi|242398942|ref|YP_002994366.1|  70 V-------FPE--I--------RYVHEDWEALLHALRDK----IIIIDEFPNLI----NENPAVLSIFQRVIDTKLV 121
                                       2.......343..3........88***************....***********....999**************** PP

                          ATPase_2 155 ekhlcvviclsSeglfie.rvyneselegrhky.ilvddldketalnflkegfkeleelskedfeeiyryvGGkPka 229
                                       + ++ +++++sS +++ e +++++s+l+gr+++ +++++l++ + + f+ +        s+e++ e+y +++G+P +
  gi|242398942|ref|YP_002994366.1| 122 NSNTKLILLGSSVSMMTEkVLSYKSPLYGRRTGsMKLKPLKFFHLKGFFPRA-------SWEELVEVYGMTDGIPFY 191
                                       ******************7789**************************9995.......9***************** PP

                          ATPase_2 230 lvel 233
                                       ++++
  gi|242398942|ref|YP_002994366.1| 192 IAQV 195
                                       *987 PP

>> DUF234  Archaea bacterial proteins of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.7   0.7   8.4e-33   1.2e-29       1      99 []     300     397 ..     300     397 .. 0.96

  Alignments for each domain:
  == domain 1  score: 102.7 bits;  conditional E-value: 8.4e-33
                            DUF234   1 wfrfvypnrseielgeseevlekikeelneyvgkvFEelvrelllelnkagklpfrftkvGrwWkkeeeiDivalde 77 
                                       wfrf+ypn s+ie+g     +++i++++n+y+g vFE++++++l+elnka+klpfrf k+GrwW+k+ee+D++al+e
  gi|242398942|ref|YP_002994366.1| 300 WFRFIYPNLSLIEEGVF--DVSEIQRDYNHYLGPVFEKIAKQFLVELNKAKKLPFRFMKIGRWWYKSEEVDLLALNE 374
                                       ***************84..458******************************************************* PP

                            DUF234  78 eekkalfgEvKwkn.sekeakki 99 
                                       +e+k l++EvKwk+ se+ea++i
  gi|242398942|ref|YP_002994366.1| 375 RERKGLLVEVKWKElSEREARGI 397
                                       **************999998876 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.2   0.0     9e-13   1.2e-09       4     127 ..      25     163 ..      23     166 .. 0.70

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 9e-13
                            AAA_14   4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe.....kllelileklke........ekkty 67 
                                       ++vi G RrvGKT l+ + +++      ++ y++++ ++++ +++++     + ++++     e         ++++
  gi|242398942|ref|YP_002994366.1|  25 LIVIYGRRRVGKTRLVLEAVRDFP----HVYYLAVEGDNLRHFKETAervfpE-IRYVH----EdweallhaLRDKI 92 
                                       799*****************8877....9999999988887666442223321.23333....1333456668999* PP

                            AAA_14  68 lflDEiqev....pewekalkslvdeg...knldvivtGSnskllskeia...tslagrva.eielyplsf 127
                                       +++DE  ++    p + ++ ++++d++   +n ++i+ GS+ +++ +++    + l gr + +++l pl+f
  gi|242398942|ref|YP_002994366.1|  93 IIIDEFPNLinenPAVLSIFQRVIDTKlvnSNTKLILLGSSVSMMTEKVLsykSPLYGRRTgSMKLKPLKF 163
                                       *****9999555545555555555544555699*********99998776444666666554999999998 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   4.9e-08   6.7e-05       2      72 ..       4      63 ..       3     115 .. 0.71
   2 ?   -2.0   0.0         3   4.1e+03      43      98 ..     369     414 ..     363     424 .. 0.66

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 4.9e-08
                            AAA_16  2 lvGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekdggif..lrgkcdqlesaipysal 72
                                      +v R eel+++++    ++s++ el++++G + vGK++lv e+ r +   ++++  ++g++ ++        +
  gi|242398942|ref|YP_002994366.1|  4 FVNRTEELKAIKER---LSSDGFELIVIYGRRRVGKTRLVLEAVRDFP--HVYYlaVEGDNLRH--------F 63
                                      88899999777765...557778*****************88877777..45551244444444........3 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3
                            AAA_16  43 ellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawr 98 
                                        l+   ++++g++++ k+++l          +   ++++l++l+++a+   le+w 
  gi|242398942|ref|YP_002994366.1| 369 LLALNERERKGLLVEVKWKEL---------SERE-ARGILKDLERKAKLVGLEEWE 414
                                       555333444577777777777.........4445.448888888888888888876 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   2.1e-07   0.00029       6      55 ..     231     281 ..     227     288 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.1e-07
                                       HHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE....E CS
                            MarR_2   6 aqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr....p 55 
                                       + +r+L a++ +     t++e+ + +g+++s ++  l+ L + GLv+r+    +
  gi|242398942|ref|YP_002994366.1| 231 TYRRILEAIALGKT---TPKEIRDFTGMKHSEITPYLRNLIETGLVVREvpltE 281
                                       789*********95...*****************************99854443 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   8.4e-06     0.012       7     130 ..      25     132 ..      21     135 .. 0.71
   2 ?   -1.4   0.0       1.8   2.5e+03      40      63 ..     219     242 ..     199     271 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 8.4e-06
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseell.eal 82 
                                       ++v++G   +GKT+l+ + ++ ++        ++ ++ v+  ++   k+ +++++ ++             ++ e  
  gi|242398942|ref|YP_002994366.1|  25 LIVIYGRRRVGKTRLVLEAVRDFP--------HVYYLAVEGDNLRHFKETAERVFPEIR------------YVhEDW 81 
                                       699*************99999884........444444444444455555555555555............233667 PP

                            AAA_22  83 eqalraravielliiDEaqhlr..seealeeLrsllnl..srkgvqliLvGt 130
                                       e  l+a ++ +++iiDE+ +l+  ++++l+ + +  +     ++++liL G 
  gi|242398942|ref|YP_002994366.1|  82 EALLHALRD-KIIIIDEFPNLIneNPAVLSIFQRVIDTklVNSNTKLILLGS 132
                                       777777777.899*******98655777777755555567779999999986 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.8
                            AAA_22  40 pevvfvtlpsstsskdllrellra 63 
                                       + +++++ ++ ++ + +l++++  
  gi|242398942|ref|YP_002994366.1| 219 DFLLRYEFTETKTYRRILEAIALG 242
                                       344455566666666666555544 PP

>> DUF4143  Domain of unknown function (DUF4143)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.6   2.2e+03      92     108 ..     211     223 ..     201     235 .. 0.79
   2 !   17.0   0.0   3.5e-06    0.0048      18     121 ..     263     386 ..     227     387 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.6
                                       xxxxxxxxxxxxxxxxx RF
                           DUF4143  92 lyyyrdkngaEvDfvie 108
                                       ++++rd    EvDf+++
  gi|242398942|ref|YP_002994366.1| 211 VSFFRD----EVDFLLR 223
                                       556666....9****96 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 3.5e-06
                                       x..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............xxxxxxxxxxxxx RF
                           DUF4143  18 k..glverlppwsespnskkrlrkspKlyfvDtGLlvallgldkeelleds.............enkGallEnlVaq 79 
                                          +l+e    ++e+p+  k   k+ ++y++D +++ +  ++ ++  l ++              ++G ++E +  q
  gi|242398942|ref|YP_002994366.1| 263 YlrNLIETGLVVREVPLTEKPNSKRGRYYVADNFIAFWFRFIYPNLSLIEEgvfdvseiqrdynHYLGPVFEKIAKQ 339
                                       1556666666677789999999*****************9999998887778**********************999 PP

                                       xxxxxxxxxxxxxxxxxxx....xxxxxxxxx.xxxxxxxxxxxxxx RF
                           DUF4143  80 eLlkysekegaklyyyrdk....ngaEvDfvi.elkggkivpiEvKs 121
                                        L+  +++++  + + +      ++ EvD++  +++++k  ++EvK+
  gi|242398942|ref|YP_002994366.1| 340 FLVELNKAKKLPFRFMKIGrwwyKSEEVDLLAlNERERKGLLVEVKW 386
                                       999965555555555555599966*******9655688889*****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 !   14.8   0.0     2e-05     0.028       2     120 ..      27     142 ..      26     147 .. 0.77
   2 ?   -2.4   0.0       4.3   5.9e+03      37      66 ..     385     412 ..     365     428 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2e-05
                                       EEESSTTSSHHHHHHHHHHHH.THEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS.......TSEEEEEETGGGH CS
                               AAA   2 llyGppGtGKTllakavakel.gvefleisgsellskyvgesekkirelfkeakeka.......kpsilfiDEidal 70 
                                       ++yG   +GKT l+   ++++ +v++l ++g +l+  +++e+++++   ++ + e         + +i++iDE+ +l
  gi|242398942|ref|YP_002994366.1|  27 VIYGRRRVGKTRLVLEAVRDFpHVYYLAVEGDNLR--HFKETAERVFPEIRYVHEDWeallhalRDKIIIIDEFPNL 101
                                       789***********999999867************..67777776544444443333444588777*********** PP

                                       HHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHH CS
                               AAA  71 aksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpall 120
                                       ++++          v++ + +++d    + s++ +i+ + +++++++++l
  gi|242398942|ref|YP_002994366.1| 102 INEN--------PAVLSIFQRVIDTKLVN-SNTKLILLGSSVSMMTEKVL 142
                                       9999........78889999999888875.55777777777777766665 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.3
                                       SSTTHHHHHHHHHHHHHHHTSTSEEEEEET CS
                               AAA  37 kyvgesekkirelfkeakekakpsilfiDE 66 
                                       k+ + se++ r+++k++++ka  + + ++E
  gi|242398942|ref|YP_002994366.1| 385 KWKELSEREARGILKDLERKA--KLVGLEE 412
                                       466678888889998888887..5555555 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   0.0   3.1e-05     0.043       9      55 ..     227     276 ..     225     293 .. 0.92
   2 ?   -2.8   0.0       4.5   6.2e+03      16      31 ..     309     324 ..     308     326 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.1e-05
                                       HCCCHCHHHH...HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEE CS
                              TrmB   9 yEakvYlaLl...klgpatadeiaeelgvprskvYevLrsLedkGlVere 55 
                                       +E k+Y  +l   +lg+ t +ei   +g  +s +  +Lr+L++ GlV re
  gi|242398942|ref|YP_002994366.1| 227 TETKTYRRILeaiALGKTTPKEIRDFTGMKHSEITPYLRNLIETGLVVRE 276
                                       589999999988899********************************987 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.5
                                       HHHHHCCCHHCHHCCC CS
                              TrmB  16 aLlklgpatadeiaee 31 
                                        L+++g  +++ei ++
  gi|242398942|ref|YP_002994366.1| 309 SLIEEGVFDVSEIQRD 324
                                       6889999999999876 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0     7e-05     0.097       2      47 ..       8      50 ..       7      53 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7e-05
                                      HHHHHHHHHHHHCTTTSCSEEEEEEESTTSSHHHHHHHHCCSHCCC CS
                            NB-ARC  2 eksvekviekLlekdelqslvvalvGmgGvGKttlakqilnksdev 47
                                      ++++++++e+L+ +d+++  ++ ++G+  vGKt l+ ++++++ +v
  gi|242398942|ref|YP_002994366.1|  8 TEELKAIKERLS-SDGFE--LIVIYGRRRVGKTRLVLEAVRDFPHV 50
                                      567899******.*****..99*******************98765 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00013      0.18       5      45 ..     233     273 ..     229     274 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00013
                                       HHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5   5 lkILklLaegelcvcelaeelglsqstvShHLkkLreaGLV 45 
                                       ++IL + a g+++  e+ + +g+  s +  +L+ L e GLV
  gi|242398942|ref|YP_002994366.1| 233 RRILEAIALGKTTPKEIRDFTGMKHSEITPYLRNLIETGLV 273
                                       79**************************************9 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.072     1e+02      21      54 ..       9      42 ..       4      52 .. 0.83
   2 ?    6.6   0.0    0.0033       4.6     112     133 ..      82     103 ..      66     121 .. 0.85
   3 ?   -3.7   0.0       4.8   6.6e+03      83      96 ..     228     241 ..     224     270 .. 0.67

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.072
                              TniB 21 erLeeLleypkrkrmpnlllvGdsnnGKtmivek 54
                                      e+L+++ e+ +++  + ++++G+  +GKt +v +
  gi|242398942|ref|YP_002994366.1|  9 EELKAIKERLSSDGFELIVIYGRRRVGKTRLVLE 42
                                      678888888888888999***********99865 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0033
                              TniB 112 lrllrelkvrvLiiDEihnlla 133
                                        +ll++l+ +++iiDE+ nl++
  gi|242398942|ref|YP_002994366.1|  82 EALLHALRDKIIIIDEFPNLIN 103
                                       57999**************986 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 4.8
                              TniB  83 ekrlyaaiLealga 96 
                                       e + y++iLea+  
  gi|242398942|ref|YP_002994366.1| 228 ETKTYRRILEAIAL 241
                                       56678888887654 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00058       0.8       1      85 [.      26     124 ..      26     129 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00058
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl............klkkkdsvys..rnpeddfwdgYt..gqevvvidDfgqv 61 
                                       i++yG++++GK++l+ e ++++   +            k++  ++v+   r + +d+    +  + ++++id+f++ 
  gi|242398942|ref|YP_002994366.1|  26 IVIYGRRRVGKTRLVLEAVRDFPHVYylavegdnlrhfKETA-ERVFPeiRYVHEDWEALLHalRDKIIIIDEFPNL 101
                                       789************998888885558888888888854443.55555555566666555556789*********** PP

                      RNA_helicase  62 kdeenpsdlaelirlvsstpypln 85 
                                        +e np  l+ + r+++++ ++ n
  gi|242398942|ref|YP_002994366.1| 102 INE-NPAVLSIFQRVIDTKLVNSN 124
                                       999.999********999877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); 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: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 2936.35
//
Query:       gi|242398943|ref|YP_002994367.1|  [L=39]
Description: hypothetical protein TSIB_0960 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                      1000  (0.0557756); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); 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: 0.39u 0.29s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 271.22
//
Query:       gi|242398944|ref|YP_002994368.1|  [L=368]
Description: hypothetical protein TSIB_0961 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0043   16.8   1.4     0.0043   16.8   1.4    2.8  2  DUF2157          Predicted membrane protein (DUF2157)
  ------ inclusion threshold ------
      0.011   15.7   3.4      0.031   14.2   0.6    2.3  2  DUF2723          Protein of unknown function (DUF2723)
      0.021   14.1  14.1       0.18   11.0   3.7    2.1  2  Na_H_antiporter  Na+/H+ antiporter family
       0.72    9.6   5.8        0.1   12.4   0.8    2.0  2  SPC25            Microsomal signal peptidase 25 kDa subunit (
        7.2    6.2   9.2       0.25   11.0   0.2    2.5  3  DUF4131          Domain of unknown function (DUF4131)


Domain annotation for each model (and alignments):
>> DUF2157  Predicted membrane protein (DUF2157)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   4.4       1.2   4.4e+03      68     109 ..     143     184 ..      55     196 .. 0.66
   2 !   16.8   1.4   1.2e-06    0.0043      23      84 ..     204     265 ..     190     281 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.2
                           DUF2157  68 llllvllllslllg.avlwrdrrvpprlgeallllaalllgaa 109
                                        l ++++l+ ++++ +v+++ ++v++++  ++l++ ++ +++a
  gi|242398944|ref|YP_002994368.1| 143 YLSISVILGGIVFAlLVTGQ-NEVKRLIEWYILTVVGIHILGA 184
                                       34444445555555333333.3566666666666666666555 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 1.2e-06
                           DUF2157  23 aeeresarrrsfleallvlGalllglGlilfvAanWqglsrlvkfllllvllllslllgavl 84 
                                       ++++   r++s++++ll+++ +ll++Gl+l++   +q+l +   +++++++++++++++++ 
  gi|242398944|ref|YP_002994368.1| 204 HKSKPVVRSKSLVNLLLGISTILLAIGLFLWFRITYQNLKNNSNVGVAIIVMAAVYFIVFLW 265
                                       222223366677********************************************998432 PP

>> DUF2723  Protein of unknown function (DUF2723)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.6   8.7e-06     0.031      23      87 ..      55     156 ..      48     168 .. 0.67
   2 ?    1.8   0.1     0.055     2e+02      51      84 ..     224     256 ..     201     324 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 8.7e-06
                           DUF2723  23 flllgrlfslladaekvalrvnllsalssaltilflfltitlllr................................ 67 
                                        +l+  l+s+ +++ +  + vn+l++l+s l++++l+ ++  ++                                 
  gi|242398944|ref|YP_002994368.1|  55 ITLITTLISIAPFMANFQVVVNMLNVLTSILAAMLLYYLVFSIILlkdlinvslrneerrnsiqrykklisdlnklq 131
                                       57888888888877778888888888877777777777766655555688888888777777766666665554444 PP

                           DUF2723  68 .....skakkiailgaglvgalafa 87 
                                            ++ + + + ++ ++g+++fa
  gi|242398944|ref|YP_002994368.1| 132 fivpiKWISLLYLSISVILGGIVFA 156
                                       4444444444446666666666666 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.055
                           DUF2723  51 saltilflfltitlllrskakkiailgaglvgal 84 
                                       + l ++ lfl      ++ +++  + + +++   
  gi|242398944|ref|YP_002994368.1| 224 TILLAIGLFLWFRITYQNLKNNSNVGV-AIIVMA 256
                                       433333333333333332222211111.111111 PP

>> Na_H_antiporter  Na+/H+ antiporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   3.7     5e-05      0.18      30     122 ..      68     163 ..      44     170 .. 0.59
   2 ?    9.6   2.5   0.00014       0.5      39     154 ..     168     280 ..     162     287 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 5e-05
                   Na_H_antiporter  30 iaalgmlvqs..ipanvysifa.llvvglvvlllrdigamlraeaeareleekeltklpiavliiltlskmpytgal 103
                                       +a++++ v++  +   ++++++ +++v+ ++ll++ i+  lr+e++   ++  + + + +  l     +k++ + +l
  gi|242398944|ref|YP_002994368.1|  68 MANFQVVVNMlnVLTSILAAMLlYYLVFSIILLKDLINVSLRNEERRNSIQRYKKLISDLNKLQFIVPIKWISLLYL 144
                                       33334444441134456666651555566666888888888888877755444333334433333334479999999 PP

                   Na_H_antiporter 104 alvaivkafivalafqntd 122
                                       ++++i+ ++++al++++ +
  gi|242398944|ref|YP_002994368.1| 145 SISVILGGIVFALLVTGQN 163
                                       9999999999999988765 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00014
                   Na_H_antiporter  39 sipanvysifallvvglvvl..llrdigamlraeaeareleekeltklpiavliiltlskmpytgalalvaivkafi 113
                                        i +++++++ + ++g++++  +  +i  ml+ ++   + +++++ + +++ l+ l +s+ ++ ++l    ++  ++
  gi|242398944|ref|YP_002994368.1| 168 LIEWYILTVVGIHILGAIQGyfVGYQISDMLSPNQ--AHKSKPVVRSKSLVNLL-LGISTILLAIGLF---LWFRIT 238
                                       5778999999999999999999999********44..46777777765666666.5554333333333...588999 PP

                   Na_H_antiporter 114 valafqntdvatalvvgalaglivatllela.slseidklln 154
                                        + + +n++v+ a++v a + +iv++ l+ + + +e+ ++l+
  gi|242398944|ref|YP_002994368.1| 239 YQNLKNNSNVGVAIIVMAAVYFIVFLWLIPYsNKHEASNILK 280
                                       9999**********************9999988888888876 PP

>> SPC25  Microsomal signal peptidase 25 kDa subunit (SPC25)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.3      0.37   1.3e+03      57      73 ..      83      99 ..      52     146 .. 0.63
   2 ?   12.4   0.8   2.8e-05       0.1      28     109 ..     216     309 ..     209     359 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.37
                             SPC25 57 pvlaiavvlYfilsgil 73
                                      ++la++++ Y ++s+il
  gi|242398944|ref|YP_002994368.1| 83 SILAAMLLYYLVFSIIL 99
                                      34444444455555554 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 2.8e-05
                             SPC25  28 vrLalGylavaiaavaflydykv..eFeesk...pvlaiavvlYfilsgiltlystfvekntifvg..........k 89 
                                       v L+lG++ +++a+++fl+   +    +++     +++++ ++Yfi+   l  ys+  e+ +i+ +          +
  gi|242398944|ref|YP_002994368.1| 216 VNLLLGISTILLAIGLFLWFRITyqNLKNNSnvgVAIIVMAAVYFIVFLWLIPYSNKHEASNILKTqlyklleladE 292
                                       679***************98765432222221112333333669999999999999999999988744444443321 PP

                             SPC25  90 rktgskrie.....kitissslkkl 109
                                                     k++i+ +++k+
  gi|242398944|ref|YP_002994368.1| 293 --------LrykseKLQIDEYSQKF 309
                                       ........02222255555555554 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.2      0.58   2.1e+03      27      46 ..      78      97 ..      53     107 .. 0.55
   2 ?   -1.9   3.1      0.65   2.3e+03      36      47 ..     141     152 ..      77     196 .. 0.48
   3 ?   11.0   0.2   7.1e-05      0.25       4      64 ..     221     280 ..     214     304 .. 0.67

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.58
                           DUF4131 27 rprrrvllllllllllallg 46
                                       +  + +l+++ll+ l+++ 
  gi|242398944|ref|YP_002994368.1| 78 LNVLTSILAAMLLYYLVFSI 97
                                      44444455555555555544 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.65
                           DUF4131  36 lllllllallgf 47 
                                       ll+l + + lg 
  gi|242398944|ref|YP_002994368.1| 141 LLYLSISVILGG 152
                                       333332222222 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 7.1e-05
                           DUF4131   4 plalvllalllllllllllllrr......rprrrvllllllllllallgfalrapqpnandlsqlle 64 
                                       +++ +lla++l+l +       r      +++  v +++++ +++ +++f++  p+ n+++ s++l+
  gi|242398944|ref|YP_002994368.1| 221 GISTILLAIGLFLWF-------RityqnlKNNSNVGVAIIVMAAVYFIVFLWLIPYSNKHEASNILK 280
                                       333344444444444.......234444488888888888888888888999999988888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1516  (0.0845557); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.65u 0.30s 00:00:00.95 Elapsed: 00:00:00.46
# Mc/sec: 2388.34
//
Query:       gi|242398945|ref|YP_002994369.1|  [L=281]
Description: hypothetical protein TSIB_0962 [Thermococcus sibiricus MM 739]
Scores for complete 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   24.0   8.6    3.1e-05   24.0   8.6    2.5  3  Rhomboid  Rhomboid family
     0.0093   16.1   0.5     0.0093   16.1   0.5    2.2  3  Pox_A14   Poxvirus virion envelope protein A14


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 ?   -3.4   0.1      0.94   8.4e+03      48     109 ..      13      21 ..       5      32 .. 0.48
   2 !   24.0   8.6   3.5e-09   3.1e-05       4     116 ..      48     172 ..      46     201 .. 0.62
   3 ?    0.8   0.6      0.05   4.5e+02     102     140 ..     220     264 ..     193     272 .. 0.69

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 0.94
                                       HHHHHHHHHHHHHHHHHH-S...-EESSHHHHHHHHHHHHHHHHCCCCGS----HC...CCC CS
                          Rhomboid  48 llyllsglagsllsllfsaesesplvGaSGaifgllgallvlvprnrkllrkliiallllll 109
                                       ++yl+                                                      ll+
  gi|242398945|ref|YP_002994369.1|  13 IMYLMI-----------------------------------------------------LLT 21 
                                       223222.....................................................222 PP

  == domain 2  score: 24.0 bits;  conditional E-value: 3.5e-09
                                       CC-TTHHHHGGG--SSHHHHHHHHHHHHHHHHHHHHHH......HH.HHHHHHHHH..HHHHHHHHHHHHH-S...- CS
                          Rhomboid   4 rgelwrlltsmflHagwlHllfNmlallvfGsplerrl......Gs.lrflllyll..sglagsllsllfsaesesp 71 
                                       +g++ rl+t  f+H+++ Hll+N+++++v+ ++l          G  +rfl++ +l    +++ +  l++ +++ ++
  gi|242398945|ref|YP_002994369.1|  48 PGDWIRLYTTHFVHVNFGHLLGNLIIFIVIFPTLYFLAeagkdvGLfKRFLVFVFLilPPILSIVDLLVMRRYDLRY 124
                                       789*********************9987766665443333333365145555544443445566666666666666* PP

                                       EESSHHHHHHHHHHHHHHHHC...CCCGS----HC...CCCCCCCCCC CS
                          Rhomboid  72 lvGaSGaifgllgallvlvpr...nrkllrkliiallllllfillnlv 116
                                        +G+SG+ ++l+ga+ +++ +   ++ +++ ++++    +++i   l+
  gi|242398945|ref|YP_002994369.1| 125 GMGFSGIDSALIGAVPYFSSNmlsRKFNFKLPPLMFSNSFMLITGGLI 172
                                       *************98665543000333333333332222222222333 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.05
                                       HC....CCCCCCCCCCHHHCTSS.....STTTHHHHHHHHHHHHH CS
                          Rhomboid 102 ia.llllllfillnlvlgllpra.....ggvsnlAHlgGllaGll 140
                                       i   +l + ++++ ++++ +pr+     g v+ + H  Gl+  l 
  gi|242398945|ref|YP_002994369.1| 220 IRnFILAISLLIVGAIWAAFPRNllgeaGLVNIFIHYLGLVSTLY 264
                                       222444455555666666667777888888999999999887544 PP

>> Pox_A14  Poxvirus virion envelope protein A14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1      0.88   7.9e+03      52      53 ..      59      60 ..      33      91 .. 0.57
   2 ?   -2.5   0.4      0.64   5.7e+03      48      65 ..      99     117 ..      56     124 .. 0.56
   3 !   16.1   0.5     1e-06    0.0093      14      70 ..     185     241 ..     170     250 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.88
                           Pox_A14 52 Fi 53
                                      F+
  gi|242398945|ref|YP_002994369.1| 59 FV 60
                                      33 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.64
                           Pox_A14  48 sivsFil.givillglllf 65 
                                         v  il  i++++ ll++
  gi|242398945|ref|YP_002994369.1|  99 VFVFLILpPILSIVDLLVM 117
                                       3333333224445555554 PP

  == domain 3  score: 16.1 bits;  conditional E-value: 1e-06
                           Pox_A14  14 vliaGiiLLilacifafvdfskststtdkawralsivsFilgivillglllfsmygr 70 
                                       +li Gi+LL+ ++  af ++  ++   +   r + i  Fil+i +l+   +++++ r
  gi|242398945|ref|YP_002994369.1| 185 LLIGGILLLVYTVSKAFREYDWNSLGKEAQKRKVVIRNFILAISLLIVGAIWAAFPR 241
                                       589********************99999999************99887777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       716  (0.0399353); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 1794.30
//
Query:       gi|242398946|ref|YP_002994370.1|  [L=396]
Description: Molybdenum cofactor biosynthesis protein MoeA [Thermococcus sibiricus MM 739]
Scores for complete 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-47  158.8   0.1    1.2e-46  158.3   0.1    1.3  1  MoeA_N         MoeA N-terminal region (domain I and II)
    1.5e-17   63.6   0.0    3.8e-17   62.3   0.0    1.7  1  MoCF_biosynth  Probable molybdopterin binding domain
    7.6e-17   61.3   0.1    3.1e-16   59.3   0.0    2.2  2  MoeA_C         MoeA C-terminal region (domain IV)
  ------ inclusion threshold ------
      0.078   12.8   0.2        1.6    8.6   0.1    2.5  2  Cyanate_lyase  Cyanate lyase C-terminal 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 !  158.3   0.1   2.8e-50   1.2e-46       2     157 .]       9     173 ..       8     173 .. 0.92

  Alignments for each domain:
  == domain 1  score: 158.3 bits;  conditional E-value: 2.8e-50
                                       -HHHHHHHHHHH-.HH-EEE.EEGGCG-TT-BBSS-EE-SS-BSSS-EESSSEEEEEEBTTB--............. CS
                            MoeA_N   2 sveealaiilaal.eleeee.vplaaealgrvlaedvvApedvPpfdnSamDGYAvraeagsgaseeep........ 68 
                                       ++ eal+++l+ + e+ee e +pl  +algrvlaedv++ +d+Ppfd+Sa+DGYAvrae++ +a+e +p        
  gi|242398946|ref|YP_002994370.1|   9 PYREALEMMLNDIkEIEEIEeLPL-DDALGRVLAEDVISLIDLPPFDRSAVDGYAVRAEDTFQAREYSPvelevide 84 
                                       689**********88877777***.99***************************************999******** PP

                                       ......-S---TT-.EEEE-TTSB--TT--EEEEGGGE.E....EETTE.S--STTTTEE-TTSSB-TTSEEE-TTB CS
                            MoeA_N  69 saageeperllpgg.avrimTGaplPegadaVvpvEdteeeeaketvev.kavkpgenvrraGedikaGevllragt 143
                                       ++ag e+++++++g av+ mTG+++P+ga+aV+ +E+++ +e +++  v ++v+pg+nv  +Ged+k+Gev+l++g+
  gi|242398946|ref|YP_002994370.1|  85 ITAGMESKKEVSNGkAVKLMTGNKMPKGANAVIEQEKVK-REGNKIY-VlRPVAPGQNVAFKGEDVKKGEVVLKKGQ 159
                                       999999999999999***********************6.2233433.269************************** PP

                                       B--CCCHHHHHHCT CS
                            MoeA_N 144 rltpaeigllasvG 157
                                       +l+p+++gll  +G
  gi|242398946|ref|YP_002994370.1| 160 ILRPQDLGLLKGIG 173
                                       **********8776 PP

>> MoCF_biosynth  Probable molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.3   0.0   8.4e-21   3.8e-17       1     142 [.     186     315 ..     186     317 .. 0.91

  Alignments for each domain:
  == domain 1  score: 62.3 bits;  conditional E-value: 8.4e-21
                                       EEEEE-HHHH.........TTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTSSEEEEESS-SS CS
                     MoCF_biosynth   1 avitvGdell.........sgkieDtngpllaellkelgvevskytvvpDdeeeikeallaaleeadviittGGtGp 68 
                                       ++i++Gdel+         +gki  +n+++l++l++++  e + y+v+pDdee i ++l++a  e d++++tGG  +
  gi|242398946|ref|YP_002994370.1| 186 GIIVTGDELIeepdeealnEGKILESNSAMLKALIRQYFGESIFYGVIPDDEELIGATLERAKCECDLVLITGGSAF 262
                                       69*********************************************************6665677*********** PP

                                       STT--HHHHHHHHHSEE-HHHHHHHHHHHHHHCCTTSHGGGGGGE.EETTEEEEE-SSHHHHHHHHHHHHHGGH CS
                     MoCF_biosynth  69 tpdDvtpealaklfekelegfeeafrrvslkpgkpvgvapgailsravgktiigLPGspkavkealeeillpal 142
                                       +++D+ ++ ++            +f++ + kpg+p+g +            i+++ G+p av + ++++++ al
  gi|242398946|ref|YP_002994370.1| 263 GEKDYAHKFVN-----------LLFHGTTIKPGRPIGYGER----------IFVMSGYPAAVFAQFHLYVKYAL 315
                                       *****998875...........56789*******9886666..........9**************99986665 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 ?   -3.1   0.1       2.1   9.2e+03      58      67 ..     145     154 ..     140     155 .. 0.81
   2 !   59.3   0.0   6.9e-20   3.1e-16       1      71 [.     329     395 ..     329     396 .] 0.95

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.1
                                       --EE-TT-EE CS
                            MoeA_C  58 tegleaGeeV 67 
                                       +e++++Ge+V
  gi|242398946|ref|YP_002994370.1| 145 GEDVKKGEVV 154
                                       6789999998 PP

  == domain 2  score: 59.3 bits;  conditional E-value: 6.9e-20
                                       EEEESS-EE--SSS-EEEEEEEES-S-EEEEEE-S---TT-GGGCTT--EEEEE-TT--EE-TT-EEEEEE CS
                            MoeA_C   1 karlaedlksdpgrreflRvilteedgeyvaeptgkqgSglLsslaeAnglivipegtegleaGeeVevil 71 
                                       karl+e+++s  gr ef+ v ++    + +a p+ k+gSg+ s+l+e+n++++ipe+ eg+++GeeV v l
  gi|242398946|ref|YP_002994370.1| 329 KARLKEKVPSSLGRHEFVKVYYE----NGEAVPIKKKGSGIMSALVESNAYLEIPEDSEGYKEGEEVWVVL 395
                                       79*********************....558*************************************9876 PP

>> Cyanate_lyase  Cyanate lyase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.07   3.2e+02      15      35 ..     208     228 ..     202     232 .. 0.86
   2 ?    8.6   0.1   0.00037       1.6      13      39 ..     343     369 ..     337     391 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.07
                     Cyanate_lyase  15 ivqvygealkelinEkfGdGi 35 
                                       i++ +   lk+li+  fG+ i
  gi|242398946|ref|YP_002994370.1| 208 ILESNSAMLKALIRQYFGESI 228
                                       56778899**********988 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00037
                     Cyanate_lyase  13 yEivqvygealkelinEkfGdGimSai 39 
                                       +E v+vy e   ++   k G GimSa+
  gi|242398946|ref|YP_002994370.1| 343 HEFVKVYYENGEAVPIKKKGSGIMSAL 369
                                       799**********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 2480.20
//
Query:       gi|242398947|ref|YP_002994371.1|  [L=176]
Description: Molybdenum cofactor biosynthesis protein B [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.3e-38  130.6   0.1    3.7e-38  130.4   0.1    1.0  1  MoCF_biosynth  Probable molybdopterin binding domain
  ------ inclusion threshold ------
      0.063   13.3   0.1         10    6.1   0.0    2.1  2  LacAB_rpiB     Ribose/Galactose Isomerase


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 !  130.4   0.1   4.2e-42   3.7e-38       1     140 [.      24     166 ..      24     173 .. 0.94

  Alignments for each domain:
  == domain 1  score: 130.4 bits;  conditional E-value: 4.2e-42
                                       EEEEE-HHHHTTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTSSEEEEESS-SSSTT--HHHH CS
                     MoCF_biosynth   1 avitvGdellsgkieDtngpllaellkelgvevskytvvpDdeeeikeallaaleeadviittGGtGptpdDvtpea 77 
                                       avitv+d+   gk+eD +g++++e+lk+ g +   y+vvpD++ +i +a+++ale+ad++ittGGtG+t++D+t ea
  gi|242398947|ref|YP_002994371.1|  24 AVITVSDTASLGKREDLSGYYIIEELKKEGNDNVYYAVVPDEKLKIIKAVIEALEKADIVITTGGTGITRRDITIEA 100
                                       79***************************************************9*********************** PP

                                       HHHHHSEE-HHHHHHHHHHHHHHCCTTSHGGGGGGE.EE.......TTE.EEEE-SSHHHHHHHHHHHHHG CS
                     MoCF_biosynth  78 laklfekelegfeeafrrvslkpgkpvgvapgailsrav.......gkt.iigLPGspkavkealeeillp 140
                                       l++lf++e +gf+e+fr  s+++     v+++a+lsra+       +++ +++LPGs +avk+ale+i+++
  gi|242398947|ref|YP_002994371.1| 101 LRPLFDEEFVGFGEIFRLKSYEE-----VGTAAVLSRATagiirdkESKiVFCLPGSLNAVKTALEIIKRE 166
                                       **********************8.....888888**********98445588***************9954 PP

>> LacAB_rpiB  Ribose/Galactose Isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1    0.0021        19      17      67 ..      46      91 ..      25      94 .. 0.59
   2 ?    6.1   0.0    0.0012        10      66     119 ..     111     164 ..     109     167 .. 0.94

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0021
                                      HHHHHHTTTEEEEECESSSS---HHHHHHHHHHHHHTTSSSEEEEEESSSH CS
                        LacAB_rpiB 17 keyLkekghevidvgteseesvdYpdfakkvaeavasgeadlgiliCgtGi 67
                                      +e+Lk++g + + + +  +   +  ++ k+v ea++  +ad++i+  gtGi
  gi|242398947|ref|YP_002994371.1| 46 IEELKKEGNDNVYYAVVPD---EKLKIIKAVIEALE--KADIVITTGGTGI 91
                                      4444444433333333222...22456666666666..589*********8 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0012
                                       SHHHHHHHHTSTT--EEE-SSHHHHHHHHHTT--SEEEEETTTS-HHHHHHHHH CS
                        LacAB_rpiB  66 GiGmsiaaNkvkgiraalchdeesAklarehnnanvlalGarvigeelakeivk 119
                                       G G    + +++++  a + +  +A   r ++   v +l++ +   ++a ei+k
  gi|242398947|ref|YP_002994371.1| 111 GFGEIFRLKSYEEVGTAAVLSRATAGIIRDKESKIVFCLPGSLNAVKTALEIIK 164
                                       88899999999*********************************9999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.44
# Mc/sec: 1212.88
//
Query:       gi|242398948|ref|YP_002994372.1|  [L=460]
Description: DEXX-box atpase [Thermococcus sibiricus MM 739]
Scores for complete 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-35  120.7   0.1    8.8e-35  120.7   0.1    1.8  3  ATPase_2     ATPase domain predominantly from Archaea
    8.3e-32  109.6   0.7    1.9e-31  108.5   0.7    1.6  1  DUF234       Archaea bacterial proteins of unknown function
    3.5e-08   33.6   0.1      1e-07   32.0   0.1    1.9  1  AAA_14       AAA domain
    3.1e-06   27.0   0.0    8.6e-06   25.5   0.0    1.8  1  HTH_5        Bacterial regulatory protein, arsR family
    4.4e-06   27.2   0.0    9.9e-06   26.0   0.0    1.6  1  AAA_16       AAA ATPase domain
      8e-05   22.6   0.0    0.00025   21.0   0.0    1.8  1  HTH_45       Winged helix-turn-helix
    0.00018   21.8   0.0    0.00041   20.6   0.0    1.5  1  AAA_22       AAA domain
    0.00024   20.8   0.0     0.0007   19.3   0.0    1.8  2  HTH_IclR     IclR helix-turn-helix domain
      0.006   16.8   0.1      0.021   15.1   0.1    1.9  1  UPF0102      Uncharacterised protein family UPF0102
  ------ inclusion threshold ------
      0.011   15.8   0.0       0.03   14.4   0.0    1.7  1  HTH_9        RNA polymerase III subunit RPC82 helix-turn-heli
      0.017   14.9   0.1       0.27   11.1   0.0    2.4  2  TFIIE_alpha  TFIIE alpha subunit
      0.028   14.8   0.0      0.099   13.1   0.0    1.9  2  AAA          ATPase family associated with various cellular a


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 !  120.7   0.1   5.9e-38   8.8e-35       1     232 [.       2     202 ..       2     203 .. 0.96
   2 ?   -3.5   0.0       5.5   8.1e+03      87     115 ..     321     349 ..     311     351 .. 0.71
   3 ?   -4.2   0.1       8.4   1.3e+04     191     207 ..     399     415 ..     382     427 .. 0.53

  Alignments for each domain:
  == domain 1  score: 120.7 bits;  conditional E-value: 5.9e-38
                          ATPase_2   1 FfdRekelkeleeilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkk 77 
                                       F++R++elk l   ++++++e++++YG++++GKtaL+ e+i +        iy+ a +++++++l++f      +++
  gi|242398948|ref|YP_002994372.1|   2 FINRKAELKLLADRVKSNKAEFVVLYGRRRIGKTALILELIRRY-----GGIYLLARETSETENLRRF------SDR 67 
                                       99***************************************998.....78*****************......999 PP

                          ATPase_2  78 lekalgiavpkaeleeilkeksklvfkaielllekikkkgkk.iiiiiDelqklidlglngaellvkeLlnlieslt 153
                                       l++++++++ +           k+ f+++++++e + +k k+ ii+ iDe+++l+    +g++ l + L+++++ ++
  gi|242398948|ref|YP_002994372.1|  68 LANYFNDDILR-----------KNPFQSWDAFFEYLHQKSKErIIVAIDEFPYLV----KGNKALPSILQEYWDLKL 129
                                       99999888887...........899**************9999************....788*************** PP

                          ATPase_2 154 kekhlcvviclsSeglfiervyneselegrhky.ilvddldketalnflkegfkeleelskedfeeiyryvGGkPka 229
                                       ++ +++++ic+sS +++ +++ ++s+ +gr++  ++++++d+ +a++fl ++       s e+f ++y ++GG+P +
  gi|242398948|ref|YP_002994372.1| 130 SKSKIFLIICGSSVSMMEKLLGYKSPIYGRRTAqLKLKPMDFFNAREFLPKY-------SPENFLRAYGVLGGSPAY 199
                                       ********************************99*****************6.......8999************** PP

                          ATPase_2 230 lve 232
                                       l e
  gi|242398948|ref|YP_002994372.1| 200 LLE 202
                                       987 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 5.5
                          ATPase_2  87 pkaeleeilkeksklvfkaielllekikk 115
                                       +  ++++++k   +++++++  ++e+++k
  gi|242398948|ref|YP_002994372.1| 321 EMEQGNALVKLVMEDIDQYLGVVFEEVTK 349
                                       44556666667778888888888888876 PP

  == domain 3  score: -4.2 bits;  conditional E-value: 8.4
                          ATPase_2 191 dldketalnflkegfke 207
                                       d+   +a+++lke+ k+
  gi|242398948|ref|YP_002994372.1| 399 DVSEGEARKILKELTKK 415
                                       33333444444444333 PP

>> DUF234  Archaea bacterial proteins of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.5   0.7   1.2e-34   1.9e-31       1      99 []     309     408 ..     309     408 .. 0.98

  Alignments for each domain:
  == domain 1  score: 108.5 bits;  conditional E-value: 1.2e-34
                            DUF234   1 wfrfvypnrseielgeseevlekikeelneyvgkvFEelvrelllelnkagklpfrftkvGrwWkkeeeiDivalde 77 
                                       wfr+v+pn ++ie+++ +++++ + e++++y+g vFEe+++++l +lnk++klp  ftk+GrwW+k+eeiD+val+e
  gi|242398948|ref|YP_002994372.1| 309 WFRYVQPNIDLIEMEQGNALVKLVMEDIDQYLGVVFEEVTKQFLARLNKMDKLPLSFTKIGRWWYKGEEIDLVALNE 385
                                       ***************************************************************************** PP

                            DUF234  78 eekkalfgEvKwkn.sekeakki 99 
                                       +e++al++EvKwk+ se ea+ki
  gi|242398948|ref|YP_002994372.1| 386 RERQALLVEVKWKDvSEGEARKI 408
                                       **************988888886 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   0.1   6.9e-11     1e-07       3     127 ..      22     171 ..      20     178 .. 0.64

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 6.9e-11
                            AAA_14   3 kilvitGaRrvGKTtllkqlikell....vkkesilyinldderdkkladpe.kllelilek.lke........... 62 
                                       + +v+ G Rr+GKT l+ +li+++              + ++ ++++l+ ++ +l +++ +  l++           
  gi|242398948|ref|YP_002994372.1|  22 EFVVLYGRRRIGKTALILELIRRYGgiylL--------ARETSETENLRRFSdRLANYFNDDiLRKnpfqswdaffe 90 
                                       5799*****************999855542........444444433333322233333333211123344445555 PP

                            AAA_14  63 ......ekktylflDEiqevpewekalkslvd.......egknldvivtGSnskllsk..eiatslag.rvaeiely 123
                                             +++ ++ +DE  ++ +  kal s+++       +++++ +i+ GS+ +++ k    ++   g r+a+++l 
  gi|242398948|ref|YP_002994372.1|  91 ylhqksKERIIVAIDEFPYLVKGNKALPSILQeywdlklSKSKIFLIICGSSVSMMEKllGYKSPIYGrRTAQLKLK 167
                                       55555568999*********66666666655544447665578999*********999444445555515569**** PP

                            AAA_14 124 plsf 127
                                       p++f
  gi|242398948|ref|YP_002994372.1| 168 PMDF 171
                                       *999 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 !   25.5   0.0   5.7e-09   8.6e-06       7      46 ..     244     283 ..     242     284 .. 0.97

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 5.7e-09
                                       HHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5   7 ILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46 
                                       I+ + a+g+++ +e++ e+gl++++v  +L++L +++LV+
  gi|242398948|ref|YP_002994372.1| 244 IMEAIAKGKTSLGEIMSETGLNRAIVGKYLSVLIDLDLVR 283
                                       9*************************************96 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   6.6e-09   9.9e-06       3     103 ..       3      98 ..       1     138 [. 0.73

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 6.6e-09
                            AAA_16   3 vGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipy.sa.laqala 77 
                                       + R++el+ L++   rv+s+  e v+l+G + +GK++l+ el r++    gi+l ++ ++ ++++++ s  la+++ 
  gi|242398948|ref|YP_002994372.1|   3 INRKAELKLLAD---RVKSNKAEFVVLYGRRRIGKTALILELIRRYG---GIYLLARETSETENLRRfSDrLANYF- 72 
                                       668888866666...7778888*****************88887555...66666666666666544466688888. PP

                            AAA_16  78 reellrqlldeaesaeleawreklee 103
                                       ++++lr+   ++ +a +e+ ++k +e
  gi|242398948|ref|YP_002994372.1|  73 NDDILRKNPFQSWDAFFEYLHQKSKE 98 
                                       66887777777666666666665555 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   1.7e-07   0.00025       9      58 ..     242     301 ..     240     303 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.7e-07
                            HTH_45   9 adILeaisegeakkTkimykanLsykllnkYLdmLvekgli..........kkskekYvl 58 
                                       ++I+eai +g+++  +im +  L+  ++ kYL+ L++ +l+          k +k+kY++
  gi|242398948|ref|YP_002994372.1| 242 FAIMEAIAKGKTSLGEIMSETGLNRAIVGKYLSVLIDLDLVrrevpvtaswKSRKGKYYI 301
                                       79**************************************97777777776667777765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   2.8e-07   0.00041       4     129 ..      20     140 ..      16     148 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.8e-07
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.sskdllrellralglelkaerlsseell 79 
                                       +a ++v++G   +GKT l+ +l +++         +  +++   +s+t +++ +  +l++ ++++  +  ++  + +
  gi|242398948|ref|YP_002994372.1|  20 KAEFVVLYGRRRIGKTALILELIRRY---------GGIYLLARETSETeNLRRFSDRLANYFNDDILR--KNPFQSW 85 
                                       6889**********************.........999999****9999**************99999..8999999 PP

                            AAA_22  80 ealeqalrarav.ielliiDEaqhlr..seealeeLrsllnl..srkgvqliLvG 129
                                       +a+ ++l+++++ + ++ iDE+ +l   ++++ + L + ++l  s++++ li++G
  gi|242398948|ref|YP_002994372.1|  86 DAFFEYLHQKSKeRIIVAIDEFPYLVkgNKALPSILQEYWDLklSKSKIFLIICG 140
                                       9999999999998899********9763233333335556665566666666666 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0         4   5.9e+03       4      16 ..      34      46 ..      32      48 .. 0.80
   2 !   19.3   0.0   4.7e-07    0.0007       6      51 ..     242     285 ..     239     286 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 4
                                      HHHHHHCT-CTTB CS
                          HTH_IclR  4 RalaiLdalaeap 16
                                      +++ iL+++++ +
  gi|242398948|ref|YP_002994372.1| 34 KTALILELIRRYG 46
                                      78889***99875 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 4.7e-07
                                       HHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                          HTH_IclR   6 laiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveqd 51 
                                       +ai++a+a++     l e+  +tgl+++ v  +L+ L+ l +v+++
  gi|242398948|ref|YP_002994372.1| 242 FAIMEAIAKGKTS--LGEIMSETGLNRAIVGKYLSVLIDLDLVRRE 285
                                       89**********6..****************************985 PP

>> UPF0102  Uncharacterised protein family UPF0102
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   1.4e-05     0.021      21      52 ..     371     405 ..     364     424 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.4e-05
                                       EEETTEEEEEEE....TTEEEEEEEEE-......-- CS
                           UPF0102  21 wrcragEiDiia....tevlvfvEVKtRssekfgsp 52 
                                       w ++  EiD++a    +++ + vEVK++  ++ g++
  gi|242398948|ref|YP_002994372.1| 371 WWYKGEEIDLVAlnerERQALLVEVKWKDVSE-GEA 405
                                       445678**********889********94322.333 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 ?   14.4   0.0     2e-05      0.03      23      57 ..     248     282 ..     244     283 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2e-05
                                       HHHSSBEHHHHHHHHSSTHHHHHHHHHHHHHTTSE CS
                             HTH_9  23 lrkgrltlrelvkktkLsldqVkksLvvLiqhrlV 57 
                                       ++kg+ +l e+ ++t+L++  V k L+vLi + lV
  gi|242398948|ref|YP_002994372.1| 248 IAKGKTSLGEIMSETGLNRAIVGKYLSVLIDLDLV 282
                                       679***************************99998 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00018      0.27       8      78 ..     232     303 ..     227     307 .. 0.81
   2 ?    0.7   0.1      0.31   4.7e+02      42      65 ..     403     427 ..     394     438 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00018
                                       HHCS-..HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTEEEEEEEEEEC CS
                       TFIIE_alpha   8 rkfyg..eeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrdeekswykyywriny 78 
                                       r++ +   + + ++++++ kg+++  ++  e+++++ +++k L  L +  lv     +  + + +k  ++in+
  gi|242398948|ref|YP_002994372.1| 232 REELDepRNYFAIMEAIA-KGKTSLGEIMSETGLNRAIVGKYLSVLIDLDLVRREVPVTASWKSRKGKYYIND 303
                                       555553467899999999.******************************999776666666666777777776 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.31
                                       HHHHHHHHHH.HHCTSEEEEEEEET CS
                       TFIIE_alpha  42 nelrklLnrL.yearlvkykrrrde 65 
                                        e rk+L +L ++a+l + k ++++
  gi|242398948|ref|YP_002994372.1| 403 GEARKILKELtKKAQLLDLKNWQED 427
                                       5789999999446899999999986 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   6.7e-05     0.099       1     119 [.      24     150 ..      24     155 .. 0.82
   2 ?   -3.6   0.0       9.3   1.4e+04      37      57 ..     396     416 ..     386     419 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.7e-05
                                       EEEESSTTSSHHHHHHHHHHHHT.HEEEEEETTTCSSS...............STTHHHHHHHHHHHHHHHTS.TSE CS
                               AAA   1 vllyGppGtGKTllakavakelg.vefleisgsellsk...............yvgesekkirelfkeakeka.kps 60 
                                       v+lyG   +GKT+l+  +++  g +++l  + se  +                + ++  ++  ++f+ + +k+ +  
  gi|242398948|ref|YP_002994372.1|  24 VVLYGRRRIGKTALILELIRRYGgIYLLARETSETENLrrfsdrlanyfnddiLRKNPFQSWDAFFEYLHQKSkERI 100
                                       689******************8546666666666654456777888888888878888899999999998888556* PP

                                       EEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHH CS
                               AAA  61 ilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpal 119
                                       i+ iDE+  l+k +         ++++ +l+e  ++k ++sk+++i+ + +++++++ l
  gi|242398948|ref|YP_002994372.1| 101 IVAIDEFPYLVKGN---------KALPSILQEYWDLKLSKSKIFLIICGSSVSMMEKLL 150
                                       **********9999.........889999999999999999999999999988887765 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 9.3
                                       SSTTHHHHHHHHHHHHHHHTS CS
                               AAA  37 kyvgesekkirelfkeakeka 57 
                                       k+   se + r+++ke+ +ka
  gi|242398948|ref|YP_002994372.1| 396 KWKDVSEGEARKILKELTKKA 416
                                       466667777777777766654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (460 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.48
# Mc/sec: 2899.91
//
Query:       gi|242398949|ref|YP_002994373.1|  [L=249]
Description: SAM-dependent methyltransferase, UbiE/COQ5 family [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-26   91.5   0.0    1.5e-25   89.7   0.0    1.9  2  Methyltransf_25  Methyltransferase domain
    3.4e-21   75.7   0.0    1.9e-20   73.3   0.0    2.0  2  Methyltransf_11  Methyltransferase domain
    2.5e-18   66.3   0.0    3.2e-18   66.0   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    9.9e-16   57.8   0.2    1.7e-15   57.0   0.2    1.3  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    2.1e-13   50.9   0.0    7.2e-13   49.1   0.0    1.8  2  Methyltransf_12  Methyltransferase domain
    2.7e-10   40.3   0.0    4.6e-10   39.6   0.0    1.4  1  Methyltransf_23  Methyltransferase domain
    6.5e-09   35.6   0.0    9.5e-09   35.0   0.0    1.2  1  MTS              Methyltransferase small domain
    3.7e-08   33.0   0.0    4.5e-08   32.7   0.0    1.2  1  TehB             Tellurite resistance protein TehB
    2.8e-05   23.6   0.0    4.4e-05   22.9   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
    7.1e-05   22.0   0.1    0.00011   21.4   0.1    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase
    0.00026   20.2   0.1    0.00034   19.9   0.1    1.2  1  Methyltransf_3   O-methyltransferase
    0.00039   20.1   0.0    0.00067   19.3   0.0    1.3  1  NodS             Nodulation protein S (NodS)
    0.00074   19.0   0.0      0.001   18.5   0.0    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
     0.0014   18.2   0.0     0.0022   17.6   0.0    1.3  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
     0.0019   18.2   0.0     0.0033   17.4   0.0    1.3  1  Methyltransf_18  Methyltransferase domain
     0.0019   18.2   0.0     0.0024   17.9   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
      0.002   17.6   0.1      0.084   12.3   0.1    2.4  2  CheR             CheR methyltransferase, SAM binding domain
     0.0021   17.8   0.1     0.0031   17.2   0.1    1.2  1  MethyltransfD12  D12 class N6 adenine-specific DNA methyltran
     0.0029   16.9   0.0     0.0044   16.3   0.0    1.2  1  Methyltransf_2   O-methyltransferase domain
     0.0065   16.6   0.0      0.042   14.0   0.0    2.2  1  FtsJ             FtsJ-like methyltransferase
     0.0065   16.1   0.0      0.013   15.1   0.0    1.5  2  TPMT             Thiopurine S-methyltransferase (TPMT)
     0.0087   15.8   0.0      0.016   14.9   0.0    1.5  1  UPF0020          Putative RNA methylase family UPF0020
  ------ inclusion threshold ------
      0.012   15.1   0.0      0.027   14.0   0.0    1.6  1  Methyltransf_4   Putative methyltransferase
      0.041   13.6   0.0      0.063   13.0   0.0    1.4  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
      0.061   14.0   0.0       0.46   11.1   0.0    2.1  2  Bin3             Bicoid-interacting protein 3 (Bin3)
      0.071   12.7   0.0        2.5    7.7   0.0    2.2  2  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
      0.078   13.3   0.2          2    8.8   0.0    2.5  2  AdoMet_MTase     Predicted AdoMet-dependent methyltransferase
       0.13   11.4   0.5        6.5    5.8   0.0    2.1  2  N2227            N2227-like protein
       0.23   10.9   0.0       0.34   10.3   0.0    1.2  1  adh_short        short chain dehydrogenase


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 !   89.7   0.0   2.5e-28   1.5e-25       1      97 []      45     139 ..      45     139 .. 0.98
   2 ?   -1.2   0.0       5.5   3.4e+03      84      97 .]     183     196 ..     168     196 .. 0.77

  Alignments for each domain:
  == domain 1  score: 89.7 bits;  conditional E-value: 2.5e-28
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEEST.GGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssga.lhh 76 
                                       +Ldl+cGtG  tl+lakr+  ++v+g+D+ eemle a+++a++egl +ef+qgda +++fe+ +fD+v+++++ +++
  gi|242398949|ref|YP_002994373.1|  45 ILDLACGTGIPTLELAKRG--YEVVGMDLHEEMLEVAKRKAKREGLTIEFIQGDALEVNFEQ-EFDAVTMFFSsIMY 118
                                       8*****************5..***************************************97.9************* PP

                                       SSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  77 lsdedlekalkeiarvLkpgG 97 
                                       +++++l+k+++ + ++LkpgG
  gi|242398949|ref|YP_002994373.1| 119 FDEKNLKKLFNSVIKALKPGG 139
                                       ********************9 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 5.5
                                       HHHHHHHHHEEEEE CS
                   Methyltransf_25  84 kalkeiarvLkpgG 97 
                                         +k++ ++Lkp+G
  gi|242398949|ref|YP_002994373.1| 183 LHFKRLVQILKPNG 196
                                       4589999*****99 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.3   0.0   3.1e-23   1.9e-20       1      95 [.      46     142 ..      46     143 .. 0.96
   2 ?   -0.3   0.0       2.8   1.7e+03      81      92 ..     185     196 ..     180     198 .. 0.85

  Alignments for each domain:
  == domain 1  score: 73.3 bits;  conditional E-value: 3.1e-23
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES.-CCC-.. CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvsse.vlhhv.. 74 
                                       Ld++cGtG+ + +lakrg++vvg+Dl +eml++ak+ka++egl++ef+++da +++fe   fD+v++++ +++++  
  gi|242398949|ref|YP_002994373.1|  46 LDLACGTGIPTLELAKRGYEVVGMDLHEEMLEVAKRKAKREGLTIEFIQGDALEVNFEQ-EFDAVTMFFsSIMYFde 121
                                       8********************************************************99.9*****99867888888 PP

                                       CCHHHHHHHHHHHEEEEEEEE CS
                   Methyltransf_11  75 edpekalkeiaRvLkpgGllv 95 
                                       ++++k+++ + + LkpgG++v
  gi|242398949|ref|YP_002994373.1| 122 KNLKKLFNSVIKALKPGGVFV 142
                                       9******************98 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 2.8
                                       HHHHHHHEEEEE CS
                   Methyltransf_11  81 lkeiaRvLkpgG 92 
                                       +k ++++Lkp+G
  gi|242398949|ref|YP_002994373.1| 185 FKRLVQILKPNG 196
                                       78999******9 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.0   0.0   5.2e-21   3.2e-18       5     113 ..      43     147 ..      39     196 .. 0.85

  Alignments for each domain:
  == domain 1  score: 66.0 bits;  conditional E-value: 5.2e-21
                   Methyltransf_31   5 lrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsn 81 
                                       +++lDl+CGtG  t+ela++   + evvG D  ee++e+A+ +a++ gl+ +eF qgd+ e +  +e + fD ++ +
  gi|242398949|ref|YP_002994373.1|  43 KKILDLACGTGIPTLELAKR---GYEVVGMDLHEEMLEVAKRKAKREGLT-IEFIQGDALEVN--FE-QEFDAVTMF 112
                                       689***************76...467***********************8.**********99..99.9****8776 PP

                   Methyltransf_31  82 ..evl.naladpdkileeiervlkpggilliedpr 113
                                         +++  + ++++k +++++++lkpgg+++++ p+
  gi|242398949|ref|YP_002994373.1| 113 fsSIMyFDEKNLKKLFNSVIKALKPGGVFVADFPC 147
                                       424447899999******************98777 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.0   0.2   2.7e-18   1.7e-15      39     150 ..      33     142 ..      23     145 .. 0.85

  Alignments for each domain:
  == domain 1  score: 57.0 bits;  conditional E-value: 2.7e-18
                                       HHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T CS
                   Ubie_methyltran  39 veklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfedd 115
                                       + k +a+++ +k+lD+a+Gtg  +++l++   + ++vv++D+ e+mL+v+++k+k+eg   ief+q++a e++fe+ 
  gi|242398949|ref|YP_002994373.1|  33 IFKGDAKREVKKILDLACGTGIPTLELAK---RGYEVVGMDLHEEMLEVAKRKAKREGL-TIEFIQGDALEVNFEQ- 104
                                       55667899999**********99998865...5779**********************7.6*************97. PP

                                       -EEEEEEES-.GGG-S-H..HHHHHHHHHHEEEEEEEE CS
                   Ubie_methyltran 116 sfDvvtvsfG.lrnvtDk..lkaLkeayrvlkpGGrlv 150
                                        fD vt+ f  +  + +k  +k ++++ + lkpGG +v
  gi|242398949|ref|YP_002994373.1| 105 EFDAVTMFFSsIMYFDEKnlKKLFNSVIKALKPGGVFV 142
                                       5******997355554332257789999*******986 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.1   0.0   1.2e-15   7.2e-13       1      99 []      46     141 ..      46     141 .. 0.88
   2 ?   -1.7   0.0       8.2   5.1e+03      87      97 ..     186     196 ..     183     197 .. 0.85

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 1.2e-15
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvas.nvl 76 
                                       L++ cGtG  + +l+++  + e++g+D++++++   +++ akre++  ++++ +al++  +   + fD+v+++ + +
  gi|242398949|ref|YP_002994373.1|  46 LDLACGTGIPTLELAKR--GYEVVGMDLHEEML-EVAKRKAKREGLTIEFIQGDALEVNFE---QEFDAVTMFfSSI 116
                                       89***************..**************.666666777777877777777776544...59*******9999 PP

                   Methyltransf_12  77 hhl..kdirevldnirklLkpgGrl 99 
                                        ++  k+++++++++ k+LkpgG++
  gi|242398949|ref|YP_002994373.1| 117 MYFdeKNLKKLFNSVIKALKPGGVF 141
                                       999********************86 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 8.2
                   Methyltransf_12  87 dnirklLkpgG 97 
                                       +++ + Lkp+G
  gi|242398949|ref|YP_002994373.1| 186 KRLVQILKPNG 196
                                       67899*****9 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   0.0   7.5e-13   4.6e-10       4     117 ..      18     143 ..      12     190 .. 0.76

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 7.5e-13
                   Methyltransf_23   4 qreeelsdklerllpk.....lraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae........kakkaq 67 
                                       +r+e++ d+++++ +      +r+ +++Ld++cGtGi + +l+++g++v+g+Dl +e+ e a+        ++ + q
  gi|242398949|ref|YP_002994373.1|  18 RRAERVGDEIDFVEEIfkgdaKREVKKILDLACGTGIPTLELAKRGYEVVGMDLHEEMLEVAKrkakreglTIEFIQ 94 
                                       45577776665555322234489999***********9999*******************99655555444222222 PP

                   Methyltransf_23  68 kdqfdeqeaaepqg......kfdlIvlre.vlehvp..dppellrqiatllkpgGylll 117
                                        d                   fd +++++ ++  ++  ++ +l++++ + lkpgG+++ 
  gi|242398949|ref|YP_002994373.1|  95 GDA----------LevnfeqEFDAVTMFFsSIMYFDekNLKKLFNSVIKALKPGGVFVA 143
                                       222..........133344478888887624666666689***************9985 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.0   1.5e-11   9.5e-09      31     135 ..      41     141 ..      24     143 .. 0.88

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 1.5e-11
                                       TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEEEEE---S CS
                               MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekkfdlivsNPPf 107
                                       + +k+lDl+cG+G+ +++lak+  e  v+ +d + + le+ak+ +++++l +e+++ d+le   e++fd++ +   f
  gi|242398949|ref|YP_002994373.1|  41 EVKKILDLACGTGIPTLELAKRGYE--VVGMDLHEEMLEVAKRKAKREGLTIEFIQGDALEVNFEQEFDAVTMF--F 113
                                       5578*****************9887..9*********************************9999******994..7 PP

                                       TTTCHCHHHHHHHHHHHHHHHEEEEEEE CS
                               MTS 108 hagkatelavaeeliaeAkeaLkegGeL 135
                                        +    +++  ++l+++  +aLk+gG +
  gi|242398949|ref|YP_002994373.1| 114 SSIMYFDEKNLKKLFNSVIKALKPGGVF 141
                                       7777888888999999999999999875 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.0   7.3e-11   4.5e-08      32     129 ..      43     140 ..      12     176 .. 0.92

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 7.3e-11
                                       -EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG----S-EEEEEE.ESSGGG CS
                              TehB  32 gkvldlgcgqgrnslylsllgydvtawdknensiafleeikekenlknistalydineaklderydfils.tvvlmf 107
                                        k+ldl cg g  +l l+  gy+v  +d  e+ ++  ++ +++e l+ i+    d  e+++++++d +      +m+
  gi|242398949|ref|YP_002994373.1|  43 KKILDLACGTGIPTLELAKRGYEVVGMDLHEEMLEVAKRKAKREGLT-IEFIQGDALEVNFEQEFDAVTMfFSSIMY 118
                                       599*******************************************9.**999*************885415679** PP

                                       S-GGGHHHHHHHHHHTEEEEEE CS
                              TehB 108 leaeripsiienmqectkvggy 129
                                       ++++ + ++ + + +  k+gg 
  gi|242398949|ref|YP_002994373.1| 119 FDEKNLKKLFNSVIKALKPGGV 140
                                       *******************995 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   7.1e-08   4.4e-05      64     163 ..      43     142 ..      31     145 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 7.1e-08
                                       -EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG-----SEEEE.ES-GGG CS
                              CMAS  64 mtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedldekvdrvvs.vgafeh 139
                                       +++Ld+ cG G  + + ++r + +vvg+ l +e  ++ak++ ++++l+ +     +   ++++++d+v   +  +  
  gi|242398949|ref|YP_002994373.1|  43 KKILDLACGTGIPTLELAKR-GYEVVGMDLHEEMLEVAKRKAKREGLTIEFIQGDALEVNFEQEFDAVTMfFSSIMY 118
                                       689*****************.************************977554333333468999****9862578999 PP

                                       TSGGGHHHHHHHHHHHS-TT-EEE CS
                              CMAS 140 vgkenydtffkklkkllkedGlll 163
                                       + ++n+++ f+ + k+lk++G+++
  gi|242398949|ref|YP_002994373.1| 119 FDEKNLKKLFNSVIKALKPGGVFV 142
                                       9*********************97 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.1   1.7e-07   0.00011      21      94 ..      32     106 ..      27     132 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.7e-07
                                       HHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTT.TCCCEEEE-S-CCGHHHHHHH CS
                            RrnaAD  21 eIldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkkls.kdeklkvvhqDflkfetpeev 94 
                                       eI++    +e +++l+++ G+Gi T eLakr  +vv + l e+++++ + k + ++  ++ ++ D+l+ ++ +e 
  gi|242398949|ref|YP_002994373.1|  32 EIFKGDAKREVKKILDLACGTGIPTLELAKRGYEVVGMDLHEEMLEVAKRKAKrEGLTIEFIQGDALEVNFEQEF 106
                                       555555567899**************************************99978889999*********99854 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.1   5.5e-07   0.00034      52     161 ..      46     149 ..      28     177 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 5.5e-07
                                       EEE--TTSHHHHHHHTTS-TT-EEEEEES-HHHHHHHHHHHHHTT-GGGEEEEES-HHHHHHHHHTSSS---EEEEE CS
                    Methyltransf_3  52 leiGvftGyslLatalalPeDGkilaididreayeialkfiqkagvaekieliegdalkvLeelvkdkklpefDfif 128
                                       l++   tG   L +a       +++ +d  +e  e+a++  ++ g+   ie+i+gdal+v  e   d   + f    
  gi|242398949|ref|YP_002994373.1|  46 LDLACGTGIPTLELAKR---GYEVVGMDLHEEMLEVAKRKAKREGLT--IEFIQGDALEVNFEQEFDAV-TMFFSSI 116
                                       55555555555555543...23699******************9985..**********9766666664.4555556 PP

                                       E-S-GGGHHHHHHHHHHTEEEEEEEEEE-TTGG CS
                    Methyltransf_3 129 vDaDkssyvnyyeklleLvkvGgliaiDntLWe 161
                                       +  D ++ ++ ++ +++ +k Gg+ + D   W+
  gi|242398949|ref|YP_002994373.1| 117 MYFDEKNLKKLFNSVIKALKPGGVFVADFPCWF 149
                                       678999**********************99995 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   1.1e-06   0.00067      40     143 ..      38     142 ..      31     148 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.1e-06
                              NodS  40 aqgsiadalevGcaaGalterlapyckrltvvdvveeaiararervke.sshiswivsdvqqfstdekfdlivv..a 113
                                       a++++ ++l++ c +G  t +la     +  +d+ ee ++ a+++ k+    i +i+ d  +++ +++fd + +  +
  gi|242398949|ref|YP_002994373.1|  38 AKREVKKILDLACGTGIPTLELAKRGYEVVGMDLHEEMLEVAKRKAKReGLTIEFIQGDALEVNFEQEFDAVTMffS 114
                                       678999**********************************999988751569******************8765225 PP

                              NodS 114 evlyyiedvaelraavrnlvsllapdgqlv 143
                                        ++y+  d ++l+   + +++ l+p+g +v
  gi|242398949|ref|YP_002994373.1| 115 SIMYF--DEKNLKKLFNSVIKALKPGGVFV 142
                                       66665..66789999999*******99988 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.7e-06     0.001     159     257 ..      39     142 ..      27     144 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.7e-06
                              PrmA 159 vkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseellk...eekadvi.. 230
                                        +e +++lD+ +G+Gi ++  ak g  +vv++D+ e  ++vak+ a++ +++ ++ +  ++++l+   e+++d +  
  gi|242398949|ref|YP_002994373.1|  39 KREVKKILDLACGTGIPTLELAKRGY-EVVGMDLHEEMLEVAKRKAKREGLTIEF-I--QGDALEvnfEQEFDAVtm 111
                                       455679*****************996.799********************99988.3..344443334678887733 PP

                              PrmA 231 .vaNIL...aevlielaedikklvkegglli 257
                                        ++ I+    + l +l +++ k++k+gg+++
  gi|242398949|ref|YP_002994373.1| 112 fFSSIMyfdEKNLKKLFNSVIKALKPGGVFV 142
                                       3678884444789999999999999999997 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 !   17.6   0.0   3.5e-06    0.0022       2      74 ..      43     111 ..      42     140 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.5e-06
                   Methyltransf_15   2 rvilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklklekikvdl 74 
                                       + ilDl +G+G  + ++a+ + +v++++  +e l++a++ a+  g    i +++gd +e+  + +++++   +
  gi|242398949|ref|YP_002994373.1|  43 KKILDLACGTGIPTLELAKRGYEVVGMDLHEEMLEVAKRKAKREGL--TIEFIQGDALEVNFEQEFDAV--TM 111
                                       679*****************99********************9965..799*****9996555555544..33 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   5.4e-06    0.0033      15      88 ..      42     111 ..      37     112 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 5.4e-06
                   Methyltransf_18  15 gsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGleklkeeevdtvvi 88 
                                        ++++D  +  g+ +++l+k+g   +v+ +D++e+ le ak++++++gl   ie++ +d le+  e+e+d+v++
  gi|242398949|ref|YP_002994373.1|  42 VKKILDLACGTGIPTLELAKRGY--EVVGMDLHEEMLEVAKRKAKREGL--TIEFIQGDALEVNFEQEFDAVTM 111
                                       56899999999999999998886..5***********************..7**********999999999875 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   3.9e-06    0.0024       9      75 ..      26      87 ..      18     132 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3.9e-06
                   Methyltransf_32  9 laelvakllkelakesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklg 75
                                       + +v++++k  +++++ ++++D+++G g  +  la      +++vvg+d++ee+ e a++ a++ g
  gi|242398949|ref|YP_002994373.1| 26 EIDFVEEIFKG-DAKREVKKILDLACGTGIPTLELAK----RGYEVVGMDLHEEMLEVAKRKAKREG 87
                                      56789998888.89999******************99....59*******************99987 PP

>> CheR  CheR methyltransferase, SAM binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0      0.12        73      61      82 ..      61      81 ..      28      88 .. 0.81
   2 !   12.3   0.1   0.00014     0.084     119     172 ..      89     142 ..      83     143 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.12
                                      SSS-EEEEEEESSCHHHHHHHH CS
                              CheR 61 aklkvkilAtDidlkvlekAka 82
                                      ++  +++++ D+ +++le Ak+
  gi|242398949|ref|YP_002994373.1| 61 KR-GYEVVGMDLHEEMLEVAKR 81
                                      33.6899999999999999987 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00014
                                       TEEEEE--TTT-SGGG--EEEEEE.-SSGGGC-CHHHHHHHHHHHCCEEEEEEEE CS
                              CheR 119 lvkFeklnllekksvlgklDvifc.rnvliYfdeetqekvlerfaeklkpgglLl 172
                                       +++F + ++le  ++++++D ++     ++Yfde++ +k+ + + ++lkpgg+ +
  gi|242398949|ref|YP_002994373.1|  89 TIEFIQGDALE-VNFEQEFDAVTMfFSSIMYFDEKNLKKLFNSVIKALKPGGVFV 142
                                       58888899999.999999999865257789**********************975 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 !   17.2   0.1     5e-06    0.0031      13      97 ..      31     123 ..      25     138 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 5e-06
                                       HCCS-.....--SEEEETT-TTSCCHHCS...SSCEEEEES-HHHHHHHHHHCCH...SHHHHHHHHH.TCTTGGC. CS
                   MethyltransfD12  13 kelipkd...kgktfvepFaGggaVffeakkqgkkvlinDinedlinlykalikn...nveelikelekllekeele 83 
                                       +e+++ d    +k++ ++ +G+g+ ++e+ k+g++v+  D++e+   ++k++ k     +e +  ++ +  +++e++
  gi|242398949|ref|YP_002994373.1|  31 EEIFKGDakrEVKKILDLACGTGIPTLELAKRGYEVVGMDLHEEMLEVAKRKAKReglTIEFIQGDALEVNFEQEFD 107
                                       44555445558999************************************988888988888888888888888887 PP

                                       TSHHHHHHHH..HHHH CS
                   MethyltransfD12  84 nereyfyelr..eefn 97 
                                         + +f  +   +e+n
  gi|242398949|ref|YP_002994373.1| 108 AVTMFFSSIMyfDEKN 123
                                       7766666665665555 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   7.1e-06    0.0044      61     161 ..      40     140 ..      26     145 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 7.1e-06
                                       GG-SEEEEET-TTSHHHHHHHHH-TT-EEEEEE-HH.HHHHHHHHS-----TTEEEEES-TTTS---.--SEEEE.. CS
                    Methyltransf_2  61 eglkslvDvGGGtGalakaivsayPtikvivfDlpe.VveaAkehlsageeervefvgGdffkdslP.eaDaill.. 133
                                       +++k+++D+  GtG    + ++   + +v+ +Dl e   e Ak++    e   +ef++Gd  + +   e Da+ +  
  gi|242398949|ref|YP_002994373.1|  40 REVKKILDLACGTGIPTLELAKR--GYEVVGMDLHEeMLEVAKRK-AKREGLTIEFIQGDALEVNFEqEFDAVTMff 113
                                       67999*********987777765..66788889975277888888.7788899*********999987789887632 PP

                                       ESSGGGS-HHHHHHHHHHHHHH--TT-E CS
                    Methyltransf_2 134 krvlhDwsdekcvklLkrvkkalpagGk 161
                                       +++++ +++++ +kl + v kal++gG 
  gi|242398949|ref|YP_002994373.1| 114 SSIMY-FDEKNLKKLFNSVIKALKPGGV 140
                                       56666.9999***************995 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   6.8e-05     0.042      21      80 ..      41     107 ..      25     195 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.8e-05
                                       TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEES.SSS.......HHH..TTEEEECS-CCCSSHHHHHC CS
                              FtsJ  21 pgktvvDlgaaPGgwsqvllqrlgakgkvvavDl.qpm.......apl..pgvttiqgditdpetiekik 80 
                                       ++k+++Dl++++G  +  l++r g    vv++Dl  +m       a++    +++iqgd ++ + ++++ 
  gi|242398949|ref|YP_002994373.1|  41 EVKKILDLACGTGIPTLELAKR-G--YEVVGMDLhEEMlevakrkAKRegLTIEFIQGDALEVNFEQEFD 107
                                       5688******************.5..68******7777999776544444578889***99988877544 PP

>> TPMT  Thiopurine S-methyltransferase (TPMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   2.2e-05     0.013      40     114 ..      44     124 ..      29     136 .. 0.70
   2 ?   -3.2   0.0       8.6   5.3e+03     130     150 ..     177     197 ..     176     203 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.2e-05
                                       EEEEET-TT-HHHHHH-BTTEEEEEE-S-HHHHHHHHHHHTT........SGGGGGEEEE--...........-TTT CS
                              TPMT  40 rvlvPlCGkaldlvwlAeqgrevvGvelselAvekffeeanl........epkvkelsgvkeysageiellcgdvFt 108
                                       ++l   CG ++    lA++g+evvG++l e  +e + ++a+         +  + e    +e +++ ++++ +++  
  gi|242398949|ref|YP_002994373.1|  44 KILDLACGTGIPTLELAKRGYEVVGMDLHEEMLEVAKRKAKRegltiefiQGDALE--VNFEQEFDAVTMFFSSIMY 118
                                       555557************************99998877766643333322222333..3333447777777777766 PP

                                       ---SS- CS
                              TPMT 109 lraeel 114
                                       +++++l
  gi|242398949|ref|YP_002994373.1| 119 FDEKNL 124
                                       666666 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 8.6
                                       -GGGHHHHHHHHHHHEEEEEE CS
                              TPMT 130 ppelreryakslaelLkpdge 150
                                       +p l + + k+l ++Lkp+ge
  gi|242398949|ref|YP_002994373.1| 177 EPGLQKLHFKRLVQILKPNGE 197
                                       677888889999999999987 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   2.6e-05     0.016      74     125 ..      61     109 ..      40     136 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.6e-05
                                       HHH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EE CS
                           UPF0020  74 raelklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvi 125
                                       ++ ++++g+Dl +++++ a+++a++ g+  +ief q da +++  e+e+d++
  gi|242398949|ref|YP_002994373.1|  61 KRGYEVVGMDLHEEMLEVAKRKAKREGL--TIEFIQGDALEVN-FEQEFDAV 109
                                       567889******************9876..79*********99.77789986 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   4.3e-05     0.027       4      82 ..      44     115 ..      41     144 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.3e-05
                                       EEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCCHHHHCS-TTSEEEEEEES CS
                    Methyltransf_4   4 vvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgdalkvllelledgslekifilF 80 
                                        +l++ cG G  +++lAk+    +++G+++++++++ + +k+++++l+ ++ ++gdal+     +e+ +++ + ++F
  gi|242398949|ref|YP_002994373.1|  44 KILDLACGTGIPTLELAKRG--YEVVGMDLHEEMLEVAKRKAKREGLT-IEFIQGDALE---VNFEQ-EFDAVTMFF 113
                                       579***************96..678***********999999999997.********44...44554.888888888 PP

                                       -- CS
                    Methyltransf_4  81 PD 82 
                                       + 
  gi|242398949|ref|YP_002994373.1| 114 SS 115
                                       75 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 ?   13.0   0.0    0.0001     0.063      73     132 ..      41      96 ..      29     143 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.0001
                                       TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES- CS
                              PCMT  73 kgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgD 132
                                       +++++L++ +G+G+ t  l    ++   vv+++  +e+ e akr+ k+++l+ + ++ gD
  gi|242398949|ref|YP_002994373.1|  41 EVKKILDLACGTGIPTLEL---AKRGYEVVGMDLHEEMLEVAKRKAKREGLT-IEFIQGD 96 
                                       6789**********99755...5788999******************99985.6666676 PP

>> Bin3  Bicoid-interacting protein 3 (Bin3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00075      0.46      18      42 ..     120     144 ..     108     149 .. 0.83
   2 ?   -0.2   0.0       2.5   1.5e+03      21      38 ..     179     197 ..     169     205 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00075
                              Bin3  18 gDeglkrlfkkiyellkpgGvlilE 42 
                                        ++ lk+lf++++++lkpgGv++ +
  gi|242398949|ref|YP_002994373.1| 120 DEKNLKKLFNSVIKALKPGGVFVAD 144
                                       4678******************965 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 2.5
                              Bin3  21 glkrl.fkkiyellkpgGv 38 
                                       gl++l fk++++ lkp+G 
  gi|242398949|ref|YP_002994373.1| 179 GLQKLhFKRLVQILKPNGE 197
                                       565543999*****99995 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 ?    7.7   0.0     0.004       2.5       7      81 ..      40     107 ..      37     112 .. 0.84
   2 ?    3.1   0.0       0.1        65     117     135 ..     124     142 ..     114     204 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.004
                                       -TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC..EE CS
                   Methyltr_RsmB-F   7 qeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlggelfD 81 
                                       +e ++ilDl+++ G  T   +el k   +vv +d ++e l+  ++  kr g+t +  +++Da +++    ++ fD
  gi|242398949|ref|YP_002994373.1|  40 REVKKILDLACGTGIPT---LELAKRGYEVVGMDLHEEMLEVAKRKAKREGLT-IEFIQGDALEVN---FEQEFD 107
                                       56678********9998...67778899*************************.9999***98873...223466 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.1
                                       HHHHHHHHCCCEEEEEEEE CS
                   Methyltr_RsmB-F 117 qkellsaaidllkkgGvlv 135
                                        k+l++++i+ lk+gGv v
  gi|242398949|ref|YP_002994373.1| 124 LKKLFNSVIKALKPGGVFV 142
                                       489*************987 PP

>> AdoMet_MTase  Predicted AdoMet-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0    0.0032         2      57      90 ..      40      73 ..      28      92 .. 0.83
   2 ?    1.9   0.1      0.46   2.8e+02      26      42 ..     159     175 ..     157     204 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0032
                      AdoMet_MTase 57 eketsfvdvgcgngllvyvlaaegykgygidlrk 90
                                       + + + d+ cg g+    la  gy+  g+dl  
  gi|242398949|ref|YP_002994373.1| 40 REVKKILDLACGTGIPTLELAKRGYEVVGMDLHE 73
                                      4566789************************975 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.46
                      AdoMet_MTase  26 wvestdplkfvfedlai 42 
                                       w estd +k v  d  i
  gi|242398949|ref|YP_002994373.1| 159 WDESTDEEKLVITDWRI 175
                                       9**********999776 PP

>> N2227  N2227-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.011       6.5      33      92 ..      18      76 ..       2      81 .. 0.77
   2 ?    3.7   0.2     0.047        29     146     200 ..      89     142 ..      77     154 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.011
                                      HHHHHHHHHHHHHHHHS-T......T-EEEEET-TT-HHHHHHHHTT-EEEEEE--HHHH CS
                             N2227 33 ERealykpiieelkelvpseskerekvkilvPGaGlGrlavelatkgyqvegnEfsyfml 92
                                       R + +   i++++e ++  + +re  kil   +G+G  ++ela+ gy+v g ++   ml
  gi|242398949|ref|YP_002994373.1| 18 RRAERVGDEIDFVEEIFKG-DAKREVKKILDLACGTGIPTLELAKRGYEVVGMDLHEEML 76
                                      5555556667788888874.6677788999999*******************99987776 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.047
                                       -EEEEES-HHHHH--SSHTT-EEEEEEE....S-TTSSS-HHHHHHHHHHHEEEEEEEE CS
                             N2227 146 nlsmaagdflevykeeeaaesydvvvtc....fFiDtaeNvleYletiekvlkpgglwi 200
                                        ++   gd lev  e+    ++d+v +      + D  +N+ + ++++ k lkpgg+++
  gi|242398949|ref|YP_002994373.1|  89 TIEFIQGDALEVNFEQ----EFDAVTMFfssiMYFD-EKNLKKLFNSVIKALKPGGVFV 142
                                       5677788888888888....9999866522222345.69*****************998 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00055      0.34      19      58 ..      58      97 ..      50     116 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00055
                                      HHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TT CS
                         adh_short 19 elakeGakvvvvdrseekleevakelkeegakalaiqvDv 58
                                      elak+G++vv +d +ee le ++ + k+eg ++ +iq+D 
  gi|242398949|ref|YP_002994373.1| 58 ELAKRGYEVVGMDLHEEMLEVAKRKAKREGLTIEFIQGDA 97
                                      89************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       670  (0.0373696); expected 358.6 (0.02)
Passed bias filter:                      606  (0.0338); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                        29  (0.00161749); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              29  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 1716.36
//
Query:       gi|242398950|ref|YP_002994374.1|  [L=52]
Description: hypothetical protein TSIB_0967 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      202  (0.0112667); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 334.12
//
Query:       gi|242398951|ref|YP_002994375.1|  [L=886]
Description: Valyl-tRNA synthetase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   1.4e-146  489.2   0.4   2.1e-145  485.3   0.4    2.0  1  tRNA-synt_1    tRNA synthetases class I (I, L, M and V)
    2.3e-38  131.5   0.8    5.1e-38  130.4   0.8    1.6  1  Anticodon_1    Anticodon-binding domain of tRNA
    3.6e-26   91.8   0.2      7e-17   61.2   0.0    3.6  3  tRNA-synt_1g   tRNA synthetases class I (M)
    4.3e-06   26.3   0.0      0.057   12.7   0.0    2.5  2  tRNA-synt_1e   tRNA synthetases class I (C) catalytic domain
    5.2e-06   26.1   0.1    3.1e-05   23.6   0.1    2.1  2  tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
      0.001   18.3   0.9          2    7.8   0.0    3.1  3  zf-TFIIB       Transcription factor zinc-finger
     0.0055   16.7   2.2       0.44   10.6   0.1    2.9  3  HypA           Hydrogenase/urease nickel incorporation, metal
  ------ inclusion threshold ------
      0.017   15.3   1.5        2.6    8.2   0.0    2.8  2  DUF2250        Uncharacterized protein conserved in archaea (
       0.03   14.4   1.9       0.37   10.9   0.4    2.6  2  Zn-ribbon_8    Zinc ribbon domain
      0.036   14.1   0.4          1    9.4   0.1    2.3  2  DZR            Double zinc ribbon
      0.064   12.8   4.7          2    8.0   0.2    3.4  3  TF_Zn_Ribbon   TFIIB zinc-binding
       0.11   13.1   0.1        1.7    9.3   0.0    2.5  2  NID            Nmi/IFP 35 domain (NID)
       0.34   10.5   5.1        7.6    6.2   0.1    3.3  3  zf_UBZ         Ubiquitin-Binding Zinc Finger
        1.7    8.5   8.2       0.92    9.3   0.7    3.2  3  zinc_ribbon_2  zinc-ribbon domain
        1.9    8.7   8.6         29    4.9   0.6    3.6  3  zf-ACC         Acetyl-coA carboxylase zinc finger domain
          2    8.0   6.0        3.8    7.0   0.4    3.0  3  zf-ribbon_3    zinc-ribbon domain
        3.8    7.5   6.0        2.6    8.0   0.1    2.9  3  DUF35_N        Rubredoxin-like zinc ribbon domain (DUF35_N)


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 !  485.3   0.4    2e-148  2.1e-145       1     599 [.      14     567 ..      14     570 .. 0.96

  Alignments for each domain:
  == domain 1  score: 485.3 bits;  conditional E-value: 2e-148
                       tRNA-synt_1   1 klyekWeeedvfkkelekekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaie 77 
                                       k++++W ee+++k     +++++ +++  +PP+  G+lH+Gh+l +t  div rykrm+G++vl+  G+D +Gl++e
  gi|242398951|ref|YP_002994375.1|  14 KWQKFWLEEGIYKYR--LDEKRPAYSIDTPPPFTSGTLHLGHVLSHTWIDIVARYKRMRGYNVLFPQGFDNHGLPTE 88 
                                       5899*********99..78899******************************************************* PP

                       tRNA-synt_1  78 akvekklgakekkerkklgreefrekvrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkg 154
                                        kvek++g+++         eef +k+ ew  + +e +r+q+ r+G s+D++ ey T+d+e+++ v++ + ++++kg
  gi|242398951|ref|YP_002994375.1|  89 LKVEKEFGISKD------QPEEFLKKCIEWTWQAIEAMRNQFIRIGYSADWELEYHTMDDEYKALVQKSLLEFYKKG 159
                                       ********9997......689******************************************************** PP

                       tRNA-synt_1 155 liyrgkklvnwstklktalselEveykdkkdalihvafpladkeevklviaTTtPeTllgdtavavnpeldyvitke 231
                                       l+y+ k++v+w++++kt+l+ +Ev y +++++l++++ p+a++e+ ++ iaTT+Pe +++ +av v+pe        
  gi|242398951|ref|YP_002994375.1| 160 LLYQDKHPVYWCPRCKTSLAKAEVGYVEEDGYLYYIKLPIAGEED-YIPIATTRPELMPACVAVFVHPE-------- 227
                                       *********************************************.***********************........ PP

                       tRNA-synt_1 232 klilaeallkslvkkesekkiledergkeLegkevelplvnrkipiiaddyvdkeaGtGvVkiaPahdedDyevgkk 308
                                                              der+k+ +gk+v+lp+ +r++piiad+ vd e+GtG+V +  + de+D    k+
  gi|242398951|ref|YP_002994375.1| 228 -----------------------DERYKNKVGKKVKLPIFEREVPIIADEDVDPEFGTGAVYNCTYGDEQDVLWQKR 281
                                       .......................9***************************************************** PP

                       tRNA-synt_1 309 ynlevinildedgtlteeaaefeglkvfdarkkvveelkekglllkaekiehsv.pfcersk..kpiiyrateqWfv 382
                                       ynl+vi +++edgt++e+a++++gl+ ++a++++v++l+e gll k+++++h v  ++ers   +pi+   ++qWf+
  gi|242398951|ref|YP_002994375.1| 282 YNLPVIITINEDGTMNENAGKYKGLTAEQAKEAIVKDLEEMGLLYKKKQVHHRVlRHTERSScrAPIELLPKKQWFI 358
                                       ***************************************************997479999853389*********** PP

                       tRNA-synt_1 383 rvkeladaalkavekvqfvpkskekryaswleniq.dWciSRqrwWGhriplfvsketeevvvreelkelvagreee 458
                                       +vkel+d+++k+ e+++++p     r ++w e +  dW+iSRqr+ G++ip++v k+ +e++          +ree+
  gi|242398951|ref|YP_002994375.1| 359 KVKELTDEIVKVSEQIRWYPPDMFLRLKDWAESMDwDWVISRQRVFGTPIPFWVCKDCGEIIP---------AREED 426
                                       ********************************9866***************************.........44455 PP

                       tRNA-synt_1 459 eaekkalekeakdkl.kkekgelekdedvlDvWFsSgswpfstlgypeedteelkkffpadmlleGlDiirgWvarl 534
                                          +  ++   +dk  k++  +le ++dvlD+W +S+ +p  + ++ +  ++ +++ fp+++  +G Diir W    
  gi|242398951|ref|YP_002994375.1| 427 LPVDPRFNGAPVDKCpKCGSTNLEGVKDVLDCWVDSSITPLVISKWQKD-EKWFSHNFPTSLRPQGTDIIRTWGFYT 502
                                       555555555666666689999*************************887.999************************ PP

                       tRNA-synt_1 535 illslaltgsePfkevlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltlilsdvgrdi 599
                                       i+ +  ltg++P+ ++l++g+v   +GrKmSKs gNv++p++vi kygadalRl+ +l++ g+d 
  gi|242398951|ref|YP_002994375.1| 503 IFRTYILTGEKPWDDILINGMVAGPDGRKMSKSYGNVVSPEEVIPKYGADALRLWTALAPPGEDH 567
                                       ***********************************************************999986 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 !  130.4   0.8   4.9e-41   5.1e-38       1     149 [.     612     760 ..     612     764 .. 0.89

  Alignments for each domain:
  == domain 1  score: 130.4 bits;  conditional E-value: 4.9e-41
                       Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkraaqevllevletllrll 77 
                                       d+wils+l++l+k +te +e+yrfn   ++l++f+w++++d y+e++k+rly+e++e+k +a++vl+e+l +++ ll
  gi|242398951|ref|YP_002994375.1| 612 DKWILSRLHRLIKFATEELEKYRFNLLTRELMTFVWHEVADDYIEMIKHRLYGEDEESKLKAKMVLYELLYNITLLL 688
                                       9****************************************************99988855**************** PP

                       Anticodon_1  78 aPfmPfitEelwqr.eeeelgkk...esimlaewpe.kaeel.ekeleeeevellkeivkairklrselkikpssel 148
                                        P +P+itEel+q+      ++k   +s++l ewpe  ++   ++e+ e+  +++ ei+ a+r+++++ +++ +++l
  gi|242398951|ref|YP_002994375.1| 689 GPLAPHITEELYQEmF----KDKvgaKSVHLLEWPEyRED-RvDEEA-ERIGKFASEIIGAMRRYKNSHGLALNAKL 759
                                       ************8663....33344489*******74443.357777.8999********************99985 PP

                       Anticodon_1 149 k 149
                                       k
  gi|242398951|ref|YP_002994375.1| 760 K 760
                                       4 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.2   0.0   6.7e-20     7e-17       3     135 ..      38     183 ..      36     187 .. 0.80
   2 ?    3.3   0.1     0.026        28     167     238 ..     339     409 ..     309     419 .. 0.80
   3 !   23.0   0.0   2.8e-08   2.9e-05     285     385 ..     487     586 ..     440     591 .. 0.71

  Alignments for each domain:
  == domain 1  score: 61.2 bits;  conditional E-value: 6.7e-20
                                       EEE--B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHT.TS...-HHHHHHHHH.... CS
                      tRNA-synt_1g   3 vttalpYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAeke.gv...tpeelvekvh.... 71 
                                       + t+ p+++g+lHlGh+l++   Di+aRykr+rg++vlf  g D+hG p+elk eke g+   +pee+ +k      
  gi|242398951|ref|YP_002994375.1|  38 IDTPPPFTSGTLHLGHVLSHTWIDIVARYKRMRGYNVLFPQGFDNHGLPTELKVEKEfGIskdQPEEFLKKCIewtw 114
                                       78899*************************************************99765522267887776541111 PP

                                       ...HHHHHHHHHTT---S..EEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GGG- CS
                      tRNA-synt_1g  72 ...eeikelfkklnisfd..kygrttseehkelvqeifkklkekgliyekeieqlycpkderflpdryv 135
                                          e+++++f +++ s d    ++t ++e k lvq+ + ++++kgl+y+ +  +++cp++++ l+  +v
  gi|242398951|ref|YP_002994375.1| 115 qaiEAMRNQFIRIGYSADweLEYHTMDDEYKALVQKSLLEFYKKGLLYQDKHPVYWCPRCKTSLAKAEV 183
                                       11144555565555555422345799999*********************************9998776 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.026
                                       ..........EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ESS-SSS-EET CS
                      tRNA-synt_1g 167 pksaisgskpevketehlffklskfekklkewieeeekeleenvkkivkewlkegLkdlaisrdldwGipvP 238
                                       ++ + + +  e+  ++++f k++++++++ +   e+ +  +  +   +k+w ++   d+ isr+  +G p+P
  gi|242398951|ref|YP_002994375.1| 339 TERSSCRAPIELLPKKQWFIKVKELTDEIVKVS-EQIRWYPPDMFLRLKDWAESMDWDWVISRQRVFGTPIP 409
                                       5555666666788899*************9988.444456777888899****9999**************9 PP

  == domain 3  score: 23.0 bits;  conditional E-value: 2.8e-08
                                       EEEEEGGGHH...HHHTHHHHHHHHTT----S-EEEE--EE.E--------------HHHHHHHH-HHHHHHHHHHH CS
                      tRNA-synt_1g 285 vhfigkdiik...FHtifwPaillgaelklpkkvvaheylt.vegkKlSkSrgvvvkakealerldadllRYylaae 357
                                           g dii+   F tif + il+g++    + +  ++++   +g+K+SkS g+vv ++e++ ++ ad+lR + a  
  gi|242398951|ref|YP_002994375.1| 487 LRPQGTDIIRtwgFYTIFRTYILTGEK--PWDDILINGMVAgPDGRKMSKSYGNVVSPEEVIPKYGADALRLWTA-L 560
                                       344577777555588888888888753..5577888888762699**************************8765.6 PP

                                       S-TTS-EEE-HHHHHHHHHHHCCCHHHH CS
                      tRNA-synt_1g 358 apekkDldfswedfvervNseLadklgn 385
                                       ap  +D  f+we +   +N    +kl n
  gi|242398951|ref|YP_002994375.1| 561 APPGEDHPFKWEIV--DYNYRFLQKLWN 586
                                       7888999**99854..455555555555 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0   0.00024      0.25      22      53 ..      48      79 ..      43      83 .. 0.90
   2 !   12.7   0.0   5.4e-05     0.057     243     280 ..     520     558 ..     505     566 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00024
                                      --BHHHHHHHHHHHHHHHHHHHTT-EEEEEEE CS
                      tRNA-synt_1e 22 ashlGhaRslvafDilrrilqalgYdvqfvqn 53
                                      + hlGh+ s   +Di++r+ +++gY+v f q 
  gi|242398951|ref|YP_002994375.1| 48 TLHLGHVLSHTWIDIVARYKRMRGYNVLFPQG 79
                                      68*************************99775 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 5.4e-05
                                       EE--EE.ETTBE--TTTT---BHHHHHTTS-HHHHHHHH CS
                      tRNA-synt_1e 243 hnghlk.iegekmsksLknfitikdvlkkfdprqlRlll 280
                                        ng++   +g+kmsks +n+++ ++v+ k+ + +lRl  
  gi|242398951|ref|YP_002994375.1| 520 INGMVAgPDGRKMSKSYGNVVSPEEVIPKYGADALRLWT 558
                                       5666652589**************************875 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 ?   -1.5   0.0       1.4   1.5e+03      12      44 ..     195     227 ..     193     234 .. 0.81
   2 !   23.6   0.1   2.9e-08   3.1e-05      86     168 ..     236     303 ..     226     322 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.4
                     tRNA-synt_1_2  12 iefkveeseeklevfttrpdtlfGvtfvalape 44 
                                       i+++++++e+ + + ttrp+ +     v + pe
  gi|242398951|ref|YP_002994375.1| 195 IKLPIAGEEDYIPIATTRPELMPACVAVFVHPE 227
                                       8899999999*********98877666666665 PP

  == domain 2  score: 23.6 bits;  conditional E-value: 2.9e-08
                     tRNA-synt_1_2  86 glkaihPitgekipiwvanyvlmeygtgavmavPahdqrDfeFakkynlpikqvikpedeekkleeseeayteegil 162
                                       g k+  Pi ++++pi   + v  e+gtgav  +   d++D  + k+ynlp++  i+++++ ++              
  gi|242398951|ref|YP_002994375.1| 236 GKKVKLPIFEREVPIIADEDVDPEFGTGAVYNCTYGDEQDVLWQKRYNLPVIITINEDGTMNE-------------- 298
                                       778899**********************************************99996553322.............. PP

                     tRNA-synt_1_2 163 vnsgef 168
                                        n+g++
  gi|242398951|ref|YP_002994375.1| 299 -NAGKY 303
                                       .22333 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0    0.0025       2.6       2      18 ..     171     187 ..     170     190 .. 0.88
   2 ?   -1.2   0.1       1.3   1.4e+03      17      26 ..     408     417 ..     401     417 .. 0.86
   3 !    7.8   0.0    0.0019         2      13      26 ..     432     445 ..     426     450 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0025
                          zf-TFIIB   2 CPkCqdeleeserggve 18 
                                       CP+C+++l ++e+g ve
  gi|242398951|ref|YP_002994375.1| 171 CPRCKTSLAKAEVGYVE 187
                                       **********9998776 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.3
                          zf-TFIIB  17 veidyCpqCr 26 
                                       +++++C +C+
  gi|242398951|ref|YP_002994375.1| 408 IPFWVCKDCG 417
                                       8999*****7 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0019
                          zf-TFIIB  13 erggveidyCpqCr 26 
                                       +++g ++d+Cp+C+
  gi|242398951|ref|YP_002994375.1| 432 RFNGAPVDKCPKCG 445
                                       67899999999997 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.033        35      38      83 ..     134     181 ..     105     191 .. 0.79
   2 !   10.6   0.1   0.00042      0.44      72     100 ..     412     452 ..     405     461 .. 0.85
   3 ?   -2.3   0.1       4.3   4.5e+03       9      33 ..     822     848 ..     818     877 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.033
                                       T--HHHHHHHHHHHHCC.TTT..T-EEEEEEE--EEEETTTS-EEECH CS
                              HypA  38 gvepeaLefafellaegtvle..gaeLeieevpvkvrCreCgkefele 83 
                                       ++e +++   +++l ++++le  ++ L +++++ +++C +C+++  ++
  gi|242398951|ref|YP_002994375.1| 134 ELEYHTMDDEYKALVQKSLLEfyKKGLLYQDKHPVYWCPRCKTSLAKA 181
                                       4566788899999999999775578899**************987754 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00042
                                       EETTTS-EEECHHHHH............S-TTTSSS-EEEE CS
                              HypA  72 rCreCgkefeleekal............rCpkCgsadveiv 100
                                        C++Cg+ +  +e++l            +CpkCgs+++e v
  gi|242398951|ref|YP_002994375.1| 412 VCKDCGEIIPAREEDLpvdprfngapvdKCPKCGSTNLEGV 452
                                       7*****9999776445678999*************998765 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 4.3
                                       HHHHHHHHHHCC..TT..EEEEEEEEE CS
                              HypA   9 sivevveeeake..aaarkvtkvkvev 33 
                                       +i   ++e+a+e  +a ++v kv+ ev
  gi|242398951|ref|YP_002994375.1| 822 KITAYLKENAEEvaKALKEVGKVEFEV 848
                                       666777777755444577888888776 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 ?    5.0   0.1     0.024        26      40      57 ..     313     330 ..     298     346 .. 0.67
   2 ?    8.2   0.0    0.0025       2.6      12      53 ..     804     845 ..     795     861 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.024
                           DUF2250  40 rellkkLeelGLlerveg 57 
                                       + ++k+Lee+GLl ++++
  gi|242398951|ref|YP_002994375.1| 313 EAIVKDLEEMGLLYKKKQ 330
                                       45789********87653 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0025
                           DUF2250  12 kvlkhlkkanvdYaksiakeleipleevrellkkLeelGLle 53 
                                       ++   +k++++ Y+k++ k +   +e+++e+ k+L+e+G +e
  gi|242398951|ref|YP_002994375.1| 804 EIKPNFKTVGPKYGKLVPKITAYLKENAEEVAKALKEVGKVE 845
                                       5566799********************************887 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.25   2.6e+02      26      38 ..     167     180 ..     161     181 .. 0.71
   2 ?   10.9   0.4   0.00035      0.37       8      37 ..     413     450 ..     411     452 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.25
                       Zn-ribbon_8  26 lta.CPeCgsevrr 38 
                                       ++  CP+C+  + +
  gi|242398951|ref|YP_002994375.1| 167 PVYwCPRCKTSLAK 180
                                       5567****987665 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00035
                       Zn-ribbon_8   8 CeeCghefe......vlqsisdaplta.CPeCgs.evr 37 
                                       C++Cg+         ++ + +  ++++ CP+Cgs +++
  gi|242398951|ref|YP_002994375.1| 413 CKDCGEIIPareedlPVDPRFNGAPVDkCPKCGStNLE 450
                                       9999977777777776666664456666******8876 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.18   1.9e+02      15      23 ..     171     179 ..     158     220 .. 0.82
   2 ?    9.4   0.1   0.00099         1      14      37 ..     412     447 ..     407     452 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.18
                               DZR  15 CseCgtklk 23 
                                       C++C+t+l 
  gi|242398951|ref|YP_002994375.1| 171 CPRCKTSLA 179
                                       666666664 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00099
                               DZR  14 fCseCgtklkavaa............edrCpsCgek 37 
                                       +C++Cg+ ++a ++             d+Cp+Cg+ 
  gi|242398951|ref|YP_002994375.1| 412 VCKDCGEIIPAREEdlpvdprfngapVDKCPKCGST 447
                                       6*******9977779******************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 ?   -0.5   0.1      0.85     9e+02       3       8 ..     171     176 ..     169     180 .. 0.81
   2 ?    4.5   0.1     0.023        25      21      29 ..     412     420 ..     410     427 .. 0.86
   3 ?    8.0   0.2    0.0019         2       2      11 ..     440     449 ..     440     457 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.85
                                       ETTTTC CS
                      TF_Zn_Ribbon   3 CPnCgs 8  
                                       CP C++
  gi|242398951|ref|YP_002994375.1| 171 CPRCKT 176
                                       999997 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.023
                                       EESSSSBEE CS
                      TF_Zn_Ribbon  21 vCtdCGlVl 29 
                                       vC+dCG+++
  gi|242398951|ref|YP_002994375.1| 412 VCKDCGEII 420
                                       9*****998 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0019
                                       EETTTTCEEC CS
                      TF_Zn_Ribbon   2 kCPnCgstnl 11 
                                       kCP+Cgstnl
  gi|242398951|ref|YP_002994375.1| 440 KCPKCGSTNL 449
                                       8*******98 PP

>> NID  Nmi/IFP 35 domain (NID)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0    0.0016       1.7       2      43 ..     642     683 ..     641     696 .. 0.88
   2 ?    0.7   0.2      0.81   8.5e+02       7      38 ..     831     862 ..     827     884 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0016
                               NID   2 litFeeeeVaqrilkkkkhkvelekkkvrvkvspvelkelkk 43 
                                       l+tF+ +eVa+  +++ kh+++ e+++ ++k++ v  + l +
  gi|242398951|ref|YP_002994375.1| 642 LMTFVWHEVADDYIEMIKHRLYGEDEESKLKAKMVLYELLYN 683
                                       79******************************9987776655 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.81
                               NID   7 eeeVaqrilkkkkhkvelekkkvrvkvspvel 38 
                                        eeVa+ + + +k ++e++ +kv++    + l
  gi|242398951|ref|YP_002994375.1| 831 AEEVAKALKEVGKVEFEVDGQKVELGKDDIVL 862
                                       589*****************999886665555 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.035        37       3      16 ..     169     182 ..     168     184 .. 0.83
   2 ?    6.2   0.1    0.0072       7.6       3      16 ..     411     424 ..     410     426 .. 0.86
   3 ?    0.4   0.3      0.49   5.2e+02       4      10 ..     440     446 ..     439     450 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.035
                            zf_UBZ   3 ylCerCgkeipese 16 
                                       y C+rC++++  +e
  gi|242398951|ref|YP_002994375.1| 169 YWCPRCKTSLAKAE 182
                                       66******998876 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0072
                            zf_UBZ   3 ylCerCgkeipese 16 
                                       ++C++Cg+ ip  e
  gi|242398951|ref|YP_002994375.1| 411 WVCKDCGEIIPARE 424
                                       79*********876 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.49
                            zf_UBZ   4 lCerCgk 10 
                                        C++Cg+
  gi|242398951|ref|YP_002994375.1| 440 KCPKCGS 446
                                       6****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 ?   -0.6   0.1       1.1   1.2e+03       2      21 ..     171     176 ..     169     180 .. 0.61
   2 ?    2.0   0.1      0.18   1.9e+02       2      11 ..     413     422 ..     412     425 .. 0.81
   3 ?    9.3   0.7   0.00088      0.92       1      14 [.     440     453 ..     440     453 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.1
                     zinc_ribbon_2   2 CpnCGaelqdnakFCpyCGt 21 
                                       Cp+C               t
  gi|242398951|ref|YP_002994375.1| 171 CPRCK--------------T 176
                                       55554..............3 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.18
                     zinc_ribbon_2   2 CpnCGaelqd 11 
                                       C+ CG+ ++ 
  gi|242398951|ref|YP_002994375.1| 413 CKDCGEIIPA 422
                                       *****98886 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.00088
                     zinc_ribbon_2   1 fCpnCGaelqdnak 14 
                                       +Cp+CG ++ +++k
  gi|242398951|ref|YP_002994375.1| 440 KCPKCGSTNLEGVK 453
                                       8********99876 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 ?    4.5   0.1     0.034        36       4      16 ..     171     183 ..     171     183 .. 0.92
   2 ?    2.3   0.1      0.18   1.9e+02       4      11 ..     413     420 ..     410     424 .. 0.80
   3 ?    4.9   0.6     0.027        29       3      10 ..     440     447 ..     440     450 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.034
                            zf-ACC   4 CpsCgemlykkeL 16 
                                       Cp+C+++l k e+
  gi|242398951|ref|YP_002994375.1| 171 CPRCKTSLAKAEV 183
                                       ********99985 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.18
                            zf-ACC   4 CpsCgeml 11 
                                       C  Cge++
  gi|242398951|ref|YP_002994375.1| 413 CKDCGEII 420
                                       ******98 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.027
                            zf-ACC   3 KCpsCgem 10 
                                       KCp+Cg++
  gi|242398951|ref|YP_002994375.1| 440 KCPKCGST 447
                                       9*****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 ?    2.1   0.1      0.13   1.4e+02       5      12 ..     171     179 ..     169     183 .. 0.77
   2 ?   -0.5   0.1      0.84   8.9e+02      18      24 ..     412     418 ..     412     420 .. 0.84
   3 ?    7.0   0.4    0.0036       3.8       4      12 ..     440     449 ..     437     451 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.13
                       zf-ribbon_3   5 CPnCGa.pl 12 
                                       CP+C++ ++
  gi|242398951|ref|YP_002994375.1| 171 CPRCKTsLA 179
                                       ****99554 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.84
                       zf-ribbon_3  18 vCpyCGt 24 
                                       vC+ CG+
  gi|242398951|ref|YP_002994375.1| 412 VCKDCGE 418
                                       6999995 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0036
                       zf-ribbon_3   4 rCPnCGa.pl 12 
                                       +CP+CG+ +l
  gi|242398951|ref|YP_002994375.1| 440 KCPKCGStNL 449
                                       7999999887 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 ?   -1.3   0.5         2   2.1e+03      25      31 ..     168     174 ..     166     178 .. 0.72
   2 ?    1.1   0.0      0.37   3.9e+02      14      25 ..     413     423 ..     412     428 .. 0.79
   3 ?    8.0   0.1    0.0025       2.6      25      37 .]     438     450 ..     436     450 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2
                           DUF35_N  25 ravCphC 31 
                                          Cp+C
  gi|242398951|ref|YP_002994375.1| 168 VYWCPRC 174
                                       5679999 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.37
                           DUF35_N  14 CpdCGtvqfPPr 25 
                                       C+dCG  + P+r
  gi|242398951|ref|YP_002994375.1| 413 CKDCGEII-PAR 423
                                       *****986.665 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0025
                           DUF35_N  25 ravCphCgsddle 37 
                                          Cp+Cgs++le
  gi|242398951|ref|YP_002994375.1| 438 VDKCPKCGSTNLE 450
                                       568********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (886 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       668  (0.0372581); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); 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: 0.82u 0.27s 00:00:01.08 Elapsed: 00:00:00.49
# Mc/sec: 5406.79
//
Query:       gi|242398952|ref|YP_002994376.1|  [L=350]
Description: Archaeal ATPase [Thermococcus sibiricus MM 739]
Scores for complete 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-24   84.9   0.6    1.1e-23   84.4   0.6    1.2  1  ATPase_2  ATPase domain predominantly from Archaea
    2.9e-09   37.0   0.0    1.2e-07   31.9   0.0    2.4  1  AAA_14    AAA domain
    1.5e-06   28.5   0.0    3.2e-06   27.4   0.0    1.5  1  AAA_22    AAA domain
    0.00027   21.4   0.0    0.00044   20.7   0.0    1.3  1  AAA_16    AAA ATPase domain


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 !   84.4   0.6   2.5e-27   1.1e-23       2     231 ..      15     243 ..      14     245 .. 0.82

  Alignments for each domain:
  == domain 1  score: 84.4 bits;  conditional E-value: 2.5e-27
                          ATPase_2   2 fdRekelkeleeilerepneiyfiYGpegsGKtaLlkeiienl..edkdkyviyyialreesiskldefieeeeekk 76 
                                       fdReke k+le+ +e   +++  i G +++GK+++l+  +++      d + +y  +    +++ +++     ++k 
  gi|242398952|ref|YP_002994376.1|  15 FDREKEFKDLEKSVEV--YPMTIILGIRRVGKSSILRAYLNENpgILIDCRNLYAESGYLTKEDLIRNL----QSKA 85 
                                       9*************99..8888899****************9932233335555554444444444444....5555 PP

                          ATPase_2  77 klekalgiavpkaeleeilk.eksklvfkaielllekikkkgkk...iiiiiDelqklidlglngaellvkeLlnli 149
                                        l +++   + k+++   lk  +++  + ++ +++e++++ g k    ii +De+q+l+ +g++g ++l++ +++++
  gi|242398952|ref|YP_002994376.1|  86 GLLNKI---TSKFKISVNLKfLTIEPGELSLREIFEELNRIGEKtgkFIIAFDEAQYLRFYGSRGGRELLALFAYAY 159
                                       555555...55666666677777777788888888888888888788****************************** PP

                          ATPase_2 150 esltkekhlcvviclsSeglfie...rvyneselegrhky.ilvddldketalnflkegfkel.eelskedfeeiyr 221
                                       ++l+   +l++++ +s+ gl+++     ++es l+gr  + i ++++dk+t+ +flk gf+e   e  +e+++++++
  gi|242398952|ref|YP_002994376.1| 160 DNLP---NLRLILTGSEIGLLHDflsITNYESSLYGRPGGeIIMKPFDKKTSIEFLKYGFNEAkVEIDEEEIKKAVE 233
                                       **76...79***********9997767789*********************************5556********** PP

                          ATPase_2 222 yvGGkPkalv 231
                                       +++G P+ lv
  gi|242398952|ref|YP_002994376.1| 234 ILDGVPGWLV 243
                                       ******9775 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.0   2.6e-11   1.2e-07       3     125 ..      32     203 ..      30     208 .. 0.64

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 2.6e-11
                            AAA_14   3 kilvitGaRrvGKTtllkqlikell..........vkkesilyinldderd.......................kkl 46 
                                       ++ +i G+RrvGK+ +l+ +++e+           +   +  y++ +d  +                          
  gi|242398952|ref|YP_002994376.1|  32 PMTIILGIRRVGKSSILRAYLNENPgilidcrnlyA---ESGYLTKED--LirnlqskagllnkitskfkisvnL-- 101
                                       5789*****************999988755543320...222222222..1334444455555444433333221.. PP

                            AAA_14  47 adpe.........kllelileklke.............ekktylflDEiqev........pewekalkslvdegknl 93 
                                          +         +                         +k ++ +DE+q++        +e+     + +d+ +nl
  gi|242398952|ref|YP_002994376.1| 102 ---KfltiepgelS----------LreifeelnrigekTGKFIIAFDEAQYLrfygsrggRELLALFAYAYDNLPNL 165
                                       ...13333344433..........0333333444566689999********************************** PP

                            AAA_14  94 dvivtGSnskllskeia.....tslagrva.eielypl 125
                                       ++i+tGS  +ll   ++     +sl gr   ei + p+
  gi|242398952|ref|YP_002994376.1| 166 RLILTGSEIGLLHDFLSitnyeSSLYGRPGgEIIMKPF 203
                                       ********999865333333336666664335666555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0   7.2e-10   3.2e-06       7     132 ..      33     175 ..      29     179 .. 0.79

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 7.2e-10
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst......sskdllrellralglelka....... 70 
                                       ++++ G   +GK+  lr +l+++          p+ +++++ ++       + +dl r+l ++ gl +k        
  gi|242398952|ref|YP_002994376.1|  33 MTIILGIRRVGKSSILRAYLNEN----------PG-ILIDCRNLYaesgylTKEDLIRNLQSKAGLLNKItskfkis 98 
                                       7899*****************96..........33.33333333332233677777777777777644448889999 PP

                            AAA_22  71 ..........erlsseellealeqalraravielliiDEaqhlr...s...eealeeLrsllnlsrkgvqliLvGtp 131
                                                  +ls++e++e l++  +++++  ++  DEaq+lr   s    e+l  +   ++ +  +++liL G +
  gi|242398952|ref|YP_002994376.1|  99 vnlkfltiepGELSLREIFEELNRIGEKTGK-FIIAFDEAQYLRfygSrggRELLALFAYAYD-NLPNLRLILTGSE 173
                                       999******99********************.99*********98873567888888866666.7999999999987 PP

                            AAA_22 132 .e 132
                                        +
  gi|242398952|ref|YP_002994376.1| 174 iG 175
                                       55 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   9.8e-08   0.00044       5     160 ..      17     157 ..      10     169 .. 0.66

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 9.8e-08
                            AAA_16   5 ReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareel 81 
                                       Re+e + L+  +e       +++++ G + vGKss++r+ l++     g  +  +c+ l      +a   +l++e+l
  gi|242398952|ref|YP_002994376.1|  17 REKEFKDLEKSVEVY-----PMTIILGIRRVGKSSILRAYLNE--NP-G--ILIDCRNL------YAESGYLTKEDL 77 
                                       555555555444422.....899******************62..22.3..56666666......234457888899 PP

                            AAA_16  82 lrqlldeaesaeleawrekleeala....avpelagaea....srllellkrllallsrderplvlvlDdlqwade. 149
                                       +r l ++a   +l+    k++ +++                   +l+e + +l +  +++++ +++ +D++q +++ 
  gi|242398952|ref|YP_002994376.1|  78 IRNLQSKAG--LLNKITSKFKISVNlkflT--------IepgeLSLREIFEELNRIGEKTGK-FIIAFDEAQYLRFy 143
                                       999988844..4555555555555522331........022347889999999988899888.*********88877 PP

                            AAA_16 150 ...aslqllaaLlr 160
                                          + ++lla+++ 
  gi|242398952|ref|YP_002994376.1| 144 gsrGGRELLALFAY 157
                                       66666666666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); 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:                         4  (0.000223102); expected 0.2 (1e-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 0.30s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2231.71
//
Query:       gi|242398953|ref|YP_002994377.1|  [L=378]
Description: TRNA m1G methyltransferase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.3e-07   29.0   0.1    1.5e-06   27.9   0.0    1.5  2  RNA_Me_trans  Predicted SAM-dependent RNA methyltransferase


Domain annotation for each model (and alignments):
>> RNA_Me_trans  Predicted SAM-dependent RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0   8.5e-11   1.5e-06      22     123 ..     138     232 ..     111     240 .. 0.72
   2 ?   -3.3   0.1      0.31   5.6e+03      10      44 ..     317     349 ..     309     357 .. 0.60

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 8.5e-11
                      RNA_Me_trans  22 iakevgaenliltslskasleslpeelkslaklelekesveellkelkevkkekvclLDpkaekelspedaeefdvf 98 
                                       i + +  ++l lt +++ ++++l +++  l+k+++ +    e+lk++ +   e+v+lLDp+a+k+ls +d + +++f
  gi|242398953|ref|YP_002994377.1| 138 IRDYLWGDRLALTWVNE-EFKEL-ANFP-LEKVTAYEGATWEFLKKE-G--IERVVLLDPWADKDLSENDFS-TEAF 207
                                       55555556777888887.45544.2222.345555555667777775.4..59***************9975.679* PP

                      RNA_Me_trans  99 lfGGIlGddpprdRTselrkkgfeg 123
                                       ++GGI+     +++T+    +++e+
  gi|242398953|ref|YP_002994377.1| 208 IIGGIVDTGGTKKKTTPKIGEELEK 232
                                       ******9988888887655555555 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 0.31
                      RNA_Me_trans  10 elseWvllEYrhiakevgaenliltslskaslesl 44 
                                       e s+W+ + ++  ++ +  ++l + +l+++++++l
  gi|242398953|ref|YP_002994377.1| 317 EYSKWLNIRWEDFVQVL--RELNFVALERKRIQQL 349
                                       55777777777777776..3455556666555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.54
# Mc/sec: 2118.14
//
Query:       gi|242398954|ref|YP_002994378.1|  [L=335]
Description: hypothetical protein TSIB_0971 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.087   13.2   0.1       0.19   12.1   0.1    1.5  1  Jag_N     Jag N-terminus


Domain annotation for each model (and alignments):
>> Jag_N  Jag N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   1.1e-05      0.19       8      28 ..      84     104 ..      83     107 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.1e-05
                             Jag_N   8 eAiekAlkeLgvsrdeveieV 28 
                                       eA+ kA++e+g++ + v+ieV
  gi|242398954|ref|YP_002994378.1|  84 EALMKAIEEMGIPPEAVKIEV 104
                                       9*******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); expected 358.6 (0.02)
Passed bias filter:                      608  (0.0339115); 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: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2319.35
//
Query:       gi|242398955|ref|YP_002994379.1|  [L=292]
Description: Probable protease htpX like protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-37  129.1   0.0    3.1e-37  128.3   0.0    1.4  1  Peptidase_M48    Peptidase family M48
    2.7e-05   23.5   0.1    4.8e-05   22.7   0.0    1.5  2  Peptidase_M56    BlaR1 peptidase M56
  ------ inclusion threshold ------
      0.019   15.3   2.0      0.054   13.8   0.0    2.1  2  DUF996           Protein of unknown function (DUF996)
        0.8    9.7   7.1        2.9    7.8   0.4    2.3  2  Abhydrolase_9_N  Alpha/beta-hydrolase family N-terminus
        2.2    8.2   9.2       0.55   10.1   0.6    3.2  3  MadM             Malonate/sodium symporter MadM subunit


Domain annotation for each model (and alignments):
>> Peptidase_M48  Peptidase family M48
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.3   0.0   8.7e-41   3.1e-37       3     195 ..      68     284 ..      66     285 .. 0.80

  Alignments for each domain:
  == domain 1  score: 128.3 bits;  conditional E-value: 8.7e-41
                                       -SSHHHHHHHHHHHHTT-..-EEEEEEE-GGGT-EEEEESSS-E.EEEEEHHHH-SSB-HHHHHHHHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48   3 reaelkevveelakeaglpkpltkvyvvnspkrNAFalgggknk.rivltdgLlkqllseeelaaVlGHElGHikhr 78 
                                       +++el e+v+ la+eag+  p++k+++v  ++ NAFa+g++ ++  +++t+gLl + l+++el++V++HEl+Hik+r
  gi|242398955|ref|YP_002994379.1|  68 EAPELYEIVRGLAQEAGI--PTPKIAIVPTETPNAFATGRNPKNaVVAVTQGLL-RILNRDELEGVIAHELSHIKNR 141
                                       678999************..9999999999999*******98777*********.********************** PP

                                       HHHHHHHHHHHHHHHHHHHHHH........HTT-SHHHHHTT--S---HHHH..HHHHHHTTHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48  79 hsvvslivsllasillllglal........lisraeedaagafldalavlig..lliillflalSRkrEyqADeagv 145
                                       +++++++ +++a  ++++++ +        +++r ++++a+++l+a+  +++  +  +l ++a+SR+rEy ADe g+
  gi|242398955|ref|YP_002994379.1| 142 DVLIQTLAAVMAGAIMMVARWAgwmlwlggFGGRDRDRDASGALGAILLIVLapIAAMLIQMAISRAREYLADETGA 218
                                       *****666666555555543321111211145566666666666555444331144556666*************** PP

                                       HTTT.HHHHHHHHHHHHHHTT--S---HHHH................HHS-SS--HHHHHHHHHH- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................xxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48 146 ellkrakdlvraliklakdlerqdvsaslrs................ellstHPplleRiqalkel 195
                                       ++  ++ +l+ral k+    +  + ++   +                el+stHPp+++Ri++l+++
  gi|242398955|ref|YP_002994379.1| 219 KISGKPWALARALEKIEHAVSMRPIKNGNPAtahmfiinpfrgvsfaELFSTHPPTQKRIERLRKI 284
                                       ****************9999887766666666788889999999999****************987 PP

>> Peptidase_M56  BlaR1 peptidase M56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   1.3e-08   4.8e-05     181     221 ..     112     152 ..      34     158 .. 0.83
   2 ?   -3.2   0.0       1.1   3.8e+03     121     138 ..     196     211 ..     185     241 .. 0.51

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.3e-08
                     Peptidase_M56 181 IvlPadflkklsdeeleyillHElaHlkrkDllvnllvavl 221
                                       + + + +l+ l+ +ele +++HEl+H+k++D+l++ l+av+
  gi|242398955|ref|YP_002994379.1| 112 VAVTQGLLRILNRDELEGVIAHELSHIKNRDVLIQTLAAVM 152
                                       445666778899*************************9986 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.1
                     Peptidase_M56 121 iaallvlkkrfvrklgkl 138
                                       iaa+l+   + +++++++
  gi|242398955|ref|YP_002994379.1| 196 IAAMLIQM-A-ISRAREY 211
                                       23322111.1.2333333 PP

>> DUF996  Protein of unknown function (DUF996)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.6       0.2   7.1e+02      71      88 ..      31      48 ..       4      66 .. 0.44
   2 ?   13.8   0.0   1.5e-05     0.054      26     105 ..     140     219 ..     130     223 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.2
                            DUF996 71 lllllvliiayvlliisa 88
                                      +++++++++a+v++ +s 
  gi|242398955|ref|YP_002994379.1| 31 TGMMFAFMFALVMNFFSY 48
                                      222333333333333333 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 1.5e-05
                            DUF996  26 fsnaliafilsiialvvailalllvlgalatalelpgleeaaslilllllvliiayvlliisavflkksyellgkrt 102
                                        +++li +++++ a +++++a  +  + ++ + + ++ ++ as+ l+ +l++++a +++++  + ++++ e l+++t
  gi|242398955|ref|YP_002994379.1| 140 NRDVLIQTLAAVMAGAIMMVARWAGWMLWLGGFGGRDRDRDASGALGAILLIVLAPIAAMLIQMAISRAREYLADET 216
                                       47899************************************************************************ PP

                            DUF996 103 gvk 105
                                       g k
  gi|242398955|ref|YP_002994379.1| 217 GAK 219
                                       987 PP

>> Abhydrolase_9_N  Alpha/beta-hydrolase family N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.4   0.00081       2.9       8      39 ..       8      39 ..       7      65 .. 0.82
   2 ?    5.0   1.5    0.0061        22      93     147 ..     143     196 ..     110     228 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00081
                   Abhydrolase_9_N  8 RtwlfqgvvsGlsaaiGYglGvllawlvrrll 39
                                      Rt ++ + ++Gl +aiGY+lG   + +++++ 
  gi|242398955|ref|YP_002994379.1|  8 RTGVLMAFLTGLLMAIGYVLGNETGMMFAFMF 39
                                      888999**************987777776665 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0061
                   Abhydrolase_9_N  93 llvllvallvfalllllgrllralvrllarllgrvlprrvaavlgvlvvvvlvvl 147
                                       +l+  +a+++++++++++r   +++ +l    gr   r ++ +lg+++++vl+ +
  gi|242398955|ref|YP_002994379.1| 143 VLIQTLAAVMAGAIMMVARWAGWML-WLGGFGGRDRDRDASGALGAILLIVLAPI 196
                                       4555677777777888888777765.77777777777777777777776666533 PP

>> MadM  Malonate/sodium symporter MadM subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.2     0.047   1.7e+02      11      31 ..      10      29 ..       5      31 .. 0.79
   2 ?   10.1   0.6   0.00015      0.55       9      34 ..      30      55 ..      27      60 .. 0.91
   3 ?   -0.0   0.1      0.23   8.2e+02      15      30 ..     149     164 ..     135     170 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.047
                              MadM 11 gLvtaFavvGllmwvSyvlSk 31
                                      g ++aF+ +Gllm + yvl++
  gi|242398955|ref|YP_002994379.1| 10 GVLMAFL-TGLLMAIGYVLGN 29
                                      6788886.6999999999876 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00015
                              MadM  9 kngLvtaFavvGllmwvSyvlSkklt 34
                                      + g+++aF++  ++ ++Sy+ S+k++
  gi|242398955|ref|YP_002994379.1| 30 ETGMMFAFMFALVMNFFSYWYSDKIV 55
                                      689********************986 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.23
                              MadM  15 aFavvGllmwvSyvlS 30 
                                       a ++ G++m+v+++ +
  gi|242398955|ref|YP_002994379.1| 149 AAVMAGAIMMVARWAG 164
                                       3455699999999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       837  (0.0466841); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); 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):               5  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.51
# Mc/sec: 1707.89
//
Query:       gi|242398956|ref|YP_002994380.1|  [L=190]
Description: adenylate kinase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-21   76.7   0.5    7.3e-21   75.1   0.2    1.8  2  AAA_18           AAA domain
    2.8e-07   31.0   0.3    9.3e-07   29.3   0.3    1.8  1  AAA              ATPase family associated with various cellul
    3.2e-07   30.9   1.0    3.8e-06   27.4   0.2    2.7  2  AAA_17           AAA domain
    3.7e-07   30.4   0.6    8.3e-06   26.0   0.6    2.1  1  SKI              Shikimate kinase
    6.1e-07   29.5   0.3      0.014   15.3   0.0    2.2  2  dNK              Deoxynucleoside kinase
    1.6e-06   28.0   0.1     0.0044   16.8   0.0    2.3  2  Cytidylate_kin   Cytidylate kinase
    1.5e-05   25.3   0.1    4.3e-05   23.8   0.0    1.7  2  AAA_28           AAA domain
    2.2e-05   24.5   0.3       0.12   12.3   0.0    2.2  2  AAA_5            AAA domain (dynein-related subfamily)
    3.3e-05   24.1   0.1     0.0012   19.0   0.1    2.4  1  AAA_33           AAA domain
    6.4e-05   23.2   0.2    0.00029   21.0   0.0    1.9  2  Cytidylate_kin2  Cytidylate kinase-like family
    0.00034   20.9   0.6     0.0029   17.9   0.6    2.1  1  AAA_22           AAA domain
    0.00073   19.3   1.0       0.44   10.2   0.2    2.2  2  Thymidylate_kin  Thymidylate kinase
      0.001   19.5   0.0     0.0015   18.9   0.0    1.6  1  AAA_16           AAA ATPase domain
     0.0011   18.3   0.1     0.0027   17.0   0.0    1.7  2  Zeta_toxin       Zeta toxin
     0.0031   17.3   0.0     0.0067   16.2   0.0    1.5  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
     0.0065   16.6   1.8      0.085   13.0   1.0    2.6  2  UPF0180          Uncharacterised protein family (UPF0180)
     0.0072   16.3   0.0     0.0087   16.0   0.0    1.3  1  NACHT            NACHT domain
  ------ inclusion threshold ------
      0.016   14.9   0.0      0.021   14.5   0.0    1.2  1  AAA_30           AAA domain
      0.018   14.9   1.1      0.041   13.8   0.2    2.0  2  NTPase_1         NTPase
       0.02   14.3   0.0      0.034   13.6   0.0    1.5  2  KTI12            Chromatin associated protein KTI12
      0.022   14.7   0.0      0.032   14.1   0.0    1.3  1  Rad17            Rad17 P-loop domain
      0.024   14.4   0.1       0.69    9.6   0.0    2.1  2  PRK              Phosphoribulokinase / Uridine kinase family
      0.025   14.5   0.1       0.15   11.9   0.0    2.0  2  AAA_3            ATPase family associated with various cellul
      0.027   14.2   0.0      0.046   13.4   0.0    1.5  1  CoaE             Dephospho-CoA kinase
      0.042   14.2   0.0      0.076   13.4   0.0    1.5  1  RNA_helicase     RNA helicase
      0.043   14.3   0.0      0.056   13.9   0.0    1.3  1  ABC_tran         ABC transporter
      0.046   13.7   0.6       0.12   12.4   0.1    1.9  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.046   13.0   0.3      0.069   12.4   0.3    1.3  1  ATP_bind_2       P-loop ATPase protein family
      0.049   13.6   0.1      0.069   13.2   0.1    1.3  1  DUF5028          Domain of unknown function (DUF5028)
      0.063   12.5   0.9      0.069   12.3   0.9    1.5  1  NB-ARC           NB-ARC domain
      0.095   12.7   0.2        0.2   11.7   0.0    1.6  2  AAA_14           AAA domain
      0.098   12.8   0.1        2.5    8.2   0.0    2.3  2  ADK              Adenylate kinase
        0.1   12.3   0.3       0.13   12.0   0.2    1.4  1  AAA_24           AAA domain
       0.13   11.7   0.1       0.26   10.7   0.1    1.4  1  ParA             NUBPL iron-transfer P-loop NTPase


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 !   75.1   0.2   1.4e-23   7.3e-21       1     129 [.       9     122 ..       9     123 .. 0.90
   2 ?   -0.6   0.0       3.5   1.9e+03      44      69 ..     134     162 ..     124     177 .. 0.69

  Alignments for each domain:
  == domain 1  score: 75.1 bits;  conditional E-value: 1.4e-23
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf.gvnlrdvakenglllevdpealdeskrldedkldklldaleenssaleegkn 76 
                                       I+++GtpGvGKtt+ak L++++g+  v lr+ a ++++ + + +e     ++++ dkl++ +++  +n        n
  gi|242398956|ref|YP_002994380.1|   9 IAVSGTPGVGKTTVAKLLAEKMGYdYVDLREFALKHRIGEIRGDE-----LEIEFDKLAYYVKEKLKN-------RN 73 
                                       89***********************99999999999888777777.....788888888777777776.......46 PP

                            AAA_18  77 lvidghlaeleseaakdikkvvLtaspeelleRlekRgyeeakikeneeaeil 129
                                        v+dghl++l + +++    ++L+a+p+   eRl++Rgy++ ki+en eae +
  gi|242398956|ref|YP_002994380.1|  74 TVLDGHLSHLMPVDQI----IILRAHPKLIGERLKERGYTKEKISENVEAELV 122
                                       8***************....******************************976 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 3.5
                            AAA_18  44 e...aldeskrldedkldklldaleenss 69 
                                       e   ++d +++  e++++++l++le+ ++
  gi|242398956|ref|YP_002994380.1| 134 EaiiEVDTTNKTPEEVVNEILSLLERGIK 162
                                       24467788888889999999988887654 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.3   1.8e-09   9.3e-07       3     127 ..      11     160 ..       9     182 .. 0.66

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 1.8e-09
                                       EESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSS..................STTHHHHHHHHHHHHHHHTS..TS CS
                               AAA   3 lyGppGtGKTllakavakelgvefleisgsellsk..................yvgesekkirelfkeakeka..kp 59 
                                       ++G+pG+GKT++ak +a+++g +++ +    l                     yv+e+ k+ + +++   ++     
  gi|242398956|ref|YP_002994380.1|  11 VSGTPGVGKTTVAKLLAEKMGYDYVDLREFALKHRigeirgdeleiefdklayYVKEKLKNRNTVLDGHLSHLmpVD 87 
                                       79*****************9866444444444433444555567777899999999999999988887544445433 PP

                                       EEEEEETGGGHHHHH.......TTCCCHHHHHHHHHHHHH..HHHTTTSSSTEEEEEEESS.GGGSTHHHHSTTSSE CS
                               AAA  60 silfiDEidalaksr.......sgseseeeervvnqLlte..ldgvkkkeskvivigatnr.pdkldpallrgRfdr 126
                                        i+++    +l+++r       +   ++ +e+v ++L+ +  l+ ++++e  +i + +tn+ p+++ +++l + ++r
  gi|242398956|ref|YP_002994380.1|  88 QIIILRAHPKLIGERlkergytK---EKISENVEAELVDVclLEALDENE-AIIEVDTTNKtPEEVVNEIL-SLLER 159
                                       88888888888888887764431...344444444444331123333322.27778888877777777777.55555 PP

                                       E CS
                               AAA 127 k 127
                                        
  gi|242398956|ref|YP_002994380.1| 160 G 160
                                       4 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.2   7.1e-09   3.8e-06       2     116 ..      13     100 ..      12     120 .. 0.73
   2 ?   -0.4   0.0       2.8   1.5e+03      35      67 ..     131     163 ..     123     169 .. 0.67

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 7.1e-09
                                       E-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEEEEE CS
                            AAA_17   2 GgPGsGKgtqceklvekygfthlsaGdllreeakrgglakardemrklpleekkelqkeaaekiaeeakkkgvlvdg 78 
                                       G PG+GK+t+++ l+ek+g+ ++     lre a +       +e+r  +le++   + ++a  ++e+ k+++ ++dg
  gi|242398956|ref|YP_002994380.1|  13 GTPGVGKTTVAKLLAEKMGYDYVD----LREFALKHRI----GEIRGDELEIEF--D-KLAYYVKEKLKNRNTVLDG 78 
                                       99**********************....9*99977776....677766666554..4.455689999999******* PP

                                       -SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHH CS
                            AAA_17  79 hprikeqagfldglpkevleelkpdaiilleadpeeil 116
                                       h +   +                +d ii+l a p+ i 
  gi|242398956|ref|YP_002994380.1|  79 HLSHLMP----------------VDQIIILRAHPKLIG 100
                                       *974322................255556666665444 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 2.8
                                       HTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHH CS
                            AAA_17  35 krgglakardemrklpleekkelqkeaaekiae 67 
                                        +++++ + d  +k p+e+ +e++ ++++ i++
  gi|242398956|ref|YP_002994380.1| 131 DENEAIIEVDTTNKTPEEVVNEILSLLERGIKR 163
                                       444555555666778888888888888877776 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.6   1.6e-08   8.3e-06       1     157 [.      15     157 ..      15     158 .. 0.77

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 1.6e-08
                                       TTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHTS-HHHHHHHHHHHHHHHHHHHHHHHHCCCSSEEEEE-TTGGGSHH CS
                               SKI   1 mGaGKstvGkllAkklglefiDlDeliekrtgksiaeifeeegeegFrelEsevlkelleeeglViatGGGavlsee 77 
                                       +G+GK+tv+kllA+k+g++++Dl e+   + + +i ei  +e e +F +l   v ++l ++ +         vl+  
  gi|242398956|ref|YP_002994380.1|  15 PGVGKTTVAKLLAEKMGYDYVDLREF---ALKHRIGEIRGDELEIEFDKLAYYVKEKLKNR-NT--------VLDGH 79 
                                       69********************8655...56678899999999999*99988777777777.44........55667 PP

                                       HHHHHHHHSEEEEEE--HHHHHHHHHHTTS.SGGGCSCHHHHHHHHHHHHHHHHHCCSSCEEEECTSSHHHHHHHHH CS
                               SKI  78 nrellkekgiviyLdvsleellerlkadke.RPllqekskeeelleelaereplyeeaadvvvdeseeskeevaeei 153
                                         +l+     +i L+++++ + erlk++   +  ++e+ ++e ++  l   e+l e+ a + vd++++++eev++ei
  gi|242398956|ref|YP_002994380.1|  80 LSHLMP-VDQIIILRAHPKLIGERLKERGYtKEKISENVEAELVDVCL--LEALDENEAIIEVDTTNKTPEEVVNEI 153
                                       777777.77788899*********999998444444444433333333..47777778899999999999*****99 PP

                                       HHHH CS
                               SKI 154 leal 157
                                       l+ l
  gi|242398956|ref|YP_002994380.1| 154 LSLL 157
                                       9866 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   2.6e-05     0.014       1      26 [.       9      34 ..       9      49 .. 0.91
   2 !   12.8   0.1   0.00015      0.08     103     150 ..      66     116 ..      53     153 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.6e-05
                                      EEEEESTTSSHHHHHHHHHCCSTCEE CS
                               dNK  1 ivveGnIgaGKstlvklLskklgvkv 26
                                      i+v+G+ g+GK+t++klL++k+g+  
  gi|242398956|ref|YP_002994380.1|  9 IAVSGTPGVGKTTVAKLLAEKMGYDY 34
                                      89********************9765 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00015
                                       HHHHHHHHHHHHHHHHHCCH-SEEEEEE--HHHHHHHHHHCTTCCCT...T CS
                               dNK 103 eeelkiykelldnlleelakpdlliYLkasletclerikkRgreeek...k 150
                                       +e+lk  + +ld  l++l  +d +i L+a+++ + er+k+Rg ++ek   +
  gi|242398956|ref|YP_002994380.1|  66 KEKLKNRNTVLDGHLSHLMPVDQIIILRAHPKLIGERLKERGYTKEKiseN 116
                                       56667777788888888888*************************995554 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   8.4e-06    0.0044       1      28 [.       9      36 ..       9      78 .. 0.94
   2 !    9.5   0.1    0.0014      0.74     182     210 ..     130     158 ..     108     159 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 8.4e-06
                                      EEEE-STTSSHHHHHHHHHHHHT-EEEE CS
                    Cytidylate_kin  1 iaiDGPagsGKssvaralaeklglkyld 28
                                      ia+ G  g GK +va++laek+g+ y+d
  gi|242398956|ref|YP_002994380.1|  9 IAVSGTPGVGKTTVAKLLAEKMGYDYVD 36
                                      8999**********************98 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0014
                                       S---TT-EEEETTTS-HHHHHHHHHHHHH CS
                    Cytidylate_kin 182 Lklaedaliidtskltieevvekilelik 210
                                       L   e  + +dt+++t eevv++il+l++
  gi|242398956|ref|YP_002994380.1| 130 LDENEAIIEVDTTNKTPEEVVNEILSLLE 158
                                       666677899***************98765 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   8.1e-08   4.3e-05       2      33 ..       9      43 ..       8      84 .. 0.73
   2 ?   -0.3   0.0       2.1   1.1e+03     106     147 ..      83     132 ..      57     143 .. 0.47

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 8.1e-08
                            AAA_28  2 ivitGgestGKTtlleaLaar.gypvv..pEaare 33
                                      i+++G+++ GKTt+++ La++ gy +v  +E+a +
  gi|242398956|ref|YP_002994380.1|  9 IAVSGTPGVGKTTVAKLLAEKmGYDYVdlREFALK 43
                                      89*****************9889999877888754 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 2.1
                            AAA_28 106 ekrydlvfllppapei..dddgeR......redleereaiderlrealre 147
                                        +  d +++l+  p++  ++ +eR        +  e+e +d +l+eal+e
  gi|242398956|ref|YP_002994380.1|  83 LMPVDQIIILRAHPKLigERLKERgytkekISENVEAELVDVCLLEALDE 132
                                       55566666666666443433333322211111223566666666666655 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 !   12.3   0.0   0.00023      0.12       5      26 ..      12      33 ..       9      40 .. 0.87
   2 !   10.3   0.1   0.00099      0.52      48      91 ..     114     159 ..      74     165 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00023
                                      E--SSSSHHHHHHHGGGGBS-- CS
                             AAA_5  5 vGppGtgKselaerlaaalnre 26
                                       G pG+gK+++a+ la+ ++  
  gi|242398956|ref|YP_002994380.1| 12 SGTPGVGKTTVAKLLAEKMGYD 33
                                      69***************99765 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00099
                                       ..........--------.G-SEEEEESGGG--HHHHHHHHHHHHS CS
                             AAA_5  48 k.ngttslvdsplvraar.egeilvlDEveraesevlnsLlsllee 91 
                                       + n +++lvd +l +a   + +i+ +D  ++ + ev+n+ lslle+
  gi|242398956|ref|YP_002994380.1| 114 SeNVEAELVDVCLLEALDeNEAIIEVDTTNKTPEEVVNEILSLLER 159
                                       147779********99997788999*******************97 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.1   2.2e-06    0.0012       1      36 [.       8      45 ..       8     165 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.2e-06
                            AAA_33  1 lvllvGlpGsGKstlaerllkklg..avllssdtlrrr 36
                                      l+ + G pG+GK+t+a+ l++k g  +v l++ +l+ r
  gi|242398956|ref|YP_002994380.1|  8 LIAVSGTPGVGKTTVAKLLAEKMGydYVDLREFALKHR 45
                                      67889*******************55555555443333 PP

>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   5.5e-07   0.00029       2      30 ..       9      37 ..       8      58 .. 0.90
   2 ?   -0.6   0.0       2.4   1.3e+03      40      66 ..     106     132 ..      90     161 .. 0.50

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 5.5e-07
                   Cytidylate_kin2  2 ITIsreyGsgGetigeaLAekLglpfydr 30
                                      I++s++ G g++t+++ LAek+g++++d 
  gi|242398956|ref|YP_002994380.1|  9 IAVSGTPGVGKTTVAKLLAEKMGYDYVDL 37
                                      99*************************95 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2.4
                   Cytidylate_kin2  40 lglseeeveevdersrlssflskllaa 66 
                                        g ++e++ e  e++ ++  l ++l++
  gi|242398956|ref|YP_002994380.1| 106 RGYTKEKISENVEAELVDVCLLEALDE 132
                                       444444443333323323333333333 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.6   5.5e-06    0.0029       5      29 ..       6      30 ..       3     169 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 5.5e-06
                            AAA_22  5 agilvvtGesGtGKTtllrrlleql 29
                                      + +++v G +G+GKTt+++ l+e+ 
  gi|242398956|ref|YP_002994380.1|  6 KMLIAVSGTPGVGKTTVAKLLAEKM 30
                                      6789*****************9985 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0     0.004       2.1       3      20 ..      13      30 ..      11      37 .. 0.89
   2 !   10.2   0.2   0.00084      0.44     119     185 .]      87     153 ..      60     153 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.004
                                      ESTTSSHHHHHHHHHHHH CS
                   Thymidylate_kin  3 GlDGaGKttqaellkerl 20
                                      G  G+GKtt+a+ll+e++
  gi|242398956|ref|YP_002994380.1| 13 GTPGVGKTTVAKLLAEKM 30
                                      778************987 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00084
                                       SEEEEEESSHHHHHTSCCTTSSTTTSHHHHHHHHHHHHHHHHHHHHTTSTEEEEETTS-.HHHHHHHH CS
                   Thymidylate_kin 119 dltflldvdpevalkRlakrdeldeeeeeqldflrkvrerylelakederiliidasks.ieevheeI 185
                                       d +++l   p+   +Rl++r+  +e++ e+ +  + v  ++le+++e+e i+ +d++++  eev++eI
  gi|242398956|ref|YP_002994380.1|  87 DQIIILRAHPKLIGERLKERGYTKEKISENVE-AELVDVCLLEALDENEAIIEVDTTNKtPEEVVNEI 153
                                       67888999999999********7777777777.8999999*****9************98999*9998 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   2.9e-06    0.0015      22      52 ..       4      43 ..       1     168 [. 0.68

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.9e-06
                            AAA_16 22 grpelvllsGesGvGKsslvrellralekd.........g 52
                                      g+  l+ +sG +GvGK+++++ l++ +  d         +
  gi|242398956|ref|YP_002994380.1|  4 GEKMLIAVSGTPGVGKTTVAKLLAEKMGYDyvdlrefalK 43
                                      5557899*****************9998885544444440 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   5.2e-06    0.0027      16      58 ..       6      46 ..       2      72 .. 0.84
   2 ?   -1.3   0.0       2.1   1.1e+03      84      84 ..     122     122 ..      93     168 .. 0.52

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 5.2e-06
                        Zeta_toxin 16 PklillgGqpGAGKselaellkdelerqgnvvrldpDdlRelh 58
                                      + li ++G pG GK+++a+ll++++  + ++v l +  l+ ++
  gi|242398956|ref|YP_002994380.1|  6 KMLIAVSGTPGVGKTTVAKLLAEKM--GYDYVDLREFALKHRI 46
                                      67999********************..8999988877666665 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.1
                        Zeta_toxin  84 v 84 
                                       v
  gi|242398956|ref|YP_002994380.1| 122 V 122
                                       3 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.3e-05    0.0067      37      60 ..      10      33 ..       5      49 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.3e-05
                            RuvB_N 37 llyGpPGlGkttlakiiakelgvk 60
                                       ++G PG+Gktt+ak++a+++g +
  gi|242398956|ref|YP_002994380.1| 10 AVSGTPGVGKTTVAKLLAEKMGYD 33
                                      578******************975 PP

>> UPF0180  Uncharacterised protein family (UPF0180)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0         1   5.4e+02      11      28 ..      21      39 ..      18      49 .. 0.75
   2 !   13.0   1.0   0.00016     0.085      12      74 ..      99     153 ..      97     155 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 1
                           UPF0180 11 nvkeaLrek.GYeVvdlet 28
                                       v++ L+ek GY+ vdl++
  gi|242398956|ref|YP_002994380.1| 21 TVAKLLAEKmGYDYVDLRE 39
                                      6778886644******996 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00016
                           UPF0180  12 vkeaLrekGYeVvdleteedaqsvdaiVvtGqdtnvmgiedtetkapvInAsgktaeeIlqev 74 
                                       + e L+e+GY+ ++++++ +a+ vd++  +  d+n   ie        ++ ++kt+ee+++e+
  gi|242398956|ref|YP_002994380.1|  99 IGERLKERGYTKEKISENVEAELVDVCLLEALDENEAIIE--------VDTTNKTPEEVVNEI 153
                                       5688************999999999999999999988888........99**********998 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.6e-05    0.0087       2      65 ..       8      72 ..       7     165 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.6e-05
                                      CEEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-......-HCHHHCCCCTS- CS
                             NACHT  2 lvilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgna...rsladllfsqlpep 65
                                      l+++ G +G+GKTt ++ la+++  ++ +    ++ + ++ +e++ ++ +     la+++ ++l+  
  gi|242398956|ref|YP_002994380.1|  8 LIAVSGTPGVGKTTVAKLLAEKMGYDYVDLR--EFALKHRIGEIRGDELEiefDKLAYYVKEKLKNR 72
                                      6899*******************99999994..7999999999888877766656666665555554 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   4.1e-05     0.021      15      79 ..       3      67 ..       1      95 [. 0.80

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.1e-05
                            AAA_30 15 tsgdrvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelgieastiakllkr 79
                                      ++++++ ++ G +G GKtt+ k l+e +  +  ++  +A +++  +  ++el+ie + +a ++k+
  gi|242398956|ref|YP_002994380.1|  3 GGEKMLIAVSGTPGVGKTTVAKLLAEKMGYDYVDLREFALKHRIGEIRGDELEIEFDKLAYYVKE 67
                                      56778999*****************9999888899999999998888888888888877777754 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   7.8e-05     0.041       2      23 ..       9      30 ..       8      43 .. 0.87
   2 ?   -1.7   0.0       4.5   2.4e+03     119     144 ..     127     153 ..     104     160 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.8e-05
                                      EEEE--TTSSHHHHHHHHHHHH CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlell 23
                                      ++++G pGvGKtT+ k ++e++
  gi|242398956|ref|YP_002994380.1|  9 IAVSGTPGVGKTTVAKLLAEKM 30
                                      789*************999987 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 4.5
                                       HHHHTTTSEEEEE--SS-.-SHHHHHH CS
                          NTPase_1 119 eevLksekpvlavihrrk.dlalveei 144
                                        e+L++++ ++ v   +k ++++v+ei
  gi|242398956|ref|YP_002994380.1| 127 LEALDENEAIIEVDTTNKtPEEVVNEI 153
                                       344554554544444444444455444 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   6.4e-05     0.034       1      26 [.       7      31 ..       7      92 .. 0.82
   2 ?   -2.8   0.0       6.5   3.4e+03     111     121 ..     135     145 ..     109     167 .. 0.54

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.4e-05
                                      E.EEEEE--TTSSHHHHHHHHHHHHH CS
                             KTI12  1 MpLvvltGlPssGKstrakeLakale 26
                                      M L+ ++G P +GK+t+ak La+++ 
  gi|242398956|ref|YP_002994380.1|  7 M-LIAVSGTPGVGKTTVAKLLAEKMG 31
                                      5.9*******************9985 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 6.5
                                       HHHHHHHHTT- CS
                             KTI12 111 vlvkwneeree 121
                                        ++++++ +++
  gi|242398956|ref|YP_002994380.1| 135 AIIEVDTTNKT 145
                                       33333322222 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   6.1e-05     0.032      45      75 ..       6      36 ..       3      83 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.1e-05
                             Rad17 45 kriLLisGPsGCgkstvvkvLskelgiklre 75
                                      k ++ +sG +G gk+tv k L+ ++g+++ +
  gi|242398956|ref|YP_002994380.1|  6 KMLIAVSGTPGVGKTTVAKLLAEKMGYDYVD 36
                                      457789*********************9876 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0    0.0013      0.69       1      28 [.       8      35 ..       8      52 .. 0.85
   2 ?    3.0   0.0      0.14        73     152     194 ..     103     143 ..      61     146 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0013
                               PRK  1 vIgvagsSGaGkttvarklekifgrekv 28
                                      +I+v+g  G Gkttva+ l + +g   v
  gi|242398956|ref|YP_002994380.1|  8 LIAVSGTPGVGKTTVAKLLAEKMGYDYV 35
                                      69*****************999886555 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.14
                               PRK 152 iaeRGrsleavldsilrrkpdyvnyikpqfseadliiqrvptv 194
                                        +eRG++ e + +++++   d   ++   ++e ++ii++  t+
  gi|242398956|ref|YP_002994380.1| 103 LKERGYTKEKISENVEAELVD--VCLLEALDENEAIIEVDTTN 143
                                       489**********99976544..45556666666666665555 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 ?   11.9   0.0   0.00028      0.15       4      27 ..      11      34 ..       8      41 .. 0.88
   2 ?   -0.3   0.0       1.7   8.9e+02      79      98 ..     123     142 ..     115     154 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00028
                             AAA_3  4 legvPGlaktllvkalakaldlef 27
                                      + g+PG++kt+++k la++++ ++
  gi|242398956|ref|YP_002994380.1| 11 VSGTPGVGKTTVAKLLAEKMGYDY 34
                                      789****************99887 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.7
                             AAA_3  79 qsalleameerqvtvegeth 98 
                                       + +llea++e++  +e +t+
  gi|242398956|ref|YP_002994380.1| 123 DVCLLEALDENEAIIEVDTT 142
                                       66899999999877665543 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   8.7e-05     0.046       1      34 [.       7      41 ..       7      73 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.7e-05
                                      EEEEEEESTTSSHHHHHHHHHH.TT-EEEEHHHHH CS
                              CoaE  1 livgltGgiasGKstvanlfad.lgvpivDaDlvA 34
                                      ++++++G  + GK+tva+l+a+ +g++ vD    A
  gi|242398956|ref|YP_002994380.1|  7 MLIAVSGTPGVGKTTVAKLLAEkMGYDYVDLREFA 41
                                      5799*****************99*******87766 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   0.00014     0.076       1      24 [.       9      32 ..       9      55 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00014
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakallk 24
                                      i ++G +g+GK+t+ak La+++  
  gi|242398956|ref|YP_002994380.1|  9 IAVSGTPGVGKTTVAKLLAEKMGY 32
                                      5689**************999875 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   0.00011     0.056      13      80 ..       8      91 ..       4     169 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00011
                                      EEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.......B-HHHCCHCEEEE-SS--S-TTSBHHHH..... CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxx..... RF
                          ABC_tran 13 kvaivGenGaGKStLlkllagllkpteGeilldgkdlke.......qeleslrkeigvlpqepqlfpeltvren..... 79
                                      ++a+ G  G GK+t++klla+++    + + l++  lk+       +ele+   +++++ +e +l+++ tv +      
  gi|242398956|ref|YP_002994380.1|  8 LIAVSGTPGVGKTTVAKLLAEKMGY--DYVDLREFALKHrigeirgDELEIEFDKLAYYVKE-KLKNRNTVLDGhlshl 83
                                      68999***************99765..55555555566555555555566665666665555.5555555555556666 PP

                                      .......H CS
                                      .......x RF
                          ABC_tran 80 .......e 80
                                              
  gi|242398956|ref|YP_002994380.1| 84 mpvdqiiI 91
                                      55555551 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   0.1   0.00023      0.12      20      49 ..       7      36 ..       2      48 .. 0.85
   2 ?   -1.4   0.1       4.3   2.2e+03     103     103 ..     145     145 ..     108     182 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00023
                                      EEEEEEESTTSSHHHHHHHHHHHTT----- CS
                              TsaE 20 dvilLeGdLGaGKTtlvrglakalgveevk 49
                                       +i+ +G  G+GKTt ++ la+++g++ v 
  gi|242398956|ref|YP_002994380.1|  7 MLIAVSGTPGVGKTTVAKLLAEKMGYDYVD 36
                                      46999*******************998665 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 4.3
                                       G CS
                              TsaE 103 l 103
                                       +
  gi|242398956|ref|YP_002994380.1| 145 T 145
                                       1 PP

>> ATP_bind_2  P-loop ATPase protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.3   0.00013     0.069       3     155 ..       8     158 ..       6     174 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00013
                                       EEEEEESTTSSHHHHHHHH.HHHTXEEEBSXXGGGHHHHHHHHH....TTTXXEEEEESTTTSXSSHHHHHHHHHTS CS
                        ATP_bind_2   3 lvivsGlsGaGksvalral.edlGyyvvdnlPlsllpklvdllkea.nsreskvavvldvrnreesaelleqaeell 77 
                                       l+ vsG  G Gk++ ++ l e +Gy  vd     l  ++ ++  +  + +  k+a  +  +  e+ ++   +++  l
  gi|242398956|ref|YP_002994380.1|   8 LIAVSGTPGVGKTTVAKLLaEKMGYDYVDLREFALKHRIGEIRGDElEIEFDKLAYYV--K--EKLKNRNTVLDGHL 80 
                                       788**********999987689*******99999999999997733022333444433..3..22233333333344 PP

                                       XT.TSEEEEEEEEXXHHHHHHHCTSSSXSSTTSXXXSSHHHHHHHHHHTHHHHHTXSEE.EECTTXXHHHHHHHHHH CS
                        ATP_bind_2  78 ek.aitprilfleadddtlvrryedtrrshPlsakdlslegiakerelleplraradli.ldtselsvrelreklrk 152
                                       ++ +   +i+ l a+ + +  r ++   +    ++++ +e ++    lle l ++  +i +dt++  ++e+ +++  
  gi|242398956|ref|YP_002994380.1|  81 SHlMPVDQIIILRAHPKLIGERLKERGYTKEKISENVEAELVD--VCLLEALDENEAIIeVDTTNKTPEEVVNEILS 155
                                       442345689999**99999999999999998899999888887..57999998887777689999999999988877 PP

                                       HHH CS
                        ATP_bind_2 153 ala 155
                                        l+
  gi|242398956|ref|YP_002994380.1| 156 LLE 158
                                       665 PP

>> DUF5028  Domain of unknown function (DUF5028)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   0.00013     0.069      30      83 ..      28      78 ..      20     123 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00013
                           DUF5028 30 tvlGyevvdtdelaekynidlpeieadeagntvkrteyvydlkvkivnkdneeG 83
                                      + +Gy+ vd +e+a k+ i+  ei+ de      +  y+++ k+k  n+   +G
  gi|242398956|ref|YP_002994380.1| 28 EKMGYDYVDLREFALKHRIG--EIRGDELEIEFDKLAYYVKEKLKNRNT-VLDG 78
                                      669*****************..*******55555555555555554444.3344 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.9   0.00013     0.069      19      43 ..       5      29 ..       1     169 [. 0.91

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                                      CSEEEEEEESTTSSHHHHHHHHCCS CS
                            NB-ARC 19 qslvvalvGmgGvGKttlakqilnk 43
                                      +++++a++G +GvGKtt+ak   +k
  gi|242398956|ref|YP_002994380.1|  5 EKMLIAVSGTPGVGKTTVAKLLAEK 29
                                      4579**************9976655 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00039       0.2       3      64 ..       7      72 ..       5      83 .. 0.60
   2 ?   -2.4   0.0       8.3   4.4e+03      31      41 ..     134     144 ..     110     167 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00039
                            AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderd.........kkla.dpekllelileklkeek 64
                                       +++++G   vGKTt++k l+++       + y++l +  +         ++l+ +++kl  +++eklk+ +
  gi|242398956|ref|YP_002994380.1|  7 MLIAVSGTPGVGKTTVAKLLAEKMG-----YDYVDLREFALkhrigeirgDELEiEFDKLAYYVKEKLKN-R 72
                                      568999**********999997766.....5555555544422233332222222344666666666654.3 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 8.3
                            AAA_14  31 esilyinldde 41 
                                       e i++++  ++
  gi|242398956|ref|YP_002994380.1| 134 EAIIEVDTTNK 144
                                       33333333332 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0    0.0047       2.5       1      23 [.      11      33 ..      11      45 .. 0.89
   2 ?    2.6   0.1      0.25   1.3e+02      99     128 ..      82     136 ..      62     158 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0047
                                      EEESTTSSHHHHHHHHHHHHTSE CS
                                      xxxxxxxxxxxxxxxxxxxxxxx RF
                               ADK  1 llGaPgaGKGtqaeklvkkygla 23
                                      + G+Pg GK t+a+ l++k+g+ 
  gi|242398956|ref|YP_002994380.1| 11 VSGTPGVGKTTVAKLLAEKMGYD 33
                                      579***************98765 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.25
                                       HTSEESEEEEEE--HHHHHHHHHT.........................GSHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx.........................xxxxxx RF
                               ADK  99 ekvkldlvleldvpeevlveRltg.........................Dneetv 128
                                       + + +d ++ l+++ +++ eRl +                         D++e++
  gi|242398956|ref|YP_002994380.1|  82 HLMPVDQIIILRAHPKLIGERLKErgytkekisenveaelvdvcllealDENEAI 136
                                       4578999999999999999999988887777777766666666666666555554 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   0.00024      0.13       3      22 ..       7      26 ..       5     110 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00024
                            AAA_24  3 lkiliyGpsgiGKTtlakel 22
                                      + i++ G +g+GKTt+ak l
  gi|242398956|ref|YP_002994380.1|  7 MLIAVSGTPGVGKTTVAKLL 26
                                      568999***********998 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1    0.0005      0.26       4      28 ..       6      30 ..       4      36 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0005
                              ParA  4 kviavlSgKGGVGKStvavnlAlaL 28
                                      k+++ +Sg  GVGK+tva  lA ++
  gi|242398956|ref|YP_002994380.1|  6 KMLIAVSGTPGVGKTTVAKLLAEKM 30
                                      567778****************877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       711  (0.0396564); expected 358.6 (0.02)
Passed bias filter:                      581  (0.0324056); expected 358.6 (0.02)
Passed Vit filter:                       118  (0.00658152); 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: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 1263.44
//
Query:       gi|242398957|ref|YP_002994381.1|  [L=42]
Description: hypothetical protein TSIB_0974 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       968  (0.0539907); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 254.77
//
Query:       gi|242398958|ref|YP_002994382.1|  [L=407]
Description: S-adenosylmethionine synthetase [Thermococcus sibiricus MM 739]
Scores for complete 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-179  595.6   5.5   4.2e-179  595.4   5.5    1.0  1  AdoMet_Synthase  S-adenosylmethionine synthetase (AdoMet synt
  ------ inclusion threshold ------
      0.036   14.7   0.1       0.29   11.8   0.0    2.5  2  S-AdoMet_synt_N  S-adenosylmethionine synthetase, N-terminal 
       0.23   11.2   0.8        7.2    6.4   0.1    2.8  2  E3_UbLigase_EDD  E3 ubiquitin ligase EDD


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 !  595.4   5.5    7e-183  4.2e-179       1     396 []       8     403 ..       8     403 .. 0.99

  Alignments for each domain:
  == domain 1  score: 595.4 bits;  conditional E-value: 7e-183
                                       --EEEEE-TTS-GTTSSEEEEEEE-TTSHHHHHHHHHHHHHHHHHHHHHHHHSS---EEEEEEEEE--EEEEETTEE CS
                   AdoMet_Synthase   1 rnivveelkkkpveeqevEivErKGiGHPDsiaDgiaeavsralskeylekfgailhhniDkvllvaGesepkfgGG 77 
                                       rni+veel ++p+e q+vE+vErKGiGHPDsiaDgiaeavsrals+ey++++g ilhhn+D+v++v+G++ p+fgGG
  gi|242398958|ref|YP_002994382.1|   8 RNIIVEELVRTPIEMQKVELVERKGIGHPDSIADGIAEAVSRALSREYIRRYGIILHHNTDQVEVVGGRAYPRFGGG 84 
                                       79*************************************************************************** PP

                                       EEEE-EEEEEEEEEEEEE.EEE--HHHHHHHHHHHHHHHH-SS--TTTSEEEEEEEEEEEEHHHHHHCH-SS...-B CS
                   AdoMet_Synthase  78 eviepieillsgratkevegekipveeialeaakeylkenlraldlekdvivdvklgkgsadLkdvferkkk.evpl 153
                                       evi+pi+illsgra++ v++e +pv+e+a++aak+ylk+++r+ld++++vi+d ++g+gs dL++vf++ k+  +pl
  gi|242398958|ref|YP_002994382.1|  85 EVIKPIYILLSGRAVEFVDKEMFPVHEVAIRAAKNYLKKRVRHLDVDNHVIIDSRIGQGSVDLVGVFNKVKEnPIPL 161
                                       ********************************************************************998879*** PP

                                       ESSSEEEEEEES--HHHHHHHHHHHHHTSHHHHHH-TTEEEEEEEEEEEETTEEEEEEEEEEEGGG--SHHHHHHHH CS
                   AdoMet_Synthase 154 aNDtSfgvgyaplseleklvleterllnskelkkklpevGeDiKvmglRekkkielTvavalvdrlvkdleeYlevk 230
                                       +NDtSfgvgyaplse+ek+vleterllns+e+kkk p+vGeDiKvmglR++++i+lT+a+a+vd+ v++ +eY+evk
  gi|242398958|ref|YP_002994382.1| 162 SNDTSFGVGYAPLSETEKIVLETERLLNSEEFKKKWPAVGEDIKVMGLRKGEEIDLTIAAAIVDSEVQNPQEYMEVK 238
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHSTTSEEEEEE-TT-BGGGTB--EESSSSGGGTT--EETTSS--TTSSB-TTS----S--TTS- CS
                   AdoMet_Synthase 231 eeikeeveelakkltkerevevevNtaDkkeeesvyltvtGtsaEegDdGsvGRGNRvnGlitpnrpmslEAaaGKN 307
                                       e i ++++el++k+t+ r+v+++vNtaD+++++++y+tvtGtsaE gDdGsvGRGNRvnGlitpnr ms+EAa GKN
  gi|242398958|ref|YP_002994382.1| 239 EGIYNAIKELTSKYTN-RDVNIYVNTADDPDKDIYYITVTGTSAEAGDDGSVGRGNRVNGLITPNRHMSMEAAGGKN 314
                                       ***************9.************************************************************ PP

                                       TTT-HHHHHHHHHHHHHHHHHHH-TTEEEEEEEEEE-TTSBTTS-SEEEEEEEESSS---HHSHHHHHHHHHHHHT- CS
                   AdoMet_Synthase 308 PvsHvGKiYnvlaneiakeiveevegvkevyvrllsqiGkpidePlvasvqvilekgvsleevekeveeiideelek 384
                                       PvsHvGKiYn+lan ia++i+eevegv+evyvr+lsqiGkpidePlvas+q i++ g+++e++e++  ei+de+l++
  gi|242398958|ref|YP_002994382.1| 315 PVSHVGKIYNILANLIARDIAEEVEGVQEVYVRILSQIGKPIDEPLVASIQAIPKPGYKVEQFERQTYEIADEWLAN 391
                                       ***************************************************************************** PP

                                       HHHHHHHHTTT- CS
                   AdoMet_Synthase 385 ieeiteeliegk 396
                                       i++i+++++e+k
  gi|242398958|ref|YP_002994382.1| 392 ITKIQKMILEDK 403
                                       ********9986 PP

>> S-AdoMet_synt_N  S-adenosylmethionine synthetase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   4.9e-05      0.29      11      53 ..      33      74 ..      24      83 .. 0.79
   2 ?   -1.1   0.1      0.54   3.2e+03      48      82 ..     221     258 ..     210     265 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.9e-05
                   S-AdoMet_synt_N 11 eGHPDkvadqisdaildailkedpkarvacetlvttglvvvag 53
                                       GHPD +ad i++a+  + l+++   r  +    +t++v v+g
  gi|242398958|ref|YP_002994382.1| 33 IGHPDSIADGIAEAVS-RALSREYIRRYGIILHHNTDQVEVVG 74
                                      6***********9975.55777777787777777777776665 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.54
                   S-AdoMet_synt_N  48 lvvvageitt.kakvdiekivrevikeig..Yekeelg 82 
                                         +v  e+++ + ++++++ + ++ike+   Y++++++
  gi|242398958|ref|YP_002994382.1| 221 AAIVDSEVQNpQEYMEVKEGIYNAIKELTskYTNRDVN 258
                                       55666777552567888888888888864225555555 PP

>> E3_UbLigase_EDD  E3 ubiquitin ligase EDD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.1    0.0012       7.2      19      37 ..       3      21 ..       1      25 [. 0.84
   2 ?    2.1   0.0     0.026   1.5e+02      28      43 ..     245     262 ..     221     266 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0012
                   E3_UbLigase_EDD 19 LqgKSRqvIiRELQrtnLd 37
                                      +  K R++I+ EL rt ++
  gi|242398958|ref|YP_002994382.1|  3 MVKKNRNIIVEELVRTPIE 21
                                      6679***********9765 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.026
                   E3_UbLigase_EDD  28 iREL..QrtnLdVNlAVN 43 
                                       i+EL    tn dVN+ VN
  gi|242398958|ref|YP_002994382.1| 245 IKELtsKYTNRDVNIYVN 262
                                       566633359********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       706  (0.0393775); expected 358.6 (0.02)
Passed bias filter:                      557  (0.031067); 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: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.48
# Mc/sec: 2533.61
//
Query:       gi|242398959|ref|YP_002994383.1|  [L=208]
Description: Translin like protein [Thermococcus sibiricus MM 739]
Scores for complete 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   0.8    5.6e-14   52.6   0.8    2.3  1  Translin  Translin family
  ------ inclusion threshold ------
       0.14   12.7   1.9       0.29   11.6   0.1    2.0  2  PIN_12    PIN domain
        2.2    8.7  13.0       0.19   12.1   1.9    3.0  3  NBD94     Nucleotide-Binding Domain 94 of RH
        4.4    7.6   9.7        2.1    8.6   0.3    3.5  4  FliS      Flagellar protein FliS


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 !   52.6   0.8   1.2e-17   5.6e-14       2     193 ..      22     183 ..      21     202 .. 0.82

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 1.2e-17
                                       HHHHHHHHHHHHHHHHHHHHHHHHTTGSSTTTHHHHHHH.HHHHHHHHHHHTTSS..........GHHHHGGGTH.H CS
                          Translin   2 rreriikasrditaaskkiifllhrvrsekteaqdkkakikkeakeklkeiakllasvaeelqgsnayrYqrqisgg 78 
                                        re+  ++ rdi ++s  +i +lhr +       + +++  k a++ ++e++++l       ++++   +   ++++
  gi|242398959|ref|YP_002994383.1|  22 MREKALRLTRDIVRLSGDCIKALHRGDL------EIAEERLKMAEKLVSELKEIL-------TEHKDLYFTGYVQNA 85 
                                       5999999******************762......222332345555555555555.......555666788899999 PP

                                       HHHHHHHHHHHHHHHHSS---HHHHHHHTT.---SSSSSS---HHHHHHHHHHHHHHHHHHHHHHHCTT--S.HHHH CS
                          Translin  79 lqeliealsfahYletqtLitleevqkilealkeneedafhltpedYllGlfdLtgELmRfainsvalgdkeekplq 155
                                        qe++ea +f+hYl ++++ + +               ++ ++++ Y lG+ d++gEL R+  n + + + e k+++
  gi|242398959|ref|YP_002994383.1|  86 HQEYVEANLFYHYLLDEEFPHPK---------------EIGIPETAYALGIGDFIGELRRYFLNLLLNDKIE-KAQE 146
                                       9*************886555544...............56788999******************99988877.**** PP

                                       HHHHHHHHHHHHHTS----HH...HHHHHTTHHHHHHH CS
                          Translin 156 ilkflrelragfellnlkndsakdlrkKldvlkqsvkK 193
                                       +++f+++l++++  l+ +  +  ++r+K+d  ++ +++
  gi|242398959|ref|YP_002994383.1| 147 VYAFMEKLYDELATLEYPK-GLVNIRQKQDQARYILER 183
                                       ******************5.468**********99987 PP

>> PIN_12  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   6.4e-05      0.29      42     128 ..       5      94 ..       3     126 .. 0.84
   2 ?    0.5   0.3      0.17   7.6e+02      76     109 ..     155     190 ..     129     206 .. 0.42

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.4e-05
                            PIN_12  42 ldEflknrekkieeskkle.kalks...lsklksakkklnekkkllslkeikkkieekveeslkkllekleaikvip 114
                                       + E+++ ++k+++e+ +++ kal+    + +l  +  k+  + +l++ +e  k++e+ v+e lk++l +++ + +  
  gi|242398959|ref|YP_002994383.1|   5 ISEIINEIRKVLDEKDEMReKALRLtrdIVRLSGDCIKALHRGDLEIAEERLKMAEKLVSE-LKEILTEHKDLYFTG 80 
                                       68*************7777777777778*************************99999887.9****9999988888 PP

                            PIN_12 115 etndevkkileraf 128
                                       + ++++++ +e  +
  gi|242398959|ref|YP_002994383.1|  81 YVQNAHQEYVEANL 94 
                                       88888888777655 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.17
                            PIN_12  76 lnekkkllslkeikkkieekvees..lkklleklea 109
                                       ++e+ +l++ k + ++ +++ +++  l++ le+l  
  gi|242398959|ref|YP_002994383.1| 155 YDELATLEYPKGLVNIRQKQDQARyiLERTLEDLTR 190
                                       333333333333333222222222333333333333 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 ?    0.5   3.6      0.18     8e+02      15      37 ..       6      28 ..       2      77 .. 0.56
   2 ?    0.2   0.1      0.23     1e+03      21      34 ..      59      72 ..      44      91 .. 0.74
   3 ?   12.1   1.9   4.3e-05      0.19       8      63 ..     138     196 ..     135     204 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.18
                             NBD94 15 kkiyeniekllnEleeiekekts 37
                                       +i ++i+k+l+E +e+ +    
  gi|242398959|ref|YP_002994383.1|  6 SEIINEIRKVLDEKDEMREKALR 28
                                      56677777777777777665544 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.23
                             NBD94 21 iekllnEleeieke 34
                                       ekl++El+ei +e
  gi|242398959|ref|YP_002994383.1| 59 AEKLVSELKEILTE 72
                                      35666666666554 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 4.3e-05
                             NBD94   8 vtkidkkkkiyeniekllnEleeiekektsle...evknielsYgrsLikllvqkIdee 63 
                                       + ki+k +++y  +ekl++El+ +e  k  ++   + ++     +r L  l   kI+++
  gi|242398959|ref|YP_002994383.1| 138 NDKIEKAQEVYAFMEKLYDELATLEYPKGLVNirqKQDQARYILERTLEDLTRAKINKN 196
                                       789*********************98775544211233333444677777777777765 PP

>> FliS  Flagellar protein FliS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.1     0.068     3e+02      50      67 ..       4      21 ..       1      31 [. 0.71
   2 ?    8.6   0.3   0.00047       2.1      30      64 ..      38      72 ..      26      79 .. 0.82
   3 ?    1.4   0.4     0.082   3.7e+02      64      82 ..     141     159 ..     123     191 .. 0.68
   4 ?   -1.1   0.0       0.5   2.2e+03      82      99 ..     185     203 ..     176     206 .. 0.62

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.068
                                      HHHHHHHHHHHTCCTTTS CS
                              FliS 50 kaqdIiseLrasLdlekg 67
                                         +Ii+e r+ Ld +++
  gi|242398959|ref|YP_002994383.1|  4 NISEIINEIRKVLDEKDE 21
                                      567999999999998663 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00047
                                      HHHHHHHHTTTHHHHHHHHHHHHHHHHHHHHTCCT CS
                              FliS 30 krakeaieekdiekkgeaiskaqdIiseLrasLdl 64
                                        +++a++++d+e ++e ++ a +++seL++ L  
  gi|242398959|ref|YP_002994383.1| 38 GDCIKALHRGDLEIAEERLKMAEKLVSELKEILTE 72
                                      56789999**********************99954 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.082
                                       TTTSCHHHHHHHHHHHHHH CS
                              FliS  64 lekggeiaknLaalYdyii 82 
                                        ek +e+ + +++lYd + 
  gi|242398959|ref|YP_002994383.1| 141 IEKAQEVYAFMEKLYDELA 159
                                       2566788888888887655 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 0.5
                                       HHHHHHHHHCT-H.HHHHH CS
                              FliS  82 irrlleanlkkda.eklde 99 
                                       ++ l++a+++k+  +kl+e
  gi|242398959|ref|YP_002994383.1| 185 LEDLTRAKINKNLeKKLEE 203
                                       5567777777666344555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1507  (0.0840538); expected 358.6 (0.02)
Passed bias filter:                      773  (0.0431145); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 1382.51
//
Query:       gi|242398960|ref|YP_002994384.1|  [L=187]
Description: Endonuclease V [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-37  129.4   0.0    4.3e-32  111.4   0.0    2.0  2  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 !  111.4   0.0   2.4e-36   4.3e-32       2     127 ..      12     132 ..      11     142 .. 0.91
   2 !   16.7   0.0   2.5e-07    0.0045     160     197 .]     141     177 ..     133     177 .. 0.87

  Alignments for each domain:
  == domain 1  score: 111.4 bits;  conditional E-value: 2.4e-36
                                       HHHCC-------SGG-SEEEEEEEEEEECTCEEEEEEEEEEETTTTEEEEEEEEEEE--S-SSTT-CHHHCHHHHHH CS
                    Endonuclease_5   2 elakkveledklkeklklvaGvDvsfvkeekkeavaalvvldlpslevvekavavvklsfpYipgfLaFRElpvllk 78 
                                       +l+k+++++++  +k+k++a+vDvs+   + ++a aa+v++++ps ev+++++ ++++ f Yip+++  RE+ ++l 
  gi|242398960|ref|YP_002994384.1|  12 KLSKRIVEKPQDISKIKTIAAVDVSY---KGNKAKAAFVLCSFPSCEVLKTKTIETEVAFSYIPTYFFLRETRPILL 85 
                                       7999*******9999***********...333457*****************************************9 PP

                                       HHCC-SS--SEEEEEC-SSSSTTS--HHHHHHHHHTS-EEEEESS-SSS CS
                    Endonuclease_5  79 aleklkqkpdvllvDGnGiaHprrlGlAshlGvlldlptiGvaKsllvg 127
                                       +l+  +   d+l+v+G+G aHpr+ GlAsh+G+l++ ptiG+aK+ l +
  gi|242398960|ref|YP_002994384.1|  86 LLKGEQ--FDLLIVEGHGKAHPRGYGLASHIGLLIGKPTIGIAKRPLPN 132
                                       998755..6***********************************99865 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 2.5e-07
                                       --EEEEEECSS-HHHHHHHHHHCS-T-SS-HHHHHHHH CS
                    Endonuclease_5 160 kpiyvSvGhrisletalelvlallkkyrlPepirqAdl 197
                                        + yvSvG+ i+l++a e+v+ + ++   P+p++ Ad+
  gi|242398960|ref|YP_002994384.1| 141 GKAYVSVGNLIDLNSAKEIVRII-NEGDYPKPLKIADK 177
                                       567***************99876.5899********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 1150.07
//
Query:       gi|242398961|ref|YP_002994385.1|  [L=211]
Description: Riboflavin kinase [Thermococcus sibiricus MM 739]
Scores for complete 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-39  135.3   0.0    1.7e-39  134.6   0.0    1.3  1  CTP-dep_RFKase  Domain of unknown function DUF120
    4.4e-07   29.4   0.1    8.3e-07   28.5   0.1    1.4  1  HTH_24          Winged helix-turn-helix DNA-binding
    5.5e-06   26.2   0.0    8.7e-06   25.5   0.0    1.3  1  MarR_2          MarR family
    7.3e-06   25.9   0.1    1.1e-05   25.3   0.1    1.3  1  HTH_Crp_2       Crp-like helix-turn-helix domain
    0.00014   21.6   0.1     0.0018   18.0   0.0    2.2  2  LexA_DNA_bind   LexA DNA binding domain
    0.00033   20.5   0.1    0.00078   19.3   0.1    1.6  1  HTH_11          HTH domain
    0.00068   19.8   0.1     0.0022   18.1   0.1    1.9  1  HTH_34          Winged helix DNA-binding domain
    0.00075   19.6   0.1      0.002   18.3   0.1    1.7  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
     0.0011   18.8   0.1     0.0022   17.8   0.1    1.5  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
     0.0019   18.1   0.1     0.0034   17.3   0.1    1.4  1  MarR            MarR family
     0.0048   16.7   0.0     0.0077   16.0   0.0    1.4  1  HTH_IclR        IclR helix-turn-helix domain
     0.0096   15.6   0.1      0.019   14.6   0.1    1.5  1  GntR            Bacterial regulatory proteins, gntR family
  ------ inclusion threshold ------
       0.01   15.3   0.0      0.016   14.6   0.0    1.2  1  RepL            Firmicute plasmid replication protein (RepL)
      0.012   15.8   0.1      0.021   15.0   0.1    1.4  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
      0.016   15.5   0.1      0.028   14.8   0.1    1.3  1  Rrf2            Transcriptional regulator
      0.018   14.7   0.0       0.03   14.0   0.0    1.3  1  HTH_53          Zap  helix turn helix N-terminal domain
      0.033   14.7   0.1      0.055   14.0   0.1    1.4  1  HTH_27          Winged helix DNA-binding domain
      0.036   14.1   0.0      0.072   13.2   0.0    1.5  1  HTH_20          Helix-turn-helix domain
      0.045   13.6   0.2       0.11   12.4   0.2    1.6  1  TrmB            Sugar-specific transcriptional regulator TrmB
      0.048   14.1   2.7        1.2    9.7   0.3    2.7  2  DUF104          Protein of unknown function DUF104
      0.065   13.3   0.0       0.11   12.6   0.0    1.3  1  FeoC            FeoC like transcriptional regulator
        0.1   12.5   0.0       0.19   11.6   0.0    1.4  1  HTH_5           Bacterial regulatory protein, arsR family
        0.1   12.3   0.1       0.27   11.0   0.0    1.6  2  DUF4364         Domain of unknown function (DUF4364)
       0.12   12.3   0.1        0.4   10.5   0.0    1.9  2  IF2_N           Translation initiation factor IF-2, N-termina
       0.16   11.7   0.1        0.3   10.8   0.1    1.4  1  Ribosomal_S19e  Ribosomal protein S19e
       0.17   11.9   0.0        0.3   11.2   0.0    1.3  1  Glyco_hydro_38  Glycosyl hydrolases family 38 C-terminal doma


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 !  134.6   0.0   2.5e-42   1.7e-39       1     121 []      92     209 ..      92     209 .. 0.97

  Alignments for each domain:
  == domain 1  score: 134.6 bits;  conditional E-value: 2.5e-42
                                       EE--SSHHHHHHCSHHHHHHHHHHHSS---SS-EEEEESCCGHHHHCHHHHS--EEE--EEETTEEE--EEEEEEEE CS
                    CTP-dep_RFKase   1 VvsGlgeGkyyvslegykeqfeeklgfepypGTLNvkldeeslelrkaleklkgieiegfedeertfgavkvypaki 77 
                                       VvsG+geGkyyv++  yke+++e+lgf+pypGTLN+ +  +  ++ +al ++++i+i+gf++++rtfg+vk+y+++i
  gi|242398961|ref|YP_002994385.1|  92 VVSGVGEGKYYVEQ--YKERIREYLGFRPYPGTLNILVVFP-KTIYEALYNVEPITIPGFSKDGRTFGDVKAYKVRI 165
                                       89***********9..********************99888.6788999**************************** PP

                                       CCEEEEEEEESS-SS.TTEEEEE-SS-HHHHTT--TT-EEEEEE CS
                    CTP-dep_RFKase  78 ekikaavvvperthyeedvlEiiapekLReklelkdgdevevev 121
                                       ++i++a+vvp+rt ++++v Eiiap  LR+kl+lkdg++v+vev
  gi|242398961|ref|YP_002994385.1| 166 NGIDGAIVVPSRTIHPPKVAEIIAPACLRKKLNLKDGSKVKVEV 209
                                       ******************************************97 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.1   1.2e-09   8.3e-07      16      47 ..      20      51 ..      16      52 .. 0.94

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 1.2e-09
                            HTH_24 16 prisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                       ri+ reL++++g Sp+ v r l+ Le+eG++
  gi|242398961|ref|YP_002994385.1| 20 VRITLRELSQEIGTSPQSVMRKLEALEKEGYV 51
                                      59*****************************9 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   1.3e-08   8.7e-06       7      61 ..       3      59 ..       1      60 [. 0.90

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 1.3e-08
                                      HHHHHHHHHCTTTS....EEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSSS CS
                            MarR_2  7 qarvLaaLgrrpgr....dltvgelarrlglsksavsrilkrLvaaGLverrpgpeDkR 61
                                      ++ +L  ++ r+g     ++t +el ++ g s+++v r l+ L++ G+v + ++   kR
  gi|242398961|ref|YP_002994385.1|  3 ELKLLISIAKRGGVgekvRITLRELSQEIGTSPQSVMRKLEALEKEGYVIKDTS--GKR 59
                                      66789999999999999999*****************************98877..555 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 !   25.3   0.1   1.6e-08   1.1e-05       6      55 ..       6      58 ..       4      67 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 1.6e-08
                                      HHHHHHCTTTC.EEEEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE..E.TE CS
                         HTH_Crp_2  6 fLlrlaeragg.eielpltqeelAsmlGltretvsrilseLkreglis..r.gr 55
                                      +L+ +a+r gg   ++++t +el++ +G+++++v r l +L++eg++   + g+
  gi|242398961|ref|YP_002994385.1|  6 LLISIAKR-GGvGEKVRITLRELSQEIGTSPQSVMRKLEALEKEGYVIkdTsGK 58
                                      67777777.55545799****************************976443343 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 !   18.0   0.0   2.7e-06    0.0018      27      60 ..      23      55 ..      22      60 .. 0.85
   2 ?    1.1   0.0       0.5   3.5e+02      21      32 ..     177     188 ..     174     205 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.7e-06
                                      -HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE-GG CS
                     LexA_DNA_bind 27 sireiaralglkSpsaveehLkaLerKGyierdp 60
                                      + re+++++g +Sp++v  +L+aLe+ Gy+  d 
  gi|242398961|ref|YP_002994385.1| 23 TLRELSQEIG-TSPQSVMRKLEALEKEGYVIKDT 55
                                      78********.67****************86554 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.5
                                       HHSS---HHHHH CS
                     LexA_DNA_bind  21 etgypPsireia 32 
                                       +t +pP ++ei 
  gi|242398961|ref|YP_002994385.1| 177 RTIHPPKVAEII 188
                                       5679******96 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1   1.1e-06   0.00078      15      51 ..      21      57 ..      17      58 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.1e-06
                            HTH_11 15 pisgeeLAeeLnvSrrtvrrdIkaLeelgvpIesepg 51
                                       i+  eL++e++ S + v r ++aLe+ g+ I  ++g
  gi|242398961|ref|YP_002994385.1| 21 RITLRELSQEIGTSPQSVMRKLEALEKEGYVIKDTSG 57
                                      49****************************9998877 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 !   18.1   0.1   3.2e-06    0.0022      15      79 ..      22      82 ..      17      83 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 3.2e-06
                            HTH_34 15 adfvelkealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreafkkyvkaLksl 79
                                      ++ +el+++++++      +l++Lek gY+   k+ +gk  rtl+++T+ G +  ++ ++++ ++
  gi|242398961|ref|YP_002994385.1| 22 ITLRELSQEIGTSPQSVMRKLEALEKEGYVI--KDTSGK--RTLVEVTSSGIQLLESIFEEIGKI 82
                                      67899************************86..888898..9**************999998876 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 !   18.3   0.1     3e-06     0.002      19      53 ..      18      52 ..      16      59 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3e-06
                                      HHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                    Fe_dep_repress 19 ekkvvktkdlaerLnvspssVsemlkkLekdGyve 53
                                      ek+ ++  +l+++++ sp sV   l+ Lek+Gyv+
  gi|242398961|ref|YP_002994385.1| 18 EKVRITLRELSQEIGTSPQSVMRKLEALEKEGYVI 52
                                      566678899*************************7 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   3.1e-06    0.0022      16      42 .]      20      46 ..      17      46 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.1e-06
                     HTH_AsnC-type 16 aRisyaeLAervGlSestvlrRvrrLe 42
                                       Ri+ +eL++++G S++ v+r +++Le
  gi|242398961|ref|YP_002994385.1| 20 VRITLRELSQEIGTSPQSVMRKLEALE 46
                                      7***********************998 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   4.9e-06    0.0034       4      49 ..       2      53 ..       1      57 [. 0.88

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.9e-06
                                      HHHHHHHHHHHSTTEEHH......HHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              MarR  4 tqfviLrilyeqgplsvs......eLakklgvskstvtrvldrLekkGlieR 49
                                       ++++L +++ +g+   +      eL   +g+s+ +v r l +Lek+G++ +
  gi|242398961|ref|YP_002994385.1|  2 EELKLLISIAKRGGVGEKvritlrELSQEIGTSPQSVMRKLEALEKEGYVIK 53
                                      578889999999998888888888*************************965 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.1e-05    0.0077      18      51 ..      16      54 ..       4      55 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.1e-05
                                      S.....-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                          HTH_IclR 18 e.....ltlselArrtglpkStvhRlLqtLvelGyveqd 51
                                             tl+el++++g ++ +v R L  L+++Gyv +d
  gi|242398961|ref|YP_002994385.1| 16 VgekvrITLRELSQEIGTSPQSVMRKLEALEKEGYVIKD 54
                                      34455579***************************9665 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   2.7e-05     0.019      24      55 ..      22      52 ..      10      62 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.7e-05
                                      ---HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              GntR 24 LPsereLaaefgVsrttvReALrrLeaeglve 55
                                      + + reL++e+g+s ++v++ L  Le eg+v+
  gi|242398961|ref|YP_002994385.1| 22 I-TLRELSQEIGTSPQSVMRKLEALEKEGYVI 52
                                      6.89*************************996 PP

>> RepL  Firmicute plasmid replication protein (RepL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   2.3e-05     0.016      74     111 ..      20      57 ..      10      63 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.3e-05
                              RepL  74 liatnRelaeetgislktvsetlkileeanilkkkanG 111
                                       + +t Rel++e g+s + v++ l +le+ ++++k ++G
  gi|242398961|ref|YP_002994385.1|  20 VRITLRELSQEIGTSPQSVMRKLEALEKEGYVIKDTSG 57 
                                       55799*******************************99 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 ?   15.0   0.1     3e-05     0.021       6      52 ..       5      55 ..       2      74 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3e-05
                    B-block_TFIIIC  6 klLelIassRysG....itqsdLakeskqdprslfyrlksLekkgLIvkqs 52
                                      klL  Ia+++  G    it ++L++e++ +p s+   l +Lek g++ k +
  gi|242398961|ref|YP_002994385.1|  5 KLLISIAKRGGVGekvrITLRELSQEIGTSPQSVMRKLEALEKEGYVIKDT 55
                                      788888888888855556899***************************987 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1     4e-05     0.028      12      55 ..       5      51 ..       3      60 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4e-05
                                      HHHHHHHHSSTCC-...B-HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                              Rrf2 12 hallyLakeeeeep...vsseeiaerqnispsylekilakLrkaglv 55
                                      ++l+ +ak+ + +    ++++e++++ ++sp+ + + l+ L+k+g+v
  gi|242398961|ref|YP_002994385.1|  5 KLLISIAKRGGVGEkvrITLRELSQEIGTSPQSVMRKLEALEKEGYV 51
                                      677778777654444559***************************98 PP

>> HTH_53  Zap  helix turn helix N-terminal 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      0.03      16      56 ..      21      61 ..      13      67 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.4e-05
                            HTH_53 16 rmaLeeLlgeveLseaqLkevLeeAGpeRFllletggeagv 56
                                      r++L+eL +e++ s++ ++  Le+   e +++ +t+g+  +
  gi|242398961|ref|YP_002994385.1| 21 RITLRELSQEIGTSPQSVMRKLEALEKEGYVIKDTSGKRTL 61
                                      89**********************************99875 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   7.9e-05     0.055      20      68 .]      23      68 ..       6      68 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.9e-05
                            HTH_27 20 kladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                      +l++l++   ++ ++++  l++L++ G+v    +++++++++v++T +G
  gi|242398961|ref|YP_002994385.1| 23 TLRELSQEIGTSPQSVMRKLEALEKEGYV---IKDTSGKRTLVEVTSSG 68
                                      789**************************...44489999******776 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0    0.0001     0.072      26      60 ..      23      57 ..      18      58 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.0001
                                      -HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                            HTH_20 26 taselaerldlskntlsyHLrvLeeagLvevvreg 60
                                      t+ el +++++s++++ + L++Le+ g+v   ++g
  gi|242398961|ref|YP_002994385.1| 23 TLRELSQEIGTSPQSVMRKLEALEKEGYVIKDTSG 57
                                      7889***********************99777766 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   0.00016      0.11      22      59 ..      21      58 ..      16      66 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00016
                                      CCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTT CS
                              TrmB 22 patadeiaeelgvprskvYevLrsLedkGlVerekgrp 59
                                      + t +e+++e+g + ++v + L+ Le+ G+V +  + +
  gi|242398961|ref|YP_002994385.1| 21 RITLRELSQEIGTSPQSVMRKLEALEKEGYVIKDTSGK 58
                                      56899**************************9988653 PP

>> DUF104  Protein of unknown function DUF104
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.2      0.12        84      25      47 ..      17      40 ..      16      54 .. 0.68
   2 ?    9.7   0.3    0.0017       1.2      18      33 ..     195     210 ..     192     211 .] 0.90

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.12
                            DUF104 25 GeevkikIee.akeilkklkgilk 47
                                      Ge+v+i+++e  +ei  + +++++
  gi|242398961|ref|YP_002994385.1| 17 GEKVRITLRElSQEIGTSPQSVMR 40
                                      9*********85555544444444 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0017
                            DUF104  18 ekvdLkEGeevkikIe 33 
                                       +k++Lk+G++vk+++ 
  gi|242398961|ref|YP_002994385.1| 195 KKLNLKDGSKVKVEVI 210
                                       89***********997 PP

>> FeoC  FeoC like 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      0.11      11      50 ..      18      57 ..      14      66 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00016
                              FeoC 11 ergrvslkeLsrhfkaspealeamLeqwvrkGrvekvaat 50
                                      e+ r+ l+eLs++  +sp+ +   Le +++ G v k + +
  gi|242398961|ref|YP_002994385.1| 18 EKVRITLRELSQEIGTSPQSVMRKLEALEKEGYVIKDTSG 57
                                      6789******************************998865 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00028      0.19      18      47 .]      24      53 ..      22      53 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00028
                                      HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5 18 vcelaeelglsqstvShHLkkLreaGLVek 47
                                        el+ e+g s+  v + L +L+++G+V k
  gi|242398961|ref|YP_002994385.1| 24 LRELSQEIGTSPQSVMRKLEALEKEGYVIK 53
                                      579*************************86 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00039      0.27      38      79 ..      40      81 ..      35      86 .. 0.90
   2 ?   -2.7   0.0       6.3   4.4e+03      80     107 ..     183     210 ..     181     211 .] 0.77

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00039
                           DUF4364 38 qalseLvesglieeeekenktlykiTekGketlelfenripk 79
                                        l+ L+++g++ ++++ ++tl ++T++G + le + ++i k
  gi|242398961|ref|YP_002994385.1| 40 RKLEALEKEGYVIKDTSGKRTLVEVTSSGIQLLESIFEEIGK 81
                                      56899*****************************99988865 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 6.3
                           DUF4364  80 sirekideylkenkeelkkesevkadyy 107
                                       ++ e i  ++ ++k +lk  s+vk++++
  gi|242398961|ref|YP_002994385.1| 183 KVAEIIAPACLRKKLNLKDGSKVKVEVI 210
                                       5667777788889999999999999876 PP

>> IF2_N  Translation initiation factor IF-2, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00058       0.4       4      28 ..      22      45 ..      20      56 .. 0.83
   2 ?   -2.0   0.0       4.8   3.3e+03      41      53 ..     104     116 ..     104     117 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00058
                             IF2_N  4 irVyeLAkeLgvkskevikkLfkel 28
                                      i+ +eL +e+g++++ v++kL++ l
  gi|242398961|ref|YP_002994385.1| 22 ITLRELSQEIGTSPQSVMRKLEA-L 45
                                      899******************55.6 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.8
                             IF2_N  41 eetaeliaeefgi 53 
                                       e+ +e i+e++g+
  gi|242398961|ref|YP_002994385.1| 104 EQYKERIREYLGF 116
                                       5788999**9997 PP

>> Ribosomal_S19e  Ribosomal protein S19e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00043       0.3      92     134 ..      35      79 ..      15      81 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00043
                                       HHHTTSSS--SSS---SS.-HHHHHTHH...HHH--SS--S--XXXX CS
                    Ribosomal_S19e  92 sgsvirkilqqLeklglv.kkekkkgrr...ltkkGqrlldriaeev 134
                                        +sv+rk l++Lek g+v k++++ +r+   +t++G +ll++i ee+
  gi|242398961|ref|YP_002994385.1|  35 PQSVMRK-LEALEKEGYViKDTSG-KRTlveVTSSGIQLLESIFEEI 79 
                                       4566666.79********776655.5542337**********99987 PP

>> Glyco_hydro_38  Glycosyl hydrolases family 38 C-terminal domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00044       0.3      24      71 ..      22      70 ..       9      71 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00044
                                      EEEEEEEGGG.S-HHHHHHHHHHS----EEEE-TTS-EE-EEEEEEEEE CS
                    Glyco_hydro_38 24 lelerlyfse.gkpeelykelkekelpeyevvdaeGeevpaevedlgvr 71
                                      ++l+ l  +  ++p++++++l+++e++ y+++d++G++  +ev+++g++
  gi|242398961|ref|YP_002994385.1| 22 ITLRELSQEIgTSPQSVMRKLEALEKEGYVIKDTSGKRTLVEVTSSGIQ 70
                                      333333333334579****************************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       709  (0.0395449); expected 358.6 (0.02)
Passed bias filter:                      650  (0.0362541); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.44u 0.20s 00:00:00.64 Elapsed: 00:00:00.36
# Mc/sec: 1740.07
//
Query:       gi|242398962|ref|YP_002994386.1|  [L=174]
Description: hypothetical protein TSIB_0979 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       884  (0.0493056); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); 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):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1227.67
//
Query:       gi|242398963|ref|YP_002994387.1|  [L=73]
Description: hypothetical protein TSIB_0980 [Thermococcus sibiricus MM 739]
Scores for complete 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-13   48.7   0.5    6.9e-13   48.5   0.5    1.0  1  PRC       PRC-barrel domain


Domain annotation for each model (and alignments):
>> PRC  PRC-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.5   0.5   3.8e-17   6.9e-13       3      74 ..       6      70 ..       5      73 .] 0.95

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 3.8e-17
                                      ECCS---TT-EEEETTSSEEEEEEEEEEETTTTEEEEEEEEETTT.....-EEEEEGG.CEECCCTEEEETT CS
                               PRC  3 efrasdliGkeVytedGeklGkVkDvvidekegrvralvvsvggflgigekevliPfdlavkigkdriivda 74
                                      ++r+s++ Gk++y++ G ++G V +v+i++++g+ r l ++  g      ++v iP++ +v++++d+i+++a
  gi|242398963|ref|YP_002994387.1|  6 VMRLSKIYGKQIYNTAGYYIGYVDEVLIEIEAGESRILALGLPG------EKVGIPYE-RVSAIGDIILIEA 70
                                      589***************************************96......9*******.***********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       244  (0.0136092); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 545.59
//
Query:       gi|242398964|ref|YP_002994388.1|  [L=490]
Description: Phosphoesterase, [Thermococcus sibiricus MM 739]
Scores for complete 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   65.0   0.7    6.8e-18   65.0   0.7    2.2  1  TrkA_N           TrkA-N domain
    3.8e-12   46.8   0.8    3.8e-12   46.8   0.8    3.2  4  DHHA1            DHHA1 domain
    1.9e-11   44.1   0.2    2.3e-10   40.6   0.1    2.2  2  DHH              DHH family
    1.8e-05   25.0   1.1    4.8e-05   23.6   0.2    2.2  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
    0.00033   20.3   1.3    0.00058   19.5   0.4    1.9  2  NmrA             NmrA-like family
    0.00078   20.0   1.7       0.18   12.4   0.6    2.9  2  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
     0.0023   17.6   1.3     0.0037   16.9   0.2    1.9  2  ApbA             Ketopantoate reductase PanE/ApbA
     0.0032   17.9   0.4      0.018   15.5   0.1    2.4  2  NAD_binding_7    Putative NAD(P)-binding
     0.0072   15.6   0.4     0.0072   15.6   0.4    2.2  2  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
  ------ inclusion threshold ------
      0.012   15.3   0.2      0.038   13.6   0.2    1.8  2  DAO              FAD dependent oxidoreductase
      0.015   15.3   0.4      0.041   13.9   0.4    1.8  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
      0.017   14.5   1.8       0.11   11.8   0.1    2.6  3  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
      0.031   13.7   0.8      0.051   12.9   0.8    1.3  1  Mannosyl_trans3  Mannosyltransferase putative
       0.07   12.6   0.1       0.13   11.7   0.1    1.4  1  CbiJ             Precorrin-6x reductase CbiJ/CobK
      0.082   12.4   0.4       0.18   11.3   0.4    1.6  1  Elong_Iki1       Elongator subunit Iki1
      0.096   12.5   5.4        5.8    6.7   0.1    3.0  3  DUF421           Protein of unknown function (DUF421)
       0.14   12.3   1.7       0.44   10.6   1.7    2.0  1  AdoHcyase_NAD    S-adenosyl-L-homocysteine hydrolase, NAD bin
       0.44   11.2   3.1        1.1   10.0   0.7    2.8  2  DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomer


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 !   65.0   0.7   6.8e-21   6.8e-18       1     104 [.       6     108 ..       6     129 .. 0.87

  Alignments for each domain:
  == domain 1  score: 65.0 bits;  conditional E-value: 6.8e-21
                                       EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHH CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatgddeani 77 
                                       ++i+G G +Grs+a+ L+ + + v++i+++e r+++l+e g++v++gd + ++ L +agiek+d+v++++ d     
  gi|242398964|ref|YP_002994388.1|   6 VLILGGGSIGRSVAQALKGEFE-VIIIEQNEIRAKSLSESGFHVIQGDFSYTASLLKAGIEKVDLVVITIMDVNGIK 81 
                                       68***************99985.***********************************************9999999 PP

                                       HHHHHHHHHTSSSEEEEEESSGGGHHH CS
                            TrkA_N  78 lavllakelnpkkkiiaraqdpehael 104
                                        ++++++++n++ +i + + d+ +++ 
  gi|242398964|ref|YP_002994388.1|  82 KTIQAIRNNNSEVPILVLIPDDTTVKE 108
                                       999999*********999999988443 PP

>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       3.7   3.7e+03     104     121 ..       4      23 ..       2      39 .. 0.80
   2 ?    2.2   1.7      0.22   2.2e+02      30      99 ..      80     153 ..      60     160 .. 0.63
   3 ?    3.8   1.4     0.072        72       8      79 ..     106     173 ..     103     185 .. 0.72
   4 !   46.8   0.8   3.8e-15   3.8e-12      27     138 .]     365     477 ..     351     477 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3.7
                                       HHHTTCCEE..EETCEEEEE CS
                             DHHA1 104 aaklgggGG..GHdlAaGag 121
                                        + l++gGG  G+  A++++
  gi|242398964|ref|YP_002994388.1|   4 MRVLILGGGsiGRSVAQALK 23 
                                       56788999999999999976 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.22
                                       HHHTCEEEC.TCEEEEEECHCCHHHHHHHHHHHHHHTHG.BT.TCEEEEEEEECTEEEEEEEESSH...SS-HHHH CS
                             DHHA1  30 llekaeevk.gvkvlvaevgeewdagalgiaadklkskl.kk.pvivfvakeegdkvkvsarskkd...gvdagel 99 
                                       + ++++ ++ + + +   v    d ++++++++++k+++ ++ ++  +v+ +   ++kv++ + k+   + +a  l
  gi|242398964|ref|YP_002994388.1|  80 IKKTIQAIRnNNSEVPILV-LIPDDTTVKEIISQIKKEFeTDvKIDYAVSPKAA-TIKVIVDTVKNlgkKKNATLL 153
                                       5555555555444444444.4667788888888888888655555555555555.888888887766654444444 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.072
                                       HHHHHHHHHCHHHHHHHHHHHHHHHTCEEEC..TCEEEEEECHCCHHHHHHHHHHHHHHTHGBT.TCEEEEEEEE CS
                             DHHA1   8 rkelekeleelkealaklkaeellekaeevk..gvkvlvaevgeewdagalgiaadklksklkk.pvivfvakee 79 
                                        ke+  ++  +ke+++++k++ +++     k  + kv+v  v ++  ++  +++ +k +s++k+    ++++ ++
  gi|242398964|ref|YP_002994388.1| 106 VKEIISQI--KKEFETDVKIDYAVSP----KaaTIKVIVDTV-KNLGKKKNATLLSKKLSEIKQkSDSLLIVMHD 173
                                       57888888..9999999999888877....233888888888.88888888888888777786645555554444 PP

  == domain 4  score: 46.8 bits;  conditional E-value: 3.8e-15
                                       HHHHHHTCEEEC.TCEEEEEECHCCHHHHHHHHHHHHHHTHGBT.TCEEEEEEEECTEEEEEEEESSH.SS-HHHHH CS
                             DHHA1  27 aeellekaeevk.gvkvlvaevgeewdagalgiaadklksklkk.pvivfvakeegdkvkvsarskkd.gvdagela 100
                                       a +++++    k  ++v++++vg  +d++a+++ ad l+    + +  v+v++  +d++ +sar++ d ++++g+++
  gi|242398964|ref|YP_002994388.1| 365 ARAIINR----KtFKNVIISNVGFITDRDAIAESADFLLR--LEgVNTVLVFGIVDDRIEISARTR-DiRINVGKVL 434
                                       4444444....23689************************..888999999999999*********.55******** PP

                                       HHHHHHTTCCEEEETCEEEEEEE.......HCHHHHHHHHHHHHH CS
                             DHHA1 101 keaaaklgggGGGHdlAaGagip.......aekleealealeeai 138
                                       kea++++g  G GH++  Ga+i        ++  + +l+++eeai
  gi|242398964|ref|YP_002994388.1| 435 KEAFTDIGSAG-GHAQSGGARIHlgifklaKD-KNSLLKLVEEAI 477
                                       **999999999.**********9899998444.488888888876 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.49   4.9e+02      56      88 ..     115     147 ..      74     159 .. 0.79
   2 !   40.6   0.1   2.4e-13   2.3e-10       3     101 .]     168     318 ..     166     318 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.49
                                       SS---SS--EEEE-SSS-HHHHHHHHHHHTT-- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DHH  56 eefetlapilflnepvgstaeivaelleekkee 88 
                                       +efet  +i +  +p ++t +++++ +++ +++
  gi|242398964|ref|YP_002994388.1| 115 KEFETDVKIDYAVSPKAATIKVIVDTVKNLGKK 147
                                       3799999999999999*******9998873333 PP

  == domain 2  score: 40.6 bits;  conditional E-value: 2.4e-13
                                       EEE-ECSSSHHHHHHHHHHHHC.................................................ECS--T CS
                                       xxxxxxxxxxxxxxxxxxxxxx.................................................xxxxxx RF
                               DHH   3 livghknpDtDsigSaialanl.................................................lvDhne 30 
                                       liv+h npD D+++Sa+al+ +                                                 lvD++ 
  gi|242398964|ref|YP_002994388.1| 168 LIVMHDNPDPDAMASAVALQVIaqntglkstivyggeithhenrafvnllgldirkvspgsyevkrhstiaLVDCQP 244
                                       799******************66666667777777777777777777777777777777777777777777****** PP

                                       CGGCGCCHHCCCSEEEEEEE-S---SS---SS-...-EEEE-SSS-HHHHHHHHHHHTT----HHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DHH  31 ksqavegeakeeaedviiiDHHrlgeefetlap...ilflnepvgstaeivaelleekkeeiskeiaellllgi 101
                                       + +  + + ++ ++  i iDHH+l +++e++ p   ++ ++++v sta+i+ae+l+  + e++ ++ + l  gi
  gi|242398964|ref|YP_002994388.1| 245 NGNLSILDDEDLKKVEILIDHHQLLQNLEEMLPrdaFVDVRPDVNSTASIMAEYLQSLNMEVNGTLGTSLFYGI 318
                                       ****9999999*************996666544111456789**************988887777777776665 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 !   23.6   0.2   4.8e-08   4.8e-05       1      80 [.       6      77 ..       6      94 .. 0.87
   2 ?   -1.9   0.0       3.8   3.8e+03      37      69 ..     269     301 ..     249     312 .. 0.58

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 4.8e-08
                                      EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-SSG CS
                   Sacchrp_dh_NADP  1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnlspp 79
                                      vli+G+Gs+G++va+ l+ +f    e++++++++ +++ l    +++ f+ i+ d +  +++L+a +++ dlvv  + +
  gi|242398964|ref|YP_002994388.1|  6 VLILGGGSIGRSVAQALKGEF----EVIIIEQNEIRAKSL----SESGFHVIQGDFSYTASLLKAGIEKVDLVVITIMD 76
                                      89***************9988....56*********7777....56899************************977777 PP

                                      G CS
                   Sacchrp_dh_NADP 80 i 80
                                      +
  gi|242398964|ref|YP_002994388.1| 77 V 77
                                      6 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.8
                                       HHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTT CS
                   Sacchrp_dh_NADP  37 lealaakalgvrfeaialdaenyeavLaallke 69 
                                       l++l + + +  f  +  d++  ++++a++l++
  gi|242398964|ref|YP_002994388.1| 269 LQNLEEMLPRDAFVDVRPDVNSTASIMAEYLQS 301
                                       444444445556666666666666666666655 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.4   5.8e-07   0.00058       3      73 ..       8      75 ..       6      93 .. 0.77
   2 ?   -2.9   0.0         4     4e+03      76     108 ..     355     388 ..     330     394 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 5.8e-07
                                      ESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEEES-.TT-HHHHHHHHTT-SEEEE--- CS
                              NmrA  3 viGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelvkgd.lddkeslvealkgvdvvfsvtg 73
                                      ++G  G++G+sv++a lk +++v ++  ++++ +aksl+e+G  +++gd  +  ++l++ +++vd+v +++ 
  gi|242398964|ref|YP_002994388.1|  8 ILG-GGSIGRSVAQA-LKGEFEVIII--EQNEIRAKSLSESGFHVIQGDfSYTASLLKAGIEKVDLVVITIM 75
                                      454.59*****9987.5788998766..677899***************45566666777*******99886 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4
                                       S-HHHHHHHHHHHHHHHS.-SEEEEEE---GG.G CS
                              NmrA  76 skeiedgkklvdAakeaG.vkhfiySslgddndr 108
                                       +  +e    l++A+ + +  k++i S++g   dr
  gi|242398964|ref|YP_002994388.1| 355 DISVETAEVLARAIINRKtFKNVIISNVGFITDR 388
                                       5556666778888888877888888887766655 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   0.6   0.00018      0.18       2      85 ..       6      91 ..       5     100 .. 0.66
   2 ?    5.3   0.0     0.029        29      10      93 ..     180     264 ..     179     266 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00018
                                      EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC......-EEECECHHHHHHH-SEEEE-S.-HHH CS
                     F420_oxidored  2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg......vkvtavdneeaaeeadvvvlav.kped 73
                                      + i+G+G++g+++a+ l  +     e++++ ++n+ +a++l e+         + ta+  +  +e+ d vv+++   + 
  gi|242398964|ref|YP_002994388.1|  6 VLILGGGSIGRSVAQALKGE----FEVIII-EQNEIRAKSLSESGFhviqgdFSYTASLLKAGIEKVDLVVITImDVNG 79
                                      6799***********65444....899988.999999999987744455555444444455556677777666524556 PP

                                      HHHHHHHCGHHH CS
                     F420_oxidored 74 veevlselakda 85
                                      ++++++++++++
  gi|242398964|ref|YP_002994388.1| 80 IKKTIQAIRNNN 91
                                      666666665554 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.029
                                       HHHHHHHHHHHTTS.-GGCEEEEEESSCCCHHHHHHHHC...-EEECECHHHHHHH-SEEEE-S-HHHHHHHHHHCG CS
                     F420_oxidored  10 mgealasgllaaga.qpheivvansrnpekaeelaeelg...vkvtavdneeaaeeadvvvlavkpedveevlsela 82 
                                       m++a+a++++a+++  ++ iv +++ + ++ +++ + lg   +kv++    e+ +++++ ++ ++p+   ++l++  
  gi|242398964|ref|YP_002994388.1| 180 MASAVALQVIAQNTgLKSTIVYGGEITHHENRAFVNLLGldiRKVSP-GSYEVKRHSTIALVDCQPNGNLSILDDE- 254
                                       99*************99****9*****************66555555.57889999**********9999999999. PP

                                       HHHHTTSEEEE CS
                     F420_oxidored  83 kdalkgklvis 93 
                                        d++k +++i+
  gi|242398964|ref|YP_002994388.1| 255 -DLKKVEILID 264
                                       .8889999988 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.2   3.7e-06    0.0037       1      76 [.       6      74 ..       6      99 .. 0.85
   2 ?   -1.1   0.3       1.3   1.3e+03      61      84 ..     120     149 ..      55     161 .. 0.53

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.7e-06
                                      EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHCEEEEETTCEEEEEECEEECCHSCCCCS-ESEEEE-S CS
                              ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr.rlealkknGlrltseggeeilrppealsaeekselepidlvivtv 76
                                      ++ilG G+iG+ +a  L k   +v++i +++ r+++l++ G+++ + +    ++ +++l ++    +e++dlv++t+
  gi|242398964|ref|YP_002994388.1|  6 VLILGGGSIGRSVAQAL-KGEFEVIIIEQNEiRAKSLSESGFHVIQGD----FSYTASLLKA---GIEKVDLVVITI 74
                                      68***************.8899*********************99999....6666666666...889999999985 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.3
                                       H......SCCCCS-ESEEEE-SSGGGHHHH CS
                              ApbA  61 e......ekselepidlvivtvKayqteea 84 
                                       +       + +++ i +++ tvK++  +++
  gi|242398964|ref|YP_002994388.1| 120 DvkidyaVSPKAATIKVIVDTVKNLGKKKN 149
                                       122333233345566666666666665555 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   1.8e-05     0.018       7      86 ..       3      91 ..       1     115 [. 0.67
   2 ?   -0.8   0.0       2.1   2.1e+03      59      59 ..     180     180 ..     113     263 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.8e-05
                     NAD_binding_7  7 gkkvlvvGgGevAarkvrklleagakvtvvapev...keele...elvklaeeel.......ekdlegadlviaatddr 72
                                        +vl+ GgG+++ + ++ l  +  +v+++ ++    k   +   + +++++ ++       ++ +e++dlv++++ d 
  gi|242398964|ref|YP_002994388.1|  3 AMRVLILGGGSIGRSVAQALKGE-FEVIIIEQNEiraK---SlseSGFHVIQGDFsytasllKAGIEKVDLVVITIMDV 77
                                      679**********9877777766.99999999943332...133333334444442222222666*****999998887 PP

                     NAD_binding_7 73 elneriaeaakarr 86
                                      +  ++  +a+++++
  gi|242398964|ref|YP_002994388.1| 78 NGIKKTIQAIRNNN 91
                                      66666666665543 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.1
                     NAD_binding_7  59 l 59 
                                       +
  gi|242398964|ref|YP_002994388.1| 180 M 180
                                       1 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.4   7.2e-06    0.0072      28     100 ..       3      75 ..       1      84 [. 0.84
   2 ?   -0.0   0.6      0.44   4.4e+02      61     122 ..     104     164 ..      82     169 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 7.2e-06
                                       --EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEE.HCHHHHHHHHHHHH-SEEEE--- CS
                       AlaDh_PNT_C  28 pakvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvev.lksqeellaeavkeadvvigtvl 100
                                       + +vl++GgG  G + +a a + + +V +++ ++ r++ l++ g ++++   + +++ll+  ++++d+v+ t+ 
  gi|242398964|ref|YP_002994388.1|   3 AMRVLILGGGSIGRS-VAQALKGEFEVIIIEQNEIRAKSLSESGFHVIQGdFSYTASLLKAGIEKVDLVVITIM 75 
                                       569**********75.66677779******************99999988456678889999*****9988764 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.44
                                       HHHHHHHHHTTTCECEEHCHHHHHHHHHHHH-SEEEE---BTTSS---SC-HHHHHTS-TTE CS
                       AlaDh_PNT_C  61 parleqleslgakfvevlksqeellaeavkeadvvigtvlipGkkaPkLvteemvksMkpgs 122
                                       ++++e +++++++ +e+  +   +++ ++++  v++ tv+  Gkk    + ++ ++++k+ s
  gi|242398964|ref|YP_002994388.1| 104 TTVKEIISQIKKE-FETDVKIDYAVSPKAATIKVIVDTVKNLGKKKNATLLSKKLSEIKQKS 164
                                       4556666667777.8999999999999999**********9999988777777777777655 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2   3.8e-05     0.038       2      35 ..       6      40 ..       5      76 .. 0.75
   2 ?   -1.7   0.0       1.7   1.7e+03      79     126 ..     240     286 ..     181     299 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.8e-05
                                      EEEECTSHHHHHHHHHHHHTT...EEEEESSSSTTSS CS
                               DAO  2 vviiGGGiiGlstAyeLarrg...Vtllekgdiagsg 35
                                      v+i GGG iG s+A +L  +g   V+++e+++i ++ 
  gi|242398964|ref|YP_002994388.1|  6 VLILGGGSIGRSVAQAL--KGefeVIIIEQNEIRAKS 40
                                      99***************..46689*******665533 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.7
                                       TSEEEEEEEEEESSHHHHHHHHHHHHHH..HHTTTTEEEEEHHHHHHHST CS
                               DAO  79 idyrrtGllslaadeeelealdkllall..leagldaelldaeevrelep 126
                                       +d +++G ls+ +de +l ++++l++    l ++l +e+l ++   ++ p
  gi|242398964|ref|YP_002994388.1| 240 VDCQPNGNLSILDDE-DLKKVEILIDHHqlL-QNL-EEMLPRDAFVDVRP 286
                                       455666666666433.466655555543212.222.24666665666665 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.4   4.1e-05     0.041      12      86 ..       3      77 ..       1     113 [. 0.78

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.1e-05
                                      T-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHH.T.ET-E.EEEGCGHHHHHHT-SEEEE-SSSS CS
                      Shikimate_DH 12 ekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeel.kgeeie.alkleelkellaeadvvisatase 86
                                        +vl++G G +++ va++L   g  +v+++  +  rak+l e+  +  +     + + lk+ ++++d+v++ ++  
  gi|242398964|ref|YP_002994388.1|  3 AMRVLILGGGSIGRSVAQALK--GEFEVIIIEQNEIRAKSLSESGfHVIQGDfSYTASLLKAGIEKVDLVVITIMDV 77
                                      679*****************7..6677**************997523222221345566788899999998877655 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00011      0.11      35      77 ..       2      43 ..       1      73 [. 0.76
   2 ?    1.2   0.1      0.21   2.1e+02      60     116 ..     134     188 ..     125     195 .. 0.73
   3 ?   -3.5   0.0       5.6   5.6e+03     131     153 ..     262     284 ..     262     288 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00011
                                      TTSEEEEES-SHHHHHHHHHHH.HTT-EEEEESSSHHHHHCHHH CS
                      2-Hacid_dh_C 35 sgktvGiiGlGrIGqavakrlk.afgmkviaydrskkkeeeeee 77
                                      s ++v i+G G+IG++va+ lk +f  +vi++++++ + ++ +e
  gi|242398964|ref|YP_002994388.1|  2 SAMRVLILGGGSIGRSVAQALKgEF--EVIIIEQNEIRAKSLSE 43
                                      56899****************9445..55555444443343444 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.21
                                       -EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-SEEEE-S--STTTTTSBSHHHHHC CS
                      2-Hacid_dh_C  60 mkviaydrskkkeeeeeelgvelvsleellaesDivslhlpltpetrhlinaeelak 116
                                       +kvi+  +++   + +++  +   +l e+ ++sD + +++  +p+   + +a +l+ 
  gi|242398964|ref|YP_002994388.1| 134 IKVIVDTVKNL-GK-KKNATLLSKKLSEIKQKSDSLLIVMHDNPDPDAMASAVALQV 188
                                       55655544444.33.4455556789*****************999999988888775 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 5.6
                                       GB-HHHHHHHHHTTSCCEEEES- CS
                      2-Hacid_dh_C 131 lvdeeaLleaLksgkiagaalDv 153
                                       l+d+  Ll+ L++   + a +Dv
  gi|242398964|ref|YP_002994388.1| 262 LIDHHQLLQNLEEMLPRDAFVDV 284
                                       68999999999999999999888 PP

>> Mannosyl_trans3  Mannosyltransferase putative
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.8   5.1e-05     0.051       4      52 ..      70     116 ..      70     167 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.1e-05
                   Mannosyl_trans3   4 IVisgggkesllalrlIkvLralgnkLPIeivikkeelekefcekilpa 52 
                                       +Vi++ +++ +   + I+++r+++++ PI ++i+++   ke +++i++ 
  gi|242398964|ref|YP_002994388.1|  70 VVITIMDVNGIK--KTIQAIRNNNSEVPILVLIPDDTTVKEIISQIKKE 116
                                       589999999999..********************888899999999983 PP

>> CbiJ  Precorrin-6x reductase CbiJ/CobK
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00013      0.13       1      56 [.       5      60 ..       5      72 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00013
                                      -EEEE-SSHHHHHHHHHHHHTT--EEEEE---SSS----S..S-EEES--S.HHHHH CS
                              CbiJ  1 rililgGTsearelaeaLaeagievvvsvateygaellpekklevrvgrlg.eegla 56
                                      r+lilgG s +r +a+aL+ + +ev++    e +a+ l+e++ +v++g ++ ++ l 
  gi|242398964|ref|YP_002994388.1|  5 RVLILGGGSIGRSVAQALKGE-FEVIIIEQNEIRAKSLSESGFHVIQGDFSyTASLL 60
                                      69****************996.****************************9754443 PP

>> Elong_Iki1  Elongator subunit Iki1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.4   0.00018      0.18      71     140 ..     106     181 ..      42     210 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00018
                        Elong_Iki1  71 lkelakeiksalspkssekk.......kkalviiDslnplaslikeeslaaflssllsspsvslvavYHtdv.eyap 139
                                       +ke++++ik++ +++ +  +           vi+D+++ l + ++++ l++ ls++ + +s sl+ v H +  + a 
  gi|242398964|ref|YP_002994388.1| 106 VKEIISQIKKEFETDVKI-DyavspkaATIKVIVDTVKNLGKKKNATLLSKKLSEIKQ-KSDSLLIVMHDNPdPDAM 180
                                       444444444444333322.1235555567789********99999************6.999999999988764444 PP

                        Elong_Iki1 140 s 140
                                       +
  gi|242398964|ref|YP_002994388.1| 181 A 181
                                       4 PP

>> DUF421  Protein of unknown function (DUF421)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   1.8    0.0092       9.2       7      92 ..      27     116 ..      21     163 .. 0.86
   2 ?    6.7   0.1    0.0059       5.8      40      88 ..     231     274 ..     193     307 .. 0.82
   3 ?   -2.7   0.0       4.8   4.8e+03      50      60 ..     303     313 ..     293     352 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0092
                            DUF421   7 pvvlienGkldeknlkklrltvdd....LleqLRqqgifslsdVkyailEtnGqlsvllkeekkpvtklplplivdG 79 
                                       +v++ie++++  k+l + ++ v +     + +L ++gi++++ V + i++ nG    ++   +++ +   l+li d 
  gi|242398964|ref|YP_002994388.1|  27 EVIIIEQNEIRAKSLSESGFHVIQgdfsYTASLLKAGIEKVDLVVITIMDVNGIKKTIQAIRNNNSEVPILVLIPDD 103
                                       57899999999999999999997533335678999******************888888777777775567899999 PP

                            DUF421  80 kiqkenLkkigkd 92 
                                       +  ke +++i+k+
  gi|242398964|ref|YP_002994388.1| 104 TTVKEIISQIKKE 116
                                       9999999999886 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0059
                            DUF421  40 ifslsdVkyailEtnGqlsvllkeekkpvtklplplivdGkiqkenLkk 88 
                                       +++ s +  +   +nG+ls+l +e+ k+v+     + +d +   +nL++
  gi|242398964|ref|YP_002994388.1| 231 VKRHSTIALVDCQPNGNLSILDDEDLKKVE-----ILIDHHQLLQNLEE 274
                                       5566677777789************99988.....77777777777776 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 4.8
                            DUF421  50 ilEtnGqlsvl 60 
                                        +E nG+l+  
  gi|242398964|ref|YP_002994388.1| 303 NMEVNGTLGTS 313
                                       57888887754 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 ?   10.6   1.7   0.00045      0.44      24     137 ..       4     115 ..       1     143 [. 0.86

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00045
                                       SEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHHHHHCTT-EE--HHHCTTT-SEEEE-SSSSSSB-HHHHCCS CS
                     AdoHcyase_NAD  24 kvavvaGyGdvGkGcaaslkglGarvivtevdPicalqaameGfevvtleevvkkadivvtttGnkdiitlehlkkm 100
                                         +++ G G +G+  a++lkg    vi+ e + i a   +  Gf+v +  +   +a+++ +     d++    ++  
  gi|242398964|ref|YP_002994388.1|   4 MRVLILGGGSIGRSVAQALKGE-FEVIIIEQNEIRAKSLSESGFHVIQ-GDFSYTASLLKAGIEKVDLVVITIMDVN 78 
                                       568999**************97.579999*****************97.5788889999999999998888888887 PP

                                       -TTEEEEE-SSTTTTBTHHHHHTTT-EEEEEETTEEE CS
                     AdoHcyase_NAD 101 kddaivcniGhfdseidvaaleanalkkeevkpqvdr 137
                                         +  +  i   +se+ +  l   +++++e+ +q+++
  gi|242398964|ref|YP_002994388.1|  79 GIKKTIQAIRNNNSEVPILVLIPDDTTVKEIISQIKK 115
                                       7777888999999999999999999999999888865 PP

>> DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.7    0.0011       1.1      46     115 ..      24      91 ..       6      96 .. 0.61
   2 ?   -0.9   0.1       2.5   2.5e+03      66      66 ..     141     141 ..      92     201 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0011
                                       HT-SEEEESSHHH.HHHHHHHHHHTTSSSEEEESHHHHHHHHCH...TT-SEEEE--SSGGGHHHHHHHHHTTS CS
                   DXP_reductoisom  46 fkpklvavadeea.aeelkealkekelktevlvGeealkelaee...eeadvvvaaivGaaGLkptlaaikagk 115
                                        + ++++++++e  a++l+e      +  +v+ G+ ++++ + +   e++d+vv  i+ + G+k t++ai++++
  gi|242398964|ref|YP_002994388.1|  24 GEFEVIIIEQNEIrAKSLSE------SGFHVIQGDFSYTASLLKagiEKVDLVVITIMDVNGIKKTIQAIRNNN 91 
                                       55555555444331222322......33455555544433322223379*********************9875 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.5
                                       H CS
                   DXP_reductoisom  66 l 66 
                                       +
  gi|242398964|ref|YP_002994388.1| 141 V 141
                                       2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (490 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       953  (0.0531541); expected 358.6 (0.02)
Passed bias filter:                      585  (0.0326287); 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: 0.75u 0.36s 00:00:01.10 Elapsed: 00:00:00.55
# Mc/sec: 2692.89
//
Query:       gi|242398965|ref|YP_002994389.1|  [L=558]
Description: hypothetical protein TSIB_0982 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
       0.27   11.9   1.3       0.95   10.1   1.3    1.9  1  DNA_ligase_A_C  ATP dependent DNA ligase C terminal region
       0.56   10.5  11.9       0.18   12.1   2.4    2.6  2  zf-C4H2         Zinc finger-containing protein
       0.68   10.4   4.2       0.76   10.2   0.7    2.9  2  YtzH            YtzH-like protein
        8.8    6.1   9.9       0.45   10.3   1.5    2.8  2  RNase_HII       Ribonuclease HII


Domain annotation for each model (and alignments):
>> 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 ?   10.1   1.3   0.00021      0.95      30      77 ..     152     197 ..     146     201 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00021
                                       HHHHHHHHHHHGGGEECTTCESS---HHHHTTEEE-TT-EEEEEESEE CS
                    DNA_ligase_A_C  30 daeleelrkklkelerkkppfaekvpeeekrdvWvePelvveVkfaei 77 
                                       +a++ee ++k k+ ++++ p ++k+ e+ek  + ++Pe++veV++ ei
  gi|242398965|ref|YP_002994389.1| 152 EAKVEETHEKPKPQKKERAPPEKKEVEKEK--KHFKPEIIVEVTGGEI 197
                                       678889999999777776666333333333..469********99887 PP

>> zf-C4H2  Zinc finger-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   2.2     0.023     1e+02      93     159 ..     120     184 ..     100     225 .. 0.66
   2 ?   12.1   2.4   3.9e-05      0.18      73     129 ..     410     466 ..     389     550 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.023
                           zf-C4H2  93 keevnelrselglekledleeeeeellkeeifekqklkaaavel.kkesstapappapptsllskssq 159
                                       k e+ne+ +e+++e   + e  e+e + e+i+++++ k +++++  k+++++ app+ ++  ++k + 
  gi|242398965|ref|YP_002994389.1| 120 KVEINEIFEENIVE---HEEIIEKERILEKILKTEEAKVEETHEkPKPQKKERAPPEKKEVEKEKKHF 184
                                       66888888888887...233445555667787877777555444044555555565544444444444 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 3.9e-05
                           zf-C4H2  73 eekekslekakklyeeykklkeevnelrselglekledleeeeeellkeeifekqkl 129
                                       ee e+  e++k+++++ ++l +e+++l++e+g++ l+ l+ee++  ++e++++++ +
  gi|242398965|ref|YP_002994389.1| 410 EEAEEVSENVKQILSKKEELEKEIEKLLQEMGVDDLSALTEEKRREVEESLLKSKVE 466
                                       56677789999*********************************9999999887654 PP

>> YtzH  YtzH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.7   0.00017      0.76       8      54 ..     379     425 ..     373     444 .. 0.92
   2 ?   -1.4   0.2      0.73   3.3e+03      32      61 ..     514     543 ..     508     556 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00017
                              YtzH   8 tlLkDiLkeqqadccgtvseceQierlvksllaneevdedvkqvLee 54 
                                       +l++ iL+ +  +    ++++  i+r+  +l + eev+e+vkq+L++
  gi|242398965|ref|YP_002994389.1| 379 ALVEGILRTHTREISKALNKYITIHRVEINLEEAEEVSENVKQILSK 425
                                       47889***************************************975 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.73
                              YtzH  32 erlvksllaneevdedvkqvLeeiYaysqe 61 
                                       e l+k++ ++  +++ ++ + ++i + s+e
  gi|242398965|ref|YP_002994389.1| 514 ESLIKAVSDDRIIEDALQMLNMSIQEISKE 543
                                       568888888887777777776777554444 PP

>> RNase_HII  Ribonuclease HII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.9      0.15   6.6e+02      70     113 ..     116     164 ..      57     201 .. 0.54
   2 ?   10.3   1.5    0.0001      0.45      23      65 ..     430     470 ..     425     552 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.15
                                       HHTTTS-HHHHHHHHHHHHHHHHHHT.....CEECCECCCE--SSHHHH CS
                         RNase_HII  70 aseneinlneikaaltlavikllekl.....gvkvdeilvdgvttpesl 113
                                       + + ++++nei ++++ + ++ +ek+       k +e +v+  ++  + 
  gi|242398965|ref|YP_002994389.1| 116 NTTPKVEINEIFEENIVEHEEIIEKErilekILKTEEAKVEETHEKPKP 164
                                       4444444454444444333333333300000334444444444442222 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0001
                                       CGHHHHHHHCTTGTTGTTS-HHHHHHHHHHHH.SEEEEEEE-HH CS
                         RNase_HII  23 ekereeelkklgvkDSKkLskqkreeLaklik.kkiekrklvae 65 
                                       eke e+ l+++gv+D   L+++kr+e+++ +      k +l+ e
  gi|242398965|ref|YP_002994389.1| 430 EKEIEKLLQEMGVDDLSALTEEKRREVEESLLkS---KVELAVE 470
                                       6777889********************9988731...2222223 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (558 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2092  (0.116682); expected 358.6 (0.02)
Passed bias filter:                      573  (0.0319594); 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):               4  [number of targets reported over threshold]
# CPU time: 0.80u 0.38s 00:00:01.18 Elapsed: 00:00:00.56
# Mc/sec: 2982.00
//
Query:       gi|242398966|ref|YP_002994390.1|  [L=289]
Description: Permease, drug/metabolite transporter (DMT) superfamily [Thermococcus sibiricus MM 739]
Scores for complete 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-45  154.3  42.0    9.2e-23   80.9  11.9    2.0  2  EamA            EamA-like transporter family
     0.0013   18.2  19.7        0.1   12.0   6.6    2.1  2  TPT             Triose-phosphate Transporter family
     0.0094   16.0  11.5        0.4   10.7   5.2    3.0  2  TMEM234         Putative transmembrane family 234
  ------ inclusion threshold ------
        4.4    5.6   6.4        6.3    5.1   6.4    1.2  1  SID-1_RNA_chan  dsRNA-gated channel SID-1


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 !   79.8  22.1   4.7e-26   2.1e-22       2     135 ..       5     140 ..       4     142 .. 0.91
   2 !   80.9  11.9   2.1e-26   9.2e-23       2     137 .]     152     287 ..     151     287 .. 0.98

  Alignments for each domain:
  == domain 1  score: 79.8 bits;  conditional E-value: 4.7e-26
                              EamA   2 lgillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegkl..aklslkdwllllllgllgtv 76 
                                       +g+llal+aa+ w+++ vl+k ++r+   +t++ +r+ i + + l i l+ ++ +   +ls++ +l  ++ gl+g+v
  gi|242398966|ref|YP_002994390.1|   5 IGALLALIAAFGWGTASVLIKLGMRNKGAITVNIIRLYITTSVYLSIFLIAGKYKgiLSLSPEIILVTFISGLFGFV 81 
                                       89**********************************99887776666666665554677777778888********* PP

                              EamA  77 lafllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvlli 135
                                       ++ +++f alk +++s+ ++its  P++t+++++ ++g+k+t  +llg+++i+l+++++
  gi|242398966|ref|YP_002994390.1|  82 IGDYFYFNALKLMGVSKTVPITSSYPLWTMLWAWMFFGKKITTQTLLGALFIFLAIVIV 140
                                       ********************************************************997 PP

  == domain 2  score: 80.9 bits;  conditional E-value: 2.1e-26
                              EamA   2 lgillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvla 78 
                                       +g ++a+la ++w+i++vl + l+ +++p++l+++r++ a+i  +++++ + + l++ +++++  l   +l+g +++
  gi|242398966|ref|YP_002994390.1| 152 KGFVYAILAPISWSIAIVLLDFLSLYIDPFSLAGLRMISAAIGISVFLPKHSKELKVVTKNEIGVLSGAALVGLIIG 228
                                       68899************************************************************************ PP

                              EamA  79 fllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllill 137
                                       +++f+++++ +++ + ++i+++ P+++ +l+v ll+e++++k ++g++l+++Gv+li++
  gi|242398966|ref|YP_002994390.1| 229 QYAFVKSVSFVGSHISTPISAINPIISSLLAVTLLKEPPNSKIFVGLILAVVGVVLIST 287
                                       ********************************************************986 PP

>> TPT  Triose-phosphate Transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   6.0   2.6e-05      0.12      32     134 ..      34     139 ..      21     170 .. 0.80
   2 !   12.0   6.6   2.2e-05       0.1      25     136 ..     174     286 ..     161     289 .] 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.6e-05
                               TPT  32 ltvsavqllvg.svlilvlwal.glkkrpkisse.flkailplalvktlghvlavvslskvaVSfthtvKasePiFt 105
                                       +tv  ++l+++ sv++++++++ ++k +  +s e  l++ +   +  ++g  +   +l+   VS t  + +s P++t
  gi|242398966|ref|YP_002994390.1|  34 ITVNIIRLYITtSVYLSIFLIAgKYKGILSLSPEiILVTFISGLFGFVIGDYFYFNALKLMGVSKTVPITSSYPLWT 110
                                       6888899987626788888888677779999999444555555566889**************************** PP

                               TPT 106 vilsrlllgeklsllvylsLlpivgGval 134
                                        + + +++g+k++++ +l  l i   +++
  gi|242398966|ref|YP_002994390.1| 111 MLWAWMFFGKKITTQTLLGALFIFLAIVI 139
                                       **************999987777766655 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 2.2e-05
                               TPT  25 lnvfpyPltvsavqllvgsvlilvlwalglkkrpkisseflkailplalvkt.lghvlavvslskvaVSfthtvKas 100
                                       l+++  P+ ++ +++++  + i+v++  + k+ + ++++ + ++   alv + +g+ + v s+s v    +  + a+
  gi|242398966|ref|YP_002994390.1| 174 LSLYIDPFSLAGLRMISAAIGISVFLPKHSKELKVVTKNEIGVLSGAALVGLiIGQYAFVKSVSFVGSHISTPISAI 250
                                       6667779999999999999999999988888888888889999999998765145555555666666666677**** PP

                               TPT 101 ePiFtvilsrlllgeklsllvylsLlpivgGvalas 136
                                       +Pi + +l+  ll+e ++ ++++ L+  v+Gv+l s
  gi|242398966|ref|YP_002994390.1| 251 NPIISSLLAVTLLKEPPNSKIFVGLILAVVGVVLIS 286
                                       ********************************9977 PP

>> TMEM234  Putative transmembrane family 234
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   5.2   8.9e-05       0.4       4     115 ..      13     140 ..      10     141 .. 0.65
   2 !    7.7   0.4    0.0008       3.6      64     115 ..     241     285 ..     199     286 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 8.9e-05
                           TMEM234   4 vgilWGitnPllkrgskgleevkeksklsqlllelkf...................lllrlkyliplllNqsgSvlf 61 
                                       +++ WG +  l+k g ++   ++ +  + +l + + +                    +  + ++  l   + g  ++
  gi|242398966|ref|YP_002994390.1|  13 AAFGWGTASVLIKLGMRNKGAITVN--IIRLYITTSVylsifliagkykgilslspEIILVTFISGLFGFVIGDYFY 87 
                                       5566666666666666655555433..2332222222234455555556654333322233344444444567789* PP

                           TMEM234  62 flllgkadlslavpiaNslafvfTvltelllgekvlkkktvlgmllvvvgialc 115
                                       f +l+ + +s +vpi+ s   + T+l +++   k ++++t+lg l+++++i+++
  gi|242398966|ref|YP_002994390.1|  88 FNALKLMGVSKTVPITSSYP-LWTMLWAWMFFGKKITTQTLLGALFIFLAIVIV 140
                                       ****************9975.789****999999999*************9986 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0008
                           TMEM234  64 llgkadlslavpiaNslafvfTvltelllgekvlkkktvlgmllvvvgialc 115
                                       +  ++++s        ++ ++  l + +l ++  ++k ++g++l vvg++l+
  gi|242398966|ref|YP_002994390.1| 241 SHISTPISA-------INPIISSLLAVTLLKEPPNSKIFVGLILAVVGVVLI 285
                                       444444444.......44455555666677889999*************997 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 ?    5.1   6.4    0.0014       6.3     401     538 ..      30     170 ..       6     175 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0014
                    SID-1_RNA_chan 401 egknkfwilfsiihllatlllslqiy...ymgrwkldvgi.lrrile.....vlkkeviqqcsrplyksrmvllvlg 468
                                       + k ++ + +  ++++++++ls+ +    y+g+++l+ +i l  +++     v+   ++ +  + +  s++v +  +
  gi|242398966|ref|YP_002994390.1|  30 N-KGAITVNIIRLYITTSVYLSIFLIagkYKGILSLSPEIiLVTFISglfgfVIGDYFYFNALKLMGVSKTVPITSS 105
                                       2.335555555556666666666543222666666643330333333566655556666667777778899998888 PP

                    SID-1_RNA_chan 469 nlvnvslavlglvlkpkdfasylLaifivnlllYlvfYiimKlrsserilllalllivltlvvwavalyf 538
                                         + ++l +++++ k+ +  + l     + l+++l+  i+ K   +er++++ +++ +l+ + w +a+++
  gi|242398966|ref|YP_002994390.1| 106 YPLWTMLWAWMFFGKKITTQTLL-----GALFIFLAIVIVRKGGLEERLSPKGFVYAILAPISWSIAIVL 170
                                       88888888888887777777666.....8999999*******************************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       743  (0.0414412); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1747.17
//
Query:       gi|242398967|ref|YP_002994391.1|  [L=159]
Description: Transcription regulator, Lrp/AsnC family [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-16   60.3   0.1    2.7e-16   59.3   0.1    1.5  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
    2.4e-13   49.4   2.5    4.6e-13   48.5   2.5    1.5  1  HTH_24          Winged helix-turn-helix DNA-binding
      4e-12   45.7   0.4    5.6e-12   45.3   0.4    1.2  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    0.00045   20.2   0.0     0.0008   19.4   0.0    1.4  1  HTH_20          Helix-turn-helix domain
    0.00047   20.0   0.3     0.0011   18.8   0.3    1.6  1  MarR            MarR family
     0.0008   19.5   0.5     0.0018   18.4   0.5    1.8  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
     0.0012   18.7   0.1     0.0023   17.8   0.1    1.5  1  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0018   18.2   0.6     0.0045   16.9   0.6    1.8  1  HTH_11          HTH domain
     0.0034   16.8   0.4     0.0047   16.4   0.4    1.2  1  RNA_pol_Rpc34   RNA polymerase Rpc34 subunit
     0.0041   17.6   0.4      0.052   14.0   0.1    2.2  2  HTH_27          Winged helix DNA-binding domain
     0.0041   17.4   0.2      0.075   13.4   0.2    2.3  2  Rrf2            Transcriptional regulator
     0.0041   17.3   0.1     0.0076   16.4   0.1    1.4  1  HTH_34          Winged helix DNA-binding domain
  ------ inclusion threshold ------
      0.018   14.8   0.1      0.062   13.1   0.1    1.8  2  LexA_DNA_bind   LexA DNA binding domain
      0.024   14.5   0.3      0.046   13.6   0.1    1.6  2  HxlR            HxlR-like helix-turn-helix
      0.037   13.6   1.4      0.059   12.9   1.4    1.3  1  DDRGK           DDRGK domain
      0.038   14.2   0.6        0.3   11.3   0.1    2.3  2  Rio2_N          Rio2, N-terminal
      0.044   14.1   4.9       0.62   10.4   0.8    2.6  3  mCpol           minimal CRISPR polymerase domain
      0.068   13.1   1.3      0.088   12.7   0.4    1.7  2  RuvB_C          RuvB C-terminal winged helix domain
        0.1   11.8   0.1       0.18   11.1   0.1    1.3  1  LYTB            LytB protein
       0.12   12.3   4.4       0.36   10.7   1.2    2.4  2  TFIIE_alpha     TFIIE alpha subunit


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 !   59.3   0.1     3e-19   2.7e-16      15      74 ..      84     142 ..      74     143 .. 0.92

  Alignments for each domain:
  == domain 1  score: 59.3 bits;  conditional E-value: 3e-19
                                       HHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEE CS
                    AsnC_trans_reg  15 efeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivle 74 
                                        ++ +l + p V+e+y+vtGdyd+llkv++++++++++fl++ +a+++++ ++++++vl+
  gi|242398967|ref|YP_002994391.1|  84 YVINKLIKNPHVLEVYKVTGDYDMLLKVKFKSINEFHEFLDT-IAKIEEIVDSTSMVVLK 142
                                       57889999**********************************.****************8 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.5   2.5   5.1e-16   4.6e-13       1      48 []       7      54 ..       7      54 .. 0.99

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 5.1e-16
                            HTH_24  1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      ld++d+k+L+ Lq++++is+reL++ ++l  s +++r+krLee+G+Ik
  gi|242398967|ref|YP_002994391.1|  7 LDKIDIKLLSMLQEDSNISIRELSKTVNLKMSELHKRIKRLEENGVIK 54
                                      79*********************************************8 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   0.4   6.2e-15   5.6e-12       1      42 []       7      48 ..       7      48 .. 0.99

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 6.2e-15
                     HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrLe 42
                                      LD+iD+k+L+ Lqed+ is +eL++ v+l  s+ ++R++rLe
  gi|242398967|ref|YP_002994391.1|  7 LDKIDIKLLSMLQEDSNISIRELSKTVNLKMSELHKRIKRLE 48
                                      8****************************************8 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   8.9e-07    0.0008      14      55 ..      13      54 ..       7      57 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 8.9e-07
                                      HHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                            HTH_20 14 rilraLaraegltaselaerldlskntlsyHLrvLeeagLve 55
                                      ++l++L ++   +  el +++ l++++l+++++ Lee g ++
  gi|242398967|ref|YP_002994391.1| 13 KLLSMLQEDSNISIRELSKTVNLKMSELHKRIKRLEENGVIK 54
                                      789************************************986 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.3   1.3e-06    0.0011       6      49 ..      12      55 ..      11      57 .. 0.95

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.3e-06
                                      HHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              MarR  6 fviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieR 49
                                      +++L +l e  ++s+ eL k ++++ s + + ++rLe++G i++
  gi|242398967|ref|YP_002994391.1| 12 IKLLSMLQEDSNISIRELSKTVNLKMSELHKRIKRLEENGVIKK 55
                                      579*************************************9986 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.5     2e-06    0.0018      22      55 ..      27      66 ..      24     144 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2e-06
                    B-block_TFIIIC 22 sdLakeskqdprslfyrlksLekkgLIvkqsii......d 55
                                      ++L+k+++ + + l++r+k Le++g I+k ++        
  gi|242398967|ref|YP_002994391.1| 27 RELSKTVNLKMSELHKRIKRLEENGVIKKFTVLlnpeklG 66
                                      789***************************9965555550 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   2.6e-06    0.0023       2      54 ..       2      55 ..       1      62 [. 0.95

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.6e-06
                                      H.HCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEE CS
                              TrmB  2 q.klGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVer 54
                                      + k++L + ++k    L +  + +++e+++ +++  s   + +++Le+ G++++
  gi|242398967|ref|YP_002994391.1|  2 KtKIDLDKIDIKLLSMLQEDSNISIRELSKTVNLKMSELHKRIKRLEENGVIKK 55
                                      6699***********************************************987 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.6     5e-06    0.0045       4      44 ..      13      56 ..      11      85 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 5e-06
                            HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg....v 44
                                      ++l +L +++++is+ eL++  n+  +  +++Ik+Lee g    +
  gi|242398967|ref|YP_002994391.1| 13 KLLSML-QEDSNISIRELSKTVNLKMSELHKRIKRLEENGvikkF 56
                                      78999*.9999*****************************55444 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 !   16.4   0.4   5.2e-06    0.0047     103     143 ..      24      64 ..      12      78 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 5.2e-06
                                       EEHHHHHHTTGXXHHHHHHHHHHHHHTTXXEEEEXSSSSSX CS
                     RNA_pol_Rpc34 103 IwsrtiksklnLhksvvkkcLksLeskkyiksvksvkaptk 143
                                       I  r++ +++nL++s+++k +k Le  + ik++  + +p+k
  gi|242398967|ref|YP_002994391.1|  24 ISIRELSKTVNLKMSELHKRIKRLEENGVIKKFTVLLNPEK 64 
                                       8899****************************999988887 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.1   5.8e-05     0.052      19      50 ..      24      55 ..      10      58 .. 0.83
   2 ?    1.4   0.0      0.53   4.7e+02      30      45 ..      77      92 ..      74     100 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.8e-05
                            HTH_27 19 kkladlcgrlnvedshisyslkkLtekGLver 50
                                       ++++l++++n+  s  ++ +k+L+e+G++++
  gi|242398967|ref|YP_002994391.1| 24 ISIRELSKTVNLKMSELHKRIKRLEENGVIKK 55
                                      456**************************976 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.53
                            HTH_27 30 vedshisyslkkLtek 45
                                      +e  + sy+++kL+++
  gi|242398967|ref|YP_002994391.1| 77 IEGKNSSYVINKLIKN 92
                                      5566667******986 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.2   8.4e-05     0.075      17      56 ..      15      54 ..       9      57 .. 0.89
   2 ?    1.6   0.0      0.39   3.5e+02      56      82 ..      75     101 ..      70     102 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.4e-05
                                      HHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2 17 LakeeeeepvsseeiaerqnispsylekilakLrkaglvk 56
                                      L++ +e++ +s++e+++ +n++ s l k +++L+++g++k
  gi|242398967|ref|YP_002994391.1| 15 LSMLQEDSNISIRELSKTVNLKMSELHKRIKRLEENGVIK 54
                                      566677778*****************************98 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.39
                                       EEETTT-TCEEESSHCCCSBHHHHHHH CS
                              Rrf2  56 ksvrGkgGGyrLakppeeItlldvvra 82 
                                         ++Gk+  y+++k  ++ ++l+v+++
  gi|242398967|ref|YP_002994391.1|  75 AKIEGKNSSYVINKLIKNPHVLEVYKV 101
                                       5679******************99975 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   8.4e-06    0.0076       3      45 ..      12      54 ..      10      64 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 8.4e-06
                            HTH_34  3 lavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYie 45
                                      +++ls+L ++++++ +el++++++  ++L + +k Le++g i+
  gi|242398967|ref|YP_002994391.1| 12 IKLLSMLQEDSNISIRELSKTVNLKMSELHKRIKRLEENGVIK 54
                                      689*************************************886 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 ?   13.1   0.1     7e-05     0.062      27      57 ..      25      54 ..      16      57 .. 0.94
   2 ?   -1.5   0.0       2.5   2.3e+03      34      51 ..     110     127 ..     106     134 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7e-05
                                      -HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE CS
                     LexA_DNA_bind 27 sireiaralglkSpsaveehLkaLerKGyie 57
                                      sire+++ ++lk  s  +++ k+Le  G+i+
  gi|242398967|ref|YP_002994391.1| 25 SIRELSKTVNLK-MSELHKRIKRLEENGVIK 54
                                      8***********.999*************97 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.5
                                       HHTS-.HHHHHHHHHHHH CS
                     LexA_DNA_bind  34 alglkSpsaveehLkaLe 51 
                                       ++++kS +  +e L + +
  gi|242398967|ref|YP_002994391.1| 110 KVKFKSINEFHEFLDTIA 127
                                       789999999988887765 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   5.1e-05     0.046      22      67 ..      27      71 ..       9      91 .. 0.85
   2 ?   -2.4   0.0         5   4.4e+03      20      33 ..     118     131 ..     107     149 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.1e-05
                                      HHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-T CS
                              HxlR 22 selkralpkisqkmLaqrLreLeqdglierevypevPpkveYslte 67
                                       el++++ ++  + L +r+++Le++g+i++ ++   P+k  ++lt+
  gi|242398967|ref|YP_002994391.1| 27 RELSKTV-NLKMSELHKRIKRLEENGVIKKFTVLLNPEKLGFNLTA 71
                                      5666666.777788******************************97 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5
                                       EHHHHHHHSTTS-H CS
                              HxlR  20 Rfselkralpkisq 33 
                                        f+e+ +++ ki +
  gi|242398967|ref|YP_002994391.1| 118 EFHEFLDTIAKIEE 131
                                       45566666665554 PP

>> DDRGK  DDRGK domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   1.4   6.6e-05     0.059     103     143 ..      13      53 ..       2      56 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.6e-05
                                       HHHHHHHH-SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS CS
                             DDRGK 103 efinyikekKvvlleelavkfklktqevierikeLeeqgsl 143
                                       +++  ++e   + + el+   +lk +e  +rik Lee+g +
  gi|242398967|ref|YP_002994391.1|  13 KLLSMLQEDSNISIRELSKTVNLKMSELHKRIKRLEENGVI 53 
                                       5677788888999*************************988 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00034       0.3      25      58 ..      24      57 ..       7      74 .. 0.81
   2 ?    1.0   0.0      0.54   4.9e+02      19      52 ..      79     112 ..      69     121 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00034
                            Rio2_N 25 Vptelieeisrlkeeevkkrlsrllkaklisrkt 58
                                      ++ ++++++ +lk++e++kr++rl +++ i++ t
  gi|242398967|ref|YP_002994391.1| 24 ISIRELSKTVNLKMSELHKRIKRLEENGVIKKFT 57
                                      7788999***********************9944 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.54
                            Rio2_N  19 mrnhevVptelieeisrlkeeevkkrlsrllkak 52 
                                        +n+++V  +li++   l+  +v+   + llk k
  gi|242398967|ref|YP_002994391.1|  79 GKNSSYVINKLIKNPHVLEVYKVTGDYDMLLKVK 112
                                       4666666667776666666666666666666655 PP

>> mCpol  minimal CRISPR polymerase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.8   0.00069      0.62       3      51 ..       4      52 ..       3      56 .. 0.90
   2 ?    0.1   0.0       1.1     1e+03      97     111 ..      69      83 ..      64      86 .. 0.84
   3 ?    4.4   0.1     0.052        47      36      84 ..      83     133 ..      78     140 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00069
                             mCpol  3 aiDGDdiGkklealllsndeeeleklskevkeaikklkkllkdelgasv 51
                                      +iD D+i  kl ++l +++  ++++lsk+v+ ++++l k +k   ++ v
  gi|242398967|ref|YP_002994391.1|  4 KIDLDKIDIKLLSMLQEDSNISIRELSKTVNLKMSELHKRIKRLEENGV 52
                                      5899***********999999********************99876665 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.1
                             mCpol  97 liaLkkAkskgknrv 111
                                       l+a+ +Ak +gkn+ 
  gi|242398967|ref|YP_002994391.1|  69 LTAFMLAKIEGKNSS 83 
                                       68999*******985 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.052
                             mCpol  36 ikklkkllkdelgasvifaaGD.silaksslee.dllvelsrvyqkitglt 84 
                                       +  ++kl+k+    +v  + GD ++l+k+++++ +++ e+  +  ki+++ 
  gi|242398967|ref|YP_002994391.1|  83 SYVINKLIKNPHVLEVYKVTGDyDMLLKVKFKSiNEFHEFLDTIAKIEEIV 133
                                       55678888888889999999*988******988888888888888887654 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 ?   12.7   0.4   9.8e-05     0.088       4      44 ..       7      44 ..       4      55 .. 0.90
   2 ?   -2.5   0.0       5.4   4.8e+03      21      29 ..     124     132 ..     114     147 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.8e-05
                                      --HHHHHHHHHHHHT.TT--B-HHHHHHHTT--HHHHHHTT CS
                            RuvB_C  4 LdeldikyLkllkekfkggpvglktlaailgeeketiedvi 44
                                      Ld++dik+L++l+   +++ ++++ l+++++++ +++ + i
  gi|242398967|ref|YP_002994391.1|  7 LDKIDIKLLSMLQ---EDSNISIRELSKTVNLKMSELHKRI 44
                                      9***********9...79**************999998776 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 5.4
                                       T--B-HHHH CS
                            RuvB_C  21 ggpvglktl 29 
                                       ++ + ++ +
  gi|242398967|ref|YP_002994391.1| 124 DTIAKIEEI 132
                                       333333333 PP

>> LYTB  LytB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1    0.0002      0.18      25     100 ..      78     149 ..      69     157 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0002
                                       CCC-SEEECS-SSS-HHHHHHHHHCTEEEESSSSTEEEE-TT---HHHHHHHHHTTEEEEE---HHHHHHHHHHHH CS
                              LYTB  25 eekkevyvlgeivHNeqvverLeekgvkfieeleevviirAhGvskeveeelkekglevvDatCplVkkvqkevkk 100
                                       e k++ yv+++++ N++v+e  +  g   +      v +++  + +e  +++++ + e+vD t ++V k++kev +
  gi|242398967|ref|YP_002994391.1|  78 EGKNSSYVINKLIKNPHVLEVYKVTGDYDMLL---KVKFKSINEFHEFLDTIAKIE-EIVDSTSMVVLKIHKEVVE 149
                                       444449**************999998665533...4889999999*********99.9***************976 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.2    0.0004      0.36      16      58 ..      12      54 ..       7      57 .. 0.94
   2 ?    2.1   0.0      0.19   1.7e+02       2      29 ..      69      96 ..      68     123 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0004
                                      HHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEE CS
                       TFIIE_alpha 16 vlvldvLlekgevteedlakelkidlnelrklLnrLyearlvk 58
                                      ++ l +L e+++++  +l+k ++++  el k + rL e +++k
  gi|242398967|ref|YP_002994391.1| 12 IKLLSMLQEDSNISIRELSKTVNLKMSELHKRIKRLEENGVIK 54
                                      678999***********************************97 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.19
                                      HHHHHHHHCS-HHHHHHHHHHHCTTSEB CS
                       TFIIE_alpha  2 llkevvrkfygeeavlvldvLlekgevt 29
                                      l ++++ k++g++   v++ L+++  v 
  gi|242398967|ref|YP_002994391.1| 69 LTAFMLAKIEGKNSSYVINKLIKNPHVL 96
                                      7789999999999999999999987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1241  (0.0692175); expected 358.6 (0.02)
Passed bias filter:                      627  (0.0349713); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); 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: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1175.21
//
Query:       gi|242398968|ref|YP_002994392.1|  [L=391]
Description: Aspartate aminotransferase [Thermococcus sibiricus MM 739]
Scores for complete 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-71  239.2   0.0    8.2e-71  239.1   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    1.5e-08   34.4   0.0    2.5e-08   33.6   0.0    1.3  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    2.2e-05   23.6   0.0       0.01   14.8   0.0    2.7  3  Aminotran_5      Aminotransferase class-V
    2.2e-05   23.1   0.0    4.4e-05   22.2   0.0    1.4  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
     0.0001   21.3   0.2     0.0055   15.6   0.2    2.2  1  Alliinase_C      Allinase
     0.0016   17.8   0.0      0.009   15.3   0.0    2.0  1  Beta_elim_lyase  Beta-eliminating lyase
  ------ inclusion threshold ------
      0.081   11.6   0.1        0.2   10.3   0.0    1.6  2  Aminotran_3      Aminotransferase class-III


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  239.1   0.0   3.2e-74   8.2e-71       2     363 .]      33     383 ..      32     383 .. 0.97

  Alignments for each domain:
  == domain 1  score: 239.1 bits;  conditional E-value: 3.2e-74
                                       EEEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHH CS
                     Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGag 78 
                                       dvi L ++e+++d    t++ +++a  +  +  ++++ y+++ gl el+ea+a+++++ +++++  e ++v ++G+g
  gi|242398968|ref|YP_002994392.1|  33 DVIHLEIGEPDFD----TPQYIKEAGCK--AILNKYTHYTHNAGLLELREAIADYYRSTQNVDISLENTLVSIGGTG 103
                                       89***********....*********99..9********************************************** PP

                                       HHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEE CS
                     Aminotran_1_2  79 aliealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilve 155
                                       al+  l ++ +   gde+l+p+p y++y+ ++++ g+   +y+l++ e+f  ++e++e+ +++       tkvi+++
  gi|242398968|ref|YP_002994392.1| 104 ALLLSLLAIVD--IGDEVLLPNPGYPPYTSMVKMIGAIPKYYSLKENESFLPNIEEIENIITN------NTKVIIIN 172
                                       *********98..**************************************************......99****** PP

                                       SS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEE CS
                     Aminotran_1_2 156 sphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGy 232
                                       +p+NPtG v++ + l+ + +la+ y l++++De+Y+ + f++l +++ +++++ee n+++ gs+sK+++++G+RvG+
  gi|242398968|ref|YP_002994392.1| 173 TPNNPTGIVYPSNILRRISELAEDYDLVVISDEVYERLIFDNLNHYS-ILKFSEEGNVIVIGSFSKSYAMTGWRVGF 248
                                       *******************************************9999.***************************** PP

                                       EEE.EHHHHHHHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS.TEEEECCSCS CS
                     Aminotran_1_2 233 ilg.naavvsqlrklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLael.glkvlasqsg 305
                                       +++ n ++++ ++ l+ ++ +  ++ +q+a+  als +++   e e+m+++++krr  +++ L+e  +++++++q++
  gi|242398968|ref|YP_002994392.1| 249 AVSnNVKIIKSMTELQEHVAIcaPAMAQKAAFVALSESQE---EAENMVKQYEKRRNLVVSLLNEFpNVSFVKPQGA 322
                                       ***666*************9999***************97...9*******************999*********** PP

                                       SEEEEEETHH..CHHHHHHHHHHTCTEEEEEGGGGTS..TTEEEEECTTS-HHHHHHHHHHH CS
                     Aminotran_1_2 306 mflltdlsae..takelskkLleevgvyvtpgtsftv..pgrlRitvAglteeeleelveal 363
                                       ++l+  +s++  +  +++++Ll +++v+v pg  f+   +g +Ri++ + +ee++ee v++l
  gi|242398968|ref|YP_002994392.1| 323 FYLFLNISHYskDSYKFAEELLLKKKVAVAPGATFGSlgEGYVRISF-ANSEENIEEGVKRL 383
                                       **********876778888888888**********************.99*******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 !   33.6   0.0   9.7e-12   2.5e-08      46     144 ..     100     204 ..      53     206 .. 0.81

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 9.7e-12
                                       SHHHHHHHHHHH.TTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-T.TTSSB-GGGCGGG--TTEEEEE...E CS
                   DegT_DnrJ_EryC1  46 sGtaAlhlaLra.lgvgpgdeVIvpsltFvatanavlelgakpvfvDvdp.dtynidpaaieaaitertkaIl...p 117
                                        Gt Al+l+L a +++g  deV+ p  ++    ++v  +ga p +   ++ +++ ++ ++ie+ it++tk I+   p
  gi|242398968|ref|YP_002994392.1| 100 GGTGALLLSLLAiVDIG--DEVLLPNPGYPPYTSMVKMIGAIPKYYSLKEnESFLPNIEEIENIITNNTKVIIintP 174
                                       59**********88888..****************************98626899*****************83443 PP

                                       B-GGGB--...-HHHHHHHHHHCT-EEEEE CS
                   DegT_DnrJ_EryC1 118 VhlyGqva...dmdalkaiaakhglkvieD 144
                                        +  G v     + ++ ++a++++l+vi+D
  gi|242398968|ref|YP_002994392.1| 175 NNPTGIVYpsnILRRISELAEDYDLVVISD 204
                                       455666542226899999**********99 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.17   4.3e+02     204     268 ..      17      82 ..       7      96 .. 0.78
   2 !   14.8   0.0   4.1e-06      0.01      69     176 ..     100     205 ..      55     208 .. 0.71
   3 !    5.7   0.0    0.0024       6.1     261     364 ..     276     374 ..     241     383 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.17
                                       SSTT-EEEEEEHHHHHTS..SS.STTSEEEEET.TEEEEHCTTGGGS.SS--HHHHHHHHHH.HHHH CS
                       Aminotran_5 204 gPtGiGvlyvrkellekleplllggemveevsl.eettfaeapskfeaGTpnvagiiglgaa.leyl 268
                                        P+Gi  ++ +   le + +l++g   ++++++ +e++++   +k+ + T n  g+  l++a ++y 
  gi|242398968|ref|YP_002994392.1|  17 PPSGIRKIFNKAMFLEDVIHLEIGEPDFDTPQYiKEAGCKAILNKYTHYTHNA-GLLELREAiADYY 82 
                                       5889999999999999999999999999**9999******9999999988775.4555554404565 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 4.1e-06
                                       SHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEE..EEBETTSCBEGGGHHHH--TTEEEE CS
                       Aminotran_5  69 Gtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkv..ipldeegeldldelekllnektklv 143
                                       G+t a+ l +l++   ++ gde+++ + ++   +   +++     a  k+  ++ +e  + +++e+e+ ++++tk++
  gi|242398968|ref|YP_002994392.1| 100 GGTGALLLSLLAI---VDIGDEVLLPNPGYPPYTSMVKMIG----AIPKYysLKENESFLPNIEEIENIITNNTKVI 169
                                       5554555555555...6777777777777766664444443....44444004555566677*************** PP

                                       EEESBETTTTEB--...HHHHHHHHHHTT-EEEEE- CS
                       Aminotran_5 144 aithvsnvtGtiqp...veeigklakkkgalvlvDa 176
                                       +i+  +n tG++ p   + +i +la +++ +v+ D 
  gi|242398968|ref|YP_002994392.1| 170 IINTPNNPTGIVYPsniLRRISELAEDYDLVVISDE 205
                                       ***********8773336789999999999999886 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.0024
                                       HHHHHHHH..HCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-CTCBSEEEEEETTCSHHHHHHHHHHT.TEE CS
                       Aminotran_5 261 lgaaleyl..eeigleaiekhekelaeyllerlkslpgvrlygpdkaerrasivsfnfkgvhaedvatlLdee.gIa 334
                                        +aa+  l  ++ ++e++ k+ ++ ++ +++ l++ p+v +++  ++ +    +++++ + ++ ++a  L  + ++a
  gi|242398968|ref|YP_002994392.1| 276 QKAAFVALseSQEEAENMVKQYEKRRNLVVSLLNEFPNVSFVK--PQGAFYLFLNISHYSKDSYKFAEELLLKkKVA 350
                                       55555555456788999************************55..58999999*****9999999987555444*** PP

                                       EEEE-TTTHHHHHHTT.S-EEEEE--TTS- CS
                       Aminotran_5 335 vrsGhhcaqplmkrlalegtvRaSlyiynt 364
                                       v  G +           eg vR+S+++  +
  gi|242398968|ref|YP_002994392.1| 351 VAPGATFG------SLGEGYVRISFANSEE 374
                                       *****999......333499****987532 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 !   22.2   0.0   1.7e-08   4.4e-05      69     175 ..      94     206 ..      67     215 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.7e-08
                                       EEEEESSHHHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHT...HHHTTCEEEEESTTSHHHHHHHCCTTEEEEE CS
                   Cys_Met_Meta_PP  69 aalavssGmaAiaaailallkaGdeivvsddlYggtqrllkkv...lkklgievkfvdtsdleelekaikentklvy 142
                                       ++l+   G++A+ +++la++  Gde+++ +  Y +  +++k +    k  +++ +     ++ee+e+ i++ntk++ 
  gi|242398968|ref|YP_002994392.1|  94 NTLVSIGGTGALLLSLLAIVDIGDEVLLPNPGYPPYTSMVKMIgaiPKYYSLKENESFLPNIEEIENIITNNTKVII 170
                                       66777889**********************9998877777765110444677777777789**************** PP

                                       EESS-TTTT----...HHHHHHHHHHTT-EEEEEGT CS
                   Cys_Met_Meta_PP 143 lEtptnpllkvvD...iekiaklakkagvlvvvDnt 175
                                       + tp np+  v     +++i++la + +++v+ D +
  gi|242398968|ref|YP_002994392.1| 171 INTPNNPTGIVYPsniLRRISELAEDYDLVVISDEV 206
                                       *******97765323367899999998888888865 PP

>> Alliinase_C  Allinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.2   2.1e-06    0.0055     137     361 ..     165     385 ..     116     387 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.1e-06
                                       S-EEEEEESS-TTT--------........-TT-EEEEEE-TT......-STTTS---S-B--SEE.EEEHHHHHS- CS
                       Alliinase_C 137 eefielvtsPnnPdgllreavv........kgseakviyDlay......YWPhytpitskadedim.LftlskltGh 198
                                       +  + ++  PnnP g++  + +        ++ +  vi D +y         hy+ ++  ++ +++ + ++sk    
  gi|242398968|ref|YP_002994392.1| 165 NTKVIIINTPNNPTGIVYPSNIlrriselaEDYDLVVISDEVYerlifdNLNHYSILKFSEEGNVIvIGSFSKSYAM 241
                                       334557889*****99865443355444445556679999999444333368999999988887651569******* PP

                                       GGG-EEEEEES-HHHHHHHHHHHHHHHSS--HHHHHHHHHHHHHHHHHTT--STTTSHHHHHHHHHHHHHHHHHHHH CS
                       Alliinase_C 199 aGsrlGWalvkdkevakklveyieknsiGvskesqlrvlkilkvvlaeiktekgtedlfefgyeklkerWeklkevv 275
                                       +G r+G+a+  + ++ k ++e  e+ +i     +q  +   l + ++e ++            ++ ++r + + +++
  gi|242398968|ref|YP_002994392.1| 242 TGWRVGFAVSNNVKIIKSMTELQEHVAICAPAMAQKAAFVALSESQEEAENM----------VKQYEKRRNLVVSLL 308
                                       *********************9999999998888877776666544444333..........344566777777788 PP

                                       HCSSSEE-----EEEETTTTSEEE---SEEEEEESSSS..-HHHHHHTTTEEEEEGGGGTS.-TTEEEEESSS-HHH CS
                       Alliinase_C 276 kesdrfslqklkseyCnyfkkvrepsPayaWlkcekeededcaevlrekkiltrsGevfea.esryvrlsllkrddd 351
                                       +e  ++s+ k + ++  +++ ++ ++ +y +           +e+l +kk+    G +f++ ++ yvr+s+ +++++
  gi|242398968|ref|YP_002994392.1| 309 NEFPNVSFVKPQGAFYLFLNISHYSKDSYKF----------AEELLLKKKVAVAPGATFGSlGEGYVRISFANSEEN 375
                                       8888888888888887777777777777644..........245777788888888888764677888888888888 PP

                                       HHHHHHHHHT CS
                       Alliinase_C 352 fdvllerlkk 361
                                        +  ++rlk+
  gi|242398968|ref|YP_002994392.1| 376 IEEGVKRLKE 385
                                       8888887776 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   3.5e-06     0.009     109     167 ..     153     204 ..      46     206 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.5e-06
                                       E-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEE CS
                   Beta_elim_lyase 109 mdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlD 167
                                        ++e++e++i++      ++k+i++ + nn   G v++ + lr+++++a++y++ ++ D
  gi|242398968|ref|YP_002994392.1| 153 PNIEEIENIITN------NTKVIIINTPNN-PTGIVYPSNILRRISELAEDYDLVVISD 204
                                       467777777777......688888877777.69*********************99988 PP

>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   7.7e-05       0.2     173     234 ..     146     206 ..     123     208 .. 0.85
   2 ?   -2.2   0.1      0.48   1.2e+03      68     113 ..     256     300 ..     239     311 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 7.7e-05
                                       HHHHHHHHHHHHHHCHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEEE-T CS
                       Aminotran_3 173 eeeaalleelealekkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvllivDEv 234
                                       +e+++ l  +e++e+ +++++  +i+ +     G+v +s + l+++ el++++d ++i DEv
  gi|242398968|ref|YP_002994392.1| 146 KENESFLPNIEEIENIITNNTKVIIINTPNNPTGIVYPS-NILRRISELAEDYDLVVISDEV 206
                                       56778888999999999***********99999987766.679******************9 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.48
                                       EEHHHHHHHHHHHHHCT-..SEEEEESSHHHHHHHHHHHHHHHHHH CS
                       Aminotran_3  68 tnepalklaekllklapkgldkvflansGseAvetAlKlarkyare 113
                                         +++ +l e ++  ap   +k   + + se+ e A  + ++y++ 
  gi|242398968|ref|YP_002994392.1| 256 IIKSMTELQEHVAICAPAMAQKA-AFVALSESQEEAENMVKQYEKR 300
                                       44555666666666777744444.4445588888888888886654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       880  (0.0490825); expected 358.6 (0.02)
Passed bias filter:                      631  (0.0351944); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.70u 0.36s 00:00:01.06 Elapsed: 00:00:00.55
# Mc/sec: 2141.40
//
Query:       gi|242398969|ref|YP_002994393.1|  [L=459]
Description: Sodium:proline symporter [Thermococcus sibiricus MM 739]
Scores for 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-56  191.6  29.5    2.6e-56  191.2  29.5    1.1  1  SSF       Sodium:solute symporter family


Domain annotation for each model (and alignments):
>> SSF  Sodium:solute symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.2  29.5   1.5e-60   2.6e-56       1     406 []      31     417 ..      31     417 .. 0.90

  Alignments for each domain:
  == domain 1  score: 191.2 bits;  conditional E-value: 1.5e-60
                               SSF   1 yflagrsltgfvlglslaasnisaasfvGlaGavaa.sGlavvllelgalllvlllllllaerlrnagalTlpdyls 76 
                                       +f+agr+l  +   +++aa+ i+++  +G+a+ ++a  G++  +  lg+   ++l++l+ a+ lr++  lTl+d++s
  gi|242398969|ref|YP_002994393.1|  31 FFVAGRRLKTWLATATIAATWIGGGITIGVAAKAYAgKGISLWATTLGLGSTLILVGLFYAKPLRKMKLLTLADFFS 107
                                       8*******************************999747999999999999999************************ PP

                               SSF  77 kRfkgkr.ilvylsalslllvitlklsvdlvggaklielalGlnyetavlllaaltalYtviGGllAvvytdtiqav 152
                                       +Rf+gk+ +   +  +  l++ ++++++++v+ga+li+ +lG++y+ta ++ +++++ Yt++GGl +v++td iq +
  gi|242398969|ref|YP_002994393.1| 108 ERFGGKKgLSGTVGFILALAY-IFAITAQIVAGARLIQVVLGWDYKTAAIVSGLIVTFYTILGGLWSVSLTDFIQLI 183
                                       *******66666666555555.5689*************************************************** PP

                               SSF 153 lmlvgalilliivllevGgleslveklkeaapkvvdlltpdslkllrdpltalslwlglvlGvaglphilvRflaak 229
                                       l+ vg +  lii + +vG +e+ v+k+ e        l  +  k+++ + + +++ + + lG + +p  ++R++  +
  gi|242398969|ref|YP_002994393.1| 184 LVFVGVFGALIIGINAVG-FEATVTKAEELGL-----LDFG--KIILAFDFWALF-IVFALGDIPAPDLMQRIFGSD 251
                                       **************9996.7777777777665.....3323..357777777777.99******************* PP

                               SSF 230 dakailkgvlkltivlilvligmisiilfaiklagavpkavgtevgvsniaypeLvvkllpnllaGlllavmlAaim 306
                                       + k++  + l  ++ +++ ++g++++ l++i+ + +      +++  +++a+p Lv+ +lp ++ Gl la  +Aa+m
  gi|242398969|ref|YP_002994393.1| 252 SEKTAQISSL--LGGISYYVMGILALLLGSIAAVKF------PNLSDPELALPMLVKSMLPAGISGLALAGLMAAVM 320
                                       ***9987765..667788888988999999988888......8999******************************* PP

                               SSF 307 stltslllsassaftkDlYkkirrkasakekelvgvsriivlvvislaillavqeeqkgvlklvelafaglasavla 383
                                       s  +s+ll+  ++++k +Y  i+  + a++  +++vsri +lv++  a++l      +g++    la++++ +  + 
  gi|242398969|ref|YP_002994393.1| 321 SNADSMLLAPGTLIAKNIYRDIINPQ-ASDEDVLKVSRISLLVIGIFALILST--TRSGIVEWLYLAWDVIFATAFF 394
                                       **************************.99999************999877654..45669999999**999999889 PP

                               SSF 384 villalfwkrvneqGAlagliiG 406
                                        + l+l+w++ + +GA+ag++ G
  gi|242398969|ref|YP_002994393.1| 395 PLTLGLWWDKTTYKGAFAGVVGG 417
                                       999****************9877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (459 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       715  (0.0398795); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); 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):               1  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.50
# Mc/sec: 2779.15
//
Query:       gi|242398970|ref|YP_002994394.1|  [L=1228]
Description: DNA topoisomerase I [Thermococcus sibiricus MM 739]
Scores for complete 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-125  418.4   0.2    2.1e-73  247.7   0.2    2.4  2  Topoisom_bac     DNA topoisomerase
    2.8e-20   72.6   0.0    2.8e-20   72.6   0.0    2.9  4  Intein_splicing  Intein splicing domain
    6.5e-19   68.1   0.0    6.5e-19   68.1   0.0    3.2  2  Toprim           Toprim domain
    4.8e-13   49.2   2.5    2.3e-12   47.1   0.0    3.2  2  LAGLIDADG_3      LAGLIDADG-like domain
      1e-12   47.6   1.6      1e-12   47.6   1.6    2.5  2  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger
  ------ inclusion threshold ------
      0.014   15.5   0.0      0.033   14.3   0.0    1.6  1  DUF1272          Protein of unknown function (DUF1272)
       0.34   10.6   8.3       0.23   11.2   0.8    3.3  3  DUF4364          Domain of unknown function (DUF4364)
       0.42   11.0   6.4        1.4    9.4   0.3    2.7  2  Lar_restr_allev  Restriction alleviation protein Lar
        1.8    8.1   4.4         25    4.5   0.1    2.7  2  zf-ribbon_3      zinc-ribbon domain
        2.9    8.0   5.3         29    4.8   0.6    2.7  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
        8.9    6.4   5.7       0.94    9.5   0.4    2.2  2  Ogr_Delta        Ogr/Delta-like zinc finger


Domain annotation for each model (and alignments):
>> Topoisom_bac  DNA topoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.2   0.0   1.8e-52   2.9e-49       2     160 ..     156     315 ..     155     319 .. 0.93
   2 !  247.7   0.2   1.3e-76   2.1e-73     161     412 ..     827    1075 ..     800    1076 .. 0.94

  Alignments for each domain:
  == domain 1  score: 168.2 bits;  conditional E-value: 1.8e-52
                      Topoisom_bac   2 inenlvdaaeaRrelDwliGinlsrlltk...klkg.kkvlsaGRVqtptLaliveRereienFvpeeyweveatlk 74 
                                       in+ ++da+ +R++lDw +G+nlsr+l+    k +g  +vls GRVq ptL+++v+Re+eienFvp++yw +++ l+
  gi|242398970|ref|YP_002994394.1| 156 INFGMADAGITRHILDWYWGVNLSRALSSairKSSGkWHVLSTGRVQGPTLKFLVDREKEIENFVPTPYWVIKMILE 232
                                       7899*************************7653333799************************************97 PP

                      Topoisom_bac  75 kekkekekkkkkkkerikdkeeaeaileklkkkeakvesvekkekkkppplpfdtttLqkeasrklglsakktlsia 151
                                       k++++    ++ +k+ri ++eea++i+e+ kk+ a ve++e +++k++pp pfd+ tLq+e  + +g+s+kktl+ia
  gi|242398970|ref|YP_002994394.1| 233 KNGEQY--TANYEKDRILNEEEAKRIVEEAKKGPAFVEKIEITQQKRSPPYPFDLGTLQRESYSAFGYSPKKTLEIA 307
                                       777776..599*******************8879******************************************* PP

                      Topoisom_bac 152 qkLYekagl 160
                                       qkLYek g+
  gi|242398970|ref|YP_002994394.1| 308 QKLYEK-GY 315
                                       *****8.87 PP

  == domain 2  score: 247.7 bits;  conditional E-value: 1.3e-76
                      Topoisom_bac  161 itYpRTdstrlseeaelkailealakkygkeylefaekllkktkkksvvknkkveaHeAIrPteelpklkelsdd 235 
                                         +YpRT s++l+++ ++++i+++lak   +ey+++a++ll k+  k v ++k++ aH+AI+Pt+e+pk  +l++d
  gi|242398970|ref|YP_002994394.1|  827 CSYPRTSSQKLPKNLNFRSIIQNLAKI--PEYKPHAHELLGKGILKPVEGKKDDPAHPAIYPTGEVPKPGDLNKD 899 
                                        69************77**********7..89*********99987767777777*************989***** PP

                      Topoisom_bac  236 ekklYelIvrrflaslmkdakyeettvkleveeeefkasgktilekGfkkvykeekkeeeeeelpelkegeevkv 310 
                                        e++lY+lIvrrfla+++++a+ e++++ +++++++f ++g++++++G++k+y +  k +e   lp++++ge+v+v
  gi|242398970|ref|YP_002994394.1|  900 EQNLYDLIVRRFLAAFAEPAIRESMKIIINSNKHHFILNGSRTIKEGWLKIYGKYVKFDE-VILPKFEKGEKVNV 973 
                                        ****************************************************66655555.48************ PP

                      Topoisom_bac  311 keveleekkTkppkryteasLikamekagiGtpaTraeiieklvergYverkkkslvptelGkalvellekf.kd 384 
                                         +++ e+kkTkpp+ry+ as+ik+me+ giGt+aTra+i+e+l++rgY+e  kk++++t+lG++++e+le+  +d
  gi|242398970|ref|YP_002994394.1|  974 IQIKKEKKKTKPPARYSPASIIKKMEDLGIGTKATRAQILETLYSRGYIEG-KKKIKVTPLGIKVIEALENNvPD 1047
                                        ***************************************************.669**************6666** PP

                      Topoisom_bac  385 lvspelTaeleekLdeIaegkadakevl 412 
                                        ++s+elT+e+e+k++eI   k++++ v+
  gi|242398970|ref|YP_002994394.1| 1048 IISVELTREFEQKMEEIMARKLKKERVI 1075
                                        *************************998 PP

>> Intein_splicing  Intein splicing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.4       5.5   8.9e+03      12      54 ..     227     272 ..     224     277 .. 0.57
   2 !   72.6   0.0   1.7e-23   2.8e-20       8     134 .]     329     826 ..     323     826 .. 0.97
   3 ?   -2.0   0.2         2   3.2e+03      74     108 ..     945     979 ..     918    1080 .. 0.61
   4 ?   -2.8   1.5       3.6   5.8e+03      33      33 ..    1110    1110 ..    1047    1151 .. 0.57

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 5.5
                                       HHHHCCECTTEEEEEETTTTEEEEEEEEEEEEEEEE...EEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxx RF
                   Intein_splicing  12 ieelvekegeevlslnledlklevksvkkliklklk...elyeikl 54 
                                       i+ ++ek+ge+  + +++d  l+ ++ k++++ ++k    + +i++
  gi|242398970|ref|YP_002994394.1| 227 IKMILEKNGEQYTANYEKDRILNEEEAKRIVEEAKKgpaFVEKIEI 272
                                       5667777777777666666666666655555555554334444444 PP

  == domain 2  score: 72.6 bits;  conditional E-value: 1.7e-23
                                       EEEEHHHHCCECTTEEEEEETTTTEEEEEEEEEEEEEEEE.EEEEEEETTS-EEEEETT-EEEECCTTEEEEEECCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Intein_splicing   8 ekvkieelvekegeevlslnledlklevksvkkliklklk.elyeiklesgrkikaTpeHkllvvrdegivEkrade 83 
                                       +k kieel   ++ ev +l++ dlkl +++  +l + +    +y+++l+  +++++T++H++l++rd+ ++ + a+e
  gi|242398970|ref|YP_002994394.1| 329 VK-KIEEL--PKEGEVFALDF-DLKLSRARY-RLLERDADeLMYKVTLSDRTELYLTGDHPVLAYRDDRLIFVPAEE 400
                                       45.89999..67999999996.688999995.55555555499************************9999****** PP

                                       --TT-EEEEE................................................................... CS
                                       xxxxxxxxxx................................................................... RF
                   Intein_splicing  84 Lkegdliavp................................................................... 93 
                                       Lk  d +++                                                                    
  gi|242398970|ref|YP_002994394.1| 401 LKDDDQVVLLinpwkfqsasetpklfdfilknassmkdyilydqsfgsvirnrikkaglkveilwkfkikeptyyky 477
                                       ********99******************************************************************* PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                   Intein_splicing  94 ............................................................................. 93 
                                                                                                                    
  gi|242398970|ref|YP_002994394.1| 478 lrgkmpvpvfkfliergviskeearevfkgfsystslsavsfefnedfwylygfvvgdchldkrgqitigardrtee 554
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                   Intein_splicing  94 ............................................................................. 93 
                                                                                                                    
  gi|242398970|ref|YP_002994394.1| 555 timaiqevansigvrfaydsrykiirlgskslvrlfellgcpygnkmkifeipgevmakpgwmasflagyydadshi 631
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                   Intein_splicing  94 ............................................................................. 93 
                                                                                                                    
  gi|242398970|ref|YP_002994394.1| 632 gtkstggrkslspqivltsknrraiytvklmwqllgvgtylwerkdkngnlmayelkvysrdslkfyeimkdhlrvk 708
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                   Intein_splicing  94 ............................................................................. 93 
                                                                                                                    
  gi|242398970|ref|YP_002994394.1| 709 rcdlekvrnaairkrksyshhysvlkvtdwngklksnkklwkefdisnqtahgrgisldklrrirdyltdedlrria 785
                                       ***************************************************************************** PP

                                       HSCEEEEEEEEEEEEECEEEEEEEEETTT-EEEECTTEEE- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Intein_splicing  94 dadvvwdkvksievedeeeyVYdltvednhNFvangiivHN 134
                                        +dv+   +ksie+ ++ ++VYdl ved+hNF+ang++vHN
  gi|242398970|ref|YP_002994394.1| 786 TGDVYILGIKSIEKFHYCGKVYDLVVEDYHNFIANGVVVHN 826
                                       ****************************************9 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 2
                                       TEEEEEECCC--TT-EEEEEHSCEEEEEEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Intein_splicing  74 egivEkradeLkegdliavpdadvvwdkvksieve 108
                                       eg++   ++ +k  ++i    +     +v +i++e
  gi|242398970|ref|YP_002994394.1| 945 EGWLKIYGKYVKFDEVILPKFEKGEKVNVIQIKKE 979
                                       44554555555554444433222222222222222 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 3.6
                                        E CS
                                        x RF
                   Intein_splicing   33 l 33  
                                         
  gi|242398970|ref|YP_002994394.1| 1110 N 1110
                                        1 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.1   0.0     4e-22   6.5e-19       1     102 [.       3     139 ..       3     140 .. 0.97
   2 ?   -2.8   4.9       4.5   7.3e+03      21      62 ..    1026    1092 ..    1001    1133 .. 0.52

  Alignments for each domain:
  == domain 1  score: 68.1 bits;  conditional E-value: 4e-22
                                       EEEEESSHHHHHHHHHTHT....................STEEEEEEESSSSEEEHS............TTEEEEE. CS
                            Toprim   1 elvivEgpsdaktiakalg....................sgfqavtaslGhildlet............efkpvye. 44 
                                       +l+i+E+p+ ak+ia al                     +++ +v + +Gh+++l+             ++ pvy  
  gi|242398970|ref|YP_002994394.1|   3 TLIIAEKPNVAKKIAYALAerkpirktigkvpyyeltrdGKKIIVAPAVGHLFSLAPkertygypvfdiDWVPVYLa 79 
                                       59***************99********************9***********************************9* PP

                                       ..ECTTTHHHHHHHHHHHHHHSEEEEECSSSHHHHHHHHHHHHHHTHHHTTTEEEEEESS CS
                            Toprim  45 ..eiedkkkvlkalkelakradeiilatDpDreGeaiawellevlkellenkigrvefse 102
                                          + ++k+++kalkelak+ade ++a+D D+eGe i++ +l++++   ++k +r++fs 
  gi|242398970|ref|YP_002994394.1|  80 ekGKSYTKDYIKALKELAKQADEFVIACDYDTEGEVIGYTALKYACGVEPSKAKRMKFSA 139
                                       999*******************************************77777*******96 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.5
                                        TEEEEEEESSSSEEEHS.............TTEEEEE............ECTTTHHHHHHHHHHHHH CS
                            Toprim   21 gfqavtaslGhildlet.............efkpvye............eiedkkkvlkalkelakr 62  
                                        ++ +vt++  ++++  +             ef++++e            + e+k+  +k+lke + +
  gi|242398970|ref|YP_002994394.1| 1026 KKIKVTPLGIKVIEALEnnvpdiisveltrEFEQKMEeimarklkkervIEESKTALIKVLKEFKNK 1092
                                        5566666666666666666666666655553333333444444444443333333333333333322 PP

>> LAGLIDADG_3  LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1      0.53   8.7e+02       5      50 ..     526     569 ..     522     594 .. 0.70
   2 !   47.1   0.0   1.4e-15   2.3e-12       2      81 ..     616     700 ..     615     702 .. 0.95

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.53
                                       HHHHHHHHHCCECCECSTTTTSEEEEES-HHHHHHHHHHHHHCT.H CS
                       LAGLIDADG_3   5 afLrGlfdaDGsvskskkkgvsisltssskelledvqrlLlrlGIe 50 
                                        +L G+  +D + +k+++    i    + +e +  +q++ + +G+ 
  gi|242398970|ref|YP_002994394.1| 526 WYLYGFVVGDCHLDKRGQI--TIGARDRTEETIMAIQEVANSIGVR 569
                                       6788999999999999964..3666666699999999998888875 PP

  == domain 2  score: 47.1 bits;  conditional E-value: 1.4e-15
                                       HHHHHHHHHHHHCCECCECSTTTTS.....EEEEES-HHHHHHHHHHHHHCT.HSCEEEEEEE-SCCCCECCCHCHC CS
                       LAGLIDADG_3   2 vkaafLrGlfdaDGsvskskkkgvs.....isltssskelledvqrlLlrlGIestiyekkkakgrgvyrlliisge 73 
                                       ++a fL+G++daD ++ +++++g++     i lts++++ ++ v+ +++ lG+ +++ e+k ++g+ + ++l + ++
  gi|242398970|ref|YP_002994394.1| 616 WMASFLAGYYDADSHIGTKSTGGRKslspqIVLTSKNRRAIYTVKLMWQLLGVGTYLWERKDKNGNLMAYELKVYSR 692
                                       5799*************9999999899*********************************999999999******** PP

                                       TTCGGGTT CS
                       LAGLIDADG_3  74 nlkrFlek 81 
                                       +  +F+e 
  gi|242398970|ref|YP_002994394.1| 693 DSLKFYEI 700
                                       **9*9986 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 !   47.6   1.6   6.2e-16     1e-12       2      37 ..    1146    1183 ..    1145    1185 .. 0.91
   2 ?    0.2   2.7      0.41   6.7e+02       2      24 ..    1193    1216 ..    1192    1228 .] 0.73

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 6.2e-16
                                        EE-SSS--EEEEEE-SSS..EEEEESST.T----EEB- CS
                    zf-C4_Topoisom    2 ekCPkCggdLvlkrgkkG..kFvGCsnYPeCkftkklk 37  
                                        + CPkCggdLv+++ ++   +FvGCsn P+C++t++l 
  gi|242398970|ref|YP_002994394.1| 1146 GSCPKCGGDLVVRYNRRTgkRFVGCSNWPNCNVTYPLL 1183
                                        79************998779***************986 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.41
                                        EE-SSS-.-EEEEEE-SSSEEEEE CS
                    zf-C4_Topoisom    2 ekCPkCg.gdLvlkrgkkGkFvGC 24  
                                        ++C +Cg +++++ + ++ ++  C
  gi|242398970|ref|YP_002994394.1| 1193 KTCSECGnAPIIKIKERNREYEVC 1216
                                        79*****78877766666677666 PP

>> DUF1272  Protein of unknown function (DUF1272)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0     2e-05     0.033      23      55 ..    1127    1159 ..    1116    1161 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2e-05
                           DUF1272   23 ricsyEctFCaeCaeevlenvCPncgGelvkRP 55  
                                        ++   E  F ++  e+++ + CP cgG+lv R 
  gi|242398970|ref|YP_002994394.1| 1127 KVIQVEADFENKGKEKIIVGSCPKCGGDLVVRY 1159
                                        45667888999999****************995 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       0.5   8.1e+02      42      70 ..      19      46 ..      13      48 .. 0.81
   2 ?   11.2   0.8   0.00014      0.23      38     110 ..    1011    1078 ..    1007    1093 .. 0.85
   3 ?    0.2   1.9      0.33   5.4e+02      73     126 ..    1089    1141 ..    1083    1146 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.5
                           DUF4364 42 eLvesglieeeekenktlykiTekGketl 70
                                       L e + i++ +  +  +y++T +Gk+++
  gi|242398970|ref|YP_002994394.1| 19 ALAERKPIRK-TIGKVPYYELTRDGKKII 46
                                      5777777886.789999*********986 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00014
                           DUF4364   38 qalseLvesglieeeekenktlykiTekGketlelfenripksirekideylkenkeelkkesevkadyykke 110 
                                        q+l+ L + g+ie     +k+ +k+T+ G +++e +en++p+ i  ++ + +++++ee+  ++  k ++++++
  gi|242398970|ref|YP_002994394.1| 1011 QILETLYSRGYIE-----GKKKIKVTPLGIKVIEALENNVPDIISVELTREFEQKMEEIMARKLKKERVIEES 1078
                                        7788888888887.....6899***********************************9988877666666555 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.33
                           DUF4364   73 fenripksirekideylkenkeelkkesevkadyykkengeytVklkikekdst 126 
                                        f+n+   +i +k+ e + en+++ k ++++  +  ++e++  +V+  + +k+++
  gi|242398970|ref|YP_002994394.1| 1089 FKNK-EGEIGKKLLETFLENEKNKKSKRKNVKELKPEEEKVIQVEADFENKGKE 1141
                                        5555.5567777788888888888888888888888888888888877777654 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 ?    9.4   0.3   0.00085       1.4       5      36 ..    1147    1178 ..    1144    1187 .. 0.88
   2 ?    3.4   1.2      0.06        98       4      36 ..    1193    1223 ..    1190    1227 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00085
                   Lar_restr_allev    5 pCPfCggravlersqrvvaeigqcvyCad...Cga 36  
                                         CP Cgg+ v+  + r+ +    +v C +   C++
  gi|242398970|ref|YP_002994394.1| 1147 SCPKCGGDLVVRYNRRTGKR---FVGCSNwpnCNV 1178
                                        6*************999998...9***88888998 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.06
                   Lar_restr_allev    4 kpCPfCggravlersqrvvaeigqcvyCad..Cga 36  
                                        k C  Cg++++++  +r+++    +  C d  C+ 
  gi|242398970|ref|YP_002994394.1| 1193 KTCSECGNAPIIKIKERNRE----YEVCLDmnCNK 1223
                                        7899***************9....99996666986 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.8     0.023        37      19      26 .]    1148    1155 ..    1147    1155 .. 0.76
   2 ?    4.5   0.1     0.015        25       3      12 ..    1193    1203 ..    1192    1209 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.023
                       zf-ribbon_3   19 CpyCGtkl 26  
                                        Cp+CG++l
  gi|242398970|ref|YP_002994394.1| 1148 CPKCGGDL 1155
                                        88888876 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.015
                       zf-ribbon_3    3 vrCPnCGa.pl 12  
                                        ++C++CG+ p+
  gi|242398970|ref|YP_002994394.1| 1193 KTCSECGNaPI 1203
                                        68*****9884 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 ?    4.8   0.6     0.018        29      21      35 ..    1148    1162 ..    1139    1177 .. 0.70
   2 ?    4.4   0.4     0.022        37      16      36 ..    1190    1210 ..    1187    1223 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.018
                     Zn_Tnp_IS1595   21 CPhCgsrkayriktr 35  
                                        CP+Cg++ + r+++r
  gi|242398970|ref|YP_002994394.1| 1148 CPKCGGDLVVRYNRR 1162
                                        *******55555552 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.022
                     Zn_Tnp_IS1595   16 pngfvCPhCgsrkayriktrg 36  
                                        p+g +C  Cg++ +++ik r 
  gi|242398970|ref|YP_002994394.1| 1190 PTGKTCSECGNAPIIKIKERN 1210
                                        67889********99999843 PP

>> Ogr_Delta  Ogr/Delta-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.4   0.00058      0.94       2      38 ..    1148    1181 ..    1147    1185 .. 0.91
   2 ?   -2.3   0.7       2.9   4.7e+03       1       9 [.    1194    1202 ..    1194    1221 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00058
                         Ogr_Delta    2 CPhCgapaaartsrnlskdvreryyqCsnf.eCgatfv 38  
                                        CP+Cg   ++r  r++ k    r+  Csn  +C  t+ 
  gi|242398970|ref|YP_002994394.1| 1148 CPKCGGDLVVRYNRRTGK----RFVGCSNWpNCNVTYP 1181
                                        **************9988....***********99985 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.9
                         Ogr_Delta    1 rCPhCgapa 9   
                                        +C +Cg++ 
  gi|242398970|ref|YP_002994394.1| 1194 TCSECGNAP 1202
                                        599999764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1286  (0.0717274); expected 358.6 (0.02)
Passed bias filter:                      642  (0.0358079); 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):              11  [number of targets reported over threshold]
# CPU time: 0.97u 0.33s 00:00:01.30 Elapsed: 00:00:00.54
# Mc/sec: 6905.77
//
Query:       gi|242398971|ref|YP_002994395.1|  [L=397]
Description: Geranylgeranyl hydrogenase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-17   63.1   0.0    3.6e-17   62.5   0.0    1.2  1  Lycopene_cycl   Lycopene cyclase protein
    3.1e-17   62.8   1.2    1.3e-14   54.2   1.2    3.0  1  FAD_binding_3   FAD binding domain
    3.8e-12   46.0   0.4    1.1e-05   24.7   0.1    3.0  3  FAD_binding_2   FAD binding domain
    2.4e-11   43.7   1.1    7.1e-11   42.1   0.3    2.1  2  FAD_oxidored    FAD dependent oxidoreductase
      9e-11   41.9   1.8    6.3e-05   22.7   0.6    2.2  2  DAO             FAD dependent oxidoreductase
    1.8e-07   30.7   0.5    0.00029   20.2   0.1    2.7  3  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    2.8e-07   29.8   0.2    0.00086   18.3   0.0    2.1  2  Trp_halogenase  Tryptophan halogenase
    4.6e-06   25.6   0.6    6.4e-05   21.8   0.3    2.1  2  HI0933_like     HI0933-like protein
    1.6e-05   25.1   0.1    5.8e-05   23.2   0.1    2.1  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    0.00013   22.4   1.5       0.42   11.2   0.2    3.2  3  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    0.00048   19.4   0.5     0.0012   18.2   0.1    1.8  2  Thi4            Thi4 family
      0.003   16.7   1.9     0.0041   16.3   0.5    1.9  2  GIDA            Glucose inhibited division protein A
     0.0034   16.0   0.0      0.038   12.5   0.0    2.0  2  GDI             GDP dissociation inhibitor
  ------ inclusion threshold ------
       0.01   15.7   1.0      0.018   14.9   0.2    1.8  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
      0.077   13.3   1.0        0.2   11.9   0.2    2.2  2  TrkA_N          TrkA-N domain
      0.085   12.4   0.0       0.18   11.3   0.0    1.5  1  DUF1188         Protein of unknown function (DUF1188)
       0.11   11.5   0.0       0.25   10.3   0.0    1.5  1  SE              Squalene epoxidase
       0.13   11.9   0.0       0.32   10.6   0.0    1.7  1  ApbA            Ketopantoate reductase PanE/ApbA


Domain annotation for each model (and alignments):
>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.5   0.0   3.6e-20   3.6e-17       1     352 [.       8     367 ..       8     377 .. 0.77

  Alignments for each domain:
  == domain 1  score: 62.5 bits;  conditional E-value: 3.6e-20
                     Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvlieaspsllfpnn.....yvWsdefedlgaleecvehsWsgtivylddg 72 
                                       Dvvv+GaG Ag  +A ++  ak g +v+li+  p +  p +        ++e++++   +++++    g+++y + g
  gi|242398971|ref|YP_002994395.1|   8 DVVVVGAGIAGPIVARNV--AKEGHSVLLIDKKPAIGAPKQcaegiNIGVFEKHNIPYDKRFINREIYGARLYSPSG 82 
                                       9*****************..***********9888855543111112455666666645789999999999999998 PP

                     Lycopene_cycl  73 kkillgraYgrvsskrlkeellerlvengvklleakv......esveeeeageslvvleggr.....kirarlvvda 138
                                        + ++   Y rvs   l++++  ++    + +  a v      + v  e+   + + +++ +     +ira + v a
  gi|242398971|ref|YP_002994395.1|  83 YTLEMR--YSRVSGVILERKVFDKMLAFYAARAGADVlprteaTDVIREDG--KIIGIKAKKegepiEIRADILVAA 155
                                       876665..****999999988888774444444443311100044444444..222222222344789999999999 PP

                     Lycopene_cycl 139 rglaslk........karrlglQtfyGvevevdnppfdldkmvlMDfrveqklkgltFlYalPldsdrllvEeTela 207
                                        g+ s           a+ + +  +y  e e+  + fd+d + l      +++    ++++ P d+dr+ v     +
  gi|242398971|ref|YP_002994395.1| 156 DGVESTIarkagintYAPPHEFDSAY--EYEMLIEGFDPDLIHLWF---GNNVAPRGYVWVFPKDEDRANVGVGINS 227
                                       99655557777775555555566665..666677789**9998853...33333457899***************** PP

                     Lycopene_cycl 208 skpeLpadalkkrlaaylralglkvkevveeEqgviPvtlggslprleqk.vlaiGaaaglvhPaTGYsvarslaea 283
                                       ++p ++a+     l + l++  +  k++ e   gviPv  gg+l++l ++ vl +G aa  v P  G  +a+++ + 
  gi|242398971|ref|YP_002994395.1| 228 DNP-MTAK---YYLDKWLKENNIPFKKILEVNVGVIPV--GGFLKELVKNnVLVVGDAARQVNPMHGGGMAEAMEAG 298
                                       ***.6665...558899*********************..******9887699************************ PP

                     Lycopene_cycl 284 pllasaiaaalres..slsarawatlwprerkrqreffrllglalllkldiegrrrfldaFfrlpkellqr 352
                                        + ++ i++al+e+  +l ++ +++ w ++ kr   ++r+   +++ +l  e    f+++ +++++e +++
  gi|242398971|ref|YP_002994395.1| 299 AIASKWIVEALKEEnfELLKNYTTEWWEKDGKRLERVLRVR--KVVEHLTDEDLDVFIQTLSGIDAEKIAG 367
                                       *9999*******99666667788889999999999999874..59999999************99998876 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.2   1.2   1.3e-17   1.3e-14       2     337 ..       7     323 ..       6     326 .. 0.72

  Alignments for each domain:
  == domain 1  score: 54.2 bits;  conditional E-value: 1.3e-17
                                       EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSS.CCSSS--EEEHHHHHHHHHTT-HHHHHHHSEECCCCEEEEE CS
                     FAD_binding_3   2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrstt.vvlpradglnqrtmellrqlGledrilaegapnelmgealy 77 
                                       +dV++VGaG aG + a+  ++ G +v+l++k     +++  a+g+n   +e   ++  ++r++++     + g  ly
  gi|242398971|ref|YP_002994395.1|   7 YDVVVVGAGIAGPIVARNVAKEGHSVLLIDKKPAIgAPKQCAEGINIGVFEK-HNIPYDKRFINRE----IYGARLY 78 
                                       79****************************9876415666899999888886.5777788887776....8899999 PP

                                       EECCCCCEEEEEHHCHHCST-CEE--HHHHHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEE CS
                     FAD_binding_3  78 nelsdtpkaradlelesspervtvypqteleriLvehaeerglqvrfktevesleqdeegvtaevrdketgeeetvr 154
                                        +      +   le++ s  +  ++  + ++++L+  a+++g++v   te + + +++ ++    + k++ge  ++r
  gi|242398971|ref|YP_002994395.1|  79 SP------SGYTLEMRYSRVSGVILERKVFDKMLAFYAARAGADVLPRTEATDVIREDGKIIGI-KAKKEGEPIEIR 148
                                       99......4445554444444556667789**********************999998887765.555568888*** PP

                                       EEEEEE--GTT-HHHHHHTGG.EEEEEEEEEEEEEEEEEEC...-SCCCTTCCEEEEECCTTEEEEEECCETEEEEE CS
                     FAD_binding_3 155 akYlvGaDGgrStvrktlgie.fegeetvyeagvldvlfda...dlsdiveplvlilsaesrgvmviPlentlerfy 227
                                       a+ lv+aDG+ St+++++gi+ +  +++   a   ++l++    dl      + + +++            + + ++
  gi|242398971|ref|YP_002994395.1| 149 ADILVAADGVESTIARKAGINtYAPPHEFDSAYEYEMLIEGfdpDLI-----HLWFGNNV-----------APRGYV 209
                                       *******************9943333333333333444333300333.....34444432...........223345 PP

                                       EEEECCE-GGGS......CCCHHHHHHHHHHHHHHTTSSCEEEEEEEEEEEEEEEEESSSEETTEEE-GGGTEEE-S CS
                     FAD_binding_3 228 vqvearaekeer......sekfteeevkarlreivgektldveieevsawtvaqrvaekyrkgrvflaGDAaHihpP 298
                                       ++++ ++++++       ++++t + + +++ ++ ++++ +    +v + +v+ +  +++ k++v+++GDAa  + P
  gi|242398971|ref|YP_002994395.1| 210 WVFPKDEDRANVgvginsDNPMTAKYYLDKWLKENNIPFKKILEVNVGVIPVGGF-LKELVKNNVLVVGDAARQVNP 285
                                       5555555555443321113445555555555555555544444444556666665.578999*************** PP

                                       TTSHHHHHHHHHHHHHHHHHHHHHTTSS-GGGGHHHHHH CS
                     FAD_binding_3 299 tgGqGlNtaiqDavnLawkLaavlkGeAkeelLdtYeee 337
                                       ++G G+  a++      + + ++lk e + elL+ Y++e
  gi|242398971|ref|YP_002994395.1| 286 MHGGGMAEAMEAGAIASKWIVEALK-EENFELLKNYTTE 323
                                       ***********9999999999****.88999*****987 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.1   1.1e-08   1.1e-05       1      44 [.       8      51 ..       8      63 .. 0.92
   2 !   16.3   0.0     4e-06    0.0039     150     203 ..     109     159 ..      89     183 .. 0.80
   3 ?    1.5   0.0      0.13   1.2e+02      95     159 ..     240     309 ..     236     344 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.1e-08
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S- CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqGg 44
                                      Dv+V+G+G+AG   A + a++G++v++++k+++ g   ++++G 
  gi|242398971|ref|YP_002994395.1|  8 DVVVVGAGIAGPIVARNVAKEGHSVLLIDKKPAIGAPKQCAEGI 51
                                      9********************************99988888885 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 4e-06
                                       HHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----G CS
                     FAD_binding_2 150 sarkagvdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgGfg 203
                                       +a +ag d+++rtea+++i+edg++ G+ ++  ++g+  +ira+ +++a+ G++
  gi|242398971|ref|YP_002994395.1| 109 YAARAGADVLPRTEATDVIREDGKIIGIKAK--KEGEPIEIRAD-ILVAADGVE 159
                                       456678*************************..*******9998.555555555 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.13
                                       HHHHTT----BCCTSSB-EEE-TT-SST...EEEE-.STT-.......HHHHHHHHHHHHHHTCT..EEEE CS
                     FAD_binding_2  95 eLeelgvpfsrtedgpvdvrelGglsat...artlhdaadarr.etlvtghallarlvesarkag..vdfq 159
                                       +L+e+ +pf++  +  v+v ++Gg+ ++     +l  ++da r ++ + g ++++++ ++a + +  v+ +
  gi|242398971|ref|YP_002994395.1| 240 WLKENNIPFKKILEVNVGVIPVGGFLKElvkNNVLV-VGDAARqVNPMHGGGMAEAMEAGAIASKwiVEAL 309
                                       999999999995555999******999988655566.888888899***********99996666554444 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   0.3   7.2e-14   7.1e-11       1     155 [.       8     169 ..       8     178 .. 0.75
   2 ?   -1.6   0.0       1.3   1.3e+03      84     123 ..     292     335 ..     260     345 .. 0.62

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 7.2e-14
                      FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaee..qvvtgiarefl.erlrqrggar 74 
                                       DvvVvG+g+aG + A   a++G +vlL+++++ +G     + + ++  +++++     + i re++ +rl    g+ 
  gi|242398971|ref|YP_002994395.1|   8 DVVVVGAGIAGPIVARNVAKEGHSVLLIDKKPAIGAPKQCAEGINIGVFEKHNipYDKRFINREIYgARLYSPSGYT 84 
                                       9*********************************9754444444444444444555556677777734555566665 PP

                      FAD_oxidored  75 lkkrskw...ntfepevakavleemlaeagvtvllntrlvevekegkriesvtveskeg.rktirAkvfiDATg.dG 146
                                       l+ r++    ++ e +v+ ++l    a+ag +vl  t++++v++e+++i +++++ keg  ++irA++ + A g + 
  gi|242398971|ref|YP_002994395.1|  85 LEMRYSRvsgVILERKVFDKMLAFYAARAGADVLPRTEATDVIREDGKIIGIKAK-KEGePIEIRADILVAADGvES 160
                                       55444432124777777777777777*******************99*******5.6644********998866467 PP

                      FAD_oxidored 147 dlaalaGvp 155
                                        +a +aG++
  gi|242398971|ref|YP_002994395.1| 161 TIARKAGIN 169
                                       777777765 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.3
                      FAD_oxidored  84 fepevakavleeml....aeagvtvllntrlvevekegkriesv 123
                                        e   a a++ +++    +e++ ++l n + +  ek+gkr+e v
  gi|242398971|ref|YP_002994395.1| 292 AEAMEAGAIASKWIvealKEENFELLKNYTTEWWEKDGKRLERV 335
                                       44444444444444444499999999999999999998887766 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.6   6.3e-08   6.3e-05       1      36 [.       8      43 ..       8      70 .. 0.84
   2 !   18.2   0.0   1.5e-06    0.0015     141     210 ..      94     166 ..      55     240 .. 0.66

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 6.3e-08
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSG CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiagsga 36
                                      dvv++G+Gi+G  +A+  a++g  V+l++k++ +g  a
  gi|242398971|ref|YP_002994395.1|  8 DVVVVGAGIAGPIVARNVAKEGhsVLLIDKKPAIG--A 43
                                      9********************99********6555..3 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 1.5e-06
                                       EEE.EHHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEE..EEE--GGGHHHHHTT CS
                               DAO 141 gqv.dpakltaalaraaealGveilegtevtgleeedgkvwgverttp.gendaada..vVnaaGawsdllgll 210
                                       g++ +   + + la  a+++G+++l +te+t++ +edgk+ g+ ++++ ge  +++a  +V a G+ s++++++
  gi|242398971|ref|YP_002994395.1|  94 GVIlERKVFDKMLAFYAARAGADVLPRTEATDVIREDGKIIGI-KAKKeGEPIEIRAdiLVAADGVESTIARKA 166
                                       5552444444556666999*************98999******.555546555556665888889998766333 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.1   2.9e-07   0.00029       1      33 [.       7      38 ..       7      76 .. 0.88
   2 !    7.9   0.0    0.0016       1.6     187     249 ..     104     167 ..      78     173 .. 0.75
   3 ?   -1.5   0.0       1.1   1.1e+03     269     285 ..     271     286 ..     248     348 .. 0.66

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 2.9e-07
                                      CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaqagakvtlveleg 33
                                      +dvvv+G+G+AG  +a+++a+ g+ v+l++ ++
  gi|242398971|ref|YP_002994395.1|  7 YDVVVVGAGIAGPIVARNVAKEGHSVLLID-KK 38
                                      69***************************5.32 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0016
                                       HHHHHHHHHTTEEEEESCEEEEEEETTE...EEE.EEETTSCEEEESEEEE-S-EEES-HHCSHCCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 187 aaleealekeGvevklgtsvkeidgnge...kle.vvledgeeidadlvvvavGvrpstelleeklg 249
                                       ++l+ +  + G +v  +t+++++++++     ++  ++++  ei ad +v a Gv+     + +k+g
  gi|242398971|ref|YP_002994395.1| 104 KMLAFYAARAGADVLPRTEATDVIREDGkiiGIKaKKEGEPIEIRADILVAADGVESTI--A-RKAG 167
                                       4455556677999**********99999555444455555556************9875..3.4455 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1.1
                                       TTEEE-GGGCTECCSS- CS
                                       xxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 269 pgiyaiGDvaggkggpe 285
                                        ++ ++GD a ++ +p+
  gi|242398971|ref|YP_002994395.1| 271 NNVLVVGDAA-RQVNPM 286
                                       4566666666.333332 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.2   0.00039      0.39       1      34 [.       8      38 ..       8      45 .. 0.87
   2 !   18.3   0.0   8.6e-07   0.00086     151     341 ..      97     296 ..      86     335 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00039
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-S CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlvese 34
                                      ++v+vG+G+aG ++A  +ak +   ++v+l++++
  gi|242398971|ref|YP_002994395.1|  8 DVVVVGAGIAGPIVARNVAKEG---HSVLLIDKK 38
                                      69******************99...899999864 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 8.6e-07
                                       E-HHHHHHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETT.S-..EEE-SEEEE-SGGG-IIIIIIT---EEE CS
                    Trp_halogenase 151 ldaalyakfLrrvaearGvtrvegkvvevqldedgrveslrled.gr..eveadlfiDcsGfrgllieqaLktgfed 224
                                       l+++ ++k+L  +a ++G +++  + ++ +++edg++ +++ ++ g+  e+ ad+ + + G ++ +  +a   g+++
  gi|242398971|ref|YP_002994395.1|  97 LERKVFDKMLAFYAARAGADVLPRTEATDVIREDGKIIGIKAKKeGEpiEIRADILVAADGVESTIARKA---GINT 170
                                       68999********************99*************9988554336789****************8...8888 PP

                                       -TTT----EEEEEEEE--H....---SSEEEEE-SSEEEEEEEETTEEEE.EEEE-TTTS-HHHHHHHHHHHCT--T CS
                    Trp_halogenase 225 wsdvLltdrAlavqvesee....lvepytrataekaGWtWkiPLqhrlgn.GyvyssahadddeAlaellaeldgkl 296
                                       ++     d+A   ++  e+    l++ + +      G +W  P  +   n G+   s+     +A   l ++l+ + 
  gi|242398971|ref|YP_002994395.1| 171 YAPPHEFDSAYEYEMLIEGfdpdLIHLWFGNNVAPRGYVWVFPKDEDRANvGVGINSDNP--MTAKYYLDKWLKENN 245
                                       8888888****9999999887777888888888899********9988887887766644..578888888888777 PP

                                       TTS-EEEE---EE......ES-SEETTEEE-CCCTEE--CCCS-HHHHHHH CS
                    Trp_halogenase 297 eaeprkirfttGr......rkqawvknvvalGlasgfvePlestsihliqa 341
                                          ++ +++++G        k+  ++nv+ +G+a+  v+P+ + +++ +++
  gi|242398971|ref|YP_002994395.1| 246 IPFKKILEVNVGVipvggfLKELVKNNVLVVGDAARQVNPMHGGGMAEAME 296
                                       777788999999999999899999*****************9999887776 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.3   6.4e-08   6.4e-05       1      36 [.       7      42 ..       7      48 .. 0.95
   2 ?    1.7   0.0     0.086        85     114     166 ..     105     160 ..      99     168 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 6.4e-08
                                      -SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                       HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllekakklg 36
                                      +dv+v+G+G AG   A ++ak+g++Vll++k++++g
  gi|242398971|ref|YP_002994395.1|  7 YDVVVVGAGIAGPIVARNVAKEGHSVLLIDKKPAIG 42
                                      59******************************9998 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.086
                                       HHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE..TTE..EEEESEEEE----SS CS
                       HI0933_like 114 allkelkeagvklrletevksvekeedgkfrvkt.ksee..eleadklvlAtGGlS 166
                                       +l   + +ag ++  +te ++v +e+++++ +k+ k++e  e++ad lv A G +S
  gi|242398971|ref|YP_002994395.1| 105 MLAFYAARAGADVLPRTEATDVIREDGKIIGIKAkKEGEpiEIRADILVAADGVES 160
                                       77777889999***********************5555544678888888888776 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.1   5.8e-08   5.8e-05       1      33 [.      11      43 ..      11      88 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 5.8e-08
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSG CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGG 33
                                      +vGaG++G   A+  ak+g++vll++k + +G 
  gi|242398971|ref|YP_002994395.1| 11 VVGAGIAGPIVARNVAKEGHSVLLIDKKPAIGA 43
                                      8******************************94 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.2   0.00042      0.42       2      35 ..       9      42 ..       8      61 .. 0.88
   2 ?   -2.2   0.0       6.5   6.5e+03      44      78 ..     104     138 ..      98     141 .. 0.74
   3 !    8.7   0.0    0.0026       2.6      42      76 ..     301     335 ..     287     340 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00042
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                      vvvvG+G  g  +A + a+ g++V +++ ++ + 
  gi|242398971|ref|YP_002994395.1|  9 VVVVGAGIAGPIVARNVAKEGHSVLLIDKKPAIG 42
                                      8*****************************9998 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 6.5
                                       HHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEEE CS
                         Pyr_redox  44 kilqeklekngievllntkveeiegsedgvesvkl 78 
                                       k+l+ +  + g +vl  t+++ +  ++ ++ ++k 
  gi|242398971|ref|YP_002994395.1| 104 KMLAFYAARAGADVLPRTEATDVIREDGKIIGIKA 138
                                       56666777888999999999999877776666665 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0026
                                       HHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEE CS
                         Pyr_redox  42 askilqeklekngievllntkveeiegsedgvesv 76 
                                       ask++ e l++++ e+l n ++e +e++++ +e+v
  gi|242398971|ref|YP_002994395.1| 301 ASKWIVEALKEENFELLKNYTTEWWEKDGKRLERV 335
                                       89*************************99976665 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   1.2e-06    0.0012      13      54 ..       2      42 ..       1      50 [. 0.93
   2 ?   -2.6   0.0       2.6   2.6e+03     117     135 ..     119     136 ..      94     164 .. 0.55

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.2e-06
                                      HHHTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS-- CS
                              Thi4 13 lkyaesDvvivGaGssGLtaayylakkpdlkvailersvspG 54
                                       ++++ Dvv+vGaG +G   a+ +ak+ +  v++++++ ++G
  gi|242398971|ref|YP_002994395.1|  2 SEIMKYDVVVVGAGIAGPIVARNVAKE-GHSVLLIDKKPAIG 42
                                      678999*********************.*********99998 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.6
                                       ESEEEEEEEEETBTEEEEE CS
                              Thi4 117 navaveDlivregegvaGv 135
                                         + + D+i  +  ++ G+
  gi|242398971|ref|YP_002994395.1| 119 PRTEATDVIRED-GKIIGI 136
                                       444444444333.333333 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.5   4.1e-06    0.0041       1      31 [.       8      38 ..       8      53 .. 0.86
   2 ?   -2.0   0.0       1.4   1.4e+03     115     149 ..     120     157 ..     108     170 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.1e-06
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEEES- CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithk 31
                                      dv+V+G+G AG   A ++a+ G++vlLi +k
  gi|242398971|ref|YP_002994395.1|  8 DVVVVGAGIAGPIVARNVAKEGHSVLLIDKK 38
                                      79*************************9554 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.4
                                       ES-EEEEEECTTEEEEEEETTS...-EEEECEEEE--T CS
                              GIDA 115 eeeveeliveekkvkgvvtedg...etikakavviatG 149
                                       + e++++i e++k+ g++ +++    +i+a++ v a G
  gi|242398971|ref|YP_002994395.1| 120 RTEATDVIREDGKIIGIKAKKEgepIEIRADILVAADG 157
                                       56888898989999998876541113466667776666 PP

>> GDI  GDP dissociation inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0   3.8e-05     0.038       4      43 ..       6      45 ..       1      71 [. 0.86
   2 ?    1.2   0.0      0.11   1.1e+02     245     273 ..     113     141 ..      99     158 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.8e-05
                                      EECEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSSCGGG CS
                               GDI  4 eydvivlGtGlkecilsGllsvdgkkvlhldrndyyGges 43
                                      +ydv+v+G+G+   i++  ++ +g+ vl +d+++  G+  
  gi|242398971|ref|YP_002994395.1|  6 KYDVVVVGAGIAGPIVARNVAKEGHSVLLIDKKPAIGAPK 45
                                      6********************************9999754 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.11
                                       T-EEETS--ECEEEE-TTS-EEEEEETTE CS
                               GDI 245 GGtymlnkpvdevvldedgkvvGvkseee 273
                                        G+ +l +     v+ edgk++G+k+++e
  gi|242398971|ref|YP_002994395.1| 113 AGADVLPRTEATDVIREDGKIIGIKAKKE 141
                                       4666676666666677*********9876 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 ?   14.9   0.2   1.8e-05     0.018       2      33 ..       9      40 ..       8      58 .. 0.90
   2 ?   -2.2   0.0       3.3   3.2e+03      68      89 ..     290     312 ..     266     319 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.8e-05
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HH CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdisee 33
                                      v v+GaG+ G  +a  +a++g++V l+d +++
  gi|242398971|ref|YP_002994395.1|  9 VVVVGAGIAGPIVARNVAKEGHSVLLIDKKPA 40
                                      89**************************9876 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.3
                                       EEES-HHHHH.C-SEEEE-S-SS CS
                           3HCDH_N  68 sfttdleeav.dadlviEavvEn 89 
                                        +++ +e+ +   ++++Ea  E+
  gi|242398971|ref|YP_002994395.1| 290 GMAEAMEAGAiASKWIVEALKEE 312
                                       45666677666889999999875 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2    0.0002       0.2       1      32 [.       9      40 ..       9      54 .. 0.88
   2 ?   -2.3   0.1       5.3   5.2e+03      44      61 ..     152     169 ..     123     171 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0002
                                      EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHH CS
                            TrkA_N  1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdee 32
                                      ++++G+G  G  +a+++ + g+ +v++idk+++
  gi|242398971|ref|YP_002994395.1|  9 VVVVGAGIAGPIVARNVAKeGH-SVLLIDKKPA 40
                                      79*****************555.7******985 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 5.3
                                       EEES-TTSHHHHHHTTGG CS
                            TrkA_N  44 vvvgdatdeevLeeagie 61 
                                        v +d+ +  + ++agi+
  gi|242398971|ref|YP_002994395.1| 152 LVAADGVESTIARKAGIN 169
                                       455777777777777775 PP

>> DUF1188  Protein of unknown function (DUF1188)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00018      0.18      41      77 ..       4      41 ..       1      44 [. 0.90

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00018
                                      E..EEEEEES-CCCHHHHHHHHCCC.EEEEEEESSGGG CS
                           DUF1188 41 leeknvlviGaYltGaaiakkLskk.eevtlvDiephl 77
                                      + + +v+v+Ga + G ++a+++ k+ + v+l+D +p++
  gi|242398971|ref|YP_002994395.1|  4 IMKYDVVVVGAGIAGPIVARNVAKEgHSVLLIDKKPAI 41
                                      556789****************************9986 PP

>> SE  Squalene epoxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00025      0.25     129     179 ..     270     320 ..     264     339 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00025
                                SE 129 kkGlillGDalnmRHPltggGmtvalnDivllskllkpledlsdeekvlee 179
                                       k+ ++++GDa     P+ ggGm+ a++  ++ sk + +    ++ e + ++
  gi|242398971|ref|YP_002994395.1| 270 KNNVLVVGDAARQVNPMHGGGMAEAMEAGAIASKWIVEALKEENFELLKNY 320
                                       56799***********************99999999887333333444444 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00032      0.32       1      32 [.       9      40 ..       9      64 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00032
                                      EEEES-SHHHHHHHHHHHHHTHCEEEE-SCHH CS
                              ApbA  1 iailGaGaiGsllaakLakagadvtlilrsrr 32
                                      ++++GaG  G ++a + ak g+ v li++++ 
  gi|242398971|ref|YP_002994395.1|  9 VVVVGAGIAGPIVARNVAKEGHSVLLIDKKPA 40
                                      689************************99884 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      561  (0.0312901); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.48
# Mc/sec: 2464.89
//
Query:       gi|242398972|ref|YP_002994396.1|  [L=67]
Description: Ferredoxin 2 [Thermococcus sibiricus MM 739]
Scores for complete 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   56.7  12.5    7.1e-09   35.1   1.4    2.1  2  Fer4          4Fe-4S binding domain
    9.8e-13   48.5  31.6    1.9e-07   31.5  11.5    2.0  3  Fer4_7        4Fe-4S dicluster domain
    1.3e-11   44.1  11.4    5.8e-08   32.5   2.1    2.1  2  Fer4_6        4Fe-4S binding domain
    2.3e-10   39.9  10.1      4e-06   26.6   1.5    2.1  2  Fer4_2        4Fe-4S binding domain
    7.5e-10   38.8  21.8    1.4e-06   28.3  11.8    2.0  2  Fer4_10       4Fe-4S dicluster domain
    5.1e-09   36.1   8.9    8.4e-09   35.4   8.9    1.4  1  Fer4_21       4Fe-4S dicluster domain
    1.2e-08   35.8   8.2    0.00035   21.5   2.6    2.1  2  Fer4_16       4Fe-4S double cluster binding domain
    1.2e-08   35.0  19.5    1.2e-06   28.6  10.9    1.9  2  Fer4_9        4Fe-4S dicluster domain
    8.5e-05   22.8  12.9     0.0021   18.5   3.9    2.2  2  Fer4_4        4Fe-4S binding domain
    0.00027   21.3  12.6      0.035   14.5   3.0    2.1  2  Fer4_8        4Fe-4S dicluster domain
    0.00045   20.7  11.9       0.11   13.1   4.3    2.2  2  Fer4_13       4Fe-4S single cluster domain of Ferredoxin I
    0.00071   20.1  12.5      0.044   14.3   2.5    2.1  2  Fer4_17       4Fe-4S dicluster domain
     0.0012   19.5   7.6       0.19   12.5   1.0    2.4  2  Fer4_15       4Fe-4S single cluster domain
     0.0017   18.5   8.8     0.0033   17.6   8.8    1.4  1  Fer4_18       4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.011   16.7  18.3      0.023   15.6   5.3    2.2  2  Fer4_3        4Fe-4S binding domain
        1.4    7.6   5.4        1.5    7.5   5.4    1.0  1  Dynactin_p62  Dynactin p62 family
        1.6    9.6  14.0        1.7    9.5   2.6    2.1  2  Fer4_22       4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   3.8   2.1e-09   2.2e-06       1      24 []       7      30 ..       7      30 .. 0.95
   2 !   35.1   1.4   6.8e-12   7.1e-09       3      24 .]      38      59 ..      36      59 .. 0.91

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 2.1e-09
                                      EEEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  1 vvideekCigCGaCvevCPvgAIt 24
                                      ++++e+kC  CG C+ vCP  AI+
  gi|242398972|ref|YP_002994396.1|  7 IIVNEDKCYLCGGCAGVCPSLAIK 30
                                      689******************996 PP

  == domain 2  score: 35.1 bits;  conditional E-value: 6.8e-12
                                      EETTTSSS-THHHHHSTTTEEE CS
                              Fer4  3 ideekCigCGaCvevCPvgAIt 24
                                      + ++kCi C +Cv +CPvgA++
  gi|242398972|ref|YP_002994396.1| 38 FFQDKCISCRICVTACPVGALE 59
                                      568*****************85 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   1.5   4.6e-06    0.0049      31      50 ..       7      26 ..       2      28 .. 0.82
   2 !   31.5  11.5   1.8e-10   1.9e-07       1      52 []      13      57 ..      13      57 .. 0.96
   3 !   21.3   3.4   2.9e-07    0.0003       1      19 [.      42      60 ..      42      65 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.6e-06
                            Fer4_7 31 veidpekClgCgaCvavCPt 50
                                      + ++++kC+ Cg C+ vCP+
  gi|242398972|ref|YP_002994396.1|  7 IIVNEDKCYLCGGCAGVCPS 26
                                      45689**************7 PP

  == domain 2  score: 31.5 bits;  conditional E-value: 1.8e-10
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                      +C  Cg C+ +Cp+ ai++  +       k+e+ ++kC++C+ Cv++CP+ga
  gi|242398972|ref|YP_002994396.1| 13 KCYLCGGCAGVCPSLAIKVSSS-------KWEFFQDKCISCRICVTACPVGA 57
                                      7******************886.......7********************98 PP

  == domain 3  score: 21.3 bits;  conditional E-value: 2.9e-07
                            Fer4_7  1 rCigCgaCvaaCpvkaiel 19
                                      +Ci C+ Cv aCpv+a+e 
  gi|242398972|ref|YP_002994396.1| 42 KCISCRICVTACPVGALEA 60
                                      7************999986 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   2.2   4.2e-06    0.0044       3      24 .]       8      29 ..       6      29 .. 0.89
   2 !   32.5   2.1   5.5e-11   5.8e-08       3      24 .]      37      58 ..      37      58 .. 0.95

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.2e-06
                            Fer4_6  3 eidpdkCigCgdCvrvCPegai 24
                                       +++dkC  Cg C+ vCP  ai
  gi|242398972|ref|YP_002994396.1|  8 IVNEDKCYLCGGCAGVCPSLAI 29
                                      69****************8765 PP

  == domain 2  score: 32.5 bits;  conditional E-value: 5.5e-11
                            Fer4_6  3 eidpdkCigCgdCvrvCPegai 24
                                      e+ +dkCi+C+ Cv++CP ga+
  gi|242398972|ref|YP_002994396.1| 37 EFFQDKCISCRICVTACPVGAL 58
                                      6899****************97 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   1.8   1.4e-06    0.0015       3      21 ..       7      25 ..       5      26 .. 0.92
   2 !   26.6   1.5   3.8e-09     4e-06       7      21 ..      40      54 ..      35      55 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.4e-06
                            Fer4_2  3 vvvdtdrCigCgaCvsaCP 21
                                      + v++d+C  Cg C  +CP
  gi|242398972|ref|YP_002994396.1|  7 IIVNEDKCYLCGGCAGVCP 25
                                      789**************** PP

  == domain 2  score: 26.6 bits;  conditional E-value: 3.8e-09
                            Fer4_2  7 tdrCigCgaCvsaCP 21
                                       d+Ci+C++Cv+aCP
  gi|242398972|ref|YP_002994396.1| 40 QDKCISCRICVTACP 54
                                      69************* PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3  11.8   1.3e-09   1.4e-06       2      56 .]       7      54 ..       6      54 .. 0.91
   2 !   21.4   2.3   1.9e-07    0.0002       4      23 ..      38      57 ..      35      67 .] 0.74

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 1.3e-09
                           Fer4_10  2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      +++++d+C  Cg C  +CP+        +++  +++ +   +kC+ c  Cv aCP
  gi|242398972|ref|YP_002994396.1|  7 IIVNEDKCYLCGGCAGVCPS-------LAIKVSSSKWEFFQDKCISCRICVTACP 54
                                      7899****************.......777777888888***************9 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 1.9e-07
                           Fer4_10  4 idddtCirCgkCvkaCPadl 23
                                      + +d+Ci C+ Cv+aCP+ +
  gi|242398972|ref|YP_002994396.1| 38 FFQDKCISCRICVTACPVGA 57
                                      5579*************943 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   8.9     8e-12   8.4e-09       3      57 ..       9      58 ..       6      60 .. 0.88

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 8e-12
                           Fer4_21  3 idedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedci 57
                                      ++edkC  Cg C+ +C+     ai++++ ++++  +d+C+ C +C++ CPv +++
  gi|242398972|ref|YP_002994396.1|  9 VNEDKCYLCGGCAGVCP---SLAIKVSS-SKWEFFQDKCISCRICVTACPV-GAL 58
                                      89***************...58999875.5679*****************9.665 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 !   18.1   0.3   3.8e-06     0.004       1      25 [.      13      36 ..      13      41 .. 0.85
   2 !   21.5   2.6   3.3e-07   0.00035       1      20 [.      42      61 ..      42      67 .] 0.88

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 3.8e-06
                           Fer4_16  1 rCgtCgkCaevCPtnaikekkekei 25
                                      +C  Cg Ca vCP+ aik   + ++
  gi|242398972|ref|YP_002994396.1| 13 KCYLCGGCAGVCPSLAIKVS-SSKW 36
                                      59***************988.4555 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 3.3e-07
                           Fer4_16  1 rCgtCgkCaevCPtnaikek 20
                                      +C++C+ C+ +CP++a++++
  gi|242398972|ref|YP_002994396.1| 42 KCISCRICVTACPVGALEAE 61
                                      6****************987 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   1.3     5e-06    0.0052      32      51 .]      10      29 ..       1      29 [. 0.73
   2 !   28.6  10.9   1.1e-09   1.2e-06       1      50 [.      13      57 ..      13      58 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 5e-06
                            Fer4_9 32 seeaCigCgaCveaCpkgai 51
                                      +e++C+ Cg C+ +Cp+ ai
  gi|242398972|ref|YP_002994396.1| 10 NEDKCYLCGGCAGVCPSLAI 29
                                      3358************8665 PP

  == domain 2  score: 28.6 bits;  conditional E-value: 1.1e-09
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50
                                      kC+ Cg C  +Cp+ +++ ++++ +  ++     +Ci+C+ Cv aCp ga
  gi|242398972|ref|YP_002994396.1| 13 KCYLCGGCAGVCPSLAIKVSSSKWEFFQD-----KCISCRICVTACPVGA 57
                                      7******************9999998874.....6************997 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   1.6    0.0012       1.3       2      15 ..      12      25 ..      11      33 .. 0.92
   2 !   18.5   3.9   1.9e-06    0.0021       1      17 []      40      56 ..      40      56 .. 0.94

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0012
                            Fer4_4  2 erCigCgsCvaaCP 15
                                      ++C  Cg C  +CP
  gi|242398972|ref|YP_002994396.1| 12 DKCYLCGGCAGVCP 25
                                      79999********* PP

  == domain 2  score: 18.5 bits;  conditional E-value: 1.9e-06
                            Fer4_4  1 qerCigCgsCvaaCPqg 17
                                      q++Ci C+ Cv aCP+g
  gi|242398972|ref|YP_002994396.1| 40 QDKCISCRICVTACPVG 56
                                      79*************86 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   1.9   0.00011      0.11       4      18 ..      13      27 ..      10      41 .. 0.73
   2 !   14.5   3.0   3.3e-05     0.035       3      18 ..      41      56 ..      39      64 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
                            Fer4_8  4 kCieCgaCqsaCpvl 18
                                      kC  Cg C   Cp+l
  gi|242398972|ref|YP_002994396.1| 13 KCYLCGGCAGVCPSL 27
                                      677777777777755 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 3.3e-05
                            Fer4_8  3 ekCieCgaCqsaCpvl 18
                                      +kCi C  C +aCpv 
  gi|242398972|ref|YP_002994396.1| 41 DKCISCRICVTACPVG 56
                                      6899999999999875 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.8   0.00017      0.18       1      18 [.       9      26 ..       9      27 .. 0.94
   2 !   13.1   4.3    0.0001      0.11       4      17 ..      41      54 ..      40      55 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00017
                           Fer4_13  1 VDrdtCiacgaCvelaPd 18
                                      V++d+C  cg C+ ++P 
  gi|242398972|ref|YP_002994396.1|  9 VNEDKCYLCGGCAGVCPS 26
                                      899**************7 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.0001
                           Fer4_13  4 dtCiacgaCvelaP 17
                                      d+Ci+c +Cv ++P
  gi|242398972|ref|YP_002994396.1| 41 DKCISCRICVTACP 54
                                      89***********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 !   11.4   2.6   0.00034      0.36      44      58 ..      12      26 ..       2      28 .. 0.83
   2 !   14.3   2.5   4.1e-05     0.044      44      58 ..      41      55 ..      28      59 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00034
                           Fer4_17 44 slCieCgeCerkCPq 58
                                      ++C  Cg+C+ +CP+
  gi|242398972|ref|YP_002994396.1| 12 DKCYLCGGCAGVCPS 26
                                      679999999999996 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 4.1e-05
                           Fer4_17 44 slCieCgeCerkCPq 58
                                      ++Ci+C+ C+++CP 
  gi|242398972|ref|YP_002994396.1| 41 DKCISCRICVTACPV 55
                                      567777777777774 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.8   0.00073      0.77       1      21 [.       7      27 ..       7      31 .. 0.90
   2 !   12.5   1.0   0.00018      0.19       5      19 ..      40      54 ..      38      65 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00073
                           Fer4_15  1 VvvDrdaCigcglCvaeapev 21
                                      + v++d+C  cg C+ ++p +
  gi|242398972|ref|YP_002994396.1|  7 IIVNEDKCYLCGGCAGVCPSL 27
                                      6799**************975 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00018
                           Fer4_15  5 rdaCigcglCvaeap 19
                                      +d+Ci+c  Cv+++p
  gi|242398972|ref|YP_002994396.1| 40 QDKCISCRICVTACP 54
                                      69************8 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   8.8   3.1e-06    0.0033      56      95 ..       9      53 ..       1      60 [. 0.78

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.1e-06
                           Fer4_18 56 kgagdcidcescvkvcPt.gidirkG....lqleciscllcidac 95
                                       ++ +c  c+ c  vcP   i +       +q +cisc  c+ ac
  gi|242398972|ref|YP_002994396.1|  9 VNEDKCYLCGGCAGVCPSlAIKVSSSkwefFQDKCISCRICVTAC 53
                                      56789************63677654323339************** PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   5.1     0.011        12       1      13 [.      14      26 ..      14      28 .. 0.90
   2 ?   15.6   5.3   2.2e-05     0.023       1      15 []      43      57 ..      43      57 .. 0.98

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.011
                            Fer4_3  1 CtgCgaCvevCPv 13
                                      C  Cg C  vCP+
  gi|242398972|ref|YP_002994396.1| 14 CYLCGGCAGVCPS 26
                                      999*99******8 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 2.2e-05
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+ C+ Cv +CPvgA
  gi|242398972|ref|YP_002994396.1| 43 CISCRICVTACPVGA 57
                                      **************9 PP

>> Dynactin_p62  Dynactin p62 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   5.4    0.0014       1.5      18      71 ..       6      62 ..       3      67 .] 0.85

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0014
                      Dynactin_p62 18 RCvteeivtyyCPnCLFevpssnvkseGnR...CtRsCfqCPiCisplavtslenee 71
                                      R +++e  +y C  C    ps  +k   ++       C  C iC++   v +le+e 
  gi|242398972|ref|YP_002994396.1|  6 RIIVNEDKCYLCGGCAGVCPSLAIKVSSSKwefFQDKCISCRICVTACPVGALEAEV 62
                                      88999*******************9777762225789*********99999998865 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   3.5     0.012        13       1      14 [.      13      26 ..      13      35 .. 0.88
   2 ?    9.5   2.6    0.0016       1.7      69      94 ..      30      55 ..      26      58 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.012
                           Fer4_22  1 rClsCgaCtlvCpt 14
                                      +C  Cg C+ vCp+
  gi|242398972|ref|YP_002994396.1| 13 KCYLCGGCAGVCPS 26
                                      79**********97 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0016
                           Fer4_22 69 klsefkekfgesgCvGCgRCieacpv 94
                                      k+s+ k +f + +C+ C  C++acpv
  gi|242398972|ref|YP_002994396.1| 30 KVSSSKWEFFQDKCISCRICVTACPV 55
                                      55556666666677777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 484.71
//
Query:       gi|242398973|ref|YP_002994397.1|  [L=224]
Description: transcription regulator, ArsR family [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.6e-11   42.6   0.0    1.5e-05   25.0   0.0    2.4  2  HTH_20         Helix-turn-helix domain
    8.3e-07   28.8   3.2    7.5e-05   22.5   1.0    2.5  2  HTH_5          Bacterial regulatory protein, arsR family
    4.8e-05   22.8   0.5      0.018   14.6   0.1    2.6  2  HTH_24         Winged helix-turn-helix DNA-binding
    0.00044   20.4   2.7       0.36   11.0   0.2    2.8  3  HTH_34         Winged helix DNA-binding domain
     0.0023   17.9   3.5       0.59   10.1   0.1    2.6  2  HTH_11         HTH domain
     0.0059   16.5   0.1       0.19   11.7   0.0    2.3  2  MarR           MarR family
     0.0076   16.4   0.1       0.02   15.0   0.1    1.7  1  FUR            Ferric uptake regulator family
     0.0079   16.1   0.1        4.9    7.1   0.0    2.2  2  MarR_2         MarR family
  ------ inclusion threshold ------
      0.015   15.1   0.1        1.7    8.5   0.0    2.3  2  HTH_AsnC-type  AsnC-type helix-turn-helix domain
      0.028   14.6   1.0      0.051   13.8   0.4    1.7  2  FliJ           Flagellar FliJ protein
       0.03   14.3   0.2      0.079   12.9   0.0    1.7  2  PadR           Transcriptional regulator PadR-like family
      0.031   13.3   1.7      0.044   12.8   1.7    1.2  1  Paf67          RNA polymerase I-associated factor PAF67
      0.034   14.2   1.0      0.034   14.2   1.0    2.0  2  DHR10          Designed helical repeat protein 10 domain
       0.05   14.2   2.6        1.9    9.1   0.3    2.4  2  SlyX           SlyX
       0.07   13.1   2.5      0.099   12.6   2.5    1.2  1  PBECR5         phage-Barnase-EndoU-ColicinE5/D-RelE like nucl
        0.1   13.2   0.6        5.1    7.8   0.0    2.6  2  Phage_rep_O    Bacteriophage replication protein O
       0.17   11.8   1.8        3.1    7.8   0.4    2.5  2  TrmB           Sugar-specific transcriptional regulator TrmB
       0.85   10.2   5.7          1    9.9   3.0    2.3  2  PCI            PCI domain
        5.4    7.0   8.4       0.57   10.1   1.0    2.9  3  Takusan        Takusan


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   1.6e-08   1.5e-05       2      52 ..       5      54 ..       4      62 .. 0.92
   2 !   15.3   0.0   1.6e-05     0.015       1      50 [.     157     206 ..     157     210 .. 0.94

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1.6e-08
                                      HHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCT CS
                            HTH_20  2 qiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeag 52
                                      +i+++L+++vRr++l++L +  +  +s l   + +s + +s+HL+++e+  
  gi|242398973|ref|YP_002994397.1|  5 DIFYILGNKVRRDLLSHL-TCTECYFSLLSSKVNVSSTAVSRHLKIMERER 54
                                      79****************.9999************************9865 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 1.6e-05
                                       HHHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHH CS
                            HTH_20   1 dqiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLee 50 
                                       d++++ +++ ++++il +L   + +t+++l + l l+  +++  +++L++
  gi|242398973|ref|YP_002994397.1| 157 DKYLKEVGDMTQLAILHYLLLYDTATVEDLSDVLNLKEREVREKVEELSK 206
                                       5789999**************************************99986 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   1.0   7.9e-08   7.5e-05       2      46 ..      13      57 ..      12      58 .. 0.92
   2 ?    6.0   0.0     0.011        10       2      27 ..     166     192 ..     165     199 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 7.9e-08
                                      HHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  2 ptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      + R+++L+ L   e++++ l+ ++++s  +vS+HLk+++ +++++
  gi|242398973|ref|YP_002994397.1| 13 KVRRDLLSHLTCTECYFSLLSSKVNVSSTAVSRHLKIMERERVLK 57
                                      679999999999***************************998876 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.011
                                       HHHHHHHHHHTT.SSEEHHHHHHHHTS CS
                             HTH_5   2 ptRlkILklLae.gelcvcelaeelgl 27 
                                        t+l IL++L     ++v +l++ l+l
  gi|242398973|ref|YP_002994397.1| 166 MTQLAILHYLLLyDTATVEDLSDVLNL 192
                                       5899********899********9998 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   1.9e-05     0.018      23      47 ..      32      56 ..      29      57 .. 0.89
   2 !    6.0   0.0    0.0091       8.6       4      41 ..     167     204 ..     165     206 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.9e-05
                            HTH_24 23 LAerlglSpstvnrrlkrLeeeGlI 47
                                      L+ ++++S+++v+r+lk +e+e ++
  gi|242398973|ref|YP_002994397.1| 32 LSSKVNVSSTAVSRHLKIMERERVL 56
                                      899*****************98765 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0091
                            HTH_24   4 tdrkILelLqknprisqreLAerlglSpstvnrrlkrL 41 
                                       t+++IL +L      +  +L++ l+l    v++ +++L
  gi|242398973|ref|YP_002994397.1| 167 TQLAILHYLLLYDTATVEDLSDVLNLKEREVREKVEEL 204
                                       7899**********************999888888877 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 !    8.8   0.0    0.0019       1.8      13      42 ..      25      54 ..      14      65 .. 0.80
   2 ?   -2.2   0.0       5.2   4.9e+03      45      61 ..     107     123 ..     101     144 .. 0.52
   3 !   11.0   0.2   0.00038      0.36       2      49 ..     168     215 ..     167     222 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0019
                            HTH_34 13 deadfvelkealeatdgnLsvhlkkLekag 42
                                       e  f+ l++++++++ + s hlk++e  +
  gi|242398973|ref|YP_002994397.1| 25 TECYFSLLSSKVNVSSTAVSRHLKIMERER 54
                                      5789**********************9876 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 5.2
                            HTH_34  45 evdkefkgkkprtllri 61 
                                       e++++  +k p+ l ++
  gi|242398973|ref|YP_002994397.1| 107 EIKLNELEKFPQDLHSM 123
                                       55555555555544443 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00038
                            HTH_34   2 RlavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdke 49 
                                        la+l+yL+  d a+ ++l++ l++ + +   +++ L k   i ++k+
  gi|242398973|ref|YP_002994397.1| 168 QLAILHYLLLYDTATVEDLSDVLNLKEREVREKVEELSKVVPIIIKKN 215
                                       59***********************99999999999988888887776 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.1   0.00063      0.59      21      41 ..      32      52 ..      29      57 .. 0.89
   2 !    7.7   0.7    0.0035       3.3       2      49 ..     168     213 ..     167     218 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00063
                            HTH_11 21 LAeeLnvSrrtvrrdIkaLee 41
                                      L+ + nvS ++v r++k++e 
  gi|242398973|ref|YP_002994397.1| 32 LSSKVNVSSTAVSRHLKIMER 52
                                      8999*************9986 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0035
                            HTH_11   2 llqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvpIese 49 
                                       +l+il+ Ll  +   + e+L++ Ln+ +r vr  +++L++   pI+ +
  gi|242398973|ref|YP_002994397.1| 168 QLAILHYLLLYDT-ATVEDLSDVLNLKEREVREKVEELSKVV-PIIIK 213
                                       6899999988887.8***********************9985.66544 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0    0.0002      0.19      19      47 ..      28      56 ..      24      63 .. 0.81
   2 ?    2.5   0.0      0.15   1.4e+02       3      30 ..     166     193 ..     165     204 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0002
                                      EHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                              MarR 19 svseLakklgvskstvtrvldrLekkGli 47
                                      + s L +k++vs+++v+r l+ +e++  +
  gi|242398973|ref|YP_002994397.1| 28 YFSLLSSKVNVSSTAVSRHLKIMERERVL 56
                                      567799******************97555 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.15
                                       HHHHHHHHHHHHSTTEEHHHHHHHHTS- CS
                              MarR   3 ltqfviLrilyeqgplsvseLakklgvs 30 
                                       +tq+ iL+ l   + ++v +L + l+++
  gi|242398973|ref|YP_002994397.1| 166 MTQLAILHYLLLYDTATVEDLSDVLNLK 193
                                       79********************999986 PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   2.1e-05      0.02      22      65 ..      20      63 ..      12      78 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.1e-05
                                      SSBEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEETT CS
                               FUR 22 ehlsaeevykelkeedpeislaTVYrtLklleeaglvkelefed 65
                                       hl+  e y +l + + ++s + V r Lk++e++ ++k+ e e+
  gi|242398973|ref|YP_002994397.1| 20 SHLTCTECYFSLLSSKVNVSSTAVSRHLKIMERERVLKSYEKEE 63
                                      5*************************************999876 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0    0.0052       4.9       8      48 ..      16      53 ..      14      63 .. 0.88
   2 !    6.8   0.0    0.0067       6.4       6      38 ..     167     197 ..     164     206 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0052
                                      HHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHT CS
                            MarR_2  8 arvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaa 48
                                      +++L +L + +   +  + l  + ++s  avsr+lk +++ 
  gi|242398973|ref|YP_002994397.1| 16 RDLLSHLTCTE---CYFSLLSSKVNVSSTAVSRHLKIMERE 53
                                      78999999999...99999*****************99876 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0067
                                       HHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHH CS
                            MarR_2   6 aqarvLaaLgrrpgrdltvgelarrlglsksav 38 
                                       +q+ +L++L   +    tv +l + l+l+   v
  gi|242398973|ref|YP_002994397.1| 167 TQLAILHYLLLYDT--ATVEDLSDVLNLKEREV 197
                                       899**********9..9*********9976555 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 ?    4.4   0.0     0.035        33      23      41 ..      32      50 ..      29      51 .. 0.83
   2 ?    8.5   0.0    0.0018       1.7       7      41 ..     170     204 ..     165     205 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.035
                     HTH_AsnC-type 23 LAervGlSestvlrRvrrL 41
                                      L+ +v++S ++v r ++ +
  gi|242398973|ref|YP_002994397.1| 32 LSSKVNVSSTAVSRHLKIM 50
                                      899*********9977766 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0018
                     HTH_AsnC-type   7 kILeaLqedaRisyaeLAervGlSestvlrRvrrL 41 
                                       +IL+ L     +++++L++ ++l e +v++ v+ L
  gi|242398973|ref|YP_002994397.1| 170 AILHYLLLYDTATVEDLSDVLNLKEREVREKVEEL 204
                                       6777777777899*****************99887 PP

>> FliJ  Flagellar FliJ protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0         3   2.8e+03      13      32 ..     102     121 ..     101     129 .. 0.72
   2 ?   13.8   0.4   5.4e-05     0.051       6      83 ..     126     205 ..     121     208 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 3
                              FliJ  13 elqqaeekleeleqyrqeyq 32 
                                       +l++ e kl+ele+  q+++
  gi|242398973|ref|YP_002994397.1| 102 KLEKLEIKLNELEKFPQDLH 121
                                       56777888888888777665 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 5.4e-05
                              FliJ   6 eLaeaqrelqqaeekleeleqyrqeyqkqlsgea.q.glsaaelrnyqafisaldeaiaqqkqelaqaekqvekare 80 
                                       ++ +a+++l+q  e l ++e+yr++++k+l++++ +   ++ +l +++  + +   +++ +  +l+ +e++v ++ e
  gi|242398973|ref|YP_002994397.1| 126 AFINANKKLEQVIEALKNIESYRNNLMKNLKDKYlKeVGDMTQLAILHYLLLYDTATVEDLSDVLNLKEREVREKVE 202
                                       57789*****************************99899999999999999999999999*********99999988 PP

                              FliJ  81 ewq 83 
                                       e+ 
  gi|242398973|ref|YP_002994397.1| 203 ELS 205
                                       886 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   8.4e-05     0.079      27      66 ..      36      76 ..      30      78 .. 0.88
   2 ?   -2.7   0.0       6.5   6.2e+03       2      22 ..     138     158 ..     137     162 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.4e-05
                                      CCTTHHHHHHHHHHHHHTTSEEEEEE-S.TSSS-EEEEEES CS
                              PadR 27 lelseGslYpaLkrLekeglvesewees.gegpprkyYrlT 66
                                      +++s + + + Lk +e+e++++s+++e+   gp+rkyY ++
  gi|242398973|ref|YP_002994397.1| 36 VNVSSTAVSRHLKIMERERVLKSYEKEEgFIGPTRKYYSIA 76
                                      56788888899*****************889*******985 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 6.5
                                       HHHHCCS-EEHHHHHHHHHCC CS
                              PadR   2 LalleeqpsyGyeiikeleel 22 
                                       ++ l++ +sy  +++k+l++ 
  gi|242398973|ref|YP_002994397.1| 138 IEALKNIESYRNNLMKNLKDK 158
                                       566777777777888888765 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 ?   12.8   1.7   4.7e-05     0.044     269     347 ..     126     204 ..      98     221 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.7e-05
                             Paf67 269 kfispaapdledaeaeed.ansekealkrqlklFlkevkqqkklptlrsylkLYttislekLasllevdeeelrsqL 344
                                        fi+++++  +  ea ++ +++ ++ +k+  + +lkev   ++l ++  yl LY t ++e L+ +l+++e e+r+++
  gi|242398973|ref|YP_002994397.1| 126 AFINANKKLEQVIEALKNiESYRNNLMKNLKDKYLKEVGDMTQL-AILHYLLLYDTATVEDLSDVLNLKEREVREKV 201
                                       58888877555566666645556***************777666.6779***********************99988 PP

                             Paf67 345 lsl 347
                                         l
  gi|242398973|ref|YP_002994397.1| 202 EEL 204
                                       765 PP

>> DHR10  Designed helical repeat protein 10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   1.0   3.6e-05     0.034       8      55 ..     107     154 ..     100     162 .. 0.72
   2 ?   -0.7   0.2       1.5   1.4e+03      59      77 ..     183     201 ..     179     207 .. 0.57

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.6e-05
                             DHR10   8 keelaelErkarelqakidalqvvekdlrsciklleeieaelakleea 55 
                                         +l+elE+  ++l+  i+a+ ++ k l+++i++l+ ie+  + l + 
  gi|242398973|ref|YP_002994397.1| 107 EIKLNELEKFPQDLHSMIKAFINANKKLEQVIEALKNIESYRNNLMKN 154
                                       445778888888888888888888888888888888888777766654 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.5
                             DHR10  59 lkelrdaleekeielrele 77 
                                       +++l+d l+ ke+e+re  
  gi|242398973|ref|YP_002994397.1| 183 VEDLSDVLNLKEREVREKV 201
                                       5566666666666666543 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.3     0.002       1.9       3      45 ..     101     143 ..     100     158 .. 0.85
   2 ?    4.9   0.1     0.044        42      11      41 ..     175     205 ..     167     211 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.002
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              SlyX   3 erleeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllae 45 
                                       e+le+LEikl  +e++ ++L  ++ +     ++l++ +++l++
  gi|242398973|ref|YP_002994397.1| 101 EKLEKLEIKLNELEKFPQDLHSMIKAFINANKKLEQVIEALKN 143
                                       689******************9998888888888888777765 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.044
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              SlyX  11 klafqedtieeLndvvaeqqqqidrlqrqlr 41 
                                        l +   t+e+L+dv+   ++++ +  ++l 
  gi|242398973|ref|YP_002994397.1| 175 LLLYDTATVEDLSDVLNLKEREVREKVEELS 205
                                       5678889*********999999988777766 PP

>> PBECR5  phage-Barnase-EndoU-ColicinE5/D-RelE like nuclease5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   2.5   0.00011     0.099      95     201 ..     101     206 ..      97     223 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00011
                            PBECR5  95 kklkeiedkieqlsrelaegafaraaslsqgqdmkdqltsegsekeLaekllndeavkaaYLadkGeevevayveke 171
                                       +kl+++e k+++l ++ ++     +a  +  ++++++++  ++++   ++l+++  +k  YL++ G+  + a+++  
  gi|242398973|ref|YP_002994397.1| 101 EKLEKLEIKLNELEKFPQDLHSMIKAFINANKKLEQVIEALKNIESYRNNLMKN--LKDKYLKEVGDMTQLAILHYL 175
                                       789999********************9999*************99999999877..4799***************99 PP

                            PBECR5 172 ktfteeqvevlekltdalgddeee..geelae 201
                                         ++   ve+l+ + +  ++ e +  +eel++
  gi|242398973|ref|YP_002994397.1| 176 LLYDTATVEDLSDVLNL-KEREVRekVEELSK 206
                                       9*********9999765.33333223444444 PP

>> Phage_rep_O  Bacteriophage replication protein O
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0    0.0054       5.1      55      87 ..      32      64 ..      23      72 .. 0.87
   2 ?    3.1   0.3      0.15   1.4e+02      53      88 ..     184     219 ..     147     223 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0054
                       Phage_rep_O 55 lveltgisrtkvskalkeLirekviikegrkvg 87
                                      l+  +++s+t+vs+ lk + re+v++  +++ g
  gi|242398973|ref|YP_002994397.1| 32 LSSKVNVSSTAVSRHLKIMERERVLKSYEKEEG 64
                                      677899*******************99887765 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.15
                       Phage_rep_O  53 sqlveltgisrtkvskalkeLirekviikegrkvgv 88 
                                       ++l+++ ++++++v++ ++eL +   ii++++ + +
  gi|242398973|ref|YP_002994397.1| 184 EDLSDVLNLKEREVREKVEELSKVVPIIIKKNIIKI 219
                                       678888889999888888888887766666655554 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0      0.13   1.2e+02      13      46 ..      27      50 ..      25      76 .. 0.61
   2 ?    7.8   0.4    0.0033       3.1      14      48 ..     172     206 ..     167     214 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.13
                                      HCHHHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHH CS
                              TrmB 13 vYlaLl.klgpatadeiaeelgvprskvYevLrsL 46
                                      +Y+ Ll ++ + + + ++++l++           +
  gi|242398973|ref|YP_002994397.1| 27 CYFSLLsSKVNVSSTAVSRHLKI-----------M 50
                                      55555544445555555555554...........3 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0033
                                       CHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHH CS
                              TrmB  14 YlaLlklgpatadeiaeelgvprskvYevLrsLed 48 
                                         +Ll ++ at+++++  l++ +  v e +++L++
  gi|242398973|ref|YP_002994397.1| 172 LHYLLLYDTATVEDLSDVLNLKEREVREKVEELSK 206
                                       568999*********************99999976 PP

>> PCI  PCI domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       1.6   1.5e+03      59      80 ..      25      46 ..       8      61 .. 0.70
   2 ?    9.9   3.0    0.0011         1      14      75 ..     143     202 ..     107     220 .. 0.58

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.6
                                      SEEEHHHHHHHHTSSHHHHHHH CS
                               PCI 59 ssislerlaklldlsvdevEki 80
                                      +   ++ l++++++s+  v + 
  gi|242398973|ref|YP_002994397.1| 25 TECYFSLLSSKVNVSSTAVSRH 46
                                      5567888899999888766554 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0011
                                       SHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHCESEEEHHHHHHHHTSSH.......H CS
                               PCI  14 nlsgfseelkdleeelladdglaqllesLekkvrerllrqvskiyssislerlaklldlsv.......d 75 
                                       n+++++ +l ++    l+d+    +l+++ + +++ ++  + + y + ++e+l++ l+l++       +
  gi|242398973|ref|YP_002994397.1| 143 NIESYRNNLMKN----LKDK----YLKEVGD-MTQLAILHYLLLYDTATVEDLSDVLNLKErevrekvE 202
                                       233333333333....3333....3333322.333333355569*****************66663333 PP

>> Takusan  Takusan
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1       1.7   1.6e+03      18      31 ..     102     115 ..      98     130 .. 0.52
   2 ?   10.1   1.0    0.0006      0.57      15      41 ..     130     156 ..     122     168 .. 0.90
   3 ?   -0.1   0.1      0.93   8.8e+02       9      23 ..     191     205 ..     186     214 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.7
                           Takusan  18 klEeLkleLrkitr 31 
                                       klE+L  +L  +++
  gi|242398973|ref|YP_002994397.1| 102 KLEKLEIKLNELEK 115
                                       45555444444333 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0006
                           Takusan  15 akkklEeLkleLrkitreRdELrdiLa 41 
                                       a+kklE+++  L++i++ R+ L + L 
  gi|242398973|ref|YP_002994397.1| 130 ANKKLEQVIEALKNIESYRNNLMKNLK 156
                                       79*********************9997 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.93
                           Takusan   9 ilekeqakkklEeLk 23 
                                        l+++++ +k+EeL 
  gi|242398973|ref|YP_002994397.1| 191 NLKEREVREKVEELS 205
                                       578999999999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1624  (0.0905795); expected 358.6 (0.02)
Passed bias filter:                      746  (0.0416086); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); 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: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 1486.23
//
Query:       gi|242398974|ref|YP_002994398.1|  [L=224]
Description: Protein disulfide oxidoreductase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.7e-24   83.7   0.0      6e-15   55.0   0.0    2.4  2  Thioredoxin_3   Thioredoxin domain
    8.5e-13   48.2   0.1    5.3e-05   23.1   0.0    2.1  2  Thioredoxin     Thioredoxin
    1.1e-12   48.1   0.0      2e-07   30.8   0.0    2.0  2  ABC_transp_aux  ABC-type uncharacterized transport system
      1e-10   41.7   4.9    2.2e-06   27.8   0.5    3.5  3  Glutaredoxin    Glutaredoxin
    4.3e-10   40.0   6.0     0.0036   17.7   0.2    4.1  2  Thioredoxin_2   Thioredoxin-like domain
    1.9e-07   30.9   0.0    0.00024   20.8   0.0    2.2  2  Thioredoxin_9   Thioredoxin
    5.8e-07   29.6   0.4    0.00077   19.3   0.0    2.9  2  TraF            F plasmid transfer operon protein
    4.4e-06   27.0   1.2    0.00026   21.3   0.4    2.5  2  DUF836          Glutaredoxin-like domain (DUF836)
     0.0028   17.9   0.3         13    6.2   0.0    3.5  3  Thioredoxin_8   Thioredoxin-like
     0.0035   17.5   0.1        0.3   11.3   0.0    2.4  2  Thioredoxin_7   Thioredoxin-like
     0.0059   16.3   0.0        1.3    8.8   0.0    2.4  2  KaiB            KaiB domain
  ------ inclusion threshold ------
      0.037   14.0   0.3        7.2    6.6   0.0    3.0  4  AhpC-TSA        AhpC/TSA family
       0.13   12.7   0.0        3.5    8.0   0.0    2.1  2  Syntaxin_2      Syntaxin-like protein
       0.15   12.0   0.0        1.3    9.0   0.0    2.2  2  HyaE            Hydrogenase-1 expression protein HyaE
       0.17   12.0   0.0         19    5.4   0.0    2.4  2  TrbC_Ftype      Type-F conjugative transfer system pilin asse


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 !   26.5   0.0   4.1e-09   4.9e-06       5      71 ..      28     102 ..      24     107 .. 0.78
   2 !   55.0   0.0     5e-18     6e-15       2      76 .]     135     221 ..     132     221 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 4.1e-09
                                       E.ESSS.STTCHHHHHHHHHHCHCCT.CECEEECCTTHHHH.HHCT-SSSSEEEC..TTC...EEEESS---CCHH CS
                     Thioredoxin_3   5 v.lgpg.CakCpklekavkeaaaekg.ikaevekvtdfeei.ekygVmsvPalvi..dgk...vvvsGkvpseeei 71 
                                       v +g+  C++C++l+++v+e+ + ++ +++e+++    +e+ eky++   Pa+v+  +gk   v++ G +p + e+
  gi|242398974|ref|YP_002994398.1|  28 VfIGKDhCQYCDQLKQLVEEISELSDlVTYELHDFDSEKELaEKYRIDIAPAVVMtqNGKdlgVRYFG-LPAGHEF 102
                                       5455555******************87**************************873345544466666.6666655 PP

  == domain 2  score: 55.0 bits;  conditional E-value: 5e-18
                                       EEEE.ESSSSTTCH.HHHHHHHHHCHCC.....TCECEEECCTTHHHH.HHCT-SSSSEEECT....TCEEEESS-- CS
                     Thioredoxin_3   2 eikv.lgpgCakCp.klekavkeaaaek.....gikaevekvtdfeei.ekygVmsvPalvid....gkvvvsGkvp 66 
                                       +i v ++p+C++Cp ++++a+k a++       +i  +++++ +f+e+ e+ygVm+vP++vi     +k+ ++G+ p
  gi|242398974|ref|YP_002994398.1| 135 QIYVfVTPTCPYCPmAVRMAHKFAIEHAlagndRILGDMIEAIEFPELaEQYGVMAVPKVVIKvngeDKISFEGAYP 211
                                       688888********87777777776643221014666************************988899********** PP

                                       -CCHHHHHHH CS
                     Thioredoxin_3  67 seeeirklle 76 
                                       ++ +++klle
  gi|242398974|ref|YP_002994398.1| 212 EKMFLEKLLE 221
                                       ********96 PP

>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   4.5e-08   5.3e-05       6      84 ..      12      88 ..       8     107 .. 0.84
   2 !   23.1   0.0   4.4e-08   5.3e-05      12      98 ..     125     216 ..     117     221 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 4.5e-08
                                      SHHHHHHHHTTTSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEEETTEE CS
                       Thioredoxin  6 tkenFeeevakekklvlveFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlklfkngke 84
                                       ke+F +++ +   ++lv    + C  C +l+  +e+++e l+d v+    d d++++la+ky ++  P++++++ngk 
  gi|242398974|ref|YP_002994398.1| 12 IKEEFFSKLVN-PVKLLVFIGKDHCQYCDQLKQLVEEISE-LSDLVTYELHDFDSEKELAEKYRIDIAPAVVMTQNGKD 88
                                      46777777777.57777877889**********9999975.6769999999**************************94 PP

  == domain 2  score: 23.1 bits;  conditional E-value: 4.4e-08
                                       HHHTT.TSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTT....TSEEEEEETTTSHHHHHHTT-SSSSEEEEEETTE CS
                       Thioredoxin  12 eevak.ekklvlveFyApwCghCkalaPeleklaeelkd....kvklakvdvdenedlakkyevegiPtlklfkngk 83 
                                       e++++ +k+  +  F  p C+ C +   + +k+a e++     ++    +++ e ++la++y+v ++P++++  ng+
  gi|242398974|ref|YP_002994398.1| 125 EALKEiNKDVQIYVFVTPTCPYCPMAVRMAHKFAIEHALagndRILGDMIEAIEFPELAEQYGVMAVPKVVIKVNGE 201
                                       4555522344455689999999999888888877766555576888889**************************** PP

                                       EEEEEESS-HHHHHH CS
                       Thioredoxin  84 evkkyegarekekla 98 
                                          ++ega +++ + 
  gi|242398974|ref|YP_002994398.1| 202 DKISFEGAYPEKMFL 216
                                       ********8866554 PP

>> ABC_transp_aux  ABC-type uncharacterized transport system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   8.3e-06    0.0099      18     108 ..      15      95 ..      13     102 .. 0.78
   2 !   30.8   0.0   1.7e-10     2e-07      11     111 ..     118     215 ..     112     221 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 8.3e-06
                    ABC_transp_aux  18 ellknleepvtikvylsenlalppelkalekevkdlLeeyaaysggkisvefidpspneeeeeeaeay..gitpvqi 92 
                                       e+ ++l +pv++ v++ ++      + ++ +++k+l ee  + s+  +++e +d ++++   e+ae+y  +i p+ +
  gi|242398974|ref|YP_002994398.1|  15 EFFSKLVNPVKLLVFIGKD------HCQYCDQLKQLVEEISELSD-LVTYELHDFDSEK---ELAEKYriDIAPAVV 81 
                                       56789999**********9......6789**************99.*********9655...666666447777666 PP

                    ABC_transp_aux  93 sveekdelktkrvymg 108
                                        +++ ++    + y+g
  gi|242398974|ref|YP_002994398.1|  82 MTQN-GK-DLGVRYFG 95 
                                       6553.33.33555555 PP

  == domain 2  score: 30.8 bits;  conditional E-value: 1.7e-10
                    ABC_transp_aux  11 tLsdatkellknleepvtikvylsenlalppelkalekevkdlLeeyaaysggkisvefidpspneeeeeeaeaygi 87 
                                        Ls++tke+lk+++++v+i+v++++     p  +   ++++++  e a +++++i  ++i++ +++   e+ae+yg+
  gi|242398974|ref|YP_002994398.1| 118 DLSEETKEALKEINKDVQIYVFVTPT---CPYCPMAVRMAHKFAIEHALAGNDRILGDMIEAIEFP---ELAEQYGV 188
                                       59************************...46667789*****************************...89999977 PP

                    ABC_transp_aux  88 tpvq...isveekdelktkrvymglvi 111
                                        +v+   i+v+++d+++++ +y+  ++
  gi|242398974|ref|YP_002994398.1| 189 MAVPkvvIKVNGEDKISFEGAYPEKMF 215
                                       7666666**************997666 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   8.4e-05       0.1       3      40 ..      29      71 ..      27      86 .. 0.80
   2 ?   -0.1   0.1       0.9   1.1e+03      29      44 ..     110     130 ..     104     135 .. 0.66
   3 !   27.8   0.5   1.9e-09   2.2e-06       2      56 ..     137     197 ..     136     201 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.4e-05
                                      EEESTSSHHHHHHHHHHHHTT.....GGEEEEEGCCSHHHHHH CS
                      Glutaredoxin  3 lftkptCpyCkkakrlLkelg.....vkfeeidvdkdeeiree 40
                                        +k  C yC + k+l +e       v +e +d d ++e+ e+
  gi|242398974|ref|YP_002994398.1| 29 FIGKDHCQYCDQLKQLVEEISelsdlVTYELHDFDSEKELAEK 71
                                      56799************99998877777888888887776665 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.9
                                       EEGCCSH.....HHHHHHHHH CS
                      Glutaredoxin  29 idvdkde.....eireelkel 44 
                                       +dv+k e     e +e+lke+
  gi|242398974|ref|YP_002994398.1| 110 VDVSKGEtdlseETKEALKEI 130
                                       566665554555788888876 PP

  == domain 3  score: 27.8 bits;  conditional E-value: 1.9e-09
                                       EEEESTSSHHHHHHHHHHHHTTGG...EEEEEGCCSH...HHHHHHHHHHTSSSSSEEEET CS
                      Glutaredoxin   2 vlftkptCpyCkkakrlLkelgvk...feeidvdkde...eireelkelsgvrtvPqvfid 56 
                                        +f++ptCpyC++a+r ++++ ++        ++ d+    +  el e  gv++vP v+i+
  gi|242398974|ref|YP_002994398.1| 137 YVFVTPTCPYCPMAVRMAHKFAIEhalAGNDRILGDMieaIEFPELAEQYGVMAVPKVVIK 197
                                       69********************9944422223444443454445555555********984 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.2     3e-06    0.0036       8      90 ..      26      87 ..      22     102 .. 0.66
   2 !   14.1   1.4   4.1e-05     0.049       4     109 .]     131     219 ..     128     219 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3e-06
                     Thioredoxin_2  8 vlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgtPtiv. 85
                                      +lv++ +++C yC++lk+ ++e++++ +             +  ++   +          +++ela+ky+++  P++v 
  gi|242398974|ref|YP_002994398.1| 26 LLVFIGKDHCQYCDQLKQLVEEISELSDL------------VTYELHDFD----------SEKELAEKYRIDIAPAVVm 82
                                      455666**************999777555............222222222..........2346777788888887664 PP

                     Thioredoxin_2 86 fldgk 90
                                      + +gk
  gi|242398974|ref|YP_002994398.1| 83 TQNGK 87
                                      55555 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 4.1e-05
                     Thioredoxin_2   4 ngkpvlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrg 80 
                                       n+   ++vf +p+CpyC    +   +  +++       l  + + +  ++  a e +          ela++ygv +
  gi|242398974|ref|YP_002994398.1| 131 NKDVQIYVFVTPTCPYCPMAVRMAHKF-AIEHA-----LAGN-DRILGDMIEAIEFP----------ELAEQYGVMA 190
                                       778899***********8754444444.44444.....6666.34444444444444..........7********* PP

                     Thioredoxin_2  81 tPtiv.fldgk.eivarlpGyvpaeeleall 109
                                       +P +v   +g+ +i    +G++p++ +++ l
  gi|242398974|ref|YP_002994398.1| 191 VPKVViKVNGEdKI--SFEGAYPEKMFLEKL 219
                                       ***66488888666..789*****9998865 PP

>> Thioredoxin_9  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0    0.0021       2.5      36     109 ..      17      87 ..       8      99 .. 0.78
   2 !   20.8   0.0     2e-07   0.00024      25     120 ..     116     213 ..     111     220 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0021
                                       HHT--S-EEEEE.E--TT-HHHHHHHHHHHHHHHH-TTEEEEEE-HHHHHHHTTTTTT-SS--SSEEEEE-TT-- CS
                     Thioredoxin_9  36 iksiekklkilv.ltedwCgDaavnvPvlakiaelnpnievkillrdenlelmdqyltngaraiPtliildeege 109
                                        +++ +++k+lv + +d C  + +    +++i+el++ ++ ++   d+++el ++y+ +     P++++  ++g+
  gi|242398974|ref|YP_002994398.1|  17 FSKLVNPVKLLVfIGKDHCQYCDQLKQLVEEISELSDLVTYELHDFDSEKELAEKYRID---IAPAVVMT-QNGK 87 
                                       55666788888845899***************************************763...33444443.4444 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 2e-07
                                       HHHHH---HHHHHT--S-EEEEEE--TT-HHHHHHHHHHHHHHHH.....-TTEEEEEE-HHHHHHHTTTTTT-SS- CS
                     Thioredoxin_9  25 kvelseeteekiksiekklkilvltedwCgDaavnvPvlakiael.....npnievkillrdenlelmdqyltngar 96 
                                       ++ lseet+e++k+i+k+++i v+ ++ C+ + + v + +k+a +     n++i  +++   e +el +qy   g  
  gi|242398974|ref|YP_002994398.1| 116 ETDLSEETKEALKEINKDVQIYVFVTPTCPYCPMAVRMAHKFAIEhalagNDRILGDMIEAIEFPELAEQY---GVM 189
                                       5789*****************************99999999885512222566777777777777777887...999 PP

                                       -SSEEEEE-TT--EEEEEESS-HH CS
                     Thioredoxin_9  97 aiPtliildeegeelgvwgerPae 120
                                       a+P+++i  ++  ++   g +P++
  gi|242398974|ref|YP_002994398.1| 190 AVPKVVIKVNGEDKISFEGAYPEK 213
                                       ******999998888877888876 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.1    0.0052       6.3     121     160 ..      14      54 ..       8      91 .. 0.68
   2 !   19.3   0.0   6.5e-07   0.00077     118     201 ..     121     199 ..     116     206 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0052
                              TraF 121 eaalkklakeygLlfFyr.gkcpyceaqapilqafadkygl 160
                                       e++ +kl + + Ll+F    +c+yc+++ + ++++ +   l
  gi|242398974|ref|YP_002994398.1|  14 EEFFSKLVNPVKLLVFIGkDHCQYCDQLKQLVEEISELSDL 54 
                                       566667777777787776266******99999988775554 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 6.5e-07
                              TraF 118 eekeaalkklakeygLlfFyrgkcpyceaqapilqafadkyglevr.aVsvdgrplpelpnarvdkgqaarlgvkrt 193
                                       ee+++alk++ k++ + +F+ ++cpyc +++ +  +fa ++ l+    +  d     e+p+       a+++gv  +
  gi|242398974|ref|YP_002994398.1| 121 EETKEALKEINKDVQIYVFVTPTCPYCPMAVRMAHKFAIEHALAGNdRILGDMIEAIEFPE------LAEQYGVMAV 191
                                       78999*********************************99988643123333333333555......7778888888 PP

                              TraF 194 Palvlvdp 201
                                       P +v+   
  gi|242398974|ref|YP_002994398.1| 192 PKVVIKVN 199
                                       87777555 PP

>> DUF836  Glutaredoxin-like domain (DUF836)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.4   2.2e-07   0.00026       2      57 ..      27      85 ..      26     128 .. 0.83
   2 ?    4.2   0.0      0.05        60       2      23 ..     136     157 ..     135     206 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 2.2e-07
                                      EEEEE-TT-HHHHHHHHHHHHHCCCTT.EEEEEEETTT-CCCHCCCCTTT.T.EEEECT CS
                            DUF836  2 ltLyskpgChlCeqakekLkelkleeg.leleviDIakdeeleakYglei.p.vlaleg 57
                                      l++++k++C  C+q+k++++e+++ ++ ++ e  D ++++el +kY  +i p v+++++
  gi|242398974|ref|YP_002994398.1| 27 LVFIGKDHCQYCDQLKQLVEEISELSDlVTYELHDFDSEKELAEKYRIDIaPaVVMTQN 85
                                      7899****************965544448888889999999*****9998432444444 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.05
                                       EEEEE-TT-HHHHHHHHHHHHH CS
                            DUF836   2 ltLyskpgChlCeqakekLkel 23 
                                       +  +++p C+ C  a    +++
  gi|242398974|ref|YP_002994398.1| 136 IYVFVTPTCPYCPMAVRMAHKF 157
                                       889*********8665555544 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1     0.018        22      57      88 ..      51      82 ..      27      88 .. 0.56
   2 ?   -2.3   0.0       4.7   5.6e+03      26      38 ..     123     136 ..     109     151 .. 0.60
   3 ?    6.2   0.0      0.01        13      73      88 ..     181     196 ..     174     201 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.018
                                      S-TTSEE.EE-TT-.HHHHTT-S--TT-SEEEE CS
                     Thioredoxin_8 57 nkkpwlsvpfddkk.rnklkkkynvkaiPtlvv 88
                                         + + ++ +d +  ++l++ky++   P +v 
  gi|242398974|ref|YP_002994398.1| 51 L-SDLVTYELHDFDsEKELAEKYRIDIAPAVVM 82
                                      2.4666677777654668888888887777554 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4.7
                                       HHHHHHH.TTSEEE CS
                     Thioredoxin_8  26 lyeklkk.kkkvei 38 
                                        +e lk+ +k+v+i
  gi|242398974|ref|YP_002994398.1| 123 TKEALKEiNKDVQI 136
                                       33444444444444 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.01
                                       HHTT-S--TT-SEEEE CS
                     Thioredoxin_8  73 klkkkynvkaiPtlvv 88 
                                       +l+++y+v+a+P++v+
  gi|242398974|ref|YP_002994398.1| 181 ELAEQYGVMAVPKVVI 196
                                       799**********765 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   0.00025       0.3      19      44 ..      25      50 ..      22      82 .. 0.87
   2 ?    3.8   0.0     0.055        66       7      33 ..     121     148 ..     117     161 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00025
                                      -EEEEE--TT-HHHHHHHHHHHH-HH CS
                     Thioredoxin_7 19 pvlvffgaswcftCqalerdflsdee 44
                                       +lvf+g++ c +C  l++ +++  e
  gi|242398974|ref|YP_002994398.1| 25 KLLVFIGKDHCQYCDQLKQLVEEISE 50
                                      68****************99987655 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.055
                                       HHHHHHHHHHT--EEE.EE--TT-HHHH CS
                     Thioredoxin_7   7 dealakaaergkpvlv.ffgaswcftCq 33 
                                       +e +++++e +k+v + +f   +c++C 
  gi|242398974|ref|YP_002994398.1| 121 EETKEALKEINKDVQIyVFVTPTCPYCP 148
                                       67889999999999998889999*9995 PP

>> KaiB  KaiB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.016        20      13      56 ..      40      81 ..      27      84 .. 0.74
   2 !    8.8   0.0    0.0011       1.3      34      58 ..     173     198 ..     159     213 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.016
                                      HHHHHHHHHCCCHCTTTEEEEEEETTTSHCHHCCTCEESCCCCC CS
                              KaiB 13 ralenlkkleeedlgfqyeLqvvdvleqPelaeedrlvatPaLi 56
                                      +++++++++ e +  + yeL   d   + elae++r+ + Pa +
  gi|242398974|ref|YP_002994398.1| 40 QLKQLVEEISELSDLVTYELH--DFDSEKELAEKYRIDIAPAVV 81
                                      666777777777666666665..6667779***********987 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0011
                                       EEETTTSHCHHCCTCEESCCCC.CCC CS
                              KaiB  34 vvdvleqPelaeedrlvatPaL.ikl 58 
                                       +++  e Pelae++ ++a+P   ik+
  gi|242398974|ref|YP_002994398.1| 173 MIEAIEFPELAEQYGVMAVPKVvIKV 198
                                       6888899*************641565 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0     0.006       7.2      27      56 ..      24      52 ..       5      59 .. 0.80
   2 ?   -1.8   0.0       2.4   2.8e+03      89     101 ..      63      75 ..      59      85 .. 0.81
   3 ?    3.8   0.0     0.043        51      19      47 ..     126     153 ..     112     169 .. 0.69
   4 ?   -2.7   0.0       4.5   5.4e+03      93     108 ..     181     190 ..     179     205 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.006
                                      EEEEEEESTST-CCHHHHHHHHHHCHHHCC CS
                          AhpC-TSA 27 pvvlffypkdwcpvCttelpalaklyeefk 56
                                      + +l+f+ kd+c++C ++l++l +++ e+ 
  gi|242398974|ref|YP_002994398.1| 24 VKLLVFIGKDHCQYC-DQLKQLVEEISELS 52
                                      5689***********.67888877777765 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.4
                                       -TTSHHHHHTT-E CS
                          AhpC-TSA  89 Deegkvakaygvl 101
                                       D+e+++a++y + 
  gi|242398974|ref|YP_002994398.1|  63 DSEKELAEKYRID 75 
                                       8999999999875 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.043
                                       ECHHH.TTSEEEEEEESTST-CCHHHHHHH CS
                          AhpC-TSA  19 slsdy.kgkpvvlffypkdwcpvCttelpa 47 
                                        l+++ k+  + +f++p+  cp+C+  ++ 
  gi|242398974|ref|YP_002994398.1| 126 ALKEInKDVQIYVFVTPT--CPYCPMAVRM 153
                                       578884444444555555..****987765 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 4.5
                                       HHHHHTT-EETTTTEC CS
                          AhpC-TSA  93 kvakaygvlkeekgla 108
                                       ++a++ygv+      a
  gi|242398974|ref|YP_002994398.1| 181 ELAEQYGVM------A 190
                                       578999998......3 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0    0.0029       3.5      26      61 ..      32      67 ..      14      85 .. 0.78
   2 ?    2.5   0.0      0.16   1.9e+02      36      54 ..     117     135 ..     102     137 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0029
                        Syntaxin_2 26 kdteelreklhelieeinelikktnellkklsqldn 61
                                      kd  ++ ++l++l+eei+el+  ++  l+++++ ++
  gi|242398974|ref|YP_002994398.1| 32 KDHCQYCDQLKQLVEEISELSDLVTYELHDFDSEKE 67
                                      67778889****************999999987555 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.16
                        Syntaxin_2  36 helieeinelikktnellk 54 
                                        +l ee++e +k++n++++
  gi|242398974|ref|YP_002994398.1| 117 TDLSEETKEALKEINKDVQ 135
                                       5677888888888888775 PP

>> HyaE  Hydrogenase-1 expression protein HyaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0    0.0011       1.3      67      98 ..      60      91 ..      39      92 .. 0.81
   2 ?    0.1   0.0      0.64   7.6e+02      74      91 ..     181     198 ..     172     209 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0011
                                      ETHHHHHHHHHCCT-TSSSEEEEEETTEEEEE CS
                              HyaE 67 adreqeealaerfgvlktPsllflrdgeylgv 98
                                       d + e++lae++++   P++++ ++g+ lgv
  gi|242398974|ref|YP_002994398.1| 60 HDFDSEKELAEKYRIDIAPAVVMTQNGKDLGV 91
                                      477899*******************9998885 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.64
                                       HHHHCCT-TSSSEEEEEE CS
                              HyaE  74 alaerfgvlktPsllflr 91 
                                       +lae++gv+ +P +++  
  gi|242398974|ref|YP_002994398.1| 181 ELAEQYGVMAVPKVVIKV 198
                                       678888888888887654 PP

>> TrbC_Ftype  Type-F conjugative transfer system pilin assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.038        46      63      82 ..      68      87 ..      24     101 .. 0.79
   2 ?    5.4   0.0     0.016        19      61      82 ..     180     201 ..     163     215 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.038
                        TrbC_Ftype 63 lFrqfkitaVPalvlaeedk 82
                                      l ++++i+  Pa+v++++ k
  gi|242398974|ref|YP_002994398.1| 68 LAEKYRIDIAPAVVMTQNGK 87
                                      5689***********99865 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.016
                        TrbC_Ftype  61 PllFrqfkitaVPalvlaeedk 82 
                                       P+l +q+++ aVP +v+  + +
  gi|242398974|ref|YP_002994398.1| 180 PELAEQYGVMAVPKVVIKVNGE 201
                                       88999***********987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       848  (0.0472977); expected 358.6 (0.02)
Passed bias filter:                      700  (0.0390429); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 1351.53
//
Query:       gi|242398975|ref|YP_002994399.1|  [L=415]
Description: Metal-dependent amidohydrolase [Thermococcus sibiricus MM 739]
Scores for complete 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-55  188.8   0.1    1.9e-55  188.5   0.1    1.0  1  Amidohydro_1  Amidohydrolase family
    3.4e-07   30.1   0.0    8.6e-05   22.2   0.0    2.3  2  Amidohydro_3  Amidohydrolase family


Domain annotation for each model (and alignments):
>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  188.5   0.1   2.2e-59   1.9e-55       2     343 ..      53     395 ..      52     396 .. 0.91

  Alignments for each domain:
  == domain 1  score: 188.5 bits;  conditional E-value: 2.2e-59
                                       EEE-EEEEEEECETTECSSS....GHHHHH..........STTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTHHHH CS
                      Amidohydro_1   2 vlPGlIDaHvHleqsllrga....tledwl..........vppetaaealesgiktalksGtttvadmgattstgie 64 
                                       ++PGl +aH+H+ ++ +rg     +l++wl           ++e+++  + +gi++a+ +G tt++d+++     + 
  gi|242398975|ref|YP_002994399.1|  53 LIPGLANAHTHVAMNRFRGFgddmPLDKWLndviwpmekeWNEEEIYKWALIGIAEAIANGSTTINDHYF----FAW 125
                                       89*************999999*************************************************....99* PP

                                       HHHHHHHTSSSEEEEEEESSEGGSGCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHHHHHHHHHH CS
                      Amidohydro_1  65 alleaaeelplglrilggkvsldrgsaetskasreklkagaaetikgkadgvvkvalapheapafsdeelkealkea 141
                                        +++aa++l  g+r+++g++++d  ++ +  +    + + + e++ +++d++++++laph+  ++s+++l e  ++a
  gi|242398975|ref|YP_002994399.1| 126 QIAKAAKKL--GVRAFIGQTMMD-LVDMPIADPKLGF-KFF-EKW-KDKDSLINATLAPHATDTVSKDLLMETKELA 196
                                       ********8..***********9.4444333333333.333.344.46799************************** PP

                                       HHHTTEEEEEETSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEEHHHHHHHHHHHHHHCEEHH CS
                      Amidohydro_1 142 kkrdlpvaiHaletkgevedaeaafgetiehgthlevaeslglldeiklilahgvhltpteaellkerlkeagvahc 218
                                       +k+ + +++H++ +++ev  +++  g      +++e+++  g l+  ++i +hg++l+ +e++l ++   +a ++hc
  gi|242398975|ref|YP_002994399.1| 197 EKKEALIHMHVSQSREEVLRVKEREG-----LSPVEYLKNTGTLKA-NFIGVHGIYLSKEEVKLYAKS--NATLVHC 265
                                       **************************.....56*************.*********************..******* PP

                                       HHHHHHSEHHHHHHHHHHHHTSCEEEEEECTTSSCCGGHHHHHHHHHHHHHHCCTTTTHCHCHHHHHHHHHTHHHHH CS
                      Amidohydro_1 219 pfsnsilrsgrealrkaldeGvkvglgtDgaasgnslnlleelrlalklqrgllyedeegglslkealrmaTingAk 295
                                       p s  +l+  + ++ + ++ G k++lg D a s+ns++++ e+++a+ l ++++++    + ++k+++++aT++gAk
  gi|242398975|ref|YP_002994399.1| 266 PVSLAKLEGYVGPILDIWKLGGKIALGNDCAVSNNSMDMILEMKFAAILNKVKNNN--PIMPTAKDVFYWATLGGAK 340
                                       *****************************99****************777766664..55689999*********** PP

                                       HTT-TTTSSSS-TTSB--EEEECC.CT........CGGGTTTCTSEEEEEEEETTEE CS
                      Amidohydro_1 296 alglddkvGsievGkdADlvvvdl.di........laafvglkkdgnvkkvivkGkl 343
                                       al+l  k+G ie G+ ADlv++++ ++        l+++v+++k   v kv+v+G+l
  gi|242398975|ref|YP_002994399.1| 341 ALNL--KAGLIENGYLADLVLINTrKLhflprenmLSHLVYSAKGSDVEKVFVGGEL 395
                                       ****..******************83355668888********************87 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.1   0.00082       7.3       6      22 ..      49      65 ..      44      76 .. 0.85
   2 !   22.2   0.0   9.6e-09   8.6e-05     358     473 .]     277     397 ..     179     397 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.00082
                      Amidohydro_3  6 kGrlvlPGFvDsHtHla 22
                                      kG l++PG+  +HtH+a
  gi|242398975|ref|YP_002994399.1| 49 KGYLLIPGLANAHTHVA 65
                                      799************54 PP

  == domain 2  score: 22.2 bits;  conditional E-value: 9.6e-09
                      Amidohydro_3 358 tpvkellnagvkvalgsD..apvgpfdpwprigaavmrktrrggevlrpdeelsleealalyTrgpAkalgledrkG 432
                                        p+  +++ g k+alg+D     +++d + ++  a  +++++++         +  +++   T g+Akal+l    G
  gi|242398975|ref|YP_002994399.1| 277 GPILDIWKLGGKIALGNDcaVSNNSMDMILEMKFAAILNKVKNN----NPIMPTAKDVFYWATLGGAKALNLKA--G 347
                                       67888888899999999955555789999999988888888886....555567899999**************..* PP

                      Amidohydro_3 433 tLevGadADlvvldadpldvdp.pelaear........vrltvvdGrvvy 473
                                        +e G+ ADlv++++  l++ p +++ + +        v+++ v+G+ +y
  gi|242398975|ref|YP_002994399.1| 348 LIENGYLADLVLINTRKLHFLPrENMLSHLvysakgsdVEKVFVGGELIY 397
                                       **************666666550444444489999999999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 2515.38
//
Query:       gi|242398976|ref|YP_002994400.1|  [L=51]
Description: hypothetical protein TSIB_0993 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score 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   15.3   1.0      0.033   14.5   0.3    1.7  2  Yos1      Yos1-like


Domain annotation for each model (and alignments):
>> Yos1  Yos1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.3   1.8e-06     0.033      45      67 ..      14      36 ..       4      37 .. 0.91
   2 ?   -0.5   0.0     0.087   1.6e+03      21      29 ..      41      49 ..      38      51 .] 0.78

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.8e-06
                              Yos1 45 svkakiinliaavrtlmripLiv 67
                                       +kak++n+i  v  +m +pLi+
  gi|242398976|ref|YP_002994400.1| 14 ILKAKVLNMILQVSVVMNMPLIF 36
                                      58********************7 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.087
                              Yos1 21 dRfLarigl 29
                                       +fLa++ +
  gi|242398976|ref|YP_002994400.1| 41 RKFLAKVLW 49
                                      579999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      158  (0.00881254); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.53
# Mc/sec: 288.95
//
Query:       gi|242398977|ref|YP_002994401.1|  [L=431]
Description: Asparaginyl-tRNA synthetase [Thermococcus sibiricus MM 739]
Scores for 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-85  284.4   0.0    1.2e-84  284.1   0.0    1.1  1  tRNA-synt_2      tRNA synthetases class II (D, K and N)
    2.8e-15   56.1   0.4    3.4e-14   52.6   0.6    2.2  2  tRNA_anti-codon  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 !  284.1   0.0   1.3e-88   1.2e-84       2     313 ..     112     425 ..     111     426 .. 0.96

  Alignments for each domain:
  == domain 1  score: 284.1 bits;  conditional E-value: 1.3e-88
                                       CCHHHHTHHHHCCSHHHHHHHHHHHHHHHHHHHHHHHTT-EE----SEESS--SSSS--EEEEETTT.TEEE....- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....x RF
                       tRNA-synt_2   2 eelrlknryldlrtekvskvlrlrstvtkavrkyleengfieietPiLsksdteegarlFkvksrekekeff....a 74 
                                        e++l+ r+l+l ++kv +v++++ t+++a r++l ++g++e+ +PiL++ ++e+ga+lFk+       ++f    +
  gi|242398977|ref|YP_002994401.1| 112 DEFLLDVRHLHLHSPKVGSVMKVKGTLMQAAREWLLQDGWYEVFPPILVTGAVEGGATLFKL-------KYFdreaY 181
                                       578999********************************************************.......56666667 PP

                                       E-S-SHHHHHHHHHCTHSEEEEEEEEE--S--BTTB-S-CEEEEEEEEET-SCHHHHHHHHHHHHHHHHHHHHCSCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2  75 LtqspqlylellivagidrvfqiaraFRaEdsrtdrhlaEFtqieaemsfieeedimqvleelikslvkevlessak 151
                                       L qs qlyle+ i + +++v++++++FRaE+srt+rhl+E++++e+e ++++  d+++v eel++++v+++le  +k
  gi|242398977|ref|YP_002994401.1| 182 LSQSAQLYLEAAIFG-LEKVWSLTPSFRAEKSRTRRHLTEYWHLELEAAWMDLWDLLEVEEELVSYMVQRTLELRKK 257
                                       ***************.*********************************************************9999 PP

                                       CCCHTTTTTS..EE-SSS-EEEEHHHHHHHHHTS......-SS--HHHHHHHHHHS--SEEEEEEEBGGGSTTCBBB CS
                                       xxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 152 diefvirrns..kdlkkpfkrltykeaieklnei......gkdldkaderalvkkeknepvfvtdfPaelkpFyark 220
                                       +ie+  +  +  k+ + pf+r++y+eai++l+++      g+d+  ++er+l++ e  +p+fv+ +P+ +k Fy+++
  gi|242398977|ref|YP_002994401.1| 258 EIEEFRKDFTtlKNSEPPFPRISYDEAIDILQSKgvkiewGEDMGADEERILTQ-EFDRPFFVYGYPKHIKAFYMKE 333
                                       999988876566777777*************999******9*************.999******************* PP

                                       STTSTTBBSEEEEEET.TE.EEEEEEEB--SHHHHHHHHHHCCHHSSSGGGGHHHHHHHHCT--SEEEEEEEHHHHH CS
                                       xxxxxxxxxxxxxxxx.xx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 221 eeddkkltesyDllin.gv.ElvgGslRiedpeeleeklkskgldeeaeekfswylealeyGapphgGlglGldRlv 295
                                       + +d++ + + D+l + g+ E++gGs+R++d+e+l +++ ++g+d   +++++wyl++++yG++ph+G+glGl+Rlv
  gi|242398977|ref|YP_002994401.1| 334 DPEDSRKALAADMLAPeGYgEVIGGSQREDDYEKLVQRILEEGMD---PKNYEWYLDLRKYGSVPHSGFGLGLERLV 407
                                       ***************9889**************************...***************************** PP

                                       HHHCT-SSGGGCSSS-XX CS
                                       xxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 296 mlllgsesIrdviaFPkl 313
                                       +++l++++Ir +++FP++
  gi|242398977|ref|YP_002994401.1| 408 AWVLKLNHIRWATLFPRT 425
                                       ****************97 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 !   52.6   0.6   3.8e-18   3.4e-14       1      76 []      20      98 ..      20      98 .. 0.98
   2 ?    0.6   0.0     0.064   5.7e+02      45      61 ..     125     141 ..     121     156 .. 0.78

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 3.8e-18
                                      EEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEET...HHHHHHHTTS-TTSEEEEEEEEEEC...TTSSEEEEEEEE CS
                   tRNA_anti-codon  1 VtvaGrvtsisdrsggkvifidlrDgtgriqvvlfr...eeatklaenlkeGdvvrvtGrvkrr...pggelelkveei 73
                                      V++aG+v ++  r+ g+ +fi+lrD +g+iq ++ +   e+a++ a+++ +++ v ++G+vk++   p+g +e+++++i
  gi|242398977|ref|YP_002994401.1| 20 VKLAGWVYRK--REVGNKVFIVLRDSSGIIQTIFMKdlsEDAYEKAKQVGIESSVIIEGTVKSDsraPTG-VEIQADKI 95
                                      89********..**********************************************************.******** PP

                                      EEE CS
                   tRNA_anti-codon 74 ell 76
                                      e+l
  gi|242398977|ref|YP_002994401.1| 96 EIL 98
                                      *97 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.064
                                       TS-TTSEEEEEEEEEEC CS
                   tRNA_anti-codon  45 nlkeGdvvrvtGrvkrr 61 
                                       + k+G+v +v+G++   
  gi|242398977|ref|YP_002994401.1| 125 SPKVGSVMKVKGTLMQA 141
                                       5689*********9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.46
# Mc/sec: 2822.91
//
Query:       gi|242398978|ref|YP_002994402.1|  [L=144]
Description: hypothetical protein TSIB_0996 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); 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: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1019.28
//
Query:       gi|242398979|ref|YP_002994403.1|  [L=155]
Description: pyrophosphatase [Thermococcus sibiricus MM 739]
Scores for complete 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   65.0   0.3    8.5e-18   64.7   0.3    1.1  1  NUDIX     NUDIX domain


Domain annotation for each model (and alignments):
>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.7   0.3   4.8e-22   8.5e-18       2     115 ..       3     123 ..       2     140 .. 0.74

  Alignments for each domain:
  == domain 1  score: 64.7 bits;  conditional E-value: 4.8e-22
                                       EEEEEEEEEEETTSEEEEEEES..SSSTTTEESSEEECBTTS.HHHHHHHHHHHHHHSEEEEEEEEEEEEEEEEEEE CS
                             NUDIX   2 lrravgvvllnekgevLlvrrs..kkpfpgWelPgGkvepgE.tpeeAArREleEEtGleaellellgrlhylapyd 75 
                                       +r  v++++ +++  +Llv++   +++   W  PgG+ve g+ ++ +AArRE++EEtGl   ++ ++ +++y + + 
  gi|242398979|ref|YP_002994403.1|   3 HRIRVAAIIVRDDS-ILLVKHVhpETKYEWWVPPGGGVENGDnSIFDAARREVWEETGL---NVNVIPEFKYIREFF 75 
                                       56677777666663.*****996555555599**************************9...668888888888888 PP

                                       EEEEEEEEEEEEEE.EEECSGCSST.......STTTEEEEEEEEHHHH CS
                             NUDIX  76 gpygdeheilyvfl.eevegelepn.......denevsevrwvpleel 115
                                       ++  ++  + ++++ e   g+l+ +       de+ +++v+w++ ee+
  gi|242398979|ref|YP_002994403.1|  76 DKENNTLNLEIFVEaEIISGDLTIKnvcgngkDEDYIKSVKWISKEEV 123
                                       888873333333334455555555556678889999**********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1173.35
//
Query:       gi|242398980|ref|YP_002994404.1|  [L=55]
Description: hypothetical protein TSIB_0998 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.065   13.3   2.7      0.078   13.1   2.7    1.1  1  Na_Pi_cotrans  Na+/Pi-cotransporter
      0.089   12.6   2.1        0.1   12.4   2.1    1.2  1  TatC           Sec-independent protein translocase protein (T
       0.11   11.5   9.6       0.12   11.4   9.6    1.0  1  DUF973         Protein of unknown function (DUF973)


Domain annotation for each model (and alignments):
>> Na_Pi_cotrans  Na+/Pi-cotransporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   2.7   1.3e-05     0.078      97     134 ..       5      42 ..       2      47 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.3e-05
                     Na_Pi_cotrans  97 lalllllvgvllllfskkkklkklgeillglgllflgl 134
                                       ++++++l+g+ll+lf   k+++++g++llg+g+ ++ l
  gi|242398980|ref|YP_002994404.1|   5 VTYIIILLGILLTLFGALKRKETYGKVLLGVGITITIL 42 
                                       57899999********999*************987655 PP

>> TatC  Sec-independent protein translocase protein (TatC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   2.1   1.7e-05       0.1      71     121 ..       5      54 ..       1      55 [] 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.7e-05
                                       HSHHHHHHHHHCCCTTTTS---STTTHHHHHHHHHHHHHHHHHHHHTHHHH CS
                              TatC  71 lasPvilyqlwafvapgLykherrlvlvfliaslllfllGaafayfvvlpl 121
                                       ++  +il+ ++  +  +L+++e  + +v+l + +++++lG++f y+++lpl
  gi|242398980|ref|YP_002994404.1|   5 VTYIIILLGILLTLFGALKRKE-TYGKVLLGVGITITILGICFIYVITLPL 54 
                                       5555677777778877888777.789**********************996 PP

>> DUF973  Protein of unknown function (DUF973)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   9.6     2e-05      0.12     103     146 ..       2      49 ..       1      54 [. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2e-05
                            DUF973 103 liligaiiiiigvilaivsll....slilslillgviilligiilali 146
                                       ++l+ +iii++g++l++++ l     +  +l+ +g++i ++gi ++ +
  gi|242398980|ref|YP_002994404.1|   2 MLLVTYIIILLGILLTLFGALkrkeTYGKVLLGVGITITILGICFIYV 49 
                                       89***************9999999888899999999999999954433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       887  (0.0494729); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 329.61
//
Query:       gi|242398981|ref|YP_002994405.1|  [L=37]
Description: hypothetical protein TSIB_0999 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       270  (0.0150594); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); 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: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.50
# Mc/sec: 222.72
//
Query:       gi|242398982|ref|YP_002994406.1|  [L=229]
Description: hypothetical protein TSIB_1000 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1467.79
//
Query:       gi|242398983|ref|YP_002994407.1|  [L=263]
Description: hypothetical protein TSIB_1001 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-05   24.9   0.0    0.00052   19.5   0.0    2.1  2  AP_endonuc_2  Xylose isomerase-like TIM barrel
  ------ inclusion threshold ------
       0.15   11.4   0.0       0.23   10.7   0.0    1.4  2  Amidohydro_1  Amidohydrolase family


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 !    3.3   0.0    0.0054        48       6      52 ..      28      71 ..      26      90 .. 0.82
   2 !   19.5   0.0   5.8e-08   0.00052     109     209 ..     110     213 ..     109     214 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.0054
                                      HCT-SEEEEECCTCSHHHHCHHHHHHHHHHHHHHTTSEEEEEEECCC CS
                      AP_endonuc_2  6 eaGfdgvElfgrdlvpvselsdeelrelrkaldelglriaslslftr 52
                                      e Gfd+v + + +    s   ++++ +l++ +de  + ++ +  f+ 
  gi|242398983|ref|YP_002994407.1| 28 ENGFDAVSFTPESIFRLS---KSKISKLKSVIDEKRIPVTIHADFNI 71
                                      679*********999998...79**************9877766554 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 5.8e-08
                                       HHHHHHHHHHHHHHHTSEEEEE--TTTTSSSTC..HHHHHHHHHHTTTTEEEEEEHHHHHHH........TTTHHHH CS
                      AP_endonuc_2 109 laeslneladyaekegvklalEtlagsgvelgd..eelarlldavdspnvgvclDtgHllia........eedvdda 175
                                       +++ l+ l+d++e +g+ ++lE  + + + l++   +++r+l   + p+ g+ lD gH++++           +++ 
  gi|242398983|ref|YP_002994407.1| 110 VIKTLEYLIDKTESKGILFGLEDFPLDSNALKNhsNQMQRIL---KCPRYGILLDLGHMNLRinnhayfkNKGIIKY 183
                                       6788999***************99999988884445555555...5666*************999995555555555 PP

                                       HHHHHGGEEEEEE.EESSTTTTSSTTEESTTSSS CS
                      AP_endonuc_2 176 lraladrikhvHikDakgdlgagrdrhvpigeGe 209
                                       +  +  +i  +H++D++      +d h+p+g+G+
  gi|242398983|ref|YP_002994407.1| 184 ITDIPVKIIELHVHDNDS----LGDKHMPPGKGV 213
                                       5555555***********....9*********97 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   2.6e-05      0.23     112     162 ..      27      76 ..      12     155 .. 0.75
   2 ?   -3.3   0.1      0.46   4.1e+03       6      16 ..     191     201 ..     164     223 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 2.6e-05
                                       CTTTCEE.EEEEECGTCCSHHHHHHHHHHHHHHHTTEEEEEETSSCHHHHHH CS
                      Amidohydro_1 112 kadgvvk.valapheapafsdeelkealkeakkrdlpvaiHaletkgeveda 162
                                       + + +++ v ++p++ + +s++ ++++ ++ +++ +pv+iHa  +  ++ ++
  gi|242398983|ref|YP_002994407.1|  27 T-ENGFDaVSFTPESIFRLSKSKISKLKSVIDEKRIPVTIHADFNISTN-EI 76 
                                       4.44556699********************************4444443.33 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 0.46
                                       EEEEEEECETT CS
                      Amidohydro_1   6 lIDaHvHleqs 16 
                                       +I +HvH ++s
  gi|242398983|ref|YP_002994407.1| 191 IIELHVHDNDS 201
                                       45556665544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       589  (0.0328518); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1700.59
//
Query:       gi|242398984|ref|YP_002994408.1|  [L=157]
Description: Hydrogenase maturation protease [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-18   66.4   0.0    3.1e-18   65.9   0.0    1.2  1  HycI      Hydrogenase maturation 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 !   65.9   0.0   1.7e-22   3.1e-18       1     128 [.      30     151 ..      30     153 .. 0.94

  Alignments for each domain:
  == domain 1  score: 65.9 bits;  conditional E-value: 1.7e-22
                                       HHHHHHHHHHEC--TTEEEEEECT-SGGGHHHHCC..-SEEEEEEE--SSS-TT-EEEEECCHHHHHHTTC.CGCCC CS
                              HycI   1 vrvvekLkrryefkenvtviDgGtqglelvgtlee..adkliivDavdfglepGevkiikddevpkklkakkmsaHq 75 
                                       v+vvekLk+r + ++ v +++ G +++++ g++    +++++ +Dav f+++pGe+++ + +        +++s+H+
  gi|242398984|ref|YP_002994408.1|  30 VYVVEKLKERISNQK-VVFLNCGEMPESYAGKIIRenPSHVVFIDAVHFEGKPGEIVLADPEGTLG----EAFSTHK 101
                                       79*******999997.**************9998779*************************9994....6699*** PP

                                       HCHHHHHHHHHHCCS--SEEEEEEE--S-BST.CCS--HHHHCCHHHHHHHCC CS
                              HycI  76 lplaevlklleekgeipkevillgvqpesledvgielseevkkavekavelil 128
                                       +pl  ++ +l+++  i++++il+g+qp+++    +e+s+e k++ e++v+++ 
  gi|242398984|ref|YP_002994408.1| 102 MPLKLLVGYLKQN--INSRFILIGAQPKQTGL-FVEMSRELKDSAERLVNILE 151
                                       ***********99..56*************98.9***************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1218.46
//
Query:       gi|242398985|ref|YP_002994409.1|  [L=241]
Description: Nucleotide-binding protein [Thermococcus sibiricus MM 739]
Scores for 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   0.1    6.4e-55  186.3   0.1    1.8  1  ParA            NUBPL iron-transfer P-loop NTPase
    3.6e-15   56.1   0.0    5.1e-15   55.7   0.0    1.2  1  CbiA            CobQ/CobB/MinD/ParA nucleotide binding domain
    1.1e-11   44.9   0.7      3e-07   30.5   0.2    2.2  2  AAA_31          AAA domain
    2.1e-07   30.5   5.4    2.2e-05   23.8   0.2    2.9  3  ArsA_ATPase     Anion-transporting ATPase
      2e-06   27.5   0.1      0.027   13.9   0.0    2.2  2  Fer4_NifH       4Fe-4S iron sulfur cluster binding proteins, 
    2.4e-06   27.0   0.0    5.1e-06   26.0   0.0    1.6  1  MipZ            ATPase MipZ
    7.4e-06   25.9   2.0      0.017   14.9   0.0    2.2  2  AAA_26          AAA domain
  ------ inclusion threshold ------
      0.039   13.9   0.1       0.13   12.2   0.0    1.9  2  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
      0.044   13.6   0.1       0.12   12.1   0.1    1.7  2  CLP1_P          mRNA cleavage and polyadenylation factor CLP1
      0.049   13.4   0.2       0.11   12.3   0.2    1.5  1  Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 famil
      0.095   11.7   0.2       0.14   11.2   0.2    1.2  1  MeaB            Methylmalonyl Co-A mutase-associated GTPase M
       0.13   11.2   0.0        0.2   10.6   0.0    1.2  1  PDH             Prephenate dehydrogenase


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 !  186.3   0.1   4.3e-58   6.4e-55       1     241 [.      15     237 ..      15     241 .] 0.92

  Alignments for each domain:
  == domain 1  score: 186.3 bits;  conditional E-value: 4.3e-58
                              ParA   1 kvkkviavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeekpeqsekkliPveakgikvmS 77 
                                       kv+++i v+SgKGGVGKS v++ lAl Lakkg+kvgllD+D +G s   +lg e ++  ++++++iP e++gik+mS
  gi|242398985|ref|YP_002994409.1|  15 KVNRIIPVVSGKGGVGKSMVSTILALVLAKKGYKVGLLDLDFHGASDHVILGFEPKEFPEEDRGVIPPEVHGIKFMS 91 
                                       5899****************************************************9999999************** PP

                              ParA  78 igfllesedeavvwrGpmkskaikqllkdvewgelDyLiiDlPPGtgDeqltvaqklplagaviVttpqevaladvk 154
                                       i +  e  d++   rG  +s a+ +ll+ ++w+elD+L+iD+PPG gD  l ++  l+  + ++V+tp ++a++++k
  gi|242398985|ref|YP_002994409.1|  92 IVYYSE--DKPTPLRGMEISDALIELLAITRWDELDFLVIDMPPGMGDQFLDILRFLKEGEFIVVATPSKLAINVIK 166
                                       *99887..99999**************************************************************** PP

                              ParA 155 kaiemfkkvkvkvlGvveNmsgfvcpkcgekteifgkgggeklaeelgvpllgeipldpeireasdegkplvlkepe 231
                                       k ie++k+ k+k++G+veN++               ++  e++a+e++vp+l  ipl +++ e++ + ++l+++e  
  gi|242398985|ref|YP_002994409.1| 167 KLIELLKEQKFKIVGLVENLKLDE------------EKDIEEIANEFNVPYLVGIPLYKDLDEKVGNVEELLKSEF- 230
                                       *******************97643............4568999******************999999998776654. PP

                              ParA 232 seaakaleei 241
                                          +k++e++
  gi|242398985|ref|YP_002994409.1| 231 ---SKKIERV 237
                                       ...4444444 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 !   55.7   0.0   3.4e-18   5.1e-15       3     123 ..      22     220 ..      20     225 .. 0.91

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 3.4e-18
                                       EEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH......................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......................... RF
                              CbiA   3 iastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep......................... 54 
                                       ++s+kGGvGK+++++ La  la++g++V l+D+D  + +++++ g e+++ p                         
  gi|242398985|ref|YP_002994409.1|  22 VVSGKGGVGKSMVSTILALVLAKKGYKVGLLDLDFHGASDHVILGFEPKEFPeedrgvippevhgikfmsivyysed 98 
                                       89********************************************99999999*********************** PP

                                       ..............................................................CCHCCCHHHHHHCHC CS
                                       ..............................................................xxxxxxxxxxxxxxx RF
                              CbiA  55 ..............................................................dlkrllellealgkk 69 
                                                                                                      +  +++l+e l+++
  gi|242398985|ref|YP_002994409.1|  99 kptplrgmeisdaliellaitrwdeldflvidmppgmgdqfldilrflkegefivvatpsklAINVIKKLIELLKEQ 175
                                       **********************************************************8888666666777777766 PP

                                       HHHH..EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  70 kalllkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeavaeapa 123
                                       k   +ki+g+v n       +  +++++ee+  +++vp l  ip  +++ e + 
  gi|242398985|ref|YP_002994409.1| 176 K---FKIVGLVENL------KLDEEKDIEEIANEFNVPYLVGIPLYKDLDEKVG 220
                                       3...8899998888......556678888888888******9*99999887765 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.2     2e-10     3e-07       2      42 ..      18      58 ..      17      72 .. 0.91
   2 !   12.6   0.0   6.2e-05     0.093     116     170 ..     122     178 ..     103     188 .. 0.81

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 2e-10
                            AAA_31  2 kvIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQa 42
                                      ++I ++  KGGvGK+  s+ la +lak+g+kv l DlD  +
  gi|242398985|ref|YP_002994409.1| 18 RIIPVVSGKGGVGKSMVSTILALVLAKKGYKVGLLDLDFHG 58
                                      89************************************765 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 6.2e-05
                            AAA_31 116 deYDyiiiDcpPsLglltenaL..vasdsviipvqaeayaleGleqllktieevkkk 170
                                       de D+ +iD+pP +g     +L  +   ++i++  ++++a++ +++l++ ++e k k
  gi|242398985|ref|YP_002994409.1| 122 DELDFLVIDMPPGMGDQFLDILrfLKEGEFIVVATPSKLAINVIKKLIELLKEQKFK 178
                                       679***********977666662266789********************99998766 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.2   1.5e-08   2.2e-05       5      38 ..      22      55 ..      17      68 .. 0.89
   2 ?    0.7   0.0      0.16   2.4e+02     103     135 ..     102     134 ..      94     148 .. 0.80
   3 !    7.0   0.4    0.0019       2.9     206     251 ..     148     193 ..     137     202 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1.5e-08
                                      EEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S CS
                       ArsA_ATPase  5 lvgGKGGVGKttvsaatavklsekgkkvllistD 38
                                      +v+GKGGVGK+ vs+ +a+ l++kg+kv l+ +D
  gi|242398985|ref|YP_002994409.1| 22 VVSGKGGVGKSMVSTILALVLAKKGYKVGLLDLD 55
                                      69**************************998887 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.16
                                       SSTTHHHHHHHHHHHHHHHCSSSSEEEEESBSC CS
                       ArsA_ATPase 103 slPGideilsfeellkyvkeeeydvvvlDtaPT 135
                                        l G++   ++ ell  ++ +e d +v+D +P 
  gi|242398985|ref|YP_002994409.1| 102 PLRGMEISDALIELLAITRWDELDFLVIDMPPG 134
                                       5668998999999999999***********993 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0019
                                       TEEEEEEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEEEE-TTCSS CS
                       ArsA_ATPase 206 rtsfrlVvipEklslkEteRaikeLkkygikvdavivNkllpeeeq 251
                                          f++V +p kl+++ ++++i+ Lk++++k+  ++ N  l+ee++
  gi|242398985|ref|YP_002994409.1| 148 EGEFIVVATPSKLAINVIKKLIELLKEQKFKIVGLVENLKLDEEKD 193
                                       55799*********************************99999875 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 !   13.9   0.0   1.8e-05     0.027       5      47 ..      23      65 ..      18      71 .. 0.85
   2 !   11.8   0.0   7.8e-05      0.12     158     217 ..     161     218 ..     106     239 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.8e-05
                         Fer4_NifH  5 iyGkGGiGksttsqnlsaalaemgkkvlivGCDPkaDstrlll 47
                                      + GkGG+Gks+ s+ l+  la++g kv ++  D    s +++l
  gi|242398985|ref|YP_002994409.1| 23 VSGKGGVGKSMVSTILALVLAKKGYKVGLLDLDFHGASDHVIL 65
                                      67*************************8888887777666666 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 7.8e-05
                         Fer4_NifH 158 anniakgiekyaksggvrlgGliinsrkvddereliekfaeelgtkvlevvPrdeivrka 217
                                       a n+ k + +  k+++ ++ Gl+ n +   de++ ie++a+e +++ l  +P+ +++ ++
  gi|242398985|ref|YP_002994409.1| 161 AINVIKKLIELLKEQKFKIVGLVENLK--LDEEKDIEEIANEFNVPYLVGIPLYKDLDEK 218
                                       457778888899999**********77..55556689***************99888765 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   3.4e-09   5.1e-06       2     108 ..      19     132 ..      18     146 .. 0.67

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 3.4e-09
                                       EEEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHHHHH..HHHHHHHHHT------...EEE-SS.. CS
                              MipZ   2 vivlgnekGGsGksttavhvavaLlkkGarvaaidldlrqrtlaryle..nraataerkglsLplp...ealals.. 71 
                                       +i +   kGG Gks ++  +a  L+kkG +v+ +dld   ++ +  l+   +   +e +g+  p+    +++++   
  gi|242398985|ref|YP_002994409.1|  19 IIPVVSGKGGVGKSMVSTILALVLAKKGYKVGLLDLDFHGASDHVILGfePKEFPEEDRGVIPPEVhgiKFMSIVyy 95 
                                       5667788********************************99998876511444444555553333211133333311 PP

                                       S-HHHHTTS-HHHHHHHHHHHHHHHHHH-SEEEEE-- CS
                              MipZ  72 eaeeaeveeeeeaevaeleelvadleaeldfividtP 108
                                       ++++ +  ++ e+++a +e l+     eldf+vid P
  gi|242398985|ref|YP_002994409.1|  96 SEDKPTPLRGMEISDALIELLAITRWDELDFLVIDMP 132
                                       2233333455666666666666777788999999986 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.5   0.00027       0.4       5      33 ..      22      50 ..      18      52 .. 0.88
   2 !   14.9   0.0   1.1e-05     0.017     131     196 ..     151     217 ..     137     219 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00027
                            AAA_26  5 vtgtdtgvGKTvvslgLvralkrkgvkvg 33
                                      v++   gvGK++vs++L+  l +kg+kvg
  gi|242398985|ref|YP_002994409.1| 22 VVSGKGGVGKSMVSTILALVLAKKGYKVG 50
                                      6777889********************98 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 1.1e-05
                            AAA_26 131 vilVargglgtinqllltiealrqknvrvlGvilN.kvrnpenvetlekksgipvlGvvPylpdlea 196
                                        i+Va++ + +in +   ie+l++++ +++G++ N k+ +++++e++ + +++p l  +P  +dl++
  gi|242398985|ref|YP_002994409.1| 151 FIVVATPSKLAINVIKKLIELLKEQKFKIVGLVENlKLDEEKDIEEIANEFNVPYLVGIPLYKDLDE 217
                                       6899999999*************************4466668******************9999986 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 ?   -1.4   0.0       1.3     2e+03      12      27 ..      36      51 ..      23      57 .. 0.80
   2 ?   12.2   0.0   8.9e-05      0.13      62     121 ..     141     201 ..     126     229 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.3
                                      HHHHHHHHTTT--EEE CS
                    NAD_Gly3P_dh_N 12 talAkvlaenghevrl 27
                                      t lA vla++g +v l
  gi|242398985|ref|YP_002994409.1| 36 TILALVLAKKGYKVGL 51
                                      7899999999999866 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 8.9e-05
                                       -HHHHHTT--EEEE---HHHHHHHHHHHCCC-.-TT-EEEE---SEET.TTEEHHHHHHHH CS
                    NAD_Gly3P_dh_N  62 dlaealkgadiivlvvPsqalrevlkklkgll.kkkailvsliKGieegtlkllsevieee 121
                                       d+ + lk+ ++iv++ Ps+   +v+kkl +ll ++k ++v l+  ++ ++ k ++e+++e+
  gi|242398985|ref|YP_002994409.1| 141 DILRFLKEGEFIVVATPSKLAINVIKKLIELLkEQKFKIVGLVENLKLDEEKDIEEIANEF 201
                                       777889999*********************9956677999999999999999999998886 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   8.3e-05      0.12       1      32 [.      25      56 ..      25      66 .. 0.91
   2 ?   -1.4   0.0       1.1   1.7e+03     116     130 ..     159     173 ..     101     209 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.3e-05
                            CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDv 32
                                      G+  +GKS ++++L+  +++kg+k+ ++DlD 
  gi|242398985|ref|YP_002994409.1| 25 GKGGVGKSMVSTILALVLAKKGYKVGLLDLDF 56
                                      66789**************************5 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.1
                            CLP1_P 116 glgaelllelieale 130
                                       +l+++++++lie+l+
  gi|242398985|ref|YP_002994409.1| 159 KLAINVIKKLIELLK 173
                                       233333333333333 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 ?   12.3   0.2   7.1e-05      0.11      21      62 ..     166     206 ..     162     221 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.1e-05
                                       HHHHHHHHTTTESEEEEETTSSSGGHHHHHHHHHHHTTEEEE CS
                    Ribosomal_L7Ae  21 kevtkalergeaklvilAedvepeekkkllealckekevpyv 62 
                                       k+ + +l+ ++ k+v l e+ + +e k+ +e +++e +vpy+
  gi|242398985|ref|YP_002994409.1| 166 KKLIELLKEQKFKIVGLVENLKLDEEKD-IEEIANEFNVPYL 206
                                       678999**********************.***********95 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   9.1e-05      0.14      34      66 ..      23      55 ..       6      66 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 9.1e-05
                                      EEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE- CS
                              MeaB 34 ltGvPGaGkstlvealglelrrrGkrvavlavD 66
                                      + G  G+Gks +   l+l l+++G++v++l +D
  gi|242398985|ref|YP_002994409.1| 23 VSGKGGVGKSMVSTILALVLAKKGYKVGLLDLD 55
                                      68999************************9988 PP

>> PDH  Prephenate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00013       0.2      33      72 ..     136     175 ..     131     199 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00013
                                       SSEEES-GGGGCCGSEEEE-S-GGGHHHHHHHHHHHS-TT CS
                               PDH  33 vdeatddieavkeadivvlavPvevilevlkelaphlked 72 
                                       +d+  d ++ +ke++++v+a+P +  ++v+k+l++ lke+
  gi|242398985|ref|YP_002994409.1| 136 GDQFLDILRFLKEGEFIVVATPSKLAINVIKKLIELLKEQ 175
                                       555556678899***********************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       720  (0.0401584); expected 358.6 (0.02)
Passed bias filter:                      584  (0.0325729); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); 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: 00:00:00.47
# Mc/sec: 1532.50
//
Query:       gi|242398986|ref|YP_002994410.1|  [L=138]
Description: Probable hydrogenase nickel incorporation protein hypA [Thermococcus sibiricus MM 739]
Scores for complete 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-28   97.4   0.4    5.4e-28   97.3   0.4    1.0  1  HypA             Hydrogenase/urease nickel incorporation, met
    7.7e-05   22.1   0.4      0.025   14.1   0.1    2.4  2  TF_Zn_Ribbon     TFIIB zinc-binding
     0.0012   19.3   0.1       0.17   12.4   0.0    2.2  2  Trm112p          Trm112p-like protein
     0.0012   18.7   0.1       0.54   10.3   0.0    2.2  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
     0.0035   17.4   0.1       0.14   12.3   0.0    2.3  2  DUF2318          Predicted membrane protein (DUF2318)
     0.0087   16.7   0.2          3    8.6   0.1    2.4  2  zf-ISL3          zinc-finger of transposase IS204/IS1001/IS10
  ------ inclusion threshold ------
      0.013   15.1   0.2        2.8    7.7   0.0    2.3  2  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
      0.014   14.8   1.2          1    8.9   0.1    2.3  2  zf-ribbon_3      zinc-ribbon domain
      0.016   15.1   3.4       0.74    9.7   1.1    2.3  2  TFIIS_C          Transcription factor S-II (TFIIS)
      0.025   15.0   2.0      0.042   14.3   1.9    1.5  1  KGK              KGK domain
      0.026   14.4   1.5      0.081   12.8   0.8    2.1  2  zf-ZPR1          ZPR1 zinc-finger domain
      0.028   14.1   4.1          3    7.7   0.4    2.4  2  zinc_ribbon_2    zinc-ribbon domain
      0.029   14.2   0.0      0.045   13.6   0.0    1.3  1  MCM_OB           MCM OB domain
      0.033   14.1   1.0       0.73    9.8   1.0    2.4  2  PhnA_Zn_Ribbon   PhnA Zinc-Ribbon
      0.036   14.5   0.1        2.7    8.4   0.0    2.2  2  Lar_restr_allev  Restriction alleviation protein Lar
      0.036   14.2   4.5        1.2    9.3   4.6    2.3  1  Zn-ribbon_8      Zinc ribbon domain
      0.041   13.8   0.8        3.3    7.7   0.1    2.4  2  zinc_ribbon_4    zinc-ribbon domain
      0.044   13.7   0.2        3.9    7.5   0.0    2.2  2  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
      0.048   13.9   1.3       0.21   11.9   0.1    2.1  2  Prim_Zn_Ribbon   Zinc-binding domain of primase-helicase
       0.06   13.1   1.1       0.67    9.8   0.1    2.2  2  zf-HYPF          HypF finger
      0.082   13.4   0.7       0.18   12.3   0.7    1.6  1  zf-3CxxC         Zinc-binding domain
      0.092   12.6   0.7       0.97    9.3   0.0    2.2  2  eIF-5_eIF-2B     Domain found in IF2B/IF5
      0.096   12.3   1.9       0.31   10.7   0.3    2.1  2  DpnI             Dam-replacing family
      0.097   12.7   5.1       0.79    9.7   0.3    2.4  2  DUF1610          Domain of unknown function (DUF1610)
       0.16   11.7   4.8        0.6    9.9   0.2    2.5  2  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI
        0.2   11.6   4.2        0.3   11.0   0.2    2.2  2  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
       0.42   10.2   2.7         14    5.4   0.3    2.2  2  Sgf11            Sgf11 (transcriptional regulation protein)
        5.2    6.9   6.8        8.5    6.2   0.7    2.3  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 !   97.3   0.4   8.4e-31   5.4e-28       1     112 []       1     133 [.       1     133 [. 0.95

  Alignments for each domain:
  == domain 1  score: 97.3 bits;  conditional E-value: 8.4e-31
                                       XCHHHHHHHHHHHHHHHHCCTT..EEEEEEEEEETTCT--HHHHHHHHHHHHCC.TTTT-EEEEEEE--EEEETTTS CS
                              HypA   1 MHElsiaesivevveeeakeaaarkvtkvkvevGelsgvepeaLefafellaegtvlegaeLeieevpvkvrCreCg 77 
                                       MHE+++a+ iv+++ e a++++ +kv + ++++Gel+ v++e+Lefa + +++gt++e+aeLe+  ++++++Cr+Cg
  gi|242398986|ref|YP_002994410.1|   1 MHEWALADGIVRTAIEFARQHGKEKVLAMRISLGELQDVNQEILEFAINEIKKGTIAEEAELEFIIEEAEFKCRNCG 77 
                                       ******************9999******************************************************* PP

                                       -EEECHH.HHH.....................S-TTTSSS-EEEEESSSEEEEEEEE CS
                              HypA  78 kefelee.kal.....................rCpkCgsadveivsGeellvksiev 112
                                       +e++l++ k +                      Cp+Cgs+d+e+++G+++++  i+v
  gi|242398986|ref|YP_002994410.1|  78 NEWKLKDvK-EsfnetikedihfipevvhaflACPNCGSRDFEVTKGRGVYLAAIKV 133
                                       ****88743.235889***********************************999875 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.012       7.4       1       8 [.      71      78 ..      61      89 .. 0.70
   2 !   14.1   0.1   3.9e-05     0.025       2      18 ..     109     125 ..     108     128 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.012
                                      EEETTTTC CS
                      TF_Zn_Ribbon  1 ykCPnCgs 8 
                                      +kC nCg+
  gi|242398986|ref|YP_002994410.1| 71 FKCRNCGN 78
                                      45555554 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 3.9e-05
                                       EETTTTCEECHEETSTT CS
                      TF_Zn_Ribbon   2 kCPnCgstnlveDperg 18 
                                        CPnCgs+++++   rg
  gi|242398986|ref|YP_002994410.1| 109 ACPNCGSRDFEVTKGRG 125
                                       5*********9988887 PP

>> Trm112p  Trm112p-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   0.00027      0.17      41      61 ..      44      78 ..      16      84 .. 0.74
   2 ?    5.1   0.0     0.052        33       4      15 ..     104     115 ..     102     135 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00027
                                      S..............CHHTTEECCCCEEEETTTTE CS
                           Trm112p 41 y..............ellleldieegeLvCpncgr 61
                                                     e+ le+ iee e+ C+ncg 
  gi|242398986|ref|YP_002994410.1| 44 LefaineikkgtiaeEAELEFIIEEAEFKCRNCGN 78
                                      2344566666666667889**************95 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.052
                                       GCCC-B-TTTHH CS
                           Trm112p   4 llniLaCpackg 15 
                                       ++ +LaCp c +
  gi|242398986|ref|YP_002994410.1| 104 VHAFLACPNCGS 115
                                       588999997755 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0     0.014         9      18      30 ..      70      83 ..      62      90 .. 0.79
   2 !   10.3   0.0   0.00085      0.54      20      38 ..     109     127 ..     105     128 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.014
                     Zn_Tnp_IS1595 18 gfvCPhCgsr.kay 30
                                       f C +Cg++ k+ 
  gi|242398986|ref|YP_002994410.1| 70 EFKCRNCGNEwKLK 83
                                      58999999987765 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00085
                     Zn_Tnp_IS1595  20 vCPhCgsrkayriktrglf 38 
                                        CP+Cgsr +  +k+rg++
  gi|242398986|ref|YP_002994410.1| 109 ACPNCGSRDFEVTKGRGVY 127
                                       5*******88888888876 PP

>> DUF2318  Predicted membrane protein (DUF2318)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   0.00022      0.14      44      68 ..      63      87 ..      41      92 .. 0.91
   2 ?    3.1   0.0      0.16     1e+02      30      47 ..     103     121 ..      98     129 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00022
                           DUF2318 44 gYvqegeelvCknCgvrfaldsige 68
                                      ++++e+ e  C+nCg++++l++++e
  gi|242398986|ref|YP_002994410.1| 63 EFIIEEAEFKCRNCGNEWKLKDVKE 87
                                      79999****************9985 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.16
                           DUF2318  30 lrvaldaCevCekkgYv.q 47 
                                       ++ a+ aC  C+++ ++  
  gi|242398986|ref|YP_002994410.1| 103 VVHAFLACPNCGSRDFEvT 121
                                       5678999999999999734 PP

>> zf-ISL3  zinc-finger of transposase IS204/IS1001/IS1096/IS1165
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.033        21       3      16 ..      71      87 ..      69      98 .. 0.71
   2 !    8.6   0.1    0.0046         3       4      12 ..     109     119 ..     107     127 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.033
                           zf-ISL3  3 hrCPnCgsk...tvvkh 16
                                       +C+nCg+    ++vk 
  gi|242398986|ref|YP_002994410.1| 71 FKCRNCGNEwklKDVKE 87
                                      57*****9974444555 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0046
                           zf-ISL3   4 rCPnCgsk..t 12 
                                       +CPnCgs+   
  gi|242398986|ref|YP_002994410.1| 109 ACPNCGSRdfE 119
                                       6******9542 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 ?    7.7   0.0    0.0044       2.8      12      24 ..      65      77 ..      59      80 .. 0.81
   2 ?    5.4   0.0     0.023        15      19      26 ..     109     116 ..     104     118 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0044
                                      --SSS----SSS- CS
                    DNA_RNApol_7kD 12 lkkgdpiRCkeCG 24
                                      +++++  +C++CG
  gi|242398986|ref|YP_002994410.1| 65 IIEEAEFKCRNCG 77
                                      7788899*****9 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.023
                                       --SSS--- CS
                    DNA_RNApol_7kD  19 RCkeCGhR 26 
                                        C +CG+R
  gi|242398986|ref|YP_002994410.1| 109 ACPNCGSR 116
                                       6*****99 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1     0.036        23      18      24 ..      72      78 ..      66      79 .. 0.80
   2 ?    8.9   0.1    0.0016         1      19      24 ..     110     115 ..     107     119 .. 0.68

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.036
                       zf-ribbon_3 18 vCpyCGt 24
                                      +C +CG 
  gi|242398986|ref|YP_002994410.1| 72 KCRNCGN 78
                                      5888886 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0016
                       zf-ribbon_3  19 CpyCGt 24 
                                       Cp+CG+
  gi|242398986|ref|YP_002994410.1| 110 CPNCGS 115
                                       555554 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 ?    9.7   1.1    0.0012      0.74      29      39 .]      71      81 ..      68      81 .. 0.92
   2 ?    5.5   0.0     0.025        16       2      10 ..     109     117 ..     106     121 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0012
                           TFIIS_C 29 ykCtkCghrWr 39
                                      +kC +Cg++W+
  gi|242398986|ref|YP_002994410.1| 71 FKCRNCGNEWK 81
                                      89********7 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.025
                           TFIIS_C   2 kCpkCgsre 10 
                                        Cp+Cgsr+
  gi|242398986|ref|YP_002994410.1| 109 ACPNCGSRD 117
                                       588888875 PP

>> KGK  KGK domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   1.9   6.5e-05     0.042      70     102 ..      39      75 ..      14      97 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.5e-05
                               KGK  70 idceiLkigskgWqkGklkikvsleFipdepe....i 102
                                       ++ eiL++  ++ +kG++  +  leFi++e e    +
  gi|242398986|ref|YP_002994410.1|  39 VNQEILEFAINEIKKGTIAEEAELEFIIEEAEfkcrN 75 
                                       7789**************************9966653 PP

>> zf-ZPR1  ZPR1 zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.2      0.69   4.4e+02      30      39 ..      70      79 ..      60      88 .. 0.76
   2 ?   12.8   0.8   0.00013     0.081      10      47 ..      87     124 ..      71     134 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.69
                           zf-ZPR1 30 sfeCehCgyk 39
                                       f+C++Cg +
  gi|242398986|ref|YP_002994410.1| 70 EFKCRNCGNE 79
                                      5899999854 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00013
                           zf-ZPR1  10 ngetrllltkiPyfkeviimsfeCehCgyknnevksag 47 
                                       ++ +++++ +i ++ ev+   + C++Cg ++ ev  + 
  gi|242398986|ref|YP_002994410.1|  87 ESFNETIKEDIHFIPEVVHAFLACPNCGSRDFEVTKGR 124
                                       3445566679***********************98875 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   0.4    0.0046         3       1       8 [.      72      79 ..      68      80 .. 0.89
   2 ?    7.4   0.2    0.0057       3.6      16      20 ..     110     114 ..     106     116 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0046
                     zinc_ribbon_2  1 fCpnCGae 8 
                                      +C nCG+e
  gi|242398986|ref|YP_002994410.1| 72 KCRNCGNE 79
                                      79999997 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0057
                     zinc_ribbon_2  16 CpyCG 20 
                                       Cp+CG
  gi|242398986|ref|YP_002994410.1| 110 CPNCG 114
                                       66666 PP

>> MCM_OB  MCM OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   7.1e-05     0.045      17      68 ..      53     121 ..      37     133 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.1e-05
                                       EEEEEEE---EEEEEEEEEEETTT-.-EEE.S---.............-S......B-..TTT-HHH-EEE- CS
                            MCM_OB  17 eGivtrasevkpklkkavfeckkcgktvev.elee.............Pr......kCeekeCeskdpfkle 68 
                                       +G++ +  e++  +++a f+c++cg++ ++ +++e             P+       C  ++C+ ++ f+++
  gi|242398986|ref|YP_002994410.1|  53 KGTIAEEAELEFIIEEAEFKCRNCGNEWKLkDVKEsfnetikedihfiPEvvhaflAC--PNCG-SRDFEVT 121
                                       6999999999999*************98864455566668888888887788888899..99*9.4666665 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.1     0.018        11      22      29 ..      73      80 ..      67      81 .. 0.87
   2 ?    9.8   1.0    0.0011      0.73       4      27 ..      72     115 ..      72     116 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.018
                    PhnA_Zn_Ribbon 22 CpeCahEw 29
                                      C +C++Ew
  gi|242398986|ref|YP_002994410.1| 73 CRNCGNEW 80
                                      99****** PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0011
                    PhnA_Zn_Ribbon   4 kCplCaSeytY....................edgallvCpeCah 27 
                                       kC +C+ e  +                    + +a l Cp+C++
  gi|242398986|ref|YP_002994410.1|  72 KCRNCGNEWKLkdvkesfnetikedihfipeVVHAFLACPNCGS 115
                                       89999999999999999999999999999999999999****86 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0      0.09        58      27      36 ..      61      78 ..      30      98 .. 0.65
   2 ?    8.4   0.0    0.0042       2.7       4      23 ..     108     127 ..     105     131 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.09
                   Lar_restr_allev 27 q........cvyCadCga 36
                                      +         + C +Cg 
  gi|242398986|ref|YP_002994410.1| 61 ElefiieeaEFKCRNCGN 78
                                      044555556899****98 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0042
                   Lar_restr_allev   4 kpCPfCggravlersqrvva 23 
                                       + CP Cg+r+  ++ +r+v+
  gi|242398986|ref|YP_002994410.1| 108 LACPNCGSRDFEVTKGRGVY 127
                                       67********9999988887 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   4.6    0.0018       1.2       5      35 ..      70     117 ..      70     119 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0018
                       Zn-ribbon_8   5 eYrCeeCghefe..............vlqsisdap.........ltaCPeCgs.e 35 
                                       e++C++Cg+e                                    aCP+Cgs +
  gi|242398986|ref|YP_002994410.1|  70 EFKCRNCGNEWKlkdvkesfnetikeD-------IhfipevvhaFLACPNCGSrD 117
                                       8********999987666555554441.......0455556665888****9955 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.1    0.0052       3.3      24      36 .]      69      81 ..      66      81 .. 0.85
   2 ?    4.3   0.0     0.061        39       4      10 ..     109     115 ..     107     120 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0052
                     zinc_ribbon_4 24 vkvrCskCghvFr 36
                                      ++ +C +Cg+ ++
  gi|242398986|ref|YP_002994410.1| 69 AEFKCRNCGNEWK 81
                                      578*******995 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.061
                     zinc_ribbon_4   4 tCpsCka 10 
                                        Cp+C++
  gi|242398986|ref|YP_002994410.1| 109 ACPNCGS 115
                                       5888875 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     0.006       3.9      43      56 ..      67      80 ..      54      90 .. 0.80
   2 ?    4.2   0.0     0.066        42      31      40 ..     110     119 ..     108     128 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.006
                    OrfB_Zn_ribbon 43 sgrtfkCpnCgfea 56
                                      ++ +fkC+nCg e+
  gi|242398986|ref|YP_002994410.1| 67 EEAEFKCRNCGNEW 80
                                      5689*******996 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.066
                    OrfB_Zn_ribbon  31 CseCgsknke 40 
                                       C++Cgs++ e
  gi|242398986|ref|YP_002994410.1| 110 CPNCGSRDFE 119
                                       9999998766 PP

>> Prim_Zn_Ribbon  Zinc-binding domain of primase-helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1       1.1   7.2e+02      28      33 ..      73      77 ..      69      83 .. 0.71
   2 ?   11.9   0.1   0.00033      0.21       5      13 ..     109     117 ..     107     127 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 1.1
                                      ETTTTB CS
                    Prim_Zn_Ribbon 28 CrqCgg 33
                                      Cr C g
  gi|242398986|ref|YP_002994410.1| 73 CRNC-G 77
                                      6666.3 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00033
                                       --TTTT-TT CS
                    Prim_Zn_Ribbon   5 pCPvCGGrD 13 
                                       +CP+CG+rD
  gi|242398986|ref|YP_002994410.1| 109 ACPNCGSRD 117
                                       7*******9 PP

>> zf-HYPF  HypF finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1       0.3   1.9e+02      24      28 ..      73      77 ..      69      82 .. 0.76
   2 ?    9.8   0.1     0.001      0.67      20      30 ..     106     116 ..     104     117 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.3
                                      -TTTS CS
                           zf-HYPF 24 CtnCG 28
                                      C nCG
  gi|242398986|ref|YP_002994410.1| 73 CRNCG 77
                                      99999 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.001
                                       TT---TTTS-- CS
                           zf-HYPF  20 qfisCtnCGPr 30 
                                        f +C+nCG r
  gi|242398986|ref|YP_002994410.1| 106 AFLACPNCGSR 116
                                       699******87 PP

>> zf-3CxxC  Zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.7   0.00028      0.18       4      31 ..      69      96 ..      67     124 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00028
                          zf-3CxxC  4 grfeCskCskkWtSakvavtfrvylerq 31
                                      ++f+C++C+++W+ + v  +f+  +++ 
  gi|242398986|ref|YP_002994410.1| 69 AEFKCRNCGNEWKLKDVKESFNETIKED 96
                                      68***************99999887765 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 ?    1.4   0.2      0.42   2.7e+02      97     116 ..      61      78 ..      53      79 .. 0.68
   2 ?    9.3   0.0    0.0015      0.97      81     107 ..     101     127 ..      85     132 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.42
                                       CEEECCSSSCEEEEESSSTC CS
                      eIF-5_eIF-2B  97 etelekeerllvlkCkaCga 116
                                       e e+++ee  +  kC++Cg+
  gi|242398986|ref|YP_002994410.1|  61 ELEFIIEEAEF--KCRNCGN 78 
                                       44555555544..9****97 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0015
                                       HHHHHHHTSTSSSTSTCEEECCSSSCE CS
                      eIF-5_eIF-2B  81 dkyieeyVlCkeCkspetelekeerll 107
                                        + ++ ++ C++C+s + e++k + ++
  gi|242398986|ref|YP_002994410.1| 101 PEVVHAFLACPNCGSRDFEVTKGRGVY 127
                                       556889*************99976665 PP

>> DpnI  Dam-replacing family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.3   0.00048      0.31      52      78 ..      69      95 ..      59     100 .. 0.90
   2 ?    1.0   0.1      0.43   2.8e+02      30      42 ..     106     118 ..      97     125 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00048
                                      -EEE-TTT--EEEEEEEESS--SEEEE CS
                              DpnI 52 aDfyCesckeefeLkskksklskkivd 78
                                      a+f C++c +e++Lk  k++++++i++
  gi|242398986|ref|YP_002994410.1| 69 AEFKCRNCGNEWKLKDVKESFNETIKE 95
                                      79*******************999975 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.43
                                       HH---TTT--SS- CS
                              DpnI  30 knlyCpkCgskkl 42 
                                         l Cp+Cgs+ +
  gi|242398986|ref|YP_002994410.1| 106 AFLACPNCGSRDF 118
                                       5567*****9854 PP

>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.6     0.048        31      16      24 .]      70      78 ..      66      78 .. 0.87
   2 ?    9.7   0.3    0.0012      0.79      18      23 ..     109     114 ..     105     115 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.048
                           DUF1610 16 vFpCPNCGE 24
                                      +F C NCG+
  gi|242398986|ref|YP_002994410.1| 70 EFKCRNCGN 78
                                      79******7 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0012
                           DUF1610  18 pCPNCG 23 
                                       +CPNCG
  gi|242398986|ref|YP_002994410.1| 109 ACPNCG 114
                                       6****9 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1     0.072        46       5      12 ..      71      78 ..      67      84 .. 0.63
   2 ?    9.9   0.2   0.00093       0.6       6      16 ..     109     119 ..     108     120 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.072
                           zf-RRN7  5 ppCgvCgc 12
                                      + C  Cg+
  gi|242398986|ref|YP_002994410.1| 71 FKCRNCGN 78
                                      55666665 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00093
                           zf-RRN7   6 pCgvCgcrsft 16 
                                       +C+ Cg+r+f 
  gi|242398986|ref|YP_002994410.1| 109 ACPNCGSRDFE 119
                                       7********95 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 ?    1.7   0.5      0.39   2.5e+02      13      18 ..      72      77 ..      72      79 .. 0.77
   2 ?   11.0   0.2   0.00047       0.3      27      37 .]     109     119 ..     106     119 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.39
                           DUF35_N 13 rCpdCG 18
                                      +C++CG
  gi|242398986|ref|YP_002994410.1| 72 KCRNCG 77
                                      688888 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00047
                           DUF35_N  27 vCphCgsddle 37 
                                       +Cp+Cgs+d+e
  gi|242398986|ref|YP_002994410.1| 109 ACPNCGSRDFE 119
                                       7********98 PP

>> Sgf11  Sgf11 (transcriptional regulation protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.3     0.021        14       3      11 ..      69      77 ..      67      79 .. 0.85
   2 ?    4.9   0.1     0.029        19       4      11 ..     107     114 ..     105     116 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.021
                                      -EEE-TTTS CS
                             Sgf11  3 eyvtCpnCg 11
                                      + ++C nCg
  gi|242398986|ref|YP_002994410.1| 69 AEFKCRNCG 77
                                      579*****8 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.029
                                       EEE-TTTS CS
                             Sgf11   4 yvtCpnCg 11 
                                       +  CpnCg
  gi|242398986|ref|YP_002994410.1| 107 FLACPNCG 114
                                       678****8 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.7     0.013       8.5       1       9 [.      71      79 ..      71      80 .. 0.86
   2 ?    3.7   0.7     0.078        50      17      22 ..     110     115 ..     109     117 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.013
                      Rubredoxin_2  1 YvCsqCGfe 9 
                                      + C++CG+e
  gi|242398986|ref|YP_002994410.1| 71 FKCRNCGNE 79
                                      78*****85 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.078
                      Rubredoxin_2  17 CpsCgs 22 
                                       Cp+Cgs
  gi|242398986|ref|YP_002994410.1| 110 CPNCGS 115
                                       999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       800  (0.0446204); expected 358.6 (0.02)
Passed bias filter:                      623  (0.0347482); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); expected 17.9 (0.001)
Passed Fwd filter:                        28  (0.00156172); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              28  [number of targets reported over threshold]
# CPU time: 0.55u 0.40s 00:00:00.95 Elapsed: 00:00:00.57
# Mc/sec: 730.63
//
Query:       gi|242398987|ref|YP_002994411.1|  [L=458]
Description: glutamate aminotransferase [Thermococcus sibiricus MM 739]
Scores for complete 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-97  326.0   0.0    3.4e-97  325.7   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 !  325.7   0.0  1.9e-101   3.4e-97       9     406 .]      35     442 ..      28     442 .. 0.94

  Alignments for each domain:
  == domain 1  score: 325.7 bits;  conditional E-value: 1.9e-101
                                       SCEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHCT- CS
                       Aminotran_3   9 lllvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllklapk 85 
                                       +++v +++ G+ ++dvdg+ ++D++++ a++ +G+ahPk+vk v+eq+ k++h ++g + ++ a+++ae+l++  p 
  gi|242398987|ref|YP_002994411.1|  35 FPVVPERGYGALIEDVDGNVFIDFLAGAAAASTGYAHPKLVKEVQEQVSKIQHSMIGYTYSKRAIEVAEILAEKSPI 111
                                       45899************************************************************************ PP

                                       ..SEEEEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEEEE-T CS
                       Aminotran_3  86 gldkvflansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevvrlky 162
                                       +  k+++  sGs+++   +K+ar       at+k+ iiaf ga+HG+t+ga sv++ ++  k++f p++p+vv ++y
  gi|242398987|ref|YP_002994411.1| 112 ENPKILFGLSGSDSIDLLMKVARF------ATRKPWIIAFIGAYHGQTYGATSVAAFQSSQKRGFSPLVPNVVWIPY 182
                                       999*********************......*********************************************** PP

                                       TBGGGTB-HH.......HHHHHHHHHHHHHH...CHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EE CS
                       Aminotran_3 163 pdeevlkene.......eeeaalleeleale...kkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvll 229
                                       p +++   n        e  +a l +le++        dev+ ++ Epiqg++G+vv++++f+++l+++ ++ ++ll
  gi|242398987|ref|YP_002994411.1| 183 PNPYRNVWNIdgyeepdELINAFLDYLENYVfahVIPPDEVSILLAEPIQGDAGIVVPPDNFFKELKKVLDEREILL 259
                                       **99987776666644344455556666665884445799************************************* PP

                                       EEE-TTTTTTTTSSSSGGGGCTS--SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTSB--TTTT-HHHHHHHHHHHH CS
                       Aminotran_3 230 ivDEvqtGfGrTGklfAlehagvspDlmtlaKaltgGlplsavlataevmqalapgshgsTfgGnplacavalavle 306
                                        +DEvqtG+GrTGk+f+ e+++v+pD++ ++K++++G+ ls v+++a +m++  +gs   T ++np+  a+a a+l+
  gi|242398987|ref|YP_002994411.1| 260 AMDEVQTGIGRTGKWFGSEWFEVEPDFISFGKGVASGMGLSGVIGKAHLMEMT-SGSALLTPAANPVISAAAYATLR 335
                                       ***************************************************99.999999***************** PP

                                       HHHHTTHHHHHHHHHHHHHHHHHHHCTT-TTEEEEEEETTEEEEEEBCCCETTC.....HHHHHHHHHCTEE-EEET CS
                       Aminotran_3 307 iieeekllenaqelgaalkegLeelqkkyevikevRgkGlmiaielkeeaevke.....keilkkakekGvlilsaG 378
                                       iieee+ll+na ++g+ +k++L e++++y+vi++vRgkGlmi++e+++++++ +      +i+ +a e G+++ s G
  gi|242398987|ref|YP_002994411.1| 336 IIEEENLLKNALKVGEFIKKRLLEMKESYDVIGDVRGKGLMIGAEIVKPNTKVPnpdltGKICWRAFELGLILPSYG 412
                                       **************************************************966699*9988**************** PP

                                       T..TEEEE---TT--HHHHHHHHHHHHHHH CS
                       Aminotran_3 379 d..nvirllppliitdeeidelleilkkal 406
                                       +  nvir++ppl+it++ ++++lei+++al
  gi|242398987|ref|YP_002994411.1| 413 MfgNVIRITPPLVITKKIAEKGLEIMEQAL 442
                                       999************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (458 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:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.52
# Mc/sec: 2625.47
//
Query:       gi|242398988|ref|YP_002994412.1|  [L=372]
Description: metallocofactor modifying protein, radical SAM superfamily [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.6e-17   63.1   0.4    8.1e-17   61.5   0.4    1.9  1  SPASM        Iron-sulfur cluster-binding domain
    1.9e-15   57.6   0.1    2.8e-15   57.1   0.1    1.3  1  Radical_SAM  Radical SAM superfamily
    8.3e-09   35.6   0.0    1.9e-08   34.4   0.0    1.6  1  Fer4_14      4Fe-4S single cluster domain
    1.8e-07   31.5   0.3    2.5e-06   27.8   0.0    2.5  3  Fer4_12      4Fe-4S single cluster domain


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 !   61.5   0.4   1.8e-20   8.1e-17       1      68 []     249     327 ..     249     327 .. 0.83

  Alignments for each domain:
  == domain 1  score: 61.5 bits;  conditional E-value: 1.8e-20
                             SPASM   1 C.fapsrslfInsdGdVvpCcvd...........kktyveelklGnireesleeIwnseeyqefrkskkfplielCr 65 
                                       C f++ + +++++dG+VvpC+             + + ve +++Gn++e+sl+eIw+s ey++fr s +++l+++C+
  gi|242398988|ref|YP_002994412.1| 249 CdFVENNVAVVRWDGEVVPCYRFlhtypeyifgrH-KKVEAYSFGNVKEKSLKEIWTSREYTWFRFSVRNSLYPSCT 324
                                       88899999************433667777777743.33344************************555899999*** PP

                             SPASM  66 nCp 68 
                                       +Cp
  gi|242398988|ref|YP_002994412.1| 325 DCP 327
                                       **7 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.1   0.1   6.3e-19   2.8e-15       1     165 [.      24     185 ..      24     195 .. 0.81

  Alignments for each domain:
  == domain 1  score: 57.1 bits;  conditional E-value: 6.3e-19
                                       EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEES.STGGGSTTHHHHHHHHHHTCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgg.gepllypdfvellerlaklavp 76 
                                       v++t+ CnlrC  C   +   +e+ + +++    l++++   + ++ k v +gg gepl++p+f + +++ +k+   
  gi|242398988|ref|YP_002994412.1|  24 VEITNRCNLRCEMCFKQY---WEDEEGDIDYNLFLKILDGTEEFPNLKMVYFGGiGEPLVHPRFMDMVKEVKKK--- 94 
                                       689**************8...9999999999999999999954444776666644******************8... PP

                                       TEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHH..HHHHHHTCTSHHHHHHHHHHHHHHTTSET.EEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
                       Radical_SAM  77 giritvetngtlpdeeklerllelgvdrvslgleaadde..kvlklmnrghtfeevlealeklreagikr.vvdriv 150
                                       g+ + ++tng+l++e  +e+l++l+vd ++++l+a+     +    m +  t+e++++  e  r+ + +   v + v
  gi|242398988|ref|YP_002994412.1|  95 GYAVGISTNGFLLTEGLIEELVKLRVDLIYISLDAIPTQptRLGHVM-PSVTVERLKKFAEVKRKENTEIpHVGVEV 170
                                       **************************************965555555.66666666666666666654446444444 PP

                                       EBTTTSHHHHHHHHH CS
                                       xxxxxxxxxxxxxxx RF
                       Radical_SAM 151 glpGendeeleelle 165
                                       +l  en  ++ el++
  gi|242398988|ref|YP_002994412.1| 171 VLTKENYTQMAELVK 185
                                       455577766666665 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   0.0   4.2e-12   1.9e-08       4      94 ..      26     109 ..      22     129 .. 0.81

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 4.2e-12
                           Fer4_14   4 rlsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltG.GePLhyenkkellklvkrlkeeyp 79 
                                        +++Cnl C +C+++  w++e g ++ +  l +il d +++  + + + + G GePL +   + ++++vk++k+++ 
  gi|242398988|ref|YP_002994412.1|  26 ITNRCNLRCEMCFKQY-WEDEEGDIDYNLFL-KIL-DGTEEFPNLKMVYFGGiGEPLVH---PRFMDMVKEVKKKG- 95 
                                       489**********999.******99988888.999.4444444456677777*****99...9*************. PP

                           Fer4_14  80 ekkiwletngtleie 94 
                                        + + + tng l  e
  gi|242398988|ref|YP_002994412.1|  96 -YAVGISTNGFLLTE 109
                                       .********988755 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      12     100 ..      27     111 ..      19     129 .. 0.79
   2 ?   -1.4   0.0      0.59   2.7e+03      49      84 ..     156     192 ..     132     200 .. 0.60
   3 ?    0.2   0.0      0.19   8.3e+02      79     106 ..     294     318 ..     289     335 .. 0.74

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 5.6e-10
                           Fer4_12  12 vsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllG..GEPllpenaeallelvkevkeekpek 86 
                                       +++Cnl+C+ Cf k+ w+ ++g +++ +l  +i++ +++  + +++++G  GEPl+    + ++++vkevk++++  
  gi|242398988|ref|YP_002994412.1|  27 TNRCNLRCEMCF-KQYWEDEEG-DIDYNLFLKILDGTEEFPNLKMVYFGgiGEPLV---HPRFMDMVKEVKKKGY-A 97 
                                       579*********.677766555.56778889999999986666666666377****...9***************.5 PP

                           Fer4_12  87 diwlytgytleels 100
                                       + ++++g+ l e +
  gi|242398988|ref|YP_002994412.1|  98 VGISTNGFLLTEGL 111
                                       99******998865 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.59
                           Fer4_12  49 kkesiegltllGGEPll.penaeallelvkevkeekp 84 
                                       k ++++++  +G E +l  en+ +++elvk++ + ++
  gi|242398988|ref|YP_002994412.1| 156 KRKENTEIPHVGVEVVLtKENYTQMAELVKYLSKFNI 192
                                       3344566666666655414566778888887776655 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.19
                           Fer4_12  79 vkeekpekdiwlytgytleelskkekee 106
                                       vke+ + k+iw +  yt++ +s +  ++
  gi|242398988|ref|YP_002994412.1| 294 VKEKSL-KEIWTSREYTWFRFSVR--NS 318
                                       677777.79*********999843..33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); 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: 0.68u 0.34s 00:00:01.02 Elapsed: 00:00:00.56
# Mc/sec: 2016.52
//
Query:       gi|242398989|ref|YP_002994413.1|  [L=82]
Description: molybdopterin converting factor, subunit 1 [Thermococcus sibiricus MM 739]
Scores for 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-21   75.9   0.2    3.3e-21   75.7   0.2    1.0  1  ThiS             ThiS family
     0.0009   19.5   0.2     0.0011   19.2   0.2    1.4  1  Urm1             Urm1 (Ubiquitin related modifier)
     0.0023   17.6   1.0       0.87    9.4   0.0    2.8  3  DUF348           G5-linked-Ubiquitin-like domain
     0.0031   16.4   0.1     0.0066   15.3   0.1    1.6  1  Transposase_mut  Transposase, Mutator family
  ------ inclusion threshold ------
      0.043   14.7   0.0      0.049   14.6   0.0    1.1  1  IL1_propep       Interleukin-1 propeptide


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 !   75.7   0.2   9.2e-25   3.3e-21       1      77 []       4      82 .]       4      82 .] 0.98

  Alignments for each domain:
  == domain 1  score: 75.7 bits;  conditional E-value: 9.2e-25
                                      EEETTCCHHHHTCEEEEESSTSBHHHHHHHHHHHTCHHG..TTTTEEEEETTEEEGC.CTTTSB--TTCEEEEEESTTC CS
                              ThiS  1 vllfaelrelageeelelaegstvaelleaLgerypela..lerrvavavNgeivpr.lwldtelkdgDevailppVaG 76
                                      v++fa+lr ++  + +++ ++ tv+elle+L  +yp+++  le++v+++vNg+++++ + l+t+lkd D v+i+ppV+G
  gi|242398989|ref|YP_002994413.1|  4 VRFFATLRNIVR-KNELELQANTVGELLEKLYSKYPKIEkeLEKGVVILVNGKNIEHlEKLNTKLKDEDLVSIFPPVGG 81
                                      89*********7.99999***********************99**************88******************** PP

                                      - CS
                              ThiS 77 G 77
                                      G
  gi|242398989|ref|YP_002994413.1| 82 G 82
                                      9 PP

>> Urm1  Urm1 (Ubiquitin related modifier)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.2   3.2e-07    0.0011      54      96 .]      39      82 .]       2      82 .] 0.78

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 3.2e-07
                                      S.TTSB-TTEEEEETTCEHHHCTCCCSB--TTEEEEEEETTT-- CS
                              Urm1 54 e.kdkvrPGilvLindaDwellgekdyelkdkDkivFistlhGG 96
                                      + ++++  G+++L+n  ++e l++++++lkd+D ++    + GG
  gi|242398989|ref|YP_002994413.1| 39 KiEKELEKGVVILVNGKNIEHLEKLNTKLKDEDLVSIFPPVGGG 82
                                      4478999**************************99877666665 PP

>> DUF348  G5-linked-Ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0   0.00024      0.87      14      26 ..      21      33 ..      15      41 .. 0.85
   2 ?   -0.5   0.0      0.29     1e+03       1       8 [.      48      55 ..      48      59 .. 0.82
   3 !    5.8   0.2    0.0032        11      23      37 ..      60      74 ..      57      75 .. 0.94

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00024
                                      ---SSHHHHHHHT CS
                            DUF348 14 TaadTVgdlLeea 26
                                        a+TVg+lLe++
  gi|242398989|ref|YP_002994413.1| 21 LQANTVGELLEKL 33
                                      579********86 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.29
                                      EEEEETTE CS
                            DUF348  1 VtltvDGk 8 
                                      V + v+Gk
  gi|242398989|ref|YP_002994413.1| 48 VVILVNGK 55
                                      7899***9 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.0032
                                      HHHTT----TT-EEE CS
                            DUF348 23 LeeagitlgeqDkVs 37
                                      Le+++ +l+++D Vs
  gi|242398989|ref|YP_002994413.1| 60 LEKLNTKLKDEDLVS 74
                                      89************8 PP

>> Transposase_mut  Transposase, Mutator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   1.9e-06    0.0066     276     317 ..       7      48 ..       2      79 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.9e-06
                   Transposase_mut 276 aealksiykaedaeearealeefleklgkkypkvaelldeaa 317
                                        ++l+ i +++++e   +++ e+lekl +kypk+++ l++++
  gi|242398989|ref|YP_002994413.1|   7 FATLRNIVRKNELELQANTVGELLEKLYSKYPKIEKELEKGV 48 
                                       5789***********************************987 PP

>> IL1_propep  Interleukin-1 propeptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.4e-05     0.049      44      99 ..      21      76 ..       8      79 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.4e-05
                        IL1_propep 44 lkedlvdkgiqlkiseqsksk.sfkesvvvvvAveklkkrrlslnqsfqddDLeaif 99
                                      l+ + v + ++   s+ +k + ++++ vv++v  + + +   +ln++++d+DL +if
  gi|242398989|ref|YP_002994413.1| 21 LQANTVGELLEKLYSKYPKIEkELEKGVVILVNGKNIEH-LEKLNTKLKDEDLVSIF 76
                                      455666666666667776666699999**9999999999.589************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1188  (0.0662614); expected 358.6 (0.02)
Passed bias filter:                      884  (0.0493056); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 572.87
//
Query:       gi|242398990|ref|YP_002994414.1|  [L=605]
Description: Tungsten-containing aldehyde ferredoxin oxidoreductase (AOR) [Thermococcus sibiricus MM 739]
Scores for 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-149  497.2   0.0   3.7e-149  496.9   0.0    1.1  1  AFOR_C    Aldehyde ferredoxin oxidoreductase, domains 2 & 3
    6.2e-89  297.1   0.1      9e-89  296.6   0.1    1.2  1  AFOR_N    Aldehyde ferredoxin oxidoreductase, N-terminal doma


Domain annotation for each model (and alignments):
>> AFOR_C  Aldehyde ferredoxin oxidoreductase, domains 2 & 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  496.9   0.0  4.1e-153  3.7e-149       2     382 .]     220     601 ..     219     601 .. 0.97

  Alignments for each domain:
  == domain 1  score: 496.9 bits;  conditional E-value: 4.1e-153
                                       HHHHHHHHHHHSH.HHHHHHHH-GGGHHHHHHHTT---BTTTTBS--TTGGGGSHHHHHHHTEEEE.E-TT-SS--E CS
                            AFOR_C   2 lgkkiqkeiksspqvtaelrkyGTaelvnianetgalptknfqegtfekaekisgealeekylvknegCfsCpiaCg 78 
                                       ++k+  k+ik++p + ++l++yGTa+lvni+ne+g++pt+nfq+g+f+ a++ sgeal  kylv+n++Cf+Cpi Cg
  gi|242398990|ref|YP_002994414.1| 220 VVKEKIKKIKENPITGGGLPQYGTAVLVNIINENGLYPTYNFQTGVFKYAYEQSGEALVAKYLVRNHSCFACPIGCG 296
                                       5788899******7777*************************************************99********* PP

                                       EEEE......ETEE---HHHHHHHTGGGT---HHHHHHHHHHHHHHTB-HHHHHHHHHHHHHHHHTTSS-HHHH.TS CS
                            AFOR_C  79 revkveegkkvkvegpeyetlaalGsnlgiddleailklnelcdelGlDtisaGntiafamelyekGllkkedt.dg 154
                                       r+   +      +egpeye+++alG+++gi+dl++i+ +n+lcde GlDtis+G+t+a amelyekG++k+e++ d 
  gi|242398990|ref|YP_002994414.1| 297 RVSYHPAVGV--TEGPEYESIWALGATCGINDLASITIANHLCDEFGLDTISTGGTLAAAMELYEKGIIKQEELgDA 371
                                       **99655553..89***********************************************************9666 PP

                                       ----TT-THHHHHHHHHHHTT-TTHHHHTT-HHHHHHCTT-GGG--EETTEE--SS-GGG-HHHHHHHHH-TTSS-S CS
                            AFOR_C 155 lelefgdaeallellekiAkregigdllAeGvkrlaeklgaeelamhvkGlelpaydprgakgmalaYatsnrGacH 231
                                        +l+fg+ e l   +ekiAkreg+gd lAeG++rlae +g++e++m+vk++elpaydprga g++++YatsnrG+cH
  gi|242398990|ref|YP_002994414.1| 372 PPLRFGNSEVLHYYIEKIAKREGFGDKLAEGSYRLAESYGHPEYSMSVKKQELPAYDPRGAEGHGVTYATSNRGGCH 448
                                       789************************************************************************** PP

                                       GGG-THHHH.....S---TT--.HHHHHHHHHHHHHHHHHHHHT--GGGG-HHH......HHHHHHHHHT----HHH CS
                            AFOR_C 232 lrayliale.....ekvdplet.egkaelvkwfqdltalvdslglCkftseaeerldlelyakllsavtGidvteee 302
                                       +r+y+i++e      k+dp++  e+ka++vk fqdlta++ds+glC+fts     l  ++ya++l+a+tG+++t++e
  gi|242398990|ref|YP_002994414.1| 449 VRGYMISPEilgvpVKLDPHDVsEEKAKWVKIFQDLTAVIDSAGLCLFTS---FALGADDYAEMLNAATGFEFTTDE 522
                                       **************99******99**************************...5678899***************** PP

                                       HHHHHHHHHHHHHHHHHHHT--H.HHS---HHHHHS---SSTTTT---..-HHHHHHHHHHHHT--TTS---HHHHH CS
                            AFOR_C 303 llkaGeRiynleRlfnlreGltr.kddtlperlleeplkegpakgkvledeleemldeyYelrGWdetGvPtketlk 378
                                        lkaGeR++nleR+fnl++Gl + kddtlp+r+leep++egp+kg+v+  +l+e l++yY+lrGWde+G Pt+e+lk
  gi|242398990|ref|YP_002994414.1| 523 WLKAGERVWNLERIFNLKAGLIPeKDDTLPKRFLEEPMPEGPNKGHVV--KLHEILPKYYKLRGWDEKGYPTEEKLK 597
                                       ********************9988***********************9..9************************** PP

                                       HCT- CS
                            AFOR_C 379 rLgL 382
                                        L+L
  gi|242398990|ref|YP_002994414.1| 598 GLDL 601
                                       9987 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 !  296.6   0.1     1e-92     9e-89       1     198 []       6     206 ..       6     206 .. 0.98

  Alignments for each domain:
  == domain 1  score: 296.6 bits;  conditional E-value: 1e-92
                                       SEEEEEETTTTEEEEEE--HHHHHHH-SCHHHHHHHHHHHS-TTS-TTSTTS-EEEEE-TTTTSSSTTB-EEEEEEE CS
                            AFOR_N   1 gkilrvdLstgkieveelpeelaekylGgrglaakllldevppgvdplspenplvfatGpltgtpapgsgrlvvvak 77 
                                       gkilrv+L+tg+i+veel+ee a++++Ggrg+a+k+ll+e++p+vdp+spen+l+fatGpltgt+ap+ gr++v++k
  gi|242398990|ref|YP_002994414.1|   6 GKILRVNLTTGEIKVEELKEEDAKNFIGGRGFASKFLLEEIDPKVDPFSPENKLIFATGPLTGTTAPTGGRYMVITK 82 
                                       79*************************************************************************** PP

                                       -TTTSSEEEEEEETCHHHHHHHCT-SEEEEES--SS-EEEEEETTEEEEEE-TTTTTS-HHHHHHHHHHHHTS...E CS
                            AFOR_N  78 sPltgtlgesnaGgrfgaelkraGydaivieGkaekpvylvieddkveiedaedlwgldtyettealkeelgd...k 151
                                       sPltg +++sn+Gg+fg+elk+aGyd+++ieGka++pvy++i+dd+vei+da++lwg+++ ett++l ee+gd   +
  gi|242398990|ref|YP_002994414.1|  83 SPLTGFIASSNSGGFFGPELKFAGYDMLIIEGKADHPVYISIKDDDVEIKDASHLWGKRVGETTDKLLEEFGDkkaR 159
                                       *********************************************************************99999888 PP

                                       EEEE-HHHHTT-TTB-E.EETTEEE-SSSHHHHHHHTTEEEEEEE-- CS
                            AFOR_N 152 vaviGpaGenlvrfAsisvddgraagrgGlGavmgsKnlkaivvrgt 198
                                       va+iGpaGe+lvr+A+i+ d++raagr+G+GavmgsKnlka+vvrgt
  gi|242398990|ref|YP_002994414.1| 160 VACIGPAGEKLVRLANIINDKHRAAGRSGVGAVMGSKNLKAVVVRGT 206
                                       99***************666999**********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (605 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.48
# Mc/sec: 3792.61
//
Query:       gi|242398991|ref|YP_002994415.1|  [L=425]
Description: CDP-alcohol phosphatidyltransferase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-15   56.7   0.0    5.7e-15   56.0   0.0    1.3  1  NTP_transf_3     MobA-like NTP transferase domain
    2.6e-14   53.4   0.0    8.5e-12   45.2   0.0    2.1  2  NTP_transferase  Nucleotidyl transferase
    6.9e-09   36.4   1.1    2.8e-08   34.4   0.1    2.4  3  CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
    3.7e-06   26.8   0.0    5.6e-06   26.3   0.0    1.3  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
  ------ inclusion threshold ------
      0.024   15.0   0.0       0.06   13.7   0.0    1.6  1  Propep_M14       Carboxypeptidase activation peptide
      0.097   12.7   0.9       0.78    9.8   0.1    2.2  2  HTH_56           Cch helix turn helix domain
       0.21   10.8   3.3       0.26   10.5   2.5    1.5  2  Voltage_CLC      Voltage gated chloride channel


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 !   56.0   0.0   2.2e-18   5.7e-15       1      97 [.       3     107 ..       3     120 .. 0.86

  Alignments for each domain:
  == domain 1  score: 56.0 bits;  conditional E-value: 2.2e-18
                                       EEEEEESS-TTTTT.....THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH...CHHHHHHTTC..TS-EEE-TT CS
                      NTP_transf_3   1 aviLAGGrSsRmgg.....dKallplggkpllervldalraagvdevvvvggd...eevlaalarl..gvrvveded 67 
                                       aviLA+G ++Rmg+     +K l++++g+ +l r++++l+++g++e v+v+++   e+ ++ l++   ++++v +  
  gi|242398991|ref|YP_002994415.1|   3 AVILAAGLGTRMGKlssklPKGLMKVAGREILYRTMKTLEKQGIEEFVIVTNPlykEKFEEFLRKNnfRYQLVINNF 79 
                                       79***********666789**********************************8866677666555336999***** PP

                                       SS-SHHHHHHHHHHHH.SSSCEEEEETT-T CS
                      NTP_transf_3  68 pgkgplaslaaalraaadadavlvlacDmP 97 
                                       p+kg ++sl+ a  ++  ++ +++++ D++
  gi|242398991|ref|YP_002994415.1|  80 PEKGNGYSLYLARLHV--SEKFVLVMSDHI 107
                                       ************9998..577777777776 PP

>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2   0.0   3.3e-15   8.5e-12       1     121 [.       2     114 ..       2     121 .. 0.87
   2 !    6.3   0.0    0.0024       6.1     174     246 ..     158     222 ..     139     224 .. 0.71

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 3.3e-15
                                       EEEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEE CS
                   NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevli 77 
                                       kavILa G GtR+  L+++l+k l+ v+g   +++ t+++l ++giee ++v+++  ++ +ee l++++ f+   l+
  gi|242398991|ref|YP_002994415.1|   2 KAVILAAGLGTRMGKLSSKLPKGLMKVAGR-EILYRTMKTLEKQGIEEFVIVTNPLYKEKFEEFLRKNN-FR-YQLV 75 
                                       79****************************.*****************9999**999999999999886.89.4455 PP

                                       EEESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHH CS
                   NTP_transferase  78 alepegkgtAdAvalaaelledeksdelvlvLggDhlikdayee 121
                                       +   ++kg   +++la++ + +++    vlv+ +Dh++++ +++
  gi|242398991|ref|YP_002994415.1|  76 INNFPEKGNGYSLYLARLHVSEKF----VLVM-SDHIYEEVFMK 114
                                       555566699***********9887....5655.79***996553 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0024
                                       EECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEEXSSHHHHHHHHHHHH CS
                   NTP_transferase 174 lassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWsDvGtldslleanekla 246
                                        +++G +v + e+++++ k l+e   ++ e+++i+++a    + +++ + ++   W+D+ t++++ +a+++l 
  gi|242398991|ref|YP_002994415.1| 158 ALDTGFFVLEAEIFDIIEKLLQEK--ESLELSEIVKEA----QLEVSEV-SGL-FWMDIDTPEDIKKAKKFLI 222
                                       567888888888888885555444..555666666665....3333322.232.6**********99998875 PP

>> CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       1.3   3.3e+03      40      56 ..     227     244 ..     202     250 .. 0.77
   2 !   34.4   0.1   1.1e-11   2.8e-08       4      66 .]     257     317 ..     254     317 .. 0.84
   3 ?   -2.0   0.1       2.6   6.7e+03      26      32 ..     361     391 ..     325     411 .. 0.54

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.3
                                       HTTHHHHHHHHTT-.--H CS
                   CDP-OH_P_transf  40 tDalDGklARrlnq.vst 56 
                                        ++ DG + R ln  +st
  gi|242398991|ref|YP_002994415.1| 227 KGSGDGIVSRYLNRrIST 244
                                       5677******99876454 PP

  == domain 2  score: 34.4 bits;  conditional E-value: 1.1e-11
                                       HHHHHHHHHHHHHHHHGGGS-H..HHHHHHHHHHHHHTTHHHHHHHHTT---HHHHHHHHHHH CS
                   CDP-OH_P_transf   4 naiTllrlllsvlailllltyyplvlailllliasltDalDGklARrlnqvstlGkllDslaD 66 
                                         +T+l+++ +++a++  +++    l+ +l+ + s++D++DG +AR   ++s++G ++Ds++D
  gi|242398991|ref|YP_002994415.1| 257 IHMTMLSFVVGIVAAVAAFFSP--PLGGVLYQLNSILDGVDGEIARAAMKTSKFGGYFDSILD 317
                                       5689999999999997664444..4777777799999***********99899********99 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 2.6
                                       ..........................HHHHH CS
                   CDP-OH_P_transf  26 p........................lvlail 32 
                                       +                        ++++il
  gi|242398991|ref|YP_002994415.1| 361 GeyfvniyktiprmkylfgkrdertFITMIL 391
                                       1444444444444444444444444222333 PP

>> IspD  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   2.2e-09   5.6e-06       2      66 ..       2      71 ..       1     105 [. 0.76

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 2.2e-09
                                      EEEEECTTSSCTT-...SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHHHHHGG...C CS
                              IspD  2 vvvipAAGsGkRmk...aglpKqflelkgqtllehtvdallaskavdkivvvvseddteefeqllld...k 66
                                       +vi AAG G+Rm+   + lpK +++++g+ +l +t+++l + + +++ v+v ++   e+fe++l +   +
  gi|242398991|ref|YP_002994415.1|  2 KAVILAAGLGTRMGklsSKLPKGLMKVAGREILYRTMKTLEK-QGIEEFVIVTNPLYKEKFEEFLRKnnfR 71
                                      69**********973335899*****************9988.8999999999999999**9999874433 PP

>> Propep_M14  Carboxypeptidase activation peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.3e-05      0.06      38      66 ..      51      79 ..      38      81 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.3e-05
                        Propep_M14 38 ilVppekledfeelLeslgisyevlieDv 66
                                      i+++p + e+fee+L++++  y+++i++ 
  gi|242398991|ref|YP_002994415.1| 51 IVTNPLYKEKFEEFLRKNNFRYQLVINNF 79
                                      88999**********************95 PP

>> HTH_56  Cch helix turn helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   0.00031      0.78      50      77 ..      57      83 ..      39      84 .. 0.92
   2 ?    0.8   0.1      0.19   4.9e+02      72      98 ..     116     143 ..      97     152 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00031
                            HTH_56 50 lknvfdkileeagFedtkvvlkelkekG 77
                                      +k++f+++l++++F  ++ v++++ ekG
  gi|242398991|ref|YP_002994415.1| 57 YKEKFEEFLRKNNF-RYQLVINNFPEKG 83
                                      799***********.***********98 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.19
                            HTH_56  72 elkekGllesekdrntkkrtv.kkkseg 98 
                                       +lk kGl++ +++++t++    k k+e+
  gi|242398991|ref|YP_002994415.1| 116 ALKGKGLVVDKEGSFTNREEAtKVKIEN 143
                                       5899*****999**99998884445544 PP

>> Voltage_CLC  Voltage gated chloride channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   2.5    0.0001      0.26      92     143 ..     265     316 ..     253     379 .. 0.74
   2 ?   -1.5   0.2      0.44   1.1e+03     181     257 ..     312     398 ..     298     411 .. 0.44

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0001
                                       HHHHHHHHHHHHT-HHHHHHHHCTTTSTSS--TTHHHHHHHHHHHHHHHHHH CS
                       Voltage_CLC  92 aaGaAAGiAAaFnaPlgGvlfalEevsrefslrallpvfvasvvaalvlrll 143
                                       ++G+ A +AA F+ PlgGvl+ l  +++ ++ +++ +++ +s ++ ++ ++l
  gi|242398991|ref|YP_002994415.1| 265 VVGIVAAVAAFFSPPLGGVLYQLNSILDGVDGEIARAAMKTSKFGGYFDSIL 316
                                       68999****************9999888887777777777777766666665 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.44
                                       HHHHHHHHHHHHHCHH.CHHHHHHHHHHHHHHHHHHHCCCSCC.CSSSSCCH.................HHHHCTT- CS
                       Voltage_CLC 181 fvrlllkverlfrkle.klkikkrlepalvgllvgllglllpasvlgggyel.................iasllegs 239
                                       f  +l +   +f  l  +l     l p + g ++++l+l+  +     +y++                 ++ l+ ++
  gi|242398991|ref|YP_002994415.1| 312 FDSILDRYVDFFVLLAlAL----HLNPDIWGWAIVSLALFGST---MVSYSTerykgeyfvniyktiprMKYLFGKR 381
                                       5555555555555553222....33344444444444444211...2222222233344445555555566666332 PP

                                       S-HHHHHH...HHHHHHH CS
                       Voltage_CLC 240 tlllsllllllllllkll 257
                                        +  ++++++l l+ k+ 
  gi|242398991|ref|YP_002994415.1| 382 -DERTFITMILCLIGKIE 398
                                       .22344444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1040  (0.0580066); expected 358.6 (0.02)
Passed bias filter:                      726  (0.0404931); 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: 0.70u 0.32s 00:00:01.02 Elapsed: 00:00:00.53
# Mc/sec: 2399.58
//
Query:       gi|242398992|ref|YP_002994416.1|  [L=501]
Description: Cobalt-activating carboxypeptidase, M32 family [Thermococcus sibiricus MM 739]
Scores for complete 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-169  564.3   0.0   2.5e-169  564.2   0.0    1.0  1  Peptidase_M32  Carboxypeptidase Taq (M32) metallopeptidase
  ------ inclusion threshold ------
       0.49    9.6   3.0        4.9    6.3   0.3    2.8  3  Peptidase_M3   Peptidase family M3


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 !  564.2   0.0  2.8e-173  2.5e-169       3     488 .]      15     499 ..      13     499 .. 0.98

  Alignments for each domain:
  == domain 1  score: 564.2 bits;  conditional E-value: 2.8e-173
                     Peptidase_M32   3 kellkkvsalesasallewDketvmpkkgaearaeqlatLselahelltseevaellekleeekeeldekekavvee 79 
                                         ++kk++a+ +a+++l wD+e++mpk g+ +r+ + + Ls l++ l+ ++++ el+ek+++ ++ l+e ek vv+ 
  gi|242398992|ref|YP_002994416.1|  15 LGHYKKIWAIGHAQSVLGWDMEVNMPKMGITERSVARGELSVLSQSLTLDPKFLELVEKAAALED-LNEYEKGVVRV 90 
                                       6799********************************************************98887.6688******* PP

                     Peptidase_M32  80 lkreykkakkvpaelvealakasakaeaaWreareandfalfepsLeevielkreiaelledlkkspYdaLldeyep 156
                                       l+r++k ak+ p e+v++l++  +ka++aW+ea+e+++f++fep+L+++iel++++ae+l ++++ pYdaLld ye+
  gi|242398992|ref|YP_002994416.1|  91 LQRDIKIAKAFPPEFVRELSEVRSKATMAWAEAKEKDNFRKFEPWLDRIIELSKKAAEYL-EYEEYPYDALLDLYEE 166
                                       ************************************************************.9*************** PP

                     Peptidase_M32 157 gltvekidalFeelkealvpllkkikeskekekkdksflereipeekqrelsrellkalgfdf.drgrldeseHPFt 232
                                       gl++  ++++F++l+++l+p+l+ki e+ ++ k++  + +++++ e+++e++ ++l+ lg+    +grld s HPFt
  gi|242398992|ref|YP_002994416.1| 167 GLRTRYLEPIFSKLEKDLKPILDKILEEGKVPKEH-PLETEKYDTESMKEVNLKILELLGYPLgVKGRLDISPHPFT 242
                                       *****************************965544.599************************99************ PP

                     Peptidase_M32 233 tsfsrkDvRittryeednllsslfsvlHEaGHalYeqnlpeelsktplgggvslgihEsqSrlyEniigrskeFwev 309
                                       t+f+ +DvRittrye  ++ ++l++v+HE+GHalYe++++e+l   p++ggvslg+hEsqSr++Eniigrs+eF+e 
  gi|242398992|ref|YP_002994416.1| 243 TEFGIHDVRITTRYEGFDFRRTLLAVVHEFGHALYELQIDEKLMFSPIAGGVSLGVHESQSRFWENIIGRSREFVEL 319
                                       ***************************************************************************** PP

                     Peptidase_M32 310 llpklkeafpeqlddvsleefyeavnkvepsliRveADEltYslHillRyelEkeliegklsvkdlpeaWnekykey 386
                                       ++p lke+ p  ++ +s+e++y ++n v+p +iRveADE+tY++HillRy+lEk ++++++++kdlpe+Wne+++++
  gi|242398992|ref|YP_002994416.1| 320 IYPVLKEKLPFMNK-YSAEDLYTYFNMVRPDYIRVEADEVTYNMHILLRYKLEKMMVNESVKAKDLPELWNEEMERL 395
                                       ********998666.************************************************************** PP

                     Peptidase_M32 387 LgidppddaeGvLQDvHWssgafGYFPtYalGniyaaqlfeamekdlpel..eiakgefseikkWLkenihqkGsly 461
                                       Lgi+p++ +eG+LQD+HW++ ++GYFPtY+lG+++a+q+ + ++kd+p++  +ia+gef++i++WL+e++h++Gs+y
  gi|242398992|ref|YP_002994416.1| 396 LGIRPKNYKEGILQDIHWAHATVGYFPTYSLGTLLATQIKSYISKDMPDFyeKIARGEFGPIREWLREKVHKYGSTY 472
                                       *************************************************9**9************************ PP

                     Peptidase_M32 462 sseellkkatgeslnaeyyidyLkeky 488
                                        ++ell++  ges+n+ey+i+yLkeky
  gi|242398992|ref|YP_002994416.1| 473 PPTELLERSFGESVNPEYFIKYLKEKY 499
                                       **************************9 PP

>> Peptidase_M3  Peptidase family M3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.3   0.00054       4.9       8     111 ..     110     210 ..     107     224 .. 0.69
   2 ?    0.8   0.0     0.025   2.2e+02     245     257 ..     267     279 ..     262     312 .. 0.84
   3 ?    1.1   0.0     0.021   1.9e+02     394     455 ..     424     494 ..     370     497 .. 0.60

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.00054
                                       HHHHHHHHHHHCTTTCCSS..THHHHHHHHHHHHHHHHHHHTT-SSHHHHHHTTSTT-S..HHHHHHHHHHHHHHHH CS
                      Peptidase_M3   8 relRkeayeashskaaeqrntlensklleellklraelAkllgyesyaelaledkmakn..petvldfleelvkklr 82 
                                        e+R +a +a+ ++ +e++n  + ++ l+++++l ++ A+ l+ye+y   al d  ++      ++ ++ +l+k l+
  gi|242398992|ref|YP_002994416.1| 110 SEVRSKATMAWAEA-KEKDNFRKFEPWLDRIIELSKKAAEYLEYEEYPYDALLDLYEEGlrTRYLEPIFSKLEKDLK 185
                                       589**********9.556666778**********************9777776644432112334456666666666 PP

                                       HHHHHHHHHHHHHHHHCCT-SSS--CCCH CS
                      Peptidase_M3  83 pllekelkllkelkkkelglegelqpwDv 111
                                       p l k l++ k  k++ l    e + +D+
  gi|242398992|ref|YP_002994416.1| 186 PILDKILEEGKVPKEHPL----ETEKYDT 210
                                       666666666665333333....3455555 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.025
                                       HHHHHHHHHHHHH CS
                      Peptidase_M3 245 tLfHEfGHsmHsl 257
                                        ++HEfGH++ +l
  gi|242398992|ref|YP_002994416.1| 267 AVVHEFGHALYEL 279
                                       579******9765 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.021
                                       HHHHHHHHHHHHHCCHHCCTT-..............CCHHHHHHHHTTTTTTSS-HHHHHHCCCSS---SHHHHHH CS
                      Peptidase_M3 394 ylyaevlaldifekffeedpln..............retGeryrkeiLsrGgskdplellkkflgrepsadallka 455
                                       y   + la++i + + + d ++              r   e  r+++ ++G++ +p ell++  g+  +++ ++k 
  gi|242398992|ref|YP_002994416.1| 424 YSLGTLLATQIKSYISK-D-MPdfyekiargefgpiR---EWLREKVHKYGSTYPPTELLERSFGESVNPEYFIKY 494
                                       55555555555555555.3.12234444432222343...67899999**************99999999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (501 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.48
# Mc/sec: 3140.54
//
Query:       gi|242398993|ref|YP_002994417.1|  [L=110]
Description: ProFAR isomerase associated, [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-16   60.6   0.9    2.3e-16   60.3   0.9    1.0  1  ASCH      ASCH domain
     0.0058   16.4   0.5      0.009   15.8   0.5    1.3  1  S4_2      S4 domain


Domain annotation for each model (and alignments):
>> ASCH  ASCH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.3   0.9   2.5e-20   2.3e-16       1     106 [.       5     107 ..       5     108 .. 0.93

  Alignments for each domain:
  == domain 1  score: 60.3 bits;  conditional E-value: 2.5e-20
                                       EEE-TTHHHHHHTTS--EEEESSTTTGGGT-CEEEEEECCCCTSEEEEEEEEEEEEEE.HHHHHHHHHCHCC--... CS
                              ASCH   1 lsfhqelaslivsGkKtaeirvwdeelpkvrgdllilaalkptgralgivevtkvevk.pfeevteehalkege... 73 
                                       + +++e+++li +GkK++e+r  de++++++ ++ i+++ k      ++v+v++++++ +f+e+ e +++   e   
  gi|242398993|ref|YP_002994417.1|   5 MGLKEEYLDLIRNGKKKVEGRLYDEKRRQINPGDVIIFEGK------LKVKVKSIKKYpSFKEMLEREGI---Ervl 72 
                                       56899********************************9999......***********************...3336 PP

                                       ....-HCHHHHHHHCCHHHHHCCEEEEEEEEEEEEEE CS
                              ASCH  74 ....sleewrevheefyeeeseeyedelvvveefelv 106
                                           ++ee ++ +++fy+ee e  ++++vv++e+e++
  gi|242398993|ref|YP_002994417.1|  73 pgvhNIEEGVKIYRQFYTEEEE--KKYGVVAIEIEPI 107
                                       7779****************77..9*********985 PP

>> S4_2  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.5     1e-06     0.009      29      60 ..      14      45 ..      10      51 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1e-06
                              S4_2 29 fiaegeVkvNGevetrRgkKlraGdvVeidge 60
                                      +i +g+ kv G   +++++++ +Gdv+ ++g+
  gi|242398993|ref|YP_002994417.1| 14 LIRNGKKKVEGRLYDEKRRQINPGDVIIFEGK 45
                                      7999999*********************9664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 717.37
//
Query:       gi|242398994|ref|YP_002994418.1|  [L=375]
Description: Geranylgeranyl hydrogenase [Thermococcus sibiricus MM 739]
Scores for complete 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-17   62.4   0.0    3.2e-13   49.7   0.0    3.0  2  FAD_binding_3   FAD binding domain
      3e-06   26.6   0.1      6e-06   25.7   0.1    1.5  1  Thi4            Thi4 family
    3.9e-06   26.0   0.2      0.092   11.6   0.0    3.0  3  Trp_halogenase  Tryptophan halogenase
    1.2e-05   25.4   0.1    6.2e-05   23.2   0.0    2.2  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
      4e-05   23.4   0.2      0.023   14.3   0.1    2.2  2  DAO             FAD dependent oxidoreductase
    0.00044   19.1   0.1    0.00096   18.0   0.1    1.5  1  HI0933_like     HI0933-like protein
     0.0018   17.4   0.1      0.016   14.3   0.0    2.2  2  Lycopene_cycl   Lycopene cyclase protein
     0.0053   16.0   0.8       0.13   11.5   0.2    2.3  3  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
      0.027   15.2   0.4      0.071   13.9   0.4    1.7  1  VAPB_antitox    Putative antitoxin
       0.12   12.6   0.3       0.43   10.8   0.0    2.0  3  TrkA_N          TrkA-N domain


Domain annotation for each model (and alignments):
>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.7   0.0   1.8e-16   3.2e-13       2     221 ..       7     203 ..       6     217 .. 0.77
   2 !    7.3   0.0    0.0013       2.4     267     308 ..     233     274 ..     221     284 .. 0.80

  Alignments for each domain:
  == domain 1  score: 49.7 bits;  conditional E-value: 1.8e-16
                                       EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS--EEEHHHHHHHHHTT-HHHHHHHSEECCCCEEEEEE CS
                     FAD_binding_3   2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpradglnqrtmellrqlGledrilaegapnelmgealyn 78 
                                       +dV+I+G+Gp+G  la+lL++   +vv++e  ++   +   +++  +  e l       ++ +e+  n+l g ++y 
  gi|242398994|ref|YP_002994418.1|   7 YDVAIIGGGPVGNYLANLLASE-FKVVVLEAKNSFGGKACTGIMGAENYEKL-------NLPKEAIINKLRGAVFYS 75 
                                       79********************.*******9888776666666666665554.......467788899999*****9 PP

                                       ECCCCCEEEEEHHCHHCST-CEE--HHHHHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEE CS
                     FAD_binding_3  79 elsdtpkaradlelesspervtvypqteleriLvehaeerglqvrfktevesleqdeegvtaevrdketgeeetvra 155
                                       +           e+e   ++ +v+  + ler L+e+a ++g++ +++++++++++ +    a v+  + +e+ +++a
  gi|242398994|ref|YP_002994418.1|  76 R-------IQSFEIERPTPQAYVVDRKLLERKLAENAIRHGAEYYMGARFLGFKNRK----AIVQ--RFNEKFEIEA 139
                                       9.......45566679999999*****************************776554....4443..3457889*** PP

                                       EEEEE--GTT-HHHHHHTGGEEEEEEEEEEEEEEEEEEC-SCCCTTCCEEEEECCTTEEEEEECCE CS
                     FAD_binding_3 156 kYlvGaDGgrStvrktlgiefegeetvyeagvldvlfdadlsdiveplvlilsaesrgvmviPlen 221
                                       ++ vGaDG +S+v++++g +  +e        ++v+ d + +d+ve +v    +++ ++ + P +n
  gi|242398994|ref|YP_002994418.1| 140 DFYVGADGLNSKVAQEIGARTDAEF--LSGYEVEVVGDFNRTDFVEIWVNKEINNEFFMWLAPINN 203
                                       ******************9865554..446777777777666666663333333444445566666 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0013
                                       EEEEEEEEEEEESSSEETTEEE-GGGTEEE-STTSHHHHHHH CS
                     FAD_binding_3 267 evsawtvaqrvaekyrkgrvflaGDAaHihpPtgGqGlNtai 308
                                       e++a +v+    +++ kg++ l+GDAa    P ++ G+  ++
  gi|242398994|ref|YP_002994418.1| 233 EIKAGNVGLGFRKPWVKGNIALVGDAALQIKPLTAGGIVYGM 274
                                       55666666667889********************99987777 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.1   3.3e-09     6e-06      12      62 ..       1      49 [.       1      66 [. 0.89

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 3.3e-09
                                      HHHHTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTST CS
                              Thi4 12 llkyaesDvvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGq 62
                                      ++k++  Dv+i+G+G+ G   a  la +  +kv++le++ s+GG a  G +
  gi|242398994|ref|YP_002994418.1|  1 MVKLMRYDVAIIGGGPVGNYLANLLASE--FKVVVLEAKNSFGGKACTGIM 49
                                      578999********************99..**************9988765 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.0   0.1    0.0025       4.6       1      33 [.       8      36 ..       8      42 .. 0.85
   2 !   11.6   0.0   5.1e-05     0.092     141     216 ..      82     155 ..      49     172 .. 0.82
   3 !    5.0   0.0     0.005         9     292     337 ..     221     271 ..     213     285 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0025
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE- CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlves 33
                                      ++ i+GGG+ G   A++la  +    +v ++e+
  gi|242398994|ref|YP_002994418.1|  8 DVAIIGGGPVGNYLANLLASEF----KVVVLEA 36
                                      699****************999....5666665 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 5.1e-05
                                       S-B-S--EEEE-HHHHHHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS-EEE-SEEEE-SGGG-IIIII CS
                    Trp_halogenase 141 glsalsyAyhldaalyakfLrrvaearGvtrvegkvvevqldedgrveslrledgreveadlfiDcsGfrgllieq 216
                                        ++ +  Ay +d++l+++ L ++a ++G +   g       + +  v++++     e+ead+++ + G ++++ ++
  gi|242398994|ref|YP_002994418.1|  82 IERPTPQAYVVDRKLLERKLAENAIRHGAEYYMGARFLGFKNRKAIVQRFNE--KFEIEADFYVGADGLNSKVAQE 155
                                       5678999***************************998888888889998876..6789***********9998776 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.005
                                       CT--TTTS-EEEE---EE....ES-SEET.TEEE-CCCTEE--CCCS-HHH CS
                    Trp_halogenase 292 ldgkleaeprkirfttGr....rkqawvk.nvvalGlasgfvePlestsih 337
                                       l++kl +e + +++++G      ++ wvk n+ ++G+a+  + Pl + +i 
  gi|242398994|ref|YP_002994418.1| 221 LKLKLLKETNIVEIKAGNvglgFRKPWVKgNIALVGDAALQIKPLTAGGIV 271
                                       66777888899999999999997777776266678************9996 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   3.4e-08   6.2e-05       1      39 [.      11      48 ..      11      61 .. 0.90
   2 ?   -2.5   0.0       3.5   6.3e+03       6      16 ..     271     281 ..     268     293 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 3.4e-08
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EEC CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasye 39
                                      I+G+G  G ++A lLa + f+v++le+ +++GG+a +  
  gi|242398994|ref|YP_002994418.1| 11 IIGGGPVGNYLANLLASE-FKVVVLEAKNSFGGKACTGI 48
                                      9***************97.***************97765 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.5
                                       HHHHHHHHHHH CS
                     NAD_binding_8   6 lsGlvaAylLa 16 
                                       + G+++ ++L+
  gi|242398994|ref|YP_002994418.1| 271 VYGMLCSHALR 281
                                       57999999998 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.1   1.3e-05     0.023       1      34 [.       8      42 ..       8      59 .. 0.85
   2 !    7.0   0.0     0.002       3.7     138     211 ..      87     154 ..      83     216 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.3e-05
                                      EEEEECTSHHHHHHHHHHHHT.TEEEEESSSSTTS CS
                               DAO  1 dvviiGGGiiGlstAyeLarr.gVtllekgdiags 34
                                      dv+iiGGG +G   A  La + +V++le+++ +g 
  gi|242398994|ref|YP_002994418.1|  8 DVAIIGGGPVGNYLANLLASEfKVVVLEAKNSFGG 42
                                      8*****************86645*******99993 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.002
                                       TTEEEEEHHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHHHHHTTC CS
                               DAO 138 pdtgqvdpakltaalaraaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsdllgllk 211
                                       p++ +vd   l + la+ a ++G+e + g++  g++++   v++  + ++ +++  ad  V a G+ s+ +   +
  gi|242398994|ref|YP_002994418.1|  87 PQAYVVDRKLLERKLAENAIRHGAEYYMGARFLGFKNRKAIVQRF-N-EKfEIE--ADFYVGADGLNSKVA---Q 154
                                       67667788888899*********************8864344444.3.444553..688999999998755...3 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1   5.4e-07   0.00096       1      77 [.       7      80 ..       7      85 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 5.4e-07
                                      -SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHHHHCGGGT-EEEETT-SGGGEEES...STTTTHHHHHHS CS
                       HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllekakklgrKilisGgGrcNvTnlseepeellsrypenpkflksalsrf 77
                                      +dv++iGgG+ G + A  + + + +V++le+++++g K  +   G  N   l+ ++e+++++   +++ ++s ++ f
  gi|242398994|ref|YP_002994418.1|  7 YDVAIIGGGPVGNYLANLL-ASEFKVVVLEAKNSFGGKACTGIMGAENYEKLNLPKEAIINK--LRGAVFYSRIQSF 80
                                      59**************888.6789**************988889999999999999999988..5667777777777 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   8.7e-06     0.016       1     175 [.       8     182 ..       8     206 .. 0.66
   2 ?    0.5   0.1      0.13   2.4e+02     313     343 ..     300     329 ..     213     342 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 8.7e-06
                     Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvlieaspsllfpnny.vWsdefedlga...leecvehsWsgtivy..ldd 71 
                                       Dv++iG+Gp g  lA+ l   + + kvv++ea +s   +++  +  +  e+ ++    +e++  + +g++ y  ++ 
  gi|242398994|ref|YP_002994418.1|   8 DVAIIGGGPVGNYLANLL---ASEFKVVVLEAKNSF--GGKAcTGIMGAENYEKlnlPKEAIINKLRGAVFYsrIQS 79 
                                       9*****************...889******998887..888778888888888844323455555555544411333 PP

                     Lycopene_cycl  72 gkkillg.raYgrvsskrlkeellerlvengvkll.eakvesveeeeageslvvleggr.kirarlvvdarglaslk 145
                                       +++   +  aY  v +k l+++l+e+ + +g++++  a+    ++ +a    v   +++ +i+a + v a gl s+ 
  gi|242398994|ref|YP_002994418.1|  80 FEIERPTpQAY-VVDRKLLERKLAENAIRHGAEYYmGARFLGFKNRKA---IVQRFNEKfEIEADFYVGADGLNSKV 152
                                       33333334455.699999999999999977777651566666666666...33333333599999999999977776 PP

                     Lycopene_cycl 146 ...karrlglQtfyGvevevdnppfdldkmvlM 175
                                           + r+      G evev  +    ++ ++ 
  gi|242398994|ref|YP_002994418.1| 153 aqeIGARTDAEFLSGYEVEVVGD---FNRTDFV 182
                                       65555566667777888888776...3444455 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.13
                     Lycopene_cycl 313 krqreffrllglalllkldiegrrrfldaFf 343
                                       k+q +f  l  + l+++l+ +++++f++ F+
  gi|242398994|ref|YP_002994418.1| 300 KKQISFG-LRIRRLFKALNQDQIEKFFEIFS 329
                                       4444443.33356788888888888888886 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 !   11.5   0.2   7.2e-05      0.13       1      41 [.       7      46 ..       7      83 .. 0.81
   2 ?    2.4   0.0     0.041        74     185     241 ..      97     152 ..      74     186 .. 0.76
   3 ?   -3.1   0.0         2   3.5e+03      57      96 ..     291     348 ..     251     363 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.2e-05
                                      CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcl 41
                                      +dv++iGgGp G  +a  la  ++kv+++e+++ + +  c 
  gi|242398994|ref|YP_002994418.1|  7 YDVAIIGGGPVGNYLANLLAS-EFKVVVLEAKNSFGGKACT 46
                                      69*************998887.9******877776666664 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.041
                                       HHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S-EEES- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 185 lsaaleealekeGvevklgtsvkeidgngeklevvledgeeidadlvvvavGvrpst 241
                                       l++ l+e   ++G e ++g+++  +++++  +    +++ ei+ad  v a G+  + 
  gi|242398994|ref|YP_002994418.1|  97 LERKLAENAIRHGAEYYMGARFLGFKNRKA-IVQRFNEKFEIEADFYVGADGLNSKV 152
                                       677888999999**************8886.7789999999*******999997765 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 2
                                       H...................HHHHCHHHH.CCCCHCCTCEEEEESCEEEEETEEECTCEE CS
                                       x...................xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  57 s...................evvkklnqg.ielllgeevvkidpgkkkvklekkkegdee 96 
                                                           + +k lnq+ ie++ +  +++ d++k  ++  ++ +++++
  gi|242398994|ref|YP_002994418.1| 291 MyedlckdikkqisfglrirRLFKALNQDqIEKFFE--IFSSDEAKNVIETYADFDDHKK 348
                                       255444444444445555555555566666666666..6666666655555444444444 PP

>> VAPB_antitox  Putative antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.4     4e-05     0.071      10      59 ..     292     338 ..     290     346 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4e-05
                      VAPB_antitox  10 YekL.kklKregeSFsdvIerLlekkkkgkkkellelfgilseeeadeiek 59 
                                       Ye L k++K+ + SF   I+rL++     ++++++++f+i s++ea+++ +
  gi|242398994|ref|YP_002994418.1| 292 YEDLcKDIKK-QISFGLRIRRLFK---ALNQDQIEKFFEIFSSDEAKNVIE 338
                                       7777467888.***********98...445679*************65543 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00024      0.43       1      30 [.       9      37 ..       9      41 .. 0.89
   2 ?   -2.4   0.0         3   5.5e+03      24      60 ..     118     158 ..      99     160 .. 0.64
   3 ?   -3.5   0.0         7   1.2e+04      86      97 ..     343     355 ..     325     361 .. 0.46

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00024
                                      EEEES-SHHHHHHHHHHHHTTEEEEEEESS CS
                            TrkA_N  1 iiiiGlGrvGrslaeeLseggkdvvvidkd 30
                                      ++iiG G vG  la+ L ++ k vvv + +
  gi|242398994|ref|YP_002994418.1|  9 VAIIGGGPVGNYLANLLASEFK-VVVLEAK 37
                                      68*****************995.9999875 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3
                                       EEEEESSHHHHHHHHHTT.SE...EEES-TTSHHHHHHTTG CS
                            TrkA_N  24 vvvidkdeerveelreeg.le...vvvgdatdeevLeeagi 60 
                                       +++  ++++ v+++ e++ +e   +v +d+ + +v +e+g+
  gi|242398994|ref|YP_002994418.1| 118 FLGFKNRKAIVQRFNEKFeIEadfYVGADGLNSKVAQEIGA 158
                                       66666667777777777764444455578888877777775 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 7
                                       HTSSSEEE.EEES CS
                            TrkA_N  86 lnpkkkii.araq 97 
                                       + ++kk+i a ++
  gi|242398994|ref|YP_002994418.1| 343 FDDHKKTIsAIVK 355
                                       2333332214444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       609  (0.0339673); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.45
# Mc/sec: 2486.71
//
Query:       gi|242398995|ref|YP_002994419.1|  [L=202]
Description: Pyrrolidone-carboxylate peptidase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.4e-74  249.9   0.9    2.7e-74  249.7   0.9    1.0  1  Peptidase_C15  Pyroglutamyl peptidase
     0.0094   15.9   0.8      0.041   13.8   0.1    1.9  2  Peptidase_C3   3C cysteine protease (picornain 3C)
  ------ inclusion threshold ------
      0.013   15.4   0.0      0.023   14.6   0.0    1.4  1  Thump_like     THUMP domain-like


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 !  249.7   0.9   4.6e-78   2.7e-74       2     200 ..       4     200 ..       3     202 .] 0.98

  Alignments for each domain:
  == domain 1  score: 249.7 bits;  conditional E-value: 4.6e-78
                                       EEEEEEE---TT-S--HHHHHHHHHTT-EETTEEEEEEEE-SSTTHHHHHHHHHHHHH--SEEEEEEE-TT--SEEE CS
                     Peptidase_C15   2 kvLvtGfdPfgkekinPaleavkeLdgaeiaeativkrevPtvfkksadvlkkaiaeikpdivlaiGqagGrsaitv 78 
                                       kvLvtGf+Pfg+ekinP++eavk+L  +ei+ea+i+k+++P++fk  ++ l k i+e  p++++  GqagGr++i v
  gi|242398995|ref|YP_002994419.1|   4 KVLVTGFEPFGEEKINPSWEAVKNLS-KEINEAEIIKKRLPVSFKAIKKKLPKIIDESMPEVIILTGQAGGRVNINV 79 
                                       9*************************.************************************************** PP

                                       E-EEES-BE-SS--TTS---ESB-SSTTS-SEEE--S-HHHHHHHHHHTT--EEEES---SSHHHHHHHHHHHHHHH CS
                     Peptidase_C15  79 ervainldDaripDnegkqlidepispdgeaaYfstlPvkamvkalkeaGvPaavsntaGtfvCnhllYqvlylldk 155
                                       ervain+ D++ +Dn+g+++ depi  +++aaYfstlP++++v+alk++ +Pa++sntaGt+vCn  +Y +l+++  
  gi|242398995|ref|YP_002994419.1|  80 ERVAINVMDSKKEDNDGYKPEDEPIFENAPAAYFSTLPIRRIVNALKHNKIPATISNTAGTYVCNTAMYVALHHTTL 156
                                       ***************************************************************************** PP

                                       HS--SEEEEEEE-B-GGGTHHHHHT-B--HHHHHHHHHHHHHHHH CS
                     Peptidase_C15 156 klpevraGfihiPylpeqvidkpetpslsldkevagvkaaieaiv 200
                                       +++++++Gfih+Py+peqv++k+ +p +sl+++ +++++ai+  +
  gi|242398995|ref|YP_002994419.1| 157 NGLNAKTGFIHVPYIPEQVLEKT-QPFMSLEMIEKAIEIAIKESI 200
                                       *********************99.9****************8665 PP

>> Peptidase_C3  3C cysteine protease (picornain 3C)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.1   6.9e-06     0.041      72     123 ..      32      83 ..      15      90 .. 0.87
   2 ?    0.5   0.0     0.086   5.1e+02      11      44 ..     125     154 ..     117     184 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.9e-06
                                       EEEEEEEEESSS--B---GGGS-SS---EEEEEEEE-SSSSTTEEEEEEEEE CS
                      Peptidase_C3  72 pldlaivklkrgekfkdirkylaarikkgkpvvllinnneagrlivsveavt 123
                                         ++ i+k +++ +fk i+k l++ i++  p+v+++  +  gr+ ++ve+v 
  gi|242398995|ref|YP_002994419.1|  32 INEAEIIKKRLPVSFKAIKKKLPKIIDESMPEVIILTGQAGGRVNINVERVA 83 
                                       458899999****************************************996 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.086
                                       HHHHEEEEEETTEEEEEE..EEEBTEEEEEGGG- CS
                      Peptidase_C3  11 lkqnvvpvttskgvftclatgvydkvillprhae 44 
                                       lk+n +p+t+s++     +t+v ++++ + +h  
  gi|242398995|ref|YP_002994419.1| 125 LKHNKIPATISNT----AGTYVCNTAMYVALHHT 154
                                       5555555555544....46777777777777755 PP

>> Thump_like  THUMP domain-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   3.9e-06     0.023      17      70 ..      25      73 ..      17      81 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.9e-06
                        Thump_like 17 lkkllrergigkanikkRgfpldpeeLrkklkl.kdggraatLvlTrvgegkagk 70
                                      +k+l   ++i +a+i+k+  p++  +++kkl    d + + +++lT      ag 
  gi|242398995|ref|YP_002994419.1| 25 VKNLS--KEINEAEIIKKRLPVSFKAIKKKLPKiIDESMPEVIILTGQ----AGG 73
                                      56665..8899********************65356777999999987....444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       715  (0.0398795); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); 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: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1227.92
//
Query:       gi|242398996|ref|YP_002994420.1|  [L=488]
Description: Prolyl-tRNA synthetase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.9e-22   78.5   0.0    1.2e-21   77.5   0.0    1.4  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
    1.6e-21   76.2   0.3    3.5e-21   75.2   0.3    1.6  1  HGTP_anticodon  Anticodon binding domain
    2.4e-14   53.3   0.9    5.6e-14   52.1   0.7    1.8  2  ProRS-C_1       Prolyl-tRNA synthetase, C-terminal
     0.0045   17.1   0.3      0.042   14.0   0.1    2.5  2  ProRS-C_2       Prolyl-tRNA synthetase, C-terminal
  ------ inclusion threshold ------
      0.076   13.6   0.0       0.19   12.3   0.0    1.7  1  TIR_2           TIR domain


Domain annotation for each model (and alignments):
>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.5   0.0   3.3e-25   1.2e-21       8     176 ..     109     277 ..     103     280 .. 0.90

  Alignments for each domain:
  == domain 1  score: 77.5 bits;  conditional E-value: 3.3e-25
                                       SEEEEE-SSSHHHHHHHHHHHEEEB.GGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEE.EEEEEEES.GGGHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx.xxxxxxxxx RF
                      tRNA-synt_2b   8 dreyiLkPtneetfvelirdevlrs.krLPlklyqiqtkyRdEksdsrGLlRvreFhq.kdgyvfha.easlddslr 81 
                                       d ++iL+Pt+e++++ +++ + +rs  +LP+k+yqi  +yR+E++ +r+L+Rvre+    + +  h   ++++ ++r
  gi|242398996|ref|YP_002994420.1| 109 DVKLILRPTSETAMYPMFNLW-IRShADLPFKIYQIVNVYRYETKHTRPLIRVREISRfFESHTAHDsFEDAERQIR 184
                                       6689***************88.***777*****************9**********873689999986588999999 PP

                                       HHHHHHHHHHHHTT.SCEEEEEE.GTTSCBTTSEEEEEEEEETTTSEEEEEEEEEEEETHHHHHTTEEEECTTSSEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b  82 dlikaisriferlglefraiiel.msaksadykdkkefeavsesltkgieigtiqklgtrlserlgatvldennrek 157
                                       + ++  +++ ++l l++ + ++  ++++ + + +++  e++++  +++++igt++  +++++++ ++t+  e++ ++
  gi|242398996|ref|YP_002994420.1| 185 EDLEIFDNLAKNLALPYIVSKRPdWDKF-PGAFYSLGAEVIMP-DGRTLQIGTMHHYKQNFAKAYEITYETEEGTHE 259
                                       9999999999999999765555467754.89999*********.9******************************** PP

                                       EEEEEEEEEEHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b 158 svimicaaigveRllsail 176
                                        v+ + ++++ eRl++ai+
  gi|242398996|ref|YP_002994420.1| 260 YVHQTTFGMS-ERLVAAIM 277
                                       **********.******97 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.2   0.3   9.7e-25   3.5e-21       1      93 [.     296     391 ..     296     392 .. 0.95

  Alignments for each domain:
  == domain 1  score: 75.2 bits;  conditional E-value: 9.7e-25
                                       SEEEEESSSS..HHHHHHHHHHHHHHHHTTTSEEEEES.SSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEET CS
                    HGTP_anticodon   1 qvvviplnek..aeeleeyakklaeeLraagirveldd.snesigkkireadllgipfavvvGekelekgtvtvrdr 74 
                                       qvvvip+ +k    ++  yak++aeeL+ ag+r+++dd ++ ++g+k+ +++ +g+p++++vG+k++e+++    +r
  gi|242398996|ref|YP_002994420.1| 296 QVVVIPIPMKesPYDVNAYAKEIAEELKTAGLRIHVDDrEDVRPGRKFYDWEIKGVPLRIEVGPKDVEENQAVFARR 372
                                       8********98855588*********************99************************************* PP

                                       TTCEEEEEETTHHHHHHHH CS
                    HGTP_anticodon  75 dtreqervsldelveklke 93 
                                       dt e+ +v++++lve+ ++
  gi|242398996|ref|YP_002994420.1| 373 DTFEKFTVKRENLVEEARK 391
                                       **************98775 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 ?   -4.1   0.0         5   1.8e+04      22      32 ..     177     187 ..     173     200 .. 0.76
   2 !   52.1   0.7   1.6e-17   5.6e-14       2      69 .]     419     488 .]     418     488 .] 0.93

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 5
                                       HHHHHHHHHHH CS
                         ProRS-C_1  22 eecEekIkeet 32 
                                       e++E++I e+ 
  gi|242398996|ref|YP_002994420.1| 177 EDAERQIREDL 187
                                       67899999875 PP

  == domain 2  score: 52.1 bits;  conditional E-value: 1.6e-17
                                       HHHHHHHHTT-.EEEEEESSGHHHHHHHHHHHS-EEEEEESSB.-SSCCCSB-TTT-SB-SEEEEEE-B- CS
                         ProRS-C_1   2 eefkealekkg.fvlapWcgeeecEekIkeetgakslcipfdq.epseegtkCivcgkpakkwvlfgrsY 69 
                                       ee k+ +e+++ +v  pWcge+ c  +++e   a++l+ip  + + + eg+kC+ cgk+ak ++ f+r+Y
  gi|242398996|ref|YP_002994420.1| 419 EEAKKLFEDRRgVVELPWCGEKGCGVEMEEILDASMLGIPYPEeTAKIEGKKCANCGKDAKYVARFARTY 488
                                       899999998888***************************997646677*********************9 PP

>> ProRS-C_2  Prolyl-tRNA synthetase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.32   1.2e+03      30      45 ..     308     323 ..     297     327 .. 0.75
   2 !   14.0   0.1   1.2e-05     0.042      12      51 ..     417     457 ..     406     474 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.32
                                       E--GGG-SHHHHHHHS CS
                         ProRS-C_2  30 PfneeiYneefeeeid 45 
                                       P++ + Y  e+ ee++
  gi|242398996|ref|YP_002994420.1| 308 PYDVNAYAKEIAEELK 323
                                       7777888888887765 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 1.2e-05
                                       .HHHHHHHCTTT-SEEEEE-.-GGG-SHHHHHHHSS-EEEE CS
                         ProRS-C_2  12 llenikeklsekkGvvLvPf.neeiYneefeeeidasvLGe 51 
                                        le+ k+ +++++Gvv +P+  e+    e+ee +das+LG 
  gi|242398996|ref|YP_002994420.1| 417 TLEEAKKLFEDRRGVVELPWcGEKGCGVEMEEILDASMLGI 457
                                       46899**************945788999***********95 PP

>> TIR_2  TIR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   5.4e-05      0.19      10      43 ..     312     346 ..     307     355 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.4e-05
                             TIR_2  10 kewaeklaeaLeaagirvwl.drwdlkpgedweee 43 
                                       +++a+++ae+L+ ag+r+++ dr+d++pg +++++
  gi|242398996|ref|YP_002994420.1| 312 NAYAKEIAEELKTAGLRIHVdDREDVRPGRKFYDW 346
                                       689**************97626699****999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (488 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       831  (0.0463495); expected 358.6 (0.02)
Passed bias filter:                      697  (0.0388756); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.67u 0.29s 00:00:00.96 Elapsed: 00:00:00.47
# Mc/sec: 3088.76
//
Query:       gi|242398997|ref|YP_002994421.1|  [L=333]
Description: D-isomer specific 2-hydroxyacid dehydrogenase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-51  174.5   0.0    1.9e-51  174.0   0.0    1.3  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
    1.8e-30  105.3   0.1    2.2e-30  105.0   0.1    1.1  1  2-Hacid_dh      D-isomer specific 2-hydroxyacid dehydrogenase
      1e-08   35.5   0.0    2.1e-08   34.5   0.0    1.5  1  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
    1.7e-08   34.9   0.0    3.5e-08   33.9   0.0    1.6  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
    2.1e-06   27.4   0.1    5.8e-06   26.0   0.0    1.7  2  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
    0.00018   21.6   0.0    0.00077   19.5   0.0    2.0  2  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
     0.0017   18.3   0.3       0.02   14.9   0.3    2.3  1  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
     0.0076   16.3   0.1      0.038   14.1   0.1    2.1  1  AdoHcyase_NAD   S-adenosyl-L-homocysteine hydrolase, NAD bind
  ------ inclusion threshold ------
       0.02   14.6   0.0      0.035   13.7   0.0    1.4  1  ApbA            Ketopantoate reductase PanE/ApbA
      0.046   13.6   0.0      0.096   12.6   0.0    1.5  1  Rossmann-like   Rossmann-like domain
      0.047   14.1   0.0       0.25   11.8   0.0    2.1  2  NAD_binding_7   Putative NAD(P)-binding


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 !  174.0   0.0   1.2e-54   1.9e-51       1     178 []     106     286 ..     106     286 .. 0.91

  Alignments for each domain:
  == domain 1  score: 174.0 bits;  conditional E-value: 1.2e-54
                                       HHHHHHHHTTHHHHHHHHHTTCCHTTCCGSBS.....-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHH CS
                      2-Hacid_dh_C   1 lalllallrrlaeadeevregewksekallgk.....elsgktvGiiGlGrIGqavakrlkafgmkviaydrskkke 72 
                                       ++l +allr++a+ d+ +r+g w+s+k++ g      +l+gk++Gi+G+G+IG+ +a+r+ka++ ++++++r++k++
  gi|242398997|ref|YP_002994421.1| 106 VGLTIALLRKIAYSDRFIRKGLWDSHKTIWGWykemeTLHGKKIGILGMGSIGKGIARRMKAMNTEIYYWSRTRKED 182
                                       5799*******************656544333334449***********************************9966 PP

                                       HCHHHHTCEECSHHHHHHH-SEEEE-S--STTTTTSBSHHHHHCSTTTEEEEESS-GGGB-HHHHHHHHHTTSCCEE CS
                      2-Hacid_dh_C  73 eeeeelgvelvsleellaesDivslhlpltpetrhlinaeelakmkkgailiNtaRGglvdeeaLleaLksgkiaga 149
                                         e+e+++++  ++++l+esDiv+l+lp tpet+h+in+e+l+++k g +l+N++RG+lvde+ L++aLk+g+++g+
  gi|242398997|ref|YP_002994421.1| 183 I-EKEVNAKWLPINDVLKESDIVILALPSTPETYHIINEETLELLK-GKYLVNVGRGSLVDEKVLIKALKEGNLKGF 257
                                       5.99999*************************************98.89**************************** PP

                                       EES--SSSSSGTCHHHHHST.TEEE-SS-T CS
                      2-Hacid_dh_C 150 alDvfeeeplpedspllelp.nviltPHia 178
                                       a+Dvfe+ep++e+ +l+e++ +++ltPH a
  gi|242398997|ref|YP_002994421.1| 258 ATDVFEKEPIQES-ELFEMEwETVLTPHHA 286
                                       ***********66.999998469*****86 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 !  105.0   0.1   1.4e-33   2.2e-30       2     134 .]       6     318 ..       5     318 .. 0.98

  Alignments for each domain:
  == domain 1  score: 105.0 bits;  conditional E-value: 1.4e-33
                                       EEEST.CHHHHHHHHHTTE.EEEEESCSSHHHCHHHHTTESEEEE-TTS-BSHHHHHHHTT--EEEESSSSCTTB-H CS
                                       xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        2-Hacid_dh   2 lileplreeelellkeegv.evevkdellteellekakdadalivrsntkvtaevlealpkLkviaragvGvDnvDl 77 
                                       l+l ++++++++llke  + +v+v   +++ee+l+ +  +d+liv   + v++e++e+ +kLkvi++ ++G+D++D+
  gi|242398997|ref|YP_002994421.1|   6 LVLFNMKSNAMKLLKE--YcDVDVMVYPTKEEVLQVIGAYDGLIVSPLNLVDKEIIEHGKKLKVISTQSAGYDHIDI 80 
                                       55557899********..66********************************************************* PP

                                       HHHHHTT-EEEE-TTTTHHHHHHHH.................................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx.................................................... RF
                        2-Hacid_dh  78 daakerGilVtnvpgystesvAElt.................................................... 102
                                       +aa+e+Gi Vt v g  +e+vAE++                                                    
  gi|242398997|ref|YP_002994421.1|  81 NAATEKGIYVTKVSGILSEAVAEFAvgltiallrkiaysdrfirkglwdshktiwgwykemetlhgkkigilgmgsi 157
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                        2-Hacid_dh 103 ............................................................................. 102
                                                                                                                    
  gi|242398997|ref|YP_002994421.1| 158 gkgiarrmkamnteiyywsrtrkediekevnakwlpindvlkesdivilalpstpetyhiineetlellkgkylvnv 234
                                       ***************************************************************************** PP

                                       ....................................................T-BHHHHHHHHHHHHHHHHHHHTTC CS
                                       ....................................................xxxxxxxxxxxxxxxxxxxxxxxxx RF
                        2-Hacid_dh 103 ....................................................aaTeeaqeniaeeaaenlvaflkge 127
                                                                                           ++ +ea+e++a +a++nl+++l g+
  gi|242398997|ref|YP_002994421.1| 235 grgslvdekvlikalkegnlkgfatdvfekepiqeselfemewetvltphhaGLAQEAMEDMALQAVNNLLEILMGN 311
                                       ***************************************************************************** PP

                                       CGTTBCS CS
                                       xxxxxxx RF
                        2-Hacid_dh 128 spanavn 134
                                        ++n vn
  gi|242398997|ref|YP_002994421.1| 312 VSENLVN 318
                                       ****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 !   34.5   0.0   1.3e-11   2.1e-08       1     110 [.     148     255 ..     148     261 .. 0.86

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 1.3e-11
                                       EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHSHC CS
                     NAD_binding_2   1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdeviegll 77 
                                       kig++G+G +G+ +a+++++ + +++ + rt++  e++ +e       i++++++ d+vi+ +++++++ ++i++  
  gi|242398997|ref|YP_002994421.1| 148 KIGILGMGSIGKGIARRMKAMNTEIYYWSRTRK--EDIEKEVNAKWLPINDVLKESDIVILALPSTPETYHIINEET 222
                                       79***************************9943..4444444444557899************************77 PP

                                       CC--TT-EEEE-S---HHHHHHHHHHHHHTT-E CS
                     NAD_binding_2  78 ealkkgdilidgstsspedtrelakelkekglk 110
                                        +l kg++l++++  s  d + l k+lke +lk
  gi|242398997|ref|YP_002994421.1| 223 LELLKGKYLVNVGRGSLVDEKVLIKALKEGNLK 255
                                       77889*****************99999997765 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 !   33.9   0.0   2.2e-11   3.5e-08       1      94 [.     148     234 ..     148     237 .. 0.83

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 2.2e-11
                                       EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-.HHHHHH CS
                     F420_oxidored   1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavk.pedvee 76 
                                       kigi+G+G++g+++a+++ a +   +ei+   sr+ +  e +++e+++k  +   +++++e+d+v+la++ +  +  
  gi|242398997|ref|YP_002994421.1| 148 KIGILGMGSIGKGIARRMKAMN---TEIYYW-SRTRK--EDIEKEVNAKWLP--INDVLKESDIVILALPsTPETYH 216
                                       7*********************...****55.88877..7888887766666..9**************95345566 PP

                                       HHHHCGHHHHTTSEEEEE CS
                     F420_oxidored  77 vlselakdalkgklvisv 94 
                                       +++e + ++lkgk ++ v
  gi|242398997|ref|YP_002994421.1| 217 IINEETLELLKGKYLVNV 234
                                       666666999999999987 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 ?   -2.2   0.0       1.6   2.7e+03      41      60 ..      80      99 ..      61     112 .. 0.56
   2 !   26.0   0.0   3.5e-09   5.8e-06       2      99 ..     144     240 ..     143     251 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.6
                                      HHHHHHTT-EEEEHHHHHHT CS
                              IlvN 41 vkkAkeegfevltvaeavkk 60
                                      ++ A+e+g+ v++v+ + ++
  gi|242398997|ref|YP_002994421.1| 80 INAATEKGIYVTKVSGILSE 99
                                      44555555555555444433 PP

  == domain 2  score: 26.0 bits;  conditional E-value: 3.5e-09
                                       HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHHH.HHHH CS
                              IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPDelq.kevy 77 
                                       l+gkki ++G+Gs G+  a+ ++    ++ +  r+ ++ ++k    + + l ++++ k++d+v++ +P + +  +++
  gi|242398997|ref|YP_002994421.1| 144 LHGKKIGILGMGSIGKGIARRMKAMNTEIYYWSRTRKEDIEKE--VNAKWLPINDVLKESDIVILALPSTPEtYHII 218
                                       899****************************999999777765..5567899****************986515789 PP

                                       HHHTGGG--TT-EEEESSSHHH CS
                              IlvN  78 eeeiepnlkegkalafahGfni 99 
                                       +ee  + lk +  +  + G  +
  gi|242398997|ref|YP_002994421.1| 219 NEETLELLKGKYLVNVGRGSLV 240
                                       9998888888888877777655 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.5   2.4e+03      47      82 ..      13      49 ..       3      74 .. 0.62
   2 !   19.5   0.0   4.8e-07   0.00077       6      96 ..     140     224 ..     138     241 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.5
                                      HHHHHHHHHHT.ET-EEEEG.CGHHHHHHT-SEEEE- CS
                      Shikimate_DH 47 erakelaeelkgeeiealkl.eelkellaeadvvisa 82
                                      ++a +l +e+ ++++ + +  ee+ +++ ++d +i++
  gi|242398997|ref|YP_002994421.1| 13 SNAMKLLKEYCDVDVMVYPTkEEVLQVIGAYDGLIVS 49
                                      5566666776565555544416788888888877765 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 4.8e-07
                                       HHS..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE- CS
                      Shikimate_DH   6 kleslkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisa 82 
                                       ++e+l++kk+ ++G G +++ +a+ + a + + +    R  +r +++ +e++++    l++++   +l+e+d+vi a
  gi|242398997|ref|YP_002994421.1| 140 EMETLHGKKIGILGMGSIGKGIARRMKAMNTE-IYYWSR--TRKEDIEKEVNAK---WLPIND---VLKESDIVILA 207
                                       67899**********************99988.665555..57899*9999666...777665...679******97 PP

                                       ...SSSSS-SB-HHHHH CS
                      Shikimate_DH  83 ...taseepilekeeve 96 
                                          t  + +i+++e +e
  gi|242398997|ref|YP_002994421.1| 208 lpsTPETYHIINEETLE 224
                                       22144456777777776 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 !   14.9   0.3   1.2e-05      0.02       1      49 [.     148     193 ..     148     259 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.2e-05
                                       -EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHHSSBTTTBT CS
                    NAD_Gly3P_dh_N   1 kiavlGaGswGtalAkvlaenghevrlwvreeelieeineehenvkyLp 49 
                                       ki++lG+Gs G  +A+ ++  + e+  w+r ++  e+i+ ++ n k Lp
  gi|242398997|ref|YP_002994421.1| 148 KIGILGMGSIGKGIARRMKAMNTEIYYWSRTRK--EDIE-KEVNAKWLP 193
                                       79***************************9875..3443.344555555 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 !   14.1   0.1   2.3e-05     0.038      21     111 ..     144     236 ..     139     260 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.3e-05
                                       -TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHHHHHCTT-EE--HHHCTTT-SEEEE-....SSSSSSB- CS
                     AdoHcyase_NAD  21 laGkvavvaGyGdvGkGcaaslkglGarvivtevdPicalqaameGfevvtleevvkkadivvtt....tGnkdiit 93 
                                       l Gk++ + G G +GkG a+ +k++ + ++         +   ++  +   +++v+k++div+ +      +  ii+
  gi|242398997|ref|YP_002994421.1| 144 LHGKKIGILGMGSIGKGIARRMKAMNTEIYYWSRTRKEDIEKEVNA-KWLPINDVLKESDIVILAlpstPETYHIIN 219
                                       689************************9998877777777777765.567899999999999965111145678999 PP

                                       HHHHCCS-TTEEEEE-SS CS
                     AdoHcyase_NAD  94 lehlkkmkddaivcniGh 111
                                        e+l+ +k + +v n+G 
  gi|242398997|ref|YP_002994421.1| 220 EETLELLKGKYLV-NVGR 236
                                       9999999988765.6665 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.2e-05     0.035       1      47 [.     149     198 ..     149     224 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.2e-05
                                       EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH..HHHH.HHHHCEEEEETT CS
                              ApbA   1 iailGaGaiGsllaakLakagadvtlilrsr..rlea.lkknGlrltseg 47 
                                       i ilG+G+iG  +a ++++ + +++ + r+r   +e+ ++ ++l ++++ 
  gi|242398997|ref|YP_002994421.1| 149 IGILGMGSIGKGIARRMKAMNTEIYYWSRTRkeDIEKeVNAKWLPINDVL 198
                                       79***************99999******9995556666777777666665 PP

>> Rossmann-like  Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   5.9e-05     0.096      12      79 ..     148     211 ..     141     228 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.9e-05
                     Rossmann-like  12 svGiisaGrvGtalgaaleraghvvvgisaisaasreraerrlPdvpvlevedvaaraellllavPda 79 
                                       ++Gi++ G +G  ++  ++  +   + i+  s + +e  e+ + + + l+++dv +++++++la+P +
  gi|242398997|ref|YP_002994421.1| 148 KIGILGMGSIGKGIARRMKAMN---TEIYYWSRTRKEDIEKEV-NAKWLPINDVLKESDIVILALPST 211
                                       79*********99987666555...678899999999999987.7899*****************964 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 ?   -0.8   0.0       1.3   2.1e+03      26      39 ..      58      71 ..      14     103 .. 0.68
   2 ?   11.8   0.0   0.00015      0.25       5      81 ..     144     220 ..     141     237 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.3
                     NAD_binding_7 26 lleagakvtvvape 39
                                      ++e g+k++v++ +
  gi|242398997|ref|YP_002994421.1| 58 IIEHGKKLKVISTQ 71
                                      45555666666555 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00015
                     NAD_binding_7   5 lkgkkvlvvGgGevAarkvrklleagakvtvvapevkeeleelvklaeeelekdlegadlviaatddrelneriaea 81 
                                       l+gkk+ + G G+++   +r++ + + ++   + + ke +e+ v+++   +++ l++ d+vi a + + +  +i ++
  gi|242398997|ref|YP_002994421.1| 144 LHGKKIGILGMGSIGKGIARRMKAMNTEIYYWSRTRKEDIEKEVNAKWLPINDVLKESDIVILALPSTPETYHIINE 220
                                       789********************************999999*9**999999*************9998887777664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); 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: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 2114.43
//
Query:       gi|242398998|ref|YP_002994422.1|  [L=304]
Description: SerA D-3-phosphoglycerate dehydrogenase [Thermococcus sibiricus MM 739]
Scores for complete 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-70  235.9   0.0    4.5e-70  234.6   0.0    1.7  2  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
    7.7e-38  129.2   0.3    8.8e-38  129.0   0.3    1.0  1  2-Hacid_dh     D-isomer specific 2-hydroxyacid dehydrogenase,
    1.7e-06   27.7   0.3    1.2e-05   25.0   0.0    2.3  3  IlvN           Acetohydroxy acid isomeroreductase, NADPH-bind
      1e-05   25.8   0.2    8.4e-05   22.8   0.0    2.2  2  NAD_binding_2  NAD binding domain of 6-phosphogluconate dehyd
    0.00061   19.1   0.0     0.0017   17.7   0.0    1.7  1  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
     0.0029   17.2   0.1     0.0067   16.0   0.1    1.6  1  NmrA           NmrA-like family
  ------ inclusion threshold ------
      0.015   15.3   0.0      0.029   14.5   0.0    1.4  1  AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD bindi
       0.11   13.1   0.0       0.26   11.8   0.0    1.7  1  XdhC_C         XdhC Rossmann domain


Domain annotation for each model (and alignments):
>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0         1   2.3e+03     146     165 ..      17      35 ..      11      45 .. 0.69
   2 !  234.6   0.0     2e-73   4.5e-70       1     178 []     105     280 ..     105     280 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1
                                       CCEEEES--SSSSSGTCHHH CS
                      2-Hacid_dh_C 146 iagaalDvfeeeplpedspl 165
                                       ++ a+l v++ee +++d +l
  gi|242398998|ref|YP_002994422.1|  17 LKNAGLEVVYEEYPDQD-RL 35 
                                       56778888888766655.44 PP

  == domain 2  score: 234.6 bits;  conditional E-value: 2e-73
                                       HHHHHHHHTTHHHHHHHHHTTCCHTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHH CS
                      2-Hacid_dh_C   1 lalllallrrlaeadeevregewksekallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeee 77 
                                       +al+++++r++a ad+++reg w  +k+ +g el+gkt+GiiG+GrIG +v k++k +gm+v+ yd++k+ e+ ++e
  gi|242398998|ref|YP_002994422.1| 105 VALMFNIARKVAFADRKIREGAW-PKKQCMGFELEGKTLGIIGFGRIGYNVGKIAKTIGMNVLLYDVYKNYER-AKE 179
                                       689********************.999*****************************************99777.*** PP

                                       HTCEECSHHHHHHH-SEEEE-S--STTTTTSBSHHHHHCSTTTEEEEESS-GGGB-HHHHHHHHHTTSCCEEEES-- CS
                      2-Hacid_dh_C  78 lgvelvsleellaesDivslhlpltpetrhlinaeelakmkkgailiNtaRGglvdeeaLleaLksgkiagaalDvf 154
                                        g+e+v+le ll++sD++++h+pl ++t+hlin+e+l++mk++a+liNt+RG++vd++aL++aL++g+iagaalDvf
  gi|242398998|ref|YP_002994422.1| 180 IGAEFVELEYLLKNSDVITIHVPLLESTYHLINEEKLKLMKSTAVLINTSRGPIVDTNALVKALEEGWIAGAALDVF 256
                                       ***************************************************************************** PP

                                       SSSSSGTCHHHHHSTTEEE-SS-T CS
                      2-Hacid_dh_C 155 eeeplpedspllelpnviltPHia 178
                                       eeeplp+d+pl++++nviltPHi+
  gi|242398998|ref|YP_002994422.1| 257 EEEPLPKDHPLTKFDNVILTPHIG 280
                                       **********************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 !  129.0   0.3   3.9e-41   8.8e-38       1     126 [.       3     304 .]       3     304 .] 0.99

  Alignments for each domain:
  == domain 1  score: 129.0 bits;  conditional E-value: 3.9e-41
                                       EEEEST.CHHHHHHHHHTTEEEEEESCSSHHHCHHHHTTESEEEE-TTS-BSHHHHHHHTT--EEEESSSSCTTB-H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        2-Hacid_dh   1 vlileplreeelellkeegvevevkdellteellekakdadalivrsntkvtaevlealpkLkviaragvGvDnvDl 77 
                                       vl+  pl+e+++e lk++g+ev++++ ++++ l+e +kd+ ++ivrs+ kvt+e+++a+p+LkviaragvG DnvD+
  gi|242398998|ref|YP_002994422.1|   3 VLVAAPLHEKAIEVLKNAGLEVVYEEYPDQDRLKELVKDVSGIIVRSKPKVTKEIIDAAPSLKVIARAGVGLDNVDV 79 
                                       6888999**********888********************************************************* PP

                                       HHHHHTT-EEEE-TTTTHHHHHHHH.................................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx.................................................... RF
                        2-Hacid_dh  78 daakerGilVtnvpgystesvAElt.................................................... 102
                                       ++ak +Gi V+n+p++s++svAEl+                                                    
  gi|242398998|ref|YP_002994422.1|  80 EYAKSKGIEVVNAPTASSRSVAELAvalmfniarkvafadrkiregawpkkqcmgfelegktlgiigfgrigynvgk 156
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                        2-Hacid_dh 103 ............................................................................. 102
                                                                                                                    
  gi|242398998|ref|YP_002994422.1| 157 iaktigmnvllydvyknyerakeigaefveleyllknsdvitihvpllestyhlineeklklmkstavlintsrgpi 233
                                       ***************************************************************************** PP

                                       ...............................................T-BHHHHHHHHHHHHHHHHHHHTT CS
                                       ...............................................xxxxxxxxxxxxxxxxxxxxxxxx RF
                        2-Hacid_dh 103 ...............................................aaTeeaqeniaeeaaenlvaflkg 126
                                                                                      a+T eaq ++++e+ae++v++l g
  gi|242398998|ref|YP_002994422.1| 234 vdtnalvkaleegwiagaaldvfeeeplpkdhpltkfdnviltphigASTVEAQARAGMEVAEKVVKVLVG 304
                                       *******************************************************************9865 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 ?   -2.3   0.0       1.3   2.8e+03      22      42 ..      16      36 ..      10      56 .. 0.72
   2 ?   -0.9   0.1      0.47   1.1e+03      39      59 ..      77      97 ..      61     112 .. 0.63
   3 !   25.0   0.0   5.3e-09   1.2e-05       2      91 ..     137     225 ..     136     240 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.3
                                      HHHHTT--EEEEE-TT-HHHH CS
                              IlvN 22 nlrdsgldvvvglregsksvk 42
                                       l+++gl+vv+  + ++  +k
  gi|242398998|ref|YP_002994422.1| 16 VLKNAGLEVVYEEYPDQDRLK 36
                                      578888888887777665554 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.47
                                      HHHHHHHHTT-EEEEHHHHHH CS
                              IlvN 39 ksvkkAkeegfevltvaeavk 59
                                        v+ Ak++g+ev+++  a++
  gi|242398998|ref|YP_002994422.1| 77 VDVEYAKSKGIEVVNAPTASS 97
                                      346667777777766655543 PP

  == domain 3  score: 25.0 bits;  conditional E-value: 5.3e-09
                                       HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-H.HHHHHHH CS
                              IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPD.elqkevy 77 
                                       l+gk++ +iG+G  G + ++  +  g++v +  ++  k++++Ake g e ++++ + k++dv++i +P  e   +++
  gi|242398998|ref|YP_002994422.1| 137 LEGKTLGIIGFGRIGYNVGKIAKTIGMNVLL--YDVYKNYERAKEIGAEFVELEYLLKNSDVITIHVPLlESTYHLI 211
                                       899*************************985..666677*****************************524455566 PP

                                       HHHTGGG--TT-EE CS
                              IlvN  78 eeeiepnlkegkal 91 
                                       +ee  + +k+ ++l
  gi|242398998|ref|YP_002994422.1| 212 NEEKLKLMKSTAVL 225
                                       66655666666655 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 ?    0.4   0.0      0.29   6.5e+02     102     131 ..      80     108 ..      32     118 .. 0.86
   2 !   22.8   0.0   3.8e-08   8.4e-05       2     106 ..     142     245 ..     141     251 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.29
                                       HHHHHTT-EEEEEEEESHHHHHHHT-EEEE CS
                     NAD_binding_2 102 kelkekglkfldaPVSGGeegAekGtLsim 131
                                       +++k+kg+++++aP   +   Ae +  ++m
  gi|242398998|ref|YP_002994422.1|  80 EYAKSKGIEVVNAPTASSRSVAELAV-ALM 108
                                       67899999999999988877777666.555 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 3.8e-08
                                       EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHS.HC CS
                     NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdevieg.ll 77 
                                       +g+iG G +G n  +  +  g++v +y++  ++ e++ + ga+ + ++e l+++ dv+ + v+  + + ++i++  l
  gi|242398998|ref|YP_002994422.1| 142 LGIIGFGRIGYNVGKIAKTIGMNVLLYDVY-KNYERAKEIGAEFV-ELEYLLKNSDVITIHVPLLESTYHLINEeKL 216
                                       79**************************87.88999999998666.5799***********************9999 PP

                                       CC--TT-EEEE-S---HHHHHHHHHHHHH CS
                     NAD_binding_2  78 ealkkgdilidgstsspedtrelakelke 106
                                       + +k+ ++li++s   + dt+ l k+l+e
  gi|242398998|ref|YP_002994422.1| 217 KLMKSTAVLINTSRGPIVDTNALVKALEE 245
                                       99*********************999987 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   7.8e-07    0.0017      32     126 ..     143     227 ..     134     248 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 7.8e-07
                                       EEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHCHHHHHHHHHHHH-SEEEE---BTTSS--. CS
                       AlaDh_PNT_C  32 lviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvevlksqeellaeavkeadvvigtvlipGkkaP. 107
                                        +iG G  G +  ++ak +g +V ++Dv ++  e+ +++ga+fve+        +  +k++dv+  t+++p  ++  
  gi|242398998|ref|YP_002994422.1| 143 GIIGFGRIGYNVGKIAKTIGMNVLLYDVYKN-YERAKEIGAEFVEL--------EYLLKNSDVI--TIHVPLLESTy 208
                                       49**************************765.677899****9987........4455556654..55555443331 PP

                                       -SC-HHHHHTS-TTEEEEE CS
                       AlaDh_PNT_C 108 kLvteemvksMkpgsVivD 126
                                       +L++ee +k Mk+ +V++ 
  gi|242398998|ref|YP_002994422.1| 209 HLINEEKLKLMKSTAVLIN 227
                                       4666666666666666553 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1     3e-06    0.0067      33      94 ..      10      72 ..       1      74 [. 0.86

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3e-06
                                      -SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT-SEEEE---GG.S-HHHHHHHHHHHHHHHS- CS
                              NmrA 33 kselakslkeaGvelvkgdlddkeslvealkgvdvvfsvtgfy.skeiedgkklvdAakeaGv 94
                                      ++++++ lk+aG e+v ++  d++ l+e++k+v ++++  + +  kei d     +++++aGv
  gi|242398998|ref|YP_002994422.1| 10 HEKAIEVLKNAGLEVVYEEYPDQDRLKELVKDVSGIIVRSKPKvTKEIIDAAPSLKVIARAGV 72
                                      6789999******************************99886678888888888888888887 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 ?   14.5   0.0   1.3e-05     0.029      21     110 ..     137     229 ..     129     248 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.3e-05
                                       -TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHHHHHCTT-EE--HHHCTTT-SEEEE-S....SSSSSB- CS
                     AdoHcyase_NAD  21 laGkvavvaGyGdvGkGcaaslkglGarvivtevdPicalqaameGfevvtleevvkkadivvttt....Gnkdiit 93 
                                       l Gk+  ++G+G +G    +  k++G  v++ +v   +  +a   G e v+le ++k++d++         +  +i+
  gi|242398998|ref|YP_002994422.1| 137 LEGKTLGIIGFGRIGYNVGKIAKTIGMNVLLYDVYK-NYERAKEIGAEFVELEYLLKNSDVITIHVplleSTYHLIN 212
                                       78******************************9975.66788888***************98654322226789*** PP

                                       HHHHCCS-TTEEEEE-S CS
                     AdoHcyase_NAD  94 lehlkkmkddaivcniG 110
                                        e+lk mk +a++ n  
  gi|242398998|ref|YP_002994422.1| 213 EEKLKLMKSTAVLINTS 229
                                       ************99965 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00012      0.26       2      66 ..     143     244 ..     142     252 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00012
                                       EEE--STTHHHHHHHHHHHTEEEEEEES-GGGG........-GGG-TT-SE.......................... CS
                            XdhC_C   2 vifGaghvaqalarlaaalgfrvtvvdpreefa........tkerfpeade.......................... 44 
                                        i+G g ++  + ++a+++g++v ++d  ++++                                            
  gi|242398998|ref|YP_002994422.1| 143 GIIGFGRIGYNVGKIAKTIGMNVLLYDVYKNYErakeigaeF--------Veleyllknsdvitihvpllestyhli 211
                                       69****************************999444444440........145555555555555556666666666 PP

                                       ..........-EEEE--.S-HHHHHHHHHHHSS CS
                            XdhC_C  45 ..........tavvvlt.hdhklDaealeaalr 66 
                                                 tav++ t +++  D++al +al+
  gi|242398998|ref|YP_002994422.1| 212 neeklklmksTAVLINTsRGPIVDTNALVKALE 244
                                       666666666677777662566889999998884 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2009.35
//
Query:       gi|242398999|ref|YP_002994423.1|  [L=215]
Description: Phosphate transport system regulator PhoU like protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-45  155.3   5.1    1.5e-45  155.2   5.1    1.0  1  PhoU_div  Protein of unknown function DUF47
     0.0011   19.4   8.2       0.26   11.8   1.7    2.5  2  PhoU      PhoU domain
  ------ inclusion threshold ------
      0.091   11.7   0.0       0.13   11.2   0.0    1.1  1  DUF3182   Protein of unknown function (DUF3182)
       0.11   12.1   0.9       0.21   11.2   0.9    1.6  1  LUC7      LUC7 N_terminus
       0.52   10.8   4.0       0.86   10.1   0.2    2.8  2  Rnk_N     Rnk N-terminus


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 !  155.2   5.1   4.1e-49   1.5e-45       5     213 ..       7     211 ..       3     212 .. 0.96

  Alignments for each domain:
  == domain 1  score: 155.2 bits;  conditional E-value: 4.1e-49
                          PhoU_div   5 fgsspekslqdhlekvsetvlkliellkallegdyekveellkeiselEreADeikreirlklekglflPvdRedll 81 
                                       ++ +++k + +hle v  t+ kl el++++l+gd ek+e+l+ke+ + Er ADe++rei+  l++g+flPv R d  
  gi|242398999|ref|YP_002994423.1|   7 KEDNVFKAIDEHLEAVGLTIKKLYELMETYLAGDIEKAEVLMKEVENQERVADELRREIEAMLYQGAFLPVNRGDYA 83 
                                       78899************************************************************************ PP

                          PhoU_div  82 elveslDeildvlediamlvtlrkvefpeelkdeflallkktveaiealaevieeleklletalskkdiveeieslE 158
                                       +l e +D+++d +e++a+ ++l k + p++lk e+l ll++++e+ +++++ ++ l++ +++a++   ++++ e  E
  gi|242398999|ref|YP_002994423.1|  84 KLSELIDSVADAAESAAHALILAKPKTPPDLKKEILDLLNASLETYKLVEKSVKMLNTNVDGAIE---YAKKTELAE 157
                                       ****************************************************************9...9******** PP

                          PhoU_div 159 deiDqlqrklikklfsredasnplevlllveiieklenvsdraedvadrisiill 213
                                       +++D+++  l+ k f+ e+ + + +  ++ + + k++ ++draed++d++ +i l
  gi|242398999|ref|YP_002994423.1| 158 EDADKIEYTLLRKVFESES-ITTFAKFIWNQVVTKIGDIADRAEDASDQVLLIAL 211
                                       ****************888.66777779**********************99976 PP

>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   1.7   7.2e-05      0.26      15      87 ..      32     107 ..      19     108 .. 0.72
   2 !   11.3   0.5    0.0001      0.37       7      84 ..     127     201 ..     121     210 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.2e-05
                                       HHHHHHCT-H...HHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              PhoU  15 alealeekdt...ela.revierddeidrlekeiersllealakrqplaedlrellsllriardlERigDhavniae 87 
                                       ++e +  +d    e + +ev ++++ +d+l++eie  l++ ++   + + d+  l++l++ + d    + ha  +a+
  gi|242398999|ref|YP_002994423.1|  32 LMETYLAGDIekaEVLmKEVENQERVADELRREIEAMLYQGAFLPVNRG-DYAKLSELIDSVADAAESAAHALILAK 107
                                       44444445541223333788889**************999997733333.688999999999999999999987775 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.0001
                                       HHHHHHHHHHHHHHCT.-H..HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHHHH CS
                              PhoU   7 iveemlddalealeek.dt..elarevierddeidrlekeiersllealakrqplaedlrellsllriardlERigD 80 
                                        +++ +++++++l ++ d   e+a++    ++++d++e+ + r+++e      + ++  +++    ++++ +  i+D
  gi|242398999|ref|YP_002994423.1| 127 ETYKLVEKSVKMLNTNvDGaiEYAKKTELAEEDADKIEYTLLRKVFESE----SITTFAKFI--WNQVVTKIGDIAD 197
                                       578999*******999443668888888889999999888888755443....333222232..2236666666666 PP

                                       HHHH CS
                              PhoU  81 havn 84 
                                        a++
  gi|242398999|ref|YP_002994423.1| 198 RAED 201
                                       6655 PP

>> DUF3182  Protein of unknown function (DUF3182)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   3.5e-05      0.13     168     237 ..      15      88 ..       7     106 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.5e-05
                           DUF3182 168 deeelaaeGlVlEedleevttySvGqvrvggllasYlGtQrltrdnsGeev....YgGsdLvvvrGgldaLlal 237
                                        +e+l+a Gl + +  e ++ty  G ++ +++l+  + +Q+ ++d+  +e+    Y G+ L v rG++++L +l
  gi|242398999|ref|YP_002994423.1|  15 IDEHLEAVGLTIKKLYELMETYLAGDIEKAEVLMKEVENQERVADELRREIeamlYQGAFLPVNRGDYAKLSEL 88 
                                       457899*************************************998776644444***************9865 PP

>> LUC7  LUC7 N_terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.9   5.8e-05      0.21     123     180 ..      14      95 ..       6     179 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5.8e-05
                                       ..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..................... CS
                              LUC7 123 kkqeqlkeleekiekllaeaeelgeeGkVdeaqklmkeveelkeekeeleqqyeaaa.................... 179
                                       + +e+l+ +  +i+kl + +e     G++++a+ lmkeve+ ++  +el+++ ea+                     
  gi|242398999|ref|YP_002994423.1|  14 AIDEHLEAVGLTIKKLYELMETY-LAGDIEKAEVLMKEVENQERVADELRREIEAMLyqgaflpvnrgdyaklseli 89 
                                       56788888999999999888876.78*************************99987666666666666666555555 PP

                                       ...... CS
                              LUC7 180 .....a 180
                                            a
  gi|242398999|ref|YP_002994423.1|  90 dsvadA 95 
                                       555550 PP

>> Rnk_N  Rnk N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.6      0.24   8.5e+02      23      36 ..      53      66 ..      28      66 .. 0.77
   2 ?   10.1   0.2   0.00024      0.86       6      31 ..      78     103 ..      77     106 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.24
                                      TSSTTHHHHHHHHH CS
                             Rnk_N 23 rdppaaeaLeaELd 36
                                      ++  +a++L +E++
  gi|242398999|ref|YP_002994423.1| 53 NQERVADELRREIE 66
                                      45577888888875 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00024
                                       EHHHHHHHHHHHHCTTTTSSTTHHHH CS
                             Rnk_N   6 telDleRLeaLldsladrdppaaeaL 31 
                                       ++ D++ L+ L+ds ad++  aa aL
  gi|242398999|ref|YP_002994423.1|  78 NRGDYAKLSELIDSVADAAESAAHAL 103
                                       566************99987887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       918  (0.051202); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); 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: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 1477.58
//
Query:       gi|242399000|ref|YP_002994424.1|  [L=300]
Description: 2-dehydropantoate 2-reductase [Thermococcus sibiricus MM 739]
Scores for complete 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  121.6   0.2    4.1e-35  120.7   0.2    1.5  1  ApbA_C           Ketopantoate reductase PanE/ApbA C terminal
    1.5e-34  118.8   0.0    3.6e-34  117.6   0.0    1.6  2  ApbA             Ketopantoate reductase PanE/ApbA
    0.00069   19.6   0.0     0.0026   17.8   0.0    1.9  2  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
    0.00081   19.0   0.6     0.0013   18.4   0.1    1.6  2  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
      0.008   16.4   0.0      0.014   15.6   0.0    1.4  1  TrkA_N           TrkA-N domain
  ------ inclusion threshold ------
      0.049   13.0   0.1       0.08   12.3   0.1    1.3  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
      0.057   14.0   0.1       0.19   12.3   0.1    2.0  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
      0.078   13.2   0.0       0.21   11.8   0.0    1.8  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
       0.16   12.5   0.3       0.16   12.5   0.3    2.4  2  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
        0.2   10.8   0.1       0.37   10.0   0.1    1.4  1  FAD_binding_3    FAD binding domain


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 !  120.7   0.2   2.3e-38   4.1e-35       1     125 []     172     295 ..     172     295 .. 0.99

  Alignments for each domain:
  == domain 1  score: 120.7 bits;  conditional E-value: 2.3e-38
                            ApbA_C   1 dirlarweKllinaainpltalldckngellespelralvrallkEalavaeaegvelseerleeaveavlektaan 77 
                                       +i++++w+K ++n+ainp++a++++kn ++le+++l +l+++++kE ++va+++gv++++    e + ++le+t++n
  gi|242399000|ref|YP_002994424.1| 172 NIEGWKWSKAIVNSAINPIGAIMEVKNVKILENEYLLKLAKEVVKEGCQVATQLGVKFEKH-PMELLIETLEQTREN 247
                                       7999*********************************************************.9************** PP

                            ApbA_C  78 rsSMlqDveagrktEidyinGavvklAeklgvetPvnellyellkale 125
                                       + SMlqD+++++ktEid+inG++++ ++k g+e+P n +l++++ka+e
  gi|242399000|ref|YP_002994424.1| 248 YNSMLQDIRRKKKTEIDFINGKIIEYGRKIGLEVPLNFALWSMVKAKE 295
                                       *********************************************986 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.6   0.0     2e-37   3.6e-34       1     151 [.       3     146 ..       3     147 .. 0.97
   2 ?   -2.0   0.0       1.3   2.4e+03      76      98 ..     199     221 ..     155     232 .. 0.70

  Alignments for each domain:
  == domain 1  score: 117.6 bits;  conditional E-value: 2e-37
                                       EEEES-SHHHHHHHHHHHHHTHCEEEE-SCHHHHHHHHHCEEEEETTCEEEEEECEEECCHSCCCCS-ESEEEE-SS CS
                              ApbA   1 iailGaGaiGsllaakLakagadvtlilrsrrlealkknGlrltseggeeilrppealsaeekselepidlvivtvK 77 
                                       i+ilGaG+iGsl++a L++ g+dv+li+r+++++++++nGl++ + + e++++p++ ++ +     ep dl+i+++K
  gi|242399000|ref|YP_002994424.1|   3 IYILGAGSIGSLFGALLSRVGEDVILIGREEHVKEINRNGLKIVGIE-EFTVYPEALTRMP----SEPPDLIILSTK 74 
                                       89*********************************************.9999999999999....79********** PP

                                       GGGHHHHHHHHGGGECTCEEEEEESSSSCHHHHHTTTSTTSEEEEEEEE-EEEEEETTEEEECS--EEEEEESS CS
                              ApbA  78 ayqteealeeikplldpntvvlllqNGlgheeelrealpkprvlggvtthgatregpgevhhagkgeikigela 151
                                       + +te+ale +++ +++nt +l++qNGlg+eee   +   ++vlgg+tt ga  e  g v++ g g + ig+++
  gi|242399000|ref|YP_002994424.1|  75 SHSTEYALECARESIGKNTWILSIQNGLGNEEEALRYT--KNVLGGITTNGAMIERWGVVKWVGRGITIIGDYP 146
                                       *******************************9999998..89*****************************986 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.3
                                       SSGGGHHHHHHHHGGGECTCEEE CS
                              ApbA  76 vKayqteealeeikplldpntvv 98 
                                       vK + +e+ l+ +k+++++ + v
  gi|242399000|ref|YP_002994424.1| 199 VKILENEYLLKLAKEVVKEGCQV 221
                                       66677777777777777776655 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   1.4e-06    0.0026       1     122 [.       2     120 ..       2     127 .. 0.79
   2 ?   -2.6   0.0       2.7   4.8e+03      33      44 ..     236     247 ..     205     256 .. 0.52

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.4e-06
                                       -EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHHSSBTTTBTT--.--TTEEEES-HHHHHTT--EEEE- CS
                    NAD_Gly3P_dh_N   1 kiavlGaGswGtalAkvlaenghevrlwvreeelieeineehenvkyLpgik.lpenlvattdlaealkgadiivlv 76 
                                       ki +lGaGs G+ + ++l++ g++v l++ree +++ein++      +++++ +pe+l+  +      +  d+i+l 
  gi|242399000|ref|YP_002994424.1|   2 KIYILGAGSIGSLFGALLSRVGEDVILIGREE-HVKEINRNGLKIVGIEEFTvYPEALTRMP-----SEPPDLIILS 72 
                                       799************************99875.67889887766666666431455555443.....5678999999 PP

                                       --HHHHHHHHHHHCCC--TT-EEEE---SE..ET.TTEEHHHHHHHHH CS
                    NAD_Gly3P_dh_N  77 vPsqalrevlkklkgllkkkailvsliKGi..eegtlkllsevieeel 122
                                         s+ ++  l+ + + + k++ ++s+  G+  ee+ l+ +++v+  ++
  gi|242399000|ref|YP_002994424.1|  73 TKSHSTEYALECARESIGKNTWILSIQNGLgnEEEALRYTKNVLGGIT 120
                                       999999999999999999999999999999877777777777776555 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.7
                                       HHHHHHHHHSSB CS
                    NAD_Gly3P_dh_N  33 elieeineehen 44 
                                        lie++++++en
  gi|242399000|ref|YP_002994424.1| 236 LLIETLEQTREN 247
                                       344555555555 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 !   18.4   0.1   7.2e-07    0.0013       1      49 [.       1      48 [.       1      61 [. 0.88
   2 ?   -3.2   0.1         3   5.4e+03     100     133 ..     183     216 ..     180     229 .. 0.58

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 7.2e-07
                                      SEEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS--T CS
                    UDPG_MGDP_dh_N  1 mkisviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipiyep 49
                                      mki ++G+G +G   +a+l+++g +vi++  + e+v+++n++ ++i+  
  gi|242399000|ref|YP_002994424.1|  1 MKIYILGAGSIGSLFGALLSRVGEDVILIGRE-EHVKEINRNGLKIVGI 48
                                      89***************************875.67*******9999855 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3
                                       HHHHHHHHHHHHHCEEEEEE-S---TTHHHHCHH CS
                    UDPG_MGDP_dh_N 100 vesaarsiaealkkgkvvvvkSTvpvgtaeelvk 133
                                       v+sa++ i+ +++ ++v +++     + a+e+vk
  gi|242399000|ref|YP_002994424.1| 183 VNSAINPIGAIMEVKNVKILENEYLLKLAKEVVK 216
                                       5566666666666666655555555554444444 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0     8e-06     0.014       1      95 [.       3      97 ..       3     110 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 8e-06
                                      EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTTSE..EEES-TTSHHHHHHTTGGGESEEEE-SSSHHHH CS
                            TrkA_N  1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreegle..vvvgdatdeevLeeagiekadaviaatgddean 76
                                      i i+G+G +G+     Ls+ g+ dv++i + ee+v+e+ ++gl+   +      +e+L ++  e  d++i  t+++ + 
  gi|242399000|ref|YP_002994424.1|  3 IYILGAGSIGSLFGALLSRvGE-DVILIGR-EEHVKEINRNGLKivGIEEFTVYPEALTRMPSEPPDLIILSTKSHSTE 79
                                      579****************777.7****99.68*********774467788899****************999887554 PP

                                      HHHHHHHHHHTSSSEEEEE CS
                            TrkA_N 77 ilavllakelnpkkkiiar 95
                                        a++ a+e  +k + i  
  gi|242399000|ref|YP_002994424.1| 80 Y-ALECARESIGKNTWILS 97
                                      3.34666666665555555 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 ?   12.3   0.1   4.4e-05      0.08      38      88 ..       2      51 ..       1      58 [. 0.90

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.4e-05
                                      EEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEECSHHHH CS
                      2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelvsleel 88
                                      ++ i+G+G+IG+ +  +l+ +g +vi + r ++ +e  +++g++ v +ee+
  gi|242399000|ref|YP_002994424.1|  2 KIYILGAGSIGSLFGALLSRVGEDVILIGREEHVKE-INRNGLKIVGIEEF 51
                                      6779***************************99777.88889999999886 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 ?   12.3   0.1   0.00011      0.19       1      97 []       2     101 ..       2     101 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00011
                                       EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC.........-EEECECHHHHHH.....H-S CS
                     F420_oxidored   1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg.........vkvtavdneeaae.....ead 63 
                                       ki i+GaG++g+ +   l++ g   ++++++    +e ++e+ ++           v      + ea++       d
  gi|242399000|ref|YP_002994424.1|   2 KIYILGAGSIGSLFGALLSRVG---EDVILI-G-REEHVKEINRNGLkivgieeftV------YPEALTrmpsePPD 67 
                                       689*******************...888877.4.44556666655444655444221......22222212222678 PP

                                       EEEE-S-HHHHHHHHHHCGHHHHTTSEEEEESSS CS
                     F420_oxidored  64 vvvlavkpedveevlselakdalkgklvisvlag 97 
                                        ++l+ k + +e +l+ ++++  k++ ++s+ +g
  gi|242399000|ref|YP_002994424.1|  68 LIILSTKSHSTEYALECARESIGKNTWILSIQNG 101
                                       9999999999999988888888888888888775 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00012      0.21       1      43 [.       3      40 ..       3      88 .. 0.74
   2 ?   -1.9   0.0       2.1   3.7e+03      49      67 ..     238     256 ..     209     265 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00012
                                      EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCH CS
                   Sacchrp_dh_NADP  1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaak 43
                                      + i+GaGs+G+ +  ll+r ++    +++++r+++   ++++ 
  gi|242399000|ref|YP_002994424.1|  3 IYILGAGSIGSLFGALLSRVGED---VILIGREEHV--KEINR 40
                                      679*****************985...9999999987..55544 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.1
                                       EEEEE--TTTHHHHHHHHH CS
                   Sacchrp_dh_NADP  49 feaialdaenyeavLaall 67 
                                       +e+ + ++eny ++L+ + 
  gi|242399000|ref|YP_002994424.1| 238 IETLEQTRENYNSMLQDIR 256
                                       5566777788877777654 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.3   9.2e-05      0.16       1      35 [.       2      36 ..       2      46 .. 0.91
   2 ?   -0.6   0.2       1.1   2.1e+03      50      69 ..     194     213 ..     154     263 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.2e-05
                                      EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                         Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                      k+ ++G+G ig  +++ l++ g +V ++ r++++ 
  gi|242399000|ref|YP_002994424.1|  2 KIYILGAGSIGSLFGALLSRVGEDVILIGREEHVK 36
                                      688***************************99987 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.1
                                       HHHTTEEEECSEEEEEEEEE CS
                         Pyr_redox  50 lekngievllntkveeiegs 69 
                                       +e +++++l n+ + ++ ++
  gi|242399000|ref|YP_002994424.1| 194 MEVKNVKILENEYLLKLAKE 213
                                       45555555555555554433 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00021      0.37       3      35 ..       2      34 ..       1      44 [. 0.89

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00021
                                      EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSS CS
                     FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlvekrst 35
                                      ++ I GaG  G + + lLs+ G +v+l+ + + 
  gi|242399000|ref|YP_002994424.1|  2 KIYILGAGSIGSLFGALLSRVGEDVILIGREEH 34
                                      578*************************99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       752  (0.0419432); expected 358.6 (0.02)
Passed bias filter:                      576  (0.0321267); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1789.12
//
Query:       gi|242399001|ref|YP_002994425.1|  [L=246]
Description: SpoU protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-36  125.7   0.0    2.2e-36  125.1   0.0    1.2  1  SpoU_methylase  SpoU rRNA Methylase family
  ------ inclusion threshold ------
       0.12   12.4   0.0       0.13   12.3   0.0    1.2  1  ELMO_CED12      ELMO/CED-12 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 !  125.1   0.0   2.5e-40   2.2e-36       2     142 .]       3     154 ..       2     154 .. 0.87

  Alignments for each domain:
  == domain 1  score: 125.1 bits;  conditional E-value: 2.5e-40
                                       EEEEEES-SSHHHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHH.EEEESSHHHHHHHHCCCTEE CS
                    SpoU_methylase   2 livvlveiedpgNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevle.lkvvdsleealkelkeegfa 77 
                                       l v+lve+e+p NlGaiaR++k+fg+++l+lv+p+   ++n+ a+ +a++a ++le +k+++sleeal+ ++ +   
  gi|242399001|ref|YP_002994425.1|   3 LKVILVEPEYPINLGAIARVMKNFGVTDLILVNPKVS-PNNKIARTFAVHAVDILEnAKIHESLEEALNTVDLA--- 75 
                                       689******************************9986.99999*******************************... PP

                                       EEEEST..T-SEGC.CS.....HHH.......TTEEEEEEBTTTBS-HHHHCTSSEEEE----TTSSS--HHHHHHH CS
                    SpoU_methylase  78 lvatsl..kgksls.ei.....dlk.......ekvalvfGnEdkGlsnelleladrlvkIpmsgeveSLNvavAvai 139
                                        ++ts+  +g+ +  ++     +++       +++ lvfG+E++Gl+ne+l+++d +v+Ip+s+e++ +N+++Ava+
  gi|242399001|ref|YP_002994425.1|  76 -IGTSGlaGGDYIPeRApispeEFAkrlsiydGEIGLVFGRESRGLDNEELKKLDFTVTIPTSEEYPIMNLSHAVAV 151
                                       .7776663333222322334442325566777********************************************* PP

                                       HHH CS
                    SpoU_methylase 140 lly 142
                                       +ly
  gi|242399001|ref|YP_002994425.1| 152 ILY 154
                                       *99 PP

>> ELMO_CED12  ELMO/CED-12 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.5e-05      0.13      97     159 ..     133     213 ..      37     215 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.5e-05
                        ELMO_CED12  97 e.....eypfavasinvtslllelleiektdeed.e.eeqkdklkt.............nntkllssnlnafeelfs 153
                                             eyp++  s +v  +l+e +++ k+++++ e + + +k +t               ++l ++++    ++++
  gi|242399001|ref|YP_002994425.1| 133 TiptseEYPIMNLSHAVAVILYEVFKQ-KLKNNPtEvKRRLRK-STrqeremlvefwakFLDTLEYPKDLEKRRFYV 207
                                       044444********************9.677777564444444.335788888877776666677777777777777 PP

                        ELMO_CED12 154 vlfllf 159
                                        +f +f
  gi|242399001|ref|YP_002994425.1| 208 LMFKRF 213
                                       777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       756  (0.0421663); expected 358.6 (0.02)
Passed bias filter:                      649  (0.0361983); 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: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.52
# Mc/sec: 1418.38
//
Query:       gi|242399002|ref|YP_002994426.1|  [L=175]
Description: Methylated-DNA--protein-cysteine methyltransferase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.1e-25   88.1   0.0    4.3e-25   87.6   0.0    1.2  1  DNA_binding_1  6-O-methylguanine DNA methyltransferase, DNA b
    1.1e-20   73.5   1.2      1e-19   70.4   0.7    2.0  2  DUF1938        Domain of unknown function (DUF1938)
  ------ inclusion threshold ------
        0.2   10.3   0.0       0.26    9.9   0.0    1.1  1  EPSP_synthase  EPSP synthase (3-phosphoshikimate 1-carboxyvin


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 !   87.6   0.0   7.2e-29   4.3e-25       1      81 []      92     170 ..      92     170 .. 0.96

  Alignments for each domain:
  == domain 1  score: 87.6 bits;  conditional E-value: 7.2e-29
                                       HHHHHHHHHHTT.S-TT-BEEHHHHHHHTT.TSCHHHHHHHHHTSSBTTTSGGGGEEBTTSBCCTTTTCHHHHHHHH CS
                     DNA_binding_1   1 afqqrVwellrq.IpyGkvttYgeiAkllgkpkaaraVgqalaanplailvPcHRVvgadgklggyagglerkralL 76 
                                       +f+++V+e+l + + +G+v+tYge+Ak+l   +++ra+g+a+++np++i+vPcHRV+++++ +g+y+ + e kr lL
  gi|242399002|ref|YP_002994426.1|  92 PFEKKVYETLTKkVKRGEVITYGELAKMLR--SSPRAIGGAMKRNPYPIIVPCHRVIASNN-IGNYTPKREYKRFLL 165
                                       699****997655*****************..***************************99.*************** PP

                                       HHTTS CS
                     DNA_binding_1  77 eaEgv 81 
                                       e Egv
  gi|242399002|ref|YP_002994426.1| 166 ETEGV 170
                                       ***97 PP

>> DUF1938  Domain of unknown function (DUF1938)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.4   0.7   1.7e-23     1e-19       1      86 [.       1      85 [.       1      88 [. 0.95
   2 ?    1.7   0.0     0.048   2.8e+02      60      88 ..      88     116 ..      87     117 .. 0.85

  Alignments for each domain:
  == domain 1  score: 70.4 bits;  conditional E-value: 1.7e-23
                                      -EEEEEEEETTEEEEEEEEESSSEEEEEEESSHHHHHH.HHHHHHHHHHHT.------B--..-SHHHHHHHHHTTSS- CS
                           DUF1938  1 ilevrkfrvkekvvyiGvlsedkvfGiifaidegelikhripdlieflekr.lskklevkegnsdysekvfkvliGkld 78
                                      +++++ f+++ek + i +l++ k++Gi f++d  + ++ r++ l+e+l  r ++++le ++  s+ +  v+k+liG++ 
  gi|242399002|ref|YP_002994426.1|  1 MISIKSFQIGEKEIVIAILFDKKIQGITFSFDGEQFLQERVNALVEHLTNRgVKVNLEERD--SELPALVYKILIGEIR 77
                                      789************************************************9988888777..**************** PP

                                      GGGGGG.. CS
                           DUF1938 79 neealefi 86
                                      n++ le++
  gi|242399002|ref|YP_002994426.1| 78 NQDGLEYL 85
                                      **999976 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.048
                                       -..-SHHHHHHHHHTTSS-GGGGGG..GB CS
                           DUF1938  60 egnsdysekvfkvliGkldneealefiel 88 
                                       eg + + +kv+ +l  k++  e++ + el
  gi|242399002|ref|YP_002994426.1|  88 EGTTPFEKKVYETLTKKVKRGEVITYGEL 116
                                       6778899**********999999887776 PP

>> EPSP_synthase  EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   4.4e-05      0.26     105     157 ..      25      76 ..      13      81 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 4.4e-05
                                       ESSEEEEE-SBTTCGS--HHHHHHHHHTT-EEEEETTEEEEEESEETSS-BEE CS
                     EPSP_synthase 105 asgevvLtGdesirkRPidrlldaLrqlGaeieveegenkaplkvkglklkgv 157
                                       +++ ++++G++ +++R ++ l++ L++ G+++++ee + ++p+ v++  ++++
  gi|242399002|ref|YP_002994426.1|  25 QGITFSFDGEQFLQER-VNALVEHLTNRGVKVNLEERDSELPALVYKILIGEI 76 
                                       347899**********.*************************99998655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); 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: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1380.63
//
Query:       gi|242399003|ref|YP_002994427.1|  [L=343]
Description: O-linked glcnac transferase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-09   38.0  29.5       0.08   13.6   0.4    7.2  6  TPR_6          Tetratricopeptide repeat
      1e-08   34.6  48.9     0.0015   18.5   2.4    8.5  8  TPR_2          Tetratricopeptide repeat
    6.1e-08   32.2  16.0    9.2e-07   28.3  15.3    3.1  2  TPR_15         Tetratricopeptide repeat
    9.4e-07   28.6  43.9     0.0054   16.8   1.0    7.0  7  TPR_8          Tetratricopeptide repeat
      2e-05   24.2  35.5      0.037   13.8   0.6    7.0  8  TPR_1          Tetratricopeptide repeat
      9e-05   22.2  24.7      0.039   14.0   1.2    7.2  7  TPR_7          Tetratricopeptide repeat
    0.00016   21.2  29.1    0.00016   21.2  29.1    2.4  2  SNAP           Soluble NSF attachment protein, SNAP
    0.00031   21.3  20.5        3.2    8.5   0.7    5.9  6  TPR_16         Tetratricopeptide repeat
     0.0018   18.9  17.7        2.1    9.4   0.2    5.8  6  TPR_14         Tetratricopeptide repeat
     0.0031   17.8  23.3      0.075   13.3   1.5    4.9  6  TPR_12         Tetratricopeptide repeat
     0.0085   16.6  18.0       0.14   12.7   1.0    4.2  4  TPR_19         Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.014   15.6   2.0         10    6.3   0.4    4.4  4  TPR_9          Tetratricopeptide repeat
      0.041   13.8   8.2       0.11   12.4   1.5    3.8  3  TPR_10         Tetratricopeptide repeat
      0.043   13.7  14.8      0.044   13.6   2.3    3.6  3  Clathrin       Region in Clathrin and VPS
        5.5    7.7   5.5         20    5.9   0.7    3.4  2  DUF883         Bacterial protein of unknown function (DUF883)


Domain annotation for each model (and alignments):
>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   1.1     0.008       9.5      13      26 ..     128     153 ..     117     154 .. 0.63
   2 !   13.2   0.7   9.3e-05      0.11       6      29 ..     159     182 ..     158     186 .. 0.88
   3 !    7.7   0.2    0.0052       6.2      10      31 ..     195     217 ..     188     217 .. 0.83
   4 !   13.6   0.4   6.7e-05      0.08       7      30 ..     224     247 ..     223     250 .. 0.94
   5 !    9.2   0.5    0.0017         2      13      28 ..     255     283 ..     246     284 .. 0.69
   6 ?    3.5   0.3      0.11   1.3e+02       6      28 ..     299     324 ..     298     325 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.008
                                       H............HHHHHHHHHHHHH CS
                             TPR_6  13 l............gdtdkAlealerl 26 
                                       +            g+++kA e++e+l
  gi|242399003|ref|YP_002994427.1| 128 GkykaaarkyekkGNYSKAAEMYEKL 153
                                       34444444444448999999999987 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 9.3e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   6 lalsyrklgdtdkAlealerlike 29 
                                       +a++y+k+ +++kA e++e+l ++
  gi|242399003|ref|YP_002994427.1| 159 AAWAYEKAEKYEKAAEIYEQLYEK 182
                                       59*****88***********9776 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0052
                                       HHH.HHHHHHHHHHHHHHHHH-T CS
                             TPR_6  10 yrk.lgdtdkAlealerlikeYP 31 
                                       y k +g+ ++A +aler  +e P
  gi|242399003|ref|YP_002994427.1| 195 YWKkAGNMERAAKALERYANEEP 217
                                       555589************99877 PP

  == domain 4  score: 13.6 bits;  conditional E-value: 6.7e-05
                                       HHHHHHHHHHHHHHHHHHHHHHH- CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeY 30 
                                       a++y++lg+ +kA+ea+e+ ++ Y
  gi|242399003|ref|YP_002994427.1| 224 AKLYEELGNEEKAKEAWEKALEYY 247
                                       899***9**************999 PP

  == domain 5  score: 9.2 bits;  conditional E-value: 0.0017
                                       H.............HHHHHHHHHHHHHHH CS
                             TPR_6  13 l.............gdtdkAlealerlik 28 
                                       +             g+ + A+ea++++++
  gi|242399003|ref|YP_002994427.1| 255 GvfwedvgniakklGNEELAKEAYQKFLE 283
                                       45555555555555*************97 PP

  == domain 6  score: 3.5 bits;  conditional E-value: 0.11
                                       HHHHHHHHHHHH...HHHHHHHHHHH CS
                             TPR_6   6 lalsyrklgdtd...kAlealerlik 28 
                                       +a++y+ lg+++   +A++ +e+ ++
  gi|242399003|ref|YP_002994427.1| 299 IAEAYEYLGEKEkveEAKKKYEEYRQ 324
                                       899999985665556***99999876 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.5    0.0031       3.7       6      26 ..     119     139 ..     117     139 .. 0.90
   2 !    7.7   3.5    0.0036       4.3       6      26 ..     132     152 ..     130     153 .. 0.88
   3 !   12.5   2.1   0.00011      0.13       8      31 ..     160     183 ..     155     186 .. 0.89
   4 ?    1.4   0.1      0.37   4.4e+02      17      27 ..     189     199 ..     188     200 .. 0.89
   5 ?    1.9   0.7      0.26   3.1e+02      12      27 ..     197     212 ..     194     217 .. 0.80
   6 !   18.5   2.4   1.3e-06    0.0015       4      32 ..     220     248 ..     217     250 .. 0.90
   7 !   12.5   0.3    0.0001      0.12       4      30 ..     258     284 ..     256     287 .. 0.91
   8 ?    3.2   3.0     0.098   1.2e+02       3      19 ..     295     311 ..     293     324 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0031
                             TPR_2   6 nlGlayyklgdyeeAleafek 26 
                                       + +++++k+g+y+ A++ +ek
  gi|242399003|ref|YP_002994427.1| 119 RSAESLEKSGKYKAAARKYEK 139
                                       66899**************98 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0036
                             TPR_2   6 nlGlayyklgdyeeAleafek 26 
                                       + ++ y+k+g+y +A+e +ek
  gi|242399003|ref|YP_002994427.1| 132 AAARKYEKKGNYSKAAEMYEK 152
                                       56889***************9 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 0.00011
                             TPR_2   8 GlayyklgdyeeAleafekAleld 31 
                                       ++ay+k+ +ye+A+e +e+  e +
  gi|242399003|ref|YP_002994427.1| 160 AWAYEKAEKYEKAAEIYEQLYEKE 183
                                       99*****************99876 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 0.37
                             TPR_2  17 yeeAleafekA 27 
                                       ++eA+e+++kA
  gi|242399003|ref|YP_002994427.1| 189 LKEAHEYWKKA 199
                                       58*******99 PP

  == domain 5  score: 1.9 bits;  conditional E-value: 0.26
                             TPR_2  12 yklgdyeeAleafekA 27 
                                        k+g+ e+A++a+e+ 
  gi|242399003|ref|YP_002994427.1| 197 KKAGNMERAAKALERY 212
                                       5899*********986 PP

  == domain 6  score: 18.5 bits;  conditional E-value: 1.3e-06
                             TPR_2   4 lynlGlayyklgdyeeAleafekAleldP 32 
                                       +   +++y++lg+ e+A+ea+ekAle++ 
  gi|242399003|ref|YP_002994427.1| 220 WEDVAKLYEELGNEEKAKEAWEKALEYYK 248
                                       777899********************986 PP

  == domain 7  score: 12.5 bits;  conditional E-value: 0.0001
                             TPR_2   4 lynlGlayyklgdyeeAleafekAlel 30 
                                       +   G+++ klg+ e A+ea++k le+
  gi|242399003|ref|YP_002994427.1| 258 WEDVGNIAKKLGNEELAKEAYQKFLEY 284
                                       6778*******************9997 PP

  == domain 8  score: 3.2 bits;  conditional E-value: 0.098
                             TPR_2   3 alynlGlayyklgdyee 19 
                                       ++  +++ay++lg+ e+
  gi|242399003|ref|YP_002994427.1| 295 WWKHIAEAYEYLGEKEK 311
                                       78888999999988776 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3  15.3   7.7e-10   9.2e-07      87     231 ..     163     310 ..     121     311 .. 0.86
   2 ?    3.2   0.1     0.035        42     241     269 ..     286     314 ..     279     322 .. 0.52

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 7.7e-10
                            TPR_15  87 llydaepkeaarlaekgwrrfrsprlLssalellerakdydriaellksleeeeaaeqsaafllaraelyrqegqtd 163
                                       + + +++++aa++ e+ +++ +++++L++a e++++a++++r a+ l++      a++++ f+  +a+ly++ g+++
  gi|242399003|ref|YP_002994427.1| 163 YEKAEKYEKAAEIYEQLYEKEKDTYYLKEAHEYWKKAGNMERAAKALER-----YANEEPWFWEDVAKLYEELGNEE 234
                                       44667899****************************************9.....8999******************* PP

                            TPR_15 164 aAlrdyreAlalapdsselraallWlli.....DlgrraeLrellkawkara....esdasLwgplaaAlllLgrpk 231
                                       +A ++ ++Al++  + ++  ++  W  +      lg+++ ++e+ +++ ++     e+d+  w+  a A+ +Lg+++
  gi|242399003|ref|YP_002994427.1| 235 KAKEAWEKALEYYKG-EAQEEGVFWEDVgniakKLGNEELAKEAYQKFLEYClkeaEEDPMWWKHIAEAYEYLGEKE 310
                                       *************99.6668899997662222234555558888887776666666999999***********9987 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.035
                            TPR_15 241 akenrkdplwllaYADaleqagradeAwr 269
                                       +ke ++dp+w    A+a e  g+ ++ ++
  gi|242399003|ref|YP_002994427.1| 286 LKEAEEDPMWWKHIAEAYEYLGEKEKVEE 314
                                       34444555555555555555555554444 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1       2.3   2.8e+03       8      20 ..     121     133 ..     118     138 .. 0.78
   2 ?    5.7   2.8     0.016        20      11      26 ..     137     152 ..     130     153 .. 0.92
   3 !    8.0   2.8    0.0032       3.8       8      28 ..     160     180 ..     155     184 .. 0.90
   4 ?    6.0   0.8     0.013        16       3      27 ..     187     212 ..     185     217 .. 0.88
   5 !   16.8   1.0   4.5e-06    0.0054       6      31 ..     222     247 ..     219     249 .. 0.89
   6 !   15.6   0.4   1.1e-05     0.014       6      30 ..     260     284 ..     257     287 .. 0.89
   7 ?    1.6   1.0      0.34   4.1e+02       7      23 ..     299     315 ..     296     325 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2.3
                                       HHHHHHTT-HHHH CS
                             TPR_8   8 gsiylklgdyeeA 20 
                                       +  ++k g+y++A
  gi|242399003|ref|YP_002994427.1| 121 AESLEKSGKYKAA 133
                                       6678899999998 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.016
                                       HHHTT-HHHHHHHHHH CS
                             TPR_8  11 ylklgdyeeAkeyyek 26 
                                       y+k+g+y +A e yek
  gi|242399003|ref|YP_002994427.1| 137 YEKKGNYSKAAEMYEK 152
                                       99*************9 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0032
                                       HHHHHHTT-HHHHHHHHHHHH CS
                             TPR_8   8 gsiylklgdyeeAkeyyekal 28 
                                       +++y+k ++ye+A e ye+  
  gi|242399003|ref|YP_002994427.1| 160 AWAYEKAEKYEKAAEIYEQLY 180
                                       79****************976 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.013
                                       HHHHHHHHH.HHTT-HHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiy.lklgdyeeAkeyyeka 27 
                                       +y++ ++ y +k g++e A +++e++
  gi|242399003|ref|YP_002994427.1| 187 YYLKEAHEYwKKAGNMERAAKALERY 212
                                       6889999**999************97 PP

  == domain 5  score: 16.8 bits;  conditional E-value: 4.5e-06
                                       HHHHHHHHTT-HHHHHHHHHHHHHHH CS
                             TPR_8   6 nlgsiylklgdyeeAkeyyekaleld 31 
                                         +++y++lg+ e+Ake+ ekale+ 
  gi|242399003|ref|YP_002994427.1| 222 DVAKLYEELGNEEKAKEAWEKALEYY 247
                                       5699*******************985 PP

  == domain 6  score: 15.6 bits;  conditional E-value: 1.1e-05
                                       HHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8   6 nlgsiylklgdyeeAkeyyekalel 30 
                                         g+i +klg+ e Ake+y+k le+
  gi|242399003|ref|YP_002994427.1| 260 DVGNIAKKLGNEELAKEAYQKFLEY 284
                                       679******************9986 PP

  == domain 7  score: 1.6 bits;  conditional E-value: 0.34
                                       HHHHHHHTT-HHHHHHH CS
                             TPR_8   7 lgsiylklgdyeeAkey 23 
                                       ++ +y+ lg++e+ +e+
  gi|242399003|ref|YP_002994427.1| 299 IAEAYEYLGEKEKVEEA 315
                                       78888888888876555 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.2      0.25   2.9e+02       9      26 ..     122     139 ..     118     139 .. 0.84
   2 !    7.3   3.0    0.0036       4.3      11      26 ..     137     152 ..     130     152 .. 0.93
   3 !    6.7   2.3    0.0055       6.5       8      26 ..     160     178 ..     160     179 .. 0.92
   4 ?   -2.0   0.1       3.1   3.7e+03      18      27 ..     190     199 ..     189     199 .. 0.87
   5 ?   -0.5   0.1       1.1   1.3e+03      13      26 ..     198     211 ..     194     212 .. 0.84
   6 !   13.8   0.6   3.1e-05     0.037       8      30 ..     224     246 ..     218     249 .. 0.90
   7 !    9.1   0.5     0.001       1.2       8      26 ..     262     280 ..     258     285 .. 0.92
   8 ?    5.3   0.0     0.016        19       4      22 ..     296     314 ..     293     315 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.25
                                       HHHHHTT-HHHHHHHHHH CS
                             TPR_1   9 nayfklgkydeAleyyek 26 
                                         + k gky+ A   yek
  gi|242399003|ref|YP_002994427.1| 122 ESLEKSGKYKAAARKYEK 139
                                       678999******988886 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0036
                                       HHHTT-HHHHHHHHHH CS
                             TPR_1  11 yfklgkydeAleyyek 26 
                                       y k+g+y +A e yek
  gi|242399003|ref|YP_002994427.1| 137 YEKKGNYSKAAEMYEK 152
                                       99************98 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0055
                                       HHHHHHTT-HHHHHHHHHH CS
                             TPR_1   8 GnayfklgkydeAleyyek 26 
                                       + ay k +ky++A e ye+
  gi|242399003|ref|YP_002994427.1| 160 AWAYEKAEKYEKAAEIYEQ 178
                                       679************9986 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 3.1
                                       HHHHHHHHHH CS
                             TPR_1  18 deAleyyekA 27 
                                       +eA ey +kA
  gi|242399003|ref|YP_002994427.1| 190 KEAHEYWKKA 199
                                       79999*9998 PP

  == domain 5  score: -0.5 bits;  conditional E-value: 1.1
                                       HTT-HHHHHHHHHH CS
                             TPR_1  13 klgkydeAleyyek 26 
                                       k g+ + A ++ e+
  gi|242399003|ref|YP_002994427.1| 198 KAGNMERAAKALER 211
                                       78999999999886 PP

  == domain 6  score: 13.8 bits;  conditional E-value: 3.1e-05
                                       HHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   8 GnayfklgkydeAleyyekALel 30 
                                       + +y +lg+ ++A e+ ekALe 
  gi|242399003|ref|YP_002994427.1| 224 AKLYEELGNEEKAKEAWEKALEY 246
                                       679******************95 PP

  == domain 7  score: 9.1 bits;  conditional E-value: 0.001
                                       HHHHHHTT-HHHHHHHHHH CS
                             TPR_1   8 GnayfklgkydeAleyyek 26 
                                       Gn+  klg+ + A e+y+k
  gi|242399003|ref|YP_002994427.1| 262 GNIAKKLGNEELAKEAYQK 280
                                       9*****************9 PP

  == domain 8  score: 5.3 bits;  conditional E-value: 0.016
                                       HHHHHHHHHHTT-HHHHHH CS
                             TPR_1   4 lynlGnayfklgkydeAle 22 
                                       ++ ++ ay +lg+ ++ +e
  gi|242399003|ref|YP_002994427.1| 296 WKHIAEAYEYLGEKEKVEE 314
                                       99***********999776 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.1     0.019        23       6      24 ..     121     139 ..     118     140 .. 0.87
   2 !   11.2   0.6   0.00025       0.3       6      24 ..     134     152 ..     130     159 .. 0.83
   3 !   14.0   1.2   3.2e-05     0.039       6      31 ..     160     185 ..     155     187 .. 0.85
   4 ?    2.3   0.1      0.18   2.1e+02       9      24 ..     196     211 ..     191     217 .. 0.87
   5 ?    3.2   0.9      0.09   1.1e+02      15      23 ..     240     248 ..     220     254 .. 0.78
   6 ?   -1.9   0.0       3.8   4.6e+03       7      27 ..     263     283 ..     260     293 .. 0.58
   7 ?    1.3   0.0      0.38   4.5e+02       4      19 ..     298     313 ..     296     315 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.019
                             TPR_7   6 arlysrlGdyeeAielyeq 24 
                                       a+  ++ G+y+ A++ ye+
  gi|242399003|ref|YP_002994427.1| 121 AESLEKSGKYKAAARKYEK 139
                                       5667899***********8 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00025
                             TPR_7   6 arlysrlGdyeeAielyeq 24 
                                       ar y++ G+y++A+e ye+
  gi|242399003|ref|YP_002994427.1| 134 ARKYEKKGNYSKAAEMYEK 152
                                       55599*************9 PP

  == domain 3  score: 14.0 bits;  conditional E-value: 3.2e-05
                             TPR_7   6 arlysrlGdyeeAielyeqsLaltkd 31 
                                       a +y++  +ye+A+e+yeq+ + +kd
  gi|242399003|ref|YP_002994427.1| 160 AWAYEKAEKYEKAAEIYEQLYEKEKD 185
                                       899****************6566665 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.18
                             TPR_7   9 ysrlGdyeeAielyeq 24 
                                       + + G++e+A++ +e+
  gi|242399003|ref|YP_002994427.1| 196 WKKAGNMERAAKALER 211
                                       6679********9998 PP

  == domain 5  score: 3.2 bits;  conditional E-value: 0.09
                             TPR_7  15 yeeAielye 23 
                                       +e+A+e+y+
  gi|242399003|ref|YP_002994427.1| 240 WEKALEYYK 248
                                       788888887 PP

  == domain 6  score: -1.9 bits;  conditional E-value: 3.8
                             TPR_7   7 rlysrlGdyeeAielyeqsLa 27 
                                       ++  +lG+ e A e y++ L+
  gi|242399003|ref|YP_002994427.1| 263 NIAKKLGNEELAKEAYQKFLE 283
                                       555666776777777777443 PP

  == domain 7  score: 1.3 bits;  conditional E-value: 0.38
                             TPR_7   4 nLarlysrlGdyeeAi 19 
                                        +a++y+ lG+ e+ +
  gi|242399003|ref|YP_002994427.1| 298 HIAEAYEYLGEKEKVE 313
                                       689********99876 PP

>> SNAP  Soluble NSF attachment protein, SNAP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2  29.1   1.4e-07   0.00016      35     186 ..     127     286 ..     111     289 .. 0.83
   2 ?    1.4   4.4      0.14   1.7e+02     119     189 ..     260     330 ..     255     335 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.4e-07
                                       HHHHHHHHHHHHHTT-THHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHT.-HHHHHHHHHHHHHHHHHTT-H CS
                              SNAP  35 adlyeqAAnayklakkweeAgeaflkaAecqeklkekdeaanayveAakcykkv.speeAvealekAieiytekgrf 110
                                       +  y+ AA++y  + ++++A+e+++k+  +++ +  + e a+ y +Aa++y++  ++e+    l++A e++ ++g++
  gi|242399003|ref|YP_002994427.1| 127 SGKYKAAARKYEKKGNYSKAAEMYEKLGWMES-AAWAYEKAEKYEKAAEIYEQLyEKEKDTYYLKEAHEYWKKAGNM 202
                                       457*************************9988.7889999*************9778899999************** PP

                                       HHHHHHH...........HHHHHHHHHTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT-HHHHHH CS
                              SNAP 111 rraAklk...........keiaelyekelgdlekAieaYekAaelyeqeeakalankcllkvAelsaelekyekAie 176
                                       +raAk             +++a+lye+  g+ ekA ea+ekA e+y++e ++     ++++v +++ +l++ e A e
  gi|242399003|ref|YP_002994427.1| 203 ERAAKALeryaneepwfwEDVAKLYEEL-GNEEKAKEAWEKALEYYKGEAQEE--GVFWEDVGNIAKKLGNEELAKE 276
                                       ****976222222222225788999955.*******************98765..5689999999999999999999 PP

                                       HHHHHHHTTS CS
                              SNAP 177 iyekvakksl 186
                                       +y+k  + +l
  gi|242399003|ref|YP_002994427.1| 277 AYQKFLEYCL 286
                                       9998777666 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.14
                                       HHHHHHHHTT--HHHHHHHHHHHHHHHHHTT.-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTTSS-T CS
                              SNAP 119 eiaelyekelgdlekAieaYekAaelyeqee.akalankcllkvAelsaelekyekAieiyekvakkslenn 189
                                       +++++ +k  g+ e A eaY+k  e+  +e        k   ++ e+  e+ek e+A + ye+  +k +++n
  gi|242399003|ref|YP_002994427.1| 260 DVGNIAKKL-GNEELAKEAYQKFLEYCLKEAeEDPMWWKHIAEAYEYLGEKEKVEEAKKKYEEYRQKIMKSN 330
                                       567776655.99999**********9888873455556666677799999*************999999887 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1      0.17     2e+02       4      21 ..     121     138 ..     118     139 .. 0.75
   2 ?    4.5   0.2     0.046        55       2      22 ..     132     152 ..     131     153 .. 0.89
   3 !    8.1   5.6    0.0035       4.2       3      55 ..     159     207 ..     158     213 .. 0.68
   4 !    8.5   0.7    0.0027       3.2       4      58 ..     224     279 ..     222     283 .. 0.81
   5 ?    2.9   0.1      0.15   1.8e+02       4      26 ..     262     284 ..     259     311 .. 0.79
   6 ?   -1.8   0.0       4.4   5.3e+03       9      23 ..     308     322 ..     299     324 .. 0.63

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.17
                            TPR_16   4 araalragdyddAaaale 21 
                                       a ++ ++g+y +Aa+ +e
  gi|242399003|ref|YP_002994427.1| 121 AESLEKSGKYKAAARKYE 138
                                       667788888888888876 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.046
                            TPR_16   2 alaraalragdyddAaaalea 22 
                                       a+ar + + g+y +Aa+++e 
  gi|242399003|ref|YP_002994427.1| 132 AAARKYEKKGNYSKAAEMYEK 152
                                       6899999************85 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0035
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaal.rqgrlaeAaa 55 
                                       +a a+ +a +y++Aa+ +e++ ++ +++      +l  +  ++ ++g++++Aa 
  gi|242399003|ref|YP_002994427.1| 159 AAWAYEKAEKYEKAAEIYEQLYEKEKDTY-----YLKEAHEYWkKAGNMERAAK 207
                                       699**********************6654.....33333333324455555554 PP

  == domain 4  score: 8.5 bits;  conditional E-value: 0.0027
                            TPR_16   4 araalragdyddAaaaleaalkrdpssPd.aaeAllllgdaalrqgrlaeAaalyr 58 
                                       a+++ ++g+ ++A +a+e al++++++ +    ++   g++a ++g+ ++A ++y+
  gi|242399003|ref|YP_002994427.1| 224 AKLYEELGNEEKAKEAWEKALEYYKGEAQeEGVFWEDVGNIAKKLGNEELAKEAYQ 279
                                       899*********************98877777777777777777777777766665 PP

  == domain 5  score: 2.9 bits;  conditional E-value: 0.15
                            TPR_16   4 araalragdyddAaaaleaalkr 26 
                                       +++a ++g+ + A +a++ +l++
  gi|242399003|ref|YP_002994427.1| 262 GNIAKKLGNEELAKEAYQKFLEY 284
                                       7889999999********99976 PP

  == domain 6  score: -1.8 bits;  conditional E-value: 4.4
                            TPR_16   9 ragdyddAaaaleaa 23 
                                       +  + ++A + +e++
  gi|242399003|ref|YP_002994427.1| 308 EKEKVEEAKKKYEEY 322
                                       444588888888776 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1     0.076        91       5      26 ..     131     152 ..     120     153 .. 0.88
   2 !    7.1   0.6    0.0097        12       7      33 ..     159     185 ..     154     196 .. 0.87
   3 ?    5.9   0.3     0.023        27      10      35 ..     194     220 ..     185     221 .. 0.75
   4 !    9.4   0.2    0.0017       2.1       1      29 [.     217     245 ..     217     258 .. 0.86
   5 ?    2.7   0.1      0.24   2.9e+02       8      43 ..     262     301 ..     256     302 .. 0.76
   6 ?    0.5   0.0       1.2   1.5e+03       4      26 ..     296     321 ..     293     325 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.076
                            TPR_14   5 lalaeallalGdpdeAiallrr 26 
                                       +a+a+ ++  G++ +A++++++
  gi|242399003|ref|YP_002994427.1| 131 KAAARKYEKKGNYSKAAEMYEK 152
                                       6778889999*********997 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0097
                            TPR_14   7 laeallalGdpdeAiallrralalaPd 33 
                                       +a+a++ ++++++A+++++++ ++  d
  gi|242399003|ref|YP_002994427.1| 159 AAWAYEKAEKYEKAAEIYEQLYEKEKD 185
                                       589*****************9998776 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.023
                            TPR_14  10 all.alGdpdeAiallrralalaPdda 35 
                                        ++  +G+ ++A+++l+r+    P+++
  gi|242399003|ref|YP_002994427.1| 194 EYWkKAGNMERAAKALERYANEEPWFW 220
                                       454269************987777766 PP

  == domain 4  score: 9.4 bits;  conditional E-value: 0.0017
                            TPR_14   1 peallalaeallalGdpdeAiallrrala 29 
                                       p+ + + a+++++lG+ ++A ++ ++al+
  gi|242399003|ref|YP_002994427.1| 217 PWFWEDVAKLYEELGNEEKAKEAWEKALE 245
                                       6789999********************98 PP

  == domain 5  score: 2.7 bits;  conditional E-value: 0.24
                            TPR_14   8 aeallalGdpdeAiallrrala....laPddaeawlllaq 43 
                                       + +   lG+ + A +++++ l+     a +d+ +w + a+
  gi|242399003|ref|YP_002994427.1| 262 GNIAKKLGNEELAKEAYQKFLEyclkEAEEDPMWWKHIAE 301
                                       6677788999999999999666555488999999998886 PP

  == domain 6  score: 0.5 bits;  conditional E-value: 1.2
                            TPR_14   4 llalaeallalGd...pdeAiallrr 26 
                                       ++ +aea++ lG+    +eA + +++
  gi|242399003|ref|YP_002994427.1| 296 WKHIAEAYEYLGEkekVEEAKKKYEE 321
                                       77889999999984445666666655 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.2    0.0099        12      48      70 ..     130     152 ..     114     153 .. 0.89
   2 !   10.4   1.2   0.00053      0.63      49      73 ..     157     181 ..     155     185 .. 0.90
   3 ?    6.0   4.2     0.012        14      25      70 ..     168     211 ..     163     214 .. 0.84
   4 !    7.4   2.1    0.0044       5.2      33      76 ..     205     248 ..     189     249 .. 0.71
   5 !   13.3   1.5   6.3e-05     0.075       8      75 ..     222     285 ..     215     287 .. 0.88
   6 ?    5.4   0.6     0.019        22       8      73 ..     260     321 ..     253     325 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0099
                            TPR_12  48 lrnLgrlyralgryeeAlellee 70 
                                       + + +r y++ g+y +A e++e+
  gi|242399003|ref|YP_002994427.1| 130 YKAAARKYEKKGNYSKAAEMYEK 152
                                       56778889999**********97 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00053
                            TPR_12  49 rnLgrlyralgryeeAlelleeala 73 
                                          +++y+++++ye+A e++e+ ++
  gi|242399003|ref|YP_002994427.1| 157 ESAAWAYEKAEKYEKAAEIYEQLYE 181
                                       5689*****************9876 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.012
                            TPR_12  25 llekaleiarrllGpdhpltattlrnLgrlyr.algryeeAlellee 70 
                                        +eka ei+++l+++++    t++   +  y+ ++g+ e A ++le+
  gi|242399003|ref|YP_002994427.1| 168 KYEKAAEIYEQLYEKEK---DTYYLKEAHEYWkKAGNMERAAKALER 211
                                       489999******98875...679999999998688999999999998 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.0044
                            TPR_12  33 arrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       a ++l+ +  ++ +   + + ly++lg+ e+A e+ e+al+ ++
  gi|242399003|ref|YP_002994427.1| 205 AAKALERYANEEPWFWEDVAKLYEELGNEEKAKEAWEKALEYYK 248
                                       44555555555666677778888888888888888888888775 PP

  == domain 5  score: 13.3 bits;  conditional E-value: 6.3e-05
                            TPR_12   8 nlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                        +a ++ +lg+ ++A e  ekale +    G +  ++     + g +  +lg+ e A e++++ l+ +
  gi|242399003|ref|YP_002994427.1| 222 DVAKLYEELGNEEKAKEAWEKALEYY---KG-EAQEEGVFWEDVGNIAKKLGNEELAKEAYQKFLEYC 285
                                       57999*********************...34.455899************************988765 PP

  == domain 6  score: 5.4 bits;  conditional E-value: 0.019
                            TPR_12   8 nlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeala 73 
                                        ++++  +lg+ + A e ++k le +     ++ ++       ++++y++lg+ e+ +e+ ++  +
  gi|242399003|ref|YP_002994427.1| 260 DVGNIAKKLGNEELAKEAYQKFLEYCL----KEAEEDPMWWKHIAEAYEYLGEKEKVEEAKKKYEE 321
                                       57999999*************999994....44455677999999999999998888887776665 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   3.7    0.0071       8.5       4      61 ..     127     188 ..     124     193 .. 0.73
   2 !    8.4   3.7    0.0026       3.1       4      56 ..     166     217 ..     163     217 .. 0.84
   3 !   12.7   1.0   0.00012      0.14       4      57 ..     199     249 ..     197     253 .. 0.88
   4 ?    4.1   0.4     0.058        69      10      47 ..     277     315 ..     270     325 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0071
                            TPR_19   4 egdyaeAlalleq..alqedpknaearllL...AeallalgqldeAealLdalpeedpddary 61 
                                       +g+y +A++ +e+   +++++++ e + ++   A a+ ++  +++A ++ ++l e+++d  +y
  gi|242399003|ref|YP_002994427.1| 127 SGKYKAAARKYEKkgNYSKAAEMYEKLGWMesaAWAYEKAEKYEKAAEIYEQLYEKEKD-TYY 188
                                       68888888888885423444445555555556699999**********99999999999.555 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0026
                            TPR_19   4 egdyaeAlalleqalqedpknaearllLAeallal.gqldeAealLdalpeedp 56 
                                       +++y+ A++++eq+++++ +  +++   A  +++  g+ + A ++L+++ +e+p
  gi|242399003|ref|YP_002994427.1| 166 AEKYEKAAEIYEQLYEKEKDTYYLKE--AHEYWKKaGNMERAAKALERYANEEP 217
                                       789***********999888888888..55555555************999986 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 0.00012
                            TPR_19   4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                       +g+ ++A+++le+    +++ ++ + + A+++ +lg+ ++A+++ ++++e ++ 
  gi|242399003|ref|YP_002994427.1| 199 AGNMERAAKALERY---ANEEPWFWEDVAKLYEELGNEEKAKEAWEKALEYYKG 249
                                       78999999999997...778999999*****************99999988776 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.058
                            TPR_19  10 A.lalleqalqedpknaearllLAeallalgqldeAeal 47 
                                       A +++le+ l+e+ +++  +   Aea+  lg+ ++ e++
  gi|242399003|ref|YP_002994427.1| 277 AyQKFLEYCLKEAEEDPMWWKHIAEAYEYLGEKEKVEEA 315
                                       55799**************************99987775 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       4.7   5.6e+03      39      53 ..     124     138 ..     116     140 .. 0.79
   2 ?    6.3   0.4    0.0088        10       7      60 ..     165     217 ..     159     218 .. 0.66
   3 ?    2.8   0.0      0.11   1.4e+02      32      57 ..     220     245 ..     215     254 .. 0.83
   4 ?    1.8   0.0      0.23   2.8e+02      32      59 ..     258     285 ..     257     307 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 4.7
                             TPR_9  39 laqlGclsaAladLe 53 
                                       l+++G ++aA++  e
  gi|242399003|ref|YP_002994427.1| 124 LEKSGKYKAAARKYE 138
                                       678899999998766 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0088
                             TPR_9   7 reedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalap 60 
                                        +e++e+a +++e l   + +d + + +      + G+++ A+++Le+y+  +p
  gi|242399003|ref|YP_002994427.1| 165 KAEKYEKAAEIYEQLYE-KEKDTYYLKEAHEYWKKAGNMERAAKALERYANEEP 217
                                       55666666666665444.3333444555556666789************98776 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.11
                             TPR_9  32 rrdRGlllaqlGclsaAladLeayla 57 
                                       + d + l+++lG+ ++A ++ e +l+
  gi|242399003|ref|YP_002994427.1| 220 WEDVAKLYEELGNEEKAKEAWEKALE 245
                                       789999******99999998877775 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.23
                             TPR_9  32 rrdRGlllaqlGclsaAladLeaylala 59 
                                       + d G +  +lG+ + A ++ + +l+ +
  gi|242399003|ref|YP_002994427.1| 258 WEDVGNIAKKLGNEELAKEAYQKFLEYC 285
                                       6789999999999999****99999765 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0       0.7   8.4e+02      15      27 ..     140     152 ..     137     152 .. 0.85
   2 ?   12.4   1.5   9.3e-05      0.11       4      37 ..     149     181 ..     146     193 .. 0.90
   3 ?    2.8   0.3     0.097   1.2e+02       9      33 ..     224     248 ..     222     249 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.7
                            TPR_10  15 rgrydeAeallee 27 
                                        g+y +A +++e+
  gi|242399003|ref|YP_002994427.1| 140 KGNYSKAAEMYEK 152
                                       699*******996 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 9.3e-05
                            TPR_10   4 slnNLanalrqrgrydeAealleealairrrllG 37 
                                        +  L+ + ++   y++Ae++ e+a +i+++l++
  gi|242399003|ref|YP_002994427.1| 149 MYEKLGWMESAAWAYEKAEKY-EKAAEIYEQLYE 181
                                       5778999**************.**********97 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.097
                            TPR_10   9 analrqrgrydeAealleealairr 33 
                                       a ++ ++g+ ++A +  e+al+ ++
  gi|242399003|ref|YP_002994427.1| 224 AKLYEELGNEEKAKEAWEKALEYYK 248
                                       5678889999999999999999886 PP

>> Clathrin  Region in Clathrin and VPS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   2.3   3.7e-05     0.044      71     140 ..     115     184 ..     106     187 .. 0.88
   2 ?    1.4   6.5      0.23   2.7e+02      81     136 ..     164     213 ..     156     254 .. 0.58
   3 ?    4.6   0.7     0.023        27      76     138 ..     223     284 ..     220     289 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.7e-05
                                       S-TTHHHHHHHT-SSHHHHHHHHHTTXTHSSHSSXSSSSHCSCHHHHTTTTTXXSHHHHHHHHHHHSSXS CS
                          Clathrin  71 ydlekvaklcekadlyeeavilykkinefkkaisllkklkdfddaieyaakvsnpelwekllealldkkp 140
                                       +d+ + a+ +ek ++y+ a   y k ++++ka+++++kl+ ++ a+ +++k+++ e ++++ e l +k++
  gi|242399003|ref|YP_002994427.1| 115 MDRFRSAESLEKSGKYKAAARKYEKKGNYSKAAEMYEKLGWMESAAWAYEKAEKYEKAAEIYEQLYEKEK 184
                                       5777778999************************************999999999999999988888876 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.23
                                       HT-SSHHHHHHHHHTTXTHSSHSSXSSSSHCSCHHHHTTTTTXXSHHHHHHHHHHH CS
                          Clathrin  81 ekadlyeeavilykkinefkkaisllkklkdfddaieyaakvsnpelweklleall 136
                                       eka++ye a ++y  + e +k      +   +++a+ey +k+ n e ++k+le + 
  gi|242399003|ref|YP_002994427.1| 164 EKAEKYEKAAEIYEQLYEKEK------DTYYLKEAHEYWKKAGNMERAAKALERYA 213
                                       444444444444443222222......11123455566666666666666655444 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.023
                                       HHHHHHT-SSHHHHHHHHHTTXTHSSHSSX.SSSSHCSCHHH.HTTTTTXXSHHHHHHHHHHHSS CS
                          Clathrin  76 vaklcekadlyeeavilykkinefkkaisl.lkklkdfddai.eyaakvsnpelwekllealldk 138
                                       vakl e+ +  e a++ + k  e+ k     +++++ f +++ ++a+k+ n+el++++ + +l++
  gi|242399003|ref|YP_002994427.1| 223 VAKLYEELGNEEKAKEAWEKALEYYK---GeAQEEGVFWEDVgNIAKKLGNEELAKEAYQKFLEY 284
                                       66666666666666666666555555...336666777777889*******99999999888876 PP

>> DUF883  Bacterial protein of unknown function (DUF883)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.7     0.016        20      50      74 ..     194     218 ..     159     221 .. 0.67
   2 ?    2.0   0.1      0.27   3.2e+02      19      43 ..     309     333 ..     297     341 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.016
                            DUF883  50 aeeavaerakeaaeaaddyVrenPw 74 
                                        + + a ++++aa+a ++y+ e+Pw
  gi|242399003|ref|YP_002994427.1| 194 EYWKKAGNMERAAKALERYANEEPW 218
                                       3445677899*************** PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.27
                            DUF883  19 keaadeageeaeelRerleerlera 43 
                                       ke+ +ea++++ee R++++++ e++
  gi|242399003|ref|YP_002994427.1| 309 KEKVEEAKKKYEEYRQKIMKSNEET 333
                                       4566889999999999999887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2074  (0.115679); expected 358.6 (0.02)
Passed bias filter:                      582  (0.0324614); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 2108.24
//
Query:       gi|242399004|ref|YP_002994428.1|  [L=113]
Description: Nascent polypeptide-associated complex protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.7e-14   52.9   4.5    4.7e-14   52.1   4.5    1.4  1  NAC            NAC domain
     0.0032   17.3   0.0     0.0047   16.7   0.0    1.3  1  UBA_4          UBA-like domain
  ------ inclusion threshold ------
      0.011   15.4   0.2      0.037   13.7   0.0    2.0  3  TAP_C          TAP C-terminal domain
      0.013   15.5   2.0        2.2    8.3   0.6    2.2  2  DUF2089        Protein of unknown function (DUF2089)
      0.021   14.9   0.7      0.037   14.0   0.3    1.7  1  HOIP-UBA       HOIP UBA domain pair
      0.022   14.4   0.0       0.41   10.4   0.0    2.4  2  CUE            CUE domain
      0.044   13.9   0.2       0.07   13.3   0.2    1.5  1  RTC4           RTC4-like domain
       0.15   12.2   1.5         12    6.2   0.4    2.4  2  DUF3389        Protein of unknown function (DUF3389)
       0.18   11.6   2.4       0.72    9.7   2.4    2.0  1  PhageMin_Tail  Phage-related minor tail protein
       0.22   11.9   0.1       0.66   10.4   0.1    1.8  2  PBD            P21-Rho-binding domain


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 !   52.1   4.5   2.6e-17   4.7e-14       1      56 [.       9      67 ..       9      68 .. 0.97

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 2.6e-17
                               NAC  1 ekKlrkalkklgl..keipgieeVtirksdgkvlvfdnPkVq..kspgsntyvvfGeaee 56
                                      +k+++k +k+lg+  +e++g++eV+i+ ++ k+++++++ V+  +++g ++y+++G+ e+
  gi|242399004|ref|YP_002994428.1|  9 PKQMQKLMKQLGIkmEELEGVKEVVIKLEN-KEIIIKDAAVTvvTAMGEKSYQIVGKEEV 67
                                      79****************************.*************************9875 PP

>> UBA_4  UBA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   2.6e-06    0.0047       2      33 ..      76     107 ..      75     108 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.6e-06
                             UBA_4   2 eliaqFqaiTGadeekArqlLeannWdLerAi 33 
                                       e i   ++ TG+d e+A++ Le + +dL  Ai
  gi|242399004|ref|YP_002994428.1|  76 EDIKLVMEQTGVDYETAKKALEETKGDLAEAI 107
                                       566667888********************998 PP

>> TAP_C  TAP C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       1.4   2.6e+03      12      22 ..       7      17 ..       5      24 .. 0.52
   2 ?   -2.9   0.0       3.1   5.5e+03      39      47 ..      68      76 ..      65      76 .. 0.70
   3 ?   13.7   0.0     2e-05     0.037       6      38 ..      81     113 .]      78     113 .] 0.91

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.4
                                      B-HHHHHHHHS CS
                             TAP_C 12 MnlewsqkcLe 22
                                      Mn++  qk+ +
  gi|242399004|ref|YP_002994428.1|  7 MNPKQMQKLMK 17
                                      55555444433 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.1
                                      G..GGS-GG CS
                             TAP_C 39 kakgkIPpe 47
                                      ++  +IP+e
  gi|242399004|ref|YP_002994428.1| 68 REVLNIPEE 76
                                      556789998 PP

  == domain 3  score: 13.7 bits;  conditional E-value: 2e-05
                                       HHHHH-B-HHHHHHHHSSTTT-HHHHHHHHHHH CS
                             TAP_C   6 fstqtgMnlewsqkcLeqnnWdyerAlqvFeel 38 
                                       +++qtg  +e ++k Le+++ d+  A+   +e+
  gi|242399004|ref|YP_002994428.1|  81 VMEQTGVDYETAKKALEETKGDLAEAIVKLQES 113
                                       799************************998875 PP

>> DUF2089  Protein of unknown function (DUF2089)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.6    0.0012       2.2      68     110 ..      10      47 ..       9      51 .. 0.87
   2 ?    6.8   0.0    0.0036       6.5      51      77 ..      77     103 ..      53     112 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0012
                           DUF2089  68 nrldeileaLgyeeeeeeeeeeeerkeileklekgeisveeAl 110
                                       +++++++++Lg+++ee      e  ke++ kle++ei +++A+
  gi|242399004|ref|YP_002994428.1|  10 KQMQKLMKQLGIKMEEL-----EGVKEVVIKLENKEIIIKDAA 47 
                                       5799*********9966.....4689***********999986 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0036
                           DUF2089  51 nlkevekelgisYpTvrnrldeileaL 77 
                                        +k v ++ g+ Y T+++ l+e   +L
  gi|242399004|ref|YP_002994428.1|  77 DIKLVMEQTGVDYETAKKALEETKGDL 103
                                       5889999*************9987666 PP

>> HOIP-UBA  HOIP UBA domain pair
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.3   2.1e-05     0.037      93     138 ..      67     112 ..      40     113 .] 0.90

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.1e-05
                          HOIP-UBA  93 vkqclreRrkKvkelaslgffdreevveaLrqsgGdvegAlveLqr 138
                                       v+++l+  ++ +k ++++  +d e + +aL++++Gd+ +A+v+Lq 
  gi|242399004|ref|YP_002994428.1|  67 VREVLNIPEEDIKLVMEQTGVDYETAKKALEETKGDLAEAIVKLQE 112
                                       66777777788899999999************************96 PP

>> CUE  CUE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.12   2.1e+02      14      27 ..      72      85 ..      72      87 .. 0.84
   2 ?   10.4   0.0   0.00023      0.41      15      38 ..      87     110 ..      86     112 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.12
                                      TS-HHHHHHHHHHC CS
                               CUE 14 dldeevIravLras 27
                                      +++ee+I+ v +++
  gi|242399004|ref|YP_002994428.1| 72 NIPEEDIKLVMEQT 85
                                      689*******9765 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00023
                                       S-HHHHHHHHHHCTTTHHHHHHHH CS
                               CUE  15 ldeevIravLrasngnvEatinaL 38 
                                       +d e+ +++L++++g++  +i +L
  gi|242399004|ref|YP_002994428.1|  87 VDYETAKKALEETKGDLAEAIVKL 110
                                       799******************887 PP

>> RTC4  RTC4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2   3.9e-05      0.07      82     113 ..      68     100 ..      29     102 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.9e-05
                              RTC4  82 qaVL.vPEvavrLimeDmkvseeeAreileesa 113
                                       ++VL +PE  ++L+me+ +v+ e+A++ lee+ 
  gi|242399004|ref|YP_002994428.1|  68 REVLnIPEEDIKLVMEQTGVDYETAKKALEETK 100
                                       566668*************************95 PP

>> DUF3389  Protein of unknown function (DUF3389)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.017        30      60      74 ..       8      22 ..       4      23 .. 0.89
   2 ?    6.2   0.4    0.0065        12      15      73 ..      30      87 ..      27      89 .. 0.69

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.017
                           DUF3389 60 neeQLeelaeelGid 74
                                      n +Q+++l ++lGi+
  gi|242399004|ref|YP_002994428.1|  8 NPKQMQKLMKQLGIK 22
                                      789**********97 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0065
                           DUF3389 15 heivvrlegeakvtLqAqvddisllgganvivadggevkWslkLDneeQLeelaeelGi 73
                                      +e+v++le+++ +   A+v  ++ +g+    ++   ev+  l++  ee ++ + e++G+
  gi|242399004|ref|YP_002994428.1| 30 KEVVIKLENKEIIIKDAAVTVVTAMGEKSYQIVGKEEVREVLNIP-EEDIKLVMEQTGV 87
                                      79********98888999999999887666555555666555553.3345555555555 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 ?    9.7   2.4    0.0004      0.72     145     184 ..       7     110 ..       1     113 [] 0.69

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0004
                     PhageMin_Tail 145 l.tkeaaealkklGist............................................................ 160
                                       + +k++++++k+lGi++                                                            
  gi|242399004|ref|YP_002994428.1|   7 MnPKQMQKLMKQLGIKMeelegvkevviklenkeiiikdaavtvvtamgeksyqivgkeevrevlnipeediklvme 83 
                                       25689999999999999777777777777777777777777777777777777777777777777777777777766 PP

                     PhageMin_Tail 161 ...kdaqgkmksldeiledlsealkkl 184
                                           d +   k l+e+ +dl+ea+ kl
  gi|242399004|ref|YP_002994428.1|  84 qtgVDYETAKKALEETKGDLAEAIVKL 110
                                       655455555566666666666666666 PP

>> PBD  P21-Rho-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00037      0.66      26      46 ..       8      28 ..       3      38 .. 0.83
   2 ?   -1.2   0.0       1.5   2.7e+03      15      20 ..      86      91 ..      64     112 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00037
                                      --CCHCCCHHHT.TTSXXXBE CS
                               PBD 26 lPpewkkllkssgItedelke 46
                                      +P++ +kl+k++gI+++el+ 
  gi|242399004|ref|YP_002994428.1|  8 NPKQMQKLMKQLGIKMEELEG 28
                                      8****************9975 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.5
                                      EEETTT CS
                               PBD 15 Gwdgds 20
                                      G d ++
  gi|242399004|ref|YP_002994428.1| 86 GVDYET 91
                                      333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1436  (0.0800937); expected 358.6 (0.02)
Passed bias filter:                      669  (0.0373138); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 815.37
//
Query:       gi|242399005|ref|YP_002994429.1|  [L=424]
Description: HflX-related GTP-binding protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.8e-21   76.6   0.4    8.2e-21   74.5   0.1    2.3  2  GTP-bdg_N    GTP-binding GTPase N-terminal
    1.8e-20   73.1   0.3    6.4e-20   71.3   0.1    2.0  2  MMR_HSR1     50S ribosome-binding GTPase
    2.1e-19   69.9   5.5    4.5e-19   68.8   5.5    1.6  1  GTP-bdg_M    GTP-binding GTPase Middle Region
    7.5e-09   35.3   0.4    1.5e-08   34.4   0.4    1.5  1  FeoB_N       Ferrous iron transport protein B
    1.4e-07   31.5   3.5    0.00048   20.1   0.1    2.7  3  RsgA_GTPase  RsgA GTPase
    3.1e-06   26.9   0.2    0.00016   21.2   0.2    2.3  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    3.7e-05   23.4   0.0    9.3e-05   22.1   0.0    1.7  1  Ras          Ras family
    5.3e-05   22.7   3.6    0.00012   21.5   2.9    2.0  1  Arf          ADP-ribosylation factor family
    5.4e-05   23.3   0.8      0.016   15.3   0.0    2.9  3  Dynamin_N    Dynamin family
    0.00093   19.0   1.6       0.13   12.0   1.0    2.9  2  PduV-EutP    Ethanolamine utilisation - propanediol utilisati
     0.0023   18.2   0.2      0.013   15.7   0.2    2.2  1  Roc          Ras of Complex, Roc, domain of DAPkinase
     0.0034   16.4   1.6     0.0068   15.4   0.4    1.9  2  Spore_IV_A   Stage IV sporulation protein A (spore_IV_A)
  ------ inclusion threshold ------
      0.017   14.4   5.6       0.37   10.0   0.2    2.3  2  Septin       Septin
      0.017   14.7   3.6        2.2    7.8   0.1    2.9  3  cobW         CobW/HypB/UreG, nucleotide-binding domain
      0.021   15.3   0.2      0.057   13.9   0.2    1.9  1  ABC_tran     ABC transporter
      0.027   14.2   0.2       0.88    9.3   0.1    2.7  2  CLP1_P       mRNA cleavage and polyadenylation factor CLP1 P-
      0.072   12.9   0.8       0.57    9.9   0.1    2.2  2  ATP_bind_1   Conserved hypothetical ATP binding protein
        2.2    7.3   5.9         21    4.1   5.7    2.6  1  APG17        Autophagy protein Apg17


Domain annotation for each model (and alignments):
>> GTP-bdg_N  GTP-binding GTPase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.5   0.1   8.3e-24   8.2e-21       5      88 ..      18     100 ..      15     101 .. 0.96
   2 ?   -1.9   0.0       5.4   5.4e+03      55      59 ..     240     244 ..     199     273 .. 0.51

  Alignments for each domain:
  == domain 1  score: 74.5 bits;  conditional E-value: 8.3e-24
                         GTP-bdg_N   5 eEleeLaktaglevvgevvqkrekpdpatyiGkGkveeikelveeeeadlvifddeLspsqqrnLekelevkViDRt 81 
                                       eE+eeL+++ag+e+++ v q r + +p++ iG Gk++e+kel++e + d vif + L+psq  n++kel++ ViD+ 
  gi|242399005|ref|YP_002994429.1|  18 EEFEELLRSAGYEILAIVEQVR-EEHPKYNIGPGKLQEVKELIKELNPDRVIFANPLTPSQSFNITKELRIDVIDKW 93 
                                       8**************8887776.789*************************************************** PP

                         GTP-bdg_N  82 qLILdIF 88 
                                       qL+L+IF
  gi|242399005|ref|YP_002994429.1|  94 QLVLEIF 100
                                       ******* PP

  == domain 2  score: -1.9 bits;  conditional E-value: 5.4
                         GTP-bdg_N  55 vifdd 59 
                                       v f d
  gi|242399005|ref|YP_002994429.1| 240 VGFID 244
                                       33333 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       4.2   4.1e+03      46      73 ..     130     154 ..     102     179 .. 0.61
   2 !   71.3   0.1   6.4e-23   6.4e-20       2     114 .]     188     307 ..     187     307 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 4.2
                                       EEEEEEECGGCSSHHHHHHHHHHHHHHH CS
                          MMR_HSR1  46 keielvDtpGliegaseekglgkaflal 73 
                                       ++i+l D +G ++g   ++  ++++l++
  gi|242399005|ref|YP_002994429.1| 130 RRIKLGDRAG-FKG--MGEYQTQQYLKH 154
                                       5678888888.541..122223333333 PP

  == domain 2  score: 71.3 bits;  conditional E-value: 6.4e-23
                                       EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHH......HHHHHHHH CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseek......glgkafla 72 
                                       +a++G++N+GKStL+n+l +e+ +++ + +tT+d++++r+ ++gk+  ++Dt+G+i+    +        +  ++++
  gi|242399005|ref|YP_002994429.1| 188 IALAGYTNAGKSTLLNTLANEEIETKMQMFTTLDTTTRRFMMNGKKTLITDTVGFID----DLppfiveAFHSTLEE 260
                                       89***************************************99***********876....2222112256666666 PP

                                       HHCTSEEEEEEETTTTCSHHHHHHHHHHHHH......TTSEEEEEEES CS
                          MMR_HSR1  73 leeadlillvvdaseeklkpldeeleellee......akkplilvlnk 114
                                       +++ad+ill++d+s e ++++++++ + +e        +kpli+vlnk
  gi|242399005|ref|YP_002994429.1| 261 IIKADIILLILDIS-EPWREIKRKFLASIEVlkelktLDKPLIIVLNK 307
                                       888*********99.667666644433322222345599********8 PP

>> GTP-bdg_M  GTP-binding GTPase Middle Region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.8   5.5   4.5e-22   4.5e-19       1      79 []     103     180 ..     103     180 .. 0.87

  Alignments for each domain:
  == domain 1  score: 68.8 bits;  conditional E-value: 4.5e-22
                                       H--SHHHHHHHHHHHHHHHHHHHCXXXXXXXXX..X....XXXXXXXXXHHHHHHHHHHHHHHHHHHHHHHHHHH.. CS
                         GTP-bdg_M   1 rArtkeaklQVelAqlkyllprLeglgkelsrqgGg..igtrGpGetkleldrrlireriaklkkeLekvkkkrelq 75 
                                       rA++keaklQVe+A+l+y+lp +   +++  r + g   g++G Ge++++ + ++ir r+ ++kkeLekvk  re++
  gi|242399005|ref|YP_002994429.1| 103 RAHSKEAKLQVEFANLQYELPLV---KEAIRRIKLGdrAGFKGMGEYQTQQYLKHIRYRMGRIKKELEKVKADREVK 176
                                       9**********************...33334442221146************************************* PP

                                       ...T CS
                         GTP-bdg_M  76 rkkR 79 
                                       rk+R
  gi|242399005|ref|YP_002994429.1| 177 RKRR 180
                                       **99 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 !   34.4   0.4   1.5e-11   1.5e-08       2     144 ..     187     343 ..     186     354 .. 0.72

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 1.5e-11
                                       EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----S.SSSSSSHHHHHHHHHHHCT CS
                            FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiY.slsayseeekvardfllee 77 
                                        +al+G  n+Gk+tl+n+l++ + +      +t + ++ ++ ++gk++ i+D  G   +l ++  e     ++    
  gi|242399005|ref|YP_002994429.1| 187 LIALAGYTNAGKSTLLNTLANEEIETKMQMFTTLDTTTRRFMMNGKKTLITDTVGFIdDLPPFIVEA-FHSTLEEII 262
                                       599*********************9999999************************861565555543.322222233 PP

                                       SSSEEEEEEEGG....GHHHHHHHHH....HHHHTTSSEEEEEETHHHHHHTTEEE-HHHHHHHHT......S-EEE CS
                            FeoB_N  78 epdvvvnvvdat....nlernLyLtl....qllelgvpvvlalnmideaekkgieidlkkLsekLg......vpvvk 140
                                       ++d+++ ++d +    +++r+++  +    +l  l++p++++ln+ d  +k+ +e  +k+L+e +         +++
  gi|242399005|ref|YP_002994429.1| 263 KADIILLILDISepwrEIKRKFLASIevlkELKTLDKPLIIVLNKKDLTSKADVEDKKKALEELITrkgiiaHSIIP 339
                                       567777777765122267887665551111566789*******************9999999987511111134555 PP

                                       EBTT CS
                            FeoB_N 141 tsak 144
                                       +sak
  gi|242399005|ref|YP_002994429.1| 340 ISAK 343
                                       5554 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       5.3   5.3e+03      65      85 ..      17      37 ..      11      44 .. 0.75
   2 !   20.1   0.1   4.8e-07   0.00048      90     161 ..     176     242 ..     143     244 .. 0.67
   3 !   11.4   0.5   0.00023      0.23      38      99 ..     290     356 ..     257     361 .. 0.66

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 5.3
                                      HHHHHHHHHHTTSEEEE--TT CS
                       RsgA_GTPase 65 leelkeelealgyevllvsak 85
                                       ee++e l+++gye+l++ ++
  gi|242399005|ref|YP_002994429.1| 17 REEFEELLRSAGYEILAIVEQ 37
                                      678899999999999988655 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 4.8e-07
                                       HHHHHHHCTTSEEEEECSTTSSHHHHHHHHCTT-----S--------------SEEEEEETTTEEEESS-SS CS
                       RsgA_GTPase  90 leelkellkdktsvlvGqSGvGKStLinallpelelktgevseklgrGkhTTtavellelaegglliDtPGf 161
                                        ++ +e++   +++l+G + +GKStL+n+l++e e++t   + ++ +   TTt++ +++ + ++l+ Dt Gf
  gi|242399005|ref|YP_002994429.1| 176 KRKRREEVGFILIALAGYTNAGKSTLLNTLANE-EIET---KMQMFTTLDTTTRRFMMNGK-KTLITDTVGF 242
                                       344445555567899****************98.3333...23334446799999998888.9******998 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.00023
                                       HHHHHHHTT-EEEEEEE-GGG--HHH......HHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTT CS
                       RsgA_GTPase  38 fLvlaeekgiepvivlnKiDlleeee......eleelkeelealgyevllvsaktkegleelkellkd 99 
                                       +L ++++ + +++ivlnK Dl+++++      +leel ++   +  +++ +sak +++l elk+ l++
  gi|242399005|ref|YP_002994429.1| 290 VLKELKTLDKPLIIVLNKKDLTSKADvedkkkALEELITRKGIIAHSIIPISAK-ENDLGELKNSLEE 356
                                       3455556666899**********9996665555555555555566667777776.6677777777776 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 !   21.2   0.2   1.6e-07   0.00016      51     190 ..     215     359 ..     184     387 .. 0.71

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.6e-07
                                       HHTSCSSCEEEEEETTCSSEEEEEEEESSSGG....GHHHHHHH....HHT-SEEEEEEETTTB......STHHHHH CS
                          GTP_EFTU  51 ergiTiksaaisleketkkylinliDtPGHvd....Fskevirg....lrvlDgavlvvdaveG......vepqtee 113
                                       +   T ++++  +    + ++  + Dt G +d    F+ e  ++    + ++D+ +l++d++e           + e
  gi|242399005|ref|YP_002994429.1| 215 QMFTTLDTTTRRFM--MNGKKTLITDTVGFIDdlppFIVEAFHStleeIIKADIILLILDISEPwreikrKFLASIE 289
                                       33357777778888..88888889999999998999999998887666789***********87666665777899* PP

                                       HHHHHHHTTTEEEEEEESCGST.HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTB..THHHHHHH CS
                          GTP_EFTU 114 vlrlalkegvpiivfiNKmDrl.kaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkge..gvktllea 187
                                       vl+ +++++ p+i+++NK D + ka+++  ++++++ +       + +g  +    +++++Sa++++  ++k+ le 
  gi|242399005|ref|YP_002994429.1| 290 VLKELKTLDKPLIIVLNKKDLTsKADVEDKKKALEELI-------TRKGIIA---HSIIPISAKENDlgELKNSLEE 356
                                       **********************7778887777777555.......3333332...3578888877775544444444 PP

                                       HHH CS
                          GTP_EFTU 188 lve 190
                                       ++ 
  gi|242399005|ref|YP_002994429.1| 357 VMF 359
                                       444 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   9.4e-08   9.3e-05       3     146 ..     189     345 ..     187     361 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 9.4e-08
                                       EEEESTTSSHHHHHHHHHHSSCSSSCTTTSSEEEEEEEEEETTEEEEEEEEEETT.........SGGGHHHHHHHHT CS
                               Ras   3 vlvGdsavGKtslllrfvkdkFkeeyesTigvdfytkeievdgkevkleiwDTAG.........qeefkslrelyyr 70 
                                        l G ++ GK++ll+  ++++ ++++++    d +t++++++gk+    i DT G          e f+s  e    
  gi|242399005|ref|YP_002994429.1| 189 ALAGYTNAGKSTLLNTLANEEIETKMQMFTTLDTTTRRFMMNGKKTL--ITDTVGfiddlppfiVEAFHSTLEEI-I 262
                                       67899*******************99987779***********9875..89****55544444448888876665.5 PP

                                       TESEEEEEEETTBHHHHHTHH.HHHHHHHHHST...TTSEEEEEEETTTGGGG-SS-HHHH..HHHHHHHT.SEE.. CS
                               Ras  71 daegillvyditsresfenvk.kwveeikrvae...envpivLvGnKvDleekravsteeg..eelakelg.lkf.. 138
                                       +a+ ill+ di++   ++++k k++  i+  +e    + p+++v nK Dl++k  v+ ++   eel  ++g +++  
  gi|242399005|ref|YP_002994429.1| 263 KADIILLILDISE--PWREIKrKFLASIEVLKElktLDKPLIIVLNKKDLTSKADVEDKKKalEELITRKGiIAHsi 337
                                       799********86..5888888999888877777665679************9999865421255666666433322 PP

                                       EEEBTTTT CS
                               Ras 139 letSAktn 146
                                       + +SAk+n
  gi|242399005|ref|YP_002994429.1| 338 IPISAKEN 345
                                       55666665 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   2.9   1.3e-07   0.00012      17     143 ..     188     326 ..     173     358 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.3e-07
                                       EEEEESTTSSHHHHHHHHHHSSCEE...CSSSSSEEEEEEEETTEEEEEEE.E-SSGGGGGGGGGGCTTE....... CS
                               Arf  17 illlGLDnaGKtTilkklkleelvt...tvPTigfnveeleiknlkftvwD.vGGqeklRplWknYfekt....... 82 
                                       i l G  naGK+T+l+ l +ee++t   +  T+  ++++ ++++ k  + D vG  + l p+  + f++t       
  gi|242399005|ref|YP_002994429.1| 188 IALAGYTNAGKSTLLNTLANEEIETkmqMFTTLDTTTRRFMMNGKKTLITDtVGFIDDLPPFIVEAFHSTleeiika 264
                                       4567999***************9885557799*********999988888857778999999887777654444444 PP

                                       SEEEEEEETT-CTTHHHHHHHHHHHCTSGCCT..TSEEEEEEE-TTSTTSS-HHHHHHHTTGG CS
                               Arf  83 davifvvDsadreRleeakeeLkalleeeelk..evallvlaNKqDlpealseeelrellgle 143
                                       d ++ ++D ++  R e  ++ L+++   +elk  + +l+++ NK+Dl++ ++ e+ +++l+  
  gi|242399005|ref|YP_002994429.1| 265 DIILLILDISEPWR-EIKRKFLASIEVLKELKtlDKPLIIVLNKKDLTSKADVEDKKKALEEL 326
                                       77888999999988.566667777655555554489*************99999988887643 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1       3.2   3.2e+03      59      89 ..     142     172 ..     104     182 .. 0.74
   2 !   15.3   0.0   1.6e-05     0.016       1      32 [.     188     219 ..     188     230 .. 0.85
   3 ?    5.4   0.0     0.017        17     122     167 ..     257     307 ..     228     308 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 3.2
                                       T-EB--CHHHHHHHHHHHHHHHTSSSS--SS CS
                         Dynamin_N  59 ekkledfsevreeieketekiagankgiskk 89 
                                          +++ +++ ++i+ ++ +i++++++++ +
  gi|242399005|ref|YP_002994429.1| 142 GMGEYQTQQYLKHIRYRMGRIKKELEKVKAD 172
                                       5567788888888888888888777777654 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 1.6e-05
                                       EEEEEBTTTTHHHHHHHHHTS--S---SSS-- CS
                         Dynamin_N   1 iavvGsqSsGKSSvlnaLlgedilprgpnptT 32 
                                       ia+ G +++GKS++ln L  e+i  + +  tT
  gi|242399005|ref|YP_002994429.1| 188 IALAGYTNAGKSTLLNTLANEEIETKMQMFTT 219
                                       7899******************9877777666 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.017
                                       HHHHHSTTEEEEEEEETTS-CCC-CHHHHHHHHSTTBTT.....EEEEEE- CS
                         Dynamin_N 122 vkeyikkadiilavtsanhdlsnsealflarevdpkgkr.....tivvltk 167
                                       + e i kadiil++++ +  + + +++fla+    k+ +      i+vl+k
  gi|242399005|ref|YP_002994429.1| 257 TLEEIIKADIILLILDISEPWREIKRKFLASIEVLKELKtldkpLIIVLNK 307
                                       55667789********************99632222222245557888876 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       3.4   3.4e+03      93     130 ..       4      39 ..       2      42 .. 0.67
   2 !   12.0   1.0   0.00013      0.13       5     142 ..     189     355 ..     186     356 .. 0.56

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3.4
                         PduV-EutP  93 iGiitkidlaedeenieaveelLksaGaekifevsave 130
                                       iGii +     ++ n e  eelL+saG e +  v+ v+
  gi|242399005|ref|YP_002994429.1|   4 IGIIRHSPN--KRVNREEFEELLRSAGYEILAIVEQVR 39 
                                       666655433..366667788999999988777777665 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00013
                         PduV-EutP   5 lliGkvgsGKttLtqalkg...................eelkYkktqaiefsdeviDtPG......eylenrklysa 56 
                                        l G +++GK tL ++l +                     ++ kkt          Dt G       ++ +  + s+
  gi|242399005|ref|YP_002994429.1| 189 ALAGYTNAGKSTLLNTLANeeietkmqmfttldtttrrFMMNGKKTLI-------TDTVGfiddlpPFIVE-AFHST 257
                                       577888888888888888833332222222222222212222223322.......3555411111133333.35555 PP

                         PduV-EutP  57 livtsaeadvialvqdateeesvfppgfa.........svfnkeviGiitkidlaedeenieaveelLks....aG. 119
                                       l    ++ad+i l++d++e++  +  +f          +++ k++i ++ k dl+ +++++e  ++ L++     G 
  gi|242399005|ref|YP_002994429.1| 258 LEE-IIKADIILLILDISEPWREIKRKFLasievlkelKTLDKPLIIVLNKKDLT-SKADVEDKKKALEElitrKGi 332
                                       554.4789*************9999998622222222246789**********99.777777666665541111563 PP

                         PduV-EutP 120 .aekifevsavekegieellkyle 142
                                        a++i+ +sa e +++ el++ le
  gi|242399005|ref|YP_002994429.1| 333 iAHSIIPISAKE-NDLGELKNSLE 355
                                       346677777654.46777777665 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.2   1.4e-05     0.013       2     119 ..     188     309 ..     187     310 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.4e-05
                                       EEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-S..GGCTTTT-HHH CS
                               Roc   2 vvlvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaG..qerfrslhply 76 
                                       + l G +++GK++ll+ + ++++++k +  + +d++t++++ ++g ++   +++    i D+     e f+s+ +  
  gi|242399005|ref|YP_002994429.1| 188 IALAGYTNAGKSTLLNTLANEEIETKMQMFTTLDTTTRRFM-MNGKKT--LITDTVGFIDDLPPfiVEAFHSTLEEI 261
                                       578899*****************************999984.555222..222222234444433357788777765 PP

                                       HCTSCEEEEEEE.GHH.HHCHHHHHHHHHHHCS....SS-EEEEEE-TT CS
                               Roc  77 lreaalailvyd.srs.senlkeWlkelkkvag....kspvilvgnkiD 119
                                       + +a++++l++d s+   e  ++ l +++   +    ++p+i+v nk D
  gi|242399005|ref|YP_002994429.1| 262 I-KADIILLILDiSEPwREIKRKFLASIEVLKElktlDKPLIIVLNKKD 309
                                       5.56677788884332134445666666544332224679999999998 PP

>> Spore_IV_A  Stage IV sporulation protein A (spore_IV_A)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.48   4.7e+02      16      41 ..     184     209 ..     147     233 .. 0.75
   2 !   15.4   0.4   6.8e-06    0.0068     168     237 ..     286     362 ..     255     405 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.48
                        Spore_IV_A  16 gdiyigvvGpvRtGKStfikrfmell 41 
                                       g i i++ G   +GKSt+++ + +  
  gi|242399005|ref|YP_002994429.1| 184 GFILIALAGYTNAGKSTLLNTLANEE 209
                                       55677777777777777776665544 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 6.8e-06
                        Spore_IV_A 168 aeervieelkeigkPfvvvlNskkpese....etkelaeeleek...ydvkvlavnveelkeedikeilekvLyefp 237
                                       a  +v++elk+++kP ++vlN k+ +s+    + k+  eel ++      ++++++++e +  ++k+ le+v++  p
  gi|242399005|ref|YP_002994429.1| 286 ASIEVLKELKTLDKPLIIVLNKKDLTSKadveDKKKALEELITRkgiIAHSIIPISAKENDLGELKNSLEEVMFTLP 362
                                       45679****************88766541111333333344333122234677777777777888888888887766 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.2   0.00037      0.37       7      56 ..     188     237 ..     181     244 .. 0.79
   2 ?    6.4   1.1    0.0048       4.8     132     200 ..     288     356 ..     281     363 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00037
                                       EEEEEBTTSSCCCCCCTTSSSS------------------S-EEEEEEEE CS
                            Septin   7 lmvvGesglGkttlintlfetdlieeekleeasekkkktveikkkkvvie 56 
                                       + ++G    Gk+tl+ntl ++++ ++ ++ ++ +++++   ++ kk++i 
  gi|242399005|ref|YP_002994429.1| 188 IALAGYTNAGKSTLLNTLANEEIETKMQMFTTLDTTTRRFMMNGKKTLIT 237
                                       457999****************9999888777777777777777666665 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0048
                                       HHHHHHHTTT.S-EEEEESSGGGS-HHHHHHHHHHHHHHHHHTT--------SSSS-SCCHHHHHHHHHH CS
                            Septin 132 velmkklsek.vnliPviaKaDtltkeElkefKkkireeleeeeikiyklpdeeededeeakelseklke 200
                                       +e++k+l++    li v+ K D   k +++  Kk + e ++++ i  +++ +++++e ++  el+++l+e
  gi|242399005|ref|YP_002994429.1| 288 IEVLKELKTLdKPLIIVLNKKDLTSKADVEDKKKALEELITRKGIIAHSIIPISAKE-NDLGELKNSLEE 356
                                       6778888775246999*****************************999988887776.555555555554 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       2.4   2.4e+03     109     144 ..      80     118 ..      62     119 .. 0.66
   2 ?    7.8   0.1    0.0023       2.2       3      28 ..     188     213 ..     186     219 .. 0.82
   3 ?    6.9   0.5    0.0044       4.3      85     170 ..     234     327 ..     213     334 .. 0.64

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.4
                                       CCCECEEEEEEETTTH....CCHCCHHHHHHHHHHTSSE CS
                              cobW 109 dltldavvavvDaknl...eaeeekieekaedqlaaadl 144
                                       ++t +  + v+D  +l     e++  +++a+ q+++a+l
  gi|242399005|ref|YP_002994429.1|  80 NITKELRIDVIDKWQLvleIFEKRAHSKEAKLQVEFANL 118
                                       566667778888866677745677777788888888875 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0023
                                       EEEEESTTCCHHHHHHHHHCT--SS- CS
                              cobW   3 tvltGflGsGKTtLlnhllenraglk 28 
                                       + l+G+  +GK+tLln+l +++ + k
  gi|242399005|ref|YP_002994429.1| 188 IALAGYTNAGKSTLLNTLANEEIETK 213
                                       6799**************97766555 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0044
                                       EEEEEECTTTTHHHH.HTT..SHHHHHCCCECEEEEEEETTTH.........CCHCCHHHHHHHHHHTSSEEEEE-H CS
                              cobW  85 viliEttGlaePapv.aft..eeelksdltldavvavvDaknl........eaeeekieekaedqlaaadllvlnKt 150
                                        ++  t+G  +  p  +++  +++l++ +++d+++ ++D ++             + +  k  + l +  ++vlnK 
  gi|242399005|ref|YP_002994429.1| 234 TLITDTVGFIDDLPPfIVEafHSTLEEIIKADIILLILDISEPwreikrkfL--ASIEVLKELKTLDKPLIIVLNKK 308
                                       5677777744433332233468999999999999999999776666543211..11222233355666679****** PP

                                       HHHCHC..HHHHHHHHHHHH CS
                              cobW 151 Dlldeeallekleerlrqln 170
                                       Dl ++++ +e  ++ l++l 
  gi|242399005|ref|YP_002994429.1| 309 DLTSKAD-VEDKKKALEELI 327
                                       ***9994.466666666655 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   5.7e-05     0.057      14      42 ..     188     216 ..     185     334 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.7e-05
                                       EEEEESTTSSHHHHHHHHTTSS--SEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  14 vaivGenGaGKStLlkllagllkpteGei 42 
                                       +a+ G + aGKStLl++la+++  t+ ++
  gi|242399005|ref|YP_002994429.1| 188 IALAGYTNAGKSTLLNTLANEEIETKMQM 216
                                       799******************99887665 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 ?    9.3   0.1   0.00088      0.88       1      28 [.     192     220 ..     192     231 .. 0.79
   2 ?    3.1   0.0     0.074        74      90     157 ..     223     290 ..     212     299 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00088
                            CLP1_P   1 GpkdsGKSTlarlLlNyalrkgrkpv.yv 28 
                                       G +++GKSTl  +L+N+ ++ +++    +
  gi|242399005|ref|YP_002994429.1| 192 GYTNAGKSTLLNTLANEEIETKMQMFtTL 220
                                       779**************988876654344 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.074
                            CLP1_P  90 eveekleenkkakasgliIntpGwvkglg...aell.leliealepdvvvvldq.eellnelkrdlplskvkv 157
                                       +++ +++ n   +++ li +t G++++l    +e     l e++++d+++++ + +e   e+kr++   +++v
  gi|242399005|ref|YP_002994429.1| 223 TTR-RFMMN---GKKTLITDTVGFIDDLPpfiVEAFhSTLEEIIKADIILLILDiSEPWREIKRKFL-ASIEV 290
                                       333.33333...7999**********98533344442456778899999998888888888888876.55555 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.29   2.9e+02       2      27 ..     191     216 ..     190     233 .. 0.72
   2 ?    9.9   0.1   0.00057      0.57     141     238 ..     284     387 ..     252     390 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.29
                        ATP_bind_1   2 vGpaGsGKttfvgalseilelrgrsv 27 
                                       +G   +GK+t+ ++l++   +++ ++
  gi|242399005|ref|YP_002994429.1| 191 AGYTNAGKSTLLNTLANEEIETKMQM 216
                                       688899*******9987655554443 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00057
                        ATP_bind_1 141 fisgllsalsamlrlelPhvvvlnkfDllkek.lekeleffedvealslllekee.......ekykklaeaiaelle 209
                                       f+ + +  l+ + +l+ P ++vlnk Dl ++   e + + +e++ + + ++ +         +   +l++++ e++ 
  gi|242399005|ref|YP_002994429.1| 284 FLAS-IEVLKELKTLDKPLIIVLNKKDLTSKAdVEDKKKALEELITRKGIIAHSIipisakeNDLGELKNSLEEVMF 359
                                       5555.555666778899***********9977888888899988888888877778997776666677777777777 PP

                        ATP_bind_1 210 efalvlrflplssekeesiedllslidea 238
                                       +     r++ + ++++e + +++++i+++
  gi|242399005|ref|YP_002994429.1| 360 TLPKY-RLFEVLVRDKEKVPKVMAMINSI 387
                                       77777.77777777777778888877765 PP

>> APG17  Autophagy protein Apg17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   5.7     0.021        21     226     255 ..     363     392 ..     101     416 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.021
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             APG17 226 reelleVlekDaaeledVvkelqerleeme 255
                                       +  l+eVl +D++ +++V++ ++++ e++ 
  gi|242399005|ref|YP_002994429.1| 363 KYRLFEVLVRDKEKVPKVMAMINSIGEILD 392
                                       6689*******************9999883 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (424 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1243  (0.069329); expected 358.6 (0.02)
Passed bias filter:                      724  (0.0403815); 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):              18  [number of targets reported over threshold]
# CPU time: 0.76u 0.38s 00:00:01.14 Elapsed: 00:00:00.52
# Mc/sec: 2434.93
//
Query:       gi|242399006|ref|YP_002994430.1|  [L=138]
Description: hypothetical protein TSIB_1025 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.2e-17   61.4   0.2    1.5e-16   60.7   0.2    1.3  1  RNA_binding  RNA binding
  ------ inclusion threshold ------
       0.06   12.9   0.0       0.16   11.5   0.0    1.6  2  ACOX         Acyl-CoA oxidase


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 !   60.7   0.2   1.7e-20   1.5e-16       1     118 [.       7     116 ..       7     117 .. 0.80

  Alignments for each domain:
  == domain 1  score: 60.7 bits;  conditional E-value: 1.7e-20
                                       EEEEEEEE-TTC-HHHHHHHHHTTSTTSE---EEEEEE-CCC-EEEEEEEEESSHHHHHHHHHHHHHHCCCCH.HHH CS
                       RNA_binding   1 kievrafvhaTEdeekVlealsnllpeeeveieeeeaeGhygnpitileaelekkkakkvlkkllellreeei.keL 76 
                                       ++ev+a+v++TEd ekV+ea+ nl+ + e        +   + ++++l +++++   kk+l+kl+el+r ++i +  
  gi|242399006|ref|YP_002994430.1|   7 EVEVEAHVYPTEDIEKVKEAMLNLVSPLE-------FHAFDKGEYILLLGKTKD---KKALQKLYELFRGQQIlDTA 73 
                                       59***********************9884.......223334455566666666...9**************96444 PP

                                       HHCCHCCB-TTSEEEEEEEHHHHHTT---BESSSS..EEEEEEE CS
                       RNA_binding  77 lkeleervdekgklylrldKQaaylgklslvegdd..vIkvkik 118
                                       +  lee +  +++++++++KQ ay+gk++++e++   +I+++i+
  gi|242399006|ref|YP_002994430.1|  74 RAMLEEGY-FGEEIIIKVHKQVAYVGKVNFNEESPlgPITIIIR 116
                                       44444433.379******************99988999999997 PP

>> ACOX  Acyl-CoA oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.18   1.6e+03     100     120 ..      14      34 ..       7      39 .. 0.75
   2 ?   11.5   0.0   1.8e-05      0.16      71     113 ..      52      94 ..      36      99 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.18
                                       SS-HHHHHHHHHHHHHHHHHH CS
                              ACOX 100 ylspdqldllreailellkel 120
                                       +   +++++++ea+l+l++ l
  gi|242399006|ref|YP_002994430.1|  14 VYPTEDIEKVKEAMLNLVSPL 34 
                                       566778899999999888755 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 1.8e-05
                                       TCHHHHHHHHHHHHHHHHHHTHHHHHHTTSS-HHHHHHHHHHH CS
                              ACOX  71 elkevLkkLckLyalstiekhlgdflesgylspdqldllreai 113
                                       + k++L+kL++L+  ++i   +  +le+gy+ ++ + ++++++
  gi|242399006|ref|YP_002994430.1|  52 KDKKALQKLYELFRGQQILDTARAMLEEGYFGEEIIIKVHKQV 94 
                                       55899***************************99999988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1039.36
//
Query:       gi|242399007|ref|YP_002994431.1|  [L=351]
Description: PepQ-2 cobalt-dependent proline dipeptidase [Thermococcus sibiricus MM 739]
Scores for complete 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-69  233.4   1.0    3.1e-69  232.8   1.0    1.3  1  Peptidase_M24  Metallopeptidase family M24
      2e-19   70.6   0.0    3.3e-19   69.8   0.0    1.4  1  Creatinase_N   Creatinase/Prolidase N-terminal domain
  ------ inclusion threshold ------
       0.12   12.4   1.0       0.32   10.9   0.7    1.9  2  Anticodon_1    Anticodon-binding domain of tRNA


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 !  232.8   1.0   5.2e-73   3.1e-69       2     208 ..     135     336 ..     134     337 .. 0.97

  Alignments for each domain:
  == domain 1  score: 232.8 bits;  conditional E-value: 5.2e-73
                                       HHHHHHHHHHHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHTTTCEESSSSEEEEGGGGGSTTTBCSSSB--TTEEEE CS
                     Peptidase_M24   2 lirkaariasaaleavleaikpgvterelaaeieattlkrhgarglafppivasgenaavlhytpndrvlkegdlvl 78 
                                       li+ a+++a+  +  ++e+i++g +e+e+aa++e+  +k +ga+++af++i+asg ++a++h++++d+++++gdlv+
  gi|242399007|ref|YP_002994431.1| 135 LIEDACKLADIGVMTAIEEIREGKREKEVAAKVEYV-MKMEGAEKPAFDTIIASGHRSALPHGIASDKRIEKGDLVV 210
                                       68899******99999999***************76.99************************************** PP

                                       EEEEEEETTEEEEEEEEEECSSGSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHHHHHTTBCCGBSSCSEE CS
                     Peptidase_M24  79 idagaeydgyasDitrTvlvGkftpeqrelyeavleaqeaaikavkpGvtlseidaaarevlesaglakffphglGH 155
                                       +d+ga y++y sDitrT++vG+++++q+e+ye+vleaq++a++a+kpG+t++e+d +ar++++++g+++ f h+lGH
  gi|242399007|ref|YP_002994431.1| 211 MDLGALYRHYNSDITRTIVVGSPNEKQKEIYEIVLEAQKKAVEAAKPGMTGKELDSIARDIITEYGYGDKFIHSLGH 287
                                       ***************************************************************************** PP

                                       EESSSSSEEEEEESSSTTCSSB--TTBEEEEEEEEEEETTTEEEEEBEEEEEE CS
                     Peptidase_M24 156 gvGlevhdegpsvsresndgrkleeGmvftiEpgiyfapgeggvriedtvlvt 208
                                       g+Gl+vh+  p+ s  + d+++l+eGmv+tiEpgiy +p  ggvriedt+++t
  gi|242399007|ref|YP_002994431.1| 288 GIGLQVHEW-PRAS--QYDETVLKEGMVITIEPGIY-IPKFGGVRIEDTIVIT 336
                                       *******75.*988..568*****************.99*************9 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 !   69.8   0.0   5.6e-23   3.3e-19       1     132 []       7     127 ..       7     127 .. 0.92

  Alignments for each domain:
  == domain 1  score: 69.8 bits;  conditional E-value: 5.6e-23
                                       HHHHHHHHHHHTT-SEEEEECCHHHHHHHSS...-SSSEEEEEEESSCEEEEEECTTHHHHHHHH.TTSEEEEESTH CS
                      Creatinase_N   1 RlerlralmeekgldallvtspenlrYltGfatetgsrglalvvtadgalllvdalryteaaeesatveevveyddp 77 
                                       R++ +r+ ++++++da+l+ts  nl+Y+ G+   +   g +lvvt+++++llv++l+y++a+ee     ev ++++ 
  gi|242399007|ref|YP_002994431.1|   7 RIKGIRNYIQKNEVDAALITSAPNLFYFVGT---APLIGGYLVVTPEEEILLVPELEYEQAKEEA--HVEVEKFKK- 77 
                                       8999***************************...888888888**********************..445555554. PP

                                       SSHHHHHHHHHHHHT-EEEE-TTSSBHHHHHHHHHHCTTSEEEETHHHHHHHHSC CS
                      Creatinase_N  78 vealadllkellesekrvgveldaltvafyealkealpdaelvdaselieelRvv 132
                                       +++l+++lk      k+++ve + ++++f + lke++  +e++ ++ +i+elR++
  gi|242399007|ref|YP_002994431.1|  78 TDELYEYLKRF----KSLAVEGT-ISLSFNNTLKEKAQIEEFKLLDDIIKELRMI 127
                                       66*********....********.8************999**************8 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 ?   10.9   0.7   5.4e-05      0.32      85     147 ..      78     138 ..      56     143 .. 0.69
   2 ?   -3.3   0.0       1.3     8e+03      30      50 ..     239     258 ..     221     270 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 5.4e-05
                       Anticodon_1  85 tEelwqreeeelgkkesimlaewpe.kaeel....ekeleeeevellkeivkairklrselkikpsse 147
                                       t+el+    e l++ +s+ ++   + +   +    ek++  ee++ll++i+k +r+++ e++ik  ++
  gi|242399007|ref|YP_002994431.1|  78 TDELY----EYLKRFKSLAVEGTISlSF--NntlkEKAQ-IEEFKLLDDIIKELRMIKTEEEIKLIED 138
                                       56677....3444444444444222111..111223333.89**********************9887 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.3
                       Anticodon_1  30 alyeffwndlcdwylelvkpr 50 
                                       ++ye ++ + ++  +e++kp 
  gi|242399007|ref|YP_002994431.1| 239 EIYE-IVLEAQKKAVEAAKPG 258
                                       4444.3333444445555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       697  (0.0388756); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); 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: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.54
# Mc/sec: 1963.19
//
Query:       gi|242399008|ref|YP_002994432.1|  [L=424]
Description: 2-methylthioadenine synthetase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.2e-27   94.5   0.7    5.6e-25   88.6   0.1    2.7  3  Radical_SAM  Radical SAM superfamily
    4.6e-20   71.5   0.0    9.7e-20   70.5   0.0    1.5  1  UPF0004      Uncharacterized protein family UPF0004
    2.5e-11   43.4   0.3    8.9e-11   41.6   0.2    2.1  2  TRAM         TRAM domain
  ------ inclusion threshold ------
      0.015   15.4   0.3       0.17   12.1   0.3    2.4  1  TRAM_2       TRAM domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.019        86     104     162 ..      29      85 ..       1     111 [. 0.60
   2 !   88.6   0.1   1.2e-28   5.6e-25       1     167 []     140     312 ..     140     312 .. 0.91
   3 ?    1.1   0.0       0.1   4.5e+02      94     146 ..     309     360 ..     307     363 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.019
                                       EEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 104 rvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvdrivglpGendeelee 162
                                       +  ++l++ad+  + + +  + +t ++  + ++ l ++g +  v+++  lp +n + ++e
  gi|242399008|ref|YP_002994432.1|  29 YEVVDLDSADYV-IMNTCAvKDPTEKHMARRIKELLDSGKR--VIVTGCLPHVNPSAIDE 85 
                                       445666666665.5555555666666666666666666555..44444444455554444 PP

  == domain 2  score: 88.6 bits;  conditional E-value: 1.2e-28
                                       EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS.....TTHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxx RF
                       Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggeplly.....pdfvellerlak 72 
                                       v++++gC ++C++Ca+++    +g+ +s  +  i++ vke+ + kg ke+ l++ +   y      ++++ll+++  
  gi|242399008|ref|YP_002994432.1| 140 VPISEGCLNACTYCATRF---ARGVLKSYKPGLIVKWVKEA-VAKGYKEIQLSSEDTGCYgfdigTNLARLLDEITS 212
                                       5799**************...8*******************.9**********999999998888889999999999 PP

                                       TCCCTEEEEEEECSSCHG....HHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET CS
                                       xxxxxxxxxxxxxxxxxx....xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  73 lavpgiritvetngtlpd....eeklerllelg.vdrvslgleaaddekvlklmnrghtfeevlealeklreagikr 144
                                       ++  ++ri+v    +       +e +e+ ++      ++l+++++d+e +lk+m+r++t+ee+ e ++ +r++ ik+
  gi|242399008|ref|YP_002994432.1| 213 IE-GEFRIRVGMMNPNNAvkvlDELIEAYKDNKiYKFLHLPVQSGDNE-ILKRMGRPYTVEEFEEIVREFRKH-IKD 286
                                       85.555555555555544789999999999999***************.************************.*** PP

                                       ...EEEEEEEBTTTSHHHHHHHHHHH CS
                                       ...xxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 145 ...vvdrivglpGendeeleellell 167
                                          ++d+ivg+pGe++e +++++el+
  gi|242399008|ref|YP_002994432.1| 287 lnlNTDIIVGFPGESEEAFQNTVELI 312
                                       **********************9986 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.1
                                       HHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  94 lerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvv 146
                                       +e++++ ++d ++++  ++ + +v  +m+++    +v+e  ++l+++++  ++
  gi|242399008|ref|YP_002994432.1| 309 VELIKRVRPDKINVSRFSPRPGTVAARMKDQIVGWRVKERSRYLHRLRLS-IS 360
                                       678899999*******************9999999999999999998776.55 PP

>> UPF0004  Uncharacterized protein family UPF0004
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.5   0.0   2.2e-23   9.7e-20       1      89 [.       2      86 ..       2      92 .. 0.93

  Alignments for each domain:
  == domain 1  score: 70.5 bits;  conditional E-value: 2.2e-23
                                      XEEEE--S-CCCCHHHHHHHHHTTTSSS----SSS--SEEEEEE--SSSSHHHHTHHHHHHHHTTST.--EEEEEEHHH CS
                           UPF0004  1 kvaietlGCqmNevdseelaslLkkegyelvedeeeAdvvlvnTCavrekaekkviqalrelkalkkpekkvvvlGCma 79
                                      +v+iet+GC++N++d+e++ +lL ++gye+v+  ++Ad+v++nTCav++ +ek++ ++++el +     k+v+v+GC++
  gi|242399008|ref|YP_002994432.1|  2 RVHIETYGCTRNKADAEMMEALLLRAGYEVVDL-DSADYVIMNTCAVKDPTEKHMARRIKELLDSG---KRVIVTGCLP 76
                                      79***************************9976.79*************************99877...89******** PP

                                      HS-HHHHHHH CS
                           UPF0004 80 qrekeellke 89
                                      + +++ + ++
  gi|242399008|ref|YP_002994432.1| 77 HVNPSAIDER 86
                                      9999888665 PP

>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0         2   8.8e+03      30      45 ..      67      87 ..      62      87 .. 0.57
   2 !   41.6   0.2     2e-14   8.9e-11       1      62 []     365     423 ..     365     423 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2
                                      EEEEETT-....-T...TEEE CS
                              TRAM 30 kvvfvpgd....lpg.IGdfV 45
                                      k v+v g     +p+ I ++V
  gi|242399008|ref|YP_002994432.1| 67 KRVIVTGClphvNPSaIDERV 87
                                      555555554444777777766 PP

  == domain 2  score: 41.6 bits;  conditional E-value: 2e-14
                                       XXXXXXEEEEEEEEE-.TTSEEEEEET.TEEEEETT--T..TEEEEEEEEEE-SSEEEEEEE CS
                              TRAM   1 rsyvGstqeVlveglsksegegiGrtdngkvvfvpgdlpgIGdfVeVkItkvkrqyLrGell 62 
                                       r+y G+++eVl  g++ ++g + Grt n+k +++p + p +G+fV+Vk+tk+++ yL Gel+
  gi|242399008|ref|YP_002994432.1| 365 RRYLGREMEVLTHGEG-KKGGIEGRTMNYKDIILPEA-P-VGEFVKVKVTKTTSTYLLGELV 423
                                       689*************.*******************6.5.5*******************97 PP

>> TRAM_2  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.3   3.8e-05      0.17      34      64 .]     397     423 ..     368     423 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.8e-05
                                       EES---T....T-EEEEEEEEEETTEEEEEE- CS
                            TRAM_2  34 vtgaeklsk.vGdfvkvkItdadeyDLiGevv 64 
                                       + +     + vG+fvkvk+t+++   L+Ge+v
  gi|242399008|ref|YP_002994432.1| 397 LPE-----ApVGEFVKVKVTKTTSTYLLGELV 423
                                       432.....147*******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (424 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       809  (0.0451224); expected 358.6 (0.02)
Passed bias filter:                      754  (0.0420548); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.46
# Mc/sec: 2760.31
//
Query:       gi|242399009|ref|YP_002994433.1|  [L=63]
Description: hypothetical protein TSIB_1028 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.016   15.3   9.9      0.017   15.2   9.9    1.0  1  Sensor     Putative sensor
       0.16   11.6   5.1       0.17   11.5   5.1    1.0  1  DUF4131    Domain of unknown function (DUF4131)
       0.29   10.1   2.8       0.35    9.8   2.8    1.0  1  DUF818     Chlamydia CHLPS protein (DUF818)
       0.61   10.3   9.9       0.81    9.9   9.9    1.2  1  TMEM238    TMEM238 protein family
       0.81    9.5   8.9        2.1    8.2   8.9    1.7  1  DUF2976    Protein of unknown function (DUF2976)
        2.7    8.0   5.9        3.1    7.8   5.9    1.1  1  RseC_MucC  Positive regulator of sigma(E), RseC/MucC
          3    7.8  13.7        3.9    7.5  13.7    1.2  1  Apq12      Nuclear pore assembly and biogenesis
        3.5    7.4  15.7        1.2    8.9   4.7    2.2  2  FixS       Cytochrome oxidase maturation protein cbb3-type
        4.4    7.3  10.7       0.54   10.3   0.7    2.4  2  FixQ       Cbb3-type cytochrome oxidase component FixQ


Domain annotation for each model (and alignments):
>> Sensor  Putative sensor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   9.9   8.3e-06     0.017       1      47 [.      11      57 ..      11      63 .] 0.94

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 8.3e-06
                            Sensor  1 YlllglplgvaafvllvtglslglgllvllvGlplLalalllargla 47
                                      +l++gl+l++a +v l+  l++   +l++++G++l+++++ l+ +l 
  gi|242399009|ref|YP_002994433.1| 11 FLIVGLALAMAFLVILTRILATYTNILITMIGIVLFVGLVGLVLWLL 57
                                      799**************************************999985 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   5.1   8.7e-05      0.17       9      52 ..      12      57 ..       5      62 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8.7e-05
                           DUF4131  9 llalllllllllllllrr..rprrrvllllllllllallgfalrap 52
                                      l++ l+l++++l++l r    +++  +++++++l+++l+g++l+ +
  gi|242399009|ref|YP_002994433.1| 12 LIVGLALAMAFLVILTRIlaTYTNILITMIGIVLFVGLVGLVLWLL 57
                                      3333333333333333335588888899***********9999976 PP

>> DUF818  Chlamydia CHLPS protein (DUF818)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   2.8   0.00017      0.35      32      64 ..      25      59 ..      20      62 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00017
                            DUF818 32 vlykilevivkivklliglilflPlg..llWvlqk 64
                                      +l++il + ++i+  +ig++lf+ l   +lW+l+k
  gi|242399009|ref|YP_002994433.1| 25 ILTRILATYTNILITMIGIVLFVGLVglVLWLLDK 59
                                      79*********************9844468*9987 PP

>> TMEM238  TMEM238 protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   9.9   0.00041      0.81       9      53 ..       7      55 ..       2      58 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00041
                           TMEM238  9 lavvfdvvGlv..lLlvGifael..lfgDllvytGaliiflSLlwwvlW 53
                                      ++ +f +vGl+  + ++ i++++  +++++l+ + ++++f++L+++vlW
  gi|242399009|ref|YP_002994433.1|  7 FGTLFLIVGLAlaMAFLVILTRIlaTYTNILITMIGIVLFVGLVGLVLW 55
                                      56677777765114455566666899*********************** PP

>> DUF2976  Protein of unknown function (DUF2976)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   8.9    0.0011       2.1      26      85 ..       9      60 ..       1      63 [] 0.81

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0011
                           DUF2976 26 dgvillgLvlaavaflaVakaalkkfneisegkaewgkfgltlvvGvvllvvviwLltkA 85
                                       +++++gL+l a+afl++ + +l+++++i       + +g++l vG  l+ +v+wLl k 
  gi|242399009|ref|YP_002994433.1|  9 TLFLIVGLAL-AMAFLVILTRILATYTNI-----LITMIGIVLFVG--LVGLVLWLLDKR 60
                                      578999**98.589***************.....677777777777..678889999875 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 ?    7.8   5.9    0.0016       3.1      76     118 ..      10      61 ..       7      63 .] 0.78

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0016
                         RseC_MucC  76 lllilgallgsall.........gssellaalgallglvlgflivrllskrl 118
                                       l+li+g++l++a+l          ++ l++++g +l++ l  l+++ll+kr 
  gi|242399009|ref|YP_002994433.1|  10 LFLIVGLALAMAFLviltrilatYTNILITMIGIVLFVGLVGLVLWLLDKRS 61 
                                       5666666666666666677668889999999999999999999999999984 PP

>> Apq12  Nuclear pore assembly and biogenesis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5  13.7     0.002       3.9       7      51 ..      12      56 ..       7      58 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.002
                             Apq12  7 illlllilyvslkildrarRvvlfwvrllvrlvfwlavvlvgayv 51
                                      +++ l+++  +l+il r+  +  + +++++ +v+++++v++++++
  gi|242399009|ref|YP_002994433.1| 12 LIVGLALAMAFLVILTRILATYTNILITMIGIVLFVGLVGLVLWL 56
                                      345566667778888888888**********************97 PP

>> FixS  Cytochrome oxidase maturation protein cbb3-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   3.2     0.017        34       3      21 ..      10      28 ..       9      34 .. 0.75
   2 ?    8.9   4.7   0.00058       1.2       1      20 [.      35      54 ..      35      58 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.017
                              FixS  3 LylLiplSlllgllalaaF 21
                                      L+l ++l+l +++l+++  
  gi|242399009|ref|YP_002994433.1| 10 LFLIVGLALAMAFLVILTR 28
                                      8899999999999887765 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00058
                              FixS  1 siLylLiplSlllgllalaa 20
                                      +iL+ +i++ l++gl++l++
  gi|242399009|ref|YP_002994433.1| 35 NILITMIGIVLFVGLVGLVL 54
                                      79***************986 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 ?    1.6   3.9      0.14   2.8e+02      13      28 ..       7      22 ..       2      34 .. 0.80
   2 ?   10.3   0.7   0.00027      0.54      16      35 ..      43      62 ..      27      63 .] 0.86

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.14
                              FixQ 13 wgllflvllfygvviy 28
                                      +g+lfl++ ++ + ++
  gi|242399009|ref|YP_002994433.1|  7 FGTLFLIVGLALAMAF 22
                                      7888888888877665 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00027
                              FixQ 16 lflvllfygvviyafrpgnr 35
                                      ++l++ ++g+v++++ +++r
  gi|242399009|ref|YP_002994433.1| 43 IVLFVGLVGLVLWLLDKRSR 62
                                      78999*********999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1387  (0.0773607); expected 358.6 (0.02)
Passed bias filter:                      627  (0.0349713); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.48u 0.32s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 385.86
//
Query:       gi|242399010|ref|YP_002994434.1|  [L=304]
Description: hypothetical protein TSIB_1029 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00013   21.6   0.0    0.00019   21.0   0.0    1.3  1  Lactamase_B_2  Beta-lactamase superfamily domain
    0.00025   21.0   0.0    0.00053   19.9   0.0    1.6  1  Lactamase_B_3  Beta-lactamase superfamily domain
      0.002   18.3   0.0        2.5    8.3   0.1    2.5  2  DIRP           DIRP
  ------ inclusion threshold ------
      0.026   14.5   0.0      0.064   13.2   0.0    1.7  1  Lactamase_B    Metallo-beta-lactamase superfamily
        0.8    9.6   4.1          8    6.4   0.2    2.7  2  CAP18_C        LPS binding domain of CAP18 (C terminal)


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 !   21.0   0.0   5.2e-08   0.00019       3     161 ..      27     206 ..      26     246 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 5.2e-08
                                       EEES--TT..............HHHHHTCGGS--S..SS--..SEEEEE-SS--HHHHGGGGCCCC....C--EE.E CS
                     Lactamase_B_2   3 iLiDagpd..............lrqqalralqPve..lrdelppidaVllthaHyDHlaglltlre....lrpkk.l 58 
                                       iLiD+g                l      alq+++    +  ++ + + ++h HyDH +  +++       +p+k  
  gi|242399010|ref|YP_002994434.1|  27 ILIDPGAAlgpkryslspakaeL-----EALQKARekIQQYSRKAQIITISHYHYDHHT--PFFEGiyesSSPEKaK 96 
                                       78888888888888766543331.....33333333233444699************95..5555544465555556 PP

                                       EEE.EEHHHHHHCCTTCGHHHCHTT........TTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSE CS
                     Lactamase_B_2  59 ply.apkgvlavleanfvylaleee........pavnvheldwgesfelgdggleitatparhksgrrldrnagdtl 126
                                       ++y  +   +++ ++n+ + +++++        ++v+  e + g+ f++gd+ +e+ + +++h+s+    ++ g ++
  gi|242399010|ref|YP_002994434.1|  97 DIYsRKTLFIKHPRENINFSQKKRAwaflkeaeKIVEKIEHADGKFFDFGDFIMEFSP-AVPHGSEG---SKLGFVV 169
                                       6884444556788888888777777999999888888888889999*******99999.59999998...5666666 PP

                                       EEEEECTTEEEEEESS-S---HHHHHHHCT..-SEEE CS
                     Lactamase_B_2 127 GlriegggkrvyyigDtgyipeeigerlgg..adlll 161
                                        +++++g++r+ ++ D + +  + +e++ +  +dll+
  gi|242399010|ref|YP_002994434.1| 170 MVMVDDGKQRLIHASDIQLLNRASKEWIIKqmPDLLI 206
                                       66666*************9997777665433455555 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   1.5e-07   0.00053      11     134 ..      19     207 ..      14     246 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.5e-07
                     Lactamase_B_3  11 lletagarilvDPf.....................kanlgyeppaeeaDlvlisqaledHahletlkql........ 58 
                                        le++   il+DP+                     ka  + ++  ++a++++is+ + dH ++   +++        
  gi|242399010|ref|YP_002994434.1|  19 FLEIGKIGILIDPGaalgpkryslspakaelealqKAREKIQQYSRKAQIITISHYHYDHHTPF-FEGIyessspek 94 
                                       57888899******7777777777766666665543345555555***************8886.666678899999 PP

                     Lactamase_B_3  59 ...............................aenvkvlee.....geslevggleiravatshdavggsergenngf 99 
                                                                      +e  k++e+     g+ +++g++ ++  ++   +++gs+ g  ++ 
  gi|242399010|ref|YP_002994434.1|  95 akdiysrktlfikhpreninfsqkkrawaflKEAEKIVEKiehadGKFFDFGDFIMEFSPAVPHGSEGSKLGFVVMV 171
                                       99999888888888888888888877777763333344433334333388999999999999999999999998888 PP

                     Lactamase_B_3 100 lleqdgltiyhlGhlahe.lsseelkelgrvDvvlt 134
                                       ++++++ +++h  ++    + s+e    + +D+++t
  gi|242399010|ref|YP_002994434.1| 172 MVDDGKQRLIHASDIQLLnRASKEWIIKQMPDLLIT 207
                                       999999999999998862123333344455666665 PP

>> DIRP  DIRP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0    0.0014       5.1      47      75 ..      37      65 ..      23      81 .. 0.86
   2 !    8.3   0.1   0.00071       2.5      15      75 ..     229     291 ..     219     299 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0014
                              DIRP 47 pRrfSeaFleeEreeLeqkRekiRelqqr 75
                                      p+r S +  + E e+L++ Reki+++ ++
  gi|242399010|ref|YP_002994434.1| 37 PKRYSLSPAKAELEALQKAREKIQQYSRK 65
                                      7899999999**************99776 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00071
                              DIRP  15 dfeelLkesfpklktrr..ltraewrkirrllgkpRrfSeaFleeEreeLeqkRekiRelqqr 75 
                                       +++e++ke+ +++   +  ++ + +  + ++l k+    ++Fl++E + Le++R++  ++ + 
  gi|242399010|ref|YP_002994434.1| 229 NLNEIIKETNAEVILDHhlIRDKRYPEFLEQLEKQALTFARFLKKEDRPLEAYRKELHKIEKG 291
                                       566666666655443332256678889999999999999*****************9998876 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.8e-05     0.064       6      57 ..      15      78 ..      11      79 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.8e-05
                                      SEEEEEEETTCEEEES--SCHHHHHHHH............HHHHHTSGGGGEEEEE-SBSSHHH CS
                       Lactamase_B  6 vnsyliegdggviLiDtGtsteaaraal............elaalglkpkdvdavilTHlHlDH 57
                                      + ++++e ++  iLiD+G     +r  l            +  ++    ++   + ++H+H+DH
  gi|242399010|ref|YP_002994434.1| 15 SLATFLEIGKIGILIDPGAALGPKRYSLspakaelealqkAREKIQQYSRKAQIITISHYHYDH 78
                                      6799*****************************99977655555555556677899******** PP

>> CAP18_C  LPS binding domain of CAP18 (C terminal)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.2    0.0022         8       3      11 ..      51      59 ..      50      61 .. 0.87
   2 ?    3.7   0.5     0.016        57       9      16 ..     129     136 ..     124     137 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0022
                                      HHHHHHHHH CS
                           CAP18_C  3 lLrkggeKI 11
                                       L+k++eKI
  gi|242399010|ref|YP_002994434.1| 51 ALQKAREKI 59
                                      69******* PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.016
                                       HHHHHHHH CS
                           CAP18_C   9 eKIgEKLk 16 
                                       eKI+EK++
  gi|242399010|ref|YP_002994434.1| 129 EKIVEKIE 136
                                       78888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       857  (0.0477997); expected 358.6 (0.02)
Passed bias filter:                      621  (0.0346366); 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: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.53
# Mc/sec: 1740.01
//
Query:       gi|242399011|ref|YP_002994435.1|  [L=354]
Description: hypothetical protein TSIB_1030 [Thermococcus sibiricus MM 739]
Scores for 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-32  109.6   0.0    1.4e-31  109.0   0.0    1.3  1  DUF835       Protein of unknown function (DUF835)
  ------ inclusion threshold ------
       0.21   12.1   8.0        1.2    9.6   0.8    2.4  2  MerC         MerC mercury resistance protein
       0.63    9.6   9.8       0.81    9.2   8.9    1.6  1  BaxI_1       Bax inhibitor 1 like
        1.8    8.9  14.0       0.45   10.8   4.9    2.4  2  YwiC         YwiC-like protein
        4.4    7.3  14.6        1.9    8.5   4.2    2.9  2  DUF1453      Protein of unknown function (DUF1453)
        5.9    6.5   7.9        2.8    7.6   0.9    2.5  3  Ilm1         Increased loss of mitochondrial DNA protein 1
        9.8    5.3   8.2         16    4.5   8.2    1.3  1  Herpes_LMP1  Herpesvirus latent membrane protein 1 (LMP1)


Domain annotation for each model (and alignments):
>> DUF835  Protein of unknown function (DUF835)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.0   0.0   5.5e-35   1.4e-31       9     136 .]     231     353 ..     224     353 .. 0.93

  Alignments for each domain:
  == domain 1  score: 109.0 bits;  conditional E-value: 5.5e-35
                            DUF835   9 keilsdlvkegvkvlaitRenpkkirekvkienvkviwltkveeentvsPtnlekltetivkflkeaekg....vvl 81 
                                        +i +++ +  ++vla++R+   +      +e++kv++l+++e+e++ sPtnl  + ++ +++++ea+++    vv+
  gi|242399011|ref|YP_002994435.1| 231 RKIKTNFED--YPVLAFVRSL--D-----APEKWKVYYLSTEEREGRLSPTNLAYMAQITSEYFREAKEKglegVVI 298
                                       477777777..9********4..2.....68************************************9999999*** PP

                            DUF835  82 iDgleyLvlengFesvlkflltlkDavllkngtlilvidkealeekelalLkref 136
                                       iD+leyL ++ngFes++kfl +l+D++l++ g+l++vi++ a+++++la+L+r f
  gi|242399011|ref|YP_002994435.1| 299 IDCLEYLSMYNGFESIAKFLAALNDFALINSGVLLVVIEEGAWNKHQLAILRRIF 353
                                       *****************************************************87 PP

>> MerC  MerC mercury resistance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.8   0.00046       1.2      38     106 ..       9      78 ..       2      84 .. 0.70
   2 ?    6.0   1.3    0.0061        16      25      84 ..     137     196 ..     100     233 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00046
                              MerC  38 lhqvllilvvaigllalvvgyrrhrktsvlvl..galGllillvalflgteaeetllfgslwqvltvlGaa 106
                                       + +vl i+++  ++  l+++y +h+ + ++ +  +++ ++++ va + + + ee +lf sl++ +++ G++
  gi|242399011|ref|YP_002994435.1|   9 FVRVLSIFIATGTFGVLAYAYLKHKIKPLFCWsaAWMFFVLMQVAFYTE-NKEEIALFYSLFSGTMIYGVL 78 
                                       5555555555555556778999999888888733566666666666666.677777899999999999876 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0061
                              MerC  25 lpllglsflasellhqvllilvvaigllalvvgyrrhrktsvlvlgalGllillvalflg 84 
                                       + l+ l++++++    +l il++++g++ l++ +r     + +v+++lG ++ +  +f++
  gi|242399011|ref|YP_002994435.1| 137 SGLVFLTMSKKQRNSLYLGILMIVFGIFVLLYPVRLSLPQLHFVWTILGTALSVGMAFFM 196
                                       233333334444466677778888899999999988888899999999988888888877 PP

>> BaxI_1  Bax inhibitor 1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   8.9   0.00032      0.81      28     180 ..      10     165 ..       5     170 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00032
                            BaxI_1  28 vktaillgvlvvtavvtwflvlaaaaalllvgalvglvlalvasfkkkvspalvllYAvleGlfl.Ggislvfeapg 103
                                       v+++ +++ +  ++v+++++++++ + l++ +a   + + + ++f  + ++ ++l Y+++ G ++ G+++++ e + 
  gi|242399011|ref|YP_002994435.1|  10 VRVLSIFIATGTFGVLAYAYLKHKIKPLFCWSAAWMFFVLMQVAFYTENKEEIALFYSLFSGTMIyGVLTYLKEHED 86 
                                       5666677777778888888877665558778888888888999*******************887366676666688 PP

                            BaxI_1 104 ivvqAvlgTlgvfavmlvlYktgairvtpkftkivvaaligil..llylvnlvlslfgvgeglrdgg.lgilfslvv 177
                                       i +     T+g++  +++lY + +i  +  +    v + +++l  ++ l++ ++ l++  ++ r++  lgil+ +++
  gi|242399011|ref|YP_002994435.1|  87 IKTLLKPETIGIIPPLFALYGMLLIHLDLPYSFSSVEVPFAVLsgIFFLFSGLVFLTMS-KKQRNSLyLGILMIVFG 162
                                       88888889**************9999875444333333333320023333322222222.23334324666666665 PP

                            BaxI_1 178 ivl 180
                                       i++
  gi|242399011|ref|YP_002994435.1| 163 IFV 165
                                       554 PP

>> YwiC  YwiC-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   1.6     0.047   1.2e+02      67     105 ..      21      60 ..       4      82 .. 0.50
   2 ?   10.8   4.9   0.00018      0.45      16     108 ..     105     205 ..      96     207 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.047
                              YwiC  67 vallllllalllqpa.llwwallflplvavavyeakrkre 105
                                         ++l+ ++l ++ + l +w ++ + +v+++v++  +++e
  gi|242399011|ref|YP_002994435.1|  21 TFGVLAYAYLKHKIKpLFCWSAAWMFFVLMQVAFYTENKE 60 
                                       2222222222223233555555555555555555444443 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00018
                              YwiC  16 llGlllag......pvwahllllvawlvgYlaffplllllka.rrrarylkplliYgavallllllalll.qpallw 84 
                                       l+G+ll +      ++   ++++v+  + +l++  ++l +++ +r+  yl  l+i  ++ +ll  + l l q +++w
  gi|242399011|ref|YP_002994435.1| 105 LYGMLLIHldlpysFSSVEVPFAVLSGIFFLFSGLVFLTMSKkQRNSLYLGILMIVFGIFVLLYPVRLSLpQLHFVW 181
                                       556665556777778999999*****9******99999998845888898888777777777776666661556999 PP

                              YwiC  85 wallflplvavavyeakrkreRsl 108
                                        +l  ++ v++a+++ k  ++R++
  gi|242399011|ref|YP_002994435.1| 182 TILGTALSVGMAFFMIKIVTSREF 205
                                       999999999999999888888876 PP

>> DUF1453  Protein of unknown function (DUF1453)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   4.2   0.00074       1.9      32     104 ..      98     172 ..      73     174 .. 0.78
   2 ?    4.0   4.5     0.018        47      30      76 ..     157     203 ..     138     212 .. 0.61

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00074
                           DUF1453  32 ilPplfmstGa.lmfvfpefrltllevleallvGalfsipliktskfevr.dgkiylkrskafifillgLlvvRl 104
                                       i+Pplf   G+ l+ +  +  ++ +ev +a+l G++f +  +++ ++  +  + +yl    +++ i++ L  vRl
  gi|242399011|ref|YP_002994435.1|  98 IIPPLFALYGMlLIHLDLPYSFSSVEVPFAVLSGIFFLFSGLVFLTMSKKqRNSLYLGILMIVFGIFVLLYPVRL 172
                                       9**********6666666788**************7665544444444444888998888888888888877776 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.018
                           DUF1453  30 kiilPplfmstGalmfvfpefrltllevleallvGalfsipliktsk 76 
                                        +i+  +f+    + + +p++++ ++ +  al vG+ f ++ i+ts+
  gi|242399011|ref|YP_002994435.1| 157 LMIVFGIFVLLYPVRLSLPQLHFVWTILGTALSVGMAFFMIKIVTSR 203
                                       222222333333355667788899999999999**988777777765 PP

>> Ilm1  Increased loss of mitochondrial DNA protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       1.8   4.7e+03      96     100 ..      45      49 ..      15      72 .. 0.60
   2 ?    4.6   0.1    0.0089        23      41      74 ..     111     145 ..      89     151 .. 0.78
   3 ?    7.6   0.9    0.0011       2.8      49     107 ..     144     207 ..     141     238 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.8
                              Ilm1  96 lffiv 100
                                       +ff++
  gi|242399011|ref|YP_002994435.1|  45 MFFVL 49 
                                       22222 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0089
                              Ilm1  41 lridaarsfskpssplAfl.gvlLlvlalvDlvll 74 
                                       +++d   sfs+ + p+A+l g+ +l+ +lv l++ 
  gi|242399011|ref|YP_002994435.1| 111 IHLDLPYSFSSVEVPFAVLsGIFFLFSGLVFLTMS 145
                                       46788889*********985799999999988765 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0011
                              Ilm1  49 fskpssplAflgvlLlvlalvDlvll...slneelavaeywgrqaplRlllffi..vslyiYls 107
                                       +sk++    +lg+l++v++++ l      sl++   v +++g+   + +++f+i  v+ + +l+
  gi|242399011|ref|YP_002994435.1| 144 MSKKQRNSLYLGILMIVFGIFVLLYPvrlSLPQLHFVWTILGTALSVGMAFFMIkiVTSREFLF 207
                                       788899999************997656779***9999999999999988888862255555555 PP

>> Herpes_LMP1  Herpesvirus latent membrane protein 1 (LMP1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   8.2    0.0063        16      61     146 ..     108     197 ..      90     206 .. 0.69

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0063
                                       XXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXX. CS
                       Herpes_LMP1  61 lliiiiliififrrdllcplgalc.llllmitlllialwnlhgqalylgivlfifgcllvl...glwiyllellwr. 132
                                       +l+i + + + f   + +p+  l  +++l+  l+++++ + + ++lylgi++++fg +++l    l +  l ++w  
  gi|242399011|ref|YP_002994435.1| 108 MLLIHLDLPYSFS-SVEVPFAVLSgIFFLFSGLVFLTMSKKQRNSLYLGILMIVFGIFVLLypvRLSLPQLHFVWTi 183
                                       4555444555554.4566777775377788899999999*****************977652113455557888873 PP

                                       XXXXXXXXXXXXXX CS
                       Herpes_LMP1 133 lgatiwqllaffla 146
                                       lg+++   +aff+ 
  gi|242399011|ref|YP_002994435.1| 184 LGTALSVGMAFFMI 197
                                       56666666777764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       862  (0.0480785); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); 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):               7  [number of targets reported over threshold]
# CPU time: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.48
# Mc/sec: 2231.94
//
Query:       gi|242399012|ref|YP_002994436.1|  [L=84]
Description: hypothetical protein TSIB_1031 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       274  (0.0152825); expected 358.6 (0.02)
Passed bias filter:                      202  (0.0112667); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 567.56
//
Query:       gi|242399013|ref|YP_002994437.1|  [L=360]
Description: hypothetical protein TSIB_1032 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score 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   15.5   0.6       0.14   12.6   0.1    2.5  3  DcpS_C    Scavenger mRNA decapping enzyme C-term binding
      0.031   14.3   0.1      0.099   12.7   0.0    1.9  2  PHD_like  Antitoxin of toxin-antitoxin, RelE / RelB, TA syste
       0.09   12.7   1.6       0.99    9.3   0.2    2.8  3  Cauli_AT  Aphid transmission protein
       0.15   12.0   0.3        1.3    9.0   0.0    2.3  2  DUF5076   Domain of unknown function (DUF5076)
       0.24   12.1   2.9         10    6.8   0.1    3.5  4  DUF5395   Family of unknown function (DUF5395)


Domain annotation for each model (and alignments):
>> 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 ?   -0.7   0.0      0.54   1.9e+03      57      86 ..      37      66 ..      23      74 .. 0.83
   2 ?   -1.0   0.0      0.67   2.4e+03      55      76 ..      89     110 ..      85     123 .. 0.77
   3 ?   12.6   0.1     4e-05      0.14      21      75 ..     128     182 ..      98     198 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.54
                                      THHHHHHHHHHHHHHHTT-T-EEEEE--SC CS
                            DcpS_C 57 pllkemrekakkvieekynevdaeelrvgv 86
                                      +ll +++++++ ++e +y +  + ++r+++
  gi|242399013|ref|YP_002994437.1| 37 KLLIQIQKQVNIIAEARYGKTIKPKFRLFL 66
                                      689999999999999999988888888886 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.67
                                       TTTHHHHHHHHHHHHHHHTT-T CS
                            DcpS_C  55 hlpllkemrekakkvieekyne 76 
                                          +++e +++++++i+e+ ++
  gi|242399013|ref|YP_002994437.1|  89 LQNWVAETHHQVYQAIQEEDEK 110
                                       5679999999999999988654 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 4e-05
                                       SSEEEEE-SS-SSSEEEEEEESS---SGGG--TTTTTHHHHHHHHHHHHHHHTT- CS
                            DcpS_C  21 ekfvvlkDikpkaklhllvipkrdikslrdLtkehlpllkemrekakkvieekyn 75 
                                         ++ ++D+ p ++ +++ i+k+  +++  L++++ + +++m++k ++ +  +++
  gi|242399013|ref|YP_002994437.1| 128 RLLTSIEDVIPPTENYFIGISKDPSEKIIRLKSKQREFVRKMKNKYQQKATVEFI 182
                                       6777899999***********************************9998776665 PP

>> PHD_like  Antitoxin of toxin-antitoxin, RelE / RelB, TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.8e-05     0.099      56      97 ..     267     308 ..     214     312 .. 0.80
   2 ?   -3.7   0.0       3.1   1.1e+04       6      30 ..     326     352 ..     324     353 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.8e-05
                                       T--EEEEEEEETTEEEEEECCGTEEEEESSHHHHHHHHHHHH CS
                          PHD_like  56 klepeieeekdgevytltldelevyvegstkeeaaedLvedl 97 
                                        + +e+e++ +g++++l  + l + + g+t +ea++dL + l
  gi|242399013|ref|YP_002994437.1| 267 PILIEMEYDMEGNLWILKHKTLSIEGYGKTYKEALKDLEDSL 308
                                       4557899*******************************8876 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 3.1
                                       EHHHHHHTHHHHHH..HHHHT.--EEE CS
                          PHD_like   6 sitearkefsalid..qvvkeykpvlv 30 
                                       s++ ++ke+s+++d     ++ykpv+v
  gi|242399013|ref|YP_002994437.1| 326 SAKRIKKELSKYLDlnDFSHKYKPVVV 352
                                       567788888888762133445566655 PP

>> Cauli_AT  Aphid transmission protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.077   2.8e+02      95     148 ..      68     121 ..      51     137 .. 0.67
   2 ?    9.3   0.2   0.00028      0.99      65      98 ..     142     175 ..     140     225 .. 0.87
   3 ?   -3.6   0.0       2.6   9.3e+03     145     159 ..     295     309 ..     289     313 .. 0.59

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.077
                          Cauli_AT  95 ifkeggedkekktklletLkeaqnrikkleeetkklaekivtekllkeevkdld 148
                                         +eg ++ + +    +tL e qn + + ++++ +  ++   + l k+++  l+
  gi|242399013|ref|YP_002994437.1|  68 EIQEGSVEATLEFSGSPTLTELQNWVAETHHQVYQAIQEEDEKTLDKTIIESLK 121
                                       448888888889999999999999777776666554444444445555554444 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00028
                          Cauli_AT  65 lsylGLekDesealsksksPfgsvfkklkkifke 98 
                                       + ++G++kD+se++ + ks   ++ +k+k+ +++
  gi|242399013|ref|YP_002994437.1| 142 NYFIGISKDPSEKIIRLKSKQREFVRKMKNKYQQ 175
                                       5689***********9999989999999988875 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 2.6
                          Cauli_AT 145 kdlderlseirdslk 159
                                       k ++e l+ ++dsl 
  gi|242399013|ref|YP_002994437.1| 295 KTYKEALKDLEDSLE 309
                                       445555555555555 PP

>> DUF5076  Domain of unknown function (DUF5076)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0   0.00036       1.3      19      74 ..      14      67 ..      13      77 .. 0.79
   2 ?    0.4   0.1      0.17   6.2e+02      46      69 ..      93     116 ..      65     124 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00036
                                      EEEEETTEEEEEE-S--.--HHHHHHHHHHHHHHHHHHHHHTSSS-HHHHHHHHHH CS
                           DUF5076 19 RvwvaegglhvalnrglweepeaWGilLadlarhiaralaeedelseeealerile 74
                                      R+w+   g +++   ++  +++++G lL+++ +++  +++++++++ + +++  l+
  gi|242399013|ref|YP_002994437.1| 14 RIWIRLDGRKIVKDHKV--DAHTFGKLLIQIQKQVNIIAEARYGKTIKPKFRLFLA 67
                                      67777777777777777..9***************999999988887777766655 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.17
                                       HHHHHHHHHHHHHHTSSS-HHHHH CS
                           DUF5076  46 Ladlarhiaralaeedelseeeal 69 
                                        a++ +++ +a +eede++ ++++
  gi|242399013|ref|YP_002994437.1|  93 VAETHHQVYQAIQEEDEKTLDKTI 116
                                       455556666666666555555544 PP

>> DUF5395  Family of unknown function (DUF5395)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.032   1.2e+02      10      40 ..      89     122 ..      82     132 .. 0.74
   2 ?   -3.2   0.1       3.9   1.4e+04      34      50 ..     165     179 ..     158     181 .. 0.63
   3 ?    1.3   0.0      0.15   5.4e+02      22      59 ..     237     277 ..     233     278 .. 0.75
   4 ?    6.8   0.1    0.0028        10       2      38 ..     270     308 ..     269     322 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.032
                           DUF5395  10 gekWiaeneelvvkg...ktleeLDenlakelkk 40 
                                        ++W+ae+++ v ++   ++ + LD+ + + lk+
  gi|242399013|ref|YP_002994437.1|  89 LQNWVAETHHQVYQAiqeEDEKTLDKTIIESLKD 122
                                       689***9988765542115566799999999987 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3.9
                           DUF5395  34 lakelkkrgdfkgksqv 50 
                                         +++k++  +++k++v
  gi|242399013|ref|YP_002994437.1| 165 FVRKMKNK--YQQKATV 179
                                       55566665..8887666 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.15
                           DUF5395  22 vkgktleeLDenlake...lkkrgdfkgksqvevfmkfDye 59 
                                       +++++++eL e l ++   l k g+f  k+ + + m++D+e
  gi|242399013|ref|YP_002994437.1| 237 ARSREMKELKEVLPQKeipLDKIGKFLLKEPILIEMEYDME 277
                                       6677777777777543333677799999999********96 PP

  == domain 4  score: 6.8 bits;  conditional E-value: 0.0028
                           DUF5395   2 lelrlvhdgekWiaeneelvvkg..ktleeLDenlakel 38 
                                       +e++   +g+ Wi ++++l ++g  kt +e  ++l++ l
  gi|242399013|ref|YP_002994437.1| 270 IEMEYDMEGNLWILKHKTLSIEGygKTYKEALKDLEDSL 308
                                       57777789***********99853377777777776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       943  (0.0525964); expected 358.6 (0.02)
Passed bias filter:                      604  (0.0336884); 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: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 2248.89
//
Query:       gi|242399014|ref|YP_002994438.1|  [L=138]
Description: hypothetical protein TSIB_1033 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); 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: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.52
# Mc/sec: 796.48
//
Query:       gi|242399015|ref|YP_002994439.1|  [L=200]
Description: hypothetical protein TSIB_1034 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.027   14.3   0.0      0.051   13.4   0.0    1.4  1  A2M        Alpha-2-macroglobulin family
       0.13   12.2   0.2       0.56   10.2   0.0    2.0  2  GreA_GreB  Transcription elongation factor, GreA/GreB, C-term


Domain annotation for each model (and alignments):
>> A2M  Alpha-2-macroglobulin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   5.7e-06     0.051      56      85 ..      20      49 ..       8      54 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.7e-06
                                      EEEEEE--SEEETTSEEEEEEEEEE-SSS- CS
                               A2M 56 ffvdlnlPysvrrgeqveikavvfNyldke 85
                                      + +++++P+ +r ge+v +++ v Ny  ++
  gi|242399015|ref|YP_002994439.1| 20 ISIHIKMPRICRIGEKVPVTVYVENYARSP 49
                                      6799**********************8776 PP

>> GreA_GreB  Transcription elongation factor, GreA/GreB, C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.17   1.5e+03      20      34 ..      52      66 ..      32      70 .. 0.78
   2 ?   10.2   0.0   6.2e-05      0.56      54      76 ..     140     162 ..     138     163 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.17
                                      --EEEE----TTT-B CS
                         GreA_GreB 20 geeetytiVgpdead 34
                                      ++ee+y iV ++   
  gi|242399015|ref|YP_002994439.1| 52 TKEEEYLIVESWAEM 66
                                      578999999888665 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 6.2e-05
                                       -TT-EE---BTTB---EEEEEEX CS
                         GreA_GreB  54 kvGdevevkapsgkikveIlkie 76 
                                       ++G+ev++   +g+++++Il+i+
  gi|242399015|ref|YP_002994439.1| 140 RIGEEVTISFEGGNVRFKILDIK 162
                                       79*******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 1135.60
//
Query:       gi|242399016|ref|YP_002994440.1|  [L=126]
Description: hypothetical protein TSIB_1035 [Thermococcus sibiricus MM 739]
Scores for complete sequence (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    6.9  11.1        1.8    6.8  11.1    1.0  1  DUF2070   Predicted membrane protein (DUF2070)


Domain annotation for each model (and alignments):
>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8  11.1    0.0001       1.8      74     174 ..      21     119 ..       8     126 .] 0.63

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0001
                           DUF2070  74 lalltelivviisllaillsallqalvllalvlslalvfalrllvlvavsdesllkavlpaliqpllailllvly.. 148
                                        al++ ++ v is++++l s    ++v+++l+l l+++ +  + +++av++e l  ++  +++  ++++ll++++  
  gi|242399016|ref|YP_002994440.1|  21 AALFMSIVGVMISVFSTLPS---GDFVTNYLILFLVIMGMTDVTMILAVAQEALEASI-GYIAGRVVGLLLMIYLgr 93 
                                       34444444455555555555...99*********999999999999999999999887.444444444444443356 PP

                           DUF2070 149 .fspesfllllllslifalavylfivv 174
                                        +   s+ ++l+++l+++l+v++ iv+
  gi|242399016|ref|YP_002994440.1|  94 mI-GVSMTPYLISLLVLLLVVVVKIVW 119
                                       42.445555666665555555554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1166  (0.0650343); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 810.36
//
Query:       gi|242399017|ref|YP_002994441.1|  [L=233]
Description: hypothetical protein TSIB_1036 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0025   17.6   0.9     0.0036   17.0   0.9    1.2  1  Tetraspanin      Tetraspanin family
     0.0025   17.4   1.3      0.004   16.7   1.3    1.3  1  BCLP             Beta-casein like protein
     0.0029   17.6   2.1     0.0051   16.8   2.1    1.4  1  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe
  ------ inclusion threshold ------
       0.02   13.8   2.7      0.027   13.3   2.7    1.1  1  SSF              Sodium:solute symporter family
      0.053   13.4   3.8      0.086   12.7   3.8    1.2  1  DUF2975          Protein of unknown function (DUF2975)
      0.062   13.0   0.3       0.12   12.0   0.0    1.6  2  DUF3990          Protein of unknown function (DUF3990)
      0.091   12.0   0.2       0.12   11.5   0.2    1.2  1  STE3             Pheromone A receptor
        0.5   10.2   7.2       0.12   12.3   3.3    1.8  2  REC1             Alpha helical recognition lobe domain
       0.83    9.7   5.0       0.29   11.1   1.3    2.1  2  DASH_Dad4        DASH complex subunit Dad4
        3.1    8.4   8.3        1.9    9.1   2.1    2.3  2  EF-G-binding_N   Elongation factor G-binding protein, N-termi


Domain annotation for each model (and alignments):
>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.9     2e-06    0.0036      46     139 ..       9     102 ..       2     106 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2e-06
                                       .......XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--HHH........HHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Tetraspanin  46 pailaillivvGvllfllgflGcigalkenkcllltfsllllvlfllelaagilgfvfsdkargkvseiinnaievk 122
                                        +++ i+++++G+++++ g+  ++ga  +  + l++ +++  ++++  +a+ +++ +   ++ +k  e +n+++ + 
  gi|242399017|ref|YP_002994441.1|   9 IKTI-IMIFAIGMFVLVGGITAVVGAKTKDDTALQFALVMANIVMVSIIALQAIATAEAVEQAKKQAELMNQSLLEM 84 
                                       3344.58999******************************99999999999999999999988999999**999988 PP

                                       HHHHHHHHHH.THHHHHH CS
                                       xxxxxxxxxx.xxxxxxx RF
                       Tetraspanin 123 yrddldlkkc.qnlldsl 139
                                        ++ l++++  ++l+ +l
  gi|242399017|ref|YP_002994441.1|  85 KKQRLNIEEFkNSLMPYL 102
                                       888888888877777665 PP

>> BCLP  Beta-casein like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   1.3   2.3e-06     0.004      42     114 ..       9      80 ..       3      95 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.3e-06
                              BCLP  42 vsnviavvs.gllsiisGivaivlsrnlknkklqwallvlsllaallsaacavgLlvavvltiankgrallakC 114
                                       +  +i +++ g+   + Gi+a+v ++ +  ++lq+al+++ ++  ++s++++ +++ a ++  a+k+ +l+++ 
  gi|242399017|ref|YP_002994441.1|   9 IKTIIMIFAiGMFVLVGGITAVVGAKTKDDTALQFALVMANIV--MVSIIALQAIATAEAVEQAKKQAELMNQS 80 
                                       56666665449**************************999987..56777777777777777777777787765 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 !   16.8   2.1   2.8e-06    0.0051      32     108 ..       7      87 ..       1      89 [. 0.83

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.8e-06
                   Phage_holin_3_6  32 ragsgagllgaagvlallalllllval.a...lalaalwlaalivaavllvlagvlalvglkklkkakplpertiee 104
                                         ++ +++++a g+++l++ ++++v++      al+++ + a iv++  ++l +++ + ++ ++kk++ l+ +++ e
  gi|242399017|ref|YP_002994441.1|   7 TNIKTIIMIFAIGMFVLVGGITAVVGAkTkddTALQFALVMANIVMVSIIALQAIATAEAVEQAKKQAELMNQSLLE 83 
                                       55778899999999999999999999963777455335588999999999****************999*******9 PP

                   Phage_holin_3_6 105 lked 108
                                       +k+ 
  gi|242399017|ref|YP_002994441.1|  84 MKKQ 87 
                                       9986 PP

>> SSF  Sodium:solute symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   2.7   1.5e-05     0.027     121     194 ..       8      88 ..       3     109 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.5e-05
                               SSF 121 etavlllaaltalYtviGGllAvvytdt.....iqavlmlvgalilliivllevGgleslveklkeaapkvvdl..l 190
                                       ++  ++++ ++ +++++GG+ Avv   t     +q  l+++  ++++ii+l +++  e++ +  k+a+   + l  +
  gi|242399017|ref|YP_002994441.1|   8 NIKTIIMIFAIGMFVLVGGITAVVGAKTkddtaLQFALVMANIVMVSIIALQAIATAEAVEQAKKQAELMNQSLleM 84 
                                       55567888999************987654444578888888888889999999997776666666665544333223 PP

                               SSF 191 tpds 194
                                       +++ 
  gi|242399017|ref|YP_002994441.1|  85 KKQR 88 
                                       3333 PP

>> DUF2975  Protein of unknown function (DUF2975)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   3.8   4.8e-05     0.086      59     122 ..       9      72 ..       5      80 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.8e-05
                           DUF2975  59 LrriglaliaaalllaagivalallaelelapgvvllllgvafaslvigllvlvlaellaeAvk 122
                                       +++i+++ ++ +++l++gi+a+ +++  ++  +++ l++ +++++ +i+l +++ ae  ++A k
  gi|242399017|ref|YP_002994441.1|   9 IKTIIMIFAIGMFVLVGGITAVVGAKTKDDTALQFALVMANIVMVSIIALQAIATAEAVEQAKK 72 
                                       68899999999***************988888*****************************977 PP

>> DUF3990  Protein of unknown function (DUF3990)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   6.9e-05      0.12      37     103 ..      59     124 ..      53     135 .. 0.85
   2 ?   -3.0   0.1       2.9   5.3e+03      32      65 ..     195     228 ..     194     232 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.9e-05
                           DUF3990  37 qAkewakrkskrkgkkevvnvyeldedelkklkikkfekadeeWldfvvknRkgkketeeyDiviGp 103
                                       qA   a++ ++ k++ e +n+  l++++ ++l+i++f+++ +  l+ v+   + +++ ++yDi+++p
  gi|242399017|ref|YP_002994441.1|  59 QAIATAEAVEQAKKQAELMNQSLLEMKK-QRLNIEEFKNSLMPYLRSVILTLEANSKRKDYDIITDP 124
                                       7777777777666777778887777777.66*********************************986 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.9
                           DUF3990  32 teskeqAkewakrkskrkgkkevvnvyeldedel 65 
                                       t++ke  ke+ k+ ++  ++ e+++  el+e+ l
  gi|242399017|ref|YP_002994441.1| 195 TRIKEKSKELLKTVESIFDEVEKMSNKELEEEIL 228
                                       5666666666666665555555555555555544 PP

>> STE3  Pheromone A receptor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   6.8e-05      0.12      20      90 ..       6      77 ..       4     123 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.8e-05
                              STE3 20 arnigalllilwllllnlisfvnaiiWsgnvvdkapvwCDisskliiaasvglpa.allcIvrrLykilslr 90
                                      + ni ++++i+ + +  l+  + a++ +++  d+a ++  +++++++++ ++l+a a++  v +  k+++l 
  gi|242399017|ref|YP_002994441.1|  6 NTNIKTIIMIFAIGMFVLVGGITAVVGAKTKDDTALQFALVMANIVMVSIIALQAiATAEAVEQAKKQAELM 77
                                      67******************************************9999999998724555555566666644 PP

>> REC1  Alpha helical recognition lobe domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1      0.69   1.2e+03      93      93 ..      83      83 ..      49     125 .. 0.51
   2 ?   12.3   3.3   6.6e-05      0.12      13      81 ..     154     231 ..     151     233 .] 0.77

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.69
                              REC1 93 k 93
                                      +
  gi|242399017|ref|YP_002994441.1| 83 E 83
                                      1 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 6.6e-05
                              REC1  13 kfideaLeslkldeeslqeflellekqkke.......dkekkelnkaekklrkeivkifkkkekk..adekkkkykk 80 
                                        fi++ Le   l+++ ++e+ +l+ k k +        +++  +++++k+l k +++if ++ek+  ++++++ +k+
  gi|242399017|ref|YP_002994441.1| 154 VFIKKFLELRGLSWQRFEEYNKLVSKFKDSktsqsekPGLATRIKEKSKELLKTVESIFDEVEKMsnKELEEEILKI 230
                                       69*********************998876677777766677789999999999999999995555435556665555 PP

                              REC1  81 l 81 
                                       l
  gi|242399017|ref|YP_002994441.1| 231 L 231
                                       5 PP

>> DASH_Dad4  DASH complex subunit Dad4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.3   0.00016      0.29      19      70 ..      66     117 ..      61     118 .. 0.92
   2 ?   -1.2   0.1       1.1     2e+03      18      38 ..     206     219 ..     192     230 .. 0.48

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00016
                         DASH_Dad4  19 nvekLnesvvelnkeleeinkkNknvelvsqlwenYqrnvqfnLeatgelke 70 
                                        ve+  ++ + +n++l e++k+  n+e +++ +  Y r+v   Lea +++k+
  gi|242399017|ref|YP_002994441.1|  66 AVEQAKKQAELMNQSLLEMKKQRLNIEEFKNSLMPYLRSVILTLEANSKRKD 117
                                       58888889999**********************************9998875 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.1
                         DASH_Dad4  18 knvekLnesvvelnkeleein 38 
                                       k+ve + + v+++       +
  gi|242399017|ref|YP_002994441.1| 206 KTVESIFDEVEKM-------S 219
                                       2333333333333.......2 PP

>> EF-G-binding_N  Elongation factor G-binding protein, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.5       0.1   1.8e+02      39      79 ..      65     102 ..      50     105 .. 0.61
   2 ?    9.1   2.1    0.0011       1.9      18      76 ..     174     232 ..     168     233 .] 0.89

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.1
                    EF-G-binding_N  39 ekIlelfpelseeqkelLeq.iddik.tkekaeklLeeLkeyV 79 
                                       e +++      ++q+el++q + + k ++ ++e++ ++L +y 
  gi|242399017|ref|YP_002994441.1|  65 EAVEQ-----AKKQAELMNQsLLEMKkQRLNIEEFKNSLMPYL 102
                                       33333.....344444443325566669999999999999986 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0011
                    EF-G-binding_N  18 lnayrsvnDkkvveavkalaaekIlelfpelseeqkelLeqiddiktkekaeklLeeLk 76 
                                       ++  +  +D+k+ +  k  +a++I+e  +el +  +++++++++ ++ke  e++L+ L+
  gi|242399017|ref|YP_002994441.1| 174 NKLVSKFKDSKTSQSEKPGLATRIKEKSKELLKTVESIFDEVEKMSNKELEEEILKILE 232
                                       66677889**************************************9999999998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2228  (0.124268); expected 358.6 (0.02)
Passed bias filter:                      822  (0.0458475); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 1578.61
//
Query:       gi|242399018|ref|YP_002994442.1|  [L=155]
Description: hypothetical protein TSIB_1037 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score 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   13.7   1.2       0.17   12.2   0.4    2.0  2  GAT       GAT domain
      0.063   13.1   1.7       0.62    9.9   0.3    2.2  2  SKA2      Spindle and kinetochore-associated protein 2
      0.068   13.7   6.0        2.5    8.6   1.3    2.1  2  FlgN      FlgN protein
       0.24    9.8   0.0       0.31    9.5   0.0    1.1  1  DcuC      C4-dicarboxylate anaerobic carrier


Domain annotation for each model (and alignments):
>> GAT  GAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.34   1.5e+03      23      47 ..      34      58 ..      23      69 .. 0.62
   2 ?   12.2   0.4   3.8e-05      0.17       5      46 ..     111     152 ..     107     155 .] 0.82

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.34
                               GAT 23 nellkeLyetckamqpriqklieet 47
                                      + l++ L +++ a ++ i   ++++
  gi|242399018|ref|YP_002994442.1| 34 ERLINTLKSELNANRRLIESNLNSL 58
                                      4566666666666666555555554 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 3.8e-05
                               GAT   5 klLsemLsstepdeellenellkeLyetckamqpriqkliee 46 
                                       +lL++ L+      +++++e +++L +++ ++ +ri+klie+
  gi|242399018|ref|YP_002994442.1| 111 NLLQQALTYNFVALTDKNKESMEDLLKRIDSLIERIIKLIEK 152
                                       789999997632335689***********************9 PP

>> SKA2  Spindle and kinetochore-associated protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1     0.026   1.2e+02      67      88 ..      32      53 ..      27      65 .. 0.81
   2 ?    9.9   0.3   0.00014      0.62       5      59 ..      97     151 ..      93     155 .] 0.84

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.026
                              SKA2 67 ekkelidkirttlvanrellqq 88
                                      ++++li+++++ l+anr l+++
  gi|242399018|ref|YP_002994442.1| 32 TRERLINTLKSELNANRRLIES 53
                                      68899***********999875 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00014
                              SKA2   5 dklealFqkaesdLdyvqhrLekefqqsypdnaeNpvkLlerlkkvkeelqaLke 59 
                                       +++ a  ++a    +++q+ L + f + +++n+e +  Ll+r+  + e++ +L e
  gi|242399018|ref|YP_002994442.1|  97 EEIIAGIYSAIDSFNLLQQALTYNFVALTDKNKESMEDLLKRIDSLIERIIKLIE 151
                                       555566667777889******************9999*********999988866 PP

>> FlgN  FlgN protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.2    0.0011       4.8      98     126 ..      35      63 ..      28      75 .. 0.88
   2 ?    8.6   1.3   0.00055       2.5       5      57 ..      97     149 ..      94     154 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0011
                                       HHHHHHHHHHHHHHHHHHHCCHHHHHHHH CS
                              FlgN  98 elleelkelnelNgrlieqslefnqrlln 126
                                        l+++lk    +N+rlie +l++++++ +
  gi|242399018|ref|YP_002994442.1|  35 RLINTLKSELNANRRLIESNLNSLKQSSD 63 
                                       689999*****************999876 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00055
                                       CHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHH CS
                              FlgN   5 eeLielleeelelleeLlelleeEteaLkagdieaLeelleekqellekleql 57 
                                       ee+i+ +   ++ ++ L++ l   + aL++++ e++e+ll+++ +l+e++ +l
  gi|242399018|ref|YP_002994442.1|  97 EEIIAGIYSAIDSFNLLQQALTYNFVALTDKNKESMEDLLKRIDSLIERIIKL 149
                                       66677777777888999*******************************99776 PP

>> DcuC  C4-dicarboxylate anaerobic carrier
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   6.8e-05      0.31     197     240 ..       6      53 ..       2      71 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 6.8e-05
                              DcuC 197 ivlrllvlviltlisiaflyfYakkikkdp....vysekdeskelfsk 240
                                       ++l+ll+ +i +li++ + ++Y ++  +++    + se +++++l + 
  gi|242399018|ref|YP_002994442.1|   6 FFLTLLAGAITALIGVHIQHWYSSRKTRERlintLKSELNANRRLIES 53 
                                       6889999*********************99555434444444444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1586  (0.08846); expected 358.6 (0.02)
Passed bias filter:                      933  (0.0520386); expected 358.6 (0.02)
Passed Vit filter:                        97  (0.00541023); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.48
# Mc/sec: 973.36
//
Query:       gi|242399019|ref|YP_002994443.1|  [L=169]
Description: hypothetical protein TSIB_1038 [Thermococcus sibiricus MM 739]
Scores for complete 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  132.9   4.7    1.4e-38  132.8   4.7    1.0  1  DUF257    Pyrococcus protein of unknown function, DUF257


Domain annotation for each model (and alignments):
>> DUF257  Pyrococcus protein of unknown function, DUF257
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.8   4.7   7.9e-43   1.4e-38      42     204 ..       3     166 ..       1     167 [. 0.95

  Alignments for each domain:
  == domain 1  score: 132.8 bits;  conditional E-value: 7.9e-43
                            DUF257  42 vdDvlDtllivlkhlkllGldvpe.esikviKigGtkevgnvvkkidfdkdpsiylskykravekvsveetv.inlv 116
                                       + D lDtl++++ +l+l+G d++  +++kviK+gG  +vg+v++++ ++ +p i  ++y+++++ +++e +v + lv
  gi|242399019|ref|YP_002994443.1|   3 IVDFLDTLYLYKAQLELAGEDTSFlNDVKVIKVGGRLNVGQVIERLRVKDEPIILAQEYTKILNSLVKEGEVaVVLV 79 
                                       789********************99********************************************7777**** PP

                            DUF257 117 lglerllllldnrrdlyklvksikkylgnknRkafylinrnllesikPellplLEeiassvieiesekealivrilK 193
                                       lg+e++ ++l+ ++ l+  ++++ +++g+++R+ fy+in+++le   Pe+lplLE+i ++v++i+++++  ++ ++K
  gi|242399019|ref|YP_002994443.1|  80 LGIEKFAPILELEKVLT-GINALLSFVGDERRIMFYFINTDVLERAIPEVLPLLEDIGTTVVRINVVEKSYTFSVVK 155
                                       *********98666555.9********************************************************** PP

                            DUF257 194 slnldivgtti 204
                                       ++n +i+g ++
  gi|242399019|ref|YP_002994443.1| 156 TINRKILGLKV 166
                                       ******99776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1069.64
//
Query:       gi|242399020|ref|YP_002994444.1|  [L=59]
Description: hypothetical protein TSIB_1039 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.025   14.0   1.3      0.026   13.9   1.3    1.1  1  EII-Sor   PTS system sorbose-specific iic component


Domain annotation for each model (and alignments):
>> EII-Sor  PTS system sorbose-specific iic component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   1.3   1.4e-06     0.026     176     212 ..      10      42 ..       2      55 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.4e-06
                           EII-Sor 176 kgLsvaGglLpavGfAmllkvmlkkkllpffllGFvl 212
                                       +g+++ G+ L++vG+A+l     ++kl+ ++++GF l
  gi|242399020|ref|YP_002994444.1|  10 TGFQTLGAGLVVVGIALL----NSNKLIGMLFIGFGL 42 
                                       79**************86....78999*******976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.26s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 435.55
//
Query:       gi|242399021|ref|YP_002994445.1|  [L=61]
Description: hypothetical protein TSIB_1040 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 436.38
//
Query:       gi|242399022|ref|YP_002994446.1|  [L=382]
Description: ATP-dependent RNA helicase, DEAD-family [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-48  165.0   0.0    3.2e-48  163.8   0.0    1.6  2  DEAD           DEAD/DEAH box helicase
    3.8e-34  117.4   0.2    6.7e-31  106.9   0.1    3.4  3  Helicase_C     Helicase conserved C-terminal domain
    3.5e-09   36.9   0.0    6.6e-09   36.0   0.0    1.4  1  ResIII         Type III restriction enzyme, res subunit
     0.0042   16.5   0.0     0.0089   15.4   0.0    1.6  1  CMS1           U3-containing 90S pre-ribosomal complex subuni
  ------ inclusion threshold ------
      0.025   13.4   0.0       0.24   10.1   0.0    2.0  2  UTP25          Utp25, U3 small nucleolar RNA-associated SSU p
      0.025   13.8   0.0      0.039   13.2   0.0    1.2  1  ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
      0.048   13.1   0.1        2.2    7.7   0.0    2.2  2  SMC_N          RecF/RecN/SMC N terminal domain


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.8   0.0   1.2e-51   3.2e-48       1     173 [.      25     189 ..      25     192 .. 0.94
   2 ?   -2.8   0.0       1.8   4.6e+03      76     104 ..     264     296 ..     243     301 .. 0.55

  Alignments for each domain:
  == domain 1  score: 163.8 bits;  conditional E-value: 1.2e-51
                                       -HHHHHHHHHHHTTC.EEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTS CS
                                       xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   1 tdiQaeaiplilggg.dvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidl 76 
                                       tdiQ+e+ip +l+g+ d++++ +TG+GKT+af++p+++ + e  + ++ +a++++PtreLa q++++++++  + ++
  gi|242399022|ref|YP_002994446.1|  25 TDIQKEVIPRLLRGDnDIIGQSQTGTGKTAAFALPLIELIDE--EIKEVQAIVITPTRELAIQVADEIRSLRGKRRI 99 
                                       89**********6644*********************99955..99999************************9999 PP

                                       EEEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  77 rvlliiggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqit 153
                                       +vl ++gg++   q+++l++gv+ivvgtpgr++d++++g+l+l+ v++++lDEadr+ld+gf ++i+ril+++    
  gi|242399022|ref|YP_002994446.1| 100 NVLPVYGGQPIGPQIRNLRRGVHIVVGTPGRVIDHIERGTLSLDGVSYFILDEADRMLDMGFIEDIERILRHT---- 172
                                       *************************************************************************.... PP

                                       TTSTTTSEEEEEESSBSHHH CS
                                       xxxxxxxxxxxxxxxxxxxx RF
                              DEAD 154 cdgklqrqvivlSATlpkdv 173
                                          +++++v+++SAT+p+++
  gi|242399022|ref|YP_002994446.1| 173 ---SEEKRVLMFSATIPREI 189
                                       ...34567*********876 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.8
                                       SEEEEE...ETTSSHHHHHHHHHTT.CSEEEEE CS
                                       xxxxxx...xxxxxxxxxxxxxxxx.xxxxxxx RF
                              DEAD  76 lrvlli...iggvaardqlskldng.vdivvgt 104
                                       ++v+++   i ++ +++ l+++++g ++++v+t
  gi|242399022|ref|YP_002994446.1| 264 YSVEALngdIPQKGRERILERFRKGkIRVLVAT 296
                                       333333112446666777777766667777777 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 ?    4.4   0.0     0.018        46       5      51 ..      59     109 ..      55     122 .. 0.79
   2 ?    2.6   0.0     0.068   1.7e+02       3      46 ..     162     205 ..     160     234 .. 0.66
   3 !  106.9   0.1   2.6e-34   6.7e-31       6     110 ..     231     333 ..     225     334 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.018
                                       HHHHHHHHTTTTSEEEEEESSHH...HHHH...HHHHHHHTTSTEEEESTTST CS
                        Helicase_C   5 allellkleeeggkilifvntid...rlek...vklllekkgikvavlhgelp 51 
                                        l+el+++e ++ +++++++t++   +      ++ l+ k+ i+v++++g  p
  gi|242399022|ref|YP_002994446.1|  59 PLIELIDEEIKEVQAIVITPTRElaiQ--VadeIRSLRGKRRINVLPVYGGQP 109
                                       5788999999999**********8663..2335899988999*****999866 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.068
                                       HHHHHHHHHHTTTTSEEEEEESSHH....HHHHHHHHHHHTTSTEEEE CS
                        Helicase_C   3 leallellkleeeggkilifvntid....rlekvklllekkgikvavl 46 
                                       +e + ++l +++e++++l+f+ ti     rl   ++l+   +++v+++
  gi|242399022|ref|YP_002994446.1| 162 IEDIERILRHTSEEKRVLMFSATIPreilRLA-RRYLK---DYEVIRI 205
                                       567788888999************96433332.45552...3444444 PP

  == domain 3  score: 106.9 bits;  conditional E-value: 2.6e-34
                                       HHHHHHHTTTTSEEEEEESSHHHHHH.HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSST CS
                        Helicase_C   6 llellkleeeggkilifvntidrlek.vklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGid 81 
                                       l+ +l   e++   ++f++t+++  + ++ l ++kg++v +l+g++pq+ re+ile+f+kg+++vL+atdva+rGid
  gi|242399022|ref|YP_002994446.1| 231 LCSIL--DEKDFYGIVFCQTKRETRElASKL-KTKGYSVEALNGDIPQKGRERILERFRKGKIRVLVATDVAARGID 304
                                       55554..56666679*******886534444.6779***************************************** PP

                                       STTESEEEESSSSSSHHHHHHHHTTSSST CS
                        Helicase_C  82 ipkvnlVinfdlprnvtsyiqriGRtgRa 110
                                       ++++++Vin+++p+n++ y++riGRtgR 
  gi|242399022|ref|YP_002994446.1| 305 VKDLTHVINYSIPQNPEAYVHRIGRTGRE 333
                                       ****************************6 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   0.0   2.6e-12   6.6e-09       4     170 ..      24     186 ..      21     187 .. 0.83

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 2.6e-12
                                       E-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHH.HHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTG CS
                            ResIII   4 lreyQeeaienlleklkskrdkrglikmaTGtGKTlva.aklierllkkgkeekflflvprkslleqtleefkkfls 79 
                                       + + Q+e+i +ll     ++d+ ++ +  TGtGKT    + lie + ++ ke +++++ p+++l  q  +e++++  
  gi|242399022|ref|YP_002994446.1|  24 PTDIQKEVIPRLL-----RGDNDIIGQSQTGTGKTAAFaLPLIELIDEEIKEVQAIVITPTRELAIQVADEIRSLRG 95 
                                       5677888888887.....89999999*********999789999999999999************************ PP

                                       G.........GEEEESSS-B--........-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.... CS
                            ResIII  80 eayke.....igkkvsgdkkka.kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgak... 147
                                       + + +           g+   +  ++ +   +i+v t  ++  ++     e+ +l+ d   ++i DEa r+ ++   
  gi|242399022|ref|YP_002994446.1|  96 KRRINvlpvyG-----GQPIGPqIRNLRRGVHIVVGTPGRVIDHI-----ERGTLSLDGVSYFILDEADRMLDMgfi 162
                                       99866554432.....332222334457899**************.....8999999*****************666 PP

                                       TTTHHHHHT---.SEEEEEESS-S CS
                            ResIII 148 kswreilekfke.avllglTATpe 170
                                       + +++il++ +e + +l ++AT++
  gi|242399022|ref|YP_002994446.1| 163 EDIERILRHTSEeKRVLMFSATIP 186
                                       6888888887555999******97 PP

>> CMS1  U3-containing 90S pre-ribosomal complex subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   3.5e-06    0.0089     177     210 ..     120     153 ..      79     172 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.5e-06
                              CMS1 177 rigiavGtpgRildLleeeslsvdeLkrivlDas 210
                                        + i vGtpgR++d +e ++ls+d + + +lD +
  gi|242399022|ref|YP_002994446.1| 120 GVHIVVGTPGRVIDHIERGTLSLDGVSYFILDEA 153
                                       37799**************************965 PP

>> UTP25  Utp25, U3 small nucleolar RNA-associated SSU processome protein 25
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0     0.058   1.5e+02      67     100 ..      62      95 ..      39     101 .. 0.83
   2 ?   10.1   0.0   9.5e-05      0.24     349     418 ..     258     325 ..     242     357 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.058
                             UTP25  67 elrdqgftrpkvLillptreaalevvelllklle 100
                                       el d+  +  + +++ ptre a++v +++ +l +
  gi|242399022|ref|YP_002994446.1|  62 ELIDEEIKEVQAIVITPTRELAIQVADEIRSLRG 95 
                                       677888899999*************999987765 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 9.5e-05
                             UTP25 349 ylkeekvsfaaiseysskkevsraRelFfkgkkkvlLyteRlhffrRykikgvkkvilYklPenpefyse 418
                                        lk++ +s  a++    +k  +r  e F kgk +vl+ t+ +   r  ++k+  +vi Y++P+npe y  
  gi|242399022|ref|YP_002994446.1| 258 KLKTKGYSVEALNGDIPQKGRERILERFRKGKIRVLVATDVAA--RGIDVKDLTHVINYSIPQNPEAYVH 325
                                       56777777777777788888899999**************885..99*******************9965 PP

>> ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.5e-05     0.039      64     149 ..     243     331 ..     217     348 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.5e-05
                     ERCC3_RAD25_C  64 ivfsDnvfaLkeyakklkkp.....yiyGetseaerlkilqkfkknpkvntiflskvgDtsiDlPeanvliqisshf 135
                                       ivf+      +e+a+klk +      + G+++++ r +il++f+k  k+++++   v+   iD+ + + +i  s  +
  gi|242399022|ref|YP_002994446.1| 243 IVFCQTKRETRELASKLKTKgysveALNGDIPQKGRERILERFRKG-KIRVLVATDVAARGIDVKDLTHVINYSIPQ 318
                                       8888888888999999875322222689****************87.89*******************999987654 PP

                     ERCC3_RAD25_C 136 gsrrqeaqrlGriL 149
                                               r+Gr  
  gi|242399022|ref|YP_002994446.1| 319 NPE-AYVHRIGRTG 331
                                       432.2345666655 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 ?    3.0   0.0     0.023        60     180     207 ..      61      89 ..      57      99 .. 0.76
   2 ?    7.7   0.0   0.00084       2.2     159     197 ..     145     183 ..     139     202 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.023
                                       HHHHHHHCTTSEEEEE-SSHHHC.CC-SC CS
                                       xxxxxxxxxxxxxxxxxxxxxxx.xxxxx RF
                             SMC_N 180 aellkeksknaQfivislreeml.ekadk 207
                                        el++e+ k++Q ivi+ ++e+  + ad+
  gi|242399022|ref|YP_002994446.1|  61 IELIDEEIKEVQAIVITPTRELAiQVADE 89 
                                       6899*************877764044455 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00084
                                       -SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 159 aplyllDeidaaLDeknvkkvaellkeksknaQfivisl 197
                                        + ++lDe d  LD   ++ + ++l+++s++  +++ s 
  gi|242399022|ref|YP_002994446.1| 145 VSYFILDEADRMLDMGFIEDIERILRHTSEEKRVLMFSA 183
                                       6779***********************999988887654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 2362.35
//
Query:       gi|242399023|ref|YP_002994447.1|  [L=576]
Description: Metallophosphoesterase, calcineurin superfamily [Thermococcus sibiricus MM 739]
Scores for complete 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   48.1   1.5    4.5e-12   46.9   1.5    1.7  1  Metallophos    Calcineurin-like phosphoesterase
    1.8e-05   25.0   0.0    3.4e-05   24.1   0.0    1.4  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
  ------ inclusion threshold ------
      0.052   13.1   0.0      0.094   12.2   0.0    1.4  1  DUF1833        Domain of unknown function (DUF1833)
      0.075   13.3   4.1       0.12   12.6   4.1    1.2  1  Shisa          Wnt and FGF inhibitory regulator
        1.2    7.5  10.6        1.8    6.8  10.6    1.2  1  DUF515         Protein of unknown function (DUF515)
        4.3    6.5   9.2        6.7    5.9   9.2    1.2  1  Med13_C        Mediator complex subunit 13 C-terminal domain
        5.5    7.4  13.5        8.7    6.8  13.5    1.2  1  MGC-24         Multi-glycosylated core protein 24 (MGC-24), s


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 !   46.9   1.5   1.8e-15   4.5e-12       1     204 []     349     527 ..     349     527 .. 0.59

  Alignments for each domain:
  == domain 1  score: 46.9 bits;  conditional E-value: 1.8e-15
                                       EEEEEEESBTB...TTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHHTSEEEEEC-TT CS
                       Metallophos   1 lrilvigDlHl...algggqlddllkllddllreekpdlvllaGDlvdrgdlekellellaalvkypipvylllGNH 74 
                                       +++l +gD+      ++++ + ++    +dl ++ +  +++  GDlv+ g +e+ ++ell++    ++pv++++GNH
  gi|242399023|ref|YP_002994447.1| 349 FTFLAFGDHRPgsgTEQPEVFFKI----RDLMNHDEGAFIINSGDLVYSGKVEE-WAELLKEWTF-NKPVFVVPGNH 419
                                       577888888733333333333333....444444577888888***********.8888666666.49********* PP

                                       SCHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEEESECEEETHHHHHHHHHHHSCHHHHCCHHHH CS
                       Metallophos  75 egfeeellnkygylgifsepwrsdaevfnnlplaslgsgslkvlllhGgspellvsldklgslnleleapepgdewl 151
                                       e ++ e +n y              ++f+    +  + g  k+++++ +      ++++      + + + +++ wl
  gi|242399023|ref|YP_002994447.1| 420 E-YRGEGKNIYH-------------KFFGPTDYSF-VLG--KYYFIFTN------NVEN------DYRLTSSQWAWL 467
                                       *.4445455433.............3343333333.344..44444444......1111......22222222**** PP

                                       HH..HHHHTTCSEEEEEESSESS...CSSSCSCCHHHHHHH.HHHTTESEE.EEESSSSE CS
                       Metallophos 152 kd..lekrekadwvivlgHsply...rgsgylfgdealedl.lkkygvdlv.isGHtHvy 204
                                       +    ++++ +++ i+  H p+      + + ++ +++++l +  +  d+  ++GH+H y
  gi|242399023|ref|YP_002994447.1| 468 ESelEKAKRLGKIPIISMHAPPIdprPEGDHAMDTNHAKKLlELMKAYDAFgLFGHIHIY 527
                                       **995555555555555566666587666666777777766444444666569*****87 PP

>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   1.3e-08   3.4e-05      13     155 ..     369     552 ..     350     564 .. 0.71

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1.3e-08
                     Metallophos_2  13 ldaleavlealkevgvdaiihaGDl.eeeepevleellela....pvlaVrGNnD...................... 62 
                                       ++ ++ ++++ +++    ii++GDl + ++ e  +ell+      pv +V+GN++                      
  gi|242399023|ref|YP_002994447.1| 369 FFKIRDLMNHDEGA---FIINSGDLvYSGKVEEWAELLKEWtfnkPVFVVPGNHEyrgegkniyhkffgptdysfvl 442
                                       55666667776666...9******998888877777776667788**********9999999999999999888888 PP

                     Metallophos_2  63 .......eevveedvlreaaelgtdlpeeaele.lagekvlliHgdpl.........gvkdalaellkeaeegsdvv 122
                                               + ve+d    + +++    e ++ + l++  +  +H  p           ++++ ++ll+ +++ +++ 
  gi|242399023|ref|YP_002994447.1| 443 gkyyfifTNNVENDYRLTSSQWAWLESELEKAKrLGKIPIISMHAPPIdprpegdhaMDTNHAKKLLELMKAYDAFG 519
                                       866665533333333333333333333222222135666888999877****99986555555555555555666** PP

                     Metallophos_2 123 vcGHtHvpevekeggvlvvnPGsvgeprdgdpe 155
                                       ++GH+H+    +++gv +v  G  g p +++p 
  gi|242399023|ref|YP_002994447.1| 520 LFGHIHIYWYGEKDGVEMVITGGGGAPLYAKPD 552
                                       ******************999999998888776 PP

>> DUF1833  Domain of unknown function (DUF1833)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   3.7e-05     0.094      16      84 ..     247     319 ..     235     339 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.7e-05
                           DUF1833  16 levlEith.qdfsepirvvkdtddlTaalea.....GkvvvftalaldlalPaededkvpeltlildNvgsvitd 84 
                                         + Ei+  + f+   r+v++ +++T+ +       G +v  tal+++++   +d ++v ++t +++N++    +
  gi|242399023|ref|YP_002994447.1| 247 WTLQEIYVeEPFIYNWRIVNG-ENITVSGGFirlvnGSKVHITALGFNVSVKIRDPKNV-QITYVIENINPSFVE 319
                                       555666541457888888887.56886655455566***************99998877.6********876555 PP

>> Shisa  Wnt and FGF inhibitory regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   4.1   4.6e-05      0.12      95     164 ..       5      79 ..       2      97 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.6e-05
                             Shisa  95 vfvivgvvvivcccgclkkkqrekr.....pgrenlssalaev..gpivte.ttsattvvhsrysepqqssssssyp 163
                                         vi++ v i+++ ++  ++++e+      + + n s+ + e+   p +t+ tt+++  v+s+    ++++++s+ p
  gi|242399023|ref|YP_002994447.1|   5 WVVILIGVLILASGCVQSPTSTESVstpttTSPTNSSQTQIETspSPSPTQtTTTTSSTVPSST---STTQTTSQKP 78 
                                       4566666666666555556665554666445556666666666443555543444444444444...4444444444 PP

                             Shisa 164 g 164
                                       g
  gi|242399023|ref|YP_002994447.1|  79 G 79 
                                       4 PP

>> DUF515  Protein of unknown function (DUF515)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8  10.6   0.00071       1.8     306     364 ..      20      78 ..       4      94 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.00071
                            DUF515 306 agsisvSEsqsqsssvseesstsssessstsespGdvsisdsssasdsssvsqstsesl 364
                                         s +  Es s+ +++s + s+ ++  +s s sp +++ + ss+  +s s++q+ts+  
  gi|242399023|ref|YP_002994447.1|  20 VQSPTSTESVSTPTTTSPTNSSQTQIETSPSPSPTQTTTTTSSTVPSSTSTTQTTSQKP 78 
                                       44556789999999999999988888889***************************964 PP

>> Med13_C  Mediator complex subunit 13 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   9.2    0.0026       6.7     156     209 ..      22      76 ..      12     109 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0026
                           Med13_C 156 srfgqsssstplst.Pqdsscthilvfptsattqstpttfasedanaedtpedss 209
                                       s ++++s+stp +t P  ss+t+i + p+   tq+t+tt+++ ++++++t++ s+
  gi|242399023|ref|YP_002994447.1|  22 SPTSTESVSTPTTTsPTNSSQTQIETSPSPSPTQTTTTTSSTVPSSTSTTQTTSQ 76 
                                       5556677899999999999999999888877778888888888877777532222 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 ?    6.8  13.5    0.0034       8.7      42     112 ..      18      88 ..      14      92 .. 0.58

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0034
                            MGC-24  42 dCsv.vnvtelcsaaskstpkptnstaktttkpsstttstsvatsgttnttvtptsqparkstFDaAsFiGG 112
                                       +C +  ++te++s+ ++++p+++++t   t+ + s+t++t++++s+ +++t t ++ +++k++ D  s+  G
  gi|242399023|ref|YP_002994447.1|  18 GCVQsPTSTESVSTPTTTSPTNSSQTQIETSPSPSPTQTTTTTSSTVPSSTSTTQT-TSQKPGIDFSSYKKG 88 
                                       56441455666777677767766555544444444444444445555666655555.569999999998655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (576 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       923  (0.0514808); expected 358.6 (0.02)
Passed bias filter:                      606  (0.0338); expected 358.6 (0.02)
Passed Vit filter:                       108  (0.00602376); 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: 0.80u 0.32s 00:00:01.12 Elapsed: 00:00:00.52
# Mc/sec: 3348.01
//
Query:       gi|242399024|ref|YP_002994448.1|  [L=411]
Description: phosphate permease [Thermococcus sibiricus MM 739]
Scores for complete 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-110  368.7  37.5   3.1e-110  368.4  37.5    1.1  1  PHO4      Phosphate transporter family
     0.0019   18.7   3.5       0.04   14.4   0.0    3.8  3  Ytca      Uncharacterised protein family
  ------ inclusion threshold ------
      0.084   12.4   1.0       0.29   10.6   1.0    1.9  1  SieB      Super-infection exclusion protein B
      0.089   12.4   5.8        1.6    8.3   0.1    3.0  2  INSIG     Insulin-induced protein (INSIG)


Domain annotation for each model (and alignments):
>> PHO4  Phosphate transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  368.4  37.5    7e-114  3.1e-110       1     337 []      27     400 ..      27     400 .. 0.88

  Alignments for each domain:
  == domain 1  score: 368.4 bits;  conditional E-value: 7e-114
                              PHO4   1 iGanDvanafatsvgskaltlrqAvilaaifeflGavllGaeVaetirkgivdvelf.dpselmlgmlaallgaavw 76 
                                       iGanD+an+++t+vg++a+t++qAv++a+++ef+Ga+l+G++V+et+rkgi+d +++ dp+++++g +aall+a +w
  gi|242399024|ref|YP_002994448.1|  27 IGANDAANSMSTAVGAGAITPKQAVLIAGVLEFIGAYLFGKSVTETVRKGIIDASQIsDPNVIVYGSIAALLAASLW 103
                                       7*****************************************************9666******************* PP

                              PHO4  77 lllatvlglPvStthslvGaliGaalaaeggeavkwkklvkivlswvlsPllggiiaallfllvkrlilvk.eklkn 152
                                       ll+a+ +glPvStths++G+++G ++a++g++ v+w+k++++v+swvlsPl g+++a++++ lv ++il++ +++++
  gi|242399024|ref|YP_002994448.1| 104 LLFASKFGLPVSTTHSIIGGIVGYGIAYAGTSIVNWSKMAQVVASWVLSPLFGAVVAFVIIKLVSKTILQQkNPIES 180
                                       ****************************999**************************************878***** PP

                              PHO4 153 alralpvlvlvtiailalsilfk............................ge....sk.kddeeteklfkflqvvs 196
                                       a++++pv + + ++++  ++ +k                                  +  +    +e +f+++qv++
  gi|242399024|ref|YP_002994448.1| 181 AKKWAPVWIGLAFVVIGSMFHIKvmhgnsllialsrygvtagigaflisyaLLkrnfQAtDPYWGAEAIFRKVQVLT 257
                                       ********8888777777766664444444444444444444444433333223222113444456667******** PP

                              PHO4 197 aalvsfahGanDvanaiGpllaalisiyk...a.sk.evplwvlllgglaialGlllgGkrviktvGekitkkltps 268
                                       +a+v+++hGanDvanaiGp+ aa++ + +   +  k +vp w+l++ggl+ia+G++++G++v++tvG+kit+ lt++
  gi|242399024|ref|YP_002994448.1| 258 SAYVALSHGANDVANAIGPV-AAVYAVATmglTgMKvPVPRWILAMGGLGIAIGVATYGYKVMETVGKKITE-LTNT 332
                                       ********************.99998888775367778899******************************5.**** PP

                              PHO4 269 rGfaaelaaaltvllasklglPvStThvlvgavvGvGlakkresavnwklvrnivlaWvlTlpvsalls 337
                                       rGf+++++aa++vl+as+lglP+StTh++vgav+GvGla+ + +a+n  +v++i+++W++T+pv+a+l+
  gi|242399024|ref|YP_002994448.1| 333 RGFSIDFSAATVVLIASWLGLPISTTHTVVGAVIGVGLAR-GVKAINKDIVKDIIISWFVTVPVAAILA 400
                                       ****************************************.79***********************986 PP

>> Ytca  Uncharacterised protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   8.8e-06      0.04      32      61 ..      77     106 ..      60     107 .. 0.78
   2 ?   -0.9   0.1      0.55   2.5e+03      13      37 ..     148     172 ..     144     179 .. 0.79
   3 ?    2.2   0.3     0.061   2.7e+02      13      32 ..     388     407 ..     378     410 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 8.8e-06
                              Ytca  32 lvrlkleleplvlvYpclviflavllWlil 61 
                                       +      + p v+vY +++++la +lWl++
  gi|242399024|ref|YP_002994448.1|  77 IIDASQISDPNVIVYGSIAALLAASLWLLF 106
                                       4444445789******************98 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.55
                              Ytca  13 aWllClaiaiaLtlvvrlvlvrlkl 37 
                                       +W+l  + +++ ++v+  ++ ++ l
  gi|242399024|ref|YP_002994448.1| 148 SWVLSPLFGAVVAFVIIKLVSKTIL 172
                                       7999999999999999888888765 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.061
                              Ytca  13 aWllClaiaiaLtlvvrlvl 32 
                                       +W++ + +a++L+ ++  +l
  gi|242399024|ref|YP_002994448.1| 388 SWFVTVPVAAILAGIMFKIL 407
                                       8************9998877 PP

>> SieB  Super-infection exclusion protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   1.0   6.4e-05      0.29       5      52 ..     158     206 ..     155     216 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 6.4e-05
                              SieB   5 iiasglllllPdsllekln.lgkfleeyglwiglvflisiayllaqvvs 52 
                                       ++a++++ l+++++l+  n ++++++    wigl+f+++ + + ++v++
  gi|242399024|ref|YP_002994448.1| 158 VVAFVIIKLVSKTILQQKNpIESAKKWAPVWIGLAFVVIGSMFHIKVMH 206
                                       58899**********99999*********************99887766 PP

>> INSIG  Insulin-induced protein (INSIG)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   3.3    0.0086        39     119     154 ..      95     129 ..      87     161 .. 0.70
   2 ?    8.3   0.1   0.00036       1.6       8      54 ..     154     200 ..     147     205 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.0086
                             INSIG 119 lalvnpfLWyliDrskpGfllsaavgllgtavllgl 154
                                        al++ +LW l+  sk G+ +s++ +++g +v +g+
  gi|242399024|ref|YP_002994448.1|  95 AALLAASLWLLF-ASKFGLPVSTTHSIIGGIVGYGI 129
                                       5889999**999.7***************9995552 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00036
                             INSIG   8 vlGvvygvlvtrlheerkllvkkeksssswrylvfwGlagvalGlll 54 
                                       ++G+v ++++ +l +++ l +k+  +s + + +v +Gla v++G+++
  gi|242399024|ref|YP_002994448.1| 154 LFGAVVAFVIIKLVSKTILQQKNPIESAKKWAPVWIGLAFVVIGSMF 200
                                       69***********99998866666999999**************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       990  (0.0552178); 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:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2638.10
//
Query:       gi|242399025|ref|YP_002994449.1|  [L=231]
Description: Phosphate transport system regulator PhoU like protein [Thermococcus sibiricus MM 739]
Scores for complete 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-46  157.7   8.5    2.9e-46  157.5   8.5    1.0  1  PhoU_div   Protein of unknown function DUF47
    4.4e-09   36.7   8.7    0.00075   19.9   1.6    2.8  2  PhoU       PhoU domain
  ------ inclusion threshold ------
      0.018   15.5   1.6       0.73   10.3   0.0    3.2  4  DUF1493    Protein of unknown function (DUF1493)
      0.053   13.5   1.9        0.1   12.5   0.3    2.2  2  MIP-T3_C   Microtubule-binding protein MIP-T3 C-terminal regi
      0.072   12.7   0.1      0.087   12.4   0.1    1.2  1  DUF885     Bacterial protein of unknown function (DUF885)
       0.11   11.7   0.5       0.67    9.1   0.0    1.9  2  PDCD9      Mitochondrial 28S ribosomal protein S30 (PDCD9)
       0.13   12.5   0.1       0.26   11.5   0.1    1.5  1  NEXCaM_BD  Regulatory region of Na+/H+ exchanger NHE binds to
        1.1    9.8   5.8       0.47   11.0   1.1    2.1  2  ArdA       Antirestriction protein (ArdA)


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 !  157.5   8.5   1.3e-49   2.9e-46       3     212 ..       9     229 ..       7     231 .] 0.96

  Alignments for each domain:
  == domain 1  score: 157.5 bits;  conditional E-value: 1.3e-49
                          PhoU_div   3 flfgsspekslqdhlekvsetvlkliellkallegdyekveellkeiselEreADeikreirlklekglflPvdRed 79 
                                        lf++sp+k+l++h+e v etv  l+ +l+a  +gdye++ + +k+++ lE  AD+ik+eir  l + lf+PvdRed
  gi|242399025|ref|YP_002994449.1|   9 KLFAKSPFKPLIKHAEVVLETVETLERALEAWENGDYENMRKYAKKVDDLEDFADKIKEEIRDSLSSKLFMPVDRED 85 
                                       69*************************************************************************** PP

                          PhoU_div  80 llelveslDeildvlediamlvtlrk.....vefpeelkdeflallkktveaiealaevieeleklletalskk... 148
                                       +l+ ++ +D+i+d +e++a+ + +r+     +e++ e+kd ++++ + +++a++++ ++i ++++++e+++ +k   
  gi|242399025|ref|YP_002994449.1|  86 ILRYLQRQDKIADAAENTAKWLLVRDpndipEEIKHEVKDLVIKMSQESIKAAKLVYDAIVQMDTVIESGFGEKeie 162
                                       ************************9854444578888999999*****************************99*** PP

                          PhoU_div 149 ...diveeieslEdeiDqlqrklikklfsredasnplevlllveiieklenvsdraedvadrisiil 212
                                           +++ei s+E++iD+l  k ++  f++ + +     ++l +i + l+ +sd a+d+a+ri++++
  gi|242399025|ref|YP_002994449.1| 163 eeyRLIKEIGSVEHKIDELDTKFMEIIFKNSSKMDWGLGMYLLNIAKTLSGISDMAKDAAERIRLMM 229
                                       *999*************************9999999999**************************97 PP

>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   1.6   3.4e-07   0.00075       8      88 ..      29     106 ..      23     107 .. 0.76
   2 !   19.9   0.8   3.5e-07   0.00078       4      89 .]     130     225 ..     122     225 .. 0.60

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 3.4e-07
                                       HHHHHHHHHHHHHCT-....HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHHHH CS
                              PhoU   8 veemlddalealeekd....telarevierddeidrlekeiersllealakrqplaedlrellsllriardlERigD 80 
                                       + e l++alea e++d    +++a++v +++d +d++ +ei++sl  +l+   p+++  ++   +lr  +    i+D
  gi|242399025|ref|YP_002994449.1|  29 TVETLERALEAWENGDyenmRKYAKKVDDLEDFADKIKEEIRDSLSSKLF--MPVDR--ED---ILRYLQRQDKIAD 98 
                                       5688999*****99994433478888888888888888888888877774..45544..33...7777888889*** PP

                                       HHHHHHHH CS
                              PhoU  81 havniaer 88 
                                        a+n a++
  gi|242399025|ref|YP_002994449.1|  99 AAENTAKW 106
                                       ******98 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 3.5e-07
                                       HHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHH.............HHHHHHHH.HHHGG-SHHHHHHH CS
                              PhoU   4 maeiveemlddalealeekdtelarevierddeidrlekei.............erslleal.akrqplaedlrell 66 
                                       m++ + ++ +++++a+++ dt  ++     ++ei++ +++i             + + +e++ ++++++  d    +
  gi|242399025|ref|YP_002994449.1| 130 MSQESIKAAKLVYDAIVQMDT-VIESG-FGEKEIEEEYRLIkeigsvehkidelDTKFMEIIfKNSSKM--DWGLGM 202
                                       555555555555555555552.22222.23444444444444444444444544556677773335555..457788 PP

                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                              PhoU  67 sllriardlERigDhavniaerv 89 
                                       +ll+ia+ l  i+D a++ aer+
  gi|242399025|ref|YP_002994449.1| 203 YLLNIAKTLSGISDMAKDAAERI 225
                                       9*******************986 PP

>> DUF1493  Protein of unknown function (DUF1493)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.35   7.9e+02      22      56 ..      21      55 ..       5      64 .. 0.80
   2 ?   -1.1   0.0       1.1   2.6e+03       5      22 ..      62      79 ..      56     109 .. 0.65
   3 ?   10.3   0.0   0.00032      0.73      86     110 .]     118     143 ..     106     143 .. 0.86
   4 ?    0.9   0.0      0.27     6e+02      23      56 ..     156     189 ..     145     218 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.35
                           DUF1493 22 kgkeveltldtdldedlkldeddaedllekffkrf 56
                                      k  ev l+  + l+  l++ e+   + + k+ k+ 
  gi|242399025|ref|YP_002994449.1| 21 KHAEVVLETVETLERALEAWENGDYENMRKYAKKV 55
                                      45667778888999999999999999999999975 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.1
                           DUF1493  5 ekevlelireelgtklfk 22
                                       +++ e ir++l+ klf+
  gi|242399025|ref|YP_002994449.1| 62 ADKIKEEIRDSLSSKLFM 79
                                      556666677777777665 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.00032
                           DUF1493  86 evere.kplTiamliesakaGrWLYd 110
                                       e+++e k+l i+m +es+ka + +Yd
  gi|242399025|ref|YP_002994449.1| 118 EIKHEvKDLVIKMSQESIKAAKLVYD 143
                                       455545****************9998 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 0.27
                           DUF1493  23 gkeveltldtdldedlkldeddaedllekffkrf 56 
                                         e+e++++++l ++++ +e+ +++l  kf +  
  gi|242399025|ref|YP_002994449.1| 156 FGEKEIEEEYRLIKEIGSVEHKIDELDTKFMEII 189
                                       5688999999999999999999999999998755 PP

>> MIP-T3_C  Microtubule-binding protein MIP-T3 C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.3   4.7e-05       0.1      66     120 ..      16      70 ..       1      76 [. 0.77
   2 ?   -1.0   0.1      0.69   1.6e+03     114     147 ..     166     196 ..     157     200 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.7e-05
                          MIP-T3_C  66 vnPLgklldfiqdDidsMqrELemWrseyrqqaeelaeerrateealeplkaqla 120
                                        +PL k  +++ + +++++r Le W +   +++ + a++    e   +++k+++ 
  gi|242399025|ref|YP_002994449.1|  16 FKPLIKHAEVVLETVETLERALEAWENGDYENMRKYAKKVDDLEDFADKIKEEIR 70 
                                       58************************98877777777776666666666666554 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.69
                          MIP-T3_C 114 plkaqlaeleeaIkdqkekisnvrakilkNeaki 147
                                       +l +++  +e++I +   k  ++   i kN +k+
  gi|242399025|ref|YP_002994449.1| 166 RLIKEIGSVEHKIDELDTKFMEI---IFKNSSKM 196
                                       45566777777777776666554...56666665 PP

>> DUF885  Bacterial protein of unknown function (DUF885)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   3.9e-05     0.087      84     190 ..      30     140 ..       9     180 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.9e-05
                                       HHHHHHHHCGTTSSCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHTT.-S-..HHHHHHHHHHHHHHHGTSSHHCCC CS
                            DUF885  84 vqqlpsllseepfateedleaylarlaavpaaldqaranlregaaaglvpp..rrqvekvieqlrgllagaaaeasa 158
                                       v++l + l++  + + e +++y+++++ + ++ d +++ +r+ ++++l++p  r+ + + ++  +++++ a+++  +
  gi|242399025|ref|YP_002994449.1|  30 VETLERALEAWENGDYENMRKYAKKVDDLEDFADKIKEEIRDSLSSKLFMPvdREDILRYLQRQDKIADAAENT-AK 105
                                       55666666777778899**********************************99999*****9999999854433.33 PP

                                       ..HH.CCCCCC....HHHHHHHHHH.HHHHHHHHH CS
                            DUF885 159 ..lvaplaele.aekealraeleaalaeavkpaya 190
                                         lv+  ++ + + k ++++ + ++ +e++k+a  
  gi|242399025|ref|YP_002994449.1| 106 wlLVRDPNDIPeEIKHEVKDLVIKMSQESIKAAKL 140
                                       45335445545555566666666666666666644 PP

>> PDCD9  Mitochondrial 28S ribosomal protein S30 (PDCD9)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1      0.12   2.6e+02     237     271 ..      53      87 ..      41     116 .. 0.69
   2 ?    9.1   0.0    0.0003      0.67      24      74 ..     130     180 ..     112     197 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.12
                             PDCD9 237 klveravvyrdkpalqiRikkqlaelvpldsedak 271
                                       k v+ +  + dk +  iR +   + ++p+d ed  
  gi|242399025|ref|YP_002994449.1|  53 KKVDDLEDFADKIKEEIRDSLSSKLFMPVDREDIL 87 
                                       34455556777777788888888888887776643 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0003
                             PDCD9  24 evaaeaaaaspeYppivasldasskaarrrraeetaeevkaaptveEKlrl 74 
                                        ++++  aa+ +Y +iv+  ++   +  ++++ee++  +k++ +ve K++ 
  gi|242399025|ref|YP_002994449.1| 130 MSQESIKAAKLVYDAIVQMDTVIESGFGEKEIEEEYRLIKEIGSVEHKIDE 180
                                       44555667778**************************************74 PP

>> NEXCaM_BD  Regulatory region of Na+/H+ exchanger NHE binds to calmodulin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00012      0.26      23      81 ..      61     122 ..      45     139 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00012
                         NEXCaM_BD  23 lskeeveeirdiLskNlykiRqR..tlsY.nrhtLvadtsekqakeilirrqkslreslrkg 81 
                                       +  +  eeird Ls+ l+    R  +l Y  r    ad+ e+ ak +l+r  + + e+++++
  gi|242399025|ref|YP_002994449.1|  61 FADKIKEEIRDSLSSKLFMPVDRedILRYlQRQDKIADAAENTAKWLLVRDPNDIPEEIKHE 122
                                       5666789*********99864444499999******************************94 PP

>> ArdA  Antirestriction protein (ArdA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   1.1   0.00021      0.47      64     135 ..      28     120 ..      16     123 .. 0.74
   2 ?    1.3   0.3      0.21   4.6e+02      50      86 ..     151     189 ..     111     226 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00021
                              ArdA  64 delnelaklleeleeh.geafaawvehfgdleeledafeeeylgeydsle....................dyAeelv 119
                                       ++++ l + le++e+   e +  ++++ +dle++ d+++ee+++++ s                      d Ae+ +
  gi|242399025|ref|YP_002994449.1|  28 ETVETLERALEAWENGdYENMRKYAKKVDDLEDFADKIKEEIRDSLSSKLfmpvdredilrylqrqdkiaDAAENTA 104
                                       45555666668888766888999999999999999999999988888877788888888888888887777777777 PP

                              ArdA 120 eelgllke.eeipesle 135
                                       + l  +++ ++ipe+++
  gi|242399025|ref|YP_002994449.1| 105 KWLL-VRDpNDIPEEIK 120
                                       6665.443477777765 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.21
                              ArdA  50 e...glpeaslge.yesidelnelaklleeleehgeafaaw 86 
                                           g++e++++e y  i+e+  + ++++el+ +   + ++
  gi|242399025|ref|YP_002994449.1| 151 ViesGFGEKEIEEeYRLIKEIGSVEHKIDELDTK--FMEII 189
                                       2445666666666688888888887666666554..44444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1236  (0.0689386); expected 358.6 (0.02)
Passed bias filter:                      645  (0.0359752); 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: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 1500.62
//
Query:       gi|242399026|ref|YP_002994450.1|  [L=68]
Description: Transcriptional regulatory protein, asnC family [Thermococcus sibiricus MM 739]
Scores for complete 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   67.9   0.4    5.7e-19   67.8   0.4    1.0  1  AsnC_trans_reg   Lrp/AsnC ligand binding domain
  ------ inclusion threshold ------
      0.017   15.2   0.0      0.027   14.5   0.0    1.3  2  Spore_YhcN_YlaJ  Sporulation lipoprotein YhcN/YlaJ (Spore_Yhc


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 !   67.8   0.4   6.4e-23   5.7e-19       6      72 ..       5      67 ..       1      68 [] 0.93

  Alignments for each domain:
  == domain 1  score: 67.8 bits;  conditional E-value: 6.4e-23
                                      -GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEE CS
                    AsnC_trans_reg  6 epghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsiv 72
                                        g+    +e+ e+l ++peV+e+y+v G+yd+++kv ++ l++l++f+ e+++++p+++ t+t+i+
  gi|242399026|ref|YP_002994450.1|  5 A-GK---EREVMEKLLTYPEVKEAYVVYGEYDLIVKVETETLKDLDHFITERIRKMPEIQMTSTMIA 67
                                      4.55...699*******************************************************98 PP

>> Spore_YhcN_YlaJ  Sporulation lipoprotein YhcN/YlaJ (Spore_YhcN_YlaJ)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   3.1e-06     0.027      63     107 ..       9      55 ..       3      60 .. 0.80
   2 ?    1.0   0.0     0.044   3.9e+02      62      80 ..      46      64 ..      39      66 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.1e-06
                   Spore_YhcN_YlaJ  63 qniaqrverlegVedarvlvtgndvlVavqtde..sdnekvkkkVke 107
                                        ++ +++ + ++V++a+v+  + d++V v+t++  +    + +++++
  gi|242399026|ref|YP_002994450.1|   9 REVMEKLLTYPEVKEAYVVYGEYDLIVKVETETlkDLDHFITERIRK 55 
                                       67889999***********************9665555555555544 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.044
                   Spore_YhcN_YlaJ 62 aqniaqrverlegVedarv 80
                                       + i++r++++++++  ++
  gi|242399026|ref|YP_002994450.1| 46 DHFITERIRKMPEIQMTST 64
                                      5669999999999998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 466.25
//
Query:       gi|242399027|ref|YP_002994451.1|  [L=40]
Description: hypothetical protein TSIB_1046 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       102  (0.00568911); expected 358.6 (0.02)
Passed bias filter:                       99  (0.00552178); 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: 0.37u 0.31s 00:00:00.68 Elapsed: 00:00:00.46
# Mc/sec: 263.94
//
Query:       gi|242399028|ref|YP_002994452.1|  [L=225]
Description: protein kinase, [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0077   16.1   0.1      0.015   15.2   0.0    1.5  2  PIP49_N        N-term cysteine-rich ER, FAM69
  ------ inclusion threshold ------
      0.058   13.8   0.1        2.9    8.3   0.0    3.0  4  Propep_M14     Carboxypeptidase activation peptide
       0.14   11.9   0.1       0.24   11.1   0.1    1.3  1  Ribo_biogen_C  Ribosome biogenesis protein, C-terminal
       0.26   11.2   0.0       0.59   10.0   0.0    1.6  2  APH            Phosphotransferase enzyme family


Domain annotation for each model (and alignments):
>> PIP49_N  N-term cysteine-rich ER, FAM69
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   3.3e-06     0.015      69     115 ..      30      76 ..      18      97 .. 0.84
   2 ?   -3.3   0.1       1.6     7e+03     100     123 ..     187     210 ..     180     223 .. 0.49

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.3e-06
                           PIP49_N  69 etlselkClsakpkeqvfsakwkdkevvikcqleealkedleklswv 115
                                       + +   k  s+ +++ +f++kw++kev+ik +  ++++++l+k++ +
  gi|242399028|ref|YP_002994452.1|  30 RGIKVEKFYSKGTTSLIFLGKWRNKEVIIKLERPDTPRKNLQKEANI 76 
                                       55555666677788899************************999875 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.6
                           PIP49_N 100 qleealkedleklswvrseasefd 123
                                       ++ e++k +   l  +r+e ++++
  gi|242399028|ref|YP_002994452.1| 187 RVREKFKINPMFLETLRKELKQYK 210
                                       455555555555555555555543 PP

>> Propep_M14  Carboxypeptidase activation peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0   0.00065       2.9      38      60 ..      13      35 ..       5      38 .. 0.86
   2 ?   -3.3   0.0       2.9   1.3e+04      45      59 ..      73      87 ..      70      90 .. 0.72
   3 ?    1.5   0.0     0.089     4e+02       6      29 ..     114     137 ..     111     152 .. 0.77
   4 ?   -1.5   0.0      0.76   3.4e+03      40      55 ..     194     209 ..     169     214 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00065
                        Propep_M14 38 ilVppekledfeelLeslgisye 60
                                       l+++e+le f+ +Le++gi++e
  gi|242399028|ref|YP_002994452.1| 13 YLISQEELERFKGFLEKRGIKVE 35
                                      6899****************987 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.9
                        Propep_M14 45 ledfeelLeslgisy 59
                                       +++++ L+ ++is+
  gi|242399028|ref|YP_002994452.1| 73 EANILRVLKGHEISP 87
                                      567778888888876 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.089
                        Propep_M14   6 eteeqlelLrdLeesseldfWkpp 29 
                                       +t e+ +lL+ Lee+++ld+++ +
  gi|242399028|ref|YP_002994452.1| 114 TTPEKDHLLQILEETYKLDLLRID 137
                                       566677889999999999999854 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 0.76
                        Propep_M14  40 VppekledfeelLesl 55 
                                       ++p  le++++ L+++
  gi|242399028|ref|YP_002994452.1| 194 INPMFLETLRKELKQY 209
                                       6777888888888876 PP

>> Ribo_biogen_C  Ribosome biogenesis protein, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   5.3e-05      0.24      74     121 ..     173     220 ..     169     224 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 5.3e-05
                                       HHHHHHTT-HHHHHHHHTSSTTHHHHHHHCHHHHHHH.TT--HHHHHH CS
                     Ribo_biogen_C  74 aaalyilglkeeaeellskfkwgeeFlelnkelleeYakckdseevve 121
                                       a a++ l+ +  ++++ +kfk    Fle  ++ l++Y+++k+ e+++e
  gi|242399028|ref|YP_002994452.1| 173 AMAMIFLNNNVISKRVREKFKINPMFLETLRKELKQYKETKNIEKIKE 220
                                       567777888888999***************************999987 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00013      0.59      14      77 ..      47     106 ..      35     128 .. 0.72
   2 ?   -2.5   0.1      0.85   3.8e+03     185     197 ..     152     162 ..     146     163 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00013
                                       EEEEETT--EEEEEE-TTS-HHHHHHHHHHHHHHHHTT-B--B-CTTBS-EEETTEEEEEEE-- CS
                               APH  14 ylvttpagryvlrrnpparaaeeirrevallrlLakagvpvPevlagdtddeeigllfalieyv 77 
                                       +l ++ +++++ ++ +p  +   +++e+ +lr+L ++++  P +++++    ++ ++f++ e+ 
  gi|242399028|ref|YP_002994452.1|  47 FLGKWRNKEVIIKLERPDTPRKNLQKEANILRVLKGHEI-SPLLIDYG---MFENREFLVREFA 106
                                       444444489******************************.89999964...4444444444444 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.85
                                       TEEEEE---TT-E CS
                               APH 185 grvtGviDfedag 197
                                            +iDfe a+
  gi|242399028|ref|YP_002994452.1| 152 RVW--IIDFEKAS 162
                                       344..9****997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       785  (0.0437838); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1568.69
//
Query:       gi|242399029|ref|YP_002994453.1|  [L=102]
Description: hypothetical protein TSIB_1048 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score 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   13.1   3.5      0.066   12.8   3.5    1.1  1  PRA1      PRA1 family protein
       0.83    9.9  10.5        1.8    8.9   6.9    2.6  2  DUF3017   Protein of unknown function (DUF3017)
       0.95    9.8   8.8        1.1    9.5   0.4    2.0  2  YwiC      YwiC-like protein
        6.1    7.1  11.7       0.71   10.1   5.7    1.9  1  TctB      Tripartite tricarboxylate transporter TctB family
        6.2    6.9  11.2        5.2    7.2   1.0    2.2  2  DUF2892   Protein of unknown function (DUF2892)


Domain annotation for each model (and alignments):
>> PRA1  PRA1 family protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   3.5   1.8e-05     0.066      42     124 ..       5      92 ..       2      96 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.8e-05
                              PRA1  42 Ylivvllvlllsll..tnplslivllllvlawlflyflrseplvlfgrelsdr.vvlivllv.vsvlllfltg.avl 113
                                       Y+++ +l++ l++    + +  +v+++l + +++ y +r++++ + +r +++   ++i++ + v +++ +l++  + 
  gi|242399029|ref|YP_002994453.1|   5 YAVLGILLMGLVIStaSKSYWGVVFAALGIPLYLAYISRERNILVRSRIFDKDlFIMIGITIiVILIFEYLLDpRIG 81 
                                       777666666555551045555577778888888888899****8888888555144444333133334455554566 PP

                              PRA1 114 vllwalligll 124
                                       ++l a+li+l+
  gi|242399029|ref|YP_002994453.1|  82 LVLAAFLIPLA 92 
                                       67777777765 PP

>> DUF3017  Protein of unknown function (DUF3017)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   6.9   0.00051       1.8       3      71 ..       6      69 ..       5      72 .. 0.73
   2 ?   -1.0   0.1      0.59   2.1e+03      26      31 ..      83      88 ..      76      99 .. 0.49

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00051
                           DUF3017  3 lvllvvavglllvaldhwRrGal..llGvalllaAvlRlvlpsrrvGlLaVRsRafDvllllvlGaaivvl 71
                                      +vl ++++gl++ ++++  +G++  +lG+ l la + R          + VRsR fD  l++++G++i+v+
  gi|242399029|ref|YP_002994453.1|  6 AVLGILLMGLVISTASKSYWGVVfaALGIPLYLAYISRE------R-NILVRSRIFDKDLFIMIGITIIVI 69
                                      688899999999888866666551156666666555442......2.367******************997 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.59
                           DUF3017 26 llGval 31
                                      +l++ l
  gi|242399029|ref|YP_002994453.1| 83 VLAAFL 88
                                      222222 PP

>> YwiC  YwiC-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.4   0.00032       1.1      66     109 ..       6      48 ..       5      54 .. 0.84
   2 ?    4.2   3.0     0.014        49      61     101 ..      59      99 ..      49     102 .] 0.81

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00032
                              YwiC  66 avallllllalllqpallwwallflplvavavyeakrkreRsll 109
                                       av ++ll+ +++ +++  +w+++f++l ++ +y+a+  reR++l
  gi|242399029|ref|YP_002994453.1|   6 AVLGILLMGLVISTASKSYWGVVFAAL-GIPLYLAYISRERNIL 48 
                                       566777888888888899999999876.789**********987 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.014
                              YwiC  61 lliYgavallllllalllqpallwwallflplvavavyeak 101
                                       +++ g+  +++l++ +ll+p++ +++++fl+ +a+ ++  +
  gi|242399029|ref|YP_002994453.1|  59 FIMIGITIIVILIFEYLLDPRIGLVLAAFLIPLAIWAWSRL 99 
                                       456677778888899999***99999999999999998765 PP

>> TctB  Tripartite tricarboxylate transporter TctB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   5.7    0.0002      0.71      73     131 ..      11      77 ..       2      80 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0002
                              TctB  73 llaalllyallleplGfilata...lflllll.g....reerkwlkalilavvlallvyllFtklLg 131
                                       ll++l++  +   + G ++a+    l+l+++        ++r + k+l++ ++++++v l+F++lL+
  gi|242399029|ref|YP_002994453.1|  11 LLMGLVISTASKSYWGVVFAALgipLYLAYISrErnilVRSRIFDKDLFIMIGITIIVILIFEYLLD 77 
                                       223444444445555777777765455544445156775678899********************96 PP

>> DUF2892  Protein of unknown function (DUF2892)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   3.4    0.0098        35      14      41 ..       6      34 ..       5      40 .. 0.81
   2 ?    7.2   1.0    0.0014       5.2       9      37 ..      55      86 ..      53      97 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0098
                           DUF2892 14 ivvGlvllllallglsggw.gwllglvGa 41
                                      +v+G++l++l++ + s++  g++++++G+
  gi|242399029|ref|YP_002994453.1|  6 AVLGILLMGLVISTASKSYwGVVFAALGI 34
                                      689*********99988766888888886 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0014
                           DUF2892  9 dRilrivvGlvllllallglsggw...gwllg 37
                                      d+ l i++G+++++++++ +   +   ++l++
  gi|242399029|ref|YP_002994453.1| 55 DKDLFIMIGITIIVILIFEYLLDPrigLVLAA 86
                                      77788***************887755333222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       915  (0.0510346); 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:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 677.54
//
Query:       gi|242399030|ref|YP_002994454.1|  [L=633]
Description: Dipeptidyl aminopeptidases/acylaminoacyl-peptidase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-52  177.7   0.0    2.9e-52  177.2   0.0    1.2  1  Peptidase_S9     Prolyl oligopeptidase family
    3.3e-11   43.3   0.0    5.1e-08   32.8   0.0    2.2  2  Peptidase_S15    X-Pro dipeptidyl-peptidase (S15 family)
      5e-06   26.3   0.3     0.0057   16.6   0.0    3.1  2  PD40             WD40-like Beta Propeller Repeat
    2.1e-05   24.3   0.0      9e-05   22.2   0.0    1.9  2  Abhydrolase_1    alpha/beta hydrolase fold
    7.4e-05   22.1   0.1     0.0047   16.2   0.0    2.2  2  Hydrolase_4      Serine aminopeptidase, S33
    0.00016   21.3   0.0    0.00039   20.1   0.0    1.6  1  DLH              Dienelactone hydrolase family
     0.0002   20.2   0.5      0.027   13.2   0.5    2.9  2  AXE1             Acetyl xylan esterase (AXE1)
     0.0055   17.3   0.0      0.014   16.0   0.0    1.7  2  Abhydrolase_6    Alpha/beta hydrolase family
  ------ inclusion threshold ------
      0.026   14.3   0.1          1    9.1   0.0    2.8  2  Abhydrolase_2    Phospholipase/Carboxylesterase
      0.028   14.3   0.1        3.3    7.7   0.1    2.9  3  Op_neuropeptide  Opioids neuropeptide
      0.048   12.8   0.0        9.5    5.3   0.0    2.4  2  DUF2920          Protein of unknown function (DUF2920)
      0.082   11.7   0.2       0.51    9.0   0.0    2.3  2  DPPIV_N          Dipeptidyl peptidase IV (DPP IV) N-terminal 
      0.092   12.4   0.1       0.26   10.9   0.0    1.7  2  Glyco_hydro_49N  Glycosyl hydrolase family 49 N-terminal Ig-l
      0.093   12.9   0.2       0.23   11.6   0.2    1.6  1  NDUF_B6          NADH:ubiquinone oxidoreductase, NDUFB6/B17 s
        0.1   11.4   0.0       0.18   10.6   0.0    1.4  1  COesterase       Carboxylesterase family


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 !  177.2   0.0   2.4e-55   2.9e-52       2     211 ..     403     614 ..     402     615 .. 0.95

  Alignments for each domain:
  == domain 1  score: 177.2 bits;  conditional E-value: 2.4e-55
                                       ---HHHHHHHCCT-EEEEE--TTSSTTHCHHHHTTSGGGGHHHHHHHHHHHHHHHHTT.S--GGGEEEEEETHHHHH CS
                      Peptidase_S9   2 sfsselqlladrGyvvvvanirGsggyGeafhdagkrklgqnefdDfiaaaealakeg.yvdserlaitGgSyGGyl 77 
                                       +f+ e+ql+a++Gy vv++n+rGs+gy e f  ++ +++g ++f+D+++++e++ + + ++d+er++itG SyGG++
  gi|242399030|ref|YP_002994454.1| 403 YFKYEMQLMAEKGYYVVFVNPRGSNGYDEGFSSRVLERTGLEDFQDILNGVEKFFELEpQADRERVGITGISYGGFM 479
                                       6889************************************************************************* PP

                                       HHHHHHH-GGG-SEEEEESE---CCCHHCSTTS...THHHCCCC--TTTCHHHHHHHHHH-CGGG-----EEEEEEE CS
                      Peptidase_S9  78 tgaalnqrpdlFkaavaevpvvdvlrydsdtdl...lteeymewgnpeeneegykelspyspldnvkaypplLlihG 151
                                       t++a++ ++dlFka+++e++++ +l+++ ++d+   + +e+ +  np  ++e+yk+lsp+ +++n  +++plLlih+
  gi|242399030|ref|YP_002994454.1| 480 TNWAVT-QSDLFKAGISENGISYWLTSYAFSDIglwFDKEVIG-DNP-LENENYKKLSPLFYAKN--VKAPLLLIHS 551
                                       ******.**************************9977778888.556.67888************..99******** PP

                                       TT-SSS-THHHHHHHHHHH--S-SEEEEEETTS-S...STTSSHHHHHHHHHHHHHHHHHCT- CS
                      Peptidase_S9 152 laDdrvppaealklvaaLqkkgknvlllifpdegH...gvgkprakveelarllaFlkealgk 211
                                       l+D+r+p+ +++++++ L++ gk++ + if+   H     g+pr+++++++ +++F++++l+k
  gi|242399030|ref|YP_002994454.1| 552 LEDYRCPLDQSVMFYHVLKDLGKEAYIAIFKRGAHghsLRGSPRHRAKRYKLFVEFFEKKLKK 614
                                       *******************************9999666568999999************9985 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 !   32.8   0.0   4.2e-11   5.1e-08      52     145 ..     402     509 ..     363     521 .. 0.79
   2 !    8.4   0.0    0.0012       1.5     209     268 ..     524     587 ..     513     588 .. 0.85

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 4.2e-11
                                       H........HHHTT-EEEEEE-TTSTT.S-S---TT.TTTHHHHHHHHHHHHHH....C.TTEEEEEEEEEECHHHH CS
                     Peptidase_S15  52 v........fvarGYavVvqdvrGtgg.SeGeftvg.dsdeaedgadvidWlak....q.pwsnGkVgmtGiSYlGt 113
                                                ++++GY vV+++ rG++g  eG+      ++  ed+ d++  + k    + +    +Vg tGiSY+G+
  gi|242399030|ref|YP_002994454.1| 402 YyfkyemqlMAEKGYYVVFVNPRGSNGyDEGFSSRVlERTGLEDFQDILNGVEKffelEpQADRERVGITGISYGGF 478
                                       0344444449**************865267887655699999***********9***96688999************ PP

                                       HHHHHCTT--TTEEEEEEECE-S-TCCCCSEC CS
                     Peptidase_S15 114 tqllaaatgvpalkaivpeaaisdlyddyyre 145
                                       + + a + +++  ka ++e +is + + y+++
  gi|242399030|ref|YP_002994454.1| 479 MTNWAVT-QSDLFKAGISENGISYWLTSYAFS 509
                                       *999888.9****************9988776 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0012
                                       -SSSHHHHTT-HHHHHCT--S-EEEEEECCSSTTC.CHHHHHHHHHCCTT-...EEEEECECTT CS
                     Peptidase_S15 209 gdydafWkdrnlsedadkvkapvllvgGwnDwnvk.ngaiklyealkapgv...klilgpwtHv 268
                                       + +++  k+ ++   a++vkap+ll++++ D     ++++ +y+ lk+ g+     i+ +++H+
  gi|242399030|ref|YP_002994454.1| 524 PLENENYKKLSPLFYAKNVKAPLLLIHSLEDYRCPlDQSVMFYHVLKDLGKeayIAIFKRGAHG 587
                                       5567777888888899***************99999************9998887888888885 PP

>> PD40  WD40-like Beta Propeller Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.0    0.0077       9.3      13      29 ..      19      35 ..      10      44 .. 0.85
   2 !   16.6   0.0   4.8e-06    0.0057      10      28 ..      62      80 ..      55      90 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0077
                                      EEEE-TTSSEEEEEEEC CS
                              PD40 13 aPsfSPDGkrlaFsSdR 29
                                      +P++S DGk+ a++ ++
  gi|242399030|ref|YP_002994454.1| 19 DPRISRDGKKVAYVLTK 35
                                      7************9886 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 4.8e-06
                                      .EEEEEE-TTSSEEEEEEE CS
                              PD40 10 negaPsfSPDGkrlaFsSd 28
                                      n  +P+fSP+Gk+++F+++
  gi|242399030|ref|YP_002994454.1| 62 NASMPRFSPNGKKITFVRS 80
                                      5679************986 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   7.6e-08     9e-05       1      92 [.     387     484 ..     387     508 .. 0.81
   2 ?   -0.9   0.0      0.88   1.1e+03     206     224 ..     517     556 ..     484     569 .. 0.68

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 7.6e-08
                                       SEEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB..CHHSHHHHHHHHH....HH.HHHCT CS
                     Abhydrolase_1   1 pvlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacin.ddygtasvaddld....ri.ldalg 71 
                                       pv+v++hG+p++ + ++ +  ++  a++g+ v+ +++rG+   + + ++++ ++ g+ +++d+l+    ++ l++  
  gi|242399030|ref|YP_002994454.1| 387 PVIVFVHGGPKGMYGYYFKYEMQLMAEKGYYVVFVNPRGSNGYDEGFSSRVlERTGLEDFQDILNgvekFFeLEPQA 463
                                       79*********999999999*******************98877777777777778888888888777544999888 PP

                                       TSSEE.EEEETHHHHHHHHHHH CS
                     Abhydrolase_1  72 ddklt.lvGhSmGGmialayaa 92 
                                       d++ + + G S+GG++  ++  
  gi|242399030|ref|YP_002994454.1| 464 DRERVgITGISYGGFMTNWA-V 484
                                       888888********975544.3 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.88
                                       C.....................THHHHSEEEEEEETTCSS CS
                     Abhydrolase_1 206 e.....................lknvlaptlvisgtsDpl 224
                                       +                      knv+ap l+i++ +D  
  gi|242399030|ref|YP_002994454.1| 517 KevigdnplenenykklsplfyAKNVKAPLLLIHSLEDYR 556
                                       255555556666666666777778*********9988855 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0     4e-06    0.0047       4      96 ..     386     485 ..     383     499 .. 0.79
   2 ?    3.6   0.0     0.027        33     187     223 ..     539     575 ..     536     588 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4e-06
                       Hydrolase_4   4 kavvvlvHGlae.hsgryae.laeaLaaqGfavyalDhrGhGrse.......gkrghvpsfddyvdDlaafvekvke 71 
                                         v+v+vHG     +g y +  ++ +a++G+ v+ ++ rG    +        +r  +++f+d+++ +++f+e ++ 
  gi|242399030|ref|YP_002994454.1| 386 APVIVFVHGGPKgMYGYYFKyEMQLMAEKGYYVVFVNPRGSNGYDegfssrvLERTGLEDFQDILNGVEKFFE-LEP 461
                                       56899***985425666666589999**************74444489889988999**************95.566 PP

                       Hydrolase_4  72 ehpelplfllGhSmGGliallyllr 96 
                                       +  ++++ + G S GG+++ +++ +
  gi|242399030|ref|YP_002994454.1| 462 QADRERVGITGISYGGFMT-NWAVT 485
                                       677778**********985.44444 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.027
                       Hydrolase_4 187 aakitlPllllhGeaDkvvdpeasrelyerlgskdkt 223
                                       a+++++Plll+h+ +D  ++ ++s  +y  l+   k+
  gi|242399030|ref|YP_002994454.1| 539 AKNVKAPLLLIHSLEDYRCPLDQSVMFYHVLKDLGKE 575
                                       67899******************98888877765444 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   3.2e-07   0.00039      75     202 ..     443     601 ..     379     615 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 3.2e-07
                               DLH  75 eekvlddlkaavaylksvpevstkkvgvvGfCmGGalalllaaevpevdaavafYG..................... 130
                                        e+  d+l+   ++ +  p+++ ++vg++G   GG ++    ++ + ++a ++  G                     
  gi|242399030|ref|YP_002994454.1| 443 LEDFQDILNGVEKFFELEPQADRERVGITGISYGGFMTNWAVTQSDLFKAGISENGisywltsyafsdiglwfdkev 519
                                       334444444445678889999*****************99999999******************************* PP

                               DLH 131 ..........lspekeleeaakikapilalfgeeDefipadevekleealkaanvdlelkvYpgagHaFandsresy 197
                                                  +  ++l +a+++kap+l ++  eD   p d+   +   lk+ ++++ + +++  +H+   + ++  
  gi|242399030|ref|YP_002994454.1| 520 igdnplenenYKKLSPLFYAKNVKAPLLLIHSLEDYRCPLDQSVMFYHVLKDLGKEAYIAIFKRGAHGHSLRGSPRH 596
                                       *****9998777788999**************************************************998888877 PP

                               DLH 198 neeaa 202
                                       ++++ 
  gi|242399030|ref|YP_002994454.1| 597 RAKRY 601
                                       76655 PP

>> AXE1  Acetyl xylan esterase (AXE1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.5   2.3e-05     0.027      67     186 ..     369     478 ..     336     496 .. 0.70
   2 ?   -0.6   0.0      0.36   4.3e+02     254     282 ..     538     566 ..     503     592 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.3e-05
                                       EEEEEEEEEES..SSSSEEEEEEEE-TT--...GGGHHHHHHHHHTT-EEEEEE-TTTS..SSB-SSCCSS-SSSST CS
                              AXE1  67 arikaklvlPke.keeklPavvefhGYegs...rgeihdllnyaaaGyavvvmdvRGqggesedkvgskgnkakGfi 139
                                        ++ +++++P+  +eek P++v  hG  ++        ++   a +Gy vv ++ RG +g+ e  ++ +  +     
  gi|242399030|ref|YP_002994454.1| 369 LELDGWYIKPDIkEEEKAPVIVFVHGGPKGmygYYFKYEMQLMAEKGYYVVFVNPRGSNGYDEGFSSRVL-E----- 439
                                       4689******96156899****99998766322445678889999*************988766333221.1..... PP

                                       TTTTTSTTT-HHHHHHHHHHHHHHHHHTS.TTEEEEEEEEEEETHHHH CS
                              AXE1 140 irGlldkeklyyrrvflDavrlveivasl.pevDeeRvavlGasqGGa 186
                                         Gl d         f D+ + ve   +l p+ D eRv+++G s GG 
  gi|242399030|ref|YP_002994454.1| 440 RTGLED---------FQDILNGVEKFFELePQADRERVGITGISYGGF 478
                                       123333.........445555555444442466666666666666665 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.36
                                       HHCC--S-EEEEEETT-SSS-HHHHHHHH CS
                              AXE1 254 lAkrvkaevllsvgLeDevcpPstvfaay 282
                                        Ak vka+ ll+ +LeD  cp       y
  gi|242399030|ref|YP_002994454.1| 538 YAKNVKAPLLLIHSLEDYRCPLDQSVMFY 566
                                       5999****************954333333 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       4.7   5.6e+03      28      60 ..      88     125 ..      78     155 .. 0.57
   2 !   16.0   0.0   1.2e-05     0.014       1      80 [.     389     481 ..     389     580 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 4.7
                                       EEEEE--TTS.T.................S-GGCS--HHHCHHHHHHHCCT CS
                     Abhydrolase_6  28 hvlapDlpGh.G.................rsdpppldledladlaalldel 60 
                                       +v+ +Dl ++ G                 +              + l++++
  gi|242399030|ref|YP_002994454.1|  88 EVWLYDLSSMsGkkvleaknildvswnedD-------------RRILITGF 125
                                       348888888877555554444333333321.............23333333 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 1.2e-05
                                       EEEE--GC.....G...CHHHHHHHHCCTCEEEEE--TTS.T......S-GGCS--HHHCHHHHHHHCCTT...... CS
                     Abhydrolase_6   1 vlllHGagssassW...lvapLaallaagvhvlapDlpGh.G......rsdpppldledladlaalldelaa..... 62 
                                       ++++HG++ + +++   + ++L a  +  v  + +  +G  G      ++    ++led +d+++ ++++ +     
  gi|242399030|ref|YP_002994454.1| 389 IVFVHGGPKGMYGYyfkYEMQLMAEKGYYV--VFVNPRGSnGydegfsSRVLERTGLEDFQDILNGVEKFFElepqa 463
                                       8*****886655554343556644444444..77****998843333222223355555555555555554489999 PP

                                       .TTSEEEEEETCHHHHHH CS
                     Abhydrolase_6  63 gggpvvlvGHSlGGalal 80 
                                       ++ +v + G S+GG++  
  gi|242399030|ref|YP_002994454.1| 464 DRERVGITGISYGGFMTN 481
                                       **************9544 PP

>> Abhydrolase_2  Phospholipase/Carboxylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1      0.17     2e+02      10      41 ..     382     413 ..     379     500 .. 0.60
   2 ?    9.1   0.0   0.00084         1     153     200 ..     540     587 ..     531     592 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.17
                                       SS---EEEEEE--TT--S.HHHHHHHH.TT--T CS
                     Abhydrolase_2  10 kdkaqavviflHGlGdsg.hawaeaakteaalp 41 
                                       ++++++v++f+HG G +g  + ++  +++   +
  gi|242399030|ref|YP_002994454.1| 382 EEEKAPVIVFVHG-GPKGmYGYYFKYEMQLMAE 413
                                       5677788888888.4444433333333333333 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00084
                                       GGGG-EEEEEEETT-SSS-HHHHHHHHHHHHTTS-GEEEEEETT--SS CS
                     Abhydrolase_2 153 vtkklpilqiHgeeDpvvplalgkaakevlkkllkkvelksyeglaHs 200
                                        ++k p l+iH  eD+  pl  + +++ vlk+l k+    +++ +aH 
  gi|242399030|ref|YP_002994454.1| 540 KNVKAPLLLIHSLEDYRCPLDQSVMFYHVLKDLGKEAYIAIFKRGAHG 587
                                       56899*************************************999995 PP

>> Op_neuropeptide  Opioids neuropeptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.068        81       7      21 ..     112     126 ..     111     126 .. 0.91
   2 ?   -2.3   0.0       3.6   4.3e+03       6      16 ..     250     260 ..     248     261 .. 0.83
   3 ?    7.7   0.1    0.0027       3.3       1       8 [.     475     482 ..     475     485 .. 0.94

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.068
                   Op_neuropeptide   7 sWdErsqkPLiTLfk 21 
                                       sW+E++++ LiT f+
  gi|242399030|ref|YP_002994454.1| 112 SWNEDDRRILITGFR 126
                                       9***********887 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.6
                   Op_neuropeptide   6 ksWdErsqkPL 16 
                                         Wd +  kPL
  gi|242399030|ref|YP_002994454.1| 250 YLWDGKEVKPL 260
                                       57********9 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0027
                   Op_neuropeptide   1 YGGFMksW 8  
                                       YGGFM+ W
  gi|242399030|ref|YP_002994454.1| 475 YGGFMTNW 482
                                       ******99 PP

>> DUF2920  Protein of unknown function (DUF2920)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0      0.01        12     160     196 ..     446     482 ..     439     500 .. 0.87
   2 ?    5.3   0.0     0.008       9.5     286     324 ..     544     582 ..     524     586 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.01
                           DUF2920 160 AlDiinalkdlvkrfpkeadlpviliGgsyGGYlalL 196
                                        +Di+n +++  +  p+   + v + G syGG++++ 
  gi|242399030|ref|YP_002994454.1| 446 FQDILNGVEKFFELEPQADRERVGITGISYGGFMTNW 482
                                       68**************999999999********9986 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.008
                           DUF2920 286 tiyvsyHsekDklapaeeKiqlakilkklgfdvelelid 324
                                          + +Hs +D   p+++ ++++++lk lg ++ + +++
  gi|242399030|ref|YP_002994454.1| 544 APLLLIHSLEDYRCPLDQSVMFYHVLKDLGKEAYIAIFK 582
                                       66789*************************999888775 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 ?    9.0   0.0   0.00043      0.51      15      63 ..      37      81 ..      23      83 .. 0.69
   2 ?   -0.6   0.0      0.35   4.2e+02     184     206 ..     106     128 ..      82     180 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00043
                                      EESSSEETTEEEEEETTTEECEEEETTTT.BSEEEEESSTTEEEEEETT CS
                           DPPIV_N 15 knwRhsytaeyyiydletneveelspgeeklqlakwSPagdklafvrnn 63
                                      +   ++y+++ ++ ++e++e + +++     +++++SP+g+k+ fvr+n
  gi|242399030|ref|YP_002994454.1| 37 NLKDNKYENTIVVEEVENGERKFIENA----SMPRFSPNGKKITFVRSN 81
                                      444456777777777777666665555....****************99 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.35
                                       EEEEEEEECTTSCCEEEEEEETT CS
                           DPPIV_N 184 eyitrvkWtsdeksllvqwlnRs 206
                                       + i +v+W +d++++l++ ++R 
  gi|242399030|ref|YP_002994454.1| 106 KNILDVSWNEDDRRILITGFRRR 128
                                       33556666666666666666555 PP

>> Glyco_hydro_49N  Glycosyl hydrolase family 49 N-terminal Ig-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       4.6   5.5e+03      49      63 ..       8      22 ..       5      34 .. 0.74
   2 ?   10.9   0.0   0.00022      0.26      14      72 ..     179     237 ..     172     253 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 4.6
                                      SS-EEE--EEE-GGG CS
                   Glyco_hydro_49N 49 eklydsfvylsiPrs 63
                                      e+ +  f+yls Pr 
  gi|242399030|ref|YP_002994454.1|  8 ENTFSKFAYLSDPRI 22
                                      577889999998874 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00022
                                       ---TTEEE-SSS---TT-EEE-SSEEEEEEETTTTSS-EEE--EEE-GGGGTGS--TT- CS
                   Glyco_hydro_49N  14 WWhdngeintqtPvqdgnvrrsslysvqvataaaseklydsfvylsiPrsGkgkidyte 72 
                                        Wh   +i       dgn++  ++y++ + + ++se++++  +y ++  +Gk+ + y +
  gi|242399030|ref|YP_002994454.1| 179 IWHGDKVIYNVPHRMDGNLQFFKFYDIYIYKDGKSERIFEGVSYAAVDSNGKAVLLYGK 237
                                       599999998888899*************************************9776655 PP

>> NDUF_B6  NADH:ubiquinone oxidoreductase, NDUFB6/B17 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   0.00019      0.23      27     141 ..     327     440 ..     317     448 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00019
                           NDUF_B6  27 erelRkkWlkDqeLsprepvvvpave.eklnpierfyrafldklykvlkpllrlyvakavrvsvfklllvlvpvyiv 102
                                       + +lR  +l D eL++      p +   ++ pi++f+ + ld     l   +     k  +++   + +   p  + 
  gi|242399030|ref|YP_002994454.1| 327 DTKLRELYLWDGELKQITDYNGPIFAkLETRPINHFHFKSLDL---ELDGWYIKPDIKEEEKAPVIVFVHGGPKGMY 400
                                       5667777777777776666666655435566777777777776...2222222222222222222222233455677 PP

                           NDUF_B6 103 aYYlKYevkdwtrkkgyevveskkkivpg.dekyd.tilek 141
                                        YY+KYe++    +kgy vv   ++  +g de++  ++le+
  gi|242399030|ref|YP_002994454.1| 401 GYYFKYEMQ-LMAEKGYYVVFVNPRGSNGyDEGFSsRVLER 440
                                       8********.999************9999888885246665 PP

>> COesterase  Carboxylesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00015      0.18      95     142 ..     378     423 ..     369     510 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00015
                                       ESSSSSTTSSEEEEEEE--STT.TS-BGCGS-THHHHHHHTSEEEEE-- CS
                        COesterase  95 PkekkeakkklPVlVwihGggf.qtgsaseydgsaLaaegnvivVtinY 142
                                       P+  ke++k  PV+V++hGg   ++g   +y+ + +a++g   vV +n 
  gi|242399030|ref|YP_002994454.1| 378 PDI-KEEEK-APVIVFVHGGPKgMYGYYFKYEMQLMAEKG-YYVVFVNP 423
                                       654.35555.5*********65156667779999998885.44444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (633 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.74u 0.30s 00:00:01.04 Elapsed: 00:00:00.47
# Mc/sec: 4025.89
//
Query:       gi|242399031|ref|YP_002994455.1|  [L=230]
Description: hypothetical protein TSIB_1050 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-35  122.9   0.0    1.5e-35  122.4   0.0    1.2  1  MAF_flag10      Protein of unknown function DUF115
  ------ inclusion threshold ------
      0.086   12.8   0.0       0.13   12.2   0.0    1.3  1  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen


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 !  122.4   0.0   1.6e-39   1.5e-35      15     168 ..      44     185 ..      31     188 .. 0.84

  Alignments for each domain:
  == domain 1  score: 122.4 bits;  conditional E-value: 1.6e-39
                        MAF_flag10  15 lkellnkfkg..nkpaiivgaGPSLeknlellkelrdkaviiaadtalkaLlkegIkPDivvs.lDpqeasyevfke 88 
                                       ++ ++    +  ++ ++++gaGPSL+k+l   k+ + + ++ia+d++++aLl++gI+PDi+v+ lD+   ++e++k+
  gi|242399031|ref|YP_002994455.1|  44 AETIK----EriKERVYVFGAGPSLDKKL---KKGKFSGTLIASDGSTSALLEQGIIPDIIVTdLDG---CFEDIKK 110
                                       22233....234579************65...555699*****************************...******* PP

                        MAF_flag10  89 aekkgdiplvfasgvnpellkkykgpkiflvtgstqalelleeekne.ilfgGgsvantaldlAvklgfkeIiliGq 164
                                       a++ g  ++v+a+g+n ++l++y +++++++ + +q+ e l    ++  +fgG++++++a++lA +lg++eI+liG+
  gi|242399031|ref|YP_002994455.1| 111 ANDLGAYVVVHAHGDNMDKLEAYVPKLKNVMGT-CQT-EPL----DIvYNFGGFTDGDRAVFLAEELGAREIFLIGF 181
                                       ****************************97775.553.333....3449**************************** PP

                        MAF_flag10 165 Dlay 168
                                       D++ 
  gi|242399031|ref|YP_002994455.1| 182 DFGE 185
                                       **96 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.4e-05      0.13      84     153 ..      12      82 ..       7      86 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.4e-05
                                       HHHHHHCCC--TT-EEEE---SE.ET.TTEEHHHHHHHHH-S--EEEEESS--HHHHHTT--EEEEEEES- CS
                    NAD_Gly3P_dh_N  84 evlkklkgllkkkailvsliKGi.eegtlkllsevieeelkeekvavlsGpslAeEvakgkptavviaskd 153
                                       +++ k+   ++++ +++ l++ +  e+++ +l e i+e +ke   ++ +Gpsl + + kgk++ + ias+ 
  gi|242399031|ref|YP_002994455.1|  12 QIVSKMGYEIEEDRKAALLLRRLlRENENYILAETIKERIKERVYVFGAGPSLDKKLKKGKFSGTLIASDG 82 
                                       567777778877777777777776888999*************88899*******************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.44
# Mc/sec: 1569.46
//
Query:       gi|242399032|ref|YP_002994456.1|  [L=63]
Description: hypothetical protein TSIB_1051 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       189  (0.0105416); expected 358.6 (0.02)
Passed bias filter:                      185  (0.0103185); 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: 0.53u 0.35s 00:00:00.88 Elapsed: 00:00:00.56
# Mc/sec: 341.43
//
Query:       gi|242399033|ref|YP_002994457.1|  [L=523]
Description: peptide ABC transporter substrate-binding protein [Thermococcus sibiricus MM 739]
Scores for complete 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-101  339.5   7.5   2.7e-101  339.2   7.5    1.1  1  SBP_bac_5     Bacterial extracellular solute-binding proteins
    0.00078   19.1   0.3      0.053   13.1   0.3    2.6  2  OpuAC         Substrate binding domain of ABC-type glycine be
  ------ inclusion threshold ------
      0.072   13.1   0.0       0.18   11.8   0.0    1.6  1  STAT6_C       STAT6 C-terminal
        0.1   12.2   0.0       0.17   11.5   0.0    1.2  1  Cu-oxidase_4  Multi-copper polyphenol oxidoreductase laccase


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 !  339.2   7.5  6.1e-105  2.7e-101       1     376 [.      82     443 ..      82     444 .. 0.95

  Alignments for each domain:
  == domain 1  score: 339.2 bits;  conditional E-value: 6.1e-105
                                       SEEESSEEEEEEEETTTTEEEEEE-TT-B-TTSSB-SHHHHHHHHHHHHTGGGHCTTHHHHHCTCTEEEEEEEETTE CS
                         SBP_bac_5   1 evvpaLAeswwevsdDgktytfkLRkgvkFsDGtpltAeDvvfsferlldpdtasgyaslleedqdikkveavddyt 77 
                                       e++paLAe+ wev++D +++tf+LRk++kF+DGtpl A+Dvv s+er++   + + +  + +    ++kvea ddyt
  gi|242399033|ref|YP_002994457.1|  82 EIEPALAEK-WEVNEDSTVWTFYLRKDLKFADGTPLKAQDVVRSIERIMTIQGDPAWLVTDF----VDKVEAKDDYT 153
                                       689******.7*********************************************999995....*********** PP

                                       EEEEESSETTTTTTHCHHHHHHHGCCHTCTCTTTTTGTTTSE-BSSSEEEEEEETTTEEEEEE-TTSTTTSCSSSSE CS
                         SBP_bac_5  78 vrftlkkpnalfltllaavpasiakkaaekeddkdkdtnekpvgtGPYklkefkpgqkivlernpdYwgggkpkldr 154
                                       v+f+l++p+a+fl+ll+ +p+ +++   ++++ ++ ++++   g GPYk++++++++++vle+np+Y+ g++pk  +
  gi|242399033|ref|YP_002994457.1| 154 VVFYLNQPTAYFLALLTTPPYFPVH---PNYSPNEIQSDQTAGGAGPYKITKWVRDEELVLEANPNYY-GEPPKTGK 226
                                       ************************6...5555555566666667***********************9.******** PP

                                       EEEEE-.SHHHHHHHHHTTSSSEE.ESTTCCTHCHHHHHTTEEEEEEEEEEEEEEEEETTTSTGGGSHHHHHHHHHH CS
                         SBP_bac_5 155 iefkvipdsdaraaalqsGeiddv.aepppsdieqlkeakglkvlyespgggvtylafNtkkppfddkrvRqAlsyA 230
                                       i++k++ d+++ ++alq+Geid++   + p+die+lk + ++ v +e pgg + y+ +Ntk +p ++++vRqAl+  
  gi|242399033|ref|YP_002994457.1| 227 IIIKFYRDASTMRLALQNGEIDIAwRTLRPTDIESLKSEGKYSV-IEVPGGFIRYICLNTKSEPTNNVKVRQALAAV 302
                                       ******9999999999*****99888999***************.******************************** PP

                                       S-HHHHHHHCTTTSSEEESSSSTTTSTTCCSCHCCCSHHSHHHHHHHHHHHTT-BCSSTSCEETCEEEEEEEEETTS CS
                         SBP_bac_5 231 iDreeivkavlegyatpansllppsspgadeeykpaykaydpekAkklLkeaGykdgdggglrekklkltlllasgs 307
                                       iDr+ei ++v++g+ +p +sl+p++++++ + +k++y +++++ Ak+lLke+Gy+ ++  ++     +l ++ + ++
  gi|242399033|ref|YP_002994457.1| 303 IDRQEISNKVFKGTVEPLYSLVPNGMWSHIDVFKNKYGDGNIDLAKQLLKETGYDENNPLKI-----QLWYTPTHYG 374
                                       *********************************************************98776.....6888888889 PP

                                       HHHHHHHHHHHHHHHHTT.EEEEEEEECHHHHHHHHHHCTTESEEEEEEECTTSTTHHHHHHHHSTTCTT CS
                         SBP_bac_5 308 paekaiaeliqqqlkkiG.ikvevktvdwaatylervkdgdfdmillgwgadypdpdnflnpflsssgag 376
                                        +e ++a+++++ql++ G i+ve+k+ +w  ty +++++g+++++llgw++dy dpd+++ pfl+s++++
  gi|242399033|ref|YP_002994457.1| 375 DTEADLAQVLKEQLEETGvIQVEIKSAEW-GTYVDYARNGQMQFYLLGWYPDYLDPDDYTTPFLKSTANS 443
                                       9999*************************.***********************************99876 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 ?    2.9   0.0     0.015        66      38      66 ..     235     262 ..     230     281 .. 0.78
   2 !   13.1   0.3   1.2e-05     0.053      16      84 ..     380     450 ..     374     485 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.015
                                       SHHHHHHHHHTTSSSEEEEEEHHHHHHHH CS
                             OpuAC  38 stavlfaalasGdiDvypeewtgtayeay 66 
                                       +  +++ al++G+iD+++    +t  e +
  gi|242399033|ref|YP_002994457.1| 235 A-STMRLALQNGEIDIAWRTLRPTDIESL 262
                                       4.67999**********987777765555 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 1.2e-05
                                       HHHHHHHHHHHTTE.EEEEEEEESHHHHHHHHHTTSSSEEEEEEHHHH..HHHHHHHHHHHHEEEEEEEESE CS
                             OpuAC  16 laeilkqllekkGy.kveltnlgstavlfaalasGdiDvypeewtgta..yeaykkaveekkglevlgplga 84 
                                       la++lk+ le+ G+ +ve  +++  ++++   ++G++++y+ +w +     ++y + + + +   ++g+ +a
  gi|242399033|ref|YP_002994457.1| 380 LAQVLKEQLEETGViQVEIKSAEW-GTYVDYARNGQMQFYLLGWYPDYldPDDYTTPFLKSTANSWAGTGYA 450
                                       79************9999999998.*******************9987664444444444444555444444 PP

>> STAT6_C  STAT6 C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   4.1e-05      0.18     126     179 ..     324     377 ..     314     385 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.1e-05
                                       XXXXXSHHHHTXSS-----HHHHHHHHH-XSSXXXXXXXXXXXXXXXXXXXXXX CS
                           STAT6_C 126 fpqetwvgedlfppllppteqdltkllleGqgeeggGslgvqpllqpshyGqsg 179
                                        p + w+  d+f       + dl+k ll+  g +   +l +q    p+hyG + 
  gi|242399033|ref|YP_002994457.1| 324 VPNGMWSHIDVFKNKYGDGNIDLAKQLLKETGYDENNPLKIQLWYTPTHYGDTE 377
                                       6999***********************************************976 PP

>> Cu-oxidase_4  Multi-copper polyphenol oxidoreductase laccase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   3.7e-05      0.17     171     210 ..     369     408 ..     343     412 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.7e-05
                                       EEEETTEEEE-HHHHHHHHHHHTT-..SEEEE---BTTT- CS
                      Cu-oxidase_4 171 aaeeegkaylDLaalarlqLeeaGvkeenieasglCTvce 210
                                       ++++ g + +DLa++ ++qLee+Gv + +i+++++ T+ +
  gi|242399033|ref|YP_002994457.1| 369 TPTHYGDTEADLAQVLKEQLEETGVIQVEIKSAEWGTYVD 408
                                       455666667****************************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (523 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       668  (0.0372581); expected 358.6 (0.02)
Passed bias filter:                      613  (0.0341904); 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: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.49
# Mc/sec: 3181.70
//
Query:       gi|242399034|ref|YP_002994458.1|  [L=339]
Description: peptide ABC transporter permease [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.8e-48  162.5  11.0    8.8e-48  162.5  11.0    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 !    1.8   0.5    0.0098   1.8e+02      25      44 ..      12      43 ..       7      94 .. 0.72
   2 !  162.5  11.0   4.9e-52   8.8e-48       1     184 [.     120     338 ..     120     339 .] 0.99

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.0098
                      BPD_transp_1 25 ivllslPsfvlaillvlvf............v 44
                                        l+ +P+++++  +v++f            v
  gi|242399034|ref|YP_002994458.1| 12 RGLMIIPTILILYTIVFIFlrilpgnpvlavV 43
                                      45788899998888887776666666544440 PP

  == domain 2  score: 162.5 bits;  conditional E-value: 4.9e-52
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf.................................. 43 
                                       g+l+G +aa +++ k+d  +r ++i+ ++l + +++++l++vf                                  
  gi|242399034|ref|YP_002994458.1| 120 GLLTGTIAAAKKSTKIDTGMRLYSIIAYTLFIPWFGMMLQYVFgihfhllptsgridpgielqritglyvldslltg 196
                                       7899************************************************************************* PP

                      BPD_transp_1  44 ...vilsilghlilpviillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglila 117
                                          +++s++ h ilp+ +l+++ +++y+rl+r++++++l++d+++ ++a+G+++w++++ ++l+na++p++t+++l+
  gi|242399034|ref|YP_002994458.1| 197 nweAFSSAVRHVILPATTLGIVLSGAYTRLVRNNMVDVLSQDFIRSYYARGVKDWKVMW-YALKNAFIPVVTLMGLQ 272
                                       ***********************************************************.***************** PP

                      BPD_transp_1 118 fggllggavlleflgswpGlgtllleailgydyseisnggvlalviavlllnlvadilqrlldprvr 184
                                       f++llggavl+e++++wpG+gt++++ i ++dy++i+ g+v++++++v l++l++di+++lldprv+
  gi|242399034|ref|YP_002994458.1| 273 FAILLGGAVLTETTFNWPGMGTFIVDRIDYRDYNAIQ-GAVVFFAFFVGLISLIVDIVYALLDPRVK 338
                                       *************************************.***************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       799  (0.0445647); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); 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: 00:00:00.51
# Mc/sec: 1998.85
//
Query:       gi|242399035|ref|YP_002994459.1|  [L=282]
Description: peptide ABC transporter permease [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.9e-27   94.2  11.1    7.9e-27   94.2  11.1    2.1  2  BPD_transp_1  Binding-protein-dependent transport system inne
    8.9e-08   32.0   3.5    8.9e-08   32.0   3.5    4.1  5  OppC_N        N-terminal TM domain of oligopeptide transport 


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.4     0.017   1.5e+02      25      44 ..      22      68 ..       8      97 .. 0.53
   2 !   94.2  11.1   8.8e-31   7.9e-27       1     183 [.      98     277 ..      98     279 .. 0.98

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.017
                      BPD_transp_1 25 ivllslPsfvlaillvlvf...........................v 44
                                       ++l++ ++v+++ +++ +                            
  gi|242399035|ref|YP_002994459.1| 22 LFGLAIVILVIIMAIFAPLiapydptkttedsfappskehlmgtnrL 68
                                      44444444444444444445555555555555555555555555553 PP

  == domain 2  score: 94.2 bits;  conditional E-value: 8.8e-31
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilp.viillllsaapyvrlirraal 76 
                                       g++lG++++ ++++k+d+ l+++++ ++++P ++lai++        +lg +    +i++++++ + y+r++r + l
  gi|242399035|ref|YP_002994459.1|  98 GVPLGLISG-YHGGKIDRGLSVIMDSIYAFPALILAIVIA------VVLGPSPVNtAIAISFVYVPTYFRMVRGQTL 167
                                       89*******.******************************......8999777777********************* PP

                      BPD_transp_1  77 rslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydysei 153
                                       +   + +veaa+alG + ++i+ k++lPn++p+i+  + l+++ ++   + l+flg    l+ +  ++ +gyd+  +
  gi|242399035|ref|YP_002994459.1| 168 SLKGQLFVEAAKALGSRNKEIMLKYILPNLAPTILVVFTLSVADAILTEAGLSFLG----LSVTPPTPDWGYDLRVG 240
                                       ********************************************************....***************** PP

                      BPD_transp_1 154 s.......nggvlalviavlllnlvadilqrlldprv 183
                                       +       +++v++ +i+++ll  ++ ++ ++l+ r+
  gi|242399035|ref|YP_002994459.1| 241 QpflldgyWWLVFFPGIMIMLLAMAFALIGEALSERI 277
                                       ********************************99997 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 !   32.0   3.5     1e-11   8.9e-08      17      51 .]      22      57 ..      20      57 .. 0.86
   2 ?    0.3   0.3     0.077   6.9e+02      18      34 ..      84     100 ..      68     107 .. 0.78
   3 ?   -0.5   1.2      0.14   1.3e+03      22      34 ..     129     141 ..     126     158 .. 0.75
   4 ?   -2.5   0.1       0.6   5.4e+03      21      32 ..     203     214 ..     200     237 .. 0.52
   5 ?   -1.1   0.5      0.21   1.9e+03      21      36 ..     258     273 ..     252     276 .. 0.56

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 1e-11
                            OppC_N 17 vvglvilllllliaifaPliaPydpqdli.qnllpP 51
                                      ++gl+i++l++++aifaPliaPydp+  + + ++pP
  gi|242399035|ref|YP_002994459.1| 22 LFGLAIVILVIIMAIFAPLIAPYDPTKTTeDSFAPP 57
                                      69***********************55553449999 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.077
                            OppC_N  18 vglvilllllliaifaP 34 
                                       +  v++++ll ++i  P
  gi|242399035|ref|YP_002994459.1|  84 LYVVFIATLLSMSIGVP 100
                                       55689999999998766 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.14
                            OppC_N  22 illlllliaifaP 34 
                                       ++l+++++++++P
  gi|242399035|ref|YP_002994459.1| 129 LILAIVIAVVLGP 141
                                       5666777777776 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 0.6
                            OppC_N  21 villlllliaif 32 
                                       v++ l ++ ai+
  gi|242399035|ref|YP_002994459.1| 203 VVFTLSVADAIL 214
                                       333333333443 PP

  == domain 5  score: -1.1 bits;  conditional E-value: 0.21
                            OppC_N  21 villlllliaifaPli 36 
                                        i ll  ++a++++ +
  gi|242399035|ref|YP_002994459.1| 258 MIMLLAMAFALIGEAL 273
                                       2333333346666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       702  (0.0391544); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1914.72
//
Query:       gi|242399036|ref|YP_002994460.1|  [L=322]
Description: ABC-type dipeptide transport system, ATPase component [Thermococcus sibiricus MM 739]
Scores for complete 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-30  104.6   0.0    8.2e-30  104.1   0.0    1.2  1  ABC_tran         ABC transporter
      5e-19   68.6   0.0    9.1e-19   67.7   0.0    1.4  1  oligo_HPY        Oligopeptide/dipeptide transporter, C-termin
    7.3e-07   29.3   0.8    0.00038   20.4   0.0    2.3  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    3.1e-06   26.8   0.5    1.4e-05   24.7   0.5    1.9  1  SMC_N            RecF/RecN/SMC N terminal domain
     0.0013   17.9   0.0     0.0019   17.3   0.0    1.2  1  T2SSE            Type II/IV secretion system protein
     0.0027   17.4   0.0     0.0046   16.7   0.0    1.4  1  AAA_29           P-loop containing region of AAA domain
     0.0032   17.6   0.0     0.0066   16.6   0.0    1.5  1  tRNA_lig_kinase  tRNA ligase kinase domain
  ------ inclusion threshold ------
      0.012   15.3   1.2       0.37   10.4   0.2    2.1  2  AAA_15           AAA ATPase domain
      0.027   13.8   0.0       0.49    9.8   0.0    2.1  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.038   14.4   0.0      0.097   13.1   0.0    1.5  1  AAA_16           AAA ATPase domain
      0.065   13.1   0.0       0.11   12.4   0.0    1.4  1  RsgA_GTPase      RsgA GTPase
      0.069   12.3   0.0       0.13   11.4   0.0    1.4  1  NB-ARC           NB-ARC domain
      0.094   13.1   0.0       0.14   12.5   0.0    1.5  1  AAA              ATPase family associated with various cellul
      0.097   13.0   0.1       0.38   11.0   0.1    2.0  1  AAA_22           AAA domain
       0.12   11.4   0.0       0.21   10.6   0.0    1.3  1  Parvo_NS1        Parvovirus non-structural protein NS1
       0.21   11.1   0.0       0.36   10.3   0.0    1.4  1  AAA_7            P-loop containing dynein motor region


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.1   0.0   7.3e-33   8.2e-30       2     136 ..      26     180 ..      25     181 .. 0.92

  Alignments for each domain:
  == domain 1  score: 104.1 bits;  conditional E-value: 7.3e-33
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--....SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS..- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxx....xxxxxxxxxxxxxxxx..x RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkp....teGeilldgkdlke....qeleslrkeigvlpqe..p 68 
                                       +nvs+ + + e v +vGe+G+GKSt++ ++++l+       +G+i +++k++ e    + +e+  kei++++q+  +
  gi|242399036|ref|YP_002994460.1|  26 ENVSFAIGKREWVSFVGESGSGKSTVAYAILNLVPSpgqiINGKIIFEDKNILEltneELREIRGKEISMIFQDpmT 102
                                       79*******************************98778889999999999999999988889999*********988 PP

                                       -S-TTSBHHHH..........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEEST CS
                                       xxxxxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  69 qlfpeltvren..........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEp 135
                                       +l+p  +++++          e++e  eka + l+ ++l+++++++ p++LSgGq+qrva+a a++ +pkll++DEp
  gi|242399036|ref|YP_002994460.1| 103 SLDPLRKIGDQiaevmiehgiEKEEAYEKAKELLKKVNLPEDRISYYPHQLSGGQRQRVAIAIAMAFNPKLLIADEP 179
                                       99999999999*********9777777888888888888889999******************************** PP

                                       T CS
                                       x RF
                          ABC_tran 136 t 136
                                       t
  gi|242399036|ref|YP_002994460.1| 180 T 180
                                       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 !   67.7   0.0   8.2e-22   9.1e-19       1      63 [.     231     292 ..     231     293 .. 0.96

  Alignments for each domain:
  == domain 1  score: 67.7 bits;  conditional E-value: 8.2e-22
                         oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekdklekikgeapslerldeGCpFapRCpfale 63 
                                       vE g++++++++plHPYT+ Ll+svp+l +ek+ ++ i+g +p+l++ ++GC+F+pRCp  +e
  gi|242399036|ref|YP_002994460.1| 231 VEFGRVEQILENPLHPYTQSLLASVPDLWSEKE-IKAIPGYPPDLRNPPSGCRFHPRCPIFKE 292
                                       8********************************.*************************8765 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 !    7.3   0.3    0.0032       3.6       4      22 ..      40      58 ..      38     110 .. 0.75
   2 !   20.4   0.0   3.4e-07   0.00038     227     301 ..     143     214 ..     104     216 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0032
                            AAA_21  4 liGpNgsGKSnLLdaldll 22
                                      ++G  gsGKS++ +a+  l
  gi|242399036|ref|YP_002994460.1| 40 FVGESGSGKSTVAYAILNL 58
                                      79**************766 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 3.4e-07
                            AAA_21 227 gdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSpll 301
                                       +d+    +++lS G+++  a++ a++  +   +ll+ DEp + L+  ++  +++l+  l+++g+ ++++TH+ +l
  gi|242399036|ref|YP_002994460.1| 143 EDRISYYPHQLSGGQRQRVAIAIAMAFNP---KLLIADEPTTALDVIVQDAIMDLIGTLKDEGTSIFFVTHDISL 214
                                       4444456899********99999999999...99**********************8888889********9877 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.5   1.2e-08   1.4e-05      25     207 ..      36     220 ..      22     231 .. 0.69

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.2e-08
                                       SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCC...CCCC--.BTTCSSTTEEEEEEEEEETTEE....SSSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxx.xxxxxxxxxxxxxxxxxxxxxx....xxxx RF
                             SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrsekl...sdlihk.skekasvkkaeveitfdnedkk....lkie 93 
                                       +  + vG+ GSGKs +  Ail +   +  + +  + +   ++++   ++e +++   e++++f+++  +     ki 
  gi|242399036|ref|YP_002994460.1|  36 EWVSFVGESGSGKSTVAYAILNLVP-SPGQIINGKIIfedKNILELtNEELREIRGKEISMIFQDPMTSldplRKIG 111
                                       556789**************77765.44434444432221233333457888889999*****98888855544555 PP

                                       SSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  94 keevsisrrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaa 170
                                       ++  +++ +   ++e  y+  ++    k+v+    +   ++++LSgG+++ va+a+ +A +   p+ l + De   a
  gi|242399036|ref|YP_002994460.1| 112 DQIAEVMIEHGIEKEEAYEKAKELL--KKVNLPEDRISYYPHQLSGGQRQRVAIAIAMAFN---PK-LLIADEPTTA 182
                                       5555555555555555554444333..334433456666777**************98864...44.7899****** PP

                                       S-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-SC CS
                                       xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx RF
                             SMC_N 171 LDeknvkkvaellkekskn.aQfivislreemlekadk 207
                                       LD     ++ +l+ + +++ + ++ ++++  + ++ + 
  gi|242399036|ref|YP_002994460.1| 183 LDVIVQDAIMDLIGTLKDEgTSIFFVTHDISLAAERSD 220
                                       *************9888776777788887666555443 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   0.0   1.7e-06    0.0019     119     193 ..      25     102 ..       4     115 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.7e-06
                             T2SSE 119 aevlrkavrerglilvsGgTgsGKttllyallkeinksderi...vtvEDpvEiqleganqvqlnakkakvtfadll 192
                                        e ++ a+ +r  + + G  gsGK+t++ya+l+ +++  + i   ++ ED   ++l +++  +++ k+ ++ f+d +
  gi|242399036|ref|YP_002994460.1|  25 VENVSFAIGKREWVSFVGESGSGKSTVAYAILNLVPSPGQIIngkIIFEDKNILELTNEELREIRGKEISMIFQDPM 101
                                       45566778889999999********************9433344457899999999999999999888888777765 PP

                             T2SSE 193 r 193
                                        
  gi|242399036|ref|YP_002994460.1| 102 T 102
                                       5 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   4.1e-06    0.0046      16      46 ..      29      59 ..      20      68 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.1e-06
                            AAA_29 16 tieidlkgatlltGpsGsGKSTllDAiqalL 46
                                      ++ i  ++ + ++G+sGsGKST+  Ai  l 
  gi|242399036|ref|YP_002994460.1| 29 SFAIGKREWVSFVGESGSGKSTVAYAILNLV 59
                                      455555668899***********99988765 PP

>> tRNA_lig_kinase  tRNA ligase kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   5.9e-06    0.0066       9      65 ..      45     103 ..      39     127 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.9e-06
                                       TSSHHHHHHHHHHH-TTSEEEEGGGS..-TT-SS-HHHHHHHTTSSTT--EEEEES--- CS
                   tRNA_lig_kinase   9 GCGkttvaltlenlfgeWghvqnDni..tgkdkkklvkealellkkdeskvvlvDrnnh 65 
                                       G Gk+tva ++ nl +  g++ n  i  ++k+  +l++e l++++ +e+++++ D   +
  gi|242399036|ref|YP_002994460.1|  45 GSGKSTVAYAILNLVPSPGQIINGKIifEDKNILELTNEELREIRGKEISMIFQDPMTS 103
                                       99***********************95445577799*****************996655 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.2   0.00033      0.37      25      68 ..      37      81 ..      23      89 .. 0.64
   2 ?    4.2   0.7     0.025        28     234     364 ..      85     210 ..      64     214 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00033
                            AAA_15 25 ltvliGkNnsGKSsilealdlFlnnk.ekknkkvikiekedleif 68
                                         ++G+ +sGKS++++a+  +     +  n k i+++k+ le +
  gi|242399036|ref|YP_002994460.1| 37 WVSFVGESGSGKSTVAYAILNLVPSPgQIINGKIIFEDKNILELT 81
                                      668***************955443221333344555555555555 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.025
                            AAA_15 234 l....eeelteklkeiqeklkeidkklaeelkkilkkkidkikkfnykgkkneeieik...ddeelplnknGsGvqr 303
                                       l     +e+ +++++  ++l+ + k+ ++ ++  ++  i+k   + y ++k+ +++++   d  + + ++ + G+++
  gi|242399036|ref|YP_002994460.1|  85 LreirGKEISMIFQDPMTSLDPLRKIGDQIAEVMIEHGIEK--EEAYEKAKELLKKVNlpeDRISYYPHQLSGGQRQ 159
                                       23333455556666666666666666655566666666666..4555555555555557779999999********* PP

                            AAA_15 304 llllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                        + +++  +++ k          l+ +EP + L    q  +++l+  l +++   +++ TH
  gi|242399036|ref|YP_002994460.1| 160 RVAIAIAMAFNPKL---------LIADEPTTALDVIVQDAIMDLIGTLKDEGT-SIFFVTH 210
                                       ***99988877666.........888888888888888888888887777775.7888888 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00043      0.49       7      48 ..      20      61 ..      16      90 .. 0.83
   2 ?    1.9   0.0      0.11   1.2e+02     174     200 ..     142     168 ..     130     217 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00043
                      Mg_chelatase  7 GqeeakraleiaaaGgHnlllvGppGsGKtmlakrlpsllpp 48
                                      G  +a + +  a+  +  + +vG +GsGK+ +a ++ +l+p+
  gi|242399036|ref|YP_002994460.1| 20 GTVKAVENVSFAIGKREWVSFVGESGSGKSTVAYAILNLVPS 61
                                      55566666666666667788*******************997 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.11
                      Mg_chelatase 174 sekeierYlsklsgplldRidlqvevk 200
                                        e++i+ Y ++lsg    R+ + +++ 
  gi|242399036|ref|YP_002994460.1| 142 PEDRISYYPHQLSGGQRQRVAIAIAMA 168
                                       566666666666666666666666653 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   8.6e-05     0.097      23      59 ..      34      69 ..      18     118 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.6e-05
                            AAA_16 23 rpelvllsGesGvGKsslvrellralekdggiflrgk 59
                                        e v ++GesG+GKs+++ ++l+ +    g  ++gk
  gi|242399036|ref|YP_002994460.1| 34 KREWVSFVGESGSGKSTVAYAILNLVPSP-GQIINGK 69
                                      4478999************9999644443.5555554 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   9.9e-05      0.11      84     119 ..      19      55 ..       3      83 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9.9e-05
                                       TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHH CS
                       RsgA_GTPase  84 aktkegleelkellkd.ktsvlvGqSGvGKStLinal 119
                                       a t +++e+++ ++ + + + +vG+SG GKSt+  a+
  gi|242399036|ref|YP_002994460.1|  19 AGTVKAVENVSFAIGKrEWVSFVGESGSGKSTVAYAI 55 
                                       556778899999998878999***********97665 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00012      0.13      18      42 ..      35      57 ..      20      64 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00012
                                      SCSEEEEEEESTTSSHHHHHHHHCC CS
                            NB-ARC 18 lqslvvalvGmgGvGKttlakqiln 42
                                          +v++vG  G+GK+t+a  iln
  gi|242399036|ref|YP_002994460.1| 35 R--EWVSFVGESGSGKSTVAYAILN 57
                                      3..49***************99987 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00013      0.14       2      52 ..      39      99 ..      38     178 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00013
                                      EEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSS..........STTHHHHHHHHHHHH CS
                               AAA  2 llyGppGtGKTllakavakelgvefleisgsellsk..........yvgesekkirelfke 52
                                       ++G  G GK+++a a+ + + ++   i+g+ ++++          + + + k+i+++f++
  gi|242399036|ref|YP_002994460.1| 39 SFVGESGSGKSTVAYAILNLVPSPGQIINGKIIFEDknileltneeLREIRGKEISMIFQD 99
                                      589*****************96665555555555111211111111334455555555554 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00034      0.38      10      31 ..      40      61 ..      33     211 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00034
                            AAA_22 10 vtGesGtGKTtllrrlleqlde 31
                                       +GesG+GK+t++  +l+  + 
  gi|242399036|ref|YP_002994460.1| 40 FVGESGSGKSTVAYAILNLVPS 61
                                      69***********999988764 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00019      0.21     110     142 ..      31      63 ..      19      70 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00019
                         Parvo_NS1 110 qlgkrntvwfyGpantGktnlaeaIakavplyg 142
                                        +gkr+ v f+G+   Gk+ +a aI + vp+ g
  gi|242399036|ref|YP_002994460.1|  31 AIGKREWVSFVGESGSGKSTVAYAILNLVPSPG 63 
                                       689**************************9865 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 ?   10.3   0.0   0.00032      0.36      29      58 ..      31      60 ..      16      91 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00032
                             AAA_7 29 llknkkpvllvGptGtGKtviikdllkkld 58
                                       + ++  v +vG++G+GK++++  +l+ ++
  gi|242399036|ref|YP_002994460.1| 31 AIGKREWVSFVGESGSGKSTVAYAILNLVP 60
                                      566788899*************99998777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       746  (0.0416086); expected 358.6 (0.02)
Passed bias filter:                      700  (0.0390429); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.47
# Mc/sec: 2071.91
//
Query:       gi|242399037|ref|YP_002994461.1|  [L=336]
Description: ABC-type dipeptide transport system, ATPase component [Thermococcus sibiricus MM 739]
Scores for complete 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  110.8   0.0    9.8e-32  110.3   0.0    1.2  1  ABC_tran     ABC transporter
    9.4e-22   77.3   0.2    2.2e-21   76.1   0.2    1.7  1  oligo_HPY    Oligopeptide/dipeptide transporter, C-terminal r
    4.3e-05   23.8   1.1    0.00068   19.9   1.1    2.1  1  AAA_22       AAA domain
  ------ inclusion threshold ------
      0.015   15.6   0.0      0.026   14.9   0.0    1.3  1  AAA_19       AAA domain
      0.016   15.6   0.0      0.021   15.2   0.0    1.3  1  AAA_16       AAA ATPase domain
      0.082   12.6   0.2       0.43   10.3   0.0    2.0  2  IstB_IS21    IstB-like ATP binding protein
      0.097   12.6   0.0       0.21   11.5   0.0    1.5  1  Rad17        Rad17 P-loop domain
       0.11   12.2   0.0       0.13   11.9   0.0    1.3  1  ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-bindi
       0.11   12.2   0.1        2.2    7.9   0.0    2.1  2  AAA_30       AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.3   0.0   4.9e-35   9.8e-32       2     136 ..      44     196 ..      43     197 .. 0.95

  Alignments for each domain:
  == domain 1  score: 110.3 bits;  conditional E-value: 4.9e-35
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG...B-HHHCCHCEEEE-SS..--S-TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxx..xxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke...qeleslrkeigvlpqe..pqlfpe 73 
                                       + +s+++++ge++a++Ge+G+GK+t  +++++l +pt G+i +dg d+++   + l+ +r+++++++q+  ++l p+
  gi|242399037|ref|YP_002994461.1|  44 DGISFEVQKGETLALIGESGCGKTTAGRVILRLIEPTDGKIIFDGVDITTlsyDALRPYRRRMQMVFQDpyASLSPR 120
                                       789**********************************************9999****************999***** PP

                                       SBHHHH..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxxx..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  74 ltvren..............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       +++++               e++e + k+l+++gl+  +d+  ++ p++LSgGq+qrv++ara++ kp+++++DE+ 
  gi|242399037|ref|YP_002994461.1| 121 MKIGDAiahpllihnlatkeEAKEMALKMLRRVGLTP-EDEFYERYPHHLSGGQRQRVVIARAMILKPEFVIADEAV 196
                                       ****************987666667999******999.999999999****************************96 PP

>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.1   0.2   1.1e-24   2.2e-21       1      65 []     248     313 ..     248     313 .. 0.97

  Alignments for each domain:
  == domain 1  score: 76.1 bits;  conditional E-value: 1.1e-24
                         oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekd.klekikgeapslerldeGCpFapRCpfaleeC 65 
                                       vE+gp+++++++p HPYT aL+++vp+l+++ + k  +i ge+p++ + ++GC+F+pRCpf++eeC
  gi|242399037|ref|YP_002994461.1| 248 VEIGPTQEVLNNPVHPYTLALIQAVPSLRKREKrKQIEITGEVPNAVNPPSGCRFHPRCPFMTEEC 313
                                       8***************************988777999***************************** PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   1.1   3.4e-07   0.00068       7     129 ..      55     226 ..      50     234 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 3.4e-07
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaee.............................................. 37 
                                        l+++GesG+GKTt  r +l+  +    +++                                              
  gi|242399037|ref|YP_002994461.1|  55 TLALIGESGCGKTTAGRVILRLIE----PTDgkiifdgvdittlsydalrpyrrrmqmvfqdpyaslsprmkigdai 127
                                       589************999999873....3335677999************999999999999999999999998886 PP

                            AAA_22  38 erpevvfvtlpsstsskdllrellralglelka..erlsseell.ealeqalrarav...ielliiDEaqhlr.... 104
                                       ++p +++  +++++  k+++ ++lr +gl  ++  ++   ++l   + ++ + ara+   +e++i DEa  ++    
  gi|242399037|ref|YP_002994461.1| 128 AHPLLIHNLATKEE-AKEMALKMLRRVGLTPEDefYERYPHHLSgGQRQRVVIARAMilkPEFVIADEAVSMIdvsm 203
                                       66665555555555.9999999999999988889988888888878888888888889*************877955 PP

                            AAA_22 105 seealeeLrsllnlsrkgvqliLvG 129
                                       ++ +le L s+ +  +++++++++ 
  gi|242399037|ref|YP_002994461.1| 204 RASILELLESFKE--EYNLSMLFIT 226
                                       5999999999999..*****98774 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   1.3e-05     0.026       9     125 ..      52     211 ..      45     226 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.3e-05
                            AAA_19   9 kekvllvtaGpGtGKTrvlkhivallvelggvkp.eeillvaftgrAakelrerlaalgae................ 68 
                                       k ++l++++  G+GKT+  + i++l++ + g    + + + ++   A +  r r++++ ++                
  gi|242399037|ref|YP_002994461.1|  52 KGETLALIGESGCGKTTAGRVILRLIEPTDGKIIfDGVDITTLSYDALRPYRRRMQMVFQDpyaslsprmkigdaia 128
                                       678899******************9998876544488999***************9999999************997 PP

                            AAA_19  69 .atTiHrlalldfddlltealelle..........................eaeeekklqeeellivDE.fqdvd.e 116
                                           iH+l   + ++ +++al++l+                              +  + + e +i DE ++++d  
  gi|242399037|ref|YP_002994461.1| 129 hPLLIHNL--ATKEEAKEMALKMLRrvgltpedefyeryphhlsggqrqrvV-IARAMILKPEFVIADEaVSMIDvS 202
                                       66679999..666666667888888999999999999999999999887753.33455558999999*955999966 PP

                            AAA_19 117 lqyrLlkal 125
                                       +  ++l+ l
  gi|242399037|ref|YP_002994461.1| 203 MRASILELL 211
                                       666665544 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   1.1e-05     0.021      22      57 ..      53      90 ..      41     214 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.1e-05
                            AAA_16 22 grpelvllsGesGvGKsslvrellralekd..ggif..lr 57
                                      g  e + l+GesG+GK++  r +lr +e +  ++if  + 
  gi|242399037|ref|YP_002994461.1| 53 G--ETLALIGESGCGKTTAGRVILRLIEPTdgKIIFdgVD 90
                                      3..7899*****************9999885324444433 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00022      0.43      25      61 ..      30      67 ..       8      78 .. 0.84
   2 ?   -0.3   0.1      0.38   7.5e+02     104     152 ..     182     232 ..     169     239 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00022
                         IstB_IS21 25 raarsldkrkvkeLatlsf.iekkenivllGpsGvGKs 61
                                      ++ r+  ++ vk++ + sf ++k e ++l+G sG GK+
  gi|242399037|ref|YP_002994461.1| 30 ETLRKEPQKYVKAVDGISFeVQKGETLALIGESGCGKT 67
                                      5567788999999*9***98999**************9 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.38
                         IstB_IS21 104 krllkvdllilDdlgllpldqaeaellfevie...kryerrsiiitsnlpfa 152
                                       + +lk++ +i D+  +  +d   ++ ++e++e   + y+ + + it ++ +a
  gi|242399037|ref|YP_002994461.1| 182 AMILKPEFVIADEA-VSMIDVSMRASILELLEsfkEEYNLSMLFITHDIAVA 232
                                       56788889999884.4555656666666665511166777777777776665 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0    0.0001      0.21      12      65 ..      20      73 ..      16      80 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0001
                             Rad17 12 kykPekaeelavhkkkieevkewlkadvLesrkkriLLisGPsGCgkstvvkvL 65
                                      ky P k   l   +k  ++  ++++  + e +k + L + G sGCgk+t+ +v+
  gi|242399037|ref|YP_002994461.1| 20 KYFPVKRGILETLRKEPQKYVKAVDGISFEVQKGETLALIGESGCGKTTAGRVI 73
                                      566666555555555555556788899999**999**************97765 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   6.7e-05      0.13       4      48 ..      42      88 ..      40     248 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.7e-05
                                      HHHHH.S-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSS.EEEEEE CS
                                      xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
                       ATP-synt_ab  4 vlDal.fpivqGqrtlipgafgvGktvisqslskqsnsdd.aiiyvg 48
                                      ++D + f + +G++++++g++g+Gkt+  + +++  + +d  ii+ g
  gi|242399037|ref|YP_002994461.1| 42 AVDGIsFEVQKGETLALIGESGCGKTTAGRVILRLIEPTDgKIIFDG 88
                                      56654377899****************99888888776666777766 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0    0.0011       2.2      20      50 ..      55      85 ..      47      98 .. 0.85
   2 ?    2.0   0.0     0.073   1.4e+02      82     113 ..     180     212 ..     125     219 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0011
                            AAA_30 20 vavltGpAGtGKttalkalreaweaaggrvi 50
                                      + +l G  G GKtta +++ +++e   g++i
  gi|242399037|ref|YP_002994461.1| 55 TLALIGESGCGKTTAGRVILRLIEPTDGKII 85
                                      67899**************999998866665 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.073
                            AAA_30  82 grarlepgtllivDEa.gmvdtkqlaallkaae 113
                                       +ra + + + +i DEa +m+d ++ a++l+ +e
  gi|242399037|ref|YP_002994461.1| 180 ARAMILKPEFVIADEAvSMIDVSMRASILELLE 212
                                       44556666999****878999999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       679  (0.0378716); expected 358.6 (0.02)
Passed bias filter:                      632  (0.0352502); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 2227.68
//
Query:       gi|242399038|ref|YP_002994462.1|  [L=157]
Description: hypothetical protein TSIB_1057 [Thermococcus sibiricus MM 739]
Scores for complete 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-44  151.1   0.0    2.5e-44  150.9   0.0    1.0  1  Mut7-C          Mut7-C RNAse domain
    1.7e-05   24.5   0.1    3.9e-05   23.3   0.1    1.6  1  DUF5615         Domain of unknown function (DUF5615)
  ------ inclusion threshold ------
      0.011   15.7   1.0        2.3    8.3   0.0    2.4  2  Rubredoxin      Rubredoxin
      0.012   15.8   0.4        1.4    9.1   0.0    2.4  2  Zn-ribbon_8     Zinc ribbon domain
       0.03   14.7   1.1       0.97    9.9   0.2    2.3  2  zf-IS66         zinc-finger binding domain of transposase IS6
      0.083   12.9   0.2         14    5.7   0.0    2.3  2  ADK_lid         Adenylate kinase, active site lid
        0.1   13.1   0.3       0.33   11.4   0.3    1.7  2  E6              Early Protein (E6)
       0.12   12.3   1.9        8.2    6.4   0.1    2.2  2  Zn_ribbon_SprT  SprT-like zinc ribbon domain
       0.18   11.4   1.9         11    5.7   0.1    2.5  2  zf_UBZ          Ubiquitin-Binding Zinc Finger
       0.43   10.7   2.2         14    5.9   0.2    2.9  3  zf-ACC          Acetyl-coA carboxylase zinc finger domain
        0.5    9.9   4.1        9.5    5.8   4.1    2.4  1  TF_Zn_Ribbon    TFIIB zinc-binding
       0.79    9.7   4.2         13    5.8   0.4    2.4  2  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)


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 !  150.9   0.0   1.7e-47   2.5e-44       2     144 ..       7     146 ..       6     148 .. 0.95

  Alignments for each domain:
  == domain 1  score: 150.9 bits;  conditional E-value: 1.7e-47
                            Mut7-C   2 rfllDamlgklakyLRllGydalyasdvedeellalaakekrillTrdreLlkraklkkgvlltsrdveeqlrevia 78 
                                       +f++D+mlg+la++LRl+Gyd++y  + +d+e+l+++++e+rillTrd  L+kr +++  +l++s+++eeq++++  
  gi|242399038|ref|YP_002994462.1|   7 KFIADMMLGRLARWLRLYGYDTVYGIE-DDDEILRISREENRILLTRDETLAKRLEDS--ILIKSNKFEEQVKQL-M 79 
                                       8***********************997.9*************************9999..***************.5 PP

                            Mut7-C  79 rlglkl.slkpelsrCvaCngeleevekeevkervpekvyeeadeftrCekCrkvfWkGshwervee 144
                                       +lg++  +l pe  rC +Cng ++++ekee++++v e vye +def+ C++C++++W G +w+++ +
  gi|242399038|ref|YP_002994462.1|  80 ELGFEFdELFPENARCPKCNGLIRRAEKEEIRGKVLEGVYEDYDEFYICTQCGQIYWPGRQWREMVK 146
                                       66777647999*****************************************************986 PP

>> DUF5615  Domain of unknown function (DUF5615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.1   2.6e-08   3.9e-05       2      56 ..       7      54 ..       6      63 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 2.6e-08
                           DUF5615  2 klllDenlsprlvellreaghdvlhvrelglegasDeeileyAkeedriivTkDk 56
                                      k+++D+ l  rl+++lr  g+d+++   ++    +D+eil++ +ee+ri++T+D+
  gi|242399038|ref|YP_002994462.1|  7 KFIADMMLG-RLARWLRLYGYDTVYG--IE----DDDEILRISREENRILLTRDE 54
                                      899999999.9**********87665..43....89******************6 PP

>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0    0.0015       2.3      25      41 ..      82      99 ..      74     107 .. 0.82
   2 ?    5.4   0.6     0.013        19       2      14 ..     126     138 ..     125     144 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0015
                                      T--GGGS.-TT-BBTTTB CS
                        Rubredoxin 25 gTkFedl.PddWvCPdCg 41
                                      g +F++l P++ +CP+C+
  gi|242399038|ref|YP_002994462.1| 82 GFEFDELfPENARCPKCN 99
                                      56788876*********6 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.013
                                       EEETTT-BEEETT CS
                        Rubredoxin   2 yeCkvCgyvYdpa 14 
                                       y C+ Cg +Y p 
  gi|242399038|ref|YP_002994462.1| 126 YICTQCGQIYWPG 138
                                       89********885 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0   0.00093       1.4      14      38 ..      84     104 ..      81     105 .. 0.70
   2 ?    4.6   0.1     0.024        36       6      14 ..     126     134 ..     121     150 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00093
                       Zn-ribbon_8  14 efevlqsisdaplta.CPeCgsevrr 38 
                                       ef++l +     + a CP+C++  rr
  gi|242399038|ref|YP_002994462.1|  84 EFDELFP-----ENArCPKCNGLIRR 104
                                       5666653.....4555*****98887 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.024
                       Zn-ribbon_8   6 YrCeeCghe 14 
                                       Y C++Cg+ 
  gi|242399038|ref|YP_002994462.1| 126 YICTQCGQI 134
                                       8899**976 PP

>> zf-IS66  zinc-finger binding domain of transposase IS66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.2   0.00065      0.97       3      20 ..      94     111 ..      93     118 .. 0.85
   2 ?    3.2   0.0     0.077   1.2e+02       3      25 ..     127     147 ..     126     149 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00065
                           zf-IS66   3 tCpcCGgllkpigedrvr 20 
                                        Cp+C+gl ++++++++r
  gi|242399038|ref|YP_002994462.1|  94 RCPKCNGLIRRAEKEEIR 111
                                       5*******9*****9998 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.077
                           zf-IS66   3 tCpcCGg.llkpigedrvreeldi 25 
                                       +C +CG+      g   +re ++i
  gi|242399038|ref|YP_002994462.1| 127 ICTQCGQiYW--PGRQ-WREMVKI 147
                                       5999998553..5555.8887776 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.014        21      21      35 ..      92     105 ..      82     105 .. 0.85
   2 ?    5.7   0.0    0.0097        14       3      11 ..     127     135 ..     126     150 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.014
                                       TTB-TTT--.-B--G CS
                           ADK_lid  21 eglCDkCGepLvqRs 35 
                                       +  C kC++ L++R+
  gi|242399038|ref|YP_002994462.1|  92 NARCPKCNG-LIRRA 105
                                       5689*****.99995 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0097
                                       E-TTT--EE CS
                           ADK_lid   3 vCpkCGrsY 11 
                                       +C +CG +Y
  gi|242399038|ref|YP_002994462.1| 127 ICTQCGQIY 135
                                       8*******9 PP

>> E6  Early Protein (E6)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0     0.002         3      66      91 ..      87     112 ..      60     117 .. 0.76
   2 ?   11.4   0.3   0.00022      0.33       1      40 [.      95     134 ..      95     144 .. 0.94

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.002
                                       TGGGSEEEETTT--B--HHHHHHHHH CS
                                E6  66 slsdleiRCvvClklLskeeKeelle 91 
                                       +l+  + RC  C  l+ ++eKee+  
  gi|242399038|ref|YP_002994462.1|  87 ELFPENARCPKCNGLIRRAEKEEIRG 112
                                       5555689***************9865 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00022
                                       BTTTXSBXXHHHHHHHHHTTXBXEEETTEEEBXXHHHHHH CS
                                E6   1 CifCkkllskleallfkekklslvwreglpygvCkkClev 40 
                                       C  C+ l++++e+ +++ k l+ v+ ++  + +C++C ++
  gi|242399038|ref|YP_002994462.1|  95 CPKCNGLIRRAEKEEIRGKVLEGVYEDYDEFYICTQCGQI 134
                                       778**********************************876 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 ?    5.3   0.1     0.012        18      23      33 ..      91     101 ..      90     107 .. 0.78
   2 ?    6.4   0.1    0.0055       8.2       5      12 ..     126     133 ..     110     135 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.012
                    Zn_ribbon_SprT  23 hnYrCrrCkgt 33 
                                       +n rC++C g 
  gi|242399038|ref|YP_002994462.1|  91 ENARCPKCNGL 101
                                       67789999875 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0055
                    Zn_ribbon_SprT   5 YrCtgCgr 12 
                                       Y Ct+Cg+
  gi|242399038|ref|YP_002994462.1| 126 YICTQCGQ 133
                                       78888884 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.2     0.013        20       4      19 ..      94     109 ..      91     109 .. 0.83
   2 ?    5.7   0.1    0.0073        11       2      11 ..     125     134 ..     124     143 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.013
                            zf_UBZ   4 lCerCgkeipeselqE 19 
                                        C++C+  i  +e++E
  gi|242399038|ref|YP_002994462.1|  94 RCPKCNGLIRRAEKEE 109
                                       6*****9999888877 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0073
                            zf_UBZ   2 tylCerCgke 11 
                                        y+C +Cg+ 
  gi|242399038|ref|YP_002994462.1| 125 FYICTQCGQI 134
                                       69******96 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       3.4   5.1e+03      12      19 ..      56      63 ..      54      63 .. 0.79
   2 ?    5.9   0.2    0.0091        14       3      14 ..      94     105 ..      93     109 .. 0.79
   3 ?    3.5   0.0     0.052        77       4       8 ..     128     132 ..     122     134 .. 0.59

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3.4
                            zf-ACC 12 ykkeLern 19
                                      ++k Le++
  gi|242399038|ref|YP_002994462.1| 56 LAKRLEDS 63
                                      68999985 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0091
                            zf-ACC   3 KCpsCgemlykk 14 
                                       +Cp+C+ ++ + 
  gi|242399038|ref|YP_002994462.1|  94 RCPKCNGLIRRA 105
                                       6****9988665 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.052
                            zf-ACC   4 CpsCg 8  
                                       C++Cg
  gi|242399038|ref|YP_002994462.1| 128 CTQCG 132
                                       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 ?    5.8   4.1    0.0064       9.5       2      26 ..      94     132 ..      93     135 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0064
                                       EETTTTCEEC.................HEETSTTCEEESSSS CS
                      TF_Zn_Ribbon   2 kCPnCgstnl.................veDpergelvCtdCG 26 
                                       +CP+C++  l                 +eD++   ++Ct CG
  gi|242399038|ref|YP_002994462.1|  94 RCPKCNG--LirraekeeirgkvlegvYEDYD-EFYICTQCG 132
                                       5899998..33678888888888888788888.666*****9 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.3     0.018        27      22      31 ..      89      98 ..      88     100 .. 0.78
   2 ?    5.8   0.4    0.0086        13      14      23 ..     128     137 ..     125     140 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.018
                           DUF35_N 22 fPPravCphC 31
                                      fP  a Cp+C
  gi|242399038|ref|YP_002994462.1| 89 FPENARCPKC 98
                                      7777999999 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0086
                           DUF35_N  14 CpdCGtvqfP 23 
                                       C+ CG+ ++P
  gi|242399038|ref|YP_002994462.1| 128 CTQCGQIYWP 137
                                       *********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       997  (0.0556082); expected 358.6 (0.02)
Passed bias filter:                      783  (0.0436723); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1093.90
//
Query:       gi|242399039|ref|YP_002994463.1|  [L=252]
Description: Phosphonate matabolism protein PhnP like protein, metallo-beta-lactamase superfamily [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-16   60.6   0.1    1.8e-16   60.2   0.1    1.1  1  Lactamase_B_2  Beta-lactamase superfamily domain
    5.6e-06   26.5   3.7    8.7e-06   25.9   2.8    1.9  1  Lactamase_B    Metallo-beta-lactamase superfamily
     0.0089   15.9   0.1      0.014   15.3   0.1    1.3  1  Lactamase_B_3  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.2   0.1   3.1e-20   1.8e-16       3     201 .]      54     219 ..      52     219 .. 0.84

  Alignments for each domain:
  == domain 1  score: 60.2 bits;  conditional E-value: 3.1e-20
                                       EEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHC CS
                     Lactamase_B_2   3 iLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylal 79 
                                       +LiD g+d+r            ++   p++a+llth H DH+ gl  lr ++++   lyap g ++ l  n      
  gi|242399039|ref|YP_002994463.1|  54 VLIDVGTDIRDL----------LHV--PLEAILLTHWHHDHIYGLYKLRWIAKR-TILYAPNGDADWLMIN------ 111
                                       677777776655..........234..9**********************8765.4589**9999999999...... PP

                                       HTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---HHHHHHHCT CS
                     Lactamase_B_2  80 eeepavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyipeeigerlgg 156
                                       +++ +++v+ +++g+ + ++   l+ita  ++h+ ++         lG++ie+++krv+ + Dt+ +pee  e l+ 
  gi|242399039|ref|YP_002994463.1| 112 DPK-NIEVKFIKAGDVLNID--SLKITALKLNHQVET---------LGYLIEEDDKRVAVLYDTKGLPEETFEILKE 176
                                       666.89999**********8..578888888888777.........************************9999998 PP

                                       ..-SEEEEE-S-SSTTHHHHHHT---STSHHHHCTTSSSSEEEEESB CS
                     Lactamase_B_2 157 ..adllllditayeddemirhmgHltpeeaveaaadlgakrlvliHi 201
                                         + l++ d+t+  + +   +++H +++e +e   +l a+r++l Hi
  gi|242399039|ref|YP_002994463.1| 177 kkLRLVISDATYSPEIN---DPYHNNVDEGAETGLKL-AERTLLSHI 219
                                       77999**9*99555533...9********99988887.556666665 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   2.8   1.5e-09   8.7e-06       8      65 ..      44      90 ..      38     148 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 1.5e-09
                                      EEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCT CS
                       Lactamase_B  8 syliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglv 65
                                        +i+ +++++LiD Gt+ +  + +           +++a++lTH+H+DHi gl +l+
  gi|242399039|ref|YP_002994463.1| 44 LAIITKNNKAVLIDVGTDIRDLLHV-----------PLEAILLTHWHHDHIYGLYKLR 90
                                      5678999****************98...........9*****************9886 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 !   15.3   0.1   2.3e-06     0.014      12     106 ..      47     155 ..      41     180 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.3e-06
                     Lactamase_B_3  12 letagarilvDPfkanlgyeppaeeaDlvlisqaledHahletlkql.........................aenvk 63 
                                       ++++++ +l+D ++     +   +  +++l+++ + dH  +  l +l                         + +vk
  gi|242399039|ref|YP_002994463.1|  47 ITKNNKAVLIDVGT--DIRDLLHVPLEAILLTHWHHDH--IYGLYKLrwiakrtilyapngdadwlmindpkNIEVK 119
                                       55578999999765..33344568899********555..5556666666********************999999* PP

                     Lactamase_B_3  64 vleegeslevggleiravatshdavggsergenngflleqdgl 106
                                       +++ g+ l++++l+i+a + +h+        e  g+l+e+d+ 
  gi|242399039|ref|YP_002994463.1| 120 FIKAGDVLNIDSLKITALKLNHQ-------VETLGYLIEEDDK 155
                                       ********************993.......4456666666544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1774.15
//
Query:       gi|242399040|ref|YP_002994464.1|  [L=191]
Description: NAD(P)H-flavin oxidoreductase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-29  103.5   0.0    1.5e-29  103.2   0.0    1.1  1  Nitroreductase  Nitroreductase family
    1.2e-11   44.6   0.0    5.7e-06   26.1   0.4    2.4  2  TM1586_NiRdase  Putative TM nitroreductase
  ------ inclusion threshold ------
       0.15   12.5   0.6       0.24   11.8   0.6    1.5  1  RecX            RecX family


Domain annotation for each model (and alignments):
>> Nitroreductase  Nitroreductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.2   0.0   2.5e-33   1.5e-29       2     170 .]       7     164 ..       6     164 .. 0.95

  Alignments for each domain:
  == domain 1  score: 103.2 bits;  conditional E-value: 2.5e-33
                                       HH--B---B-S----HHHHHHHHHHHHTS--GGG---EEEEEE.-CCCHHHHHHHHHHHHHHHHTT-SS-GGGGGG. CS
                    Nitroreductase   2 rkRrSiRkFddepvpkeelekileaarraPsagnlqpwrfvvvqdkelryklaeaalelllkaeaqaelaqryrke. 77 
                                       ++R+++RkF++e++p e++ ki+eaa  aPs++n+qpw+f+++++ e +++++ ++ e  +k  ++++ +  ++ + 
  gi|242399040|ref|YP_002994464.1|   7 KRRKTVRKFKKEKPPIEKILKIIEAAKEAPSGMNAQPWHFIIIETPERKREIRGLCEEGEKKFYEKMKGKLGKWLQd 83 
                                       79*****************************************9999999999999999999999999999888774 PP

                                       HHHHHHHHHHHHSSEEEEE---TTS---HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE-GGGGGHHHHHHHH CS
                    Nitroreductase  78 elklkaqkalagapvlivivatldkserkaaerayryalldagaaaqnllLaAtalGlgscpiggfdeaaeevrkll 154
                                       +    ++++l +ap l+++            + ++++a++ + +a+  llLa++++Glg++  + ++ ++  + +l 
  gi|242399040|ref|YP_002994464.1|  84 KGFTWKKPFLSDAPYLLLV----------FTDVRAPFAVQATWLAIGYLLLALEEEGLGTVTYTPPNPRE--IEELV 148
                                       55568899***********..........*****************************************..***** PP

                                       T-S..SEEEEEEEEE- CS
                    Nitroreductase 155 glpdeeeivvliavGy 170
                                       + p++++++ +++vGy
  gi|242399040|ref|YP_002994464.1| 149 NAPKHYKLQTILPVGY 164
                                       ***************9 PP

>> TM1586_NiRdase  Putative TM nitroreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.4   9.5e-10   5.7e-06     139     184 ..       6      49 ..       2      73 .. 0.80
   2 !   16.0   0.0   1.1e-06    0.0066      64     154 ..      94     186 ..      70     191 .] 0.76

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 9.5e-10
                                       .-----HHHHBSS-GGGS-HHHHHHHHHHHTS--GGG----EEE.E CS
                    TM1586_NiRdase 139 eakrkpleelcevkeeelpewfkeileaarlAPsAlNqqpwrfelk 184
                                       +++rk++ ++ + k     e++ +i+eaa  APs +N qpw+f + 
  gi|242399040|ref|YP_002994464.1|   6 AKRRKTVRKFKKEKP--PIEKILKIIEAAKEAPSGMNAQPWHFIII 49 
                                       566777777774443..4699**********************865 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 1.1e-06
                                       SSSSEEEE----SSHHHHHHHHHHHH.HHHHHHHHTT-EEEEES--SST............T-S-EEEEE-BS---- CS
                    TM1586_NiRdase  64 kgvpnyialvgekkedleekaGYyge.qlvLkltalGlgtcWvggtykk.kkakvelkkgeklvivIalGyaktklv 138
                                       +++p+ ++++ + +  + ++a ++    l+L l ++Glgt       ++  ++ v+++k  kl  ++ +Gy+++++ 
  gi|242399040|ref|YP_002994464.1|  94 SDAPYLLLVFTDVRAPFAVQATWLAIgYLLLALEEEGLGTVTYTPPNPReIEELVNAPKHYKLQTILPVGYPNDEKP 170
                                       56666666666666666666666554147788999*****755544444366779999******************* PP

                                       .-----HHHHBSS-GG CS
                    TM1586_NiRdase 139 eakrkpleelcevkee 154
                                       + +rk+le+++++++ 
  gi|242399040|ref|YP_002994464.1| 171 KYERKALEDVISFEKF 186
                                       ***********99875 PP

>> RecX  RecX family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.6   4.1e-05      0.24      75     110 ..      58      89 ..       9      92 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.1e-05
                                       HHHHHHHHHHHTTTS-HHHHHHHHHHHHHHTT--HH CS
                              RecX  75 arelaekklkklkkeedekekqklvrfLarrGFsse 110
                                       +r l+e   kk      ek+k kl ++L+ +GF+++
  gi|242399040|ref|YP_002994464.1|  58 IRGLCEEGEKKF----YEKMKGKLGKWLQDKGFTWK 89 
                                       444555555555....49****************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1213.43
//
Query:       gi|242399041|ref|YP_002994465.1|  [L=149]
Description: Protein tyrosine/serine/threonine phosphatase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-19   69.0   0.0    3.7e-19   68.8   0.0    1.1  1  DSPc             Dual specificity phosphatase, catalytic doma
    1.7e-07   31.1   0.0    2.1e-07   30.7   0.0    1.1  1  Y_phosphatase    Protein-tyrosine phosphatase
    4.9e-06   26.3   0.0    6.5e-06   25.9   0.0    1.2  1  CDKN3            Cyclin-dependent kinase inhibitor 3 (CDKN3)
    0.00041   20.5   0.0     0.0047   17.1   0.0    2.0  2  PTPlike_phytase  Inositol hexakisphosphate
     0.0033   17.4   0.0     0.0036   17.3   0.0    1.2  1  Y_phosphatase3   Tyrosine phosphatase family
  ------ inclusion threshold ------
       0.04   14.2   0.0      0.054   13.8   0.0    1.3  1  Init_tRNA_PT     Rit1 DUSP-like domain


Domain annotation for each model (and alignments):
>> DSPc  Dual specificity phosphatase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.8   0.0   1.2e-22   3.7e-19      32     132 ..      42     144 ..      18     145 .. 0.85

  Alignments for each domain:
  == domain 1  score: 68.8 bits;  conditional E-value: 1.2e-22
                                       C...ECCTTTTSEEEEECCESSTTSCCGGGHHHHHHHHHHHHHTT-EEEEEESSSSSHHHHHHHHHHHHHHTSCHHH CS
                              DSPc  32 a...nalkkseieklripvedehetkiskyleeavefidkakqkgkkvlVHCqaGisRSatliiaYlmktknlslne 105
                                       +    +l+k++ie l  p++d  +    ++l e+v+ i+k +++gkkvlVHC  G  RS+t+++aYlm++++ls ++
  gi|242399041|ref|YP_002994465.1|  42 YydlEELSKNGIEVLYSPIKD-FSVPPLEELIEIVKWIEKKARNGKKVLVHCLSGKGRSGTIVTAYLMYSEGLSFRD 117
                                       334545677788888888888.8888899999********************************************* PP

                                       HHHHHHHHSTT-SSTHHHHHHHHHHHH CS
                              DSPc 106 ayeflkerrpaispnagfirqLleyek 132
                                       a+  +++ +p+ ++++++i+ L + e+
  gi|242399041|ref|YP_002994465.1| 118 ALARVRSLKPSAVETEEQIGILKDLEN 144
                                       *******************99988775 PP

>> Y_phosphatase  Protein-tyrosine phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.0   7.2e-11   2.1e-07     146     226 ..      63     136 ..      45     142 .. 0.87

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 7.2e-11
                                       SSSGSCCHHHHHHHHHHHHHHSTTSS-EEEECSSSSHHHHHHHHHHHHHHHHHHHSEEEHHHHHHHHHTTSTTSS-S CS
                     Y_phosphatase 146 hgvpesaksllklirkvekskeaksgpvvVhCsaGvgRtgtfvaldillqqleaeeevdvlqivkelrkqRpgmvqt 222
                                        +vp+  ++l+++++ +ek+   + + v+VhC  G gR+gt+v++ +++++      ++  +++ ++r+ +p++v+t
  gi|242399041|ref|YP_002994465.1|  63 FSVPP-LEELIEIVKWIEKKA-RNGKKVLVHCLSGKGRSGTIVTAYLMYSEG-----LSFRDALARVRSLKPSAVET 132
                                       55664.678999999999999.8999******************99988754.....56999*************** PP

                                       HHHH CS
                     Y_phosphatase 223 leqy 226
                                       +eq 
  gi|242399041|ref|YP_002994465.1| 133 EEQI 136
                                       **96 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 !   25.9   0.0   2.2e-09   6.5e-06      97     161 ..      49     112 ..      35     119 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 2.2e-09
                                       HHTT-EEEE----TTS---HHHHHHHHHHHHHHHHTT--EEEE-SSSSSHHHHHHHHHHHHH-SS CS
                             CDKN3  97 qqygivthhhpiadggtpdiascleimeelatclknyrktlihcygglgrsclvaaclllylsds 161
                                        + gi   + pi d   p +   +ei++ +    +n +k l+hc  g grs  + ++ l+y s+ 
  gi|242399041|ref|YP_002994465.1|  49 SKNGIEVLYSPIKDFSVPPLEELIEIVKWIEKKARNGKKVLVHCLSGKGRSGTIVTAYLMY-SEG 112
                                       567999999******************************************9988888887.445 PP

>> PTPlike_phytase  Inositol hexakisphosphate
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.11   3.2e+02      99     125 ..      10      36 ..       4      41 .. 0.82
   2 !   17.1   0.0   1.6e-06    0.0047     106     154 ..      59     108 ..      42     110 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.11
                                       T-EEEEEEE-TTS---HHHHHHHHHHH CS
                   PTPlike_phytase  99 slrYaRipitdekapeeedfdalvsil 125
                                       ++ ++ +p +++   ++++fda+v ++
  gi|242399041|ref|YP_002994465.1|  10 KVAFSSVPYPEDIPKLAKEFDAFVVLI 36 
                                       56677789999************9776 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 1.6e-06
                                       EE-TTS---HHHHHHHHHHHHTS.-TT-EEEEE-SSSSHHHHHHHHHHHH CS
                   PTPlike_phytase 106 pitdekapeeedfdalvsilkea.pektalvfnCqmGrgRTTtamviatL 154
                                       pi+d   p  e++ ++v+ +++   + + ++++C  G+gR+ t ++++ +
  gi|242399041|ref|YP_002994465.1|  59 PIKDFSVPPLEELIEIVKWIEKKaRNGKKVLVHCLSGKGRSGTIVTAYLM 108
                                       89999999999999999999988788****************99888876 PP

>> Y_phosphatase3  Tyrosine phosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.2e-06    0.0036     110     142 ..      71     107 ..      14     118 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.2e-06
                    Y_phosphatase3 110 yrkvfealadee....pvlfHCtaGKDRTGvlaalll 142
                                       + ++++ + +++     vl+HC +GK R G ++   l
  gi|242399041|ref|YP_002994465.1|  71 LIEIVKWIEKKArngkKVLVHCLSGKGRSGTIVTAYL 107
                                       44444455552235689*************9876555 PP

>> Init_tRNA_PT  Rit1 DUSP-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.8e-05     0.054      20      61 ..      70     109 ..      57     141 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.8e-05
                      Init_tRNA_PT  20 alpkivdfvrkrlsedkkkkilvacetGkdlsvgvaLailck 61 
                                       +l +iv++++k+ +++k  k+lv+c +Gk  s  ++ a l++
  gi|242399041|ref|YP_002994465.1|  70 ELIEIVKWIEKKARNGK--KVLVHCLSGKGRSGTIVTAYLMY 109
                                       78899******988877..9***********99999988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         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: 913.47
//
Query:       gi|242399042|ref|YP_002994466.1|  [L=531]
Description: hypothetical protein TSIB_1061 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score 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   13.1   0.7      0.036   12.5   0.7    1.2  1  DcuC            C4-dicarboxylate anaerobic carrier
       0.16   11.6   0.1       0.54    9.8   0.1    1.8  1  tRNA_anti-like  tRNA_anti-like


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 ?   12.5   0.7     4e-06     0.036     251     341 ..       5      93 ..       1     112 [. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4e-06
                              DcuC 251 krqkvvlilfvlplilvllg...lafvivngewylpeiavlflamgilvefiaklnglkekeiveafveGaaellgv 324
                                       k++ v l+l++l++ l+++     ++ i++g +  p+i+ +f+a+g ++ + +k++  +  +  +a + G      +
  gi|242399042|ref|YP_002994466.1|   5 KKEDVRLFLPFLVFALIIWLfrpWFHGIIMGFYRNPTIIYIFIALGAILVYASKQKLTEGYTRKNASISGI-----F 76 
                                       56778899999999999996555444555556999**************9999877777788888888886.....6 PP

                              DcuC 325 alvvglargveviaegg 341
                                       al++ l++  +v+ + +
  gi|242399042|ref|YP_002994466.1|  77 ALIILLLVVLSVLTGAL 93 
                                       77888887777776655 PP

>> tRNA_anti-like  tRNA_anti-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   6.1e-05      0.54      90     144 ..     464     519 ..     460     523 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 6.1e-05
                                       EEEEEEEEEEE.-STT-E.EEEEE-TT-S-S--EEEEEEGGHHHHHH--TTSEEEEE CS
                    tRNA_anti-like  90 eVeGvvsdikk.ieassv.vvlardddgltnVrclledeateasaakiskGqkvtiv 144
                                       eV+Gv+++i   i++ ++ +vl+  ++ l     +l+de  ++++ +++ G++vt++
  gi|242399042|ref|YP_002994466.1| 464 EVSGVIEGIYSyIKNGNThWVLIIGNETLYLSSDQLSDEL-ILKVLNLKEGDNVTVK 519
                                       79*******7779999999****99999999999999999.**************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (531 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1054  (0.0587874); expected 358.6 (0.02)
Passed bias filter:                      753  (0.041999); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.35s 00:00:01.08 Elapsed: 00:00:00.55
# Mc/sec: 2927.00
//
Query:       gi|242399043|ref|YP_002994467.1|  [L=37]
Description: hypothetical protein TSIB_1062 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       500  (0.0278878); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 262.85
//
Query:       gi|242399044|ref|YP_002994468.1|  [L=150]
Description: hypothetical protein TSIB_1063 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1006.33
//
Query:       gi|242399045|ref|YP_002994469.1|  [L=265]
Description: hypothetical protein TSIB_1064 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score 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   13.6   2.1      0.027   13.2   2.1    1.1  1  TRP       Transient receptor potential (TRP) ion channel
        1.4    8.2   5.8        2.4    7.4   5.8    1.4  1  DUF3810   Protein of unknown function (DUF3810)


Domain annotation for each model (and alignments):
>> TRP  Transient receptor potential (TRP) ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   2.1   3.1e-06     0.027     155     288 ..       6     134 ..       4     137 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.1e-06
                               TRP 155 fliliallvvlvllfKlllellarkklikedrlkefrknwlgilkgallrlilifffqllvlclfeftqrdsaavvv 231
                                       ++++++ +v+l+ll+ + + +++   ++  ++l+ +  + l i++  ++  +li++f   + +l  + +++sa v  
  gi|242399045|ref|YP_002994469.1|   6 LAMILVSIVLLLLLIPISIAVMILLDISDISKLFPYSVSSLIITGIGIVLSALIVGFLAKIAALKIYKEEKSAKVAF 82 
                                       56677778889999999999999999998899997777777777777777778888888888888889999****** PP

                               TRP 232 lAvillalflgvllffafrvlitarkskrlhknpaylLysdkkvlnky.Gflyeqyra 288
                                       lAv+++a+++     +++++ +++   ++      y+Ly+++ ++n y G ++  + +
  gi|242399045|ref|YP_002994469.1|  83 LAVFFIAVLISA---YSINIPRIGPSPQKVI---YYTLYENEVYVNPYfGKISLPFEE 134
                                       *****9999966...7888888888866663...589****99999652666666655 PP

>> DUF3810  Protein of unknown function (DUF3810)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   5.8   0.00026       2.4      13      70 ..      32      92 ..      11     101 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00026
                           DUF3810 13 lsrlsglfpFSvgellivllillvilylvlai....klkkrkkkkkrllkvllrvllvllvv 70
                                      +s +s+lfp+Sv  l+i+ + +++ +++v ++       k  k++k+++ ++l+v+++++++
  gi|242399045|ref|YP_002994469.1| 32 ISDISKLFPYSVSSLIITGIGIVLSALIVGFLakiaA-LKIYKEEKSAKVAFLAVFFIAVLI 92
                                      6889*************88888888888888877642.334444455555555554444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1374  (0.0766356); expected 358.6 (0.02)
Passed bias filter:                      815  (0.0454571); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 1679.08
//
Query:       gi|242399046|ref|YP_002994470.1|  [L=267]
Description: dioxygenase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-18   67.0   0.0    1.6e-18   66.8   0.0    1.0  1  LigB      Catalytic LigB subunit of aromatic ring-opening dio
     0.0073   15.5   0.0      0.034   13.3   0.0    1.9  2  Memo      Memo-like protein


Domain annotation for each model (and alignments):
>> 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 !   66.8   0.0   1.8e-22   1.6e-18       2     271 ..      11     262 ..      10     264 .. 0.83

  Alignments for each domain:
  == domain 1  score: 66.8 bits;  conditional E-value: 1.8e-22
                              LigB   2 alllsHvppilaavdgkeqealrekvikgyesireriaek.sPdtiivvsphhltdvnpvfvlgvaeefeaiddfgk 77 
                                       a+++sH+ p+l  +d +e  +    + + +++i+++   + + ++ +++sph +    ++ v+ v++   ++  f  
  gi|242399046|ref|YP_002994470.1|  11 AAIMSHGNPVLKPED-EETRK----LAEALKEIGRE---FsKAEAYVIISPHNVRMSEAIGVIMVEN-LISWLGFD- 77 
                                       6889******77777.33333....33444555544...3577889999***998666555555555.66677778. PP

                              LigB  78 flprleyelkgnpeLaekiaealkksgidlav........esnsmklDHGtlvPLelmlpdeakvpvikvslntvay 146
                                        +  l +e+k ++eLa++i++ +k +g +++         e  + +l +G l+PL ++ +        +++l t   
  gi|242399046|ref|YP_002994470.1|  78 -GVHLPGEYKTEKELAKEIYQRAKVKGLPVVDinfaslggEYSRFPLTWGELIPLHFLEK-------RPIVLLT-PA 145
                                       .9***************************754999*****999***************99.......4666666.22 PP

                              LigB 147 pllsferlykLGeAlrkaveeldknvlilgsGglsHqlegdeaakadaqtlllneefdeelldllkegrveelckms 223
                                          s   l k+Ge +++  ee+dk+v +++s +  H  +g+ +++      + ++e+de ++ ++ke+r+e+l+++s
  gi|242399046|ref|YP_002994470.1| 146 RKVSRDTLVKFGEVIGEVLEEYDKKVTFVASADHAHA-HGNGPYGHA----PEAKEYDELIMRIIKENRLEKLLEIS 217
                                       35577789****************************7.677777444....59************************ PP

                              LigB 224 keelsaaagheeeelvplvvalGalsgdkaelrkelvsyeglpavsav 271
                                        e +++a     +   +l+v+ G+l+ ++ +l+ + +++ ++++++a+
  gi|242399046|ref|YP_002994470.1| 218 DELINKA---LPDSYWQLLVLYGVLKRAPMKLKLSAYVCPTYFGMGAA 262
                                       9999999...59999***********9999999999999999988876 PP

>> Memo  Memo-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0     0.061   5.5e+02     155     177 ..      27      52 ..      20      68 .. 0.58
   2 !   13.3   0.0   3.8e-06     0.034     152     216 ..     149     215 ..     132     228 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.061
                              Memo 155 takevgealakvikdes...nlviiS 177
                                        +++++eal+++ +++s   + viiS
  gi|242399046|ref|YP_002994470.1|  27 ETRKLAEALKEIGREFSkaeAYVIIS 52 
                                       34445555555555544443334443 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 3.8e-06
                              Memo 152 seetakevgealakvikdes..nlviiSsDlsHygrrFg....spqeiaesieDrevikaleelneeelke 216
                                       s +t  ++ge++ +v+++++  + +++S D  H +   g      +++a++  D+ ++  ++e + e+l e
  gi|242399046|ref|YP_002994470.1| 149 SRDTLVKFGEVIGEVLEEYDkkVTFVASADHAHAH---GngpyGHAPEAKEY-DELIMRIIKENRLEKLLE 215
                                       6788899**********9998899*********98...32233334444444.9****9999987776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       737  (0.0411066); expected 358.6 (0.02)
Passed bias filter:                      685  (0.0382063); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 1955.34
//
Query:       gi|242399047|ref|YP_002994471.1|  [L=380]
Description: Threonine synthase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-74  250.2   0.0    3.1e-74  250.0   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 !  250.0   0.0   1.7e-78   3.1e-74       2     294 .]      58     353 ..      57     353 .. 0.94

  Alignments for each domain:
  == domain 1  score: 250.0 bits;  conditional E-value: 1.7e-78
                                       GGCSSS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT CS
                              PALP   2 tlgigpTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaallG 78 
                                       +lg+g+TPl +++rlskelgv+l+lK+E lnpt SfKdRg    ++r+ e  g   + + s+GN+++++Aa++a++G
  gi|242399047|ref|YP_002994471.1|  58 SLGEGDTPLTKAKRLSKELGVELYLKNETLNPTWSFKDRGTFIGIHRALEL-GFNKIGTVSTGNMAASVAAYGARFG 133
                                       6799***********************************************.************************* PP

                                       -EEEEEEETTS-HHHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHHHTHHHHHHHHTT CS
                              PALP  79 lkvtivvpadaspekvallrllGaevvevggdydeavaaaaelaaegegaylvsqfdnptviegygtiglEileqlg 155
                                       l+ +i+v+++  +ek+++l+ +Ga+v++v gdy     +  e+ ++ +g+y++++  +p ++egy++ig+Ei+e++ 
  gi|242399047|ref|YP_002994471.1| 134 LETYILVSSTIVEEKLKALEVYGAKVIKVRGDYGGLYYRSLEIGQR-KGIYFINSD-DPFRVEGYKSIGFEIAEEVT 208
                                       ***************************************99*****.*******99.8**************99996 PP

                                       TTEEEEEEE-SSSHHHHHHHHHHHH..HSTT......-EEEEEEECTTCGGTTCC..S..S.SS..B....SSS.CC CS
                              PALP 156 gkpdavvvpvGgGgliaGiaaglke..rrpd......vrvigvepegsdalarsl..ragrrvtvpvs...dtiadg 219
                                         pd+vv p+++Ggl+ Gi++g+ e  +  +      +++++v++eg++++ +++   + + ++       +tia +
  gi|242399047|ref|YP_002994471.1| 209 --PDYVVIPTSSGGLFRGIVKGFLElkE--SgliedlPTFVAVQAEGCSPICKAFneSRQKIER---FenpHTIAHA 278
                                       ..***********************651..4455679******************333333344...3455****** PP

                                       STCS..CGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHHHHHHHHCCTTCEEEEEEE-B CS
                              PALP 220 lavg..spselafelldrlvdeivtvsdeealeamrllarregivvepssaaalaalklreagelkegdrvvviltg 294
                                       ++++   +++ +++ll +l + +v+vsdee+lea++ l  regi+v p+sa+++aa+  + +g+++e+ +vv iltg
  gi|242399047|ref|YP_002994471.1| 279 IENPypPSGNAVLRLLNELKGLCVAVSDEEILEAQQDLG-REGIFVQPASATGIAAI-KKLRGRIEEDTKVVSILTG 353
                                       *****9999******************************.*****************.******************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2487.81
//
Query:       gi|242399048|ref|YP_002994472.1|  [L=285]
Description: Arginase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-75  254.4   0.0    1.7e-75  254.1   0.0    1.1  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 !  254.1   0.0   9.5e-80   1.7e-75       3     279 ..      13     271 ..      11     272 .. 0.90

  Alignments for each domain:
  == domain 1  score: 254.1 bits;  conditional E-value: 9.5e-80
                                       EEEEEEE--TTTSSSGGGGGHHHHHHHHHHTSBTHCHEETTTTE.SCCSEEEEEEEEE--SSCHHHHHHHHHHHHHH CS
                          Arginase   3 vallGvPfdaagsgrpGarfGPraireasarleealeynlelgv.leelkivdlgdvavtpvdneevleqieeavae 78 
                                       + +lG+P+d + s+r+G+++GP+airea+++   + ++n +l +  e++++ dlgdv+v+  + ee++e++ + v++
  gi|242399048|ref|YP_002994472.1|  13 LYILGIPWDNSSSYRRGCDKGPEAIREATSEEL-YNSFNESLVNlAEHWRYKDLGDVKVE--NFEELVERVDDLVKR 86 
                                       679*************************54332.4556665555899***********98..556667877777777 PP

                                       HHHTTCEEEEEESSGGGHHHHHHHHHHHHSTTEEEEEESSS----SSCTTTBSSSTTSHHHHHHHHTSECGCEEEEE CS
                          Arginase  79 ilkagklpivlGGDHsialgilralaekygkplgvihfDAHaDlrtpetegsgnshGtpfrraaeegllkpkklvqi 155
                                       +   g+l ++lGGDHsi+++++ral+++ ++++g+i fDAH Dl  ++ eg+++sh++ +rr +ee+l+k k++vqi
  gi|242399048|ref|YP_002994472.1|  87 HY-TGELFLFLGGDHSITYATFRALKKVSQEEFGLIYFDAHPDLYPEY-EGDKYSHACTVRRLVEEDLVKGKDVVQI 161
                                       54.479******************************************.9*************************** PP

                                       EE-STCSHHHHHHHHTTSEEEEHHHHHHHHHHHHHHHHHHHHTCTTSEEEEEEEGGGBBTTTSTSSSS-BSS-B-HH CS
                          Arginase 156 GirsvdneeyelakelgirvitmreidelglkavveeilervgaeedpvylSfDiDvlDpavaPGtGtpepgGltlr 232
                                       G+r++++++ e+a+e+gi++i++ ei +       ++++  ++    + ylSfD+DvlDpa+aPG+G pe gGlt+r
  gi|242399048|ref|YP_002994472.1| 162 GVRAPTKQQIEFAEEHGIKIISASEIYR------CQKVDVPFK----KAYLSFDMDVLDPAFAPGVGNPESGGLTTR 228
                                       **************************98......556777774....78**************************** PP

                                       HHHHHHHHHHCHSEEEEEEEE-B-GGGSSTTTHHHHHHHHHHHHHHH CS
                          Arginase 233 ellallrelaeklnlvgaDvvEvnPaldteaeqtarlaarlvrelll 279
                                       el ++++ ++   ++v++DvvE+nP++d ++ +ta +aa++vre+ l
  gi|242399048|ref|YP_002994472.1| 229 ELVEVIKSIKT--EVVAFDVVELNPSYDYKG-ITAFAAAKIVREI-L 271
                                       *********66..8***************76.************5.5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); 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: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 1767.74
//
Query:       gi|242399049|ref|YP_002994473.1|  [L=109]
Description: tRNA-binding protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.7e-26   90.7   0.0    5.3e-26   90.6   0.0    1.0  1  tRNA_bind  Putative tRNA binding domain


Domain annotation for each model (and alignments):
>> tRNA_bind  Putative tRNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.6   0.0   2.9e-30   5.3e-26       1      96 []      14     107 ..      14     107 .. 0.98

  Alignments for each domain:
  == domain 1  score: 90.6 bits;  conditional E-value: 2.9e-30
                                       EEEEEEEEEEEETTSSTEEEEEEEESSSSEEEEEESCTTTSTHHHHTTEEEEEETTSESEEETTEEESSEE-EEECC CS
                         tRNA_bind   1 lrvGkvleaeehpnadkLlvlkvdvGeeeprqivsgaknvyepeelvakkvvvvanlkpkklrGveSeGMilsaeel 77 
                                       lrvG v  ae+++  +kL++l+vd+G+e+ r+iv+g+++ y+pe+l +kk v v nlkpkkl GveS+GM++ ae+ 
  gi|242399049|ref|YP_002994473.1|  14 LRVGLVKRAEKLKRTKKLIKLEVDFGKEQ-RTIVTGLADQYSPEDLEGKKFVFVLNLKPKKLSGVESQGMLIVAEN- 88 
                                       79***************************.*********************************************6. PP

                                       ESSCEEEEEESST--TTCE CS
                         tRNA_bind  78 dekevgilelpadveaGek 96 
                                       ++++v +l +p++v++G+k
  gi|242399049|ref|YP_002994473.1|  89 ENGKVYLLPVPDEVPIGTK 107
                                       *****************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); 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: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 713.17
//
Query:       gi|242399050|ref|YP_002994474.1|  [L=189]
Description: Multimeric flavodoxin (WrbA) domain containing protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.6e-20   71.0   0.0    1.7e-19   70.1   0.0    1.4  2  FMN_red       NADPH-dependent FMN reductase
     0.0071   16.1   0.0     0.0095   15.7   0.0    1.2  1  Flavodoxin_2  Flavodoxin-like fold


Domain annotation for each model (and alignments):
>> FMN_red  NADPH-dependent FMN reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.1   0.0   1.9e-23   1.7e-19       1     125 [.       1     130 [.       1     142 [. 0.83
   2 ?   -2.3   0.0      0.37   3.4e+03      78      84 ..     140     146 ..     138     149 .. 0.89

  Alignments for each domain:
  == domain 1  score: 70.1 bits;  conditional E-value: 1.9e-23
                                       -EEEEEES--STT-HHHHHHHHHHCCT-T.T-CEEEEETTTS..--....---HCHGHTCGGSHHHHHHHHHHHH-S CS
                           FMN_red   1 mkilvisGSlrkgsntrklaewaaealkeagaevelidladl.ilpc..alcdkdlesegqtsddvaellekiaaad 74 
                                       mk+l+i+ S+rk++n+ kl++++++ l+++++++el++ +d+   pc  + +   +  e++ +dd+  ++ek ++ad
  gi|242399050|ref|YP_002994474.1|   1 MKVLGIAFSARKNGNSAKLLQYCLDNLEKRKFDTELLEAHDFqLTPCshCNYE-CFSGECPIKDDIPLFYEKAMKAD 76 
                                       9*********************************************9765555.344559***************** PP

                                       CEEEEEEECTTCE-HHHHHHHHCHT-..SSCHCCT..T-EEEEEEE-SSTTTTH CS
                           FMN_red  75 aliivtPeYngsysgllKnalDrlsr.trgkkelr..gKpvalvavgggrrggl 125
                                       +li++ P+Y g +sgl  ++ +r  +  ++++e++  ++ + ++ vg   +gg 
  gi|242399050|ref|YP_002994474.1|  77 ILIFAVPTYGGHASGLYRAFCERGQAiFKSYDEWNnfARKLNFIFVGNLSSGGD 130
                                       ***********************9998556666663334444444555555554 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.37
                                       EEEEECT CS
                           FMN_red  78 ivtPeYn 84 
                                       i+tPeY+
  gi|242399050|ref|YP_002994474.1| 140 IATPEYW 146
                                       79****9 PP

>> Flavodoxin_2  Flavodoxin-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.1e-06    0.0095       1     102 [.       1      99 [.       1     118 [. 0.81

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.1e-06
                                       -EEEEEE--TTGGCCHHHCHHHHHHHHHCCCTT..TEEEEEEHHCCT-----CCCCHCCHHHHTTCHHHHHHH.HHH CS
                      Flavodoxin_2   1 mkiLiinahprpeksfssalaqafvealekagp..hevtvrdLyadflpvlttrdlaaklayeekpadveseq.iek 74 
                                       mk+L i  + r+ + +s +l+q  ++ lek +   +  + +d   +++ +++ ++++++      p++ +     ek
  gi|242399050|ref|YP_002994474.1|   1 MKVLGIAFSARK-NGNSAKLLQYCLDNLEKRKFdtELLEAHDFQLTPCSHCNYECFSGE-C----PIKDDIPLfYEK 71 
                                       9***********.6999**************9764336667777779999999999832.1....3444444445** PP

                                       HHCSSEEEEEEE-BTTB--HHHHHHHHH CS
                      Flavodoxin_2  75 llaadaivlqfPlwwfgvPailKgwiDr 102
                                          ad++++++P +  + + ++ ++ +r
  gi|242399050|ref|YP_002994474.1|  72 AMKADILIFAVPTYGGHASGLYRAFCER 99 
                                       ***************9999999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 1144.23
//
Query:       gi|242399051|ref|YP_002994475.1|  [L=273]
Description: N-acetyltransferase, GNAT family [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.3e-12   45.4   0.0    2.1e-11   44.1   0.0    1.6  2  Acetyltransf_1   Acetyltransferase (GNAT) family
    3.4e-07   30.6   0.0    6.6e-07   29.7   0.0    1.5  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    0.00083   19.5   0.1      0.046   13.9   0.0    2.4  2  Acetyltransf_4   Acetyltransferase (GNAT) domain
     0.0044   16.9   0.0      0.015   15.2   0.0    1.8  2  FR47             FR47-like protein
     0.0067   17.1   0.0      0.013   16.1   0.0    1.5  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.011   15.7   0.0       0.02   14.8   0.0    1.4  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
        0.1   12.7   0.0       0.58   10.2   0.0    2.1  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
        0.1   12.8   0.2       0.27   11.5   0.2    1.6  1  Myb_DNA-binding  Myb-like DNA-binding domain
       0.15   12.4   0.0        5.6    7.4   0.0    2.9  3  B5               tRNA synthetase B5 domain


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.1   0.0     1e-14   2.1e-11      16     117 .]      26     126 ..      11     126 .. 0.79
   2 ?   -3.6   0.0       6.2   1.2e+04     107     117 .]     244     254 ..     228     258 .. 0.64

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 1e-14
                                       HHHHHHHHHHHHHHSTTCEEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHH...HHH CS
                    Acetyltransf_1  16 nedaseeefeesfsleaegllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLleale...era 89 
                                        ed    +f e+  l ++ ++v e dg++iG++ l+  p    +v+++e+l V+p+y+++G G++  + ++    ++
  gi|242399051|ref|YP_002994475.1|  26 GEDYLASVFDEW--LKDGNFYVLELDGKVIGTAKLTFLPG---KVGWLEGLRVHPSYQKRGFGRLIQNFMLhkgNEL 97 
                                       233333336666..355678999*****************...***********************99999555445 PP

                                       HHTTE.SEEEEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  90 reegi.kkivlaveedndaairlYeklGF 117
                                        e+gi +++++ +   n+ +i++ +k GF
  gi|242399051|ref|YP_002994475.1|  98 AEKGIiNALEFSTYFLNKESIAMAKKDGF 126
                                       5559999999999999*******977887 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 6.2
                                       HHHHHHHHTTE CS
                    Acetyltransf_1 107 aairlYeklGF 117
                                         i+l+++lGF
  gi|242399051|ref|YP_002994475.1| 244 DLIELLKELGF 254
                                       34555533555 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) 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   6.6e-07       2      56 ..      40     107 ..      39     128 .. 0.70

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 3.3e-10
                                       TEEEEEEEETTEEEEEEEEEEES...TCTEEEEE-GGGTTSSHHHHHHHH.....TT...SEEE..EE CS
                    Acetyltransf_7   2 kgevfVaeddgkivGfialslld...aeitrlaVdpeyrgkGiGraLlea.....ae...kgii..le 56 
                                       +g+++V+e dgk++G++ l+ l    +++++l V+p+y+++G Gr + ++     +e   kgii  le
  gi|242399051|ref|YP_002994475.1|  40 DGNFYVLELDGKVIGTAKLTFLPgkvGWLEGLRVHPSYQKRGFGRLIQNFmlhkgNElaeKGIInaLE 107
                                       689************9999998887777777**************99997555551134456444433 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   2.3e-05     0.046      25     143 ..      22     135 ..       5     143 .. 0.75
   2 ?    3.3   0.0     0.042        83     109     142 ..     229     262 ..     186     263 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.3e-05
                    Acetyltransf_4  25 itfeyevssveefekflealdsekeyvflvae.sdrivGyaylgqfkkrakdwkaelsvylaerdnnkeglgrelid 100
                                       +t+e e + +  f+ +l++        f v+e +++++G+a+l  f +    + ++l+ + ++   +k+g gr + +
  gi|242399051|ref|YP_002994475.1|  22 LTWEGEDYLASVFDEWLKDG------NFYVLElDGKVIGTAKLT-FLP---GKVGWLEGLRVHPSYQKRGFGRLIQN 88 
                                       56777777777777777775......4667777***********.555...36677777777788999999999888 PP

                    Acetyltransf_4 101 ale...qvl.keqnienllaeiaspnensiqfhkalGFelvgifkkc 143
                                       ++    + l  +  i+ l+ +++  n++si+++k+ GF++v +f+ +
  gi|242399051|ref|YP_002994475.1|  89 FMLhkgNELaEKGIINALEFSTYFLNKESIAMAKKDGFKIVERFYYI 135
                                       76545666636666799******99****************999765 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.042
                    Acetyltransf_4 109 qnienllaeiaspnensiqfhkalGFelvgifkk 142
                                        ++ ++ + +  +++  i+++k+lGF++  +fk+
  gi|242399051|ref|YP_002994475.1| 229 IGYDSIDIMLPEEKQDLIELLKELGFKNWTDFKE 262
                                       333333333333345589*********9998875 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   7.6e-06     0.015      20      82 ..      64     131 ..      55     135 .. 0.81
   2 ?   -1.8   0.0       1.6   3.2e+03      69      79 ..     246     256 ..     227     259 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 7.6e-06
                                       TTSSEEEEEE-GGG-SSSHHHHHHHHHHH...HHHHS-S-EEEEEET..T-HHHHHHHHHHT-EEEEE CS
                              FR47  20 dggelgalqvlpehrrrGlgsrlvkalak...eiaergktvllvvva..sNtpsirlyeklGfekiee 82 
                                       ++g l +l v+p+ ++rG+g+++ + + +   e+ae+g++  l   +   N++si++ +k Gf+  e 
  gi|242399051|ref|YP_002994475.1|  64 KVGWLEGLRVHPSYQKRGFGRLIQNFMLHkgnELAEKGIINALEFSTyfLNKESIAMAKKDGFKIVER 131
                                       57999*****************9999986333699999998886655226999999999999987755 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.6
                                       HHHHHHHT-EE CS
                              FR47  69 irlyeklGfek 79 
                                       i+l++ lGf+ 
  gi|242399051|ref|YP_002994475.1| 246 IELLKELGFKN 256
                                       78999999986 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   6.7e-06     0.013      45     138 .]      37     127 ..       8     127 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 6.7e-06
                    Acetyltransf_3  45 waeeseeegygwaivlkdtgviGsvglrdleeedeeaelgymlapsfwgkGyateavralleyafeel...glerlv 118
                                       w      ++ ++ + + d++viG++ l+ l+++ ++   g++++ps++ +G+++   + +l+  +e      ++ l+
  gi|242399051|ref|YP_002994475.1|  37 WL-----KDGNFYVLELDGKVIGTAKLTFLPGKVGW-LEGLRVHPSYQKRGFGRLIQNFMLHKGNELAekgIINALE 107
                                       32.....33356665777768************995.55*************************64444448999** PP

                    Acetyltransf_3 119 avidkeNeaSirvleklGfe 138
                                         +   N+ Si+ ++k Gf+
  gi|242399051|ref|YP_002994475.1| 108 FSTYFLNKESIAMAKKDGFK 127
                                       ******************97 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0     1e-05      0.02      24      81 ..      36      95 ..      18     112 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1e-05
                   Acetyltransf_10 24 erieegealllvaeeggkivGviel.rdgs...hisllfVdpeyrgqGigkaLleaveeeae 81
                                      e++  ++  ++v+e +gk++G+++l    +    ++ l V+p+y+++G g+ + ++++++ +
  gi|242399051|ref|YP_002994475.1| 36 EWL--KDGNFYVLELDGKVIGTAKLtFLPGkvgWLEGLRVHPSYQKRGFGRLIQNFMLHKGN 95
                                      555..4556899999********77433334679999***************9999998853 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00029      0.58       2     105 ..       5     100 ..       4     129 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00029
                                       EEEE-GGGHHHHHHHHHHHTT----H..HHHHHHHHHHTTSEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEEE CS
                    Acetyltransf_9   2 irelteedldevlellkyaFqdeespleeireyfrklleesrvlgaedngelvgqlallplelnvpGktlkaagvtg 78 
                                       ir + +ed + + e+ +  ++ e+  +      f++ l++++++++e +g+++g+++l+ l    pG   k++++ g
  gi|242399051|ref|YP_002994475.1|   5 IRLAHKEDKPFIEEIARLTWEGEDYLA----SVFDEWLKDGNFYVLELDGKVIGTAKLTFL----PG---KVGWLEG 70 
                                       788999999999999999999999985....689999******************999865....44...5789999 PP

                                       EEE-CCGTTS-H...HHHHHHHHHHHHHHT CS
                    Acetyltransf_9  79 Vavapehrgrgv...lskLlaraleemree 105
                                         v+p +++rg+   ++ ++ +  +e++e+
  gi|242399051|ref|YP_002994475.1|  71 LRVHPSYQKRGFgrlIQNFMLHKGNELAEK 100
                                       999999999997555666665555555555 PP

>> Myb_DNA-binding  Myb-like DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   0.00014      0.27       6      24 ..     239     258 ..     238     260 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00014
                                       HHHHHHHHHHHHHHT.TCHH CS
                   Myb_DNA-binding   6 eeEdelLleavkkhG.nrWk 24 
                                       +eE + L+e++k++G ++W+
  gi|242399051|ref|YP_002994475.1| 239 PEEKQDLIELLKELGfKNWT 258
                                       8******************7 PP

>> B5  tRNA synthetase B5 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.15   2.9e+02      53      64 ..       9      22 ..       3      23 .. 0.72
   2 ?    7.4   0.0    0.0028       5.6      15      51 ..     209     245 ..     131     251 .. 0.92
   3 ?    0.4   0.0      0.41   8.1e+02      18      31 ..     242     255 ..     240     264 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.15
                                      SHHH..HHHHHHHH CS
                                      xxxx..xxxxxxxx RF
                                B5 53 reeD..liEEvaRl 64
                                      ++eD  +iEE+aRl
  gi|242399051|ref|YP_002994475.1|  9 HKEDkpFIEEIARL 22
                                      5555558******8 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0028
                                       ---HHHHHHHHHHTT-E.EESSTTCEEEE--TT-TT- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                                B5  15 dlseeeiikiLkrlgceriekdkdlllVtvPswRsDl 51 
                                       +ls + i++iL ++ +e+ + + d +++  P  ++Dl
  gi|242399051|ref|YP_002994475.1| 209 KLSIAAIKNILPAMSFETRNIGYDSIDIMLPEEKQDL 245
                                       78999**************************999998 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.41
                                       HHHHHHHHHHTT-E CS
                                       xxxxxxxxxxxxxx RF
                                B5  18 eeeiikiLkrlgce 31 
                                       +++ i++Lk+lg++
  gi|242399051|ref|YP_002994475.1| 242 KQDLIELLKELGFK 255
                                       578999******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); 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 0.26s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1815.20
//
Query:       gi|242399052|ref|YP_002994476.1|  [L=312]
Description: Threonine synthase [Thermococcus sibiricus MM 739]
Scores for complete 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-54  183.0   0.0      1e-53  182.7   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 !  182.7   0.0   5.7e-58     1e-53       6     294 .]      11     301 ..       7     301 .. 0.93

  Alignments for each domain:
  == domain 1  score: 182.7 bits;  conditional E-value: 5.7e-58
                                       SS--EEEECCTCCCCCCE.EEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT-EE CS
                              PALP   6 gpTPlvrlprlskelgvp.lflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaallGlkv 81 
                                       g+ Pl+r+++l++ lg+  +++KlEs+nptg +KdR a   +++  +  g   +++++ GN g+++A+ a+++Glk+
  gi|242399052|ref|YP_002994476.1|  11 GGPPLIRAQKLEEYLGISkIYIKLESFNPTGTHKDRIARVHVEEVNKL-GFSAITTGTCGNYGISIAYFAQKYGLKA 86 
                                       778*****************************************9999.**************************** PP

                                       EEEEETTS-HHHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTTSHH.HHHHHHTHHHHHHHHTTTT CS
                              PALP  82 tivvpadaspekvallrllGaevvevggdydeavaaaaelaaegegaylvsqfdnpt.viegygtiglEileqlggk 157
                                       +i++p+  s+ +++ l+ +Gaevv+++g+y+eav   +++a+e +++y +++++ p+   egy+ i  Ei++ +   
  gi|242399052|ref|YP_002994476.1|  87 HIFIPRAYSNIRLKELEKYGAEVVFINGSYEEAVFESKKFAKE-NNIYDANPGSKPWiDYEGYAAISREIAKNV--T 160
                                       *******************************************.*************66888********7666..4 PP

                                       EEEEEEE-SSSHHHHHHHHHHHHHSTT-EEEEEEEC.TTCGGTTCCS..S.SS..B.......SSS.CCSTCSCGTT CS
                              PALP 158 pdavvvpvGgGgliaGiaaglkerrpdvrvigvepe.gsdalarslragrrvtvpvs......dtiadglavgspse 227
                                       p av+vpvG+G ++ Gi++g+++ + ++++igv ++ g+  l++++ +++ ++v+        + ++++++ +   +
  gi|242399052|ref|YP_002994476.1| 161 PYAVFVPVGNGTTLVGIYHGFRQLGFTPHMIGVTTSfGNQVLNAFY-TKSFDEVKDFaetkfnEPLVSSISFD--FD 234
                                       99**********************************7777777777.55555555557766666666666666..9* PP

                                       CCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHH.HHHHHHCCTTCEEEEEEE-B CS
                              PALP 228 lafelldrlvdeivtvsdeealeamrllarregivvepssaaalaal.klreagelkegdrvvviltg 294
                                        a+e++ ++ +++ +  d+  ++ + ll r egi + p+sa +la+l k +++  +++  + v+iltg
  gi|242399052|ref|YP_002994476.1| 235 NALEAIYDSDGYVFGFADDVSFKYAYLLERFEGIKAFPASALVLAGLvKFVKKFGVNGR-NFVLILTG 301
                                       ***********************************************************.******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.32s 00:00:00.95 Elapsed: 00:00:00.53
# Mc/sec: 1770.43
//
Query:       gi|242399053|ref|YP_002994477.1|  [L=363]
Description: hypothetical protein TSIB_1074 [Thermococcus sibiricus MM 739]
Scores for complete 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-65  220.1   0.0    2.2e-65  219.7   0.0    1.1  1  DUF1611    Domain of unknown function (DUF1611_C) P-loop doma
    1.6e-30  105.1   0.0    3.6e-30  104.1   0.0    1.6  1  DUF1611_N  Domain of unknown function (DUF1611_N) Rossmann-li
    0.00032   20.8   0.0      0.041   14.0   0.0    2.6  2  DapB_N     Dihydrodipicolinate reductase, N-terminus
  ------ inclusion threshold ------
      0.068   13.2   0.1          1    9.4   0.0    2.7  3  CbiA       CobQ/CobB/MinD/ParA nucleotide binding domain
       0.09   13.0   0.0       0.66   10.2   0.0    2.5  3  PK_C       Pyruvate kinase, alpha/beta domain


Domain annotation for each model (and alignments):
>> DUF1611  Domain of unknown function (DUF1611_C) P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  219.7   0.0   6.2e-69   2.2e-65       3     200 .]     143     339 ..     141     339 .. 0.99

  Alignments for each domain:
  == domain 1  score: 219.7 bits;  conditional E-value: 6.2e-69
                           DUF1611   3 adgkarevkakrvlvvGTdcavGKrttaleleealeerGlkaafvaTgqtgili.agegvvldavvvdfvaGavegl 78 
                                       ++gk++ev+a +v+v+GTd a+GKrtta++l+ea+++ G k+ f+a+gqtg+++  ++ +v+d++v+dfvaGa+e++
  gi|242399053|ref|YP_002994477.1| 143 FSGKIEEVNAIKVAVLGTDGAIGKRTTAIMLHEAFNRFGKKSIFIAMGQTGWMQgFKYAIVMDSIVNDFVAGAIEDV 219
                                       6899************************************************************************* PP

                           DUF1611  79 vkkaaeeeepdlilveGQgsLthpaysgvtlglLlGsqPdalvLchrpgrkhirglpeialppleeeieliealaak 155
                                       +++a++ee+pd+i+ +G gsL+hpay+g  ++l+ +++Pd++vL+h+p+rk+++++p++++pple++i+lie l++k
  gi|242399053|ref|YP_002994477.1| 220 IWRAWKEENPDVIVTHGEGSLLHPAYPG-GFELIASGRPDYIVLQHAPARKYFDDFPQYEIPPLEKYIQLIELLSGK 295
                                       ****************************.************************************************ PP

                           DUF1611 156 kkvvgislNtknlseeeakealeeleeelglpvvdpvregaeklv 200
                                       k  ++i++N++nls+e+a ++++e+e+++g+ +  p+ e+++++v
  gi|242399053|ref|YP_002994477.1| 296 K-PIAITINSENLSKEDAFKIAREIESTYGILTKVPLYESIDEIV 339
                                       9.***************************************9996 PP

>> DUF1611_N  Domain of unknown function (DUF1611_N) Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.1   0.0   9.9e-34   3.6e-30       2      93 ..      39     134 ..      38     135 .. 0.98

  Alignments for each domain:
  == domain 1  score: 104.1 bits;  conditional E-value: 9.9e-34
                         DUF1611_N   2 ekaGkdagelldd..rgipvvssleea..laagaevlviGiapeggklpeswreavkeAleaGldvvsGlHerLsdd 74 
                                       ++aG+dage+ld+  rgip+++s+eea  +++++++l+iG+a++gg+lp  +re vk+A+++Gl++vsGlH++Ls++
  gi|242399053|ref|YP_002994477.1|  39 TLAGRDAGEVLDGvyRGIPIYGSFEEAitENPDVKYLIIGVATPGGYLPSVYREIVKKAIKRGLNIVSGLHYFLSSE 115
                                       689*********99*************************************************************** PP

                         DUF1611_N  75 pelaalakkkgvkiiDvRk 93 
                                       +e+a+lak+++v++iDvRk
  gi|242399053|ref|YP_002994477.1| 116 SEFARLAKRYKVQLIDVRK 134
                                       ******************8 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   1.1e-05     0.041      13      97 ..      17     107 ..      15     130 .. 0.81
   2 ?    4.0   0.1     0.014        51       1      21 [.     153     173 ..     153     196 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.1e-05
                                       HHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEBSSHHHHHHH.-S...EEEE-S-H.....HHH CS
                            DapB_N  13 Gkevvkaveeaedlelvaavdrkeselegkdagellglgklgvavtddleevlek.ad...vliDFTtp.....eav 80 
                                       Gk+   +v+ ++++++v++vd++   l g+dage+l+    g++++ ++ee++++  d    +i   tp     ++ 
  gi|242399053|ref|YP_002994477.1|  17 GKTAHGLVRYSQRYQIVGVVDST---LAGRDAGEVLDGVYRGIPIYGSFEEAITEnPDvkyLIIGVATPggylpSVY 90 
                                       6777778889999********97...59************************9998775556888887522222667 PP

                                       HHHHHHHHHTT-EEEE- CS
                            DapB_N  81 lenlklalekgvklViG 97 
                                        e +k a+++g ++V G
  gi|242399053|ref|YP_002994477.1|  91 REIVKKAIKRGLNIVSG 107
                                       78999999999999998 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.014
                                       EEEEEETTTSHHHHHHHHHHH CS
                            DapB_N   1 ikvavvGasGrmGkevvkave 21 
                                       ikvav+G  G +Gk+ +  + 
  gi|242399053|ref|YP_002994477.1| 153 IKVAVLGTDGAIGKRTTAIML 173
                                       79************9876654 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 ?   -2.8   0.0       1.7   6.1e+03      73      93 ..      29      49 ..      18      73 .. 0.64
   2 ?    0.9   0.0      0.13   4.5e+02      81     113 ..     102     136 ..      88     152 .. 0.65
   3 ?    9.4   0.0   0.00028         1       1      33 [.     155     187 ..     155     345 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.7
                                      H..EEEEEEEEESS...-TTC CS
                                      xxxxxxxxxxxxxxxxxxxxx RF
                              CbiA 73 llkiagvvlnrvdgeneetll 93
                                        +i+gvv+    g+++ + l
  gi|242399053|ref|YP_002994477.1| 29 RYQIVGVVDSTLAGRDAGEVL 49
                                      367888888888888655544 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.13
                                       EEEESS...-TTCHHHHHHHHHHCTS-EEE..EEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxx RF
                              CbiA  81 lnrvdgeneetllkealeelkqrygvpvlg..vip 113
                                       ln v g +++ + ++ +++l +ry+v++++  +i 
  gi|242399053|ref|YP_002994477.1| 102 LNIVSGLHYFLSSESEFARLAKRYKVQLIDvrKIF 136
                                       56666666666677777777777777776655443 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.00028
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllv 33 
                                       +a+ +t G  GK t+a+ L+ a++r g++ + +
  gi|242399053|ref|YP_002994477.1| 155 VAVLGTDGAIGKRTTAIMLHEAFNRFGKKSIFI 187
                                       689************************997766 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 ?   10.2   0.0   0.00018      0.66      23      76 ..      14      64 ..      12     130 .. 0.76
   2 ?   -2.9   0.0       2.1   7.6e+03      78     103 ..     208     237 ..     201     239 .. 0.60
   3 ?   -2.3   0.0       1.4   4.9e+03      80      87 ..     311     318 ..     283     351 .. 0.48

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00018
                                      -SSSHHHHHHHHT-TSSEEEEEESHHHHHHHHH.HCTTEEHHH.HHHHH...TTS CS
                              PK_C 23 tesGetArliskyrpkvpiiavtpneltarqla.lyrGvypvlvekaktaestde 76
                                      t+ G+tA+ + +y ++ +i+ v ++ l+ r    ++ Gvy+   ++   + s++e
  gi|242399053|ref|YP_002994477.1| 14 TSDGKTAHGLVRYSQRYQIVGVVDSTLAGRDAGeVLDGVYRGI-PI---YGSFEE 64
                                      899*********************9999888877888888763.44...333444 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.1
                                       HHHHHHHHHH....TTSS-STSEEEEEE-S CS
                              PK_C  78 lreavkvake....aglvkkgdevvvtaGt 103
                                       ++++v+ a+e    + + +++ +v+vt+G 
  gi|242399053|ref|YP_002994477.1| 208 VNDFVAGAIEdviwRAWKEENPDVIVTHGE 237
                                       455555555544434555677789999985 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 1.4
                                       HHHHHHHH CS
                              PK_C  80 eavkvake 87 
                                       +a+k+a e
  gi|242399053|ref|YP_002994477.1| 311 DAFKIARE 318
                                       33333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); 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: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2431.62
//
Query:       gi|242399054|ref|YP_002994478.1|  [L=485]
Description: hypothetical protein TSIB_1075 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score 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   13.7   0.8       0.11   12.5   0.8    1.5  1  Amidase_6  Putative amidase domain


Domain annotation for each model (and alignments):
>> Amidase_6  Putative amidase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.8   6.4e-06      0.11      45      84 ..     184     222 ..     178     235 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.4e-06
                         Amidase_6  45 glpedktgaea.eWnyyndskssasWagaeefknylssskk 84 
                                       g+ +      a +W+++n+s++++ W++++ ++n++ s+ k
  gi|242399054|ref|YP_002994478.1| 184 GHWKVAL--TAyKWFEKNESNTKKVWSNVDRLYNFIESNMK 222
                                       4444444..2335*99999999999***********99854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (485 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       709  (0.0395449); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); 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: 0.63u 0.27s 00:00:00.90 Elapsed: 00:00:00.45
# Mc/sec: 3271.85
//
Query:       gi|242399055|ref|YP_002994479.1|  [L=148]
Description: acetyl transferase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-13   50.6   0.1    2.4e-13   50.3   0.1    1.1  1  Acetyltransf_1   Acetyltransferase (GNAT) family
      4e-09   36.5   0.0    5.2e-09   36.1   0.0    1.1  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    3.1e-06   27.5   0.2      5e-06   26.8   0.2    1.3  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.031   14.4   0.1      0.057   13.6   0.1    1.4  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
      0.092   12.7   0.0       0.31   11.0   0.0    1.7  2  FR47             FR47-like protein
       0.13   13.0   0.0       0.15   12.7   0.0    1.2  1  Acetyltransf_3   Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.3   0.1   8.1e-17   2.4e-13       9     117 .]      26     137 ..      18     137 .. 0.84

  Alignments for each domain:
  == domain 1  score: 50.3 bits;  conditional E-value: 8.1e-17
                                       HHHTHHHHHHHHHHH...HHHHHHSTTCEEEE.EEETTEEEEEEEEEEEET..TSTTEEEEEEEEESGGGTTSSHHH CS
                    Acetyltransf_1   9 vesffppnedaseee...feesfsleaegllv.aeedgeliGfisllkipd..ekggvayieslaVspeyrgkGlGs 79 
                                        + f++p+ + se++    +e +s+ +  ++v   ++g+ +G++ l++  d   + + ayi+++ V+    g G+Gs
  gi|242399055|ref|YP_002994479.1|  26 FLKFPIPFDEYSERYeklIRELLSRGEHKFFVaLGKNGKFLGHVWLCMTLDtvDYVKIAYIYDIEVKQ--KGEGIGS 100
                                       4556677777777776556777888888777769999*******998888888999**********87..59***** PP

                                       HHHHHHHHHHHHTTESEEEEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  80 aLlealeerareegikkivlaveedndaairlYeklGF 117
                                       aLl+ +ee+a+e+g+kk+vl v+ +n +a + Y++ G+
  gi|242399055|ref|YP_002994479.1| 101 ALLKRAEEFAKEKGAKKVVLRVDLSN-PALEWYKRKGY 137
                                       ********************999998.******88997 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.0   1.7e-12   5.2e-09      19     109 ..      39     140 ..      23     147 .. 0.77

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 1.7e-12
                   Acetyltransf_10  19 p..ealrerieegealllvaeeg.gkivGviel.rdgs.....hisllf.VdpeyrgqGigkaLleaveeeaekdgi 85 
                                       +  + +re ++ ge++++va  + gk +G++ l ++ +     +i+ ++ ++ +++g Gig+aLl+++ee a+++g 
  gi|242399055|ref|YP_002994479.1|  39 RyeKLIRELLSRGEHKFFVALGKnGKFLGHVWLcMTLDtvdyvKIAYIYdIEVKQKGEGIGSALLKRAEEFAKEKGA 115
                                       33245666667888888877654499*****5544444456665555544778999********************* PP

                   Acetyltransf_10  86 kl.eltvnaspyavpfYeklGFkav 109
                                       k+  l v+ s+ a + Y++ G+++ 
  gi|242399055|ref|YP_002994479.1| 116 KKvVLRVDLSNPALEWYKRKGYTER 140
                                       *9********************976 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.2   1.7e-09     5e-06       3      76 .]      53     139 ..      51     139 .. 0.72

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 1.7e-09
                                       EEEEEEEET.TEEEEEEEEEEES.....TCTEEEE.E-GGGTTSSHHHHHHH.HTT....SEEE.EE.EEEETHHHH CS
                    Acetyltransf_7   3 gevfVaedd.gkivGfialslld.....aeitrla.VdpeyrgkGiGraLle.aae....kgii.le.qlelnaeka 65 
                                       +++fVa  + gk++G + l+ +        i +++ +  +  g GiG+aLl+ a+e    kg + ++ ++ l++ +a
  gi|242399055|ref|YP_002994479.1|  53 HKFFVALGKnGKFLGHVWLCMTLdtvdyVKIAYIYdIEVKQKGEGIGSALLKrAEEfakeKGAKkVVlRVDLSN-PA 128
                                       67999866578888988888887887655555577999999**********96522444566332234456655.8* PP

                                       HHHHHHTTEEE CS
                    Acetyltransf_7  66 ikfYeklGFee 76 
                                       +++Y++ G++e
  gi|242399055|ref|YP_002994479.1| 129 LEWYKRKGYTE 139
                                       *********85 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   1.9e-05     0.057      27      59 ..      86     116 ..      73     121 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.9e-05
                   Acetyltransf_CG  27 fthTeVpeelrGkGiAkkLvkaalddareeglk 59 
                                       ++ +eV+   +G+Gi+++L k+a ++a+e+g k
  gi|242399055|ref|YP_002994479.1|  86 IYDIEVK--QKGEGIGSALLKRAEEFAKEKGAK 116
                                       5556665..4799*****************986 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.68     2e+03      45      65 ..      42      62 ..      40      64 .. 0.78
   2 ?   11.0   0.0   0.00011      0.31      26      80 ..      88     140 ..      78     145 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.68
                                      HHHHHHHHS-S-EEEEEETT- CS
                              FR47 45 alakeiaergktvllvvvasN 65
                                      +l++e+  rg++ + v+  +N
  gi|242399055|ref|YP_002994479.1| 42 KLIRELLSRGEHKFFVALGKN 62
                                      688999999999988776555 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00011
                                       EEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EEEEEETT-HHHHHHHHHHT-EEE CS
                              FR47  26 alqvlpehrrrGlgsrlvkalakeiaergktvllvvvasNtpsirlyeklGfeki 80 
                                        ++v  + +++G gs l k   +   e+g + +++ v   +p+ + y++ G++++
  gi|242399055|ref|YP_002994479.1|  88 DIEV--KQKGEGIGSALLKRAEEFAKEKGAKKVVLRVDLSNPALEWYKRKGYTER 140
                                       4444..4689********997777777******9999999************987 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   5.2e-05      0.15      32     127 ..      31     128 ..       5     142 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.2e-05
                    Acetyltransf_3  32 ltleeaeewlerawaeeseeegygwaivl.kdtgviGsvglrdleeedeeaelgymlaps..fwgkGyateavrall 105
                                        + +e  e++e+  +e   + +  + + l k+++++G v l    +  + + + y+ + +    g G+++  ++ + 
  gi|242399055|ref|YP_002994479.1|  31 IPFDEYSERYEKLIRELLSRGEHKFFVALgKNGKFLGHVWLCMTLDTVDYVKIAYIYDIEvkQKGEGIGSALLKRAE 107
                                       44455555555443322222334566656477778****6665554445599999888551366889********** PP

                    Acetyltransf_3 106 eyafeelglerlvavidkeNea 127
                                       e+a +e g++++v ++d +N+a
  gi|242399055|ref|YP_002994479.1| 108 EFA-KEKGAKKVVLRVDLSNPA 128
                                       ***.7888*********99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); 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:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 971.40
//
Query:       gi|242399056|ref|YP_002994480.1|  [L=388]
Description: hypothetical protein TSIB_1077 [Thermococcus sibiricus MM 739]
Scores for complete 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-13   48.8  28.3    4.5e-13   48.8  28.3    2.0  2  MFS_1     Major Facilitator Superfamily


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.8  28.3   2.5e-17   4.5e-13       1     347 [.       9     341 ..       9     345 .. 0.70
   2 !   13.5  22.9   1.4e-06     0.025       2     175 ..     208     383 ..     207     388 .] 0.87

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 2.5e-17
                             MFS_1   1 lllaaflsalarsilgpalplalaedlgispseigllltlyalga....avaslplGrlsdrfGrrr.vlllglllf 72 
                                       lll+++l +++ +i ++alp++l ++  +  s++g     y+l++    ++a +++Gr+ d+   +  + +++l++ 
  gi|242399056|ref|YP_002994480.1|   9 LLLTTVLRTIGDAIENIALPWHLLDETASLLSVAG-----YSLASmlpwVIAPPLMGRFLDKTEKKVrLAFIALFIQ 80 
                                       578999999999999*****988777552222222.....4444444449999999******976666777777777 PP

                             MFS_1  73 alglllll.fasslwlllvlrvlqGlgagalfpagaaliadwfpk.eergraigllsagfslGailgpllggllass 147
                                       ++ +l+ + fas++w++++l  l ++   +    g +lia ++ + +e  + ++ +++   + ++l  ++ g+la +
  gi|242399056|ref|YP_002994480.1|  81 SFLALATIkFASNIWAFYILISLISALDVLHRYFGFTLIASMTLEeSELQKLNAKVQTVGEATSLLVFPIVGYLAYL 157
                                       77745555899********************************9989****************************** PP

                             MFS_1 148 lgWravfyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfs 224
                                       +g r++ ++ a+++l++++l + ++  + ++++r + + +         ++ ++  ++   +  + ++ll++f++  
  gi|242399056|ref|YP_002994480.1| 158 FGVRLM-LLDAVFLLIGALLLIPYINIPVRQEERIEYESK--------SAQ-FEVSRRIV-FVGIALVLLFNFAIAP 223
                                       ****65.899999999988666666555555555544444........222.22233333.3223333333333333 PP

                             MFS_1 225 g.lltllplylqevlgls...glllaglllallalvgailallagrlsdr..lgrrrrlllallllllaalglalla 295
                                       + +++++ l  ++v       gll ++    l++l+g   a  ++ ++++  +g  ++l++++ll +la l+l l +
  gi|242399056|ref|YP_002994480.1| 224 ArIFVFSAL--NDVAIGEivyGLLNSV--GTLGSLIG---AAGIAIFARKykIGISKPLVIGMLLESLAILILGLHS 293
                                       355555555..4444444444444444..45555555...4445555566114555555555555555555555555 PP

                             MFS_1 296 vtssavllllvlvliGfglgfvfpsllalasdlappeeagtasglfntagsl 347
                                       +     ll ++++++ fg  + ++s+ +l ++++p e+ gt+ g+f  + +l
  gi|242399056|ref|YP_002994480.1| 294 LL----LLFAGILILNFGRQILNISFDSLFQRVIPLEKLGTYKGVFDALATL 341
                                       55....66669999*******************************9877765 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 1.4e-06
                             MFS_1   2 llaaflsalarsilgpalplalaedlg...ispseigllltlyalgaavaslplGrlsdrf..Grrrvlllglllfa 73 
                                       +++++l+ l  ++++pa   ++ ++l+   i + ++gll ++ +lg+++++  ++ ++ ++  G  + l++g+ll +
  gi|242399056|ref|YP_002994480.1| 208 FVGIALVLLFNFAIAPARI-FVFSALNdvaIGEIVYGLLNSVGTLGSLIGAAGIAIFARKYkiGISKPLVIGMLLES 283
                                       5666666677777777666.554454444499999************9999999999998766************** PP

                             MFS_1  74 lglllllfasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgW 150
                                       l++l+l + +sl ll+++ ++  +g  +l+ +  +l+ ++ p e+ g + g++ a + l + l  l  ++l+++ g 
  gi|242399056|ref|YP_002994480.1| 284 LAILILGL-HSLLLLFAGILILNFGRQILNISFDSLFQRVIPLEKLGTYKGVFDALATLIIPLSQLSFAWLIEQ-GI 358
                                       **777777.9999***********************************************************77.89 PP

                             MFS_1 151 ravfyilaivsllafvlfllllpee 175
                                        ++ +++++++l ++  ++++++ +
  gi|242399056|ref|YP_002994480.1| 359 NVSILAVGVFGLGVLTAVGFFILIN 383
                                       *************988888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       784  (0.043728); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.50
# Mc/sec: 2337.27
//
Query:       gi|242399057|ref|YP_002994481.1|  [L=342]
Description: permease, major facilitator superfamily [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-12   47.6  24.9    2.6e-06   26.6  16.1    2.0  2  MFS_1         Major Facilitator Superfamily
  ------ inclusion threshold ------
       0.25   10.6   0.0       0.41    9.9   0.0    1.3  1  Syntaxin-5_N  Syntaxin-5 N-terminal, Sly1p-binding domain
        7.8    6.1   7.8         11    5.6   2.4    2.8  2  NapE          Periplasmic nitrate reductase protein NapE


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 !   26.1   5.0     6e-10   3.6e-06      46     257 ..       4     209 ..       1     210 [. 0.82
   2 !   26.6  16.1   4.4e-10   2.6e-06      38     174 ..     195     332 ..     191     341 .. 0.89

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 6e-10
                             MFS_1  46 avaslplGrlsdrfGrrrvlllglllfalg.lllllfa...sslw.lllvlrvlqGlgagalfpagaaliadwfpke 117
                                       + +++++Gr+ +r+  ++ l++  +l +++ +l++ +a   +  + +l+++rv+  l + +l+p+ +a+   ++p++
  gi|242399057|ref|YP_002994481.1|   4 SPSTYLFGRFFNRWDIKKGLIAIDVLDGIAyVLYG-LAkgvIA-PlMLFAGRVIEKLST-MLYPLYQAYEQVIYPED 77 
                                       668899************************44444.4544444.449***********6.***************** PP

                             MFS_1 118 ergraigllsagfslGailgpllggllasslg.....Wravfyilaivsllafvlfllllpeepperkrkspkeeek 189
                                       +    +++      +++i+  ++ g++++++      +r+vf++ +++s++   +++l ++ + + r+   + e   
  gi|242399057|ref|YP_002994481.1|  78 KYEEIFAWHLRLPEIATIVSFPVIGYFLDYVYnrpehYRLVFLFSGLFSVVT--VAYLGFFLPSVGREERISPEG-- 150
                                       ********************8888888877778*******************..667888888888888888888.. PP

                             MFS_1 190 gtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlglsglllaglllallalvg 257
                                         + +++ + +k ll+   l  l +a+ l+   f ++ + ++++ ++v+  + l+ ++  ++l+ ++g
  gi|242399057|ref|YP_002994481.1| 151 --FTFKVGE-FKVLLTFEAL--LTLAWGLAP-EFILINYVVFVLHKTVFEVT-LIAVA--SSLMRIIG 209
                                       ..8999999.*****99977..555555554.55556666666667888888.67776..77777776 PP

  == domain 2  score: 26.6 bits;  conditional E-value: 4.4e-10
                             MFS_1  38 ltlyalgaavaslplGrlsdrfGrrr.vlllglllfalglllllfa..sslwlllvlrvlqGlgagalfpagaalia 111
                                       +tl a++++++ +++ + s+r+  r+ ++ +++ +f+ +++ l++a  +++wl l + ++  +g ++ fp   ++i 
  gi|242399057|ref|YP_002994481.1| 195 VTLIAVASSLMRIIGTYASERVPKRKgFYAIAFGMFLNAFYTLTMAlaPPFWLALTVYAIGDFGNALWFPFYRSWIF 271
                                       789999***********************99999999996666665559**************************** PP

                             MFS_1 112 dwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllllpe 174
                                       ++ pke+ +   + +s+ + l  +++p ++g+la s+  ++++ +  +++l+a+ + +++lp+
  gi|242399057|ref|YP_002994481.1| 272 KIIPKERTSEFHAAISSYNRLIGLITPFVAGALA-SIHATLPYGASLVLFLMAGAM-FWVLPR 332
                                       *****9999999**********************.8889999**********9995.344444 PP

>> Syntaxin-5_N  Syntaxin-5 N-terminal, Sly1p-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   6.8e-05      0.41       9      19 ..     278     288 ..     276     291 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 6.8e-05
                      Syntaxin-5_N   9 RTsEFqSivks 19 
                                       RTsEF+++  s
  gi|242399057|ref|YP_002994481.1| 278 RTSEFHAAISS 288
                                       *******9987 PP

>> NapE  Periplasmic nitrate reductase protein NapE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.3     0.017     1e+02      15      40 ..     113     135 ..     109     137 .. 0.64
   2 ?    5.6   2.4    0.0019        11      16      44 ..     231     263 ..     228     266 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.017
                              NapE  15 ElkaflfltvvlfPiLsValVggYGf 40 
                                       E   ++fl   lf +++Va  g   f
  gi|242399057|ref|YP_002994481.1| 113 EHYRLVFLFSGLFSVVTVAYLG---F 135
                                       6666777777777666666555...4 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0019
                              NapE  16 lkaflfltvvlfP....iLsValVggYGfivWm 44 
                                       l+af  lt+ l+P    +L+V  +g +G ++W+
  gi|242399057|ref|YP_002994481.1| 231 LNAFYTLTMALAPpfwlALTVYAIGDFGNALWF 263
                                       578999999999977778**************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      202  (0.0112667); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2498.62
//
Query:       gi|242399058|ref|YP_002994482.1|  [L=581]
Description: ABC transporter ATP-binding protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-56  191.9  12.2      2e-56  191.6  12.2    1.1  1  ABC_membrane    ABC transporter transmembrane region
    2.1e-32  112.5   0.0    3.3e-32  111.9   0.0    1.3  1  ABC_tran        ABC transporter
     0.0037   17.7   0.1       0.72   10.3   0.0    2.4  2  AAA             ATPase family associated with various cellula
  ------ inclusion threshold ------
      0.016   14.6   0.1       0.48    9.8   0.0    2.0  2  SMC_N           RecF/RecN/SMC N terminal domain
      0.021   14.9   0.1      0.048   13.8   0.1    1.5  1  DUF87           Helicase HerA, central domain
      0.095   11.9   0.0        0.2   10.8   0.0    1.5  1  NB-ARC          NB-ARC domain
      0.095   13.0   0.1        0.4   11.0   0.1    2.1  1  AAA_22          AAA domain
       0.14   11.9   1.2        4.7    6.9   0.1    2.3  2  AAA_21          AAA domain, putative AbiEii toxin, Type IV TA
       0.15   12.5   0.3       0.32   11.5   0.3    1.4  1  AAA_23          AAA domain
       0.16   11.3   8.6       0.01   15.3   3.6    1.5  2  ABC_membrane_2  ABC transporter transmembrane region 2
       0.18   10.7   0.0       0.33    9.8   0.0    1.4  1  AAA_10          AAA-like domain
       0.24   11.1   0.2       0.86    9.3   0.2    1.9  1  AAA_30          AAA domain


Domain annotation for each model (and alignments):
>> ABC_membrane  ABC transporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.6  12.2   1.4e-59     2e-56       1     273 [.      27     297 ..      27     298 .. 0.99

  Alignments for each domain:
  == domain 1  score: 191.6 bits;  conditional E-value: 1.4e-59
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      ABC_membrane   1 liliillailagvlsplfplvlgrildtlldkgdpetealnvysllllllglaqfilallqsyllnvtgerlskrlr 77 
                                       li++++++i + ++ ++ p++l+  +d ++  g+ +     +++ll+l+++ aq+++a+lq++++ v g+++  +lr
  gi|242399058|ref|YP_002994482.1|  27 LIIVVVSIIGSALATLAPPYILSVAIDRYILAGNYNR--FWFIALLYLSALTAQWFFATLQTFYIEVFGQKVLCDLR 101
                                       68999**************************999999..************************************** PP

                                       HHHHHHHHCSTHHHHHHSCHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHH CS
                      ABC_membrane  78 rklfkkilrqpmsffdtnsvGellsrltndvsklrdglgeklglffqslltfvgglivmfylgwkltlvllailpli 154
                                       ++l +k+lr  ++ff ++s+G+l+sr+ nd+  ++d+l + l+  + sll+++g++i mf+l +kltlv+la +pl+
  gi|242399058|ref|YP_002994482.1| 102 ARLHEKVLRSRLEFFKDKSTGDLVSRIVNDTGIVNDVLVSGLFGSLGSLLSLIGIIIAMFLLDVKLTLVTLASIPLM 178
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      ABC_membrane 155 ilvsaviakilkklkkkeqkavakassvaeEslsgirtVkafgreeyflekfekaleeakkagikkaianglligit 231
                                       ilv+++++ +++++ ++  +++ak+ssv+eEs+ g++t++afg+e +++++f   ++e  ka++++a++ gl+++ +
  gi|242399058|ref|YP_002994482.1| 179 ILVAYYFGGKMRRAYRETRQKIAKISSVVEESVAGVETIRAFGKEGEVEREFSRVSRETIKAYLRVAVYMGLFWPLM 255
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHTTSSTHHHHHHHHHHHHHHHHH CS
                      ABC_membrane 232 qllgllsyalalwfGttlvisgelsvgdlvvflslfailfga 273
                                       ++ +l+s+++++ +G++l  +g++s+g +++f++++  + g+
  gi|242399058|ref|YP_002994482.1| 256 NITSLVSVIIVIAYGGYLAYQGAMSIGVVIAFIQYAQRFRGP 297
                                       ***********************************9888776 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.9   0.0   2.2e-35   3.3e-32       1     136 [.     358     506 ..     358     507 .. 0.94

  Alignments for each domain:
  == domain 1  score: 111.9 bits;  conditional E-value: 2.2e-35
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       lk ++l++ + +k+aivG++GaGK+t++ l+++ ++pteG++l+dg d k+++++slr++ig++pqe+ lfp++ + 
  gi|242399058|ref|YP_002994482.1| 358 LKGINLQIPPASKIAIVGRTGAGKTTIAGLIMRFYDPTEGRVLYDGVDGKRISRKSLRRRIGYVPQETYLFPGT-IM 433
                                       789***********************************************************************.99 PP

                                       HH.......HHHTCHHHHHHHSTTGG.......TTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx.......xxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.......esdeeiekalsklglke.......lkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       en       +s+e++ ++ ++lg ++         +t +++ ++ LS G++q ++larall++p++++lDE+ 
  gi|242399058|ref|YP_002994482.1| 434 ENilmanpeASEEDVIRVCKELGVQDfimrlpkGYNTSAGEAGKLLSVGERQLISLARALLEDPDIVILDEAL 506
                                       999*****98888899999999999988887776788888888****************************96 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.021        31       3      20 ..     373     390 ..     371     429 .. 0.83
   2 !   10.3   0.0   0.00048      0.72      18      98 ..     451     530 ..     448     555 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.021
                                       EESSTTSSHHHHHHHHHH CS
                               AAA   3 lyGppGtGKTllakavak 20 
                                       ++G  G GKT++a  +++
  gi|242399058|ref|YP_002994482.1| 373 IVGRTGAGKTTIAGLIMR 390
                                       789**********99886 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00048
                                       HHHHHTHEEEEEETTTCSSSSTTHHHHHH....HHHHHHHHHTS.TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHH CS
                               AAA  18 vakelgvefleisgsellskyvgesekki....relfkeakeka.kpsilfiDEidalaksrsgseseeeervvnqL 89 
                                       v+kelgv+ + + +++  +   ge+ k +    r+l++ a++   +p i+++DE+ + +  +       e+ v++++
  gi|242399058|ref|YP_002994482.1| 451 VCKELGVQDFIMRLPKGYNTSAGEAGKLLsvgeRQLISLARALLeDPDIVILDEALSSVDPK------TERLVQDAM 521
                                       67777777666666666666666666655333345555556555679*******99888877......899****** PP

                                       HHHHHHTTT CS
                               AAA  90 lteldgvkk 98 
                                       l+ ++g ++
  gi|242399058|ref|YP_002994482.1| 522 LKLMEGRTS 530
                                       ******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 ?    2.1   0.0     0.075   1.1e+02      26      41 ..     370     385 ..     354     392 .. 0.82
   2 ?    9.8   0.0   0.00032      0.48     136     212 ..     478     550 ..     431     555 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.075
                                       EEEEEESTTSSHHHHH CS
                                       xxxxxxxxxxxxxxxx RF
                             SMC_N  26 ftaivGpNGSGKsnll 41 
                                         aivG+ G+GK+ + 
  gi|242399058|ref|YP_002994482.1| 370 KIAIVGRTGAGKTTIA 385
                                       469**********986 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00032
                                       CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadklvgvt 212
                                       lLS Ge++L++la        +   +++lDe  +  D k  + v + + +  +    i+i++r ++++ adk+v v 
  gi|242399058|ref|YP_002994482.1| 478 LLSVGERQLISLARA----LLEDPDIVILDEALSSVDPKTERLVQDAMLKLMEGRTSIIIAHRLGITRFADKVVVVE 550
                                       79*******998754....35666799*******************9999999******************999875 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   3.2e-05     0.048      25      45 ..     370     390 ..     365     392 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.2e-05
                             DUF87  25 HlAilgsTGsGKSntvavLle 45 
                                        +Ai+g+TG+GK++ ++++++
  gi|242399058|ref|YP_002994482.1| 370 KIAIVGRTGAGKTTIAGLIMR 390
                                       58****************986 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00013       0.2      23      53 ..     371     403 ..     364     419 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00013
                                       EEEEESTTSSHHHHHHHHCCSHCCCCC..CBTE CS
                            NB-ARC  23 valvGmgGvGKttlakqilnksdeveg..rFds 53 
                                       +a+vG+ G GKtt+a  i++ +d +eg   +d+
  gi|242399058|ref|YP_002994482.1| 371 IAIVGRTGAGKTTIAGLIMRFYDPTEGrvLYDG 403
                                       89**************99998888777444665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00027       0.4       8      38 ..     371     416 ..     367     528 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00027
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee...................e 38 
                                       ++++G +G+GKTt +  +++ +d      e                   +
  gi|242399058|ref|YP_002994482.1| 371 IAIVGRTGAGKTTIAGLIMRFYDPT----EgrvlydgvdgkrisrkslrR 416
                                       89************99999998643....223335555555554444440 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1      0.04        60       3      19 ..     372     388 ..     371     418 .. 0.81
   2 ?    6.9   0.1    0.0032       4.7     237     282 ..     475     521 ..     460     534 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.04
                            AAA_21   3 vliGpNgsGKSnLLdal 19 
                                       +++G+ g+GK+++  ++
  gi|242399058|ref|YP_002994482.1| 372 AIVGRTGAGKTTIAGLI 388
                                       79**********96665 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0032
                            AAA_21 237 l....SdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell 282
                                       +    S G ++l+ l+ all+++   +++++DE  ++ +Pk  r + + +
  gi|242399058|ref|YP_002994482.1| 475 AgkllSVGERQLISLARALLEDP---DIVILDEALSSVDPKTERLVQDAM 521
                                       44445****************99...9***********995444433555 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.3   0.00021      0.32      23      36 ..     372     385 ..     357     389 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00021
                            AAA_23  23 lItGpNGaGKTTil 36 
                                       +I+G +GaGKTTi 
  gi|242399058|ref|YP_002994482.1| 372 AIVGRTGAGKTTIA 385
                                       8***********96 PP

>> ABC_membrane_2  ABC transporter transmembrane region 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   3.6   6.7e-06      0.01      19     179 ..      29     194 ..      12     208 .. 0.72
   2 ?   -4.0   0.2       5.1   7.6e+03     138     168 ..     237     267 ..     229     276 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 6.7e-06
                    ABC_membrane_2  19 vlllllvlrtllsvlv.aqldgklvkalvaknvraFvlsllkfallavpasfvnsalkYltqkLalafRkrLtkhll 94 
                                       +++++++ + l ++     l+ ++ ++++a+n++ F++  l ++ ++ +  f + ++ ++ + +  ++   L + l+
  gi|242399058|ref|YP_002994482.1|  29 IVVVSIIGSALATLAPpYILSVAIDRYILAGNYNRFWFIALLYLSALTAQWFFATLQTFYIEVFGQKVLCDLRARLH 105
                                       333333333333333203456678899************************************************** PP

                    ABC_membrane_2  95 seYlknr.tyYkvsnlderidnp..DqritqDvekFts.slssLlsglvkpildvilftfiLwslsgtlglllllly 167
                                       ++ l+ r  ++k ++ ++ ++ +  D  i +Dv       ++  l++l+  i+ ++l  ++L+ ++ +  +l++l+ 
  gi|242399058|ref|YP_002994482.1| 106 EKVLRSRlEFFKDKSTGDLVSRIvnDTGIVNDVLVSGLfGSLGSLLSLIGIIIAMFLLDVKLTLVTLASIPLMILVA 182
                                       *******9****99999955432226666666644332333333445666666677777777777777777999999 PP

                    ABC_membrane_2 168 vllatvilriig 179
                                       +++++ + r+++
  gi|242399058|ref|YP_002994482.1| 183 YYFGGKMRRAYR 194
                                       999999888876 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 5.1
                    ABC_membrane_2 138 lvkpildvilftfiLwslsgtlgllllllyv 168
                                        +k+ l v++++   w l++  +l+++++++
  gi|242399058|ref|YP_002994482.1| 237 TIKAYLRVAVYMGLFWPLMNITSLVSVIIVI 267
                                       5677777777777777777766665555544 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00022      0.33      17      68 ..     364     418 ..     345     439 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00022
                            AAA_10  17 sktnasasliiGdlGnGKSvlakllvlyisllggkali..iDpkke.rekfketl 68 
                                       +   as+ +i+G +G+GK  +a l++ +    +g++l+  +D k+  r+  ++++
  gi|242399058|ref|YP_002994482.1| 364 QIPPASKIAIVGRTGAGKTTIAGLIMRFYDPTEGRVLYdgVDGKRIsRKSLRRRI 418
                                       44558889*****************************988898887455566666 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.2   0.00057      0.86      22      55 ..     372     405 ..     367     526 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00057
                            AAA_30  22 vltGpAGtGKttalkalreaweaaggrviglApt 55 
                                       +++G+ G+GKtt+ + + + ++  +grv+     
  gi|242399058|ref|YP_002994482.1| 372 AIVGRTGAGKTTIAGLIMRFYDPTEGRVLYDGVD 405
                                       699**************99999997777654444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (581 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       786  (0.0438396); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                        97  (0.00541023); 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: 0.74u 0.33s 00:00:01.07 Elapsed: 00:00:00.49
# Mc/sec: 3590.54
//
Query:       gi|242399059|ref|YP_002994483.1|  [L=41]
Description: ABC transporter ATP-binding protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       111  (0.00619109); expected 358.6 (0.02)
Passed bias filter:                       94  (0.0052429); 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: 0.39u 0.31s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 265.03
//
Query:       gi|242399060|ref|YP_002994484.1|  [L=579]
Description: ABC transporter, ATP-binding protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-45  155.3  16.3    3.4e-45  154.8  16.3    1.2  1  ABC_membrane     ABC transporter transmembrane region
    6.6e-36  123.8   0.0    1.2e-35  123.0   0.0    1.5  1  ABC_tran         ABC transporter
    4.1e-06   27.3   0.0      1e-05   26.0   0.0    1.7  1  AAA_16           AAA ATPase domain
    9.1e-05   22.4   0.2      0.056   13.2   0.0    2.4  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    0.00014   21.5   0.0    0.00033   20.3   0.0    1.5  1  AAA_29           P-loop containing region of AAA domain
    0.00028   21.5   0.0    0.00095   19.7   0.0    1.9  1  AAA_18           AAA domain
    0.00055   19.1   0.0     0.0011   18.1   0.0    1.5  1  T2SSE            Type II/IV secretion system protein
    0.00087   19.1   0.0     0.0022   17.7   0.0    1.6  1  AAA_30           AAA domain
    0.00092   19.5   0.0     0.0025   18.1   0.0    1.7  1  AAA_22           AAA domain
      0.001   18.7   0.0     0.0021   17.7   0.0    1.5  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
     0.0014   18.1   0.2       0.18   11.2   0.2    2.3  1  SMC_N            RecF/RecN/SMC N terminal domain
     0.0021   18.5   0.0     0.0066   16.9   0.0    2.0  1  AAA              ATPase family associated with various cellul
     0.0033   17.4   0.0     0.0078   16.1   0.0    1.7  1  NTPase_1         NTPase
     0.0052   16.7   0.0      0.011   15.7   0.0    1.5  1  Rad17            Rad17 P-loop domain
     0.0054   17.0   0.0       0.01   16.1   0.0    1.5  1  AAA_28           AAA domain
     0.0097   15.2   0.0      0.026   13.8   0.0    1.6  1  Zeta_toxin       Zeta toxin
  ------ inclusion threshold ------
      0.019   14.7   0.0      0.031   14.0   0.0    1.3  1  AAA_24           AAA domain
       0.02   14.9   0.0      0.059   13.4   0.0    1.8  1  AAA_5            AAA domain (dynein-related subfamily)
      0.022   14.7   0.0       0.07   13.0   0.0    1.8  1  ATPase_2         ATPase domain predominantly from Archaea
      0.026   14.3   0.2        0.1   12.3   0.0    2.0  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      0.034   13.5   0.0      0.064   12.6   0.0    1.4  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.037   12.8   0.0        5.2    5.8   0.0    2.5  2  ABC_ATPase       Predicted ATPase of the ABC class
       0.04   13.8   0.0      0.088   12.7   0.0    1.6  1  NACHT            NACHT domain
      0.044   12.8   0.0      0.075   12.0   0.0    1.3  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
      0.046   12.9   0.0       0.12   11.5   0.0    1.6  1  DUF815           Protein of unknown function (DUF815)
      0.047   13.9   0.0        0.1   12.8   0.0    1.6  1  AAA_33           AAA domain
      0.047   14.2   0.1       0.12   12.8   0.1    1.6  1  AAA_23           AAA domain
       0.05   12.8   0.0      0.074   12.2   0.0    1.2  1  G-alpha          G-protein alpha subunit
      0.053   13.9   0.0       0.18   12.1   0.0    1.9  1  AAA_19           AAA domain
      0.059   12.5   0.0        0.1   11.8   0.0    1.3  1  DAP3             Mitochondrial ribosomal death-associated pro
      0.074   12.6   0.0       0.16   11.5   0.0    1.5  1  AAA_25           AAA domain
        0.1   13.0   0.0        0.2   12.1   0.0    1.5  1  AAA_17           AAA domain
       0.11   12.5   0.0       0.29   11.2   0.0    1.6  1  AAA_14           AAA domain
       0.12   11.3   0.0       0.17   10.8   0.0    1.2  1  AAA_10           AAA-like domain
       0.13   12.8   0.2         22    5.6   0.1    2.7  2  RuvA_C           RuvA, C-terminal domain
       0.13   12.0   0.0        0.2   11.4   0.0    1.3  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
       0.18   12.2   0.0       0.51   10.8   0.0    1.9  1  RNA_helicase     RNA helicase
       0.24   10.0   0.0         12    4.4   0.0    2.1  2  AAA_13           AAA domain


Domain annotation for each model (and alignments):
>> ABC_membrane  ABC transporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.8  16.3   7.2e-48   3.4e-45       7     274 .]      28     293 ..      22     293 .. 0.97

  Alignments for each domain:
  == domain 1  score: 154.8 bits;  conditional E-value: 7.2e-48
                                       HHHHHHHHHHHHHHHHHHHHHHHHSSTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      ABC_membrane   7 lailagvlsplfplvlgrildtlldkgdpetealnvysllllllglaqfilallqsyllnvtgerlskrlrrklfkk 83 
                                         +l   ++ ++p+++   +d  +++g+ +    ++y+l++ll+++++++++++  yll +++++++ +lr ++f++
  gi|242399060|ref|YP_002994484.1|  28 IVLLMSYTNGIIPVLIREAIDGGITTGEYHV--AVRYALIVLLVAVLNGVFSFGGRYLLVKAAQYAVYHLRMDAFRA 102
                                       55666778899********************..******************************************** PP

                                       HHCSTHHHHHHSCHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHH CS
                      ABC_membrane  84 ilrqpmsffdtnsvGellsrltndvsklrdglgeklglffqslltfvgglivmfylgwkltlvllailpliilvsav 160
                                       i r  m+ffd++ +G+l+sr+tnd++++  +l++++ +f+ s+++++++l +m+ +++ lt v l+++ +++ ++  
  gi|242399060|ref|YP_002994484.1| 103 IQRHQMEFFDKTYSGQLISRITNDTERITRFLSFRVRMFVYSIFLILVSLYYMIMMNVTLTGVALVTIAVVVALNTT 179
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      ABC_membrane 161 iakilkklkkkeqkavakassvaeEslsgirtVkafgreeyflekfekaleeakkagikkaianglligitqllgll 237
                                       +a++++++ +k   +++ + sv + s+ g++t+ka+  ee+ + kf k++ee ++ ++ ++++++l + + +l++ +
  gi|242399060|ref|YP_002994484.1| 180 YARKVRPIYDKVRHQTGVIASVSTGSIAGVKTIKALSVEENIQGKFSKENEELYSLNVEATKITALYGNAPFLIMGT 256
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHTTSSTHHHHHHHHHHHHHHHHHH CS
                      ABC_membrane 238 syalalwfGttlvisgelsvgdlvvflslfailfgal 274
                                       +++++l++G+  +++++l+vg+l++fl+++ +++++l
  gi|242399060|ref|YP_002994484.1| 257 AMSAMLYYGGRAIMANTLTVGELTAFLTYMLTMTWPL 293
                                       **********************************996 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.0   0.0   2.6e-38   1.2e-35       1     136 [.     355     503 ..     355     504 .. 0.93

  Alignments for each domain:
  == domain 1  score: 123.0 bits;  conditional E-value: 2.6e-38
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       lk ++lk+k+ge++ i+G+ G+GKStLlkl+a+ ++p+ G++l+d+ d+++++++slrk ++++pqep++f+++ +r
  gi|242399060|ref|YP_002994484.1| 355 LKGLNLKIKPGERILITGPPGSGKSTLLKLIARFYEPERGQVLVDDVDVRKIKTSSLRKTVAYIPQEPFIFNRS-LR 430
                                       7899**********************************************************************.** PP

                                       HH................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       en                ++ ++i++++++l   +  +tvv++++ +LSgGq+qr+alarall +p++lllD+p 
  gi|242399060|ref|YP_002994484.1| 431 ENialakpdasmeeiiraAKIAKIHDFIASLPEGY--ETVVGEKGVTLSGGQRQRIALARALLLEPRILLLDDPV 503
                                       ******88877777766666666888888888777..*************************************7 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   2.2e-08     1e-05      25     143 ..     366     501 ..     357     530 .. 0.56

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 2.2e-08
                            AAA_16  25 elvllsGesGvGKsslvrellralekdggiflrgkcdql...esa.....ipysa.laqalareellrqllde.... 88 
                                       e +l++G++G+GKs+l++ ++r +e ++g +l  + d     + +     ++y++    ++ +++l + ++ +    
  gi|242399060|ref|YP_002994484.1| 366 ERILITGPPGSGKSTLLKLIARFYEPERGQVLVDDVDVRkikT-SslrktVAYIPqEPFIF-NRSLRENIALAkpda 440
                                       679************************9999888888874431.12333355544222222.334444444442222 PP

                            AAA_16  89 .....aesaeleawrekleeala.....................avpelagaeasrllellkrllallsrderplvl 139
                                                          +a++                         ++ ++ +r + +l+r+l ll+    p +l
  gi|242399060|ref|YP_002994484.1| 441 smeeiI-------------RAAKiakihdfiaslpegyetvvgeK--GVTLSGGQRQRIALARAL-LLE----PRIL 497
                                       222221.............22223333344444444555655332..222222244444555555.222....3566 PP

                            AAA_16 140 vlDd 143
                                       +lDd
  gi|242399060|ref|YP_002994484.1| 498 LLDD 501
                                       6665 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   0.00012     0.056       3      62 ..     369     437 ..     368     447 .. 0.66
   2 ?    6.6   0.1     0.013       6.1     237     279 ..     476     515 ..     472     531 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00012
                            AAA_21   3 vliGpNgsGKSnLLdaldllarl............drdvegltdelsggggirkipslldlydpeipfefei 62 
                                       +++Gp gsGKS+LL+++     +             +  +  t++l++++ ++ ++ ++++++ ++ ++++ 
  gi|242399060|ref|YP_002994484.1| 369 LITGPPGSGKSTLLKLIAR---FyepergqvlvddVDVRKIKTSSLRKTVAYIPQEPFIFNRSLRENIALAK 437
                                       699**************55...44557777777744444444555666666666666666666666666655 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.013
                            AAA_21 237 lSdGtkrllalltallralkkgsllliDEpEngLHPkllrrll 279
                                       lS G+++ +al+ all  +   ++ll+D+p ++L+ +  ++l+
  gi|242399060|ref|YP_002994484.1| 476 LSGGQRQRIALARALLLEP---RILLLDDPVSNLDAETEEKLV 515
                                       7999999999999999999...************998877777 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0     7e-07   0.00033      15      39 ..     358     382 ..     353     392 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 7e-07
                            AAA_29  15 htieidlkgatlltGpsGsGKSTll 39 
                                         ++i++ + +l+tGp GsGKSTll
  gi|242399060|ref|YP_002994484.1| 358 LNLKIKPGERILITGPPGSGKSTLL 382
                                       5678998889**************8 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0     2e-06   0.00095       1      36 [.     368     405 ..     368     445 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 2e-06
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf....gvnlrdvakeng 36 
                                       Il+tG+pG+GK+tl k +++   +    g++l d +  + 
  gi|242399060|ref|YP_002994484.1| 368 ILITGPPGSGKSTLLKLIARF--YeperGQVLVDDVDVRK 405
                                       99***************9763..34455666666555555 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 !   18.1   0.0   2.4e-06    0.0011     102     165 ..     338     400 ..     316     442 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.4e-06
                             T2SSE 102 eltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeinksderivtvED 165
                                       +++++++  + ++ +++ + l+  ++    il++G+ gsGK+tll  +  + + + +  v+v D
  gi|242399060|ref|YP_002994484.1| 338 KIEFRNVHLTYHTGKTVLKGLNLKIKPGERILITGPPGSGKSTLLKLIARFYEPE-RGQVLVDD 400
                                       567777778888889999999999999******************9888777766.55556655 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   4.7e-06    0.0022      21      50 ..     368     397 ..     362     403 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4.7e-06
                            AAA_30  21 avltGpAGtGKttalkalreaweaaggrvi 50 
                                        ++tGp+G+GK+t+lk +++ +e + g+v+
  gi|242399060|ref|YP_002994484.1| 368 ILITGPPGSGKSTLLKLIARFYEPERGQVL 397
                                       579********************9977876 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   5.3e-06    0.0025       8      32 ..     368     392 ..     363     438 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 5.3e-06
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldee 32 
                                       +++tG++G+GK+tll+ +++ ++ e
  gi|242399060|ref|YP_002994484.1| 368 ILITGPPGSGKSTLLKLIARFYEPE 392
                                       79******************99643 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 !   17.7   0.0   4.4e-06    0.0021       3      49 ..     368     414 ..     366     420 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4.4e-06
                                       EEEEESTTCCHHHHHHHHHCT--SS-EEEEESS-SSCHCCCCCCHCC CS
                              cobW   3 tvltGflGsGKTtLlnhllenraglklavivNefgevsiDaellret 49 
                                       +++tG++GsGK+tLl+ + +  + ++  v+v ++   +i  + lr+t
  gi|242399060|ref|YP_002994484.1| 368 ILITGPPGSGKSTLLKLIARFYEPERGQVLVDDVDVRKIKTSSLRKT 414
                                       689******************************99878877777776 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 !   11.2   0.2   0.00038      0.18     135     211 ..     454     546 ..     356     552 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00038
                                       T....................CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSE CS
                                       x....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 135 e....................lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQ 191
                                                            +LSgG+++ +ala  +     +p+ + llD+  ++LD++  +k++  lk   +   
  gi|242399060|ref|YP_002994484.1| 454 IhdfiaslpegyetvvgekgvTLSGGQRQRIALARALL---LEPR-ILLLDDPVSNLDAETEEKLVGDLKDILEGKT 526
                                       14445555555555555556689*****9988876543...3454.77999999*****************999999 PP

                                       EEEE-SSHHHCCC-SCEEEE CS
                                       xxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 192 fivislreemlekadklvgv 211
                                        +++s r  m++  d+++ +
  gi|242399060|ref|YP_002994484.1| 527 ALIVSQRLSMVKLTDRVIVM 546
                                       ************99998755 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.4e-05    0.0066       1      38 [.     368     423 ..     368     546 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.4e-05
                                       EEEESSTTSSHHHHHHHHHHHH..........THEEEEEETTTCSSS........S CS
                               AAA   1 vllyGppGtGKTllakavakel..........gvefleisgsellsk........y 38 
                                       +l++GppG GK++l k +a+            +v++ +i+ s+l++         +
  gi|242399060|ref|YP_002994484.1| 368 ILITGPPGSGKSTLLKLIARFYepergqvlvdDVDVRKIKTSSLRKTvayipqepF 423
                                       699*****************974444433444477888888888844555555550 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.6e-05    0.0078       1      22 [.     367     388 ..     367     412 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.6e-05
                                       EEEEE--TTSSHHHHHHHHHHH CS
                          NTPase_1   1 kvfiTGppGvGKtTlvkkvlel 22 
                                       +++iTGppG+GK+Tl+k +++ 
  gi|242399060|ref|YP_002994484.1| 367 RILITGPPGSGKSTLLKLIARF 388
                                       699*************999875 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   2.3e-05     0.011      33      71 ..     353     391 ..     348     414 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.3e-05
                             Rad17  33 ewlkadvLesrkkriLLisGPsGCgkstvvkvLskelgi 71 
                                       + lk   L+ ++ + +Li+GP+G gkst +k +++ + +
  gi|242399060|ref|YP_002994484.1| 353 TVLKGLNLKIKPGERILITGPPGSGKSTLLKLIARFYEP 391
                                       56777778888888899***************9987655 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   2.1e-05      0.01       1      29 [.     367     400 ..     367     439 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.1e-05
                            AAA_28   1 kivitGgestGKTtlleaLa.....argypvvpE 29 
                                       +i itG++++GK+tll+ +a     +rg + v +
  gi|242399060|ref|YP_002994484.1| 367 RILITGPPGSGKSTLLKLIArfyepERGQVLVDD 400
                                       799***************9965555556666655 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   5.6e-05     0.026      19      56 ..     368     405 ..     360     413 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.6e-05
                        Zeta_toxin  19 illgGqpGAGKselaellkdelerqgnvvrldpDdlRe 56 
                                       il+ G pG+GKs+l++l+++  e++++ v +d  d+R+
  gi|242399060|ref|YP_002994484.1| 368 ILITGPPGSGKSTLLKLIARFYEPERGQVLVDDVDVRK 405
                                       899********************999999999888886 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   6.6e-05     0.031       4      46 ..     367     406 ..     365     469 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.6e-05
                            AAA_24   4 kiliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdi 46 
                                       +ili+Gp+g+GK+tl+k +   + f   e+G   +d+ ++ +i
  gi|242399060|ref|YP_002994484.1| 367 RILITGPPGSGKSTLLKLI---ARFYEPERGQVLVDDVDVRKI 406
                                       89***************99...555666666655555555555 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   0.00013     0.059       2      23 ..     368     389 ..     367     401 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00013
                                       EEEE--SSSSHHHHHHHGGGGB CS
                             AAA_5   2 vlLvGppGtgKselaerlaaal 23 
                                       +l+ GppG+gKs+l + +a+++
  gi|242399060|ref|YP_002994484.1| 368 ILITGPPGSGKSTLLKLIARFY 389
                                       6899***************998 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   0.00015      0.07      19      98 ..     364     450 ..     358     465 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00015
                          ATPase_2  19 pneiyfiYGpegsGKtaLlkeiienledkdkyviyyi..alreesiskldefie.....eeeekkklekalgiavpk 88 
                                       p e ++i+Gp gsGK++Llk i+    + +   + ++  ++r++++s+l+++++         +++l++ ++ a p 
  gi|242399060|ref|YP_002994484.1| 364 PGERILITGPPGSGKSTLLKLIARFY-EPERGQVLVDdvDVRKIKTSSLRKTVAyipqePFIFNRSLRENIALAKPD 439
                                       667789*************9877666.43445555551156677777777776655443222344444555555555 PP

                          ATPase_2  89 aeleeilk.ek 98 
                                       a++eei+   k
  gi|242399060|ref|YP_002994484.1| 440 ASMEEIIRaAK 450
                                       55555555544 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       6.6   3.1e+03      43      97 ..     164     216 ..     157     223 .. 0.73
   2 ?   12.3   0.0   0.00022       0.1      31      58 ..     363     390 ..     347     470 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 6.6
                            RuvB_N  43 GlGkttlakiiakelgvklkitsgPvlekagdlaalltnleekdvlfideihrls 97 
                                       G+   t+a ++a   +++      P+ +k +  ++++++++++ +  +  i  ls
  gi|242399060|ref|YP_002994484.1| 164 GVALVTIAVVVAL--NTTYARKVRPIYDKVRHQTGVIASVSTGSIAGVKTIKALS 216
                                       5555677777774..5555566679999999999999999988888877777665 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00022
                            RuvB_N  31 ealdhvllyGpPGlGkttlakiiakelg 58 
                                       ++ + +l++GpPG Gk+tl k+ia+  +
  gi|242399060|ref|YP_002994484.1| 363 KPGERILITGPPGSGKSTLLKLIARFYE 390
                                       556789*****************98554 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00014     0.064      21      78 ..     364     423 ..     350     445 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00014
                      Mg_chelatase  21 GgHnlllvGppGsGKtmlakrlpsllpplseeealevakiasvag..kkeeekllkrrpf 78 
                                        g  +l++GppGsGK+ l k ++    p   +  ++   ++ +++   +++ +++ + pf
  gi|242399060|ref|YP_002994484.1| 364 PGERILITGPPGSGKSTLLKLIARFYEPERGQVLVDDVDVRKIKTssLRKTVAYIPQEPF 423
                                       56789***************9999888877776666666665555223444555666666 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 ?    5.8   0.0     0.011       5.2     233     265 ..     350     386 ..     322     391 .. 0.74
   2 ?    4.3   0.0     0.031        15     297     349 ..     449     502 ..     436     548 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.011
                                       TTEEE.EEEE..E-SS.EEEEEE-TTSSHHHHHHHHH CS
                        ABC_ATPase 233 ngkkv.sGmg..ipkG.vtlIvGggfhGKsTLLeAle 265
                                        gk+v +G+   i+ G  +lI+G+   GKsTLL+ ++
  gi|242399060|ref|YP_002994484.1| 350 TGKTVlKGLNlkIKPGeRILITGPPGSGKSTLLKLIA 386
                                       4444436765226677789**************9775 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.031
                                       EEEE--TTTB---CCC--ST.TEEESS--HHHHHHHHHHHHHHTT-SEEEEEGG CS
                        ABC_ATPase 297 vkgvDispFinnLPegkdtt.kfstedASGStsqAanimealeagakllLiDED 349
                                        k + i  Fi +LPeg +t       + SG   q  ++++al ++ ++lL+D  
  gi|242399060|ref|YP_002994484.1| 449 AKIAKIHDFIASLPEGYETVvGEKGVTLSGGQRQRIALARALLLEPRILLLDDP 502
                                       5567899************955555678***********************975 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00019     0.088       2      22 ..     367     387 ..     366     396 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00019
                                       CEEEEC-TTTCHHHHHHHHHH CS
                             NACHT   2 lvilqGeaGsGKTtLlqklal 22 
                                        ++++G++GsGK+tLl+ +a+
  gi|242399060|ref|YP_002994484.1| 367 RILITGPPGSGKSTLLKLIAR 387
                                       589*************99985 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 ?   12.0   0.0   0.00016     0.075      15      54 ..     351     390 ..     341     408 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00016
                                       HHHHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHH CS
                              MeaB  15 akellerllakaGraqvvGltGvPGaGkstlvealglelr 54 
                                        k++l+ l  k    +++ +tG PG+Gkstl++ ++  + 
  gi|242399060|ref|YP_002994484.1| 351 GKTVLKGLNLKIKPGERILITGPPGSGKSTLLKLIARFYE 390
                                       56777777777777899**************976655544 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00025      0.12      50     106 ..     362     422 ..     349     426 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00025
                            DUF815  50 glpannvLLwGarGtGKSslvkallneyaeeg....Lrlievekedlkelpklvellrerp 106
                                        +p + +L++G  G+GKS+l+k + + y+ e     +  ++v+k + ++l k v+ + ++p
  gi|242399060|ref|YP_002994484.1| 362 IKPGERILITGPPGSGKSTLLKLIARFYEPERgqvlVDDVDVRKIKTSSLRKTVAYIPQEP 422
                                       578899*******************999988766555556777777777777777766555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00022       0.1       2      32 ..     368     401 ..     368     460 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00022
                            AAA_33   2 vllvGlpGsGKstlaerllkklg...avllssdt 32 
                                       +l+ G+pGsGKstl++ +++      +++l  d+
  gi|242399060|ref|YP_002994484.1| 368 ILITGPPGSGKSTLLKLIARFYEperGQVLVDDV 401
                                       5789**********99775433333355555554 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   0.00026      0.12      22      39 ..     368     385 ..     340     387 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00026
                            AAA_23  22 tlItGpNGaGKTTildAi 39 
                                        lItGp G+GK+T+l  i
  gi|242399060|ref|YP_002994484.1| 368 ILITGPPGSGKSTLLKLI 385
                                       49*************877 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00016     0.074      25      58 ..     367     405 ..     347     503 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00016
                                       EEEEEESTTSSHHHHHHHHHHHCS--.....--HHHHHC CS
                           G-alpha  25 kllllGqseSGKsTilkqlkllykkg.....fseeelat 58 
                                       ++l+ G  +SGKsT+lk + ++y+++     +++ ++++
  gi|242399060|ref|YP_002994484.1| 367 RILITGPPGSGKSTLLKLIARFYEPErgqvlVDDVDVRK 405
                                       8**********************9986676655555544 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00039      0.18      11      37 ..     366     392 ..     360     413 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00039
                            AAA_19  11 kvllvtaGpGtGKTrvlkhivallvel 37 
                                       + +l+t++pG+GK+++lk i + ++ +
  gi|242399060|ref|YP_002994484.1| 366 ERILITGPPGSGKSTLLKLIARFYEPE 392
                                       6789**************999887655 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 ?   11.8   0.0   0.00021       0.1      19      40 ..     361     382 ..     352     406 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00021
                                       SSS---EEEEE-SSSSSTTTTH CS
                              DAP3  19 kkkkvkrlvltGekgsGKSvlL 40 
                                       k k+ +r+++tG +gsGKS+lL
  gi|242399060|ref|YP_002994484.1| 361 KIKPGERILITGPPGSGKSTLL 382
                                       568899**************99 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00035      0.16      31      54 ..     363     386 ..     352     410 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00035
                            AAA_25  31 pagelallaGapgtGKttlaldla 54 
                                         ge +l++G+pg+GK+tl+  +a
  gi|242399060|ref|YP_002994484.1| 363 KPGERILITGPPGSGKSTLLKLIA 386
                                       6799**************986555 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00043       0.2       1      19 [.     371     389 ..     371     448 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00043
                                       EE-TTSSHHHHHHHHHHHH CS
                            AAA_17   1 lGgPGsGKgtqceklveky 19 
                                       +G+PGsGK+t+++ +++ y
  gi|242399060|ref|YP_002994484.1| 371 TGPPGSGKSTLLKLIARFY 389
                                       7***********9888766 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00061      0.29       5      42 ..     368     405 ..     365     432 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00061
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldder 42 
                                       ++itG+  +GK+tllk +++ +  ++ ++l  ++d  +
  gi|242399060|ref|YP_002994484.1| 368 ILITGPPGSGKSTLLKLIARFYEPERGQVLVDDVDVRK 405
                                       79*************99987666344444444444433 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00036      0.17      23      55 ..     367     401 ..     342     433 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00036
                            AAA_10  23 asliiGdlGnGKSvlakllvlyisllggkali..i 55 
                                         li+G++G GKS l kl+  +     g++l+  +
  gi|242399060|ref|YP_002994484.1| 367 RILITGPPGSGKSTLLKLIARFYEPERGQVLVddV 401
                                       569******************99999999887334 PP

>> RuvA_C  RuvA, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0      0.13        64      10      29 ..     293     312 ..     293     324 .. 0.84
   2 ?    5.6   0.1     0.048        22      28      42 ..     436     449 ..     431     449 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.13
                                       HHHCTS-HHHHHHHHHHHHC CS
                            RuvA_C  10 LlaLGYkekeaekAvakvla 29 
                                       L aLG++  ++++ +a++++
  gi|242399060|ref|YP_002994484.1| 293 LRALGFTIGDIQRSLAAASR 312
                                       78*************99975 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.048
                                       HC-TTS-HHHHHHHH CS
                            RuvA_C  28 lanpgasveelIraA 42 
                                       + +p+as ee+IraA
  gi|242399060|ref|YP_002994484.1| 436 A-KPDASMEEIIRAA 449
                                       3.9***********9 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00042       0.2       1      21 [.     368     388 ..     368     417 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00042
                   Viral_helicase1   1 ivvhGvpGcGKStlirkllrt 21 
                                       i++ G pG+GKStl++ ++r 
  gi|242399060|ref|YP_002994484.1| 368 ILITGPPGSGKSTLLKLIARF 388
                                       6899************99987 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0    0.0011      0.51       1      20 [.     368     387 ..     368     455 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0011
                      RNA_helicase   1 iwlyGpsgeGKStlakeLak 20 
                                       i+++Gp+g GKStl k +a+
  gi|242399060|ref|YP_002994484.1| 368 ILITGPPGSGKSTLLKLIAR 387
                                       689************99776 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.055        26      20      69 ..     369     428 ..     361     442 .. 0.66
   2 ?    4.4   0.0     0.025        12     525     542 ..     492     509 ..     480     516 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.055
                            AAA_13  20 liYGwNGaGKTtLSrllrslelgetepkfangsi............eitnge........eldirVfNrd 69 
                                       li G  G+GK+tL +l++ + + e       g++            +    +        +++ ++fNr 
  gi|242399060|ref|YP_002994484.1| 369 LITGPPGSGKSTLLKLIARFYEPE------RGQVlvddvdvrkiktS----SlrktvayiPQEPFIFNRS 428
                                       677999************995433......23333344444533330....1233444447888888875 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.025
                            AAA_13 525 gkdkivviDDPvSSLDsn 542
                                        + +i  +DDPvS LD++
  gi|242399060|ref|YP_002994484.1| 492 LEPRILLLDDPVSNLDAE 509
                                       5899************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (579 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1005  (0.0560544); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); expected 358.6 (0.02)
Passed Vit filter:                       122  (0.00680462); expected 17.9 (0.001)
Passed Fwd filter:                        40  (0.00223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              38  [number of targets reported over threshold]
# CPU time: 0.80u 0.33s 00:00:01.13 Elapsed: 00:00:00.51
# Mc/sec: 3436.34
//
Query:       gi|242399061|ref|YP_002994485.1|  [L=186]
Description: Nicotinamide-nucleotide adenylyltransferase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-19   69.3   0.0    4.6e-18   65.8   0.0    2.2  1  CTP_transf_like  Cytidylyltransferase-like
    0.00055   19.3   0.1       0.14   11.3   0.0    2.1  2  HIGH_NTase1      HIGH Nucleotidyl Transferase


Domain annotation for each model (and alignments):
>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.8   0.0   5.1e-22   4.6e-18       1     143 []       4     135 ..       4     135 .. 0.90

  Alignments for each domain:
  == domain 1  score: 65.8 bits;  conditional E-value: 5.1e-22
                                       EEEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHHHHH CS
                   CTP_transf_like   1 lagGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkkkplasaeeRlemlelakevdevisvdpweltrevl 77 
                                       l++G+F+p+H+GHl+ le +++++ee +i+g+ s+++++   k++++ +eR+eml +a +++  i+  ++ l+   l
  gi|242399061|ref|YP_002994485.1|   4 LFVGRFQPVHNGHLKALEYVFEEVEE-VIIGIGSAQVSHTL-KNPFTTSERMEMLIRALDEKG-IPRGKYFLVA--L 75 
                                       79************************.************99.****************66655.7777777775..5 PP

                                       HHTTTTEEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEEEHTTCEEEEEEECCTTTCSHHHHHHH CS
                   CTP_transf_like  78 kklkpdklylvigadvledfsewkeleeilgnvklvvvsrpekqanvllkaekrtngiSstkirer 143
                                        +++ +  +++   +++       +++ +++ + lv + ++e+ ++v++ ++ r    S+t+ir+r
  gi|242399061|ref|YP_002994485.1|  76 PDINFN-SIWAPYVEAIVP-----KFDIVFTGNSLVAQLFRERGYKVIVQPMFRKDILSATEIRRR 135
                                       555553.599999999988.....8***************************************97 PP

>> HIGH_NTase1  HIGH Nucleotidyl Transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1   0.0   0.00062       5.5      10      34 ..       9      32 ..       5      40 .. 0.80
   2 !   11.3   0.0   1.6e-05      0.14     201     238 ..     124     158 ..     110     183 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.00062
                       HIGH_NTase1 10 YNPfHnGHlyhlekakeltgadvvi 34
                                      + P HnGHl  le + e+++ +v+i
  gi|242399061|ref|YP_002994485.1|  9 FQPVHNGHLKALEYVFEEVE-EVII 32
                                      78***********9999855.4444 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 1.6e-05
                       HIGH_NTase1 201 eeiaSAtaiRkalkeekkleelkklvPestleilkeel 238
                                       ++i SAt iR+ + e+   ++ ++lvP+s++e++ke  
  gi|242399061|ref|YP_002994485.1| 124 KDILSATEIRRRMIED---QTWEELVPKSVVEYIKEIK 158
                                       579**********555...689***********98762 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); 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: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1219.80
//
Query:       gi|242399062|ref|YP_002994486.1|  [L=258]
Description: hypothetical protein TSIB_1083 [Thermococcus sibiricus MM 739]
Scores for complete 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  262.2   0.0    4.2e-78  262.0   0.0    1.0  1  SAM_adeno_trans  S-adenosyl-l-methionine hydroxide adenosyltr


Domain annotation for each model (and alignments):
>> SAM_adeno_trans  S-adenosyl-l-methionine hydroxide adenosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  262.0   0.0   2.3e-82   4.2e-78       1     235 []       2     250 ..       2     250 .. 0.91

  Alignments for each domain:
  == domain 1  score: 262.0 bits;  conditional E-value: 2.3e-82
                                       EEEEESSTSSSSHHHHHHHHHHHH-TTSEEEEEES-S-TT-HHHHHHHHHHHHGGS-TTEEEEEE--TTTTSS--EE CS
                   SAM_adeno_trans   1 itLlTDFGlkdpyvgamkgvilsiapdarivDitHdippfdvreaaflLaaalpyfpkgtvhlavVDpgvgterral 77 
                                       itL+TDFGlk+pyvg mkg+il+i+p+++++DitH+i+++++ e++f++++a++yfp++t+h+ v+Dpgvgt rra+
  gi|242399062|ref|YP_002994486.1|   2 ITLTTDFGLKGPYVGEMKGAILAINPEVEVIDITHSITRHSIIEGSFVMEQAVKYFPADTIHVGVIDPGVGTRRRAI 78 
                                       9**************************************************************************** PP

                                       EEEETTSEEEEESSSTTHHHH...SEEEEEEGSSCC........--TS-HHHHTHHHHHHHHHCT--GGGCSEEESG CS
                   SAM_adeno_trans  78 vveakggyfvgPDNGlltlal...lleeaveieeee........ssatFhgrDvFapvaarlaagvsleelgeeldp 143
                                       ++e ++ ++v PDNG+ tl l    +++a+ei+ ++         s+tFhgrDvF p++a l+ g +++++g+e+d 
  gi|242399062|ref|YP_002994486.1|  79 IIEGHQ-FLVVPDNGIATLPLkwiDAKSAYEIDLQKmeaiigrkISSTFHGRDVFGPAGALLSLGYEPSRFGKEIDL 154
                                       **9655.***********8887765599****96666899999988******************************* PP

                                       GGS-SSS....E.CSCEEEEEEEE-TTS-EEEEEE...EHHHHHTTCEE....EEEEESSGGGSTTTSEEEEE-TTS CS
                   SAM_adeno_trans 144 eelvrle....e.derlegevlyvDrFGNvitniskelleelekerkva....klkkvetyaevaegellalvnssg 211
                                       e++++le    + ++++  +v+y+D+FGNvi+n+++    ++      +    ++  +ety++v+ ge lal +s++
  gi|242399062|ref|YP_002994486.1| 155 EKVIKLElepkKeEDSWILSVIYIDDFGNVILNLENYEKPKYV-----EvlgrRIPYIETYGKVNIGEFLALPGSHD 226
                                       ***999997752477888****************944443332.....1235566677******************* PP

                                       EEEEEETTC-HHHHHT--TT-EEE CS
                   SAM_adeno_trans 212 lleiavnkgsaaellglkvgdeve 235
                                       +leia+n+gsaa++lglkvgdeve
  gi|242399062|ref|YP_002994486.1| 227 YLEIAINQGSAADVLGLKVGDEVE 250
                                       *********************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1753.80
//
Query:       gi|242399063|ref|YP_002994487.1|  [L=536]
Description: hypothetical protein TSIB_1084 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-05   24.8   0.0    3.9e-05   24.1   0.0    1.4  1  Transglut_core  Transglutaminase-like superfamily
     0.0015   18.8   0.0        0.2   11.9   0.0    2.7  2  CARDB           CARDB
     0.0021   18.8   0.0          2    9.2   0.0    2.6  2  N_BRCA1_IG      Ig-like domain from next to BRCA1 gene
  ------ inclusion threshold ------
      0.076   13.1   0.0       0.18   12.0   0.0    1.6  1  UBA_2           Ubiquitin associated domain (UBA)
        1.9    8.4   5.3        4.5    7.2   0.3    3.5  3  DUF2393         Protein of unknown function (DUF2393)


Domain annotation for each model (and alignments):
>> Transglut_core  Transglutaminase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   1.1e-08   3.9e-05       7     111 ..     298     389 ..     292     390 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1.1e-08
                    Transglut_core   7 ltagakdplekakaiyewvrknveysaprrtpgsrdaeavletgkGncedfaslfvallRalGipaRvvtgylsgee 83 
                                       + +ga++++e+a+++y+++ ++++     ++++s ++++++ ++    e+ + lf+ +lR+l ip+Rv++ y+ ++ 
  gi|242399063|ref|YP_002994487.1| 298 VINGAQSEKEAAQKVYNFITSKYSLG---NNTTSLNLTEIMSKKEISYEEATLLFTGALRSLNIPSRVISLYNGTD- 370
                                       55899***************888777...9999999**********************************999843. PP

                    Transglut_core  84 ekeqsvasedaHawvevylegygWvplD 111
                                              + +  +  e+y   + W+++D
  gi|242399063|ref|YP_002994487.1| 371 -------CTQ-NVISEFYS-AGLWYVVD 389
                                       .......333.47777777.66677776 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.018        66       9      84 ..      31     108 ..      26     115 .. 0.63
   2 !   11.9   0.0   5.6e-05       0.2       4      84 ..     139     224 ..     136     241 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.018
                                       EEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEE.......SEE-CTEEEEEEEEEE-S-S-CEE CS
                             CARDB   9 tlnpseafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtv.......psLaagesttvsftwtteategev 78 
                                       t+  s + +++ + + v+++N+G+ a + ++  lyl++   +   +       ++L  g+ ++     t++  +g +
  gi|242399063|ref|YP_002994487.1|  31 TVDKSVVKEENVFHLIVKINNTGKVAITGIN--LYLNDPRFK---IsqnpkfdAPLGVGQAREFIWILTAPKDAGRY 102
                                       455566666777788899*****99887665..666666542...22223456666666666666666666666666 PP

                                       EEEEEE CS
                             CARDB  79 tltvvv 84 
                                        l+v+v
  gi|242399063|ref|YP_002994487.1| 103 FLKVSV 108
                                       666666 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 5.6e-05
                                       EEE...EEEC-SEEETTSEEEEEEEEEE-SSS-.EEEEEEEEEETTEEE.EEEEE.SEE-CTEEEEEEEEEE-S-S- CS
                             CARDB   4 Ltv..tntlnpseafvgeentitvtvkNqGtaa.sgatkvalyldgelv.gtvtv.psLaagesttvsftwtteate 75 
                                       L +    +++p+e+  g+++++++t++N G++    +    + l+g +v +t ++ + +++ge ++ ++t++t+  +
  gi|242399063|ref|YP_002994487.1| 139 LGIlnAIITSPTEVMGGNDFQLQITLQNVGNGPvKIKGIFVYPLEGMEVtKTPSLpNDISPGEVIKLNYTIKTPYMP 215
                                       5555567899**********************95334444444777777466667778***************9544 PP

                                       CEEEEEEEE CS
                             CARDB  76 gevtltvvv 84 
                                       ++ +lt+++
  gi|242399063|ref|YP_002994487.1| 216 KTGYLTISI 224
                                       444444443 PP

>> N_BRCA1_IG  Ig-like domain from next to BRCA1 gene
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0   0.00057         2       4      79 ..      33     103 ..      31     119 .. 0.83
   2 !    6.9   0.0     0.003        11       5      75 ..     149     215 ..     145     245 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00057
                        N_BRCA1_IG   4 dgtvvppgteftktWrlrNtGseaWpagtklvfvgGdkmgsasaeessvsvpavapgeevevsvelkaPskpgryi 79 
                                       d++vv+ ++ f  + +++NtG++a  +g++l + +  ++ + s +++++   ++  g+  e+   l+aP+ +gry 
  gi|242399063|ref|YP_002994487.1|  33 DKSVVKEENVFHLIVKINNTGKVAI-TGINLYLND-PRF-KIS-QNPKF-DAPLGVGQAREFIWILTAPKDAGRYF 103
                                       8899********************7.999999888.445.322.33444.557999******************95 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.003
                        N_BRCA1_IG   5 gtvvppgteftktWrlrNtGseaW.pagtklvfvgGdkmgsasaeessvsvpavapgeevevsvelkaPskp 75 
                                        t+v  g+ f+ + +l+N G+ +   +g+ +   +G ++     +++    ++++pge+++++ ++k+P  p
  gi|242399063|ref|YP_002994487.1| 149 PTEVMGGNDFQLQITLQNVGNGPVkIKGIFVYPLEGMEV-----TKTPSLPNDISPGEVIKLNYTIKTPYMP 215
                                       57888899999999****999976346666666666666.....334456788****************655 PP

>> UBA_2  Ubiquitin associated domain (UBA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   4.9e-05      0.18       4      34 ..     109     139 ..     106     146 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.9e-05
                             UBA_2   4 dvvsaLsktM.GYdkdeIieaLekaekskssn 34 
                                       +v+++L++t  G+ k+ Ii+++ek+++   s 
  gi|242399063|ref|YP_002994487.1| 109 EVIDELQRTWgGFYKEFIINVIEKENEI-PSL 139
                                       79********99**************98.444 PP

>> DUF2393  Protein of unknown function (DUF2393)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.3    0.0013       4.5      66     142 ..      46     107 ..       2     111 .. 0.61
   2 ?   -1.1   0.1      0.47   1.7e+03      51      77 ..     146     172 ..     141     176 .. 0.84
   3 ?   -2.8   0.1       1.6   5.6e+03      41      64 ..     324     347 ..     316     349 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0013
                           DUF2393  66 dgtitNeGkftikeCkleiklvnkshnkkskellkklkplvsksevikedlkpgeskeFrviidyfpyfknysvklt 142
                                        ++i N+Gk +i++                + +l+  +++ s+++ ++++l  g+ +eF +i   +++ + y +k++
  gi|242399063|ref|YP_002994487.1|  46 IVKINNTGKVAITGI---------------NLYLNDPRFKISQNPKFDAPLGVGQAREFIWILTAPKDAGRYFLKVS 107
                                       344444444444444...............44555556666667777777777777777777777777776666665 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.47
                           DUF2393  51 ilsqkrllyteafvvdgtitNeGkfti 77 
                                       i+s + ++  ++f +++t +N G+ ++
  gi|242399063|ref|YP_002994487.1| 146 ITSPTEVMGGNDFQLQITLQNVGNGPV 172
                                       66778899999***********98665 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 1.6
                           DUF2393  41 dkylkkaeltilsqkrllyteafv 64 
                                       ++++  + ++i+s+k ++y+ea++
  gi|242399063|ref|YP_002994487.1| 324 NNTTSLNLTEIMSKKEISYEEATL 347
                                       566677778899999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (536 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       689  (0.0384294); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); 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: 0.67u 0.29s 00:00:00.96 Elapsed: 00:00:00.51
# Mc/sec: 3168.00
//
Query:       gi|242399064|ref|YP_002994488.1|  [L=180]
Description: hypothetical protein TSIB_1085 [Thermococcus sibiricus MM 739]
Scores for complete 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  168.3   0.1    7.5e-50  167.8   0.1    1.2  1  Trm56           tRNA ribose 2'-O-methyltransferase, aTrm56
     0.0056   16.9   0.0     0.0081   16.3   0.0    1.3  1  SpoU_methylase  SpoU rRNA Methylase family
  ------ inclusion threshold ------
      0.055   12.9   0.0      0.075   12.4   0.0    1.2  1  DUF4058         Protein of unknown function (DUF4058)


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 !  167.8   0.1   1.3e-53   7.5e-50       1     119 []      54     171 ..      54     171 .. 0.98

  Alignments for each domain:
  == domain 1  score: 167.8 bits;  conditional E-value: 1.3e-53
                                       H-S--EEE.E--HHHHHHC-S...SEEEEE-TTSEEHHHHHHHHHC-SE...EEEEE------TCHHHHSSEEEESS CS
                             Trm56   1 wGgefkvevakslkklikefkkeggivvhltmyGenieevieeikkkek..dllvvvGaekvprevyeladynvsvg 75 
                                       wGg+f+ve++ +++++++e+k   g++vhltmyG++i++++ eik++ k  d+l+vvGaekvprevye+a+ynv+vg
  gi|242399064|ref|YP_002994488.1|  54 WGGPFEVEFNPHWRQVLREWK---GKIVHLTMYGIHIDKALPEIKEALKieDILIVVGAEKVPREVYEIAHYNVAVG 127
                                       *********************...**********************76666************************** PP

                                       SS---HHHHHHHHHHHHC.--TTT---TT-SSEEE--SSS-EEE CS
                             Trm56  76 nqPhsevaalaifldrllegkelekefedaklkviPsergkkvv 119
                                       nqPhsevaala+fldr+l+g+ l+k+f++ak+k+iP+ergkkv+
  gi|242399064|ref|YP_002994488.1| 128 NQPHSEVAALAVFLDRVLDGEGLRKDFKNAKVKIIPQERGKKVI 171
                                       ******************************************96 PP

>> SpoU_methylase  SpoU rRNA Methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.4e-06    0.0081      18     122 ..      21     126 ..      13     139 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.4e-06
                                       HHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHHEEEESSHHHHHHHHCCCTEEEEEESTT-SEGC....C CS
                    SpoU_methylase  18 iaRtakafgaselvlvkprsadllnpeakraaagalevlelkvvdsleealkelkeegfalvatslkgksls....e 90 
                                       +a ta+afga+++++ ++r ++++++ ++ + +     +e++  ++++++l+e+k +   +v ++ +g +++    e
  gi|242399064|ref|YP_002994488.1|  21 VALTARAFGADKIIIAAERDEHVYDS-VMDVVTRWGGPFEVEFNPHWRQVLREWKGK---IVHLTMYGIHIDkalpE 93 
                                       66799************999877776.666666666677777999**********99...55555555555522224 PP

                                       SHHH...TTEEEEEEBTTTBS-HHHHCTSSEEEE- CS
                    SpoU_methylase  91 idlk...ekvalvfGnEdkGlsnelleladrlvkI 122
                                       i+ +   e +++v+G E+  +++e+ e a++ v +
  gi|242399064|ref|YP_002994488.1|  94 IKEAlkiEDILIVVGAEK--VPREVYEIAHYNVAV 126
                                       4444668**********7..788888877777665 PP

>> DUF4058  Protein of unknown function (DUF4058)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.3e-05     0.075     186     237 ..      79     130 ..      53     138 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.3e-05
                           DUF4058 186 eaelyafnlrdalptiplPLrkedeevlldlqallnevYeraaYdlaidYek 237
                                       +  +y +++ +alp+i   L+ ed  +++  +++ +evYe a+Y+ a+  ++
  gi|242399064|ref|YP_002994488.1|  79 HLTMYGIHIDKALPEIKEALKIEDILIVVGAEKVPREVYEIAHYNVAVGNQP 130
                                       4578*****************************************9997655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); 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: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1192.86
//
Query:       gi|242399065|ref|YP_002994489.1|  [L=186]
Description: CDP-alcohol phosphatidyltransferase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-14   54.2   1.4    1.8e-14   54.2   1.4    1.7  2  CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase


Domain annotation for each model (and alignments):
>> CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.2   1.4     1e-18   1.8e-14       2      66 .]      26      89 ..      25      89 .. 0.89
   2 ?   -1.7   0.1      0.29   5.1e+03      12      12 ..     148     148 ..     102     174 .. 0.59

  Alignments for each domain:
  == domain 1  score: 54.2 bits;  conditional E-value: 1e-18
                                      -HHHHHHHHHHHHHHHHHGGGS-H..HHHHHHHHHHHHHTTHHHHHHHHTT---HHHHHHHHHHH CS
                   CDP-OH_P_transf  2 lPnaiTllrlllsvlailllltyyplvlailllliasltDalDGklARrlnqvstlGkllDslaD 66
                                      +Pn++Tl++ll+s++ +++++  +   +a+l+ll+ sl+DalDG lAR ++++s++G++lDs  D
  gi|242399065|ref|YP_002994489.1| 26 TPNQLTLIGLLISLTGAYFFAHGS-QQIAALVLLFGSLVDALDGTLARVTRKSSRFGAFLDSTFD 89
                                      8*************9998775555.58888999999999*************888*******987 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.29
                                       H CS
                   CDP-OH_P_transf  12 l 12 
                                       l
  gi|242399065|ref|YP_002994489.1| 148 L 148
                                       1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1185.05
//
Query:       gi|242399066|ref|YP_002994490.1|  [L=236]
Description: 2-haloalkanoic acid dehalogenase-like hydrolase [Thermococcus sibiricus MM 739]
Scores for complete 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  100.3   0.3    1.9e-28   99.8   0.3    1.3  1  HAD_2            Haloacid dehalogenase-like hydrolase
    5.4e-18   66.0   0.2      3e-17   63.6   0.0    2.1  2  Hydrolase        haloacid dehalogenase-like hydrolase
    1.7e-09   37.6   0.0      1e-07   31.9   0.0    2.4  2  Hydrolase_like   HAD-hyrolase-like
    3.5e-06   27.6   0.0      5e-06   27.0   0.0    1.2  1  HAD              haloacid dehalogenase-like hydrolase
     0.0011   19.0   0.3     0.0051   16.8   0.3    1.9  2  Mad3_BUB1_I      Mad3/BUB1 homology region 1
  ------ inclusion threshold ------
       0.14   11.5   0.1        1.5    8.2   0.0    2.4  3  Put_Phosphatase  Putative Phosphatase


Domain annotation for each model (and alignments):
>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.8   0.3   6.4e-32   1.9e-28       2     176 ..       6     201 ..       5     203 .. 0.82

  Alignments for each domain:
  == domain 1  score: 99.8 bits;  conditional E-value: 6.4e-32
                             HAD_2   2 iFDlDgTlldte...eliiqafnelleey............glselseeelrkliglslrellrklgeseeeee... 60 
                                        FD+ gTll +e    ++ ++++e+l++             +++ l+ e+++++ g ++ + +r l+e+  ee    
  gi|242399066|ref|YP_002994490.1|   6 FFDFVGTLLSKEfedITHQNIIREALRRVkaenvdplkvweEYEALTSEKFKEYAGKPY-KPIRVLEEEIVEEIakk 81 
                                       68999999987522124455666666655788899999999888888888888888887.33444444333222445 PP

                             HAD_2  61 ....kieellrkyneekkkkevkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvek 133
                                             +++++++ + +++ + k+yd+++e+L++Lk +gy++g +T+++++ +  +l++lgi ++Fd i tse+++ 
  gi|242399066|ref|YP_002994490.1|  82 yefeVPHDFWEIHLKMHQQ-YGKLYDEAIEVLKTLKVNGYHIGMITDSDNDYLHAQLKALGILEFFDSITTSEEAGF 157
                                       6666888898888888877.********************************************************* PP

                             HAD_2 134 kKPdpeviekaleklklkkeeviyvGDsp.tDieaakkagikvi 176
                                        KP+p+++e al+k +lk ee+iyvGD+p +D  +++ + ++++
  gi|242399066|ref|YP_002994490.1| 158 YKPHPRMFELALQKANLKGEEAIYVGDNPlKDCVGSRTVDMTSV 201
                                       *************************************9999876 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.6   0.0     1e-20     3e-17       1     200 [.       2     186 ..       2     190 .. 0.77
   2 ?   -2.0   0.0       1.2   3.5e+03       6      26 ..     196     216 ..     195     227 .. 0.82

  Alignments for each domain:
  == domain 1  score: 63.6 bits;  conditional E-value: 1e-20
                                       SSEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHH.HHCHHHHHHHHHHHHH.HHHHHHHHHETTTEHHHHTHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase   1 iktvvfDkdGTLttgepsvedvivsaalalaaaletg.sehpigkalvaaakar.sgaltgfatfigrgayaigkpe 75 
                                       ik+v+fD+ GTL+  e   ed++ ++   +++al+ + +e     ++ ++++a+ s++ +++a      +  +  + 
  gi|242399066|ref|YP_002994490.1|   2 IKAVFFDFVGTLLSKE--FEDITHQN--IIREALRRVkAENVDPLKVWEEYEALtSEKFKEYAG-----KPYKPIRV 69 
                                       89***********777..99999999..333333333222222222222233322333333333.....33333333 PP

                                       HHHHHHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  76 wltaldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraa 152
                                       + +     + +++   +++ +    +++    l +     +  +++ea e++++Lk +g+ ++++t ++    ++ +
  gi|242399066|ref|YP_002994490.1|  70 LEE-----EIVEEIAKKYEFEVPHDFWE--IHLKMHQQYGK--LYDEAIEVLKTLKVNGYHIGMITDSDNDYLHAQL 137
                                       333.....44778888888889999999..88888888888..********************************** PP

                                       HHTT.GGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSH CS
                                       xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 153 nqlG.ddyfdaviasdietvakpspegkvaaireLqgkpeevamVGDgv 200
                                       + lG  ++fd + +s++ ++ kp+p++++ a+++ + k+ee + VGD++
  gi|242399066|ref|YP_002994490.1| 138 KALGiLEFFDSITTSEEAGFYKPHPRMFELALQKANLKGEEAIYVGDNP 186
                                       ****99999**************************************86 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.2
                                       EESBTTTBCHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase   6 fDkdGTLttgepsvedvivsa 26 
                                        D++ +L++ +   ++++++ 
  gi|242399066|ref|YP_002994490.1| 196 VDMTSVLLNKKGDKKEFWKEC 216
                                       699999999998888888876 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.034     1e+02       9      39 ..     104     136 ..     101     138 .. 0.82
   2 !   31.9   0.0   3.3e-11     1e-07       4      49 ..     159     204 ..     157     226 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.034
                                       HHHHHHHHH...---GGGEEEEES-TTTHHHHHH CS
                    Hydrolase_like   9 mydfalevl...gsdpeevlmiGDrlatDiagAn 39 
                                       +yd+a evl   +++  ++ mi D+ + D + A+
  gi|242399066|ref|YP_002994490.1| 104 LYDEAIEVLktlKVNGYHIGMITDS-DNDYLHAQ 136
                                       68888888876677788899*****.*9988775 PP

  == domain 2  score: 31.9 bits;  conditional E-value: 3.3e-11
                                       TTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEES CS
                    Hydrolase_like   4 KPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVl 49 
                                       KP+p m++ al++ +++ ee +++GD++  D  g + + ++svL  
  gi|242399066|ref|YP_002994490.1| 159 KPHPRMFELALQKANLKGEEAIYVGDNPLKDCVGSRTVDMTSVLLN 204
                                       9*****************************************9974 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.0   1.7e-09     5e-06       1     180 [.       5     185 ..       5     187 .. 0.70

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 1.7e-09
                               HAD   1 alfDfDgTLldgdslelllrfllrrgaprlwralreklllal..frellrldraglaelleallaglseelaaeler 75 
                                       ++fDf gTLl +  +e ++++ + r a+r+ +a ++ +l+ +  ++ l + + +++a   ++  + l+ee+ +e+++
  gi|242399066|ref|YP_002994490.1|   5 VFFDFVGTLLSK-EFEDITHQNIIREALRRVKAENVDPLKVWeeYEALTSEKFKEYAGKPYKPIRVLEEEIVEEIAK 80 
                                       79**********.5666666666666777777777777777755445555544555555555555555555555555 PP

                               HAD  76 fv..............aevirpklldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrl 138
                                        +               + +  kl+  +a e+l+  + +G+++ +++ +   ++++ l++lg+ e+ ++        
  gi|242399066|ref|YP_002994490.1|  81 KYefevphdfweihlkMHQQYGKLY-DEAIEVLKTLKVNGYHIGMITDSDNDYLHAQLKALGILEFFDS------IT 150
                                       5555555555665555333333456.99******999*************************9999999......88 PP

                               HAD 139 tgelglegkpvrgegkvaalrewlaaegegidleevvayGDs 180
                                       t e   e ++ + + +  +l+     ++++++ ee +++GD 
  gi|242399066|ref|YP_002994490.1| 151 TSE---EAGFYKPHPRMFELAL----QKANLKGEEAIYVGDN 185
                                       888...6666666666777777....6666777778999996 PP

>> Mad3_BUB1_I  Mad3/BUB1 homology region 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.3   1.7e-06    0.0051       7      91 ..      28     119 ..      22     126 .. 0.75
   2 ?   -0.6   0.0       0.4   1.2e+03      51      77 ..     149     175 ..     129     188 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.7e-06
                                       HHHHHTG.....-THHHHHHHHHHHHHH-TT.-T.TT-HHHHH.HHHHHHTTTSGGGTT-HHHHHHHHHHHTTS... CS
                       Mad3_BUB1_I   7 eeeleea.eegdDpLelwlryikwieesypq.sskesgllell.erclkkfkdderYknDpRylklwlkyadlv... 77 
                                       +e+l+    e+ DpL++w +y   ++e++++ ++k  + +++l e++++++ ++ +++  + + ++ lk+ +++   
  gi|242399066|ref|YP_002994490.1|  28 REALRRVkAENVDPLKVWEEYEALTSEKFKEyAGKPYKPIRVLeEEIVEEIAKKYEFEVPHDFWEIHLKMHQQYgkl 104
                                       455666555567********************777777777772578999999999988888766666666555455 PP

                                       .S-HHHHHHHHHHHT CS
                       Mad3_BUB1_I  78 .eepreifkflaskk 91 
                                        +e+ e+ k+l  ++
  gi|242399066|ref|YP_002994490.1| 105 yDEAIEVLKTLKVNG 119
                                       599999999998775 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.4
                                       HHHTTTSGGGTT-HHHHHHHHHHHTTS CS
                       Mad3_BUB1_I  51 lkkfkdderYknDpRylklwlkyadlv 77 
                                       +++ ++   Yk  pR+ +l l+ a+l 
  gi|242399066|ref|YP_002994490.1| 149 ITTSEEAGFYKPHPRMFELALQKANLK 175
                                       445667788999999999999888765 PP

>> Put_Phosphatase  Putative Phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.45   1.3e+03       3      29 ..       5      31 ..       4      61 .. 0.61
   2 ?    8.2   0.0    0.0005       1.5      76     121 ..     108     151 ..      93     156 .. 0.89
   3 ?   -0.4   0.0      0.21   6.3e+02     165     180 ..     172     187 ..     164     211 .. 0.64

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.45
                   Put_Phosphatase  3 vvfDFDktiidedsdnwvvdelpatel 29
                                      v fDF  t+++++ +++  + +  ++l
  gi|242399066|ref|YP_002994490.1|  5 VFFDFVGTLLSKEFEDITHQNIIREAL 31
                                      568888888887766665555544443 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0005
                   Put_Phosphatase  76 lvelikslakkkleldliiiSDaNsffieeileaagledlFseift 121
                                        +e++k+l  k +++ + +i D+ + ++   l+a+g+ ++F++i t
  gi|242399066|ref|YP_002994490.1| 108 AIEVLKTL--KVNGYHIGMITDSDNDYLHAQLKALGILEFFDSITT 151
                                       57899999..5679*****************************998 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.21
                   Put_Phosphatase 165 egveyerliYvGDgan 180
                                        + + e  iYvGD   
  gi|242399066|ref|YP_002994490.1| 172 ANLKGEEAIYVGDNPL 187
                                       45567899*****753 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       695  (0.038764); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.29s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 1603.30
//
Query:       gi|242399067|ref|YP_002994491.1|  [L=100]
Description: hypothetical protein TSIB_1088 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.068   13.4   0.1      0.077   13.3   0.1    1.1  1  DUF4230   Protein of unknown function (DUF4230)


Domain annotation for each model (and alignments):
>> DUF4230  Protein of unknown function (DUF4230)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   4.3e-06     0.077       8      55 ..      34      92 ..      27      99 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.3e-06
                           DUF4230  8 eLetaeytvdkvvtiedek....lllk.........ekklliiargtvkagvDLsklkeed 55
                                       ++  ey++  + ++++++    +  k         ek  ++ +++++k g+DL++++ + 
  gi|242399067|ref|YP_002994491.1| 34 HWAYGEYNFISILDFDNSReleeF--KeklrhligdEKFKVYLVKYEAKNGIDLNDISNDF 92
                                      578889*************77651..1456677887888899***************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       726  (0.0404931); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); 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: 0.46u 0.31s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 639.51
//
Query:       gi|242399068|ref|YP_002994492.1|  [L=189]
Description: hypothetical protein TSIB_1089 [Thermococcus sibiricus MM 739]
Scores for complete 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-20   72.1   0.3    1.2e-19   70.9   0.1    1.6  2  ASCH            ASCH domain
     0.0024   18.2   0.2      0.049   14.0   0.0    2.4  2  SAP30_Sin3_bdg  Sin3 binding region of histone deacetylase co


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 !   70.9   0.1   1.3e-23   1.2e-19       1     106 [.       4     102 ..       4     103 .. 0.94
   2 ?   -1.9   0.0      0.56     5e+03      77      91 ..     167     181 ..     153     185 .. 0.69

  Alignments for each domain:
  == domain 1  score: 70.9 bits;  conditional E-value: 1.3e-23
                                       EEE-TTHHHHHHTTS--EEEESSTTTGGGT-CEEEEEECCCCTSEEEEEEEEEEEEEEHHHHHHHHHCHCC--.-HC CS
                              ASCH   1 lsfhqelaslivsGkKtaeirvwdeelpkvrgdllilaalkptgralgivevtkvevkpfeevteehalkege.sle 76 
                                       l+f+ ++++l+++GkK+a+ir+++ ++ +   ++++l  +++ g  lg+++v++ve+k+++e+t+e+a+++g+ + e
  gi|242399068|ref|YP_002994492.1|   4 LKFDGKYKELLLNGKKRATIRFGKVNMAP---GDEVL--IHSAGYVLGKAKVKRVEKKKVSELTDEDAKLDGFkDRE 75 
                                       68999*********************666...78888..89************************************ PP

                                       HHHHHHHCCHHHHHCCEEEEEEEEEEEEEE CS
                              ASCH  77 ewrevheefyeeeseeyedelvvveefelv 106
                                       +++e+++++y++ +   +d +v+++efe+v
  gi|242399068|ref|YP_002994492.1|  76 KLMEALRDHYKNIK---PDAEVTLIEFEFV 102
                                       ************87...6**********98 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.56
                                       HHHHHHHCCHHHHHC CS
                              ASCH  77 ewrevheefyeeese 91 
                                       + re +++ yee+++
  gi|242399068|ref|YP_002994492.1| 167 KIREILRKAYEELKK 181
                                       456777777777654 PP

>> SAP30_Sin3_bdg  Sin3 binding region of histone deacetylase complex subunit SAP30
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   5.5e-06     0.049      22      49 ..      72      99 ..      67     103 .. 0.93
   2 ?    1.6   0.0      0.04   3.6e+02      26      51 ..     123     148 ..     116     149 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.5e-06
                    SAP30_Sin3_bdg 22 sskeqLaeaVarHFkaqpvdEkevitsF 49
                                      + +e+L+ea+++H+k++++d + ++ +F
  gi|242399068|ref|YP_002994492.1| 72 KDREKLMEALRDHYKNIKPDAEVTLIEF 99
                                      579*********************9999 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.04
                    SAP30_Sin3_bdg  26 qLaeaVarHFkaqpvdEkevitsFly 51 
                                       ++ae   +H +++  +E   +  Fl+
  gi|242399068|ref|YP_002994492.1| 123 EIAELALKHLNNLSFEEVVLLKLFLQ 148
                                       67788899************999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       778  (0.0433934); expected 358.6 (0.02)
Passed bias filter:                      560  (0.0312343); 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: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1324.74
//
Query:       gi|242399069|ref|YP_002994493.1|  [L=120]
Description: hypothetical protein TSIB_1090 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.6e-12   46.0   0.2    7.8e-12   45.7   0.2    1.1  1  ASCH      ASCH domain
  ------ inclusion threshold ------
      0.091   12.8   0.1       0.13   12.3   0.1    1.3  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 !   45.7   0.2   8.7e-16   7.8e-12       2     106 ..       7     108 ..       6     109 .. 0.92

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 8.7e-16
                                       EE-TTHHHHHHTTS--EEEESSTTTGGGT-CEEEEEECCCCTSEEEEEEEEEEEEEE.HHHHHHHHHCHCC--.... CS
                              ASCH   2 sfhqelaslivsGkKtaeirvwdeelpkvrgdllilaalkptgralgivevtkvevk.pfeevteehalkege.... 73 
                                        +++e+++ i sGkK +e+rv +++l++++ +++i+++ +      + +ev  ++ + +f++v +e++    +    
  gi|242399069|ref|YP_002994493.1|   7 YVREEYLEMIESGKKDIEVRVAYPQLRNIKPKDKIIFNNT------IPAEVLTIKRYeTFRQVLREESVERIFpdkp 77 
                                       6899********************************9988......99******9999***********44447777 PP

                                       -HCHHHHHHHCCHHHHHCCEEEEEEEEEEEEEE CS
                              ASCH  74 sleewrevheefyeeeseeyedelvvveefelv 106
                                       s+e+ ++ ++++y++++e  ++++v++++f+l+
  gi|242399069|ref|YP_002994493.1|  78 SFEQAVKRFHNMYPKWKE--NRYGVLAIKFRLL 108
                                       ****************99..**********986 PP

>> DUF3850  Domain of unknown function (DUF3850)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   1.5e-05      0.13       2      51 ..       4      55 ..       3      67 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.5e-05
                           DUF3850  2 heLkilpeyfeaVvsGkKtfeirk...nDrdyqvGDlLvLkeideedgeytGr 51
                                       +L + +ey e ++sGkK  e+r    + r+ +  D ++++++ + ++  t++
  gi|242399069|ref|YP_002994493.1|  4 YKLYVREEYLEMIESGKKDIEVRVaypQLRNIKPKDKIIFNNTIP-AEVLTIK 55
                                      689999*****************8555679999999999998876.5666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 792.49
//
Query:       gi|242399070|ref|YP_002994494.1|  [L=375]
Description: Archaeal signal peptidase, A24 family [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-26   92.4   2.0    3.9e-26   91.4   2.0    1.5  1  Arc_PepC       Archaeal Peptidase A24 C-terminal Domain
      2e-06   28.2   1.1    5.6e-06   26.8   0.0    2.3  2  Arc_PepC_II    Archaeal Peptidase A24 C-terminus Type II
    3.5e-06   27.4   9.5    3.5e-06   27.4   9.5    2.6  3  Peptidase_A24  Type IV leader peptidase family


Domain annotation for each model (and alignments):
>> 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 !   91.4   2.0   6.5e-30   3.9e-26       4     112 .]     233     341 ..     230     341 .. 0.96

  Alignments for each domain:
  == domain 1  score: 91.4 bits;  conditional E-value: 6.5e-30
                          Arc_PepC   4 vsitelkliskvikaltkeelsdkkkveeLkEGdiladiilekeddevtvddksllkrlkealktgdvskietk.gk 79 
                                        + + +k+  +++ +++ e+l++k+ v+eLkE+dil++ i+ek d+++++d+++ +++l +alkt +v++++    k
  gi|242399070|ref|YP_002994494.1| 233 LTFYLFKTFFSLVSIMRVEVLTKKVSVNELKEWDILGEWIYEK-DGKIQRDREGSFDKLIRALKTLNVNALRVYyDK 308
                                       5678899999*********************************.99**************************999** PP

                          Arc_PepC  80 vlvsdlaeGLtkediellkkLvsegKiedefrv 112
                                        ++  +aeGLtke+ie lk Lv+e K+edef v
  gi|242399070|ref|YP_002994494.1| 309 LIAYPTAEGLTKENIEILKRLVEEEKLEDEFLV 341
                                       *******************************76 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 ?   -1.8   0.2      0.76   4.5e+03      59      84 ..      22      48 ..       4      50 .. 0.71
   2 !   26.8   0.0   9.4e-10   5.6e-06       8      92 .]     253     364 ..     248     364 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.76
                       Arc_PepC_II 59 kkglieet.vWvtygvPflipitaGfi 84
                                      k g+i+++ v+   g+  l ++ +Gf 
  gi|242399070|ref|YP_002994494.1| 22 KTGFIDDKhVFPIAGLGILYYLYMGFF 48
                                      567777666777777777777777776 PP

  == domain 2  score: 26.8 bits;  conditional E-value: 9.4e-10
                       Arc_PepC_II   8 igyrvkvkellkkflflleefeekdgkikrkfisvekeld............................eelrkelkk 56 
                                       + ++v+v+el k++ +l e + ekdgki+r    + ++l                             +e ++ lk+
  gi|242399070|ref|YP_002994494.1| 253 LTKKVSVNEL-KEWDILGEWIYEKDGKIQRDREGSFDKLIralktlnvnalrvyydkliayptaegltKENIEILKR 328
                                       6788999999.899999999999999999966555544447999999******************9999******** PP

                       Arc_PepC_II  57 ykkkglieetvWvtygvPflipitaGfiialvlGDl 92 
                                       +++++++e++  v  ++Pf + +++Gf+i++++GDl
  gi|242399070|ref|YP_002994494.1| 329 LVEEEKLEDEFLVRNAMPFAPALFLGFLISVLYGDL 364
                                       ***********************************6 PP

>> Peptidase_A24  Type IV leader peptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   9.5   5.8e-10   3.5e-06       2     102 ..       8     126 ..       7     138 .. 0.79
   2 ?   -3.0   3.2       1.6   9.7e+03      54      59 ..     193     198 ..     157     248 .. 0.53
   3 ?   -3.0   0.2       1.6   9.8e+03      29      36 ..     351     358 ..     340     369 .. 0.54

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 5.8e-10
                     Peptidase_A24   2 vlltillvlsviDldtrtlpdeltlpllllgvlfaqllllglpnlaqavlgalvgalvllli..slvdeqamGgGDv 76 
                                       + +++ ++ s++D++t  ++d+ ++p++ lg+l+  ++ + +++ + ++l++++g++  +l+  +l+ ++++  GD+
  gi|242399070|ref|YP_002994494.1|   8 LGVIMGILTSYTDIKTGFIDDKHVFPIAGLGILYYLYMGFFIKHNTIFALSGIIGLGTGFLLgyFLYMMGGWASGDI 84 
                                       6788999***************************9556667777777777877777777776667999********* PP

                     Peptidase_A24  77 klaavlgaflgwerl................llavlvaillg 102
                                        ++++ +a+l+                    l ++l++il+ 
  gi|242399070|ref|YP_002994494.1|  85 VILMGYSALLPYASRyakvippyaskyplhsLTLLLNSILAI 126
                                       ***********6555566677777788888544444444443 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.6
                     Peptidase_A24  54 lvgalv 59 
                                       + +al+
  gi|242399070|ref|YP_002994494.1| 193 ITIALM 198
                                       222222 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 1.6
                     Peptidase_A24  29 lllgvlfa 36 
                                       l+lg+l+ 
  gi|242399070|ref|YP_002994494.1| 351 LFLGFLIS 358
                                       22222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       785  (0.0437838); 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:                         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: 0.59u 0.25s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 2485.72
//
Query:       gi|242399071|ref|YP_002994495.1|  [L=210]
Description: Phosphoserine phosphatase [Thermococcus sibiricus MM 739]
Scores for complete 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   67.6   0.1    2.2e-18   67.4   0.1    1.1  1  HAD              haloacid dehalogenase-like hydrolase
    7.9e-15   55.7   0.0    2.9e-14   53.9   0.0    1.8  1  Hydrolase        haloacid dehalogenase-like hydrolase
    5.2e-08   32.9   0.2    5.5e-06   26.3   0.2    2.7  3  Hydrolase_3      haloacid dehalogenase-like hydrolase
    6.3e-08   32.9   0.1    1.4e-06   28.5   0.1    2.3  1  HAD_2            Haloacid dehalogenase-like hydrolase
     0.0023   17.4   0.0      0.051   13.0   0.0    2.2  2  Put_Phosphatase  Putative Phosphatase
  ------ inclusion threshold ------
      0.032   14.0   0.0      0.052   13.3   0.0    1.3  1  HD_2             HD containing hydrolase-like enzyme
      0.083   12.4   0.0       0.17   11.4   0.0    1.7  2  S6PP             Sucrose-6F-phosphate phosphohydrolase


Domain annotation for each model (and alignments):
>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.4   0.1   8.5e-22   2.2e-18       1     188 []       4     171 ..       4     171 .. 0.78

  Alignments for each domain:
  == domain 1  score: 67.4 bits;  conditional E-value: 8.5e-22
                               HAD   1 alfDfDgTLldgdslelllrfllrrgaprlwralreklllalfrellrldraglaelleallagls.eelaaelerf 76 
                                       + fD+ gTL+ + s   +++ + r g ++ +++++e++++    +++++     a+l ++l++g s  e+ +++e  
  gi|242399071|ref|YP_002994495.1|   4 IAFDLEGTLVKSKSS--WVELHKRFGTWDKGEEYAERFFKGE-FDYATW-----AKLDASLWRGKSrKEIMEWVESV 72 
                                       57**********665..5555556667777777777766666.355555.....89999999999988888888888 PP

                               HAD  77 vaevirpklldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevdd..rltgelglegkpvrg 151
                                                + +g++el++  +++ ++++++Sggl+ l+e++ +el ad v+a+el +d+  ++tg   +   + ++
  gi|242399071|ref|YP_002994495.1|  73 E--------YFEGVKELFEFLKRNKFKIAIISGGLKCLAERIGKELKADFVYANELLFDEeeKVTGD--VLSWVDFR 139
                                       8........5599999999999*********************************************..44444444 PP

                               HAD 152 egkvaalrewlaaegegidleevvayGDspsDlpllr 188
                                        +k + l e     +e+++++ +va+GD+++D+++++
  gi|242399071|ref|YP_002994495.1| 140 -NKGDILLE--L--KEKLKPKLTVAVGDGHNDIAMFK 171
                                       .23333333..2..33444455*************86 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.9   0.0   1.1e-17   2.9e-14       3     210 .]       3     174 ..       1     174 [. 0.81

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 1.1e-17
                                       EEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETTTEHHHHTHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase   3 tvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakarsgaltgfatfigrgayaigkpewlta 79 
                                       +++fD+ GTL++++      +v++                     ++  + + + +++a+     ++ +g+ ++ t+
  gi|242399071|ref|YP_002994495.1|   3 LIAFDLEGTLVKSK----SSWVEL---------------------HKRFGTWDKGEEYAE-----RFFKGEFDYATW 49 
                                       79*********888....667777.....................6666999********.....************ PP

                                       HHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  80 ldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlG 156
                                                       +   + +  +   ++ +  ++ + +++++e+++ Lk++++++++++g+ +  aer+ ++l 
  gi|242399071|ref|YP_002994495.1|  50 A---------------KLDASLWRGKSRKEIMEWVESVEYFEGVKELFEFLKRNKFKIAIISGGLKCLAERIGKELK 111
                                       *...............6666666666666666677777799************************************ PP

                                       GGGE.SEEEEHHCES..STTT........SHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                       xxxx.xxxxxxxxxx..xxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 157 ddyf.daviasdiet..vakp........spegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                       +d++ ++++  d+e+   + +        + ++++++ ++L  kp+ +++VGDg nD+a+++ A+
  gi|242399071|ref|YP_002994495.1| 112 ADFVyANELLFDEEEkvTGDVlswvdfrnKGDILLELKEKL--KPKLTVAVGDGHNDIAMFKVAD 174
                                       55555777777777777455566665555555555555555..6777***************997 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.025        64       1      15 [.       4      18 ..       4      25 .. 0.86
   2 ?   -1.1   0.0       0.5   1.3e+03      20      54 ..      78     112 ..      69     120 .. 0.62
   3 !   26.3   0.2   2.1e-09   5.5e-06     187     229 ..     140     180 ..     104     183 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.025
                                      EEEEIIIIIS-TTS- CS
                       Hydrolase_3  1 ialDlDGTLlnsdkk 15
                                      ia+Dl GTL++s+++
  gi|242399071|ref|YP_002994495.1|  4 IAFDLEGTLVKSKSS 18
                                      89********99876 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.5
                                       HHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCC CS
                       Hydrolase_3  20 tkeaikklkekgikvviATGRslravlpvleelgl 54 
                                        ke ++ lk + +k++i +G     ++++ +el+ 
  gi|242399071|ref|YP_002994495.1|  78 VKELFEFLKRNKFKIAIISGGLKCLAERIGKELKA 112
                                       45555666666666666666666666666666555 PP

  == domain 3  score: 26.3 bits;  conditional E-value: 2.1e-09
                                       SHHHHHHHHHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEET CS
                       Hydrolase_3 187 sKgtalkklakelnisleeviafGDgeNDieMLeaaglgvAmg 229
                                       +Kg  l +l +  +++++ ++a+GDg+NDi+M+++a++++A++
  gi|242399071|ref|YP_002994495.1| 140 NKGDILLELKE--KLKPKLTVAVGDGHNDIAMFKVADVSIAIN 180
                                       56666666664..4567889*********************85 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.1   5.6e-10   1.4e-06       1     173 [.       4     175 ..       4     179 .. 0.68

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 5.6e-10
                             HAD_2   1 iiFDlDgTlldteeliiqafnelleeyglselseeelrkliglslr.ellrklgeseeeeekieellrkyneekkkk 76 
                                       i FDl gTl+ ++  +++  ++        +  ee+ ++++  + +  +  kl  s +  ++++e++++++      
  gi|242399071|ref|YP_002994495.1|   4 IAFDLEGTLVKSKSSWVELHKRFG----TWDKGEEYAERFFKGEFDyATWAKLDASLWRGKSRKEIMEWVE------ 70 
                                       67***********99998877766....4456677777776655541556677777776666666644443...... PP

                             HAD_2  77 evkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekkKPdpeviekalekl..... 148
                                       +v+ ++gvkel e Lk++++k++i++ + +  +e+  ++l+ + ++   +  ++ ek     +v+            
  gi|242399071|ref|YP_002994495.1|  71 SVEYFEGVKELFEFLKRNKFKIAIISGGLKCLAERIGKELKADFVYANELLFDEEEKV--TGDVLSW----Vdfrnk 141
                                       47779*************************9999999999986444433333333333..2333222....222234 PP

                             HAD_2 149 .........klkkeeviyvGDsptDieaakkagi 173
                                                klk++ ++ vGD ++Di   k a +
  gi|242399071|ref|YP_002994495.1| 142 gdillelkeKLKPKLTVAVGDGHNDIAMFKVADV 175
                                       4666666677888888888888888877776666 PP

>> Put_Phosphatase  Putative Phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0     2e-05     0.051       1      98 [.       2      98 ..       2     129 .. 0.84
   2 ?    2.2   0.0     0.039     1e+02     163     183 ..     148     168 ..     139     178 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2e-05
                   Put_Phosphatase  1 ilvvfDFDktiidedsd.nwvvdelpatelfeelretlrkglwnelmdrvlkelheqgvseadikkvlrsiplspglve 78
                                      +l++fD + t+++++s    + +  ++ ++ ee  e + kg +       l     +g+s ++i + ++s+    g+ e
  gi|242399071|ref|YP_002994495.1|  2 YLIAFDLEGTLVKSKSSwVELHKRFGTWDKGEEYAERFFKGEFDYATWAKLDASLWRGKSRKEIMEWVESVEYFEGVKE 80
                                      589*********8776514578899999999999999999988877777777777789********************* PP

                   Put_Phosphatase 79 likslakkkleldliiiSDa 98
                                      l+++l+  ++++ + iiS  
  gi|242399071|ref|YP_002994495.1| 81 LFEFLK--RNKFKIAIISGG 98
                                      *****4..578******965 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.039
                   Put_Phosphatase 163 aregveyerliYvGDganDlC 183
                                       ++e+ + +  + vGDg nD+ 
  gi|242399071|ref|YP_002994495.1| 148 LKEKLKPKLTVAVGDGHNDIA 168
                                       345567788899*******86 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 ?   13.3   0.0     2e-05     0.052      31      83 ..      90     141 ..      79     153 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2e-05
                              HD_2  31 levaliahalalienkkfggkldaerlallalyHDasEiitGDlptpvKyanp 83 
                                       +++a+i+  l +++++  g++l a+ +++  l+ D +E +tGD+ + v ++n+
  gi|242399071|ref|YP_002994495.1|  90 FKIAIISGGLKCLAERI-GKELKADFVYANELLFDEEEKVTGDVLSWVDFRNK 141
                                       78999**9**9999965.9***************************9998876 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      0.95   2.4e+03       4      24 ..       3      22 ..       2      32 .. 0.74
   2 ?   11.4   0.0   6.5e-05      0.17     173     210 ..     146     183 ..      62     204 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.95
                                      EEEE-TBTTTB.S-HHHHHHH CS
                              S6PP  4 llvsdLDntlvdgdnealarl 24
                                      l++ dL +tlv +++++  +l
  gi|242399071|ref|YP_002994495.1|  3 LIAFDLEGTLV-KSKSSWVEL 22
                                      78999*****9.666555555 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 6.5e-05
                                       HHHHHT--GGGEEEEE-SGGGHHHHTSSSEEEE-TT-- CS
                              S6PP 173 LakkleleleqilvcGdsgnDeellignvlgVvVgnaq 210
                                       L  k +l+++ ++ +Gd  nD+++++    ++ +  ++
  gi|242399071|ref|YP_002994495.1| 146 LELKEKLKPKLTVAVGDGHNDIAMFKVADVSIAINPHE 183
                                       55566778999**************9888888887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); 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: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1314.03
//
Query:       gi|242399072|ref|YP_002994496.1|  [L=221]
Description: Pcm; protein-L-isoaspartate O-methyltransferase [Thermococcus sibiricus MM 739]
Scores for complete 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-67  225.6   0.0    6.3e-67  225.4   0.0    1.0  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    5.8e-07   29.4   0.0    8.5e-07   28.9   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    2.5e-06   28.1   0.0    4.1e-06   27.4   0.0    1.3  1  Methyltransf_25  Methyltransferase domain
    1.4e-05   24.3   0.0    1.7e-05   24.0   0.0    1.1  1  RrnaAD           Ribosomal RNA adenine dimethylase
    9.2e-05   22.3   0.0    0.00014   21.8   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
    0.00075   19.1   0.0     0.0013   18.3   0.0    1.3  1  MTS              Methyltransferase small domain
      0.006   15.8   0.0     0.0085   15.3   0.0    1.4  1  Methyltransf_3   O-methyltransferase
     0.0062   17.2   0.0      0.011   16.4   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
     0.0073   15.6   0.0      0.011   15.1   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
     0.0095   15.9   0.0      0.015   15.3   0.0    1.2  1  Methyltransf_18  Methyltransferase domain
  ------ inclusion threshold ------
      0.016   15.0   0.0      0.022   14.5   0.0    1.2  1  Methyltransf_16  Lysine methyltransferase
      0.033   13.9   0.0      0.046   13.4   0.0    1.2  1  GCD14            tRNA methyltransferase complex GCD14 subunit
      0.041   13.3   0.0      0.059   12.8   0.0    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm


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 !  225.4   0.0   4.5e-70   6.3e-67       5     208 ..      12     216 ..       8     218 .. 0.95

  Alignments for each domain:
  == domain 1  score: 225.4 bits;  conditional E-value: 4.5e-70
                                       HHHHHHHHTTS---HHHHHHHHHS-GGGGSSCGGGGGTTSSS-EEEETTEEE--HHHHHHHHHHTT--TT-EEEEES CS
                              PCMT   5 alieelkkkgviksdkvaealeevdReefvpesfkekaYedaplsigynatiSaphmvalalellelkkgarvLevG 81 
                                       +l+e+l+++g+iks+kv  a++ v+R +fv + +ke+a++d pl+i +++tiSaphmva++lel el+ g++vLevG
  gi|242399072|ref|YP_002994496.1|  12 RLVENLEREGIIKSEKVKRAFLRVPRYKFVSDRYKEYAHVDEPLPIPAGQTISAPHMVAIMLELAELEGGMNVLEVG 88 
                                       69*************************************************************************** PP

                                       -TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTC.SEEEEES-GGGTTGGG-SEEEEEESSBBSS--H CS
                              PCMT  82 sGsGyltavlarlvgekgrvvsierikelveeakrnlkkldle.nvivvvgDGrkGyeekaPYdaihvgaaapeiPe 157
                                       +GsG+++a++++lv+++    +ier+ +lve a++nl++ +++ +v+v+ gDG kGy+++aPYd+i+v+a+ap++Pe
  gi|242399072|ref|YP_002994496.1|  89 AGSGWNAALIYELVKREV--YTIERVSDLVEFARKNLERAGYKdKVHVIWGDGSKGYPPNAPYDRIIVTAGAPKVPE 163
                                       ***************997..99*******************9889******************************** PP

                                       HHHHTEEEEEEEEEEESB.SSSEEE.EEEEEETTTEEEEEEEEEE---B-BCC CS
                              PCMT 158 alidQLkeGGrlvvPvge.eeeQvl.klvdkkadgkvvikkleevrfvpltdk 208
                                       +li+QLk GG+l++Pvg+ +  Q+l ++++ ++d++++ik+   v+fvpl ++
  gi|242399072|ref|YP_002994496.1| 164 PLIEQLKVGGKLLIPVGSyHLWQELlEVIKLDEDNNTKIKNHGGVAFVPLIGE 216
                                       *****************9877787615556677899**************876 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0   6.2e-10   8.5e-07       2     129 ..      79     199 ..      78     220 .. 0.81

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 6.2e-10
                   Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdiee.leklledekfD 76 
                                       + g++vl++G+G+G  +  ++e++  k ev+ i++  + +e+Ar+n+++ g++  v++  gd  +  + +   +++D
  gi|242399072|ref|YP_002994496.1|  79 EGGMNVLEVGAGSGWNAALIYELV--KREVYTIERVSDLVEFARKNLERAGYKdKVHVIWGDGSKgYPPN---APYD 150
                                       679***********9999999655..689************************9**********999954...9999 PP

                   Methyltransf_31  77 lilsnevlnaladpdkileeiervlkpggilliedpr..llaelpakveeeskay 129
                                        i+       +a  +k+ e +++ lk gg lli   +  l++el++ ++ +++++
  gi|242399072|ref|YP_002994496.1| 151 RIIV------TAGAPKVPEPLIEQLKVGGKLLIPVGSyhLWQELLEVIKLDEDNN 199
                                       9988......566777777788888888888876555557777776666666544 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0     3e-09   4.1e-06       1      75 [.      84     159 ..      84     171 .. 0.88

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 3e-09
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEEESTGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvssgalh 75 
                                       vL++G+G+G +++ + + + k +v+ ++  ++++e ar+++e++g+  +v+++ gd ++   +++ +D ++++ +  
  gi|242399072|ref|YP_002994496.1|  84 VLEVGAGSGWNAALIYELV-KREVYTIERVSDLVEFARKNLERAGYkdKVHVIWGDGSKGYPPNAPYDRIIVTAGAP 159
                                       9*****************9.6**********************99999*********99888999****99964444 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   1.2e-08   1.7e-05      22     105 ..      72     153 ..      62     209 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1.2e-08
                                       HHHHH-GGTTSEEEEES-TTTCCHHHHHCC-.SEEEEE-S-HHHHHHHHCHTT...TCCCEEEE-S-CCGHHHHHHH CS
                            RrnaAD  22 IldklnleekltvleigpGkGilTeeLakra.kqvvvlElderLakllqkkls...kdeklkvvhqDflkfetpeev 94 
                                        l+ ++le  ++vle+g+G G   + + + + ++v  +E  ++L+++ +k+l+    + k+ v+  D+ k   p+  
  gi|242399072|ref|YP_002994496.1|  72 MLELAELEGGMNVLEVGAGSGWNAALIYELVkREVYTIERVSDLVEFARKNLEragYKDKVHVIWGDGSKGYPPNAP 148
                                       567789999**********************999*******************9988999****9999988888744 PP

                                       CTTTCCCCEEE CS
                            RrnaAD  95 tekdsihqefl 105
                                       +      ++++
  gi|242399072|ref|YP_002994496.1| 149 Y------DRII 153
                                       3......4444 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0     1e-07   0.00014      14     143 ..      73     202 ..      61     220 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1e-07
                   Methyltransf_23  14 erllpklraggrvLdiGcGtGillevlrengf.svtgvDlspeaveiae.......kakkaqkdqfdeqeaaepqgk 82 
                                       ++l++ l+ g++vL++G+G+G ++ ++ e ++ +v+ ++  + +ve a+        ++k +    d ++  +p++ 
  gi|242399072|ref|YP_002994496.1|  73 LELAE-LEGGMNVLEVGAGSGWNAALIYELVKrEVYTIERVSDLVEFARknleragYKDKVHVIWGDGSKGYPPNAP 148
                                       45654.8999***************9988888899999999999999877774444222222222333355569999 PP

                   Methyltransf_23  83 fdlIvlrevlehvpdppellrqiatllkpgGylllseplaslkedrllldwlylvpagrhi 143
                                       +d I+ + +   vp p        + lk gG ll+ +  +++ + +ll+ ++++ +++++i
  gi|242399072|ref|YP_002994496.1| 149 YDRIIVTAGAPKVPEPLI------EQLKVGGKLLIPVG-SYHLWQELLEVIKLDEDNNTKI 202
                                       999999998888887643......44455666665554.3445666666666666555555 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   9.5e-07    0.0013      30     102 ..      79     153 ..      68     156 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 9.5e-07
                                       CTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTTTST.TS-EEEEE CS
                               MTS  30 elsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..vevvasdvleeve.ekkfdliv 102
                                       e   +vl +G+G G  +a + +  ++ ev  ++     +e+a++nle+ + +  v+v++ d+ +  + ++ +d i+
  gi|242399072|ref|YP_002994496.1|  79 EGGMNVLEVGAGSGWNAALIYELVKR-EVYTIERVSDLVEFARKNLERAGYKdkVHVIWGDGSKGYPpNAPYDRII 153
                                       45668**********99998887777.9***********************999**********998578899988 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   6.2e-06    0.0085      42     110 ..      75     141 ..      60     204 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 6.2e-06
                                       HHHHHT--EEEEE--TTSHHHHHHHTTS-TT-EEEEEES-HHHHHHHHHHHHHTT-GGGEEEEES-HHH CS
                    Methyltransf_3  42 LvklvnakrvleiGvftGyslLatalalPeDGkilaididreayeialkfiqkagvaekieliegdalk 110
                                       L +l +  +vle+G   G+ +  +   +    ++ +i+   + +e a+k +++ag+++k+++i gd+ k
  gi|242399072|ref|YP_002994496.1|  75 LAELEGGMNVLEVGAGSGWNAALIYELVK--REVYTIERVSDLVEFARKNLERAGYKDKVHVIWGDGSK 141
                                       66889999***********8755544443..479*******************************9876 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   7.6e-06     0.011       1      54 [.      85     141 ..      85     165 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 7.6e-06
                                       EEET-TTSHHHHHHHHTT.SEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCC CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg.arvvgvDlskemlklakekaseegl..kvefvvadaek 54 
                                       L+vG+G+G +a+ + + + ++v++++    +++ a+++ +++g   kv ++ +d +k
  gi|242399072|ref|YP_002994496.1|  85 LEVGAGSGWNAALIYELVkREVYTIERVSDLVEFARKNLERAGYkdKVHVIWGDGSK 141
                                       89*************9999**********************9998877888788776 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   7.7e-06     0.011      52     118 ..      70     136 ..      64     158 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 7.7e-06
                                       HHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEE CS
                              CMAS  52 dlileklelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevkl 118
                                        ++le +el+ Gm++L++G+G G  +    e    +v  +   ++  + a+k++++++ ++kv+v  
  gi|242399072|ref|YP_002994496.1|  70 AIMLELAELEGGMNVLEVGAGSGWNAALIYELVKREVYTIERVSDLVEFARKNLERAGYKDKVHVIW 136
                                       5789999***********9875555444444444699999999999****************99865 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.1e-05     0.015      31      88 ..      96     154 ..      75     159 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.1e-05
                   Methyltransf_18  31 ylvkegkakkviasDinegplekakeniekagledkievrlsdGleklkeee.vdtvvi 88 
                                       +l+ e   ++v+ ++  +  +e a++n+e+ag++dk++v+ +dG + + ++  +d +++
  gi|242399072|ref|YP_002994496.1|  96 ALIYELVKREVYTIERVSDLVEFARKNLERAGYKDKVHVIWGDGSKGYPPNApYDRIIV 154
                                       455556667899999999******************************99988986654 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.6e-05     0.022      47     125 ..      81     153 ..      64     156 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.6e-05
                   Methyltransf_16  47 klsvlELGsGtGlvGlavaellpeakviltDleellellkknielnknalkskvkvevLdWgeeleedllekeevDl 123
                                       +++vlE+G+G+G     + el+++   ++  +++l+e+ +kn+e   +  k+kv+v    Wg+   +    + ++D 
  gi|242399072|ref|YP_002994496.1|  81 GMNVLEVGAGSGWNAALIYELVKREVYTIERVSDLVEFARKNLER--AGYKDKVHV---IWGDGS-KGYPPNAPYDR 151
                                       689**********9999999988888889999*************..559999987...466654.44555555665 PP

                   Methyltransf_16 124 il 125
                                       i+
  gi|242399072|ref|YP_002994496.1| 152 II 153
                                       55 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   3.3e-05     0.046      30     100 ..      69     138 ..      59     152 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.3e-05
                             GCD14  30 sliimkL.elkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehelsqlvtvthrD 100
                                         i+ +L el+ G  v+e G+Gsg  +  i   v+    ++t+e   + +e+ar+++++ + ++ v+v   D
  gi|242399072|ref|YP_002994496.1|  69 VAIMLELaELEGGMNVLEVGAGSGWNAALIYELVK--REVYTIERVSDLVEFARKNLERAGYKDKVHVIWGD 138
                                       334443337899************99999999886..57**************************9997666 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   4.3e-05     0.059     159     231 ..      78     153 ..      67     167 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.3e-05
                              PrmA 159 vkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseellk....eekadviv 231
                                       +++g +vl vG+GSG  a     L  ++v+ +   +  v+ a++N+e+ + ++k++v+  ++  k    ++++d i+
  gi|242399072|ref|YP_002994496.1|  78 LEGGMNVLEVGAGSGWNAALIYELVKREVYTIERVSDLVEFARKNLERAGYKDKVHVIW-GDGSKgyppNAPYDRII 153
                                       46678**************************************************9953.33333233367777555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        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 0.34s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 1299.12
//
Query:       gi|242399073|ref|YP_002994497.1|  [L=218]
Description: Archaea-specific Zn-finger-containing protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-05   24.6   1.0    3.6e-05   23.6   1.0    1.5  1  eIF-5_eIF-2B     Domain found in IF2B/IF5
    7.2e-05   22.2   0.2    0.00018   20.9   0.2    1.8  1  TF_Zn_Ribbon     TFIIB zinc-binding
    0.00028   20.9   0.4    0.00064   19.7   0.1    1.7  1  Elf1             Transcription elongation factor Elf1 like
     0.0043   17.7   0.2     0.0085   16.8   0.2    1.4  1  Ribosomal_L27A   Ribosomal proteins 50S-L15, 50S-L18e, 60S-L2
     0.0047   17.0   5.5      0.028   14.5   0.1    2.4  2  UPF0547          Uncharacterised protein family UPF0547
      0.006   16.5   1.7       0.17   11.9   0.1    2.4  2  PhnA_Zn_Ribbon   PhnA Zinc-Ribbon
      0.008   16.1   0.4      0.014   15.3   0.4    1.4  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
  ------ inclusion threshold ------
      0.011   15.2   0.6      0.015   14.7   0.6    1.2  1  NMD3             NMD3 family
      0.016   15.4   0.1        8.2    6.6   0.0    2.4  2  Zn-ribbon_8      Zinc ribbon domain
      0.036   14.1   2.6       0.92    9.6   2.0    2.7  2  HypA             Hydrogenase/urease nickel incorporation, met
      0.052   13.5   6.0      0.073   13.0   3.8    2.4  2  zinc_ribbon_4    zinc-ribbon domain
      0.062   13.7   0.2        0.1   13.0   0.2    1.4  1  Lar_restr_allev  Restriction alleviation protein Lar
      0.082   12.6   0.5       0.23   11.2   0.5    1.8  1  zinc_ribbon_10   Predicted integral membrane zinc-ribbon meta
       0.13   11.5   0.0       0.16   11.2   0.0    1.2  1  CcmF_C           Cytochrome c-type biogenesis protein CcmF C-
       0.19   11.6   4.9        6.5    6.7   4.7    2.2  2  TFIIS_C          Transcription factor S-II (TFIIS)
       0.21   12.0   1.2        1.5    9.2   1.6    2.0  2  DUF4379          Probable Zinc-ribbon domain
       0.39   10.8   4.6        4.9    7.3   0.5    3.2  3  zf-ACC           Acetyl-coA carboxylase zinc finger domain
       0.71    9.8   4.9       0.25   11.3   0.5    2.4  3  DUF951           Bacterial protein of unknown function (DUF95
          1    9.1   4.1        5.3    6.8   4.0    2.2  1  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
        1.3    8.8   5.8        2.2    8.1   3.1    2.7  2  zinc_ribbon_5    zinc-ribbon domain


Domain annotation for each model (and alignments):
>> eIF-5_eIF-2B  Domain found in IF2B/IF5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   1.0     4e-08   3.6e-05      84     116 ..      18      51 ..      15      52 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 4e-08
                                       HHHHTSTSSSTSTCEEECC.SSSCEEEEESSSTC CS
                      eIF-5_eIF-2B  84 ieeyVlCkeCkspetelek.eerllvlkCkaCga 116
                                       +eey +C+eCks ++e++k ++r l+l+C +Cg+
  gi|242399073|ref|YP_002994497.1|  18 MEEYFVCPECKSEDVEIIKeRGRDLTLRCAECGH 51 
                                       589****************6578888******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 !   20.9   0.2     2e-07   0.00018       1      30 [.      22      54 ..      22      62 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2e-07
                                      EEETTTTCEEC...HEETSTTCEEESSSSBEEE CS
                      TF_Zn_Ribbon  1 ykCPnCgstnl...veDpergelvCtdCGlVle 30
                                      ++CP+C+s+++    e     +l+C +CG V++
  gi|242399073|ref|YP_002994497.1| 22 FVCPECKSEDVeiiKERGRDLTLRCAECGHVWQ 54
                                      79******986554444566788********97 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.1   7.1e-07   0.00064      12      59 ..      12      57 ..       4      67 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 7.1e-07
                              Elf1 12 kkkkkklptkFdCpfCnheksvevkldkkek.iaevsCkvCgesfetkv 59
                                      + ++k+++++F Cp C++e   +v++ k+++   +++C  Cg   ++ v
  gi|242399073|ref|YP_002994497.1| 12 RSEVKEMEEYFVCPECKSE---DVEIIKERGrDLTLRCAECGHVWQIIV 57
                                      344556*************...6666665553789*******9887665 PP

>> Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.2   9.5e-06    0.0085      28     124 ..      62     168 ..      51     171 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 9.5e-06
                                       --.........---GGG..---EEEEHHHHHHTTTTGTTS--...----EEEGGGTTTTSSS.....SE.EEE--S. CS
                    Ribosomal_L27A  28 qmplyrrlpkrGfknskfkkeykvvnlkdLdelideerlela...deaeeidleelaeaglikk.kdgv.Kvlgkg. 98 
                                       q+p++    ++ fk++++   ++++ ++d++el d+e++      ++++ ++ +e+++ +++ + +  + Kv+g   
  gi|242399073|ref|YP_002994497.1|  62 QVPIIVSKHEKSFKKTVELPVDEEIRVGDIVELEDDEVRISSielEDNKRVEKAEIKDVKVLWGeSLAYpKVIGVSi 138
                                       6777777777888876766777***********99998863357889999999999888888776677899999876 PP

                                       ....---.--EEEESEE-HHHHHHHHHTT- CS
                    Ribosomal_L27A  99 ....eltkklkvkaskfSkkAkekIeaaGG 124
                                            +t+ +kvk+++  + A+ ++ ++GG
  gi|242399073|ref|YP_002994497.1| 139 ylpkGITQSFKVKVDREEEFAIGEVLEVGG 168
                                       66668899*********************9 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   1.6     0.061        55       2       8 ..      23      29 ..      23      30 .. 0.81
   2 !   14.5   0.1   3.2e-05     0.028      16      25 ..      45      54 ..      43      55 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.061
                           UPF0547  2 vCPeCea 8 
                                      vCPeC +
  gi|242399073|ref|YP_002994497.1| 23 VCPECKS 29
                                      7****86 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 3.2e-05
                           UPF0547 16 fCphCGyvFq 25
                                      +C++CG+v+q
  gi|242399073|ref|YP_002994497.1| 45 RCAECGHVWQ 54
                                      7********8 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.1   0.00019      0.17      17      28 ..      19      30 ..       4      30 .. 0.86
   2 ?    3.5   0.2     0.076        68      22      29 ..      46      53 ..      42      54 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00019
                    PhnA_Zn_Ribbon 17 gallvCpeCahE 28
                                       + +vCpeC++E
  gi|242399073|ref|YP_002994497.1| 19 EEYFVCPECKSE 30
                                      6789******98 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.076
                    PhnA_Zn_Ribbon 22 CpeCahEw 29
                                      C eC+h w
  gi|242399073|ref|YP_002994497.1| 46 CAECGHVW 53
                                      ******88 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 !   15.3   0.4   1.6e-05     0.014      19      45 ..      22      51 ..      16      52 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.6e-05
                     Zn_Tnp_IS1595 19 fvCPhCgsr..kayrikt.rglfqCkeCrk 45
                                      fvCP C+s+  ++++ ++    ++C+eC++
  gi|242399073|ref|YP_002994497.1| 22 FVCPECKSEdvEIIKERGrDLTLRCAECGH 51
                                      9********55555555533459*****98 PP

>> NMD3  NMD3 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.6   1.7e-05     0.015      13      99 ..      19     111 ..      11     159 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.7e-05
                              NMD3  13 ng..lCedCllkevditegiekievevCkeCgryl..pkgkWvk...aeleseellaeclkklvekgLkvseeve.. 80 
                                       ++  +C++C  ++v+i++   +  +  C+eCg ++    gk ++      ++e++ ++ ++  v ++++v + ve  
  gi|242399073|ref|YP_002994497.1|  19 EEyfVCPECKSEDVEIIKERGRDLTLRCAECGHVWqiIVGKMIQvpiIVSKHEKSFKKTVELPVDEEIRVGDIVEle 95 
                                       33569*************999977789*******9885557777555445666666777777777777766655533 PP

                              NMD3  81 evkvelvdaefiwtephsk 99 
                                       + +v+    + i  e++++
  gi|242399073|ref|YP_002994497.1|  96 DDEVR---ISSIELEDNKR 111
                                       44444...33333444333 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0     0.011        10      28      37 ..      23      33 ..      10      35 .. 0.72
   2 ?    6.6   0.0    0.0091       8.2       7      19 ..      45      57 ..      43      66 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.011
                       Zn-ribbon_8 28 aCPeCgs.evr 37
                                      +CPeC+s +v+
  gi|242399073|ref|YP_002994497.1| 23 VCPECKSeDVE 33
                                      3*****97775 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0091
                       Zn-ribbon_8  7 rCeeCghefevlq 19
                                      rC eCgh+  +++
  gi|242399073|ref|YP_002994497.1| 45 RCAECGHVWQIIV 57
                                      9******998765 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   2.0     0.001      0.92      83     107 ..      18      44 ..       9      49 .. 0.68
   2 ?    3.0   0.1      0.11        99      69      82 ..      42      55 ..      38      92 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.001
                                       HHHHHS-TTTSSS-EEEEE..SSSEEE CS
                              HypA  83 eekalrCpkCgsadveivs..Geellv 107
                                        e+ + Cp+C+s+dvei++  G++l++
  gi|242399073|ref|YP_002994497.1|  18 MEEYFVCPECKSEDVEIIKerGRDLTL 44 
                                       223579***********9744666665 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.11
                                      -EEEETTTS-EEEC CS
                              HypA 69 vkvrCreCgkefel 82
                                      +++rC eCg+ +++
  gi|242399073|ref|YP_002994497.1| 42 LTLRCAECGHVWQI 55
                                      56677888777764 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   3.8   8.1e-05     0.073       3      35 ..      22      53 ..      21      54 .. 0.81
   2 ?   -2.7   0.0       6.6   5.9e+03      12      24 ..     171     181 ..     169     184 .. 0.51

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.1e-05
                     zinc_ribbon_4  3 itCpsCkakyeiddeklpakgv..kvrCskCghvF 35
                                      ++Cp+Ck++   d e ++++g+   +rC+ Cghv+
  gi|242399073|ref|YP_002994497.1| 22 FVCPECKSE---DVEIIKERGRdlTLRCAECGHVW 53
                                      579999998...66667777776699********* PP

  == domain 2  score: -2.7 bits;  conditional E-value: 6.6
                     zinc_ribbon_4  12 yeiddeklpakgv 24 
                                       ++id  k+ +  +
  gi|242399073|ref|YP_002994497.1| 171 FKIDKIKIEG--K 181
                                       5566555544..3 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 ?   13.0   0.2   0.00012       0.1       5      36 ..      23      51 ..      19      74 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00012
                   Lar_restr_allev  5 pCPfCggravlersqrvvaeigqcvyCadCga 36
                                       CP C++++v +  +r++     +  Ca+Cg 
  gi|242399073|ref|YP_002994497.1| 23 VCPECKSEDVEIIKERGRDL---TLRCAECGH 51
                                      5**********999999999...*******97 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.5   0.00026      0.23      22      53 ..      21      52 ..       6      53 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00026
                    zinc_ribbon_10 22 alICskChshnGlapkeeleevkyrCpkCgal 53
                                        +C++C+s      ke+ ++++ rC++Cg++
  gi|242399073|ref|YP_002994497.1| 21 YFVCPECKSEDVEIIKERGRDLTLRCAECGHV 52
                                      579*****9998888***************85 PP

>> CcmF_C  Cytochrome c-type biogenesis protein CcmF C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00018      0.16     174     226 ..     121     177 ..      66     189 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00018
                            CcmF_C 174 rsawGmvlAH...lGvavtv.lGvalvsayeverdvrlkpgesvevagyefefegve 226
                                       +  wG  lA    +Gv + +  G++ + +++v+r+ + ++ge +ev+gy+f++++++
  gi|242399073|ref|YP_002994497.1| 121 KVLWGESLAYpkvIGVSIYLpKGITQSFKVKVDREEEFAIGEVLEVGGYTFKIDKIK 177
                                       4568888887544677776645*******************************9986 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 ?    3.7   0.5     0.061        55      28      36 ..      21      29 ..      11      31 .. 0.65
   2 ?    6.7   4.7    0.0073       6.5       2      39 .]      23      54 ..      22      54 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.061
                           TFIIS_C 28 fykCtkCgh 36
                                      +++C +C+ 
  gi|242399073|ref|YP_002994497.1| 21 YFVCPECKS 29
                                      566666653 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0073
                           TFIIS_C  2 kCpkCgsreayffqlQtRsaDEpmtvfykCtkCghrWr 39
                                       Cp+C+s+++  +       + +  +  +C++Cgh W+
  gi|242399073|ref|YP_002994497.1| 23 VCPECKSEDVEII------KERGRDLTLRCAECGHVWQ 54
                                      5777777777776......4445558899********6 PP

>> DUF4379  Probable Zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1       2.6   2.3e+03      52      56 .]      20      27 ..      10      27 .. 0.61
   2 ?    9.2   1.6    0.0017       1.5      21      44 ..      35      58 ..      24      63 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2.6
                           DUF4379 52 k...CpkC 56
                                      +   Cp+C
  gi|242399073|ref|YP_002994497.1| 20 EyfvCPEC 27
                                      24559*99 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0017
                           DUF4379 21 tpgskkkvwWkCakCgheWeasvs 44
                                       +  ++ +  +Ca+Cgh W+  v 
  gi|242399073|ref|YP_002994497.1| 35 IKERGRDLTLRCAECGHVWQIIVG 58
                                      55566777789********97765 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.5    0.0054       4.9      19      26 .]      20      27 ..      16      27 .. 0.85
   2 ?    1.8   0.1      0.29   2.6e+02       3       9 ..      45      51 ..      44      52 .. 0.84
   3 ?    1.4   0.0      0.38   3.4e+02      14      22 ..     104     112 ..     101     112 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0054
                            zf-ACC 19 nlyVCPkC 26
                                       ++VCP+C
  gi|242399073|ref|YP_002994497.1| 20 EYFVCPEC 27
                                      69****** PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.29
                            zf-ACC  3 KCpsCge 9 
                                      +C +Cg+
  gi|242399073|ref|YP_002994497.1| 45 RCAECGH 51
                                      6****97 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.38
                            zf-ACC  14 keLernlyV 22 
                                        eLe+n+ V
  gi|242399073|ref|YP_002994497.1| 104 IELEDNKRV 112
                                       79****988 PP

>> DUF951  Bacterial protein of unknown function (DUF951)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.5   0.00028      0.25      15      39 ..      27      52 ..      25      61 .. 0.89
   2 ?   -3.2   0.1       9.3   8.3e+03      45      54 ..      68      77 ..      62      78 .. 0.75
   3 ?   -0.9   0.0       1.8   1.6e+03       1       9 [.      86      94 ..      86      95 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00028
                            DUF951 15 CgsneweilR.vGadiklkClgcgre 39
                                      C+s++ ei++  G d+ l+C +cg++
  gi|242399073|ref|YP_002994497.1| 27 CKSEDVEIIKeRGRDLTLRCAECGHV 52
                                      999999999747*************7 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 9.3
                            DUF951 45 skfekkikkv 54
                                      sk ek++kk 
  gi|242399073|ref|YP_002994497.1| 68 SKHEKSFKKT 77
                                      5778888885 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 1.8
                            DUF951  1 yklgdivem 9 
                                      +++gdive+
  gi|242399073|ref|YP_002994497.1| 86 IRVGDIVEL 94
                                      589****97 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 ?    6.8   4.0    0.0059       5.3       2      25 ..      23      51 ..      22      53 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0059
                                      B-SSS--.B----SSS....----SSS-- CS
                    DNA_RNApol_7kD  2 iCgeCga.evslkkgd....piRCkeCGh 25
                                       C eC++ +v+++k+      +RC eCGh
  gi|242399073|ref|YP_002994497.1| 23 VCPECKSeDVEIIKERgrdlTLRCAECGH 51
                                      6999986257766543233479******9 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   3.1    0.0024       2.2       5      35 ..      24      53 ..      21      55 .. 0.75
   2 ?   -1.2   0.0         2   1.8e+03      11      24 ..     170     181 ..     168     187 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0024
                     zinc_ribbon_5  5 CpdCdtkFklvdsklKksgk..kVrCakCaevF 35
                                      Cp+C++    + + +K+ g     rCa C++v 
  gi|242399073|ref|YP_002994497.1| 24 CPECKSE---DVEIIKERGRdlTLRCAECGHVW 53
                                      8888876...66667888763357********7 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2
                     zinc_ribbon_5  11 kFklvdsklKksgk 24 
                                       +Fk++  k+K  gk
  gi|242399073|ref|YP_002994497.1| 170 TFKID--KIKIEGK 181
                                       67775..6666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.53
# Mc/sec: 1231.75
//
Query:       gi|242399074|ref|YP_002994498.1|  [L=281]
Description: hypothetical protein TSIB_1095 [Thermococcus sibiricus MM 739]
Scores for complete 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-08   32.2   0.0    1.4e-07   31.3   0.0    1.4  1  MarR_2           MarR family
    2.8e-07   30.4   0.1    4.7e-07   29.6   0.1    1.3  1  MarR             MarR family
    9.3e-06   25.4   0.5      2e-05   24.4   0.5    1.6  1  TrmB             Sugar-specific transcriptional regulator Trm
    2.6e-05   24.0   0.1    5.1e-05   23.1   0.1    1.5  1  HTH_5            Bacterial regulatory protein, arsR family
    0.00011   22.7   0.2    0.00023   21.6   0.2    1.5  1  HTH_27           Winged helix DNA-binding domain
    0.00092   19.2   0.0     0.0015   18.6   0.0    1.3  1  HTH_20           Helix-turn-helix domain
     0.0014   18.6   0.1     0.0026   17.7   0.1    1.4  1  HTH_Crp_2        Crp-like helix-turn-helix domain
     0.0026   17.3   0.1     0.0045   16.5   0.1    1.5  1  HTH_24           Winged helix-turn-helix DNA-binding
     0.0029   17.4   0.0     0.0044   16.8   0.0    1.3  1  HTH_IclR         IclR helix-turn-helix domain
     0.0032   17.5   0.0     0.0049   17.0   0.0    1.2  1  DprA_WH          DprA winged helix domain
     0.0096   16.0   0.2      0.018   15.1   0.2    1.4  1  DUF2250          Uncharacterized protein conserved in archaea
  ------ inclusion threshold ------
      0.035   14.5   0.1      0.062   13.7   0.1    1.4  1  HTH_26           Cro/C1-type HTH DNA-binding domain
       0.12   12.4   0.0       0.26   11.2   0.0    1.5  1  HTH_37           Helix-turn-helix domain
       0.12   12.7   0.1       0.24   11.8   0.1    1.4  1  Penicillinase_R  Penicillinase repressor
       0.12   12.4   1.0       0.23   11.5   0.3    1.8  2  Sulfolobus_pRN   Sulfolobus plasmid regulatory protein
       0.16   12.2   0.1       0.36   11.1   0.1    1.6  1  DUF4841          Domain of unknown function (DUF4841)


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 !   31.3   0.0   1.2e-10   1.4e-07      12      60 ..     229     271 ..     223     273 .. 0.86

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 1.2e-10
                                       HHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSS CS
                            MarR_2  12 aaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeDk 60 
                                         L+ rp   + ++el++rlg sk+ vs +lk ++++GL+er+++   +
  gi|242399074|ref|YP_002994498.1| 229 EILRERP---MYQSELVKRLGFSKAKVSLLLKNMEKRGLIERVKD---G 271
                                       4455665...9********************************85...4 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.1   4.2e-10   4.7e-07      12      52 ..     230     270 ..     226     272 .. 0.91

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 4.2e-10
                                       HHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE CS
                              MarR  12 lyeqgplsvseLakklgvskstvtrvldrLekkGlieRsks 52 
                                       + ++ p+++seL k+lg sk+ v+ +l+ +ek+GlieR k+
  gi|242399074|ref|YP_002994498.1| 230 ILRERPMYQSELVKRLGFSKAKVSLLLKNMEKRGLIERVKD 270
                                       556789********************************987 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   0.5   1.7e-08     2e-05       9      62 ..     223     276 ..     216     281 .] 0.82

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 1.7e-08
                                       HCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES.STTTEE CS
                              TrmB   9 yEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerek.grpklY 62 
                                        E kv + +l++ p+  +e+ ++lg +++kv   L+++e++Gl+er+k gr++l 
  gi|242399074|ref|YP_002994498.1| 223 DEEKV-IEILRERPMYQSELVKRLGFSKAKVSLLLKNMEKRGLIERVKdGRTYLV 276
                                       55555.5678999**********************************94445555 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.1   4.5e-08   5.1e-05       6      46 ..     226     266 ..     225     267 .. 0.96

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 4.5e-08
                                       HHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5   6 kILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46 
                                       k++ +L+e++++ +el++ lg s+++vS  Lk +++ GL+e
  gi|242399074|ref|YP_002994498.1| 226 KVIEILRERPMYQSELVKRLGFSKAKVSLLLKNMEKRGLIE 266
                                       68999**********************************97 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.2   2.1e-07   0.00023      12      63 ..     231     277 ..     223     278 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 2.1e-07
                            HTH_27  12 irhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvr 63 
                                       +r  +r++ +++l++rl ++++ +s  lk ++++GL+er    +d+r+ +v+
  gi|242399074|ref|YP_002994498.1| 231 LR--ERPMYQSELVKRLGFSKAKVSLLLKNMEKRGLIERV---KDGRTYLVK 277
                                       44..899999***************************999...778998886 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.3e-06    0.0015      15      61 .]     227     272 ..     226     272 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.3e-06
                                       HHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTEE CS
                            HTH_20  15 ilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvregr 61 
                                       +   L r++++  sel +rl+ sk+ +s  L+ +e+ gL+e+v+ gr
  gi|242399074|ref|YP_002994498.1| 227 VIEIL-RERPMYQSELVKRLGFSKAKVSLLLKNMEKRGLIERVKDGR 272
                                       66778.9*************************************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 !   17.7   0.1   2.3e-06    0.0026      18      55 ..     232     272 ..     209     281 .] 0.75

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.3e-06
                                       EEEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE..E.TE CS
                         HTH_Crp_2  18 ielpltqeelAsmlGltretvsrilseLkreglis..r.gr 55 
                                        e p+ q el  +lG +   vs +l+ ++++gli+  + gr
  gi|242399074|ref|YP_002994498.1| 232 RERPMYQSELVKRLGFSKAKVSLLLKNMEKRGLIErvKdGR 272
                                       3569*******************************532334 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1     4e-06    0.0045      18      48 .]     236     266 ..     224     266 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4e-06
                            HTH_24  18 isqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                                       + q+eL +rlg S++ v+  lk++e+ GlI+
  gi|242399074|ref|YP_002994498.1| 236 MYQSELVKRLGFSKAKVSLLLKNMEKRGLIE 266
                                       5599**************************7 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0     4e-06    0.0044      16      50 ..     233     267 ..     226     269 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 4e-06
                                       BSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR  16 pqeltlselArrtglpkStvhRlLqtLvelGyveq 50 
                                        +++  sel +r+g +k++v+ lL+ ++++G++e+
  gi|242399074|ref|YP_002994498.1| 233 ERPMYQSELVKRLGFSKAKVSLLLKNMEKRGLIER 267
                                       466889***************************98 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   4.3e-06    0.0049      10      61 .]     220     271 ..     213     271 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.3e-06
                           DprA_WH  10 lddlerrvLaaLgpePvhvDqLvrrtglpaaevsaaLleLELaGlverlpGg 61 
                                       l ++e++v + L   P+   +Lv+r+g++ a vs +L ++E  Gl+er  +g
  gi|242399074|ref|YP_002994498.1| 220 LRSDEEKVIEILRERPMYQSELVKRLGFSKAKVSLLLKNMEKRGLIERVKDG 271
                                       6689********************************************8766 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 !   15.1   0.2   1.6e-05     0.018      12      57 ..     226     270 ..     217     280 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.6e-05
                           DUF2250  12 kvlkhlkkanvdYaksiakeleipleevrellkkLeelGLlerveg 57 
                                       kv+++l++  + Y   ++k+l  ++ +v+ llk++e+ GL+erv+ 
  gi|242399074|ref|YP_002994498.1| 226 KVIEILRE-RPMYQSELVKRLGFSKAKVSLLLKNMEKRGLIERVKD 270
                                       56666654.5779999***************************984 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   5.5e-05     0.062       4      34 ..     229     259 ..     226     268 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.5e-05
                            HTH_26   4 elmadrgitkseLargtgisaatlsrlvkgk 34 
                                       e++++r + +seL +++g+s+a++s l+k+ 
  gi|242399074|ref|YP_002994498.1| 229 EILRERPMYQSELVKRLGFSKAKVSLLLKNM 259
                                       7999************************984 PP

>> HTH_37  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   0.00024      0.26      23      55 ..     227     259 ..     214     270 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00024
                                       HHHHHHHCT--HHHHHHHHT--HHHHHHHHTT- CS
                            HTH_37  23 iaeliekrelsqseaaqllgiaqPkvsrllrgk 55 
                                       ++e++++r   qse+ ++lg +++kvs ll+  
  gi|242399074|ref|YP_002994498.1| 227 VIEILRERPMYQSELVKRLGFSKAKVSLLLKNM 259
                                       78999*************************855 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00021      0.24       5      60 ..     224     274 ..     222     277 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00021
                                       -SHHHHHHHHHS-EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEETTEE CS
                   Penicillinase_R   5 EaevmeilwekgeatvkevveeleeekelaysTVktllrrLvkKgllsrekegraf 60 
                                       E++v+eil+e+  +  +e+v++l      +++ V  ll++++k+gl++r k+gr++
  gi|242399074|ref|YP_002994498.1| 224 EEKVIEILRERP-MYQSELVKRL----GFSKAKVSLLLKNMEKRGLIERVKDGRTY 274
                                       556666665543.3334445555....456889*********************99 PP

>> Sulfolobus_pRN  Sulfolobus plasmid regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       5.9   6.6e+03      53      67 ..     107     121 ..     103     123 .. 0.84
   2 ?   11.5   0.3    0.0002      0.23       7      50 ..     224     267 ..     218     277 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 5.9
                    Sulfolobus_pRN  53 rkiaGkkvreyclky 67 
                                       + i Gkk   y lk+
  gi|242399074|ref|YP_002994498.1| 107 QDINGKKQFSYYLKF 121
                                       678999999999996 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.0002
                    Sulfolobus_pRN   7 sekillilsrrcatleeleektGiekeellvyltrlykrGlisr 50 
                                        ek++ il  r +   el  + G  k ++ + l  + krGli r
  gi|242399074|ref|YP_002994498.1| 224 EEKVIEILRERPMYQSELVKRLGFSKAKVSLLLKNMEKRGLIER 267
                                       689999************************************98 PP

>> DUF4841  Domain of unknown function (DUF4841)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00032      0.36      23      67 ..      28      70 ..      19      73 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00032
                           DUF4841 23 vdesksieLeiPtavqtlYvqYptasGkkevkevpvkvstradks 67
                                       +++ +i+ ++P +  t Y qYp  +  ++++e++   ++ a+ s
  gi|242399074|ref|YP_002994498.1| 28 ETIEITISPNVPLSRYTFYSQYPIENP-EAIVEINGR-TQIANVS 70
                                      455668999****************99.999999866.6666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); 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: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1849.19
//
Query:       gi|242399075|ref|YP_002994499.1|  [L=628]
Description: phosphoadenosine 5'-phosphosulfate reductase, fused to RNA-binding PUA and 4Fe-4S binding domains [Thermococcus sibiricus MM 739]
Scores for complete 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-43  148.1   0.0    7.6e-43  146.6   0.0    1.9  1  PAPS_reduct     Phosphoadenosine phosphosulfate reductase fam
    1.4e-14   53.8   1.8    1.4e-14   53.8   1.8    1.8  1  PUA             PUA domain
    6.3e-11   41.6  16.4      8e-06   25.5   4.9    2.7  2  Fer4            4Fe-4S binding domain
    1.1e-09   38.7  11.3    3.4e-09   37.1  11.3    1.8  1  Fer4_7          4Fe-4S dicluster domain
    4.6e-09   36.3   9.8    1.4e-08   34.8   9.8    1.9  1  Fer4_9          4Fe-4S dicluster domain
    2.1e-07   30.9  10.3    2.1e-07   30.9  10.3    1.9  1  Fer4_10         4Fe-4S dicluster domain
    5.1e-07   29.7   9.1    1.5e-06   28.2   9.1    1.8  1  Fer4_21         4Fe-4S dicluster domain
    1.8e-06   27.7  11.8    0.00017   21.4   2.3    2.7  2  Fer4_2          4Fe-4S binding domain
    1.9e-06   28.7   8.7      0.018   16.0   0.2    3.7  3  Fer4_16         4Fe-4S double cluster binding domain
    3.2e-06   27.5   5.8      0.027   14.9   0.8    2.9  2  Fer4_8          4Fe-4S dicluster domain
    6.8e-06   25.9  15.6    6.5e-05   22.8   2.4    2.7  2  Fer4_6          4Fe-4S binding domain
    6.4e-05   23.4  13.5      0.015   15.8   1.1    2.9  2  Fer4_17         4Fe-4S dicluster domain
    0.00057   20.2  17.0     0.0038   17.6   1.9    3.1  2  Fer4_4          4Fe-4S binding domain
     0.0038   18.0   4.6        0.2   12.5   0.3    2.9  2  Fer4_22         4Fe-4S dicluster domain
     0.0075   16.8   9.9      0.086   13.4   1.3    2.8  2  Fer4_13         4Fe-4S single cluster domain of Ferredoxin I
     0.0077   16.0   0.0      0.021   14.6   0.0    1.8  1  ATP_bind_3      PP-loop family
  ------ inclusion threshold ------
      0.013   15.7   0.2      0.037   14.3   0.2    1.8  1  UPF0113         UPF0113 PUA domain
      0.014   16.3   3.6      0.014   16.3   3.6    3.0  2  Fer4_3          4Fe-4S binding domain
      0.029   15.1  10.9       0.19   12.5   1.2    3.2  3  Fer4_15         4Fe-4S single cluster domain
      0.078   12.8   0.3       0.18   11.7   0.3    1.6  1  PUA_3           PUA-like domain
      0.089   13.0  10.7       0.31   11.3   2.3    2.5  2  Fer4_18         4Fe-4S dicluster domain
       0.21   11.5   3.8        0.9    9.5   0.2    2.8  3  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an


Domain annotation for each model (and alignments):
>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.6   0.0   9.3e-46   7.6e-43       4     173 ..     253     427 ..     250     428 .. 0.97

  Alignments for each domain:
  == domain 1  score: 146.6 bits;  conditional E-value: 9.3e-46
                                       EE--SSCTCHHHHHHHHHHCTT.HEEEEEE-STB-HHHHHHHHHHHHHT...T-EEEEEE-SCHHHHHHHHHH-S-T CS
                       PAPS_reduct   4 vsvsgGkdslVllhLalkafkp.vpvvfvdtghefpetiefvdeleery...glrlkvyepeeevaekinaekhgss 76 
                                       v++sgGkdsl++l L+l+ f + + v+f +tg efpet+e++d ++e++   ++++++++ ++ +++++  ++ + +
  gi|242399075|ref|YP_002994499.1| 253 VAFSGGKDSLAVLGLMLEEFGEnFFVFFNNTGIEFPETLEYIDMVKENLkekNIKFIIADAKDAFWRALSIFSPPGR 329
                                       79******************99668************************999999********************** PP

                                       HHHCHHHHHHTHHHHHHHHHCT..TECEEE----CCCTTTTTTSSSEEECTTT-SCEEE-CCCT--HHHHHHHHHHC CS
                       PAPS_reduct  77 lyeeaaeriaKveplkkaLekl..dedalltGaRrdesksraklpiveidedfekslrvfPllnWteedvwqyilre 151
                                       +y++ +++++K+ p++ +++++  d +++++G+R++es +r k+p v+++ + ++ +   P+++W+  +vw yi ++
  gi|242399075|ref|YP_002994499.1| 330 DYRW-CCKVTKLGPITLTIKRYypDGVLMFVGQRKYESIQRYKQPRVWKNPWVPNEIGASPIFHWNALEVWLYIFSR 405
                                       ****.*****************9999*************************************************** PP

                                       T--B-CCCCTT-SS--BCTTB- CS
                       PAPS_reduct 152 nipynpLydqgfrsiGcvpctg 173
                                       +++ynpLy++  ++iGc++c++
  gi|242399075|ref|YP_002994499.1| 406 ELKYNPLYENRVDRIGCFMCPS 427
                                       ********************86 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.8   1.8   1.7e-17   1.4e-14       2      72 ..     133     204 ..     132     205 .. 0.95

  Alignments for each domain:
  == domain 1  score: 53.8 bits;  conditional E-value: 1.7e-17
                                       EEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHC.TSEEEEEEE CS
                               PUA   2 rvvvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakik.ggksveier 72 
                                        v+vd+gA + +++ga++l+ G++e+e +++ gd V++v+edg ++a G+a+  +e l + + +g +v++++
  gi|242399075|ref|YP_002994499.1| 133 WVIVDKGAKEPIKNGANVLPVGIIEAEASIKVGDDVVVVSEDGDVIATGIAKKGWEKLIDKNeRGTGVKTRH 204
                                       79******************************************************9988888999999887 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   3.7   2.2e-07   0.00018       7      23 ..     572     588 ..     568     589 .. 0.92
   2 !   25.5   4.9   9.8e-09     8e-06       1      19 [.     597     615 ..     597     616 .. 0.95

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 2.2e-07
                                       TSSS-THHHHHSTTTEE CS
                              Fer4   7 kCigCGaCvevCPvgAI 23 
                                        C+gCG Cv  CP +A+
  gi|242399075|ref|YP_002994499.1| 572 ECVGCGVCVGRCPENAL 588
                                       6***************8 PP

  == domain 2  score: 25.5 bits;  conditional E-value: 9.8e-09
                                       EEEETTTSSS-THHHHHST CS
                              Fer4   1 vvideekCigCGaCvevCP 19 
                                       +++d+ekCi+C +CvevCP
  gi|242399075|ref|YP_002994499.1| 597 IEVDWEKCIHCRECVEVCP 615
                                       589**************** PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1  11.3   4.2e-12   3.4e-09       2      49 ..     573     615 ..     572     616 .. 0.95

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 4.2e-12
                            Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCP 49 
                                       C+gCg Cv  Cp +a++++       t+k+e+d ekC++C++Cv+vCP
  gi|242399075|ref|YP_002994499.1| 573 CVGCGVCVGRCPENALRINSN-----TRKIEVDWEKCIHCRECVEVCP 615
                                       ******************987.....789******************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 !   34.8   9.8   1.7e-11   1.4e-08       1      47 [.     572     615 ..     572     619 .. 0.93

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 1.7e-11
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCp 47 
                                       +C+gCg Cv  Cp ++ +  +++rk+++++   e+Ci+C++Cve+Cp
  gi|242399075|ref|YP_002994499.1| 572 ECVGCGVCVGRCPENALRINSNTRKIEVDW---EKCIHCRECVEVCP 615
                                       5**************************976...58***********9 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9  10.3   2.6e-10   2.1e-07       8      56 .]     572     615 ..     566     615 .. 0.94

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 2.6e-10
                           Fer4_10   8 tCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                        C++Cg Cv  CP      +a  ++s+  +++++ ekC++c +Cve+CP
  gi|242399075|ref|YP_002994499.1| 572 ECVGCGVCVGRCPE-----NALRINSNTRKIEVDWEKCIHCRECVEVCP 615
                                       6*************.....999**************************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 !   28.2   9.1   1.9e-09   1.5e-06       7      53 ..     572     616 ..     566     620 .. 0.85

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 1.9e-09
                           Fer4_21   7 kCigCgkCliaCedtshqaieidak.tvlkvvedeCvGCnlCssvCPv 53 
                                       +C+gCg C+  C++   +a++i+++ ++++v  ++C+ C  C++vCP+
  gi|242399075|ref|YP_002994499.1| 572 ECVGCGVCVGRCPE---NALRINSNtRKIEVDWEKCIHCRECVEVCPL 616
                                       7************7...7788776515779999**************7 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   2.2   0.00056      0.45      10      22 .]     573     585 ..     565     585 .. 0.91
   2 !   21.4   2.3   2.1e-07   0.00017       2      21 ..     596     615 ..     595     616 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00056
                            Fer4_2  10 CigCgaCvsaCPa 22 
                                       C+gCg Cv  CP+
  gi|242399075|ref|YP_002994499.1| 573 CVGCGVCVGRCPE 585
                                       ***********95 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 2.1e-07
                            Fer4_2   2 pvvvdtdrCigCgaCvsaCP 21 
                                       +++vd ++Ci+C+ Cv +CP
  gi|242399075|ref|YP_002994499.1| 596 KIEVDWEKCIHCRECVEVCP 615
                                       689****************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 ?   -1.0   0.0       4.3   3.5e+03      11      40 ..     424     453 ..     420     460 .. 0.69
   2 !   16.0   0.2   2.2e-05     0.018       2      20 ..     573     591 ..     555     601 .. 0.86
   3 !   13.7   2.6   0.00012     0.094       1      22 [.     603     624 ..     603     627 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 4.3
                           Fer4_16  11 vCPtnaikekkekeiearecisyntaekkd 40 
                                       +CP++ + e +  + e++e  ++ ++e ++
  gi|242399075|ref|YP_002994499.1| 424 MCPSSSLAEFQTLKEEKPEIWKNWENELRK 453
                                       799999998866666666666665555555 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 2.2e-05
                           Fer4_16   2 CgtCgkCaevCPtnaikek 20 
                                       C++Cg C+  CP+na++ +
  gi|242399075|ref|YP_002994499.1| 573 CVGCGVCVGRCPENALRIN 591
                                       9999999999999999866 PP

  == domain 3  score: 13.7 bits;  conditional E-value: 0.00012
                           Fer4_16   1 rCgtCgkCaevCPtnaikekke 22 
                                       +C+ C++C+evCP   ik+++e
  gi|242399075|ref|YP_002994499.1| 603 KCIHCRECVEVCPLLKIKNPQE 624
                                       5************999999855 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.1   6.5e-05     0.053      44      64 ..     562     586 ..     533     587 .. 0.73
   2 !   14.9   0.8   3.4e-05     0.027       3      22 ..     602     621 ..     600     627 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.5e-05
                            Fer4_8  44 e....eealwsCttcgaCtevCpvg 64 
                                       +     + +++C++cg C+ +Cp++
  gi|242399075|ref|YP_002994499.1| 562 QayylIKRAYECVGCGVCVGRCPEN 586
                                       1444467789999999999999986 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 3.4e-05
                            Fer4_8   3 ekCieCgaCqsaCpvlrrtk 22 
                                       ekCi+C  C + Cp+l+ ++
  gi|242399075|ref|YP_002994499.1| 602 EKCIHCRECVEVCPLLKIKN 621
                                       79999999999999998776 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   5.5    0.0043       3.5       9      24 .]     573     588 ..     573     588 .. 0.97
   2 !   22.8   2.4     8e-08   6.5e-05       1      20 [.     596     615 ..     596     620 .. 0.95

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0043
                            Fer4_6   9 CigCgdCvrvCPegai 24 
                                       C+gCg Cv  CPe+a+
  gi|242399075|ref|YP_002994499.1| 573 CVGCGVCVGRCPENAL 588
                                       **************97 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 8e-08
                            Fer4_6   1 vveidpdkCigCgdCvrvCP 20 
                                       ++e+d +kCi+C++Cv vCP
  gi|242399075|ref|YP_002994499.1| 596 KIEVDWEKCIHCRECVEVCP 615
                                       689999*************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 !   15.8   1.1   1.8e-05     0.015      34      59 ..     557     586 ..     540     588 .. 0.74
   2 !   13.7   3.1   8.3e-05     0.067      40      57 ..     598     615 ..     586     619 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.8e-05
                           Fer4_17  34 leeaeke....ekaslCieCgeCerkCPqg 59 
                                        +e+++     ++a +C++Cg C+ +CP++
  gi|242399075|ref|YP_002994499.1| 557 ENEIMQAyyliKRAYECVGCGVCVGRCPEN 586
                                       33333335676899**************97 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 8.3e-05
                           Fer4_17  40 eekaslCieCgeCerkCP 57 
                                       e  +++Ci+C+eC+++CP
  gi|242399075|ref|YP_002994499.1| 598 EVDWEKCIHCRECVEVCP 615
                                       34799************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 !   11.2   2.7   0.00052      0.42       3      16 ..     572     585 ..     568     589 .. 0.89
   2 !   17.6   1.9   4.7e-06    0.0038       2      15 ..     602     615 ..     601     624 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00052
                            Fer4_4   3 rCigCgsCvaaCPq 16 
                                        C+gCg+Cv  CP 
  gi|242399075|ref|YP_002994499.1| 572 ECVGCGVCVGRCPE 585
                                       5*********9995 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 4.7e-06
                            Fer4_4   2 erCigCgsCvaaCP 15 
                                       e+Ci+C+ Cv +CP
  gi|242399075|ref|YP_002994499.1| 602 EKCIHCRECVEVCP 615
                                       89************ PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.3   0.00024       0.2      78      95 ..     569     586 ..     541     587 .. 0.79
   2 ?    5.8   0.5      0.03        25       1      13 [.     603     615 ..     598     624 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00024
                           Fer4_22  78 gesgCvGCgRCieacpvk 95 
                                        ++ CvGCg C+ +cp++
  gi|242399075|ref|YP_002994499.1| 569 RAYECVGCGVCVGRCPEN 586
                                       5689***********986 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.03
                           Fer4_22   1 rClsCgaCtlvCp 13 
                                       +C++C +C  vCp
  gi|242399075|ref|YP_002994499.1| 603 KCIHCRECVEVCP 615
                                       6999999999998 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 ?    7.0   1.8     0.011       8.7       5      18 ..     572     585 ..     570     586 .. 0.93
   2 !   13.4   1.3   0.00011     0.086       1      17 [.     599     615 ..     599     624 .. 0.95

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.011
                           Fer4_13   5 tCiacgaCvelaPd 18 
                                       +C++cg+Cv  +P+
  gi|242399075|ref|YP_002994499.1| 572 ECVGCGVCVGRCPE 585
                                       7************8 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00011
                           Fer4_13   1 VDrdtCiacgaCvelaP 17 
                                       VD ++Ci c  Cve++P
  gi|242399075|ref|YP_002994499.1| 599 VDWEKCIHCRECVEVCP 615
                                       899*************9 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   2.6e-05     0.021       2      67 ..     251     314 ..     250     334 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.6e-05
                                       EEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSS.TCHHHHHHHHHHHHHHTT-EEEEEE-- CS
                        ATP_bind_3   2 vlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglr.eeskeeaelvkelckklnikleiekvd 67 
                                       v vA+SgG DS+a l l+ ++   +g +++++  + g+  +e+ e  ++vke  k+ nik++i++++
  gi|242399075|ref|YP_002994499.1| 251 VGVAFSGGKDSLAVLGLMLEE---FGENFFVFFNNTGIEfPETLEYIDMVKENLKEKNIKFIIADAK 314
                                       569*************99998...55699**********99********************999877 PP

>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.2   4.6e-05     0.037       2      54 ..     134     186 ..     133     205 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.6e-05
                           UPF0113   2 vvvkekaeklFLYGrdvlkesilkitesvkenqvvvVlnengeplGiGkirkd 54 
                                       v+v++ a++ +  G +vl  +i++ + s+k ++ vvV++e+g++++ G+++k 
  gi|242399075|ref|YP_002994499.1| 134 VIVDKGAKEPIKNGANVLPVGIIEAEASIKVGDDVVVVSEDGDVIATGIAKKG 186
                                       67888888888889***********************************9764 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   7.4     0.015        12       1      15 []     573     587 ..     573     587 .. 0.98
   2 ?   16.3   3.6   1.7e-05     0.014       1      12 [.     604     615 ..     604     619 .. 0.95

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.015
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C+gCg Cv  CP++A
  gi|242399075|ref|YP_002994499.1| 573 CVGCGVCVGRCPENA 587
                                       *************98 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 1.7e-05
                            Fer4_3   1 CtgCgaCvevCP 12 
                                       C++C+ CvevCP
  gi|242399075|ref|YP_002994499.1| 604 CIHCRECVEVCP 615
                                       ************ PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       9.2   7.5e+03       9      22 ..     420     433 ..     419     446 .. 0.70
   2 ?    6.6   1.7     0.016        13       7      20 ..     572     585 ..     570     589 .. 0.91
   3 ?   12.5   1.2   0.00024      0.19       1      19 [.     597     615 ..     597     622 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 9.2
                           Fer4_15   9 igcglCvaeapevf 22 
                                       igc++C   +   f
  gi|242399075|ref|YP_002994499.1| 420 IGCFMCPSSSLAEF 433
                                       79****87765444 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.016
                           Fer4_15   7 aCigcglCvaeape 20 
                                       +C gcg+Cv ++pe
  gi|242399075|ref|YP_002994499.1| 572 ECVGCGVCVGRCPE 585
                                       6***********97 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 0.00024
                           Fer4_15   1 VvvDrdaCigcglCvaeap 19 
                                       ++vD+++Ci c  Cv+++p
  gi|242399075|ref|YP_002994499.1| 597 IEVDWEKCIHCRECVEVCP 615
                                       79****************8 PP

>> PUA_3  PUA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.3   0.00022      0.18       1      51 [.     134     183 ..     134     186 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00022
                             PUA_3   1 viLkkkaekrlrqGhPwvfsneiasvegeledGdvVdvfsekgkflGtGyy 51 
                                       vi+ k+a   +++G   +  + i+  +  ++ Gd V v+se+g  ++tG+ 
  gi|242399075|ref|YP_002994499.1| 134 VIVDKGAKEPIKNGANVLPVGIIEAEA-SIKVGDDVVVVSEDGDVIATGIA 183
                                       789999999999999888777777666.7********************86 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3  11.5     0.026        21      56      95 ..     568     614 ..     547     614 .. 0.69
   2 ?   11.3   2.3   0.00038      0.31      53      73 ..     596     616 ..     585     627 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.026
                           Fer4_18  56 kgagdcidcescvkvcPtg.idirkGlq.l.....eciscllcidac 95 
                                       k a +c+ c++cv  cP + + i    + +     +ci c +c++ c
  gi|242399075|ref|YP_002994499.1| 568 KRAYECVGCGVCVGRCPENaLRINSNTRkIevdweKCIHCRECVEVC 614
                                       56789************7524554332212122336********999 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00038
                           Fer4_18  53 rkekgagdcidcescvkvcPt 73 
                                       + e +  +ci+c+ cv+vcP 
  gi|242399075|ref|YP_002994499.1| 596 KIEVDWEKCIHCRECVEVCPL 616
                                       44556789************6 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 ?   -3.1   0.0       9.8     8e+03      12      19 ..      42      49 ..      42      58 .. 0.74
   2 ?    9.5   0.2    0.0011       0.9      10      38 ..     150     178 ..     145     185 .. 0.80
   3 ?    2.3   0.1      0.21   1.7e+02      13      31 ..     480     498 ..     480     507 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 9.8
                                      -CCCHHHC CS
                    MazE_antitoxin 12 Pkevrfel 19
                                      P++vrf+ 
  gi|242399075|ref|YP_002994499.1| 42 PADVRFAF 49
                                      99***986 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0011
                                       EE-CCCHHHC.CEECTCEEEEEECTTCCCC CS
                    MazE_antitoxin  10 riPkevrfel.gireGdevelevdgdkiil 38 
                                       ++P  + ++   i++Gd+v+++ +++ +++
  gi|242399075|ref|YP_002994499.1| 150 VLPVGIIEAEaSIKVGDDVVVVSEDG-DVI 178
                                       78999999999**********87775.554 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.21
                                       CCCHHHCCEECTCEEEEEE CS
                    MazE_antitoxin  13 kevrfelgireGdevelev 31 
                                       k+v++elgi+   + ++e+
  gi|242399075|ref|YP_002994499.1| 480 KAVARELGIKIPEKRIWEP 498
                                       89*********99999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (628 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       926  (0.0516482); expected 358.6 (0.02)
Passed bias filter:                      658  (0.0367003); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.70u 0.33s 00:00:01.03 Elapsed: 00:00:00.48
# Mc/sec: 3954.00
//
Query:       gi|242399076|ref|YP_002994500.1|  [L=78]
Description: hypothetical protein TSIB_1097 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); 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 0.30s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 506.64
//
Query:       gi|242399077|ref|YP_002994501.1|  [L=444]
Description: hypothetical protein TSIB_1098 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0036   17.1   0.0       0.12   12.1   0.0    2.4  1  DUF4139   Domain of unknown function (DUF4139)
  ------ inclusion threshold ------
      0.023   14.4   0.1       0.11   12.2   0.0    2.2  2  LSM       LSM domain
      0.075   13.2   0.2       0.42   10.8   0.1    2.2  3  SM-ATX    Ataxin 2 SM domain


Domain annotation for each model (and alignments):
>> DUF4139  Domain of unknown function (DUF4139)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0     2e-05      0.12     171     206 ..     409     444 .]     176     444 .] 0.63

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2e-05
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DUF4139 171 epskaevdkdtgilewklklapgekkkiefsyevky 206
                                       e+s +  +++ +++e k+++ pgek++i f+yev+y
  gi|242399077|ref|YP_002994501.1| 409 ESSISPINETADYVEFKVTVNPGEKEEIIFDYEVRY 444
                                       3344455778889*********************98 PP

>> LSM  LSM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.8e-05      0.11       3      28 ..     101     126 ..      99     128 .. 0.87
   2 ?   -2.9   0.0      0.98   5.8e+03      36      58 ..     362     383 ..     360     384 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.8e-05
                                       HHHTTTSEEEEEETTSEEEEEEEEEE CS
                               LSM   3 lkklinkkvtvelkngrelrGtLkgf 28 
                                       ++  i+k++t++lk+g++++G++ g+
  gi|242399077|ref|YP_002994501.1| 101 IEANIGKEITIKLKSGETISGKFLGY 126
                                       56679****************99876 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.98
                                       EEEEEEEETTETEEEEEEEEEEE CS
                               LSM  36 LedveetlkdkkekrklglvliR 58 
                                       L+ ++e+l++  ++ ++g++ iR
  gi|242399077|ref|YP_002994501.1| 362 LKGTTEVLEER-HDDHYGYYKIR 383
                                       77889999888.99999998887 PP

>> SM-ATX  Ataxin 2 SM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.3   7.8e+03      29      44 ..      24      40 ..      24      57 .. 0.80
   2 ?   10.8   0.1     7e-05      0.42       8      33 ..     101     126 ..      99     136 .. 0.85
   3 ?   -2.3   0.0      0.88   5.3e+03       6      16 ..     241     251 ..     240     251 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.3
                                      EEEEE-T...T--EEEE CS
                            SM-ATX 29 ifstvsl.ekdfsvvLk 44
                                      if+ ++  e+++s++L 
  gi|242399077|ref|YP_002994501.1| 24 IFHQTQAqEDQTSIALY 40
                                      89999998889999885 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 7e-05
                                       HHTTTTSEEEEEETTS-EEEEEEEEE CS
                            SM-ATX   8 ltslvGkevevtvknGevyeGifstv 33 
                                       + + +Gke+++++k+Ge+++G f ++
  gi|242399077|ref|YP_002994501.1| 101 IEANIGKEITIKLKSGETISGKFLGY 126
                                       6778*****************88665 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 0.88
                                       HHHHTTTTSEE CS
                            SM-ATX   6 flltslvGkev 16 
                                       +++ s+vGkev
  gi|242399077|ref|YP_002994501.1| 241 YATESMVGKEV 251
                                       8999*****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (444 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); 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: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 2717.81
//
Query:       gi|242399078|ref|YP_002994502.1|  [L=232]
Description: Acetyl-CoA synthetase I (ACSI, ADP-forming), subunit beta [Thermococcus sibiricus MM 739]
Scores for complete 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-81  273.3   0.5    1.5e-81  273.1   0.5    1.0  1  ATP-grasp_5      ATP-grasp domain
    4.3e-10   39.5   0.9    7.5e-10   38.7   0.9    1.5  1  ATP-grasp_2      ATP-grasp domain
    7.8e-05   22.5   0.3    0.00019   21.3   0.1    1.7  2  GARS_A           Phosphoribosylglycinamide synthetase, ATP-gr
    0.00013   21.6   0.0    0.00024   20.7   0.0    1.4  1  ATP-grasp        ATP-grasp domain
    0.00029   20.4   0.2    0.00085   18.9   0.1    1.8  2  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
  ------ inclusion threshold ------
      0.091   12.7   0.0       0.26   11.3   0.0    1.7  2  PI_PP_C          Phosphoinositide phosphatase C-terminal doma
       0.28   10.9   1.1        5.8    6.7   0.1    2.5  2  Ribosom_S30AE_C  Sigma 54 modulation/S30EA ribosomal protein 


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 !  273.1   0.5   5.7e-85   1.5e-81       5     221 ..      16     231 ..      12     232 .] 0.98

  Alignments for each domain:
  == domain 1  score: 273.1 bits;  conditional E-value: 5.7e-85
                       ATP-grasp_5   5 egrtlLteaeakelleaygipvvetrlassaeeaveaaeeigypvvlKivspdilhKtdvgGvrlnlkdaeevraaa 81 
                                       ++++ L e eake+l+ yg+pv+e+++a+++eeav+ a+eigypvv+Kivsp+i+hK+d+gGv++n+k++ee ++a+
  gi|242399078|ref|YP_002994502.1|  16 AENRPLVEPEAKEILQLYGVPVPEFKVATNEEEAVQFAREIGYPVVMKIVSPQIIHKSDAGGVKVNIKSDEEAKEAF 92 
                                       5567799********************************************************************** PP

                       ATP-grasp_5  82 eeilervkekspeariegvlVqemakrggrElivgvteDpvFGpvilfGlGGtavevlkdvavalpplnstlareli 158
                                       ++i++++k+++p+a + gv++ +m +  g E+ivg+ +Dp+FGp i+fGlGG+ ve+lkdv+++++p+++++a e+i
  gi|242399078|ref|YP_002994502.1|  93 NTIMKNAKNYKPDADLWGVIIYKMLP-LGKEVIVGMIRDPQFGPAIMFGLGGIFVEILKDVSFRVAPISKEEALEMI 168
                                       ************************99.9************************************************* PP

                       ATP-grasp_5 159 ertkaskllkgvrgekkadlaaleellvrlsqLvvdlpeIreldinPllveeegvvalDarir 221
                                       +++ka+++l g rgek+++++al+e+++++ +L+ +lpe++eldinP++++e+  va+Dari 
  gi|242399078|ref|YP_002994502.1| 169 KEIKAYPILAGARGEKPVNIEALAEIIMKVGELALELPEVKELDINPVFAYEDTSVAVDARIL 231
                                       *************************************************************95 PP

>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.7   0.9   2.9e-13   7.5e-10       2     199 ..      21     215 ..      20     218 .. 0.65

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 2.9e-13
                                       E-HHHHHHHHHCTT----SEEEESSHHHHHHHHHHHTSSSE..EEEE--SSSTCCCTTCEEEESSHHHHHHHHHCCT CS
                       ATP-grasp_2   2 lhEyqakeilakygvkvpegevaesaeeaeeaakklgekel..vvKaQvlaGGRGKagGvklvkskeeakeaakell 76 
                                       l E +akeil+ ygv+vpe++va+++eea + a+++g  ++  +v  Q+    +  agGvk+  + +e ++ a + +
  gi|242399078|ref|YP_002994502.1|  21 LVEPEAKEILQLYGVPVPEFKVATNEEEAVQFAREIGYPVVmkIVSPQIIH--KSDAGGVKVNIKSDEEAKEAFNTI 95 
                                       67889********************************99842245567775..789*****9655555444444555 PP

                                       TSEEE-TTS-TT-EEE--EEEEE---ECEEEEEEEEEETTTTEEEEEEESSTTS-HHHHHHH-GGGEEEEEEB.TTT CS
                       ATP-grasp_2  77 gkelvtkqtgkeGkkvekvlveealdikkElYlsivlDraskkvvviaSseGGvdiEevaakkPekiikvaid.pak 152
                                        k+ + +   k       v++ ++l++ kE+ ++++ D +  ++ +++   GG+ +E + + +  +++ ++ + + +
  gi|242399078|ref|YP_002994502.1|  96 MKNAKNY---KPDADLWGVIIYKMLPLGKEVIVGMIRDPQF-GPAIMF-GLGGIFVEILKDVS-FRVAPISKEeALE 166
                                       5555634...445668889999************9988664.455555.46777776443333.3333333320233 PP

                                       B--HHHHHHHHHHC.T--CHHHHHHHHHHHHHHHHHHHT.TEEEEEEEE CS
                       ATP-grasp_2 153 glkeeqareiakkl.glekelvkkaakiikklyklfvel.datlvEiNP 199
                                        +ke +a  i+  + g +   ++ +a+ii+k+ +l +el + + ++iNP
  gi|242399078|ref|YP_002994502.1| 167 MIKEIKAYPILAGArGEKPVNIEALAEIIMKVGELALELpEVKELDINP 215
                                       3344444444443303444566777777777777776653667777777 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 !   21.3   0.1   7.3e-08   0.00019       6      77 ..      26     102 ..      25     134 .. 0.72
   2 ?   -2.3   0.0       1.2   3.1e+03      59      71 ..     160     172 ..     154     192 .. 0.71

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 7.3e-08
                                       HHHHHHHTT--B--EEEESSHHHHHHHHHHHSSSEEEEE...ESC-..GGGT-EEEE.SSHHHHHHHHHHHCTS-TT CS
                            GARS_A   6 akdllkkagiptaeyeaftdpeeakeyieeatakalVvK...adgl..aagKgviva.kseeealkavkeilekkkf 76 
                                       ak++l+ +g+p +e+++ t+ eea ++ +e + ++ V+K   ++ +  +   gv+v  ks eea +a + i+++ k 
  gi|242399078|ref|YP_002994502.1|  26 AKEILQLYGVPVPEFKVATNEEEAVQFAREIGYPV-VMKivsPQIIhkSDAGGVKVNiKSDEEAKEAFNTIMKNAKN 101
                                       699*******************************9.65511144342233458888668899**********98765 PP

                                       C CS
                            GARS_A  77 G 77 
                                        
  gi|242399078|ref|YP_002994502.1| 102 Y 102
                                       4 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.2
                                       SHHHHHHHHHHHC CS
                            GARS_A  59 seeealkavkeil 71 
                                       s+eeal+++kei 
  gi|242399078|ref|YP_002994502.1| 160 SKEEALEMIKEIK 172
                                       6788888888874 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   9.2e-08   0.00024       4      84 ..      33     129 ..      30     143 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 9.2e-08
                                       TT--B-EEEEECCHHHHHHHHHHH-SCEEEE....ESSS-CTTTTEEE.ECTCCGHHCHHHHC...........GTT CS
                         ATP-grasp   4 lglpvprflaveskeeleeaaeelglpvvvK....arrlgydGkGqsv.vrseedleqaleal...........kee 64 
                                        g+pvp+f +++++ee+ ++a+e+g+pvv+K    + ++ +d  G +v ++s+e++++a++++           +  
  gi|242399078|ref|YP_002994502.1|  33 YGVPVPEFKVATNEEEAVQFAREIGYPVVMKivspQIIHKSDAGGVKVnIKSDEEAKEAFNTImknaknykpdaDLW 109
                                       69*****************************4444457889988887669999999999998877766666655555 PP

                                       CEEEEE----SEEEEEEEEE CS
                         ATP-grasp  65 kvivEefvpfekElsvlvvr 84 
                                        vi+ ++ p+ kE+ v ++r
  gi|242399078|ref|YP_002994502.1| 110 GVIIYKMLPLGKEVIVGMIR 129
                                       67777777777777666666 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 !   18.9   0.1   3.3e-07   0.00085       5     102 ..      26     130 ..      23     161 .. 0.60
   2 ?   -1.1   0.0      0.44   1.1e+03      22      42 ..     156     177 ..     143     183 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 3.3e-07
                                       HHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETT.......CCTTTTEEEESSHHHHHHHHHHHHHHH CS
                       CPSase_L_D2   5 akealkkinvpvvpssaapvetleealaiakeigyPviikaaf.......glGGkGmrvarneeelaelvkkalaea 74 
                                       ake+l+  +vpv + + a  +++eea+++a+eigyPv++k            GG    + +++ee +e++++ +++a
  gi|242399078|ref|YP_002994502.1|  26 AKEILQLYGVPVPEFKVA--TNEEEAVQFAREIGYPVVMKIVSpqiihksDAGGVKVNI-KSDEEAKEAFNTIMKNA 99 
                                       677777888887776666..99***************9884321111111233333333.44455556666555555 PP

                                       HHHHSTS...-EEEEE--SSSEEEEEEEEEE CS
                       CPSase_L_D2  75 kaafgnk...qvlvekslkgpkeiEvevlrD 102
                                       k    ++    v + k+l   ke+ v ++rD
  gi|242399078|ref|YP_002994502.1| 100 KNYKPDAdlwGVIIYKMLPLGKEVIVGMIRD 130
                                       4322222111355666666666666666665 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.44
                                       SSBSSHHHHHHHHHHH-.SSEE CS
                       CPSase_L_D2  22 apvetleealaiakeig.yPvi 42 
                                       ++  + eeal++ kei+ yP++
  gi|242399078|ref|YP_002994502.1| 156 VAPISKEEALEMIKEIKaYPIL 177
                                       4455778999999998549987 PP

>> PI_PP_C  Phosphoinositide phosphatase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0    0.0001      0.26      12      74 ..      90     150 ..      83     153 .. 0.93
   2 ?   -2.4   0.0       1.7   4.5e+03      57      73 ..     183     199 ..     166     205 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0001
                                       HHHHHHHTSGGGG---GGG-SSGGGTTS-S-HHHHHHHHHCSS---TTHHHHHHHHHHHHHHT CS
                           PI_PP_C  12 daLsalineeklfqekkkswslsffesssaPtGieqikellqdkksgkdnvlrlakIfeevle 74 
                                       +a + ++++ k +++ ++ w++ ++  +  P G e i  ++ d++ g + ++ l  If e+l+
  gi|242399078|ref|YP_002994502.1|  90 EAFNTIMKNAKNYKPDADLWGVIIY--KMLPLGKEVIVGMIRDPQFGPAIMFGLGGIFVEILK 150
                                       567899*******************..********************999999******9986 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.7
                                       -TTHHHHHHHHHHHHHH CS
                           PI_PP_C  57 sgkdnvlrlakIfeevl 73 
                                       ++  n++ la+I+++v 
  gi|242399078|ref|YP_002994502.1| 183 EKPVNIEALAEIIMKVG 199
                                       45567888999998885 PP

>> Ribosom_S30AE_C  Sigma 54 modulation/S30EA ribosomal protein C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1     0.046   1.2e+02       3      43 ..       7      47 ..       5      57 .. 0.81
   2 ?    6.7   0.1    0.0023       5.8       5      28 ..     147     170 ..     145     174 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.046
                                      XX-EEEEE-S--S-B-HHHHHHHHHHHT-SEEEEEETTTTE CS
                   Ribosom_S30AE_C  3 epeivrtkrfelkpmsveeAilqmellghdFfvFrnaetge 43
                                      ++ei+++ + e +p+ + eA++ ++l g ++  F+ a ++e
  gi|242399078|ref|YP_002994502.1|  7 AKEIIEKAKAENRPLVEPEAKEILQLYGVPVPEFKVATNEE 47
                                      6899*********************9998776666665555 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0023
                                       -EEEEE-S--S-B-HHHHHHHHHH CS
                   Ribosom_S30AE_C   5 eivrtkrfelkpmsveeAilqmel 28 
                                       ei +  +f + p+s eeA++ +++
  gi|242399078|ref|YP_002994502.1| 147 EILKDVSFRVAPISKEEALEMIKE 170
                                       799999************998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); 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: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1582.50
//
Query:       gi|242399079|ref|YP_002994503.1|  [L=265]
Description: hypothetical protein TSIB_1100 [Thermococcus sibiricus MM 739]
Scores for complete 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-65  218.9   5.6    9.1e-65  218.7   5.6    1.0  1  GCHY-1    Type I GTP cyclohydrolase folE2
  ------ inclusion threshold ------
       0.13   12.9   3.5        9.2    6.9   0.2    3.1  3  ATP-cone  ATP cone 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 !  218.7   5.6     1e-68   9.1e-65       2     259 .]       2     261 ..       1     261 [. 0.92

  Alignments for each domain:
  == domain 1  score: 218.7 bits;  conditional E-value: 1e-68
                                       XXXXXXXXXX----SEEEEEEEEEEEEE--TTTS-EEEEEEEEEEEES-SS--GGGGGHHHHHHH.HS-SSEEG... CS
                            GCHY-1   2 pDvqsekderkipldrVGvkgvklpvkvkdkekkaqtlvaevdlfvdLpaekkGihmSRlvevle.eaeeelee... 74 
                                        ++q+e +e++ +l+rVG++++++  +++ k+k   t++ ++++++d+p+ekkGihmSRlve+++ + +e++ee   
  gi|242399079|ref|YP_002994503.1|   2 FETQEEIPEIRERLHRVGITNLRTIARINWKGK-FYTFIPTFEITIDVPEEKKGIHMSRLVESITeTMSEAVEEevk 77 
                                       5789999***********************886.56*****************************555577776666 PP

                                       ...GGHHH....HHHHHHHHTT.-SEEEEEEEEEEEEEEE-TTT--EEEEEEEEEEEEEE..TTEEEEEEEEEEEEE CS
                            GCHY-1  75 ...kslee....ileellekleyaeraevelkfeyfiekkapvsgkeglesyevtleaelerkeevkltvgvevpvt 144
                                          +slee    i+++l +k+   +rae  +k+++++e+++p+s+k +le+y+v++ + +e  e+v+++++v + + 
  gi|242399079|ref|YP_002994503.1|  78 eahTSLEElglaIIRRLEKKHP-HRRAEAWIKTQLIMERETPASKKVTLETYDVEVGVIKEP-EKVEKVLKVIAIGN 152
                                       5665555599999999999999.9*********************99**********99965.37************ PP

                                       EE-HHHHHHS....SS---EEEEEEEEEEEE......--HHHHHHHHHHHSSEE--S---HHHHHHHHHHHHTS--- CS
                            GCHY-1 145 tlCPCskeisrelleagaHnQRsvvtvkvelaeeekeveiedlielvessassevyellKReDEkavtekayenpkF 221
                                       t+CP +++      +  +H QR+++t++++ ++ ++e+++ed+i++ve+s+ss++y+llK +DE+av++++y+npkF
  gi|242399079|ref|YP_002994503.1| 153 TACPHAMANN----QGKTHIQRAIATLEIR-TDYDEEIPLEDMIDVVEESFSSPTYTLLKTADENAVVQAMYSNPKF 224
                                       **********....99**************.77999***************************************** PP

                                       HHHHHHHHHHHHHS-TTEEEEEEEEEEE-TTTSSEEEE CS
                            GCHY-1 222 vEDvvRevaaaleeeerveefsveveneESiHnHnavA 259
                                       vEDv+Re++ ++ +++   +++v+v ++ESiH+H+++A
  gi|242399079|ref|YP_002994503.1| 225 VEDVAREIIFKA-RQRFKGNIHVRVLSHESIHKHDVIA 261
                                       ************.55566688***************98 PP

>> ATP-cone  ATP cone domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1      0.11   9.5e+02      34      66 ..      62      95 ..      51     108 .. 0.57
   2 ?    6.9   0.2     0.001       9.2      15      65 ..     141     198 ..     135     210 .. 0.68
   3 ?    4.6   0.0    0.0056        50      19      56 ..     211     248 ..     207     251 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.11
                                      HHHHHHHHHHHHHH.HIIT-BHHHHHHHHHHHHH CS
                          ATP-cone 34 deiaeeveaevrkr.lrdgisteeIqdlvektli 66
                                      + i+e++ + v+++ +++  s ee++  +++ l 
  gi|242399079|ref|YP_002994503.1| 62 ESITETMSEAVEEEvKEAHTSLEELGLAIIRRLE 95
                                      3444444444444434444555665555555554 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.001
                                       HHHHHHHHHHHHHH......-HHHHHHHHHHHH.HHHHHHHIIT-BHHHHHHHHHHHH CS
                          ATP-cone  15 vekIkraiekAceg......seeeideiaeeve.aevrkrlrdgisteeIqdlvektl 65 
                                       vek+ + i+    +      ++++   i + ++ +e+r  ++++i+ e++ d+ve+  
  gi|242399079|ref|YP_002994503.1| 141 VEKVLKVIAIGNTAcphamaNNQGKTHIQRAIAtLEIRTDYDEEIPLEDMIDVVEESF 198
                                       45555555444333445666677766666666557999999999***********975 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.0056
                                       HHHHHHHHHH-HHHHHHHHHHHHHHHHHHHIIT-BHHH CS
                          ATP-cone  19 kraiekAcegseeeideiaeeveaevrkrlrdgistee 56 
                                       ++a+  A+ ++++ ++++a+e++ ++r+r++ +i++  
  gi|242399079|ref|YP_002994503.1| 211 ENAVVQAMYSNPKFVEDVAREIIFKARQRFKGNIHVRV 248
                                       57899999999********************9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1103  (0.0615204); expected 358.6 (0.02)
Passed bias filter:                      649  (0.0361983); 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: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 1686.27
//
Query:       gi|242399080|ref|YP_002994504.1|  [L=247]
Description: hypothetical protein TSIB_1101 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-05   25.6   0.0     0.0013   19.0   0.0    2.2  2  DUF4129          Domain of unknown function (DUF4129)
     0.0015   19.0   0.0     0.0024   18.4   0.0    1.3  1  Syntaxin-6_N     Syntaxin 6, N-terminal
  ------ inclusion threshold ------
       0.03   13.7   6.8      0.042   13.2   6.8    1.2  1  Glucos_trans_II  Glucosyl transferase GtrII
      0.092   12.5   3.9        1.5    8.6   3.9    2.2  1  Oxidored_q3      NADH-ubiquinone/plastoquinone oxidoreductase
       0.36   11.3   3.7        2.7    8.5   0.5    2.6  2  ATP_synt_H       ATP synthase subunit H
        3.9    7.7   7.3         39    4.4   4.2    2.2  2  RDD              RDD family


Domain annotation for each model (and alignments):
>> DUF4129  Domain of unknown function (DUF4129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.015        44      17      29 ..      58      70 ..      56      89 .. 0.78
   2 !   19.0   0.0   4.3e-07    0.0013       2      68 ..     174     239 ..     173     240 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.015
                           DUF4129 17 rpgeTprEyarrv 29
                                      r+ +T +Ey+r++
  gi|242399080|ref|YP_002994504.1| 58 RRKRTKGEYLREL 70
                                      889*********9 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 4.3e-07
                           DUF4129   2 yrallraLaergldrrpgeTprEyarrv.riapspaaalaalaelfeearYGgrpasaeeyrrlveal 68 
                                       y  +++ L  rg++++ ++T  E    +  i+  + + l+ ++++fe+a Y g  ++ e+ + ++e +
  gi|242399080|ref|YP_002994504.1| 174 YKNVVAGLIKRGYPYQKSWTHWEHEDKLkDIFE-DLEDLDNITRVFEKAKY-GYKLDKEDIKIARESY 239
                                       6678899999******************76644.5567999**********.8999999888777765 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 !   18.4   0.0   7.9e-07    0.0024      39      86 ..     190     237 ..     168     244 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 7.9e-07
                      Syntaxin-6_N  39 ldetrteLrkalrsiewdledLeetvriveknpskfkidekelsrrra 86 
                                        ++t+ e + +l++i +dledL++  r+ ek ++ +k+d+++++  r+
  gi|242399080|ref|YP_002994504.1| 190 KSWTHWEHEDKLKDIFEDLEDLDNITRVFEKAKYGYKLDKEDIKIARE 237
                                       57999999*********************************9987665 PP

>> Glucos_trans_II  Glucosyl transferase GtrII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   6.8   1.4e-05     0.042     151     256 ..       3     148 ..       1     153 [. 0.69

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.4e-05
                   Glucos_trans_II 151 a.lllilllrdl..ldekkklkeilkkllllllvliisfvlylllykiilklfglelsy...........isellqn 213
                                         l++++l+r+     ++++  eil +++  l+++++++++++l  k i  ++ +  ++           i  +   
  gi|242399080|ref|YP_002994504.1|   3 LlLFITMLFRATveHGQSSFNIEILYLAWATLFFGFLGYAIWFLFKKGIPIMSVKRRKRtkgeylreliiILAIVIA 79 
                                       336677777777755666777899999999999************99988888888877999998888764444555 PP

                   Glucos_trans_II 214 lkryys..........................isnygvkpkklllililliliilllalllkkkkkkkk 256
                                       l+  +s                          + +y   p + + i i+++++i+ ++l ++kk+++k+
  gi|242399080|ref|YP_002994504.1|  80 LRALFSkrvepyrgikapvikypklgfsndtfTITYEPLPDYAYFIPIFVFIVIIAVLLFYRKKEPQKI 148
                                       555555888999999999999999999999774444444444444444444444444444444444444 PP

>> Oxidored_q3  NADH-ubiquinone/plastoquinone oxidoreductase chain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   3.9    0.0005       1.5      50      98 ..       1      62 [.       1     205 [. 0.67

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0005
                                      HHHHHHHHHHSSTTS----TTCHHHHHHHHHHHHHHHHHHHTT--................... CS
                       Oxidored_q3 50 lvlflFvimllesaeeeepeslsrslalaalligllllallllllles...............s 98
                                      ++l+lF++ml++  ++e  +s   ++ +++l+ + l++ +l +++ +                +
  gi|242399080|ref|YP_002994504.1|  1 MILLLFITMLFRA-TVEHGQSSF-NIEILYLAWATLFFGFLGYAIWFLfkkgipimsvkrrkrT 62
                                      89********833.333333333.3333334444444444444433322223333333333330 PP

>> ATP_synt_H  ATP synthase subunit H
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.5   0.00091       2.7       3      35 ..      30      74 ..      28      85 .. 0.70
   2 ?    3.2   0.2     0.041   1.2e+02       6      27 ..     127     147 ..     122     153 .. 0.53

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00091
                                      HHHHHHHHHHHTCSCSSS-S................TTHHHHHHHHHH CS
                        ATP_synt_H  3 lvgtiifavlgvvatfvvpkg...............enrglirvlvil 35
                                       + t++f +lg +++f+++kg                   l  +++il
  gi|242399080|ref|YP_002994504.1| 30 AWATLFFGFLGYAIWFLFKKGipimsvkrrkrtkgeY---LRELIIIL 74
                                      578****************998888777776553321...33333333 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.041
                                       HHHHHHHHTCSCSSS-S.TTHH CS
                        ATP_synt_H   6 tiifavlgvvatfvvpkgenrg 27 
                                        ++f+v+ +v+ f+ +k ++ +
  gi|242399080|ref|YP_002994504.1| 127 IFVFIVIIAVLLFYRKKEPQ-K 147
                                       44555555555555555444.4 PP

>> RDD  RDD family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   4.2     0.013        39      22      71 ..       4      50 ..       1      51 [. 0.75
   2 ?    4.2   0.0     0.015        46     100     128 ..      69     139 ..      57     148 .. 0.48

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.013
                               RDD 22 slllallivall.nakasaneavagslllllllvlllvllvyqllllskkg 71
                                      +l++++l    + ++ +  +++++  +l+l+++ l++ +l y +++l kkg
  gi|242399080|ref|YP_002994504.1|  4 LLFITML----FrATVEHGQSSFNIEILYLAWATLFFGFLGYAIWFLFKKG 50
                                      2222222....2347788999999999999999*************99987 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.015
                               RDD 100 alllllllv..........................................lglslvlllllligflfvlf 128
                                       +l+++l +v                                           + +++ +++++++++++lf
  gi|242399080|ref|YP_002994504.1|  69 ELIIILAIVialralfskrvepyrgikapvikypklgfsndtftityeplpDYAYFIPIFVFIVIIAVLLF 139
                                       44444444444455555555555555555555555555555555555555533333333333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1104  (0.0615762); expected 358.6 (0.02)
Passed bias filter:                      702  (0.0391544); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 1542.55
//
Query:       gi|242399081|ref|YP_002994505.1|  [L=129]
Description: DNA-binding protein, containing HTH domain of resolvase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-09   37.7   0.3    2.2e-09   37.1   0.3    1.3  1  DUF1699       Protein of unknown function (DUF1699)
    2.2e-05   24.1   0.0    4.2e-05   23.2   0.0    1.5  1  HTH_23        Homeodomain-like domain
    0.00018   22.1   0.1     0.0003   21.3   0.1    1.4  1  HTH_32        Homeodomain-like domain
    0.00074   19.5   0.5     0.0013   18.8   0.5    1.4  1  HTH_7         Helix-turn-helix domain of resolvase
  ------ inclusion threshold ------
      0.017   15.6   0.3       0.92   10.0   0.0    2.6  3  HTH_40        Helix-turn-helix domain
      0.023   14.8   0.0      0.025   14.6   0.0    1.1  1  DUF3071       Protein of unknown function (DUF3071)
      0.023   14.6   0.1       0.53   10.2   0.0    2.4  2  TrmB          Sugar-specific transcriptional regulator TrmB
      0.028   14.5   0.1      0.063   13.4   0.1    1.6  1  MerR_1        MerR HTH family regulatory protein
      0.041   13.6   0.0      0.092   12.4   0.0    1.6  1  Sigma70_r4_2  Sigma-70, region 4
      0.042   13.9   0.0        3.6    7.7   0.0    2.2  2  HTH_29        Winged helix-turn helix
      0.059   12.9   0.0        0.1   12.2   0.0    1.4  1  GerE          Bacterial regulatory proteins, luxR family
      0.074   13.2   0.0        0.2   11.8   0.0    1.7  1  HTH_28        Helix-turn-helix domain
       0.11   12.5   0.6        1.1    9.3   0.0    2.6  3  HTH_3         Helix-turn-helix


Domain annotation for each model (and alignments):
>> DUF1699  Protein of unknown function (DUF1699)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   0.3   1.6e-12   2.2e-09      13     115 ..      19     116 ..      13     127 .. 0.87

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 1.6e-12
                           DUF1699  13 etlnenekivHlafrpsntdilslvkkcpklkaiqvpeSykktlsksakmfleiqgiellegdvwghrkdineyyev 89 
                                       etln + + v +  rp +  ++++++++p++k+i+ p+S + ++sk +   l+  gi+l+  + ++ r    + y  
  gi|242399081|ref|YP_002994505.1|  19 ETLNGEVTEVYINLRPTKVILVKILERAPNVKIIKCPSSLYPKVSKKIIRALSQMGIKLVPANHSRGRP---KKY-- 90 
                                       5788888899**************************************************987555544...333.. PP

                           DUF1699  90 seevierikelkseglseeeiaekls 115
                                       + ++i++i+el ++g++ +ei+++l+
  gi|242399081|ref|YP_002994505.1|  91 DAAIIKQIEELVRKGKTPKEISQELK 116
                                       689******************99986 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0     3e-08   4.2e-05      12      39 ..      96     127 ..      92     128 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 3e-08
                            HTH_23  12 lllae....GlsvreIAreLgvsrrTvyrwlk 39 
                                       +   e    G++++eI++eL ++ rTvy +++
  gi|242399081|ref|YP_002994505.1|  96 KQIEElvrkGKTPKEISQELKIPLRTVYYIIN 127
                                       555555555*******************9985 PP

>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.1   2.2e-07    0.0003      17      72 ..      77     125 ..      62     126 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 2.2e-07
                            HTH_32  17 Lkdr.prrgrprklsdevrariiallreeprWsprqlaarlaeregvkvShstvyri 72 
                                       L ++ ++rgrp+k +++  ++i +l+ ++   +p++++++l      k+  +tvy i
  gi|242399081|ref|YP_002994505.1|  77 LVPAnHSRGRPKKYDAAIIKQIEELV-RK-GKTPKEISQEL------KIPLRTVYYI 125
                                       444425669*****************.66.67*********......8999999987 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.5   9.2e-07    0.0013       1      42 [.      85     126 ..      85     129 .] 0.95

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 9.2e-07
                                       S---SS-HHHHGGGGSSTTTT--STTTSSSS---SSSS--SS CS
                             HTH_7   1 GRpsklskndinrvvkLleeGisiskIAkevnisRsTvYRyl 42 
                                       GRp+k++   i ++ +L+++G + ++I  e++i   TvY + 
  gi|242399081|ref|YP_002994505.1|  85 GRPKKYDAAIIKQIEELVRKGKTPKEISQELKIPLRTVYYII 126
                                       9**************************************765 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0       0.1   1.4e+02      65      82 ..      10      27 ..       2      33 .. 0.71
   2 ?   -1.1   0.0       1.9   2.6e+03      55      65 ..      64      74 ..      39     100 .. 0.62
   3 ?   10.0   0.0   0.00067      0.92       7      30 ..     100     123 ..      95     126 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.1
                            HTH_40 65 gseklkpikealpeevsy 82
                                      ++e lk+i e l++ev+ 
  gi|242399081|ref|YP_002994505.1| 10 NEELLKKIDETLNGEVTE 27
                                      2344**********9985 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.9
                            HTH_40 55 keIeeaiekvg 65
                                      k+I+ a+ ++g
  gi|242399081|ref|YP_002994505.1| 64 KKIIRALSQMG 74
                                      45555555544 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00067
                            HTH_40   7 elleeglsieeIAkerglkesTIe 30 
                                       el+++g++++eI++e ++   T++
  gi|242399081|ref|YP_002994505.1| 100 ELVRKGKTPKEISQELKIPLRTVY 123
                                       689*******************97 PP

>> DUF3071  Protein of unknown function (DUF3071)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.8e-05     0.025      27      83 ..      14     122 ..       2     124 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.8e-05
                           DUF3071  27 flavddeLraalree.....................................................serqaeaee 50 
                                         ++d++L+  ++e                                                      + ++ + ++
  gi|242399081|ref|YP_002994505.1|  14 LKKIDETLNGEVTEVyinlrptkvilvkilerapnvkiikcpsslypkvskkiiralsqmgiklvpanH-SRGRPKK 89 
                                       556666666666663344556666777777777777777777777777777777777777777766532.2455666 PP

                           DUF3071  51 esslrpreIQariRaGasveevaeeagvsverv 83 
                                        +   +++I + +R+G++++e+++e++++ + v
  gi|242399081|ref|YP_002994505.1|  90 YDAAIIKQIEELVRKGKTPKEISQELKIPLRTV 122
                                       777899********************9998876 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.15   2.1e+02      41      65 ..      65      93 ..      50      96 .. 0.71
   2 ?   10.2   0.0   0.00038      0.53      20      44 ..     103     127 ..      99     128 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.15
                                      HHHHHHHHCT..SEEEESST..TTEEEE- CS
                              TrmB 41 evLrsLedkG..lVerekgr..pklYrav 65
                                      +++r L+++G  lV  +++r  pk+Y a+
  gi|242399081|ref|YP_002994505.1| 65 KIIRALSQMGikLVPANHSRgrPKKYDAA 93
                                      56777777773345555544559999885 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00038
                                       HCCCHHCHHCCCTTSSCHCHHHHHH CS
                              TrmB  20 lgpatadeiaeelgvprskvYevLr 44 
                                       ++ +t +ei++el++p  +vY +++
  gi|242399081|ref|YP_002994505.1| 103 RKGKTPKEISQELKIPLRTVYYIIN 127
                                       6789*****************9876 PP

>> MerR_1  MerR HTH family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   4.6e-05     0.063      12      66 ..      62     115 ..      59     117 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.6e-05
                                       S-HHHHHHHHHHTT.-S-EE-TTS-.EEEEHHHHHHHHHHHHHHHTT--GGG---XX CS
                            MerR_1  12 vtthtlrywekegl.lkpkrteggr.ryYtdedierLklikyLlkrGltlkgikkll 66 
                                       v+++ +r   + g  l+p+ +++gr   Y+    + +k+i +L  +G t k+i++ l
  gi|242399081|ref|YP_002994505.1|  62 VSKKIIRALSQMGIkLVPANHSRGRpKKYDA---AIIKQIEELVRKGKTPKEISQEL 115
                                       889999******************9999976...5789999************9866 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   6.7e-05     0.092      25      44 ..     104     123 ..      98     126 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.7e-05
                                       S---HHHHHHHHT--HHHHH CS
                      Sigma70_r4_2  25 eglsykEIAellgisegtVk 44 
                                       +g++ kEI+++l+i+ +tV+
  gi|242399081|ref|YP_002994505.1| 104 KGKTPKEISQELKIPLRTVY 123
                                       69999**************7 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.029        40      33      61 ..      67      94 ..      61      96 .. 0.76
   2 ?    7.7   0.0    0.0026       3.6       2      33 ..      96     126 ..      96     127 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.029
                            HTH_29 33 lkrfeegGlaalld.rrrsgrprnrlseeq 61
                                      +++  + G+ +l + ++++grp++  +++ 
  gi|242399081|ref|YP_002994505.1| 67 IRALSQMGI-KLVPaNHSRGRPKK-YDAAI 94
                                      566666776.678888999***96.89875 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0026
                            HTH_29   2 aqallllaeGvstvsqiAkllglsrrtvyrwl 33 
                                       +q+  l+++G  t+++i + l +  rtvy ++
  gi|242399081|ref|YP_002994505.1|  96 KQIEELVRKGK-TPKEISQELKIPLRTVYYII 126
                                       57788999**9.9***************9766 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   7.4e-05       0.1      12      34 ..     100     122 ..      96     126 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.4e-05
                                       HHHCTTS-HHHHHHHHTS-HHHH CS
                              GerE  12 rllaeGksnkeIAeelniSekTV 34 
                                       +l+ +Gk+ keI++el i  +TV
  gi|242399081|ref|YP_002994505.1| 100 ELVRKGKTPKEISQELKIPLRTV 122
                                       67889****************99 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00014       0.2       8      34 ..     101     127 ..      93     128 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00014
                            HTH_28   8 llaaGhsvreaArelgisrrtvyrWik 34 
                                       l+ +G++ +e+++el i  rtvy  i+
  gi|242399081|ref|YP_002994505.1| 101 LVRKGKTPKEISQELKIPLRTVYYIIN 127
                                       455799*****************9885 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.52   7.2e+02      39      54 ..      12      27 ..      10      28 .. 0.81
   2 ?   -2.3   0.0       3.6   4.9e+03      41      50 ..      40      49 ..      33      52 .. 0.53
   3 ?    9.3   0.0   0.00081       1.1       6      32 ..     102     128 ..      98     129 .] 0.90

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.52
                                      HHHHHHHHHHTSEHHH CS
                             HTH_3 39 etlkklakaLgvslde 54
                                      e lkk+ ++L+ + +e
  gi|242399081|ref|YP_002994505.1| 12 ELLKKIDETLNGEVTE 27
                                      889*******987766 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.6
                                      HHHHHHHHTS CS
                             HTH_3 41 lkklakaLgv 50
                                      +k l++a +v
  gi|242399081|ref|YP_002994505.1| 40 VKILERAPNV 49
                                      4445555555 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.00081
                                       HHTTHHHHHHHHHHTSSHHHHHHHHTT CS
                             HTH_3   6 kqlglsqeeLAeklGvsrstisriEnG 32 
                                         +g + +e++++l ++ +t++ i+nG
  gi|242399081|ref|YP_002994505.1| 102 VRKGKTPKEISQELKIPLRTVYYIING 128
                                       568***********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       983  (0.0548274); expected 358.6 (0.02)
Passed bias filter:                      801  (0.0446762); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 828.59
//
Query:       gi|242399082|ref|YP_002994506.1|  [L=416]
Description: hypothetical protein TSIB_1103 [Thermococcus sibiricus MM 739]
Scores for complete 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-21   74.2  17.4    1.1e-17   63.6   8.9    3.5  2  DUF530    Protein of unknown function (DUF530)


Domain annotation for each model (and alignments):
>> DUF530  Protein of unknown function (DUF530)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.6   8.9   6.2e-22   1.1e-17      99     281 ..      85     258 ..       3     265 .. 0.83
   2 !   12.7   1.4   1.6e-06     0.029     377     520 ..     265     414 ..     257     415 .. 0.66

  Alignments for each domain:
  == domain 1  score: 63.6 bits;  conditional E-value: 6.2e-22
                            DUF530  99 kKnildrVksAiasHkiAignleeyaelkCksCekkyklseleleskkCecgseefklkvnkegiyRleiipyLpls 175
                                       +   l+r + Ai++HkiA++ ++ + ++   + +k   +++++   +k ++ +  +k+  ++    Rle++p+L++s
  gi|242399082|ref|YP_002994506.1|  85 RMLTLERLRIAITAHKIALATIDSHYTF--YKGKKGVDIKNIT---NKRDLEK--LKVAEKSIKLGRLEVLPHLAYS 154
                                       45579******************95443..4455555555554...4444444..55555555667*********** PP

                            DUF530 176 GdYmvklSelskyareafkkilrilkqekkGivksislvikvledgkwirkrvkidsedesnyEeelrkryGknvri 252
                                       Gd +  lS+  +  r++fk i + lk++++ + k i + + + ++g+ ++ r+    e  ++ ++elrkr+G+  r 
  gi|242399082|ref|YP_002994506.1| 155 GDVLKILSQQDNKVRDTFKEIKSKLKEKGQIRKKGIRIEVEYWQEGRLKKERLDFPVE--ADIDSELRKRFGQKYRW 229
                                       **************************99998899999999999****99998777766..78*************** PP

                            DUF530 253 ellqfhrkKpsiinDkyvrtalalaYvkl 281
                                        +l + ++K  +i  +y+ +++alaY++ 
  gi|242399082|ref|YP_002994506.1| 230 RVLSYVKTKGVLITSHYTVDNIALAYAST 258
                                       **************************875 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 1.6e-06
                            DUF530 377 tlilwDilkYYLttSadrRkrysgpFPnlrpeldrqqlkvfeefekkvvellekkleekiiaiknldevllkkfelE 453
                                       + +  D ++YY  tS+ +R+   + +P+++p +d +   +f+  + +  e      +        +  ++ kk e+E
  gi|242399082|ref|YP_002994506.1| 265 KALALDFFRYYYLTSEKERES-ISLYPQIKPCIDCH-YSIFDVPFMNEPEF-----RTGF---GSM--LIIKKCEIE 329
                                       66788**************99.678*********75.67888654433222.....2222...222..455555666 PP

                            DUF530 454 kklkglnlkl...nyaalGaailnseseieieeiakllsvdvkevkkek.............knikklek..pssdk 512
                                       + l g + ++    +  lG +il+  s  + +++++ll++d+ e+k  +             +++ k+ek  p+sdk
  gi|242399082|ref|YP_002994506.1| 330 SFLSGRRSEIsniPNYLLGGVILYGVSSFDEKKVSNLLQIDETELKDAIekfvlsglhislfEDVGKFEKfmPKSDK 406
                                       55544443331003357999********************999998765111222222222234456776555699* PP

                            DUF530 513 akkFLeli 520
                                       ak+FLel+
  gi|242399082|ref|YP_002994506.1| 407 AKQFLELL 414
                                       ****9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       966  (0.0538792); expected 358.6 (0.02)
Passed bias filter:                      640  (0.0356964); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 2797.36
//
Query:       gi|242399083|ref|YP_002994507.1|  [L=381]
Description: Type II DNA topoisomerase VI subunit A [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-19   68.9   0.0    4.9e-19   68.1   0.0    1.4  1  TP6A_N    Type IIB DNA topoisomerase
      0.003   17.5   0.0     0.0056   16.6   0.0    1.5  1  DUF2399   Protein of unknown function C-terminus (DUF2399)


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 !   68.1   0.0   5.5e-23   4.9e-19       1      62 []      78     147 ..      78     147 .. 0.98

  Alignments for each domain:
  == domain 1  score: 68.1 bits;  conditional E-value: 5.5e-23
                                       HHHHHHHHHHHHHHHHHHTT--EEHHHHHHH........GGGS-SSHHHHHHHHHHHHHHHTS-GGGGTE CS
                            TP6A_N   1 rkfaqllkvlelihelleegkvvTkRdiYYr........dvelFksQaesdrliddievllgvsReeLnv 62 
                                       rkf+q+l++ + i++l++egk++++R+ YY         ++++F++Q+esd +i+d+e+++gv+Ree+++
  gi|242399083|ref|YP_002994507.1|  78 RKFMQTLLISAYIKRLVSEGKHASLREAYYAnkhtipgsKENTFEDQSESDPIIEDLERMFGVLREEMHI 147
                                       79**********************************9999*****************************8 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 !   16.6   0.0   6.2e-07    0.0056      21      88 ..     196     266 ..     183     292 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 6.2e-07
                           DUF2399  21 avyVvENpavlaaaadr..lgakaaplvctsGqpsaaalelldkl.aaagarlrYhGDfDwpGlaiankla 88 
                                       +v VvE +a+   ++++    +++a +v t+Gq s+ + +l+++l  ++g  + +  D D+ G  i  ++ 
  gi|242399083|ref|YP_002994507.1| 196 YVLVVETAAMADRLIEEkyPKKEKALVVATQGQASRGVRRLIHRLhYEEGLPIIVFTDGDPYGWYIYSTIK 266
                                       599************99533336666789****************8899***********99988877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); 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: 0.62u 0.35s 00:00:00.97 Elapsed: 00:00:00.54
# Mc/sec: 2124.33
//
Query:       gi|242399084|ref|YP_002994508.1|  [L=566]
Description: Type 2 DNA topoisomerase 6 subunit B [Thermococcus sibiricus MM 739]
Scores for complete 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-55  187.1   0.0    3.3e-55  186.2   0.0    1.4  1  Topo-VIb_trans  Topoisomerase VI B subunit, transducer
    3.2e-11   43.7   0.2    6.4e-11   42.8   0.2    1.5  1  HATPase_c       Histidine kinase-, DNA gyrase B-, and HSP90-l
    2.3e-09   37.2   0.0    4.6e-09   36.2   0.0    1.5  1  HATPase_c_3     Histidine kinase-, DNA gyrase B-, and HSP90-l
  ------ inclusion threshold ------
        0.1   11.5   2.6       0.08   11.8   0.4    1.8  2  Phage_min_cap2  Phage minor capsid protein 2


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 !  186.2   0.0   7.4e-59   3.3e-55       1     154 [.     357     510 ..     357     516 .. 0.95

  Alignments for each domain:
  == domain 1  score: 186.2 bits;  conditional E-value: 7.4e-59
                    Topo-VIb_trans   1 Pstdclspigeeliekglkkelkpefvaavtrkpkvyegh.pfivEvgiayGGelekeekaeilRfaNrvPLlydeg 76 
                                       P+t+ l+pigee+iekgl+ +l+pefv++vtr+pkvy+g  pf vEvg+a+GGel  ++  ++lR+aNrvPLl+d+g
  gi|242399084|ref|YP_002994508.1| 357 PPTHGLRPIGEENIEKGLTGILRPEFVTSVTRPPKVYRGGiPFQVEVGLAFGGEL--SSGFDLLRYANRVPLLFDAG 431
                                       999***********************************988************87..6789**************** PP

                    Topo-VIb_trans  77 advitkavksinwkrYkleq.pedpvvvlvhvastkvPfksegKeaiadveeiekeiklalqevarkLkkylskkek 152
                                       ++vit+a+++i+wkrY++++ ++ p+++lv+v+s++vP++s+gK+++a+ eei++ei+la+++var+L kyl  k++
  gi|242399084|ref|YP_002994508.1| 432 SCVITSAARNIDWKRYRVDDvDRAPLALLVNVVSVHVPYTSTGKQSVANEEEIYEEIRLAVMDVARRLAKYLGGKHR 508
                                       *******************96666************************************************98887 PP

                    Topo-VIb_trans 153 ek 154
                                       + 
  gi|242399084|ref|YP_002994508.1| 509 KL 510
                                       65 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 !   42.8   0.2   1.4e-14   6.4e-11       2      93 ..      34     132 ..      33     183 .. 0.66

  Alignments for each domain:
  == domain 1  score: 42.8 bits;  conditional E-value: 1.4e-14
                                       HHHHHHHHHHHHHHHHHHHHSTTT...EEEEEEEEEE...TEEEEEEEESSSSSTTHHHTGTCSTTCH.....HCST CS
                         HATPase_c   2 dekrLrqiisnlvdNavkfatkag...eieveikase...ddlvisveDnGiGipkedlkklfekfsq.....ddst 67 
                                       + + L+ +i ++v+N++++  +ag    ++vei+  e   ++++i veDnG+Gip++ + ++f+k+        + +
  gi|242399084|ref|YP_002994508.1|  34 KLRSLTTLIHEAVTNSLDACEEAGilpYVRVEIE--ElgtEHYKIIVEDNGPGIPEKFIAHVFGKMLAgtkahRNIQ 108
                                       567899************9555554447788988..44567***********************7666687555555 PP

                                       CHTSTSSSH.HHHHHHHHHHHTTTEEE CS
                         HATPase_c  68 krggggtGl.GlsivkklvelmgGeiw 93 
                                       +rg++g G+ G+ +  ++++   G+ +
  gi|242399084|ref|YP_002994508.1| 109 SRGQQGIGIsGAVMFAQITS---GKAT 132
                                       55555555533333333433...3332 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 !   36.2   0.0     1e-12   4.6e-09       7     118 ..      42     165 ..      36     177 .. 0.77

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 1e-12
                       HATPase_c_3   7 laelvdNsldAdaen.....vkievnknrgktgeivieDdGkGmseeelknalrlatsskeakrkstslGkkGiGl. 77 
                                       + e v NsldA  e      v +e+++  +++ +i +eD+G G++e+ +  ++  +   ++a+r+ +s+G+ GiG+ 
  gi|242399084|ref|YP_002994508.1|  42 IHEAVTNSLDACEEAgilpyVRVEIEELGTEHYKIIVEDNGPGIPEKFIAHVFGKMLAGTKAHRNIQSRGQQGIGIs 118
                                       6799*******999999999999999999999******************988655555555789999******962 PP

                       HATPase_c_3  78 ...klAslslgkkltvitkkegess...tltldvdkidkenekvlee 118
                                           +A + +gk   +it++ +e+     + +dvdk + + +k+++ 
  gi|242399084|ref|YP_002994508.1| 119 gavMFAQITSGKATRIITSTGEEEIieaWVGIDVDKNEGKIFKKIKH 165
                                       22246777889999999988777764444666666666555555554 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 ?   -1.2   0.1      0.16   7.4e+02      63      96 ..     263     293 ..     247     342 .. 0.67
   2 ?   11.8   0.4   1.8e-05      0.08      15      96 ..     483     563 ..     475     566 .] 0.89

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.16
                    Phage_min_cap2  63 iskltgksekelrkllkeagdkaiksddkelaiy 96 
                                       i + +++s+k++++l++ +    + ++++   ++
  gi|242399084|ref|YP_002994508.1| 263 IGEFSRISDKKIDELVQYITALRLIKEEE---EQ 293
                                       56677777777777777766666655552...22 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 1.8e-05
                    Phage_min_cap2  15 dlysaleqeiiediarrikktgeltntaewqieklaelgllnreilkliskltgksekelrkllkeagdkaiksddk 91 
                                       ++y+++   ++ d+arr++k+   +    +q+++ + l++   e+ +++s ltg  e e++k+l ++ +k+++s d+
  gi|242399084|ref|YP_002994508.1| 483 EIYEEIRLAVM-DVARRLAKYLGGKHRKLYQVKRRKTLEKYVPEVSRALSILTGLPEGEIKKMLVTIIEKKFESIDE 558
                                       56666666665.89***********************************************************9997 PP

                    Phage_min_cap2  92 elaiy 96 
                                        ++++
  gi|242399084|ref|YP_002994508.1| 559 AVEAE 563
                                       77765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (566 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       711  (0.0396564); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); 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: 0.67u 0.32s 00:00:00.99 Elapsed: 00:00:00.50
# Mc/sec: 3436.20
//
Query:       gi|242399085|ref|YP_002994509.1|  [L=220]
Description: RNA-binding protein, containing KH domain [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-17   63.6   7.8    3.6e-10   39.5   0.3    2.4  2  KH_1      KH domain
    3.9e-07   30.1   0.0    6.8e-07   29.3   0.0    1.4  1  KH_8      Krr1 KH1 domain
    6.9e-06   25.8   9.6     0.0002   21.1   0.7    2.8  2  KH_2      KH domain
     0.0057   16.5   6.0       0.31   11.0   0.5    2.9  2  KH_4      KH domain
  ------ inclusion threshold ------
       0.71   10.0   6.5        8.6    6.5   0.9    2.4  2  KH_5      NusA-like 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 !   39.5   0.3     1e-13   3.6e-10       2      55 ..      37      84 ..      35      99 .. 0.86
   2 !   27.2   2.1   6.9e-10   2.5e-06      10      65 ..     140     187 ..     132     188 .. 0.90

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 1e-13
                                      EEEEEGGGHHHHHHTGGGHHHHHHHHHHT-EEEEESSTT...T.-EEEEEESHH CS
                              KH_1  2 lrilvPsslvgriIGkgGsnIkeIreetgakIkvpksedegsderevtisGspe 55
                                      + + +P++ +g +IGk+G++ k+I++ t++kI+++ s     +  ev i+ ++e
  gi|242399085|ref|YP_002994509.1| 37 EFVRIPKERIGVVIGKNGETKKKIEDATKTKIDID-S-----NTGEVFITSTEE 84
                                      4579*****************************76.5.....467899998777 PP

  == domain 2  score: 27.2 bits;  conditional E-value: 6.9e-10
                                       HHHHHHTGGGHHHHHHHHHHT-EEEEESSTT...T.-EEEEEESHHHHHHHHHHHH CS
                              KH_1  10 lvgriIGkgGsnIkeIreetgakIkvpksedegsderevtisGspeavekAkelie 65 
                                         griIG++G++   I+e +g+ I v  +       ++v i+G+p +v+ Ak +ie
  gi|242399085|ref|YP_002994509.1| 140 VRGRIIGRKGRTREIIEEMSGTEISVY-G-------KTVAIIGNPLQVQVAKTAIE 187
                                       57**********99999999*****87.5.......58*****9999*****9997 PP

>> KH_8  Krr1 KH1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.0   1.9e-10   6.8e-07      25      80 ..      60     115 ..      40     116 .. 0.87

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 1.9e-10
                              KH_8  25 lleekklklevdlkerslkvsTtekTrDPyiilkardlikLisrgvpleeakkvle 80 
                                       + +  k k+++d + + + +  te+T DP  + kard++  i+rg + e+a ++l+
  gi|242399085|ref|YP_002994509.1|  60 IEDATKTKIDIDSNTGEVFITSTEETEDPLAVWKARDIVLAIGRGFSPERAFRLLN 115
                                       335678999******************************************99987 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.7   5.5e-08    0.0002      25      60 ..      35      70 ..       9      88 .. 0.70
   2 !    8.9   1.8   0.00037       1.3      37      68 ..     142     172 ..     140     207 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 5.5e-08
                                      CEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHH CS
                              KH_2 25 nrviiviresqpgivIGkgGsnikkigkelrkdiek 60
                                      +   + i +++ g+vIGk+G++ kki+ + + +i++
  gi|242399085|ref|YP_002994509.1| 35 QEEFVRIPKERIGVVIGKNGETKKKIEDATKTKIDI 70
                                      4555668899*********************99963 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00037
                                       HHHHTGGGHHHHHHHHHHHHHHHHHHTTCEEE CS
                              KH_2  37 givIGkgGsnikkigkelrkdieklegkkVkl 68 
                                       g++IG++G++ + i++  + +i  + gk V +
  gi|242399085|ref|YP_002994509.1| 142 GRIIGRKGRTREIIEEMSGTEIS-VYGKTVAI 172
                                       99********************5.88888764 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.5   8.6e-05      0.31      33      50 ..      39      56 ..      21      61 .. 0.84
   2 !    7.4   0.4    0.0011         4      41      50 ..     142     151 ..     138     158 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 8.6e-05
                              KH_4 33 lnvegedlGrvIGkrGrt 50
                                      +++ +e +G+vIGk+G+t
  gi|242399085|ref|YP_002994509.1| 39 VRIPKERIGVVIGKNGET 56
                                      67889***********98 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0011
                              KH_4  41 GrvIGkrGrt 50 
                                       Gr+IG++Grt
  gi|242399085|ref|YP_002994509.1| 142 GRIIGRKGRT 151
                                       9********9 PP

>> KH_5  NusA-like KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.9    0.0024       8.6      18      44 ..      45      70 ..      30      74 .. 0.90
   2 ?    6.1   0.5    0.0032        12      20      44 ..     142     165 ..     125     174 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0024
                              KH_5 18 pvGaivgkkGsrikavsseLkgekidv 44
                                       +G ++gk+G+  k++++   ++kid+
  gi|242399085|ref|YP_002994509.1| 45 RIGVVIGKNGETKKKIEDAT-KTKIDI 70
                                      59*****************9.999998 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0032
                              KH_5  20 GaivgkkGsrikavsseLkgekidv 44 
                                       G i+g+kG r +++++e++g+ i v
  gi|242399085|ref|YP_002994509.1| 142 GRIIGRKG-RTREIIEEMSGTEISV 165
                                       89******.5799******999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); 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:                         5  (0.000278878); expected 0.2 (1e-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: 1290.21
//
Query:       gi|242399086|ref|YP_002994510.1|  [L=258]
Description: Rio1 protein, [Thermococcus sibiricus MM 739]
Scores for complete 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  182.7   0.2    7.2e-54  182.3   0.2    1.1  1  RIO1            RIO1 family
    3.8e-05   23.2   0.1    0.00019   20.9   0.1    2.0  1  Pkinase         Protein kinase domain
    0.00027   20.9   0.0    0.00094   19.2   0.0    1.7  2  APH             Phosphotransferase enzyme family
  ------ inclusion threshold ------
      0.076   11.8   0.0       0.11   11.3   0.0    1.3  1  Pkinase_fungal  Fungal protein 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 !  182.3   0.2   1.6e-57   7.2e-54       1     182 [.      65     245 ..      65     251 .. 0.96

  Alignments for each domain:
  == domain 1  score: 182.3 bits;  conditional E-value: 1.6e-57
                                       EEEEEEETTTEEEEEEEE-S---SS-HHHHCTTTSTTSTCG--GS-HHHHHHHHHHHHHHHHHHHHHTT--S--EEE CS
                              RIO1   1 nVyhavsedgkevaiKiyktstteFkkrkkyvsgekrfkdrksktnprklvklwaekEfrnLkrleeagvpvPkpie 77 
                                       nV+++v+edg+ vaiK+y+t tteF+++ +y   ++r +  +  ++ rk+v +w+++Ef+nL+r+ +  v++P+pi 
  gi|242399086|ref|YP_002994510.1|  65 NVFKGVDEDGNYVAIKVYRTYTTEFRRIWEYLAADPRIS--YLPKDIRKMVFVWTRREFKNLQRAMKYAVRAPEPIV 139
                                       79***********************************55..779********************************* PP

                                       EETTEEEEE--EETTEEGGBHHHCG.-..HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETTEEEE--GTT CS
                              RIO1  78 lkrhvlvmefigedgvaapklkdve.e..eeeaeelyeevleemrklykeaglvHaDLSeyNvlvdedkvviIDvsQ 151
                                       + ++vl+me+ig d+ +ap+lkdve +  ++e eelye  +e+++kl k+  +vH+DLSeyN+l++e+ +viID+sQ
  gi|242399086|ref|YP_002994510.1| 140 FSNNVLIMEYIG-DESPAPRLKDVErDldKKEFEELYEFAMESIEKLWKRGDMVHGDLSEYNILIWEK-PVIIDWSQ 214
                                       ************.************758899**********************************975.******** PP

                                       EEETTSTTHHHHHHHHHHHHHHHHHTTC--- CS
                              RIO1 152 aveldhpnalefLerDveniikfFrrkgvek 182
                                       a+  ++++al++L rD++ni ++F +kg++ 
  gi|242399086|ref|YP_002994510.1| 215 ATVRRNRMALTLLYRDLRNITNYFAKKGIKV 245
                                       ****************************983 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.1   4.3e-08   0.00019       7     151 ..      58     221 ..      52     248 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 4.3e-08
                                       EEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHH..............HHHHHHHHHHHHHSCTTB--EEEEEEE CS
                           Pkinase   7 lGeGsfGkVykaveketgkivAvKkikkekakkkke..............kkvlrEikilkklkhpnivrlyevfee 69 
                                       + +G+ ++V+k+v +e+g+ vA+K+ ++  ++ ++               k++++ + +  + + +n+ r +++  +
  gi|242399086|ref|YP_002994510.1|  58 ISTGKEANVFKGV-DEDGNYVAIKVYRTYTTEFRRIweylaadprisylpKDIRKMVFVWTRREFKNLQRAMKYAVR 133
                                       66899999*****.699999****99988776655444555555555554445554555555555555555554444 PP

                                       ......SSEEEEEEE--TTEBHHHHHH.HHSS--HHHHHHHHHHHHHHHHHHHHTT.EE-SS-SGGGEEEETTTEEE CS
                           Pkinase  70 ......kdelylvleyveggeladlle.rkgslseeeakkiakqilegleylHskg.iiHrDlKpeNiLidekgelK 138
                                              ++ +l++ey+  ++ a +l+  ++ l+++e +++ +  +e++e l+++g ++H Dl   NiLi   ++  
  gi|242399086|ref|YP_002994510.1| 134 apepivFSNNVLIMEYIGDESPAPRLKdVERDLDKKEFEELYEFAMESIEKLWKRGdMVHGDLSEYNILIW--EKPV 208
                                       99999989999**********88888855556*********************9988*************9..5666 PP

                                       E-SGTTSEESSSS CS
                           Pkinase 139 itDFGlakeless 151
                                       i+D+  a+  +++
  gi|242399086|ref|YP_002994510.1| 209 IIDWSQATVRRNR 221
                                       8888887766655 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.16   7.3e+02      37      84 ..     117     157 ..      72     178 .. 0.60
   2 !   19.2   0.0   2.1e-07   0.00094     139     197 ..     164     216 ..     147     218 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.16
                                       HHHHHHHHHHHHHTT-B--B-CTTBS-EEETTEEEEEEE----EE-SS CS
                               APH  37 irrevallrlLakagvpvPevlagdtddeeigllfalieyvpgrsllr 84 
                                       +rre++ l+   k  v++Pe++ +  ++      ++++ey++ +s+++
  gi|242399086|ref|YP_002994510.1| 117 TRREFKNLQRAMKYAVRAPEPIVF--SN-----NVLIMEYIGDESPAP 157
                                       334555555555555577888773..22.....344566666666655 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 2.1e-07
                                       CCTCC.HHHHHHHHHHHHHHHH--SSS-EEEE-SS-SGGGEEEC..TTEEEEE---TT-E CS
                               APH 139 selld.lleeleeqvlaalaallpgelptvllHgDlhpgNllvdpddgrvtGviDfedag 197
                                       ++l++ + eel e +++ +++l+    +   +HgDl+  N+l+   + +v  +iD+  a+
  gi|242399086|ref|YP_002994510.1| 164 RDLDKkEFEELYEFAMESIEKLWK---RGDMVHGDLSEYNILIW--EKPV--IIDWSQAT 216
                                       333335566777778888889998...7889*************..8999..****9887 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   2.4e-05      0.11     315     343 ..     178     206 ..     157     226 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.4e-05
                    Pkinase_fungal 315 aIkghrsLflkagiLHrDiSenNilitds 343
                                       a +  ++L + + ++H D Se+Nili ++
  gi|242399086|ref|YP_002994510.1| 178 AMESIEKLWKRGDMVHGDLSEYNILIWEK 206
                                       6777889999****************964 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       715  (0.0398795); expected 358.6 (0.02)
Passed bias filter:                      566  (0.031569); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 1591.40
//
Query:       gi|242399087|ref|YP_002994511.1|  [L=152]
Description: Translation initiation factor 1A [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.2e-21   73.6   2.7    1.1e-20   73.1   2.0    1.6  2  eIF-1a    Translation initiation factor 1A / IF-1
     0.0001   22.0   0.1     0.0002   21.1   0.1    1.5  1  RsgA_N    RsgA N-terminal domain


Domain annotation for each model (and alignments):
>> eIF-1a  Translation initiation factor 1A / IF-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0      0.72   6.4e+03      14      23 ..       8      17 ..       3      33 .. 0.63
   2 !   73.1   2.0   1.3e-24   1.1e-20       1      64 []      63     126 ..      63     126 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.72
                                      TEEEEEE.SS CS
                            eIF-1a 14 nlfrVelpdn 23
                                        f+V l+ +
  gi|242399087|ref|YP_002994511.1|  8 KIFKVALTTD 17
                                      5677777533 PP

  == domain 2  score: 73.1 bits;  conditional E-value: 1.3e-24
                                       EEEEEEEEEEETTTEEEEEE.SSSSBEEEEE-HHHHCT----TT-EEEEEE-TT-TT.EEEEES- CS
                            eIF-1a   1 gevigkViealgnnlfrVelpdngkevlaeipgkfRnkiwikrGdyVlVelspydlt.kGrIvyr 64 
                                       ++v g+V++alg++ + V++ d +k + ++ipg++R+k+wi+ Gd+V+Ve+++ + + +G+Ivyr
  gi|242399087|ref|YP_002994511.1|  63 NQVFGVVEQALGSGWMDVRCVD-NKIRRCRIPGRLRRKMWIRIGDVVIVEPWEVQSDeRGDIVYR 126
                                       69******************96.******************************99555******8 PP

>> RsgA_N  RsgA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.1   2.2e-08    0.0002       9      46 ..      75     112 ..      67     123 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2.2e-08
                            RsgA_N   9 sgfYyVk.eegeiyecRaRGkFRkkkisplVGDrVefel 46 
                                       sg+ +V+  +++i +cR+ G++R+k + + +GD V +e 
  gi|242399087|ref|YP_002994511.1|  75 SGWMDVRcVDNKIRRCRIPGRLRRK-MWIRIGDVVIVEP 112
                                       79*****7888************55.7888*****9984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 1153.41
//
Query:       gi|242399088|ref|YP_002994512.1|  [L=387]
Description: hypothetical protein TSIB_1109 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00074   20.0   0.0     0.0018   18.7   0.0    1.7  1  AAA_17    AAA domain
  ------ inclusion threshold ------
       0.11   12.7   1.8       0.44   10.8   1.1    2.4  2  SRP54_N   SRP54-type protein, helical bundle 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 !   18.7   0.0     2e-07    0.0018      14     136 .]      24     153 ..       8     153 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2e-07
                                       HHHHHHTEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHH...HHHHHHHHHHHHHHHH..HSSEE.EEEE-SEEEE CS
                            AAA_17  14 klvekygfthlsaGdllreeakrgglakardemrklplee...kkelqkeaaekiaeea..kkkgv.lvdghprike 84 
                                       +l+++ +f+++   d+l e  +++g + +r+++ +  +++    + +++ea ++i++e   ++k + lv + + +++
  gi|242399088|ref|YP_002994512.1|  24 RLAKNENFQYYHVFDYLKEIGREKGVKITRKNVLDFAISHpdlMNTIRDEAFKRIRDEIdrSDKSFhLVSTPALFRW 100
                                       56788899999999***9999999998899988865555411267889*******999544555566999******* PP

                                       TTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHHTT.ST-TS-SHHHHH CS
                            AAA_17  85 qagfldglpkevleelkpdaiilleadpeeilerrlkdrt.rgrdddneesik 136
                                        +g + g++   l+ lkp+ +i++ +d   +++r + d++  +r   nee ik
  gi|242399088|ref|YP_002994512.1| 101 GSGSVLGFTLSNLKLLKPSRVIIVLDDILSVRRRIIHDEEwFERFRRNEENIK 153
                                       ***********************999999********9765899999999986 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 ?   -1.1   0.0      0.26   2.3e+03      42      74 ..     166     204 ..     164     204 .. 0.71
   2 ?   10.8   1.1   4.9e-05      0.44       4      41 ..     269     305 ..     267     313 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.26
                                       HHHHHHHHHHHHHHHCTTS......S-HHHHHHHHHHHH CS
                           SRP54_N  42 kvvkklienvkkkavgekk......lkpkqqvkkivkde 74 
                                       + vk l+ ++ k+++  +         p+q++++++++e
  gi|242399088|ref|YP_002994512.1| 166 NHVKTLVHELNKEEIQVRYvlhfgiRHPHQTFIDLIFHE 204
                                       568888888888777755577777544888888888876 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 4.9e-05
                                       HHHHHHHHHCCSSCGHHHHHHHHHHHHHHHHHHTT--H CS
                           SRP54_N   4 klnsalkklsgkskideedleealkeleeaLleaDVgv 41 
                                       k+++++ +  + +++d +d+e+a + l+++L+e D ++
  gi|242399088|ref|YP_002994512.1| 269 KIKNIFDG-EEIEELDRDDIEQATDILRRQLVERDFNL 305
                                       67888877.566689********************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       780  (0.0435049); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.23s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2774.23
//
Query:       gi|242399089|ref|YP_002994513.1|  [L=419]
Description: Glutamate dehydrogenase [Thermococcus sibiricus MM 739]
Scores for 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  257.9   0.6    1.3e-76  257.5   0.6    1.2  1  ELFV_dehydrog    Glutamate/Leucine/Phenylalanine/Valine dehyd
    1.4e-53  180.3   0.0    3.1e-53  179.1   0.0    1.6  1  ELFV_dehydrog_N  Glu/Leu/Phe/Val dehydrogenase, dimerisation 
    0.00013   21.4   0.1    0.00026   20.4   0.1    1.5  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas


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 !  257.5   0.6   2.2e-80   1.3e-76       1     243 []     182     415 ..     182     415 .. 0.98

  Alignments for each domain:
  == domain 1  score: 257.5 bits;  conditional E-value: 2.2e-80
                                       T--TTTTTHHHHHHHHHHHHHHHHTTTS-STTEEEEEE--SHHHHHHHHHHHHC.T-EEEEEEESSEEEEETTEE-H CS
                     ELFV_dehydrog   1 GGsldrpeaTglGvvyyveemlkklkldslegkrvaisGsGnvgsyaallltel.gakvvavsDssGviydpeGldi 76 
                                       GGsl+r +aT+ G+v++v+e++k l++d l+gk++a++G+Gn g y+a+l++e+ g+kvvavsDs+G iy+p+Gld 
  gi|242399089|ref|YP_002994513.1| 182 GGSLGRGTATAQGAVFTVREAAKALGID-LNGKTIAVQGYGNAGYYMAKLSKEQlGMKVVAVSDSKGGIYNPDGLDP 257
                                       9***************************.*********************98755********************** PP

                                       HHHHHHHHCSSSSTTHSHHSTSTSEEESHHSHHHHSS-SEEEE-SSTTSB-HHHHTHTHHTT-SEEE-SSSS-B-HH CS
                     ELFV_dehydrog  77 eellelkeerksvkeykkssekkaeyieneeellelkvdilvPcAtqneideenakalikngvklvvEgANlpttqe 153
                                       +e+l++kee++svk+++     +a+ i+ne ellel+v++l P+A++ +i+++na+ ++k  +k+v+E+AN+p+t+e
  gi|242399089|ref|YP_002994513.1| 258 DEVLKWKEEHGSVKDFP-----GATNITNE-ELLELEVEVLAPSAIEGVINKDNAD-KVK--AKIVAEVANGPVTPE 325
                                       *****************.....5789***7.*************************.999..*************** PP

                                       HHHHHHHTT-EEE-HHHHTTHHHHHHHHHHHHHHCT----HHHHHHHHHHHHHHHHHHHHHHHHHCT-THHHHHHHH CS
                     ELFV_dehydrog 154 AkeileeagvlvvpdkaaNaGGVtvSslEmlqnlarlswteeevdeklkkimkeifkavveeaeeykqelvkgania 230
                                       A++il+e+g+l +pd+++NaGGVtvS++E++qnl++++wte+ev+ekl+++m+e+f  v++  +e++ +++++a++ 
  gi|242399089|ref|YP_002994513.1| 326 ADDILHEKGILQIPDFLCNAGGVTVSYFEWVQNLMGYYWTEDEVREKLDRKMTEAFWGVYNIHKEKNIHMRDAAYVR 402
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHCT CS
                     ELFV_dehydrog 231 gfekvaeamkaqG 243
                                       ++ +v eamka+G
  gi|242399089|ref|YP_002994513.1| 403 AVSRVYEAMKARG 415
                                       ***********99 PP

>> ELFV_dehydrog_N  Glu/Leu/Phe/Val dehydrogenase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.1   0.0   5.1e-57   3.1e-53       1     129 [.      34     161 ..      34     162 .. 0.99

  Alignments for each domain:
  == domain 1  score: 179.1 bits;  conditional E-value: 5.1e-57
                                       -SEEEEEEEEEE-TTSBEEEEEEEEEEEE-TTSSEEEEEEEETT--HHHHHHHHHHHHHHHHHTTSS-EEEEEEEES CS
                   ELFV_dehydrog_N   1 pervlqvtvpvkrdnGelevikgyraqhssalgPakGGiRfhpsvnldevkaLaalmtyKnalvdlpfGGakggvki 77 
                                       p+r+l+v++pv++d+G+++v++g+r+qh+ algP+kGGiR hp+ +l++vkaLa +mt+K+a ++lp+GG+kggv++
  gi|242399089|ref|YP_002994513.1|  34 PQRILEVSIPVEMDDGSVKVFTGFRVQHNWALGPTKGGIRWHPEETLSTVKALATWMTWKCATLGLPYGGGKGGVIV 110
                                       89*************************************************************************** PP

                                       -GGGS-HHHHHHHHHHHHHHHG.GG-BTTTEEEEBBTTB-HHHHHHHHHHHH CS
                   ELFV_dehydrog_N  78 dpkklseeeleritrrfvrelakkfiGpgiDvpApDvgtgaremawladeyk 129
                                       dpkkls++e e++ r ++r+++ ++i p +DvpApDv+t+++ maw++dey+
  gi|242399089|ref|YP_002994513.1| 111 DPKKLSDREKEKLARGYIRAIY-DIISPYTDVPAPDVYTNPQIMAWMMDEYE 161
                                       **********************.****************************7 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.1   4.3e-08   0.00026      24      69 ..     200     246 ..     185     263 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 4.3e-08
                                       HTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHH.HTT-EEEEESSSH CS
                      2-Hacid_dh_C  24 ksekallgkelsgktvGiiGlGrIGqavakrlk.afgmkviaydrsk 69 
                                       ++ ++ lg +l+gkt+++ G+G+ G  +ak+ k ++gmkv+a++ sk
  gi|242399089|ref|YP_002994513.1| 200 REAAKALGIDLNGKTIAVQGYGNAGYYMAKLSKeQLGMKVVAVSDSK 246
                                       556788999************************99*******99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (419 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       716  (0.0399353); expected 358.6 (0.02)
Passed bias filter:                      620  (0.0345808); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 2824.45
//
Query:       gi|242399090|ref|YP_002994514.1|  [L=522]
Description: Na+dependent transporter [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-51  176.0  34.8    1.5e-28   99.8  14.1    2.2  2  SNF       Sodium:neurotransmitter symporter family


Domain annotation for each model (and alignments):
>> SNF  Sodium:neurotransmitter symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.2  12.6   1.8e-27   3.3e-23       1     115 [.       4     132 ..       4     137 .. 0.81
   2 !   99.8  14.1   8.3e-33   1.5e-28     189     509 ..     166     496 ..     137     509 .. 0.81

  Alignments for each domain:
  == domain 1  score: 82.2 bits;  conditional E-value: 1.8e-27
                               SNF   1 RetwskkldfilsvvGfavgLgnvWRFPYlcyknGGGafliPYlilllvaGiPlfflelalGqytre...Gait..v 72 
                                       R++w +kl  il+++G a+gLgn WRFPY +  nGGGaf+iPY+++l++ G+P++++e   G+y  +   G+++   
  gi|242399090|ref|YP_002994514.1|   4 RDRWATKLGLILAMAGNAIGLGNFWRFPYQAAVNGGGAFMIPYFVALFLLGVPIMWVEWVTGRYGGKyghGTLGptF 80 
                                       899***********************************************************996432125543222 PP

                               SNF  73 w....rkicP....llkgi.GyasivvalyvglyYnvilawalfYlfssftt 115
                                       +    + + P    ++  i G+ ++ v+++++ yY  i++w++ Y++ s+t 
  gi|242399090|ref|YP_002994514.1|  81 YlmarESLKPrsavIFGMIgGMLAFSVTTLLNSYYLHIVGWSAAYTYFSITG 132
                                       32222455562222566664466778999********************985 PP

  == domain 2  score: 99.8 bits;  conditional E-value: 8.3e-33
                               SNF 189 vvvylailkGvkssgkvvyftatfPyvvllvllvrgvlLpG.......avkgikfyltpdlekllepkvWidaatqi 258
                                       + v  ++ kG++   kv++ + +  yv  ++l++r+++L         ++kg +f+ +p +++++  +   +aa qi
  gi|242399090|ref|YP_002994514.1| 166 IAVGQGVSKGIERWVKVMMPA-L--YVAAILLVLRSLTLGSpvkpewsSIKGFEFLWEPRFSEVTFKS-ALAAAGQI 238
                                       234456778888888887764.4..899999999****96422222226799***********98766.578999** PP

                               SNF 259 ffslgigfGvlialasYnkfennvyrdallvslinsltsvlaglvvFsvlGfmaeeqgekisevaeeGpgLaFiayp 335
                                       ff+l++g+G++  +asY   e++v  ++l +  +n + +v+ g  +   + f     ++ i      G gLa+ia p
  gi|242399090|ref|YP_002994514.1| 239 FFTLSLGMGIIQNYASYLGPEDDVALSGLATVSLNEFAEVILGGSIAIPIAFAYLGPEKAI----AGGVGLAYIALP 311
                                       ****************************************999888777777666666655....58********** PP

                               SNF 336 ealtklplsplwsvlFFlmlillgldsqfgtvegiitavvDefkvllrrrelltlivavlaflvglllv...teg.. 407
                                       ++  ++p ++l++ ++Fl l ++g++s++++ + +++ + +++k+   +r++  +iv++l++++gl +v   t++  
  gi|242399090|ref|YP_002994514.1| 312 NVFMRMPGGQLFGAVWFLLLWFAGFTSAIAMYNYLTALLEEDLKI---NRKTGAAIVFILYLILGLPVVldpTKAtl 385
                                       *******************************99998888889999...9999999999999999*999866544422 PP

                               SNF 408 Giyvltlldkyaaslsllvvvlleaiavawvyglkkflddikemlgfrpllflklcwkfvspllllvlliasivklk 484
                                        +y+lt ld+++ s+ l+v+ l+++i+ +w+++ ++f +++++    ++  ++k ++++++p+  ++ll+ s   + 
  gi|242399090|ref|YP_002994514.1| 386 DLYYLTELDNWVGSYLLVVLGLFDIIVAVWLFKPDNFWEELHKGAYIKVPGWIKPIIVYIAPIYTIILLLGSTRDYY 462
                                       57999***********************************************************************9 PP

                               SNF 485 pltynayv........yPkwae.algwllalssv 509
                                       + +y + v        y +w+  a g++l ++ +
  gi|242399090|ref|YP_002994514.1| 463 KAGYFKAVpgyvgapeYANWVWfARGMMLFILII 496
                                       9999886667668555555532122333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (522 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       763  (0.0425568); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.46
# Mc/sec: 3376.56
//
Query:       gi|242399091|ref|YP_002994515.1|  [L=37]
Description: hypothetical protein TSIB_1112 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.055   13.5   0.2      0.055   13.5   0.2    1.1  1  DUF1358   Protein of unknown function (DUF1358)


Domain annotation for each model (and alignments):
>> DUF1358  Protein of unknown function (DUF1358)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.2   3.1e-06     0.055      63      83 ..       3      23 ..       1      34 [. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.1e-06
                           DUF1358 63 kesGaslalralGWGslyall 83
                                      k +G++la+ al WG ++ ++
  gi|242399091|ref|YP_002994515.1|  3 KMKGSALAFMALAWGIIFIWM 23
                                      668**************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 269.40
//
Query:       gi|242399092|ref|YP_002994516.1|  [L=242]
Description: Alpha-glucosidase [Thermococcus sibiricus MM 739]
Scores for complete 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   0.3     0.0008   19.3   0.3    1.1  1  DUF4515   Domain of unknown function (DUF4515)
  ------ inclusion threshold ------
       0.02   15.3   1.1      0.032   14.6   1.1    1.3  1  TINF2_N   TERF1-interacting nuclear factor 2 N-terminus
       0.98    9.7   6.5       0.83    9.9   2.6    2.5  2  DUF4181   Domain of unknown function (DUF4181)


Domain annotation for each model (and alignments):
>> DUF4515  Domain of unknown function (DUF4515)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.3   1.3e-07    0.0008      56     158 ..       7     107 ..       4     122 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.3e-07
                           DUF4515  56 LlqkekeqaklkkeLqalediaklkeqqe.rkiqtLeeekekvqaetaeklrelklqfLkekaalekqleelkllel 131
                                       L++ +++  ++++++++l+ ++ +k+q+  ++i + +e+ +k+ +e    + el + fLk+ ++l+  ++++ + +l
  gi|242399092|ref|YP_002994516.1|   7 LKETAEILEEVEERIRNLNSLSPRKKQNAlNQIREAKENFRKMASEVVIDNDELASFFLKRANKLKNSTNDKTIEKL 83 
                                       7778888999***************9997478********************************************* PP

                           DUF4515 132 gkratkelkkkakalklaAkkalseft 158
                                       g++   +     +a+    k a  +f 
  gi|242399092|ref|YP_002994516.1|  84 GEKTYMK---DVEAMYKYSKAAPYDFA 107
                                       *998776...44455555555555555 PP

>> TINF2_N  TERF1-interacting nuclear factor 2 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   1.1   5.3e-06     0.032      52     112 ..       7      67 ..       5      97 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.3e-06
                           TINF2_N  52 rkekaadlkaiqshlerlrasaakstkkkdekveeaqenflklvqsLledpeerekflqee 112
                                       +ke+a+ l+++++ + +l++ + +++++ +++++ea+enf k+  +++ d++e ++f+ + 
  gi|242399092|ref|YP_002994516.1|   7 LKETAEILEEVEERIRNLNSLSPRKKQNALNQIREAKENFRKMASEVVIDNDELASFFLKR 67 
                                       56778999************999**********************************9665 PP

>> DUF4181  Domain of unknown function (DUF4181)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   2.6   0.00014      0.83      20      74 ..     106     156 ..      95     190 .. 0.83
   2 ?   -2.6   0.1       1.1   6.7e+03      42      50 ..     222     230 ..     205     239 .. 0.48

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00014
                           DUF4181  20 kfsyekhvnklhkkielilrvlfiifiilsliiilsreyvdiiilifvflvvlel 74 
                                       +++y k+vn+ +k+  ++    ++ f++++ + +l+++ + +i+li+++l++l+l
  gi|242399092|ref|YP_002994516.1| 106 FAGYMKYVNRGYKAYVWG----MVSFFVVTAFLPLEFKITSLILLIPIILSLLSL 156
                                       567889999999999888....677778888888999999999888888888765 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.1
                           DUF4181  42 fiifiilsl 50 
                                         +f++++ 
  gi|242399092|ref|YP_002994516.1| 222 AEVFLLSYA 230
                                       223333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1686  (0.0940376); expected 358.6 (0.02)
Passed bias filter:                      836  (0.0466284); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 1799.63
//
Query:       gi|242399093|ref|YP_002994517.1|  [L=108]
Description: Nitrogen regulatory protein P-II [Thermococcus sibiricus MM 739]
Scores for 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  101.2   1.3    9.1e-29  100.1   1.3    1.5  1  P-II      Nitrogen regulatory protein P-II


Domain annotation for each model (and alignments):
>> P-II  Nitrogen regulatory protein P-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.1   1.3   5.1e-33   9.1e-29       1     102 []       7     100 ..       7     100 .. 0.95

  Alignments for each domain:
  == domain 1  score: 100.1 bits;  conditional E-value: 5.1e-33
                                       EEEEEEGGGHHHHHHHHHHTTGGCEEEEEEEEEESTCCEEEECTTEEEEEEEEEEEEEEEEEEGGGHHHHHHHHHHH CS
                              P-II   1 ieaiirpekleevkeaLekagvkgltvtevkGrGkqkghtelyrgaeyevellpkvkleivvsdedvekvveaiika 77 
                                       ieai+r e++++v++aL+++g+  +t+  vkGrG q g            el+pk+k+eivv+dedvekvv++ii++
  gi|242399093|ref|YP_002994517.1|   7 IEAIVREEEFDRVHKALKQMGIVPMTAYPVKGRGVQGGVP--------PYELMPKMKIEIVVKDEDVEKVVNVIIQN 75 
                                       89**********************************9543........3479************************* PP

                                       H-SSSTTSEEEEEEEESEEEETTTT CS
                              P-II  78 aktgeiGDGkiFvlpveevirirtg 102
                                       a+ g +GDGkiF+lpv e+irirt+
  gi|242399093|ref|YP_002994517.1|  76 ARRGIPGDGKIFILPVYEAIRIRTE 100
                                       ***********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); 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: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 742.96
//
Query:       gi|242399094|ref|YP_002994518.1|  [L=566]
Description: Alpha-amylase (intracellular) [Thermococcus sibiricus MM 739]
Scores for complete 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-77  259.9   8.2    1.5e-76  257.7   8.2    2.2  1  Glyco_hydro_57  Glycosyl hydrolase family 57
    7.3e-31  106.6   4.3    7.5e-30  103.3   0.1    3.1  3  DUF1957         Domain of unknown function (DUF1957)
  ------ inclusion threshold ------
       0.01   15.9   0.0       0.01   15.9   0.0    1.8  2  DUF1285         Protein of unknown function (DUF1285)
       0.97    9.9   4.9        1.6    9.2   1.3    2.8  3  FRB_dom         FKBP12-rapamycin binding domain


Domain annotation for each model (and alignments):
>> Glyco_hydro_57  Glycosyl hydrolase family 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  257.7   8.2   3.4e-80   1.5e-76       1     320 [.       6     400 ..       6     406 .. 0.93

  Alignments for each domain:
  == domain 1  score: 257.7 bits;  conditional E-value: 3.4e-80
                                       EEEEEE-----TTS-SSSSSHHHHHHHHHHTHHHHHHHHHHHHHTT----EEEEE-HHHHHHHT-H..HHHHHHHHH CS
                    Glyco_hydro_57   1 afvfhqHqplykkpgkgeytlpwvrehaaedYiklalilekfpkvhvtfeLsgsLiaqLeeylnge..kksylpate 75 
                                       +fvfh+H+p+++k+gk++++++wv+e++ e+Yi+l++++e+f+k+ v+f+L + +++ L+e+l++e  kk++++++e
  gi|242399094|ref|YP_002994518.1|   6 TFVFHTHIPYVRKHGKWPFGEEWVFEAISETYIPLLMEFERFKKKGVKFQLMIGITPILAEQLADEymKKEFEQYME 82 
                                       69*************************************************************************** PP

                                       HHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHT.TT-HHHHHHHHHHCTSEEEEEE-TT-B-GGG-S-HHH CS
                    Glyco_hydro_57  76 ellelieeglerctelkldlavlfnlaisgplleqiqkwlnkevlelfrelqesgqvElltspyyHpllpllpdsed 152
                                       ++l+ ++e+le++ + +l+ a+ ++++++  ++e+++++ n+++l  fr+lq++g++E++ts+++H++lpll+++e+
  gi|242399094|ref|YP_002994518.1|  83 RKLKAMQEDLEKYDDERLKNAISYMIKYFMEVYEYWKNI-NGDILGVFRQLQDEGYIEIITSAATHGYLPLLERDEA 158
                                       ************************************887.************************************* PP

                                       HHHHHHHHHHHHHHHHSS--SBEE-GGG-B--S................HHHHHHHTT--EEEE-C........... CS
                    Glyco_hydro_57 153 ieaqvkkarelyeeyfgqePrgfwlpElavspe................ileilaelGfeylftde........... 202
                                       ie q+ +++ +ye++fg++P+g+wlpE+a++pe                ++++l++ G +++f+++           
  gi|242399094|ref|YP_002994518.1| 159 IEGQITNGILTYEKHFGRKPKGIWLPECAYRPEglwqspssgeivwrkgLEKFLEKHGLKFFFVEShlidegpasfg 235
                                       ***************************************************************************** PP

                                       ------------TTS-EE-TTS.-EEEE--CHH.....-TTTSGGG-.............................. CS
                    Glyco_hydro_57 203 laeiledkskespyrpyllknggiavffRdreL.....sddigFrys.............................. 244
                                       + +il+ k+k+s++rpy++k ++iavf+R+re+     s+dig++++                              
  gi|242399094|ref|YP_002994518.1| 236 YGKILPAKTKKSTLRPYFIKGTNIAVFARNRETglqvwSADIGYPGDfwyrefhkkaeksggqywritskaiglgek 312
                                       *********************************************99****************************99 PP

                                       .....................TTSB....................-TT---TTT--BB-TT-S---HHHHHHHHHHH CS
                    Glyco_hydro_57 245 .........eqypleavddfinwlkkvkka..........ksevvtialdgEnwghypetgkkeFleklyeeleeng 302
                                                e+  +  ++ f+  +k    +           + +v+   d E +gh+   g+k +l k  e + e+ 
  gi|242399094|ref|YP_002994518.1| 313 epyvpekalERVEE-HAKHFVGLVK----SlleeyerehgAKGIVVAPYDTELFGHWWFEGVK-WLGKVLELMAEEN 383
                                       98886555422222.4444555444....24444899998888999999************98.9999999999999 PP

                                       HHHHHHHHHHHHHHSS-E CS
                    Glyco_hydro_57 303 lielvtpsefikklkpkg 320
                                        ie++t+s+f++ ++ ++
  gi|242399094|ref|YP_002994518.1| 384 -IETITISKFLENYQGER 400
                                       .*********99776655 PP

>> DUF1957  Domain of unknown function (DUF1957)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.3      0.15   6.9e+02      46      82 ..      64     100 ..      62     120 .. 0.63
   2 ?    2.0   0.0      0.06   2.7e+02      53      76 ..     318     341 ..     312     352 .. 0.81
   3 !  103.3   0.1   1.7e-33   7.5e-30       1     101 []     430     535 ..     430     535 .. 0.95

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.15
                                       HHTTSSHHHHHHHHHHHHHHHHHHH.HHHHHS---HHH CS
                           DUF1957  46 ittgtaveYAekrikehlerftely.ealesgeideel 82 
                                       + ++ a eY++k +++ +er  + + e+le+ + de+l
  gi|242399094|ref|YP_002994518.1|  64 LAEQLADEYMKKEFEQYMERKLKAMqEDLEKYD-DERL 100
                                       566778899999999999876554404444433.4443 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.06
                                       HHHHHHHHHHHHHHHHHHHHHHHS CS
                           DUF1957  53 eYAekrikehlerftelyealesg 76 
                                       e A +r++eh+++f  l ++l ++
  gi|242399094|ref|YP_002994518.1| 318 EKALERVEEHAKHFVGLVKSLLEE 341
                                       67999*********9999988554 PP

  == domain 3  score: 103.3 bits;  conditional E-value: 1.7e-33
                                       HHHHHHHHHHHHHHHHTTSSHHHHHHHHHHHHHHHHHHBTHHHHHHHTTSSHHHHHHHHHHHHHHHHHHHHHH.... CS
                           DUF1957   1 hlhkaeermvelakkfpeadelkervlnqaaRElLLaqssdWafiittgtaveYAekrikehlerftelyeal.... 73 
                                       h+h ae+rmv+la+k+ ++d+  +rvl+q+ RElLL++ssdW+f++tt +a+eY ++r  eh++ f++l++al    
  gi|242399094|ref|YP_002994518.1| 430 HIHLAERRMVALASKYLHKDKFGDRVLEQLGRELLLIESSDWPFLVTTSQAKEYGKRRLLEHANSFHHLANALekyf 506
                                       89***********************************************************************8888 PP

                                       HHS-.--HHHHHHHHHHS---S--....- CS
                           DUF1957  74 esge.ideelleeleekdniFpeidyrvy 101
                                       +sge  d ++lee+eekdn+F+ id+ vy
  gi|242399094|ref|YP_002994518.1| 507 QSGEfKDMKFLEEIEEKDNPFSSIDIDVY 535
                                       777745677*****************998 PP

>> DUF1285  Protein of unknown function (DUF1285)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.8   1.4         4   1.8e+04       7      14 ..     362     369 ..     362     370 .. 0.86
   2 ?   15.9   0.0   2.3e-06      0.01       8      74 ..     425     492 ..     421     504 .. 0.89

  Alignments for each domain:
  == domain 1  score: -4.8 bits;  conditional E-value: 4
                                       S-EEETTE CS
                           DUF1285   7 GeWfyegs 14 
                                       G+W++eg 
  gi|242399094|ref|YP_002994518.1| 362 GHWWFEGV 369
                                       89****95 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 2.3e-06
                                       -EEETTEE---HHHHHHHHTTEEEETT.EEEEE-.SS-EEEEEESS-SEEEEEEEEES-GGG-EEEEE CS
                           DUF1285   8 eWfyegspikRealvkLFasvLrkeedgeyfLvt.PveklrIeVeDapflavevevegegeeqvlefr 74 
                                       eW++e  ++  +++v L ++ L+k++ g+ +L     e l Ie  D pfl++  ++++ g+++ le  
  gi|242399094|ref|YP_002994518.1| 425 EWMWEHIHLAERRMVALASKYLHKDKFGDRVLEQlGRELLLIESSDWPFLVTTSQAKEYGKRRLLEHA 492
                                       8*******************************86368999*******************999999865 PP

>> FRB_dom  FKBP12-rapamycin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   1.3   0.00036       1.6      36      95 ..      60     116 ..      32     120 .. 0.79
   2 ?   -1.6   0.0      0.81   3.6e+03      40      62 ..     375     398 ..     368     403 .. 0.71
   3 ?   -0.2   0.1      0.31   1.4e+03      13      37 ..     494     517 ..     488     526 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00036
                           FRB_dom  36 lleplhellekgpetlreasFaqafgreLkeaeewlkkykkteneedlnqawdiyyevfr 95 
                                       +   l e+l      ++ ++F q  +r+Lk  +e l+ky  ++ ++ ++ + + + ev++
  gi|242399094|ref|YP_002994518.1|  60 ITPILAEQLAD---EYMKKEFEQYMERKLKAMQEDLEKYDDERLKNAISYMIKYFMEVYE 116
                                       55555555555...57899**************************************997 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.81
                           FRB_dom  40 lhellek.gpetlreasFaqafgr 62 
                                         el+ + + et+  ++F+++++ 
  gi|242399094|ref|YP_002994518.1| 375 VLELMAEeNIETITISKFLENYQG 398
                                       44555441558999999*999986 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.31
                           FRB_dom  13 whegLeeAsrlyfgeknveamlkll 37 
                                        ++ L +A ++yf++ ++++m k+l
  gi|242399094|ref|YP_002994518.1| 494 SFHHLANALEKYFQSGEFKDM-KFL 517
                                       567899999999999999887.444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (566 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       913  (0.0509231); expected 358.6 (0.02)
Passed bias filter:                      593  (0.0330749); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.77u 0.34s 00:00:01.11 Elapsed: 00:00:00.53
# Mc/sec: 3203.18
//
Query:       gi|242399095|ref|YP_002994519.1|  [L=334]
Description: Aspartate-semialdehyde dehydrogenase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-30  105.6   0.0      5e-30  104.9   0.0    1.3  1  Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation dom
    1.9e-27   96.1   0.0    3.7e-27   95.2   0.0    1.5  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
     0.0026   17.9   0.0     0.0046   17.1   0.0    1.4  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
     0.0099   15.4   0.0      0.015   14.8   0.0    1.2  1  Epimerase        NAD dependent epimerase/dehydratase family
  ------ inclusion threshold ------
       0.13   12.9   0.0        0.3   11.8   0.0    1.6  1  DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomer
       0.16   12.8   0.0       0.33   11.8   0.0    1.5  1  GARS_N           Phosphoribosylglycinamide synthetase, N doma
       0.16   12.8   0.0       0.39   11.5   0.0    1.7  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 


Domain annotation for each model (and alignments):
>> Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.9   0.0     2e-33     5e-30       1     183 [.     151     314 ..     151     315 .. 0.85

  Alignments for each domain:
  == domain 1  score: 104.9 bits;  conditional E-value: 2e-33
                                       HHHHHHCTT.EEEEEEEEEEEGGGCHHHHHHHHHHHHHHHHHSTTS.CTTTSSHHTTSEESTCSTBTTTTCHCBHHH CS
                   Semialdhyde_dhC   1 LkPLldalgelervivatyqavSGaGkkgvreLlkqvaelqrsdeakpgvfgvpiagNlipyidkeedkgepetree 77 
                                       L+PL+d  ++++rv+vat+qa+SGaG                      g + ++i +N+ip+i +ee k+e+e+r++
  gi|242399095|ref|YP_002994519.1| 151 LAPLRD--FGIKRVHVATMQAISGAGF--------------------FGLSALAIHDNVIPFISGEEWKIENESRKI 205
                                       89****..56*****************....................7***************************** PP

                                       HHHHHHHHHHCTESCSEEEEEEEESBSSEEEEEEEEEES.SSHHHHHHHHHHHHCS.......TTEEEEESSHCHHS CS
                   Semialdhyde_dhC  78 lkavaetkkileftekvsatcvrVPvlrGhseavtiklk.lkdveveeveellaaa.......pevkvvvneeedrP 146
                                       l+++++ + + + +e vsa+++rVPvl Gh+eav+i+l+  ++++++e++e +           e+ +v     ++P
  gi|242399095|ref|YP_002994519.1| 206 LGKIENGRIKPALFE-VSAIATRVPVLHGHTEAVFIELEhGSTEKIKEAFESFDPLkslslpsYEKPLVYT---EVP 278
                                       **************8.**********************876777777777777777777777734444444...356 PP

                                       SHH..HHTTCSSSEEEEEEEEETTCTTEEEEEEEEETTT CS
                   Semialdhyde_dhC 147 tpa..avaggtnsvsVGRirkdemgdeglklvvvgDNll 183
                                       +p+    +g++++v+VGR++     +  +k+v++g+Nl+
  gi|242399095|ref|YP_002994519.1| 279 QPRfhRERGKGLTVTVGRVEGSD--S-AFKYVITGHNLV 314
                                       6661156666*******998766..4.499********8 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 !   95.2   0.0   1.4e-30   3.7e-27       1     119 [.       2     121 ..       2     123 .. 0.93

  Alignments for each domain:
  == domain 1  score: 95.2 bits;  conditional E-value: 1.4e-30
                                       EEEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSG.GGTTTECEBEEEGGGGGC.TT-SEEEE-SC CS
                    Semialdhyde_dh   1 kvaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavk.aleegkdlkvedvdeeel.kevdivflalp 75 
                                       kva++GatG+vG+ +++lLe hp++e+  l++s+rsaG ++ e+v+ ++ee +d++v + ++     +vd+vf alp
  gi|242399095|ref|YP_002994519.1|   2 KVAVLGATGMVGRTFVKLLEGHPWFEVEKLVASERSAGIRYGELVEdSPEEFRDFEVISLEDFLKdPGVDLVFNALP 78 
                                       7*********************************************9999999999999444433599********* PP

                                       HHHHHHHHHHHHHTTSEEEESSSTTTTSTTSEBE-HHHHGGGGG CS
                    Semialdhyde_dh  76 agvskelapklaeagvkviDlssdfRlkddavyvlpevnreaik 119
                                       a+ + +++++l ++++ ++ ++  +R++dd+++ +pevn+e+++
  gi|242399095|ref|YP_002994519.1|  79 ASLAGDVEERL-AKDIPIFTNARVHRYDDDVPILVPEVNPEHLR 121
                                       ***********.899***************************86 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.8e-06    0.0046       1      53 [.       1      51 [.       1      81 [. 0.82

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.8e-06
                                      EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS-- CS
                            DapB_N  1 ikvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglgkl 53
                                      +kvav+Ga+G +G++ vk++e ++ +e+ + v +++    g   gel++ ++ 
  gi|242399095|ref|YP_002994519.1|  1 MKVAVLGATGMVGRTFVKLLEGHPWFEVEKLVASER--SAGIRYGELVEDSPE 51
                                      89*****************************99987..577888888776654 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   5.8e-06     0.015       2      79 ..       4      87 ..       3     101 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.8e-06
                                      EEETTTSHHHHHHHHHHHHCT...SEEEEEES-STTTTCHHCHHC...EEEE--TT-HHHHHHHHHHHT-SEEEE-..- CS
                         Epimerase  2 lVtGatGfiGsalvkallekg...yevigldrlssasntarledl...elveldltdrsalerlfkeeqpdavihl..A 72
                                       V+GatG++G+ +vk l+ +    +e ++ + +s + + ++l +    e+ +    +  +le+++k+ ++d v+++  A
  gi|242399095|ref|YP_002994519.1|  4 AVLGATGMVGRTFVKLLEGHPwfeVEKLVASERSAGIRYGELVEDspeEFRDF---EVISLEDFLKDPGVDLVFNAlpA 79
                                      69****************98877666666777767777776666644444444...444899*************9766 PP

                                      S.---HHH CS
                         Epimerase 73 a.vggvaa 79
                                         g+v++
  gi|242399095|ref|YP_002994519.1| 80 SlAGDVEE 87
                                      65555555 PP

>> DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00012       0.3       1      36 [.       3      37 ..       3      48 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00012
                                      EEEESTTSHHHHHHHHHHHHCTTTEEEEEEEESSTH CS
                   DXP_reductoisom  1 vviLGsTGSIGtqtLdvieenpdkfevvalaagsnv 36
                                      v++LG+TG +G+  ++++e +p  fev+ l+a+++ 
  gi|242399095|ref|YP_002994519.1|  3 VAVLGATGMVGRTFVKLLEGHP-WFEVEKLVASERS 37
                                      78********************.9******997765 PP

>> GARS_N  Phosphoribosylglycinamide synthetase, N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00013      0.33       1      81 [.       1      97 [.       1     101 [. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00013
                                      EEEEEEESSHHHHHHHHHHTTS.T..TESEEEEEE--CGG.............TTHH..HHHHHHHHCTESEEEE-SHH CS
                            GARS_N  1 mkvLvvGsGGRehalawklaqs.p..kvekvyvapgNagt.............edle..alvefakeekidlvvvGpea 61
                                      mkv v+G  G       kl +  p  +vek+++  + ag+              d+e  +l +f k+ ++dlv+ +  a
  gi|242399095|ref|YP_002994519.1|  1 MKVAVLGATGMVGRTFVKLLEGhPwfEVEKLVASERSAGIrygelvedspeefRDFEviSLEDFLKDPGVDLVFNALPA 79
                                      888899888776655555555423337899**********999999877755533333359****************** PP

                                      HHHTTHHHHHHHHHT-EEES CS
                            GARS_N 62 pLvaGvadaleeekgikvfG 81
                                       L+ +v+++l  +k+i++f 
  gi|242399095|ref|YP_002994519.1| 80 SLAGDVEERL--AKDIPIFT 97
                                      **********..55899996 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 ?   11.5   0.0   0.00015      0.39       1      84 [.       1      91 [.       1      96 [. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00015
                                      EEEEEETT.SHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHH.......HHHTTHEEESSHHHHHTCTTESEEEE-S- CS
                      GFO_IDH_MocA  1 lrvaiiGa.Gkigskhlrplnesqrleevvalldpdaeraeav.......aesfgveaysdleelladpeidavivatp 71
                                      ++va+ Ga G++g+ ++ +l e +++ ev  l+ ++ ++  +         e+f+   + +le+ l+dp +d+v+ a p
  gi|242399095|ref|YP_002994519.1|  1 MKVAVLGAtGMVGRTFV-KLLEGHPWFEVEKLVASERSAGIRYgelvedsPEEFRDFEVISLEDFLKDPGVDLVFNALP 78
                                      689*****8888****9.888888*********9999888887665444444444445555****************** PP

                                      GGGHHHHHHHHHH CS
                      GFO_IDH_MocA 72 ngtheelakaale 84
                                      +++  ++++++++
  gi|242399095|ref|YP_002994519.1| 79 ASLAGDVEERLAK 91
                                      *999999988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 2133.31
//
Query:       gi|242399096|ref|YP_002994520.1|  [L=392]
Description: Threonine synthase [Thermococcus sibiricus MM 739]
Scores for complete 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-82  275.5   0.2    6.1e-82  275.3   0.2    1.0  1  PALP           Pyridoxal-phosphate dependent enzyme
  ------ inclusion threshold ------
      0.067   13.4   0.0         41    4.4   0.0    3.1  3  ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthas


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  275.3   0.2   6.8e-86   6.1e-82       2     294 .]      61     361 ..      60     361 .. 0.96

  Alignments for each domain:
  == domain 1  score: 275.3 bits;  conditional E-value: 6.8e-86
                                       GGCSSS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT CS
                              PALP   2 tlgigpTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaallG 78 
                                       +l +g+TPl +l++l+k +gv++++K+E+ nptgSfKdRg++  ++++ e  g + v++as+GN+ ++lAa+aa++G
  gi|242399096|ref|YP_002994520.1|  61 SLNEGGTPLYKLKNLEKGFGVEIYAKNEGANPTGSFKDRGMTVGVSKALEL-GMDKVICASTGNTSASLAAYAARAG 136
                                       6789***********************************************.************************* PP

                                       -EEEEEEETTS-H.HHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHHHTHHHHHHHHT CS
                              PALP  79 lkvtivvpadasp.ekvallrllGaevvevggdydeavaaaaelaaegegaylvsqfdnptviegygtiglEileql 154
                                       +k++++vp+++ + +k+a+   +Ga+vv v g++d+a++++ e+ a+  g+y++++  np + eg++ti+lEi++ql
  gi|242399096|ref|YP_002994520.1| 137 IKAYVLVPSGKIAlGKLAQAIIYGARVVPVRGNFDDALRVVVEASAK-LGVYMLNSI-NPFRLEGQKTIALEIYDQL 211
                                       ************88*********************************.*********.9****************** PP

                                       TTTEEEEEEE-SSSHHHHHHHHHHHH....HSTT....-EEEEEEECTTCGGTTCCS..S.SS...B.SSS.CCSTC CS
                              PALP 155 ggkpdavvvpvGgGgliaGiaaglke....rrpd....vrvigvepegsdalarslragrrvt.vpvsdtiadglav 222
                                       g +pd +v+pvG++g+i++i++g+ke    +       +r++g+++eg+++l r++++g+  + +++++t a+++++
  gi|242399096|ref|YP_002994520.1| 212 GFVPDNIVLPVGNAGNISAIWKGFKElyekG--IteklPRMMGIQAEGASPLVRAWKTGEKFKpIEKPETVATAIRI 286
                                       **************************76641..14678******************999876516777********* PP

                                       S..CGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHH.HHHHHHCCTTCEEEEEEE-B CS
                              PALP 223 g..spselafelldrlvdeivtvsdeealeamrllarregivvepssaaalaal.klreagelkegdrvvviltg 294
                                       g  ++ ++a+++++++++ + +vsdee+l+a++lla++eg++vep+saa+la+l kl+e ge++++++ v+i tg
  gi|242399096|ref|YP_002994520.1| 287 GnpANWPKAWRAVKESGGLFESVSDEEILQAQQLLASKEGLFVEPASAASLAGLiKLLEIGEVDRSESYVLITTG 361
                                       *8888899***************************************************************9997 PP

>> ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.02   1.8e+02      27      56 ..     105     132 ..      97     163 .. 0.78
   2 ?    4.4   0.0    0.0045        41      21      50 ..     201     230 ..     197     243 .. 0.90
   3 ?    2.4   0.0     0.019   1.7e+02      50      81 ..     333     364 ..     331     372 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.02
                                       HHHHHT--GGGB--THHHH-B-GGGHHHHH CS
                     ACP_syn_III_C  27 vakklglpeekvvvnldeyGntsaasipla 56 
                                       v k l+l ++kv  + + +Gntsa+   +a
  gi|242399096|ref|YP_002994520.1| 105 VSKALELGMDKV--ICASTGNTSASLAAYA 132
                                       678889999998..7899*****9866555 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0045
                                       HHHHHHHHHHHT--GGGB--THHHH-B-GG CS
                     ACP_syn_III_C  21 lriidavakklglpeekvvvnldeyGntsa 50 
                                       ++i  ++ ++lg+ ++ +v  + + Gn+sa
  gi|242399096|ref|YP_002994520.1| 201 KTIALEIYDQLGFVPDNIVLPVGNAGNISA 230
                                       56778899*********************9 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.019
                                       GGHHHHHHHHHHHTTSS-TT-EEEEEEEETTT CS
                     ACP_syn_III_C  50 aasiplaLdeaveegklkpgdlvllvgfGaGl 81 
                                       +a ++  L +++e g++++ +  +l+++G Gl
  gi|242399096|ref|YP_002994520.1| 333 SAASLAGLIKLLEIGEVDRSESYVLITTGHGL 364
                                       67778889999999*****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); 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: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 2302.27
//
Query:       gi|242399097|ref|YP_002994521.1|  [L=292]
Description: Homoserine kinase [Thermococcus sibiricus MM 739]
Scores for complete 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   0.0      1e-11   45.0   0.0    1.4  1  GHMP_kinases_C  GHMP kinases C terminal
    1.6e-11   44.3   0.4    1.6e-11   44.3   0.4    2.3  2  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 !   45.0   0.0   1.2e-15     1e-11       2      79 ..     198     267 ..     197     273 .. 0.85

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 1.2e-15
                    GHMP_kinases_C   2 lealergdlellgellnlsqrselkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkdeaeqvara 78 
                                       + al+++dl+++g+ll +  +  +  +++ l+ + e++ ea++e+Ga+g+++sG+  Gp+vfa++   ++++q+   
  gi|242399097|ref|YP_002994521.1| 198 ILALKENDLQTVGRLLDDRIA-LP--YRKQLMQWYETVREAALEAGAYGFSVSGS--GPAVFAIG---EDVAQIGKV 266
                                       66899************7777.36..*****************************..********...555555544 PP

                    GHMP_kinases_C  79 l 79 
                                       +
  gi|242399097|ref|YP_002994521.1| 267 I 267
                                       4 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 !   44.3   0.4   1.7e-15   1.6e-11       3      65 ..      75     138 ..      73     139 .. 0.92
   2 ?   -1.0   0.1      0.24   2.2e+03      59      59 ..     246     246 ..     192     281 .. 0.55

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 1.7e-15
                                       EEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHH.HH.HHHHHHHHHHHHHHHHHSHHHHHHHHS CS
                    GHMP_kinases_N   3 vikseiPvgaGLGSSAAlavalvaAllallglsl.ee.aklaleaerlaqggngsggDvaasvyG 65 
                                       ++++ i +++G+GSS+A ++a+++A+++ lg++  e+ ++ a e+er a  g+ +g++v +++yG
  gi|242399097|ref|YP_002994521.1|  75 KLTKGIRPKSGIGSSGASSLAGALAMAKVLGVEDdEMiLRAAMEGERVAS-GSVHGDNVIPAYYG 138
                                       67899*9************************9973669*********999.889**********9 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.24
                                       H CS
                    GHMP_kinases_N  59 v 59 
                                       v
  gi|242399097|ref|YP_002994521.1| 246 V 246
                                       1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       343  (0.019131); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1996.17
//
Query:       gi|242399098|ref|YP_002994522.1|  [L=344]
Description: Aspartokinase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      2e-43  148.7   0.1    2.5e-43  148.4   0.1    1.1  1  AA_kinase  Amino acid kinase family


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.4   0.1   1.4e-47   2.5e-43       1     238 [.       3     259 ..       3     262 .. 0.83

  Alignments for each domain:
  == domain 1  score: 148.4 bits;  conditional E-value: 1.4e-47
                                       TEEEEEE-TTCCCCTCCHHHHHHHHHHHHHHHHTTEEEEEE--.HHHHHHHHHH.............TCCCCCHHHC CS
                         AA_kinase   1 krvVvKlGGssltdkeeaslrrlaeqiaalkesgnklvvVhGg.gsftdgllal.............ksglssgela 63 
                                       k+ VvK+GGss+++     + ++++ ++ l  +g klvvV+++ +++t +l++l                       
  gi|242399098|ref|YP_002994522.1|   3 KLRVVKFGGSSVKNS----FWSALKLVEYL-LEGSKLVVVVSAlKGVTEKLIQLseqsdlgifesiiL--------- 65 
                                       578**********55....88999999999.9**********************77555444444440......... PP

                                       ......................E..HHHHHHHHHHHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE.....HH CS
                         AA_kinase  64 a..................glrstleeagevatrdalaslgerlvaallaaglpavglsaaaldateagr...degs 119
                                       +                   ++   + + ++a rd+++s+ge+l+aal+a++l++ g++a +ldate      ++g+
  gi|242399098|ref|YP_002994522.1|  66 EhskmanrlgvdiepilsdLEKAITKRRHDLAWRDYILSFGEKLSAALFAKALENEGVPALSLDATEVLMlrgSFGN 142
                                       1444444444444433335444555555555555*********************************999**99999 PP

                                       HTTTCEEECCHHHHHHHT..T-EEEEESEEEEETTTE...EEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTT CS
                         AA_kinase 120 dgnvesvdaeaieellea..gvvpvltgfigldeege...lgrgssDtiaallAealgAdkliiltdVdGVydadpk 191
                                       ++ + s +   +++l e   +vvpv+tgfi  + +g    lgrg+sD++a++l+++l+A+ ++i++dV+G+y+adp+
  gi|242399098|ref|YP_002994522.1| 143 AKIDFSASLPHVQKLGELteKVVPVVTGFI-GNLNGRtatLGRGGSDYTASALGAMLKAKAVLIMSDVEGIYTADPR 218
                                       999999998888888744325********9.555555689************************************* PP

                                       TCCTTCECCEEEHHHCHHCSSS.TTTHHHHCHHHHHHHHHCTT-EEE CS
                         AA_kinase 192 kvpdarllpeisvdeaeesaselatgGmkvkhpaalaaarrggipvv 238
                                        vp arl++ is d a+      a+ Gmk++hp+al+++++  ip++
  gi|242399098|ref|YP_002994522.1| 219 LVPEARLFHFISRDRAML----AARLGMKALHPEALKPLQG--IPLI 259
                                       ******************....*****************76..6765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       260  (0.0145016); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 2297.50
//
Query:       gi|242399099|ref|YP_002994523.1|  [L=62]
Description: hypothetical protein TSIB_1120, partial [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       244  (0.0136092); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); 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 0.27s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 413.05
//
Query:       gi|242399100|ref|YP_002994524.1|  [L=650]
Description: fibronectin-binding protein [Thermococcus sibiricus MM 739]
Scores for 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-84  282.7  28.2    6.6e-84  282.3  28.2    1.1  1  FbpA           Fibronectin-binding protein A N-terminus (FbpA
    3.6e-29  101.6   0.0      9e-29  100.3   0.0    1.7  1  NFACT-R_1      NFACT protein RNA binding domain
    5.2e-05   23.1   0.0    5.2e-05   23.1   0.0    2.4  3  H2TH           Formamidopyrimidine-DNA glycosylase H2TH domai
     0.0088   16.4   0.2     0.0088   16.4   0.2    3.4  4  Ribosomal_S13  Ribosomal protein S13/S18
  ------ inclusion threshold ------
       0.24   10.3  10.1       0.35    9.7  10.1    1.3  1  LMBR1          LMBR1-like membrane protein
       0.96   10.2   0.0       0.96   10.2   0.0    3.5  3  FliD_N         Flagellar hook-associated protein 2 N-terminus
        4.4    4.8   8.6        6.5    4.2   8.6    1.2  1  ACR_tran       AcrB/AcrD/AcrF family


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 !  282.3  28.2   2.6e-87   6.6e-84       2     423 ..       7     435 ..       6     453 .. 0.94

  Alignments for each domain:
  == domain 1  score: 282.3 bits;  conditional E-value: 2.6e-87
                                       HHHHHHHHHHHHHHHTTXEEEEEEEEETTEEEEEEE.ETTEEEEEEEEXXTTTXEEEEXXXXXXXXSSXXHHHHHHH CS
                              FbpA   2 glvlaavvaELqkellggridkiyqpekdelvltlr.anrgrhkLllsahpsyarihltekpkenpkeppnFcmlLR 77 
                                       +++++ +v+EL+  l+g+r+dkiyq +k+ ++++l+ +++gr++L ++a   ++rihlt++ ke p+ p++F+mlLR
  gi|242399100|ref|YP_002994524.1|   7 SVDIKYIVEELKT-LEGARVDKIYQ-DKNRVRIKLHtTGEGRNDLIIEA---GKRIHLTTYIKEAPQHPSSFTMLLR 78 
                                       68999*******9.**********7.7899******99999999*****...************************* PP

                                       HHHTTXEEEEEEEXTTSSEEEEEEEEEXTTSXEEEEEEEEEXXGGGXEEEEEETTTEEEEESSXBXXXSSXSXXBST CS
                              FbpA  78 kyLkgarivsieqlgfdRivelsiekrdElgdeeeytLivEimgrhSNiiLvdeenkIidaikhvspkqsrvReilp 154
                                       kyL+g+r+++ieq++fdRiv+l+i +          tLi+E++ + +NiiLvde+n Ii a++  ++k   +R+i p
  gi|242399100|ref|YP_002994524.1|  79 KYLSGSRVEKIEQHDFDRIVKLKIGNY---------TLIAELFQK-GNIILVDENNVIISAMRYEEFK---DRTIKP 142
                                       ************************999.........*********.**********************...9***** PP

                                       TXBXXXSXXXSXBXTTSXXH.HHHHHHHHHS.XXXHHHHHHHBTTXXHHHHHHHHTTXSSSH............... CS
                              FbpA 155 gekYelPpsqdklnPleaeeleefkellskkekdlvkaLvkafqGlspllaeelleragldketsakelseedlerl 231
                                        + Y lPp+  + nP ++   e+f+el+s ++ ++v+aL++++ ++++l+aee+l rag++k+++a++l+e++l+ +
  gi|242399100|ref|YP_002994524.1| 143 QHVYLLPPA--RENPVDILW-ENFRELISSQDVEIVRALARKL-NMGGLYAEEILLRAGIEKTKRANALDENELKVI 215
                                       *********..*******99.9*********************.********************************* PP

                                       HHHHHHHHTXXX....XXEE.....XSSSEESSXXTTXX.SSXXXXSXHHHHHHHHTTTXXX--SHHHHHHHHHHH. CS
                              FbpA 232 yealqelleeleeekfepqlvlkeekpeefsvvplkslselekesfdslsealdeyYakkaerdrveqkrsdlekr. 307
                                       +e+++e+++  +    + ++++k+++p ++ +++lk +++++k+ f+++sealdey++k + + +  ++ ++l+++ 
  gi|242399100|ref|YP_002994524.1| 216 FEKIKEVFNAPK----KANIIYKNDNPIDVVPIELKWYESYKKKFFTTFSEALDEYFGKILLESAKIERTKKLQNKk 288
                                       ************....78999999889999999999999*********************99999999999999888 PP

                                       ..HHHHHHHHHHHHHHHHHHHHCCGGH.....HHHHCCHH-----------------------.--........... CS
                              FbpA 308 ..veneleklekklkklekelekaeka.....enyrligelltaylyaikkgmsevelenyydege........... 366
                                         +e++l+k+e+ ++ ++++++++++       n+  i++ll+ +++a+ ++  + e ++  ++g+           
  gi|242399100|ref|YP_002994524.1| 289 rqLEATLRKQEEMINGFKNQIQENQEIgdliyTNFAFIENLLKELSKAV-EKLGWKEFKERVENGKksgnkiaqiik 364
                                       89***********************************************.667899999999984458999****** PP

                                       ..............---------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT- CS
                              FbpA 367 ..............evtIpLdprkspsenAqkyfkkykKlkraveaveeqieetkeeleylesveaaleqa 423
                                                     + +++L  +ks+ enA+ y++k+kK+k++ e+++++ +et ++++ +e++ ++ e+ 
  gi|242399100|ref|YP_002994524.1| 365 nidakekavtieldGKKVKLYLNKSVGENAEIYYEKAKKAKHKLEGAQKAHKETLKKIKEIEKLIEEEEKK 435
                                       **********999999**********************************999999999999998888743 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 !  100.3   0.0   3.5e-32     9e-29       1     109 []     452     561 ..     452     561 .. 0.97

  Alignments for each domain:
  == domain 1  score: 100.3 bits;  conditional E-value: 3.5e-32
                         NFACT-R_1   1 kvfwFkssdgylvimGkDkqeneelikkyleesdvwfhvdkessahvylrlsegeleeipeelleeaaqlakanSia 77 
                                       k++wF ss+g+l+i+GkD+++ne+++k+y++e+d+++h+d+ +++hv+++  +g+  +  e++l ea+q+a+++S+a
  gi|242399100|ref|YP_002994524.1| 452 KFRWFLSSEGFLIIAGKDATTNEIVVKRYMSENDLYCHADIYGAPHVVIK--DGK--KAGEKTLFEACQFAVSMSRA 524
                                       8*************************************************..666..89****************** PP

                         NFACT-R_1  78 .gnklssvdvvyvpasnlsktap....ldtGsvgfkg 109
                                        ++ l s d++++ +++++k+ap    l +G+++++g
  gi|242399100|ref|YP_002994524.1| 525 wKEGLYSGDAYWTDPNQVTKKAPsgeyLGKGAFMVYG 561
                                       **********************************986 PP

>> H2TH  Formamidopyrimidine-DNA glycosylase H2TH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0     2e-08   5.2e-05      39      79 ..     184     224 ..     163     232 .. 0.94
   2 ?   -2.0   0.1       1.4   3.7e+03      16      38 ..     281     304 ..     272     311 .. 0.71
   3 ?   -3.7   0.2         5   1.3e+04      52      70 ..     407     425 ..     404     431 .. 0.52

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 2e-08
                                       --HHHHHHHHHHTT--TTSBGGGS-HHHHHHHHHHHHHHHH CS
                              H2TH  39 lGNiyadEvLfrakihPerlakslskeelellhqeikevlk 79 
                                       +G +ya+E+L ra+i+ ++ a+ l ++el+++ ++ikev++
  gi|242399100|ref|YP_002994524.1| 184 MGGLYAEEILLRAGIEKTKRANALDENELKVIFEKIKEVFN 224
                                       7999**********************************986 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.4
                                       HHHHHT--SBHHHHHHCTT.TSCS CS
                              H2TH  16 aerlkkkkrkiktlLLDqk.lvaG 38 
                                       +++l++kkr++ + L  q+ ++ G
  gi|242399100|ref|YP_002994524.1| 281 TKKLQNKKRQLEATLRKQEeMING 304
                                       578999999999998877425555 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 5
                                       T--TTSBGGGS-HHHHHHH CS
                              H2TH  52 kihPerlakslskeelell 70 
                                       k++++++a++ + ++++ +
  gi|242399100|ref|YP_002994524.1| 407 KLEGAQKAHKETLKKIKEI 425
                                       4555555555555544444 PP

>> Ribosomal_S13  Ribosomal protein S13/S18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.2   3.5e-06    0.0088      10      64 ..     171     225 ..     167     242 .. 0.83
   2 ?   -1.1   1.0      0.88   2.3e+03      34      60 ..     306     332 ..     273     380 .. 0.55
   3 ?   -2.1   1.6       1.9   4.8e+03      30      60 ..     361     392 ..     351     434 .. 0.48
   4 ?   -0.6   0.9      0.63   1.6e+03      34      66 ..     405     437 ..     373     460 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.5e-06
                     Ribosomal_S13  10 kkkveialtaikGiGrrkakiilkkadvdedkrigelteeeiekieeivenkaqy 64 
                                       + +++ al+    +G  +a++il +a+++++kr++ l+e+e++ i e +++  + 
  gi|242399100|ref|YP_002994524.1| 171 DVEIVRALARKLNMGGLYAEEILLRAGIEKTKRANALDENELKVIFEKIKEVFNA 225
                                       55788999999999*********************************99985443 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.88
                     Ribosomal_S13  34 kadvdedkrigelteeeiekieeiven 60 
                                       k +++e++ ig+l   +   ie+++++
  gi|242399100|ref|YP_002994524.1| 306 KNQIQENQEIGDLIYTNFAFIENLLKE 332
                                       445555555666555555555554444 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1.9
                     Ribosomal_S13  30 iilkkadvdedkrigelteeeiek.ieeiven 60 
                                       +i+k++d +e++++ el+ ++++  +++ v +
  gi|242399100|ref|YP_002994524.1| 361 QIIKNIDAKEKAVTIELDGKKVKLyLNKSVGE 392
                                       45566666666666666655554212233332 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 0.63
                     Ribosomal_S13  34 kadvdedkrigelteeeiekieeivenkaqyki 66 
                                       k +++  +++++ t ++i++ie+++e++ +++ 
  gi|242399100|ref|YP_002994524.1| 405 KHKLEGAQKAHKETLKKIKEIEKLIEEEEKKEL 437
                                       445667778888888888888888888555443 PP

>> LMBR1  LMBR1-like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7  10.1   0.00013      0.35     209     343 ..     281     455 ..     199     466 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00013
                             LMBR1 209 aaklntekeeaereledllkevkklrksisesd.........plrkyleeilk........................ 252
                                        +kl+++k + e  l++  + ++  +++i+e++         +                                  
  gi|242399100|ref|YP_002994524.1| 281 TKKLQNKKRQLEATLRKQEEMINGFKNQIQENQeigdliytnF---------Afienllkelskaveklgwkefker 348
                                       2344444444444444445555555555555553333333331.........1333333344456666666666666 PP

                             LMBR1 253 .....kvPeeiaeklks...................nenkteeslakle........kqlikalqkrertekqwkrl 297
                                            k+ ++ia+ +k+                           l+k+         ++ +ka +k e  +k  k+ 
  gi|242399100|ref|YP_002994524.1| 349 vengkKSGNKIAQIIKNidakekavtieldgkkvklY-------LNKSVgenaeiyyEKAKKAKHKLEGAQKAHKET 418
                                       6667666666666666666666667777765554442.......3333333334445899999************** PP

                             LMBR1 298 lekalelediiknksskekefkssessrrgefakqgklkltptley 343
                                       l+k+ e+e++i+++++ke  ++++e++++++f k++         +
  gi|242399100|ref|YP_002994524.1| 419 LKKIKEIEKLIEEEEKKELSVRKLEKRKKKWFEKFR---------W 455
                                       ************************998888887774.........2 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 ?   10.2   0.0   0.00037      0.96       1      34 [.       6      39 ..       6      49 .. 0.87
   2 ?   -1.2   3.9       1.3   3.4e+03      17      48 ..     278     309 ..     270     378 .. 0.68
   3 ?    0.5   0.5       0.4     1e+03      21      51 ..     399     429 ..     386     478 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00037
                                      ..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXH CS
                            FliD_N  1 SglDtdslvkqlmkaerakldkleqkktklewkq 34
                                      S +D++ +v++l + e a++dk++q+k+ +  k 
  gi|242399100|ref|YP_002994524.1|  6 SSVDIKYIVEELKTLEGARVDKIYQDKNRVRIKL 39
                                      789***********************99887665 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.3
                                       XXXXXXXXXXXXXXXXXHHHHHHHHHHHHHHH CS
                            FliD_N  17 rakldkleqkktklewkqsayrelnsklsnlk 48 
                                         + +kl++kk +le+   + +e+ + ++n +
  gi|242399100|ref|YP_002994524.1| 278 IERTKKLQNKKRQLEATLRKQEEMINGFKNQI 309
                                       23555688888888777776666666555543 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.4
                                       XXXXXXXXXXXXXHHHHHHHHHHHHHHHHHH CS
                            FliD_N  21 dkleqkktklewkqsayrelnsklsnlksal 51 
                                       +k +++k kle  q+a +e  +k++++++ +
  gi|242399100|ref|YP_002994524.1| 399 EKAKKAKHKLEGAQKAHKETLKKIKEIEKLI 429
                                       5667777777777777777777777666644 PP

>> ACR_tran  AcrB/AcrD/AcrF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   8.6    0.0026       6.5     571     713 ..     293     436 ..     279     448 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.0026
                                       B-HHHHHHHHHHHHHHHHTTTTEEEEEEEECECS.SE..ECCCEEEEEEEES-GCGS-SGGGSHHHHHHHHHHHCTT CS
                          ACR_tran 571 vsleqtqkvlkqvekilkekpevesvfavtGfae.sgdtagpnsakvfisLkpekerkeeeksvealierlrkelkk 646
                                       ++l +++++++ +++ ++e++e+ +++ ++ fa+ ++  ++ ++a      k  ker e+ k++ + i+++ k++++
  gi|242399100|ref|YP_002994524.1| 293 ATLRKQEEMINGFKNQIQENQEIGDLIYTN-FAFiENLLKELSKAVEKLGWKEFKERVENGKKSGNKIAQIIKNIDA 368
                                       6899999*****************998766.4566999********************9999999999999999988 PP

                                       STSSEEEEEETTSSCC.CSSSSCEEEEEEE.SSSSHHHHHHHHHHHHHHHHCCSTTEEEEEESS-S-E CS
                          ACR_tran 647 ipganvellapiqlre.letlsgvrselqvklfgddleaLseaaeqllaalkelpelsdvrseqqedq 713
                                        ++a  + l+  +++  l+++ g ++e+ +  + +  ++L+ a+++ ++ lk+++e++++  e ++++
  gi|242399100|ref|YP_002994524.1| 369 KEKAVTIELDGKKVKLyLNKSVGENAEIYYEKAKKAKHKLEGAQKAHKETLKKIKEIEKLIEEEEKKE 436
                                       88888888888888877999*************************************99887766654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (650 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2601  (0.145072); expected 358.6 (0.02)
Passed bias filter:                      736  (0.0410508); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); 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):               7  [number of targets reported over threshold]
# CPU time: 0.88u 0.37s 00:00:01.25 Elapsed: 00:00:00.54
# Mc/sec: 3643.66
//
Query:       gi|242399101|ref|YP_002994525.1|  [L=146]
Description: hypothetical protein TSIB_1122 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); 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 0.29s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 1002.23
//
Query:       gi|242399102|ref|YP_002994526.1|  [L=365]
Description: Pyruvate formate-lyase activating enzyme related protein [Thermococcus sibiricus MM 739]
Scores for complete 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   40.7   0.0    5.7e-10   39.8   0.0    1.6  1  Radical_SAM  Radical SAM superfamily
    1.1e-06   28.8   0.0    2.2e-06   27.8   0.0    1.5  1  Fer4_14      4Fe-4S single cluster domain
    0.00022   21.5   0.1    0.00064   20.0   0.0    1.8  2  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 !   39.8   0.0   9.6e-14   5.7e-10       4     121 ..      37     157 ..      34     231 .. 0.80

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 9.6e-14
                                       ESEESS--TTTSCCTT....HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC.C CS
                                       xxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x RF
                       Radical_SAM   4 trgCnlrCsfCarpet....vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla.v 75 
                                       t  C++ C +C+ +      v+      ++ v +i+ee+k+      + +  ++gg+pl + d ++++ +  k+   
  gi|242399102|ref|YP_002994526.1|  37 TGICPRECFYCPLSPWrredVSYANERPIKNVNDIIEEAKIQE----ALGAGVTGGDPLSRIDRTVKYIKTLKENfG 109
                                       778********99975644444444455555555555554443....88999************999999999999* PP

                                       CTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHH..HHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxx RF
                       Radical_SAM  76 pgiritvetngtlpdeeklerllelgvdrvslgleaadde..kvlklm 121
                                       ++++i++ t g+l +ee l +l ++g+d + ++ +++++    +++ +
  gi|242399102|ref|YP_002994526.1| 110 KKFHIHLYTTGLLATEENLGKLYDAGLDEIRFHPDIFNPNsnIFQREI 157
                                       **************************************9855444443 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 !   27.8   0.0   3.7e-10   2.2e-06       2      94 ..      35     125 ..      33     139 .. 0.77

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 3.7e-10
                           Fer4_14   2 fvrlsgCnlsCkgCdnketwks...elgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlk 75 
                                       f  ++ C+ +C  C  +  w+    ++ ++   + +++i++++k +e    g  +tGG+PL   + +  +k +k lk
  gi|242399102|ref|YP_002994526.1|  35 FT-TGICPRECFYCPLSP-WRRedvSYANERPIKNVNDIIEEAKIQEA--LGAGVTGGDPL--SRIDRTVKYIKTLK 105
                                       44.899********9665.65522255555555566677766666665..56789******..899*********** PP

                           Fer4_14  76 eey.pekkiwletngtleie 94 
                                       e++ ++++i+l+t g+l+ e
  gi|242399102|ref|YP_002994526.1| 106 ENFgKKFHIHLYTTGLLATE 125
                                       ***899*********99865 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   1.1e-07   0.00064       4      92 ..      28     118 ..      25     136 .. 0.80
   2 ?   -2.7   0.0       1.1   6.5e+03      71     102 ..     186     217 ..     170     235 .. 0.68

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.1e-07
                           Fer4_12   4 eGvrlslfvsg.CnlsCkgCfnketw..sfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvk 77 
                                       +G+ l+lf++g C+++C +C    ++  ++++ +e + +  + iie++k ++  g  ++GG+Pl     +  ++ +k
  gi|242399102|ref|YP_002994526.1|  28 KGTKLVLFTTGiCPRECFYCPLSPWRreDVSYANERPIKNVNDIIEEAKIQEALGAGVTGGDPLS--RIDRTVKYIK 102
                                       588999**6655********866665445668888888889999****99***************..8999999999 PP

                           Fer4_12  78 evkeekpek.diwlyt 92 
                                        +ke++ +k  i lyt
  gi|242399102|ref|YP_002994526.1| 103 TLKENFGKKfHIHLYT 118
                                       9999999541444444 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.1
                           Fer4_12  71 allelvkevkeekpekdiwlytgytleelskk 102
                                         +e++++  +++++ + ++++ + le+l+++
  gi|242399102|ref|YP_002994526.1| 186 WYAEFLDKHGAKFLNINELEFSETNLEALLSR 217
                                       45677888888888888888888888888764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); 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: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 2231.94
//
Query:       gi|242399103|ref|YP_002994527.1|  [L=1070]
Description: Isoleucyl-tRNA synthetase [Thermococcus sibiricus MM 739]
Scores for complete 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-188  625.6   7.2   1.1e-187  625.0   7.2    1.3  1  tRNA-synt_1    tRNA synthetases class I (I, L, M and V)
    2.5e-37  128.2   2.0    3.2e-37  127.8   0.5    2.0  2  Anticodon_1    Anticodon-binding domain of tRNA
    8.4e-25   87.3   4.3      2e-08   33.4   0.0    4.2  3  tRNA-synt_1g   tRNA synthetases class I (M)
    8.4e-08   31.9   0.2    3.5e-05   23.3   0.0    2.9  3  tRNA-synt_1e   tRNA synthetases class I (C) catalytic domain
    5.5e-05   22.2   0.0      0.028   13.4   0.0    2.5  2  tRNA-synt_1f   tRNA synthetases class I (K)
    0.00056   19.5   0.0     0.0022   17.5   0.0    2.1  1  tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
     0.0086   15.9   0.0       0.91    9.4   0.0    2.6  2  DUF4720        Domain of unknown function (DUF4720)
  ------ inclusion threshold ------
       0.19   11.6   0.1       0.19   11.6   0.1    1.9  2  zf-FPG_IleRS   Zinc finger found in FPG and IleRS


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 !  625.0   7.2    5e-191  1.1e-187       3     601 ..      20     664 ..      18     665 .. 0.95

  Alignments for each domain:
  == domain 1  score: 625.0 bits;  conditional E-value: 5e-191
                       tRNA-synt_1   3 yekWeeedvfkkelekekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaieak 79 
                                        + W+e+++++k ++++++ +++ + dgPPyv G++H+G a++k++kd+vir+++m+G++v+++pG+D++Gl+ie k
  gi|242399103|ref|YP_002994527.1|  20 EKLWKENEIYNKVKKARETGPDYYFLDGPPYVSGAIHLGTAWNKIIKDMVIRFRSMQGYNVRRQPGFDMHGLPIEVK 96 
                                       579**********9*************************************************************** PP

                       tRNA-synt_1  80 vekklgakekke.rkklgreefrekvrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkgl 155
                                       ve+ lg k kk+  +k+g+e+f++k+r+++ +  + +++q+k lGv++D+d++y+T+++e+ e+ + +++r  ++gl
  gi|242399103|ref|YP_002994527.1|  97 VEQALGLKYKKDiEEKVGVENFIKKCRDFALTNLKIMTEQFKMLGVWMDWDNPYMTIKNEYIESAWFTLKRAWENGL 173
                                       ******9977762679************************************************************* PP

                       tRNA-synt_1 156 iyrgkklvnwstklktalselEv..eykdkkdalihvafpladkeevklviaTTtPeTllgdtavavnpeldyv... 227
                                       + + +++++w+++++tal+e Ev  eyk  +d++i+v+fp+++k++ ++ i+TTtP+Tl++++av+v+pe +y+   
  gi|242399103|ref|YP_002994527.1| 174 LEKDQRVLHWCPRCETALAEHEVrgEYKIREDPSIYVKFPVEGKDNEYVLIWTTTPWTLPANLAVTVHPEYEYAkvk 250
                                       **********************************************9***************************999 PP

                       tRNA-synt_1 228 ....itkeklilaeallkslvkke.sekkiledergkeLegkevelpl.............vnrkipiiaddyvdke 286
                                            ++e++i+a+al+  +++++  + +i+e+++g+eLeg+++ +p+              + + ++i +++v+  
  gi|242399103|ref|YP_002994527.1| 251 vsheGKEEYWIVAKALVGRILEETgAKGEIVEEFKGEELEGLRYVHPFleeyprqkefrekYKWAHKLILGEHVTLG 327
                                       9987788999*************97888****************************99988888899********** PP

                       tRNA-synt_1 287 aGtGvVkiaPahdedDyevgkkynlevinildedgtlteeaaefeglkvfdarkkvveelkekglllkaekiehsvp 363
                                       +GtG+V++aP+h+e+D+e+gk+y++++ ++ld++g++ e  ++++g  v+da+  +ve+l+ekglllka +ieh++p
  gi|242399103|ref|YP_002994527.1| 328 EGTGLVHTAPGHGEEDFEIGKQYGIPIYSPLDDEGRYYE--GKWKGKFVKDADPEIVEYLREKGLLLKAGTIEHKYP 402
                                       *************************************98..69********************************** PP

                       tRNA-synt_1 364 fcerskkpiiyrateqWfvrvkeladaalkave.kvqfvpkskekryaswleniqdWciSRqrwWGhriplfvsket 439
                                       +c+r k+p+i+rat+qWf ++++++d+++++++ kv+++p++ + ry + +    dWciSRqr+WG ++p++ s++ 
  gi|242399103|ref|YP_002994527.1| 403 HCWRCKTPLIFRATDQWFLKISKVKDKIIEENDkKVTWYPDWVKIRYDNGVMHSGDWCISRQRYWGIPLPIWSSED- 478
                                       ******************************9998*****************************************9. PP

                       tRNA-synt_1 440 eevvvreelkelvagreeee..aekkalekeakdkl......................kkekgelekdedvlDvWFs 492
                                       +e++++   +elv+  ++ e  +e+ +l ++  +kl                      k +++e+++++dvlDvWF+
  gi|242399103|ref|YP_002994527.1| 479 GEIYIVGTFEELVELSVAIEvnGERIELPESYDEKLrvieeklgpedlhrpyvdafviKVNNKEMKRVKDVLDVWFD 555
                                       5688888877777765544400445555567777778889999********************************** PP

                       tRNA-synt_1 493 SgswpfstlgypeedteelkkffpadmlleGlDiirgWvarlillslaltgsePfkevlvhglvrdeeGrKmSKslg 569
                                       Sg    ++l+yp + ++ +++ +pad+++eG D++  W+++    s+  ++ +P+++v +hg v+de+G KmSKslg
  gi|242399103|ref|YP_002994527.1| 556 SGIASWASLDYPRR-KDLFERLWPADFIVEGEDQVTKWFYSQQAASVVAFDTVPYRKVAMHGYVLDEKGDKMSKSLG 631
                                       **************.999*********************************************************** PP

                       tRNA-synt_1 570 NvidpldvikkygadalRltli.lsdvgrdinl 601
                                       N+i p+dvi+k g d  R++++  ++  +++++
  gi|242399103|ref|YP_002994527.1| 632 NIIRPEDVIQKDGRDPFRFYMLwATTPWENLRF 664
                                       *********************977777776665 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 !  127.8   0.5   1.4e-40   3.2e-37       1     151 [.     711     862 ..     711     864 .. 0.93
   2 ?   -2.1   0.0       1.5   3.3e+03      91     140 ..     935    1007 ..     930    1018 .. 0.52

  Alignments for each domain:
  == domain 1  score: 127.8 bits;  conditional E-value: 1.4e-40
                       Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkra.aqevllevletllrl 76 
                                       d+wils++n+l+++v++ +e++ + ka + + +f+++dl++wy++++++rl+ e +++++  a+++l+++++ llrl
  gi|242399103|ref|YP_002994527.1| 711 DKWILSKVNNLISTVEDGLESFYLTKATRGIENFIIEDLSRWYVRVIRKRLWVERDDPDKLaAYWTLWKIFDVLLRL 787
                                       9****************************************************99988877799************* PP

                       Anticodon_1  77 laPfmPfitEelwqr..eeeelgkkesimlaewpekaeel.ekeleeeevellkeivkairklrselkikpsselkv 150
                                       +aPf+P+itEe++q+  +   + +kes++l++wp+k+e + +++l e+e+e++++iv+a  ++r++ kik + ++k 
  gi|242399103|ref|YP_002994527.1| 788 MAPFTPYITEEIYQNliR--PFSNKESVHLEDWPKKDESWvDGDL-EKEMEIVRKIVEAGSAARQKAKIKLRYPVKQ 861
                                       ***************763..356789********98889998888.99**********************9999765 PP

                       Anticodon_1 151 v 151
                                       v
  gi|242399103|ref|YP_002994527.1| 862 V 862
                                       4 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.5
                       Anticodon_1   91 r............eeeelgkkesimlaewpe.kaeelekel.e..............eeevellkeivkairklr 137 
                                        r            +e +++k+  im +e pe    e+     +                   l++e v+ i+++r
  gi|242399103|ref|YP_002994527.1|  935 RlmqgklkvevgdKEFTIEKEHIIMEEELPEfLIGEE---FdHgkvfvdkiitrelmT--EGLAREFVRRIQEMR 1004
                                        4444455556665556678888899999996333222...122334454555544331..122334555555555 PP

                       Anticodon_1  138 sel 140 
                                        ++l
  gi|242399103|ref|YP_002994527.1| 1005 KQL 1007
                                        555 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 !   33.4   0.0   9.1e-12     2e-08       8     138 ..      49     199 ..      46     205 .. 0.76
   2 !   20.1   0.1   9.6e-08   0.00022     165     247 ..     400     483 ..     384     493 .. 0.80
   3 !   31.9   0.3   2.5e-11   5.6e-08     240     373 ..     545     671 ..     496     682 .. 0.79

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 9.1e-12
                                       B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHH...........HTTS-HHHHHHHHH.. CS
                      tRNA-synt_1g   8 pYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAe...........kegvtpeelvekvh.. 71 
                                       pY++g++HlG + + i+ D+++R++ ++g++v    g D+hG pie+k e           +e+v +e++++k +  
  gi|242399103|ref|YP_002994527.1|  49 PYVSGAIHLGTAWNKIIKDMVIRFRSMQGYNVRRQPGFDMHGLPIEVKVEqalglkykkdiEEKVGVENFIKKCRdf 125
                                       8*********************************************9876222332222224667777777765422 PP

                                       .....HHHHHHHHHTT-..--SEEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GGG-EE. CS
                      tRNA-synt_1g  72 .....eeikelfkklni..sfdkygrttseehkelvqeifkklkekgliyekeieqlycpkderflpdryvegt 138
                                            ++++e+fk l++   +d+ + t ++e  e +   +k+  e+gl+++ +    +cp++e+ l++ +v+g+
  gi|242399103|ref|YP_002994527.1| 126 altnlKIMTEQFKMLGVwmDWDNPYMTIKNEYIESAWFTLKRAWENGLLEKDQRVLHWCPRCETALAEHEVRGE 199
                                       22222566777787776224566677777777777777778888999999999999999999999999999886 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 9.6e-08
                                       ............EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHHH..HH.HHHHT----EE-ESS-SSS-EET. CS
                      tRNA-synt_1g 165 inpksaisgskpevketehlffklskfekklkewieeeekeleenvkk..ivkewlkegLkdlaisrdldwGipvP. 238
                                       + p++  +++  +++ t+++f+k+sk+++k+ e  +++  ++     k  + + ++++   d++isr+  wGip+P 
  gi|242399103|ref|YP_002994527.1| 400 KYPHCWRCKTPLIFRATDQWFLKISKVKDKIIEENDKKV-TWYPDWVKirYDNGVMHS--GDWCISRQRYWGIPLPi 473
                                       4699*************************9977664444.455544440044555666..7***************9 PP

                                       .TECCEEE-H CS
                      tRNA-synt_1g 239 .gaekkvlYV 247
                                         +e+  +Y+
  gi|242399103|ref|YP_002994527.1| 474 wSSEDGEIYI 483
                                       9888888885 PP

  == domain 3  score: 31.9 bits;  conditional E-value: 2.5e-11
                                       ECCEEE-HHHHHHHHHHHTTTTT-...TTSGGGG.G--S......EEEEEGGGHH.HHHTHHHHHHHHTT----S-E CS
                      tRNA-synt_1g 240 aekkvlYVWldAligYisatkelakkkgeeekwkeyWakdkevelvhfigkdiik.FHtifwPaillgaelklpkkv 315
                                       + k vl VW+d  i   +++ +      +++ +++ W +d       + g d ++ +      a + + +    +kv
  gi|242399103|ref|YP_002994527.1| 545 RVKDVLDVWFDSGIASWASLDYPR----RKDLFERLWPAD-----FIVEGEDQVTkWFYSQQAASVVAFDTVPYRKV 612
                                       44668999***9999999999986....45799999*442.....233377766424444556777788888999** PP

                                       EEE--EE.E--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE-HHHHHH CS
                      tRNA-synt_1g 316 vaheylt.vegkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfswedfve 373
                                       + h+y+   +g+K+SkS g+++ +++++++   d +R+y++ ++   ++l fsw+ + +
  gi|242399103|ref|YP_002994527.1| 613 AMHGYVLdEKGDKMSKSLGNIIRPEDVIQKDGRDPFRFYMLWATTPWENLRFSWKGLAQ 671
                                       *****762679*******************************************98765 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.3   0.0    0.0048        11      18      49 ..      50      81 ..      37      83 .. 0.91
   2 !   23.3   0.0   1.5e-08   3.5e-05     225     299 ..     596     672 ..     580     674 .. 0.81
   3 ?   -3.7   0.1       2.7   6.1e+03      56      65 ..    1010    1019 ..     978    1046 .. 0.41

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0048
                                      BTTS--BHHHHHHHHHHHHHHHHHHHTT-EEE CS
                      tRNA-synt_1e 18 tvydashlGhaRslvafDilrrilqalgYdvq 49
                                       v  a+hlG a + ++ D++ r+  ++gY+v+
  gi|242399103|ref|YP_002994527.1| 50 YVSGAIHLGTAWNKIIKDMVIRFRSMQGYNVR 81
                                      57889*************************96 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 1.5e-08
                                       HHHHHHHHSS.S--EEEEEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHSS-.TTS-EEE-HHHHHHH CS
                      tRNA-synt_1e 225 elaqseaafd.kqlvkyflhnghlkiegekmsksLknfitikdvlkkfdprqlRllllsah.yrsqldfkeelleea 299
                                         a s  afd  ++ k  +h  +l  +g+kmsksL+n+i+ +dv++k     +R+++l a    ++l f+ + l+++
  gi|242399103|ref|YP_002994527.1| 596 QQAASVVAFDtVPYRKVAMHGYVLDEKGDKMSKSLGNIIRPEDVIQKDGRDPFRFYMLWATtPWENLRFSWKGLAQV 672
                                       56888999998999****************************************99875431234566666666655 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 2.7
                                        --SHHHHHHH CS
                      tRNA-synt_1e   56 DidDkiikra 65  
                                        D++D+i++  
  gi|242399103|ref|YP_002994527.1| 1010 DVNDRIMAYV 1019
                                        3333333322 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 !    6.2   0.0    0.0019       4.2      10      61 ..      27      79 ..      21      83 .. 0.76
   2 !   13.4   0.0   1.2e-05     0.028     270     321 ..     614     666 ..     585     675 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0019
                      tRNA-synt_1f 10 klieerkkkka.ekdevvvesGispSGliHiGnlrevltadlvaralrkrgee 61
                                      ++ ++ kk+++ + d++ ++    +SG iH+G++ + +  d+v r  + +g +
  gi|242399103|ref|YP_002994527.1| 27 EIYNKVKKAREtGPDYYFLDGPPYVSGAIHLGTAWNKIIKDMVIRFRSMQGYN 79
                                      455555555665888999999999******************99876666655 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 1.2e-05
                      tRNA-synt_1f 270 vYelillkggekmssSkGnvltledwlevaepevlrflil.rrkPkkakkldl 321
                                       +  ++l+++g+kms+S Gn++ +ed+++   ++  rf++l  + P ++++++ 
  gi|242399103|ref|YP_002994527.1| 614 MHGYVLDEKGDKMSKSLGNIIRPEDVIQKDGRDPFRFYMLwATTPWENLRFSW 666
                                       667899******************************99872456666666665 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 !   17.5   0.0   9.9e-07    0.0022      10     138 ..     208     356 ..     202     377 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 9.9e-07
                     tRNA-synt_1_2  10 leiefkvees.eeklevfttrpdtlfGvtfvalapehplvekl.....aekkke....laafieevkkkseserele 76 
                                       + ++f+ve++ +e + ++tt p tl     v++ pe + ++       +   +e     +a++ ++ +++ ++ e+ 
  gi|242399103|ref|YP_002994527.1| 208 IYVKFPVEGKdNEYVLIWTTTPWTLPANLAVTVHPEYEYAKVKvshegK---EEywivAKALVGRILEETGAKGEIV 281
                                       57899999997789999********999999999999999866553321...2222213456666666666666666 PP

                     tRNA-synt_1_2  77 tkekeGvftglkaihPitgek.............ipiwvanyvlmeygtgavmavPahdqrDfeFakkynlpikq 138
                                       ++ k    +gl  +hP+ +e                + + ++v  + gtg v + P+h ++Dfe  k+y++pi  
  gi|242399103|ref|YP_002994527.1| 282 EEFKGEELEGLRYVHPFLEEYprqkefrekykwaHKLILGEHVTLGEGTGLVHTAPGHGEEDFEIGKQYGIPIYS 356
                                       655555589999999999887788899999999889999*********************************976 PP

>> DUF4720  Domain of unknown function (DUF4720)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.032        71      38      65 ..      71      98 ..      63     109 .. 0.80
   2 !    9.4   0.0    0.0004      0.91      25      52 ..     560     587 ..     556     604 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.032
                           DUF4720 38 ffrtlqayflrr..Gldlekfpaafsikne 65
                                       fr++q y +rr  G d++ +p + ++  e
  gi|242399103|ref|YP_002994527.1| 71 RFRSMQGYNVRRqpGFDMHGLPIEVKV--E 98
                                      59*********9889***999988776..3 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0004
                           DUF4720  25 kWkslenPrnrdlffrtlqayflrrGld 52 
                                       +W sl+ Pr +dlf r   a f+  G d
  gi|242399103|ref|YP_002994527.1| 560 SWASLDYPRRKDLFERLWPADFIVEGED 587
                                       7*********************999977 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 ?   11.6   0.1   8.4e-05      0.19      16      28 ..     176     188 ..     174     190 .. 0.87
   2 ?   -4.5   1.8         8   1.8e+04       5       9 ..     402     406 ..     402     410 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.4e-05
                                       CTTEEEEE-TTTT CS
                      zf-FPG_IleRS  16 qagrstyfCprCq 28 
                                       +++r  ++CprC 
  gi|242399103|ref|YP_002994527.1| 176 KDQRVLHWCPRCE 188
                                       689*********6 PP

  == domain 2  score: -4.5 bits;  conditional E-value: 8
                                       TTT-- CS
                      zf-FPG_IleRS   5 pRCwr 9  
                                       p+Cwr
  gi|242399103|ref|YP_002994527.1| 402 PHCWR 406
                                       67776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1070 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1117  (0.0623013); expected 358.6 (0.02)
Passed bias filter:                      738  (0.0411624); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); 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: 0.92u 0.32s 00:00:01.24 Elapsed: 00:00:00.51
# Mc/sec: 6302.22
//
Query:       gi|242399104|ref|YP_002994528.1|  [L=40]
Description: hypothetical protein TSIB_1125 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       146  (0.00814323); expected 358.6 (0.02)
Passed bias filter:                      138  (0.00769703); 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: 0.40u 0.30s 00:00:00.70 Elapsed: 00:00:00.47
# Mc/sec: 253.26
//
Query:       gi|242399105|ref|YP_002994529.1|  [L=396]
Description: hypothetical protein TSIB_1126 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-64  219.1  30.8    1.5e-64  218.8  30.8    1.0  1  DUF401    Protein of unknown function (DUF401)
  ------ inclusion threshold ------
      0.029   14.5   0.1      0.098   12.8   0.0    1.9  2  DUF2615   Protein of unknown function (DUF2615)


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 !  218.8  30.8   1.7e-68   1.5e-64       5     384 ..       5     389 ..       2     394 .. 0.86

  Alignments for each domain:
  == domain 1  score: 218.8 bits;  conditional E-value: 1.7e-68
                            DUF401   5 llllfsvivvlilik.klsisllifvivailalkv.lileillvtlksladsfti...eivvvvllalllGyseksf 76 
                                       l ll s  v+   i+ +++i++ i +++++l ++  l+ + ll  l  ++ + ++   +i+++v +  l+G+  +  
  gi|242399105|ref|YP_002994529.1|   5 LYLLVSFGVIIGFIRlRINIGISILLGSLLLGVLFgLGPKKLLTSLY-ISSTEWStmrLIIIIVSITALTGIFSQI- 79 
                                       555666666666665479***************99999999998876.5555554222788888888999999887. PP

                            DUF401  77 Gdlekvseelreif..skyvdllvPlliGllPmPGGalisavilknllkeerisseklalknywfrhvivtfwPlyP 151
                                       G l+ + +  ++ f   ky+   +P+liGllPmP Gal+sa++++    +  +s+e+ ++ nywfrh+++  wP+y 
  gi|242399105|ref|YP_002994529.1|  80 GYLKLMEKATKDLFpnEKYSLAALPALIGLLPMPAGALVSAPMIETIADKLNVSPERKTIINYWFRHIWEHSWPMYQ 156
                                       888888888888883347888889***************************************************** PP

                            DUF401 152 avvlvaelvnvdyfkvalalfPvfvialtlG.ltltrkqerrlrksrs...lfdsli.nlyPliillilsvlllldk 223
                                       a+++++++ ++   +++  +f +  + +++G l++ r  + +  k+++    +  ++   yP+++++ +s++l  d+
  gi|242399105|ref|YP_002994529.1| 157 AIIIASAILDISVREFSTKMFLLTLVMVLIGyLFFLRPIKSQEDKNKNtkkGLKLFLkSTYPIMVIILVSIVLGYDM 233
                                       *******************************98888766555555555111334343268***************** PP

                            DUF401 224 llalvvlllavsiyavakledllkilkrvvdkkvilllfavyvykvvvensGvaesl.aedvrlnlsapillilltl 299
                                       + + ++ +l+  i   + + + ++++k  ++ k+i+llf v+ +k ++e +G+ e+l  + ++lnl+  +++ l ++
  gi|242399105|ref|YP_002994529.1| 234 VYGALIGFLSALIP-HFNKINHKEVVKYALQPKIIFLLFSVMYFKKLLEVTGAVEALpKTIIELNLPVVLVIALTPF 309
                                       ***99999998775.56667789**********************************99****************** PP

                            DUF401 300 lvGiatGieqaavsialPlltevtssgivvakylvlviaaaviGvilsPvhlcvvlsakyfevevfdilkklllilv 376
                                       l+G+ tGi  a+v++a+Pll+ +++s      ++ l ++ +++G+++sP+hlc+v+sa+y++ +++++++++ll+  
  gi|242399105|ref|YP_002994529.1| 310 LIGLMTGISFAYVGMAFPLLLPFFTS----FDKIALAYLSGYMGMLFSPIHLCLVFSAEYYNADLGKVYREMLLPGL 382
                                       **************************....5667899************************************9955 PP

                            DUF401 377 ltlilval 384
                                       +  +l+ +
  gi|242399105|ref|YP_002994529.1| 383 VLFLLG-V 389
                                       444443.3 PP

>> DUF2615  Protein of unknown function (DUF2615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0         1   9.1e+03      11      25 ..      52      66 ..      51      70 .. 0.77
   2 ?   12.8   0.0   1.1e-05     0.098      49      89 ..     168     206 ..     161     211 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1
                           DUF2615 11 iwshelamrrLlsll 25
                                      i s+e++  rL+ ++
  gi|242399105|ref|YP_002994529.1| 52 ISSTEWSTMRLIIII 66
                                      778888888888766 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 1.1e-05
                           DUF2615  49 skeggsslfliallwlvvaavlfllrPsslrnasaknkpsr 89 
                                       s +++s+ +++++l++v++  lf+lrP + ++  +knk+++
  gi|242399105|ref|YP_002994529.1| 168 SVREFSTKMFLLTLVMVLIGYLFFLRPIKSQE--DKNKNTK 206
                                       56788999*******************97665..4444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1008  (0.0562218); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 3049.44
//
Query:       gi|242399106|ref|YP_002994530.1|  [L=355]
Description: hypothetical protein TSIB_1127 [Thermococcus sibiricus MM 739]
Scores for 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-130  434.8   0.6   2.2e-130  434.6   0.6    1.0  1  DUF1464   Protein of unknown function (DUF1464)
  ------ inclusion threshold ------
      0.089   12.4   0.0       0.14   11.8   0.0    1.2  1  AMNp_N    Bacterial AMP nucleoside phosphorylase N-terminus


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 !  434.6   0.6  2.5e-134  2.2e-130       1     326 [.       5     350 ..       5     351 .. 0.99

  Alignments for each domain:
  == domain 1  score: 434.6 bits;  conditional E-value: 2.5e-134
                           DUF1464   1 GiDPGtksydvvvvddlgkvvlekeiptdevekdpsvlvkaieearadivalpSGyGlPlkriselaereillltla 77 
                                       G+DPGtks+dv++++d g++ l+  +p+++v+++p+ +vk+ie++ a+++++pSGyG+Plk+isel++++++++tl+
  gi|242399106|ref|YP_002994530.1|   5 GVDPGTKSFDVIGLED-GRIRLDLTFPSEVVAEKPEQIVKVIENFDANLIIGPSGYGVPLKHISELTDKDRFEMTLV 80 
                                       9***************.************************************************************ PP

                           DUF1464  78 eeseegl....vGLrellkelaskelnaftiPgVieLptvPewRKvnkiDmGtADKlasavlavadeaeee..eyre 148
                                       + +e+++    +GL++++ e+a+k++n+++iPgVi+LptvPewRK+nkiDmGtADK+a++vl+++d+a++   ey++
  gi|242399106|ref|YP_002994530.1|  81 RGEEMKKipvlIGLQKMVDEMAEKDMNVWFIPGVIHLPTVPEWRKYNKIDMGTADKMAITVLGIYDQAKRLgvEYND 157
                                       ****9999999***********************************************************99***** PP

                           DUF1464 149 lsFilvEvGsgfnaviaVknGkivDGlGgtilpG..flsaGalDgEvAyllgkvakiekslifsgGvasiagea... 220
                                       +sF+l+EvG+g+n++  Vk+GkivDG+Ggti+pG  ++++GalDgEvAyllg   k+ek+++f+gG+++ia+++   
  gi|242399106|ref|YP_002994530.1| 158 VSFVLLEVGFGYNYAGGVKGGKIVDGIGGTIFPGpaYVNSGALDGEVAYLLG---KVEKWHLFWGGATVIAANEilp 231
                                       **********************************99****************...9****************999** PP

                           DUF1464 221 ..elekklsee....aferlke.vvksvaellsskykleeiivSGrlkrikelgkklesrleev......kllelas 284
                                         e++k+l+ee    a+e++k+ ++k+va+ l+ + +++ei++SGrl+ri+el+k++++ +ee+      k+++l++
  gi|242399106|ref|YP_002994530.1| 232 peEFAKRLDEEsfsrAWEAMKDgFIKAVAAELAIVRNPREIVLSGRLMRIEELRKDVKDTFEELfglpvvKQRGLEG 308
                                       **********99***************************************************9************* PP

                           DUF1464 285 kaKeaaqGaAiianalaGgryrelvdhleiekssgtvldyvk 326
                                       kaKeaaqG+Aiia++laGg+++elv+h+ei+ks+g++ldyvk
  gi|242399106|ref|YP_002994530.1| 309 KAKEAAQGSAIIADGLAGGEFKELVEHVEIRKSRGSILDYVK 350
                                       ****************************************97 PP

>> AMNp_N  Bacterial AMP nucleoside phosphorylase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   1.6e-05      0.14      66     146 ..      20     103 ..       7     108 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.6e-05
                                       SEEEEEE---TTTTHHHHHHHHHHHHHCC--EEEEEEEEEE--GGGCCTSS.T---SCCCH..HHHHHCS--B-STX CS
                            AMNp_N  66 pGtYsttvtrPdlfreYlleqlelLlrnygvevevgeSdqeiPlhyvldes.elelegals..aeladvfdvpdLaa 139
                                        G+ +  +t P+ + +   eq+  +++n+++++ +g+S   +Pl+++ + + +++ e +l   +e++++  +  L++
  gi|242399106|ref|YP_002994530.1|  20 DGRIRLDLTFPSEVVAEKPEQIVKVIENFDANLIIGPSGYGVPLKHISELTdKDRFEMTLVrgEEMKKIPVLIGLQK 96 
                                       5777778888999999999****************************887745555555545578888888888888 PP

                                       XXXXXXX CS
                            AMNp_N 140 idDeiad 146
                                       + De+a+
  gi|242399106|ref|YP_002994530.1|  97 MVDEMAE 103
                                       8888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2410.93
//
Query:       gi|242399107|ref|YP_002994531.1|  [L=85]
Description: hypothetical protein TSIB_1128 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       164  (0.00914719); expected 358.6 (0.02)
Passed bias filter:                      148  (0.00825478); 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: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 607.89
//
Query:       gi|242399108|ref|YP_002994532.1|  [L=353]
Description: hypothetical protein TSIB_1129 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-30  104.8   0.2    4.2e-30  104.2   0.2    1.3  1  DUF835    Protein of unknown function (DUF835)
  ------ inclusion threshold ------
        8.2    5.8   8.9        2.4    7.5   1.4    2.2  2  DUF373    Domain of unknown function (DUF373)


Domain annotation for each model (and alignments):
>> DUF835  Protein of unknown function (DUF835)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.2   0.2   4.7e-34   4.2e-30      10     135 ..     231     351 ..     223     352 .. 0.93

  Alignments for each domain:
  == domain 1  score: 104.2 bits;  conditional E-value: 4.7e-34
                            DUF835  10 eilsdlvkegvkvlaitRenpkkirekvkienvkviwltkveeentvsPtnlekltetivkflkeaekg....vvli 82 
                                        i ++l k  v++la++R+     +    +++++ ++++++e  n+vsPtnl ++ +t v++lkea+++    v++i
  gi|242399108|ref|YP_002994532.1| 231 TIKEKLEK--VSALAFVRDL----K---APKTWNTFFVSTTEVRNSVSPTNLAFIIDTSVRYLKEAKNKgfggVIII 298
                                       56677777..999*****94....2...5899***********************************999******* PP

                            DUF835  83 DgleyLvlengFesvlkflltlkDavllkngtlilvidkealeekelalLkre 135
                                       D+ eyL ++ngFes +kf+ +lkD++++++gtlilvi+++a++e+el++Lkr 
  gi|242399108|ref|YP_002994532.1| 299 DCPEYLKAYNGFESLAKFFASLKDFTISYEGTLILVIEEKAWDERELQILKRI 351
                                       ***************************************************97 PP

>> DUF373  Domain of unknown function (DUF373)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   1.5    0.0093        84     264     327 ..      62     135 ..       7     143 .. 0.61
   2 ?    7.5   1.4   0.00027       2.4     160     219 ..     153     222 ..     139     335 .. 0.68

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.0093
                            DUF373 264 gavewlalailtaslgkiideylkre.ekdiarllllpflvlaiglvlygasaylls..........lsilalsl 327
                                       ga++   l + t++l +  + +  ++ +   +++l+++ ++++++ +l+g+ +y  +          +s l +++
  gi|242399108|ref|YP_002994532.1|  62 GAFWATFLFYGTLILLEENEIVS-GKiRGWCWKTLSAIPVATSLYGILIGVIGYSSDwfallglpyaVSALFIVV 135
                                       33333333333333333333333.344778999999**************9999955888887665333333333 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00027
                            DUF373 160 plGlllliyallll..........lglpelalaiillllGlylllrGfgldelleelleklkesleegri 219
                                       +lG +l++y+l  l          + ++++al++i+++l +y++++ +  +e ++    +++ +++ g +
  gi|242399108|ref|YP_002994532.1| 153 YLGGILFVYGLHQLdfpilrlvewFAPIGFALGSIFTVLSAYFMIKFVFAEEFIRVEKPSVEIYFKPGVM 222
                                       567778888888888888888**999********************888888777666666666555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.33s 00:00:00.84 Elapsed: 00:00:01.20
# Mc/sec: 890.90
//
Query:       gi|242399109|ref|YP_002994533.1|  [L=204]
Description: hypothetical protein TSIB_1130 [Thermococcus sibiricus MM 739]
Scores for 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  141.1   0.2    2.4e-41  140.8   0.2    1.0  1  DUF116    Protein of unknown function DUF116


Domain annotation for each model (and alignments):
>> DUF116  Protein of unknown function DUF116
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.8   0.2   1.3e-45   2.4e-41       4     154 ..      24     180 ..      21     181 .. 0.95

  Alignments for each domain:
  == domain 1  score: 140.8 bits;  conditional E-value: 1.3e-45
                            DUF116   4 kllgrllgldkdklkrvfievnnklvrkkfkkvppekrllllPhClraa.dCpaklteeglnCkrCgkCkigelkkl 79 
                                       ++ ++l+++d++  +++++e++nk+++++f ++p ekr++++P+Clr+  +Cpa+  e g +C++CgkC ige++++
  gi|242399109|ref|YP_002994533.1|  24 RMALSLISEDEELTDQIYVEIKNKAYKEDFTRIPIEKRAVFIPQCLRNVkECPAEFGEYGWECTKCGKCAIGEIIEY 100
                                       567788999**************************************877*************************** PP

                            DUF116  80 aeklgy.kvyivtggtlarkiikekkpk....aiigvaCerdltegiqdlkklpvigqlvllekggCinTkvdveel 151
                                        eklgy ++yiv+gg+l++k++kek p+    a ig+aC  +l+e+ ++l+ l+++ q v+l ++gCinT vd+++ 
  gi|242399109|ref|YP_002994533.1| 101 GEKLGYkHFYIVPGGSLVKKVLKEKVPRgeikAAIGIACWPELAEASEKLSILKIPLQAVPLLRTGCINTIVDIKRA 177
                                       ******99****************998877779******************************************98 PP

                            DUF116 152 eel 154
                                       +e+
  gi|242399109|ref|YP_002994533.1| 178 KEV 180
                                       887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       697  (0.0388756); expected 358.6 (0.02)
Passed bias filter:                      564  (0.0314574); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1323.24
//
Query:       gi|242399110|ref|YP_002994534.1|  [L=290]
Description: Permease, drug/metabolite transporter (DMT) superfamily [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      1e-35  122.9  27.9    1.2e-19   70.9  10.1    2.1  2  EamA       EamA-like transporter family
    4.9e-05   22.8   8.7    0.00088   18.7   5.9    2.1  2  TPT        Triose-phosphate Transporter family


Domain annotation for each model (and alignments):
>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.9  10.1   1.3e-23   1.2e-19       2     136 ..      16     144 ..      15     145 .. 0.89
   2 !   58.2   9.8     1e-19   9.3e-16       2     133 ..     152     282 ..     151     283 .. 0.94

  Alignments for each domain:
  == domain 1  score: 70.9 bits;  conditional E-value: 1.3e-23
                              EamA   2 lgillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvla 78 
                                       +++l++l  +++w+++f+++k+ l+++sp+ ++++rf +a++l+l++   +  k+     + ++  ++lg    +++
  gi|242399110|ref|YP_002994534.1|  16 KAELVLLGITVIWGLTFPVMKVSLEYLSPVLFLTYRFGVASLLMLLFFGRTVLKK-----ETLFEGFVLG-STLFFG 86 
                                       578999*******************************999998866555444444.....5555556666.7999** PP

                              EamA  79 fllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                       +  ++ +lk+tsasn ++itsl +vft + ++ llg kl+ k++l+++ +++G++li+
  gi|242399110|ref|YP_002994534.1|  87 HASQIVGLKYTSASNSAFITSLYVVFTPFVAYGLLGDKLKGKDFLSLGAAIVGLYLIS 144
                                       ********************************************************96 PP

  == domain 2  score: 58.2 bits;  conditional E-value: 1e-19
                              EamA   2 lgillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkd..wllllllgllgtv 76 
                                        g+ll +l a+++a+ +vl  + +++ + l+l+f++++  +++ l +al+ eg    +s++   +  +l++++l+tv
  gi|242399110|ref|YP_002994534.1| 152 YGDLLTVLCAISFAFQIVLVHK-FKEKDYLSLAFWQIFWNFVFSLSYALIVEGFA--FSRETapLVGILYTAVLATV 225
                                       599*****************88.6***********************99999999..67666347777********* PP

                              EamA  77 lafllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvl 133
                                       ++f ++++ +k+t+a +a+li s eP+f  i s+l  ge l+l+ +lg++lil++++
  gi|242399110|ref|YP_002994534.1| 226 IGFTFQIKYQKETKAHKAALIYSAEPIFGHISSFLTIGEVLSLRGYLGAILILVAIW 282
                                       *****************************************************9985 PP

>> TPT  Triose-phosphate Transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   5.9   9.9e-08   0.00088      31     205 ..      44     208 ..      29     234 .. 0.79
   2 !    5.0   0.3    0.0015        13      94     130 ..     243     279 ..     213     282 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 9.9e-08
                               TPT  31 PltvsavqllvgsvlilvlwalglkkrpkisseflkailplalvktlghvlavvslskvaVSfthtvKasePiFtvi 107
                                       P++  + ++ v s+l+l+++   + k+       l   ++l+ + ++gh +  v l+ ++ S +  + ++  +Ft  
  gi|242399110|ref|YP_002994534.1|  44 PVLFLTYRFGVASLLMLLFFGRTVLKKET-----LFEGFVLGSTLFFGHASQIVGLKYTSASNSAFITSLYVVFTPF 115
                                       66666667777777777777776666444.....4444556777799****************************** PP

                               TPT 108 lsrlllgeklsllvylsLlpivgGvalasvtElsFnligfisAlisnltfslrnifsKkllkklkdldalnlfaiit 184
                                       ++  llg+kl+ + +lsL   ++G+ l s   l+Fn   +++ l   ++f+++ ++  k+ +k    d l l +   
  gi|242399110|ref|YP_002994534.1| 116 VAYGLLGDKLKGKDFLSLGAAIVGLYLISDATLHFNYGDLLTVLC-AISFAFQIVLVHKFKEK----DYLSLAFWQI 187
                                       *************************************99998665.699*******9998666....5556666666 PP

                               TPT 185 ilslllllPvallvegvlktp 205
                                       +  ++++l  al+veg+  + 
  gi|242399110|ref|YP_002994534.1| 188 FWNFVFSLSYALIVEGFAFSR 208
                                       788999999999999954443 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0015
                               TPT  94 thtvKasePiFtvilsrlllgeklsllvylsLlpivg 130
                                       +  + ++ePiF  i s l +ge+lsl  yl  + i++
  gi|242399110|ref|YP_002994534.1| 243 AALIYSAEPIFGHISSFLTIGEVLSLRGYLGAILILV 279
                                       678999********************99998777764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.54
# Mc/sec: 1626.02
//
Query:       gi|242399111|ref|YP_002994535.1|  [L=183]
Description: oxidoreductase, Fe-S subunit [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-13   49.0  33.6    1.1e-05   25.2   3.5    4.2  4  Fer4_6    4Fe-4S binding domain
    9.5e-12   44.3  33.5    1.4e-06   28.1   2.7    4.2  4  Fer4_2    4Fe-4S binding domain
    1.6e-11   44.2  14.0    1.6e-11   44.2  14.0    2.1  2  Fer4_11   4Fe-4S dicluster domain
      6e-11   42.8  24.1      4e-07   30.5  12.3    3.3  3  Fer4_7    4Fe-4S dicluster domain
    1.5e-10   41.1  49.6    1.4e-06   28.4  12.7    2.8  4  Fer4_9    4Fe-4S dicluster domain
    2.8e-09   36.9  42.1    4.4e-06   26.7  15.2    3.3  3  Fer4_10   4Fe-4S dicluster domain
    8.7e-09   35.4  28.9    0.00042   20.4  13.2    3.6  4  Fer4_21   4Fe-4S dicluster domain
    3.3e-08   33.0  22.1    5.3e-07   29.2   4.8    5.2  6  Fer4      4Fe-4S binding domain
    1.3e-07   31.5  32.1     0.0014   19.0   2.3    4.3  4  Fer4_4    4Fe-4S binding domain
    0.00039   21.2  41.9       0.04   14.9   4.6    4.3  4  Fer4_3    4Fe-4S binding domain
     0.0046   17.9  28.9       0.15   13.0   1.3    4.3  4  Fer4_16   4Fe-4S double cluster binding domain
  ------ inclusion threshold ------
      0.024   15.2  24.2       0.86   10.2   0.5    4.1  3  Fer4_17   4Fe-4S dicluster domain
      0.028   15.0   5.3      0.028   15.0   5.3    4.0  4  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
       0.74   10.3  31.3         17    5.9   9.6    3.8  2  Fer4_8    4Fe-4S dicluster domain
        1.6    9.5  23.3        1.8    9.3   9.0    4.1  3  Fer4_15   4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.9   1.4e-06    0.0017       4      21 ..      21      41 ..      19      44 .. 0.80
   2 !   14.7   4.1     2e-05     0.024       6      24 .]      63      83 ..      58      83 .. 0.85
   3 !   25.2   3.5   9.5e-09   1.1e-05       2      20 ..      92     110 ..      91     114 .. 0.92
   4 !    8.1   2.7    0.0024       2.9       9      21 ..     126     141 ..     124     147 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.4e-06
                            Fer4_6  4 idpdkCigCgdCvrvCP...e 21
                                      i pdkC gC+ C++ C    e
  gi|242399111|ref|YP_002994535.1| 21 ITPDKCSGCRLCEITCSlehE 41
                                      679*************86544 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 2e-05
                            Fer4_6  6 pdkCigC..gdCvrvCPegai 24
                                      p+ C++C  ++Cv++CP +a+
  gi|242399111|ref|YP_002994535.1| 63 PQTCVQCpdYPCVKACPVDAL 83
                                      899****8666******9996 PP

  == domain 3  score: 25.2 bits;  conditional E-value: 9.5e-09
                            Fer4_6   2 veidpdkCigCgdCvrvCP 20 
                                       v +d++kCi Cg+C+++CP
  gi|242399111|ref|YP_002994535.1|  92 VLVDEEKCIECGACITACP 110
                                       679***************9 PP

  == domain 4  score: 8.1 bits;  conditional E-value: 0.0024
                            Fer4_6   9 CigC.gd..CvrvCPe 21 
                                       C+ C g+  Cv vC e
  gi|242399111|ref|YP_002994535.1| 126 CDLCgGEpkCVEVCHE 141
                                       ****655*******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 !   12.0   1.8   0.00014      0.17       5      20 ..      21      36 ..      16      37 .. 0.85
   2 !   13.8   5.0   3.9e-05     0.047       6      21 ..      62      79 ..      57      80 .. 0.83
   3 !   28.1   2.7   1.1e-09   1.4e-06       3      21 ..      92     110 ..      90     110 .. 0.94
   4 !    7.8   1.4    0.0032       3.8       9      20 ..     125     139 ..     113     141 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00014
                            Fer4_2  5 vdtdrCigCgaCvsaC 20
                                      + +d+C gC+ C   C
  gi|242399111|ref|YP_002994535.1| 21 ITPDKCSGCRLCEITC 36
                                      669*********8888 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 3.9e-05
                            Fer4_2  6 dtdrCigC..gaCvsaCP 21
                                      ++++C++C   +Cv+aCP
  gi|242399111|ref|YP_002994535.1| 62 VPQTCVQCpdYPCVKACP 79
                                      499*****777******* PP

  == domain 3  score: 28.1 bits;  conditional E-value: 1.1e-09
                            Fer4_2   3 vvvdtdrCigCgaCvsaCP 21 
                                       v vd+++Ci+CgaC++aCP
  gi|242399111|ref|YP_002994535.1|  92 VLVDEEKCIECGACITACP 110
                                       789***************9 PP

  == domain 4  score: 7.8 bits;  conditional E-value: 0.0032
                            Fer4_2   9 rCigCg...aCvsaC 20 
                                       +C  Cg   +Cv +C
  gi|242399111|ref|YP_002994535.1| 125 ICDLCGgepKCVEVC 139
                                       7****99******** PP

>> Fer4_11  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.3      0.48   5.7e+02       2      14 ..      18      30 ..      17      48 .. 0.72
   2 !   44.2  14.0   1.4e-14   1.6e-11       6      91 ..      62     140 ..      59     145 .. 0.95

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.48
                           Fer4_11  2 ewlflpeqCrhCl 14
                                      ++l++p++C  C 
  gi|242399111|ref|YP_002994535.1| 18 WILITPDKCSGCR 30
                                      5678899999885 PP

  == domain 2  score: 44.2 bits;  conditional E-value: 1.4e-14
                           Fer4_11   6 lpeqCrhCleppCvasapseaivkdeetGaVlldektkkeevrevveacPykivrkneetgkvekCdmcldrveaGl 82 
                                       +p++C +C + pCv+++p++a+  +e+tGaVl+de+++  e+ ++++acP k++r  +++g v  Cd+c      G 
  gi|242399111|ref|YP_002994535.1|  62 VPQTCVQCPDYPCVKACPVDALSVNEKTGAVLVDEEKCI-ECGACITACPGKVPRIPTDKGSVVICDLC------GG 131
                                       79************************************7.*****************************......77 PP

                           Fer4_11  83 lpacvescp 91 
                                       +p+cve+c 
  gi|242399111|ref|YP_002994535.1| 132 EPKCVEVCH 140
                                       899999995 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.5   4.7e-05     0.057      32      48 ..      20      36 ..       2      40 .. 0.74
   2 !   30.5  12.3   3.4e-10     4e-07       1      50 [.      65     111 ..      65     113 .. 0.90
   3 ?    5.8   0.2     0.018        21       2      18 ..     126     148 ..     125     175 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.7e-05
                            Fer4_7 32 eidpekClgCgaCvavC 48
                                       i p+kC+gC+ C+ +C
  gi|242399111|ref|YP_002994535.1| 20 LITPDKCSGCRLCEITC 36
                                      5789**********999 PP

  == domain 2  score: 30.5 bits;  conditional E-value: 3.4e-10
                            Fer4_7   1 rCigCg..aCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPt 50 
                                       +C++C    Cv+aCpv+a++++e+     t  v +d+ekC+ CgaC+++CP 
  gi|242399111|ref|YP_002994535.1|  65 TCVQCPdyPCVKACPVDALSVNEK-----TGAVLVDEEKCIECGACITACPG 111
                                       5****7669************998.....56899*****************5 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.018
                            Fer4_7   2 CigCg...aCvaaCp...vkaie 18 
                                       C  Cg   +Cv++C    ++a++
  gi|242399111|ref|YP_002994535.1| 126 CDLCGgepKCVEVCHeagHDALK 148
                                       77787777999999644444444 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   1.7    0.0029       3.4      35      47 ..      25      37 ..       5      44 .. 0.69
   2 !   17.4   8.9     3e-06    0.0036       1      50 [.      25      82 ..      25      83 .. 0.76
   3 !   28.4  12.7   1.2e-09   1.4e-06       2      49 ..      66     112 ..      65     113 .. 0.89
   4 !   20.6  12.0   3.1e-07   0.00037       1      48 [.      98     141 ..      98     144 .. 0.95

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0029
                            Fer4_9 35 aCigCgaCveaCp 47
                                      +C gC+ C+  C 
  gi|242399111|ref|YP_002994535.1| 25 KCSGCRLCEITCS 37
                                      5666666666664 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 3e-06
                            Fer4_9  1 kCtgCgaCveaC..pagvvvedaaerkarlraase....eaCigCga..CveaCpkga 50
                                      kC gC+ C+  C  +++ ++  +a r++  +        + C++C +  Cv+aCp +a
  gi|242399111|ref|YP_002994535.1| 25 KCSGCRLCEITCslEHEGIIWPEASRIRVFELLPGvnvpQTCVQCPDypCVKACPVDA 82
                                      7***********77555555555555555544443888889**************987 PP

  == domain 3  score: 28.4 bits;  conditional E-value: 1.2e-09
                            Fer4_9   2 CtgCga..CveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkg 49 
                                       C++C    Cv+aCp ++ +  ++++ + +++   e+Ci+CgaC+ aCp +
  gi|242399111|ref|YP_002994535.1|  66 CVQCPDypCVKACPVDALSVNEKTGAVLVDE---EKCIECGACITACPGK 112
                                       ****6556*******************9976...48************65 PP

  == domain 4  score: 20.6 bits;  conditional E-value: 3.1e-07
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCga...CveaCpk 48 
                                       kC++CgaC++aCp +v +    ++ + +       C  Cg    Cve+C +
  gi|242399111|ref|YP_002994535.1|  98 KCIECGACITACPGKVPRIPTDKGSVVI-------CDLCGGepkCVEVCHE 141
                                       7**************************8.......*****9999*****86 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.3   0.00013      0.15       3      19 ..      20      36 ..      18      53 .. 0.82
   2 !   26.7  15.2   3.7e-09   4.4e-06       5      56 .]      62     110 ..      59     110 .. 0.92
   3 !   20.8  13.2   2.5e-07    0.0003       2      55 ..      92     139 ..      91     140 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                           Fer4_10  3 vidddtCirCgkCvkaC 19
                                       i +d+C +C+ C   C
  gi|242399111|ref|YP_002994535.1| 20 LITPDKCSGCRLCEITC 36
                                      6899************* PP

  == domain 2  score: 26.7 bits;  conditional E-value: 3.7e-09
                           Fer4_10   5 dddtCirCg..kCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                        ++tC++C    CvkaCP+     +a   +++ +av ++ ekC++cgaC+ aCP
  gi|242399111|ref|YP_002994535.1|  62 VPQTCVQCPdyPCVKACPV-----DALSVNEKTGAVLVDEEKCIECGACITACP 110
                                       589*****9999*******.....9999999999999999*************9 PP

  == domain 3  score: 20.8 bits;  conditional E-value: 2.5e-07
                           Fer4_10   2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcg...aCveaC 55 
                                       v +d+++Ci+Cg+C +aCP          +  ++ ++++ v  C+ cg   +Cve+C
  gi|242399111|ref|YP_002994535.1|  92 VLVDEEKCIECGACITACPG---------KVPRIPTDKGSVVICDLCGgepKCVEVC 139
                                       6789***************9.........3333333333444588887777****** PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4  10.9   2.7e-05     0.032       3      57 ..      21      83 ..      19      86 .. 0.72
   2 !   20.4  13.2   3.5e-07   0.00042       6      52 ..      64     110 ..      59     116 .. 0.87
   3 !   18.5  12.1   1.3e-06    0.0016       3      51 ..      94     139 ..      91     139 .. 0.85
   4 !   10.7   0.7   0.00038      0.46       8      36 ..     129     157 ..     122     163 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.7e-05
                           Fer4_21  3 idedkCigCgkCliaCedtshqaieidaktvl........kvvedeCvGCn..lCssvCPvedci 57
                                      i +dkC gC +C i+C+   h+ i   +++++          v ++Cv C    C++ CPv d++
  gi|242399111|ref|YP_002994535.1| 21 ITPDKCSGCRLCEITCSL-EHEGIIWPEASRIrvfellpgVNVPQTCVQCPdyPCVKACPV-DAL 83
                                      889**************5.67777444443332335555334589*****6336******9.665 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 3.5e-07
                           Fer4_21   6 dkCigCgk..CliaCedtshqaieidaktvlkvv.edeCvGCnlCssvCP 52 
                                       ++C++C    C++aC+   ++a+++++kt + +v e++C+ C  C++ CP
  gi|242399111|ref|YP_002994535.1|  64 QTCVQCPDypCVKACP---VDALSVNEKTGAVLVdEEKCIECGACITACP 110
                                       79****7555******...8*****999987665499************* PP

  == domain 3  score: 18.5 bits;  conditional E-value: 1.3e-06
                           Fer4_21   3 idedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvC 51 
                                       +de+kCi+Cg C++aC+ + +  i +  ++   v+ d C G   C++vC
  gi|242399111|ref|YP_002994535.1|  94 VDEEKCIECGACITACP-GKVPRIPT--DKGSVVICDLCGGEPKCVEVC 139
                                       89***************.45555655..5666699************** PP

  == domain 4  score: 10.7 bits;  conditional E-value: 0.00038
                           Fer4_21   8 CigCgkCliaCedtshqaieidaktvlkv 36 
                                       C g  kC+ +C++++h+a+++ + ++  v
  gi|242399111|ref|YP_002994535.1| 129 CGGEPKCVEVCHEAGHDALKLVKGNYRSV 157
                                       555569*************9888776655 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   2.1   1.4e-05     0.017       3      18 ..      21      36 ..      19      37 .. 0.91
   2 ?   -1.6   0.1       2.3   2.8e+03       7      11 ..      65      69 ..      62      69 .. 0.77
   3 !   12.6   0.8   7.7e-05     0.092      14      23 ..      74      83 ..      73      84 .. 0.93
   4 !   29.2   4.8   4.4e-10   5.3e-07       2      20 ..      93     111 ..      92     115 .. 0.89
   5 ?   -2.8   1.6       5.6   6.7e+03       8      12 ..     126     130 ..     125     131 .. 0.81
   6 ?    0.3   2.1       0.6   7.2e+02      14      18 ..     135     139 ..     134     139 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.4e-05
                                      EETTTSSS-THHHHHS CS
                              Fer4  3 ideekCigCGaCvevC 18
                                      i ++kC gC +C+  C
  gi|242399111|ref|YP_002994535.1| 21 ITPDKCSGCRLCEITC 36
                                      789**********999 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.3
                                      TSSS- CS
                              Fer4  7 kCigC 11
                                       C+ C
  gi|242399111|ref|YP_002994535.1| 65 TCVQC 69
                                      69999 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 7.7e-05
                                      HHHHSTTTEE CS
                              Fer4 14 CvevCPvgAI 23
                                      Cv++CPv+A+
  gi|242399111|ref|YP_002994535.1| 74 CVKACPVDAL 83
                                      *********8 PP

  == domain 4  score: 29.2 bits;  conditional E-value: 4.4e-10
                                       EEETTTSSS-THHHHHSTT CS
                              Fer4   2 videekCigCGaCvevCPv 20 
                                        +deekCi CGaC+ +CP 
  gi|242399111|ref|YP_002994535.1|  93 LVDEEKCIECGACITACPG 111
                                       59****************6 PP

  == domain 5  score: -2.8 bits;  conditional E-value: 5.6
                                       SSS-T CS
                              Fer4   8 CigCG 12 
                                       C  CG
  gi|242399111|ref|YP_002994535.1| 126 CDLCG 130
                                       88888 PP

  == domain 6  score: 0.3 bits;  conditional E-value: 0.6
                                       HHHHS CS
                              Fer4  14 CvevC 18 
                                       CvevC
  gi|242399111|ref|YP_002994535.1| 135 CVEVC 139
                                       ***** 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   3.0   5.5e-05     0.066       1      15 [.      23      37 ..      23      39 .. 0.91
   2 !   11.5   3.3   0.00029      0.35       1      16 [.      63      80 ..      63      84 .. 0.90
   3 !   19.0   2.3   1.2e-06    0.0014       2      15 ..      97     110 ..      96     121 .. 0.91
   4 ?    4.4   1.1     0.055        66       4      15 ..     129     140 ..     125     151 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.5e-05
                            Fer4_4  1 qerCigCgsCvaaCP 15
                                      +++C gC+ C+++C+
  gi|242399111|ref|YP_002994535.1| 23 PDKCSGCRLCEITCS 37
                                      69************7 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00029
                            Fer4_4  1 qerCigCgs..CvaaCPq 16
                                      +++C++C+   Cv aCP+
  gi|242399111|ref|YP_002994535.1| 63 PQTCVQCPDypCVKACPV 80
                                      589*****889******7 PP

  == domain 3  score: 19.0 bits;  conditional E-value: 1.2e-06
                            Fer4_4   2 erCigCgsCvaaCP 15 
                                       e+Ci+Cg+C+ aCP
  gi|242399111|ref|YP_002994535.1|  97 EKCIECGACITACP 110
                                       89************ PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.055
                            Fer4_4   4 CigCgsCvaaCP 15 
                                       C g ++Cv +C 
  gi|242399111|ref|YP_002994535.1| 129 CGGEPKCVEVCH 140
                                       556779*****6 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   3.9      0.31   3.7e+02       1      11 [.      26      36 ..      26      38 .. 0.90
   2 !   12.6   5.9   0.00017       0.2       1      15 []      66      82 ..      66      82 .. 0.91
   3 !   14.9   4.6   3.3e-05      0.04       1      14 [.      99     112 ..      99     113 .. 0.93
   4 !    9.8   3.8    0.0014       1.6       1      11 [.     126     139 ..     126     143 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.31
                            Fer4_3  1 CtgCgaCvevC 11
                                      C gC++C+  C
  gi|242399111|ref|YP_002994535.1| 26 CSGCRLCEITC 36
                                      99*****9888 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00017
                            Fer4_3  1 CtgC..gaCvevCPvgA 15
                                      C++C  ++Cv++CPv+A
  gi|242399111|ref|YP_002994535.1| 66 CVQCpdYPCVKACPVDA 82
                                      9***7669*******98 PP

  == domain 3  score: 14.9 bits;  conditional E-value: 3.3e-05
                            Fer4_3   1 CtgCgaCvevCPvg 14 
                                       C+ CgaC  +CP +
  gi|242399111|ref|YP_002994535.1|  99 CIECGACITACPGK 112
                                       ************86 PP

  == domain 4  score: 9.8 bits;  conditional E-value: 0.0014
                            Fer4_3   1 CtgCg...aCvevC 11 
                                       C+ Cg    CvevC
  gi|242399111|ref|YP_002994535.1| 126 CDLCGgepKCVEVC 139
                                       ****99999***** PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.4     0.015        17      52      65 ..      24      37 ..       3      39 .. 0.80
   2 !   13.0   1.3   0.00013      0.15       1      21 [.      65      87 ..      65      96 .. 0.86
   3 !   10.8   6.3    0.0006      0.72       1      16 [.      98     113 ..      98     127 .. 0.84
   4 ?    1.7   2.0      0.42   5.1e+02       2      14 ..     129     141 ..     125     176 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.015
                           Fer4_16 52 eaitgCdiCqdvCP 65
                                       ++ gC+ C+ +C 
  gi|242399111|ref|YP_002994535.1| 24 DKCSGCRLCEITCS 37
                                      56889999999995 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00013
                           Fer4_16  1 rCgtCgk..CaevCPtnaikekk 21
                                      +C++C    C+++CP++a++ ++
  gi|242399111|ref|YP_002994535.1| 65 TCVQCPDypCVKACPVDALSVNE 87
                                      5****9889**********9874 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.0006
                           Fer4_16   1 rCgtCgkCaevCPtna 16 
                                       +C++Cg+C+ +CP ++
  gi|242399111|ref|YP_002994535.1|  98 KCIECGACITACPGKV 113
                                       6************876 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.42
                           Fer4_16   2 CgtCgkCaevCPt 14 
                                       Cg+  kC+evC +
  gi|242399111|ref|YP_002994535.1| 129 CGGEPKCVEVCHE 141
                                       5555589999965 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.5   0.00072      0.86      44      57 ..      24      37 ..       6      40 .. 0.83
   2 ?    3.9  12.9     0.065        78      43      60 ..      96     113 ..      65     114 .. 0.55
   3 ?    2.2   0.1      0.23   2.8e+02       2      14 ..     126     141 ..     125     175 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00072
                           Fer4_17 44 slCieCgeCerkCP 57
                                      ++C++C++Ce  C 
  gi|242399111|ref|YP_002994535.1| 24 DKCSGCRLCEITCS 37
                                      78999999999995 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.065
                           Fer4_17  43 aslCieCgeCerkCPqgl 60 
                                        ++CieCg C ++CP ++
  gi|242399111|ref|YP_002994535.1|  96 EEKCIECGACITACPGKV 113
                                       378***********9876 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.23
                           Fer4_17   2 CiqCgy...ClpeCps 14 
                                       C  Cg    C+++C  
  gi|242399111|ref|YP_002994535.1| 126 CDLCGGepkCVEVCHE 141
                                       6667744557777765 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   2.2     0.053        63       3      16 ..      23      36 ..      21      38 .. 0.87
   2 ?    2.0   0.2      0.25     3e+02      49      57 ..      76      84 ..      72      85 .. 0.81
   3 ?   15.0   5.3   2.3e-05     0.028       1      17 [.      94     110 ..      94     127 .. 0.90
   4 ?   -1.6   0.5       3.5   4.2e+03       5      17 ..     128     140 ..     124     142 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.053
                           Fer4_13  3 rdtCiacgaCvela 16
                                       d+C++c +C  ++
  gi|242399111|ref|YP_002994535.1| 23 PDKCSGCRLCEITC 36
                                      589*******9998 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.25
                           Fer4_13 49 daCPvesIg 57
                                      +aCPv++  
  gi|242399111|ref|YP_002994535.1| 76 KACPVDALS 84
                                      79**99976 PP

  == domain 3  score: 15.0 bits;  conditional E-value: 2.3e-05
                           Fer4_13   1 VDrdtCiacgaCvelaP 17 
                                       VD+++Ci+cgaC  ++P
  gi|242399111|ref|YP_002994535.1|  94 VDEEKCIECGACITACP 110
                                       9**************** PP

  == domain 4  score: -1.6 bits;  conditional E-value: 3.5
                           Fer4_13   5 tCiacgaCvelaP 17 
                                        C +  +Cve++ 
  gi|242399111|ref|YP_002994535.1| 128 LCGGEPKCVEVCH 140
                                       5777778999985 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   9.6     0.015        17       3      64 ..      24      81 ..      22      82 .. 0.83
   2 ?    4.8  13.8     0.033        40       3      16 ..      97     110 ..      95     167 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.015
                            Fer4_8  3 ekCieCgaCqsaCpvlrrtk.khlldargeaaedvqeeqvleeeealwsCttcga..CtevCpvg 64
                                      +kC +C +C+ +C +l++++  ++  +r ++ e           +  ++C++c    C+++Cpv+
  gi|242399111|ref|YP_002994535.1| 24 DKCSGCRLCEITC-SLEHEGiIWPEASRIRVFELLPGV------NVPQTCVQCPDypCVKACPVD 81
                                      69***********.677777799999999999833333......4599*****9999******96 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.033
                            Fer4_8   3 ekCieCgaCqsaCp 16 
                                       ekCieCgaC +aCp
  gi|242399111|ref|YP_002994535.1|  97 EKCIECGACITACP 110
                                       69***********9 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.9      0.18   2.1e+02       5      15 ..      23      33 ..      19      43 .. 0.81
   2 ?    4.3   0.5     0.058        69      56      66 .]      75      85 ..      74      85 .. 0.87
   3 ?    9.3   9.0    0.0015       1.8       1      27 [.      92     118 ..      92     152 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.18
                           Fer4_15  5 rdaCigcglCv 15
                                       d+C gc lC 
  gi|242399111|ref|YP_002994535.1| 23 PDKCSGCRLCE 33
                                      69********5 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.058
                           Fer4_15 56 araCPvdAIrv 66
                                      ++aCPvdA++v
  gi|242399111|ref|YP_002994535.1| 75 VKACPVDALSV 85
                                      589*****987 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.0015
                           Fer4_15   1 VvvDrdaCigcglCvaeapevfelded 27 
                                       V vD+++Ci cg+C++++p  +     
  gi|242399111|ref|YP_002994535.1|  92 VLVDEEKCIECGACITACPGKVPRIPT 118
                                       78****************976655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); 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):              15  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1222.95
//
Query:       gi|242399112|ref|YP_002994536.1|  [L=626]
Description: Tungsten-containing aldehyde:ferredoxin oxidoreductase (AOR) [Thermococcus sibiricus MM 739]
Scores for 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-81  271.7   0.0    1.5e-80  271.1   0.0    1.3  1  AFOR_C    Aldehyde ferredoxin oxidoreductase, domains 2 & 3
    7.6e-61  205.4   0.3    1.1e-60  205.0   0.3    1.2  1  AFOR_N    Aldehyde ferredoxin oxidoreductase, N-terminal doma


Domain annotation for each model (and alignments):
>> AFOR_C  Aldehyde ferredoxin oxidoreductase, domains 2 & 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  271.1   0.0   1.7e-84   1.5e-80       8     382 .]     238     610 ..     232     610 .. 0.91

  Alignments for each domain:
  == domain 1  score: 271.1 bits;  conditional E-value: 1.7e-84
                                       HHHHHSH.HHHHHHHH-G.GGHHHHHHHTT---BTTTTBS--TTGGGGSHHHHHHHTEEEE.E.-TT-SS--EEEEE CS
                            AFOR_C   8 keiksspqvtaelrkyGT.aelvnianetgalptknfqegtfekaekisgealeekylvkneg.CfsCpiaCgrevk 82 
                                       +e+++++  +  +r+ GT a+ +++ ++ +  p++n+qe++ +  e+is  ++e++  +k+    ++Cpi+C +   
  gi|242399112|ref|YP_002994536.1| 238 REFWKKSFLSTTFREWGTgAGGYSVGHDRSSEPIRNWQEEYHN-NEEISVVNFEDRAWIKKYWaDYGCPINCMKISY 313
                                       5566666677799*****77888899*************9843.699********999999667899********** PP

                                       .......ET.EE---HHHHHHHTGGGT---HHHHHHHHHHHHHHTB-HHHHHHHHHHHHHHHHTTSS-HHHHTS--- CS
                            AFOR_C  83 veegkk.vk.vegpeyetlaalGsnlgiddleailklnelcdelGlDtisaGntiafamelyekGllkkedtdglel 157
                                        + g++ +  ++ p+ye  a++Gsnlgi+++e+i++l++l+delGlD i+aGnt++f+ ely++G+l+k+d+ g+el
  gi|242399112|ref|YP_002994536.1| 314 LRYGPYkGAiTDAPDYELQAYMGSNLGIFEPEKIVYLSYLVDELGLDGINAGNTLGFVAELYQRGILTKDDI-GFEL 389
                                       999999555**************************************************************9.**** PP

                                       -TT-THHHHHHHHHHHTT-TTHHHHTT-HHHHHHCTT......-GGG--EETTEE--SS-GGG..-HHHHHHHHH-T CS
                            AFOR_C 158 efgdaeallellekiAkregigdllAeGvkrlaeklg......aeelamhvkGlelpaydprg..akgmalaYatsn 226
                                       ++gd++a+ +ll+ iA++e+ig++lA+G++r+a k+        +++a+hvkG+ + a+  r    ++  ++Ya+s 
  gi|242399112|ref|YP_002994536.1| 390 NWGDEKAFAKLLHLIANKEEIGEILADGTYRAALKVSkikgidVTKYAVHVKGIGIGAHGIRSelDYTKDISYAVSV 466
                                       *********************************55554446779******************723455679****** PP

                                       TSS-SGGG-THHHHS---TT--HHHHHHHHHHHHHHHHHHHHT--GGGG-HHH......HHHHHHHHHT----HHH. CS
                            AFOR_C 227 rGacHlraylialeekvdpletegkaelvkwfqdltalvdslglCkftseaeerldlelyakllsavtGidvteee. 302
                                       +G++H +              t g ++     +++++++ds+++C f++    +  +e++ ++ +avtG+++++e+ 
  gi|242399112|ref|YP_002994536.1| 467 QGGDHTS--------------TAGLPAKSYEGEMVNTFYDSAVICFFVT----QPGFENILEFGNAVTGFNISPEQw 525
                                       *****98..............3466777778888899************....6789****************9984 PP

                                       HHHHHHHHHHHHHHHHHHHT--.....HHHS---HHHHHS---SSTTTT---...-HHHHHHHHHHHHT--TTS--- CS
                            AFOR_C 303 llkaGeRiynleRlfnlreGlt.....rkddtlperlleeplkegpakgkvl.edeleemldeyYelrGWdetGvPt 373
                                       l ++G+Ri+ l+R++ l  G +     rkdd+ p+r++ epl++gp +gk + e+e+++ +++yYe+ G+de+G+P+
  gi|242399112|ref|YP_002994536.1| 526 LNEIGRRIIHLQRILLLLGGPDvywdpRKDDDNPPRFY-EPLPSGPMRGKAPsEEEIKAKVKQYYEEIGYDENGIPK 601
                                       679*****************99999988*********9.9************8888********************* PP

                                       HHHHHHCT- CS
                            AFOR_C 374 ketlkrLgL 382
                                       +e l++LgL
  gi|242399112|ref|YP_002994536.1| 602 EEVLEELGL 610
                                       ********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 !  205.0   0.3   1.2e-64   1.1e-60       1     197 [.       8     220 ..       8     221 .. 0.93

  Alignments for each domain:
  == domain 1  score: 205.0 bits;  conditional E-value: 1.2e-64
                                       SEEEEEETTTTEEEEEE--HHHHHHH-SCHHHHHHHHHHHS..-.TTS-TTSTTS-EEEEE-TTTTSSSTTB-EEEE CS
                            AFOR_N   1 gkilrvdLstgkieveelpeelaekylGgrglaakllldev..p.pgvdplspenplvfatGpltgtpapgsgrlvv 74 
                                       gk+l ++L+++ki++ +l+ee+++k+ Ggrgl+++ll++e+  + ++vdpl++en l++  Gpltg+ +p   +++v
  gi|242399112|ref|YP_002994536.1|   8 GKLLDINLTKEKIKETKLDEEILKKFYGGRGLGTYLLWKELgdRwETVDPLDEENLLLILSGPLTGY-YP-GMKTAV 82 
                                       699************************************996535889******************9.77.6899** PP

                                       EEE-TTTSSEEEEEEETCHHHHHHHCT-SEEEEES--SS-EEEEEETTEEEEEE-TTTTTS-HHHHHHHHHHHHTS. CS
                            AFOR_N  75 vaksPltgtlgesnaGgrfgaelkraGydaivieGkaekpvylvieddkveiedaedlwgldtyettealkeelgd. 150
                                       ++ksP ++++  s   ++++ elk +Gyd+++i+Gka++pvyl++++d+vei+da+++wg++  e+ ++l +e+++ 
  gi|242399112|ref|YP_002994536.1|  83 ISKSPESNGVVGSVLSSEVALELKTSGYDGVIIRGKAKSPVYLFVHNDTVEIRDANKYWGMGGTELYKTLLKEVHEe 159
                                       *************************************************************9999999977755555 PP

                                       ..............EEEEE-HHHHTT-TTB-E.EETTEEE-SSSHHHHHHHTTEEEEEEE- CS
                            AFOR_N 151 ..............kvaviGpaGenlvrfAsisvddgraagrgGlGavmgsKnlkaivvrg 197
                                                      +++iG aGen+vr+A+i+++  +aag gG GavmgsKnlkai v+g
  gi|242399112|ref|YP_002994536.1| 160 ikkkemlkgipkepAMMYIGRAGENQVRIAAIMTKLMHAAGYGGYGAVMGSKNLKAILVKG 220
                                       66788999999987777***************77788999*******************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (626 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); 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: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.45
# Mc/sec: 4221.33
//
Query:       gi|242399113|ref|YP_002994537.1|  [L=158]
Description: OsmC-like protein [Thermococcus sibiricus MM 739]
Scores for complete 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   89.3   0.0    2.8e-25   88.7   0.0    1.2  1  OsmC      OsmC-like protein
     0.0044   16.7   0.0     0.0061   16.2   0.0    1.3  1  DUF4978   Domain of unknown function (DUF4978)
  ------ inclusion threshold ------
       0.14   11.1   0.0       0.16   11.0   0.0    1.1  1  DUF4026   Protein of unknown function (DUF4026)


Domain annotation for each model (and alignments):
>> OsmC  OsmC-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.7   0.0   4.7e-29   2.8e-25       2     100 .]      51     154 ..      50     154 .. 0.95

  Alignments for each domain:
  == domain 1  score: 88.7 bits;  conditional E-value: 4.7e-29
                                       TXSSB-HHHHHHHHHHHHHHHHHHHHTCCCT---SCEEEEEEEEEECCECT.......CEEEEEEEEEEE-SS-H.. CS
                              OsmC   2 dgsgpsPeelllaalasCfaitlravakkkgikledleveveaerdpegak.......giteirlkvevkipgadse 71 
                                       +g++psP e++laala+C++i +  va+++gi++edl+veve+ ++p+++        g++ei+ k++vk++ ++  
  gi|242399113|ref|YP_002994537.1|  51 GGEAPSPIEYVLAALAGCINIVATLVAQDMGINIEDLSVEVEGVFNPAKFLgqengraGYKEITAKIKVKTDADE-- 125
                                       578********************************************9999******************977755.. PP

                                       HHHHHHHHHHHHHSHHHHHHCT-SSSEEE CS
                              OsmC  72 eklkkllekaekrCpvsntlkngvkvele 100
                                       e+lkk le++e+rCpvs+ l n++++++e
  gi|242399113|ref|YP_002994537.1| 126 ETLKKWLEQVEERCPVSDNLSNPTPIKVE 154
                                       **************************986 PP

>> DUF4978  Domain of unknown function (DUF4978)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0     1e-06    0.0061      59     103 ..      19      67 ..      13      98 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1e-06
                           DUF4978  59 yktnakkvkge.ls..ayasiagnfrliaeidakdansPv.yqlaalag 103
                                       yk+ + kv ge ls  ++   agnf ++++  + +a sP+ y+laalag
  gi|242399113|ref|YP_002994537.1|  19 YKDMVLKVVGErLSpmKMKVRAGNFEMVMDKLGGEAPSPIeYVLAALAG 67 
                                       77777777776333337788899****************8799****98 PP

>> DUF4026  Protein of unknown function (DUF4026)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   2.6e-05      0.16     244     314 ..      67     138 ..      34     142 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 2.6e-05
                           DUF4026 244 eGirqinkktpldqlkpleeieyklqn.aaeneflGdmddrdeyhqhPsvllfrvneseevletffkgyeed 314
                                         i+ +    + d    +e++ ++ ++     +flG+ + r  y +  + +  +++ +ee l+ ++ + ee 
  gi|242399113|ref|YP_002994537.1|  67 GCINIVATLVAQDMGINIEDLSVEVEGvFNPAKFLGQENGRAGYKEITAKIKVKTDADEETLKKWLEQVEER 138
                                       55666677777788889**********777899*******************************99999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       805  (0.0448993); expected 358.6 (0.02)
Passed bias filter:                      709  (0.0395449); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.36s 00:00:00.94 Elapsed: 00:00:00.55
# Mc/sec: 865.13
//
Query:       gi|242399114|ref|YP_002994538.1|  [L=108]
Description: hypothetical protein TSIB_1135 [Thermococcus sibiricus MM 739]
Scores for complete 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   17.8   0.0     0.0041   17.4   0.0    1.1  1  DUF2277   Uncharacterized conserved protein (DUF2277)


Domain annotation for each model (and alignments):
>> DUF2277  Uncharacterized conserved protein (DUF2277)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   2.3e-07    0.0041      12      66 ..      51     105 ..      48     108 .] 0.87

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.3e-07
                           DUF2277  12 ePpateeeiraAAlqyVRK.vsGvrkpsaaneeaferAveeiaaaterLLdeLetr 66 
                                        P ateee  + A ++  K + G++kp + ++  +++A ee+ +  ++LL+eL+++
  gi|242399114|ref|YP_002994538.1|  51 LPGATEEEALENAIRFFEKlIIGLEKP-KIKSSPLKEAPEEVYTKLRELLEELKNE 105
                                       599*************99945788887.667889*******************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.34s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 609.55
//
Query:       gi|242399115|ref|YP_002994539.1|  [L=73]
Description: hypothetical protein TSIB_1136 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.9e-10   41.2   0.1    2.1e-10   41.1   0.1    1.0  1  ThiS       ThiS family
     0.0069   16.4   0.1      0.044   13.8   0.1    2.0  1  TGS        TGS domain
  ------ inclusion threshold ------
      0.013   15.4   0.1      0.019   14.8   0.1    1.3  1  Ub-Mut7C   Mut7-C ubiquitin
      0.071   13.5   0.0       0.16   12.4   0.0    1.6  2  FHA        FHA domain
       0.11   12.6   0.1       0.18   11.9   0.1    1.5  1  ThiS-like  ThiS-like ubiquitin
       0.11   12.1   0.1        5.1    6.8   0.0    2.8  3  SH3_1      SH3 domain


Domain annotation for each model (and alignments):
>> ThiS  ThiS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   0.1   7.2e-14   2.1e-10       1      77 []       5      73 .]       5      73 .] 0.98

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 7.2e-14
                                      EEETTCCHHHHT.CEEEEESSTSBHHHHHHHHHHHTCHHGTTTTEEEEETTEEEGCCTTTSB--TTCEEEEEESTTC- CS
                              ThiS  1 vllfaelrelag.eeelelaegstvaelleaLgerypelalerrvavavNgeivprlwldtelkdgDevailppVaGG 77
                                      v+l++el  + g e e+e++ ++tv+++l+ L              + +N++ v++   +++lk+gD++ +l +V GG
  gi|242399115|ref|YP_002994539.1|  5 VRLYGELALKHGaEVEIEIEKEATVGDILKLLRISE------SEHHLILNEKKVSK---NHPLKEGDTLKVLSVVYGG 73
                                      899*******************************99......9*************...******************9 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.1   1.5e-05     0.044      38      59 ..      46      67 ..      11      68 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.5e-05
                                      EECSEEEETTSBB-SSEEEEEE CS
                               TGS 38 lVnGqrvgldhvLedgdvveIv 59
                                      + n ++v  +h+L++gd+++++
  gi|242399115|ref|YP_002994539.1| 46 ILNEKKVSKNHPLKEGDTLKVL 67
                                      56889**************986 PP

>> Ub-Mut7C  Mut7-C ubiquitin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1   6.2e-06     0.019      22      76 ..      16      69 ..       1      71 [. 0.83

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 6.2e-06
                          Ub-Mut7C 22 eralavafdeaatvkhviEalGVPhtEVelilvnGesvgfshiledGdrvavypv 76
                                        +++ ++++ atv++++  l +   E  li +n ++v+ +h l++Gd ++v  v
  gi|242399115|ref|YP_002994539.1| 16 GAEVEIEIEKEATVGDILKLLRISESEHHLI-LNEKKVSKNHPLKEGDTLKVLSV 69
                                      45688999*******************8776.69*****************9876 PP

>> FHA  FHA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.99     3e+03      58      68 ..      11      21 ..       4      22 .. 0.76
   2 ?   12.4   0.0   5.3e-05      0.16      36      67 ..      36      65 ..      16      66 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.99
                                      EEE-TTEEEEE CS
                               FHA 58 veLksgdviel 68
                                        Lk+g ++e+
  gi|242399115|ref|YP_002994539.1| 11 LALKHGAEVEI 21
                                      67999999886 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 5.3e-05
                                      EEEESSSSSEEETTEEESTTSEEEE-TTEEEE CS
                               FHA 36 leDlgSknGtfvNgqrigkgepveLksgdvie 67
                                      l+   S +   +N+++++k   ++Lk+gd+++
  gi|242399115|ref|YP_002994539.1| 36 LRISESEHHLILNEKKVSK--NHPLKEGDTLK 65
                                      444469999*********9..9*******997 PP

>> ThiS-like  ThiS-like ubiquitin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   6.1e-05      0.18       8      51 ..      19      64 ..      17      68 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.1e-05
                         ThiS-like  8 keveveegttlealke..kikpdaDvvIlNGFpikeDteLkegDev 51
                                       e+e+e+++t+ ++ +  +i+++++ +IlN   ++++ +LkegD +
  gi|242399115|ref|YP_002994539.1| 19 VEIEIEKEATVGDILKllRISESEHHLILNEKKVSKNHPLKEGDTL 64
                                      57888888888888774456677779******************87 PP

>> SH3_1  SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.11   3.4e+02      12      24 ..       9      21 ..       8      28 .. 0.84
   2 ?    0.8   0.0      0.12   3.7e+02      18      30 ..      29      41 ..      26      43 .. 0.83
   3 ?    6.8   0.0    0.0017       5.1      15      29 ..      57      71 ..      50      73 .] 0.86

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.11
                                      TBXEBSTTEEEEE CS
                             SH3_1 12 dELsfkkGDviiv 24
                                      +EL +k G ++++
  gi|242399115|ref|YP_002994539.1|  9 GELALKHGAEVEI 21
                                      59******99987 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.12
                                      TTEEEEEEEECSS CS
                             SH3_1 18 kGDviivleksed 30
                                       GD++++l  se+
  gi|242399115|ref|YP_002994539.1| 29 VGDILKLLRISES 41
                                      69*****998886 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0017
                                      EBSTTEEEEEEEECS CS
                             SH3_1 15 sfkkGDviivlekse 29
                                      ++k+GD+++vl+ + 
  gi|242399115|ref|YP_002994539.1| 57 PLKEGDTLKVLSVVY 71
                                      69*********9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 487.40
//
Query:       gi|242399116|ref|YP_002994540.1|  [L=94]
Description: hypothetical protein TSIB_1137 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0019   18.2   0.2     0.0029   17.6   0.2    1.3  1  RNR_N         Ribonucleotide reductase N-terminal
  ------ inclusion threshold ------
      0.019   14.1   0.1       0.02   14.1   0.1    1.1  1  Hemocyanin_M  Hemocyanin, copper containing domain


Domain annotation for each model (and alignments):
>> RNR_N  Ribonucleotide reductase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.2   3.3e-07    0.0029      29      75 ..      28      74 ..      24      79 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.3e-07
                             RNR_N 29 YlkehvnpntvkfesleekldyLvendYyeeevlekYskefieelyk 75
                                      Y+   ++++t  f+  ++k++ L e  Y  +e +e+++++ +e++ k
  gi|242399116|ref|YP_002994540.1| 28 YVPLVIEERTIVFDRQNQKIKVLEEGRYLSPEEIERFEEKILENIKK 74
                                      6666799***********************************99987 PP

>> Hemocyanin_M  Hemocyanin, copper containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   2.2e-06      0.02     114     186 ..       2      78 ..       1      90 [. 0.81

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.2e-06
                                       HHHHTT--S-----TTSE....ES--B---EETTC..E---B-TTEETTSGGGHHHHHHHHHHHHHHHHHHHHSEE. CS
                      Hemocyanin_M 114 ERlsnglgeieefswyep....ieegYdpqlsyynGlsfpsRpnyyeletegnyeklekvedlekrirdaidsgyvl 186
                                       ERl   l++i++   y +    ++  Y p ++    + f   ++++++ +eg+y + e++e++e++i + i++g v 
  gi|242399116|ref|YP_002994540.1|   2 ERLKLYLEHISRKAGYAEelygVRIRYVPLVIEERTIVFDRQNQKIKVLEEGRYLSPEEIERFEEKILENIKKGVVE 78 
                                       55555555555554443311115667**********************9*************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 666.60
//
Query:       gi|242399117|ref|YP_002994541.1|  [L=599]
Description: glycoside hydrolase [Thermococcus sibiricus MM 739]
Scores for complete 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-08   31.8   0.2    8.4e-08   31.8   0.2    2.0  3  Glyco_hydro_57  Glycosyl hydrolase family 57


Domain annotation for each model (and alignments):
>> Glyco_hydro_57  Glycosyl hydrolase family 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.2   4.7e-12   8.4e-08     130     320 ..     104     295 ..      48     300 .. 0.74
   2 ?   -1.9   0.1     0.084   1.5e+03     225     245 ..     343     383 ..     319     422 .. 0.64
   3 ?   -3.5   0.2      0.26   4.6e+03      29      81 ..     450     497 ..     438     501 .. 0.61

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 4.7e-12
                                       TSEEEEEE-TT-B-GGG-S-HHHHHHHHHHHH..HHHHHHHS.S--SBEE-GGG-B--SHHHHHHH.TT--EEEE-C CS
                    Glyco_hydro_57 130 gqvElltspyyHpllpllpdsedieaqvkkar..elyeeyfg.qePrgfwlpElavspeileilae.lGfeylftde 202
                                        +vE + ++  Hp++p l++   +e+++  ++  ++ye  +  ++ +g wlpE + ++e+++i+ae    e+lf  +
  gi|242399117|ref|YP_002994541.1| 104 NKVEPVPTTSFHPIMPHLST---FEQEILAKIsfDFYEPFIKdKNVVGYWLPENVITKETAKIVAEsTQREVLFLLD 177
                                       47899999999********9...666665444005666655578999******************943445555555 PP

                                       -----------..-TTS-EE-TTS.-EEEE--CHH-TTTSGGG-..............TTSB.............-T CS
                    Glyco_hydro_57 203 laeiledkske..spyrpyllknggiavffRdreLsddigFryseqypl..eavddfinwlkkvkka...ksevvti 272
                                       +++++  +  +   +   y+ +++ ++vf Rd++Lsd+ +F+  + + l  + v+  ++ +k    +    + +v +
  gi|242399117|ref|YP_002994541.1| 178 ERQFVGLHFPQakFSCNTYKCDDKIVYVFGRDHQLSDAFAFNTLDANGLvrAVVEGKVDVFK----EnsgIPYLVYL 250
                                       5555555545433566778888777****************977433330013333333333....23457889999 PP

                                       T---TTT--BB-TT-S---HHHHHHHHHHHHHHHHHHHHHHHHHSS-E CS
                    Glyco_hydro_57 273 aldgEnwghypetgkkeFleklyeeleenglielvtpsefikklkpkg 320
                                       a d E +   p++ +k Fl++   +lee++ +e++   +fi+k k+ +
  gi|242399117|ref|YP_002994541.1| 251 ASDLEALLSNPQQLDK-FLSWIS-KLEERE-VEVINAVDFIRKKKNGE 295
                                       9999998888888876.9*9975.699999.99999999999777655 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.084
                                       ..-EEEE--CHH-TTTSGGG-.................... CS
                    Glyco_hydro_57 225 g.iavffRdreLsddigFrys...................e 245
                                       + i+    dr+ s+++ F +                    +
  gi|242399117|ref|YP_002994541.1| 343 RvINRIYKDRKVSQLWKFAFTklfrelnrsirfgvidlvrK 383
                                       36667778888888888888855555544444444444333 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 0.26
                                       HHTHHHHHHHHHHHHHTT----EEEEE-HHHHHHHT-HHHHHHHHHHHHHHHH CS
                    Glyco_hydro_57  29 aedYiklalilekfpkvhvtfeLsgsLiaqLeeylngekksylpateelleli 81 
                                         ++++ +     f +v+   ++s  Li+ ++ y++  ++ y++a+ ++le++
  gi|242399117|ref|YP_002994541.1| 450 DPRFWENIDTRVTFGNVS---AISKALIELMKVYIE--ENMYEKANYLFLEYM 497
                                       555555555555555555...555666666665555..777777777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (599 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); 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: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 3754.79
//
Query:       gi|242399118|ref|YP_002994542.1|  [L=449]
Description: CCA-adding enzyme [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-36  125.2   0.0    2.5e-36  124.4   0.0    1.5  1  tRNA_NucTransf2  tRNA nucleotidyltransferase, second domain
    1.3e-10   41.5   0.2    1.3e-10   41.5   0.2    2.7  4  NTP_transf_2     Nucleotidyltransferase domain
      3e-05   24.3   0.0    5.9e-05   23.3   0.0    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 !  124.4   0.0   4.2e-40   2.5e-36       1     113 []     152     273 ..     152     273 .. 0.90

  Alignments for each domain:
  == domain 1  score: 124.4 bits;  conditional E-value: 4.2e-40
                                       HHHHHHHHHHHHTT-BSSSTTT-SB-HHHHHHHHHHHSSHHHHHHHHTT--TTEEEE...............EEE.. CS
                   tRNA_NucTransf2   1 devrllKkflkgigvYGselkvkGfsGYlaEllvleygsfeevleaaakwkpkvvidleekea.........llkkf 68 
                                       devrllK+flkgi++YGse++v+GfsGYl+Ell+++ygsf +++e+++   +  +idle   +         + ++ 
  gi|242399118|ref|YP_002994542.1| 152 DEVRLLKRFLKGINAYGSEVYVRGFSGYLTELLIIKYGSFLKLMENIEFLGKIKIIDLEGWLKkepeiayktIEREG 228
                                       89*********************************************999999999966554445566555344555 PP

                                       -SS-EEEETTEEEEETTTTS-HHHHHHHHHHHHHHHHS--GGGGS CS
                   tRNA_NucTransf2  69 deplvviDPvDpkRNvaaalsleklaefilaareflkkpseefff 113
                                       ++plvviDPvDp+RNva+als+ek+  f+++a+e+ ++ ++efff
  gi|242399118|ref|YP_002994542.1| 229 EKPLVVIDPVDPRRNVASALSWEKFGVFYFKAMELKENLKLEFFF 273
                                       88*****************************************96 PP

>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.5   0.2   2.1e-14   1.3e-10       8      94 ..      36     138 ..      26     139 .. 0.91
   2 ?   -1.8   0.1      0.68   4.1e+03      50      83 ..     200     232 ..     181     242 .. 0.51
   3 ?   -2.4   0.0         1   6.1e+03      36      70 ..     294     320 ..     287     343 .. 0.63
   4 ?   -3.8   0.0       2.8   1.7e+04      35      47 ..     422     434 ..     421     445 .. 0.60

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 2.1e-14
                                       HHHHTTTSEEEEEHHHHCTTSCTT.SSEEEEEEESTTCHHH...............HHHEHHHHHHHHCCCEEECTT CS
                      NTP_transf_2   8 lkelepvakvvlfGSyarGtalkg.SDiDllvvlpeevsre...............kkeegleklaeiikfleellg 68 
                                       +++ e+ + ++l+GS a++t+l+g +DiDl++ +p + s e                 e+++  +ae++++    +g
  gi|242399118|ref|YP_002994542.1|  36 IEKVESEVTLHLVGSIAKDTYLSGdHDIDLFLAFPLDYSLEelrkrglelakaignHFENYEVTYAEHPYVRAIYKG 112
                                       444455899****************************9999***************888889*************** PP

                                       EEEEEECEEECCCCTEEEEEECEEEH CS
                      NTP_transf_2  69 levdlvtrekledpllvksileerpl 94 
                                         vd+v+++ +++++ v++++++ +l
  gi|242399118|ref|YP_002994542.1| 113 FDVDIVPCYNVKSWKEVRTAVDRSIL 138
                                       *******************9998775 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.68
                                       HEHHHHHHHHCCCEEECTTEEEEEECEEECCCCT CS
                      NTP_transf_2  50 eegleklaeiikfleellglevdlvtrekledpl 83 
                                       + g+ k++  + +l++ + + +  ++re  + pl
  gi|242399118|ref|YP_002994542.1| 200 FLGKIKIIDLEGWLKKEPEIAYKTIEREGEK-PL 232
                                       3334444444444444444444444444444.44 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1
                                       EEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEE CS
                      NTP_transf_2  36 llvvlpeevsrekkeegleklaeiikfleellgle 70 
                                       +++++p++           +++ i++ + + +gle
  gi|242399118|ref|YP_002994542.1| 294 IVILFPKPEL--------VDDVLIPQLERSAKGLE 320
                                       6788888843........33444444444444444 PP

  == domain 4  score: -3.8 bits;  conditional E-value: 2.8
                                       EEEEEESTTCHHH CS
                      NTP_transf_2  35 Dllvvlpeevsre 47 
                                       D+l+ +  +  +e
  gi|242399118|ref|YP_002994542.1| 422 DILINFVPHELEE 434
                                       8888888885443 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 !   23.3   0.0   9.8e-09   5.9e-05       7     134 ..       4     124 ..       1     137 [. 0.82

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 9.8e-09
                             SMODS   7 FkeflsnielsqttkdsissrvkaitkrLnkdfrelkskiaesllvGSyardTaikpvsdkdmlfeldvdllvvvne 83 
                                       ++e l  i++s++++  i++ ++++ +  +++ ++++s+++ + lvGS a+dT + +  d d+   ++ d+ ++   
  gi|242399118|ref|YP_002994542.1|   4 LEEVLGMIKPSEEERRLINEVIREVVDIAKAEIEKVESEVTLH-LVGSIAKDTYLSGDHDIDLFLAFPLDYSLEELR 79 
                                       56778889*************************9999888776.9*************************7776666 PP

                             SMODS  84 vegdepsdlleklkkalkktyksseirqdrqvvvvelneikidvvPavenk 134
                                       ++g    +l +++ + ++++     +  +++ v+  ++++++d+vP+ + k
  gi|242399118|ref|YP_002994542.1|  80 KRGL---ELAKAIGNHFENYEV---TYAEHPYVRAIYKGFDVDIVPCYNVK 124
                                       5555...455555566654333...367799****************8765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (449 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.65u 0.30s 00:00:00.95 Elapsed: 00:00:00.52
# Mc/sec: 2620.38
//
Query:       gi|242399119|ref|YP_002994543.1|  [L=185]
Description: 2'-5' RNA ligase [Thermococcus sibiricus MM 739]
Scores for 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  117.1   0.1    1.6e-19   69.9   0.1    2.0  2  LigT_PEase       LigT like Phosphoesterase
    1.8e-16   60.6   1.3    2.2e-16   60.4   1.3    1.1  1  AKAP7_NLS        AKAP7 2'5' RNA ligase-like domain
    2.2e-13   50.4   0.0    2.8e-13   50.0   0.0    1.1  1  2_5_RNA_ligase2  2'-5' RNA ligase superfamily
     0.0036   17.4   1.3       0.12   12.5   0.1    2.9  3  PYRIN            PAAD/DAPIN/Pyrin domain
     0.0067   15.9   0.1       0.01   15.4   0.1    1.4  1  HVSL             Uncharacterised conserved protein
  ------ inclusion threshold ------
      0.022   15.2   0.6       0.04   14.3   0.6    1.4  1  DUF4600          Domain of unknown function (DUF4600)
      0.035   14.6   1.5       0.12   12.8   0.1    2.4  3  RBFA             Ribosome-binding factor A
      0.072   13.1   0.1      0.072   13.1   0.1    2.2  3  DUF2680          Protein of unknown function (DUF2680)
        0.1   12.6   0.3       0.15   12.1   0.3    1.3  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
       0.11   11.8   0.0       0.14   11.5   0.0    1.1  1  Phi_1            Phosphate-induced protein 1 conserved region


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 !   69.9   0.1   8.9e-23   1.6e-19       1      87 []       7      92 ..       7      92 .. 0.97
   2 !   45.6   0.0   3.4e-15   6.2e-12       9      87 .]      99     175 ..      94     175 .. 0.94

  Alignments for each domain:
  == domain 1  score: 69.9 bits;  conditional E-value: 8.9e-23
                                      EE-CHHHHHHHHHHHHHHHHHHCCTTEEETSGGGSEEEEEEEEEESHHHHHHHHHHHHHHHHTSBEEEEEEEEEEEEEE CS
                        LigT_PEase  1 lgppeeiaeelarlaaeleralaklglkpvrpfnpHiTLaflgevdeekvpellealaeiasgaepfelkvdgvglfps 79
                                      +++++e++++l +++++++ + +++++k+v+p+n HiTL+flge++ee+++++++ l++ia+  ++ e++++gvg+fp+
  gi|242399119|ref|YP_002994543.1|  7 VEINDEVRKKLVEIQEKID-RTKSAKIKFVEPENIHITLKFLGEITEEQAEDIKRILESIAKNHKKHEVNAKGVGVFPN 84
                                      67899**************.78899****************************************************** PP

                                      CCSCCEEE CS
                        LigT_PEase 80 rlrprviy 87
                                       ++ rvi+
  gi|242399119|ref|YP_002994543.1| 85 YNYVRVIW 92
                                      99*****9 PP

  == domain 2  score: 45.6 bits;  conditional E-value: 3.4e-15
                                       HHHHHHHHHHHHHHCCTTEEETSGGGSEEEEEEEEEES.HHHHHHHHHHHHHHHHTSBEEEEEEEEEEEEEECC.SC CS
                        LigT_PEase   9 eelarlaaeleralaklglkpvrpfnpHiTLaflgevd.eekvpellealaeiasgaepfelkvdgvglfpsrl.rp 83 
                                       ee+ ++a+e+++al +lg+k +++f  HiT+++++ v+ +  +  +l++l++ ++g+    +kv+ + l +s+l ++
  gi|242399119|ref|YP_002994543.1|  99 EEIKKMAEEIDNALFQLGFKREKNFVSHITIGRVKFVKdKVGLMLVLKELSNEEFGK----FKVEAIELKKSTLtPK 171
                                       699**********************************9888999*********8885....**************** PP

                                       CEEE CS
                        LigT_PEase  84 rviy 87 
                                       ++iy
  gi|242399119|ref|YP_002994543.1| 172 GPIY 175
                                       ***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 !   60.4   1.3   1.2e-19   2.2e-16       4     206 ..       4     182 ..       3     183 .. 0.88

  Alignments for each domain:
  == domain 1  score: 60.4 bits;  conditional E-value: 1.2e-19
                                       EEEEE---HHHHHHHHHHHHHHHHH-GGGGGGB.--TT--EEEEEEE---SHHHHHHHHHHHHHHHHHHHHHHTTS- CS
                         AKAP7_NLS   4 FlsiplnsnklrkklekfqesvlsklpgldeslfikpeklHlTllvlkLknkeeiaaakevLkevkeeikdaldnkp 80 
                                       F+++ +n+ ++rkkl ++qe++ +      +  f++pe++H+Tl  l   ++e+ ++ k++L+++ ++       k+
  gi|242399119|ref|YP_002994543.1|   4 FIAVEIND-EVRKKLVEIQEKIDRTKS--AKIKFVEPENIHITLKFLGEITEEQAEDIKRILESIAKNH------KK 71 
                                       77777764.6************88655..555569*************99************9996333......77 PP

                                       -EEEEEEEEEE.....TTTEEEEEE--SHHHHHHHHHHHHHHHHHHTTT--B--SS-.---EEEEEEGGG-THHHHT CS
                         AKAP7_NLS  81 lslrlkGletfnddpakarVlYakveeesneekLqeladriikafeeaglvlekdkkkvklHaTlmnsrkrkkkqak 157
                                        +++ kG+++f  +   +rV++a+v+   n e+++++a+ i +a+ + g++ ek+   +  H+T+  +++ k+k   
  gi|242399119|ref|YP_002994543.1|  72 HEVNAKGVGVFP-NYNYVRVIWAGVD---NDEEIKKMAEEIDNALFQLGFKREKN---FVSHITIGRVKFVKDKVGL 141
                                       79*********5.5555********9...568******************99998...779***********99997 PP

                                       T--S--GG.GGGGGTT-EEEEEE--EEEEEESSS---TTS--EEEEEEE CS
                         AKAP7_NLS 158 skesfdareilkqfkdfefgeekineihLsqlesddesdgyYkviasvk 206
                                                +lk+ +++efg+ k+++i+L + + + +    Y+++a+++
  gi|242399119|ref|YP_002994543.1| 142 ML-------VLKELSNEEFGKFKVEAIELKKSTLTPK-GPIYETLARFE 182
                                       77.......*********************9999988.99999998876 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 !   50.0   0.0   1.6e-16   2.8e-13       5     117 ..      20     133 ..      11     167 .. 0.85

  Alignments for each domain:
  == domain 1  score: 50.0 bits;  conditional E-value: 1.6e-16
                   2_5_RNA_ligase2   5 laapiealrrslydkayprwppHitLlypfvededl.adlaellsrlaketepfevrldgfgvFeh.kks.vvylsv 78 
                                       ++++i++ + s+  k ++    HitL++++++ e   +d+++ l+ +ak++++ ev  +g+gvF+      v+++ v
  gi|242399119|ref|YP_002994543.1|  20 IQEKIDRTK-SAKIKFVEPENIHITLKFLGEITEEQaEDIKRILESIAKNHKKHEVNAKGVGVFPNyNYVrVIWAGV 95 
                                       566677888.99999999************9998888*****************************97778****** PP

                   2_5_RNA_ligase2  79 sdsealqalraallealpeagdkedsgeftPHlTiaqsa 117
                                       +++e+++++ +++ +al + g k++ ++f+ H+Ti++ +
  gi|242399119|ref|YP_002994543.1|  96 DNDEEIKKMAEEIDNALFQLGFKRE-KNFVSHITIGRVK 133
                                       **********************997.**********876 PP

>> PYRIN  PAAD/DAPIN/Pyrin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.71   1.3e+03      55      74 ..      11      30 ..      10      31 .. 0.80
   2 ?    2.0   0.0      0.13   2.3e+02       3      24 ..      44      65 ..      42      80 .. 0.74
   3 !   12.5   0.1     7e-05      0.12       2      19 ..     141     158 ..     140     174 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.71
                                      CCCHHHHHHHHHHTTTHHHH CS
                             PYRIN 55 daavevtlkvlekinlkdla 74
                                      d++ ++++++ eki++++ a
  gi|242399119|ref|YP_002994543.1| 11 DEVRKKLVEIQEKIDRTKSA 30
                                      56778999999999998766 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.13
                                      CCCCCCC-HHHHHHHHHHHHH. CS
                             PYRIN  3 llyLeeLseeelkkFKslLkee 24
                                      l+ L e++ee+ + +K+ L++ 
  gi|242399119|ref|YP_002994543.1| 44 LKFLGEITEEQAEDIKRILESI 65
                                      677999*************543 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 7e-05
                                       HCCCCCCC-HHHHHHHHH CS
                             PYRIN   2 LllyLeeLseeelkkFKs 19 
                                       L+l+L+eLs+ee+ kFK 
  gi|242399119|ref|YP_002994543.1| 141 LMLVLKELSNEEFGKFKV 158
                                       899*************95 PP

>> HVSL  Uncharacterised conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   5.6e-06      0.01      51     172 ..      10     118 ..       2     164 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 5.6e-06
                              HVSL  51 seeekellsellkkleekl...eeevklhslltsdlgaplplHiSLSrplvlrthqkdsfldslkkelkssakrrFe 124
                                       ++           ++++kl   +e+++ ++  + ++ +p++ Hi+L     ++++q +++ + l++  k+ +k + e
  gi|242399119|ref|YP_002994543.1|  10 ND-----------EVRKKLveiQEKIDRTKSAKIKFVEPENIHITLKFLGEITEEQAEDIKRILESIAKN-HK-KHE 73 
                                       33...........333333333344444556777899999999999999999999999988888777744.33.689 PP

                              HVSL 125 vsfsglkwvsndektRsFlvlrvkspendeLkklleavnkvleefglp 172
                                       v+++g+ +++n++  R+ ++  v +   +e+kk+ e+++++l + g +
  gi|242399119|ref|YP_002994543.1|  74 VNAKGVGVFPNYNYVRVIWAG-VDND--EEIKKMAEEIDNALFQLGFK 118
                                       9999*******9999987776.5444..69999999999998776655 PP

>> DUF4600  Domain of unknown function (DUF4600)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.6   2.2e-05      0.04      11      72 ..       5      75 ..       1      80 [. 0.73

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.2e-05
                           DUF4600 11 tqlelNdqLekqiailkeklekir......gnpsdrlasirvleklte...eelnqllkqLekekkslenq 72
                                      + +e+Nd+ +k+++ ++ek++ ++       +p+++  +++ l ++te   e+++++l+ + k+ k+ e +
  gi|242399119|ref|YP_002994543.1|  5 IAVEINDEVRKKLVEIQEKIDRTKsakikfVEPENIHITLKFLGEITEeqaEDIKRILESIAKNHKKHEVN 75
                                      568********************988888855555555555555555411167888899888888876665 PP

>> RBFA  Ribosome-binding factor A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1       1.4   2.5e+03       8      87 ..      12      32 ..       7      46 .. 0.47
   2 ?   12.8   0.1   6.8e-05      0.12       6      93 ..      55     138 ..      49     140 .. 0.72
   3 ?    5.7   0.1     0.011        21       3      48 ..     102     145 ..     101     169 .. 0.64

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.4
                                      HHHHHHHHHHHHCT-HCCTGHHCEEEEEEESTTSSEEEEEEEESS-HHHHHHHHHHHHHTHHHHHHHHHHHC-SSSG-E CS
                              RBFA  8 liqrelseilqeelkdprlgklvtiteVkvsrDlskakVyvsvlgseeekeevlkaLkkaagflrrelakrlklrktPe 86
                                      +++++l ei  e+                                                          ++  k  +
  gi|242399119|ref|YP_002994543.1| 12 EVRKKLVEIQ-EK----------------------------------------------------------IDRTKSAK 31
                                      4445554443.22..........................................................22222223 PP

                                      E CS
                              RBFA 87 L 87
                                      +
  gi|242399119|ref|YP_002994543.1| 32 I 32
                                      3 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 6.8e-05
                                       HHHHHHHHHHHHHHCT-HCCTGHHCEEEEEEESTTSSEEEEEEEESS-HHHHHHHHHHHHHTHHHHHHHHHHH.C-S CS
                              RBFA   6 aeliqrelseilqeelkdprlgklvtiteVkvsrDlskakVyvsvlgseeekeevlkaLkkaagflrrelakr.lkl 81 
                                       ae i+r l++i     k+++  + v+ ++V v +++ +++V +  ++++ee +++++++++a  +l  +  k+ ++ 
  gi|242399119|ref|YP_002994543.1|  55 AEDIKRILESIA----KNHKK-HEVNAKGVGVFPNYNYVRVIWAGVDNDEEIKKMAEEIDNALFQLGFKREKNfVSH 126
                                       455566666555....44433.48999***************99777777888888888888877777777775556 PP

                                       SSG-EEEEESSS CS
                              RBFA  82 rktPeLkFvlDe 93 
                                        ++ ++kFv+D+
  gi|242399119|ref|YP_002994543.1| 127 ITIGRVKFVKDK 138
                                       666788888886 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.011
                                       HHHHHHHHHHHHHHHHHCT-HCCTGHHCEEEEEEESTTSSEEEEEE CS
                              RBFA   3 ervaeliqrelseilqeelkdprlgklvtiteVkvsrDlskakVyv 48 
                                       +++ae+i ++l ++  +  +++ + +++ti +Vk  +D      ++
  gi|242399119|ref|YP_002994543.1| 102 KKMAEEIDNALFQLGFK-REKNFV-SHITIGRVKFVKDKVGLMLVL 145
                                       57888888888887722.223344.5********999965554444 PP

>> DUF2680  Protein of unknown function (DUF2680)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.2         2   3.6e+03      18      25 ..      12      19 ..      10      24 .. 0.59
   2 ?   13.1   0.1     4e-05     0.072      31      54 ..      48      71 ..      46      82 .. 0.87
   3 ?   -3.3   0.1       5.1   9.2e+03      40      44 ..     103     107 ..      98     114 .. 0.49

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2
                           DUF2680 18 elrKqivd 25
                                      e+rK++v+
  gi|242399119|ref|YP_002994543.1| 12 EVRKKLVE 19
                                      45566554 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 4e-05
                           DUF2680 31 GllTkeqgekikkniDkrlkylke 54
                                      G++T+eq+e ik  ++   k+ k+
  gi|242399119|ref|YP_002994543.1| 48 GEITEEQAEDIKRILESIAKNHKK 71
                                      9************99998888776 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 5.1
                           DUF2680  40 kikkn 44 
                                       k+ + 
  gi|242399119|ref|YP_002994543.1| 103 KMAEE 107
                                       23333 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.3   8.4e-05      0.15      54     104 ..      42     115 ..       8     140 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.4e-05
                                       H..............CCHCCCHHHHHHCHCHHHH...........EEEEEEEEESS...-TTCHHHHHHHHHHC CS
                                       x..............xxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  54 p..............dlkrllellealgkkkall.........lkiagvvlnrvdgeneetllkealeelkqry 104
                                                      d+kr+le++++  kk++++          ++++v+   vd+++e++++ e +++ ++++
  gi|242399119|ref|YP_002994543.1|  42 ItlkflgeiteeqaeDIKRILESIAKNHKKHEVNakgvgvfpnYNYVRVIWAGVDNDEEIKKMAEEIDNALFQL 115
                                       033444444444466*********999999999999*********************99999999999988777 PP

>> Phi_1  Phosphate-induced protein 1 conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   7.6e-05      0.14      11     128 ..      38     155 ..      33     174 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.6e-05
                             Phi_1  11 gkikvsllwYGkftpaqkaiiadfleslsssseakaaasps..vasWWktvekykekkaakavsakvklakqvsdek 85 
                                       ++i+++l + G+ t++q + i+  les+ +++++++ ++    v   ++ v+     ++ ++ ++  k+a+++ ++ 
  gi|242399119|ref|YP_002994543.1|  38 ENIHITLKFLGEITEEQAEDIKRILESIAKNHKKHEVNAKGvgVFPNYNYVRVIW--AGVDNDEEIKKMAEEIDNAL 112
                                       589**************************66665555544401455566666666..34443455567888888999 PP

                             Phi_1  86 yslGksLtreqieklaakaveekkkgialvLtakdvavegfCs 128
                                       ++lG + +++ ++++    v+  k+++ l+L  k+ + e+f +
  gi|242399119|ref|YP_002994543.1| 113 FQLGFKREKNFVSHITIGRVKFVKDKVGLMLVLKELSNEEFGK 155
                                       999*999999999999999998888888888888998888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1343  (0.0749066); expected 358.6 (0.02)
Passed bias filter:                      759  (0.0423336); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 1202.97
//
Query:       gi|242399120|ref|YP_002994544.1|  [L=159]
Description: Xanthine-guanine phosphoribosyltransferase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.5e-27   94.0   0.2    7.9e-27   93.7   0.2    1.0  1  Pribosyltran    Phosphoribosyl transferase domain
    0.00021   20.8   0.0    0.00027   20.5   0.0    1.1  1  UPRTase         Uracil phosphoribosyltransferase
  ------ inclusion threshold ------
      0.035   13.6   0.1      0.048   13.2   0.1    1.1  1  PRTase_2        Phosphoribosyl transferase
      0.042   13.9   1.1      0.056   13.5   1.1    1.2  1  Pribosyl_synth  Phosphoribosyl synthetase-associated domain


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 !   93.7   0.2   1.8e-30   7.9e-27      19     154 ..      18     151 ..       5     154 .. 0.88

  Alignments for each domain:
  == domain 1  score: 93.7 bits;  conditional E-value: 1.8e-30
                                       TEEEEEE--GGGEEEEEEETTTHHHHHHHHHHS.TT-EE-EEEEEE-TTT--EE........EE----TTSEEEEE- CS
                      Pribosyltran  19 aaeileeyngkpdvvvgiargGvpfakiladeL.evplayvrkvkyrpdgseeaargssdesrlledpagkkVliVD 94 
                                       +a+ l+   ++pd++vgi rgG+++a +l++ L +v + +++++ y + +     ++++ +    ++++gk+V+iVD
  gi|242399120|ref|YP_002994544.1|  18 LADVLRR--YNPDTIVGISRGGLIPAVRLSHILgDVDFKVIDVKFYKGIDERAEEPKITIP--IHGSLEGKRVVIVD 90 
                                       4444444..7***********************************9998888888777655..99************ PP

                                       SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE-HHHHHHHHHH-TTS......EEEEEEE-S CS
                      Pribosyltran  95 DildtGgTllaalelLkekgpeevriavlvdkpateeevdknakrvfsls.pdnfvavvgf 154
                                       D+ dtG+Tl+ +++ +k+kg++ +++a+l+ kp t   +d++++r+++ + + +++++v +
  gi|242399120|ref|YP_002994544.1|  91 DVSDTGKTLQVVIDEVKKKGAKDIKVACLAMKPWTLVVPDFYVFRTDKWIvFPWEEFPVVV 151
                                       ***********************************************88888888888765 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0     6e-08   0.00027      70     157 ..      29     119 ..      19     125 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 6e-08
                           UPRTase  70 alVpilRaGegmeealrellpea..rvghlglqreeetlepveyynkLPkki..aertvlllDpviaTGgsaaaaiq 142
                                       ++V i R+G+  +  l+ +l ++  +v+ ++ ++  +  +++e    +P +   + ++v+++D v  TG++++ +i+
  gi|242399120|ref|YP_002994544.1|  29 TIVGISRGGLIPAVRLSHILGDVdfKVIDVKFYKGID-ERAEEPKITIPIHGslEGKRVVIVDDVSDTGKTLQVVID 104
                                       5788889999999999999999866778888777543.23344444455554449999******************* PP

                           UPRTase 143 lLkergvgeekIlvl 157
                                        +k++g++  k+ +l
  gi|242399120|ref|YP_002994544.1| 105 EVKKKGAKDIKVACL 119
                                       ****99875555544 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   1.1e-05     0.048     121     158 ..      83     121 ..      74     127 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.1e-05
                          PRTase_2 121 akelvLvDDEistGktalnliralqeklpr.kryvvvsl 158
                                        k++v+vDD   tGkt+  +i+++++k  +  +++++++
  gi|242399120|ref|YP_002994544.1|  83 GKRVVIVDDVSDTGKTLQVVIDEVKKKGAKdIKVACLAM 121
                                       5789*********************99776466666665 PP

>> Pribosyl_synth  Phosphoribosyl synthetase-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   1.1   1.3e-05     0.056      64     116 ..      64     116 ..      47     123 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.3e-05
                                       -------------EES--TTSEEEEEEEEE-S-HHHHHHHHHHHHTT--EEEE CS
                    Pribosyl_synth  64 lpellakekppltvvGdvgGriaiivddliddvesfvaaaevlkerGaykiyv 116
                                       + e +   k  + + G ++G+  +ivdd+ d  +++    + +k++Ga  i v
  gi|242399120|ref|YP_002994544.1|  64 IDERAEEPKITIPIHGSLEGKRVVIVDDVSDTGKTLQVVIDEVKKKGAKDIKV 116
                                       555556666677789*********************************87765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); 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: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1069.07
//
Query:       gi|242399121|ref|YP_002994545.1|  [L=897]
Description: Ribonucleotide reductase alpha subunit [Thermococcus sibiricus MM 739]
Scores for complete 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-226  753.2   0.0   1.9e-226  752.7   0.0    1.2  1  Ribonuc_red_lgC  Ribonucleotide reductase, barrel domain
    1.2e-29  102.2   0.1    3.3e-29  100.7   0.1    1.9  1  Ribonuc_red_lgN  Ribonucleotide reductase, all-alpha domain
    1.4e-21   76.8   0.9    4.6e-21   75.2   0.9    2.0  1  ATP-cone         ATP cone 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 !  752.7   0.0  3.1e-230  1.9e-226       1     524 []     271     771 ..     271     771 .. 0.98

  Alignments for each domain:
  == domain 1  score: 752.7 bits;  conditional E-value: 3.1e-230
                                       EEE.....BSS-EEEE-X..............XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC   1 ssCfvlsvedslesIletvkeaallskaggGvGlnlsklRakgslvkgtegaasGpvsfmklidavadvvkqgGkRr 77 
                                       s+Cfv+ +ed++esI+++++++a + k ggG+Gln+sk+R++g+lv++t+gaasGp+sfm+lidav++v+kqgG+Rr
  gi|242399121|ref|YP_002994545.1| 271 SACFVVPIEDDMESIMKAAHDVAIIQKMGGGTGLNFSKIRPEGDLVGTTTGAASGPISFMHLIDAVSNVIKQGGVRR 347
                                       79*************************************************************************** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX............ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC  78 GAamvylevwHpDiekfidaKekntgeeenrlsnlnisvgvpdlFmeavkedkdwtLfsPrtvvkleklygeefeee 154
                                       GA+m++levwHpDiekfi+aKe+n+g  +n lsn+nisvg++ +F+ea+ke+k+++L++Prt +k            
  gi|242399121|ref|YP_002994545.1| 348 GANMGILEVWHPDIEKFIHAKEQNVG--TNILSNFNISVGMWADFWEALKEGKKYPLINPRTGKK------------ 410
                                       **************************..*********************************5444............ PP

                                       .............XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC 155 yeeleekakikkkevkakeLfeeiaesawetgePgvlfkDtiNrrnvlekakggkIratNlCgEiplleyesvavCn 231
                                                   ke+++++Lfee+a++aw++++Pgv+f+D+iN+rnvl +akg+kIratN+CgE+pl++yes   Cn
  gi|242399121|ref|YP_002994545.1| 411 -----------VKEIDPRSLFEELAYMAWAKADPGVVFFDVINKRNVLVPAKGEKIRATNPCGEEPLYDYES---CN 473
                                       ...........569**********************************************************...** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC 232 LasinLakfvkkdeegkkefdwdelkkviqlvvraLdnvidvnkyplpeiekntkktRriGlGvmgladalaklgip 308
                                       LasinLakfvk+d+egk++f+wde++kvi +v+++Ldn+idvnk+plpei++ntk +RriG+G+mgladal+klgi+
  gi|242399121|ref|YP_002994545.1| 474 LASINLAKFVKYDDEGKPYFEWDEYAKVIMKVAKYLDNAIDVNKFPLPEIDYNTKLSRRIGVGIMGLADALFKLGIR 550
                                       ***************************************************************************** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX........XXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC 309 ydseealkfarkitelltyyaykaSvelAkergpfplfekskyskgilpvdefeeke..kedweeLreeikkyGlrn 383
                                       y+s+e+ +f+rk+te+lt+yayk+S+++Akergpfpl++k++y +g+lp++++ +ke  +  w+eL+e+++kyG+rn
  gi|242399121|ref|YP_002994545.1| 551 YNSKEGYDFMRKATEYLTFYAYKYSIRAAKERGPFPLYHKTEYPEGKLPIEGYYHKEiwNLPWDELVEDLRKYGVRN 627
                                       *****************************************************655566999*************** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxx RF
                   Ribonuc_red_lgC 384 amvtalaPTgsiSliagtssgiePifalvykksvtvgeflevnpvfeeeLkklglwseellkki...lesvqgleei 457
                                       amvt+++PTgs+S+ia+tssgiePifalvykksvtvgef++v+p fe+eLkk+gl+++e+l+ki   ++svqgleei
  gi|242399121|ref|YP_002994545.1| 628 AMVTTCPPTGSVSMIADTSSGIEPIFALVYKKSVTVGEFYYVDPIFEAELKKRGLYTDEILQKIsdnYGSVQGLEEI 704
                                       ****************************************************************988888******* PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC 458 peeikrvfktaldidqedhikaqaaiqkwidqsiSktinlpneatvedvkelyllAwklGlKgvtyY 524
                                       pe+++++f+ta+di++ dh+ aqa+iq w+++s+Sktin+pn+atvedvk++yllA+ lG+Kgvt+Y
  gi|242399121|ref|YP_002994545.1| 705 PEDVQKIFVTAMDIHWFDHLLAQASIQLWLTDSASKTINMPNDATVEDVKAAYLLAHALGCKGVTVY 771
                                       ******************************************************************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 !  100.7   0.1   5.5e-33   3.3e-29       1      83 []     113     268 ..     113     268 .. 0.99

  Alignments for each domain:
  == domain 1  score: 100.7 bits;  conditional E-value: 5.5e-33
                   Ribonuc_red_lgN   1 kkltynalkvledrYllkdengeivEspqqmfmRvAlalaiaealyd.............................. 47 
                                       k++++n+l+vl++rYl+k+e+g+ivE+p ++f+RvA+++ai+++lyd                              
  gi|242399121|ref|YP_002994545.1| 113 KRFSINGLRVLASRYLIKNEEGKIVETPKELFERVAILAAIPDLLYDermfskegtyiqdlkrveyylqnfenfdsi 189
                                       689************************************************************************** PP

                   Ribonuc_red_lgN  48 ...........................................kleedkdlaeefydlmssqkflpasPtlmnaGte 81 
                                                                                  ++++++ ++eef++lm++q f+p++P+l+n+G++
  gi|242399121|ref|YP_002994545.1| 190 ytigrfklnkyqfermvnlyrelaekgkmkvsideflnmlkngEFDKYEGVIEEFFNLMVNQVFMPNTPALINSGRP 266
                                       ****************************************************************************9 PP

                   Ribonuc_red_lgN  82 lg 83 
                                       lg
  gi|242399121|ref|YP_002994545.1| 267 LG 268
                                       86 PP

>> ATP-cone  ATP cone domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.2   0.9   7.6e-25   4.6e-21       2      85 ..       5      93 ..       4      94 .. 0.83

  Alignments for each domain:
  == domain 1  score: 75.2 bits;  conditional E-value: 7.6e-25
                                      EEE-TTS-EEE--HHHHHHHHHHHHHH....-HHHHHHHHHHHHHHHHHHHIIT.-BHHHHHHHHHHHHHHSS-HHHHH CS
                          ATP-cone  2 kViKRdGtvepfdvekIkraiekAceg....seeeideiaeeveaevrkrlrdg.isteeIqdlvektliehpdyavaa 75
                                      kV KRdG+++pfd+++I+ ai++A+ +    +++ +d++++ v++++ + ++ + +++e Iqd+ve +l++++ ++va+
  gi|242399121|ref|YP_002994545.1|  5 KVMKRDGRIVPFDESRIRWAIQRAMWEvgvrDDNLLDKVVKDVIDRINELYEGQvPHIENIQDIVELELMRNGLFEVAK 83
                                      79*************************5554444455555555555555555559************************ PP

                                      HHHHHHHHHH CS
                          ATP-cone 76 ayilyrnlrk 85
                                      ayi+yr+++ 
  gi|242399121|ref|YP_002994545.1| 84 AYIIYRKKKA 93
                                      ******9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (897 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       732  (0.0408277); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 5760.02
//
Query:       gi|242399122|ref|YP_002994546.1|  [L=146]
Description: hypothetical protein TSIB_1143 [Thermococcus sibiricus MM 739]
Scores for complete 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   41.4   5.4      1e-09   38.9   5.1    1.9  1  Rubrerythrin  Rubrerythrin
     0.0083   16.1   5.4       0.14   12.1   5.5    2.3  1  Ferritin      Ferritin-like domain
  ------ inclusion threshold ------
      0.015   14.9   0.6      0.018   14.6   0.6    1.1  1  MiaE          tRNA-(MS[2]IO[6]A)-hydroxylase (MiaE)


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 !   38.9   5.1   1.7e-13     1e-09       1     134 [.       5     138 ..       5     141 .. 0.86

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 1.7e-13
                                       HHHHHHHHHHHHHHHHHHHHHHCHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSBBS-------T CS
                      Rubrerythrin   1 eiLekAiagEssarrlYkelaekakegypqiaelFeelAeeEreHakilnklleklepelelevkekvreyaeakpk 77 
                                       e+L++ i  E + ++lYk  +  a  ++p + e F++lA eE +H++ ++++l++  +e+   +  ++ e +  +p 
  gi|242399122|ref|YP_002994546.1|   5 ELLKNIIHQENELYNLYKLGETFATYENPILIEHFQWLASEELRHRQTIENFLKSGSLENT--PVVDYLETLSLEPY 79 
                                       678888999999999999777777799****************************888877..66666666666776 PP

                                       TGGHHH...HHHHHHHHHHHHHHCHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHHHHH CS
                      Rubrerythrin  78 flttak...nLeeaiegayaeeeemyrfyeelaekegneeakklfkklaeaEkkHeerlr 134
                                       f  t+    ++e++i  a  +e+ +y+ y++l e ++ +  k++f  ++++E kH++rl+
  gi|242399122|ref|YP_002994546.1|  80 FQDTRAepeSIEDLILEALVREKHSYELYKKLGEIMKGS-LKEIFGMMSQEELKHAYRLK 138
                                       666544333899**********************99988.******************98 PP

>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   5.5   2.4e-05      0.14       2     133 ..       5     138 ..       4     145 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.4e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHHHH..HTTS....SHHHHHH..... CS
                          Ferritin   2 kaLneqladeltaayqylamawyvkgpgleglaeffdeqaeeerehadklaeril..alGgtpvltraelee..... 71 
                                       ++L + +  e +++++y+     +   + + l e+f+  a+ee+ h + + ++++   l+ tpv+++ e        
  gi|242399122|ref|YP_002994546.1|   5 ELLKNIIHQENELYNLYKLG-ETFATYENPILIEHFQWLASEELRHRQTIENFLKsgSLENTPVVDYLETLSlepyf 80 
                                       689999***********876.567777888999*****************999974469*********998866653 PP

                                       C-SSSS..CSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHH CS
                          Ferritin  72 ieapke..fgsveevleaalehekkvteslrelielaeeegDpatadfledfleeqeehewele 133
                                          + +   +s+e+ + +al +ek+  e +++l e+ +      + ++++ + +e+ +h+  l+
  gi|242399122|ref|YP_002994546.1|  81 Q--DTRaePESIEDLILEALVREKHSYELYKKLGEIMKGS----LKEIFGMMSQEELKHAYRLK 138
                                       2..3335466***********************9999985....88999999999999988776 PP

>> MiaE  tRNA-(MS[2]IO[6]A)-hydroxylase (MiaE)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.6   3.1e-06     0.018     101     198 ..      34     133 ..       8     143 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.1e-06
                              MiaE 101 dlvdklvrlikeelehfeqvlelleaRnielakisasrYakglkaav..rthepqrllDkLivgayi.eaRsceRla 174
                                        l++++  l+ eel+h + ++++l+   +e +++     + +l+     ++ ep+ + D  i  a++ e  s e ++
  gi|242399122|ref|YP_002994546.1|  34 ILIEHFQWLASEELRHRQTIENFLKSGSLENTPVVDYLETLSLEPYFqdTRAEPESIEDL-ILEALVrEKHSYELYK 109
                                       48999*********************9998888877666677776552256799998885.5555554999****** PP

                              MiaE 175 kLapyldeelakfyvsLlrseaRh 198
                                       kL + +   l++ +  + + e +h
  gi|242399122|ref|YP_002994546.1| 110 KLGEIMKGSLKEIFGMMSQEELKH 133
                                       ************999888888777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 983.87
//
Query:       gi|242399123|ref|YP_002994547.1|  [L=286]
Description: Cobalt/zinc/cadmium cation efflux pump protein [Thermococcus sibiricus MM 739]
Scores for complete 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-46  156.7  14.5      7e-46  156.5  14.5    1.1  1  Cation_efflux  Cation efflux family
    1.6e-22   79.4   4.7    3.5e-22   78.3   4.7    1.6  1  ZT_dimer       Dimerisation domain of Zinc Transporter
  ------ inclusion threshold ------
        0.1   13.0   2.7       0.11   13.0   0.3    2.3  2  Asp23          Asp23 family, cell envelope-related function
       0.57    9.7   0.0       0.57    9.7   0.0    2.6  3  DUF1576        Protein of unknown function (DUF1576)
        8.7    6.1  12.3        0.6    9.9   0.8    3.3  3  PAP2           PAP2 superfamily


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 !  156.5  14.5   1.9e-49     7e-46       1     198 [.       8     200 ..       8     201 .. 0.98

  Alignments for each domain:
  == domain 1  score: 156.5 bits;  conditional E-value: 1.9e-49
                     Cation_efflux   1 lilsllanlilalvelivglltnSlalladafhslsdlvsllllllalklsrkppderfpfGygrlevlgalvsgll 77 
                                       li+s++ n++la+v+++vg+l  Slal++d++hslsd++++++++++ k+++kp+d+++pfG+ r+e+++a++ g+ 
  gi|242399123|ref|YP_002994547.1|   8 LIVSIFGNIVLAIVKITVGVLYSSLALISDGVHSLSDVITSIFGYFGAKIASKPADQTHPFGHSRFESFFAFFIGMA 84 
                                       79*************************************************************************** PP

                     Cation_efflux  78 llglavfllleaiqklikegereihaglalvvalvslvvnlalllilrragrklrsaalkaaalhvlgDaltslgvl 154
                                       l+++a+ +  +ai++++ ++   + ++++++v+l+s++ + a+  +  ++gr+l++++l a+a+h+++Dal+s++vl
  gi|242399123|ref|YP_002994547.1|  85 LFLVAYEIGKDAIKRIF-GDSTIEVNAIMIGVVLLSIFSKEAMTQYSLKVGRRLNNQILIADAYHHRSDALSSVAVL 160
                                       *****************.*********************************************************** PP

                     Cation_efflux 155 vsalvillfnlksgplaDpvaslligliilysalkllkeslseL 198
                                       v++ ++ ++      + D++as++++++i + a++++ +++  L
  gi|242399123|ref|YP_002994547.1| 161 VGLGLQRFG----FRYGDALASVVVVILIGKVAVEIVLKNVGYL 200
                                       ********7....4679**********************99877 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 !   78.3   4.7   9.7e-26   3.5e-22       2      77 ..     206     280 ..     205     282 .. 0.95

  Alignments for each domain:
  == domain 1  score: 78.3 bits;  conditional E-value: 9.7e-26
                                       ...HHHHHHHHHTT-SS-EEEEEEEEE-S----EEEEEEEE-TTS-HHHHHHHHHHHHHHHHHH-TT--EEEEEEE CS
                          ZT_dimer   2 deeeeeeireiiksvpgvkgvhdlrtrksGskifvdlhievdgdlsvkeaHeiadevekrikeefpgvadvliHve 77 
                                       ++e++eei+++++sv+gv++vhdlr++++G++++v+lhiev+++l++keaH+i++ v+kri+ ++++v+  ++Hv+
  gi|242399123|ref|YP_002994547.1| 206 PHEILEEIKNAALSVTGVVDVHDLRAHYVGPRLHVELHIEVPPELTLKEAHDISETVKKRIE-RLEEVELAFVHVD 280
                                       7899*********************************************************5.88999888***98 PP

>> Asp23  Asp23 family, cell envelope-related function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1         2     7e+03       6      26 ..      91     111 ..      89     116 .. 0.69
   2 ?   13.0   0.3   2.9e-05      0.11      59     107 ..     237     284 ..     179     285 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2
                             Asp23   6 eisdeViakiagiaaeeveGv 26 
                                       ei +++i+ i g ++ ev+ +
  gi|242399123|ref|YP_002994547.1|  91 EIGKDAIKRIFGDSTIEVNAI 111
                                       566777777777777777655 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 2.9e-05
                             Asp23  59 qvavdlyvvveYGvkipevaenvqekVkeaveemtglevseVnvhVqgv 107
                                       +++v+l++ v  +  ++e a+++ e Vk+++e++ ++e++ V+v ++g+
  gi|242399123|ref|YP_002994547.1| 237 RLHVELHIEVPPELTLKE-AHDISETVKKRIERLEEVELAFVHVDIKGI 284
                                       567888888888888887.899**************************9 PP

>> DUF1576  Protein of unknown function (DUF1576)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   1.1     0.033   1.2e+02      69     143 ..      11      88 ..       7      94 .. 0.66
   2 ?    9.7   0.0   0.00016      0.57      71     102 ..     101     132 ..      99     135 .. 0.91
   3 ?   -1.8   0.1      0.52   1.9e+03     121     144 ..     169     193 ..     151     204 .. 0.57

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.033
                           DUF1576  69 safGknllNiipillGvlLyalvk...kesfkkyilaalfgtaLaPivgellfslelel.glvlgilvGiiaGfllp 141
                                       s+fG+ +l i+ i++Gvl  +l+      ++ + +++ +fg   a i+++    +++++ +  +  ++++++G+ l 
  gi|242399123|ref|YP_002994547.1|  11 SIFGNIVLAIVKITVGVLYSSLALisdGVHSLSDVITSIFGYFGAKIASKP-ADQTHPFgHSRFESFFAFFIGMALF 86 
                                       789999999999999997666554666666667777777887777777777.4444444444555555566666555 PP

                           DUF1576 142 al 143
                                        +
  gi|242399123|ref|YP_002994547.1|  87 LV 88 
                                       55 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00016
                           DUF1576  71 fGknllNiipillGvlLyalvkkesfkkyila 102
                                       fG   + + +i++Gv+L+++++ke +++y l 
  gi|242399123|ref|YP_002994547.1| 101 FGDSTIEVNAIMIGVVLLSIFSKEAMTQYSLK 132
                                       8999999********************99875 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.52
                           DUF1576 121 elel.glvlgilvGiiaGfllpala 144
                                        +++  ++ +++v i++G + + ++
  gi|242399123|ref|YP_002994547.1| 169 GFRYgDALASVVVVILIGKVAVEIV 193
                                       4444455666666677776655443 PP

>> PAP2  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.8   0.00017       0.6      85     119 ..      17      50 ..       4      60 .. 0.80
   2 ?    1.5   0.1     0.065   2.3e+02     108     132 ..      70      94 ..      69      98 .. 0.81
   3 ?    0.5   0.7      0.13   4.6e+02     104     119 ..     144     159 ..     141     197 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00017
                              PAP2  85 vllalillllavlvalsRlylgvHflsDvlaGlli 119
                                       vl+++ +++ +++ +l+ +++gvH lsDv++++ +
  gi|242399123|ref|YP_002994547.1|  17 VLAIVKITVGVLYSSLALISDGVHSLSDVITSI-F 50 
                                       566677888899999***************994.4 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.065
                              PAP2 108 HflsDvlaGlliGialaalayrlvq 132
                                       H ++  +++++iG al+++ay + +
  gi|242399123|ref|YP_002994547.1|  70 HSRFESFFAFFIGMALFLVAYEIGK 94 
                                       7788889999999999999987765 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.13
                              PAP2 104 ylgvHflsDvlaGlli 119
                                       ++ +H++sD l ++++
  gi|242399123|ref|YP_002994547.1| 144 ADAYHHRSDALSSVAV 159
                                       6778888888887543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       668  (0.0372581); 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:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2058.40
//
Query:       gi|242399124|ref|YP_002994548.1|  [L=43]
Description: hypothetical protein TSIB_1145 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       266  (0.0148363); expected 358.6 (0.02)
Passed bias filter:                      180  (0.0100396); 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: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.44
# Mc/sec: 294.44
//
Query:       gi|242399125|ref|YP_002994549.1|  [L=278]
Description: Biotin synthase-related protein, radical SAM superfamily [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.4e-13   49.9   0.6    2.9e-09   37.5   0.3    2.4  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 !   37.5   0.3   1.6e-13   2.9e-09       4     152 ..      23     163 ..      20     165 .. 0.87
   2 !   10.3   0.0   3.7e-05      0.67      91     154 ..     172     234 ..     163     242 .. 0.84

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 1.6e-13
                                       ESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   4 trgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlaklavpgir 79 
                                       ++ C+l+C +C  ++     +  + + + ++++  k l ++ g ++ +++gg++  l  ++  +++++++++ ++ +
  gi|242399125|ref|YP_002994549.1|  23 GNYCTLDCAHCGKHY----LESMKKVEKSNLVDYCKNL-EKEGyKGCLLSGGMDSRLKVPLDIYTDEIKQIK-KETK 93 
                                       678***********7....7888888888888888888.77777999************************7.9999 PP

                                       EEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  80 itvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivgl 152
                                       + + +  + +de  le l+   vd+vsl+    dd  +++  + ++ +e++l+ +e+l+++gik+  +++vgl
  gi|242399125|ref|YP_002994549.1|  94 LKLNVHVGFIDESDLEWLKY--VDVVSLDFVGEDDV-IKRVYKIKKRVEDYLKIIELLTSNGIKVAPHITVGL 163
                                       99999999996666666666..6************8.******99*******************877777775 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 3.7e-05
                                       HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET.EEEEEEEBTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                       Radical_SAM  91 eeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikr.vvdrivglpG 154
                                        + +e+l+ ++vd++ l++ +++   +   +   +++++ le+++++r+  ++   +++++ +pG
  gi|242399125|ref|YP_002994549.1| 172 YKAIELLAHYPVDVLVLDVLIPTRG-TEMENTTSPSVDKSLEVVKYARDT-FNGeLSIGCMRPPG 234
                                       5789********************9.66555599***************9.66446666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); 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 0.26s 00:00:00.77 Elapsed: 00:00:00.56
# Mc/sec: 1505.62
//
Query:       gi|242399126|ref|YP_002994550.1|  [L=308]
Description: Na+/Ca2+ exchange integral membrane protein [Thermococcus sibiricus MM 739]
Scores for complete 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  164.9  37.7    4.7e-27   94.8  14.2    2.0  2  Na_Ca_ex      Sodium/calcium exchanger protein
  ------ inclusion threshold ------
      0.013   16.0   1.5      0.013   16.0   1.5    3.8  5  DUF3917       Protein of unknown function (DUF3917)
      0.032   14.4   0.0       0.99    9.6   0.0    2.7  3  DUF739        Protein of unknown function (DUF739)
        0.1   12.2   0.0       0.18   11.4   0.0    1.4  1  Baculo_LEF-2  lef-2
        1.3    9.3  10.6       0.13   12.6   1.4    2.9  3  DUF2189       Predicted integral membrane protein (DUF2189)


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 !   76.4  15.5     6e-25   2.1e-21       3     150 ..       9     147 ..       7     148 .. 0.90
   2 !   94.8  14.2   1.3e-30   4.7e-27       3     150 ..     167     307 ..     165     308 .] 0.92

  Alignments for each domain:
  == domain 1  score: 76.4 bits;  conditional E-value: 6e-25
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex   3 fvlfilslllisvladflvssaeeiakslgisgsvlGltllAlgnslpElissiiaaltgevdlaignvlGsnifnl 79 
                                       f+lfil+l++++ ++d++v++a+ +ak +g+s+ +++l+l +++++lpE+++s ia  +g   +a+gn++Gs+++n+
  gi|242399126|ref|YP_002994550.1|   9 FGLFILGLVILIKGSDLFVEAATRVAKGFGVSEFIIALVLASIATTLPEVTTSAIASYKGLSGIALGNAVGSALANI 85 
                                       889************************************************************************** PP

                                       HTHHHHHHHHHHBTTSSCECCHHHHHHHHHHHHHHHHHHHTCHHHHHHTEEHHHHHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex  80 llviGlialigslkvdseslkldlgllllvallllllvlllllplfvpgrltvleglvllllYalylvlsl 150
                                        l++G++  i++l vd+  +k++l   +++a+ l   +++ll    ++ ++++ eg  l+l+Y+ +l++++
  gi|242399126|ref|YP_002994550.1|  86 ALILGVSSMIMPLDVDEIAWKNSL---FMIAVTL---YAWLL---MGDLTISRIEGGSLILIYGGFLYYLY 147
                                       **********99999987777666...5555555...33433...257********************986 PP

  == domain 2  score: 94.8 bits;  conditional E-value: 1.3e-30
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex   3 fvlfilslllisvladflvssaeeiakslgisgsvlGltllAlgnslpElissiiaaltgevdlaignvlGsnifnl 79 
                                       +v++++s l+++v+a ++v+sa +ia  lgi++ v+Gltl+++g+slpE++ s++a l++ +++++gn++G+ni+n+
  gi|242399126|ref|YP_002994550.1| 167 VVILFVSGLIVVVGARLVVDSAVKIAIALGIPEVVVGLTLVSIGTSLPEFANSLTATLKKIPNISVGNIVGANILNI 243
                                       68999999******************999************************************************ PP

                                       HTHHHHHHHHHHBTTSSCECCHHHHHHHHHHHHHHHHHHHTCHHHHHHTEEHHHHHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex  80 llviGlialigslkvdseslkldlgllllvallllllvlllllplfvpgrltvleglvllllYalylvlsl 150
                                       l+viG++ali ++kvds  + ++++l+l+v+++l + ++l l      +r+ + +++vll+lY+ +l+ ++
  gi|242399126|ref|YP_002994550.1| 244 LMVIGIAALINPIKVDSGIYSFTVPLTLVVMMVL-A-ISLKL-----NNRVGRKTSAVLLILYGYFLYANF 307
                                       ************************8877777766.2.23323.....4*******************9876 PP

>> DUF3917  Protein of unknown function (DUF3917)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1       2.9   1.1e+04       7      21 ..      38      52 ..      33      55 .. 0.70
   2 ?   16.0   1.5   3.5e-06     0.013      14      55 ..      79     122 ..      70     139 .. 0.85
   3 ?   -1.6   0.7         1   3.7e+03      66      66 ..     179     179 ..     167     222 .. 0.59
   4 ?   -1.1   2.1      0.74   2.6e+03      49      66 ..     236     253 ..     199     261 .. 0.74
   5 ?   -3.8   0.3         5   1.8e+04      55      61 ..     272     278 ..     262     281 .. 0.58

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.9
                           DUF3917  7 GlkrfvpGsilaGia 21
                                      G+  f+   +la ia
  gi|242399126|ref|YP_002994550.1| 38 GVSEFIIALVLASIA 52
                                      666777777788777 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 3.5e-06
                           DUF3917  14 GsilaGialityvasifv..esvsvevsaslvfvaitlfaGsim 55 
                                       Gs la iali  v+s+ +  +   + +  sl ++a+tl+a  +m
  gi|242399126|ref|YP_002994550.1|  79 GSALANIALILGVSSMIMplDVDEIAWKNSLFMIAVTLYAWLLM 122
                                       9**************876224446789*************8777 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 1
                           DUF3917  66 i 66 
                                       +
  gi|242399126|ref|YP_002994550.1| 179 V 179
                                       1 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 0.74
                           DUF3917  49 lfaGsimvlmvaGivlfi 66 
                                       + a  + +lmv Gi  +i
  gi|242399126|ref|YP_002994550.1| 236 VGANILNILMVIGIAALI 253
                                       445566789999987665 PP

  == domain 5  score: -3.8 bits;  conditional E-value: 5
                           DUF3917  55 mvlmvaG 61 
                                       +v+mv  
  gi|242399126|ref|YP_002994550.1| 272 VVMMVLA 278
                                       4444433 PP

>> DUF739  Protein of unknown function (DUF739)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0       0.1   3.6e+02      21      54 ..      84     116 ..      66     120 .. 0.77
   2 ?   -3.0   0.0       2.4   8.6e+03      22      36 ..     191     205 ..     189     207 .. 0.78
   3 ?    9.6   0.0   0.00028      0.99      32      49 ..     278     295 ..     260     298 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.1
                            DUF739  21 nfaialgLserslslkLndkvsWkddeilkavdl 54 
                                       n a  lg+s   + l + d ++Wk++  + av l
  gi|242399126|ref|YP_002994550.1|  84 NIALILGVSSMIMPLDV-DEIAWKNSLFMIAVTL 116
                                       66666777766666665.679****998888876 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.4
                            DUF739  22 faialgLserslslk 36 
                                        aialg+ e  + l 
  gi|242399126|ref|YP_002994550.1| 191 IAIALGIPEVVVGLT 205
                                       699999999877665 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00028
                            DUF739  32 slslkLndkvsWkddeil 49 
                                       ++slkLn++v+ k++ +l
  gi|242399126|ref|YP_002994550.1| 278 AISLKLNNRVGRKTSAVL 295
                                       68***********99775 PP

>> Baculo_LEF-2  lef-2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   5.1e-05      0.18      38      79 ..     130     169 ..     116     184 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.1e-05
                      Baculo_LEF-2  38 lnGGrlikvvGlrllnlleksksieeiknskvkkrakkkvcl 79 
                                       ++GG li++ G  l+ l  k  ++ee   s+ k++ kk+v +
  gi|242399126|ref|YP_002994550.1| 130 IEGGSLILIYGGFLYYLYRKHVTLEE--PSEGKENPKKDVVI 169
                                       68************************..9999******8864 PP

>> DUF2189  Predicted integral membrane protein (DUF2189)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   1.4   3.5e-05      0.13      65     123 ..      39      96 ..      37     101 .. 0.87
   2 ?   -2.4   0.1       1.5   5.3e+03      54      68 ..     111     125 ..     106     136 .. 0.68
   3 ?    1.9   0.3     0.068   2.4e+02      79     117 ..     201     248 ..     158     253 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.5e-05
                           DUF2189  65 aaallfallfgtapleslsafledvlltpeglaflivgllvGavlAalvFaisvvslPl 123
                                       ++ +++al++ ++  ++l ++++ ++ + +gl+ +++g++vG++lA +++++ v s+ +
  gi|242399126|ref|YP_002994550.1|  39 VSEFIIALVL-ASIATTLPEVTTSAIASYKGLSGIALGNAVGSALANIALILGVSSMIM 96 
                                       5778999999.566789*******************************99999988744 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.5
                           DUF2189  54 llallfllWvraaal 68 
                                       ++a+ + +W+++  l
  gi|242399126|ref|YP_002994550.1| 111 MIAVTLYAWLLMGDL 125
                                       566667777776655 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.068
                           DUF2189  79 l.........eslsafledvlltpeglaflivgllvGavlAalvFais 117
                                       +         +sl +f++ +  t +++  + vg++vGa +  ++ +i 
  gi|242399126|ref|YP_002994550.1| 201 VvgltlvsigTSLPEFANSLTATLKKIPNISVGNIVGANILNILMVIG 248
                                       233333355689999999999999999999999999998877776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       870  (0.0485247); 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:                         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: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2096.84
//
Query:       gi|242399127|ref|YP_002994551.1|  [L=219]
Description: deoxyribose-phosphate aldolase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.6e-21   75.5   4.6    5.3e-21   75.3   4.6    1.0  1  DeoC      DeoC/LacD family aldolase
     0.0005   19.4   2.6    0.00074   18.8   2.2    1.5  1  DHO_dh    Dihydroorotate dehydrogenase


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 !   75.3   4.6   5.9e-25   5.3e-21       2     232 ..       3     212 ..       2     215 .. 0.89

  Alignments for each domain:
  == domain 1  score: 75.3 bits;  conditional E-value: 5.9e-25
                                       EEEEECCSHHHHHHHHCTSSHHHHHHHHHHHHHHGGGSSEEEEETTTHHHHHHCSCT...TSEEEEETECSSCCTTS CS
                              DeoC   2 vilavDqrvankddtasaqneqledlkalvkealtpgasavlldpgviasaskeyak...diallvkldkgtyllks 75 
                                       v++++D++  +k+ t++      ed+ +l++ea++ +  av+++p ++  a+ +++    ++a +++++ g + ++ 
  gi|242399127|ref|YP_002994551.1|   3 VAKYIDHTN-LKAYTSK------EDIIKLCEEAKKYNFYAVCVNPYRVKLAKEHLKGtdiKVASVIGFPLGATPTEV 72 
                                       678888875.4566666......7********************************99***********77766666 PP

                                       TTEEEETTCHHHHHHHTT-SEEEEEEEEHTTTTCHHHHHHHHHHHHHHHHHHHT..EEEEEE.EEE-CTTBSSTTCH CS
                              DeoC  76 kqrdvdevasveeakalGAdavkvvvyyradgseeeqqklaeikrvkeacheeg..lplile.lylrdeaikdekvd 149
                                       k      v ++ +a+++GAd++++v+++ a+++++ + + ++i+ v + +he g   ++i+e +yl +e+    k  
  gi|242399127|ref|YP_002994551.1|  73 K------VFEANKALEDGADELDMVINIGALKDKDYEYVKKDIEDVTKVAHEKGaiVKVIIEtCYLTEEE----K-- 137
                                       6......99******************************************8775478999999998888....3.. PP

                                       HHHHHHHHHHHTCCT-SEEEE--SSCC.B.HHHHHHHHHHHHHCHSSTEEEEETTSSHHHHHHHHHHHHH..HHTH. CS
                              DeoC 150 pdlvaeAarvsaelGaDiiKvevpkevvnateedaevfkdvikaapvpgvvlsGGvseedfletvedAvk..eaga. 223
                                           + A ++++e+ aD++K++++     at ed++ +++v+++    gv+ +GG+      +t edA++  +aga 
  gi|242399127|ref|YP_002994551.1| 138 ----EIACKLAMEARADFVKTSTGFGTGGATIEDVKLMRRVVGDK--LGVKAAGGI------RTYEDALAmiNAGAn 202
                                       ....4599****************88899**************77..66*******......999999988899999 PP

                                       .CEEEESHHH CS
                              DeoC 224 .sGvlsGRai 232
                                        +G +sG +i
  gi|242399127|ref|YP_002994551.1| 203 rIGTSSGVKI 212
                                       9999999776 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   2.2   8.2e-08   0.00074     212     275 ..     150     209 ..     102     217 .. 0.66

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 8.2e-08
                                       CCCTTSSE.EEEEGGGHHHHHHHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHH CS
                            DHO_dh 212 nvkanktG.GlsGkalkdialkvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvyta 275
                                          + +tG G +G+ + d     +  +++++ +++ + + GGi + eDal +i+aGA  +   ++
  gi|242399127|ref|YP_002994551.1| 150 DFVKTSTGfGTGGATIED-----VKLMRRVVGDKLGVKAAGGIRTYEDALAMINAGANRIGTSSG 209
                                       333334444577777766.....556899999*************************98776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); 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: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1392.31
//
Query:       gi|242399128|ref|YP_002994552.1|  [L=200]
Description: hypothetical protein TSIB_1149 [Thermococcus sibiricus MM 739]
Scores for complete 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-39  133.4  22.4    8.1e-39  133.4  22.4    1.5  1  ECF-ribofla_trS  ECF-type riboflavin transporter, S component
    7.4e-06   26.2  20.7    7.4e-06   26.2  20.7    2.2  2  ECF_trnsprt      ECF transporter, substrate-specific componen
     0.0022   17.8  13.5     0.0031   17.3  13.3    1.3  1  7TM-7TMR_HD      7TM receptor with intracellular HD hydrolase
  ------ inclusion threshold ------
       0.14   11.9   0.5       0.35   10.7   0.5    1.7  1  Gemini_mov       Geminivirus putative movement protein
        2.3    7.8   6.4       0.58    9.8   2.5    1.9  2  DUF4131          Domain of unknown function (DUF4131)


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 !  133.4  22.4   2.3e-42   8.1e-39       7     168 ..      39     185 ..      33     189 .. 0.94

  Alignments for each domain:
  == domain 1  score: 133.4 bits;  conditional E-value: 2.3e-42
                                       HHHHHHHHHHHHHHHHH---B-S.SS-B--TTHHHHHHHHHHSS--STHHHHHHHHHHHHHHHSS-GGGHHHHHHHH CS
                   ECF-ribofla_trS   7 vvatailaAlvvvltlfisIplpantegsinlgdavlalaallfGpvvGflvGaiGsalaDllsgYgiwapftliik 83 
                                       v++ +++aAlv+v+t+ i+Ip+p  t g+in+gd++++l+a+lfGp++G+++G++Gs +aD+++gY++wapftl+ik
  gi|242399128|ref|YP_002994552.1|  39 VALSGVMAALVAVVTMAIQIPTP-LTSGYINVGDSMVMLVAVLFGPTIGAFAGGFGSGMADIITGYAHWAPFTLVIK 114
                                       7899******************9.999************************************************** PP

                                       HHHHHHHHHH--S-S-SSH...HHHHHHHHHHHHHHHHHHHHHHHH..........S-HHHHHHHHHHHHHHHHHHH CS
                   ECF-ribofla_trS  84 gliGlivGliakklkknkengvfkilalvlfaivmvigyviaegllpildiiiysepaekvalqsipaniiqavvga 160
                                       g++G++vG+i+ k+    + +++ +la++l++++mv+gy+ +e+ +          +++  a++++p+ni+qav+g+
  gi|242399128|ref|YP_002994552.1| 115 GVEGFVVGYITSKK----DDFTTVLLATILGGALMVLGYFMIEIYV----------YGWGGAVAEVPGNILQAVTGI 177
                                       ************99....33567999********************..........********************* PP

                                       HHHHHHHH CS
                   ECF-ribofla_trS 161 iialpLlk 168
                                       +++  + +
  gi|242399128|ref|YP_002994552.1| 178 VVGGGVGH 185
                                       **966555 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 !    6.1   7.4     0.003        11      81     122 ..      14      55 ..       5      65 .. 0.69
   2 !   26.2  20.7   2.1e-09   7.4e-06       3     130 ..      39     158 ..      37     197 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.003
                                       HCHHHHHHHHHHCCCHTTHHHHHHHHHHHHCCCCCHHHHHHH CS
                       ECF_trnsprt  81 iligliagllykkgkkknlkeivvsfilagvlgtivatllvl 122
                                       i+++ i ++ y ++ kk+ +e+ v+++l+gv+ ++va+++ +
  gi|242399128|ref|YP_002994552.1|  14 IIAVAILYFAYLFILKKKIFEAAVGVALSGVMAALVAVVTMA 55 
                                       455666667777777777777788888888888888887644 PP

  == domain 2  score: 26.2 bits;  conditional E-value: 2.1e-09
                                       HHHHHHHHHHHHHHHHHHEEE.STS..EEESHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHCHT-SSTTHHHHHHHH CS
                       ECF_trnsprt   3 lvitglliAisivlsllgyiplpni..kitiihipvllggllfGpikGailgiitsvlkailtggtgalssfvpiaf 77 
                                       ++++g+++A+ +v+ ++  ip+p     i   +  v+l+++lfGp  Ga++g+++s ++ i+  g + ++   p+  
  gi|242399128|ref|YP_002994552.1|  39 VALSGVMAALVAVVTMAIQIPTPLTsgYINVGDSMVMLVAVLFGPTIGAFAGGFGSGMADII-TGYAHWA---PFTL 111
                                       799************64666666444469999******************************.4655555...**** PP

                                       HHHHCHHHHHHHHHHCCCHTTHHHHHHHHHHHHCCCCCHHHHHHHCCC.HHHHS CS
                       ECF_trnsprt  78 lsriligliagllykkgkkknlkeivvsfilagvlgtivatllvllii.lplyl 130
                                       ++ ++ g+++g++   +kk      +  ++la++lg  +++l  +++i + +y+
  gi|242399128|ref|YP_002994552.1| 112 VIKGVEGFVVGYIT--SKKDD----FTTVLLATILGGALMVLG-YFMIeIYVYG 158
                                       ***********777..44444....678888888888888886.5555544443 PP

>> 7TM-7TMR_HD  7TM receptor with intracellular HD hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3  13.3   8.5e-07    0.0031       4     172 ..       9     177 ..       6     183 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 8.5e-07
                       7TM-7TMR_HD   4 llgllllvlllllilllflrrfrkelrernkkllllslllllvlllsklvvl.issiesiiylvplaavalLlslll 79 
                                       ++  +++++ +l++ +lf+   +k+++e    + l +++ +lv +++ ++ + ++   + +y+ +   + +L+++l+
  gi|242399128|ref|YP_002994552.1|   9 YAKWIIIAVAILYFAYLFI--LKKKIFEAAVGVALSGVMAALVAVVTMAIQIpTP--LTSGYINVGDSMVMLVAVLF 81 
                                       5666788888888888888..5679999998888888888888888888777777..99****************** PP

                       7TM-7TMR_HD  80 dsrlalvvsvllsllisilf...gnnlellllalvsglvgallvrklrsRsdllragllvalvnvlvilalsliqss 153
                                       +++++ +++ + s ++ i++   +  +  l++  v g+v++++ +k    + +l+a +l ++  vl ++ ++++  +
  gi|242399128|ref|YP_002994552.1|  82 GPTIGAFAGGFGSGMADIITgyaHWAPFTLVIKGVEGFVVGYITSKKDDFTTVLLATILGGALMVLGYFMIEIYVYG 158
                                       *******************9566666788888889999999999999999999999999999999999999986555 PP

                       7TM-7TMR_HD 154 nlswleiltllvlafisgl 172
                                       + +    ++  +l ++ g+
  gi|242399128|ref|YP_002994552.1| 159 WGGAVAEVPGNILQAVTGI 177
                                       5454555555555555555 PP

>> Gemini_mov  Geminivirus putative movement protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.5   9.8e-05      0.35      43      64 ..      12      33 ..       3      36 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 9.8e-05
                        Gemini_mov 43 ltlvavlvlYLlytlvlkDlil 64
                                       +++av +lY +y+++lk  i+
  gi|242399128|ref|YP_002994552.1| 12 WIIIAVAILYFAYLFILKKKIF 33
                                      689***************8887 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   2.5   0.00016      0.58       4      57 ..       8      64 ..       6      82 .. 0.72
   2 ?   -0.6   0.2      0.25   8.8e+02      35      35 ..     133     133 ..      71     159 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00016
                           DUF4131  4 plalvllalllllllllllllrr...rprrrvllllllllllallgfalrapqpnan 57
                                      p+a ++++++++l+++ l++l++        v+l+  +++l+a++ +a++ p+p ++
  gi|242399128|ref|YP_002994552.1|  8 PYAKWIIIAVAILYFAYLFILKKkifEAAVGVALSGVMAALVAVVTMAIQIPTPLTS 64
                                      8999***************98875554444446666677777777777777776664 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.25
                           DUF4131  35 l 35 
                                       +
  gi|242399128|ref|YP_002994552.1| 133 T 133
                                       1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1137  (0.0634168); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 1293.50
//
Query:       gi|242399129|ref|YP_002994553.1|  [L=447]
Description: Pyridoxal phosphate-dependent aminotransferase [Thermococcus sibiricus MM 739]
Scores for complete 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-114  381.4   0.0   4.7e-114  381.2   0.0    1.0  1  Aminotran_3  Aminotransferase class-III
  ------ inclusion threshold ------
       0.85    9.7   3.0        1.5    8.9   0.2    2.4  2  ComZ         ComZ


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 !  381.2   0.0  5.3e-118  4.7e-114       7     406 .]      34     442 ..      28     442 .. 0.94

  Alignments for each domain:
  == domain 1  score: 381.2 bits;  conditional E-value: 5.3e-118
                                       --SCEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHC CS
                       Aminotran_3   7 dnlllvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllkla 83 
                                       ++ +lvi+++eG+y  dvdg+++lD+ s+i v+n G ++P++v+a+k+q++kl h     + n  +++l+ekl ++a
  gi|242399129|ref|YP_002994553.1|  34 NEYFLVIERTEGNYWIDVDGNKILDFSSGIGVLNAGLRNPRLVEALKKQLDKLIHGAGTDYYNPYQVALVEKLDSIA 110
                                       45789****************************************************88888888899********* PP

                                       T-..S.EEEEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEEE CS
                       Aminotran_3  84 pkgld.kvflansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevvr 159
                                       p++++ k+fl nsG+eA+e+A+K+a+       +t+++ +iaf gafHGrt+g++s+t+sk+ +++ + p++p+v +
  gi|242399129|ref|YP_002994553.1| 111 PGDFEkKTFLSNSGTEANEAAIKIAKW------STKRKLFIAFIGAFHGRTHGTMSLTASKPVHRSRMFPTMPGVEH 181
                                       ***9999********************......******************************************** PP

                                       E-TTBGGGTB-HH.......HHHHHHHHHHHHHH...CHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT CS
                       Aminotran_3 160 lkypdeevlkene.......eeeaalleeleale...kkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhd 226
                                       ++yp +++ + +        e  +++le++e++     +  +eva+vi EpiqgegG+vv++ +f+++l+++ +kh+
  gi|242399129|ref|YP_002994553.1| 182 VPYPNPYRNPWHIdgyeepdELVNRVLEYIEDYLlahYVPPEEVAGVIAEPIQGEGGYVVPPMNFFKELKKVLDKHG 258
                                       *****999887655666444445566666666668877889************************************ PP

                                       -EEEEE-TTTTTTTTSSSSGGGGCTS--SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTSB--TTTT-HHHHHHHHH CS
                       Aminotran_3 227 vllivDEvqtGfGrTGklfAlehagvspDlmtlaKaltgGlplsavlataevmqalapgshgsTfgGnplacavala 303
                                       +ll+ DEvq G+GrTGk+fA+eh+gv+pD++ laKal+gG p+ a++ ++++   + +g h++T+gGn lac++al 
  gi|242399129|ref|YP_002994553.1| 259 ILLMDDEVQMGMGRTGKMFAIEHFGVAPDIISLAKALGGGVPIGATIFRKDLDFGI-SGVHSNTYGGNALACVAALT 334
                                       ****************************************************9999.899***************** PP

                                       HHHHHHHTTHHHHHHHHHHHHHHHHHHHCTT-TTEEEEEEETTEEEEEEBCCCETTC......HHHHHHHHHCTEE- CS
                       Aminotran_3 304 vleiieeekllenaqelgaalkegLeelqkkyevikevRgkGlmiaielkeeaevke......keilkkakekGvli 374
                                       v++ +e+  l+enaq+l+  +ke+L+e+ +kye i++vRg+Gl  aie+++++++ke      ++++ +a++ G+ +
  gi|242399129|ref|YP_002994553.1| 335 VIDELEN-GLIENAQKLEPLFKERLQEMYDKYELIGDVRGLGLAWAIEFVKDRKTKEyasnerNKVVVEALKRGLAT 410
                                       *****86.7*********************************************999******99************ PP

                                       EEETTTEEEE---TT--HHHHHHHHHHHHHHH CS
                       Aminotran_3 375 lsaGdnvirllppliitdeeidelleilkkal 406
                                       l++G++++rl+ppl+i +ee++ +l+il++a+
  gi|242399129|ref|YP_002994553.1| 411 LGCGKSALRLIPPLTIDEEEAKIGLDILEEAI 442
                                       ****************************9987 PP

>> ComZ  ComZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.2   0.00017       1.5      11      34 ..     244     267 ..     242     271 .. 0.92
   2 ?    0.1   0.2     0.091   8.2e+02      25      50 ..     342     367 ..     337     370 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00017
                              ComZ  11 mkylPeakkeLekkGIelsmeelq 34 
                                       m+++ e kk L+k+GI l  +e+q
  gi|242399129|ref|YP_002994553.1| 244 MNFFKELKKVLDKHGILLMDDEVQ 267
                                       99****************999988 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.091
                              ComZ  25 GIelsmeelqPlleLllkVmnEAYEL 50 
                                       G+  + ++l+Pl++  l+ m + YEL
  gi|242399129|ref|YP_002994553.1| 342 GLIENAQKLEPLFKERLQEMYDKYEL 367
                                       44447789999999999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); 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 0.33s 00:00:00.92 Elapsed: 00:00:00.49
# Mc/sec: 2739.55
//
Query:       gi|242399130|ref|YP_002994554.1|  [L=334]
Description: Thioredoxin reductase [Thermococcus sibiricus MM 739]
Scores for complete 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-57  193.5   1.4    5.4e-57  193.3   1.4    1.0  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    1.4e-30  106.6   2.2    1.7e-25   89.9   0.2    2.1  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    3.7e-21   75.5   8.2    1.9e-19   70.0   1.8    3.5  3  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    4.3e-14   52.4   2.0    0.00012   21.3   0.1    4.1  4  GIDA            Glucose inhibited division protein A
    1.2e-09   37.8   3.8    0.00011   21.5   0.2    4.1  4  FAD_binding_2   FAD binding domain
    2.8e-09   36.7   0.1    0.00033   20.0   0.0    2.3  2  FAD_binding_3   FAD binding domain
    4.5e-08   32.2   0.2     0.0027   16.5   0.1    3.6  4  HI0933_like     HI0933-like protein
    1.1e-07   31.6   1.5    2.3e-05   23.9   0.0    2.9  3  FAD_oxidored    FAD dependent oxidoreductase
    2.5e-07   30.6   5.5      0.028   14.0   0.6    3.9  4  DAO             FAD dependent oxidoreductase
    4.1e-07   30.4   0.3    0.00044   20.7   0.1    3.0  3  NAD_binding_7   Putative NAD(P)-binding
    2.3e-06   27.7   0.2    0.00017   21.8   0.0    2.3  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    5.7e-06   25.8   0.1      0.001   18.3   0.1    2.4  2  Thi4            Thi4 family
    1.3e-05   24.5   0.0     0.0054   15.9   0.0    3.2  3  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
    0.00025   20.2   0.4       0.52    9.3   0.1    3.1  3  Lycopene_cycl   Lycopene cyclase protein
     0.0006   19.2   1.4       0.21   10.8   0.0    2.6  3  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
     0.0017   18.4   0.4       0.26   11.3   0.1    2.9  3  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
     0.0025   16.7   0.4       0.18   10.6   0.1    2.3  2  Trp_halogenase  Tryptophan halogenase
     0.0046   16.4   0.2      0.039   13.4   0.1    2.3  2  PALP            Pyridoxal-phosphate dependent enzyme
     0.0047   17.4   0.0      0.092   13.3   0.0    2.4  2  XdhC_C          XdhC Rossmann domain
  ------ inclusion threshold ------
      0.021   14.4   0.1      0.047   13.3   0.1    1.7  1  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
      0.034   12.6   0.0       0.04   12.3   0.0    1.2  1  FMO-like        Flavin-binding monooxygenase-like
       0.08   12.2   0.0       0.19   11.0   0.0    1.6  2  Amino_oxidase   Flavin containing amine 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 !  193.3   1.4   6.6e-60   5.4e-57       2     294 .]      22     313 ..      21     313 .. 0.86

  Alignments for each domain:
  == domain 1  score: 193.3 bits;  conditional E-value: 6.6e-60
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH.........HHHHCHHHHCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxx RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias.........evvkklnqgiel 69 
                                       d+++iG+GpAG++aa++ a++g++++++ +++   +g + l+ +++++++++e ++         e+vkkln     
  gi|242399130|ref|YP_002994554.1|  22 DILIIGAGPAGFTAAIYSARYGFDTLII-SKD--IGGNVALTDIIENYPGFPEGVKgselankmhEQVKKLNVP--I 93 
                                       899*************************.554..6888999************999*97777777777777655..2 PP

                                       CHCCTCEEEEESC.EEEEETEEEC.....TCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS CS
                                       xxxxxxxxxxxxx.xxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  70 llgeevvkidpgk.kkvklekkke.....gdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkl 140
                                       + + ev ++dp++ + ++     +     ++++ +++ ++++A G++pr+l++pG+ + +g++v++++++++     
  gi|242399130|ref|YP_002994554.1|  94 VFD-EVERVDPAEcAYYEGPC--KfevktKNGKVYKARSVIIAVGAEPRKLKVPGEDKFYGRGVSYCATCDGPLFRG 167
                                       233.57777766623333332..1346668999***************************************96665 PP

                                       -TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTE... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                       Pyr_redox_2 141 lpkrivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgnge... 214
                                       +  +++vvGgG++++  A +l+++g++vtlv++r+++       + ++l+e+++k G+ v l+++v+ei+gn++   
  gi|242399130|ref|YP_002994554.1| 168 K--HVIVVGGGNTALQEALYLNEIGVNVTLVHRREEFR------ADKILQERFKKAGIPVLLNNVVVEIKGNQKves 236
                                       5..6*********************************7......99***************************9664 PP

                                       .EEE.EEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GGGCTECCSS--HHH CS
                                       .xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 215 .kle.vvledgeeidadlvvvavGvrpstelleeklglelderggivvdeflrtnvpgiyaiGDvaggkggpelaqa 289
                                         l+  ++++  e ++d v+v +G++p+t+++ ++lg+ +de+g+i+vd ++rtn++g++a+GD++   ++++++ +
  gi|242399130|ref|YP_002994554.1| 237 vLLRnIKTGEIFEKKVDGVFVFIGYEPKTDFV-KHLGI-TDEQGYILVDMYMRTNIKGLFAAGDIT---NVFKQIAV 308
                                       32334555555559******************.*****.58*************************...******** PP

                                       HHHHH CS
                                       xxxxx RF
                       Pyr_redox_2 290 AvqqG 294
                                       Av qG
  gi|242399130|ref|YP_002994554.1| 309 AVGQG 313
                                       **998 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.2   4.2e-06    0.0034       1      33 [.      24      55 ..      24      68 .. 0.80
   2 !   89.9   0.2   2.1e-28   1.7e-25      78     305 .]      73     297 ..      62     297 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.2e-06
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgnig 33
                                      +IiGaGPaG +aai   + g+ d li+ k+  g
  gi|242399130|ref|YP_002994554.1| 24 LIIGAGPAGFTAAIYSARYGF-DTLIISKDIGG 55
                                      6********************.78999986433 PP

  == domain 2  score: 89.9 bits;  conditional E-value: 2.1e-28
                       Pyr_redox_3  78 lsrkealeYlrevaksfelpiklfeeVesvkked.......egfevetske.tyeAkkviiAtGefdkPnklnipGe 146
                                       +++ e+++ + e +k+ ++pi  f eVe+v++++        +fev+t+++ +y+A++viiA G    P+kl++pGe
  gi|242399130|ref|YP_002994554.1|  73 VKGSELANKMHEQVKKLNVPIV-FDEVERVDPAEcayyegpCKFEVKTKNGkVYKARSVIIAVGA--EPRKLKVPGE 146
                                       5677778888888888888885.667999998542333222359*****9879***********9..********** PP

                       Pyr_redox_3 147 ek...lvkhyskvkefhkyagqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrlee 220
                                       +k     + y    +   ++g++v+V+Gg+n+a   Al l + g +Vt+v+r++e ++++         + ++r+++
  gi|242399130|ref|YP_002994554.1| 147 DKfygRGVSYCATCDGPLFRGKHVIVVGGGNTALQEALYLNEIGVNVTLVHRREEFRADK---------ILQERFKK 214
                                       *9733345555555776899*********************************9877764.........67788877 PP

                       Pyr_redox_3 221 lvkeekikvlfnaevkeikekeeeykvk...tedgkkvevkddvvla.tGykpdlsflkkslfeldedgrpvlteet 293
                                       +     i vl n+ v eik +++   v     ++g+ +e+k d v++ +Gy+p+++f+k +l  +de+g+++++   
  gi|242399130|ref|YP_002994554.1| 215 A----GIPVLLNNVVVEIKGNQKVESVLlrnIKTGEIFEKKVDGVFVfIGYEPKTDFVK-HLGITDEQGYILVD-MY 285
                                       4....4899999999999966544444322378888899988888888**********9.55556799999886.68 PP

                       Pyr_redox_3 294 eetnvpglflaG 305
                                       + tn++glf aG
  gi|242399130|ref|YP_002994554.1| 286 MRTNIKGLFAAG 297
                                       **********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 ?    6.8   0.1     0.012       9.6       2      59 ..      23      95 ..      22     103 .. 0.69
   2 !   70.0   1.8   2.3e-22   1.9e-19       1      79 [.     169     240 ..     169     246 .. 0.97
   3 ?   -1.9   0.0       6.2     5e+03       3      17 ..     308     322 ..     307     329 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.012
                                      EEEECSSHHHHHHHHHHHHTT..............SEEEEEESSSSSS.TTSSHHHHHHHHHHHHHTTEEEEC CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelg..............kkVtvversdkll.rllDeeaskilqeklekngievll 59
                                      ++++G+G  g  +A + a++g              + + ++e+ + +   + + e+++ ++e+++k+++ +++
  gi|242399130|ref|YP_002994554.1| 23 ILIIGAGPAGFTAAIYSARYGfdtliiskdiggnvALTDIIENYPGFPeGVKGSELANKMHEQVKKLNVPIVF 95
                                      799************9977774444444444444444466777777777777777777777777777777765 PP

  == domain 2  score: 70.0 bits;  conditional E-value: 2.3e-22
                                       EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEE CS
                         Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedgvesvk 77 
                                       +v+vvGgG+++l +A +l+e+g +Vt+v+r+++++      a kilqe+++k gi vlln++v+ei+g+++ vesv 
  gi|242399130|ref|YP_002994554.1| 169 HVIVVGGGNTALQEALYLNEIGVNVTLVHRREEFR------ADKILQERFKKAGIPVLLNNVVVEIKGNQK-VESVL 238
                                       79*********************************......*****************************9.****9 PP

                                       EE CS
                         Pyr_redox  78 lk 79 
                                       l+
  gi|242399130|ref|YP_002994554.1| 239 LR 240
                                       97 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 6.2
                                       EEECSSHHHHHHHHH CS
                         Pyr_redox   3 vvvGgGyiglElAga 17 
                                       v vG G i+   A+ 
  gi|242399130|ref|YP_002994554.1| 308 VAVGQGAIAANSAKD 322
                                       669*****9988875 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.1   1.5e-07   0.00012       1      32 [.      22      53 ..      22      65 .. 0.87
   2 !   12.9   0.0   5.5e-05     0.044      97     150 ..      78     136 ..      72     160 .. 0.82
   3 !    6.8   0.0    0.0039       3.1       2      29 ..     170     197 ..     169     217 .. 0.86
   4 !    8.3   0.1    0.0013       1.1     349     387 ..     285     323 ..     276     328 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.5e-07
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEEES-G CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithkl 32
                                      d+ +iG+G AG+ AA+ +ar G+++l+i +++
  gi|242399130|ref|YP_002994554.1| 22 DILIIGAGPAGFTAAIYSARYGFDTLIISKDI 53
                                      789***********************996554 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 5.5e-05
                                       HHHHHHHHHHTSTTEEEEES-EEEEEECT.....TEEEE.EEETTS-EEEECEEEE--TT CS
                              GIDA  97 yskevteklenepnleiieeeveelivee.....kkvkg.vvtedgetikakavviatGt 150
                                        +++++e++++  n+ i+ +eve++++ e     + +k  v+t++g+++ka++v+ia G+
  gi|242399130|ref|YP_002994554.1|  78 LANKMHEQVKK-LNVPIVFDEVERVDPAEcayyeGPCKFeVKTKNGKVYKARSVIIAVGA 136
                                       67899999999.9**************9999999666655*******************9 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0039
                                       EEEE-SSHHHHHHHHHHHHTT--EEEEE CS
                              GIDA   2 viViGgGhAGceAAlaaarlGakvlLit 29 
                                       viV+GgG   +  Al + + G++v+L+ 
  gi|242399130|ref|YP_002994554.1| 170 VIVVGGGNTALQEALYLNEIGVNVTLVH 197
                                       9*************************92 PP

  == domain 4  score: 8.3 bits;  conditional E-value: 0.0013
                                       TSBBSSSBTEEE-CGGGTB.-SHHHHHHHHHHHHHHHHHH CS
                              GIDA 349 tLetkkvkgLflAGqinGt.eGYeEaaaqGllAGinaark 387
                                        ++t+ +kgLf+AG+i+ + +    a++qG +A+  a+  
  gi|242399130|ref|YP_002994554.1| 285 YMRTN-IKGLFAAGDITNVfKQIAVAVGQGAIAANSAKDI 323
                                       56776.9************554555778*****9888765 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.2   1.3e-07   0.00011       1      31 [.      22      52 ..      22      60 .. 0.94
   2 !    8.4   0.0    0.0012         1       2      35 ..     170     203 ..     169     207 .. 0.94
   3 ?    1.1   0.0       0.2   1.6e+02     147     193 ..     208     253 ..     205     258 .. 0.86
   4 ?    4.7   0.0     0.017        14     378     402 ..     282     300 ..     274     312 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.3e-07
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESS CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavveke 31
                                      D+++iG+G AG +AA+  a+ G ++++++k 
  gi|242399130|ref|YP_002994554.1| 22 DILIIGAGPAGFTAAIYSARYGFDTLIISKD 52
                                      99***************************96 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0012
                                       EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGG CS
                     FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavvekeqefg 35 
                                       viV+G+G   L  Al ++e G +v++v   +ef+
  gi|242399130|ref|YP_002994554.1| 170 VIVVGGGNTALQEALYLNEIGVNVTLVHRREEFR 203
                                       9**************************9999987 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.2
                                       HHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEES CS
                     FAD_binding_2 147 lvesarkagvdfqerteadeLivedgrvtGavvenpesgrevrirak 193
                                       l e+++kag+ ++ +  ++e+   +++v  + ++n ++g++++ + +
  gi|242399130|ref|YP_002994554.1| 208 LQERFKKAGIPVLLNNVVVEI-KGNQKVESVLLRNIKTGEIFEKKVD 253
                                       78999999************9.5599**************9986555 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.017
                                       BETTSBESTTEEESSBTEEE-STCE CS
                     FAD_binding_2 378 tdengrvldadgqpipGLYAaGeva 402
                                       +d  +r+      +i+GL+AaG  +
  gi|242399130|ref|YP_002994554.1| 282 VDMYMRT------NIKGLFAAGDIT 300
                                       5666666......*********988 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   4.1e-07   0.00033       3      32 ..      22      51 ..      20      56 .. 0.94
   2 !   14.5   0.0   1.9e-05     0.015       3      36 ..     169     202 ..     168     219 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 4.1e-07
                                      EEEEE--SHHHHHHHHHHHHTTHHEEEEES CS
                     FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlvek 32
                                      d+lI+GaGpaG+++a   +++G +++++ k
  gi|242399130|ref|YP_002994554.1| 22 DILIIGAGPAGFTAAIYSARYGFDTLIISK 51
                                      89**************************98 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 1.9e-05
                                       EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSS CS
                     FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekrstt 36 
                                        V++VG+G + l  al L e Gv+v+lv +r++ 
  gi|242399130|ref|YP_002994554.1| 169 HVIVVGGGNTALQEALYLNEIGVNVTLVHRREEF 202
                                       59****************************9875 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   3.3e-06    0.0027       2      31 ..      22      51 ..      21      59 .. 0.92
   2 !    6.7   0.0    0.0032       2.6     102     164 ..      69     136 ..      67     139 .. 0.78
   3 ?    4.9   0.0     0.011       8.8       2      35 ..     169     202 ..     168     240 .. 0.92
   4 ?   -4.0   0.0       5.5   4.4e+03     373     387 ..     288     302 ..     284     302 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.3e-06
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-S CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllek 31
                                      d+++iG+G+AG+ aAi  a+ g ++l++ k
  gi|242399130|ref|YP_002994554.1| 22 DILIIGAGPAGFTAAIYSARYGFDTLIISK 51
                                      799**********************99976 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0032
                                       EETT.-CHHHHHHHHHHHHHHT-EEE-S--EEEE......ECETTE.EEEEE.TTEEEEESEEEE---- CS
                       HI0933_like 102 Fpvsdkaedivdallkelkeagvklrletevksv......ekeedgkfrvktkseeeleadklvlAtGG 164
                                       Fp+  k +++ + + +++k+ +v +  + ev++v       +e   kf+vktk+++ ++a+++++A+G 
  gi|242399130|ref|YP_002994554.1|  69 FPEGVKGSELANKMHEQVKKLNVPIVFD-EVERVdpaecaYYEGPCKFEVKTKNGKVYKARSVIIAVGA 136
                                       7777888888888888899999888765.445554445555667778********************96 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.011
                                       SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS CS
                       HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakkl 35 
                                       +viv+GgG   l  A+ +++ g +V+l+ + +++
  gi|242399130|ref|YP_002994554.1| 169 HVIVVGGGNTALQEALYLNEIGVNVTLVHRREEF 202
                                       79*************************9988775 PP

  == domain 4  score: -4.0 bits;  conditional E-value: 5.5
                                       TTSTTEEE-GGGBSE CS
                       HI0933_like 373 kkvpgLffaGEvlDv 387
                                        +++gLf aG + +v
  gi|242399130|ref|YP_002994554.1| 288 TNIKGLFAAGDITNV 302
                                       5789******98765 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   2.8e-08   2.3e-05       1      37 [.      22      56 ..      22      89 .. 0.91
   2 ?    1.6   0.1      0.17   1.4e+02       2      32 ..     170     200 ..     169     202 .. 0.94
   3 ?    4.0   0.0     0.031        26      89     129 ..     204     243 ..     199     252 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 2.8e-08
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGl 37
                                      D++++G+gpaG++AAi +ar G  +l+++++  +GG+
  gi|242399130|ref|YP_002994554.1| 22 DILIIGAGPAGFTAAIYSARYGFDTLIISKD--IGGN 56
                                      9***************************975..6766 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.17
                      FAD_oxidored   2 vvVvGGgpaGvaAAiaAaraGakvlLveerg 32 
                                       v+VvGGg   +  A+   + G +v Lv++r+
  gi|242399130|ref|YP_002994554.1| 170 VIVVGGGNTALQEALYLNEIGVNVTLVHRRE 200
                                       9**************************9986 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.031
                      FAD_oxidored  89 akavleemlaeagvtvllntrlvevekegkriesvtveske 129
                                       a ++l+e  ++ag+ vlln ++ve++ ++ ++esv +++ +
  gi|242399130|ref|YP_002994554.1| 204 ADKILQERFKKAGIPVLLNNVVVEIKGNQ-KVESVLLRNIK 243
                                       778999999*****************985.9****997755 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.6   3.5e-05     0.028       1      32 [.      22      54 ..      22      58 .. 0.91
   2 !    6.4   0.0    0.0073       5.9     146     207 ..      76     141 ..      68     163 .. 0.73
   3 !    9.2   0.1     0.001      0.83       1      32 [.     169     202 ..     169     206 .. 0.91
   4 ?    0.8   0.0      0.36     3e+02     152     190 ..     208     247 ..     202     283 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.5e-05
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSSST CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdia 32
                                      d++iiG+G +G ++A + ar g  ++++ k+ i 
  gi|242399130|ref|YP_002994554.1| 22 DILIIGAGPAGFTAAIYSARYGfdTLIISKD-IG 54
                                      8**********************99999998.54 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0073
                                       HHHHHHHHHHHHHTT-EEEESECEEEEEEEE......TCEEEEEEECT.EEEEEEEEEEE--GGGHHHH CS
                               DAO 146 akltaalaraaealGveilegtevtgleeed......gkvwgverttp.gendaadavVnaaGawsdll 207
                                        +l++ + +++++l v i++  ev++++  +          +v  +t+ g + +a+ v++a Ga  ++l
  gi|242399130|ref|YP_002994554.1|  76 SELANKMHEQVKKLNVPIVFD-EVERVDPAEcayyegPCKFEV--KTKnGKVYKARSVIIAVGAEPRKL 141
                                       678999999***********9.****96543444433333444..666698866699******997654 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.001
                                       EEEEECTSHHHHHHHHHHHHTT..EEEEESSSST CS
                               DAO   1 dvviiGGGiiGlstAyeLarrg..Vtllekgdia 32 
                                       +v+++GGG + l  A++L + g  Vtl+ +++++
  gi|242399130|ref|YP_002994554.1| 169 HVIVVGGGNTALQEALYLNEIGvnVTLVHRREEF 202
                                       79****************7779*******99765 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 0.36
                                       HHHHHHHTT-EEEESECEEEEEEEETCEEEEE..EECTEEE CS
                               DAO 152 laraaealGveilegtevtgleeedgkvwgve..rttpgen 190
                                       l+++++++G+ +l++  v++++  + kv  v   + + ge+
  gi|242399130|ref|YP_002994554.1| 208 LQERFKKAGIPVLLNNVVVEIK-GNQKVESVLlrNIKTGEI 247
                                       678899*********9999994.346777777853333655 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 ?    5.9   0.0     0.021        17       9      41 ..      22      56 ..      17     109 .. 0.77
   2 !   20.7   0.1   5.4e-07   0.00044       5      46 ..     165     215 ..     164     280 .. 0.64
   3 ?   -0.6   0.0       2.2   1.8e+03      10      28 ..     307     325 ..     299     328 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.021
                     NAD_binding_7  9 kvlvvGgGevAarkvrklleagakvtvvapev..k 41
                                       +l++G+G+ + + +   +++g +  ++++++  +
  gi|242399130|ref|YP_002994554.1| 22 DILIIGAGPAGFTAAIYSARYGFDTLIISKDIggN 56
                                      68****************************97441 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 5.4e-07
                     NAD_binding_7   5 lkgkkvlvvGgGevAarkvrklleagakvtvvapevkeele..........e 46 
                                       ++gk+v+vvGgG+ A++ +  l e g +vt+v  +  e+             
  gi|242399130|ref|YP_002994554.1| 165 FRGKHVIVVGGGNTALQEALYLNEIGVNVTLVHRRE-EFRAdkilqerfkkA 215
                                       689*****************************9993.333322322233230 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 2.2
                     NAD_binding_7  10 vlvvGgGevAarkvrklle 28 
                                        + vG G +Aa+ ++ +le
  gi|242399130|ref|YP_002994554.1| 307 AVAVGQGAIAANSAKDILE 325
                                       5669*******99998887 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0     2e-07   0.00017       1      36 [.      25      58 ..      25      85 .. 0.89
   2 ?    3.7   0.0     0.087        71       1      29 [.     172     200 ..     172     204 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 2e-07
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG- CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraa 36
                                      I+GaG +G +aA + a++gfd l++ k  ++GG++a
  gi|242399130|ref|YP_002994554.1| 25 IIGAGPAGFTAAIYSARYGFDTLIISK--DIGGNVA 58
                                      9************************77..6999986 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.087
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSS CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrd 29 
                                       +vG+G ++l  A +L + g++v+l+ +r+
  gi|242399130|ref|YP_002994554.1| 172 VVGGGNTALQEALYLNEIGVNVTLVHRRE 200
                                       8**********************998776 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1   1.3e-06     0.001      13      51 ..      16      53 ..       7      60 .. 0.86
   2 ?    4.9   0.0     0.017        14      18      50 ..     168     199 ..     163     204 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.3e-06
                                      HHHTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSS CS
                              Thi4 13 lkyaesDvvivGaGssGLtaayylakkpdlkvailersv 51
                                      ++    D++i+GaG++G taa y a+  ++ ++i+ + +
  gi|242399130|ref|YP_002994554.1| 16 DETKTWDILIIGAGPAGFTAAIYSARY-GFDTLIISKDI 53
                                      566778********************9.*****998865 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.017
                                       EEEEEE--SHHHHHHHHHHHHCTTS-EEEEESS CS
                              Thi4  18 sDvvivGaGssGLtaayylakkpdlkvailers 50 
                                         v++vG+G + L  a yl +  +++v+++ r+
  gi|242399130|ref|YP_002994554.1| 168 KHVIVVGGGNTALQEALYLNEI-GVNVTLVHRR 199
                                       579****************999.9999988765 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.17   1.4e+02       2      23 ..      20      41 ..      19      52 .. 0.81
   2 !   15.9   0.0   6.7e-06    0.0054     118     229 ..      97     203 ..      82     206 .. 0.69
   3 ?    3.0   0.0     0.055        45     298     341 ..     220     262 ..     205     263 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.17
                       K_oxygenase  2 ilDligiGiGpsnLsLaillee 23
                                      + D+ +iG+Gp+  + ai ++ 
  gi|242399130|ref|YP_002994554.1| 20 TWDILIIGAGPAGFTAAIYSAR 41
                                      689*********9999887765 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 6.7e-06
                       K_oxygenase 118 eveevepdeeeee...elltveskdaegeeeelearnlvlgvGtepkiPevleklegkervv.Hsseylerkee.ll 189
                                       eve+v+p e +       ++v++     + + ++ar+++++vG ep     l+   g+++++    +y  + +  l 
  gi|242399130|ref|YP_002994554.1|  97 EVERVDPAECAYYegpCKFEVKT----KNGKVYKARSVIIAVGAEPR---KLKV-PGEDKFYgRGVSYCATCDGpLF 165
                                       68888888864332324477776....46789***********9985...3332.2223333023355555544589 PP

                       K_oxygenase 190 akkriaVvGsGqSaaeifedllrrqkkvelklvtrseale 229
                                       ++k+++VvG+G +a +  e l+ ++  v+++lv r+e+++
  gi|242399130|ref|YP_002994554.1| 166 RGKHVIVVGGGNTALQ--EALYLNEIGVNVTLVHRREEFR 203
                                       9************976..4555555667999999999986 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.055
                       K_oxygenase 298 lpnrevesaeaegkgeveltlrneesgeeetlevdavvlATGYr 341
                                       l n  v +++ ++k    + lrn ++ge ++ +vd v++  GY+
  gi|242399130|ref|YP_002994554.1| 220 LLNNVVVEIKGNQK-VESVLLRNIKTGEIFEKKVDGVFVFIGYE 262
                                       55666777777775.667899*******************9997 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.1   0.00063      0.52       1      35 [.      22      52 ..      22      66 .. 0.86
   2 ?    3.7   0.0     0.032        26      87     160 ..      76     154 ..      70     161 .. 0.74
   3 ?    3.9   0.0     0.027        22       2      32 ..     170     198 ..     169     217 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00063
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieasps 35
                                      D+++iGaGpAg   A  +  a++g   ++i  s++
  gi|242399130|ref|YP_002994554.1| 22 DILIIGAGPAGFTAAIYS--ARYGFDTLII--SKD 52
                                      9************99999..9999988888..555 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.032
                     Lycopene_cycl  87 krlkeellerlvengvklleakvesveeeeag......eslvvleggrkirarlvvdarglaslkkarrlglQtfyG 157
                                       ++l+++++e++ + +v  +   ve+v ++e +      +  v +++g+  +ar v+ a g a+++k +  g  +fyG
  gi|242399130|ref|YP_002994554.1|  76 SELANKMHEQVKKLNVPIVFDEVERVDPAECAyyegpcKFEVKTKNGKVYKARSVIIAVG-AEPRKLKVPGEDKFYG 151
                                       6677777777777777777777777776664312122256789999**************.9999999999999999 PP

                     Lycopene_cycl 158 vev 160
                                         v
  gi|242399130|ref|YP_002994554.1| 152 RGV 154
                                       766 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.027
                     Lycopene_cycl   2 vvviGaGpAglslAarlteakpglkvvliea 32 
                                       v+v+G+G   l+ A  l  ++ g++v+l+  
  gi|242399130|ref|YP_002994554.1| 170 VIVVGGGNTALQEALYL--NEIGVNVTLVHR 198
                                       89***************..*********965 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   0.00026      0.21      21      60 ..      13      52 ..       2      93 .. 0.85
   2 !    7.1   0.1    0.0035       2.9      29      63 ..     168     202 ..     148     260 .. 0.81
   3 ?   -3.3   0.1       5.7   4.6e+03      17      44 ..     293     320 ..     283     323 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00026
                                      CEETCB---EEEEESTSHHHHHHHHHHHHTT-EEEEEESS CS
                       AlaDh_PNT_C 21 GgvpgvepakvlviGgGvaGlqAiatakglgakVtvlDvr 60
                                      +g+ +++   +l+iG+G aG  A+  +++ g ++ ++ ++
  gi|242399130|ref|YP_002994554.1| 13 SGIDETKTWDILIIGAGPAGFTAAIYSARYGFDTLIISKD 52
                                      6788888999*******************99998887665 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0035
                                       -EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHH CS
                       AlaDh_PNT_C  29 akvlviGgGvaGlqAiatakglgakVtvlDvrpar 63 
                                        +v+v+GgG   lq +   +++g +Vt++  r++ 
  gi|242399130|ref|YP_002994554.1| 168 KHVIVVGGGNTALQEALYLNEIGVNVTLVHRREEF 202
                                       589*************************9998875 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 5.7
                                       EETTCEETCB---EEEEESTSHHHHHHH CS
                       AlaDh_PNT_C  17 gtlaGgvpgvepakvlviGgGvaGlqAi 44 
                                         +aG ++ v +   + +G G    +++
  gi|242399130|ref|YP_002994554.1| 293 LFAAGDITNVFKQIAVAVGQGAIAANSA 320
                                       5677777777777777777776666655 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.065        53       3      35 ..      11      43 ..       9      51 .. 0.73
   2 !   11.3   0.1   0.00032      0.26      10      59 ..     165     214 ..     158     234 .. 0.81
   3 ?   -2.0   0.0       4.1   3.4e+03      13      34 ..     305     326 ..     296     331 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.065
                                      HHHHHS..TT-EEEEES-SHHHHHHHHHHHCCT CS
                      Shikimate_DH  3 akkkleslkekkvlliGaGemaelvakhLlakg 35
                                       ++ +++ k+  +l+iGaG  +  +a + ++ g
  gi|242399130|ref|YP_002994554.1| 11 SQSGIDETKTWDILIIGAGPAGFTAAIYSARYG 43
                                      566778899999*******99887776655555 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00032
                                       .TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.E CS
                      Shikimate_DH  10 lkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkge 59 
                                       +++k+v+++G G++a + a +L + gv+  +v  R+  ra+++ +e  ++
  gi|242399130|ref|YP_002994554.1| 165 FRGKHVIVVGGGNTALQEALYLNEIGVNVTLVHRREEFRADKILQERFKK 214
                                       57899***********************8899999999**9987664333 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 4.1
                                       -EEEEES-SHHHHHHHHHHHCC CS
                      Shikimate_DH  13 kkvlliGaGemaelvakhLlak 34 
                                       + ++ +G G +a   ak +l++
  gi|242399130|ref|YP_002994554.1| 305 QIAVAVGQGAIAANSAKDILEN 326
                                       4567799999999999988765 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.1   0.00023      0.18       1      34 [.      22      51 ..      22      57 .. 0.79
   2 ?    4.4   0.0     0.017        14       2      34 ..     170     199 ..     169     243 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00023
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-S CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlvese 34
                                      +i+i+G+G+aG++aA++ a+++ +    tl+ s+
  gi|242399130|ref|YP_002994554.1| 22 DILIIGAGPAGFTAAIYSARYGFD----TLIISK 51
                                      69****************999843....455455 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.017
                                       EEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-S CS
                    Trp_halogenase   2 ivivGGGtaGwlaAaalakalkgklevtlvese 34 
                                       +++vGGG  +   A +l++ +   ++vtlv   
  gi|242399130|ref|YP_002994554.1| 170 VIVVGGGNTALQEALYLNEIG---VNVTLVHRR 199
                                       89******************9...99***9865 PP

>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.29   2.4e+02      55      84 ..      20      49 ..       6      62 .. 0.81
   2 !   13.4   0.1   4.8e-05     0.039      52      90 ..     152     202 ..     113     328 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.29
                                      TSEEEEEBSSHHHHHHHHHHHHHT-EEEEE CS
                              PALP 55 aktvveassGNhgralAaaaallGlkvtiv 84
                                      +  ++  ++G +g  +A+++a++G++  i 
  gi|242399130|ref|YP_002994554.1| 20 TWDILIIGAGPAGFTAAIYSARYGFDTLII 49
                                      556777889999************987664 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 4.8e-05
                                       T............TTTSEEEEEBSSHHHHHHHHHHHHHT-EEEEEEETTS- CS
                              PALP  52 g............tgaktvveassGNhgralAaaaallGlkvtivvpadas 90 
                                                     ++k+v++ ++GN+++  A++ + +G+ vt+v  +   
  gi|242399130|ref|YP_002994554.1| 152 RgvsycatcdgplFRGKHVIVVGGGNTALQEALYLNEIGVNVTLVHRREEF 202
                                       0444444444455899****************************9776655 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.52   4.3e+02       2      29 ..      24      51 ..      23      70 .. 0.91
   2 !   13.3   0.0   0.00011     0.092       1      64 [.     170     242 ..     170     269 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.52
                                      EEE--STTHHHHHHHHHHHTEEEEEEES CS
                            XdhC_C  2 vifGaghvaqalarlaaalgfrvtvvdp 29
                                      +i+Gag+ +   a + a+ gf++ ++ +
  gi|242399130|ref|YP_002994554.1| 24 LIIGAGPAGFTAAIYSARYGFDTLIISK 51
                                      79*********************99976 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.00011
                                       EEEE--STTHHHHHHHHHHHTEEEEEEES-GGGG....-GGG-TT-SE.....-EEEE--S-HHHHHHHHHHH CS
                            XdhC_C   1 lvifGaghvaqalarlaaalgfrvtvvdpreefa....tkerfpeade.....tavvvlthdhklDaealeaa 64 
                                       ++++G+g+ a + a +++++g++vt+v  reef+     +erf++a       ++vv +  ++k +  +l+++
  gi|242399130|ref|YP_002994554.1| 170 VIVVGGGNTALQEALYLNEIGVNVTLVHRREEFRadkiLQERFKKAGIpvllnNVVVEIKGNQKVESVLLRNI 242
                                       689****************************999666655666644337777666666666666666666555 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   5.7e-05     0.047       2      50 ..     165     213 ..     164     254 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.7e-05
                                       HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-E CS
                              IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfe 50 
                                       ++gk++ v+G G+ +  +al l + g++v++  r+++  ++k  +e f+
  gi|242399130|ref|YP_002994554.1| 165 FRGKHVIVVGGGNTALQEALYLNEIGVNVTLVHRREEFRADKILQERFK 213
                                       579*****************************99999777766666555 PP

>> FMO-like  Flavin-binding monooxygenase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   4.9e-05      0.04     158     268 ..     142     261 ..      61     308 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.9e-05
                          FMO-like 158 sfpGiekfkGqyfhsrdykepevfkgkrvlviGlGnsggdiavelsrtaeqvllstrsGsw....vl.srvsdsGyp 229
                                         pG +kf G+ +      +   f+gk v+v+G Gn++ + a  l +   +v l  r+  +    +l +r  + G p
  gi|242399130|ref|YP_002994554.1| 142 KVPGEDKFYGRGVSYCATCDGPLFRGKHVIVVGGGNTALQEALYLNEIGVNVTLVHRREEFradkILqERFKKAGIP 218
                                       57999999999998888888899*****************************9999876652222332577778888 PP

                          FMO-like 230 w...dmllvtrfksllknilptalsn.wlvekklnkrfnheny 268
                                       +   ++++  + ++ ++ +l +++ +  + ekk++  f    y
  gi|242399130|ref|YP_002994554.1| 219 VllnNVVVEIKGNQKVESVLLRNIKTgEIFEKKVDGVFVFIGY 261
                                       5444777888888888888888776525777877777765544 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00023      0.19     183     266 ..      38     140 ..       6     150 .. 0.79
   2 ?   -3.0   0.0       4.1   3.3e+03     415     449 ..     287     318 ..     281     319 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00023
                                       CBHHHHTCCCCHHHHHTSCCCEE............TTHTHHHHHHHHH..TTTTEEEETSEEEEEEEE.......ET CS
                     Amino_oxidase 183 lsaklalpllwelegfggslllp............rgGlsqlpealae..elrgldirlntrVkeikr.......eg 238
                                       +sa+  +++l   ++ gg++ l+             +G s+l++ ++e  +++++ i ++ +V +++        ++
  gi|242399130|ref|YP_002994554.1|  38 YSARYGFDTLIISKDIGGNVALTdiienypgfpegVKG-SELANKMHEqvKKLNVPIVFD-EVERVDPaecayyeGP 112
                                       66666677777777777777777777777777666666.899999999999999999999.9999999999988777 PP

                                       TCEEEEETTSTEEEESEEEE-S-HHHHH CS
                     Amino_oxidase 239 dgvtvtledgevveaDaVvvTvplgvlk 266
                                        +  v++++g+v++a++V+++v     k
  gi|242399130|ref|YP_002994554.1| 113 CKFEVKTKNGKVYKARSVIIAVGAEPRK 140
                                       77********************887666 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4.1
                                       CHHCSTTEEE.SGGGCTTTTTSHHHHHHHHHHHHH CS
                     Amino_oxidase 415 kpegdprlffAGehtsreypgtvegAilSGlraAa 449
                                       ++ ++++lf AG+ t   ++  +  A+  G  aA+
  gi|242399130|ref|YP_002994554.1| 287 RT-NIKGLFAAGDITN--VFKQIAVAVGQGAIAAN 318
                                       45.7999******998..88888888888888885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       744  (0.041497); expected 358.6 (0.02)
Passed bias filter:                      631  (0.0351944); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); 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: 0.70u 0.34s 00:00:01.04 Elapsed: 00:00:00.50
# Mc/sec: 1990.89
//
Query:       gi|242399131|ref|YP_002994555.1|  [L=177]
Description: membrane-bound metal-dependent hydrolase [Thermococcus sibiricus MM 739]
Scores for 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   50.9   3.8    1.4e-13   50.5   3.8    1.1  1  YdjM      LexA-binding, inner membrane-associated putative hy


Domain annotation for each model (and alignments):
>> YdjM  LexA-binding, inner membrane-associated putative hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.5   3.8   7.8e-18   1.4e-13       1     112 [.       1     171 [.       1     173 [. 0.88

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 7.8e-18
                              YdjM   1 MdgltHallGaalglalaallgaake.............avllavavlgAllPDiDhpsstlgrklgllskklak.. 62 
                                       Md   H+l+G+++  ++  + +  k+             +  +av vlg+ lPD+Dhp + + r ++++ +++    
  gi|242399131|ref|YP_002994555.1|   1 MDYNGHVLSGLLTYPLAVLFASFLKQyagipfkmslmatIFGYAVYVLGSDLPDLDHPEALIHRGIKPIVSVMVGsv 77 
                                       9999*******99777666666555566799*9**999888999999************************88889* PP

                              YdjM  63 ........................................lvgHRgftHSllflallalvlllllrlfgrsa....l 95 
                                                                               + +HRg+ HSl+f+ + +l + +l+r     +    +
  gi|242399131|ref|YP_002994555.1|  78 vvvkirdsisfgndtwmdgsvswaigalfavgawyafgavIPKHRGVVHSLMFASIYGLSIFALCRYGLIFRfeeaF 154
                                       ****************************************9************999988888777544444344448 PP

                              YdjM  96 rlglllllgvlsHlllD 112
                                       +++++ +lg+ +Hl+ D
  gi|242399131|ref|YP_002994555.1| 155 FVAFMAFLGYTLHLVED 171
                                       89999**********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1273.40
//
Query:       gi|242399132|ref|YP_002994556.1|  [L=403]
Description: ATPase, AAA superfamily [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00013   21.9   0.7    0.00049   20.1   0.7    1.9  1  ATPase_2       ATPase domain predominantly from Archaea
     0.0013   18.6   0.2       0.82    9.6   0.0    3.1  3  NACHT          NACHT domain
     0.0016   18.9   0.6      0.011   16.2   0.6    2.2  1  AAA            ATPase family associated with various cellular
     0.0018   18.5   0.0     0.0051   17.1   0.0    1.7  1  AAA_22         AAA domain
     0.0031   16.9   0.1     0.0058   16.0   0.1    1.4  1  ATPase         KaiC
  ------ inclusion threshold ------
      0.022   15.2   0.0      0.043   14.2   0.0    1.5  1  AAA_16         AAA ATPase domain
      0.023   14.7   2.2       0.35   10.9   0.2    2.6  2  AAA_14         AAA domain
      0.025   14.1   0.1      0.042   13.4   0.1    1.3  1  AAA_7          P-loop containing dynein motor region
      0.026   15.0   0.0      0.051   14.1   0.0    1.7  1  ABC_tran       ABC transporter
      0.026   14.5   0.0      0.041   13.9   0.0    1.3  1  ResIII         Type III restriction enzyme, res subunit
      0.038   12.8   0.1      0.061   12.1   0.1    1.2  1  AAA_35         AAA-like domain
      0.041   13.1   0.0       0.67    9.1   0.0    2.4  2  NB-ARC         NB-ARC domain
       0.05   12.5   0.5       0.11   11.4   0.5    1.5  1  AAA_10         AAA-like domain
      0.051   13.5   0.0       0.28   11.1   0.0    2.2  2  TrmB           Sugar-specific transcriptional regulator TrmB
      0.054   12.4   0.1       0.11   11.4   0.1    1.4  1  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
      0.071   12.5   0.2       0.34   10.3   0.2    2.0  1  TniB           Bacterial TniB protein
       0.12   12.2   0.0          3    7.8   0.0    2.6  2  HTH_5          Bacterial regulatory protein, arsR family
       0.12   11.5   0.0        0.2   10.8   0.0    1.3  1  DUF815         Protein of unknown function (DUF815)


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 !   20.1   0.7   4.9e-07   0.00049      14     230 ..      59     287 ..      54     290 .. 0.64

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 4.9e-07
                          ATPase_2  14 ilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefie.....eeeekkklekalgia 85 
                                       i+ ++++    + Gp g GKt+ lk i++  ++++ + iy+    ++ ++ ++++++     +++ + ++e+  ++ 
  gi|242399132|ref|YP_002994556.1|  59 IIGNQSSIAFSLVGPLGMGKTQRLKTIYKTISEQGGKAIYIKVDTNDILKLTRDMFNglkppKTRTNIFFENLSKKL 135
                                       5555555555578********************99999998766666666666666688887777777777777777 PP

                          ATPase_2  86 vpkaeleeilkeksklvfkaielllekikkkgkk...iiiiiDelqklidlglngaellvkeLlnliesltkekhlc 159
                                          ++le++l++++++  + i++    ++k+  k     +++Del ++    +++++ l  e+l+ + s  +  + c
  gi|242399132|ref|YP_002994556.1| 136 GFIDRLEKMLSSTKEYKSRDIAE---MLTKELSKypySTVLLDELENMQ-TASEEEKILFFEMLRHFIS--NMPRGC 206
                                       77788888877655554555554...444555555558999*******9.7888999999999998887..444445 PP

                          ATPase_2 160 vviclsSeglfiervyneselegrhky.ilvddldketalnflkegfkel..eel.......skedfeeiyryvGGk 226
                                       +v  +       e+         r  y  +++++  +++ +++k+  +++  ++        ++e + +i ++  G+
  gi|242399132|ref|YP_002994556.1| 207 IVGFACIPDAYEEYSKIFPAFFMRLHYeFKLRPMSLDETFELVKKRLNQVriRDTddpiypfTEEAVRLIHQLAKGN 283
                                       55333333344443333344455555556666666666666666655555432224555555555555555566666 PP

                          ATPase_2 227 Pkal 230
                                       P+++
  gi|242399132|ref|YP_002994556.1| 284 PRQI 287
                                       6555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1     0.054        53       5      28 ..      70      93 ..      67     101 .. 0.86
   2 !    9.6   0.0   0.00082      0.82      82     163 ..     170     253 ..     122     255 .. 0.78
   3 ?    1.5   0.0      0.25   2.5e+02      19      80 ..     274     329 ..     271     342 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.054
                                      EEC-TTTCHHHHHHHHHHHHCTS- CS
                             NACHT  5 lqGeaGsGKTtLlqklalawaegk 28
                                      l G+ G+GKT  l+ +  ++ e+ 
  gi|242399132|ref|YP_002994556.1| 70 LVGPLGMGKTQRLKTIYKTISEQG 93
                                      7899************99988765 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00082
                                       CEEEEEE-STT-SS-TCH.........HHHHHCTTTTT--EEEEEEECCCHHHHCTTSSCE.......EEEE--TCC CS
                             NACHT  82 rlLlilDglDelvtdlgqkekqpvrtlLselirkkllpeasllltvrpralrdleeqleea.....ivlevegfses 153
                                       ++  +lD l+ ++t  ++ ek    ++L++ i+  +++++ +  ++ p+a ++  + +        + ++++++s +
  gi|242399132|ref|YP_002994556.1| 170 ST-VLLDELENMQTASEE-EKILFFEMLRHFISN-MPRGCIVGFACIPDAYEEYSKIFPAFfmrlhYEFKLRPMSLD 243
                                       33.679*******98877.9999*******9998.******************888888888888999********* PP

                                       HHHHHHHHCT CS
                             NACHT 154 rrkqlvrkyf 163
                                       ++ +lv k +
  gi|242399132|ref|YP_002994556.1| 244 ETFELVKKRL 253
                                       *****99865 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.25
                                       HHHHHHCTS-SCCCC-SEEEEEETTTTTTS-...-HCHHHCCCCTS--SSS-CCHHHHCCSC CS
                             NACHT  19 klalawaegklpqgafklvFflslrelsrsgnarsladllfsqlpepaapvsevwavllelp 80 
                                       +l++++a+g++ q     +F+  l+e s+++    ++d+++   +e+ +  +e   +l+++p
  gi|242399132|ref|YP_002994556.1| 274 RLIHQLAKGNPRQ--ILRLFHYVLGEASKHKFD-PIDDYVVTTILEEPKSLEE---YLMRIP 329
                                       79999*****999..799999999999999877.9999**9999999999999...666666 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   0.6   1.1e-05     0.011       3      74 ..      70     184 ..      68     219 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.1e-05
                                       EESSTTSSHHHHHHHHHHHH.....THEEEEEETTTCSSS..................................... CS
                               AAA   3 lyGppGtGKTllakavakel.....gvefleisgsellsk..................................... 37 
                                       l+Gp G+GKT   k + k++     ++ +++++  ++l k                                     
  gi|242399132|ref|YP_002994556.1|  70 LVGPLGMGKTQRLKTIYKTIseqggKAIYIKVDTNDIL-Kltrdmfnglkppktrtniffenlskklgfidrlekml 145
                                       89*****************9444433668999999999.55778877666666666666666666666666666663 PP

                                       ..STTHHHHHHHHHHHHHHHTS.TS.EEEEEETGGGHHHHH CS
                               AAA  38 ..yvgesekkirelfkeakeka.kp.silfiDEidalaksr 74 
                                         + + ++++i+e++++  e +  p s +++DE++++ +++
  gi|242399132|ref|YP_002994556.1| 146 ssTKEYKSRDIAEMLTK--ELSkYPySTVLLDELENMQTAS 184
                                       33333333334333333..2223355666666666665554 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   5.1e-06    0.0051      10     111 ..      70     197 ..      63     213 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 5.1e-06
                            AAA_22  10 vtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka................ 70 
                                       ++G+ G+GKT  l+++ ++  e+      + + +++++       +l r++++ l+ ++ +                
  gi|242399132|ref|YP_002994556.1|  70 LVGPLGMGKTQRLKTIYKTISEQ------GGKAIYIKVDTND-ILKLTRDMFNGLKPPKTRtniffenlskklgfid 139
                                       89*****************9866......5555555544444.6666677777777666667777777777777777 PP

                            AAA_22  71 .........erlsseellealeqalraravielliiDEaqhlr..s.......eealee 111
                                                ++ +s+++ e+l++ l+++   + +++DE +++   s        e+l++
  gi|242399132|ref|YP_002994556.1| 140 rlekmlsstKEYKSRDIAEMLTKELSKYPY-STVLLDELENMQtaSeeekilfFEMLRH 197
                                       777777777777999999************.***********66525555444444444 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   5.8e-06    0.0058      22     139 ..      68     189 ..      53     208 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 5.8e-06
                            ATPase  22 vlitGepGtGKtifalqFlikgaekygepgvfvtveepa.........edlrenakslGwdlekleeegklaiidas 89 
                                         ++G  G GKt   l+ ++k +++ g + +++ v+ +          + l+   ++  + +e+l ++  l +id  
  gi|242399132|ref|YP_002994556.1|  68 FSLVGPLGMGKTQR-LKTIYKTISEQGGKAIYIKVDTNDilkltrdmfNGLKPPKTRTNIFFENLSKK--LGFIDRL 141
                                       5688999****975.6679*****************99999999888888888888899999999998..9999999 PP

                            ATPase  90 esaeesaeekdkedleelieelaeaikeikakrvviDsitgl.ayeekeav 139
                                       e++  s+   ++++ + ++e l++ ++++  + v++D ++++ + +e+e+ 
  gi|242399132|ref|YP_002994556.1| 142 EKMLSST---KEYKSRDIAEMLTKELSKYPYSTVLLDELENMqTASEEEKI 189
                                       9987755...59999999999*********************433333333 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   4.4e-05     0.043      28     106 ..      69     136 ..      55     207 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.4e-05
                            AAA_16  28 llsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekleea 104
                                        l+G+ G+GK+  ++++++ ++++gg +++ k d +         +  l+r + ++ l+ +  ++  + + e l + 
  gi|242399132|ref|YP_002994556.1|  69 SLVGPLGMGKTQRLKTIYKTISEQGGKAIYIKVDTN--------DILKLTR-DMFNGLKPP--KTRTNIFFENLSKK 134
                                       699*******************************99........3333324.555555544..22344444444444 PP

                            AAA_16 105 la 106
                                       l+
  gi|242399132|ref|YP_002994556.1| 135 LG 136
                                       44 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.2   0.00035      0.35       5      72 ..      68     130 ..      64     152 .. 0.65
   2 ?    3.7   0.5      0.06        60      46      81 ..     151     185 ..     124     246 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00035
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDE 72 
                                         ++G+  +GKT  lk+++k+   +  + +yi++d+++  kl+    + + ++    ++ +t +f+  
  gi|242399132|ref|YP_002994556.1|  68 FSLVGPLGMGKTQRLKTIYKTISEQGGKAIYIKVDTNDILKLTRD--MFNGLKP---PKTRTNIFFEN 130
                                       5689**************988889999*********999776633..2222222...12222233333 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.06
                            AAA_14  46 ladpekllelileklkeekktylflDEiqevpewek 81 
                                       ++ ++++ e++ ++l++   + ++lDE  +++++++
  gi|242399132|ref|YP_002994556.1| 151 YK-SRDIAEMLTKELSKYPYSTVLLDELENMQTASE 185
                                       22.22566666666544344569*****99966554 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   4.2e-05     0.042       9      84 ..      39     116 ..      33     168 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.2e-05
                             AAA_7   9 fseilVptvdtvrysyllelllknkkpvl..lvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdiie 83 
                                       +++i V     +r+s++++ ++ n+ ++   lvGp G GKt  +k++ k+++++  + + i++  +   + ++d+++
  gi|242399132|ref|YP_002994556.1|  39 VESIHVYQEVDMRLSMMISEIIGNQSSIAfsLVGPLGMGKTQRLKTIYKTISEQGGKAIYIKVDTNDILKLTRDMFN 115
                                       678889888999**********99887652279*****************999988888888777766666666665 PP

                             AAA_7  84 s 84 
                                        
  gi|242399132|ref|YP_002994556.1| 116 G 116
                                       4 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   5.1e-05     0.051      15      53 ..      69     116 ..      62     282 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.1e-05
                                       EEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.........B- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xx RF
                          ABC_tran  15 aivGenGaGKStLlkllagllkpteGeilldgkdlke.........qe 53 
                                        +vG+ G GK+  lk++++  + + G+  + + d+++         + 
  gi|242399132|ref|YP_002994556.1|  69 SLVGPLGMGKTQRLKTIYKTISEQGGKAIYIKVDTNDilkltrdmfNG 116
                                       79************************9844444444432255444433 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 ?   13.9   0.0   4.1e-05     0.041      26     118 ..      67     155 ..      33     214 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.1e-05
                                       EEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B--...... CS
                            ResIII  26 rglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseaykeigkkvsgdkkkakekdst 102
                                        + ++ + G+GKT  +  + + ++++g+ + + + v+++++l+ t++ f+ ++++++  ++ ++++ +kk   ++++
  gi|242399132|ref|YP_002994556.1|  67 AFSLVGPLGMGKTQRLKTIYKTISEQGG-KAIYIKVDTNDILKLTRDMFNGLKPPKTR-TNIFFENLSKKL--GFID 139
                                       45588899*****987777777777655.799999**************999999865.444444444444..4444 PP

                                       .-SEEEEEHHHHHHTH CS
                            ResIII 103 nkkilvttiqsldads 118
                                         + +++++++ +++ 
  gi|242399132|ref|YP_002994556.1| 140 RLEKMLSSTKEYKSRD 155
                                       4444444444433333 PP

>> AAA_35  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   6.1e-05     0.061      31     157 ..      65     199 ..      35     205 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.1e-05
                            AAA_35  31 GalirikapkkmGKtSLlarilakakqqgyktvsldlqlad.....keilsdldk...flrwfcanvsrqLklenkl 99 
                                            + +p  mGKt  l++i ++ ++qg k++++++++ d     +++++ l+      + f  n+s++L++ ++l
  gi|242399132|ref|YP_002994556.1|  65 SIAFSLVGPLGMGKTQRLKTIYKTISEQGGKAIYIKVDTNDilkltRDMFNGLKPpktRTNIFFENLSKKLGFIDRL 141
                                       33567889***************************8876553222266766654333378899************** PP

                            AAA_35 100 deyWdeelgskvsctayleeylLkeidkplvLaldevdrlfeypeiak.dflslLRswh 157
                                       +++  ++ + k++  a + +  L++   + vL lde++++ + +e  k  f+++LR++ 
  gi|242399132|ref|YP_002994556.1| 142 EKMLSSTKEYKSRDIAEMLTKELSKYPYSTVL-LDELENMQTASEEEKiLFFEMLRHFI 199
                                       *9999766666554444444445555555554.66666665544433314999999875 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0   0.00067      0.67      17      92 ..      62     137 ..      47     190 .. 0.67
   2 ?    1.5   0.0      0.14   1.4e+02     151     202 ..     232     288 ..     226     359 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00067
                                       TSCSEEEEEEESTTSSHHHHHHHHCCSHCCCCCCBTEEEEEEEESXXHHHHHHHXXHHHHHCCCTTSSSS-STTS.. CS
                            NB-ARC  17 elqslvvalvGmgGvGKttlakqilnksdevegrFdsvawvvvsktdkseeiletilkeLslseddleekeeves.. 91 
                                       +  s+  +lvG  G+GKt  +k i++  +e  g     +++ v +t ++ ++++++ + L+  +  ++++ e+ s  
  gi|242399132|ref|YP_002994556.1|  62 NQSSIAFSLVGPLGMGKTQRLKTIYKTISEQGG---KAIYIKV-DTNDILKLTRDMFNGLKPPKTRTNIFFENLSkk 134
                                       45567899*******************555554...4555555.455566666666666666666666665555433 PP

                                       ..H CS
                            NB-ARC  92 ..l 92 
                                          
  gi|242399132|ref|YP_002994556.1| 135 lgF 137
                                       332 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.14
                                       EEEEEESS--HHHHHHHHHHCCTS-GGCHH.......CHHHHHHHHHHCTT-HHHHH CS
                            NB-ARC 151 sekievelLekdeawellenkvfekkleekes.....leevakeivekckGlPlalk 202
                                       ++ ++++ ++ de +el+++  ++ +  + ++      ee  + i +  kG+P  + 
  gi|242399132|ref|YP_002994556.1| 232 HYEFKLRPMSLDETFELVKKRLNQVRIRDTDDpiypfTEEAVRLIHQLAKGNPRQIL 288
                                       5677888899999******99999999877778899889999999999999997764 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.5   0.00011      0.11      12      60 ..      57     104 ..      46     190 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00011
                            AAA_10  12 qevkgsktnasasliiGdlGnGKSvlakllvlyisllggkaliiDpkke 60 
                                        e+ g+ + + a  ++G+lG GK    k++   is  ggka++i    +
  gi|242399132|ref|YP_002994556.1|  57 SEIIGN-QSSIAFSLVGPLGMGKTQRLKTIYKTISEQGGKAIYIKVDTN 104
                                       566663.345557899***************************965544 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       2.3   2.3e+03      36      62 ..     121     151 ..     111     172 .. 0.60
   2 ?   11.1   0.0   0.00028      0.28      21      52 ..     346     377 ..     337     391 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 2.3
                                       CHCHHHHHHHHHHC.TSEEEESST...TTEE CS
                              TrmB  36 rskvYevLrsLedk.GlVerekgr...pklY 62 
                                       +++ +   ++L++k G+++r ++    +k Y
  gi|242399132|ref|YP_002994556.1| 121 KTRTNIFFENLSKKlGFIDRLEKMlssTKEY 151
                                       5555555566654446665554333333333 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00028
                                       CCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSE CS
                              TrmB  21 gpatadeiaeelgvprskvYevLrsLedkGlV 52 
                                       gpa+  +ia+e++ p  +vY+ L++L++ G+ 
  gi|242399132|ref|YP_002994556.1| 346 GPASYIQIAKEVKKPGVQVYDHLEELIRLGFL 377
                                       6778889***********************85 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00011      0.11      18      47 ..      68      97 ..      59     108 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00011
                     TrwB_AAD_bind 18 ilivGttGsGKtqalekllrairargdrai 47
                                      + +vG  G+GKtq l+ + ++i ++g +ai
  gi|242399132|ref|YP_002994556.1| 68 FSLVGPLGMGKTQRLKTIYKTISEQGGKAI 97
                                      6799***********************998 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.2   0.00034      0.34     100     158 ..     149     208 ..      44     213 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00034
                              TniB 100 ararvskleqqvlrllrelkvrvLiiDEihnllagsarkqreflnalks.Lgnelkipiv 158
                                       ++ +  ++ ++  + l+++    +++DE++n+ ++s +++  f+++l+  ++n  +  iv
  gi|242399132|ref|YP_002994556.1| 149 KEYKSRDIAEMLTKELSKYPYSTVLLDELENMQTASEEEKILFFEMLRHfISNMPRGCIV 208
                                       2234556677777889999999*************************9615555555555 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1      0.38   3.8e+02      10      26 ..     144     161 ..     143     166 .. 0.85
   2 ?    7.8   0.0     0.003         3       7      44 ..     339     376 ..     338     377 .. 0.95

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.38
                                       HHTT.SSEEHHHHHHHHT CS
                             HTH_5  10 lLae.gelcvcelaeelg 26 
                                       +L++ +e+++ ++ae+l 
  gi|242399132|ref|YP_002994556.1| 144 MLSStKEYKSRDIAEMLT 161
                                       7888899********985 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.003
                                       HHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTS CS
                             HTH_5   7 ILklLaegelcvcelaeelglsqstvShHLkkLreaGL 44 
                                       I+++ + g+++  ++a+e++++   v  HL  L  +G+
  gi|242399132|ref|YP_002994556.1| 339 IVYQFNGGPASYIQIAKEVKKPGVQVYDHLEELIRLGF 376
                                       999******************************99997 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0    0.0002       0.2      30     117 ..      42     132 ..      23     148 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0002
                            DUF815  30 LvgidkqkealventeqfleglpannvLLwGarGtGKSslvkallneyaeeg..Lrlievekedlkelp.klvellr 103
                                       ++ +++   +l   +++ + ++++    L+G  G+GK   +k++ ++++e+g     i+v+ +d+ +l  ++++ l+
  gi|242399132|ref|YP_002994556.1|  42 IHVYQEVDMRLSMMISEIIGNQSSIAFSLVGPLGMGKTQRLKTIYKTISEQGgkAIYIKVDTNDILKLTrDMFNGLK 118
                                       55555666666666677777777777889***********************6555678888888887537999999 PP

                            DUF815 104 erperfilfvDDLs 117
                                         ++r  +f   Ls
  gi|242399132|ref|YP_002994556.1| 119 PPKTRTNIFFENLS 132
                                       99999999999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       775  (0.0432261); expected 358.6 (0.02)
Passed bias filter:                      627  (0.0349713); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.67u 0.32s 00:00:00.99 Elapsed: 00:00:00.48
# Mc/sec: 2533.64
//
Query:       gi|242399133|ref|YP_002994557.1|  [L=171]
Description: RNA-binding protein, containing THUMP domain [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-17   62.7   1.7    5.3e-17   62.3   1.7    1.2  1  THUMP     THUMP domain


Domain annotation for each model (and alignments):
>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.3   1.7   2.9e-21   5.3e-17      13     143 ..      33     159 ..      26     160 .. 0.77

  Alignments for each domain:
  == domain 1  score: 62.3 bits;  conditional E-value: 2.9e-21
                                       H-SEEEEETTEEEEECTEEEEEETHHHHHHHHHTST.TECEEEEEEEEEESSHHHHHHHHHHHHHHHHHHCT-EEEE CS
                             THUMP  13 nverveagkgrivvelkgekpeedeellkealekar.giqrvipvcevceadledileaakeivkkkfeeeketFaV 88 
                                       ++++++a++++++++ ++ ++  + e++ke     +  i +v+p +  +  + e i e   ++ k++++ e+e+FaV
  gi|242399133|ref|YP_002994557.1|  33 DARVRRAKWRGVLIVKTRLEKDDALERIKEFD---TtAIFKVLPLEKLVMSKKEVIMEEGFAMAKERIK-ETESFAV 105
                                       6789999********98776444444444433...2467899999544444444444444444444443.445**** PP

                                       EEEESSSTSSSHHHHHHHHHHHHHHCCTT-EE-SSS-SEEEEEEEETTEEEEEEE CS
                             THUMP  89 rvkrrgkhfeftsreinrevGkaivektglkVdlenPdivvrveiikdkayisid 143
                                       r+krrg+    + +ei+ e+G+ i+e +++ Vdl+nPd+ v++e+++++++is+ 
  gi|242399133|ref|YP_002994557.1| 106 RCKRRGNW-ISSGKEIEIELGAKIKETINANVDLTNPDWYVWIEVLGKQTGISVI 159
                                       *******9.9******************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 1099.37
//
Query:       gi|242399134|ref|YP_002994558.1|  [L=241]
Description: Archaeosine biosynthesis protein queC [Thermococcus sibiricus MM 739]
Scores for complete 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-62  210.2   0.0    2.7e-62  210.0   0.0    1.0  1  QueC             Queuosine biosynthesis protein QueC
      2e-06   27.7   0.0    0.00014   21.7   0.0    2.1  2  ATP_bind_3       PP-loop family
    1.2e-05   25.0   0.0      0.039   13.5   0.0    2.3  2  ThiI             Thiamine biosynthesis protein (ThiI)
    4.1e-05   23.0   0.0    6.2e-05   22.5   0.0    1.2  1  Arginosuc_synth  Arginosuccinate synthase
     0.0013   18.2   0.0     0.0022   17.5   0.0    1.3  1  Diphthami_syn_2  Diphthamide synthase
  ------ inclusion threshold ------
      0.014   15.1   0.0      0.018   14.7   0.0    1.1  1  Asn_synthase     Asparagine synthase
      0.023   14.8   0.0      0.045   13.8   0.0    1.8  1  PAPS_reduct      Phosphoadenosine phosphosulfate reductase fa
      0.041   12.7   0.0      0.059   12.2   0.0    1.2  1  tRNA_Me_trans    tRNA methyl transferase
       0.13   12.6   0.1        2.3    8.6   0.0    2.1  2  Phage_int_SAM_5  Phage integrase SAM-like domain


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 !  210.0   0.0   1.3e-65   2.7e-62       1     207 [.       5     225 ..       5     228 .. 0.91

  Alignments for each domain:
  == domain 1  score: 210.0 bits;  conditional E-value: 1.3e-65
                                       EEEEE--SSHHHHHHHHHHHHH-SEEEEEEEESS-T.TSHHHHHHHHHHHHT--.-EEEEE-GGGGGGS...CGGG- CS
                              QueC   1 kavvllSGGlDSttvlalakkegkevealtfdYgqr.hkkeleaakkiakelgveehkildldllkelg...gsaLt 73 
                                       +avvl+SGGlDSt++l++ak++++ev++lt++Yg++ +k+ +++a+ ++kel++   ki++ld+l+e++   g++L+
  gi|242399134|ref|YP_002994558.1|   5 RAVVLFSGGLDSTACLYWAKENYDEVIMLTINYGSNeEKVINKIAEFFSKELNI-PLKIIHLDFLEEFSklrGTTLV 80 
                                       69**********************************66666777888899****.**********998766689999 PP

                                       -----.-----........--------TTHHHHHHHHHHHHHHHHT-SEEEE---S-STT--GGGSHHHHHHHHHHH CS
                              QueC  74 deeie.vpkeelee.....eelpntfVpaRNliflslaasyaealgaeaiiiGvneedfsgYPDcrdefvkalnkal 144
                                        +e+  v++++le+     e++++++VpaRNl+++s+aas+ +alg  +ii+G+n+e+  ++PD+++efv+++n++l
  gi|242399134|ref|YP_002994558.1|  81 GGETPkVTSKDLENtekaqETAKSVWVPARNLVLISVAASLLDALGGGDIIVGFNAEEGMTFPDNTPEFVEKMNNML 157
                                       988765777444444445599******************************************************** PP

                                       HHHHTS--EEE-TTTT--HHHHHHHHHHTTHHHHH-B-STTS......-BTTTTSSSHHHHHHHHHHH CS
                              QueC 145 nlgedkkieieaPlidlsKaeivklgkelgvpleetlsCYege.....eegkaCgeCdaCalRkkgfe 207
                                       ++g+ ++++++aPli lsK+ i++l ke g+++e++ sCY ++      +  +CgeC++C++R++g+ 
  gi|242399134|ref|YP_002994558.1| 158 KYGSMSDVKVVAPLIGLSKKGIARLLKEFGAKYEYSNSCYMPKgftedGKPIHCGECESCIRRHRGLV 225
                                       ******************************************9999777778**************86 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0     7e-08   0.00014       3      68 ..       7      67 ..       5      79 .. 0.85
   2 ?    4.0   0.0     0.019        37     126     164 ..     153     191 ..     139     198 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 7e-08
                                      EEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE--H CS
                        ATP_bind_3  3 lvAvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvkelckklnikleiekvdv 68
                                      +v +SgGlDS+a l++++++ +    +++++++++g   e k  +++ + ++k+lni+l+i ++d 
  gi|242399134|ref|YP_002994558.1|  7 VVLFSGGLDSTACLYWAKENYD----EVIMLTINYGSN-EEKVINKIAEFFSKELNIPLKIIHLDF 67
                                      7889*************99988....89*******975.567789999************999886 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.019
                                       HH-S-SEEEETTCCEE-CCCT--HHHHHHHHHHTT---B CS
                        ATP_bind_3 126 lagikeaseiasirlvRPlLkvskeeleeylkekkikwv 164
                                       +  + ++ +++++++v Pl+ +sk+ + ++lke + k+ 
  gi|242399134|ref|YP_002994558.1| 153 MNNMLKYGSMSDVKVVAPLIGLSKKGIARLLKEFGAKYE 191
                                       55566667778899******************9888885 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0   0.00044      0.88       5      58 ..       5      54 ..       2      79 .. 0.71
   2 !   13.5   0.0     2e-05     0.039     127     165 ..     154     193 ..     151     208 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00044
                              ThiI  5 kvlaLlSgGiDSpVaaylllkRGcrvvlvhlknepgtseeaiekveklaellae 58
                                      ++++L SgG+DS    y + +   +v ++++ n+  ++   +++++k+ae +++
  gi|242399134|ref|YP_002994558.1|  5 RAVVLFSGGLDSTACLYWAKENYDEVIMLTI-NYGSNE---EKVINKIAEFFSK 54
                                      7899*********999999988888888888.444444...4555666666555 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 2e-05
                              ThiI 127 eNlrvisavvnllilrPLigldKeeiiklAkeigt.yeis 165
                                       +N+    +++++ ++ PLigl+K+ i +l ke g  ye s
  gi|242399134|ref|YP_002994558.1| 154 NNMLKYGSMSDVKVVAPLIGLSKKGIARLLKEFGAkYEYS 193
                                       6777777899**********************99646666 PP

>> Arginosuc_synth  Arginosuccinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   3.1e-08   6.2e-05       2      63 ..       8      71 ..       7      76 .. 0.70

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 3.1e-08
                   Arginosuc_synth  2 LaysGGlDtsviikllkeklgeeviavavdvGqeeed.ldevke...kalklgavksvvvDakeef 63
                                      + +sGGlD + ++ + ke++ +evi ++++ G +ee+ +++++e   k l++  +k +  D  eef
  gi|242399134|ref|YP_002994558.1|  8 VLFSGGLDSTACLYWAKENY-DEVIMLTINYGSNEEKvINKIAEffsKELNIP-LKIIHLDFLEEF 71
                                      569*****************.9**********998762344443111333332.355556666666 PP

>> Diphthami_syn_2  Diphthamide synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   1.1e-06    0.0022       2      38 ..       5      42 ..       4      77 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.1e-06
                   Diphthami_syn_2  2 kvavlysGGkDsilaLykalke.sevesLvsvisenke 38
                                      +++vl+sGG Ds+  Ly+a ++  ev++L      n+e
  gi|242399134|ref|YP_002994558.1|  5 RAVVLFSGGLDSTACLYWAKENyDEVIMLTINYGSNEE 42
                                      789*****************996678888766666766 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0     9e-06     0.018      21      71 ..       7      53 ..       1      74 [. 0.88

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 9e-06
                      Asn_synthase 21 GalLSGGlDSSliaalaarqsksplktFsigfeekgsdeakyakevaehlg 71
                                       +l+SGGlDS++  + a++  + ++   +i +   gs+e k+  ++ae + 
  gi|242399134|ref|YP_002994558.1|  7 VVLFSGGLDSTACLYWAKENYD-EVIMLTINY---GSNEEKVINKIAEFFS 53
                                      5899****************98.9********...9***********9886 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.3e-05     0.045       2      57 ..       6      62 ..       5     192 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.3e-05
                                      EEEE--SSCTCHHHHHHHHHHCTTHEEEEEE-STB-HHHHHHHHHH.HHHTT-EEEE CS
                       PAPS_reduct  2 lvvsvsgGkdslVllhLalkafkpvpvvfvdtghefpetiefvdel.eeryglrlkv 57
                                       vv++sgG ds++ l  a ++ ++v ++ ++ g + +++i+ + e+ ++++++ lk+
  gi|242399134|ref|YP_002994558.1|  6 AVVLFSGGLDSTACLYWAKENYDEVIMLTINYGSNEEKVINKIAEFfSKELNIPLKI 62
                                      699**********************99999999999999998887614455777544 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.9e-05     0.059       3      67 ..       6      62 ..       4      85 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.9e-05
                     tRNA_Me_trans  3 vvvalSgGVDSsvaaallkeqgyevigvflklweeedeegkeccaeedlkdaervaeklgiplev 67
                                       vv++SgG DS+  ++  ke++ evi ++++  ++e++           k ae  +++l+ipl++
  gi|242399134|ref|YP_002994558.1|  6 AVVLFSGGLDSTACLYWAKENYDEVIMLTINYGSNEEKVI--------NKIAEFFSKELNIPLKI 62
                                      689***********************99998888765554........23345556666666554 PP

>> Phage_int_SAM_5  Phage integrase SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0    0.0012       2.3      18      56 ..      34      73 ..      19     112 .. 0.84
   2 ?    1.9   0.0      0.14   2.8e+02      35      74 ..     134     184 ..     130     193 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0012
                                      -HHHHHHHHHHHHHTTTS-...S---TTT--HHHHHHHHH CS
                   Phage_int_SAM_5 18 skgtlrnykstlkhlkkFl.kkkditfeeidkefleeFed 56
                                      + ++ +n +++++++ +F  k+ +i+++ i  +fleeF +
  gi|242399134|ref|YP_002994558.1| 34 TINYGSNEEKVINKIAEFFsKELNIPLKIIHLDFLEEFSK 73
                                      567778999**********56688**************75 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.14
                                       S-..S---TTT--HHHHHHHHHHH.....HHTS........---HHHHHHHHH CS
                   Phage_int_SAM_5  35 FlkkkditfeeidkefleeFedYL.....kkkk........glsentiskyfk 74 
                                       F+ ++ +tf + ++ef+e+  + L     +           gls+ +i++ +k
  gi|242399134|ref|YP_002994558.1| 134 FNAEEGMTFPDNTPEFVEKMNNMLkygsmS--DvkvvapliGLSKKGIARLLK 184
                                       77778899999999*999999888433331..033444555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      611  (0.0340789); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 1572.60
//
Query:       gi|242399135|ref|YP_002994559.1|  [L=107]
Description: hypothetical protein TSIB_1156 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); 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: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 674.11
//
Query:       gi|242399136|ref|YP_002994560.1|  [L=114]
Description: hypothetical protein TSIB_1157 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 789.12
//
Query:       gi|242399137|ref|YP_002994561.1|  [L=74]
Description: hypothetical protein TSIB_1158 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       255  (0.0142228); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 524.95
//
Query:       gi|242399138|ref|YP_002994562.1|  [L=69]
Description: hypothetical protein TSIB_1159 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.061   12.7   0.1      0.061   12.7   0.1    1.1  1  DUF5305   Family of unknown function (DUF5305)


Domain annotation for each model (and alignments):
>> DUF5305  Family of unknown function (DUF5305)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   3.4e-06     0.061      93     135 ..      27      67 ..       3      69 .] 0.78

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.4e-06
                           DUF5305  93 etdeengeitetvtvkespslaegilliilgllaliglvvlir 135
                                       e++++++++ et + +e+ ++    ++++l ++ali++++li+
  gi|242399138|ref|YP_002994562.1|  27 EEKNNQETLPETDKGTENSDQST--AICLLPIIALIAFILLIK 67 
                                       44567777777777777777766..99************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 494.07
//
Query:       gi|242399139|ref|YP_002994563.1|  [L=39]
Description: hypothetical proteinn [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       109  (0.00607954); expected 358.6 (0.02)
Passed bias filter:                       74  (0.00412739); expected 358.6 (0.02)
Passed Vit filter:                         2  (0.000111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 253.03
//
Query:       gi|242399140|ref|YP_002994564.1|  [L=195]
Description: hypothetical protein TSIB_1161 [Thermococcus sibiricus MM 739]
Scores for complete 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-64  214.5   0.3    8.4e-64  214.3   0.3    1.0  1  DUF99     Protein of unknown function DUF99
  ------ inclusion threshold ------
      0.093   13.1   0.0       0.15   12.4   0.0    1.3  1  DUF243    Domain of unknown function (DUF243)


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 !  214.3   0.3   9.4e-68   8.4e-64       2     183 .]       8     188 ..       7     188 .. 0.97

  Alignments for each domain:
  == domain 1  score: 214.3 bits;  conditional E-value: 9.4e-68
                                       GSEEEEEEEEE.......-SS-EEEEEEEEETT.EEEEEEEEEE-TT-S-HHHHHHHHHCC-TTTTEEEEEESSSEE CS
                             DUF99   2 eirvlGiddsffe..rkkkdgksvlvGvvmradrvvdgvafgrvtvdGtDateaiielvkrleredirvvlldGiti 76 
                                       +irv+G+dd++f+  +k k++k++lvGvvm++++ v gv+ + ++vdG+Date++ie + +++++d+r+++l+Git+
  gi|242399140|ref|YP_002994564.1|   8 QIRVIGFDDGTFSfkSKIKRDKTILVGVVMKGSQDVVGVVTRWIEVDGRDATEKMIEAIHNSRFKDLRIIMLKGITY 84 
                                       79**********9765558********************************************************** PP

                                       TTTEE--HHHHHHHH---EEEEESS---HHHHHHCCT.TSTTHHHHHHHHHHC.---EEETT....EEEEEESS-HH CS
                             DUF99  77 agFNvvDlerlheetglPviavtreepdlgklekaLrkhfpdeeeRlelieklgerieevektgeelyvravGiele 153
                                       agFNvvD+e+l++et +Pvi+v+r++pdl+++ekaL+khf+d+ee+++l++k+ ++i+e+    ++ly++a+G++ +
  gi|242399140|ref|YP_002994564.1|  85 AGFNVVDVEELSRETRMPVIIVIRKKPDLQAMEKALKKHFSDAEEKISLLHKA-GKIKELIP--GKLYYQAIGVSYD 158
                                       *****************************************************.******99..99*********** PP

                                       HHHHHHHHC-SSSSS-HHHHHHHHHHHHHH CS
                             DUF99 154 eaaklvrkltlegriPEPlRvAhliAsalv 183
                                       +a++++r +++ + iPEPlR+Ah+iAsa++
  gi|242399140|ref|YP_002994564.1| 159 QAEEIIRLTQKSSLIPEPLRLAHMIASAVM 188
                                       ***************************985 PP

>> DUF243  Domain of unknown function (DUF243)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.7e-05      0.15      16      90 ..      57     130 ..      51     133 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.7e-05
                            DUF243  16 eeeekeleqlakalkknykvvFikaPenkaleaaalalakqqaeekTviYVLskkadeaelakklaaieqtkssk 90 
                                       +++ek +e ++++  k+++++ +k+ +  +++   +++  +++    vi V+ kk+d ++++k+l++  + +++k
  gi|242399140|ref|YP_002994564.1|  57 DATEKMIEAIHNSRFKDLRIIMLKGITYAGFNVVDVEEL-SRETRMPVIIVIRKKPDLQAMEKALKKHFSDAEEK 130
                                       456777888899999****************99999999.7788889**************99999877766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       792  (0.0441742); expected 358.6 (0.02)
Passed bias filter:                      596  (0.0332422); 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: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.54
# Mc/sec: 1084.86
//
Query:       gi|242399141|ref|YP_002994565.1|  [L=104]
Description: Divalent cation tolerance protein [Thermococcus sibiricus MM 739]
Scores for complete 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-32  109.6   0.2    5.9e-32  109.5   0.2    1.0  1  CutA1     CutA1 divalent ion tolerance protein


Domain annotation for each model (and alignments):
>> CutA1  CutA1 divalent ion tolerance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.5   0.2   3.3e-36   5.9e-32       1      97 [.       5     100 ..       5     102 .. 0.97

  Alignments for each domain:
  == domain 1  score: 109.5 bits;  conditional E-value: 3.3e-36
                                       EEEEEEESSHHHHHHHHHHHHHTTS-SEEEEEEEEEEEEEETTEEEEEEEEEEEEEEEGGGHHHHHHHHHHHSSSSS CS
                             CutA1   1 vlvlvtapseeeakklaralveeklaACvnilpkieSvYrWkgkieedkEvllliktreekveelekrvkelhpyev 77 
                                       +lv++t+p+ e+a++++++l+e++l+AC+n+ +  +++Y+W+g+ie+d+E+  l+kt+ + ++el+++++elhpy+v
  gi|242399141|ref|YP_002994565.1|   5 ILVYTTFPNWESAERITKELLERRLIACANLRE-HKAFYWWQGQIENDNEIGALLKTKVDLWSELKDALRELHPYTV 80 
                                       589***************************887.******************************************* PP

                                       -EEEEEEESEEEHHHHHHHH CS
                             CutA1  78 peiialpieagseaYlkWie 97 
                                       p+ii +++++++++Yl+W+ 
  gi|242399141|ref|YP_002994565.1|  81 PAIIRIDVDHVNKEYLNWLL 100
                                       ******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); 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: 0.54u 0.34s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 592.81
//
Query:       gi|242399142|ref|YP_002994566.1|  [L=91]
Description: Acylphosphatase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-26   92.7   0.1    1.5e-26   92.6   0.1    1.0  1  Acylphosphatase  Acylphosphatase


Domain annotation for each model (and alignments):
>> Acylphosphatase  Acylphosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.6   0.1   8.6e-31   1.5e-26       2      84 ..       7      88 ..       6      89 .. 0.96

  Alignments for each domain:
  == domain 1  score: 92.6 bits;  conditional E-value: 8.6e-31
                   Acylphosphatase  2 rllvtGrVQgvgFRkfvrrlAkelglkGyvrNlsdgsVeivaegeeekvekfleelksgppkarvdeveveeleeeeef 80
                                      +l+++GrVQgvgFR+ ++r+Ak+lg++G+vrNl++gsVe+v+ege+e ve+++ + ++gp  arv++vev +++ ++e 
  gi|242399142|ref|YP_002994566.1|  7 HLRIYGRVQGVGFRWSMQREAKKLGVNGWVRNLPNGSVEAVIEGERERVEALIGWAHQGPSWARVTRVEVGWETPKGE- 84
                                      689*********************************************************************999998. PP

                   Acylphosphatase 81 kdFe 84
                                      k+F+
  gi|242399142|ref|YP_002994566.1| 85 KGFR 88
                                      9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       284  (0.0158403); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 678.48
//
Query:       gi|242399143|ref|YP_002994567.1|  [L=197]
Description: hypothetical protein TSIB_1164 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       698  (0.0389313); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); 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: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 1149.88
//
Query:       gi|242399144|ref|YP_002994568.1|  [L=662]
Description: hypothetical protein TSIB_1165 [Thermococcus sibiricus MM 739]
Scores for complete 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-49  165.3   0.1    1.9e-48  163.7   0.1    1.9  1  DUF460      Protein of unknown function (DUF460)
    2.5e-05   24.6   0.0    6.3e-05   23.3   0.0    1.6  1  acVLRF1     Actinobacteria/chloroflexi VLRF1 release factor
  ------ inclusion threshold ------
        1.3    9.4   9.5       0.26   11.6   3.5    3.1  2  TSC22       TSC-22/dip/bun family
        1.9    9.2  16.5        0.3   11.8   6.2    3.8  4  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 !  163.7   0.1   4.3e-52   1.9e-48       1     141 []     209     349 ..     209     349 .. 0.97

  Alignments for each domain:
  == domain 1  score: 163.7 bits;  conditional E-value: 4.3e-52
                            DUF460   1 kvkskdvkvevesvekdkiefeplkkkr....kkklivGiDPGittgiavldldgevlalkssreldreevielise 73 
                                       ++++ d++v++++ve++++ef+plk++r    +k++ivG+DPGit+gia+ldl+g+vl ++s+r++  ++vi++ise
  gi|242399144|ref|YP_002994568.1| 209 PMRGGDIEVRIRPVERKTFEFVPLKSERaireRKSVIVGLDPGITVGIAALDLNGQVLMTYSERNMAISDVIKFISE 285
                                       5899*******************9888788889******************************************** PP

                            DUF460  74 lGkpvivAtDvspppetvkklarslkavlyvPeedlsveeKeelaeklsekekvkykddHeRDalaAA 141
                                       +G+p+i++tDv+p+p +v+k+ars+ka l+vP+e+l+veeK+el+++      v+++ddH+RDal+AA
  gi|242399144|ref|YP_002994568.1| 286 IGHPIIISTDVNPAPGLVEKIARSFKALLFVPRESLKVEEKNELLRN----LGVTVEDDHQRDALTAA 349
                                       ***********************************************....77889***********8 PP

>> acVLRF1  Actinobacteria/chloroflexi VLRF1 release factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   1.4e-08   6.3e-05      13      68 ..     123     173 ..     111     190 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 1.4e-08
                           acVLRF1  13 favgvveggelvaskvgtrdvqgrtaaGGwSqqRfaRrrenqadalleavaeaaar 68 
                                       ++v  +e++ + ++++g++       +GGwSq R+ Rr  n +++ +++++e++++
  gi|242399144|ref|YP_002994568.1| 123 YEVLAFEDEVIIKVSRGRS-----QGKGGWSQDRYRRRLHNLIQNKVREIEETLKK 173
                                       6666666555555555554.....479***********************999876 PP

>> TSC22  TSC-22/dip/bun family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1       2.3     1e+04      32      42 ..     322     332 ..     320     334 .. 0.79
   2 ?   11.6   3.5   5.8e-05      0.26      21      46 ..     423     448 ..     422     461 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.3
                             TSC22  32 eleeENslLka 42 
                                       ++ee N+lL++
  gi|242399144|ref|YP_002994568.1| 322 KVEEKNELLRN 332
                                       56889999996 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 5.8e-05
                             TSC22  21 ekIkeLeernseleeENslLkalasp 46 
                                       ekIkeLe++++ le+EN+ L+a++ +
  gi|242399144|ref|YP_002994568.1| 423 EKIKELEKTIEFLEKENQELRAMIEE 448
                                       79*******************98765 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1       3.1   1.4e+04      41      53 ..     158     170 ..     150     175 .. 0.53
   2 ?    0.3   0.0      0.24   1.1e+03      24      55 ..     344     375 ..     340     380 .. 0.80
   3 ?   11.8   6.2   6.6e-05       0.3       3      50 ..     423     470 ..     422     483 .. 0.90
   4 ?    1.3   0.1      0.12   5.3e+02       2      27 ..     481     506 ..     480     515 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 3.1
                                       HHHHHT-XXXXXX CS
                              SlyX  41 rllaerlkelees 53 
                                       +l++++++e+ee+
  gi|242399144|ref|YP_002994568.1| 158 NLIQNKVREIEET 170
                                       3344566666665 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.24
                                       HHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXX CS
                              SlyX  24 dvvaeqqqqidrlqrqlrllaerlkeleessg 55 
                                       d++++  +   rl+ +l+++  +l+ele + +
  gi|242399144|ref|YP_002994568.1| 344 DALTAAYKAYLRLKPKLDHVDAKLRELEIEGK 375
                                       77888888889999999999999999997755 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 6.6e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXX CS
                              SlyX   3 erleeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkel 50 
                                       e+++eLE  + f+e+  +eL +++ eq++ i+ l+++++   e+++e 
  gi|242399144|ref|YP_002994568.1| 423 EKIKELEKTIEFLEKENQELRAMIEEQRKIIENLETKIATYDEKIREK 470
                                       689**************************************9999764 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 0.12
                                       HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              SlyX   2 eerleeLEiklafqedtieeLndvva 27 
                                       e+r+  LE +l      ie+L++ ++
  gi|242399144|ref|YP_002994568.1| 481 EKRIAYLEKELREAKSIIEKLSKDLV 506
                                       67888888888888888888887554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (662 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2463  (0.137375); expected 358.6 (0.02)
Passed bias filter:                      871  (0.0485805); expected 358.6 (0.02)
Passed Vit filter:                       129  (0.00719505); 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):               4  [number of targets reported over threshold]
# CPU time: 0.96u 0.34s 00:00:01.30 Elapsed: 00:00:00.53
# Mc/sec: 3765.09
//
Query:       gi|242399145|ref|YP_002994569.1|  [L=50]
Description: hypothetical protein TSIB_1166 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 297.04
//
Query:       gi|242399146|ref|YP_002994570.1|  [L=337]
Description: Pyruvate formate-lyase activating enzyme [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-11   45.4   0.1      2e-11   44.5   0.1    1.4  1  Radical_SAM     Radical SAM superfamily
     0.0024   17.9   0.2     0.0024   17.9   0.2    3.1  3  DZR             Double zinc ribbon
     0.0085   16.2   0.1     0.0085   16.2   0.1    1.9  2  DiS_P_DiS       Bacterial Peptidase A24 N-terminal domain
  ------ inclusion threshold ------
      0.018   15.0   0.8       0.94    9.5   0.0    3.4  3  ADK_lid         Adenylate kinase, active site lid
       0.15   11.8   5.7        1.6    8.5   0.1    3.5  3  zinc_ribbon_2   zinc-ribbon domain
       0.17   11.0   0.1       0.17   11.0   0.1    2.1  2  CoiA            Competence protein CoiA-like family
        0.2   11.5   0.0        0.2   11.5   0.0    4.1  4  zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
       0.33   10.4   0.1       0.33   10.4   0.1    3.4  3  zf-ribbon_3     zinc-ribbon domain
       0.69   10.0   5.9      0.098   12.7   0.8    2.3  2  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
        1.2    8.8   5.7        3.2    7.4   0.2    3.1  3  zf_UBZ          Ubiquitin-Binding Zinc Finger
        1.6    8.9  10.7       0.43   10.7   1.5    3.4  3  UPF0547         Uncharacterised protein family UPF0547
        6.4    7.0   9.2        2.8    8.1   0.0    3.6  4  Zn-ribbon_8     Zinc ribbon domain
        7.7    6.9   9.4       0.62   10.4   1.0    2.5  2  DUF2039         Uncharacterized conserved protein (DUF2039)


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.5   0.1   1.5e-14     2e-11       6     142 ..      80     207 ..      76     229 .. 0.86

  Alignments for each domain:
  == domain 1  score: 44.5 bits;  conditional E-value: 1.5e-14
                                       EESS--TTTSCCTT..HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEE CS
                                       xxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   6 gCnlrCsfCarpet..vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiri 80 
                                       gCn+ C++C++++   ++  +  r+ ++ee+++++ + +     +++  +  ep+  + +  ++++la +  +g+  
  gi|242399146|ref|YP_002994570.1|  80 GCNFYCPWCQNYHLsfSKLPENTRETPPEELVDLALRSR----NDGLCASFNEPTTLYTYLLDTFELAGR--RGLYS 150
                                       9***********999999*****************9998....99*************************..7**** PP

                                       EEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  81 tvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagi 142
                                       +++tng+    + l+rl e g   +s++++   + kvl  +    +  +v ++ + + ++g 
  gi|242399146|ref|YP_002994570.1| 151 CLVTNGYFT-TKALRRLIESGASGFSIDIKGCPKMKVLSTV----DHRKVFRNAKEALNLGA 207
                                       ********8.*********************9998666666....34555555555555554 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   2.2       1.3   1.8e+03      26      41 ..      11      26 ..       4      34 .. 0.75
   2 ?    0.3   0.3      0.51   7.1e+02      13      20 ..      83      90 ..      80     104 .. 0.80
   3 !   17.9   0.2   1.7e-06    0.0024       9      40 ..     289     330 ..     286     335 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.3
                               DZR 26 aaedrCpsCgekvdpe 41
                                      ++ ++C  C++ ++ +
  gi|242399146|ref|YP_002994570.1| 11 NETIKCLVCERRCSIK 26
                                      4478899999998765 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.51
                               DZR 13 rfCseCgt 20
                                       +C++C++
  gi|242399146|ref|YP_002994570.1| 83 FYCPWCQN 90
                                      57888875 PP

  == domain 3  score: 17.9 bits;  conditional E-value: 1.7e-06
                               DZR   9 ppdarfCseCgtklkavaa..........edrCpsCgekvdp 40 
                                       +++  +C++Cg+kl   ++           +rCp+C++k++ 
  gi|242399146|ref|YP_002994570.1| 289 KHETTYCPTCGEKLVIRSEyrvlkwnlekDNRCPRCSQKIPI 330
                                       56788********97555599****************99875 PP

>> DiS_P_DiS  Bacterial Peptidase A24 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.4       6.7   9.2e+03      54      64 ..      15      25 ..      13      44 .. 0.66
   2 !   16.2   0.1   6.2e-06    0.0085      22      64 ..     287     330 ..     230     335 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 6.7
                         DiS_P_DiS 54 rCraCkakisl 64
                                      +C  C+++ s+
  gi|242399146|ref|YP_002994570.1| 15 KCLVCERRCSI 25
                                      45555555544 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 6.2e-06
                         DiS_P_DiS  22 slvkprSrCpkCghklkwleliPvlSylllr.grCraCkakisl 64 
                                       s+ ++   Cp+Cg+kl ++    vl + l +  rC +C++ki++
  gi|242399146|ref|YP_002994570.1| 287 SVKHETTYCPTCGEKLVIRSEYRVLKWNLEKdNRCPRCSQKIPI 330
                                       7778899********************886638*********97 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 ?    1.6   0.1       0.2   2.8e+02       4      25 ..      85     124 ..      83     132 .. 0.65
   2 ?    9.5   0.0   0.00068      0.94      20      35 ..     291     306 ..     270     306 .. 0.89
   3 ?   -1.4   0.1       1.7   2.4e+03      20      29 ..     317     326 ..     312     328 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.2
                                       -TTT--EEETTT.B--S..................STTB-T CS
                           ADK_lid   4 CpkCGrsYhvvf.npPk..................veglCD 25 
                                       Cp C+  Yh+ f + P                   ++glC 
  gi|242399146|ref|YP_002994570.1|  85 CPWCQ-NYHLSFsKLPEntretppeelvdlalrsrNDGLCA 124
                                       66664.59988877787566666656666666666777775 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00068
                                       STTB-TTT--.-B--G CS
                           ADK_lid  20 veglCDkCGepLvqRs 35 
                                       +   C  CGe+Lv Rs
  gi|242399146|ref|YP_002994570.1| 291 ETTYCPTCGEKLVIRS 306
                                       5678***********7 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 1.7
                                       STTB-TTT-- CS
                           ADK_lid  20 veglCDkCGe 29 
                                       +++ C  C+ 
  gi|242399146|ref|YP_002994570.1| 317 KDNRCPRCSQ 326
                                       6888999976 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.2       0.3   4.2e+02       1       7 [.      84      90 ..      84      94 .. 0.75
   2 ?    8.5   0.1    0.0012       1.6      14      23 .]     293     302 ..     288     306 .. 0.72
   3 ?    2.9   0.2      0.07        97       1       7 [.     320     326 ..     314     330 .. 0.61

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.3
                     zinc_ribbon_2  1 fCpnCGa 7 
                                      +Cp C +
  gi|242399146|ref|YP_002994570.1| 84 YCPWCQN 90
                                      6888865 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0012
                     zinc_ribbon_2  14 kFCpyCGtpl 23 
                                       ++Cp CG++l
  gi|242399146|ref|YP_002994570.1| 293 TYCPTCGEKL 302
                                       5677777665 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.07
                     zinc_ribbon_2   1 fCpnCGa 7  
                                       +Cp+C  
  gi|242399146|ref|YP_002994570.1| 320 RCPRCSQ 326
                                       4666655 PP

>> CoiA  Competence protein CoiA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -5.0   2.7       8.7   1.2e+04      27      48 ..       9      30 ..       5      33 .. 0.85
   2 ?   11.0   0.1   0.00013      0.17      28      45 ..     289     306 ..     267     323 .. 0.85

  Alignments for each domain:
  == domain 1  score: -5.0 bits;  conditional E-value: 8.7
                              CoiA 27 qkkerfyCpaCksklvikiGsq 48
                                      +++e + C +C+ +  ik G++
  gi|242399146|ref|YP_002994570.1|  9 KYNETIKCLVCERRCSIKEGKK 30
                                      6888999************987 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00013
                              CoiA  28 kkerfyCpaCksklviki 45 
                                       k+e  yCp+C++klvi++
  gi|242399146|ref|YP_002994570.1| 289 KHETTYCPTCGEKLVIRS 306
                                       68899***********97 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 ?   -2.9   2.4       4.5   6.3e+03       3      20 ..      15      32 ..      13      37 .. 0.75
   2 ?    1.4   0.1       0.2   2.8e+02       3       8 ..      84      89 ..      82      94 .. 0.79
   3 ?   11.5   0.0   0.00015       0.2       3      15 ..     294     306 ..     292     309 .. 0.89
   4 ?    1.7   0.2      0.17   2.3e+02       2      11 ..     319     328 ..     318     330 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 4.5
                                      E-SSS--EEEEEE-SSSE CS
                    zf-C4_Topoisom  3 kCPkCggdLvlkrgkkGk 20
                                      kC  C     +k+gkkG 
  gi|242399146|ref|YP_002994570.1| 15 KCLVCERRCSIKEGKKGI 32
                                      777788888899999984 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.2
                                      E-SSS- CS
                    zf-C4_Topoisom  3 kCPkCg 8 
                                       CP+C 
  gi|242399146|ref|YP_002994570.1| 84 YCPWCQ 89
                                      5****8 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.00015
                                       E-SSS--EEEEEE CS
                    zf-C4_Topoisom   3 kCPkCggdLvlkr 15 
                                        CP Cg++Lv+++
  gi|242399146|ref|YP_002994570.1| 294 YCPTCGEKLVIRS 306
                                       7**********97 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.17
                                       EE-SSS--EE CS
                    zf-C4_Topoisom   2 ekCPkCggdL 11 
                                       + CP C +++
  gi|242399146|ref|YP_002994570.1| 319 NRCPRCSQKI 328
                                       68****9875 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.3      0.26   3.6e+02      19      23 ..      85      89 ..      83      94 .. 0.84
   2 ?   10.4   0.1   0.00024      0.33       1      11 [.     291     302 ..     291     307 .. 0.81
   3 ?    1.6   0.4      0.15     2e+02       4       8 ..     320     324 ..     317     329 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.26
                       zf-ribbon_3 19 CpyCG 23
                                      Cp+C+
  gi|242399146|ref|YP_002994570.1| 85 CPWCQ 89
                                      89996 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00024
                       zf-ribbon_3   1 stvrCPnCGa.p 11 
                                       +t++CP CG+ +
  gi|242399146|ref|YP_002994570.1| 291 ETTYCPTCGEkL 302
                                       589******955 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.15
                       zf-ribbon_3   4 rCPnC 8  
                                       rCP+C
  gi|242399146|ref|YP_002994570.1| 320 RCPRC 324
                                       89999 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.4         5   6.9e+03       2       5 ..      85      88 ..      84      89 .. 0.79
   2 ?   12.7   0.8   7.1e-05     0.098       2      22 ..     295     323 ..     294     326 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 5
                    DNA_ligase_ZBD  2 CPvC 5 
                                      CP C
  gi|242399146|ref|YP_002994570.1| 85 CPWC 88
                                      9998 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 7.1e-05
                    DNA_ligase_ZBD   2 CPvCGsavv.Ree......g.eaiyRCtn 22 
                                       CP CG ++v R e      + e + RC++
  gi|242399146|ref|YP_002994570.1| 295 CPTCGEKLViRSEyrvlkwNlEKDNRCPR 323
                                       *********99996666552799999998 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       1.4   1.9e+03       3      12 ..      83      92 ..      82     100 .. 0.69
   2 ?    2.8   0.1     0.065        89       2      12 ..     292     302 ..     291     307 .. 0.81
   3 ?    7.4   0.2    0.0023       3.2       4      14 ..     320     330 ..     317     332 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.4
                            zf_UBZ  3 ylCerCgkei 12
                                      + C+ C+ + 
  gi|242399146|ref|YP_002994570.1| 83 FYCPWCQNYH 92
                                      88**998765 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.065
                            zf_UBZ   2 tylCerCgkei 12 
                                       t  C+ Cg+++
  gi|242399146|ref|YP_002994570.1| 292 TTYCPTCGEKL 302
                                       678*****986 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0023
                            zf_UBZ   4 lCerCgkeipe 14 
                                        C+rC ++ip+
  gi|242399146|ref|YP_002994570.1| 320 RCPRCSQKIPI 330
                                       6********96 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.3       2.5   3.5e+03       3       7 ..      85      89 ..      84      90 .. 0.61
   2 ?    2.7   0.1     0.098   1.4e+02      17      21 ..     295     299 ..     287     303 .. 0.63
   3 ?   10.7   1.5   0.00031      0.43       2      12 ..     320     330 ..     320     330 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2.5
                           UPF0547  3 CPeCe 7 
                                      CP C+
  gi|242399146|ref|YP_002994570.1| 85 CPWCQ 89
                                      66664 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.098
                           UPF0547  17 CphCG 21 
                                       Cp CG
  gi|242399146|ref|YP_002994570.1| 295 CPTCG 299
                                       55555 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00031
                           UPF0547   2 vCPeCeakvPv 12 
                                       +CP+C++k+P+
  gi|242399146|ref|YP_002994570.1| 320 RCPRCSQKIPI 330
                                       6*********7 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   1.0       4.8   6.6e+03      15      33 ..       3      20 ..       2      24 .. 0.51
   2 ?   -1.1   0.1       1.6   2.2e+03      29      34 ..      85      90 ..      82      97 .. 0.73
   3 ?    8.1   0.0    0.0021       2.8      26      36 ..     291     302 ..     284     305 .. 0.73
   4 ?    2.8   0.0     0.095   1.3e+02      25      34 ..     317     326 ..     307     329 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 4.8
                       Zn-ribbon_8 15 fevlqsisdaplta.CPeCg 33
                                      fe l++    ++t  C  C 
  gi|242399146|ref|YP_002994570.1|  3 FENLCEKY--NETIkCLVCE 20
                                      55555433..2444477775 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.6
                       Zn-ribbon_8 29 CPeCgs 34
                                      CP C+ 
  gi|242399146|ref|YP_002994570.1| 85 CPWCQN 90
                                      888864 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0021
                       Zn-ribbon_8  26 lta.CPeCgsev 36 
                                       +t+ CP+Cg+++
  gi|242399146|ref|YP_002994570.1| 291 ETTyCPTCGEKL 302
                                       6677*****954 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.095
                       Zn-ribbon_8  25 pltaCPeCgs 34 
                                       ++  CP+C +
  gi|242399146|ref|YP_002994570.1| 317 KDNRCPRCSQ 326
                                       4556****76 PP

>> DUF2039  Uncharacterized conserved protein (DUF2039)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   1.9       0.7   9.6e+02      52      75 ..      11      35 ..       2      41 .. 0.77
   2 ?   10.4   1.0   0.00045      0.62      28      63 ..     291     327 ..     268     330 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.7
                           DUF2039 52 tkkkkCvkCeek.tvkkaYhkiCkk 75
                                      +++ kC  Ce++ ++k+  + iC++
  gi|242399146|ref|YP_002994570.1| 11 NETIKCLVCERRcSIKEGKKGICRN 35
                                      4667999999884588888888875 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00045
                           DUF2039  28 vegvCerCkdkieWkvkykkYk.altkkkkCvkCeek 63 
                                        ++ C +C +k+  + +y+  k +l+k ++C +C++k
  gi|242399146|ref|YP_002994570.1| 291 ETTYCPTCGEKLVIRSEYRVLKwNLEKDNRCPRCSQK 327
                                       4567888999998998888887345688889999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       870  (0.0485247); expected 358.6 (0.02)
Passed bias filter:                      570  (0.0317921); 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):              13  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.51
# Mc/sec: 1995.56
//
Query:       gi|242399147|ref|YP_002994571.1|  [L=331]
Description: ATPase, PP-loop superfamily [Thermococcus sibiricus MM 739]
Scores for complete 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   58.7   0.0    1.4e-15   57.5   0.0    1.7  1  ATP_bind_3     PP-loop family
    9.7e-05   22.5   0.0    0.00024   21.2   0.0    1.7  1  PAPS_reduct    Phosphoadenosine phosphosulfate reductase fami
    0.00038   19.4   0.0     0.0007   18.5   0.0    1.4  1  tRNA_Me_trans  tRNA methyl transferase
     0.0088   16.3   1.2      0.088   13.0   0.1    2.9  3  CTU2           Cytoplasmic tRNA 2-thiolation protein 2
  ------ inclusion threshold ------
       0.01   15.4   0.0      0.022   14.3   0.0    1.7  1  QueC           Queuosine biosynthesis protein QueC
       0.01   15.0   0.0      0.018   14.2   0.0    1.4  1  NAD_synthase   NAD synthase
      0.021   14.5   0.0      0.056   13.1   0.0    1.6  2  Asn_synthase   Asparagine synthase
      0.032   13.7   1.2      0.032   13.7   1.2    2.8  3  zn-ribbon_14   Zinc-ribbon
       0.07   13.0   0.9       0.07   13.0   0.9    2.6  4  zf-trcl        Probable zinc-ribbon domain
      0.086   13.2   0.3      0.086   13.2   0.3    3.0  3  C1_2           C1 domain
        5.4    6.9   8.1        6.4    6.6   0.5    3.3  3  zinc_ribbon_2  zinc-ribbon domain
        9.4    5.9  11.1       0.66    9.6   1.8    2.7  3  RecR           RecR protein


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 !   57.5   0.0   9.7e-19   1.4e-15       2     162 ..      60     238 ..      59     257 .. 0.82

  Alignments for each domain:
  == domain 1  score: 57.5 bits;  conditional E-value: 9.7e-19
                                       EEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE--H........HH CS
                        ATP_bind_3   2 vlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvkelckklnikleiekvdv........ak 70 
                                       ++v+vSgG DS++Ll++l+kl++k+ ++++ai++d g+     e  e+ k+ +kkl+i+++i +++           
  gi|242399147|ref|YP_002994571.1|  60 IAVGVSGGKDSVVLLHILHKLSQKFPFEIIAITIDEGIEGYRPESVEIAKRNAKKLGIEHKIYSFKEyigfsldeTV 136
                                       78****************************************************************999**999834 PP

                                       CTTSTCCCHHH........HHHHHHHHHCHHCCT.CEEE---BHHHHHHHHHHHHCCT--CCHHH-S-SEEEETT.. CS
                        ATP_bind_3  71 kkgknleeaAR........elRYevlkealkkegievlllAhhadDqaEtfllrlargsglaglagikeaseias.. 137
                                       +   ++e++ R         +R  +++ a++  +++ l+++h+ dD + +fl+++ rg   +     + ++ i++  
  gi|242399147|ref|YP_002994571.1| 137 SIMGSFEKRERvgacsycgVWRRWLINYAAQDLEADKLAVGHNLDDEVQMFLMNVMRGDVARLGRTGPYYEVIHEgl 213
                                       445666666663322222268999**********************************9987666666666666623 PP

                                       CCEE-CCCT--HHHHHHHHHHTT-- CS
                        ATP_bind_3 138 irlvRPlLkvskeeleeylkekkik 162
                                       +  + Pl +v  +e+  y+  ++i+
  gi|242399147|ref|YP_002994571.1| 214 VPRIKPLREVPEKEIVLYAILNNIE 238
                                       4556799999999988887766665 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   1.6e-07   0.00024       2     154 ..      60     238 ..      59     240 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.6e-07
                                       EEEE--SSCTCHHHHHHHHHHCTTH....EEEEEE-STB..-HHHHHHHHHHHHHTT-EEEEEE-SCHHHHHHHHHH CS
                       PAPS_reduct   2 lvvsvsgGkdslVllhLalkafkpv....pvvfvdtghe..fpetiefvdeleeryglrlkvyepeeevaekinaek 72 
                                       ++v vsgGkds+Vllh++ k  +++      + +d g e   pe +e  ++ ++++g++ k+y+ +e +  ++ +  
  gi|242399147|ref|YP_002994571.1|  60 IAVGVSGGKDSVVLLHILHKLSQKFpfeiIAITIDEGIEgyRPESVEIAKRNAKKLGIEHKIYSFKEYIGFSLDETV 136
                                       6889******************997555568999999885569****************888877777666666665 PP

                                       -S-THHHC.......HHHHHHTHHHHHHHHHCTTECEEE----CCCTTTTTTSSSEEECTTT-S............. CS
                       PAPS_reduct  73 hgsslyee.......aaeriaKveplkkaLekldedalltGaRrdesksraklpiveidedfek............. 129
                                            +e+        ++ + +   ++ a ++l++d l +G   d++ +   +++++ d +                
  gi|242399147|ref|YP_002994571.1| 137 SIMGSFEKrervgacSYCGVWRRWLINYAAQDLEADKLAVGHNLDDEVQMFLMNVMRGDVARLGrtgpyyevihegl 213
                                       55555666668888888888888888888888888888888888888888888888877775447888888888887 PP

                                       CEEE-CCCT--HHHHHHHHHHCT-- CS
                       PAPS_reduct 130 slrvfPllnWteedvwqyilrenip 154
                                       + r+ Pl +  e+++  y+  +ni+
  gi|242399147|ref|YP_002994571.1| 214 VPRIKPLREVPEKEIVLYAILNNIE 238
                                       7788888888888888888888886 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   4.7e-07    0.0007       2     125 ..      59     179 ..      58     195 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 4.7e-07
                     tRNA_Me_trans   2 kvvvalSgGVDSsvaaallkeqgyevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdfeke..yke 76 
                                       +++v++SgG DS v +++l++  ++    +++++ +e+ eg      e ++ a+r a+klgi++++ +f++   +  
  gi|242399147|ref|YP_002994571.1|  59 RIAVGVSGGKDSVVLLHILHKLSQKFPFEIIAITIDEGIEG---YRPESVEIAKRNAKKLGIEHKIYSFKEYigFSL 132
                                       89*****************9988777666666655555555...78899********************87423555 PP

                     tRNA_Me_trans  77 kvfeefleeyeeGrTPnPdvlCNkeiKfgallekakeelgadalatGHY 125
                                       +   +++ ++e+ +    +  C   +  + l+++a ++l+ad+la GH 
  gi|242399147|ref|YP_002994571.1| 133 DETVSIMGSFEKRERVGACSYCG--VWRRWLINYAAQDLEADKLAVGHN 179
                                       55556778999999999999995..778889999999999999999995 PP

>> CTU2  Cytoplasmic tRNA 2-thiolation protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1       1.3     2e+03      44      82 ..       9      47 ..       6      56 .. 0.68
   2 ?   -2.1   0.0       2.9   4.4e+03      41      53 ..     125     156 ..      96     174 .. 0.62
   3 !   13.0   0.1   5.9e-05     0.088       7      55 ..     256     303 ..     253     331 .] 0.71

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.3
                              CTU2 44 tsekCalCglplddkakewkrtitiselseteseeekee 82
                                      ++ kC+ Cg ++  +a+ + +    ++ +e+++++ k++
  gi|242399147|ref|YP_002994571.1|  9 RKMKCTKCGREAVYHARYEGKFYCHKHFNEMVESKVKQT 47
                                      567899999988777777666666666666666665555 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.9
                              CTU2  41 e...................letsekCalCgl 53 
                                       +                    e+   C+ Cg+
  gi|242399147|ref|YP_002994571.1| 125 KeyigfsldetvsimgsfekRERVGACSYCGV 156
                                       34555555555555555544566677888875 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 5.9e-05
                              CTU2   7 ekFilklekdfpstvstvvrTgeKLvknksseeaeletsekCalCglpl 55 
                                       +++i+++e++ p t   ++r+ +K+    +++ a  ++ ++C++C+ p 
  gi|242399147|ref|YP_002994571.1| 256 RDWINEMEEKHPGTKYQILRSYDKMFPLLAKAYA-NRDLNRCKICDQPT 303
                                       689*********************9988776544.56777777777776 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.5e-05     0.022       4      70 ..      62     130 ..      59     185 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.5e-05
                                       EE--SSHHHHHHHHHHHHH-....SEEEEEEEESS-T..TSHHHHHHHHHHHHT--.-EEEEE-GGGGGGSCG CS
                              QueC   4 vllSGGlDSttvlalakkeg....kevealtfdYgqr..hkkeleaakkiakelgveehkildldllkelggs 70 
                                       v +SGG DS ++l + +k       e++a+t+d g    + + +e+ak+ ak+lg+ ehki + +   e  g 
  gi|242399147|ref|YP_002994571.1|  62 VGVSGGKDSVVLLHILHKLSqkfpFEIIAITIDEGIEgyRPESVEIAKRNAKKLGI-EHKIYSFK---EYIGF 130
                                       679*********99988765223469********99875667799***********.99987765...44444 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.2e-05     0.018       7      88 ..      42     131 ..      36     151 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.2e-05
                                       HHHHHHHHHCTT....SEEEEEE-SSHHHHHHHHHHHHHHTC..GEEEEEE--..SSSTTHHHHHHHHHHHHHHTSE CS
                      NAD_synthase   7 dflkeyvkkaga....kgvvlGlSGGvDSslvaalavkalgk..envlalllP..ssvsseedvedalalaenlgie 75 
                                         +k+ v+k+g     + + +G+SGG DS +   +  k+ +k   +++a+ +    +   +e+ve a+  a++lgie
  gi|242399147|ref|YP_002994571.1|  42 SKVKQTVRKYGLikrgDRIAVGVSGGKDSVVLLHILHKLSQKfpFEIIAITIDegIEGYRPESVEIAKRNAKKLGIE 118
                                       56777777777643336799**********99998888775411578999998423345899*************** PP

                                       EEE---HHHHHHH CS
                      NAD_synthase  76 vktidikpivraf 88 
                                        k ++ k+++  +
  gi|242399147|ref|YP_002994571.1| 119 HKIYSFKEYIGFS 131
                                       *****99988655 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   3.8e-05     0.056      20      82 ..      60     127 ..      40     148 .. 0.78
   2 ?   -2.0   0.0       1.5   2.2e+03     285     321 ..     238     275 ..     220     296 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.8e-05
                      Asn_synthase  20 vGalLSGGlDSSliaalaarqsk.splktFsigfee....kgsdeakyakevaehlgtehtelvltee 82 
                                       +++  SGG DS ++ +++ + s+  p+   +i+ +e     + + ++ ak+ a++lg+eh  + ++e 
  gi|242399147|ref|YP_002994571.1|  60 IAVGVSGGKDSVVLLHILHKLSQkFPFEIIAITIDEgiegYRPESVEIAKRNAKKLGIEHKIYSFKEY 127
                                       66778****************997455555555533343355566799************99988875 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.5
                      Asn_synthase 285 Kegfsa.pvgewklkgelrelaeellsdsrlakeglld 321
                                        ++fs  p +   +++e+r++++e+ ++ + +k+++l+
  gi|242399147|ref|YP_002994571.1| 238 EVDFSEcPYAVEAFRAEIRDWINEMEEKHPGTKYQILR 275
                                       56677777778888899999999988888888877654 PP

>> zn-ribbon_14  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   1.4     0.099   1.5e+02       2       7 ..      12      17 ..      11      18 .. 0.88
   2 ?   -1.3   0.2       1.1   1.6e+03       1       8 [.     149     156 ..     149     157 .. 0.82
   3 ?   13.7   1.2   2.1e-05     0.032       1      19 [.     294     312 ..     294     313 .. 0.94

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.099
                      zn-ribbon_14  2 kCerCG 7 
                                      kC++CG
  gi|242399147|ref|YP_002994571.1| 12 KCTKCG 17
                                      9****9 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.1
                      zn-ribbon_14   1 gkCerCGy 8  
                                       g C+ CG 
  gi|242399147|ref|YP_002994571.1| 149 GACSYCGV 156
                                       57****95 PP

  == domain 3  score: 13.7 bits;  conditional E-value: 2.1e-05
                      zn-ribbon_14   1 gkCerCGylSSqkiCkACv 19 
                                       ++C+ C+  +  ++CkAC+
  gi|242399147|ref|YP_002994571.1| 294 NRCKICDQPTTGEVCKACN 312
                                       69****************7 PP

>> zf-trcl  Probable zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.9   4.7e-05      0.07       4      30 ..      10      37 ..       7      41 .. 0.88
   2 ?   -2.8   0.1       4.3   6.4e+03       6      14 ..     150     158 ..     147     161 .. 0.76
   3 ?   -1.9   0.2       2.1   3.2e+03      34      39 ..     294     299 ..     287     304 .. 0.75
   4 ?   -2.4   0.2       3.1   4.6e+03       6      11 ..     307     312 ..     305     314 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.7e-05
                           zf-trcl  4 tltCkdCgaefvFtag.eQeFyaekgfd 30
                                      +++C++Cg+e v+ a  e +Fy  k f+
  gi|242399147|ref|YP_002994571.1| 10 KMKCTKCGREAVYHARyEGKFYCHKHFN 37
                                      689***********9669******9995 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.3
                           zf-trcl   6 tCkdCgaef 14 
                                        C  Cg + 
  gi|242399147|ref|YP_002994571.1| 150 ACSYCGVWR 158
                                       599999875 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 2.1
                           zf-trcl  34 kRCkaC 39 
                                        RCk C
  gi|242399147|ref|YP_002994571.1| 294 NRCKIC 299
                                       578777 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 3.1
                           zf-trcl   6 tCkdCg 11 
                                       +Ck C+
  gi|242399147|ref|YP_002994571.1| 307 VCKACN 312
                                       677775 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.7      0.14   2.1e+02      15      35 ..       7      32 ..       2      37 .. 0.65
   2 ?   -1.1   0.0       1.6   2.4e+03      15      25 ..     145     155 ..     132     160 .. 0.79
   3 ?   13.2   0.3   5.7e-05     0.086      17      44 ..     292     317 ..     280     318 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.14
                              C1_2 15 ssesfnCsaCgrk....idgff....YsC 35
                                      +  +++C  Cgr+        +    ++C
  gi|242399147|ref|YP_002994571.1|  7 EARKMKCTKCGREavyhA---RyegkFYC 32
                                      567899******974321...21334555 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.6
                              C1_2  15 ssesfnCsaCg 25 
                                       ++  + Cs Cg
  gi|242399147|ref|YP_002994571.1| 145 RERVGACSYCG 155
                                       55567899997 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 5.7e-05
                              C1_2  17 esfnCsaCgrkidgffYsCseCdfslhv 44 
                                       +  +C++C+++++g+   C+ C+f+l v
  gi|242399147|ref|YP_002994571.1| 292 DLNRCKICDQPTTGE--VCKACNFKLQV 317
                                       5689*******9999..9*99***9965 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   0.5    0.0043       6.4       1       8 [.      12      19 ..      12      21 .. 0.89
   2 ?    3.4   0.2     0.044        66      15      20 ..     150     155 ..     144     156 .. 0.82
   3 ?   -1.2   0.1       1.3   1.9e+03       2      10 ..     308     316 ..     307     319 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0043
                     zinc_ribbon_2  1 fCpnCGae 8 
                                      +C++CG+e
  gi|242399147|ref|YP_002994571.1| 12 KCTKCGRE 19
                                      7*****97 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.044
                     zinc_ribbon_2  15 FCpyCG 20 
                                        C+yCG
  gi|242399147|ref|YP_002994571.1| 150 ACSYCG 155
                                       5****9 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.3
                     zinc_ribbon_2   2 CpnCGaelq 10 
                                       C+ C  +lq
  gi|242399147|ref|YP_002994571.1| 308 CKACNFKLQ 316
                                       999998886 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.3       5.7   8.4e+03      18      23 ..      12      17 ..      11      17 .. 0.82
   2 ?    2.4   0.1     0.081   1.2e+02      13      23 ..     145     155 ..     143     158 .. 0.88
   3 ?    9.6   1.8   0.00044      0.66      13      35 ..     290     312 ..     287     313 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 5.7
                                      E-TTT- CS
                              RecR 18 hCsrCg 23
                                       C +Cg
  gi|242399147|ref|YP_002994571.1| 12 KCTKCG 17
                                      599997 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.081
                                       HHH-EE-TTT- CS
                              RecR  13 kekvrhCsrCg 23 
                                       +e+v+ Cs Cg
  gi|242399147|ref|YP_002994571.1| 145 RERVGACSYCG 155
                                       799*******9 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00044
                                       HHH-EE-TTT--EESSSS-CCCC CS
                              RecR  13 kekvrhCsrCgnlteedlCaICs 35 
                                        +++ +C++C   t+ ++C  C+
  gi|242399147|ref|YP_002994571.1| 290 NRDLNRCKICDQPTTGEVCKACN 312
                                       567889****************5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       943  (0.0525964); expected 358.6 (0.02)
Passed bias filter:                      710  (0.0396006); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 2370.60
//
Query:       gi|242399148|ref|YP_002994572.1|  [L=71]
Description: hypothetical protein TSIB_1169 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00018   20.4   0.1    0.00021   20.3   0.1    1.0  1  Spore_permease   Spore germination protein
     0.0021   18.3   0.5     0.0024   18.1   0.5    1.1  1  DUF948           Bacterial protein of unknown function (DUF94
     0.0069   16.1   1.3     0.0084   15.9   1.3    1.1  1  DivIC            Septum formation initiator
  ------ inclusion threshold ------
      0.016   14.4   0.1      0.018   14.3   0.1    1.0  1  DLP_helical      Dynamin-like helical domain
      0.018   14.9   1.5      0.022   14.6   1.5    1.1  1  betaPIX_CC       betaPIX coiled coil
      0.018   15.3   0.0      0.022   15.1   0.0    1.1  1  DUF4064          Protein of unknown function (DUF4064)
      0.019   15.6   0.6      0.022   15.4   0.6    1.1  1  DUF3139          Protein of unknown function (DUF3139)
      0.026   14.5   0.0      0.028   14.4   0.0    1.0  1  Cytomega_TRL10   Cytomegalovirus TRL10 protein
      0.041   14.0   0.0      0.041   14.0   0.0    1.1  1  PEP-utilisers_N  PEP-utilising enzyme, N-terminal
      0.045   13.4   0.0      0.055   13.1   0.0    1.2  1  ABC_membrane     ABC transporter transmembrane region
       0.06   13.8   0.1      0.063   13.7   0.1    1.1  1  SecD-TM1         SecD export protein N-terminal TM region
      0.062   12.1   0.0      0.065   12.0   0.0    1.0  1  DUF2207          Predicted membrane protein (DUF2207)
      0.066   13.0   0.5      0.075   12.9   0.5    1.0  1  Spc29            Spindle Pole Component 29
      0.069   13.6   0.8      0.099   13.1   0.8    1.2  1  FeoB_associated  FeoB-associated Cys-rich membrane protein
      0.085   12.7   2.7        0.1   12.5   2.7    1.2  1  CAMSAP_CC1       Spectrin-binding region of Ca2+-Calmodulin
      0.091   12.8   0.0      0.099   12.6   0.0    1.1  1  Cpta_toxin       Membrane-bound toxin component of toxin-anti
        0.1   13.0   2.9       0.13   12.7   2.9    1.2  1  FlaC_arch        Flagella accessory protein C (FlaC)
       0.11   12.8   0.0       0.11   12.7   0.0    1.1  1  DUF4381          Domain of unknown function (DUF4381)
       0.16   12.0   3.7        0.2   11.7   3.7    1.2  1  Bap31_Bap29_C    Bap31/Bap29 cytoplasmic coiled-coil domain
       0.16   12.2   0.1       0.18   12.0   0.1    1.1  1  WXG100           Proteins of 100 residues with WXG
       0.43   10.6   4.7        4.7    7.3   1.2    2.1  2  SNARE            SNARE domain
        7.5    6.4   6.9         39    4.1   7.0    1.8  1  DUF2570          Protein of unknown function (DUF2570)


Domain annotation for each model (and alignments):
>> Spore_permease  Spore germination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.1   2.5e-07   0.00021      32      61 ..      12      41 ..       7      52 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2.5e-07
                    Spore_permease 32 tpdgWisvllagiiililvllmlkllkkfp 61
                                      tp+gWis++l++ii ++lv  +++l k  +
  gi|242399148|ref|YP_002994572.1| 12 TPSGWISIILGLIILVVLVFAFYQLNKTLN 41
                                      799*********************998754 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 !   18.1   0.5     3e-06    0.0024      12      58 ..      24      70 ..      18      71 .] 0.88

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 3e-06
                            DUF948 12 vLviflivvllklkktldeaaatieelekqvdpilkevedllakvne 58
                                      ++ ++l+ ++ +l+ktl+e++  ie l++ ++++ k++e++ +k +e
  gi|242399148|ref|YP_002994572.1| 24 IILVVLVFAFYQLNKTLNEFKVEIERLKNALEETRKNTEEVKKKLEE 70
                                      5667899999******************9999999999999888765 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   1.3     1e-05    0.0084       3      48 ..      24      69 ..      21      71 .] 0.82

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1e-05
                                      XXXXXXXXXXXXXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                             DivIC  3 llfllllifgkkgllaykqlkqeiaalqaelaklkaeneeLeaevk 48
                                      +++++l++ + +   ++ + k ei++l++ l++ ++  ee +++++
  gi|242399148|ref|YP_002994572.1| 24 IILVVLVFAFYQLNKTLNEFKVEIERLKNALEETRKNTEEVKKKLE 69
                                      455666666666667899************************9887 PP

>> DLP_helical  Dynamin-like helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   2.2e-05     0.018     241     301 ..       4      63 ..       2      69 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.2e-05
                       DLP_helical 241 PWgAvkLAknlnkalaiiGavlelalevwdslkqskkekelkelkeelveklkdqrkeile 301
                                       PWg v +    +++++ii  ++ l + v+  ++  k  +e+k  +e l++ l+++rk++ e
  gi|242399148|ref|YP_002994572.1|   4 PWGGVYMST-PSGWISIILGLIILVVLVFAFYQLNKTLNEFKVEIERLKNALEETRKNTEE 63 
                                       999999988.89****9977999*********************************99765 PP

>> betaPIX_CC  betaPIX coiled coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   1.5   2.7e-05     0.022      33      74 ..      29      67 ..      27      71 .] 0.79

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.7e-05
                        betaPIX_CC 33 lVDtVYaLkdevqelkqenkklkksleeEqkaRkdLEkvvrk 74
                                      lV + Y+L   ++e+k e  +lk +lee +k     E+v +k
  gi|242399148|ref|YP_002994572.1| 29 LVFAFYQLNKTLNEFKVEIERLKNALEETRKN---TEEVKKK 67
                                      78899**********************97665...4443333 PP

>> DUF4064  Protein of unknown function (DUF4064)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   2.7e-05     0.022       9      43 ..      15      54 ..      14      70 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.7e-05
                           DUF4064  9 glIGgilgillglllllflfllssgefsqeltee.....q 43
                                      g+I++ilg+++ ++l++++ +l+++ ++++ ++e      
  gi|242399148|ref|YP_002994572.1| 15 GWISIILGLIILVVLVFAFYQLNKTLNEFKVEIErlknaL 54
                                      8********9999999998888877777666665654331 PP

>> DUF3139  Protein of unknown function (DUF3139)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.6   2.8e-05     0.022       5      55 ..      18      66 ..      15      71 .] 0.73

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.8e-05
                           DUF3139  5 iiililliillvivkvflglvgskpikkylan.kkldkylqekgykeddIks 55
                                       iil+l+i+++++   f  ++ +k ++++ ++ ++l++ l+e   + +++k+
  gi|242399148|ref|YP_002994572.1| 18 SIILGLIILVVLV---FAFYQLNKTLNEFKVEiERLKNALEETRKNTEEVKK 66
                                      4555555555444...44679999999999999*******888888888887 PP

>> Cytomega_TRL10  Cytomegalovirus TRL10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   3.4e-05     0.028      61     113 ..      15      67 ..       4      71 .] 0.83

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.4e-05
                    Cytomega_TRL10  61 gagsfvatlivllvvffviyareeeknntgtevdqclayrsltrkkleqhaak 113
                                       g  s++  li+l+v+ f  y  ++  n+   e++++    + trk  e+   k
  gi|242399148|ref|YP_002994572.1|  15 GWISIILGLIILVVLVFAFYQLNKTLNEFKVEIERLKNALEETRKNTEEVKKK 67 
                                       4458999****************************999999999998876555 PP

>> PEP-utilisers_N  PEP-utilising enzyme, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0     5e-05     0.041      26      54 ..      40      68 ..      17      71 .] 0.81

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5e-05
                                      .GGHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   PEP-utilisers_N 26 aedveaelerleeAlekvreelealaeka 54
                                       ++ + e+erl++Ale++r+  e++++k+
  gi|242399148|ref|YP_002994572.1| 40 LNEFKVEIERLKNALEETRKNTEEVKKKL 68
                                      456789******************98765 PP

>> ABC_membrane  ABC transporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   6.7e-05     0.055     131     171 ..       6      46 ..       3      65 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.7e-05
                                       HHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      ABC_membrane 131 gglivmfylgwkltlvllailpliilvsaviakilkklkkk 171
                                       gg+ ++  +gw   +++l+il+++++ ++ ++k+l+++k +
  gi|242399148|ref|YP_002994572.1|   6 GGVYMSTPSGWISIILGLIILVVLVFAFYQLNKTLNEFKVE 46 
                                       78999999****************************99976 PP

>> SecD-TM1  SecD export protein N-terminal TM region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   7.7e-05     0.063      11      59 ..      23      70 ..      10      71 .] 0.71

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.7e-05
                          SecD-TM1 11 lilvvlligllyalPnlygedpavqisaakatlkvdeatlskveqaLke 59
                                      li++v+l+ ++y l +   ++  v+i+  k++l+ + + +++v+++L+e
  gi|242399148|ref|YP_002994572.1| 23 LIILVVLVFAFYQLNKTL-NEFKVEIERLKNALEETRKNTEEVKKKLEE 70
                                      345555555555554444.5789***********************986 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0     8e-05     0.065     408     458 ..      10      57 ..       3      70 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8e-05
                           DUF2207 408 llvfllilllillliaiivlllfsrllgrrteeGaellakwkgFkkyLeDf 458
                                       ++++ +++++il+li+++vl+++   ++++++  +e + +++ +k+ Le+ 
  gi|242399148|ref|YP_002994572.1|  10 MSTPSGWISIILGLIILVVLVFA---FYQLNKTLNEFKVEIERLKNALEET 57 
                                       3788999999*****99999997...889999*************999843 PP

>> Spc29  Spindle Pole Component 29
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.5   9.2e-05     0.075     121     156 ..      35      70 ..      29      71 .] 0.92

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.2e-05
                             Spc29 121 elekklddqkleIkeLkreleqqrtvnseLqekvae 156
                                       +l+k l++ k+eI+ Lk++le+ r   +e ++k++e
  gi|242399148|ref|YP_002994572.1|  35 QLNKTLNEFKVEIERLKNALEETRKNTEEVKKKLEE 70 
                                       6899*****************************988 PP

>> FeoB_associated  FeoB-associated Cys-rich membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.8   0.00012     0.099       2      21 ..      18      37 ..      17      42 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00012
                   FeoB_associated  2 tiIVgliiaaavafvirrli 21
                                       iI glii+++++f+++ l 
  gi|242399148|ref|YP_002994572.1| 18 SIILGLIILVVLVFAFYQLN 37
                                      69**************9875 PP

>> CAMSAP_CC1  Spectrin-binding region of Ca2+-Calmodulin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   2.7   0.00012       0.1      14      40 ..      45      71 .]      32      71 .] 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00012
                        CAMSAP_CC1 14 selselrlkLEEKRRaIEaqKrkiEaa 40
                                       e+  l+  LEE R+  E+ K+k+E++
  gi|242399148|ref|YP_002994572.1| 45 VEIERLKNALEETRKNTEEVKKKLEEI 71
                                      577788888****************75 PP

>> Cpta_toxin  Membrane-bound toxin component of toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00012     0.099      32      72 ..      10      52 ..       7      68 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00012
                        Cpta_toxin 32 apwPedyallwllllllv..vfecvrsqrkikkrqGelvllad 72
                                      +  P++++ + l l++lv  vf +++ ++ +++ + e+  l++
  gi|242399148|ref|YP_002994572.1| 10 MSTPSGWISIILGLIILVvlVFAFYQLNKTLNEFKVEIERLKN 52
                                      5679999998887777661156667777889999888877665 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   2.9   0.00016      0.13       6      38 ..      37      69 ..      34      71 .] 0.61

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00016
                         FlaC_arch  6 EnklsklsteletvkkeneelsksveelkenVk 38
                                       + l+++++e+e +k+ +ee +k+ ee+k++ +
  gi|242399148|ref|YP_002994572.1| 37 NKTLNEFKVEIERLKNALEETRKNTEEVKKKLE 69
                                      566666666666666666666666666666554 PP

>> DUF4381  Domain of unknown function (DUF4381)
   #    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      19      63 ..      14      59 ..       6      71 .] 0.52

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00014
                           DUF4381 19 pGwwlllaalllllllvlalwllrrrkrnrreAlreLaalr....adea 63
                                       Gw  ++++l++l++lv+a+++l +  ++      e+++l+    ++++
  gi|242399148|ref|YP_002994572.1| 14 SGWISIILGLIILVVLVFAFYQLNKTLNE---FKVEIERLKnaleETRK 59
                                      47777776766677777777766655544...33333333311122223 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 ?   11.7   3.7   0.00025       0.2       2      25 ..      46      69 ..      45      71 .] 0.95

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00025
                     Bap31_Bap29_C  2 eiekLkkeLkkkkkDlealKkQae 25
                                      eie+Lk+ L++++k+ e +Kk+ e
  gi|242399148|ref|YP_002994572.1| 46 EIERLKNALEETRKNTEEVKKKLE 69
                                      9********************988 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 ?   12.0   0.1   0.00022      0.18      50      83 ..      37      70 ..      32      71 .] 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00022
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100 50 qaefeewkqaaqklvdaLeeisealkqaanafed 83
                                      +++++e+k ++++l++aLee++++++++++++e+
  gi|242399148|ref|YP_002994572.1| 37 NKTLNEFKVEIERLKNALEETRKNTEEVKKKLEE 70
                                      678999***********************99987 PP

>> SNARE  SNARE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   1.2    0.0058       4.7      37      52 ..      16      31 ..       8      32 .. 0.61
   2 ?    5.0   0.1      0.03        25       3      24 ..      47      68 ..      46      70 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0058
                                      XXXXXXXXXXXXXXXX CS
                             SNARE 37 lkciillilviillvv 52
                                      +  iil+++++++lv+
  gi|242399148|ref|YP_002994572.1| 16 WISIILGLIILVVLVF 31
                                      5666666666666665 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.03
                                      HHHHHHHHHHHHHHHHHHHHHH CS
                             SNARE  3 vDrIdtnVenaqsnveraqkeL 24
                                      + r+ +  e+++ n+e+++k+L
  gi|242399148|ref|YP_002994572.1| 47 IERLKNALEETRKNTEEVKKKL 68
                                      67888999**********9998 PP

>> DUF2570  Protein of unknown function (DUF2570)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   7.0     0.048        39       3      54 ..      17      69 ..      15      70 .. 0.50

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.048
                           DUF2570  3 ivgklaliilgLgvwlwsqs.qkidsLraenkaqaqlieeqqkanqrLteqLe 54
                                      i+  l+liil + v+ ++q  ++++  + e +   + +ee +k  ++++++Le
  gi|242399148|ref|YP_002994572.1| 17 ISIILGLIILVVLVFAFYQLnKTLNEFKVEIERLKNALEETRKNTEEVKKKLE 69
                                      55555666555555555554134555666655555555555555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2831  (0.157901); expected 358.6 (0.02)
Passed bias filter:                     1679  (0.0936472); expected 358.6 (0.02)
Passed Vit filter:                       336  (0.0187406); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.54u 0.34s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 452.76
//
Query:       gi|242399149|ref|YP_002994573.1|  [L=97]
Description: Transcriptional regulator, arsR family [Thermococcus sibiricus MM 739]
Scores for complete 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   51.9   0.2    8.2e-14   51.2   0.2    1.4  1  HTH_5           Bacterial regulatory protein, arsR family
    1.9e-13   50.2   0.0    2.7e-13   49.8   0.0    1.2  1  HTH_20          Helix-turn-helix domain
    1.1e-07   31.7   0.1    1.5e-07   31.2   0.1    1.2  1  TrmB            Sugar-specific transcriptional regulator TrmB
    2.3e-06   27.5   1.8      9e-06   25.6   1.8    1.8  1  PadR            Transcriptional regulator PadR-like family
    1.5e-05   24.8   0.5    1.5e-05   24.8   0.5    1.5  1  HTH_11          HTH domain
    0.00011   21.7   2.2    0.00059   19.3   0.2    2.4  2  HTH_24          Winged helix-turn-helix DNA-binding
    0.00014   22.0   0.1    0.00018   21.6   0.1    1.2  1  HTH_34          Winged helix DNA-binding domain
    0.00046   20.0   0.0    0.00074   19.4   0.0    1.4  1  MarR            MarR family
    0.00049   19.9   0.0    0.00067   19.5   0.0    1.3  1  MarR_2          MarR family
     0.0014   19.0   0.1       0.43   11.0   0.1    2.2  2  HTH_26          Cro/C1-type HTH DNA-binding domain
     0.0025   18.1   0.3     0.0082   16.5   0.1    1.7  2  Rrf2            Transcriptional regulator
     0.0036   17.0   0.3      0.031   13.9   0.1    2.1  2  HTH_41          Helix-turn-helix domain
     0.0042   17.6   0.1     0.0051   17.4   0.1    1.2  1  Mga             Mga helix-turn-helix domain
     0.0047   16.7   0.2     0.0087   15.8   0.2    1.5  1  HTH_23          Homeodomain-like domain
     0.0056   16.5   0.3     0.0072   16.1   0.3    1.3  1  HxlR            HxlR-like helix-turn-helix
     0.0093   16.1   0.1      0.018   15.2   0.1    1.4  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
  ------ inclusion threshold ------
      0.016   15.3   0.0      0.025   14.7   0.0    1.4  1  HTH_28          Helix-turn-helix domain
      0.018   14.6   0.0      0.049   13.2   0.0    1.7  2  HTH_CodY        CodY helix-turn-helix domain
       0.02   14.9   0.2      0.036   14.1   0.2    1.4  1  BLACT_WH        Beta-lactamase associated winged helix domain
      0.024   14.5   0.7      0.028   14.3   0.7    1.2  1  TFIIE_alpha     TFIIE alpha subunit
      0.024   14.7   0.1      0.032   14.3   0.1    1.3  1  DUF2250         Uncharacterized protein conserved in archaea 
      0.048   13.5   0.1       0.11   12.3   0.0    1.6  1  HTH_10          HTH DNA binding domain
      0.049   13.2   0.1      0.055   13.1   0.1    1.1  1  ArsR            ArsR transcriptional regulator
      0.068   13.2   0.0      0.093   12.8   0.0    1.3  1  HTH_29          Winged helix-turn helix
      0.088   13.1   0.0       0.11   12.8   0.0    1.2  1  HTH_Tnp_1       Transposase
      0.097   12.3   0.2       0.24   11.1   0.2    1.6  1  GntR            Bacterial regulatory proteins, gntR family
       0.19   11.7   2.5        2.3    8.2   2.0    2.2  2  HTH_36          Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.2   0.2   1.2e-16   8.2e-14       1      47 []      17      63 ..      17      63 .. 0.98

  Alignments for each domain:
  == domain 1  score: 51.2 bits;  conditional E-value: 1.2e-16
                                      SHHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5  1 dptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                      +p R+kILklL+++e +v ela+el++s+  +  HLkkL++aGLVe+
  gi|242399149|ref|YP_002994573.1| 17 NPVRIKILKLLCQKEWYVYELAKELEISRQLLYLHLKKLENAGLVES 63
                                      699******************************************96 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.8   0.0   4.1e-16   2.7e-13       2      57 ..      10      64 ..       9      66 .. 0.96

  Alignments for each domain:
  == domain 1  score: 49.8 bits;  conditional E-value: 4.1e-16
                                      HHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                            HTH_20  2 qiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevv 57
                                      +i eAL++PvR +il++L   ++  + ela++l++s++ l+ HL++Le agLve++
  gi|242399149|ref|YP_002994573.1| 10 KICEALSNPVRIKILKLL-CQKEWYVYELAKELEISRQLLYLHLKKLENAGLVESE 64
                                      799***************.**********************************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 !   31.2   0.1   2.3e-10   1.5e-07      15      64 ..      24      80 ..      23      84 .. 0.88

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 2.3e-10
                                      HHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.......TTEEEE CS
                              TrmB 15 laLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.......pklYra 64
                                      l+Ll++++  ++e+a+el+++r+  Y  L++Le++GlVe e +        +k+Yra
  gi|242399149|ref|YP_002994573.1| 24 LKLLCQKEWYVYELAKELEISRQLLYLHLKKLENAGLVESELRLepddpraKKYYRA 80
                                      58*************************************997656677777777776 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   1.8   1.4e-08     9e-06       1      64 [.      23      79 ..      23      82 .. 0.91

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1.4e-08
                                      HHHHHCCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-S.TSSS-EEEEE CS
                              PadR  1 iLalleeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglvesewees.gegpprkyYr 64
                                      iL+ll +++ y ye++kele +           lY  Lk+Le+ glvese + + ++ +++kyYr
  gi|242399149|ref|YP_002994573.1| 23 ILKLLCQKEWYVYELAKELEIS--------RQLLYLHLKKLENAGLVESELRLEpDDPRAKKYYR 79
                                      89****************9987........347*****************999978889999*98 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.5   2.3e-08   1.5e-05       3      48 ..      21      63 ..      19      67 .. 0.88

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 2.3e-08
                            HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvpIes 48
                                       +il+lL +++  +   eLA+eL++Sr+  + ++k+Le +g  +es
  gi|242399149|ref|YP_002994573.1| 21 IKILKLLCQKE--WYVYELAKELEISRQLLYLHLKKLENAG-LVES 63
                                      68999996666..99*************************9.5555 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.25   1.6e+02       3      14 ..      18      29 ..      16      31 .. 0.80
   2 !   19.3   0.2   8.9e-07   0.00059      22      48 .]      36      62 ..      36      62 .. 0.97

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.25
                            HTH_24  3 etdrkILelLqk 14
                                        ++kIL+lL +
  gi|242399149|ref|YP_002994573.1| 18 PVRIKILKLLCQ 29
                                      6689*****987 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 8.9e-07
                            HTH_24 22 eLAerlglSpstvnrrlkrLeeeGlIk 48
                                      eLA++l +S++ +  +lk+Le++Gl++
  gi|242399149|ref|YP_002994573.1| 36 ELAKELEISRQLLYLHLKKLENAGLVE 62
                                      8************************96 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.1   2.8e-07   0.00018       1      55 [.      19      72 ..      19      76 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 2.8e-07
                            HTH_34  1 vRlavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdkefkgkkp 55
                                      vR+++l +L ++++    el ++le++   L+ hlkkLe+ag +e ++ ++   p
  gi|242399149|ref|YP_002994573.1| 19 VRIKILKLLCQKEWYV-YELAKELEISRQLLYLHLKKLENAGLVESELRLEPDDP 72
                                      89********999876.589999*********************99988776655 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   1.1e-06   0.00074      12      50 ..      26      64 ..      17      74 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.1e-06
                                      HHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR 12 lyeqgplsvseLakklgvskstvtrvldrLekkGlieRs 50
                                      l +q + +v eLak l++s+  +   l++Le +Gl+e++
  gi|242399149|ref|YP_002994573.1| 26 LLCQKEWYVYELAKELEISRQLLYLHLKKLENAGLVESE 64
                                      446778899***************************975 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     1e-06   0.00067      24      55 ..      34      67 ..      18      76 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1e-06
                                      HHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE..E CS
                            MarR_2 24 vgelarrlglsksavsrilkrLvaaGLverr..p 55
                                      v ela++l +s++ +  +lk+L+ aGLve +   
  gi|242399149|ref|YP_002994573.1| 34 VYELAKELEISRQLLYLHLKKLENAGLVESElrL 67
                                      779*************************877542 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.025        17      39      50 ..       4      15 ..       3      18 .. 0.90
   2 !   11.0   0.1   0.00065      0.43       1      32 [.      22      53 ..      22      59 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.025
                            HTH_26 39 sldtLdkiCdaL 50
                                      s+++L+kiC+aL
  gi|242399149|ref|YP_002994573.1|  4 SIEELAKICEAL 15
                                      6799*******9 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00065
                            HTH_26  1 kLrelmadrgitkseLargtgisaatlsrlvk 32
                                      k+ +l+ +++  ++eLa+ ++is++ l+ ++k
  gi|242399149|ref|YP_002994573.1| 22 KILKLLCQKEWYVYELAKELEISRQLLYLHLK 53
                                      57799********************9998776 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0       1.6     1e+03      27      52 ..       4      30 ..       2      34 .. 0.76
   2 !   16.5   0.1   1.2e-05    0.0082      28      58 ..      34      64 ..      23      65 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 1.6
                                      -HHHHHH.HHTS-HHHHHHHHHHHHHT CS
                              Rrf2 27 sseeiae.rqnispsylekilakLrka 52
                                      s+ee+a+ +  +s ++  kil+ L ++
  gi|242399149|ref|YP_002994573.1|  4 SIEELAKiCEALSNPVRIKILKLLCQK 30
                                      678888866688888888999888776 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 1.2e-05
                                      HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              Rrf2 28 seeiaerqnispsylekilakLrkaglvksv 58
                                      + e+a++ +is++ l   l+kL++aglv+s+
  gi|242399149|ref|YP_002994573.1| 34 VYELAKELEISRQLLYLHLKKLENAGLVESE 64
                                      679**************************95 PP

>> HTH_41  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      0.59   3.9e+02       6      17 ..       2      13 ..       1      17 [. 0.85
   2 !   13.9   0.1   4.7e-05     0.031       9      39 ..      34      64 ..      33      66 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.59
                            HTH_41  6 lktIeelakele 17
                                      +++Ieelak +e
  gi|242399149|ref|YP_002994573.1|  2 VQSIEELAKICE 13
                                      689*****9887 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 4.7e-05
                            HTH_41  9 IeelakeleLSvGlvQkALklLeddkaisle 39
                                      + elakele+S+ l    Lk+Le+++ ++ e
  gi|242399149|ref|YP_002994573.1| 34 VYELAKELEISRQLLYLHLKKLENAGLVESE 64
                                      569***********************99765 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   7.7e-06    0.0051      17      65 ..      19      67 ..       3      76 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 7.7e-06
                                      HHHHHHHHHHHHSEEEHHHHHHHCT--HHHHHHHHHHHHHH.CHCCT-EE CS
                               Mga 17 lkyqllkflfeeeevsieelaqelyiSestlkrkikelnkl.Lkefdlel 65
                                      + +++lk+l  ++e  ++ela+el iS+  l+ ++k+l++  L e +l+l
  gi|242399149|ref|YP_002994573.1| 19 VRIKILKLLC-QKEWYVYELAKELEISRQLLYLHLKKLENAgLVESELRL 67
                                      5667777665.9*************************9764366666666 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.2   1.3e-05    0.0087       6      46 ..      19      60 ..      14      63 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.3e-05
                            HTH_23  6 eRlrillllae.GlsvreIAreLgvsrrTvyrwlkryreeGl 46
                                       R++il+ll +  + v e A+eL +sr+ +y  lk+ ++ Gl
  gi|242399149|ref|YP_002994573.1| 19 VRIKILKLLCQkEWYVYELAKELEISRQLLYLHLKKLENAGL 60
                                      59*****************************99999866775 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.3   1.1e-05    0.0072       9      53 ..      22      65 ..      14      87 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.1e-05
                                      HHHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEE CS
                              HxlR  9 lilvellkgkkRfselkralpkisqkmLaqrLreLeqdglierev 53
                                       il  l +++    el+++l +is+++L  +L++Le+ gl+e e 
  gi|242399149|ref|YP_002994573.1| 22 KILKLLCQKEWYVYELAKEL-EISRQLLYLHLKKLENAGLVESEL 65
                                      57777788888889******.********************9875 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 !   15.2   0.1   2.7e-05     0.018      23      50 ..      36      63 ..      32      67 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.7e-05
                    B-block_TFIIIC 23 dLakeskqdprslfyrlksLekkgLIvk 50
                                      +Lake++++   l+ +lk+Le+ gL++ 
  gi|242399149|ref|YP_002994573.1| 36 ELAKELEISRQLLYLHLKKLENAGLVES 63
                                      79************************85 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   3.7e-05     0.025       2      41 ..      20      60 ..      19      76 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.7e-05
                            HTH_28  2 RleiikllaaGh.svreaArelgisrrtvyrWikryeegGi 41
                                      R++i+kll + +  v e+A+el isr+ +y  +k++e  G+
  gi|242399149|ref|YP_002994573.1| 20 RIKILKLLCQKEwYVYELAKELEISRQLLYLHLKKLENAGL 60
                                      77777776665557889*********************886 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 ?   13.2   0.0   7.4e-05     0.049      10      36 ..      37      63 ..      33      66 .. 0.92
   2 ?   -2.7   0.1         7   4.6e+03      16      23 ..      87      94 ..      84      95 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.4e-05
                          HTH_CodY 10 iaDriGitrsvivnaLrkLesaGiies 36
                                      +a ++ i r  +   L+kLe aG++es
  gi|242399149|ref|YP_002994573.1| 37 LAKELEISRQLLYLHLKKLENAGLVES 63
                                      688999********************9 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 7
                          HTH_CodY 16 itrsvivn 23
                                      i   vivn
  gi|242399149|ref|YP_002994573.1| 87 IDNDVIVN 94
                                      66678888 PP

>> BLACT_WH  Beta-lactamase associated winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.2   5.4e-05     0.036      25      41 ..      48      64 ..      42      70 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.4e-05
                          BLACT_WH 25 vlahLeKLeeeGkVkre 41
                                      +++hL+KLe+ G+V++e
  gi|242399149|ref|YP_002994573.1| 48 LYLHLKKLENAGLVESE 64
                                      789***********976 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.7   4.2e-05     0.028      16      77 ..      21      81 ..       6      91 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.2e-05
                                      HHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTEEEEEEEEEE CS
                       TFIIE_alpha 16 vlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrdeekswykyywrin 77
                                      +++l+ L  + e    +lakel+i ++ l   L +L +a+lv+   r +++    k y+r  
  gi|242399149|ref|YP_002994573.1| 21 IKILKLLC-QKEWYVYELAKELEISRQLLYLHLKKLENAGLVESELRLEPDDPRAKKYYRAR 81
                                      56777777.55666679********************************8888888888765 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 ?   14.3   0.1   4.9e-05     0.032       7      54 ..      17      63 ..      11      81 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.9e-05
                           DUF2250  7 delalkvlkhlkkanvdYaksiakeleipleevrellkkLeelGLler 54
                                      +++ +k+lk l + +  Y   +akelei+++     lkkLe++GL+e 
  gi|242399149|ref|YP_002994573.1| 17 NPVRIKILKLLCQKE-WYVYELAKELEISRQLLYLHLKKLENAGLVES 63
                                      677888888887655.59999*************************96 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00017      0.11      27      49 ..      35      57 ..      29      58 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00017
                            HTH_10 27 keLAkelGIskstlsehLrkaes 49
                                       eLAkel Is++ l+ hL+k e+
  gi|242399149|ref|YP_002994573.1| 35 YELAKELEISRQLLYLHLKKLEN 57
                                      69*****************9886 PP

>> ArsR  ArsR transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   8.2e-05     0.055       3      76 ..       4      80 ..       2      93 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.2e-05
                              ArsR  3 dpveLvpllqvfdsetkkkvyeelsk.eWlteeeleeklgee...veealklLkkikliEsqWrmpepgekpekeYht 76
                                       + eL  + +++++++  k+++ l++ eW+   el+++l+ +       lk L++++l+Es  r        +k Y++
  gi|242399149|ref|YP_002994573.1|  4 SIEELAKICEALSNPVRIKILKLLCQkEWYV-YELAKELEISrqlLYLHLKKLENAGLVESELRLEPDDPRAKKYYRA 80
                                      57899999***************98626775.5677766655335667789999*********998877788888886 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00014     0.093       6      41 ..      26      60 ..      20      81 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00014
                            HTH_29  6 lllaeGvstvsqiAkllglsrrtvyrwlkrfeegGl 41
                                      ll+ ++++ v ++Ak l +sr+  y +lk  e+ Gl
  gi|242399149|ref|YP_002994573.1| 26 LLCQKEWY-VYELAKELEISRQLLYLHLKKLENAGL 60
                                      67788887.**********************99995 PP

>> HTH_Tnp_1  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00017      0.11      11      57 ..      19      66 ..      15      84 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00017
                         HTH_Tnp_1 11 fKariVreslepgksvsevArrhgvspnqLykWrrqyr.egeeaspae 57
                                      ++++i+++  +    v e+A+++++s++ Ly   ++ + +g+ +s+++
  gi|242399149|ref|YP_002994573.1| 19 VRIKILKLLCQKEWYVYELAKELEISRQLLYLHLKKLEnAGLVESELR 66
                                      78999999999********************98888887777777776 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   0.00036      0.24      29      57 ..      36      64 ..      33      66 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00036
                                      HHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              GntR 29 eLaaefgVsrttvReALrrLeaeglverr 57
                                      eLa+e+++sr+ +   L++Le +glve++
  gi|242399149|ref|YP_002994573.1| 36 ELAKELEISRQLLYLHLKKLENAGLVESE 64
                                      9*************************975 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.2      0.15        98      27      54 ..       4      32 ..       3      34 .. 0.77
   2 ?    8.2   2.0    0.0035       2.3      19      55 .]      29      61 ..      21      61 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.15
                            HTH_36 27 sqetlakrl.glsknTvsraikeLeqlGy 54
                                      s e lak + +ls    ++++k+L q+ +
  gi|242399149|ref|YP_002994573.1|  4 SIEELAKICeALSNPVRIKILKLLCQKEW 32
                                      56778888855666666899999999988 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0035
                            HTH_36 19 nknggcfpsqetlakrlglsknTvsraikeLeqlGyi 55
                                      +k+++    +  lak l++s++  + ++k+Le +G++
  gi|242399149|ref|YP_002994573.1| 29 QKEWY----VYELAKELEISRQLLYLHLKKLENAGLV 61
                                      55555....5679**********************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 668.75
//
Query:       gi|242399150|ref|YP_002994574.1|  [L=224]
Description: hypothetical protein TSIB_1171 [Thermococcus sibiricus MM 739]
Scores for complete 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-63  212.3   1.5    4.1e-63  212.1   1.5    1.0  1  DUF2202       Uncharacterized protein domain (DUF2202)
  ------ inclusion threshold ------
      0.015   15.7   0.0      0.029   14.8   0.0    1.6  1  Rubrerythrin  Rubrerythrin
      0.063   13.0   0.3        1.3    8.8   0.1    2.8  3  DnaB_2        Replication initiation and membrane attachment
       0.16   11.6   0.0       0.28   10.8   0.0    1.4  1  DUF3231       Protein of unknown function (DUF3231)


Domain annotation for each model (and alignments):
>> DUF2202  Uncharacterized protein domain (DUF2202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  212.1   1.5   9.1e-67   4.1e-63       1     159 [.      64     223 ..      64     224 .] 0.98

  Alignments for each domain:
  == domain 1  score: 212.1 bits;  conditional E-value: 9.1e-67
                           DUF2202   1 ekdsllymreeeklarDvYlelYdrwklqiflniakseqthtdavksllekYeledpvkederGkfedeelqelYnk 77 
                                       e++ +lymreeeklarDvYl lY++++l+if+niakseqth+dav  l+ekY+l+dp +    G f+ +e+qelY++
  gi|242399150|ref|YP_002994574.1|  64 EIEAILYMREEEKLARDVYLVLYNKTGLSIFNNIAKSEQTHMDAVLGLIEKYNLTDPLEGMGIGEFNSTEMQELYER 140
                                       6899************************************************************************* PP

                           DUF2202  78 LvekgsksledaLkvgatiedldiaDlekalketdnkdikevYenllkGsrnhlRsfvrklee.rgkeYepqyisee 153
                                       Lv++gs+  ++aLkvga+ie++di+Dl+++lk tdn+dik+v+  l  Gs+nhlR+f+r l+e +g  Y+pq +see
  gi|242399150|ref|YP_002994574.1| 141 LVAQGSEGEVEALKVGALIEEIDIKDLDEWLKRTDNEDIKAVFGSLRMGSENHLRAFTRLLREnYGVVYTPQVLSEE 217
                                       *************************************************************652799********** PP

                           DUF2202 154 efdeiv 159
                                       e++ iv
  gi|242399150|ref|YP_002994574.1| 218 EYESIV 223
                                       *****9 PP

>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   6.5e-06     0.029      10     136 ..      75     200 ..      66     201 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 6.5e-06
                                       HHHHHHHHHHHHHCHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSBBS-------TTGGHHHHHH CS
                      Rubrerythrin  10 EssarrlYkelaekakegypqiaelFeelAeeEreHakilnklleklepelelevkekvreyaeakpkflttaknLe 86 
                                       E  ar +Y  l+ k+         +F+ +A+ E+ H + +  l+ek++++     +   ++++  ++  +++++ + 
  gi|242399150|ref|YP_002994574.1|  75 EKLARDVYLVLYNKTG------LSIFNNIAKSEQTHMDAVLGLIEKYNLTDP--LEGMGIGEFNSTEMQELYERLVA 143
                                       6677888888888888......569***********************9988..34444444444444444444444 PP

                                       .......HHHHHHHHHHHCHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Rubrerythrin  87 .......eaiegayaeeeemyrfyeelaekegneeakklfkklaeaEkkHeerlrkl 136
                                              ea++ +   ee  ++ + e ++++ ne++k +f +l    + H + + +l
  gi|242399150|ref|YP_002994574.1| 144 qgsegevEALKVGALIEEIDIKDLDEWLKRTDNEDIKAVFGSLRMGSENHLRAFTRL 200
                                       4555666677776666777779*********************99999999999887 PP

>> DnaB_2  Replication initiation and membrane attachment
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.1    0.0003       1.3      11      41 ..      59      89 ..      57     110 .. 0.85
   2 ?   -2.0   0.0       0.7   3.1e+03      14      30 ..     102     118 ..      92     121 .. 0.78
   3 ?    0.7   0.0     0.097   4.4e+02       8      27 ..     155     174 ..     149     202 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0003
                                      S--HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            DnaB_2 11 plspseletilywlddlglspevilllleya 41
                                       lsp e+e ily+ ++ +l  +v l+l+ ++
  gi|242399150|ref|YP_002994574.1| 59 ELSPDEIEAILYMREEEKLARDVYLVLYNKT 89
                                      59*********************99998876 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.7
                                       HHHHHHHHHHHHHHHHH CS
                            DnaB_2  14 pseletilywlddlgls 30 
                                       ++ ++ +l ++++++l+
  gi|242399150|ref|YP_002994574.1| 102 QTHMDAVLGLIEKYNLT 118
                                       56778888889999887 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.097
                                       S-.S--HHHHHHHHHHHHHH CS
                            DnaB_2   8 fgrplspseletilywlddl 27 
                                        g ++ +++++++++wl+  
  gi|242399150|ref|YP_002994574.1| 155 VGALIEEIDIKDLDEWLKRT 174
                                       6778889999******9964 PP

>> DUF3231  Protein of unknown function (DUF3231)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   6.2e-05      0.28      30      72 ..     162     204 ..     146     218 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 6.2e-05
                           DUF3231  30 lgialitgFlqvaedkeikelleralelsnkhikelkelLkee 72 
                                       + i  +  +l+++++++ik+++   ++ s++h++ +++lL e+
  gi|242399150|ref|YP_002994574.1| 162 IDIKDLDEWLKRTDNEDIKAVFGSLRMGSENHLRAFTRLLREN 204
                                       55666778899*****************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); 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: 0.58u 0.36s 00:00:00.94 Elapsed: 00:00:00.53
# Mc/sec: 1277.62
//
Query:       gi|242399151|ref|YP_002994575.1|  [L=216]
Description: hypothetical protein TSIB_1172 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.8e-14   52.0   3.2    7.8e-14   52.0   3.2    2.3  3  DUF4405   Domain of unknown function (DUF4405)
    6.8e-07   29.0   0.2    9.8e-06   25.3   0.0    2.7  3  IF2_N     Translation initiation factor IF-2, N-terminal regi
  ------ inclusion threshold ------
        2.9    7.9   4.2        3.3    7.7   0.0    2.7  3  OppC_N    N-terminal TM domain of oligopeptide transport perm


Domain annotation for each model (and alignments):
>> DUF4405  Domain of unknown function (DUF4405)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.0   3.2   1.3e-17   7.8e-14       1      63 [.      17      80 ..      17      84 .. 0.96
   2 ?   -1.0   0.0      0.46   2.7e+03       9      20 ..      85      96 ..      81     104 .. 0.82
   3 ?   -2.5   0.0       1.3   7.7e+03      14      23 ..     144     153 ..     143     159 .. 0.77

  Alignments for each domain:
  == domain 1  score: 52.0 bits;  conditional E-value: 1.3e-17
                           DUF4405  1 iidlllllsflvlaiSGillsfavlpsgrgaywa...flglskhqwrdiHeilgllflilvvlHlg 63
                                      +idlll+++f++ +++Gi l+ a  psgr+a ++   flg++k+++  iH+++g+++ +lv++Hl+
  gi|242399151|ref|YP_002994575.1| 17 VIDLLLVVTFVAELFTGIGLYLA--PSGRIAETIgwtFLGFDKDTLDLIHTYFGFAMAGLVMVHLV 80
                                      69*******************99..******99999****************************97 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.46
                           DUF4405  9 sflvlaiSGill 20
                                      s+lv++ SG+  
  gi|242399151|ref|YP_002994575.1| 85 SMLVMLKSGFRK 96
                                      899999999865 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 1.3
                           DUF4405  14 aiSGillsfa 23 
                                        i+G ++ + 
  gi|242399151|ref|YP_002994575.1| 144 YITGTMMKYY 153
                                       5999999876 PP

>> IF2_N  Translation initiation factor IF-2, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.17     1e+03      40      53 ..      56      69 ..      55      70 .. 0.91
   2 !   25.3   0.0   1.6e-09   9.8e-06       4      39 ..     153     186 ..     150     190 .. 0.89
   3 ?   -0.7   0.0      0.22   1.3e+03      36      51 ..     192     207 ..     188     210 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.17
                             IF2_N 40 Deetaeliaeefgi 53
                                      D++t+ li  +fg+
  gi|242399151|ref|YP_002994575.1| 56 DKDTLDLIHTYFGF 69
                                      89**********96 PP

  == domain 2  score: 25.3 bits;  conditional E-value: 1.6e-09
                             IF2_N   4 irVyeLAkeLgvkskevikkLfkelGievkshsssL 39 
                                         V++LA+e +v+++++i+kL k  Gie +s++++L
  gi|242399151|ref|YP_002994575.1| 153 YIVRQLADEFNVEVTDLIEKLSK-NGIE-ASPDDTL 186
                                       5599*****************66.****.****998 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.22
                             IF2_N  36 sssLDeetaeliaeef 51 
                                       + +LD e+ ++ +ee+
  gi|242399151|ref|YP_002994575.1| 192 NYGLDHEEFKAMLEEI 207
                                       7899***999999987 PP

>> OppC_N  N-terminal TM domain of oligopeptide transport permease C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.2      0.24   1.4e+03      25      36 ..      20      31 ..      12      42 .. 0.70
   2 ?   -0.7   0.7      0.24   1.4e+03      16      27 ..      70      81 ..      69      84 .. 0.80
   3 ?    7.7   0.0   0.00056       3.3      10      39 ..      94     122 ..      89     136 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.24
                            OppC_N 25 lllliaifaPli 36
                                      lll++ ++a+l+
  gi|242399151|ref|YP_002994575.1| 20 LLLVVTFVAELF 31
                                      567777888777 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.24
                            OppC_N 16 Avvglvilllll 27
                                      A++glv++ l++
  gi|242399151|ref|YP_002994575.1| 70 AMAGLVMVHLVI 81
                                      9*****987665 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.00056
                            OppC_N  10 FkrNklAvvglvilllllliaifaPliaPy 39 
                                       F++ kl  v+ v++ llll+a + P++a y
  gi|242399151|ref|YP_002994575.1|  94 FRKSKLRTVAAVFVPLLLLVAGY-PVFAWY 122
                                       9********************88.888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       687  (0.0383178); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 1367.90
//
Query:       gi|242399152|ref|YP_002994576.1|  [L=290]
Description: hypothetical protein TSIB_1173 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-66  223.4   0.6    1.7e-66  223.1   0.6    1.1  1  DUF2202   Uncharacterized protein domain (DUF2202)


Domain annotation for each model (and alignments):
>> DUF2202  Uncharacterized protein domain (DUF2202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  223.1   0.6   9.3e-71   1.7e-66       1     161 [.      60     220 ..      60     221 .. 0.99

  Alignments for each domain:
  == domain 1  score: 223.1 bits;  conditional E-value: 9.3e-71
                           DUF2202   1 ekdsllymreeeklarDvYlelYdrwklqiflniakseqthtdavksllekYeledpvkederGkfedeelqelYnk 77 
                                       e+d+llym eeeklarDvYl+lY++w l +f nia+se th++av sl+ekY+l+ p++ d++G+f++eelq+lY++
  gi|242399152|ref|YP_002994576.1|  60 EIDGLLYMVEEEKLARDVYLTLYEQWSLPVFGNIAESEGTHMNAVLSLIEKYNLTAPDTLDQVGVFQNEELQALYDQ 136
                                       789************************************************************************** PP

                           DUF2202  78 LvekgsksledaLkvgatiedldiaDlekalketdnkdikevYenllkGsrnhlRsfvrkleergkeYepqyiseee 154
                                       Lve gs sle+aLkvga+ie+ di+Dle ++ +tdn+dik+vY nl++Gs+nhlR+fv +le+ g +Y++q + +e+
  gi|242399152|ref|YP_002994576.1| 137 LVEMGSASLEEALKVGALIEETDIKDLEDWIVQTDNEDIKTVYTNLMAGSENHLRAFVGQLERLGVDYTAQVLPQEQ 213
                                       ***************************************************************************** PP

                           DUF2202 155 fdeivss 161
                                       +dei+ss
  gi|242399152|ref|YP_002994576.1| 214 VDEILSS 220
                                       *****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); 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 0.30s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 1863.88
//
Query:       gi|242399153|ref|YP_002994577.1|  [L=38]
Description: hypothetical protein TSIB_1174 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      159  (0.00886831); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 244.30
//
Query:       gi|242399154|ref|YP_002994578.1|  [L=248]
Description: hypothetical protein TSIB_1175 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-06   26.7   0.2    8.2e-06   25.3   0.0    1.7  2  ATPase    KaiC
  ------ inclusion threshold ------
      0.057   13.5   0.2         15    5.8   0.0    2.7  2  FKBP26_C  FKBP26_C-terminal


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 !   25.3   0.0   9.2e-10   8.2e-06       1      98 [.       8     104 ..       8     138 .. 0.86
   2 ?   -1.0   0.0       0.1     9e+02     188     225 ..     209     246 ..     170     248 .] 0.80

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 9.2e-10
                            ATPase   1 vktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekl 77 
                                       +kt I+ lDe l gGi e+++vlit ++ +   ++a + l + +e+ g+ gv++    p + l  + k++  dl++ 
  gi|242399154|ref|YP_002994578.1|   8 IKTKIPQLDEALGGGILEDSIVLITYDTYSQGWTLAFEILRNRIED-GDFGVIINSVVPISMLNLELKRINFDLNEK 83 
                                       69***********************988777777899*********.****************************** PP

                            ATPase  78 eeegklaiidasesaeesaee 98 
                                        e+g l iid+++s  +++ e
  gi|242399154|ref|YP_002994578.1|  84 GENGDLGIIDIFASFYGIEYE 104
                                       *************99887666 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.1
                            ATPase 188 dlkeieeelvRtleivkmRgtkhskkehpfeIteegik 225
                                       d +++e++++  + i+k    + ++ +++f+I+++ + 
  gi|242399154|ref|YP_002994578.1| 209 DFNSQESQMEEKMLIRKSPLPSFKPTKLNFKIENGKVL 246
                                       55566778888999999999999999999999987665 PP

>> FKBP26_C  FKBP26_C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0    0.0017        15       5      35 ..       4      34 ..       3      38 .. 0.85
   2 ?    4.8   0.0    0.0033        30       6      33 ..     220     248 .]     218     248 .] 0.88

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0017
                                      HHHHHHHH-TT--..--EEEEETTEEEEE-- CS
                          FKBP26_C  5 ikelIkryiPnidlekfkieiedktvtIelp 35
                                      i elIk  iP++d       +ed++v I+ +
  gi|242399154|ref|YP_002994578.1|  4 IMELIKTKIPQLDEALGGGILEDSIVLITYD 34
                                      889**********777778889999999876 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0033
                                       HHHHHHH.-TT--..--EEEEETTEEEEE CS
                          FKBP26_C   6 kelIkry.iPnidlekfkieiedktvtIe 33 
                                       k lI +  +P  + +k++++ie+++v I+
  gi|242399154|ref|YP_002994578.1| 220 KMLIRKSpLPSFKPTKLNFKIENGKVLIT 248
                                       568877778*****************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); 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: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 1424.33
//
Query:       gi|242399155|ref|YP_002994579.1|  [L=170]
Description: Oxidoreductase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-32  111.2   0.2    3.7e-32  111.1   0.2    1.0  1  LDcluster4       SLOG cluster4 family
    1.4e-08   34.9   0.9    4.8e-07   29.9   0.2    2.2  2  Lysine_decarbox  Possible lysine decarboxylase
     0.0036   16.8   1.0        0.7    9.3   0.4    2.5  2  TPALS            TIR- and PNP-associating SLOG family
     0.0073   15.6   0.1        0.3   10.3   0.0    2.0  2  LSDAT_prok       SLOG in TRPM, prokaryote
  ------ inclusion threshold ------
      0.033   13.6   0.0      0.059   12.7   0.0    1.4  1  SPOUT_MTase_2    AF2226-like SPOUT RNA Methylase fused to THU


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 !  111.1   0.2     1e-35   3.7e-32       2     149 ..       2     151 ..       1     162 [. 0.88

  Alignments for each domain:
  == domain 1  score: 111.1 bits;  conditional E-value: 1e-35
                        LDcluster4   2 lkigVmGsaeteakeealelaeelGrliAk..egavlltGgrtGvmeaaskGakeagGltvGilpassekehsnkyv 76 
                                       ++i++ Gs++te  ++a+e+++e  +++Ak    +vlltGgr+G+me as+   + gGl+vGilp++++ ++ n+  
  gi|242399155|ref|YP_002994579.1|   2 IQIAIAGSSDTEPLPKAVEKTKEFIKELAKykDTVVLLTGGRGGIMEIASREFARFGGLVVGILPERQKGNEFNT-- 76 
                                       89********998999*************7335799******************************766666665.. PP

                        LDcluster4  77 diiiyTGlglagRnlilvlssdvviaiggrsGTlsEialaleegkpvivlkgt...dellseiiekkekderkviv 149
                                        i i TG+++a R+ i+++s+dv++++gg++GT+ E  +a++++k ++v+++t   ++ l+ ++++ + d++k+++
  gi|242399155|ref|YP_002994579.1|  77 -IRIKTGMDFAERSAIMINSADVLVVLGGGIGTMVEALMAYDYSKVLVVVTDTgypSDRLELLASNGYFDHKKLVQ 151
                                       .**************************************************9999988888888888888884443 PP

>> Lysine_decarbox  Possible lysine decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.9   0.0    0.0071        26      47      69 ..      27      49 ..      15      51 .. 0.84
   2 !   29.9   0.2   1.3e-10   4.8e-07       1      74 [.      47     117 ..      47     164 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0071
                                      HHHHHHESEEEE-S-SHHHHHHH CS
                   Lysine_decarbox 47 ealveladafvilPGGiGTleEl 69
                                      + l++++d +v+l GG G + E+
  gi|242399155|ref|YP_002994579.1| 27 KELAKYKDTVVLLTGGRGGIMEI 49
                                      56899*************88775 PP

  == domain 2  score: 29.9 bits;  conditional E-value: 1.3e-10
                                       HHHHHHHHHHTTS-EEEEEECCHHHHHCCTTT-SEEEEESSHHHHHHHHHHHESEEEE-S-SHHHHHHHHHHHH CS
                   Lysine_decarbox   1 meavakgaleaggrviGiipkillaeeapneevnelvivedmeeRkealveladafvilPGGiGTleElleilt 74 
                                       me +++  ++ gg v+Gi p+  +++e ++ +++   +  d++eR + +++ ad +v+l GGiGT+ E+l ++ 
  gi|242399155|ref|YP_002994579.1|  47 MEIASREFARFGGLVVGILPERQKGNEFNTIRIK---TGMDFAERSAIMINSADVLVVLGGGIGTMVEALMAYD 117
                                       7778888889999999999988888886666665...55699************************99987665 PP

>> TPALS  TIR- and PNP-associating SLOG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.7   0.0    0.0024       8.5       6      33 ..       4      31 ..       2      46 .. 0.92
   2 !    9.3   0.4    0.0002       0.7     125     152 ..      86     113 ..      65     125 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0024
                             TPALS  6 ihIaGSiskeaskaaverAhelvralvk 33
                                      i IaGS   e  ++ave+ +e++++l+k
  gi|242399155|ref|YP_002994579.1|  4 IAIAGSSDTEPLPKAVEKTKEFIKELAK 31
                                      89************************98 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0002
                             TPALS 125 gkrieaqarvgdalialGGgkGVsylAn 152
                                       ++r    ++ +d+l++lGGg G  + A 
  gi|242399155|ref|YP_002994579.1|  86 AERSAIMINSADVLVVLGGGIGTMVEAL 113
                                       5555677899************988775 PP

>> LSDAT_prok  SLOG in TRPM, prokaryote
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.6   0.0    0.0093        33      26      72 ..      23      67 ..       4      73 .. 0.73
   2 !   10.3   0.0   8.4e-05       0.3     118     164 ..      90     139 ..      77     168 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.0093
                        LSDAT_prok 26 ravlaplaealgavvidgGtdtGvmkllgraraaveatfpLiGVApe 72
                                      ++ + +la+  ++vv+ +G   G+m++  r  a+ ++   ++G+ pe
  gi|242399155|ref|YP_002994579.1| 23 KEFIKELAKYKDTVVLLTGGRGGIMEIASREFARFGGL--VVGILPE 67
                                      55667788888889999999999999988877775544..5677665 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 8.4e-05
                        LSDAT_prok 118 alaekkpsvtvlvnGgeitlkdiresvkagrpilvvaGsgrladei...a 164
                                       a+  +   v v+++Gg  t+ ++ ++    + ++vv+ +g   d++   a
  gi|242399155|ref|YP_002994579.1|  90 AIMINSADVLVVLGGGIGTMVEALMAYDYSKVLVVVTDTGYPSDRLellA 139
                                       3447788999*********************************9985432 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 ?   12.7   0.0   1.6e-05     0.059     100     150 ..      12      66 ..      10      79 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.6e-05
                     SPOUT_MTase_2 100 tdPeGeeisevkeelaealrkakevvvlvGsReGiP....kGlfrfadfvvDlaP 150
                                       t+P  + +++ ke ++e  ++++ vv+l G R Gi     +   rf  +vv + P
  gi|242399155|ref|YP_002994579.1|  12 TEPLPKAVEKTKEFIKELAKYKDTVVLLTGGRGGIMeiasREFARFGGLVVGILP 66 
                                       799999****************************961111345567777777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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: 1152.34
//
Query:       gi|242399156|ref|YP_002994580.1|  [L=380]
Description: Membrane-associated metalloprotease, M50 family, containing PDZ domain [Thermococcus sibiricus MM 739]
Scores for complete 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   74.6   6.3    2.3e-20   72.9   5.6    2.0  1  Peptidase_M50  Peptidase family M50
    3.6e-09   36.8   0.0    5.9e-09   36.1   0.0    1.3  1  PDZ_2          PDZ domain
    7.1e-06   25.8   0.0    1.2e-05   25.0   0.0    1.4  1  PDZ_6          PDZ domain
    2.2e-05   24.7   0.2    4.1e-05   23.9   0.2    1.4  1  PDZ            PDZ domain
  ------ inclusion threshold ------
      0.089   12.8   0.0       0.26   11.3   0.0    1.7  2  PDZ_1          PDZ-like domain
       0.94    9.4   5.4        1.3    8.9   0.2    3.1  3  Maff2          Maff2 family


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 !   72.9   5.6   7.6e-24   2.3e-20       2     248 ..     118     366 ..     117     369 .. 0.83

  Alignments for each domain:
  == domain 1  score: 72.9 bits;  conditional E-value: 7.6e-24
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50   2 filllgilvvvHElGHflvAklcgvkveefsigfGpkllsfkkgeteYaiallpLGGyVkmageepeeelseeeaka 78 
                                        ++ l+++++vHEl H++vA+++++ ++++++ +               + ++p G++V+ ++e             
  gi|242399156|ref|YP_002994580.1| 118 GLIGLIVVMFVHELSHGFVARAENLPLKSVGLVL---------------FFVIP-GAFVEPDEEA------------ 166
                                       5799************************999999...............999**.********99............ PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.......................-EEECE..CTTTSCEE-SEEEC-X CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......................xxxxxx..xxxxxxxxxxxxxxxx RF
                     Peptidase_M50  79 flkkspwqrllivlAGplanfilailvfvv.......................pkkske..seeekrgviGvspkpv 130
                                       ++k+++++rl++ +AG + n++ ai+++++                       p         +++  +iG++ +  
  gi|242399156|ref|YP_002994580.1| 167 LNKAPLLSRLRVYAAGSMGNIVTAIVALLLlsfvltpiiqpagvevsnlaesgP----ArdYLQKGDIIIGINGHE- 238
                                       999**************************9**********99999877766553....134788999999999888. PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXX......XXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXX.......XXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx.......xxxx RF
                     Peptidase_M50 131 kkegllealkegvektlkvvvltvk......algklitgklslk.tlggpisiaqlaseaaeagls.......sflq 193
                                          + +e + + ++kt+   ++ v+       l+  i    +++   +g ++++ +     + g++         l+
  gi|242399156|ref|YP_002994580.1| 239 --IKTVEEFFDIMNKTIAGQIIEVEllrngnKLKFTIPLGSHPDnPEKGYLGVYPAQHIISKVGFDnivlpvsFSLY 313
                                       ..66677777777777666666666445566666666666677745678899999998888999988888886779* PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50 194 llalisvnLgilNLlPipvLDGghllfalleairrkplserkeevanlvglalll 248
                                       +++++++ +g++NL+Pi +LDGg++l   l+a+   p+++ k  +  ++g+ + l
  gi|242399156|ref|YP_002994580.1| 314 WIYMLNLGIGLMNLFPIVPLDGGKMLDDSLKAFL--PSRVAKSITYLFIGIGIFL 366
                                       **********************************..7777777766677666655 PP

>> PDZ_2  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.0     2e-12   5.9e-09      14      82 .]     208     275 ..     200     275 .. 0.94

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 2e-12
                                       .-EEEEEE-TTSGGGGT.--TT-EEEEETTB--SSHHHHHHHHHTS-TT-EEEEEEEETTEEEEEEEE- CS
                             PDZ_2  14 ggvlvvsVkeggPaakaglkagDvilkvdgkkvksledlislllkkkpGdtVkltvlRdgkkktvevkl 82 
                                        gv v +  e+gPa +  l++gD+i+ ++g+++k+ e++   ++k+ +G+ +++++lR+g+k+++++ l
  gi|242399156|ref|YP_002994580.1| 208 AGVEVSNLAESGPARDY-LQKGDIIIGINGHEIKTVEEFFDIMNKTIAGQIIEVELLRNGNKLKFTIPL 275
                                       489999*******9988.**********************************************99865 PP

>> PDZ_6  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0     4e-09   1.2e-05       6      56 .]     216     264 ..     211     264 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 4e-09
                             PDZ_6   6 dpgsPAdrAG.lrvGDiilsvNGqpveglsladvaallr.gsagesvvlvvrr 56 
                                        + +PA     l+ GDii+ +NG+++  ++++++ +++  + ag+++++++ r
  gi|242399156|ref|YP_002994580.1| 216 AESGPAR--DyLQKGDIIIGINGHEI--KTVEEFFDIMNkTIAGQIIEVELLR 264
                                       5668888..44***************..**********999999999998766 PP

>> PDZ  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.2   1.4e-08   4.1e-05      26      75 ..     208     255 ..     200     263 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 1.4e-08
                                       SSEEEEEECTTSHHHHHTSSTTEEEEEETTEETTTSHHHHHHHHHHTTTS CS
                               PDZ  26 kgifvsevlpggaaeadglkvGDkIlsvNgvdvenvsheeavqaikgskg 75 
                                        g+ vs++ + g+a    l++GD+I+++Ng  +++v +e   +++k + g
  gi|242399156|ref|YP_002994580.1| 208 AGVEVSNLAESGPARDY-LQKGDIIIGINGHEIKTV-EEFFDIMNKTIAG 255
                                       5899*************.***************999.5566666665555 PP

>> PDZ_1  PDZ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       2.7     8e+03      15      32 ..     128     146 ..     126     149 .. 0.67
   2 ?   11.3   0.0   8.8e-05      0.26      32      74 ..     210     251 ..     203     253 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.7
                             PDZ_1  15 fhdLsyq.larsyaipvkg 32 
                                       +h+Ls+  +ar  ++p+k 
  gi|242399156|ref|YP_002994580.1| 128 VHELSHGfVARAENLPLKS 146
                                       7999996346777777665 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 8.8e-05
                             PDZ_1  32 gvyvseasgsfklsskekkgviitsinnqptpnLdefievvkk 74 
                                       + + + a+ +++ ++  +kg ii  in++++++++ef ++++k
  gi|242399156|ref|YP_002994580.1| 210 VEVSNLAESGPARDY-LQKGDIIIGINGHEIKTVEEFFDIMNK 251
                                       445555667776777.99***********************86 PP

>> Maff2  Maff2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.2     0.095   2.8e+02      14      33 ..       7      26 ..       2      33 .. 0.81
   2 ?   -2.3   0.0       1.4   4.1e+03       4      27 ..      88     111 ..      86     119 .. 0.69
   3 ?    8.9   0.2   0.00043       1.3      44      70 .]     353     379 ..     347     379 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.095
                             Maff2 14 lvvalGaglgvWGvvnlleG 33
                                      l+  l   +g WG++ l+ G
  gi|242399156|ref|YP_002994580.1|  7 LITVLAVIVGFWGILYLIGG 26
                                      6777888899*****99987 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.4
                             Maff2   4 ftsavdvlktlvvalGaglgvWGv 27 
                                       f+ a++ l+t v + G  l + Gv
  gi|242399156|ref|YP_002994580.1|  88 FSLALQNLRTKVATPGVQLVIPGV 111
                                       666777777777777777777665 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.00043
                             Maff2  44 qGikqlmaGgGviligvtlvPllsgll 70 
                                       + i  l  G G+ l++v l P l+gll
  gi|242399156|ref|YP_002994580.1| 353 KSITYLFIGIGIFLLAVNLFPALKGLL 379
                                       56788999****************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       679  (0.0378716); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2691.59
//
Query:       gi|242399157|ref|YP_002994581.1|  [L=252]
Description: LplA-like lipoate-protein ligase A related [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.9e-12   45.9   0.0    8.8e-12   45.1   0.0    1.4  1  BPL_LplA_LipB  Biotin/lipoate A/B protein ligase family


Domain annotation for each model (and alignments):
>> BPL_LplA_LipB  Biotin/lipoate A/B protein ligase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.1   0.0   4.9e-16   8.8e-12      15     125 ..      58     160 ..      49     165 .. 0.78

  Alignments for each domain:
  == domain 1  score: 45.1 bits;  conditional E-value: 4.9e-16
                                       .GCGGG--TT-EEEEEEESS-B-B--B-TTSEEEEEEEEESS...-CCGTHHHHHHHHHHHHHHH......HHTT-T CS
                     BPL_LplA_LipB  15 slnsselesgglvvvrrqtgGrnvwhspkgeltyslllspeqktfqnrvlelyvsllvlavlealgyrdskpgiegi 91 
                                       ++ +++ ++ g+ vvrr tgG  v+h+ +ge+tys ++ ++  +   +++e   ++++   +eal     + g +g 
  gi|242399157|ref|YP_002994581.1|  58 DVDLEKCKKLGIPVVRRITGGGSVFHDQYGEITYSAVIGEDSYKGL-KNVEESYRTIASPLVEAL----REVGLNGG 129
                                       5667788999*****************************7765555.555555666666666666....12266666 PP

                                       TEEEETTTEEEETTEEEEEEEEEEEETTS-EEEE CS
                     BPL_LplA_LipB  92 pvfikwpnDlyvngrKlaGiavtstrgktlhhiv 125
                                              nD+ +ng+K++G+a+t+++g++l+h++
  gi|242399157|ref|YP_002994581.1| 130 FSG---LNDIIANGKKISGSAQTRRKGVILQHGT 160
                                       655...**************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); 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: 00:00:00.43
# Mc/sec: 1767.35
//
Query:       gi|242399158|ref|YP_002994582.1|  [L=170]
Description: signal peptidase I [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-07   31.1   0.1    4.2e-07   29.8   0.1    1.8  1  Peptidase_S24  Peptidase S24-like


Domain annotation for each model (and alignments):
>> Peptidase_S24  Peptidase S24-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.1   2.4e-11   4.2e-07       2      48 ..      44      92 ..      43     116 .. 0.78

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 2.4e-11
                                      XXSSTTCCTXXTTXEEEEECTS..---TTSEEEEEETTCE-EEEEEEEE CS
                     Peptidase_S24  2 vpGdSMeptlldGdlilVdkfs..epkrGdivvfrlpgeeeayiKrvig 48
                                      v ++SMept+  Gd++l +     e+k+G +vv r p  +  +i+rv+ 
  gi|242399158|ref|YP_002994582.1| 44 VISGSMEPTFYRGDVVLLKGVLpdEIKPGNVVVYRRPYTRYPIIHRVKN 92
                                      669***************844478****************666666662 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1227.39
//
Query:       gi|242399159|ref|YP_002994583.1|  [L=194]
Description: hypothetical protein TSIB_1180 [Thermococcus sibiricus MM 739]
Scores for complete 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-77  258.8   0.0    2.9e-77  258.6   0.0    1.0  1  DUF531          Protein of unknown function (DUF531)
    0.00094   18.6   0.0     0.0014   18.1   0.0    1.2  1  SPOUT_MTase_2   AF2226-like SPOUT RNA Methylase fused to THUM
  ------ inclusion threshold ------
       0.19   11.9   0.0       0.44   10.7   0.0    1.6  1  SpoU_methylase  SpoU rRNA Methylase family


Domain annotation for each model (and alignments):
>> DUF531  Protein of unknown function (DUF531)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  258.6   0.0   4.9e-81   2.9e-77       1     169 [.      12     182 ..      12     183 .. 0.98

  Alignments for each domain:
  == domain 1  score: 258.6 bits;  conditional E-value: 4.9e-81
                            DUF531   1 mltlglvntYDkkklheaHkRaiARaapicyafdfnLalldFplk.keekelvdvvaekttiGesGkylkelaeknr 76 
                                       mltl l+n+YD+kklheaH+RaiARaapicyafdf+Lal++Fp++ k++ e+  +++++ttiGesGkyl ela++n+
  gi|242399159|ref|YP_002994583.1|  12 MLTLSLYNSYDPKKLHEAHLRAIARAAPICYAFDFHLALVGFPFEtKKPLEIGSEISKSTTIGESGKYLLELAKTNK 88 
                                       89******************************************956889*************************** PP

                            DUF531  77 llvldlpkkgfpaqfGevvattskpdekkaitpeevaeeilrkksvllliGlGrkGlPkellklakyhldit.ekgv 152
                                       +++ld+pk gfp+qfG++vatt+kpde+k+i++ ++ae +lr++s++l++GlGr+GlPke++klakyhldit +k++
  gi|242399159|ref|YP_002994583.1|  89 FHLLDFPKLGFPPQFGQIVATTRKPDENKNISSLQLAERALRGESFMLVVGLGRHGLPKEIFKLAKYHLDITdGKRI 165
                                       ************************************************************************889** PP

                            DUF531 153 slEtctAigaiaaviat 169
                                       slEtctAig+i+++i t
  gi|242399159|ref|YP_002994583.1| 166 SLETCTAIGSIPTKIRT 182
                                       **************986 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 !   18.1   0.0   2.3e-07    0.0014     113     163 ..     123     176 ..     104     187 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.3e-07
                     SPOUT_MTase_2 113 elaealrkakevvvlvG.sReGiPkGlfrfadfvvDlaPgvtlate..yaiaaa 163
                                       +lae+  + +  +++vG  R+G+Pk +f++a + +D++ g  ++ e  +ai ++
  gi|242399159|ref|YP_002994583.1| 123 QLAERALRGESFMLVVGlGRHGLPKEIFKLAKYHLDITDGKRISLEtcTAIGSI 176
                                       4555555566667777757*******************9866655511555554 PP

>> SpoU_methylase  SpoU rRNA Methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   7.4e-05      0.44      77     123 ..     105     160 ..      98     174 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 7.4e-05
                                       EEEEEST...T-SEGCCSHHH......TTEEEEEEBTTTBS-HHHHCTSSEEEE-- CS
                    SpoU_methylase  77 alvatsl...kgkslseidlk......ekvalvfGnEdkGlsnelleladrlvkIp 123
                                       ++vat++   ++k++s ++l+      e+ +lv+G  ++Gl++e+ +la++++ I 
  gi|242399159|ref|YP_002994583.1| 105 QIVATTRkpdENKNISSLQLAeralrgESFMLVVGLGRHGLPKEIFKLAKYHLDIT 160
                                       57888884444455554544467888999*********************999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1311.04
//
Query:       gi|242399160|ref|YP_002994584.1|  [L=356]
Description: TRP-repeat-containing protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.7e-05   23.1   1.1        7.1    7.0   0.0    5.2  7  TPR_12        Tetratricopeptide repeat
     0.0048   16.3   0.0      0.008   15.6   0.0    1.3  1  ThrE          Putative threonine/serine exporter
     0.0093   16.1   0.2        5.5    7.3   0.0    2.6  2  Gemini_V2     Geminivirus V2 protein
  ------ inclusion threshold ------
      0.045   13.8   1.2        0.1   12.7   0.0    2.2  2  Cullin_Nedd8  Cullin protein neddylation domain
      0.053   14.0   2.8        5.5    7.6   0.0    4.0  5  TPR_19        Tetratricopeptide repeat
      0.088   12.7   4.3         35    4.4   0.1    4.5  4  TPR_1         Tetratricopeptide repeat
      0.088   13.0   7.6         29    5.1   0.0    5.2  6  TPR_2         Tetratricopeptide repeat
       0.12   12.0   0.0       0.42   10.2   0.0    1.9  2  LUC7          LUC7 N_terminus
       0.27   11.6   5.9        7.5    7.0   0.0    5.3  7  PPR           PPR repeat


Domain annotation for each model (and alignments):
>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.4     0.017        33      17      48 ..      14      36 ..       8      42 .. 0.54
   2 ?    1.6   0.0      0.17   3.4e+02      12      32 ..      23      43 ..      22      64 .. 0.80
   3 ?    1.8   0.0      0.15     3e+02      43      60 ..      70      87 ..      46     100 .. 0.56
   4 ?    2.6   0.0     0.084   1.7e+02       3      36 ..      72     105 ..      70     121 .. 0.82
   5 !    7.0   0.0    0.0036       7.1      21      77 .]     130     188 ..     118     188 .. 0.85
   6 !    6.1   0.0     0.007        14      21      45 ..     174     198 ..     172     210 .. 0.79
   7 ?   -0.3   0.0      0.69   1.4e+03      24      67 ..     292     333 ..     287     347 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.017
                            TPR_12 17 grydeAlellekaleiarrllGpdhpltattl 48
                                      +r       +e+ale++ +l  + +++ a tl
  gi|242399160|ref|YP_002994584.1| 14 KR-------YEEALELVHQL--EGNLEKALTL 36
                                      44.......55555555555..3345555555 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.17
                            TPR_12 12 vlrrlgrydeAlellekalei 32
                                      v++  g++++Al+l   a e+
  gi|242399160|ref|YP_002994584.1| 23 VHQLEGNLEKALTLGAMAKEV 43
                                      678888888888876666555 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.15
                            TPR_12 43 ltattlrnLgrlyralgr 60
                                      + a++l n + +y ++ +
  gi|242399160|ref|YP_002994584.1| 70 EKAIALANVASVYVLMRD 87
                                      455555555555544433 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.084
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrl 36 
                                       a+al n+a+v+  + + d   +l+ekal   +++
  gi|242399160|ref|YP_002994584.1|  72 AIALANVASVYVLMRDVDYGMALFEKALKETEKI 105
                                       6777799999999999999999999999877776 PP

  == domain 5  score: 7.0 bits;  conditional E-value: 0.0036
                            TPR_12  21 eAlellekaleiarrllGpdhpltattlrnLgrlyralgr...yeeAlelleealaiaek 77 
                                        +++l+ek  +i+ +l   ++    ++l +Lg++ ++ g+     eAl ++++a +++ek
  gi|242399160|ref|YP_002994584.1| 130 FSFDLFEKIFDIIINL-KVNYVKKTEYLLDLGDMMEKVGDelvSPEALTFYKRAHDLFEK 188
                                       5788999999999888.47899999999999999999999666699********999986 PP

  == domain 6  score: 6.1 bits;  conditional E-value: 0.007
                            TPR_12  21 eAlellekaleiarrllGpdhplta 45 
                                       eAl+++++a++++++l+ p + +t+
  gi|242399160|ref|YP_002994584.1| 174 EALTFYKRAHDLFEKLHVPAKVATL 198
                                       8999999999999999877665555 PP

  == domain 7  score: -0.3 bits;  conditional E-value: 0.69
                            TPR_12  24 ellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlel 67 
                                       e +++al++  ++  +d +l ++ +  +++   ++g+ + A +l
  gi|242399160|ref|YP_002994584.1| 292 ERFKTALALSMKI--EDVYLRSEFMGEIAIGMIKSGEIDGAMKL 333
                                       5566666666666..66666666666666655555555555555 PP

>> ThrE  Putative threonine/serine exporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0     4e-06     0.008      30     125 ..      35     131 ..      24     145 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4e-06
                              ThrE  30 algleevevfvtptsiivsvdeeeesitt.vrrvrsrgvnleklsevnelsreiaageisleeaeerLdeIerskpr 105
                                       +lg    evf + ++i +s+ e+ e +++ +++ +++ + l  ++ v  l+r++  g    e+a ++ ++I+++k++
  gi|242399160|ref|YP_002994584.1|  35 TLGAMAKEVFHIDETIAYSLLEDAEYFSEkIKNKKEKAIALANVASVYVLMRDVDYGMALFEKALKETEKIKNAKEK 111
                                       67777889999999******65788888878888******************************************* PP

                              ThrE 106 yprwlvvlaaglaaaafall 125
                                        ++++ ++ ++ +++ + + 
  gi|242399160|ref|YP_002994584.1| 112 IKPLIEIAYYMGISGLVEFS 131
                                       ***********999987665 PP

>> Gemini_V2  Geminivirus V2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0    0.0027       5.5      41      70 ..       3      32 ..       1      36 [. 0.85
   2 !    6.4   0.0    0.0053        11      21      61 ..     267     304 ..     255     317 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0027
                         Gemini_V2 41 lirdLisvlRarnyveatrRyshfhsrleg 70
                                       i+dLi + R ++y+ea +  ++++ +le+
  gi|242399160|ref|YP_002994584.1|  3 EIEDLIYLARNKRYEEALELVHQLEGNLEK 32
                                      589**************9988888877765 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0053
                         Gemini_V2  21 AvkylqevektyspdtvgyelirdLisvlRarnyveatrRy 61 
                                       A+kyl++++  +spd++ y +ir Li++ R ++    + + 
  gi|242399160|ref|YP_002994584.1| 267 ALKYLKNIQ--LSPDSIEY-VIRLLIELERFKTALALSMKI 304
                                       99******9..99****66.79******9999866555555 PP

>> Cullin_Nedd8  Cullin protein neddylation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.4       2.4   4.8e+03      41      56 ..     105     120 ..     100     121 .. 0.78
   2 ?   12.7   0.0   5.1e-05       0.1      14      54 ..     252     291 ..     248     294 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.4
                      Cullin_Nedd8  41 iadikkrIesLiekeY 56 
                                       i+  k+ I+ Lie  Y
  gi|242399160|ref|YP_002994584.1| 105 IKNAKEKIKPLIEIAY 120
                                       5667899999999766 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 5.1e-05
                      Cullin_Nedd8  14 MKsrktlshneLvsevieqlskrftpsiadikkrIesLiek 54 
                                       MK++ tl +n++v+  ++ l k+ ++s+  i  +I  Lie 
  gi|242399160|ref|YP_002994584.1| 252 MKKNATLGYNQIVNTALKYL-KNIQLSPDSIEYVIRLLIEL 291
                                       *******************9.99****************95 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1       0.3   5.9e+02       4      16 ..      13      25 ..       9      41 .. 0.62
   2 ?   -2.1   0.0       2.9   5.8e+03      11      20 ..      92     101 ..      65     110 .. 0.61
   3 ?   -3.4   0.0       7.3   1.5e+04      10      19 ..     175     184 ..     174     189 .. 0.60
   4 ?    3.3   0.0     0.058   1.2e+02       9      46 ..     266     299 ..     264     306 .. 0.83
   5 ?    7.6   0.0    0.0028       5.5      13      55 ..     293     341 ..     288     349 .. 0.72

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.3
                            TPR_19  4 egdyaeAlalleq 16
                                      +++y+eAl+l  q
  gi|242399160|ref|YP_002994584.1| 13 NKRYEEALELVHQ 25
                                      4566666666655 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.9
                            TPR_19  11 lalleqalqe 20 
                                       +al+e+al+e
  gi|242399160|ref|YP_002994584.1|  92 MALFEKALKE 101
                                       3444444443 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 7.3
                            TPR_19  10 Alalleqalq 19 
                                       Al ++++a +
  gi|242399160|ref|YP_002994584.1| 175 ALTFYKRAHD 184
                                       6777777654 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.058
                            TPR_19   9 eAlalleqalqedpknaearllLAeallalgqldeAea 46 
                                        Al++l+++ q +p++ e  +   ++l++l +++ A a
  gi|242399160|ref|YP_002994584.1| 266 TALKYLKNI-QLSPDSIEYVI---RLLIELERFKTALA 299
                                       699*****5.****9888777...88888888888876 PP

  == domain 5  score: 7.6 bits;  conditional E-value: 0.0028
                            TPR_19  13 lleqalqedpk......naearllLAeallalgqldeAealLdalpeed 55 
                                       +++ al+ + k       +e     A+ ++++g++d A++l +++p+e 
  gi|242399160|ref|YP_002994584.1| 293 RFKTALALSMKiedvylRSEFMGEIAIGMIKSGEIDGAMKLAERIPDEH 341
                                       55555555555333333444444668889*****************986 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1     0.062   1.2e+02      13      22 ..      12      21 ..       9      25 .. 0.82
   2 ?    0.0   0.0      0.44   8.7e+02      10      21 ..      23      34 ..      22      36 .. 0.80
   3 ?    4.4   0.1     0.018        35       1      29 [.      72     100 ..      72     101 .. 0.94
   4 ?    3.0   0.0     0.052     1e+02      19      31 ..     174     186 ..     173     189 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.062
                                      HTT-HHHHHH CS
                             TPR_1 13 klgkydeAle 22
                                      ++++y+eAle
  gi|242399160|ref|YP_002994584.1| 12 RNKRYEEALE 21
                                      6799999998 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.44
                                      HHHHTT-HHHHH CS
                             TPR_1 10 ayfklgkydeAl 21
                                      +++  g++++Al
  gi|242399160|ref|YP_002994584.1| 23 VHQLEGNLEKAL 34
                                      577889999998 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.018
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALe 29 
                                       a al n + +y  + + d   + +ekAL+
  gi|242399160|ref|YP_002994584.1|  72 AIALANVASVYVLMRDVDYGMALFEKALK 100
                                       67999***********************7 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.052
                                       HHHHHHHHHHHHS CS
                             TPR_1  19 eAleyyekALeln 31 
                                       eAl +y++A  l 
  gi|242399160|ref|YP_002994584.1| 174 EALTFYKRAHDLF 186
                                       8********9886 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.3     0.016        31      11      24 ..      10      23 ..       8      27 .. 0.83
   2 ?   -0.2   0.0      0.71   1.4e+03      10      22 ..      23      35 ..      22      36 .. 0.79
   3 ?    5.1   0.0     0.014        29       1      30 [.      72     101 ..      72     105 .. 0.89
   4 ?    2.4   0.1      0.11   2.1e+02      19      32 ..     174     187 ..     173     189 .. 0.80
   5 ?   -4.5   0.1         9   1.8e+04      24      30 ..     294     300 ..     290     300 .. 0.61
   6 ?   -0.9   0.0       1.2   2.4e+03       7      26 ..     317     336 ..     312     337 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.016
                             TPR_2 11 yyklgdyeeAleaf 24
                                      ++++++yeeAle+ 
  gi|242399160|ref|YP_002994584.1| 10 LARNKRYEEALELV 23
                                      7899*******975 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.71
                             TPR_2 10 ayyklgdyeeAle 22
                                      ++   g++e+Al 
  gi|242399160|ref|YP_002994584.1| 23 VHQLEGNLEKALT 35
                                      57778999*9985 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.014
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAlel 30 
                                       a al n + +y  + d +   ++fekAl+ 
  gi|242399160|ref|YP_002994584.1|  72 AIALANVASVYVLMRDVDYGMALFEKALKE 101
                                       678999999*******************97 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.11
                             TPR_2  19 eAleafekAleldP 32 
                                       eAl ++++A  l +
  gi|242399160|ref|YP_002994584.1| 174 EALTFYKRAHDLFE 187
                                       89999999988865 PP

  == domain 5  score: -4.5 bits;  conditional E-value: 9
                             TPR_2  24 fekAlel 30 
                                       f+ Al+l
  gi|242399160|ref|YP_002994584.1| 294 FKTALAL 300
                                       6667765 PP

  == domain 6  score: -0.9 bits;  conditional E-value: 1.2
                             TPR_2   7 lGlayyklgdyeeAleafek 26 
                                       ++   +k+g+ + A ++ e+
  gi|242399160|ref|YP_002994584.1| 317 IAIGMIKSGEIDGAMKLAER 336
                                       56677899******999886 PP

>> LUC7  LUC7 N_terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.73   1.5e+03     148     206 ..      27      87 ..      12      93 .. 0.53
   2 ?   10.2   0.0   0.00021      0.42     122     161 ..      97     138 ..      40     146 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.73
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              LUC7 148 eGkVdeaqklmkeveelkeekeeleqqyeaaa..aneeseasqekkmkvCeiCGaflivgD 206
                                       eG+ ++a +l ++++e+ +  e++  +  + a   +e+ ++++ek + + ++ + ++++ D
  gi|242399160|ref|YP_002994584.1|  27 EGNLEKALTLGAMAKEVFHIDETIAYSLLEDAeyFSEKIKNKKEKAIALANVASVYVLMRD 87 
                                       4555555555444444444444433333222222345566666666666666666666666 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00021
                                       .....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              LUC7 122 a..kkqeqlkeleekiekllaeaeelgeeGkVdeaqklmkev 161
                                       +  k++e++k+ +eki+ l++ a  +g++G V+ + +l++++
  gi|242399160|ref|YP_002994584.1|  97 KalKETEKIKNAKEKIKPLIEIAYYMGISGLVEFSFDLFEKI 138
                                       145899*******************************99886 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0    0.0038       7.5      10      27 ..      10      27 ..       9      29 .. 0.87
   2 ?   -1.7   0.0       2.3   4.5e+03      13      22 ..      27      36 ..      26      36 .. 0.85
   3 ?   -0.1   0.1      0.73   1.5e+03       8      26 ..      80      98 ..      77     101 .. 0.82
   4 ?   -0.3   0.0      0.82   1.6e+03      13      26 ..     125     138 ..     122     140 .. 0.86
   5 ?   -2.3   0.0       3.6   7.1e+03      16      26 ..     179     189 ..     178     190 .. 0.81
   6 ?   -2.2   0.0       3.5   6.9e+03      11      23 ..     220     232 ..     216     234 .. 0.80
   7 ?    1.2   0.0      0.28   5.5e+02       9      25 ..     320     336 ..     319     342 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0038
                               PPR 10 ycknGkleeAlelfkeMk 27
                                      +++n ++eeAlel ++++
  gi|242399160|ref|YP_002994584.1| 10 LARNKRYEEALELVHQLE 27
                                      689**********98876 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.3
                               PPR 13 nGkleeAlel 22
                                      +G+le+Al l
  gi|242399160|ref|YP_002994584.1| 27 EGNLEKALTL 36
                                      69*****975 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.73
                               PPR  8 sgycknGkleeAlelfkeM 26
                                      s+y+  ++++  + lf++ 
  gi|242399160|ref|YP_002994584.1| 80 SVYVLMRDVDYGMALFEKA 98
                                      7899999999999999985 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 0.82
                               PPR  13 nGkleeAlelfkeM 26 
                                       +G++e  ++lf+++
  gi|242399160|ref|YP_002994584.1| 125 SGLVEFSFDLFEKI 138
                                       7999*******985 PP

  == domain 5  score: -2.3 bits;  conditional E-value: 3.6
                               PPR  16 leeAlelfkeM 26 
                                       ++ A +lf+++
  gi|242399160|ref|YP_002994584.1| 179 YKRAHDLFEKL 189
                                       57899***986 PP

  == domain 6  score: -2.2 bits;  conditional E-value: 3.5
                               PPR  11 cknGkleeAlelf 23 
                                       +k+Gk+  A +l+
  gi|242399160|ref|YP_002994584.1| 220 VKEGKYIYATKLL 232
                                       7999999999987 PP

  == domain 7  score: 1.2 bits;  conditional E-value: 0.28
                               PPR   9 gycknGkleeAlelfke 25 
                                       g  k+G+++ A++l ++
  gi|242399160|ref|YP_002994584.1| 320 GMIKSGEIDGAMKLAER 336
                                       5679********99665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       762  (0.042501); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); 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: 0.65u 0.34s 00:00:00.99 Elapsed: 00:00:00.55
# Mc/sec: 1950.55
//
Query:       gi|242399161|ref|YP_002994585.1|  [L=311]
Description: Microsomal dipeptidase like protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.3e-93  312.8   0.0    2.6e-93  312.7   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 !  312.7   0.0   1.5e-97   2.6e-93       8     318 ..       2     307 ..       1     308 [. 0.97

  Alignments for each domain:
  == domain 1  score: 312.7 bits;  conditional E-value: 1.5e-97
                                       EEEEEE-HHHHHHHCTTTTT-TTTHCTSSS-HHHHHHHTEEEEEEEEE--CCCCCCCHHHHHHHHHHHHHHHHHHGT CS
                     Peptidase_M19   8 viDghndlplklrqekkeslllekdselqtdlerlraggvsavlfaifvpedasyeeavkatleqidlirrlvrknp 84 
                                       ++D+h+dlp+++++++ke +    ++ l+ +++++    ++  ++a++  +++++ +a++++le ++ +++ + ++p
  gi|242399161|ref|YP_002994585.1|   2 IFDAHCDLPTYIYEKRKEGK----NAVLENEFAKFFGKYITSRVMAVW-SRPEKRATALRYALEVVNTLHKDIIESP 73 
                                       89*********999999876....99999******************9.44569*********************** PP

                                       TTEEE-SSHHHHHHHHHTT-EEEEEEEESCGGGTT-HHHHHHHHHTTEEEEES-SSS-BSSB-BCCGTT.SSSSB-H CS
                     Peptidase_M19  85 eqlklvrtaddierakkegkiavllgiegaealgddlallrafyalGvrvlgltynrnnkfAdgaleekdedgGLse 161
                                       + +++v+t+d++++a k+gk+a++lg+eg+e+++d+l+ll+ fy+lGvrvl+lt+n +n ++dg  e+  ++gGL++
  gi|242399161|ref|YP_002994585.1|  74 S-FAFVTTTDEMRNAVKNGKVALWLGLEGGEPIEDSLDLLEIFYKLGVRVLTLTWNLRNAIGDGTFER--TKGGLTN 147
                                       8.*****************************************************************9..******* PP

                                       HHHHHHHHHHHHT-EEE-TTB-HHHHHHHHHH-SSE.EECCEEBTTTS--TTSB-HHHHHHHHHTT-EEEE-SSHHH CS
                     Peptidase_M19 162 fGkelVrelNrlgiliDlShlsektfldvlelSkaPvvaSHSnaralcdhpRNltDeqlkaiaesgGvvgvtfvpaf 238
                                       fG e++ ++++lgiliD+Shl+e++f++v+e++ +P++aSHSna+++c+h RNl+D+q+kai+e++Gv+gv  +paf
  gi|242399161|ref|YP_002994585.1| 148 FGVEVLGKAEELGILIDVSHLNEQGFWNVIETTAFPIIASHSNAYSICEHVRNLKDDQIKAISERKGVIGVSSIPAF 224
                                       ***************************************************************************** PP

                                       CTTTS--BHHHHHHHHHHHHHHT-GGGEEE---T.....TTTSS-BBTBSSGGGHHHHHHHHHHTTS-HHHHHHHHT CS
                     Peptidase_M19 239 lkekaeatledvvdhidyivelaGidhVGlGsDf.....dgggelpegledvsklpnltaeLlrrgyseadiekilg 310
                                       +++ + +tle++v+hi+yi++l+G+++VG+G Df     +++ge ++g+e+ +++p l+a+L +  +s+++ie+i+ 
  gi|242399161|ref|YP_002994585.1| 225 VDK-EAPTLEKMVNHIEYIADLVGYKYVGFGFDFvyylsWWKGESVKGFENEERIPALLAKLDD-LFSKKEIEAITF 299
                                       *98.9**********************************888999*****************66.************ PP

                                       HHHHHHHH CS
                     Peptidase_M19 311 gNflrvle 318
                                       gNf rv+e
  gi|242399161|ref|YP_002994585.1| 300 GNFERVFE 307
                                       ******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1946.50
//
Query:       gi|242399162|ref|YP_002994586.1|  [L=279]
Description: SAM-dependent methyltransferase, UPF0020 family [Thermococcus sibiricus MM 739]
Scores for complete 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-09   37.8   0.0    4.2e-09   37.0   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
    2.8e-08   34.3   0.0    5.6e-08   33.3   0.0    1.5  1  Methyltransf_11  Methyltransferase domain
    6.5e-07   29.0   0.0    1.1e-06   28.3   0.0    1.3  1  MTS              Methyltransferase small domain
    1.1e-06   28.3   0.0    1.9e-06   27.6   0.0    1.3  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
    1.5e-06   28.0   0.0    2.1e-06   27.5   0.0    1.4  1  Cons_hypoth95    Conserved hypothetical protein 95
    2.4e-06   27.4   0.0    4.1e-06   26.7   0.0    1.4  1  Methyltransf_31  Methyltransferase domain
    1.9e-05   24.1   0.0    3.3e-05   23.4   0.0    1.4  1  Spermine_synth   Spermine/spermidine synthase domain
    4.8e-05   23.2   0.0     0.0001   22.2   0.0    1.6  1  Methyltransf_30  S-adenosyl-L-methionine-dependent methyltran
    0.00021   21.1   0.1    0.00063   19.5   0.0    1.7  2  Met_10           Met-10+ like-protein
     0.0016   17.6   0.0     0.0022   17.1   0.0    1.3  1  RrnaAD           Ribosomal RNA adenine dimethylase
     0.0017   17.7   0.0      0.025   13.9   0.0    2.2  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family
     0.0057   16.4   0.1       0.55    9.9   0.0    2.8  3  N6_N4_Mtase      DNA methylase
  ------ inclusion threshold ------
      0.012   15.4   0.0      0.023   14.6   0.0    1.4  1  Methyltransf_23  Methyltransferase domain
      0.021   14.2   0.0      0.051   13.0   0.0    1.6  1  SAM_MT           Putative SAM-dependent methyltransferase
      0.043   13.5   0.0      0.076   12.7   0.0    1.4  1  UPF0020          Putative RNA methylase family UPF0020
      0.051   13.2   0.0       0.12   12.0   0.0    1.6  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
       0.11   13.5   0.0        0.2   12.7   0.0    1.4  1  Methyltransf_24  Methyltransferase domain
       0.17   11.7   0.0       0.39   10.5   0.0    1.6  1  Palm_thioest     Palmitoyl protein thioesterase


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 !   37.0   0.0   4.2e-12   4.2e-09       1      97 []     130     231 ..     130     231 .. 0.89

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 4.2e-12
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT....TEEEEESBCCGB..SSSTTTEEEEEEE CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl....nvefvqgdaedl..pfedgsfDlvvss 71 
                                       vLd + G G ++++ akr+  a v+ ++ +++ +e ar +  + ++    n++++qgda+++  +f+d++f++++  
  gi|242399162|ref|YP_002994586.1| 130 VLDTCMGLGYTAIESAKRG--AYVMTIEKDPNVIELARLNPWSWEVfnsqNIQVIQGDASEIikKFNDETFNVIIHD 204
                                       9*****************5..*****************999887677778*********9974469**********6 PP

                                       ST.GGGSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  72 ga.lhhlsdedlekalkeiarvLkpgG 97 
                                          +++  +   e+++ke++rvLkp+G
  gi|242399162|ref|YP_002994586.1| 205 PPrFSLAGHLYSEAFYKELFRVLKPKG 231
                                       66677666667899***********99 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.0   5.6e-11   5.6e-08       1      95 [.     131     234 ..     131     235 .. 0.87

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 5.6e-11
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-....EEEETTEECCCT..SS-TT-EEEEEEES.. CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl....kvefvvadaekl..pfednsfDlvvsse.. 69 
                                       Ld  +G G+ a + akrga v++++ ++++++la+ +    ++    +++++++da+++  +f+d++f +++     
  gi|242399162|ref|YP_002994586.1| 131 LDTCMGLGYTAIESAKRGAYVMTIEKDPNVIELARLNPWSWEVfnsqNIQVIQGDASEIikKFNDETFNVIIHDPpr 207
                                       6777899***************************99998888899999**********6568**********97644 PP

                                       ..-CCC-CCHHHHHHHHHHHEEEEEEEE CS
                   Methyltransf_11  70 ..vlhhvedpekalkeiaRvLkpgGllv 95 
                                            h+   e++ ke+ RvLkp G+l+
  gi|242399162|ref|YP_002994586.1| 208 fsLAGHL-YSEAFYKELFRVLKPKGRLF 234
                                       4344444.79***************996 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.0   1.1e-09   1.1e-06      26     149 ..     121     249 ..     114     267 .. 0.78

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 1.1e-09
                                       HCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC....EEEEE...-STTTTSTT CS
                               MTS  26 tlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle....vevva...sdvleevee 95 
                                       t++ ++s+ vlD + G G+ +++ ak+     v  +++d + +e+a+ n  + ++     ++v++   s++++++++
  gi|242399162|ref|YP_002994586.1| 121 TVNPRESEFVLDTCMGLGYTAIESAKRGAY--VMTIEKDPNVIELARLNPWSWEVFnsqnIQVIQgdaSEIIKKFND 195
                                       556667888*****************8887..99*************99544332223346666511156778888* PP

                                       S-EEEEEE---STTTCHCHHHHHHHHHHHHHHHEEEEEEEE.EEEETTSCHHHH.H CS
                               MTS  96 kkfdlivsNPPfhagkatelavaeeliaeAkeaLkegGeLl.iVanrklgyesl.l 149
                                       + f++i+  PP  +     +   e++ +e  ++Lk++G+L+  V n   +y+++ l
  gi|242399162|ref|YP_002994586.1| 196 ETFNVIIHDPPRFSLAG--HLYSEAFYKELFRVLKPKGRLFhYVGNPGAKYRKKdL 249
                                       ***********655544..67899999************98469999999987654 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 !   27.6   0.0   1.9e-09   1.9e-06       2      80 ..     128     206 ..     127     218 .. 0.93

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 1.9e-09
                   Methyltransf_15   2 rvilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgv..sdkitlvlgdvfellaklklekikvdlvf 76 
                                       + +lD + G G  +i+ a+ +  v++ie++++ +++a  N  +++v  s++i++++gd  e+++k++ e+   ++++
  gi|242399162|ref|YP_002994586.1| 128 EFVLDTCMGLGYTAIESAKRGAYVMTIEKDPNVIELARLNPWSWEVfnSQNIQVIQGDASEIIKKFNDETF--NVII 202
                                       579***************************************99998889***************988877..9999 PP

                   Methyltransf_15  77 lSpP 80 
                                         pP
  gi|242399162|ref|YP_002994586.1| 203 HDPP 206
                                       9998 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.0   2.1e-09   2.1e-06      42     122 ..     127     206 ..     100     266 .. 0.82

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 2.1e-09
                                       C-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--T..TTEEEEES-HHHHCTS--SS-EEEE CS
                     Cons_hypoth95  42 garvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelklee..etaelkedaleallklakkkeefdi 116
                                        + vLD + G G  ++E + Rga  ++ +ekd++++++ + n  + ++ +  ++++++ da+e ++k   ++e f++
  gi|242399162|ref|YP_002994586.1| 127 SEFVLDTCMGLGYTAIESAKRGA-YVMTIEKDPNVIELARLNPWSWEVFNsqNIQVIQGDASEIIKKF--NDETFNV 200
                                       4559******************6.57889***********9977777666546788888887777776..8899*** PP

                                       EEE--S CS
                     Cons_hypoth95 117 vflDPP 122
                                       +  DPP
  gi|242399162|ref|YP_002994586.1| 201 IIHDPP 206
                                       ****** PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0   4.1e-09   4.1e-06       7     108 ..     130     234 ..     125     270 .. 0.84

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 4.1e-09
                   Methyltransf_31   7 vlDlGCGtGeltfelaeelgpkaevvGiDiseeaielAre...naqklgldnveFeqgdiee.leklledekfDlil 79 
                                       vlD   G G+ ++e a++   +a v+ i+ ++++ielAr      +  +++n+++ qgd+ e ++k ++de+f++i+
  gi|242399162|ref|YP_002994586.1| 130 VLDTCMGLGYTAIESAKR---GAYVMTIEKDPNVIELARLnpwSWEVFNSQNIQVIQGDASEiIKK-FNDETFNVII 202
                                       677777888888888854...688***************966657788889***********6665.********** PP

                   Methyltransf_31  80 snevl...naladpdkileeiervlkpggill 108
                                        + +    +    ++++++e++rvlkp+g+l 
  gi|242399162|ref|YP_002994586.1| 203 HDPPRfslAGHLYSEAFYKELFRVLKPKGRLF 234
                                       *944455577777899*************985 PP

>> Spermine_synth  Spermine/spermidine synthase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   3.3e-08   3.3e-05      46     131 ..     152     236 ..     134     268 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 3.3e-08
                                       EEEES-HHHHHHHHHHSHHHHTTCGGCTTEEEEESTCHHHHCTCSS.-EEEEEEECCSTTCSSCGCSSHHHHHHHHH CS
                    Spermine_synth  46 tlvdiDqkvidfskkflpslaisafndarvklvlgdgfkflkayek.kfdvvivdsldpvgpaenlFskeffdllkk 121
                                         ++ D +vi++ +      + + fn + ++++ gd+ + +k+ ++ +f v+i d     + a +l+s+ f++ l +
  gi|242399162|ref|YP_002994586.1| 152 MTIEKDPNVIELARL--NPWSWEVFNSQNIQVIQGDASEIIKKFNDeTFNVIIHDPPR-FSLAGHLYSEAFYKELFR 225
                                       6789999****9995..55555568*********************9********988.888888************ PP

                                       TEEEEE.EEEE CS
                    Spermine_synth 122 vlkedG.viil 131
                                       vlk+ G +++ 
  gi|242399162|ref|YP_002994586.1| 226 VLKPKGrLFHY 236
                                       ****9934444 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 !   22.2   0.0     1e-07    0.0001      30      90 ..     176     237 ..     169     272 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1e-07
                                       TEEEEEEES-HHHHHHHC-.T-EEEEEE-SS-TTTSGGGCSHHHHHHHHHHEEEEEEEEES- CS
                   Methyltransf_30  30 evtlklligdarealkeld.ekadawFlDgFsPaknPelwseellkelarllkkkgtlatys 90 
                                       + +++++ gda+e +k+ + e ++++ +D+   + +  l+se ++kel+r+lk+kg+l  y 
  gi|242399162|ref|YP_002994586.1| 176 SQNIQVIQGDASEIIKKFNdETFNVIIHDPPRFSLAGHLYSEAFYKELFRVLKPKGRLFHYV 237
                                       56899*************99**********9999***********************99885 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       1.8   1.8e+03      79      99 ..      42      62 ..       9      74 .. 0.56
   2 !   19.5   0.0   6.3e-07   0.00063      99     170 ..     125     195 ..     110     240 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.8
                                      TTS---GGGHHHHHHHHTT-- CS
                            Met_10 79 skvyfsskleaErerlaklve 99
                                       kv f  + e E+  l k+++
  gi|242399162|ref|YP_002994586.1| 42 DKVVFPDESEIEKDILKKIAK 62
                                      344444444444444444444 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 6.3e-07
                                       -TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-..TTCEEEEES-GGG---TT-EE CS
                            Met_10  99 eegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkv..ekvvkpileDgrevireqlad 170
                                       +e e V+d   G G+ ai  ak  ++  v++i+++P+ +++ + n    +v  ++ +++i++D+ e+i+ ++ d
  gi|242399162|ref|YP_002994586.1| 125 RESEFVLDTCMGLGYTAIESAK--RGAYVMTIEKDPNVIELARLNPWSWEVfnSQNIQVIQGDASEIIK-KFND 195
                                       6789******************..99*****************99998888556889*********996.3333 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   2.2e-06    0.0022      23      88 ..     119     189 ..     108     261 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.2e-06
                                       HHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTT.....TCCCEEEE-S-CCGH CS
                            RrnaAD  23 ldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkkls.....kdeklkvvhqDflkf 88 
                                       +d++n++e+  vl+   G G +  e akr   v  +E+d++ ++l + ++      ++++++v++ D+ + 
  gi|242399162|ref|YP_002994586.1| 119 VDTVNPRESEFVLDTCMGLGYTAIESAKRGAYVMTIEKDPNVIELARLNPWswevfNSQNIQVIQGDASEI 189
                                       899***************************************999887665666779**********8654 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   2.5e-05     0.025      40     150 ..     119     234 ..     110     238 .. 0.82
   2 ?    1.2   0.0       0.2   1.9e+02     204     228 ..     253     277 ..     244     278 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.5e-05
                                       HHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSS...TEEEEE--TTT-..T CS
                   Ubie_methyltran  40 eklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegki...nieflqanaeeL..p 111
                                        ++v++++++ vlD + G g  a++   s+++   v+ ++ ++n+++ ++       +    ni+ +q++a e+  +
  gi|242399162|ref|YP_002994586.1| 119 VDTVNPRESEFVLDTCMGLGYTAIE---SAKRGAYVMTIEKDPNVIELARLNPWSWEVFnsqNIQVIQGDASEIikK 192
                                       46788999999*******9988875...66677789999999999999987755444333569********998557 PP

                                       TS-T-EEEEEEE...S-GGG-S-HHHHHHHHHHHEEEEEEEE CS
                   Ubie_methyltran 112 feddsfDvvtvs...fGlrnvtDklkaLkeayrvlkpGGrlv 150
                                       f+d++f+v+      f l      +   ke++rvlkp Grl+
  gi|242399162|ref|YP_002994586.1| 193 FNDETFNVIIHDpprFSLAGHLYSEAFYKELFRVLKPKGRLF 234
                                       99*****997634449***999999**************985 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.2
                                       HHHHHHHTTEEEEEEEEEGGGTEEE CS
                   Ubie_methyltran 204 lkeliedaGfksveyesltgGvvai 228
                                       + e +++aGf++v+  + + Gvva+
  gi|242399162|ref|YP_002994586.1| 253 VIERLRNAGFTKVRKVEEALGVVAT 277
                                       556789****************996 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.78   7.7e+02      37      86 ..      30      77 ..       9      96 .. 0.68
   2 !    9.9   0.0   0.00055      0.55     191     229 ..     126     164 ..     117     166 .. 0.91
   3 ?    2.8   0.0     0.083        83      36      66 ..     217     246 ..     213     266 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.78
                                      HHHHHHHHHEEEEEEEEEEE-CCCHHTHHHHHHHHHTT-EEEEEEEEEEE CS
                       N6_N4_Mtase 37 kvlkevrrvLkddgsifiniddseikkelkaladeifggffllnvivwkk 86
                                      k  ++++ + k+d+++f   +++e    lk++a+++    ++l++ ++ k
  gi|242399162|ref|YP_002994586.1| 30 KTNRIHKVIVKEDKVVFPDESEIEKDI-LKKIAKDENT-VYFLKDSHIYK 77
                                      445566667777777777666666554.6666666666.55555544444 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00055
                                       TT-EEEETT-TTTHHHHHHHHTT-EEEEEESSHHHHHHH CS
                       N6_N4_Mtase 191 kgdivlDpFaGSGtTavaakelgrkfiGieieeeyvela 229
                                       + + vlD  +G G+Ta++ ++ g     ie++++ +ela
  gi|242399162|ref|YP_002994586.1| 126 ESEFVLDTCMGLGYTAIESAKRGAYVMTIEKDPNVIELA 164
                                       5789*******************99999******99987 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.083
                                       HHHHHHHHHHEEEEEEEEEEE-CCCHHTHHH CS
                       N6_N4_Mtase  36 ekvlkevrrvLkddgsifiniddseikkelk 66 
                                       e + ke+ rvLk+ g +f  ++   +k+ +k
  gi|242399162|ref|YP_002994586.1| 217 EAFYKELFRVLKPKGRLFHYVGNPGAKY-RK 246
                                       56789*************9999988886.44 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   2.3e-05     0.023      20     120 ..     124     238 ..     104     269 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.3e-05
                   Methyltransf_23  20 lraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae...........kakkaqkdqfdeqeaaepqgkfdl 85 
                                        r++  vLd   G G+++ + +++g+ v  ++ +p+ +e+a+           + ++ ++  + e+  ++++++f++
  gi|242399162|ref|YP_002994586.1| 124 PRESEFVLDTCMGLGYTAIESAKRGAYVMTIEKDPNVIELARlnpwswevfnsQNIQVIQGDASEIIKKFNDETFNV 200
                                       466778******************************************9998866666666666888888999**** PP

                   Methyltransf_23  86 Ivl...revlehvpdppellrqiatllkpgGylllsep 120
                                       I+    r++l    + ++  + +++ lkp G+l++ + 
  gi|242399162|ref|YP_002994586.1| 201 IIHdppRFSLAGHLYSEAFYKELFRVLKPKGRLFHYVG 238
                                       *9655577777777779999999999999999987663 PP

>> SAM_MT  Putative SAM-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   5.2e-05     0.051      48     156 ..     103     205 ..      97     209 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.2e-05
                            SAM_MT  48 ahRrkfgggrgeaiakavglkkgvlptvlDaTaGlGrDafvlaslGckvtliErhpvvaaLLedglkRakqdaeige 124
                                        hR k ++  +++  k+  ++   +  vlD+  GlG  a+  a  G+ v  iE++p v  L      R +  +  + 
  gi|242399162|ref|YP_002994586.1| 103 MHRTKDTNPLKDTRSKVDTVNPRESEFVLDTCMGLGYTAIESAKRGAYVMTIEKDPNVIEL-----ARLNPWS-WEV 173
                                       577777777777777777788888899******************************9976.....5655433.344 PP

                            SAM_MT 125 llaerlkLlaasslealakleeekpdvvYlDP 156
                                       + +++++++++++ e+++k ++e+ +v+  DP
  gi|242399162|ref|YP_002994586.1| 174 FNSQNIQVIQGDASEIIKKFNDETFNVIIHDP 205
                                       56899****************99999999998 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   7.6e-05     0.076      67     154 ..     139     229 ..     101     237 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.6e-05
                                       HHHHHHHHHH--EEEEES-HHHHHHHHHHHHHTT-..GGGEEEEE--GGG--..STTS---EEEE----------HH CS
                           UPF0020  67 aeaeeearaelklygsDldrrvvqgareNaekagv..gdliefsqadaakLr..lkegevdvivtnpPYGerlgskk 139
                                        +a e+a++ + ++ +++d++v++ ar N  + +v  ++ i++ q da ++    +++ ++vi+ +pP   +l  + 
  gi|242399162|ref|YP_002994586.1| 139 YTAIESAKRGAYVMTIEKDPNVIELARLNPWSWEVfnSQNIQVIQGDASEIIkkFNDETFNVIIHDPPR-FSLAGHL 214
                                       56777777888899***************9988874467899*******9986544558*********3.3444455 PP

                                       HHHHHHHHHHHHHHH CS
                           UPF0020 140 alekLYseflrelkr 154
                                         e++Y+e+ r lk 
  gi|242399162|ref|YP_002994586.1| 215 YSEAFYKELFRVLKP 229
                                       558888888887775 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 ?   12.0   0.0   0.00012      0.12       3      88 ..     121     206 ..     119     212 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00012
                                       HH---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHH...HHHTT--SEEEEES-CTCCHHHHC CS
                   Methyltr_RsmB-F   3 lLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaen...lkrLgvtntivleaDarkidkvlg 76 
                                       + +p+e e++lD c + G   t i    k  + v+ ++++ + ++    n    + ++ +n++v+++Da++i k   
  gi|242399162|ref|YP_002994586.1| 121 TVNPRESEFVLDTCMGLGY--TAIESA-KRGAYVMTIEKDPNVIELARLNpwsWEVFNSQNIQVIQGDASEIIKKFN 194
                                       679************9884..455554.88899999888877666555552226788999***************** PP

                                       C..EEEEEEEE- CS
                   Methyltr_RsmB-F  77 gelfDriLlDaP 88 
                                       +e+f  i+ D P
  gi|242399162|ref|YP_002994586.1| 195 DETFNVIIHDPP 206
                                       *****9999988 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0    0.0002       0.2      25      78 ..     150     206 ..     133     235 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.0002
                   Methyltransf_24  25 rlvavdhdpgaeeaaalare......aglddrvrlikadseealaslaagsiDllfiDgg 78 
                                        ++++++dp   ++ +lar          ++++++i++d++e +++++++++ +++ D +
  gi|242399162|ref|YP_002994586.1| 150 YVMTIEKDP---NVIELARLnpwsweVFNSQNIQVIQGDASEIIKKFNDETFNVIIHDPP 206
                                       577888888...66666663344444788999*************************953 PP

>> Palm_thioest  Palmitoyl protein thioesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00039      0.39     173     219 ..      27      78 ..      11      85 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00039
                      Palm_thioest 173 nllkleklvlvgfsdDtvvvPkeSslfgfykeks....eev.pleetelYke 219
                                        l k ++++ v  ++D+vv P+eS++ +++ +k     ++v  l+++++Yk+
  gi|242399162|ref|YP_002994586.1|  27 DLRKTNRIHKVIVKEDKVVFPDESEIEKDILKKIakdeNTVyFLKDSHIYKA 78 
                                       57899********************987655533555344568888888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1832.38
//
Query:       gi|242399163|ref|YP_002994587.1|  [L=349]
Description: Hydrogenase expression/formation protein HypE [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.6e-17   62.3   0.0    9.3e-17   61.6   0.0    1.4  1  AIRS_C    AIR synthase related protein, C-terminal domain
    2.6e-14   53.6   0.0    5.4e-14   52.6   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 !   61.6   0.0     1e-20   9.3e-17       1     154 [.     174     329 ..     174     331 .. 0.81

  Alignments for each domain:
  == domain 1  score: 61.6 bits;  conditional E-value: 1e-20
                                       STTEEEEEEETSSCTCCHHHHHHHCHHHCTSHTT.....TSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHH CS
                            AIRS_C   1 kpGdvliltgslGlggagtslkrkileeegldds.....avqlgdvlleptliyvkralaalkglvkaahDvTgGGL 72 
                                       kpGd +i t+++ +  a+  +++   ee +  ++      + l + + ++t+++ ++++   k+ ++++hDvT+GGL
  gi|242399163|ref|YP_002994587.1| 174 KPGDDIIITKGIAIEFAV-GAAWFRTEELK--KIlspsqISSLREMYTLETVVKDALLA---KKFARGMHDVTEGGL 244
                                       79*********9999999.99995555544..554444333344444444454444444...556*********998 PP

                                       HHHHHHHHHTTTEEEEEECG...THHHHHHHH..HHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEE CS
                            AIRS_C  73 lgalaemapasgvgaeidld...kvpifdele..splemllsensGrllvavppeeadavlaileeeglpeaavIGe 144
                                       + +l+e+a+ s+vg+e++++    +p+++++    +  +l + + G l+++ p+e+  +++++l+++g+ +a+ +G+
  gi|242399163|ref|YP_002994587.1| 245 T-TLHEIADNSEVGFEVYYEklhMPPLVKKVVkfYGVNPLTVSSTGTLIIISPQENTSKLIKALHSHGI-NASTVGK 319
                                       5.8********************9999999888888999999****99999999999************.8****** PP

                                       EEESSSEEEE CS
                            AIRS_C 145 vtakeelsvi 154
                                        t+++e ++i
  gi|242399163|ref|YP_002994587.1| 320 FTEEKERALI 329
                                       ***9987765 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 !   52.6   0.0     6e-18   5.4e-14       2      94 .]      57     163 ..      56     163 .. 0.85

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 6e-18
                                       SSEE.........EEEEEEEE.EECCTCCCCHHHHHHHHHHHHHHTTTEEEEEEEEEEEEC......HHHHHHHHHH CS
                              AIRS   2 Daav.........vvttdshnrpvlvepvhfiGakavavnlsDlaamGArPlalllslalp......wleevvrgla 63 
                                       Daav         v++td     + v + hf G  + + + sD+a+ GA P +l+++l lp      +l+ v+r+l+
  gi|242399163|ref|YP_002994587.1|  57 DAAVleydeknylVIATD---PILGVPKEHF-GFFTYHFASSDVAVFGAIPKWLIVNLLLPngtteeDLNSVMRELN 129
                                       788333444444477777...3333455677.********************************************* PP

                                       HHHHHTT-EEEEEEEEEESS...EEEEEEEEEEE CS
                              AIRS  64 eaaeelgvplvgGdtsfsne...ptisvtavGlv 94 
                                       e ++++g++++gG+t +++    +t ++ta+Glv
  gi|242399163|ref|YP_002994587.1| 130 EECKKYGTSIIGGHTGVYSTtrsFTATTTAIGLV 163
                                       *****************977789*********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); 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 0.25s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2361.00
//
Query:       gi|242399164|ref|YP_002994588.1|  [L=364]
Description: Cell division like protein pelota [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-32  112.5   1.1    2.5e-32  111.6   1.1    1.4  1  eRF1_1          eRF1 domain 1
    1.8e-23   83.1   3.0    1.8e-23   83.1   3.0    2.1  2  eRF1_3          eRF1 domain 3
    5.3e-15   55.9   0.1    1.2e-14   54.7   0.1    1.6  1  eRF1_2          eRF1 domain 2
      0.004   17.7   0.6      0.023   15.3   0.1    2.3  2  baeRF_family12  Bacterial archaeo-eukaryotic release factor f
  ------ inclusion threshold ------
      0.018   15.3   1.5      0.035   14.4   0.2    2.2  2  baeRF_family10  Bacterial archaeo-eukaryotic release factor f
      0.037   14.0   0.8       0.38   10.7   0.8    2.3  1  IQ_SEC7_PH      PH domain


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 !  111.6   1.1   8.3e-36   2.5e-32       3     128 ..      11     135 ..       9     136 .. 0.89

  Alignments for each domain:
  == domain 1  score: 111.6 bits;  conditional E-value: 8.3e-36
                                       EEEECTBTTSCCEEEEEE-SCHHHHHHHHHCHTTHEEEEEEEECHHH........--CEEEEEEEEEEEEEEECTTS CS
                            eRF1_1   3 llkrdlekdgsgsvtLipeddedlwhlynliapgdsvrastvrkvqr.esstgsreservklkLtikvekvdfdkda 78 
                                       ++++d +   +g +++ +e+ +dlwhly++i++gd v a+t+rk  + + s    + +++ + L ikvekv+f+k a
  gi|242399164|ref|YP_002994588.1|  11 IIHQDPK---EGKIKVKVETLDDLWHLYHVIEEGDIVYAKTFRKQSQrSDSLRPEKVQTIPVFLGIKVEKVNFHKFA 84 
                                       5555554...899*******************************877233444455899****************** PP

                                       SEEEEEEEEEEGGGG.--TTSEEEEEE-TTSEEEEEECEESHHHHHHHHHH CS
                            eRF1_1  79 gvlrisGkvieeneh.vklgafhtldlelkrpftiikeewdsfalerLkea 128
                                       + lri+G +++++++ v++g++htl +e ++ +ti+ke+w+++++erL+ea
  gi|242399164|ref|YP_002994588.1|  85 NSLRITGPIVSSSREeVPIGKYHTLAIEENNTITIQKEKWKRHHIERLEEA 135
                                       ********99877655**********************************9 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       1.1   3.4e+03      76      88 ..     137     149 ..     103     195 .. 0.56
   2 !   83.1   3.0   6.2e-27   1.8e-23       2     113 .]     269     363 ..     268     363 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.1
                                       HHHHHTT-EEEEE CS
                            eRF1_3  76 enveesgakveii 88 
                                       +  +  +  +++i
  gi|242399164|ref|YP_002994588.1| 137 KASQRARVMITVI 149
                                       3333332222222 PP

  == domain 2  score: 83.1 bits;  conditional E-value: 6.2e-27
                                       HHHHHHHHHHHHHHHCTCSSEEESHHHHHHHHHTT-EEEEEEEHCHHTSSSHHHHHS-HHH-HHHHHHHHHHHHHHH CS
                            eRF1_3   2 iqekklleefleelakdtgkavYGveevlkalemgAvetLLvseelersrdtlkekvketgeelelvelieelvenv 78 
                                       ++e++l+e+++ee++++ +++vYG +ev++a+ +gA+etLLv++el + +  +k+k             ie+++e v
  gi|242399164|ref|YP_002994588.1| 269 AKEVQLVEKVIEEISRG-KLVVYGLKEVEEAASYGAIETLLVIDELMKGE--YKDK-------------IEQIMEFV 329
                                       79*************99.******************************98..5666.............9******* PP

                                       HHTT-EEEEE-TTSHHHHHHHHHTTTEEEEESS-- CS
                            eRF1_3  79 eesgakveiisseseeGeqlvkafgGiaaiLRykv 113
                                       + ++++v i+sse+e Ge+l ka+gGiaa+LRyk+
  gi|242399164|ref|YP_002994588.1| 330 RGTRGEVLIVSSEHEGGEKL-KALGGIAALLRYKI 363
                                       ********************.************97 PP

>> eRF1_2  eRF1 domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.7   0.1   4.1e-18   1.2e-14       4     126 ..     146     256 ..     143     265 .. 0.89

  Alignments for each domain:
  == domain 1  score: 54.7 bits;  conditional E-value: 4.1e-18
                                       EEEEETTEEEEEEEESSCEEEEEEEE------BSTTBSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCHTTTESEE CS
                            eRF1_2   4 livldegeAtigllkgsrtevlkkievsvPkKhkrGgqsarrfeRlreekleeflkkvaeaankafllvdkdklkgi 80 
                                       + v+degeA i++++++ +e +++i+ ++ +K+     +a+     re + ++f++ + + + +    ++++ ++  
  gi|242399164|ref|YP_002994588.1| 146 ITVIDEGEADIAVVREYGVEHIANITHNLGGKRY----NAD-----RESEEKKFFHDLSKTMLEI---MERERVDKA 210
                                       779******************************7....455.....4677788888888888777...79******* PP

                                       EEEESSTHHHHHHHHHHHHHHHHTCCEEEEE-S-TSCHHHHHHHHC CS
                            eRF1_2  81 ilagpgfvkeefldkdlldaelkkkviklvdvsyggesglnevlek 126
                                       i+agpgf+ke+f++ +  ++   +k++++ d+s +g  g+ ev++ 
  gi|242399164|ref|YP_002994588.1| 211 IVAGPGFTKENFYKFLSENYPDLAKKVVIEDTSVTGSTGIYEVIRR 256
                                       ********************************************97 PP

>> baeRF_family12  Bacterial archaeo-eukaryotic release factor family 12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1      0.48   1.4e+03      62      98 ..     112     148 ..      94     157 .. 0.70
   2 !   15.3   0.1   7.6e-06     0.023      64     113 ..     180     229 ..     160     241 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.48
                    baeRF_family12  62 eetdfkeqeeerFakeladeLkkrakegkferlvlva 98 
                                       ee ++ + ++e++ ++  ++L++++k+++  r+ +++
  gi|242399164|ref|YP_002994588.1| 112 EENNTITIQKEKWKRHHIERLEEAVKASQRARVMITV 148
                                       4445555578888888888888888888777777766 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 7.6e-06
                    baeRF_family12  64 tdfkeqeeerFakeladeLkkrakegkferlvlvappetlgelrkhlhke 113
                                        + +e ee++F+++l++++ + ++++++++ ++ +p +t + + k l+++
  gi|242399164|ref|YP_002994588.1| 180 NADRESEEKKFFHDLSKTMLEIMERERVDKAIVAGPGFTKENFYKFLSEN 229
                                       3445569*********************************9999998876 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 ?   14.4   0.2   1.2e-05     0.035      23     124 ..     139     246 ..      98     257 .. 0.81
   2 ?   -2.6   0.1         2   6.1e+03      77     103 ..     272     298 ..     264     300 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.2e-05
                    baeRF_family10  23 reraRlfevylgelee.veevegevpgrtk..tggwksqdrfqrreeeqaerhlkevAellaklleergverlvlgG 96 
                                        +raR++   ++e e    +v++  +++ +  t+   + +r+ + +e   +++++++ +++ +++e+++v+  +++G
  gi|242399164|ref|YP_002994588.1| 139 SQRARVMITVIDEGEAdIAVVREYGVEHIAniTHNL-GGKRYNADRESEEKKFFHDLSKTMLEIMERERVDKAIVAG 214
                                       578888888888888867777777777666666666.99************************************** PP

                    baeRF_family10  97 deeetaalldrlpk...alrarvvgt.lplpv 124
                                       +   ++++ + l++   +l+++vv + +++ +
  gi|242399164|ref|YP_002994588.1| 215 PGFTKENFYKFLSEnypDLAKKVVIEdTSVTG 246
                                       *8888877777776111566666655566665 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2
                    baeRF_family10  77 AellaklleergverlvlgGdeeetaa 103
                                       ++l++k++ee     lv+ G +e+++a
  gi|242399164|ref|YP_002994588.1| 272 VQLVEKVIEEISRGKLVVYGLKEVEEA 298
                                       578888888888888888888777665 PP

>> IQ_SEC7_PH  PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.8   0.00013      0.38     100     132 ..     178     208 ..      37     212 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00013
                        IQ_SEC7_PH 100 tfnakneedrkkfvedlkesilEveemeklrie 132
                                        +na  e++ kkf++dl +++lE+ e  ++r++
  gi|242399164|ref|YP_002994588.1| 178 RYNADRESEEKKFFHDLSKTMLEIME--RERVD 208
                                       589********************955..55554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       828  (0.0461822); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 2432.96
//
Query:       gi|242399165|ref|YP_002994589.1|  [L=201]
Description: 50S ribosomal protein L15e [Thermococcus sibiricus MM 739]
Scores for complete 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-88  293.4   7.3    7.5e-88  293.3   7.3    1.0  1  Ribosomal_L15e  Ribosomal L15


Domain annotation for each model (and alignments):
>> Ribosomal_L15e  Ribosomal L15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  293.3   7.3   4.2e-92   7.5e-88       1     191 []       9     196 ..       9     196 .. 0.99

  Alignments for each domain:
  == domain 1  score: 293.3 bits;  conditional E-value: 4.2e-92
                                       -SHHHHHHHTTSTTSHHHHHHHHHHHHHHTTS-SEEEESS-SSHHHHHHHT--SSTTEEEEEEEEE-SS---..--- CS
                    Ribosomal_L15e   1 gaykylrelwkkkqsdvlrellrerlweyrqepavvrverptrldrArrLGYkakqGivvvrvrvrrGgrkkkvskg 77 
                                       g+yky+re+wk+++++++  ll++r++++r+ep +vr+erptrldrAr+LGY+akqG+v+vrvrvr+Ggrk+  ++ 
  gi|242399165|ref|YP_002994589.1|   9 GMYKYIREAWKNPKKTYVGDLLKQRMIKWRREPGIVRIERPTRLDRARNLGYQAKQGYVLVRVRVRKGGRKR--PRW 83 
                                       79**********************************************************************..*** PP

                                       SS---GGGG-SSS---SS-HHHHHHHHHHHHSTTSEEEEEEEEEEESSEEEEEEEEE-TTSHHHHT-TTTGGGGSGG CS
                    Ribosomal_L15e  78 ktgrkpkrqgvnklkpakslqaiaeervgrklpnlrvLnSYwvgeDgtykyyEvilvDpshkairndkkinwickkv 154
                                       k grkp+++g  k++p+kslq+iaee+++rk+pnl+vLnSYwvgeDg+y+++EvilvDp+h++i++d+ki wi+ k 
  gi|242399165|ref|YP_002994589.1|  84 KGGRKPSKMGQVKYSPKKSLQWIAEEKAARKFPNLEVLNSYWVGEDGMYRWFEVILVDPHHPVIKSDSKIAWIAGKA 160
                                       ***************************************************************************** PP

                                       GTTGGGGT-SHHHHHHTT-S-SS.TT-TTTSS-TGGG CS
                    Ribosomal_L15e 155 hkhRelrGltsagkksRGlrkkglkgaekirgsrran 191
                                       hk+R++rGltsagkksRGlr+kg kgaek+r+s+ra+
  gi|242399165|ref|YP_002994589.1| 161 HKGRVFRGLTSAGKKSRGLRNKG-KGAEKVRPSIRAH 196
                                       ***********************.**********995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); 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 0.27s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1222.48
//
Query:       gi|242399166|ref|YP_002994590.1|  [L=312]
Description: hypothetical protein TSIB_1187 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score 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   14.5   0.1      0.067   13.5   0.1    1.4  1  DUF1548   Domain of Unknown Function (DUF1548)


Domain annotation for each model (and alignments):
>> DUF1548  Domain of Unknown Function (DUF1548)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   3.7e-06     0.067      16      73 ..      66     127 ..      57     134 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.7e-06
                           DUF1548  16 yGeeLGLivdnlakildaltlr..ltsrlilkkkekYkrllk..eFlqaYkasvseLveyil 73 
                                       y e+LG iv+  +++++ +t++   t++ i    + Y   ++  +F ++Yk+   +L+ey+ 
  gi|242399166|ref|YP_002994590.1|  66 YIENLGFIVNTFGRYFSDYTTTacTTGEDISGWINPYLIYKNgiNFDSQYKNMLDNLIEYLN 127
                                       6689***************9863368999********55444557***************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); 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: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 1949.56
//
Query:       gi|242399167|ref|YP_002994591.1|  [L=498]
Description: hypothetical protein TSIB_1188 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-09   36.6   0.0    5.6e-07   29.0   0.0    2.3  2  SQHop_cyclase_C  Squalene-hopene cyclase C-terminal domain
  ------ inclusion threshold ------
       0.12   11.9   0.2       0.28   10.8   0.2    1.6  1  Baculo_11_kDa    Baculovirus 11 kDa family


Domain annotation for each model (and alignments):
>> SQHop_cyclase_C  Squalene-hopene cyclase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.0   6.3e-11   5.6e-07     190     289 ..      58     160 ..      51     171 .. 0.82
   2 !    5.2   0.0    0.0011       9.4     239     279 ..     396     436 ..     376     443 .. 0.81

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 6.3e-11
                                       HHHHHHHHHHTT--TTSHHHHHHHHHHHTT--TTSSBB--.GGGGT..-GGGTT-SSBBHHHHHHHHHHHHHTTGG. CS
                   SQHop_cyclase_C 190 twsvlsalaavgedleepvirkavdWlksvqnedGGWGes.aesyk..dpklagkgestasqtaWallallaagev. 262
                                           ++ala  + ++++p +++ v+ +ks+q +dG +    ++ y   + +++   +s a+ ta allall age+ 
  gi|242399167|ref|YP_002994591.1|  58 SCLKVIALARSSFPKDSPDFQRLVEEIKSKQLKDGSFPPIiTDDYPkeEGEWFYWEKSKAAGTALALLALLEAGESp 134
                                       55667889999999***********************875267787324467788*******************983 PP

                                       GSHHHHHHHHHHHHH--TTS-----S- CS
                   SQHop_cyclase_C 263 eseavkrGiaylletqkedGtWeeeay 289
                                       +se v++Gi++ll++++ed  W+ + y
  gi|242399167|ref|YP_002994591.1| 135 NSEVVTKGIKFLLANKTED-YWTSTVY 160
                                       677899*******998655.7877665 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0011
                                       TT-SSBBHHHHHHHHHHHHHTTGGGSHHHHHHHHHHHHH-- CS
                   SQHop_cyclase_C 239 agkgestasqtaWallallaageveseavkrGiaylletqk 279
                                        g+ +    +t+ al+ l  age++ +  k+Gi++ll++ +
  gi|242399167|ref|YP_002994591.1| 396 DGSWNHDVYSTSIALIWLYLAGETDYNGFKKGIEFLLRNDR 436
                                       555555667899************************99875 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 ?   10.8   0.2   3.1e-05      0.28      43      83 ..       3      43 ..       1      44 [. 0.93

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3.1e-05
                     Baculo_11_kDa 43 lvvfvvivlfilLlvvilknaeaeeaekekrektllaNldl 83
                                      ++v+vv+vl++ L ++++++++ e+  + ++ + +++N+++
  gi|242399167|ref|YP_002994591.1|  3 IFVVVVLVLLLSLPFSLAQSVSVEKDYQMRTLHSYAKNYGI 43
                                      67999999999****************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (498 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       676  (0.0377043); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.51
# Mc/sec: 2952.20
//
Query:       gi|242399168|ref|YP_002994592.1|  [L=50]
Description: hypothetical protein TSIB_1189 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 357.43
//
Query:       gi|242399169|ref|YP_002994593.1|  [L=154]
Description: exosome subunit, DUF54 family [Thermococcus sibiricus MM 739]
Scores for complete 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  134.3   0.8    2.9e-39  134.0   0.8    1.1  1  RNA_binding  RNA binding
     0.0048   16.3   0.2     0.0072   15.8   0.2    1.2  1  DUF3552      Domain of unknown function (DUF3552)


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 !  134.0   0.8   3.2e-43   2.9e-39       2     119 .]      12     134 ..      11     134 .. 0.98

  Alignments for each domain:
  == domain 1  score: 134.0 bits;  conditional E-value: 3.2e-43
                                       EEEEEEE-TTC-HHHHHHHHHTTSTTS....E---EEEEEE-CCC-EEEEEEEEESSHHH.HHHHHHHHHHHCCCCH CS
                       RNA_binding   2 ievrafvhaTEdeekVlealsnllpee....eveieeeeaeGhygnpitileaelekkka.kkvlkkllellreeei 73 
                                       i+v++f haTEd ekVlea+ +++pe+    ++e+e+ e+eG++gnpi++++ae+++++  kk+l+++++ll+ee++
  gi|242399169|ref|YP_002994593.1|  12 IRVSTFGHATEDPEKVLEAMGTFFPEDipseDIEFEIIETEGYFGNPIKVINAEVKRSRSvKKMLEHIKNLLSEEDK 88 
                                       99***********************99***9999******************************************* PP

                                       HHHHHCCHCCB-TTSEEEEEEEHHHHHTT---BESSSSEEEEEEEE CS
                       RNA_binding  74 keLlkeleervdekgklylrldKQaaylgklslvegddvIkvkikv 119
                                       ++Ll++lee+vde g++++r++KQ+aylg+  + eg+dvI+vkikv
  gi|242399169|ref|YP_002994593.1|  89 EYLLENLEEKVDEAGTFFIRFSKQRAYLGEAVIGEGEDVIQVKIKV 134
                                       ********************************************96 PP

>> DUF3552  Domain of unknown function (DUF3552)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.2     8e-07    0.0072     134     178 ..      70     114 ..      57     118 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 8e-07
                           DUF3552 134 eeqrqeLerisgLtkeeAkeilleeveeelkheaAkmikeieeea 178
                                       ++ ++ Le+i +L +ee ke+lle++ee++++  +  i+ ++++a
  gi|242399169|ref|YP_002994593.1|  70 RSVKKMLEHIKNLLSEEDKEYLLENLEEKVDEAGTFFIRFSKQRA 114
                                       455789**************************9999999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1218  (0.0679346); expected 358.6 (0.02)
Passed bias filter:                      762  (0.042501); 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: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.51
# Mc/sec: 915.44
//
Query:       gi|242399170|ref|YP_002994594.1|  [L=214]
Description: Ribonuclease P protein component 3 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.5e-34  117.8   0.0    5.2e-34  117.6   0.0    1.0  1  RNase_P_p30    RNase P subunit p30
  ------ inclusion threshold ------
      0.078   13.0   0.1       0.14   12.2   0.1    1.3  1  Ribosomal_L29  Ribosomal L29 protein


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 !  117.6   0.0   5.8e-38   5.2e-34      27     214 ..      21     201 ..       5     202 .. 0.87

  Alignments for each domain:
  == domain 1  score: 117.6 bits;  conditional E-value: 5.8e-38
                                       -SEEEEEEEEEESS---HHHHH.......HHHHHHHH...HHSSEEEEEEES-.H.HHHHHHHHH--EEEEE--SHH CS
                       RNase_P_p30  27 ytgvainftveaekekkpnasepikeelkelkkelsg.lkllsRvtlvvsdps.klqrlskvrqkfdllavrPttek 101
                                       y++v+++++v       ++++     ++ elk++++g  + + ++ l + + + +l r  k r    l++v++++ +
  gi|242399170|ref|YP_002994594.1|  21 YDEVVFTKKVY-----LRDSP-----NFGELKSDVKGlKEKYGKIALLLITEKpSLIREVKKRIPNALIYVQGGNLR 87 
                                       45555444444.....22333.....36788999999777999999988888845677888888889********** PP

                                       HHHHHHHT.T-SEEE-TTTTSSS-S--HHHHHHHHHHT-EEEEESHHHHHS-HHHHHHHHHHHHHHHHHHHH..--E CS
                       RNase_P_p30 102 alraacenldvDiisidltsrlpfglkhktiraAvergvafEinyspllrdsglaRrnfisnarkllrltrg..kgv 176
                                       ++r+a+en +vD i+ +  +r+++gl+h+++r+A+++ va+ +++spllr++ ++R+n+++ +++++rl+++   + 
  gi|242399170|ref|YP_002994594.1|  88 VVRFAIEN-KVDAIISPEYGRKDSGLDHVLARLAASNDVAIGFSLSPLLRANSYERANILKFMMRNWRLVDKykVPR 163
                                       ******99.9******************************************************************* PP

                                       EEE--BSSGGG---HHHHHHHHHHHT--HHHHHHTTTH CS
                       RNase_P_p30 177 viSSgAesplelRnpydiinLlktlGLeedrakeavse 214
                                       +++S+Aes++e+R+p+d+++L+  +G+e  +ak+++s 
  gi|242399170|ref|YP_002994594.1| 164 FLTSSAESKWEVRSPKDLMSLGINIGMEIPQAKSSLSF 201
                                       **********************************9986 PP

>> Ribosomal_L29  Ribosomal L29 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   1.6e-05      0.14      10      47 ..      40      74 ..      37      78 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.6e-05
                                      HHHHHHHHHHHHHHHHHHHHHHTSSS-CHHHHHHHHHH CS
                     Ribosomal_L29 10 eLkeklkelkkeLfnLrfqkatgqlenpsrirkvRkdI 47
                                      eLk  +k lk+++ +  +   t+   +ps ir+v+k+I
  gi|242399170|ref|YP_002994594.1| 40 ELKSDVKGLKEKYGKIALLLITE---KPSLIREVKKRI 74
                                      99999****************99...**********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1365.71
//
Query:       gi|242399171|ref|YP_002994595.1|  [L=373]
Description: hypothetical protein TSIB_1192 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-32  112.5   1.6    1.9e-32  111.8   1.6    1.3  1  DUF835    Protein of unknown function (DUF835)


Domain annotation for each model (and alignments):
>> DUF835  Protein of unknown function (DUF835)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.8   1.6   1.1e-36   1.9e-32       7     135 ..     240     368 ..     236     369 .. 0.88

  Alignments for each domain:
  == domain 1  score: 111.8 bits;  conditional E-value: 1.1e-36
                            DUF835   7 kakeilsdlvkegvkvlaitRenpkkirekvkienvkviwltkveeentvsPtnlekltetivkflkeaekg....v 79 
                                       k + il++  k + +vla++R+ ++   + v  e   ++ +tk+ + n +sPtnle++te   ++l+  e++    v
  gi|242399171|ref|YP_002994595.1| 240 KRYAILKEKLK-DIPVLAFVRDLKEA--SDV-WERYFITTITKEGKDNFISPTNLERITELSYRYLRMMEEKgsrgV 312
                                       55667766666.4*********7555..345.7888899999999999****************998777666778* PP

                            DUF835  80 vliDgleyLvlengFesvlkflltlkDavllkngtlilvidkealeekelalLkre 135
                                       +++D++eyL+++n+F+sv+kfl ++kD+v+ ++gtli+v++kea+e++++alL+r 
  gi|242399171|ref|YP_002994595.1| 313 IVLDCVEYLLMYNDFSSVMKFLNKIKDFVMHYKGTLIIVVEKEAFEDQQWALLMRL 368
                                       ******************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       838  (0.0467399); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 2183.77
//
Query:       gi|242399172|ref|YP_002994596.1|  [L=352]
Description: hypothetical protein TSIB_1193 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.26   10.6   0.0       0.41   10.0   0.0    1.2  1  PNMA      PNMA


Domain annotation for each model (and alignments):
>> PNMA  PNMA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   2.3e-05      0.41      25      60 ..     176     209 ..     174     231 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 2.3e-05
                              PNMA  25 gipedceeaeieetLqaaLkpLGryrVlgkiFrree 60 
                                       gi ++ +e+ +ee+L++ L pL ry    +iF +++
  gi|242399172|ref|YP_002994596.1| 176 GIKQELKEKRLEEVLEGRLGPLARYT--KRIFEKDR 209
                                       99***********************5..78888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 2175.51
//
Query:       gi|242399173|ref|YP_002994597.1|  [L=423]
Description: hypothetical protein TSIB_1194 [Thermococcus sibiricus MM 739]
Scores for 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-08   31.7   0.0    1.1e-07   30.8   0.0    1.4  1  AMP-binding  AMP-binding enzyme
     0.0025   16.7   0.0       0.18   10.7   0.0    2.1  2  GH3          GH3 auxin-responsive promoter


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.0   1.3e-11   1.1e-07     165     323 ..      80     232 ..      67     256 .. 0.81

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 1.3e-11
                                       EEE--SSSS-EEEEEEHHHHHHHHHHHH...HHHCSCCTTT-EEEES.S-TTSCHHHHHHHHHHHHTT-EEEE-TTC CS
                       AMP-binding 165 iYTSGTTGkPKGVmlshrnlvanvaslk...letrfklkeddvvlsi.lplahifglilelllallsGatvvllpkd 237
                                       + TSGTTG PK V  +h+      +++    le    l e++ + s+ +pl  + g+ l++ ++  +  + + +p  
  gi|242399173|ref|YP_002994597.1|  80 MRTSGTTGDPKRVAFTHDDKKRYRRQARswaLE---YL-EGSIMASFtAPLPSSSGI-LAIEGFSDANIRYHQIPIQ 151
                                       66***************6664444443221122...22.578999987999999996.9999999999999999988 PP

                                       GCCHHHHHHHHHHHHT-SEEEEEHHHHHHH.HHCCCHHCHHHHCCGTT.-SEEEEESS-EBHHHHHHHHHHHTC.EE CS
                       AMP-binding 238 aaldpklllelieklkvtviagvPrvleal.lesgalkaakkakdlss.lrlvllggeplspellrffralfge.ev 311
                                         ++ ++l++ ++ +k+t i+g  +++  l l    ++      d    ++l+++gge l +el++ + + f++  +
  gi|242399173|ref|YP_002994597.1| 152 YLRMRDALIKELRGIKATGIFGLTAAIYNLsLTL--PE------DIRNdIQLIIMGGETLTKELAKVVLDNFPNaVI 220
                                       777789999************9999888884555..34......55566*************************99* PP

                                       EEEEEEGGGSSE CS
                       AMP-binding 312 legYGlTEttgv 323
                                       ++++G TE +  
  gi|242399173|ref|YP_002994597.1| 221 FDVFGNTEDGLT 232
                                       ********8765 PP

>> GH3  GH3 auxin-responsive promoter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0     2e-05      0.18      80     118 ..      80     117 ..      74     168 .. 0.79
   2 !    3.9   0.0    0.0022        20     370     421 ..     284     330 ..     280     354 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 2e-05
                                       EEECCEETTEEEEEEESHHHHHHHHHH.HHHHHHHHHHH CS
                               GH3  80 alsSGTtsgksKliPvteeslkelallvlallaallsry 118
                                         +SGTt g +K + +t++  k++++++ +++ ++l+  
  gi|242399173|ref|YP_002994597.1|  80 MRTSGTT-GDPKRVAFTHDDKKRYRRQARSWALEYLEGS 117
                                       57*****.*******************999999998533 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.0022
                                       -SSEEECEEEEEEEEETTEEEEEEEECCTEEE-SSSS-CCHHHHHHHHH.HH CS
                               GH3 370 LyRYrigDvvrvtgfynkaPrleFvgRknvvlsidgeklteeelqkaveeaa 421
                                       L+ Y+igD+ +v++      r+  + R + v+s+ g kl+ +++++ v++  
  gi|242399173|ref|YP_002994597.1| 284 LFNYKIGDLAKVVDD-----RVVNIIRVKDVISLSGAKLHIDQVMDIVHRYP 330
                                       678************.....9*************************999544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 2666.20
//
Query:       gi|242399174|ref|YP_002994598.1|  [L=419]
Description: Metal-dependent phosphohydrolase, HD superfamily [Thermococcus sibiricus MM 739]
Scores for complete 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   1.0    2.5e-16   60.0   1.0    2.2  2  HD        HD domain
     0.0041   16.6   0.0     0.0077   15.7   0.0    1.4  1  HDOD      HDOD domain


Domain annotation for each model (and alignments):
>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.0   1.0   2.8e-20   2.5e-16       1      70 [.      55     125 ..      55     185 .. 0.76
   2 ?   -2.0   0.1      0.43   3.9e+03      64     101 ..     285     321 ..     283     339 .. 0.48

  Alignments for each domain:
  == domain 1  score: 60.0 bits;  conditional E-value: 2.8e-20
                                       HHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHH CS
                                HD   1 rleHsleVaklarrlaedlge.eedrellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrev 70 
                                       r+eHsl+++++a+rl+++l++ ee+r +l+++aLlHDiG+gpf+++fe++ e++ ++++H+  g  i+   
  gi|242399174|ref|YP_002994598.1|  55 RFEHSLGTYNIAKRLGQELELsEEERTILEAGALLHDIGHGPFSHTFEQIYEHYVREYDHMHLGQNIILGK 125
                                       79*************************************************9***********99887654 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.43
                                       HHHHHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHH....HH CS
                                HD  64 aeilrevekrlgldledvaklirehheswegkkrpr....gl 101
                                       aei+++v++r+     ++ ++ + + +   ++++++    ++
  gi|242399174|ref|YP_002994598.1| 285 AEIVKRVKYRD-----LFKAALLLNADELTTEEKREllnvYK 321
                                       57777777777.....33333333333333333332333333 PP

>> HDOD  HDOD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   8.6e-07    0.0077      96     151 ..      56     113 ..      49     123 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 8.6e-07
                                       HHHHHHHHHHHHHHHHHTT-S-HHHHHH..HHHTTTHHHHHHHHHSHHHHHHHHHHHH CS
                              HDOD  96 wehslavAlvarelaeelgledpeeafl..aGLLhdiGklvllsllpeeleellekva 151
                                        ehsl +  +a++l +el+l+++e+  l  ++LLhdiG   + +++++ +e  ++++ 
  gi|242399174|ref|YP_002994598.1|  56 FEHSLGTYNIAKRLGQELELSEEERTILeaGALLHDIGHGPFSHTFEQIYEHYVREYD 113
                                       58********************8877653378******************99988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (419 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       665  (0.0370907); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); 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 0.33s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2576.78
//
Query:       gi|242399175|ref|YP_002994599.1|  [L=319]
Description: HTH-type transcriptional regulatory protein TK0539 [Thermococcus sibiricus MM 739]
Scores for complete 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   0.7    3.7e-11   42.9   0.2    2.0  2  HTH_3           Helix-turn-helix
    2.1e-10   40.8   0.2    9.9e-10   38.6   0.1    2.0  2  HTH_31          Helix-turn-helix domain
      5e-07   29.6   0.2      3e-06   27.2   0.1    2.3  2  HTH_19          Helix-turn-helix domain
    0.00038   20.6   0.0      0.025   14.8   0.0    2.7  2  HTH_17          Helix-turn-helix domain
      0.004   17.1   0.0      0.015   15.2   0.0    2.0  1  HTH_11          HTH domain
     0.0053   17.2   0.0      0.016   15.6   0.0    1.9  1  HTH_26          Cro/C1-type HTH DNA-binding domain
     0.0058   16.4   0.0      0.016   15.0   0.0    1.8  1  MerR            MerR family regulatory protein
     0.0062   16.4   0.3      0.015   15.1   0.0    1.8  1  HTH_25          Helix-turn-helix domain
     0.0081   15.9   0.1      0.031   14.1   0.0    2.0  2  HTH_23          Homeodomain-like domain
  ------ inclusion threshold ------
      0.015   15.2   0.0       0.16   11.9   0.0    2.4  2  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox
      0.015   15.1   0.0      0.077   12.8   0.0    2.2  2  HTH_8           Bacterial regulatory protein, Fis family
      0.019   15.1   0.0       0.41   10.8   0.0    2.5  2  HTH_28          Helix-turn-helix domain
      0.023   14.7   0.0      0.077   13.0   0.0    2.0  3  DUF1870         Domain of unknown function (DUF1870)
      0.026   14.6   0.1        0.1   12.7   0.0    2.1  2  MerR_1          MerR HTH family regulatory protein
      0.053   13.7   0.6       0.31   11.2   0.2    2.5  1  GP3_package     DNA-packaging protein gp3
      0.081   12.6   0.4       0.21   11.3   0.1    1.8  2  YcxB            YcxB-like protein
       0.44   10.3   0.0       0.44   10.3   0.0    3.0  4  Sigma70_r4_2    Sigma-70, region 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 ?   -1.6   0.0       2.8   2.9e+03      39      49 ..      60      70 ..      58      74 .. 0.78
   2 !   42.9   0.2   3.5e-14   3.7e-11       1      50 [.     132     181 ..     132     185 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.8
                                      HHHHHHHHHHT CS
                             HTH_3 39 etlkklakaLg 49
                                      e lk+lak + 
  gi|242399175|ref|YP_002994599.1| 60 EDLKRLAKLFE 70
                                      78999999986 PP

  == domain 2  score: 42.9 bits;  conditional E-value: 3.5e-14
                                       HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTS CS
                             HTH_3   1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgv 50 
                                       l+elR+ +g+s  eLAe+lGvsr +++++E+Ge++ sle++++l++ ++ 
  gi|242399175|ref|YP_002994599.1| 132 LRELRESHGYSVGELAELLGVSRKSLQNYEKGEQAMSLEIALRLEELFDA 181
                                       89********************************************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 ?   -1.2   0.0       2.6   2.7e+03      44      58 ..      59      73 ..      47      74 .. 0.83
   2 !   38.6   0.1   9.4e-13   9.9e-10       3      59 ..     129     184 ..     129     185 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.6
                            HTH_31 44 pavlealaralgldp 58
                                       ++l +la ++ ++p
  gi|242399175|ref|YP_002994599.1| 59 AEDLKRLAKLFEASP 73
                                      679999999998876 PP

  == domain 2  score: 38.6 bits;  conditional E-value: 9.4e-13
                            HTH_31   3 GalLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralgldpa 59 
                                       G +Lr+lRe +G s  e+Ae+lgvs+  l  +E G++  +s++   +l +++++++a
  gi|242399175|ref|YP_002994599.1| 129 GKYLRELRESHGYSVGELAELLGVSRKSLQNYEKGEQ-AMSLEIALRLEELFDAPVA 184
                                       789**********************************.5**************9986 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       2.1   2.2e+03      42      54 ..      59      71 ..      47      73 .. 0.76
   2 !   27.2   0.1   2.8e-09     3e-06       1      37 [.     129     165 ..     129     184 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2.1
                            HTH_19 42 aelllkiaealgi 54
                                      ae+l+++a++++ 
  gi|242399175|ref|YP_002994599.1| 59 AEDLKRLAKLFEA 71
                                      8999****99985 PP

  == domain 2  score: 27.2 bits;  conditional E-value: 2.8e-09
                            HTH_19   1 GerLkeaReelgltqeelaerlgisrskisaiEngkk 37 
                                       G+ L+e+Re  g++  elae lg+sr+++ ++E+g+ 
  gi|242399175|ref|YP_002994599.1| 129 GKYLRELRESHGYSVGELAELLGVSRKSLQNYEKGEQ 165
                                       899********************************54 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0      0.13   1.4e+02      14      34 ..     100     122 ..      98     135 .. 0.73
   2 !   14.8   0.0   2.3e-05     0.025       2      21 ..     141     160 ..     141     164 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.13
                            HTH_17  14 srstvyrlirrgelpaa..kiGr 34 
                                        ++t+y+ + ++elpa    +G+
  gi|242399175|ref|YP_002994599.1| 100 NPQTLYNALVENELPAIfaERGG 122
                                       689***99989999888542544 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 2.3e-05
                            HTH_17   2 ltveEaAelLgvsrstvyrl 21 
                                       ++v E+AelLgvsr++++++
  gi|242399175|ref|YP_002994599.1| 141 YSVGELAELLGVSRKSLQNY 160
                                       89***************986 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.4e-05     0.015       6      35 ..     132     160 ..     130     162 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.4e-05
                            HTH_11   6 lelLleargpisgeeLAeeLnvSrrtvrrd 35 
                                       l+ L+e++g  s  eLAe L+vSr+  +++
  gi|242399175|ref|YP_002994599.1| 132 LRELRESHG-YSVGELAELLGVSRKSLQNY 160
                                       788999999.7**************99886 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.6e-05     0.016       2      42 ..     132     171 ..     131     181 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.6e-05
                            HTH_26   2 LrelmadrgitkseLargtgisaatlsrlvkgkpervsldt 42 
                                       Lrel   +g+++ eLa+ +g+s+ +l+++ kg+ + +sl+ 
  gi|242399175|ref|YP_002994599.1| 132 LRELRESHGYSVGELAELLGVSRKSLQNYEKGE-QAMSLEI 171
                                       899*****************************9.8999875 PP

>> MerR  MerR family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.5e-05     0.016       1      21 [.     142     162 ..     142     163 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.5e-05
                                       EHHHHHHHHTTTHHHHHHHHH CS
                              MerR   1 tIgevAeltGvsprtLRyYEr 21 
                                       ++ge+Ael+Gvs + L  YE+
  gi|242399175|ref|YP_002994599.1| 142 SVGELAELLGVSRKSLQNYEK 162
                                       68******************7 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.4e-05     0.015       1      34 [.     131     164 ..     131     167 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.4e-05
                                       HHHHHHHTTT--HHHHHHHSS--HHHHHHHHCT- CS
                            HTH_25   1 rLraaRearglsleevaketkIrkdylealEedd 34 
                                       +Lr+ Re+ g+s+ e+a+ + ++ + l+  E+++
  gi|242399175|ref|YP_002994599.1| 131 YLRELRESHGYSVGELAELLGVSRKSLQNYEKGE 164
                                       69**************************988875 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0     3e-05     0.031      12      39 ..     133     162 ..     131     166 .. 0.88
   2 ?   -3.1   0.0       7.2   7.6e+03       3       9 ..     251     257 ..     242     262 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3e-05
                            HTH_23  12 lllae..GlsvreIAreLgvsrrTvyrwlk 39 
                                       + l+e  G+sv e A++Lgvsr  ++++ k
  gi|242399175|ref|YP_002994599.1| 133 RELREshGYSVGELAELLGVSRKSLQNYEK 162
                                       6677789******************99876 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 7.2
                            HTH_23   3 sereRlr 9  
                                       s ++R++
  gi|242399175|ref|YP_002994599.1| 251 STLKRAQ 257
                                       3445555 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 ?   -0.2   0.0      0.85     9e+02      40      57 ..      11      28 ..       8      32 .. 0.86
   2 ?   11.9   0.0   0.00015      0.16      12      46 ..     144     178 ..     140     184 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.85
                    YdaS_antitoxin 40 vpeIekatnGeVtreeLR 57
                                      v  I+k t+++V r e R
  gi|242399175|ref|YP_002994599.1| 11 VEGIFKGTGFKVARMEFR 28
                                      56699*********9988 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00015
                    YdaS_antitoxin  12 kaLAealgvsqqaVsqWlkgkkqvpaervpeIeka 46 
                                        +LAe+lgvs++  ++  kg++ ++ e  + +e++
  gi|242399175|ref|YP_002994599.1| 144 GELAELLGVSRKSLQNYEKGEQAMSLEIALRLEEL 178
                                       68******************999*******99997 PP

>> HTH_8  Bacterial regulatory protein, Fis family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       2.4   2.6e+03      30      39 ..      99     108 ..      99     109 .. 0.86
   2 ?   12.8   0.0   7.3e-05     0.077      15      36 ..     137     158 ..     130     159 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 2.4
                                       S-HHHHHHHH CS
                             HTH_8  30 isRrtLyrKL 39 
                                       ++++tLy+ L
  gi|242399175|ref|YP_002994599.1|  99 LNPQTLYNAL 108
                                       689****987 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 7.3e-05
                                       HHTTT-HHHHHHHHTS-HHHHH CS
                             HTH_8  15 ertgGnkskAArlLGisRrtLy 36 
                                       e++g+ + + A+lLG+sR++L 
  gi|242399175|ref|YP_002994599.1| 137 ESHGYSVGELAELLGVSRKSLQ 158
                                       799****************995 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.37   3.9e+02      36      47 ..      91     102 ..      90     108 .. 0.77
   2 ?   10.8   0.0   0.00039      0.41      11      30 ..     139     158 ..     131     165 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.37
                            HTH_28  36 yeegGiagLvpr 47 
                                       ye +Gi++L+p+
  gi|242399175|ref|YP_002994599.1|  91 YERHGIHALNPQ 102
                                       777888888875 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00039
                            HTH_28  11 aGhsvreaArelgisrrtvy 30 
                                       +G sv e+A++lg+sr +++
  gi|242399175|ref|YP_002994599.1| 139 HGYSVGELAELLGVSRKSLQ 158
                                       366*************9986 PP

>> DUF1870  Domain of unknown function (DUF1870)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   7.3e-05     0.077       2      57 ..     128     181 ..     127     220 .. 0.86
   2 ?   -2.0   0.0       3.3   3.5e+03      65      87 ..     240     262 ..     203     285 .. 0.62
   3 ?   -2.9   0.0       6.2   6.6e+03      45      55 ..     300     310 ..     271     317 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.3e-05
                                       -HHHHHHHHHHTT--HHHHHHHTSSS--HHHHHHHHTTSS---HHHHHHHHHHHHH CS
                           DUF1870   2 naleLqAlRkilaltveeaaeyigkavdsatWknWesgalpipdeivaelkelkkl 57 
                                       n+  L  lR++ ++ v e ae +g   + ++ +n+e+g+++++ ei  +l+el + 
  gi|242399175|ref|YP_002994599.1| 128 NGKYLRELRESHGYSVGELAELLGV--SRKSLQNYEKGEQAMSLEIALRLEELFDA 181
                                       6778999*************99985..5899********************99765 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.3
                                       HHHHHCCS-S--EEE--SSHHHH CS
                           DUF1870  65 iveklndrignstlryystltef 87 
                                       i+ ++ +r  +stl+  +  +e 
  gi|242399175|ref|YP_002994599.1| 240 ILTGISERRTTSTLKRAQMVNEV 262
                                       36667777777777655555444 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 6.2
                                       HHHHHHHHHHH CS
                           DUF1870  45 deivaelkelk 55 
                                       de+++ ++elk
  gi|242399175|ref|YP_002994599.1| 300 DELMEMIEELK 310
                                       33333344443 PP

>> MerR_1  MerR HTH family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       7.7   8.1e+03      39      52 ..      55      68 ..      45      71 .. 0.57
   2 ?   12.7   0.0   9.7e-05       0.1       1      22 [.     141     162 ..     141     167 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 7.7
                                      EHHHHHHHHHHHHH CS
                            MerR_1 39 tdedierLklikyL 52
                                      t+e+ e Lk+  +L
  gi|242399175|ref|YP_002994599.1| 55 TEEQAEDLKRLAKL 68
                                      44555555555544 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 9.7e-05
                                       EEHHHHHHHHTS-HHHHHHHHH CS
                            MerR_1   1 ysigevakilgvtthtlrywek 22 
                                       ys+ge+a++lgv+ + l+ +ek
  gi|242399175|ref|YP_002994599.1| 141 YSVGELAELLGVSRKSLQNYEK 162
                                       9*******************98 PP

>> GP3_package  DNA-packaging protein gp3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   0.00029      0.31      41      69 ..     139     167 ..     119     276 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00029
                                       ----HHHHHHHHT--HHHHHHHGG..SHH CS
                       GP3_package  41 raptvtGLalyLgisrstlkeyekrkref 69 
                                         ++v  La  Lg+sr++l++yek ++ +
  gi|242399175|ref|YP_002994599.1| 139 HGYSVGELAELLGVSRKSLQNYEKGEQAM 167
                                       5689999*****************88644 PP

>> YcxB  YcxB-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       4.1   4.3e+03      49      60 ..      54      65 ..      52      66 .. 0.81
   2 ?   11.3   0.1    0.0002      0.21      20      61 .]     260     306 ..     260     306 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 4.1
                              YcxB 49 ftkeeaeafrel 60
                                      +t+e+ae+++ l
  gi|242399175|ref|YP_002994599.1| 54 LTEEQAEDLKRL 65
                                      6899***99876 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.0002
                              YcxB  20 dsiekvkEtkdyfyLflsggs....afiiPKraf.tkeeaeafrell 61 
                                       ++++k++ ++ +f+L   +++    + +iPK+ + +  +a++++e++
  gi|242399175|ref|YP_002994599.1| 260 NEVSKIIHSDGLFILKKTKTEvvgeIPLIPKNKLdEIKDADELMEMI 306
                                       589*************776663433579******9999999998875 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       7.2   7.6e+03       5      16 ..      48      59 ..      46      60 .. 0.75
   2 ?   10.3   0.0   0.00042      0.44      21      45 ..     135     159 ..     134     160 .. 0.88
   3 ?   -1.7   0.1       2.3   2.4e+03      36      50 ..     242     256 ..     240     256 .. 0.89
   4 ?   -0.8   0.1       1.2   1.2e+03       2      13 ..     300     311 ..     299     318 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 7.2
                                      HHHHTTS-HHHH CS
                      Sigma70_r4_2  5 realaeLperqr 16
                                      ++ +++L+e+q 
  gi|242399175|ref|YP_002994599.1| 48 LQNIDSLTEEQA 59
                                      556899999997 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00042
                                       HHHTS---HHHHHHHHT--HHHHHH CS
                      Sigma70_r4_2  21 lryleglsykEIAellgisegtVks 45 
                                       lr+ +g+s  E Aellg+s ++ ++
  gi|242399175|ref|YP_002994599.1| 135 LRESHGYSVGELAELLGVSRKSLQN 159
                                       77889**************999776 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 2.3
                                       HT--HHHHHHHHHHH CS
                      Sigma70_r4_2  36 lgisegtVksrlsRA 50 
                                       +gise+   s l+RA
  gi|242399175|ref|YP_002994599.1| 242 TGISERRTTSTLKRA 256
                                       79****999999998 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 1.2
                                       HHHHHHHTTS-H CS
                      Sigma70_r4_2   2 qalrealaeLpe 13 
                                       ++l+e+++eL +
  gi|242399175|ref|YP_002994599.1| 300 DELMEMIEELKK 311
                                       579999999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1105  (0.061632); expected 358.6 (0.02)
Passed bias filter:                      707  (0.0394333); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.65u 0.33s 00:00:00.98 Elapsed: 00:00:00.53
# Mc/sec: 1820.38
//
Query:       gi|242399176|ref|YP_002994600.1|  [L=429]
Description: transcription-associated protein TFIIS [Thermococcus sibiricus MM 739]
Scores for complete 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-39  133.6   0.0    8.5e-39  132.2   0.0    1.8  2  DUF1743          Domain of unknown function (DUF1743)
    5.9e-09   35.8   0.1    1.4e-08   34.6   0.1    1.6  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
    0.00023   21.3   0.0    0.00048   20.3   0.0    1.5  1  tRNA_anti_2      OB-fold nucleic acid binding domain
  ------ inclusion threshold ------
      0.013   15.0   0.8      0.027   14.0   0.8    1.5  1  TF_Zn_Ribbon     TFIIB zinc-binding
      0.014   15.4   1.0      0.022   14.7   1.0    1.2  1  zinc-ribbons_6   zinc-ribbons
       0.09   12.5   0.1       0.25   11.0   0.0    1.7  2  HIN              HIN-200/IF120x domain
       0.24   11.7   3.3       0.42   10.9   3.3    1.3  1  IBR              IBR domain, a half RING-finger domain
       0.64   10.0   4.0        1.4    9.0   4.0    1.5  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
          1    9.3   3.8          2    8.4   3.8    1.4  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
        3.6    7.4   5.5        3.5    7.4   2.3    2.2  2  YdjO             Cold-inducible protein YdjO
        3.7    7.5   6.5        7.9    6.4   6.5    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 ?   -2.8   0.0         4   6.5e+03      66      96 ..      44      82 ..      41      94 .. 0.62
   2 !  132.2   0.0   5.2e-42   8.5e-39       1     116 []     141     254 ..     141     254 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 4
                                      CCS-STTSS........EEEEEEES-HHHHHHHHHCSEE CS
                           DUF1743 66 vlvPhtpdp........vlfGirgedpeallkaakeils 96
                                       l+P++p +          f  r+ed  ++++ + e+ +
  gi|242399176|ref|YP_002994600.1| 44 RLNPNVPYKtrgngavaMSFDAREEDILKIKNLVLEMVK 82
                                      577888888777777666666666666666555444444 PP

  == domain 2  score: 132.2 bits;  conditional E-value: 5.2e-42
                                       TTHHHHHHHHHH-..-TTS-EEEEEEEE-GGGTT.---EEHHHHHHHHHHHTTCECTSEBTTTTCECCS-STTSSEE CS
                           DUF1743   1 grgiiGAtaalganialedstyEllaYreperwg.erevdeesvieadektypetfdnvDlshklvvlvPhtpdpvl 76 
                                       grgiiGA+aa+g+  +l+ +tyEllaYr +e wg  r+v++esv+++d+ typ t+dnvDls++ v+++Ph++dpvl
  gi|242399176|ref|YP_002994600.1| 141 GRGIIGALAAIGH--PLKVFTYELLAYRTREFWGtARKVNKESVFAVDHLTYPFTYDNVDLSKGSVLITPHGKDPVL 215
                                       89***********..5567********************************************************** PP

                                       EEEEES-HHHHHHHHHCSEE..S-EECEEEEEESTTS-TT CS
                           DUF1743  77 fGirgedpeallkaakeilskeeeseemavfrtnqgtdah 116
                                        Girg d+++++ a+++i   ee+++ +++++tnq+td+h
  gi|242399176|ref|YP_002994600.1| 216 VGIRGIDKNKVIWAFENITF-EEPIDFFQIYKTNQNTDDH 254
                                       ********************.9*****************9 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 !   34.6   0.1   8.5e-12   1.4e-08       3      75 ..     271     343 ..     269     344 .. 0.95

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 8.5e-12
                                       EEEEEEEEEEEEETTEEEEEEEETTEEEEEEEET..HHHHHHHTTS-TTSEEEEEEEEEECTTSSEEEEEEEEEE CS
                   tRNA_anti-codon   3 vaGrvtsisdrsggkvifidlrDgtgriqvvlfr..eeatklaenlkeGdvvrvtGrvkrrpggelelkveeiel 75 
                                       v+G+v+++   ++g+++f+++ D+tg+++v +f   ++++k+   l eGd + + G vk+++g  l+l+ e++ +
  gi|242399176|ref|YP_002994600.1| 271 VRGKVIKKY-WEKGRHVFFEISDDTGKLRVAAFEptKGFRKYVRMLIEGDEIIAAGGVKEFNGV-LTLNLEKFYP 343
                                       889999998.99****************************************************.***9999876 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 !   20.3   0.0   2.9e-07   0.00048      20      80 ..     267     329 ..     256     340 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2.9e-07
                       tRNA_anti_2  20 kavwvrGeisnlkr.kasghvYftLkDekakisavifr..sraaklkftledGmkVlvkgrlsv 80 
                                       ++  vrG + +    ++  hv+f+++D++ k++++ f+  + ++k    l +G++++++g ++ 
  gi|242399176|ref|YP_002994600.1| 267 DSAIVRGKVIKK-YwEKGRHVFFEISDDTGKLRVAAFEptKGFRKYVRMLIEGDEIIAAGGVKE 329
                                       4589******99.424566*******************544445555669**********9875 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.8   1.6e-05     0.027       2      36 ..     356     387 ..     355     389 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.6e-05
                                       EETTTTCEECHEETSTTCE.EESSSSBEEEECCCCC CS
                      TF_Zn_Ribbon   2 kCPnCgstnlveDpergel.vCtdCGlVlednside 36 
                                       kCP+C++t+     + ge+  C++CG+ +    i +
  gi|242399176|ref|YP_002994600.1| 356 KCPKCKGTM----KSKGEYlKCKKCGYKMKKVLIPK 387
                                       8******99....89999989******999888766 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   1.0   1.3e-05     0.022       2      29 ..     356     383 ..     355     389 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.3e-05
                                       --SSS-S--EE-SSEEE-TTT--EEEEE CS
                    zinc-ribbons_6   2 kCpeCqqelekrgeqyhCeaCqedlkke 29 
                                       kCp+C+  ++++ge ++C++C  ++kk+
  gi|242399176|ref|YP_002994600.1| 356 KCPKCKGTMKSKGEYLKCKKCGYKMKKV 383
                                       7********************9988875 PP

>> HIN  HIN-200/IF120x domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00016      0.25     102     148 ..     259     303 ..     243     309 .. 0.75
   2 ?   -3.2   0.0       3.7     6e+03      10      56 ..     344     388 ..     343     389 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00016
                                       -HHHHTTSSTTEEEEEEEEEEEEEEESSEEEEEEEETTEEEEEEEEC CS
                               HIN 102 kikklkkqasgtivnGlfkvqkktvkkkniiyeikDntgkmevvvsg 148
                                       ki +lk ++s  iv G  +++k  +k  ++++ei+D+tgk+ v+ ++
  gi|242399176|ref|YP_002994600.1| 259 KIAELKPLDS-AIVRGK-VIKKYWEKGRHVFFEISDDTGKLRVAAFE 303
                                       5555555443.567774.5777778888***************9875 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3.7
                                       EEE---EEEECTTTCEEEEEEEEEESSCEEEEEE--GGGTCTC-TTE CS
                               HIN  10 LkatepFeyeskeeekkmfhAtvateseffrvkVfnvklkekFtkkk 56 
                                       +k te+ +ye ++  k     t+ ++ e+++ k    k+k+  ++k+
  gi|242399176|ref|YP_002994600.1| 344 IKLTEKITYEKPKCPK--CKGTMKSKGEYLKCKKCGYKMKKVLIPKR 388
                                       5777888888777666..67777788888888888888887777776 PP

>> IBR  IBR domain, a half RING-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   3.3   0.00026      0.42      12      47 ..     350     379 ..     339     380 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00026
                               IBR  12 lesdpnlkwCprpdCeaiieksegcksvtCskCgfe 47 
                                       ++   ++ +Cp  +C++ ++++ +  +++C+kCg++
  gi|242399176|ref|YP_002994600.1| 350 ITY--EKPKCP--KCKGTMKSKGE--YLKCKKCGYK 379
                                       333..3458**..***99977666..889*****97 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   4.0   0.00083       1.4      18      45 ..     354     378 ..     348     379 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00083
                     Zn_Tnp_IS1595  18 gfvCPhCgsrkayriktrglfqCkeCrk 45 
                                       ++ CP+C+     + k+ ++++Ck+C++
  gi|242399176|ref|YP_002994600.1| 354 KPKCPKCK--GTMKSKG-EYLKCKKCGY 378
                                       699*****..8888999.9*******98 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 ?    8.4   3.8    0.0012         2      30      56 ..     356     380 ..     354     382 .. 0.94

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0012
                    OrfB_Zn_ribbon  30 tCseCgsknkealsgrtfkCpnCgfea 56 
                                       +C++C  ++k   +g+ +kC++Cg+++
  gi|242399176|ref|YP_002994600.1| 356 KCPKCKGTMKS--KGEYLKCKKCGYKM 380
                                       7**********..***********986 PP

>> YdjO  Cold-inducible protein YdjO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   2.3    0.0021       3.5      38      55 ..     353     370 ..     350     373 .. 0.83
   2 ?    0.8   0.2      0.25   4.1e+02      41      51 ..     372     382 ..     368     384 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0021
                              YdjO  38 eePtCplCkseMvkevrm 55 
                                       e+P+Cp Ck  M+++  +
  gi|242399176|ref|YP_002994600.1| 353 EKPKCPKCKGTMKSKGEY 370
                                       89***********97655 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.25
                              YdjO  41 tCplCkseMvk 51 
                                       +C  C+ +M+k
  gi|242399176|ref|YP_002994600.1| 372 KCKKCGYKMKK 382
                                       7********97 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   6.5    0.0049       7.9       4      30 ..     357     379 ..     357     381 .. 0.96

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0049
                                       ESTTTSBEEEEECSCCCEEEESSSS-E CS
                    RNA_POL_M_15KD   4 CpkCgNlLlpkedkegknfeCrqCgYe 30 
                                       CpkC+  + +k+  ++    C +CgY+
  gi|242399176|ref|YP_002994600.1| 357 CPKCKGTMKSKGEYLK----CKKCGYK 379
                                       ****************....******7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); 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: 00:00:00.50
# Mc/sec: 2579.82
//
Query:       gi|242399177|ref|YP_002994601.1|  [L=451]
Description: Adenylosuccinate lyase [Thermococcus sibiricus MM 739]
Scores for complete 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  198.5   1.2    2.3e-58  198.0   1.2    1.2  1  Lyase_1   Lyase
    4.9e-21   75.1   0.3    8.5e-20   71.1   0.1    2.5  2  ADSL_C    Adenylosuccinate lyase C-terminus
    3.8e-07   30.2   0.2    1.3e-06   28.5   0.2    1.9  1  ASL_C     Adenylosuccinate lyase C-terminal
  ------ inclusion threshold ------
      0.028   14.4   0.2      0.063   13.2   0.2    1.6  1  SafA      Two-component-system connector protein
      0.096   13.5   0.1       0.98   10.2   0.0    2.7  3  ASL_C2    Argininosuccinate lyase C-terminal


Domain annotation for each model (and alignments):
>> Lyase_1  Lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.0   1.2   6.5e-62   2.3e-58      10     310 ..      15     295 ..       8     297 .. 0.84

  Alignments for each domain:
  == domain 1  score: 198.0 bits;  conditional E-value: 6.5e-62
                                       HHHHHHHHHHHHGGGHHHHHCHHHHHHHHHHHTTSSTHHHHHHHHHHHHHHHCHCHHCGGHHHBSSSSSHHHHHHHH CS
                           Lyase_1  10 lmgiftersrenfrlseedikalaalkkaaakanvdlkeeaaaiikaldevleegklddqfvlkviqegsgtavnmn 86 
                                       +  i+ e++++++ l+     ++aal++a a+++ +++e a+ i + ++ +   +k ++ ++++    ++  av  +
  gi|242399177|ref|YP_002994601.1|  15 MKRIWDEENKLQKLLD-----VEAALARAHAQLGNIPEESAKIISERANTNW--VKVERVNEIEEEIHHDIMAVVKA 84 
                                       4445555555555555.....9***************666666666555544..47775555555544444445455 PP

                                       HHHHHHHHTTHSSGIIIIITTT--HHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHTTT-EEEEEETTEEE CS
                           Lyase_1  87 lnevigellgekvepndkvhtgqSsnDqvpTalrlalkkalsekLlpaleqLidalkekakefkdvvkiGrThlqdA 163
                                       l+ev g       e  +++h g++snD+++Ta +l++k++l e +l++l++L+++lk  ake+k++v iGrTh+q+A
  gi|242399177|ref|YP_002994601.1|  85 LSEVCG-------EHGKYIHLGATSNDIIDTANALLIKESL-EIVLKDLKELRTILKSLAKEHKYTVCIGRTHGQHA 153
                                       666666.......99**************************.88********************************* PP

                                       EEEEHHHHHHHHHHHHHHHHHHHHHHHHHHTCEETTTTTTTSSTTTSCC.THHHHHHHHHHHHHCSTEESSSHHHHH CS
                           Lyase_1 164 tPvtlgqelsayaealerdrerlkellkrllvellgggtavgtglnadp.efaelvakelakvtglpvkapnsfeav 239
                                       +P+t g++++ + ++ +r++er++e++kr+lv++++g++++ + ++    + +elv++ l+ +     k++ + +++
  gi|242399177|ref|YP_002994601.1| 154 VPTTYGMKFAIWLDETQRHIERIEEAKKRILVGQMSGAVGTMASFGEMGlKIQELVMEDLG-L-----KSALISNQI 224
                                       *************************************888777776544477889999998.4.....558888899 PP

                                       HC-HHHHHHHHHHHHHHHHHHHHHHHHHHHTSTTTSSEEEEGCCTSSC-TTSTTTEBTHHHHHHHHHHHHH CS
                           Lyase_1 240 sdrDavvellgalkllatsLskfaeDlrllssgeaglvelslaesepGSSiMPgKvNPvqlElltgvagrv 310
                                        +rD ++el+++l+++a  L k+a ++r l+ +e+ ++ + + +++ GSS+MP+K+NP+ +E + g a+ +
  gi|242399177|ref|YP_002994601.1| 225 IQRDVYAELMSILAIIASTLDKIALEIRNLQRTEILEISEPFGKKQVGSSTMPHKRNPIRSEKISGLARVI 295
                                       ********************************998888888888888*****************9998766 PP

>> ADSL_C  Adenylosuccinate lyase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.16   5.7e+02      48      69 ..      18      41 ..      11      44 .. 0.77
   2 !   71.1   0.1   2.4e-23   8.5e-20       2      73 .]     362     438 ..     361     438 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.16
                                      C..HHCHHHHHT-GGGCCTTHHHH CS
                            ADSL_C 48 k..seeeldalfdpayylgsadei 69
                                         +e++l++l+d ++ l +a ++
  gi|242399177|ref|YP_002994601.1| 18 IwdEENKLQKLLDVEAALARAHAQ 41
                                      2546779***********999887 PP

  == domain 2  score: 71.1 bits;  conditional E-value: 2.4e-23
                                       GGGHHHHHHHHH.HTH-HHHHHHHHHHHHHHHHHC...HHHHHHT-HHHH.C.HHCHHHHHT-GGGCCTTHHHHHHH CS
                            ADSL_C   2 lifservllaLv.kglgReeAyelVqeaamkawee...llelLaadpevk.k.seeeldalfdpayylgsadeivdr 72 
                                       li++e ++l+L+ kg+gR+eA+elV+++amka +e   lle+L + +e + + ++++l a ++p++y+g a++ivd 
  gi|242399177|ref|YP_002994601.1| 362 LIMAEPLMLKLTeKGMGRQEAHELVRRLAMKAFKEnrdLLEVLSESKEAReYlTDDDL-ASLKPENYIGMAPRIVDN 437
                                       9***********88************************************66988788.667*************98 PP

                                       H CS
                            ADSL_C  73 v 73 
                                       v
  gi|242399177|ref|YP_002994601.1| 438 V 438
                                       7 PP

>> ASL_C  Adenylosuccinate lyase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.2   3.5e-10   1.3e-06       4     115 .]     311     428 ..     309     428 .. 0.76

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 3.5e-10
                                       T--TCHHHHHTTCH.HHHHHHHHHHHHHHHHHCCEEE-HHHHHHHHHT-.GGGGHHHHHHHHHHT..T-TTHHHHHH CS
                             ASL_C   4 QRDLtdStvlRnlg.valahslialksllkglsklevneealaedLden.wevlaEaiqtvlrre..giekpYeklk 76 
                                        RDLt+S+v R +   ++      lk+++k l  le+  e+++++L  +   ++aE++   l ++  g ++++e ++
  gi|242399177|ref|YP_002994601.1| 311 ERDLTNSSVERVILpETFVLLDEMLKNMKKVLLGLEFFPENIKKNLYLTkNLIMAEPLMLKLTEKgmGRQEAHELVR 387
                                       6**********8741445555556788888888899999999999987625689******99977225689****** PP

                                       HHHTTS---HHHHHHHHHCS.-S-HH.HHHHHHC--CCC-- CS
                             ASL_C  77 eltrgkkitkeslkefiesl.evsee.akeeLkaltpatYi 115
                                       +l  ++  ++++l e++++  e +e  + ++L +l+p++Yi
  gi|242399177|ref|YP_002994601.1| 388 RLAMKAFKENRDLLEVLSESkEAREYlTDDDLASLKPENYI 428
                                       ****997777777777766615555425689*********8 PP

>> SafA  Two-component-system connector protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   1.8e-05     0.063       5      35 ..     219     248 ..     215     264 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.8e-05
                              SafA   5 tvknkitqrdnykeimsvivvvllltltlia 35 
                                        + n+i qrd y e+ms++ ++   tl  ia
  gi|242399177|ref|YP_002994601.1| 219 LISNQIIQRDVYAELMSILAII-ASTLDKIA 248
                                       578**************87654.55666666 PP

>> ASL_C2  Argininosuccinate lyase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.8   6.4e+03      25      60 ..     192     231 ..     190     241 .. 0.57
   2 ?   -2.9   0.0       3.5   1.3e+04      54      68 ..     314     329 ..     300     329 .. 0.76
   3 ?   10.2   0.0   0.00027      0.98      11      67 ..     372     427 ..     368     429 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.8
                                       HHHHHHHHHHTT--GGG--HHHHHHH-TT.....--GGGGG CS
                            ASL_C2  25 vgravrlaeekgkeleeltleelkeispl.....leedvee 60 
                                       vg +++   e g++++el +e+l   s l     ++ dv++
  gi|242399177|ref|YP_002994601.1| 192 VGTMASF-GEMGLKIQELVMEDLGLKSALisnqiIQRDVYA 231
                                       5566655.566888888888888733322122225556655 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.5
                                       --.GGGGGGSSHHHHT CS
                            ASL_C2  54 le.edveeaLdpeasV 68 
                                       l+ + ve+++ pe++V
  gi|242399177|ref|YP_002994601.1| 314 LTnSSVERVILPETFV 329
                                       5658899999999987 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.00027
                                       HHHCTS-HHHHHHHHHHHHHHHHHTT--GGG--HHHHHHH-TT--.GGGGGGSSHHHH CS
                            ASL_C2  11 LvrkGlpFReAHeivgravrlaeekgkeleeltleelkeisplle.edveeaLdpeas 67 
                                       L++kG+   eAHe+v r++ +a +++++l e+  e  + + + l+ +d  + L+pe+ 
  gi|242399177|ref|YP_002994601.1| 372 LTEKGMGRQEAHELVRRLAMKAFKENRDLLEVLSESKE-AREYLTdDD-LASLKPENY 427
                                       788999999*******************9988666655.445577466.667888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       784  (0.043728); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); 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: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.48
# Mc/sec: 2840.94
//
Query:       gi|242399178|ref|YP_002994602.1|  [L=94]
Description: DNA/RNA-binding protein Alba [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-20   72.2   0.8    2.8e-20   71.9   0.8    1.1  1  Alba      Alba
      0.004   17.1   0.1     0.0049   16.8   0.1    1.3  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 !   71.9   0.8   3.1e-24   2.8e-20       2      66 ..       9      70 ..       8      71 .. 0.94

  Alignments for each domain:
  == domain 1  score: 71.9 bits;  conditional E-value: 3.1e-24
                                      EEEE-STS-HHHHHHHHHHHHTHTTESEEEEEEETTHHHHHHHHHHHHHHHTCTT.EEEEEEEEE CS
                              Alba  2 eiyVsskspimsyvkralklLsnkkeeeVvlkatGraIskAvsvaeilkrrfgkglyqvnvltss 66
                                      ++++++ +p+m+yv+++++++ n++++eV + a+GraIs+Av+vaei+++rf+++ + v++++++
  gi|242399178|ref|YP_002994602.1|  9 VVFIGK-KPVMNYVLAVITQF-NEGAKEVSVRARGRAISRAVDVAEIVRNRFLPE-VRVKEIKIG 70
                                      7999*9.**************.******************************965.999999875 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 !   16.8   0.1   5.5e-07    0.0049      58      93 ..      29      64 ..      17      79 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.5e-07
                             Rpp20 58 elkkeeVfvkatGrAiekalsvgrwfqekeeykvrv 93
                                      ++  +eV v+a GrAi +a+ v++  +++   +vrv
  gi|242399178|ref|YP_002994602.1| 29 NEGAKEVSVRARGRAISRAVDVAEIVRNRFLPEVRV 64
                                      56789******************9997776444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 639.46
//
Query:       gi|242399179|ref|YP_002994603.1|  [L=199]
Description: Transcription regulator, ArsR family [Thermococcus sibiricus MM 739]
Scores for complete 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    1.1e-12   47.8   0.0    1.4  1  HTH_20           Helix-turn-helix domain
    6.6e-10   38.7   0.1    1.7e-09   37.4   0.1    1.7  1  HTH_5            Bacterial regulatory protein, arsR family
    3.9e-09   35.9   0.1      9e-09   34.8   0.1    1.6  1  HTH_24           Winged helix-turn-helix DNA-binding
      1e-06   28.5   0.4    3.2e-06   26.9   0.1    1.9  2  TrmB             Sugar-specific transcriptional regulator Trm
    1.9e-05   24.5   0.1    3.5e-05   23.6   0.1    1.4  1  MarR             MarR family
    2.1e-05   24.3   0.0      4e-05   23.4   0.0    1.5  1  MarR_2           MarR family
    2.5e-05   24.0   0.0      6e-05   22.8   0.0    1.6  1  HTH_IclR         IclR helix-turn-helix domain
    0.00034   21.0   0.1    0.00086   19.7   0.1    1.8  2  HTH_40           Helix-turn-helix domain
     0.0019   17.7   0.0     0.0043   16.5   0.0    1.6  1  Sigma70_r4       Sigma-70, region 4
      0.002   17.8   0.1     0.0049   16.5   0.1    1.6  1  Sigma70_r4_2     Sigma-70, region 4
     0.0026   17.5   0.0     0.0049   16.7   0.0    1.5  1  DUF742           Protein of unknown function (DUF742)
     0.0027   17.2   0.0     0.0063   16.0   0.0    1.6  1  GerE             Bacterial regulatory proteins, luxR family
     0.0027   17.4   0.0     0.0064   16.2   0.0    1.6  1  HTH_38           Helix-turn-helix domain
     0.0028   17.8   0.1     0.0058   16.8   0.1    1.5  1  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
     0.0041   17.0   0.1      0.011   15.6   0.1    1.8  1  HTH_11           HTH domain
     0.0047   16.7   0.2      0.013   15.3   0.0    1.8  2  HTH_10           HTH DNA binding domain
     0.0051   17.3   0.2      0.013   16.0   0.2    1.6  1  PCI              PCI domain
     0.0063   16.3   0.0      0.015   15.0   0.0    1.6  1  HTH_23           Homeodomain-like domain
       0.01   16.2   0.1       0.02   15.2   0.1    1.5  1  Rrf2             Transcriptional regulator
  ------ inclusion threshold ------
      0.022   14.8   0.1      0.045   13.8   0.1    1.4  1  HTH_45           Winged helix-turn-helix
      0.035   14.6   0.0      0.083   13.4   0.0    1.6  1  HTH_27           Winged helix DNA-binding domain
      0.072   13.2   0.1       0.22   11.6   0.0    1.9  1  HTH_3            Helix-turn-helix
      0.084   12.8   0.1       0.19   11.7   0.1    1.6  1  HTH_12           Ribonuclease R winged-helix domain
       0.17   11.9   0.0       0.44   10.6   0.0    1.7  1  Phage_terminase  Phage terminase small subunit


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 !   47.8   0.0   1.5e-15   1.1e-12       2      56 ..      15      68 ..      14      72 .. 0.95

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 1.5e-15
                                      HHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20  2 qiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56
                                      ++a +La+ + + il++L +++ l+ se+a++ld++ +t+syHL+++ ++g++e 
  gi|242399179|ref|YP_002994603.1| 15 ELAQILANDTALSILSLL-QEKTLSMSEIAKELDIPISTVSYHLDKMIRVGFIEI 68
                                      68999*************.**********************************96 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   0.1   2.2e-12   1.7e-09       2      46 ..      23      67 ..      22      67 .. 0.95

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 2.2e-12
                                      HHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  2 ptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                       t l IL+lL+e+ l+ +e+a+el+++ stvS+HL k+   G++e
  gi|242399179|ref|YP_002994603.1| 23 DTALSILSLLQEKTLSMSEIAKELDIPISTVSYHLDKMIRVGFIE 67
                                      57899***********************************99986 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   0.1   1.2e-11     9e-09       2      48 .]      22      67 ..      22      67 .. 0.96

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 1.2e-11
                            HTH_24  2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      ++t + IL+lLq+   +s++e+A++l++++stv+++l+++++ G+I+
  gi|242399179|ref|YP_002994603.1| 22 NDTALSILSLLQE-KTLSMSEIAKELDIPISTVSYHLDKMIRVGFIE 67
                                      689999*******.9***************************99996 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.1   4.3e-09   3.2e-06      15      64 ..      29      85 ..      26      88 .. 0.91
   2 ?   -1.6   0.0       3.4   2.5e+03      37      48 ..     123     134 ..     117     135 .. 0.77

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 4.3e-09
                                      HHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.......TTEEEE CS
                              TrmB 15 laLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.......pklYra 64
                                      l Ll+++ ++++eia+el++p s+v   L ++++ G++e+  ++        klYra
  gi|242399179|ref|YP_002994603.1| 29 LSLLQEKTLSMSEIAKELDIPISTVSYHLDKMIRVGFIEIAGKKygkrlqeVKLYRA 85
                                      579*************************************98888888888888887 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.4
                                       HCHHHHHHHHHH CS
                              TrmB  37 skvYevLrsLed 48 
                                       s  Y vL++L++
  gi|242399179|ref|YP_002994603.1| 123 SGTYLVLEKLVS 134
                                       567999999985 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.1   4.8e-08   3.5e-05       7      48 ..      27      67 ..      22      68 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 4.8e-08
                                      HHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR  7 viLrilyeqgplsvseLakklgvskstvtrvldrLekkGlie 48
                                      +iL  l ++  ls+se+ak l + +stv+  ld++++ G+ie
  gi|242399179|ref|YP_002994603.1| 27 SILS-LLQEKTLSMSEIAKELDIPISTVSYHLDKMIRVGFIE 67
                                      5554.457789******************************7 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   5.4e-08     4e-05      20      52 ..      30      67 ..      11      76 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 5.4e-08
                                      S.....EEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                            MarR_2 20 r.....dltvgelarrlglsksavsrilkrLvaaGLve 52
                                             l+++e+a++l+++ s+vs++l+++ + G++e
  gi|242399179|ref|YP_002994603.1| 30 SllqekTLSMSEIAKELDIPISTVSYHLDKMIRVGFIE 67
                                      03333349****************************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 !   22.8   0.0     8e-08     6e-05       5      49 ..      25      67 ..      23      68 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 8e-08
                                      HHHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR  5 alaiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                      al+iL +l e +     se+A+++++p Stv+ +L  +++ G++e
  gi|242399179|ref|YP_002994603.1| 25 ALSILSLLQEKTLS--MSEIAKELDIPISTVSYHLDKMIRVGFIE 67
                                      89999999999885..7**************************97 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.1   1.2e-06   0.00086       6      45 ..      29      68 ..      24     114 .. 0.81
   2 ?   -1.5   0.0       4.8   3.6e+03      36      65 ..     120     149 ..     101     164 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.2e-06
                            HTH_40  6 lell.eeglsieeIAkerglkesTIegHLaelieegeeidl 45
                                      l+ll e+ ls+ eIAke  +  sT+  HL ++i+ g  i++
  gi|242399179|ref|YP_002994603.1| 29 LSLLqEKTLSMSEIAKELDIPISTVSYHLDKMIRVGF-IEI 68
                                      67776899**************************997.655 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 4.8
                            HTH_40  36 lieegeeidlerlvseeeekeIeeaiekvg 65 
                                       l+ +g  + le+lvse+ +  +e+a +  +
  gi|242399179|ref|YP_002994603.1| 120 LLASGTYLVLEKLVSERSILGLENATRLTK 149
                                       455565567778888877777777766544 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   5.8e-06    0.0043      11      42 ..      27      58 ..      22      62 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5.8e-06
                                      HHHHHHHTTT--HHHHHHHHTS-HHHHHHHHH CS
                        Sigma70_r4 11 evlelrfgeglTleEIgerlgiSrerVrqiek 42
                                       +l+l  ++ l+++EI+++l+i+ ++V+ ++ 
  gi|242399179|ref|YP_002994603.1| 27 SILSLLQEKTLSMSEIAKELDIPISTVSYHLD 58
                                      58999999*******************97665 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   6.6e-06    0.0049      18      47 ..      28      57 ..      27      59 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.6e-06
                                      HHHHHHTS---HHHHHHHHT--HHHHHHHH CS
                      Sigma70_r4_2 18 ifllryleglsykEIAellgisegtVksrl 47
                                      i+ l +++ ls  EIA++l+i+ +tV ++l
  gi|242399179|ref|YP_002994603.1| 28 ILSLLQEKTLSMSEIAKELDIPISTVSYHL 57
                                      667778999******************998 PP

>> DUF742  Protein of unknown function (DUF742)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   6.6e-06    0.0049      41      90 ..      21      71 ..       5      88 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 6.6e-06
                            DUF742 41 lqpehrailrLcre.plsVaelaAelklPvgvvrvLlsdLldaglltvrap 90
                                      +++ + +il L +e +ls  e+a el++P+++v   l  ++  g +++   
  gi|242399179|ref|YP_002994603.1| 21 ANDTALSILSLLQEkTLSMSEIAKELDIPISTVSYHLDKMIRVGFIEIAGK 71
                                      4566789*****9999*****************999999999998887655 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   8.4e-06    0.0063      18      42 ..      37      61 ..      27      62 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 8.4e-06
                                      S-HHHHHHHHTS-HHHHHHHHHHHH CS
                              GerE 18 ksnkeIAeelniSekTVkvhksnim 42
                                      +s+ eIA+el+i   TV++h+  + 
  gi|242399179|ref|YP_002994603.1| 37 LSMSEIAKELDIPISTVSYHLDKMI 61
                                      6899****************99886 PP

>> HTH_38  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   8.5e-06    0.0064      13      41 ..      28      57 ..      26      59 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 8.5e-06
                            HTH_38 13 IerllaeG.lslreIArrLgrspsTIsREl 41
                                      I  ll+e+ ls++eIA++L+   sT+s++l
  gi|242399179|ref|YP_002994603.1| 28 ILSLLQEKtLSMSEIAKELDIPISTVSYHL 57
                                      788999888******************987 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   7.7e-06    0.0058      19      58 ..      33      72 ..      27      73 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 7.7e-06
                                      HHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT CS
                    Fe_dep_repress 19 ekkvvktkdlaerLnvspssVsemlkkLekdGyveyekyk 58
                                      ++k  + +++a++L++  s+Vs  l k+ + G++e +++k
  gi|242399179|ref|YP_002994603.1| 33 QEKTLSMSEIAKELDIPISTVSYHLDKMIRVGFIEIAGKK 72
                                      4677899**************************9998876 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   1.5e-05     0.011       3      50 ..      26      72 ..      24      74 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.5e-05
                            HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg.vpIesep 50
                                      l+il lL +++ ++s +e+A+eL++  +tv  +++++   g ++I +++
  gi|242399179|ref|YP_002994603.1| 26 LSILSLL-QEK-TLSMSEIAKELDIPISTVSYHLDKMIRVGfIEIAGKK 72
                                      6799999.555.4**********************99999977777765 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1         5   3.8e+03      22      33 ..       9      20 ..       9      29 .. 0.80
   2 !   15.3   0.0   1.8e-05     0.013      22      48 ..      35      61 ..      33      63 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 5
                            HTH_10 22 RrvtlkeLAkel 33
                                      R+ +++eLA++l
  gi|242399179|ref|YP_002994603.1|  9 RDEKARELAQIL 20
                                      566789999876 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 1.8e-05
                            HTH_10 22 RrvtlkeLAkelGIskstlsehLrkae 48
                                      ++ +++e+Akel+I  st+s+hL k +
  gi|242399179|ref|YP_002994603.1| 35 KTLSMSEIAKELDIPISTVSYHLDKMI 61
                                      677899*****************9876 PP

>> PCI  PCI domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.2   1.7e-05     0.013      57      91 ..      33      67 ..       9      69 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.7e-05
                                      CESEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSSS CS
                               PCI 57 iyssislerlaklldlsvdevEkilvklIrdgeir 91
                                        +++s++++ak ld++ + v + l k+Ir g+i+
  gi|242399179|ref|YP_002994603.1| 33 QEKTLSMSEIAKELDIPISTVSYHLDKMIRVGFIE 67
                                      5789****************************996 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   2.1e-05     0.015       8      35 ..      26      54 ..      24      59 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.1e-05
                            HTH_23  8 lrillllae.GlsvreIAreLgvsrrTvy 35
                                      l+il ll+e  ls +eIA+eL+++ +Tv+
  gi|242399179|ref|YP_002994603.1| 26 LSILSLLQEkTLSMSEIAKELDIPISTVS 54
                                      57999999999*****************8 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   2.7e-05      0.02      13      67 ..      25      77 ..      23      81 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.7e-05
                                      HHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT-TCEEE CS
                              Rrf2 13 allyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvrGkgGGyrL 67
                                      al +L++ +e++ +s++eia++ +i+ s ++  l k+ + g+++   Gk+ G rL
  gi|242399179|ref|YP_002994603.1| 25 ALSILSLLQEKT-LSMSEIAKELDIPISTVSYHLDKMIRVGFIEI-AGKKYGKRL 77
                                      788899999987.******************************85.566666555 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1     6e-05     0.045       9      56 ..      26      73 ..      22      77 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6e-05
                            HTH_45  9 adILeaisegeakkTkimykanLsykllnkYLdmLvekglikkskekY 56
                                      ++IL+ ++e+  ++++i ++ ++  ++++  Ld+++  g+i+  ++kY
  gi|242399179|ref|YP_002994603.1| 26 LSILSLLQEKTLSMSEIAKELDIPISTVSYHLDKMIRVGFIEIAGKKY 73
                                      68***************************************9999888 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 ?   13.4   0.0   0.00011     0.083      16      54 ..      34      72 ..      22      87 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00011
                            HTH_27 16 rrrkkladlcgrlnvedshisyslkkLtekGLvertgde 54
                                      + + + +++++ l++  s++sy l+k+++ G++e  g++
  gi|242399179|ref|YP_002994603.1| 34 EKTLSMSEIAKELDIPISTVSYHLDKMIRVGFIEIAGKK 72
                                      4455569**************************877765 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0    0.0003      0.22       3      27 ..      30      54 ..      28      55 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0003
                                      HHHHHTTHHHHHHHHHHTSSHHHHH CS
                             HTH_3  3 elRkqlglsqeeLAeklGvsrstis 27
                                       l++++ ls+ e+A++l+++ st+s
  gi|242399179|ref|YP_002994603.1| 30 SLLQEKTLSMSEIAKELDIPISTVS 54
                                      57899*******************9 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00026      0.19       2      58 ..      27      77 ..      26      82 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00026
                            HTH_12  2 eILkilaesdkpigakeiaeeLkkrgydigeravRyrLrkleergltrrvgya.grel 58
                                       IL++l+e++  ++  eia+eL     di   +v y+L k+ + g+++  g+  g++l
  gi|242399179|ref|YP_002994603.1| 27 SILSLLQEKT--LSMSEIAKEL-----DIPISTVSYHLDKMIRVGFIEIAGKKyGKRL 77
                                      5899999876..58889***99.....566699**************98776655655 PP

>> Phage_terminase  Phage terminase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00059      0.44      20      40 ..      34      54 ..      22      57 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00059
                   Phage_terminase 20 ggtlklkdIAkvLdvsestvr 40
                                       +tl + +IAk+Ld++ stv+
  gi|242399179|ref|YP_002994603.1| 34 EKTLSMSEIAKELDIPISTVS 54
                                      58999**************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       798  (0.0445089); expected 358.6 (0.02)
Passed bias filter:                      598  (0.0333538); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); 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 0.34s 00:00:00.94 Elapsed: 00:00:00.53
# Mc/sec: 1131.47
//
Query:       gi|242399180|ref|YP_002994604.1|  [L=180]
Description: Inosine-5'-monophosphate dehydrogenase related protein II [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.8e-21   75.3   7.4    4.7e-11   43.0   1.7    2.5  3  CBS           CBS domain
  ------ inclusion threshold ------
      0.015   15.1   0.8       0.57   10.0   0.0    2.2  2  Rubredoxin_2  Rubredoxin metal binding domain
      0.067   13.1   1.7       0.14   12.1   1.7    1.4  1  Nudix_N_2     Nudix N-terminal
        0.2   11.7   1.0         13    5.9   0.2    2.4  2  ADK_lid       Adenylate kinase, active site lid
       0.23   11.5   4.4        1.1    9.2   4.5    2.0  1  zf-dskA_traR  Prokaryotic dksA/traR C4-type zinc finger


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.0   1.7   1.3e-14   4.7e-11       1      55 [.       9      62 ..       9      64 .. 0.87
   2 !   35.4   0.1   3.1e-12   1.1e-08       1      55 [.      74     127 ..      74     129 .. 0.94
   3 ?   -2.6   0.0       2.2   7.9e+03      15      23 ..     136     144 ..     135     148 .. 0.64

  Alignments for each domain:
  == domain 1  score: 43.0 bits;  conditional E-value: 1.3e-14
                                      HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55
                                      V++i  r+ ++++p++t+e +++++++++vs+  VV e ++++Givt+rD+l+++
  gi|242399180|ref|YP_002994604.1|  9 VEQIVKRKAIVIKPTETVERVAKILAKNKVSSA-VVMEKDEIIGIVTDRDILNKV 62
                                      7899999******************77779999.6536667***********986 PP

  == domain 2  score: 35.4 bits;  conditional E-value: 3.1e-12
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                       V++imt+ ++t+  d ++ +a+elm  kgv+rl+V+   g + G vt  Dll al
  gi|242399180|ref|YP_002994604.1|  74 VSSIMTKTPITIEYDYDIQDAIELMMGKGVRRLLVT-RLGMPMGFVTAADLLAAL 127
                                       899*********************879******888.8999***********998 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 2.2
                                       TSBHHHHHH CS
                               CBS  15 dttleeale 23 
                                       ++++eea e
  gi|242399180|ref|YP_002994604.1| 136 EESIEEAGE 144
                                       677777765 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00016      0.57      10      27 ..     142     159 ..     140     160 .. 0.86
   2 ?    3.5   0.3     0.016        58      15      22 ..     169     176 ..     168     177 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00016
                      Rubredoxin_2  10 sakwfGrCpsCgsWntlk 27 
                                       +  ++G C  Cg++ +l+
  gi|242399180|ref|YP_002994604.1| 142 AGEVYGICEVCGQYAQLH 159
                                       6789*********99886 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.016
                      Rubredoxin_2  15 GrCpsCgs 22 
                                       + C sC++
  gi|242399180|ref|YP_002994604.1| 169 WVCESCKD 176
                                       99999986 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.7   3.8e-05      0.14       3      29 ..     149     175 ..     149     176 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.8e-05
                                       -TTT--B-EEE--TT-SS-EEEETTTT CS
                         Nudix_N_2   3 CsqCGtpvelripdgDnreRlvCpaCg 29 
                                       C+ CG+  +l+    +  eR vC++C 
  gi|242399180|ref|YP_002994604.1| 149 CEVCGQYAQLHRVIREGYERWVCESCK 175
                                       9********999999***********5 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 ?    4.0   0.0     0.014        48      20      29 ..     145     154 ..     128     158 .. 0.76
   2 ?    5.9   0.2    0.0036        13       1       8 [.     168     175 ..     168     177 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.014
                                       STTB-TTT-- CS
                           ADK_lid  20 veglCDkCGe 29 
                                       v g+C +CG 
  gi|242399180|ref|YP_002994604.1| 145 VYGICEVCGQ 154
                                       779*****96 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0036
                                       EEE-TTT- CS
                           ADK_lid   1 RrvCpkCG 8  
                                       R+vC++C+
  gi|242399180|ref|YP_002994604.1| 168 RWVCESCK 175
                                       9******8 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 ?    9.2   4.5   0.00031       1.1       3      23 ..     146     166 ..     144     176 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00031
                      zf-dskA_traR   3 ygsCeeCGEpIpeaRlralPg 23 
                                       yg+Ce+CG+    +R+ + ++
  gi|242399180|ref|YP_002994604.1| 146 YGICEVCGQYAQLHRVIREGY 166
                                       9*********99999777664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       921  (0.0513693); expected 358.6 (0.02)
Passed bias filter:                      634  (0.0353617); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 1254.21
//
Query:       gi|242399181|ref|YP_002994605.1|  [L=199]
Description: Proteasome, beta subunit 2 [Thermococcus sibiricus MM 739]
Scores for complete 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-51  173.1   0.1    4.8e-51  173.0   0.1    1.0  1  Proteasome  Proteasome subunit


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  173.0   0.1   2.7e-55   4.8e-51       2     184 ..       4     178 ..       3     185 .. 0.95

  Alignments for each domain:
  == domain 1  score: 173.0 bits;  conditional E-value: 2.7e-55
                                       HHS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSG CS
                        Proteasome   2 kkGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygrp 78 
                                       k+Gtt+vGik kdgvvlaad++a+  +++ ++ +++Ki  i+d+i++++aG+++D ++l+r+++aea+ y++++g+p
  gi|242399181|ref|YP_002994605.1|   4 KTGTTTVGIKLKDGVVLAADTQASLDHMV-ETLNIKKILPITDRIAITTAGSVGDLQALARMLEAEAKYYQFTWGKP 79 
                                       79**********************99999.8888******************************************* PP

                                       TCHHHHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHHS CS
                        Proteasome  79 ipverlvarvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekeyk 155
                                       ++ +    ++a++l++ + +s+  p++v+++i+g+ e  +p L ++dp G +i + +++++Gsgs +a+++le+ yk
  gi|242399181|ref|YP_002994605.1|  80 MTAK----AMANLLSNILNESKWFPYMVQIIIGGYVE--EPTLASLDPLGGLIFD-NYTTTGSGSPFAIAILEDGYK 149
                                       ****....99999999999*****************3..49**************.7******************** PP

                                       TTBSHHHHHHHHHHHHHHHHHHBTTSCSS CS
                        Proteasome 156 edltleeavelavkalkealerdklsgkn 184
                                       ed++ e+a ela+ka++ a +rd+++g+ 
  gi|242399181|ref|YP_002994605.1| 150 EDMSIEDARELAIKAVRTAGKRDVYTGER 178
                                       *************************9953 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); 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: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1308.49
//
Query:       gi|242399182|ref|YP_002994606.1|  [L=374]
Description: hypothetical protein TSIB_1203 [Thermococcus sibiricus MM 739]
Scores for complete 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-06   26.6   0.1      9e-06   25.8   0.1    1.3  1  DUF4157   Domain of unknown function (DUF4157)


Domain annotation for each model (and alignments):
>> DUF4157  Domain of unknown function (DUF4157)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.1     5e-10     9e-06      40      76 ..     124     160 ..     111     161 .. 0.93

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 5e-10
                           DUF4157  40 AfTlgndivfaageyqpesaagrellaHELtHvvqqr 76 
                                       A T g+++++ ++++ ++ ++ +++laHE tHv q++
  gi|242399182|ref|YP_002994606.1| 124 AATSGDKVYIISENFFKTGKTSQRVLAHEFTHVLQKQ 160
                                       99*********************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       838  (0.0467399); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.36s 00:00:01.04 Elapsed: 00:00:00.54
# Mc/sec: 2085.70
//
Query:       gi|242399183|ref|YP_002994607.1|  [L=481]
Description: GTPase-like protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.9e-06   25.8   0.0    1.6e-05   24.6   0.0    1.6  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
    6.2e-05   23.0   0.0          2    8.5   0.0    4.1  4  B12-binding      B12 binding domain
    0.00036   21.2   3.3        2.2    9.1   0.0    4.4  4  PTS_IIB          PTS system, Lactose/Cellobiose specific IIB 
     0.0015   18.5   0.1      0.021   14.9   0.2    2.5  3  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
     0.0052   16.5   0.0      0.012   15.3   0.0    1.6  1  Thymidylate_kin  Thymidylate kinase
      0.007   16.1   0.0      0.021   14.5   0.0    1.8  2  SWI2_SNF2        SWI2/SNF2 ATPase
  ------ inclusion threshold ------
      0.015   14.8   0.1      0.054   13.0   0.1    1.9  2  PPK2             Polyphosphate kinase 2 (PPK2)
      0.015   14.6   0.0      0.064   12.5   0.0    2.0  2  MipZ             ATPase MipZ
      0.031   15.1   0.0         18    6.2   0.0    2.9  2  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
       0.04   13.9   0.4        9.6    6.1   0.0    3.5  4  Glyco_tran_WecB  Glycosyl transferase WecB/TagA/CpsF family
      0.052   13.9   0.8        1.2    9.5   0.0    2.9  3  RuvX             Holliday junction resolvase
      0.055   13.7   0.1        3.4    7.9   0.0    3.6  5  UPF0180          Uncharacterised protein family (UPF0180)
      0.064   12.9   0.2        2.4    7.7   0.0    2.7  3  SRP54            SRP54-type protein, GTPase domain
      0.067   13.1   0.6       0.22   11.4   0.1    2.1  1  AAA_31           AAA domain
      0.073   12.3   0.1       0.16   11.2   0.1    1.6  1  Zeta_toxin       Zeta toxin
      0.086   12.7   0.1        1.1    9.1   0.0    2.4  2  RsgA_GTPase      RsgA GTPase
       0.09   12.9   0.8          6    7.0   0.0    3.8  4  DUF2325          Uncharacterized protein conserved in bacteri
      0.094   13.0   0.1         18    5.6   0.0    2.7  3  AAA_22           AAA domain
      0.096   12.5   1.1        1.9    8.4   0.1    3.0  3  DAHP_snth_FXD    DAHP synthase ferredoxin-like domain
       0.12   12.2   0.1        1.2    9.0   0.0    2.4  2  AAA_26           AAA domain
       0.12   13.3   0.0       0.37   11.8   0.0    1.8  1  LytR_C           LytR cell envelope-related transcriptional a
       0.14   12.1   0.1        9.6    6.2   0.0    3.2  3  PB1              PB1 domain
       0.17   11.7   5.5        0.6    9.9   0.3    3.5  3  DUF2179          Uncharacterized protein conserved in bacteri
       0.21   11.3   0.2        8.6    6.1   0.0    2.7  3  ATP_bind_1       Conserved hypothetical ATP binding protein
       0.25   11.0   0.5        1.6    8.4   0.3    2.4  2  AAA_30           AAA domain


Domain annotation for each model (and alignments):
>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   2.2e-08   1.6e-05     128     176 ..     286     333 ..     266     334 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 2.2e-08
                                       HCCHHHHHHHHHHTSSEEEEE-HHHHCHC..HHHHHHHHHHHHTTS-EE CS
                              cobW 128 eekieekaedqlaaadllvlnKtDlldeeallekleerlrqlnpeakvl 176
                                       +e + + +e  + aad++++nK+D+++ e +++k++e ++++np+a v+
  gi|242399183|ref|YP_002994607.1| 286 HELKYHPGETNFRAADVIIINKIDTANRE-DVQKVRESIEKINPKAIVI 333
                                       45555667899*****************9.66************99876 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       1.7   1.2e+03      33      59 ..      22      48 ..      10      77 .. 0.71
   2 !    8.2   0.0    0.0034       2.4      40      81 ..     102     142 ..      90     147 .. 0.88
   3 !    8.5   0.0    0.0027         2      51      88 ..     299     336 ..     295     362 .. 0.85
   4 ?   -1.1   0.0       2.5   1.8e+03      37      57 ..     414     435 ..     388     447 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.7
                       B12-binding 33 llganvenedivaairaekpdvvglSa 59
                                      +++++v++ ++++ +++ + +vv l a
  gi|242399183|ref|YP_002994607.1| 22 NIDCKVKTFEVIKMAEKKRKRVVILGA 48
                                      677777777777777777777766544 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0034
                       B12-binding  40 nedivaairaekpdvvglSalltsqleavkelvellkrirpr 81 
                                        +d+++ i++++ d+v++   +  ++e+v +l+ ++++++++
  gi|242399183|ref|YP_002994607.1| 102 EDDLEKIIKEHDIDIVVFAY-SDVSHEHVMHLASRAHSAGAD 142
                                       599***************76.************998888765 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0027
                       B12-binding  51 kpdvvglSalltsqleavkelvellkrirprvkvvvGG 88 
                                       ++dv+ +  + t++ e+v+++ e +++i+p+++v+ G 
  gi|242399183|ref|YP_002994607.1| 299 AADVIIINKIDTANREDVQKVRESIEKINPKAIVIDGA 336
                                       79*****************************9998765 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 2.5
                       B12-binding  37 nven.edivaairaekpdvvgl 57 
                                        +++ +++++ i + ++d+v++
  gi|242399183|ref|YP_002994607.1| 414 GAKQiKELEETINRADADLVVI 435
                                       4444588888999999998876 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 !    9.1   0.0     0.003       2.2      19      72 ..     104     164 ..     101     184 .. 0.75
   2 ?    0.6   0.0       1.3   9.1e+02       2      33 ..     161     191 ..     160     204 .. 0.84
   3 ?    1.8   0.1      0.56     4e+02      46      79 ..     298     332 ..     288     341 .. 0.71
   4 ?    7.2   0.0     0.011         8      35      89 ..     416     471 ..     398     472 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.003
                                       HHHHHHHHCTEEEEETTEE........GGGHHHHHHT-SEEEEEESSGG.CTHHHHTTSEEEE CS
                           PTS_IIB  19 klekaakelgieaegeagv........eleaeeiaddaDlvllapqvrv.kdlarfagkpvav 72 
                                        lek+ ke++i++++ a +         l + + ++ aD+ ll+p  ++ k++++ ++  v  
  gi|242399183|ref|YP_002994607.1| 104 DLEKIIKEHDIDIVVFAYSdvshehvmHLASRAHSAGADFWLLGPKSTMiKSTKPVVA--VTA 164
                                       689*******88855555555555567999999999*********9999888877777..333 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 1.3
                                       EEEEESSSHHHHHHHHHHHHHHHHHCTEEEEE CS
                           PTS_IIB   2 illaCgaGmatSlmaaeklekaakelgieaeg 33 
                                       +++a  +G + S+    k+ + ++e+g +++ 
  gi|242399183|ref|YP_002994607.1| 161 AVTAVRTGSGKSQTS-RKVAQLLQEMGYKVVA 191
                                       6888889******99.***********77765 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.56
                                       HT-SEEEEEE.SSGG.CTHHHHTTSEEEEECTTHHH CS
                           PTS_IIB  46 ddaDlvllap.qvrv.kdlarfagkpvavinikdal 79 
                                         aD++++ + +++  +d+++  +  +++in k+++
  gi|242399183|ref|YP_002994607.1| 298 RAADVIIINKiDTANrEDVQKVRE-SIEKINPKAIV 332
                                       459999999945554666666666.68888888855 PP

  == domain 4  score: 7.2 bits;  conditional E-value: 0.011
                                       TEE.GGGHHHHHHT-SEEEEEESSGGCTHHHHTTSE..EEEECTTHHHCCHCHHHHHH CS
                           PTS_IIB  35 agv.eleaeeiaddaDlvllapqvrvkdlarfagkp..vavinikdalgimdgekvlk 89 
                                       +++ ele   + +daDlv++++ ++      + +kp   +++ +++ +g  + + +lk
  gi|242399183|ref|YP_002994607.1| 416 KQIkELEETINRADADLVVIGTPIDL-RRVMKLNKPavRVRYELEE-IGEPKLKDILK 471
                                       45567888999999********9997.2222222452244555555.66666666665 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 !   14.9   0.2   2.9e-05     0.021       1      33 [.     160     192 ..     160     194 .. 0.94
   2 ?   -1.3   0.0         3   2.2e+03      79      99 ..     303     325 ..     288     347 .. 0.73
   3 ?   -0.7   0.0       1.9   1.3e+03      27      69 ..     349     428 ..     344     467 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.9e-05
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllv 33 
                                       +a+++   G+GK+ ++ + a++l++ g++V+++
  gi|242399183|ref|YP_002994607.1| 160 VAVTAVRTGSGKSQTSRKVAQLLQEMGYKVVAI 192
                                       6899999***********************986 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 3
                                       EEEEEESS...-TT..CHHHHHH CS
                                       xxxxxxxxxxxxxx..xxxxxxx RF
                              CbiA  79 vvlnrvdgeneetl..lkealee 99 
                                       +++n++d  n+e     +e++e+
  gi|242399183|ref|YP_002994607.1| 303 IIINKIDTANREDVqkVRESIEK 325
                                       78999998865543003344444 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.9
                                       T--EEEEEEEESSCCCCH.............HTTEB-HHHH...........................CCHCCCHHH CS
                                       xxxxxxxxxxxxxxxxxx.............xxxxxxxxxx...........................xxxxxxxxx RF
                              CbiA  27 glrVllvDaDpqannlai.............leglendiep...........................dlkrllell 63 
                                       g+rVl+v  +p    l++              +g ++ i+p                           ++k+++el 
  gi|242399183|ref|YP_002994607.1| 349 GKRVLVVEDGPT---LTHggmkygagyvaakKFGAREIIDPrpyavgsiidtykkynhldvilpamgyGAKQIKELE 422
                                       778888874444...44334433333333333333333333777777777777777778888888888777777776 PP

                                       HHHCHC CS
                                       xxxxxx RF
                              CbiA  64 ealgkk 69 
                                       e++ + 
  gi|242399183|ref|YP_002994607.1| 423 ETINRA 428
                                       666655 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.7e-05     0.012       6      53 ..     168     213 ..     167     235 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.7e-05
                                       TSSHHHHHHHHHHHHHHTTE..EEEESSSTTSHHHHHHHHHHHTCS--- CS
                   Thymidylate_kin   6 GaGKttqaellkerlkeegik.vvltrepggteiGekirelllkeeele 53 
                                       G+GK++ ++++++ l+e+g+k v ++++   ++++++i +      ++e
  gi|242399183|ref|YP_002994607.1| 168 GSGKSQTSRKVAQLLQEMGYKvVAIRHPMPYGDLRKQIVQR---FATYE 213
                                       9********************77777777666666555443...33333 PP

>> SWI2_SNF2  SWI2/SNF2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       7.9   5.7e+03     120     157 ..      40      75 ..      26      78 .. 0.57
   2 !   14.5   0.0   2.9e-05     0.021      27     151 ..     167     333 ..     152     336 .. 0.71

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 7.9
                         SWI2_SNF2 120 eniivlvDEaHRsqygelakklrkalpnaafigFTGTP 157
                                       ++ +v+   a R  + ++++  r   p++ +++FT T 
  gi|242399183|ref|YP_002994607.1|  40 RKRVVILGAAGRD-FHNFNTFFR-NNPEYEVVAFTATQ 75 
                                       4445555555443.333443333.34778888888885 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 2.9e-05
                         SWI2_SNF2  27 qGSGKsltmvflakklleeelknpkvvvvtDRkdLdkQlsktfaka..geekpkqaesrkeLkellekesekiiftt 101
                                       +GSGKs t+ ++a+ l+e   k   +   +   dL kQ+ + fa+    ++++ ++e+r+e +  +  +++ ++ + 
  gi|242399183|ref|YP_002994607.1| 167 TGSGKSQTSRKVAQLLQEMGYKVVAIRHPMPYGDLRKQIVQRFATYedLDKHECTIEEREEYEPYI--DRGMVVYAG 241
                                       8***************99544445555556678***********9844345556899999999999..457777776 PP

                         SWI2_SNF2 102 iqKfe....eeek.....................................eklevlsereniivl..vDEaHRsqyg 135
                                       ++  +    + ek                                     +  e+  +  ++i++  +D a R   +
  gi|242399183|ref|YP_002994607.1| 242 VDYEKilreA-EKeadiilwdggnndfpfyipdlwivvadphrpghelkyHPGETNFRAADVIIInkIDTANREDVQ 317
                                       6533333321.224678888888888888888888888888888877654222333344456665557888888888 PP

                         SWI2_SNF2 136 elakklrkalpnaafi 151
                                       +++++++k+ p+a +i
  gi|242399183|ref|YP_002994607.1| 318 KVRESIEKINPKAIVI 333
                                       8888888888887765 PP

>> PPK2  Polyphosphate kinase 2 (PPK2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       3.9   2.8e+03     125     159 ..     104     138 ..     102     146 .. 0.71
   2 ?   13.0   0.1   7.6e-05     0.054      22     122 ..     149     250 ..     132     264 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 3.9
                                       HHHHHHHHTTEEEEEEEEE--HHHHHHHHHHHHHS CS
                              PPK2 125 efErmlvesgillvKfwlsiskeeqleRfkeRred 159
                                       ++E+ + e++i +v f +s  ++e  + + +R ++
  gi|242399183|ref|YP_002994607.1| 104 DLEKIIKEHDIDIVVFAYSDVSHEHVMHLASRAHS 138
                                       68999999999888886655555566677777665 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 7.6e-05
                                       HHSGGGGG-EEEEEEEESTTS-HHHHHHHHHTTS-GGG-EEEE--S--HH.HHTS-TTHHHHTT--.-TT-EEEEES CS
                              PPK2  22 qekvkaegkklvvifegrDaAGKgGaikrvtealnprvarvvalkaPtee.EksqwylqRyvehlP.akgeivlFdR 96 
                                       ++ + ++ k +v++   r + GK  + ++v + l+  +++vva+++P    +  ++  qR+ +     k e ++ +R
  gi|242399183|ref|YP_002994607.1| 149 KSTMIKSTKPVVAVTAVRTGSGKSQTSRKVAQLLQEMGYKVVAIRHPMPYgDLRKQIVQRFATYEDlDKHECTIEER 225
                                       6778889999*************************************975267888899997654314667777777 PP

                                       -GGGGGTHHHHHTSS-HHHHHHHHHH CS
                              PPK2  97 swYnragvervmgfctdkeaerflre 122
                                         Y+   ++r m + +  ++e+ lre
  gi|242399183|ref|YP_002994607.1| 226 EEYEP-YIDRGMVVYAGVDYEKILRE 250
                                       77764.45666666666666666666 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     9e-05     0.064       3     109 ..     160     264 ..     158     270 .. 0.63
   2 ?   -1.7   0.0       1.9   1.4e+03      86     116 ..     418     446 ..     411     451 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9e-05
                                       EEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHHHHHHHHHHHH...HHT------EEE-SSS-HHH CS
                              MipZ   3 ivlgnekGGsGksttavhvavaLlkkGarvaaidldlrqrtlarylenraatae...rkglsLplpealalseaeea 76 
                                       + ++  + GsGks t+  va  L ++G +v ai   +    l + +  r at e   +++ ++++ e ++       
  gi|242399183|ref|YP_002994607.1| 160 VAVTAVRTGSGKSQTSRKVAQLLQEMGYKVVAIRHPMPYGDLRKQIVQRFATYEdldKHECTIEEREEYEP------ 230
                                       66777889*************************87655555555555555554300033333333333222...... PP

                                       HTTS-H.HHHHHHHHHHHHHHHHH-SEEEEE--S CS
                              MipZ  77 eveeee.eaevaeleelvadleaeldfividtPG 109
                                        ++++      ++ e++++++e+e+d+i+ d   
  gi|242399183|ref|YP_002994607.1| 231 YIDRGMvVYAGVDYEKILREAEKEADIILWDGGN 264
                                       2333220223356678889999999999888654 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.9
                                       HHHHHHHHHHHHHH-SEEEEE--SS--HHHH CS
                              MipZ  86 vaeleelvadleaeldfividtPGsdsalsr 116
                                       ++elee +++  a++d++vi tP    ++++
  gi|242399183|ref|YP_002994607.1| 418 IKELEETINR--ADADLVVIGTPIDLRRVMK 446
                                       4455555554..4689******987777666 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 ?    5.6   0.0     0.038        27       2      81 ..      42     132 ..      41     140 .. 0.76
   2 ?    6.2   0.0     0.025        18       7      73 ..     369     440 ..     367     452 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.038
                                       EEEEETTSHHHHHH..HHHHHHTTTTEEEEEEECSSHHHHHHH..HHHTTHEEESS.........HHHHHTCTTESE CS
                      GFO_IDH_MocA   2 rvaiiGaGkigskh..lrplnesqrleevvalldpdaeraeav..aesfgveaysd.........leelladpeida 65 
                                       rv+i Ga  +g+++  ++ + ++++++evva+  ++ +  e      ++  e y +         le++ ++ +id+
  gi|242399183|ref|YP_002994607.1|  42 RVVILGA--AGRDFhnFNTFFRNNPEYEVVAFTATQIPDIEGRiyPPELAGELYPNgipiwseddLEKIIKEHDIDI 116
                                       8999999..555552456667777888****999999998866677777777888888888888899****99**** PP

                                       EEE-S-GGGHHHHHHH CS
                      GFO_IDH_MocA  66 vivatpngtheelaka 81 
                                       v+ a    +he ++  
  gi|242399183|ref|YP_002994607.1| 117 VVFAYSDVSHEHVMHL 132
                                       *999999887766554 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.025
                                       TTSHH.HHHHHHHHHHTTTTEEEEEEECSSHH.HHHHH...HHHTTHEEESSHHHHHTCTTESEEEE-S-GG CS
                      GFO_IDH_MocA   7 GaGki.gskhlrplnesqrleevvalldpdae.raeav...aesfgveaysdleelladpeidavivatpng 73 
                                       GaG++ ++k+++      r + v  ++d+ ++ ++ +v   a  +g++  ++lee  +  ++d+v+++tp +
  gi|242399183|ref|YP_002994607.1| 369 GAGYVaAKKFGAREIIDPRPYAVGSIIDTYKKyNHLDVilpAMGYGAKQIKELEETINRADADLVVIGTPID 440
                                       777775555544434444777888888887762344458899999************************965 PP

>> Glyco_tran_WecB  Glycosyl transferase WecB/TagA/CpsF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0      0.16   1.1e+02      35     117 ..      31     134 ..      15     147 .. 0.68
   2 ?    1.0   0.0      0.51   3.7e+02      34     105 ..     130     195 ..     125     210 .. 0.63
   3 ?   -2.0   0.1       4.3   3.1e+03      81     102 ..     312     333 ..     294     336 .. 0.76
   4 ?    6.1   0.0     0.013       9.6      66     104 ..     399     437 ..     390     444 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.16
                   Glyco_tran_WecB  35 elleraeeeglrvfllGgkpevlekaaerlrekypglriagthdg.........yk.............eeeeeaii 89 
                                       e+++ ae++++rv++lG++     ++ + +r++ p+ +++ + +          y+                e+++ 
  gi|242399183|ref|YP_002994607.1|  31 EVIKMAEKKRKRVVILGAAGRDFHNFNTFFRNN-PEYEVVAFTATqipdiegriYPpelagelypngipIWSEDDLE 106
                                       567778888899999999888777777777666.5555555544434444444410334444444556456778888 PP

                   Glyco_tran_WecB  90 eainaskpdlllvglGapkqEkwiarlk 117
                                       + i++++ d+++ +      E++++  +
  gi|242399183|ref|YP_002994607.1| 107 KIIKEHDIDIVVFAYSDVSHEHVMHLAS 134
                                       8889999999999988888888777555 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.51
                   Glyco_tran_WecB  34 eelleraeeeglrvfllGgkpevlekaaerlrekypglriagthdgy.keeeeeaiieainaskpdlllvglG 105
                                       ++l +ra+++g  ++llG k  ++++++       p + +  ++ g  k++ ++++++ +++ + +++ +   
  gi|242399183|ref|YP_002994607.1| 130 MHLASRAHSAGADFWLLGPKSTMIKSTK-------PVVAVTAVRTGSgKSQTSRKVAQLLQEMGYKVVAIRHP 195
                                       5666667666777777777744444333.......33334444444445678888888888888888776555 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 4.3
                   Glyco_tran_WecB  81 keeeeeaiieainaskpdlllv 102
                                       ++e+ +++ e i++ +p+ +++
  gi|242399183|ref|YP_002994607.1| 312 NREDVQKVRESIEKINPKAIVI 333
                                       3588999999999999999876 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.013
                   Glyco_tran_WecB  66 ekypglriagthdgykeeeeeaiieainaskpdlllvgl 104
                                       +ky++l++     gy +++ +++ e+in++++dl+++g 
  gi|242399183|ref|YP_002994607.1| 399 KKYNHLDVILPAMGYGAKQIKELEETINRADADLVVIGT 437
                                       57889999999999966999*****************96 PP

>> RuvX  Holliday junction resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       6.1   4.4e+03      41      57 ..     103     119 ..     101     136 .. 0.85
   2 ?    1.0   0.1      0.73   5.2e+02      34      57 ..     310     333 ..     294     343 .. 0.77
   3 ?    9.5   0.0    0.0017       1.2      36      65 ..     414     443 ..     396     461 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 6.1
                                       HHHHHHHHHTT--EEEE CS
                              RuvX  41 eelkelvkeeeveeiVv 57 
                                       ++l++++ke++++ +V 
  gi|242399183|ref|YP_002994607.1| 103 DDLEKIIKEHDIDIVVF 119
                                       57999*******99996 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.73
                                       --HHHHHHHHHHHHHHTT--EEEE CS
                              RuvX  34 kskekdleelkelvkeeeveeiVv 57 
                                       +++++d+++++e +++ ++++iV+
  gi|242399183|ref|YP_002994607.1| 310 TANREDVQKVRESIEKINPKAIVI 333
                                       224689****************98 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.0017
                                       HHHHHHHHHHHHHHTT--EEEEE------S CS
                              RuvX  36 kekdleelkelvkeeeveeiVvGlPlnldg 65 
                                       + k+++el+e++++ +++ +V+G P++l+ 
  gi|242399183|ref|YP_002994607.1| 414 GAKQIKELEETINRADADLVVIGTPIDLRR 443
                                       4789*********************98864 PP

>> UPF0180  Uncharacterised protein family (UPF0180)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       9.4   6.8e+03      22      61 ..      31      47 ..      26      62 .. 0.54
   2 ?    7.9   0.0    0.0047       3.4      11      28 ..     177     194 ..     173     232 .. 0.84
   3 ?   -2.6   0.0       9.1   6.5e+03      29      47 ..     249     267 ..     239     268 .. 0.74
   4 ?    0.4   0.0         1   7.2e+02      33      61 ..     298     334 ..     282     354 .. 0.61
   5 ?   -2.1   0.0       6.4   4.6e+03      17      40 ..     409     435 ..     403     451 .. 0.57

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 9.4
                           UPF0180 22 eVvdleteedaqsvdaiVvtGqdtnvmgiedtetkapvIn 61
                                      eV+++ +   +                    +  ++++  
  gi|242399183|ref|YP_002994607.1| 31 EVIKMAE---K--------------------KRKRVVILG 47
                                      5555553...2....................333333333 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0047
                           UPF0180  11 nvkeaLrekGYeVvdlet 28 
                                       +v++ L+e GY+Vv +++
  gi|242399183|ref|YP_002994607.1| 177 KVAQLLQEMGYKVVAIRH 194
                                       699***********9997 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 9.1
                           UPF0180  29 eedaqsvdaiVvtGqdtnv 47 
                                        e+++++d+i  +G ++++
  gi|242399183|ref|YP_002994607.1| 249 REAEKEADIILWDGGNNDF 267
                                       4568999999999999875 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 1
                           UPF0180  33 qsvdaiVvtGqdtnv........mgiedtetkapvIn 61 
                                       + +d+i+++  dt +          ie+++ ka+vI+
  gi|242399183|ref|YP_002994607.1| 298 RAADVIIINKIDTANredvqkvrESIEKINPKAIVID 334
                                       5566666644332222222443345555666666665 PP

  == domain 5  score: -2.1 bits;  conditional E-value: 6.4
                           UPF0180  17 rekGYeVvdlet...eedaqsvdaiVv 40 
                                        + GY   ++++     +  ++d +V+
  gi|242399183|ref|YP_002994607.1| 409 PAMGYGAKQIKEleeTINRADADLVVI 435
                                       556675555555421444555555555 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.23   1.7e+02      67      98 ..      24      55 ..       2      61 .. 0.79
   2 ?    7.7   0.0    0.0034       2.4      10      34 ..     167     191 ..     158     198 .. 0.88
   3 ?   -2.9   0.0       5.9   4.2e+03      85      99 ..     301     318 ..     295     336 .. 0.55

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.23
                                      CHHHHHHHHHHHHHHTTSSEEEEEE--SSTTH CS
                             SRP54 67 dpaavakeavekakeekidvvlvDTaGrlqnd 98
                                      d    ++e +++a++++  vv++  aGr   +
  gi|242399183|ref|YP_002994607.1| 24 DCKVKTFEVIKMAEKKRKRVVILGAAGRDFHN 55
                                      555567899999****************7665 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0034
                                       TTSSHHHHHHHHHHHHHHTTS-EEE CS
                             SRP54  10 qGaGKTttlaKLaallkkegkkvll 34 
                                       +G+GK +t  K+a+ll+++g+kv+ 
  gi|242399183|ref|YP_002994607.1| 167 TGSGKSQTSRKVAQLLQEMGYKVVA 191
                                       8*********************975 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 5.9
                                       SEEE...EEE--SSTTHH CS
                             SRP54  85 dvvl...vDTaGrlqndk 99 
                                       dv++   +DTa r   +k
  gi|242399183|ref|YP_002994607.1| 301 DVIIinkIDTANREDVQK 318
                                       555523336666655443 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1    0.0003      0.22       3      36 ..     159     192 ..     157     196 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0003
                            AAA_31   3 vIaianqKGGvGKTTtsvnlaaalaklgkkvLlv 36 
                                       v+a++  + G GK+ ts ++a+ l ++g+kv  +
  gi|242399183|ref|YP_002994607.1| 159 VVAVTAVRTGSGKSQTSRKVAQLLQEMGYKVVAI 192
                                       89999**************************987 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00023      0.16      10      49 ..     152     192 ..     145     205 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00023
                        Zeta_toxin  10 ypsqerPklillgGqpGAGKselaellkdele.rqgnvvrl 49 
                                       ++++ +P++ + +  +G+GKs++++++++ l+ ++ +vv +
  gi|242399183|ref|YP_002994607.1| 152 MIKSTKPVVAVTAVRTGSGKSQTSRKVAQLLQeMGYKVVAI 192
                                       67789***********************9998556666655 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0       0.6   4.3e+02      48      81 ..     157     191 ..     101     210 .. 0.61
   2 ?    9.1   0.0    0.0016       1.1      49      83 ..     301     334 ..     295     353 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.6
                                       EEEEEEE-GGG--HHH.HHHHHHHHHHHTTSEEEE CS
                       RsgA_GTPase  48 epvivlnKiDlleeee.eleelkeelealgyevll 81 
                                       +pv++++ +   + ++ + +++++ l+++gy+v++
  gi|242399183|ref|YP_002994607.1| 157 KPVVAVTAVRTGSGKSqTSRKVAQLLQEMGYKVVA 191
                                       33333333333332222345555555555555555 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0016
                                       EEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE-- CS
                       RsgA_GTPase  49 pvivlnKiDlleeeeeleelkeelealgyevllvs 83 
                                        vi++nKiD +++e+ +++++e +e+++ + ++++
  gi|242399183|ref|YP_002994607.1| 301 DVIIINKIDTANRED-VQKVRESIEKINPKAIVID 334
                                       68*************.***********99998876 PP

>> DUF2325  Uncharacterized protein conserved in bacteria (DUF2325)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       5.8   4.1e+03      64      81 ..      31      48 ..      27      53 .. 0.80
   2 ?    7.0   0.0    0.0084         6      46      79 ..     113     146 ..     101     153 .. 0.80
   3 ?   -0.4   0.0       1.8   1.3e+03      10      32 ..     314     336 ..     285     345 .. 0.71
   4 ?    0.1   0.0       1.3   9.1e+02      32      53 ..     413     434 ..     390     438 .. 0.61

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 5.8
                           DUF2325 64 kvkkeakkkgkpvvrlhs 81
                                      +v k a+kk k+vv+l  
  gi|242399183|ref|YP_002994607.1| 31 EVIKMAEKKRKRVVILGA 48
                                      577899999999999865 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0084
                           DUF2325  46 kaDlvvlftdtvsHkavkkvkkeakkkgkpvvrl 79 
                                       + D+vv+  + vsH+ v ++ + a+  g  +++l
  gi|242399183|ref|YP_002994607.1| 113 DIDIVVFAYSDVSHEHVMHLASRAHSAGADFWLL 146
                                       4699******************999999998877 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1.8
                           DUF2325  10 rmeeqyrklleklggklkvfdgr 32 
                                       + ++++r+ +ek + k++v+dg 
  gi|242399183|ref|YP_002994607.1| 314 EDVQKVRESIEKINPKAIVIDGA 336
                                       34556666677777777776665 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 1.3
                           DUF2325  32 rkekkkkkleskigkaDlvvlf 53 
                                       +  k+ k+le+ i++aD+ +++
  gi|242399183|ref|YP_002994607.1| 413 YGAKQIKELEETINRADADLVV 434
                                       3444555999999988764444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.025        18      13      65 ..     166     210 ..     153     228 .. 0.75
   2 ?   -2.3   0.0       6.9   4.9e+03      77     100 ..     314     336 ..     305     347 .. 0.78
   3 ?    4.3   0.0     0.065        47     106     137 .]     415     445 ..     402     445 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.025
                            AAA_22  13 esGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralg 65 
                                        +G+GK+ + r++++ l+        + ++  v + +++   dl++++++ + 
  gi|242399183|ref|YP_002994607.1| 166 RTGSGKSQTSRKVAQLLQ--------EMGYKVVAIRHPMPYGDLRKQIVQRFA 210
                                       58***************7........566666666666667777777777665 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 6.9
                            AAA_22  77 ellealeqalraravielliiDEa 100
                                       e ++++++ +++    ++++iD a
  gi|242399183|ref|YP_002994607.1| 314 EDVQKVRESIEKINP-KAIVIDGA 336
                                       556778888888888.99999987 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.065
                            AAA_22 106 eealeeLrsllnlsrkgvqliLvGtp.elrkll 137
                                       +++++eL +  n  r +  l+++Gtp +lr+++
  gi|242399183|ref|YP_002994607.1| 415 AKQIKELEETIN--RADADLVVIGTPiDLRRVM 445
                                       678899999999..***************9875 PP

>> DAHP_snth_FXD  DAHP synthase ferredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0       0.5   3.6e+02      13      31 ..     174     192 ..     166     193 .. 0.82
   2 ?    8.4   0.1    0.0027       1.9       7      34 ..     309     336 ..     302     339 .. 0.83
   3 ?   -2.8   0.0       8.4   6.1e+03      11      25 ..     415     429 ..     410     435 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.5
                     DAHP_snth_FXD  13 qieevierieelGlkvhvs 31 
                                         ++v + ++e+G+kv  +
  gi|242399183|ref|YP_002994607.1| 174 TSRKVAQLLQEMGYKVVAI 192
                                       557999*********9766 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0027
                     DAHP_snth_FXD   7 kgateeqieevierieelGlkvhvskGe 34 
                                        +a+ e++++v e ie+ + k+ v+ G+
  gi|242399183|ref|YP_002994607.1| 309 DTANREDVQKVRESIEKINPKAIVIDGA 336
                                       47899********************998 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 8.4
                     DAHP_snth_FXD  11 eeqieevierieelG 25 
                                        +qi+e+ e+i++ +
  gi|242399183|ref|YP_002994607.1| 415 AKQIKELEETINRAD 429
                                       678899988888766 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0    0.0016       1.2       4     103 ..     161     259 ..     159     264 .. 0.65
   2 ?   -0.2   0.0         1   7.2e+02      85     111 ..     313     340 ..     298     344 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0016
                            AAA_26   4 fvtgtdtgvGKTvvslgLvralkrkgvk.vgyfKPiqtgieededselikellgldqtyelpeplalsaplspelaa 79 
                                        vt+++tg+GK+ +s  +++ l++ g+k v+   P+  g  +++ +++ +++ +ld++++ +e     +p+ ++   
  gi|242399183|ref|YP_002994607.1| 161 AVTAVRTGSGKSQTSRKVAQLLQEMGYKvVAIRHPMPYGDLRKQIVQRFATYEDLDKHECTIEEREEYEPYIDRGMV 237
                                       69*************************95556667888888777777777777777666654443222233222222 PP

                            AAA_26  80 rqegedidlekivkelekdadivv 103
                                             +d eki +e ek+adi++
  gi|242399183|ref|YP_002994607.1| 238 VY--AGVDYEKILREAEKEADIIL 259
                                       22..23455666666666666665 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1
                            AAA_26  85 didlekivkelek.dadivvVEGagglg 111
                                         d++k+ +++ek + + +v++Ga++l 
  gi|242399183|ref|YP_002994607.1| 313 REDVQKVRESIEKiNPKAIVIDGASPLY 340
                                       3456666666666555778888887765 PP

>> LytR_C  LytR cell envelope-related transcriptional attenuator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00052      0.37       5      34 ..     164     193 ..     160     219 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00052
                            LytR_C   5 eVlNgtgvsGlAarvadaLeerGftvgevg 34 
                                       +V+ g+g+s+  ++va++L+e G++v+++ 
  gi|242399183|ref|YP_002994607.1| 164 AVRTGSGKSQTSRKVAQLLQEMGYKVVAIR 193
                                       68889*********************9865 PP

>> PB1  PB1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       3.8   2.8e+03      34      50 ..       7      24 ..       1      25 [. 0.73
   2 ?    1.7   0.0      0.34   2.4e+02      54      70 ..      97     113 ..      95     121 .. 0.89
   3 ?    6.2   0.0     0.013       9.6      16      63 ..     190     229 ..     182     234 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3.8
                                      HHTST.CCSEEEEEEETT CS
                               PB1 34 rfkls.dedvklkYpded 50
                                      ++ ls +++ k++Yp+ d
  gi|242399183|ref|YP_002994607.1|  7 KISLSnKNSYKCQYPNID 24
                                      455557899999*99866 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.34
                                       EEESSHHHHHHHHHHHH CS
                               PB1  54 VtitsDeDLeealeear 70 
                                       ++i s++DLe++++e++
  gi|242399183|ref|YP_002994607.1|  97 IPIWSEDDLEKIIKEHD 113
                                       7999**********986 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.013
                                       EEEGSSS-HHHHHHHHHHHHTSTCCSEEEEEEETTSSEEEESSHHHHH CS
                               PB1  16 lsvssnisfeeLrakvekrfklsdedvklkYpdedgdlVtitsDeDLe 63 
                                       + ++++ ++ +Lr+++ +rf+         Y+d d++++ti + e++e
  gi|242399183|ref|YP_002994607.1| 190 VAIRHPMPYGDLRKQIVQRFAT--------YEDLDKHECTIEEREEYE 229
                                       6789999**************9........999999999999988876 PP

>> DUF2179  Uncharacterized protein conserved in bacteria (DUF2179)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.2      0.53   3.8e+02      31      46 ..     104     119 ..     102     126 .. 0.79
   2 ?    9.9   0.3   0.00083       0.6      24      46 ..     311     333 ..     310     334 .. 0.94
   3 ?    0.5   0.0      0.72   5.2e+02      27      46 ..     416     435 ..     414     440 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.53
                           DUF2179  31 klkeiikeiDpkAFii 46 
                                       +l++iike+D +  ++
  gi|242399183|ref|YP_002994607.1| 104 DLEKIIKEHDIDIVVF 119
                                       799*******887665 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00083
                           DUF2179  24 vsrkelsklkeiikeiDpkAFii 46 
                                       ++r +++k++e i++i pkA +i
  gi|242399183|ref|YP_002994607.1| 311 ANREDVQKVRESIEKINPKAIVI 333
                                       689*****************997 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.72
                           DUF2179  27 kelsklkeiikeiDpkAFii 46 
                                       k++++l+e+i++ D +  +i
  gi|242399183|ref|YP_002994607.1| 416 KQIKELEETINRADADLVVI 435
                                       79***********9886665 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.1      0.26   1.8e+02       5      28 ..     167     190 ..     166     193 .. 0.89
   2 ?   -1.9   0.0       3.1   2.3e+03     159     175 ..     301     318 ..     277     335 .. 0.69
   3 ?    6.1   0.0     0.012       8.6      69      99 ..     408     438 ..     395     447 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.26
                        ATP_bind_1   5 aGsGKttfvgalseilelrgrsva 28 
                                        GsGK+   ++++++l++ g++v 
  gi|242399183|ref|YP_002994607.1| 167 TGSGKSQTSRKVAQLLQEMGYKVV 190
                                       59*****************99876 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.1
                        ATP_bind_1 159 hvvvlnkfDllkek.lek 175
                                        v+++nk+D ++++  +k
  gi|242399183|ref|YP_002994607.1| 301 DVIIINKIDTANREdVQK 318
                                       577888888866332222 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.012
                        ATP_bind_1  69 vvaleflresldwldeelekeeddyllfDtP 99 
                                         a+ ++++++ +l+e++++ ++d+++++tP
  gi|242399183|ref|YP_002994607.1| 408 LPAMGYGAKQIKELEETINRADADLVVIGTP 438
                                       56999*************77799*******9 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.3    0.0023       1.6      17      51 ..     156     191 ..     150     194 .. 0.78
   2 ?   -1.7   0.0       2.8     2e+03     101     126 ..     414     439 ..     410     472 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0023
                            AAA_30  17 gdrvavltG.pAGtGKttalkalreaweaaggrvig 51 
                                       ++ v+++t+ + G+GK+ + +++++++++ g++v++
  gi|242399183|ref|YP_002994607.1| 156 TKPVVAVTAvRTGSGKSQTSRKVAQLLQEMGYKVVA 191
                                       444444444278**********************96 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.8
                            AAA_30 101 dtkqlaallkaaekagakvilvGDer 126
                                       ++kq+++l + +++a+a ++++G + 
  gi|242399183|ref|YP_002994607.1| 414 GAKQIKELEETINRADADLVVIGTPI 439
                                       67899999999999999999999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (481 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       870  (0.0485247); expected 358.6 (0.02)
Passed bias filter:                      746  (0.0416086); expected 358.6 (0.02)
Passed Vit filter:                       102  (0.00568911); 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: 0.75u 0.37s 00:00:01.12 Elapsed: 00:00:00.54
# Mc/sec: 2705.51
//
Query:       gi|242399184|ref|YP_002994608.1|  [L=409]
Description: Glucose-dependent multidrug resistance protein [Thermococcus sibiricus MM 739]
Scores for complete 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-27   94.8  18.0    5.3e-27   94.4  18.0    1.0  1  MFS_3     Transmembrane secretion effector
      5e-27   94.8  22.8      5e-27   94.8  22.8    1.9  2  MFS_1     Major Facilitator Superfamily
    4.3e-07   28.9   2.2    4.3e-07   28.9   2.2    3.1  3  MFS_2     MFS/sugar transport protein


Domain annotation for each model (and alignments):
>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.4  18.0   8.9e-31   5.3e-27      18     394 ..      12     392 ..       2     401 .. 0.85

  Alignments for each domain:
  == domain 1  score: 94.4 bits;  conditional E-value: 8.9e-31
                             MFS_3  18 aslvsnlGtliqevaasWlmtdisasplmvAlvqaaatLPifllsilaGalaDnfdrRkvllavqlllalvsvlltv 94 
                                          +s+ G++iq++a+   + d + s + + +  +a  +P +l+  +aG++ D ++r++++++     ++  vll  
  gi|242399184|ref|YP_002994608.1|  12 GRWISQAGWVIQDIAVPLYVLDKTGSGTIMSIFIIAELIPRLLVNPIAGVIGDRYNRKNLMVWLD---IARGVLLFG 85 
                                       456999*******************************************************9854...567889999 PP

                             MFS_3  95 laalgllspwlllaltlligiGaalndPaWqAsvgelvkrrdvpaAvaLnsvginiaRsvGPAlgGvlvaavGaala 171
                                       + a++ll+  +lla+ ++++i  a+ +   + + ++lvkr+++ +A      g  i R +GP lgGv+ a+ G  la
  gi|242399184|ref|YP_002994608.1|  86 VIAFNLLDIQSLLAVQVVMSIMGAFFSAGISGMFPDLVKREELAQANSPLQSGGQIIRIAGPILGGVIYAFGGLKLA 162
                                       9999*****************************************9987778999********************** PP

                             MFS_3 172 favnalsyla..livallrwkrevrksslprEkllealraglRftaasreikavlvRaalFglsasavla.LLPlva 245
                                         +na+s++   l   l++ k+e rk s ++E + e + +g++f + s+++ + +  a++       ++a +LP + 
  gi|242399184|ref|YP_002994608.1| 163 ILINAVSFFGsgLFEMLIEYKWESRKISSLNE-VWEDMLEGFKFIKDSKSLLVLVSLAIALNTLLNPIFAvILPYLS 238
                                       ********9633788999*******9999988.5678889***********9999999999988888888469**** PP

                             MFS_3 246 rdqldgdalvyGillgalGvGAilgallls.rLRerlsserlvllaavalAlvllslalass......lwvavlvl. 314
                                       r  l+  ++ +G + +a  +GA++g +l + +L+e  sse+l+  a +a  ++ll l++  +      ++ a+l + 
  gi|242399184|ref|YP_002994608.1| 239 RVILGFSSVQFGSIQTATTIGALAGNVLIAgKLKE--SSENLLFKALFAQLICLLLLSVIVHplirpvAYPALLGIf 313
                                       *************************9765427777..6999999999999999999987544122111333444441 PP

                             MFS_3 315 llgGaaWitalstlnvavqlavPrWvvgRalavYltvlaGglaaGsllWGavaealsvtlaLlaaaaalllaaaill 391
                                       ++gG   i++   l +  q +vP+ v++R ++ + t+++ +  +G ++ G + + + v++ L ++ ++l l a i +
  gi|242399184|ref|YP_002994608.1| 314 MMGGFFNILVNVPLITKLQKSVPNEVRARFFSAFETAIMATTPLGMAVVGPLLDIIEVST-LVITLVTLSLLASIYY 389
                                       455556688888999*************************************99999964.5555555444444444 PP

                             MFS_3 392 llk 394
                                        ++
  gi|242399184|ref|YP_002994608.1| 390 YIN 392
                                       444 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.8  22.8   8.4e-31     5e-27       4     351 ..      12     357 ..       9     359 .. 0.82
   2 ?    2.0   1.1     0.013        77     254     297 ..     355     394 ..     344     402 .. 0.55

  Alignments for each domain:
  == domain 1  score: 94.8 bits;  conditional E-value: 8.4e-31
                             MFS_1   4 aaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll 80 
                                       + ++s +++ i  +a+pl++ +  g s++ +++ + +  +  ++ ++++G+++dr+ r+ ++++  ++ ++  l+++
  gi|242399184|ref|YP_002994608.1|  12 GRWISQAGWVIQDIAVPLYVLDKTG-SGTIMSIFIIAELIPRLLVNPIAGVIGDRYNRKNLMVWLDIARGVL-LFGV 86 
                                       5678889999999999987777777.7777776666667777**************9999***********9.5555 PP

                             MFS_1  81 ..fa.sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravf 154
                                         f    +  ll++ v+++++++++ +++  ++ d++++ee ++a++ l++g ++  i gp+lgg++++ +g  ++ 
  gi|242399184|ref|YP_002994608.1|  87 iaFNlLDIQSLLAVQVVMSIMGAFFSAGISGMFPDLVKREELAQANSPLQSGGQIIRIAGPILGGVIYAFGGLKLAI 163
                                       2342444556******************************************************************* PP

                             MFS_1 155 yilaivsllafv..lfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlw.illialllfffgfsgllt 228
                                       +i+a+ ++ +++  + + + +e+++ ++ ++ +e+        +++++k ++ ++ l+ ++ +a++l+++ + ++ +
  gi|242399184|ref|YP_002994608.1| 164 LINAVSFFGSGLfeMLIEYKWESRKISSLNEVWED--------MLEGFKFIKDSKSLLvLVSLAIALNTLLNPIFAV 232
                                       **********9933322333555555555555555........8999********9976677777777778888999 PP

                             MFS_1 229 llplylqevlgls....glllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavt.... 297
                                        lp + +  lg+s    g ++++    ++al+g +l  +ag+l     +++ l+ al++ l+++l+l ++ ++    
  gi|242399184|ref|YP_002994608.1| 233 ILPYLSRVILGFSsvqfGSIQTA--TTIGALAGNVL--IAGKLKES--SENLLFKALFAQLICLLLLSVIVHPlirp 303
                                       999999*******7766556666..66666666666..88888765..78899999999999999999999997777 PP

                             MFS_1 298 ssavllllvlvliGfglgfvfpsllalasdlappeeagtasglfntagslggal 351
                                         +++ll ++++ Gf+  +v+++l++ +++++p+e +++ +++f ta  + + l
  gi|242399184|ref|YP_002994608.1| 304 VAYPALLGIFMMGGFFNILVNVPLITKLQKSVPNEVRARFFSAFETAIMATTPL 357
                                       77777777888888899999************************9998766655 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.013
                             MFS_1 254 alvgailallagrlsdrlgrrrrlllallllllaalglallavt 297
                                         +g   + ++g l+d +    +l+++l+ l+l+a +++++++ 
  gi|242399184|ref|YP_002994608.1| 355 TPLG---MAVVGPLLDIIE-VSTLVITLVTLSLLASIYYYINFK 394
                                       2222...456666666655.366666666666666666666665 PP

>> MFS_2  MFS/sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   2.2   7.2e-11   4.3e-07     223     347 ..       3     127 ..       1     133 [. 0.89
   2 !    5.2   7.1    0.0011       6.7     212     330 ..     198     322 ..     153     331 .. 0.83
   3 !    5.1   1.1    0.0012         7     125     192 ..     333     392 ..     322     402 .. 0.74

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 7.2e-11
                             MFS_2 223 nraflillllfllaalalgvlnglllYyltyvlgngsaasvfllvvtisallgiplwqplakrlgkkntyllgallt 299
                                       n+ f++ +++  + +++ +++  ++ +y+ +  g+g+ +s+f ++  i+ ll+ p++ ++  r+++kn++++  ++ 
  gi|242399184|ref|YP_002994608.1|   3 NKNFWLYAVGRWISQAGWVIQDIAVPLYVLDKTGSGTIMSIFIIAELIPRLLVNPIAGVIGDRYNRKNLMVWLDIAR 79 
                                       999************************************************************************** PP

                             MFS_2 300 ivllvlvlllqpsnlllflvllviagfgvgvaallpwsmladvvDyge 347
                                        vll++v++++  ++  +l+++v+ ++  +++   +  m++d+v   e
  gi|242399184|ref|YP_002994608.1|  80 GVLLFGVIAFNLLDIQSLLAVQVVMSIMGAFFSAGISGMFPDLVKREE 127
                                       **********77777777777777777766666667778888887666 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0011
                             MFS_2 212 slleqlkevfrnraflill.llfllaalalgvlnglllYyltyvlg.ngsaasvfllvvtisallgiplwqplakrl 286
                                        +le++k + +++ +l+l+ l++ l++l   + + +l Y  + +lg +  ++  + +++ti+al+g +l++   k  
  gi|242399184|ref|YP_002994608.1| 198 DMLEGFKFIKDSKSLLVLVsLAIALNTLLNPIFAVILPYLSRVILGfSSVQFGSIQTATTIGALAGNVLIAGKLKES 274
                                       5677888888888888887245568888888999999***********************************99999 PP

                             MFS_2 287 gkkntyllgalltivllvlvlll....qpsnlllflvllviagfgvgv 330
                                       +   ++ + ++ +i ll+l +++    +p  + ++l +++++gf+ ++
  gi|242399184|ref|YP_002994608.1| 275 SENLLFKALFAQLICLLLLSVIVhpliRPVAYPALLGIFMMGGFFNIL 322
                                       999888888888888888888888888999999999999999998655 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.0012
                             MFS_2 125 ltkdydeRtsltsvrsflsvlggvlaailafllvlilgglkserkgylifaliialLmllgviivvlg 192
                                        +  ++ R +++s  +++ ++++ l+++++++l+ i ++     ++  i++++ +lL+ + ++   + 
  gi|242399184|ref|YP_002994608.1| 333 KSVPNEVRARFFSAFETAIMATTPLGMAVVGPLLDIIEV-----STLVITLVTLSLLASIYYY---IN 392
                                       5678999*******************************9.....4444444444444444444...33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       757  (0.0422221); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 2591.92
//
Query:       gi|242399185|ref|YP_002994609.1|  [L=241]
Description: hypothetical protein TSIB_1206 [Thermococcus sibiricus MM 739]
Scores for complete 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-13   48.6  13.8    8.9e-12   45.2  13.8    2.4  1  CPBP      CPBP intramembrane metalloprotease
  ------ inclusion threshold ------
       0.12   12.1   0.2          5    6.8   0.0    2.3  2  DUF5381   Family of unknown function (DUF5381)
        3.4    5.9   5.9        9.4    4.4   5.9    1.6  1  DUF2070   Predicted membrane protein (DUF2070)


Domain annotation for each model (and alignments):
>> CPBP  CPBP intramembrane metalloprotease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2  13.8   1.5e-15   8.9e-12       9      91 ..     137     236 ..      33     237 .. 0.88

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 1.5e-15
                                       HHHHHHHHHHHHHHHTTCHHHHHHHH.S-HHHHHHHHHHHHHCSGGG..........HHHH.........HHHHHHH CS
                              CPBP   9 llalllapllEEllfRglllqllqergsstlailissilFglaHlpn..........gpsv.........llaalaG 66 
                                       ++ +l+  + EE+++R+ l+++l++  ++  a+++ ++lFglaH+p+          g  +         l   ++G
  gi|242399185|ref|YP_002994609.1| 137 IIGFLSPSFKEEWFYRATLQSKLERALGQNKAWFFGGLLFGLAHIPTnffgplweasG--YsmaaalfrlLGQCAFG 211
                                       4477888999****************6668*****************77766555551..0555566666******* PP

                                       HHHHHHHHHTT-HHHHHHHHHHHHH CS
                              CPBP  67 lvlgylylktgsllaaillHallnl 91 
                                       +++g+ly+k++s+++a+++H ++++
  gi|242399185|ref|YP_002994609.1| 212 WLWGILYMKNRSIFPAVIAHYFADF 236
                                       *********************9997 PP

>> DUF5381  Family of unknown function (DUF5381)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   1.4     0.034     2e+02      16      63 ..      36      84 ..      31      94 .. 0.80
   2 ?    6.8   0.0   0.00084         5     132     166 ..     122     156 ..     119     159 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.034
                           DUF5381 16 flatvglglaglfllfeglkfes.kysllyiiigiigtifgliillmvl 63
                                      ++ tv + l+ ++ +++++ f s +y  ++i++  +   f+l +ll +l
  gi|242399185|ref|YP_002994609.1| 36 LFETVTIWLINFVSITYIVLFGSeSYPSVAIGGIRFSAHFFLALLLPFL 84
                                      5789999999999********9988888888877788888888888665 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.00084
                           DUF5381 132 nllseeefekvvekyilpylteeakknWekrkdke 166
                                         l e +++k v+k i+ +l+++ k++W  r + +
  gi|242399185|ref|YP_002994609.1| 122 AFLFEGSVSKGVDKLIIGFLSPSFKEEWFYRATLQ 156
                                       57889999********************9888765 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   5.9    0.0016       9.4      20     161 ..      42     231 ..      30     235 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0016
                           DUF2070  20 liillalligllaflssk.............lfgillfglpalvaflltlpvlrilggr..ltykrslflallteli 81 
                                       ++++  + i++++   s+             ++ +l+++lp+lv +++ ++  r lg r  + +k ++ l  + +++
  gi|242399185|ref|YP_002994609.1|  42 IWLINFVSITYIVLFGSEsypsvaiggirfsAHFFLALLLPFLVEVVIHKRGARELGFRtpIAWKPAAALVGFGMFF 118
                                       3333333333333333334678888888888888999999****************999888999999999999999 PP

                           DUF2070  82 vviisllaillsallqalvllalvls.................................lalvfalrllvlvavsde 125
                                        ++ +l+   +s  + +l++ +l  s                                 la +  + +  l+  s++
  gi|242399185|ref|YP_002994609.1| 119 GFFAFLFEGSVSKGVDKLIIGFLSPSfkeewfyratlqskleralgqnkawffggllfgLAHIPTNFFGPLWEASGY 195
                                       88888888877755544444444444666677777777777777777777777777777777777777778888888 PP

                           DUF2070 126 sllkavlpaliqpllailllvlyfspesflllllls 161
                                       s+  a++  l q ++++l  +ly+++ s++++++++
  gi|242399185|ref|YP_002994609.1| 196 SMAAALFRLLGQCAFGWLWGILYMKNRSIFPAVIAH 231
                                       888888888888888888888887777777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 1500.64
//
Query:       gi|242399186|ref|YP_002994610.1|  [L=41]
Description: hypothetical protein TSIB_1207 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); 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: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 261.45
//
Query:       gi|242399187|ref|YP_002994611.1|  [L=92]
Description: Methyltransferase type 11 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-10   41.6   0.0      9e-10   39.1   0.0    1.9  2  Methyltransf_25  Methyltransferase domain
    3.4e-08   33.5   0.0    3.6e-08   33.4   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
    2.2e-07   31.4   0.0      1e-06   29.3   0.0    1.8  2  Methyltransf_11  Methyltransferase domain
    4.3e-07   30.6   0.0    6.6e-07   30.0   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
    1.4e-06   28.2   0.0    1.7e-06   27.9   0.0    1.1  1  Methyltransf_31  Methyltransferase domain
     0.0013   18.2   0.0     0.0015   18.0   0.0    1.1  1  TehB             Tellurite resistance protein TehB
     0.0021   17.4   0.0     0.0057   16.0   0.0    1.6  2  CMAS             Mycolic acid cyclopropane synthetase
      0.004   16.4   0.0      0.004   16.4   0.0    1.1  1  N2227            N2227-like protein
     0.0087   15.7   0.0       0.01   15.4   0.0    1.1  1  MetW             Methionine biosynthesis protein MetW
  ------ inclusion threshold ------
      0.013   14.8   0.0      0.015   14.6   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
      0.017   14.7   0.0      0.021   14.4   0.0    1.1  1  MTS              Methyltransferase small domain
       0.16   11.4   0.0       0.21   11.1   0.0    1.2  1  Methyltransf_4   Putative methyltransferase
       0.18   11.5   0.0       0.19   11.5   0.0    1.1  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.74     1e+03      76      95 ..       5      23 ..       1      24 [. 0.78
   2 !   39.1   0.0   6.5e-13     9e-10       1      41 [.      42      80 ..      42      89 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.74
                                      GSSHHHHHHHHHHHHHHEEE CS
                   Methyltransf_25 76 hlsdedlekalkeiarvLkp 95
                                      h++ +++e +++e++++L+p
  gi|242399187|ref|YP_002994611.1|  5 HYK-SEYEGFFAEFYDILQP 23
                                      443.57899*********98 PP

  == domain 2  score: 39.1 bits;  conditional E-value: 6.5e-13
                                      EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHH CS
                   Methyltransf_25  1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaarera 41
                                      +L+lGcGtGrl++ +ak++   k+tg+D s eml+++r+++
  gi|242399187|ref|YP_002994611.1| 42 ILELGCGTGRLLIPIAKKG--FKITGIDSSREMLAICRSKI 80
                                      8*****************5..*****************987 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.0   2.6e-11   3.6e-08      25      61 ..      41      77 ..       6      87 .. 0.79

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 2.6e-11
                   Methyltransf_23 25 rvLdiGcGtGillevlrengfsvtgvDlspeaveiae 61
                                       +L++GcGtG+ll  ++++gf++tg+D s+e+ +i +
  gi|242399187|ref|YP_002994611.1| 41 PILELGCGTGRLLIPIAKKGFKITGIDSSREMLAICR 77
                                      79*****************************988765 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       1.1   1.5e+03      75      90 ..       8      23 ..       3      26 .. 0.81
   2 !   29.3   0.0   7.6e-10     1e-06       1      38 [.      43      80 ..      43      89 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.1
                                      CCHHHHHHHHHHHEEE CS
                   Methyltransf_11 75 edpekalkeiaRvLkp 90
                                       + e +++e++ +L+p
  gi|242399187|ref|YP_002994611.1|  8 SEYEGFFAEFYDILQP 23
                                      678999******9998 PP

  == domain 2  score: 29.3 bits;  conditional E-value: 7.6e-10
                                      EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHC CS
                   Methyltransf_11  1 LdvGcGtGrlaealakrgarvvgvDlskemlklakeka 38
                                      L++GcGtGrl+ ++ak+g +++g+D s eml+++++k+
  gi|242399187|ref|YP_002994611.1| 43 LELGCGTGRLLIPIAKKGFKITGIDSSREMLAICRSKI 80
                                      89********************************9986 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.0   4.8e-10   6.6e-07       1      39 [.      43      79 ..      43      88 .. 0.91

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 4.8e-10
                   Methyltransf_12  1 LeiGcGtGsllralleklpdieytgvDispsaiedakek 39
                                      Le+GcGtG+ll ++++k  + ++tg+D s+++++  + k
  gi|242399187|ref|YP_002994611.1| 43 LELGCGTGRLLIPIAKK--GFKITGIDSSREMLAICRSK 79
                                      8****************..**************777766 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0   1.2e-09   1.7e-06       5      46 ..      40      78 ..      36      87 .. 0.87

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 1.2e-09
                   Methyltransf_31  5 lrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielAre 46
                                       ++l+lGCGtG+l++ +a++   + +++GiD s e++  +r+
  gi|242399187|ref|YP_002994611.1| 40 DPILELGCGTGRLLIPIAKK---GFKITGIDSSREMLAICRS 78
                                      689***************54...458***********99886 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   1.1e-06    0.0015       6      69 ..      11      77 ..       6      91 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.1e-06
                                      CCHHHHHHT--.---HHHHHHCCCS-S-E..EEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHH CS
                              TehB  6 edyfskkynlt.athsevveavkivkpgk..vldlgcgqgrnslylsllgydvtawdknensiafle 69
                                      e +f++ y++  +t  +    vk  k     +l+lgcg gr  + ++ +g+++t +d   + +a  +
  gi|242399187|ref|YP_002994611.1| 11 EGFFAEFYDILqPTVHDAPAYVKFAKEFGdpILELGCGTGRLLIPIAKKGFKITGIDSSREMLAICR 77
                                      667888887641344444444444443213389************************9988877654 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1      0.71   9.8e+02     142     158 ..       7      23 ..       3      26 .. 0.79
   2 !   16.0   0.0   4.1e-06    0.0057      58     105 ..      34      80 ..      27      87 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.71
                                       GGGHHHHHHHHHHHS-T CS
                              CMAS 142 kenydtffkklkkllke 158
                                       k++y+ ff++++++l++
  gi|242399187|ref|YP_002994611.1|   7 KSEYEGFFAEFYDILQP 23 
                                       46799999999999875 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 4.1e-06
                                       TT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHH CS
                              CMAS  58 lelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrv 105
                                          + G+ +L++GcG G l++  +++ + k+ g+  S+e  + ++ ++
  gi|242399187|ref|YP_002994611.1|  34 FAKEFGDPILELGCGTGRLLIPIAKK-GFKITGIDSSREMLAICRSKI 80 
                                       556779*******************9.*************99999876 PP

>> N2227  N2227-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   2.9e-06     0.004      61      94 ..      42      76 ..       4      90 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.9e-06
                                      EEEET-TT-HHHHHHHHTT-EEEEEE--HHHH.HH CS
                             N2227 61 ilvPGaGlGrlavelatkgyqvegnEfsyfml.la 94
                                      il  G+G+Grl + +a+kg++  g++ s  ml ++
  gi|242399187|ref|YP_002994611.1| 42 ILELGCGTGRLLIPIAKKGFKITGIDSSREMLaIC 76
                                      6677***********************99998344 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   7.5e-06      0.01      15      56 ..      40      80 ..      29      88 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 7.5e-06
                              MetW 15 srvldlGcGdGellellkeekqvdgrGleldeegvaecvakG 56
                                        +l+lGcG G ll  +++ k+ +  G++ ++e +a c +k 
  gi|242399187|ref|YP_002994611.1| 40 DPILELGCGTGRLLIPIAK-KGFKITGIDSSREMLAICRSKI 80
                                      568************9965.***************9998875 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.1e-05     0.015      46      98 ..      37      86 ..      19      90 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.1e-05
                                      --TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSS CS
                   Ubie_methyltran 46 krgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegki 98
                                        g  +l++ +Gtg l + ++   ++ +k++++D + +mL + + k+  ++  
  gi|242399187|ref|YP_002994611.1| 37 EFGDPILELGCGTGRLLIPIA---KKGFKITGIDSSREMLAICRSKILIKAAL 86
                                      557889********9988775...5789****************998766655 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.5e-05     0.021      28      74 ..      35      79 ..      31      90 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.5e-05
                                      HCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHH CS
                               MTS 28 pkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesaken 74
                                       ke+ + +l lGcG+G l + +ak+  +  +t +d + + l++++  
  gi|242399187|ref|YP_002994611.1| 35 AKEFGDPILELGCGTGRLLIPIAKKGFK--ITGIDSSREMLAICRSK 79
                                      55577789****************8776..99999999988888765 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   0.00015      0.21       5      41 ..      42      76 ..      40      89 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00015
                                      EEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHH CS
                    Methyltransf_4  5 vleiGcGkGeflvalAkknPdknflGiEirvkvvakv 41
                                      +le+GcG G++l+ +Akk    ++ Gi+ +++++a +
  gi|242399187|ref|YP_002994611.1| 42 ILELGCGTGRLLIPIAKKGF--KITGIDSSREMLAIC 76
                                      69**************9964..445666666665555 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00014      0.19      73     123 ..      38      85 ..      18      92 .] 0.77

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00014
                                       TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTT CS
                              PCMT  73 kgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldl 123
                                        g+ +Le+G+G+G l   l  + ++ +++ +i+ ++e+ +  + ++  +++
  gi|242399187|ref|YP_002994611.1|  38 FGDPILELGCGTGRL---LIPIAKKGFKITGIDSSREMLAICRSKILIKAA 85 
                                       4789*********86...677888999***********9999988765555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       236  (0.013163); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 626.67
//
Query:       gi|242399188|ref|YP_002994612.1|  [L=394]
Description: Aldo/keto reductase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-74  250.8   0.0    3.6e-74  249.6   0.0    1.5  2  Aldo_ket_red  Aldo/keto reductase family
     0.0018   17.7   0.0        1.2    8.5   0.0    2.6  2  AP_endonuc_2  Xylose isomerase-like TIM barrel


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 !  249.6   0.0     4e-78   3.6e-74       1     291 [.      18     302 ..      18     305 .. 0.97
   2 ?   -1.8   0.0      0.15   1.4e+03      74     106 ..     307     339 ..     303     351 .. 0.80

  Alignments for each domain:
  == domain 1  score: 249.6 bits;  conditional E-value: 4e-78
                                       .EEEE-SSS-ST..TS-HHHHHHHHHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH-TTTGGG-EEEEEE--SSST CS
                      Aldo_ket_red   1 elglGtwqlgsk.eeiskeealellrraleaGinffDtAevYgkgqseellGealkksrkkreeviiatKvdlrdae 76 
                                       e+g+Gt +l++  ++++ ee  ++++ra+e G+nffDtAe+Y  g +e++lGe++k+    re+v iatKv + ++ 
  gi|242399188|ref|YP_002994612.1|  18 EIGIGTYALSGAyGRKDLEEFKRMINRAYELGVNFFDTAEAY--GNAEQILGEIIKS---FREDVYIATKV-GVKEG 88 
                                       69****************************************..*************...***********.***** PP

                                       TSSSS-HHHHHHHHHHHHHHHT-S-EEEEEE-S--TTS-.HHHHHHHHHHHHHTTSEEEEEEES--HHHHHHHHHTT CS
                      Aldo_ket_red  77 iksglskeniresleeslkrLgtdyvDllllHrpdpslpsieevldaleelvkeGkiraiGvSnfsveqlekakkkk 153
                                       ik++lske i +++eeslk+L+tdy+Dl+++H  dp++p iee+++al+elv+eGkir++Gv   + +  e++   +
  gi|242399188|ref|YP_002994612.1|  89 IKPNLSKEYIKKACEESLKKLQTDYIDLYQVHFHDPTTP-IEETIEALDELVEEGKIRYYGVGHLPLDVTEEY--CR 162
                                       ***************************************.*******************************99..67 PP

                                       T--EEEEE-B-BTT-HHHHTTHHHHHHHTT-EEEEBSTTGGGTTGTTTSS---SSSCCC-------..TS-HHHHHH CS
                      Aldo_ket_red 154 kvkivavqveynllreleeegllelckkkgvpliaysplggGlltgkyqseedkedkeprkdlkrd..ertsknlda 228
                                         k+ ++ +e++ + ++  e+ll+l++k+++++ia+s+ g+Glltgk ++++++e+++ r     +  er++  l  
  gi|242399188|ref|YP_002994612.1| 163 LGKPFSILAEFSAVARESYEKLLPLYRKYNLGIIAFSTTGRGLLTGKFKENQKFEPGDIRYLDPLFqrERFQYGLRI 239
                                       777788889**********************************************9999987655589********* PP

                                       HHHHHHHHHHTT--HHHHHHHHHTTSTT-SEEEE--SSHHHHHHHHGGGG----HHHHHHHHH CS
                      Aldo_ket_red 229 aeelselakehgvslaqlalryalsqpavgivipgasnieqlednldalelklseeevaelde 291
                                       a+++ el++++g+++ q+a++++l++++v++++ g+s++++le+n++a  ++++ e+++el+e
  gi|242399188|ref|YP_002994612.1| 240 AKKFAELGEKYGKTPVQVAIAWVLAHEGVICALTGPSTVKHLEENVEASGWEIPREDLRELEE 302
                                       ************************************************************998 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.15
                                       SSTTSSSS-HHHHHHHHHHHHHHHT-S-EEEEE CS
                      Aldo_ket_red  74 daeiksglskeniresleeslkrLgtdyvDlll 106
                                        +e+ ++ +ke+i + l e l++ ++  vDl++
  gi|242399188|ref|YP_002994612.1| 307 EDEWLRQKQKESIKQILTEPLQEPHRAFVDLIY 339
                                       566777788889999999999888888888876 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 !    8.5   0.0   0.00014       1.2      49     126 ..      21      86 ..       5     144 .. 0.79
   2 !    6.8   0.0   0.00045       4.1      27     124 ..     178     308 ..     155     348 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00014
                                       ECCCHSTCTHCHTTCSHHHHHHHHHHHHHHHHHHTBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTS CS
                      AP_endonuc_2  49 lftrfgypdederearreesvdalkraielaaaLGapllvlhpGtagagpkgseeeawerlaeslneladyaekegv 125
                                       + t   +     + ++    ++++kr+i +a++LG+ +  +        + g++e+ +  +++s++e + +a k+gv
  gi|242399188|ref|YP_002994612.1|  21 IGTYALS--GAYGRKD----LEEFKRMINRAYELGVNFFDTA------EAYGNAEQILGEIIKSFREDVYIATKVGV 85 
                                       4433333..3457788....***************9887777......66777777777777777777777777777 PP

                                       E CS
                      AP_endonuc_2 126 k 126
                                       k
  gi|242399188|ref|YP_002994612.1|  86 K 86 
                                       6 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.00045
                                       HHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHC................HTTCS.HHHHHHHHHHHHHHHHHH.... CS
                      AP_endonuc_2  27 deelrelrkaldelglriaslslftrfgypded................erear.reesvdalkraielaaaL.... 82 
                                       +e  ++l  + ++++l i ++s+++r    +                  + +++  +  ++ +k+ +el ++     
  gi|242399188|ref|YP_002994612.1| 178 RESYEKLLPLYRKYNLGIIAFSTTGRGLLTGKFkenqkfepgdiryldpLFQRErFQYGLRIAKKFAELGEKYgktp 254
                                       56778888899999999999999999998776677777776666644442222234444444444444444445555 PP

                                       ............TBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHHHHHHT CS
                      AP_endonuc_2  83 ............GapllvlhpGtagagpkgseeeawerlaeslneladyaekeg 124
                                                   G+ +  ++p+t  +++++ e++ we  +e+l+el +++++e+
  gi|242399188|ref|YP_002994612.1| 255 vqvaiawvlaheGVICALTGPSTVKHLEENVEASGWEIPREDLRELEEFFKRED 308
                                       555555555555555555555558899999999***************999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1002  (0.0558871); expected 358.6 (0.02)
Passed bias filter:                      773  (0.0431145); 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: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 2762.39
//
Query:       gi|242399189|ref|YP_002994613.1|  [L=258]
Description: hypothetical protein TSIB_1210 [Thermococcus sibiricus MM 739]
Scores for complete 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   17.8   0.0     0.0058   17.0   0.0    1.5  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.015   15.5   0.1      0.036   14.3   0.0    1.7  2  Acetyltransf_1   Acetyltransferase (GNAT) family
      0.062   13.2   0.1       0.12   12.4   0.1    1.4  1  Acetyltransf_10  Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   9.7e-07    0.0058      35      76 .]      92     141 ..      37     141 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 9.7e-07
                                       GGTTSSHHHHHHHH.TT..SEEE....EEEEEE.THH....HHHHHHHHTTEEE CS
                    Acetyltransf_7  35 eyrgkGiGraLlea.ae..kgii....leqlel.nae....kaikfYeklGFee 76 
                                       e++gkGi+r ++e  +e  +g +    l  ++  + +      ++f+++ GF+e
  gi|242399189|ref|YP_002994613.1|  92 EAQGKGIARSMVEKlIEkvRG-KyeflL--THAfD-TreflSQAEFFKRSGFRE 141
                                       89**********963224666.222321..22232.124556689*******86 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0     6e-06     0.036      34      98 ..      49     117 ..      19     139 .. 0.67
   2 ?   -2.8   0.0       1.2   7.4e+03      15      26 ..     163     174 ..     153     202 .. 0.44

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6e-06
                                       EEEEEEETTEEEEEEEEEEEET.....TSTTEEEEEEEEE.SGGGTTSSHHHHHHHHHHHHHHHT.TESEEE CS
                    Acetyltransf_1  34 gllvaeedgeliGfisllkipd.....ekggvayieslaV.speyrgkGlGsaLlealeeraree.gikkiv 98 
                                        +lva+++g++++ +  ++         +++v +++ ++    e++gkG+++ ++e+l+e++r + ++    
  gi|242399189|ref|YP_002994613.1|  49 VGLVAYFNGKPAAQLLTYPEKAdptslKRENVLVVNCIYNpLVEAQGKGIARSMVEKLIEKVRGKyEF---L 117
                                       566677777777777555555566665555556665555445578***************99988333...3 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHH CS
                    Acetyltransf_1  15 pnedaseeefee 26 
                                        +++ +e+++ +
  gi|242399189|ref|YP_002994613.1| 163 FWKEGEEYRRSD 174
                                       344444444222 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   1.9e-05      0.12      62     112 ..      92     145 ..      90     148 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.9e-05
                   Acetyltransf_10  62 eyrgqGigkaLleaveeeaekdgikl....eltvnaspyavpfYeklGFkavgee 112
                                       e++g+Gi+++++e+++e+++ + ++     ++  ++   + +f+++ GF+++++e
  gi|242399189|ref|YP_002994613.1|  92 EAQGKGIARSMVEKLIEKVRGK-YEFllthAFDTREFLSQAEFFKRSGFREMTKE 145
                                       79****************8544.3322345666666668999*******998665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1620.37
//
Query:       gi|242399190|ref|YP_002994614.1|  [L=274]
Description: hypothetical protein TSIB_1211 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); 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):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1848.95
//
Query:       gi|242399191|ref|YP_002994615.1|  [L=61]
Description: hypothetical protein TSIB_1212 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-07   30.5   0.6    2.6e-07   30.5   0.6    1.5  1  PLDc_N           Phospholipase_D-nuclease N-terminal
     0.0034   17.0   4.2     0.0038   16.8   4.2    1.0  1  Bac_rhodopsin    Bacteriorhodopsin-like protein
     0.0039   16.8   1.1      0.004   16.8   1.1    1.0  1  DUF4131          Domain of unknown function (DUF4131)
  ------ inclusion threshold ------
      0.029   13.6   1.6      0.031   13.5   1.6    1.0  1  LGT              Prolipoprotein diacylglyceryl transferase
      0.073   13.2   0.4       0.16   12.1   0.0    1.7  2  Insulin_TMD      Insulin receptor trans-membrane segment
       0.14   12.6   1.7          4    7.9   0.1    2.1  2  FeoB_associated  FeoB-associated Cys-rich membrane protein
       0.29   10.7   1.4       0.29   10.7   1.4    1.0  1  DUF5336          Family of unknown function (DUF5336)
        1.1    8.6   2.5        1.1    8.6   2.5    1.1  1  TMEM156          TMEM156 protein family


Domain annotation for each model (and alignments):
>> PLDc_N  Phospholipase_D-nuclease N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.6   1.2e-10   2.6e-07       4      40 ..      18      57 ..      14      58 .. 0.85

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 1.2e-10
                            PLDc_N  4 iialidiird...rnpssklaWllvilflPvlGailYllf 40
                                      +++++dii++    ++++k  W+++ l++ ++Ga +Y+++
  gi|242399191|ref|YP_002994615.1| 18 LWVVYDIIKNqkdMSTARKGFWIVLTLLFSLIGAGAYYVV 57
                                      6********555666666*******************986 PP

>> Bac_rhodopsin  Bacteriorhodopsin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   4.2   1.7e-06    0.0038     123     177 ..       1      56 [.       1      58 [. 0.87

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.7e-06
                                       HHHHHHHHHHHHHHHHHHHHHTHHHHHHTTSTHHHHHHHHHHHHHHHHH.HHHHHH CS
                     Bac_rhodopsin 123 yrwvyftisvaallvvlylllgelaraakslsserrslfntLrnlvvvl.wilYpv 177
                                       ++w+++t+s ++ l+ l +++ ++ ++ k++s++r+ +  +L++l+ ++   +Y v
  gi|242399191|ref|YP_002994615.1|   1 MAWTWWTMSLVVGLLSLLWVVYDIIKNQKDMSTARKGFWIVLTLLFSLIgAGAYYV 56 
                                       69********************************9999999999887763445555 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   1.1   1.8e-06     0.004       5      51 ..       3      57 ..       1      61 [] 0.82

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.8e-06
                           DUF4131  5 lalvllalllllllllllllrr........rprrrvllllllllllallgfalra 51
                                      + ++++ l++ ll ll++++            r+ ++++l+ll+ l+++g+++ +
  gi|242399191|ref|YP_002994615.1|  3 WTWWTMSLVVGLLSLLWVVYDIiknqkdmsTARKGFWIVLTLLFSLIGAGAYYVV 57
                                      6788888888888888888777899999998899999999999999999998766 PP

>> LGT  Prolipoprotein diacylglyceryl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   1.6   1.4e-05     0.031      12      66 ..       4      57 ..       1      60 [. 0.77

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.4e-05
                                      xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               LGT 12 rwYgllialgfllavllakrrakke.glkeekdkvddlliyavilgiiGaRlgyvl 66
                                       w+ + +++g+l  +++++ ++k++ ++++ + k   +++ ++++++iGa  +yv+
  gi|242399191|ref|YP_002994615.1|  4 TWWTMSLVVGLLSLLWVVYDIIKNQkDMSTAR-KGFWIVL-TLLFSLIGAGAYYVV 57
                                      69********************9963344433.3444444.4459*********97 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 ?   -1.3   0.1       1.1   2.4e+03      31      35 ..      17      21 ..       8      29 .. 0.50
   2 ?   12.1   0.0     7e-05      0.16      22      42 ..      40      60 ..      39      61 .] 0.93

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.1
                       Insulin_TMD 31 vigav 35
                                      +  +v
  gi|242399191|ref|YP_002994615.1| 17 LLWVV 21
                                      22233 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 7e-05
                       Insulin_TMD 22 viciillllvigavfvvvkKr 42
                                      +++ +l +l+++++++vv Kr
  gi|242399191|ref|YP_002994615.1| 40 IVLTLLFSLIGAGAYYVVEKR 60
                                      7889999*************9 PP

>> FeoB_associated  FeoB-associated Cys-rich membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.1    0.0018         4      10      25 ..      14      29 ..       5      37 .. 0.71
   2 ?    4.6   0.3     0.019        42       3      23 ..      39      59 ..      36      61 .] 0.88

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0018
                   FeoB_associated 10 aaavafvirrlikkkk 25
                                      ++ +++v++ +ik++k
  gi|242399191|ref|YP_002994615.1| 14 LLSLLWVVYDIIKNQK 29
                                      3456788888888877 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.019
                   FeoB_associated  3 iIVgliiaaavafvirrlikk 23
                                      +IV+ ++++++++  ++++ k
  gi|242399191|ref|YP_002994615.1| 39 WIVLTLLFSLIGAGAYYVVEK 59
                                      7********999999999877 PP

>> DUF5336  Family of unknown function (DUF5336)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.4   0.00013      0.29     105     142 ..       8      46 ..       2      57 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00013
                           DUF5336 105 vaAvlsvlgfLlvlaevinapegvsia.wglwvvlvlal 142
                                       +  v+ +l++L v++ +i+ ++++s+a  g+w+vl+l +
  gi|242399191|ref|YP_002994615.1|   8 MSLVVGLLSLLWVVYDIIKNQKDMSTArKGFWIVLTLLF 46 
                                       5568999***********999998875268999976532 PP

>> TMEM156  TMEM156 protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   2.5   0.00051       1.1     176     205 ..       3      32 ..       1      45 [. 0.88

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00051
                           TMEM156 176 itWyvlvllvfifliiliihKileehrrvq 205
                                        tW+++ l+v ++ +  +++ i+++++ + 
  gi|242399191|ref|YP_002994615.1|   3 WTWWTMSLVVGLLSLLWVVYDIIKNQKDMS 32 
                                       69**********************999665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       962  (0.0536561); expected 358.6 (0.02)
Passed bias filter:                      577  (0.0321825); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 397.16
//
Query:       gi|242399192|ref|YP_002994616.1|  [L=643]
Description: ERCC2/XPD/Rad3-related DNA repair helicase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-68  230.4   0.1    2.9e-68  229.3   0.1    1.6  1  HBB           Helical and beta-bridge domain
    1.9e-37  129.1   0.2    1.6e-36  126.1   0.0    2.3  2  Helicase_C_2  Helicase C-terminal domain
    3.1e-31  108.3   1.0    5.6e-31  107.5   1.0    1.4  1  DEAD_2        DEAD_2
    2.8e-07   30.7   1.0    1.7e-06   28.2   1.0    2.1  1  ResIII        Type III restriction enzyme, res subunit
      3e-06   27.1   0.1    0.00031   20.6   0.0    3.1  3  DEAD          DEAD/DEAH box helicase
     0.0038   17.0   0.0     0.0077   16.0   0.0    1.5  1  AAA_30        AAA domain
  ------ inclusion threshold ------
      0.012   15.1   0.1        1.5    8.2   0.0    2.4  2  PhoH          PhoH-like protein
      0.033   14.5   0.3          2    8.7   0.0    2.6  2  AAA_22        AAA domain
      0.058   12.2   0.0       0.12   11.2   0.0    1.5  1  AAA_35        AAA-like domain


Domain annotation for each model (and alignments):
>> HBB  Helical and beta-bridge domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  229.3   0.1   1.5e-71   2.9e-68       1     190 []     238     428 ..     238     428 .. 0.99

  Alignments for each domain:
  == domain 1  score: 229.3 bits;  conditional E-value: 1.5e-71
                                       HCHCHCCCCHHCCCCCCCHHHHHHHHHCCCCHHHHSTTTECCHCHHHHHCHCHHHCHHHHHHHHHHHHHHHHHHHCC CS
                               HBB   1 aikeaketdepklqdeysrLvegLreaeeereeeyvleeepilpdeileeavpglirsaehflsllkrlveygkarr 77 
                                       aikea+e++e+++++++s++++gL+++++e+ ++  ++e+pi+p++i+ +++++l++++++++++l ++v++g+a+r
  gi|242399192|ref|YP_002994616.1| 238 AIKEADEYKEHEIANFLSIFLKGLENLYQEKLRDLKIDEVPIIPESIFYHVFDVLKINEKQLIRILDQMVKAGDAIR 314
                                       69*************************************************************************** PP

                                       HHCCCTCC-SHHHHHHHHHHHHHHHT.S.TTTEEEEEE.STT.EECCCCS-TCCHHHHHHHCHCCCCCCTS-SSHHH CS
                               HBB  78 eekieksesPrsflsrlaefllawls.sdeedYvrlvskeegesLeavcldPskalrflkerlssllmsgtltplee 153
                                       e+kie+s +Prs+++r++efll w++ +++edY++l+s+e+g+sLe+v+ldPskal+f+k+++s+++msgt+tple+
  gi|242399192|ref|YP_002994616.1| 315 EDKIERSLPPRSYVGRVGEFLLLWFAlIGKEDYLFLMSREKGFSLELVALDPSKALSFVKNVQSAIFMSGTMTPLEA 391
                                       ***************************************************************************** PP

                                       HHHHHT....EEE.S..S.GGHCCCCCCCCCSHTCCC CS
                               HBB 154 ysdiiGleaklkkfpspfpkEnlivlfatdVsTkyke 190
                                       ++di+G+e klkkfp++++kEn+ivl+a+dVsT+++e
  gi|242399192|ref|YP_002994616.1| 392 FADIMGIEGKLKKFPRIVKKENAIVLVAKDVSTRGDE 428
                                       **********************************986 PP

>> Helicase_C_2  Helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.2      0.34   6.8e+02       7      57 ..      55     107 ..      50     161 .. 0.63
   2 !  126.1   0.0   7.9e-40   1.6e-36       1     170 [.     441     615 ..     441     616 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.34
                      Helicase_C_2   7 vvpggvlvffpSyklleevverlkeeleskki...eifveekeesrekvleeyk 57 
                                        + ++++ +   +k++++v+e+lk+  +++++   e+    ke   ++ ++++ 
  gi|242399192|ref|YP_002994616.1|  55 EMGYKIIYLARTHKQMDRVIEELKAISNKTQVsgvEFRSR-KELCLHQYVQNFA 107
                                       5666777788888888888888887443333311122222.4444444444444 PP

  == domain 2  score: 126.1 bits;  conditional E-value: 7.9e-40
                      Helicase_C_2   1 llellevvpggvlvffpSyklleevverlkeel..eskkieifvee...keesrekvleeykek.kkkgaillavcr 71 
                                       ++e ++ +p++v vf+ Sy++le + ++  +    e +++++f e+   ++++++ ++  +ke+ k++ga+ll+v++
  gi|242399192|ref|YP_002994616.1| 441 IVEAVKLIPKNVGVFTASYEVLEGLLSANVDIQiqEVSGKKVFIEKrgaSSKENDLLVMAFKEEaKRDGAVLLGVMG 517
                                       578899******************9987655322255677999999998889999999****965************ PP

                      Helicase_C_2  72 GklsEGidfsddllraviivglPfpnpkdpeveakreyldekgkknsgkewylpealravnQaiGRliRhkdDygai 148
                                       G+ sEG d+s+d+++ vi+vg+P++ p  p+v+a+ +y+++k+ +++  + y  +a +++ Qa+GR+ R+++++ga+
  gi|242399192|ref|YP_002994616.1| 518 GRNSEGQDYSGDEMNGVILVGIPYARP-TPKVQAQIRYFENKFPRKGRYYGYVLPAHKKLVQAAGRVHRSEEEKGAV 593
                                       ***************************.7***************66667789************************* PP

                      Helicase_C_2 149 vllDeRfakeeireklpkwlre 170
                                       v+lD R+  +++r+ lp+w++e
  gi|242399192|ref|YP_002994616.1| 594 VVLDYRLLWSNVRKDLPDWMKE 615
                                       ********************97 PP

>> DEAD_2  DEAD_2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.5   1.0   2.8e-34   5.6e-31       1     173 [.      62     232 ..      62     235 .. 0.88

  Alignments for each domain:
  == domain 1  score: 107.5 bits;  conditional E-value: 2.8e-34
                                       EEESSHHHHHHHHHHHHHHHHHCHHHS---EEEE--CCCC-SCHHCCCHHC.CCCHHHHHHHHHCCHHCCHTTTTTT CS
                            DEAD_2   1 ycsRThsqleqvvkelkklesykkkkekvkvviLgSRknlCineevkkekk.ekavneaCkelkkkkaeekeekCsf 76 
                                       y +RTh+q+++v++elk +++    k++v  v   SRk+lC+++ v++      ++  +Ck+lkk        kC+f
  gi|242399192|ref|YP_002994616.1|  62 YLARTHKQMDRVIEELKAISN----KTQVSGVEFRSRKELCLHQYVQNFAPdAYNAMIVCKNLKKLG------KCEF 128
                                       899***************963....457******************997764556667899999888......7*** PP

                                       -SCC....CCHHHHHHHHHHC---CHHHHHHHHHCT--HHHHHHHHHCCTSEEEEEHHHHTSCCCHHHHH...T..G CS
                            DEAD_2  77 fenl....eelkklkkllleevvdiedlvelgeklklCPYylsrelledadiiilpYqyLldekireslk...gisl 146
                                       fenl    ee+++l + + +++ +   +    + l +CPY l+r+++ + d+i+++Y y++d+ ire++     ++ 
  gi|242399192|ref|YP_002994616.1| 129 FENLkkkkEEFDELAQYFVQKPAEPMMILTHSKMLDFCPYELTRKIAFNSDVIVASYLYMIDPAIRENFMayfDFDY 205
                                       ***95555555555788888888888899999************************************98888899* PP

                                       CGCEEEECTCCCHHHHHHHCC-EEEEC CS
                            DEAD_2 147 knsivilDEAhNiedvceeaasveise 173
                                       ++ ivi+DEAhN+ + +++a+s ++s 
  gi|242399192|ref|YP_002994616.1| 206 SDLIVIFDEAHNLPNQAINALSDRLSV 232
                                       *********************998875 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 !   28.2   1.0   8.4e-10   1.7e-06       4     149 ..      10     231 ..       8     251 .. 0.68

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 8.4e-10
                                       E-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHG...... CS
                            ResIII   4 lreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleef...... 74 
                                       lr+ Qe+ i+ +   +  ++ ++++i+++TG GKT+  ++ +  ++k+ ++ k++ l+ + + +++ +ee+      
  gi|242399192|ref|YP_002994616.1|  10 LRPNQEDFIKLVDTVV--RNGENLVIEAPTGFGKTISVLAGALPYAKEMGY-KIIYLARTHKQMDRVIEELkaisnk 83 
                                       7888999888776555..688999**************9999999998776.*******************999999 PP

                                       ....................GGGTGG...............GEEEESSS-B--........................ CS
                            ResIII  75 ....................kkflseayke...........igkkvsgdkkka........................ 96 
                                                           ++f+++ay++           +++++++ kkk+                        
  gi|242399192|ref|YP_002994616.1|  84 tqvsgvefrsrkelclhqyvQNFAPDAYNAmivcknlkklgKCEFFENLKKKKeefdelaqyfvqkpaepmmilths 160
                                       99999999999999999999888888887788665555555444444444444555566666666666665555555 PP

                                       .................-SEEEEEHHHHHHTH........HHHTTT-S.EEEEETGGGTTS.T........T CS
                            ResIII  97 ..........kekdstnkkilvttiqsldadseeeeeeseellrdrfd.viiiDEaHrlgakk........s 149
                                                 ++k + n++++v+++  +  +  + e+    ++ d++d ++i+DEaH+l  ++        s
  gi|242399192|ref|YP_002994616.1| 161 kmldfcpyelTRKIAFNSDVIVASYLYMIDPAIR-ENFMAYFDFDYSDlIVIFDEAHNLPNQAinalsdrlS 231
                                       5555555555444445555555554333333322.4444444444444699********9962333333442 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   1.5e-07   0.00031       3      75 ..      13      85 ..      11     105 .. 0.83
   2 ?    2.8   0.0     0.046        91     124     138 ..     209     223 ..     116     246 .. 0.84
   3 ?   -1.9   0.0       1.2   2.4e+03      31      75 ..     568     618 ..     567     632 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.5e-07
                                      HHHHHHHHHH....TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTST CS
                                      xxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  3 iQaeaiplil....gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyid 75
                                       Q+  i+l+     +g++++++a+TG GKT   l  +l       ++ g k+++++ t++ +  ++++lk + ++++
  gi|242399192|ref|YP_002994616.1| 13 NQEDFIKLVDtvvrNGENLVIEAPTGFGKTISVLAGALPYA----KEMGYKIIYLARTHKQMDRVIEELKAISNKTQ 85
                                      57777777666667999*******************99666....789**********************9998765 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.046
                                       EEEEETHHHHHHTTT CS
                                       xxxxxxxxxxxxxxx RF
                              DEAD 124 flVlDEadrlldqgf 138
                                       ++++DEa++l +q  
  gi|242399192|ref|YP_002994616.1| 209 IVIFDEAHNLPNQAI 223
                                       699******999854 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHS.....TTSTS-EEEEEESSHHHHHHHHHHHHHHTTT.ST CS
                                       xxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx RF
                              DEAD  31 flipvlqivyet.....kgktgpkalivePtreLaeqtlnnlkkfkky.id 75 
                                       +++p+ +++++      ++++++ a++v   r L  ++ ++l  ++k+ i+
  gi|242399192|ref|YP_002994616.1| 568 YVLPAHKKLVQAagrvhRSEEEKGAVVVLDYRLLWSNVRKDLPDWMKEtIK 618
                                       567777777777777777888889999999999999999999888886344 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   3.9e-06    0.0077       9      68 ..      20      79 ..       9     101 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.9e-06
                            AAA_30  9 avealltsgdrvavltGpAGtGKttalkalreaweaa.ggrviglAptgkaAkvLaeelgi 68
                                      +v++++ +g+   v+++p G GKt ++ a +  ++++ g+++i lA t+k+ +++ eel +
  gi|242399192|ref|YP_002994616.1| 20 LVDTVVRNGE-NLVIEAPTGFGKTISVLAGALPYAKEmGYKIIYLARTHKQMDRVIEELKA 79
                                      4556677775.899**********98888777777777**************999888775 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0   0.00076       1.5       7      64 ..      12      73 ..       8      87 .. 0.79
   2 ?    4.3   0.0     0.012        23     120     144 ..     207     231 ..     204     249 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00076
                                      HHHHHHHHHHH....H-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S--TT-- CS
                              PhoH  7 keQkeylealk....kndivfaiGpaGtGKtylavalavealkkkkvkriiltrpaveagee 64
                                       +Q+++++ ++    + + +++ +p+G GKt   +a a+ + k+  +k i l+r + ++++ 
  gi|242399192|ref|YP_002994616.1| 12 PNQEDFIKLVDtvvrNGENLVIEAPTGFGKTISVLAGALPYAKEMGYKIIYLARTHKQMDRV 73
                                      57777777776666566788999**********9*****99999999999999988777655 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.012
                                       SEEEEE-SGGG--HHHHHHHHTTB- CS
                              PhoH 120 dafvilDEAQnttkeqmkmfltRlG 144
                                       d +vi+DEA n+ ++ ++ +  Rl 
  gi|242399192|ref|YP_002994616.1| 207 DLIVIFDEAHNLPNQAINALSDRLS 231
                                       779**************99988875 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.049        98       6      24 ..      29      47 ..      25     135 .. 0.69
   2 ?    8.7   0.0   0.00098         2      91     117 ..     202     231 ..     123     242 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.049
                            AAA_22  6 gilvvtGesGtGKTtllrr 24
                                        lv+ +++G GKT ++  
  gi|242399192|ref|YP_002994616.1| 29 ENLVIEAPTGFGKTISVLA 47
                                      678999********99765 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00098
                            AAA_22  91 v....ielliiDEaqhlrseealeeLrslln 117
                                       +      ++i DEa++l +++a++ L+++l 
  gi|242399192|ref|YP_002994616.1| 202 DfdysDLIVIFDEAHNL-PNQAINALSDRLS 231
                                       45554578999******.********99876 PP

>> AAA_35  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0     6e-05      0.12      23      68 ..      20      66 ..       7     119 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6e-05
                            AAA_35 23 cyeeiekpGalirikapkkmGKt.SLlarilakakqqgyktvsldlq 68
                                      +++++ ++G+ + i+ap   GKt S+la  l +ak+ gyk ++l   
  gi|242399192|ref|YP_002994616.1| 20 LVDTVVRNGENLVIEAPTGFGKTiSVLAGALPYAKEMGYKIIYLART 66
                                      567899*****************99******************9644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (643 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       889  (0.0495845); expected 358.6 (0.02)
Passed bias filter:                      672  (0.0374812); 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: 0.75u 0.33s 00:00:01.08 Elapsed: 00:00:00.50
# Mc/sec: 3876.08
//
Query:       gi|242399193|ref|YP_002994617.1|  [L=87]
Description: hypothetical protein TSIB_1214 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.044   13.8   0.5      0.054   13.5   0.5    1.2  1  DUF1422     Protein of unknown function (DUF1422)
       0.12   12.0   0.3       0.15   11.6   0.3    1.3  1  TRAP-gamma  Translocon-associated protein, gamma subunit (TRA


Domain annotation for each model (and alignments):
>> DUF1422  Protein of unknown function (DUF1422)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.5     6e-06     0.054      38      82 ..      15      60 ..       4      80 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6e-06
                           DUF1422 38 plialvlavyclyqrYlnksleeglPllalacfll.Gvlgysalvr 82
                                       +i ++la +  yq+Yl  + + glPl   + fl+ G+l+ +a++ 
  gi|242399193|ref|YP_002994617.1| 15 GFIIMILAYFFYYQNYLLYKWHCGLPLPSKTPFLIaGILTGTAYIL 60
                                      57899***********************999998769999888874 PP

>> TRAP-gamma  Translocon-associated protein, gamma subunit (TRAP-gamma)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.3   1.6e-05      0.15      47      83 ..      43      82 ..      13      87 .] 0.75

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.6e-05
                        TRAP-gamma 47 slilfvivtll..styllalayknvkfvlkhkiavk.Ree 83
                                      s   f+i+ +l  ++y+l  ayk   +++khkia+  Ree
  gi|242399193|ref|YP_002994617.1| 43 SKTPFLIAGILtgTAYILYKAYKIYPEIQKHKIANVlREE 82
                                      555667766552279******************9752554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 585.35
//
Query:       gi|242399194|ref|YP_002994618.1|  [L=348]
Description: Endoglucanase (intracellular) [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   3.3e-113  377.6   0.3   3.8e-113  377.3   0.3    1.0  1  Peptidase_M42  M42 glutamyl aminopeptidase
      1e-11   44.9   0.1    1.9e-11   44.0   0.1    1.4  1  Peptidase_M20  Peptidase family M20/M25/M40
    5.2e-06   26.3   0.1     0.0001   22.0   0.0    2.1  2  Peptidase_M28  Peptidase family M28
     0.0088   14.9   0.1      0.039   12.8   0.0    1.8  2  Peptidase_M18  Aminopeptidase I zinc metalloprotease (M18)


Domain annotation for each model (and alignments):
>> Peptidase_M42  M42 glutamyl aminopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  377.3   0.3  8.5e-117  3.8e-113       1     292 []      45     335 ..      45     335 .. 0.99

  Alignments for each domain:
  == domain 1  score: 377.3 bits;  conditional E-value: 8.5e-117
                                       S-EEEEEESSTTSSEEEEEEE--B-EEEEEEEETTSEEEEEEESS--GGGTTTEEEEEEETTE.EEEEEEEE--CGG CS
                     Peptidase_M42   1 GnliakkkgkekepkvmiaAHmDeiGfmVkeIkedGflrfekvGGvdpkvlegqrvkiltkkg.kisGvigskppHl 76 
                                       Gn+ia+kkg  ++pkvm+a+HmD+iG+mV++I+++Gflr++++GG+dp++l++qr+k+  +k   ++Gv gs+ppH+
  gi|242399194|ref|YP_002994618.1|  45 GNVIAHKKG--DGPKVMLAGHMDQIGLMVTHIEKNGFLRVAPIGGIDPRTLIAQRFKVWVDKDkFVYGVGGSVPPHI 119
                                       9********..****************************************************99************ PP

                                       CHHHHHHCT--GCGEEEEGSGSSHHHHHHTTS-TT-EEEES---EEETTECEEETTHHHHHHHHHHHHHHHHHCTSS CS
                     Peptidase_M42  77 lkeeerkkaleikelfiDigakskeeaeelGisvGdivvfdkefvelangkivskalDdragvavllellkelkeee 153
                                       +k+e+r+ka++++++fiDiga+skeeaee+G+++G+++++d + ++l+++++vs a+Ddr++v+ l+e++++lke++
  gi|242399194|ref|YP_002994618.1| 120 QKPEDRQKAPDWDQIFIDIGAESKEEAEEIGVKIGTVITWDGRLERLGKHRFVSIAFDDRIAVYTLVETARQLKESN 196
                                       ***************************************************************************98 PP

                                       -SSEEEEEEESTCTTTSHHHHHHHHHH--SEEEEEEEEEE-CSTTSTTTTSS..TTS-CEEEEEETTCCSHHHHHHH CS
                     Peptidase_M42 154 leatvylvatvqEEvGlrGaktsaekikpdiaiavDvtaagdtpgskekeak..lgkGpvirvkDasgiyhpklrkk 228
                                         a++y+vatvqEEvGlrGa+tsa+ i+pd+ +avDvt+a+d pg++e+++   lgkG++i+++D+s+i+hp+++k+
  gi|242399194|ref|YP_002994618.1| 197 --ADIYFVATVQEEVGLRGARTSAFGIEPDYGFAVDVTIAADVPGTPEHKQVtqLGKGTAIKIMDRSVICHPTIVKW 271
                                       ..************************************************8899*********************** PP

                                       HHHHHHHTT--EEEEEESSSSSTHHHHHTSTTTSEEEEEEEEEBSTTSTTEEEEHHHHHHHHHH CS
                     Peptidase_M42 229 llelAkknnipyqlevlsgggtDAgaihltgegvptalisiptryiHspvevahlddleatvkL 292
                                       ++elAkk++ipyq+++l gggtDAgaihl+++gvpt++isip ryiHs+ ev++ +d++a vkL
  gi|242399194|ref|YP_002994618.1| 272 MEELAKKYEIPYQWDILLGGGTDAGAIHLNKAGVPTGAISIPSRYIHSNTEVVDERDVDASVKL 335
                                       ************************************************************9998 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 !   44.0   0.1   4.3e-15   1.9e-11      35     206 ..     175     341 ..     164     342 .. 0.83

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 4.3e-15
                                       TTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTTTHHHHHHHHHH.TTTCESEEEEEEEESSSBTCHSTE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20  35 addmkggvlaalealralkdegikpkgtivllfqpdEEggrgGakallegle.erekvdavfelhieepgileagkl 110
                                       a d+   v +++e +r+lk++    + +i +++++ EE+g +Ga+  + g+e + +++   + +    pg +e +k 
  gi|242399194|ref|YP_002994618.1| 175 AFDDRIAVYTLVETARQLKES----NADIYFVATVQEEVGLRGARTSAFGIEpD-YGFAVDVTIAADVPGTPE-HKQ 245
                                       57899999*************....68***********988***9999999844.566666666666778888.555 PP

                                       TEEEEE.EEEEEEEEESHEEECCHHHHHHHHHHHHHHHTSC.EEEEEESSSBHTHHHH....TTTEEEEEEESSGGC CS
                                       xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxx RF
                     Peptidase_M20 111 aigvvk.vevelleggapvtlndsplvkalaeaaeelfgek.velivsgpggtdarff....agiptvmifgpgsgl 181
                                       + +++k   ++     ++v +  + +vk+++e a+++     + +i  g ggtda+ +    ag+pt  i  p+   
  gi|242399194|ref|YP_002994618.1| 246 VTQLGKgTAIK--IMDRSVICH-PTIVKWMEELAKKY-EIPyQWDILLG-GGTDAGAIhlnkAGVPTGAISIPS-RY 316
                                       66677656666..567778888.*************6.55533334799.9********988888*99888899.9* PP

                                       TTSTTTEEEHHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20 182 aHspnEyvdledlekgikvlarlle 206
                                       +Hs+ E vd++d+ + +k+++++le
  gi|242399194|ref|YP_002994618.1| 317 IHSNTEVVDERDVDASVKLMVKVLE 341
                                       *********************9987 PP

>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.032   1.4e+02       1      26 [.      46      69 ..      46      80 .. 0.82
   2 !   22.0   0.0   2.3e-08    0.0001      35     183 ..     175     328 ..     160     341 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.032
                                      EEEEEESTTCESEEEEEEEE--B-TT CS
                     Peptidase_M28  1 NviatlegkatdevlllgAHyDsvgv 26
                                      Nvia  +g+     ++l++H+D +g 
  gi|242399194|ref|YP_002994618.1| 46 NVIAHKKGDG--PKVMLAGHMDQIGL 69
                                      8999888888..479*******9875 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 2.3e-08
                                       TTTTHHHHHHHHHHHHHCHHGGCCSSEEEEEEEESSCSGSSHHHHHHHH..HHCCCTTEEEEEEECS-SSSS--EEE CS
                     Peptidase_M28  35 AdDnAsgvaalLelarvlaasgsrpkrgvrflffdaEEagllGSkafak..akpelkkiaavlnlDmvgsggkellf 109
                                       A D+   v +l+e+ar+l++    ++ ++ f+++  EE gl G++  a   + +   ++++ +  D  g+++ + ++
  gi|242399194|ref|YP_002994618.1| 175 AFDDRIAVYTLVETARQLKE----SNADIYFVATVQEEVGLRGARTSAFgiEPDYGFAVDVTIAADVPGTPEHKQVT 247
                                       6788899************8....569*******************9987554489999*****************9 PP

                                       ...........HHHHHHCHHHHHHHHHHHHHTT-TTSCCEEEEES.STT-STTHHHH..TTT--EEEECTSSS-TTT CS
                     Peptidase_M28 110 ...........esgdkssselekelkalakpvgraaaedpfders.grgrsDhspfl..kagvpvldlaetgfpevy 172
                                                   ++   ++++ k++++lak+++      p + +    g +D+ +++  kagvp+  +     p++y
  gi|242399194|ref|YP_002994618.1| 248 qlgkgtaikimDRSVICHPTIVKWMEELAKKYE-----IPYQWDIlLGGGTDAGAIHlnKAGVPTGAI---SIPSRY 316
                                       666666543333333334444444444444444.....445555534555887655544999999988...677777 PP

                                       .TSTTSSGGGB- CS
                     Peptidase_M28 173 .HtprDtldnid 183
                                        H++   +d+ d
  gi|242399194|ref|YP_002994618.1| 317 iHSNTEVVDERD 328
                                       787776666555 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 ?   -0.6   0.0     0.097   4.3e+02     229     277 ..     171     214 ..     131     220 .. 0.76
   2 !   12.8   0.0   8.6e-06     0.039     330     428 ..     242     336 ..     232     339 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.097
                                       EEESSHHHHHHHHHHHHHHCCCCHT-TTTS-SEEEEEEESSCCGTS-ST CS
                     Peptidase_M18 229 lfaprlDnkvscfaaleallesaedsleeedkvrivalfDnEEvGStsa 277
                                         +   D+++++++ +e+  +++e+    +  +  va + +EEvG  +a
  gi|242399194|ref|YP_002994618.1| 171 FVSIAFDDRIAVYTLVETARQLKES----NADIYFVATV-QEEVGLRGA 214
                                       4567789999999999888887666....3344455544.688886655 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 8.6e-06
                                       -TTTS--TTSEEEEEEETTSSSTT-HHHHHHHHHHHHHHC-EEEEEEE-TTS----HCHHHHHHHHT-EEEEEE-EE CS
                     Peptidase_M18 330 eenhapllnkGvvikvnanqryatnsagaallkevaqkanvklQelvvrndspcGstigpilaaktGirtiDlGaaq 406
                                       e+++  +l+kG+ ik+        + + ++ ++e+a+k +++ Q  ++     +G+  g+i   k G+ t  + ++ 
  gi|242399194|ref|YP_002994618.1| 242 EHKQVTQLGKGTAIKIMD-RSVICHPTIVKWMEELAKKYEIPYQWDILL---GGGTDAGAIHLNKAGVPTGAISIPS 314
                                       55667899******9964.456778888899*************87774...68999******************** PP

                                       BSTTSSSEEEECCHHHHHHHHH CS
                     Peptidase_M18 407 lsmHSireltgskdveeavklf 428
                                         +HS  e++++ dv   vkl 
  gi|242399194|ref|YP_002994618.1| 315 RYIHSNTEVVDERDVDASVKLM 336
                                       ***************9999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 2147.16
//
Query:       gi|242399195|ref|YP_002994619.1|  [L=230]
Description: Sugar fermentation stimulation protein [Thermococcus sibiricus MM 739]
Scores for complete 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-39  133.0   0.0    8.2e-39  132.7   0.0    1.1  1  SfsA      Sugar fermentation stimulation protein RE domain
    2.9e-10   40.2   0.0    5.9e-10   39.1   0.0    1.6  1  SfsA_N    SfsA N-terminal OB domain


Domain annotation for each model (and alignments):
>> SfsA  Sugar fermentation stimulation protein RE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.7   0.0   9.1e-43   8.2e-39       3     136 ..      82     215 ..      80     217 .. 0.96

  Alignments for each domain:
  == domain 1  score: 132.7 bits;  conditional E-value: 9.1e-43
                                       HHHHHHHHHEE...........EEES-EETTEE-SEEEE-S.SSEEEEEEEE--EE..EEEEE-SS--HHHHHHHHH CS
                              SfsA   3 pnklveealesgli.elagyeeikrevkygnsriDfllekeeeekcyvEVKsvtleeggialfPdapteRgqkhlee 78 
                                       + k++e+a+e gli  l+g++  krevk+gnsr+D+ll+++ +e+++vE Ks++l+eg +a++Pd+p+ Rgqkh++e
  gi|242399195|ref|YP_002994619.1|  82 QAKAFERAIELGLIeWLKGCKIKKREVKVGNSRLDYLLDCN-GEEVFVEMKSAVLREGDYAMYPDCPSLRGQKHIKE 157
                                       67899****99***88************************9.***************99****************** PP

                                       HHHHHHTT-EEEEEEEE-SSS--EEEE-TTT-HHHHHHHHHHHHHT-EEEEEEEEE-T CS
                              SfsA  79 LaelvkegyravvlfvvqredarefkpnkeidpefaealreaaeaGVevlaydckvtp 136
                                       L++l+++g+ra+++f+   +++r+fk + + dpe+a++lrea + GVe++a+++++ p
  gi|242399195|ref|YP_002994619.1| 158 LIRLRENGKRAMIVFIGALPGVRKFKSYTQGDPEIARLLREADKVGVEIHALGISLLP 215
                                       ***************************************************9987765 PP

>> SfsA_N  SfsA N-terminal OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1   0.0   6.6e-14   5.9e-10       1      54 [.      13      67 ..      13      77 .. 0.87

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 6.6e-14
                                      EEEEETTEEEEEEE.....EE----S--TTT--TT-EEEEE....ESSS-SEEEEEE CS
                            SfsA_N  1 lrRpnRFladveldg...tvHvpntGrlkelllpGarvllsksdnpkrKtkytleav 54
                                      ++R nRFl+ +e++g   ++ + ntGrl+e ++ G+++++   ++++ Kt++ l+ +
  gi|242399195|ref|YP_002994619.1| 13 IKRLNRFLGVIEVNGelkKALITNTGRLEEFMIRGRKAFCI--PKQEGKTNFVLIGF 67
                                      89************86756**********************..57899****99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 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:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1505.60
//
Query:       gi|242399196|ref|YP_002994620.1|  [L=388]
Description: glycosyl transferase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-37  128.9   0.0    3.3e-37  128.6   0.0    1.1  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    3.2e-30  105.2   0.0    4.6e-30  104.7   0.0    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
      4e-28   98.7   1.0    6.9e-28   97.9   1.0    1.3  1  Glyco_trans_2_3  Glycosyl transferase family group 2
    1.8e-14   53.6   0.0    2.7e-14   53.0   0.0    1.2  1  Glyco_transf_21  Glycosyl transferase family 21
    2.9e-11   43.4   0.0    1.1e-10   41.4   0.0    1.8  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
    4.1e-09   35.6   0.2     0.0008   18.1   0.9    3.0  3  Chitin_synth_2   Chitin synthase
     0.0077   16.7   0.0      0.015   15.8   0.0    1.5  1  Glyco_tranf_2_4  Glycosyl transferase family 2
  ------ inclusion threshold ------
       0.62    9.9   0.1       0.62    9.9   0.1    2.5  3  Prion_bPrPp      Major prion protein bPrPp - N terminal


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 !  128.6   0.0   1.5e-40   3.3e-37       1     230 []      33     259 ..      33     259 .. 0.91

  Alignments for each domain:
  == domain 1  score: 128.6 bits;  conditional E-value: 1.5e-40
                   Glyco_tranf_2_3   1 prdlavlVptfneedvlgevlesllaqeypr..vevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgk 75 
                                       p+ +++l+p+ ne  v++++l++ ++ +yp   +ev + +d+s+++t++ aee+ +++p +  +v++++  +gs gk
  gi|242399196|ref|YP_002994620.1|  33 PS-VTILIPARNEGLVIRDTLRAMANLDYPKdkLEVLLLDDGSTDDTAKIAEEVSKDYPFI--KVIRVEG-GGS-GK 104
                                       67.9*************************66679*************************96..8888866.776.** PP

                   Glyco_tranf_2_3  76 sralnealravksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvflln.rstlvsalgalefaerhlrflaa 151
                                       s+ ln +l+ +k++++++ D+D++ eP++lk l++ + +++  av+++v ++n  ++ +++  ++e+   +l   a 
  gi|242399196|ref|YP_002994620.1| 105 SYVLNYGLKLAKGEVIAVYDADNRPEPGALKDLVAML-SDETPAVTGKVKTMNwNRNILTRFICMEYLYFQLAGQAG 180
                                       ************************************9.99999******9998677888888888855555544444 PP

                   Glyco_tranf_2_3 152 rral.gvltlnGsgslirrevlkelegldplflltdDyelglrlrragfrtayvpgaavrevfpsslkayikqrnRw 227
                                          + ++++l G+ ++ir e+l+el+g+d+   l++D+el++r+  +g ++ay p a+++e++p+sl   ++qr+Rw
  gi|242399196|ref|YP_002994620.1| 181 KSKFyKTAILPGTNFVIRKELLEELGGWDE-EALAEDLELSFRIILTGKKIAYTPLAVTWEQEPESLRVWFRQRTRW 256
                                       44444589999*******************.********************************************** PP

                   Glyco_tranf_2_3 228 vyg 230
                                       + g
  gi|242399196|ref|YP_002994620.1| 257 AAG 259
                                       975 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 !  104.7   0.0   2.1e-33   4.6e-30       1     170 []      36     206 ..      36     206 .. 0.96

  Alignments for each domain:
  == domain 1  score: 104.7 bits;  conditional E-value: 2.1e-33
                                       EEEEEESS-TTTHHHHHHHHHHH.GGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-.HHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaq.dpypdfeiivvDDgStDetveileelakedprvrvirreenv.Gkagalnagl 75 
                                       ++ ip+ Ne   ++ tl++ ++  +p++++e++++DDgStD+t++i+ee +k +p ++vir e +  Gk+  ln gl
  gi|242399196|ref|YP_002994620.1|  36 TILIPARNEGLVIRDTLRAMANLdYPKDKLEVLLLDDGSTDDTAKIAEEVSKDYPFIKVIRVEGGGsGKSYVLNYGL 112
                                       589************************************************************************** PP

                                       HH--SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCST CS
                   Glycos_transf_2  76 raatgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnls 152
                                       + a+g++i++ DaD  p+p+ l++lv+ l ++ + +v g++   +++++  +r   +++ +        +s++++++
  gi|242399196|ref|YP_002994620.1| 113 KLAKGEVIAVYDADNRPEPGALKDLVAMLSDETP-AVTGKVKTMNWNRNILTRFICMEYLYFQLAGQAGKSKFYKTA 188
                                       *******************************555.99***************999998888888888999999**** PP

                                       TCSTCCCEEEEHHHHHCH CS
                   Glycos_transf_2 153 feigsaallrrealeell 170
                                       +  g+++++r+e+leel+
  gi|242399196|ref|YP_002994620.1| 189 ILPGTNFVIRKELLEELG 206
                                       ***************985 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 !   97.9   1.0   3.1e-31   6.9e-28       1     195 [.     119     330 ..     119     333 .. 0.76

  Alignments for each domain:
  == domain 1  score: 97.9 bits;  conditional E-value: 3.1e-31
                   Glyco_trans_2_3   1 iilllDaDtvlppdclreiaaelaspevaivqgpvlvmnv.anwleelaalffaedhgkdilvrealgrvvpsvGsg 76 
                                       +i++ DaD+++ p  l++++a+l++ e  +v+g+v  mn+ +n+l++++++++    +  +   +++ +++ ++G +
  gi|242399196|ref|YP_002994620.1| 119 VIAVYDADNRPEPGALKDLVAMLSD-ETPAVTGKVKTMNWnRNILTRFICMEYLYFQLAGQAGKSKFYKTAILPGTN 194
                                       58999******************87.9***********8768**********96655555566669*********** PP

                   Glyco_trans_2_3  77 aflrrsalqevggwdgdessvsEDfdmglrlqrkGyrvrfvpeslvkekspltlraalrQrkRwayGc........e 145
                                       +++r ++l+e+ggwd  e++++ED+++++r+   G ++ + p ++++e+ p +lr ++rQr+Rwa G+        +
  gi|242399196|ref|YP_002994620.1| 195 FVIRKELLEELGGWD--EEALAEDLELSFRIILTGKKIAYTPLAVTWEQEPESLRVWFRQRTRWAAGNvhtvkeyvK 269
                                       ***************..**************************************************8776543331 PP

                   Glyco_trans_2_3 146 l......eklillvrllgylgsllwsalp...lhlallllfslla..lalvlllllllaal 195
                                              + l++ + l  +   ll++a+    +++++lll+s +   + +++l +++la+l
  gi|242399196|ref|YP_002994620.1| 270 RfkeipsWGLRFDLFLTLMVYYLLAMAVIvadVAFVALLLTSGSVtwFTWSVLGFVYLAFL 330
                                       1333333222223333344444555554434433334444443333455555555555554 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 !   53.0   0.0   1.2e-17   2.7e-14      12     172 ..      98     257 ..      91     258 .. 0.86

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 1.2e-17
                   Glyco_transf_21  12 pvgvnpKvnnllqaleaakydllvisDsdvrvkpdyLeellaaledpkvglVts.lpvgsdakglaaaleaaflntl 87 
                                       + g + K + l+++l+ ak +++ + D+d r +p +L++l+a+l+d ++  Vt+ +      +++ +++ +     +
  gi|242399196|ref|YP_002994620.1|  98 EGGGSGKSYVLNYGLKLAKGEVIAVYDADNRPEPGALKDLVAMLSD-ETPAVTGkVKTMNWNRNILTRFICMEYLYF 173
                                       5567789999***********************************9.899999834455556789999988887444 PP

                   Glyco_transf_21  88 agvlqa...klsglgfavGksmalrreaLeaiGGfealadeLAeDyalgkllraaGlkvvlspapiaqtsvprrssl 161
                                       + + qa   k+ ++ +  G   ++r+e Le++GG  +  + LAeD++l+ ++   G+k++  p ++ +++ p+  sl
  gi|242399196|ref|YP_002994620.1| 174 QLAGQAgksKFYKTAILPGTNFVIRKELLEELGGWDE--EALAEDLELSFRIILTGKKIAYTPLAVTWEQEPE--SL 246
                                       44444433689999***********************..**************************99988774..9* PP

                   Glyco_transf_21 162 rallaRqlrWa 172
                                       r ++++ +rWa
  gi|242399196|ref|YP_002994620.1| 247 RVWFRQRTRWA 257
                                       **********8 PP

>> Glyco_tranf_2_2  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.4   0.0   5.1e-14   1.1e-10       3     230 ..      36     252 ..      34     277 .. 0.76

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 5.1e-14
                   Glyco_tranf_2_2   3 viplraseerhyieervlqkaky.y.deeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarNrGa 77 
                                        i + a +e   i+++++  a+  y  +++e++++ddgS++++++  + + +    + +   +    +++   N G 
  gi|242399196|ref|YP_002994620.1|  36 TILIPARNEGLVIRDTLRAMANLdYpKDKLEVLLLDDGSTDDTAKIAEEVSKDYPFIKVIRVEGGGSGKSYVLNYGL 112
                                       444444455556*****887764246899***************9999999999999878887889999999***** PP

                   Glyco_tranf_2_2  78 skaesdlvlFlDaDcfissDkfekilklitikklrenidaavvlpv...vdlnkedsevlkdvedltassrvledll 151
                                       + a+++++   DaD    +  ++ ++       l++  +++ v      +++n++    +  +e+l+ +   +    
  gi|242399196|ref|YP_002994620.1| 113 KLAKGEVIAVYDADNRPEPGALKDLVA-----MLSD--ETPAVTGKvktMNWNRNILTRFICMEYLYFQLAGQ---- 178
                                       ****************99999988887.....3443..33334443000444555555566677777777766.... PP

                   Glyco_tranf_2_2 152 aakstlvkffapssssilinrraflevGGyDErfrGhgaEDfdlllRlakaikslekmpvellykarakslsnykGf 228
                                       a ks + k  +  + +++i+++ + e+GG+DE+     aED +l  R+ +  k+++  p  ++++++ +sl+    f
  gi|242399196|ref|YP_002994620.1| 179 AGKSKFYKTAILPGTNFVIRKELLEELGGWDEEA---LAEDLELSFRIILTGKKIAYTPLAVTWEQEPESLR--VWF 250
                                       6788888876667899****************98...79***************************999999..334 PP

                   Glyco_tranf_2_2 229 rr 230
                                       r+
  gi|242399196|ref|YP_002994620.1| 251 RQ 252
                                       43 PP

>> Chitin_synth_2  Chitin synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.014        32      27      66 ..      35      73 ..      19      85 .. 0.80
   2 !   10.3   0.0   8.8e-05       0.2     196     283 ..     111     196 ..     106     208 .. 0.88
   3 !   18.1   0.9   3.6e-07    0.0008     342     442 ..     228     331 ..     212     365 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.014
                    Chitin_synth_2 27 ticlvtaysegeeglrttldslastdyddkrklllvvcdG 66
                                      + +l++a  eg   +r tl ++a++dy++ +  +l++ dG
  gi|242399196|ref|YP_002994620.1| 35 VTILIPARNEG-LVIRDTLRAMANLDYPKDKLEVLLLDDG 73
                                      45677777776.469*************988888888887 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 8.8e-05
                    Chitin_synth_2 196 GvspdfyeivlmvdadtkvapdsltrlvaalvkdpeilglcGetkiankkeswvtaiqvfeyyishhlskafesvfG 272
                                       G++ +  e++ + dad + +p +l+ lva+l++++   ++ G+ k  n +   +t     ey       +a +s f 
  gi|242399196|ref|YP_002994620.1| 111 GLKLAKGEVIAVYDADNRPEPGALKDLVAMLSDETP--AVTGKVKTMNWNRNILTRFICMEYLYFQLAGQAGKSKFY 185
                                       5566667899999****************9988765..889*********************9999999******** PP

                    Chitin_synth_2 273 svtclPGcfsl 283
                                         + lPG   +
  gi|242399196|ref|YP_002994620.1| 186 KTAILPGTNFV 196
                                       ******97554 PP

  == domain 3  score: 18.1 bits;  conditional E-value: 3.6e-07
                    Chitin_synth_2 342 rktvfvpqakcktvaPdtfkvllsqrrrwinstvhnllelvlvrdlcGtfcfsmrfvvfieligtvvlPvaiaftly 418
                                       +k  + p a+++   P++ +v + qr rw    vh + e v+   +  +  + +rf +f+ l+   +l +a++    
  gi|242399196|ref|YP_002994620.1| 228 KKIAYTPLAVTWEQEPESLRVWFRQRTRWAAGNVHTVKEYVK--RFKEIPSWGLRFDLFLTLMVYYLLAMAVIVADV 302
                                       67899**********************************985..455566778888888887777666666555444 PP

                    Chitin_synth_2 419 livasilk.....sklvpviplvllaivl 442
                                         va +l+          v+ +v la +l
  gi|242399196|ref|YP_002994620.1| 303 AFVALLLTsgsvtWFTWSVLGFVYLAFLL 331
                                       44444444000004445555666665555 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 !   15.8   0.0   6.7e-06     0.015       1      55 [.      42     104 ..      42     131 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 6.7e-06
                   Glyco_tranf_2_4   1 rneadiLpeflahhlalgf..dr..ilvydndstDgtrailke....lpevkllhvdksyede 55 
                                       rne  ++  +l++  +l++  d+  +l++d++stD+t++i +e    +p +k+++v++  +++
  gi|242399196|ref|YP_002994620.1|  42 RNEGLVIRDTLRAMANLDYpkDKleVLLLDDGSTDDTAKIAEEvskdYPFIKVIRVEGGGSGK 104
                                       89****************86642459***************8855546779999888655543 PP

>> Prion_bPrPp  Major prion protein bPrPp - N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1       3.3   7.3e+03      14      20 ..     137     143 ..     137     143 .. 0.91
   2 ?   -2.3   0.2       1.8   4.1e+03       8      22 ..     290     303 ..     287     304 .. 0.62
   3 ?    9.9   0.1   0.00028      0.62       6      15 ..     345     354 ..     340     357 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3.3
                       Prion_bPrPp  14 fvatwsD 20 
                                       +va++sD
  gi|242399196|ref|YP_002994620.1| 137 LVAMLSD 143
                                       79***99 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.8
                       Prion_bPrPp   8 cWLLvLfvatwsDVg 22 
                                       + LL++  ++ +DV+
  gi|242399196|ref|YP_002994620.1| 290 YYLLAMA-VIVADVA 303
                                       6677654.4667776 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.00028
                       Prion_bPrPp   6 lgcWLLvLfv 15 
                                       +gcWLL+L+ 
  gi|242399196|ref|YP_002994620.1| 345 PGCWLLALLM 354
                                       7*******95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 2937.46
//
Query:       gi|242399197|ref|YP_002994621.1|  [L=286]
Description: TOPRIM-domain-containing protein, potential nuclease [Thermococcus sibiricus MM 739]
Scores for complete 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-10   38.8   1.0    1.1e-07   32.1   0.1    3.1  3  Toprim       Toprim domain
     0.0038   17.6   0.0     0.0079   16.6   0.0    1.6  1  Toprim_2     Toprim-like
  ------ inclusion threshold ------
      0.011   15.1   4.2        1.2    8.5   3.2    2.1  2  Cluap1       Clusterin-associated protein-1
      0.012   15.8  11.3      0.035   14.3   3.4    2.6  2  HALZ         Homeobox associated leucine zipper
      0.013   15.5   5.7       0.18   11.9   2.1    2.4  2  DASH_Dad3    DASH complex subunit Dad3
      0.029   13.0   2.3      0.048   12.3   2.3    1.3  1  FapA         Flagellar Assembly Protein A
       0.11   13.0   0.3       0.43   11.1   0.3    2.1  1  Toprim_4     Toprim domain
          1    9.0  11.4       0.37   10.4   5.5    2.4  3  GrpE         GrpE
        2.5    8.6  18.4       0.23   11.9  12.2    2.4  2  ZapB         Cell division protein ZapB
        7.2    6.8  13.2       0.66   10.1   3.4    2.7  2  bZIP_1       bZIP transcription factor
          8    7.2   8.7        1.2    9.9   4.0    2.2  2  Ku_C         Ku70/Ku80 C-terminal arm


Domain annotation for each model (and alignments):
>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.1   6.5e-11   1.1e-07       3      99 ..      13      95 ..      11      97 .. 0.82
   2 ?    1.9   0.0      0.16   2.7e+02      37      71 ..     144     199 ..     114     203 .. 0.62
   3 ?    1.7   0.0      0.18     3e+02      11      38 ..     217     252 ..     212     279 .. 0.66

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 6.5e-11
                                      EEESSHHHHHHHHHTHT.....STEEEEEEESSSSEEEHSTTEEEEEECTTTHHHHHHHHHHHHHHSEEEEECSSSHHH CS
                            Toprim  3 vivEgpsdaktiakalg.....sgfqavtaslGhildletefkpvyeeiedkkkvlkalkelakradeiilatDpDreG 76
                                      ++vEg sd++ ++kal+     s+++++++ +   ++le                    k+ a  ad +i+atD+Dr G
  gi|242399197|ref|YP_002994621.1| 13 ILVEGASDVEVVSKALQglalgSEYNITISAIIPTTNLEI------------------AKSAAAGADLLIIATDADRVG 73
                                      89*************9999995666666666666666666..................88888**************** PP

                                      HHHHHHHHHHHTHHHTTTEEEEE CS
                            Toprim 77 eaiawellevlkellenkigrve 99
                                      +++a +++  l+el+ + + r++
  gi|242399197|ref|YP_002994621.1| 74 RELAERMFRELGELVGQ-VERMK 95
                                      ********888866666.66665 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.16
                                       S..........TTEEEEE...........ECTTTHHHHHH.........HHHHHHHHSEEEEECS CS
                            Toprim  37 t..........efkpvye...........eiedkkkvlka.........lkelakradeiilatD 71 
                                                  e+k++y+           e                   lke++k+  +++ +tD
  gi|242399197|ref|YP_002994621.1| 144 GkhemlmqeneELKKNYQeleqkygelleE---------YsqvleennrLKESLKKRANVFKLTD 199
                                       355555556677777777444444443333.........03333345558888888778887777 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.18
                                       HHHHHHTHTSTEEEEEEESSSSEEEHS..........T CS
                            Toprim  11 aktiakalgsgfqavtaslGhildlet..........e 38 
                                       a++++k+  + +++++  +Ghi++ ++           
  gi|242399197|ref|YP_002994621.1| 217 AEAVEKL--NLGGKIIVGQGHIYSEDEdlivellrivH 252
                                       6777888..79999**********99954443333330 PP

>> Toprim_2  Toprim-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   4.8e-06    0.0079      20      86 ..      34     102 ..      13     105 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 4.8e-06
                          Toprim_2  20 ktnvvalgGtalteaalkllerype..kkvvlalDnDkaGrkaakrlaellreagvrekirelpegkDw 86 
                                        +++  + +  ++ ++l++ ++ ++  + +++a+D+D+ Gr+ a+r+ + l e   +++ +++p g D+
  gi|242399197|ref|YP_002994621.1|  34 GSEYNITISAIIPTTNLEIAKSAAAgaDLLIIATDADRVGRELAERMFRELGELVGQVERMKIPMGHDL 102
                                       4455555555456666666665533225599********************99999********99996 PP

>> Cluap1  Clusterin-associated protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   3.2   0.00071       1.2     159     238 ..     103     182 ..      59     204 .. 0.76
   2 ?    5.7   0.0    0.0053       8.6      53     109 ..     216     272 ..     211     283 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00071
                            Cluap1 159 rqleleeiekalkeaikkvkeelektkkalenlesdeanLeakiekkkqeleraqkrLqslqsvrPafmdeyeklee 235
                                       +++++e + k+lk+++ ++  +  ++  +   l+++   L+ k e   qe e  +k +q+l++     ++ey ++ e
  gi|242399197|ref|YP_002994621.1| 103 EHIDVELVRKELKNTLVRAGLKSLQVLPEYMALRNQLFDLKGKHEMLMQENEELKKNYQELEQKYGELLEEYSQVLE 179
                                       45677778888888888888888888888888888888888888888888888888888888888888888888776 PP

                            Cluap1 236 eLq 238
                                       e +
  gi|242399197|ref|YP_002994621.1| 180 ENN 182
                                       644 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0053
                            Cluap1  53 iksvaeflatkasikLntkkLYaAdgaAvkELlkiaslLykalksaeeekeeeekst 109
                                       i +++e l    +i +    +Y  d+  + ELl+i++l ++  k+++ee + ee++t
  gi|242399197|ref|YP_002994621.1| 216 IAEAVEKLNLGGKIIVGQGHIYSEDEDLIVELLRIVHLSLSMAKTQKEEPQVEEEKT 272
                                       66777777777888888889****************998777777755555555544 PP

>> HALZ  Homeobox associated leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   3.4   2.1e-05     0.035       6      41 ..     131     166 ..     130     167 .. 0.95
   2 ?    7.5   5.1     0.003       4.9       5      36 ..     158     189 ..     158     190 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.1e-05
                              HALZ   6 DYdvLKasYdaLksdydsLkkenekLkaelqeLkek 41 
                                       +Y +L+ +   Lk +++ L +ene+Lk+  qeL +k
  gi|242399197|ref|YP_002994621.1| 131 EYMALRNQLFDLKGKHEMLMQENEELKKNYQELEQK 166
                                       799******************************987 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.003
                              HALZ   5 rDYdvLKasYdaLksdydsLkkenekLkaelq 36 
                                       + Y  L ++Y  L  +y ++++en++Lk  l+
  gi|242399197|ref|YP_002994621.1| 158 KNYQELEQKYGELLEEYSQVLEENNRLKESLK 189
                                       56999**********************98765 PP

>> DASH_Dad3  DASH complex subunit Dad3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   2.1   0.00011      0.18       7      49 ..     127     168 ..     124     171 .. 0.91
   2 ?    4.9   0.1     0.017        27       6      22 ..     175     197 ..     169     260 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                         DASH_Dad3   7 evLdeYerLaenlktLaselkeLasnsteeildgLReLErkig 49 
                                       +vL eY  L ++l +L+ + + L ++ +ee+ ++ +eLE+k g
  gi|242399197|ref|YP_002994621.1| 127 QVLPEYMALRNQLFDLKGKHEMLMQE-NEELKKNYQELEQKYG 168
                                       8*******************777776.99************87 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.017
                         DASH_Dad3   6 qevLdeYerLaenlkt......L 22 
                                       ++vL+e +rL+e+lk+      L
  gi|242399197|ref|YP_002994621.1| 175 SQVLEENNRLKESLKKranvfkL 197
                                       46677777777777764444441 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   2.3     3e-05     0.048     323     413 ..     116     193 ..      79     210 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3e-05
                              FapA 323 kteievgldepelkeklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleelee 399
                                       +t +++gl+ +++  ++ +l+++l +l+ + e+l ++              +e k+ +++l++++ +l ee++++ e
  gi|242399197|ref|YP_002994621.1| 116 NTLVRAGLKSLQVLPEYMALRNQLFDLKGKHEMLMQEN-------------EELKKNYQELEQKYGELLEEYSQVLE 179
                                       45555555555555555555555555555555555553.............44556899999999999999999999 PP

                              FapA 400 elkelkeeleskke 413
                                       e ++lke+l+++++
  gi|242399197|ref|YP_002994621.1| 180 ENNRLKESLKKRAN 193
                                       99999999998843 PP

>> Toprim_4  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.3   0.00026      0.43      50      80 ..      56      86 ..      11      95 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00026
                          Toprim_4 50 aekkvkevilaldgDaeGeataerlaellle 80
                                      a   ++ +i+a+d+D  G + aer  ++l+e
  gi|242399197|ref|YP_002994621.1| 56 AAAGADLLIIATDADRVGRELAERMFRELGE 86
                                      44556889****************9997743 PP

>> GrpE  GrpE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.11   1.8e+02      94     115 ..     106     127 ..      85     132 .. 0.90
   2 ?   10.4   5.5   0.00023      0.37      10      61 ..     142     193 ..     134     204 .. 0.84
   3 ?   -3.1   0.1       3.4   5.5e+03       8       8 ..     264     264 ..     241     279 .. 0.50

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.11
                                       HHHHHHHHHHHHHHHTT-EE-- CS
                              GrpE  94 GvemtlkqllkiLekhgvekie 115
                                        ve+++k+l+++L + g++ ++
  gi|242399197|ref|YP_002994621.1| 106 DVELVRKELKNTLVRAGLKSLQ 127
                                       699**************99876 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00023
                                       THHHHCCCCCCTTCHHHCTTSCCCCCCTTTTTTTTHHHHHHHHHHHHHHHHH CS
                              GrpE  10 eedeeeeleeeleelekevkelkekllrllaefenlrkrtekekeeakkfai 61 
                                       ++ + e l +e eel+k+++el++k+ +ll+e+ ++ +  ++ ke +kk a+
  gi|242399197|ref|YP_002994621.1| 142 LKGKHEMLMQENEELKKNYQELEQKYGELLEEYSQVLEENNRLKESLKKRAN 193
                                       6667888999999999999999999999999999999999999999999875 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 3.4
                                       T CS
                              GrpE   8 e 8  
                                       e
  gi|242399197|ref|YP_002994621.1| 264 E 264
                                       1 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  12.2   0.00014      0.23      21      64 ..     147     190 ..     124     193 .. 0.68
   2 ?   -2.7   0.4       5.4   8.7e+03      29      40 ..     259     270 ..     249     278 .. 0.50

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00014
                              ZapB  21 tlLqmeieeLkeeneelkeenreleeeneqlkeereawqerlkk 64 
                                       + L +e+eeLk+  +el+++  el ee +q  ee + ++e lkk
  gi|242399197|ref|YP_002994621.1| 147 EMLMQENEELKKNYQELEQKYGELLEEYSQVLEENNRLKESLKK 190
                                       34556666666666666666666666666666666666666664 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.4
                              ZapB  29 eLkeeneelkee 40 
                                       + ++e  + +ee
  gi|242399197|ref|YP_002994621.1| 259 KTQKEEPQVEEE 270
                                       333333333333 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   3.4   0.00041      0.66      31      62 ..     135     166 ..     130     168 .. 0.85
   2 ?    2.4   4.0       0.1   1.6e+02      31      57 ..     163     189 ..     162     197 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00041
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  31 LerrvkaLekeNksLkseleelkkevekLksk 62 
                                       L ++   L+++ ++L +e+eelkk++++L++k
  gi|242399197|ref|YP_002994621.1| 135 LRNQLFDLKGKHEMLMQENEELKKNYQELEQK 166
                                       666667899999***************99987 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.1
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  31 LerrvkaLekeNksLkseleelkkeve 57 
                                       Le++  +L +e ++  +e+++lk+  +
  gi|242399197|ref|YP_002994621.1| 163 LEQKYGELLEEYSQVLEENNRLKESLK 189
                                       666666666666666666666666554 PP

>> Ku_C  Ku70/Ku80 C-terminal arm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   4.0   0.00075       1.2      27      73 ..     148     191 ..     131     222 .. 0.80
   2 ?   -2.4   0.1       4.9     8e+03      31      36 ..     266     271 ..     250     280 .. 0.49

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00075
                                       --...---SS--HHHHHHHHH-....HHHHHHHHHHHHH..HHHHH.. CS
                              Ku_C  27 dlpe.eledktlpkyeaidkragslleewkelfeleeedkekkkekrk 73 
                                       +  + +++++++++y++++++ g+llee+ + +e+++  k  ++ k+ 
  gi|242399197|ref|YP_002994621.1| 148 M--LmQENEELKKNYQELEQKYGELLEEYSQVLEENNRLK--ESLKKR 191
                                       3..336666666679*********************9984..444433 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.9
                                       ---SS- CS
                              Ku_C  31 eledkt 36 
                                       + e+++
  gi|242399197|ref|YP_002994621.1| 266 QVEEEK 271
                                       222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1617  (0.0901891); expected 358.6 (0.02)
Passed bias filter:                      861  (0.0480228); expected 358.6 (0.02)
Passed Vit filter:                       141  (0.00786435); 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):              11  [number of targets reported over threshold]
# CPU time: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.46
# Mc/sec: 1868.94
//
Query:       gi|242399198|ref|YP_002994622.1|  [L=278]
Description: tyrosine recombinase [Thermococcus sibiricus MM 739]
Scores for complete 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-52  178.0   0.0      2e-52  177.5   0.0    1.3  1  Phage_integrase  Phage integrase family
    1.3e-08   35.0   1.5    7.8e-08   32.5   0.5    2.7  2  Phage_int_SAM_1  Phage integrase, N-terminal SAM-like domain
      2e-07   31.4   1.7    1.1e-06   29.0   1.0    2.6  3  Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain
    4.5e-07   29.9   0.8     0.0021   18.0   0.2    2.6  2  Phage_integr_3   Archaeal phage integrase
  ------ inclusion threshold ------
      0.084   12.7   0.0         23    5.0   0.0    3.5  4  HTH_23           Homeodomain-like domain
        1.4    9.5   4.3         32    5.1   1.7    3.2  2  Pox_D5           Poxvirus D5 protein-like


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 !  177.5   0.0   6.6e-56     2e-52       2     170 ..      96     259 ..      95     261 .. 0.97

  Alignments for each domain:
  == domain 1  score: 177.5 bits;  conditional E-value: 6.6e-56
                                       HHHHHHHHHHHHCCGCHHHHHHHHHHHHHHHHT--HHHHTT-BGGGEECTTTEEEEEEEECSSSSEEEEECTHHHHH CS
                   Phage_integrase   2 vltedeverllaaleeslkirdklllellyetGlRisEllsLrvkdldlengvilvheregKgskeravplseeale 78 
                                        lt ++v+rll+a++  +  rd+l++ lly+tGlR+sE+++L++kd+d+++gv++v  + gKg k+r+vpls ++l+
  gi|242399198|ref|YP_002994622.1|  96 SLTREDVKRLLNAVPP-TRKRDRLIILLLYGTGLRVSEVCNLKIKDIDFNRGVLTV--EGGKGAKDRIVPLSGSLLK 169
                                       699************9.***************************************..******************* PP

                                       HHHHHHHHHCHCCTTTSBSSBET...TSSB--HHHHHHHHHHHHHHCT-SSC--TTHHHHHHHHHHHHHCTSHHHHH CS
                   Phage_integrase  79 llkellskaleeaeksellfask...rgkplsrqtvrkafkraveeagiekpltpHtlRhsfataLleagvdlrvvq 152
                                        ++++l+++   +++se+lf++    +++++s +tv+  +k+++++a+++  +tpH+lRhsfat++le+gvd+rv+q
  gi|242399198|ref|YP_002994622.1| 170 EIEKYLETR---KDGSEYLFVEIrreKKDKISPKTVWYLLKKYGNKANVS--VTPHMLRHSFATHMLERGVDIRVIQ 241
                                       *********...*********987789999********************..************************* PP

                                       HHHT-SSCCHHHHHHCCC CS
                   Phage_integrase 153 kllGHssisttqiYthva 170
                                       ++lGHss+sttqiYt+v+
  gi|242399198|ref|YP_002994622.1| 242 EILGHSSLSTTQIYTKVT 259
                                       ***************997 PP

>> Phage_int_SAM_1  Phage integrase, N-terminal SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   0.5   2.6e-11   7.8e-08       1      79 [.       5      74 ..       5      76 .. 0.94
   2 ?   -0.6   0.0      0.57   1.7e+03      25      58 ..     236     268 ..     216     272 .. 0.73

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 2.6e-11
                                      HHHHHHHHHHTT-S-HHHHHHHHHHHHHHHHHHHH.TS--TTT--HHHHHHHHHS----------HHHHHHHHHHHHHH CS
                   Phage_int_SAM_1  1 leqfleyLikerglspnTlraYrrdLrrflkflaergkesleqlttedvraflaeleeeglsatslarrlsalrsFfqf 79
                                      +e+f+ yL++e   sp+T+r Y + ++rflk         +e+ + ++ ++fla+l++eg+s +sl+++  al+s+f+f
  gi|242399198|ref|YP_002994622.1|  5 IEEFKTYLELEGK-SPQTVRMYTYYVERFLKD--------VENPNYRSALRFLAKLKKEGYSNKSLNLVVQALKSYFRF 74
                                      799********99.************998864........566***********************************9 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.57
                                       HHHHHHHHHHH.TS--TTT--HHHHHHHHHS--- CS
                   Phage_int_SAM_1  25 dLrrflkflaergkesleqlttedvraflaelee 58 
                                       d+r +++ l +    s +q+ t+  ++ l++  e
  gi|242399198|ref|YP_002994622.1| 236 DIRVIQEILGH-SSLSTTQIYTKVTVEHLKKAQE 268
                                       67778888888.6666666666666666666555 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 !   29.0   1.0   3.7e-10   1.1e-06       3      76 ..       6      73 ..       5      80 .. 0.93
   2 ?   -3.0   0.0       3.6   1.1e+04      38      50 ..      94     106 ..      91     109 .. 0.78
   3 ?   -1.4   0.0       1.1   3.3e+03      29      60 ..     205     236 ..     193     264 .. 0.67

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 3.7e-10
                   Phage_int_SAM_4  3 erfrealrlaglserTiksYlsaikrflrflkkkapeeltkedieaYlnyLanerklsastqknalnalsffyk 76
                                      e+f  +l+l+g+s++T++ Y+++++rfl+ ++       + + + ++l++L  ++ +s ++ +   +al+++++
  gi|242399198|ref|YP_002994622.1|  6 EEFKTYLELEGKSPQTVRMYTYYVERFLKDVE-----NPNYRSALRFLAKLK-KEGYSNKSLNLVVQALKSYFR 73
                                      89**************************9999.....55678899*******.9999****************8 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.6
                   Phage_int_SAM_4  38 peeltkedieaYl 50 
                                       p++lt+ed+++ l
  gi|242399198|ref|YP_002994622.1|  94 PKSLTREDVKRLL 106
                                       7899999998655 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 1.1
                   Phage_int_SAM_4  29 flrflkkkapeeltkedie.aYlnyLanerkls 60 
                                       +l+++ +ka  ++t++ ++ ++ ++++ er + 
  gi|242399198|ref|YP_002994622.1| 205 LLKKYGNKANVSVTPHMLRhSFATHML-ERGVD 236
                                       566666666666666666535666666.66655 PP

>> Phage_integr_3  Archaeal phage integrase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0   0.00022      0.66       5      43 ..      98     136 ..      95     152 .. 0.86
   2 !   18.0   0.2   6.9e-07    0.0021      89     153 ..     196     269 ..     170     275 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00022
                                       -HHHHHHHHHHHHHH-HHHHHHHHHHHHH---HHHHHHH CS
                    Phage_integr_3   5 tdeevrealeelkekseevelvykllvfsGiRLkevlkl 43 
                                       t e+v++ l+ +  + ++ +l+ +ll  +G+R +ev +l
  gi|242399198|ref|YP_002994622.1|  98 TREDVKRLLNAVPPTRKRDRLIILLLYGTGLRVSEVCNL 136
                                       789*********************************987 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 6.9e-07
                                       B--HHHHHHHHHT-T......--GHHHHHHHHHHHHHTT--HHHHHHHTTSS-...CCTTSCHHCHHHHHHHHH CS
                    Phage_integr_3  89 elseeavkefeakkk......vkakyiRkwvatklaelgvpeevidFiqGrkp...ssvlekhYlnllvlAdea 153
                                       ++s ++v +  +k++      v+ +++R+ +at ++e+gv+  vi+ i G+ +   +++ +k  ++ l++A+e+
  gi|242399198|ref|YP_002994622.1| 196 KISPKTVWYLLKKYGnkanvsVTPHMLRHSFATHMLERGVDIRVIQEILGHSSlstTQIYTKVTVEHLKKAQEK 269
                                       5666677666666556666789*****************************99666777788888888888776 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       2.5   7.4e+03      28      35 ..      16      23 ..      13      23 .. 0.79
   2 ?    5.0   0.0    0.0075        23       2      24 ..     112     134 ..     111     136 .. 0.91
   3 ?    3.2   0.0     0.026        79      29      41 ..     197     209 ..     196     215 .. 0.89
   4 ?   -2.2   0.0       1.4     4e+03      12      28 ..     229     245 ..     222     252 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.5
                            HTH_23 28 gvsrrTvy 35
                                      g s++Tv+
  gi|242399198|ref|YP_002994622.1| 16 GKSPQTVR 23
                                      88999996 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0075
                            HTH_23   2 asereRlrillllaeGlsvreIA 24 
                                        ++r+Rl illl+  Gl+v+e++
  gi|242399198|ref|YP_002994622.1| 112 TRKRDRLIILLLYGTGLRVSEVC 134
                                       5899****************998 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.026
                            HTH_23  29 vsrrTvyrwlkry 41 
                                       +s+ Tv+  lk+y
  gi|242399198|ref|YP_002994622.1| 197 ISPKTVWYLLKKY 209
                                       9***********9 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 1.4
                            HTH_23  12 lllaeGlsvreIAreLg 28 
                                       ++l +G  +r I ++Lg
  gi|242399198|ref|YP_002994622.1| 229 HMLERGVDIRVIQEILG 245
                                       67777999999999997 PP

>> Pox_D5  Poxvirus D5 protein-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   1.7     0.011        32      18      56 ..      34      71 ..       1      89 [. 0.55
   2 ?    2.0   0.0       0.1     3e+02      14      59 ..     186     232 ..     171     266 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.011
                            Pox_D5 18 kstrvpsdvlYeaYkafcekngykpvlskrtFqkrlkki 56
                                      k   +p++    +++a ++k+gy +  s++   + lk++
  gi|242399198|ref|YP_002994622.1| 34 KDVENPNYRSALRFLAKLKKEGYSN-KSLNLVVQALKSY 71
                                      3333444444445555555555555.6666666666665 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.1
                            Pox_D5  14 feee...kstrvpsdvlYeaYkafcekngykpvlskrtFqkrlkkilee 59 
                                       f+e    k +++  + ++   k++  k ++    + +++ +++++++ e
  gi|242399198|ref|YP_002994622.1| 186 FVEIrreKKDKISPKTVWYLLKKYGNKANVSV--TPHMLRHSFATHMLE 232
                                       33323338888888888888888888888876..777777777777755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1984.38
//
Query:       gi|242399199|ref|YP_002994623.1|  [L=461]
Description: ADP-dependent 6-phosphofructokinase (PFK) [Thermococcus sibiricus MM 739]
Scores for 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-106  357.1   0.0   1.1e-106  356.9   0.0    1.0  1  ADP_PFK_GK  ADP-specific Phosphofructokinase/Glucokinase cons


Domain annotation for each model (and alignments):
>> ADP_PFK_GK  ADP-specific Phosphofructokinase/Glucokinase conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  356.9   0.0  6.4e-111  1.1e-106       3     423 ..      13     449 ..      11     450 .. 0.94

  Alignments for each domain:
  == domain 1  score: 356.9 bits;  conditional E-value: 6.4e-111
                                       EEEES--EEEEE.....HHHHHHHHCC-HH.HHHHHHC--SSBSSHHHHHHHHHHHHHHT--EEEEB--HHHHHHHH CS
                        ADP_PFK_GK   3 vavGynanvDai.....vdavelleklgleevkekseedhdeikskedlletfayffkkGaaaErfvenkelfeelv 74 
                                       + ++yn+nvDai     + +++l++++g+e+vk++++e+++ei+++ d++++++++ k+G+++ +++ + e+ +++ 
  gi|242399199|ref|YP_002994623.1|  13 MYLAYNTNVDAIiylneKHIQTLIKEFGAENVKKRMQEYPREINEPLDFVARLIHALKTGKPQSVPLMSYEVDKWFN 89 
                                       789************************************************************************** PP

                                       ....CC--SEEEEESHHHHHHHHHCCTT-.EEEEE-.---HHHHTTS-SS......EE.....EEEEGGG-S-...- CS
                        ADP_PFK_GK  75 kaakklkkaelrmGGnagimanrlakega.kvllga.klskklkellsek......iv.....vlgkpseaske..k 136
                                       +   ++++  +r+GG++gi+an+la++++ kv+++   l+kk++e++ ++      +v     +l+kp ea+ke   
  gi|242399199|ref|YP_002994623.1|  90 S---RFEHGVERIGGQVGIIANLLANLDFkKVIAYSpLLGKKQAEMFVRRdnllypVVengklILKKPLEAYKEddP 163
                                       9...**********************************************888777225777799*********655 PP

                                       --EEEEEEE-TT-EE...TE.EE-SS-EEEEEE--STCG.GTS--HHHCTTHHHHH..-SEEEE--GGG--TB-TTS CS
                        ADP_PFK_GK 137 deiHlIlEykkgekw...ge.ieapraNRfIissdpenl.rlsileefkealkefk..pdllvlsGlqmleeqykeg 206
                                        +i++I+E+++g ++   +e ie+p + RfI++ + e++ r++++ +fk +l+e++  +d+++lsG+q ++++y +g
  gi|242399199|ref|YP_002994623.1| 164 VKINRIFEFRAGMRFnlgNEvIEVPYSGRFIVACRSEEFaRVETSSNFKPYLPEIGemVDGAILSGYQGIRNHYTDG 240
                                       5****************8778*************9998769************************************ PP

                                       TCHHHHHHHHHHHHHHHC.C.T-EEEEE----S-HHHHHHHHHHCGGG-SEEEE-HHHHHHHHHHTT-HHHCCSS.. CS
                        ADP_PFK_GK 207 kereerlekvkeqlkslk.n.kikiHlElAsfqdeellkeilekilpyvdslGlnEqElanllsvlggeekeltevs 281
                                       k+ +++l+k+ke++k lk + ++kiH+E+As+qd++l+k+++ +i+p +ds+G++E E+a +lsvlg  +++l++  
  gi|242399199|ref|YP_002994623.1| 241 KNANYYLRKAKEDIKLLKkKkDVKIHVEFASIQDRDLRKKVIFNIFPLADSVGMDEAEIAHILSVLG--YRDLSDRI 315
                                       ******************845*********************************************5..55566666 PP

                                       .CC--HHHHHHHHHHHHH.....HHTT-SEEEEEETTEEEEEEETTSSS-HHHHHHHHHHHHHHHHHHHHH...-SH CS
                        ADP_PFK_GK 282 dkepriakvlealrkllkllkkskkrkltrihvHtlayqiiltkkesewkneaakkalakaallAarkacn...sdl 355
                                        +++ri++++ +++ ll+     +  +l+ +++Ht++y +++t++++++++ + +k+l+ +++lAa++a     + +
  gi|242399199|ref|YP_002994623.1| 316 FTYNRIEDTILGAKILLD-----EL-NLEVLQIHTIYYLMYITHRDNPLSEGDLLKSLEVGTTLAATRALLgdiKRP 386
                                       799***************.....99.*********************************************76669* PP

                                       HHHHHHH..........HS-B-TT.HHHHHHHHCC....EETTEEEEEEE-B--SS-S--TTHHHHHHHHHHH CS
                        ADP_PFK_GK 356 eklelklddsfsvskskkiplnek.epvscweeei....eleevevclaPvlvckkpkkTvGlGDtISaaglv 423
                                       e+++++l          +ip+nek e v+   ee     +++e++++++P++++k+p++TvGlGDtISa++++
  gi|242399199|ref|YP_002994623.1| 387 EDVKVGL----------NIPFNEKgEYVKLRLEEAlskmRTREYKIVITPTRIVKNPVSTVGLGDTISAGAFA 449
                                       *******..........*******65555544444899999******************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (461 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 2760.82
//
Query:       gi|242399200|ref|YP_002994624.1|  [L=237]
Description: maleate cis-trans isomerase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-34  119.3   0.0    2.1e-34  119.1   0.0    1.0  1  Amdase        Arylmalonate decarboxylase
    1.6e-14   54.3   0.0    2.1e-14   53.9   0.0    1.2  1  Asp_Glu_race  Asp/Glu/Hydantoin racemase


Domain annotation for each model (and alignments):
>> Amdase  Arylmalonate decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.1   0.0   2.3e-38   2.1e-34      16     217 .]      35     234 ..      22     234 .. 0.94

  Alignments for each domain:
  == domain 1  score: 119.1 bits;  conditional E-value: 2.3e-38
                            Amdase  16 AeGLglkelskegydevidrvveaArelaerGaqavslmGtsLsFyRGaafneeLvarleeatgLPattmssavvea 92 
                                          + l+++++e   ++    ++ A+ l+++ ++ +    ts sF  G +f++eL  r+e+   LP+ t s+a++ea
  gi|242399200|ref|YP_002994624.1|  35 TARMPLRNVTEEELLAMSSLAIDSAKLLKDADVDLILYGCTSGSFIGGGEFDKELSMRIEDEVKLPVITTSTAILEA 111
                                       55567888888888888889999*************9999************************************* PP

                            Amdase  93 lralgarRvAvataYidevnerLvayLeesglevaalesLdiedveavakvtaeelvelgkkavaaapeadallisC 169
                                       l+ l a+++ v+t Y+de+n+r +++Le++ lev  +++L+i d +++ +++  e   + k ++  ++eada++isC
  gi|242399200|ref|YP_002994624.1| 112 LKILDAQKILVVTPYTDEINQREREFLEANELEVIDIRGLGIVDNTKIGRLEPYEAYRMIKALF--TDEADAVFISC 186
                                       ***********************************************************99999..678******** PP

                            Amdase 170 GGLrtldvvreledelglpvvssalAGlwdavrlagldaraagegrlf 217
                                          rt ++++ led+ g+pvv+s +A lw a+r ++  ++ +  grlf
  gi|242399200|ref|YP_002994624.1| 187 TNFRTFEIIELLEDDFGIPVVTSNQASLWLALRELDVGEKIPWLGRLF 234
                                       ***********************************9999888888876 PP

>> Asp_Glu_race  Asp/Glu/Hydantoin racemase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.9   0.0   2.3e-18   2.1e-14       1     221 [.       8     215 ..       8     218 .. 0.82

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 2.3e-18
                                       EEECSCCCCHHHHHHHHHHBTTSSGGGS..EEEEE-CCS-TCHHHHHCH.T..THH.HHHHHHHHHHCTTESEEEE- CS
                      Asp_Glu_race   1 IGgmgpeatlsvlrklveatpaesdqehlplivlndsaipdrteaieeesgddpvl.klleaakkLekagadaivia 76 
                                       IG + p++++++  +l+ a+p+         ++ + +    +te+         +     ++ak L++a++d+i++ 
  gi|242399200|ref|YP_002994624.1|   8 IGLIVPSSNTTMEMELHSALPEGV------SLYTARMPLRNVTEEELLA-----MSsLAIDSAKLLKDADVDLILYG 73 
                                       788899999999999999999888......4444444444666666333.....333889***************** PP

                                       -CHHHHHHHHHH..........HH-SSEEEECHHHHHHHHHHHSS-EEEEEE-HHHHHCTHHHHHHHHHGT.EEE.. CS
                      Asp_Glu_race  77 CnTahavadelq..........kkikiPvlgiveataealkatgvkkvglLgTrgtlksglyqkeleanqgievvvp 143
                                       C++ + ++ + +          +++k+Pv+    a +ealk  +++k++++++++   ++  +++lean ++     
  gi|242399200|ref|YP_002994624.1|  74 CTSGS-FIGGGEfdkelsmrieDEVKLPVITTSTAILEALKILDAQKILVVTPYTDEINQREREFLEAN-EL----- 143
                                       ****5.444333356667999899*******88888888888**************************7.99..... PP

                                       ..T-CCCHHCCHCHHHHTT-TTSHHHHHHHHHHHHHHTTT-SEEEE-STTHHHHHHHHHHCC-TT.SEEEEHHHHHH CS
                      Asp_Glu_race 144 seelqssvnqaiyeelkaGevteearrailkllerlaergadaviLGCTelplllekaealekeksvpvidptdila 220
                                         e+++     i +  k G++++ ++++++k+l     ++adav++ CT+++++ e +e le++ ++pv+ ++++  
  gi|242399200|ref|YP_002994624.1| 144 --EVIDIRGLGIVDNTKIGRLEPYEAYRMIKALF---TDEADAVFISCTNFRTF-EIIELLEDDFGIPVVTSNQASL 214
                                       ..555544456778999*******9999999999...9**************99.9999999988********9876 PP

                                       H CS
                      Asp_Glu_race 221 r 221
                                       +
  gi|242399200|ref|YP_002994624.1| 215 W 215
                                       6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 1376.72
//
Query:       gi|242399201|ref|YP_002994625.1|  [L=292]
Description: hypothetical protein TSIB_1222 [Thermococcus sibiricus MM 739]
Scores for complete 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-71  239.8   0.0    3.3e-71  239.6   0.0    1.0  1  Memo      Memo-like protein
     0.0032   16.6   0.0     0.0052   15.9   0.0    1.4  1  LigB      Catalytic LigB subunit of aromatic ring-opening dio


Domain annotation for each model (and alignments):
>> Memo  Memo-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  239.6   0.0   3.7e-75   3.3e-71       2     271 .]       5     288 ..       4     288 .. 0.95

  Alignments for each domain:
  == domain 1  score: 239.6 bits;  conditional E-value: 3.7e-75
                              Memo   2 aavAGsfYpedeeelkkqleeflekntgkkeiarviis...PHagyvysgevaakayaeles.skvervvilGpsHt 74 
                                       ++vAGsfYp   eelk++l+ef+++  + +e +r+i     PHagyv+sg +a++ y+++ +   +e++v++Gp+Ht
  gi|242399201|ref|YP_002994625.1|   5 PTVAGSFYPTG-EELKMMLKEFFRDLGELGE-ERKITAgvaPHAGYVFSGFTASRTYKAIYEdGLPETFVVIGPNHT 79 
                                       89*******87.68******99988766665.788877789*******************99999************ PP

                              Memo  75 ilgskvsvlaaseleTPlGdlkvDeelveeLvkkeeiadldetaalaEHSlEvqlpfLkellkek..kfkivPilvs 149
                                       +lgs+v++++ +++ TP+G +kvDe+l++++ +++ iadlde a+++EHS+Evq+pf++++ +++  +++ivPi+++
  gi|242399201|ref|YP_002994625.1|  80 GLGSPVAIYPEGKWITPMGGIKVDEDLAKAIARHSGIADLDELAHKYEHSIEVQIPFIQYISQKAeeEVRIVPITLG 156
                                       *************************************************************9999899********* PP

                              Memo 150 aqseetakevgealakvikdes..nlviiSsDlsHygrrFg......spqeiaesie..Drevikaleelneeelke 216
                                        q+ee+a+++g+a+ ++ ++    ++vi+S+D+ Hyg  +g        +++  +i+  D ++i+++ e +++++ +
  gi|242399201|ref|YP_002994625.1| 157 LQDEEVAEDLGKAIFEASQELGrdIVVIASTDMMHYGYAYGyvpfraRGDDLLGRIKewDFRIIQKILEFDHKGMFD 233
                                       ********************9999*************9999****99777888887779****************** PP

                              Memo 217 ylektnnticGekpiavilkalkklgakkakllkYaqssdvtsdtdsvVsyaslv 271
                                        + k+n t+cG + +a ++  ++ +ga + ++l+Y++s +v+ +td+ V+y s+v
  gi|242399201|ref|YP_002994625.1| 234 EIRKMNHTMCGPGGVATAIVFSRLAGAVETEVLHYTTSFEVSRSTDAIVGYVSIV 288
                                       ***************************************************9975 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 !   15.9   0.0   5.8e-07    0.0052      42     222 ..      67     238 ..      42     276 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5.8e-07
                              LigB  42 sPdtiivvsphhltdvnpvfvlgvaeefeaiddfgkflprleyelkgnpeLaekiaealkksgidlavesnsmklDH 118
                                        P+t +v+ p h+   +pv+++  ++              + + +k++ +La++ia +   ++ d  +  ++  ++ 
  gi|242399201|ref|YP_002994625.1|  67 LPETFVVIGPNHTGLGSPVAIYPEGK-----------WITPMGGIKVDEDLAKAIARHSGIADLDELAHKYEHSIE- 131
                                       66666666666666666553333333...........3346678999999****9999999999966644444444. PP

                              LigB 119 GtlvPL.elmlpdeakvpvikvslntvaypllsferlykLGeAlrkaveeldknvlilgsGglsHqlegde..aaka 192
                                        + +P+ +++ +      + +v +++++ +l + e   +LG+A+ +a +el + +++++s ++ H+  +    ++ a
  gi|242399201|ref|YP_002994625.1| 132 -VQIPFiQYISQ----KAEEEVRIVPITLGLQDEEVAEDLGKAIFEASQELGRDIVVIASTDMMHYGYAYGyvPFRA 203
                                       .45565233333....4455666666667899*********************************865444113333 PP

                              LigB 193 daqtll.lneefdeelldllke....grveelckm 222
                                         + ll   +e+d ++++++ e    g ++e+ km
  gi|242399201|ref|YP_002994625.1| 204 RGDDLLgRIKEWDFRIIQKILEfdhkGMFDEIRKM 238
                                       33333446677777777776664444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        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 0.28s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2042.42
//
Query:       gi|242399202|ref|YP_002994626.1|  [L=74]
Description: hypothetical protein TSIB_1223 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.53
# Mc/sec: 419.05
//
Query:       gi|242399203|ref|YP_002994627.1|  [L=125]
Description: Nucleotidyltransferase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.8e-15   56.2   0.1    4.7e-15   55.4   0.1    1.3  1  Polbeta       Polymerase beta, Nucleotidyltransferase
    2.4e-11   43.8   0.1    3.1e-11   43.4   0.1    1.3  1  NTP_transf_2  Nucleotidyltransferase domain
  ------ inclusion threshold ------
      0.066   12.8   0.0      0.083   12.5   0.0    1.1  1  RlaP          RNA repair pathway DNA polymerase beta family


Domain annotation for each model (and alignments):
>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.4   0.1   7.8e-19   4.7e-15       2      91 ..       9      93 ..       6      95 .. 0.84

  Alignments for each domain:
  == domain 1  score: 55.4 bits;  conditional E-value: 7.8e-19
                                      STTTTHHHHHHHHSTTEEEEEE-S------EEEEEEEESS---HHHHHHHHHHHHHH.SSSEEEEEETTTS-HHHHHHH CS
                           Polbeta  2 kikeilekekeielaylFGSrakgkareeSDiDlavllkekldleeelelaaelediklgkkvDlvdlneapplllyei 80
                                      ki ++ ++  ++++++l+GS a+gkar++SDiDl+++++ +  + e +++ +++    l ++ D+++++  p  +++e+
  gi|242399203|ref|YP_002994627.1|  9 KILSLDRE-RKVKFIILYGSHARGKARKDSDIDLCIYYDGT--KREAFQFRMKVLGE-LPDNYDIQIFDLLPVFIRKEC 83
                                      45444444.5******************************9..66777777777666.67999******9988999999 PP

                                      HHS-EEEES-S CS
                           Polbeta 81 lkegkllyskd 91
                                      lk g +l++kd
  gi|242399203|ref|YP_002994627.1| 84 LK-GVILFCKD 93
                                      99.******98 PP

>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.4   0.1   5.2e-15   3.1e-11       8      48 ..      13      70 ..       2     119 .. 0.67

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 5.2e-15
                                      HHHHTTTSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHH..................H CS
                      NTP_transf_2  8 lkelepvakvvlfGSyarGtalkgSDiDllvvlpeevsre..................k 48
                                      l ++++v+ ++l+GS arG+a+k+SDiDl+++++  + re                  +
  gi|242399203|ref|YP_002994627.1| 13 LDRERKVKFIILYGSHARGKARKDSDIDLCIYYDGTK-REafqfrmkvlgelpdnydiQ 70
                                      3444459*****************************5.555666666444443333330 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 ?   12.5   0.0   1.4e-05     0.083      16      64 ..      15      62 ..       2      78 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.4e-05
                              RlaP 16 eevkilyacesGSrawGfpspdsDyDvrfiyiepaewylglertrdvie 64
                                      +e k+ + ++ GS+a G + +dsD+D+   y   ++  +++ r++   e
  gi|242399203|ref|YP_002994627.1| 15 RERKVKFIILYGSHARGKARKDSDIDLCIYYDGTKREAFQF-RMKVLGE 62
                                      3569999*******************965555555555555.4444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 811.15
//
Query:       gi|242399204|ref|YP_002994628.1|  [L=140]
Description: hypothetical protein TSIB_1225 [Thermococcus sibiricus MM 739]
Scores for complete 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   80.6   1.3    9.5e-23   80.3   1.3    1.1  1  DUF86     Protein of unknown function DUF86
     0.0012   18.9   2.4       0.02   15.0   0.6    2.2  2  DUF4145   Domain of unknown function (DUF4145)


Domain annotation for each model (and alignments):
>> DUF86  Protein of unknown function DUF86
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.3   1.3   1.1e-26   9.5e-23       1     119 []      13     132 ..      10     132 .. 0.96

  Alignments for each domain:
  == domain 1  score: 80.3 bits;  conditional E-value: 1.1e-26
                                       HHHHHHHHCCHH...TSTSCCGSHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----SSC..HHHHHHHTTSS-HHH CS
                             DUF86   1 ikealeklkefteeldeeeflsdeleydavernlqvigEaaidiakhlakklgikkpgdy..ifeilaekgviaeep 75 
                                       i+e+l+++++ +   d e+f++  l +d +++  + + ++++di++ +  +l++  p+++  i+e+l ++++i+ee 
  gi|242399204|ref|YP_002994628.1|  13 ILESLKLIEKHL-PDDVEDFKKLGLIKDGIYKRTEFALQNVLDICAIINTDLKLSLPETEddILETLSRARIISEEL 88 
                                       679999999998.999**********************************999999999889*************** PP

                                       HHHHHHHHCCHHHHHT-CCCTTHHHHHHHHHHTCHHHHHHHHHH CS
                             DUF86  76 eepwrkmiglRNrLvHgYlgidpeivwsiikenlpdleeflesi 119
                                       +++++ m+g+RN+LvH+Y +i+++  +s+++enl+d+  f+e+i
  gi|242399204|ref|YP_002994628.1|  89 KNKLKLMKGFRNILVHRYGRINDDLAFSVLRENLKDIYTFIEAI 132
                                       ****************************************9976 PP

>> DUF4145  Domain of unknown function (DUF4145)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.0   0.1     0.006        54      18      54 ..       6      41 ..       5      52 .. 0.86
   2 !   15.0   0.6   2.3e-06      0.02      21      78 ..      48     112 ..      45     130 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.006
                           DUF4145 18 iRraLEkllkdkgiakgkdLknkiealvekgvipekl 54
                                      iR+ +E++l  ++ ++ k L + +e++ + g i++ +
  gi|242399204|ref|YP_002994628.1|  6 IRSKIEEILESLKLIE-KHLPDDVEDFKKLGLIKDGI 41
                                      79999********555.69************999877 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 2.3e-06
                           DUF4145  21 aLEkllkdkgiakgkdL........knkiealvekgvipeklkelldairviGNdgaHelkditke 78 
                                       aL+ +l+  +i+ ++dL         + +e+l+ +++i+e+lk++l+ ++ ++N+ +H++  i+ +
  gi|242399204|ref|YP_002994628.1|  48 ALQNVLDICAII-NTDLklslpeteDDILETLSRARIISEELKNKLKLMKGFRNILVHRYGRINDD 112
                                       566666666633.34555566777777899****************************97766654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); 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: 0.55u 0.34s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 792.80
//
Query:       gi|242399205|ref|YP_002994629.1|  [L=333]
Description: Mevalonate kinase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-17   63.1   2.2    4.2e-17   62.1   2.2    1.6  1  GHMP_kinases_N   GHMP kinases N terminal domain
    2.6e-13   50.1   0.4    2.6e-13   50.1   0.4    2.4  2  GHMP_kinases_C   GHMP kinases C terminal
     0.0033   17.0   0.0     0.0096   15.5   0.0    1.8  1  GalKase_gal_bdg  Galactokinase galactose-binding signature
  ------ inclusion threshold ------
      0.032   14.2   0.4        7.6    6.5   0.1    2.2  2  DUF2150          Uncharacterized protein conserved in archaea
      0.045   14.0   0.2        2.8    8.2   0.0    2.8  2  Flagellin_IN     Flagellin hook IN motif


Domain annotation for each model (and alignments):
>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.1   2.2   1.2e-20   4.2e-17       2      66 .]     102     168 ..     101     168 .. 0.94

  Alignments for each domain:
  == domain 1  score: 62.1 bits;  conditional E-value: 1.2e-20
                                       EEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHH..HH.HHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
                    GHMP_kinases_N   2 ivikseiPvgaGLGSSAAlavalvaAllallglsl..ee.aklaleaerlaqggngsggDvaasvyGg 66 
                                       ++i+s iPvgaGLGSSAA+ava++ A+ +l+gl+l  ee akl+ + e l+q g +sg+D ++s+ Gg
  gi|242399205|ref|YP_002994629.1| 102 VSITSQIPVGAGLGSSAAVAVATIGAVSRLFGLELtpEEvAKLGHKVELLVQ-GASSGIDPTVSAIGG 168
                                       789*******************************986558************.999********9998 PP

>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.4      0.98   3.5e+03      55      64 ..     111     120 ..      80     132 .. 0.78
   2 !   50.1   0.4   7.2e-17   2.6e-13      10      79 ..     244     309 ..     226     313 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.98
                    GHMP_kinases_C  55 GaGgGptvfa 64 
                                       GaG+G++ ++
  gi|242399205|ref|YP_002994629.1| 111 GAGLGSSAAV 120
                                       8888888776 PP

  == domain 2  score: 50.1 bits;  conditional E-value: 7.2e-17
                    GHMP_kinases_C  10 lellgellnlsqrselkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkdeaeqvaral 79 
                                       +++lg l+n ++   l++ +g+++ +l +l+ a +e+Galgak++GaGgG++ +al+  ++++++va a+
  gi|242399205|ref|YP_002994629.1| 244 FKRLGTLMNINHG--LLDALGVSTKSLSDLVYASREAGALGAKITGAGGGGCMYALA--PEKQSEVATAI 309
                                       789**********..9*****************************************..77777777776 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 !   15.5   0.0   2.7e-06    0.0096      12      45 ..       3      36 ..       2      39 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.7e-06
                                      EEEEEEEEEEEE--S-TTTT-EEEEEEEEEEEEE CS
                   GalKase_gal_bdg 12 fvasAPGRvnLiGEHtDYngGfVlpmAieqdiyi 45
                                      ++asAP  + L GEH    g   +++Ai++++y+
  gi|242399205|ref|YP_002994629.1|  3 VLASAPAKIILFGEHSVVYGKPAIAAAIDLRTYV 36
                                      589******************************8 PP

>> DUF2150  Uncharacterized protein conserved in archaea (DUF2150)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1    0.0021       7.6      62     152 ..      25     114 ..       5     132 .. 0.70
   2 ?    5.9   0.0    0.0033        12      74     119 ..     202     247 ..     197     250 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0021
                           DUF2150  62 Aleeleevreivleeveeddeekeeliesvqtsllvvfaaaeeyieggvakekdieelvkaaaeaeaeedleaalei 138
                                       A++   + r  v +e +e+     e  +     l v f   + y+e ++ k +++ ++v++a++    e+ e+  ++
  gi|242399205|ref|YP_002994629.1|  25 AIAAAIDLRTYVKAEFNENGRIRIEAKDIRTPGLTVSFSEDQIYFETDYGKAAEVLSYVREAINLV-MEEAEKQKGV 100
                                       555555666666666666554445555555556888999999*********************998.6667777677 PP

                           DUF2150 139 vaqiGakvidgekl 152
                                        ++i +++  g+ l
  gi|242399205|ref|YP_002994629.1| 101 TVSITSQIPVGAGL 114
                                       77666666555555 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0033
                           DUF2150  74 leeveeddeekeeliesvqtsllvvfaaaeeyieggvakekdieel 119
                                       +++v ++ ee+ e+i+ + +s+  +++ a+e i  +++ke +++ l
  gi|242399205|ref|YP_002994629.1| 202 VAKVRKNYEEMPEIIDPILNSMGRLVEKAREVILAEYDKEIKFKRL 247
                                       46788889******************************99988876 PP

>> Flagellin_IN  Flagellin hook IN motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.039   1.4e+02      26      56 .]      26      52 ..      25      52 .. 0.83
   2 ?    8.2   0.0   0.00077       2.8      23      45 ..      80     106 ..      74     114 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.039
                                      HHHHHHHHCCTTTEEEEEEEECEEEEEEEEE CS
                      Flagellin_IN 26 iadaINavssktGVsAsidadggrLvltskd 56
                                      ia+aI      t V+A  +++ gr+ + +kd
  gi|242399205|ref|YP_002994629.1| 26 IAAAID---LRTYVKAEFNEN-GRIRIEAKD 52
                                      666666...6899********.***999886 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00077
                                       CHHHHHHHH....HHCCTTTEEEEEEE CS
                      Flagellin_IN  23 lddiadaIN....avssktGVsAsida 45 
                                       l+ +++aIN     + ++ GV+ si++
  gi|242399205|ref|YP_002994629.1|  80 LSYVREAINlvmeEAEKQKGVTVSITS 106
                                       5669********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       692  (0.0385967); expected 358.6 (0.02)
Passed bias filter:                      592  (0.0330191); 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: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2132.02
//
Query:       gi|242399206|ref|YP_002994630.1|  [L=46]
Description: hypothetical protein TSIB_1227 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); 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: 288.00
//
Query:       gi|242399207|ref|YP_002994631.1|  [L=251]
Description: hypothetical protein TSIB_1228 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); 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: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.53
# Mc/sec: 1432.46
//
Query:       gi|242399208|ref|YP_002994632.1|  [L=644]
Description: hypothetical protein TSIB_1229 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.6e-06   25.8   2.1          7    6.5   0.1    6.7  5  Prenyltrans      Prenyltransferase and squalene oxidase repea
    0.00063   18.9   0.1       0.43    9.6   0.0    3.6  4  SQHop_cyclase_C  Squalene-hopene cyclase C-terminal domain
  ------ inclusion threshold ------
      0.019   14.1   0.1         46    3.0   0.1    3.6  3  SQHop_cyclase_N  Squalene-hopene cyclase N-terminal domain


Domain annotation for each model (and alignments):
>> Prenyltrans  Prenyltransferase and squalene oxidase repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.04   2.4e+02      14      35 ..      67      89 ..      64      98 .. 0.70
   2 ?    3.4   0.5      0.01        62      32      44 .]     319     331 ..     295     331 .. 0.86
   3 ?    2.6   0.0     0.019   1.2e+02       3      25 ..     472     494 ..     470     507 .. 0.86
   4 !    6.5   0.1    0.0012         7       7      44 .]     523     554 ..     520     554 .. 0.75
   5 ?    3.2   0.0     0.013        75       2      21 ..     559     578 ..     558     600 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.04
                                      SHTTS-BBSSTTS.SBBHHHHHH CS
                       Prenyltrans 14 QnedGGwggrpgs.esdtyytyw 35
                                      Q +dGG+ +  +   +d   ty+
  gi|242399208|ref|YP_002994632.1| 67 QTPDGGFTEIVDNvIPDILSTYY 89
                                      77*****8875556667777776 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.01
                                       HHHHHHHHHHHCT CS
                       Prenyltrans  32 ytywalaaLallG 44 
                                       +ty+a+ aL+l+G
  gi|242399208|ref|YP_002994632.1| 319 GTYYAVEALILIG 331
                                       79999***99998 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.019
                                       HHHHHHHHHHHSHTTS-BBSSTT CS
                       Prenyltrans   3 vekavefLlscQnedGGwggrpg 25 
                                       +++++e +l   n dG +g + g
  gi|242399208|ref|YP_002994632.1| 472 KNQLIEKILAQRNQDGTFGNHSG 494
                                       78999*************98766 PP

  == domain 4  score: 6.5 bits;  conditional E-value: 0.0012
                                       HHHHHHHSHTTS-BBSSTTSSBBHHHHHHHHHHHHHCT CS
                       Prenyltrans   7 vefLlscQnedGGwggrpgsesdtyytywalaaLallG 44 
                                       vefLl+ Q   GGwg       d+y ty+++ aL  +G
  gi|242399208|ref|YP_002994632.1| 523 VEFLLNSQ-TNGGWGAP-----DLYTTYYVVRALRTIG 554
                                       77888888.77887754.....9999999998888776 PP

  == domain 5  score: 3.2 bits;  conditional E-value: 0.013
                                       HHHHHHHHHHHHSHTTS-BB CS
                       Prenyltrans   2 dvekavefLlscQnedGGwg 21 
                                       dv+ ++ fL++ Q + GG++
  gi|242399208|ref|YP_002994632.1| 559 DVDGLLSFLKRVQYPYGGFN 578
                                       78999*************96 PP

>> SQHop_cyclase_C  Squalene-hopene cyclase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.3   0.0    0.0031        18     129     157 ..     163     191 ..     149     241 .. 0.85
   2 ?   -2.1   0.0      0.26   1.6e+03     168     236 ..     297     362 ..     273     372 .. 0.66
   3 ?   -0.8   0.0      0.11   6.5e+02     189     231 ..     451     494 ..     446     507 .. 0.76
   4 !    9.6   0.0   7.2e-05      0.43     148     225 ..     509     576 ..     499     588 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.0031
                                       SSS-SSB--BHHHHHHHHHHHHHHT--TT CS
                   SQHop_cyclase_C 129 dhealldpptadvtarvlellaqlgeeed 157
                                       d ++++d   +d+t + le+l+ lg++ +
  gi|242399208|ref|YP_002994632.1| 163 DNGSFIDDDGTDMTEKALEMLSALGYNVA 191
                                       8899********************99743 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.26
                                       HHHHS-TTS----SSBSSHH..HHHHHHHHHHHHTT--TTSHHHHHHHHHHHTT--TTSSBB--GGGGT-G CS
                   SQHop_cyclase_C 168 lkkeqepdGsWfGrWGvnyi..yGtwsvlsalaavgedleepvirkavdWlksvqnedGGWGesaesykdp 236
                                       l +e+  dG  f  +G++y    Gt+ ++ al  +g+  e+++    +++++++  + GG+  + +s+ dp
  gi|242399208|ref|YP_002994632.1| 297 LMEEKLWDGG-FNLFGLDYGepQGTYYAVEALILIGKMPERDT----INFIHERETPLGGFIFCYQSFGDP 362
                                       5555555554.55667777422689999999999998777665....467777777777776666666665 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.11
                                       HHHHHHHHH.HHTT--TTSHHHHHHHHHHHTT--TTSSBB--GG CS
                   SQHop_cyclase_C 189 Gtwsvlsal.aavgedleepvirkavdWlksvqnedGGWGesae 231
                                       G w  l+ l +++g+ l+e++ ++ ++ + +++n+dG +G+++ 
  gi|242399208|ref|YP_002994632.1| 451 GSWISLIKLgKEIGVVLDEKTKNQLIEKILAQRNQDGTFGNHSG 494
                                       67777777745788888888888999999999999999998654 PP

  == domain 4  score: 9.6 bits;  conditional E-value: 7.2e-05
                                       HHHHHT--TTSHHHHHHHHHHHHHS-TTS----SSBSSHHHHHHHHHHHHHHTT--TTSHHHHHHHHHHHTT--TTS CS
                   SQHop_cyclase_C 148 llaqlgeeedsealkraveylkkeqepdGsWfGrWGvnyiyGtwsvlsalaavgedleepvirkavdWlksvqnedG 224
                                       ll +lg++      +r+ve+l + q +     G WG+  +y t+ v++al+++g+  ++  +   +++lk+vq + G
  gi|242399208|ref|YP_002994632.1| 509 LLEELGYKYR---DERTVEFLLNSQTN-----GGWGAPDLYTTYYVVRALRTIGVCPKD--VDGLLSFLKRVQYPYG 575
                                       5555555443...46899****99987.....559******************987554..4555666777776666 PP

                                       S CS
                   SQHop_cyclase_C 225 G 225
                                       G
  gi|242399208|ref|YP_002994632.1| 576 G 576
                                       6 PP

>> SQHop_cyclase_N  Squalene-hopene cyclase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.011        63      43      94 ..     286     337 ..     272     351 .. 0.83
   2 ?    3.0   0.1    0.0078        46      43      93 ..     468     519 ..     455     545 .. 0.74
   3 ?    2.8   0.0    0.0089        53      49      87 ..     562     600 ..     556     612 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.011
                   SQHop_cyclase_N  43 deeeeekiakylrsqqredGgWelypggpgdlsttveaYlALkllGdspdap 94 
                                       ++e ++++ k l++++  dGg++l+  + g+   t  a  AL l+G+ p+ +
  gi|242399208|ref|YP_002994632.1| 286 TDEIKSATYKILMEEKLWDGGFNLFGLDYGEPQGTYYAVEALILIGKMPERD 337
                                       45677888999**************888888888888888999999988876 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.0078
                   SQHop_cyclase_N  43 deeeeekiakylrsqqredGgWelypggp.gdlsttveaYlALkllGdspda 93 
                                       de++++++ + +++q+++dG+++ + g+   +l  t  a l L  lG++  +
  gi|242399208|ref|YP_002994632.1| 468 DEKTKNQLIEKILAQRNQDGTFGNHSGNIyKKLLYTSHAVLLLEELGYKYRD 519
                                       6778888889999999999999988877656666666666666666655544 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.0089
                   SQHop_cyclase_N  49 kiakylrsqqredGgWelypggpgdlsttveaYlALkll 87 
                                        +  +l + q + Gg++ y g++       e+YlAL++l
  gi|242399208|ref|YP_002994632.1| 562 GLLSFLKRVQYPYGGFNFYEGQENAYGGLYETYLALRIL 600
                                       56788999****************99999********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (644 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); 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: 0.73u 0.31s 00:00:01.04 Elapsed: 00:00:00.51
# Mc/sec: 3805.51
//
Query:       gi|242399209|ref|YP_002994633.1|  [L=260]
Description: Amino acid kinase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.9e-46  158.6   0.0    2.2e-46  158.4   0.0    1.0  1  AA_kinase  Amino acid kinase family
  ------ inclusion threshold ------
      0.013   15.9   0.0      0.069   13.6   0.0    2.1  2  GluRS_N    Glutamate--tRNA ligase N-terminal domain


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.4   0.0   2.4e-50   2.2e-46       2     237 ..       1     233 [.       1     237 [. 0.94

  Alignments for each domain:
  == domain 1  score: 158.4 bits;  conditional E-value: 2.4e-50
                                       EEEEEE-TTCCCCTCC......HHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHHTCCCCCHHHC....E..HH CS
                         AA_kinase   2 rvVvKlGGssltdkee......aslrrlaeqiaalkesgnklvvVhGggsftdgllalksglssgelaaglrstlee 72 
                                       ++++KlGGs+++dk++      ++++++ae+ia++   ++  ++VhGggsf++  +++ +++ +g +    +++ + 
  gi|242399209|ref|YP_002994633.1|   1 MIIIKLGGSVISDKNTpysfnrEVVEEIAEEIAQF-YPKESFILVHGGGSFGHPNARE-YKIREGLIG---DVKRKR 72 
                                       58*********************************.666677****************.******998...8***** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE..HHHTTTCEEECCHHHHHHHTT-EEEEESEEEE CS
                         AA_kinase  73 agevatrdalaslgerlvaallaaglpavglsaaaldateagrdegsdgnvesvdaeaieelleagvvpvltgfigl 149
                                        g+  t++a+++l+  + + +l++glpa+++s++++ ++e+g        +   + e +++lle+g++pvl g+ ++
  gi|242399209|ref|YP_002994633.1|  73 IGFSKTHQAMLKLNNLIIEVFLEKGLPAYSVSSSSIFLIENGE-------IIYGELEILRKLLEKGFIPVLFGDTAV 142
                                       *************************************997666.......99999********************** PP

                                       ETTTEEEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHH......CSSS.TTTHHH CS
                         AA_kinase 150 deegelgrgssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaee......saselatgGmk 220
                                         e+++ ++s+D+ia +lA+ l+A+k+i+l dVdG+yd++p++   a+l++e++ + +e       sa+ ++tgG+ 
  gi|242399209|ref|YP_002994633.1| 143 ALEKGIDILSGDQIAGYLAKILRAEKVIFLMDVDGIYDKNPREK-GAKLITELTKEGIEHllesseSAGIDVTGGIG 218
                                       *****99************************************8.********9888888888************** PP

                                       HCHHHHHHHHHCTT-EE CS
                         AA_kinase 221 vkhpaalaaarrggipv 237
                                        k+++al++a+ +  +v
  gi|242399209|ref|YP_002994633.1| 219 NKLKKALEIAHYS--DV 233
                                       *********9865..44 PP

>> GluRS_N  Glutamate--tRNA ligase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.28   2.5e+03      44      54 ..      22      32 ..       6      37 .. 0.62
   2 ?   13.6   0.0   7.7e-06     0.069      26      53 ..     103     130 ..      95     131 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.28
                           GluRS_N 44 edvLnkLaekf 54
                                       +v++ +ae++
  gi|242399209|ref|YP_002994633.1| 22 REVVEEIAEEI 32
                                      56666666654 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 7.7e-06
                           GluRS_N  26 dfdssvkLtdggktivdsedvLnkLaek 53 
                                       +++ss+ L  +g++i++++++L+kL ek
  gi|242399209|ref|YP_002994633.1| 103 VSSSSIFLIENGEIIYGELEILRKLLEK 130
                                       55777788*****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 1665.68
//
Query:       gi|242399210|ref|YP_002994634.1|  [L=374]
Description: Isopentenyl-diphosphate delta-isomerase [Thermococcus sibiricus MM 739]
Scores for complete 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-29  100.7   1.3    9.6e-17   61.0   1.4    2.1  2  FMN_dh        FMN-dependent dehydrogenase
    2.6e-05   23.4   8.2    0.00053   19.1   0.3    3.5  4  IMPDH         IMP dehydrogenase / GMP reductase domain
    0.00038   19.9   2.7    0.00065   19.2   1.4    1.9  2  NMO           Nitronate monooxygenase
     0.0031   16.7   0.5       0.16   11.1   0.3    2.3  2  Glu_synthase  Conserved region in glutamate synthase
  ------ inclusion threshold ------
      0.017   14.3   0.0      0.041   13.0   0.0    1.6  2  DUF561        Protein of unknown function (DUF561)
      0.082   12.4   0.1          5    6.5   0.0    2.9  3  His_biosynth  Histidine biosynthesis protein


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 !   37.7   0.0   3.8e-13   1.1e-09       8      96 ..      13     105 ..       6     120 .. 0.81
   2 !   61.0   1.4   3.2e-20   9.6e-17     205     343 ..     186     346 ..     120     350 .. 0.89

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 3.8e-13
                                       HHHHHHH--STTSHHHHHHHHGGGGEEE---SSSS-SS-..B--EEETTEEESSSEEE--B.STGGGTSTTHHHH.. CS
                            FMN_dh   8 kafayvaggagdevtlrenraaferirlrprvlrdvskv..dlsttllGqklslPvliaPv.glaklahpdgela.. 79 
                                       ++f++++ + +++v ++   ++fe+i++++  l ++ k   dls+++lG+k+++P++ia + g +k  +  g+++  
  gi|242399210|ref|YP_002994634.1|  13 RKFEHIEHCLKKQVEAHV-STQFENIHFVHTSLPEIDKDeiDLSVEVLGRKFDYPIMIAGMtGGTKGSQLAGKINkt 88 
                                       578888888888887765.567************9987555*******************97555555555555444 PP

                                       HHHHHHHHTS-EEEETT CS
                            FMN_dh  80 laraaakagipfvlstv 96 
                                       la+aa++++ip++++++
  gi|242399210|ref|YP_002994634.1|  89 LAKAAQELNIPMGVGSQ 105
                                       *************9986 PP

  == domain 2  score: 61.0 bits;  conditional E-value: 3.2e-20
                                       HHHHHHHHHHHSSEEEEEEE...-SHHHHHHHHHTTESEEEE--GGG.....................TSSTT---H CS
                            FMN_dh 205 wddikwlreqtklplvvKGv...ltaedakraveaGvdgivvSNHGG.....................Rqldgapat 257
                                        + +++l+ +++ p++ K+    ++ e a ++  +G+d+i v   GG                     +  d  ++t
  gi|242399210|ref|YP_002994634.1| 186 ITALAELKGELSYPIIAKETgagVSMEVAIKLESIGIDAIDVGGLGGtswssveyyrakdeksknlalKFWDWGIPT 262
                                       457999************9988999****************************************999999*99999 PP

                                       HHCHHHHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                            FMN_dh 258 idvLpeiveavggrievlvDgGirrGsDvlkAlalGAdavllGRpflyglaagGeeGvervleilraelertmallG 334
                                            e++ a g  +++++ gGir G  ++kAlalGA++ +++ p+l  +  g  eGv ++l+   +el+++m l+G
  gi|242399210|ref|YP_002994634.1| 263 ALSVAEVRYATG--LPIIATGGIRDGIMIAKALALGANLAGVALPLLKPAVNGDVEGVIKILQQYIDELRNVMFLVG 337
                                       9999***99999..*************************************************************** PP

                                       -SBHHHHHC CS
                            FMN_dh 335 vksvaeldr 343
                                       + sv+el++
  gi|242399210|ref|YP_002994634.1| 338 AGSVKELKK 346
                                       ******986 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.31   9.2e+02     249     278 ..      88     119 ..      65     131 .. 0.62
   2 ?    1.1   0.4     0.053   1.6e+02     129     173 ..     182     228 ..     174     238 .. 0.78
   3 !   19.1   0.3   1.8e-07   0.00053     197     232 ..     264     299 ..     257     304 .. 0.88
   4 !    5.2   0.0     0.003       8.8     299     327 ..     318     346 ..     309     356 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.31
                                       EEEETTEEEEEEEETTSHHHH.HH.-SS-TTS CS
                                       xxxxxxxxxxxxxxxxxxxxx.xx.xxxxxxx RF
                             IMPDH 249 viliegrkyKeyrGmgslgam.kk.gskdryf 278
                                       ++    +++    G+gs +am +k +++++y+
  gi|242399210|ref|YP_002994634.1|  88 TLAKAAQELNIPMGVGSQRAMiRKpETWESYY 119
                                       33444566666778888888853235666664 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.053
                                       SHHHHHHHHHHHHHTTTSEEE...EEEE-SHHHHHHHHHTT-SEEEE- CS
                                       xxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 129 sekvleavkeikkkveevevi...aGnvataegakaLieagadavkvG 173
                                        ++v++a++e+k ++ +  +i   +G  ++ e a +L + g+da+ vG
  gi|242399210|ref|YP_002994634.1| 182 YKGVITALAELKGEL-SYPIIakeTGAGVSMEVAIKLESIGIDAIDVG 228
                                       567899999999998.56677333588899999**************8 PP

  == domain 3  score: 19.1 bits;  conditional E-value: 1.8e-07
                                       HHHHHHHCTCT-EEEEES---SHHHHHHHHHTT-SE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 197 aevaeaakkagvpviaDGGikysgdivkAlaaGada 232
                                       ++vae+   +g p+ia GGi+    i+kAla+Ga+ 
  gi|242399210|ref|YP_002994634.1| 264 LSVAEVRYATGLPIIATGGIRDGIMIAKALALGANL 299
                                       4678888999************************86 PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.003
                                       HHHHHHHHHHHHHHHHHHHT-SSHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 299 vkevveqlvgglrsgmgylGaktieelke 327
                                       v ++++q + +lr+ m  +Ga +++elk+
  gi|242399210|ref|YP_002994634.1| 318 VIKILQQYIDELRNVMFLVGAGSVKELKK 346
                                       4578999********************87 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.59   1.8e+03      11      31 ..      65      85 ..      59     101 .. 0.81
   2 !   19.2   1.4   2.2e-07   0.00065     185     221 ..     266     302 ..     257     310 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.59
                               NMO 11 kppvvqpgmggiskarLaaav 31
                                      +p++++++ gg  + +La+ +
  gi|242399210|ref|YP_002994634.1| 65 YPIMIAGMTGGTKGSQLAGKI 85
                                      577788888889999999876 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 2.2e-07
                               NMO 185 vpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqi 221
                                       v++v+ a  +P+iA+GGi d+  +a aLalGA+ + +
  gi|242399210|ref|YP_002994634.1| 266 VAEVRYATGLPIIATGGIRDGIMIAKALALGANLAGV 302
                                       677888888***********************75544 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 !    3.7   0.0    0.0093        28      30     101 ..      25     104 ..       5     161 .. 0.69
   2 !   11.1   0.3   5.2e-05      0.16     266     303 ..     266     303 ..     182     308 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.0093
                                       HHTS.-S-SGGGGEEE--SS--.--GGGS--HHHH.....HTTEE---B-TTT....S-HHHHHHHHHHHHHHT-B- CS
                      Glu_synthase  30 leerevlkakrdlleldaaeealikleevepalki.....kkriltsamSyGa....lseeahealakamnrlgtks 97 
                                       + e+ ++ ++ + +++ ++  ++i ++e++  +++     + +i++++m  G+    l+ + +++laka+++l + +
  gi|242399210|ref|YP_002994634.1|  25 QVEA-HVSTQFENIHFVHTSLPEIDKDEIDLSVEVlgrkfDYPIMIAGMTGGTkgsqLAGKINKTLAKAAQELNIPM 100
                                       3344.556666777777777777666666655544121116689999999886333466677889999999988887 PP

                                       EETT CS
                      Glu_synthase  98 ntGE 101
                                         G 
  gi|242399210|ref|YP_002994634.1| 101 GVGS 104
                                       7765 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 5.2e-05
                                       HHHTT-GGG-EEEEESS--SHHHHHHHHHHT-SEEE-S CS
                      Glu_synthase 266 lkeeglrdrvsliadGglktgadvvkalalGAdavgig 303
                                       + e      + +ia+Gg++ g  ++kalalGA+  g++
  gi|242399210|ref|YP_002994634.1| 266 VAEVRYATGLPIIATGGIRDGIMIAKALALGANLAGVA 303
                                       345555667889********************987766 PP

>> DUF561  Protein of unknown function (DUF561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.4e-05     0.041     135     217 ..     211     306 ..     207     333 .. 0.69
   2 ?   -2.5   0.0      0.79   2.4e+03      55      72 ..     340     357 ..     318     361 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.4e-05
                            DUF561 135 vkLakkLeslgvdliqteG.kitsis.......kakkvndlieksls.....tlastyeiskkvslPvicasGlsd. 197
                                       +++a kLes+g+d i   G + ts s       k +k ++l  k        t  s+ e+  ++ lP+i++ G+ d 
  gi|242399210|ref|YP_002994634.1| 211 MEVAIKLESIGIDAIDVGGlGGTSWSsveyyraKDEKSKNLALKF-WdwgipTALSVAEVRYATGLPIIATGGIRDg 286
                                       57899**********998732344445778775333333322222.134444999999****************864 PP

                            DUF561 198 vtvplalslgasGiGigsav 217
                                       + +  al+lga   G+   +
  gi|242399210|ref|YP_002994634.1| 287 IMIAKALALGANLAGVALPL 306
                                       78888999999877776554 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.79
                            DUF561  55 kvksvsniPiCvsaveak 72 
                                       +vk+  ++Pi v +   +
  gi|242399210|ref|YP_002994634.1| 340 SVKELKKVPIVVTGFARE 357
                                       689999999999887655 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0     0.073   2.2e+02      82     142 ..      12      73 ..      11     100 .. 0.76
   2 ?    1.3   0.0     0.065   1.9e+02      63     132 ..      87     159 ..      66     231 .. 0.77
   3 ?    6.5   0.0    0.0017         5      65      97 ..     266     298 ..     259     308 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.073
                                       SSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEEC...EEEEETTTT CS
                      His_biosynth  82 IrsledveelleagadkviigtaavknpelikelaekfgsqkivvaiDarrg...ykvaikgwr 142
                                       Ir++e++e+ l+  ++  +  +  ++n ++++  + ++ +++i +++++      y ++i g +
  gi|242399210|ref|YP_002994634.1|  12 IRKFEHIEHCLKKQVEAHV--STQFENIHFVHTSLPEIDKDEIDLSVEVLGRkfdYPIMIAGMT 73 
                                       8999999999999998766..67899999****9999999999999998773344555555544 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.065
                                       HHHHHHHHH-SSEEEEESS...SSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEE CS
                      His_biosynth  63 dlveeiaeevfipvqvGGG...IrsledveelleagadkviigtaavknpelikelaekfgsqkivvaiDarr 132
                                       + +++ a+e++ip+ vG+    Ir+ e+ e++  + +   i     +  p++ +++ +++g ++   a+++ +
  gi|242399210|ref|YP_002994634.1|  87 KTLAKAAQELNIPMGVGSQramIRKPETWESYYVRDVAPDIFLVGNLGAPQFAENMPNRYGVEEALKAVETIQ 159
                                       5567888888888888877888999999999888888877777777888888888888888888777777666 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.0017
                                       HHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-S CS
                      His_biosynth  65 veeiaeevfipvqvGGGIrsledveelleagad 97 
                                       v+e++ ++ +p+   GGIr+   ++++l +ga+
  gi|242399210|ref|YP_002994634.1| 266 VAEVRYATGLPIIATGGIRDGIMIAKALALGAN 298
                                       678888889999999999999999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); 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: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.45
# Mc/sec: 2514.75
//
Query:       gi|242399211|ref|YP_002994635.1|  [L=440]
Description: Metallo-beta-lactamase superfamily protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-13   50.8   3.2    2.6e-12   46.5   0.1    3.0  3  RMMBL          Zn-dependent metallo-hydrolase RNA specificity
    1.8e-13   50.9   0.0    3.1e-13   50.2   0.0    1.4  1  Lactamase_B    Metallo-beta-lactamase superfamily
    3.7e-08   33.1   0.7      6e-08   32.4   0.1    1.6  2  Lactamase_B_2  Beta-lactamase superfamily domain
     0.0017   17.8   0.4     0.0046   16.4   0.4    1.8  1  Lactamase_B_6  Metallo-beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.024   13.1   0.0      0.041   12.4   0.0    1.3  1  DUF2114        Uncharacterized protein conserved in archaea (
      0.025   13.7   0.7      0.085   12.0   0.4    1.9  2  PDEase_II      cAMP phosphodiesterases class-II


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 ?    3.8   0.0     0.018        55      29      51 ..      66      91 ..      64     124 .. 0.81
   2 ?   -2.4   0.2       1.6   4.7e+03      33      42 ..     155     164 ..     144     166 .. 0.75
   3 !   46.5   0.1   8.6e-16   2.6e-12       4      56 ..     371     421 ..     370     431 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.018
                             RMMBL 29 lkprn...vilvHGeeeatsalarll 51
                                      +k+++   ++l HG+ +++ a a+l+
  gi|242399211|ref|YP_002994635.1| 66 IKNKKvvaIALSHGHLDHIGAIAKLA 91
                                      788888889*************9987 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.6
                             RMMBL  33 nvilvHGeee 42 
                                        +++vH  e 
  gi|242399211|ref|YP_002994635.1| 155 SIVVVHTPEG 164
                                       399***9875 PP

  == domain 3  score: 46.5 bits;  conditional E-value: 8.6e-16
                             RMMBL   4 vkarieeidfSgHadknellelirklkprnvilvHGeeeatsalarllkeeeg 56 
                                       v++ ++++++SgH+ +++++ li++l+p+n i+ HGe +++ ++a+l+ eeeg
  gi|242399211|ref|YP_002994635.1| 371 VRM-VKDLHVSGHSSREDHRYLIKLLNPENMIPAHGEFRMLTHYAELA-EEEG 421
                                       566.899*****************************************.8888 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.2   0.0   1.1e-16   3.1e-13       4     162 ..      13     183 ..      10     241 .. 0.90

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 1.1e-16
                                       CSSEEEEEEETTCEEEES--SCHHHHHHHH.................HHHHHTSGGGGEEEEE-SBSSHHHHTTGGG CS
                       Lactamase_B   4 dpvnsyliegdggviLiDtGtsteaaraal.................elaalglkpkdvdavilTHlHlDHiGglgg 63 
                                       ++ n++ ie +++vi+iD G+  ++ ++ +                 ++ +  +k k+v a+ l+H+HlDHiG+ ++
  gi|242399211|ref|YP_002994635.1|  13 VGKNMTAIEYENEVIIIDMGIRLDRVLIHEdvnfqkmssrdlkklgaIPDDTIIKNKKVVAIALSHGHLDHIGAIAK 89 
                                       6779************************99*********************************************** PP

                                       CTTHHCCEETCCEHHHHCCHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEE CS
                       Lactamase_B  64 lveatdvpvgavaeeapalfmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvvey 140
                                       l+ ++ +++++   ++ +l + e+  ++ ++       +++      e+ ++ +    +++++ +  ++++ +vv+ 
  gi|242399211|ref|YP_002994635.1|  90 LAPHYSNVPIYGTPYTIKLAKGEVRSEQYFE-----VTNPMYETQYGEIVQVSENLTIEFVQVTHSIPHSSIVVVHT 161
                                       ************************6655554.....37888888888999999999********************* PP

                                       TTCCEEEECTTTSSHHCCCCCC CS
                       Lactamase_B 141 gggkvlftGDallagetgridl 162
                                       ++g v+++ D  + + +++++ 
  gi|242399211|ref|YP_002994635.1| 162 PEGAVVYACDYKFDNHNPLGEN 183
                                       ************9999999887 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 !   32.4   0.1     2e-11     6e-08      29     144 ..      69     173 ..      53     183 .. 0.83
   2 ?   -3.4   0.1       1.9   5.6e+03     175     200 ..     379     404 ..     362     404 .. 0.78

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 2e-11
                                       .SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTTTTEEEEEE-TTSEEEECSTTEEE CS
                     Lactamase_B_2  29 ppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleeepavnvheldwgesfelgdgglei 105
                                       +++ a+ l+h+H DH+  +  l++ +++++p+y+++ +++  + +   ++  e  + ++ e + ge +++  ++l+i
  gi|242399211|ref|YP_002994635.1|  69 KKVVAIALSHGHLDHIGAIAKLAP-HYSNVPIYGTPYTIKLAKGEVRSEQYFEV-TNPMYETQYGEIVQVS-ENLTI 142
                                       6899********************.6778**********988777665555555.99999**********7.69*** PP

                                       EEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S CS
                     Lactamase_B_2 106 tatparhksgrrldrnagdtlGlriegggkrvyyigDtg 144
                                       +++++ h+ +            +++ +++ +v+y+ D +
  gi|242399211|ref|YP_002994635.1| 143 EFVQVTHSIPH--------SSIVVVHTPEGAVVYACDYK 173
                                       ********999........55555557888888887765 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.9
                                       HHT---STSHHHHCTTSSSSEEEEES CS
                     Lactamase_B_2 175 hmgHltpeeaveaaadlgakrlvliH 200
                                         gH++ e+   +++ l+++ +++ H
  gi|242399211|ref|YP_002994635.1| 379 VSGHSSREDHRYLIKLLNPENMIPAH 404
                                       56888889999999999999999988 PP

>> Lactamase_B_6  Metallo-beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.4   1.5e-06    0.0046       6      84 ..      24     114 ..      19     178 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.5e-06
                     Lactamase_B_6   6 nvkiLlDvGwdeskvslesalkelekvi.................ptvdliLLshatlehlGayallyakfksklll 65 
                                       n  i++D+G +  +v +++++++ +                    ++v +i Lsh  l+h+Ga a l  +      +
  gi|242399211|ref|YP_002994635.1|  24 NEVIIIDMGIRLDRVLIHEDVNFQKMSSrdlkklgaipddtiiknKKVVAIALSHGHLDHIGAIAKLAPH-----YS 95 
                                       5555566665544444444433322211112222333444455778999*************97655544.....48 PP

                     Lactamase_B_6  66 nipvyatlpvvkLGrvsll 84 
                                       n+p+y+t  ++kL++  + 
  gi|242399211|ref|YP_002994635.1|  96 NVPIYGTPYTIKLAKGEVR 114
                                       *************986664 PP

>> DUF2114  Uncharacterized protein conserved in archaea (DUF2114)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.4e-05     0.041     188     245 ..      14      72 ..       6      92 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.4e-05
                           DUF2114 188 gakwtdvdfrnPcisidfGttLdGrivndeePyaktvgnfcGlaGaipd.aivrGtglv 245
                                       g  +t +++ n +i id+G  Ld  +++++  + k+ +  +   Gaipd +i++  ++v
  gi|242399211|ref|YP_002994635.1|  14 GKNMTAIEYENEVIIIDMGIRLDRVLIHEDVNFQKMSSRDLKKLGAIPDdTIIKNKKVV 72 
                                       67789******************************************963688877766 PP

>> PDEase_II  cAMP phosphodiesterases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.4   2.8e-05     0.085      79     125 ..      69     110 ..      39     157 .. 0.76
   2 ?   -1.3   0.0       0.3     9e+02     318     336 ..     185     203 ..     138     204 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.8e-05
                                       HTEEEEE-S---GGGTHHHHHHGGGGGS-S.--EEEEE-HHHHHHHH CS
                         PDEase_II  79 nniksylItHsHLDHvsglvinSaefykaqlkkktivGlpytInalq 125
                                       +++    ++H HLDH++++    +  y     +  i+G pytI   +
  gi|242399211|ref|YP_002994635.1|  69 KKVVAIALSHGHLDHIGAIAKLAP-HYS----NVPIYGTPYTIKLAK 110
                                       35777789********87644433.444....468********8665 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.3
                                       HHHHHHHHTT---EEEE-- CS
                         PDEase_II 318 elekLkeaenlgvrisIal 336
                                        +++Lke+ + gv+i I++
  gi|242399211|ref|YP_002994635.1| 185 DYKRLKEIGQEGVKILIPE 203
                                       5889999999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (440 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 2936.35
//
Query:       gi|242399212|ref|YP_002994636.1|  [L=341]
Description: Bifunctional short chain isoprenyl diphosphate synthase [Thermococcus sibiricus MM 739]
Scores for 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-72  241.8   0.0    8.3e-72  241.3   0.0    1.2  1  polyprenyl_synt  Polyprenyl synthetase
     0.0067   16.0   0.0       0.45   10.0   0.0    2.2  2  SQS_PSY          Squalene/phytoene synthase
  ------ inclusion threshold ------
      0.083   13.0   0.2       0.17   12.0   0.2    1.5  1  POTRA_TamA_1     POTRA domain TamA domain 1


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 !  241.3   0.0   1.4e-75   8.3e-72       3     241 ..      32     267 ..      30     280 .. 0.93

  Alignments for each domain:
  == domain 1  score: 241.3 bits;  conditional E-value: 1.4e-75
                                       HHHHHHHHHHHSSS--HHHHHHHHHHHHHSCGHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEETTEE-HHHCTC CS
                   polyprenyl_synt   3 lleealeylveagGKrlRpllvllaaealkeeeeelekaavlawivellhaasLvhDDimDdsetRRGqpcahrlvG 79 
                                       ++++a++++  agGKr+Rp +vl + ea++ +    eka  +a++vellh++sLvhDDimD +e RRG+p++h+++G
  gi|242399212|ref|YP_002994636.1|  32 IIYDAARHYPLAGGKRIRPFIVLTSTEAVGGN---PEKAVYAAAAVELLHNYSLVHDDIMDMDEKRRGRPTVHKVWG 105
                                       67778888888*******************44...489*************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHH..STT.HHHHHHHHHHHHHHHHHHHHHHHHTTTTTCCC.SHHHHHHHHHHHTHH CS
                   polyprenyl_synt  80 nklAindgdfllarafellaklf..eks.lellelfsevllqtveGqlldleeekdddlskfsleeyleivkyKTay 153
                                       +++Ai++gd+l++++fe +ak+    ++ +++l+++s+++ +++eGq+ dle e++++++   ++ey++++  KT++
  gi|242399212|ref|YP_002994636.1| 106 VNMAILAGDLLFSKVFEAVAKIPveAEKvVKVLDVISKTSNELCEGQARDLEFENKETVT---IDEYMKMISGKTGA 179
                                       **********************9974446**********************999989999...************** PP

                                       HCHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHSS-TSHHHHTT---HHHHHHHHCT-HH CS
                   polyprenyl_synt 154 lfalpvalaallagasdeelealkdiglelGlaFQiqDDylDlfgdpevlgKpagtDiqegkctlpilkalelaspe 230
                                       l+ +++ ++ l++  ++e ++al+++g+++G+aFQi DD+lDl +d+e+lgKp+g+Di++gk t+++ + le+as+e
  gi|242399212|ref|YP_002994636.1| 180 LIDASATIGGLIGTENNEYIQALSKYGRNVGIAFQIWDDVLDLIADEEKLGKPVGSDIRKGKKTIIVAHFLENASEE 256
                                       **************988989*******************************************************99 PP

                                       HHHHHHHHTTS CS
                   polyprenyl_synt 231 qrkvlkeilgk 241
                                       ++ ++ +++gk
  gi|242399212|ref|YP_002994636.1| 257 DKLKFFKVFGK 267
                                       98777777765 PP

>> SQS_PSY  Squalene/phytoene synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0   7.5e-05      0.45      75     156 ..     129     217 ..      70     231 .. 0.71
   2 !    4.0   0.0    0.0051        31     201     233 ..     299     331 ..     271     338 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 7.5e-05
                                       HHHHHHHHHHT--HHHHHHHHHHTS--SS-....--SHHHHHHHHHHHHHHHHHHHHHHH-S...S-H...HHHHHH CS
                           SQS_PSY  75 ralaqlirtyklpkellleliegmeadlef..tryetlddLeeYcyrvagvVgelclrllgar..rsd...ralaea 144
                                        + +++++  +++++   el+eg ++dlef  ++ +t+d++++      g+++  ++ + g+   +++   +al ++
  gi|242399212|ref|YP_002994636.1| 129 VEAEKVVKVLDVISKTSNELCEGQARDLEFenKETVTIDEYMKMISGKTGALIDASATIGGLIgtENNeyiQALSKY 205
                                       456667777778999999***********95445889***9999999999999999998877533333688999999 PP

                                       HHHHHHHHHHHH CS
                           SQS_PSY 145 arrlGkalQltn 156
                                       +r++G+a+Q+  
  gi|242399212|ref|YP_002994636.1| 206 GRNVGIAFQIWD 217
                                       *********965 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.0051
                                       HHHHHHHHHHHHHHHHHTGGGS.-HHHHHHHHH CS
                           SQS_PSY 201 lrrlaerArelldearellkqlpdrrarpalll 233
                                        ++ a  Ar+l++ea e lk+lp+ +ar  l l
  gi|242399212|ref|YP_002994636.1| 299 TDYAANLARKLIEEAKEALKALPESEARKHLEL 331
                                       457889999************999999987665 PP

>> POTRA_TamA_1  POTRA domain TamA domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   2.8e-05      0.17       5      51 ..     275     320 ..     271     320 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.8e-05
                      POTRA_TamA_1   5 eG.ldgeleeNvrayLsliseeesesserlerllrraeeeirkALral 51 
                                       eG ++++++e+v+++++l+++  s++    ++l r++ ee+++AL+al
  gi|242399212|ref|YP_002994636.1| 275 EGiIEEDIQEEVKKAIDLLKKYGSTDYA--ANLARKLIEEAKEALKAL 320
                                       566778********************99..****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       671  (0.0374254); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); 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: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.50
# Mc/sec: 2049.23
//
Query:       gi|242399213|ref|YP_002994637.1|  [L=631]
Description: archaeal serine protease [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.5e-15   54.7   0.9    1.8e-14   53.8   0.9    1.4  1  Lon_C            Lon protease (S16) C-terminal proteolytic do
    0.00057   19.7   0.2     0.0033   17.2   0.0    2.4  3  ChlI             Subunit ChlI of Mg-chelatase
  ------ inclusion threshold ------
       0.12   12.6   0.1       0.44   10.8   0.1    2.0  1  Ntox28           Bacterial toxin 28
       0.14   12.7   0.8       0.85   10.1   0.2    2.5  2  Glyco_hydro_108  Glycosyl hydrolase 108
       0.16   11.8   1.2        9.7    6.1   0.1    2.5  2  Hypoth_Ymh       Protein of unknown function (Hypoth_ymh)
        1.8    8.3   5.6        1.7    8.3   0.4    2.8  3  DUF745           Protein of unknown function (DUF745)
        3.6    8.3   6.7        6.1    7.5   0.1    3.8  4  DUF4398          Domain of unknown function (DUF4398)
        6.7    6.9  12.2        1.3    9.2   0.3    3.5  3  HEPN             HEPN 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 !   53.8   0.9   8.1e-18   1.8e-14      51     178 ..      57     180 ..      39     204 .. 0.81

  Alignments for each domain:
  == domain 1  score: 53.8 bits;  conditional E-value: 8.1e-18
                                       SS-S-EEE.EES--HH.HHHHHHHHHHHHTSS-GGGSS-SS-TTT-EEEEEE-S-B-GGGGGGGHHHHHHHHHHHHT CS
                             Lon_C  51 pgkgklkl.tGklgdv.mkesaqaalsyvrsraeelgidkevfekkdihihvPeGavPkdGPsaGvtlatalvsllt 125
                                       pg+g++ + t  l +v m+ sa+ a+ +     + l++d   ++k+d+ i v + a    GPsaG t+++ ++++l 
  gi|242399213|ref|YP_002994637.1|  57 PGNGHVYVeTWPLAEVdMQASARLAAQIAG---KVLDVD---MNKYDVFIQVKSDAPIIGGPSAGGTMTVGIIAALE 127
                                       566655432666666666666666654432...223333...35789*********99******************* PP

                                       S--B-TTBEE--EE-TT-BEE--S-HHHHHHHHHHTT-SBEEEEGGGGGGTTT CS
                             Lon_C 126 gkkvrkdvamtGeitLrGrvlpiGGlkekllaakragikkvilPkenekdled 178
                                       g +vrkdv mtG i   G + p+GG+ ek  aa   g k  ++P+  + ++ +
  gi|242399213|ref|YP_002994637.1| 128 GWEVRKDVMMTGMINPDGSIGPVGGILEKASAAYSVGSKLFLIPEGQRIQIIQ 180
                                       ********************************************998877655 PP

>> ChlI  Subunit ChlI of Mg-chelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   1.5e-06    0.0033      65     119 ..     118     172 ..      69     174 .. 0.95
   2 ?   -1.2   0.0       0.8   1.8e+03       1      33 [.     266     298 ..     266     308 .. 0.85
   3 ?   -3.9   0.0       5.4   1.2e+04      12      32 ..     356     377 ..     349     380 .. 0.62

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.5e-06
                              ChlI  65 iAigilaaleqieaeeetlflGeLsldGslrpvkgvlpialaakkegikkvivpk 119
                                       + +gi+aale  e+++++++ G ++ dGs+ pv g+l+ a aa + g k +++p+
  gi|242399213|ref|YP_002994637.1| 118 MTVGIIAALEGWEVRKDVMMTGMINPDGSIGPVGGILEKASAAYSVGSKLFLIPE 172
                                       789**************************************************97 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.8
                              ChlI   1 vevdvskglpkftivGlpdtavkeskervrsal 33 
                                       ve +++  + ++t    +++a +e+k r  +a 
  gi|242399213|ref|YP_002994637.1| 266 VENKLKTSNMGYTTYSYLKEALNEAKSRLDEAK 298
                                       678888888999999999**********98875 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 5.4
                              ChlI  12 ftivGlpd.tavkeskervrsa 32 
                                       +ti G+   +av  s+er+++a
  gi|242399213|ref|YP_002994637.1| 356 LTIRGISMlQAVAASEERIEQA 377
                                       5555543226777788887765 PP

>> Ntox28  Bacterial toxin 28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1    0.0002      0.44      64     103 ..     263     302 ..     245     303 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0002
                            Ntox28  64 rralekelenppdsdteRevLerklkeavleLdrvedfle 103
                                        +++e++l+ ++ + t+   L+++l+ea  +Ld  ++ le
  gi|242399213|ref|YP_002994637.1| 263 YEQVENKLKTSNMGYTTYSYLKEALNEAKSRLDEAKKALE 302
                                       5799*****************************9988765 PP

>> Glyco_hydro_108  Glycosyl hydrolase 108
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.3   2.9e+03      46      61 ..     211     226 ..     190     244 .. 0.74
   2 ?   10.1   0.2   0.00038      0.85      22      75 ..     357     409 ..     340     415 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.3
                                       CS-HHHHHHCHHHHTT CS
                   Glyco_hydro_108  46 altreeaaaiykedYw 61 
                                        l+ +e+++iy + Y+
  gi|242399213|ref|YP_002994637.1| 211 GLEVKEIKDIYDAVYY 226
                                       566789999**99776 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00038
                                       EECTEEHHHCCCTT-BS....-CCCS-HHHHHHCHHHHTTCCCTGGGSS.HHHHH CS
                   Glyco_hydro_108  22 TnkGItkktlralrkekaidadvkaltreeaaaiykedYwkklkldelp.asval 75 
                                       T +GI+   + a+++e+   ++ k+l +e + ++y ++Yw++++  +++ +++++
  gi|242399213|ref|YP_002994637.1| 357 TIRGISMLQAVAASEER--IEQAKSLLKEAWSDYYDANYWDAVSNAAFAyERIQT 409
                                       66666655444443333..3389*******************9988887666665 PP

>> Hypoth_Ymh  Protein of unknown function (Hypoth_ymh)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.2     0.021        47       6      32 ..     379     405 ..     376     424 .. 0.89
   2 ?    6.1   0.1    0.0043       9.7      12      66 ..     469     525 ..     463     558 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.021
                        Hypoth_Ymh   6 eilkaarkellaenyreAvseAikale 32 
                                       ++lk a++++ + ny +Avs+A+ a+e
  gi|242399213|ref|YP_002994637.1| 379 SLLKEAWSDYYDANYWDAVSNAAFAYE 405
                                       578999****************98887 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0043
                        Hypoth_Ymh  12 rkellaenyreAvseAikaledr..vreksgltkdgkeLmqeafsakk.pllaindls 66 
                                       + ++++++y  A+++A++a +++  + + +g++ +++ Lm++  + k+ +++ai +++
  gi|242399213|ref|YP_002994637.1| 469 EGYYQDGKYSAAIFSAMEARIQAeiILDTLGID-NETILMDKLQRMKEnAKVAIAQAQ 525
                                       678*************97644331134444444.688888888777774445555554 PP

>> DUF745  Protein of unknown function (DUF745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0     0.095   2.1e+02     100     127 ..     274     301 ..     250     308 .. 0.67
   2 ?    8.3   0.4   0.00075       1.7     108     164 ..     334     390 ..     327     408 .. 0.88
   3 ?   -2.7   0.2       1.8     4e+03      85      97 ..     510     522 ..     478     527 .. 0.57

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.095
                            DUF745 100 kqaqqqlealkallkaakenlenaeqva 127
                                       +   + ++ lk++l++ak++l++a+++ 
  gi|242399213|ref|YP_002994637.1| 274 NMGYTTYSYLKEALNEAKSRLDEAKKAL 301
                                       4445566667777777777777766654 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00075
                            DUF745 108 alkallkaakenlenaeqvaagaqqelaektqlleaAkkRveeLkkqlkearkdlek 164
                                        l++llk+++++++++e++ ++      +  q ++a+++R+e+ k+ lkea +d+ +
  gi|242399213|ref|YP_002994637.1| 334 DLENLLKNVNDEIKSTENAISNLTIRGISMLQAVAASEERIEQAKSLLKEAWSDYYD 390
                                       5899**************************************************964 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 1.8
                            DUF745  85 lqsseanakaaak 97 
                                       lq+ ++nak+a +
  gi|242399213|ref|YP_002994637.1| 510 LQRMKENAKVAIA 522
                                       2222222222222 PP

>> DUF4398  Domain of unknown function (DUF4398)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.1    0.0027       6.1      23      47 ..     284     308 ..     279     335 .. 0.82
   2 ?    0.7   0.7      0.38   8.5e+02      21      60 ..     368     408 ..     344     421 .. 0.60
   3 ?   -1.4   0.0       1.6   3.6e+03      35      61 ..     467     493 ..     457     497 .. 0.83
   4 ?   -0.4   0.0      0.84   1.9e+03       4      17 ..     515     528 ..     510     541 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0027
                           DUF4398  23 paeleeAreaLaqAeaamaekdyee 47 
                                       +++l+eA+  L++A++a ++++y +
  gi|242399213|ref|YP_002994637.1| 284 KEALNEAKSRLDEAKKALEDGRYYT 308
                                       678**************99999965 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.38
                           DUF4398  21 yApae.leeAreaLaqAeaamaekdyeeAdhlaylAerdae 60 
                                        A++e  e+A+  L++A ++  +++y +A   a  A ++++
  gi|242399213|ref|YP_002994637.1| 368 AASEErIEQAKSLLKEAWSDYYDANYWDAVSNAAFAYERIQ 408
                                       33344455555555555554445555555555555555555 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 1.6
                           DUF4398  35 qAeaamaekdyeeAdhlaylAerdael 61 
                                       ++e   ++++y++A   a +A+ +ae+
  gi|242399213|ref|YP_002994637.1| 467 EGEGYYQDGKYSAAIFSAMEARIQAEI 493
                                       5566667899999999999**999997 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 0.84
                           DUF4398   4 adAraaleaAraag 17 
                                       ++A+ a+++A+ +g
  gi|242399213|ref|YP_002994637.1| 515 ENAKVAIAQAQKEG 528
                                       46777777777776 PP

>> HEPN  HEPN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.3   0.00058       1.3       3      28 ..     285     310 ..     283     317 .. 0.86
   2 ?   -3.3   0.0       4.2   9.4e+03      54      71 ..     333     350 ..     328     357 .. 0.69
   3 ?    1.2   4.2      0.17   3.9e+02       2      41 ..     371     410 ..     370     497 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00058
                                       HHHHHHHHHHHHHHHHHHTT-HHHHH CS
                              HEPN   3 ewlrrAeedleaAellleegdydlac 28 
                                       e l++A+++l++A+++le+g+y  ++
  gi|242399213|ref|YP_002994637.1| 285 EALNEAKSRLDEAKKALEDGRYYTTL 310
                                       6789******************8876 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 4.2
                                       CHHHHHHCCHHHT...-H CS
                              HEPN  54 hdlreLleelkkelkese 71 
                                        dl  Ll+++ +e+k+ e
  gi|242399213|ref|YP_002994637.1| 333 ADLENLLKNVNDEIKSTE 350
                                       688889998888887433 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.17
                                       HHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH CS
                              HEPN   2 eewlrrAeedleaAellleegdydlacfhaqqaaekalKA 41 
                                       ee +++A++ l++A  ++ +  y +a+++a  a e +  A
  gi|242399213|ref|YP_002994637.1| 371 EERIEQAKSLLKEAWSDYYDANYWDAVSNAAFAYERIQTA 410
                                       7899**********************99998888766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (631 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1267  (0.0706676); expected 358.6 (0.02)
Passed bias filter:                      765  (0.0426683); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.77u 0.32s 00:00:01.09 Elapsed: 00:00:00.49
# Mc/sec: 3835.76
//
Query:       gi|242399214|ref|YP_002994638.1|  [L=375]
Description: amino acid racemase [Thermococcus sibiricus MM 739]
Scores for complete 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    2.3e-29  102.6   0.0    1.1  1  Ala_racemase_N  Alanine racemase, N-terminal domain
    2.8e-10   40.7   0.0      8e-10   39.3   0.0    1.8  2  D-ser_dehydrat  Putative serine dehydratase domain
  ------ inclusion threshold ------
      0.011   15.4   0.0       0.47   10.1   0.0    2.3  1  CbiC            Precorrin-8X methylmutase


Domain annotation for each model (and alignments):
>> Ala_racemase_N  Alanine racemase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.6   0.0   3.8e-33   2.3e-29       1     218 [.      14     242 ..      14     243 .. 0.91

  Alignments for each domain:
  == domain 1  score: 102.6 bits;  conditional E-value: 3.8e-33
                                       EEHHHHHHHHHHHHHHS.CTTSEEEEE-HHHHHTTHHHHHHHHHHHTTESEEEESSHHHHHHHHHTTSCSEEEEESC CS
                    Ala_racemase_N   1 idldalrhNlrrlrala.gpgaklmavvKanayghgavevaralaeggadgfgvatleEalelreagitapilvleg 76 
                                       +dld+l+ N++ +++ a +++++l+++vK+    h  v va  ++++ga gf + t++Ea++l+eag+ + +++  +
  gi|242399214|ref|YP_002994638.1|  14 VDLDKLEFNIKEVAKEAkKHNKQLFPMVKT----HKSVYVANLQKKAGAGGFLCGTIDEAEALAEAGLGETLMLAYP 86 
                                       79***************777999*******....99999999999999*******************9999999988 PP

                                       .STGGGHHHHHH.....TTEEEEESSHHHHHHHHHHHHHTTS-EEEEEEBESSSSSSSBSCHHHHHHHHHHHHTTTE CS
                    Ala_racemase_N  77 .fspeelaalae.....ydltvtvdsleqlealaaaareagkplrvhlkidtgmgRlGftpeeleellealaalpgl 147
                                        +++e ++++a+      ++   +ds + +e l+a +++ g +++  + +dtg+ R G++pe++  +++++++ ++l
  gi|242399214|ref|YP_002994638.1|  87 iMDKENFSRVARliedgLRVIFRIDSVDAAEFLDAELKKRGLRAEFTIIVDTGGVRYGIEPEKVGNFAKRVKEYSNL 163
                                       88*******999999977999********************************99********************** PP

                                       EEEEEE-S-SST......TSTSHHHHHHHHHHHHHHHHHHHTTGGGSEEEEESHHHHHHSG.GG.TTEEEESGGGGT CS
                    Ala_racemase_N 148 rleglmtHfasa......depdeeteaqlarfeealeelekaglrppvvslanSaaillaa.ah.fdmvRpGialyG 216
                                       +++g++tH+++       +e ++ +e+  + ++ al  l++ +++p++v +++++++ + +  + ++++ pG ++y 
  gi|242399214|ref|YP_002994638.1| 164 EFVGITTHPGHVynatnpKEVKAIAEQATKGMKIALRSLRQWNMNPEIVGIGSTPTFRFDIeEEiYTHLFPGNYVYY 240
                                       ***********98775543333445557888899999999989*****************53448********9997 PP

                                       -S CS
                    Ala_racemase_N 217 ls 218
                                       ++
  gi|242399214|ref|YP_002994638.1| 241 DR 242
                                       75 PP

>> D-ser_dehydrat  Putative serine dehydratase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.1   6.9e+03      17      48 ..     134     163 ..     124     195 .. 0.61
   2 !   39.3   0.0   1.3e-13     8e-10       1      94 [.     257     349 ..     257     351 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.1
                                       EEES--HHHH-S-SS--BT-EEE-TTSEEEEB CS
                    D-ser_dehydrat  17 alvdaGskalsldssgpgfgkvvagleegwvv 48 
                                       ++vd G    + +    ++g+ ++  +e + +
  gi|242399214|ref|YP_002994638.1| 134 IIVDTGGVRYGIEP--EKVGNFAKRVKEYSNL 163
                                       68888888888883..2233444333333333 PP

  == domain 2  score: 39.3 bits;  conditional E-value: 1.3e-13
                                       -EEEEEEEEEEETTTT...EEES--HHHH-S-S.S--B.T-EEE-TTSEEEEB-..EE-SS-EEEE--TT-GGGS-T CS
                    D-ser_dehydrat   1 AlavlatVvSrptarr...alvdaGskalslds.sgpg.fgkvvagleegwvvsvrrlsdEhgiltleeesaddlrv 72 
                                       Al++  tV S  ++ +    l++aGs+ +++   ++ g fg++v+   +++++    ls+E g +++++e  +d++v
  gi|242399214|ref|YP_002994638.1| 257 ALTIFVTVTSIAERCGkrfGLINAGSLYFDKRGhEILGsFGQAVEY--PRAKLI--GLSQEVGKIDVTNE--PDVKV 327
                                       89999*****9997666679************87888889999955..566644..9**********966..8**** PP

                                       T-EEEEE-S-HHHHHTT-SEEE CS
                    D-ser_dehydrat  73 GdvvrlipnHaCptvnlhdayv 94 
                                       G+++ +ipnH+C   n  ++++
  gi|242399214|ref|YP_002994638.1| 328 GEKINVIPNHSCFSNNATSYII 349
                                       *************999888775 PP

>> CbiC  Precorrin-8X methylmutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   7.8e-05      0.47      56     135 ..     127     224 ..     111     234 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 7.8e-05
                                       HHHCT-EEEESSHHHHCCS-HHHHHTT..................C-EEEECTC-HHHHHHHHHHTS-HHHHHHHHH CS
                              CbiC  56 alkagapivtDvemvkaGitkkrlekl..................gnevlclladpevaelakekgitrsaaameka 114
                                        l+a+ +i++D+  v+ Gi+ ++  ++                    +v+ +++ +ev+++a++  +   + a++ +
  gi|242399214|ref|YP_002994638.1| 127 GLRAEFTIIVDTGGVRYGIEPEKVGNFakrvkeysnlefvgitthPGHVYNATNPKEVKAIAEQATK-GMKIALRSL 202
                                       5888999999999999999999888885555666655555555444556666666666655444333.334455555 PP

                                       HH.CTTTCEEEESS-HHHHHHH CS
                              CbiC 115 ae.elegaivviGnAPtALlel 135
                                       ++ +++ +iv iG+ Pt  + +
  gi|242399214|ref|YP_002994638.1| 203 RQwNMNPEIVGIGSTPTFRFDI 224
                                       5567788899999998876665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.38
# Mc/sec: 2936.64
//
Query:       gi|242399215|ref|YP_002994639.1|  [L=232]
Description: NAD(P)H-flavin oxidoreductase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.9e-32  111.7   0.0    4.6e-32  111.4   0.0    1.1  1  Nitroreductase  Nitroreductase family
    1.4e-07   31.3   0.1      0.022   14.3   0.0    2.5  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 !  111.4   0.0   5.1e-36   4.6e-32       1     170 []      58     231 ..      58     231 .. 0.94

  Alignments for each domain:
  == domain 1  score: 111.4 bits;  conditional E-value: 5.1e-36
                                       HHH--B---B-S----HHHHHHHHHHH........HTS--GGG---EEEEEE..-CCCH....HHHHHHHHHHHHHH CS
                    Nitroreductase   1 irkRrSiRkFddepvpkeelekileaa........rraPsagnlqpwrfvvv.qdkelr....yklaeaalelllka 64 
                                       i+kR+SiR+++++p+++e+l+++l+a         r aPsag ++p++++vv  + e +    y +++  ++ +l++
  gi|242399215|ref|YP_002994639.1|  58 IAKRKSIRTYKNQPLKLEDLSQLLWACqgithdkkRSAPSAGATYPFEIFVVvGSVERLkpgiYHYNPFEHSITLVK 134
                                       79****************************9999999***********999976666668***88888888888888 PP

                                       HTT-SS-GGGGGGHHHHHHHHHHHHSSEEEEE---TTS---HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE- CS
                    Nitroreductase  65 eaqaelaqryrkeelklkaqkalagapvlivivatldkserkaaerayryalldagaaaqnllLaAtalGlgscpig 141
                                       e + ++  +++     ++ qk++++a++ i++va++++ ++ ++er+ ry +++ag++ qn++L Atal+lg++ ig
  gi|242399215|ref|YP_002994639.1| 135 EGDFRKELQKA-----ALDQKWVGDAAIDIILVAFYERTTKVYGERGIRYVHMEAGHIGQNIYLQATALNLGTVAIG 206
                                       88888888877.....************************************************************* PP

                                       GGGGGHHHHHHHHT-S..SEEEEEEEEE- CS
                    Nitroreductase 142 gfdeaaeevrkllglpdeeeivvliavGy 170
                                       +f++++  v++++g      ++++++vG+
  gi|242399215|ref|YP_002994639.1| 207 AFYDEE--VAEIIGTN--GAPLYIFPVGR 231
                                       ******..********..9********95 PP

>> TM1586_NiRdase  Putative TM nitroreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   2.6e-06     0.023       3      37 ..      55      89 ..      53      97 .. 0.85
   2 ?   -2.0   0.0      0.25   2.2e+03     168     189 ..      93     113 ..      90     131 .. 0.71
   3 !   14.3   0.0   2.5e-06     0.022      73     118 ..     172     218 ..     166     231 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.6e-06
                                      HHHHHH--B---B--S---HHHHHHHHH-----S. CS
                    TM1586_NiRdase  3 yeaiekRhsvRkYkdealeeelleelkeaieeink 37
                                       eai kR+s+R+Yk+++l+ e l++l  a + i +
  gi|242399215|ref|YP_002994639.1| 55 EEAIAKRKSIRTYKNQPLKLEDLSQLLWACQGITH 89
                                      69*****************9999999877777665 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.25
                                       HTS--GGG----EEE.E-SSEE CS
                    TM1586_NiRdase 168 rlAPsAlNqqpwrfelkdddei 189
                                       r APsA  + p+++ ++  +++
  gi|242399215|ref|YP_002994639.1|  93 RSAPSAGATYPFEIFVVV-GSV 113
                                       679999999999876555.344 PP

  == domain 3  score: 14.3 bits;  conditional E-value: 2.5e-06
                                       ---SS.HHHHHHHHHHHHHHHHHHHHTT-EEEEES--SST....... CS
                    TM1586_NiRdase  73 vgekk.edleekaGYygeqlvLkltalGlgtcWvggtykkkkakvel 118
                                       +ge   + ++++aG +g+++ L++tal+lgt  +g+ y+++ a++  
  gi|242399215|ref|YP_002994639.1| 172 YGERGiRYVHMEAGHIGQNIYLQATALNLGTVAIGAFYDEEVAEIIG 218
                                       55555566789************************999997765554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 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:                        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: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1480.60
//
Query:       gi|242399216|ref|YP_002994640.1|  [L=59]
Description: hypothetical protein TSIB_1237 [Thermococcus sibiricus MM 739]
Scores for complete 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   22.4   3.0    0.00012   22.3   3.0    1.0  1  DUF4079         Protein of unknown function (DUF4079)
  ------ inclusion threshold ------
      0.014   15.9   7.2      0.018   15.4   7.2    1.1  1  DUF2768         Protein of unknown function (DUF2768)
      0.016   15.8   5.0      0.027   15.0   5.1    1.4  1  DUF4405         Domain of unknown function (DUF4405)
      0.048   12.5   2.5      0.054   12.3   2.5    1.0  1  LptF_LptG       Lipopolysaccharide export system permease Lpt
      0.073   13.2   4.2       0.12   12.5   4.2    1.4  1  Cytochrom_B561  Eukaryotic cytochrome b561
       0.29    9.8   7.4       0.32    9.7   7.4    1.1  1  DUF2206         Predicted membrane protein (DUF2206)


Domain annotation for each model (and alignments):
>> DUF4079  Protein of unknown function (DUF4079)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   3.0     4e-08   0.00012      83     131 ..       5      55 ..       1      57 [. 0.86

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 4e-08
                           DUF4079  83 sHlyaGlavvvLlalsaalvpeiqkgks..taRtlHialnvlalllfawqa 131
                                        H+  G +  +L+ ls+ +   i+ +k+   + +lHi++ +la +l++w +
  gi|242399216|ref|YP_002994640.1|   5 DHYTLGYITFGLMNLSMLSGAFIFLSKKkgLWTKLHILISILAYILMVWTI 55 
                                       6****************99999986666468*****************987 PP

>> DUF2768  Protein of unknown function (DUF2768)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   7.2   6.1e-06     0.018       3      46 ..      11      54 ..      10      58 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 6.1e-06
                           DUF2768  3 wiSlasiglmflsvlliilsreklknkflkiivaliAyilllvs 46
                                      +i ++ + l +ls  +i+ls++k     l i+++++Ayil++  
  gi|242399216|ref|YP_002994640.1| 11 YITFGLMNLSMLSGAFIFLSKKKGLWTKLHILISILAYILMVWT 54
                                      79999999999999*********99889*************865 PP

>> DUF4405  Domain of unknown function (DUF4405)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   5.1   9.1e-06     0.027       6      60 ..      13      53 ..       8      57 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 9.1e-06
                           DUF4405  6 lllsflvlaiSGillsfavlpsgrgaywaflglskhqwrdiHeilgllflilvvl 60
                                      ++ ++ + ++SG  ++ +               +k+ w+++H+++++l  il+v+
  gi|242399216|ref|YP_002994640.1| 13 TFGLMNLSMLSGAFIFLS--------------KKKGLWTKLHILISILAYILMVW 53
                                      566677777777777744..............38999****************97 PP

>> LptF_LptG  Lipopolysaccharide export system permease LptF/LptG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   2.5   1.8e-05     0.054     280     320 ..      14      57 ..      11      59 .] 0.91

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.8e-05
                         LptF_LptG 280 laclvfaliaaplglvkrrggrglr..lliaillfvl.yyvlls 320
                                       +  + + +++ ++ + +++ g++++  +li+il ++l ++++++
  gi|242399216|ref|YP_002994640.1|  14 FGLMNLSMLSGAFIFLSKKKGLWTKlhILISILAYILmVWTIWI 57 
                                       6678899******************************9999987 PP

>> Cytochrom_B561  Eukaryotic cytochrome b561
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   4.2   4.1e-05      0.12      72     126 ..       6      55 ..       2      58 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.1e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHTSS---HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    Cytochrom_B561  72 HswlGlvtvilfllqlvlGfvlfllpklskklralllplHvllGlvifvlaivta 126
                                       H  lG +t+ l+ l++++G ++fl      k + l  +lH+l+ +++++l + t+
  gi|242399216|ref|YP_002994640.1|   6 HYTLGYITFGLMNLSMLSGAFIFLS-----KKKGLWTKLHILISILAYILMVWTI 55 
                                       7789999999999999999999992.....2345788999999999999998886 PP

>> DUF2206  Predicted membrane protein (DUF2206)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   7.4   0.00011      0.32      13      64 ..       3      53 ..       1      58 [. 0.67

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00011
                           DUF2206 13 vvSHYglsyivllllalayllliilrlyikedksqilnftyvlifv..vlalaW 64
                                      v+ HY+l+yi++ l+ l++l   ++  ++k  k+ + +  ++li +   + ++W
  gi|242399216|ref|YP_002994640.1|  3 VLDHYTLGYITFGLMNLSMLSGAFIF-LSK--KKGLWTKLHILISIlaYILMVW 53
                                      889****************9999888.344..4444444444444400455556 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       753  (0.041999); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 411.40
//
Query:       gi|242399217|ref|YP_002994641.1|  [L=122]
Description: carbohydrate binding protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-16   59.9   0.1    2.3e-16   59.3   0.1    1.3  1  Cupin_2          Cupin domain
    7.9e-09   35.5   0.1      1e-08   35.1   0.1    1.1  1  AraC_binding     AraC-like ligand binding domain
    6.9e-06   25.7   0.0      8e-06   25.5   0.0    1.1  1  Cupin_1          Cupin
    1.6e-05   24.9   0.1    1.7e-05   24.8   0.1    1.1  1  MannoseP_isomer  Mannose-6-phosphate isomerase
     0.0011   18.6   0.0     0.0016   18.1   0.0    1.3  1  Cupin_3          Protein of unknown function (DUF861)
     0.0012   18.5   0.1     0.0021   17.8   0.1    1.4  1  Auxin_BP         Auxin binding protein
     0.0025   18.0   0.0     0.0028   17.8   0.0    1.0  1  Ectoine_synth    Ectoine synthase
  ------ inclusion threshold ------
      0.051   13.0   0.0      0.066   12.7   0.0    1.2  1  PCO_ADO          PCO_ADO
       0.13   12.2   0.3       0.18   11.7   0.3    1.4  1  Cupin_7          ChrR Cupin-like domain


Domain annotation for each model (and alignments):
>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.3   0.1   1.2e-19   2.3e-16       2      70 ..      41     108 ..      40     109 .. 0.96

  Alignments for each domain:
  == domain 1  score: 59.3 bits;  conditional E-value: 1.2e-19
                                       EEEEETTEEEEEECSSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEEEE-SSS-EEEEEE CS
                           Cupin_2   2 lvelppGesapshrHpgedeffyVleGegeltvdgeeveleaGdsvyfpagtpHrfrNtgdeparllvv 70 
                                       ++++++G+++p h H++e + +++++Geg +t + +++++ +G ++y+p+++pH+++N+++e +++l++
  gi|242399217|ref|YP_002994641.1|  41 YFVIKKGGKIPIHQHDWE-HEIFIVKGEGYITNGRKTIKVVPGSFLYVPPNEPHAYENPESETFEFLCL 108
                                       6789**************.***********************************************996 PP

>> AraC_binding  AraC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.1   5.2e-12     1e-08      18      74 ..      52     108 ..      42     113 .. 0.91

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 5.2e-12
                                       EETT-SEEEEEEEEE-EEEEETTEEEEE-TT-EEEE-TTS-EEEEE-TTSEEEEEEE CS
                      AraC_binding  18 phvhdeyvihyvteGtgrlrlngrtydlgpGdlfLlppgepHdyesdsedgweyrwl 74 
                                        h+hd+ + + +++G+g+++ +++t  + pG+ + +pp+epH ye  +++ +e+ +l
  gi|242399217|ref|YP_002994641.1|  52 IHQHDWEHEIFIVKGEGYITNGRKTIKVVPGSFLYVPPNEPHAYENPESETFEFLCL 108
                                       49***88889999********************************999998887766 PP

>> Cupin_1  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0     4e-09     8e-06      34     114 ..      38     109 ..      11     118 .. 0.82

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 4e-09
                                       EEEEEEE.TTEEEEEEEESSS-EEEEEEESEEEEEEEETTSS.EEEEEEEETTEEEEE-TT-EEEEEEESSSSEEEE CS
                           Cupin_1  34 saarvdlepgglllPhyhpnateiayvlqGegrvgfvvpgngnrdfhkklreGdvfvvPaglvhfqynsgdepavai 110
                                       ++  +++++gg +++h h + +ei ++++Geg+   +++g+     + k+ +G  ++vP++ +h+  n + ++++++
  gi|242399217|ref|YP_002994641.1|  38 AMRYFVIKKGGKIPIHQHDWEHEI-FIVKGEGY---ITNGR----KTIKVVPGSFLYVPPNEPHAYENPE-SETFEF 105
                                       44456669**********888887.5679****...77775....334588******************7.****** PP

                                       EEEE CS
                           Cupin_1 111 vvfd 114
                                        ++ 
  gi|242399217|ref|YP_002994641.1| 106 LCLI 109
                                       9975 PP

>> MannoseP_isomer  Mannose-6-phosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.1   8.5e-09   1.7e-05      60     131 ..      34     104 ..       5     115 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 8.5e-09
                   MannoseP_isomer  60 geryqvkritvkPgeklslqkhhhraehWvvvkGtakvtvddevlllkenestyiplgaihrlenpGkiple 131
                                       ++++ ++  ++k g k+ +++h    e + +vkG   +t++ +++++      y+p ++ h+ enp   ++e
  gi|242399217|ref|YP_002994641.1|  34 AKNFAMRYFVIKKGGKIPIHQHDWEHEIF-IVKGEGYITNGRKTIKVVPGSFLYVPPNEPHAYENPESETFE 104
                                       57899***********9987776655544.58**********************************887665 PP

>> Cupin_3  Protein of unknown function (DUF861)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   8.1e-07    0.0016      10      60 ..      41      91 ..      33     106 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 8.1e-07
                                      EEEEEECEEEEECESSEEEE.EEEECEEEEEETTTEEEEEETTEEEEE-TTE CS
                           Cupin_3 10 giwectpGkfrltyeedEfc.yileGevkvtpeggetvelraGDlvvlpkgl 60
                                      + +  + Gk + +   +E+  +i++Ge  +t  g +t+++ +G+++++p++ 
  gi|242399217|ref|YP_002994641.1| 41 YFVIKKGGKIPIHQHDWEHEiFIVKGEGYITN-GRKTIKVVPGSFLYVPPNE 91
                                      556678899999999999877***********.****************976 PP

>> Auxin_BP  Auxin binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1     1e-06    0.0021      15     103 ..       6      87 ..       1     113 [. 0.71

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1e-06
                                       GGGS--B-TT-TTEEEEEEE-HH..HH--SSEEEEEEEE-TT-B--EEEESS-EEEEEEE--EEEEE--SSSSS--S CS
                          Auxin_BP  15 iselpqdnygreglshitvagsv..lhgmkevevwlqtlapgsrtpihrhsceevfvvlkgkgtlylasssskypgk 89 
                                         ++ +++  +eg+  +t+   +  + g k+  +    +  g + pih+h  e  + ++kg+g +  +  +      
  gi|242399217|ref|YP_002994641.1|   6 YQDVEEKEVTMEGVENTTIRWLIspKIGAKNFAMRYFVIKKGGKIPIHQHDWEHEIFIVKGEGYITNGRKT------ 76 
                                       566777788889999999976552267999**********************9888888****87766333...... PP

                                       -EEEEE-TTEEEEE CS
                          Auxin_BP  90 pqelpifanstlsi 103
                                          +++ + s l +
  gi|242399217|ref|YP_002994641.1|  77 ---IKVVPGSFLYV 87 
                                       ...33333344444 PP

>> Ectoine_synth  Ectoine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   1.4e-06    0.0028       1     105 [.       1     107 [.       1     116 [. 0.81

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.4e-06
                                       -EEEEHHHHTTSTTEEEETTEEEEEEE-GGGSSS...SEEEEEEE-TT--EEEE-TT-EEEEEEEE--EEEEETTT- CS
                     Ectoine_synth   1 mivrtleeiekterevksenweskRlllkddgmG...fslhettikagtetelkYknHleavycieGegeveeledg 74 
                                       m+v +++++e+ e ++++ + +  R l+   ++G   f++   +ik+g +  ++ ++    +++++Geg +++    
  gi|242399217|ref|YP_002994641.1|   1 MFVSHYQDVEEKEVTMEGVENTTIRWLISP-KIGaknFAMRYFVIKKGGKIPIHQHDWEHEIFIVKGEGYITNG--R 74 
                                       8999******99999999999999988854.344344*****************9998889**********986..5 PP

                                       -EEEE-TTEEEEETTT-EEEEEESS..-EEEEE CS
                     Ectoine_synth  75 evyeikpgtlYlldkhdkHllrakk..elrlvc 105
                                       ++ ++ pg++  +  ++ H  +  +   ++ +c
  gi|242399217|ref|YP_002994641.1|  75 KTIKVVPGSFLYVPPNEPHAYENPEseTFEFLC 107
                                       889999998877777888876654334566666 PP

>> PCO_ADO  PCO_ADO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.3e-05     0.066      42      62 ..      35      55 ..       5      59 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.3e-05
                           PCO_ADO 42 dsfslgvFvlppgaviPLHdH 62
                                      ++f++  Fv+++g  iP+H H
  gi|242399217|ref|YP_002994641.1| 35 KNFAMRYFVIKKGGKIPIHQH 55
                                      79******************9 PP

>> Cupin_7  ChrR Cupin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.3   9.2e-05      0.18      31      78 ..      44      95 ..      16     112 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.2e-05
                                      E-TTEE---EE-TT-EEEEEEEEEEEETTEEE....ETTEEEEE-TT-EE-- CS
                           Cupin_7 31 yapgsafsahkHpggeeilVLeGvfsdeegdy....paGsylrnppgsshap 78
                                      +++g + + h+H+   ei++++G+    +g+       Gs+l  pp++ ha 
  gi|242399217|ref|YP_002994641.1| 44 IKKGGKIPIHQHDWEHEIFIVKGEGYITNGRKtikvVPGSFLYVPPNEPHAY 95
                                      688999*****************97777776434446899999999988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.33s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 692.45
//
Query:       gi|242399218|ref|YP_002994642.1|  [L=427]
Description: purine permease [Thermococcus sibiricus MM 739]
Scores for complete 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-97  324.9  38.1    6.7e-97  324.6  38.1    1.0  1  Xan_ur_permease  Permease family


Domain annotation for each model (and alignments):
>> Xan_ur_permease  Permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  324.6  38.1  3.7e-101   6.7e-97       2     387 ..      17     393 ..      16     395 .. 0.97

  Alignments for each domain:
  == domain 1  score: 324.6 bits;  conditional E-value: 3.7e-101
                                       HHHHHHHHHHHHHHHHHHHHHHTTTS-..........H.HHHHHHHHHHHHHHHHHTTT-----EEE-GGGHHHHHG CS
                   Xan_ur_permease   2 qllllglQhllamfaalvvvPllvgdalgl.aeelrqlisatllasGiatllqllifgirlpillgssfafvtalmi 77 
                                       +++llg+Qh+lamf+a+v+vPl+vg a+gl  ++++ li++ lla Giatllq++ +g+r pi++gssfaf++  +i
  gi|242399218|ref|YP_002994642.1|  17 KVILLGFQHVLAMFGATVTVPLVVGTAIGLnGRDIALLIQVVLLAMGIATLLQTT-IGSRYPIVQGSSFAFIP-GLI 91 
                                       789************************99999***********************.*****************.*** PP

                                       GG-....HHHHHHHHHHHHHHHHHHHHHHHTT-SH.HHHHH--HHHHHHHHHHHHHHHHHHHHHHTTSS-..BTT.B CS
                   Xan_ur_permease  78 alGsaedieialagllgallvagvlfilisltglrgrlarlipPvvtgpvvlliGlslaqiavkkvgggwaaveglt 154
                                        +G+    + +l+++ gal++ g++  +i+++g+ g+l +l+ Pvvtg++++liG+sla +avk   +  a+ +g  
  gi|242399218|ref|YP_002994642.1|  92 SIGN----NLGLPAVEGALIIGGLIEATIGTFGIIGKLKKLFSPVVTGVTIMLIGFSLAHVAVKYTFNFFADPNG-- 162
                                       ***6....*************************************************************955555.. PP

                                       ---HHHHHHHHHHHHHHHHHHHSSSTTTTTHHHHHHHHHHHHHHHHHHHTTSSHHHHS-SS-----------HH..H CS
                   Xan_ur_permease 155 vvslkllllavvvllvilllsvflkglfsqlpiLigiiagwllalfmgivnlspevseapwfqlpsplkfgtplfnl 231
                                       +  +k + +a+++ ++++ ++   k  ++ +p+  g ++g+ +++++g+ +++  v+e+p++ +p+pl++gtp fn+
  gi|242399218|ref|YP_002994642.1| 163 TSIPKAFFIALITFATTMYIALKGKRSLRAMPVIAGAFVGYTASIILGMADFTL-VRELPLINIPKPLPWGTPVFNA 238
                                       999***************************************************.********************** PP

                                       .HHHHTHHH.HHHHHHHHHHHHHHHHHHTS-TIIIIIHHHHHHHHHHHHHHHHHHT---EEE-HHHHHHHHHHTB-- CS
                   Xan_ur_permease 232 gliltvlavalvavvesvGdiravakvvgrslkpkpdlrralladGlatllsgllGalpvttyaeniGvvaltkvas 308
                                        +i+t+l+ ++v+++esvGd++a++ +++ +++ +++++r+++ +Gla+ l+g+lGa ++t+y+eniG+valtk+as
  gi|242399218|ref|YP_002994642.1| 239 TAIITLLFAFMVSIIESVGDYHAISAIAEAPIT-NKNINRGIMSEGLACSLAGILGACGTTSYSENIGLVALTKIAS 314
                                       *****************************9999.******************************************* PP

                                       HHHHHHHHHHHHHHT--HHHHHHHTTS-HHHHHHHHHHHHHHHHHHHHHHHHHTTS-.SHHHHHHHHHHHHHHHH-- CS
                   Xan_ur_permease 309 rrvmvtagvilillglipklaallssIPepvlgGvllvvfgmiaasgvsnlqtvdld.sarnllivavslvlGlgva 384
                                       r v++++gvil+ll++ipk++  l+s P pvlgG +++++gmi ++g++ +++ +++ + rn++i+a +l++Glg++
  gi|242399218|ref|YP_002994642.1| 315 RQVVQVGGVILVLLAMIPKFSGILASMPHPVLGGLTIALYGMISVTGLRLIKD-KVElNDRNMFIIASALIIGLGAP 390
                                       ************************************************97765.45558*****************9 PP

                                       --- CS
                   Xan_ur_permease 385 tvp 387
                                       ++p
  gi|242399218|ref|YP_002994642.1| 391 QLP 393
                                       987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       740  (0.0412739); 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:                         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: 0.65u 0.33s 00:00:00.98 Elapsed: 00:00:00.52
# Mc/sec: 2469.75
//
Query:       gi|242399219|ref|YP_002994643.1|  [L=232]
Description: Probable uracil phosphoribosyltransferase [Thermococcus sibiricus MM 739]
Scores for complete 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-50  170.7   0.0    3.2e-50  170.5   0.0    1.0  1  UPRTase       Uracil phosphoribosyltransferase
    4.1e-10   39.4   0.7    5.4e-10   39.0   0.7    1.2  1  Pribosyltran  Phosphoribosyl transferase domain
  ------ inclusion threshold ------
      0.094   12.2   0.0       0.23   10.9   0.0    1.6  2  PRTase_2      Phosphoribosyl transferase


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 !  170.5   0.0   5.3e-54   3.2e-50       3     207 .]      15     218 ..      13     218 .. 0.96

  Alignments for each domain:
  == domain 1  score: 170.5 bits;  conditional E-value: 5.3e-54
                           UPRTase   3 shpllkakltilRdastsrkdfrelvdriarllaeealsallpveevtvttplgkeysgelldeekialVpilRaGe 79 
                                       ++p l  +lt lR+++t++  fr+ + +++r++++e+++  + ve+ +++tpl++++   ++d++++++V +lRa  
  gi|242399219|ref|YP_002994643.1|  15 DSPYLMEILTELRNKDTDSIAFRKGLVKLGRYMGYEIIKT-MDVEKIKIETPLEETEGIIVKDRKNVVIVTVLRAAV 90 
                                       5788999********************************8.************************************ PP

                           UPRTase  80 gmeealrellpearvghlglqree.etlepveyynkLPkkiaertvlllDpviaTGgsaaaaiqlLkergvgeekIl 155
                                       +++e+l +++ +ar+g +   r +  + e ++ y k+P+   e+tv++ Dp+iaTG++++++++ +k+ g + ++ +
  gi|242399219|ref|YP_002994643.1|  91 PLMEGLVKVFEHARIGIVSASRGKaPKFEIEMNYVKIPQITPEDTVIVADPMIATGSTLITVMEEIKKYGTP-KRLI 166
                                       ********************9977246788899***********************************9975.89** PP

                           UPRTase 156 vlsvlaseegvkrlaeefpkvkvvtaavDeeldekgyivpGlGDfGDRlFgT 207
                                       vl +la++eg++r+ e+fp+ +++++++D++l+ kgyi+pGlGD+GDR Fg+
  gi|242399219|ref|YP_002994643.1| 167 VLGILAAPEGINRIKEKFPEAEIFVTQIDRGLNSKGYILPGLGDAGDRAFGA 218
                                       **************************************************96 PP

>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   0.7   9.1e-14   5.4e-10      27     130 ..      76     177 ..      50     195 .. 0.80

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 9.1e-14
                                       -GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........EE----TTSEEEEE-SEESSSHHH CS
                      Pribosyltran  27 ngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdesrlledpagkkVliVDDildtGgTl 103
                                       ++k++v+v+++r +vp+   l + +e     + + ++ + ++ e+  + ++    + ++   +V++ D +++tG+Tl
  gi|242399219|ref|YP_002994643.1|  76 DRKNVVIVTVLRAAVPLMEGLVKVFEHARIGIVSASRGKAPKFEIEMNYVK---IPQITPEDTVIVADPMIATGSTL 149
                                       59***********************87766666666655555555555554...8999******************* PP

                                       HHHHHHHHCC-.BSEEEEEEEEE-HHHH CS
                      Pribosyltran 104 laalelLkekg.peevriavlvdkpate 130
                                       + ++e +k++g p+++++  +++ p++ 
  gi|242399219|ref|YP_002994643.1| 150 ITVMEEIKKYGtPKRLIVLGILAAPEGI 177
                                       *****88887747788887777766665 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.27   1.6e+03      50      86 ..      75     112 ..      42     124 .. 0.64
   2 ?   10.9   0.0   3.9e-05      0.23     118     161 ..     130     173 ..     115     195 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.27
                          PRTase_2  50 elpepvlvigfAEtAtaLghgvadal.eeealylhtTR 86 
                                       + +++v+++ +  +A+ L +g+++ + ++++ ++ + R
  gi|242399219|ref|YP_002994643.1|  75 KDRKNVVIVTVLRAAVPLMEGLVKVFeHARIGIVSASR 112
                                       44566777777777777777777777333555555555 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 3.9e-05
                          PRTase_2 118 laaakelvLvDDEistGktalnliralqeklprkryvvvslvdw 161
                                       ++ ++++++ D  i+tG+t++ +++++++  + kr++v+ ++  
  gi|242399219|ref|YP_002994643.1| 130 ITPEDTVIVADPMIATGSTLITVMEEIKKYGTPKRLIVLGILAA 173
                                       556788999999******************99999999998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); 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:                         3  (0.000167327); expected 0.2 (1e-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 0.32s 00:00:00.94 Elapsed: 00:00:00.54
# Mc/sec: 1284.01
//
Query:       gi|242399220|ref|YP_002994644.1|  [L=163]
Description: Transcription regulator, Lrp/AsnC family [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-13   49.7   0.5      3e-12   46.1   0.2    2.3  2  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    2.3e-12   46.2   2.6      4e-12   45.5   1.0    2.2  2  HTH_24          Winged helix-turn-helix DNA-binding
    3.5e-07   30.1   0.0    8.7e-07   28.8   0.0    1.9  2  AsnC_trans_reg  Lrp/AsnC ligand binding domain
    1.6e-05   24.7   0.1    3.7e-05   23.6   0.1    1.5  1  MarR            MarR family
    3.3e-05   23.7   1.1    7.1e-05   22.7   0.3    2.0  1  HTH_11          HTH domain
    0.00019   21.4   0.1    0.00073   19.6   0.0    2.0  2  HTH_20          Helix-turn-helix domain
    0.00032   20.1   0.0      0.021   14.4   0.0    2.5  2  Sigma70_r4      Sigma-70, region 4
    0.00062   19.6   0.2     0.0026   17.6   0.0    2.0  2  MarR_2          MarR family
    0.00083   19.2   0.7     0.0019   18.0   0.2    1.9  2  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0021   18.1   0.7     0.0052   16.8   0.2    2.0  2  HTH_Mga         M protein trans-acting positive regulator (MG
     0.0039   17.0   0.5      0.089   12.6   0.0    2.5  2  HTH_IclR        IclR helix-turn-helix domain
     0.0093   16.0   2.1       0.21   11.7   0.1    2.7  3  HTH_9           RNA polymerase III subunit RPC82 helix-turn-h
  ------ inclusion threshold ------
      0.027   14.1   0.1      0.039   13.6   0.1    1.2  1  E3_UFM1_ligase  E3 UFM1-protein ligase 1
      0.041   13.9   2.7        4.6    7.3   0.0    3.3  4  HTH_45          Winged helix-turn-helix
      0.042   13.5   0.0       0.11   12.1   0.0    1.7  1  HTH_41          Helix-turn-helix domain
      0.044   13.1   0.0       0.06   12.6   0.0    1.3  1  Dcc1            Sister chromatid cohesion protein Dcc1
      0.082   13.1   0.1       0.16   12.1   0.1    1.6  1  HTH_34          Winged helix DNA-binding domain
      0.083   13.0   0.0       0.23   11.6   0.0    1.7  1  FeoC            FeoC like transcriptional regulator
       0.13   13.0   0.0       0.23   12.1   0.0    1.5  1  RPA_C           Replication protein A C terminal
       0.19   11.4   1.1       0.77    9.4   0.2    2.4  2  HTH_50          Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.1   0.2   3.4e-15     3e-12       2      42 .]       5      45 ..       4      45 .. 0.99
   2 ?    1.4   0.0      0.32   2.8e+02       9      18 ..      72      81 ..      72      91 .. 0.77

  Alignments for each domain:
  == domain 1  score: 46.1 bits;  conditional E-value: 3.4e-15
                     HTH_AsnC-type  2 DeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrLe 42
                                      DeiD+k+L +L++++R++ +eL++++GlS + + +Rv++Le
  gi|242399220|ref|YP_002994644.1|  5 DEIDKKLLIELRKNGRATLTELSKKLGLSVASIKNRVDKLE 45
                                      9***************************************8 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.32
                     HTH_AsnC-type  9 LeaLqedaRi 18
                                      Le+L ed+R+
  gi|242399220|ref|YP_002994644.1| 72 LELLVEDPRT 81
                                      89*****886 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 !   45.5   1.0   4.5e-15     4e-12       2      48 .]       5      51 ..       4      51 .. 0.96
   2 ?   -1.1   0.0       1.6   1.5e+03       9      18 ..      72      81 ..      65      84 .. 0.84

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 4.5e-15
                            HTH_24  2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      de+d+k+L +L+kn+r + +eL+++lglS++ ++ r+++Le+ G Ik
  gi|242399220|ref|YP_002994644.1|  5 DEIDKKLLIELRKNGRATLTELSKKLGLSVASIKNRVDKLERVGAIK 51
                                      9****************************************988775 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.6
                            HTH_24  9 LelLqknpri 18
                                      LelL ++pr+
  gi|242399220|ref|YP_002994644.1| 72 LELLVEDPRT 81
                                      7888899985 PP

>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       8.9     8e+03      56      69 ..      42      55 ..      36      57 .. 0.61
   2 !   28.8   0.0   9.7e-10   8.7e-07      17      58 ..      85     125 ..      61     145 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 8.9
                                      HTTTTSTTEEEEEE CS
                    AsnC_trans_reg 56 eklaslpgvartet 69
                                      +kl ++  ++ ++t
  gi|242399220|ref|YP_002994644.1| 42 DKLERVGAIKGYST 55
                                      45666666666666 PP

  == domain 2  score: 28.8 bits;  conditional E-value: 9.7e-10
                                       HHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTT CS
                    AsnC_trans_reg  17 eealaelpeVvecyrvtGdydyllkvvvrdlealerflrekl 58 
                                        +++ +l++V+ +y+ tG++++l+++ ++++e+l++fl+  l
  gi|242399220|ref|YP_002994644.1|  85 LHEIGKLDNVLGIYKKTGEFQILIRANFKSMEDLREFLDL-L 125
                                       678999*******************************864.3 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.1   4.1e-08   3.7e-05       8      47 ..      11      50 ..       9      53 .. 0.95

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 4.1e-08
                                      HHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                              MarR  8 iLrilyeqgplsvseLakklgvskstvtrvldrLekkGli 47
                                      +L  l+ +g ++++eL kklg+s +++ + +d+Le+ G i
  gi|242399220|ref|YP_002994644.1| 11 LLIELRKNGRATLTELSKKLGLSVASIKNRVDKLERVGAI 50
                                      8999********************************9988 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.3   7.9e-08   7.1e-05       3      44 ..       9      49 ..       8      54 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 7.9e-08
                            HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                      +++l+ L +++g  +  eL+++L++S + + +++++Le  g+
  gi|242399220|ref|YP_002994644.1|  9 KKLLIEL-RKNGRATLTELSKKLGLSVASIKNRVDKLERVGA 49
                                      5789999.556669************************9994 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   8.1e-07   0.00073      17      56 ..      13      52 ..       4      55 .. 0.90
   2 ?   -2.4   0.0       5.9   5.3e+03      29      46 ..     117     135 ..     113     136 .. 0.59

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 8.1e-07
                                      HHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20 17 raLaraegltaselaerldlskntlsyHLrvLeeagLvev 56
                                       +L+ ++ +t++el + l+ls +++ +++++Le++g++++
  gi|242399220|ref|YP_002994644.1| 13 IELRKNGRATLTELSKKLGLSVASIKNRVDKLERVGAIKG 52
                                      56788999*****************************986 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5.9
                                       HHHHHHT.S-HHHHHHHHH CS
                            HTH_20  29 elaerld.lskntlsyHLr 46 
                                       +l e ld lsk+ l+++Lr
  gi|242399220|ref|YP_002994644.1| 117 DLREFLDlLSKKYLRKNLR 135
                                       5556666455555777766 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   2.3e-05     0.021      10      41 ..      10      41 ..       7      44 .. 0.89
   2 ?    3.2   0.0     0.073        65      20      28 ..      82      90 ..      70      94 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.3e-05
                                      HHHHHHHHTTT--HHHHHHHHTS-HHHHHHHH CS
                        Sigma70_r4 10 revlelrfgeglTleEIgerlgiSrerVrqie 41
                                      +  +elr     Tl E++++lg+S   ++ + 
  gi|242399220|ref|YP_002994644.1| 10 KLLIELRKNGRATLTELSKKLGLSVASIKNRV 41
                                      5679****9999**************999886 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.073
                                      T--HHHHHH CS
                        Sigma70_r4 20 glTleEIge 28
                                      +lTl+EIg+
  gi|242399220|ref|YP_002994644.1| 82 DLTLHEIGK 90
                                      89******8 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0     3e-06    0.0026      10      50 ..      11      49 ..       8      56 .. 0.92
   2 ?   -1.7   0.0       3.1   2.8e+03      14      27 ..      74      88 ..      66      91 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3e-06
                                      HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTS CS
                            MarR_2 10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGL 50
                                      +L +L+ +++   t +el ++lgls +++ +++++L++ G 
  gi|242399220|ref|YP_002994644.1| 11 LLIELRKNGR--ATLTELSKKLGLSVASIKNRVDKLERVGA 49
                                      7999****98..9***********************98775 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.1
                                      HHCTTTS.EEEHHHH CS
                            MarR_2 14 Lgrrpgr.dltvgel 27
                                      L  +++r dlt  e+
  gi|242399220|ref|YP_002994644.1| 74 LLVEDPRtDLTLHEI 88
                                      444555558888887 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.2   2.2e-06    0.0019       8      53 ..       6      51 ..       4      59 .. 0.94
   2 ?   -3.1   0.0       8.3   7.5e+03      36      50 ..     136     150 ..     132     157 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.2e-06
                                      HHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEE CS
                              TrmB  8 eyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVe 53
                                      e + k  + L k+g+at +e++++lg++ +++ + + +Le+ G ++
  gi|242399220|ref|YP_002994644.1|  6 EIDKKLLIELRKNGRATLTELSKKLGLSVASIKNRVDKLERVGAIK 51
                                      67889999999********************************986 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 8.3
                                       CHCHHHHHHHHHHCT CS
                              TrmB  36 rskvYevLrsLedkG 50 
                                       r +v  vL+ L+d G
  gi|242399220|ref|YP_002994644.1| 136 RWRVTIVLEVLKDGG 150
                                       566777888887766 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 !   16.8   0.2   5.8e-06    0.0052       9      44 ..      10      44 ..       5      47 .. 0.84
   2 ?   -2.8   0.0       7.8     7e+03      39      53 ..     116     130 ..     115     132 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.8e-06
                           HTH_Mga  9 kLlelLteneksltldelakeLglseltlqsdiseL 44
                                      kLl  L + +++ tl+el+k+Lgls  ++++++++L
  gi|242399220|ref|YP_002994644.1| 10 KLLIELRK-NGRATLTELSKKLGLSVASIKNRVDKL 44
                                      55555667.999********************9998 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 7.8
                           HTH_Mga  39 sdiseLnelFpeels 53 
                                       +d++e+ +l++++++
  gi|242399220|ref|YP_002994644.1| 116 EDLREFLDLLSKKYL 130
                                       567777777777765 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 !   12.6   0.0    0.0001     0.089      15      48 ..      17      50 ..      11      52 .. 0.87
   2 ?    2.0   0.1      0.21   1.8e+02      38      52 .]      65      79 ..      62      79 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.0001
                                      TBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          HTH_IclR 15 apqeltlselArrtglpkStvhRlLqtLvelGyv 48
                                       +++ tl+el++++gl+ ++  + +  L++ G +
  gi|242399220|ref|YP_002994644.1| 17 KNGRATLTELSKKLGLSVASIKNRVDKLERVGAI 50
                                      55667****************9999999999976 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.21
                                      HHHHHHHTTSEE... CS
                          HTH_IclR 38 lLqtLvelGyveqdg 52
                                      +Lq L+el ++  d+
  gi|242399220|ref|YP_002994644.1| 65 YLQALIELELLVEDP 79
                                      8**********9986 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.1   0.00023      0.21      22      46 ..      15      39 ..       5      44 .. 0.89
   2 ?    3.3   0.0       0.1        92      20      46 ..     105     132 ..     104     135 .. 0.86
   3 ?   -2.4   0.0         6   5.4e+03      15      31 ..     139     155 ..     138     157 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00023
                                      HHHHSSBEHHHHHHHHSSTHHHHHH CS
                             HTH_9 22 LlrkgrltlrelvkktkLsldqVkk 46
                                      L ++gr tl+el+kk++Ls  ++k+
  gi|242399220|ref|YP_002994644.1| 15 LRKNGRATLTELSKKLGLSVASIKN 39
                                      6789*******************97 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.1
                                       HHHHHHSSBEHHHHHHHHS.STHHHHHH CS
                             HTH_9  20 etLlrkgrltlrelvkktk.LsldqVkk 46 
                                       + L+r +++++ +l ++++ Ls++  +k
  gi|242399220|ref|YP_002994644.1| 105 QILIRANFKSMEDLREFLDlLSKKYLRK 132
                                       68*****************999887776 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 6
                                       HHHHHHHHHHHSSBEHH CS
                             HTH_9  15 vakVvetLlrkgrltlr 31 
                                       v  V e+L + g + +r
  gi|242399220|ref|YP_002994644.1| 139 VTIVLEVLKDGGVSLSR 155
                                       67788899888887776 PP

>> E3_UFM1_ligase  E3 UFM1-protein ligase 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   4.4e-05     0.039      54      97 ..       5      47 ..       3      79 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.4e-05
                    E3_UFM1_ligase 54 eqLekeikdelekagGRvnlvdLakilnvdlshiekkaeeivke 97
                                      ++++k++  el+k+ GR +l++L+k l++ +  i+++++++ + 
  gi|242399220|ref|YP_002994644.1|  5 DEIDKKLLIELRKN-GRATLTELSKKLGLSVASIKNRVDKLERV 47
                                      67888999999999.9**********************999443 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0    0.0051       4.6      15      51 ..      16      52 ..       5      61 .. 0.86
   2 ?    4.5   0.1     0.038        34      36      56 ..      62      83 ..      53     105 .. 0.79
   3 ?   -0.1   0.1         1   9.4e+02      24      48 ..     105     130 ..      91     140 .. 0.68
   4 ?   -0.6   0.0       1.4   1.3e+03       1      13 [.     135     147 ..     135     152 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0051
                            HTH_45 15 isegeakkTkimykanLsykllnkYLdmLvekglikk 51
                                       ++g+a+ T++ +k  Ls   +++ +d+L   g ik 
  gi|242399220|ref|YP_002994644.1| 16 RKNGRATLTELSKKLGLSVASIKNRVDKLERVGAIKG 52
                                      4699***************************999975 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.038
                            HTH_45 36 lnkYLdmLvekgli.kkskekY 56
                                      l++YL+ L+e +l+ ++  +  
  gi|242399220|ref|YP_002994644.1| 62 LEEYLQALIELELLvEDPRTDL 83
                                      799*********9725555555 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 1
                            HTH_45  24 kimykanL.sykllnkYLdmLvekgl 48 
                                       +i+ +an  s + l+++Ld L +k l
  gi|242399220|ref|YP_002994644.1| 105 QILIRANFkSMEDLREFLDLLSKKYL 130
                                       57777777456778888887766544 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 1.4
                            HTH_45   1 rRskleIiadILe 13 
                                       rR ++ I++++L+
  gi|242399220|ref|YP_002994644.1| 135 RRWRVTIVLEVLK 147
                                       8999******997 PP

>> HTH_41  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00013      0.11       8      37 ..      22      51 ..      18      53 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00013
                            HTH_41  8 tIeelakeleLSvGlvQkALklLeddkais 37
                                      t +el+k+l+LSv  +   + +Le  +ai+
  gi|242399220|ref|YP_002994644.1| 22 TLTELSKKLGLSVASIKNRVDKLERVGAIK 51
                                      889************************995 PP

>> Dcc1  Sister chromatid cohesion protein Dcc1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   6.7e-05      0.06     126     179 ..      18      72 ..       4     100 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.7e-05
                                       S-S-SHHHHHHTSSS-HHHHHHHHHHCTEE.EETTEEEEE-HHHHHHHHHHHHHH CS
                              Dcc1 126 kekytleeLlenvqaSeaElkkaLkelgal.eidGrlrllspsylselLelvlal 179
                                       + + tl+eL +++  S a +k+  ++l+ +  i+G+  l++p++l+e L+++++l
  gi|242399220|ref|YP_002994644.1|  18 NGRATLTELSKKLGLSVASIKNRVDKLERVgAIKGYSTLVEPTFLEEYLQALIEL 72 
                                       33489************************99********************9975 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00018      0.16       5      45 ..      11      51 ..       8      69 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00018
                            HTH_34  5 vlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYie 45
                                      +l  L ++ +a+ +el+++l+++ + +   ++kLe  g i+
  gi|242399220|ref|YP_002994644.1| 11 LLIELRKNGRATLTELSKKLGLSVASIKNRVDKLERVGAIK 51
                                      56678899****************************99887 PP

>> FeoC  FeoC like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00025      0.23       9      45 ..      15      51 ..      10      55 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00025
                              FeoC  9 leergrvslkeLsrhfkaspealeamLeqwvrkGrve 45
                                      l+++gr+ l eLs+++  s + ++  ++ ++r G ++
  gi|242399220|ref|YP_002994644.1| 15 LRKNGRATLTELSKKLGLSVASIKNRVDKLERVGAIK 51
                                      689*****************************99876 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 ?   12.1   0.0   0.00026      0.23      70     100 ..      23      55 ..      14      58 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00026
                                       HHHHHHHSTSXHHHHHHHHHHHHHTTSE..EES CS
                             RPA_C  70 vdeiaqklrlsvndvkqavdeLsneGii..YsT 100
                                       + e+++kl+lsv+++k+ vd+L+  G i  YsT
  gi|242399220|ref|YP_002994644.1|  23 LTELSKKLGLSVASIKNRVDKLERVGAIkgYST 55 
                                       6799**********************9988887 PP

>> HTH_50  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.2   0.00086      0.77       8      46 ..       4      43 ..       2      45 .. 0.84
   2 ?   -1.0   0.1       1.5   1.4e+03       3      22 ..     117     136 ..     115     138 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00086
                            HTH_50  8 veefErelikkayekYpSt.RklAkrLGvShtaianklrk 46
                                      v+e++++l++++ ++   t   l k+LG+S + i n++ k
  gi|242399220|ref|YP_002994644.1|  4 VDEIDKKLLIELRKNGRATlTELSKKLGLSVASIKNRVDK 43
                                      88999999999988877762569**************976 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.5
                            HTH_50   3 sLkeyveefErelikkayek 22 
                                       +L+e ++   ++ + k +++
  gi|242399220|ref|YP_002994644.1| 117 DLREFLDLLSKKYLRKNLRR 136
                                       79999999999999888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       836  (0.0466284); expected 358.6 (0.02)
Passed bias filter:                      644  (0.0359195); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.48u 0.32s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1070.65
//
Query:       gi|242399221|ref|YP_002994645.1|  [L=834]
Description: DEAD/DEAH box RNA helicase [Thermococcus sibiricus MM 739]
Scores for complete 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-25   88.4   0.0    1.2e-24   87.0   0.0    1.7  1  DEAD        DEAD/DEAH box helicase
    5.9e-14   52.4   0.0    2.3e-13   50.5   0.0    2.1  1  Helicase_C  Helicase conserved C-terminal domain
    4.6e-08   33.2   0.0    9.2e-08   32.3   0.0    1.5  1  ResIII      Type III restriction enzyme, res subunit
  ------ inclusion threshold ------
      0.033   12.9   0.0       0.11   11.2   0.0    1.5  1  SNF2_N      SNF2 family N-terminal domain
       0.15   12.1   0.2       0.35   10.9   0.2    1.5  1  LRV_FeS     LRV protein FeS4 cluster


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 !   87.0   0.0   3.3e-28   1.2e-24       2     170 ..     220     383 ..     219     388 .. 0.90

  Alignments for each domain:
  == domain 1  score: 87.0 bits;  conditional E-value: 3.3e-28
                                       HHHHHHHHHHH.TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSE CS
                                       xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   2 diQaeaiplil.gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlr 77 
                                       ++Q+ ai++ l +g+++lv  +T+sGKTl+  +  + +       +g+k l+++P+ +La+q ++++kk+ ++++l+
  gi|242399221|ref|YP_002994645.1| 220 PVQSLAIKNGLlEGENLLVVSATASGKTLIGELGGVPKA-----FNGKKLLFLVPLVALANQKYEDFKKRYSKLGLK 291
                                       789999999887*********************999666.....7899***************************99 PP

                                       EEEEET..TSSHHHHHHHHHTT..CSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSH CS
                                       xxxxxx..xxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  78 vlliig..gvaardqlskldng..vdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlp 150
                                       v   +g    +++d+l ++d g  +di+vgt + +d ll+ g+ ++ +v ++V+DE+++l d++++  ++ ++++l+
  gi|242399221|ref|YP_002994645.1| 292 VAIRVGmsRIKTKDELVVVDTGidADIIVGTYEGIDYLLRAGR-KIGNVGTIVIDEIHMLDDEERGARLDGLIARLR 367
                                       997766447788999999998899***************8777.8*******************************8 PP

                                       HHCTTSTTTSEEEEEESSBS CS
                                       xxxxxxxxxxxxxxxxxxxx RF
                              DEAD 151 qitcdgklqrqvivlSATlp 170
                                       + + +     q+i lSAT+ 
  gi|242399221|ref|YP_002994645.1| 368 KLYPN----AQFIGLSATIG 383
                                       77665....44*******96 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.5   0.0   6.3e-17   2.3e-13      15     109 ..     439     537 ..     418     538 .. 0.85

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 6.3e-17
                                       TTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEEES CS
                        Helicase_C  15 eggkilifvntidrlekvklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvnlVinf 91 
                                        +g+ ++f+ +++r++++  +l++kg+k+ ++h+ lp  +r+ +  +f+++  dv+++t +++ G+d+p  ++++  
  gi|242399221|ref|YP_002994645.1| 439 FKGQNIVFTYSRKRCHELAAFLTSKGLKAKPYHSGLPYHQRKLTEMEFQAQMLDVVVTTAALGAGVDFPASQVIF-E 514
                                       57899**********9988888999********************************************666555.4 PP

                                       SSS.....SSHHHHHHHHTTSSS CS
                        Helicase_C  92 dlp.....rnvtsyiqriGRtgR 109
                                       +l       +v++++q+ GR+gR
  gi|242399221|ref|YP_002994645.1| 515 SLAmgnkwLSVREFHQMLGRAGR 537
                                       44445554569***********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 !   32.3   0.0   2.6e-11   9.2e-08       6     169 ..     220     382 ..     215     384 .. 0.77

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 2.6e-11
                                       HHHHHHHHHHT......TTSEEEEEESTTSTHHHHH.HHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG. CS
                            ResIII   6 eyQeeaienlleklkskrdkrglikmaTGtGKTlva.aklierllkkgkeekflflvprkslleqtleefkkflsea 81 
                                       + Q  ai+n l      + +++l++ aT +GKTl+  +  + + ++    +k lflvp  +l +q +e+fkk +s+ 
  gi|242399221|ref|YP_002994645.1| 220 PVQSLAIKNGL-----LEGENLLVVSATASGKTLIGeLGGVPKAFNG---KKLLFLVPLVALANQKYEDFKKRYSKL 288
                                       56666666665.....3457999************998888887773...59***********************99 PP

                                       .........GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T.... CS
                            ResIII  82 yke......igkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk.... 148
                                         +       + ++++d+         +++i+v t++ +d  +      +   + ++   i+iDE H l +++    
  gi|242399221|ref|YP_002994645.1| 289 GLKvairvgMSRIKTKDELVV-VDTGIDADIIVGTYEGIDYLL------RAGRKIGNVGTIVIDEIHMLDDEErgar 358
                                       887777666455555555555.666677899999999999988......6667777777************855555 PP

                                       ...TTHHHHHT---SEEEEEESS- CS
                            ResIII 149 ...swreilekfkeavllglTATp 169
                                           + ++ + +++a  +gl+AT+
  gi|242399221|ref|YP_002994645.1| 359 ldgLIARLRKLYPNAQFIGLSATI 382
                                       5555566677778899*******7 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 ?   11.2   0.0   3.1e-05      0.11      99     194 ..     264     355 ..     172     370 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.1e-05
                                       EEEE--H.HHHHHHHHHHHHH-TTS-EEE--SSHHHH-----------------EEEE-HHHHHHHT......TTS- CS
                                       xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N  99 tLivvPa.slldqWeneierhvsssalrvlvyggqkkmkkkntkvapklladydvvittYdvlsreaelqkkrsvlk 174
                                        L +vP  +l++q ++++++  s+  l+v +  g ++ k k + v  ++  d+d+++ tY+ +         r   k
  gi|242399221|ref|YP_002994645.1| 264 LLFLVPLvALANQKYEDFKKRYSKLGLKVAIRVGMSRIKTKDELVVVDTGIDADIIVGTYEGIDYLL-----RAGRK 335
                                       678999999******************************************************9666.....34444 PP

                                       S-S-SEEEES-GGGT--TTS CS
                                       xxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N 175 qvewkrvvlDEghtlknsts 194
                                         +   +v+DE h+l  +++
  gi|242399221|ref|YP_002994645.1| 336 IGNVGTIVIDEIHMLDDEER 355
                                       455678*********98853 PP

>> LRV_FeS  LRV protein FeS4 cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.2   9.8e-05      0.35       9      51 ..     123     165 ..     117     166 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 9.8e-05
                           LRV_FeS   9 vdCasCehrellaeGrCelgkaCvadryarridRFfrwnpeLA 51 
                                         C+sC+ +el++e r + +   + d+  + ++RF + n+ +A
  gi|242399221|ref|YP_002994645.1| 123 FICESCAEEELKNELRYRFRSLGMFDQAKKLLERFRDLNKVMA 165
                                       56*************************************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (834 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       792  (0.0441742); expected 358.6 (0.02)
Passed bias filter:                      667  (0.0372023); 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: 0.86u 0.37s 00:00:01.23 Elapsed: 00:00:00.59
# Mc/sec: 4272.38
//
Query:       gi|242399222|ref|YP_002994646.1|  [L=466]
Description: hypothetical protein TSIB_1243 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    0.00076   18.9  10.0     0.0014   18.0  10.0    1.3  1  Peptidase_U4  Sporulation factor SpoIIGA
  ------ inclusion threshold ------
        1.5    9.1   6.6       0.97    9.7   4.3    2.0  2  VirB3         Type IV secretory pathway, VirB3-like protein


Domain annotation for each model (and alignments):
>> Peptidase_U4  Sporulation factor SpoIIGA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0  10.0   1.5e-07    0.0014      27     136 ..     348     450 ..     331     463 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.5e-07
                      Peptidase_U4  27 klkikklrlllaAllGalyvvlvlflpklesillsillkilvsllmv.liafgpkslkeflkalllfylvsfllgGi 102
                                       +l   k+r l+ +l+ ++  ++++++p++ +i  ++++ki +++ ++ l+++++++l  fl a +lf++  +++ G+
  gi|242399222|ref|YP_002994646.1| 348 RL---KKRELILSLVSSIG-AIAVLYPTIDDISPQVMFKIYIAWTLIvLATYRKHTLFGFLLAPVLFFVGLAAIMGL 420
                                       22...34666667777777.44467788999*********98888874778**********99999999999999*9 PP

                      Peptidase_U4 103 lfalsylllksknllvlllgalvaylllkllvki 136
                                       +++ ++l++    l v +++++v++l+lkl + +
  gi|242399222|ref|YP_002994646.1| 421 ITMRYSLFV----LTVGTISTFVLWLILKLNYLL 450
                                       998888777....89999*********9954433 PP

>> VirB3  Type IV secretory pathway, VirB3-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.0         2   1.8e+04      42      50 ..     332     340 ..     326     348 .. 0.49
   2 ?    9.7   4.3   0.00011      0.97       5      65 ..     390     452 ..     380     465 .. 0.80

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 2
                             VirB3  42 illllvplh 50 
                                        ll++v ++
  gi|242399222|ref|YP_002994646.1| 332 TLLVAVSIV 340
                                       233333222 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00011
                             VirB3   5 lfkaltRpamllGvplelvllnllvsvilfl..vglslwillllvplhlvlrliakrDpqmfr 65 
                                       +++a  R+ +l+G  l +vl+ +++++i+ l  +  sl++l +  ++ +vl+li k    +++
  gi|242399222|ref|YP_002994646.1| 390 IVLATYRKHTLFGFLLAPVLFFVGLAAIMGLitMRYSLFVLTVGTISTFVLWLILKLNYLLLE 452
                                       789999********************99999555566777777779*******9987666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (466 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       756  (0.0421663); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); 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: 0.72u 0.34s 00:00:01.06 Elapsed: 00:00:00.56
# Mc/sec: 2500.45
//
Query:       gi|242399223|ref|YP_002994647.1|  [L=366]
Description: hypothetical protein TSIB_1244 [Thermococcus sibiricus MM 739]
Scores for complete 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-16   58.9   0.0    1.2e-15   58.2   0.0    1.3  1  Radical_SAM  Radical SAM superfamily
    1.1e-08   35.4   0.2    1.3e-07   32.0   0.1    2.3  2  Fer4_12      4Fe-4S single cluster domain
    7.3e-08   32.6   0.0      2e-07   31.1   0.0    1.8  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 !   58.2   0.0   2.1e-19   1.2e-15       3     165 ..      27     198 ..      25     200 .. 0.87

  Alignments for each domain:
  == domain 1  score: 58.2 bits;  conditional E-value: 2.1e-19
                                       EESEESS--TTTSCCTT...HHHHHHHHHHHHHHHHHHHHHHH.HHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTC CS
                                       xxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxx.xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   3 vtrgCnlrCsfCarpet...vrregrgrslsveeileevkelk.aekg.vkevilgggepllypdfvellerlakla 74 
                                       +t  CnlrC++C+ p++   ++    ++ ++   il  ++++k +ek  + +v++ ggepll +d v  l ++    
  gi|242399223|ref|YP_002994647.1|  27 PTLNCNLRCPYCYEPRDkfeESIKIMPEKVQESLILFTIDQIKkHEKIkAIGVTWYGGEPLLASDVVLSLSKRLMGI 103
                                       6789*************999888999999999999999999998777667888888*******99998887666555 PP

                                       ....CCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHH..HHHHHHTCTSHHHHHHHHHHHHHHTTSETE CS
                                       ....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  75 ....vpgiritvetngtlpdeeklerllelgvdrvslgleaadde..kvlklmnrghtfeevlealeklreagikrv 145
                                             +++ +++tngtl++e+ l+ ll+ ++ +++++ +   +   k++ + n+++tf++v + +++l e+++k +
  gi|242399223|ref|YP_002994647.1| 104 adeyGLKYTSSIVTNGTLLTEKLLKNLLQFNMSQFQITFDGDKPHhdKTRVYPNGKGTFDQVFQKFRLLLEHDVK-I 179
                                       6999***************************99999999999998777777777*********************.8 PP

                                       EEEEEEBTTTSHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 146 vdrivglpGendeeleelle 165
                                       ++ri +   en e + +ll+
  gi|242399223|ref|YP_002994647.1| 180 SVRINVSS-ENYESIPNLLD 198
                                       88887766.77777766665 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   0.1   2.1e-11   1.3e-07      14     102 ..      30     128 ..      24     165 .. 0.67
   2 ?    1.0   0.0     0.077   4.6e+02      96     125 ..     162     189 ..     146     196 .. 0.79

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 2.1e-11
                           Fer4_12  14 gCnlsCkgCfnketwsfksgkeftkelleeii....edlkkesi...egltllGGEPllpenaeallelvkevkeek 83 
                                        Cnl+C++C+ +  +  +s k ++++++e +i    +++kk+++   +g+t  GGEPll    +++l+l k++   +
  gi|242399223|ref|YP_002994647.1|  30 NCNLRCPYCYEPRDKFEESIKIMPEKVQESLIlftiDQIKKHEKikaIGVTWYGGEPLL--ASDVVLSLSKRLMGIA 104
                                       6*********99999999999999888888761111555554446889***********..9999999999986554 PP

                           Fer4_12  84 ...p..ekdiwlytgytleelskk 102
                                               + ++++g+ l e + k
  gi|242399223|ref|YP_002994647.1| 105 deyGlkYTSSIVTNGTLLTEKLLK 128
                                       111222234455555555443333 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.077
                           Fer4_12  96 leelskkekeellkeidvlvdGkfeesled 125
                                       ++++   +k +ll e+dv ++++ + s e+
  gi|242399223|ref|YP_002994647.1| 162 FDQVF--QKFRLLLEHDVKISVRINVSSEN 189
                                       44443..5789************9998887 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 !   31.1   0.0   3.4e-11     2e-07       7     113 ..      30     140 ..      27     145 .. 0.64

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 3.4e-11
                           Fer4_14   7 gCnlsCkgCd.....nketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeey 78 
                                        Cnl C+ C+      +e+ k   +k+q++ +l +i + +k+++ik+ g++  GGePL     +++l l krl    
  gi|242399223|ref|YP_002994647.1|  30 NCNLRCPYCYeprdkFEESIKIMPEKVQESLILFTIDQIKKHEKIKAIGVTWYGGEPL--LASDVVLSLSKRLMGIA 104
                                       6*********8554434444444555555555555555789999**************..77999****99987766 PP

                           Fer4_14  79 pe....kkiwletngtleielektpdlkeklealskidl 113
                                        e    +   + tngtl  e       +  ++ +s+ ++
  gi|242399223|ref|YP_002994647.1| 105 DEyglkYTSSIVTNGTLLTEKL---LKNLLQFNMSQFQI 140
                                       5511115555666666653322...22234455555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 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:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.54
# Mc/sec: 2050.90
//
Query:       gi|242399224|ref|YP_002994648.1|  [L=288]
Description: ABC transporter [Thermococcus sibiricus MM 739]
Scores for complete 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-68  230.8  17.3    3.9e-68  230.6  17.3    1.0  1  DUF63            Membrane protein of unknown function DUF63
  ------ inclusion threshold ------
        1.8    9.1   3.0         78    3.8   1.0    3.4  3  FeoB_associated  FeoB-associated Cys-rich membrane protein


Domain annotation for each model (and alignments):
>> DUF63  Membrane protein of unknown function DUF63
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  230.6  17.3   4.3e-72   3.9e-68       2     272 .]      30     286 ..      29     286 .. 0.97

  Alignments for each domain:
  == domain 1  score: 230.6 bits;  conditional E-value: 4.3e-72
                             DUF63   2 seFiykyYidpivykegYnivntltyaiiLivavyliykllkkl.kikidekfvlatipyvilgsslRvveDagllk 77 
                                       + F+++++i+p++++egYn+ ntl+yaiiL++a++++y+++ k  kik+dek+++a++p++++g+++R++ D g+l 
  gi|242399224|ref|YP_002994648.1|  30 ERFLWEHFIRPMYTREGYNPYNTLVYAIILGLAIIYTYRWIIKPlKIKVDEKLFYAVTPMTVFGATVRALIDGGVL- 105
                                       68**************************************98765*******************************. PP

                             DUF63  78 pplsyllitPliyflvflitlavlliskklekklkkdykklyaavGvvlvlvvlllLllteevvnlevlllvlllaa 154
                                        + + l++tP+i+f++f+++l++l+++++l     k+y k+++ +G++l+l++++lL+  ++v+++e + l+l  ++
  gi|242399224|ref|YP_002994648.1| 106 -EPHPLILTPGIFFTAFFLILPALFADSRL-----KTYPKITVGWGTILALYANYLLI--THVKSWEPYELTLFYTV 174
                                       .889**************************.....9**********************..9999*********9999 PP

                             DUF63 155 vltalvllllrklklellsdklnlllllahllDasatfvgidllgYvEqHvvpsfLidltGtalvmyplkllvlipv 231
                                       v+++ +l+ ++       ++kl+ll + ah++D  +t+v+i+++gY E H+++++L++ +G a+v+yp+ + +l+ v
  gi|242399224|ref|YP_002994648.1| 175 VFFLPILVYYKFRP----FEKLYLLPISAHIFDIGSTVVAIHYYGYREVHWLENILVQKFG-AFVYYPWIVFILVVV 246
                                       99999999999999....99*****************************************.*************** PP

                             DUF63 232 lyildkevkeeeelrnlvklailvlGlaPgiRnllrmvlgv 272
                                       +y l   v +ee  r++++lai++lGl+P+iR+ ++mvl++
  gi|242399224|ref|YP_002994648.1| 247 YYGLRYLVPDEE-ERKYWYLAIYILGLGPAIRDPAQMVLQI 286
                                       ***********9.9*************************97 PP

>> FeoB_associated  FeoB-associated Cys-rich membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   1.0    0.0087        78       2      22 ..      51      72 ..      50      75 .. 0.72
   2 ?    0.0   0.0      0.13   1.2e+03       6      23 ..     145     162 ..     145     164 .. 0.87
   3 ?    2.2   0.0     0.027   2.4e+02       3      21 ..     238     254 ..     237     260 .. 0.62

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.0087
                   FeoB_associated  2 tiIVgliia.aavafvirrlik 22
                                      + +V +ii+ +a+++  r +ik
  gi|242399224|ref|YP_002994648.1| 51 NTLVYAIILgLAIIYTYRWIIK 72
                                      67899****5566666666665 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.13
                   FeoB_associated   6 gliiaaavafvirrlikk 23 
                                       g i+a+++ ++++ ++k+
  gi|242399224|ref|YP_002994648.1| 145 GTILALYANYLLITHVKS 162
                                       569999******999995 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.027
                   FeoB_associated   3 iIVgliiaaavafvirrli 21 
                                       +IV ++++++ +  +r+l+
  gi|242399224|ref|YP_002994648.1| 238 WIVFILVVVYYG--LRYLV 254
                                       567777775544..66655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); 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: 0.56u 0.35s 00:00:00.91 Elapsed: 00:00:00.54
# Mc/sec: 1601.89
//
Query:       gi|242399225|ref|YP_002994649.1|  [L=124]
Description: hypothetical protein TSIB_1246 [Thermococcus sibiricus MM 739]
Scores for complete 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   18.0  28.2     0.0018   18.0  28.2    1.5  1  Yip1            Yip1 domain
  ------ inclusion threshold ------
      0.083   13.2  22.3       0.11   12.8  22.3    1.1  1  TctB            Tripartite tricarboxylate transporter TctB fa


Domain annotation for each model (and alignments):
>> Yip1  Yip1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0  28.2     2e-07    0.0018      61     168 ..      11     104 ..       2     118 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2e-07
                              Yip1  61 sllgaiiggylglllgllllalllhliakllg.gkgsfkq.tlsvvgyallPlilgaliaillllllgtllllvgll 135
                                        ++++ ++++l++l++l++ +++l ++ak++g  ++++++ +++vvg + l+l++g+++                ++
  gi|242399225|ref|YP_002994649.1|  11 LFAAMGFMAVLVILIALIIAGFFLMIGAKFAGiEDVTLGKsMIAVVGGGILALLIGWIP----------------AI 71 
                                       44555677777779*******************99999885778888889999999999................56 PP

                              Yip1 136 aliWslvllylglkaahnlskkkallaalilll 168
                                       ++i ++++ ++ +k+++n++++ka++a l+ ++
  gi|242399225|ref|YP_002994649.1|  72 GWILGIIAYIWVIKTVFNTDWGKAAIAWLMTIV 104
                                       89999999999******************9444 PP

>> TctB  Tripartite tricarboxylate transporter TctB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8  22.3   1.2e-05      0.11      29     133 ..      16     120 ..       1     121 [. 0.55

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.2e-05
                              TctB  29 gffPll.lgvllallgllllvaadgekeekearedwrkllklvlallaalll.yallleplGfilatalflllll.. 101
                                       gf+  l + ++l+++g +l++ a+ +++e+       k++ + ++   ++l+  +  ++ +G+il+++++++++   
  gi|242399225|ref|YP_002994649.1|  16 GFMAVLvILIALIIAGFFLMIGAKFAGIED---VTLGKSM-IAVV-GGGILAlLIGWIPAIGWILGIIAYIWVIKtv 87 
                                       122222135555555666666433333333...3344444.2333.334444255589999*******999777676 PP

                              TctB 102 g...reerkwlkalilavvlallvyllFtklLgvp 133
                                       +   ++  k   a ++++v+ ++v+++F +lLg++
  gi|242399225|ref|YP_002994649.1|  88 FntdWG--KAAIAWLMTIVVEIIVMFAFMVLLGIS 120
                                       453333..4567777788888889********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1429  (0.0797033); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); 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):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 908.26
//
Query:       gi|242399226|ref|YP_002994650.1|  [L=343]
Description: hypothetical protein TSIB_1247 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.8e-11   42.0   1.4    6.8e-11   42.0   1.4    1.7  2  DUF5305   Family of unknown function (DUF5305)


Domain annotation for each model (and alignments):
>> DUF5305  Family of unknown function (DUF5305)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.16   2.8e+03     174     187 ..       4      17 ..       2      37 .. 0.80
   2 !   42.0   1.4   3.8e-15   6.8e-11       7     219 .]     132     337 ..     129     337 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.16
                           DUF5305 174 ekvievdsledLvd 187
                                       +++i+v++l+ Lv 
  gi|242399226|ref|YP_002994650.1|   4 KSMINVENLKKLVT 17 
                                       46888888888885 PP

  == domain 2  score: 42.0 bits;  conditional E-value: 3.8e-15
                           DUF5305   7 lasettqeveskeltisesvsinlseyndrieeieeelglsvgtseltvvlevnvegeidgesieesktsrlpi..p 81 
                                       l++++ + +++k   + ++ ++nl+e+++r++ei ++lgl+  + e++ +++v+veg+  g++i+e++ +  ++  +
  gi|242399226|ref|YP_002994650.1| 132 LFKDSGELKDGK---FITEYNLNLTELDRRTAEIMDQLGLKRLNREIVFTTNVHVEGKAFGKEINENFGHVSTLikD 205
                                       555556655555...8999******************************************8888887665555235 PP

                           DUF5305  82 lteqtyeikkdetdeengeitetvtvkespslae.......gilliilgllaliglvvlirriiftsskaekyelel 151
                                        +++ y ++++ ++ +++ i+ + + ++  ++              ++ llal++l+ +i   + +      + ++ 
  gi|242399226|ref|YP_002994650.1| 206 TGSGLYYFTNEKESVQKSIIERQAQRTRVSKYGVtmyadtaK---KVIPLLALLFLTPVIGGVYTI------KSQRP 273
                                       699******999987777777777766666665564553331...344444444444433332222......33577 PP

                           DUF5305 152 ekilkeYdewIvkgslppdlgdekvievdsledLvdvaielnepvlydeeedeegkFvvvddevvYvY 219
                                       ++ +k+ + +I++g   + ++   ++ + + +dL +  + l++p+l+++e + e  +v++d++++Y Y
  gi|242399226|ref|YP_002994650.1| 274 KNEFKDLAPYITEGAPVEVEK---RVILATKDDLKKTFDLLDKPILHYTEGG-EDIYVIIDGGIAYEY 337
                                       99999999*****98777764...78899999******************99.99***********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2449.04
//
Query:       gi|242399227|ref|YP_002994651.1|  [L=306]
Description: hypothetical protein TSIB_1248 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0005   19.9   0.0    0.00074   19.3   0.0    1.2  1  DUF4139   Domain of unknown function (DUF4139)
     0.0017   18.6   0.0     0.0037   17.5   0.0    1.5  1  DUF11     Domain of unknown function DUF11
     0.0048   17.2   3.3          1    9.8   0.3    3.3  3  SpaA      Prealbumin-like fold domain
  ------ inclusion threshold ------
      0.043   13.3   0.0      0.081   12.4   0.0    1.4  1  DUF4925   Domain of unknown function (DUF4925)
       0.11   12.6   0.0       0.27   11.4   0.0    1.7  1  DUF4232   Protein of unknown function (DUF4232)
       0.33   11.0   2.8       0.68   10.0   0.1    2.7  3  Rib       Rib/alpha-like repeat


Domain annotation for each model (and alignments):
>> DUF4139  Domain of unknown function (DUF4139)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   2.5e-07   0.00074     129     205 ..     182     257 ..     172     260 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 2.5e-07
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DUF4139 129 rrveyaytitvkNtksepvtlkvedqvPvSrdeeikveledaepskaevdkdtgilewklklapgekkkiefsyevk 205
                                       + +e+ ++i+v+N+  ++ +l+++d +P   d +++ + +++   + ++  ++++lew+++l pge++ ++++++ +
  gi|242399227|ref|YP_002994651.1| 182 TYQEWVFQIEVTNSG-TAQNLTIKDVIPGEFDVDLNRTSASKGNYTFTRHGKSDQLEWNVELDPGESAHMNITISTR 257
                                       56899*******976.678*********9999999997766666667888999***************999988766 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   1.3e-06    0.0037      15      77 ..     185     255 ..     173     263 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.3e-06
                             DUF11  15 tvtytltvtNtgpasangvvvtDtlP..aglayvsvsas.........qgtasaltsvgsLeagesatlsftvr 77 
                                       + ++ + vtN+g+a+   ++++D+ P    + + + sas           + + +++  +L +gesa +++t++
  gi|242399227|ref|YP_002994651.1| 185 EWVFQIEVTNSGTAQN--LTIKDVIPgeFDVDLNRTSASkgnytftrhGKSDQLEWN-VELDPGESAHMNITIS 255
                                       66899*******8765..********6655666777777444444443333444444.599*********9986 PP

>> SpaA  Prealbumin-like fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.5   0.0     0.007        21      35      57 ..      55      77 ..      24      82 .. 0.84
   2 ?    0.5   0.0      0.27     8e+02      44      58 ..     122     136 ..     112     137 .. 0.91
   3 !    9.8   0.3   0.00033         1      38      77 ..     259     296 ..     188     300 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.007
                                      ESEEE-BTTSEEEEEEEESEEEE CS
                              SpaA 35 vttlttdenGkatfegLplGtYl 57
                                      ++t+  d+n ++tf++L +G+Yl
  gi|242399227|ref|YP_002994651.1| 55 AATVIIDQNSELTFDALTVGNYL 77
                                      578899****************6 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.27
                                       SEEEEEEEESEEEEE CS
                              SpaA  44 GkatfegLplGtYll 58 
                                       G++++++ ++GtY +
  gi|242399227|ref|YP_002994651.1| 122 GNISVGNADPGTYEV 136
                                       899**********86 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.00033
                                       EE-BTTSEEEEEEEESEEEEEEEEE-STTEEE-SSEEEEE CS
                              SpaA  38 lttdenGkatfegLplGtYllvEtkaPegYvldkepfevt 77 
                                       ++t+++Gk +f+    GtY l E     gY+++++ ++v 
  gi|242399227|ref|YP_002994651.1| 259 VETGKDGKWEFT--SCGTYPLNEGAKIVGYNITSNSITVV 296
                                       57**********..88*********************995 PP

>> DUF4925  Domain of unknown function (DUF4925)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   2.7e-05     0.081      19      57 ..     193     229 ..     187     257 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.7e-05
                           DUF4925  19 tedsetgtltLndiiPGeketkiesikLseeedeYtFsG 57 
                                       t+ +    lt++d+iPGe ++ +++   s  +++YtF  
  gi|242399227|ref|YP_002994651.1| 193 TNSGTAQNLTIKDVIPGEFDVDLNRT--SASKGNYTFTR 229
                                       55666678***************876..45789999974 PP

>> DUF4232  Protein of unknown function (DUF4232)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   9.1e-05      0.27      56     100 ..     228     277 ..     186     300 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9.1e-05
                           DUF4232  56 eregpaavp...vtLapGesAyaglrwtnaggdgdgecta..aglrvtpp 100
                                       +r+g++ +    v L+pGesA++++++++   +++++ +   ++   +p 
  gi|242399227|ref|YP_002994651.1| 228 TRHGKSDQLewnVELDPGESAHMNITISTRWVETGKDGKWefTSCGTYPL 277
                                       455554444788*************7766555555444444445555555 PP

>> Rib  Rib/alpha-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1      0.56   1.7e+03      19      59 ..      92     138 ..      88     144 .. 0.54
   2 ?   10.0   0.1   0.00023      0.68      16      42 ..     173     199 ..     171     208 .. 0.90
   3 ?   -1.7   0.0      0.96   2.9e+03      33      50 ..     259     276 ..     245     282 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.56
                               Rib  19 sdlPdGTkytWke.......tpdttksGekeavvvVtYPDGskdevpv 59 
                                       s+lP+G  + W e       ++d  +  +  + + V   D  + evp+
  gi|242399227|ref|YP_002994651.1|  92 SNLPSGVEM-WIEsedgitrPIDSQEYYTFWGNISVGNADPGTYEVPI 138
                                       788888776.33322334445555544444555555555555555555 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00023
                               Rib  16 kNksdlPdGTkytWketpdttksGeke 42 
                                       +N  d+P  T  +W+ ++++t+sG+ +
  gi|242399227|ref|YP_002994651.1| 173 GNTTDIPLKTYQEWVFQIEVTNSGTAQ 199
                                       799*********************865 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.96
                               Rib  33 pdttksGekeavvvVtYP 50 
                                       ++t k G+ e +   tYP
  gi|242399227|ref|YP_002994651.1| 259 VETGKDGKWEFTSCGTYP 276
                                       688899999999889998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1973.88
//
Query:       gi|242399228|ref|YP_002994652.1|  [L=356]
Description: Signal peptidase I [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.3e-12   46.2   0.1    7.7e-12   45.0   0.1    1.6  1  Peptidase_S24  Peptidase S24-like
  ------ inclusion threshold ------
       0.15   11.8   0.4        1.6    8.6   0.0    2.5  3  IRK            Inward rectifier potassium channel transmembra
       0.24   11.9   0.2       0.24   11.9   0.2    2.9  3  FtsX           FtsX-like permease family


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 !   45.0   0.1   1.3e-15   7.7e-12       1      61 [.      34      94 ..      34     101 .. 0.89

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 1.3e-15
                                      EXXSSTTCCTXXTTXEEEEECTS.---TTSEEEEEETTCE-EEEEEEEEETTEEEEE.SST.T CS
                     Peptidase_S24  1 rvpGdSMeptlldGdlilVdkfs.epkrGdivvfrlpgeeeayiKrviglpgdrvllasnn.e 61
                                      +v +dSM ptl+ Gdl ++++fs +++ Gd++vf+l g    +++rv+   +d + ++ +n  
  gi|242399228|ref|YP_002994652.1| 34 YVSSDSMTPTLNKGDLFFINPFSrSADVGDVIVFNLRGS--WTVHRVVAIVEDGYITKGDNnV 94
                                      699********************9***************..6******999999998877743 PP

>> IRK  Inward rectifier potassium channel transmembrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1      0.27   1.6e+03     112     128 ..      11      27 ..       3      36 .. 0.66
   2 ?    8.6   0.0   0.00026       1.6      16      56 ..     165     205 ..     161     227 .. 0.87
   3 ?   -0.8   0.0       0.2   1.2e+03      38      72 ..     308     341 ..     286     350 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.27
                               IRK 112 eailllviqsivgllid 128
                                        ai+ +v+ sivg+l+d
  gi|242399228|ref|YP_002994652.1|  11 LAITAFVVGSIVGALLD 27 
                                       45666666666666666 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00026
                               IRK  16 ekslrylkDlfttlvdlkwryllllfvlsfvlswllfallw 56 
                                       +k+ ++++  f tl  l   +ll++f+ls ++sw +f + +
  gi|242399228|ref|YP_002994652.1| 165 KKRPKFIRVKFKTLYILASAFLLIMFSLSIFISWQMFPMEY 205
                                       5677899999999999999******************8765 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.2
                               IRK  38 lllfvlsfvlswllfallwylialahgDleeeeke 72 
                                       l +f++ f +s  ++++l+++  + + D+ + +++
  gi|242399228|ref|YP_002994652.1| 308 LPVFAILFEIS-AFLGVLYFISGIGNEDVLKIRNK 341
                                       55677777666.46799999999999998754444 PP

>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   4.1e-05      0.24      21      72 ..       4      52 ..       1      56 [. 0.81
   2 ?   -2.4   3.8       1.1   6.7e+03      67      86 ..     180     195 ..     140     205 .. 0.51
   3 ?   -1.9   0.1      0.78   4.7e+03      20      34 ..     313     327 ..     294     338 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.1e-05
                              FtsX 21 llteillitlvalviGlglgllaaqllsdvllssvfsselkisidlitvlii 72
                                      ++   l++++ a+v+G ++g+l+  +++  + ss   ++++++++  ++++i
  gi|242399228|ref|YP_002994652.1|  4 FIEYFLILAITAFVVGSIVGALLDRPVFMSYVSS---DSMTPTLNKGDLFFI 52
                                      44556778999***************88888777...999999998888887 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.1
                              FtsX  67 itvliiivlllllallagll 86 
                                       i   +++++++ l     ++
  gi|242399228|ref|YP_002994652.1| 180 ILASAFLLIMFSLS----IF 195
                                       22222222222222....22 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.78
                              FtsX  20 lllteillitlvalv 34 
                                       +l+  +++++++ ++
  gi|242399228|ref|YP_002994652.1| 313 ILFEISAFLGVLYFI 327
                                       222223333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2394.89
//
Query:       gi|242399229|ref|YP_002994653.1|  [L=168]
Description: hypothetical protein TSIB_1250 [Thermococcus sibiricus MM 739]
Scores for complete 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-30  104.4   0.6    6.9e-30  104.1   0.6    1.1  1  DUF1102   Protein of unknown function (DUF1102)


Domain annotation for each model (and alignments):
>> DUF1102  Protein of unknown function (DUF1102)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.1   0.6   3.9e-34   6.9e-30       8     141 .]      40     167 ..      33     167 .. 0.92

  Alignments for each domain:
  == domain 1  score: 104.1 bits;  conditional E-value: 3.9e-34
                           DUF1102   8 lidL.tpvqpYayidnGkLvidisennpnypgyGdGlspnseYvFdevfevsndlweneespivveiksenssvkly 83 
                                        +++ +p+ pYay++ G L idis++ p ypg+G+Glspns+YvF++vfe+ n+ +e++ s i+v i+s  s++ l+
  gi|242399229|ref|YP_002994653.1|  40 SVSIeNPLPPYAYLSGGYLKIDISNQSPLYPGFGEGLSPNSVYVFNNVFEIYNNESETGFSEICVVISSPVSVIGLF 116
                                       444426999******************************************************************** PP

                           DUF1102  84 agevddgqtasiadaaesieftveegeevsvGlildateeslGvkkaeltikayagec 141
                                        + ++           +sief v  +++v++G+ +d+t+  lG +++++ti+a+ g+c
  gi|242399229|ref|YP_002994653.1| 117 VSPYT-------GTWNQSIEFEVLANQSVNLGMRFDTTGLPLGDYNQNITIQAFGGSC 167
                                       *9988.......445589***********************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); 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 0.28s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1095.92
//
Query:       gi|242399230|ref|YP_002994654.1|  [L=184]
Description: hypothetical protein TSIB_1251 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-36  125.8   0.5    1.8e-36  125.4   0.5    1.1  1  DUF1102   Protein of unknown function (DUF1102)
  ------ inclusion threshold ------
      0.036   14.1   0.9       0.12   12.4   0.4    1.9  2  DUF3185   Protein of unknown function (DUF3185)


Domain annotation for each model (and alignments):
>> DUF1102  Protein of unknown function (DUF1102)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.4   0.5     2e-40   1.8e-36       1     141 []      43     180 ..      43     180 .. 0.93

  Alignments for each domain:
  == domain 1  score: 125.4 bits;  conditional E-value: 2e-40
                           DUF1102   1 ivsDdnelidLtpvqpYayi.dnGkLvidisennpn.ypgyGdGlspnseYvFdevfevsndlweneespivveik. 74 
                                       iv DdnelidL p+qpYayi +nG Lvid+s  n n   g G+G+sp+s YvF++vf vsn+lwen +  i+++i+ 
  gi|242399230|ref|YP_002994654.1|  43 IVPDDNELIDLVPLQPYAYInSNGMLVIDLSSANGNwEEGLGEGVSPDSIYVFEHVFGVSNHLWENVT--ICMNIEy 117
                                       899*****************99**************889*****************************..******9 PP

                           DUF1102  75 senssvklyagevddgqtasiadaaesieftveegeevsvGlildateeslG.vkkaeltikayagec 141
                                       s    ++++ ge++ ++t       + +++t+  ge +++G+i+d+ + + G   +++l+++a  gec
  gi|242399230|ref|YP_002994654.1| 118 SGSGAISFFEGEYT-NET----VGVDTLHVTILPGETAEIGMIIDSEGLDDGdALSGTLNFDAKLGEC 180
                                       99**********99.222....223789**********************998999999999999988 PP

>> DUF3185  Protein of unknown function (DUF3185)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.4   1.3e-05      0.12       1      21 [.       8      28 ..       8      35 .. 0.87
   2 ?   -0.8   0.0      0.18   1.6e+03      27      42 ..     120     135 ..     116     137 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.3e-05
                           DUF3185  1 riiGiiLlvaGivLlvfGyna 21
                                      +i+Gi +l+aGiv++v+  +a
  gi|242399230|ref|YP_002994654.1|  8 KILGIFMLIAGIVIAVTASSA 28
                                      8**************987666 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.18
                           DUF3185  27 sqvseaftGsttdktl 42 
                                       s +  +f G++t++t+
  gi|242399230|ref|YP_002994654.1| 120 SGAISFFEGEYTNETV 135
                                       56677999****9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); 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: 0.49u 0.32s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1160.18
//
Query:       gi|242399231|ref|YP_002994655.1|  [L=221]
Description: hypothetical protein TSIB_1252 [Thermococcus sibiricus MM 739]
Scores for complete 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-35  120.6   1.1    9.4e-34  116.6   1.1    2.0  1  DUF1102   Protein of unknown function (DUF1102)


Domain annotation for each model (and alignments):
>> DUF1102  Protein of unknown function (DUF1102)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.6   1.1   5.2e-38   9.4e-34       1     138 [.      56     209 ..      56     212 .. 0.85

  Alignments for each domain:
  == domain 1  score: 116.6 bits;  conditional E-value: 5.2e-38
                           DUF1102   1 ivsDdnelidLtpvqpYayi.dnGkLvidisennpnypgy............GdGlspnseYvFdevfevsndlwen 64 
                                       +v+Dd+elidL+p qpYayi d GkLvid+s++npn pgy            G G+sp+s+Y+Fd+vf vsn+lwe+
  gi|242399231|ref|YP_002994655.1|  56 VVADDVELIDLHPGQPYAYInDRGKLVIDFSVENPNWPGYidspyyipnwtgGLGISPQSRYNFDHVFYVSNHLWEQ 132
                                       799*****************99****************9854444455556667**********************9 PP

                           DUF1102  65 eespivveik.senssvklyage.....vddgqtasiadaa.esieftveegeevsvGlildateeslGvkkaelti 134
                                       ++  ivv++  s+  + ++y ++     + + ++++ +d+a  +++f+++ gee  vG+++   + + G   +++ti
  gi|242399231|ref|YP_002994655.1| 133 TS--IVVQVIsSDPGTFSFYDNTknmyvTGTTTKPYNSDTAdGDVCFVLQPGEELGVGMEIA--GGERGDFYGNVTI 205
                                       99..88887737788999**99888875445677889999999****************985..5667888888888 PP

                           DUF1102 135 kaya 138
                                       ka+ 
  gi|242399231|ref|YP_002994655.1| 206 KAWP 209
                                       8875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1617.17
//
Query:       gi|242399232|ref|YP_002994656.1|  [L=166]
Description: hypothetical protein TSIB_1253 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score 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   13.3   0.0      0.073   12.8   0.0    1.1  1  PMM       Eukaryotic phosphomannomutase


Domain annotation for each model (and alignments):
>> PMM  Eukaryotic phosphomannomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   4.1e-06     0.073      33      95 ..      43     105 ..      32     111 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.1e-06
                                       THHHH-SEEEEGGGTEEEETTEEEEE--HHHHH-HHHHHHHHHHHHHHHHCS--S---S-SEE CS
                               PMM  33 evldefdyvfsenGlvaykkgkelasqsiiealgeeklkklinfvlryladldlPvkrGtfie 95 
                                       ++ d  d++  e+G v  ++ k++ +  +++++++ +   +i+f  + ++ l++P     ++e
  gi|242399232|ref|YP_002994656.1|  43 DLRDIVDFIAKEEGKVDRRHRKSVYVSLVQTHIPKMERAGMIRFDHHVVTLLKIPENVDVYME 105
                                       566788*************************************************99888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       815  (0.0454571); expected 358.6 (0.02)
Passed bias filter:                      559  (0.0311785); 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: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1042.93
//
Query:       gi|242399233|ref|YP_002994657.1|  [L=76]
Description: hypothetical protein TSIB_1254 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0013   19.0   0.1     0.0018   18.5   0.1    1.4  1  Vps39_1        Vacuolar sorting protein 39 domain 1
  ------ inclusion threshold ------
      0.093   12.5   1.0       0.22   11.3   1.0    1.7  1  Arg_repressor  Arginine repressor, DNA binding domain
      0.095   13.0   0.2       0.11   12.8   0.2    1.1  1  DUF5071        Domain of unknown function (DUF5071)


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 !   18.5   0.1     3e-07    0.0018      17      61 ..      27      74 ..      11      76 .] 0.71

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 3e-07
                           Vps39_1 17 vgpLlrleN....aCdlkdveeiLkkekkykeLidlYygkklheeALeL 61
                                      v+ + r  N    +C+ ++ve++L+k   +  L++++y++++h++   L
  gi|242399233|ref|YP_002994657.1| 27 VAFITRFLNergvECTRQKVEKTLEK-MFIAGLVEFFYKNGNHRRHYRL 74
                                      44444444422226**********87.589*************987666 PP

>> Arg_repressor  Arginine repressor, DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   1.0   3.7e-05      0.22       7      59 ..      12      67 ..       4      76 .] 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.7e-05
                                      HHHHHHHHHHS---SHHHHHHHHHTTT----HHHHHHHHHHH...T-EEEETTSTS CS
                     Arg_repressor  7 qklikkiikeekissQkelvelLkeeGidvtQatvSRdLkel...glvkvraenge 59
                                       k i+k++ke++  + + +   L+e G++ t  +v   L+++   glv    +ng+
  gi|242399233|ref|YP_002994657.1| 12 EKEILKLLKEKDELTVAFITRFLNERGVECTRQKVEKTLEKMfiaGLVEFFYKNGN 67
                                      688999****99999999*********************99955555655444444 PP

>> DUF5071  Domain of unknown function (DUF5071)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   1.8e-05      0.11      54      99 ..       9      54 ..       1      58 [. 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.8e-05
                                      GGTHHHHHHHHHSS-HHHHHHHHHHHGGGS-HHHHHHHHHHHHHHH CS
                           DUF5071 54 eelvkeiaeiLeknDeewkyfvleflveklpveskkklkeelerlv 99
                                        ++kei ++L+++De   +f+  fl+e+ ++  ++k++++le++ 
  gi|242399233|ref|YP_002994657.1|  9 ISIEKEILKLLKEKDELTVAFITRFLNERGVECTRQKVEKTLEKMF 54
                                      5789**************************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1037  (0.0578393); expected 358.6 (0.02)
Passed bias filter:                      643  (0.0358637); 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: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 512.49
//
Query:       gi|242399234|ref|YP_002994658.1|  [L=45]
Description: hypothetical protein TSIB_1255 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); 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: 0.37u 0.28s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 312.41
//
Query:       gi|242399235|ref|YP_002994659.1|  [L=251]
Description: ABC-type cobalt transport system, permease component [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-28   99.5  13.3      2e-28   99.5  13.3    1.5  2  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 !   99.5  13.3   1.1e-32     2e-28       3     215 ..      10     210 ..       8     213 .. 0.87
   2 ?   -3.4   0.2      0.34   6.1e+03      36      44 ..     229     237 ..     223     248 .. 0.50

  Alignments for each domain:
  == domain 1  score: 99.5 bits;  conditional E-value: 1.1e-32
                                       CCCCS-HHHHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHTTS---HHHHHHHCCCHCHHHHHHHHHHE...... CS
                              CbiQ   3 svlhrldprvkliwlfllllalvlapnlvtlliiiallllllllvilprvlaqalilpllflllgllillfqlitte 79 
                                       s+lh+ldprvk i  fl ++a++l +++ +l +++  ++l+l+l ++  +  ++ +   l +l+ + i+++      
  gi|242399235|ref|YP_002994659.1|  10 SFLHKLDPRVKIIGSFLGIIAFILFNSPSLLFVLFLTIVLTLVLIGKIHIREIFTV---LKPLIPIAIVAM------ 77 
                                       79*****************************8887777777777777755555555...556665555555...... PP

                                       .EECTTEEE...E-TTHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHHHHCCCSS--HHHHHHHHHHHHHHHHHHHH CS
                              CbiQ  80 gefvfagggqisitseGllrglllalRiltllslllllalTTppeeltsslerlgvPlelalillLayRfiflLlee 156
                                          +++++  ++ ++ Gl+ g+  ++R l++ +l+l l++TT+  +l+ ++ r+g+P e+ l+l++a+R+i++L+  
  gi|242399235|ref|YP_002994659.1|  78 ---IIWPFI-LKPWYFGLFIGAGYGIRLLSVALLTLGLIMTTSQKDLVLGFIRMGMPYEIGLTLTIALRYIPTLYML 150
                                       ...233333.357779*************99999999**************************************** PP

                                       HHHHHHHHHHTTTTS...SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS-SS.... CS
                              CbiQ 157 vqrikqAqklRlgds.klgirrslrslgkliaalflralkraervalAmeaRGYtgseer 215
                                       +q+i++Aqk+R+++  k ++ +++r + +++++l++ ++k a ++ +A+e+R +  s++r
  gi|242399235|ref|YP_002994659.1| 151 TQTIMDAQKSRGLELeKGNFFQRARNTVPVLIPLIVASIKTAHELSIALESRAFGASKRR 210
                                       ******************************************************986555 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 0.34
                                       HHHHHHHHH CS
                              CbiQ  36 iiallllll 44 
                                       +i+l l++l
  gi|242399235|ref|YP_002994659.1| 229 LIVLFLFAL 237
                                       222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       944  (0.0526521); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1558.16
//
Query:       gi|242399236|ref|YP_002994660.1|  [L=262]
Description: ABC-type cobalt transport system, ATPase component [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-29  103.6   0.0    1.7e-29  103.1   0.0    1.2  1  ABC_tran      ABC transporter
    7.7e-11   41.8   0.1    1.7e-09   37.4   0.1    2.1  1  SMC_N         RecF/RecN/SMC N terminal domain
    1.9e-09   37.7   0.2     0.0014   18.5   0.3    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    9.3e-05   21.9   0.0    0.00014   21.3   0.0    1.2  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
    0.00015   21.6   0.0    0.00019   21.2   0.0    1.4  1  AAA_15        AAA ATPase domain
    0.00051   20.6   0.1    0.00061   20.3   0.1    1.3  1  AAA_23        AAA domain
    0.00051   20.0   0.4     0.0077   16.2   0.1    2.1  2  NTPase_1      NTPase
    0.00055   20.4   0.0     0.0013   19.1   0.0    1.7  1  AAA_16        AAA ATPase domain
    0.00056   18.7   0.1       0.14   10.7   0.1    2.1  2  AAA_13        AAA domain
    0.00097   18.8   0.3     0.0022   17.7   0.3    1.6  1  AAA_29        P-loop containing region of AAA domain
    0.00098   18.8   0.0     0.0015   18.2   0.0    1.2  1  SRP54         SRP54-type protein, GTPase domain
     0.0015   19.1   0.0     0.0047   17.5   0.0    1.8  2  AAA_18        AAA domain
     0.0018   18.4   0.0     0.0032   17.6   0.0    1.4  1  AAA_33        AAA domain
      0.002   18.3   0.0      0.085   13.1   0.0    2.3  1  SbcCD_C       Putative exonuclease SbcCD, C subunit
     0.0026   17.7   0.3     0.0085   16.0   0.0    1.9  2  NACHT         NACHT domain
      0.003   17.6   0.0      0.051   13.6   0.0    2.2  2  AAA_14        AAA domain
     0.0033   17.4   0.0      0.006   16.6   0.0    1.4  1  AAA_5         AAA domain (dynein-related subfamily)
     0.0037   17.5   0.1      0.008   16.5   0.1    1.8  1  AAA_22        AAA domain
     0.0041   16.9   0.0     0.0069   16.1   0.0    1.3  1  AAA_30        AAA domain
     0.0045   16.3   0.0     0.0083   15.4   0.0    1.3  1  Zeta_toxin    Zeta toxin
     0.0051   17.1   0.0      0.018   15.3   0.0    2.0  1  AAA_28        AAA domain
     0.0055   17.1   0.0      0.015   15.7   0.0    1.7  2  AAA           ATPase family associated with various cellular 
     0.0055   16.4   0.0      0.024   14.3   0.0    1.9  2  AAA_24        AAA domain
  ------ inclusion threshold ------
      0.011   15.5   0.2       0.26   11.0   0.1    2.1  2  IstB_IS21     IstB-like ATP binding protein
      0.012   14.8   0.1      0.021   14.0   0.1    1.3  1  NB-ARC        NB-ARC domain
      0.016   15.1   0.0      0.029   14.3   0.0    1.5  1  ATPase_2      ATPase domain predominantly from Archaea
       0.02   14.8   0.0      0.033   14.1   0.0    1.3  1  RsgA_GTPase   RsgA GTPase
      0.025   13.6   0.0      0.044   12.8   0.0    1.3  1  T2SSE         Type II/IV secretion system protein
      0.036   13.6   0.0       0.14   11.7   0.0    2.0  2  AAA_25        AAA domain
      0.056   13.2   0.0       0.09   12.5   0.0    1.3  1  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
      0.067   13.2   0.1       0.12   12.3   0.1    1.4  1  TsaE          Threonylcarbamoyl adenosine biosynthesis protei
      0.081   11.8   0.1       0.11   11.4   0.1    1.1  1  DLIC          Dynein light intermediate chain (DLIC)
        0.1   13.0   0.0        0.2   12.0   0.0    1.5  1  RNA_helicase  RNA helicase
       0.12   11.9   0.1       0.18   11.3   0.1    1.2  1  cobW          CobW/HypB/UreG, nucleotide-binding domain
       0.12   11.8   0.1       0.26   10.7   0.1    1.4  1  PhoH          PhoH-like protein
       0.13   12.1   0.0       0.26   11.2   0.0    1.4  1  APS_kinase    Adenylylsulphate kinase
       0.31    9.8   0.7        5.7    5.6   0.4    2.1  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 !  103.1   0.0   3.5e-32   1.7e-29      11     136 ..      27     162 ..      18     163 .. 0.92

  Alignments for each domain:
  == domain 1  score: 103.1 bits;  conditional E-value: 3.5e-32
                                       TSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBHHHH....... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx....... RF
                          ABC_tran  11 gekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltvren....... 79 
                                       +e+va+vG+nG+GK+tL+k l gllkpt+G++ +dg d++e +  +l + +g+++q+ +++f e +v ++       
  gi|242399236|ref|YP_002994660.1|  27 NEIVALVGPNGSGKTTLAKHLNGLLKPTKGNVVVDGMDTREYSVAELARVVGYVFQNpENMFFEENVFKEvsfgpkn 103
                                       599******************************************************76666666666668****** PP

                                       ......HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       ......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  80 ......esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                             e ++++  al++ +l + +d+      +sLSgG+kqr+a+a++l+ kpk ++lDEpt
  gi|242399236|ref|YP_002994660.1| 104 lglsedEVEARVRWALKETNLGGYEDRSP----YSLSGGEKQRLAIACILAMKPKYIILDEPT 162
                                       ***98888888************999998....*****************************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 !   37.4   0.1   3.5e-12   1.7e-09      17     213 ..      20     209 ..       9     214 .. 0.76

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 3.5e-12
                                       EEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--..BTTCSSTTEEEEE.EEEEETTEES CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxx.xxxxxxxxxx RF
                             SMC_N  17 tvilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk..skekasvkkaeve.itfdnedkkl 90 
                                        v+l + +++ a+vGpNGSGK+ l   +    G      l+ +k + ++    ++e + ++ a+v   +f+n+++ +
  gi|242399236|ref|YP_002994660.1|  20 GVDLTIGNEIVALVGPNGSGKTTLAKHL---NG-----LLKPTKGNVVVDGmdTREYSVAELARVVgYVFQNPENMF 88 
                                       5677888999**************9988...23.....577888888888755566677777876526789999997 PP

                                       SSSSSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  91 kiekeevsisrrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDei 167
                                        +e+   ++s   k+ g se +++ +     + ++l   ++ s+ +LSgGek+ +a+a ++A++   p+   +lDe 
  gi|242399236|ref|YP_002994660.1|  89 FEENVFKEVSFGPKNLGLSEDEVEARVRWALKETNLGGYEDRSPYSLSGGEKQRLAIACILAMK---PK-YIILDEP 161
                                       666666666666666666777776666555555666666677788***************9975...44.4689*** PP

                                       TTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHH.CCC-SCEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx.xxxxxxxxxxxx RF
                             SMC_N 168 daaLDeknvkkvaellkekskn.aQfivislreem.lekadklvgvtk 213
                                          LDekn +++ +++++  ++   ++ i+++ ++ le a+++v ++k
  gi|242399236|ref|YP_002994660.1| 162 TTGLDEKNAEAIKSIIRKLYSDgHGILLITHEMDLvLELAERVVLLYK 209
                                       *****************88666589999***98861566788877776 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 !   18.5   0.3     3e-06    0.0014       1      23 [.      29      51 ..      29      89 .. 0.85
   2 !   17.6   0.0   5.6e-06    0.0027     225     301 ..     123     196 ..      81     199 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 3e-06
                            AAA_21  1 lnvliGpNgsGKSnLLdaldlla 23
                                      + +l+GpNgsGK++L + l +l 
  gi|242399236|ref|YP_002994660.1| 29 IVALVGPNGSGKTTLAKHLNGLL 51
                                      579************99998885 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 5.6e-06
                            AAA_21 225 engdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSpll 301
                                         g++ ++++++lS G k+ la++ +l+  +   + +++DEp +gL+ k  + +  ++++l + g  ++l TH   l
  gi|242399236|ref|YP_002994660.1| 123 NLGGYEDRSPYSLSGGEKQRLAIACILAMKP---KYIILDEPTTGLDEKNAEAIKSIIRKLYSDGHGILLITHEMDL 196
                                       557888999***********77777777766...56************9999999999888888999******8554 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0     3e-07   0.00014       7      56 ..      13      61 ..       8      86 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 3e-07
                      Mg_chelatase  7 GqeeakraleiaaaGgHnlllvGppGsGKtmlakrlpsllpplseeeale 56
                                      G+++a r ++++ +G+  + lvGp GsGKt lak l++ll p + + +++
  gi|242399236|ref|YP_002994660.1| 13 GKKAAIRGVDLT-IGNEIVALVGPNGSGKTTLAKHLNGLLKPTKGNVVVD 61
                                      677777777775.699999*********************9988776655 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0     4e-07   0.00019      15      55 ..      19      68 ..      17     179 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 4e-07
                            AAA_15 15 kdveidlseeltvliGkNnsGKSsilealdlFlnnkekkn..........k 55
                                      + v++ + +e+  l+G+N+sGK+++++ l+ +l+ + k n          +
  gi|242399236|ref|YP_002994660.1| 19 RGVDLTIGNEIVALVGPNGSGKTTLAKHLNGLLKPT-KGNvvvdgmdtreY 68
                                      5577889999********************999977.44445544444440 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.1   1.3e-06   0.00061      12      42 ..      20      50 ..      14     180 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.3e-06
                            AAA_23 12 dqeidFskgltlItGpNGaGKTTildAikla 42
                                      ++++  ++ +++++GpNG+GKTT+   +   
  gi|242399236|ref|YP_002994660.1| 20 GVDLTIGNEIVALVGPNGSGKTTLAKHLNGL 50
                                      556667999***************9877655 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   1.6e-05    0.0077       2      39 ..      30      69 ..      29      83 .. 0.84
   2 ?    1.8   0.0       0.4     2e+02      83     143 ..     142     203 ..     113     215 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.6e-05
                                      EEEE--TTSSHHHHHHHHHHHH.....GGGEEEEEEEEE- CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlellkss..gvkvgGfyteevr 39
                                      v++ Gp G+GKtTl k +  llk    +v v+G+ t+e+ 
  gi|242399236|ref|YP_002994660.1| 30 VALVGPNGSGKTTLAKHLNGLLKPTkgNVVVDGMDTREYS 69
                                      6789******************965559********9986 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.4
                                       HHHHHHHHHHHHHH-EEEE--..-STTGGG-HHHHHHHHHHHTTTSEEEEE--SS-.-SHHHHH CS
                          NTPase_1  83 elalealrkalseadviviDE..iGkmElkskkfkeaveevLksekpvlavihrrk.dlalvee 143
                                       +la++ +     ++  i++DE   G  E +++ +k+ ++++ + +  +l + h+ +  l+l e+
  gi|242399236|ref|YP_002994660.1| 142 RLAIACILA--MKPKYIILDEptTGLDEKNAEAIKSIIRKLYSDGHGILLITHEMDlVLELAER 203
                                       555555543..4677889999767889999999*********9888888888888444444444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   2.7e-06    0.0013      25      88 ..      28      83 ..      15     217 .. 0.52

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 2.7e-06
                            AAA_16 25 elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqllde 88
                                      e+v l+G+ G+GK++l+++l   l+ ++     g+ +  +++++ + +a+++   +++  + ++
  gi|242399236|ref|YP_002994660.1| 28 EIVALVGPNGSGKTTLAKHLNGLLKPTK-----GNVVVDGMDTREYSVAELA---RVVGYVFQN 83
                                      89******************97666663.....3333333332222333333...444444444 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.1    0.0003      0.14      23      41 ..      34      52 ..      19     144 .. 0.69
   2 !    6.7   0.0    0.0049       2.4     526     581 ..     152     204 ..      98     235 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0003
                            AAA_13 23 GwNGaGKTtLSrllrslel 41
                                      G NG+GKTtL++ l+ l +
  gi|242399236|ref|YP_002994660.1| 34 GPNGSGKTTLAKHLNGLLK 52
                                      99************99832 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0049
                            AAA_13 526 kdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleffkevkknt 581
                                       k k +++D P   LD +    + s i++ +   ++   +++ TH +++  e+ +++
  gi|242399236|ref|YP_002994660.1| 152 KPKYIILDEPTTGLDEKNAEAIKSIIRKLY---SDGHGILLITHEMDLVLELAERV 204
                                       7889*************************9...99999**********99998765 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   0.3   4.5e-06    0.0022       9      50 ..       8      55 ..       2      59 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4.5e-06
                            AAA_29  9 Wgtfdghtieid.....lkg.atlltGpsGsGKSTllDAiqalLvpak 50
                                      W+ ++g+++ i+       + ++ l+Gp+GsGK+Tl   ++ lL p+k
  gi|242399236|ref|YP_002994660.1|  8 WHVYNGKKAAIRgvdltIGNeIVALVGPNGSGKTTLAKHLNGLLKPTK 55
                                      666666544433111114446899************877777777765 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   3.1e-06    0.0015       3      39 ..      29      65 ..      27      79 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.1e-06
                                      EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEEST CS
                             SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvllvaaDt 39
                                      +++lvG++G+GKTt +  L  llk  + +v++  +Dt
  gi|242399236|ref|YP_002994660.1| 29 IVALVGPNGSGKTTLAKHLNGLLKPTKGNVVVDGMDT 65
                                      799*****************************99998 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   9.7e-06    0.0047       1      43 [.      30      82 ..      30      98 .. 0.63
   2 ?   -1.7   0.0         8   3.9e+03      53      88 ..     166     198 ..     153     219 .. 0.60

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 9.7e-06
                            AAA_18  1 IlltGtpGvGKttlakeLskrlgf..........gvnlrdvakenglllevdp 43
                                      ++l G+ G+GKttlak+L+ +l+            ++  +va   + + +v++
  gi|242399236|ref|YP_002994660.1| 30 VALVGPNGSGKTTLAKHLNGLLKPtkgnvvvdgmDTREYSVAELARVVGYVFQ 82
                                      6899**************76652245445666664444444444444444444 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 8
                            AAA_18  53 dedkldklldaleenssaleegknlvidghlaeles 88 
                                       de++ +++ +++++ +    +g+ +++  h  +l+ 
  gi|242399236|ref|YP_002994660.1| 166 DEKNAEAIKSIIRKLY---SDGHGILLITHEMDLVL 198
                                       4444444444444443...35555555555444444 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   6.6e-06    0.0032       2      24 ..      30      55 ..      29      95 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 6.6e-06
                            AAA_33  2 vllvGlpGsGKstlaerl...lkklg 24
                                      v lvG++GsGK+tla++l   lk+++
  gi|242399236|ref|YP_002994660.1| 30 VALVGPNGSGKTTLAKHLnglLKPTK 55
                                      789*************9855455555 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0   0.00018     0.085      27      88 ..     129     177 ..     110     179 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00018
                           SbcCD_C  27 srssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllell 88 
                                       +rs  +lSGGekq la  +++               +++ ++LDE   +lDe++++++ +++
  gi|242399236|ref|YP_002994660.1| 129 DRSPYSLSGGEKQRLAIACIL-------------AMKPKYIILDEPTTGLDEKNAEAIKSII 177
                                       6777899*****999999988.............2357789999999999999998876665 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.7e-05    0.0085       2      25 ..      29      52 ..      28      61 .. 0.85
   2 ?   -1.9   0.0       5.5   2.7e+03      70      86 ..     192     207 ..     161     222 .. 0.61

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.7e-05
                                      CEEEEC-TTTCHHHHHHHHHHHHC CS
                             NACHT  2 lvilqGeaGsGKTtLlqklalawa 25
                                      +v+l G++GsGKTtL+++l  +++
  gi|242399236|ref|YP_002994660.1| 29 IVALVGPNGSGKTTLAKHLNGLLK 52
                                      689***************977766 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 5.5
                                       -CCHHHHCCSCCCEEEE CS
                             NACHT  70 sevwavllelperlLli 86 
                                          + ++lel+er++l+
  gi|242399236|ref|YP_002994660.1| 192 H-EMDLVLELAERVVLL 207
                                       2.366667777777654 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   0.00011     0.051       2      58 ..      27      82 ..      26     114 .. 0.76
   2 ?    2.0   0.0       0.4   1.9e+02      64      88 ..     152     182 ..     127     221 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00011
                            AAA_14  2 rkilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelile 58
                                      ++i++++G+  +GKTtl+k+l   ll + +  + ++  d r+++ a+ +++  ++++
  gi|242399236|ref|YP_002994660.1| 27 NEIVALVGPNGSGKTTLAKHLN-GLLKPTKGNVVVDGMDTREYSVAELARVVGYVFQ 82
                                      689**************99995.4444777777777777777666655555555544 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.4
                            AAA_14  64 kktylflDEiqev......pewekalkslvd 88 
                                       k +y++lDE          + +++++++l+ 
  gi|242399236|ref|YP_002994660.1| 152 KPKYIILDEPTTGldeknaEAIKSIIRKLYS 182
                                       6789999996543333222444444444444 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 !   16.6   0.0   1.2e-05     0.006       2      29 ..      30      58 ..      29      79 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.2e-05
                                      EEEE--SSSSHHHHHHHGGGGB.S--EEE CS
                             AAA_5  2 vlLvGppGtgKselaerlaaal.nrevey 29
                                      v LvGp G+gK++la++l  +l  ++ ++
  gi|242399236|ref|YP_002994660.1| 30 VALVGPNGSGKTTLAKHLNGLLkPTKGNV 58
                                      679****************9997444433 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   1.6e-05     0.008       6      29 ..      28      51 ..      25     213 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.6e-05
                            AAA_22  6 gilvvtGesGtGKTtllrrlleql 29
                                       i++++G+ G+GKTtl++ l   l
  gi|242399236|ref|YP_002994660.1| 28 EIVALVGPNGSGKTTLAKHLNGLL 51
                                      6899**************998776 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.4e-05    0.0069      14      51 ..      23      60 ..      11      91 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.4e-05
                            AAA_30 14 ltsgdrvavltGpAGtGKttalkalreaweaaggrvig 51
                                      lt g+ +++l+Gp G+GKtt+ k+l+ +++  +g+v++
  gi|242399236|ref|YP_002994660.1| 23 LTIGNEIVALVGPNGSGKTTLAKHLNGLLKPTKGNVVV 60
                                      4556779********************99999777765 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   1.7e-05    0.0083      18      57 ..      29      68 ..      27      78 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.7e-05
                        Zeta_toxin 18 lillgGqpGAGKselaellkdelerqgnvvrldpDdlRel 57
                                      ++ l+G  G+GK++la+ l+  l+++++ v++d+ d Re+
  gi|242399236|ref|YP_002994660.1| 29 IVALVGPNGSGKTTLAKHLNGLLKPTKGNVVVDGMDTREY 68
                                      67899*******************99999999*9999998 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   3.8e-05     0.018       2      27 ..      30      60 ..      29     196 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.8e-05
                            AAA_28  2 ivitGgestGKTtlleaLa.....argypvv 27
                                      ++++G+ ++GKTtl+++L+      +g +vv
  gi|242399236|ref|YP_002994660.1| 30 VALVGPNGSGKTTLAKHLNgllkpTKGNVVV 60
                                      799***************9555432344444 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   3.1e-05     0.015       2      51 ..      31      82 ..      30      97 .. 0.72
   2 ?   -2.0   0.0         9   4.4e+03      41      64 ..     168     190 ..     134     201 .. 0.59

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.1e-05
                                      EEESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCSSSSTTHHHHHHHHHHH CS
                               AAA  2 llyGppGtGKTllakavakelg..vefleisgsellskyvgesekkirelfk 51
                                       l+Gp G GKT+lak +   l+     + ++g++ ++  v e ++ +  +f+
  gi|242399236|ref|YP_002994660.1| 31 ALVGPNGSGKTTLAKHLNGLLKptKGNVVVDGMDTREYSVAELARVVGYVFQ 82
                                      69**************999987433346677777775555555555555555 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 9
                                       HHHHHHHHHHHHHHHTSTSEEEEE CS
                               AAA  41 esekkirelfkeakekakpsilfi 64 
                                       ++++ i+ +++++ +   + il+i
  gi|242399236|ref|YP_002994660.1| 168 KNAEAIKSIIRKLYSDG-HGILLI 190
                                       33444444554444443.555544 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     5e-05     0.024       5      23 ..      30      52 ..      27      72 .. 0.81
   2 ?   -0.7   0.0         2   9.7e+02     158     171 ..     188     201 ..     155     217 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5e-05
                            AAA_24  5 iliyGpsgiGKTtlakel....g 23
                                      ++++Gp+g+GKTtlak+l    +
  gi|242399236|ref|YP_002994660.1| 30 VALVGPNGSGKTTLAKHLngllK 52
                                      789**************955551 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2
                            AAA_24 158 nelkeevDlvlran 171
                                        ++++e+Dlvl++ 
  gi|242399236|ref|YP_002994660.1| 188 LLITHEMDLVLELA 201
                                       45777777777766 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 ?   11.0   0.1   0.00053      0.26      37      67 ..      17      47 ..       9      59 .. 0.87
   2 ?    2.4   0.0      0.24   1.2e+02     106     140 ..     150     183 ..     137     197 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00053
                         IstB_IS21 37 eLatlsfiekkenivllGpsGvGKshlaial 67
                                      ++++ + +  +e ++l+Gp G GK+ la  l
  gi|242399236|ref|YP_002994660.1| 17 AIRGVDLTIGNEIVALVGPNGSGKTTLAKHL 47
                                      6777888888999**************9765 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.24
                         IstB_IS21 106 llkvdllilDdlgllpldqaeaellfeviekryer 140
                                        +k++ +ilD+   + ld+++ae +  +i k y  
  gi|242399236|ref|YP_002994660.1| 150 AMKPKYIILDEPT-TGLDEKNAEAIKSIIRKLYSD 183
                                       5688999***975.68999************9964 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   0.1   4.4e-05     0.021      19      41 ..      26      48 ..      20      58 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.4e-05
                                      CSEEEEEEESTTSSHHHHHHHHC CS
                            NB-ARC 19 qslvvalvGmgGvGKttlakqil 41
                                      +  +valvG  G+GKttlak+ +
  gi|242399236|ref|YP_002994660.1| 26 GNEIVALVGPNGSGKTTLAKHLN 48
                                      5569***************9876 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 ?   14.3   0.0     6e-05     0.029      20      82 ..      27      93 ..      24     220 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6e-05
                          ATPase_2 20 neiyfiYGpegsGKtaLlkeiienl.edkdkyviyyialreesiskldefie...eeeekkklekal 82
                                      nei+ + Gp gsGKt+L k++   l   k+  v+  ++ re+s ++l + ++   ++ e+ ++e+ +
  gi|242399236|ref|YP_002994660.1| 27 NEIVALVGPNGSGKTTLAKHLNGLLkPTKGNVVVDGMDTREYSVAELARVVGyvfQNPENMFFEENV 93
                                      7899999*************99988445566777788888888888888877777555555555555 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   6.8e-05     0.033      86     124 ..      14      52 ..       4      76 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.8e-05
                                       THTTHHHHHHHCTTSEEEEECSTTSSHHHHHHHHCTT-- CS
                       RsgA_GTPase  86 tkegleelkellkdktsvlvGqSGvGKStLinallpele 124
                                       +k++++ +   + +++++lvG+ G GK+tL ++l++ l+
  gi|242399236|ref|YP_002994660.1|  14 KKAAIRGVDLTIGNEIVALVGPNGSGKTTLAKHLNGLLK 52 
                                       56777778888999*******************998655 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     9e-05     0.044     131     174 ..      29      73 ..      14      86 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9e-05
                             T2SSE 131 lilvsGgTgsGKttllyallkeinksderivt.vEDpvEiqlega 174
                                       ++ + G+ gsGKttl+  l   ++ ++ ++v+   D++E+ +++ 
  gi|242399236|ref|YP_002994660.1|  29 IVALVGPNGSGKTTLAKHLNGLLKPTKGNVVVdGMDTREYSVAEL 73 
                                       45677******************9998887652469999998765 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   0.00029      0.14      31      53 ..      25      47 ..      15      91 .. 0.90
   2 ?   -1.0   0.0       2.2   1.1e+03     139     170 ..     150     178 ..     106     185 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00029
                            AAA_25 31 pagelallaGapgtGKttlaldl 53
                                      + +e+++l+G+ g+GKttla +l
  gi|242399236|ref|YP_002994660.1| 25 IGNEIVALVGPNGSGKTTLAKHL 47
                                      568999*************9765 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.2
                            AAA_25 139 evegvrlvviDplsralggdensnsdvgalve 170
                                       +  +++ +++D    ++g de++++++++++ 
  gi|242399236|ref|YP_002994660.1| 150 A-MKPKYIILDE--PTTGLDEKNAEAIKSIIR 178
                                       3.2356666663..345556666666666665 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00019      0.09       3      23 ..      29      49 ..      27      58 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00019
                         PduV-EutP  3 killiGkvgsGKttLtqalkg 23
                                       + l+G+ gsGKttL+++l+g
  gi|242399236|ref|YP_002994660.1| 29 IVALVGPNGSGKTTLAKHLNG 49
                                      5789***************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 ?   12.3   0.1   0.00026      0.12      19      40 ..      27      48 ..      11      59 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00026
                                      TEEEEEEESTTSSHHHHHHHHH CS
                              TsaE 19 gdvilLeGdLGaGKTtlvrgla 40
                                      +++++L G+ G+GKTtl+++l 
  gi|242399236|ref|YP_002994660.1| 27 NEIVALVGPNGSGKTTLAKHLN 48
                                      578****************985 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00022      0.11      25      55 ..      27      57 ..       3      78 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00022
                              DLIC 25 gksvlvlGedgsGkttliaklqGveeekkGr 55
                                      +  v ++G +gsGkttl   l G+ ++ kG+
  gi|242399236|ref|YP_002994660.1| 27 NEIVALVGPNGSGKTTLAKHLNGLLKPTKGN 57
                                      4456789**********************96 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00042       0.2       2      35 ..      31      59 ..      30      74 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00042
                      RNA_helicase  2 wlyGpsgeGKStlakeLakallkklklkkkdsvy 35
                                       l+Gp+g GK+tlak+L + l     +++k++v+
  gi|242399236|ref|YP_002994660.1| 31 ALVGPNGSGKTTLAKHL-NGL----LKPTKGNVV 59
                                      689*************4.333....345555555 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00038      0.18       3      26 ..      30      53 ..      28      70 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00038
                                      EEEEESTTCCHHHHHHHHHCT--S CS
                              cobW  3 tvltGflGsGKTtLlnhllenrag 26
                                      + l+G+ GsGKTtL +hl    + 
  gi|242399236|ref|YP_002994660.1| 30 VALVGPNGSGKTTLAKHLNGLLKP 53
                                      689***********9998644444 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00053      0.26      17      37 ..      25      45 ..      13      52 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00053
                                      HH-SEEEEE--TTSSTTHHHH CS
                              PhoH 17 kkndivfaiGpaGtGKtylav 37
                                        n+iv  +Gp G+GKt la 
  gi|242399236|ref|YP_002994660.1| 25 IGNEIVALVGPNGSGKTTLAK 45
                                      4799***************96 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00054      0.26       4      43 ..      29      67 ..      27      79 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00054
                                      EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTT CS
                        APS_kinase  4 vvwltGlsgsGKstianalekkLvekgisvylLdGdnvRh 43
                                      +v l G  gsGK+t+a++l+  L+ ++ + +++dG   R+
  gi|242399236|ref|YP_002994660.1| 29 IVALVGPNGSGKTTLAKHLNGLLKPTKGN-VVVDGMDTRE 67
                                      67899**************9777666544.5678877765 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 ?    5.6   0.4     0.012       5.7     234     264 ..      15      47 ..       8      62 .. 0.83
   2 ?    2.3   0.0      0.12        57     357     411 ..     157     207 ..     150     218 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.012
                                       TEEEEEEEE-SS..EEEEEE-TTSSHHHHHHHH CS
                        ABC_ATPase 234 gkkvsGmgipkG..vtlIvGggfhGKsTLLeAl 264
                                       + +++G+ +  G  ++++vG++  GK+TL + l
  gi|242399236|ref|YP_002994660.1|  15 KAAIRGVDLTIGneIVALVGPNGSGKTTLAKHL 47 
                                       56788876665555***************9877 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.12
                                       ---HHHHHHS-GGG--B--HHHCHHHHHHHH--EEEEEESS-GCCTTT-SEEEEE CS
                        ABC_ATPase 357 irDermqelvskekepitplvdrvrelykklgvstilvvggsgdyldvAdtvilm 411
                                       i De    l +k++e+i++++ ++ ++    g  ++l++  ++  l++A++v+l+
  gi|242399236|ref|YP_002994660.1| 157 ILDEPTTGLDEKNAEAIKSIIRKLYSD----GHGILLITHEMDLVLELAERVVLL 207
                                       668888888899999999999888777....7788999**************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      573  (0.0319594); 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: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.48
# Mc/sec: 1656.36
//
Query:       gi|242399237|ref|YP_002994661.1|  [L=171]
Description: Biotin biosynthesis protein BioY [Thermococcus sibiricus MM 739]
Scores for 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-37  126.3  17.9    1.1e-36  125.8  17.9    1.2  1  BioY         BioY family
    8.5e-06   26.0  21.2    1.1e-05   25.6  21.2    1.1  1  ECF_trnsprt  ECF transporter, substrate-specific component
  ------ inclusion threshold ------
        3.1    7.7  18.3        0.6   10.1  13.6    2.2  2  Colicin_V    Colicin V production protein


Domain annotation for each model (and alignments):
>> BioY  BioY family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.8  17.9   1.9e-40   1.1e-36       2     134 ..      27     166 ..      26     167 .. 0.94

  Alignments for each domain:
  == domain 1  score: 125.8 bits;  conditional E-value: 1.9e-40
                              BioY   2 gpvpitlqtlavllaglllgprrgalavllYlllGalglPvfag.ggGlavllgptgGYllGFlvaalvvgll...k 74 
                                       g vpit+q l+vll+gl+lgp +g+l++l+Y+++Ga+glPvfa+ +gG+a++ gptgGYl++F++aa+++g++   +
  gi|242399237|ref|YP_002994661.1|  27 GTVPITFQLLFVLLSGLILGPHLGFLSQLIYVFMGAIGLPVFASfSGGFAYIYGPTGGYLMAFPIAAYLAGFFskrE 103
                                       78******************************************77***************************8642 PP

                              BioY  75 k.laelllallagllviyalGvlwlalv..lslaaalaagvlpfipgdlvkavlaallakalr 134
                                       + + +++l  ++++ v+y+lG++ l l+   ++++a+++gv+pf++ dl k +l +l+ak+++
  gi|242399237|ref|YP_002994661.1| 104 EnILNYILGTFLAISVVYLLGWFRLGLFmgGDFKKAFIVGVAPFVLIDLGKGALSILIAKRVK 166
                                       2699999*9******************74556****************************986 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 !   25.6  21.2   1.8e-09   1.1e-05       1     168 [.       4     162 ..       4     166 .. 0.68

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1.8e-09
                                       HHHHHHHHHHHHHHHHHHHHEEE.STSEEESHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHCHT-SSTTHHHH.... CS
                       ECF_trnsprt   1 kklvitglliAisivlsllgyiplpnikitiihipvllggllfGpikGailgiitsvlkailtggtgalssfv.... 73 
                                       k ++ ++l++A+ +v++    ip+++++it+  + vll+gl++Gp  G++  +i  +++ai  + +   +sf     
  gi|242399237|ref|YP_002994661.1|   4 KDIAYSALFVALTAVGA-QISIPIGTVPITFQLLFVLLSGLILGPHLGFLSQLIYVFMGAIGLPVF---ASFSggfa 76 
                                       67899************.7777777889999999999*************************6444...44444578 PP

                                       HHHHHHHHCHHHHHHHHHHCCCHTTHHHHHHHHHHHHCCCCCHHHHHHHCCC.HHHHS.............--HHHH CS
                       ECF_trnsprt  74 piaflsriligliagllykkgkkknlkeivvsfilagvlgtivatllvllii.lplylklktakaiaiagkallaai 149
                                        i+ ++++ ++  +   y  g   ++ e ++ +il+++l   v  ll ++ + l++ + +          k+++++ 
  gi|242399237|ref|YP_002994661.1|  77 YIYGPTGGYLMAFPIAAYLAGFFSKREENILNYILGTFLAISVVYLLGWFRLgLFMGG-DF---------KKAFIVG 143
                                       5555555555555555666666666666566666666555444444433333133333.22.........3666677 PP

                                       HHHHHCCTTCCHHHHHHHH CS
                       ECF_trnsprt 150 lgpiivkglieaiiaaiiv 168
                                       + p ++ +l +++++++i+
  gi|242399237|ref|YP_002994661.1| 144 VAPFVLIDLGKGALSILIA 162
                                       7777777777777777765 PP

>> Colicin_V  Colicin V production protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.1       1.5   8.9e+03      63      75 ..       7      19 ..       5      24 .. 0.51
   2 ?   10.1  13.6    0.0001       0.6       3      81 ..      33     131 ..      31     169 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.5
                         Colicin_V 63 aflllfllvlliv 75
                                      a+ +lf++  +++
  gi|242399237|ref|YP_002994661.1|  7 AYSALFVALTAVG 19
                                      4444555444443 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0001
                         Colicin_V   3 liillilllsallGlrrGfvrevlsllgwvvafvvasllypslaellae...................lilspalaa 60 
                                       + +l++ll +++lG   Gf+ +++++ + ++++ v + ++  +a ++++                     +++ l +
  gi|242399237|ref|YP_002994661.1|  33 FQLLFVLLSGLILGPHLGFLSQLIYVFMGAIGLPVFASFSGGFAYIYGPtggylmafpiaaylagffsKREENILNY 109
                                       6689*************************************************************998778899999 PP

                         Colicin_V  61 iiaflllfllvllivsl.lgal 81 
                                       i++ +l+  +v+l++++ lg +
  gi|242399237|ref|YP_002994661.1| 110 ILGTFLAISVVYLLGWFrLGLF 131
                                       9999999999999977624444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1107.45
//
Query:       gi|242399238|ref|YP_002994662.1|  [L=193]
Description: molybdopterin-guanine dinucleotide biosynthesis protein A [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.1e-05   22.9   0.0    0.00012   22.5   0.0    1.1  1  NTP_transf_3  MobA-like NTP transferase 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 !   22.5   0.0   6.7e-09   0.00012      18     139 ..      13     131 ..      10     153 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 6.7e-09
                                       HHCCCCCCHHHHHHHHHCTT..-CEEEEECSHCHHHHHHTTCTS-EEE-.TTSS-SHHHHHHHHHHHH.SSSCEEEE CS
                      NTP_transf_3  18 llplggkpllervldalraag.vdevvvvggdeevlaalarlgvrvved.edpgkgplaslaaalraaadadavlvl 92 
                                       ll ++++p+++ v ++l a++ +dev++  + +e++    ++ +++ +  +   k+ l++l+ al +   +  v+++
  gi|242399238|ref|YP_002994662.1|  13 LLSINEEPMMRIVERRLLASKrIDEVIMLIRKNELK----KFSLHTSNLkPLDAKNKLEALYKALPS---SGEVFLV 82 
                                       8999***************9659*********9876....566665444144469**********85...58***** PP

                                       ETT-TT--HHHHHHHHHCHHHHTSSEEEEESSSEEEECC..EEEGGGHH CS
                      NTP_transf_3  93 acDmPlltpelverllaaaaasgadvvvptyegerghpl..lfrarlls 139
                                        + mPl+ p lv++l   + + ++++++p ++++  +    ++ +++l+
  gi|242399238|ref|YP_002994662.1|  83 EGNMPLIMPFLVNYLSTMFYELEYEALIPGWADGTLEVThgFYDSKALK 131
                                       *********************************9988886666554443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1249.98
//
Query:       gi|242399239|ref|YP_002994663.1|  [L=38]
Description: hypothetical protein TSIB_1260 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      186  (0.0103743); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.32s 00:00:00.67 Elapsed: 00:00:00.45
# Mc/sec: 253.97
//
Query:       gi|242399240|ref|YP_002994664.1|  [L=206]
Description: hypothetical protein TSIB_1261 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       783  (0.0436723); expected 358.6 (0.02)
Passed bias filter:                      568  (0.0316805); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1311.88
//
Query:       gi|242399241|ref|YP_002994665.1|  [L=122]
Description: metalloprotease, containing Jab1/MPN domain [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-10   41.3   0.0    1.6e-10   40.8   0.0    1.2  1  Prok-JAB  Prokaryotic homologs of the 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 !   40.8   0.0     9e-15   1.6e-10       6     106 ..      11      99 ..       7     108 .. 0.83

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 9e-15
                          Prok-JAB   6 salvaharrahpeEtcGlllgkeseseevivvplvnewsnrfeipdpedslarlkfearerglevvgiwHSHpggsa 82 
                                       + l++ a+  +p+E +G+l  k  + eev ++p              ++s+  ++ ++  +++++ g++HSHpg+s+
  gi|242399241|ref|YP_002994665.1|  11 DYLIQLAKDFYPNEFGGFLREKNGIFEEVLIIPKG---------YFGKESIYFDT-WLLPHDENIKGTVHSHPGPSP 77 
                                       55677788889999999999999999999999965.........25788888999.********************* PP

                          Prok-JAB  83 rPSetDrrdaaalarvkalliivg 106
                                       rPS+ D + +++ +  +++lii+ 
  gi|242399241|ref|YP_002994665.1|  78 RPSQVDKKFFSKFG--GVHLIIAY 99 
                                       ************87..78888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 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:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 938.48
//
Query:       gi|242399242|ref|YP_002994666.1|  [L=108]
Description: Transcriptional regulator [Thermococcus sibiricus MM 739]
Scores for complete 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   46.0   1.2    4.4e-12   45.7   0.2    1.8  2  HTH_5        Bacterial regulatory protein, arsR family
    1.4e-07   31.5   0.0    2.2e-07   30.9   0.0    1.3  1  HTH_20       Helix-turn-helix domain
  ------ inclusion threshold ------
      0.022   14.4   0.3      0.039   13.5   0.2    1.6  1  ArsR         ArsR transcriptional regulator
       0.11   13.1   0.1       0.29   11.6   0.1    1.7  2  HTH_27       Winged helix DNA-binding domain
        3.5    7.6   0.0        3.5    7.6   0.0    3.3  3  Nore1-SARAH  Novel Ras effector 1 C-terminal SARAH (Sav/Rassf


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 !   45.7   0.2   1.2e-15   4.4e-12       1      45 [.      34      78 ..      34      80 .. 0.96
   2 ?   -2.5   0.1       1.3   4.7e+03      35      41 ..      99     105 ..      96     106 .. 0.76

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 1.2e-15
                                      SHHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5  1 dptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLV 45
                                      +p R  I+k+L ++ +cvc +a++l+  q  +ShHL+ L++++L+
  gi|242399242|ref|YP_002994666.1| 34 NPIRAGIIKMLKKRWMCVCLIAKALNQDQTLISHHLRTLKNMNLL 78
                                      699****************************************98 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.3
                                       HHHHHHH CS
                             HTH_5  35 HLkkLre 41 
                                       +L++L++
  gi|242399242|ref|YP_002994666.1|  99 YLSILEK 105
                                       7899987 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.0     6e-11   2.2e-07       3      61 .]      28      85 ..      26      85 .. 0.93

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 6e-11
                                      HHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTEE CS
                            HTH_20  3 iaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvregr 61
                                       +++L++P R++i ++L  ++ +++  +a++l  +++ +s+HLr+L    L++ +reg+
  gi|242399242|ref|YP_002994666.1| 28 FIKVLSNPIRAGIIKML-KKRWMCVCLIAKALNQDQTLISHHLRTLKNMNLLHERREGK 85
                                      5799*************.**************777777*******************96 PP

>> ArsR  ArsR transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.2   1.1e-05     0.039       6      60 ..      24      81 ..      20     107 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.1e-05
                              ArsR  6 eLvpllqvfdsetkkkvyeelskeWlteeeleeklgee...veealklLkkikliEsq 60
                                      eL   ++v++++    + + l+k+W+    +++ l+++    ++ l+ Lk+++l+ ++
  gi|242399242|ref|YP_002994666.1| 24 ELTNFIKVLSNPIRAGIIKMLKKRWMCVCLIAKALNQDqtlISHHLRTLKNMNLLHER 81
                                      677889999999999*********************997777899*********9876 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.5   5.4e+03      17      25 ..      37      45 ..      24      50 .. 0.46
   2 ?   11.6   0.1   8.2e-05      0.29      24      60 ..      54      84 ..      53      91 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.5
                            HTH_27 17 rrkkladlc 25
                                      r  ++++l 
  gi|242399242|ref|YP_002994666.1| 37 RAGIIKMLK 45
                                      333333333 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 8.2e-05
                            HTH_27 24 lcgrlnvedshisyslkkLtekGLvertgdeadrrek 60
                                      ++++ln +++ is  l+ L ++ L+      ++rre 
  gi|242399242|ref|YP_002994666.1| 54 IAKALNQDQTLISHHLRTLKNMNLL------HERREG 84
                                      789**********************......445543 PP

>> Nore1-SARAH  Novel Ras effector 1 C-terminal SARAH (Sav/Rassf/Hpo) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   3.1         1   3.8e+03      12      21 ..       9      18 ..       9      20 .. 0.80
   2 ?    7.6   0.0   0.00096       3.5       5      14 ..      23      32 ..      22      34 .. 0.92
   3 ?    2.6   0.5     0.037   1.3e+02       6      17 ..      95     106 ..      92     106 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1
                       Nore1-SARAH 12 riLeeEEeee 21
                                      +iL+ EEe e
  gi|242399242|ref|YP_002994666.1|  9 EILDLEEEIE 18
                                      59*****965 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00096
                       Nore1-SARAH  5 PELqnFLriL 14
                                      PEL nF+++L
  gi|242399242|ref|YP_002994666.1| 23 PELTNFIKVL 32
                                      9*******99 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.037
                       Nore1-SARAH   6 ELqnFLriLeeE 17 
                                       EL   L iLe+E
  gi|242399242|ref|YP_002994666.1|  95 ELKKYLSILEKE 106
                                       9999*******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       792  (0.0441742); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); 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: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 701.30
//
Query:       gi|242399243|ref|YP_002994667.1|  [L=100]
Description: regulatory protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-14   53.4   1.2    2.8e-14   53.0   0.5    1.5  2  MazG           MazG nucleotide pyrophosphohydrolase domain
     0.0015   18.8   0.2     0.0017   18.6   0.2    1.1  1  dUTPase_2      dUTPase
  ------ inclusion threshold ------
      0.021   14.0   0.1      0.024   13.7   0.1    1.0  1  hDGE_amylase   Glycogen debranching enzyme, glucanotransferas
       0.03   14.9   0.1      0.048   14.2   0.1    1.5  1  Colicin_immun  Bacterial self-protective colicin-like immunit
      0.051   13.8   0.3      0.072   13.4   0.3    1.3  1  MazG-like      MazG-like family


Domain annotation for each model (and alignments):
>> MazG  MazG nucleotide pyrophosphohydrolase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.6   5.8e+03      24      34 ..       6      16 ..       4      16 .. 0.77
   2 !   53.0   0.5   7.9e-18   2.8e-14       5      73 ..      23      94 ..      20      95 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.6
                                      T-HHHHHHHHH CS
                              MazG 24 edrdeleeELG 34
                                      e+ d+l +E G
  gi|242399243|ref|YP_002994667.1|  6 EKVDSLIKEFG 16
                                      67889999977 PP

  == domain 2  score: 53.0 bits;  conditional E-value: 7.9e-18
                                      HHHHHHHHHHHHHHHHHHT.......T-HHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHH-GGG CS
                              MazG  5 tllaylleEvgEvaeaIkk.......edrdeleeELGDvLlqvlflaniaeeeggidledvaetileKlerRhphv 73
                                      ++la+++eE gE+  +I k       ++  ++eeELGDvL+ ++++an     ++id+e+++++++ K+++R++++
  gi|242399243|ref|YP_002994667.1| 23 AMLAAVIEELGELSNEILKlediktsKEIPKVEEELGDVLFALFCIANY----YNIDVEKALNKTIIKYSSRDKER 94
                                      7899*************9976666555555******************8....********************976 PP

>> dUTPase_2  dUTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.2   4.7e-07    0.0017       6     100 ..       2      86 ..       1      98 [. 0.79

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 4.7e-07
                                       HHHHHHHHHHHSTTH.....HH-HHHHH....HHHHHHHHHHHTTS.---SSSSTT---HHHHHHHHHHHHHHHHHH CS
                         dUTPase_2   6 lelQkeLderiekkwnlkkkrkklsdwleekllAllvElaElanetrsfKyWknkkksdlekvleElvDilHFllsl 82 
                                        +lQ++ d+ i++     +  + +  +l     A++ El+El ne+   K    k+ +++ kv eEl D+l  l  +
  gi|242399243|ref|YP_002994667.1|   2 KNLQEKVDSLIKEFG---GYWE-PFAML----AAVIEELGELSNEI--LKLEDIKTSKEIPKVEEELGDVLFALFCI 68 
                                       567888888888877...2222.33344....888889********..9999999999******************* PP

                                       HHCHHCT-GGGGCSSCCC CS
                         dUTPase_2  83 alelkdekeeasvekels 100
                                       a+ ++++ e+a  ++ ++
  gi|242399243|ref|YP_002994667.1|  69 ANYYNIDVEKALNKTIIK 86 
                                       ****99999985555544 PP

>> hDGE_amylase  Glycogen debranching enzyme, glucanotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   6.8e-06     0.024     135     200 ..      31      93 ..      18      99 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.8e-06
                                       CCCTCCCHCCTSSS-SS---HCHHHHHHHHHHHHTCGGCTTGTTTS--CHHHHHHHHHSTTSS--- CS
                      hDGE_amylase 135 allefskeleklglpteikseedlekvmealkeevleklklweyyvvdvekeveelkealeesekk 200
                                       +l e+s+e+ kl   ++ik+++++ kv e+l + +++ + + +yy +dvek+++++  ++++++k+
  gi|242399243|ref|YP_002994667.1|  31 ELGELSNEILKL---EDIKTSKEIPKVEEELGDVLFALFCIANYYNIDVEKALNKTIIKYSSRDKE 93 
                                       455666666554...59************************************9999888666443 PP

>> Colicin_immun  Bacterial self-protective colicin-like immunity
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   1.3e-05     0.048      37      66 ..      49      78 ..      29      94 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.3e-05
                     Colicin_immun 37 gsllklneklsevldslFlavdlYnpdsel 66
                                      + + k++e+l  vl +lF+ +++Yn d e 
  gi|242399243|ref|YP_002994667.1| 49 KEIPKVEEELGDVLFALFCIANYYNIDVEK 78
                                      45669**********************874 PP

>> MazG-like  MazG-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.3     2e-05     0.072      14      66 ..      38      87 ..      25      98 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2e-05
                         MazG-like 14 ellksveelfkallkgseeeildeLAdviiylylLAdrlGidfee.ideklkkk 66
                                      e+l    +l    ++++  ++ +eL dv+  l+  A+  +id+e+ +++++ k 
  gi|242399243|ref|YP_002994667.1| 38 EIL----KLEDIKTSKEIPKVEEELGDVLFALFCIANYYNIDVEKaLNKTIIKY 87
                                      333....3333334478889*************************999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       734  (0.0409393); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); 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: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.51
# Mc/sec: 594.00
//
Query:       gi|242399244|ref|YP_002994668.1|  [L=149]
Description: transcription regulator, Lrp/AsnC family [Thermococcus sibiricus MM 739]
Scores for complete 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   50.2   2.5    4.3e-13   48.6   0.7    2.3  2  HTH_24          Winged helix-turn-helix DNA-binding
    2.7e-11   43.1   1.7    5.9e-11   42.0   1.3    1.8  2  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    2.5e-08   33.8   0.2    2.1e-07   30.8   0.1    2.0  2  HTH_Crp_2       Crp-like helix-turn-helix domain
    0.00021   21.1   0.8     0.0022   17.8   0.3    2.3  2  TrmB            Sugar-specific transcriptional regulator TrmB
    0.00034   20.4   0.3    0.00066   19.5   0.3    1.4  1  MarR_2          MarR family
    0.00037   20.6   0.1     0.0011   19.2   0.1    1.8  2  HTH_34          Winged helix DNA-binding domain
    0.00041   20.4   0.3    0.00084   19.4   0.2    1.6  1  HTH_28          Helix-turn-helix domain
    0.00056   19.8   0.3     0.0016   18.3   0.3    1.7  1  MarR            MarR family
    0.00082   19.3   0.6     0.0031   17.4   0.1    2.1  2  HTH_11          HTH domain
     0.0019   18.5   0.1      0.012   16.0   0.1    2.1  2  Rrf2            Transcriptional regulator
     0.0037   17.2   0.1     0.0076   16.2   0.1    1.5  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
     0.0081   16.2   0.1      0.014   15.5   0.1    1.3  1  HTH_20          Helix-turn-helix domain
  ------ inclusion threshold ------
      0.013   15.5   0.2       0.02   14.9   0.2    1.3  1  Replic_Relax    Replication-relaxation
      0.016   15.0   0.7      0.042   13.7   0.7    1.8  1  HTH_23          Homeodomain-like domain
      0.022   14.8   0.1      0.044   13.9   0.1    1.4  1  FeoC            FeoC like transcriptional regulator
      0.033   13.9   0.5      0.059   13.0   0.5    1.4  1  Crp             Bacterial regulatory proteins, crp family
      0.033   14.0   0.9       0.16   11.8   0.2    2.2  2  HxlR            HxlR-like helix-turn-helix
      0.038   14.0   0.1      0.072   13.1   0.1    1.4  1  FAM180          FAM180 family
      0.038   13.7   0.9       0.12   12.0   0.4    1.9  2  Stk19           Serine-threonine protein kinase 19
      0.049   14.0   1.0          3    8.3   0.1    2.6  2  ATR13           Avirulence protein ATR13, RxLR effector
       0.06   13.0   0.4       0.13   12.0   0.4    1.5  1  GntR            Bacterial regulatory proteins, gntR family
      0.072   12.4   0.1       0.13   11.5   0.1    1.4  1  EAP30           EAP30/Vps36 family
      0.084   13.3   1.7        3.4    8.1   0.3    2.1  2  DUF1690         Protein of Unknown function (DUF1690)
      0.087   13.4   0.3        0.5   11.0   0.0    2.0  2  Phage_rep_O     Bacteriophage replication protein O
       0.12   12.2   4.4       0.24   11.2   1.1    2.3  2  HTH_DeoR        DeoR-like helix-turn-helix domain
       0.16   12.1   2.6       0.18   11.9   0.2    2.0  2  DUF2250         Uncharacterized protein conserved in archaea 
       0.18   11.5   2.2        0.9    9.2   0.1    2.4  2  DUF4423         Domain of unknown function (DUF4423)


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.6   0.7   6.4e-16   4.3e-13       2      48 .]       6      52 ..       5      52 .. 0.97
   2 ?    0.6   0.0      0.62   4.1e+02       6      17 ..      81      92 ..      78      96 .. 0.83

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 6.4e-16
                            HTH_24  2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      d+ d++I+++L kn+r ++r+LAe l+ +++ v rrl+rLe+eG Ik
  gi|242399244|ref|YP_002994668.1|  6 DKFDLQIMSVLAKNARVNYRQLAELLNTTRQRVARRLERLEREGTIK 52
                                      99******************************************997 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.62
                            HTH_24  6 rkILelLqknpr 17
                                       kI+e+L+++ +
  gi|242399244|ref|YP_002994668.1| 81 EKIIETLKEDDD 92
                                      69*******976 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.0   1.3   8.8e-14   5.9e-11       1      42 []       5      46 ..       5      46 .. 0.98
   2 ?   -2.1   0.0       5.4   3.6e+03       7      15 ..      82      90 ..      81      95 .. 0.87

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 8.8e-14
                     HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrLe 42
                                      +D++D++I++ L ++aR  y++LAe ++ ++++v+rR++rLe
  gi|242399244|ref|YP_002994668.1|  5 IDKFDLQIMSVLAKNARVNYRQLAELLNTTRQRVARRLERLE 46
                                      6****************************************8 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 5.4
                     HTH_AsnC-type  7 kILeaLqed 15
                                      kI+e L ed
  gi|242399244|ref|YP_002994668.1| 82 KIIETLKED 90
                                      899999998 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 !   30.8   0.1   3.1e-10   2.1e-07      21      65 ..      21      63 ..       9      65 .. 0.90
   2 ?    0.8   0.0      0.72   4.8e+02      32      59 ..      77     109 ..      76     118 .. 0.69

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 3.1e-10
                                      EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETEEEEES-HHHH CS
                         HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglisrgrririldleaL 65
                                      +++ ++lA++l++tr+ v r l +L+reg i++    +i+d ++L
  gi|242399244|ref|YP_002994668.1| 21 RVNYRQLAELLNTTRQRVARRLERLEREGTIKKY--TIIPDFDKL 63
                                      68899***************************75..699999998 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.72
                                       TSSHHHHHHHHHHHHHTTSEEE..T.EE..EEE CS
                         HTH_Crp_2  32 GltretvsrilseLkreglisr..g.rr..iri 59 
                                       G++ e +  +l+e  + ++i+r  g ++  ++i
  gi|242399244|ref|YP_002994668.1|  77 GTSIEKIIETLKEDDDVKVIQRaiGyHQliVHI 109
                                       899999999999999999999434633344445 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.3   3.3e-06    0.0022      10      56 ..       9      55 ..       4      73 .. 0.85
   2 ?    1.5   0.0       0.4   2.7e+02      35      58 ..      76      99 ..      69     119 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.3e-06
                                      CCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                              TrmB 10 EakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerek 56
                                      + ++  +L k+ + + +++ae l+  r++v + L++Le+ G +++  
  gi|242399244|ref|YP_002994668.1|  9 DLQIMSVLAKNARVNYRQLAELLNTTRQRVARRLERLEREGTIKKYT 55
                                      677778999*********************************99865 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.4
                                      SCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB 35 prskvYevLrsLedkGlVerekgr 58
                                      p +++ ++++ L++ + V+++++ 
  gi|242399244|ref|YP_002994668.1| 76 PGTSIEKIIETLKEDDDVKVIQRA 99
                                      678999*********999999875 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.3   9.9e-07   0.00066       9      52 ..      11      52 ..       9      56 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 9.9e-07
                                      HHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                            MarR_2  9 rvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                                      +++ +L+ + +  ++ ++la+ l+ ++++v r+l+rL++ G + 
  gi|242399244|ref|YP_002994668.1| 11 QIMSVLAKNAR--VNYRQLAELLNTTRQRVARRLERLEREGTIK 52
                                      67788888887..999************************9886 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 !   19.2   0.1   1.6e-06    0.0011       3      45 ..      10      52 ..       8      56 .. 0.95
   2 ?   -2.4   0.0       8.6   5.7e+03      39      55 ..      61      76 ..      57      81 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.6e-06
                            HTH_34  3 lavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYie 45
                                      l+++s+La++ ++++++l e l++t  + +  l+ Le  g i+
  gi|242399244|ref|YP_002994668.1| 10 LQIMSVLAKNARVNYRQLAELLNTTRQRVARRLERLEREGTIK 52
                                      89************************************99886 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 8.6
                            HTH_34 39 ekagYievdkefkgkkp 55
                                       k gY+ v ++ + k p
  gi|242399244|ref|YP_002994668.1| 61 DKLGYLYVAIGISIK-P 76
                                      688998888777655.5 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.2   1.3e-06   0.00084      10      40 ..      19      49 ..      10      53 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.3e-06
                            HTH_28 10 aaGhsvreaArelgisrrtvyrWikryeegG 40
                                       a +++r++A++l+++r++v r + r+e +G
  gi|242399244|ref|YP_002994668.1| 19 NARVNYRQLAELLNTTRQRVARRLERLEREG 49
                                      3567************************999 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.3   2.4e-06    0.0016       8      50 ..      12      54 ..       9      56 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.4e-06
                                      HHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR  8 iLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRs 50
                                      i+  l+ +   +  +La+ l++++  v r l rLe++G i+++
  gi|242399244|ref|YP_002994668.1| 12 IMSVLAKNARVNYRQLAELLNTTRQRVARRLERLEREGTIKKY 54
                                      77778888889999**************************987 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   4.7e-06    0.0031       3      44 ..      10      54 ..       9      65 .. 0.85
   2 ?   -0.9   0.0       2.5   1.7e+03       3      12 ..      81      90 ..      78     102 .. 0.62

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.7e-06
                            HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg....v 44
                                      lqi+  L +++  ++  +LAe Ln +r+ v r++++Le  g    +
  gi|242399244|ref|YP_002994668.1| 10 LQIMSVL-AKNARVNYRQLAELLNTTRQRVARRLERLEREGtikkY 54
                                      5888999.66666**************************9965554 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.5
                            HTH_11  3 lqilelLlea 12
                                      ++i+e L+e 
  gi|242399244|ref|YP_002994668.1| 81 EKIIETLKED 90
                                      4566666443 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   1.8e-05     0.012      11      56 ..      10      52 ..       3      55 .. 0.91
   2 ?   -0.2   0.0       1.9   1.3e+03      41      57 ..      79      95 ..      74     105 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.8e-05
                                      HHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2 11 lhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvk 56
                                      l+++ +Lak+++   v+ +++ae  n+ ++ +++ l++L+++g +k
  gi|242399244|ref|YP_002994668.1| 10 LQIMSVLAKNAR---VNYRQLAELLNTTRQRVARRLERLEREGTIK 52
                                      788999999988...99**************************998 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.9
                                      HHHHHHHHHHHTTSEEE CS
                              Rrf2 41 ylekilakLrkaglvks 57
                                       +eki+++L++ + vk+
  gi|242399244|ref|YP_002994668.1| 79 SIEKIIETLKEDDDVKV 95
                                      68999999999887776 PP

>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   1.1e-05    0.0076       1      73 [.      70     141 ..      70     143 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.1e-05
                                       EEEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEES.SHHHHHHHHHHTTTTSTTEEEEEEEEEE CS
                    AsnC_trans_reg   1 vlvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvr.dlealerflreklaslpgvartetsivl 73 
                                       +++s++pg   ++e+++e l+e + V+ + r  G +++++++v++ +++++e+ ++e   +++g++ ++ s+v 
  gi|242399244|ref|YP_002994668.1|  70 IGISIKPGT--SIEKIIETLKEDDDVKVIQRAIGYHQLIVHIVAPkNMKEIEKKIHELSKKVEGLEGMDMSFVT 141
                                       689999999..9*******************************9549*************************97 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   2.1e-05     0.014      13      54 ..      10      51 ..       5      55 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.1e-05
                                      HHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTE CS
                            HTH_20 13 rrilraLaraegltaselaerldlskntlsyHLrvLeeagLv 54
                                      + i++ La ++ +   +lae+l ++++ + ++L+ Le+ g +
  gi|242399244|ref|YP_002994668.1| 10 LQIMSVLAKNARVNYRQLAELLNTTRQRVARRLERLEREGTI 51
                                      67999999999**************************98866 PP

>> Replic_Relax  Replication-relaxation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.2   3.1e-05      0.02       4      43 ..      16      54 ..      13      67 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.1e-05
                      Replic_Relax  4 LaehrvlTtrqiarllfashratarrrLarLrelgllsrl 43
                                      La+    + rq+a+ll+ ++++ + rrL rL+++g ++++
  gi|242399244|ref|YP_002994668.1| 16 LAKNARVNYRQLAELLNTTRQR-VARRLERLEREGTIKKY 54
                                      566666788*************.*************9985 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.7   6.3e-05     0.042      15      45 ..      17      49 ..      10      54 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.3e-05
                            HTH_23 15 ae..GlsvreIAreLgvsrrTvyrwlkryreeG 45
                                      a+  + ++r+ A++L+ +r+ v r l+r ++eG
  gi|242399244|ref|YP_002994668.1| 17 AKnaRVNYRQLAELLNTTRQRVARRLERLEREG 49
                                      3335899*********************98898 PP

>> FeoC  FeoC like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   6.6e-05     0.044       4      47 ..      11      54 ..      10      57 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.6e-05
                              FeoC  4 elkeyleergrvslkeLsrhfkaspealeamLeqwvrkGrvekv 47
                                      ++ + l+++ rv+ ++L+  ++++ + +   Le ++r G ++k 
  gi|242399244|ref|YP_002994668.1| 11 QIMSVLAKNARVNYRQLAELLNTTRQRVARRLERLEREGTIKKY 54
                                      566789***********************************986 PP

>> Crp  Bacterial regulatory proteins, crp family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.5   8.9e-05     0.059       7      32 .]      26      51 ..      23      51 .. 0.96

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.9e-05
                                      HHHHHHTS-HHHHHHHHHHHHHTTSE CS
                               Crp  7 dIAdylGlTrETVSRlLtrLrekGLI 32
                                      ++A++l +Tr  V R L rL+++G+I
  gi|242399244|ref|YP_002994668.1| 26 QLAELLNTTRQRVARRLERLEREGTI 51
                                      79**********************98 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   0.00025      0.16       5      74 ..       7      76 ..       5      92 .. 0.79
   2 ?    0.1   0.0       1.1   7.2e+02      17      35 ..     111     129 ..      95     133 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00025
                                      TTHHHHHHHHTT.S-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHH CS
                              HxlR  5 kWkllilvellk.gkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrslep 74
                                      k  l i+  l k  +  + +l++ l + +++  a+rL +Le++g i++ ++     k  Y   + G s++p
  gi|242399244|ref|YP_002994668.1|  7 KFDLQIMSVLAKnARVNYRQLAELL-NTTRQRVARRLERLEREGTIKKYTIIPDFDKLGYLYVAIGISIKP 76
                                      5566677777663555789999999.8899999***************99988889999998888777765 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.1
                                       S-EEHHHHHHHSTTS-HHH CS
                              HxlR  17 gkkRfselkralpkisqkm 35 
                                        +k ++e+++++ ++s+k+
  gi|242399244|ref|YP_002994668.1| 111 APKNMKEIEKKIHELSKKV 129
                                       4667888999988888876 PP

>> FAM180  FAM180 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   0.00011     0.072      40      95 ..      80     136 ..      74     142 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00011
                            FAM180  40 ldksgelsikDeELaSlrkarkle.viceeviPkkledirrliaelsrksgpLkkeD 95 
                                       ++k  e + +D+++  +++a  ++ +i++ v Pk++++i + i+els+k + L+  D
  gi|242399244|ref|YP_002994668.1|  80 IEKIIETLKEDDDVKVIQRAIGYHqLIVHIVAPKNMKEIEKKIHELSKKVEGLEGMD 136
                                       55555666677888888888777615555567*****************99998877 PP

>> Stk19  Serine-threonine protein kinase 19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.4   0.00018      0.12      33      67 ..      22      56 ..       8      99 .. 0.87
   2 ?   -1.1   0.0       1.9   1.3e+03      45     219 ..     114     137 ..      90     142 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00018
                             Stk19 33 vtvahlhsllaqsptkvereleelirkgklrklvi 67
                                      v   +l  ll++++ +v r+le+l r+g+++k +i
  gi|242399244|ref|YP_002994668.1| 22 VNYRQLAELLNTTRQRVARRLERLEREGTIKKYTI 56
                                      66789*****99********************887 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.9
                             Stk19  45 sptkvereleelirkgklrklvingrgkdisklgevlvltedyeklikesseleeeekvlekFlellkenptalsis 121
                                       + +++e+++ el                                                                 
  gi|242399244|ref|YP_002994668.1| 114 NMKEIEKKIHELS---------------------------------------------------------------- 126
                                       3333333333333................................................................ PP

                             Stk19 122 asslseeeisaLvraGfLtssaneiesaeyslslPntGtflkllsagrkhLlslLkkskykEaleslLeerWeGave 198
                                                                                                                    
  gi|242399244|ref|YP_002994668.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                             Stk19 199 gdkklsaakrkkwkefygldf 219
                                                 kk + + g+d+
  gi|242399244|ref|YP_002994668.1| 127 ----------KKVEGLEGMDM 137
                                       ..........45555555555 PP

>> ATR13  Avirulence protein ATR13, RxLR effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0       0.1        67      39      67 ..       5      35 ..       1      56 [. 0.71
   2 ?    8.3   0.1    0.0045         3      66      87 ..      74      95 ..      65     106 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.1
                                      TTSS--SSS-..-SS---SS------TTTS- CS
                             ATR13 39 ieahdlhvsk..skeapiqyasvaeylkkiy 67
                                      i+  dl +    +k+a ++y ++ae l+ + 
  gi|242399244|ref|YP_002994668.1|  5 IDKFDLQIMSvlAKNARVNYRQLAELLNTTR 35
                                      677787765323799**********998764 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0045
                                      S--SHHHHHHHHHHHHHT-TTT CS
                             ATR13 66 iysdkdierivstlerhdevga 87
                                      i ++  ie+i+ tl++ d+v+ 
  gi|242399244|ref|YP_002994668.1| 74 IKPGTSIEKIIETLKEDDDVKV 95
                                      67899**************986 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.4   0.00019      0.13      20      54 ..      18      51 ..       8      53 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00019
                                      TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                              GntR 20 pGdkLPsereLaaefgVsrttvReALrrLeaeglv 54
                                       +++    r+La+ ++++r+ v + L rLe+eg +
  gi|242399244|ref|YP_002994668.1| 18 KNARV-NYRQLAELLNTTRQRVARRLERLEREGTI 51
                                      55666.779***********************976 PP

>> EAP30  EAP30/Vps36 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1    0.0002      0.13     185     232 ..      10      51 ..       2      52 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0002
                             EAP30 185 krlvsllaekssgggvtaselaeeeenlgwsvarakeaLeelereGll 232
                                        ++ s+la++ +   v+ ++lae    l+ +++r+ + Le+lereG++
  gi|242399244|ref|YP_002994668.1|  10 LQIMSVLAKNAR---VNYRQLAEL---LNTTRQRVARRLERLEREGTI 51 
                                       567777777776...9*****888...*******************86 PP

>> DUF1690  Protein of Unknown function (DUF1690)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.3    0.0051       3.4       9      50 ..       8      48 ..       2      56 .. 0.80
   2 ?    4.7   0.0     0.057        38      73      96 ..     110     133 ..      78     144 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0051
                           DUF1690  9 fSqslvsqLessketdasraqalekliqerVaeeLkkLraee 50
                                      f  +++s L++++  ++ +  +l +  ++rVa +L++L ++e
  gi|242399244|ref|YP_002994668.1|  8 FDLQIMSVLAKNARVNYRQLAELLNTTRQRVARRLERL-ERE 48
                                      667788899999999999999999999***********.333 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.057
                           DUF1690  73 kdelsskalnekieeLrkkleefk 96 
                                          ++ k++++ki+eL+kk+e ++
  gi|242399244|ref|YP_002994668.1| 110 VAPKNMKEIEKKIHELSKKVEGLE 133
                                       5567889999********999866 PP

>> Phage_rep_O  Bacteriophage replication protein O
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00075       0.5      46      81 ..      18      53 ..      10      63 .. 0.91
   2 ?    0.3   0.0       1.6   1.1e+03      36      78 ..      95     137 ..      81     146 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00075
                       Phage_rep_O 46 ksdwisnsqlveltgisrtkvskalkeLirekviik 81
                                      k+++++  ql+el +++r++v + l+ L re+ i+k
  gi|242399244|ref|YP_002994668.1| 18 KNARVNYRQLAELLNTTRQRVARRLERLEREGTIKK 53
                                      7889999************************99976 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.6
                       Phage_rep_O  36 virktYgfkkksdwisnsqlveltgisrtkvskalkeLirekv 78 
                                       vi++ +g+++   +i   + ++ ++ + +++sk ++ L  +++
  gi|242399244|ref|YP_002994668.1|  95 VIQRAIGYHQLIVHIVAPKNMKEIEKKIHELSKKVEGLEGMDM 137
                                       6677777777777776666666666666677777777766666 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 ?   11.2   1.1   0.00036      0.24       4      46 ..      11      53 ..       9      55 .. 0.95
   2 ?    1.7   0.1      0.33   2.2e+02       2      18 ..      80      96 ..      80     100 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00036
                          HTH_DeoR  4 qilellkqqgklsveelvellgvSeaTiRRDLneLeeqglltR 46
                                      qi+  l++   ++  +l+ell+++ + + R L+ Le +g++++
  gi|242399244|ref|YP_002994668.1| 11 QIMSVLAKNARVNYRQLAELLNTTRQRVARRLERLEREGTIKK 53
                                      8999************************************987 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.33
                          HTH_DeoR  2 ieqilellkqqgklsve 18
                                      ie+i+e lk+++ ++v 
  gi|242399244|ref|YP_002994668.1| 80 IEKIIETLKEDDDVKVI 96
                                      689*********99986 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   0.2   0.00027      0.18       8      56 ..       7      55 ..       2      57 .. 0.84
   2 ?   -0.1   0.2       1.6   1.1e+03      29      44 ..     115     130 ..      84     137 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00027
                           DUF2250  8 elalkvlkhl.kkanvdYaksiakeleipleevrellkkLeelGLlerve 56
                                      + +l+++  l k+a v+Y +++a+ l+  +++v + l++Le+ G +++++
  gi|242399244|ref|YP_002994668.1|  7 KFDLQIMSVLaKNARVNY-RQLAELLNTTRQRVARRLERLEREGTIKKYT 55
                                      566777776526789999.7899***********************9986 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.6
                           DUF2250  29 akeleipleevrellk 44 
                                       +ke+e++++e +++++
  gi|242399244|ref|YP_002994668.1| 115 MKEIEKKIHELSKKVE 130
                                       4445555555555555 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.1    0.0014       0.9      33      70 ..      18      53 ..       2      56 .. 0.88
   2 ?    1.6   0.1      0.29   1.9e+02     127     146 ..     111     130 ..     102     144 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0014
                           DUF4423 33 kdfkadpeelakrlrpkisaeevekalefLlklgllkk 70
                                      k+++ ++++la+ l+   + ++v++ le+L++ g +kk
  gi|242399244|ref|YP_002994668.1| 18 KNARVNYRQLAELLN--TTRQRVARRLERLEREGTIKK 53
                                      5567799********..*******************98 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.29
                           DUF4423 127 skedyekikkeirefrkkil 146
                                         +++++i+k+i e+ kk+ 
  gi|242399244|ref|YP_002994668.1| 111 APKNMKEIEKKIHELSKKVE 130
                                       56788889999988888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1544  (0.0861175); expected 358.6 (0.02)
Passed bias filter:                      983  (0.0548274); expected 358.6 (0.02)
Passed Vit filter:                       124  (0.00691617); 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: 0.62u 0.33s 00:00:00.95 Elapsed: 00:00:00.51
# Mc/sec: 876.59
//
Query:       gi|242399245|ref|YP_002994669.1|  [L=233]
Description: Integral membrane protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-51  175.4   8.7    2.1e-51  174.6   8.7    1.3  1  DUF92     Integral membrane protein DUF92


Domain annotation for each model (and alignments):
>> DUF92  Integral membrane protein DUF92
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  174.6   8.7   1.2e-55   2.1e-51       2     201 ..       8     210 ..       7     223 .. 0.88

  Alignments for each domain:
  == domain 1  score: 174.6 bits;  conditional E-value: 1.2e-55
                             DUF92   2 ltlllalralrkksLtpsGalaavlvgvlialaplgllffllllvFfllgslltkvkkkvKa..kleeekegaRdav 76 
                                       ++ +l+++a++ ++L+ +G laa+++gv+++   +g+ +fl+ll+F + g l+tk+k ++K   ++++e +g R++ 
  gi|242399245|ref|YP_002994669.1|   8 IIGILGVMAYKFRALDGKGTLAAAFLGVFTLEL-GGIYPFLALLTFVIFGILATKYKFSEKIkkGIAQEGKGIRSWR 83 
                                       67899***********************88877.7889*****************886654433999998999**** PP

                             DUF92  77 qVlanslvalllally..lasdlllvgivasyAavaaDTlaSElGkilskskprlittlkkvppGtnGgVsllGlla 151
                                       +V++n+l+al++ ++   +++d++++++++++A+++aDTlaSElGki++k +pr+ittl++  pG +G+Vsl G +a
  gi|242399245|ref|YP_002994669.1|  84 NVFGNGLAALIFLIVEyyTKQDIFWAATFSAIATANADTLASELGKIWGK-HPRIITTLEPALPGDEGAVSLQGEVA 159
                                       **********99988854339****************************9.************************** PP

                             DUF92 152 sllGalliallavlllllel.lillltlaGllGsllDSlLGatlqasvvdk 201
                                       +l+G+++ial+a++l+  ++ +++++tl G+lG+++DS++Gatl+++++ +
  gi|242399245|ref|YP_002994669.1| 160 ALIGGFAIALFALFLTQNKTeIFVAVTLGGFLGCNIDSVIGATLERKGLVN 210
                                       *********9965554443379999*********************95443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       660  (0.0368119); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); 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):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1514.54
//
Query:       gi|242399246|ref|YP_002994670.1|  [L=200]
Description: 30S ribosomal protein S3Ae [Thermococcus sibiricus MM 739]
Scores for complete 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  229.9   1.2    2.5e-68  229.7   1.2    1.0  1  Ribosomal_S3Ae  Ribosomal S3Ae family
  ------ inclusion threshold ------
      0.096   12.7   0.0       0.14   12.2   0.0    1.3  1  Transglut_i_TM  Inactive transglutaminase fused to 7 transmem


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 !  229.7   1.2   2.8e-72   2.5e-68       4     202 .]      11     198 ..       8     198 .. 0.97

  Alignments for each domain:
  == domain 1  score: 229.7 bits;  conditional E-value: 2.8e-72
                                       ---S-TCCSEEEEEEEB-TTSSSSEEEEEEEE--BSSSESHHSHTT-EEEEESHHHHTCSHTSSSEEEEEEEEEEES CS
                    Ribosomal_S3Ae   4 kkvvDkfkkKeWydvkaPslfgkreiGktlvnrtqgtkiaseklkgrvvevslaDLtndekeqafrklklkieevqg 80 
                                         ++Dk+k K+Wy v+aP++fg++eiG t++       +++ek+kgr++e++l+D+t+d+  + ++kl+++i++v+g
  gi|242399246|ref|YP_002994670.1|  11 AAAKDKWKLKDWYIVYAPEFFGNVEIGLTPA-------DEPEKVKGRIIETTLRDVTGDF-TKGHVKLYFRIHDVKG 79 
                                       5689***************************.......**********************.557************* PP

                                       SEEEEEEEEEEE-HHHHHHH--SSB-EEEEEEEEEESSSEEEEEEEEEEE-STTB---HHHHHHHHHHHHHHHHHHH CS
                    Ribosomal_S3Ae  81 knaltnFkgmeltrDklrslvrkwsslIeaivdvktkDgyllrvfvvafTkkrnsYakssqkkaIrkkmveilteea 157
                                       +na+t+Fkg++l+r ++rslvr+++++I+ i++v+tkDgy+lrv+ +++  +r   ++ssq++a+r++m+++++++a
  gi|242399246|ref|YP_002994670.1|  80 QNAYTKFKGHKLARSYIRSLVRRRTTRIDGIFNVTTKDGYKLRVMGMVIAIRR---IQSSQERAVREVMEDLIRKKA 153
                                       *****************************************************...********************* PP

                                       HHS-HHHHHHHHTTTHHHHHHHHHHTTTS-EEEEEEEEEEEEE-S CS
                    Ribosomal_S3Ae 158 seldlkelvkklipeslgkeiekeakkIyplrnveirKvkvlkkP 202
                                       +el+++e+v + ++ ++g+e+ +eakkIypl++ eirK+kvl +P
  gi|242399246|ref|YP_002994670.1| 154 EELTFTEFVLEAVNGKMGAELAREAKKIYPLKRAEIRKIKVLAEP 198
                                       **************77**************************988 PP

>> Transglut_i_TM  Inactive transglutaminase fused to 7 transmembrane helices
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.5e-05      0.14      80     148 ..      65     169 ..      41     176 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.5e-05
                    Transglut_i_TM  80 kGkqtLYYraqlvkdkkakeesksepepespt....................................leepekaaa 120
                                       kG+ +LY+r++ vk ++a ++ k ++ ++s+                                     ++++++ a+
  gi|242399246|ref|YP_002994670.1|  65 KGHVKLYFRIHDVKGQNAYTKFKGHKLARSYIrslvrrrttridgifnvttkdgyklrvmgmviairrIQSSQERAV 141
                                       78889999999999888877777776666655677789999999999999999999999999999999999****** PP

                    Transglut_i_TM 121 eslleearersadtltfarelikrlnnp 148
                                       ++++e++ ++ a++ltf++ +++ +n +
  gi|242399246|ref|YP_002994670.1| 142 REVMEDLIRKKAEELTFTEFVLEAVNGK 169
                                       *******************999998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       753  (0.041999); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); 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: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1336.81
//
Query:       gi|242399247|ref|YP_002994671.1|  [L=81]
Description: hypothetical protein TSIB_1268 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score 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   12.6   0.0       0.14   12.6   0.0    1.1  1  FAM177    FAM177 family


Domain annotation for each model (and alignments):
>> FAM177  FAM177 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   7.7e-06      0.14      40      83 ..      15      58 ..       5      76 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.7e-06
                            FAM177 40 eekeekdlasqldeskltwgpylrfkalrvatkslsgcdylGer 83
                                      +ek  + +a ++d  +l++++ ++fk+    ++++  ++ylGe 
  gi|242399247|ref|YP_002994671.1| 15 SEKIARAIAGAVDVDNLNLPKNFKFKTHCEDNRVITKVKYLGEI 58
                                      44445568899*******************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); 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 0.29s 00:00:00.71 Elapsed: 00:00:00.47
# Mc/sec: 521.82
//
Query:       gi|242399248|ref|YP_002994672.1|  [L=476]
Description: SsDNA-specific exonuclease [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.6e-23   81.3   4.6    1.6e-22   80.4   1.7    2.8  3  DHHA1     DHHA1 domain
     0.0061   16.8   0.5      0.017   15.3   0.2    2.0  2  DHH       DHH family
  ------ inclusion threshold ------
       0.05   13.7   0.1       0.23   11.6   0.1    2.1  2  YqzH      YqzH-like protein


Domain annotation for each model (and alignments):
>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.48   2.9e+03      44      67 ..      49      72 ..      26      97 .. 0.60
   2 ?   -1.3   0.0      0.45   2.7e+03      13      64 ..     253     304 ..     245     316 .. 0.58
   3 !   80.4   1.7   2.6e-26   1.6e-22       9     137 ..     327     463 ..     323     464 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.48
                                      EEECHCCHHHHHHHHHHHHHHTHG CS
                             DHHA1 44 vaevgeewdagalgiaadklkskl 67
                                      +a+ g++ +  +++++ ++l ++l
  gi|242399248|ref|YP_002994672.1| 49 IAREGADFHLSIVKQLSEDLIKEL 72
                                      344445555555555555555554 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.45
                                       HHHHCHHHHHHHHHHHHHHHTCEEEC...TCEEEEEECHCCHHHHHHHHHHHHHH CS
                             DHHA1  13 keleelkealaklkaeellekaeevk...gvkvlvaevgeewdagalgiaadklk 64 
                                       k    l++al + ++++  +k e+++   g+ +l+ ++ e+  ++  ++ a+ l+
  gi|242399248|ref|YP_002994672.1| 253 KRK--LHDALVIHLIKNNASK-EDIDrliGDVILIRKYPEGDPRHEAREFATLLN 304
                                       322..5555555555555444.333356688888877744444466666666555 PP

  == domain 3  score: 80.4 bits;  conditional E-value: 2.6e-26
                                       HHHHHHHHCHHHHHHHHHHHHHHHTCEEECTCEEEEEECHCCHHHHHHHHHHHHHHTHG...BT.TCEEEEEEEECT CS
                             DHHA1   9 kelekeleelkealaklkaeellekaeevkgvkvlvaevgeewdagalgiaadklkskl...kk.pvivfvakeegd 81 
                                       +++ k +ee+k++  ++ +  +++ +  ++++  +v + g++++ +++giaa+   +     ++ pv+v++ +ee+ 
  gi|242399248|ref|YP_002994672.1| 327 RDALKLVEEYKKEQIEMRKYLIQNWNSAIEKDHAYVFYAGKNIKDTMVGIAATIAINAQltnPEkPVVVLADSEEDG 403
                                       6777888888888888888777777777776667777777***********99888843466666999999999988 PP

                                       EEEEEEEESSH....SS-HHHHHHHHHHHTTCCEEEETCEEEEEEEHCHHHHHHHHHHHH CS
                             DHHA1  82 kvkvsarskkd....gvdagelakeaaaklgggGGGHdlAaGagipaekleealealeea 137
                                        +k+sar++k+    g+++ge++++aa+ lgg GGGH+ AaG +ip++kl+e+ e+++++
  gi|242399248|ref|YP_002994672.1| 404 LIKGSARTTKRgiekGYNLGEALRRAAEVLGGEGGGHAIAAGIRIPKDKLDEFTELIDKL 463
                                       *********99*********************************************9987 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.2   2.9e-06     0.017       2      72 ..      28     129 ..      27     165 .. 0.69
   2 ?   -2.2   0.0      0.82   4.9e+03      33      50 ..     169     184 ..     135     200 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.9e-06
                                       EEEE-ECSSSHHHHHH.HHHHHH................................CECS--TCGGCGCCHHCCCSEE CS
                                       xxxxxxxxxxxxxxxx.xxxxxx................................xxxxxxxxxxxxxxxxxxxxxx RF
                               DHH   2 ilivghknpDtDsigS.aialan................................llvDhneksqavegeakeeaed 45 
                                       i i  + + D+D+i++ ai+ ++                                +  D ++ s   ++     + +
  gi|242399248|ref|YP_002994672.1|  28 IRI--ISHRDADGITAgAILAKAiaregadfhlsivkqlsedlikelaeedqkiyIFSDLGSGSIRFIE-RYLADAT 101
                                       556..6778999****88888887777777777777777777777777777777669999999999998.5556678 PP

                                       EEEEE-S---S.S---SS--EEEE-SSS CS
                                       xxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                               DHH  46 viiiDHHrlge.efetlapilflnepvg 72 
                                       v+i DHH +++ e+e+ +++++  ++ g
  gi|242399248|ref|YP_002994672.1| 102 VVIADHHPPEDgEIEQENHVIVNPTQFG 129
                                       9999****99885555555554444444 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.82
                                       GCGCCHHCCCSEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxx RF
                               DHH  33 qavegeakeeaedviiiD 50 
                                       q+v+g  ++++ +v+iiD
  gi|242399248|ref|YP_002994672.1| 169 QEVDG--QFHGINVEIID 184
                                       44555..67777777777 PP

>> YqzH  YqzH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   3.8e-05      0.23      17      58 ..     239     282 ..     231     283 .. 0.90
   2 ?   -3.6   0.0       2.1   1.3e+04      30      44 ..     455     469 ..     453     472 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.8e-05
                              YqzH  17 YgrdtelmplseeeqkeLver..iqekkkeqedeDlyeiveDiv 58 
                                       + +d++   l eee+++L ++  i   k++ ++eD+  ++ D++
  gi|242399248|ref|YP_002994672.1| 239 FDPDVNYWQLKEEEKRKLHDAlvIHLIKNNASKEDIDRLIGDVI 282
                                       66899999***********98557899***************98 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 2.1
                              YqzH  30 eqkeLveriqekkke 44 
                                       e+ eL++++  ++++
  gi|242399248|ref|YP_002994672.1| 455 EFTELIDKLLGQQNS 469
                                       788888888877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (476 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       674  (0.0375927); expected 358.6 (0.02)
Passed bias filter:                      559  (0.0311785); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.33s 00:00:00.95 Elapsed: 00:00:00.51
# Mc/sec: 2800.52
//
Query:       gi|242399249|ref|YP_002994673.1|  [L=151]
Description: 30S ribosomal protein S15P/S13e [Thermococcus sibiricus MM 739]
Scores for 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-27   93.7   0.1      1e-26   92.8   0.1    1.5  1  Ribosomal_S13_N  Ribosomal S13/S15 N-terminal domain
    9.5e-19   67.4   0.7    1.4e-18   66.9   0.7    1.3  1  Ribosomal_S15    Ribosomal protein S15
     0.0032   17.5   0.1       0.24   11.6   0.1    2.3  2  DUF5340          Family of unknown function (DUF5340)
  ------ inclusion threshold ------
      0.023   14.8   0.0        2.2    8.5   0.0    2.5  2  cwf21            cwf21 domain
      0.085   12.7   0.1        2.1    8.2   0.1    2.5  2  DUF4817          Helix-turn-helix domain (DUF4817)
       0.17   11.7   0.0       0.43   10.5   0.0    1.7  2  UPF0728          Uncharacterised protein family UPF0728


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 !   92.8   0.1   3.4e-30     1e-26       1      60 []       1      60 [.       1      60 [. 1.00

  Alignments for each domain:
  == domain 1  score: 92.8 bits;  conditional E-value: 3.4e-30
                                      X--SSSSSS--------S-SS--TTS---HHHHHHHHHHHHHTT--HHHHHHHHHHCCT- CS
                   Ribosomal_S13_N  1 MarmhsrgkGkSgSarPyrreapsWlklskeeveelivklakkGltpSqIGviLRDqyGv 60
                                      Mar+h+r++GkSgS++P r+ +p+W+++++eeve+l+vkl+k+G++ ++IG+iLRDqyG+
  gi|242399249|ref|YP_002994673.1|  1 MARLHARKRGKSGSKKPPRTAPPTWVDYTAEEVENLVVKLRKDGHSVAMIGTILRDQYGI 60
                                      ***********************************************************9 PP

>> Ribosomal_S15  Ribosomal protein S15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.9   0.7   4.7e-22   1.4e-18       3      80 ..      73     148 ..      70     149 .. 0.95

  Alignments for each domain:
  == domain 1  score: 66.9 bits;  conditional E-value: 4.7e-22
                                       HHHHHHSSSTT-TSSHHHHHHHHHHHHHHHHHHHHCTTT-HHHHHHHHHHHHHHHHHHHHHHHH-H..HHHHHHHHH CS
                     Ribosomal_S15   3 elikefqrhekDtGspevqiallterInnltehlkenkkDkhsrrgLlklvskRrkllkYLkrkdv..erYkkliek 77 
                                       ++++e++ ++    ++++++++l++++++l++hl++++kD hsrrgL++++sk+r+l+kY++++ +  +++++  e+
  gi|242399249|ref|YP_002994673.1|  73 KILEENNLAP----ELPEDLMFLIRKAVKLRKHLEQHPKDLHSRRGLQLTESKIRRLVKYYRETGRlpANWRYDPEQ 145
                                       6799999999....9**************************************************999*******99 PP

                                       CTS CS
                     Ribosomal_S15  78 lgl 80 
                                       ++l
  gi|242399249|ref|YP_002994673.1| 146 AKL 148
                                       987 PP

>> DUF5340  Family of unknown function (DUF5340)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.021        63      34      46 ..      30      42 ..      24      47 .. 0.88
   2 !   11.6   0.1     8e-05      0.24      25      58 ..      73     106 ..      64     123 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.021
                           DUF5340 34 reqvqqliitLRK 46
                                       e+v++l+++LRK
  gi|242399249|ref|YP_002994673.1| 30 AEEVENLVVKLRK 42
                                      689*********9 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 8e-05
                           DUF5340  25 aaveqnsalreqvqqliitLRKAlaqQkqLEesc 58 
                                       +++e+n+ + e  ++l+  +RKA+ + k+LE++ 
  gi|242399249|ref|YP_002994673.1|  73 KILEENNLAPELPEDLMFLIRKAVKLRKHLEQHP 106
                                       556677777777789****************975 PP

>> cwf21  cwf21 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.019        57      25      39 ..      28      42 ..       3      43 .. 0.84
   2 ?    8.5   0.0   0.00075       2.2      14      39 ..      96     131 ..      73     132 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.019
                             cwf21 25 lseeeIeervdelRe 39
                                      ++ ee+e  v +lR+
  gi|242399249|ref|YP_002994673.1| 28 YTAEEVENLVVKLRK 42
                                      689***********7 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00075
                             cwf21  14 lelrdeLEeeg..........lseeeIeervdelRe 39 
                                       ++lr  LE             l+e  I   v+ +Re
  gi|242399249|ref|YP_002994673.1|  96 VKLRKHLEQHPkdlhsrrglqLTESKIRRLVKYYRE 131
                                       6788888884346777777868*************8 PP

>> DUF4817  Helix-turn-helix domain (DUF4817)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.12   3.7e+02      38      53 ..      30      45 ..      29      47 .. 0.85
   2 ?    8.2   0.1    0.0007       2.1      37      52 ..     118     133 ..     116     135 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.12
                           DUF4817 38 rstirrlvkkfeetGs 53
                                      ++ + +lv k+++ G 
  gi|242399249|ref|YP_002994673.1| 30 AEEVENLVVKLRKDGH 45
                                      67899********995 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0007
                           DUF4817  37 srstirrlvkkfeetG 52 
                                       ++s irrlvk ++etG
  gi|242399249|ref|YP_002994673.1| 118 TESKIRRLVKYYRETG 133
                                       6899************ PP

>> UPF0728  Uncharacterised protein family UPF0728
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00014      0.43      20      50 ..      26      56 ..      18      67 .. 0.87
   2 ?   -2.5   0.1       1.6   4.8e+03      24      38 ..     119     133 ..     113     135 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00014
                           UPF0728 20 vkhrterleglqavlkkdGheveLektedyn 50
                                      v++ +e +e+l  +l+kdGh+v +  t  ++
  gi|242399249|ref|YP_002994673.1| 26 VDYTAEEVENLVVKLRKDGHSVAMIGTILRD 56
                                      8999******************998877665 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.6
                           UPF0728  24 terleglqavlkkdG 38 
                                        ++++ l ++++++G
  gi|242399249|ref|YP_002994673.1| 119 ESKIRRLVKYYRETG 133
                                       578888999999888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); 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: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.51
# Mc/sec: 894.84
//
Query:       gi|242399250|ref|YP_002994674.1|  [L=37]
Description: hypothetical protein TSIB_1271 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       141  (0.00786435); expected 358.6 (0.02)
Passed bias filter:                      126  (0.00702772); expected 358.6 (0.02)
Passed Vit filter:                         2  (0.000111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 263.90
//
Query:       gi|242399251|ref|YP_002994675.1|  [L=244]
Description: hypothetical protein TSIB_1272 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-32  112.2   1.4    2.9e-32  112.2   1.4    1.6  2  Cas_Cas6  CRISPR associated protein Cas6


Domain annotation for each model (and alignments):
>> Cas_Cas6  CRISPR associated protein Cas6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.27   4.8e+03      66      79 ..      21      34 ..       7      74 .. 0.53
   2 !  112.2   1.4   1.6e-36   2.9e-32       2     146 .]      95     238 ..      94     238 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.27
                                      HHHHHHHHHHHHHH CS
                          Cas_Cas6 66 sellkenlkkkyka 79
                                      ++++++ l++k+ +
  gi|242399251|ref|YP_002994675.1| 21 NDEIHDQLLEKIFL 34
                                      55555555555322 PP

  == domain 2  score: 112.2 bits;  conditional E-value: 1.6e-36
                                       HHCS-EEEETTEEEEEEEEEE----S--TCEE.EEESS-BBEEEEEEETTCCEEEEE-TTSTTHHHHHHHHHHHHHH CS
                          Cas_Cas6   2 llknkeirlgnnefkveevellkepeitssevvfktlSPivvrstkkengkkktyylspddeeFsellkenlkkkyk 78 
                                       + +n+ +++g+++f++ ++e+l ep i+++++ f+tlSPivvr+ k e++k k ++l p++e F+++l++ ++ k++
  gi|242399251|ref|YP_002994675.1|  95 FVSNPILKIGKATFSMVKIEILREPPISDGTL-FSTLSPIVVRTAKFEDNKVKIWDLYPNNEGFQDKLRKVMLTKFS 170
                                       789999*********************99977.**********99******************************** PP

                                       HHHSS...SS---EEEEEEEEE......TEEEEEEEEEEEEEE-HHHHHHHHHC-SCS-CCCT-S-EEE CS
                          Cas_Cas6  79 alygee.keeklsikpdkkvkkivvkkketyirGylgrfelegdpellklaydaGlGeknsqGFGmvev 146
                                       ++yg+  ++ +++i+++k +k + +k  + y rG+l+ f+ +g++e+ k++y++G+G k+s GFGmv+v
  gi|242399251|ref|YP_002994675.1| 171 EIYGNLpEDTDFHIDVIK-FKPVRIKVGKNYYRGSLMVFRYYGSKEIGKFGYENGFGDKTSYGFGMVKV 238
                                       ****98767777777777.99988888899*************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.34s 00:00:00.93 Elapsed: 00:00:00.55
# Mc/sec: 1333.07
//
Query:       gi|242399252|ref|YP_002994676.1|  [L=298]
Description: UDP-N-acetylglucosamine--dolichyl-phosphate N- acetylglucosaminephosphotransferase [Thermococcus sibiricus MM 739]
Scores for complete 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-32  111.9  15.5    5.8e-32  110.9  15.5    1.6  1  Glycos_transf_4  Glycosyl transferase family 4
  ------ inclusion threshold ------
        2.8    8.0   0.0        2.8    8.0   0.0    3.0  3  DUF3278          Protein of unknown function (DUF3278)


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 !  110.9  15.5   6.5e-36   5.8e-32       4     159 ..      67     213 ..      64     214 .. 0.88

  Alignments for each domain:
  == domain 1  score: 110.9 bits;  conditional E-value: 6.5e-36
                   Glycos_transf_4   4 llltillilllGflDDvlglkarlKlilqilaalililtldlslttlgllltqvlielglilavlltllvivgvtNa 80 
                                       +ll+ l+++++G+lDD+ +lk+ +K+il++l++l ++ +     t+++lll+  +ielg +l++l+++l+++g++N 
  gi|242399252|ref|YP_002994676.1|  67 ALLVFLAFGVIGVLDDIANLKQSHKVILSLLVSLGVLAL-P-LDTKVNLLLF--SIELG-VLYYLFSILFVTGAANL 138
                                       6788999**************************998664.3.3567777777..8****.9999************* PP

                   Glycos_transf_4  81 vNliDGldGlaagvsiiialalvvlaavdgrsellllalallgallGfllfNrypAkvFmGDsgslflGlvlavlai 157
                                       vNl++G++Gl++g+s+i++++l++ +  +g+ ++l++  + +++ lGfl++N+ypAkvF GD+g+l+lG++++v+ i
  gi|242399252|ref|YP_002994676.1| 139 VNLLAGFNGLEVGTSVIALFFLGLTT--SGDAQVLAF--TGVAVGLGFLWWNKYPAKVFPGDTGTLSLGALIGVVGI 211
                                       ************************99..566665555..555555******************************99 PP

                   Glycos_transf_4 158 lg 159
                                       lg
  gi|242399252|ref|YP_002994676.1| 212 LG 213
                                       87 PP

>> DUF3278  Protein of unknown function (DUF3278)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0   0.00031       2.8      72     105 ..       6      39 ..       1      61 [. 0.83
   2 ?    0.0   1.4     0.093   8.3e+02      45      77 ..      95     129 ..      69     142 .. 0.67
   3 ?   -1.8   0.2      0.34     3e+03      49      77 ..     262     290 ..     259     294 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00031
                           DUF3278  72 nlllvvlvsglYiliaskklglatkeveakdyek 105
                                       + +l  lv   Yi++ ++k+g++ +++++ d+++
  gi|242399252|ref|YP_002994676.1|   6 IGFLISLVLTPYIASLMRKAGIVGRDIHKLDRPE 39 
                                       44666778899******************99876 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.093
                           DUF3278  45 llilslvalllakktpeselilglvl..tnlllvv 77 
                                        l++sl +l+l+  t+ ++l++ + l  +  l+++
  gi|242399252|ref|YP_002994676.1|  95 SLLVSLGVLALPLDTKVNLLLFSIELgvLYYLFSI 129
                                       56677777888888888777765433113333333 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.34
                           DUF3278  49 slvalllakktpeselilglvl.tnlllvv 77 
                                       +l +++ +kk +e++l+ ++v  +  +l+v
  gi|242399252|ref|YP_002994676.1| 262 FLGIIMRMKKVKEYQLV-AIVWgIETFLGV 290
                                       55667778888888887.666556666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1995.43
//
Query:       gi|242399253|ref|YP_002994677.1|  [L=443]
Description: Bifunctional phosphatase/dolichol-phosphate glucosyltransferase [Thermococcus sibiricus MM 739]
Scores for complete 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-26   91.2   0.1    4.1e-25   88.5   0.0    2.3  2  Glycos_transf_2  Glycosyl transferase family 2
    4.7e-23   82.2   1.3    1.9e-22   80.2   0.1    2.4  3  HAD_2            Haloacid dehalogenase-like hydrolase
      4e-13   50.1   0.1    1.1e-08   35.6   0.0    2.6  3  Hydrolase        haloacid dehalogenase-like hydrolase
      8e-08   32.9   0.0    1.6e-07   31.9   0.0    1.5  1  HAD              haloacid dehalogenase-like hydrolase
    5.3e-05   23.2   0.0    9.1e-05   22.4   0.0    1.3  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
     0.0001   22.3   0.0    0.00048   20.2   0.0    2.3  1  Hydrolase_6      Haloacid dehalogenase-like hydrolase
    0.00029   20.8   0.0     0.0007   19.6   0.0    1.7  1  Hydrolase_like   HAD-hyrolase-like
    0.00074   20.0   0.0     0.0016   18.9   0.0    1.6  1  Glyco_tranf_2_4  Glycosyl transferase family 2
  ------ inclusion threshold ------
      0.034   14.0   0.1       0.22   11.4   0.1    2.3  1  Acid_PPase       Acid Phosphatase
      0.049   13.3   0.1       0.33   10.6   0.0    2.3  2  PNK3P            Polynucleotide kinase 3 phosphatase


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.78   1.4e+03      99     137 ..      92     129 ..      89     151 .. 0.75
   2 !   88.5   0.0   2.3e-28   4.1e-25       2     131 ..     224     349 ..     223     380 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.78
                                       HHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEEC CS
                   Glycos_transf_2  99 klvealekdgadvvlgqrprifgetdeiernkrvgener 137
                                       +l+e+l++ g +++l++r  ++  +++ +++k   e  +
  gi|242399253|ref|YP_002994677.1|  92 ELLEFLKDKGLKLALMTRSSRKATEFTLKKHKIK-EFFN 129
                                       7999999999999999999999999999998863.3333 PP

  == domain 2  score: 88.5 bits;  conditional E-value: 2.3e-28
                                       EEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH- CS
                   Glycos_transf_2   2 vviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraa 78 
                                       vv+p+yNeekt+ ++le ll+    +++eiivv+DgS+D+t+ei+ e      +v v+ +  n+G++gal +g+r+a
  gi|242399253|ref|YP_002994677.1| 224 VVVPAYNEEKTIGNVLEDLLKY--FKEKEIIVVNDGSKDRTKEIAIEK-----GVVVLSHLVNRGLGGALGTGIRYA 293
                                       9********************8..***********************9.....9**********************9 PP

                                       -SS...EEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-S CS
                   Glycos_transf_2  79 tgd...yilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkr 131
                                         +   +i+++DaD ++  ++  k++++  ++ ad ++g+r + + +  ++ +  +
  gi|242399253|ref|YP_002994677.1| 294 LLKgaeIIITFDADGQHLVEDALKVMKPVIEGKADFAIGSRLKGDISQMPFVKKIG 349
                                       888889***********************************999988888877766 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.2   0.1   1.1e-25   1.9e-22       1     175 [.       9     183 ..       9     186 .. 0.82
   2 ?   -0.5   0.0      0.64   1.1e+03      17      56 ..     213     250 ..     206     273 .. 0.62
   3 ?   -1.9   0.0       1.7   3.1e+03      65      89 ..     412     436 ..     384     441 .. 0.66

  Alignments for each domain:
  == domain 1  score: 80.2 bits;  conditional E-value: 1.1e-25
                             HAD_2   1 iiFDlDgTlldteeliiqafnelleeyglselseeelrkliglslrellrklgeseeeee.kieellrkyneekkkk 76 
                                       ++FDlDgTl+  +    ++ ++l ++  l+e  +eel   + + ++ l++ +++ +  +   ++++l   + e  k 
  gi|242399253|ref|YP_002994677.1|   9 VVFDLDGTLIGASMDFTEIKRKLRNKL-LEEGIPEELIGDLTPMYETLVQISQK-TGISFeHLHSFLVNLEVERSK- 82 
                                       79**********999999999998887.66555666655555555444443333.333334555555555555555. PP

                             HAD_2  77 evkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekk..KPdpeviekaleklklk 151
                                       e  +++g++elLe Lk++g+kl+++T +sr+a+e  l++++i+++F+ i+t +dv+ k  KP+   ++ +l+ + + 
  gi|242399253|ref|YP_002994677.1|  83 ESYLFEGARELLEFLKDKGLKLALMTRSSRKATEFTLKKHKIKEFFNLIITRDDVSWKdvKPNNGHLKVILDYFRIP 159
                                       7******************************************************98888***************** PP

                             HAD_2 152 keeviyvGDsptDieaakkagikv 175
                                       + +v++vGD+ +D++ ak++g+ +
  gi|242399253|ref|YP_002994677.1| 160 STKVVVVGDHGYDLIPAKALGTLS 183
                                       *******************99755 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.64
                             HAD_2  17 iqafnelleeyglselseeelrkliglslrellrklgese 56 
                                       i+ f++ll+ y +  ++  + +k ig  l++ll++++e+e
  gi|242399253|ref|YP_002994677.1| 213 IDLFKRLLNTYVV--VPAYNEEKTIGNVLEDLLKYFKEKE 250
                                       5566666666633..4444455666666666666666643 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.7
                             HAD_2  65 llrkyneekkkkevkpydgvkelLe 89 
                                       ++ +y e  kkk +++++gvk + +
  gi|242399253|ref|YP_002994677.1| 412 IRAIYTEYTKKKGTNVLEGVKIAFN 436
                                       3345666667788999999887665 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   0.00012      0.21       2      37 ..       7      39 ..       6      72 .. 0.79
   2 !   35.6   0.0   6.2e-12   1.1e-08     114     210 .]      81     180 ..      65     180 .. 0.91
   3 ?   -2.7   0.0       3.3   5.9e+03     125     201 ..     241     259 ..     214     278 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00012
                                      SEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  2 ktvvfDkdGTLttgepsvedvivsaalalaaaletg 37
                                       +vvfD+dGTL+  ++  +++ +++   +++ le g
  gi|242399253|ref|YP_002994677.1|  7 QLVVFDLDGTLIGASMDFTEIKRKL---RNKLLEEG 39
                                      68**********9999999999999...66666665 PP

  == domain 2  score: 35.6 bits;  conditional E-value: 6.2e-12
                                       HHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT.GGGESEEEEHHCES..STTTSHHHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxx RF
                         Hydrolase 114 adplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlG.ddyfdaviasdiet..vakpspegkvaaireLq 187
                                       + + +++++a+e+++ Lk++g++++l+t ++++  e ++++   +++f+ +i++d++     kp+  +++ +++ ++
  gi|242399253|ref|YP_002994677.1|  81 SKESYLFEGARELLEFLKDKGLKLALMTRSSRKATEFTLKKHKiKEFFNLIITRDDVSwkDVKPNNGHLKVILDYFR 157
                                       456689******************************999999999999**********999999999********** PP

                                       STGGGEEEEESSHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 188 gkpeevamVGDgvnDaaalaaAg 210
                                       ++  +v++VGD   D+  ++a g
  gi|242399253|ref|YP_002994677.1| 158 IPSTKVVVVGDHGYDLIPAKALG 180
                                       **************999888865 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 3.3
                                       HHHHHHHHTTEEEEEEESSEHHHHHHHHHHTTGGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 125 eavasLkaagievvlltgdnpetaeraanqlGddyfdaviasdietvakpspegkvaaireLqgkpeevamVGDgvn 201
                                       ++++++k++ i                                                          ++V Dg  
  gi|242399253|ref|YP_002994677.1| 241 DLLKYFKEKEI----------------------------------------------------------IVVNDGSK 259
                                       44444444444..........................................................44444433 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.0   8.9e-11   1.6e-07       1     184 [.       9     173 ..       9     175 .. 0.67

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 8.9e-11
                               HAD   1 alfDfDgTLldgdsle.lllrfllrrgaprlwralreklllal..frellrldraglaelleallagls.eelaael 73 
                                       ++fD+DgTL+  ++++ ++ r +lr++ +++   + e+l  +l  ++e l +              g s e+l+  l
  gi|242399253|ref|YP_002994677.1|   9 VVFDLDGTLIGASMDFtEIKR-KLRNKLLEE--GIPEELIGDLtpMYETLVQIS---------QKTGISfEHLHSFL 73 
                                       79**********988856666.999877654..333333333333666666633.........34444444444444 PP

                               HAD  74 erfvaevirpk.lldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelglegkpv 149
                                         +  e  ++  l+ +ga+ell+  +++G ++++ + + r  +e +l+++ ++e+ +        +t+   +++k+v
  gi|242399253|ref|YP_002994677.1|  74 VNLEVERSKESyLF-EGARELLEFLKDKGLKLALMTRSSRKATEFTLKKHKIKEFFNL------IITRD-DVSWKDV 142
                                       44443333333166.************************************8888888......66666.4444444 PP

                               HAD 150 rgegkv.aalrewlaaegegidleevvayGDspsDl 184
                                       + ++   ++           i+  +vv++GD+  Dl
  gi|242399253|ref|YP_002994677.1| 143 KPNNGHlKV-----ILDYFRIPSTKVVVVGDHGYDL 173
                                       442222022.....334667777889999**99997 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   5.1e-08   9.1e-05       4      97 ..     222     307 ..     221     334 .. 0.71

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 5.1e-08
                   Glyco_tranf_2_3   4 lavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksraln 80 
                                       ++v+Vp++nee+++g+vle+ll++   + e++vv d+s++ t e a e      + +v+v+  ++    +g   al 
  gi|242399253|ref|YP_002994677.1| 222 TYVVVPAYNEEKTIGNVLEDLLKY-FKEKEIIVVNDGSKDRTKEIAIE------K-GVVVL--SHLVN-RGLGGALG 287
                                       69*********************5.599**************998866......3.34444..33222.33334444 PP

                   Glyco_tranf_2_3  81 ealravk...sdlvllvDdD 97 
                                        ++r +     ++++ +D+D
  gi|242399253|ref|YP_002994677.1| 288 TGIRYALlkgAEIIITFDAD 307
                                       55553322344466666666 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   2.7e-07   0.00048       1      51 [.       9     122 ..       9     172 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 2.7e-07
                                       EEEESTTTSE...............................................................ETTE CS
                       Hydrolase_6   1 flfDidGvLw...............................................................rgdk 14 
                                       ++fD+dG+L+                                                               +++ 
  gi|242399253|ref|YP_002994677.1|   9 VVFDLDGTLIgasmdfteikrklrnklleegipeeligdltpmyetlvqisqktgisfehlhsflvnleversKESY 85 
                                       69*******************************************************************9999999* PP

                                       E-TTHHHHHHHHHHTT-EEEEEE---SS-HHHHHHHH CS
                       Hydrolase_6  15 aipgaaealnalraagkpvvllTNnsskseeeyakkl 51 
                                       +++ga e+l++l+++g +++l+T +s+k  e  +kk 
  gi|242399253|ref|YP_002994677.1|  86 LFEGARELLEFLKDKGLKLALMTRSSRKATEFTLKKH 122
                                       ************************9999987776665 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   3.9e-07    0.0007       4      74 ..     143     211 ..     142     212 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 3.9e-07
                                       TTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESSSSS-TTTHHHHHHHHT---SEEES CS
                    Hydrolase_like   4 KPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVltGvtrpedleepehkptyvaddlae 74 
                                       KP+ + ++ +l  + +++ +v+++GD    D++ A++ G  svL+++  +++   +   +++t+ +++++e
  gi|242399253|ref|YP_002994677.1| 143 KPNNGHLKVILDYFRIPSTKVVVVGDH-GYDLIPAKALGTLSVLITSNESGRMSFK-IDEEATFEVKTIKE 211
                                       9**************************.*******************998886644.55677776666666 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 !   18.9   0.0   9.1e-07    0.0016       1      82 [.     229     308 ..     229     319 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 9.1e-07
                   Glyco_tranf_2_4   1 rneadiLpeflahhlalgf..drilvydndstDgtrailkelpevkllhvdksyederrqvellkallaryaeadwv 75 
                                       +ne+++++++l+ +l++ f  ++i+v++++s+D+t +i  e   v l h ++   + + +  ++ all+    a+ +
  gi|242399253|ref|YP_002994677.1| 229 YNEEKTIGNVLEDLLKY-FkeKEIIVVNDGSKDRTKEIAIEKGVVVLSHLVNRGLGGALGTGIRYALLKG---AEII 301
                                       69**********99997.42268******************99999999999888899999999999955...6999 PP

                   Glyco_tranf_2_4  76 lvvDaDE 82 
                                       +++DaD 
  gi|242399253|ref|YP_002994677.1| 302 ITFDADG 308
                                       9999995 PP

>> Acid_PPase  Acid Phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00012      0.22       4      73 ..       7     113 ..       5     186 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00012
                                       SEEEE-STTTSSSS-TTTS..................................S-S-EEE-TTS............. CS
                        Acid_PPase   4 klivFDLDyTLWpfevdtl..................................vsaplkkeskks............ 34 
                                       +l+vFDLD TL    +d                                     +         +            
  gi|242399253|ref|YP_002994677.1|   7 QLVVFDLDGTLIGASMDFTeikrklrnklleegipeeligdltpmyetlvqisQK---------Tgisfehlhsflv 74 
                                       79***************99999999999999999999999999976666555522.........2223333344557 PP

                                       -EEETT--EE---TTHHHHHHHHHHTT--EEEEE--S-H CS
                        Acid_PPase  35 evvDrrgeelklypdveeileelkskevklavaSrtdep 73 
                                       ++  +r++e  l++ ++e+le+lk+k+ kla+  r+++ 
  gi|242399253|ref|YP_002994677.1|  75 NLEVERSKESYLFEGARELLEFLKDKGLKLALMTRSSRK 113
                                       555678999999999999999999999999998887654 PP

>> PNK3P  Polynucleotide kinase 3 phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00018      0.33       2      59 ..       8      66 ..       7     170 .. 0.83
   2 ?   -0.1   0.0      0.36   6.5e+02      46      86 ..     182     226 ..     172     255 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00018
                             PNK3P  2 iaaFDlDstliktksgkefakdaddwkllsesvlekLkklkeegyk.ivifsNqggvve 59
                                      +++FDlD+tli ++   ++ k +   kll+e ++e+L    +  y+ +v +s + g++ 
  gi|242399253|ref|YP_002994677.1|  8 LVVFDLDGTLIGASMDFTEIKRKLRNKLLEEGIPEELIGDLTPMYEtLVQISQKTGISF 66
                                      689*********99977767778888**********99887776541555777777765 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.36
                             PNK3P  46 ykivifsNqggvvek....ktkkslekfkekieallkeldvpllv 86 
                                        +++i sN++g ++     + + +++++ke i+ + + l++ ++v
  gi|242399253|ref|YP_002994677.1| 182 LSVLITSNESGRMSFkideEATFEVKTIKEAIDLFKRLLNTYVVV 226
                                       578999999987775465566667777777777777766665544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (443 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       674  (0.0375927); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.48
# Mc/sec: 2782.86
//
Query:       gi|242399254|ref|YP_002994678.1|  [L=128]
Description: UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-22   80.3   4.1    1.2e-22   80.1   4.1    1.1  1  DUF2304   Uncharacterized conserved protein (DUF2304)
  ------ inclusion threshold ------
       0.14   12.2   0.4       0.14   12.2   0.4    2.3  2  DUF4577   Domain of unknown function (DUF4577)
       0.28   11.5   0.1       0.28   11.5   0.1    2.0  3  DUF948    Bacterial protein of unknown function (DUF948)
       0.59    9.0   4.3       0.63    8.9   2.5    1.7  2  LMBR1     LMBR1-like membrane protein


Domain annotation for each model (and alignments):
>> DUF2304  Uncharacterized conserved protein (DUF2304)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.1   4.1   2.7e-26   1.2e-22       2     103 ..       4     106 ..       3     109 .. 0.98

  Alignments for each domain:
  == domain 1  score: 80.1 bits;  conditional E-value: 2.7e-26
                           DUF2304   2 lqiiliivsvllllliirlvrkkklkleysllwlllalilivlslfp.qiltvlanllGvgrgtnllfllgivfllv 77 
                                       +q i+++++  l++++i ++ kk+l++++ +lw  l li++v+sl p +i + +++llG+grg+++lf+++i ++++
  gi|242399254|ref|YP_002994678.1|   4 IQYIALLIISGLIIYLIGKYGKKELDWQDLILWESLLLIMLVISLKPiEISMTIKRLLGLGRGLDALFVVSIGLSYL 80 
                                       89*********************************************99**************************** PP

                           DUF2304  78 ilfslslklskleekikeLaqeiAll 103
                                       ilf+l+++++k e++i+eL+++iA++
  gi|242399254|ref|YP_002994678.1|  81 ILFRLYMTIDKTEREITELTRQIAIE 106
                                       ************************96 PP

>> DUF4577  Domain of unknown function (DUF4577)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.4      0.14   6.5e+02      67      76 ..      40      49 ..      20      69 .. 0.68
   2 ?   12.2   0.4     3e-05      0.14      70     113 ..      70     118 ..      58     122 .. 0.69

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.14
                           DUF4577 67 liivlivsla 76
                                      l+i+l++sl 
  gi|242399254|ref|YP_002994678.1| 40 LLIMLVISLK 49
                                      3445555554 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 3e-05
                           DUF4577  70 vlivslalvsfvif...lii.qtgskmddvsrrltaegkdi.delkkin 113
                                       +++vs+ l  +++f   ++i +t  ++ +++r+++ e +di +elkk++
  gi|242399254|ref|YP_002994678.1|  70 LFVVSIGLSYLILFrlyMTIdKTEREITELTRQIAIEFQDIkEELKKLE 118
                                       3455655555444411155525667789*************557**986 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1      0.78   3.5e+03       1      13 [.       7      19 ..       5      25 .. 0.61
   2 ?   -3.2   0.1       2.3     1e+04      15      22 ..      42      49 ..      39      60 .. 0.51
   3 ?   11.5   0.1   6.3e-05      0.28      10      57 ..      71     118 ..      69     122 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.78
                            DUF948  1 IAglIaAiAFvvL 13
                                      IA+lI+ + ++ L
  gi|242399254|ref|YP_002994678.1|  7 IALLIISGLIIYL 19
                                      5666666544443 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2.3
                            DUF948 15 iflivvll 22
                                      i+l++ l+
  gi|242399254|ref|YP_002994678.1| 42 IMLVISLK 49
                                      33443333 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 6.3e-05
                            DUF948  10 FvvLviflivvllklkktldeaaatieelekqvdpilkevedllakvn 57 
                                       Fvv + +   +l++l  t+d++++ i+el++q+    +++++ l+k +
  gi|242399254|ref|YP_002994678.1|  71 FVVSIGLSYLILFRLYMTIDKTEREITELTRQIAIEFQDIKEELKKLE 118
                                       777777888889999999999999999999999888888777777765 PP

>> LMBR1  LMBR1-like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   2.5   0.00014      0.63       3      64 ..       2      67 ..       1     109 [. 0.76
   2 ?    1.1   0.1     0.032   1.4e+02     174     221 ..      70     119 ..      60     125 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00014
                             LMBR1  3 liillllflllfllallllrrykrkkdqeavvkllvllalalsflivlllPlDiastiyrq......n 64
                                      ++i ++++l+++ l+++l+ +y++ k+ ++   l+ + +l+l +l++ l P+ i+ ti+r        
  gi|242399254|ref|YP_002994678.1|  2 YAIQYIALLIISGLIIYLIGKYGK-KELDW-QDLILWESLLLIMLVISLKPIEISMTIKRLlglgrgL 67
                                      5678899*****************.55555.5666778899999************999876666661 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.032
                             LMBR1 174 llilllGyGlvelPrslwr...eiksdldeelkklyfeaaklntekeeaer 221
                                       l+++++G  +  l + l+    + ++++ e ++++ +e + +++e+++ e+
  gi|242399254|ref|YP_002994678.1|  70 LFVVSIGLSYLIL-FRLYMtidKTEREITELTRQIAIEFQDIKEELKKLEK 119
                                       5555555555555.4444446666666666666666666666655555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1466  (0.081767); expected 358.6 (0.02)
Passed bias filter:                      916  (0.0510904); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 809.82
//
Query:       gi|242399255|ref|YP_002994679.1|  [L=180]
Description: Deoxycytidylate deaminase [Thermococcus sibiricus MM 739]
Scores for complete 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-28   97.2   0.1    6.6e-28   96.6   0.1    1.3  1  dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-
    4.3e-20   71.9   0.0    5.9e-20   71.4   0.0    1.2  1  MafB19-deam      MafB19-like deaminase
  ------ inclusion threshold ------
       0.01   16.0   0.0      0.017   15.3   0.0    1.5  1  APOBEC3          APOBEC3
      0.029   14.5   0.1      0.048   13.7   0.1    1.5  1  Bd3614-deam      Bd3614-like deaminase


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 !   96.6   0.1   1.5e-31   6.6e-28       2      99 ..      21     131 ..      20     133 .. 0.97

  Alignments for each domain:
  == domain 1  score: 96.6 bits;  conditional E-value: 1.5e-31
                                       HHHHHHHHHHHHHHHHHHTTTSCSEEEEEEETTEEEEEEESBHHCCTG...............TTB-HHHHHHHHHH CS
                   dCMP_cyt_deam_1   2 ekdekllelalkaakeaqkcsnfkVGavivkngeiistgyngepaggs...............ktiHAEvnAilkaa 63 
                                       +kde+++ +a+++  +a +c++ kVGav vk+g i++tgyng p++ +               + +HAE+n i+ aa
  gi|242399255|ref|YP_002994679.1|  21 TKDEYFMLIAKLVGLRA-TCPRLKVGAVAVKDGYILATGYNGAPRNMDhcidvgclvvdghchRAVHAEQNVIAMAA 96 
                                       579**************.*********************************************************** PP

                                       HHTSSCETTEEEEEEE--BHHHHHHHHHHT-SEEEE CS
                   dCMP_cyt_deam_1  64 knggsklegatlyvtlePCsmCakaiiqsgikkvvv 99 
                                       ++ g++legatlyvt++PC +C k+++++gi+++++
  gi|242399255|ref|YP_002994679.1|  97 RK-GISLEGATLYVTHFPCDTCFKLLVNAGIREIIY 131
                                       99.999***************************998 PP

>> MafB19-deam  MafB19-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.4   0.0   1.3e-23   5.9e-20       2     133 ..      21     172 ..      20     177 .. 0.84

  Alignments for each domain:
  == domain 1  score: 71.4 bits;  conditional E-value: 1.3e-23
                       MafB19-deam   2 dkekafrkalaevekatkikedkigavivkdkkviargsn...............ekelnakataHaEiaalqqAak 63 
                                       +k+++f+ ++++v+ ++ +   k+gav vkd+ ++a+g+n                 +++ +   HaE +++  Aa 
  gi|242399255|ref|YP_002994679.1|  21 TKDEYFMLIAKLVGLRATCPRLKVGAVAVKDGYILATGYNgaprnmdhcidvgclVVDGHCHRAVHAEQNVIAMAAR 97 
                                       5899***************************************************7777889999**********88 PP

                       MafB19-deam  64 klkskrlddatlyvtlepCdmCagaivqaglkklvygagnpkslnkLkvkekngrvelv.......eddckeilkgf 133
                                       k++s   ++atlyvt+ pCd C +++v+ag+++++y   +p+  ++L +ke  ++  +        ++ +k  l+++
  gi|242399255|ref|YP_002994679.1|  98 KGISL--EGATLYVTHFPCDTCFKLLVNAGIREIIYEDIYPNKATELLLKEAQEKGIVKirqfkvpKERVKLFLEEL 172
                                       88877..*********************************9997777766655544222334444455554445554 PP

>> APOBEC3  APOBEC3
   #    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      29      72 ..      83     123 ..      64     174 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.7e-06
                           APOBEC3  29 ekkHAEerfidkirslnldslkqykitcylswsPcpkCaeelve 72 
                                       +  HAE+  i   + + ++ +     t+y++  Pc +C + lv+
  gi|242399255|ref|YP_002994679.1|  83 RAVHAEQNVIAMAARKGISLEG---ATLYVTHFPCDTCFKLLVN 123
                                       568**********998888777...8****************98 PP

>> Bd3614-deam  Bd3614-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   1.1e-05     0.048      60      99 ..      86     126 ..      44     143 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.1e-05
                       Bd3614-deam  60 iadrdgdgeeerrple.egarllvtlqcCkmCAalvvaaad 99 
                                        a+++    ++r+ +  ega+l+vt+ +C  C  l+v+a+ 
  gi|242399255|ref|YP_002994679.1|  86 HAEQNVIAMAARKGISlEGATLYVTHFPCDTCFKLLVNAGI 126
                                       556666667778877658***************99999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.49
# Mc/sec: 1096.75
//
Query:       gi|242399256|ref|YP_002994680.1|  [L=260]
Description: Zinc-dependent protease HtpX like rotein, M48 family [Thermococcus sibiricus MM 739]
Scores for complete 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   83.9   0.0      2e-23   83.2   0.0    1.3  1  Peptidase_M48   Peptidase family M48
      3e-06   26.6   0.9    1.7e-05   24.2   0.1    2.0  2  Peptidase_M56   BlaR1 peptidase M56
     0.0068   16.2   0.3      0.022   14.6   0.3    1.8  2  AGTRAP          Angiotensin II, type I receptor-associated pr
  ------ inclusion threshold ------
        7.1    7.1   8.3         45    4.6   0.0    2.3  2  PhoR            Phosphate regulon sensor protein PhoR


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 !   83.2   0.0   4.4e-27     2e-23       5     192 ..      57     245 ..      54     249 .. 0.81

  Alignments for each domain:
  == domain 1  score: 83.2 bits;  conditional E-value: 4.4e-27
                                       SHHHHHHHHHHHHTT-..-EEEEEEE-GGGT-EEEEESSS-EEEEEEHHHH-SSB-HHHHHHHHHHHHHHHHTTHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48   5 aelkevveelakeaglpkpltkvyvvnspkrNAFalgggknkrivltdgLlkqllseeelaaVlGHElGHikhrhsv 81 
                                       ++l + + ++a++ag+  +++++y++++   NA+  g++    ivl+ gL+ + l+e+ ++aV +HE+GHik+r++v
  gi|242399256|ref|YP_002994680.1|  57 PWLYDGIVRMANKAGI--ATPDIYILDDYIPNAYSFGNS----IVLSLGLF-EVLDEDGILAVTAHEIGHIKNRDTV 126
                                       67888899********..********************9....********.************************7 PP

                                       HHHHHHHHHHHHHHHHHHHHTT-SHHHHHTT--S---HHHHHHHHHHTTHHHHHHHHHHHHHHHHTTT.HHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48  82 vslivsllasillllglallisraeedaagafldalavliglliillflalSRkrEyqADeagvellkrakdlvral 158
                                       +  +vs++  +++ ++++     + ++  + +++ + v++++l  +  + + RkrE++AD  +++l++r+  l +al
  gi|242399256|ref|YP_002994680.1| 127 IFPLVSYIRYLMIPMVVL-----NALFSKSLMVALASVMLYILYEVERVHYLRKREFKADDTALRLVSRPLSLKEAL 198
                                       777777666666655555.....55555555555555677777788888**************************** PP

                                       HHHHHHTT-......-S---HHHH.............HHS-SS--HHHHHHHH CS
                                       xxxxxxxxx......xxxxxxxxx.............xxxxxxxxxxxxxxxx RF
                     Peptidase_M48 159 iklakdler......qdvsaslrs.............ellstHPplleRiqal 192
                                        +l +  +             +                +++tHP+  eRi ++
  gi|242399256|ref|YP_002994680.1| 199 EELRYYEDLrinvkvS-----E-VpsiepgierkyhnPIFATHPSYDERIWRI 245
                                       9998765543332220.....2.2346788888888899***********877 PP

>> Peptidase_M56  BlaR1 peptidase M56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.1   3.7e-09   1.7e-05     110     225 ..      22     138 ..       7     151 .. 0.83
   2 ?    1.0   0.1     0.043   1.9e+02     107     164 ..     153     211 ..     142     219 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 3.7e-09
                     Peptidase_M56 110 ivgalilllyliaallvlkkrfvrklgklraeelkeaLkeakeemqlkrnik...ir.lsssidsPavlgllkprIv 182
                                       +v++l++++ l+  +l+  ++f+rk+++l + e+   L +   +m+ k  i+   i+ l + i +  ++g   + Iv
  gi|242399256|ref|YP_002994680.1|  22 LVIILVTFFALMILYLWTTRKFLRKNQNLLSFEEMPWLYDGIVRMANKAGIAtpdIYiLDDYIPNAYSFG---NSIV 95 
                                       7899999999******99999*****************99999999787665222541345666666666...78** PP

                     Peptidase_M56 183 lPadflkklsdeeleyillHElaHlkrkDllvnllvavlqclf 225
                                       l+  +++ l+++ +  + +HE  H+k++D+++  lv  +  l+
  gi|242399256|ref|YP_002994680.1|  96 LSLGLFEVLDEDGILAVTAHEIGHIKNRDTVIFPLVSYIRYLM 138
                                       ********************************99998888776 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.043
                     Peptidase_M56 107 liWivgalilllyliaallvlkkr.fvrklgklraeelkeaLkeakeemqlkrnikirl 164
                                       ++ ++ +++ +ly +  + +l+kr f     +lr  +    Lkea ee  +  +++i +
  gi|242399256|ref|YP_002994680.1| 153 MVALASVMLYILYEVERVHYLRKReFKADDTALRLVSRPLSLKEALEELRYYEDLRINV 211
                                       34455666778899999999999989888889998888889999999988877766654 PP

>> AGTRAP  Angiotensin II, type I receptor-associated protein (AGTRAP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.3   4.8e-06     0.022      15      74 ..      79     141 ..      77     169 .. 0.74
   2 ?   -1.1   0.1      0.33   1.5e+03      58      97 ..     153     194 ..     137     202 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.8e-06
                            AGTRAP  15 vlaeylsgaYawanftvlavgvWaiaqrdsidAismfliglvl...tillDiihlsiyyprka 74 
                                       +l++y+++aY+++n  vl +g++ + ++d i A++   ig +    t+++ +++ + y    +
  gi|242399256|ref|YP_002994680.1|  79 ILDDYIPNAYSFGNSIVLSLGLFEVLDEDGILAVTAHEIGHIKnrdTVIFPLVSYIRYLMIPM 141
                                       5889*******************************9999987533377777777766665543 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.33
                            AGTRAP  58 tillDiihlsiyyprka..lsdvkrfsagmailsLllkPvsc 97 
                                        + l  ++l i y+ ++      ++f a  + l L+ +P+s+
  gi|242399256|ref|YP_002994680.1| 153 MVALASVMLYILYEVERvhYLRKREFKADDTALRLVSRPLSL 194
                                       444455666666766551133456688888888888888886 PP

>> PhoR  Phosphate regulon sensor protein PhoR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   5.3     0.027   1.2e+02      10      50 ..       4      45 ..       1      54 [. 0.73
   2 ?    4.6   0.0      0.01        45       9      48 ..     134     173 ..     129     182 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.027
                              PhoR 10 allllaallvgllvgalaalll.lalllllawhlyqllrLsr 50
                                      +++l+ +l+  l++g+++++++ ++ ++l++  l+ ++++ r
  gi|242399256|ref|YP_002994680.1|  4 LIFLAQLLMTLLYLGKFGLVIIlVTFFALMILYLWTTRKFLR 45
                                      345555668889999999998877777778888888877754 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.01
                              PhoR   9 lallllaallvgllvgalaallllalllllawhlyqllrL 48 
                                       + +l+++++++ +l+++  ++ l++++l++++ + +++ L
  gi|242399256|ref|YP_002994680.1| 134 IRYLMIPMVVLNALFSKSLMVALASVMLYILYEVERVHYL 173
                                       5678999999999999999999999999998887776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       950  (0.0529868); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); 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):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 1634.77
//
Query:       gi|242399257|ref|YP_002994681.1|  [L=121]
Description: transcription regulator, penicillinase repressor family [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-18   66.1   0.4    3.9e-18   65.9   0.4    1.1  1  Penicillinase_R  Penicillinase repressor
     0.0014   18.6   0.4     0.0035   17.3   0.4    1.6  1  Cdc6_C           CDC6, C terminal winged helix domain
  ------ inclusion threshold ------
      0.013   15.7   0.1      0.019   15.1   0.1    1.4  1  FUR              Ferric uptake regulator family
      0.079   13.0   0.0        0.1   12.6   0.0    1.1  1  Replic_Relax     Replication-relaxation
      0.097   12.9   0.0        0.2   11.9   0.0    1.5  1  PPR_2            PPR repeat family
       0.11   12.5   0.0       0.17   12.0   0.0    1.2  1  HTH_20           Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.9   0.4   1.3e-21   3.9e-18       3      95 ..      19     116 ..      17     121 .] 0.89

  Alignments for each domain:
  == domain 1  score: 65.9 bits;  conditional E-value: 1.3e-21
                                       -S-SHHHHHHHHHS-EEHHHHHHT--GG.G---HHHHHHHHHHHHHTTS-EEEEE....TTEEEEE----XXXXXXX CS
                   Penicillinase_R   3 elEaevmeilwekgeatvkevveeleee.kelaysTVktllrrLvkKgllsreke....grafiYsplvseeeavas 74 
                                       ++Eae+me++w+ + at++ev ++l+++  +l +sTV  l++rL+++gll+r+ +    g +++Ys ++s+ee+ ++
  gi|242399257|ref|YP_002994681.1|  19 PMEAEIMEYMWRVKVATAGEVYDHLKKRhESLRRSTVSILMNRLCERGLLKRKVDtgrgGMKYVYSVATSKEEFEKK 95 
                                       68**************************7888*******************99766233569*************** PP

                                       XXXXXXXXXXXXXXXXXXXXX CS
                   Penicillinase_R  75 avkqlldklfegsvkelvaaf 95 
                                        v+++l++l+++  +++va +
  gi|242399257|ref|YP_002994681.1|  96 VVESILNSLMNNFKEATVAYL 116
                                       **********98777777765 PP

>> Cdc6_C  CDC6, C terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.4   1.2e-06    0.0035      20      82 ..      38      93 ..      30      95 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.2e-06
                                      HHHHHHHHHHHHTT-----HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEESSSCHHHH CS
                            Cdc6_C 20 evyevYkslCesegvdpltqrevsdllseLemlgileleksskGrregrtrkisLnvdpddvl 82
                                      evy+  k+       + l +++vs l+++L  +g+l++++   Gr +g+++ +s+ +++++ +
  gi|242399257|ref|YP_002994681.1| 38 EVYDHLKKR-----HESLRRSTVSILMNRLCERGLLKRKVD-TGR-GGMKYVYSVATSKEEFE 93
                                      444444433.....45699*******************987.888.7*********9999876 PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.1   6.2e-06     0.019      23      73 ..      33      84 ..      17     113 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 6.2e-06
                                      SBEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEE.EEETTSEEEEEES CS
                               FUR 23 hlsaeevykelkeedpeislaTVYrtLklleeaglvke.lefedgesryela 73
                                        +a evy++lk++++++  +TV   ++ l e+gl+k+ +++  g ++y  +
  gi|242399257|ref|YP_002994681.1| 33 VATAGEVYDHLKKRHESLRRSTVSILMNRLCERGLLKRkVDTGRGGMKYVYS 84
                                      47999*******************************9636676666666444 PP

>> Replic_Relax  Replication-relaxation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   3.5e-05       0.1       7      61 ..      31      85 ..      26      92 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.5e-05
                      Replic_Relax  7 hrvlTtrqiarllfashra....tarrrLarLrelgllsr.lrkrvggarggsepyvYaL 61
                                      ++v+T+  ++ +l + h++    t++  ++rL+e+gll+r ++     ++g   +yvY  
  gi|242399257|ref|YP_002994681.1| 31 VKVATAGEVYDHLKKRHESlrrsTVSILMNRLCERGLLKRkVDTG---RGG--MKYVYSV 85
                                      6889999999999999988888899999************44444...444..5778865 PP

>> PPR_2  PPR repeat family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   6.7e-05       0.2      13      49 ..      27      63 ..      23      64 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.7e-05
                             PPR_2 13 lckkgkveeAfklfneMkkrglePnsyTysilikglc 49
                                      ++ + kv  A ++++  kkr  +   +T sil++ lc
  gi|242399257|ref|YP_002994681.1| 27 YMWRVKVATAGEVYDHLKKRHESLRRSTVSILMNRLC 63
                                      6677789999*************************** PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   5.6e-05      0.17       4      56 ..      13      70 ..      11      73 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.6e-05
                                      HHHHS-HHHHHHHHHHSTCTTB-HHHHHHHH.....TS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20  4 aeALahPvRrrilraLaraegltaselaerl.....dlskntlsyHLrvLeeagLvev 56
                                      ++A++ P+ ++i+ + +r + +ta+e+ + l     +l+++t+s  ++ L e gL+++
  gi|242399257|ref|YP_002994681.1| 13 LKAILPPMEAEIMEYMWRVKVATAGEVYDHLkkrheSLRRSTVSILMNRLCERGLLKR 70
                                      578889999**********************877766*****************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       981  (0.0547158); expected 358.6 (0.02)
Passed bias filter:                      621  (0.0346366); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 884.54
//
Query:       gi|242399258|ref|YP_002994682.1|  [L=416]
Description: transaminase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-44  152.9   0.0    1.5e-44  152.7   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    3.1e-08   32.8   0.0    1.2e-07   30.9   0.0    1.9  1  Aminotran_MocR   Alanine-glyoxylate amino-transferase
    9.3e-06   25.1   0.0    1.7e-05   24.2   0.0    1.4  1  Beta_elim_lyase  Beta-eliminating lyase
    0.00032   20.1   0.0    0.00048   19.5   0.0    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family


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 !  152.7   0.0   3.3e-48   1.5e-44       3     362 ..      45     405 ..      43     406 .. 0.92

  Alignments for each domain:
  == domain 1  score: 152.7 bits;  conditional E-value: 3.3e-48
                                       EEESSSSSTTSTTSSHHHHHHHHHHHH.HHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHH CS
                     Aminotran_1_2   3 vinLgsneylgdsgkptlpevakaeke.galaggtlneygpidglpeleealakflgrseklklkreaavvvgsGag 78 
                                       ++ L++++++ d     + +v+ + ++  ++ +++   y+p  g pel+e++  fl++  +l++ +e ++v++ G +
  gi|242399258|ref|YP_002994682.1|  45 LVSLAAGDPDPD---LIPRKVLGEIAReVLQNQPKSVMYTPANGIPELREEISVFLKKYDNLEVSPE-NIVLTIGGT 117
                                       688999999999...5666666666668999999999********************999*******.888888888 PP

                                       HHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEE. CS
                     Aminotran_1_2  79 aliealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilv. 154
                                        ++++l ++l ++pgd+i+  +p+y +   +++  g+++  + ++   + ++ ++ lee++ke++++ +k+k+i++ 
  gi|242399258|ref|YP_002994682.1| 118 GALDLLGRVL-IDPGDVIITENPSYINTLLAFEQLGAKIEGVIVD---NEGMRVDLLEEKIKELKAKGQKIKFIYTi 190
                                       8888999999.89*************************9999955...889***********************963 PP

                                       ESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EE CS
                     Aminotran_1_2 155 esphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvG 231
                                        + +NP G+ ++ +  ++ll+la ky ll++ D aY ++ ++  d v+ +  +++e  ++++g++sK +G +G+RvG
  gi|242399258|ref|YP_002994682.1| 191 PTGQNPMGVTMSMDRRKALLELASKYDLLIIEDTAYNAMRYEGGDIVP-LKALDNEGRVIVAGTFSKVLG-TGFRVG 265
                                       799***************************************999888.5555565668***********.8***** PP

                                       EEEEEHHHHHHHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS..TEEEECCSC CS
                     Aminotran_1_2 232 yilgnaavvsqlrklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLael..glkvlasqs 304
                                       +i++  ++++ +   ++p+ +  ++l q+++++ l+   +++ +l+ +   ++++r+ + ++L+e   + k++++ +
  gi|242399258|ref|YP_002994682.1| 266 WIIAEGDILKKVLMQKQPIDFcaPALSQYIALEYLRRGYFEKYHLNSALLGYKEKRDLMLKALEENlpDAKFTKPIA 342
                                       *************9999998888****************9999********************999*********** PP

                                       SSEEEEEETHH.CHHHHHHHHHHTCTEEEEEGGGGTS....TTEEEEECTTS-HHHHHHHHHH CS
                     Aminotran_1_2 305 gmflltdlsae.takelskkLleevgvyvtpgtsftv....pgrlRitvAglteeeleelvea 362
                                       gmf++  l++e +  +++ +L e++gv+v+pg++f++    ++ +R++++  ++e++   +e+
  gi|242399258|ref|YP_002994682.1| 343 GMFVMLFLPEEaDGIAFASELMEKEGVVVVPGKPFYTdesgKNAIRLNFSRPSKEDIPVGIEK 405
                                       ***********888999999********************999******99999999888776 PP

>> Aminotran_MocR  Alanine-glyoxylate amino-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.0   2.7e-11   1.2e-07     126     405 ..     133     406 ..      83     411 .. 0.72

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 2.7e-11
                                       EEEEEES--HHHHHHHHHHT-EEEEEEEETTEE-HH....HHHHHHHC-TTEEEEEE-SSS-TTT-----HHHHHHH CS
                    Aminotran_MocR 126 kllvtvpGydrhfllleelGielltvdlqddGpdvd....aveklvaedasvkGilavpkysnptGetiseevarrl 198
                                        ++   p y   +l  e+lG ++  v ++++G  vd    ++++l a+   +k i+++p+  np G t+s ++ + l
  gi|242399258|ref|YP_002994682.1| 133 VIITENPSYINTLLAFEQLGAKIEGVIVDNEGMRVDlleeKIKELKAKGQKIKFIYTIPTGQNPMGVTMSMDRRKAL 209
                                       577889*****************9999999999987333357889**************************988888 PP

                                       HT---SSTT-EEEEE-TTSS-BS.SSSS----HHHHHHHHT-TTSEEEEEESTTTS-TTSS-EEEEE-HHHHHHHH. CS
                    Aminotran_MocR 199 aalkaaapdfrifaddayavhdlvaeedkdanivalardaGhpdrafvlastskitfaGaGvafvassedniawlk. 274
                                         l  +  d+ i  d ay++     e     +iv+l +      r +v  + sk+  +G  v+ + +  d ++ +  
  gi|242399258|ref|YP_002994682.1| 210 LELA-SKYDLLIIEDTAYNAMRY--E---GGDIVPLKA-LDNEGRVIVAGTFSKVLGTGFRVGWIIAEGDILKKVLm 279
                                       8874.568**********99877..3...346777643.44567888888889999999999999888888776540 PP

                                       HHHHHC-S---HHHHHHHHHHHHHSTHHHHHHHHHHHHHHH..HHHHHHHHHHHHHTTTSSEEE---SBSS-EEE.. CS
                    Aminotran_MocR 275 kylGlqsiGpdkveqlrhvkflkdyeGlealmrdhaeliap..kfeavlevleaelggaevatwteprGGyfisl.. 347
                                       +   ++   p  + q   + +l+   G   + +  ++l+    k + +l++le++l     a +t+p  G f+ l  
  gi|242399258|ref|YP_002994682.1| 280 QKQPIDFCAP-ALSQYIALEYLRR--GYFEKYHLNSALLGYkeKRDLMLKALEENLPD---AKFTKPIAGMFVMLfl 350
                                       3344444444.4666666666654..44444444455554400444456667777664...5578888888888744 PP

                                       .EESSS-HHHHHHHHHHCTEE---TTTTSSTT--SSS-EEEE--SSS-HHHHHHHHHHH CS
                    Aminotran_MocR 348 .dtldgvakrvvklaeeaGvsltaaGatypaGedpkdrnirlaptlppleevetamdvv 405
                                        + +dg+a    +l e+ Gv + +    + + e  k+  irl  ++p+ e++ + ++ +
  gi|242399258|ref|YP_002994682.1| 351 pEEADGIAF-ASELMEKEGVVVVPGKP-FYTDESGKN-AIRLNFSRPSKEDIPVGIEKL 406
                                       445666664.45788888888877544.434444443.588888888888887776665 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   3.9e-09   1.7e-05      48     169 ..     108     225 ..      92     255 .. 0.88

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 3.9e-09
                                       SEEEEES-HHHHHHHHHHHH--TTEEEEEETT-HHHHSSTTHHHHC.C--EEEEE-EBTTTBE-HHHHHHHS--S-T CS
                   Beta_elim_lyase  48 eaalfvpqGtaAnsillkillqrgeevivtepahihfdetgaiael.agvklrdlknkeaGkmdlekleaaikevga 123
                                       e ++ +  Gt+A  +l ++l+ +g+ +i ++p+ i   +  a ++l a      +  ++   m ++ le++ike +a
  gi|242399258|ref|YP_002994682.1| 108 ENIVLTIGGTGALDLLGRVLIDPGDVIITENPSYI--NTLLAFEQLgAK--IEGVIVDN-EGMRVDLLEEKIKELKA 179
                                       66789999*****************9999999855..678889888444..55555555.55************988 PP

                                       TS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEET CS
                   Beta_elim_lyase 124 heekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgA 169
                                         +kik+i++  T +   G  +s++  +++ ++a ky++ ++ D A
  gi|242399258|ref|YP_002994682.1| 180 KGQKIKFIYTIPTGQNPMGVTMSMDRRKALLELASKYDLLIIEDTA 225
                                       99*************************************9999987 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 !   19.5   0.0   1.1e-07   0.00048      45     146 ..     114     225 ..     103     247 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.1e-07
                                       SSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EE..EEE-B-TTTSSB-GGGCGGG--TTE..EEEEE CS
                   DegT_DnrJ_EryC1  45 ssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakp..vfvDvdpdtynidpaaieaaitert..kaIlp 117
                                         Gt Al l+ r+  ++pgd +I+   +++ t  a  +lgak   v vD +   + +  ++i+++  +    k I +
  gi|242399258|ref|YP_002994682.1| 114 IGGTGALDLLGRV-LIDPGDVIITENPSYINTLLAFEQLGAKIegVIVDNEGMRVDLLEEKIKELKAKGQkiKFIYT 189
                                       5688888886555.599************************852277777777777777777765544335699998 PP

                                       B-G....GGB---HH...HHHHHHHHCT-EEEEE-T CS
                   DegT_DnrJ_EryC1 118 Vhl....yGqvadmd...alkaiaakhglkvieDaA 146
                                       + +    +G  + md   al ++a+k++l +ieD+A
  gi|242399258|ref|YP_002994682.1| 190 IPTgqnpMGVTMSMDrrkALLELASKYDLLIIEDTA 225
                                       8662222677778875557999************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      570  (0.0317921); 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 0.28s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 2642.59
//
Query:       gi|242399259|ref|YP_002994683.1|  [L=334]
Description: Glyoxylate reductase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-70  235.8   0.0    2.9e-70  235.3   0.0    1.3  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
    7.6e-40  135.7   0.0    8.7e-40  135.5   0.0    1.0  1  2-Hacid_dh     D-isomer specific 2-hydroxyacid dehydrogenase,
    2.3e-08   34.4   0.1    4.8e-08   33.3   0.1    1.5  1  NAD_binding_2  NAD binding domain of 6-phosphogluconate dehyd
    1.7e-05   24.5   0.1      4e-05   23.2   0.0    1.6  2  IlvN           Acetohydroxy acid isomeroreductase, NADPH-bind
    0.00075   20.0   0.0     0.0018   18.8   0.0    1.7  1  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
  ------ inclusion threshold ------
      0.039   13.2   0.1       0.11   11.8   0.1    1.7  1  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
      0.057   13.9   0.1       0.28   11.6   0.0    2.0  2  NAD_binding_7  Putative NAD(P)-binding


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 !  235.3   0.0   1.1e-73   2.9e-70       2     178 .]     110     290 ..     109     290 .. 0.97

  Alignments for each domain:
  == domain 1  score: 235.3 bits;  conditional E-value: 1.1e-73
                                       HHHHHHHTTHHHHHHHHHTTCC......HTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHH CS
                      2-Hacid_dh_C   2 alllallrrlaeadeevregew......ksekallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkke 72 
                                       +llla++rrl ead+ vr+gew      + +  +lg+ l+gkt+GiiGlGrIGqavakr+k+fgmkv++y+r++k+e
  gi|242399259|ref|YP_002994683.1| 110 TLLLATARRLIEADQFVRSGEWkksgvgWHPLMFLGYGLKGKTLGIIGLGRIGQAVAKRAKGFGMKVLYYSRTRKTE 186
                                       799*******************9999988899*****************************************9977 PP

                                       HCHHHHTCEECSHHHHHHH-SEEEE-S--STTTTTSBSHHHHHCSTTTEEEEESS-GGGB-HHHHHHHHHTTSCCEE CS
                      2-Hacid_dh_C  73 eeeeelgvelvsleellaesDivslhlpltpetrhlinaeelakmkkgailiNtaRGglvdeeaLleaLksgkiaga 149
                                       + e+e g+++v++e+ll++sD++s+h+plt++t+h+i+++el++mk++ail+NtaRG++vd++aL++aLk+g+iaga
  gi|242399259|ref|YP_002994683.1| 187 A-EKEIGADYVDFETLLKKSDFISIHVPLTKKTYHMIGEKELQLMKPNAILVNTARGAIVDTKALVKALKEGWIAGA 262
                                       7.999************************************************************************ PP

                                       EES--SSSSSGTCHHHHHSTTEEE-SS-T CS
                      2-Hacid_dh_C 150 alDvfeeeplpedspllelpnviltPHia 178
                                       +lDvfeeep+  d +l++l+nv+l PHi+
  gi|242399259|ref|YP_002994683.1| 263 GLDVFEEEPYY-DRELFSLKNVVLAPHIG 290
                                       ***********.55*************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 !  135.5   0.0   3.4e-43   8.7e-40       1     134 []       5     322 ..       5     322 .. 0.99

  Alignments for each domain:
  == domain 1  score: 135.5 bits;  conditional E-value: 3.4e-43
                                       EEEEST.CHHHHHHHHHTTEEEEEES...CSSHHHCHHHHTTESEEEE-TTS-BSHHHHHHHTT--EEEESSSSCTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        2-Hacid_dh   1 vlileplreeelellkeegvevevkd...ellteellekakdadalivrsntkvtaevlealpkLkviaragvGvDn 74 
                                       v+i+++++e++++ +k+  +e+ev++   +++++ llek++d+dal++  + kv++e+l+ +p+Lk+ia+++vG+Dn
  gi|242399259|ref|YP_002994683.1|   5 VFITREIPENGIKMIKK-FYEIEVWKdqkAPPRDVLLEKIRDFDALVTLLTEKVDKELLDSAPNLKIIAQYAVGYDN 80 
                                       689999***********.55******9*99*********************************************** PP

                                       B-HHHHHHTT-EEEE-TTTTHHHHHHHH................................................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx................................................. RF
                        2-Hacid_dh  75 vDldaakerGilVtnvpgystesvAElt................................................. 102
                                       +D++ a++rG+ Vtn+pg+ t+++A+l+                                                 
  gi|242399259|ref|YP_002994683.1|  81 IDVEEATKRGVYVTNTPGVLTDATADLAftlllatarrlieadqfvrsgewkksgvgwhplmflgyglkgktlgiig 157
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                        2-Hacid_dh 103 ............................................................................. 102
                                                                                                                    
  gi|242399259|ref|YP_002994683.1| 158 lgrigqavakrakgfgmkvlyysrtrkteaekeigadyvdfetllkksdfisihvpltkktyhmigekelqlmkpna 234
                                       ***************************************************************************** PP

                                       ........................................................T-BHHHHHHHHHHHHHHHHHH CS
                                       ........................................................xxxxxxxxxxxxxxxxxxxxx RF
                        2-Hacid_dh 103 ........................................................aaTeeaqeniaeeaaenlvaf 123
                                                                                               +aT+ea+e +a+ +aenl+af
  gi|242399259|ref|YP_002994683.1| 235 ilvntargaivdtkalvkalkegwiagagldvfeeepyydrelfslknvvlaphigSATHEAREGMARLVAENLIAF 311
                                       ***************************************************************************** PP

                                       HTTCCGTTBCS CS
                                       xxxxxxxxxxx RF
                        2-Hacid_dh 124 lkgespanavn 134
                                       ++ge p+n +n
  gi|242399259|ref|YP_002994683.1| 312 ARGEIPPNLIN 322
                                       ********997 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 !   33.3   0.1   1.9e-11   4.8e-08       2     106 ..     153     256 ..     152     264 .. 0.91

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 1.9e-11
                                       EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHS.HC CS
                     NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdevieg.ll 77 
                                       +g+iGlG +G+  a++ +  g+kv  y rt  k+e+  + ga+   + e l+++ d++ + v+ +k++ ++i +  l
  gi|242399259|ref|YP_002994683.1| 153 LGIIGLGRIGQAVAKRAKGFGMKVLYYSRT-RKTEAEKEIGADY-VDFETLLKKSDFISIHVPLTKKTYHMIGEkEL 227
                                       79**************************99.6677767677755.56799**********************99899 PP

                                       CC--TT-EEEE-S---HHHHHHHHHHHHH CS
                     NAD_binding_2  78 ealkkgdilidgstsspedtrelakelke 106
                                       + +k+++il++++  ++ dt+ l k+lke
  gi|242399259|ref|YP_002994683.1| 228 QLMKPNAILVNTARGAIVDTKALVKALKE 256
                                       *************************9997 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 ?   -2.6   0.0       1.4   3.6e+03      38      54 ..      80      96 ..      51     112 .. 0.58
   2 !   23.2   0.0   1.6e-08     4e-05       2      74 ..     148     218 ..     147     252 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.4
                                      -HHHHHHHHTT-EEEEH CS
                              IlvN 38 sksvkkAkeegfevltv 54
                                      +  v++A+++g+ v+++
  gi|242399259|ref|YP_002994683.1| 80 NIDVEEATKRGVYVTNT 96
                                      23445555555555554 PP

  == domain 2  score: 23.2 bits;  conditional E-value: 1.6e-08
                                       HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHHHH CS
                              IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPDelqk 74 
                                       lkgk++ +iG G  G+a a+  +  g++v +  r+ +  ++  ke g + ++ + + kk+d++ i +P + ++
  gi|242399259|ref|YP_002994683.1| 148 LKGKTLGIIGLGRIGQAVAKRAKGFGMKVLYYSRTRK--TEAEKEIGADYVDFETLLKKSDFISIHVPLTKKT 218
                                       89****************************9988887..555677899********************65543 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 !   18.8   0.0     7e-07    0.0018       2      72 ..     153     215 ..     152     235 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 7e-07
                                       EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HH CS
                     F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpe 72 
                                       +giiG G++g+a+a+++   g    +++   sr+ +  +e+++e+  ++  vd e++++++d++ + v+ +
  gi|242399259|ref|YP_002994683.1| 153 LGIIGLGRIGQAVAKRAKGFG---MKVL-YYSRTRK--TEAEKEI--GADYVDFETLLKKSDFISIHVPLT 215
                                       8***************99999...9999.5477666..4555555..577778*********999888865 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   4.3e-05      0.11      32     132 ..     154     242 ..     145     256 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.3e-05
                                       EEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHCHHHHHHHHHHHH-SEEEE---BT.TSS-- CS
                       AlaDh_PNT_C  32 lviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvevlksqeellaeavkeadvvigtvlip.GkkaP 107
                                        +iG G  G++ ++ akg+g kV  +   +++ e  +++ga            ++  +k++d +  ++++p  kk+ 
  gi|242399259|ref|YP_002994683.1| 154 GIIGLGRIGQAVAKRAKGFGMKVLYYSR-TRKTEAEKEIGAD--------YVDFETLLKKSDFI--SIHVPlTKKTY 219
                                       59*********************88754.3334444447777........45678899999987..67777457788 PP

                                       -SC-HHHHHTS-TTEEEEETTGGGT CS
                       AlaDh_PNT_C 108 kLvteemvksMkpgsVivDvAidqG 132
                                       +++ e+ ++ Mkp++++v  A  +G
  gi|242399259|ref|YP_002994683.1| 220 HMIGEKELQLMKPNAILVNTA--RG 242
                                       9***************99866..45 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 ?   -0.7   0.0      0.77     2e+03      25      46 ..      42      66 ..      39     121 .. 0.57
   2 ?   11.6   0.0   0.00011      0.28       5      91 ..     148     239 ..     144     248 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.77
                     NAD_binding_7 25 klleagakvtvvapevkeele...e 46
                                      k+ +++a vt+++++v +el     
  gi|242399259|ref|YP_002994683.1| 42 KIRDFDALVTLLTEKVDKELLdsaP 66
                                      6667788888888886332222331 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00011
                     NAD_binding_7   5 lkgkkvlvvGgGevAarkvrklleagakvtvvapevkeeleelvklaeeelekdlegadlviaatdd.relneriae 80 
                                       lkgk+  ++G G++++  +++   +g kv  ++ + k e+e+ + +   ++e  l++ d++ + ++  ++  + i e
  gi|242399259|ref|YP_002994683.1| 148 LKGKTLGIIGLGRIGQAVAKRAKGFGMKVLYYSRTRKTEAEKEIGADYVDFETLLKKSDFISIHVPLtKKTYHMIGE 224
                                       799********************************999999999999999999999998776555430333333333 PP

                     NAD_binding_7  81 ....aakarrilvnv 91 
                                           ++k + ilvn 
  gi|242399259|ref|YP_002994683.1| 225 kelqLMKPNAILVNT 239
                                       222233446666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         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: 2224.30
//
Query:       gi|242399260|ref|YP_002994684.1|  [L=239]
Description: hypothetical protein TSIB_1281 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-37  130.0   0.9    1.7e-37  129.6   0.9    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 !  129.6   0.9   9.7e-42   1.7e-37      13     215 ..      15     233 ..      12     236 .. 0.80

  Alignments for each domain:
  == domain 1  score: 129.6 bits;  conditional E-value: 9.7e-42
                                       HHCCT-SEEEE-HHCCSSS-HHHHHHHHCTS-TT-EEEEE--CCCCCS....................G.-.SCHHH CS
                             DUF72  13 yYarhfntVEinstFYalpspetvakwaaqtpedFrFavKapraithe...............r....n.e.daeea 68 
                                        Y+r fntVE+++tFY+l +++t++kw +++p+dF F++Ka++ +th                +    +   d+   
  gi|242399260|ref|YP_002994684.1|  15 KYFRDFNTVEVQQTFYKLIQDKTLQKWEQEAPKDFIFSIKAFQGVTHPptsptwrrsnvkptpGvgllRpTpDVFRY 91 
                                       7**********************************************544455555555444414443222245555 PP

                                       HHHHHHH.CHHHCT-EEEEEEE--TT--S.HHHHHHHHHHTTTS-...S.EEEE--BGGGH.H.HHHHHHHTT-EEE CS
                             DUF72  69 lerflesalepLgeklgpllfQlppsfkfdeenlerLeaflaalp...l.lavEvRhrswf.e.llellrehgvavv 139
                                       +e  l++  e Lg k   +l+Qlp+sfk +ee++++ e+f+++++     ++vE+R   w  + + e++re +++ v
  gi|242399260|ref|YP_002994684.1|  92 WELTLRE-AEILGAK--FVLIQLPKSFKETEESFNNAEKFFSKIEkrdFtIVVELRG--WSeKgIKEFVREFNLIDV 163
                                       5555555.5666655..4*********99999********9988888955******8..87767*********9988 PP

                                       EE--SSC--------SSTEEEEEE--S....HHTTB----HHHHHHHHHHHHHHHTCSSEEEEEE-SBCCCHHHHHH CS
                             DUF72 140 ldepkkpklpledvttadfvyvRlhgr....eeryayrYseeelaewaerikawaaegrevyvffnndaegqaplna 212
                                       +d      l  e+   ++  y+Rlhg     +  y+++Y++eel+ +a+++k+w++  +e yv+fnn +   ++++a
  gi|242399260|ref|YP_002994684.1| 164 TD-----PLVREPLHVGKINYYRLHGAyqkgRIIYKHKYTQEELQGIAKKVKEWNK--KESYVYFNNAY---MCEDA 230
                                       88.....23346666689**********9974679*******************99..89*******55...56666 PP

                                       HHH CS
                             DUF72 213 raL 215
                                       r +
  gi|242399260|ref|YP_002994684.1| 231 RSF 233
                                       655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       970  (0.0541023); expected 358.6 (0.02)
Passed bias filter:                      588  (0.032796); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1752.17
//
Query:       gi|242399261|ref|YP_002994685.1|  [L=152]
Description: Membrane-bound hydrogenase MBH 2, subunit Mbh2N (hydrogenase subunit) [Thermococcus sibiricus MM 739]
Scores for complete 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   53.7  19.7    3.4e-09   37.2  10.9    2.1  2  Fer4_7    4Fe-4S dicluster domain
    5.7e-13   48.1  12.5    1.3e-08   34.3   3.1    2.3  2  Fer4      4Fe-4S binding domain
    2.9e-11   43.3   8.1    4.4e-11   42.7   8.1    1.3  1  Fer4_10   4Fe-4S dicluster domain
    1.8e-09   37.1  12.1    4.9e-08   32.6   2.6    2.3  2  Fer4_2    4Fe-4S binding domain
    2.9e-09   36.6  12.6      2e-08   34.0   3.0    2.3  2  Fer4_6    4Fe-4S binding domain
    1.5e-08   34.7   8.7    2.4e-08   34.0   8.7    1.3  1  Fer4_9    4Fe-4S dicluster domain
    3.1e-08   33.6  10.2    9.4e-08   32.1  10.3    1.7  1  Fer4_21   4Fe-4S dicluster domain
    1.7e-06   28.9  10.6     0.0038   18.1   2.8    2.3  3  Fer4_16   4Fe-4S double cluster binding domain
    2.2e-05   25.1   4.6       0.02   15.6   0.9    2.4  2  Fer4_15   4Fe-4S single cluster domain
    2.2e-05   24.6  11.4     0.0016   18.8   3.0    2.3  2  Fer4_4    4Fe-4S binding domain
    2.9e-05   24.7  17.2      0.017   16.0   4.5    2.3  2  Fer4_3    4Fe-4S binding domain
    0.00011   22.6   9.3      0.065   13.8   0.7    2.2  3  Fer4_17   4Fe-4S dicluster domain
    0.00025   21.4   8.8      0.095   13.2   1.7    2.2  3  Fer4_8    4Fe-4S dicluster domain
     0.0055   17.2   9.4       0.13   12.9   2.4    2.4  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
  ------ inclusion threshold ------
      0.016   15.4  10.3       0.14   12.3  10.3    2.0  1  Fer4_18   4Fe-4S dicluster domain
      0.069   14.0   6.4       0.55   11.1   0.8    2.2  2  Fer4_22   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   1.5   1.7e-09   1.9e-06      29      52 .]      57      80 ..      24      80 .. 0.70
   2 !   37.2  10.9     3e-12   3.4e-09       1      49 [.      65     108 ..      65     111 .. 0.95

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 1.7e-09
                            Fer4_7 29 ekveidpekClgCgaCvavCPtga 52
                                       k+++dpe+C+gC+ C++vCP++a
  gi|242399261|ref|YP_002994685.1| 57 GKIHYDPERCIGCRLCITVCPANA 80
                                      6889*****************997 PP

  == domain 2  score: 37.2 bits;  conditional E-value: 3e-12
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCP 49 
                                       rCigC+ C  +Cp++a+e+ +e      +k+++  ++C++C  Cv+vCP
  gi|242399261|ref|YP_002994685.1|  65 RCIGCRLCITVCPANAMEWIPE-----LRKIRHYVSRCMFCALCVDVCP 108
                                       8******************997.....68899***************** PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   3.1   1.2e-11   1.3e-08       2      23 ..      60      81 ..      59      82 .. 0.92
   2 !   19.2   2.0   6.5e-07   0.00073       6      19 ..      95     108 ..      90     110 .. 0.89

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 1.2e-11
                                      EEETTTSSS-THHHHHSTTTEE CS
                              Fer4  2 videekCigCGaCvevCPvgAI 23
                                       +d+e+CigC +C+ vCP +A 
  gi|242399261|ref|YP_002994685.1| 60 HYDPERCIGCRLCITVCPANAM 81
                                      68******************97 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 6.5e-07
                                       TTSSS-THHHHHST CS
                              Fer4   6 ekCigCGaCvevCP 19 
                                       ++C++C +Cv+vCP
  gi|242399261|ref|YP_002994685.1|  95 SRCMFCALCVDVCP 108
                                       89************ PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.7   8.1   3.9e-14   4.4e-11       1      56 []      58     108 ..      58     108 .. 0.97

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 3.9e-14
                           Fer4_10   1 kvvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       k+++d+++Ci+C+ C ++CPa     +a + + e  ++r+ v++C++c  Cv++CP
  gi|242399261|ref|YP_002994685.1|  58 KIHYDPERCIGCRLCITVCPA-----NAMEWIPELRKIRHYVSRCMFCALCVDVCP 108
                                       5789*****************.....*****************************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 !   32.6   2.6   4.4e-11   4.9e-08       2      22 .]      58      78 ..      57      78 .. 0.95
   2 !    9.7   2.2   0.00087      0.97       8      21 ..      95     108 ..      88     108 .. 0.84

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 4.4e-11
                            Fer4_2  2 pvvvdtdrCigCgaCvsaCPa 22
                                      ++++d++rCigC+ C+++CPa
  gi|242399261|ref|YP_002994685.1| 58 KIHYDPERCIGCRLCITVCPA 78
                                      79******************8 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00087
                            Fer4_2   8 drCigCgaCvsaCP 21 
                                        rC+ C  Cv++CP
  gi|242399261|ref|YP_002994685.1|  95 SRCMFCALCVDVCP 108
                                       67999********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 !   34.0   3.0   1.7e-11     2e-08       1      23 [.      58      80 ..      58      81 .. 0.95
   2 !    7.8   2.2    0.0031       3.5       8      20 ..      96     108 ..      94     117 .. 0.85

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 1.7e-11
                            Fer4_6  1 vveidpdkCigCgdCvrvCPega 23
                                      ++++dp++CigC+ C++vCP++a
  gi|242399261|ref|YP_002994685.1| 58 KIHYDPERCIGCRLCITVCPANA 80
                                      689******************98 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0031
                            Fer4_6   8 kCigCgdCvrvCP 20 
                                       +C  C  Cv+vCP
  gi|242399261|ref|YP_002994685.1|  96 RCMFCALCVDVCP 108
                                       5666999*****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 !   34.0   8.7   2.2e-11   2.4e-08       1      48 [.      65     109 ..      65     111 .. 0.93

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 2.2e-11
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpk 48 
                                       +C+gC+ C+++Cpa++++     rk+r+      +C++C  Cv++Cp 
  gi|242399261|ref|YP_002994685.1|  65 RCIGCRLCITVCPANAMEWIPELRKIRHYVS---RCMFCALCVDVCPG 109
                                       6*********************999999875...7***********96 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  10.3   8.4e-11   9.4e-08       4      52 ..      62     108 ..      59     112 .. 0.85

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 8.4e-11
                           Fer4_21   4 dedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCP 52 
                                       d+++CigC +C+++C+ ++++ i     +++++  ++C+ C+lC++vCP
  gi|242399261|ref|YP_002994685.1|  62 DPERCIGCRLCITVCPANAMEWIPEL--RKIRHYVSRCMFCALCVDVCP 108
                                       899*************9999988643..455667789************ 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 !   18.1   2.8   3.4e-06    0.0038       1      18 [.      65      82 ..      65      92 .. 0.89
   2 !   14.2   1.1   5.5e-05     0.062      50      65 ..      93     108 ..      82     110 .. 0.72
   3 !   14.9   1.1   3.6e-05      0.04       1      28 [.      96     122 ..      96     150 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 3.4e-06
                           Fer4_16  1 rCgtCgkCaevCPtnaik 18
                                      rC++C+ C+ vCP+na++
  gi|242399261|ref|YP_002994685.1| 65 RCIGCRLCITVCPANAME 82
                                      6***************97 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 5.5e-05
                           Fer4_16  50 kqeaitgCdiCqdvCP 65 
                                          ++++C+ C+dvCP
  gi|242399261|ref|YP_002994685.1|  93 YVSRCMFCALCVDVCP 108
                                       358899*********9 PP

  == domain 3  score: 14.9 bits;  conditional E-value: 3.6e-05
                           Fer4_16   1 rCgtCgkCaevCPtnaikekkekeiear 28 
                                       rC  C  C++vCP + + ++ ek+++a 
  gi|242399261|ref|YP_002994685.1|  96 RCMFCALCVDVCPGKKFPGE-EKSVKAL 122
                                       59999999999999999988.4555544 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.9   1.8e-05      0.02       1      20 [.      59      78 ..      59      83 .. 0.90
   2 !   11.0   0.1   0.00051      0.57       6      20 ..      95     109 ..      94     143 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.8e-05
                           Fer4_15  1 VvvDrdaCigcglCvaeape 20
                                      +++D ++Cigc lC++++p 
  gi|242399261|ref|YP_002994685.1| 59 IHYDPERCIGCRLCITVCPA 78
                                      679***************96 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00051
                           Fer4_15   6 daCigcglCvaeape 20 
                                       ++C+ c+lCv+++p 
  gi|242399261|ref|YP_002994685.1|  95 SRCMFCALCVDVCPG 109
                                       59***********63 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   3.0   1.4e-06    0.0016       1      16 [.      63      78 ..      63      79 .. 0.92
   2 !   10.7   1.3   0.00058      0.65       3      15 ..      96     108 ..      95     123 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.4e-06
                            Fer4_4  1 qerCigCgsCvaaCPq 16
                                      +erCigC+ C+ +CP 
  gi|242399261|ref|YP_002994685.1| 63 PERCIGCRLCITVCPA 78
                                      69*************7 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00058
                            Fer4_4   3 rCigCgsCvaaCP 15 
                                       rC  C  Cv++CP
  gi|242399261|ref|YP_002994685.1|  96 RCMFCALCVDVCP 108
                                       788899******* PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   4.5   1.5e-05     0.017       1      15 []      66      80 ..      66      80 .. 0.96
   2 !   14.4   4.8   4.9e-05     0.055       1      14 [.      97     110 ..      97     111 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.5e-05
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+gC++C  vCP +A
  gi|242399261|ref|YP_002994685.1| 66 CIGCRLCITVCPANA 80
                                      ************987 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 4.9e-05
                            Fer4_3   1 CtgCgaCvevCPvg 14 
                                       C+ C +Cv+vCP +
  gi|242399261|ref|YP_002994685.1|  97 CMFCALCVDVCPGK 110
                                       99**********75 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   2.1     7e-05     0.079      44      59 ..      64      79 ..      42      81 .. 0.78
   2 !   13.5   1.5   7.1e-05     0.079       1      15 [.      65      79 ..      65      93 .. 0.76
   3 !   13.8   0.7   5.8e-05     0.065      38      58 ..      89     109 ..      78     111 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7e-05
                           Fer4_17 44 slCieCgeCerkCPqg 59
                                      ++Ci+C++C ++CP++
  gi|242399261|ref|YP_002994685.1| 64 ERCIGCRLCITVCPAN 79
                                      5677777777777754 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 7.1e-05
                           Fer4_17  1 rCiqCgyClpeCpsy 15
                                      rCi+C+ C+ +Cp +
  gi|242399261|ref|YP_002994685.1| 65 RCIGCRLCITVCPAN 79
                                      588888888888864 PP

  == domain 3  score: 13.8 bits;  conditional E-value: 5.8e-05
                           Fer4_17  38 ekeekaslCieCgeCerkCPq 58 
                                       + ++++s+C+ C +C+ +CP 
  gi|242399261|ref|YP_002994685.1|  89 KIRHYVSRCMFCALCVDVCPG 109
                                       446899*************95 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   1.7   8.5e-05     0.095      49      63 ..      64      78 ..      26      80 .. 0.73
   2 !   11.2   1.7   0.00035      0.39      45      62 ..      91     108 ..      79     111 .. 0.76
   3 !   11.5   1.1   0.00028      0.31       3      16 ..      95     108 ..      92     144 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.5e-05
                            Fer4_8 49 wsCttcgaCtevCpv 63
                                      ++C +c+ C +vCp 
  gi|242399261|ref|YP_002994685.1| 64 ERCIGCRLCITVCPA 78
                                      556666666666665 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00035
                            Fer4_8  45 eealwsCttcgaCtevCp 62 
                                       ++++ +C+ c  C++vCp
  gi|242399261|ref|YP_002994685.1|  91 RHYVSRCMFCALCVDVCP 108
                                       577888999999999998 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.00028
                            Fer4_8   3 ekCieCgaCqsaCp 16 
                                       ++C+ C +C + Cp
  gi|242399261|ref|YP_002994685.1|  95 SRCMFCALCVDVCP 108
                                       56777777777776 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   2.4   0.00011      0.13       2      18 ..      62      78 ..      61      79 .. 0.93
   2 !    8.3   0.7    0.0029       3.3       5      17 ..      96     108 ..      94     117 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
                           Fer4_13  2 DrdtCiacgaCvelaPd 18
                                      D ++Ci+c +C  ++P 
  gi|242399261|ref|YP_002994685.1| 62 DPERCIGCRLCITVCPA 78
                                      789*************6 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0029
                           Fer4_13   5 tCiacgaCvelaP 17 
                                       +C+ c++Cv+++P
  gi|242399261|ref|YP_002994685.1|  96 RCMFCALCVDVCP 108
                                       8***********9 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3  10.3   0.00013      0.14      59      95 ..      64     107 ..      53     109 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                           Fer4_18  59 gdcidcescvkvcPtgi.....dirkGlql..eciscllcidac 95 
                                         ci c+ c++vcP +      ++rk   +   c+ c+lc+d c
  gi|242399261|ref|YP_002994685.1|  64 ERCIGCRLCITVCPANAmewipELRKIRHYvsRCMFCALCVDVC 107
                                       57************9743333556765443238*********** 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   0.8   0.00049      0.55      77      95 ..      61      79 ..      53      80 .. 0.78
   2 ?    5.9   0.6      0.02        23       1      13 [.      96     108 ..      89     118 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00049
                           Fer4_22 77 fgesgCvGCgRCieacpvk 95
                                      ++ + C+GC  Ci++cp++
  gi|242399261|ref|YP_002994685.1| 61 YDPERCIGCRLCITVCPAN 79
                                      5667899999999999875 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.02
                           Fer4_22   1 rClsCgaCtlvCp 13 
                                       rC+ C+ C  vCp
  gi|242399261|ref|YP_002994685.1|  96 RCMFCALCVDVCP 108
                                       5888888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 959.50
//
Query:       gi|242399262|ref|YP_002994686.1|  [L=322]
Description: Membrane-bound hydrogenase MBH 2, subunit Mbh2M (hydrogenase subunit) [Thermococcus sibiricus MM 739]
Scores for complete 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-66  222.6  24.8      8e-66  222.4  24.8    1.0  1  NADHdh    NADH dehydrogenase
  ------ inclusion threshold ------
       0.22   11.5   0.8        9.5    6.2   0.0    2.3  2  DUF4714   Domain of unknown function (DUF4714)


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 !  222.4  24.8   8.9e-70     8e-66      11     298 ..      17     317 ..       7     318 .. 0.91

  Alignments for each domain:
  == domain 1  score: 222.4 bits;  conditional E-value: 8.9e-70
                                       HHHHHHHHHHHHHHHHHHTTS--S-SSTTTTTTHHHHHHHHHCCS-----TTS-HHHHHHHHHHHHHHHHCTTTTS- CS
                            NADHdh  11 llvvalltlleRkvlAriqdRlGPnrvGplGllqplaDalKlllKediipkkadkllfllapvlalilallafaviP 87 
                                       +++ +++ +++R+v+Ar+ +R+GP      ++ qp+ D+ KlllKe+i+p++a k++f+++p+lal+++++++++iP
  gi|242399262|ref|YP_002994686.1|  17 VFLGLVYKGIDRRVSARMTSRIGP------PIRQPFWDVGKLLLKETIVPANAVKWIFNAMPILALASSMTLLLYIP 87 
                                       344458999***************......9********************************************** PP

                                       SSSSSS--TT..HHHHHHHHHHHCHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-SS-HHHH CS
                            NADHdh  88 fgevladlnv..glllilalsslgvygillaGwasnskYallGalRsaaqmisyEvalglsllavvllagslslsei 162
                                       fg + a+l+   +l++il+l++l++++++++G+as+s+++ +Ga R+++ m+syE+++++++ +++l+++s+sls+i
  gi|242399262|ref|YP_002994686.1|  88 FGIIKAPLEGygDLVVILYLLTLQALAMAIGGFASGSPFSSVGAQREMVLMMSYEMPFAIVITGFALIYKSFSLSTI 164
                                       **7666665456***************************************************************** PP

                                       HHCCCTT-C......CCCHHHHHHHHHHHHHHCCTCTTBTTTTSTTSSSSCCCTT-HCHHHHHHHHHHHHHHHHHHH CS
                            NADHdh 163 veaqeeiwf......illqllafiifliallaetnraPFDlpeaesELvaGfhtEYsgmkfalfflaeyanmvlvsa 233
                                        +  + +w        +  +l++i+fl+++ ae+ + PFD++eae+E+++G+  EYsg ++alf+l+  ++ ++++a
  gi|242399262|ref|YP_002994686.1| 165 AS--TPVWTivgplgGIGIFLLLIAFLLVTPAELAKLPFDIAEAETEIAEGMLAEYSGRNLALFYLSDAVRGFAMMA 239
                                       44..45687778889555599******************************************************** PP

                                       HHHHHCT.SS-HCCS.................HHHHHHHHHHHHHHHHH.HHHHC----TCHHHHHHHCCTCHHHHH CS
                            NADHdh 234 lavllFlgGwllpfs.................gllwfllKvllllflfi.wiratlpRlRydqlmklgwkvllplal 292
                                       + v+lF+                         ++lwfl+Kvl++++ ++ ++r++++R+R++q+ +l w ++  + l
  gi|242399262|ref|YP_002994686.1| 240 IEVVLFIPF-----TlsylfglnlsgatlyivEALWFLFKVLVFYVSAVtLVRTSFARFRIEQASRLFWVYVNIIGL 311
                                       *******54.....333445899*******************999876659************************99 PP

                                       HHHHHH CS
                            NADHdh 293 anlllt 298
                                       + lll+
  gi|242399262|ref|YP_002994686.1| 312 LGLLLI 317
                                       999875 PP

>> DUF4714  Domain of unknown function (DUF4714)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1    0.0073        65      77     101 ..      93     117 ..      88     123 .. 0.92
   2 ?    6.2   0.0    0.0011       9.5      75     102 ..     172     199 ..     162     210 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.0073
                           DUF4714  77 spvhgrgafllllallvltclalai 101
                                       +p++g g ++++l ll l  la+ai
  gi|242399262|ref|YP_002994686.1|  93 APLEGYGDLVVILYLLTLQALAMAI 117
                                       699999*****************98 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0011
                           DUF4714  75 gcspvhgrgafllllallvltclalail 102
                                         +p+ g g flll+a+l++t   la l
  gi|242399262|ref|YP_002994686.1| 172 IVGPLGGIGIFLLLIAFLLVTPAELAKL 199
                                       56899999*************9888866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1981.26
//
Query:       gi|242399263|ref|YP_002994687.1|  [L=412]
Description: Membrane-bound hydrogenase MBH 2, subunit Mbh2L (NiFe hydrogenase catalytic subunit) [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.5e-62  210.0   0.2    2.3e-60  204.0   0.2    2.1  1  Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd s
    1.9e-18   66.7   3.0      1e-13   51.0   0.0    3.3  3  NiFeSe_Hases    Nickel-dependent hydrogenase


Domain annotation for each model (and alignments):
>> Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  204.0   0.2   2.5e-64   2.3e-60       2     271 .]     120     376 ..     119     376 .. 0.95

  Alignments for each domain:
  == domain 1  score: 204.0 bits;  conditional E-value: 2.5e-64
                                       TT-HHHHHHHHHHHHHHHHHHHHHHSSSSS-TTBESSBBSS---TTHHHHHHHHHHHHHHHHHHHHHHHHSSSSHHH CS
                    Complex1_49kDa   2 lGaltvflyafreRekildlleevtGaRltasyiriGGvarDlpegllekikeflkelekkldeleklltknrifkk 78 
                                       +G  ++++++++ Rek+ld+le++tG+R+++s+++iGGv+rDl+e+ ++ +k++++++ +  +++++++ +++++k+
  gi|242399263|ref|YP_002994687.1| 120 IGFDSLLFWTWKGREKVLDILEAITGNRINYSMYMIGGVRRDLKESHIRVLKDMITYYWEFTEHMKEVFLSDPVYKA 196
                                       79999************************************************************************ PP

                                       HHSSSS-BSHHHHHHHTT-SSSSGGGT-TTTHHHHSS-SSGGGS------......-SSBSHHHHHHHHHHHHHHHH CS
                    Complex1_49kDa  79 RtkgvgvlskeealelgltGpvlRasGvkyDlRkaepYeaYdeldfdvpv......geegDvydRylvrveEmrqSl 149
                                       Rt+gv+ +sk+ al+l l+Gp++Ra+G+++D+R++ pY+aY ++d + +v      + +gD+yd ++vr+ E++qSl
  gi|242399263|ref|YP_002994687.1| 197 RTRGVAQVSKDVALKLNLVGPTARAAGLRMDIRQDIPYDAYADIDVKAVVpqdivgEARGDAYDVTMVRIYEIEQSL 273
                                       **********************************************9999888887888****************** PP

                                       HHHHHHHHT--.S-SB---TTTS---GGGGGT-HHHHHHHHHHHHS-----SEEEEEEEEETTEEEEEEEEEESSSS CS
                    Complex1_49kDa 150 kIieqaleklpegpvlaedkkvalpkkeevkksmealihhfklvtegfkvpkgevyaavEapkGelgvylvsdgssk 226
                                       +Iie ++++lpeg++la       p+       +         + +++k  +ge + a Eap+Ge+++y+  dg+++
  gi|242399263|ref|YP_002994687.1| 274 DIIEYCIDNLPEGKILAI------PN------YI--------ALLNKIKKTEGEGIGAHEAPRGEVVHYFRYDGTRD 330
                                       **************8872......32......22........2234567889************************9 PP

                                       .-SEEEEE-HHHHTTTTHHHHTTTS-SGGGTHHHHTT---HHHHH- CS
                    Complex1_49kDa 227 .pyrlkirapsfvnlqaleellkgellaDvvailgsldivlgevDR 271
                                        p  +k+ aps++n++++ + l g+ +aD++++++ +d+++ + DR
  gi|242399263|ref|YP_002994687.1| 331 gPAVWKVIAPSYNNINSWGYCLLGAEVADIPVVVAYIDPCMCCNDR 376
                                       9*****************************************9998 PP

>> NiFeSe_Hases  Nickel-dependent hydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.0   0.0   1.2e-17     1e-13       1      69 [.      44     112 ..      44     117 .. 0.98
   2 !    3.2   0.0    0.0037        34     167     224 ..     141     197 ..     132     249 .. 0.81
   3 !   11.5   0.3   1.1e-05       0.1     397     444 ..     280     328 ..     215     374 .. 0.72

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 1.2e-17
                                       --HHHHTTTS-GGGHHHHHHTT-SSSTTHHHHHHHHHHHHHHT----HHHHHHHHHHHHHHHHHHHHHH CS
                      NiFeSe_Hases   1 RGlElilkgrdprdawalvqRiCGVCttvHalasvravedAlgikipknarlirnliaaalllhdhivh 69 
                                       RG+E +   r+  ++ +l +RiCG+C  +H  a v   e+Algi+ p  a++ir++ia  + +h+hi++
  gi|242399263|ref|YP_002994687.1|  44 RGIEYMGMKRNAIQTLYLSERICGICSISHPYAFVIGSEKALGIEAPPRAQYIRTIIAELERIHSHILW 112
                                       9******************************************************************98 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.0037
                                       HHHHHSSSSS--.EBTTBESSGBGSBSHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHH CS
                      NiFeSe_Hases 167 vaifggknPhpqslvvGGvtcaidllnaerlaevkslikevkefveevylpDvlaiak 224
                                        ai g +    + +++GGv   ++  +++ l+++ +++ e +e+++ev+l D +  a+
  gi|242399263|ref|YP_002994687.1| 141 EAITGNRINYSM-YMIGGVRRDLKESHIRVLKDMITYYWEFTEHMKEVFLSDPVYKAR 197
                                       466666666666.*********998999999999999999999999999999766554 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 1.1e-05
                                       HHHHHTTB---B--TT-SGGGS-.SEEEEEEEEEETTEEEEEEEEEETT CS
                      NiFeSe_Hases 397 venikkgdtetaneekldkkevp.keakGvglveapRGaLsHwikikdg 444
                                       ++n+ +g   ++ ++    ++++ +e +G+g +eapRG   H+ + + +
  gi|242399263|ref|YP_002994687.1| 280 IDNLPEGKILAIPNYIALLNKIKkTEGEGIGAHEAPRGEVVHYFRYDGT 328
                                       344444433333344334455562589****************997654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 2725.26
//
Query:       gi|242399264|ref|YP_002994688.1|  [L=186]
Description: Membrane-bound hydrogenase MBH 2, subunit Mbh2K (hydrogenase subunit) [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-19   70.8   0.0    2.1e-19   70.3   0.0    1.1  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 !   70.3   0.0   1.2e-23   2.1e-19       2     115 ..      44     159 ..      43     164 .. 0.91

  Alignments for each domain:
  == domain 1  score: 70.3 bits;  conditional E-value: 1.2e-23
                                       E--HHHHHHHHHHHHH...TT--EEEEEEEEETTSSSEEEEEEEE--S-.....-EEEEEE....-S-BEE--TTT- CS
                    Complex1_30kDa   2 vvepedllevakflkdeeelgfdvlsdltavDekeerfevvyhllslekn....erirvkvevdeeepevpSvtdlf 74 
                                       ++++++++++++++ +    ++ +l  +t+ D  +e+++++y +  ++++    ++i++k ++++++ ++p++tdl+
  gi|242399264|ref|YP_002994688.1|  44 EIDKNAFRRAIEAIFK---IEYPHLHFITGEDI-GESIRMIYSFGLFHEHpwgeVSIVIKFDLPKNKLVLPTITDLM 116
                                       5788889999999998...89***********7.699*******98855568889********************** PP

                                       STHHHHHHHHHHHSHHBCTTSSTSS-SSSSTTS..SS-TTSTT CS
                    Complex1_30kDa  75 pgadwyEREayDmfGivfeghpdlrrillpedf..eghPLRkd 115
                                        ga+  ERE+++m+G++f+g ++ r ++lp+d+   ++P+R+d
  gi|242399264|ref|YP_002994688.1| 117 MGAETNEREIREMLGVEFDGLKNKRHLFLPDDWpeGKYPWRRD 159
                                       *********************************85556***99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.32s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1130.83
//
Query:       gi|242399265|ref|YP_002994689.1|  [L=148]
Description: Membrane-bound hydrogenase MBH 2, subunit Mbh2J (hydrogenase subunit) [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.1e-28   98.8   0.1    2.4e-28   98.6   0.1    1.1  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 !   98.6   0.1   1.4e-32   2.4e-28       1     130 [.      21     131 ..      21     132 .. 0.94

  Alignments for each domain:
  == domain 1  score: 98.6 bits;  conditional E-value: 1.4e-32
                                       -SHHHHHHT-TTTTHHHHHHTEEEEEETTT-S--HHHHHHTHTTTSEEEEEESBE...EEEHHHHHHHHGGGSSEEE CS
                       Oxidored_q6   1 CtGcsisllaleedlldllelielryhetlladskeeeieakekeadvlvveGavtrkpkealellkelaekakavi 77 
                                       C++c+i++ a+ ++ +d+     +r++++l+ +++         +advl+v+Ga++++ +++l++++e+++++kavi
  gi|242399265|ref|YP_002994689.1|  21 CNACDIEIIAALTPRYDA-----ERFGIKLVGSPR---------HADVLLVTGAIPKDFADKLRRIYEQMPDPKAVI 83 
                                       ********99999999*9.....9***********.........********************************* PP

                                       EESHHHHH-TGGGSTT-TEE-HHHHHHHC.S-E.EEE-SSS--HHHHHHHHHH CS
                       Oxidored_q6  78 avGtCAafGGipaaannpsvgeevgellevvpvdinipGCPphpeailetlla 130
                                        +G+C ++GG++  ++  s+   +g+++e +pvd+++pGCPp+peai++++++
  gi|242399265|ref|YP_002994689.1|  84 VIGNCGTSGGVF--YD--SYN-IAGPIDEIIPVDVYVPGCPPRPEAIVDAVVK 131
                                       ************..55..332.258************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); 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: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1009.62
//
Query:       gi|242399266|ref|YP_002994690.1|  [L=113]
Description: Membrane-bound hydrogenase MBH 2, subunit Mbh2I (Na+/H+ transporter subunit) [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       616  (0.0343577); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 663.48
//
Query:       gi|242399267|ref|YP_002994691.1|  [L=517]
Description: Membrane-bound hydrogenase MBH 2, subunit Mbh2H (hydrogenase subunit) [Thermococcus sibiricus MM 739]
Scores for complete 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-51  173.0  23.8    8.1e-51  173.0  23.8    2.5  3  Proton_antipo_M  Proton-conducting membrane transporter
     0.0001   22.3   1.2     0.0001   22.3   1.2    4.3  5  Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), 
  ------ inclusion threshold ------
        7.6    5.8   5.1        2.1    7.7   1.2    2.1  2  TMEM43           Transmembrane protein 43


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 ?   -3.0   0.8      0.53   3.2e+03      89     130 ..      18      58 ..       6      65 .. 0.60
   2 ?   -3.6   0.2      0.83   4.9e+03       7      22 ..      90     105 ..      79     127 .. 0.57
   3 !  173.0  23.8   1.4e-54   8.1e-51       2     293 .]     138     441 ..     137     441 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.53
                   Proton_antipo_M  89 lvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvl 130
                                       +++ l+K     ++ W   +  + +++ s+ll   +v+ g++
  gi|242399267|ref|YP_002994691.1|  18 FIAPLFKKHHEGVSIWAIFV-TGISVVLSLLLTKEVVTNGII 58 
                                       45555666666666666666.666666666665555555555 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 0.83
                   Proton_antipo_M   7 lylglElvllplylLi 22 
                                        ++++ ++l++++  i
  gi|242399267|ref|YP_002994691.1|  90 AFMAISATLMSFIGAI 105
                                       3444444444443333 PP

  == domain 3  score: 173.0 bits;  conditional E-value: 1.4e-54
                   Proton_antipo_M   2 ndLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskalelglns 78 
                                       +dL+ l+++lE+ +++   L+g++ ++ +++eA++k++++++++sl+ L+++++ly++ g+l++ +++k+   +  +
  gi|242399267|ref|YP_002994691.1| 138 GDLFNLFVFLEIAGIAGSALVGFRNYRGEASEAGIKYLIVSAVASLMVLFAVSILYGQYGNLNLAYIAKN---VSFN 211
                                       69********************************************************************...5566 PP

                   Proton_antipo_M  79 lelllllllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirllllla....vssneisqlll 151
                                       +  +++l ll+ ++++K ++vp+h W+pday e P+ +   l  ++  a++++l+r+++ l+    +    +  ++ 
  gi|242399267|ref|YP_002994691.1| 212 MVDMIALGLLFTSFAMKCGAVPMHYWVPDAYTEVPAGINPPL-LVATYASLYALFRVSFTLFanvvIDLARVGWIMS 287
                                       667899999***************************988766.58899*********99888664444555667899 PP

                   Proton_antipo_M 152 ilaiismllgslvalaqtdiKrllAySsishlGymlialav.....a........tqygveaaiihllthalfkall 215
                                       il++++m++g ++al q d+Krl+    is+ Gyml++++v     +        + +++++ ++h++  ++ k+ll
  gi|242399267|ref|YP_002994691.1| 288 ILGVLTMFIGVTMALIQKDVKRLMSHHAISQTGYMLLGVGVgltvlHdpsklaefGRDAMAGGVFHIINNIIYKSLL 364
                                       9*************************************998533330333333335678888899999999999999 PP

                   Proton_antipo_M 216 FllagsviyerektrdirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavslillvlavvasvl 292
                                        + ag++ y +  tr+++++ggLa kmPi+ + ++v++ +++GlPp+ gF skfli e +++ +++l v+a+v+svl
  gi|242399267|ref|YP_002994691.1| 365 LMTAGALFYVT-GTRNLNEMGGLARKMPITTISFMVGAAAISGLPPFNGFASKFLIYETSYRLNPLLTVFAMVTSVL 440
                                       99998887766.9**************************************************************99 PP

                   Proton_antipo_M 293 t 293
                                       t
  gi|242399267|ref|YP_002994691.1| 441 T 441
                                       7 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 ?   -2.9   0.5       1.2   7.3e+03      25      35 ..      33      43 ..      31      49 .. 0.55
   2 !   22.3   1.2   1.7e-08    0.0001      10      57 ..      77     124 ..      71     125 .. 0.92
   3 ?   -2.6   1.8         1   6.1e+03      27      41 ..     175     189 ..     172     193 .. 0.78
   4 ?   -2.0   0.1      0.65   3.9e+03      29      36 ..     392     399 ..     390     401 .. 0.87
   5 ?    1.3   0.0     0.063   3.7e+02      15      44 ..     423     454 ..     414     463 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.2
                   Proton_antipo_N 25 mllvvtfvsll 35
                                       +++vt++s++
  gi|242399267|ref|YP_002994691.1| 33 WAIFVTGISVV 43
                                      44556666543 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 1.7e-08
                   Proton_antipo_N  10 lsieigfllDklsalmllvvtfvsllvhlYSigYMaddegyqRFfayl 57 
                                       + i i f +D + a m++  t+ s++  +YS +  ++d+g  +++a+l
  gi|242399267|ref|YP_002994691.1|  77 VPIRIMFEVDAMGAFMAISATLMSFIGAIYSYSHVKKDTGLEKYYALL 124
                                       678999****************************************98 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 1
                   Proton_antipo_N  27 lvvtfvsllvhlYSi 41 
                                       l+v+ v++l  l+++
  gi|242399267|ref|YP_002994691.1| 175 LIVSAVASLMVLFAV 189
                                       788888888888876 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 0.65
                   Proton_antipo_N  29 vtfvsllv 36 
                                       +t++s++v
  gi|242399267|ref|YP_002994691.1| 392 ITTISFMV 399
                                       89*****9 PP

  == domain 5  score: 1.3 bits;  conditional E-value: 0.063
                   Proton_antipo_N  15 gfllDklsalmllv..vtfvsllvhlYSigYM 44 
                                       +++l++l  ++++v  v +++++v ++++ ++
  gi|242399267|ref|YP_002994691.1| 423 SYRLNPLLTVFAMVtsVLTLASFVKVFASAFL 454
                                       66666665554444227788889999988765 PP

>> TMEM43  Transmembrane protein 43
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   1.2   0.00035       2.1     174     205 ..     271     302 ..     258     333 .. 0.75
   2 ?   -2.3   0.1      0.38   2.3e+03     191     214 ..     429     452 ..     412     491 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00035
                            TMEM43 174 mfakeksenklltwllRllGfllmflglllll 205
                                       +fa+   + ++  w++ +lG+l+mf+g++++l
  gi|242399267|ref|YP_002994691.1| 271 LFANVVIDLARVGWIMSILGVLTMFIGVTMAL 302
                                       6788888889999**************98754 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.38
                            TMEM43 191 llGfllmflglllllsplsvlvsl 214
                                       ll ++ m+ ++l+l+s ++v++s 
  gi|242399267|ref|YP_002994691.1| 429 LLTVFAMVTSVLTLASFVKVFASA 452
                                       555666666666666666666653 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (517 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       941  (0.0524848); 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:                         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: 0.69u 0.30s 00:00:00.99 Elapsed: 00:00:00.50
# Mc/sec: 3136.74
//
Query:       gi|242399268|ref|YP_002994692.1|  [L=121]
Description: Membrane-bound hydrogenase MBH 2, subunit Mbh2G (Na+/H+ transporter subunit) [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-29  102.0   3.9    1.5e-29  101.7   3.9    1.0  1  Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase cha


Domain annotation for each model (and alignments):
>> Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase chain 4L
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.7   3.9   8.4e-34   1.5e-29       3     104 ..      11     117 ..       9     118 .. 0.96

  Alignments for each domain:
  == domain 1  score: 101.7 bits;  conditional E-value: 8.4e-34
                                       HHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHHHHHHHHC..................TTSCGGHHHHHHH CS
                       Oxidored_q2   3 llliallfliGlygvllrrnllkvliglelisnavnlllvlagvftegtlvi.....tnpatefadplpqalvLtai 74 
                                       ++++all ++G+y + ++rnl+kv+ig+e+++ avn+++v++g+ ++g ++i     ++   +++ p pqal+Lt i
  gi|242399268|ref|YP_002994692.1|  11 FIVVALLLALGFYTIGFKRNLIKVVIGVEILEGAVNMFIVALGYVKGGYTPIytqapQEAVGKMVLPTPQALTLTSI 87 
                                       689***************************************************99999999*************** PP

                                       HHHHHHHHHHHHHHHHHHHHSSS-BCCG-- CS
                       Oxidored_q2  75 vigaaetavgLallvrlyreygtddvqelr 104
                                       vig+a+ta++La +v++yr+ygt+dv  +r
  gi|242399268|ref|YP_002994692.1|  88 VIGVAVTALMLAFAVNIYRHYGTLDVTRVR 117
                                       **************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       815  (0.0454571); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        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):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 738.55
//
Query:       gi|242399269|ref|YP_002994693.1|  [L=155]
Description: Membrane-bound hydrogenase MBH 2, subunit Mbh2F (Na+/H+ transporter subunit) [Thermococcus sibiricus MM 739]
Scores for complete 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-28   98.0   9.7    6.1e-28   97.6   9.7    1.1  1  MnhB      Domain related to MnhB subunit of Na+/H+ antiporter
  ------ inclusion threshold ------
       0.11   12.2   4.6      0.035   13.8   2.2    1.6  2  DUF2105   Predicted membrane protein (DUF2105)


Domain annotation for each model (and alignments):
>> MnhB  Domain related to MnhB subunit of Na+/H+ antiporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.6   9.7   6.8e-32   6.1e-28       1     123 [.       5     138 ..       5     139 .. 0.85

  Alignments for each domain:
  == domain 1  score: 97.6 bits;  conditional E-value: 6.8e-32
                              MnhB   1 ilrtvarllvplillvslylllrGhnsPGGGFqgGlilaaalillylafgleelekll.rvklaprileglglllav 76 
                                       i++t++rll+plil+++ y++l+Gh++PGGGFqgG+++a++lill++a+ ++++++l  +  l  + le+lg+l ++
  gi|242399269|ref|YP_002994693.1|   5 IIKTTTRLLAPLILVFGSYIILHGHLTPGGGFQGGAVFASGLILLIVANTRDKVQELFeKTPL--TQLESLGALGFL 79 
                                       79***************************************************6665515554..59********** PP

                              MnhB  77 ltgllglllg.fltslflelel.....llg.....eve..lgtallfdlgVylvVvggll 123
                                       ++gllgl+   fl++++++ ++             + +   gt+ +++++V+ +V++gl+
  gi|242399269|ref|YP_002994693.1|  80 GIGLLGLMGYtFLKNAIANSGFlfggtT-PqginpGYLntGGTLSYLNIFVGTKVLAGLT 138
                                       *******87799*999999877555440.04444422256****************9985 PP

>> DUF2105  Predicted membrane protein (DUF2105)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   2.2   3.9e-06     0.035      96     143 ..       4      60 ..       1     104 [. 0.70
   2 ?   -3.0   0.0      0.54   4.9e+03      15      15 ..     139     139 ..     118     153 .. 0.51

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.9e-06
                           DUF2105  96 evlktaPkflalvLvvyG..iil.......sGftGGavaasGlllyllskrvrekev 143
                                        ++kt+ ++la +++v+G  iil        Gf GGav asGl+l +++++  ++++
  gi|242399269|ref|YP_002994693.1|   4 TIIKTTTRLLAPLILVFGsyIILhghltpgGGFQGGAVFASGLILLIVANTRDKVQE 60 
                                       57788888888777777744444233323348*************999876655443 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.54
                           DUF2105  15 v 15 
                                        
  gi|242399269|ref|YP_002994693.1| 139 S 139
                                       1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.32s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 973.67
//
Query:       gi|242399270|ref|YP_002994694.1|  [L=91]
Description: Membrane-bound hydrogenase MBH 2, subunit Mbh2E (Na+/H+ transporter subunit) [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.31s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 567.51
//
Query:       gi|242399271|ref|YP_002994695.1|  [L=87]
Description: Membrane-bound hydrogenase MBH 2, subunit Mbh2D (Na+/H+ transporter subunit) [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-19   69.4   6.0    2.7e-19   69.1   6.0    1.2  1  DUF4040   Domain of unknown function (DUF4040)
  ------ inclusion threshold ------
       0.65   10.1   2.5       0.85    9.7   2.5    1.2  1  SLATT_3   SMODS and SLOG-associating 2TM effector domain 3


Domain annotation for each model (and alignments):
>> DUF4040  Domain of unknown function (DUF4040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.1   6.0   3.1e-23   2.7e-19       2      65 ..      17      80 ..      16      82 .. 0.96

  Alignments for each domain:
  == domain 1  score: 69.1 bits;  conditional E-value: 3.1e-23
                           DUF4040  2 llvlaalaavlardrlaavillgvvGllvallfvllgAPDvAlTqaavveglttvllllalrrl 65
                                       l+ +++aa++ +++++avi+++v++l++++ f++l+APDvA+++a v++gltt+++lla+r +
  gi|242399271|ref|YP_002994695.1| 17 ALLGSSIAAIRFKNLISAVIAMAVFSLALSVEFYILQAPDVAIAEAGVGAGLTTAMYLLAIRNT 80
                                      57899********************************************************987 PP

>> SLATT_3  SMODS and SLOG-associating 2TM effector domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   2.5   9.5e-05      0.85      17      68 ..       5      53 ..       2      61 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 9.5e-05
                           SLATT_3 17 eylrllrlrlvllvvAAlaaalslkvgsvdlaallaalafllalvievvlar 68
                                      ++++++++ ++++++++ +aa+ +k     + a++a+++f lal +e+++ +
  gi|242399271|ref|YP_002994695.1|  5 TFFWAIQVLIAIALLGSSIAAIRFKN---LISAVIAMAVFSLALSVEFYILQ 53
                                      56788888889999999988888666...5999***************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       786  (0.0438396); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 558.99
//
Query:       gi|242399272|ref|YP_002994696.1|  [L=116]
Description: Membrane-bound hydrogenase MBH 2, subunit Mbh2C (Na+/H+ transporter subunit) [Thermococcus sibiricus MM 739]
Scores for complete 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   92.3   7.6    2.1e-26   92.0   7.6    1.1  1  PhaG_MnhG_YufB   Na+/H+ antiporter subunit
  ------ inclusion threshold ------
      0.052   12.9   2.3      0.032   13.6   1.0    1.4  2  DUF4191          Domain of unknown function (DUF4191)


Domain annotation for each model (and alignments):
>> PhaG_MnhG_YufB  Na+/H+ antiporter subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.0   7.6   2.3e-30   2.1e-26       1      78 [.       9      97 ..       9      98 .. 0.97

  Alignments for each domain:
  == domain 1  score: 92.0 bits;  conditional E-value: 2.3e-30
                    PhaG_MnhG_YufB  1 llllGalfvllgaigllrlpdvytRlhaatkadtlGlllillGlllrf.slaa..........slkllliilfllltaP 68
                                      ll++G+ f ll++ig+lr+pdvytR+ha tk++t+G+++i+l+++++   +++           ++  l+++fl+lt+P
  gi|242399272|ref|YP_002994696.1|  9 LLAIGVSFNLLASIGILRFPDVYTRIHASTKCTTFGTIFIVLAAVIYSaYNWRlthdvawitmGIHSALVVIFLVLTNP 87
                                      799*******************************************99888889************************* PP

                    PhaG_MnhG_YufB 69 vaahliaraa 78
                                      v+ah+++raa
  gi|242399272|ref|YP_002994696.1| 88 VGAHALGRAA 97
                                      *********8 PP

>> DUF4191  Domain of unknown function (DUF4191)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.21   1.9e+03      52      65 ..       8      21 ..       2      44 .. 0.59
   2 ?   13.6   1.0   3.6e-06     0.032      22      87 ..      38     102 ..      23     115 .. 0.68

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.21
                           DUF4191 52 lllilgillgllva 65
                                      +ll +g+ + ll+ 
  gi|242399272|ref|YP_002994696.1|  8 VLLAIGVSFNLLAS 21
                                      23333333444433 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 3.6e-06
                           DUF4191  22 dkkllwlllaaflvvvvvfvvlglllgslilllilgillgllvalivltrraekaayaqiegqpGa 87 
                                        k +++ ++ + ++++v+  ++ + l++ + ++ +gi  +l+v ++vlt+ + + a  ++  + G 
  gi|242399272|ref|YP_002994696.1|  38 TKCTTFGTIFI-VLAAVIYSAYNWRLTHDVAWITMGIHSALVVIFLVLTNPVGAHALGRAARKSGI 102
                                       44433333322.3333333333444468**********************9999999998888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       795  (0.0443416); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 863.83
//
Query:       gi|242399273|ref|YP_002994697.1|  [L=84]
Description: Membrane-bound hydrogenase MBH 2, subunit Mbh2B (Na+/H+ transporter subunit) [Thermococcus sibiricus MM 739]
Scores for complete 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-18   64.4   8.8    8.9e-18   64.4   8.8    1.7  2  MrpF_PhaF  Multiple resistance and pH regulation protein F (M
  ------ inclusion threshold ------
      0.069   13.2   3.2      0.083   12.9   3.2    1.3  1  MtN3_slv   Sugar efflux transporter for intercellular exchang


Domain annotation for each model (and alignments):
>> MrpF_PhaF  Multiple resistance and pH regulation protein F (MrpF / PhaF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.6      0.34     3e+03      35      40 ..       4       9 ..       1      19 [. 0.46
   2 !   64.4   8.8   9.9e-22   8.9e-18       1      52 [.      25      76 ..      25      77 .. 0.99

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.34
                         MrpF_PhaF 35 lvlAll 40
                                      +vl  +
  gi|242399273|ref|YP_002994697.1|  4 MVLLFI 9 
                                      222222 PP

  == domain 2  score: 64.4 bits;  conditional E-value: 9.9e-22
                         MrpF_PhaF  1 aDRvvAlDllgtllvallallailtgrpayldvalvlAllgFvgtvafarfl 52
                                      +DR+vAlD+l+t+++++++l++i+t++++++dvalv+A+l++++t+++ar+l
  gi|242399273|ref|YP_002994697.1| 25 PDRAVALDALTTTTAGAMVLYGIITKQAVMIDVALVYAVLSYIATLYIARYL 76
                                      8**************************************************8 PP

>> MtN3_slv  Sugar efflux transporter for intercellular exchange
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   3.2   9.3e-06     0.083      30      86 ..      23      79 ..       1      80 [. 0.76

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.3e-06
                          MtN3_slv 30 sveelsfllflagllsallWllYGllkkdaliiivNlvgvlleliylllflvyakkk 86
                                      ++ +  ++l  +++ +a   +lYG+ +k a++i v lv ++l+ i +l+ + y  kk
  gi|242399273|ref|YP_002994697.1| 23 TIPDRAVALDALTTTTAGAMVLYGIITKQAVMIDVALVYAVLSYIATLYIARYLVKK 79
                                      55555556666778889999***********************99999999888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 580.84
//
Query:       gi|242399274|ref|YP_002994698.1|  [L=167]
Description: Membrane-bound hydrogenase MBH 2, subunit Mbh2A (Na+/H+ transporter subunit) [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-36  125.8   0.1    1.2e-36  125.6   0.1    1.0  1  MNHE             Na+/H+ ion antiporter subunit
  ------ inclusion threshold ------
      0.088   11.9   2.8       0.21   10.7   3.0    1.5  2  AI-2E_transport  AI-2E family transporter
      0.089   13.0   0.2       0.13   12.5   0.2    1.2  1  HPP              HPP family
      0.094   13.2   2.1       0.14   12.6   2.1    1.3  1  Caps_synth_CapC  Capsule biosynthesis CapC
       0.21   11.6   2.1        0.3   11.1   2.1    1.2  1  Rhomboid         Rhomboid family
       0.24   11.9   3.5        0.4   11.2   3.5    1.4  1  FtsX             FtsX-like permease 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 !  125.6   0.1   4.2e-40   1.2e-36       1     146 []       7     165 ..       7     165 .. 0.92

  Alignments for each domain:
  == domain 1  score: 125.6 bits;  conditional E-value: 4.2e-40
                              MNHE   1 llllflvWllltgs........lgelllGlllallvalllrrll.......lplrrvllrllayllvflweivkanl 62 
                                       +l++++v+l+lt+         ++el++G+++a+l+ +++r+++       ++++r++l +++ l+ f+  +++anl
  gi|242399274|ref|YP_002994698.1|   7 FLWSLIVYLVLTAGsgsvllwsPEELIAGIVIAALIGYATRNIMserldyfFNPKRWVLFIIYALGPFFLAMARANL 83 
                                       689*********99999***********************999999999998899999978888899********** PP

                              MNHE  63 dVakrvlrpklpirpgivkvplrlksdlaltllansitltPGTltvdvdedrrvlyvHvldv.edeeeeareeikgr 138
                                       dVa+rv+++  +irpgivk+  +l+ d  +tllansitltPGT t+++de++  +yvH+++v + +e+   ee++g 
  gi|242399274|ref|YP_002994698.1|  84 DVAYRVITG--KIRPGIVKISPNLTRDESRTLLANSITLTPGTFTLEIDEEG-NFYVHWINVpPGKEKPTPEELCGY 157
                                       ********5..5************************************9776.8********666688889999999 PP

                              MNHE 139 lErrllei 146
                                       l +++++i
  gi|242399274|ref|YP_002994698.1| 158 LPKWARRI 165
                                       99999886 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 ?   10.7   3.0   6.9e-05      0.21       6      60 ..      17      72 ..       6      81 .. 0.75
   2 ?   -2.9   0.0      0.98   2.9e+03     163     184 ..      93     114 ..      91     118 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 6.9e-05
                   AI-2E_transport  6 vllllllalypfiselllplliAlvlayll.npvvkfLkkrgvkrvlavllvllll 60
                                      +++  + +l++   el+  ++iA+++ y++ n+  ++L++++ +++++ +++++l 
  gi|242399274|ref|YP_002994698.1| 17 LTAGSGSVLLWSPEELIAGIVIAALIGYATrNIMSERLDYFFNPKRWVLFIIYALG 72
                                      23333445555555************99994567789****************984 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.98
                   AI-2E_transport 163 klrqgilkllpervrervkail 184
                                       k+r+gi+k+ p+ +r++++ +l
  gi|242399274|ref|YP_002994698.1|  93 KIRPGIVKISPNLTRDESRTLL 114
                                       6889999999999999998877 PP

>> HPP  HPP family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   4.2e-05      0.13      10      64 ..      16      78 ..       9      86 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.2e-05
                               HPP 10 vllfavpesplaqPrnvvgGhlisalvGvaiaklfgl........sllwlaaalavalaialm 64
                                      vl  +  +  l +P ++++G +i+al+G+a+ +++++        + ++l +  a++   ++m
  gi|242399274|ref|YP_002994698.1| 16 VLTAGSGSVLLWSPEELIAGIVIAALIGYATRNIMSErldyffnpKRWVLFIIYALGPFFLAM 78
                                      6666666677889*****************999998877777774333335555555544444 PP

>> Caps_synth_CapC  Capsule biosynthesis CapC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   2.1   4.6e-05      0.14      37     105 ..       4      71 ..       1      87 [. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.6e-05
                   Caps_synth_CapC  37 lvtllialltylivrllsrflilyGrrrfvavlllgvlvklllelllllllpaelveeleviGlivpgL 105
                                        + +l +l++yl++++ s  ++l   ++++a ++++ l+ ++++ +++  l+  +    +++ +i+ +L
  gi|242399274|ref|YP_002994698.1|   4 TTSFLWSLIVYLVLTAGSGSVLLWSPEELIAGIVIAALIGYATRNIMSERLDYFFN-PKRWVLFIIYAL 71 
                                       567899*****************************************998876664.888888888776 PP

>> Rhomboid  Rhomboid family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   2.1    0.0001       0.3      51     123 ..      15      82 ..       3      94 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0001
                                       HHHHHHHHHHHHHHH-S...-EESSHHHHHHHHHHHHHHHHCCCCGS----HC...CCCCCCCCCCHHHCTSS CS
                          Rhomboid  51 llsglagsllsllfsaesesplvGaSGaifgllgallvlvprnrkllrkliiallllllfillnlvlgllpra 123
                                       l+  +ags  +ll s+e   +++G   +i++l+g+++ ++ ++r  +++ +  ++l+++++l  ++l++ + +
  gi|242399274|ref|YP_002994698.1|  15 LV-LTAGSGSVLLWSPEE--LIAGI--VIAALIGYATRNIMSERLDYFFNPKRWVLFIIYALGPFFLAMARAN 82 
                                       32.334444445555554..77775..9*************************99999999999998887766 PP

>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   3.5   0.00014       0.4      18      85 ..       8      79 ..       1      87 [. 0.74

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00014
                              FtsX 18 lllllteillitlvalviG.....lglgllaaqllsdvllssvfsselkisidlitvliiivlllllallagl 85
                                      l+ l++ ++l++  ++v+      l++g+++a l+     ++++  +l++++++  ++++i+ +l  + la++
  gi|242399274|ref|YP_002994698.1|  8 LWSLIVYLVLTAGSGSVLLwspeeLIAGIVIAALIGYATRNIMS-ERLDYFFNPKRWVLFIIYALGPFFLAMA 79
                                      333444444444444444444444555*******9999999999.*************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1041.59
//
Query:       gi|242399275|ref|YP_002994699.1|  [L=189]
Description: Membrane-bound hydrogenase MBH 1, subunit Mbh1N (hydrogenase subunit) [Thermococcus sibiricus MM 739]
Scores for 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  101.1  32.2    6.1e-08   32.2   3.8    4.2  4  Fer4      4Fe-4S binding domain
    1.3e-26   92.9  64.4    3.4e-10   40.4  11.5    3.2  4  Fer4_7    4Fe-4S dicluster domain
    1.2e-18   66.3  34.3    3.8e-06   26.7   3.1    4.2  4  Fer4_6    4Fe-4S binding domain
    4.3e-17   62.0  56.2    5.4e-07   29.6  12.9    4.0  4  Fer4_21   4Fe-4S dicluster domain
    1.3e-16   60.4  51.6    8.3e-09   35.4  10.5    2.9  3  Fer4_10   4Fe-4S dicluster domain
    3.3e-16   59.2  29.2    3.9e-10   39.7   8.0    3.0  3  Fer4_9    4Fe-4S dicluster domain
    5.3e-16   57.7  26.9    2.4e-05   24.1   1.3    4.2  4  Fer4_2    4Fe-4S binding domain
    7.6e-16   58.8  26.0    3.4e-05   24.7   0.1    4.2  4  Fer4_16   4Fe-4S double cluster binding domain
      1e-10   42.0  24.8     0.0001   22.8  11.1    3.6  4  Fer4_17   4Fe-4S dicluster domain
    1.8e-10   40.5  34.9     0.0013   19.1   2.7    4.2  4  Fer4_4    4Fe-4S binding domain
    2.8e-10   40.5  29.0      4e-05   24.0   8.9    3.5  4  Fer4_8    4Fe-4S dicluster domain
      5e-09   36.6  23.1    0.00019   21.9   0.4    4.3  4  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
    9.2e-07   29.4  44.2     0.0055   17.6   6.4    4.2  4  Fer4_3    4Fe-4S binding domain
    0.00023   21.9  28.7        0.2   12.6   1.2    4.1  4  Fer4_22   4Fe-4S dicluster domain
     0.0042   17.8  30.9       0.46   11.3   1.6    4.3  4  Fer4_15   4Fe-4S single cluster domain
     0.0049   17.1  30.7       0.17   12.1   2.6    3.6  3  Fer4_18   4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.071   13.2  21.2       0.11   12.7   1.9    3.9  4  ETF_QO    Electron transfer flavoprotein-ubiquinone oxidoredu


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   2.4   2.9e-10     3e-07       2      23 ..      40      61 ..      39      62 .. 0.89
   2 !   29.7   1.0   3.5e-10   3.7e-07       6      24 .]      75      93 ..      70      93 .. 0.89
   3 !   27.0   2.6   2.5e-09   2.6e-06       2      24 .]     133     155 ..     132     155 .. 0.94
   4 !   32.2   3.8   5.8e-11   6.1e-08       2      24 .]     163     185 ..     162     185 .. 0.94

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 2.9e-10
                                      EEETTTSSS-THHHHHSTTTEE CS
                              Fer4  2 videekCigCGaCvevCPvgAI 23
                                      v++ +kCigC++C++vCP g+ 
  gi|242399275|ref|YP_002994699.1| 40 VYHVDKCIGCKLCMNVCPAGVF 61
                                      6778**************9975 PP

  == domain 2  score: 29.7 bits;  conditional E-value: 3.5e-10
                                      TTSSS-THHHHHSTTTEEE CS
                              Fer4  6 ekCigCGaCvevCPvgAIt 24
                                       +C++C +Cv+vCPv+A++
  gi|242399275|ref|YP_002994699.1| 75 GRCVFCQQCVDVCPVNALE 93
                                      69***************85 PP

  == domain 3  score: 27.0 bits;  conditional E-value: 2.5e-09
                                       EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4   2 videekCigCGaCvevCPvgAIt 24 
                                        i+ ekC gC +C+  CP +AI+
  gi|242399275|ref|YP_002994699.1| 133 RIIAEKCKGCTLCARNCPQNAIE 155
                                       6999******************6 PP

  == domain 4  score: 32.2 bits;  conditional E-value: 5.8e-11
                                       EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4   2 videekCigCGaCvevCPvgAIt 24 
                                       +i++ekCigCG+C+ +C + AI+
  gi|242399275|ref|YP_002994699.1| 163 KINPEKCIGCGICATICKFSAIE 185
                                       79*******************96 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   2.0   3.4e-08   3.6e-05      29      52 .]      37      60 ..      18      60 .. 0.79
   2 !   40.4  11.5   3.2e-13   3.4e-10       1      52 []      45      91 ..      45      91 .. 0.96
   3 !   34.2  14.5   2.6e-11   2.8e-08       1      52 []      76     153 ..      76     153 .. 0.73
   4 !   31.8  12.9   1.5e-10   1.6e-07       1      52 []     138     183 ..     138     183 .. 0.91

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 3.4e-08
                            Fer4_7 29 ekveidpekClgCgaCvavCPtga 52
                                       k++++ +kC+gC+ C++vCP+g+
  gi|242399275|ref|YP_002994699.1| 37 GKLVYHVDKCIGCKLCMNVCPAGV 60
                                      67899****************996 PP

  == domain 2  score: 40.4 bits;  conditional E-value: 3.2e-13
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                      +CigC+ C+++Cp++++e+ +e     ++kv++   +C++C++Cv+vCP++a
  gi|242399275|ref|YP_002994699.1| 45 KCIGCKLCMNVCPAGVFEYVPE-----IKKVTLWLGRCVFCQQCVDVCPVNA 91
                                      7******************997.....899********************97 PP

  == domain 3  score: 34.2 bits;  conditional E-value: 2.6e-11
                            Fer4_7   1 rCigCgaCvaaCpvkaield...........eeenek...................gtekveidpekClgCgaCvav 47 
                                       rC+ C++Cv++Cpv+a+e+            +    +                   +t+k++i +ekC gC+ C++ 
  gi|242399275|ref|YP_002994699.1|  76 RCVFCQQCVDVCPVNALEMSgefllatydkyD----DnlrwlkneeieemiaqksgKTKKYRIIAEKCKGCTLCARN 148
                                       8*****************98555554443320....1344444444555555555556999**************** PP

                            Fer4_7  48 CPtga 52 
                                       CP +a
  gi|242399275|ref|YP_002994699.1| 149 CPQNA 153
                                       **997 PP

  == domain 4  score: 31.8 bits;  conditional E-value: 1.5e-10
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                       +C gC  C+++Cp++aie  ++         +i+pekC+gCg C++ C + a
  gi|242399275|ref|YP_002994699.1| 138 KCKGCTLCARNCPQNAIEGAPRV------VHKINPEKCIGCGICATICKFSA 183
                                       7******************9983......4589***************9875 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   1.8   4.2e-09   4.4e-06       3      23 ..      40      60 ..      38      61 .. 0.88
   2 !   10.4   3.2   0.00053      0.56       8      24 .]      76      92 ..      75      92 .. 0.90
   3 !   20.4   3.3   3.6e-07   0.00038       4      24 .]     134     154 ..     133     154 .. 0.93
   4 !   26.7   3.1   3.6e-09   3.8e-06       4      24 .]     164     184 ..     163     184 .. 0.95

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 4.2e-09
                            Fer4_6  3 eidpdkCigCgdCvrvCPega 23
                                      ++  dkCigC  C++vCP+g+
  gi|242399275|ref|YP_002994699.1| 40 VYHVDKCIGCKLCMNVCPAGV 60
                                      56679**************98 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00053
                            Fer4_6  8 kCigCgdCvrvCPegai 24
                                      +C+ C  Cv+vCP +a+
  gi|242399275|ref|YP_002994699.1| 76 RCVFCQQCVDVCPVNAL 92
                                      688899********997 PP

  == domain 3  score: 20.4 bits;  conditional E-value: 3.6e-07
                            Fer4_6   4 idpdkCigCgdCvrvCPegai 24 
                                       i ++kC gC  C+r+CP +ai
  gi|242399275|ref|YP_002994699.1| 134 IIAEKCKGCTLCARNCPQNAI 154
                                       7899*************9998 PP

  == domain 4  score: 26.7 bits;  conditional E-value: 3.6e-09
                            Fer4_6   4 idpdkCigCgdCvrvCPegai 24 
                                       i+p+kCigCg C+++C + ai
  gi|242399275|ref|YP_002994699.1| 164 INPEKCIGCGICATICKFSAI 184
                                       8****************9998 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   3.7   3.8e-07    0.0004      37      53 ..      42      58 ..      34      65 .. 0.84
   2 !   25.8  14.7   7.9e-09   8.3e-06       5      59 .]      43      94 ..      41      94 .. 0.83
   3 !   23.5   1.6   4.3e-08   4.5e-05      30      58 ..     128     155 ..     115     156 .. 0.78
   4 !   29.6  12.9   5.1e-10   5.4e-07       3      52 ..     134     180 ..     133     186 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 3.8e-07
                           Fer4_21 37 vedeCvGCnlCssvCPv 53
                                        d+C+GC+lC++vCP 
  gi|242399275|ref|YP_002994699.1| 42 HVDKCIGCKLCMNVCPA 58
                                      469*************5 PP

  == domain 2  score: 25.8 bits;  conditional E-value: 7.9e-09
                           Fer4_21  5 edkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedciem 59
                                       dkCigC++C+ +C+ +  + +     +++++   +Cv C+ C++vCPv +++em
  gi|242399275|ref|YP_002994699.1| 43 VDKCIGCKLCMNVCPAGVFEYVPEI--KKVTLWLGRCVFCQQCVDVCPV-NALEM 94
                                      589************8777777433..45567789*************9.88887 PP

  == domain 3  score: 23.5 bits;  conditional E-value: 4.3e-08
                           Fer4_21  30 aktvlkvvedeCvGCnlCssvCPvedcie 58 
                                       + +++++++++C GC+lC+  CP +++ie
  gi|242399275|ref|YP_002994699.1| 128 KTKKYRIIAEKCKGCTLCARNCP-QNAIE 155
                                       44567899***************.69886 PP

  == domain 4  score: 29.6 bits;  conditional E-value: 5.1e-10
                           Fer4_21   3 idedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCP 52 
                                       i  +kC gC++C+  C+    +aie++++ v+k+  ++C+GC +C+++C 
  gi|242399275|ref|YP_002994699.1| 134 IIAEKCKGCTLCARNCP---QNAIEGAPRVVHKINPEKCIGCGICATICK 180
                                       6679*************...59***************************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 !   35.4  10.5   7.9e-12   8.3e-09       2      56 .]      39      88 ..      38      88 .. 0.91
   2 !   27.1  11.2   3.2e-09   3.3e-06       8      56 .]      76     150 ..      69     150 .. 0.89
   3 !   23.3  13.9   4.8e-08     5e-05       3      55 ..     133     179 ..     131     180 .. 0.85

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 7.9e-12
                           Fer4_10  2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      +v+  d+Ci+C+ C+++CPa     g+ ++  e+++v   +++C +c +Cv++CP
  gi|242399275|ref|YP_002994699.1| 39 LVYHVDKCIGCKLCMNVCPA-----GVFEYVPEIKKVTLWLGRCVFCQQCVDVCP 88
                                      67899***************.....888888888888889**************9 PP

  == domain 2  score: 27.1 bits;  conditional E-value: 3.2e-09
                           Fer4_10   8 tCirCgkCvkaCPadl..........................tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       +C+ C++Cv++CP+++                           +    ++  + ++ r+  ekC gc+ C++ CP
  gi|242399275|ref|YP_002994699.1|  76 RCVFCQQCVDVCPVNAlemsgefllatydkyddnlrwlkneeIEEMIAQKSGKTKKYRIIAEKCKGCTLCARNCP 150
                                       8*************99************************9656666666666677778***************9 PP

  == domain 3  score: 23.3 bits;  conditional E-value: 4.8e-08
                           Fer4_10   3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaC 55 
                                       +i +++C +C+ C + CP+      +  e  +  + ++++ekC+gcg C+ +C
  gi|242399275|ref|YP_002994699.1| 133 RIIAEKCKGCTLCARNCPQ------NAIEGAPRVVHKINPEKCIGCGICATIC 179
                                       68899**************......6666666666777*************** PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.7   8.0   3.7e-13   3.9e-10       1      50 [.      45      91 ..      45      92 .. 0.90
   2 !   16.8   3.3   5.3e-06    0.0056      20      51 .]     124     154 ..     115     154 .. 0.72
   3 !   22.3  13.7     1e-07   0.00011       1      51 []     138     184 ..     138     184 .. 0.79

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 3.7e-13
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50
                                      kC+gC+ C+++Cpagv+++    +k+ l      +C++C++Cv++Cp +a
  gi|242399275|ref|YP_002994699.1| 45 KCIGCKLCMNVCPAGVFEYVPEIKKVTLWL---GRCVFCQQCVDVCPVNA 91
                                      7*****************999999999843...37************986 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 5.3e-06
                            Fer4_9  20 daaerkarlraaseeaCigCgaCveaCpkgai 51 
                                       ++++++ ++r+  e +C gC  C+  Cp++ai
  gi|242399275|ref|YP_002994699.1| 124 QKSGKTKKYRIIAE-KCKGCTLCARNCPQNAI 154
                                       44444455555544.9*************997 PP

  == domain 3  score: 22.3 bits;  conditional E-value: 1e-07
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                       kC gC+ C + Cp++++++        +     e+CigCg C+ +C+  ai
  gi|242399275|ref|YP_002994699.1| 138 KCKGCTLCARNCPQNAIEGAPRVVHKINP----EKCIGCGICATICKFSAI 184
                                       7****************665544443332....37***********98766 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   1.3   2.3e-08   2.4e-05       3      22 .]      39      58 ..      37      58 .. 0.90
   2 !   10.9   0.9   0.00037      0.39       9      21 ..      76      88 ..      62      89 .. 0.90
   3 !   16.2   1.7   7.9e-06    0.0083       3      22 .]     132     151 ..     130     151 .. 0.88
   4 !   22.7   1.7   6.7e-08   7.1e-05       4      20 ..     163     179 ..     160     181 .. 0.91

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 2.3e-08
                            Fer4_2  3 vvvdtdrCigCgaCvsaCPa 22
                                       v+  d+CigC+ C ++CPa
  gi|242399275|ref|YP_002994699.1| 39 LVYHVDKCIGCKLCMNVCPA 58
                                      578899*************8 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00037
                            Fer4_2  9 rCigCgaCvsaCP 21
                                      rC+ C  Cv++CP
  gi|242399275|ref|YP_002994699.1| 76 RCVFCQQCVDVCP 88
                                      7999********* PP

  == domain 3  score: 16.2 bits;  conditional E-value: 7.9e-06
                            Fer4_2   3 vvvdtdrCigCgaCvsaCPa 22 
                                       + + +++C gC  C  +CP+
  gi|242399275|ref|YP_002994699.1| 132 YRIIAEKCKGCTLCARNCPQ 151
                                       567899*************6 PP

  == domain 4  score: 22.7 bits;  conditional E-value: 6.7e-08
                            Fer4_2   4 vvdtdrCigCgaCvsaC 20 
                                       ++++++CigCg+C + C
  gi|242399275|ref|YP_002994699.1| 163 KINPEKCIGCGICATIC 179
                                       69*************** PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   1.0   6.9e-06    0.0073       1      19 [.      45      63 ..      41      71 .. 0.77
   2 !   24.7   0.1   3.2e-08   3.4e-05       1      33 [.      76     106 ..      76     136 .. 0.64
   3 !   18.9   3.2     2e-06    0.0021       1      21 [.     138     158 ..     138     168 .. 0.81
   4 !   12.3   2.5   0.00023      0.24       1      20 [.     168     187 ..     168     189 .] 0.89

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 6.9e-06
                           Fer4_16  1 rCgtCgkCaevCPtnaike 19
                                      +C++C+ C++vCP+++++ 
  gi|242399275|ref|YP_002994699.1| 45 KCIGCKLCMNVCPAGVFEY 63
                                      5888888888888888765 PP

  == domain 2  score: 24.7 bits;  conditional E-value: 3.2e-08
                           Fer4_16   1 rCgtCgkCaevCPtnaikekkekeiearecisy 33 
                                       rC+ C++C++vCP+na+++  e+ +++ ++  y
  gi|242399275|ref|YP_002994699.1|  76 RCVFCQQCVDVCPVNALEMSGEFLLATYDK--Y 106
                                       6*****************995544443333..3 PP

  == domain 3  score: 18.9 bits;  conditional E-value: 2e-06
                           Fer4_16   1 rCgtCgkCaevCPtnaikekk 21 
                                       +C++C+ Ca  CP+nai++  
  gi|242399275|ref|YP_002994699.1| 138 KCKGCTLCARNCPQNAIEGAP 158
                                       5****************9883 PP

  == domain 4  score: 12.3 bits;  conditional E-value: 0.00023
                           Fer4_16   1 rCgtCgkCaevCPtnaikek 20 
                                       +C++Cg Ca +C  +ai+e 
  gi|242399275|ref|YP_002994699.1| 168 KCIGCGICATICKFSAIEEY 187
                                       5****************987 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.3   7.8e-06    0.0082      43      60 ..      43      60 ..      26      61 .. 0.84
   2 !   11.4   1.8   0.00034      0.35      43      58 ..      74      89 ..      65      93 .. 0.81
   3 !   22.8  11.1   9.6e-08    0.0001       1      59 [.      76     152 ..      76     153 .. 0.60
   4 !   10.3   1.2   0.00078      0.82       1      15 [.     168     182 ..     163     189 .] 0.76

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 7.8e-06
                           Fer4_17 43 aslCieCgeCerkCPqgl 60
                                      +++Ci+C++C  +CP+g+
  gi|242399275|ref|YP_002994699.1| 43 VDKCIGCKLCMNVCPAGV 60
                                      678999999999999876 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00034
                           Fer4_17 43 aslCieCgeCerkCPq 58
                                       ++C+ C++C+ +CP 
  gi|242399275|ref|YP_002994699.1| 74 LGRCVFCQQCVDVCPV 89
                                      5789999999999996 PP

  == domain 3  score: 22.8 bits;  conditional E-value: 9.6e-08
                           Fer4_17   1 rCiqCgyClpeCpsyea..........ydnepk..kllraaklglleeaeke.........ekaslCieCgeCerkC 56 
                                       rC  C+ C+++Cp ++           yd++ +  ++l++   +++ee++++           a++C +C +C+r C
  gi|242399275|ref|YP_002994699.1|  76 RCVFCQQCVDVCPVNALemsgefllatYDKYDDnlRWLKN---EEIEEMIAQksgktkkyrIIAEKCKGCTLCARNC 149
                                       799**********855544444444444433331123333...333333222333444343489************* PP

                           Fer4_17  57 Pqg 59 
                                       Pq+
  gi|242399275|ref|YP_002994699.1| 150 PQN 152
                                       *97 PP

  == domain 4  score: 10.3 bits;  conditional E-value: 0.00078
                           Fer4_17   1 rCiqCgyClpeCpsy 15 
                                       +Ci+Cg C+  C + 
  gi|242399275|ref|YP_002994699.1| 168 KCIGCGICATICKFS 182
                                       588888888888764 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   2.7   1.2e-06    0.0013       2      17 .]      44      59 ..      44      60 .. 0.93
   2 !   16.3   1.7   9.2e-06    0.0097       3      17 .]      76      90 ..      74      96 .. 0.91
   3 !    8.9   4.3    0.0023       2.4       2      17 .]     137     152 ..     136     152 .. 0.93
   4 !   13.9   3.2   5.5e-05     0.058       1      16 [.     166     181 ..     166     182 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.2e-06
                            Fer4_4  2 erCigCgsCvaaCPqg 17
                                      ++CigC+ C+++CP g
  gi|242399275|ref|YP_002994699.1| 44 DKCIGCKLCMNVCPAG 59
                                      79************75 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 9.2e-06
                            Fer4_4  3 rCigCgsCvaaCPqg 17
                                      rC+ C +Cv++CP++
  gi|242399275|ref|YP_002994699.1| 76 RCVFCQQCVDVCPVN 90
                                      9************75 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0023
                            Fer4_4   2 erCigCgsCvaaCPqg 17 
                                       e+C gC  C + CPq+
  gi|242399275|ref|YP_002994699.1| 137 EKCKGCTLCARNCPQN 152
                                       89************86 PP

  == domain 4  score: 13.9 bits;  conditional E-value: 5.5e-05
                            Fer4_4   1 qerCigCgsCvaaCPq 16 
                                       +e+CigCg C  +C++
  gi|242399275|ref|YP_002994699.1| 166 PEKCIGCGICATICKF 181
                                       69************85 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   3.3   1.1e-05     0.011       2      17 ..      43      58 ..      42      72 .. 0.84
   2 !   13.1   2.2   9.5e-05       0.1      48      64 ..      74      90 ..      64      91 .. 0.87
   3 !   24.0   8.9   3.8e-08     4e-05       3      64 ..      75     152 ..      73     153 .. 0.78
   4 !   11.6   1.5   0.00029       0.3       3      17 ..     167     181 ..     165     188 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.1e-05
                            Fer4_8  2 lekCieCgaCqsaCpv 17
                                      ++kCi+C +C++ Cp+
  gi|242399275|ref|YP_002994699.1| 43 VDKCIGCKLCMNVCPA 58
                                      689***********94 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 9.5e-05
                            Fer4_8 48 lwsCttcgaCtevCpvg 64
                                      l++C+ c++C++vCpv+
  gi|242399275|ref|YP_002994699.1| 74 LGRCVFCQQCVDVCPVN 90
                                      679************97 PP

  == domain 3  score: 24.0 bits;  conditional E-value: 3.8e-08
                            Fer4_8   3 ekCieCgaCqsaCp..vlrrtkkhlldargeaaedvqeeqvlee...............eealwsCttcgaCtevCp 62 
                                        +C+ C+ C + Cp  +l+ ++++ll ++++  + + ++ ++ee               + ++++C +c  C+++Cp
  gi|242399275|ref|YP_002994699.1|  75 GRCVFCQQCVDVCPvnALEMSGEFLLATYDKYDD-NLRWLKNEEieemiaqksgktkkyRIIAEKCKGCTLCARNCP 150
                                       58************54444455676666666666.777777666777777888888999999*************** PP

                            Fer4_8  63 vg 64 
                                       ++
  gi|242399275|ref|YP_002994699.1| 151 QN 152
                                       87 PP

  == domain 4  score: 11.6 bits;  conditional E-value: 0.00029
                            Fer4_8   3 ekCieCgaCqsaCpv 17 
                                       ekCi+Cg C + C +
  gi|242399275|ref|YP_002994699.1| 167 EKCIGCGICATICKF 181
                                       69***********76 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.4   1.8e-07   0.00019       4      29 ..      44      70 ..      43      73 .. 0.88
   2 !    9.2   0.1    0.0016       1.7       5      17 ..      76      88 ..      74     125 .. 0.79
   3 ?    6.5   2.9     0.011        12       4      18 ..     137     151 ..     135     152 .. 0.92
   4 !   11.3   2.1   0.00036      0.38       1      16 [.     164     179 ..     164     181 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.8e-07
                           Fer4_13  4 dtCiacgaCvelaPd.vFeeddeggas 29
                                      d+Ci+c++C +++P  vFe+ +e +++
  gi|242399275|ref|YP_002994699.1| 44 DKCIGCKLCMNVCPAgVFEYVPEIKKV 70
                                      59************77******98775 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0016
                           Fer4_13  5 tCiacgaCvelaP 17
                                      +C+ c++Cv+++P
  gi|242399275|ref|YP_002994699.1| 76 RCVFCQQCVDVCP 88
                                      79**********9 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.011
                           Fer4_13   4 dtCiacgaCvelaPd 18 
                                       ++C +c++C+  +P+
  gi|242399275|ref|YP_002994699.1| 137 EKCKGCTLCARNCPQ 151
                                       79************6 PP

  == domain 4  score: 11.3 bits;  conditional E-value: 0.00036
                           Fer4_13   1 VDrdtCiacgaCvela 16 
                                       ++ ++Ci+cg+C+ ++
  gi|242399275|ref|YP_002994699.1| 164 INPEKCIGCGICATIC 179
                                       7899**********99 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   5.8   6.1e-05     0.064       1      14 [.      46      59 ..      46      60 .. 0.93
   2 !   17.6   6.4   5.2e-06    0.0055       1      15 []      77      91 ..      77      91 .. 0.98
   3 !    9.2   5.4    0.0024       2.5       1      15 []     139     153 ..     139     153 .. 0.97
   4 ?    7.3   2.8      0.01        11       1      12 [.     169     180 ..     169     183 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6.1e-05
                            Fer4_3  1 CtgCgaCvevCPvg 14
                                      C+gC +C++vCP g
  gi|242399275|ref|YP_002994699.1| 46 CIGCKLCMNVCPAG 59
                                      ************76 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 5.2e-06
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+ C++Cv+vCPv+A
  gi|242399275|ref|YP_002994699.1| 77 CVFCQQCVDVCPVNA 91
                                      *************99 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0024
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C gC +C + CP +A
  gi|242399275|ref|YP_002994699.1| 139 CKGCTLCARNCPQNA 153
                                       9***********998 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.01
                            Fer4_3   1 CtgCgaCvevCP 12 
                                       C+gCg C   C 
  gi|242399275|ref|YP_002994699.1| 169 CIGCGICATICK 180
                                       ***********6 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   1.7     0.002       2.2      79      95 ..      43      59 ..      36      60 .. 0.76
   2 ?    4.6   3.1     0.056        59       1      14 [.      76      89 ..      76     102 .. 0.79
   3 !   12.6   1.2   0.00019       0.2      52      95 ..     108     152 ..      94     153 .. 0.80
   4 !   12.2   1.0   0.00025      0.26      74      93 ..     161     180 ..     155     183 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.002
                           Fer4_22 79 esgCvGCgRCieacpvk 95
                                        +C+GC  C+++cp++
  gi|242399275|ref|YP_002994699.1| 43 VDKCIGCKLCMNVCPAG 59
                                      56788888888888875 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.056
                           Fer4_22  1 rClsCgaCtlvCpt 14
                                      rC+ C++C  vCp 
  gi|242399275|ref|YP_002994699.1| 76 RCVFCQQCVDVCPV 89
                                      57777777777774 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 0.00019
                           Fer4_22  52 envrkekkerlrqrllhklsefke.kfgesgCvGCgRCieacpvk 95 
                                       +n+r  k+e +++ + +k  ++k+ ++ +++C GC  C ++cp++
  gi|242399275|ref|YP_002994699.1| 108 DNLRWLKNEEIEEMIAQKSGKTKKyRIIAEKCKGCTLCARNCPQN 152
                                       567888889999999999876554267999************986 PP

  == domain 4  score: 12.2 bits;  conditional E-value: 0.00025
                           Fer4_22  74 kekfgesgCvGCgRCieacp 93 
                                       ++k++ ++C+GCg C + c+
  gi|242399275|ref|YP_002994699.1| 161 VHKINPEKCIGCGICATICK 180
                                       56778899********9997 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   1.7    0.0012       1.3       6      20 ..      44      58 ..      40      72 .. 0.84
   2 ?    5.6   3.2     0.025        26       7      19 ..      76      88 ..      70     121 .. 0.86
   3 !    8.9   1.8    0.0023       2.5       6      20 ..     137     151 ..     136     165 .. 0.77
   4 !   11.3   1.6   0.00044      0.46       3      19 ..     164     180 ..     163     188 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0012
                           Fer4_15  6 daCigcglCvaeape 20
                                      d+Cigc lC+ ++p 
  gi|242399275|ref|YP_002994699.1| 44 DKCIGCKLCMNVCPA 58
                                      89***********85 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.025
                           Fer4_15  7 aCigcglCvaeap 19
                                      +C  c +Cv+++p
  gi|242399275|ref|YP_002994699.1| 76 RCVFCQQCVDVCP 88
                                      8**********98 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0023
                           Fer4_15   6 daCigcglCvaeape 20 
                                       ++C gc lC++++p+
  gi|242399275|ref|YP_002994699.1| 137 EKCKGCTLCARNCPQ 151
                                       68***********74 PP

  == domain 4  score: 11.3 bits;  conditional E-value: 0.00044
                           Fer4_15   3 vDrdaCigcglCvaeap 19 
                                       ++ ++Cigcg C++ ++
  gi|242399275|ref|YP_002994699.1| 164 INPEKCIGCGICATICK 180
                                       7789**********995 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   2.6   0.00016      0.17      58      75 ..      43      60 ..      36      69 .. 0.90
   2 !   10.8   3.3   0.00039      0.41      59      74 ..      75      90 ..      65      96 .. 0.87
   3 ?    5.4   9.1     0.019        20      39      96 ..     117     180 ..      91     185 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00016
                           Fer4_18 58 agdcidcescvkvcPtgi 75
                                      + +ci c+ c++vcP g+
  gi|242399275|ref|YP_002994699.1| 43 VDKCIGCKLCMNVCPAGV 60
                                      578************997 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00039
                           Fer4_18 59 gdcidcescvkvcPtg 74
                                      g c+ c++cv+vcP++
  gi|242399275|ref|YP_002994699.1| 75 GRCVFCQQCVDVCPVN 90
                                      78************85 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.019
                           Fer4_18  39 grkkekkalkekeerkekgagdcidcescvkvcPtg.id.....irkGlqleciscllcidacd 96 
                                       + ++  ++++ k ++ +  a +c  c  c + cP + i+     + k    +ci c+ c   c+
  gi|242399275|ref|YP_002994699.1| 117 EIEEMIAQKSGKTKKYRIIAEKCKGCTLCARNCPQNaIEgaprvVHKINPEKCIGCGICATICK 180
                                       2223333334444455556789************862443333244555568*******99996 PP

>> ETF_QO  Electron transfer flavoprotein-ubiquinone oxidoreductase, 4Fe-4S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.4      0.31   3.3e+02      67      81 ..      38      52 ..      27      54 .. 0.85
   2 ?   12.7   1.9    0.0001      0.11      46      82 ..      52      84 ..      50      96 .. 0.79
   3 ?    9.8   0.6   0.00082      0.86      39      91 ..     103     155 ..      91     159 .. 0.86
   4 ?    2.7   1.2      0.13   1.4e+02      68      82 ..     162     176 ..     152     186 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.31
                                      EEEE-CCC--S--HH CS
                            ETF_QO 67 klqinaqnCvhCktC 81
                                      kl+     C+ Ck C
  gi|242399275|ref|YP_002994699.1| 38 KLVYHVDKCIGCKLC 52
                                      67788899******9 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.0001
                                      HHHH-TTS-EEEEETTTTSSEEEEE-CCC--S--HHH CS
                            ETF_QO 46 eqryCPagvyeivedeeakekklqinaqnCvhCktCd 82
                                      +  +CPagv+e+v +     kk+++    Cv C+ C 
  gi|242399275|ref|YP_002994699.1| 52 CMNVCPAGVFEYVPEI----KKVTLWLGRCVFCQQCV 84
                                      5679*********876....466777789*****994 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.00082
                                       HHHHS-THHHH-TTS-EEEEETTTTSSEEEEE-CCC--S--HHHHH-TT--EE CS
                            ETF_QO  39 lekyagpeqryCPagvyeivedeeakekklqinaqnCvhCktCdikdpsqnie 91 
                                       ++ky++  +      + e++ +++ k+kk++i a+ C  C  C    p++ ie
  gi|242399275|ref|YP_002994699.1| 103 YDKYDDNLRWLKNEEIEEMIAQKSGKTKKYRIIAEKCKGCTLCARNCPQNAIE 155
                                       667777777777788999*****99******************9999998886 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.13
                                       EEE-CCC--S--HHH CS
                            ETF_QO  68 lqinaqnCvhCktCd 82 
                                        +in + C+ C  C 
  gi|242399275|ref|YP_002994699.1| 162 HKINPEKCIGCGICA 176
                                       68**********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       799  (0.0445647); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); 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: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 1288.67
//
Query:       gi|242399276|ref|YP_002994700.1|  [L=329]
Description: Membrane-bound hydrogenase MBH 1, subunit Mbh1M (hydrogenase subunit) [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-57  195.6  15.7    1.4e-57  195.3  15.7    1.0  1  NADHdh    NADH dehydrogenase


Domain annotation for each model (and alignments):
>> NADHdh  NADH dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.3  15.7   7.7e-62   1.4e-57       4     298 ..      11     320 ..       8     321 .. 0.89

  Alignments for each domain:
  == domain 1  score: 195.3 bits;  conditional E-value: 7.7e-62
                                       HHHHHHHHHHHHHHHHHHHHHHHHHTTS--S-SSTTTTTTHHHHHHHHHCCS-----TTS-HHHHHHHHHHHHHHHH CS
                            NADHdh   4 llllvvlllvvalltlleRkvlAriqdRlGPnrvGplGllqplaDalKlllKediipkkadkllfllapvlalilal 80 
                                       +++ + + +v ++  +l+Rk++Ar+q+R+GP      +llqp++D+lKl+ Ke+iip++++k +f ++p+lal++++
  gi|242399276|ref|YP_002994700.1|  11 IAVYIYVSFVSLVWDGLDRKLVARMQRRVGP------PLLQPFYDFLKLVGKESIIPRDSNK-MFEASPILALAASI 80 
                                       344444555556999****************......***********************65.89************ PP

                                       CTTTTS-SS.SSSS--TTHHHHHHHHHHHCHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-S CS
                            NADHdh  81 lafaviPfg.evladlnvglllilalsslgvygillaGwasnskYallGalRsaaqmisyEvalglsllavvllags 156
                                       +++a+ P+g   +   + ++l++++l++l +++ ++++++s+s+Ya +Ga R+++++ s E +++l l+a+++   +
  gi|242399276|ref|YP_002994700.1|  81 TLLAYTPIGfGPILATKGDVLVFIYLLALIAFIRVIGAVSSGSPYAQIGAQREVIMLASREAPMMLGLFAILWRLAK 157
                                       *******99545666778********************************************************999 PP

                                       S-HHHHH....HCCCTT-C......CCCHHHHHHHHHHHHHHCCTCTTBTTTTSTTSSSSCCCTT-HCHHHHHHHHH CS
                            NADHdh 157 lslseiv....eaqeeiwf......illqllafiifliallaetnraPFDlpeaesELvaGfhtEYsgmkfalffla 223
                                       l++++       +q++iw       i+  l+++i+f++ l  e++   F++peae+E+++G++ EYsg  +alf l+
  gi|242399276|ref|YP_002994700.1| 158 LDVEKPFsletLYQHNIWEigtpltIVGSLVLLIVFIFWLASEIEVGYFNIPEAETEVAEGPMAEYSGRDLALFKLS 234
                                       9666654222247888886677888888899999999999************************************* PP

                                       HHHHHHHHHHHHHHHCT.SS-HCCS...............HHHHHHHHHHHHHHHHH.HHHHC----TCHHHHHHHC CS
                            NADHdh 224 eyanmvlvsalavllFlgGwllpfs...............gllwfllKvllllflfi.wiratlpRlRydqlmklgw 284
                                       + ++ ++ ++l+v++F+  w    +               +l++ ++Kv+++lf+ + ++ra+  RlR+ q+++l w
  gi|242399276|ref|YP_002994700.1| 235 NSLKEYASASLVVAVFF-PW----GlsqylgisgieamlvDLVFHTIKVFVILFVSMsLFRAITGRLRVTQAVNLFW 306
                                       *************9999.34....3334567999999999**************99879****************** PP

                                       CTCHHHHHHHHHHH CS
                            NADHdh 285 kvllplalanlllt 298
                                       + +lp +++  +l+
  gi|242399276|ref|YP_002994700.1| 307 SRILPASMIGAILL 320
                                       ********998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       654  (0.0364772); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.30s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 2035.18
//
Query:       gi|242399277|ref|YP_002994701.1|  [L=430]
Description: Membrane-bound hydrogenase MBH 1, subunit Mbh1L (NiFe hydrogenase catalytic subunit) [Thermococcus sibiricus MM 739]
Scores for complete 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-56  190.7   0.1    1.3e-54  185.1   0.1    2.1  1  Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd s
    7.2e-20   71.4   4.4    1.7e-14   53.6   0.2    3.1  3  NiFeSe_Hases    Nickel-dependent hydrogenase
  ------ inclusion threshold ------
      0.023   15.0   0.0      0.047   14.0   0.0    1.4  1  DUF1722         Protein of unknown function (DUF1722)


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 !  185.1   0.1   2.2e-58   1.3e-54       2     271 .]     123     380 ..     122     380 .. 0.92

  Alignments for each domain:
  == domain 1  score: 185.1 bits;  conditional E-value: 2.2e-58
                                       TT-HHHHHHHHHHHHHHHHHHHHHHSSSSS-TTBESSBBSS---TTHHHHHHHHHHHHHH.HHHHHHHHHHSSSSHH CS
                    Complex1_49kDa   2 lGaltvflyafreRekildlleevtGaRltasyiriGGvarDlpegllekikeflkelek.kldeleklltknrifk 77 
                                       +G  tv+   +  Re+++d+le++ G+R+++++  iGGv+rD++e+  ++i +++k++++  + ++e+++  ++++ 
  gi|242399277|ref|YP_002994701.1| 123 IGYDTVLHLSWLARERVMDILEAIGGNRVNYAMNTIGGVRRDIEEKHKRMILDMIKHYREeVMPKVEEIFLYDPTVE 199
                                       78999**************************************************988651578************* PP

                                       HHHSSSS-BSHHHHHHHTT-SSSSGGGT-TTTHHHHSS-SSGGGS------......-SSBSHHHHHHHHHHHHHHH CS
                    Complex1_49kDa  78 kRtkgvgvlskeealelgltGpvlRasGvkyDlRkaepYeaYdeldfdvpv......geegDvydRylvrveEmrqS 148
                                       +R+++ gv+ k+ ale+++ Gp++R+sG+k D+R +e   +Y el  + ++        +gDv+dR++vrv E++qS
  gi|242399277|ref|YP_002994701.1| 200 ARLRDAGVIPKRIALEYSAQGPTARGSGIKKDVRYNERLGVYPELGIKPITpkeftgVIKGDVFDRMVVRVGELWQS 276
                                       ************************************************999777666668***************** PP

                                       HHHHHHHHHT--.S-SB---TTTS---GGGGGT-HHHHHHHHHHHHS-----SEEEEEEEEETTEEEEEEEEEE.SS CS
                    Complex1_49kDa 149 lkIieqaleklpegpvlaedkkvalpkkeevkksmealihhfklvtegfkvpkgevyaavEapkGelgvylvsd.gs 224
                                       ++Iie+a++++peg++++ +k            +  +l+        ++k ++g  + + Eap+Ge+ +y+ ++ g+
  gi|242399277|ref|YP_002994701.1| 277 MEIIEKAFDQMPEGKIKTFSK------------DNVTLT--------KLKKAEGAGIGRYEAPRGETIHYVRANpGT 333
                                       ***************877322............222232........456889******************998577 PP

                                       SS-SEEEEE-HHHHTTTTHHHHTTTS-SGGGTHHHHTT---HHHHH- CS
                    Complex1_49kDa 225 skpyrlkirapsfvnlqaleellkgellaDvvailgsldivlgevDR 271
                                       ++p ++k r+p+f nl a+++ l ge+laDv+++++s+d++l+++DR
  gi|242399277|ref|YP_002994701.1| 334 DTPAKWKAREPTFPNLFAVARALVGEQLADVPVAIASIDPCLSCTDR 380
                                       77********************************************9 PP

>> NiFeSe_Hases  Nickel-dependent hydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.6   0.2   2.8e-18   1.7e-14       1      68 [.      47     114 ..      47     125 .. 0.98
   2 ?   -1.2   0.0      0.12   7.3e+02     159     218 ..     136     195 ..     127     203 .. 0.68
   3 !   17.5   0.3   2.6e-07    0.0016     390     503 ..     277     378 ..     258     379 .. 0.78

  Alignments for each domain:
  == domain 1  score: 53.6 bits;  conditional E-value: 2.8e-18
                                       --HHHHTTTS-GGGHHHHHHTT-SSSTTHHHHHHHHHHHHHHT----HHHHHHHHHHHHHHHHHHHHH CS
                      NiFeSe_Hases   1 RGlElilkgrdprdawalvqRiCGVCttvHalasvravedAlgikipknarlirnliaaalllhdhiv 68 
                                       RGlE i   r+  +  +lv+RiCG+C  +H ++ +rave+  gi++p+ a++ir +i   + +h+h++
  gi|242399277|ref|YP_002994701.1|  47 RGLEWIAMRRNYIQLLYLVERICGICSFSHNHTYTRAVEEMAGIEVPERAEYIRAIIGELERIHSHLL 114
                                       9*****************************************************************97 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.12
                                       HHHHHTHHHHHHHSSSSS--.EBTTBESSGBGS.BSHHHHHHHHHHHHHHHHHHHHTHHHH CS
                      NiFeSe_Hases 159 lqrkaakivaifggknPhpqslvvGGvtcaidl.lnaerlaevkslikevkefveevylpD 218
                                        +r +  + a +gg   +    ++GGv   i+   +   l+ +k++ +ev   vee++l D
  gi|242399277|ref|YP_002994701.1| 136 RERVMDILEA-IGGNRVNYAMNTIGGVRRDIEEkHKRMILDMIKHYREEVMPKVEEIFLYD 195
                                       4444444444.5555555556899***9998874445556778888888888888888877 PP

  == domain 3  score: 17.5 bits;  conditional E-value: 2.6e-07
                                       HHHHHHHHHHHHTTB---B--TT-SGGGS-S.EEEEEEEEEETTEEEEEEEEEETTEEEEEEEE-HHHHHH--S-TT CS
                      NiFeSe_Hases 390 kewldelvenikkgdtetaneekldkkevpk.eakGvglveapRGaLsHwikikdgkienYqavvPsTWnasPrdak 465
                                       +e +++  +++ +g  +t+++++++ ++++k e  G+g +eapRG   H+++ + g         P+ W a      
  gi|242399277|ref|YP_002994701.1| 277 MEIIEKAFDQMPEGKIKTFSKDNVTLTKLKKaEGAGIGRYEAPRGETIHYVRANPGTD------TPAKWKAREPTF- 346
                                       4556666677788888899999999999995599******************987754......599998865444. PP

                                       ----HHHHHHTT-B-SSTTS-HHHHHHHHHT--BHHHH CS
                      NiFeSe_Hases 466 gqkgayEaaLigtpvadpekPleilrtihSfDPClACa 503
                                        +  a+ +aL+g ++ad+  P+     i S DPCl+C+
  gi|242399277|ref|YP_002994701.1| 347 PNLFAVARALVGEQLADV--PV----AIASIDPCLSCT 378
                                       456789999999999875..55....567999999995 PP

>> DUF1722  Protein of unknown function (DUF1722)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   7.8e-06     0.047      49      88 ..     148     187 ..     137     193 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.8e-06
                           DUF1722  49 kkhinvlqhilgyfkkklsaeekqelleliekYregkvpl 88 
                                       ++ +n +++ +g ++++++++ k+ +l++i++Yre+ +p 
  gi|242399277|ref|YP_002994701.1| 148 GNRVNYAMNTIGGVRRDIEEKHKRMILDMIKHYREEVMPK 187
                                       7899*******************************99885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.48
# Mc/sec: 2717.54
//
Query:       gi|242399278|ref|YP_002994702.1|  [L=174]
Description: Membrane-bound hydrogenase MBH 1, subunit Mbh1K (hydrogenase subunit) [Thermococcus sibiricus MM 739]
Scores for complete 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   74.2   0.0    2.1e-20   73.6   0.0    1.2  1  Complex1_30kDa  Respiratory-chain NADH dehydrogenase, 30 Kd s
  ------ inclusion threshold ------
      0.055   13.6   0.0      0.083   13.1   0.0    1.2  1  DOPA_dioxygen   Dopa 4,5-dioxygenase family


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 !   73.6   0.0   2.3e-24   2.1e-20       2     116 ..      35     151 ..      34     155 .. 0.86

  Alignments for each domain:
  == domain 1  score: 73.6 bits;  conditional E-value: 2.3e-24
                                       E--HHHHHHHHHHHHH...TT--EEEEEEEEETTSSSEEEEEEEE--S-....-EEEEEE....-S-BEE--TTT-S CS
                    Complex1_30kDa   2 vvepedllevakflkdeeelgfdvlsdltavDekeerfevvyhllslekn...erirvkvevdeeepevpSvtdlfp 75 
                                       +++++d++e++k+ ++      +++s + + D+ +++++  yhl+ + +n    ++ v +++++e+p++pS+ d+fp
  gi|242399278|ref|YP_002994702.1|  35 EISRNDFKELMKYFQEI--DPHTQFSIIIGEDR-GDHLSATYHLELFCENspsLSVAVITSCPKEDPKIPSLGDVFP 108
                                       688999*********94..34678999999997.6**********8844445577777778899************* PP

                                       THHHHHHHHHHHSHHBCTTSSTSS-SSSSTTS..SS-TTSTTS CS
                    Complex1_30kDa  76 gadwyEREayDmfGivfeghpdlrrillpedf..eghPLRkdf 116
                                       +   yERE ++++Gi feg pd rr++lp+df    +PLR d 
  gi|242399278|ref|YP_002994702.1| 109 SSVPYERENQEFLGIIFEGIPDSRRLFLPDDFpeGIYPLRLDE 151
                                       ********************************85456***885 PP

>> DOPA_dioxygen  Dopa 4,5-dioxygenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   9.3e-06     0.083      19      87 ..       4      69 ..       2      88 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.3e-06
                                      HHHHHHHHHHTTTT..E---BSS--TT-SSEEEEEEE.-HHHHHHHHHHHHHH..-TT--EEEEEESS-HH CS
                     DOPA_dioxygen 19 keLrekirrefeeelrvgklaekpiGPhpvamfevdvftpeqfgkvvswlaln..rgplsvLiHpntgdel 87
                                      +eL ++i+++fe e  ++  +++   Php +   +++ +++ f++++++++    ++++s++i    gd+l
  gi|242399278|ref|YP_002994702.1|  4 EELIKRIKERFEVE--IY--TSQTKTPHPRERIWIEI-SRNDFKELMKYFQEIdpHTQFSIIIGEDRGDHL 69
                                      57889999999664..66..667778***********.9***********974337889999866666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.55
# Mc/sec: 947.58
//
Query:       gi|242399279|ref|YP_002994703.1|  [L=156]
Description: Membrane-bound hydrogenase MBH 1, subunit Mbh1J (hydrogenase subunit) [Thermococcus sibiricus MM 739]
Scores for complete 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-27   93.8   0.0    9.1e-27   93.5   0.0    1.1  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 !   93.5   0.0   5.1e-31   9.1e-27       1     128 [.      32     140 ..      32     142 .. 0.93

  Alignments for each domain:
  == domain 1  score: 93.5 bits;  conditional E-value: 5.1e-31
                                       -SHHHHHHT-TTTTHHHHHHTEEEEEETTT-S--HHHHHHTHTTTSEEEEEESBE...EEEHHHHHHHHGGGSSEEE CS
                       Oxidored_q6   1 CtGcsisllaleedlldllelielryhetlladskeeeieakekeadvlvveGavtrkpkealellkelaekakavi 77 
                                       C+Gc+i++ a+ ++ +d+     +r++++l+ +++         +ad+l+v+G++t ++ e+++l++e+++++k+v+
  gi|242399279|ref|YP_002994703.1|  32 CNGCDIEIIAALTPRYDA-----ERFGIKLVGTPR---------HADILLVTGPITDQSLERVKLIYEQTPDPKVVV 94 
                                       ********99999999*9.....9***********.........********************************* PP

                                       EESHHHHH-TGGGSTT-TEE-HHHHHHHC.S-E.EEE-SSS--HHHHHHHH CS
                       Oxidored_q6  78 avGtCAafGGipaaannpsvgeevgellevvpvdinipGCPphpeailetl 128
                                       a+G+C + G ++  ++    +    +l++++pvd++ipGCPp+pea+l+++
  gi|242399279|ref|YP_002994703.1|  95 AIGACPTGGSVFFESP---FT--NAPLDRHIPVDVFIPGCPPRPEAVLYGV 140
                                       ************5555...23..459*********************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1106.83
//
Query:       gi|242399280|ref|YP_002994704.1|  [L=115]
Description: Membrane-bound hydrogenase MBH 1, subunit Mbh1I (Na+/H+ transporter subunit) [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0082   15.5   0.4     0.0093   15.4   0.4    1.0  1  Glucos_trans_II  Glucosyl transferase GtrII
  ------ inclusion threshold ------
       0.14   12.1   0.2       0.47   10.4   0.0    1.9  2  UcrQ             UcrQ family
       0.63    9.9   4.5        7.1    6.5   0.2    2.2  2  LapA_dom         Lipopolysaccharide assembly protein A domain


Domain annotation for each model (and alignments):
>> Glucos_trans_II  Glucosyl transferase GtrII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.4   1.6e-06    0.0093     175     245 ..       7     114 ..       3     115 .] 0.85

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.6e-06
                   Glucos_trans_II 175 llllllvliisfvlylllykiilklfglelsy................................isellqnlkryys 219
                                       +l++++++i+++++++ll+k+  k++  + +                                 + ++++ +++++ 
  gi|242399280|ref|YP_002994704.1|   7 ALYFIYAFIVGLLISYLLMKWAEKVSVGTRKEgdgskiyisgedqdkvipqfehlqgyftgrhvMWGFIRGINKMFL 83 
                                       6788999*******************999988**********************99999999995567888888888 PP

                   Glucos_trans_II 220 .....isnygvkpkklllililliliillla 245
                                            +  + ++++++lli++ ++l + +++
  gi|242399280|ref|YP_002994704.1|  84 tfrreHTGLLTDYVSYLLITVAIVLGAMVIW 114
                                       8877777777788888888887777776665 PP

>> UcrQ  UcrQ family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   7.8e-05      0.47      46      65 ..      12      31 ..       7      41 .. 0.80
   2 ?   -1.1   0.0       0.3   1.8e+03      34      47 ..      81      94 ..      72     112 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 7.8e-05
                                      HHHHHHHHHHHHHHHHHHHH CS
                              UcrQ 46 lyvlppfiiayliykwakee 65
                                      + +++ ++i+yl++kwa++ 
  gi|242399280|ref|YP_002994704.1| 12 YAFIVGLLISYLLMKWAEKV 31
                                      678999***********985 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.3
                                      SSSTTCTTTTTHHH CS
                              UcrQ 34 ifntlrRtksqvly 47
                                      +f t+rR  + +l+
  gi|242399280|ref|YP_002994704.1| 81 MFLTFRREHTGLLT 94
                                      56666665544443 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 ?    6.5   0.2    0.0012       7.1      24      40 ..      11      27 ..       7      37 .. 0.84
   2 ?    5.0   0.7    0.0036        21      20      35 ..      99     114 ..      94     115 .] 0.93

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0012
                          LapA_dom 24 lvafgiGallgwllslw 40
                                      + af++G+l+ +ll+ w
  gi|242399280|ref|YP_002994704.1| 11 IYAFIVGLLISYLLMKW 27
                                      679***********988 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0036
                          LapA_dom  20 sllllvafgiGallgw 35 
                                       +ll+ va+++Ga+++w
  gi|242399280|ref|YP_002994704.1|  99 YLLITVAIVLGAMVIW 114
                                       69***********999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       688  (0.0383736); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.44
# Mc/sec: 790.87
//
Query:       gi|242399281|ref|YP_002994705.1|  [L=528]
Description: Membrane-bound hydrogenase MBH 1, subunit Mbh1H (hydrogenase subunit) [Thermococcus sibiricus MM 739]
Scores for complete 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-57  195.3  26.5    1.2e-57  195.3  26.5    2.5  2  Proton_antipo_M  Proton-conducting membrane transporter
    8.7e-10   38.5   0.3    8.7e-10   38.5   0.3    2.7  2  Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), 
    1.2e-08   34.6   7.3    1.2e-08   34.6   7.3    2.9  2  NADHdeh_related  NADH dehydrogenase I, subunit N related prot


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.4         1     6e+03      36      61 ..      88     113 ..      84     126 .. 0.62
   2 !  195.3  26.5   2.1e-61   1.2e-57       2     293 .]     135     448 ..     134     448 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 1
                   Proton_antipo_M  36 lklflltllgsliLLlgilllynltg 61 
                                       l ++ +t+++ l++L+++ ++ + tg
  gi|242399281|ref|YP_002994705.1|  88 LLALTVTFVSFLAILYSLEYMKHDTG 113
                                       44555666666666666666666555 PP

  == domain 2  score: 195.3 bits;  conditional E-value: 2.1e-61
                   Proton_antipo_M   2 ndLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskalelglns 78 
                                       +d++ +y++lE++++++y L++++ +  + +eA++k++++++l+s+++Llgi+lly++ gtl + +l++ +  +   
  gi|242399281|ref|YP_002994705.1| 135 GDIFNFYVFLEIMSIASYALVAFRNDTWEGIEAGVKYMFVGSLASSFILLGIALLYGQYGTLTMAYLAMKIAENP-T 210
                                       58899**************************************************************99943333.3 PP

                   Proton_antipo_M  79 lelllllllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkag.vlllirllllla.............. 140
                                       l   ++l +l+ gll+Ks++vp+h+Wl da+ +aP ++sa+l++++ kag v++++r+++ ++              
  gi|242399281|ref|YP_002994705.1| 211 LISKVALAFLIGGLLFKSGAVPVHMWLSDAHPAAPSSISAMLSGLVIKAGgVYAIARIIFGIFnpglhgylktfgmp 287
                                       334456677889********************************999997368888876644333322322333333 PP

                   Proton_antipo_M 141 .vssneisqlllilaiismllgslvalaqtdiKrllAySsishlGymlialav........atqygveaaiihllth 208
                                        +  n++  ++++ a +++++g+ +a++q+d+Krl A+Ss++++Gy+l+++++         +++++++a+ h++ h
  gi|242399281|ref|YP_002994705.1| 288 aFNLNTLGWIIIFFACLTLVIGNAMAVVQNDMKRLFAFSSVGQIGYILLGFGIgivaygdkIGEIALTGAVYHIVNH 364
                                       44567777889999***********************************999855544443377899********** PP

                   Proton_antipo_M 209 alfkallFllagsviyerektrdirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavslillvl 285
                                       a++k llF +ag+vi++   t+++++++gLa +mP++ + +++++ ++ GlPp+ gF sk+li e++  +++il+v+
  gi|242399281|ref|YP_002994705.1| 365 AVIKGLLFFIAGAVIHQV-GTKNLNELSGLARRMPFTTISFIIGATAIIGLPPLNGFASKWLIYESSAMYNPILAVV 440
                                       ************998876.9********************************************************* PP

                   Proton_antipo_M 286 avvasvlt 293
                                       av+++v++
  gi|242399281|ref|YP_002994705.1| 441 AVIGTVFS 448
                                       *****996 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 !   38.5   0.3   1.5e-13   8.7e-10      10      56 ..      74     120 ..      68     122 .. 0.91
   2 ?   -4.0   2.2       2.7   1.6e+04      25      36 ..     481     491 ..     475     497 .. 0.49

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 1.5e-13
                   Proton_antipo_N  10 lsieigfllDklsalmllvvtfvsllvhlYSigYMaddegyqRFfay 56 
                                       + i i   +D + al +l+vtfvs+l +lYS++YM++d+g  +++++
  gi|242399281|ref|YP_002994705.1|  74 FPIRIIWEVDLFGALLALTVTFVSFLAILYSLEYMKHDTGLDKYYTL 120
                                       67788889************************************976 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 2.7
                   Proton_antipo_N  25 mllvvtfvsllv 36 
                                       ml++v ++ l+ 
  gi|242399281|ref|YP_002994705.1| 481 MLVLVIII-LVM 491
                                       44444444.333 PP

>> NADHdeh_related  NADH dehydrogenase I, subunit N related protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   7.3     2e-12   1.2e-08      74     183 ..     120     234 ..      95     257 .. 0.84
   2 ?   -0.9   9.4      0.15   8.9e+02     105     182 ..     339     417 ..     297     459 .. 0.65

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 2e-12
                   NADHdeh_related  74 laivcglatlgavvtgdvfnftlflaliGianiGivaavkkef.vleaafnyGlvaliatlplfggaalilastGtl 149
                                       l +v  l  +g+v+tgd+fnf +fl ++ ia   +va  ++ +  +ea  +y +v  +a+ +++ g al+ ++ Gtl
  gi|242399281|ref|YP_002994705.1| 120 LTLVLELGMIGVVITGDIFNFYVFLEIMSIASYALVAFRNDTWeGIEAGVKYMFVGSLASSFILLGIALLYGQYGTL 196
                                       78899999*****************************999998469******************************* PP

                   NADHdeh_related 150 sifela.klagdvlliakl...llvlGvvGetGvaPfy 183
                                       ++  la k+a +  li+k+   +l+ G++  +G  P +
  gi|242399281|ref|YP_002994705.1| 197 TMAYLAmKIAENPTLISKValaFLIGGLLFKSGAVPVH 234
                                       **988615677755555541115666777777777765 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.15
                   NADHdeh_related 105 niGivaavkk..efvleaafnyGlv..aliatlplfggaalilastGtlsifelaklagdvlliaklllvlGvvGet 177
                                        iGiva   k  e +l+ a  y +v  a+i  l lf  a+ ++ + Gt  + el++la   + ++ + +++G     
  gi|242399281|ref|YP_002994705.1| 339 GIGIVAYGDKigEIALTGAV-YHIVnhAVIKGL-LFFIAGAVIHQVGTKNLNELSGLARR-MPFTTISFIIGATAII 412
                                       57888654432366777664.445422566666.55566777899*************98.5567788889988888 PP

                   NADHdeh_related 178 GvaPf 182
                                       G+ P+
  gi|242399281|ref|YP_002994705.1| 413 GLPPL 417
                                       88776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (528 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1047  (0.058397); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.79u 0.33s 00:00:01.12 Elapsed: 00:00:00.57
# Mc/sec: 2778.23
//
Query:       gi|242399282|ref|YP_002994706.1|  [L=120]
Description: Membrane-bound hydrogenase MBH 1, subunit Mbh1G (Na+/H+ transporter subunit) [Thermococcus sibiricus MM 739]
Scores for complete 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-25   88.0   4.0    3.4e-25   87.7   4.0    1.0  1  Oxidored_q2   NADH-ubiquinone/plastoquinone oxidoreductase ch
     0.0015   18.5   2.3     0.0015   18.5   2.3    1.8  2  DUF2108       Predicted membrane protein (DUF2108)
  ------ inclusion threshold ------
      0.069   11.4   2.3      0.085   11.1   2.3    1.0  1  YfhO          Bacterial membrane protein YfhO
       0.99    9.0   3.3       0.65    9.6   0.2    1.8  2  Saf_2TM       SAVED-fused 2TM effector domain
        4.5    7.1   7.4        2.4    8.0   0.6    2.3  2  Adeno_E3_CR2  Adenovirus E3 region protein CR2


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 !   87.7   4.0   9.6e-29   3.4e-25       3     105 .]       6     117 ..       4     118 .. 0.97

  Alignments for each domain:
  == domain 1  score: 87.7 bits;  conditional E-value: 9.6e-29
                                       HHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHHHHHHHHC......................TTSCGGHHH CS
                       Oxidored_q2   3 llliallfliGlygvllrrnllkvliglelisnavnlllvlagvftegtlvi.........tnpatefadplpqalv 70 
                                       +++++l++++G+y +l++rnl+k +++l+l+  +++lll+ +g++ e+ l +         t + t ++ p+pqalv
  gi|242399282|ref|YP_002994706.1|   6 FVTAFLMIFMGIYAFLYKRNLIKLILALNLVDAGIHLLLISLGYRLENGLLPtapiytgyeTLKGTPMVGPIPQALV 82 
                                       789*********************************************99999************************ PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHSSS-BCCG--X CS
                       Oxidored_q2  71 LtaivigaaetavgLallvrlyreygtddvqelrr 105
                                       Lt ivig++++++++al++++y++y+t+dv++lrr
  gi|242399282|ref|YP_002994706.1|  83 LTSIVIGVCVLSLAMALTINAYQHYETLDVSKLRR 117
                                       ********************************975 PP

>> DUF2108  Predicted membrane protein (DUF2108)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   2.3   4.2e-07    0.0015       3      46 ..       5      49 ..       3      50 .. 0.92
   2 ?   -2.0   0.8         1   3.7e+03      53      66 ..      84      97 ..      80     102 .. 0.55

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 4.2e-07
                           DUF2108  3 llvalalaliGaigvillkkpldKli.mlalleaGlillivakgY 46
                                      + v ++l+++ +i++ l k++l Kli +l l++aG+ ll+++ gY
  gi|242399282|ref|YP_002994706.1|  5 QFVTAFLMIFMGIYAFLYKRNLIKLIlALNLVDAGIHLLLISLGY 49
                                      67999*******************99469*************999 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1
                           DUF2108 53 vallePvstiilll 66
                                      ++++  v+++ l +
  gi|242399282|ref|YP_002994706.1| 84 TSIVIGVCVLSLAM 97
                                      45555555554444 PP

>> YfhO  Bacterial membrane protein YfhO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   2.3   2.4e-05     0.085     342     453 ..       4     113 ..       3     117 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2.4e-05
                              YfhO 342 fsfilsflllllaaealkelkqlkklkllaailllvllll.iilllknkksynfltssqlllgllllllalllllll 417
                                       f+f+ +fl++++ ++a+ ++++l  +kl++a+ l+ +++  + + l +   +n l  ++ +++ + +l ++ +++++
  gi|242399282|ref|YP_002994706.1|   4 FQFVTAFLMIFMGIYAFLYKRNL--IKLILALNLVDAGIHlLLISLGY-RLENGLLPTAPIYTGYETLKGTPMVGPI 77 
                                       89*******************99..66666666665555514444444.445667778******************* PP

                              YfhO 418 llkkkkkklvllllllvlvlelggnaylslnkisys 453
                                              ++v+ +++l l++ l++nay  ++++++s
  gi|242399282|ref|YP_002994706.1|  78 PQALVLTSIVIGVCVLSLAMALTINAYQHYETLDVS 113
                                       **************************9999888765 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 ?    0.2   0.6      0.14   5.1e+02      69      85 ..       3      19 ..       1      30 [. 0.75
   2 ?    9.6   0.2   0.00018      0.65      25      90 ..      35     104 ..      20     112 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.14
                           Saf_2TM 69 aiilvigvllivvGavl 85
                                      a+ +v+++l+i +G++ 
  gi|242399282|ref|YP_002994706.1|  3 AFQFVTAFLMIFMGIYA 19
                                      67799999999999763 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00018
                           Saf_2TM  25 lftigvalllailgt...dwalkialklaggslevsfssse.ipeivlaiilvigvllivvGavllilry 90 
                                       l+  g+ lll +lg    + +l  a    g++   +  + + ip++++++++vigv+ + + + l i  y
  gi|242399282|ref|YP_002994706.1|  35 LVDAGIHLLLISLGYrleNGLLPTAPIYTGYETLKGTPMVGpIPQALVLTSIVIGVCVLSLAMALTINAY 104
                                       777899999999998886777777777778888888999999*********************9999887 PP

>> Adeno_E3_CR2  Adenovirus E3 region protein CR2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.6   0.00066       2.4      18      33 ..      10      25 ..       6      28 .. 0.86
   2 ?    2.4   1.2     0.037   1.3e+02       1      21 [.      77      99 ..      77     105 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00066
                      Adeno_E3_CR2 18 iIiicmlyYaCcYrkh 33
                                       + i m +Ya+ Y++ 
  gi|242399282|ref|YP_002994706.1| 10 FLMIFMGIYAFLYKRN 25
                                      57899*********95 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.037
                      Adeno_E3_CR2  1 IPssti..aIivaVvvGlaiIii 21
                                      IP++++  +I+ +V v  + +++
  gi|242399282|ref|YP_002994706.1| 77 IPQALVltSIVIGVCVLSLAMAL 99
                                      67776666899999875555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       768  (0.0428356); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 811.51
//
Query:       gi|242399283|ref|YP_002994707.1|  [L=151]
Description: Membrane-bound hydrogenase MBH 1, subunit Mbh1F (Na+/H+ transporter subunit) [Thermococcus sibiricus MM 739]
Scores for complete 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-25   89.0  15.1    3.4e-25   88.7  15.1    1.1  1  MnhB      Domain related to MnhB subunit of Na+/H+ antiporter
  ------ inclusion threshold ------
       0.19   11.3   0.6       0.28   10.8   0.6    1.4  1  TMEM100   Transmembrane protein 100


Domain annotation for each model (and alignments):
>> MnhB  Domain related to MnhB subunit of Na+/H+ antiporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.7  15.1   3.8e-29   3.4e-25       1     123 [.      11     137 ..      11     138 .. 0.89

  Alignments for each domain:
  == domain 1  score: 88.7 bits;  conditional E-value: 3.8e-29
                              MnhB   1 ilrtvarllvplillvslylllrGhnsPGGGFqgGlilaaalillylafglee.lekllrvklaprileglglllav 76 
                                       i++t+ar  +pli ++++y++ +Gh +PGGGFqgG+++a a +l+++afgl+e +ek+++    + +leg+g l+++
  gi|242399283|ref|YP_002994707.1|  11 IVKTMARATIPLIGIFGAYVIAHGHITPGGGFQGGATIAGAGVLFLVAFGLSEaKEKINKNF--YSVLEGIGGLVFL 85 
                                       79***************************************************888888888..67*********** PP

                              MnhB  77 ltgllglllgfltslflel.el...llgeve..lgtallfdlgVylvVvggll 123
                                       ++g+lgl + f++++ ++   +     g+ +  +g + +++l+V+l+V +gl+
  gi|242399283|ref|YP_002994707.1|  86 AAGMLGLGVAFFYNILWHKgPVfngEAGT-LlsAGYLSMMNLAVGLKVYTGLV 137
                                       *******9999999999994445443333.24799999**********99875 PP

>> TMEM100  Transmembrane protein 100
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.6   3.2e-05      0.28      61     109 ..      81     132 ..      46     135 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3.2e-05
                           TMEM100  61 gvvvLvaGvvvtavaytfnshgs...visvlglvLLsaGlvllassavCWkv 109
                                       g v L aG+ + +va+ +n   +   v +  +  LLsaG + ++  av  kv
  gi|242399283|ref|YP_002994707.1|  81 GLVFLAAGMLGLGVAFFYNILWHkgpVFNGEAGTLLSAGYLSMMNLAVGLKV 132
                                       6899***************865411155555679*****9999988887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.54
# Mc/sec: 844.69
//
Query:       gi|242399284|ref|YP_002994708.1|  [L=97]
Description: Membrane-bound hydrogenase MBH 1, subunit Mbh1E (Na+/H+ transporter subunit) [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.044   13.3   0.1      0.065   12.8   0.1    1.2  1  DUF2106   Predicted membrane protein (DUF2106)


Domain annotation for each model (and alignments):
>> DUF2106  Predicted membrane protein (DUF2106)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   3.7e-06     0.065     116     145 ..      58      87 ..      42      92 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.7e-06
                           DUF2106 116 GiideilyytrGldtvlessillvafvias 145
                                        i+ +i++  rG dt+ e+++l+++ + a 
  gi|242399284|ref|YP_002994708.1|  58 NIVTDIVFDYRGYDTLGEATVLFTSIAGAV 87 
                                       3899*******************9987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 667.15
//
Query:       gi|242399285|ref|YP_002994709.1|  [L=80]
Description: Membrane-bound hydrogenase MBH 1, subunit Mbh1D (Na+/H+ transporter subunit) [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.8e-18   64.2   4.9      1e-17   64.0   4.9    1.1  1  DUF4040      Domain of unknown function (DUF4040)
     0.0055   16.4   0.0     0.0075   16.0   0.0    1.2  1  Oxidored_q3  NADH-ubiquinone/plastoquinone oxidoreductase cha
  ------ inclusion threshold ------
      0.013   15.5   3.9      0.015   15.3   3.9    1.0  1  TspO_MBR     TspO/MBR family


Domain annotation for each model (and alignments):
>> DUF4040  Domain of unknown function (DUF4040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.0   4.9   1.7e-21     1e-17       2      67 .]       9      74 ..       8      74 .. 0.97

  Alignments for each domain:
  == domain 1  score: 64.0 bits;  conditional E-value: 1.7e-21
                           DUF4040  2 llvlaalaavlardrlaavillgvvGllvallfvllgAPDvAlTqaavveglttvllllalrrlpr 67
                                      ++++++++++++rd+l+a++++ +++ll++l f++l+APDvA+++aav++g++t+++++ +++++r
  gi|242399285|ref|YP_002994709.1|  9 GILISSYWMITTRDLLSAALASTAMSLLLSLEFYMLHAPDVAIAEAAVGAGVVTAIVVYGISKTER 74
                                      799***********************************************************9986 PP

>> Oxidored_q3  NADH-ubiquinone/plastoquinone oxidoreductase chain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.3e-06    0.0075       2      58 ..      14      70 ..      13      79 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.3e-06
                                      HHHHHH-SBHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHIIIIIHHHHHHHHHH CS
                       Oxidored_q3  2 allvitsknpvysalfLilsfvgvaglfillgaeFlallqilvYvGAilvlflFvim 58
                                      +  +it++ ++ +al+  ++ +++++ f++l a+ +a++   v +G ++ ++++ i+
  gi|242399285|ref|YP_002994709.1| 14 SYWMITTRDLLSAALASTAMSLLLSLEFYMLHAPDVAIAEAAVGAGVVTAIVVYGIS 70
                                      5679**************************************************997 PP

>> TspO_MBR  TspO/MBR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   3.9   2.6e-06     0.015      44     111 ..       4      72 ..       1      76 [. 0.79

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.6e-06
                                       HHHHHHHHHHHHHHHHH...HHHHHHHHHHHHTSGGCTTTTTSGGGHHHHHHHHHHHHHHHHHHCCCC-HH CS
                          TspO_MBR  44 tvlyilmgvaaylvwka...lalyavqlvlnllwsplffglkspvlalvdivallglvvalilafskvdkl 111
                                        +l + +++++y ++++   l + +++ ++ ll s+ f  l+ p +a+++ ++ +g+v+a++  ++ ++k+
  gi|242399285|ref|YP_002994709.1|   4 VALLVGILISSYWMITTrdlLSAALASTAMSLLLSLEFYMLHAPDVAIAEAAVGAGVVTAIV--VYGISKT 72 
                                       566777788886655556998899999**************************999999999..3444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.48
# Mc/sec: 496.03
//
Query:       gi|242399286|ref|YP_002994710.1|  [L=121]
Description: Membrane-bound hydrogenase MBH 1, subunit Mbh1C (Na+/H+ transporter subunit) [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-23   82.5   3.6    2.2e-23   82.3   3.6    1.1  1  PhaG_MnhG_YufB  Na+/H+ antiporter subunit
     0.0019   17.9   2.3     0.0023   17.6   2.3    1.1  1  MASE3           Membrane-associated sensor domain
  ------ inclusion threshold ------
      0.011   14.9   0.4      0.011   14.9   0.4    1.4  2  7TM_GPCR_Sri    Serpentine type 7TM GPCR chemoreceptor Sri
      0.032   14.2   3.5      0.057   13.4   3.5    1.4  1  Rhomboid        Rhomboid family
      0.078   12.3   1.9       0.09   12.2   1.9    1.0  1  TssN            Type VI secretion system, TssN
      0.099   13.0   2.2       0.12   12.7   2.2    1.1  1  DUF3021         Protein of unknown function (DUF3021)


Domain annotation for each model (and alignments):
>> PhaG_MnhG_YufB  Na+/H+ antiporter subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.3   3.6   7.3e-27   2.2e-23       1      79 []       9      98 ..       9      98 .. 0.95

  Alignments for each domain:
  == domain 1  score: 82.3 bits;  conditional E-value: 7.3e-27
                    PhaG_MnhG_YufB  1 llllGalfvllgaigllrlpdvytRlhaatkadtlGlllillGlllrf.slaa..........slkllliilfllltaP 68
                                      +l++++ f +lg++ l r+pdvytRlh atk++t+G+++ +++++l+  ++ +          +l+ ++++++l+lt+P
  gi|242399286|ref|YP_002994710.1|  9 FLAVSITFNILGSLSLHRFPDVYTRLHGATKCTTFGTIFAVFAVVLHSiWQLRetndpkylqmALHSMVALIALMLTNP 87
                                      7899******************************************88555559************************* PP

                    PhaG_MnhG_YufB 69 vaahliaraay 79
                                      ++ah+ia+aa+
  gi|242399286|ref|YP_002994710.1| 88 TGAHAIAKAAH 98
                                      *********97 PP

>> MASE3  Membrane-associated sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   2.3   7.7e-07    0.0023     109     184 ..       7      81 ..       2      96 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 7.7e-07
                             MASE3 109 lvyalvtlll.llsifypkifPalfiegsGlTpfkiisEyliilllllalllllrrrkkfekkvlrlllaalvllil 184
                                       +++++v++++ +l  + ++ fP++++  +G T+       +i +++++ l  +++ r+ +++k+l++ l ++v+li+
  gi|242399286|ref|YP_002994710.1|   7 YAFLAVSITFnILGSLSLHRFPDVYTRLHGATKCTTFG--TIFAVFAVVLHSIWQLRETNDPKYLQMALHSMVALIA 81 
                                       344444444325566679*************9877765..788999999999****************999999886 PP

>> 7TM_GPCR_Sri  Serpentine type 7TM GPCR chemoreceptor Sri
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.3         1   3.1e+03      20      29 ..      11      20 ..       2      25 .. 0.53
   2 ?   14.9   0.4   3.8e-06     0.011     248     297 ..      38      87 ..      34      88 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1
                      7TM_GPCR_Sri 20 viSlvlnllg 29
                                      ++S+ +n+lg
  gi|242399286|ref|YP_002994710.1| 11 AVSITFNILG 20
                                      3455555554 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 3.8e-06
                      7TM_GPCR_Sri 248 tslvlllPllvlvvvvlfelenlqeiveillaifslhSsvnslvlilttp 297
                                       t +  +  ++++++vvl+++ +l+e+     + ++lhS+v  + l+lt+p
  gi|242399286|ref|YP_002994710.1|  38 TKCTTFGTIFAVFAVVLHSIWQLRETNDPKYLQMALHSMVALIALMLTNP 87 
                                       55667788999**************************************9 PP

>> Rhomboid  Rhomboid family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   3.5   1.9e-05     0.057      71     134 ..      33     101 ..       1     103 [. 0.64

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.9e-05
                                       -EESSH.....HHHHHHHHHHHHHHHCCCCGS----HC...CCCCCCCCCCHHHCTSSSTTTHHHHHHH CS
                          Rhomboid  71 plvGaS.....GaifgllgallvlvprnrkllrkliiallllllfillnlvlgllpraggvsnlAHlgG 134
                                        l Ga+     G if++++++l  +++ r++ +   +++ l  +++l+ l+l   ++a +++ +AHl+G
  gi|242399286|ref|YP_002994710.1|  33 RLHGATkcttfGTIFAVFAVVLHSIWQLRETNDPKYLQMALHSMVALIALMLTNPTGAHAIAKAAHLSG 101
                                       445554444448899999999999999999999999994444444444444444444499*******99 PP

>> TssN  Type VI secretion system, TssN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.9     3e-05      0.09      56     141 ..       3      86 ..       1      94 [. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3e-05
                              TssN  56 efvpygyillqilylllGilhlylllkkffkelkekk.ilfeilltlivillglvlfvlv.fnllselqygvwaats 130
                                       e++ y ++++ i + +lG+l l ++ +++ +    +k  +f      i++++++vl++++    +++ +y  +a+ s
  gi|242399286|ref|YP_002994710.1|   3 EIIIYAFLAVSITFNILGSLSLHRFPDVYTRLHGATKcTTF----GTIFAVFAVVLHSIWqLRETNDPKYLQMALHS 75 
                                       57889******************999999998888884333....44444455555554425778999999999999 PP

                              TssN 131 llvfiipllfl 141
                                       +++ i  +l++
  gi|242399286|ref|YP_002994710.1|  76 MVALIALMLTN 86 
                                       99998888776 PP

>> DUF3021  Protein of unknown function (DUF3021)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   2.2   4.1e-05      0.12       2      84 ..       2      86 ..       1      92 [. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.1e-05
                           DUF3021  2 krillgiliGiligliislvislfsgettllestavlkqvllsaliGvlfalaslifese..rlsllkqtlihflvvll 78
                                       +i++++++++ i + i   +sl    ++++ ++ ++k++ +  ++ v++ ++  i++    + +  +q+++h +v l+
  gi|242399286|ref|YP_002994710.1|  2 IEIIIYAFLAVSITFNILGSLSLHRFPDVYTRLHGATKCTTFGTIFAVFAVVLHSIWQLRetNDPKYLQMALHSMVALI 80
                                      5688888888888887777777777777888**************************9884466788999********9 PP

                           DUF3021 79 lvllla 84
                                      +++l++
  gi|242399286|ref|YP_002994710.1| 81 ALMLTN 86
                                      999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       709  (0.0395449); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         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: 723.94
//
Query:       gi|242399287|ref|YP_002994711.1|  [L=94]
Description: Membrane-bound hydrogenase MBH 1, subunit Mbh1B (Na+/H+ transporter subunit) [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.3e-20   73.5   6.2    1.3e-20   73.5   6.2    2.0  2  MrpF_PhaF  Multiple resistance and pH regulation protein F (M
  ------ inclusion threshold ------
        0.7    9.9  11.6      0.039   13.9   5.9    1.8  2  DUF2108    Predicted membrane protein (DUF2108)


Domain annotation for each model (and alignments):
>> MrpF_PhaF  Multiple resistance and pH regulation protein F (MrpF / PhaF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.4     0.049   4.4e+02      30      44 ..      13      27 ..      10      33 .. 0.70
   2 !   73.5   6.2   1.5e-24   1.3e-20       1      52 [.      38      89 ..      38      90 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.049
                         MrpF_PhaF 30 yldvalvlAllgFvg 44
                                      ++  ++ +Al gF+ 
  gi|242399287|ref|YP_002994711.1| 13 FFYGMIGVALAGFIT 27
                                      666777777777764 PP

  == domain 2  score: 73.5 bits;  conditional E-value: 1.5e-24
                         MrpF_PhaF  1 aDRvvAlDllgtllvallallailtgrpayldvalvlAllgFvgtvafarfl 52
                                      +DRvv++D+l+tl+va ++ll++ ++r +y+d+a+v+All+++gt+++a++l
  gi|242399287|ref|YP_002994711.1| 38 PDRVVGVDTLNTLIVAGMILLGVAYDRVIYIDIAIVYALLSYIGTLIIAKYL 89
                                      8**************************************************9 PP

>> DUF2108  Predicted membrane protein (DUF2108)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.3      0.28   2.5e+03      29      39 ..      17      27 ..      14      33 .. 0.69
   2 ?   13.9   5.9   4.4e-06     0.039      32      65 ..      50      86 ..      41      90 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.28
                           DUF2108 29 mlalleaGlil 39
                                      m+++  aG+i 
  gi|242399287|ref|YP_002994711.1| 17 MIGVALAGFIT 27
                                      56666666665 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 4.4e-06
                           DUF2108 32 lleaGlillivakg...YLDVaiavallePvstiill 65
                                      l+ aG+ill va     Y+D+ai+ all  ++t+i+ 
  gi|242399287|ref|YP_002994711.1| 50 LIVAGMILLGVAYDrviYIDIAIVYALLSYIGTLIIA 86
                                      67788888877643344******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.34s 00:00:00.78 Elapsed: 00:00:00.50
# Mc/sec: 568.97
//
Query:       gi|242399288|ref|YP_002994712.1|  [L=169]
Description: Membrane-bound hydrogenase MBH 1, subunit Mbh1A (Na+/H+ transporter subunit) [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-42  145.4   0.8    1.1e-42  145.2   0.8    1.0  1  MNHE      Na+/H+ ion antiporter subunit
  ------ inclusion threshold ------
        1.2    9.2   3.3          2    8.5   3.3    1.3  1  DUF1003   Protein of unknown function (DUF1003)


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 !  145.2   0.8   1.3e-46   1.1e-42       1     145 [.      10     166 ..      10     167 .. 0.91

  Alignments for each domain:
  == domain 1  score: 145.2 bits;  conditional E-value: 1.3e-46
                              MNHE   1 llllflvWllltgs.......lgelllGlllallvalllrrll.......lplrrvllrllayl.lvflweivkanl 62 
                                       ++++f++Wl+lt+        ++el++G ++a +va+ +r+++       l+++r +l++++y+ + ++w +vkanl
  gi|242399288|ref|YP_002994712.1|  10 FIWSFVLWLVLTAGtkgmlwsAEELIAGSIFASIVAFSTRNIIgekttrfLNPVR-WLGFVVYAmGPLFWGMVKANL 85 
                                       69**********999************************9999988875554455.555666654779********* PP

                              MNHE  63 dVakrvlrpklpirpgivkvplrlksdlaltllansitltPGTltvdvdedrrvlyvHvldvedeeeeareeikgrl 139
                                       dVa+rv+++  +i+pgivkvp++l++d++ t+l+nsitltPGTlt+d+  ++++lyvH+++v++ee + +e i g++
  gi|242399288|ref|YP_002994712.1|  86 DVAYRVITG--KIKPGIVKVPVDLENDAQYTILSNSITLTPGTLTIDACPEEKALYVHWIHVTEEEPKTSEIIAGSF 160
                                       ********5..5**************************************************99899999999**** PP

                              MNHE 140 Errlle 145
                                       E+++++
  gi|242399288|ref|YP_002994712.1| 161 EKWARR 166
                                       ***997 PP

>> DUF1003  Protein of unknown function (DUF1003)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   3.3   0.00023         2       1      48 [.       1      46 [.       1      52 [. 0.79

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00023
                           DUF1003  1 mGsakFlvlftaivilWialnllvlpglkpfDpypFillnlvlslqaa 48
                                      mG ++F++ f+  ++lW++l      +   +   + i   ++ s+ a 
  gi|242399288|ref|YP_002994712.1|  1 MGKMSFIIAFIWSFVLWLVLTAGT--KGMLWSAEELIAGSIFASIVAF 46
                                      8******************99775..6666777777777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.50
# Mc/sec: 1023.91
//
Query:       gi|242399289|ref|YP_002994713.1|  [L=71]
Description: RNA-binding protein, containing TRAM domain [Thermococcus sibiricus MM 739]
Scores for complete 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-15   54.5   2.8    9.7e-15   54.3   2.8    1.0  1  TRAM      TRAM domain
  ------ inclusion threshold ------
      0.033   13.9   2.6      0.071   12.9   0.8    2.2  2  Hexapep   Bacterial transferase hexapeptide (six repeats)


Domain annotation for each model (and alignments):
>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.3   2.8   1.1e-18   9.7e-15       2      62 .]      15      71 .]      14      71 .] 0.97

  Alignments for each domain:
  == domain 1  score: 54.3 bits;  conditional E-value: 1.1e-18
                                      XXXXXEEEEEEEEE-.TTSEEEEEET.TEEEEETT--T..TEEEEEEEEEE-SSEEEEEEE CS
                              TRAM  2 syvGstqeVlveglsksegegiGrtdngkvvfvpgdlpgIGdfVeVkItkvkrqyLrGell 62
                                      ++vG+ + V++e  +   g+gi+r++ g+vvfvp+++   Gd+Ve+ I  vkr+++++e++
  gi|242399289|ref|YP_002994713.1| 15 VKVGERYKVKIESIG-QGGDGIARIK-GFVVFVPNTKV--GDEVEIVINSVKRKFAFAEVI 71
                                      68*************.**********.*********99..*******************96 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0     0.071   6.3e+02      18      25 ..      13      20 ..      11      27 .. 0.77
   2 ?   12.9   0.8     8e-06     0.071       9      28 ..      37      56 ..      33      61 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.071
                                      TTEEE-TT CS
                           Hexapep 18 gnVkIGdn 25
                                      ++Vk+G++
  gi|242399289|ref|YP_002994713.1| 13 APVKVGER 20
                                      57888874 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 8e-06
                                      EE-TTEEEETTEEE-TTEEE CS
                           Hexapep  9 lIgpfaviggnVkIGdnvkI 28
                                       I  f+v+ +n+k+Gd v I
  gi|242399289|ref|YP_002994713.1| 37 RIKGFVVFVPNTKVGDEVEI 56
                                      6888**************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.44
# Mc/sec: 482.19
//
Query:       gi|242399290|ref|YP_002994714.1|  [L=420]
Description: Sugar-phosphate nucleotydyltransferase [Thermococcus sibiricus MM 739]
Scores for complete 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-44  151.6   0.2    3.8e-44  151.1   0.2    1.2  1  NTP_transferase  Nucleotidyl transferase
    6.4e-20   70.1  27.7    8.7e-10   37.9   2.5    4.8  6  Hexapep          Bacterial transferase hexapeptide (six repea
      4e-17   63.0   0.0    5.7e-17   62.5   0.0    1.2  1  NTP_transf_3     MobA-like NTP transferase domain
    3.4e-12   45.9  18.1    5.1e-07   29.3   0.3    4.5  4  Hexapep_2        Hexapeptide repeat of succinyl-transferase
    4.1e-05   23.4   0.0    6.4e-05   22.8   0.0    1.4  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
    0.00038   20.3   0.0    0.00057   19.7   0.0    1.4  1  Glycos_transf_2  Glycosyl transferase family 2
  ------ inclusion threshold ------
      0.097   12.1   0.1        0.2   11.1   0.0    1.6  2  ABC_transp_aux   ABC-type uncharacterized transport system
       0.15   12.0   0.0        0.2   11.5   0.0    1.3  1  Glyco_tranf_2_3  Glycosyltransferase like family 2


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.1   0.2   1.7e-47   3.8e-44       1     246 [.       2     232 ..       2     234 .. 0.95

  Alignments for each domain:
  == domain 1  score: 151.1 bits;  conditional E-value: 1.7e-47
                                       EEEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEE CS
                   NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevli 77 
                                       k+vILa G+G+RL PLt +++k ++ v++k  +i++ l++l    ++e  +++ +++++ + e+l++++k +  v++
  gi|242399290|ref|YP_002994714.1|   2 KGVILAAGKGERLNPLTDDRPKVMLKVANK-AIIDYLLENLH-PFVDE-FIIIVRYQKEKLMEYLGDEYKGK-PVTY 74 
                                       79****************************.**********9.57888.8888899999**********988.9*** PP

                                       EEESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEEST.THHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEE CS
                   NTP_transferase  78 alepegkgtAdAvalaaelledeksdelvlvLggDhlikd.ayeeavkkaiekaakgtvtfgivpveeateyGviea 153
                                       + + eg+gtA+A++ a+e++ed++    +l ++gD++++   ++++++ +++++a  ++++++++ ++ + +G+i++
  gi|242399290|ref|YP_002994714.1|  75 VEQVEGEGTAKAIYSAIEYIEDKE----FLAVNGDIYFERdGIKDLLQAFRKSNA--DAALLVKEFKDLSHFGMIKV 145
                                       *********************999....8*********998**************..9******************* PP

                                       CTTSBEEEEECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EE CS
                   NTP_transferase 154 deegrverfvEKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWs 230
                                       ++ + ve+ +EKP +   s +a+ G Y+f++ev++f+ ++ ++++rge eitd+++ +++egk+  +++ ++  yW+
  gi|242399290|ref|YP_002994714.1| 146 KG-DLVEEVKEKPGAV--SGYANLGAYLFKPEVFKFI-ENTSQSQRGEYEITDTINLMIKEGKKVTYAVYEG--YWN 216
                                       98.59********984..69*****************.88********************************..9** PP

                                       EXSSHHHHHHHHHHHH CS
                   NTP_transferase 231 DvGtldslleanekla 246
                                       D+G +  lle ne ++
  gi|242399290|ref|YP_002994714.1| 217 DIGRPWNLLELNEYIL 232
                                       **********998776 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.3   8.1e-07    0.0018      12      34 ..     246     268 ..     243     269 .. 0.91
   2 !   37.9   2.5   3.9e-13   8.7e-10       2      35 ..     254     287 ..     253     288 .. 0.95
   3 !   24.6   0.6   6.3e-09   1.4e-05       3      30 ..     279     306 ..     279     307 .. 0.94
   4 !   13.5   1.0   1.9e-05     0.043       2      28 ..     290     315 ..     289     321 .. 0.88
   5 !    8.1   0.8     0.001       2.3       2      33 ..     307     337 ..     306     340 .. 0.79
   6 !   24.9   4.7   5.2e-09   1.2e-05       1      35 [.     365     399 ..     365     400 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 8.1e-07
                                       TTEEEETTEEE-TTEEEETTEEE CS
                           Hexapep  12 pfaviggnVkIGdnvkIgagvvi 34 
                                        +a+++++V+IG++++I +gv+i
  gi|242399290|ref|YP_002994714.1| 246 EGATVLPPVEIGEGTVIRSGVYI 268
                                       689******************99 PP

  == domain 2  score: 37.9 bits;  conditional E-value: 3.9e-13
                                       EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                       + IG++++I+++++i g+VkIG+n+kIg+++ i+
  gi|242399290|ref|YP_002994714.1| 254 VEIGEGTVIRSGVYIIGPVKIGKNSKIGPNCFIR 287
                                       78*****************************997 PP

  == domain 3  score: 24.6 bits;  conditional E-value: 6.3e-09
                                       EEETTEEE-TTEEEETTEEE-TTEEEET CS
                           Hexapep   3 vIGsnvlIgpfaviggnVkIGdnvkIga 30 
                                       +IG n++I+p++ ig+ ++IG+ v I +
  gi|242399290|ref|YP_002994714.1| 279 KIGPNCFIRPYTSIGDKCHIGNAVEIKN 306
                                       6*********************999976 PP

  == domain 4  score: 13.5 bits;  conditional E-value: 1.9e-05
                                       EEEETTEEE-TTEEEETTEEE-TTEEE CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkI 28 
                                       t IG++++Ig +av   n +I d++ +
  gi|242399290|ref|YP_002994714.1| 290 TSIGDKCHIG-NAVEIKNSIIMDHSNV 315
                                       78********.8888899999999876 PP

  == domain 5  score: 8.1 bits;  conditional E-value: 0.001
                                       EEEETTEEE-TTEEEETTEEE-TTEEEETTEE CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvv 33 
                                       ++I +++ + +  ++ g+ +IG+n+ +gag+ 
  gi|242399290|ref|YP_002994714.1| 307 SIIMDHSNVPHLNYV-GDSIIGENSNLGAGTI 337
                                       567777777777788.8999*********985 PP

  == domain 6  score: 24.9 bits;  conditional E-value: 5.2e-09
                                       TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                           Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                       +++IG nv+ g +++i+++ kIG+n+ +g+gv + 
  gi|242399290|ref|YP_002994714.1| 365 GAIIGHNVKTGINVTIYPGRKIGSNSFVGPGVIVD 399
                                       589*****************************985 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.5   0.0   2.5e-20   5.7e-17       1     127 [.       3     136 ..       3     191 .. 0.84

  Alignments for each domain:
  == domain 1  score: 62.5 bits;  conditional E-value: 2.5e-20
                                       EEEEEESS-TTTT.....TTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..C....HHHHHHTTCTS-EEE-T CS
                      NTP_transf_3   1 aviLAGGrSsRmg.....gdKallplggkpllervldalraagvdevvvvggd..e....evlaalarlgvrvvede 66 
                                       +viLA+G++ R++     ++K +l++++k +++++l++l++  vde ++++++  e     + +++++++v++ve+ 
  gi|242399290|ref|YP_002994714.1|   3 GVILAAGKGERLNpltddRPKVMLKVANKAIIDYLLENLHPF-VDEFIIIVRYqkEklmeYLGDEYKGKPVTYVEQV 78 
                                       79**********7554436***********************.********99543333234446678899999995 PP

                                       TSS-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESSSEE CS
                      NTP_transf_3  67 dpgkgplaslaaalraaadadavlvlacDmPlltpelverllaaaaasgadvvvptyeger 127
                                        +g+g+++++++a++ + +++ +l + +D+ + +++ ++ ll+a+++s+ad++ ++ e + 
  gi|242399290|ref|YP_002994714.1|  79 -EGEGTAKAIYSAIEYI-EDKEFLAVNGDIYF-ERDGIKDLLQAFRKSNADAALLVKEFKD 136
                                       .7**************9.89**********66.*******************999988665 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 !    7.8   0.2    0.0012       2.7      15      32 ..     249     268 ..     246     269 .. 0.86
   2 !   29.3   0.3   2.3e-10   5.1e-07       1      28 [.     271     300 ..     271     304 .. 0.94
   3 !    6.4   0.2    0.0034       7.5       3      14 ..     325     336 ..     324     338 .. 0.85
   4 !   12.0   2.1   6.1e-05      0.14       3      34 .]     367     400 ..     365     400 .. 0.95

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0012
                                       EE..SEEE-TT-EE-TT-EE CS
                         Hexapep_2  15 gi..GvslGdncvvgaGvvi 32 
                                       ++  +v++G++ v+ +Gv+i
  gi|242399290|ref|YP_002994714.1| 249 TVlpPVEIGEGTVIRSGVYI 268
                                       55568**************9 PP

  == domain 2  score: 29.3 bits;  conditional E-value: 2.3e-10
                                       .EEE-TT-EE-TT-EE.S.EEE-TT-EE-T CS
                         Hexapep_2   1 pviIGdnCliGanagi.G.vslGdncvvga 28 
                                       pv+IG+n+ iG+n+ i + +s+Gd+c++g+
  gi|242399290|ref|YP_002994714.1| 271 PVKIGKNSKIGPNCFIrPyTSIGDKCHIGN 300
                                       8***************988*********98 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0034
                                       EE-TT-EE-TT- CS
                         Hexapep_2   3 iIGdnCliGana 14 
                                       iIG+n+++Ga  
  gi|242399290|ref|YP_002994714.1| 325 IIGENSNLGAGT 336
                                       799999999976 PP

  == domain 4  score: 12.0 bits;  conditional E-value: 6.1e-05
                                       EE-TT-EE-TT-EE..SEEE-TT-EE-TT-EE-S CS
                         Hexapep_2   3 iIGdnCliGanagi..GvslGdncvvgaGvvita 34 
                                       iIG n+  G n +i  G ++G n+ vg+Gv++++
  gi|242399290|ref|YP_002994714.1| 367 IIGHNVKTGINVTIypGRKIGSNSFVGPGVIVDK 400
                                       9*******************************86 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 !   22.8   0.0   2.9e-08   6.4e-05       4      97 ..       4     102 ..       1     213 [. 0.76

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 2.9e-08
                                       EEECTTSSCTT-...SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHHHHHGG....CCEEEEE. CS
                              IspD   4 vipAAGsGkRmk...aglpKqflelkgqtllehtvdallaskavdkivvvvseddteefeqllld....ksiqlva. 72 
                                       vi AAG+G+R++    ++pK  l++++++++   ++ l  ++ vd+ +++v+ ++ e+ ++ l+d    k+++ v+ 
  gi|242399290|ref|YP_002994714.1|   4 VILAAGKGERLNpltDDRPKVMLKVANKAIIDYLLENL--HPFVDEFIIIVRYQK-EKLMEYLGDeykgKPVTYVEq 77 
                                       89********8533389*******************98..569*******99999.666666666699966666652 PP

                                       .--SSHHHHHHHHHHTTSSTTSEEEE CS
                              IspD  73 .GGdeRaesVlnglkalegeakfVLv 97 
                                         G+  a++++ +++ +e++ +f  v
  gi|242399290|ref|YP_002994714.1|  78 vEGEGTAKAIYSAIEYIEDK-EFLAV 102
                                       247778999******99888.55544 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 !   19.7   0.0   2.6e-07   0.00057      49     119 ..      62     135 ..      34     203 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 2.6e-07
                                       GCH...C-TTEEEEEESSS-HHHHHHHHHHHH--SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEE CS
                   Glycos_transf_2  49 lak...edprvrvirreenvGkagalnaglraatgdyilflDaDdepdpdwleklvealekdgadvvlgqrpri 119
                                       +     ++++v+++ + e++G a+a+  ++++   + +l ++ D ++++d +++l++a+ k +ad++l    ++
  gi|242399290|ref|YP_002994714.1|  62 YLGdeyKGKPVTYVEQVEGEGTAKAIYSAIEYIEDKEFLAVNGDIYFERDGIKDLLQAFRKSNADAALLVKEFK 135
                                       333455699********************************************************998766555 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 ?   11.1   0.0   8.9e-05       0.2      88     161 ..      70     217 ..      34     254 .. 0.71
   2 ?   -2.7   0.0       1.5   3.3e+03      62      76 ..     345     359 ..     338     390 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 8.9e-05
                    ABC_transp_aux  88 tpvqisveekdelktkrvymglvieygdke............................................... 117
                                       +pv + ++ ++e  +k +y+ +  ++   +                                               
  gi|242399290|ref|YP_002994714.1|  70 KPVTYVEQVEGEGTAKAIYSAIEYIED--Keflavngdiyferdgikdllqafrksnadaallvkefkdlshfgmik 144
                                       555555554555455666665553333..224666666666666666666666666777777777777777777777 PP

                    ABC_transp_aux 118 .............................etipllkn.tsesnlEyeltsairkltdkkkpkvgfltghgelsl 161
                                                                    e+ ++++n +++++ Eye+t+ i  ++++  +kv++    g  ++
  gi|242399290|ref|YP_002994714.1| 145 vkgdlveevkekpgavsgyanlgaylfkpEVFKFIENtSQSQRGEYEITDTINLMIKEG-KKVTYAVYEGYWND 217
                                       77777777777777777777777777777999999996667899*********999988.88888876665555 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.5
                    ABC_transp_aux  62 ggkisvefidpspne 76 
                                       +++i+ve+ d  +++
  gi|242399290|ref|YP_002994714.1| 345 NKNIKVEIKDKLEDS 359
                                       568888888887766 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 ?   11.5   0.0   8.7e-05       0.2      24     133 ..      37     158 ..      21     267 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8.7e-05
                   Glyco_tranf_2_3  24 llaqeypr.vevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralnealravksdlvllvDdDtv 99 
                                       ll + +p  +e++++v   +++  e    l +++++  v++v + +  g  g++ a++ a++ ++++  l v++D  
  gi|242399290|ref|YP_002994714.1|  37 LLENLHPFvDEFIIIVRYQKEKLME---YLGDEYKGKPVTYVEQVE--G-EGTAKAIYSAIEYIEDKEFLAVNGDIY 107
                                       4554444446667777444444444...3457999999**996666..6.488899********************* PP

                   Glyco_tranf_2_3 100 vePdtlkrllqffltpkvgavgtpvfllnrstl.................v 133
                                        e d +k llq+f+ ++++a+   ++++  s++                  
  gi|242399290|ref|YP_002994714.1| 108 FERDGIKDLLQAFRKSNADAALLVKEFKDLSHFgmikvkgdlveevkekpG 158
                                       *************99999999988888877776555555555555555550 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (420 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2667.37
//
Query:       gi|242399291|ref|YP_002994715.1|  [L=368]
Description: hypothetical protein TSIB_1313 [Thermococcus sibiricus MM 739]
Scores for 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-33  112.8   1.9    1.4e-32  112.3   1.9    1.2  1  DUF835    Protein of unknown function (DUF835)
  ------ inclusion threshold ------
      0.061   11.6  10.1       0.08   11.2  10.1    1.1  1  DUF2070   Predicted membrane protein (DUF2070)


Domain annotation for each model (and alignments):
>> DUF835  Protein of unknown function (DUF835)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.3   1.9   1.5e-36   1.4e-32       2     136 .]     229     364 ..     228     364 .. 0.95

  Alignments for each domain:
  == domain 1  score: 112.3 bits;  conditional E-value: 1.5e-36
                            DUF835   2 vkkkekakeilsdlvkegvkvlaitRenpkkirekvkienvkviwltkveeen........tvsPtnlekltetivk 70 
                                       +k+ke+ k+ + ++ +   +v++itRe pk+   kv +en+ v+wltk ee           +sPt++++l++ + k
  gi|242399291|ref|YP_002994715.1| 229 FKSKEELKKAIPNFFD--QNVIMITRELPKD---KV-PENMLVYWLTKMEEDTikadgkiyPISPTRIDVLLHLLTK 299
                                       6899999*********..7*********999...44.*************966778899999*************** PP

                            DUF835  71 flkeaekgvvliDgleyLvlengFesvlkflltlkDavllkngtlilvidkealeekelalLkref 136
                                       +l+++++  v+iDg+eyL++engF+ v+kfll lkD+vl+k+ ++ l+id+++l +k++alL+ref
  gi|242399291|ref|YP_002994715.1| 300 NLESGYN-AVYIDGFEYLMIENGFDIVIKFLLDLKDRVLNKGDVITLIIDPRILTDKQMALLEREF 364
                                       ******6.*********************************************************9 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2  10.1   8.9e-06      0.08      19     211 ..      34     245 ..      18     250 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 8.9e-06
                           DUF2070  19 lliillalligllaflssk...lfgillfglpalvaflltlpvlrilggrltykrslflalltelivviisllaill 92 
                                       + ++ll+ ++++ +++  +    +++ ++ + a +  +l   +l + +++l+ +rs f  ++++ i+v+  ++ ++l
  gi|242399291|ref|YP_002994715.1|  34 ITTALLINALDVESYILTPlgvSIKSGAYDVAAKIPNFLIAGLLVWGSIQLKKERSDFKDVTILGIFVVAAYIWLFL 110
                                       33333333344444444445565555666666778888888888888888999999998888888877765544443 PP

                           DUF2070  93 sall......qalvllalvlslalvfalrllvlvavsdesllkav...lpaliqpllailllvly......fspesf 154
                                        a         ++++ +l+ s+a+ +++ +l +++ s    +k +   +p  +++l a+ l++++      ++p+ f
  gi|242399291|ref|YP_002994715.1| 111 LASEffdrfeHSFTIKSLFPSFAFGASFIYLGYTLRSYVISKKTLeelFPIGLILLGALNLTYPFtrniqaIAPAMF 187
                                       333244888877777777777888888888888766655555555443444444444444455557*********** PP

                           DUF2070 155 llllllslifalavylfivvvdrplkrnlgvsaldllsaFlahileg.skelEeffee 211
                                       ll++++ l+ +++++ f ++    + +  +  + ++   F+    e+ +k++ +ff++
  gi|242399291|ref|YP_002994715.1| 188 LLAAIFRLMAVIGALKFAIYPAAIFAKPKEQMPSKIRGTFMFKSKEElKKAIPNFFDQ 245
                                       *********************9999999999999999999999999999999999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2536.56
//
Query:       gi|242399292|ref|YP_002994716.1|  [L=390]
Description: inosine monophosphate dehydrogenase-like protein [Thermococcus sibiricus MM 739]
Scores for complete 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-36  122.8  15.8    8.7e-17   61.3   0.6    4.4  4  CBS          CBS domain
  ------ inclusion threshold ------
       0.09   13.3   0.2       0.39   11.3   0.1    2.0  2  Hrs_helical  Hepatocyte growth factor-regulated tyrosine kina
       0.18   11.7   0.0       0.84    9.5   0.0    2.0  2  DUF1508      Domain of unknown function (DUF1508)


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 !   19.6   0.1   1.5e-07   0.00091       1      51 [.       6      55 ..       6      60 .. 0.81
   2 !   15.3   0.2   3.4e-06      0.02      11      56 ..      78     123 ..      69     124 .. 0.74
   3 !   61.3   0.6   1.5e-20   8.7e-17       1      52 [.     132     183 ..     132     187 .. 0.97
   4 !   34.8   1.3   2.7e-12   1.6e-08       2      52 ..     211     261 ..     210     265 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.5e-07
                                      HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTB.EEEEEEHHHH CS
                               CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgk.lvGivtlrDl 51
                                      V ++mt+++  ++ +++l+ea+ ++ ek+   l VV  dgk + G++t+  +
  gi|242399292|ref|YP_002994716.1|  6 VQEVMTEKFAKIDINAPLSEAIGIF-EKEDPDLIVV-FDGKiYKGVLTQDLI 55
                                      789**********************.5554677687.5787355****8655 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 3.4e-06
                                       EEETTSBHHHHHHHHHHHTSSEEEEEETTTB.EEEEEEHHHHHHHHH CS
                               CBS  11 tvppdttleealelmrekgvsrlPVVdedgk.lvGivtlrDllrall 56 
                                        +  d++l+ a++lm e+++++lPV  +d+k ++G++++  ll+ ++
  gi|242399292|ref|YP_002994716.1|  78 ILELDEDLSIAAKLMFETDLRSLPVG-KDKKtILGVISDITLLERIA 123
                                       455677799*****65888******7.5554288********99886 PP

  == domain 3  score: 61.3 bits;  conditional E-value: 1.5e-20
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDll 52 
                                       V+d+mt+dvvt++ ++t+++al +mr++++sr+PVVde+gkl G+vtl+Dl+
  gi|242399292|ref|YP_002994716.1| 132 VEDFMTKDVVTLRSSDTVAKALATMRDYAISRIPVVDENGKLEGLVTLHDLI 183
                                       89*************************************************8 PP

  == domain 4  score: 34.8 bits;  conditional E-value: 2.7e-12
                                       HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHH CS
                               CBS   2 gdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDll 52 
                                       +d+m + v+tv+p+t ++ea+ l++e+++++l +++ ++ + G++t +Dll
  gi|242399292|ref|YP_002994716.1| 211 RDVMIKGVITVYPETMVREAISLIKEYDIDGLVIINQENVVKGVLTVKDLL 261
                                       79**********************9999****6679888666********9 PP

>> Hrs_helical  Hepatocyte growth factor-regulated tyrosine kinase substrate
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.57   3.4e+03      45      66 ..     116     137 ..      82     160 .. 0.76
   2 ?   11.3   0.1   6.5e-05      0.39      10      59 ..     328     380 ..     322     387 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.57
                       Hrs_helical  45 sqllkriqeqeekraeyeslqd 66 
                                        +ll+ri+++e  ++++e +  
  gi|242399292|ref|YP_002994716.1| 116 ITLLERIAKEEFGKKKVEDFMT 137
                                       4688999999888888887654 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 6.5e-05
                       Hrs_helical  10 veifvnrmksnsarGrsianDs...avqslFqkltamhsqllkriqeqeekra 59 
                                       v +++ rm+ ++ +G+ +a+ +   a+q+++  + a++ q+l++++ q e+++
  gi|242399292|ref|YP_002994716.1| 328 VHLYQARMRLVTDKGQFMATGEtwgAIQAVHDAIRAIERQILQKVELQRETKH 380
                                       788999*************9973336*******************99988775 PP

>> DUF1508  Domain of unknown function (DUF1508)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       0.5     3e+03      24      39 ..     284     299 ..     283     301 .. 0.83
   2 ?    9.5   0.0   0.00014      0.84       6      39 ..     333     366 ..     332     370 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.5
                                       BSSHHHHHHHHHHHHH CS
                           DUF1508  24 YsskaaaenGIesVkk 39 
                                       Y s  ++e+ Ie V+k
  gi|242399292|ref|YP_002994716.1| 284 YLSDFSRERIIEDVRK 299
                                       55666899******98 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00014
                                       EEEEEE-TTS-EEEEEEEBSSHHHHHHHHHHHHH CS
                           DUF1508   6 frFrLkaaNgevIatsegYsskaaaenGIesVkk 39 
                                        r rL+ + g+ +at+e+  + +a+ ++I+++ +
  gi|242399292|ref|YP_002994716.1| 333 ARMRLVTDKGQFMATGETWGAIQAVHDAIRAIER 366
                                       688***************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 2505.85
//
Query:       gi|242399293|ref|YP_002994717.1|  [L=167]
Description: hypothetical protein TSIB_1315 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0033   17.2   0.6     0.0049   16.7   0.6    1.2  1  DUF2238   Predicted membrane protein (DUF2238)
      0.004   17.8   0.9     0.0074   16.9   0.9    1.5  1  VanZ      VanZ like family
     0.0087   16.4   0.0      0.028   14.8   0.0    1.8  1  COX7a     Cytochrome c oxidase subunit VII


Domain annotation for each model (and alignments):
>> DUF2238  Predicted membrane protein (DUF2238)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.6   8.2e-07    0.0049      33     109 ..      40     120 ..      23     128 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 8.2e-07
                           DUF2238  33 vGghYtYaevplddwlkelfglernkYDrlvHfaqGlllalvvrelllrkkkl......rkwllllavlvvlaisal 103
                                       ++ h    +vp+   + +lf+ e  + D + Hf+ G+++ ++ +e+ll+ ++       r+ l+l ++l++  +s  
  gi|242399293|ref|YP_002994717.1|  40 IAVHVSLVNVPFT--TIDLFHKEWRNADMVSHFLGGMVVWVITAEILLNLSNEkylnlaRRKLILYSFLALFFLSFG 114
                                       5555556677776..668999999999*******************8776655456886556888888888999999 PP

                           DUF2238 104 YEliEw 109
                                       +E++E 
  gi|242399293|ref|YP_002994717.1| 115 WEVVEK 120
                                       999996 PP

>> VanZ  VanZ like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.9   1.2e-06    0.0074      36     122 ..      46     154 ..      20     158 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.2e-06
                              VanZ  36 l..ipfkeikrllke.re..lea.livgnvalfvplGfllplllkkk...flk......vlllgfllslsiElhQlf 97 
                                       l  +pf++i  + ke r+  +   ++ g v++ +   +ll l  +k      +      ++l  f+ls++ E++  +
  gi|242399293|ref|YP_002994717.1|  46 LvnVPFTTIDLFHKEwRNadMVShFLGGMVVWVITAEILLNLSNEKYlnlA-RrklilySFLALFFLSFGWEVVEKL 121
                                       334799999999544322334443446677777777777777776657651.1455666888899**********99 PP

                              VanZ  98 vp........gRsfdvdDvilntlGallGilly 122
                                                   + +v+D i+ntlG+l +++l+
  gi|242399293|ref|YP_002994717.1| 122 SEseisfiheSTVNKVRDSIMNTLGGLSALYLV 154
                                       999*****995599*************887766 PP

>> COX7a  Cytochrome c oxidase subunit VII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   4.7e-06     0.028      19      42 ..      92     115 ..      88     118 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.7e-06
                             COX7a  19 wlrgprsklylypyyalfavgllg 42 
                                       +l   r+kl+ly ++alf+ ++++
  gi|242399293|ref|YP_002994717.1|  92 YLNLARRKLILYSFLALFFLSFGW 115
                                       89999****************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       774  (0.0431703); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); 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: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 1247.39
//
Query:       gi|242399294|ref|YP_002994718.1|  [L=204]
Description: ABC-type cobalt transport system, CbiM permease component [Thermococcus sibiricus MM 739]
Scores for complete 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-62  209.1  19.7    6.9e-62  209.0  19.7    1.0  1  CbiM             Cobalt uptake substrate-specific transmembra
     0.0016   18.0   0.2       0.12   12.1   0.0    3.3  3  DUF3149          Protein of unknown function (DUF3149)


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 !  209.0  19.7   7.7e-66   6.9e-62       1     206 [.       2     198 ..       2     199 .. 0.97

  Alignments for each domain:
  == domain 1  score: 209.0 bits;  conditional E-value: 7.7e-66
                              CbiM   1 HipdgiLspavllaayavalallalalrrlrkeldearvpllallaafifaaqminipipggtslHllgavlaaiLl 77 
                                       Hipdg+Ls++v++++y++++++l+++lr+l++   e+++pll+l+aa ifaaqm+n+pi gg+s+Hllgavlaa+Ll
  gi|242399294|ref|YP_002994718.1|   2 HIPDGLLSLPVIAITYVLTIGILGYSLRKLKDF-PEEKIPLLGLFAAGIFAAQMVNFPIIGGVSGHLLGAVLAAVLL 77 
                                       *******************************98.9999*************************************** PP

                              CbiM  78 GpwaaflavavvlllqallfgdGGitaLGaNilnmavigvllaylvyrllsrlasskkrvalaaflaallsvvlaal 154
                                       Gp+aa+l+++ vll+q+llfgdGGita+GaNilnm++ g++++y++y  l     ++ ++a++++la + +vvl+a+
  gi|242399294|ref|YP_002994718.1|  78 GPYAAVLIMTAVLLIQTLLFGDGGITAIGANILNMGITGAFAGYWIYSKL-----KNFSEAFGIALASWSAVVLGAF 149
                                       ************************************************99.....45579***************** PP

                              CbiM 155 lvalelalsgleaslsltaalaamllvhlpvgilEgviTaaivkalkkvrpe 206
                                       l+++e+++s++   l++ ++l +m+  h ++gi+E++iT+++v+alk+  pe
  gi|242399294|ref|YP_002994718.1| 150 LASVEIGVSHS---LPFGKVLGLMVGYHTVIGIGEALITLFVVNALKSRLPE 198
                                       *********55...59******************************998776 PP

>> DUF3149  Protein of unknown function (DUF3149)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   1.3e-05      0.12      10      35 ..       6      31 ..       4      35 .. 0.93
   2 ?   -1.5   0.1      0.23   2.1e+03      22      33 ..     113     124 ..     110     128 .. 0.85
   3 ?    1.4   0.0     0.028   2.5e+02      20      35 ..     176     191 ..     174     194 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.3e-05
                           DUF3149 10 GLlSliVIvftigmgaffiryFirKm 35
                                      GLlSl VI++t ++   +++y +rK 
  gi|242399294|ref|YP_002994718.1|  6 GLLSLPVIAITYVLTIGILGYSLRKL 31
                                      9********************99996 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.23
                           DUF3149  22 gmgaffiryFir 33 
                                       g+ + f++y i+
  gi|242399294|ref|YP_002994718.1| 113 GITGAFAGYWIY 124
                                       889999999887 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.028
                           DUF3149  20 tigmgaffiryFirKm 35 
                                       +ig+g   i++F+++ 
  gi|242399294|ref|YP_002994718.1| 176 VIGIGEALITLFVVNA 191
                                       89**********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       759  (0.0423336); 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:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1397.38
//
Query:       gi|242399295|ref|YP_002994719.1|  [L=82]
Description: hypothetical protein TSIB_1318 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-05   24.8   3.0    1.9e-05   24.5   0.0    2.1  2  PDGLE     PDGLE domain
  ------ inclusion threshold ------
      0.042   13.9   3.7       0.15   12.1   0.1    2.2  2  PsbX      Photosystem II reaction centre X protein (PsbX)


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 !   24.5   0.0   2.1e-09   1.9e-05       3      31 ..      11      39 ..       8      51 .. 0.81
   2 ?    0.7   0.9     0.057   5.1e+02      71      88 ..      59      76 ..      42      77 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 2.1e-09
                             PDGLE  3 alliggvlswfASanPdGLEwsiekvagt 31
                                       l++  ++ +fAS nPdGLE ++ekv  +
  gi|242399295|ref|YP_002994719.1| 11 ILILLAIALPFASDNPDGLEATMEKVHLE 39
                                      5667778889***************9544 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.057
                             PDGLE 71 vAgivGvlltlalaglig 88
                                      + g +G+ l+++ ++++g
  gi|242399295|ref|YP_002994719.1| 59 IMGAIGITLVFGAVYGLG 76
                                      568899999999888876 PP

>> PsbX  Photosystem II reaction centre X protein (PsbX)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   1.7e-05      0.15      11      31 ..       3      23 ..       1      26 [. 0.91
   2 ?    2.8   0.6     0.013   1.2e+02      11      29 ..      57      69 ..      53      75 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.7e-05
                                      HHHHHH.HHHHHHHHHHHHHH CS
                              PsbX 11 SLvaGalvVvipiaaaLifvS 31
                                      S+v G l+++i +a+aL f S
  gi|242399295|ref|YP_002994719.1|  3 SIVKGLLIILILLAIALPFAS 23
                                      9****************9987 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.013
                                      HHHHHH.HHHHHHHHHHHH CS
                              PsbX 11 SLvaGalvVvipiaaaLif 29
                                      SL++Ga      i + L+f
  gi|242399295|ref|YP_002994719.1| 57 SLIMGA------IGITLVF 69
                                      555555......5544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 499.36
//
Query:       gi|242399296|ref|YP_002994720.1|  [L=218]
Description: ABC-type cobalt transport system, CbiQ permease component [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-27   94.9  11.6    6.6e-27   94.5  11.6    1.1  1  CbiQ      Cobalt transport protein


Domain annotation for each model (and alignments):
>> CbiQ  Cobalt transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.5  11.6   3.7e-31   6.6e-27      14     211 ..       3     193 ..       1     199 [. 0.86

  Alignments for each domain:
  == domain 1  score: 94.5 bits;  conditional E-value: 3.7e-31
                                       HHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHTTS---..HHHHHHHCCCHCHHHHHHHHHHE.......EECTTEEE CS
                              CbiQ  14 liwlfllllalvlapnlvtlliiiallllllllvilp..rvlaqalilpllflllgllillfqlittegefvfaggg 88 
                                       li++f++ l++v  ++l  l    +l +l++l+ +++  r+l++ l+  +l+ + g+l++l  l+t+ + +v++++g
  gi|242399296|ref|YP_002994720.1|   3 LIFIFIYALVIVTRTSLAEL--FYFLPILMVLILLFKpkRMLFKHLG--FLLGFEGFLFILA-LFTPGDPLVTTPLG 74 
                                       66666666666665555555..4455444444444444488888888..8888888888888.789999******** PP

                                       ...E-TTHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHHHHCCCSS--HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              CbiQ  89 qisitseGllrglllalRiltllslllllalTTppeeltsslerlgvPlelalillLayRfiflLleevqrikqAqk 165
                                         +itseG++r  ll+++ + ++s+++ ++ +  ++ l+ ++e l+ P+ l+l+l+ +yR++ l+ ee+ r+k+A +
  gi|242399296|ref|YP_002994720.1|  75 --TITSEGIQRFSLLLGKAFLSSSAVVVISNSLGFPYLLGEMEALRFPRILVLTLAFTYRYLELFEEEALRMKRALD 149
                                       ..*************************************************************************** PP

                                       HTTTTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS-SS CS
                              CbiQ 166 lRlgdsklgirrslrslgkliaalflralkraervalAmeaRGYtg 211
                                       +R++++  g  + +r+lg li++ f ra+ r+ ++  Am +RG+  
  gi|242399296|ref|YP_002994720.1| 150 SRAFNI--GKIEYYRKLGALIGETFARAYIRSIKIHWAMLSRGFGE 193
                                       ******..99999*******************************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1430.04
//
Query:       gi|242399297|ref|YP_002994721.1|  [L=262]
Description: ABC-type cobalt transport system, ATPase component [Thermococcus sibiricus MM 739]
Scores for complete 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  106.3   0.0    2.5e-30  105.8   0.0    1.2  1  ABC_tran     ABC transporter
    7.2e-09   35.9   1.5    0.00017   21.5   0.1    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    2.3e-08   33.7   0.1    1.1e-07   31.6   0.1    1.8  1  SMC_N        RecF/RecN/SMC N terminal domain
    0.00047   19.9   0.0    0.00083   19.0   0.0    1.4  1  AAA_29       P-loop containing region of AAA domain
    0.00095   19.7   1.3     0.0011   19.6   1.3    1.5  1  AAA_23       AAA domain
     0.0011   19.0   0.9       0.09   12.7   0.1    2.1  2  NTPase_1     NTPase
     0.0026   17.7   0.1     0.0045   16.9   0.1    1.3  1  RsgA_GTPase  RsgA GTPase
     0.0061   15.6   0.0     0.0087   15.1   0.0    1.2  1  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
  ------ inclusion threshold ------
      0.028   14.0   0.1      0.053   13.1   0.1    1.4  1  cobW         CobW/HypB/UreG, nucleotide-binding domain
      0.056   13.1   1.0       0.17   11.5   0.4    1.7  2  AAA_15       AAA ATPase domain
      0.081   12.8   0.0       0.17   11.8   0.0    1.5  1  Elf4         Early Flowering 4 domain
      0.084   13.1   0.1        1.4    9.2   0.1    2.1  1  SbcCD_C      Putative exonuclease SbcCD, C subunit
       0.12   12.2   0.0       0.32   10.9   0.0    1.6  2  Rad17        Rad17 P-loop domain
       0.12   11.1   0.1       0.17   10.7   0.1    1.1  1  DLIC         Dynein light intermediate chain (DLIC)
       0.16   11.7   0.1         15    5.3   0.0    2.2  2  IstB_IS21    IstB-like ATP binding protein
       0.16   12.1   0.1       0.24   11.5   0.1    1.5  1  MMR_HSR1     50S ribosome-binding GTPase
       0.17   11.6   0.0       0.29   10.8   0.0    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 !  105.8   0.0   2.4e-33   2.5e-30       1     137 []      17     162 ..      17     162 .. 0.91

  Alignments for each domain:
  == domain 1  score: 105.8 bits;  conditional E-value: 2.4e-33
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS..--S-TTSB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe..pqlfpelt 75 
                                       lk++slk++ ge+ +i+G+nGaGKStL+  l g lkp+eG++ ++g ++++ + +++rk +g+++q+  +qlf+ + 
  gi|242399297|ref|YP_002994721.1|  17 LKDISLKINDGEVFGILGPNGAGKSTLILHLNGILKPKEGKVIVNGIEVNK-KPKEARKIVGIVFQDpnDQLFSPK- 91 
                                       79*************************************************.88999**********888888888. PP

                                       HHHH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  76 vren.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       v +              e +e++ kal+ +g+ +   +      ++LS G+k+rva+a +l+ +p++l++DEp+a
  gi|242399297|ref|YP_002994721.1|  92 VFDDvafgpynlglrgrELEERVVKALRLVGMGDYIYRET----KELSFGEKKRVAIATVLAMEPEILVFDEPFA 162
                                       77778********988888888888888888888555555....*****************************85 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.9   3.4e-05     0.035       2      23 ..      30      51 ..      29      95 .. 0.73
   2 !   21.5   0.1   1.7e-07   0.00017     219     298 ..      96     191 ..      45     195 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.4e-05
                            AAA_21  2 nvliGpNgsGKSnLLdaldlla 23
                                       ++ GpNg+GKS+L+  l ++ 
  gi|242399297|ref|YP_002994721.1| 30 FGILGPNGAGKSTLILHLNGIL 51
                                      689***********98887774 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 1.7e-07
                            AAA_21 219 r....................gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHP... 272
                                       +                     ++++ +gd+  +   elS G k+  a++t l+  +    +l++DEp ++L+    
  gi|242399297|ref|YP_002994721.1|  96 VafgpynlglrgreleervvkALRLVGMGDYIYRETKELSFGEKKRVAIATVLAMEP---EILVFDEPFANLDFrgk 169
                                       0444555555555555556668888999999999999******************99...9*************888 PP

                            AAA_21 273 kllrrllellkelsrngaQviltTHS 298
                                       k+lr+l+e ++ +      +il++H 
  gi|242399297|ref|YP_002994721.1| 170 KMLRELIEKFRGE----KTIILSSHE 191
                                       8888888777444....459999995 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 !   31.6   0.1     1e-10   1.1e-07      25     211 ..      28     204 ..       4     210 .. 0.83

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 1e-10
                                       SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--..BTTCSSTTEEEEEEEEEETTEESSSSSSCEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk..skekasvkkaeveitfdnedkklkiekeevsi 99 
                                       ++  i+GpNG+GKs l+  +    G      l+ ++ + +++    ++k++  +  v i+f++++++l   k    +
  gi|242399297|ref|YP_002994721.1|  28 EVFGILGPNGAGKSTLILHL---NG-----ILKPKEGKVIVNGieVNKKPKEARKIVGIVFQDPNDQLFSPKVFDDV 96 
                                       35579**********97555...44.....47778877777774334445555556***********8888888888 PP

                                       EEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 100 srrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknv 176
                                           ++ g    +++++ v+   +  +      + ++LS Gek+ va+a ++A++   p+ + ++De  a+LD++  
  gi|242399297|ref|YP_002994721.1|  97 AFGPYNLGLRGRELEERVVKALRLVGMGDYIYRETKELSFGEKKRVAIATVLAME---PE-ILVFDEPFANLDFRGK 169
                                       88899999999999999999999999999999999****************9985...44.789************* PP

                                       HHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 177 kkvaellkeksknaQfivislreemlekadklvgv 211
                                       k + el+++ + +  +i  s+++e l+ +d++v +
  gi|242399297|ref|YP_002994721.1| 170 KMLRELIEKFRGEKTIILSSHEAEYLTLCDRIVLL 204
                                       ****************************9998865 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   7.9e-07   0.00083      14      52 ..      19      58 ..       7      63 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 7.9e-07
                            AAA_29 14 ghtieidlkgatlltGpsGsGKSTllDAiqalLvpak.kv 52
                                      + +++i+  +++ + Gp+G+GKSTl+  ++ +L p++ kv
  gi|242399297|ref|YP_002994721.1| 19 DISLKINDGEVFGILGPNGAGKSTLILHLNGILKPKEgKV 58
                                      4566777445999************988888887776555 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   1.3     1e-06    0.0011      15      42 ..      20      50 ..       8     260 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1e-06
                            AAA_23 15 idF...skgltlItGpNGaGKTTildAikla 42
                                      i +   +  ++ I GpNGaGK+T++  +  +
  gi|242399297|ref|YP_002994721.1| 20 ISLkinDGEVFGILGPNGAGKSTLILHLNGI 50
                                      4445545579**************9666555 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.1   8.6e-05      0.09       3      45 ..      31      75 ..      29     122 .. 0.77
   2 ?    5.0   0.1      0.02        21      94     156 ..     150     213 ..     121     222 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.6e-05
                                      EEE--TTSSHHHHHHHHHHHH.....GGGEEEEEEEEE------- CS
                          NTPase_1  3 fiTGppGvGKtTlvkkvlellkss..gvkvgGfyteevreggrri 45
                                       i Gp G GK+Tl+  +   lk +   v v+G+ +++  ++ r+i
  gi|242399297|ref|YP_002994721.1| 31 GILGPNGAGKSTLILHLNGILKPKegKVIVNGIEVNKKPKEARKI 75
                                      577******************876446899999999888777776 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.02
                                       HHH-EEEE--.-STTGGG-HHHHHHHHHHHTTTSEEEEE--SS--SHHHHHHHT-TT-EEEE-- CS
                          NTPase_1  94 seadviviDE.iGkmElkskkfkeaveevLksekpvlavihrrkdlalveeirerkdvkvfevt 156
                                        e++++v DE   ++ +  kk+ +++ e ++ ek ++   h+++ l l ++i   +++k++++ 
  gi|242399297|ref|YP_002994721.1| 150 MEPEILVFDEpFANLDFRGKKMLRELIEKFRGEKTIILSSHEAEYLTLCDRIVLLSEGKIVKIG 213
                                       6899999999668999999***999999***************************99*999985 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   4.3e-06    0.0045      81     126 ..       8      54 ..       2      63 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.3e-06
                                       E--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT---- CS
                       RsgA_GTPase  81 lvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallpelelk 126
                                         s +++e l++++ +++d ++  ++G+ G+GKStLi +l++ l+ k
  gi|242399297|ref|YP_002994721.1|   8 HFSYNNREVLKDISLKINDgEVFGILGPNGAGKSTLILHLNGILKPK 54 
                                       5677889999****9999999****************9999866655 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 !   15.1   0.0   8.2e-06    0.0087       7      62 ..       4      60 ..       1      70 [. 0.84

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 8.2e-06
                                      HHH--SH.HHHHHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEE CS
                              MeaB  7 lveserp.eakellerllakaGraqvvGltGvPGaGkstlvealglelrrrGkrvav 62
                                      lv+ + + + +e+l+ ++ k    +v G+ G  GaGkstl+ +l   l+ +  +v v
  gi|242399297|ref|YP_002994721.1|  4 LVNVHFSyNNREVLKDISLKINDGEVFGILGPNGAGKSTLILHLNGILKPKEGKVIV 60
                                      555555557899*******************************99999888777766 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 ?   13.1   0.1   5.1e-05     0.053       2      37 ..      29      64 ..      28      75 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.1e-05
                                      EEEEEESTTCCHHHHHHHHHCT--SS-EEEEESS-S CS
                              cobW  2 vtvltGflGsGKTtLlnhllenraglklavivNefg 37
                                      v+++ G+ G+GK+tL+ hl    + ++  vivN + 
  gi|242399297|ref|YP_002994721.1| 29 VFGILGPNGAGKSTLILHLNGILKPKEGKVIVNGIE 64
                                      67899**************98888899999999876 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.4   0.00016      0.17      14      67 ..      17      67 ..      12      89 .. 0.76
   2 ?    0.3   0.1      0.44   4.6e+02     282     364 ..     111     190 ..      61     195 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00016
                            AAA_15 14 lkdveidlsee.ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedlei 67
                                      lkd+++++++  +  + G+N++GKS+++  l+ +l+ k    + ++ ++  ++++
  gi|242399297|ref|YP_002994721.1| 17 LKDISLKINDGeVFGILGPNGAGKSTLILHLNGILKPK----EGKVIVNGIEVNK 67
                                      6888888888778899****************999999....3333333333333 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.44
                            AAA_15 282 eeieik........ddeelplnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllke 350
                                       ee+ +k        d  + + ++ ++G +  + +++ +++ e        + il+++EP a+L    +k+l +l+ +
  gi|242399297|ref|YP_002994721.1| 111 EERVVKalrlvgmgDYIYRETKELSFGEKKRVAIATVLAM-E--------PEILVFDEPFANLDFRGKKMLRELIEK 178
                                       5555555555555444444555556666666665554432.2........347889998888877777777777776 PP

                            AAA_15 351 landnktQviitTH 364
                                          ++   +i+++H
  gi|242399297|ref|YP_002994721.1| 179 FRGEKT--IILSSH 190
                                       666663..777776 PP

>> Elf4  Early Flowering 4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00016      0.17      40      80 ..     215     255 ..     210     258 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00016
                              Elf4  40 pdnlsrnvaLirelNgNIskvvslYsdLslsfsksveasse 80 
                                       p+++ rn +L+re N  +   ++l+s L l+  +s+e++++
  gi|242399297|ref|YP_002994721.1| 215 PEEILRNAGLLREHNLDVPSLIDLFSSLGLEIPRSLEEAKR 255
                                       8999**************************99999998876 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 ?    9.2   0.1    0.0013       1.4      27      88 ..     128     176 ..     109     178 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0013
                           SbcCD_C  27 srssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllell 88 
                                       +r++++lS Gek + +++a ++a              ++++++DE F++lD +  + l el+
  gi|242399297|ref|YP_002994721.1| 128 YRETKELSFGEK-KRVAIATVLA------M------EPEILVFDEPFANLDFRGKKMLRELI 176
                                       555666666666.3333333322......2......4789**********987776666665 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0    0.0003      0.32      33      89 ..      15      72 ..       7      96 .. 0.79
   2 ?   -2.5   0.0       3.8     4e+03     108     137 ..     160     187 ..     139     189 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0003
                             Rad17 33 ewlkadvLesrkkriLLisGPsGCgkstvvkvLskelgiklre.wlnpvslkepdnqk 89
                                      e lk  +L+ +  ++  i GP G gkst +  L  +l +k  +  +n++++++ + + 
  gi|242399297|ref|YP_002994721.1| 15 EVLKDISLKINDGEVFGILGPNGAGKSTLILHLNGILKPKEGKvIVNGIEVNKKPKEA 72
                                      56777778888888999*******************9998755156888876666554 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.8
                             Rad17 108 sfkeleLkdakylklqklGddlrtdkklil 137
                                        f +l  ++ k   l+ l ++ r++k +il
  gi|242399297|ref|YP_002994721.1| 160 PFANLDFRGKKM--LRELIEKFRGEKTIIL 187
                                       455566666655..6667777777777776 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00016      0.17      17      56 ..      19      58 ..       9      78 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00016
                              DLIC 17 rsssklPsgksvlvlGedgsGkttliaklqGveeekkGrG 56
                                        s k+  g    +lG +g+Gk+tli  l G+ ++k G+ 
  gi|242399297|ref|YP_002994721.1| 19 DISLKINDGEVFGILGPNGAGKSTLILHLNGILKPKEGKV 58
                                      55667777777889**********************9985 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.014        15      44      65 ..      24      45 ..       8      57 .. 0.84
   2 ?    4.3   0.0     0.028        30     106     148 ..     149     190 ..     111     194 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.014
                         IstB_IS21 44 iekkenivllGpsGvGKshlai 65
                                      i++ e + +lGp G+GKs l  
  gi|242399297|ref|YP_002994721.1| 24 INDGEVFGILGPNGAGKSTLIL 45
                                      67788899**********8865 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.028
                         IstB_IS21 106 llkvdllilDdlgllpldqaeaellfeviekryerrsiiitsn 148
                                        +++++l+ D+  + +ld   +++l e+iek  + ++ii++s 
  gi|242399297|ref|YP_002994721.1| 149 AMEPEILVFDE-PFANLDFRGKKMLRELIEKFRGEKTIILSSH 190
                                       34568999999.5889999*********************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 ?   11.5   0.1   0.00023      0.24       2      42 ..      30      81 ..      29     186 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00023
                                      EEEEESTTSSHHHHHHHHHT...........STEEESSSTTSSSSEEEEEEE CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltg...........ekaivsdkpgtTrdinegrvk 42
                                      ++i+G   +GKStLi  l g           +  +v++kp   r+i+ + ++
  gi|242399297|ref|YP_002994721.1| 30 FGILGPNGAGKSTLILHLNGilkpkegkvivNGIEVNKKPKEARKIVGIVFQ 81
                                      589************9998766666554443345778888877777766665 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   0.00028      0.29      19      51 ..      28      60 ..      20      68 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00028
                            AAA_30 19 rvavltGpAGtGKttalkalreaweaaggrvig 51
                                       v  + Gp G+GK+t++ +l+ +++ ++g+vi+
  gi|242399297|ref|YP_002994721.1| 28 EVFGILGPNGAGKSTLILHLNGILKPKEGKVIV 60
                                      478899******************999888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); expected 358.6 (0.02)
Passed Vit filter:                        97  (0.00541023); 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: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 1770.55
//
Query:       gi|242399298|ref|YP_002994722.1|  [L=831]
Description: Phosphorylase [Thermococcus sibiricus MM 739]
Scores for complete 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-43  147.1   0.0    1.8e-30  105.9   0.0    4.1  3  Phosphorylase  Carbohydrate phosphorylase
    4.4e-29  101.1   2.9    4.4e-29  101.1   2.9    2.2  2  DUF3417        Protein of unknown function (DUF3417)


Domain annotation for each model (and alignments):
>> Phosphorylase  Carbohydrate phosphorylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0   7.5e-11   6.7e-07      22      73 ..     123     175 ..     118     229 .. 0.86
   2 !  105.9   0.0     2e-34   1.8e-30     216     581 ..     266     610 ..     260     621 .. 0.84
   3 !    4.1   0.2    0.0013        12     669     709 ..     647     688 ..     633     690 .. 0.81

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 7.5e-11
                                       SSHHHHHHHHHHHHHHHTT-EEEEEEE--SCESEEEEE.ETTEEEEEEEBTTC CS
                     Phosphorylase  22 nGGLGRLAacfldslatlelpavGygirYeyGlFkQki.edgaqveepdeWlk 73 
                                        GGLG LA  +l +++ l+lp +G+g+ Y++G FkQ+i ++g+q+e+  e+  
  gi|242399298|ref|YP_002994722.1| 123 SGGLGILAGDHLKTASDLGLPFIGIGLLYKHGYFKQQIdKNGNQIEVFPEYDP 175
                                       59************************************889****98666555 PP

  == domain 2  score: 105.9 bits;  conditional E-value: 2e-34
                                       HHEEEEEESSTTTTHHHHHHHHH.HHCC---HHHHHHHHCCCEEEEE--SSGGGS-EEEHHHHHHHSHHHHHHHHHH CS
                     Phosphorylase 216 ekvaiqlnDtHPalaipelmriL.vdeeglewdeaweitkktfaytnhtvlpealekwpvellekllprhleiieei 291
                                       e+++i+ln+ HPa+a  ++ ri    eegl++ ea++i+++t+ +t ht +p   +k+p+  +ek l + le i + 
  gi|242399298|ref|YP_002994722.1| 266 ESAVIHLNEGHPAFA--NFQRIAwYMEEGLNFLEALTIVRATTIFTTHTPVPAGHDKFPIVEVEKRLAKFLEGIPK- 339
                                       5789********987..55665314788*******************************99999988877765543. PP

                                       HHHHHHHHHHHSTT-HHHHHHHSSEETSCEEEHHHHHHHCCSEEEESSHHHHHHHHHTTTHHHHHHSGGGE..EE-- CS
                     Phosphorylase 292 nerfleevekklpedeeklerlsiieeekkvrmanlaivgshsvngvaalhsellkkevlkdfyelypekf..nnkt 366
                                        e+fl+                   +e ++ +m  l+i +s+ vn+v++lh+ + k+   + +  + p+ +  + +t
  gi|242399298|ref|YP_002994722.1| 340 -EEFLNLG-----------------REGEEFNMTLLSIRTSSYVNAVSKLHTAVTKEMWKELWKGVPPDEMpvEGIT 398
                                       .3343332.................2346789*********************99988878888888887633789* PP

                                       --B-CHHHCCCTSHHHHHHHHHHCSSGGCCSGGGGGGGGGGCCSHHHHHHHHHHHHHHHHHHHHHHHHHHSS-.... CS
                     Phosphorylase 367 nGitprrwlllanpelaelitekigeewvkdleeLkkLekladdkefleelaeikqenKerlaelikekegve.... 439
                                       nG+ ++ wl+   +e+++li++ ig+ w  d  eL+ L   ++ +   eel e++ + K++l +lik++++ +    
  gi|242399298|ref|YP_002994722.1| 399 NGVHTKTWLH---NEIKKLIDRYIGRVWR-DYAELEGLWYGVE-RIPNEELWEAHLKAKKELIDLIKRNMKERnkrl 470
                                       *********7...5899***********6.6789999976654.444556666677777777777777543333345 PP

                                       ........--TTSEEEEEES-SCCCCTHHHHHHHHHHHHHHHHHSTTS----EEEEEE----TT-HHHHHHHHHHHH CS
                     Phosphorylase 440 ........vdpeslfdvqvkRlheYkRqlLnvLhiitlYneikenpekkvvprtvifggkaapgYalAkkiiklins 508
                                               +++++l     +R+  YkR ++ +++ +++ ++i +np     p  +ifggka p  +  k+ +k + +
  gi|242399298|ref|YP_002994722.1| 471 gieepipeINENALLIGFARRFATYKRATM-IFNDLERLKKIANNP---ERPVYIIFGGKAHPMDTSGKEFLKRLYE 543
                                       555666669******************998.788888888888887...7899************************ PP

                                       HHHHHCC-TTTCCCEEEEEETT-SHHHHHHHGGG-SEEEE---TTTSSS-SHHHHHHHTT-EEEEESSTCHHH CS
                     Phosphorylase 509 vaevvnndpevkdklkvvflenynvslaekiipaadlseqistagkeASGTgnmkfmlnGaltigtlDGanvE 581
                                       v+++    pe k+  k++++eny++  a  +i++ d+  +      eASGT+ mk  lnG l ++ +DG  vE
  gi|242399298|ref|YP_002994722.1| 544 VSQM----PEFKG--KIIIFENYDMGSARAMISGVDVWLNTPRRPLEASGTSGMKAGLNGVLNLSVYDGWWVE 610
                                       9987....77777..58999*************************************************8887 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.0013
                                       HHHHHHHCSHHHHHHHHHHHHHCG.GGGBHHHHHHHHHHHTT CS
                     Phosphorylase 669 ekveeaYkdkkewakksilniaks.gkFssDrtikeYaeeiW 709
                                       e + + Y+++++w  ++  +i ++  +Fs+ r +keY ++ +
  gi|242399298|ref|YP_002994722.1| 647 EVIPTYYENRQRWIYMMKESIKSIaPRFSTHRMLKEYVNKFY 688
                                       4466789*******9999999875169**********99866 PP

>> DUF3417  Protein of unknown function (DUF3417)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.1   2.9   4.9e-33   4.4e-29       1     109 []      12     119 ..      12     119 .. 0.96
   2 ?   -4.0   0.1         2   1.8e+04      22      37 ..     367     382 ..     363     385 .. 0.62

  Alignments for each domain:
  == domain 1  score: 101.1 bits;  conditional E-value: 4.9e-33
                           DUF3417   1 lpeeLekLeeLaknlwwswneeareLFksldpelweevghnPvklLeevsqerleelaedeeflarleavveefeey 77 
                                       lpe+Le L +L +n+ww+wn++a++L+++++pe w+e  +nPvklL ++++erl+el++d++f++ +e v+++f++y
  gi|242399298|ref|YP_002994722.1|  12 LPENLEGLLDLGYNYWWNWNRRATKLWEKINPEHWRE-YKNPVKLLLDTPEERLKELSKDDDFINLYELVIDQFRHY 87 
                                       8************************************.99************************************* PP

                           DUF3417  78 leek.twfqkkaeeekkeaiAYFsaEfGlhesL 109
                                       +e++ tw++++   + +e + Y+++E+G+++sL
  gi|242399298|ref|YP_002994722.1|  88 MESEnTWLSTNW-PKWEEPVIYLCMEYGISKSL 119
                                       **9989999998.67888899*********997 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 2
                           DUF3417  22 eareLFksldpelwee 37 
                                       ++++L++++ +e+w+e
  gi|242399298|ref|YP_002994722.1| 367 AVSKLHTAVTKEMWKE 382
                                       5566777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (831 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       663  (0.0369792); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); 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: 0.81u 0.31s 00:00:01.12 Elapsed: 00:00:00.51
# Mc/sec: 4947.38
//
Query:       gi|242399299|ref|YP_002994723.1|  [L=225]
Description: Probable uridylate kinase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.2e-35  122.4   0.4    4.3e-35  121.5   0.4    1.4  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 !  121.5   0.4   2.4e-39   4.3e-35       1     240 [.       1     202 [.       1     203 [. 0.90

  Alignments for each domain:
  == domain 1  score: 121.5 bits;  conditional E-value: 2.4e-39
                                       TEEEEEE-TTCCC.CTCC.HHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHHTCCCCCHHHC....E..HHHHH CS
                         AA_kinase   1 krvVvKlGGsslt.dkee.aslrrlaeqiaalkesgnklvvVhGggsftdgllalksglssgelaaglrstleeage 75 
                                       +r+V  +GGs+l  d+ + ++++++a q+ ++ +++++++vV+Ggg ++++++++++ ++++e              
  gi|242399299|ref|YP_002994723.1|   1 MRIVFDIGGSVLVpDEPDvKFIEEIAYQLTKI-SEDHEVAVVVGGGRVAREYIQAAKSFTPNETF------------ 64 
                                       7999******999555559*************.999*******************5555555554............ PP

                                       HHHHHHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE..HHHTTTCEEECCHHHHHHHTT-EEEEESEEEEETT CS
                         AA_kinase  76 vatrdalaslgerlvaallaaglpavglsaaaldateagrdegsdgnvesvdaeaieelleagvvpvltgfigldee 152
                                          +d+++++ +r +a+ll a+l+++ ++   +d + + +                 e ++ +++p+++g     ++
  gi|242399299|ref|YP_002994723.1|  65 ---KDYIGIHITRANAMLLIAALREKAYPFVVSDFR-KAW-----------------EVMQLKKIPIMGGT----HP 116
                                       ...3************************98888844.333.................4555579******5....48 PP

                                       TEEEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHH..CSSS.TTTHHHHCHHHHH CS
                         AA_kinase 153 gelgrgssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaee..saselatgGmkvkhpaal 227
                                       g+    ++D +aallAe+l+Ad l+++t+VdGVyd+dpkk+p+a++l++is +++ e   +se   gG  v++  a+
  gi|242399299|ref|YP_002994723.1| 117 GH----TTDAVAALLAEYLQADLLVVITNVDGVYDSDPKKNPNAKKLDRISTEKLVEiaMQSESKAGGSGVVDALAA 189
                                       88....9********************************************************************** PP

                                       HHHHCTT-EEEEE CS
                         AA_kinase 228 aaarrggipvvIt 240
                                       ++++rg+i++ I+
  gi|242399299|ref|YP_002994723.1| 190 KFIQRGEIKTLII 202
                                       **********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1471.10
//
Query:       gi|242399300|ref|YP_002994724.1|  [L=439]
Description: NoxA-2 NADH oxidase [Thermococcus sibiricus MM 739]
Scores for complete 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-66  223.8   2.1    2.8e-66  223.8   2.1    1.4  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    1.2e-22   80.2   8.3      5e-17   62.2   0.9    4.4  4  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    1.1e-17   64.3   0.4    3.9e-17   62.5   0.0    2.1  2  Pyr_redox_dim   Pyridine nucleotide-disulphide oxidoreductase
    8.6e-11   41.6   0.2    2.2e-09   37.0   0.1    2.2  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    3.6e-07   29.2   6.3       0.48    9.1   0.0    4.1  4  HI0933_like     HI0933-like protein
    1.2e-05   24.6   0.4      0.083   12.0   0.1    3.2  3  GIDA            Glucose inhibited division protein A
    1.3e-05   24.6   0.1       0.04   13.2   0.1    2.4  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
    1.8e-05   24.0   4.7       0.06   12.4   1.2    3.3  3  FAD_binding_2   FAD binding domain
    2.8e-05   23.9   5.8       0.62    9.6   0.1    4.1  4  DAO             FAD dependent oxidoreductase
     0.0003   21.0   0.3       0.64   10.3   0.1    2.5  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
     0.0052   16.2   0.2      0.045   13.1   0.0    2.1  2  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
     0.0055   16.3   0.4      0.046   13.3   0.1    2.4  2  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
     0.0071   16.2   0.6       0.22   11.4   0.1    2.6  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
  ------ inclusion threshold ------
      0.039   13.4   1.0        3.6    7.0   0.1    2.6  3  Glu_dehyd_C     Glucose dehydrogenase C-terminus
      0.043   12.9   0.3       0.69    9.0   0.0    2.5  3  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
      0.058   12.4   2.7          2    7.4   0.0    3.0  3  Lycopene_cycl   Lycopene cyclase protein
       0.11   12.9   0.9          7    7.2   0.3    2.5  2  NAD_binding_7   Putative NAD(P)-binding
       0.58    9.3   2.9        3.8    6.7   1.4    2.5  3  FAD_binding_3   FAD binding domain
       0.59    8.9   0.0       0.59    8.9   0.0    2.1  3  Trp_halogenase  Tryptophan halogenase


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 !  223.8   2.1   2.9e-69   2.8e-66       2     279 ..       2     283 ..       1     298 [. 0.90
   2 ?   -4.2   0.0       8.4   7.9e+03     189     203 ..     334     348 ..     332     353 .. 0.82

  Alignments for each domain:
  == domain 1  score: 223.8 bits;  conditional E-value: 2.9e-69
                                       SEEEE--SHHHHHHHHHHHH..HTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH.......HHHHCHHHHCCC CS
                                       xxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxx RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaq..agakvtlvelegtclnggcllskallgvaedaeias.......evvkklnqgiel 69 
                                       ++vviG+G AG ++al++++   +a+++++++e+t+ +  c l+ +l g   + e +        e     +q+i++
  gi|242399300|ref|YP_002994724.1|   2 KIVVIGSGTAGSNFALFARKldRKAEIIVIGKEKTMQYSPCALPFVLSGKIPKLEDIVvfpnefyE-----KQKIQM 73 
                                       89******************888********************99999998888888899854442.....568*** PP

                                       CHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-T...S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...x RF
                       Pyr_redox_2  70 llgeevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllp...k 143
                                       +l++e+ +id+++ kv ++     d+ ++ ydklvlAtGs+++ ++i+Gv++ +++ ++++++++++++  ++   k
  gi|242399300|ref|YP_002994724.1|  74 MLETEAKTIDRKR-KVIIT-----DKDEVPYDKLVLATGSKAFVPPIKGVEKRGVFTLKEMRDVREIQEYIKErkpK 144
                                       **********999.88884.....3458**********************99999999999999999988888888* PP

                                       EEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSS.TTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 144 rivvvGgGyiGvElAaalaklgkevtlveardrll.raldkelsaaleealekeGvevklgtsvkeidgngeklevv 219
                                       ++vv+G+G+iG+E A a+++lg ev +ve +++ll  +ldk+++ +++ +le++G+++++g  v ei+g++   + v
  gi|242399300|ref|YP_002994724.1| 145 KAVVIGAGLIGLEGAVAFRELGMEVLVVELLEHLLpTMLDKDIASIVQSHLEERGIQFRFGVGVSEIIGDPV--TAV 219
                                       ***********************************999*********************************7..766 PP

                                       ETTSCEEEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GGGC.......T CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......x RF
                       Pyr_redox_2 220 ledgeeidadlvvvavGvrpstelleeklglelderggivvdeflrtnvpgiyaiGDva.......g 279
                                          +e+i+ d v+va+Gvr++ +l+ +++gle+  ++givvde+lrt++p+iyaiGD+a       g
  gi|242399300|ref|YP_002994724.1| 220 KIGEEKIESDIVLVATGVRANVDLA-REAGLEI--KRGIVVDEYLRTSDPDIYAIGDCAevydavtG 283
                                       666666*******************.*******..999*********************66555543 PP

  == domain 2  score: -4.2 bits;  conditional E-value: 8.4
                                       HHHHHHHTTEEEEES CS
                                       xxxxxxxxxxxxxxx RF
                       Pyr_redox_2 189 leealekeGvevklg 203
                                        +e+ +keG+ev++g
  gi|242399300|ref|YP_002994724.1| 334 TQERARKEGIEVVVG 348
                                       578999999999876 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   0.00014      0.13       1      31 [.       2      32 ..       2      41 .. 0.87
   2 ?    3.5   0.1      0.12   1.1e+02      50      71 ..      66      87 ..      56      94 .. 0.82
   3 !   62.2   0.9   5.3e-20     5e-17       1      78 [.     145     221 ..     145     224 .. 0.94
   4 ?    3.1   0.0      0.15   1.5e+02      34      60 ..     319     348 ..     290     351 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00014
                                      EEEEECSSHHHHHHHHHHHHTTSEEEEEESS CS
                         Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvvers 31
                                      k+vv+G+G+ g  +A ++++l  k  +++ +
  gi|242399300|ref|YP_002994724.1|  2 KIVVIGSGTAGSNFALFARKLDRKAEIIVIG 32
                                      79*******************9998887655 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.12
                                      HHHTTEEEECSEEEEEEEEETT CS
                         Pyr_redox 50 lekngievllntkveeiegsed 71
                                       ek++i+++l+t+++ i+ + +
  gi|242399300|ref|YP_002994724.1| 66 YEKQKIQMMLETEAKTIDRKRK 87
                                      6899*************97665 PP

  == domain 3  score: 62.2 bits;  conditional E-value: 5.3e-20
                                       EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS.TTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEE CS
                         Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkll.rllDeeaskilqeklekngievllntkveeiegsedgvesv 76 
                                       k+vv+G+G+iglE A a++elg +V vve  ++ll  +lD+++++i+q +le++gi+++++  v ei g++   ++v
  gi|242399300|ref|YP_002994724.1| 145 KAVVIGAGLIGLEGAVAFRELGMEVLVVELLEHLLpTMLDKDIASIVQSHLEERGIQFRFGVGVSEIIGDPV--TAV 219
                                       68******************************************************************9995..566 PP

                                       EE CS
                         Pyr_redox  77 kl 78 
                                       k+
  gi|242399300|ref|YP_002994724.1| 220 KI 221
                                       65 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.15
                                       SS.TTSSHHHHH..HHHHHHHHTTEEEECS CS
                         Pyr_redox  34 ll.rllDeeask..ilqeklekngievlln 60 
                                           l+D e+++  i+qe+ +k+giev+ +
  gi|242399300|ref|YP_002994724.1| 319 AItELFDLEIGTfgITQERARKEGIEVVVG 348
                                       44467777777733679*********9876 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 ?   -2.5   0.1       6.6   6.3e+03      58      80 ..     144     166 ..     141     169 .. 0.79
   2 !   62.5   0.0   4.1e-20   3.9e-17       7     105 ..     324     423 ..     318     426 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 6.6
                                       TTTBEEEEEEECTTHHHHHHHHH CS
                     Pyr_redox_dim  58 ktgkvlGahivGpgageliqela 80 
                                       k+  v+Ga ++G + + ++ el 
  gi|242399300|ref|YP_002994724.1| 144 KKAVVIGAGLIGLEGAVAFRELG 166
                                       667899*****999888887776 PP

  == domain 2  score: 62.5 bits;  conditional E-value: 4.1e-20
                                       SSSEEEEEES-HHHHHHHHSGEEEEEEEEECGHHHCHTTH.TEEEEEEEEETTTTBEEEEEEEC.TTHHHHHHHHHH CS
                     Pyr_redox_dim   7 tdpevasvGlteeeAkaagieikvgkfpfkangralayae.tkgfvKlvadaktgkvlGahivG.pgageliqelav 81 
                                       +d+e+++ G+t+e A+++g  i+v+  +fk +++  +y+  + ++vKl+++++++k++Ga+ivG +++  +i +l++
  gi|242399300|ref|YP_002994724.1| 324 FDLEIGTFGITQERARKEG--IEVVVGKFKGSTKPEYYPGgKPITVKLIFRKDNKKLIGAQIVGgERVWGRIMALSF 398
                                       79*****************..55555667779999999999**********************9788999******* PP

                                       HHHTTSBHHH.HHTSBSSSSSTGGG CS
                     Pyr_redox_dim  82 aikagltved.ladtihihPtlsea 105
                                       a ++++tved +  + +++P++s +
  gi|242399300|ref|YP_002994724.1| 399 AAQKEATVEDiAYGETAYAPPISPT 423
                                       *********65899******99965 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.055        52       1      30 [.       4      34 ..       4      41 .. 0.80
   2 !   37.0   0.1   2.4e-12   2.2e-09      71     305 .]      46     272 ..      30     272 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.055
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagle.dylilEkg 30
                                      ++iG G aG ++a+ ++k++ + +++++ k+
  gi|242399300|ref|YP_002994724.1|  4 VVIGSGTAGSNFALFARKLDRKaEIIVIGKE 34
                                      79****************9995145666665 PP

  == domain 2  score: 37.0 bits;  conditional E-value: 2.4e-12
                       Pyr_redox_3  71 fslkeeklsrkealeYlrevaksfelpiklfeeVesvkkedegfevetsketyeAkkviiAtGefdkPnklnipGee 147
                                       f l+ + ++ ++++ + +e  ++++++ +l++e +++++++   ++ t+k+++  +k+++AtG   k  ++ i+G e
  gi|242399300|ref|YP_002994724.1|  46 FVLSGKIPKLEDIVVFPNEFYEKQKIQMMLETEAKTIDRKR--KVIITDKDEVPYDKLVLATGS--KAFVPPIKGVE 118
                                       66777788889999999999******************986..589*****************9..99999999999 PP

                       Pyr_redox_3 148 k....lvkhyskvkefhky....agqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdien 216
                                       k    + k  + v+e+++y    + +k vViG++  + + A+ + + g+eV vv   +++  +    +  +  ++++
  gi|242399300|ref|YP_002994724.1| 119 KrgvfTLKEMRDVREIQEYikerKPKKAVVIGAGLIGLEGAVAFRELGMEVLVVELLEHLLPT--MLDKDIASIVQS 193
                                       7444334456666777666222245789**************************999977775..355666777777 PP

                       Pyr_redox_3 217 rleelvkeekikvlfnaevkeikekeeeykvktedgkkvevkddvvlatGykpdlsflkkslfeldedgrpvlteet 293
                                        lee    + i++ f   v ei  + ++  vk  + +k+e +d v++atG + ++++ +++++e+   +r  + +e 
  gi|242399300|ref|YP_002994724.1| 194 HLEE----RGIQFRFGVGVSEIIGDPVT-AVKIGE-EKIE-SDIVLVATGVRANVDLAREAGLEI---KRGIVVDEY 260
                                       7766....459***********987665.566666.4555.5899999***********999999...455556677 PP

                       Pyr_redox_3 294 eetnvpglflaG 305
                                         t  p+++ +G
  gi|242399300|ref|YP_002994724.1| 261 LRTSDPDIYAIG 272
                                       788888888887 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1     0.016        15       2      29 ..       2      29 ..       1      38 [. 0.72
   2 !    9.1   0.0   0.00051      0.48     111     167 ..      58     110 ..      53     128 .. 0.79
   3 !    7.0   0.9    0.0022       2.1       2      31 ..     145     174 ..     144     180 .. 0.91
   4 !    9.0   0.0   0.00052       0.5     109     165 ..     185     238 ..     178     244 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.016
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlll 29
                                      +++viG G AG   A+ a+k +++  ++
  gi|242399300|ref|YP_002994724.1|  2 KIVVIGSGTAGSNFALFARKLDRKAEII 29
                                      79**********9999997666554443 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00051
                                       HHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----SS- CS
                       HI0933_like 111 ivdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGGlSi 167
                                       iv +  +  ++++++++lete k++++  ++   + t +++e+  dklvlAtG++++
  gi|242399300|ref|YP_002994724.1|  58 IVVFPNEFYEKQKIQMMLETEAKTIDR--KR-KVIIT-DKDEVPYDKLVLATGSKAF 110
                                       5555556678999************44..33.44666.89*************9985 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0022
                                       SEEEE--SHHHHHHHHHHHHTT--EEEE-S CS
                       HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllek 31 
                                       + +viG+G  Gl +A++ ++ g +Vl++e 
  gi|242399300|ref|YP_002994724.1| 145 KAVVIGAGLIGLEGAVAFRELGMEVLVVEL 174
                                       689************************995 PP

  == domain 4  score: 9.0 bits;  conditional E-value: 0.00052
                                       HHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----S CS
                       HI0933_like 109 edivdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGGl 165
                                       +di ++ +++l+e+g+++r    v+++    d +  vk+ +ee++e+d +++AtG  
  gi|242399300|ref|YP_002994724.1| 185 KDIASIVQSHLEERGIQFRFGVGVSEI--IGDPVTAVKI-GEEKIESDIVLVATGVR 238
                                       7899999********************..5567789***.9*************965 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0    0.0016       1.5       1      34 [.       2      35 ..       2      51 .. 0.78
   2 ?    0.8   0.0      0.21     2e+02     115     150 ..      76     107 ..      63     128 .. 0.72
   3 !   12.0   0.1   8.8e-05     0.083       2      29 ..     146     176 ..     145     197 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0016
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGG CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithkldt 34
                                      +++ViG G AG+  Al a +l  k  +i+   ++
  gi|242399300|ref|YP_002994724.1|  2 KIVVIGSGTAGSNFALFARKLDRKAEIIVIGKEK 35
                                      69******************99999988433333 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.21
                                       ES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT CS
                              GIDA 115 eeeveeliveekkvkgvvtedgetikakavviatGt 150
                                       e e++ ++    + + v+ +d+ ++  ++ v+atG+
  gi|242399300|ref|YP_002994724.1|  76 ETEAKTID----RKRKVIITDKDEVPYDKLVLATGS 107
                                       44444442....45667888888899999******9 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 8.8e-05
                                       EEEE-SSHHHHHHHHHHHHTT--EEEE...E CS
                              GIDA   2 viViGgGhAGceAAlaaarlGakvlLi...t 29 
                                        +ViG+G+ G+e A+a  +lG++vl +    
  gi|242399300|ref|YP_002994724.1| 146 AVVIGAGLIGLEGAVAFRELGMEVLVVellE 176
                                       69**********************9884441 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0    0.0008      0.75      30      67 ..       2      39 ..       1      90 [. 0.83
   2 !   13.2   0.1   4.2e-05      0.04      25      60 ..     140     175 ..     135     226 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0008
                                      EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHH CS
                       AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleql 67
                                      k++viG G+aG + +  a++l+ k +++ + +++  q 
  gi|242399300|ref|YP_002994724.1|  2 KIVVIGSGTAGSNFALFARKLDRKAEIIVIGKEKTMQY 39
                                      89*******************99988887776666665 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 4.2e-05
                                       CB---EEEEESTSHHHHHHHHHHHHTT-EEEEEESS CS
                       AlaDh_PNT_C  25 gvepakvlviGgGvaGlqAiatakglgakVtvlDvr 60 
                                       + +p k +viG+G  Gl+ + + ++lg +V v+++ 
  gi|242399300|ref|YP_002994724.1| 140 ERKPKKAVVIGAGLIGLEGAVAFRELGMEVLVVELL 175
                                       56799*************************999875 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.0   0.00081      0.76       2      33 ..       3      36 ..       2      50 .. 0.84
   2 !   12.4   1.2   6.3e-05      0.06       2      31 ..     146     175 ..     145     178 .. 0.93
   3 ?    2.4   0.0     0.071        67     374     404 ..     253     276 ..     190     283 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00081
                                      EEEE--SHHHHHHHHHHHH..TTT-EEEEESSSG CS
                     FAD_binding_2  2 viViGsGlAGLaAAleaae..aGlkvavvekeqe 33
                                      ++ViGsG AG   Al a++  + ++++v+ ke+ 
  gi|242399300|ref|YP_002994724.1|  3 IVVIGSGTAGSNFALFARKldRKAEIIVIGKEKT 36
                                      79****************9644458999988875 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 6.3e-05
                                       EEEE--SHHHHHHHHHHHHTTT-EEEEESS CS
                     FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavveke 31 
                                       ++ViG+Gl GL  A++ +e G +v+vve  
  gi|242399300|ref|YP_002994724.1| 146 AVVIGAGLIGLEGAVAFRELGMEVLVVELL 175
                                       69*************************975 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.071
                                       -EEEBETTSBESTTEEESSBTEEE-STCEES CS
                     FAD_binding_2 374 gGvetdengrvldadgqpipGLYAaGevaag 404
                                        G+++de +r+        p+ YA+G +a  
  gi|242399300|ref|YP_002994724.1| 253 RGIVVDEYLRT------SDPDIYAIGDCA-E 276
                                       69*********......99*********9.4 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.012        12       1      29 [.       2      34 ..       2      38 .. 0.80
   2 ?    3.2   0.0     0.055        52     158     218 ..      68     115 ..      64     139 .. 0.66
   3 ?    4.1   1.9     0.031        29       2      27 ..     146     173 ..     145     174 .. 0.89
   4 !    9.6   0.1   0.00066      0.62     154     210 ..     193     247 ..     186     283 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.012
                                      EEEEECTSHHHHHHHHHHHHTT....EEEEESS CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg....Vtllekg 29
                                      ++v+iG+G +G+  A+++ +      ++++ k+
  gi|242399300|ref|YP_002994724.1|  2 KIVVIGSGTAGSNFALFARKLDrkaeIIVIGKE 34
                                      59****************543335788888765 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.055
                                       HTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHHHHHTTCTTTSEEE CS
                               DAO 158 alGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsdllgllkeldlpis 218
                                       ++ +++ ++te++ ++++  + + +  t + +    +d++V+a+G  + ++   +    pi+
  gi|242399300|ref|YP_002994724.1|  68 KQKIQMMLETEAKTIDRK--RKVII--TDKdEV--PYDKLVLATGSKA-FV---P----PIK 115
                                       556778889999999775..33344..333243..68********664.33...2....444 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.031
                                       EEEECTSHHHHHHHHHHHHTT..EEEEE CS
                               DAO   2 vviiGGGiiGlstAyeLarrg..Vtlle 27 
                                        v+iG+G iGl  A +  + g  V+++e
  gi|242399300|ref|YP_002994724.1| 146 AVVIGAGLIGLEGAVAFRELGmeVLVVE 173
                                       69**********9999977799999998 PP

  == domain 4  score: 9.6 bits;  conditional E-value: 0.00066
                                       HHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEE.EEEEEEEE--GGGHH.HH.HTT CS
                               DAO 154 raaealGveilegtevtgleeedgkvwgverttp.gen.daadavVnaaGawsd.ll.gll 210
                                       + +e++G+++++g  v ++  +   v+ v    + ge+  + d v +a+G+ ++  l + +
  gi|242399300|ref|YP_002994724.1| 193 SHLEERGIQFRFGVGVSEIIGD--PVTAV----KiGEEkIESDIVLVATGVRANvDLaREA 247
                                       5689*************98332..37777....33444333488*******9998553333 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0027       2.6       1      24 [.       5      30 ..       5      36 .. 0.78
   2 !   10.3   0.1   0.00068      0.64       1      31 [.     148     178 ..     148     202 .. 0.94

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0027
                                      EE--SHHHHHHHHHHHCC..TEEEEE CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLaka..gfdvll 24
                                      ++G+G +G+ +A +++k   ++++ +
  gi|242399300|ref|YP_002994724.1|  5 VIGSGTAGSNFALFARKLdrKAEIIV 30
                                      8***************9622445555 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00068
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSSSS CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrl 31 
                                       ++GaGl Gl  A + ++ g +vl++e  ++l
  gi|242399300|ref|YP_002994724.1| 148 VIGAGLIGLEGAVAFRELGMEVLVVELLEHL 178
                                       8************************987775 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 ?    0.4   0.0      0.39   3.7e+02      38      61 ..       2      25 ..       1      43 [. 0.80
   2 !   13.1   0.0   4.7e-05     0.045      27      66 ..     134     173 ..     119     185 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.39
                                      EEEEES-SHHHHHHHHHHHHTT-E CS
                      2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlkafgmk 61
                                      ++ +iG G  G+++a  +++++ k
  gi|242399300|ref|YP_002994724.1|  2 KIVVIGSGTAGSNFALFARKLDRK 25
                                      689************999988753 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 4.7e-05
                                       CCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEES CS
                      2-Hacid_dh_C  27 kallgkelsgktvGiiGlGrIGqavakrlkafgmkviayd 66 
                                        +  +ke + k+  +iG+G IG + a  ++++gm+v++++
  gi|242399300|ref|YP_002994724.1| 134 IQEYIKERKPKKAVVIGAGLIGLEGAVAFRELGMEVLVVE 173
                                       5667889999***************************986 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 ?   -0.0   0.0      0.59   5.6e+02       1      19 [.       1      19 [.       1      38 [. 0.70
   2 !   13.3   0.1   4.9e-05     0.046       2      53 ..     145     197 ..     144     209 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.59
                                      SEEEEE--STTHHHHHHHH CS
                    UDPG_MGDP_dh_N  1 mkisviGlGYvGlvtaavl 19
                                      mki+viG+G  G   a+  
  gi|242399300|ref|YP_002994724.1|  1 MKIVVIGSGTAGSNFALFA 19
                                      89*******9998766544 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 4.9e-05
                                       EEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHH.HCTTS-SS--TTHHH CS
                    UDPG_MGDP_dh_N   2 kisviGlGYvGlvtaavlaeighevigvDideekvdk.lnsgkipiyepgLee 53 
                                       k +viG+G +Gl  a+++ e+g+ev++v   e+   + l ++  +i++  Lee
  gi|242399300|ref|YP_002994724.1| 145 KAVVIGAGLIGLEGAVAFRELGMEVLVVELLEHLLPTmLDKDIASIVQSHLEE 197
                                       568*************************9988887541566666777777765 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 ?    2.5   0.0      0.13   1.2e+02       1      18 [.       2      19 ..       2      38 .. 0.77
   2 !   11.4   0.1   0.00024      0.22       2      39 ..     146     183 ..     145     211 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.13
                                      EEEEE--SCCHHHHHHHH CS
                           3HCDH_N  1 kvaviGaGtmGagiaavf 18
                                      k+ viG+Gt G+  a  +
  gi|242399300|ref|YP_002994724.1|  2 KIVVIGSGTAGSNFALFA 19
                                      689**********99655 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00024
                                       EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHH CS
                           3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdiseealekal 39 
                                         viGaG++G + a +f + g+eV +v+  e+ l + l
  gi|242399300|ref|YP_002994724.1| 146 AVVIGAGLIGLEGAVAFRELGMEVLVVELLEHLLPTML 183
                                       579************************99777665554 PP

>> Glu_dehyd_C  Glucose dehydrogenase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.027        26      57     132 ..      55     128 ..      46     139 .. 0.83
   2 ?    7.0   0.1    0.0038       3.6      28      57 ..     140     167 ..     129     183 .. 0.79
   3 ?   -2.5   0.0       3.2     3e+03      93     112 ..     220     239 ..     206     256 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.027
                       Glu_dehyd_C  57 lervyvlgrrdrpdptidlveelGatYvdsretpvdeipeaseemdlvvEaTGsakhafeaiealapnGvaaLlGv 132
                                       le++ v+  + +++++i+++ e  a  +d r+ +v    + + + d +v aTGs k+ +  i+ ++  Gv +L  +
  gi|242399300|ref|YP_002994724.1|  55 LEDIVVFPNEFYEKQKIQMMLETEAKTID-RKRKVIITDKDEVPYDKLVLATGS-KAFVPPIKGVEKRGVFTLKEM 128
                                       6777788888889999************9.6777877888999**********8.566789*********999765 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0038
                       Glu_dehyd_C  28 ewepesalvlGaGslGLLalalleaeergl 57 
                                       e +p++a+v+GaG +GL  +++++    g+
  gi|242399300|ref|YP_002994724.1| 140 ERKPKKAVVIGAGLIGLEGAVAFRE--LGM 167
                                       468**************98887774..444 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 3.2
                       Glu_dehyd_C  93 eipeaseemdlvvEaTGsak 112
                                       +i e++ e d+v+ aTG  +
  gi|242399300|ref|YP_002994724.1| 220 KIGEEKIESDIVLVATGVRA 239
                                       45566777888888888654 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.25   2.4e+02     193     223 ..       2      32 ..       1      49 [. 0.73
   2 ?    9.0   0.0   0.00073      0.69     144     204 ..      93     156 ..      61     168 .. 0.74
   3 ?   -1.7   0.0       1.3   1.2e+03     326     341 ..     223     238 ..     219     239 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.25
                       K_oxygenase 193 riaVvGsGqSaaeifedllrrqkkvelklvt 223
                                       +i+V+GsG  +++ +  + +  +k+e+ ++ 
  gi|242399300|ref|YP_002994724.1|   2 KIVVIGSGTAGSNFALFARKLDRKAEIIVIG 32 
                                       799*****99998776666666666665555 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00073
                       K_oxygenase 144 eeelearnlvlgvGtepkiPevleklegkervvHsseylerkee.....llakkriaVvGsGqSaa 204
                                       ++e+   +lvl++G+++ +P++   +e k  v+  +e+   +e      ++++k+ +V+G+G  + 
  gi|242399300|ref|YP_002994724.1|  93 KDEVPYDKLVLATGSKAFVPPIK-GVE-KRGVFTLKEMRDVREIqeyikERKPKKAVVIGAGLIGL 156
                                       45666679************975.466.3666666655443322457779999*********8665 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 1.3
                       K_oxygenase 326 eetlevdavvlATGYr 341
                                       ee++e+d+v++ATG r
  gi|242399300|ref|YP_002994724.1| 223 EEKIESDIVLVATGVR 238
                                       68899*********76 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.13   1.2e+02       2      18 ..       3      19 ..       2      45 .. 0.71
   2 ?    1.6   0.8      0.12   1.2e+02       3      33 ..     147     175 ..     146     182 .. 0.87
   3 ?    7.4   0.0    0.0021         2      88     177 ..     186     274 ..     180     290 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.13
                     Lycopene_cycl  2 vvviGaGpAglslAarl 18
                                      +vviG+G Ag   A   
  gi|242399300|ref|YP_002994724.1|  3 IVVIGSGTAGSNFALFA 19
                                      89********8877544 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.12
                     Lycopene_cycl   3 vviGaGpAglslAarlteakpglkvvlieas 33 
                                       vviGaG+ gl  A      + g++v+++e  
  gi|242399300|ref|YP_002994724.1| 147 VVIGAGLIGLEGAVAF--RELGMEVLVVELL 175
                                       8**********99999..999****999865 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0021
                     Lycopene_cycl  88 rlkeellerlvengvkllea.kvesveeeeageslvvleggrkirarlvvdarglaslk.karrlglQtfyGvevev 162
                                       ++++ ++ +l e g++++ +  v ++  +++   ++v  g++ki++ +v++a+g+ ++   ar+ gl + +G++v  
  gi|242399300|ref|YP_002994724.1| 186 DIASIVQSHLEERGIQFRFGvGVSEIIGDPV---TAVKIGEEKIESDIVLVATGVRANVdLAREAGLEIKRGIVVDE 259
                                       5556666666677777665425888888888...77778999************76555699*************99 PP

                     Lycopene_cycl 163 dnppfdldkmvlMDf 177
                                            d+d   + D 
  gi|242399300|ref|YP_002994724.1| 260 YLRTSDPDIYAIGDC 274
                                       888889998877775 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 ?    3.9   0.0     0.077        73       9      46 ..       2      57 ..       1     109 [. 0.62
   2 ?    7.2   0.3    0.0074         7       7      39 ..     143     175 ..     139     258 .. 0.66

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.077
                     NAD_binding_7  9 kvlvvGgGevAarkvrkl..leagakvtvvapevkeele................e 46
                                      k++v+G G+ + + +     l+ +a+++v+ +e + + +                +
  gi|242399300|ref|YP_002994724.1|  2 KIVVIGSGTAGSNFALFArkLDRKAEIIVIGKEKTMQYSpcalpfvlsgkipkleD 57
                                      789******99976655411556799***999964444455566666655554431 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0074
                     NAD_binding_7   7 gkkvlvvGgGevAarkvrklleagakvtvvape 39 
                                        kk +v+G+G ++++ +  + e g +v vv   
  gi|242399300|ref|YP_002994724.1| 143 PKKAVVIGAGLIGLEGAVAFRELGMEVLVVELL 175
                                       6899*************************8654 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.36   3.4e+02       3      34 ..       2      35 ..       1      44 [. 0.64
   2 ?    6.7   1.4     0.004       3.8       4      34 ..     146     176 ..     144     182 .. 0.89
   3 ?   -1.0   0.0      0.85     8e+02     107     131 ..     187     211 ..     181     251 .. 0.68

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.36
                                      EEEEE--SHHHHHHHHH...HHHTTHHEEEEESSS CS
                     FAD_binding_3  3 dVlIVGaGpaGlmlall...LseaGvrvvlvekrs 34
                                      +++++G+G aG   al+   L ++  + +++ k +
  gi|242399300|ref|YP_002994724.1|  2 KIVVIGSGTAGSNFALFarkLDRK-AEIIVIGKEK 35
                                      679********8776652225555.5566665555 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.004
                                       EEEE--SHHHHHHHHHHHHTTHHEEEEESSS CS
                     FAD_binding_3   4 VlIVGaGpaGlmlallLseaGvrvvlvekrs 34 
                                        +++GaG+ Gl  a   +e G +v++ve  +
  gi|242399300|ref|YP_002994724.1| 146 AVVIGAGLIGLEGAVAFRELGMEVLVVELLE 176
                                       589************************9765 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.85
                                       HHHHHHHHHHHHTEEETCSEEEECC CS
                     FAD_binding_3 107 leriLvehaeerglqvrfktevesl 131
                                       +  i+ +h+eerg+q+rf+  v  +
  gi|242399300|ref|YP_002994724.1| 187 IASIVQSHLEERGIQFRFGVGVSEI 211
                                       56788899*********99886533 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0   0.00062      0.59       1      37 [.       2      37 ..       2      41 .. 0.84
   2 ?   -3.1   0.6       2.7   2.5e+03       2      32 ..     146     173 ..     145     177 .. 0.80
   3 ?   -2.0   0.1       1.3   1.2e+03     159     211 ..     190     239 ..     185     263 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00062
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS- CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlveseeig 37
                                      kiv++G GtaG+  A  +a+ l++k+e+ ++ +e++ 
  gi|242399300|ref|YP_002994724.1|  2 KIVVIGSGTAGSNFAL-FARKLDRKAEIIVIGKEKTM 37
                                      79**********9986.56667688******999875 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.7
                                       EEEE--SHHHHHHHHHHHHHTTTSSEEEEEE CS
                    Trp_halogenase   2 ivivGGGtaGwlaAaalakalkgklevtlve 32 
                                        v++G+G  G   A a+++ +   +ev++ve
  gi|242399300|ref|YP_002994724.1| 146 AVVIGAGLIGLEGAVAFRELG---MEVLVVE 173
                                       599**************9999...5566555 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1.3
                                       HHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS-EEE-SEEEE-SGGG- CS
                    Trp_halogenase 159 fLrrvaearGvtrvegkvvevqldedgrveslrledgreveadlfiDcsGfrg 211
                                       + + + e+rG++ + g    v     + v+++++  ++++e d+++ ++G r+
  gi|242399300|ref|YP_002994724.1| 190 IVQSHLEERGIQFRFGVG--VSEIIGDPVTAVKI-GEEKIESDIVLVATGVRA 239
                                       556666777777777754..44444788999999.566699999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.43
# Mc/sec: 3035.45
//
Query:       gi|242399301|ref|YP_002994725.1|  [L=427]
Description: transporter [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-62  211.7  34.0    6.2e-37  127.5  16.8    2.1  2  SNF       Sodium:neurotransmitter symporter family


Domain annotation for each model (and alignments):
>> SNF  Sodium:neurotransmitter symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.3   9.2   6.5e-30   1.2e-25       1     118 [.       3     120 ..       3     130 .. 0.97
   2 !  127.5  16.8   3.5e-41   6.2e-37     178     480 ..     140     424 ..     128     426 .. 0.87

  Alignments for each domain:
  == domain 1  score: 90.3 bits;  conditional E-value: 6.5e-30
                               SNF   1 RetwskkldfilsvvGfavgLgnvWRFPYlcyknGGGafliPYlilllvaGiPlfflelalGqytreGaitvwrkic 77 
                                       Retw++++ f+ +++G+avgLgn+W FP  +   GG afl+PYl+ll+++G+  + +e +lG+ t+ G i ++ k  
  gi|242399301|ref|YP_002994725.1|   3 RETWGSRVGFVAASIGSAVGLGNIWMFPMRAGLYGGAAFLVPYLVLLFTVGVVGLTVEWTLGRSTKGGPIEAFAKAL 79 
                                       9**************************************************************************** PP

                               SNF  78 PllkgiGyasivvalyvglyYnvilawalfYlfssftteLp 118
                                       P  k +G  + ++++++  +Y ++l+w l Y+++++t eL 
  gi|242399301|ref|YP_002994725.1|  80 PGGKYLGILVNIIMIMIFAFYSLVLGWILRYFIATLTGELT 120
                                       *************************************9997 PP

  == domain 2  score: 127.5 bits;  conditional E-value: 3.5e-41
                               SNF 178 weltlcllvawvvvylailkGvkssgkvvyftatfPyvvllvllvrgvlLpGavkgikfyltpdlekllepkvWida 254
                                       w+++ ++ +++ +v ++++kG++ + k+++ +    +v+l++l +r+v+Lp a++g+kfyl pd++k+++ k W+ a
  gi|242399301|ref|YP_002994725.1| 140 WQFI-VIAITVGIVAMGVQKGIERANKIMMPAL---FVLLIMLTIRSVTLPNAYEGLKFYLLPDWSKMMSGKTWMIA 212
                                       5554.46778899***************99865...5**************************************** PP

                               SNF 255 atqiffslgigfGvlialasYnkfennvyrdallvslinsltsvlaglvvF.svlGfmaeeqgekisevaeeGpgLa 330
                                        +q+ffsl++   +++ ++sY k ++++  +a+ +++ ++++ v+ag+ +F +v+ f  e          + GpgL+
  gi|242399301|ref|YP_002994725.1| 213 LSQMFFSLSVLGTTMVVYGSYLKESDDIPLSAIATAFGDTAVAVTAGFLIFpAVFSFGVE---------PTAGPGLV 280
                                       **********999**************************************445555433.........357***** PP

                               SNF 331 FiaypealtklplsplwsvlFFlmlillgldsqfgtvegiitavvDefkvllrrrelltlivavlaflvglllvteg 407
                                       F++ p + +k+p + ++++lFFl li++gl s+++++e+ + + + ++++   +r+   +++ +++flvg     + 
  gi|242399301|ref|YP_002994725.1| 281 FVTLPMVFQKMPGGIFFGMLFFLLLIFAGLSSTVSMLEVYVDSAITKLNM---SRKNASVLLGLATFLVGAPSALSP 354
                                       *******************************************9999999...8888899999******98765443 PP

                               SNF 408 Giyvltlldkyaaslsllvvvlleaiavawvyglkkflddikemlgfrpllflklcwkfvspllllvlliasi 480
                                          +++++ + ++ +   + +l+ a+a+    g++k ++++++    ++   +k  +k++ p++++v+ i+++
  gi|242399301|ref|YP_002994725.1| 355 --SYFDWIANISTVYIGPLGALIAALALIR-LGIEKAYEELRKGALIEVPEAWKPWVKYLYPIVIIVIYISQF 424
                                       ..3467777777665545556666666544.599999999999999999999999999999999999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       999  (0.0557198); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); 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):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.34s 00:00:00.97 Elapsed: 00:00:00.50
# Mc/sec: 2544.98
//
Query:       gi|242399302|ref|YP_002994726.1|  [L=38]
Description: hypothetical protein TSIB_1325 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       802  (0.044732); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); 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: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 241.29
//
Query:       gi|242399303|ref|YP_002994727.1|  [L=349]
Description: histidinol-phosphate aminotransferase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-50  172.6   0.0    1.6e-50  172.3   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    1.4e-05   24.2   0.0     0.0002   20.4   0.0    2.1  2  Aminotran_5      Aminotransferase class-V
    0.00011   20.9   0.0    0.00013   20.7   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
     0.0037   16.2   0.0      0.026   13.4   0.0    1.9  2  Alliinase_C      Allinase
     0.0042   16.4   0.0     0.0063   15.8   0.0    1.3  1  Beta_elim_lyase  Beta-eliminating lyase
  ------ inclusion threshold ------
      0.011   15.1   0.0      0.015   14.6   0.0    1.1  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
      0.021   13.4   0.1      0.029   12.9   0.1    1.1  1  Met_gamma_lyase  Methionine gamma-lyase
       0.15   12.5   0.4        1.1    9.7   0.0    2.1  2  PepX_N           X-Prolyl dipeptidyl aminopeptidase PepX, N-t


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 !  172.3   0.0   7.2e-54   1.6e-50      19     363 .]      34     344 ..      20     344 .. 0.90

  Alignments for each domain:
  == domain 1  score: 172.3 bits;  conditional E-value: 7.2e-54
                                       HHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-E CS
                     Aminotran_1_2  19 tlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgde 95 
                                        ++ v+++ k+  l++++++ y+++d   +l+eala+f++      +k++ ++ +g+G+  +++ ++ ll+  pg++
  gi|242399303|ref|YP_002994727.1|  34 CPTLVIEELKK--LSFHDIHLYPNND--EKLKEALAEFWN------VKND-QIFLGTGSMGCLQKINKLLT--PGSV 97 
                                       56668888888..*************..************......6666.*******************9..**** PP

                                       EEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHH CS
                     Aminotran_1_2  96 ilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleelek 172
                                       +l  +p + +y+n++rl+g+  +++pl  eedf++d+  ++++++e      +t +i+v +p+NPtG++++l+e+e+
  gi|242399303|ref|YP_002994727.1|  98 VLGYSPQFLPYINDARLNGAVYHYVPLLREEDFTIDVSRIIAQIDE------RTTFIYVDNPNNPTGQIFKLKEIEE 168
                                       **********************************************......************************* PP

                                       HHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEE.EHHHHHHHHHHHH CS
                     Aminotran_1_2 173 lldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilg.naavvsqlrklsr 248
                                       l++ a +++++l+vDea+++f+ +  +      n+ e+pn++i++s+sK fGlaG+R+Gy+++  +++++ l k+  
  gi|242399303|ref|YP_002994727.1| 169 LAEEAGRKGAILIVDEAFGEFMEKRNS----AINL-EYPNVVITRSFSKGFGLAGLRIGYCVVkGKEMKELLFKVDF 240
                                       ************************543....4555.68*************************889*********** PP

                                       HHTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS.TEEEECCSCSSEEEEEETHHCHHHHHHHH CS
                     Aminotran_1_2 249 pflsssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLael.glkvlasqsgmflltdlsaetakelskkL 324
                                       pf ++++  +a+++al+d++    +l+++ ++ +k+ ++  +eL +   ++ + + + +fl  + +       +   
  gi|242399303|ref|YP_002994727.1| 241 PFSITNISIRAALKALEDTE----FLKKTIKKTKKSKEKTMKELGRRfHIAKTHKTTPIFLCGGQKD-----TYGYF 308
                                       ********************....6777777777777777777766657777777778887744444.....47889 PP

                                       HHTCTEEEEEGGGGTS..TTEEEEECTTS-HHHHHHHHHHH CS
                     Aminotran_1_2 325 leevgvyvtpgtsftv..pgrlRitvAglteeeleelveal 363
                                       l++ g++ +pg++f     + +Ri v    +++++el++++
  gi|242399303|ref|YP_002994727.1| 309 LQK-GILTVPGSEFMNldDSYVRIRV----PKDVDELLTRI 344
                                       999.**********999*99******....88888888876 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0     9e-08    0.0002      97     177 ..     100     185 ..      53     192 .. 0.71
   2 ?    1.5   0.0     0.052   1.2e+02     210     249 ..     246     285 ..     239     315 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 9e-08
                                       SHGGGTHHHHHHHHHHTEEEEEEEB..ETTSCBEGGGHHHH--TTEEEEEEESBETTTTEB--HHHHHHHHHH...T CS
                       Aminotran_5  97 ehhanlvpwqelakrtgakvkvipl..deegeldldelekllnektklvaithvsnvtGtiqpveeigklakk...k 168
                                       ++  +++p  + a+  ga  +++pl  +e+ ++d++++ ++++e+t  +++   +n tG i+ ++ei +la +   k
  gi|242399303|ref|YP_002994727.1| 100 GYSPQFLPYINDARLNGAVYHYVPLlrEEDFTIDVSRIIAQIDERTTFIYVDNPNNPTGQIFKLKEIEELAEEagrK 176
                                       556666777677777788888888722456678899*************************9999999888875435 PP

                                       T-EEEEE-T CS
                       Aminotran_5 169 galvlvDaa 177
                                       ga+++vD a
  gi|242399303|ref|YP_002994727.1| 177 GAILIVDEA 185
                                       9******87 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.052
                                       EEEEEHHHHHTS..SS.STTSEEEEET.TEEEEHCTTGGGS CS
                       Aminotran_5 210 vlyvrkellekleplllggemveevsl.eettfaeapskfe 249
                                        +++r  +l++le +++ ++++++ +  +e+t++e  ++f+
  gi|242399303|ref|YP_002994727.1| 246 NISIRA-ALKALEDTEFLKKTIKKTKKsKEKTMKELGRRFH 285
                                       566666.8999999999999999999989999999999997 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 !   20.7   0.0   5.7e-08   0.00013     126     177 ..     133     187 ..      59     215 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 5.7e-08
                                       SHHHHHHHCCTTEEEEEEESS-TTTT----HHHHHHHHHHTT...-EEEEEGTTT CS
                   Cys_Met_Meta_PP 126 dleelekaikentklvylEtptnpllkvvDiekiaklakkag...vlvvvDntfa 177
                                       d++++ ++i+e+t  +y++ p np+ ++  +++i +la +ag   ++++vD +f 
  gi|242399303|ref|YP_002994727.1| 133 DVSRIIAQIDERTTFIYVDNPNNPTGQIFKLKEIEELAEEAGrkgAILIVDEAFG 187
                                       56788899*********************9999999999987778******9996 PP

>> Alliinase_C  Allinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   1.2e-05     0.026     142     251 ..     149     273 ..     130     293 .. 0.65
   2 ?    0.1   0.0      0.13   2.8e+02     313     348 ..     300     336 ..     285     345 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.2e-05
                                       EEESS-TTT-----.---.......-TT-EEEEEE-TT...-STTTS---S-B--SEEEEEHHHHHS-GGG-EEEEE CS
                       Alliinase_C 142 lvtsPnnPdgllre.avv.......kgseakviyDlay...YWPhytpitskadedimLftlskltGhaGsrlGWal 207
                                        v  PnnP g++ + + +        ++ a++i+D a+      + ++i+ +  + ++  ++sk  G aG r+G+ +
  gi|242399303|ref|YP_002994727.1| 149 YVDNPNNPTGQIFKlKEIeelaeeaGRKGAILIVDEAFgefMEKRNSAINLEYPNVVITRSFSKGFGLAGLRIGYCV 225
                                       578999999987432222233444234556789999863323456789999999999999***************** PP

                                       ES-HHHHHHHHHH.HHHHHSS--HHHHHHHHH...HHHHHHHHTT--S CS
                       Alliinase_C 208 vkdkevakklvey.ieknsiGvskesqlrvlk...ilkvvlaeiktek 251
                                       vk ke+ + l +     +   +s  + l++l+    lk+ ++++k++k
  gi|242399303|ref|YP_002994727.1| 226 VKGKEMKELLFKVdFPFSITNISIRAALKALEdteFLKKTIKKTKKSK 273
                                       *****9988765422333344565666665541114444444444333 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.13
                                       S..-HHHHHHTTTEEEEEGGGG.TS-TTEEEEESSS- CS
                       Alliinase_C 313 ededcaevlrekkiltrsGevf.eaesryvrlsllkr 348
                                       +++d +  + +k+ilt  G++f + + +yvr+ + k 
  gi|242399303|ref|YP_002994727.1| 300 GQKDTYGYFLQKGILTVPGSEFmNLDDSYVRIRVPKD 336
                                       4679999999*******9988736799****976543 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   2.8e-06    0.0063     102     169 ..     125     185 ..      59     186 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.8e-06
                                       -EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEET CS
                   Beta_elim_lyase 102 knkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgA 169
                                         +e+ ++d+ ++ a i+e      ++ +i++ + nn   Gq+ +l+e++e+a+ a ++g  l++D A
  gi|242399303|ref|YP_002994727.1| 125 LREEDFTIDVSRIIAQIDE------RTTFIYVDNPNNP-TGQIFKLKEIEELAEEAGRKGAILIVDEA 185
                                       4555455555555555555......799*********5.9***********************99976 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   6.8e-06     0.015      25     138 ..      57     174 ..      39     192 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6.8e-06
                                       HHHHHHHHHHHHT.-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B.-TTTSSB CS
                   DegT_DnrJ_EryC1  25 veeFEkafaaylg.vkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDv.dpdtyni 99 
                                        e++ +a+a++ + ++  i + +G+ + +  ++ l ++pg  V+  s  F+  +n ++ +ga+  +v    +++++i
  gi|242399303|ref|YP_002994727.1|  57 DEKLKEALAEFWNvKNDQIFLGTGSMGCLQKINKL-LTPGSVVLGYSPQFLPYINDARLNGAVYHYVPLlREEDFTI 132
                                       56677777777773334677777777766666554.56799999999999999999999999999998626789*** PP

                                       -GGGCGGG--TTEEEEE...EB-GGGB---HHHHHHHHHHCT CS
                   DegT_DnrJ_EryC1 100 dpaaieaaitertkaIl...pVhlyGqvadmdalkaiaakhg 138
                                       d+++i a i ert  I    p +  Gq++ +++++++a++ g
  gi|242399303|ref|YP_002994727.1| 133 DVSRIIAQIDERTTFIYvdnPNNPTGQIFKLKEIEELAEEAG 174
                                       ****************833356789************99764 PP

>> Met_gamma_lyase  Methionine gamma-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   1.3e-05     0.029     131     208 ..     118     194 ..     108     240 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.3e-05
                   Met_gamma_lyase 131 kykevdlleeg..kvdieavkeaikektkliliqrskGyserkslsieeieeiiklvkeinedvivfvdncyGefve 205
                                        y+ v+ll e   ++d++++ ++i e+t +i +   +   + + ++++eiee+ +     ++  i+ vd+ +Gef+e
  gi|242399303|ref|YP_002994727.1| 118 VYHYVPLLREEdfTIDVSRIIAQIDERTTFIYVDNPNN-PTGQIFKLKEIEELAEEA--GRKGAILIVDEAFGEFME 191
                                       688899875441279******************98765.556789999999998864..56789999********** PP

                   Met_gamma_lyase 206 eke 208
                                       +++
  gi|242399303|ref|YP_002994727.1| 192 KRN 194
                                       986 PP

>> PepX_N  X-Prolyl dipeptidyl aminopeptidase PepX, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1      0.33   7.3e+02      17      47 ..      39      67 ..      35      75 .. 0.63
   2 ?    9.7   0.0   0.00049       1.1       6      54 ..     242     291 ..     241     323 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.33
                            PepX_N 17 leELkkigfldedlekestekallktflkka 47
                                      +eELkk+ f d +l    ++ + lk+ l+++
  gi|242399303|ref|YP_002994727.1| 39 IEELKKLSFHDIHLYP--NNDEKLKEALAEF 67
                                      6899999995544444..4445565555554 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00049
                            PepX_N   6 FayiktdfetaleELkkigfldedlekestek.allktflkkafleakse 54 
                                       F++++ +   al+ L++ +fl+++++k++++k +++k++ +++++  + +
  gi|242399303|ref|YP_002994727.1| 242 FSITNISIRAALKALEDTEFLKKTIKKTKKSKeKTMKELGRRFHIAKTHK 291
                                       999**********************9987765156788888888776663 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       794  (0.0442858); expected 358.6 (0.02)
Passed bias filter:                      613  (0.0341904); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 2236.46
//
Query:       gi|242399304|ref|YP_002994728.1|  [L=87]
Description: hypothetical protein TSIB_1327 [Thermococcus sibiricus MM 739]
Scores for complete 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   79.0   5.1    2.7e-22   78.9   5.1    1.0  1  UPF0016   Uncharacterized protein family UPF0016
  ------ inclusion threshold ------
        0.9    9.7   0.2        0.9    9.7   0.2    2.2  2  SdpI      SdpI/YhfL protein family


Domain annotation for each model (and alignments):
>> UPF0016  Uncharacterized protein family UPF0016
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.9   5.1   3.1e-26   2.7e-22       3      75 .]       7      79 ..       5      79 .. 0.98

  Alignments for each domain:
  == domain 1  score: 78.9 bits;  conditional E-value: 3.1e-26
                           UPF0016  3 aflliflaElGDkTqlaaalLaarykplpVflGavlAlalmtvlsvllGsslakrlperlielvaavlFllfG 75
                                      +f++iflaElGDkTqla++++a++y +++ flGavl+l+ +++++++lG+++++ lp +li+  a+vlF+lfG
  gi|242399304|ref|YP_002994728.1|  7 VFVAIFLAELGDKTQLATIAFASKYGWVKAFLGAVLGLVSVNLIGAILGDKIGDALPFELIHKGAGVLFILFG 79
                                      79**********************************************************************9 PP

>> SdpI  SdpI/YhfL protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   1.8     0.096   8.6e+02      40      62 ..      24      45 ..       4      55 .. 0.48
   2 ?    9.7   0.2    0.0001       0.9      24      42 ..      66      84 ..      62      86 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.096
                              SdpI 40 lllla....lgavvlvllvlvlllviv 62
                                      ++++a    +     v  +l ++l +v
  gi|242399304|ref|YP_002994728.1| 24 TIAFAskygW-----VKAFLGAVLGLV 45
                                      3333333331.....333333333322 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0001
                              SdpI 24 kahrfagklwiiaGlilll 42
                                        h+ ag l+i+ G+++ll
  gi|242399304|ref|YP_002994728.1| 66 LIHKGAGVLFILFGILMLL 84
                                      67***************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 625.35
//
Query:       gi|242399305|ref|YP_002994729.1|  [L=398]
Description: Aspartate transaminase [Thermococcus sibiricus MM 739]
Scores for complete 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  244.3   0.0    2.5e-72  244.1   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    1.2e-08   34.3   0.0    9.1e-05   21.6   0.0    2.2  2  Aminotran_5      Aminotransferase class-V
    1.2e-06   28.0   0.0    2.2e-06   27.3   0.0    1.3  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
      0.001   18.4   0.0     0.0018   17.6   0.0    1.3  1  Beta_elim_lyase  Beta-eliminating lyase
  ------ inclusion threshold ------
      0.012   14.1   0.0      0.021   13.4   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
      0.044   12.6   0.1       0.42    9.4   0.2    2.2  2  Alliinase_C      Allinase
       0.06   13.2   0.0       0.33   10.8   0.0    2.2  3  HU-CCDC81_bac_1  CCDC81-like prokaryotic HU domain 1
      0.079   13.2   1.1       0.29   11.3   0.4    2.3  2  DUF2774          Protein of unknown function (DUF2774)
       0.13   11.4   0.0        0.9    8.6   0.0    2.0  2  DUF2303          Uncharacterized conserved protein (DUF2303)


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 !  244.1   0.0   1.2e-75   2.5e-72       1     362 [.      40     390 ..      40     391 .. 0.95

  Alignments for each domain:
  == domain 1  score: 244.1 bits;  conditional E-value: 1.2e-75
                                       SEEEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHH CS
                     Aminotran_1_2   1 tdvinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGa 77 
                                       ++vi Lg++e+++d    t++++++a+k+  +  ++++ y+p+ g +el++a+ +++ +++++ ++++ +v+v+ Ga
  gi|242399305|ref|YP_002994729.1|  40 KNVISLGIGEPDFD----TPKNIKEAAKR--ALDEGWTHYTPNAGIAELRNAISEYYVSHYGMRIQPQ-NVLVTAGA 109
                                       589***********....**********9..88899********************************.******** PP

                                       HHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEE CS
                     Aminotran_1_2  78 galiealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilv 154
                                        ++  +++  l l+ gde+++pdp +  y ++++ sg++ +r pl++e++f+ d ++l+e++++      +t++i++
  gi|242399305|ref|YP_002994729.1| 110 YEATYLAFESL-LEEGDEVIIPDPAFVCYVEDAKVSGAKYIRLPLKEENEFQPDTDELLELITK------RTRMIVL 179
                                       ***********.****************************************************......******* PP

                                       ESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTT.EEEEEESSSTTSSGGG-E CS
                     Aminotran_1_2 155 esphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepn.llivgslsKafGlaGeRv 230
                                       + p+NPtG+ +++e  ++++d+a+ yn+++++De Y++f ++  ++v+   + ++  + +++++s+sK f+++G+R+
  gi|242399305|ref|YP_002994729.1| 180 NYPNNPTGATLDEEVAKAVADIAQDYNIYILSDEPYEHFLYDGAKHVP-MIKYAP--DnTILANSFSKTFAMTGWRL 253
                                       ******************************************665444.444444..359***************** PP

                                       EEEEEEHHHHHHHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS.TEEEECCSC CS
                     Aminotran_1_2 231 Gyilgnaavvsqlrklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLael.glkvlasqs 304
                                       G++++ ++vv+ + kl++ ++    s +q a +aal+ +    + +eemr++++krrk + ++L+e   +k +++++
  gi|242399305|ref|YP_002994729.1| 254 GFTIAPEDVVKDMIKLHAYIIGnvASFVQIAGVAALREEASW-KAVEEMRKEYEKRRKLVLEHLKEMpHIKAFEPKG 329
                                       *******************99999**************9976.5********************999********** PP

                                       SSEEEEEETHH..CHHHHHHHHHHTCTEEEEEGGGGTS..TTEEEEECTTS-HHHHHHHHHH CS
                     Aminotran_1_2 305 gmflltdlsae..takelskkLleevgvyvtpgtsftv..pgrlRitvAglteeeleelvea 362
                                       +++++  ++    + +e+++ Ll++ gv+v+pgt f+   +g +Ri++ ++++e+l e++ +
  gi|242399305|ref|YP_002994729.1| 330 AFYVFANITGTgmKSEEFAEWLLDKAGVVVIPGTAFGPagEGYIRISY-ATSQENLLEAMAR 390
                                       ***********9999*********************************.9999999888765 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   4.6e-08   9.1e-05      62     175 ..     101     212 ..      94     214 .. 0.84
   2 !   10.6   0.0    0.0001       0.2     254     342 ..     282     366 ..     275     384 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 4.6e-08
                                       GGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBE..GGGHHHH- CS
                       Aminotran_5  62 eeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeld..ldelekll 136
                                       +++++t G+ ea  l+  sl   l++gde+++ +     ++v+ +e ak  gak   +pl+ee e +  +del +l+
  gi|242399305|ref|YP_002994729.1| 101 QNVLVTAGAYEATYLAFESL---LEEGDEVIIPDP----AFVCYVEDAKVSGAKYIRLPLKEENEFQpdTDELLELI 170
                                       79******************...*********985....455677778899**99999999988876458999**** PP

                                       -TTEEEEEEESBETTTTEB--...HHHHHHHHHHTT-EEEEE CS
                       Aminotran_5 137 nektklvaithvsnvtGtiqp...veeigklakkkgalvlvD 175
                                       +++t+++ ++  +n tG   +    ++++++a+++++++l D
  gi|242399305|ref|YP_002994729.1| 171 TKRTRMIVLNYPNNPTGATLDeevAKAVADIAQDYNIYILSD 212
                                       *****************9554232467888888899998877 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0001
                                       -HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-CTCBSEEEEEETTCSHHHHHH.HHH CS
                       Aminotran_5 254 nvagiiglgaaleyleeigleaiekhekelaeyllerlkslpgvrlygpdkaerrasivsfnfkgvhaedvat.lLd 329
                                       ++ag+ +l++ + +     +e+++k+ ++ ++ +le lk++p+++ ++p  + +     +++ +g+++e++a  lLd
  gi|242399305|ref|YP_002994729.1| 282 QIAGVAALREEASWK---AVEEMRKEYEKRRKLVLEHLKEMPHIKAFEP--KGAFYVFANITGTGMKSEEFAEwLLD 353
                                       578888888888887...8999999*********************886..7999999************9982456 PP

                                       HTTEEEEEE-TTT CS
                       Aminotran_5 330 eegIavrsGhhca 342
                                       ++g+ v  G +  
  gi|242399305|ref|YP_002994729.1| 354 KAGVVVIPGTAFG 366
                                       66****9998876 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 !   27.3   0.0   1.1e-09   2.2e-06       4     144 ..      56     212 ..      53     219 .. 0.79

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 1.1e-09
                                       HHHHHHHHHHHTSS-SSS..SHHHHHHHHHHHHH........HT-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEES CS
                   DegT_DnrJ_EryC1   4 eeeleaveevlksgwlts..gpeveeFEkafaay........lgvkhaiavssGtaAlhlaLralgvgpgdeVIvps 70 
                                       ++++ea++++l+ gw+    +  ++e+ +a+++y        ++ ++++ ++ + +A  la + l  + gdeVI+p 
  gi|242399305|ref|YP_002994729.1|  56 KNIKEAAKRALDEGWTHYtpNAGIAELRNAISEYyvshygmrIQPQNVLVTAGAYEATYLAFESLLEE-GDEVIIPD 131
                                       56778888888888887766777888888888882222222223456778888889999999997555.9******* PP

                                       SS-THHHHHHHHTT-EEEEE-B-.TTTSSB-GGGCGGG--TTEEEEE...EB-GGGB---...HHHHHHHHHHCT-E CS
                   DegT_DnrJ_EryC1  71 ltFvatanavlelgakpvfvDvd.pdtynidpaaieaaitertkaIl...pVhlyGqvad...mdalkaiaakhglk 140
                                         Fv  ++ +  +gak + +  + ++ +++d +++ ++it+rt+ I+   p +  G+  d    +a+ +ia++++++
  gi|242399305|ref|YP_002994729.1| 132 PAFVCYVEDAKVSGAKYIRLPLKeENEFQPDTDELLELITKRTRMIVlnyPNNPTGATLDeevAKAVADIAQDYNIY 208
                                       ******************999872578*******************94445688888886333468999******** PP

                                       EEEE CS
                   DegT_DnrJ_EryC1 141 vieD 144
                                       +++D
  gi|242399305|ref|YP_002994729.1| 209 ILSD 212
                                       *999 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   8.8e-07    0.0018      54     167 ..     107     212 ..      54     214 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 8.8e-07
                                       S-HHHHHHHHHHHH--TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTT..TBE-HHHHHHHS--S-TTS-EE CS
                   Beta_elim_lyase  54 pqGtaAnsillkillqrgeevivtepahihfdetgaiaelagvklrdlknkea..Gkmdlekleaaikevgaheeki 128
                                       +    A  ++++ ll+ g+evi+ +pa ++  e   +   +g+k + l+ ke+   + d ++l ++i++      ++
  gi|242399305|ref|YP_002994729.1| 107 AGAYEATYLAFESLLEEGDEVIIPDPAFVCYVEDAKV---SGAKYIRLPLKEEneFQPDTDELLELITK------RT 174
                                       333468899************************9887...55555555555551166678889999998......69 PP

                                       EEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEE CS
                   Beta_elim_lyase 129 klisltvTnntagGqvvsleelrevaaiakkygiplhlD 167
                                       ++i+l   nn   G  +  e  ++va+ia++y+i ++ D
  gi|242399305|ref|YP_002994729.1| 175 RMIVLNYPNNP-TGATLDEEVAKAVADIAQDYNIYILSD 212
                                       9*********5.9*********************99887 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.1e-05     0.021      69     173 ..     102     212 ..      97     216 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.1e-05
                                       EEEEESSHHHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHH...TTCEEEEESTTSHHHHHHHCCTTEEEEE CS
                   Cys_Met_Meta_PP  69 aalavssGmaAiaaailallkaGdeivvsddlYggtqrllkkvlkk...lgievkfvdtsdleelekaikentklvy 142
                                       ++l+++    A+ +a+ +ll++Gde+++ d ++ +  +  k    k   l ++ +   + d++el + i+++t+++ 
  gi|242399305|ref|YP_002994729.1| 102 NVLVTAGAYEATYLAFESLLEEGDEVIIPDPAFVCYVEDAKVSGAKyirLPLKEENEFQPDTDELLELITKRTRMIV 178
                                       56777777789999****************9888777666655444311445555555578899************* PP

                                       EESS-TTTT----...HHHHHHHHHHTT-EEEEE CS
                   Cys_Met_Meta_PP 143 lEtptnpllkvvD...iekiaklakkagvlvvvD 173
                                       l  p np+  ++D    +++a++a++ ++ ++ D
  gi|242399305|ref|YP_002994729.1| 179 LNYPNNPTGATLDeevAKAVADIAQDYNIYILSD 212
                                       ************9443356788888888877766 PP

>> Alliinase_C  Allinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.2   0.00021      0.42     142     224 ..     178     276 ..     122     311 .. 0.66
   2 ?    0.1   0.0      0.15   2.9e+02     315     361 ..     345     393 ..     320     395 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00021
                                       EEESS-TTT--.------.......-TT-EEEEEE-TT-S......TTTS---S-B--SEEEEEHHHHHS-GGG-EE CS
                       Alliinase_C 142 lvtsPnnPdgl.lreavv.......kgseakviyDlayYW......PhytpitskadedimLftlskltGhaGsrlG 204
                                       +   PnnP g+ l e+v        ++ +  ++ D  y         h   i+++ d+ i   ++sk+   +G rlG
  gi|242399305|ref|YP_002994729.1| 178 VLNYPNNPTGAtLDEEVAkavadiaQDYNIYILSDEPYEHflydgaKHVPMIKYAPDNTILANSFSKTFAMTGWRLG 254
                                       3456888887524444432222222222222333333321111122356679************************* PP

                                       EEEES-HHHHH..HHHHHHHHH CS
                       Alliinase_C 205 Walvkdkevak..klveyiekn 224
                                       +++  +  v +  kl  yi  n
  gi|242399305|ref|YP_002994729.1| 255 FTIAPEDVVKDmiKLHAYIIGN 276
                                       *998776664322666677665 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.15
                                       .-HHH.HHHTTTEEEEEGGGGT.S-TTEEEEESSS-HHHHHHHHHHHHT CS
                       Alliinase_C 315 edcae.vlrekkiltrsGevfe.aesryvrlsllkrdddfdvllerlkk 361
                                       e+ ae +l +++++   G+ f+ a++ y+r+s   ++++    ++r+kk
  gi|242399305|ref|YP_002994729.1| 345 EEFAEwLLDKAGVVVIPGTAFGpAGEGYIRISYATSQENLLEAMARMKK 393
                                       444441456889999999999867899**********999999999886 PP

>> HU-CCDC81_bac_1  CCDC81-like prokaryotic HU domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       5.9   1.2e+04      23      35 ..       3      15 ..       3      20 .. 0.80
   2 ?   10.8   0.0   0.00017      0.33       9      54 ..     118     162 ..     115     165 .. 0.92
   3 ?   -2.1   0.0       1.8   3.7e+03       9      22 ..     349     362 ..     345     364 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 5.9
                   HU-CCDC81_bac_1 23 lGGFvahyvpAry 35
                                      lGG ++ y++ +y
  gi|242399305|ref|YP_002994729.1|  3 LGGWIMRYKKHKY 15
                                      7999999988776 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00017
                   HU-CCDC81_bac_1   9 ekLLlehdcVivPglGGFvahyvpArydeeenlflPpkrtigFNpq 54 
                                       e LL e d Vi+P+  +Fv+   +A+++  + + lP k++ +F p+
  gi|242399305|ref|YP_002994729.1| 118 ESLLEEGDEVIIPDP-AFVCYVEDAKVSGAKYIRLPLKEENEFQPD 162
                                       89************6.*********************999999875 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1.8
                   HU-CCDC81_bac_1   9 ekLLlehdcVivPg 22 
                                       e LL +   V++Pg
  gi|242399305|ref|YP_002994729.1| 349 EWLLDKAGVVVIPG 362
                                       568888999****7 PP

>> DUF2774  Protein of unknown function (DUF2774)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.6   3.2e+03      10      25 ..     192     207 ..     189     208 .. 0.66
   2 ?   11.3   0.4   0.00015      0.29      14      51 ..     278     312 ..     266     315 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.6
                           DUF2774  10 hesgknFveIAkkldi 25 
                                       +e  k   +IA+ ++i
  gi|242399305|ref|YP_002994729.1| 192 EEVAKAVADIAQDYNI 207
                                       5666666778888776 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00015
                           DUF2774  14 knFveIAkkldirakdvaklwveveearekfktrEkVV 51 
                                        +Fv+IA    + a      w+ vee+r+++++r k V
  gi|242399305|ref|YP_002994729.1| 278 ASFVQIAG---VAALREEASWKAVEEMRKEYEKRRKLV 312
                                       58999995...555555678***************998 PP

>> DUF2303  Uncharacterized conserved protein (DUF2303)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0      0.19   3.9e+02      87     131 ..     264     311 ..     244     316 .. 0.82
   2 ?    8.6   0.0   0.00045       0.9     114     160 ..     330     379 ..     323     395 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.19
                           DUF2303  87 vavfdlgta...dapghadhrAtlklkktaefkawtgidgkklsqael 131
                                       ++++ l++    + +++ + + + +l++ a++ka++++ ++  ++++l
  gi|242399305|ref|YP_002994729.1| 264 KDMIKLHAYiigNVASFVQIAGVAALREEASWKAVEEMRKEYEKRRKL 311
                                       55666666666677888888888999999*******999888777766 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00045
                           DUF2303 114 efkawtgidgkklsqaelaeflEdnakdiv...ngkspdgetlleiaral 160
                                       +f    +i g  ++ +e+ae+l d a  +v   +++ p+ge  + i+ a 
  gi|242399305|ref|YP_002994729.1| 330 AFYVFANITGTGMKSEEFAEWLLDKAGVVVipgTAFGPAGEGYIRISYAT 379
                                       577788999*******************************9999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       807  (0.0450109); expected 358.6 (0.02)
Passed bias filter:                      706  (0.0393775); 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: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.49
# Mc/sec: 2440.41
//
Query:       gi|242399306|ref|YP_002994730.1|  [L=136]
Description: hypothetical protein TSIB_1329 [Thermococcus sibiricus MM 739]
Scores for complete 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   28.7   0.1    1.6e-06   28.3   0.1    1.1  1  CGI-121      Kinase binding protein CGI-121
  ------ inclusion threshold ------
      0.063   13.2   0.1        0.1   12.5   0.1    1.4  1  PTSIIA_gutA  PTS system glucitol/sorbitol-specific IIA compon


Domain annotation for each model (and alignments):
>> CGI-121  Kinase binding protein CGI-121
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.1   1.8e-10   1.6e-06      35     123 ..      37     119 ..      31     134 .. 0.86

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 1.8e-10
                                       HHHHHHHHHHHHHHHHS---SSSHHHHHHHHHSSSS-HHHHHHHHB--TT-S-EEEEEEESSS--HHHHHHHHHHHS CS
                           CGI-121  35 ehllsAvlrallaaargklktktlhsEilfsLspnnnIgealkrfgisdkttsllvvkvssseadeeevlkslkevv 111
                                       e+++ A+  al + +rg+ k kt+  Eil++ s+n +I++a++  g ++ ++  ++v ++++   +e++l+++   +
  gi|242399306|ref|YP_002994730.1|  37 EKVVFATVLALKSFERGTNKAKTIRGEILLRVSGNLQIKDAINLVGAKKGEN--FIVAFGEN---AEKDLAEVLLKI 108
                                       578999******************************************9999..88889887...789999999999 PP

                                       -SEEE--SHHHH CS
                           CGI-121 112 egelvpleeele 123
                                         ++++l++ +e
  gi|242399306|ref|YP_002994730.1| 109 GAKELQLTN-CE 119
                                       888888888.32 PP

>> PTSIIA_gutA  PTS system glucitol/sorbitol-specific IIA component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   1.1e-05       0.1      12      46 ..      80     114 ..      70     130 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.1e-05
                                       TT--TTS.-EEEEE-TTS-HHHHTTCEEEE-T.GG CS
                       PTSIIA_gutA  12 eaeefleekmlIlFgeeapdeLadysviheveelk 46 
                                        + +++ e++++ Fge+a+++La++ + +  +el+
  gi|242399306|ref|YP_002994730.1|  80 LVGAKKGENFIVAFGENAEKDLAEVLLKIGAKELQ 114
                                       67778899****************99888877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 910.61
//
Query:       gi|242399307|ref|YP_002994731.1|  [L=63]
Description: transcriptional regulators containing the CopG/Arc/MetJ DNA- binding domain and a metal-binding domain [Thermococcus sibiricus MM 739]
Scores for 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-10   38.1   0.1    1.3e-09   37.6   0.1    1.2  1  RHH_1           Ribbon-helix-helix protein, copG family
    2.2e-05   24.6   0.0    2.2e-05   24.6   0.0    1.1  1  RHH_8           Ribbon-Helix-Helix transcriptional regulator 
     0.0061   16.5   0.4     0.0089   15.9   0.4    1.5  1  VapB_antitoxin  Bacterial antitoxin of type II TA system, Vap
  ------ inclusion threshold ------
      0.074   12.7   0.0      0.082   12.5   0.0    1.1  1  DUF5440         Family of unknown function (DUF5440)


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 !   37.6   0.1     3e-13   1.3e-09       2      39 .]       7      45 ..       7      45 .. 0.97

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 3e-13
                                      EEEEEEHHHHHHHHHHHHHHT.SSHHHHHHHHHHHHHHH CS
                             RHH_1  2 vsirldeellerLdelarrrg.rSrSelIReAlreyler 39
                                      +s+ l++ l+ +Ld l+rr+  ++rSe+IReA+re+++r
  gi|242399307|ref|YP_002994731.1|  7 ISVQLPQGLINALDVLVRRGVyPNRSEAIREAIRELVKR 45
                                      79**********************************987 PP

>> RHH_8  Ribbon-Helix-Helix transcriptional regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0     5e-09   2.2e-05      15      48 ..      16      49 ..       2      62 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 5e-09
                             RHH_8 15 LgqiDlLveeGfYsnRtDlirtairaqLakhdda 48
                                      +  +D+Lv+ G Y nR++ ir+air+ ++++  +
  gi|242399307|ref|YP_002994731.1| 16 INALDVLVRRGVYPNRSEAIREAIRELVKRELYV 49
                                      5679*********************987766544 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   0.4     2e-06    0.0089      17      40 ..      24      47 ..      17      60 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2e-06
                                      XXXXXXXXXXXXXXXXXX------ CS
                    VapB_antitoxin 17 rltglktKrEaVnlALreLiqrrk 40
                                      r++ +  ++Ea+++A+reL++r+ 
  gi|242399307|ref|YP_002994731.1| 24 RRGVYPNRSEAIREAIRELVKREL 47
                                      67778899*************986 PP

>> DUF5440  Family of unknown function (DUF5440)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.8e-05     0.082       5      52 ..      10      58 ..       6      62 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.8e-05
                           DUF5440  5 qlpqglrtelevvsakGvtGnktWvlrd.vktdkayelapatiegWdiP 52
                                      qlpqgl   l+v+ ++Gv  n++  +r+ ++   + el     e+ +iP
  gi|242399307|ref|YP_002994731.1| 10 QLPQGLINALDVLVRRGVYPNRSEAIREaIRELVKRELYVMESEEREIP 58
                                      99*********************99997233444556655555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); 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: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 440.57
//
Query:       gi|242399308|ref|YP_002994732.1|  [L=414]
Description: Cell division ftsZ like protein [Thermococcus sibiricus MM 739]
Scores for 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-41  140.2   0.2    2.2e-40  139.0   0.2    1.7  1  Tubulin   Tubulin/FtsZ family, GTPase domain
    3.5e-23   81.7   0.9    1.3e-22   79.9   0.9    2.0  1  FtsZ_C    FtsZ family, C-terminal domain


Domain annotation for each model (and alignments):
>> Tubulin  Tubulin/FtsZ family, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.0   0.2   2.5e-44   2.2e-40       1     196 [.      37     205 ..      37     206 .. 0.96

  Alignments for each domain:
  == domain 1  score: 139.0 bits;  conditional E-value: 2.5e-44
                                       EEEEEEEHHHHHHHHHHHHH...HHHCH....HHHT.....TTEEEEE....EEESBHHHHHTS-GS......EEEE CS
                           Tubulin   1 eiivigvGqcGnqignelwellakehgiqsdgdslesfFsesgkveyiprsvaidtdpqvlneikagselfnpnkll 77 
                                       +i +ig+G++Gn+++++l+e      g+             +g +e+i    a++td+q+l+++ka+      +++l
  gi|242399308|ref|YP_002994732.1|  37 KIAIIGIGGSGNNTITRLYE----L-GV-------------EG-AELI----AMNTDAQHLARTKAH------RRIL 84 
                                       5899****************....4.88.............77.8888....***************......**** PP

                                       --CCCCTTC--TT-HHHHHHHHHHTHHHHHHHHTT-SE.SEEEEEEETTSSHHHHHHHHHHHHHHHTSTT......S CS
                           Tubulin  78 lgkegagnngaggypevgkeaaeeileeirkevekcdslqgffitaslgGGTGSGlgpvilevlkeeypk......a 148
                                       lgk+ ++++g+gg+p +g+ aae++++ei + ++++d+   +f+ta++g+GTG+G++pvi++++kee ++       
  gi|242399308|ref|YP_002994732.1|  85 LGKNITHGKGSGGNPRIGYLAAEASRDEIAEVARDVDL---VFLTAGMGNGTGTGAAPVIAKIIKEEARNrgriqeP 158
                                       **************************************...**************************7667888889 PP

                                       EEEEEEEE--GG.G-HHHHHHHHHHHHHHHHT-SEEEEEEHHHHHCCS CS
                           Tubulin 149 lvvtvvvlPsefsevvvepynailalkelieesdavividNdaLlkil 196
                                       l+++vv++P+++ e+++++++a  ++++l ++sd+vi+i+Nd+Ll+++
  gi|242399308|ref|YP_002994732.1| 159 LIISVVTYPFKN-EGTRRIEKAKTGIQALLKYSDTVIIIENDKLLELV 205
                                       ***********9.*******************************9875 PP

>> FtsZ_C  FtsZ family, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.9   0.9   1.4e-26   1.3e-22       1      94 [.     253     346 ..     253     347 .. 0.99

  Alignments for each domain:
  == domain 1  score: 79.9 bits;  conditional E-value: 1.4e-26
                                       EEEEEEEEEEESTTHHHHHHHHHHTSGGGT--GGG-SEEEEEEEE-TT--HHHHHHHHHHHHHHS-TTSEEEEEEEE CS
                            FtsZ_C   1 GvAmmgvGeasgedraeeaaeaaisspLLdvdlsgAkgvlvnitggsdltlkEveevaetireevdeeanvivGavi 77 
                                       G A++g+Ge++++ ra +a ++a+ + +L+v++ + +++lv++t g+d++l E++++++ ++e++  ++++ +Ga+i
  gi|242399308|ref|YP_002994732.1| 253 GAALIGIGESDSNRRAVDAINNALTNKMLEVEFGSGESALVHFTVGPDVSLGEINDAMQIVYEKLGAKSEIKWGARI 329
                                       89*************************************************************************** PP

                                       -TT--SEEEEEEEEES- CS
                            FtsZ_C  78 deeledeirvtvvatgl 94 
                                       d+el  ++r +v++tg+
  gi|242399308|ref|YP_002994732.1| 330 DKELGKVVRAMVIMTGI 346
                                       ****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); 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: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 2910.01
//
Query:       gi|242399309|ref|YP_002994733.1|  [L=148]
Description: Glycerol-3-phosphate cytidyltransferase [Thermococcus sibiricus MM 739]
Scores for 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-23   80.9   0.1    1.2e-22   80.7   0.1    1.0  1  CTP_transf_like  Cytidylyltransferase-like
     0.0001   22.3   0.8    0.00062   19.7   0.8    2.1  1  FAD_syn          FAD synthetase
  ------ inclusion threshold ------
      0.024   14.2   0.2       0.04   13.5   0.1    1.3  1  Peripla_BP_2     Periplasmic binding protein
      0.061   12.5   0.0      0.091   11.9   0.0    1.3  1  HIGH_NTase1      HIGH Nucleotidyl Transferase


Domain annotation for each model (and alignments):
>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.7   0.1   2.6e-26   1.2e-22       1     142 [.      10     140 ..      10     141 .. 0.94

  Alignments for each domain:
  == domain 1  score: 80.7 bits;  conditional E-value: 2.6e-26
                                       EEEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-..SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHHH CS
                   CTP_transf_like   1 lagGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkk..kplasaeeRlemlelakevdevisvdpweltre 75 
                                       ++gG+FD++H GH++ l+qak+l++e l+v+v+ d+++   k  +p+ s +eR e l+++k vdev+  +p  +  e
  gi|242399309|ref|YP_002994733.1|  10 VTGGVFDILHVGHIHFLKQAKELGDE-LVVIVAHDKTVEERKgrRPINSMYERAEVLKALKMVDEVVIGEPNCISFE 85 
                                       58************************.***********999669********************************* PP

                                       HHHHTTTTEEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEEEHTTCEEEEEEECCTTTCSHHHHHH CS
                   CTP_transf_like  76 vlkklkpdklylvigadvledfsewkeleeilgnvklvvvsrpekqanvllkaekrtngiSstkire 142
                                       ++k+l+pd  ++++g d+  d     +l+e l+++++  ++++       ++ ++++    ++ki++
  gi|242399309|ref|YP_002994733.1|  86 IVKQLNPD--IIALGPDQNFD---VSALKEELKKKNINAEVIR-------IPYAYKSDVAKTSKIIQ 140
                                       ********..*******9888...59************99888.......88888888889999987 PP

>> FAD_syn  FAD synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.8   1.4e-07   0.00062       4      81 ..       4      75 ..       1     137 [. 0.80

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.4e-07
                           FAD_syn  4 edegavvtlGnFDGvHlGHqallkkaveaakekglpsvvvtFephPrevlakekapar.Lttleeklelleelg.vdav 80
                                      +++  vvt G FD +H+GH + lk+a+e+ +e     v+v  +    ++++ e++  r ++++ e++e+l++l  vd+v
  gi|242399309|ref|YP_002994733.1|  4 KKKIRVVTGGVFDILHVGHIHFLKQAKELGDELV---VIVAHD----KTVE-ERKGRRpINSMYERAEVLKALKmVDEV 74
                                      566789*******************999986543...333333....2344.233444488888888888888767777 PP

                           FAD_syn 81 l 81
                                      +
  gi|242399309|ref|YP_002994733.1| 75 V 75
                                      6 PP

>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   8.9e-06      0.04      39      83 ..      63     117 ..      33     123 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.9e-06
                                       .........TS-BSBESSSB-HHHHHHH--SEEEE-GGG.....GGGHHHHHHHS CS
                      Peripla_BP_2  39 e........aivevgadgeidvEklaalkPDlvilskgl..gltdedeellksgi 83 
                                       e        + v++g ++ i++E + +l PD++ l +++  ++ +  eel k++i
  gi|242399309|ref|YP_002994733.1|  63 EvlkalkmvDEVVIGEPNCISFEIVKQLNPDIIALGPDQnfDVSALKEELKKKNI 117
                                       344445555779***************************9888888888888877 PP

>> HIGH_NTase1  HIGH Nucleotidyl Transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0     2e-05     0.091      13      75 ..      18      83 ..      15      89 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2e-05
                       HIGH_NTase1 13 fHnGHlyhlekakeltgadvviavmSGnFvq..RGepAildKwtRaem..ALenGvDlViElPvvya 75
                                      +H GH + l++akel g+++v++v   + v+  +G   i + ++Rae+  AL++  ++Vi  P +++
  gi|242399309|ref|YP_002994733.1| 18 LHVGHIHFLKQAKEL-GDELVVIVAHDKTVEerKGRRPINSMYERAEVlkALKMVDEVVIGEPNCIS 83
                                      7*************7.677666666666663336999999999999976688888888888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); 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:                         4  (0.000223102); expected 0.2 (1e-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 0.31s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 973.76
//
Query:       gi|242399310|ref|YP_002994734.1|  [L=170]
Description: RNA-binding protein, containing PUA domain [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-24   85.7   1.1    3.3e-24   84.7   1.1    1.6  1  PUA       PUA domain
    1.5e-06   28.4   3.6    8.1e-06   26.0   3.6    2.3  1  DUF1947   Domain of unknown function (DUF1947)
    1.6e-05   25.1   0.9    8.8e-05   22.7   0.1    2.1  2  UPF0113   UPF0113 PUA domain
    0.00059   20.5   0.2    0.00093   19.8   0.2    1.3  1  Pre-PUA   Pre-PUA-like domain


Domain annotation for each model (and alignments):
>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.7   1.1   7.3e-28   3.3e-24       2      73 ..      87     159 ..      86     160 .. 0.98

  Alignments for each domain:
  == domain 1  score: 84.7 bits;  conditional E-value: 7.3e-28
                                       EEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETT.SCEEEEEEESS-HHHHHHHCTSEEEEEEEE CS
                               PUA   2 rvvvddgAvkallsgasLlapGvvevegdfeegdvVaivded.gelvavGlanysseelakikggksveierv 73 
                                       rvvvd+gAv  +l+ga+++ pG+v+v+++++egd V iv e+ g+++a+G+a+++++ +++ k+gk+v+++++
  gi|242399310|ref|YP_002994734.1|  87 RVVVDQGAVPYILNGADVMTPGIVDVDEEIKEGDFVFIVEEKyGRPLAIGIALLDGKTMKEKKKGKAVKVIHH 159
                                       8**********************************************************************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 !   26.0   3.6   1.8e-09   8.1e-06       2      65 ..       4      74 ..       3      75 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 1.8e-09
                                      -EE--HHHHHHHHHHHHTTT.....---TT--..-EEEE-S.S-EEEEETTEEEEEE.SSSEEE-HHHHHH CS
                           DUF1947  2 RHfLSkKeakeileklkeky.....isislesdkiEieeek.keklYlingvpilfe.eekliPtLklLlk 65
                                      +H LSkKe ++i+e +k+       +++  +sd++ i+e + k  ++++n++p +++ e+ ++P + +L++
  gi|242399310|ref|YP_002994734.1|  4 KHPLSKKEVRQIMEDMKRIFgkevaEKLISKSDQVLIGEFDkKTQILFVNKKPRFIKrEDLIFPLVIALYE 74
                                      799*************976411111466677888****9654889*******************9999875 PP

>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.13   5.7e+02      13      42 ..      22      55 ..       9      59 .. 0.76
   2 !   22.7   0.1     2e-08   8.8e-05       2      63 ..      88     153 ..      87     163 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.13
                           UPF0113 13 LYGrdvlkesilkit....esvkenqvvvVlnen 42
                                      ++G++v ++ i k +    ++++++ +++++n++
  gi|242399310|ref|YP_002994734.1| 22 IFGKEVAEKLISKSDqvliGEFDKKTQILFVNKK 55
                                      6888888888888877777777777777777776 PP

  == domain 2  score: 22.7 bits;  conditional E-value: 2e-08
                           UPF0113   2 vvvkekaeklFLYGrdvlkesilkitesvkenqvvvV.lnengeplGiGkirkdt...kaspgkiv 63 
                                       vvv++ a   +L G dv+  +i+ ++e++ke+++v++   ++g+pl+iG++  d+   k +++++ 
  gi|242399310|ref|YP_002994734.1|  88 VVVDQGAVPYILNGADVMTPGIVDVDEEIKEGDFVFIvEEKYGRPLAIGIALLDGktmKEKKKGKA 153
                                       78889999999*******************988887637889*********999976533444444 PP

>> Pre-PUA  Pre-PUA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.2   2.1e-07   0.00093      11      85 ..       5      74 ..       1      75 [. 0.82

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 2.1e-07
                           Pre-PUA 11 tqlksSdrrkLraklleqfpslseeqleellpkkeevkvvklqgehvelyvvdgeplffqdregellPtlytlwk 85
                                      ++l++++ r++ ++ +  f    +e+ e+l+ k  +v +  +  +++++++v+++p f++  e+ ++P + +l++
  gi|242399310|ref|YP_002994734.1|  5 HPLSKKEVRQIMEDMKRIF---GKEVAEKLISKSDQVLIGEFD-KKTQILFVNKKPRFIKR-EDLIFPLVIALYE 74
                                      5566666666665555554...6789*****************.***************99.99******99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.34s 00:00:00.92 Elapsed: 00:00:00.55
# Mc/sec: 925.35
//
Query:       gi|242399311|ref|YP_002994735.1|  [L=199]
Description: hypothetical protein TSIB_1334 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.9e-42  142.7   0.1    7.3e-42  142.1   0.1    1.3  1  DUF4443         Domain of unknown function (DUF4443)
     0.0016   18.0   0.1     0.0037   16.9   0.1    1.6  1  HrcA_DNA-bdg    Winged helix-turn-helix transcription repress
      0.006   16.5   0.9      0.015   15.2   0.1    2.2  3  HTH_12          Ribonuclease R winged-helix domain
     0.0089   15.7   0.1      0.015   15.0   0.1    1.3  1  Ribosomal_S19e  Ribosomal protein S19e
     0.0098   15.7   0.4      0.025   14.4   0.1    1.9  2  HTH_5           Bacterial regulatory protein, arsR family
  ------ inclusion threshold ------
      0.011   15.4   0.4      0.027   14.1   0.4    1.7  1  HTH_41          Helix-turn-helix domain
      0.016   15.2   0.1       0.03   14.3   0.1    1.4  1  HTH_45          Winged helix-turn-helix
      0.061   14.0   0.0       0.12   13.0   0.0    1.5  1  WGG             Pre-rRNA-processing protein TSR2
      0.065   13.1   0.0       0.14   12.1   0.0    1.6  1  TrmB            Sugar-specific transcriptional regulator TrmB
      0.069   12.7   0.4       0.14   11.7   0.4    1.5  1  HTH_24          Winged helix-turn-helix DNA-binding
        0.1   12.1   0.0       0.59    9.7   0.0    2.1  2  Sigma70_r4      Sigma-70, region 4
       0.17   12.1   0.0       0.52   10.5   0.0    1.9  1  HTH_28          Helix-turn-helix domain
       0.22   11.4   0.8         16    5.4   0.0    3.0  3  HTH_IclR        IclR helix-turn-helix domain


Domain annotation for each model (and alignments):
>> DUF4443  Domain of unknown function (DUF4443)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.1   0.1   5.3e-45   7.3e-42       1     112 []      80     190 ..      80     190 .. 0.96

  Alignments for each domain:
  == domain 1  score: 142.1 bits;  conditional E-value: 5.3e-45
                           DUF4443   1 fseahfvgkvdgmpayaivvknppqfksielrdeairffakgamilivkngepvfpederplrdtmeelamnieevl 77 
                                       fse   v  ++ + ayaivvk+ppqfksielrdeairffa+gamil   nge +fped+rpl++t+ e+a ++e+ l
  gi|242399311|ref|YP_002994735.1|  80 FSEPVEVCSIEDFLAYAIVVKDPPQFKSIELRDEAIRFFARGAMILRYLNGEVIFPEDNRPLKETLPEIAEDLEK-L 155
                                       788888999999************************************************************986.8 PP

                           DUF4443  78 nfsdgdlivvtwaenpsdamksayhvaltlkndei 112
                                        + dgdliv+twaen  da+ksa hval lk ++i
  gi|242399311|ref|YP_002994735.1| 156 PLEDGDLIVITWAENRIDAVKSAIHVALVLKGEQI 190
                                       9******************************8876 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 !   16.9   0.1   2.7e-06    0.0037      27      56 ..      30      59 ..      12      64 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.7e-06
                      HrcA_DNA-bdg 27 eeiAevlkrneGtvRNqlqsLkalgLvegv 56
                                      ++i e l+  eGt+R  l+ L al+L++++
  gi|242399311|ref|YP_002994735.1| 30 KQISEELNLGEGTIRTLLKKLAALNLIKSQ 59
                                      68*************************996 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   1.1e-05     0.015       3      64 ..      16      71 ..      14      73 .. 0.85
   2 ?   -3.5   0.0       7.5     1e+04      24      36 ..     109     116 ..     106     117 .. 0.51
   3 ?   -2.7   0.0       4.4   6.1e+03      18      25 ..     147     154 ..     136     156 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.1e-05
                            HTH_12  3 ILkilaesdkpigakeiaeeLkkrgydigeravRyrLrkleergltrrvgyagreltEkGle 64
                                      IL  l   ++p g+k+i eeL+     +ge ++R  L+kl   +l++ + ++   l EkG +
  gi|242399311|ref|YP_002994735.1| 16 ILVTLFLLKTPKGRKQISEELN-----LGEGTIRTLLKKLAALNLIKSQQKG-HSLSEKGFK 71
                                      777777788999********97.....577778999**********999876.99****986 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 7.5
                            HTH_12  24 kkrgydigeravR 36 
                                       ++r+++     +R
  gi|242399311|ref|YP_002994735.1| 109 ELRDEA-----IR 116
                                       455555.....44 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 4.4
                            HTH_12  18 eiaeeLkk 25 
                                       eiae+L+k
  gi|242399311|ref|YP_002994735.1| 147 EIAEDLEK 154
                                       78888876 PP

>> Ribosomal_S19e  Ribosomal protein S19e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   1.1e-05     0.015      93     130 ..      40      76 ..      23      81 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.1e-05
                                       HHTTSSS--SSS---SS-HHHHHTHHHHH--SS--S-- CS
                    Ribosomal_S19e  93 gsvirkilqqLeklglvkkekkkgrrltkkGqrlldri 130
                                       +  ir++l++L +l+l+k+++k g+ l++kG + ++ i
  gi|242399311|ref|YP_002994735.1|  40 EGTIRTLLKKLAALNLIKSQQK-GHSLSEKGFKVVEAI 76 
                                       6789*************88855.********9999877 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   0.1   1.8e-05     0.025      11      47 .]      22      58 ..      16      58 .. 0.86
   2 ?   -3.3   0.0       6.4   8.8e+03      20      27 ..     147     154 ..     143     155 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.8e-05
                                      HTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5 11 LaegelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                      L + ++   +++eel+l ++t++  LkkL  ++L+++
  gi|242399311|ref|YP_002994735.1| 22 LLKTPKGRKQISEELNLGEGTIRTLLKKLAALNLIKS 58
                                      666667778*************************985 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 6.4
                                       HHHHHHTS CS
                             HTH_5  20 elaeelgl 27 
                                       e+ae+l++
  gi|242399311|ref|YP_002994735.1| 147 EIAEDLEK 154
                                       89999985 PP

>> HTH_41  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.4     2e-05     0.027      11      43 ..      31      63 ..      30      66 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2e-05
                            HTH_41 11 elakeleLSvGlvQkALklLeddkaislerrGr 43
                                      ++++el L+ G++   Lk+L +   i+ + +G+
  gi|242399311|ref|YP_002994735.1| 31 QISEELNLGEGTIRTLLKKLAALNLIKSQQKGH 63
                                      5799****************************9 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   2.2e-05      0.03      20      70 ..      27      77 ..      13      82 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.2e-05
                            HTH_45 20 akkTkimykanLsykllnkYLdmLvekglikkskekYvlTekGlelleklk 70
                                      +   +i  + nL   +++  L++L   +lik +++  +l ekG +++e + 
  gi|242399311|ref|YP_002994735.1| 27 KGRKQISEELNLGEGTIRTLLKKLAALNLIKSQQKGHSLSEKGFKVVEAIL 77
                                      555679999************************************999875 PP

>> WGG  Pre-rRNA-processing protein TSR2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0     9e-05      0.12       7      62 ..      45      97 ..      40     100 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9e-05
                               WGG  7 lilhlWtaLklavengwggpdsadkrdwlagaivdlfkakeeldqedvedvLlqvm 62
                                       +l++  aL+l+ +++  g++ ++k  ++++ai dlf  +e +++  +ed+L  ++
  gi|242399311|ref|YP_002994735.1| 45 TLLKKLAALNLIKSQQK-GHSLSEKGFKVVEAILDLF--SEPVEVCSIEDFLAYAI 97
                                      56666677888777665.577999*************..689**********8765 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0    0.0001      0.14      19      58 ..      23      62 ..      13      76 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0001
                                      HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB 19 klgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                       + p+  ++i+eel++ + ++   L++L    l++ +++ 
  gi|242399311|ref|YP_002994735.1| 23 LKTPKGRKQISEELNLGEGTIRTLLKKLAALNLIKSQQKG 62
                                      57788889***************************99865 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.4    0.0001      0.14      21      48 .]      30      57 ..      29      57 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0001
                            HTH_24 21 reLAerlglSpstvnrrlkrLeeeGlIk 48
                                      ++++e+l+l  +t+++ lk+L    lIk
  gi|242399311|ref|YP_002994735.1| 30 KQISEELNLGEGTIRTLLKKLAALNLIK 57
                                      79********************999997 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00042      0.59      24      43 ..      30      49 ..      24      52 .. 0.93
   2 ?   -0.7   0.0      0.77   1.1e+03      22      30 ..     144     152 ..     122     154 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00042
                                      HHHHHHHTS-HHHHHHHHHH CS
                        Sigma70_r4 24 eEIgerlgiSrerVrqiekr 43
                                      ++I+e+l++ ++++r ++k+
  gi|242399311|ref|YP_002994735.1| 30 KQISEELNLGEGTIRTLLKK 49
                                      79***************997 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.77
                                       -HHHHHHHH CS
                        Sigma70_r4  22 TleEIgerl 30 
                                       Tl EI+e l
  gi|242399311|ref|YP_002994735.1| 144 TLPEIAEDL 152
                                       888888876 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00038      0.52      14      37 ..      28      51 ..      21      62 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00038
                            HTH_28 14 svreaArelgisrrtvyrWikrye 37
                                       ++++++el++++ t++ ++k++ 
  gi|242399311|ref|YP_002994735.1| 28 GRKQISEELNLGEGTIRTLLKKLA 51
                                      5899*****************976 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 ?    5.4   0.0     0.012        16      22      50 ..      30      58 ..      22      60 .. 0.90
   2 ?   -2.9   0.0       4.5   6.2e+03       7      14 ..      75      82 ..      73      82 .. 0.86
   3 ?    3.0   0.0     0.064        89       4      14 ..     120     130 ..     119     153 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.012
                                      HHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR 22 selArrtglpkStvhRlLqtLvelGyveq 50
                                      +++++++ l   t + lL+ L  l +++ 
  gi|242399311|ref|YP_002994735.1| 30 KQISEELNLGEGTIRTLLKKLAALNLIKS 58
                                      69*********************999875 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4.5
                                      HHHCT-CT CS
                          HTH_IclR  7 aiLdalae 14
                                      aiLd+++e
  gi|242399311|ref|YP_002994735.1| 75 AILDLFSE 82
                                      79***986 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.064
                                       HHHHHHCT-CT CS
                          HTH_IclR   4 RalaiLdalae 14 
                                       R+++iL++l+ 
  gi|242399311|ref|YP_002994735.1| 120 RGAMILRYLNG 130
                                       999***99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); 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: 00:00:00.51
# Mc/sec: 1169.81
//
Query:       gi|242399312|ref|YP_002994736.1|  [L=380]
Description: ATP-dependent DNA ligase [Thermococcus sibiricus MM 739]
Scores for complete 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-26   91.7   0.5    6.3e-26   90.8   0.1    1.7  2  Lig_C           Ligase Pab1020 C-terminal region
    2.5e-19   70.2   0.2    3.9e-19   69.5   0.2    1.3  1  RNA_ligase      RNA ligase
      4e-08   33.2   0.1     0.0042   16.8   0.2    2.2  2  DNA_ligase_A_M  ATP dependent DNA ligase domain
  ------ inclusion threshold ------
      0.054   13.5   0.0       0.12   12.3   0.0    1.6  1  SwrA            Swarming motility protein


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 ?   -2.8   0.0       1.3   5.9e+03      78      95 ..     212     229 ..     205     248 .. 0.56
   2 !   90.8   0.1   1.4e-29   6.3e-26       3     124 ..     253     375 ..     251     376 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.3
                                       HHHHHHHHCTT--EEEEE CS
                             Lig_C  78 eellehLrrlgvkaevee 95 
                                       +el+e Lr+++ + +v +
  gi|242399312|ref|YP_002994736.1| 212 RELIENLREQRREGIVMK 229
                                       444555554444433333 PP

  == domain 2  score: 90.8 bits;  conditional E-value: 1.4e-29
                                       CCSCCGS-STSCHHHHHHHHHHHHHH--SHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---EEEEEEE-SSHHHHHH CS
                             Lig_C   3 fsylfelgrdFlfsRviReafqavefeeseeelrerakeLGesiLepmvetikkvkeeekvkeefrvrfkdeeniee 79 
                                       ++ +fel + ++++R+ R +f + e++  ++e+++ a  LG+++Lep ve+i +v+ +e+++e f+vr+k  e++ +
  gi|242399312|ref|YP_002994736.1| 253 ARVFFELPHGYFMQRIKRLGFYLSEKKIRDAEFEKYATALGKALLEPFVESIWDVSGGEEIAEVFTVRVKHIETAYK 329
                                       67899************************************************************************ PP

                                       HHHHHHCTT--EEEEEEE...TTEEEEE..EE-HHHHHHHHHHHTT CS
                             Lig_C  80 llehLrrlgvkaeveekeke.dgelvvkfkkiaqsttdkikslLeG 124
                                       +++h++rlg+k+++ee e+  ++++ ++fk+++ ++t  i +l++G
  gi|242399312|ref|YP_002994736.1| 330 MVSHFERLGLKIHIEEIEEMpNDYWRISFKRVYPEATREILELWNG 375
                                       ******************888******************9999999 PP

>> RNA_ligase  RNA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.5   0.2   8.7e-23   3.9e-19       2     161 .]      86     240 ..      85     240 .. 0.75

  Alignments for each domain:
  == domain 1  score: 69.5 bits;  conditional E-value: 8.7e-23
                                       EEEEEEE-SSEEEEEEEETT.EEEEETTCEB.CTTTHHHHHHTHHHHHHHH.HHHHH..ECCEEEEEEEES.SS... CS
                        RNA_ligase   2 evvvtEKlDGtnfriylvke.vgvasRsqil.pfgeekfkefkrwaaalrk.klkeklaneelilyGElighsi... 72 
                                       +++v+EK+DG+n+r+   ++ v +++R++++ pf++e++++         + ++ ++   ++l+l+GE+ g+     
  gi|242399312|ref|YP_002994736.1|  86 PFYVEEKVDGYNVRVAQIEGrVFAFTRGGFIcPFTTERIED-------FVNmEFFKD--YPNLVLCGEMAGPESpyl 153
                                       799*************99667**********6544444422.......221222333..456*********444234 PP

                                       ......TTSS.EEEEEEEEEEECTTBECE--HHHHHHHHHCCT..B..EEEEE.SSHHHHHCCC..HHHHTC--EEE CS
                        RNA_ligase  73 ....kygglpkefyvFdifdirdkeeqrylspdevealakglg..tvpvlyegkflaaeellell.lskgnkrEGlV 142
                                           +y + + +f++Fdi    +k++++ l+ +e+ ++a+++g  +v +++ +++++ ++l+el+ +  +++rEG+V
  gi|242399312|ref|YP_002994736.1| 154 vegpPYVKEDIKFFLFDIQ---EKRTGKSLPVKERVKIAEEYGipSVEIFGIYDISKINDLRELIeNLREQRREGIV 227
                                       4444444434499999999...677***************9*********999999777777773335677****** PP

                                       EEESSSSBETTEBSEEEEE CS
                        RNA_ligase 143 ikpeselyknkgraifKvk 161
                                       +k+ ++      ++i+K++
  gi|242399312|ref|YP_002994736.1| 228 MKSFDM------KRIIKYV 240
                                       **6666......9999996 PP

>> DNA_ligase_A_M  ATP dependent DNA ligase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   6.1e-06     0.028      10      80 ..      74     145 ..      67     151 .. 0.86
   2 !   16.8   0.2   9.4e-07    0.0042     114     188 ..     163     232 ..     158     237 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.1e-06
                                       HHHHHHHT.TTSEEEEEEEESSEEEEEEEETTEEEEEETTS-B-GGGCHHHHHHHHHHBSTTESEEEEEEEE CS
                    DNA_ligase_A_M  10 iekalkkl.eekafivEiKyDGeRaqvhkegdkvklfSRrlkditaakpelvkalkeafkkdeksvilDGEl 80 
                                       +e+ +k++ ++k+f+vE+K+DG+ ++v + +++v  f+R +   + + +++  +++  f+kd  +++l GE+
  gi|242399312|ref|YP_002994736.1|  74 LENGVKRVfKRKPFYVEEKVDGYNVRVAQIEGRVFAFTRGGFICPFTTERIEDFVNMEFFKDYPNLVLCGEM 145
                                       4555554325689***************999**********99999999999999999*99999****9998 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 9.4e-07
                                       EEEEEEEEEEEETTEEHTTSCHHHHHHHHHHHB--BTTTEEE--EEEESSHHHHHHHHHHHHHTTECEEEEEETT CS
                    DNA_ligase_A_M 114 elclfvFDiLyldgesltdeplkeRrklLeeilkesedrvelaeslevkdveeleelleeaiseglEGlvvKnpd 188
                                        + +f+FDi   ++ +   +p+keR k+ ee+       ve+   ++++++++l+el+e+  +++ EG+v+K+ d
  gi|242399312|ref|YP_002994736.1| 163 DIKFFLFDIQ--EKRTGKSLPVKERVKIAEEYG---IPSVEIFGIYDISKINDLRELIENLREQRREGIVMKSFD 232
                                       5679999999..44445689***********98...45688899999999999*******************976 PP

>> SwrA  Swarming motility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.7e-05      0.12       8      83 ..     207     279 ..     203     286 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.7e-05
                              SwrA   8 kekkyqelleelkvkstevtssaskavkllrlfsrylvnytsvkevedidkdcveeyfsylidnhkrlslsltdik 83 
                                       k +  +el+e+l+++++e  +  s+++k    + +y++ y+ ++++    +   e+   y+++  krl++ l++ k
  gi|242399312|ref|YP_002994736.1| 207 KINDLRELIENLREQRREGIVMKSFDMK---RIIKYVTPYANINDIRIGARVFFELPHGYFMQRIKRLGFYLSEKK 279
                                       5566789*******************55...5579***********99999999***************9998755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); 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: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2361.27
//
Query:       gi|242399313|ref|YP_002994737.1|  [L=241]
Description: tRNA-binding protein [Thermococcus sibiricus MM 739]
Scores for complete 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-56  188.8   0.5    4.7e-56  188.4   0.5    1.1  1  Alpha_Helical  Alpha helical domain
    1.9e-20   72.7   0.1    3.3e-20   72.0   0.1    1.3  1  tRNA_bind      Putative tRNA binding domain


Domain annotation for each model (and alignments):
>> Alpha_Helical  Alpha helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  188.4   0.5   5.2e-60   4.7e-56       1     127 []       1     127 [.       1     127 [. 1.00

  Alignments for each domain:
  == domain 1  score: 188.4 bits;  conditional E-value: 5.2e-60
                     Alpha_Helical   1 mwDtskDYRllvaekavelferivegaklrgkwnkkkalelakemeselqslkysylepedLakseevkklkekaee 77 
                                       mwDts+DYRllvaeka+elf++++egak++gkw+kk+a++lak+m +elq+l+ysylep++L++++++k+lkek+e 
  gi|242399313|ref|YP_002994737.1|   1 MWDTSNDYRLLVAEKAIELFLKTIEGAKFKGKWDKKRAVQLAKRMIPELQALRYSYLEPSELIETPQMKDLKEKVEG 77 
                                       9**************************************************************************** PP

                     Alpha_Helical  78 iiealggeewsekfleeaekeekekteesiakvkfflrtllglkkRlalG 127
                                       iiealggeew+ +fle a+++e+ek+eesiakv+ffl+t+++l+kRlalG
  gi|242399313|ref|YP_002994737.1|  78 IIEALGGEEWYVRFLELADRHEREKLEESIAKVRFFLNTIMNLDKRLALG 127
                                       *************************************************9 PP

>> tRNA_bind  Putative tRNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.0   0.1   3.7e-24   3.3e-20       1      92 [.     138     224 ..     138     226 .. 0.95

  Alignments for each domain:
  == domain 1  score: 72.0 bits;  conditional E-value: 3.7e-24
                                       EEEEEEEEEEEETTSSTEEEEEEEESSSSEEEEEESCTTTSTHHHHTTEEEEEETTSESEEETTEEESSEE-EEEC. CS
                         tRNA_bind   1 lrvGkvleaeehpnadkLlvlkvdvGeeeprqivsgaknvyepeelvakkvvvvanlkpkklrGveSeGMilsaee. 76 
                                       ++vG+v++a +hpnadkLlv++v++G+++ +++v+++ +v e      ++ v+va+l p ++rG++SeGM+l+a+e 
  gi|242399313|ref|YP_002994737.1| 138 IKVGEVMSAGKHPNADKLLVCNVNIGDKA-ITVVTNDLSVKE------GHRVAVALLPPVNFRGITSEGMFLGASEg 207
                                       78***************************.************......****************************9 PP

                                       .CESSCEEEEEESST-- CS
                         tRNA_bind  77 .ldekevgilelpadve 92 
                                        l++ + +i  lp+ ++
  gi|242399313|ref|YP_002994737.1| 208 vLKDVNGEIGGLPKGIP 224
                                       99999999988888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1570.87
//
Query:       gi|242399314|ref|YP_002994738.1|  [L=356]
Description: hypothetical protein TSIB_1337 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.029   14.3   0.1      0.098   12.6   0.0    1.9  2  APT       Aerolysin/Pertussis toxin (APT) domain
      0.051   13.8   2.5         14    6.2   0.0    4.3  3  TPR_8     Tetratricopeptide repeat
        0.1   12.9   5.5         10    6.5   0.1    4.3  4  TPR_12    Tetratricopeptide repeat
        3.8    7.9  13.2         41    4.6   0.0    5.0  5  TPR_2     Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> APT  Aerolysin/Pertussis toxin (APT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.81   3.6e+03      19      45 ..     179     205 ..     165     209 .. 0.72
   2 ?   12.6   0.0   2.2e-05     0.098      16      47 ..     316     347 ..     289     352 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.81
                                       TB--TTEEE--HHHHHH-HHHHHHHHC CS
                               APT  19 erCanktRaltvaelrgsaelksylrn 45 
                                       e   n  R l   elr +a l +   +
  gi|242399314|ref|YP_002994738.1| 179 EIYENIRRNLIARELRKKASLIEAATQ 205
                                       555677888999999998887766555 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 2.2e-05
                                       ECTTB--TTEEE--HHHHHH-HHHHHHHHCC- CS
                               APT  16 gayerCanktRaltvaelrgsaelksylrnvt 47 
                                        ay r ++k +a+tvae+ ++ ++k+ + + +
  gi|242399314|ref|YP_002994738.1| 316 LAYARKGDKLKAVTVAEAISNENVKKEILKAI 347
                                       58999********************9987655 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1     0.057   2.6e+02       1      17 [.      68      84 ..      68      85 .. 0.91
   2 ?    1.7   0.2     0.084   3.8e+02      19      33 ..     169     183 ..     169     184 .. 0.86
   3 ?    6.2   0.0    0.0032        14       2      25 ..     309     332 ..     308     335 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.057
                                      CCHHHHHHHHHHHTT-H CS
                             TPR_8  1 aeayynlgsiylklgdy 17
                                      a+a+ ++g+++l  gd 
  gi|242399314|ref|YP_002994738.1| 68 ARALALIGYTLLASGDS 84
                                      799**********9996 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.084
                                       HHHHHHHHHHHHHHH CS
                             TPR_8  19 eAkeyyekaleldpd 33 
                                       +A e+ye a e+ ++
  gi|242399314|ref|YP_002994738.1| 169 NAREFYELAAEIYEN 183
                                       6999*****999875 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.0032
                                       CHHHHHHHHHHHTT-HHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyye 25 
                                       ++  +++++y  +gd+ +A+ + e
  gi|242399314|ref|YP_002994738.1| 309 QVFARIALAYARKGDKLKAVTVAE 332
                                       67889*************998765 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.032   1.4e+02      31      61 ..      56      84 ..      40      86 .. 0.77
   2 ?    6.5   0.1    0.0023        10      35      73 ..      99     135 ..      88     137 .. 0.82
   3 ?    2.3   0.1     0.046   2.1e+02      21      36 ..     169     184 ..     166     200 .. 0.78
   4 ?    0.1   0.0      0.23     1e+03      29      66 ..     294     329 ..     288     333 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.032
                            TPR_12 31 eiarrllGpdhpltattlrnLgrlyralgry 61
                                      e + +l  +++++ a++l  +g +++a+g+ 
  gi|242399314|ref|YP_002994738.1| 56 ETVDSL--KESLEKARALALIGYTLLASGDS 84
                                      455555..67888888888888888888885 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0023
                            TPR_12  35 rllGpdhpltattlrnLgrlyralgryeeAlelleeala 73 
                                       ++  +  ++ a  +  L+ +  ++g+y +A ++++ +++
  gi|242399314|ref|YP_002994738.1|  99 SI--DSTLWRADGYGYLAYYMALSGKYSDAFYYYNVSYE 135
                                       55..556788888999999999*************9987 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.046
                            TPR_12  21 eAlellekaleiarrl 36 
                                        A+e++e a ei++++
  gi|242399314|ref|YP_002994738.1| 169 NAREFYELAAEIYENI 184
                                       5788888888888766 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 0.23
                            TPR_12  29 aleiarrllGpdhpltattlrnLgrlyralgryeeAle 66 
                                       al ia  +  ++++ ++++   ++ +y + g+  +A+ 
  gi|242399314|ref|YP_002994738.1| 294 ALTIAAII--TNKEIASQVFARIALAYARKGDKLKAVT 329
                                       66666555..7777888888889999999999888875 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0         2   8.8e+03      12      23 ..       9      20 ..       8      23 .. 0.77
   2 ?   -0.5   0.0      0.39   1.8e+03       1      16 [.      68      83 ..      68      85 .. 0.88
   3 ?    3.4   3.5     0.023     1e+02       1      25 [.     107     131 ..     107     135 .. 0.91
   4 ?    2.0   0.1     0.064   2.9e+02      20      33 ..     170     183 ..     167     184 .. 0.89
   5 ?    4.6   0.0    0.0092        41       4      23 ..     311     330 ..     308     334 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2
                             TPR_2 12 yklgdyeeAlea 23
                                      +++gd+  Al++
  gi|242399314|ref|YP_002994738.1|  9 MERGDFGSALDL 20
                                      678999999876 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.39
                             TPR_2  1 aealynlGlayyklgd 16
                                      a+al  +G+ ++++gd
  gi|242399314|ref|YP_002994738.1| 68 ARALALIGYTLLASGD 83
                                      689999*****99998 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.023
                             TPR_2   1 aealynlGlayyklgdyeeAleafe 25 
                                       a+++ +l++  + +g+y +A  +++
  gi|242399314|ref|YP_002994738.1| 107 ADGYGYLAYYMALSGKYSDAFYYYN 131
                                       67899*****************997 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.064
                             TPR_2  20 AleafekAleldPn 33 
                                       A+e++e A e+++n
  gi|242399314|ref|YP_002994738.1| 170 AREFYELAAEIYEN 183
                                       9*********9987 PP

  == domain 5  score: 4.6 bits;  conditional E-value: 0.0092
                             TPR_2   4 lynlGlayyklgdyeeAlea 23 
                                         +++lay+++gd  +A+  
  gi|242399314|ref|YP_002994738.1| 311 FARIALAYARKGDKLKAVTV 330
                                       6789**********999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); 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: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2357.89
//
Query:       gi|242399315|ref|YP_002994739.1|  [L=110]
Description: hypothetical protein TSIB_1338 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-05   24.1   1.2       0.12   12.5   0.3    2.5  2  zf-ACC          Acetyl-coA carboxylase zinc finger domain
    0.00097   18.6   1.7       0.94    9.0   0.2    2.5  2  TF_Zn_Ribbon    TFIIB zinc-binding
     0.0015   17.9   0.8        1.1    8.7   0.2    2.2  2  zf-ribbon_3     zinc-ribbon domain
  ------ inclusion threshold ------
      0.014   15.6   0.3        5.2    7.4   0.1    2.2  2  zf-Di19         Drought induced 19 protein (Di19), zinc-bindi
       0.02   14.7   0.4          6    6.8   0.0    2.6  2  Rad50_zn_hook   Rad50 zinc hook motif
      0.038   14.5   1.1        1.8    9.2   0.3    2.4  2  zf-C2H2         Zinc finger, C2H2 type
      0.038   13.7   0.5        6.3    6.6   0.1    2.3  2  YacG            DNA gyrase inhibitor YacG
      0.038   14.1   0.6       0.33   11.1   0.6    2.2  1  MqsA_antitoxin  Antitoxin component of bacterial toxin-antito
      0.048   13.6   0.6        4.2    7.4   0.1    2.3  2  zinc_ribbon_4   zinc-ribbon domain
       0.05   13.2   0.8        1.8    8.2   0.1    2.4  2  zf_UBZ          Ubiquitin-Binding Zinc Finger
      0.051   13.3   4.4       0.51   10.1   0.7    2.5  2  zinc_ribbon_2   zinc-ribbon domain
      0.064   13.2   0.4        9.6    6.3   0.0    2.2  2  Ogr_Delta       Ogr/Delta-like zinc finger
       0.11   13.4   2.0        3.3    8.8   0.2    2.4  2  zf-C2H2_4       C2H2-type zinc finger
       0.11   12.5   2.5        6.2    6.9   0.1    2.4  2  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
       0.11   12.6   2.8        1.1    9.5   0.7    2.4  2  Zn-ribbon_8     Zinc ribbon domain
       0.12   12.5   0.1        2.6    8.2   0.0    2.2  2  DiS_P_DiS       Bacterial Peptidase A24 N-terminal domain
       0.13   12.2   0.9         13    5.8   0.1    2.2  2  Prok-RING_1     Prokaryotic RING finger family 1
       0.13   12.2   1.0        2.9    7.9   0.1    2.2  2  Zn_ribbon_SprT  SprT-like zinc ribbon domain
       0.14   12.1   1.7        7.5    6.6   0.2    2.3  2  YhfH            YhfH-like protein
       0.18   11.7   1.5         24    4.9   0.3    2.8  3  Cys_rich_CPXG   Cysteine-rich CPXCG
        0.2   11.4   1.6        1.9    8.2   0.1    2.1  2  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
        0.2   12.2   2.6        8.8    6.9   0.3    2.5  2  Zn-C2H2_12      Autophagy receptor zinc finger-C2H2 domain
        0.3   11.2   1.4        3.2    7.8   1.4    2.2  1  CpXC            CpXC protein
       0.34   10.9   8.9       0.19   11.7   1.9    2.2  2  DUF1610         Domain of unknown function (DUF1610)
       0.51   10.4   1.8        2.7    8.1   0.2    2.3  2  zf-C2H2_6       C2H2-type zinc finger
       0.65   10.5   3.8        2.8    8.5   0.7    2.2  2  zf-H2C2_2       Zinc-finger double domain
       0.74    9.4   5.2        1.3    8.7   1.2    2.2  2  zf_C2H2_10      C2H2 type zinc-finger
        5.1    7.1   7.6        5.3    7.1   2.0    2.2  2  zf-C2HC_2       zinc-finger of a C2HC-type


Domain annotation for each model (and alignments):
>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0    0.0011      0.69       3      20 ..       3      20 ..       2      22 .. 0.88
   2 !   12.5   0.3   0.00018      0.12       2      19 ..      45      62 ..      45      62 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0011
                            zf-ACC  3 KCpsCgemlykkeLernl 20
                                      +Cp Cge++  ++L +++
  gi|242399315|ref|YP_002994739.1|  3 RCPLCGEVIKWEDLVEQM 20
                                      8************99876 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00018
                            zf-ACC  2 tKCpsCgemlykkeLern 19
                                      +KCp+Cge  y + L +n
  gi|242399315|ref|YP_002994739.1| 45 FKCPKCGEEFYGNNLNQN 62
                                      5*******9999988766 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.1    0.0019       1.2      21      35 ..       3      17 ..       1      20 [. 0.80
   2 !    9.0   0.2    0.0015      0.94       1      11 [.      45      55 ..      45      65 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0019
                                      EESSSSBEEEECCCC CS
                      TF_Zn_Ribbon 21 vCtdCGlVlednsid 35
                                      +C+ CG+V+  ++ +
  gi|242399315|ref|YP_002994739.1|  3 RCPLCGEVIKWEDLV 17
                                      7*******9876665 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0015
                                      EEETTTTCEEC CS
                      TF_Zn_Ribbon  1 ykCPnCgstnl 11
                                      +kCP+Cg +++
  gi|242399315|ref|YP_002994739.1| 45 FKCPKCGEEFY 55
                                      79*****9875 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0    0.0034       2.2       3      13 ..       2      12 ..       1      17 [. 0.79
   2 !    8.7   0.2    0.0018       1.1       4      10 ..      46      52 ..      43      54 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0034
                       zf-ribbon_3  3 vrCPnCGapls 13
                                       rCP CG++++
  gi|242399315|ref|YP_002994739.1|  2 SRCPLCGEVIK 12
                                      58*****9776 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0018
                       zf-ribbon_3  4 rCPnCGa 10
                                      +CP+CG+
  gi|242399315|ref|YP_002994739.1| 46 KCPKCGE 52
                                      5666664 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 ?    6.3   0.0     0.019        12       5      19 ..       4      18 ..       2      25 .. 0.61
   2 ?    7.4   0.1    0.0081       5.2       3      17 ..      45      59 ..      43      66 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.019
                           zf-Di19  5 CPyCgkeltvkeLve 19
                                      CP Cg+ ++ + Lve
  gi|242399315|ref|YP_002994739.1|  4 CPLCGEVIKWEDLVE 18
                                      666666665555555 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0081
                           zf-Di19  3 ftCPyCgkeltvkeL 17
                                      f+CP Cg+e+  ++L
  gi|242399315|ref|YP_002994739.1| 45 FKCPKCGEEFYGNNL 59
                                      9*******9987776 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 ?    5.9   0.1     0.018        12      21      27 ..       3       9 ..       2      21 .. 0.80
   2 ?    6.8   0.0    0.0094         6      21      31 ..      46      56 ..      27      67 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.018
                                      E-TTT-- CS
                     Rad50_zn_hook 21 cCPlCgR 27
                                      +CPlCg 
  gi|242399315|ref|YP_002994739.1|  3 RCPLCGE 9 
                                      7****96 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0094
                                      E-TTT--EE-H CS
                     Rad50_zn_hook 21 cCPlCgRelde 31
                                      +CP Cg e+  
  gi|242399315|ref|YP_002994739.1| 46 KCPKCGEEFYG 56
                                      9******9965 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0      0.14        90       2       9 ..       3      10 ..       2      17 .. 0.81
   2 ?    9.2   0.3    0.0028       1.8       1      11 [.      45      55 ..      45      61 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.14
                                      EETTTTEE CS
                           zf-C2H2  2 kCpdCgks 9 
                                      +Cp Cg++
  gi|242399315|ref|YP_002994739.1|  3 RCPLCGEV 10
                                      7*****87 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0028
                                      EEETTTTEEES CS
                           zf-C2H2  1 ykCpdCgksFk 11
                                      +kCp+Cg+ F 
  gi|242399315|ref|YP_002994739.1| 45 FKCPKCGEEFY 55
                                      8******9995 PP

>> YacG  DNA gyrase inhibitor YacG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1    0.0098       6.3       2      14 ..       3      15 ..       2      20 .. 0.87
   2 ?    5.5   0.1     0.021        14       2      13 ..      46      57 ..      45      64 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0098
                              YacG  2 kCPtCkkevewse 14
                                      +CP C++ ++w++
  gi|242399315|ref|YP_002994739.1|  3 RCPLCGEVIKWED 15
                                      8*********986 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.021
                              YacG  2 kCPtCkkevews 13
                                      kCP+C++e+  +
  gi|242399315|ref|YP_002994739.1| 46 KCPKCGEEFYGN 57
                                      8*****997655 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 ?   11.1   0.6   0.00051      0.33      35      69 ..      45      79 ..       2      97 .. 0.52

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00051
                    MqsA_antitoxin 35 dfCarCGegvldeeeedrlseellefrkkvnaelv 69
                                        C++CGe +++++ +++ ++++ e+ ++ n+++ 
  gi|242399315|ref|YP_002994739.1| 45 FKCPKCGEEFYGNNLNQNEASKVFELLNEFNGSID 79
                                      34999999998887666666666666666666552 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.047        30      27      35 ..       3      11 ..       1      12 [. 0.86
   2 ?    7.4   0.1    0.0066       4.2      26      35 ..      45      54 ..      41      55 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.047
                     zinc_ribbon_4 27 rCskCghvF 35
                                      rC+ Cg+v+
  gi|242399315|ref|YP_002994739.1|  3 RCPLCGEVI 11
                                      9*****997 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0066
                     zinc_ribbon_4 26 vrCskCghvF 35
                                       +C+kCg+ F
  gi|242399315|ref|YP_002994739.1| 45 FKCPKCGEEF 54
                                      6899998766 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1       0.1        64       5      16 ..       4      15 ..       1      18 [. 0.79
   2 ?    8.2   0.1    0.0028       1.8       3      12 ..      45      54 ..      44      60 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.1
                            zf_UBZ  5 CerCgkeipese 16
                                      C+ Cg+ i  ++
  gi|242399315|ref|YP_002994739.1|  4 CPLCGEVIKWED 15
                                      *******98655 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0028
                            zf_UBZ  3 ylCerCgkei 12
                                      + C++Cg+e+
  gi|242399315|ref|YP_002994739.1| 45 FKCPKCGEEF 54
                                      89*****998 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.2     0.058        37       1       8 [.       3      10 ..       3      12 .. 0.70
   2 ?   10.1   0.7    0.0008      0.51       1       8 [.      46      53 ..      41      54 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.058
                     zinc_ribbon_2  1 fCpnCGae 8 
                                      +Cp CG+ 
  gi|242399315|ref|YP_002994739.1|  3 RCPLCGEV 10
                                      58888875 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0008
                     zinc_ribbon_2  1 fCpnCGae 8 
                                      +Cp+CG+e
  gi|242399315|ref|YP_002994739.1| 46 KCPKCGEE 53
                                      56666664 PP

>> Ogr_Delta  Ogr/Delta-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1     0.032        20       1       8 [.       3      10 ..       3      13 .. 0.85
   2 ?    6.3   0.0     0.015       9.6       1      13 [.      46      58 ..      46      65 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.032
                         Ogr_Delta  1 rCPhCgap 8 
                                      rCP+Cg+ 
  gi|242399315|ref|YP_002994739.1|  3 RCPLCGEV 10
                                      7*****86 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.015
                         Ogr_Delta  1 rCPhCgapaaart 13
                                      +CP+Cg++ +  +
  gi|242399315|ref|YP_002994739.1| 46 KCPKCGEEFYGNN 58
                                      6*****9877665 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   0.1      0.18   1.2e+02       2       9 ..       3      10 ..       2      15 .. 0.87
   2 ?    8.8   0.2    0.0052       3.3       1      10 [.      45      54 ..      45      61 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.18
                         zf-C2H2_4  2 kCpiCgks 9 
                                      +Cp+Cg++
  gi|242399315|ref|YP_002994739.1|  3 RCPLCGEV 10
                                      6****975 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0052
                         zf-C2H2_4  1 fkCpiCgksF 10
                                      fkCp Cg+ F
  gi|242399315|ref|YP_002994739.1| 45 FKCPKCGEEF 54
                                      8*******99 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.4     0.031        20       2       9 ..       1       8 [.       1       8 [. 0.88
   2 ?    6.9   0.1    0.0096       6.2      22      29 ..      47      54 ..      43      55 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.031
                    PhnA_Zn_Ribbon 2 lpkCplCa 9
                                     ++ CplC+
  gi|242399315|ref|YP_002994739.1| 1 MSRCPLCG 8
                                     799****5 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0096
                    PhnA_Zn_Ribbon 22 CpeCahEw 29
                                      Cp+C++E+
  gi|242399315|ref|YP_002994739.1| 47 CPKCGEEF 54
                                      88888775 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0       0.2   1.3e+02      28      34 ..       3       9 ..       1      18 [. 0.71
   2 ?    9.5   0.7    0.0017       1.1       4      15 ..      43      54 ..      42      67 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.2
                       Zn-ribbon_8 28 aCPeCgs 34
                                       CP Cg+
  gi|242399315|ref|YP_002994739.1|  3 RCPLCGE 9 
                                      3666664 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0017
                       Zn-ribbon_8  4 YeYrCeeCghef 15
                                      + ++C +Cg+ef
  gi|242399315|ref|YP_002994739.1| 43 FAFKCPKCGEEF 54
                                      6799*****999 PP

>> DiS_P_DiS  Bacterial Peptidase A24 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0    0.0041       2.6      28      43 ..       2      17 ..       1      18 [. 0.92
   2 ?    2.4   0.0      0.27   1.7e+02      28      36 ..      45      53 ..      21      59 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0041
                         DiS_P_DiS 28 SrCpkCghklkwleli 43
                                      SrCp Cg+ +kw +l+
  gi|242399315|ref|YP_002994739.1|  2 SRCPLCGEVIKWEDLV 17
                                      9***********9986 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.27
                         DiS_P_DiS 28 SrCpkCghk 36
                                       +CpkCg++
  gi|242399315|ref|YP_002994739.1| 45 FKCPKCGEE 53
                                      579999886 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 ?    5.1   0.0     0.034        22       6      20 ..       3      16 ..       1      18 [. 0.81
   2 ?    5.8   0.1     0.021        13       4      15 ..      44      55 ..      41      58 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.034
                       Prok-RING_1  6 kCpvCgkelkeedDi 20
                                      +Cp+Cg+ +k e D+
  gi|242399315|ref|YP_002994739.1|  3 RCPLCGEVIKWE-DL 16
                                      7******99988.55 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.021
                       Prok-RING_1  4 gkkCpvCgkelk 15
                                        kCp Cg+e+ 
  gi|242399315|ref|YP_002994739.1| 44 AFKCPKCGEEFY 55
                                      569999999996 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 ?    3.0   0.2      0.15        94       6      11 ..       3       8 ..       2      12 .. 0.71
   2 ?    7.9   0.1    0.0045       2.9       3      15 ..      43      55 ..      41      58 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.15
                    Zn_ribbon_SprT  6 rCtgCg 11
                                      rC+ Cg
  gi|242399315|ref|YP_002994739.1|  3 RCPLCG 8 
                                      688888 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0045
                    Zn_ribbon_SprT  3 yvYrCtgCgreyt 15
                                      ++ +C+ Cg+e++
  gi|242399315|ref|YP_002994739.1| 43 FAFKCPKCGEEFY 55
                                      7889****99875 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1      0.05        32      15      24 ..       3      12 ..       1      14 [. 0.88
   2 ?    6.6   0.2     0.012       7.5      15      23 ..      46      54 ..      45      58 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.05
                              YhfH 15 kCteCGkeie 24
                                       C+ CG++i+
  gi|242399315|ref|YP_002994739.1|  3 RCPLCGEVIK 12
                                      5******995 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.012
                              YhfH 15 kCteCGkei 23
                                      kC++CG+e+
  gi|242399315|ref|YP_002994739.1| 46 KCPKCGEEF 54
                                      7*****986 PP

>> Cys_rich_CPXG  Cysteine-rich CPXCG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.046        29       2      11 ..       3      12 ..       2      17 .. 0.85
   2 ?    4.9   0.3     0.038        24       2      10 ..      46      54 ..      45      56 .. 0.88
   3 ?   -1.2   0.0         3   1.9e+03      34      50 ..      72      88 ..      71      90 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.046
                     Cys_rich_CPXG  2 qCPyCgeeie 11
                                       CP Cge i+
  gi|242399315|ref|YP_002994739.1|  3 RCPLCGEVIK 12
                                      5*****9876 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.038
                     Cys_rich_CPXG  2 qCPyCgeei 10
                                      +CP Cgee+
  gi|242399315|ref|YP_002994739.1| 46 KCPKCGEEF 54
                                      7******97 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 3
                     Cys_rich_CPXG 34 ivlqvevdeeegeveve 50
                                      ++++ ++d e+++v+++
  gi|242399315|ref|YP_002994739.1| 72 NEFNGSIDYENNKVRLK 88
                                      56788899999999886 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 ?    2.3   0.1      0.21   1.4e+02       6      10 ..       4       8 ..       2      12 .. 0.72
   2 ?    8.2   0.1    0.0029       1.9      23      32 .]      46      55 ..      42      55 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.21
                     zf-NADH-PPase  6 CgrCG 10
                                      C+ CG
  gi|242399315|ref|YP_002994739.1|  4 CPLCG 8 
                                      77777 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0029
                     zf-NADH-PPase 23 vCpaCglehY 32
                                       Cp Cg+e+Y
  gi|242399315|ref|YP_002994739.1| 46 KCPKCGEEFY 55
                                      6******999 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 ?    6.9   0.3     0.014       8.8       3       9 ..       4      10 ..       3      12 .. 0.89
   2 ?    4.8   0.1      0.06        39       2      10 ..      46      54 ..      46      63 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.014
                        Zn-C2H2_12  3 CPlCseq 9 
                                      CPlC+e+
  gi|242399315|ref|YP_002994739.1|  4 CPLCGEV 10
                                      *****96 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.06
                        Zn-C2H2_12  2 eCPlCseqF 10
                                      +CP C+e F
  gi|242399315|ref|YP_002994739.1| 46 KCPKCGEEF 54
                                      7****9987 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   1.4    0.0049       3.2      34      47 ..      41      54 ..       3      58 .. 0.61

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0049
                              CpXC 34 slfeatCpkCgata 47
                                      + f ++CpkCg+++
  gi|242399315|ref|YP_002994739.1| 41 NSFAFKCPKCGEEF 54
                                      45789999999987 PP

>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.8      0.12        77      19      24 .]       4       9 ..       3       9 .. 0.94
   2 ?   11.7   1.9    0.0003      0.19      16      24 .]      44      52 ..      41      52 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.12
                           DUF1610 19 CPNCGE 24
                                      CP CGE
  gi|242399315|ref|YP_002994739.1|  4 CPLCGE 9 
                                      *****9 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.0003
                           DUF1610 16 vFpCPNCGE 24
                                      +F CP+CGE
  gi|242399315|ref|YP_002994739.1| 44 AFKCPKCGE 52
                                      79******9 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 ?    1.3   0.1      0.57   3.6e+02       3      10 ..       3      10 ..       3      10 .. 0.86
   2 ?    8.1   0.2    0.0042       2.7       1      11 [.      44      54 ..      44      59 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.57
                         zf-C2H2_6  3 eCsvCsks 10
                                      +C+ C+++
  gi|242399315|ref|YP_002994739.1|  3 RCPLCGEV 10
                                      7****986 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0042
                         zf-C2H2_6  1 vheCsvCsksF 11
                                      +++C+ C+++F
  gi|242399315|ref|YP_002994739.1| 44 AFKCPKCGEEF 54
                                      69*******99 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 ?    2.9   0.1      0.27   1.7e+02      17      22 ..       4       9 ..       3      12 .. 0.81
   2 ?    8.5   0.7    0.0043       2.8      13      24 ..      43      54 ..      38      55 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.27
                         zf-H2C2_2 17 CplCdk 22
                                      CplC+ 
  gi|242399315|ref|YP_002994739.1|  4 CPLCGE 9 
                                      ****85 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0043
                         zf-H2C2_2 13 kpyeCplCdkaF 24
                                      + ++Cp+C+  F
  gi|242399315|ref|YP_002994739.1| 43 FAFKCPKCGEEF 54
                                      569*****9887 PP

>> zf_C2H2_10  C2H2 type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1      0.19   1.2e+02       5      11 ..       4      10 ..       2      12 .. 0.89
   2 ?    8.7   1.2     0.002       1.3       3      10 ..      45      52 ..      44      54 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.19
                        zf_C2H2_10  5 CPKCqek 11
                                      CP C+e+
  gi|242399315|ref|YP_002994739.1|  4 CPLCGEV 10
                                      *****97 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.002
                        zf_C2H2_10  3 fsCPKCqe 10
                                      f CPKC+e
  gi|242399315|ref|YP_002994739.1| 45 FKCPKCGE 52
                                      88****98 PP

>> zf-C2HC_2  zinc-finger of a C2HC-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.3      0.13        84       4       9 ..       3       8 ..       1       9 [. 0.83
   2 ?    7.1   2.0    0.0083       5.3       4      12 ..      46      54 ..      45      54 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.13
                         zf-C2HC_2 4 pCpkCg 9
                                      Cp Cg
  gi|242399315|ref|YP_002994739.1| 3 RCPLCG 8
                                     7****9 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0083
                         zf-C2HC_2  4 pCpkCgRsF 12
                                      +CpkCg  F
  gi|242399315|ref|YP_002994739.1| 46 KCPKCGEEF 54
                                      8*****998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       836  (0.0466284); expected 358.6 (0.02)
Passed bias filter:                      583  (0.0325172); expected 358.6 (0.02)
Passed Vit filter:                       109  (0.00607954); 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: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 663.28
//
Query:       gi|242399316|ref|YP_002994740.1|  [L=326]
Description: phosphohydrolase, DHH family [Thermococcus sibiricus MM 739]
Scores for complete 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-13   49.0   1.8    6.8e-12   46.0   1.8    2.2  2  DHHA1     DHHA1 domain
    2.8e-12   46.8   0.1      7e-12   45.5   0.1    1.7  1  DHH       DHH family
  ------ inclusion threshold ------
      0.037   14.0   0.6        3.7    7.4   0.2    2.3  2  SPOC      SPOC 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 ?    0.4   0.0      0.14   8.2e+02      25      60 ..       5      38 ..       2      60 .. 0.78
   2 !   46.0   1.8   1.1e-15   6.8e-12      58     137 ..     238     317 ..     196     318 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.14
                                      HHHHHHHHTCEEECTCEEEEEECHCCHHHHHHHHHH CS
                             DHHA1 25 lkaeellekaeevkgvkvlvaevgeewdagalgiaa 60
                                      +k + +l+ka++  ++++++    +++d++ lg+a+
  gi|242399316|ref|YP_002994740.1|  5 IKLKRFLNKAKKN-NYSFMLLCH-HNADPDSLGSAI 38
                                      5666777777765.888888888.999999999985 PP

  == domain 2  score: 46.0 bits;  conditional E-value: 1.1e-15
                                       HHHHHHHTHGBTTCEEEEEEEECTEEEEEEEESSH....SS-HHHHHHHHHHHTTCCEEEETCEEEEEEEHCHHHHH CS
                             DHHA1  58 iaadklksklkkpvivfvakeegdkvkvsarskkd....gvdagelakeaaaklgggGGGHdlAaGagipaekleea 130
                                        a+  +++    + +++v +e++  v++s r+k+     g+++g++++++ +++ g+GGGH  AaGa+ +  +l+ea
  gi|242399316|ref|YP_002994740.1| 238 LACKTFLQ--LGADVAIVGSEKN-GVRISSRAKEHlikkGLHLGKIMEKVGPIIDGSGGGHSGAAGANGK-KNLDEA 310
                                       34555555..5578888888887.9********99**********************************6.99**** PP

                                       HHHHHHH CS
                             DHHA1 131 lealeea 137
                                       +++l + 
  gi|242399316|ref|YP_002994740.1| 311 VKFLVKE 317
                                       **99876 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.5   0.1   1.2e-15     7e-12       2      86 ..      21     148 ..      20     163 .. 0.69

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 1.2e-15
                                       EEEE-ECSSSHHHHHHHHHHHH.........................................CECS--TCGGCGCC CS
                                       xxxxxxxxxxxxxxxxxxxxxx.........................................xxxxxxxxxxxxxx RF
                               DHH   2 ilivghknpDtDsigSaialan.........................................llvDhneksqaveg 37 
                                       +++++h+n D Ds+gSaia+++                                         ++ D+++ +q    
  gi|242399316|ref|YP_002994740.1|  21 FMLLCHHNADPDSLGSAIAFSRyltsmglknrigvaqsissyakrllqfaeveknpkveedviIIFDTSSLEQLDPI 97 
                                       56789*****************5555555555555555555554444444444444444444445555555555433 PP

                                       HHCCCSEEEEEEE-S---SS---SS--EEEE-SSS-HHHHHHHHHHH....TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xx RF
                               DHH  38 eakeeaedviiiDHHrlgeefetlapilflnepvgstaeivaellee....kk 86 
                                           e+++vi+iDHH  + e+   a+i +++++  staeiv++l+++    ++
  gi|242399316|ref|YP_002994740.1|  98 -NLPEGKIVIVIDHHVEK-ENPIKADIKIVDSSRTSTAEIVWDLFKYlgfrDE 148
                                       .8999************9.6666669*******************99654322 PP

>> SPOC  SPOC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0    0.0053        32      54     101 ..       8      57 ..       3      99 .. 0.81
   2 ?    7.4   0.2   0.00062       3.7      38      69 ..     206     238 ..     169     253 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0053
                                       HHHHHH-S......EEEEEEEE.ESSGGGHHHHHHHHHHHHTTTEEEE.. CS
                              SPOC  54 kkyldevsrri.tadllavalf.psdesdesgfaelvdYLksKqraGvvn 101
                                       k +l + ++   + +ll  + + p++  +  +f ++ +++  K+r+Gv +
  gi|242399316|ref|YP_002994740.1|   8 KRFLNKAKKNNySFMLLCHHNAdPDSLGSAIAFSRYLTSMGLKNRIGVAQ 57 
                                       5667777766644477777777789999999999**************44 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.00062
                                       -.-SEEEE-EEEEHHHHHHHHHH-S.....EEE CS
                              SPOC  38 s.pslLritqRlrldqvkkyldevsrritadll 69 
                                       + + +L+ +qR+++++vk+y+ ++s+  + + l
  gi|242399316|ref|YP_002994740.1| 206 KrMAILKACQRMEIKKVKNYIIAISKVSSYESL 238
                                       23667****************999987655444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       834  (0.0465168); expected 358.6 (0.02)
Passed bias filter:                      560  (0.0312343); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.34s 00:00:00.93 Elapsed: 00:00:00.52
# Mc/sec: 1877.35
//
Query:       gi|242399317|ref|YP_002994741.1|  [L=102]
Description: hypothetical protein TSIB_1340 [Thermococcus sibiricus MM 739]
Scores for complete 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-23   80.7   3.2    9.3e-23   80.4   3.2    1.1  1  DUF3194   Protein of unknown function (DUF3194)


Domain annotation for each model (and alignments):
>> DUF3194  Protein of unknown function (DUF3194)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.4   3.2   5.2e-27   9.3e-23       1      81 [.       9      90 ..       9      91 .. 0.98

  Alignments for each domain:
  == domain 1  score: 80.4 bits;  conditional E-value: 5.2e-27
                                      ----SHHHHHHHHHHHHHHHHHHHHTTS-TTTEEEEEEEEEEEESSSEEEEEEEEEEE-TT----TT.HHHHHHHHHHH CS
                           DUF3194  1 LkkLteedldeiseflaeviekkifkkvskkevldlditvevkeneeLdvdveveleldelskldqe.lideavdeaye 78
                                      L++L ee+l + +e+++e+++++if ++ ++ev+d+++t++++++++Ld+++e++le++ ++k+d++ l+++a++eay+
  gi|242399317|ref|YP_002994741.1|  9 LPELNEEELVKLGELAQETAIEYIFAHLTRSEVKDIEVTTKLNQGDTLDLELEIYLEVPIFVKVDVDnLVEKALEEAYK 87
                                      79****************************************************************99*********** PP

                                      HHH CS
                           DUF3194 79 eld 81
                                      +++
  gi|242399317|ref|YP_002994741.1| 88 KVE 90
                                      *98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       782  (0.0436165); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.33s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 620.67
//
Query:       gi|242399318|ref|YP_002994742.1|  [L=133]
Description: Prefoldin subunit beta [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.7e-22   78.0  18.5    5.3e-22   77.8  18.5    1.0  1  Prefoldin_2      Prefoldin subunit
    0.00023   20.6   4.9    0.00028   20.3   4.9    1.1  1  ALIX_LYPXL_bnd   ALIX V-shaped domain binding to HIV
    0.00029   19.2   9.6    0.00035   18.9   9.6    1.0  1  FPP              Filament-like plant protein, long coiled-coi
    0.00064   19.5  11.5      0.013   15.3   0.5    2.2  2  CdvA             CdvA-like coiled-coil domain
    0.00068   20.3   6.6     0.0067   17.1   6.6    2.0  1  Ead_Ea22         Ead/Ea22-like protein
     0.0014   17.6  13.9      0.094   11.6   0.6    2.0  2  Spc7             Spc7 kinetochore protein
     0.0016   18.6   7.8       0.36   11.0   2.7    2.2  2  RasGAP_C         RasGAP C-terminus
     0.0023   18.0  15.7      0.073   13.1   7.4    2.0  2  DHR10            Designed helical repeat protein 10 domain
     0.0025   18.1   1.0     0.0034   17.7   1.0    1.1  1  DUF3416          Domain of unknown function (DUF3416)
     0.0046   16.6  13.0     0.0091   15.6  13.0    1.4  1  PspA_IM30        PspA/IM30 family
     0.0052   16.1  14.3      0.015   14.6   3.9    2.0  2  DUF3450          Protein of unknown function (DUF3450)
     0.0054   16.7  10.7     0.0077   16.2  10.7    1.3  1  Laminin_II       Laminin Domain II
     0.0057   16.0  11.2       0.15   11.4   5.0    2.0  2  GAS              Growth-arrest specific micro-tubule binding
     0.0066   16.6   6.0     0.0066   16.6   6.0    2.2  2  XhlA             Haemolysin XhlA
     0.0072   16.4   4.5     0.0094   16.1   2.8    1.8  2  DUF2120          Uncharacterized protein conserved in archaea
     0.0076   16.6  12.4      0.015   15.7   4.6    2.8  3  FlaC_arch        Flagella accessory protein C (FlaC)
     0.0082   16.8   7.2       0.82   10.4   0.3    2.2  2  DUF4404          Domain of unknown function (DUF4404)
  ------ inclusion threshold ------
      0.011   13.2   1.6      0.013   13.0   1.6    1.0  1  Bac_GDH          Bacterial NAD-glutamate dehydrogenase
      0.012   16.1  16.4       0.38   11.3   0.8    2.0  2  APG6_N           Apg6 coiled-coil region
      0.013   15.6  12.4       0.13   12.5   5.9    2.1  2  Tropomyosin_1    Tropomyosin like
      0.019   14.8   3.3      0.022   14.5   3.3    1.0  1  AAA_11           AAA domain
      0.021   12.8   3.6      0.027   12.4   3.6    1.2  1  V_ATPase_I       V-type ATPase 116kDa subunit family
      0.021   15.4   0.3       0.84   10.3   0.0    2.2  2  MCM_N            MCM N-terminal domain
      0.024   14.8  11.7      0.032   14.4  11.7    1.1  1  DUF3958          Protein of unknown function (DUF3958)
      0.028   14.5  12.8       0.41   10.8   3.2    2.3  2  TolA_bind_tri    TolA binding protein trimerisation
      0.029   14.3  12.7       0.66    9.9   1.6    2.1  2  YscO             Type III secretion protein YscO
      0.032   14.3  12.7       0.92    9.5   6.5    2.1  2  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
      0.033   12.2   7.1      0.045   11.7   7.1    1.2  1  Prominin         Prominin
      0.036   14.1  14.7       0.29   11.2   5.6    2.1  2  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
      0.047   13.9  10.8       0.38   11.0   2.5    2.4  2  FliJ             Flagellar FliJ protein
      0.048   13.2   3.9      0.056   13.0   3.9    1.1  1  Exonuc_VII_L     Exonuclease VII, large subunit
      0.052   13.5   8.9        0.1   12.6   8.9    1.5  1  SOAR             STIM1 Orai1-activating region
       0.06   12.7   4.7      0.073   12.4   4.7    1.2  1  DUF4407          Domain of unknown function (DUF4407)
      0.065   11.8   9.1      0.081   11.5   9.1    1.1  1  FapA             Flagellar Assembly Protein A
      0.069   13.2  13.2       0.26   11.4   6.5    2.1  2  ADIP             Afadin- and alpha -actinin-Binding
      0.071   13.3   0.2       0.11   12.7   0.2    1.5  1  TA0956           Thermoplasma acidophilum protein TA0956
      0.074   11.6   0.2      0.087   11.4   0.2    1.0  1  FUSC             Fusaric acid resistance protein family
      0.088   13.1   7.9       0.16   12.3   2.4    2.0  2  DUF641           Plant protein of unknown function (DUF641)
        0.1   13.1   9.2       0.31   11.5   2.0    2.2  2  NPV_P10          Nucleopolyhedrovirus P10 protein
       0.12   13.0  13.3       0.16   12.6   1.9    2.1  2  YabA             Initiation control protein YabA
       0.13   12.7  12.2         25    5.4  12.2    2.3  1  DUF4140          N-terminal domain of unknown function (DUF41
       0.14   12.6   0.0         11    6.4   0.0    2.1  2  Lambda_tail_I    Bacteriophage lambda tail assembly protein I
       0.15   12.0  17.7       0.13   12.2   6.9    2.4  2  Prefoldin        Prefoldin subunit
       0.15   12.4  10.1        2.2    8.7   4.8    2.3  2  CLZ              C-terminal leucine zipper domain of cyclic n
       0.17   11.6   6.1       0.16   11.7   1.2    2.0  2  DUF4988          Domain of unknown function
        0.2   11.2  15.3        0.7    9.4   5.4    2.0  2  Filament         Intermediate filament protein
       0.21   11.7   7.9        3.2    7.8   2.4    2.1  2  COG2             COG (conserved oligomeric Golgi) complex com
       0.23   10.6  10.8      0.077   12.2   7.5    1.6  1  DLP_helical      Dynamin-like helical domain
       0.23    9.6  14.3       0.35    9.0  14.3    1.3  1  EzrA             Septation ring formation regulator, EzrA
       0.46   10.8   9.4        2.5    8.4   0.8    2.3  2  DUF4164          Domain of unknown function (DUF4164)
       0.47   10.6   9.6       0.81    9.9   9.6    1.4  1  Uds1             Up-regulated During Septation
       0.57   10.4  17.0    1.5e+02    2.7  17.0    2.1  1  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
       0.65    9.6  15.5         14    5.2   2.5    2.0  2  PI3K_P85_iSH2    Phosphatidylinositol 3-kinase regulatory sub
       0.74   10.9   5.7        6.8    7.8   1.3    2.2  2  DUF5320          Family of unknown function (DUF5320)
       0.79    9.0  17.7        1.6    8.0   7.8    2.0  2  Tropomyosin      Tropomyosin
       0.79   10.1  10.4       0.48   10.8   2.0    2.3  2  E2F_CC-MB        E2F transcription factor CC-MB domain
       0.79   10.2   4.4        2.8    8.4   0.3    2.3  2  FAA_hydro_N_2    Fumarylacetoacetase N-terminal domain 2
       0.89    8.4   3.6        1.1    8.1   3.6    1.1  1  LMBR1            LMBR1-like membrane protein
        0.9    8.4  12.8        1.4    7.8  12.8    1.2  1  IFT57            Intra-flagellar transport protein 57
       0.93    9.4  12.1          2    8.3   2.0    2.1  2  Sec34            Sec34-like family
       0.96    9.7   4.7       0.46   10.7   1.2    2.2  2  CinA_KH          Damage-inducible protein CinA KH domain
          1    8.8  18.9        1.6    8.1   7.1    2.0  2  DUF4618          Domain of unknown function (DUF4618)
        1.5    9.0  12.6        7.5    6.7  12.6    2.0  1  Fib_alpha        Fibrinogen alpha/beta chain family
        1.9    8.7  14.1        2.4    8.3   1.5    2.1  2  CENP-Q           CENP-Q, a CENPA-CAD centromere complex subun
        1.9    7.0  12.3        3.5    6.2  12.3    1.3  1  AAA_13           AAA domain
        1.9    9.0  11.7      0.086   13.3   3.0    2.3  2  HSCB_C           HSCB C-terminal oligomerisation domain
          2    8.5  19.9        1.4    8.9   4.3    2.5  2  FlxA             FlxA-like protein
        2.1    8.4  10.8       0.56   10.3   3.3    2.0  2  MCU              Mitochondrial calcium uniporter
        2.4    7.9  12.9        0.9    9.3   4.6    2.0  2  zf-CpG_bind_C    CpG binding protein zinc finger C terminal d
        2.4    8.4   9.7          1    9.7   2.6    2.2  2  DUF948           Bacterial protein of unknown function (DUF94
        3.1    7.4  15.5         29    4.2  15.5    1.9  1  DUF4795          Domain of unknown function (DUF4795)
        3.3    8.2  20.1       0.19   12.3   6.7    2.1  2  DUF16            Protein of unknown function DUF16
        3.5    8.1  19.1        2.1    8.9   5.6    2.2  2  Snapin_Pallidin  Snapin/Pallidin
        4.3    7.3  14.3       0.12   12.2   4.9    2.2  2  GIT_CC           GIT coiled-coil Rho guanine nucleotide excha
        4.8    7.9  15.2       0.75   10.5   4.3    2.3  2  SlyX             SlyX
          5    7.7   9.6         17    6.1   8.1    2.0  2  Syntaxin-6_N     Syntaxin 6, N-terminal
        5.3    6.9  17.4        1.1    9.0   5.7    2.2  2  DivIC            Septum formation initiator
        5.5    5.7  10.4         11    4.8  10.4    1.4  1  Fmp27_WPPW       RNA pol II promoter Fmp27 protein domain
        5.6    7.3  14.3    4.3e+02    1.3  14.4    2.2  1  BLOC1_2          Biogenesis of lysosome-related organelles co
        6.5    7.3  12.2    1.9e+02    2.6  12.2    2.1  1  DUF2408          Protein of unknown function (DUF2408)
        7.1    6.0   7.6        6.4    6.2   4.1    1.9  2  Allexi_40kDa     Allexivirus 40kDa protein
        7.1    5.8  17.6         47    3.1  17.6    1.9  1  HemX             HemX, putative uroporphyrinogen-III C-methyl
        7.3    6.5   8.7         24    4.8   8.7    1.8  1  EMP24_GP25L      emp24/gp25L/p24 family/GOLD
        7.5    6.8  12.5        4.6    7.5   3.8    3.1  2  DUF2802          Protein of unknown function (DUF2802)
        8.7    7.1  11.0    5.4e+02    1.3  11.0    2.1  1  DUF2203          Uncharacterized conserved protein (DUF2203)
        8.8    6.6  15.2        6.2    7.1   5.8    2.2  2  Spc24            Spc24 subunit of Ndc80
          9    7.0  12.5       0.34   11.6   4.1    2.3  2  DUF5398          Family of unknown function (DUF5398)


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 !   77.8  18.5   2.6e-24   5.3e-22       1     104 [.      25     128 ..      25     130 .. 0.98

  Alignments for each domain:
  == domain 1  score: 77.8 bits;  conditional E-value: 2.6e-24
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-TT--EEEEETTEEEEE-HHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2   1 qelinkfqqlqqqlqqlaqqikqletqlkelelvleelelldedtkvyklvGdvlvkqdkeevkeeLeerketleke 77 
                                       q+l+ +++ +qqq+q + qq++ ++ +l++++++lee+e+ +e t++yk vG + vk +k +++ee++e+ etle +
  gi|242399318|ref|YP_002994742.1|  25 QALLGQLESYQQQIQLVIQQKQRVQVELNDAKKALEEIEKTEEGTPIYKTVGTLIVKSTKSKALEEVKEKVETLEVR 101
                                       8999************************************************************************* PP

                                       HHHHHHHHHHHHHHHHHHHHHHHCCTS CS
                       Prefoldin_2  78 iktlekqleklekeleelkeelqkklq 104
                                       +k+le+q++kl+++++el +++q++l 
  gi|242399318|ref|YP_002994742.1| 102 LKALERQEQKLNEKIKELTQQIQSALR 128
                                       ***********************9875 PP

>> ALIX_LYPXL_bnd  ALIX V-shaped domain binding to HIV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   4.9   1.4e-06   0.00028      75     168 ..      25     124 ..      12     127 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.4e-06
                    ALIX_LYPXL_bnd  75 aelraelqkyreileeAsesDkivrqklqenkedlelLsgpeeeleaa......lpssssaaasesveeqirklrsl 145
                                       + l  +l++y++ ++   +  + v+ +l++ k++le+++++ee +  +      + +s++++a e+v+e++++l+  
  gi|242399318|ref|YP_002994742.1|  25 QALLGQLESYQQQIQLVIQQKQRVQVELNDAKKALEEIEKTEEGTPIYktvgtlIVKSTKSKALEEVKEKVETLEVR 101
                                       78999*********************************998887777766666555888888889999999999977 PP

                    ALIX_LYPXL_bnd 146 lekldelkaereqllkdlkekae 168
                                       l+ l++ +++ ++ +k+l ++++
  gi|242399318|ref|YP_002994742.1| 102 LKALERQEQKLNEKIKELTQQIQ 124
                                       77777777777777777766655 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 !   18.9   9.6   1.7e-06   0.00035     710     812 ..      23     126 ..      14     130 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.7e-06
                               FPP 710 elksatenleslkaqlqesEqllaelkseLeslkeskslaetqlkcmkesyesletrate..leaelnelkqkieaL 784
                                       +++    +les + q+q   q+ + ++ eL+ +k++ + +e+  ++ + +y+++ t   +    + l+e+k+k+e+L
  gi|242399318|ref|YP_002994742.1|  23 QVQALLGQLESYQQQIQLVIQQKQRVQVELNDAKKALEEIEK-TEEGTPIYKTVGTLIVKstKSKALEEVKEKVETL 98 
                                       667777899********************************9.899999*****997544104567*********** PP

                               FPP 785 eveLeeekksheeleakckelqeqlerv 812
                                       ev L+  ++  ++l+ k+kel +q++++
  gi|242399318|ref|YP_002994742.1|  99 EVRLKALERQEQKLNEKIKELTQQIQSA 126
                                       **************************96 PP

>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.5   6.4e-05     0.013      78     115 ..      32      69 ..      30      76 .. 0.93
   2 !    8.5   4.7    0.0084       1.7      18      57 ..      86     124 ..      78     129 .. 0.50

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 6.4e-05
                              CdvA  78 eaYksaieairellesaleekeeikklleklsklelee 115
                                       e+Y+++i+ + +++++++ e++++kk+le+++k e+++
  gi|242399318|ref|YP_002994742.1|  32 ESYQQQIQLVIQQKQRVQVELNDAKKALEEIEKTEEGT 69 
                                       69*******************************99876 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0084
                              CdvA  18 styeeikeklee...alkklkekakelkeklkkrlkeledqik 57 
                                       ++ ee+kek+e+    lk+l++++++l+ek+    kel +qi+
  gi|242399318|ref|YP_002994742.1|  86 KALEEVKEKVETlevRLKALERQEQKLNEKI----KELTQQIQ 124
                                       4455566555441114555555555555555....55555554 PP

>> Ead_Ea22  Ead/Ea22-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   6.6   3.2e-05    0.0067      61     126 ..      15     100 ..       1     128 [. 0.70

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.2e-05
                          Ead_Ea22  61 iaaan.patvlaLLDelekkqqrikeleeeaenedialtvgklrveleaaekrl....................... 113
                                       +a  n p+ v+aLL +le++qq+i+++ +    ++++    +++++le++ek                         
  gi|242399318|ref|YP_002994742.1|  15 VAMQNiPPQVQALLGQLESYQQQIQLVIQQ--KQRVQVELNDAKKALEEIEKTEegtpiyktvgtlivkstkskale 89 
                                       455455**********************66..999999999999988888887677799999999888777777644 PP

                          Ead_Ea22 114 ....ekenveqadaaev 126
                                           +       +  ev
  gi|242399318|ref|YP_002994742.1|  90 evkeK------VETLEV 100
                                       43330......233333 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.6   0.00046     0.094     216     262 ..      18      64 ..      12      69 .. 0.86
   2 !   10.7   6.8   0.00087      0.18     198     244 ..      85     124 ..      77     128 .. 0.49

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00046
                              Spc7 216 eekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckg 262
                                       ++   +++ l  qle+ +++i+ + +qk++++ e++ a++ lee ++
  gi|242399318|ref|YP_002994742.1|  18 QNIPPQVQALLGQLESYQQQIQLVIQQKQRVQVELNDAKKALEEIEK 64 
                                       555567889999*****************************998665 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00087
                              Spc7 198 keeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqks 244
                                       ++       +l+e+k+++e ++ +l+ l++q ++l+eki+el++q++
  gi|242399318|ref|YP_002994742.1|  85 SK-------ALEEVKEKVETLEVRLKALERQEQKLNEKIKELTQQIQ 124
                                       33.......34444444444444444444444455555544444444 PP

>> RasGAP_C  RasGAP C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.2    0.0024       0.5      66     106 ..      24      64 ..      15      78 .. 0.74
   2 !   11.0   2.7    0.0017      0.36      40      84 ..      83     127 ..      79     129 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0024
                          RasGAP_C  66 nnylesqlesYkayienvleqlkkkkgklpfskqyfkkrel 106
                                        + l  qlesY++ i+ v++q ++ + +l+  k++ ++ e+
  gi|242399318|ref|YP_002994742.1|  24 VQALLGQLESYQQQIQLVIQQKQRVQVELNDAKKALEEIEK 64 
                                       567889***************99887667766655555444 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.0017
                          RasGAP_C  40 nkgrlrekrkeElesleetlktLseknnylesqlesYkayienvl 84 
                                       +k+++ e++ke +e+le  lk+L+ ++++l+++++++ + i+++l
  gi|242399318|ref|YP_002994742.1|  83 TKSKALEEVKEKVETLEVRLKALERQEQKLNEKIKELTQQIQSAL 127
                                       6788899***********************************997 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 !   10.1   1.2     0.003      0.62      11      47 ..      28      64 ..      17      70 .. 0.46
   2 !   13.1   7.4   0.00036     0.073      62     102 ..      84     124 ..      77     128 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.003
                             DHR10 11 laelErkarelqakidalqvvekdlrsciklleeiea 47
                                      l +lE  ++++q  i   q+v+ +l+ + k+leeie+
  gi|242399318|ref|YP_002994742.1| 28 LGQLESYQQQIQLVIQQKQRVQVELNDAKKALEEIEK 64
                                      3333333344444444444444444444444444433 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00036
                             DHR10  62 lrdaleekeielrelerkeerlqrqlenaeeklerlreqae 102
                                        ++alee +++++ le + + l+rq ++ +ek+  l++q +
  gi|242399318|ref|YP_002994742.1|  84 KSKALEEVKEKVETLEVRLKALERQEQKLNEKIKELTQQIQ 124
                                       56899999999999999999999999999999999999986 PP

>> DUF3416  Domain of unknown function (DUF3416)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   1.0   1.7e-05    0.0034      84     161 ..      24     123 ..      22     128 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.7e-05
                           DUF3416  84 veAWvDpfatWrhdlekkveagqdveleleeGarlleraaeraea.................aalraaaaal..... 138
                                       v+A   ++++++++++  ++++q+v++el+ +++ le++ +++e                  +al+++ +++     
  gi|242399318|ref|YP_002994742.1|  24 VQALLGQLESYQQQIQLVIQQKQRVQVELNDAKKALEEIEKTEEGtpiyktvgtlivkstksKALEEVKEKVetlev 100
                                       78888899********************************8886699999999999987777444444444422233 PP

                           DUF3416 139 rddpeerlaaalseevaallary 161
                                       r ++ er +  l+e++++l ++ 
  gi|242399318|ref|YP_002994742.1| 101 RLKALERQEQKLNEKIKELTQQI 123
                                       33367788888888888887765 PP

>> PspA_IM30  PspA/IM30 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6  13.0   4.4e-05    0.0091     111     205 ..      21     123 ..      14     129 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.4e-05
                         PspA_IM30 111 rsaveqlrkqlealetkieelkakkellkarekaa.kaqeavqkslgkls..........tesatdslerieeKiee 176
                                         +v+ l +qle   ++i+ ++++k+ +++ ++ a ka e+++k+ ++             ++ +++le+++eK+e 
  gi|242399318|ref|YP_002994742.1|  21 PPQVQALLGQLESYQQQIQLVIQQKQRVQVELNDAkKALEEIEKTEEGTPiyktvgtlivKSTKSKALEEVKEKVET 97 
                                       567888999**********************99772588999998777667777779998888999*********** PP

                         PspA_IM30 177 rearadaaaelaesaqdldakleaagiqk 205
                                       +e r +a +  +   q l +k++++  q 
  gi|242399318|ref|YP_002994742.1|  98 LEVRLKALERQE---QKLNEKIKELTQQI 123
                                       *******99888...66688888776664 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   2.7     0.013       2.6      56      96 ..      24      67 ..      16      72 .. 0.56
   2 !   14.6   3.9   7.1e-05     0.015      47      91 ..      82     126 ..      80     130 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.013
                           DUF3450 56 lkeeleslevyneqlerlvasqeq...eiasleeqieeieeier 96
                                      +++ l +le y++q + ++++ ++   e+++ ++ +eeie++e+
  gi|242399318|ref|YP_002994742.1| 24 VQALLGQLESYQQQIQLVIQQKQRvqvELNDAKKALEEIEKTEE 67
                                      44445556666666665555544411156666666666666665 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 7.1e-05
                           DUF3450  47 qellaeyralkeeleslevyneqlerlvasqeqeiasleeqieei 91 
                                       ++ ++ ++++ke++e lev  + ler+ ++++++i++l++qi+++
  gi|242399318|ref|YP_002994742.1|  82 STKSKALEEVKEKVETLEVRLKALERQEQKLNEKIKELTQQIQSA 126
                                       56778899**********************************986 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2  10.7   3.7e-05    0.0077       6     102 ..      32     126 ..      17     128 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.7e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXX--TTTTTGGGHHHHHH CS
                        Laminin_II   6 aeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdAr..rsvkkLeklapqLldklkelkq 80 
                                       ++ +++++ v +q++ ++++l+  k+ l+ei+++ ee +   k   + i+     ++  +++++++ L+ +lk l+ 
  gi|242399318|ref|YP_002994742.1|  32 ESYQQQIQLVIQQKQRVQVELNDAKKALEEIEKT-EEGTPIYKTVGTLIVKSTksKALEEVKEKVETLEVRLKALER 107
                                       566788999*************************.887877777776666543013467778899************ PP

                                       HHHH...HHHHHHHHHHHHHHH CS
                        Laminin_II  81 leeassslsdniseikelIaqA 102
                                       +e++   l ++i+e+ ++I+ A
  gi|242399318|ref|YP_002994742.1| 108 QEQK---LNEKIKELTQQIQSA 126
                                       **99...99**********987 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.4     0.005         1     150     192 ..      23      65 ..       6      70 .. 0.75
   2 !   11.4   5.0   0.00072      0.15      83     124 ..      84     125 ..      77     129 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.005
                               GAS 150 klkalqeelEkkeaqleevlaaanldpaalsavsekleevles 192
                                       +++al  +lE+ ++q++ v+++++  + +l+ +++ lee+ ++
  gi|242399318|ref|YP_002994742.1|  23 QVQALLGQLESYQQQIQLVIQQKQRVQVELNDAKKALEEIEKT 65 
                                       5677777777777777777777777777777777777776554 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00072
                               GAS  83 dkqslknlkarlkelekelkdlkwehevleqrfekvekerde 124
                                       + ++l+++k+++++le  lk+l+ + + l+++++++ ++++ 
  gi|242399318|ref|YP_002994742.1|  84 KSKALEEVKEKVETLEVRLKALERQEQKLNEKIKELTQQIQS 125
                                       456788888888888888888888888888888888877665 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   1.2      0.44        90      12      47 ..      30      65 ..      23      67 .. 0.85
   2 !   16.6   6.0   3.2e-05    0.0066       5      42 ..      87     124 ..      84     125 .. 0.94

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.44
                              XhlA 12 kldnleervdkleekaaeaeekiknleedlkklesn 47
                                      +l++++++++ + + + +++ ++  + + l+++e++
  gi|242399318|ref|YP_002994742.1| 30 QLESYQQQIQLVIQQKQRVQVELNDAKKALEEIEKT 65
                                      688899999999999999999999999999999975 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 3.2e-05
                              XhlA   5 rlerietkldnleervdkleekaaeaeekiknleedlk 42 
                                        le++++k+++le r++ le+ + +  ekik+l+ ++ 
  gi|242399318|ref|YP_002994742.1|  87 ALEEVKEKVETLEVRLKALERQEQKLNEKIKELTQQIQ 124
                                       699********************************997 PP

>> DUF2120  Uncharacterized protein conserved in archaea (DUF2120)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1      0.73   1.5e+02      20      50 ..      34      64 ..      17      69 .. 0.62
   2 !   16.1   2.8   4.6e-05    0.0094       3      76 ..      55     128 ..      53     132 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.73
                           DUF2120 20 ldkeeiLivrgvsrkkeeleeleskleelle 50
                                      ++++  L+++ + r + el++ ++ lee+ +
  gi|242399318|ref|YP_002994742.1| 34 YQQQIQLVIQQKQRVQVELNDAKKALEEIEK 64
                                      4444456666666666666666666666654 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 4.6e-05
                           DUF2120   3 agkimkeldaFkGSkplldkeeiLivrgvsrkkeeleeleskleelleklda..eevdleseeakkliekldesir 76 
                                       a+k ++e++  +   p++++  +Liv+++  k   lee+++k+e l  +l+a  ++ +  +e++k+l++++++ +r
  gi|242399318|ref|YP_002994742.1|  55 AKKALEEIEKTEEGTPIYKTVGTLIVKSTKSK--ALEEVKEKVETLEVRLKAleRQEQKLNEKIKELTQQIQSALR 128
                                       577888888888899***********986444..469999999999888875212334456677777777777665 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       7.9   1.6e+03      13      24 ..      28      39 ..      15      48 .. 0.47
   2 ?    4.9   0.9      0.17        35      10      29 ..      46      65 ..      28      79 .. 0.83
   3 !   15.7   4.6   7.2e-05     0.015       3      39 ..      89     125 ..      87     128 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 7.9
                         FlaC_arch 13 steletvkkene 24
                                        +le+ +++++
  gi|242399318|ref|YP_002994742.1| 28 LGQLESYQQQIQ 39
                                      223333333332 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.17
                         FlaC_arch 10 sklsteletvkkeneelsks 29
                                      +++++el+ +kk +ee++k+
  gi|242399318|ref|YP_002994742.1| 46 QRVQVELNDAKKALEEIEKT 65
                                      56778888888888888876 PP

  == domain 3  score: 15.7 bits;  conditional E-value: 7.2e-05
                         FlaC_arch   3 delEnklsklsteletvkkeneelsksveelkenVkd 39 
                                       +e+ +k++ l+++l+ ++++ ++l+++++el ++++ 
  gi|242399318|ref|YP_002994742.1|  89 EEVKEKVETLEVRLKALERQEQKLNEKIKELTQQIQS 125
                                       8999******************************986 PP

>> DUF4404  Domain of unknown function (DUF4404)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.3     0.004      0.82      21      62 ..      26      64 ..      16      82 .. 0.74
   2 !    9.6   1.9    0.0068       1.4       2      38 ..      92     128 ..      91     132 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.004
                           DUF4404 21 etralLeslaedieellaeedaaaeeeelaerlneaverFee 62
                                      +  ++Les +++i+ ++++++  + e  l++ +++a+e+ e+
  gi|242399318|ref|YP_002994742.1| 26 ALLGQLESYQQQIQLVIQQKQRVQVE--LND-AKKALEEIEK 64
                                      56689******************999..444.4555554443 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0068
                           DUF4404   2 kelLekLheeLeqnesldeetralLeslaedieella 38 
                                       ke++e+L+  L+  e+ +++ ++++++l ++i+ +l+
  gi|242399318|ref|YP_002994742.1|  92 KEKVETLEVRLKALERQEQKLNEKIKELTQQIQSALR 128
                                       899******************************9997 PP

>> Bac_GDH  Bacterial NAD-glutamate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   1.6   6.5e-05     0.013      21     132 ..      14     125 ..       3     130 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.5e-05
                           Bac_GDH  21 eivtddmpFlvdsvtaelnrqgltvhlvvhpvleverdkegklleveeekeeaekaekeslilieidrqsdaeelee 97 
                                        +  +++p  v ++  +l++ + +++lv+++  +v+ + +++ +++ee ++++e +   +++   i + +++++lee
  gi|242399318|ref|YP_002994742.1|  14 GVAMQNIPPQVQALLGQLESYQQQIQLVIQQKQRVQVELNDAKKALEEIEKTEEGTPIYKTVGTLIVKSTKSKALEE 90 
                                       6788999999********************99999999888888888888888877776666666666679999*** PP

                           Bac_GDH  98 leeelekvledvraaveDwkkmreklkelaeelek 132
                                       ++e++e+    ++a  +  +k++ek+kel++++++
  gi|242399318|ref|YP_002994742.1|  91 VKEKVETLEVRLKALERQEQKLNEKIKELTQQIQS 125
                                       *****************************999985 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.8    0.0018      0.38      54      99 ..      22      67 ..       4      70 .. 0.85
   2 ?    9.7   8.9    0.0055       1.1      53      92 ..      85     124 ..      79     127 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0018
                            APG6_N 54 eeleklekeeeelleeLkelekereeleaelaaleeelealeeeee 99
                                       ++++l  + e+ +++++ + +++++++ el+++++ le++e+ ee
  gi|242399318|ref|YP_002994742.1| 22 PQVQALLGQLESYQQQIQLVIQQKQRVQVELNDAKKALEEIEKTEE 67
                                      5678888999999999999999999999999999999999999987 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0055
                            APG6_N  53 eeeleklekeeeelleeLkelekereeleaelaaleeele 92 
                                        + le+++++ e+l+  Lk+le+++++l++++++l+++ +
  gi|242399318|ref|YP_002994742.1|  85 SKALEEVKEKVETLEVRLKALERQEQKLNEKIKELTQQIQ 124
                                       5779999999999999999999999999999999999876 PP

>> Tropomyosin_1  Tropomyosin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.4     0.023       4.8      74     110 ..      30      66 ..      19      71 .. 0.66
   2 ?   12.5   5.9   0.00061      0.13     103     140 ..      88     125 ..      79     128 .. 0.56

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.023
                     Tropomyosin_1  74 nnealtrkiqlLEeeleesdkkLkettekLretdvka 110
                                       + e+++++iql+ ++  + + +L+++ + L+e++++ 
  gi|242399318|ref|YP_002994742.1|  30 QLESYQQQIQLVIQQKQRVQVELNDAKKALEEIEKTE 66 
                                       4566666666666666666666666666666666554 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00061
                     Tropomyosin_1 103 LretdvkaeelERkvkaLeqerdewekkyeeleekyke 140
                                       L+e+  k e+lE + kaLe+++++ ++k+ el+++ ++
  gi|242399318|ref|YP_002994742.1|  88 LEEVKEKVETLEVRLKALERQEQKLNEKIKELTQQIQS 125
                                       55555555555555555555555555555555555544 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   3.3   0.00011     0.022     114     190 ..      35     125 ..      12     129 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 0.00011
                            AAA_11 114 ekrlekeekaqlakeiskeleklakelrafeeeeek................eklkkskekskskleqerrklkker 174
                                       +++++    +q++++++ el++ +k+l++ e++ee                  k +++ +++ ++le+++++l+++ 
  gi|242399318|ref|YP_002994742.1|  35 QQQIQ--LVIQQKQRVQVELNDAKKALEEIEKTEEGtpiyktvgtlivkstkSKALEEVKEKVETLEVRLKALERQE 109
                                       22222..268889999999999999998888887769*************9988889999999999999******** PP

                            AAA_11 175 kelskeleeaeeslee 190
                                       ++l+++++e ++++++
  gi|242399318|ref|YP_002994742.1| 110 QKLNEKIKELTQQIQS 125
                                       ********99999975 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 ?   12.4   3.6   0.00013     0.027      40     106 ..      57     123 ..      12     129 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00013
                        V_ATPase_I  40 rfleeeieklekavikeeea...........eesleapeekeldeleeelekleeelkelnenleklkkelnelvel 105
                                       + lee iek          +           +   +++++k l+e++e++e+le +lk l+++++kl+++ +el+++
  gi|242399318|ref|YP_002994742.1|  57 KALEE-IEK----------TeegtpiyktvgTLIVKSTKSKALEEVKEKVETLEVRLKALERQEQKLNEKIKELTQQ 122
                                       22222.222..........122334444445778888999999***************************9999987 PP

                        V_ATPase_I 106 k 106
                                        
  gi|242399318|ref|YP_002994742.1| 123 I 123
                                       5 PP

>> MCM_N  MCM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1      0.47        97      22      45 ..      32      54 ..       7      69 .. 0.82
   2 ?   10.3   0.0    0.0041      0.84      33      69 ..      92     128 ..      85     132 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.47
                             MCM_N 22 kkYrdqlqemaerekttLevdldd 45
                                        Y +q+q +++++ +++ v+l+d
  gi|242399318|ref|YP_002994742.1| 32 ESYQQQIQLVIQQK-QRVQVELND 54
                                      57999999987765.578888887 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0041
                             MCM_N  33 erekttLevdlddLaafdeeLaeailenpkeylplle 69 
                                       +++ +tLev l+ L+  +++L e+i e ++++  +l+
  gi|242399318|ref|YP_002994742.1|  92 KEKVETLEVRLKALERQEQKLNEKIKELTQQIQSALR 128
                                       56789**********************9999998886 PP

>> DUF3958  Protein of unknown function (DUF3958)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4  11.7   0.00016     0.032       2      98 ..      30     124 ..      29     128 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 0.00016
                           DUF3958   2 kleelnqelrelaekqeenekelkkqeqlkeeyeehfnqskrlfdelletfrkdeeshlfeklrdevqrlsrklred 78 
                                       +le+++q+++ + +++++++ el+  ++  ee+e+  ++++  ++ +++   k+++s  +e++++ v  l+  l++ 
  gi|242399318|ref|YP_002994742.1|  30 QLESYQQQIQLVIQQKQRVQVELNDAKKALEEIEKT-EEGTPIYKTVGTLIVKSTKSKALEEVKEKVETLEVRLKA- 104
                                       789******************************986.689*********************************985. PP

                           DUF3958  79 LEeeeeeLkrekrqLedqee 98 
                                       LE++e++L+++ ++L +q++
  gi|242399318|ref|YP_002994742.1| 105 LERQEQKLNEKIKELTQQIQ 124
                                       *****************997 PP

>> TolA_bind_tri  TolA binding protein trimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   3.2     0.002      0.41      32      71 ..      22      61 ..       4      66 .. 0.84
   2 ?    9.3   2.2    0.0058       1.2       4      39 ..      93     129 ..      90     131 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.002
                     TolA_bind_tri 32 qelreLRGqiEelqyqleqleerQrdlYldlDerlrklea 71
                                       +++ L Gq+E  q q++ ++++ +   ++l+   ++le+
  gi|242399318|ref|YP_002994742.1| 22 PQVQALLGQLESYQQQIQLVIQQKQRVQVELNDAKKALEE 61
                                      58999****************9999999999888887775 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0058
                     TolA_bind_tri   4 drvarLErilearsqlllelqqqlealqqelre.LRG 39 
                                       ++v++LE  l+a ++   +l +++++l q++++ LRG
  gi|242399318|ref|YP_002994742.1|  93 EKVETLEVRLKALERQEQKLNEKIKELTQQIQSaLRG 129
                                       5666666666666666666666666666666533555 PP

>> YscO  Type III secretion protein YscO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   1.6    0.0032      0.66      84     123 ..      26      65 ..      20      69 .. 0.66
   2 ?    9.8   3.8    0.0036      0.74      61     106 ..      81     126 ..      75     129 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0032
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YscO  84 elekqveeakqqleaerealrqarkelqearraveKfael 123
                                        l  q+e  +qq +  ++++++ ++el  a++a+e++++ 
  gi|242399318|ref|YP_002994742.1|  26 ALLGQLESYQQQIQLVIQQKQRVQVELNDAKKALEEIEKT 65 
                                       5555667777777777777777777777777777776654 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0036
                                       TT--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YscO  61 klvllkelekvkqqvalLrekeaelekqveeakqqleaerealrqa 106
                                       k  + k+le+vk++v  L+ + + le q ++++++ ++  ++ ++a
  gi|242399318|ref|YP_002994742.1|  81 KSTKSKALEEVKEKVETLEVRLKALERQEQKLNEKIKELTQQIQSA 126
                                       6667889999998888888888888888888887777777766665 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   0.4     0.008       1.6      60     102 ..      23      65 ..      13      70 .. 0.66
   2 ?    9.5   6.5    0.0045      0.92      49      91 ..      83     125 ..      76     128 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.008
                    CENP-F_leu_zip  60 eieelaeelreleldLvalrsekeeLekelqkkqervseLesl 102
                                       +++ l  +l+  +++++ + ++k+ ++ el++ ++  +e e++
  gi|242399318|ref|YP_002994742.1|  23 QVQALLGQLESYQQQIQLVIQQKQRVQVELNDAKKALEEIEKT 65 
                                       6666666677777777777777777777777777777776665 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0045
                    CENP-F_leu_zip  49 tskaevetlkeeieelaeelreleldLvalrsekeeLekelqk 91 
                                       t+ +++e++ke++e+l+ +l+ le + ++l +  +eL++++q 
  gi|242399318|ref|YP_002994742.1|  83 TKSKALEEVKEKVETLEVRLKALERQEQKLNEKIKELTQQIQS 125
                                       4556789999999999999999999999999999999999885 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   7.1   0.00022     0.045     604     704 ..      30     126 ..      16     128 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00022
                          Prominin 604 glskihsslyleqlckkltkvnletlaekleelanelsngkknlkqslkneaqdlraiqqelvlplessvkklkksv 680
                                       +l++++ +  l   +k+ ++v+l+  ++ lee+ ++ +     + + +      +++ +++  ++++++v++l+ ++
  gi|242399318|ref|YP_002994742.1|  30 QLESYQQQIQLVIQQKQRVQVELNDAKKALEEIEKTEEGT--PIYKTV--GTLIVKSTKSKALEEVKEKVETLEVRL 102
                                       5677777777777788889999999999999998887444..444443..345578888999999999999999999 PP

                          Prominin 681 kkldeensdlqesikkllaavera 704
                                       k+l++++++l+e+ik+l++++++a
  gi|242399318|ref|YP_002994742.1| 103 KALERQEQKLNEKIKELTQQIQSA 126
                                       999999999999999999999886 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   1.7     0.011       2.3      59      99 ..      24      64 ..      21      68 .. 0.68
   2 ?   11.2   5.6    0.0014      0.29      52      93 ..      81     122 ..      76     127 .. 0.56

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.011
                        TPR_MLP1_2 59 lqalreelnelkaeiaelkaeaesakaeleeseesweeqke 99
                                      +qal  +l++++++i+ + ++ ++++ el+ +++++ee ++
  gi|242399318|ref|YP_002994742.1| 24 VQALLGQLESYQQQIQLVIQQKQRVQVELNDAKKALEEIEK 64
                                      56666677777777777777777777777777777776554 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.0014
                        TPR_MLP1_2  52 haedvkelqalreelnelkaeiaelkaeaesakaeleesees 93 
                                       +++ +k+l++++e++++l+ +++ l+ + ++++++++e +++
  gi|242399318|ref|YP_002994742.1|  81 KSTKSKALEEVKEKVETLEVRLKALERQEQKLNEKIKELTQQ 122
                                       455555555555555555555555555555555555555544 PP

>> FliJ  Flagellar FliJ protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   2.5    0.0018      0.38      47      96 ..      17      66 ..       6      68 .. 0.85
   2 ?    7.7   1.3     0.019       3.9       4      28 ..      99     123 ..      78     131 .. 0.52

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0018
                              FliJ 47 lrnyqafisaldeaiaqqkqelaqaekqvekareewqearqerkklekLk 96
                                      ++n+  + +al  ++++++q+++   +q ++ + e+  a++ ++ +ek +
  gi|242399318|ref|YP_002994742.1| 17 MQNIPPQVQALLGQLESYQQQIQLVIQQKQRVQVELNDAKKALEEIEKTE 66
                                      67777788899999999999999999999999999999999999999865 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.019
                              FliJ   4 areLaeaqrelqqaeekleeleqyr 28 
                                       + +L++ +r+ q+ +ek+ el+q++
  gi|242399318|ref|YP_002994742.1|  99 EVRLKALERQEQKLNEKIKELTQQI 123
                                       2334444444444444444444443 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   3.9   0.00027     0.056     143     258 ..      25     121 ..       4     132 .. 0.49

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00027
                      Exonuc_VII_L 143 aeleeqleelerrlekaikrlleekkqrleklasrlkspeellerkrqrldeleerleralkkqlkkkrerleelke 219
                                       + l+                                     +le+ +q+++ + ++ +r ++ +l+ ++++lee+++
  gi|242399318|ref|YP_002994742.1|  25 QALLG------------------------------------QLESYQQQIQLVIQQKQR-VQVELNDAKKALEEIEK 64 
                                       33333....................................344444444444444333.44444444444444442 PP

                      Exonuc_VII_L 220 rlk..................ekleekkerlkklkerlelleekkerleeleeklea 258
                                       + +                  + lee ke++++l+ rl+ le+++++l+e +++l++
  gi|242399318|ref|YP_002994742.1|  65 TEEgtpiyktvgtlivkstksKALEEVKEKVETLEVRLKALERQEQKLNEKIKELTQ 121
                                       222344444555555544444445555555555555555555555555555544443 PP

>> SOAR  STIM1 Orai1-activating region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   8.9   0.00049       0.1       4      92 ..      21     118 ..      18     127 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00049
                              SOAR   4 peeLqqlLq..lTyelElkylnkkkqeaekqlqeAkeeveklkkkrs.....sllgsl..rlahssslddvdkkile 71 
                                       p ++q lL   ++y++  + + ++kq+ + +l+ Ak+++e ++k  +     + +g+l  ++++s+ l++v +k+ +
  gi|242399318|ref|YP_002994742.1|  21 PPQVQALLGqlESYQQQIQLVIQQKQRVQVELNDAKKALEEIEKTEEgtpiyKTVGTLivKSTKSKALEEVKEKVET 97 
                                       7788888862259*******************************9863333357887533778************99 PP

                              SOAR  72 akqaleevtkelkerqeRWqq 92 
                                       +  +l+ ++++ +  +e+ ++
  gi|242399318|ref|YP_002994742.1|  98 LEVRLKALERQEQKLNEKIKE 118
                                       998877777666555554444 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   4.7   0.00035     0.073     131     235 ..      27     125 ..       1     130 [. 0.43

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00035
                           DUF4407 131 ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtk.gtgttgvaGkgpaakekkaqldaaqaelaelkakl 206
                                       l  +l+  ++qi+   ++ +  + +l++++++++ e++ t  gt + ++ G   +  +k ++l++ ++++++l+ + 
  gi|242399318|ref|YP_002994742.1|  27 LLGQLESYQQQIQLVIQQKQRVQVELNDAKKALE-EIEKTEeGTPIYKTVGTLIVKSTKSKALEEVKEKVETLEVR- 101
                                       3334444444444333333333333333333333.22222224444444455555555555555555555554444. PP

                           DUF4407 207 datarlaalraelaeleaerakeraasqa 235
                                            l+al+++ ++l++++++ +++ q+
  gi|242399318|ref|YP_002994742.1| 102 -----LKALERQEQKLNEKIKELTQQIQS 125
                                       .....444444444444444443333333 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   9.1   0.00039     0.081     333     414 ..      39     122 ..      22     131 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00039
                              FapA 333 pelkeklkeleeeleeleeeleklkkk.....ikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkel 404
                                       + ++++ ++++ el++ ++ le+++k+     i    k+  +  ++s+k++ l++++e+ e l+ +l++le++ ++l
  gi|242399318|ref|YP_002994742.1|  39 QLVIQQKQRVQVELNDAKKALEEIEKTeegtpI---YKTVGTLIVKSTKSKALEEVKEKVETLEVRLKALERQEQKL 112
                                       456677799999999999999999999874441...33333567788888999999999999999999999999999 PP

                              FapA 405 keeleskkee 414
                                       +e++++ +++
  gi|242399318|ref|YP_002994742.1| 113 NEKIKELTQQ 122
                                       9998888433 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.5     0.045       9.3      75     112 ..      23      60 ..       2      68 .. 0.77
   2 ?   11.4   6.5    0.0012      0.26      71     113 ..      83     125 ..      79     128 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.045
                              ADIP  75 kierlktqleqlerelalvqakerqlekklktleqklk 112
                                       +++ l  qle+++++++lv ++++  + +l +++++l 
  gi|242399318|ref|YP_002994742.1|  23 QVQALLGQLESYQQQIQLVIQQKQRVQVELNDAKKALE 60 
                                       56777789999999999888888888888888777664 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.0012
                              ADIP  71 rlqskierlktqleqlerelalvqakerqlekklktleqklkn 113
                                        ++++ e +k+++e le +l++++++e++l+ k+k+l+q++++
  gi|242399318|ref|YP_002994742.1|  83 TKSKALEEVKEKVETLEVRLKALERQEQKLNEKIKELTQQIQS 125
                                       56788999******************************99875 PP

>> TA0956  Thermoplasma acidophilum protein TA0956
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   0.00055      0.11      26      79 ..      31      88 ..      13     126 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00055
                                      HHHHHHHHHHHTTS-..-CCHHHH...HHHHH---S---TTSEEEEEEEEETTTTEEE CS
                            TA0956 26 lreslealadvldse.lieeslee...fieefartdeimPedktvGfviinsdkkvls 79
                                      l++  ++++ v++++  ++  l++    +ee  +t+e  P  ktvG +i+ s+k    
  gi|242399318|ref|YP_002994742.1| 31 LESYQQQIQLVIQQKqRVQVELNDakkALEEIEKTEEGTPIYKTVGTLIVKSTKSKAL 88
                                      444444455555433134444544222689**********************996543 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   0.00042     0.087     221     312 ..      17     128 ..       8     132 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00042
                              FUSC 221 lrrllsrmlallallsslarllarlraeeaaavpe...laallaelaal.................eaaaaaealea 277
                                       ++ +  +++all +l s++++ + + +++++ + e    ++ l+e+++                  ++++a e+ ++
  gi|242399318|ref|YP_002994742.1|  17 MQNIPPQVQALLGQLESYQQQIQLVIQQKQRVQVElndAKKALEEIEKTeegtpiyktvgtlivksTKSKALEEVKE 93 
                                       5666678899999999999999999999888888844455555555555*****************88899****** PP

                              FUSC 278 alaalrarlralrraleadadtaalllarlaella 312
                                       ++++l+ rl+al+r++++ ++   +l ++ ++ l+
  gi|242399318|ref|YP_002994742.1|  94 KVETLEVRLKALERQEQKLNEKIKELTQQIQSALR 128
                                       *****************888877777777777666 PP

>> DUF641  Plant protein of unknown function (DUF641)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.3      0.23        48      84     122 ..      25      66 ..       3      70 .. 0.64
   2 ?   12.3   2.4   0.00078      0.16      77     119 ..      85     127 ..      72     130 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.23
                            DUF641  84 rsllktyeitvkkleaelkak...dseieeLkekLeeaeksn 122
                                       + ll  +e   ++++  +++k   ++e++  k+ Lee+ek +
  gi|242399318|ref|YP_002994742.1|  25 QALLGQLESYQQQIQLVIQQKqrvQVELNDAKKALEEIEKTE 66 
                                       444445555555555555554112678889999999988775 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00078
                            DUF641  77 eaeiqeqrsllktyeitvkkleaelkakdseieeLkekLeeae 119
                                       ++ ++e +++++t+e+++k+le++ ++ +++i+eL +++++a 
  gi|242399318|ref|YP_002994742.1|  85 SKALEEVKEKVETLEVRLKALERQEQKLNEKIKELTQQIQSAL 127
                                       556789999*****************************99876 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.8     0.077        16      11      56 ..      22      64 ..      16      76 .. 0.66
   2 ?   11.5   2.0    0.0015      0.31      12      53 ..      87     125 ..      79     128 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.077
                           NPV_P10 11 adikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaelet 56
                                        ++a+  ++++ qqq++ v ++ + v+    +L++  ++L+e+e+
  gi|242399318|ref|YP_002994742.1| 22 PQVQALLGQLESYQQQIQLVIQQKQRVQ---VELNDAKKALEEIEK 64
                                      4566666666777777766666666644...667777777777665 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.0015
                           NPV_P10  12 dikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLae 53 
                                       + ++v++kV+ l+ +++ ++ + ++   lnek+ ++++q+++
  gi|242399318|ref|YP_002994742.1|  87 ALEEVKEKVETLEVRLKALERQEQK---LNEKIKELTQQIQS 125
                                       788999***********99998888...99999999999875 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   1.9   0.00079      0.16      10      60 ..      17      67 ..      14      78 .. 0.86
   2 ?    5.8   4.0      0.11        22       8      36 ..      93     121 ..      80     129 .. 0.40

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00079
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXX CS
                              YabA 10 leeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkek 60
                                      ++++  q+++ll +le+ +++++ ++++ +++++e +  ++ lee ek+e+
  gi|242399318|ref|YP_002994742.1| 17 MQNIPPQVQALLGQLESYQQQIQLVIQQKQRVQVELNDAKKALEEIEKTEE 67
                                      7788899************************************76666554 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.11
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YabA   8 dkleeleeqleelleeleelkeelaelle 36 
                                       +k+e+le +l++l ++ ++l+e+++el++
  gi|242399318|ref|YP_002994742.1|  93 EKVETLEVRLKALERQEQKLNEKIKELTQ 121
                                       22333333333333333333333333222 PP

>> DUF4140  N-terminal domain of unknown function (DUF4140)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4  12.2      0.12        25      57      96 ..      85     124 ..       4     126 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.12
                           DUF4140  57 vpnreaeeeelkalraeleeledelaaledelaaaearla 96 
                                       +   e+++e++++l+ +l++le++ ++l+++++ + ++++
  gi|242399318|ref|YP_002994742.1|  85 SKALEEVKEKVETLEVRLKALERQEQKLNEKIKELTQQIQ 124
                                       2223333336999999999999999999999999999986 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 ?    4.5   0.0      0.22        45      27      57 ..      21      54 ..       2      69 .. 0.73
   2 ?    6.4   0.0     0.055        11      18      59 ..      90     130 ..      78     133 .] 0.91

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.22
                     Lambda_tail_I 27 eeairalssqldafkellq...rskfavrvagvd 57
                                      +  ++al+ ql+ +++ +q   + k  v+v + d
  gi|242399318|ref|YP_002994742.1| 21 PPQVQALLGQLESYQQQIQlviQQKQRVQVELND 54
                                      3449*************99888777777777666 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.055
                     Lambda_tail_I  18 dvveavktleeairalssqldafkellqrskfavrvagvdVg 59 
                                       +v+e v+tle  ++al  q+    e++++   +++ a+++ g
  gi|242399318|ref|YP_002994742.1|  90 EVKEKVETLEVRLKALERQEQKLNEKIKELTQQIQSALRG-G 130
                                       67899***********************999999999998.6 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   3.3     0.088        18       2      36 ..      35      66 ..      23      82 .. 0.54
   2 ?   12.2   6.9   0.00061      0.13      76     116 ..      85     125 ..      77     128 .. 0.58

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.088
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT.- CS
                         Prefoldin  2 keeleslqaelaqlkeaieelektletlktlkked 36
                                      +++++ + ++    +  + el++++++l++++k +
  gi|242399318|ref|YP_002994742.1| 35 QQQIQLVIQQK---QRVQVELNDAKKALEEIEKTE 66
                                      33333333333...333344444444444444422 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00061
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  76 eeAiellkkkleelekqlekleeeleklkdqittleanlaq 116
                                        +A e +k+k+e+le  l+ le + +kl ++i++l ++++ 
  gi|242399318|ref|YP_002994742.1|  85 SKALEEVKEKVETLEVRLKALERQEQKLNEKIKELTQQIQS 125
                                       55666666666666666666666666666666666665554 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   0.2     0.046       9.4      31      69 ..      22      60 ..       9      65 .. 0.77
   2 ?    8.7   4.8     0.011       2.2      26      63 ..      88     125 ..      77     128 .. 0.64

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.046
                               CLZ 31 ekverLessLeaLqtrlarLlaeyessqrkLkqRitkLE 69
                                       +v+ L ++Le+ q++++ ++++ + +q +L+   ++LE
  gi|242399318|ref|YP_002994742.1| 22 PQVQALLGQLESYQQQIQLVIQQKQRVQVELNDAKKALE 60
                                      568888888888888888888888888888877666666 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.011
                               CLZ  26 qkeleekverLessLeaLqtrlarLlaeyessqrkLkq 63 
                                        +e++ekve Le +L+aL+ + ++L ++ ++  +++++
  gi|242399318|ref|YP_002994742.1|  88 LEEVKEKVETLEVRLKALERQEQKLNEKIKELTQQIQS 125
                                       45666677777777777766666666666666666554 PP

>> DUF4988  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.3      0.44        91       5      48 ..      24      68 ..      20      89 .. 0.70
   2 ?   11.7   1.2   0.00076      0.16       2      32 ..      92     122 ..      91     127 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.44
                           DUF4988  5 vndlkdrvaaleeqvkelndniealk.klleegkviteveensdg 48
                                      v++l  + ++ ++q++ + ++ + ++ +l + +k++ e+e++++g
  gi|242399318|ref|YP_002994742.1| 24 VQALLGQLESYQQQIQLVIQQKQRVQvELNDAKKALEEIEKTEEG 68
                                      666777777788888877777777662455778888888888877 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00076
                           DUF4988   2 eddvndlkdrvaaleeqvkelndniealkkl 32 
                                       +++v+ l+ r +ale+q ++ln++i+ l + 
  gi|242399318|ref|YP_002994742.1|  92 KEKVETLEVRLKALERQEQKLNEKIKELTQQ 122
                                       789**********************999764 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   2.5     0.016       3.4      54      89 ..      29      64 ..      15      69 .. 0.77
   2 ?    9.4   5.4    0.0034       0.7     215     257 ..      85     127 ..      73     130 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.016
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          Filament 54 keleelrkqldeltkerarlqleldnlreeledlrk 89
                                       +le+ ++q++ + ++++r+q+el++++++le++ k
  gi|242399318|ref|YP_002994742.1| 29 GQLESYQQQIQLVIQQKQRVQVELNDAKKALEEIEK 64
                                      467788888888888888888888888888888765 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0034
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 215 keeitelrrqiqsleieleslkkqkasleaqlaeleerleael 257
                                        + ++e++ ++++le+ l++l+ q+++l+++++el ++++++l
  gi|242399318|ref|YP_002994742.1|  85 SKALEEVKEKVETLEVRLKALERQEQKLNEKIKELTQQIQSAL 127
                                       356899******************************9999876 PP

>> COG2  COG (conserved oligomeric Golgi) complex component, COG2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.3     0.024         5      62      98 ..      29      65 ..      17      75 .. 0.83
   2 ?    7.8   2.4     0.016       3.2      61     103 ..      85     127 ..      83     129 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.024
                              COG2 62 ghLvglqeeleevesplaaarkkvesvreklsereee 98
                                      g+L ++q++++ v ++ ++++ ++++++++l+e e++
  gi|242399318|ref|YP_002994742.1| 29 GQLESYQQQIQLVIQQKQRVQVELNDAKKALEEIEKT 65
                                      6888889999999888888888888888888887765 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.016
                              COG2  61 SghLvglqeeleevesplaaarkkvesvreklsereeeveskl 103
                                       S++L  ++e++e++e+ l+a+ ++ ++++ek++e  ++++s l
  gi|242399318|ref|YP_002994742.1|  85 SKALEEVKEKVETLEVRLKALERQEQKLNEKIKELTQQIQSAL 127
                                       7789999999999999999999999999999999999988876 PP

>> DLP_helical  Dynamin-like helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   7.5   0.00038     0.077      41     114 ..      54     126 ..      49     129 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00038
                       DLP_helical  41 eLqdateekikknggelalieetkksvirdvlerqlpeaeerleelekevekleesakriekelaelkkeieea 114
                                       + ++a ee+ k++ g+  + +  +  +++   ++ l+e++e++e le  ++ le + ++++++++el ++i+ a
  gi|242399318|ref|YP_002994742.1|  54 DAKKALEEIEKTEEGT-PIYKTVGTLIVKSTKSKALEEVKEKVETLEVRLKALERQEQKLNEKIKELTQQIQSA 126
                                       5578888988899999.******************************************************987 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0  14.3    0.0017      0.35     315     426 ..      17     126 ..       4     129 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0017
                                       HHT--HHHHTTGGG-TTTS-GGGSSTTTSTTHHHHHHHHHHHHHHHHHHHHHHS-SS---STTGGGT.HH.HHHHHH CS
                              EzrA 315 lehlekqnkelkeeldrlkqsYeLseeeleklrelekelkelekdyeeleekleekkvaYSelqeel.ee.leekle 389
                                       ++++  q++ l  +l+  +q+ +L    +++ + ++ el++ +k +ee+e+ +ee++  Y ++   + ++  ++ le
  gi|242399318|ref|YP_002994742.1|  17 MQNIPPQVQALLGQLESYQQQIQL---VIQQKQRVQVELNDAKKALEEIEK-TEEGTPIYKTVGTLIvKStKSKALE 89 
                                       677788999999999999999999...8999999999*****999999875.66677777666655514314578** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              EzrA 390 eieekqeeileslkslrkdEkrAreqldeikkelkei 426
                                       e++ek+e+++  lk+l+++E++ +e+++e+ ++++++
  gi|242399318|ref|YP_002994742.1|  90 EVKEKVETLEVRLKALERQEQKLNEKIKELTQQIQSA 126
                                       *********************************9876 PP

>> DUF4164  Domain of unknown function (DUF4164)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.8     0.012       2.5      33      69 ..      30      66 ..      23      69 .. 0.89
   2 ?    6.7   2.1     0.042       8.7      43      79 ..      90     126 ..      80     129 .. 0.51

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.012
                           DUF4164 33 krdeleaeiealgedrsRLaeeLdqaearaarleevn 69
                                      + ++++++i+++ + ++R   eL +a+  ++++e++ 
  gi|242399318|ref|YP_002994742.1| 30 QLESYQQQIQLVIQQKQRVQVELNDAKKALEEIEKTE 66
                                      557899**********************999999986 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.042
                           DUF4164  43 algedrsRLaeeLdqaearaarleevnrEvsrrLkaa 79 
                                       +++e  + L+ +L + e  +++l+e  +E+ +++++a
  gi|242399318|ref|YP_002994742.1|  90 EVKEKVETLEVRLKALERQEQKLNEKIKELTQQIQSA 126
                                       4444444455555555555555555555555555444 PP

>> Uds1  Up-regulated During Septation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   9.6    0.0039      0.81      22     119 ..      23     116 ..      21     126 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0039
                              Uds1  22 eVeelkkelkaLeerlea.lrkkLaletklrdaarsLsrlyssskksakssaarsnskssreslakaeeelaeserk 97 
                                       +V++l  +l++ +++++  +++k  ++  l da ++L++   +++        ++ ++ +   + ++ ++l+e ++k
  gi|242399318|ref|YP_002994742.1|  23 QVQALLGQLESYQQQIQLvIQQKQRVQVELNDAKKALEEIEKTEEGT-P--IYKTVGTLI--VKSTKSKALEEVKEK 94 
                                       5777777888889999852688999****************444444.3..222333333..667778888999999 PP

                              Uds1  98 vdelaselekleeraaevrrrL 119
                                       v+ l+  l+ le++++++++++
  gi|242399318|ref|YP_002994742.1|  95 VETLEVRLKALERQEQKLNEKI 116
                                       9999999999999998888775 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 ?    2.7  17.0      0.72   1.5e+02      54     104 ..      74     123 ..      16     126 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.72
                                       HHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCTS CS
                      Seryl_tRNA_N  54 elskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaeleklllai 104
                                       +++  I k  k+ +  ee++++v++l  +lkale ++++l++++++l+++i
  gi|242399318|ref|YP_002994742.1|  74 TVGTLIVKSTKS-KALEEVKEKVETLEVRLKALERQEQKLNEKIKELTQQI 123
                                       333444444444.6999*****************************99988 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 ?    5.2   2.5     0.068        14      82     123 ..      23      64 ..       1      70 [. 0.67
   2 ?    3.7  16.2      0.21        43      44     120 ..      39     125 ..      23     129 .. 0.61

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.068
                     PI3K_P85_iSH2  82 EieklqenleqlksrlkelhsskekLeedlkqqkeeereleR 123
                                        ++ l  +le  +++++ + ++k++++ +l+  k+   e+e+
  gi|242399318|ref|YP_002994742.1|  23 QVQALLGQLESYQQQIQLVIQQKQRVQVELNDAKKALEEIEK 64 
                                       456666677777777777777777777777777777766665 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.21
                     PI3K_P85_iSH2  44 seeiqlkrqaleaFneaikmFeeqiklqekfskea..........qehEieklqenleqlksrlkelhsskekLeed 110
                                       +  iq k+  +   n+a k +ee  k+ e                +++  e+++e +e l+ rlk l+ + +kL+e+
  gi|242399318|ref|YP_002994742.1|  39 QLVIQQKQRVQVELNDAKKALEEIEKTEEGTPIYKtvgtlivkstKSKALEEVKEKVETLEVRLKALERQEQKLNEK 115
                                       222333333333344444444443333333322223333333333599999************************** PP

                     PI3K_P85_iSH2 111 lkqqkeeere 120
                                       +k+ +++ ++
  gi|242399318|ref|YP_002994742.1| 116 IKELTQQIQS 125
                                       **99998775 PP

>> DUF5320  Family of unknown function (DUF5320)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.2      0.18        37      66      98 ..      29      61 ..       6      62 .. 0.80
   2 ?    7.8   1.3     0.033       6.8      70      99 .]      90     119 ..      69     125 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.18
                           DUF5320 66 taeaskeeekelLeeqaeaLeeeleaikkrlke 98
                                       + +s +++++l  +q++  + el++ kk l+e
  gi|242399318|ref|YP_002994742.1| 29 GQLESYQQQIQLVIQQKQRVQVELNDAKKALEE 61
                                      45567789999999***************9998 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.033
                           DUF5320  70 skeeekelLeeqaeaLeeeleaikkrlkel 99 
                                       + +e+ e Le + +aLe++ +++++++kel
  gi|242399318|ref|YP_002994742.1|  90 EVKEKVETLEVRLKALERQEQKLNEKIKEL 119
                                       455666777777777777777777777765 PP

>> Tropomyosin  Tropomyosin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   2.3     0.018       3.7      39      74 ..      32      67 ..      23      77 .. 0.87
   2 ?    8.0   7.8    0.0077       1.6      61     104 ..      83     126 ..      73     129 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.018
                       Tropomyosin 39 aalnrriqlleeelerteerleealekLeeaekaad 74
                                      ++ +++iql+ ++ +r++ +l++a++ Lee ek+ +
  gi|242399318|ref|YP_002994742.1| 32 ESYQQQIQLVIQQKQRVQVELNDAKKALEEIEKTEE 67
                                      68899**************************99754 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0077
                       Tropomyosin  61 ealekLeeaekaadeserarKvlEnrelkdeekleeleaqlkea 104
                                       ++ + Lee++++ +  e  +K+lE +e+k +ek++el +q++ a
  gi|242399318|ref|YP_002994742.1|  83 TKSKALEEVKEKVETLEVRLKALERQEQKLNEKIKELTQQIQSA 126
                                       44566777777777778888888888888888888888888776 PP

>> E2F_CC-MB  E2F transcription factor CC-MB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   1.4      0.25        52      47      75 ..      30      66 ..      23      95 .. 0.69
   2 ?   10.8   2.0    0.0024      0.48       4      28 ..     101     125 ..      98     128 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.25
                         E2F_CC-MB 47 siasfkeqtviaikAppgtqlevpdpee........e 75
                                      +++s+++q+ ++i+  +  q+e  d ++        e
  gi|242399318|ref|YP_002994742.1| 30 QLESYQQQIQLVIQQKQRVQVELNDAKKaleeiektE 66
                                      6788999999999999999999998763333444440 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0024
                         E2F_CC-MB   4 elesleeeeqkLDelieklteqlkn 28 
                                        l+ le++eqkL+e i++lt+q+++
  gi|242399318|ref|YP_002994742.1| 101 RLKALERQEQKLNEKIKELTQQIQS 125
                                       6899******************985 PP

>> FAA_hydro_N_2  Fumarylacetoacetase N-terminal domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.4      0.51   1.1e+02      32      58 ..      35      61 ..      12      74 .. 0.61
   2 ?    8.4   0.3     0.013       2.8      13      59 ..      76     122 ..      72     128 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.51
                     FAA_hydro_N_2 32 aptlqaaLdnWdevepaLeelyeaLna 58
                                       +++q ++++ ++v+ +L+++ +aL++
  gi|242399318|ref|YP_002994742.1| 35 QQQIQLVIQQKQRVQVELNDAKKALEE 61
                                      345555666666666666666666665 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.013
                     FAA_hydro_N_2  13 GeLvvVsrdlkkavdaseiaptlqaaLdnWdevepaLeelyeaLnag 59 
                                       G+L+v s   k+  +++e ++tl   L   ++ e++L+e+ ++L ++
  gi|242399318|ref|YP_002994742.1|  76 GTLIVKSTKSKALEEVKEKVETLEVRLKALERQEQKLNEKIKELTQQ 122
                                       899999999999999**********9999999999999999999865 PP

>> LMBR1  LMBR1-like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   3.6    0.0052       1.1     201     307 ..      30     123 ..      12     129 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0052
                             LMBR1 201 elkklyfeaaklntekeeaereledllkevkklrksisesdplrkylee.ilkkvPeeiaeklksnenkteeslakl 276
                                       +l++++ +++ + ++k+  + el+d +k++++++k+ + +  ++k + + i+k++ +           k++e++++ 
  gi|242399318|ref|YP_002994742.1|  30 QLESYQQQIQLVIQQKQRVQVELNDAKKALEEIEKTEEGTP-IYKTVGTlIVKSTKS-----------KALEEVKEK 94 
                                       78999999999999999999999999999999988877777.444444403333333...........444455555 PP

                             LMBR1 277 ekqlikalqkrertekqwkrllekaleledi 307
                                        + l  +l+  er+e+++++ +++   +++i
  gi|242399318|ref|YP_002994742.1|  95 VETLEVRLKALERQEQKLNEKIKEL--TQQI 123
                                       5555555555555555555555554..3333 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8  12.8    0.0067       1.4     226     323 ..      28     125 ..      17     128 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0067
                             IFT57 226 leqmkkhkksieeslpetksqlkklhedisktlekiesrEk..ylnsqleellqeyreaqeelsevkekykqlsegv 300
                                       l q+++++++i+  +++ k+ ++   +d +k+le+ie+ E+   + + + +l+ + +++++ l+evkek+++l+ ++
  gi|242399318|ref|YP_002994742.1|  28 LGQLESYQQQIQLVIQQ-KQRVQVELNDAKKALEEIEKTEEgtPIYKTVGTLIVK-STKSKALEEVKEKVETLEVRL 102
                                       678999999**999999.99999999*************9633699999999998.677889*************** PP

                             IFT57 301 seltrelaeiseelekvkqemee 323
                                       ++l+r+ ++++e+++++ q++++
  gi|242399318|ref|YP_002994742.1| 103 KALERQEQKLNEKIKELTQQIQS 125
                                       ********************996 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   2.0    0.0097         2       2      39 ..      28      65 ..      27      84 .. 0.90
   2 ?    6.2   3.2     0.043       8.9      25      66 ..      87     121 ..      73     128 .. 0.43

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0097
                             Sec34  2 ldqLeskeeecdelleqtdealeqLeeleekfksvsek 39
                                      l qLes++++++ +++q ++++ +L++ ++  +++++ 
  gi|242399318|ref|YP_002994742.1| 28 LGQLESYQQQIQLVIQQKQRVQVELNDAKKALEEIEKT 65
                                      569*****************************999875 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.043
                             Sec34  25 qLeeleekfksvsektsslheaceqlleeqkrleelaeeiee 66 
                                        Lee++ek+++ + + ++l+++ ++l e+ k+l+       +
  gi|242399318|ref|YP_002994742.1|  87 ALEEVKEKVETLEVRLKALERQEQKLNEKIKELT-------Q 121
                                       3333333333333333333333333333222222.......2 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 ?    0.2   0.1       4.2   8.6e+02      41      60 ..      47      66 ..      23      79 .. 0.68
   2 ?   10.7   1.2    0.0022      0.46      36      68 ..      96     128 ..      71     131 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 4.2
                                      EEE...EEHHHHHHHHH... CS
                           CinA_KH 41 Rltakaaneeeaealiapve 60
                                      R+ ++ +++++a + i+++e
  gi|242399318|ref|YP_002994742.1| 47 RVQVELNDAKKALEEIEKTE 66
                                      44444455555555555555 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0022
                                       TEEEEEEE...EEHHHHHHHHH....HHHHHTT CS
                           CinA_KH  36 gevtvRltakaaneeeaealiapveeeirerlg 68 
                                       +  +vRl a  ++e++ ++ i++++++i+++l 
  gi|242399318|ref|YP_002994742.1|  96 ETLEVRLKALERQEQKLNEKIKELTQQIQSALR 128
                                       5789************************99885 PP

>> DUF4618  Domain of unknown function (DUF4618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   4.0     0.018       3.7      39      80 ..      23      67 ..      19      74 .. 0.80
   2 ?    8.1   7.1    0.0077       1.6      67     105 ..      86     124 ..      69     128 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.018
                           DUF4618 39 kvrklLqqyeklktvisil.ekss..kkqleqakaeLqeweekee 80
                                      +v++lL q e +++ i+ + ++++  + +l++ak+ L+e+e++ee
  gi|242399318|ref|YP_002994742.1| 23 QVQALLGQLESYQQQIQLViQQKQrvQVELNDAKKALEEIEKTEE 67
                                      6999********9999876244441156789***********998 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0077
                           DUF4618  67 qakaeLqeweekeekklekLeqqleqlnakvqklqeeln 105
                                       +a +e +e+ e++e +l+ Le+q ++ln+k+++l ++++
  gi|242399318|ref|YP_002994742.1|  86 KALEEVKEKVETLEVRLKALERQEQKLNEKIKELTQQIQ 124
                                       45567778888899999***************9999986 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 ?    6.7  12.6     0.036       7.5      38     127 ..      25     125 ..      15     129 .. 0.56

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.036
                                       CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH.............HHHHHHHHHHHHHHCCCHHHHHHHCCH CS
                         Fib_alpha  38 ekleneleeisnstkeaeelvkeikdslrekqkskkd.............ndnvikksskeleeeilrlketidaqe 101
                                       + l  +le+++++ + + +  ++++  l++++k  ++               ++i ks+k   +  +++ke++ + e
  gi|242399318|ref|YP_002994742.1|  25 QALLGQLESYQQQIQLVIQQKQRVQVELNDAKKALEEiekteegtpiyktVGTLIVKSTK--SKALEEVKEKVETLE 99 
                                       444444444444444444444444444444444333333333222222112333333333..345779999999999 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 102 snirvLqnvlesneqkiqkLeqdidq 127
                                        ++++L    +++++ki++L q+i++
  gi|242399318|ref|YP_002994742.1| 100 VRLKALERQEQKLNEKIKELTQQIQS 125
                                       99999999999999999999999976 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 ?    8.3   1.5     0.012       2.4      34      75 ..      24      65 ..      16      68 .. 0.92
   2 ?    5.8   5.3     0.073        15      60      96 ..      86     122 ..      80     129 .. 0.57

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.012
                            CENP-Q 34 kaaleaqLspelhslelLeaeiekeeralerdyeaLreLekn 75
                                       +al  qL+  +++++l  +++++++ +l   ++aL+e ek+
  gi|242399318|ref|YP_002994742.1| 24 VQALLGQLESYQQQIQLVIQQKQRVQVELNDAKKALEEIEKT 65
                                      578899********************************9996 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.073
                            CENP-Q  60 ralerdyeaLreLeknakaearerkeklkkehvllqe 96 
                                       +ale+ +e+ ++Le   ka++r++++  +k   l+q+
  gi|242399318|ref|YP_002994742.1|  86 KALEEVKEKVETLEVRLKALERQEQKLNEKIKELTQQ 122
                                       5666666666666666666666655544444445553 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2  12.3     0.017       3.5     363     457 ..      23     127 ..      13     130 .. 0.63

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.017
                            AAA_13 363 kiesikklvaeineliakhNekvanleeekeeakkklelhlveeleseldeyk............kkykklekaiek 427
                                       +++++  ++++ +++i+   ++ ++++ e ++akk+le  +    e+    yk            k+++++++++e 
  gi|242399318|ref|YP_002994742.1|  23 QVQALLGQLESYQQQIQLVIQQKQRVQVELNDAKKALEEIEK--TEEGTPIYKtvgtlivkstksKALEEVKEKVET 97 
                                       555555556666666666666666677777777777776443..333222233333444444455777788888888 PP

                            AAA_13 428 lekelkeeeaelkkleeeikeLekqlrdek 457
                                       le +lk+ e++ +kl+e+ikeL +q+++  
  gi|242399318|ref|YP_002994742.1|  98 LEVRLKALERQEQKLNEKIKELTQQIQSAL 127
                                       888999999999999999999988888765 PP

>> HSCB_C  HSCB C-terminal oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   1.6       4.5   9.3e+02      54      63 ..      51      60 ..      22      69 .. 0.49
   2 ?   13.3   3.0   0.00042     0.086      11      50 ..      90     127 ..      86     131 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 4.5
                                      -HHHHHHHHH CS
                            HSCB_C 54 dleaaadllr 63
                                      +l++a+++l 
  gi|242399318|ref|YP_002994742.1| 51 ELNDAKKALE 60
                                      3333333332 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.00042
                                       HHHHHHHCGGGSSSHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            HSCB_C  11 elrEeleeaeeaadkeeleelkaeveerieeleaeleeaf 50 
                                       e++E++e +e      +le+ +++++e+i+el++++++a+
  gi|242399318|ref|YP_002994742.1|  90 EVKEKVETLE-V-RLKALERQEQKLNEKIKELTQQIQSAL 127
                                       6778888883.3.45***********************98 PP

>> FlxA  FlxA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   7.7      0.12        25      52      91 ..      18      57 ..      15      70 .. 0.60
   2 ?    8.9   4.3     0.007       1.4      22      66 ..      91     124 ..      76     127 .. 0.46

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.12
                              FlxA 52 qliqaQIqqlqaQIaqlqqqqaekaqekqqsekeeksksk 91
                                      q i  Q+q+l  Q++  qqq +   q+kq  ++e + ++k
  gi|242399318|ref|YP_002994742.1| 18 QNIPPQVQALLGQLESYQQQIQLVIQQKQRVQVELNDAKK 57
                                      5566677777777777777777666666666666554444 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.007
                              FlxA  22 LqkQiknlqkqLkelsesdeltkeekkkqqqliqaQIqqlqaQIa 66 
                                        ++ +++l+  Lk l             q+q + ++I+ l +QI+
  gi|242399318|ref|YP_002994742.1|  91 VKEKVETLEVRLKALE-----------RQEQKLNEKIKELTQQIQ 124
                                       3333333333333333...........344444444444444443 PP

>> MCU  Mitochondrial calcium uniporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   1.2      0.35        72      43      82 ..      25      64 ..       6      70 .. 0.55
   2 ?   10.3   3.3    0.0027      0.56       8      72 ..      69     125 ..      62     129 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.35
                                      X-SSSSSSTSSSSSHHHHHHHHHHHHH-SHHHHHHHHTCC CS
                               MCU 43 esalnveeeqlkkereleekleelreelepleekkeeide 82
                                      +++l   e  +++ + + +++++++ el+ ++++ eei++
  gi|242399318|ref|YP_002994742.1| 25 QALLGQLESYQQQIQLVIQQKQRVQVELNDAKKALEEIEK 64
                                      3333333344444444444555555555555555555543 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0027
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-SSSSSSTSSSSSHHHHHHHHHHHHH-SH CS
                               MCU   8 aavlsesgvvialstlleeeeakvllrvkqlvkalesalnveeeqlkkereleekleelreelep 72 
                                         ++++ g+ i+ st     ++k l++vk+ v++le  l++    +++e++l+ek++el++++++
  gi|242399318|ref|YP_002994742.1|  69 TPIYKTVGTLIVKST-----KSKALEEVKEKVETLEVRLKAL---ERQEQKLNEKIKELTQQIQS 125
                                       567788888888888.....7899999999999999999666...67777888888888888876 PP

>> zf-CpG_bind_C  CpG binding protein zinc finger C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   1.0      0.17        36      40      75 ..      23      58 ..      15      72 .. 0.71
   2 ?    9.3   4.6    0.0044       0.9      23      64 ..      80     121 ..      69     128 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.17
                     zf-CpG_bind_C 40 eakkklkelekklkkLeeliekakklslkeeeeeee 75
                                      ++++ l +le+ +++++ +i+++++++++ ++ +++
  gi|242399318|ref|YP_002994742.1| 23 QVQALLGQLESYQQQIQLVIQQKQRVQVELNDAKKA 58
                                      567778889999999999999888888887776542 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0044
                     zf-CpG_bind_C  23 aeeenkkklekirkeqeeakkklkelekklkkLeeliekakk 64 
                                       +++++ k+le++++++e+++ +lk+le++ +kL+e i++  +
  gi|242399318|ref|YP_002994742.1|  80 VKSTKSKALEEVKEKVETLEVRLKALERQEQKLNEKIKELTQ 121
                                       567888999999999999999999999999999999987655 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.7      0.43        89      28      68 ..      24      57 ..      12      79 .. 0.46
   2 ?    9.7   2.6     0.005         1      25      66 ..      85     126 ..      70     129 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.43
                            DUF948 28 ldeaaatieelekqvdpilkevedllakvnelledvnekle 68
                                      ++++  ++e+ ++q++ ++++ +++  + n+         +
  gi|242399318|ref|YP_002994742.1| 24 VQALLGQLESYQQQIQLVIQQKQRVQVELND-------AKK 57
                                      3333333444444444444444444444444.......222 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.005
                            DUF948  25 kktldeaaatieelekqvdpilkevedllakvnelledvnek 66 
                                       +k l+e+++ +e+le +++++ ++ ++l +k++el++++++ 
  gi|242399318|ref|YP_002994742.1|  85 SKALEEVKEKVETLEVRLKALERQEQKLNEKIKELTQQIQSA 126
                                       799***********************************9976 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2  15.5      0.14        29       9     101 ..      17     127 ..       9     128 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.14
                           DUF4795   9 lkklqeaieklqeelekleekvkelekrledkekklealkkqieelekvk...............adkeeveeelae 70 
                                       ++++  +++ l  +le+ +++ + + +++++ +++l+  kk++ee ek+                  k++  ee++e
  gi|242399318|ref|YP_002994742.1|  17 MQNIPPQVQALLGQLESYQQQIQLVIQQKQRVQVELNDAKKALEEIEKTEegtpiyktvgtlivkSTKSKALEEVKE 93 
                                       56666666666677777777777777777777777777777777777776666666677788877777777788888 PP

                           DUF4795  71 kadkeaLatkvsrdq...fDeakkeLekmleell 101
                                       k+ +  ++ k+ + q   + e++keL+++++++l
  gi|242399318|ref|YP_002994742.1|  94 KVETLEVRLKALERQeqkLNEKIKELTQQIQSAL 127
                                       8888888888766666778888888888888776 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   5.4         1   2.1e+02      46      83 ..      30      64 ..      13      79 .. 0.47
   2 ?   12.3   6.7   0.00091      0.19      32      72 ..      84     124 ..      72     129 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 1
                                      ..HHHHHHHHHHHHHHHHHHHHHHHHHHHHH....... CS
                             DUF16 46 lgeqinkleqkvekqgekikelkveqkaqgeelnkvde 83
                                      + e+ +++ q v +q +++   +ve +  +++l+++++
  gi|242399318|ref|YP_002994742.1| 30 QLESYQQQIQLVIQQKQRV---QVELNDAKKALEEIEK 64
                                      2233333334443444333...3333333333333333 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00091
                                       BHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHH CS
                             DUF16  32 nkqrLkkieakvdklgeqinkleqkvekqgekikelkveqk 72 
                                         + L+++++kv++l++++++le + +k++ekikel+++++
  gi|242399318|ref|YP_002994742.1|  84 KSKALEEVKEKVETLEVRLKALERQEQKLNEKIKELTQQIQ 124
                                       45679*******************************99876 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   5.6      0.13        28      10      52 ..      26      69 ..      23      87 .. 0.86
   2 ?    8.9   5.6      0.01       2.1       8      46 ..      88     126 ..      85     129 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.13
                   Snapin_Pallidin 10 llepkldeldeklkelrqsQeeLleqldrlnekLkeleeaqe.a 52
                                       l  +l+  +++++ ++q+ + ++ +l+  +++L+e+e+++e +
  gi|242399318|ref|YP_002994742.1| 26 ALLGQLESYQQQIQLVIQQKQRVQVELNDAKKALEEIEKTEEgT 69
                                      56678999*******************************99844 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.01
                   Snapin_Pallidin   8 lellepkldeldeklkelrqsQeeLleqldrlnekLkel 46 
                                       le ++ k+++l+ +lk+l+++ ++L+e++++l+++++++
  gi|242399318|ref|YP_002994742.1|  88 LEEVKEKVETLEVRLKALERQEQKLNEKIKELTQQIQSA 126
                                       5668899****************************9975 PP

>> GIT_CC  GIT coiled-coil Rho guanine nucleotide exchange factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   2.0       2.9   5.9e+02      34      57 ..      30      53 ..      13      63 .. 0.58
   2 ?   12.2   4.9    0.0006      0.12      20      55 ..      90     125 ..      87     128 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 2.9
                            GIT_CC 34 qLlkvNtslsdelrlLQskvqkLq 57
                                      qL    ++++  +++ Q+++ +L+
  gi|242399318|ref|YP_002994742.1| 30 QLESYQQQIQLVIQQKQRVQVELN 53
                                      344444444444444455444444 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.0006
                            GIT_CC  20 elKkalaaseakiqqLlkvNtslsdelrlLQskvqk 55 
                                       e+K+++ + e+++++L +  ++l++++++L +++q+
  gi|242399318|ref|YP_002994742.1|  90 EVKEKVETLEVRLKALERQEQKLNEKIKELTQQIQS 125
                                       9*****************************888875 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   3.2      0.76   1.6e+02      22      56 ..      27      61 ..      17      70 .. 0.59
   2 ?   10.5   4.3    0.0036      0.75       2      35 ..      92     125 ..      91     128 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.76
                                      HHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXX CS
                              SlyX 22 Lndvvaeqqqqidrlqrqlrllaerlkeleessga 56
                                      L  ++   qqqi+   +q ++++ +l++++++ ++
  gi|242399318|ref|YP_002994742.1| 27 LLGQLESYQQQIQLVIQQKQRVQVELNDAKKALEE 61
                                      44555556666666666666666666555555443 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0036
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              SlyX   2 eerleeLEiklafqedtieeLndvvaeqqqqidr 35 
                                       +e++e LE++l  +e++ ++Ln+ + e  qqi+ 
  gi|242399318|ref|YP_002994742.1|  92 KEKVETLEVRLKALERQEQKLNEKIKELTQQIQS 125
                                       6899***************************985 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.6      0.35        73      15      54 ..      29      63 ..      17      68 .. 0.38
   2 ?    6.1   8.1     0.081        17       7      85 ..      45     123 ..      42     129 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.35
                      Syntaxin-6_N 15 nkaeslyrrwerlledtssstseeldetrteLrkalrsie 54
                                       ++es  ++ +    + ++ +++ ++   ++ +kal++ie
  gi|242399318|ref|YP_002994742.1| 29 GQLESYQQQIQ----LVIQ-QKQRVQVELNDAKKALEEIE 63
                                      33333333332....1111.13333333333333333333 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.081
                      Syntaxin-6_N   7 keeVqkslnkaeslyrrwerlledtss.stseeldetrteLrkalrsiewdledLeetvriveknpskfkidekels 82 
                                       k+ Vq +ln a++ +++ e++ e t+  + +      ++   kal+++++++e Le   +++e++++k + + kel+
  gi|242399318|ref|YP_002994742.1|  45 KQRVQVELNDAKKALEEIEKTEEGTPIyK-TVGTLIVKSTKSKALEEVKEKVETLEVRLKALERQEQKLNEKIKELT 120
                                       78899999999999999998777766644.44445555555789999999999999999999999999999999988 PP

                      Syntaxin-6_N  83 rrr 85 
                                       ++ 
  gi|242399318|ref|YP_002994742.1| 121 QQI 123
                                       875 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   3.8      0.26        53      19      59 ..      24      64 ..      15      65 .. 0.84
   2 ?    9.0   5.7    0.0055       1.1      18      52 ..      87     121 ..      77     126 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.26
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXXXXX CS
                             DivIC 19 ykqlkqeiaalqaelaklkaeneeLeaevkdLksdedyiee 59
                                      +++l  +++  q++++ + +++++ + e++d k+  + ie+
  gi|242399318|ref|YP_002994742.1| 24 VQALLGQLESYQQQIQLVIQQKQRVQVELNDAKKALEEIEK 64
                                      56677788889999999999999999999999988888887 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0055
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XX CS
                             DivIC  18 aykqlkqeiaalqaelaklkaeneeLeaevkdLks 52 
                                       a+ ++k+++++l+  l++l  ++++L++++k+L++
  gi|242399318|ref|YP_002994742.1|  87 ALEEVKEKVETLEVRLKALERQEQKLNEKIKELTQ 121
                                       67789999999999999999999999999999964 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 ?    4.8  10.4     0.051        11     161     244 ..      27     113 ..      21     129 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.051
                        Fmp27_WPPW 161 ilgkendpervqkelleeRleeleeqiekleekleelelkseke...........deelkeeieelekeikelkekl 226
                                       +lg+  ++ + q +l+ + +++++ ++++ +++lee+e+++e +           +++        +k ++e+kek+
  gi|242399318|ref|YP_002994742.1|  27 LLGQ-LESYQQQIQLVIQQKQRVQVELNDAKKALEEIEKTEEGTpiyktvgtlivKST-------KSKALEEVKEKV 95 
                                       5677.6688999****************************999888654443333333.......334455555555 PP

                        Fmp27_WPPW 227 efletlledlkeseesse 244
                                       e+le  l+ l+++e++ +
  gi|242399318|ref|YP_002994742.1|  96 ETLEVRLKALERQEQKLN 113
                                       555555555555554222 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3  14.4       2.1   4.3e+02      52      95 ..      80     123 ..      23     124 .. 0.61

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 2.1
                           BLOC1_2  52 klnekyeelqpylqqidqiekqvteLeeavseLDeyskeLEakf 95 
                                         + k+++l++ +++++ +e +++ Le   ++L+e +keL +++
  gi|242399318|ref|YP_002994742.1|  80 VKSTKSKALEEVKEKVETLEVRLKALERQEQKLNEKIKELTQQI 123
                                       34667778888888888888888888888888888888887665 PP

>> DUF2408  Protein of unknown function (DUF2408)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6  12.2      0.92   1.9e+02       3     112 ..      19     120 ..      17     131 .. 0.56

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.92
                           DUF2408   3 elspelepiyekLvsirrsLlslaakskaeeakeseevkeelkelkeeLkkieskrdeegkFkseegkevvekgqav 79 
                                       +++p++++++ +L s ++++  ++ ++++        v+ el++ k+ L++ie++ + +  +k+  +  v++++ + 
  gi|242399318|ref|YP_002994742.1|  19 NIPPQVQALLGQLESYQQQIQLVIQQKQR--------VQVELNDAKKALEEIEKTEEGTPIYKTVGTLIVKSTKSKA 87 
                                       66677777777777766666544444443........5666666666666666666665666555555555555555 PP

                           DUF2408  80 lngLlddcfdlvedlkaqdgeekkvasslqpiY 112
                                       l++  ++   l   lka + +e+k++++++++ 
  gi|242399318|ref|YP_002994742.1|  88 LEEVKEKVETLEVRLKALERQEQKLNEKIKELT 120
                                       555555555555555555545555555555443 PP

>> Allexi_40kDa  Allexivirus 40kDa protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.4      0.87   1.8e+02      85     130 ..      26      62 ..      11      69 .. 0.43
   2 ?    6.2   4.1     0.031       6.4      75     141 ..      83     123 ..      49     130 .. 0.51

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.87
                      Allexi_40kDa  85 dalrtltklldklksvekklelsaetasdskllkklesietsleel 130
                                       + l +l++  ++++         +++++  +   +l+  ++ lee+
  gi|242399318|ref|YP_002994742.1|  26 ALLGQLESYQQQIQL-------VIQQKQRVQ--VELNDAKKALEEI 62 
                                       333334444444443.......333333222..2233333333332 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.031
                      Allexi_40kDa  75 sqttlLselrdalrtltklldklksvekklelsaetasdskllkklesietsleelhakldelssse 141
                                       ++++ L e++++++tl+                           +l+++e++ ++l++k++el+++ 
  gi|242399318|ref|YP_002994742.1|  83 TKSKALEEVKEKVETLEV--------------------------RLKALERQEQKLNEKIKELTQQI 123
                                       233344444444444444..........................45555555555555555555444 PP

>> HemX  HemX, putative uroporphyrinogen-III C-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1  17.6      0.23        47      25      98 ..      40     125 ..      12     129 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.23
                              HemX  25 lgqqqvqeltaevaelqqqlaaleqqlaq...............veaekeqkqeleerlqqlaeklealekeleqlq 86 
                                       l  qq+q+ + e ++ +++l+++e+   +                +++ +  +e++e++++l+ +l+ale++ ++l+
  gi|242399318|ref|YP_002994742.1|  40 LVIQQKQRVQVELNDAKKALEEIEK---TeegtpiyktvgtlivKSTKSKALEEVKEKVETLEVRLKALERQEQKLN 113
                                       2223333444444444444444444...1556********9985555566778899999999999************ PP

                              HemX  87 kqleelqqqlsk 98 
                                       ++++el+qq++ 
  gi|242399318|ref|YP_002994742.1| 114 EKIKELTQQIQS 125
                                       *******99986 PP

>> EMP24_GP25L  emp24/gp25L/p24 family/GOLD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   8.7      0.12        24     103     150 ..      60     125 ..      17     128 .. 0.68

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.12
                       EMP24_GP25L 103 d..................ykdsakkekletleselkkleekldsikreqkylrereerlrdtnes 150
                                       +                  + +s k++ le++++++++le +l+ ++r+ + l+e+ ++l ++++s
  gi|242399318|ref|YP_002994742.1|  60 EeiekteegtpiyktvgtlIVKSTKSKALEEVKEKVETLEVRLKALERQEQKLNEKIKELTQQIQS 125
                                       144445555556666666677777888888888888888888888888777777777777766665 PP

>> DUF2802  Protein of unknown function (DUF2802)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   1.5      0.52   1.1e+02       7      34 ..      46      73 ..      18      88 .. 0.78
   2 ?    7.5   3.8     0.022       4.6       5      28 ..     101     124 ..      85     128 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.52
                           DUF2802  7 aelekrlkqleerleeleqqdpqsklYs 34
                                      ++++ +l+  ++ lee+e++++ ++ Y 
  gi|242399318|ref|YP_002994742.1| 46 QRVQVELNDAKKALEEIEKTEEGTPIYK 73
                                      4566667777788888888888888886 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.022
                           DUF2802   5 rlaelekrlkqleerleeleqqdp 28 
                                       rl++le++ ++l+e+++el qq +
  gi|242399318|ref|YP_002994742.1| 101 RLKALERQEQKLNEKIKELTQQIQ 124
                                       899****************88865 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3  11.0       2.6   5.4e+02      47      69 ..      70     123 ..      15     129 .. 0.46

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 2.6
                           DUF2203  47 e...............................aaeleaeleeleaeieelveei 69 
                                                                        ++le+++++l+++i+el+++i
  gi|242399318|ref|YP_002994742.1|  70 PiyktvgtlivkstkskaleevkekvetlevrLKALERQEQKLNEKIKELTQQI 123
                                       244333333332222222222222222222334444444444444444444444 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   3.0      0.22        46      11      42 ..      36      67 ..      17      89 .. 0.56
   2 ?    7.1   5.8      0.03       6.2       9      41 ..      91     123 ..      80     129 .. 0.52

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.22
                             Spc24 11 kelsdleselesleselaelkeeleeleeese 42
                                      ++++ + ++ ++++ el++ k+ lee+e+ +e
  gi|242399318|ref|YP_002994742.1| 36 QQIQLVIQQKQRVQVELNDAKKALEEIEKTEE 67
                                      33333444445555555555555555555443 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.03
                             Spc24   9 iakelsdleselesleselaelkeeleeleees 41 
                                       + ++++ le  l++le + ++l+e+++el ++ 
  gi|242399318|ref|YP_002994742.1|  91 VKEKVETLEVRLKALERQEQKLNEKIKELTQQI 123
                                       334445555555555555555555555555554 PP

>> DUF5398  Family of unknown function (DUF5398)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   1.2       5.4   1.1e+03      34      55 ..      45      66 ..      21      80 .. 0.71
   2 ?   11.6   4.1    0.0016      0.34       7      52 ..      85     131 ..      79     132 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 5.4
                           DUF5398 34 kqkvesriqkikeaLReGenke 55
                                      kq+v+  + + k+aL e e+ e
  gi|242399318|ref|YP_002994742.1| 45 KQRVQVELNDAKKALEEIEKTE 66
                                      6666666677777776655555 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.0016
                           DUF5398   7 qkkgekseeflfelEkdlkdvkka.keikqkvesriqkikeaLReGe 52 
                                       +k+ e  +e +  lE  lk + ++ +++++k+++  q+i++aLR+G 
  gi|242399318|ref|YP_002994742.1|  85 SKALEEVKEKVETLEVRLKALERQeQKLNEKIKELTQQIQSALRGGV 131
                                       566667778888899999999765278******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2901  (0.161805); expected 358.6 (0.02)
Passed bias filter:                     1042  (0.0581181); expected 358.6 (0.02)
Passed Vit filter:                       207  (0.0115455); expected 17.9 (0.001)
Passed Fwd filter:                       102  (0.00568911); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              87  [number of targets reported over threshold]
# CPU time: 0.89u 0.38s 00:00:01.27 Elapsed: 00:00:00.54
# Mc/sec: 742.55
//
Query:       gi|242399319|ref|YP_002994743.1|  [L=80]
Description: hypothetical protein TSIB_1342 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-15   55.5   0.0    5.2e-15   55.3   0.0    1.0  1  Pcc1      Transcription factor Pcc1


Domain annotation for each model (and alignments):
>> Pcc1  Transcription factor Pcc1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.3   0.0   2.9e-19   5.2e-15       3      73 ..       7      78 ..       5      79 .. 0.96

  Alignments for each domain:
  == domain 1  score: 55.3 bits;  conditional E-value: 2.9e-19
                                      EEEEE-SSHHHHHHHHHHHHHHCHC-TTE.CEEEEEEETTEEEEEEEESSHHHHHHHHHHHHHHHHHHHHHH CS
                              Pcc1  3 tisvpfpterlAsialrtLqvDkelspla.vkrslslegnvLqveykAttnrmLRvavngfleslglvletm 73
                                      +i+++fp+e+ A+i+++++  +++  p   ++ ++sl+g+++ ++++A++n +LR ++n++l++++++l++ 
  gi|242399319|ref|YP_002994743.1|  7 SIELEFPNEEIAKIVYESVLFEHKSVPYRrSRLDFSLKGSKIIMRFTAEDNSALRGTINSYLRWIKVALDVA 78
                                      79********************99999998***************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); 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: 0.31u 0.27s 00:00:00.58 Elapsed: 00:00:00.40
# Mc/sec: 604.08
//
Query:       gi|242399320|ref|YP_002994744.1|  [L=210]
Description: Probable brix domain-containing ribosomal biogenesis protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.33s 00:00:00.87 Elapsed: 00:00:00.53
# Mc/sec: 1200.59
//
Query:       gi|242399321|ref|YP_002994745.1|  [L=53]
Description: DNA-directed RNA polymerase subunit P [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.5e-09   34.8   6.2    1.5e-08   34.2   6.2    1.3  1  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
    2.8e-05   24.1   0.2      3e-05   24.0   0.2    1.1  1  HypA             Hydrogenase/urease nickel incorporation, met
      3e-05   24.1   0.5    4.3e-05   23.5   0.5    1.3  1  Zn-ribbon_8      Zinc ribbon domain
    0.00012   21.4   3.2     0.0072   15.7   0.1    2.1  2  zf-ribbon_3      zinc-ribbon domain
    0.00078   19.3   0.8       0.26   11.2   0.3    2.1  2  Cys_rich_CPXG    Cysteine-rich CPXCG
     0.0018   17.8   0.9      0.076   12.6   0.0    2.1  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
     0.0018   18.6   0.1     0.0026   18.1   0.1    1.2  1  DUF4379          Probable Zinc-ribbon domain
     0.0019   18.2   0.4     0.0031   17.5   0.4    1.4  1  DZR              Double zinc ribbon
     0.0022   17.8   1.5     0.0031   17.4   1.0    1.5  2  Zn_ribbon_SprT   SprT-like zinc ribbon domain
     0.0024   17.8   0.4        0.7    9.9   0.2    2.1  2  Ogr_Delta        Ogr/Delta-like zinc finger
     0.0029   17.4   2.4        0.1   12.4   0.3    2.1  2  TFIIS_C          Transcription factor S-II (TFIIS)
     0.0038   17.3   1.2        1.2    9.2   0.1    2.1  2  CpXC             CpXC protein
      0.004   17.1   0.6     0.0059   16.5   0.6    1.3  1  Prok-RING_1      Prokaryotic RING finger family 1
      0.005   16.5   6.0        0.1   12.3   0.2    2.1  2  zinc_ribbon_2    zinc-ribbon domain
     0.0051   17.2   2.1       0.57   10.7   0.4    2.2  2  zf-H2C2_2        Zinc-finger double domain
      0.006   16.3   1.7        1.2    9.0   0.2    2.3  2  zinc_ribbon_5    zinc-ribbon domain
     0.0061   16.4   1.0       0.25   11.3   0.0    2.1  2  DUF951           Bacterial protein of unknown function (DUF95
     0.0085   16.0   1.3          2    8.5   0.2    2.1  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
      0.009   15.9   2.9       0.35   10.8   2.9    2.2  1  zinc_ribbon_4    zinc-ribbon domain
     0.0092   15.9   3.0        1.2    9.1   0.1    2.2  2  zf-C2HC_2        zinc-finger of a C2HC-type
  ------ inclusion threshold ------
      0.011   16.2   2.3       0.25   11.9   0.2    2.1  2  Zn_ribbon_recom  Recombinase zinc beta ribbon domain
      0.012   15.4   0.6      0.014   15.3   0.6    1.1  1  zf-C3HC4_3       Zinc finger, C3HC4 type (RING finger)
      0.013   15.7   0.6        1.9    8.7   0.1    2.1  2  zf-AN1           AN1-like Zinc finger
      0.014   15.4   2.5        0.2   11.7   0.2    2.1  2  zf-C2H2_6        C2H2-type zinc finger
      0.016   15.7   4.4       0.51   10.9   0.9    2.2  2  zf-C2H2          Zinc finger, C2H2 type
      0.018   15.4   0.5       0.31   11.4   0.0    2.0  2  DUF3268          zinc-finger-containing domain
      0.018   15.2   0.1      0.019   15.1   0.1    1.1  1  FYVE             FYVE zinc finger
      0.019   14.7   0.6        2.5    7.9   0.1    2.1  2  zinc_ribbon_10   Predicted integral membrane zinc-ribbon meta
      0.019   15.2   0.3      0.022   15.0   0.3    1.1  1  DUF2072          Zn-ribbon containing protein
      0.026   14.3   2.6       0.19   11.6   0.2    2.1  2  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger
      0.026   14.4   1.0      0.058   13.3   0.9    1.6  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
      0.027   15.3   1.4        4.3    8.4   0.1    2.2  2  zf-C2H2_4        C2H2-type zinc finger
      0.033   14.2   0.5      0.068   13.2   0.5    1.5  1  zf-C2HC5         Putative zinc finger motif, C2HC5-type
      0.037   14.0   0.6      0.064   13.2   0.6    1.4  1  zinc-ribbons_6   zinc-ribbons
      0.045   13.8   0.8        3.8    7.6   0.1    2.1  2  zf-BED           BED zinc finger
      0.055   13.2   0.5        1.1    9.0   0.1    2.1  2  YacG             DNA gyrase inhibitor YacG
      0.055   13.5   2.4          2    8.5   0.4    2.1  2  YhfH             YhfH-like protein
      0.066   13.1   0.6        9.2    6.3   0.1    2.2  2  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
      0.092   12.6   0.2       0.13   12.1   0.2    1.3  1  NinF             NinF protein
        0.1   12.1   2.4       0.55    9.8   2.4    1.9  1  TF_Zn_Ribbon     TFIIB zinc-binding
       0.12   12.3   4.2        2.7    8.0   0.2    2.1  2  PyrI_C           Aspartate carbamoyltransferase regulatory ch
       0.16   12.7   0.7        0.2   12.3   0.7    1.2  1  FYDLN_acid       Protein of unknown function (FYDLN_acid)
       0.18   12.1   1.3        1.1    9.6   0.2    2.0  2  zf-Di19          Drought induced 19 protein (Di19), zinc-bind
       0.76    9.4   6.7        5.3    6.8   0.1    2.6  3  zf-tcix          Putative treble-clef, zinc-finger, Zn-bindin


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 !   34.2   6.2   3.7e-11   1.5e-08       1      32 []      10      43 ..      10      43 .. 0.95

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 3.7e-11
                                      -B-SSS--B--..--SSS----SSS-----B--- CS
                    DNA_RNApol_7kD  1 YiCgeCgaevs..lkkgdpiRCkeCGhRilYKkR 32
                                      Y+C++Cg+e++  l     iRC +CG +i+YK+R
  gi|242399321|ref|YP_002994745.1| 10 YKCAKCGKEFKmdLAVVREIRCPYCGAKIIYKPR 43
                                      9********9977889999*************99 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.2   7.3e-08     3e-05      63      95 ..       2      37 ..       1      45 [. 0.84

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 7.3e-08
                                      EEEEE--EEEETTTS-EEECHH..H.HHS-TTTSSS CS
                              HypA 63 eieevpvkvrCreCgkefelee..k.alrCpkCgsa 95
                                       i+ v+v ++C +Cgkef+++     ++rCp Cg++
  gi|242399321|ref|YP_002994745.1|  2 VITMVEVLYKCAKCGKEFKMDLavVrEIRCPYCGAK 37
                                      58899**************876442688******86 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.5   1.1e-07   4.3e-05       6      35 ..      10      37 ..       9      39 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.1e-07
                       Zn-ribbon_8  6 YrCeeCghefe.vlqsisdapltaCPeCgse 35
                                      Y+C +Cg+ef   l+ +    ++ CP Cg++
  gi|242399321|ref|YP_002994745.1| 10 YKCAKCGKEFKmDLAVVR---EIRCPYCGAK 37
                                      9**********7333233...888*****85 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.5     0.015         6      18      25 ..      11      18 ..      10      19 .. 0.81
   2 !   15.7   0.1   1.8e-05    0.0072       2      11 ..      28      38 ..      27      41 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.015
                       zf-ribbon_3 18 vCpyCGtk 25
                                      +C++CG++
  gi|242399321|ref|YP_002994745.1| 11 KCAKCGKE 18
                                      69999986 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 1.8e-05
                       zf-ribbon_3  2 tvrCPnCGa.p 11
                                      ++rCP+CGa +
  gi|242399321|ref|YP_002994745.1| 28 EIRCPYCGAkI 38
                                      78999999955 PP

>> Cys_rich_CPXG  Cysteine-rich CPXCG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0     0.014       5.5       1      14 [.      10      23 ..      10      28 .. 0.85
   2 !   11.2   0.3   0.00063      0.26       1      10 [.      29      38 ..      29      43 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.014
                     Cys_rich_CPXG  1 iqCPyCgeeievlv 14
                                      ++C+ Cg+e+++++
  gi|242399321|ref|YP_002994745.1| 10 YKCAKCGKEFKMDL 23
                                      78********9986 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00063
                     Cys_rich_CPXG  1 iqCPyCgeei 10
                                      i CPyCg++i
  gi|242399321|ref|YP_002994745.1| 29 IRCPYCGAKI 38
                                      78*****998 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   0.00019     0.076       3      15 ..      10      22 ..       8      25 .. 0.88
   2 ?    4.3   0.2     0.077        31       3      12 ..      29      38 ..      27      40 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00019
                            zf_UBZ  3 ylCerCgkeipes 15
                                      y C++Cgke+ ++
  gi|242399321|ref|YP_002994745.1| 10 YKCAKCGKEFKMD 22
                                      99*******9986 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.077
                            zf_UBZ  3 ylCerCgkei 12
                                      + C+ Cg++i
  gi|242399321|ref|YP_002994745.1| 29 IRCPYCGAKI 38
                                      57*****998 PP

>> DUF4379  Probable Zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1   6.4e-06    0.0026      27      56 .]       7      34 ..       3      34 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 6.4e-06
                           DUF4379 27 kvwWkCakCgheWeasvsnrtkgsskCpkC 56
                                      +v+ kCakCg+e+++ ++     + +Cp+C
  gi|242399321|ref|YP_002994745.1|  7 EVLYKCAKCGKEFKMDLAVVR--EIRCPYC 34
                                      6899***********999887..444**** PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.4   7.5e-06    0.0031      15      39 ..      12      39 ..       7      44 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 7.5e-06
                               DZR 15 CseCgtklkavaa...edrCpsCgekvd 39
                                      C +Cg++ k   a   e+rCp Cg+k+ 
  gi|242399321|ref|YP_002994745.1| 12 CAKCGKEFKMDLAvvrEIRCPYCGAKII 39
                                      9999999876555888999999999865 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 !   17.4   1.0   7.7e-06    0.0031       5      35 ..      10      39 ..       9      42 .. 0.86
   2 ?    6.7   0.8     0.017         7       6      21 ..      30      45 ..      30      51 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 7.7e-06
                    Zn_ribbon_SprT  5 YrCtgCgreythhlsi.rrhnYrCrrCkgtLr 35
                                      Y+C  Cg+e++  l + r    rC++C+ ++ 
  gi|242399321|ref|YP_002994745.1| 10 YKCAKCGKEFKMDLAVvREI--RCPYCGAKII 39
                                      ****************7774..6****97765 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.017
                    Zn_ribbon_SprT  6 rCtgCgreythhlsir 21
                                      rC+ Cg ++ +  + +
  gi|242399321|ref|YP_002994745.1| 30 RCPYCGAKIIYKPRPK 45
                                      6777777777766665 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     0.017       6.7      21      46 ..       5      28 ..       1      29 [. 0.81
   2 !    9.9   0.2    0.0017       0.7       1      10 [.      30      39 ..      30      49 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.017
                         Ogr_Delta 21 vreryyqCsnfeCgatfvaaeeiert 46
                                        e+ y C    Cg  f++ ++++r 
  gi|242399321|ref|YP_002994745.1|  5 MVEVLYKCAK--CGKEFKMDLAVVRE 28
                                      5578899999..99999999999886 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0017
                         Ogr_Delta  1 rCPhCgapaa 10
                                      rCP+Cga++ 
  gi|242399321|ref|YP_002994745.1| 30 RCPYCGAKII 39
                                      7******975 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.3   0.00026       0.1      27      39 .]       8      20 ..       6      20 .. 0.90
   2 ?    5.3   0.1     0.045        18       1      12 [.      29      40 ..      29      41 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00026
                           TFIIS_C 27 vfykCtkCghrWr 39
                                      v ykC+kCg++++
  gi|242399321|ref|YP_002994745.1|  8 VLYKCAKCGKEFK 20
                                      68********997 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.045
                           TFIIS_C  1 akCpkCgsreay 12
                                      ++Cp Cg + +y
  gi|242399321|ref|YP_002994745.1| 29 IRCPYCGAKIIY 40
                                      58*****98665 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.1     0.007       2.8      39      51 ..      11      23 ..       7      28 .. 0.65
   2 !    9.2   0.1    0.0029       1.2      36      48 ..      27      39 ..      24      45 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.007
                              CpXC 39 tCpkCgataklea 51
                                      +C kCg+++k++ 
  gi|242399321|ref|YP_002994745.1| 11 KCAKCGKEFKMDL 23
                                      5666666666654 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0029
                              CpXC 36 featCpkCgatak 48
                                      +e++Cp+Cga++ 
  gi|242399321|ref|YP_002994745.1| 27 REIRCPYCGAKII 39
                                      789******9976 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.6   1.4e-05    0.0059       5      28 ..      10      36 ..       7      39 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.4e-05
                       Prok-RING_1  5 kkCpvCgkelkeedDiVv...CpeCgt 28
                                       kC  Cgke+k +  +V    Cp Cg+
  gi|242399321|ref|YP_002994745.1| 10 YKCAKCGKEFKMDLAVVReirCPYCGA 36
                                      69***********88874445*****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 ?    6.5   1.6     0.017       6.8       1       8 [.      11      18 ..      11      19 .. 0.80
   2 !   12.3   0.2   0.00026       0.1      16      22 ..      31      37 ..      27      38 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.017
                     zinc_ribbon_2  1 fCpnCGae 8 
                                      +C +CG+e
  gi|242399321|ref|YP_002994745.1| 11 KCAKCGKE 18
                                      68888886 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00026
                     zinc_ribbon_2 16 CpyCGtp 22
                                      CpyCG++
  gi|242399321|ref|YP_002994745.1| 31 CPYCGAK 37
                                      7777776 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 !   10.7   0.4    0.0014      0.57      15      25 ..      10      20 ..       4      20 .. 0.90
   2 ?    6.4   0.1     0.032        13      14      21 ..      28      35 ..      25      38 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0014
                         zf-H2C2_2 15 yeCplCdkaFk 25
                                      y+C +C+k Fk
  gi|242399321|ref|YP_002994745.1| 10 YKCAKCGKEFK 20
                                      9*********8 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.032
                         zf-H2C2_2 14 pyeCplCd 21
                                      +  Cp+C+
  gi|242399321|ref|YP_002994745.1| 28 EIRCPYCG 35
                                      679****8 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.2    0.0029       1.2      27      35 ..      11      19 ..       6      22 .. 0.74
   2 ?    6.6   0.1     0.016       6.4       3      11 ..      29      37 ..      28      40 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0029
                     zinc_ribbon_5 27 rCakCaevF 35
                                      +CakC++ F
  gi|242399321|ref|YP_002994745.1| 11 KCAKCGKEF 19
                                      788888755 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.016
                     zinc_ribbon_5  3 irCpdCdtk 11
                                      irCp C+ k
  gi|242399321|ref|YP_002994745.1| 29 IRCPYCGAK 37
                                      9*****986 PP

>> DUF951  Bacterial protein of unknown function (DUF951)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.2     0.075        31      32      43 ..      11      22 ..       6      28 .. 0.84
   2 !   11.3   0.0   0.00062      0.25      31      54 ..      29      53 .]      24      53 .] 0.91

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.075
                            DUF951 32 kClgcgrevmlp 43
                                      kC +cg+e+ ++
  gi|242399321|ref|YP_002994745.1| 11 KCAKCGKEFKMD 22
                                      9******99775 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00062
                            DUF951 31 lkClgcgrevm.lpRskfekkikkv 54
                                      ++C  cg +++  pR k+ +++k +
  gi|242399321|ref|YP_002994745.1| 29 IRCPYCGAKIIyKPRPKVGRRVKAI 53
                                      9******999978**********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 ?    7.0   0.0     0.014       5.5      37      45 ..       9      17 ..       3      18 .. 0.86
   2 !    8.5   0.2    0.0049         2      19      30 ..      29      40 ..      26      49 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.014
                     Zn_Tnp_IS1595 37 lfqCkeCrk 45
                                      l++C++C+k
  gi|242399321|ref|YP_002994745.1|  9 LYKCAKCGK 17
                                      79*****98 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0049
                     Zn_Tnp_IS1595 19 fvCPhCgsrkay 30
                                       +CP+Cg + +y
  gi|242399321|ref|YP_002994745.1| 29 IRCPYCGAKIIY 40
                                      58*****87555 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   2.9   0.00086      0.35       4      35 ..      11      38 ..       9      39 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00086
                     zinc_ribbon_4  4 tCpsCkakyeiddeklpakgvkvrCskCghvF 35
                                       C +C+++++ d +      +++rC+ Cg+++
  gi|242399321|ref|YP_002994745.1| 11 KCAKCGKEFKMDLA----VVREIRCPYCGAKI 38
                                      59999999999995....56789*****9876 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 !    9.1   0.1    0.0029       1.2       3      14 ..      10      21 ..       9      22 .. 0.83
   2 ?    7.2   0.6     0.012       4.9       3       9 ..      29      35 ..      27      35 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0029
                         zf-C2HC_2  3 vpCpkCgRsFnp 14
                                       +C kCg  F+ 
  gi|242399321|ref|YP_002994745.1| 10 YKCAKCGKEFKM 21
                                      68********75 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.012
                         zf-C2HC_2  3 vpCpkCg 9 
                                      + Cp+Cg
  gi|242399321|ref|YP_002994745.1| 29 IRCPYCG 35
                                      79****9 PP

>> Zn_ribbon_recom  Recombinase zinc beta ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1      0.12        48       6      15 ..      10      19 ..       8      22 .. 0.81
   2 ?   11.9   0.2   0.00062      0.25       6      24 ..      29      49 ..      28      52 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.12
                   Zn_ribbon_recom  6 lrCgeCGspm 15
                                       +C++CG+ +
  gi|242399321|ref|YP_002994745.1| 10 YKCAKCGKEF 19
                                      58*****865 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00062
                   Zn_ribbon_recom  6 lrCgeCGspmtrrkrk..gkr 24
                                      +rC +CG++ +++ r   g+r
  gi|242399321|ref|YP_002994745.1| 29 IRCPYCGAKIIYKPRPkvGRR 49
                                      79*******999877644555 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 ?   15.3   0.6   3.4e-05     0.014      25      47 ..      11      38 ..       2      41 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.4e-05
                                      E-HHHHHHHHH.....TT-B-TTT--B- CS
                        zf-C3HC4_3 25 lCeeCaekllk.....rkkkCpiCrrpi 47
                                       C +C ++++      r+ +Cp+C ++i
  gi|242399321|ref|YP_002994745.1| 11 KCAKCGKEFKMdlavvREIRCPYCGAKI 38
                                      6********989*************998 PP

>> zf-AN1  AN1-like Zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.1    0.0046       1.9      12      23 ..       8      19 ..       3      19 .. 0.82
   2 ?    5.8   0.0     0.038        16      13      21 ..      28      36 ..      20      38 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0046
                            zf-AN1 12 lpfkCryCgkvF 23
                                      + +kC +Cgk+F
  gi|242399321|ref|YP_002994745.1|  8 VLYKCAKCGKEF 19
                                      569*******99 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.038
                            zf-AN1 13 pfkCryCgk 21
                                       ++C+yCg 
  gi|242399321|ref|YP_002994745.1| 28 EIRCPYCGA 36
                                      389****96 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 ?   11.7   0.2   0.00048       0.2       2      12 ..      10      20 ..       9      21 .. 0.91
   2 ?    4.1   0.1      0.12        49       3       9 ..      30      36 ..      30      37 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00048
                         zf-C2H2_6  2 heCsvCsksFp 12
                                      ++C  C+k+F+
  gi|242399321|ref|YP_002994745.1| 10 YKCAKCGKEFK 20
                                      9*********8 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.12
                         zf-C2H2_6  3 eCsvCsk 9 
                                      +C++C++
  gi|242399321|ref|YP_002994745.1| 30 RCPYCGA 36
                                      7****97 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.9    0.0012      0.51       1      11 [.      10      20 ..      10      21 .. 0.95
   2 ?    6.4   0.1     0.034        14       2       7 ..      30      35 ..      29      43 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0012
                                      EEETTTTEEES CS
                           zf-C2H2  1 ykCpdCgksFk 11
                                      ykC +Cgk Fk
  gi|242399321|ref|YP_002994745.1| 10 YKCAKCGKEFK 20
                                      9*********8 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.034
                                      EETTTT CS
                           zf-C2H2  2 kCpdCg 7 
                                      +Cp+Cg
  gi|242399321|ref|YP_002994745.1| 30 RCPYCG 35
                                      8****9 PP

>> DUF3268  zinc-finger-containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1      0.34   1.4e+02      28      39 ..       7      18 ..       3      24 .. 0.76
   2 ?   11.4   0.0   0.00076      0.31       3      18 ..      29      44 ..      27      52 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.34
                           DUF3268 28 kllylCpkCday 39
                                      ++ly C kC+  
  gi|242399321|ref|YP_002994745.1|  7 EVLYKCAKCGKE 18
                                      678999999865 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00076
                           DUF3268  3 trCpyCGekvilvsas 18
                                      +rCpyCG+k+i++   
  gi|242399321|ref|YP_002994745.1| 29 IRCPYCGAKIIYKPRP 44
                                      79********998665 PP

>> FYVE  FYVE zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.1   4.7e-05     0.019      10      34 ..      10      37 ..       4      47 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.7e-05
                                      SB-TTT--B--S...SS--EE-TTT--E CS
                              FYVE 10 kkCeiCakkFsl...lrrrhhCrlCGkv 34
                                       kC +C k+F++   ++r   C  CG  
  gi|242399321|ref|YP_002994745.1| 10 YKCAKCGKEFKMdlaVVREIRCPYCGAK 37
                                      58********975557**********75 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 ?    7.9   0.1    0.0062       2.5      41      52 ..       6      17 ..       2      19 .. 0.84
   2 ?    5.7   0.0      0.03        12      46      53 ..      30      37 ..      22      38 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0062
                    zinc_ribbon_10 41 eevkyrCpkCga 52
                                       ev y+C+kCg 
  gi|242399321|ref|YP_002994745.1|  6 VEVLYKCAKCGK 17
                                      6789******95 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.03
                    zinc_ribbon_10 46 rCpkCgal 53
                                      rCp+Cga+
  gi|242399321|ref|YP_002994745.1| 30 RCPYCGAK 37
                                      8*****97 PP

>> DUF2072  Zn-ribbon containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.3   5.4e-05     0.022       3      28 ..      11      37 ..      10      50 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 5.4e-05
                           DUF2072  3 kCtkCekvfedgskeilk.GCpsCGgk 28
                                      kC+kC+k+f+   +++++  Cp CG k
  gi|242399321|ref|YP_002994745.1| 11 KCAKCGKEFKMDLAVVREiRCPYCGAK 37
                                      9*********8888787647*****87 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.2      0.18        74       3      10 ..      11      18 ..      10      21 .. 0.86
   2 ?   11.6   0.2   0.00046      0.19       2      14 ..      29      41 ..      28      47 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.18
                                      E-SSS--E CS
                    zf-C4_Topoisom  3 kCPkCggd 10
                                      kC kCg++
  gi|242399321|ref|YP_002994745.1| 11 KCAKCGKE 18
                                      8*****76 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00046
                                      EE-SSS--EEEEE CS
                    zf-C4_Topoisom  2 ekCPkCggdLvlk 14
                                      + CP Cg+++++k
  gi|242399321|ref|YP_002994745.1| 29 IRCPYCGAKIIYK 41
                                      57*********99 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   0.9   0.00014     0.058      30      55 ..      11      37 ..      10      41 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00014
                    OrfB_Zn_ribbon 30 tCseCgsknke.alsgrtfkCpnCgfe 55
                                      +C++Cg++ k      r+ +Cp Cg++
  gi|242399321|ref|YP_002994745.1| 11 KCAKCGKEFKMdLAVVREIRCPYCGAK 37
                                      7********9988899*********87 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 ?    8.4   0.1     0.011       4.3       1      11 [.      10      20 ..      10      26 .. 0.90
   2 ?    6.4   0.2     0.049        20       2       8 ..      30      36 ..      29      41 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.011
                         zf-C2H2_4  1 fkCpiCgksFs 11
                                      +kC  Cgk F+
  gi|242399321|ref|YP_002994745.1| 10 YKCAKCGKEFK 20
                                      89********7 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.049
                         zf-C2H2_4  2 kCpiCgk 8 
                                      +Cp+Cg+
  gi|242399321|ref|YP_002994745.1| 30 RCPYCGA 36
                                      7****86 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 ?   13.2   0.5   0.00017     0.068      14      46 ..       6      40 ..       3      45 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00017
                          zf-C2HC5 14 leaapnClnCGkiiCakegls..kpCsfCgsplls 46
                                      +e++  C +CGk      +++   +C++Cg++++ 
  gi|242399321|ref|YP_002994745.1|  6 VEVLYKCAKCGKEFKMDLAVVreIRCPYCGAKIIY 40
                                      577889******9887777777789*****99985 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.6   0.00016     0.064      16      39 ..       9      38 ..       2      41 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00016
                                      EEE-TTT--......EEEEEEE-SSS-S-- CS
                    zinc-ribbons_6 16 qyhCeaCqe......dlkkealCpeCeqel 39
                                       y+C +C +       + +e  Cp C+ ++
  gi|242399321|ref|YP_002994745.1|  9 LYKCAKCGKefkmdlAVVREIRCPYCGAKI 38
                                      589999999555555555678999999875 PP

>> zf-BED  BED zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1     0.051        21      18      27 ..      11      20 ..       7      25 .. 0.88
   2 ?    7.6   0.1    0.0093       3.8      17      28 ..      29      40 ..      26      47 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.051
                                      EETTTTEE-- CS
                            zf-BED 18 vCryCgkils 27
                                      +C  Cgk+++
  gi|242399321|ref|YP_002994745.1| 11 KCAKCGKEFK 20
                                      7******987 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0093
                                      -EETTTTEE--- CS
                            zf-BED 17 avCryCgkilsr 28
                                      ++C yCg+++ +
  gi|242399321|ref|YP_002994745.1| 29 IRCPYCGAKIIY 40
                                      89*****99865 PP

>> YacG  DNA gyrase inhibitor YacG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0       0.2        82       2      13 ..      11      22 ..      10      26 .. 0.85
   2 ?    9.0   0.1    0.0028       1.1       1      14 [.      29      42 ..      29      52 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.2
                              YacG  2 kCPtCkkevews 13
                                      kC +C+ke++++
  gi|242399321|ref|YP_002994745.1| 11 KCAKCGKEFKMD 22
                                      8******99875 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0028
                              YacG  1 vkCPtCkkevewse 14
                                      ++CP C++++ +++
  gi|242399321|ref|YP_002994745.1| 29 IRCPYCGAKIIYKP 42
                                      69*******99998 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.4    0.0048         2      15      23 ..      11      19 ..      10      22 .. 0.87
   2 ?    5.1   0.1     0.056        23      16      23 ..      31      38 ..      29      41 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0048
                              YhfH 15 kCteCGkei 23
                                      kC++CGke+
  gi|242399321|ref|YP_002994745.1| 11 KCAKCGKEF 19
                                      7******96 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.056
                              YhfH 16 CteCGkei 23
                                      C+ CG +i
  gi|242399321|ref|YP_002994745.1| 31 CPYCGAKI 38
                                      *****998 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 ?    5.6   0.1     0.037        15      11      19 ..       9      17 ..       8      19 .. 0.81
   2 ?    6.3   0.1     0.023       9.2      26      33 ..      29      36 ..      25      38 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.037
                           DUF35_N 11 gqrCpdCGt 19
                                      + +C++CG+
  gi|242399321|ref|YP_002994745.1|  9 LYKCAKCGK 17
                                      679****97 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.023
                           DUF35_N 26 avCphCgs 33
                                        Cp+Cg+
  gi|242399321|ref|YP_002994745.1| 29 IRCPYCGA 36
                                      78****97 PP

>> NinF  NinF protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   0.00032      0.13      20      46 ..      12      42 ..       4      46 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00032
                              NinF 20 CanCskkLevdevhv....CeeCvaeliyyr 46
                                      Ca C+k+ + d   v    C  C a++iy  
  gi|242399321|ref|YP_002994745.1| 12 CAKCGKEFKMDLAVVreirCPYCGAKIIYKP 42
                                      ******988776555334488999****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 ?    9.8   2.4    0.0014      0.55       1      29 [.      10      38 ..      10      42 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0014
                                      EEETTTTCEE.C...HEETSTTCEEESSSSBEE CS
                      TF_Zn_Ribbon  1 ykCPnCgstn.l...veDpergelvCtdCGlVl 29
                                      ykC +Cg ++ +   v+     e++C+ CG+ +
  gi|242399321|ref|YP_002994745.1| 10 YKCAKCGKEFkMdlaVVR----EIRCPYCGAKI 38
                                      799999988755666555....999****9876 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 ?    6.5   0.4     0.019       7.6      30      45 ..       6      21 ..       1      24 [. 0.82
   2 ?    8.0   0.2    0.0067       2.7      33      43 ..      28      38 ..      24      42 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.019
                                      TTTEEEETTT--EEEH CS
                            PyrI_C 30 ekvklkCkYCekeise 45
                                       +v +kC  C+ke++ 
  gi|242399321|ref|YP_002994745.1|  6 VEVLYKCAKCGKEFKM 21
                                      5789*********986 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0067
                                      EEEETTT--EE CS
                            PyrI_C 33 klkCkYCekei 43
                                      +++C YC+ +i
  gi|242399321|ref|YP_002994745.1| 28 EIRCPYCGAKI 38
                                      68*****9987 PP

>> FYDLN_acid  Protein of unknown function (FYDLN_acid)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.7    0.0005       0.2      12      40 ..      12      42 ..      10      52 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0005
                        FYDLN_acid 12 CpscgakF.YDLnk.dPivcpkcgeefepee 40
                                      C +cg+ F  DL   + i cp+cg+++  ++
  gi|242399321|ref|YP_002994745.1| 12 CAKCGKEFkMDLAVvREIRCPYCGAKIIYKP 42
                                      ********88**98899*******9875554 PP

>> zf-Di19  Drought induced 19 protein (Di19), zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1      0.71   2.9e+02       4      44 ..      11      22 ..       7      25 .. 0.56
   2 ?    9.6   0.2    0.0028       1.1       2      11 ..      28      37 ..      27      42 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.71
                           zf-Di19  4 tCPyCgkeltvkeLveHvedeHrveskevvCPvCaekvtkd 44
                                      +                             C  C ++ ++d
  gi|242399321|ref|YP_002994745.1| 11 K-----------------------------CAKCGKEFKMD 22
                                      4.............................55555555555 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0028
                           zf-Di19  2 sftCPyCgke 11
                                      ++ CPyCg +
  gi|242399321|ref|YP_002994745.1| 28 EIRCPYCGAK 37
                                      679****986 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 ?    6.1   0.4     0.021       8.5      12      17 ..      11      16 ..       8      18 .. 0.85
   2 ?    6.8   0.1     0.013       5.3       8      18 ..      27      36 ..      21      38 .. 0.78
   3 ?   -1.3   0.2       4.2   1.7e+03       2      12 ..      42      52 ..      41      52 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.021
                           zf-tcix 12 kCpkCG 17
                                      kC+kCG
  gi|242399321|ref|YP_002994745.1| 11 KCAKCG 16
                                      9***** PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.013
                           zf-tcix  8 RGvrkCpkCGt 18
                                      R +r Cp CG+
  gi|242399321|ref|YP_002994745.1| 27 REIR-CPYCGA 36
                                      5555.*****8 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 4.2
                           zf-tcix  2 lgrktlRGvrk 12
                                      +++k+ R+v++
  gi|242399321|ref|YP_002994745.1| 42 PRPKVGRRVKA 52
                                      56788899985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                       129  (0.00719505); 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: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 328.77
//
Query:       gi|242399322|ref|YP_002994746.1|  [L=85]
Description: 50S ribosomal protein L37Ae [Thermococcus sibiricus MM 739]
Scores for complete 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  120.3   3.8    3.1e-35  120.1   3.8    1.0  1  Ribosomal_L37ae  Ribosomal L37ae protein family
    2.1e-06   27.6   3.4    3.1e-06   27.0   3.4    1.3  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
     0.0001   22.1   0.8    0.00014   21.7   0.8    1.2  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
    0.00051   20.1   2.1      0.053   13.7   0.5    2.2  2  Zn-ribbon_8      Zinc ribbon domain
    0.00099   18.9   0.2     0.0012   18.6   0.2    1.1  1  Rep_fac-A_C      Replication factor-A C terminal domain
     0.0022   17.6   0.6     0.0031   17.1   0.6    1.3  1  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI
     0.0027   18.1   0.2        1.4    9.5   0.1    2.2  2  zf-H2C2_2        Zinc-finger double domain
     0.0075   16.1   1.5       0.01   15.7   1.5    1.1  1  C1_1             Phorbol esters/diacylglycerol binding domain
     0.0088   16.4   0.4      0.013   15.9   0.4    1.4  1  Lar_restr_allev  Restriction alleviation protein Lar
  ------ inclusion threshold ------
      0.014   15.4   2.8      0.028   14.4   2.8    1.5  1  DNA_ligase_ZBD   NAD-dependent DNA ligase C4 zinc finger doma
      0.021   14.3   0.4      0.039   13.5   0.4    1.4  1  TF_Zn_Ribbon     TFIIB zinc-binding
      0.026   14.5   0.4        3.9    7.5   0.0    2.2  2  ADK_lid          Adenylate kinase, active site lid
      0.031   14.3   2.2      0.061   13.4   2.2    1.5  1  Elf1             Transcription elongation factor Elf1 like
      0.035   14.7   0.1      0.048   14.2   0.1    1.2  1  RPA_interact_C   Replication protein A interacting C-terminal
      0.048   14.1   1.1        6.4    7.4   0.1    2.3  2  zf-C2H2          Zinc finger, C2H2 type
      0.062   13.1   0.2       0.09   12.6   0.2    1.3  1  Rad50_zn_hook    Rad50 zinc hook motif
      0.062   13.0   2.2       0.23   11.2   2.2    1.8  1  A2L_zn_ribbon    A2L zinc ribbon domain
      0.074   12.9   0.6         14    5.6   0.2    2.2  2  zf-C2H2_3        zinc-finger of acetyl-transferase ESCO
      0.093   13.6   1.2         15    6.7   0.1    2.3  2  zf-C2H2_4        C2H2-type zinc finger
       0.11   12.9   1.9        3.4    8.1   0.1    2.2  2  DUF4379          Probable Zinc-ribbon domain
       0.15   12.1   2.1        2.7    8.1   0.1    2.2  2  zf-BED           BED zinc finger
       0.16   11.9   4.3       0.41   10.6   4.3    1.6  1  Zn_ribbon_SprT   SprT-like zinc ribbon domain
       0.18   12.0   3.0       0.21   11.8   0.6    1.9  2  NOB1_Zn_bind     Nin one binding (NOB1) Zn-ribbon like
       0.18   11.7   4.9       0.37   10.7   4.9    1.6  1  HalOD2           Halobacterial output domain 2
        0.2   11.8   2.9       0.25   11.5   2.9    1.2  1  zf-RING_13       RING/Ubox like zinc-binding domain
        0.2   11.7   2.6          7    6.8   0.1    2.2  2  zf-C2H2_6        C2H2-type zinc finger
        0.2   11.7   3.0        1.8    8.6   3.3    1.8  2  DZR              Double zinc ribbon
        0.2   11.6   5.7        1.7    8.6   1.0    2.3  2  zf-C2HC_2        zinc-finger of a C2HC-type
       0.26   11.3   4.1         10    6.2   4.1    2.2  1  Ogr_Delta        Ogr/Delta-like zinc finger
       0.27   10.9   0.9        4.5    6.9   0.0    2.2  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
       0.27   11.2   4.7        2.3    8.2   0.2    2.6  3  Nudix_N_2        Nudix N-terminal
       0.33   10.7   4.4       0.64    9.8   0.6    2.1  2  Rubredoxin_2     Rubredoxin metal binding domain
       0.67    9.8   0.2       0.67    9.8   0.2    2.0  2  zf-C2H2_11       zinc-finger C2H2-type
        0.8    9.8   3.5         12    5.9   0.2    2.2  2  CpXC             CpXC protein
       0.81   10.0   7.4        2.9    8.2   7.4    1.9  1  Prim_Zn_Ribbon   Zinc-binding domain of primase-helicase
       0.92    9.2   6.5       0.52   10.0   0.5    2.5  2  zf-tcix          Putative treble-clef, zinc-finger, Zn-bindin
        1.7    8.5   5.7         12    5.8   0.5    2.2  2  zinc_ribbon_2    zinc-ribbon domain


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 !  120.1   3.8   6.4e-38   3.1e-35       1      81 [.       3      83 ..       3      84 .. 0.98

  Alignments for each domain:
  == domain 1  score: 120.1 bits;  conditional E-value: 6.4e-38
                                      XXXXXX-GGGGTTSS-HHHHHHHHHHHHHHHS-BEESSSSSSEEEEEETTEEEETTTTEEEE-BSSSSS-HHHHHHHH- CS
                   Ribosomal_L37ae  1 rtkkvgiaGkygtrYGaslrkrvkkieisqhakytCpfcgktkvkRkavgiwkCkkcgktvaGgAytpettsaktvksa 79
                                      rtkkvg+aG++g+rYG ++r+rv+ +e+++++k+tCp cg+++v+R ++giw+C+kcg+t+aGgAy p t++++++k+ 
  gi|242399322|ref|YP_002994746.1|  3 RTKKVGSAGRFGPRYGLKIRRRVAAVEEKMRQKHTCPVCGRKAVRRISTGIWQCQKCGATFAGGAYLPATPAGRIAKRG 81
                                      79**************************************************************************998 PP

                                      XX CS
                   Ribosomal_L37ae 80 ir 81
                                      i+
  gi|242399322|ref|YP_002994746.1| 82 IS 83
                                      75 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 !   27.0   3.4   6.5e-09   3.1e-06      17      45 ..      34      61 ..      29      62 .. 0.92

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 6.5e-09
                     Zn_Tnp_IS1595 17 ngfvCPhCgsrkayriktrglfqCkeCrk 45
                                      ++++CP Cg + ++ri+t g +qC++C++
  gi|242399322|ref|YP_002994746.1| 34 QKHTCPVCGRKAVRRIST-GIWQCQKCGA 61
                                      6799*****99*******.********97 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.8   2.9e-07   0.00014      29      56 ..      36      63 ..      18      64 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 2.9e-07
                    OrfB_Zn_ribbon 29 ktCseCgsknkealsgrtfkCpnCgfea 56
                                       tC++Cg+k  ++ s+  ++C++Cg+++
  gi|242399322|ref|YP_002994746.1| 36 HTCPVCGRKAVRRISTGIWQCQKCGATF 63
                                      59***********************975 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.5   0.00011     0.053      22      38 ..      33      48 ..      22      49 .. 0.68
   2 ?    6.0   0.0     0.027        13       7      15 ..      55      63 ..      54      71 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00011
                       Zn-ribbon_8 22 sdaplta.CPeCgs.evrr 38
                                          +++ CP Cg  +vrr
  gi|242399322|ref|YP_002994746.1| 33 R---QKHtCPVCGRkAVRR 48
                                      3...4444******66666 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.027
                       Zn-ribbon_8  7 rCeeCghef 15
                                      +C++Cg +f
  gi|242399322|ref|YP_002994746.1| 55 QCQKCGATF 63
                                      699999998 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 !   18.6   0.2   2.4e-06    0.0012       8      48 ..      25      64 ..      19      69 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.4e-06
                                      EEEEETTTTEEEB--STT---B-EEE.TTTEEEETTTTEEES CS
                       Rep_fac-A_C  8 vsfikkdnlvYkACpsedCnkKvvee.edgewrCekCdkeve 48
                                      v  +++++   + Cp   C +K v++ + g w+C+kC  +++
  gi|242399322|ref|YP_002994746.1| 25 VAAVEEKMRQKHTCP--VCGRKAVRRiSTGIWQCQKCGATFA 64
                                      6667777777899**..*********899********98875 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 !   17.1   0.6   6.4e-06    0.0031       6      28 ..      37      60 ..      32      62 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 6.4e-06
                           zf-RRN7  6 pCgvCgcrsftl.ddGfyyCrrCh 28
                                       C+vCg + ++    G + C+ C+
  gi|242399322|ref|YP_002994746.1| 37 TCPVCGRKAVRRiSTGIWQCQKCG 60
                                      6**********************9 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   0.1    0.0029       1.4      14      24 ..      35      45 ..      29      47 .. 0.77
   2 ?    6.8   0.0      0.02       9.9      14      25 ..      53      64 ..      49      64 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0029
                         zf-H2C2_2 14 pyeCplCdkaF 24
                                      +++Cp+C+ + 
  gi|242399322|ref|YP_002994746.1| 35 KHTCPVCGRKA 45
                                      59*****9886 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.02
                         zf-H2C2_2 14 pyeCplCdkaFk 25
                                      +++C +C+ +F+
  gi|242399322|ref|YP_002994746.1| 53 IWQCQKCGATFA 64
                                      589******995 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   1.5   2.1e-05      0.01       5      37 ..      29      62 ..      24      64 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.1e-05
                                      EE--SS--B-TTT-SB--S.SSS-EEEETTT--E CS
                              C1_1  5 hrnfkqptfCkhCgeflwg.kekqglkCswCkll 37
                                      + +++q+++C  Cg    +  ++ +++C+ C+ +
  gi|242399322|ref|YP_002994746.1| 29 EEKMRQKHTCPVCGRKAVRrISTGIWQCQKCGAT 62
                                      56789*********9997879**********976 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.4   2.7e-05     0.013       5      36 ..      37      61 ..      33      80 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.7e-05
                   Lar_restr_allev  5 pCPfCggravlersqrvvaeigqcvyCadCga 36
                                       CP Cg +av   s++ +       +C++Cga
  gi|242399322|ref|YP_002994746.1| 37 TCPVCGRKAVRRISTGIW-------QCQKCGA 61
                                      7***********999998.......5*****9 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   2.8   5.8e-05     0.028       1      20 [.      37      56 ..      37      61 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.8e-05
                    DNA_ligase_ZBD  1 hCPvCGsavvReegeaiyRC 20
                                      +CPvCG ++vR     i+ C
  gi|242399322|ref|YP_002994746.1| 37 TCPVCGRKAVRRISTGIWQC 56
                                      7*********9877666666 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.4     8e-05     0.039       2      27 ..      37      61 ..      36      63 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8e-05
                                      EETTTTCEECHEETSTTCEEESSSSB CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGl 27
                                      +CP+Cg +  v+  ++g   C +CG+
  gi|242399322|ref|YP_002994746.1| 37 TCPVCGRKA-VRRISTGIWQCQKCGA 61
                                      8*****985.**************96 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.1     0.038        18      23      34 ..      37      48 ..      26      49 .. 0.71
   2 ?    7.5   0.0     0.008       3.9       2      11 ..      54      63 ..      54      73 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.038
                                      B-TTT--.-B-- CS
                           ADK_lid 23 lCDkCGepLvqR 34
                                       C +CG + v+R
  gi|242399322|ref|YP_002994746.1| 37 TCPVCGRKAVRR 48
                                      677777666666 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.008
                                      EE-TTT--EE CS
                           ADK_lid  2 rvCpkCGrsY 11
                                      + C kCG+++
  gi|242399322|ref|YP_002994746.1| 54 WQCQKCGATF 63
                                      78******98 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   2.2   0.00013     0.061      11      55 ..      25      63 ..      16      71 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00013
                              Elf1 11 kkkkkkklptkFdCpfCnheksvevkldkkekiaevsCkvCgesf 55
                                           +k+ +k +Cp+C+ + +      ++ ++++ +C++Cg++f
  gi|242399322|ref|YP_002994746.1| 25 VAAVEEKMRQKHTCPVCGRK-A-----VRRISTGIWQCQKCGATF 63
                                      4455677999**********.3.....3566899*******9987 PP

>> RPA_interact_C  Replication protein A interacting C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   9.9e-05     0.048       1      26 [.      37      64 ..      37      74 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 9.9e-05
                    RPA_interact_C  1 lCPvCkkrklkets.evifCe.Cglrle 26
                                      +CPvC ++ +++ s  + +C+ Cg +++
  gi|242399322|ref|YP_002994746.1| 37 TCPVCGRKAVRRIStGIWQCQkCGATFA 64
                                      5**********98857789*99**9886 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.1     0.013       6.4       1       9 [.      36      44 ..      36      50 .. 0.80
   2 ?    5.5   0.1     0.053        26       2      10 ..      55      63 ..      54      65 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.013
                                      EEETTTTEE CS
                           zf-C2H2  1 ykCpdCgks 9 
                                      ++Cp+Cg++
  gi|242399322|ref|YP_002994746.1| 36 HTCPVCGRK 44
                                      79*****86 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.053
                                      EETTTTEEE CS
                           zf-C2H2  2 kCpdCgksF 10
                                      +C +Cg +F
  gi|242399322|ref|YP_002994746.1| 55 QCQKCGATF 63
                                      8*****999 PP

>> Rad50_zn_hook  Rad50 zinc hook motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   0.00018      0.09      17      28 ..      34      44 ..      20      44 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00018
                                      T-SEE-TTT--E CS
                     Rad50_zn_hook 17 eakgcCPlCgRe 28
                                      + k+ CP+CgR+
  gi|242399322|ref|YP_002994746.1| 34 Q-KHTCPVCGRK 44
                                      4.44*******6 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   2.2   0.00047      0.23       5      31 ..      37      63 ..      33      64 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00047
                     A2L_zn_ribbon  5 vCsvCggngilnseqgylvCieCgasf 31
                                      +C vCg+  +     g+ +C++Cga+f
  gi|242399322|ref|YP_002994746.1| 37 TCPVCGRKAVRRISTGIWQCQKCGATF 63
                                      677777777776677999*******99 PP

>> zf-C2H2_3  zinc-finger of acetyl-transferase ESCO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.2     0.028        14      10      20 ..      32      42 ..      27      43 .. 0.76
   2 ?    5.6   0.0     0.028        14      12      24 ..      52      64 ..      48      67 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.028
                         zf-C2H2_3 10 sfgasqCkeCg 20
                                        ++++C++Cg
  gi|242399322|ref|YP_002994746.1| 32 MRQKHTCPVCG 42
                                      445688****8 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.028
                         zf-C2H2_3 12 gasqCkeCgMvYn 24
                                      g  qC +Cg +++
  gi|242399322|ref|YP_002994746.1| 52 GIWQCQKCGATFA 64
                                      6689*****8875 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.2     0.061        30       1       9 [.      36      44 ..      36      48 .. 0.82
   2 ?    6.7   0.1     0.032        15       2      11 ..      55      64 ..      54      69 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.061
                         zf-C2H2_4  1 fkCpiCgks 9 
                                      ++Cp+Cg+ 
  gi|242399322|ref|YP_002994746.1| 36 HTCPVCGRK 44
                                      68****985 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.032
                         zf-C2H2_4  2 kCpiCgksFs 11
                                      +C  Cg++F 
  gi|242399322|ref|YP_002994746.1| 55 QCQKCGATFA 64
                                      8********6 PP

>> DUF4379  Probable Zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.2      0.11        52      41      56 .]      26      41 ..      19      41 .. 0.78
   2 ?    8.1   0.1     0.007       3.4      29      39 ..      53      63 ..      48      68 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.11
                           DUF4379 41 asvsnrtkgsskCpkC 56
                                      a+v+++++++ +Cp C
  gi|242399322|ref|YP_002994746.1| 26 AAVEEKMRQKHTCPVC 41
                                      567777866666**** PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.007
                           DUF4379 29 wWkCakCgheW 39
                                       W+C+kCg ++
  gi|242399322|ref|YP_002994746.1| 53 IWQCQKCGATF 63
                                      5*******876 PP

>> zf-BED  BED zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.2     0.044        21      13      29 ..      32      48 ..      26      54 .. 0.80
   2 ?    8.1   0.1    0.0055       2.7      15      29 ..      52      66 ..      46      83 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.044
                                      GSS--EETTTTEE---- CS
                            zf-BED 13 keqkavCryCgkilsrg 29
                                       +qk +C  Cg++  r+
  gi|242399322|ref|YP_002994746.1| 32 MRQKHTCPVCGRKAVRR 48
                                      58999*******99998 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0055
                                      S--EETTTTEE---- CS
                            zf-BED 15 qkavCryCgkilsrg 29
                                      + ++C  Cg+++++g
  gi|242399322|ref|YP_002994746.1| 52 GIWQCQKCGATFAGG 66
                                      789********9987 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   4.3   0.00084      0.41       4      34 ..      35      63 ..      35      65 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00084
                    Zn_ribbon_SprT  4 vYrCtgCgreythhlsirrhnYrCrrCkgtL 34
                                      +++C+ Cgr  ++ ++i +  + C++C+ t+
  gi|242399322|ref|YP_002994746.1| 35 KHTCPVCGR--KAVRRISTGIWQCQKCGATF 63
                                      579*****6..555555555599****9876 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 ?   11.8   0.6   0.00042      0.21      20      40 ..      32      52 ..      24      58 .. 0.83
   2 ?    0.1   0.2       1.9     9e+02      26      31 ..      56      61 ..      54      64 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00042
                      NOB1_Zn_bind 20 dmtkkFCpkCGnktLkrvavs 40
                                        +k+ Cp CG k ++r+++ 
  gi|242399322|ref|YP_002994746.1| 32 MRQKHTCPVCGRKAVRRISTG 52
                                      468999************975 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.9
                      NOB1_Zn_bind 26 CpkCGn 31
                                      C+kCG 
  gi|242399322|ref|YP_002994746.1| 56 CQKCGA 61
                                      999996 PP

>> HalOD2  Halobacterial output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   4.9   0.00075      0.37      23      43 ..      45      65 ..      35      76 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00075
                            HalOD2 23 GyrqLGayvWkCtrCGevqaa 43
                                       +r++ + +W+C +CG++ a+
  gi|242399322|ref|YP_002994746.1| 45 AVRRISTGIWQCQKCGATFAG 65
                                      68888999*********9886 PP

>> zf-RING_13  RING/Ubox like zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   2.9   0.00052      0.25       3      33 ..      37      67 ..      35      75 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00052
                                      --TTTSS--SEEETTS-EE-TTTHHHTTTSS CS
                        zf-RING_13  3 vctvcgaapvaksacggwfcgncvpyhaghc 33
                                       c vcg   v + + g w c +c    ag  
  gi|242399322|ref|YP_002994746.1| 37 TCPVCGRKAVRRISTGIWQCQKCGATFAGGA 67
                                      69*********************99999865 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 ?    4.9   0.4     0.055        26       2       9 ..      36      43 ..      35      44 .. 0.89
   2 ?    6.8   0.1     0.014         7       4      11 ..      56      63 ..      54      64 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.055
                         zf-C2H2_6  2 heCsvCsk 9 
                                      h C+vC++
  gi|242399322|ref|YP_002994746.1| 36 HTCPVCGR 43
                                      99****96 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.014
                         zf-C2H2_6  4 CsvCsksF 11
                                      C+ C+++F
  gi|242399322|ref|YP_002994746.1| 56 CQKCGATF 63
                                      ******** PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   3.3    0.0037       1.8      27      49 .]      34      60 ..      15      60 .. 0.69
   2 ?    8.3   2.2    0.0046       2.3       1      22 [.      38      63 ..      38      71 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0037
                               DZR 27 aedrCpsCgekvdpearf....CpeCG 49
                                      ++++Cp Cg+k+  + ++    C++CG
  gi|242399322|ref|YP_002994746.1| 34 QKHTCPVCGRKAVRRISTgiwqCQKCG 60
                                      278888888886665555567788887 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0046
                               DZR  1 CpqCgee....lppdarfCseCgtkl 22
                                      Cp Cg++    ++ +   C++Cg++ 
  gi|242399322|ref|YP_002994746.1| 38 CPVCGRKavrrISTGIWQCQKCGATF 63
                                      89999887777777777999999875 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 ?    8.6   1.0    0.0036       1.7       4      11 ..      37      44 ..      34      44 .. 0.87
   2 ?    5.3   0.3     0.039        19       4      12 ..      55      63 ..      55      64 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0036
                         zf-C2HC_2  4 pCpkCgRs 11
                                       Cp CgR+
  gi|242399322|ref|YP_002994746.1| 37 TCPVCGRK 44
                                      7******8 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.039
                         zf-C2HC_2  4 pCpkCgRsF 12
                                      +C+kCg +F
  gi|242399322|ref|YP_002994746.1| 55 QCQKCGATF 63
                                      8*****777 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 ?    6.2   4.1     0.021        10       1      16 [.      37      52 ..      37      66 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.021
                         Ogr_Delta  1 rCPhCgapaaartsrn 16
                                      +CP Cg +a+ r s+ 
  gi|242399322|ref|YP_002994746.1| 37 TCPVCGRKAVRRISTG 52
                                      6********9998876 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.3      0.21     1e+02       2      10 ..      35      43 ..      34      45 .. 0.83
   2 ?    6.9   0.0    0.0093       4.5       3      12 ..      54      63 ..      52      67 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.21
                            zf_UBZ  2 tylCerCgk 10
                                       ++C+ Cg+
  gi|242399322|ref|YP_002994746.1| 35 KHTCPVCGR 43
                                      579****97 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0093
                            zf_UBZ  3 ylCerCgkei 12
                                      ++C++Cg+++
  gi|242399322|ref|YP_002994746.1| 54 WQCQKCGATF 63
                                      79*****988 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   1.0    0.0093       4.5      11      29 ..      22      42 ..      15      43 .. 0.70
   2 ?    8.2   0.2    0.0048       2.3       3      17 ..      38      52 ..      35      52 .. 0.89
   3 ?    3.6   0.2      0.13        64       3       9 ..      56      62 ..      55      71 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0093
                                      EEE--TT-SS-E..EEETTTT CS
                         Nudix_N_2 11 elripdgDnreR..lvCpaCg 29
                                      ++r+ + ++++R  ++Cp Cg
  gi|242399322|ref|YP_002994746.1| 22 RRRVAAVEEKMRqkHTCPVCG 42
                                      566666666555449*****9 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0048
                                      -TTT--B-EEE--TT CS
                         Nudix_N_2  3 CsqCGtpvelripdg 17
                                      C+ CG +  +ri  g
  gi|242399322|ref|YP_002994746.1| 38 CPVCGRKAVRRISTG 52
                                      9******99999765 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.13
                                      -TTT--B CS
                         Nudix_N_2  3 CsqCGtp 9 
                                      C++CG++
  gi|242399322|ref|YP_002994746.1| 56 CQKCGAT 62
                                      7777764 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.2      0.26   1.2e+02      17      21 ..      38      42 ..      36      47 .. 0.79
   2 ?    9.8   0.6    0.0013      0.64       1      10 [.      54      63 ..      54      65 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.26
                      Rubredoxin_2 17 CpsCg 21
                                      Cp Cg
  gi|242399322|ref|YP_002994746.1| 38 CPVCG 42
                                      88887 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0013
                      Rubredoxin_2  1 YvCsqCGfes 10
                                      ++C++CG+++
  gi|242399322|ref|YP_002994746.1| 54 WQCQKCGATF 63
                                      7999999987 PP

>> zf-C2H2_11  zinc-finger C2H2-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.4       1.4   6.7e+02       6      13 ..      37      44 ..      35      44 .. 0.81
   2 ?    9.8   0.2    0.0014      0.67       6      15 ..      55      64 ..      51      67 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.4
                        zf-C2H2_11  6 qCleCGlc 13
                                       C  CG++
  gi|242399322|ref|YP_002994746.1| 37 TCPVCGRK 44
                                      5999**96 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0014
                        zf-C2H2_11  6 qCleCGlcft 15
                                      qC++CG  f+
  gi|242399322|ref|YP_002994746.1| 55 QCQKCGATFA 64
                                      *******997 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.2     0.026        12      34      47 ..      32      45 ..      20      51 .. 0.76
   2 ?    5.8   0.3     0.027        13      37      47 ..      53      63 ..      43      69 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.026
                              CpXC 34 slfeatCpkCgata 47
                                        +++tCp Cg++a
  gi|242399322|ref|YP_002994746.1| 32 MRQKHTCPVCGRKA 45
                                      557899****9986 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.027
                              CpXC 37 eatCpkCgata 47
                                       ++C+kCgat+
  gi|242399322|ref|YP_002994746.1| 53 IWQCQKCGATF 63
                                      68999999987 PP

>> Prim_Zn_Ribbon  Zinc-binding domain of primase-helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   7.4    0.0061       2.9       4      33 ..      36      60 ..      33      67 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0061
                                      E--TTTT-TTTEEETT....S-EEETTTTB CS
                    Prim_Zn_Ribbon  4 spCPvCGGrDrFrfddkdgrGtwfCrqCgg 33
                                        CPvCG++   r++     G w C++C g
  gi|242399322|ref|YP_002994746.1| 36 HTCPVCGRKAVRRIST----GIWQCQKC-G 60
                                      57*******9999998....********.5 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 ?    1.9   0.9      0.35   1.7e+02      12      17 ..      37      42 ..      32      45 .. 0.85
   2 ?   10.0   0.5    0.0011      0.52       4      18 ..      47      61 ..      44      65 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.35
                           zf-tcix 12 kCpkCG 17
                                       Cp CG
  gi|242399322|ref|YP_002994746.1| 37 TCPVCG 42
                                      6****9 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0011
                           zf-tcix  4 rktlRGvrkCpkCGt 18
                                      r++  G+ +C kCG+
  gi|242399322|ref|YP_002994746.1| 47 RRISTGIWQCQKCGA 61
                                      89999*********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 ?    5.8   0.5     0.024        12       2       7 ..      38      43 ..      35      45 .. 0.62
   2 ?    5.1   0.6     0.039        19       2       7 ..      56      61 ..      55      62 .. 0.66

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.024
                     zinc_ribbon_2  2 CpnCGa 7 
                                      Cp CG+
  gi|242399322|ref|YP_002994746.1| 38 CPVCGR 43
                                      555555 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.039
                     zinc_ribbon_2  2 CpnCGa 7 
                                      C +CGa
  gi|242399322|ref|YP_002994746.1| 56 CQKCGA 61
                                      777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       686  (0.038262); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); 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: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 597.37
//
Query:       gi|242399323|ref|YP_002994747.1|  [L=106]
Description: hypothetical protein TSIB_1346, partial [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.3e-14   51.7   0.1    8.2e-14   51.5   0.1    1.0  1  DUF835    Protein of unknown function (DUF835)


Domain annotation for each model (and alignments):
>> DUF835  Protein of unknown function (DUF835)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.5   0.1   4.5e-18   8.2e-14      40     136 .]       3     102 ..       1     102 [. 0.92

  Alignments for each domain:
  == domain 1  score: 51.5 bits;  conditional E-value: 4.5e-18
                            DUF835  40 envkviwltkveeen...tvsPtnlekltetivkflkeaekgvvliDgleyLvlengFesvlkflltlkDavllkng 113
                                        n +v+w+t++  +n   t +P+ + +  et+   l +++ +vvl++++e L++e + ++++k l t+kD+++ +++
  gi|242399323|ref|YP_002994747.1|   3 RNIPVVWITSKAAKNgiiTLKPRFIVESPETLCGDLFQEGYKVVLLESIESLLVEFDEREIAKALMTMKDIAIQNDC 79 
                                       6899********988788889999998889988777777778*********************************** PP

                            DUF835 114 tlilvidkealeekelalLkref 136
                                       +++l+ +kea+ ++ +a+L++e+
  gi|242399323|ref|YP_002994747.1|  80 YILLQGEKEAFTPRMWAMLTSEM 102
                                       *********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 796.82
//
Query:       gi|242399324|ref|YP_002994748.1|  [L=196]
Description: Rubrerythrin subfamily, [Thermococcus sibiricus MM 739]
Scores for complete 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   80.2   8.2    2.5e-22   79.8   8.2    1.2  1  Rubrerythrin  Rubrerythrin
     0.0045   17.3   0.7       0.15   12.4   0.1    2.2  2  DUF2383       Domain of unknown function (DUF2383)
  ------ inclusion threshold ------
      0.056   13.7   0.3       0.11   12.8   0.3    1.4  1  MutS_II       MutS domain II
      0.058   13.4   0.1       0.16   12.0   0.1    1.7  2  DUF892        Domain of unknown function (DUF892)
      0.095   12.9   0.9       0.33   11.2   1.0    1.7  1  Ferritin_2    Ferritin-like domain
        0.1   12.5   1.2       0.27   11.2   0.9    1.9  1  Ferritin      Ferritin-like 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 !   79.8   8.2   8.3e-26   2.5e-22       1     137 []      25     159 ..      25     159 .. 0.96

  Alignments for each domain:
  == domain 1  score: 79.8 bits;  conditional E-value: 8.3e-26
                                       HHHHHHHHHHHHHHHHHHHHHHCHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH..B.SSBBS------- CS
                      Rubrerythrin   1 eiLekAiagEssarrlYkelaekakegypqiaelFeelAeeEreHakilnklleklepele.levkekvreyaeakp 76 
                                       e+L++Ai +E +++++Y+ela+++k    +i+ lF ++++e +eH+++l++l++kl+ ++e ++v++  +e++  + 
  gi|242399324|ref|YP_002994748.1|  25 EVLSYAIFNEDEETKYYEELARRVK--RDSIKVLFIQMSDESKEHRDRLYRLFKKLYTDEEpVKVDAPPVEVFPYYS 99 
                                       89***********************..************************************************** PP

                                       TTGGHHHHHHHHHHHHHHHHHCHH..HHHHHHHHHTTSHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Rubrerythrin  77 kflttaknLeeaiegayaeeeemy..rfyeelaekegneeakklfkklaeaEkkHeerlrkll 137
                                       +f++ +++Le   +++y++ +e++  ++ye+l + ++ne+ + +f +la +E++H+ r rk++
  gi|242399324|ref|YP_002994748.1| 100 EFEKANDYLE---ALEYCMKSELFakKVYEMLISYAENEDSRGIFSQLALMERDHYLRIRKAY 159
                                       **********...77777777777669*******************************99986 PP

>> DUF2383  Domain of unknown function (DUF2383)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.1   5.1e-05      0.15      17      53 ..      38      74 ..      26      84 .. 0.86
   2 ?    3.3   0.0     0.033        98       3      66 ..     108     171 ..     106     177 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.1e-05
                                      HHHHHHHHHT--SHHHHHHHHHHHHHHHHHHHHHHHH CS
                           DUF2383 17 eegykeaaekvkdpqlktlleriaeereeaaeeLqse 53
                                       + y+e a++vk++++k l+ ++++e +e+ ++L   
  gi|242399324|ref|YP_002994748.1| 38 TKYYEELARRVKRDSIKVLFIQMSDESKEHRDRLYRL 74
                                      578***********************99999888665 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.033
                                       HHHHHHHHHHHHHHHHHHHHHHHT--SHHHHHHHHHHHHHHHHHHHHHHHHHHHCT-------- CS
                           DUF2383   3 ieaLndLietlkdgeegykeaaekvkdpqlktlleriaeereeaaeeLqseiralggepedggs 66 
                                       +eaL+  ++ +  +++ y+  +  +++++ + ++ + a   +++  ++++  +  gg  +++ +
  gi|242399324|ref|YP_002994748.1| 108 LEALEYCMKSELFAKKVYEMLISYAENEDSRGIFSQLALMERDHYLRIRKAYEFIGGFMDKKKT 171
                                       56777777888889999*******************9999999988888877777776666665 PP

>> MutS_II  MutS domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.3   3.7e-05      0.11      33      99 ..       8      78 ..       3      92 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.7e-05
                                      EE.-HHHHHHHHHH-ESEEEEESS-SCCCHHHHHHCHCTTT-EEEEE...SCCCCSHCCHHHHCHHHB--S CS
                           MutS_II 33 ed.feeleaeLsrlsPkElllpedlsestaeeessklrelrsrvgvr...etvefesekaserleedfsve 99
                                       + f+ +  +L+ l PkE+l    ++e+++++++++l ++++r +      ++++es++ + rl + f++ 
  gi|242399324|ref|YP_002994748.1|  8 DEyFSSVIERLKCLRPKEVLSYAIFNEDEETKYYEELARRVKRDSIKvlfIQMSDESKEHRDRLYRLFKKL 78
                                      347999**********************9988888877666655444113556677777777888888775 PP

>> DUF892  Domain of unknown function (DUF892)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   5.3e-05      0.16      14     120 ..      31     132 ..      24     145 .. 0.74
   2 ?    0.2   0.1      0.22   6.5e+02      16      63 ..     117     164 ..     103     177 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.3e-05
                                       HHHHHHHHHHHHHHHHH-SSHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-------.-HHHHTTT-----------T CS
                            DUF892  14 yaaEkqllkalpkmakaaespeLkaaleqHleeTegqierLeqvferlgesasekkcdamegliaegqelieeaaed 90 
                                          E + +k  +++a++++++ +k  + q  +e +++ +rL ++f++l ++ + +k da      e+     e+ + 
  gi|242399324|ref|YP_002994748.1|  31 IFNEDEETKYYEELARRVKRDSIKVLFIQMSDESKEHRDRLYRLFKKLYTDEEPVKVDA---PPVEVFPYYSEFEKA 104
                                       55688889999*************************************99999988444...334444444445555 PP

                                       HHHHHHH...HHHHHHHHHHHHHHHHHHHH CS
                            DUF892  91 eslkdaaliaaaqavehyEiAsYgtLialA 120
                                       ++ + a+    +++ e +    Y++Li++A
  gi|242399324|ref|YP_002994748.1| 105 NDYLEAL--EYCMKSELFAKKVYEMLISYA 132
                                       5555555..555666666666666666655 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.22
                                       HHHHHHHHHHHHHHH-SSHHHHHHHHHHHHHHHHHHHHHHHHHHHTT- CS
                            DUF892  16 aEkqllkalpkmakaaespeLkaaleqHleeTegqierLeqvferlge 63 
                                        E  + k+ + +++ ae+++ +  + q     +++  r+++  e +g 
  gi|242399324|ref|YP_002994748.1| 117 SELFAKKVYEMLISYAENEDSRGIFSQLALMERDHYLRIRKAYEFIGG 164
                                       444445555555555666666666666555666666666666665555 PP

>> Ferritin_2  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.0   0.00011      0.33       4     131 ..      25     156 ..      22     160 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00011
                        Ferritin_2   4 diLnfAlnlEyleaafYtaalegaslddkalldaevrevaeeiakheeaHveflkaaleGaaav..akptfdf.... 74 
                                       ++L++A+  E  e+++Y++ + + +      ++    ++  e ++h+   ++++k+  + +++v  ++p +++    
  gi|242399324|ref|YP_002994748.1|  25 EVLSYAIFNEDEETKYYEELARRVK---RDSIKVLFIQMSDESKEHRDRLYRLFKKLYTDEEPVkvDAPPVEVfpyy 98 
                                       79*******************9765...3445555555555555555555555555555555554444444445777 PP

                        Ferritin_2  75 .afdpfadeksflalaavlEdvgvsAYlgaapllsnkelltaaasIlsvEArHaavir 131
                                        +f++ +d+ + l+  +  E  + + Y   + + +n++ +    +++  E  H   ir
  gi|242399324|ref|YP_002994748.1|  99 sEFEKANDYLEALEYCMKSELFAKKVYEMLISYAENEDSRGIFSQLALMERDHYLRIR 156
                                       7888888888888888888888888888888888888888888888877777766666 PP

>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.9     9e-05      0.27      21     111 ..      41     136 ..      36     151 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 9e-05
                                       HHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS....SHHHHHH..........C-SSSS...CS.SHHH CS
                          Ferritin  21 mawyvkgpgleglaeffdeqaeeerehadklaerilalGgtpvltraelee..........ieapke...fg.svee 83 
                                       +   ++ +++++++ +f + ++e  eh d+l+   ++l       + e  +          ++   +    + + +e
  gi|242399324|ref|YP_002994748.1|  41 YEELARRVKRDSIKVLFIQMSDESKEHRDRLYRLFKKLYT-----DEEPVKvdappvevfpYY---SefeKAnDYLE 109
                                       5556677888899999999999999999999998888866.....333333111334433333...2444445**** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHTT- CS
                          Ferritin  84 vleaalehekkvteslrelielaeeegD 111
                                       +le ++++e  + + ++ li +ae e D
  gi|242399324|ref|YP_002994748.1| 110 ALEYCMKSELFAKKVYEMLISYAENE-D 136
                                       ************************87.4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       847  (0.0472419); expected 358.6 (0.02)
Passed bias filter:                      571  (0.0318478); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.47u 0.21s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 1501.52
//
Query:       gi|242399325|ref|YP_002994749.1|  [L=269]
Description: Probable exosome complex exonuclease 2 [Thermococcus sibiricus MM 739]
Scores for complete 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  108.5   0.0    5.4e-31  107.8   0.0    1.3  1  RNase_PH    3' exoribonuclease family, domain 1
    3.7e-15   55.7   0.0    8.2e-15   54.6   0.0    1.6  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 !  107.8   0.0     6e-35   5.4e-31       1     132 []      29     164 ..      29     164 .. 0.95

  Alignments for each domain:
  == domain 1  score: 107.8 bits;  conditional E-value: 6e-35
                                       EEEEEEEEESSSSTTSEEEEEEECCEEEEEEEEEEEEEE-TCCG--CCEEEECCCCECCCCEC-C...S...HHHHH CS
                          RNase_PH   1 elRslsietgvlsqanGSaylelGdtkvlasvtgpieerpseerddaegaldveveyapfasgerrregrpsdeeie 77 
                                       ++R+l++et+v+++a+GSa+++lG+t+vl++++++  e p+++ +d+ g+++++ve+ p+as++++  g p++++ie
  gi|242399325|ref|YP_002994749.1|  29 DFRPLTVETNVIEKAEGSALVKLGNTQVLVGIKVELGE-PFPDLPDM-GVITTNVEFVPLASPTFEP-GPPDESAIE 102
                                       69**********************************99.77777666.79***************77.9******** PP

                                       HHHHHHHHHCCTC-C........CGCCTCEEEEEEEEEECCCS-CHHHCHHHHHHHHHCTCEE CS
                          RNase_PH  78 lsrlleralrpsill........ekkpkstididitvlssdggslldalinaaslALadagip 132
                                       l+r+++r +r+s  +        ++k    i id++vl++dg +llda+ ++a++AL++++ip
  gi|242399325|ref|YP_002994749.1| 103 LARIIDRGIRESQAIdleklvivPGKLVRVIFIDVHVLDHDG-NLLDASGIGAIAALLSTKIP 164
                                       **************99999999999999**************.*******************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 !   54.6   0.0   9.2e-19   8.2e-15       2      66 ..     189     253 ..     188     254 .. 0.98

  Alignments for each domain:
  == domain 1  score: 54.6 bits;  conditional E-value: 9.2e-19
                                       --EEEEEEEETTEEEES--HHHHHHSSEEEEEEEETTSEEEEEEEECSSCEEHHHHHHHHHHHHH CS
                        RNase_PH_C   2 pviavtvgkvddqfvlDptkeEedlsegdltlavagtkevvtlmkeggsqldeetlleaielAkk 66 
                                       ++i vt +k+++++v+Dp+ eEe++++g++t++ ++++ + +++k++g++++ e+++ a++lA+k
  gi|242399325|ref|YP_002994749.1| 189 IPIPVTLAKIGGNLVVDPNFEEEQVMDGKITITTDENGYISAVQKSEGGSFKLEEVVYAVDLAYK 253
                                       7999***********************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1948.49
//
Query:       gi|242399326|ref|YP_002994750.1|  [L=246]
Description: Probable exosome complex exonuclease 1 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      4e-36  124.4   0.0    6.1e-36  123.8   0.0    1.3  1  RNase_PH    3' exoribonuclease family, domain 1
    1.8e-17   63.1   0.4    3.5e-17   62.2   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 !  123.8   0.0   6.8e-40   6.1e-36       1     132 []      24     153 ..      24     153 .. 0.93

  Alignments for each domain:
  == domain 1  score: 123.8 bits;  conditional E-value: 6.8e-40
                                       EEEEEEEEESSSSTTSEEEEEEECCEEEEEEEEEEEEEE-TCCG..--CCEEEECCCCECCCCEC-C...S...HHH CS
                          RNase_PH   1 elRslsietgvlsqanGSaylelGdtkvlasvtgpieerpseer..ddaegaldveveyapfasgerrregrpsdee 75 
                                       elR++++e gvl++a+GSay+e G++k++a+v+gp+e +p+  +  d+a   l v++++apf+ +er++   p++++
  gi|242399326|ref|YP_002994750.1|  24 ELRKIKMEVGVLKSADGSAYVEWGKNKIMAAVYGPREIHPKHLQkpDRAI--LRVRYNMAPFSVEERKK-PGPDRRS 97 
                                       79**********************************99666554335555..***************77.56***** PP

                                       HHHHHHHHHHHCCTC-CCGCCTCEEEEEEEEEECCCS-CHHHCHHHHHHHHHCTCEE CS
                          RNase_PH  76 ielsrlleralrpsillekkpkstididitvlssdggslldalinaaslALadagip 132
                                       +e+s+++  al+p ++le +p++ idi+i+vl++d  ++  a i+aaslALadagip
  gi|242399326|ref|YP_002994750.1|  98 VEISKVIRGALEPAVILELFPRTSIDIFIEVLQADA-GTRVAGITAASLALADAGIP 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 !   62.2   0.4   3.9e-21   3.5e-17       1      67 []     156     221 ..     156     221 .. 0.97

  Alignments for each domain:
  == domain 1  score: 62.2 bits;  conditional E-value: 3.9e-21
                                       S--EEEEEEEETTEEEES--HHHHHHSSEEEEEEEETTSEEEEEEEECSSCEEHHHHHHHHHHHHHH CS
                        RNase_PH_C   1 apviavtvgkvddqfvlDptkeEedlsegdltlavagtkevvtlmkeggsqldeetlleaielAkkg 67 
                                       ++v+a++ gk+d+++vlD++keE++++e+d+++a+   k+ +tl++++g  l+ e++lea++lA kg
  gi|242399326|ref|YP_002994750.1| 156 DLVAACAAGKIDGEIVLDLNKEEDNYGEADVPVAIMPIKNDITLLQMDGY-LTKEEFLEAVKLAIKG 221
                                       58************************************************.*************885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); 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: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1636.39
//
Query:       gi|242399327|ref|YP_002994751.1|  [L=251]
Description: Probable exosome complex RNA-binding protein 1 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.6e-09   36.2   2.2    5.9e-09   36.1   0.7    1.8  2  KH_6      KH domain
    3.4e-07   30.0   0.3    6.5e-07   29.1   0.3    1.5  1  KH_1      KH domain
    6.6e-07   29.0   0.0    1.4e-06   28.0   0.0    1.6  1  ECR1_N    Exosome complex exonuclease RRP4 N-terminal region
    5.1e-06   26.2   2.1    8.5e-06   25.5   1.3    1.8  2  KH_2      KH domain


Domain annotation for each model (and alignments):
>> KH_6  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.7   1.3e-12   5.9e-09       1      43 [.     149     194 ..     149     197 .. 0.86
   2 ?   -2.5   0.0       1.5   6.7e+03      11      25 ..     222     236 ..     221     242 .. 0.70

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 1.3e-12
                              KH_6   1 GmlfeVslslvrRllnhvLeeLgka...gpfeiavGlNGriWvkse 43 
                                       G+l+++++s+v+Rl+ + ++++++     +  i+vG+NG++Wv++ 
  gi|242399327|ref|YP_002994751.1| 149 GQLVKITPSKVPRLIGKGGSMINMIknlTGTRIIVGQNGWVWVSGR 194
                                       99*************777777776566677*************986 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.5
                              KH_6  11 vrRllnhvLeeLgka 25 
                                       vr +l++ L eL+++
  gi|242399327|ref|YP_002994751.1| 222 VREMLVKRLNELKEQ 236
                                       677777777787765 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.3   1.4e-10   6.5e-07       4      55 ..     152     197 ..     150     208 .. 0.76

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 1.4e-10
                                       EEEGGGHHHHHHTGGGHHHHHHHHHHT-EEEEESSTT...T.-EEEEEE.SHH CS
                              KH_1   4 ilvPsslvgriIGkgGsnIkeIreetgakIkvpksedegsderevtisG.spe 55 
                                       +++  s+v+r+IGkgGs+I+ I++ tg++I v +       +  v +sG ++e
  gi|242399327|ref|YP_002994751.1| 152 VKITPSKVPRLIGKGGSMINMIKNLTGTRIIVGQ-------NGWVWVSGrKEE 197
                                       5788899************************753.......235777775555 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 !   28.0   0.0   3.1e-10   1.4e-06       1      37 [.      11      46 ..      11      47 .. 0.95

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 3.1e-10
                                      EE-TT-EEEETTTSEE-TTEEEETTEEEESSSEEEEE CS
                            ECR1_N  1 iVtPGevlttdeefmrGhGTYvrggtiyAsvaGtvev 37
                                      +V+PG+ l  +  f+ G GT+ +g+ +y+sv+G v+v
  gi|242399327|ref|YP_002994751.1| 11 LVVPGTLL-AQGSFKNGRGTFKEGNRLYSSVVGLVRV 46
                                      69******.9999**********************97 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       2.2   9.7e+03      47      59 ..     102     114 ..     101     120 .. 0.76
   2 !   25.5   1.3   1.9e-09   8.5e-06      29      69 ..     152     192 ..     146     208 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2.2
                                       HHHHHHHHHHHHH CS
                              KH_2  47 ikkigkelrkdie 59 
                                       ++ ++++lrk+++
  gi|242399327|ref|YP_002994751.1| 102 VDVLKTDLRKIFD 114
                                       6778889999875 PP

  == domain 2  score: 25.5 bits;  conditional E-value: 1.9e-09
                                       EEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTCEEEE CS
                              KH_2  29 iviresqpgivIGkgGsnikkigkelrkdieklegkkVkln 69 
                                       + i+ s+  ++IGkgGs+i++i+   + +i + ++++V++ 
  gi|242399327|ref|YP_002994751.1| 152 VKITPSKVPRLIGKGGSMINMIKNLTGTRIIVGQNGWVWVS 192
                                       78999********************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       633  (0.0353059); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); 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: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1740.01
//
Query:       gi|242399328|ref|YP_002994752.1|  [L=236]
Description: RNA-associated protein [Thermococcus sibiricus MM 739]
Scores for complete 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-25   89.1   0.1    2.7e-25   88.2   0.1    1.4  1  SBDS      Shwachman-Bodian-Diamond syndrome (SBDS) protein
    1.9e-18   66.5   0.0    3.1e-18   65.9   0.0    1.4  1  SBDS_C    SBDS protein C-terminal domain


Domain annotation for each model (and alignments):
>> SBDS  Shwachman-Bodian-Diamond syndrome (SBDS) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.2   0.1     3e-29   2.7e-25       2      88 .]       8      94 ..       7      94 .. 0.98

  Alignments for each domain:
  == domain 1  score: 88.2 bits;  conditional E-value: 3e-29
                                      -EEEEEEETTEEEEEEE-HHHHHHHHCTT---HHHHBSSSS-EEETTTTEE--HHHHHHHHS---HHHHHHHHHHHSEE CS
                              SBDS  2 vsivrykkgkkrFeiavyknklleyregkeidLsevlqsekiFtnaskGetaskselekafgteskdeiikeILkkGei 80
                                      ++i+r+k +++ Fei+v++  + +++egke +++e+l+++ iF++a+kG++as+ e+ek+fgt++  ei+k+IL+kGe+
  gi|242399328|ref|YP_002994752.1|  8 AVIARLKTHGEIFEILVDPYLARDFKEGKELPVEEILATPYIFKDAHKGDKASEHEMEKIFGTNDPYEIAKIILRKGEV 86
                                      6899*************************************************************************** PP

                                      E--HHHHH CS
                              SBDS 81 qvsaeerk 88
                                      q++ae+rk
  gi|242399328|ref|YP_002994752.1| 87 QLTAEQRK 94
                                      *****997 PP

>> SBDS_C  SBDS protein C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.9   0.0   3.5e-22   3.1e-18       2      99 ..     101     201 ..     100     223 .. 0.76

  Alignments for each domain:
  == domain 1  score: 65.9 bits;  conditional E-value: 3.5e-22
                                       HHHHHHHHHHHEEBTTTTB---HHHHHHHHHHTT----TTS-CCCCHHHHHHHHTTTS--EE-EEEEEEEE-...CC CS
                            SBDS_C   2 ekeiieivaeklvnpqtkrpytttmIekalkelgtsvktnksaksQalevikaLiqeipiqrarmrlritcptsikd 78 
                                       +k+i+ i+++++v+p++++p+++ +I ka++e+g++v++ k a++Q+ e+ikaL++ +p + +   +++++p    +
  gi|242399328|ref|YP_002994752.1| 101 KKQIAMIIHRNAVDPRSGYPHPPDRILKAMEEVGVRVDIFKDAQAQVPEIIKALRRVLPLKIETKVIAVKIP---SE 174
                                       79**********************************************************************...66 PP

                                       CHHHHHHHH.HH.....S.EE.....E CS
                            SBDS_C  79 kilklieqv.esqkvaekewe.....v 99 
                                       +  k++ +v +  +++ +ew      +
  gi|242399328|ref|YP_002994752.1| 175 YSGKAYGEVrTFGNIKREEWAsdgswM 201
                                       666666666333333334433333321 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 1503.61
//
Query:       gi|242399329|ref|YP_002994753.1|  [L=260]
Description: Proteasome subunit alpha [Thermococcus sibiricus MM 739]
Scores for complete 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-69  232.1   1.4    1.1e-68  230.5   0.0    1.9  2  Proteasome      Proteasome subunit
    4.8e-13   48.5   0.8    1.2e-12   47.2   0.2    1.9  2  Proteasome_A_N  Proteasome subunit A N-terminal signature
  ------ inclusion threshold ------
      0.091   12.8   0.2       0.18   11.8   0.2    1.5  1  CARD_2          Caspase recruitment domain


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 !  230.5   0.0   1.9e-72   1.1e-68       1     190 []      33     215 ..      33     215 .. 0.98
   2 ?    0.4   0.4     0.064   3.8e+02     152     177 ..     219     244 ..     216     251 .. 0.80

  Alignments for each domain:
  == domain 1  score: 230.5 bits;  conditional E-value: 1.9e-72
                                       HHHS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSS CS
                        Proteasome   1 vkkGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygr 77 
                                       vk+G t+vG+k+kdgvvla++kr+t  skl+++++ eKif+iddhi++a +G +aDar+lv+rar eaq yrl+yg+
  gi|242399329|ref|YP_002994753.1|  33 VKRGATAVGVKCKDGVVLAVEKRVT--SKLIEPESYEKIFQIDDHIAAASSGIIADARVLVDRARLEAQIYRLTYGE 107
                                       79***********************..************************************************** PP

                                       GTCHHHHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHH CS
                        Proteasome  78 pipverlvarvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekey 154
                                       p+p+ +lv+++++++q +tq++g+rpfg++ll+agv+  ++peL+++dpsG+y+e+k avaiGsg++ a++++e++y
  gi|242399329|ref|YP_002994753.1| 108 PVPLTVLVKKICDLKQMHTQYGGVRPFGAALLMAGVN--EKPELFETDPSGAYFEWK-AVAIGSGRNTAMAIFEEKY 181
                                       *************************************..459**************8.******************* PP

                                       STTBSHHHHHHHHHHHHHHHHHHBTTSCSSEEEEEE CS
                        Proteasome 155 kedltleeavelavkalkealerdklsgknievavi 190
                                       ++++tleea++lav al++++e  + s++ ievavi
  gi|242399329|ref|YP_002994753.1| 182 RDEMTLEEAIKLAVLALSKIME--EPSPESIEVAVI 215
                                       **********************..68********97 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.064
                                       HHHSTTBSHHHHHHHHHHHHHHHHHH CS
                        Proteasome 152 keykedltleeavelavkalkealer 177
                                       ++ ++++t ee  +  ++alke+  +
  gi|242399329|ref|YP_002994753.1| 219 EKKFKKITPEEVAKCLEEALKEVEAE 244
                                       555699**************998765 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 !   47.2   0.2     2e-16   1.2e-12       1      23 []      10      32 ..      10      32 .. 0.99
   2 ?   -1.0   0.0      0.24   1.4e+03      13      18 ..      68      73 ..      68      73 .. 0.88

  Alignments for each domain:
  == domain 1  score: 47.2 bits;  conditional E-value: 2e-16
                    Proteasome_A_N  1 YDrslttFSPdGRLfQVEYAmkA 23
                                      YDr++t+FSPdGRLfQV YA +A
  gi|242399329|ref|YP_002994753.1| 10 YDRAITVFSPDGRLFQVQYAREA 32
                                      *********************99 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.24
                    Proteasome_A_N 13 RLfQVE 18
                                      ++fQ++
  gi|242399329|ref|YP_002994753.1| 68 KIFQID 73
                                      79**97 PP

>> CARD_2  Caspase recruitment domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2     3e-05      0.18       7      49 ..     213     254 ..     208     258 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3e-05
                                       .HHHHTHHHH.TT--HHHHGGG-T.TS-HHHHHHHHHHHHHHH CS
                            CARD_2   7 rllrllrprlketikpseilphltecLteedkeeIraeeenkG 49 
                                       +++++ ++++k+ i+p+e+ + l+e L+e + ee+  +ee ++
  gi|242399329|ref|YP_002994753.1| 213 AVISVKEKKFKK-ITPEEVAKCLEEALKEVEAEEVPEKEEDYS 254
                                       577888899977.**********************99998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       966  (0.0538792); expected 358.6 (0.02)
Passed bias filter:                      686  (0.038262); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.51
# Mc/sec: 1521.44
//
Query:       gi|242399330|ref|YP_002994754.1|  [L=120]
Description: Ribonuclease P protein component 2 [Thermococcus sibiricus MM 739]
Scores for complete 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-22   79.0   0.1      3e-22   78.8   0.1    1.0  1  RNase_P_Rpp14  Rpp14/Pop5 family


Domain annotation for each model (and alignments):
>> RNase_P_Rpp14  Rpp14/Pop5 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.8   0.1   1.7e-26     3e-22       1     102 [.      17     113 ..      17     114 .. 0.96

  Alignments for each domain:
  == domain 1  score: 78.8 bits;  conditional E-value: 1.7e-26
                                       EEEEEEEEESS......-HHHHHHHHHHHHHHHHHHHHHHH--..EEEEEETTTTEEEEEEEGGGHHHHHHHHHT-- CS
                     RNase_P_Rpp14   1 RYllveilypdeeeelteksllkairesvqelfGdyglgklgsslsvkyfspatstaiiRcsresyrlvwaaLtlit 77 
                                       RY+++++  +++   ++++ + kai++   +++G++g+++++   + ++f+++t+t+i+Rc+r+++++++ +Ltlit
  gi|242399330|ref|YP_002994754.1|  17 RYIAFQVTGERP---FKKEMIKKAIWDVSLKTLGELGTARAKP--WFIKFDEKTQTGIVRCDRKYVEEIRFVLTLIT 88 
                                       9**********4...679*************************..9******************************* PP

                                       EETTEEEEEEEEEEESSHHHHHHHT CS
                     RNase_P_Rpp14  78 kiegrpvvfrvvrvsGTikkaeeea 102
                                       +i+g ++++r+++vsGTik+++ ++
  gi|242399330|ref|YP_002994754.1|  89 EINGSKAIVRTLGVSGTIKRLKMKF 113
                                       ********************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 891.38
//
Query:       gi|242399331|ref|YP_002994755.1|  [L=385]
Description: hypothetical protein TSIB_1354 [Thermococcus sibiricus MM 739]
Scores for complete 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-124  414.4   0.0   5.1e-124  413.5   0.0    1.4  2  DUF763    Protein of unknown function (DUF763)


Domain annotation for each model (and alignments):
>> DUF763  Protein of unknown function (DUF763)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  413.5   0.0  2.8e-128  5.1e-124       1     312 []       5     339 ..       5     339 .. 0.96
   2 ?   -2.8   0.1      0.16   2.9e+03      91     113 ..     357     379 ..     356     382 .. 0.86

  Alignments for each domain:
  == domain 1  score: 413.5 bits;  conditional E-value: 2.8e-128
                            DUF763   1 GiadLpLhegkvPewllermkkLskaiveliveeygkeellerlsdPlwFqslgnvlGmdWdsSGsTtvvlgalkea 77 
                                       Gia+LpLh+g+vP+wl+ rmk+L+ ++++l+v+eyg++ +lerl+dP+wFq+l+n++GmdWdsSGsTtv+ g++k++
  gi|242399331|ref|YP_002994755.1|   5 GIAELPLHGGHVPRWLALRMKRLADLVIKLLVDEYGTQGVLERLADPVWFQALNNLIGMDWDSSGSTTVTAGMVKDV 81 
                                       89*************************************************************************** PP

                            DUF763  78 lkseelgilvaGGkGkksrktpeeleklaeklgldeeklvkasrlvakvdnaalqdgyqlYlhalivsekgkwaviq 154
                                       l++e+lgi+ aGGkG+ksrktpeel++++e +gld+++++k+s+lvakvd++alq gyqlY+h+++v+++g+w+++q
  gi|242399331|ref|YP_002994755.1|  82 LSKEDLGIKAAGGKGTKSRKTPEELKQISEIYGLDADEYIKTSKLVAKVDTVALQTGYQLYHHVFFVDQDGRWTIVQ 158
                                       ***************************************************************************** PP

                            DUF763 155 QGmneeerlARRYhwlseelesfveephsgiagekkeeevlnlvskeseearkaildlvkekpekllkelkelkall 231
                                       QGmn + +lARRYhw+se++esf+ eph+gi+g  k++  ln+++kes+e +k++ld+++e+p+k+++e+k+++al 
  gi|242399331|ref|YP_002994755.1| 159 QGMNPSIKLARRYHWFSEKIESFTLEPHKGISG-IKSDYSLNTIAKESKEYQKTLLDIISESPTKIEREVKSIEALS 234
                                       *********************************.88999************************************99 PP

                            DUF763 232 kgekkl.................klpakhev......lekvlekayelqpedfeellllkgvGpktlraLalvaeli 285
                                       kg + l                 +             ++k+le a el++++++elll+kg+Gp+tlraL+lv el+
  gi|242399331|ref|YP_002994755.1| 235 KGYTPLfykpyekrevlpiveryQ------SfgrfelNKKALELARELSVSNYDELLLIKGLGPSTLRALSLVLELV 305
                                       999998988777666665554443......0555565**************************************** PP

                            DUF763 286 ygekasfkDPv.......kysfavGgKdgvPypv 312
                                       y+ ++s+kDPv       k+++avGgKd+vP+p+
  gi|242399331|ref|YP_002994755.1| 306 YDVHPSWKDPVthppdpfKFAYAVGGKDKVPFPI 339
                                       *********************************7 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.16
                            DUF763  91 kGkksrktpeeleklaeklglde 113
                                       kGk+ r++ ++++k++ek+++ e
  gi|242399331|ref|YP_002994755.1| 357 KGKEEREVVKQVTKISEKWKFPE 379
                                       89999********9999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 2384.94
//
Query:       gi|242399332|ref|YP_002994756.1|  [L=55]
Description: hypothetical protein TSIB_1355 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       137  (0.00764125); expected 358.6 (0.02)
Passed bias filter:                      130  (0.00725082); 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 0.31s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 346.91
//
Query:       gi|242399333|ref|YP_002994757.1|  [L=184]
Description: hypothetical protein TSIB_1356 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.6e-13   48.2   1.2    1.8e-12   47.2   1.2    1.5  1  HNH            HNH endonuclease
    1.3e-07   31.3   1.2    2.3e-07   30.6   1.2    1.4  1  HNH_5          HNH endonuclease
  ------ inclusion threshold ------
       0.06   13.3   0.2       0.11   12.5   0.2    1.6  1  Cytochrome_C7  Cytochrome c7 and related cytochrome c
      0.072   14.0   0.2      0.072   14.0   0.2    1.9  2  zf-C2H2_4      C2H2-type zinc finger
      0.095   13.2   0.3      0.095   13.2   0.3    1.8  2  SPT2           SPT2 chromatin protein
       0.12   12.9   0.2       0.12   12.9   0.2    2.3  2  zf-C2H2        Zinc finger, C2H2 type
       0.13   12.7   1.5       0.37   11.2   1.5    1.8  1  DUF1677        Protein of unknown function (DUF1677)
        1.3    9.0  11.7          3    7.9   8.0    2.5  2  DUF4674        Domain of unknown function (DUF4674)


Domain annotation for each model (and alignments):
>> HNH  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.2   1.2     8e-16   1.8e-12       1      43 [.      43      84 ..      43      87 .. 0.95

  Alignments for each domain:
  == domain 1  score: 47.2 bits;  conditional E-value: 8e-16
                               HNH  1 CeyCgrkfhksealevdHiipisqggaddieNlqllCksCHnk 43
                                      CeyCgr +  + a  ++Hi+pi +gg+++ +N++ lC +CH++
  gi|242399333|ref|YP_002994757.1| 43 CEYCGRRVSTT-AGYIHHIKPIREGGKTTPSNIIVLCGTCHRN 84
                                      *******9886.*****************************97 PP

>> HNH_5  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   1.2     1e-10   2.3e-07       1      45 [.      43      87 ..      43      96 .. 0.93

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 1e-10
                             HNH_5  1 CiyCgkeiaekelseeHIiPeslGGkltisnlvtlCkkCNqkkgq 45
                                      C yCg+++ ++   + HI P   GGk+t+sn+ +lC +C+ +  +
  gi|242399333|ref|YP_002994757.1| 43 CEYCGRRVSTTAGYIHHIKPIREGGKTTPSNIIVLCGTCHRNADN 87
                                      99********999***************************98765 PP

>> Cytochrome_C7  Cytochrome c7 and related cytochrome c
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   4.8e-05      0.11      11      60 ..      38      88 ..      29     130 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.8e-05
                     Cytochrome_C7 11 atgykCtdCHskl.feskakkk.maemekgkskkaeves.ltCgaCHdgknaf 60
                                      ++g+kC+ C   + ++++  ++ +   e gk   +  ++ + Cg+CH++  + 
  gi|242399333|ref|YP_002994757.1| 38 VVGRKCEYCGRRVsTTAGYIHHiKPIREGGKT--TPSNIiVLCGTCHRNADNA 88
                                      46789999999993333333442333333333..44555577*****987765 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.2   3.2e-05     0.072       2      21 ..      42      61 ..      41      62 .. 0.94
   2 ?   -3.3   0.2         8   1.8e+04       3       8 ..      78      83 ..      77      85 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.2e-05
                         zf-C2H2_4  2 kCpiCgksFsskkaLlrHlk 21
                                      kC++Cg++ s+  ++ +H+k
  gi|242399333|ref|YP_002994757.1| 42 KCEYCGRRVSTTAGYIHHIK 61
                                      8*****************97 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 8
                         zf-C2H2_4  3 CpiCgk 8 
                                      C  C++
  gi|242399333|ref|YP_002994757.1| 78 CGTCHR 83
                                      666755 PP

>> SPT2  SPT2 chromatin protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.3   4.2e-05     0.095      24      65 ..      87     131 ..      81     140 .. 0.63
   2 ?   -3.1   1.7         5   1.1e+04      46      46 ..     171     171 ..     143     181 .. 0.50

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.2e-05
                              SPT2  24 dfieddeeeeeerrr...yarseIwaifnkdkk.kyesrddaesdd 65 
                                       + i + +e +e+ r+   ++++ I++i+n++k+ k +s+ + +++ 
  gi|242399333|ref|YP_002994757.1|  87 NAIISRKELKEKVRSrskNVQDSIRRILNRNKSgK-SSSTKSKEQF 131
                                       5555444444443334559**************53.3334444444 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 5
                              SPT2  46 a 46 
                                        
  gi|242399333|ref|YP_002994757.1| 171 G 171
                                       1 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   5.2e-05      0.12       2      21 ..      42      61 ..      42      61 .. 0.96
   2 ?   -1.0   0.2       1.4   3.2e+03       3       8 ..      78      83 ..      77      85 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.2e-05
                                      EETTTTEEESSHHHHHHHHH CS
                           zf-C2H2  2 kCpdCgksFkrksnLkrHir 21
                                      kC++Cg++ ++   + +Hi+
  gi|242399333|ref|YP_002994757.1| 42 KCEYCGRRVSTTAGYIHHIK 61
                                      7*****************96 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.4
                                      ETTTTE CS
                           zf-C2H2  3 CpdCgk 8 
                                      C+ C++
  gi|242399333|ref|YP_002994757.1| 78 CGTCHR 83
                                      999987 PP

>> DUF1677  Protein of unknown function (DUF1677)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.5   0.00016      0.37       4      65 ..      41     118 ..      38     139 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00016
                           DUF1677   4 akCecCglteectaeYiarvrerfsG.k.......wvCGLCaeavkeele.r.......skkkisveeAlkahmafc 64 
                                        kCe Cg +   ta Yi++++   +G k        +CG C     + +  r       ++++++v++ +++  +  
  gi|242399333|ref|YP_002994757.1|  41 RKCEYCGRRVSTTAGYIHHIKPIREGgKttpsniiVLCGTCHRNADNAIIsRkelkekvRSRSKNVQDSIRRILNRN 117
                                       59******************976555233344444689999876655543143443333334444444444444444 PP

                           DUF1677  65 k 65 
                                       k
  gi|242399333|ref|YP_002994757.1| 118 K 118
                                       4 PP

>> DUF4674  Domain of unknown function (DUF4674)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1      0.52   1.2e+03      16      26 ..      41      51 ..      30      65 .. 0.72
   2 ?    7.9   8.0    0.0013         3      71     126 ..      70     128 ..      60     153 .. 0.68

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.52
                           DUF4674 16 piCpyCfqllv 26
                                      + C yC+   +
  gi|242399333|ref|YP_002994757.1| 41 RKCEYCGRRVS 51
                                      36888887555 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0013
                           DUF4674  71 sksvLlitCkvCnkttkhkgksrsflaplkskeetpksksslk...tkkkktksskkkt 126
                                         s++++ C +C +++  +  sr+ l+++  ++++  + s +     +k+ ++ss+k +
  gi|242399333|ref|YP_002994757.1|  70 TPSNIIVLCGTCHRNADNAIISRKELKEKVRSRSKNVQDSIRRilnRNKSGKSSSTKSK 128
                                       568999********************998855555554444440004444444444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1316  (0.0734006); expected 358.6 (0.02)
Passed bias filter:                      691  (0.0385409); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1103.55
//
Query:       gi|242399334|ref|YP_002994758.1|  [L=95]
Description: hypothetical protein TSIB_1357 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-29  101.8   1.8    1.9e-29  101.6   1.8    1.1  1  DUF357    Protein of unknown function (DUF357)


Domain annotation for each model (and alignments):
>> DUF357  Protein of unknown function (DUF357)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.6   1.8     1e-33   1.9e-29       1      73 []      12      84 ..      12      84 .. 0.99

  Alignments for each domain:
  == domain 1  score: 101.6 bits;  conditional E-value: 1e-33
                                      HHHHHHHHHHHHHH.....TS---HHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTSTS CS
                            DUF357  1 rYirlleealekvkiapdeesplgeaaeevlemaesYleDakyflekgdlvnAlasfsYaeGwLDagarlgll 73
                                      +Y++++++ale+++ia++e+s l+ +a+++l+ma+sY++Da+y+++kgd+v+A+a+++Ya+G++Dag+rlg++
  gi|242399334|ref|YP_002994758.1| 12 KYFEITKQALERLEIAVHEKSLLFSVAQDFLTMAKSYYSDAEYYYKKGDYVTAFAALNYAHGFIDAGVRLGVF 84
                                      7**********************************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       914  (0.0509789); expected 358.6 (0.02)
Passed bias filter:                      642  (0.0358079); 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: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 587.50
//
Query:       gi|242399335|ref|YP_002994759.1|  [L=130]
Description: hypothetical protein TSIB_1358 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-41  141.1   0.7    1.5e-41  140.8   0.7    1.1  1  DUF555          Protein of unknown function (DUF555)
  ------ inclusion threshold ------
       0.05   13.5   0.0      0.075   12.9   0.0    1.2  1  FdhE            Protein involved in formate dehydrogenase for
      0.055   13.3   0.1       0.14   12.0   0.1    1.7  1  Rad50_zn_hook   Rad50 zinc hook motif
      0.072   13.1   0.9       0.16   12.0   0.9    1.6  1  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai


Domain annotation for each model (and alignments):
>> DUF555  Protein of unknown function (DUF555)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.8   0.7   3.3e-45   1.5e-41       1     101 []       3     104 ..       3     104 .. 0.99

  Alignments for each domain:
  == domain 1  score: 140.8 bits;  conditional E-value: 3.3e-45
                            DUF555   1 dyevvleaawivrdvksvddAigiAiseagkrlnpe.ldfveievgetecPkcgeelesalvvadtalvglllemkv 76 
                                       dy vvlea++ivr+v+s+ddAi++A+s+++k ln+e ldfv++e+g+++cP cg+++esa+v+++++lvg++l++kv
  gi|242399335|ref|YP_002994759.1|   3 DYIVVLEAPIIVREVESADDAINVAVSKVAKALNKEkLDFVRVEIGYSQCPVCGSPFESAFVIGNVGLVGIYLTLKV 79 
                                       89*********************************99**************************************** PP

                            DUF555  77 fnaeseEhaeriakseigkaledvP 101
                                       fna+s Ehaeriak+++gkal++vP
  gi|242399335|ref|YP_002994759.1|  80 FNAQSLEHAERIAKAVVGKALKKVP 104
                                       ************************9 PP

>> FdhE  Protein involved in formate dehydrogenase formation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.7e-05     0.075     143     183 ..      22      64 ..      14      72 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.7e-05
                                       HHHHHHHHHHHHT--TTSSS-.-TT..-SS-TTT---EEEEEE CS
                              FdhE 143 aAlqvvwtklaaaldakalaelaee..kglCPvCgsaPvasvv 183
                                        A++v+++k+a+al++++l  ++ e   + CPvCgs+  ++ v
  gi|242399335|ref|YP_002994759.1|  22 DAINVAVSKVAKALNKEKLDFVRVEigYSQCPVCGSPFESAFV 64 
                                       5899***********999865555511567*****97555544 PP

>> Rad50_zn_hook  Rad50 zinc hook motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   3.1e-05      0.14      21      31 ..      51      61 ..      46      62 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.1e-05
                                      E-TTT--EE-H CS
                     Rad50_zn_hook 21 cCPlCgRelde 31
                                       CP+Cg+++++
  gi|242399335|ref|YP_002994759.1| 51 QCPVCGSPFES 61
                                      7********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 ?   12.0   0.9   3.7e-05      0.16       1       8 [.      51      58 ..      51      62 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.7e-05
                    DNA_ligase_ZBD  1 hCPvCGsa 8 
                                      +CPvCGs+
  gi|242399335|ref|YP_002994759.1| 51 QCPVCGSP 58
                                      5******9 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:                      754  (0.0420548); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 969.03
//
Query:       gi|242399336|ref|YP_002994760.1|  [L=544]
Description: CTP synthase [Thermococcus sibiricus MM 739]
Scores for complete 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-126  420.8   1.0   2.5e-126  420.4   1.0    1.2  1  CTP_synth_N    CTP synthase N-terminus
    2.9e-58  196.8   0.0    6.2e-58  195.7   0.0    1.6  2  GATase         Glutamine amidotransferase class-I
    6.6e-07   29.3   0.1    4.6e-05   23.3   0.0    3.3  3  Peptidase_C26  Peptidase C26
  ------ inclusion threshold ------
      0.052   13.6   0.0       0.11   12.5   0.0    1.6  1  CbiA           CobQ/CobB/MinD/ParA nucleotide binding domain
      0.097   12.6   0.2       0.51   10.2   0.2    2.0  1  AAA_31         AAA domain
       0.15   11.9   0.1       0.74    9.6   0.0    2.0  2  DJ-1_PfpI      DJ-1/PfpI family


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 !  420.4   1.0  8.5e-130  2.5e-126       1     264 [.      15     276 ..      15     277 .. 0.99

  Alignments for each domain:
  == domain 1  score: 420.4 bits;  conditional E-value: 8.5e-130
                                       EEEEEEE--STTTTHHHHHHHHHHHHHCTT--EEEEEEE-SSSSSSTT--CCCC--EEE-TT--EEETHHHHHHHHH CS
                       CTP_synth_N   1 kyilvtGGvvSglGkGiiaaslgallksrglkvtlikiDPYlnvdagtlsplehGEvfvlddGaetDlDlGnYeRfl 77 
                                       k i+vtGGvvSglGkGi++aslg+l+ksrglk t ikiDPYln+dagt+sp++hGEvfvlddG+e+DlDlGnYeRfl
  gi|242399336|ref|YP_002994760.1|  15 KIIFVTGGVVSGLGKGITSASLGMLMKSRGLKTTNIKIDPYLNYDAGTMSPYQHGEVFVLDDGGEVDLDLGNYERFL 91 
                                       78*************************************************************************** PP

                                       T----GGGEEEHHHHHHHHHHHHHTTTTTT----CCCHHHHHHHHHHHHHH.HCT-SEEEEEE-S-TTSGGGHHHHH CS
                       CTP_synth_N  78 dikltkennittGkiyksviekerrGdylGktvqviphvtdeikeriekvakkveadvviveigGtvgdieslpfle 154
                                       +++lt ++nittGk+y++viekerrGdylG+tvqviph+t+eiker++k+a+  e dvv+veigGtvgdies+pfle
  gi|242399336|ref|YP_002994760.1|  92 NTSLTFDHNITTGKVYSTVIEKERRGDYLGATVQVIPHITNEIKERVRKIAD--EYDVVVVEIGGTVGDIESMPFLE 166
                                       ***************************************************9..9********************** PP

                                       HHHHHHHHH-TTTEEEEEEEE--B-TTTSSB-HHHHHHHHHHHHHHT---SEEEEEESS---HHHHHHHHHHCT--G CS
                       CTP_synth_N 155 airqlklelgkenvllihvtlvpvlkaagelktkptqhsvkelrslGiqpdiivcrsekeleeevkekialfcnvek 231
                                       a rq++le g++nv+++hvt+vp lk  ge+ktkptqhsvkelrslGiqpd i++rse++lee++k+ki+lf+nv++
  gi|242399336|ref|YP_002994760.1| 167 AARQMQLEEGRDNVAFVHVTYVPKLKVVGEQKTKPTQHSVKELRSLGIQPDAIIARSEDPLEENAKKKISLFTNVPT 243
                                       ***************************************************************************** PP

                                       GGEEEEE--S-GGGHHHHHHHCTHHHHHHHHTT CS
                       CTP_synth_N 232 eavisvkdvesiyevpllleeqglaelileklk 264
                                       eavis+ dve++yevpllle++gl ++++++l 
  gi|242399336|ref|YP_002994760.1| 244 EAVISAYDVEDTYEVPLLLEKEGLGKYLTKRLG 276
                                       ******************************997 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0         2   5.9e+03      18      49 ..     118     151 ..     110     170 .. 0.63
   2 !  195.7   0.0   2.1e-61   6.2e-58       2     190 .]     312     537 ..     311     537 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2
                                       HHTT-EEEEEETTS.HHHHHHH.THHSTSEEEEE CS
                            GATase  18 velgvkvevvpida.saeeile.llknpdgilvs 49 
                                         lg++v+v+p+ + +++e    +++++d ++v 
  gi|242399336|ref|YP_002994760.1| 118 DYLGATVQVIPHITnEIKERVRkIADEYDVVVVE 151
                                       5577778887765423333322347777777764 PP

  == domain 2  score: 195.7 bits;  conditional E-value: 2.1e-61
                                       EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHH..THHSTSEEEEEEESSCTTTTTHHHHHHHHCTSTS-EEE CS
                            GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeile..llknpdgilvsgGpgspgvegkieaikearenkiPiLG 76 
                                       l D+y s++e+l+h++v+++vkv +++i+a+++e++   ll+n+dgi+v+gG+g++g egki+a+k+aren+iP+LG
  gi|242399336|ref|YP_002994760.1| 312 LADSYLSIKEALKHSSVANEVKVRIRWIEAEDLEKEGvkLLENVDGIIVPGGFGARGSEGKIMAVKYARENNIPFLG 388
                                       78*********************************77855************************************* PP

                                       ETHHHHHHHHHTTTEEE.......................EEECEEEEEEEEEEEETTT........CGGTTTTSEE CS
                            GATase  77 ICLGmQllaiefgrkvv.......................kekekehhggtmrlgddet........allyglknev 122
                                       IC+G+Ql++ ef+r+v                        ++++ +++ggtmrlg+++         ++ly + + +
  gi|242399336|ref|YP_002994760.1| 389 ICFGFQLTVVEFARHVLgfkgansteidphtpypiidlmeEQRDLDKLGGTMRLGAYPIkikkdtlaHKLYAK-ELI 464
                                       **************888888888888999999999999999999************9999*******999998.*** PP

                                       EEEEEEEEEEESG...CHHHTTEEEEEEEETTEEEEEEEEETT.T.EEEESSBTTSTTSTTHHHHHHHHHHHH CS
                            GATase 123 ierhrHryevnpk...elepaglevtakseddeelmeiiekkn.p.fvgvQFHPEststpegpellfnflika 190
                                       +erhrHr+evnp+   ele+agl++++   dde++mei e+++   f+++QFHPE++s+p++p+++f++l+ka
  gi|242399336|ref|YP_002994760.1| 465 YERHRHRWEVNPDfinELEKAGLVFSGIAGDDERRMEILELPDkHyFIATQFHPEFKSRPMNPAPVFKGLVKA 537
                                       *******************************************769***********************9985 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.52   1.6e+03      45      94 ..     131     181 ..     107     188 .. 0.70
   2 ?    1.6   0.0     0.067     2e+02      49      67 ..     345     363 ..     303     367 .. 0.82
   3 !   23.3   0.0   1.5e-08   4.6e-05      95     216 .]     373     519 ..     365     519 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.52
                     Peptidase_C26  45 ieedeedvkaildkldglll.tGgq..dvePslygeepsekeeeadpeRdale 94 
                                       ++e +e v++i d+ d +++  Gg   d+e + + e+   ++ + +++Rd + 
  gi|242399336|ref|YP_002994760.1| 131 TNEIKERVRKIADEYDVVVVeIGGTvgDIESMPFLEA--ARQMQLEEGRDNVA 181
                                       3445788999999999888734666677777777777..66777777777765 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.067
                     Peptidase_C26  49 eedvkaildkldgllltGg 67 
                                       e++  ++l+++dg++++Gg
  gi|242399336|ref|YP_002994760.1| 345 EKEGVKLLENVDGIIVPGG 363
                                       4555689***********9 PP

  == domain 3  score: 23.3 bits;  conditional E-value: 1.5e-08
                     Peptidase_C26  95 laLiraalergvPilgiCrGlqllnvalG.......Gtlyqdieeqsgltdhrehe...............q..... 144
                                       ++ ++ a e+++P lgiC G+ql  v +        G   ++i+          h+               +     
  gi|242399336|ref|YP_002994760.1| 373 IMAVKYARENNIPFLGICFGFQLTVVEFArhvlgfkGANSTEIDP---------HTpypiidlmeeqrdldKlggtm 440
                                       566788999**************9997641111122444444443.........11223444444445555155556 PP

                     Peptidase_C26 145 saashavkvekgsllaellgseeievnslHhqaike........laeelrveAvaeDgviEaieseeakafvlgvQw 213
                                          +  +k++k++l ++l+ +e i     H+  ++          +  +  +A ++   +E +e+++++  +++ Q+
  gi|242399336|ref|YP_002994760.1| 441 RLGAYPIKIKKDTLAHKLYAKELIYERHRHRWEVNPdfinelekAGLVFSGIAGDDERRMEILELPDKH-YFIATQF 516
                                       88899**************8777777777777666555555422444444455566678********66.899**** PP

                     Peptidase_C26 214 HPE 216
                                       HPE
  gi|242399336|ref|YP_002994760.1| 517 HPE 519
                                       **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 ?   12.5   0.0   3.8e-05      0.11       8      43 ..      25      60 ..      17     309 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.8e-05
                                      TTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCC CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  8 GGvGKTtlaanLaralarrglrVllvDaDpqannla 43
                                      +G GK  ++a+L+ +++ rgl++  ++ Dp  n +a
  gi|242399336|ref|YP_002994760.1| 25 SGLGKGITSASLGMLMKSRGLKTTNIKIDPYLNYDA 60
                                      99****************************987766 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.2   0.00017      0.51      12     125 ..      26     152 ..      14     168 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00017
                            AAA_31  12 GvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgiekneiektlyev.............lieeknikeaiik 75 
                                       G GK  ts  l++ + ++g k+  + +Dp  n   g+    ++ e  +++              +++++ + +  i+
  gi|242399336|ref|YP_002994760.1|  26 GLGKGITSASLGMLMKSRGLKTTNIKIDPYLNYDAGTMSPYQHGEVFVLDDggevdldlgnyerFLNTSLTFDHNIT 102
                                       88******************************998665544443332222222211111111111112212222221 PP

                            AAA_31  76 tkvenldlipssidLaeaeielvelekk..............eeilkellekvkdeYDyiiiDc 125
                                       t     ++i  +               +              ++ +ke ++k+ deYD++++ +
  gi|242399336|ref|YP_002994760.1| 103 TGKVYSTVIEKER--------------RgdylgatvqviphiTNEIKERVRKIADEYDVVVVEI 152
                                       2222223333333..............2222222222233335557899999999999998765 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 ?   -1.1   0.0      0.47   1.4e+03      55      72 ..     139     156 ..     103     181 .. 0.69
   2 ?    9.6   0.0   0.00025      0.74      60     107 ..     353     396 ..     342     402 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.47
                                       GGCTCCG-SEEEE.--BHH CS
                         DJ-1_PfpI  55 ddvkaaeyDalvl.pGGra 72 
                                        +++ +eyD++v+ +GG+ 
  gi|242399336|ref|YP_002994760.1| 139 RKIA-DEYDVVVVeIGGTV 156
                                       4544.45999998567766 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00025
                                       CG-SEEEE--BHHHHHHHHTSHHHHHHHHHHHHTT-EEEEETTTHHHH CS
                         DJ-1_PfpI  60 aeyDalvlpGGragperlrenekvvelvkefaekgklvaaICagpqlL 107
                                       ++ D +++pGG       r +e  +  vk + e++ ++  IC g ql 
  gi|242399336|ref|YP_002994760.1| 353 ENVDGIIVPGGFG----ARGSEGKIMAVKYARENNIPFLGICFGFQLT 396
                                       578**********....7777888999****************98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (544 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); 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: 0.61u 0.23s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 3697.23
//
Query:       gi|242399337|ref|YP_002994761.1|  [L=298]
Description: hypothetical protein TSIB_1360 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1021  (0.0569468); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 1934.95
//
Query:       gi|242399338|ref|YP_002994762.1|  [L=344]
Description: cysteine synthase [Thermococcus sibiricus MM 739]
Scores for complete 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-72  243.4   0.0    3.8e-72  243.2   0.0    1.0  1  PALP      Pyridoxal-phosphate dependent enzyme
    0.00027   21.0   0.0    0.00054   20.0   0.0    1.4  1  ABM       Antibiotic biosynthesis monooxygenase


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 !  243.2   0.0   4.3e-76   3.8e-72       4     294 .]      16     313 ..      14     313 .. 0.94

  Alignments for each domain:
  == domain 1  score: 243.2 bits;  conditional E-value: 4.3e-76
                                       CSSS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHHHHTT...TTTSEEEEEBSSHHHHHHHHHHHHH CS
                              PALP   4 gigpTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllarlkeg...tgaktvveassGNhgralAaaaall 77 
                                        ig+TP+vrl ++ k++  ++++K+E++nptgS+KdR a+y++++++++   ++++t++ a++GN+g+a Aa ++ +
  gi|242399338|ref|YP_002994762.1|  16 LIGDTPIVRLSKIDKDYPFEIWAKCEFMNPTGSVKDRMAYYMIKEAEKQgklKPGMTIAIATTGNTGIAFAAWGSYF 92 
                                       589******************************************66666*************************** PP

                                       T-EEEEEEETTS-HHHHHHHHHTT-EEEEE...CCHHHHHHHHHHHHHHH.STTCEE--TTTSHHHHHH.HHTHHHH CS
                              PALP  78 GlkvtivvpadaspekvallrllGaevvev...ggdydeavaaaaelaae.gegaylvsqfdnptvieg.ygtiglE 149
                                       G++v iv+p+ +s e+++l  l+Ga+++ +   ++d + a+++a++l++e  +++++++q+d+++++ + y+t+g E
  gi|242399338|ref|YP_002994762.1|  93 GYDVLIVMPEEMSYERKLLDMLFGAKLIYTpggESDAMGALEYAKKLEKEnPDKYVVLDQWDDEANFKAhYETTGRE 169
                                       ******************************6444447777888******978889999******************* PP

                                       HHHHTT.TTEEEEEEE-SSSHHHHHHHHHHHHHSTT-EEEEEEECTTCGGTTCCS..S.SS..B.SSS.CCSTCSCG CS
                              PALP 150 ileqlg.gkpdavvvpvGgGgliaGiaaglkerrpdvrvigvepegsdalarslragrrvtvpvsdtiadglavgsp 225
                                       i+eqlg ++++ +v++vG+Gg++ Gia+ lk+++p +   g ep+++++  + ++ g+   +   ++ ++g++ g  
  gi|242399338|ref|YP_002994762.1| 170 IIEQLGaENIKGFVAGVGSGGTLVGIAKRLKDANPRIITAGMEPAECPTAEGWFKSGELGAWG--RHEVEGIGDG-F 243
                                       ***********************************99999**************777665544..9*********.7 PP

                                       TTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHH.HHHHHHCCTTCEEEEEEE-B CS
                              PALP 226 selafelldrlvdeivtvsdeealeamrllarregivvepssaaalaal.klreagelkegdrvvviltg 294
                                        +  +e +++++d+ vtvs++ea+e++r+ arre + v+ ss+a++ a+ kl+e+ +++egdrvv+il++
  gi|242399338|ref|YP_002994762.1| 244 VPSLVEKYKQYIDDWVTVSSDEAIEMARRIARREALGVGISSGANVVAAiKLAERHNFGEGDRVVTILPD 313
                                       77778899***********************************************************986 PP

>> ABM  Antibiotic biosynthesis monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   6.1e-08   0.00054      35      69 ..     131     165 ..     123     172 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 6.1e-08
                                       TEEEEEEEEEETSTTEEEEEEEESSHHHHHHHHTS CS
                               ABM  35 GclgyellrstedpdevvvieeWeseaaleahlks 69 
                                       G l+y+  +++e+pd++vv+ +W++ea ++ah ++
  gi|242399338|ref|YP_002994762.1| 131 GALEYAKKLEKENPDKYVVLDQWDDEANFKAHYET 165
                                       66777777899*********************766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 2236.23
//
Query:       gi|242399339|ref|YP_002994763.1|  [L=183]
Description: agmatinase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-38  131.5   0.0    5.3e-38  131.1   0.0    1.1  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 !  131.1   0.0     3e-42   5.3e-38     143     277 ..       7     140 ..       3     142 .. 0.94

  Alignments for each domain:
  == domain 1  score: 131.1 bits;  conditional E-value: 3e-42
                                       HHTSECGCEEEEEEE-STCSH..HHHHHHHTTSEEEEHHHHHHHHHHHHHHHHHHHHTCTTSEEEEEEEGGGBBTTT CS
                          Arginase 143 eegllkpkklvqiGirsvdne..eyelakelgirvitmreidelglkavveeilervgaeedpvylSfDiDvlDpav 217
                                       eegl  +++++qiG r+ +++  e + a+elg++++t++e+ +lg+++v+++i+ervg    +v+++fDiD++D a+
  gi|242399339|ref|YP_002994763.1|   7 EEGLFLTEHSIQIGKRGSTYSkdEIDKARELGFEIVTAEEMFKLGIDKVAQMIQERVG--YVKVFVTFDIDFIDSAY 81 
                                       67888899********999997788888*****************************8..78*************** PP

                                       STSSSS-BSS-B-HHHHHHHHHH.HHCHSEEEEEEEE-B-GGGSSTTTHHHHHHHHHHHHH CS
                          Arginase 218 aPGtGtpepgGltlrellallre.laeklnlvgaDvvEvnPaldteaeqtarlaarlvrel 277
                                       aPGtGtpe+gG t+re+l+l+r+ l++ ln++g+D+vEv P++d+ + +ta+la+++v+e+
  gi|242399339|ref|YP_002994763.1|  82 APGTGTPEVGGPTSREALELIRKgLKG-LNFAGFDLVEVYPQYDP-GFITALLAVNIVFEF 140
                                       ***********************9999.*****************.77***********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1276.23
//
Query:       gi|242399340|ref|YP_002994764.1|  [L=133]
Description: 30S ribosomal protein S8e [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-32  113.2   4.6    1.2e-32  112.9   4.6    1.0  1  Ribosomal_S8e  Ribosomal protein S8e


Domain annotation for each model (and alignments):
>> Ribosomal_S8e  Ribosomal protein S8e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.9   4.6   6.7e-37   1.2e-32       3     137 .]       5     128 ..       3     128 .. 0.96

  Alignments for each domain:
  == domain 1  score: 112.9 bits;  conditional E-value: 6.7e-37
                                       XBXXCCCSEESSTEEXXXSSXXXCCSBXXXXXXXEE..SSHEEEEEEETTCEEEEEEESESEEEEEETTTTEEEEEE CS
                     Ribosomal_S8e   3 isrdskhkrkltGgkakllrkkrkielgrkekatkl..gaervkvvrvrgGkrkkralrlkkanvthpeekvtkklk 77 
                                       + +++++ +k +Gg+    rkkrk elgr+++ t++  ++e  k +r+ gG+rk+r++++ +anv    +++ kk+k
  gi|242399340|ref|YP_002994764.1|   5 AIWQGRSLKKPSGGRIIFTRKKRKRELGREPALTRVveEKEERKIIRTYGGNRKVRLVKTIYANVFE--NGKGKKAK 79 
                                       6799********************************65599************************97..888999** PP

                                       EEEEECSSSTCHHHHTTC--TTEEEEEESHHHHHHHHTTEEEEEEESEHHHHSSEEEEEE CS
                     Ribosomal_S8e  78 IlgVkknpsnneyvrlgvltKgaiievdvseLgevtqsgkvvAqvtsrPgqdGcvnavlL 137
                                       I++V++np+n++yvr++++tKgai+++++++           A vtsrPgqdG+vnavlL
  gi|242399340|ref|YP_002994764.1|  80 IISVVENPANRQYVRRNIVTKGAIVQTEIGK-----------ALVTSRPGQDGVVNAVLL 128
                                       *******************************...........*****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 811.89
//
Query:       gi|242399341|ref|YP_002994765.1|  [L=297]
Description: hypothetical protein TSIB_1364 [Thermococcus sibiricus MM 739]
Scores for complete 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-08   33.8  11.1    3.7e-08   33.3  11.1    1.2  1  DZR             Double zinc ribbon
    6.2e-06   26.9   7.4     0.0071   17.1   0.5    2.7  2  zinc_ribbon_15  zinc-ribbon family
    5.6e-05   22.4  18.6     0.0028   17.0   6.1    2.9  3  zf-ribbon_3     zinc-ribbon domain
    0.00046   19.8  19.8      0.046   13.4   5.5    3.0  2  zinc_ribbon_2   zinc-ribbon domain
     0.0043   15.9   8.3      0.012   14.4   7.9    1.7  2  DUF2207         Predicted membrane protein (DUF2207)
  ------ inclusion threshold ------
      0.014   15.8   1.1      0.028   14.9   1.1    1.4  1  T3SSipB         Type III cell invasion protein SipB
      0.016   15.9   5.0      0.016   15.9   5.0    2.6  2  Occludin_ELL    Occludin homology domain
      0.081   13.3   0.4       0.18   12.2   0.1    1.8  2  Syntaxin_2      Syntaxin-like protein
       0.12   11.5   2.0       0.19   10.8   2.0    1.3  1  DUF2330         Uncharacterized protein conserved in bacteria
       0.13   12.1   2.7       0.22   11.3   2.7    1.4  1  Cys_rich_KTR    Cysteine-rich KTR
       0.14   12.5  11.5       0.41   11.0   6.2    2.3  2  DUF2524         Protein of unknown function (DUF2524)
       0.14   12.6   3.2       0.71   10.3   2.0    2.2  2  Terminase_4     Phage terminase, small subunit
       0.18   11.6   0.1          4    7.3   0.0    2.2  2  Lipase_3        Lipase (class 3)
       0.79    9.8   8.9       0.63   10.1   0.5    2.7  3  HypA            Hydrogenase/urease nickel incorporation, meta
          3    8.3   6.3        4.3    7.8   6.3    1.2  1  AAA_23          AAA domain
        4.3    7.5  16.5         48    4.2  11.0    3.1  2  UPF0547         Uncharacterised protein family UPF0547


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 !   33.3  11.1   3.3e-11   3.7e-08       1      49 []     253     296 ..     253     296 .. 0.99

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 3.3e-11
                               DZR   1 CpqCgeelppdarfCseCgtklkavaaedrCpsCgekvdpearfCpeCG 49 
                                       C +Cg ++++d   C++Cg+klk     ++C +Cg+  +   +fCp+CG
  gi|242399341|ref|YP_002994765.1| 253 CYNCGFPIKDDYLNCPNCGAKLK-----EKCEHCGALKPIHLQFCPYCG 296
                                       9*********************8.....9*******************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 !   17.1   0.5   6.3e-06    0.0071      60      86 .]     245     271 ..     226     271 .. 0.79
   2 !   12.7   1.3   0.00015      0.17      65      86 .]     275     296 ..     272     296 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 6.3e-06
                    zinc_ribbon_15  60 kessekkeCknCgkeveeefkyCpkCg 86 
                                       k+++ +++C nCg  +++++  Cp+Cg
  gi|242399341|ref|YP_002994765.1| 245 KRRIAQNKCYNCGFPIKDDYLNCPNCG 271
                                       3444599*******************9 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00015
                    zinc_ribbon_15  65 kkeCknCgkeveeefkyCpkCg 86 
                                       k++C++Cg+    + ++Cp+Cg
  gi|242399341|ref|YP_002994765.1| 275 KEKCEHCGALKPIHLQFCPYCG 296
                                       579******************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 !   17.0   6.1   2.5e-06    0.0028       4      26 .]     252     274 ..     249     274 .. 0.93
   2 !   11.2   4.6   0.00017      0.19       4      24 ..     266     283 ..     264     284 .. 0.80
   3 !   10.7   4.2   0.00024      0.27       3      24 ..     276     297 .]     274     297 .] 0.90

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.5e-06
                       zf-ribbon_3   4 rCPnCGaplssddnvCpyCGtkl 26 
                                       +C nCG p+++d  +Cp+CG+kl
  gi|242399341|ref|YP_002994765.1| 252 KCYNCGFPIKDDYLNCPNCGAKL 274
                                       799****99***********997 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00017
                       zf-ribbon_3   4 rCPnCGaplssddnvCpyCGt 24 
                                       +CPnCGa+l     +C +CG+
  gi|242399341|ref|YP_002994765.1| 266 NCPNCGAKL---KEKCEHCGA 283
                                       6******74...568999986 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00024
                       zf-ribbon_3   3 vrCPnCGa.plssddnvCpyCGt 24 
                                        +C +CGa +     ++CpyCG+
  gi|242399341|ref|YP_002994765.1| 276 EKCEHCGAlK-PIHLQFCPYCGQ 297
                                       589*****88.99*********5 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   5.5   4.1e-05     0.046       1      23 []     252     274 ..     252     274 .. 0.94
   2 !   11.1   6.1   0.00023      0.25       1      20 [.     277     296 ..     277     297 .] 0.96

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.1e-05
                     zinc_ribbon_2   1 fCpnCGaelqdnakFCpyCGtpl 23 
                                       +C nCG +++d+   Cp+CG++l
  gi|242399341|ref|YP_002994765.1| 252 KCYNCGFPIKDDYLNCPNCGAKL 274
                                       688******************97 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00023
                     zinc_ribbon_2   1 fCpnCGaelqdnakFCpyCG 20 
                                       +C +CGa  +   +FCpyCG
  gi|242399341|ref|YP_002994765.1| 277 KCEHCGALKPIHLQFCPYCG 296
                                       8*******9**********9 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   7.9   1.1e-05     0.012     221     422 ..      17     221 ..       5     239 .. 0.57
   2 ?    3.3   0.4     0.026        29     203     252 ..     205     247 ..     202     252 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.1e-05
                           DUF2207 221 llllllliklllwkkygrepkvkevdpeYerdvPedlsPavvg..ylvkg........dkvdengltAtlldLavkg 287
                                       +lll  + +l+ + +   +p +++ +++Y      +++P++ +  +l+          +k ++n   A  ++L ++ 
  gi|242399341|ref|YP_002994765.1|  17 FLLLASINFLRELENIPQRPDYTYYQEKY------GITPLLENqsRLMELdrelyegyKKAESNLTEAERVYLFKRE 87 
                                       22222222222344466677777777777......677776666666666667777787788888888888888888 PP

                           DUF2207 288 yitieeekkkkkkgkdtltilkkndeeldpyEkalldlLfdkseegkslkeikkyakkskkkakkfkkalkkwksav 364
                                         ++  e+ +  k     ++ +++ +   +yEka l++L  k        +           ++ ++++l+++ s++
  gi|242399341|ref|YP_002994765.1|  88 EYRVALESGNATK-----ELEQEYLKAKEEYEKAYLKYLGAK--------S----------AYDDVHNKLQELSSQI 141
                                       7666666666543.....677777777799999999999922........2..........4444444444444444 PP

                           DUF2207 365 kk...kergyfdkkgkkklkklsalglgliilglilillallllvll...................lvfllilllil 419
                                       ++   k+++ ++++ + ++ k+ +l l++++ +++++ll+l  +  +                    ++  + ++++
  gi|242399341|ref|YP_002994765.1| 142 QElmqKANEEYTRAYQVYRLKVLMLKLAFVLPIFVMSLLLLRKYKNIytssliaysallllyltisAIWNIVHIIGI 218
                                       44333356677777788888888888888777777777665555554888877764444444443322222222222 PP

                           DUF2207 420 lli 422
                                        l+
  gi|242399341|ref|YP_002994765.1| 219 SLF 221
                                       222 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.026
                           DUF2207 203 rlslallillilllilllllllllliklllwkkygrepkvkevdpeYerd 252
                                       ++s +++i+ i+ + l+++++ l++++      y r+  +k+ ++ Y r 
  gi|242399341|ref|YP_002994765.1| 205 TISAIWNIVHIIGISLFGAVATLAALY------YLRKEYFKP-ERVYKRR 247
                                       567788899999999999999999999......777777777.7777775 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 ?   14.9   1.1   2.5e-05     0.028      48      95 ..      99     146 ..      86     159 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.5e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--- CS
                           T3SSipB  48 lqtalseakgatddleaaiekadqaksaadaatkkvdeaqkrlkeLaP 95 
                                        +++ +e  +a++++e+a  k+  aksa+d++++k++e   +++eL  
  gi|242399341|ref|YP_002994765.1|  99 TKELEQEYLKAKEEYEKAYLKYLGAKSAYDDVHNKLQELSSQIQELMQ 146
                                       56667788899**********************************932 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.4       1.4   1.6e+03      34      64 ..      53      66 ..       2      88 .. 0.63
   2 ?   15.9   5.0   1.5e-05     0.016       8      63 ..     104     159 ..      96     166 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.4
                      Occludin_ELL 34 vskkfseLerelkelkegskeykkieeeilq 64
                                       ++++ eL+rel                 ++
  gi|242399341|ref|YP_002994765.1| 53 NQSRLMELDREL-----------------YE 66
                                      333333333333.................33 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1.5e-05
                      Occludin_ELL   8 eqrerYkaeFnkeYkeYkelhaeleevskkfseLerelkelkegskeykkieeeil 63 
                                       +++ + k+e++k Y +Y   ++  ++v +k++eL+++++el ++ +e+ +++ +++
  gi|242399341|ref|YP_002994765.1| 104 QEYLKAKEEYEKAYLKYLGAKSAYDDVHNKLQELSSQIQELMQKANEEYTRAYQVY 159
                                       44555599************************************998777777765 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       7.2     8e+03      73      99 ..      55      81 ..      41      83 .. 0.65
   2 ?   12.2   0.1   0.00016      0.18      17      55 ..     116     154 ..      98     162 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 7.2
                        Syntaxin_2 73 ekLkkdfkealqeFqkiqrqyaekekq 99
                                      ++L++  +e+ + ++k+  + +e+e+ 
  gi|242399341|ref|YP_002994765.1| 55 SRLMELDRELYEGYKKAESNLTEAERV 81
                                      455555555555666666666666665 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00016
                        Syntaxin_2  17 klvkqLgtkkdteelreklhelieeinelikktnellkk 55 
                                        ++k Lg k   +++++kl+el ++i+el +k ne   +
  gi|242399341|ref|YP_002994765.1| 116 AYLKYLGAKSAYDDVHNKLQELSSQIQELMQKANEEYTR 154
                                       57888****************************997665 PP

>> DUF2330  Uncharacterized protein conserved in bacteria (DUF2330)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   2.0   0.00017      0.19     221     298 ..      75     154 ..      63     160 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00017
                           DUF2330 221 aanartvklpenidvpvflkqsnfykalfeeav.akeavkavfveyagdvaaadpcaeeLreltaaweaylTrlhve 296
                                        ++a++v l +  +  v+l+ +n  k+l +e + ake +++   +y g  +a d+  ++L+el+++ ++ + + + e
  gi|242399341|ref|YP_002994765.1|  75 LTEAERVYLFKREEYRVALESGNATKELEQEYLkAKEEYEKAYLKYLGAKSAYDDVHNKLQELSSQIQELMQKANEE 151
                                       56788999999999**************9998736899*****************************9999999888 PP

                           DUF2330 297 i.e 298
                                       + +
  gi|242399341|ref|YP_002994765.1| 152 YtR 154
                                       844 PP

>> Cys_rich_KTR  Cysteine-rich KTR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   2.7    0.0002      0.22       3      34 ..     264     296 ..     262     297 .] 0.90

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0002
                      Cys_rich_KTR   3 WvlcPvCgnkTRlkiredTvLknfpL.fCPKCk 34 
                                       ++ cP Cg+k ++k  +   Lk   L fCP C 
  gi|242399341|ref|YP_002994765.1| 264 YLNCPNCGAKLKEKCEHCGALKPIHLqFCPYCG 296
                                       689*******************98777*****6 PP

>> DUF2524  Protein of unknown function (DUF2524)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.7     0.026        30      16      53 ..      66     102 ..      53     104 .. 0.81
   2 ?   11.0   6.2   0.00037      0.41      12      66 ..     100     154 ..      95     172 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.026
                           DUF2524  16 qaieeaeeqfeeakrqehyndeeYteAqlkLEeavneL 53 
                                       + +++ae++++ea+r+  ++ eeY  A++   +a++eL
  gi|242399341|ref|YP_002994765.1|  66 EGYKKAESNLTEAERVYLFKREEYRVALES-GNATKEL 102
                                       56899*******************998754.4555555 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00037
                           DUF2524  12 qkceqaieeaeeqfeeakrqehyndeeYteAqlkLEeavneLeklaksandqQre 66 
                                       +  eq + +a+e++e+a  +    +++Y +  +kL e++ ++++l+++an++   
  gi|242399341|ref|YP_002994765.1| 100 KELEQEYLKAKEEYEKAYLKYLGAKSAYDDVHNKLQELSSQIQELMQKANEEYTR 154
                                       67799999******************************************99654 PP

>> Terminase_4  Phage terminase, small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   2.0   0.00064      0.71       8      79 ..      47     121 ..      45     151 .. 0.71
   2 ?    1.5   0.1      0.36     4e+02       1      37 [.     123     160 ..     123     167 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00064
                       Terminase_4   8 iikeLdelgilseldseaLaayceayaryreaekki..ekeGvtittaegeg.akkknpavtilnsaekelrkla 79 
                                       i++ L++++ l eld+e+ ++y +a ++  eae+ +  ++e + +  ++g+  ++ ++ ++++++++ek ++k++
  gi|242399341|ref|YP_002994765.1|  47 ITPLLENQSRLMELDRELYEGYKKAESNLTEAERVYlfKREEYRVALESGNAtKELEQEYLKAKEEYEKAYLKYL 121
                                       899****************************99887663333333333333344445555556666666555554 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.36
                       Terminase_4   1 AkkeWkriikeLdelgi.lseldseaLaayceayaryr 37 
                                       Ak  ++ + ++L+el+  ++el ++a + y  ay+ yr
  gi|242399341|ref|YP_002994765.1| 123 AKSAYDDVHNKLQELSSqIQELMQKANEEYTRAYQVYR 160
                                       78888899999999876689999999999999998886 PP

>> Lipase_3  Lipase (class 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.2      0.13   1.5e+02      34      64 ..     112     143 ..      65     159 .. 0.70
   2 ?    7.3   0.0    0.0036         4      68      97 ..     214     243 ..     185     261 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.13
                                       EEEHHHHHHHH.....S-HHHHHHHHHHHHHHHTT- CS
                          Lipase_3  34 kvhsgfleaye.....eslreqvlkelkrllekype 64 
                                       + ++ +          +s++++v+++l++l ++ +e
  gi|242399341|ref|YP_002994765.1| 112 EYEKAY----LkylgaKSAYDDVHNKLQELSSQIQE 143
                                       333333....24444778889999999888887664 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0036
                                       EEEEETHHHHHHHHHHHHHHHTT-SS---E CS
                          Lipase_3  68 vvtGHSLGgalAlLaaldlvengenekkkv 97 
                                        + G SL ga+A+Laal++ +++  + ++v
  gi|242399341|ref|YP_002994765.1| 214 HIIGISLFGAVATLAALYYLRKEYFKPERV 243
                                       57899************9999998864443 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       2.9   3.2e+03      10      39 ..     141     171 ..     130     196 .. 0.64
   2 ?   10.1   0.5   0.00056      0.63      66      95 ..     246     273 ..     205     276 .. 0.82
   3 ?    4.5   1.3     0.031        35      70      94 ..     275     297 .]     272     297 .] 0.73

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.9
                                       HHHHHHHHHCC.TT..EEEEEEEEEETTCT- CS
                              HypA  10 ivevveeeake.aaarkvtkvkvevGelsgv 39 
                                       i e+++++ +e ++a +v ++kv + +l+ v
  gi|242399341|ref|YP_002994765.1| 141 IQELMQKANEEyTRAYQVYRLKVLMLKLAFV 171
                                       3333333334445566777777766666655 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00056
                                       EE--EEEETTTS-EEECHHHHHS-TTTSSS CS
                              HypA  66 evpvkvrCreCgkefeleekalrCpkCgsa 95 
                                       +  ++ +C +Cg  ++ +   l+Cp+Cg++
  gi|242399341|ref|YP_002994765.1| 246 RRIAQNKCYNCGFPIKDD--YLNCPNCGAK 273
                                       5567889*****666544..689****985 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.031
                                       EEEETTTS-EEECHHHHHS-TTTSS CS
                              HypA  70 kvrCreCgkefeleekalrCpkCgs 94 
                                       k +C++Cg+   ++ +   Cp Cg+
  gi|242399341|ref|YP_002994765.1| 275 KEKCEHCGALKPIHLQ--FCPYCGQ 297
                                       668*****76666534..5****95 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   6.3    0.0038       4.3     153     198 ..      66     147 ..      18     149 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0038
                            AAA_23 153 e..................rleelekeleeledekkllekleqekekek..................eleeleeele 193
                                       e                  + ee++ +le  +++k+l ++ +++ke+ +                  +l+el ++++
  gi|242399341|ref|YP_002994765.1|  66 EgykkaesnlteaervylfKREEYRVALESGNATKELEQEYLKAKEEYEkaylkylgaksayddvhnKLQELSSQIQ 142
                                       133333345555667888899**********99999999997777766669999******99999999999999999 PP

                            AAA_23 194 eilke 198
                                       e++++
  gi|242399341|ref|YP_002994765.1| 143 ELMQK 147
                                       99997 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.2      0.89     1e+03      14      22 ..     250     258 ..     248     259 .. 0.79
   2 ?    4.2  11.0     0.043        48       2      21 ..     266     296 ..     266     296 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.89
                           UPF0547  14 aqfCphCGy 22 
                                         +C  CG+
  gi|242399341|ref|YP_002994765.1| 250 QNKCYNCGF 258
                                       568999**8 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.043
                           UPF0547   2 vCPeCeakvPvaaqfC...........phCG 21 
                                       +CP C ak+++ ++ C           p+CG
  gi|242399341|ref|YP_002994765.1| 266 NCPNCGAKLKEKCEHCgalkpihlqfcPYCG 296
                                       7**********99999999999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2370  (0.132188); expected 358.6 (0.02)
Passed bias filter:                     1016  (0.056668); expected 358.6 (0.02)
Passed Vit filter:                       179  (0.00998383); 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):              16  [number of targets reported over threshold]
# CPU time: 0.76u 0.39s 00:00:01.14 Elapsed: 00:00:00.57
# Mc/sec: 1578.89
//
Query:       gi|242399342|ref|YP_002994766.1|  [L=351]
Description: GTPase, containing NOG1 domain [Thermococcus sibiricus MM 739]
Scores for complete 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-52  176.2   1.3    8.3e-52  175.4   1.3    1.4  1  NOG1_N        NOG1 N-terminal helical domain
    3.9e-25   87.4   0.0    8.8e-25   86.3   0.0    1.6  1  NOG1          Nucleolar GTP-binding protein 1 (NOG1)
    4.2e-21   75.1   0.0      1e-20   73.9   0.0    1.6  1  MMR_HSR1      50S ribosome-binding GTPase
    2.1e-18   66.3   0.0    3.2e-18   65.8   0.0    1.3  1  FeoB_N        Ferrous iron transport protein B
      2e-08   34.3   0.1      0.004   17.1   0.0    2.8  2  RsgA_GTPase   RsgA GTPase
    1.7e-05   24.8   0.0    0.00017   21.6   0.0    2.3  2  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
    6.5e-05   22.5   0.2       0.17   11.4   0.0    3.3  3  GTP_EFTU      Elongation factor Tu GTP binding domain
    6.7e-05   22.4   0.0       0.11   12.0   0.0    2.4  2  Arf           ADP-ribosylation factor family
    7.3e-05   22.4   0.0    0.00058   19.5   0.0    2.1  1  Ras           Ras family
     0.0001   22.0   0.3     0.0034   17.1   0.2    2.8  2  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
     0.0017   18.0   0.0       0.93    9.1   0.0    2.2  2  cobW          CobW/HypB/UreG, nucleotide-binding domain
     0.0053   16.0   0.2      0.094   11.9   0.1    2.3  2  G-alpha       G-protein alpha subunit
     0.0063   16.3   0.0       0.45   10.3   0.0    2.6  2  ATP_bind_1    Conserved hypothetical ATP binding protein
  ------ inclusion threshold ------
      0.012   15.9   0.0       0.12   12.6   0.0    2.3  1  Roc           Ras of Complex, Roc, domain of DAPkinase
      0.014   16.0   0.0       0.07   13.7   0.0    2.2  2  AAA_18        AAA domain
      0.018   15.1   0.1        5.6    7.0   0.0    2.8  3  Dynamin_N     Dynamin family
      0.023   15.0   0.0      0.075   13.3   0.0    1.8  1  AAA_22        AAA domain
      0.026   13.8   0.0      0.056   12.8   0.0    1.6  1  AIG1          AIG1 family
      0.042   13.3   0.0      0.076   12.4   0.0    1.5  1  SRPRB         Signal recognition particle receptor beta subun
      0.053   13.8   0.0       0.17   12.1   0.0    1.9  1  AAA_28        AAA domain
      0.061   13.7   0.0       0.14   12.6   0.0    1.7  1  AAA_16        AAA ATPase domain
      0.067   13.1   0.3        1.8    8.4   0.0    2.4  2  ATPase_2      ATPase domain predominantly from Archaea
      0.087   12.2   0.0       0.33   10.3   0.0    2.0  2  TniB          Bacterial TniB protein
       0.12   12.2   1.0       0.39   10.6   0.1    2.4  2  NTPase_1      NTPase
       0.12   11.8   0.0       0.35   10.3   0.0    1.8  2  KTI12         Chromatin associated protein KTI12
       0.16   12.3   0.0        0.3   11.5   0.0    1.4  1  RNA_helicase  RNA helicase
       0.19   10.7   0.7        4.8    6.1   0.0    2.5  3  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea


Domain annotation for each model (and alignments):
>> NOG1_N  NOG1 N-terminal helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.4   1.3   1.3e-54   8.3e-52       1     160 []       5     164 ..       5     164 .. 1.00

  Alignments for each domain:
  == domain 1  score: 175.4 bits;  conditional E-value: 1.3e-54
                            NOG1_N   1 FekiptvptseelidkalrrakraakttkkkkneikrlrnlearkvrtasntlsdkLeeivkkfPnldelhpFyrel 77 
                                       Fek+pt++ ++e+idka+rra++aa++++ ++n i+++r++e+ +vrt+sn+ +d L+++++++P +++l+pFy+el
  gi|242399342|ref|YP_002994766.1|   5 FEKMPTILLADEIIDKAFRRAEKAASAFTPRGNIISKARQREELRVRTVSNVTRDSLRKVLDRTPGVSTLPPFYQEL 81 
                                       9**************************************************************************** PP

                            NOG1_N  78 ldvlvdkdelkksLaqvkwarklirkigkeyvnklkkaddkkeakelrreafgrvasvlkkvdkaldfLedvrkkLr 154
                                       ld+lvdk  ++k+La+++wa k+ir ++++yv+k+++++d+ke+++lrre++grvas+lk ++++l++L+++r  L+
  gi|242399342|ref|YP_002994766.1|  82 LDTLVDKRMFHKALASINWAIKTIRGLEERYVEKIRYSRDPKEIAKLRREFYGRVASILKDINDNLEYLNKARDVLK 158
                                       ***************************************************************************** PP

                            NOG1_N 155 kLpaiD 160
                                       ++p+iD
  gi|242399342|ref|YP_002994766.1| 159 DMPVID 164
                                       *****9 PP

>> NOG1  Nucleolar GTP-binding protein 1 (NOG1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.3   0.0   1.3e-27   8.8e-25       1      58 []     234     291 ..     234     291 .. 0.99

  Alignments for each domain:
  == domain 1  score: 86.3 bits;  conditional E-value: 1.3e-27
                              NOG1   1 eIEkqAiaALkhladavlFllDpseecgysleeQlsLleeikelfankpvivvlnKiD 58 
                                       eIEkqAi+AL+hl ++v++++Dpse cgy++e+Q++L+eei+e+f++ p+ivvlnK+D
  gi|242399342|ref|YP_002994766.1| 234 EIEKQAILALRHLGKLVIYIFDPSEYCGYPIEDQMHLFEEIYEEFGDFPFIVVLNKTD 291
                                       6*******************************************************99 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.9   0.0   1.5e-23     1e-20       2     114 .]     170     289 ..     169     289 .. 0.77

  Alignments for each domain:
  == domain 1  score: 73.9 bits;  conditional E-value: 1.5e-23
                                       EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSS..HHHHHHHHHHHHHHHHCT CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGlie..gaseekglgkaflaleea 76 
                                       ++i+G+pNvGKStL+++lt++k +v+ +p+tT+ in g+++++  +++++DtpGl++   +++++ +++a+lal+  
  gi|242399342|ref|YP_002994766.1| 170 IVIAGHPNVGKSTLLRKLTNAKPEVATYPFTTKGINVGQFEEHWLKYQVIDTPGLLDrpISERNEIEKQAILALRHL 246
                                       89**************************************966699********98644344455789999999985 PP

                                       .SEEEEEEETT....TTCSHHHHHHHHHHHHH.TTSEEEEEEES CS
                          MMR_HSR1  77 .dlillvvdas....eeklkpldeeleellee.akkplilvlnk 114
                                        +l+++++d s       ++++ + +ee+ ee  + p+i+vlnk
  gi|242399342|ref|YP_002994766.1| 247 gKLVIYIFDPSeycgY-PIEDQMHLFEEIYEEfGDFPFIVVLNK 289
                                       5********7744430.233333333444333566789999998 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 !   65.8   0.0   4.8e-21   3.2e-18       2     156 .]     169     330 ..     168     330 .. 0.88

  Alignments for each domain:
  == domain 1  score: 65.8 bits;  conditional E-value: 4.8e-21
                                       EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHHHHHHHHHH..C CS
                            FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYslsayseeekvardfll..e 76 
                                       t++++G pnvGk+tl+ +lt+ak +v+ +p +t   + g+++ +  +++++D PG  +  ++se +++ ++ +l  +
  gi|242399342|ref|YP_002994766.1| 169 TIVIAGHPNVGKSTLLRKLTNAKPEVATYPFTTKGINVGQFEEHWLKYQVIDTPGLLD-RPISERNEIEKQAILalR 244
                                       699***************************************888**********987.789999999999998445 PP

                                       TSSSEEEEEEEGGG.....HHHHHHHHHHHHHT..TSSEEEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTTT CS
                            FeoB_N  77 eepdvvvnvvdatn.....lernLyLtlqllel..gvpvvlalnmideaekkgieidlkkLsekLgvpvvktsakkk 146
                                       +  ++v+ + d ++     +e +++L+ ++ e   + p++++ln++d a++++i+  ++ L+ + g++ ++++a+k+
  gi|242399342|ref|YP_002994766.1| 245 HLGKLVIYIFDPSEycgypIEDQMHLFEEIYEEfgDFPFIVVLNKTDIASEDKIRKVEEFLQ-RRGIKSLRIAAEKG 320
                                       5679*******875444559**********9843359****************996666665.56************ PP

                                       BTHHHHHHHH CS
                            FeoB_N 147 egieellkai 156
                                        gi+el++++
  gi|242399342|ref|YP_002994766.1| 321 IGIDELKSKV 330
                                       ******9875 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   4.7e-05     0.031      97     161 ..     165     224 ..     129     228 .. 0.65
   2 !   17.1   0.0   6.1e-06     0.004      47      97 ..     281     330 ..     274     335 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.7e-05
                                       CTTSEEEEECSTTSSHHHHHHHHCTT-.----S--------------SEEEEEETTTEEEESS-SS CS
                       RsgA_GTPase  97 lkdktsvlvGqSGvGKStLinallpel.elktgevseklgrGkhTTtavellelaegglliDtPGf 161
                                       l+  t+v++G+  vGKStL+ +l++ + e++t        +G +  +  e      +  +iDtPG+
  gi|242399342|ref|YP_002994766.1| 165 LTLPTIVIAGHPNVGKSTLLRKLTNAKpEVATYPFT---TKGINVGQFEEHWL---KYQVIDTPGL 224
                                       555789*****************9962144443332...33444444333222...2347777775 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 6.1e-06
                                       -EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHC CS
                       RsgA_GTPase  47 iepvivlnKiDlleeeeeleelkeelealgyevllvsaktkegleelkell 97 
                                        + ++vlnK+D+++e++ +++++e l++ g++ l + a+++ g++elk+++
  gi|242399342|ref|YP_002994766.1| 281 FPFIVVLNKTDIASEDK-IRKVEEFLQRRGIKSLRIAAEKGIGIDELKSKV 330
                                       56799************.*****************************9876 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 ?    0.2   0.0       1.2   7.7e+02      43      63 ..      79      99 ..      72     126 .. 0.87
   2 !   21.6   0.0   2.6e-07   0.00017      57     102 ..     282     332 ..     269     335 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.2
                      MMR_HSR1_Xtn 43 DdlidviegnrvYipclyvlN 63
                                      ++l d++ ++r++ ++l  +N
  gi|242399342|ref|YP_002994766.1| 79 QELLDTLVDKRMFHKALASIN 99
                                      5899************99998 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 2.6e-07
                      MMR_HSR1_Xtn  57 pclyvlNKiDlisleeldelare.....pnsvviSaekelnldeLkekiwe 102
                                       p ++vlNK+D +s+++++++++       +s+ i+aek++++deLk+k+ e
  gi|242399342|ref|YP_002994766.1| 282 PFIVVLNKTDIASEDKIRKVEEFlqrrgIKSLRIAAEKGIGIDELKSKVIE 332
                                       889***************999944454459999*************99866 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 !   11.4   0.0   0.00026      0.17       5      28 ..     169     192 ..     166     202 .. 0.86
   2 ?    1.5   0.0      0.29   1.9e+02      62      79 ..     208     223 ..     199     226 .. 0.73
   3 ?    5.4   0.0     0.017        12     123     149 ..     281     308 ..     269     339 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00026
                                       EEEEEESTTSSHHHHHHHHHHHTT CS
                          GTP_EFTU   5 nigiighvDhGKtTLtdrLlyktg 28 
                                       +i+i+gh + GK+TL+ +L+ ++ 
  gi|242399342|ref|YP_002994766.1| 169 TIVIAGHPNVGKSTLLRKLTNAKP 192
                                       799***************997665 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.29
                                       EEETTCSSEEEEEEEESS CS
                          GTP_EFTU  62 sleketkkylinliDtPG 79 
                                       ++e  ++  ++++iDtPG
  gi|242399342|ref|YP_002994766.1| 208 QFE--EHWLKYQVIDTPG 223
                                       555..7778999****** PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.017
                                       TEEEEEEESCGST.HHHHHHHHHHHHHH CS
                          GTP_EFTU 123 vpiivfiNKmDrl.kaelkeiveevkqk 149
                                        p+iv++NK D + +++++++ e ++++
  gi|242399342|ref|YP_002994766.1| 281 FPFIVVLNKTDIAsEDKIRKVEEFLQRR 308
                                       689********99555566655555544 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   0.00016      0.11      17      67 ..     170     223 ..     156     229 .. 0.85
   2 !    8.0   0.0    0.0027       1.8     111     147 ..     276     312 ..     247     335 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00016
                                       EEEEESTTSSHHHHHHHHHHSS.CEECSS..SSSEEEEEEEETTEEEEEEEE-S CS
                               Arf  17 illlGLDnaGKtTilkklklee.lvttvP..TigfnveeleiknlkftvwDvGG 67 
                                       i++ G  n GK+T+l kl++ +  v t P  T g nv + e + lk++v D  G
  gi|242399342|ref|YP_002994766.1| 170 IVIAGHPNVGKSTLLRKLTNAKpEVATYPftTKGINVGQFEEHWLKYQVIDTPG 223
                                       899999************876525667776699*******99999999999655 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0027
                                       GCCTTSEEEEEEE-TTSTTSS-HHHHHHHTTGGGSSS CS
                               Arf 111 eelkevallvlaNKqDlpealseeelrellgleelkg 147
                                       ee  + +++v+ NK D+++  + ++++e l+ + +k+
  gi|242399342|ref|YP_002994766.1| 276 EEFGDFPFIVVLNKTDIASEDKIRKVEEFLQRRGIKS 312
                                       677899**********************999999883 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   8.8e-07   0.00058       2     158 ..     170     332 ..     169     336 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 8.8e-07
                                       EEEEESTTSSHHHHHHHHHHSSCSSSCTTTSSEEEEEEEEEETTEEEEEEEEEETT......SGGGHHHHHHHH... CS
                               Ras   2 lvlvGdsavGKtslllrfvkdkFkeeyesTigvdfytkeievdgkevkleiwDTAG......qeefkslrelyy... 69 
                                       +v+ G  +vGK++ll + ++ k +    +     + ++  +++++ +k ++ DT G       e+ ++++++ +   
  gi|242399342|ref|YP_002994766.1| 170 IVIAGHPNVGKSTLLRKLTNAKPEVATYPFT--TKGINVGQFEEHWLKYQVIDTPGlldrpiSER-NEIEKQAIlal 243
                                       7999*************99987554433322..23444445569999*********554443233.33333333111 PP

                                       TT.ESEEEEEEETTBHHHH..HTHHHHHHHHHHHSTTTSEEEEEEETTTGGGG-SS-HHHHHHHHHHHTSEEEEEBT CS
                               Ras  70 rd.aegillvyditsresf..envkkwveeikrvaeenvpivLvGnKvDleekravsteegeelakelglkfletSA 143
                                       r+ ++ ++ ++d ++   +  e+  +++eei +    ++p+++v nK+D++++ ++++  +ee+ ++ g+k l ++A
  gi|242399342|ref|YP_002994766.1| 244 RHlGKLVIYIFDPSEYCGYpiEDQMHLFEEIYEEFG-DFPFIVVLNKTDIASEDKIRK--VEEFLQRRGIKSLRIAA 317
                                       321344555666666666633555689999999999.5**************999976..669************** PP

                                       TTTCTHHHHHHHHHH CS
                               Ras 144 ktnenveeafeellr 158
                                       ++  +++e+  ++++
  gi|242399342|ref|YP_002994766.1| 318 EKGIGIDELKSKVIE 332
                                       ******998877776 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       3.6   2.4e+03      48     115 ..      86     157 ..      77     162 .. 0.59
   2 !   17.1   0.2   5.1e-06    0.0034       4     139 ..     170     328 ..     168     332 .. 0.64

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 3.6
                         PduV-EutP  48 lenrklysalivtsaeadvialvqdateeesvfp..pgfasvfnkeviGiitki..dlaedeenieaveelL 115
                                       +++r + +al+++    + i  + +   e+  ++  p+  + +++e  G +  i  d+ ++ e ++++++ L
  gi|242399342|ref|YP_002994766.1|  86 VDKRMFHKALASINWAIKTIRGLEERYVEKIRYSrdPKEIAKLRREFYGRVASIlkDINDNLEYLNKARDVL 157
                                       567777777777777777777666666555555522344455666666666655445555555555555555 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 5.1e-06
                         PduV-EutP   4 illiGkvgsGKttLtqalkg...eelkYk.ktqaie........fsdeviDtPGey...lenrkl..ysalivtsae 63 
                                       i++ G+ ++GK tL ++l++   e  +Y   t+ i+        ++ +viDtPG     + +r+    +a+ ++ + 
  gi|242399342|ref|YP_002994766.1| 170 IVIAGHPNVGKSTLLRKLTNakpEVATYPfTTKGINvgqfeehwLKYQVIDTPGLLdrpISERNEieKQAILALRHL 246
                                       56677777888888888877555334453133334311111111345678888854223444443113455555556 PP

                         PduV-EutP  64 advialvqd........ateeesvfppgfasvfnkeviGiitkidlaedeenieaveelLksaGaekifevsaveke 132
                                        +++  + d        +++++++f + + ++   + i ++ k+d+a +e++i++vee+L+  G+++  ++ a + +
  gi|242399342|ref|YP_002994766.1| 247 GKLVIYIFDpseycgypIEDQMHLFEEIYEEFGDFPFIVVLNKTDIA-SEDKIRKVEEFLQRRGIKS-LRIAAEKGI 321
                                       666666655111111113457788888888888999***********.99***************87.69******* PP

                         PduV-EutP 133 gieellk 139
                                       gi+el++
  gi|242399342|ref|YP_002994766.1| 322 GIDELKS 328
                                       ****986 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.0    0.0069       4.6       1      24 [.     168     191 ..     168     196 .. 0.86
   2 !    9.1   0.0    0.0014      0.93     107     167 ..     242     306 ..     204     312 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0069
                                       EEEEEEESTTCCHHHHHHHHHCT- CS
                              cobW   1 pvtvltGflGsGKTtLlnhllenr 24 
                                       p++v++G +  GK+tLl++l++ +
  gi|242399342|ref|YP_002994766.1| 168 PTIVIAGHPNVGKSTLLRKLTNAK 191
                                       689****************99654 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0014
                                       HHCCCECEEEEEEETTTH......CCHCCHHHHHHHHHHTSSEEEEE-HHHHCHC..HHHHHHHHH CS
                              cobW 107 ksdltldavvavvDaknl.....eaeeekieekaedqlaaadllvlnKtDlldeeallekleerlr 167
                                       + +   + v+++ D +++     e++ +  ee +e+   +  ++vlnKtD ++e++ ++k+ee l+
  gi|242399342|ref|YP_002994766.1| 242 ALRHLGKLVIYIFDPSEYcgypiEDQMHLFEEIYEEFGDFPFIVVLNKTDIASEDK-IRKVEEFLQ 306
                                       3456667899999999999999877788888888888889999**********995.488887665 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.18   1.2e+02      19      44 ..     151     188 ..     135     197 .. 0.70
   2 !   11.9   0.1   0.00014     0.094     251     289 ..     264     301 ..     200     343 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.18
                                       XE..EE............EEEEEESTTSSHHHHHHHHH CS
                           G-alpha  19 kkkrev............kllllGqseSGKsTilkqlk 44 
                                       +k+r+v            ++++ G+   GKsT+l++l 
  gi|242399342|ref|YP_002994766.1| 151 NKARDVlkdmpvidltlpTIVIAGHPNVGKSTLLRKLT 188
                                       44444444445567777789999***********9986 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00014
                                       HHHHHHHHHCCCC-GGGTTSEEEEEEE-HHHHHH.HCCCS CS
                           G-alpha 251 leeslklFkeicnnkllkntpiiLflnKlDilee.Klkkg 289
                                       +e+ ++lF+ei +  ++ + p+i++lnK+Di +e K++k+
  gi|242399342|ref|YP_002994766.1| 264 IEDQMHLFEEIYE--EFGDFPFIVVLNKTDIASEdKIRKV 301
                                       45669******99..8**************9754266655 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 ?    3.2   0.0     0.095        63       1      22 [.     172     193 ..     172     200 .. 0.86
   2 !   10.3   0.0   0.00067      0.45     156     186 ..     280     310 ..     204     347 .. 0.65

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.095
                        ATP_bind_1   1 vvGpaGsGKttfvgalseilel 22 
                                       ++G++ +GK+t+ ++l++  ++
  gi|242399342|ref|YP_002994766.1| 172 IAGHPNVGKSTLLRKLTNAKPE 193
                                       68************99987665 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00067
                        ATP_bind_1 156 elPhvvvlnkfDllkeklekeleffedveal 186
                                       + P++vvlnk+D+++e++ +++e f +   +
  gi|242399342|ref|YP_002994766.1| 280 DFPFIVVLNKTDIASEDKIRKVEEFLQRRGI 310
                                       68***********998866666666544333 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 ?   12.6   0.0   0.00018      0.12       2      37 ..     170     207 ..     169     292 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00018
                                       EEEESSTTSSHHHHHHCHCT-CCC-EE..ETTTTEEEE CS
                               Roc   2 vvlvGdsgvGKtsllkrfvedkfseke..kstigvdfl 37 
                                       +v+ G  +vGK++ll+++++ k +  +   +t g+++ 
  gi|242399342|ref|YP_002994766.1| 170 IVIAGHPNVGKSTLLRKLTNAKPEVATypFTTKGINVG 207
                                       899****************8776533301334444443 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       4.8   3.2e+03      36      69 ..     115     145 ..     109     163 .. 0.71
   2 ?   13.7   0.0   0.00011      0.07       1      27 [.     170     205 ..     170     241 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 4.8
                            AAA_18  36 glllevdpealdeskrldedkldklldaleenss 69 
                                        +++++dp+   e  +l++++  ++ ++l+ +++
  gi|242399342|ref|YP_002994766.1| 115 KIRYSRDPK---EIAKLRREFYGRVASILKDIND 145
                                       567777887...8888888888888888888876 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 0.00011
                            AAA_18   1 IlltGtpGvGKttlakeLskrl.gf........gvn 27 
                                       I+++G p vGK+tl + L +   ++        g+n
  gi|242399342|ref|YP_002994766.1| 170 IVIAGHPNVGKSTLLRKLTNAKpEVatypfttkGIN 205
                                       99****************665433344444555444 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       4.1   2.7e+03      35      78 ..     113     156 ..     101     166 .. 0.61
   2 ?    4.8   0.0     0.039        26       1      22 [.     170     191 ..     170     206 .. 0.80
   3 ?    7.0   0.0    0.0085       5.6      89     125 ..     202     238 ..     192     245 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 4.1
                                       -EEEEECCT---CCS...SSEEEET-EB--CHHHHHHHHHHHHH CS
                         Dynamin_N  35 plelqlgeeeeaseravkeelkekekkledfsevreeieketek 78 
                                       + ++++++++++  + ++e ++  ++ l+d+++  e+++k+++ 
  gi|242399342|ref|YP_002994766.1| 113 VEKIRYSRDPKEIAKLRREFYGRVASILKDINDNLEYLNKARDV 156
                                       55677777777553333333333366666666666666666554 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.039
                                       EEEEEBTTTTHHHHHHHHHTS- CS
                         Dynamin_N   1 iavvGsqSsGKSSvlnaLlged 22 
                                       i++ G+ + GKS++l +L+ ++
  gi|242399342|ref|YP_002994766.1| 170 IVIAGHPNVGKSTLLRKLTNAK 191
                                       8999***********9998876 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0085
                                       S-EEEEEEETTS-SEEEEE---B-SSSGTTSHHHHHH CS
                         Dynamin_N  89 kvillkilsllvkgltlvDlPGldsvnkrdqelvkey 125
                                       k i++  ++ +  ++ ++D+PGl +++  + + ++++
  gi|242399342|ref|YP_002994766.1| 202 KGINVGQFEEHWLKYQVIDTPGLLDRPISERNEIEKQ 238
                                       567788888999999*********9999998887775 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   0.00011     0.075       8      33 ..     170     195 ..     168     219 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00011
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeea 33 
                                       +v+ G++ +GK+tllr+l++ ++e+a
  gi|242399342|ref|YP_002994766.1| 170 IVIAGHPNVGKSTLLRKLTNAKPEVA 195
                                       799*****************988765 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   8.5e-05     0.056      40     142 ..     205     309 ..     168     319 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.5e-05
                                       EEEEEEETTEEEEEEE--SCCCTTCC.HHCHHHHHHHHHHHCTT-ESEEEEEEETT...B-SHHHHH.HHHHHHHHH CS
                              AIG1  40 qkksrtwdgkkinViDTPglfdlsvs.adkiskeivrclllseegihalllvlslg...rfteedek.alktlkelF 111
                                       +  + +++  k +ViDTPgl+d   s  ++i+k+ +  l l + g   ++++++ +    +  ed++ +++++ e F
  gi|242399342|ref|YP_002994766.1| 205 NVGQFEEHWLKYQVIDTPGLLDRPISeRNEIEKQAI--LALRHLG-KLVIYIFDPSeycGYPIEDQMhLFEEIYEEF 278
                                       3333366667889*********98762444555444..3444443.4566666555113455677651457788888 PP

                                       CGGGGGGEEEEEEEGGGGTTCC...HHHHHHHHH CS
                              AIG1 112 Gekilkylivvftrkddledds...ledylskss 142
                                       G+     +ivv+ + d + +d+   +e++l+++ 
  gi|242399342|ref|YP_002994766.1| 279 GD---FPFIVVLNKTDIASEDKirkVEEFLQRRG 309
                                       87...67899999999988888788889988765 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00011     0.076       4      58 ..     168     223 ..     166     319 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00011
                                       -EEEEE-STTSSHHHHHHHHHHSS--.-B---SS-EEETTG...GGTT-SEEEETT CS
                             SRPRB   4 pavllvGlsdsGKTslftrLttdsvk.ktvtSqessaalkvksekgskltliDfPG 58 
                                       p+++++G  + GK +l+ +Lt+ + +  t+    + +     +e+  k ++iD PG
  gi|242399342|ref|YP_002994766.1| 168 PTIVIAGHPNVGKSTLLRKLTNAKPEvATYPFTTKGINVGQFEEHWLKYQVIDTPG 223
                                       79*******************98544044444444343333377788999999999 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00026      0.17       2      28 ..     170     197 ..     169     329 .. 0.52

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00026
                            AAA_28   2 ivitGgestGKTtlleaLaargypvv.p 28 
                                       ivi G +  GK+tll++L++ + +v   
  gi|242399342|ref|YP_002994766.1| 170 IVIAGHPNVGKSTLLRKLTNAKPEVAtY 197
                                       9******************997666532 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0    0.0002      0.14      25      51 ..     168     193 ..     131     235 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.0002
                            AAA_16  25 elvllsGesGvGKsslvrellralekd 51 
                                       + +++ G++ vGKs+l+r+l   ++ +
  gi|242399342|ref|YP_002994766.1| 168 PTIVIAGHPNVGKSTLLRKLT-NAKPE 193
                                       899****************99.45555 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0    0.0027       1.8      22      46 ..     169     193 ..     164     216 .. 0.83
   2 ?    2.2   0.2      0.22   1.4e+02      38     119 ..     237     311 ..     233     342 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0027
                          ATPase_2  22 iyfiYGpegsGKtaLlkeiienled 46 
                                        ++i G  ++GK++Ll+++ + + +
  gi|242399342|ref|YP_002994766.1| 169 TIVIAGHPNVGKSTLLRKLTNAKPE 193
                                       589***************9998755 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.22
                          ATPase_2  38 keiienledkdkyviyyialreesiskldefieeeeekkklekalgiavpkaeleeilkeksklvfkaielllekik 114
                                       k++i  l++++k viy+++ +e+    +++          l + + ++++ + +  +l+++    + +i ++ e ++
  gi|242399342|ref|YP_002994766.1| 237 KQAILALRHLGKLVIYIFDPSEYCGYPIEDQ-------MHLFEEIYEEFGDFPFIVVLNKTDIASEDKIRKVEEFLQ 306
                                       6788888999999999999999988888886.......556666777777777777777666666778888888888 PP

                          ATPase_2 115 kkgkk 119
                                       ++g k
  gi|242399342|ref|YP_002994766.1| 307 RRGIK 311
                                       87766 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       3.2   2.1e+03      76      97 ..      67      88 ..      44     106 .. 0.75
   2 ?   10.3   0.0    0.0005      0.33      33      62 ..     165     194 ..     133     206 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3.2
                              TniB 76 qappkpdekrlyaaiLealgap 97
                                      ++p  ++   +y+++L++l  +
  gi|242399342|ref|YP_002994766.1| 67 RTPGVSTLPPFYQELLDTLVDK 88
                                      6777777888999999888654 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0005
                              TniB  33 krmpnlllvGdsnnGKtmivekFarlhppe 62 
                                          p ++++G++n+GK+++++k ++ +p+ 
  gi|242399342|ref|YP_002994766.1| 165 LTLPTIVIAGHPNVGKSTLLRKLTNAKPEV 194
                                       456999****************99998865 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       4.7   3.1e+03     139     164 ..      37      62 ..      25      66 .. 0.79
   2 ?   10.6   0.1   0.00059      0.39       2      22 ..     170     190 ..     169     212 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 4.7
                                       HHHHHHHT-TT-EEEE--TTTTTTHH CS
                          NTPase_1 139 alveeirerkdvkvfevteenrdall 164
                                       +++ + r+r++ +v +v++  rd+l 
  gi|242399342|ref|YP_002994766.1|  37 NIISKARQREELRVRTVSNVTRDSLR 62 
                                       56778888999999999888888775 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00059
                                       EEEE--TTSSHHHHHHHHHHH CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlel 22 
                                       ++i G+p vGK+Tl++k++++
  gi|242399342|ref|YP_002994766.1| 170 IVIAGHPNVGKSTLLRKLTNA 190
                                       89***************9875 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       5.5   3.7e+03     237     248 ..     122     133 ..      81     151 .. 0.65
   2 ?   10.3   0.0   0.00053      0.35       2      24 ..     168     190 ..     167     221 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 5.5
                                       HHHHHHHHHHHH CS
                             KTI12 237 laeLsrlrrqFv 248
                                        +e+ +lrr+F 
  gi|242399342|ref|YP_002994766.1| 122 PKEIAKLRREFY 133
                                       345556666664 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00053
                                       .EEEEE--TTSSHHHHHHHHHHH CS
                             KTI12   2 pLvvltGlPssGKstrakeLaka 24 
                                       p +v+ G+P +GKst+ ++L +a
  gi|242399342|ref|YP_002994766.1| 168 PTIVIAGHPNVGKSTLLRKLTNA 190
                                       78**************9999875 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   0.00045       0.3       1      48 [.     170     217 ..     170     230 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00045
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdgYt 48 
                                       i++ G++++GKStl ++L++a  +   ++ + + +  +  +++w +Y+
  gi|242399342|ref|YP_002994766.1| 170 IVIAGHPNVGKSTLLRKLTNAKPEVATYPFTTKGINVGQFEEHWLKYQ 217
                                       7899**************999888888888888888888888888886 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 ?   -3.6   0.0       6.5   4.3e+03     226     252 ..      26      52 ..      15      66 .. 0.50
   2 ?    6.1   0.0    0.0072       4.8      32      51 ..     170     189 ..     149     193 .. 0.86
   3 ?    2.0   0.1      0.12        82     205     228 ..     310     333 ..     276     345 .. 0.67

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 6.5
                                       HHHHHHHHHTTHHHHHHHHHHHHHHHH CS
                              MeaB 226 eehrevlkktGllekrrrerakeelre 252
                                       e+ +++ +  G++  + r+r++  +r+
  gi|242399342|ref|YP_002994766.1|  26 EKAASAFTPRGNIISKARQREELRVRT 52 
                                       444445555555555555555444333 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0072
                                       EEEEE-TTSSHHHHHHHHHH CS
                              MeaB  32 vGltGvPGaGkstlvealgl 51 
                                       + + G P +Gkstl+ +l+ 
  gi|242399342|ref|YP_002994766.1| 170 IVIAGHPNVGKSTLLRKLTN 189
                                       6799************9985 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.12
                                       -EEEEEBCCCTBSHHHHHHHHHHH CS
                              MeaB 205 pkvlktsavegeGidelvdaieeh 228
                                        k l+++a +g Gidel +++ e 
  gi|242399342|ref|YP_002994766.1| 310 IKSLRIAAEKGIGIDELKSKVIEI 333
                                       456889999999999999998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); 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: 0.72u 0.37s 00:00:01.08 Elapsed: 00:00:00.53
# Mc/sec: 1976.77
//
Query:       gi|242399343|ref|YP_002994767.1|  [L=441]
Description: Zinc-dependent protease, TldD/PmbA family [Thermococcus sibiricus MM 739]
Scores for complete 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  158.2   0.2    4.7e-46  157.9   0.2    1.1  1  PmbA_TldD  Putative modulator of DNA gyrase
  ------ inclusion threshold ------
      0.045   14.3   0.0       0.13   12.8   0.0    1.8  1  YjbR       YjbR


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 !  157.9   0.2   5.3e-50   4.7e-46       2     279 .]      17     304 ..      16     304 .. 0.84

  Alignments for each domain:
  == domain 1  score: 157.9 bits;  conditional E-value: 5.3e-50
                                       EEEEEEEEEEEEEEEETTEEEEEEEEEEEEEEEEEEETTEEEEEE...ESSHHHHHHHHHHHHHHCCS---TT-... CS
                         PmbA_TldD   2 aevrleesestsvrfengevetnsssedsglgvrvikggrlgfastldtsdealeeaveraveiaklapedpea... 75 
                                        e+ + +++ +sv++e +ev+t+  +e+    vr +k+++lg++  +++++e+++e +era+++akl+++d+++   
  gi|242399343|ref|YP_002994767.1|  17 LEIAIYKNRDASVNIELNEVSTSALRERVVTVVRGVKDKKLGVSIVDTADEEKIKESIERAYKMAKLNKPDEKWisl 93 
                                       68999*****************99999999*************665666668**********************666 PP

                                       GGS-HHHHHHHHHHHHHH.CHCST.........TEEEEEEEEEE......EEE.EEEEEEETTSEEEEEEEEEEEEE CS
                         PmbA_TldD  76 eevsaeekielleelekalrsadp.........kienskgarisgvsaslsaskeeklianSeGldveqtrtrvsls 143
                                       +   +  k    ++++k l++++p          ie++++ +i+ + +   a++ e+li+nS+G++v+q+   + ++
  gi|242399343|ref|YP_002994767.1|  94 P---EPGKYRKPRKVDKELKEVSPdyfvelarkGIELAREEGIVVAGGGGGAEWRESLIINSHGINVSQEGGGAFFY 167
                                       2...4444434455555555555566555555445555577999999999*************************** PP

                                       EEEEE..STCSETEEEEEEEESSHHH.....S..SSHHHHHHHHHHCTTT-B---SEEEEEEE-HHHHHHHHHGHHH CS
                         PmbA_TldD 144 lsvia.ddggsgdgmgggsgyedlee.....edleeiaeeaaekalasleakplppgkypVvlspeavgsllheavg 214
                                       ++ +  ++g+     +g +   d+++      ++ee++++a +k++++ + ++ ++ + +V+l+pe + sll +a+ 
  gi|242399343|ref|YP_002994767.1| 168 IELVGmKEGRV---TPGIF---DFDAklslnLNVEEVIRKALQKVKWAFNVEKSKTEEAKVILEPEPISSLLTYALF 238
                                       *****666333...22333...34444556689999**************8888*********************** PP

                                       HHTBHHHHHTT--TTTT-TTSB-S-TT--EEEETT-......-SB-TTSBB---EEEEETTEE--- CS
                         PmbA_TldD 215 haleadavlegrSflkdklGekvaselltivddpts.gglgsypfDdEGvptqrtvlIenGvLkny 279
                                       +a++++ + +g+++l++k++e + +ellti+ddp+   +++    DdEGvpt+++vl+e+G+++++
  gi|242399343|ref|YP_002994767.1| 239 PAFSGEKLVKGTTPLASKVNESISNELLTIYDDPLHeLSINPVIADDEGVPTRKNVLVEKGIFNGF 304
                                       ***************88*****************96555556777******************998 PP

>> YjbR  YjbR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.4e-05      0.13      26      85 ..      20      79 ..       8      80 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.4e-05
                                      EEEECCCCGEEEES-HHHHHHHHHSSTTEEE-TS.TTTEEEEETTSS-HHHHHHHHHHHHH CS
                              YjbR 26 allgleeeslnlkcdpeeaeaLreqypaiapgyh.kkhWitvlldgvpddeleelideSYr 85
                                      a++ + ++s+n+ +++    aLre+  ++++g + kk  ++++ d +++++++e i+++Y+
  gi|242399343|ref|YP_002994767.1| 20 AIYKNRDASVNIELNEVSTSALRERVVTVVRGVKdKKLGVSIV-DTADEEKIKESIERAYK 79
                                      566667777****************98899***9888889998.8899************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.34s 00:00:01.00 Elapsed: 00:00:00.53
# Mc/sec: 2500.46
//
Query:       gi|242399344|ref|YP_002994768.1|  [L=315]
Description: Carbohydrate/pyrimidine kinase, PfkB family [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-48  165.7   0.1    1.8e-48  165.4   0.1    1.0  1  PfkB      pfkB family carbohydrate kinase


Domain annotation for each model (and alignments):
>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.4   0.1     1e-52   1.8e-48       3     298 ..      26     295 ..      24     297 .. 0.94

  Alignments for each domain:
  == domain 1  score: 165.4 bits;  conditional E-value: 1e-52
                                       EEEEEEEEEEEEEEECSSH..TTSEEEESEEEEEEESHHHHHHHHHHHTT-EEEEEEEEESSHHHHHHHHHHHHTTE CS
                              PfkB   3 kvvviGealidliavsekl..egelvevktveksaGGagaNvAvalarlgadvafigavGdDnfGeflleelkkegv 77 
                                       ++v+iG +++d+ + +e++  + e v +k+ +++ GGa+ N+A  l+++g +v figavG+D++Ge +++++kk gv
  gi|242399344|ref|YP_002994768.1|  26 DIVAIGNLNYDVTLLVERFpeFHEKVIAKKAHFGLGGAAGNTASWLSQMGLKVGFIGAVGNDEIGEAHISYFKKIGV 102
                                       699*****************999****************************************************** PP

                                       EETTEEEESSSEEEEEEEEETTTSEEEEEEEEGGGGGHHHHHHHHHHHHHGCTSEEEEESEECTTSHHHHHHHHHHH CS
                              PfkB  78 dtdyvkidedtrtglalivvdedgertivfnrgaaadltkeeleededlleeadllyisgllsselpeavleelaea 154
                                       d++++k++++ + g+a+ +++++ +  iv ++ga+a+ + +     +++l+ a ++++s+      p+++ e++a+ 
  gi|242399344|ref|YP_002994768.1| 103 DVEGIKVVNE-PSGIAISMIKNE-DKRIVKHLGANAHREID-----LEYLSRARYIHMSS-----NPKEIIEKTAKF 167
                                       ******7777.**********87.89**************5.....78***********9.....99********** PP

                                       HHHTTEEEEEECESSSHHHHHHHHHHHCTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTSSEEEEEEGGGE CS
                              PfkB 155 aknggtfdpnlldplgaqfkeallellaladllkpneeElealtgekledieealaalhklkakgaktvvvtlGkeG 231
                                       a++ +  +p++ld  +a   e  +++  ++++l +ne+E+++  g+      e l+a++       k++++tl   G
  gi|242399344|ref|YP_002994768.1| 168 AHKRD--IPVFLDIGEA---ELPKSVEDKITYLLMNEDEFKRKYGSL-----ENLQAVKS------KNLIITLNGGG 228
                                       *****..*********5...7788888**************999999.....55666665......8********** PP

                                       EEEEE.TTEEEEEEE.SSSS-SBGTTHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHTSSSSSTC CS
                              PfkB 232 alvve.kdgelkvpavpkvkvvDttGAGDsfvggflaallegksleealrfanavAalvvqkkgaias 298
                                       al+ + +++ +kv+   + kv+D+tGAGD+f +gf++++ +g++l+ea+ +++ +A l+vqk ga+++
  gi|242399344|ref|YP_002994768.1| 229 ALLRNeRGEIFKVKG-LSAKVIDSTGAGDAFDAGFIYGIIKGWRLKEAATLGTFLAYLSVQKVGARTA 295
                                       *****8899999999.57***********************************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2491.00
//
Query:       gi|242399345|ref|YP_002994769.1|  [L=273]
Description: ABC-type multidrug transport system, permease component [Thermococcus sibiricus MM 739]
Scores for complete 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-13   48.7  26.0    5.9e-13   48.7  26.0    1.5  2  ABC2_membrane    ABC-2 type transporter
    5.6e-06   25.7  29.8    5.6e-06   25.7  29.8    1.4  1  ABC2_membrane_3  ABC-2 family transporter protein
  ------ inclusion threshold ------
       0.05   13.5   1.0       0.05   13.5   1.0    3.7  3  Transport_MerF   Membrane transport protein MerF


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 !   48.7  26.0   9.9e-17   5.9e-13      15     208 ..      18     228 ..       9     230 .. 0.84
   2 ?   -2.9   0.0       0.6   3.6e+03     170     182 ..     241     253 ..     237     262 .. 0.60

  Alignments for each domain:
  == domain 1  score: 48.7 bits;  conditional E-value: 9.9e-17
                     ABC2_membrane  15 wrdpslgllwrliqplllalvfgtvfgn....lg..nsedglnr...........pgllffsvlflafsaltsvapv 74 
                                       wr  +++ lw +   ++ ++++g +       +g  ns                   +l+f+vl +++++l++ + +
  gi|242399345|ref|YP_002994769.1|  18 WRIFTSYKLWLVSDVMMGFFFVGQALLIgiglTGerNSLA---LqqitgyadyvtFAVLGFMVLGFGLTFLSGFVWS 91 
                                       7777777777777777777777777764433322333333...1335888899998888888888887777777666 PP

                     ABC2_membrane  75 ferer..gvlerelvsplyslsayvlakvlvelpvsllqalifllivyflvgldls..rfflflllllltalaassl 147
                                       ++ e   g++e  +++p+ ++ ++++++vl+ l +s+l   +++ i+++l++++ +  +f+ +l++ll+ a+ +++l
  gi|242399345|ref|YP_002994769.1|  92 VVEELyaGTIEYSFAAPM-RRITFFMGNVLIRLFLSFLYMSVYVPIFILLFDVRFNflNFVKALPFLLVGAVGMIGL 167
                                       666643399*********.*************************************9999***************** PP

                     ABC2_membrane 148 gllisalapsfedasqlaslvllpllllsGffipidsmpkwlqwiaylnPltyavealrsn 208
                                       g++ + l+ +++d + +++++ ++ + lsG+++pi+ +p+ lq +a+++P++ + ea+r++
  gi|242399345|ref|YP_002994769.1| 168 GMAAAGLVLYLKDPGPFITILEMLVFALSGAMYPISILPMGLQILAKALPYAPTSEAVRKI 228
                                       ***********************************************************97 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.6
                     ABC2_membrane 170 lpllllsGffipi 182
                                       + l+llsGf+  i
  gi|242399345|ref|YP_002994769.1| 241 SYLVLLSGFYAII 253
                                       4566677766544 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 !   25.7  29.8   9.4e-10   5.6e-06     157     344 ..      62     255 ..      53     256 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 9.4e-10
                   ABC2_membrane_3 157 snvasflvg.liliilifitasfiavsi...veEkesrikelqlvsgvsplqywlskilgdflvyllqlllil...l 226
                                       +++a+++ + ++ ++++ ++++f++ ++   veE   +++e  + +++++++++++++l+ +++++l + +++   +
  gi|242399345|ref|YP_002994769.1|  62 TGYADYVTFaVLGFMVLGFGLTFLSGFVwsvVEELYAGTIEYSFAAPMRRITFFMGNVLIRLFLSFLYMSVYVpifI 138
                                       5677775555666666666766666644444*************************************988764324 PP

                   ABC2_membrane_3 227 lafglgipfgnlglllllfllfglayialgyllsslfknsetaqilifivilllsgffgglfpledlpsalkwifsi 303
                                       l+f++ ++f n++ +l ++l+++  +i lg++   l+   ++   +i+i+ +l ++++g+++p++ lp +l++++  
  gi|242399345|ref|YP_002994769.1| 139 LLFDVRFNFLNFVKALPFLLVGAVGMIGLGMAAAGLVLYLKDPGPFITILEMLVFALSGAMYPISILPMGLQILAKA 215
                                       59**788888******************************************************************* PP

                   ABC2_membrane_3 304 iPffapglgllrli.tgdplweillsliilalfavvylllal 344
                                       +P    +++  +++ +g+        + +l+l++ +y ++++
  gi|242399345|ref|YP_002994769.1| 216 LPYAPTSEAVRKIVaYGY--TASVNEISYLVLLSGFYAIIGY 255
                                       *************84555..3444899999999999988876 PP

>> Transport_MerF  Membrane transport protein MerF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   1.0   8.3e-06      0.05      13      37 ..      58      85 ..      42      89 .. 0.81
   2 ?   -2.1   2.1      0.63   3.8e+03       4      14 ..     158     168 ..     155     178 .. 0.64
   3 ?    2.2   1.2     0.029   1.7e+02      12      22 ..     248     258 ..     242     259 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.3e-06
                    Transport_MerF 13 LsAlvGYLDYVLlPaLaifi...gLtvy 37
                                      L  ++GY DYV + +L++++   gLt++
  gi|242399345|ref|YP_002994769.1| 58 LQQITGYADYVTFAVLGFMVlgfGLTFL 85
                                      66789**************944446665 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.63
                    Transport_MerF   4 LVillGvvGLs 14 
                                       LV  +G++GL+
  gi|242399345|ref|YP_002994769.1| 158 LVGAVGMIGLG 168
                                       55567777776 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.029
                    Transport_MerF  12 GLsAlvGYLDY 22 
                                       G+ A++GYL Y
  gi|242399345|ref|YP_002994769.1| 248 GFYAIIGYLSY 258
                                       889******99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1655.48
//
Query:       gi|242399346|ref|YP_002994770.1|  [L=267]
Description: ABC-type multidrug transport system, permease component [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-13   50.8  29.3    1.3e-13   50.8  29.3    2.0  2  ABC2_membrane    ABC-2 type transporter
    1.1e-06   28.0  28.2    1.1e-06   28.0  28.2    1.7  1  ABC2_membrane_3  ABC-2 family transporter protein
  ------ inclusion threshold ------
        7.3    6.7   5.8         22    5.1   5.8    1.9  1  DUF4342          Domain of unknown function (DUF4342)


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 !   50.8  29.3   2.3e-17   1.3e-13       5     209 ..       5     222 ..       2     223 .. 0.80
   2 ?    0.7   0.3     0.049   2.9e+02     101     125 ..     230     254 ..     228     263 .. 0.82

  Alignments for each domain:
  == domain 1  score: 50.8 bits;  conditional E-value: 2.3e-17
                     ABC2_membrane   5 allkreflqrwrdpslgllwrliqplllalvfgtvfgn...lgnsedglnr...............pgllffsvlfl 63 
                                       a++ +ef+ ++r p l ++++++  +++  ++ +vf++   lg       r                ++l++ vl++
  gi|242399346|ref|YP_002994770.1|   5 AVVEKEFRMFFRYP-LRVISSILVGIVF--LLQFVFFGqavLGG------RysallevstgmgdypTYALIGYVLWW 72 
                                       67888999999999.4436555555443..33455554233221......123344457788888966666666666 PP

                     ABC2_membrane  64 afsaltsv...apvferergvlerelvsplyslsayvlakvlvelpvsllqalifllivyflvgldls..rfflfll 135
                                       + ++ +++   ++ +e +rg++e    sp+ +  + + + +++ l++  ++ +i+++i +++++++l+   ++  l+
  gi|242399346|ref|YP_002994770.1|  73 VSVSPMEAyvwGVRRELQRGTFEMNVLSPT-KIVELLSGLAISWLLMDSVLMMIVFAIGVVIFDIPLTllIILKSLP 148
                                       54433333222578999*************.************************************97555***** PP

                     ABC2_membrane 136 lllltalaasslgllisalapsfedasqlaslvllpllllsGffipidsmpkwlqwiaylnPltyavealrsnl 209
                                       +++++++a++++g++++ l++ +++++ +a+++ + +l++sG+f+p++ mp+ ++++++l Plt+a  ++rs +
  gi|242399346|ref|YP_002994770.1| 149 IVVASLIAFLGFGFVFAGLVMMLKNIGPFAQIFEFAMLFFSGVFFPLNVMPEAMIAFSKLFPLTHAAAVVRSLF 222
                                       **************************************************99******************9976 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.049
                     ABC2_membrane 101 vlvelpvsllqalifllivyflvgl 125
                                       v++e+++ l+++ i++ i y+l+ +
  gi|242399346|ref|YP_002994770.1| 230 VWGEVAWLLVLIPIYWGIGYLLFKW 254
                                       6788999999999999999998776 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0  28.2   1.8e-10   1.1e-06     161     344 ..      63     249 ..      47     250 .. 0.87

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 1.8e-10
                   ABC2_membrane_3 161 sflvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilll...afglgip 234
                                       + l+g++l+ ++  ++   + ++ +E ++++ e+ ++s+ +  +++ +  ++ +l+  + +++++++   +f+  ip
  gi|242399346|ref|YP_002994770.1|  63 YALIGYVLWWVSVSPMEAYVWGVRRELQRGTFEMNVLSPTKIVELLSGLAISWLLMDSVLMMIVFAIgvvIFD--IP 137
                                       346667777667777777888999********************99999999999999999999987667899..99 PP

                   ABC2_membrane_3 235 fgnlgl..llllfllfglayialgyllsslfknsetaqilifivilllsgffgglfpledlpsalkwifsiiPffap 309
                                        + l++   l  ++  ++a++ +g+++  l+   ++   ++ i+ + +++f+g++fpl+ +p+a+  ++ ++P+++ 
  gi|242399346|ref|YP_002994770.1| 138 LTLLIIlkSLPIVVASLIAFLGFGFVFAGLVMMLKNIGPFAQIFEFAMLFFSGVFFPLNVMPEAMIAFSKLFPLTHA 214
                                       987766345588888899****************************88889999999******************** PP

                   ABC2_membrane_3 310 glgllrlitgdplweillsliilalfavvylllal 344
                                       + +  +l  g  + e++  +++l++++ +y+ +++
  gi|242399346|ref|YP_002994770.1| 215 AAVVRSLFVGRGYLEVWGEVAWLLVLIPIYWGIGY 249
                                       ********999889****************98876 PP

>> DUF4342  Domain of unknown function (DUF4342)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   5.8    0.0037        22      37      68 ..     130     161 ..     120     171 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0037
                           DUF4342  37 gktlleiPltaGvvggviavllapllaalgai 68 
                                       g ++++iPlt+ +++  + +++a l+a+lg+ 
  gi|242399346|ref|YP_002994770.1| 130 GVVIFDIPLTLLIILKSLPIVVASLIAFLGFG 161
                                       6699***********99999999999999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       949  (0.052931); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1821.66
//
Query:       gi|242399347|ref|YP_002994771.1|  [L=329]
Description: ABC-type multidrug transport system, ATPase component [Thermococcus sibiricus MM 739]
Scores for complete 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-30  106.6   0.0    2.5e-30  105.8   0.0    1.4  1  ABC_tran    ABC transporter
    1.4e-10   41.5   0.6    5.2e-06   26.5   0.0    2.2  2  AAA_21      AAA domain, putative AbiEii toxin, Type IV TA sys
    2.1e-06   28.4   0.3    7.5e-06   26.6   0.3    2.0  1  DUF4162     Domain of unknown function (DUF4162)
    6.7e-05   23.5   0.0     0.0001   22.9   0.0    1.4  1  AAA_23      AAA domain
    0.00032   20.7   2.0       0.03   14.3   0.0    2.5  3  NTPase_1    NTPase
     0.0025   18.1   0.3      0.017   15.4   0.3    2.1  1  AAA_22      AAA domain
     0.0033   17.1   0.1     0.0072   16.0   0.1    1.5  1  AAA_29      P-loop containing region of AAA domain
     0.0081   15.9   0.0       0.24   11.1   0.0    2.1  2  AAA_15      AAA ATPase domain
  ------ inclusion threshold ------
      0.012   15.4   0.0      0.079   12.7   0.0    2.0  2  AAA_30      AAA domain
      0.013   15.9   0.2       0.11   12.9   0.1    2.3  1  AAA         ATPase family associated with various cellular ac
      0.023   14.6   0.0       0.04   13.8   0.0    1.4  1  Rad17       Rad17 P-loop domain
      0.026   14.2   0.0      0.086   12.5   0.0    1.9  2  AAA_24      AAA domain
      0.044   13.1   0.0        0.1   11.9   0.0    1.5  1  Zeta_toxin  Zeta toxin
      0.048   13.3   0.0       0.11   12.2   0.0    1.5  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 !  105.8   0.0     2e-33   2.5e-30       2     136 ..      39     182 ..      38     183 .. 0.95

  Alignments for each domain:
  == domain 1  score: 105.8 bits;  conditional E-value: 2e-33
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltvr 77 
                                       k +s+k+k+ge+ +++G+nGaGK+t +k+l+ ll+pt G+ ++ g d++e ++++ r++i  + +   +l  +l+ +
  gi|242399347|ref|YP_002994771.1|  39 KGISFKVKKGELFGLLGPNGAGKTTTIKMLTTLLEPTDGSARILGYDIRE-NTREIRRRINLVAEGeRTLYWRLSGY 114
                                       789***********************************************.777788888888887699999999** PP

                                       HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       en             e++e+ie +l+ +gl e++++ v     ++S G+kqr+a+a+al+++p++l+lDEpt
  gi|242399347|ref|YP_002994771.1| 115 ENlkyfariyyvskeEERERIEFLLKLVGLWEKRNDLV----MNYSRGMKQRLAIAKALVNDPEVLFLDEPT 182
                                       ************99888888******************....*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.2   2.2e-05     0.029       2      42 ..      51      74 ..      50     106 .. 0.68
   2 !   26.5   0.0   4.1e-09   5.2e-06     142     297 ..      94     213 ..      74     217 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.2e-05
                            AAA_21  2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggi 42
                                       +l GpNg+GK++ ++ l  l                   +
  gi|242399347|ref|YP_002994771.1| 51 FGLLGPNGAGKTTTIKMLTTLLE-----------------P 74
                                      689***************88853.................2 PP

  == domain 2  score: 26.5 bits;  conditional E-value: 4.1e-09
                            AAA_21 142 kaltditsrawsllllldglrke..rigllnifadyfgfakekrllqrlvrslklveielsdlgegeeliasvderl 216
                                       +++++++++ +++l +  +++++  ++++  ++ ++  + +++++l +lv+ + ++++ +++               
  gi|242399347|ref|YP_002994771.1|  94 RRRINLVAEGERTLYWRLSGYENlkYFARIYYVSKEE-ERERIEFLLKLVGLWEKRNDLVMNY-------------- 155
                                       5555555556666666666663333333333332222.4444444445555555555555555.............. PP

                            AAA_21 217 rergvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQv 292
                                                            S G+k+ la++ al  ++    +l++DEp +gL+ +    + e++++l +  g  v
  gi|242399347|ref|YP_002994771.1| 156 ---------------------SRGMKQRLAIAKALVNDP---EVLFLDEPTLGLDVQSSIFVREFVRKLVDeQGKTV 208
                                       .....................****************99...9*************5555555888555555899** PP

                            AAA_21 293 iltTH 297
                                       +ltTH
  gi|242399347|ref|YP_002994771.1| 209 LLTTH 213
                                       ***** PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.3   5.8e-09   7.5e-06       4      81 .]     240     323 ..     238     323 .. 0.67

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 5.8e-09
                                       HHHHTTS.-SSEEEEE-------..--.-EEEE-TT..S-EEEEE-.------------.----EEEEEEEE---HH CS
                           DUF4162   4 eeiKrsy.gknrieveadaeelleepg.veeveeeg..gelelkle.deeaanellkal.tsgveirsFeeeePsLn 74 
                                       + +K+    ++ +e++ +    +e+p  + +ve++   +  +l+ + dee  +++ + l +++++i s+e++eP+L+
  gi|242399347|ref|YP_002994771.1| 240 DNLKKLVmDEDVVEIRLKGNVPEEIPWrLAIVERDVesNFTVLRGTvDEEELPKVVEWLvRRKAKIISVEQKEPTLE 316
                                       566666656677778855444455544444443332224444444435799********88**************** PP

                                       HHHHHHH CS
                           DUF4162  75 dIFiekv 81 
                                       d+Fi+++
  gi|242399347|ref|YP_002994771.1| 317 DVFIRLT 323
                                       ****975 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   8.1e-08    0.0001       2      45 ..      12      74 ..      11     183 .. 0.66

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 8.1e-08
                            AAA_23  2 LkienfrsfrdqeidF...................skgltlItGpNGaGKTTildAiklaLyg 45
                                      ++++n++++  ++i F                   +  l+ + GpNGaGKTT +  ++  L  
  gi|242399347|ref|YP_002994771.1| 12 IEVNNLKKYYPKKIPFplrkiewveavkgisfkvkKGELFGLLGPNGAGKTTTIKMLTTLLEP 74
                                      67888888888888888888888888888877886668*******************999853 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   2.3e-05      0.03       4      68 ..      53     116 ..      51     153 .. 0.79
   2 ?    5.7   0.1      0.01        13      94     156 ..     171     237 ..     146     248 .. 0.75
   3 ?   -2.9   0.1       4.2   5.4e+03     130     157 ..     284     310 ..     270     315 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.3e-05
                                       EE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE-------EEEEEET.T--EEEEEETT---S CS
                          NTPase_1   4 iTGppGvGKtTlvkkvlellkssgvkvgGfyteevreggrrigFkivdlasgeegiLarveakre 68 
                                       + Gp G GKtT +k ++ ll+  + + + ++  ++re+ r i  +i  +a+ge++   r ++ ++
  gi|242399347|ref|YP_002994771.1|  53 LLGPNGAGKTTTIKMLTTLLEPTDGSAR-ILGYDIRENTREIRRRINLVAEGERTLYWRLSGYEN 116
                                       569*****************88877665.8999*********************99888874433 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.01
                                       HHH-EEEE--..-STTGGG-HHH.HHHHHHHHT.TTSEEEEE--SS-.-SHHHHHHHT-TT-EEEE-- CS
                          NTPase_1  94 seadviviDE..iGkmElkskkf.keaveevLk.sekpvlavihrrk.dlalveeirerkdvkvfevt 156
                                       ++++v+ +DE   G + ++s  f +e v+++++ ++k vl + h     ++l ++i     +k++ ++
  gi|242399347|ref|YP_002994771.1| 171 NDPEVLFLDEptLG-LDVQSSIFvREFVRKLVDeQGKTVLLTTHYMAeAEQLCDRIAIIDHGKIIALD 237
                                       66677777774333.5556665526789*****99*********9998999****9999889988874 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 4.2
                                       EE--SS--SHHHHHHHT-TT-EEEE--T CS
                          NTPase_1 130 avihrrkdlalveeirerkdvkvfevte 157
                                       +++ +++ +++ve + +r ++k+++v +
  gi|242399347|ref|YP_002994771.1| 284 GTVDEEELPKVVEWLVRR-KAKIISVEQ 310
                                       577777666777777776.688887765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.3   1.3e-05     0.017      10     127 ..      53     210 ..      46     261 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.3e-05
                            AAA_22  10 vtGesGtGKTtllrrlleqldeeakaee.....................erpevvfvtlpsstsskdllrellralg 65 
                                       + G+ G+GKTt++++l+  l+     ++                     e+ ++++  l++ +++k ++r      +
  gi|242399347|ref|YP_002994771.1|  53 LLGPNGAGKTTTIKMLTTLLEPTDGSARilgydirentreirrrinlvaEGERTLYWRLSGYENLKYFARIYYVSKE 129
                                       67*****************9766555559999999999999888888887777777777777777777666666666 PP

                            AAA_22  66 lelka............erlsseell.ealeqalrarav....ielliiDEaqh.lr...seealeeLrsllnlsrk 121
                                       +e+++            +r+++   + + + q l  +++    +e+l +DE    l+   s  + e++r+l++  ++
  gi|242399347|ref|YP_002994771.1| 130 EERERiefllklvglweKRNDLVMNYsRGMKQRLAIAKAlvndPEVLFLDEPTLgLDvqsSIFVREFVRKLVD--EQ 204
                                       6666677777777777655555555544444444444447888888888888887777644777777777777..55 PP

                            AAA_22 122 gvqliL 127
                                       g +++L
  gi|242399347|ref|YP_002994771.1| 205 GKTVLL 210
                                       555544 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 !   16.0   0.1   5.7e-06    0.0072       9      50 ..      34      76 ..      29      80 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 5.7e-06
                            AAA_29  9 Wgtfdg.htieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                      W +  +  +++++  + + l Gp+G+GK+T +  +++lL p+ 
  gi|242399347|ref|YP_002994771.1| 34 WVEAVKgISFKVKKGELFGLLGPNGAGKTTTIKMLTTLLEPTD 76
                                      65554447788885558999******************99975 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   0.00019      0.24      24      50 ..      40      75 ..       9     136 .. 0.71
   2 ?    2.7   0.0     0.063        81     322     364 ..     171     213 ..     116     214 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00019
                            AAA_15 24 e.........ltvliGkNnsGKSsilealdlFlnnk 50
                                                l  l G+N++GK++ +++l  +l+ +
  gi|242399347|ref|YP_002994771.1| 40 GisfkvkkgeLFGLLGPNGAGKTTTIKMLTTLLEPT 75
                                      055555555678899**************9999866 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.063
                            AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                       +++ +l+++EP + L  q    + +  ++l+++  + v++tTH
  gi|242399347|ref|YP_002994771.1| 171 NDPEVLFLDEPTLGLDVQSSIFVREFVRKLVDEQGKTVLLTTH 213
                                       57899**********99999999999********99******* PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   6.1e-05     0.079      20      46 ..      50      77 ..      41     107 .. 0.80
   2 ?    0.1   0.0      0.45   5.7e+02      38      68 ..     197     227 ..     190     271 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.1e-05
                            AAA_30 20 vavltGpAGtGKttalkalreaweaa.g 46
                                      +  l Gp G+GKtt++k l+ ++e   g
  gi|242399347|ref|YP_002994771.1| 50 LFGLLGPNGAGKTTTIKMLTTLLEPTdG 77
                                      67789***************99998733 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.45
                            AAA_30  38 lreaweaaggrviglAptgkaAkvLaeelgi 68 
                                       +r++++++g++v++ ++  + A++L + + i
  gi|242399347|ref|YP_002994771.1| 197 VRKLVDEQGKTVLLTTHYMAEAEQLCDRIAI 227
                                       5888888999999999999999999877664 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 ?   12.9   0.1   8.6e-05      0.11       3      66 ..      53     180 ..      51     226 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.6e-05
                                       EESSTTSSHHHHHHHHHHHH.....THEEEEEETTTCSSS..................................... CS
                               AAA   3 lyGppGtGKTllakavakel.....gvefleisgsellsk..................................... 37 
                                       l Gp G GKT+++k + + l     +    +i g +++++                                     
  gi|242399347|ref|YP_002994771.1|  53 LLGPNGAGKTTTIKMLTTLLeptdgS---ARILGYDIRENtreirrrinlvaegertlywrlsgyenlkyfariyyv 126
                                       78***************998433321...333333333222234444554444445555555555555556666666 PP

                                       ........................STTHHHHHHHHHHHHHHHTS.TSEEEEEET CS
                               AAA  38 ........................yvgesekkirelfkeakeka.kpsilfiDE 66 
                                                               +v + ++ +++ ++ ak+   +p +lf+DE
  gi|242399347|ref|YP_002994771.1| 127 skeeereriefllklvglwekrndLVMNYSRGMKQRLAIAKALVnDPEVLFLDE 180
                                       666666666666666666666666666666666666666555556677888877 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.1e-05      0.04      26      69 ..      30      72 ..      16      95 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.1e-05
                             Rad17 26 kkieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLskel 69
                                      +kie v+ ++k  + + +k ++  + GP G gk+t++k+L+  l
  gi|242399347|ref|YP_002994771.1| 30 RKIEWVE-AVKGISFKVKKGELFGLLGPNGAGKTTTIKMLTTLL 72
                                      6777664.6778888888899999***************98655 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   6.8e-05     0.086       7      38 ..      53      82 ..      48     135 .. 0.81
   2 ?   -1.5   0.0       1.4   1.8e+03     122     134 ..     205     217 ..     192     249 .. 0.51

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.8e-05
                            AAA_24  7 iyGpsgiGKTtlakelgpkplfidtekGlksl 38
                                      + Gp+g+GKTt++k+l  ++l+  t+++++ l
  gi|242399347|ref|YP_002994771.1| 53 LLGPNGAGKTTTIKML--TTLLEPTDGSARIL 82
                                      89**************..88888888866444 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.4
                            AAA_24 122 rknvifiahektr 134
                                       +k+v ++ h   +
  gi|242399347|ref|YP_002994771.1| 205 GKTVLLTTHYMAE 217
                                       4455555554433 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   7.8e-05       0.1      23      60 ..      55      92 ..      39     102 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.8e-05
                        Zeta_toxin 23 GqpGAGKselaellkdelerqgnvvrldpDdlRelhPe 60
                                      G  GAGK++++++l++ le++++  r+ + d+Re  +e
  gi|242399347|ref|YP_002994771.1| 55 GPNGAGKTTTIKMLTTLLEPTDGSARILGYDIRENTRE 92
                                      889*************************9999997765 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   8.3e-05      0.11       6      34 ..      53      81 ..      49      88 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.3e-05
                                      EEESTTSSHHHHHHHHHHHHHHTTS-EEE CS
                             SRP54  6 lvGlqGaGKTttlaKLaallkkegkkvll 34
                                      l+G++GaGKTtt+  L  ll+    ++ +
  gi|242399347|ref|YP_002994771.1| 53 LLGPNGAGKTTTIKMLTTLLEPTDGSARI 81
                                      79***********9999988876555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       711  (0.0396564); expected 358.6 (0.02)
Passed bias filter:                      631  (0.0351944); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.48
# Mc/sec: 2052.28
//
Query:       gi|242399348|ref|YP_002994772.1|  [L=65]
Description: hypothetical protein TSIB_1372 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       239  (0.0133304); expected 358.6 (0.02)
Passed bias filter:                      174  (0.00970495); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.54
# Mc/sec: 360.16
//
Query:       gi|242399349|ref|YP_002994773.1|  [L=93]
Description: hypothetical protein TSIB_1373 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); 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: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 571.94
//
Query:       gi|242399350|ref|YP_002994774.1|  [L=176]
Description: Probable archaeal transcription factor, related to transcription factor TFIIE, alpha subunit [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-25   88.5   6.9    2.2e-25   88.5   6.9    1.8  2  TFIIE_alpha      TFIIE alpha subunit
    6.7e-05   22.6   0.5    6.7e-05   22.6   0.5    3.3  3  Rad50_zn_hook    Rad50 zinc hook motif
    0.00052   19.5   0.1     0.0011   18.5   0.1    1.5  1  TF_Zn_Ribbon     TFIIB zinc-binding
      0.001   19.0   9.7      0.023   14.6   0.1    3.3  3  Prefoldin_2      Prefoldin subunit
     0.0042   16.9   0.1      0.011   15.6   0.1    1.8  1  TrmB             Sugar-specific transcriptional regulator Trm
     0.0054   16.7   4.5     0.0054   16.7   4.5    3.1  3  PLC-beta_C       PLC-beta C terminal
      0.009   16.1   0.2      0.009   16.1   0.2    2.5  3  Sigma70_r3       Sigma-70 region 3
     0.0091   16.1   0.0      0.024   14.7   0.0    1.6  1  HTH_9            RNA polymerase III subunit RPC82 helix-turn-
  ------ inclusion threshold ------
      0.012   15.7   0.6        1.7    8.8   0.1    2.3  2  MqsA_antitoxin   Antitoxin component of bacterial toxin-antit
      0.017   15.3  11.9        3.6    7.9   0.1    3.4  3  ABC_tran_CTD     ABC transporter C-terminal domain
      0.018   15.0   0.0      0.042   13.8   0.0    1.6  1  HTH_Crp_2        Crp-like helix-turn-helix domain
      0.019   14.7   2.0      0.076   12.8   0.7    2.0  2  UPF0167          Uncharacterised protein family (UPF0167)
      0.033   13.8   0.9       0.46   10.1   0.0    2.6  2  HTH_24           Winged helix-turn-helix DNA-binding
      0.048   13.3   0.3        2.3    8.0   0.0    2.5  2  Sigma70_r4_2     Sigma-70, region 4
      0.082   12.7   1.9       0.39   10.5   0.1    2.2  2  COQ7             Ubiquinone biosynthesis protein COQ7
       0.11   12.3   0.2        1.7    8.6   0.0    2.4  2  HTH_AsnC-type    AsnC-type helix-turn-helix domain
       0.13   12.7   3.2      0.052   13.9   0.9    1.5  1  Ribosomal_S13    Ribosomal protein S13/S18
       0.13   12.3   0.1         17    5.5   0.0    2.8  2  Ogr_Delta        Ogr/Delta-like zinc finger
       0.16   12.1   2.5       0.17   12.0   0.1    2.2  3  Mrr_N            Mrr N-terminal domain
       0.16   12.0   2.2        1.8    8.7   0.0    3.0  3  HTH_3            Helix-turn-helix
       0.26   11.8   2.8         40    4.7   0.3    3.0  3  DUF4140          N-terminal domain of unknown function (DUF41
       0.42   11.1   3.7         21    5.6   0.1    2.7  3  DUF4094          Domain of unknown function (DUF4094)
       0.68    9.8   5.5         15    5.5   2.3    2.3  2  rRNA_proc-arch   rRNA-processing arch domain
       0.95   10.0   5.3        1.1    9.7   0.3    2.7  3  HTH_40           Helix-turn-helix domain
          1    9.9   5.7        1.7    9.3   0.0    3.2  3  MerR-DNA-bind    MerR, DNA binding
        3.2    7.9   7.7        1.3    9.2   0.2    3.1  3  MetOD2           Metanogen output domain 2
        4.2    7.5   7.0        2.6    8.2   0.4    2.7  3  IFP_35_N         Interferon-induced 35 kDa protein (IFP 35) N
        4.4    6.8  12.1       0.06   12.9   2.0    2.5  3  4HB_MCP_1        Four helix bundle sensory module for signal 


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 !   88.5   6.9   3.4e-28   2.2e-25       2     104 ..      14     115 ..      13     116 .. 0.96
   2 ?   -0.6   0.1       1.9   1.2e+03      84      99 ..     157     171 ..     148     174 .. 0.56

  Alignments for each domain:
  == domain 1  score: 88.5 bits;  conditional E-value: 3.4e-28
                                       HHHHHHHHCS-HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTEEEEEEEEEEC CS
                       TFIIE_alpha   2 llkevvrkfygeeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrdeekswykyywriny 78 
                                       llk+ v ++ geea++v+++L +k+e t+e+la+ ++i  n +rk+L+ Ly+ +l++++r rd +++wy yyw ++ 
  gi|242399350|ref|YP_002994774.1|  14 LLKF-VEEIGGEEAKEVIKALEKKVEATDEELAEITGIRVNTVRKILYSLYDNQLAEFRRTRDKDTGWYYYYWHLET 89 
                                       5665.589999****************************************************************** PP

                                       CCHCCCHHHHHHHHHHHHHHHHCCCT CS
                       TFIIE_alpha  79 eklvdvvkrkleevvkkLeeklekee 104
                                       ++l d+++ k+ + +kkL+e+le+e+
  gi|242399350|ref|YP_002994774.1|  90 KRLSDIIRSKKMQELKKLKEALEEET 115
                                       ***********************997 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.9
                                       CHHHHHHHHHHHHHHH CS
                       TFIIE_alpha  84 vvkrkleevvkkLeek 99 
                                       vv ++l+e +kkLe++
  gi|242399350|ref|YP_002994774.1| 157 VV-KELQERIKKLEKE 171
                                       22.2445555555555 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 ?    5.0   0.4     0.033        21      29      52 .]      21      44 ..      19      44 .. 0.90
   2 ?    0.0   1.0       1.2   7.9e+02      39      51 ..     102     114 ..      89     118 .. 0.63
   3 !   22.6   0.5   1.1e-07   6.7e-05      21      52 .]     141     172 ..     132     172 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.033
                                      E-HHHHHHHHHHHHHHHHHHH... CS
                     Rad50_zn_hook 29 ldeehrseLikelqsklerlpeel 52
                                      ++ e+++e+ik l++k e   eel
  gi|242399350|ref|YP_002994774.1| 21 IGGEEAKEVIKALEKKVEATDEEL 44
                                      67899**************99986 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHH.. CS
                     Rad50_zn_hook  39 kelqsklerlpee 51 
                                       +el++  e l+ee
  gi|242399350|ref|YP_002994774.1| 102 QELKKLKEALEEE 114
                                       4444444444444 PP

  == domain 3  score: 22.6 bits;  conditional E-value: 1.1e-07
                                       E-TTT--EE-HHHHHHHHHHHHHHHHHHH... CS
                     Rad50_zn_hook  21 cCPlCgReldeehrseLikelqsklerlpeel 52 
                                       +CPlCg  l + + se++kelq+++++l++el
  gi|242399350|ref|YP_002994774.1| 141 RCPLCGEMLMQYDNSEVVKELQERIKKLEKEL 172
                                       9*****************************96 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1   1.7e-06    0.0011       9      35 ..     128     155 ..     121     161 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.7e-06
                                       EECHEE.TSTTCEEESSSSBEEEECCCC CS
                      TF_Zn_Ribbon   9 tnlveD.pergelvCtdCGlVlednsid 35 
                                       ++l++D +++ e++C+ CG++l   +++
  gi|242399350|ref|YP_002994774.1| 128 PRLTFDeAMEYEFRCPLCGEMLMQYDNS 155
                                       33688889**************987776 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.8     0.026        17      72      95 ..      24      47 ..       6      51 .. 0.85
   2 ?    3.4   0.4      0.11        70      90     101 ..     102     113 ..      87     123 .. 0.53
   3 !   14.6   0.1   3.6e-05     0.023      50      78 ..     144     172 ..     142     173 .. 0.95

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.026
                                      HHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2 72 etlekeiktlekqleklekeleel 95
                                      e+++++ik+lek+ e   +el+e+
  gi|242399350|ref|YP_002994774.1| 24 EEAKEVIKALEKKVEATDEELAEI 47
                                      677888999999999988888875 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.11
                                       HHHHHHHHHHHC CS
                       Prefoldin_2  90 keleelkeelqk 101
                                       +el++lke l +
  gi|242399350|ref|YP_002994774.1| 102 QELKKLKEALEE 113
                                       222222222222 PP

  == domain 3  score: 14.6 bits;  conditional E-value: 3.6e-05
                                       EETTEEEEE-HHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  50 lvGdvlvkqdkeevkeeLeerketlekei 78 
                                       l+G++l++ d  ev +eL+er+++leke+
  gi|242399350|ref|YP_002994774.1| 144 LCGEMLMQYDNSEVVKELQERIKKLEKEL 172
                                       58*************************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 !   15.6   0.1   1.7e-05     0.011      15      62 ..      31      84 ..      20      90 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.7e-05
                                      HHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST......TTEE CS
                              TrmB 15 laLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr......pklY 62
                                      +aL k+ +at +e+ae++g+  ++v ++L sL d  l e ++ r      +++Y
  gi|242399350|ref|YP_002994774.1| 31 KALEKKVEATDEELAEITGIRVNTVRKILYSLYDNQLAEFRRTRdkdtgwYYYY 84
                                      66779999******************************9998776676655544 PP

>> PLC-beta_C  PLC-beta C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   1.7     0.093        59      43      73 ..       6      36 ..       4      53 .. 0.85
   2 !   16.7   4.5   8.5e-06    0.0054      36      66 ..      88     118 ..      55     122 .. 0.91
   3 ?    2.4   0.3      0.21   1.4e+02     143     160 ..     154     171 ..     147     174 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.093
                        PLC-beta_C 43 larekqaaelKkLkeisekekKelkKkleak 73
                                      +ar k +  lK   ei  +e Ke+ K le+k
  gi|242399350|ref|YP_002994774.1|  6 MARRKNKELLKFVEEIGGEEAKEVIKALEKK 36
                                      6888888899999999999999999999998 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 8.5e-06
                        PLC-beta_C  36 qiqkllelarekqaaelKkLkeisekekKel 66 
                                       ++++l ++ r+k+ +elKkLke+ e+e+Ke+
  gi|242399350|ref|YP_002994774.1|  88 ETKRLSDIIRSKKMQELKKLKEALEEETKEI 118
                                       5789**************************8 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.21
                        PLC-beta_C 143 qeeldeeyeeklkrLpae 160
                                       ++e+ +e++e++k+L++e
  gi|242399350|ref|YP_002994774.1| 154 NSEVVKELQERIKKLEKE 171
                                       467888888888888887 PP

>> Sigma70_r3  Sigma-70 region 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.2   1.4e-05     0.009       7      43 ..      27      61 ..      23      78 .. 0.83
   2 ?   -2.0   0.6       6.2     4e+03       3      17 ..     101     115 ..      99     117 .. 0.71
   3 ?   -1.0   0.2       2.9   1.9e+03       4      20 ..     159     175 ..     156     176 .] 0.71

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.4e-05
                                      HHHHHHHHHHHSSXXXHHHHHHHHTXXHHHHHHHHHH CS
                        Sigma70_r3  7 kraqreLeqelgrePtpeEiAeeLglseekVrevlea 43
                                      k++++ Le +   e+t+eE+Ae +g+ ++ Vr++l  
  gi|242399350|ref|YP_002994774.1| 27 KEVIKALEKKV--EATDEELAEITGIRVNTVRKILYS 61
                                      78889999999..*********************975 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 6.2
                                       HHHHHHHHHHHHHHH CS
                        Sigma70_r3   3 lnkikraqreLeqel 17 
                                        +++k+ ++ Le+e+
  gi|242399350|ref|YP_002994774.1| 101 MQELKKLKEALEEET 115
                                       567788888888776 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 2.9
                                       HHHHHHHHHHHHHHSSX CS
                        Sigma70_r3   4 nkikraqreLeqelgre 20 
                                       +++ + +++Le elg  
  gi|242399350|ref|YP_002994774.1| 159 KELQERIKKLEKELGIK 175
                                       56677788999999875 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 !   14.7   0.0   3.7e-05     0.024       7      59 ..      18      70 ..      15      72 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.7e-05
                                      HHHCSTTHHHHHHHHHHHHSSBEHHHHHHHHSSTHHHHHHHHHHHHHTTSEEE CS
                             HTH_9  7 ieehFGevvakVvetLlrkgrltlrelvkktkLsldqVkksLvvLiqhrlVqy 59
                                      +ee+ Ge ++ V++ L +k   t  el++ t++  + V+k+L++L  + l+ +
  gi|242399350|ref|YP_002994774.1| 18 VEEIGGEEAKEVIKALEKKVEATDEELAEITGIRVNTVRKILYSLYDNQLAEF 70
                                      788889***************************************98888766 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 ?    5.5   0.1     0.028        18      53      98 ..      10      54 ..       3      67 .. 0.80
   2 ?    8.8   0.1    0.0026       1.7      28      62 ..     132     167 ..     100     174 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.028
                    MqsA_antitoxin 53 lseellefrkkvnaelvdpafiarvrkkleldqreaaeifGgGvna 98
                                        +ell+f +++ +e  + + i+ + kk+e + +e+aei G  vn+
  gi|242399350|ref|YP_002994774.1| 10 KNKELLKFVEEIGGEE-AKEVIKALEKKVEATDEELAEITGIRVNT 54
                                      5566777888887776.66789999999999999999999988886 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0026
                    MqsA_antitoxin  28 vikavtgdf.CarCGegvldeeeedrlseellefrk 62 
                                       + +a++ +f C+ CGe++++ ++++ + e + +++k
  gi|242399350|ref|YP_002994774.1| 132 FDEAMEYEFrCPLCGEMLMQYDNSEVVKELQERIKK 167
                                       5567777878**********9999998888777665 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 ?    6.9   1.1     0.011       7.3       8      27 ..      27      47 ..       9      54 .. 0.69
   2 ?    6.5   0.8     0.016        10      40      61 ..      98     119 ..      89     120 .. 0.81
   3 ?    7.9   0.1    0.0056       3.6      37      57 ..     152     172 ..     144     175 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.011
                      ABC_tran_CTD  8 re.leeleaeIeaLEeeiael 27
                                      +e +++le++ ea +ee+ae+
  gi|242399350|ref|YP_002994774.1| 27 KEvIKALEKKVEATDEELAEI 47
                                      333455555555555555555 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.016
                      ABC_tran_CTD  40 peklaelsaeleeleaeLeely 61 
                                       ++k++el + +e+le+e +e y
  gi|242399350|ref|YP_002994774.1|  98 SKKMQELKKLKEALEEETKEIY 119
                                       5799999999999999988866 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0056
                      ABC_tran_CTD  37 ysdpeklaelsaeleeleaeL 57 
                                       y ++e ++el++++++le+eL
  gi|242399350|ref|YP_002994774.1| 152 YDNSEVVKELQERIKKLEKEL 172
                                       667788999999999999998 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   6.5e-05     0.042      18      54 ..      35      72 ..      13      77 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.5e-05
                                      EEEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ET CS
                         HTH_Crp_2 18 ielpltqeelAsmlGltretvsrilseLkreglis.rg 54
                                       ++  t eelA++ G++  tv +il  L + +l + r+
  gi|242399350|ref|YP_002994774.1| 35 KKVEATDEELAEITGIRVNTVRKILYSLYDNQLAEfRR 72
                                      467899************************99999554 PP

>> UPF0167  Uncharacterised protein family (UPF0167)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.43   2.7e+02     106     157 ..      14      68 ..      10      75 .. 0.62
   2 ?   12.8   0.7   0.00012     0.076      92     172 ..      78     153 ..      63     154 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.43
                           UPF0167 106 acaflgevgaeelealkiklekeelaaikddle.s...kieellellekdgeltgy 157
                                         +f++e+g ee +++ ++lek+ + a++++l+     ++++++++l +  +++  
  gi|242399350|ref|YP_002994774.1|  14 LLKFVEEIGGEEAKEVIKALEKKVE-ATDEELAeItgiRVNTVRKILYSLYDNQLA 68 
                                       5678888888888887777776533.333333312244777777777666666655 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00012
                           UPF0167  92 iswqqeqWlahCddacaflgevgaeelealkiklekeelaaikddleskieellellekdgeltgylFrClhcgkhr 168
                                       ++w + +W          ++  +++el++lk++le+e +++i  ++  + ++ + ++++   +  y FrC  cg++ 
  gi|242399350|ref|YP_002994774.1|  78 TGWYYYYWHLETKRLSDIIRSKKMQELKKLKEALEEE-TKEIYYHCG-TPSHPRLTFDE---AMEYEFRCPLCGEML 149
                                       69******************************99995.667777777.45555555544...466**********99 PP

                           UPF0167 169 lyiD 172
                                       ++ D
  gi|242399350|ref|YP_002994774.1| 150 MQYD 153
                                       9887 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00072      0.46       7      37 ..      28      58 ..      26      65 .. 0.91
   2 ?    1.4   0.3      0.36   2.3e+02      36      44 ..     163     171 ..     159     171 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00072
                            HTH_24  7 kILelLqknprisqreLAerlglSpstvnrr 37
                                      +++++L+k+   +  eLAe +g+ ++tv++ 
  gi|242399350|ref|YP_002994774.1| 28 EVIKALEKKVEATDEELAEITGIRVNTVRKI 58
                                      78999***********************986 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.36
                            HTH_24  36 rrlkrLeee 44 
                                       +r+k+Le+e
  gi|242399350|ref|YP_002994774.1| 163 ERIKKLEKE 171
                                       79*****96 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0    0.0036       2.3      30      46 ..      42      58 ..      40      60 .. 0.89
   2 ?    2.9   0.1      0.14        87       2      20 ..     102     120 ..     101     122 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0036
                                      HHHHHHHT--HHHHHHH CS
                      Sigma70_r4_2 30 kEIAellgisegtVksr 46
                                      +E Ae++gi ++tV++ 
  gi|242399350|ref|YP_002994774.1| 42 EELAEITGIRVNTVRKI 58
                                      799***********985 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.14
                                       HHHHHHHTTS-HHHHHHHH CS
                      Sigma70_r4_2   2 qalrealaeLperqreifl 20 
                                       q+l +++++L e+ +ei+ 
  gi|242399350|ref|YP_002994774.1| 102 QELKKLKEALEEETKEIYY 120
                                       78999***********986 PP

>> COQ7  Ubiquinone biosynthesis protein COQ7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.2      0.34   2.2e+02     116     146 ..       8      38 ..       2      56 .. 0.74
   2 ?   10.5   0.1   0.00062      0.39     102     150 ..      61     120 ..      50     126 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.34
                              COQ7 116 eeedkelleiikqfrddEleHldtAvendae 146
                                       ++++kell+ ++++  +E++    A+e++ e
  gi|242399350|ref|YP_002994774.1|   8 RRKNKELLKFVEEIGGEEAKEVIKALEKKVE 38 
                                       4677888888888888888888888877544 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00062
                              COQ7 102 eHYneqlreleelee...........eedkelleiikqfrddEleHldtAvendaekapa 150
                                       + Y++ql+e +++++            e k+l++ii++ + +El++l+ A+e++++++  
  gi|242399350|ref|YP_002994774.1|  61 SLYDNQLAEFRRTRDkdtgwyyyywhLETKRLSDIIRSKKMQELKKLKEALEEETKEIYY 120
                                       5699*****99888799********999*************************9998765 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 ?    8.6   0.0    0.0026       1.7       9      35 ..      30      56 ..      27      57 .. 0.92
   2 ?    1.1   0.1      0.58   3.7e+02      34      42 .]     161     169 ..     159     169 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0026
                     HTH_AsnC-type  9 LeaLqedaRisyaeLAervGlSestvl 35
                                      ++aL++   ++ +eLAe +G+  +tv+
  gi|242399350|ref|YP_002994774.1| 30 IKALEKKVEATDEELAEITGIRVNTVR 56
                                      789**********************98 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.58
                     HTH_AsnC-type  34 vlrRvrrLe 42 
                                        ++R+++Le
  gi|242399350|ref|YP_002994774.1| 161 LQERIKKLE 169
                                       689*****8 PP

>> Ribosomal_S13  Ribosomal protein S13/S18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.9   8.1e-05     0.052      17     106 ..      15     104 ..       5     115 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 8.1e-05
                     Ribosomal_S13  17 ltaikGiGrrkakiilkkad..vd.edkrigelteeeiekieeivenkaqykipnwinrqkdikdGkdshvvendlr 90 
                                       l+ ++ iG ++ak+++k+++  v+ +d  + e+t   ++++++i+    ++   + + r +d  +G +++   + l+
  gi|242399350|ref|YP_002994774.1|  15 LKFVEEIGGEEAKEVIKALEkkVEaTDEELAEITGIRVNTVRKILYSLYDN-QLAEFRRTRDKDTGWYYY--YWHLE 88 
                                       677889**********99872244245677888889999999999995544.445567888888887665..68899 PP

                     Ribosomal_S13  91 rklredieRlkkirsy 106
                                       +k+ +di R kk++  
  gi|242399350|ref|YP_002994774.1|  89 TKRLSDIIRSKKMQEL 104
                                       9999*****9998865 PP

>> Ogr_Delta  Ogr/Delta-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.027        17      16      28 ..     110     122 ..     106     137 .. 0.87
   2 ?    3.7   0.1     0.093        60       1       7 [.     141     147 ..     141     156 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.027
                         Ogr_Delta  16 nlskdvreryyqC 28 
                                       +l + ++e+yy C
  gi|242399350|ref|YP_002994774.1| 110 ALEEETKEIYYHC 122
                                       678899******* PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.093
                         Ogr_Delta   1 rCPhCga 7  
                                       rCP+Cg+
  gi|242399350|ref|YP_002994774.1| 141 RCPLCGE 147
                                       7****96 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00026      0.17       6      42 ..      12      48 ..      10      75 .. 0.89
   2 ?   -2.4   0.0       8.3   5.3e+03      20      29 ..     104     113 ..      92     122 .. 0.56
   3 ?   -1.7   0.0         5   3.2e+03      21      32 ..     155     167 ..     148     172 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00026
                             Mrr_N  6 lplLealad.gsehrlkeirervaerfglseeeraell 42
                                      ++lL+++++ g e+  ke++++++++++ ++ee+ae +
  gi|242399350|ref|YP_002994774.1| 12 KELLKFVEEiGGEEA-KEVIKALEKKVEATDEELAEIT 48
                                      579******988888.9******************987 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 8.3
                             Mrr_N  20 lkeirervae 29 
                                       lk+++e+++e
  gi|242399350|ref|YP_002994774.1| 104 LKKLKEALEE 113
                                       3444444443 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 5
                             Mrr_N  21 keirervaerf.g 32 
                                       +e++++++er+ +
  gi|242399350|ref|YP_002994774.1| 155 SEVVKELQERIkK 167
                                       5555555555533 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0    0.0029       1.8      11      29 ..      40      58 ..      29      63 .. 0.89
   2 ?   -1.2   0.1       3.6   2.3e+03      26      43 ..      92     109 ..      90     116 .. 0.60
   3 ?    1.5   0.0       0.5   3.2e+02      38      51 ..     162     175 ..     162     176 .] 0.83

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0029
                                      HHHHHHHHHTSSHHHHHHH CS
                             HTH_3 11 sqeeLAeklGvsrstisri 29
                                      + eeLAe +G+ ++t+++i
  gi|242399350|ref|YP_002994774.1| 40 TDEELAEITGIRVNTVRKI 58
                                      569**************99 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 3.6
                                       HHHHHTTSSCSBHHHHHH CS
                             HTH_3  26 isriEnGernPsletlkk 43 
                                       +s+i++ + +  l++lk+
  gi|242399350|ref|YP_002994774.1|  92 LSDIIRSKKMQELKKLKE 109
                                       566666666555555543 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.5
                                       HHHHHHHHHHHTSE CS
                             HTH_3  38 letlkklakaLgvs 51 
                                       +e++kkl+k Lg++
  gi|242399350|ref|YP_002994774.1| 162 QERIKKLEKELGIK 175
                                       58999999999975 PP

>> DUF4140  N-terminal domain of unknown function (DUF4140)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.3     0.062        40      62      86 ..      25      49 ..       7      59 .. 0.75
   2 ?    1.5   0.0      0.64   4.1e+02      66      82 ..     100     116 ..      65     120 .. 0.60
   3 ?    4.4   0.0     0.077        49      64      81 ..     154     172 ..     128     173 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.062
                           DUF4140 62 aeeee.lkalraeleeledelaaled 86
                                      +++ e +kal++++e+  +ela+++ 
  gi|242399350|ref|YP_002994774.1| 25 EAK-EvIKALEKKVEATDEELAEITG 49
                                      233.4499999999999999999876 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.64
                           DUF4140  66 elkalraeleeledela 82 
                                       ++++l++  e+le+e +
  gi|242399350|ref|YP_002994774.1| 100 KMQELKKLKEALEEETK 116
                                       24444444444444433 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.077
                           DUF4140  64 eee.lkalraeleeledel 81 
                                       ++e +k+l++++++le+el
  gi|242399350|ref|YP_002994774.1| 154 NSEvVKELQERIKKLEKEL 172
                                       44669***********997 PP

>> DUF4094  Domain of unknown function (DUF4094)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.2     0.036        23      63      83 ..      25      45 ..       5      47 .. 0.83
   2 ?   -1.2   0.0       4.5   2.9e+03      29      44 ..      94     110 ..      84     120 .. 0.50
   3 ?    5.6   0.1     0.032        21      64      82 ..     154     172 ..     145     175 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.036
                           DUF4094 63 kthkaiqtLdktissLemeLa 83
                                      +++++i++L+k++ +   eLa
  gi|242399350|ref|YP_002994774.1| 25 EAKEVIKALEKKVEATDEELA 45
                                      6789****************8 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 4.5
                           DUF4094  29 diirqs.keelklvsed 44 
                                       diir++ ++elk  +e 
  gi|242399350|ref|YP_002994774.1|  94 DIIRSKkMQELKKLKEA 110
                                       55555533555444433 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.032
                           DUF4094  64 thkaiqtLdktissLemeL 82 
                                        +++++ L+ +i +Le eL
  gi|242399350|ref|YP_002994774.1| 154 NSEVVKELQERIKKLEKEL 172
                                       56899*************9 PP

>> rRNA_proc-arch  rRNA-processing arch domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   2.3     0.023        15      17      66 ..      30     125 ..      25     129 .. 0.69
   2 ?    5.0   0.1      0.03        19       9      31 ..     150     172 ..     136     173 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.023
                                       HHHHHHHHHHHHHHHHTC--TT............HHH...................................HHHHH CS
                    rRNA_proc-arch  17 lpelekklkeleeelksitied............eed...................................ieeyy 46 
                                       + +lekk+++++eel++it                 +                                   ++e  
  gi|242399350|ref|YP_002994774.1|  30 IKALEKKVEATDEELAEITGIRvntvrkilyslyD-NqlaefrrtrdkdtgwyyyywhletkrlsdiirskkMQELK 105
                                       678999*********99884435555555555550.05555556666666777777777777777777777799999 PP

                                       HHHHHHHHHHHHHHHHHCSH CS
                    rRNA_proc-arch  47 klrqqleelreeirkiltkp 66 
                                       kl+++lee ++ei+    +p
  gi|242399350|ref|YP_002994774.1| 106 KLKEALEEETKEIYYHCGTP 125
                                       99999999999998766555 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.03
                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                    rRNA_proc-arch   9 sqfqnqkslpelekklkeleeel 31 
                                       +q+ n + + el++++k+le+el
  gi|242399350|ref|YP_002994774.1| 150 MQYDNSEVVKELQERIKKLEKEL 172
                                       46777777777777777777765 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.2      0.47     3e+02      52      81 ..       9      38 ..       2      41 .. 0.80
   2 ?    9.7   0.3    0.0017       1.1      16      80 ..      42     115 ..      36     120 .. 0.79
   3 ?   -1.7   0.0       6.4   4.1e+03      52      65 ..     156     169 ..     146     175 .. 0.58

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.47
                            HTH_40 52 eeekeIeeaiekvgseklkpikealpeevs 81
                                      ++ ke+ + +e++g e+ k++ +al+++v+
  gi|242399350|ref|YP_002994774.1|  9 RKNKELLKFVEEIGGEEAKEVIKALEKKVE 38
                                      677888999999999999999999888876 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0017
                            HTH_40  16 eeIAkerglkesTIegHLaelieeg.........eeidlerlvseeeekeIeeaiekvgseklkpikealpeev 80 
                                       ee A++ g+ ++T+ + L +l+ ++         ++  +  ++ + e k++ ++i+  + ++lk++keal+ee 
  gi|242399350|ref|YP_002994774.1|  42 EELAEITGIRVNTVRKILYSLYDNQlaefrrtrdKDTGWYYYYWHLETKRLSDIIRSKKMQELKKLKEALEEET 115
                                       78999999999999999999999944444444445667766777888899999999988889********9985 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 6.4
                            HTH_40  52 eeekeIeeaiekvg 65 
                                       e  ke++e i+k++
  gi|242399350|ref|YP_002994774.1| 156 EVVKELQERIKKLE 169
                                       44555555555544 PP

>> MerR-DNA-bind  MerR, DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0    0.0026       1.7      21      59 ..      12      51 ..      10      54 .. 0.94
   2 ?    0.5   0.3       1.4   9.1e+02      50      63 ..      99     112 ..      91     113 .. 0.86
   3 ?    0.6   0.2       1.3   8.6e+02      46      56 ..     159     169 ..     155     172 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0026
                                      HHHHHHHHS.TTTBHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     MerR-DNA-bind 21 relLalydd.rappcqdvrallarklaeleeriaeLqalr 59
                                      +elL + ++ ++ ++ +v + l++k++  +e +ae++ +r
  gi|242399350|ref|YP_002994774.1| 12 KELLKFVEEiGGEEAKEVIKALEKKVEATDEELAEITGIR 51
                                      69999999999*************************9887 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1.4
                                       HHHHHHHHHHHHHH CS
                     MerR-DNA-bind  50 eriaeLqalraeLa 63 
                                       ++++eL++l++ L+
  gi|242399350|ref|YP_002994774.1|  99 KKMQELKKLKEALE 112
                                       68999999999987 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 1.3
                                       HHHHHHHHHHH CS
                     MerR-DNA-bind  46 aeleeriaeLq 56 
                                       +el+eri++L+
  gi|242399350|ref|YP_002994774.1| 159 KELQERIKKLE 169
                                       67888888776 PP

>> MetOD2  Metanogen output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.2    0.0021       1.3      56      82 ..      23      49 ..       9      55 .. 0.88
   2 ?    0.2   0.3       1.3   8.5e+02      58      73 ..      99     114 ..      86     120 .. 0.61
   3 ?    1.2   0.2       0.6   3.9e+02      52      70 ..     154     172 ..     147     175 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0021
                            MetOD2 56 seeieaalknlekkleaqeerlkqikk 82
                                      +ee ++ +k lekk+ea  e+l++i +
  gi|242399350|ref|YP_002994774.1| 23 GEEAKEVIKALEKKVEATDEELAEITG 49
                                      678899******************976 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.3
                            MetOD2  58 eieaalknlekkleaq 73 
                                       +  ++lk l++ le++
  gi|242399350|ref|YP_002994774.1|  99 KKMQELKKLKEALEEE 114
                                       3345566666666555 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.6
                            MetOD2  52 kaevseeieaalknlekkl 70 
                                       + ev +e+++ +k lek+l
  gi|242399350|ref|YP_002994774.1| 154 NSEVVKELQERIKKLEKEL 172
                                       3455666666666666654 PP

>> IFP_35_N  Interferon-induced 35 kDa protein (IFP 35) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       7.3   4.7e+03      14      24 ..      28      38 ..      18      53 .. 0.58
   2 ?    2.8   0.1       0.2   1.3e+02      14      30 ..     102     118 ..      92     130 .. 0.81
   3 ?    8.2   0.4     0.004       2.6      10      23 ..     159     172 ..     152     176 .] 0.87

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 7.3
                          IFP_35_N 14 eeiqkLeaELQ 24
                                      e i+ Le    
  gi|242399350|ref|YP_002994774.1| 28 EVIKALEKKVE 38
                                      44444443333 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.2
                          IFP_35_N  14 eeiqkLeaELQettref 30 
                                       +e++kL   L e+t+e 
  gi|242399350|ref|YP_002994774.1| 102 QELKKLKEALEEETKEI 118
                                       69999999999999995 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.004
                          IFP_35_N  10 iqLkeeiqkLeaEL 23 
                                       ++L+e+i+kLe EL
  gi|242399350|ref|YP_002994774.1| 159 KELQERIKKLEKEL 172
                                       78***********9 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 ?   12.9   2.0   9.4e-05      0.06      59     127 ..       8      76 ..       5      77 .. 0.91
   2 ?   -0.3   0.3         1   6.6e+02      67      91 ..      94     118 ..      86     121 .. 0.62
   3 ?   -0.8   0.1       1.5   9.3e+02      72      90 ..     153     171 ..     147     173 .. 0.47

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.4e-05
                         4HB_MCP_1  59 relradlleliltkdkaekdellkdieeleaeidkllekyektilteeEkelleefkeqlnaYrevrkk 127
                                       r+++  ll+ + +   +e +e++k++e++ + +d++l+++  + +++  k l++ +++ql+++r+ r+k
  gi|242399350|ref|YP_002994774.1|   8 RRKNKELLKFVEEIGGEEAKEVIKALEKKVEATDEELAEITGIRVNTVRKILYSLYDNQLAEFRRTRDK 76 
                                       5667777777778888999**********************************************9986 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1
                         4HB_MCP_1  67 eliltkdkaekdellkdieeleaei 91 
                                       ++i +k ++e ++l++++ee  +ei
  gi|242399350|ref|YP_002994774.1|  94 DIIRSKKMQELKKLKEALEEETKEI 118
                                       5566666666666666666665554 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 1.5
                         4HB_MCP_1  72 kdkaekdellkdieeleae 90 
                                       ++++  +el+++i++le+e
  gi|242399350|ref|YP_002994774.1| 153 DNSEVVKELQERIKKLEKE 171
                                       3444444444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2049  (0.114284); expected 358.6 (0.02)
Passed bias filter:                      981  (0.0547158); expected 358.6 (0.02)
Passed Vit filter:                       144  (0.00803168); expected 17.9 (0.001)
Passed Fwd filter:                        32  (0.00178482); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              28  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.48
# Mc/sec: 1101.29
//
Query:       gi|242399351|ref|YP_002994775.1|  [L=243]
Description: hypothetical protein TSIB_1375 [Thermococcus sibiricus MM 739]
Scores for 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-70  234.7   0.2      1e-69  234.6   0.2    1.0  1  DUF2110   Uncharacterized protein conserved in archaea (DUF21


Domain annotation for each model (and alignments):
>> DUF2110  Uncharacterized protein conserved in archaea (DUF2110)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  234.6   0.2   5.7e-74     1e-69       1     219 [.       5     234 ..       5     239 .. 0.98

  Alignments for each domain:
  == domain 1  score: 234.6 bits;  conditional E-value: 5.7e-74
                           DUF2110   1 latkvYdareralesleslvenelkdLdveleisvreddfvkvtleGedeevaanllreefgeitke...veegevy 74 
                                       +++k+Y  +++ +++l++++++ ++dL+v+++i+++++++vk+tleGed e+++nl+reefge++++   ++ege+y
  gi|242399351|ref|YP_002994775.1|   5 ILEKIY-GDRSGFQKLDKKLDSLIGDLEVSWKIGITQKQWVKITLEGEDTEISTNLIREEFGEVPYKlnsIKEGETY 80 
                                       689***.9999******************************************************999999****** PP

                           DUF2110  75 vGtlesldedgf..vldigvevripkdelkpLge.......gspeqiaerFGlvqhlpleveveeveeeekeiearl 142
                                       +G++ +l+++g+  + digv  + pkd+l pL+        + ++q++++FG+v++lp+e+++++ve  ++e+ea++
  gi|242399351|ref|YP_002994775.1|  81 KGRFIDLGKVGYgvYTDIGVFSPTPKDALIPLYYlksifgeKPVRQMIREFGWVDYLPIEIKIKKVEFGTREVEAEF 157
                                       ************999************************9999********************************** PP

                           DUF2110 143 tdeqvdrlyewkkgkedrlivnsatrsevkaalnraGhardivtverlglleqsvvcredtdapGlvaeiGpylpae 219
                                       t+eq++r+ +w ++++d+++v +++++++++al  +Gh+rd++++e+lgl+e+ ++++++t+apG+++eiGpy++++
  gi|242399351|ref|YP_002994775.1| 158 TEEQIKRIEKWLSDGHDKIFVTGTISENIEKALLETGHSRDVIRLEELGLMETLLILKKGTQAPGIIKEIGPYVRSA 234
                                       **************************************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 1686.57
//
Query:       gi|242399352|ref|YP_002994776.1|  [L=459]
Description: hypothetical protein TSIB_1376 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.19   12.2   0.0       0.31   11.5   0.0    1.3  1  ZapA      Cell division protein ZapA


Domain annotation for each model (and alignments):
>> ZapA  Cell division protein ZapA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   1.7e-05      0.31       6      41 ..      37      70 ..      37      76 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 1.7e-05
                              ZapA  6 lgreytlaceegeeeylreaaklvdekikeireagg 41
                                      +gr+y +   +ge ey ++ ak++dek+++++e+g 
  gi|242399352|ref|YP_002994776.1| 37 NGRSYHV--LPGESEYSKAWAKYLDEKLSRFKEKGE 70
                                      6999999..45579******************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (459 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       956  (0.0533214); 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:                         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: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 2854.90
//
Query:       gi|242399353|ref|YP_002994777.1|  [L=293]
Description: ATPase [Thermococcus sibiricus MM 739]
Scores for complete 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-95  319.6   0.9    1.5e-95  319.3   0.9    1.1  1  ParA           NUBPL iron-transfer P-loop NTPase
    4.3e-16   59.1   0.0    7.9e-16   58.3   0.0    1.4  1  CbiA           CobQ/CobB/MinD/ParA nucleotide binding domain
    3.8e-13   49.7   0.5    1.9e-12   47.4   0.5    1.9  1  AAA_31         AAA domain
    4.5e-08   32.7   0.1    7.6e-07   28.7   0.0    2.1  2  MipZ           ATPase MipZ
    1.2e-06   28.2   0.8      7e-06   25.7   0.8    2.0  1  Fer4_NifH      4Fe-4S iron sulfur cluster binding proteins, N
    3.1e-06   26.6   3.2    3.8e-05   23.0   0.4    2.3  2  ArsA_ATPase    Anion-transporting ATPase
    2.5e-05   24.0   0.0    4.2e-05   23.2   0.0    1.4  1  AAA_25         AAA domain
    0.00011   22.1   0.0    0.00021   21.2   0.0    1.4  1  APS_kinase     Adenylylsulphate kinase
    0.00078   19.3   0.0      0.002   17.9   0.0    1.7  2  CLP1_P         mRNA cleavage and polyadenylation factor CLP1 
     0.0057   15.7   0.0      0.012   14.6   0.0    1.6  1  MeaB           Methylmalonyl Co-A mutase-associated GTPase Me
     0.0061   17.0   0.0      0.012   16.0   0.0    1.5  1  AAA_16         AAA ATPase domain
     0.0062   16.1   0.3      0.023   14.2   0.3    1.9  1  CBP_BcsQ       Cellulose biosynthesis protein BcsQ
     0.0066   16.4   0.3      0.013   15.4   0.0    1.6  1  RsgA_GTPase    RsgA GTPase
     0.0098   15.2   0.0      0.019   14.3   0.0    1.4  1  VirC1          VirC1 protein
  ------ inclusion threshold ------
      0.011   15.2   0.1       0.03   13.8   0.0    1.7  2  RecA           recA bacterial DNA recombination protein
      0.012   14.9   0.0      0.019   14.3   0.0    1.2  1  DnaB_C         DnaB-like helicase C terminal domain
      0.033   14.0   0.2        8.6    6.1   0.1    2.2  2  AAA_26         AAA domain
      0.036   14.6   0.1      0.082   13.4   0.1    1.6  1  AAA_18         AAA domain
      0.046   13.0   0.1      0.086   12.1   0.1    1.4  1  Zeta_toxin     Zeta toxin
      0.047   13.6   0.7       0.14   12.1   0.1    2.0  2  NTPase_1       NTPase
      0.053   12.7   0.1      0.085   12.0   0.1    1.2  1  DAP3           Mitochondrial ribosomal death-associated prote
      0.066   12.8   0.8       0.13   11.9   0.2    1.8  2  SRP54          SRP54-type protein, GTPase domain
      0.066   13.1   0.0       0.13   12.1   0.0    1.5  1  MobB           Molybdopterin guanine dinucleotide synthesis p
      0.082   12.6   0.1       0.15   11.7   0.1    1.5  1  AAA_30         AAA domain
      0.084   12.3   0.2       0.22   11.0   0.0    1.8  2  PhoH           PhoH-like protein
      0.085   12.9   0.0       0.16   11.9   0.0    1.5  1  AAA_5          AAA domain (dynein-related subfamily)
      0.094   12.5   0.3       0.18   11.5   0.3    1.5  1  zinc_ribbon_2  zinc-ribbon domain
        0.1   12.0   0.0       0.17   11.3   0.0    1.3  1  KTI12          Chromatin associated protein KTI12
       0.11   12.9   0.0       0.24   11.8   0.0    1.6  1  RNA_helicase   RNA helicase
       0.12   11.6   0.1       0.19   10.9   0.1    1.3  1  TIP49          TIP49 P-loop domain
       0.14   11.8   0.1       0.36   10.5   0.1    1.6  1  IstB_IS21      IstB-like ATP binding protein
       0.16   11.2   0.1       0.28   10.3   0.1    1.4  1  NB-ARC         NB-ARC domain
       0.18   12.0   0.0       0.69   10.2   0.0    1.9  2  AAA_22         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 !  319.3   0.9   2.8e-98   1.5e-95       3     245 ..      31     282 ..      29     283 .. 0.94

  Alignments for each domain:
  == domain 1  score: 319.3 bits;  conditional E-value: 2.8e-98
                              ParA   3 kkviavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeekpeqs.....ekkliPvea.... 70 
                                       k +iavlSgKGGVGKStvavnlA+aLak+g+ vg+lDaD++Gp+++++lgv+++++ ++     + ++iP ++    
  gi|242399353|ref|YP_002994777.1|  31 KYKIAVLSGKGGVGKSTVAVNLAAALAKQGYFVGVLDADVHGPNVAKMLGVDKAEVLAEkledgHFEMIPPMNdflg 107
                                       789**************************************************666444343235568877766888 PP

                              ParA  71 ..kgikvmSigfllesedeavvwrGpmkskaikqllkdvewgelDyLiiDlPPGtgDeqltvaqklplagaviVttp 145
                                         + ikvmS+gf+++ ed++++wrG++++kaikqll dv+wg+lD++iiD+PPGtgD  ltv+q+l+l++a+iVttp
  gi|242399353|ref|YP_002994777.1| 108 qtTPIKVMSMGFMVP-EDQPIIWRGALVTKAIKQLLGDVKWGNLDFMIIDFPPGTGDQILTVTQTLNLEAAIIVTTP 183
                                       7778***********.************************************************************* PP

                              ParA 146 qevaladvkkaiemfkkvkvkvlGvveNmsgfvcpkcgekteifgkgggeklaeelgvpllgeipldpeireasdeg 222
                                       qeval d+ ka++m+k+++v+ ++v+eNms+++cp+cg+k+++fg+gggeklae+ gv+++g++p+dp+ reasd+g
  gi|242399353|ref|YP_002994777.1| 184 QEVALLDTGKAVNMMKQMQVPYVAVIENMSYLICPHCGNKIDLFGEGGGEKLAEKEGVDFIGKVPIDPKAREASDNG 260
                                       ***************************************************************************** PP

                              ParA 223 kplvlkepeseaakaleeiaekv 245
                                        p+vl e +++aa+a++eia+++
  gi|242399353|ref|YP_002994777.1| 261 VPIVLYE-DTSAARAFMEIAKNL 282
                                       ****996.78899*******987 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.3   0.0   1.5e-18   7.9e-16       1     128 []      34     263 ..      34     263 .. 0.89

  Alignments for each domain:
  == domain 1  score: 58.3 bits;  conditional E-value: 1.5e-18
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH....................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................... RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep....................... 54 
                                       ia+ s+kGGvGK+t+a+nLa+ala++g+ V ++DaD+ ++n a  + l  d+++                       
  gi|242399353|ref|YP_002994777.1|  34 IAVLSGKGGVGKSTVAVNLAAALAKQGYFVGVLDADVHGPNVA--KMLGVDKAEvlaekledghfemippmndflgq 108
                                       89***************************************99..66666777777999****************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|242399353|ref|YP_002994777.1| 109 ttpikvmsmgfmvpedqpiiwrgalvtkaikqllgdvkwgnldfmiidfppgtgdqiltvtqtlnleaaiivttpqe 185
                                       *************************************************************9999999999999999 PP

                                       ....CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHHTS- CS
                                       ....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  55 ....dlkrllellealgkkkalllkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeavaeapargep 127
                                           d  + ++++++++ ++   ++ +++++  + g++ +   + + e+l ++ gv ++g++p d +  ea  +g p
  gi|242399353|ref|YP_002994777.1| 186 vallDTGKAVNMMKQMQVPYVAVIENMSYLICPHCGNKIDLFGEGGGEKLAEKEGVDFIGKVPIDPKAREASDNGVP 262
                                       99998888899999999888777777777777777766555556566666655599999999999999999999987 PP

                                       H CS
                                       x RF
                              CbiA 128 v 128
                                       +
  gi|242399353|ref|YP_002994777.1| 263 I 263
                                       6 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.4   0.5   3.5e-15   1.9e-12       3     168 ..      33     202 ..      31     211 .. 0.75

  Alignments for each domain:
  == domain 1  score: 47.4 bits;  conditional E-value: 3.5e-15
                            AAA_31   3 vIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQa.nattglgiekne.iektlyevlieeknikeaiiktk 77 
                                        Ia+   KGGvGK+T +vnlaaalak+g+ v + D+D  + n +  lg++k e + ++l +  +e            
  gi|242399353|ref|YP_002994777.1|  33 KIAVLSGKGGVGKSTVAVNLAAALAKQGYFVGVLDADVHGpNVAKMLGVDKAEvLAEKLEDGHFEM----------I 99 
                                       599**********************************9876999999*988873344444443322..........2 PP

                            AAA_31  78 venldlipssidLaeaeielvelekk.........eeilkellekvk.deYDyiiiDcpPsLg..lltenaLvasds 142
                                         ++d++  ++ +  +++ ++  e++         ++++k+ll +vk  + D++iiD pP  g  +lt++  +  + 
  gi|242399353|ref|YP_002994777.1| 100 PPMNDFLGQTTPIKVMSMGFMVPEDQpiiwrgalvTKAIKQLLGDVKwGNLDFMIIDFPPGTGdqILTVTQTLNLEA 176
                                       33444555444444444444444444344433344777899999999558**********98755899999999999 PP

                            AAA_31 143 viipvqaeayaleGleqllktieevk 168
                                        ii++ +++ al    + ++++++++
  gi|242399353|ref|YP_002994777.1| 177 AIIVTTPQEVALLDTGKAVNMMKQMQ 202
                                       9*********9998888888888877 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.0   1.4e-09   7.6e-07       3      53 ..      34      84 ..      32     107 .. 0.84
   2 ?    2.1   0.0      0.18        99      92     121 ..     141     172 ..     115     204 .. 0.69

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 1.4e-09
                                      EEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHHHHHHHHH CS
                              MipZ  3 ivlgnekGGsGksttavhvavaLlkkGarvaaidldlrqrtlarylenraa 53
                                      i +   kGG Gkst+av +a aL+k+G  v+++d d+    +a+ l+  +a
  gi|242399353|ref|YP_002994777.1| 34 IAVLSGKGGVGKSTVAVNLAAALAKQGYFVGVLDADVHGPNVAKMLGVDKA 84
                                      556678******************************998888888775555 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.18
                                       HHHHHH.HH-SEEEEE--.SS--HHHHHHHHT CS
                              MipZ  92 lvadle.aeldfividtP.Gsdsalsrlahsl 121
                                       l+ d++  +ldf++id P G+ +++  ++++l
  gi|242399353|ref|YP_002994777.1| 141 LLGDVKwGNLDFMIIDFPpGTGDQILTVTQTL 172
                                       5555542478******7538777766555442 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 !   25.7   0.8   1.3e-08     7e-06       4     247 ..      36     285 ..      32     290 .. 0.72

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 1.3e-08
                         Fer4_NifH   4 aiyGkGGiGksttsqnlsaalaemgkkvlivGCDPkaDstrlllggkaqetvldtlrekgavedvkv.edvvkkGyg 79 
                                        + GkGG+Gkst + nl+aala++g  v ++  D        +lg  + e + + l++ g+ e +   +d + +  +
  gi|242399353|ref|YP_002994777.1|  36 VLSGKGGVGKSTVAVNLAAALAKQGYFVGVLDADVHGPNVAKMLGVDKAEVLAEKLED-GHFEMIPPmNDFLGQ-TT 110
                                       346********************************99999888888777666666655.556998751555555.88 PP

                         Fer4_NifH  80 gvkcvesG..GPep.GvGCaGrgvitaielleelgayddlDfvlyDv...LGDvvCGGfalPiredk.aqevyivts 149
                                        +k++  G   Pe   +   G  v +ai+ l     + +lDf++ D+    GD       l + +    +  +ivt+
  gi|242399353|ref|YP_002994777.1| 111 PIKVMSMGfmVPEDqPIIWRGALVTKAIKQLLGDVKWGNLDFMIIDFppgTGDQ-----ILTVTQTLnLEAAIIVTT 182
                                       89988888334664146678999******9999999**********93333454.....444444431466788888 PP

                         Fer4_NifH 150 gelmalyaanniakgiekya...ksggvrlgGliins..rkvdd.ereliekfaeelgtkvlevvPrdeivrkaelr 220
                                        +  al    +  + +++++        +++ li+ +   k+d  +++  ek+ae+ g++ + +vP d + r+a+ +
  gi|242399353|ref|YP_002994777.1| 183 PQEVALLDTGKAVNMMKQMQvpyVAVIENMSYLICPHcgNKIDLfGEGGGEKLAEKEGVDFIGKVPIDPKAREASDN 259
                                       8888888655544444443300023333577888863112343214455689***********************99 PP

                         Fer4_NifH 221 kktvieyapeseqakeyrelarkilen 247
                                          ++ y+++s  a  + e+a++++++
  gi|242399353|ref|YP_002994777.1| 260 GVPIVLYEDTSA-ARAFMEIAKNLVKK 285
                                       999998887766.99******998765 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.4   6.9e-08   3.8e-05       2      38 ..      33      69 ..      32      86 .. 0.89
   2 ?    3.5   0.1      0.06        32     208     244 ..     176     212 ..     162     222 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 6.9e-08
                                      EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S CS
                       ArsA_ATPase  2 kvilvgGKGGVGKttvsaatavklsekgkkvllistD 38
                                      k+ +++GKGGVGK+tv+  +a+ l+++g+ v ++  D
  gi|242399353|ref|YP_002994777.1| 33 KIAVLSGKGGVGKSTVAVNLAAALAKQGYFVGVLDAD 69
                                      67889***********************988777666 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.06
                                       EEEEEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEEE CS
                       ArsA_ATPase 208 sfrlVvipEklslkEteRaikeLkkygikvdavivNk 244
                                       + ++V++p +++l +t +a++ +k++++   avi N 
  gi|242399353|ref|YP_002994777.1| 176 AAIIVTTPQEVALLDTGKAVNMMKQMQVPYVAVIENM 212
                                       5689*****************************9986 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   7.7e-08   4.2e-05      34     149 ..      33     156 ..      18     157 .. 0.63

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 7.7e-08
                            AAA_25  34 elallaGapgtGKttlaldlalavatGkpwlg..pvapeqgkVlyvsaEdsedelrrRlravgeal.....rddarl 103
                                       ++a+l G +g+GK+t+a++la+a+a+   + g  +  +   +V    + d+++ l+++l+  + ++     ++ ++ 
  gi|242399353|ref|YP_002994777.1|  33 KIAVLSGKGGVGKSTVAVNLAAALAKQGYFVGvlDADVHGPNVAKMLGVDKAEVLAEKLEDGHFEMippmnDFLGQT 109
                                       5789*********************6666999885455555555444444444888888876655556555444444 PP

                            AAA_25 104 lvldlagv.eslpLfak.drggtlltadvdaleaaieevegvrlvviD 149
                                       + ++++++   +p  ++ + +g+l+t ++++l  +++   ++++ +iD
  gi|242399353|ref|YP_002994777.1| 110 TPIKVMSMgFMVPEDQPiIWRGALVTKAIKQLLGDVKW-GNLDFMIID 156
                                       44443333222221111124555666666666666666.566666666 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   3.8e-07   0.00021       6      55 ..      36      85 ..      31      91 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 3.8e-07
                                      EEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT--SSHHH CS
                        APS_kinase  6 wltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdLgfseed 55
                                       l+G  g GKst+a++l+ +L ++g+ v +Ld d+   ++ k Lg ++++
  gi|242399353|ref|YP_002994777.1| 36 VLSGKGGVGKSTVAVNLAAALAKQGYFVGVLDADVHGPNVAKMLGVDKAE 85
                                      699********************************999999999998876 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   3.8e-06     0.002       1      75 [.      39     113 ..      39     121 .. 0.80
   2 ?   -2.4   0.0       6.5   3.5e+03     123     144 ..     175     196 ..     133     210 .. 0.60

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3.8e-06
                            CLP1_P   1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDvGqseispPgtislalverpidveegfsldaplvyffGdtspsd 75 
                                       G+  +GKST+a +L+  ++++g+ + ++D+Dv  ++++    +  a v  +   + +f++  p+  f G+t+p +
  gi|242399353|ref|YP_002994777.1|  39 GKGGVGKSTVAVNLAAALAKQGYFVGVLDADVHGPNVAKMLGVDKAEVLAEKLEDGHFEMIPPMNDFLGQTTPIK 113
                                       66789***************************9999776555555555555555677888888888888888865 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 6.5
                            CLP1_P 123 leliealepdvvvvldqeelln 144
                                       +++i +  p+ v++ld  +  n
  gi|242399353|ref|YP_002994777.1| 175 EAAIIVTTPQEVALLDTGKAVN 196
                                       3334444444444444444444 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 !   14.6   0.0   2.2e-05     0.012      33      70 ..      36      73 ..      11     102 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.2e-05
                                      EEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE----- CS
                              MeaB 33 GltGvPGaGkstlvealglelrrrGkrvavlavDPssp 70
                                       l G  G+Gkst+  +l++ l+++G+ v+vl  D   p
  gi|242399353|ref|YP_002994777.1| 36 VLSGKGGVGKSTVAVNLAAALAKQGYFVGVLDADVHGP 73
                                      57899**************************9987665 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   2.2e-05     0.012      25      56 ..      33      63 ..      17     103 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.2e-05
                            AAA_16 25 elvllsGesGvGKsslvrellralekdggifl 56
                                       + +lsG  GvGKs+++  l+ al k+ g+f+
  gi|242399353|ref|YP_002994777.1| 33 KIAVLSGKGGVGKSTVAVNLAAALAKQ-GYFV 63
                                      6889*************9999999999.6663 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.3   4.2e-05     0.023       5     138 ..      36     172 ..      32     191 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.2e-05
                          CBP_BcsQ   5 alqGvRGGvGttsllaaLawalhelgesvlviDlspd..nlLrlh.Fnvdieqregwaraeldgapwrqaaleyapg 78 
                                       +l+G +GGvG++++++ La al ++g+ v v+D+ +   n+ ++   + +   +e +   +++  p  +  l  ++ 
  gi|242399353|ref|YP_002994777.1|  36 VLSG-KGGVGKSTVAVNLAAALAKQGYFVGVLDADVHgpNVAKMLgVDKAEVLAEKLEDGHFEMIPPMNDFLGQTTP 111
                                       4555.8*********************99999875431133333202222223444555555555555666666666 PP

                          CBP_BcsQ  79 ldllPfGelnveekenlqqlaekaeallaalkelk.eqyrwillDlpagasaltrellala 138
                                       ++++  G +  e++  +   a  ++a+++ l  +k ++ +++++D p g+ ++  +++++ 
  gi|242399353|ref|YP_002994777.1| 112 IKVMSMGFMVPEDQPIIWRGALVTKAIKQLLGDVKwGNLDFMIIDFPPGTGDQILTVTQTL 172
                                       6666666666666665555555556666666666666666666666666666555555544 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   2.5e-05     0.013      88     121 ..      21      54 ..       7      69 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.5e-05
                                       TTHHHHHHHCTTSEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  88 egleelkellkdktsvlvGqSGvGKStLinallp 121
                                       + ++e ++++k k++vl G+ GvGKSt+  +l+ 
  gi|242399353|ref|YP_002994777.1|  21 QRIKEKAKQWKYKIAVLSGKGGVGKSTVAVNLAA 54 
                                       456667788899***************9877765 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   3.4e-05     0.019       4      43 ..      34      73 ..      32      78 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.4e-05
                             VirC1  4 itfcslkGGaGkttalmglcsalasdgkrvalfeadenrP 43
                                      i++ s kGG Gk+t  + l +ala +g  v++++ad   P
  gi|242399353|ref|YP_002994777.1| 34 IAVLSGKGGVGKSTVAVNLAAALAKQGYFVGVLDADVHGP 73
                                      567899*****************************97665 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   5.6e-05      0.03      55     116 ..      34      94 ..      29     118 .. 0.87
   2 ?   -1.8   0.0       3.1   1.7e+03     113     143 ..     159     189 ..     144     204 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.6e-05
                                       EEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEESS----HHHHHHTT--GGG-EEE--SSH CS
                              RecA  55 iieiyGpessGkttlalhaiaeaqkkggvaafidaehaldpkyakklGvdidellvsqpdtG 116
                                       i  + G    Gk+t+a+++ a   k+g ++  +da+    p+ ak lGvd  e+l  + + G
  gi|242399353|ref|YP_002994777.1|  34 IAVLSGKGGVGKSTVAVNLAAALAKQGYFVGVLDADV-HGPNVAKMLGVDKAEVLAEKLEDG 94 
                                       5556788889*************************84.58***********99998776666 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.1
                                       -SSHHHHHHHHHHHHTTT--SEEEEE-TTT- CS
                              RecA 113 pdtGeqaleiadalvrsgaidlivvdsvaal 143
                                       p tG+q l ++++l   +ai +   + va l
  gi|242399353|ref|YP_002994777.1| 159 PGTGDQILTVTQTLNLEAAIIVTTPQEVALL 189
                                       6799999999999988888876666666655 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   3.4e-05     0.019      20     118 ..      33     134 ..      20     159 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.4e-05
                                       XEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHHHHHHHHHHHTXXHHHHHHTTSXH....HHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxx RF
                            DnaB_C  20 dliiiAarpsmGktalalniaenaavkeklpvavfslemsaeqlvqRllsseaeidskklrtgklke....edwekl 92 
                                       ++ ++ ++ ++Gk+++a+n+a++ a+ +   v v   + +  ++++ l   +ae+ ++kl+ g+++     +d+   
  gi|242399353|ref|YP_002994777.1|  33 KIAVLSGKGGVGKSTVAVNLAAALAK-QGYFVGVLDADVHGPNVAKMLGVDKAEVLAEKLEDGHFEMippmNDFLGQ 108
                                       5789******************9995.6778************999999999**********998742222333333 PP

                                       HHHHHHHHHSEEEEEEXSSXCHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C  93 teaieelseaklfiddtpaltvseir 118
                                       t+ i+ +s   ++ +d+p +    + 
  gi|242399353|ref|YP_002994777.1| 109 TTPIKVMSMGFMVPEDQPIIWRGALV 134
                                       33344444444444555555555554 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.1     0.016       8.6       5      32 ..      36      63 ..      33      77 .. 0.80
   2 ?    5.8   0.0     0.019        11     124     196 ..     169     255 ..     158     257 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.016
                            AAA_26  5 vtgtdtgvGKTvvslgLvralkrkgvkv 32
                                      v +   gvGK++v+  L++al ++g+ v
  gi|242399353|ref|YP_002994777.1| 36 VLSGKGGVGKSTVAVNLAAALAKQGYFV 63
                                      5566679**************6555555 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.019
                            AAA_26 124 aknlgap.vilVargglgtinqllltiealrqknvrvlGvilNk....vrnp......e.....nvetlekksgipv 184
                                        ++l+++  i+V+++++ ++ ++  ++++++q +v+ ++vi N     +  p      +       e+l +k g++ 
  gi|242399353|ref|YP_002994777.1| 169 TQTLNLEaAIIVTTPQEVALLDTGKAVNMMKQMQVPYVAVIENMsyliC--PhcgnkiDlfgegGGEKLAEKEGVDF 243
                                       55666652377888888899999999***************99855322..2455545155666899999999**** PP

                            AAA_26 185 lGvvPylpdlea 196
                                       +G vP +p+ ++
  gi|242399353|ref|YP_002994777.1| 244 IGKVPIDPKARE 255
                                       *****9998876 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   0.00015     0.082       3      22 ..      37      56 ..      36      93 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00015
                            AAA_18  3 ltGtpGvGKttlakeLskrl 22
                                      l+G+ GvGK+t+a +L+  l
  gi|242399353|ref|YP_002994777.1| 37 LSGKGGVGKSTVAVNLAAAL 56
                                      89**************8886 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00016     0.086       9      51 ..      24      68 ..      17      76 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00016
                        Zeta_toxin  9 k.ypsqerPklillgGqpGAGKselaellkdelerqgnvv.rldp 51
                                      k   +q + k+ +l+G  G GKs++a  l+++l++qg +v +ld+
  gi|242399353|ref|YP_002994777.1| 24 KeKAKQWKYKIAVLSGKGGVGKSTVAVNLAAALAKQGYFVgVLDA 68
                                      33446666678899********************99999833455 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00025      0.14       3      31 ..      36      64 ..      34      71 .. 0.91
   2 ?   -1.3   0.1       3.4   1.8e+03     118     144 ..     168     192 ..     165     213 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00025
                                      EEE--TTSSHHHHHHHHHHHH...GGGEE CS
                          NTPase_1  3 fiTGppGvGKtTlvkkvlellkssgvkvg 31
                                      +++G+ GvGK+T+  +++ +l+++g+ vg
  gi|242399353|ref|YP_002994777.1| 36 VLSGKGGVGKSTVAVNLAAALAKQGYFVG 64
                                      689*********************99774 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 3.4
                                       HHHHHTTTSEEEEE--SS--SHHHHHH CS
                          NTPase_1 118 veevLksekpvlavihrrkdlalveei 144
                                       v+++L+ e  ++++ +++   al+++ 
  gi|242399353|ref|YP_002994777.1| 168 VTQTLNLEAAIIVTTPQEV--ALLDTG 192
                                       7888998888888888873..344333 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 ?   12.0   0.1   0.00016     0.085      10      54 ..      19      63 ..      16      68 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00016
                                      HHHHHTTS-SSS---EEEEE-SSSSSTTTTHHHHHHHGGGS--EE CS
                              DAP3 10 likklkkadkkkkvkrlvltGekgsGKSvlLlqalayAlekgwvv 54
                                      l++++k++ k+ k k  vl+G+ g+GKS++ + + a  +++g++v
  gi|242399353|ref|YP_002994777.1| 19 LTQRIKEKAKQWKYKIAVLSGKGGVGKSTVAVNLAAALAKQGYFV 63
                                      7999************************99887777666666665 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   0.00024      0.13       3      40 ..      34      71 ..      32      92 .. 0.89
   2 ?   -2.2   0.0       5.1   2.8e+03     147     149 ..     180     182 ..     135     208 .. 0.52

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00024
                                      EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTS CS
                             SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvllvaaDtf 40
                                      + +l G  G+GK t +  Laa l k+g+ v +  aD+ 
  gi|242399353|ref|YP_002994777.1| 34 IAVLSGKGGVGKSTVAVNLAAALAKQGYFVGVLDADVH 71
                                      67899*************************99999975 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 5.1
                                       EES CS
                             SRP54 147 ltk 149
                                       +t 
  gi|242399353|ref|YP_002994777.1| 180 VTT 182
                                       222 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00024      0.13       4      43 ..      37      76 ..      34      86 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00024
                              MobB  4 ivgksgsGKTtLleklipelkarglrvgtiKhahhgfdvd 43
                                      + gk g GK t   +l ++l+++g+ vg++  ++hg +v 
  gi|242399353|ref|YP_002994777.1| 37 LSGKGGVGKSTVAVNLAAALAKQGYFVGVLDADVHGPNVA 76
                                      67999*****************************997765 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00028      0.15      18      51 ..      32      65 ..      21     109 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00028
                            AAA_30 18 drvavltGpAGtGKttalkalreaweaaggrvig 51
                                       ++avl G  G GK+t+   l++a++++g+ v +
  gi|242399353|ref|YP_002994777.1| 32 YKIAVLSGKGGVGKSTVAVNLAAALAKQGYFVGV 65
                                      5689************************976644 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0    0.0004      0.22      17      49 ..      29      62 ..      16     119 .. 0.84
   2 ?   -1.4   0.0       2.5   1.4e+03      20      43 ..     151     174 ..     135     213 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0004
                                      H.H-SEEEEE--TTSSTTHHHHHHHHHHHHTTS- CS
                              PhoH 17 k.kndivfaiGpaGtGKtylavalavealkkkkv 49
                                      + k++i +  G+ G GK+ +av la+++ k++ +
  gi|242399353|ref|YP_002994777.1| 29 QwKYKIAVLSGKGGVGKSTVAVNLAAALAKQGYF 62
                                      35899**********************9999866 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.5
                                       SEEEEE--TTSSTTHHHHHHHHHH CS
                              PhoH  20 divfaiGpaGtGKtylavalavea 43 
                                       d++++  p GtG   l+v+  +++
  gi|242399353|ref|YP_002994777.1| 151 DFMIIDFPPGTGDQILTVTQTLNL 174
                                       556666678888888888776654 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0    0.0003      0.16       3      35 ..      36      69 ..      34      87 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0003
                                      EEE--SSSSHHHHHHHGGGGB.S--EEEEE--TT CS
                             AAA_5  3 lLvGppGtgKselaerlaaal.nreveyvqltrd 35
                                      +L G+ G+gKs++a  laaal ++ +++  l +d
  gi|242399353|ref|YP_002994777.1| 36 VLSGKGGVGKSTVAVNLAAALaKQGYFVGVLDAD 69
                                      699******************9999998888777 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.3   0.00034      0.18       2      10 ..     217     225 ..     216     226 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00034
                     zinc_ribbon_2   2 CpnCGaelq 10 
                                       Cp+CG++++
  gi|242399353|ref|YP_002994777.1| 217 CPHCGNKID 225
                                       *******96 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00032      0.17       5      39 ..      36      70 ..      34      85 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00032
                                      EEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THH CS
                             KTI12  5 vltGlPssGKstrakeLakaleeekrsvvviddes 39
                                      vl+G   +GKst+a +La al+++++ v v+d + 
  gi|242399353|ref|YP_002994777.1| 36 VLSGKGGVGKSTVAVNLAAALAKQGYFVGVLDADV 70
                                      7899999*********************9999775 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00043      0.24       2      25 ..      36      59 ..      35      91 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00043
                      RNA_helicase  2 wlyGpsgeGKStlakeLakallkk 25
                                      +l+G+ g+GKSt+a +La+al+k+
  gi|242399353|ref|YP_002994777.1| 36 VLSGKGGVGKSTVAVNLAAALAKQ 59
                                      689******************976 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00035      0.19      48      95 ..      30      77 ..      19      93 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00035
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49 48 laGravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkk 95
                                         +  +l+G+ g Gk+ +a+ ++ +l+++  fv +  ++v+  +v k
  gi|242399353|ref|YP_002994777.1| 30 WKYKIAVLSGKGGVGKSTVAVNLAAALAKQGYFVGVLDADVHGPNVAK 77
                                      45577799**************************99999999877655 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 ?   10.5   0.1   0.00066      0.36      50      78 ..      35      63 ..      21      85 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00066
                         IstB_IS21 50 ivllGpsGvGKshlaialgveavraglsv 78
                                       vl G  GvGKs +a+ l+ + +++g+ v
  gi|242399353|ref|YP_002994777.1| 35 AVLSGKGGVGKSTVAVNLAAALAKQGYFV 63
                                      5899*********************9876 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00052      0.28      11      41 ..      22      53 ..      15      66 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00052
                                      HHHC.TTTSCSEEEEEEESTTSSHHHHHHHHC CS
                            NB-ARC 11 kLle.kdelqslvvalvGmgGvGKttlakqil 41
                                      +  e  ++ +  +  l+G+gGvGK+t+a +  
  gi|242399353|ref|YP_002994777.1| 22 RIKEkAKQWKYKIAVLSGKGGVGKSTVAVNLA 53
                                      4444234555568899***********98765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0    0.0013      0.69       6      31 ..      33      58 ..      30      92 .. 0.81
   2 ?   -1.4   0.0       4.7   2.6e+03      38      69 ..     259     291 ..     245     293 .] 0.60

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0013
                            AAA_22  6 gilvvtGesGtGKTtllrrlleqlde 31
                                      +i v+ G  G+GK+t++ +l+  l +
  gi|242399353|ref|YP_002994777.1| 33 KIAVLSGKGGVGKSTVAVNLAAALAK 58
                                      6899****************999854 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 4.7
                            AAA_22  38 erpevvfvtlpsst.sskdllrellralglelk 69 
                                       +++++v+++ +s      +++++l+++l++++k
  gi|242399353|ref|YP_002994777.1| 259 NGVPIVLYEDTSAArAFMEIAKNLVKKLEERAK 291
                                       555666666666666677777777777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       727  (0.0405488); expected 358.6 (0.02)
Passed bias filter:                      667  (0.0372023); expected 358.6 (0.02)
Passed Vit filter:                       137  (0.00764125); 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: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2016.77
//
Query:       gi|242399354|ref|YP_002994778.1|  [L=315]
Description: Pyruvate:ferredoxin oxidoreductase (POR), subunit beta [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-26   93.3   0.2    2.4e-26   92.3   0.2    1.5  1  TPP_enzyme_C    Thiamine pyrophosphate enzyme, C-terminal TPP
  ------ inclusion threshold ------
      0.032   13.5   0.1      0.054   12.7   0.1    1.3  1  DXP_synthase_N  1-deoxy-D-xylulose-5-phosphate synthase
       0.21   11.5   1.2       0.33   10.8   0.0    1.9  2  Rep_1B          Replicase polyprotein 1ab


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 !   92.3   0.2   4.1e-30   2.4e-26       2     153 .]      57     218 ..      56     218 .. 0.91

  Alignments for each domain:
  == domain 1  score: 92.3 bits;  conditional E-value: 4.1e-30
                                       SSHHHHHHHHHHTTSSSSEEEC.ETTTS-TTTHHHHHHHHHHH....STTSEEEEEEEHHHHHHT.GGGHHHHHHTT CS
                      TPP_enzyme_C   2 iGcltlwaarllkvkrprsylt.sgglgtmGyglpaAiGakla....kpdrevvaivGDGgflmi.lqelatavrrn 72 
                                       +Gc++++ a +     p++ ++ + +++++ ++ +aA+G+++a     ++ ++ ai GDGg+++i lq+l+ + +r+
  gi|242399354|ref|YP_002994778.1|  57 TGCMEVVSAVF-----PYTAWKaPWIHVAFENAAAAASGVEAAwkklGRKGKILAIGGDGGTADIgLQALSGMLERR 128
                                       79999977777.....778777588*****************654332356************************** PP

                                       -SEEEEEEE-SBCCCHHHH...HHHHTCCTTTTSBB......BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHH CS
                      TPP_enzyme_C  73 lpitvvvlnNegygmtggq...qepfggkrksgpagk.....dlkpvdfaklaealGak.garvekadveeleealk 140
                                       +++++++++Ne+y++tg q   ++p+g++++++p gk     d++++ +a +a+a+ ++ +a+ +  d+ ++ +++k
  gi|242399354|ref|YP_002994778.1| 129 HNVVYLMYDNEAYMNTGIQrssSTPYGAWTTTSPPGKysigeDKPKKWVALIAAAHQVPyVATASIGDPYDFYRKMK 205
                                       ****************************************977888899999999****9999999999******** PP

                                       HHHCSSSEEEEEE CS
                      TPP_enzyme_C 141 ealekkgpaliev 153
                                       +a + +gpa+++v
  gi|242399354|ref|YP_002994778.1| 206 KAASVDGPAFVQV 218
                                       ***********87 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 ?   12.7   0.1     9e-06     0.054     116     176 ..      84     143 ..      78     156 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9e-06
                    DXP_synthase_N 116 sisaalGlavardlkgekkkvvaviGDgaltgGmafealnnigelkkkllvilNdNemsis 176
                                       + +aa G+ +a ++ g+k k++a+ GDg+ t+ + ++al  + e +++++ ++ dNe  ++
  gi|242399354|ref|YP_002994778.1|  84 AAAAASGVEAAWKKLGRKGKILAIGGDGG-TADIGLQALSGMLERRHNVVYLMYDNEAYMN 143
                                       56899***********************9.999***********************98665 PP

>> Rep_1B  Replicase polyprotein 1ab
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.3      0.81   4.8e+03      40      45 ..      22      27 ..      17      30 .. 0.77
   2 ?   10.8   0.0   5.6e-05      0.33      14      32 ..     159     181 ..     155     184 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.81
                                      BSS-SC CS
                            Rep_1B 40 fGcGPG 45
                                       GcGP 
  gi|242399354|ref|YP_002994778.1| 22 AGCGPA 27
                                      599995 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 5.6e-05
                                       ECSSSEEEESS....SSEEEEE- CS
                            Rep_1B  14 ttsPPGrykvG....hkvvavva 32 
                                       ttsPPG+y +G     k va++a
  gi|242399354|ref|YP_002994778.1| 159 TTSPPGKYSIGedkpKKWVALIA 181
                                       9*********9333335666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); 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:                         3  (0.000167327); expected 0.2 (1e-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 0.33s 00:00:00.92 Elapsed: 00:00:00.52
# Mc/sec: 1824.05
//
Query:       gi|242399355|ref|YP_002994779.1|  [L=394]
Description: Pyruvate:ferredoxin oxidoreductase (POR), subunit alpha [Thermococcus sibiricus MM 739]
Scores for 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-77  261.0   0.7    1.4e-77  260.6   0.7    1.1  1  POR_N            Pyruvate flavodoxin/ferredoxin oxidoreductas
      7e-25   87.3   0.0    1.3e-24   86.4   0.0    1.5  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
    4.1e-05   23.4   0.2     0.0001   22.2   0.0    1.8  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 !  260.6   0.7   2.3e-81   1.4e-77       2     230 ..      16     240 ..      15     241 .. 0.98

  Alignments for each domain:
  == domain 1  score: 260.6 bits;  conditional E-value: 2.3e-81
                                       HHHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCC CS
                             POR_N   2 aaiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmien 78 
                                       aa+ a+++v+aa+PITPs+ + e+++e++a+ge+ d+e++++esE++aisa++GA+aaG+ra+TaT++qGl+Lm+e 
  gi|242399355|ref|YP_002994779.1|  16 AAKLAKPKVVAAFPITPSTLVPEKISEFVADGEM-DAEFIKVESEHSAISACVGASAAGVRAFTATASQGLALMHEV 91 
                                       68999****************************8.9***************************************** PP

                                       HHHHHHTT--EEEEEEEEE-STTBEEEEE--TTCHHHHS---EEEE-SSHHHHHHHHHHHHHHHHH..CTSEEEEEE CS
                             POR_N  79 lglaageelPvvivvvaRalpstglsirtdqsDlmaardtglivlasenvqeafdlalvAfnlAek..vrvPvivlf 153
                                       l++aag++lP+v+++ +R+l+++ ++i++d++D +  rdtg++++++en+qea dl+l+Af++Ae+  v +P++v f
  gi|242399355|ref|YP_002994779.1|  92 LFIAAGMRLPIVMAIGNRSLSAP-INIWNDWQDTISERDTGWMQFYAENNQEALDLILIAFKVAEDerVLLPAMVGF 167
                                       ***********************.*****************************************999********* PP

                                       EHHHH.HEEEEEEC-SGG.GS-----SBXXXXXXXXSXXXBXXTXXTSSXXEEESBXBXTTSXBXXXXHHHHHHHHH CS
                             POR_N 154 Dgfllshevekvelpdeedelklikekleeyerkeyaldpekpiargtaanpdtglehrekgneaedaaekvveeve 230
                                       D+f+l+h+ve+ve+pd+e    +++e+l ey +k+++ dp kpi++g+  +p++++e+r +++ea+++a++v++e++
  gi|242399355|ref|YP_002994779.1| 168 DAFILTHTVEPVEIPDQE----VVDEFLGEYVPKHAYFDPAKPITQGALGFPAHYMEARFTVWEAMENARQVIAEAF 240
                                       ******************....**************************************************99875 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 !   86.4   0.0   2.2e-28   1.3e-24       1     101 [.     262     364 ..     262     365 .. 0.97

  Alignments for each domain:
  == domain 1  score: 86.4 bits;  conditional E-value: 2.2e-28
                                       -SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHHHHHHH CS
                           PFOR_II   1 AevvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlveevkaa 77 
                                       Ae+++++mGs+agt+k+ +d+ Reeg+k+G  +++++rPFP ee++ l+kk+k ++ l+++isfg+ G+++ +  +a
  gi|242399355|ref|YP_002994779.1| 262 AEIILLTMGSLAGTLKEFIDKKREEGLKIGAAKMTVYRPFPIEEFRALAKKAKVLAILEKDISFGIGGAVFADAGRA 338
                                       9**************************************************************************99 PP

                                       TGGG..TSEEEEEE--GGG----HHH CS
                           PFOR_II  78 lkks..kvkvvnfvaglgGrditved 101
                                       l ++  k+ +++f+ glgGrd+t e+
  gi|242399355|ref|YP_002994779.1| 339 LVNEkeKPILLDFIIGLGGRDVTFEN 364
                                       9988889999*************987 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       1.4   8.3e+03      11      26 ..      90     105 ..      89     108 .. 0.84
   2 !   22.2   0.0   1.7e-08    0.0001       6     121 ..     258     373 ..     255     376 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.4
                                       SEEEEEETTHHHHHHH CS
                   Transketolase_C  11 dvtlvayGsmveeale 26 
                                       +v+++a G+ ++ +++
  gi|242399355|ref|YP_002994779.1|  90 EVLFIAAGMRLPIVMA 105
                                       7999****99998886 PP

  == domain 2  score: 22.2 bits;  conditional E-value: 1.7e-08
                                       EETTSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEESTTSHHHHHHH CS
                   Transketolase_C   6 lregkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeavkrgGigsevaa 82 
                                       + +  +++l+++Gs   +  e +++ ++eg+++    +   +p+  e +++++kk + l ++e   +++Gig +v a
  gi|242399355|ref|YP_002994779.1| 258 KTDDAEIILLTMGSLAGTLKEFIDKKREEGLKIGAAKMTVYRPFPIEEFRALAKKAKVLAILEK-DISFGIGGAVFA 333
                                       566789********************************************77777766666666.556********* PP

                                       HHHHCCCTTCSSEEEEEEE-SS.SSSSGHHHHHHHTT-SH CS
                   Transketolase_C  83 alaeeafdgldapvkrvggpdv.iepgsaeelekafglda 121
                                          + ++++ ++p++   +    ++  ++e+le+ + +++
  gi|242399355|ref|YP_002994779.1| 334 DAGRALVNEKEKPILLDFIIGLgGRDVTFENLEDVVEISK 373
                                       9999999999999987777777777777777777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); 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: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2740.84
//
Query:       gi|242399356|ref|YP_002994780.1|  [L=105]
Description: Pyruvate:ferredoxin oxidoreductase (POR), subunit delta [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-13   48.7  15.2    1.9e-08   33.8   4.8    2.3  2  Fer4      4Fe-4S binding domain
    1.9e-12   46.7  13.7    1.5e-06   28.0   3.2    2.2  2  Fer4_6    4Fe-4S binding domain
    4.9e-11   42.6   6.5    6.7e-11   42.1   6.5    1.2  1  Fer4_21   4Fe-4S dicluster domain
    1.6e-10   40.4  10.8    5.2e-05   23.1   1.1    2.4  2  Fer4_2    4Fe-4S binding domain
    2.8e-08   34.2   9.1    7.3e-08   32.9   9.2    1.6  1  Fer4_7    4Fe-4S dicluster domain
      1e-07   32.0  17.4    3.5e-06   27.1   9.5    1.7  2  Fer4_9    4Fe-4S dicluster domain
    3.9e-07   30.9  10.6    0.00054   20.9   3.3    2.4  2  Fer4_16   4Fe-4S double cluster binding domain
    4.3e-07   29.9  22.3    4.7e-05   23.4  12.4    2.3  2  Fer4_10   4Fe-4S dicluster domain
    1.1e-05   26.1  10.0     0.0098   16.6   0.7    2.6  2  Fer4_15   4Fe-4S single cluster domain
     0.0017   18.7  13.0        0.2   12.1   3.5    2.3  2  Fer4_8    4Fe-4S dicluster domain
     0.0028   18.2  11.1       0.27   11.8   1.2    2.3  2  Fer4_17   4Fe-4S dicluster domain
     0.0057   17.2  13.5      0.024   15.2   2.1    2.5  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
     0.0088   16.5  12.3       0.32   11.6   4.0    2.2  2  Fer4_4    4Fe-4S binding domain
  ------ inclusion threshold ------
       0.06   14.2  10.5       0.27   12.1   1.6    2.4  3  Fer4_22   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   2.7   2.1e-07   0.00027       1      24 []      46      69 ..      46      69 .. 0.94
   2 !   33.8   4.8   1.5e-11   1.9e-08       1      24 []      76      99 ..      76      99 .. 0.95

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.1e-07
                                      EEEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  1 vvideekCigCGaCvevCPvgAIt 24
                                      +++d++kCi+C +C+  CP  AI+
  gi|242399356|ref|YP_002994780.1| 46 PKFDKDKCIRCFICYTLCPEPAIY 69
                                      579*****************9996 PP

  == domain 2  score: 33.8 bits;  conditional E-value: 1.5e-11
                                      EEEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  1 vvideekCigCGaCvevCPvgAIt 24
                                      +v+d++ C gCG+C++ CP+ AI+
  gi|242399356|ref|YP_002994780.1| 76 PVFDYDYCKGCGICANECPTKAIE 99
                                      689********************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 !   24.4   2.9   1.6e-08     2e-05       2      24 .]      46      68 ..      45      68 .. 0.93
   2 !   28.0   3.2   1.2e-09   1.5e-06       2      24 .]      76      98 ..      75      98 .. 0.96

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 1.6e-08
                            Fer4_6  2 veidpdkCigCgdCvrvCPegai 24
                                      + +d+dkCi C  C++ CPe ai
  gi|242399356|ref|YP_002994780.1| 46 PKFDKDKCIRCFICYTLCPEPAI 68
                                      78*****************9876 PP

  == domain 2  score: 28.0 bits;  conditional E-value: 1.2e-09
                            Fer4_6  2 veidpdkCigCgdCvrvCPegai 24
                                      +++d+d C gCg C++ CP++ai
  gi|242399356|ref|YP_002994780.1| 76 PVFDYDYCKGCGICANECPTKAI 98
                                      89*******************98 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   6.5   5.3e-14   6.7e-11       3      59 .]      48     100 ..      46     100 .. 0.93

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 5.3e-14
                           Fer4_21   3 idedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedciem 59 
                                       +d+dkCi C  C++ C++    ai +d++++     d C GC +C++ CP+ ++iem
  gi|242399356|ref|YP_002994780.1|  48 FDKDKCIRCFICYTLCPE---PAIYLDEESYPVFDYDYCKGCGICANECPT-KAIEM 100
                                       799**************7...99****999988889**************7.99998 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   1.1     4e-08   5.2e-05       3      22 .]      46      65 ..      44      65 .. 0.93
   2 !   22.0   2.8   9.1e-08   0.00012       2      22 .]      75      95 ..      74      95 .. 0.94

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 4e-08
                            Fer4_2  3 vvvdtdrCigCgaCvsaCPa 22
                                      +++d d+Ci+C +C++ CP+
  gi|242399356|ref|YP_002994780.1| 46 PKFDKDKCIRCFICYTLCPE 65
                                      79*****************5 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 9.1e-08
                            Fer4_2  2 pvvvdtdrCigCgaCvsaCPa 22
                                      ++v+d d C gCg+C + CP+
  gi|242399356|ref|YP_002994780.1| 75 YPVFDYDYCKGCGICANECPT 95
                                      689*****************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 !   32.9   9.2   5.7e-11   7.3e-08       1      52 []      52      97 ..      52      97 .. 0.94

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 5.7e-11
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                      +Ci C  C   Cp  ai+ldee       ++++d+++C gCg C+++CPt+a
  gi|242399356|ref|YP_002994780.1| 52 KCIRCFICYTLCPEPAIYLDEE------SYPVFDYDYCKGCGICANECPTKA 97
                                      7******************998......4689******************87 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   1.0     9e-06     0.012      33      51 .]      43      68 ..       9      68 .. 0.72
   2 !   27.1   9.5   2.7e-09   3.5e-06       1      51 []      52      98 ..      52      98 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 9e-06
                            Fer4_9 33 e.......eaCigCgaCveaCpkgai 51
                                              ++Ci C  C+  Cp+ ai
  gi|242399356|ref|YP_002994780.1| 43 VfmpkfdkDKCIRCFICYTLCPEPAI 68
                                      0333334489************9766 PP

  == domain 2  score: 27.1 bits;  conditional E-value: 2.7e-09
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                      kC++C  C + Cp  ++  d+  + +    +    C gCg C++ Cp++ai
  gi|242399356|ref|YP_002994780.1| 52 KCIRCFICYTLCPEPAIYLDEESYPVFDYDY----CKGCGICANECPTKAI 98
                                      7******************999999998765....*************997 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.3   3.1e-05      0.04       1      21 [.      52      72 ..      52      81 .. 0.83
   2 !   20.9   3.3   4.2e-07   0.00054       2      22 ..      83     103 ..      82     105 .] 0.88

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.1e-05
                           Fer4_16  1 rCgtCgkCaevCPtnaikekk 21
                                      +C++C  C   CP+ ai  ++
  gi|242399356|ref|YP_002994780.1| 52 KCIRCFICYTLCPEPAIYLDE 72
                                      6***************98873 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 4.2e-07
                           Fer4_16   2 CgtCgkCaevCPtnaikekke 22 
                                       C++Cg Ca+ CPt+ai++ +e
  gi|242399356|ref|YP_002994780.1|  83 CKGCGICANECPTKAIEMVRE 103
                                       ****************98754 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4  12.4   3.7e-08   4.7e-05       3      56 .]      47      94 ..      45      94 .. 0.78
   2 !   18.1   2.2   1.7e-06    0.0022       3      23 ..      77      97 ..      75     105 .] 0.81

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 3.7e-08
                           Fer4_10  3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrk.kvekCtgcgaCveaCP 56
                                      ++d+d+CirC  C + CP         +++ +ee   + +++ C gcg C+ +CP
  gi|242399356|ref|YP_002994780.1| 47 KFDKDKCIRCFICYTLCPE-------PAIYLDEESYPVfDYDYCKGCGICANECP 94
                                      789****************.......33333333333348**************9 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 1.7e-06
                           Fer4_10  3 vidddtCirCgkCvkaCPadl 23
                                      v+d d C +Cg C + CP+++
  gi|242399356|ref|YP_002994780.1| 77 VFDYDYCKGCGICANECPTKA 97
                                      7899**************954 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.7   7.6e-06    0.0098       3      20 ..      48      65 ..      47      74 .. 0.91
   2 !   13.2   2.9   9.2e-05      0.12       2      20 ..      77      95 ..      77     101 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 7.6e-06
                           Fer4_15  3 vDrdaCigcglCvaeape 20
                                      +D+d+Ci c+ C++++pe
  gi|242399356|ref|YP_002994780.1| 48 FDKDKCIRCFICYTLCPE 65
                                      8***************97 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 9.2e-05
                           Fer4_15  2 vvDrdaCigcglCvaeape 20
                                      v+D d C gcg C+ e+p+
  gi|242399356|ref|YP_002994780.1| 77 VFDYDYCKGCGICANECPT 95
                                      58***************85 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3  13.4      0.01        13       3      64 ..      51      96 ..      49      97 .. 0.65
   2 !   12.1   3.5   0.00016       0.2       3      63 ..      81      95 ..      79     105 .] 0.65

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.01
                            Fer4_8  3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64
                                      +kCi+C+ C + Cp        +    +e +   +           ++C +cg C+++Cp++
  gi|242399356|ref|YP_002994780.1| 51 DKCIRCFICYTLCPE-------PAIYLDEESY-PVF--------DYDYCKGCGICANECPTK 96
                                      689999999999982.......2222222111.111........147899999999999986 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00016
                            Fer4_8  3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpv 63
                                      ++C +Cg C ++Cp                                              +
  gi|242399356|ref|YP_002994780.1| 81 DYCKGCGICANECP----------------------------------------------T 95
                                      46777777777776..............................................3 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   1.2   0.00021      0.27       1      23 [.      52      74 ..      52      82 .. 0.83
   2 !   11.0   2.8   0.00037      0.47       2      15 ..      83      96 ..      82     104 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00021
                           Fer4_17  1 rCiqCgyClpeCpsyeaydnepk 23
                                      +Ci+C  C   Cp  ++y +e+ 
  gi|242399356|ref|YP_002994780.1| 52 KCIRCFICYTLCPEPAIYLDEES 74
                                      6************9988888765 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00037
                           Fer4_17  2 CiqCgyClpeCpsy 15
                                      C +Cg C++eCp+ 
  gi|242399356|ref|YP_002994780.1| 83 CKGCGICANECPTK 96
                                      99999999999975 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   2.1   1.9e-05     0.024       2      18 ..      49      65 ..      48      77 .. 0.92
   2 !    7.4   3.6    0.0049       6.3       2      17 ..      79      94 ..      77      96 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.9e-05
                           Fer4_13  2 DrdtCiacgaCvelaPd 18
                                      D+d+Ci c +C+ l+P+
  gi|242399356|ref|YP_002994780.1| 49 DKDKCIRCFICYTLCPE 65
                                      99**************8 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0049
                           Fer4_13  2 DrdtCiacgaCvelaP 17
                                      D d C +cg+C++ +P
  gi|242399356|ref|YP_002994780.1| 79 DYDYCKGCGICANECP 94
                                      6689************ PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   1.2   0.00082         1       1      15 [.      50      64 ..      50      75 .. 0.91
   2 !   11.6   4.0   0.00025      0.32       2      16 ..      81      95 ..      80      96 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00082
                            Fer4_4  1 qerCigCgsCvaaCP 15
                                      +++Ci+C  C+  CP
  gi|242399356|ref|YP_002994780.1| 50 KDKCIRCFICYTLCP 64
                                      69************9 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00025
                            Fer4_4  2 erCigCgsCvaaCPq 16
                                      + C gCg C + CP+
  gi|242399356|ref|YP_002994780.1| 81 DYCKGCGICANECPT 95
                                      89************8 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   1.4    0.0066       8.5      74      94 ..      45      65 ..      32      68 .. 0.72
   2 ?    5.5   1.8     0.024        31       1      14 [.      52      65 ..      52      75 .. 0.87
   3 ?   12.1   1.6   0.00021      0.27      76      95 ..      77      96 ..      69      97 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0066
                           Fer4_22 74 kekfgesgCvGCgRCieacpv 94
                                      + kf++ +C+ C  C + cp+
  gi|242399356|ref|YP_002994780.1| 45 MPKFDKDKCIRCFICYTLCPE 65
                                      566677777777777777764 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.024
                           Fer4_22  1 rClsCgaCtlvCpt 14
                                      +C++C  C ++Cp 
  gi|242399356|ref|YP_002994780.1| 52 KCIRCFICYTLCPE 65
                                      7***********96 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 0.00021
                           Fer4_22 76 kfgesgCvGCgRCieacpvk 95
                                       f+   C GCg C + cp+k
  gi|242399356|ref|YP_002994780.1| 77 VFDYDYCKGCGICANECPTK 96
                                      578899***********975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 646.94
//
Query:       gi|242399357|ref|YP_002994781.1|  [L=311]
Description: 2-ketoisovalerate:ferredoxin oxidoreductase (VOR) subunit beta [Thermococcus sibiricus MM 739]
Scores for complete 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   66.5   0.0    3.2e-18   66.0   0.0    1.3  1  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b


Domain annotation for each model (and alignments):
>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.0   0.0   1.8e-22   3.2e-18      19     152 ..      64     218 ..      52     219 .. 0.84

  Alignments for each domain:
  == domain 1  score: 66.0 bits;  conditional E-value: 1.8e-22
                                       SEEEC.ETTTS-TTTHHHHHHHHHHH..........STTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEEEEEEE-S CS
                      TPP_enzyme_C  19 rsylt.sgglgtmGyglpaAiGakla..........kpdrevvaivGDGgflmi.lqelatavrrnlpitvvvlnNe 83 
                                       +s ++ + +++++  + ++  G+++a          + +  vv  +GDGg+++i lq+l+ + +r+++ ++++++Ne
  gi|242399357|ref|YP_002994781.1|  64 YSAFNaPLFHTAFETTGAVIGGIEAAlkakgykvkgEDGVMVVGWAGDGGTADIgLQALSGFLERGHDGLYIMYDNE 140
                                       55555445677777777777777773334455543344689************************************ PP

                                       BCCCHHHH...HHHHTCCTTTTSBB......BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHHHHCSSSEEEE CS
                      TPP_enzyme_C  84 gygmtggq...qepfggkrksgpagk.....dlkpvdfaklaealGak.garvekadveeleealkealekkgpali 151
                                       +y++tg q   ++p+g++++ +p gk      ++++++  ++ a+    +a+ ++a++e++ ++lk+a + kgp++i
  gi|242399357|ref|YP_002994781.1| 141 AYMNTGIQrssSTPYGAWTTNTPGGKkrfleRKPKKKVIDIVIAHKPAyAATASVAYPEDFMRKLKKAKTIKGPSFI 217
                                       *****************************9768999*********888788999**********************9 PP

                                       E CS
                      TPP_enzyme_C 152 e 152
                                       +
  gi|242399357|ref|YP_002994781.1| 218 Q 218
                                       7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); 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: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 1856.75
//
Query:       gi|242399358|ref|YP_002994782.1|  [L=393]
Description: 2-ketoisovalerate:ferredoxin oxidoreductase (VOR) subunit alpha [Thermococcus sibiricus MM 739]
Scores for complete 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-77  260.0   0.8    2.7e-77  259.6   0.8    1.1  1  POR_N            Pyruvate flavodoxin/ferredoxin oxidoreductas
    1.8e-32  111.7   0.0    4.2e-32  110.5   0.0    1.7  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
    0.00016   21.5   0.0    0.00061   19.7   0.0    1.9  2  Transketolase_C  Transketolase, C-terminal domain
     0.0099   15.5   0.2      0.039   13.5   0.0    1.9  2  Phosphonate-bd   ABC transporter, phosphonate, periplasmic su
  ------ inclusion threshold ------
       0.03   14.0   1.5      0.062   12.9   1.5    1.5  1  TPP_enzyme_N     Thiamine pyrophosphate enzyme, N-terminal TP
      0.078   13.4   0.0       0.22   11.9   0.0    1.7  2  Syntaxin_2       Syntaxin-like protein


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 !  259.6   0.8   9.1e-81   2.7e-77       2     230 ..      15     240 ..      14     241 .. 0.99

  Alignments for each domain:
  == domain 1  score: 259.6 bits;  conditional E-value: 9.1e-81
                                       HHHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCC CS
                             POR_N   2 aaiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmien 78 
                                       aa++a+v+v+aaYPITP+++i+e++ae++a+gev++ e+v +esE++a++a+iGA+aaGar++TaTS+qGl+Lm+e+
  gi|242399358|ref|YP_002994782.1|  15 AAKHARVEVVAAYPITPQTSIIEKIAEFIANGEVENLEYVPVESEHSAMAACIGASAAGARTFTATSAQGLALMHEM 91 
                                       899*******************************99***************************************** PP

                                       HHHHHHTT--EEEEEEEEE-STTBEEEEE--TTCHHHHS---EEEE-SSHHHHHHHHHHHHHHHHH..CTSEEEEEE CS
                             POR_N  79 lglaageelPvvivvvaRalpstglsirtdqsDlmaardtglivlasenvqeafdlalvAfnlAek..vrvPvivlf 153
                                       l++aag++lPvv+v+v+Ra++ + +s++ dq+D +a rdtg++++++en+qe++d +l+Af++ e+  v++Pv+v+ 
  gi|242399358|ref|YP_002994782.1|  92 LHWAAGARLPVVMVDVNRAMAPP-WSVWDDQTDSLAQRDTGWLQFYAENNQEVYDGVLMAFKIGEHekVNLPVMVIE 167
                                       ***********************.*****************************************999********* PP

                                       EHHHH.HEEEEEEC-SGG.GS-----SBXXXXXXXXSXXXBXXTXXTSSXXEEESBXBXTTSXBXXXXHHHHHHHHH CS
                             POR_N 154 Dgfllshevekvelpdeedelklikekleeyerkeyaldpekpiargtaanpdtglehrekgneaedaaekvveeve 230
                                        +f+lsh+++ v+++++e     ++e+l+++++ ++ +d+++p  +g+  +p+ ++e+r+k  +a+++a+k+++ev 
  gi|242399358|ref|YP_002994782.1| 168 SAFILSHTYDIVDMLEQE----EVDEFLPPRKPLYSLTDFDNPFSIGALGTPADYYEFRYKIAKAMEEAKKIIKEVG 240
                                       ******************....***************************************************9985 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 !  110.5   0.0   1.4e-35   4.2e-32       1     102 []     263     366 ..     263     366 .. 0.98

  Alignments for each domain:
  == domain 1  score: 110.5 bits;  conditional E-value: 1.4e-35
                                       -SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHHHHHHH CS
                           PFOR_II   1 AevvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlveevkaa 77 
                                       A++v+++mGs++gt+k+avd +R eg+kvG  ++r++rPFP+eel el+k+v+ ++vldrn+sfg+eG+l++e k  
  gi|242399358|ref|YP_002994782.1| 263 ADIVFMGMGSLMGTVKEAVDIFRSEGYKVGAAKVRWFRPFPREELYELAKSVEGIAVLDRNFSFGQEGILFNEAKGI 339
                                       9**************************************************************************** PP

                                       TGGG..TSEEEEEE--GGG----HHHH CS
                           PFOR_II  78 lkks..kvkvvnfvaglgGrditvedi 102
                                       l++   ++ + n++ glgGrd+tv+d+
  gi|242399358|ref|YP_002994782.1| 340 LYNTdaNPIMKNYIVGLGGRDLTVNDV 366
                                       ***99899999*************997 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       2.2   6.5e+03      34      48 ..      17      31 ..       9      52 .. 0.52
   2 !   19.7   0.0     2e-07   0.00061       6      68 ..     259     321 ..     257     330 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.2
                                      TTTCEEEEE-SEEES CS
                   Transketolase_C 34 egisaeVvdlrtvkp 48
                                      +  ++eVv ++ + p
  gi|242399358|ref|YP_002994782.1| 17 KHARVEVVAAYPITP 31
                                      334444444333333 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 2e-07
                                       EETTSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEE CS
                   Transketolase_C   6 lregkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvve 68 
                                       + e  d+++ ++Gs + ++ eA++  ++eg+++    +r+++p+ +e + e++k+ + + v++
  gi|242399358|ref|YP_002994782.1| 259 KTEDADIVFMGMGSLMGTVKEAVDIFRSEGYKVGAAKVRWFRPFPREELYELAKSVEGIAVLD 321
                                       56789************************************************9987777665 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 ?   -0.9   0.0      0.34     1e+03     152     190 ..       4      41 ..       2      48 .. 0.79
   2 !   13.5   0.0   1.3e-05     0.039      24      61 ..     236     273 ..     214     287 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.34
                                       HHHTTSSSEEEEEHHHHHHHHHH-HHHHTTEEEEEEEEE CS
                    Phosphonate-bd 152 avlsgdadaaavsadaledlvaegpedkdelrviasspp 190
                                        v+sg++ aa   ++a+ ++va+ p + +++ +i+++++
  gi|242399358|ref|YP_002994782.1|   4 KVISGNYAAAYAAKHARVEVVAAYP-ITPQTSIIEKIAE 41 
                                       6899999999999999999999877.5677777777665 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 1.3e-05
                                       HHHHSSEEEEE--SSHHHHHHHHHTTS-SEEE--HHHH CS
                    Phosphonate-bd  24 seelGvevelvvatdyaavvealragqvDiaflgplay 61 
                                        +e+G+e+  ++++dy++++e  +++ +Di+f+g  + 
  gi|242399358|ref|YP_002994782.1| 236 IKEVGKEFGEKFGRDYSQMIELYKTEDADIVFMGMGSL 273
                                       3567*****************************97765 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   1.5   2.1e-05     0.062       9      98 ..      14     107 ..       7     126 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.1e-05
                                       HHHHHCT--EEEE---CCCHHHHCCHHCT.......TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHC CS
                      TPP_enzyme_N   9 raLkalgvehvfgvpGsrilplldalseeq......girvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatna 79 
                                        a k ++ve+v ++p +  ++++++++e        ++++v + +E +a++a  g + a   +  + +ts  G++ +
  gi|242399358|ref|YP_002994782.1|  14 YAAKHARVEVVAAYPITPQTSIIEKIAEFIangeveNLEYVPVESEHSAMAACIGASAAG-ART-FTATSAQGLALM 88 
                                       555778999999999988888888877755555889*************99999987775.444.5555667***** PP

                                       HHHHHHHHHHT--EEEEEE CS
                      TPP_enzyme_N  80 ltalaeAkvdriPllvlsg 98 
                                          l+ A+ +r+P++++  
  gi|242399358|ref|YP_002994782.1|  89 HEMLHWAAGARLPVVMVDV 107
                                       ***************9855 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   7.2e-05      0.22      21      52 ..     211     242 ..     199     245 .. 0.88
   2 ?   -2.9   0.0       2.9   8.8e+03      27      40 ..     365     378 ..     351     383 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.2e-05
                        Syntaxin_2  21 qLgtkkdteelreklhelieeinelikktnel 52 
                                        Lgt+ d  e+r k+ + +ee++++ik++ + 
  gi|242399358|ref|YP_002994782.1| 211 ALGTPADYYEFRYKIAKAMEEAKKIIKEVGKE 242
                                       59**************************9875 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.9
                        Syntaxin_2  27 dteelreklhelie 40 
                                       d +++ ++++++ie
  gi|242399358|ref|YP_002994782.1| 365 DVRKIASNMKKIIE 378
                                       44444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       740  (0.0412739); expected 358.6 (0.02)
Passed bias filter:                      609  (0.0339673); 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: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 2770.88
//
Query:       gi|242399359|ref|YP_002994783.1|  [L=105]
Description: 2-ketoisovalerate:ferredoxin oxidoreductase (VOR) subunit delta [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.6e-15   54.4  17.1    3.8e-08   32.8   4.8    2.2  2  Fer4      4Fe-4S binding domain
    2.7e-11   43.4   8.9    3.5e-11   43.1   8.9    1.2  1  Fer4_21   4Fe-4S dicluster domain
    1.3e-10   40.9  15.2    7.4e-06   25.8   3.9    2.2  2  Fer4_6    4Fe-4S binding domain
    2.4e-08   34.0  20.0      1e-06   28.8  10.8    1.5  2  Fer4_9    4Fe-4S dicluster domain
    5.3e-08   33.3  10.8    9.9e-08   32.5  10.8    1.5  1  Fer4_7    4Fe-4S dicluster domain
    9.5e-08   31.7  11.7    0.00025   21.0   3.0    2.3  2  Fer4_2    4Fe-4S binding domain
    1.1e-07   31.8  22.9    7.5e-06   26.0  12.8    2.1  2  Fer4_10   4Fe-4S dicluster domain
    3.9e-07   30.9  10.7    0.00044   21.1   3.0    2.4  2  Fer4_16   4Fe-4S double cluster binding domain
    1.8e-05   25.4   9.2      0.032   15.0   3.1    2.7  2  Fer4_15   4Fe-4S single cluster domain
    4.5e-05   23.9  13.2      0.001   19.6   2.5    2.4  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
  ------ inclusion threshold ------
      0.011   16.3  11.5       0.35   11.4   2.6    2.3  2  Fer4_17   4Fe-4S dicluster domain
      0.027   14.9  13.1       0.32   11.6   4.0    2.2  2  Fer4_4    4Fe-4S binding domain
      0.051   14.0  13.1       0.27   11.7   3.8    2.2  2  Fer4_8    4Fe-4S dicluster domain
       0.21   12.5  10.3       0.71   10.7   2.4    2.3  3  Fer4_22   4Fe-4S dicluster domain
        1.6    9.0   8.5         14    5.9   8.5    2.0  1  Fer4_18   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   4.4   1.3e-09   1.5e-06       1      24 []      46      69 ..      46      69 .. 0.95
   2 !   32.8   4.8   3.2e-11   3.8e-08       2      24 .]      77      99 ..      76      99 .. 0.94

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 1.3e-09
                                      EEEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  1 vvideekCigCGaCvevCPvgAIt 24
                                      +v+de+kCi+C +C + CP  AI+
  gi|242399359|ref|YP_002994783.1| 46 PVVDESKCIKCYICWKFCPEPAIY 69
                                      69******************9996 PP

  == domain 2  score: 32.8 bits;  conditional E-value: 3.2e-11
                                      EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  2 videekCigCGaCvevCPvgAIt 24
                                       +d++ C gCG+C++ CP+ AI+
  gi|242399359|ref|YP_002994783.1| 77 AVDYDYCKGCGICANECPTKAIS 99
                                      69*******************96 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.1   8.9   2.9e-14   3.5e-11       2      59 .]      47     100 ..      46     100 .. 0.95

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 2.9e-14
                           Fer4_21   2 ridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedciem 59 
                                       ++de+kCi+C  C + C++    ai i+++ +++v  d C GC +C++ CP+ ++i+m
  gi|242399359|ref|YP_002994783.1|  47 VVDESKCIKCYICWKFCPE---PAIYIKEDGYVAVDYDYCKGCGICANECPT-KAISM 100
                                       69****************7...99***************************7.99998 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   3.5   2.1e-07   0.00025       2      24 .]      46      68 ..      45      68 .. 0.93
   2 !   25.8   3.9   6.2e-09   7.4e-06       2      24 .]      76      98 ..      75      98 .. 0.96

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.1e-07
                            Fer4_6  2 veidpdkCigCgdCvrvCPegai 24
                                      +++d++kCi C+ C + CPe ai
  gi|242399359|ref|YP_002994783.1| 46 PVVDESKCIKCYICWKFCPEPAI 68
                                      89*****************9876 PP

  == domain 2  score: 25.8 bits;  conditional E-value: 6.2e-09
                            Fer4_6  2 veidpdkCigCgdCvrvCPegai 24
                                      v++d+d C gCg C++ CP++ai
  gi|242399359|ref|YP_002994783.1| 76 VAVDYDYCKGCGICANECPTKAI 98
                                      79*******************98 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   1.7   5.8e-06    0.0069      33      51 .]      43      68 ..       8      68 .. 0.74
   2 !   28.8  10.8   8.4e-10     1e-06       1      51 []      52      98 ..      52      98 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5.8e-06
                            Fer4_9 33 e.......eaCigCgaCveaCpkgai 51
                                      +       ++Ci+C  C + Cp+ ai
  gi|242399359|ref|YP_002994783.1| 43 NfmpvvdeSKCIKCYICWKFCPEPAI 68
                                      1444555579************9766 PP

  == domain 2  score: 28.8 bits;  conditional E-value: 8.4e-10
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                      kC++C  C + Cp  ++  ++ ++ a    +    C gCg C++ Cp++ai
  gi|242399359|ref|YP_002994783.1| 52 KCIKCYICWKFCPEPAIYIKEDGYVAVDYDY----CKGCGICANECPTKAI 98
                                      7***********************9998765....*************997 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5  10.8   8.3e-11   9.9e-08       1      52 []      52      97 ..      52      97 .. 0.95

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 8.3e-11
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                      +Ci+C  C + Cp  ai+++e+       +v++d+++C gCg C+++CPt+a
  gi|242399359|ref|YP_002994783.1| 52 KCIKCYICWKFCPEPAIYIKED------GYVAVDYDYCKGCGICANECPTKA 97
                                      7******************997......589*******************87 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   1.5   8.1e-06    0.0097       3      22 .]      46      65 ..      44      65 .. 0.90
   2 !   21.0   3.0   2.1e-07   0.00025       2      22 .]      75      95 ..      74      95 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 8.1e-06
                            Fer4_2  3 vvvdtdrCigCgaCvsaCPa 22
                                      +vvd+ +Ci C +C + CP+
  gi|242399359|ref|YP_002994783.1| 46 PVVDESKCIKCYICWKFCPE 65
                                      89************888*95 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 2.1e-07
                            Fer4_2  2 pvvvdtdrCigCgaCvsaCPa 22
                                      +v+vd d C gCg+C + CP+
  gi|242399359|ref|YP_002994783.1| 75 YVAVDYDYCKGCGICANECPT 95
                                      6899****************7 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0  12.8   6.3e-09   7.5e-06       2      56 .]      46      94 ..      45      94 .. 0.90
   2 !   17.4   2.4   2.9e-06    0.0035       3      24 ..      77      98 ..      75     105 .] 0.79

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 6.3e-09
                           Fer4_10  2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      +v+d+++Ci+C  C k+CP          +++e++ v ++++ C gcg C+ +CP
  gi|242399359|ref|YP_002994783.1| 46 PVVDESKCIKCYICWKFCPE------PAIYIKEDGYVAVDYDYCKGCGICANECP 94
                                      6899****************......67777788888889**************9 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 2.9e-06
                           Fer4_10  3 vidddtCirCgkCvkaCPadlt 24
                                       +d d C +Cg C + CP+++ 
  gi|242399359|ref|YP_002994783.1| 77 AVDYDYCKGCGICANECPTKAI 98
                                      5799***************653 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.9     5e-05      0.06       1      20 [.      52      71 ..      52      79 .. 0.85
   2 !   21.1   3.0   3.7e-07   0.00044       2      22 ..      83     103 ..      82     105 .] 0.88

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5e-05
                           Fer4_16  1 rCgtCgkCaevCPtnaikek 20
                                      +C++C  C + CP+ ai  k
  gi|242399359|ref|YP_002994783.1| 52 KCIKCYICWKFCPEPAIYIK 71
                                      6***************9765 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 3.7e-07
                           Fer4_16   2 CgtCgkCaevCPtnaikekke 22 
                                       C++Cg Ca+ CPt+ai++ +e
  gi|242399359|ref|YP_002994783.1|  83 CKGCGICANECPTKAISMVRE 103
                                       ****************98855 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 !   13.3   0.5     9e-05      0.11       2      20 ..      47      65 ..      47      75 .. 0.82
   2 !   15.0   3.1   2.7e-05     0.032       1      20 [.      76      95 ..      76      98 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9e-05
                           Fer4_15  2 vvDrdaCigcglCvaeape 20
                                      vvD+++Ci c  C++ +pe
  gi|242399359|ref|YP_002994783.1| 47 VVDESKCIKCYICWKFCPE 65
                                      69***************87 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 2.7e-05
                           Fer4_15  1 VvvDrdaCigcglCvaeape 20
                                      V vD d C gcg C+ e+p+
  gi|242399359|ref|YP_002994783.1| 76 VAVDYDYCKGCGICANECPT 95
                                      88****************95 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 !   19.6   2.5   8.4e-07     0.001       1      19 [.      48      66 ..      48      78 .. 0.79
   2 !   10.2   3.0   0.00071      0.85       1      17 [.      78      94 ..      78      96 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 8.4e-07
                           Fer4_13  1 VDrdtCiacgaCvelaPdv 19
                                      VD+++Ci c +C++++P+ 
  gi|242399359|ref|YP_002994783.1| 48 VDESKCIKCYICWKFCPEP 66
                                      9****************85 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00071
                           Fer4_13  1 VDrdtCiacgaCvelaP 17
                                      VD d C +cg+C++ +P
  gi|242399359|ref|YP_002994783.1| 78 VDYDYCKGCGICANECP 94
                                      899************** PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   1.6    0.0009       1.1       1      18 [.      52      69 ..      52      82 .. 0.79
   2 ?   11.4   2.6   0.00029      0.35       2      16 ..      83      97 ..      82     105 .] 0.79

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0009
                           Fer4_17  1 rCiqCgyClpeCpsyeay 18
                                      +Ci+C  C + Cp  ++y
  gi|242399359|ref|YP_002994783.1| 52 KCIKCYICWKFCPEPAIY 69
                                      6***********986554 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00029
                           Fer4_17  2 CiqCgyClpeCpsye 16
                                      C +Cg C++eCp+ +
  gi|242399359|ref|YP_002994783.1| 83 CKGCGICANECPTKA 97
                                      999999999999755 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   1.8    0.0022       2.6       2      15 ..      51      64 ..      50      74 .. 0.90
   2 ?   11.6   4.0   0.00027      0.32       2      16 ..      81      95 ..      80      96 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0022
                            Fer4_4  2 erCigCgsCvaaCP 15
                                      ++Ci C  C  +CP
  gi|242399359|ref|YP_002994783.1| 51 SKCIKCYICWKFCP 64
                                      58***********9 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00027
                            Fer4_4  2 erCigCgsCvaaCPq 16
                                      + C gCg C + CP+
  gi|242399359|ref|YP_002994783.1| 81 DYCKGCGICANECPT 95
                                      89************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 ?    4.4  13.2     0.043        51       4      64 ..      52      96 ..      49      97 .. 0.59
   2 ?   11.7   3.8   0.00023      0.27       3      63 ..      81      95 ..      79     104 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.043
                            Fer4_8  4 kCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64
                                      kCi+C  C + Cp      +   + +++        +        ++C +cg C+++Cp++
  gi|242399359|ref|YP_002994783.1| 52 KCIKCYICWKFCP------EPAIYIKEDGYV---AVD-------YDYCKGCGICANECPTK 96
                                      6777777777776......222222222112...112.......47899999999999986 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00023
                            Fer4_8  3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpv 63
                                      ++C +Cg C ++Cp                                              +
  gi|242399359|ref|YP_002994783.1| 81 DYCKGCGICANECP----------------------------------------------T 95
                                      45666666666666..............................................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 ?    6.4   1.1     0.014        17      74      94 ..      45      65 ..      32      68 .. 0.69
   2 ?    5.2   1.3     0.032        38       1      15 [.      52      66 ..      52      80 .. 0.82
   3 ?   10.7   2.4    0.0006      0.71      77      95 ..      78      96 ..      68      97 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.014
                           Fer4_22 74 kekfgesgCvGCgRCieacpv 94
                                      +  ++es+C+ C  C + cp+
  gi|242399359|ref|YP_002994783.1| 45 MPVVDESKCIKCYICWKFCPE 65
                                      555667777777777777764 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.032
                           Fer4_22  1 rClsCgaCtlvCptC 15
                                      +C++C  C   Cp  
  gi|242399359|ref|YP_002994783.1| 52 KCIKCYICWKFCPEP 66
                                      7***********965 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.0006
                           Fer4_22 77 fgesgCvGCgRCieacpvk 95
                                      ++   C GCg C + cp+k
  gi|242399359|ref|YP_002994783.1| 78 VDYDYCKGCGICANECPTK 96
                                      57789***********975 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   8.5     0.012        14      57      96 ..      49      94 ..      41     102 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.012
                           Fer4_18 57 gagdcidcescvkvcPt.gidirk.G...lqle.ciscllcidacd 96
                                      ++++ci+c  c k cP   i i++ G   + ++ c  c+ c + c 
  gi|242399359|ref|YP_002994783.1| 49 DESKCIKCYICWKFCPEpAIYIKEdGyvaVDYDyCKGCGICANECP 94
                                      5789************746899862421123335999999999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 742.57
//
Query:       gi|242399360|ref|YP_002994784.1|  [L=186]
Description: pyruvate:ferredoxin oxidoreductase (POR) and 2-ketoisovalerate:ferredoxin oxidoreductase (VOR) subunit gamma [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.4e-44  151.5   0.6    2.8e-44  151.3   0.6    1.0  1  POR         Pyruvate ferredoxin/flavodoxin oxidoreductase
  ------ inclusion threshold ------
      0.041   13.6   0.0      0.058   13.1   0.0    1.2  1  MAF_flag10  Protein of unknown function DUF115


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 !  151.3   0.6   3.1e-48   2.8e-44       1     177 []      11     179 ..      11     179 .. 0.96

  Alignments for each domain:
  == domain 1  score: 151.3 bits;  conditional E-value: 3.1e-48
                                       CTSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHH..HHGGG CS
                               POR   1 GGqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetls..ehldg 75 
                                       GGqG+vta++ila+ a+ +G+yvqa++++g e+rG+++++  ri+++pi+   +++e+d++v+ld+++l+  ++ +g
  gi|242399360|ref|YP_002994784.1|  11 GGQGAVTAANILAEGAFLEGKYVQAFPFFGVERRGAPVTAFTRIDEKPIRIKTQIYEPDVVVVLDPSLLDtvDVTAG 87 
                                       9*************************************************99999**************99****** PP

                                       EEEEEEEEEECTCGTT-CCHHHCTS-HHHHHHHT-EEEEE-HHHHHHHCCC.CCHHHHHHHHHHHHHHT.S-HHHHH CS
                               POR  76 lkpggiiiynseelkpdelkkakeeerelkerlgvrvygvdatkiakeiggneraaNtvmlGalaallg.lpleale 151
                                       lk+gg++i+n+e++k+++l+k k   +        ++  vdat ia ei+g  +++Nt +lGa+a+++g +++e++e
  gi|242399360|ref|YP_002994784.1|  88 LKEGGLVIVNTEKTKEEVLEKLKKKPA--------KLALVDATTIALEILG-LPITNTSILGAVAKATGiVKIESVE 155
                                       ************999999999887543........5779************.************************* PP

                                       HHHHCCS-CH.HHHHHHHHHHHHHHH CS
                               POR 152 eaikkrfpkkkeviekNlkafragye 177
                                       eaik++f +  e+ ekN ka+r+++e
  gi|242399360|ref|YP_002994784.1| 156 EAIKEAFSG--ELGEKNAKAAREAFE 179
                                       ********9..8***********986 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 ?   13.1   0.0   6.4e-06     0.058      69     125 ..      67     125 ..      61     147 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.4e-06
                        MAF_flag10  69 kPDivvslDpqeasyevfkeaekkgdiplvfasgvnpellkkykgpki..flvtgstqa 125
                                       +PD+vv lDp+ ++  ++    k+g  ++v+++ +++e+l+k+k++ +   lv+++t+a
  gi|242399360|ref|YP_002994784.1|  67 EPDVVVVLDPSLLDTVDVTAGLKEGGLVIVNTEKTKEEVLEKLKKKPAklALVDATTIA 125
                                       6*********888887777777778****************998763322556665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       654  (0.0364772); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1242.91
//
Query:       gi|242399361|ref|YP_002994785.1|  [L=38]
Description: hypothetical protein TSIB_1385 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      197  (0.0109878); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.29s 00:00:00.65 Elapsed: 00:00:00.45
# Mc/sec: 251.64
//
Query:       gi|242399362|ref|YP_002994786.1|  [L=327]
Description: Sodium/phosphate symporter [Thermococcus sibiricus MM 739]
Scores for complete 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-70  236.5  33.2    2.9e-69  233.7  33.2    1.9  1  PHO4      Phosphate transporter family


Domain annotation for each model (and alignments):
>> PHO4  Phosphate transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  233.7  33.2   1.6e-73   2.9e-69       1     336 [.      26     313 ..      26     314 .. 0.93

  Alignments for each domain:
  == domain 1  score: 233.7 bits;  conditional E-value: 1.6e-73
                              PHO4   1 iGanDvanafatsvgskaltlrqAvilaaifeflGavllGaeVaetirkgivdvelfdpselm.lgmlaallgaavw 76 
                                       iGanD ana++t+vg++ l+ rqA +  +if +lGa+l G++V++ti+kgiv      p+ l   ++++all+a++w
  gi|242399362|ref|YP_002994786.1|  26 IGANDSANAMGTAVGAGLLSFRQATLTITIFVVLGAYLKGSKVMKTIGKGIV-----PPEYLSlELAIIALLAAGTW 97 
                                       7***************************************************.....566666459999******** PP

                              PHO4  77 lllatvlglPvStthslvGaliGaalaaeggeavkwkklvkivlswvlsPllggiiaallfllvkrlilvkeklkna 153
                                       +++at+ glPvStt+s+vG+++G+++a   +  +kw++lvki+ +wv+sP+l++++a +lf +  +l+         
  gi|242399362|ref|YP_002994786.1|  98 VTIATIKGLPVSTTQSIVGGVVGIGIA--TNAPIKWETLVKIAGAWVFSPILAALFALILFKFYGKLVN-------D 165
                                       ***************************..4679**********************************44.......3 PP

                              PHO4 154 lralpvlvlvtiailalsilfkgeskkddeeteklfkflqvvsaalvsfahGanDvanaiGpllaalisiykaskev 230
                                       +++l                          ++e l+k+l v+ +++++f  Gan+vana+Gpl+ a +        +
  gi|242399362|ref|YP_002994786.1| 166 IKSL-------------------------GRIEFLYKWLAVLGGSYMAFNFGANEVANATGPLVGAGF-------FD 210
                                       4444.........................478999****************************66654.......35 PP

                              PHO4 231 plwvlllgglaialGlllgGkrviktvGekitkkltpsrGfaaelaaaltvllasklglPvStThvlvgavvGvGla 307
                                       p    ++g+l++alG +++ + vi tvG+kit +l p+++f+a++++a+ v la+ +glPvS+++++vg+v+GvG+a
  gi|242399362|ref|YP_002994786.1| 211 PKTAGMFGALSLALGAFTFSYAVIYTVGKKIT-SLGPISAFSAQFGSAIAVSLANIFGLPVSSSQAIVGGVIGVGIA 286
                                       88899***************************.6******************************************* PP

                              PHO4 308 kkresavnwklvrnivlaWvlTlpvsall 336
                                        +   +v+ +++++i+++W+ T   + ++
  gi|242399362|ref|YP_002994786.1| 287 SG--MKVEKGIIKDIAIGWIATPTTALII 313
                                       *6..6*****************9988887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       755  (0.0421105); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         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: 00:00:00.45
# Mc/sec: 2196.13
//
Query:       gi|242399363|ref|YP_002994787.1|  [L=425]
Description: ABC transporter [Thermococcus sibiricus MM 739]
Scores for complete 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  139.3  24.5    1.8e-40  139.1  24.5    1.0  1  ABC2_membrane_3  ABC-2 family transporter protein
    1.1e-29  103.6  19.6    1.6e-29  103.1  19.6    1.2  1  ABC2_membrane_2  ABC-2 family transporter protein
    1.5e-13   50.6  20.8    1.5e-13   50.6  20.8    2.6  3  ABC2_membrane    ABC-2 type transporter
    3.1e-06   27.3  14.7    3.1e-06   27.3  14.7    3.3  3  ABC2_membrane_4  ABC-2 family transporter protein
    5.7e-06   26.0  26.2    5.7e-06   26.0  26.2    2.5  3  ABC2_membrane_5  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.1  24.5   5.1e-44   1.8e-40       1     344 [.      19     406 ..      19     407 .. 0.87

  Alignments for each domain:
  == domain 1  score: 139.1 bits;  conditional E-value: 5.1e-44
                   ABC2_membrane_3   1 ksfliitlllPiilvlllglifsnsve.ddentpiavvdednsslsqqlvealeaspsve.lvyevdseeeakkalk 75 
                                       k++++ ++++P+il+  lg ++++++  ++e+t+i +v+ d  ++ + l++ lea p+v+ +++e+ +++ea k+ +
  gi|242399363|ref|YP_002994787.1|  19 KGLIFGIIVVPLILYPALGQMMQIGFQqAQEETKIVLVNFDEGDYGNLLIKTLEAAPNVTvTIIEALNLDEALKKAQ 95 
                                       678899999**************999999*******************************9**************** PP

                   ABC2_membrane_3  76 ngdidgilvipkgfskdllkgesatvtvlinssnlnss..........kailnalns.llqqlnasalv.lqseats 140
                                       ++d+++i+vi k+fsk++++++ a+v+++   ++ +            +ail  +n+ l + ++++++   ++ ++ 
  gi|242399363|ref|YP_002994787.1|  96 EEDYNMIVVISKNFSKSIESNQKAQVEIYGIVKGISGGmresisegrvNAILTVINDyLAKLKIQQNMEgDPEAILR 172
                                       ********************99******99999999999999******88888888866655555554453333333 PP

                   ABC2_membrane_3 141 tsaninvestql..........eeelsnv..asflvgliliilifitasfiavsiveEkesrikelqlvsgvsplqy 205
                                          +i+ +s++           +  +s +  +sf ++++++i+i+++a++ a s++ Eke++++e +l+ +v+++++
  gi|242399363|ref|YP_002994787.1| 173 ---PIDARSYTVirgrivpvppSLVASLItsQSFSMPIVIFIMIIMVAQMSAGSMAMEKENKTLETLLTLPVKRITI 246
                                       ...3333333334457787777555544411556677**************************************** PP

                   ABC2_membrane_3 206 wlskilgdflvyllqlllill.l..afgl...............gipfg..nlglllllfllfglayialgyllssl 262
                                       + +k++g+++++++ ++ +++ +  ++g                g++++  +  l++l ++l +  ++++++ll ++
  gi|242399363|ref|YP_002994787.1| 247 VAGKMVGTAIIGIIAAVTYMIgMrsYLGNmisssgeigisledlGLTVTpqGAALFVLIMFLAITFALSFAMLLAVF 323
                                       *****************9999877777778999****99999995555543667777999999************** PP

                   ABC2_membrane_3 263 fknsetaqilifivilllsgffgglfp..ledlpsalkwifsiiPffapglgllrlitgdplweillsliilalfav 337
                                         ++++a++++++ i++l +  ++l++  +e+lp a+k+++  +Pf++p+l+   +++g+ ++++  s+++l +++ 
  gi|242399363|ref|YP_002994787.1| 324 AEDTKSANAVVSAGIMPLAFPTFILMFadIETLPLAIKYLLLALPFSHPILASRAMLMGQ-YSSMYVSVLYLGILST 399
                                       ****************888888877777********************************.88999*********** PP

                   ABC2_membrane_3 338 vylllal 344
                                       v+l++++
  gi|242399363|ref|YP_002994787.1| 400 VTLVITA 406
                                       ****987 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 !  103.1  19.6   4.4e-33   1.6e-29       1     287 [.       5     413 ..       5     414 .. 0.83

  Alignments for each domain:
  == domain 1  score: 103.1 bits;  conditional E-value: 4.4e-33
                   ABC2_membrane_2   1 laiakkEfrdlvrsrrfllltvllpli............................................dvalay 33 
                                       ++i+kkE+rdl+r++ ++   +++pli                                             v +++
  gi|242399363|ref|YP_002994787.1|   5 WIIVKKELRDLLRDKGLIFGIIVVPLIlypalgqmmqigfqqaqeetkivlvnfdegdygnlliktleaapNVTVTI 81 
                                       89*************************88888888888888888888888888888888888888888888777888 PP

                   ABC2_membrane_2  34 lkdlgsslqseakaikeatlaleyveaasasdeaedtdqdlkv.................................. 76 
                                       +++l  ++  +++++ +    +  ++  s+ ++ ++++++ ++                                  
  gi|242399363|ref|YP_002994787.1|  82 IEALNLDEALKKAQEEDYNMIVVISKNFSK-SIESNQKAQVEIygivkgisggmresisegrvnailtvindylakl 157
                                       777777777766666655555555554444.66666666666699999999999999999999999*********** PP

                   ABC2_membrane_2  77 ..............................................vstimavlipviaalfgadaiagEkergTlk 107
                                                                                     ++ i+++++ ++ a ++a + a Eke++Tl+
  gi|242399363|ref|YP_002994787.1| 158 kiqqnmegdpeailrpidarsytvirgrivpvppslvaslitsqsfSMPIVIFIMIIMVAQMSAGSMAMEKENKTLE 234
                                       *********************************************7666777777778999**************** PP

                   ABC2_membrane_2 108 llLskPvsRdeillgKfigglaiglaiavallatvll..alaiilalgivlaledllllv......vasvlllllv. 175
                                        lL++Pv R +i++gK++g ++ig++ av++++++    + +i+ +++i ++ledl l+v      +++++++l++ 
  gi|242399363|ref|YP_002994787.1| 235 TLLTLPVKRITIVAGKMVGTAIIGIIAAVTYMIGMRSylGNMISSSGEIGISLEDLGLTVtpqgaaLFVLIMFLAIt 311
                                       *************************99999999965555778899999999*****999744444356666666669 PP

                   ABC2_membrane_2 176 vflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavpqeindflsllsptsayntllneilag 252
                                       ++l++++ll+++a ++++a a++ + ++ la+    + + +a++++ p +       l+l  p+s+  ++ +++l+g
  gi|242399363|ref|YP_002994787.1| 312 FALSFAMLLAVFAEDTKSANAVVSAGIMPLAFP--TFILMFADIETLPLA----IKYLLLALPFSHPILASRAMLMG 382
                                       99************7776666655555555444..333334444444433....24488999999999********* PP

                   ABC2_membrane_2 253 sdlnalgstatnllilllllavllvlgyvlFkrkD 287
                                       +    + s   ++l+l +l +v lv+++ +F +++
  gi|242399363|ref|YP_002994787.1| 383 Q----YSSMYVSVLYLGILSTVTLVITARFFTTEK 413
                                       *....789999********************9886 PP

>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.5   0.0    0.0028       9.9       3      41 ..       4      41 ..       2      81 .. 0.87
   2 !   50.6  20.8   4.2e-17   1.5e-13      33     209 ..     196     380 ..     176     381 .. 0.83
   3 ?   -3.4   0.3       1.5   5.3e+03      59      77 ..     390     406 ..     384     419 .. 0.42

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0028
                     ABC2_membrane  3 ikallkreflqrwrdpslgllwrliqplllalvfgtvfg 41
                                      +++++k+e++  +rd+ l+ +  ++ pl+l   +g +  
  gi|242399363|ref|YP_002994787.1|  4 FWIIVKKELRDLLRDKGLI-FGIIVVPLILYPALGQMMQ 41
                                      89****************9.9**********99999886 PP

  == domain 2  score: 50.6 bits;  conditional E-value: 4.2e-17
                     ABC2_membrane  33 alvfgtvfgnlgnsedglnrpgllffsvlflafsaltsvapvferergvlerelvsplyslsayvlakvlvelpvsl 109
                                       +l+              +++p ++f++++++a ++ +++ + +e+e+++le +l+ p+ ++ ++v++k+++ +++++
  gi|242399363|ref|YP_002994787.1| 196 SLITSQ----------SFSMPIVIFIMIIMVA-QMSAGS-MAMEKENKTLETLLTLPV-KRITIVAGKMVGTAIIGI 259
                                       444444..........4458************.555555.******************.****************** PP

                     ABC2_membrane 110 lqalifllivyflv.................gldls.rf.flflllllltalaasslgllisalapsfedasqlasl 167
                                       ++a+ +++ +   +                 gl+++ ++ +lf+l+++l + +a+s+++l++++a++ + a+ ++s+
  gi|242399363|ref|YP_002994787.1| 260 IAAVTYMIGMRSYLgnmisssgeigisledlGLTVTpQGaALFVLIMFLAITFALSFAMLLAVFAEDTKSANAVVSA 336
                                       ********98886534446666665555555555557558************************************* PP

                     ABC2_membrane 168 vllplll..lsGffipidsmpkwlqwiaylnPltyavealrsnl 209
                                        ++pl +  +  +f  i+++p  ++++  ++P+++ + a r+ l
  gi|242399363|ref|YP_002994787.1| 337 GIMPLAFptFILMFADIETLPLAIKYLLLALPFSHPILASRAML 380
                                       ****9984455567888999*9999***********99988765 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 1.5
                     ABC2_membrane  59 svlflafsaltsvapvfer 77 
                                       svl+l+  +l++v +v+  
  gi|242399363|ref|YP_002994787.1| 390 SVLYLG--ILSTVTLVITA 406
                                       333333..22222222222 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 ?    0.7   0.0      0.13   4.6e+02       2      44 ..       8      50 ..       7      71 .. 0.76
   2 !   27.3  14.7   8.7e-10   3.1e-06      48     148 ..     199     314 ..     189     333 .. 0.57
   3 ?   -7.2  13.1         5   1.8e+04      16     120 ..     304     399 ..     299     419 .. 0.45

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.13
                   ABC2_membrane_4  2 iktEflKlkrskivwllvlaallvpllallyfnllgktgldpa 44
                                      +k E+  l r k ++++++++ l+ ++al  ++++g ++++++
  gi|242399363|ref|YP_002994787.1|  8 VKKELRDLLRDKGLIFGIIVVPLILYPALGQMMQIGFQQAQEE 50
                                      5667777889999999999999999999999988876666544 PP

  == domain 2  score: 27.3 bits;  conditional E-value: 8.7e-10
                   ABC2_membrane_4  48 slsvfgftlllllplilgi.iasylifrEeqndtlknLltiPvsrtklllaKlivllllsvllmlvtf..litvlfa 121
                                       + ++f++ +++++++i++  +++ ++ +E++n+tl  Llt+Pv+r +++++K++ ++++ ++  ++ +  + + l  
  gi|242399363|ref|YP_002994787.1| 199 TSQSFSMPIVIFIMIIMVAqMSAGSMAMEKENKTLETLLTLPVKRITIVAGKMVGTAIIGIIAAVTYMigMRSYLGN 275
                                       445666665544444444448999*******************************9999998876644112233444 PP

                   ABC2_membrane_4 122 llsgfvgfsvkl............vlellkkclelgllv 148
                                       ++s + ++ ++l             l++l ++l ++  +
  gi|242399363|ref|YP_002994787.1| 276 MISSSGEIGISLedlgltvtpqgaALFVLIMFLAITFAL 314
                                       444332222221111111111111222222222222222 PP

  == domain 3  score: -7.2 bits;  conditional E-value: 5
                   ABC2_membrane_4  16 wllvlaallvpllallyfnllgktgldpaefyslsvfgftlllllplilgiiasylifrEeqndtlknLl.tiPvsr 91 
                                       ++++la+ ++  +a+l+   +++t+ +        ++ +    ++pl +  +  +    E+    +k+Ll  +P s 
  gi|242399363|ref|YP_002994787.1| 304 LIMFLAITFALSFAMLLAVFAEDTK-S--------ANAVVSAGIMPLAFPTFILMFADIETLPLAIKYLLlALPFSH 371
                                       2222222222223333222111111.1........111112224555555555566677777777777764677776 PP

                   ABC2_membrane_4  92 tklllaKlivllllsvllmlvtflitvlf 120
                                         +l++  +++  +s +++ v++l  + +
  gi|242399363|ref|YP_002994787.1| 372 P-ILASRAMLMGQYSSMYVSVLYLGILST 399
                                       5.666666666666665555555444433 PP

>> ABC2_membrane_5  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1      0.29     1e+03     150     183 ..      22      55 ..      16      58 .. 0.65
   2 !   26.0  26.2   1.6e-09   5.7e-06      27     175 ..     194     361 ..     186     405 .. 0.70
   3 ?   -1.7   0.6      0.51   1.8e+03      81     100 ..     386     405 ..     379     416 .. 0.59

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.29
                   ABC2_membrane_5 150 liiiifgiifllvaifslsklelslidlsnyill 183
                                       ++ ii++  +l++a+ +++++ +++ + ++ i+l
  gi|242399363|ref|YP_002994787.1|  22 IFGIIVVPLILYPALGQMMQIGFQQAQEETKIVL 55 
                                       4444555555778888888888887777766665 PP

  == domain 2  score: 26.0 bits;  conditional E-value: 1.6e-09
                   ABC2_membrane_5  27 iiliflndsvllifsilslvis.iililttlsyDekskwnkylltLPvtrkeiVksKYlfvlililiailitllll. 101
                                       + ++++++s+++ ++i++++i+ +++   +++ ++ +k+   lltLPv+r +iV+ K ++++i+++ia + +++ + 
  gi|242399363|ref|YP_002994787.1| 194 VASLITSQSFSMPIVIFIMIIMvAQMSAGSMAMEKENKTLETLLTLPVKRITIVAGKMVGTAIIGIIAAVTYMIGMr 270
                                       44555566666666666665554888899*******************************************99965 PP

                   ABC2_membrane_5 102 .iiavlikgn...........vtisevllsiliglvialiflaivlPlyfkfgvekgrivliiiifg...iif..ll 161
                                        +++++i+++           +t+ +   ++++ +++  i +a+++ +++   +e ++ ++ ++++g   ++f  ++
  gi|242399363|ref|YP_002994787.1| 271 sYLGNMISSSgeigisledlgLTVTPQGAALFVLIMFLAITFALSFAMLLAVFAEDTKSANAVVSAGimpLAFptFI 347
                                       48999999999999777777744445555555555555555666666666666666666666666651113333233 PP

                   ABC2_membrane_5 162 vaifslsklelsli 175
                                         +  +++l l++ 
  gi|242399363|ref|YP_002994787.1| 348 LMFADIETLPLAIK 361
                                       33333444444433 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.51
                   ABC2_membrane_5  81 sKYlfvlililiailitlll 100
                                       s Y++vl l++++++ ++++
  gi|242399363|ref|YP_002994787.1| 386 SMYVSVLYLGILSTVTLVIT 405
                                       34555555555555544443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1417  (0.079034); expected 358.6 (0.02)
Passed bias filter:                      632  (0.0352502); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2771.43
//
Query:       gi|242399364|ref|YP_002994788.1|  [L=249]
Description: Daunorubicin resistance ATP-binding like protein drrA [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.9e-27   94.3   0.0    1.2e-26   93.8   0.0    1.2  1  ABC_tran     ABC transporter
    4.3e-12   46.5   0.2    7.5e-05   22.7   0.1    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    2.7e-05   24.7   0.1    3.6e-05   24.3   0.1    1.3  1  AAA_23       AAA domain
    4.9e-05   23.0   0.1     0.0001   21.9   0.1    1.5  1  AAA_29       P-loop containing region of AAA domain
     0.0013   18.2   0.2        1.7    8.1   0.0    2.3  2  SMC_N        RecF/RecN/SMC N terminal domain
     0.0022   17.8   0.0     0.0034   17.2   0.0    1.5  1  AAA_15       AAA ATPase domain
     0.0079   16.1   0.0      0.016   15.1   0.0    1.4  1  Rad17        Rad17 P-loop domain
  ------ inclusion threshold ------
      0.019   14.6   0.0      0.033   13.8   0.0    1.4  1  AAA_27       AAA domain
       0.02   14.5   0.1       0.23   11.1   0.1    2.2  2  SRP54        SRP54-type protein, GTPase domain
      0.024   14.3   0.3      0.037   13.7   0.3    1.5  1  AAA_30       AAA domain
      0.032   13.6   0.4       0.16   11.2   0.1    2.1  2  AAA_8        P-loop containing dynein motor region D4
      0.034   14.4   0.1       0.07   13.4   0.1    1.6  1  AAA_22       AAA domain
      0.051   14.1   0.1       0.14   12.7   0.0    1.7  2  AAA_18       AAA domain
      0.078   12.0   0.1       0.15   11.0   0.1    1.5  1  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
       0.12   12.4   0.3         18    5.3   0.1    2.2  2  MutS_V       MutS domain V
       0.14   12.1   0.5       0.35   10.8   0.1    1.9  3  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 !   93.8   0.0   1.1e-29   1.2e-26       1     136 [.      19     162 ..      19     163 .. 0.84

  Alignments for each domain:
  == domain 1  score: 93.8 bits;  conditional E-value: 1.1e-29
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l+ +s+++kege+ +++G+nGaGKSt lk+la ll+pt G+ ++ g+d+ + +  ++rk i++lp+e+   ++l+  
  gi|242399364|ref|YP_002994788.1|  19 LRGISFEIKEGEIFGLIGPNGAGKSTTLKILATLLTPTGGRAEVFGHDVVK-DGDEVRKLISYLPEEAGAYKNLKGI 94 
                                       6789**********************************************9.9999***********9999999855 PP

                                       HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       e               ++e +e  ++  gl +  +    ++ s++S+G+ +++ laral+ +pkl +lDEp 
  gi|242399364|ref|YP_002994788.1|  95 EYlqfmaklyaktgkSYEEMLEVGVKLSGLGDRLN----DKISTYSKGMTRKLLLARALMVEPKLAILDEPA 162
                                       55699999998555333333444444444444445....555*****************************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 !   22.7   0.1   6.7e-08   7.5e-05       1      26 [.      31      58 ..      31     100 .. 0.65
   2 !   22.0   0.0   1.1e-07   0.00012     194     300 ..     116     196 ..     105     199 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 6.7e-08
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllarl..d 26
                                      + +liGpNg+GKS+ L++l  l      
  gi|242399364|ref|YP_002994788.1| 31 IFGLIGPNGAGKSTTLKILATLLTPtgG 58
                                      578****************888643442 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 1.1e-07
                            AAA_21 194 lveielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngL 270
                                       +v+ +ls lg++ ++                         ++  S G+ r l l+ al   +   +l ++DEp +gL
  gi|242399364|ref|YP_002994788.1| 116 EVGVKLSGLGDRLNDK------------------------ISTYSKGMTRKLLLARALMVEP---KLAILDEPASGL 165
                                       5555555554444443........................4455*******66666666666...89********** PP

                            AAA_21 271 HPkllrrllellkelsr.ngaQviltTHSpl 300
                                       +     ++ + +k+ +r +g+ +++++H+ l
  gi|242399364|ref|YP_002994788.1| 166 DIINAYSIRQTIKQFAReKGVTFLVSSHNML 196
                                       ************999999**********976 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.1   3.3e-08   3.6e-05      15     133 ..      22     140 ..      12     244 .. 0.72

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 3.3e-08
                            AAA_23  15 idF...skgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiesegkvkayvelt......fenk 82 
                                       i F   +  ++ ++GpNGaGK+T l  +   L+   +      +   + +dv  +++++v++ ++        ++n 
  gi|242399364|ref|YP_002994788.1|  22 ISFeikEGEIFGLIGPNGAGKSTTLKILATLLTPTGG------RAEVFGHDVV-KDGDEVRKLISYLpeeagaYKNL 91 
                                       4444466689***********************7422......3345666664.23334444455556666666665 PP

                            AAA_23  83 dgrytrsiererelskkkgkttkkaklelleideleqfisellgskkiiln 133
                                       +g+  + ++++ +l+ k gk++ +  + +++ + l ++++++++   + ++
  gi|242399364|ref|YP_002994788.1|  92 KGI--EYLQFMAKLYAKTGKSYEEMLEVGVKLSGLGDRLNDKISTYSKGMT 140
                                       564..6788899999999999999999999998888888887765555444 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   0.1   9.3e-08    0.0001      16      50 ..      23      57 ..      15      62 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 9.3e-08
                            AAA_29 16 tieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                      ++ei++ +++ l+Gp+G+GKST l  +++lL+p+ 
  gi|242399364|ref|YP_002994788.1| 23 SFEIKEGEIFGLIGPNGAGKSTTLKILATLLTPTG 57
                                      57787666999**********************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 !    8.0   0.1    0.0015       1.7      26      42 ..      31      47 ..      14      60 .. 0.78
   2 !    8.1   0.0    0.0015       1.7     149     199 ..     143     195 ..     137     212 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0015
                                      EEEEEESTTSSHHHHHH CS
                                      xxxxxxxxxxxxxxxxx RF
                             SMC_N 26 ftaivGpNGSGKsnlld 42
                                      +  ++GpNG+GKs  l 
  gi|242399364|ref|YP_002994788.1| 31 IFGLIGPNGAGKSTTLK 47
                                      55699********8765 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0015
                                       HHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHH..HHCTTSEEEEE-SSH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxx RF
                             SMC_N 149 LlfAiqkvkpaplyllDeidaaLDeknvkkvaellk..eksknaQfivislre 199
                                       Ll+A   +    l +lDe ++ LD  n   + + +k  +++k + f+v s++ 
  gi|242399364|ref|YP_002994788.1| 143 LLLARALMVEPKLAILDEPASGLDIINAYSIRQTIKqfAREKGVTFLVSSHNM 195
                                       66665444445589**********************43355669999999875 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0     3e-06    0.0034      17      50 ..      22      56 ..      15     140 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3e-06
                            AAA_15 17 veidlsee.ltvliGkNnsGKSsilealdlFlnnk 50
                                      ++ +++e  +  liG+N++GKS+ l++l  +l+ +
  gi|242399364|ref|YP_002994788.1| 22 ISFEIKEGeIFGLIGPNGAGKSTTLKILATLLTPT 56
                                      344444444889****************9999855 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.4e-05     0.016      34      70 ..      18      54 ..       8      59 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.4e-05
                             Rad17 34 wlkadvLesrkkriLLisGPsGCgkstvvkvLskelg 70
                                      +l+  + e ++ +i  + GP G gkst++k+L+  l+
  gi|242399364|ref|YP_002994788.1| 18 ALRGISFEIKEGEIFGLIGPNGAGKSTTLKILATLLT 54
                                      5666677778888999****************98775 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0     3e-05     0.033      10      50 ..      12      53 ..       5      66 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3e-05
                            AAA_27 10 ryGkftd.rsldfsaeeadlhliyGpNEAGKstalrAisdll 50
                                       yGk++  r ++f+ +e ++  ++GpN AGKst+l+ +  ll
  gi|242399364|ref|YP_002994788.1| 12 DYGKVKAlRGISFEIKEGEIFGLIGPNGAGKSTTLKILATLL 53
                                      577776535688888888888889***********9998887 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1    0.0002      0.23       6      39 ..      34      67 ..      30      72 .. 0.82
   2 ?    0.6   0.0      0.33   3.7e+02     163     195 ..     112     144 ..     105     145 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0002
                                      EEESTTSSHHHHHHHHHHHHHHTTS-EEEEEEST CS
                             SRP54  6 lvGlqGaGKTttlaKLaallkkegkkvllvaaDt 39
                                      l+G++GaGK ttl  La ll+  g ++ +   D+
  gi|242399364|ref|YP_002994788.1| 34 LIGPNGAGKSTTLKILATLLTPTGGRAEVFGHDV 67
                                      89****************9998877766666665 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.33
                                       HHHHTS-EEEEE-SSSTTGEEE--HHHHHHHHH CS
                             SRP54 163 aaelklPikfigvGekiedleefdperlvsrll 195
                                       +++l++ +k+ g+G++++d     ++ + ++ll
  gi|242399364|ref|YP_002994788.1| 112 EEMLEVGVKLSGLGDRLNDKISTYSKGMTRKLL 144
                                       6789999**********9988888888888886 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.3   3.3e-05     0.037      20      49 ..      31      60 ..      24     180 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.3e-05
                            AAA_30 20 vavltGpAGtGKttalkalreaweaaggrv 49
                                      +  l Gp G+GK+t+lk l+ +++  ggr 
  gi|242399364|ref|YP_002994788.1| 31 IFGLIGPNGAGKSTTLKILATLLTPTGGRA 60
                                      67799*****************99997544 PP

>> AAA_8  P-loop containing dynein motor region D4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.55   6.2e+02      29      46 ..      34      51 ..      24      58 .. 0.75
   2 ?   11.2   0.1   0.00015      0.16      70     125 ..     173     227 ..     170     244 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.55
                             AAA_8 29 lvGvgGsGrqsltkLAaf 46
                                      l+G +G G+ +  k+ a 
  gi|242399364|ref|YP_002994788.1| 34 LIGPNGAGKSTTLKILAT 51
                                      89*******987765443 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00015
                             AAA_8  70 lkkllkkagikqkevvfllsdnqiieesfledinnlLntGevpnLfskeekeeiie 125
                                       +++++k+ + ++k v+fl+s+++++e +fl d   l+n+G + ++ + +e++e +e
  gi|242399364|ref|YP_002994788.1| 173 IRQTIKQFA-REKGVTFLVSSHNMLEVEFLCDRVALINKGVIVEIGTPKELKEKYE 227
                                       566666666.5578*******************************99999887655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   6.2e-05      0.07       9      52 ..      33      90 ..      26     197 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.2e-05
                            AAA_22  9 vvtGesGtGKTtllrrlleqldeeakaee...........erpevvfvtlpsst...s 52
                                       ++G+ G+GK+t+l+ l+  l+     +e           e ++++++ + + +   +
  gi|242399364|ref|YP_002994788.1| 33 GLIGPNGAGKSTTLKILATLLTPTGGRAEvfghdvvkdgdEVRKLISYLPEEAGaykN 90
                                      589***************9997555555577777777665444444444444444443 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00012      0.14       3      44 ..      34      86 ..      33     113 .. 0.77
   2 ?   -2.0   0.0       4.5   5.1e+03      65      83 ..     178     194 ..     156     230 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00012
                            AAA_18  3 ltGtpGvGKttlakeLskrl.gf..........gvnlrdvakenglllevdpe 44
                                      l G+ G+GK+t  k L+ +l             +v+ +d +++  ++l++++ 
  gi|242399364|ref|YP_002994788.1| 34 LIGPNGAGKSTTLKILATLLtPTggraevfghdVVKDGDEVRKLISYLPEEAG 86
                                      89**************9997444888888888877777777777777776666 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.5
                            AAA_18  65 eenssaleegknlvidghl 83 
                                       ++   a+e+g + ++++h 
  gi|242399364|ref|YP_002994788.1| 178 KQF--AREKGVTFLVSSHN 194
                                       333..46777777777775 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   0.1   0.00014      0.15      25      63 ..      25      63 ..       6      69 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00014
                                      G-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEE CS
                              MeaB 25 kaGraqvvGltGvPGaGkstlvealglelrrrGkrvavl 63
                                      +  + +  Gl G  GaGkst+++ l++ l+  G r  v 
  gi|242399364|ref|YP_002994788.1| 25 EIKEGEIFGLIGPNGAGKSTTLKILATLLTPTGGRAEVF 63
                                      55566789************************9998876 PP

>> MutS_V  MutS domain V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.1     0.016        18       4      20 ..      35      51 ..      33      58 .. 0.83
   2 ?    5.2   0.0     0.017        19      49     120 ..     123     194 ..     109     232 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.016
                                      E-STTSSHHHHHHHHHH CS
                            MutS_V  4 tGpnmaGkstylrqval 20
                                       Gpn aGkst l+  a 
  gi|242399364|ref|YP_002994788.1| 35 IGPNGAGKSTTLKILAT 51
                                      6***********98764 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.017
                                       --------SS-HHHHHHHHHHHHHTT-.-TTSEEEEESTS-SS-HHHHHHHHHHHHHHHHHTT--EEEEEES- CS
                            MutS_V  49 gasDdlakgkstFmvEmlEtasilkna.tekslvilDElGRGtstydGlaialavaeyllekikaktlfatHy 120
                                       g +D+l+ + st+   m+    + +    e  l ilDE   G  + + ++i +++ ++   ++  + l + H 
  gi|242399364|ref|YP_002994788.1| 123 GLGDRLNDKISTYSKGMTRKLLLARALmVEPKLAILDEPASGLDIINAYSIRQTIKQFAR-EKGVTFLVSSHN 194
                                       56799999999999999876544444325779*******************999876655.567777888874 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00031      0.35      81     120 ..      10      50 ..       1      59 [. 0.79
   2 ?   -1.7   0.0       2.2   2.4e+03      36      83 ..     140     192 ..     133     217 .. 0.60
   3 ?   -3.3   0.0       6.7   7.5e+03      63      83 ..     218     237 ..     195     244 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00031
                                       E--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHC CS
                       RsgA_GTPase  81 lvsaktkegleelkellkd.ktsvlvGqSGvGKStLinall 120
                                         +  + ++l+ ++ ++k+ ++  l+G+ G+GKSt ++ l+
  gi|242399364|ref|YP_002994788.1|  10 EKDYGKVKALRGISFEIKEgEIFGLIGPNGAGKSTTLKILA 50 
                                       45555567788888999988999************998886 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.2
                                       HHHHHHHHHTT-EEEEEE.....E-GGG--HHHHHHHHHHHHHHTTSEEEE-- CS
                       RsgA_GTPase  36 drfLvlaeekgiepvivl.....nKiDlleeeeeleelkeelealgyevllvs 83 
                                       +r L+la +  +ep +++     + +D+++  +  +++k+  ++ g+++l+ s
  gi|242399364|ref|YP_002994788.1| 140 TRKLLLARALMVEPKLAIldepaSGLDIINAYSIRQTIKQFAREKGVTFLVSS 192
                                       56666666666666665533333445666666644445555555555555444 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 6.7
                                       HHHHHHHHHHHHTTSEEEE-- CS
                       RsgA_GTPase  63 eeleelkeelealgyevllvs 83 
                                       +  +elke++ea ++e +++s
  gi|242399364|ref|YP_002994788.1| 218 T-PKELKEKYEAENLEEVFMS 237
                                       3.5566666666666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); 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: 0.61u 0.35s 00:00:00.96 Elapsed: 00:00:00.53
# Mc/sec: 1417.53
//
Query:       gi|242399365|ref|YP_002994789.1|  [L=65]
Description: transcription regulator, containing DNA-binding HTH domain [Thermococcus sibiricus MM 739]
Scores for complete 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-20   71.1   0.2    6.3e-20   71.0   0.2    1.0  1  HTH_3           Helix-turn-helix
    1.6e-15   56.9   0.3    1.8e-15   56.7   0.3    1.0  1  HTH_19          Helix-turn-helix domain
    3.5e-10   40.1   0.0    3.8e-10   40.0   0.0    1.0  1  HTH_31          Helix-turn-helix domain
    3.7e-08   33.7   0.0    4.2e-08   33.5   0.0    1.0  1  HTH_26          Cro/C1-type HTH DNA-binding domain
    2.2e-07   30.6   0.3    2.8e-07   30.3   0.3    1.2  1  HTH_25          Helix-turn-helix domain
    0.00024   20.5   0.2    0.00038   19.9   0.2    1.3  1  Sigma70_r4      Sigma-70, region 4
    0.00033   20.5   0.3     0.0005   20.0   0.3    1.3  1  HTH_11          HTH domain
    0.00079   19.4   0.0     0.0013   18.6   0.0    1.4  1  HTH_Crp_2       Crp-like helix-turn-helix domain
      0.001   18.8   0.0     0.0016   18.2   0.0    1.3  1  HTH_23          Homeodomain-like domain
     0.0051   16.7   0.1     0.0073   16.2   0.1    1.2  1  MarR_2          MarR family
     0.0059   16.5   0.0      0.027   14.4   0.0    1.8  2  MarR            MarR family
     0.0063   16.4   0.0     0.0099   15.8   0.0    1.3  1  HTH_37          Helix-turn-helix domain
     0.0082   15.2   0.0     0.0082   15.2   0.0    1.1  1  TnsD            Tn7-like transposition protein D
  ------ inclusion threshold ------
      0.012   15.4   0.1      0.025   14.3   0.1    1.6  2  HTH_38          Helix-turn-helix domain
      0.014   14.9   0.1       0.02   14.4   0.1    1.3  1  HTH_24          Winged helix-turn-helix DNA-binding
      0.015   15.0   0.0      0.024   14.3   0.0    1.3  1  Sigma70_r4_2    Sigma-70, region 4
      0.018   14.8   0.0      0.021   14.5   0.0    1.0  1  Sigma54_DBD     Sigma-54, DNA binding domain
      0.019   14.8   0.0      0.024   14.5   0.0    1.2  1  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox
      0.033   14.2   0.6      0.069   13.2   0.1    1.7  2  HTH_7           Helix-turn-helix domain of resolvase
      0.072   13.0   0.0      0.086   12.7   0.0    1.1  1  Sigma70_ECF     ECF sigma factor
       0.11   12.9   0.0       0.34   11.3   0.0    1.7  2  WYL_3           WYL 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 !   71.0   0.2   7.4e-23   6.3e-20       1      54 [.       5      58 ..       5      59 .. 0.97

  Alignments for each domain:
  == domain 1  score: 71.0 bits;  conditional E-value: 7.4e-23
                                      HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSEHHH CS
                             HTH_3  1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgvslde 54
                                      l+elR+ +gl+qe+LA+ lGv+r+ti +iE+G+  Psl+ ++k+ak+++v++++
  gi|242399365|ref|YP_002994789.1|  5 LRELRELKGLTQEDLAKTLGVTRQTIIAIEKGKYDPSLRLAFKIAKFFKVKIED 58
                                      8**************************************************987 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.7   0.3   2.1e-18   1.8e-15       3      60 ..       4      60 ..       3      64 .. 0.96

  Alignments for each domain:
  == domain 1  score: 56.7 bits;  conditional E-value: 2.1e-18
                            HTH_19  3 rLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealgidleyll 60
                                      rL+e+Re +gltqe+la++lg++r  i+aiE+gk+ +ps +l  kia+++++ +e ++
  gi|242399365|ref|YP_002994789.1|  4 RLRELRELKGLTQEDLAKTLGVTRQTIIAIEKGKY-DPSLRLAFKIAKFFKVKIEDIF 60
                                      9*********************************9.****************998765 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   0.0   4.5e-13   3.8e-10       5      56 ..       4      54 ..       3      59 .. 0.93

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 4.5e-13
                            HTH_31  5 lLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralgl 56
                                      +Lr+lRe  GL+qe++A+ lgv++ t+  +E G+ + ps++   ++a  + +
  gi|242399365|ref|YP_002994789.1|  4 RLRELRELKGLTQEDLAKTLGVTRQTIIAIEKGKYD-PSLRLAFKIAKFFKV 54
                                      8**********************************7.****99999987766 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.0   4.9e-11   4.2e-08       1      62 [.       4      64 ..       4      65 .] 0.97

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 4.9e-11
                            HTH_26  1 kLrelmadrgitkseLargtgisaatlsrlvkgkpervsldtLdkiCdaLgctpgDLleyep 62
                                      +Lrel   +g+t+ +La+ +g++++t+  + kgk   +sl    ki++ ++++++D+++ye+
  gi|242399365|ref|YP_002994789.1|  4 RLRELRELKGLTQEDLAKTLGVTRQTIIAIEKGK-YDPSLRLAFKIAKFFKVKIEDIFIYED 64
                                      7********************************9.6************************97 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.3   3.3e-10   2.8e-07       1      36 [.       4      39 ..       4      45 .. 0.97

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 3.3e-10
                                      HHHHHHHTTT--HHHHHHHSS--HHHHHHHHCT--T CS
                            HTH_25  1 rLraaRearglsleevaketkIrkdylealEeddfd 36
                                      rLr+ Re +gl+ e++ak + +  +++ a+E++++d
  gi|242399365|ref|YP_002994789.1|  4 RLRELRELKGLTQEDLAKTLGVTRQTIIAIEKGKYD 39
                                      7********************************998 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.2   4.4e-07   0.00038      14      42 ..       7      35 ..       4      36 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 4.4e-07
                                      HHHHTTT--HHHHHHHHTS-HHHHHHHHH CS
                        Sigma70_r4 14 elrfgeglTleEIgerlgiSrerVrqiek 42
                                      elr ++glT+e+++++lg++r ++  iek
  gi|242399365|ref|YP_002994789.1|  7 ELRELKGLTQEDLAKTLGVTRQTIIAIEK 35
                                      57789*******************88886 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.3   5.9e-07    0.0005       6      33 ..       5      31 ..       2      32 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 5.9e-07
                            HTH_11  6 lelLleargpisgeeLAeeLnvSrrtvr 33
                                      l+ L+e +g ++ e+LA+ L+v+r+t+ 
  gi|242399365|ref|YP_002994789.1|  5 LRELRELKG-LTQEDLAKTLGVTRQTII 31
                                      678999999.****************95 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.6e-06    0.0013      21      39 ..      13      31 ..       2      34 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.6e-06
                                      EHHHHHHHHHTTSSHHHHH CS
                         HTH_Crp_2 21 pltqeelAsmlGltretvs 39
                                       ltqe+lA  lG+tr+t+ 
  gi|242399365|ref|YP_002994789.1| 13 GLTQEDLAKTLGVTRQTII 31
                                      49***************86 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.8e-06    0.0016       8      35 ..       5      31 ..       1      37 [. 0.77

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.8e-06
                            HTH_23  8 lrillllae..GlsvreIAreLgvsrrTvy 35
                                      lr l   +e  Gl++++ A+ Lgv+r+T+ 
  gi|242399365|ref|YP_002994789.1|  5 LREL---RElkGLTQEDLAKTLGVTRQTII 31
                                      4444...4455*****************95 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   8.5e-06    0.0073      11      38 ..       5      30 ..       5      33 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 8.5e-06
                                      HHHHHCTTTSEEEHHHHHHHHTSSHHHH CS
                            MarR_2 11 LaaLgrrpgrdltvgelarrlglsksav 38
                                      L +L+   g  lt+ +la++lg++++++
  gi|242399365|ref|YP_002994789.1|  5 LRELRELKG--LTQEDLAKTLGVTRQTI 30
                                      789999999..***************97 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   3.1e-05     0.027       9      34 ..       5      30 ..       4      33 .. 0.95
   2 ?   -0.3   0.0       1.2     1e+03      16      30 ..      40      55 ..      37      57 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.1e-05
                                      HHHHHHSTTEEHHHHHHHHTS-HHHH CS
                              MarR  9 LrilyeqgplsvseLakklgvskstv 34
                                      Lr l+e  +l++ +Lak lgv++ t+
  gi|242399365|ref|YP_002994789.1|  5 LRELRELKGLTQEDLAKTLGVTRQTI 30
                                      899********************997 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.2
                                      TTEEHH.HHHHHHTS- CS
                              MarR 16 gplsvs.eLakklgvs 30
                                      ++l+++ ++ak+++v+
  gi|242399365|ref|YP_002994789.1| 40 PSLRLAfKIAKFFKVK 55
                                      566777799*999986 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.2e-05    0.0099      23      56 ..       5      38 ..       1      41 [. 0.92

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.2e-05
                                      HHHHHHHCT--HHHHHHHHT--HHHHHHHHTT-- CS
                            HTH_37 23 iaeliekrelsqseaaqllgiaqPkvsrllrgkl 56
                                      ++el+e ++l+q+++a+ lg+++  + ++++gk 
  gi|242399365|ref|YP_002994789.1|  5 LRELRELKGLTQEDLAKTLGVTRQTIIAIEKGKY 38
                                      899**************************99986 PP

>> TnsD  Tn7-like transposition protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   9.6e-06    0.0082     188     222 ..       2      36 ..       1      58 [. 0.91

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 9.6e-06
                              TnsD 188 eerlkeLveeeglslkeiAkelgvdiktVlryakk 222
                                       ++rl+eL e +gl++++ Ak+lgv+ +t++ + k 
  gi|242399365|ref|YP_002994789.1|   2 KNRLRELRELKGLTQEDLAKTLGVTRQTIIAIEKG 36 
                                       789**************************998875 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   2.9e-05     0.025      12      37 ..       4      30 ..       2      31 .. 0.88
   2 ?   -2.2   0.0       4.4   3.7e+03      24      28 ..      45      50 ..      33      54 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.9e-05
                            HTH_38 12 eIerlla.eGlslreIArrLgrspsTI 37
                                      ++  l++ +Gl++ + A+ Lg+ ++TI
  gi|242399365|ref|YP_002994789.1|  4 RLRELRElKGLTQEDLAKTLGVTRQTI 30
                                      667788769*****************9 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 4.4
                            HTH_38 24 r.eIAr 28
                                      + +IA+
  gi|242399365|ref|YP_002994789.1| 45 AfKIAK 50
                                      246776 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   2.4e-05      0.02       9      34 ..       5      30 ..       5      33 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.4e-05
                            HTH_24  9 LelLqknprisqreLAerlglSpstv 34
                                      L++L++  +++q +LA+ lg++++t+
  gi|242399365|ref|YP_002994789.1|  5 LRELRELKGLTQEDLAKTLGVTRQTI 30
                                      778888889***************98 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   2.8e-05     0.024      20      43 ..       7      30 ..       7      30 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.8e-05
                                      HHHHTS---HHHHHHHHT--HHHH CS
                      Sigma70_r4_2 20 llryleglsykEIAellgisegtV 43
                                      +lr+l+gl++++ A+ lg++ +t+
  gi|242399365|ref|YP_002994789.1|  7 ELRELKGLTQEDLAKTLGVTRQTI 30
                                      69******************9996 PP

>> Sigma54_DBD  Sigma-54, DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   2.5e-05     0.021      45      93 ..       9      57 ..       3      60 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.5e-05
                                      XXXXXXXHHHHHTTSSSXHHHHHHHHHHXEEEXSSXEEECSCCXXXCSS CS
                       Sigma54_DBD 45 ealrpltlrevaealelhesTvSRvvsnkyiktprGvfelkafFsssvs 93
                                      ++l+ lt +++a++l++ + T+  + ++ky  + r  f++ +fF  +++
  gi|242399365|ref|YP_002994789.1|  9 RELKGLTQEDLAKTLGVTRQTIIAIEKGKYDPSLRLAFKIAKFFKVKIE 57
                                      789******************************************9986 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 ?   14.5   0.0   2.8e-05     0.024      10      52 ..      15      55 ..      12      59 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.8e-05
                    YdaS_antitoxin 10 gqkaLAealgvsqqaVsqWlkgkkqvpaervpeIekatnGeVt 52
                                      +q  LA+ lgv++q++    kgk   + +   +I k+ +  V+
  gi|242399365|ref|YP_002994789.1| 15 TQEDLAKTLGVTRQTIIAIEKGKYDPSLRLAFKIAKFFK--VK 55
                                      5899************99998888888888888888776..44 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   8.1e-05     0.069      12      38 ..       3      30 ..       1      31 [. 0.88
   2 ?   -1.4   0.0         3   2.6e+03      26      33 ..      47      54 ..      45      54 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.1e-05
                                      GGGGSSTTTT.--STTTSSSS---SSSS CS
                             HTH_7 12 nrvvkLleeG.isiskIAkevnisRsTv 38
                                      nr+++L+e +  +  ++Ak ++++R+T+
  gi|242399365|ref|YP_002994789.1|  3 NRLRELRELKgLTQEDLAKTLGVTRQTI 30
                                      788899986559***************8 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3
                                      TTSSSS-- CS
                             HTH_7 26 kIAkevni 33
                                      kIAk +++
  gi|242399365|ref|YP_002994789.1| 47 KIAKFFKV 54
                                      89999886 PP

>> Sigma70_ECF  ECF sigma factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0    0.0001     0.086     142     168 ..       4      30 ..       1      35 [. 0.91

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.0001
                       Sigma70_ECF 142 rlvelrkleGlsveEiAeklgvskrtv 168
                                       rl elr l+Gl+ e++A++lgv ++t+
  gi|242399365|ref|YP_002994789.1|   4 RLRELRELKGLTQEDLAKTLGVTRQTI 30 
                                       6779********************997 PP

>> WYL_3  WYL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0    0.0004      0.34      14      30 ..      12      28 ..       2      39 .. 0.79
   2 ?    0.2   0.0       1.2     1e+03      17      33 ..      34      50 ..      31      58 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0004
                             WYL_3 14 dgvtkedyAkkLgIadk 30
                                      +g t+ed Ak+Lg++ +
  gi|242399365|ref|YP_002994789.1| 12 KGLTQEDLAKTLGVTRQ 28
                                      799***********987 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.2
                             WYL_3 17 tkedyAkkLgIadkiak 33
                                       k +y   L++a kiak
  gi|242399365|ref|YP_002994789.1| 34 EKGKYDPSLRLAFKIAK 50
                                      67888899999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 444.07
//
Query:       gi|242399366|ref|YP_002994790.1|  [L=131]
Description: hypothetical protein TSIB_1390 [Thermococcus sibiricus MM 739]
Scores for complete 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-13   48.6   1.5    1.2e-12   47.9   1.6    1.3  1  DUF2178   Predicted membrane protein (DUF2178)
  ------ inclusion threshold ------
       0.57   10.3   0.1       0.57   10.3   0.1    2.2  2  SPC12     Microsomal signal peptidase 12 kDa subunit (SPC12)
       0.83   10.3   0.2       0.83   10.3   0.2    4.3  4  LPAM_1    Prokaryotic membrane lipoprotein lipid attachment s


Domain annotation for each model (and alignments):
>> DUF2178  Predicted membrane protein (DUF2178)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.9   1.6     2e-16   1.2e-12       3      98 ..      17     116 ..      11     123 .. 0.71

  Alignments for each domain:
  == domain 1  score: 47.9 bits;  conditional E-value: 2e-16
                           DUF2178   3 iivavialvglgiwaaignvllaviavaaGvllaillkkkve...evveDERlariaekAsrktlqillfliallgv 76 
                                        +va++ +vg+ +  ++g+ +l +ia+a+  + + l  + +e    ++eDER+ ri+e Asr+tlqi++++ a++++
  gi|242399366|ref|YP_002994790.1|  17 AVVALGWIVGWVT--NSGKSELSLIAFALTAIFVNLYFSYLEkkgFILEDERTLRINEIASRRTLQITSISLAVAML 91 
                                       4566666666666..7777777777777777777777777766669******************************9 PP

                           DUF2178  77 vliv..lksdfpey.trvgfllafs 98 
                                       +l+    + ++++    +g++la+ 
  gi|242399366|ref|YP_002994790.1|  92 LLSGklSDPKMEGAfLTAGLVLAVM 116
                                       9987333333333334555555544 PP

>> SPC12  Microsomal signal peptidase 12 kDa subunit (SPC12)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   9.5e-05      0.57      15      48 ..      13      44 ..       5      58 .. 0.71
   2 ?   -0.1   0.8      0.17     1e+03      22      52 ..      88     118 ..      73     122 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 9.5e-05
                             SPC12 15 vilvlsaviafivGyitqdlkltlyillagvvlt 48
                                       +l++++++++ivG++t++ k  l ++++  +lt
  gi|242399366|ref|YP_002994790.1| 13 PALLAVVALGWIVGWVTNSGKSELSLIAF--ALT 44
                                      57899999*********998766544333..222 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.17
                             SPC12  22 viafivGyitqdlkltlyillagvvltllvv 52 
                                       v+ +++   ++d k+   +l ag+vl+++++
  gi|242399366|ref|YP_002994790.1|  88 VAMLLLSGKLSDPKMEGAFLTAGLVLAVMLT 118
                                       3333444444555555555666666666665 PP

>> LPAM_1  Prokaryotic membrane lipoprotein lipid attachment site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   1.0     0.019   1.1e+02       2      13 ..       8      19 ..       8      21 .. 0.81
   2 ?   -0.3   1.3      0.31   1.9e+03       5      10 ..      40      45 ..      38      48 .. 0.51
   3 ?   10.3   0.2   0.00014      0.83       4      16 ..      83      95 ..      76      95 .. 0.91
   4 ?    2.7   0.3     0.035   2.1e+02       5      14 ..     106     115 ..     101     118 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.019
                            LPAM_1  2 KKillalgalll 13
                                      KK+ll ++++++
  gi|242399366|ref|YP_002994790.1|  8 KKMLLPALLAVV 19
                                      99*998888765 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.31
                            LPAM_1  5 llalga 10
                                       +al+a
  gi|242399366|ref|YP_002994790.1| 40 AFALTA 45
                                      355555 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.00014
                            LPAM_1  4 illalgalllLsG 16
                                      ++++++a+llLsG
  gi|242399366|ref|YP_002994790.1| 83 SISLAVAMLLLSG 95
                                      599*********9 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.035
                            LPAM_1   5 llalgalllL 14 
                                       +l++g++l++
  gi|242399366|ref|YP_002994790.1| 106 FLTAGLVLAV 115
                                       6778888764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       885  (0.0493614); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 786.05
//
Query:       gi|242399367|ref|YP_002994791.1|  [L=87]
Description: hypothetical protein TSIB_1391 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); 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: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.52
# Mc/sec: 504.68
//
Query:       gi|242399368|ref|YP_002994792.1|  [L=101]
Description: PRC-barrel domain protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-14   53.4   0.6    2.5e-14   53.1   0.6    1.1  1  PRC       PRC-barrel domain
  ------ inclusion threshold ------
       0.13   12.5   0.2        1.2    9.4   0.0    2.3  2  EB1       EB1-like C-terminal motif


Domain annotation for each model (and alignments):
>> PRC  PRC-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.1   0.6   2.8e-18   2.5e-14       1      76 [.       1      81 [.       1      84 [. 0.95

  Alignments for each domain:
  == domain 1  score: 53.1 bits;  conditional E-value: 2.8e-18
                                      XEECCS---TT-EEEETTSSEEEEEEEEEEETTTTEEEEEEEEETTT...........-EEEEEGG.CEECCCTEEEET CS
                               PRC  1 edefrasdliGkeVytedGeklGkVkDvvidekegrvralvvsvggflgi......gekevliPfdlavkigkdriivd 73
                                      +  + as+l+++e++t++G +lG+++D+ +de++g+v+ +v +  + l+       +e  +liP++ avk+++  i+vd
  gi|242399368|ref|YP_002994792.1|  1 MVKVKASKLRDMEIITDTGIRLGWLYDLSFDEDTGEVLVIVAEPDENLDTsefvtdHEGLLLIPMK-AVKSIGEFIVVD 78
                                      567899****************************************9999****************.***********9 PP

                                      TS- CS
                               PRC 74 apk 76
                                        k
  gi|242399368|ref|YP_002994792.1| 79 HNK 81
                                      876 PP

>> EB1  EB1-like C-terminal motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00013       1.2      10      22 ..       7      43 ..       7      71 .. 0.67
   2 ?    0.5   0.2     0.081   7.3e+02      10      18 ..      86      94 ..      86      99 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00013
                                      HHHHHHHHHHHH........................T CS
                               EB1 10 sKLRdIEilcqt........................e 22
                                      sKLRd Ei+  t                        e
  gi|242399368|ref|YP_002994792.1|  7 SKLRDMEIITDTgirlgwlydlsfdedtgevlvivaE 43
                                      8*********988888888888776555555555542 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.081
                                      HHHHHHHHH CS
                               EB1 10 sKLRdIEil 18
                                      sKLR I i+
  gi|242399368|ref|YP_002994792.1| 86 SKLRRISII 94
                                      7****9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.29s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 672.38
//
Query:       gi|242399369|ref|YP_002994793.1|  [L=839]
Description: Pk-cdcA protein [Thermococcus sibiricus MM 739]
Scores for 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-103  339.9   0.0    6.1e-52  175.5   0.0    2.8  2  AAA              ATPase family associated with various cellul
    6.8e-32  109.0   1.1    1.3e-16   60.1   0.4    2.7  2  AAA_lid_3        AAA+ lid domain
    2.4e-31  107.7   0.1    3.6e-30  104.0   0.6    2.7  2  CDC48_N          Cell division protein 48 (CDC48), N-terminal
    5.7e-17   61.9   0.0      2e-08   34.2   0.0    3.4  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    4.8e-16   59.4   0.0    6.9e-09   36.0   0.0    2.7  2  AAA_2            AAA domain (Cdc48 subfamily)
    6.5e-16   59.2   0.0    1.5e-06   28.7   0.0    4.0  2  AAA_16           AAA ATPase domain
    9.3e-14   51.0   0.3    6.5e-13   48.3   0.1    2.4  2  CDC48_2          Cell division protein 48 (CDC48), domain 2
    1.4e-13   51.3   0.2    0.00018   21.8   0.0    4.8  3  AAA_22           AAA domain
    2.2e-11   43.5   0.1    0.00043   19.6   0.0    3.5  3  TIP49            TIP49 P-loop domain
    3.8e-11   43.1   0.0    1.4e-05   25.1   0.0    2.6  2  AAA_14           AAA domain
      6e-11   42.5   1.6    0.00018   21.5   0.1    4.6  2  AAA_5            AAA domain (dynein-related subfamily)
    3.3e-10   40.3   0.0    0.00046   20.4   0.0    2.8  2  AAA_33           AAA domain
    1.1e-08   35.7   0.1      0.016   15.7   0.0    3.6  2  AAA_18           AAA domain
    5.1e-08   32.9   0.0     0.0052   16.5   0.0    2.6  2  AAA_24           AAA domain
    5.1e-08   32.9   0.1     0.0084   15.9   0.0    2.7  2  IstB_IS21        IstB-like ATP binding protein
    1.4e-07   31.4   1.4     0.0024   17.8   0.1    3.3  2  Vps4_C           Vps4 C terminal oligomerisation domain
    1.6e-07   31.6   0.0      0.017   15.5   0.0    2.8  2  RNA_helicase     RNA helicase
    1.8e-07   31.0   2.1     0.0097   15.5   0.2    4.0  3  AAA_25           AAA domain
    4.1e-07   29.9   0.3      0.038   13.7   0.0    4.0  4  Sigma54_activat  Sigma-54 interaction domain
    5.3e-07   30.0   0.0       0.02   15.1   0.0    2.8  2  AAA_28           AAA domain
    5.9e-07   29.6   2.4     0.0079   16.1   0.0    4.0  3  ATPase_2         ATPase domain predominantly from Archaea
    1.1e-06   28.0   0.0      0.024   13.8   0.0    2.4  2  DUF815           Protein of unknown function (DUF815)
    1.1e-06   28.2   1.9      0.038   13.4   0.0    2.9  3  Mg_chelatase     Magnesium chelatase, subunit ChlI
    1.8e-06   28.0   0.0      0.025   14.4   0.0    3.2  3  Bac_DnaA         Bacterial dnaA  protein
    6.7e-06   25.7   0.0        0.1   12.1   0.0    2.7  2  AAA_7            P-loop containing dynein motor region
    9.7e-06   25.6   0.0       0.13   12.2   0.0    2.8  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
    1.8e-05   25.2   0.0       0.47   11.0   0.0    3.0  2  ABC_tran         ABC transporter
    2.9e-05   23.5   1.2       0.33   10.2   0.0    3.5  4  Zeta_toxin       Zeta toxin
    5.5e-05   23.1   0.1        1.1    9.2   0.0    3.7  4  NACHT            NACHT domain
    7.2e-05   22.0   0.1       0.36    9.9   0.0    2.3  2  Parvo_NS1        Parvovirus non-structural protein NS1
    7.9e-05   22.0   0.0       0.11   11.7   0.0    2.4  2  DUF2075          Uncharacterized conserved protein (DUF2075)
    9.9e-05   21.9   0.4       0.38   10.2   0.0    2.6  2  PhoH             PhoH-like protein
    0.00015   21.6   0.0       0.57   10.0   0.0    2.5  2  AAA_3            ATPase family associated with various cellul
    0.00022   21.1   0.5       0.87    9.3   0.0    3.1  3  AAA_11           AAA domain
    0.00023   20.4   0.0        0.9    8.7   0.0    2.8  2  NB-ARC           NB-ARC domain
    0.00027   20.4   7.8       0.49    9.7   0.0    4.8  6  ATPase           KaiC
    0.00038   20.2   0.2        1.3    8.7   0.0    2.8  2  AAA_30           AAA domain
     0.0014   19.0   1.9        2.8    8.4   0.0    4.1  3  AAA_17           AAA domain
     0.0023   18.3   2.4        2.5    8.4   0.1    3.1  2  AAA_19           AAA domain
     0.0024   17.7   1.5        6.2    6.5   0.0    4.0  4  Cytidylate_kin   Cytidylate kinase
     0.0043   17.0   6.1        3.9    7.4   0.0    5.0  5  NTPase_1         NTPase
     0.0051   15.9   0.0          2    7.4   0.0    2.7  2  T2SSE            Type II/IV secretion system protein
     0.0064   16.6   0.0        5.4    7.1   0.0    2.7  2  Sigma54_activ_2  Sigma-54 interaction domain
  ------ inclusion threshold ------
      0.012   14.5   0.0        5.4    5.8   0.0    2.7  2  AFG1_ATPase      AFG1-like ATPase
      0.015   15.1   0.0        0.8    9.4   0.0    2.3  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.016   15.3   1.1         12    6.0   0.0    3.8  3  SKI              Shikimate kinase
      0.023   14.3   0.0        2.2    7.9   0.0    3.0  2  Zot              Zonular occludens toxin (Zot)
      0.027   13.7   0.5         24    4.0   0.0    3.8  4  KAP_NTPase       KAP family P-loop domain
       0.04   13.3   0.0         17    4.8   0.0    3.3  3  TniB             Bacterial TniB protein
      0.041   13.9   0.0         20    5.1   0.0    3.0  2  ResIII           Type III restriction enzyme, res subunit
       0.11   12.2   0.0         22    4.8   0.0    2.7  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
       0.13   11.7   0.6         15    4.9   0.0    2.9  2  IPT              Isopentenyl transferase
       0.13   12.0   0.0         27    4.6   0.0    2.4  2  AAA_29           P-loop containing region of AAA domain
       0.15   12.6   4.0       0.12   13.0   0.7    2.8  1  ATP-cone         ATP cone domain
       0.16   11.5   0.1         19    4.8   0.0    2.6  2  cobW             CobW/HypB/UreG, nucleotide-binding domain
        1.6    8.9   3.7        1.3    9.2   0.1    2.7  2  FPRL1_inhibitor  Formyl peptide receptor-like 1 inhibitory pr


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 !  175.5   0.0   1.9e-54   6.1e-52       1     131 [.     250     379 ..     250     380 .. 0.98
   2 !  161.5   0.0   4.1e-50   1.3e-47       1     131 [.     585     714 ..     585     715 .. 0.97

  Alignments for each domain:
  == domain 1  score: 175.5 bits;  conditional E-value: 1.9e-54
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTC CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgs 77 
                                       vllyGppGtGKTllakava+e++++f+ i+g+e++sky gese+++r++fkea+e+a psi+fiDEida+a++r++ 
  gi|242399369|ref|YP_002994793.1| 250 VLLYGPPGTGKTLLAKAVANEANAHFIAINGPEIMSKYYGESEERLRDIFKEAEENA-PSIIFIDEIDAIAPKREEV 325
                                       79******************************************************9.******************* PP

                                       CCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  78 eseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                       + e+e+rvv+qLlt +dg+k++ +kvivigatnrpd ldpal+r gRfdr+ie++
  gi|242399369|ref|YP_002994793.1| 326 TGEVEKRVVSQLLTLMDGLKSR-GKVIVIGATNRPDALDPALRRpGRFDREIEVG 379
                                       *********************6.77***************************986 PP

  == domain 2  score: 161.5 bits;  conditional E-value: 4.1e-50
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTC CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgs 77 
                                       +llyGppGtGKTllakava+e++++f+ i g+e+lsk+vgesek+ire+f++a++ a p+++fiDE+d++a+ r g+
  gi|242399369|ref|YP_002994793.1| 585 ILLYGPPGTGKTLLAKAVANESEANFIGIRGPEVLSKWVGESEKRIREIFRKARQAA-PTVVFIDEVDSIAPMRGGE 660
                                       69******************************************************9.****************99* PP

                                       CCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  78 eseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                        +++++r++nqLlte+dg +++ s v+vi+atnrpd ldpallr gRfdr i ++
  gi|242399369|ref|YP_002994793.1| 661 GDRVTDRLINQLLTEMDGIEEN-SGVVVIAATNRPDILDPALLRpGRFDRLILVP 714
                                       *********************7.55*************************99876 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.7   0.0   6.2e-15     2e-12       4      37 ..     465     498 ..     462     524 .. 0.88
   2 !   60.1   0.4   4.1e-19   1.3e-16       1      37 [.     737     773 ..     737     798 .. 0.86

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 6.2e-15
                         AAA_lid_3   4 lkeLAerTeGySGADlaalcreAallAlrrgike 37 
                                       l+eLAe+T+G++GADlaal reAa++ lrr i+e
  gi|242399369|ref|YP_002994793.1| 465 LEELAEKTHGFVGADLAALAREAAMVVLRRLITE 498
                                       89****************************8885 PP

  == domain 2  score: 60.1 bits;  conditional E-value: 4.1e-19
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgike 37 
                                       dv+l+eLA++TeGySGADlaal+reAa++Alrr    
  gi|242399369|ref|YP_002994793.1| 737 DVSLQELAKKTEGYSGADLAALVREAAFVALRRAVSI 773
                                       9********************************7543 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 !  104.0   0.6   1.1e-32   3.6e-30       1      85 []      16     100 ..      16     100 .. 0.98
   2 ?   -1.6   0.0       9.8   3.1e+03      20      64 ..     235     280 ..     235     281 .. 0.60

  Alignments for each domain:
  == domain 1  score: 104.0 bits;  conditional E-value: 1.1e-32
                                       CEEEECCSS-CSSTTEEEE-HHHHHHHTS-TTSEEEEECCCCEEEEEEEBSTTSTTTTEEEE-HHHHHHHT--TTEE CS
                           CDC48_N   1 rLrVaeapqedvgrgivridpedmeelglepgdvveiegkrkTvaivwpaepedegkgiIrmdgvtRknagvsiGdk 77 
                                       +LrVaea ++dvgrg+vrid++  ++lg+epgd+ve+eg+rkT+ai+ +a+p+d+g +iIrmdg++R+nagvsiGd 
  gi|242399369|ref|YP_002994793.1|  16 KLRVAEALKRDVGRGVVRIDRKYQRQLGIEPGDIVELEGERKTAAIAENAHPDDKGLDIIRMDGYIRRNAGVSIGDY 92 
                                       69*************************************************************************** PP

                                       EEEEEE-- CS
                           CDC48_N  78 VtVrkaev 85 
                                       ++ rkaev
  gi|242399369|ref|YP_002994793.1|  93 IILRKAEV 100
                                       *****985 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 9.8
                                       -HHHHHHHTS-TTSEEEEEC...CCCEE.EEEEEBSTTSTTTTEEEE-H CS
                           CDC48_N  20 dpedmeelglepgdvveieg...krkTv.aivwpaepedegkgiIrmdg 64 
                                       +pe +e+lg+ep + v + g   + kT  a+++++e    +   I+++g
  gi|242399369|ref|YP_002994793.1| 235 HPELFERLGIEPPKGVLLYGppgTGKTLlAKAVANEA---NAHFIAING 280
                                       5899999999999999887641133333344444433...356666665 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 !   34.2   0.0   6.1e-11     2e-08      34     104 ..     248     326 ..     224     374 .. 0.78
   2 !   23.5   0.0   1.2e-07   3.7e-05      34      96 ..     583     653 ..     546     658 .. 0.76

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 6.1e-11
                            RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihrlsravee 102
                                         vllyGpPG Gkt lak +a+e ++++ +  gP +      e +  l  ++++ ee+   ++fidei  ++++ ee
  gi|242399369|ref|YP_002994793.1| 248 KGVLLYGPPGTGKTLLAKAVANEANAHFIAINGPEImskyygESEERLRDIFKEAEENapSIIFIDEIDAIAPKREE 324
                                       679*******************************994433333456799999998876447***************9 PP

                            RuvB_N 103 vl 104
                                       v 
  gi|242399369|ref|YP_002994793.1| 325 VT 326
                                       86 PP

  == domain 2  score: 23.5 bits;  conditional E-value: 1.2e-07
                            RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihrl 96 
                                         +llyGpPG Gkt lak +a+e ++++    gP +      e ++ +  ++ + ++    v+fide+  +
  gi|242399369|ref|YP_002994793.1| 583 KGILLYGPPGTGKTLLAKAVANESEANFIGIRGPEVlskwvgESEKRIREIFRKARQAapTVVFIDEVDSI 653
                                       569*************************9999996533333344566778877766542268999998766 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   0.0   2.2e-11   6.9e-09       6     105 ..     250     343 ..     246     350 .. 0.91
   2 !   20.2   0.0   1.6e-06   0.00051       6     100 ..     585     673 ..     581     687 .. 0.81

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 2.2e-11
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKi 80 
                                       +ll gp g+Gkt+laka+a+  ++    ++i ++  e++     + + ++++  ++  ++aee+   i+++DEid i
  gi|242399369|ref|YP_002994793.1| 250 VLLYGPPGTGKTLLAKAVANEANA----HFIAINGPEIMS----KYYGESEERLRDIFKEAEENApsIIFIDEIDAI 318
                                       6889******************96....************....********************************* PP

                                       ---.---------HHHHHHHHHHHH- CS
                             AAA_2  81 hpk.essgadvSregVqrdLLqileg 105
                                       +pk e+ + +v +  V+  LL +++g
  gi|242399369|ref|YP_002994793.1| 319 APKrEEVTGEVEK-RVVSQLLTLMDG 343
                                       **97777777766.588889999997 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 1.6e-06
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKi 80 
                                       ill gp g+Gkt+laka+a+  ++    ++i +   e+l     + + ++++  ++   +a +    +v++DE+d i
  gi|242399369|ref|YP_002994793.1| 585 ILLYGPPGTGKTLLAKAVANESEA----NFIGIRGPEVLS----KWVGESEKRIREIFRKARQAAptVVFIDEVDSI 653
                                       8999****************9985....************....77777777778888888887789********** PP

                                       ------------HHHHHHHH CS
                             AAA_2  81 hpkessgadvSregVqrdLL 100
                                       +p +  + d   +   + LL
  gi|242399369|ref|YP_002994793.1| 654 APMRGGEGDRVTDRLINQLL 673
                                       **855555555555555555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.0   4.6e-09   1.5e-06      16     140 ..     239     352 ..     236     362 .. 0.71
   2 !   22.5   0.0   3.7e-07   0.00012      18     123 ..     576     672 ..     572     688 .. 0.62

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 4.6e-09
                            AAA_16  16 lervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysa.laqalareellrqlldeaes 91 
                                       +er+    p  vll+G++G+GK+ l+++++++++++   f++ +  +      +s  + +    ee lr++  eae+
  gi|242399369|ref|YP_002994793.1| 239 FERLGIEPPKGVLLYGPPGTGKTLLAKAVANEANAH---FIAINGPEI-----MSKyYGES---EERLRDIFKEAEE 304
                                       55555556799*******************977755...998888888.....33322222...2445555555444 PP

                            AAA_16  92 .aeleawrekleealaavpelagaeasrllellkrllallsrderplvlv 140
                                        a    + +++++ +    e++g+ ++r+  +l  l++ l+++++ ++ v
  gi|242399369|ref|YP_002994793.1| 305 nAPSIIFIDEIDAIAPKREEVTGEVEKRVVSQLLTLMDGLKSRGK-VI-V 352
                                       04444555556666668888888888***********99999888.43.3 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 3.7e-07
                            AAA_16  18 rvrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesael 94 
                                       r+    p  +ll+G++G+GK+ l+++++++ e++   f+  +  +      +s ++     e+ +r++ ++a++  +
  gi|242399369|ref|YP_002994793.1| 576 RLGITPPKGILLYGPPGTGKTLLAKAVANESEAN---FIGIRGPEV-----LSKWVGES--EKRIREIFRKARQ--A 640
                                       555555699*******************988888...655555555.....22455555..3788888888444..3 PP

                            AAA_16  95 eawrekleealaavpelagaea....srllell 123
                                       +     + +++ ++++++g e      rl ++l
  gi|242399369|ref|YP_002994793.1| 641 A-PTVVFIDEVDSIAPMRGGEGdrvtDRLINQL 672
                                       3.3333334445566777777733344443333 PP

>> CDC48_2  Cell division protein 48 (CDC48), domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       4.4   1.4e+03      33      62 ..      14      47 ..       5      49 .. 0.80
   2 !   48.3   0.1     2e-15   6.5e-13       9      64 .]     123     202 ..     118     202 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 4.4
                                      CEEEEEEEECCCC....SCEEECTSCCEEESTTC CS
                           CDC48_2 33 eiklvVvstePkg....pvgitetTeielgtkpv 62
                                      eikl+V++    +    +v+i+++ + +lg +p 
  gi|242399369|ref|YP_002994793.1| 14 EIKLRVAEALKRDvgrgVVRIDRKYQRQLGIEPG 47
                                      6778887777666777799999999999999886 PP

  == domain 2  score: 48.3 bits;  conditional E-value: 2e-15
                                       HHHCCCTTEEE-TTEEE.............EECCT...........CCCEEEEEEEECCCCSCEEECTSCCEEESTT CS
                           CDC48_2   9 ylkrqFlgrpvtkGdlv.............vfefk...........gqeiklvVvstePkgpvgitetTeielgtkp 61 
                                        +kr++lgrpvtkGdlv             +f+ +            +e+k+ Vv+t Pkg+v it +Teie+ +++
  gi|242399369|ref|YP_002994793.1| 123 LVKRNLLGRPVTKGDLVvasgreteiyagsPFDELfrgffeslplgFGELKFIVVNTAPKGIVQITYNTEIEVLPQA 199
                                       79***************8887777777777444436666888888899**************************999 PP

                                       CCE CS
                           CDC48_2  62 vev 64 
                                       vev
  gi|242399369|ref|YP_002994793.1| 200 VEV 202
                                       985 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   5.8e-07   0.00018       8      61 ..     250     303 ..     245     362 .. 0.72
   2 !   16.8   0.0   1.9e-05    0.0061       8      30 ..     585     607 ..     580     635 .. 0.79
   3 ?    3.7   0.0      0.22        72      78     117 ..     630     677 ..     623     697 .. 0.59

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 5.8e-07
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevv.fvtlpsstsskdllrell 61 
                                       ++++G++GtGKT+l++ ++++++++  a  ++pe++ +++  s++ ++d+++e  
  gi|242399369|ref|YP_002994793.1| 250 VLLYGPPGTGKTLLAKAVANEANAHFIAI-NGPEIMsKYYGESEERLRDIFKEAE 303
                                       689******************95443333.3555555555555556666655544 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 1.9e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleqld 30 
                                       ++++G++GtGKT+l++ ++++ +
  gi|242399369|ref|YP_002994793.1| 585 ILLYGPPGTGKTLLAKAVANESE 607
                                       79*****************9973 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.22
                            AAA_22  78 llealeqalraravielliiDEaqhlr....s......eealeeLrslln 117
                                       ++e +++a +a+  + ++ iDE++ +            ++++++L + ++
  gi|242399369|ref|YP_002994793.1| 630 IREIFRKARQAA--PTVVFIDEVDSIApmrgGegdrvtDRLINQLLTEMD 677
                                       333333333333..46*********9766541455556777776655444 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   1.3e-06   0.00043      51      97 ..     248     292 ..     243     317 .. 0.87
   2 ?   -0.5   0.0       1.7   5.5e+02      20      48 ..     469     501 ..     414     503 .. 0.73
   3 !   19.0   0.0     2e-06   0.00066      51     106 ..     583     637 ..     577     654 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.3e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte 97 
                                       ++vLl Gp+gtGkt la a+++e +   +f+a++g e+ s     +e
  gi|242399369|ref|YP_002994793.1| 248 KGVLLYGPPGTGKTLLAKAVANEAN--AHFIAINGPEIMSKYYGESE 292
                                       89********************977..89*********998776654 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.7
                                       XXXXXXXXXX...XXXXXXXXXXX.XXXXXXXX CS
                             TIP49  20 ekeeeglvGq...kkareaagviv.elikekkl 48 
                                        ++++g+vG      areaa v++ +li e+k+
  gi|242399369|ref|YP_002994793.1| 469 AEKTHGFVGAdlaALAREAAMVVLrRLITEGKV 501
                                       455668888622235788887654268888775 PP

  == domain 3  score: 19.0 bits;  conditional E-value: 2e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXX CS
                             TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkktev.ltqalrks 106
                                       +++Ll Gp+gtGkt la a+++e   +  f+ + g ev s  v  +e  + + +rk+
  gi|242399369|ref|YP_002994793.1| 583 KGILLYGPPGTGKTLLAKAVANES--EANFIGIRGPEVLSKWVGESEKrIREIFRKA 637
                                       89********************95..689**************99985377889987 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   4.5e-08   1.4e-05       5     100 ..     250     355 ..     247     373 .. 0.80
   2 !   15.1   0.0   5.6e-05     0.018       5      76 ..     585     653 ..     582     692 .. 0.82

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 4.5e-08
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe.kllelileklkeekktylflDEiqev.... 76 
                                       +++ G+  +GKT l+k +++e      +++ in  +   k + ++e +l ++++e  +e+  +++f+DEi  +    
  gi|242399369|ref|YP_002994793.1| 250 VLLYGPPGTGKTLLAKAVANEAN---AHFIAINGPEIMSKYYGESEeRLRDIFKEA-EENAPSIIFIDEIDAIapkr 322
                                       7899***************9888...********9999988776652566666665.55699***********8888 PP

                            AAA_14  77 ........pewekalkslvd.egknldvivtGS 100
                                               +++ + l  l+d  +++++viv G 
  gi|242399369|ref|YP_002994793.1| 323 eevtgeveKRVVSQLLTLMDgLKSRGKVIVIGA 355
                                       888888887788888888885335778888776 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 5.6e-05
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev 76 
                                       +++ G+  +GKT l+k +++e+     +++ i   +   k   ++ek +++i++k+++   t++f+DE+  +
  gi|242399369|ref|YP_002994793.1| 585 ILLYGPPGTGKTLLAKAVANESE---ANFIGIRGPEVLSKWVGESEKRIREIFRKARQAAPTVVFIDEVDSI 653
                                       7899***************9988...99999999998888777666555555555455589********887 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.1   5.8e-07   0.00018       1     136 [.     249     368 ..     249     369 .. 0.69
   2 !   15.0   0.2   5.8e-05     0.018       2      79 ..     585     655 ..     584     704 .. 0.64

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 5.8e-07
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEve 75 
                                       +vlL GppGtgK+ la+ +a   n+ +  +++++ +++          +++++l+  +++ +a+   ++i+++DE++
  gi|242399369|ref|YP_002994793.1| 249 GVLLYGPPGTGKTLLAKAVANEANAHFIAINGPEIMSKYYG-------ESEERLR-DIFK-EAEenAPSIIFIDEID 316
                                       59*******************************97765322.......2233333.3444.44446899******** PP

                                       G--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHHT CS
                             AAA_5  76 raesevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalrs 136
                                        + ++  ++     e+r ++  ++ +l++  +     ++ vi+++n++d     l+palr+
  gi|242399369|ref|YP_002994793.1| 317 AIAPKREEVT-GEVEKRVVS--QLLTLMDGLKS--RGKVIVIGATNRPD----ALDPALRR 368
                                       9886543333.333444444..55555555442..22399999999999....88888876 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 5.8e-05
                                       EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGGG CS
                             AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEver 76 
                                       +lL GppGtgK+ la+ +a   ++++  + +++      ++ ++    g+ + +  ++ r+ar   + ++++DEv+ 
  gi|242399369|ref|YP_002994793.1| 585 ILLYGPPGTGKTLLAKAVANESEANFIGIRGPE------VLSKWV---GESEKRIREIFRKARqaAPTVVFIDEVDS 652
                                       89***************9988877777666665......555555...34444445555555556667777777776 PP

                                       --H CS
                             AAA_5  77 aes 79 
                                       + +
  gi|242399369|ref|YP_002994793.1| 653 IAP 655
                                       666 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   1.4e-06   0.00046       2      79 ..     250     357 ..     250     434 .. 0.78
   2 !   17.0   0.0   1.6e-05     0.005       2      63 ..     585     676 ..     585     739 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.4e-06
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt............................dy 48 
                                       vll G+pG+GK+ la+ ++++    ++ ++ ++++++++g+ +++++                              
  gi|242399369|ref|YP_002994793.1| 250 VLLYGPPGTGKTLLAKAVANEANahFIAINGPEIMSKYYGESEERLRdifkeaeenapsiifideidaiapkreeVT 326
                                       7899***************99889999************98888887666666667777777777777766555433 PP

                            AAA_33  49 trvldrlyqilnelarkalsagrnvildatn 79 
                                        +v++r+  +l  l +   s+g+ +++ atn
  gi|242399369|ref|YP_002994793.1| 327 GEVEKRVVSQLLTLMDGLKSRGKVIVIGATN 357
                                       3466666666666666655666666666665 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 1.6e-05
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt............................dy 48 
                                       +ll G+pG+GK+ la+ ++++    ++ ++ ++++++ +g+ +++++                            + 
  gi|242399369|ref|YP_002994793.1| 585 ILLYGPPGTGKTLLAKAVANESEanFIGIRGPEVLSKWVGESEKRIReifrkarqaaptvvfidevdsiapmrggEG 661
                                       6789***************999999999*****99999998877777555555555566666666666666666544 PP

                            AAA_33  49 trvldrlyqilnela 63 
                                        rv+drl+++l    
  gi|242399369|ref|YP_002994793.1| 662 DRVTDRLINQLLTEM 676
                                       455566555554444 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   5.1e-05     0.016       1      41 [.     250     308 ..     250     358 .. 0.63
   2 !   15.6   0.0   5.6e-05     0.018       1      25 [.     585     634 ..     585     720 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 5.1e-05
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf..................gvnlrdvakenglllev 41 
                                       +ll G+pG+GKt lak+++++ +                    ++lrd++ke +   + 
  gi|242399369|ref|YP_002994793.1| 250 VLLYGPPGTGKTLLAKAVANEANAhfiaingpeimskyygesEERLRDIFKEAEENAPS 308
                                       799***************99864467888888888888888866666666655444443 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 5.6e-05
                            AAA_18   1 IlltGtpGvGKttlakeLskrl..gf.......................g 25 
                                       Ill G+pG+GKt lak+++++   +f                        
  gi|242399369|ref|YP_002994793.1| 585 ILLYGPPGTGKTLLAKAVANESeaNFigirgpevlskwvgesekrireiF 634
                                       99****************76643244877776666666666644433333 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.6e-05    0.0052       5      77 ..     250     318 ..     247     332 .. 0.78
   2 !   13.5   0.0   0.00014     0.045       5      25 ..     585     607 ..     582     669 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.6e-05
                            AAA_24   5 iliyGpsgiGKTtlakel..gpkplfidtekGlksldadkfpdieswedfldevvelaaeladyktlviDtidel 77 
                                       +l+yGp+g+GKT lak    + ++ fi +++   ++  + +   es e ++d ++e +++ +  ++++iD id +
  gi|242399369|ref|YP_002994793.1| 250 VLLYGPPGTGKTLLAKAVanEANAHFIAING--PEIMSKYYG--ESEERLRDIFKEAEENAP--SIIFIDEIDAI 318
                                       89****************9988888888887..333333333..377999999999888877..89999999976 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.00014
                            AAA_24   5 iliyGpsgiGKTtlakel..gpk 25 
                                       il+yGp+g+GKT lak    + +
  gi|242399369|ref|YP_002994793.1| 585 ILLYGPPGTGKTLLAKAVanESE 607
                                       89*************99855444 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   2.6e-05    0.0084      47      73 ..     247     273 ..     236     282 .. 0.86
   2 !   14.0   0.0   9.6e-05     0.031      48      71 ..     583     606 ..     578     650 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.6e-05
                         IstB_IS21  47 kenivllGpsGvGKshlaialgveavr 73 
                                        ++++l Gp+G+GK+ la a++ ea +
  gi|242399369|ref|YP_002994793.1| 247 PKGVLLYGPPGTGKTLLAKAVANEANA 273
                                       57899*****************99966 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 9.6e-05
                         IstB_IS21  48 enivllGpsGvGKshlaialgvea 71 
                                       ++i+l Gp+G+GK+ la a++ e 
  gi|242399369|ref|YP_002994793.1| 583 KGILLYGPPGTGKTLLAKAVANES 606
                                       6799***************99875 PP

>> Vps4_C  Vps4 C terminal oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0    0.0012      0.38      17      44 ..     506     533 ..     497     539 .. 0.88
   2 !   17.8   0.1   7.5e-06    0.0024      12      57 ..     771     820 ..     768     822 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0012
                            Vps4_C  17 mdipsdkllePpvtlkDflkalkkarpt 44 
                                       ++ip++ l e +vt +Df +alk   p+
  gi|242399369|ref|YP_002994793.1| 506 EKIPPEVLQELKVTKNDFYEALKMIEPS 533
                                       5799999****************99998 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 7.5e-06
                            Vps4_C  12 iemtwmdip...sdklleP.pvtlkDflkalkkarptVskeDLekheeFT 57 
                                       + +t +d+    +++ le  +v+  Df++a+kk++p+++   L+ ++ F 
  gi|242399369|ref|YP_002994793.1| 771 VSITSRDLVedqAEEFLEKlKVSKGDFEDAMKKVKPSITRYMLDYYKTFE 820
                                       55566664435577778888************************999995 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   5.3e-05     0.017       1      34 [.     250     283 ..     250     325 .. 0.71
   2 !   13.3   0.0   0.00025      0.08       1      26 [.     585     610 ..     585     693 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 5.3e-05
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl...klkkkdsv 34 
                                       ++lyGp+g+GK++lak +a++   ++   +    +++
  gi|242399369|ref|YP_002994793.1| 250 VLLYGPPGTGKTLLAKAVANEANAHFiaiN---GPEI 283
                                       689**************9999998873332...3333 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.00025
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl 26 
                                       i+lyGp+g+GK++lak +a++ + ++
  gi|242399369|ref|YP_002994793.1| 585 ILLYGPPGTGKTLLAKAVANESEANF 610
                                       789**************999877665 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0049       1.6      36      52 ..     250     266 ..     244     271 .. 0.87
   2 ?    3.5   0.0      0.14        45     129     176 ..     294     341 ..     282     355 .. 0.85
   3 !   15.5   0.2     3e-05    0.0097      36     148 ..     585     688 ..     579     693 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0049
                            AAA_25  36 allaGapgtGKttlald 52 
                                       +ll+G+pgtGKt la  
  gi|242399369|ref|YP_002994793.1| 250 VLLYGPPGTGKTLLAKA 266
                                       69***********9965 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.14
                            AAA_25 129 dvdaleaaieevegvrlvviDplsralggdensnsdv.galvealeria 176
                                        ++++ +++ee + +  + iD ++++ +  e+   +v +++v++l  + 
  gi|242399369|ref|YP_002994793.1| 294 RLRDIFKEAEE-NAPSIIFIDEIDAIAPKREEVTGEVeKRVVSQLLTLM 341
                                       56778889999.67***************99999999999999997765 PP

  == domain 3  score: 15.5 bits;  conditional E-value: 3e-05
                            AAA_25  36 allaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgealrddarllvldlagve 112
                                       +ll+G+pgtGKt la  +a +  +  ++ g++ pe    ++   E    ++r+ +r++++a+      +v+ +++v+
  gi|242399369|ref|YP_002994793.1| 585 ILLYGPPGTGKTLLAKAVANE--SEANFIGIRGPEVLSKWVGESEK---RIREIFRKARQAA-----PTVVFIDEVD 651
                                       69**********988655544..45679996544555544444333...3444444444444.....3344443445 PP

                            AAA_25 113 slpLfakdrggtlltadvdaleaaieeveg.vrlvvi 148
                                       s+  +  + g+ ++++ +++l  +++ +e+  ++vvi
  gi|242399369|ref|YP_002994793.1| 652 SIAPMRGGEGDRVTDRLINQLLTEMDGIEEnSGVVVI 688
                                       676666778888899***********99887888887 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   0.00012     0.038      23      61 ..     248     283 ..     239     359 .. 0.85
   2 ?   -1.3   0.0       4.9   1.6e+03       6      64 ..     424     486 ..     421     492 .. 0.71
   3 !   10.4   0.0    0.0012       0.4      23      48 ..     583     608 ..     570     614 .. 0.86
   4 ?   -1.7   0.0       6.3     2e+03      90     108 ..     638     656 ..     631     696 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00012
                                       S-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS CS
                   Sigma54_activat  23 lsvlitGesGtGKellaraiheaskrkekpfvavncaai 61 
                                         vl+ G  GtGK+lla+a+ ++   ++++f+a+n  +i
  gi|242399369|ref|YP_002994793.1| 248 KGVLLYGPPGTGKTLLAKAVANE---ANAHFIAINGPEI 283
                                       569****************9765...5689999997765 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 4.9
                                       HHHHHHHHHHHHHCTSS.S-EEEECSTTSSHHHHHHHHHH...HSTTTTS-EEEEETTTS-TT CS
                   Sigma54_activat   6 ealkelleqikkvaktd.lsvlitGesGtGKellaraihe...askrkekpfvavncaaipee 64 
                                       e+++e++++i+++ + + +++ ++ +    Ke+ ar+i +   +  +k++ fv  + aa+++e
  gi|242399369|ref|YP_002994793.1| 424 ERIEEMIQKIENAKEESdIKITLKEDGELYKEVRARLIDSmleELAEKTHGFVGADLAALARE 486
                                       678888888888875433888887777788999999886644355667778888888888665 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.0012
                                       S-EEEECSTTSSHHHHHHHHHHHSTT CS
                   Sigma54_activat  23 lsvlitGesGtGKellaraiheaskr 48 
                                         +l+ G  GtGK+lla+a+ ++s+ 
  gi|242399369|ref|YP_002994793.1| 583 KGILLYGPPGTGKTLLAKAVANESEA 608
                                       569*****************998874 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 6.3
                                       HHTTTSEEEEETGGGS-HH CS
                   Sigma54_activat  90 ekadgGtlfLDeigelple 108
                                       ++a   ++f+De+ ++ + 
  gi|242399369|ref|YP_002994793.1| 638 RQAAPTVVFIDEVDSIAPM 656
                                       5677788999999887654 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   6.2e-05      0.02       2      49 ..     250     302 ..     249     342 .. 0.73
   2 !   11.9   0.0   0.00064       0.2       2      32 ..     585     620 ..     584     649 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 6.2e-05
                            AAA_28   2 ivitGgestGKTtlleaLaar....gypvv.pEaareileeklakgedalpwv 49 
                                       + + G+++tGKT l++a a++     + +  pE++ +++ e  ++ +d+ +++
  gi|242399369|ref|YP_002994793.1| 250 VLLYGPPGTGKTLLAKAVANEanahFIAINgPEIMSKYYGESEERLRDIFKEA 302
                                       6799***************6543324444488888888888877777766654 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00064
                            AAA_28   2 ivitGgestGKTtlleaLaar...gypvv..pEaar 32 
                                       i + G+++tGKT l++a a++   ++  +  pE+  
  gi|242399369|ref|YP_002994793.1| 585 ILLYGPPGTGKTLLAKAVANEseaNFIGIrgPEVLS 620
                                       7899***************76534322223455444 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   0.0   2.5e-05    0.0079      15     122 ..     242     353 ..     236     356 .. 0.69
   2 !    8.5   0.0    0.0052       1.7      23      45 ..     585     607 ..     576     614 .. 0.85
   3 ?    1.7   0.0      0.64   2.1e+02     110     150 ..     630     677 ..     613     693 .. 0.60

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.5e-05
                          ATPase_2  15 lerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekal......... 82 
                                       l  ep + +++YGp g GKt L k ++++ +     ++  i+  e+ ++++ e+  ee+ ++ +++a          
  gi|242399369|ref|YP_002994793.1| 242 LGIEPPKGVLLYGPPGTGKTLLAKAVANEANA----HFIAINGPEIMSKYYGES--EERLRDIFKEAEenapsiifi 312
                                       5667788899**********999999999843....455677777777777777..333333333333445555556 PP

                          ATPase_2  83 .giavpkaeleeilkeksklvfkaielllekikkkgkkiii 122
                                         i+    + ee+  e  k v +++  l++ +k +gk i+i
  gi|242399369|ref|YP_002994793.1| 313 dEIDAIAPKREEVTGEVEKRVVSQLLTLMDGLKSRGKVIVI 353
                                       64444444556677788999999999999999999997766 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0052
                          ATPase_2  23 yfiYGpegsGKtaLlkeiienle 45 
                                       +++YGp g GKt L k +++++e
  gi|242399369|ref|YP_002994793.1| 585 ILLYGPPGTGKTLLAKAVANESE 607
                                       789*************9999875 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.64
                          ATPase_2 110 lekikkkgkk...iiiiiDelqklidlgln....gaellvkeLlnlie 150
                                       +++i +k+++    +++iDe+  +  +           l+++Ll+ ++
  gi|242399369|ref|YP_002994793.1| 630 IREIFRKARQaapTVVFIDEVDSIAPMRGGegdrVTDRLINQLLTEMD 677
                                       445556666666689********9977655222223344455444444 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   0.00035      0.11      52      91 ..     246     287 ..     237     356 .. 0.75
   2 !   13.8   0.0   7.5e-05     0.024      21     115 ..     541     649 ..     525     697 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00035
                            DUF815  52 pannvLLwGarGtGKSslvkallneyaeegLrli..eveked 91 
                                       p + vLL+G  GtGK  l ka+ ne++++ +++   e+  + 
  gi|242399369|ref|YP_002994793.1| 246 PPKGVLLYGPPGTGKTLLAKAVANEANAHFIAINgpEIMSKY 287
                                       56789*********************9998766322554443 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 7.5e-05
                            DUF815  21 evdevklddLvgidkqkealvente.......qf..leglpannvLLwGarGtGKSslvkallneyaeeg..Lrlie 86 
                                       ev +v++dd+ g+++ k++l+e +e       +f  l  +p + +LL+G  GtGK  l ka+ ne +++   +r  e
  gi|242399369|ref|YP_002994793.1| 541 EVPNVRWDDIGGLENVKQELKEAVEwplkypkAFqrLGITPPKGILLYGPPGTGKTLLAKAVANESEANFigIRGPE 617
                                       56788999999999999999998872222222221123356688********************9988864466667 PP

                            DUF815  87 vekedlkelpklvell.r..erperfilfvDD 115
                                       v  + + e +k ++++ r  +++   ++f+D 
  gi|242399369|ref|YP_002994793.1| 618 VLSKWVGESEKRIREIfRkaRQAAPTVVFIDE 649
                                       76666655544333331311223345667665 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       7.5   2.4e+03     116     142 ..      13      39 ..       8      41 .. 0.83
   2 !   12.9   0.0   0.00016     0.052      25      42 ..     250     267 ..     247     272 .. 0.90
   3 !   13.4   0.0   0.00012     0.038      25      42 ..     585     602 ..     576     609 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 7.5
                      Mg_chelatase 116 pefkrkvlevLRePledgevtisraka 142
                                        e+k +v e+L++ + +g v+i r+ +
  gi|242399369|ref|YP_002994793.1|  13 DEIKLRVAEALKRDVGRGVVRIDRKYQ 39 
                                       48999*****************99865 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00016
                      Mg_chelatase  25 lllvGppGsGKtmlakrl 42 
                                       +ll+GppG+GKt+lak++
  gi|242399369|ref|YP_002994793.1| 250 VLLYGPPGTGKTLLAKAV 267
                                       79*************987 PP

  == domain 3  score: 13.4 bits;  conditional E-value: 0.00012
                      Mg_chelatase  25 lllvGppGsGKtmlakrl 42 
                                       +ll+GppG+GKt+lak++
  gi|242399369|ref|YP_002994793.1| 585 ILLYGPPGTGKTLLAKAV 602
                                       89*************987 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   7.7e-05     0.025      37     176 ..     250     391 ..     245     440 .. 0.77
   2 ?   -0.4   0.1       2.7   8.8e+02     143     193 ..     460     515 ..     417     532 .. 0.65
   3 !    9.2   0.0    0.0031      0.98      37     109 ..     585     653 ..     580     747 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 7.7e-05
                                       EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHHHTT-.SEEEEE-GGGGTT- CS
                          Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkkaeefkeklrkv.DvLliDDiqflagk 112
                                       +++yg+ G Gkt L ka++ne+ +++     + +++ e +++     +++  + fke   ++  ++ iD+i  +a k
  gi|242399369|ref|YP_002994793.1| 250 VLLYGPPGTGKTLLAKAVANEANAHF-----IAINGPEIMSKYYGESEERLRDIFKEAEENApSIIFIDEIDAIAPK 321
                                       79****************99886655.....567888888888888899999999998875527899*******988 PP

                                       H.........HHHHHHHHHHHHHHTTT-EEEEEESS-TTT-SS--HHHHHHHHSSEEEE-----HHHHHHHHH CS
                          Bac_DnaA 113 e.........ktqeelfhtfnalleegkqvvlssDrsPkeleeledrlrsrfeaGlvvdieppdletrlailk 176
                                                 ++  +l+++++ l   gk +v+ +   P +l+        rf++   +++  pd++ r +il+
  gi|242399369|ref|YP_002994793.1| 322 ReevtgevekRVVSQLLTLMDGLKSRGKVIVIGATNRPDALDPALR-RPGRFDRE--IEVGVPDKQGRKEILQ 391
                                       52222211112445688888889999999*********99876433.35677765..4555577777777776 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 2.7
                                       T-SS--HHHHHHHHSSEEEE-----HHHHHHHHHHHHHHTT--.....--TTHHHH CS
                          Bac_DnaA 143 eleeledrlrsrfeaGlvvdieppdletrlailkkkieaekle.....vpeevlef 193
                                        ++++ + l  + +  + +d+    +e ++ +l++ i + k++     +p+evl+ 
  gi|242399369|ref|YP_002994793.1| 460 LIDSMLEELAEKTHGFVGADLAALAREAAMVVLRRLITEGKVNpeeekIPPEVLQE 515
                                       45666666666766667788888888888888888888777776667799999875 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0031
                                       EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHHHT.T-SEEEEE-GGGG CS
                          Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkkaeefkeklr.kvDvLliDDiqfl 109
                                       +++yg+ G Gkt L ka++ne ++n+   r     + e l++ v   +++  e f++  + +  v+ iD++  +
  gi|242399369|ref|YP_002994793.1| 585 ILLYGPPGTGKTLLAKAVANESEANFIGIR-----GPEVLSKWVGESEKRIREIFRKARQaAPTVVFIDEVDSI 653
                                       79*****************99888776544.....555555566555555555555544413345556666555 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 !   12.1   0.0   0.00032       0.1      33      61 ..     247     274 ..     238     323 .. 0.87
   2 !   10.4   0.0     0.001      0.33      33      58 ..     582     607 ..     572     614 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00032
                             AAA_7  33 kkpvllvGptGtGKtviikdllkkldkek 61 
                                        k vll+Gp GtGKt+++k + ++ +  +
  gi|242399369|ref|YP_002994793.1| 247 PKGVLLYGPPGTGKTLLAKAVANEAN-AH 274
                                       5789****************999888.33 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.001
                             AAA_7  33 kkpvllvGptGtGKtviikdllkkld 58 
                                        k +ll+Gp GtGKt+++k + ++ +
  gi|242399369|ref|YP_002994793.1| 582 PKGILLYGPPGTGKTLLAKAVANESE 607
                                       5789***************9988766 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   0.00042      0.13      19      59 ..     247     287 ..     220     310 .. 0.78
   2 !   10.3   0.0    0.0017      0.54      19      45 ..     582     608 ..     548     617 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00042
                                       TEEEEEEESTTSSHHHHHHHHHHHTT--..----TTTTSEEEE CS
                              TsaE  19 gdvilLeGdLGaGKTtlvrglakalgve..evkSPTFtlveeY 59 
                                        + +lL+G+ G+GKT l++++a++ + +  +++ P   ++++Y
  gi|242399369|ref|YP_002994793.1| 247 PKGVLLYGPPGTGKTLLAKAVANEANAHfiAINGP--EIMSKY 287
                                       4459*******************998887778777..456555 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0017
                                       TEEEEEEESTTSSHHHHHHHHHHHTT- CS
                              TsaE  19 gdvilLeGdLGaGKTtlvrglakalgv 45 
                                        + ilL+G+ G+GKT l++++a++ + 
  gi|242399369|ref|YP_002994793.1| 582 PKGILLYGPPGTGKTLLAKAVANESEA 608
                                       3449*****************998765 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0    0.0017      0.55       7      67 ..     243     301 ..     241     368 .. 0.79
   2 !   11.0   0.0    0.0015      0.47       9      72 ..     580     642 ..     576     693 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0017
                                       EEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   7 klkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe 67 
                                        +++ + v + G+ G+GK+ L+k++a++ +  +  i ++g ++ ++   +++++++ +++e
  gi|242399369|ref|YP_002994793.1| 243 GIEPPKGVLLYGPPGTGKTLLAKAVANEAN--AHFIAINGPEIMSKYYGESEERLRDIFKE 301
                                       677788899*****************9986..45666677777766666666666666655 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.0015
                                       ETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-T CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx RF
                          ABC_tran   9 kegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfp 72 
                                        + + + + G+ G+GK+ L+k++a++++  +  i ++g ++ ++   +++k+i+ ++ +  q  p
  gi|242399369|ref|YP_002994793.1| 580 TPPKGILLYGPPGTGKTLLAKAVANESE--ANFIGIRGPEVLSKWVGESEKRIREIFRKaRQAAP 642
                                       555668899****************986..67888888888888888888888888877444444 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0     0.001      0.33      14      51 ..     245     280 ..     237     297 .. 0.88
   2 ?   -1.7   0.1       4.4   1.4e+03     164     195 ..     424     454 ..     389     457 .. 0.77
   3 !    9.6   0.0    0.0016      0.51      16      49 ..     582     613 ..     574     618 .. 0.88
   4 ?   -2.7   0.0       8.9   2.9e+03     142     177 ..     759     794 ..     753     807 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.001
                        Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnvvrldp 51 
                                       e Pk +ll G pG GK+ la+++++e   +  ++ +++
  gi|242399369|ref|YP_002994793.1| 245 EPPKGVLLYGPPGTGKTLLAKAVANEA--NAHFIAING 280
                                       56999*********************8..788888776 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 4.4
                        Zeta_toxin 164 eglresvealeeekqldrvkikdrdgktvlyd 195
                                       e+++e ++++e++k  +++ki+ +++  +ly+
  gi|242399369|ref|YP_002994793.1| 424 ERIEEMIQKIENAKEESDIKITLKED-GELYK 454
                                       56789999999999999999988888.66665 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.0016
                        Zeta_toxin  16 PklillgGqpGAGKselaellkdelerqgnvvrl 49 
                                       Pk ill G pG GK+ la+++++e   + n++ +
  gi|242399369|ref|YP_002994793.1| 582 PKGILLYGPPGTGKTLLAKAVANES--EANFIGI 613
                                       999*********************8..6777766 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 8.9
                        Zeta_toxin 142 dRyeeevaegRlvpkeehdeafeglresvealeeek 177
                                        R+ + va  R v++++ d + ++++e +e+l+++k
  gi|242399369|ref|YP_002994793.1| 759 VREAAFVALRRAVSITSRDLVEDQAEEFLEKLKVSK 794
                                       555555444589999999999999999999988876 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0    0.0033       1.1       3      24 ..     250     271 ..     248     275 .. 0.89
   2 ?   -1.8   0.0       8.1   2.6e+03      64     115 ..     290     343 ..     282     380 .. 0.60
   3 !    8.1   0.0    0.0072       2.3       3      23 ..     585     605 ..     583     609 .. 0.89
   4 ?    0.4   0.0       1.7   5.5e+02      63     115 ..     624     675 ..     616     703 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0033
                                       EEEEC-TTTCHHHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklalaw 24 
                                       v+l G++G GKT L++ +a ++
  gi|242399369|ref|YP_002994793.1| 250 VLLYGPPGTGKTLLAKAVANEA 271
                                       799**************99876 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 8.1
                                       S--SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH.............HHHHHCT CS
                             NACHT  64 epaapvsevwavllelperlLlilDglDelvtdlgq....kekqpvrtlLselirk 115
                                       e++++ + ++++  e++ ++ + +D +D ++ + ++      +++v   L +l+ +
  gi|242399369|ref|YP_002994793.1| 290 ESEERLRDIFKEAEENAPSIIF-IDEIDAIAPKREEvtgeV-EKRVVSQLLTLMDG 343
                                       5566666666666666666666.588888887777677743.33333333356555 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0072
                                       EEEEC-TTTCHHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                       ++l G++G GKT L++ +a +
  gi|242399369|ref|YP_002994793.1| 585 ILLYGPPGTGKTLLAKAVANE 605
                                       7899************99875 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 1.7
                                       TS--SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH.........HHHHHCT CS
                             NACHT  63 pepaapvsevwavllelperlLlilDglDelvtdlgqkekqpvrtlLselirk 115
                                        e++++++e +   ++++  ++  +D +D ++   g ++ + +++l+++l+++
  gi|242399369|ref|YP_002994793.1| 624 GESEKRIRE-IFRKARQAAPTVVFIDEVDSIAPMRGGEGDRVTDRLINQLLTE 675
                                       566667777.333355666777889******9999999999999999999987 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 !    9.6   0.0    0.0013      0.43     117     136 ..     250     269 ..     245     276 .. 0.90
   2 !    9.9   0.0    0.0011      0.36     117     137 ..     585     605 ..     579     608 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0013
                         Parvo_NS1 117 vwfyGpantGktnlaeaIak 136
                                       v++yGp+ tGkt la+a a+
  gi|242399369|ref|YP_002994793.1| 250 VLLYGPPGTGKTLLAKAVAN 269
                                       89***************997 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0011
                         Parvo_NS1 117 vwfyGpantGktnlaeaIaka 137
                                       +++yGp+ tGkt la+a a+ 
  gi|242399369|ref|YP_002994793.1| 585 ILLYGPPGTGKTLLAKAVANE 605
                                       89***************9985 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   0.00035      0.11       4      66 ..     250     305 ..     247     332 .. 0.70
   2 !    8.1   0.0    0.0044       1.4       4      25 ..     585     606 ..     582     646 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00035
                           DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvl.vlrealakkeekkkkkeafek 66 
                                       vl  G +GtGKt+++ ++++e+       +a+++  N+p+++ +++ + +++  +  +kea e+
  gi|242399369|ref|YP_002994793.1| 250 VLLYGPPGTGKTLLAKAVANEA-------NAHFIAINGPEIMsKYYGESEERL-RDIFKEAEEN 305
                                       6789****************99.......778888888876625555555555.5555554444 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0044
                           DUF2075   4 vlVtGvaGtGKtvvllnllael 25 
                                       +l  G +GtGKt+++ ++++e 
  gi|242399369|ref|YP_002994793.1| 585 ILLYGPPGTGKTLLAKAVANES 606
                                       6789************999987 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0    0.0012      0.38      22      43 ..     250     271 ..     243     277 .. 0.86
   2 !    8.9   0.1    0.0028      0.91      23      41 ..     586     604 ..     578     610 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0012
                                       EEEE--TTSSTTHHHHHHHHHH CS
                              PhoH  22 vfaiGpaGtGKtylavalavea 43 
                                       v   Gp GtGKt+la a+a ea
  gi|242399369|ref|YP_002994793.1| 250 VLLYGPPGTGKTLLAKAVANEA 271
                                       6789************999765 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0028
                                       EEE--TTSSTTHHHHHHHH CS
                              PhoH  23 faiGpaGtGKtylavalav 41 
                                          Gp GtGKt+la a+a 
  gi|242399369|ref|YP_002994793.1| 586 LLYGPPGTGKTLLAKAVAN 604
                                       578***********99985 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0    0.0018      0.57       2      30 ..     250     278 ..     249     332 .. 0.88
   2 !    9.1   0.0    0.0036       1.1       2      30 ..     585     613 ..     584     647 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0018
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkri 30 
                                       vll g PG++ktll+ka+a+  +++f  i
  gi|242399369|ref|YP_002994793.1| 250 VLLYGPPGTGKTLLAKAVANEANAHFIAI 278
                                       7999*****************99999776 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0036
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkri 30 
                                       +ll g PG++ktll+ka+a+  +++f  i
  gi|242399369|ref|YP_002994793.1| 585 ILLYGPPGTGKTLLAKAVANESEANFIGI 613
                                       7999****************999998665 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0    0.0027      0.87      20      42 ..     250     272 ..     232     354 .. 0.82
   2 ?   -0.4   0.2       2.5   8.1e+02      88     122 ..     406     445 ..     371     521 .. 0.66
   3 !    7.9   0.0    0.0072       2.3      20      41 ..     585     606 ..     563     645 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0027
                            AAA_11  20 tliqGPPGtgKTktivellsqll 42 
                                       +l+ GPPGtgKT    ++ ++++
  gi|242399369|ref|YP_002994793.1| 250 VLLYGPPGTGKTLLAKAVANEAN 272
                                       799*********88888887776 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 2.5
                            AAA_11  88 pkivRvgneeeriseavksvsleekvekrlekee......k 122
                                        +++Rv n+  + +ea  +  +ee+++k  +++e      +
  gi|242399369|ref|YP_002994793.1| 406 RSVLRVLNSL-KNREAFDKERIEEMIQKIENAKEesdikiT 445
                                       4555555555.455555555555555555555442222220 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0072
                            AAA_11  20 tliqGPPGtgKTktivellsql 41 
                                        l+ GPPGtgKT    ++ ++ 
  gi|242399369|ref|YP_002994793.1| 585 ILLYGPPGTGKTLLAKAVANES 606
                                       5899********7776666665 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0    0.0033       1.1      23      43 ..     250     270 ..     237     278 .. 0.84
   2 !    8.7   0.0    0.0028       0.9      23      44 ..     585     606 ..     574     613 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0033
                                       EEEEESTTSSHHHHHHHHCCS CS
                            NB-ARC  23 valvGmgGvGKttlakqilnk 43 
                                       v l+G +G GKt lak + n+
  gi|242399369|ref|YP_002994793.1| 250 VLLYGPPGTGKTLLAKAVANE 270
                                       789***************998 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0028
                                       EEEEESTTSSHHHHHHHHCCSH CS
                            NB-ARC  23 valvGmgGvGKttlakqilnks 44 
                                       + l+G +G GKt lak + n+s
  gi|242399369|ref|YP_002994793.1| 585 ILLYGPPGTGKTLLAKAVANES 606
                                       679***************9994 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0    0.0015      0.49      15      37 ..     243     265 ..     235     282 .. 0.84
   2 ?    0.2   0.0       1.2   3.9e+02     108     153 ..     292     343 ..     265     355 .. 0.67
   3 ?   -2.0   0.1       5.9   1.9e+03     106     121 ..     428     443 ..     400     518 .. 0.52
   4 !    9.7   0.0    0.0016       0.5      15      38 ..     578     601 ..     557     613 .. 0.87
   5 ?   -1.0   0.0       2.8   8.9e+02     110     133 ..     629     654 ..     617     687 .. 0.53
   6 ?   -0.8   0.1       2.5   7.9e+02      70     135 ..     751     822 ..     730     836 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0015
                            ATPase  15 GipegrvvlitGepGtGKtifal 37 
                                       Gi   + vl++G pGtGKt++a+
  gi|242399369|ref|YP_002994793.1| 243 GIEPPKGVLLYGPPGTGKTLLAK 265
                                       77777889*************97 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.2
                            ATPase 108 ieelaeaikeika...krvviDsitgl...ayeekeavaReilrqlvrvlkk 153
                                        e+l+++ ke ++   + + iD i+++    +e + +v ++ + ql++ + +
  gi|242399369|ref|YP_002994793.1| 292 EERLRDIFKEAEEnapSIIFIDEIDAIapkREEVTGEVEKRVVSQLLTLMDG 343
                                       5566666666655444889999999994312223334456667777777755 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 5.9
                            ATPase 106 elieelaeaikeikak 121
                                       e+i+++++a +e  +k
  gi|242399369|ref|YP_002994793.1| 428 EMIQKIENAKEESDIK 443
                                       3333333333332222 PP

  == domain 4  score: 9.7 bits;  conditional E-value: 0.0016
                            ATPase  15 GipegrvvlitGepGtGKtifalq 38 
                                       Gi   + +l++G pGtGKt++a+ 
  gi|242399369|ref|YP_002994793.1| 578 GITPPKGILLYGPPGTGKTLLAKA 601
                                       67777889*************985 PP

  == domain 5  score: -1.0 bits;  conditional E-value: 2.8
                            ATPase 110 elaeaikeika...krvviDsitglay 133
                                       +++e+ ++ ++   + v iD ++++  
  gi|242399369|ref|YP_002994793.1| 629 RIREIFRKARQaapTVVFIDEVDSI-A 654
                                       4444444443333366777666655.2 PP

  == domain 6  score: -0.8 bits;  conditional E-value: 2.5
                            ATPase  70 lGwdlekleeegklaiidasesaeesaee.....kdkedleelieelaeaikeika..krvviDsitglayee 135
                                        G dl +l +e  ++ +  + s + +        +  e+l+  + ++++a+k++k   +r ++D  +++ +e+
  gi|242399369|ref|YP_002994793.1| 751 SGADLAALVREAAFVALRRAVSITSRDLVedqaeEFLEKLKVSKGDFEDAMKKVKPsiTRYMLDYYKTF-EES 822
                                       577888888777666655433333222112322244445555567788888888876678888877777.443 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0     0.004       1.3      21      43 ..     250     272 ..     237     280 .. 0.82
   2 !    8.5   0.1    0.0047       1.5      21      44 ..     585     608 ..     572     654 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.004
                            AAA_30  21 avltGpAGtGKttalkalreawe 43 
                                       ++l Gp+GtGKt + ka+++ ++
  gi|242399369|ref|YP_002994793.1| 250 VLLYGPPGTGKTLLAKAVANEAN 272
                                       6789************9976555 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0047
                            AAA_30  21 avltGpAGtGKttalkalreawea 44 
                                        +l Gp+GtGKt + ka+++  ea
  gi|242399369|ref|YP_002994793.1| 585 ILLYGPPGTGKTLLAKAVANESEA 608
                                       5789************99876665 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0    0.0087       2.8       1      25 [.     253     277 ..     253     331 .. 0.72
   2 ?   -0.4   0.5       4.5   1.4e+03      37      69 ..     433     468 ..     411     508 .. 0.57
   3 ?    6.8   0.0     0.026       8.4       1      25 [.     588     614 ..     588     741 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0087
                                       EE-TTSSHHHHHHHHHHHHTEEEEE CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthls 25 
                                       +G+PG GK+ +++ ++ + + +++ 
  gi|242399369|ref|YP_002994793.1| 253 YGPPGTGKTLLAKAVANEANAHFIA 277
                                       7**************9998765543 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 4.5
                                       TTSHSSHHHHC...TSHHHHHHHHHHHHHHHHHHHH CS
                            AAA_17  37 gglakardemr...klpleekkelqkeaaekiaeea 69 
                                        + ak++++++   k++ e  ke+++++++++ ee 
  gi|242399369|ref|YP_002994793.1| 433 IENAKEESDIKitlKEDGELYKEVRARLIDSMLEEL 468
                                       233333333333334444445555555555555543 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.026
                                       EE-TTSSHHHHHHHHHHHH..TEEEEE CS
                            AAA_17   1 lGgPGsGKgtqceklveky..gfthls 25 
                                       +G+PG GK+ +++ ++ +   +f  + 
  gi|242399369|ref|YP_002994793.1| 588 YGPPGTGKTLLAKAVANESeaNFIGIR 614
                                       7***********999976522444444 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.1     0.013       4.1      11      32 ..     248     269 ..     244     284 .. 0.81
   2 !    8.4   0.1    0.0079       2.5      10      34 ..     582     606 ..     575     654 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.013
                            AAA_19  11 kvllvtaGpGtGKTrvlkhiva 32 
                                       k +l+ ++pGtGKT + k++ +
  gi|242399369|ref|YP_002994793.1| 248 KGVLLYGPPGTGKTLLAKAVAN 269
                                       56899*********98777665 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0079
                            AAA_19  10 ekvllvtaGpGtGKTrvlkhivall 34 
                                        k +l+ ++pGtGKT + k++ ++ 
  gi|242399369|ref|YP_002994793.1| 582 PKGILLYGPPGTGKTLLAKAVANES 606
                                       56789**********9887776654 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0     0.019       6.2       4      27 ..     253     276 ..     250     280 .. 0.90
   2 ?   -0.6   0.1       2.9   9.4e+02     156     188 ..     404     436 ..     393     459 .. 0.79
   3 ?    5.1   0.0     0.051        16       3      27 ..     587     611 ..     585     613 .. 0.89
   4 ?    1.5   0.0      0.64   2.1e+02      23      59 ..     749     785 ..     736     806 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.019
                                       E-STTSSHHHHHHHHHHHHT-EEE CS
                    Cytidylate_kin   4 DGPagsGKssvaralaeklglkyl 27 
                                        GP g+GK  +a+a+a++ +++++
  gi|242399369|ref|YP_002994793.1| 253 YGPPGTGKTLLAKAVANEANAHFI 276
                                       6*******************9997 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2.9
                                       ----HHHHHHHHHHHHHHHHCTSSS-S---TT- CS
                    Cytidylate_kin 156 tsvsleellaeikeRDklDkerevgpLklaeda 188
                                        + s+ ++l+++k+R + Dker  + +++ e+a
  gi|242399369|ref|YP_002994793.1| 404 DKRSVLRVLNSLKNREAFDKERIEEMIQKIENA 436
                                       556677899999999999999987776665555 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.051
                                       EE-STTSSHHHHHHHHHHHHT-EEE CS
                    Cytidylate_kin   3 iDGPagsGKssvaralaeklglkyl 27 
                                       + GP g+GK  +a+a+a++ +++++
  gi|242399369|ref|YP_002994793.1| 587 LYGPPGTGKTLLAKAVANESEANFI 611
                                       67****************9998886 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 0.64
                                       T-EEEEHHHHHHHHHHHHHHTT--TT-HHHHHHHHHT CS
                    Cytidylate_kin  23 glkyldtgalYRalalaalrrkvdlldeaalvelake 59 
                                       g++  d +al R  a++alrr v +++ + +++ a+e
  gi|242399369|ref|YP_002994793.1| 749 GYSGADLAALVREAAFVALRRAVSITSRDLVEDQAEE 785
                                       56777888999*************9999888776655 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.039        12       2      26 ..     250     274 ..     249     281 .. 0.81
   2 ?    0.5   0.1       1.5   4.9e+02      82     120 ..     292     331 ..     284     358 .. 0.72
   3 ?    1.1   0.0         1   3.3e+02     102     123 ..     548     569 ..     521     575 .. 0.84
   4 ?    7.4   0.0     0.012       3.9       2      39 ..     585     619 ..     584     631 .. 0.78
   5 ?   -1.5   0.0       6.5   2.1e+03      80     104 ..     625     650 ..     612     653 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.039
                                       EEEE--TTSSHHHHHHHHHHHH... CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkss 26 
                                       v++ GppG+GKt l k v+++ + +
  gi|242399369|ref|YP_002994793.1| 250 VLLYGPPGTGKTLLAKAVANEANAH 274
                                       6788*************99987665 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1.5
                                       HHHHHHHHHHHH.HHH-EEEE---STTGGG-HHHHHHHHH CS
                          NTPase_1  82 eelalealrkal.seadviviDEiGkmElkskkfkeavee 120
                                       ee   +++++a  + + +i iDEi  +  k +++  +ve+
  gi|242399369|ref|YP_002994793.1| 292 EERLRDIFKEAEeNAPSIIFIDEIDAIAPKREEVTGEVEK 331
                                       45555666666645566******98776666666666654 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 1
                                       ---STTGGG-HHHHHHHHHHHT CS
                          NTPase_1 102 DEiGkmElkskkfkeaveevLk 123
                                       D iG +E   +++keave  Lk
  gi|242399369|ref|YP_002994793.1| 548 DDIGGLENVKQELKEAVEWPLK 569
                                       99***************97776 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.012
                                       EEEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE- CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgGfyteevr 39 
                                       +++ GppG+GKt l k v+++    + +  G+  +ev 
  gi|242399369|ref|YP_002994793.1| 585 ILLYGPPGTGKTLLAKAVANES---EANFIGIRGPEVL 619
                                       6788********9999999887...4556677666665 PP

  == domain 5  score: -1.5 bits;  conditional E-value: 6.5
                                       HHHHHHHHHHHHHH.HHH-EEEE--- CS
                          NTPase_1  80 sfeelalealrkal.seadviviDEi 104
                                       + e+ + e++rka    + v+ iDE+
  gi|242399369|ref|YP_002994793.1| 625 ESEKRIREIFRKARqAAPTVVFIDEV 650
                                       567778889999984455599****8 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0    0.0061         2      93     156 ..     200     274 ..     179     282 .. 0.65
   2 ?    5.4   0.0     0.025       8.1     127     152 ..     580     605 ..     467     613 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0061
                             T2SSE  93 lviRkksakeltlddlgaeealkekiaevlrkavre...........rglilvsGgTgsGKttllyallkeinks 156
                                       + +R++++ e+t++d+g  ++  +ki+e+++ ++++            + +l+ G+ g+GKt l+ a+ +e n++
  gi|242399369|ref|YP_002994793.1| 200 VEVREEKVPEVTYEDIGGLKDAVQKIREMVELPLKHpelferlgiepPKGVLLYGPPGTGKTLLAKAVANEANAH 274
                                       5566666666677777666655544444444443321111111110146689******************99987 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.025
                             T2SSE 127 rerglilvsGgTgsGKttllyallke 152
                                       +  + il+ G+ g+GKt l+ a+ +e
  gi|242399369|ref|YP_002994793.1| 580 TPPKGILLYGPPGTGKTLLAKAVANE 605
                                       346789*************9998776 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0     0.017       5.4      24      47 ..     250     273 ..     245     324 .. 0.71
   2 ?    6.4   0.0     0.028         9      24      47 ..     585     608 ..     580     656 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.017
                                       EEEEEETT--HHHHHHCC--TTS- CS
                   Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgp 47 
                                       v+l G++G+gk+l A++ ++++  
  gi|242399369|ref|YP_002994793.1| 250 VLLYGPPGTGKTLLAKAVANEANA 273
                                       9****************9987654 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.028
                                       EEEEEETT--HHHHHHCC--TTS- CS
                   Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgp 47 
                                       ++l G++G+gk+l A++ +++s+ 
  gi|242399369|ref|YP_002994793.1| 585 ILLYGPPGTGKTLLAKAVANESEA 608
                                       799***************999876 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       5.4      58      80 ..     243     265 ..     200     279 .. 0.83
   2 ?    5.6   0.0     0.019       6.2      50      79 ..     572     599 ..     548     606 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.017
                       AFG1_ATPase  58 svepvrglYlwGgvGrGKtylmd 80 
                                         ep++g+ l+G+ G GKt l  
  gi|242399369|ref|YP_002994793.1| 243 GIEPPKGVLLYGPPGTGKTLLAK 265
                                       468****************9865 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.019
                       AFG1_ATPase  50 klfgrkrksvepvrglYlwGgvGrGKtylm 79 
                                       k f+r     +p++g+ l+G+ G GKt l 
  gi|242399369|ref|YP_002994793.1| 572 KAFQRL--GITPPKGILLYGPPGTGKTLLA 599
                                       455533..578****************985 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0      0.19        60       5      71 ..     254     315 ..     250     320 .. 0.67
   2 ?    9.4   0.0    0.0025       0.8       4      71 ..     588     650 ..     585     654 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.19
                   Viral_helicase1   5 GvpGcGKStlirkllrts..liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                       G pG GK+ l + ++++   + + +++   e+ ++   +++ +    ++++++++       i+++DE+
  gi|242399369|ref|YP_002994793.1| 254 GPPGTGKTLLAKAVANEAnaHFI-AING-PEIMSKYYGESEERLRDIFKEAEENAP-----SIIFIDEI 315
                                       78***************663333.3333.355555555666666666666666553.....48899987 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0025
                   Viral_helicase1   4 hGvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                        G pG GK+ l + ++++s  ++  +r   e+l++++ +++++  + ++++ +a+       ++++DE 
  gi|242399369|ref|YP_002994793.1| 588 YGPPGTGKTLLAKAVANESeANFIGIRG-PEVLSKWVGESEKRIREIFRKARQAAPT-----VVFIDEV 650
                                       588*****************99999999.********99999999999999998754.....8999995 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0       2.4   7.8e+02       7      45 ..      18      56 ..      15      62 .. 0.89
   2 ?    6.0   0.0     0.038        12       1      24 [.     256     279 ..     256     306 .. 0.71
   3 ?    4.8   0.0     0.089        28       1      31 [.     591     623 ..     591     641 .. 0.70

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 2.4
                                      HHHHHHHHHHTSEEEEHHHHHHHHHTS-HHHHHHHHHHH CS
                               SKI  7 tvGkllAkklglefiDlDeliekrtgksiaeifeeegee 45
                                       v+++l + +g+ ++ +D+  +++ g +  +i+e ege 
  gi|242399369|ref|YP_002994793.1| 18 RVAEALKRDVGRGVVRIDRKYQRQLGIEPGDIVELEGER 56
                                      57778888899999***********************96 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.038
                                       TTSSHHHHHHHHHHHHTSEEEEHH CS
                               SKI   1 mGaGKstvGkllAkklglefiDlD 24 
                                       +G+GK+ ++k++A++ + +fi + 
  gi|242399369|ref|YP_002994793.1| 256 PGTGKTLLAKAVANEANAHFIAIN 279
                                       69******************9664 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.089
                                       TTSSHHHHHHHHHHHHTSEEEEH..HHHHHHHH CS
                               SKI   1 mGaGKstvGkllAkklglefiDl..Deliekrt 31 
                                       +G+GK+ ++k++A++ + +fi +   e+++k +
  gi|242399369|ref|YP_002994793.1| 591 PGTGKTLLAKAVANESEANFIGIrgPEVLSKWV 623
                                       69*****************99653345555544 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0     0.007       2.2       4      62 ..     251     319 ..     250     342 .. 0.79
   2 ?    2.6   0.0      0.29        92       5      61 ..     587     648 ..     585     675 .. 0.55

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.007
                               Zot   4 lvtGapGsgKts..gavkkdllpalk..egRkiitnidGlrlerieqvlgekvs.tarlirid.....n 62 
                                       l +G+pG+gKt+  +av ++++      +g +i+ +  G   er++ +++e+ + ++ +i+id      
  gi|242399369|ref|YP_002994793.1| 251 LLYGPPGTGKTLlaKAVANEANAHFIaiNGPEIMSKYYGESEERLRDIFKEAEEnAPSIIFIDeidaiA 319
                                       679********733679998888444357**********************9999999***99544433 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.29
                               Zot   5 vtGapGsgKtsga..vkkdllpalk..egRkiitnidGlrlerieqvlgekvs.tarlirid 61 
                                        +G+pG+gKt+ a  v ++         g ++  +  G   +ri+ +++++ + ++ +++id
  gi|242399369|ref|YP_002994793.1| 587 LYGPPGTGKTLLAkaVANESEANFIgiRGPEVLSKWVGESEKRIREIFRKARQaAPTVVFID 648
                                       57777777776431144433322222235555555555555555555555555555555555 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       0.3        97      18      47 ..     245     274 ..     232     280 .. 0.81
   2 ?    4.0   0.0     0.074        24     156     201 ..     290     334 ..     275     341 .. 0.81
   3 ?    0.6   0.0       0.8   2.6e+02      19      43 ..     581     605 ..     572     611 .. 0.83
   4 ?    0.4   0.0      0.96   3.1e+02     170     187 ..     636     655 ..     617     697 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.3
                        KAP_NTPase  18 atpivvgLygkWGsGKssllnkledelkef 47 
                                       ++p  v Lyg+ G+GK+ l + + +e + +
  gi|242399369|ref|YP_002994793.1| 245 EPPKGVLLYGPPGTGKTLLAKAVANEANAH 274
                                       5677799************99999988765 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.074
                        KAP_NTPase 156 eveelladmektLdalqkrlVvviDdLDrceteevlqlleavkllf 201
                                       e ee l d++k+ ++ + + +++iD++D + +++   + e+ k ++
  gi|242399369|ref|YP_002994793.1| 290 ESEERLRDIFKEAEE-NAPSIIFIDEIDAIAPKREEVTGEVEKRVV 334
                                       667788899998888.999**********99999888777766665 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.8
                        KAP_NTPase  19 tpivvgLygkWGsGKssllnklede 43 
                                       +p  + Lyg+ G+GK+ l + + +e
  gi|242399369|ref|YP_002994793.1| 581 PPKGILLYGPPGTGKTLLAKAVANE 605
                                       666799**********999988776 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 0.96
                        KAP_NTPase 170 a..lqkrlVvviDdLDrcet 187
                                       +  +  + Vv+iD+ D++ +
  gi|242399369|ref|YP_002994793.1| 636 KarQAAPTVVFIDEVDSIAP 655
                                       24468899********9866 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     0.053        17      26      59 ..     238     271 ..     223     282 .. 0.82
   2 ?    4.2   0.0     0.076        24      35      59 ..     582     606 ..     555     614 .. 0.80
   3 ?   -1.8   0.0       5.4   1.7e+03     110     132 ..     632     654 ..     621     668 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.053
                              TniB  26 LleypkrkrmpnlllvGdsnnGKtmivekFarlh 59 
                                       L+e+   + ++ +ll+G++ +GKt +++  a++ 
  gi|242399369|ref|YP_002994793.1| 238 LFERLGIEPPKGVLLYGPPGTGKTLLAKAVANEA 271
                                       5556666667899*************99887765 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.076
                              TniB  35 mpnlllvGdsnnGKtmivekFarlh 59 
                                       ++ +ll+G++ +GKt +++  a++ 
  gi|242399369|ref|YP_002994793.1| 582 PKGILLYGPPGTGKTLLAKAVANES 606
                                       5789*************99887765 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 5.4
                              TniB 110 qvlrllrelkvrvLiiDEihnll 132
                                       ++ r  r+  + v+ iDE++++ 
  gi|242399369|ref|YP_002994793.1| 632 EIFRKARQAAPTVVFIDEVDSIA 654
                                       445556788899*******9986 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 ?    5.1   0.0     0.062        20      21      49 ..     240     272 ..     217     329 .. 0.75
   2 ?    5.0   0.0      0.07        22      13      46 ..     554     604 ..     545     615 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.062
                                       ......TTSEEEEEESTTSTHHHHHHHHHHHH- CS
                            ResIII  21 s....krdkrglikmaTGtGKTlvaaklierll 49 
                                       +    +  k +l+  + GtGKTl+a +++ +  
  gi|242399369|ref|YP_002994793.1| 240 ErlgiEPPKGVLLYGPPGTGKTLLAKAVANEAN 272
                                       045547788899999********9987777655 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.07
                                       HHHT.......................TTSEEEEEESTTSTHHHHHHHHHH CS
                            ResIII  13 enlleklks.................krdkrglikmaTGtGKTlvaaklie 46 
                                       en++++lk+                 +  k +l+  + GtGKTl+a +++ 
  gi|242399369|ref|YP_002994793.1| 554 ENVKQELKEavewplkypkafqrlgiTPPKGILLYGPPGTGKTLLAKAVAN 604
                                       566666666666777777777777777888999***********9966655 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.085        27       2      24 ..     248     270 ..     247     275 .. 0.89
   2 ?    4.8   0.0     0.069        22       2      24 ..     583     605 ..     582     609 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.085
                         PduV-EutP   2 kkilliGkvgsGKttLtqalkge 24 
                                       k +ll G+ g+GKt L++a+ +e
  gi|242399369|ref|YP_002994793.1| 248 KGVLLYGPPGTGKTLLAKAVANE 270
                                       5699***************9987 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.069
                         PduV-EutP   2 kkilliGkvgsGKttLtqalkge 24 
                                       k ill G+ g+GKt L++a+ +e
  gi|242399369|ref|YP_002994793.1| 583 KGILLYGPPGTGKTLLAKAVANE 605
                                       6699***************9987 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.047        15       5      32 ..     251     278 ..     248     280 .. 0.90
   2 ?    3.7   0.0      0.11        34       5      29 ..     586     610 ..     583     614 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.047
                               IPT   5 lifGatttGKtaeaiklaketgapvivl 32 
                                       l++G+ +tGKt  a ++a+e  a  i++
  gi|242399369|ref|YP_002994793.1| 251 LLYGPPGTGKTLLAKAVANEANAHFIAI 278
                                       89*****************999888775 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.11
                               IPT   5 lifGatttGKtaeaiklaketgapv 29 
                                       l++G+ +tGKt  a ++a+e  a  
  gi|242399369|ref|YP_002994793.1| 586 LLYGPPGTGKTLLAKAVANESEANF 610
                                       89****************9987665 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 ?    4.6   0.0     0.086        28      21      39 ..     247     264 ..     238     269 .. 0.77
   2 ?    4.6   0.0     0.083        27      21      39 ..     582     599 ..     572     604 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.086
                            AAA_29  21 lkgatlltGpsGsGKSTll 39 
                                       +kg +ll Gp G+GK+ l 
  gi|242399369|ref|YP_002994793.1| 247 PKG-VLLYGPPGTGKTLLA 264
                                       356.9**********8765 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.083
                            AAA_29  21 lkgatlltGpsGsGKSTll 39 
                                       +kg +ll Gp G+GK+ l 
  gi|242399369|ref|YP_002994793.1| 582 PKG-ILLYGPPGTGKTLLA 599
                                       456.9**********8765 PP

>> ATP-cone  ATP cone domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.7   0.00038      0.12       8      66 ..     416     470 ..     409     491 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00038
                                       S-EEE--HHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHIIT-BHHHHHHHHHHHHH CS
                          ATP-cone   8 GtvepfdvekIkraiekAcegseeeideiaeeveaevrkrlrdgisteeIqdlvektli 66 
                                       + +e fd+e+I+++i+k  +++ee   +    + ++   +l++++    I+ ++e+ + 
  gi|242399369|ref|YP_002994793.1| 416 KNREAFDKERIEEMIQKIENAKEESDIK----ITLKEDGELYKEVRARLIDSMLEELAE 470
                                       679***************7774444444....444446779999999999999998876 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0      0.06        19       4      30 ..     251     277 ..     249     287 .. 0.78
   2 ?    3.6   0.0      0.13        43       4      25 ..     586     607 ..     584     613 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.06
                                       EEEESTTCCHHHHHHHHHCT--SS-EE CS
                              cobW   4 vltGflGsGKTtLlnhllenraglkla 30 
                                       +l G++G+GKT L +++ ++++   +a
  gi|242399369|ref|YP_002994793.1| 251 LLYGPPGTGKTLLAKAVANEANAHFIA 277
                                       688*******98888887766655555 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.13
                                       EEEESTTCCHHHHHHHHHCT-- CS
                              cobW   4 vltGflGsGKTtLlnhllenra 25 
                                       +l G++G+GKT L +++ ++++
  gi|242399369|ref|YP_002994793.1| 586 LLYGPPGTGKTLLAKAVANESE 607
                                       689********99888776655 PP

>> FPRL1_inhibitor  Formyl peptide receptor-like 1 inhibitory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1       6.4   2.1e+03      43      74 ..      10      41 ..       5      73 .. 0.70
   2 ?    9.2   0.1    0.0041       1.3      49     103 ..     786     838 ..     774     839 .] 0.86

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 6.4
                   FPRL1_inhibitor 43 etvndlylivkklsqgdvkkavvrikdggprd 74
                                      e  +++ l v +  + dv + vvri     r+
  gi|242399369|ref|YP_002994793.1| 10 EVKDEIKLRVAEALKRDVGRGVVRIDRKYQRQ 41
                                      56667788888888999999999998766665 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0041
                   FPRL1_inhibitor  49 ylivkklsqgdvkkavvrikdggprdyytfdltrpleenrknikvvkngeidsit 103
                                       +l   k+s+gd + a+ ++k    r  y +d  + +ee rk +k  +  e+d  t
  gi|242399369|ref|YP_002994793.1| 786 FLEKLKVSKGDFEDAMKKVKPSITR--YMLDYYKTFEESRKGVKGEERREVDYFT 838
                                       5566799*************98877..999**************99999999766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (839 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1162  (0.0648112); expected 358.6 (0.02)
Passed bias filter:                      915  (0.0510346); expected 358.6 (0.02)
Passed Vit filter:                       136  (0.00758548); 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):              56  [number of targets reported over threshold]
# CPU time: 1.03u 0.37s 00:00:01.40 Elapsed: 00:00:00.52
# Mc/sec: 4864.08
//
Query:       gi|242399370|ref|YP_002994794.1|  [L=254]
Description: hypothetical protein TSIB_1394 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.038   13.3   0.0      0.058   12.7   0.0    1.3  1  DUF1235   Protein of unknown function (DUF1235)
      0.091   13.2   0.0       0.22   11.9   0.0    1.7  1  RuvX      Holliday junction resolvase
       0.17   12.1   0.0       0.61   10.3   0.0    1.8  2  MG4       Macroglobulin domain MG4


Domain annotation for each model (and alignments):
>> DUF1235  Protein of unknown function (DUF1235)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   9.7e-06     0.058      47     124 ..      52     133 ..       9     136 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.7e-06
                           DUF1235  47 lvknlisikvvdkyelkk....elinsnlskiivCiqsakkGGliividkelnekkilklnvdkivilspLseytvs 119
                                        ++  ++i vv+++ +       +  +++ +i + i+   + G+ +v d+ + e + lk ++d  vil+ L +y  +
  gi|242399370|ref|YP_002994794.1|  52 AINFPVKIAVVNENFIDSllnkLEGRERFKNIYIAIDPGERPGVAVVADNRVIEVHHLKSPKDIDVILNLLEKYPGA 128
                                       5666788889888766654432445678899*******************************************887 PP

                           DUF1235 120 kvvkG 124
                                       +v+ G
  gi|242399370|ref|YP_002994794.1| 129 RVKIG 133
                                       77655 PP

>> RuvX  Holliday junction resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   3.7e-05      0.22       2     101 ..      83     168 ..      82     179 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.7e-05
                                       -EEEEEESSSEEEEEEE-S--SS---EEEEE---HHHHHHHHHHHHHHTT--EEEEE------SSS---SSTTHHHH CS
                              RuvX   2 rilglDvGtkriGvAvsdplgilaspletierkskekdleelkelvkeeeveeiVvGlPlnldgsegesakkvrkfa 78 
                                       +++++D G+ r GvAv  +++++   +  ++   + kd++ + +l++++  +++ +G     +g +  ++ + +++a
  gi|242399370|ref|YP_002994794.1|  83 IYIAIDPGE-RPGVAVVADNRVI--EVHHLK---SPKDIDVILNLLEKYPGARVKIG-----HGAKRYRSLMLKNLA 148
                                       689*****8.57****9999886..333333...4699************9999999.....5788899999***** PP

                                       HHHHHT..T-EEEEE--S----X CS
                              RuvX  79 eeLakrlkklpvelvDErlttve 101
                                       + L + +   p++lv+Er+tt +
  gi|242399370|ref|YP_002994794.1| 149 NILGEDF---PIFLVNERRTTPK 168
                                       ***9998...**********965 PP

>> MG4  Macroglobulin domain MG4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0    0.0001      0.61      11      50 ..      33      70 ..      29      82 .. 0.79
   2 ?   -1.3   0.0      0.42   2.5e+03      49      76 ..     216     243 ..     183     252 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0001
                               MG4 11 KpGlPfsikVlvkdpdgspaknvpVkiealkseteekesl 50
                                      +  +Pf+++V ++ +++  a n pVki++++   ++ +sl
  gi|242399370|ref|YP_002994794.1| 33 RDEIPFDVEVVLTSEEEYNAINFPVKIAVVN--ENFIDSL 70
                                      5679*************************75..4555554 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.42
                               MG4  49 slttdedGtakfsintpedaksltitvk 76 
                                       +  + ++G++ +s  ++++ ++ ++t +
  gi|242399370|ref|YP_002994794.1| 216 RSRELSNGMITISSRLAREVAKGNLTLE 243
                                       3445678888888888877776666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 1758.08
//
Query:       gi|242399371|ref|YP_002994795.1|  [L=64]
Description: hypothetical protein TSIB_1395 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
        2.2    8.0   9.1        2.4    7.9   9.1    1.0  1  Pox_Ag35         Pox virus Ag35 surface protein


Domain annotation for each model (and alignments):
>> Pox_Ag35  Pox virus Ag35 surface protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   9.1   0.00013       2.4      70     119 ..      14      63 ..       2      64 .] 0.71

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00013
                          Pox_Ag35  70 kkkeeekeeaaeeeeledseedeenendedeseesvqaeeeksnestedd 119
                                        kk++ ++ ++eee le++ ede +e+ e++ ee+ + e+e+ +e++edd
  gi|242399371|ref|YP_002994795.1|  14 PKKKKVEDFEEEEEILEEDWEDEFDEDWEEDWEEEEDWEDEDWEEEDEDD 63 
                                       23333444455566788888999999999999999999999999997775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1334  (0.0744046); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.32s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 406.96
//
Query:       gi|242399372|ref|YP_002994796.1|  [L=400]
Description: Molybdenum cofactor biosynthesis protein MoeA [Thermococcus sibiricus MM 739]
Scores for complete 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-41  141.1   0.1    7.6e-41  139.5   0.0    1.8  2  MoeA_N         MoeA N-terminal region (domain I and II)
    4.4e-25   88.0   0.0    7.6e-25   87.3   0.0    1.4  1  MoCF_biosynth  Probable molybdopterin binding domain
    2.6e-18   66.0   0.0    7.6e-18   64.5   0.0    1.9  1  MoeA_C         MoeA C-terminal region (domain IV)
  ------ inclusion threshold ------
       0.18   10.4   0.1       0.33    9.5   0.1    1.4  1  MutL           MutL protein


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 !  139.5   0.0   1.7e-44   7.6e-41       2     157 .]       8     171 ..       7     171 .. 0.89
   2 ?   -1.5   0.0      0.43   1.9e+03     118     138 ..     185     205 ..     173     216 .. 0.70

  Alignments for each domain:
  == domain 1  score: 139.5 bits;  conditional E-value: 1.7e-44
                                       -HHHHHHHHHHH-.HH-EEEEEGGCG-TT-BBSS-EE-SS-BSSS-EESSSEEEEEEBTTB--.............. CS
                            MoeA_N   2 sveealaiilaal.eleeeevplaaealgrvlaedvvApedvPpfdnSamDGYAvraeagsgaseeep........s 69 
                                       ++e al+i+ ++  +++ ee+pl ++algr+laedv++p++vPpfd++++DGYAv++e++++a+e++p        +
  gi|242399372|ref|YP_002994796.1|   8 PLERALNIVNSLPlNAKIEEIPL-ENALGRILAEDVTSPVNVPPFDRATVDGYAVKSENTWNANESNPvrlkvigeV 83 
                                       68999997777754446666***.99**************************************************8 PP

                                       .....-S---TT-.EEEE-TTSB--TT--EEEEGGGE.E....EETTE.S--STTTTEE-TTSSB-TTSEEE-TTBB CS
                            MoeA_N  70 aageeperllpgg.avrimTGaplPegadaVvpvEdteeeeaketvev.kavkpgenvrraGedikaGevllragtr 144
                                       +ageep+ ++++g av+i TGa+lP+g+daV+  E ++  ++ ++v + k++ p++ v +aG di +G++ll++g +
  gi|242399372|ref|YP_002994796.1|  84 HAGEEPNIEINSGeAVYISTGAVLPKGTDAVIEFEIVD--REGDEVLIyKPIYPQAGVMKAGTDIPKGKLLLKKGMK 158
                                       88888888888888***********************5..22333344799************************** PP

                                       --CCCHHHHHHCT CS
                            MoeA_N 145 ltpaeigllasvG 157
                                       l+  e +ll +vG
  gi|242399372|ref|YP_002994796.1| 159 LGFKETALLSAVG 171
                                       ***********98 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.43
                                       --STTTTEE-TTSSB-TTSEE CS
                            MoeA_N 118 avkpgenvrraGedikaGevl 138
                                        ++ g+ v   Ge++k G++ 
  gi|242399372|ref|YP_002994796.1| 185 IISTGNEVILPGEELKPGKIY 205
                                       566788888888888888775 PP

>> MoCF_biosynth  Probable molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.3   0.0   1.7e-28   7.6e-25       1     143 [.     184     319 ..     184     320 .. 0.95

  Alignments for each domain:
  == domain 1  score: 87.3 bits;  conditional E-value: 1.7e-28
                                       EEEEE-HHHH.......TTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTSSEEEEESS-SSST CS
                     MoCF_biosynth   1 avitvGdell.......sgkieDtngpllaellkelgvevskytvvpDdeeeikeallaaleeadviittGGtGptp 70 
                                       a+i++G+e++       +gki+D ng  l +++kelg + + +++ +D+ee ++ ++l+ l++ d+++++GG + + 
  gi|242399372|ref|YP_002994796.1| 184 AIISTGNEVIlpgeelkPGKIYDINGRALNDAVKELGGDPHFLGIARDNEESLRTKILEGLKY-DIVLLSGGASGGT 259
                                       69999999999999999*******************************************777.************* PP

                                       T--HHHHHHHHHSEE-HHHHHHHHHHHHHHCCTTSHGGGGGGE.EETTEEEEE-SSHHHHHHHHHHHHHGGHH CS
                     MoCF_biosynth  71 dDvtpealaklfekelegfeeafrrvslkpgkpvgvapgailsravgktiigLPGspkavkealeeillpale 143
                                       +D+t  ++ +l+e       + +++++ +pgkp++++ +   +++    i+gLPG+p ++ + + +++ p ++
  gi|242399372|ref|YP_002994796.1| 260 RDLTASIIDELGE-------VRIHGIAIQPGKPTIIGVI---NEK---AIFGLPGYPTSCLTNFTLLVAPLIR 319
                                       *************.......89***********999999...544...7*******************99987 PP

>> MoeA_C  MoeA C-terminal region (domain IV)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.5   0.0   1.7e-21   7.6e-18       3      72 .]     334     398 ..     332     398 .. 0.96

  Alignments for each domain:
  == domain 1  score: 64.5 bits;  conditional E-value: 1.7e-21
                                       EESS-EE--SSS-EEEEEEEES-S-EEEEEE-S---TT-GGGCTT--EEEEE-TT--EE-TT-EEEEEE- CS
                            MoeA_C   3 rlaedlksdpgrreflRvilteedgeyvaeptgkqgSglLsslaeAnglivipegtegleaGeeVevill 72 
                                       rl++++ s +grr+fl+v+++    e +a p+ ++gSg+++s+ +A+g++++pe++e le+GeeV+vil+
  gi|242399372|ref|YP_002994796.1| 334 RLTHKVFSVKGRRQFLPVKIK----EETAIPI-MKGSGAITSFINADGFVEVPENVEILEEGEEVNVILF 398
                                       899******************....669****.***********************************97 PP

>> MutL  MutL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1   7.3e-05      0.33     112     141 ..     237     266 ..     209     287 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 7.3e-05
                              MutL 112 dleelrelrpdiiLLaGGtDgGnkevllen 141
                                       + + l+ l+ di+LL+GG  gG+++     
  gi|242399372|ref|YP_002994796.1| 237 RTKILEGLKYDIVLLSGGASGGTRDLTASI 266
                                       6778999****************9987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.37
# Mc/sec: 3218.58
//
Query:       gi|242399373|ref|YP_002994797.1|  [L=455]
Description: Seryl-tRNA synthetase [Thermococcus sibiricus MM 739]
Scores for complete 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-38  130.8   0.0    8.7e-38  130.1   0.0    1.3  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
    1.4e-25   89.6  10.2    2.7e-25   88.7  10.2    1.5  1  Seryl_tRNA_N    Seryl-tRNA synthetase N-terminal domain
  ------ inclusion threshold ------
      0.078   13.0   4.9       0.16   12.0   4.9    1.4  1  CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein C
       0.14   11.9   1.1       0.32   10.7   1.1    1.6  1  HAUS2           HAUS augmin-like complex subunit 2
       0.32   10.7   7.6       0.56    9.9   7.6    1.3  1  YkyA            Putative cell-wall binding lipoprotein


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 !  130.1   0.0   2.4e-41   8.7e-38       7     178 ..     243     420 ..     238     421 .. 0.95

  Alignments for each domain:
  == domain 1  score: 130.1 bits;  conditional E-value: 2.4e-41
                                       TSEEEEE-SSSHHHHHHHHHHHEEEBGGSSEEEEEEEEEEBTTTS....TBCTTTB-SEEEEEEEEEEESGGGHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b   7 ndreyiLkPtneetfvelirdevlrskrLPlklyqiqtkyRdEks....dsrGLlRvreFhqkdgyvfhaeasldds 79 
                                       ++++++L+Pt+e++++ ++++e+l   +LP+ ++ +++++R+E+     d++G++Rv++Fh+ +++v+  ++++++ 
  gi|242399373|ref|YP_002994797.1| 243 EGEDLYLIPTSEHPLAGMHSNEILDGHNLPILYAGVSPCFRKEAGtagkDTKGIFRVHQFHKVEQFVYARPEESWEW 319
                                       4689******************8899******************77899**************************** PP

                                       HHHHHHHHHHHHHHTT.SCEEEEEEGTTSCBTTSEEEEEEEEETTTSEEEEEEEEEEEETHHHHHTTEEEECTTS.S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x RF
                      tRNA-synt_2b  80 lrdlikaisriferlglefraiielmsaksadykdkkefeavsesltkgieigtiqklgtrlserlgatvldenn.r 155
                                        ++l++ +++if++l +++r +  ++++    +++k+++ea++  ++k++e+++++++ + +++rl++++ d+ n +
  gi|242399373|ref|YP_002994797.1| 320 HEKLLQNAEEIFQALEIPYRIVNICTGDLGYAAAKKYDIEAWMSAQGKFREVVSCSNCTEWQARRLNIRFRDKPNeK 396
                                       ******************9988888*********************************99************97758 PP

                                       EEEEEEEEEE.EEHHHHHHHHHHH CS
                                       xxxxxxxxxx.xxxxxxxxxxxxx RF
                      tRNA-synt_2b 156 eksvimicaa.igveRllsaileq 178
                                        ++v++++ + i+++R + ai+e+
  gi|242399373|ref|YP_002994797.1| 397 PRFVHTLNSTaIATSRAIVAIIEN 420
                                       89*******99***********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 !   88.7  10.2   7.5e-29   2.7e-25       1     107 [.       1     109 [.       1     110 [. 0.97

  Alignments for each domain:
  == domain 1  score: 88.7 bits;  conditional E-value: 7.5e-29
                                       ---HHHHHH-HHHHHHHHCCCT..CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCC CS
                      Seryl_tRNA_N   1 MLDiklirenpeavkeklkkRg..edkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliae 75 
                                       M+Diklirenp+++k  l kRg  e    +de+leld+k+re  +e+++l++erN+l+ eIgk kk++e ++eli++
  gi|242399373|ref|YP_002994797.1|   1 MIDIKLIRENPDLIKGDLIKRGelEKLRWIDEILELDKKWRENLKEINNLRRERNKLAIEIGKRKKSGEAIDELIKK 77 
                                       9*********************6656667************************************************ PP

                                       CHHHHHHHHHHHHHHHHHHHHHHHHHCTS--- CS
                      Seryl_tRNA_N  76 vkelkeelkaleaelkeleaeleklllaiPNi 107
                                       ++++ ++++++e+e + ++++++ +l+++PNi
  gi|242399373|ref|YP_002994797.1|  78 SDNIAKRIEEIEKENNIIREKIDYYLWRLPNI 109
                                       *******************************9 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 ?   12.0   4.9   4.4e-05      0.16      53     123 ..      23      98 ..      17     106 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.4e-05
                    CENP-F_leu_zip  53 evetlk..eeieelaeelreleldLvalrsekeeLekelqkkq...ervseLeslnsslenlleekEqekvqmkee 123
                                       e+e+l+  +ei el ++ re   ++++lr+e+++L+ e+ k +   e ++eL +    + + +ee E+e+  ++e+
  gi|242399373|ref|YP_002994797.1|  23 ELEKLRwiDEILELDKKWRENLKEINNLRRERNKLAIEIGKRKksgEAIDELIKKSDNIAKRIEEIEKENNIIREK 98 
                                       666654337999*************************99876633368*********************9888876 PP

>> HAUS2  HAUS augmin-like complex subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.1   8.8e-05      0.32      43      94 ..      43      96 ..      23     101 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 8.8e-05
                             HAUS2 43 vLrelsavqrelaklnlElqlrkddkdvad..lthvselekkcealqrvtthLk 94
                                       L+e+ ++ re +kl +E+ +rk+  +++d  +   ++++k++e++++ +++++
  gi|242399373|ref|YP_002994797.1| 43 NLKEINNLRRERNKLAIEIGKRKKSGEAIDelIKKSDNIAKRIEEIEKENNIIR 96
                                      69**********************99999875556789*********9999875 PP

>> YkyA  Putative cell-wall binding lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   7.6   0.00016      0.56      10      79 ..      30      97 ..      25     100 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00016
                              YkyA 10 leeavelEkefeeqqekLtelekkeqelyeeiielgmdefdkikklsdealenveeReellekekesiee 79
                                      ++e+ el+k+ +e+ +++++l ++ ++l  ei  + ++  ++i +l+++  +n+ +R e++eke+++i e
  gi|242399373|ref|YP_002994797.1| 30 IDEILELDKKWRENLKEINNLRRERNKLAIEIG-KRKKSGEAIDELIKK-SDNIAKRIEEIEKENNIIRE 97
                                      5788999*************************6.577777999999998.5799***********99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (455 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1058  (0.0590105); expected 358.6 (0.02)
Passed bias filter:                      680  (0.0379274); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); expected 17.9 (0.001)
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: 0.65u 0.30s 00:00:00.95 Elapsed: 00:00:00.48
# Mc/sec: 2838.09
//
Query:       gi|242399374|ref|YP_002994798.1|  [L=120]
Description: Ribonuclease P protein component 4 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-18   65.5   0.3    3.8e-18   65.5   0.3    1.5  2  Rpr2      RNAse P Rpr2/Rpp21/SNM1 subunit domain
  ------ inclusion threshold ------
      0.015   14.8   2.7      0.022   14.2   2.7    1.4  1  NMD3      NMD3 family
      0.036   13.8   0.5      0.036   13.8   0.5    1.5  1  FEZ       FEZ-like protein


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 ?   -3.8   0.3       2.7   1.6e+04      71      77 ..       8      14 ..       3      18 .. 0.40
   2 !   65.5   0.3   6.4e-22   3.8e-18       1      90 []      21     100 ..      21     100 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 2.7
                                      -E..... CS
                              Rpr2 71 kkkkkkk 77
                                      +k++++k
  gi|242399374|ref|YP_002994798.1|  8 RKEQREK 14
                                      2222222 PP

  == domain 2  score: 65.5 bits;  conditional E-value: 6.4e-22
                                       HHHHHHHHHH.HHHHH-HHHHHHHHHHHHHHHHHCT---SSTCCCTB-TTT--B--CTTTEEEEEE-SSS-E..... CS
                              Rpr2   1 rlnfLyqaahlqlaeaspalsrylakqlrevskkaqlrlppsvkrtvCkkCgsvlipgvtcsvrvenkskkkkkkkk 77 
                                       r+++L+++a+    +  ++l++++++ + +v++ka++r+p+++kr++CkkC+s+l+pgv+++vr+++k+ +      
  gi|242399374|ref|YP_002994798.1|  21 RIDILFNLAER-VFAYDKELANRYVEIALAVQQKAKVRMPRKWKRRYCKKCHSFLVPGVNARVRLRQKRMP------ 90 
                                       89999999998.9999*************************************************865554...... PP

                                       ....EEEEETTTT CS
                              Rpr2  78 kadvlvvtClaCg 90 
                                         + +v++Cl+Cg
  gi|242399374|ref|YP_002994798.1|  91 --H-VVIKCLECG 100
                                       ..3.58******7 PP

>> NMD3  NMD3 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   2.7   3.7e-06     0.022     109     156 ..      48      89 ..       3     114 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.7e-06
                              NMD3 109 gevrgenetilqqevevevkvkrqqCprCsriaggyyeaivQvRqkre 156
                                         v      + + +v+++ k+kr+ C++C+ +     +a v++Rqkr 
  gi|242399374|ref|YP_002994798.1|  48 LAV------QQKAKVRMPRKWKRRYCKKCHSFLVPGVNARVRLRQKRM 89 
                                       222......12346677789**************************54 PP

>> FEZ  FEZ-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.5   6.1e-06     0.036     197     235 ..      28      65 ..      16      70 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.1e-06
                               FEZ 197 LAlRdELefeKEvKnsFIslLlavQnrrreqrelekkrk 235
                                       LA R    ++KE+ n ++ + lavQ++ +     + kr+
  gi|242399374|ref|YP_002994798.1|  28 LAER-VFAYDKELANRYVEIALAVQQKAKVRMPRKWKRR 65 
                                       5555.368*******************999875555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1072  (0.0597914); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 816.09
//
Query:       gi|242399375|ref|YP_002994799.1|  [L=515]
Description: hypothetical protein TSIB_1399 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (515 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 3300.44
//
Query:       gi|242399376|ref|YP_002994800.1|  [L=133]
Description: Methylmalonyl-CoA epimerase [Thermococcus sibiricus MM 739]
Scores for complete 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   84.3   0.0    7.7e-24   84.1   0.0    1.0  1  Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxyge
    1.9e-14   53.9   0.0    2.1e-14   53.8   0.0    1.0  1  Glyoxalase    Glyoxalase/Bleomycin resistance protein/Dioxyge
    1.5e-10   41.5   0.0    1.6e-10   41.4   0.0    1.0  1  Glyoxalase_3  Glyoxalase-like domain
  ------ inclusion threshold ------
      0.054   12.7   0.0          4    6.5   0.0    2.0  2  DUF1338       Domain of unknown function (DUF1338)
       0.13   12.2   0.0        1.9    8.4   0.0    2.1  2  PASTA         PASTA domain


Domain annotation for each model (and alignments):
>> Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.1   0.0   2.2e-27   7.7e-24       1     109 []       6     115 ..       6     115 .. 0.95

  Alignments for each domain:
  == domain 1  score: 84.1 bits;  conditional E-value: 2.2e-27
                                       EEEEEE-S-HHHHHHHHHH.TT-EESS--E.EETTTTEEEEEEEETTEEEEEEEESSTT....-THHHTS-EEEEEE CS
                      Glyoxalase_4   1 dQigivVeDleaavarfsallGvgpwqryrdepqevdlafallgsgsvqieLieplegp....eflaehgeglhhla 73 
                                       d+igi+V+Dle+a++ ++  lG++++++ ++++q+v++a++++g++  +ieL e   ++    +f++++geg+hh+a
  gi|242399376|ref|YP_002994800.1|   6 DHIGIAVRDLEEAIKIWES-LGLKVEEIEEVPDQKVRTAIFHAGET--RIELLEGTTEDspvsKFVEKRGEGIHHIA 79 
                                       6*****************8.*************************6..9*****88877567788888********* PP

                                       EEES-HHHHHHHHCTTTEEEEEEEE-GGGTT-EEEE CS
                      Glyoxalase_4  74 ywvddldaavarleeqGfevvqkgvragaagrrfay 109
                                       + vd++++ +++l+e+Gf++++  +r g +g ++a+
  gi|242399376|ref|YP_002994800.1|  80 LGVDNIEEHLQKLKENGFRLIDVTPRIGVGGAKIAF 115
                                       ****************************99999998 PP

>> Glyoxalase  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.8   0.0   5.8e-18   2.1e-14       1     116 [.       4     114 ..       4     128 .. 0.89

  Alignments for each domain:
  == domain 1  score: 53.8 bits;  conditional E-value: 5.8e-18
                                       EEEEEEEEESHHHHHHHHHHHHHTSEEEEEEEEEESTEEEEEEEEETTTSEEEEEEEECCTTSCTHHCCBSCTSEEE CS
                        Glyoxalase   1 gidhvallvgdleksldFYtkvLGfklvkktdnteeteglriaffhaggghielvlneapsgaakhvkkieetvhhv 77 
                                       ++dh+ ++v+dle++++ ++  LG+k+ + ++   +++++r a fhag+++iel+   +++++ +++  +e+ ++++
  gi|242399376|ref|YP_002994800.1|   4 KVDHIGIAVRDLEEAIKIWES-LGLKVEEIEE--VPDQKVRTAIFHAGETRIELLEGTTEDSPVSKF--VEKRGEGI 75 
                                       589******************.**********..***********************9999999999..67689*** PP

                                       EEEEEEHCHHHHHHHHHHHTTGEEEEEEECHHCTEEEEE CS
                        Glyoxalase  78 afialdvedvgkaldrlkeagvkvvaepgrhyfgalysf 116
                                       ++ial v+++++ l++lke+g++  ++  r + g+  ++
  gi|242399376|ref|YP_002994800.1|  76 HHIALGVDNIEEHLQKLKENGFRLIDVTPRIGVGGAKIA 114
                                       ***********************9999999888777766 PP

>> Glyoxalase_3  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.4   0.0   4.5e-14   1.6e-10       2     111 ..       6     106 ..       5     132 .. 0.81

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 4.5e-14
                      Glyoxalase_3   2 DHvvlavpdleeaaarfarrlGftvtpggehpglgtaNalvmfgdgYlElla.vdpeapaperprlfgldrlakgeg 77 
                                       DH+++av+dleea++ + + lG++v++  e p+   + a+++ g++ +Ell+   ++ p     + f     ++geg
  gi|242399376|ref|YP_002994800.1|   6 DHIGIAVRDLEEAIKIW-ESLGLKVEEIEEVPDQKVRTAIFHAGETRIELLEgTTEDSPVS---K-FVE---KRGEG 74 
                                       ***************77.9**************9999999999********9677777763...3.322...369** PP

                      Glyoxalase_3  78 lhtlalrtddidataarlraaGvdeagrrvrpdg 111
                                       +h++al +d+i++  ++l+++G+   + +v+p  
  gi|242399376|ref|YP_002994800.1|  75 IHHIALGVDNIEEHLQKLKENGFR--LIDVTPRI 106
                                       **********************85..44444444 PP

>> DUF1338  Domain of unknown function (DUF1338)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0    0.0011         4     207     270 ..       4      60 ..       2      71 .. 0.82
   2 ?    5.0   0.0    0.0032        12     203     235 ..      70     102 ..      59     110 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0011
                           DUF1338 207 aiNHlTprvldidalqafleergiklkdeieGpptvspdglLrQtSfkAleeevkfaegsgeev 270
                                        + H+ ++v d++++ +  e+ g+k++ eie    + pd  +r   f+A e+++++ eg   ++
  gi|242399376|ref|YP_002994800.1|   4 KVDHIGIAVRDLEEAIKIWESLGLKVE-EIE----EVPDQKVRTAIFHAGETRIELLEGT--TE 60 
                                       589***********************9.666....57999***999*********99444..44 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0032
                           DUF1338 203 vngyaiNHlTprvldidalqafleergiklkde 235
                                        +g  i H++  v +i++  ++l+e+g++l d+
  gi|242399376|ref|YP_002994800.1|  70 KRGEGIHHIALGVDNIEEHLQKLKENGFRLIDV 102
                                       5788999**********************9876 PP

>> PASTA  PASTA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0   0.00052       1.9      10      34 ..      14      38 ..       9      41 .. 0.90
   2 ?    1.4   0.0     0.081   2.9e+02      11      29 ..      85     103 ..      83     122 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00052
                                      BHHHHHHHHHHTT--CCCEEEECTC CS
                             PASTA 10 svdeAkatLkalGlkiktveetsdd 34
                                      +++eA+++ ++lGlk+ ++ee++d+
  gi|242399376|ref|YP_002994800.1| 14 DLEEAIKIWESLGLKVEEIEEVPDQ 38
                                      79******************98875 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.081
                                       HHHHHHHHHHTT--CCCEE CS
                             PASTA  11 vdeAkatLkalGlkiktve 29 
                                       ++e  + Lk++G++   v+
  gi|242399376|ref|YP_002994800.1|  85 IEEHLQKLKENGFRLIDVT 103
                                       56777999*****655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 873.38
//
Query:       gi|242399377|ref|YP_002994801.1|  [L=322]
Description: Lysine/arginine/ornithine transport system kinase [Thermococcus sibiricus MM 739]
Scores for complete 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-103  343.0   3.0     1e-102  342.7   3.0    1.0  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
    1.6e-07   31.0   2.6    1.5e-06   28.0   2.6    2.3  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
    2.4e-06   27.3   0.1    3.2e-05   23.6   0.1    2.3  1  GTP_EFTU         Elongation factor Tu GTP binding domain
    1.6e-05   24.9   0.1    5.5e-05   23.1   0.1    1.9  1  NTPase_1         NTPase
    1.9e-05   24.6   0.1    0.00037   20.4   0.0    2.2  2  ATP_bind_1       Conserved hypothetical ATP binding protein
    0.00014   21.6   0.1     0.0006   19.5   0.1    2.0  1  SRP54            SRP54-type protein, GTPase domain
    0.00015   22.1   0.0    0.00032   21.0   0.0    1.7  1  AAA_22           AAA domain
    0.00023   20.5   0.0    0.00023   20.5   0.0    1.3  1  KAP_NTPase       KAP family P-loop domain
    0.00026   21.4   0.0    0.00047   20.6   0.0    1.4  1  AAA_16           AAA ATPase domain
    0.00039   21.0   0.1    0.00094   19.7   0.1    1.7  1  AAA_18           AAA domain
    0.00052   20.5   0.1    0.00085   19.8   0.1    1.4  1  ABC_tran         ABC transporter
    0.00076   19.2   0.2     0.0016   18.2   0.2    1.5  1  AAA_29           P-loop containing region of AAA domain
     0.0011   18.2   0.1     0.0019   17.5   0.1    1.3  1  NB-ARC           NB-ARC domain
     0.0016   18.3   0.0     0.0075   16.2   0.0    2.0  2  MobB             Molybdopterin guanine dinucleotide synthesis
     0.0022   17.9   0.6     0.0048   16.8   0.1    1.8  2  ATPase_2         ATPase domain predominantly from Archaea
      0.003   17.6   0.8      0.022   14.8   0.8    2.4  1  MMR_HSR1         50S ribosome-binding GTPase
     0.0035   16.7   0.1     0.0065   15.8   0.1    1.4  1  Zeta_toxin       Zeta toxin
     0.0036   17.5   0.2      0.015   15.4   0.0    1.9  2  AAA_33           AAA domain
     0.0037   17.0   0.0     0.0076   16.0   0.0    1.5  1  AAA_30           AAA domain
     0.0058   16.5   0.0       0.15   11.8   0.0    2.1  2  AAA_11           AAA domain
     0.0074   16.7   1.6      0.049   14.1   0.1    2.6  2  AAA_17           AAA domain
  ------ inclusion threshold ------
      0.011   14.8   0.0      0.021   13.9   0.0    1.4  1  T2SSE            Type II/IV secretion system protein
      0.013   15.4   0.0      0.029   14.3   0.0    1.5  1  NACHT            NACHT domain
      0.014   14.9   0.3        1.3    8.4   0.0    2.3  2  RecA             recA bacterial DNA recombination protein
      0.014   14.3   0.1      0.024   13.5   0.1    1.3  1  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
      0.015   15.3   0.0      0.087   12.7   0.0    2.1  2  RsgA_GTPase      RsgA GTPase
      0.017   15.4   0.0      0.083   13.2   0.1    2.1  2  AAA_19           AAA domain
      0.018   15.4   0.0      0.058   13.8   0.0    1.9  1  RNA_helicase     RNA helicase
      0.018   15.1   0.0      0.037   14.0   0.0    1.5  1  AAA_14           AAA domain
      0.022   14.0   0.0      0.031   13.4   0.0    1.2  1  PIF1             PIF1-like helicase
      0.022   14.3   0.0       0.51    9.9   0.0    2.6  2  FeoB_N           Ferrous iron transport protein B
      0.025   13.3   0.0      0.045   12.5   0.0    1.4  1  RNA12            RNA12 protein
      0.025   14.0   0.1      0.067   12.6   0.0    1.7  1  KTI12            Chromatin associated protein KTI12
      0.028   14.5   0.4      0.059   13.5   0.1    1.7  1  DUF87            Helicase HerA, central domain
      0.043   14.3   0.0       0.18   12.2   0.0    2.1  1  AAA              ATPase family associated with various cellul
      0.055   13.2   0.0       0.16   11.7   0.0    1.8  1  AAA_24           AAA domain
      0.085   13.1   0.1       0.17   12.1   0.1    1.5  1  AAA_28           AAA domain
      0.085   12.9   0.0       0.25   11.4   0.0    1.8  1  AAA_5            AAA domain (dynein-related subfamily)
      0.089   12.7   0.0       0.17   11.8   0.0    1.4  1  Rad17            Rad17 P-loop domain
       0.14   11.9   0.1       0.22   11.2   0.1    1.3  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
       0.31   11.5   1.5       0.42   11.1   0.2    1.8  1  AAA_23           AAA domain


Domain annotation for each model (and alignments):
>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  342.7   3.0  2.3e-105    1e-102       2     265 ..      21     286 ..      20     288 .. 0.98

  Alignments for each domain:
  == domain 1  score: 342.7 bits;  conditional E-value: 2.3e-105
                                       HHHHHHHH--SHHHHHHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE------------- CS
                              MeaB   2 araitlveserpeakellerllakaGraqvvGltGvPGaGkstlvealglelrrrGkrvavlavDPsspftGGsilG 78 
                                       ar+itlve+++ +a+e+++++ +k+Gra  +G+tG PG+Gkstlv++l+ + r++G+ v+v+a+DP+spftGG++lG
  gi|242399377|ref|YP_002994801.1|  21 ARLITLVENDEEKAREIVKKIYSKTGRAYIIGITGPPGSGKSTLVDKLIKKARDEGNIVGVIAIDPTSPFTGGALLG 97 
                                       89*************************************************************************** PP

                                       -----HCCCTSTTEEEEEE-----HHHHHHHHHHHHHHHHHTT-SEEEEEEESSTTHHHHHHTT-SEEEEEEESSTT CS
                              MeaB  79 DklRleelavdegvfiRslpsrGalGGlaaktrevvllleaaGfDvvlietvGvGqsevdvaevvdtfvvlllpeaG 155
                                       D++R++++++d+gvfiRs+++rG lGGla++t++++++l+a G D++ +etvGvGq evd+++ +dt+v++++p+ G
  gi|242399377|ref|YP_002994801.1|  98 DRIRMQRHSTDPGVFIRSMATRGSLGGLAKATNDAIKILDAYGCDIIFVETVGVGQIEVDIVKTADTVVLVTVPGLG 174
                                       ***************************************************************************** PP

                                       TTTTT--CCCHHH-SEEEEE---HHHHHHHHHHHHHHHHHCSTT..BTTB--EEEEEBCCCTBSHHHHHHHHHHHHH CS
                              MeaB 156 DelqgikkGileiaDiivvnkaDkkeaekaarelraaleleeek..ekeWrpkvlktsavegeGidelvdaieehre 230
                                       D++q+ik+G++eiaDi+vvnkaDk++ae +  el+ +l+le+ k  +++Wrp+v+ t a +++G+del+ ai+ehre
  gi|242399377|ref|YP_002994801.1| 175 DDIQAIKAGLMEIADIFVVNKADKEGAEATMFELELMLDLEKDKwqKSGWRPPVVSTIAFTNKGVDELWGAINEHRE 251
                                       **************************************9999977799***************************** PP

                                       HHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHC- CS
                              MeaB 231 vlkktGllekrrrerakeelrelvedellkrvkaa 265
                                       +l ++G++e++r+ r+ ee++++v++++ +++ ++
  gi|242399377|ref|YP_002994801.1| 252 FLLNSGKIEEKRKFRVGEEIKAIVSSKIARKIGEK 286
                                       ***************************99988665 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 !   28.0   2.6   3.3e-09   1.5e-06       2     158 ..      50     204 ..      49     218 .. 0.73

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 3.3e-09
                                       EEEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SSCHCCCCCC......HCCCT.........EEEETT.TTE CS
                              cobW   2 vtvltGflGsGKTtLlnhll..enraglklavivNefgevsiDaell......retgve........ivelen.Gci 61 
                                       ++++tG++GsGK+tL+ +l+  ++ +g+ + vi  +  +    ++ll      +             i ++++ G +
  gi|242399377|ref|YP_002994801.1|  50 IIGITGPPGSGKSTLVDKLIkkARDEGNIVGVIAIDPTSPFTGGALLgdrirmQ----RhstdpgvfIRSMATrGSL 122
                                       578*****************8777788999*****9997777777774444431....0344567778888763666 PP

                                       CCHCTT-HHHHHHHHHHHHTT-SEEEEEECTTTTHHHHHTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHH CS
                              cobW  62 CctlredllkelealeereerldviliEttGlaePapvafteeelksdltldavvavvDaknleaeeekieekaedq 138
                                             ++++ + ++++ +   d+i++Et+G+ +              ++   +v++v +      +++i+      
  gi|242399377|ref|YP_002994801.1| 123 GGL--AKATNDAIKILDAY-GCDIIFVETVGVGQIEVD---------IVKTADTVVLVTVP---GLGDDIQAIKAGL 184
                                       665..44555555666666.5**********9875443.........44444455555663...4589999999999 PP

                                       HHTSSEEEEE-HHHHCHC.. CS
                              cobW 139 laaadllvlnKtDlldeeal 158
                                       ++ ad++v+nK+D   +ea+
  gi|242399377|ref|YP_002994801.1| 185 MEIADIFVVNKADKEGAEAT 204
                                       *************9887755 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.1   7.2e-08   3.2e-05       5     191 ..      50     249 ..      47     251 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 7.2e-08
                                       EEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHH...HHHST............HCHSHHHHHHTSCSSCEEEEEE.. CS
                          GTP_EFTU   5 nigiighvDhGKtTLtdrLlyktgaiskkgeka...eeerv............lDtlkeErergiTiksaaisle.. 64 
                                        igi g   +GK+TL+d+L++k+ +  +   +        +            +  + +    g+ i s a+  +  
  gi|242399377|ref|YP_002994801.1|  50 IIGITGPPGSGKSTLVDKLIKKARDEGNIVGVIaidP---TspftggallgdrIRMQRHSTDPGVFIRSMATRGSlg 123
                                       699********************99999777774431...2456778888777777777888899999999988888 PP

                                       ..TTCSSEEEEEEEESS.SGGGHHHHHHH......HHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESC CS
                          GTP_EFTU  65 ..ketkkylinliDtPG.HvdFskevirg......lrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKm 132
                                         ++ ++  i+++D+ G ++ F+++v  g      ++++D +vlv     G   q       a  +++  i+++NK+
  gi|242399377|ref|YP_002994801.1| 124 glAKATNDAIKILDAYGcDIIFVETVGVGqievdiVKTADTVVLVTVPGLGDDIQAI----KAGLMEIADIFVVNKA 196
                                       87699999*********4456*****9997776667777777777666666666654....467789999******* PP

                                       GSTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHHH CS
                          GTP_EFTU 133 DrlkaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvktllealvel 191
                                       D+ +ae  +   e+  +l  +++k++k g +     pvv + a++++gv++l  a+ e+
  gi|242399377|ref|YP_002994801.1| 197 DKEGAEATMFELELMLDL--EKDKWQKSGWRP----PVVSTIAFTNKGVDELWGAINEH 249
                                       *****9999999999888..777888887776....8***************9998876 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.1   1.3e-07   5.5e-05       2      32 ..      51      80 ..      50      89 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1.3e-07
                                      EEEE--TTSSHHHHHHHHHHHH...GGGEEE CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvkvgG 32
                                      + iTGppG+GK+Tlv+k++++ +++g  v G
  gi|242399377|ref|YP_002994801.1| 51 IGITGPPGSGKSTLVDKLIKKARDEGNIV-G 80
                                      67********************9987655.4 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 !   20.4   0.0   8.5e-07   0.00037       1      36 [.      53      88 ..      53      91 .. 0.95
   2 ?    2.0   0.0      0.34   1.5e+02     155     186 ..     185     217 ..     146     258 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 8.5e-07
                        ATP_bind_1  1 vvGpaGsGKttfvgalseilelrgrsvavvNLDPAa 36
                                      ++Gp+GsGK+t+v +l++ ++++g  v v+ +DP +
  gi|242399377|ref|YP_002994801.1| 53 ITGPPGSGKSTLVDKLIKKARDEGNIVGVIAIDPTS 88
                                      68********************************75 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.34
                        ATP_bind_1 155 lelPhvvvlnkfDllkek.lekeleffedveal 186
                                       +e+  + v+nk+D    + + +ele + d+e+ 
  gi|242399377|ref|YP_002994801.1| 185 MEIADIFVVNKADKEGAEaTMFELELMLDLEKD 217
                                       7899999******97777899999999998764 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.1   1.4e-06    0.0006       4     111 ..      51     168 ..      48     203 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.4e-06
                                       EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEEST...SSTTHH..H..HHHHHHHHTTEEEEE.SSTTS..CHHH CS
                             SRP54   4 illvGlqGaGKTttlaKLaallkkegkkvllvaaDt...fRaaAv..e..QLktlaeklgvpvik.kkeea..dpaa 70 
                                       i + G+ G+GK t + KL ++ ++eg+ v ++a D    f  +A+  +   ++ + +  gv + + +++++    a+
  gi|242399377|ref|YP_002994801.1|  51 IGITGPPGSGKSTLVDKLIKKARDEGNIVGVIAIDPtspFTGGALlgDriRMQRHSTDPGVFIRSmATRGSlgGLAK 127
                                       6688999****************************634477788744422466666666665555433333446899 PP

                                       HHHHHHHHHHHTTSSEEEEEE--SSTTHHHHHHHHHHHHHH CS
                             SRP54  71 vakeavekakeekidvvlvDTaGrlqndkelmeelkkikkv 111
                                        +++a++  ++ ++d+++v T G  q++ ++++  +++  v
  gi|242399377|ref|YP_002994801.1| 128 ATNDAIKILDAYGCDIIFVETVGVGQIEVDIVKTADTVVLV 168
                                       99************************999999887776655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   7.3e-07   0.00032       4      55 ..      47      94 ..      19     136 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 7.3e-07
                            AAA_22  4 tagilvvtGesGtGKTtllrrlleqldeeakaee.erpevvfvtlpsstsskd 55
                                      +a+i+ +tG++G+GK+tl+ +l +++       e + ++v+ ++++s+ +   
  gi|242399377|ref|YP_002994801.1| 47 RAYIIGITGPPGSGKSTLVDKLIKKARD-----EgNIVGVIAIDPTSPFTGGA 94
                                      689999******************9842.....23677788888888876555 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 !   20.5   0.0   5.2e-07   0.00023       6      62 ..      35      88 ..      31     298 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 5.2e-07
                        KAP_NTPase  6 saladilseptlatpivvgLygkWGsGKssllnkledelkefakpvrflfaefnaws 62
                                        +++ + + t ++ +++g++g+ GsGKs+l+ kl+++ +++   + + ++ +++ s
  gi|242399377|ref|YP_002994801.1| 35 REIVKKIYSKT-GRAYIIGITGPPGSGKSTLVDKLIKKARDE--GNIVGVIAIDPTS 88
                                      56778888776.9*************************9999..5555555555544 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   1.1e-06   0.00047      21      55 ..      45      79 ..      32     106 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.1e-06
                            AAA_16 21 sgrpelvllsGesGvGKsslvrellralekdggif 55
                                      +gr  ++ ++G++G+GKs+lv++l + ++++g i+
  gi|242399377|ref|YP_002994801.1| 45 TGRAYIIGITGPPGSGKSTLVDKLIKKARDEGNIV 79
                                      56667889******************999996444 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.1   2.2e-06   0.00094       1      22 [.      51      72 ..      51     121 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 2.2e-06
                            AAA_18  1 IlltGtpGvGKttlakeLskrl 22
                                      I++tG+pG+GK+tl + L k+ 
  gi|242399377|ref|YP_002994801.1| 51 IGITGPPGSGKSTLVDKLIKKA 72
                                      89****************5552 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.1     2e-06   0.00085      12      42 ..      49      78 ..      38     140 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 2e-06
                                      SEEEEEESTTSSHHHHHHHHTTSS--SEEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 12 ekvaivGenGaGKStLlkllagllkpteGei 42
                                       +++i+G+ G+GKStL+  l+++ + +eG+i
  gi|242399377|ref|YP_002994801.1| 49 YIIGITGPPGSGKSTLVDKLIKKAR-DEGNI 78
                                      589******************9998.57776 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.2   3.6e-06    0.0016      26      41 ..      52      67 ..      41      70 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.6e-06
                            AAA_29 26 lltGpsGsGKSTllDA 41
                                       +tGp GsGKSTl+D 
  gi|242399377|ref|YP_002994801.1| 52 GITGPPGSGKSTLVDK 67
                                      49*************5 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   4.3e-06    0.0019       3      44 ..      32      72 ..      30      84 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4.3e-06
                                      HHHHHHHHHHHCTTTSCSEEEEEEESTTSSHHHHHHHHCCSH CS
                            NB-ARC  3 ksvekviekLlekdelqslvvalvGmgGvGKttlakqilnks 44
                                      ++ +++ +k   k +    ++++ G +G+GK+tl+ + ++k 
  gi|242399377|ref|YP_002994801.1| 32 EKAREIVKKIYSKTGRA-YIIGITGPPGSGKSTLVDKLIKKA 72
                                      56778899999777776.9******************99983 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.7e-05    0.0075       1      33 [.      50      82 ..      50      89 .. 0.94
   2 ?   -1.5   0.0       4.9   2.1e+03      81      97 ..     129     147 ..     112     164 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.7e-05
                              MobB  1 vlgivgksgsGKTtLleklipelkarglrvgti 33
                                      ++gi+g  gsGK tL+ kli++ +++g  vg+i
  gi|242399377|ref|YP_002994801.1| 50 IIGITGPPGSGKSTLVDKLIKKARDEGNIVGVI 82
                                      799****************************98 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 4.9
                              MobB  81 leellarlse..vDlvlvE 97 
                                       +++ ++ l++  +D+++vE
  gi|242399377|ref|YP_002994801.1| 129 TNDAIKILDAygCDIIFVE 147
                                       4555666655569999998 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 !   16.8   0.1   1.1e-05    0.0048      11      49 ..      38      77 ..      29      87 .. 0.77
   2 ?   -1.9   0.1       5.8   2.6e+03      55      96 ..     254     297 ..     241     316 .. 0.55

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.1e-05
                          ATPase_2 11 leeile.repneiyfiYGpegsGKtaLlkeiienledkdk 49
                                      +++i++ ++++ i+ i+Gp gsGK++L+ ++i++ +d + 
  gi|242399377|ref|YP_002994801.1| 38 VKKIYSkTGRAYIIGITGPPGSGKSTLVDKLIKKARDEGN 77
                                      455554156678999*******************999876 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 5.8
                          ATPase_2  55 ialreesiskldefie..eeeekkklekalgiavpkaeleeilk 96 
                                        +  +++++++ +  e  +  +++k+++++g++++++ +  +++
  gi|242399377|ref|YP_002994801.1| 254 LNSGKIEEKRKFRVGEeiKAIVSSKIARKIGEKMGEDDIAVLIE 297
                                       44445444444444333333445556666666666666554444 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.8   5.1e-05     0.022       2      30 ..      51      79 ..      50     205 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.1e-05
                                      EEEEESTTSSHHHHHHHHHTSTEEESSST CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltgekaivsdkp 30
                                      ++i G p +GKStL+ +l++++   +++ 
  gi|242399377|ref|YP_002994801.1| 51 IGITGPPGSGKSTLVDKLIKKARDEGNIV 79
                                      89*****************9754444444 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   1.5e-05    0.0065      10      49 ..      42      81 ..      33      86 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.5e-05
                        Zeta_toxin 10 ypsqerPklillgGqpGAGKselaellkdelerqgnvvrl 49
                                      y +  r  +i + G pG+GKs+l ++l ++ + +gn+v +
  gi|242399377|ref|YP_002994801.1| 42 YSKTGRAYIIGITGPPGSGKSTLVDKLIKKARDEGNIVGV 81
                                      5566777888899***********************9976 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       3.5   1.5e+03      31      64 ..       6      39 ..       5      52 .. 0.56
   2 !   15.4   0.0   3.5e-05     0.015       4      24 ..      53      73 ..      50      85 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 3.5
                            AAA_33 31 dtlrrrlfgtdqqsktdytrvldrlyqilnelar 64
                                      d+l++r+f+ d++ + +++++ ++  +  +e+++
  gi|242399377|ref|YP_002994801.1|  6 DDLIERMFKGDKRATARLITLVENDEEKAREIVK 39
                                      7788888887777776666655543333333333 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 3.5e-05
                            AAA_33  4 lvGlpGsGKstlaerllkklg 24
                                      + G+pGsGKstl+++l+kk  
  gi|242399377|ref|YP_002994801.1| 53 ITGPPGSGKSTLVDKLIKKAR 73
                                      57**************99865 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.7e-05    0.0076      17      53 ..      47      83 ..      31      90 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.7e-05
                            AAA_30 17 gdrvavltGpAGtGKttalkalreaweaaggrviglA 53
                                      ++ +  +tGp+G+GK+t++ +l + ++++g  v ++A
  gi|242399377|ref|YP_002994801.1| 47 RAYIIGITGPPGSGKSTLVDKLIKKARDEGNIVGVIA 83
                                      3345568***************999999996555555 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   0.00035      0.15       7      41 ..      35      72 ..      28     115 .. 0.80
   2 ?    2.6   0.0      0.22        95      53     105 ..     225     280 ..     185     309 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00035
                            AAA_11  7 reaiksalsese...itliqGPPGtgKTktivellsql 41
                                      re +k+++s+++   i  i GPPG+gK++ + +l++++
  gi|242399377|ref|YP_002994801.1| 35 REIVKKIYSKTGrayIIGITGPPGSGKSTLVDKLIKKA 72
                                      5556777777777778899***************9987 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.22
                            AAA_11  53 akpriLvCapSNaAvDellerllr..glldsegekykpkivRvgnee.eriseavk 105
                                       ++p +   a +N+ vDel   + +  ++l ++g+ ++ +  Rvg e    +s+++ 
  gi|242399377|ref|YP_002994801.1| 225 RPPVVSTIAFTNKGVDELWGAINEhrEFLLNSGKIEEKRKFRVGEEIkAIVSSKIA 280
                                       55555666789**********9999999999*************998422333333 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.1   0.00011     0.049       1      19 [.      54      72 ..      54      80 .. 0.91
   2 ?    0.7   0.2       1.5   6.6e+02      39      74 ..     258     292 ..     250     309 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 0.00011
                                      EE-TTSSHHHHHHHHHHHH CS
                            AAA_17  1 lGgPGsGKgtqceklveky 19
                                      +G+PGsGK+t+++kl +k 
  gi|242399377|ref|YP_002994801.1| 54 TGPPGSGKSTLVDKLIKKA 72
                                      7**************9986 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1.5
                                       SHSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEE CS
                            AAA_17  39 lakardemrklpleekkelqkeaaekiaeeakkkgv 74 
                                        ++++ ++ ++ +e+k  +  ++a+ki e+ +++++
  gi|242399377|ref|YP_002994801.1| 258 KIEEKRKF-RVGEEIKAIVSSKIARKIGEKMGEDDI 292
                                       44566666.466789999999999999998766653 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 ?   13.9   0.0   4.7e-05     0.021     116     161 ..      36      79 ..      13      86 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.7e-05
                             T2SSE 116 ekiaevlrkavrerglilvsGgTgsGKttllyallkeinksderiv 161
                                       e ++++ +k   + ++i ++G+ gsGK+tl+  l+k+  ++  +iv
  gi|242399377|ref|YP_002994801.1|  36 EIVKKIYSKT-GRAYIIGITGPPGSGKSTLVDKLIKKARDE-GNIV 79 
                                       2333333333.4566777*****************999888.7777 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   6.6e-05     0.029       4      26 ..      52      74 ..      49      79 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.6e-05
                                      EEEC-TTTCHHHHHHHHHHHHCT CS
                             NACHT  4 ilqGeaGsGKTtLlqklalawae 26
                                       ++G++GsGK+tL+ kl+ ++++
  gi|242399377|ref|YP_002994801.1| 52 GITGPPGSGKSTLVDKLIKKARD 74
                                      589***************99876 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0     0.003       1.3      52      88 ..      47      83 ..      41      91 .. 0.88
   2 ?    4.1   0.1     0.062        27       8      47 ..     281     320 ..     273     321 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.003
                                      TTSEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEE CS
                              RecA 52 kGriieiyGpessGkttlalhaiaeaqkkggvaafid 88
                                      +  ii i Gp  sGk+tl  ++i +a+ +g+++  i 
  gi|242399377|ref|YP_002994801.1| 47 RAYIIGITGPPGSGKSTLVDKLIKKARDEGNIVGVIA 83
                                      5569**************************9998775 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.062
                                       HHHHHHH-TTSS--TTS--.-----EE--S-HHHHHHTSS CS
                              RecA   8 kqiekkfGkgsimklgdekeklkvetissGslaldialGi 47 
                                       ++i  k+G++ i  l +  +k +++ +s+  l l+ alG+
  gi|242399377|ref|YP_002994801.1| 281 RKIGEKMGEDDIAVLIEMIAKREIDPYSAADLVLEKALGV 320
                                       679999*********************************8 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   5.6e-05     0.024      18      56 ..      51      91 ..      38      94 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.6e-05
                     TrwB_AAD_bind 18 ilivGttGsGKtqalekllrairarg..draivlDltGafv 56
                                      i i+G  GsGK++ + kl++++r  g    +i +D+t  f+
  gi|242399377|ref|YP_002994801.1| 51 IGITGPPGSGKSTLVDKLIKKARDEGniVGVIAIDPTSPFT 91
                                      6799*********************9444678889888776 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0    0.0002     0.087      82     123 ..      26      72 ..       2      82 .. 0.63
   2 ?   -0.6   0.0       2.4   1.1e+03      46     100 ..     186     249 ..     179     257 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.0002
                                       --TTTHTTHHHHHHHCTT.....SEEEEECSTTSSHHHHHHHHCTT- CS
                       RsgA_GTPase  82 vsaktkegleelkellkd.....ktsvlvGqSGvGKStLinallpel 123
                                       + ++++e+++e+ +++ +      ++ + G+ G GKStL+++l+ ++
  gi|242399377|ref|YP_002994801.1|  26 LVENDEEKAREIVKKIYSktgraYIIGITGPPGSGKSTLVDKLIKKA 72 
                                       334444444444444433111034566899*************9875 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2.4
                                       T-EEEEEEE-GGG--HHH.........HHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTTS CS
                       RsgA_GTPase  46 giepvivlnKiDlleeee.........eleelkeelealgyevllvsaktkegleelkellkdk 100
                                       +i  + v+nK+D    e          +le+ k + + +  +v+ + a t++g++el  +++++
  gi|242399377|ref|YP_002994801.1| 186 EIADIFVVNKADKEGAEAtmfelelmlDLEKDKWQKSGWRPPVVSTIAFTNKGVDELWGAINEH 249
                                       5666788999998877776777777666666666777777777777777888888877666665 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   0.00019     0.083      10      50 ..      48      86 ..      35      91 .. 0.80
   2 ?   -1.7   0.0       7.6   3.3e+03      41      59 ..     225     243 ..     217     252 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00019
                            AAA_19 10 ekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaf 50
                                      + ++ +t++pG+GK++++ + ++ + ++g++    ++++ +
  gi|242399377|ref|YP_002994801.1| 48 AYIIGITGPPGSGKSTLVDKLIKKARDEGNI--VGVIAIDP 86
                                      556889*****************99999865..55555555 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 7.6
                            AAA_19  41 kpeeillvaftgrAakelr 59 
                                        p  +  +aft++ ++el 
  gi|242399377|ref|YP_002994801.1| 225 RPPVVSTIAFTNKGVDELW 243
                                       55667889*****999986 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   0.00013     0.058       3      24 ..      53      74 ..      51      91 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00013
                      RNA_helicase  3 lyGpsgeGKStlakeLakallk 24
                                      ++Gp+g GKStl+++L+k+  +
  gi|242399377|ref|YP_002994801.1| 53 ITGPPGSGKSTLVDKLIKKARD 74
                                      89***************98765 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   8.5e-05     0.037       4      34 ..      50      79 ..      47      91 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 8.5e-05
                            AAA_14  4 ilvitGaRrvGKTtllkqlikellvkkesil 34
                                      i+ itG+  +GK+tl+ +lik+   ++ +i+
  gi|242399377|ref|YP_002994801.1| 50 IIGITGPPGSGKSTLVDKLIKKAR-DEGNIV 79
                                      899*****************9988.666665 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   7.2e-05     0.031       4      57 ..      28      83 ..      25      87 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.2e-05
                                      HHHHHHHHHH......HCTS-..EEEEESTTSSCHHHHHHHHHHCHCTCCCEEEEE CS
                              PIF1  4 eeQkkvfdaiieavlnekgkl..fFvtGsgGtgKtflwkallkklrsegkivlavA 57
                                      e+ ++ +++i++ ++++ g+   + +tG  G+gK+ l  +l+kk r eg+iv ++A
  gi|242399377|ref|YP_002994801.1| 28 ENDEEKAREIVKKIYSKTGRAyiIGITGPPGSGKSTLVDKLIKKARDEGNIVGVIA 83
                                      566677789999999999885225689*************************9998 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 ?    9.9   0.0    0.0012      0.51       3      33 ..      51      81 ..      49      90 .. 0.91
   2 ?    1.5   0.0      0.43   1.9e+02     136     154 ..     226     244 ..     177     246 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0012
                                      EEEEESTTSSHHHHHHHHHTTSEEEEESTTS CS
                            FeoB_N  3 valvGnpnvGkttlfnaltgakqkvgNwpGv 33
                                      + + G p +Gk+tl+++l ++  + gN  Gv
  gi|242399377|ref|YP_002994801.1| 51 IGITGPPGSGKSTLVDKLIKKARDEGNIVGV 81
                                      6789***********************9998 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.43
                                       S-EEEEBTTTTBTHHHHHH CS
                            FeoB_N 136 vpvvktsakkkegieellk 154
                                        pvv+t+a +++g++el  
  gi|242399377|ref|YP_002994801.1| 226 PPVVSTIAFTNKGVDELWG 244
                                       5899*********999975 PP

>> RNA12  RNA12 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0    0.0001     0.045      16      45 ..      46      81 ..      31      88 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.0001
                             RNA12 16 vntFiv.vkGPrGSGkkeLvldrvlkdrkk......v 45
                                        ++i+ ++GP+GSGk+ Lv d+ +k+ ++      v
  gi|242399377|ref|YP_002994801.1| 46 GRAYIIgITGPPGSGKSTLV-DKLIKKARDegnivgV 81
                                      45566559************.9999987765555444 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00015     0.067       4      36 ..      51      83 ..      49      90 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00015
                                      EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE- CS
                             KTI12  4 vvltGlPssGKstrakeLakaleeekrsvvvid 36
                                      + +tG P sGKst++++L k+ ++e+  v vi 
  gi|242399377|ref|YP_002994801.1| 51 IGITGPPGSGKSTLVDKLIKKARDEGNIVGVIA 83
                                      559*******************99998887775 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   0.00013     0.059      27      63 ..      52      89 ..      50     138 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00013
                             DUF87 27 AilgsTGsGKSntvavLleelle.kkgatililDpHGE 63
                                      +i g  GsGKS++v  L++++    + + ++ +Dp + 
  gi|242399377|ref|YP_002994801.1| 52 GITGPPGSGKSTLVDKLIKKARDeGNIVGVIAIDPTSP 89
                                      788888****************9555559*****9865 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00042      0.18       3      23 ..      53      73 ..      51     120 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00042
                                      EESSTTSSHHHHHHHHHHHHT CS
                               AAA  3 lyGppGtGKTllakavakelg 23
                                      ++GppG GK++l+  ++k++ 
  gi|242399377|ref|YP_002994801.1| 53 ITGPPGSGKSTLVDKLIKKAR 73
                                      68**************99984 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   0.00036      0.16       2      22 ..      48      68 ..      47      85 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00036
                            AAA_24  2 klkiliyGpsgiGKTtlakel 22
                                      ++ i i+Gp+g+GK+tl+ +l
  gi|242399377|ref|YP_002994801.1| 48 AYIIGITGPPGSGKSTLVDKL 68
                                      67899************9998 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00039      0.17       2      20 ..      51      69 ..      50      82 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00039
                            AAA_28  2 ivitGgestGKTtlleaLa 20
                                      i itG++++GK+tl+ +L 
  gi|242399377|ref|YP_002994801.1| 51 IGITGPPGSGKSTLVDKLI 69
                                      569************9996 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00057      0.25       4      30 ..      53      79 ..      51     138 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00057
                                      EE--SSSSHHHHHHHGGGGBS--EEEE CS
                             AAA_5  4 LvGppGtgKselaerlaaalnreveyv 30
                                      + GppG+gKs+l+++l +  ++e ++v
  gi|242399377|ref|YP_002994801.1| 53 ITGPPGSGKSTLVDKLIKKARDEGNIV 79
                                      58*************998886655554 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   0.00039      0.17      46      68 ..      49      71 ..      31      79 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00039
                             Rad17 46 riLLisGPsGCgkstvvkvLske 68
                                       i+ i+GP+G gkst v  L k+
  gi|242399377|ref|YP_002994801.1| 49 YIIGITGPPGSGKSTLVDKLIKK 71
                                      3899*************999886 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1    0.0005      0.22       3      21 ..      53      71 ..      51      87 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0005
                   Viral_helicase1  3 vhGvpGcGKStlirkllrt 21
                                      + G pG+GKStl+ kl+++
  gi|242399377|ref|YP_002994801.1| 53 ITGPPGSGKSTLVDKLIKK 71
                                      7899*************98 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   0.00095      0.42      21      37 ..      50      66 ..      47      69 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00095
                            AAA_23 21 ltlItGpNGaGKTTild 37
                                      +  ItGp G+GK+T++d
  gi|242399377|ref|YP_002994801.1| 50 IIGITGPPGSGKSTLVD 66
                                      678************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       830  (0.0462937); expected 358.6 (0.02)
Passed bias filter:                      687  (0.0383178); expected 358.6 (0.02)
Passed Vit filter:                       125  (0.00697194); 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: 0.70u 0.34s 00:00:01.04 Elapsed: 00:00:00.51
# Mc/sec: 1882.39
//
Query:       gi|242399378|ref|YP_002994802.1|  [L=144]
Description: Methylmalonyl-CoA mutase, C-terminus of large subunit, partial [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.5e-24   84.1   0.3    8.8e-24   83.9   0.3    1.1  1  B12-binding    B12 binding domain
  ------ inclusion threshold ------
      0.027   14.2   0.2       0.23   11.1   0.0    2.1  2  MoCF_biosynth  Probable molybdopterin binding domain
      0.082   13.3   0.2         17    5.8   0.0    2.8  3  Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor
       0.12   12.6   0.0       0.22   11.7   0.0    1.4  1  DUF1611_N      Domain of unknown function (DUF1611_N) Rossman
       0.16   11.0   0.0       0.19   10.7   0.0    1.1  1  IMPDH          IMP dehydrogenase / GMP reductase domain


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 !   83.9   0.3   2.5e-27   8.8e-24       2     114 ..       8     121 ..       7     127 .. 0.91

  Alignments for each domain:
  == domain 1  score: 83.9 bits;  conditional E-value: 2.5e-27
                       B12-binding   2 kvllatvggdlhplGlavlaaalrdagfeVqllganvenedivaairaekpdvvglSalltsqleavkelvel.... 74 
                                       +vl+a+ g d h++G++v+a+alrdagfeV+++g+ +++e+i++++ +e+ dv+glS+l+++++  + ++++l    
  gi|242399378|ref|YP_002994802.1|   8 RVLIAKPGLDGHDRGAKVIARALRDAGFEVIYTGIRQTPEQIAESVVQEDIDVLGLSILSGAHMVLIPKILKLleek 84 
                                       799**********************************************************************9956 PP

                       B12-binding  75 .lkrirprvkvvvGGahpsldpeetleaklgiddvvvgege 114
                                        + +++++v v++GG++p  d++e le+ +g +  v+g g 
  gi|242399378|ref|YP_002994802.1|  85 gI-KANEDVLVLAGGIIPPDDAQE-LEK-MG-VGRVFGPGS 121
                                       33.34579****************.665.**.999***996 PP

>> MoCF_biosynth  Probable molybdopterin binding domain
   #    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      15      53 ..      19      56 ..      14      70 .. 0.83
   2 ?    0.8   0.0     0.098   3.5e+02      51      66 ..      86      99 ..      69     107 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 6.5e-05
                                      GBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHH CS
                     MoCF_biosynth 15 eDtngpllaellkelgvevskytvvpDdeeeikeallaa 53
                                       D+ ++++a++l+++g+ev+ yt ++  +e+i+e++ ++
  gi|242399378|ref|YP_002994802.1| 19 HDRGAKVIARALRDAGFEVI-YTGIRQTPEQIAESVVQE 56
                                      69999***************.8889**********9544 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.098
                                      HHHHHTSSEEEEESS- CS
                     MoCF_biosynth 51 laaleeadviittGGt 66
                                      ++a +e dv+++ GG+
  gi|242399378|ref|YP_002994802.1| 86 IKA-NE-DVLVLAGGI 99
                                      333.44.9******98 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 ?    4.1   0.1     0.016        58      41      82 ..      21      42 ..       2      60 .. 0.59
   2 ?    0.6   0.0       0.2   7.3e+02      41      58 ..      44      61 ..      40      68 .. 0.88
   3 ?    5.8   0.0    0.0047        17      51      90 ..      87     127 ..      75     131 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.016
                                      CSSTHHHHHHHHTT-SEEEESSSCHHHHHHHCTTTSEEEES.- CS
                     Nitro_FeMo-Co 41 ggggklaqllaeegvdvvivgkiGpralakleaagievykg.a 82
                                      +g + +a+ l ++g +v++                     +  
  gi|242399378|ref|YP_002994802.1| 21 RGAKVIARALRDAGFEVIY---------------------TgI 42
                                      5555555555555555555.....................444 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.2
                                      CSSTHHHHHHHHTT-SEE CS
                     Nitro_FeMo-Co 41 ggggklaqllaeegvdvv 58
                                      + ++++a+++ +e++dv+
  gi|242399378|ref|YP_002994802.1| 44 QTPEQIAESVVQEDIDVL 61
                                      578999*********997 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.0047
                                       HH.TT-SEEEESSSCHHHHHHHCTTTSEEEES-SSBHHHHH CS
                     Nitro_FeMo-Co  51 ae.egvdvvivgkiGpralakleaagievykgaggtveeal 90 
                                       ++ e+v v+  g i p  +++le+ g+  + g+g ++ee++
  gi|242399378|ref|YP_002994802.1|  87 KAnEDVLVLAGGIIPPDDAQELEKMGVGRVFGPGSPIEEII 127
                                       44489999999999*****************9******997 PP

>> DUF1611_N  Domain of unknown function (DUF1611_N) Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   6.3e-05      0.22      22      87 ..      28      87 ..      12      90 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.3e-05
                         DUF1611_N 22 sleealaagaevlviGiapeggklpeswreavkeAle.aGldvvsGlHerLsddpelaalakkkgvk 87
                                            +ag ev++ Gi    +++     ++v+e ++ +Gl++ sG+H  L   p++ +l+++kg+k
  gi|242399378|ref|YP_002994802.1| 28 RAL--RDAGFEVIYTGIRQTPEQI---AESVVQEDIDvLGLSILSGAHMVLI--PKILKLLEEKGIK 87
                                      332..5689999999999999999...556777788648**********998..9999999888875 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   5.3e-05      0.19     100     178 ..      41     121 ..      21     123 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 5.3e-05
                                       -SSTTHHHHHHHHHHTT-SEEEEE-STSSSHHHHHHHHHHHHHTT.....TSEEEEEEE-SHHHHHHHHHTT-SEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 100 gvkedalervkalveagvdvlvvdsahghsekvleavkeikkkve.....eveviaGnvataegakaLieagadavk 171
                                       g+++  ++ ++ +v++++dvl + +  g     + ++ ++ ++       +v v+aG +   + a++L ++g+  v 
  gi|242399378|ref|YP_002994802.1|  41 GIRQTPEQIAESVVQEDIDVLGLSILSGAHMVLIPKILKLLEEKGikaneDVLVLAGGIIPPDDAQELEKMGVGRV- 116
                                       667777888999************99998887776665543332212222699*******************9877. PP

                                       E-SS-ST CS
                                       xxxxxxx RF
                             IMPDH 172 vGiGpGs 178
                                          GpGs
  gi|242399378|ref|YP_002994802.1| 117 --FGPGS 121
                                       ..56665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1071.75
//
Query:       gi|242399379|ref|YP_002994803.1|  [L=215]
Description: phosphotransferase, php family [Thermococcus sibiricus MM 739]
Scores for complete 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-11   43.5   0.2    1.1e-10   42.1   0.1    1.8  2  PHP       PHP domain
     0.0002   21.0   0.0    0.00072   19.3   0.0    1.9  2  PHP_C     PHP-associated
  ------ inclusion threshold ------
      0.056   12.9   0.0       0.91    8.9   0.0    2.3  2  PGA_cap   Bacterial capsule synthesis protein PGA_cap


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 !   42.1   0.1   1.9e-14   1.1e-10       1     166 [.       2     157 ..       2     158 .. 0.76
   2 ?   -3.2   0.0       1.5   9.1e+03      45      65 ..     165     182 ..     164     187 .. 0.72

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 1.9e-14
                                       EEEE--CCC.--.S-H..HHHHHHHHHCT-SEEEEEEEEBTT......HHHHHHHHHHHHTTTTSEEEEEEE..... CS
                                       xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               PHP   1 dlHvHteys.lldgalsieelvkkakelglkaiaiTDhgnlf......gyvefykaakkkykagikpiiGleayvad 70 
                                       dlH+Ht +s +  g +   + +++a+++gl  ++i+Dh ++f      +y+  +++akk  +++  ++ G+ea++ +
  gi|242399379|ref|YP_002994803.1|   2 DLHTHTRFSdGI-GDI--RDNIAEAERKGLRIVGISDHIHFFtphvlnSYLSLINQAKK--DSETIVLAGMEANILP 73 
                                       89*******666.788..***************************************64..45799*********** PP

                                       .............E....EHHHHHHHHHHHHH..........HHHHHH............S................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............xxxxxxxxxxxxxxxxx RF
                               PHP  71 dsekerpshltllaknqeGyknllkllskaylegfyrkpridkellek............hsegLivlsgclkGevf 135
                                       ++           +   +++++ l+ ++++   +f+   + +  +l k            h            G+vf
  gi|242399379|ref|YP_002994803.1|  74 EG-----------VDITDDLRKRLDYVIASVHMYFNPGSHHKYLELVKtaiqdenvdiigH-----------FGNVF 128
                                       *9...........655566777766666666655522222222222223555556665555...........79999 PP

                                       ..TTGGHHHHHHHHHHHHHHHC.T-EEEEEG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               PHP 136 ealdlieveekaeealeelakifgdyiEint 166
                                        ++ + ++++  +e+++  +++ g+++Ei t
  gi|242399379|ref|YP_002994803.1| 129 SYIGHPSIKD-YKEIIDLAEEY-GKGFEIST 157
                                       9998889999.99999999997.99999976 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.5
                                       HHHHHHHHHTTTTSEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                               PHP  45 efykaakkkykagikpiiGle 65 
                                       +f+k +    k g+k+++G +
  gi|242399379|ref|YP_002994803.1| 165 DFIKFC---IKRGVKLVFGSD 182
                                       566666...567799999987 PP

>> PHP_C  PHP-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       1.4   8.1e+03      11      23 ..      23      35 ..      20      35 .. 0.82
   2 !   19.3   0.0   1.2e-07   0.00072       9      32 ..     168     191 ..     167     197 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.4
                             PHP_C 11 AeklglpgtgGSD 23
                                      Ae+ gl  +g SD
  gi|242399379|ref|YP_002994803.1| 23 AERKGLRIVGISD 35
                                      8999999998777 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 1.2e-07
                             PHP_C   9 rfAeklglpgtgGSDAHrleeVGr 32 
                                       +f +k+g+  + GSDAH++++VG+
  gi|242399379|ref|YP_002994803.1| 168 KFCIKRGVKLVFGSDAHQPKDVGN 191
                                       7899*******************8 PP

>> PGA_cap  Bacterial capsule synthesis protein PGA_cap
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0     0.029   1.7e+02     186     201 ..      81      96 ..      43     127 .. 0.76
   2 ?    8.9   0.0   0.00015      0.91     214     239 ..     165     190 ..     152     211 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.029
                           PGA_cap 186 earkeadlvivslHwg 201
                                        +rk+ d+vi+s+H+ 
  gi|242399379|ref|YP_002994803.1|  81 DLRKRLDYVIASVHMY 96 
                                       4677899*******94 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00015
                           PGA_cap 214 elaralidaGadvviGhhpHvlqgie 239
                                       ++ + +i+ G+++v+G+ +H ++++ 
  gi|242399379|ref|YP_002994803.1| 165 DFIKFCIKRGVKLVFGSDAHQPKDVG 190
                                       7899*****************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1400.22
//
Query:       gi|242399380|ref|YP_002994804.1|  [L=185]
Description: Maf-like protein [Thermococcus sibiricus MM 739]
Scores for complete 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-55  185.6   0.0    6.9e-55  185.4   0.0    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 !  185.4   0.0   3.8e-59   6.9e-55       1     161 [.       2     176 ..       2     179 .. 0.93

  Alignments for each domain:
  == domain 1  score: 185.4 bits;  conditional E-value: 3.8e-59
                                       EEEEE---HHHHHHHHCT-..EEEE------......HHHHHHHHHHHHHHHHH....TCEEEEEEEEEE...CE-- CS
                               Maf   1 kliLASaSprRkelLeqlg..fevvpsdvde......aeelvlrlAeaKaeava....alvigaDtvvvl...ilgK 62 
                                       kliLAS+SprR+e+L ++   f+v+ps+++e      + + v ++A++Ka +v+     +vigaDtvv+l   ilgK
  gi|242399380|ref|YP_002994804.1|   2 KLILASQSPRRREILGRFFrdFDVIPSQISEesnfqdSIAHVIEVARKKAWDVYkehdGTVIGADTVVTLdgkILGK 78 
                                       69***************65599********99***9944579**************9967*********97766*** PP

                                       -SSHHHHHHHHHHHTTSEEEEEEEEEEEEEEE..EEEEEEEEEE----HHHHHHHHHCTSGCCSTTS--TTCGGGGG CS
                               Maf  63 PkdeeealemLkklsgrthevvTgvavlkekevksfvettevtfkelsdeeieaYvatgepldkAGaygiqgllgla 139
                                       Pk+ eea +mL  lsg+ hev+Tg ++++e++++  +e t+v+f+el+++eie+Yv+tge ldkAGaygiqg+ g++
  gi|242399380|ref|YP_002994804.1|  79 PKTPEEAKQMLGLLSGKVHEVITGYCIIHEGKEILGHEVTKVKFRELDKDEIEWYVSTGESLDKAGAYGIQGK-GGV 154
                                       *****************************7778888************************************9.666 PP

                                       CEEEECS-HHHHHT--HHHHHH CS
                               Maf 140 lverieGsysnVvGLPlaelle 161
                                       lve i+G+y+nV+G+P++ ++e
  gi|242399380|ref|YP_002994804.1| 155 LVEWIKGDYYNVIGFPMKIIVE 176
                                       ****************987766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); 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 0.29s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1150.59
//
Query:       gi|242399381|ref|YP_002994805.1|  [L=605]
Description: ATPase, AAA superfamily, containing PIN and KH nucleic acid- binding domains [Thermococcus sibiricus MM 739]
Scores for complete 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   32.2   0.1    1.2e-07   31.0   0.1    1.5  1  T2SSE            Type II/IV secretion system protein
    2.1e-07   31.4   0.2    6.8e-07   29.8   0.2    1.9  1  PIN              PIN domain
    7.3e-05   23.1   4.7      0.002   18.4   0.2    3.2  2  PIN_9            PIN like domain
    9.2e-05   22.2   0.8    0.00027   20.7   0.8    1.8  1  KH_1             KH domain
    0.00028   21.2   0.1    0.00065   20.0   0.1    1.6  1  PIN_4            PIN domain
    0.00038   20.1   0.1     0.0021   17.7   0.0    2.1  2  AAA_25           AAA domain
    0.00045   19.6   0.0      0.016   14.6   0.0    2.4  2  DnaB_C           DnaB-like helicase C terminal domain
     0.0021   17.8   0.0     0.0041   16.9   0.0    1.4  1  IstB_IS21        IstB-like ATP binding protein
     0.0022   18.5   0.1      0.011   16.2   0.0    2.3  1  AAA_18           AAA domain
     0.0027   17.5   1.3     0.0027   17.5   1.3    3.4  2  KH_2             KH domain
     0.0076   15.9   0.2      0.039   13.6   0.2    2.3  2  Thymidylate_kin  Thymidylate kinase
     0.0092   16.0   1.7       0.03   14.4   0.2    2.7  1  KH_5             NusA-like KH domain
  ------ inclusion threshold ------
      0.013   15.6   0.4      0.077   13.0   0.0    2.5  3  AAA_14           AAA domain
      0.015   15.6   0.2      0.055   13.7   0.0    2.1  1  AAA_28           AAA domain
      0.016   15.6   0.0      0.063   13.6   0.0    2.0  2  AAA_16           AAA ATPase domain
      0.026   14.5   0.0       0.11   12.5   0.0    2.1  2  AAA_5            AAA domain (dynein-related subfamily)
      0.027   14.4   0.1      0.058   13.3   0.1    1.5  1  NACHT            NACHT domain
      0.047   13.6   0.1       0.22   11.4   0.0    2.2  1  NTPase_1         NTPase
      0.048   14.0   0.0       0.13   12.7   0.0    1.8  1  RNA_helicase     RNA helicase
      0.049   13.3   0.4        0.1   12.3   0.1    1.7  1  AAA_30           AAA domain
      0.053   14.0   0.1       0.18   12.2   0.1    2.0  1  AAA              ATPase family associated with various cellul
      0.055   13.2   0.1       0.28   10.9   0.1    2.2  2  ATP_bind_1       Conserved hypothetical ATP binding protein
      0.059   12.6   0.0       0.15   11.4   0.0    1.6  1  Zeta_toxin       Zeta toxin
      0.066   13.4   0.0       0.62   10.2   0.0    2.3  2  AAA_33           AAA domain
      0.075   13.3   0.4       0.17   12.2   0.4    1.6  1  Hydin_ADK        Hydin Adenylate kinase-like domain
      0.083   12.3   0.0        0.2   11.1   0.0    1.6  1  KTI12            Chromatin associated protein KTI12
        0.1   13.1   0.0        0.4   11.2   0.0    2.0  1  ABC_tran         ABC transporter
       0.18   12.1   0.1        2.6    8.3   0.0    2.5  2  AAA_22           AAA domain
       0.19   11.7   1.0       0.63   10.0   0.0    2.3  2  ResIII           Type III restriction enzyme, res subunit


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 !   31.0   0.1     2e-10   1.2e-07      76     244 ..     216     373 ..     185     396 .. 0.77

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 2e-10
                             T2SSE  76 kgvrlrvvllPvvag.ealviRkksakeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallk 151
                                       +++r+ ++ +P +   e  ++R     +l+++d+   e+l e   ++  k       i+++G+ g GKtt++ al +
  gi|242399381|ref|YP_002994805.1| 216 RNYRIVIAKPPFADRiEITAVR--PITKLSIEDYDLPEKLLE---RLTDK----AEGIIIAGAPGEGKTTFAQALAE 283
                                       5778888888888887778888..445667777776655433...33334....58899****************** PP

                             T2SSE 152 einksderivtvEDpvEiqlega..nqvqlnakkakvtfadllraaLRlrPDrimvGEiRdketlei.lkAvnTGHl 225
                                       + +++ + + t+E p+ +q++++  ++++l        +++    +L  rPD  +  E+R +  ++i       G  
  gi|242399381|ref|YP_002994805.1| 284 YYASTGKIVKTMEKPRDLQVSEEitQYTALGG-----RMEKTGDVLLLVRPDYTIFDEMRKTSDFKIyADLRLAG-V 354
                                       ***9988888**********654113333333.....4555556678899*****************54444555.5 PP

                             T2SSE 226 gslsTlHansaagalerLe 244
                                       g ++ +Ha ++++a++r  
  gi|242399381|ref|YP_002994805.1| 355 GMVGVVHATKPIDAVQRFI 373
                                       5599************974 PP

>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.2   1.1e-09   6.8e-07       2     120 ..       8     120 ..       7     122 .. 0.90

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 1.1e-09
                                       EE-HHHHHHHHTTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHS.SCHCHHHHHHHHHHHHHHHTSEEEEBCHHH CS
                               PIN   2 vlDTsvliallrgeekaeaarklleeleelvtsalvlaEllyvlar.rkskrekaaelvelllllsalkilpidaei 77 
                                       v+DTsv++   +g+  + ++++ ++e  ++v++++v+aE+ + ++  +  ++  ++el++l+ l+++ +il    + 
  gi|242399381|ref|YP_002994805.1|   8 VVDTSVIV---DGRL-T-QYLDGINEKVKVVIPEAVVAEIEHQANEgKAIGHTGLEELKKLRNLAENERILLEFYGE 79 
                                       89******...3333.3.355556666*******************9999**********************9**** PP

                                       HHHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHHHHH CS
                               PIN  78 aeeaaeialkygllpnDaliaAtAkehgikliatfDedfrrva 120
                                       +   ++i++ +  + +D +i  +A+e +++li t D   r+va
  gi|242399381|ref|YP_002994805.1|  80 RPDLWQIRRAK-SGEIDHIIREVARELNATLI-TGDQVQRDVA 120
                                       *********99.********************.***9999887 PP

>> PIN_9  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.1     0.035        21      22      49 ..      23      50 ..       7      56 .. 0.80
   2 !   18.4   0.2   3.3e-06     0.002      38     114 ..      57     131 ..      52     133 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.035
                             PIN_9 22 lerllgsvelvvpkavleELerlakagk 49
                                      l+ + ++v++v+p+av++E+e+ a++gk
  gi|242399381|ref|YP_002994805.1| 23 LDGINEKVKVVIPEAVVAEIEHQANEGK 50
                                      566667899************9876665 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 3.3e-06
                             PIN_9  38 leELerlakagkgkertaakvalsLaerceiveaeeekaDdailelakeldaavlvTnDreLkkrllekgipvilLR 114
                                       leEL++l ++ +++er   +   +  +  +i +a++++ D +i e+a+el+a+ + T D+  ++ ++ kg++vi+L 
  gi|242399381|ref|YP_002994805.1|  57 LEELKKL-RNLAENERILLEFYGERPDLWQIRRAKSGEIDHIIREVARELNATLI-TGDQVQRDVAIAKGVEVIYLE 131
                                       799***9.99999999999999999999***********************8888.*******************96 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.8   4.4e-07   0.00027      11      39 ..     496     525 ..     484     547 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 4.4e-07
                                       HHHHHTGGGHHHHHHHHHHT-EEEEES.ST CS
                              KH_1  11 vgriIGkgGsnIkeIreetgakIkvpk.se 39 
                                       ++ iIGk+G++I eI+++ g +I+v + +e
  gi|242399381|ref|YP_002994805.1| 496 IPTIIGKKGKRITEIEKKLGISIDVRSfDE 525
                                       789**************77*****984333 PP

>> PIN_4  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.1   1.1e-06   0.00065       1     124 [.       7     124 ..       7     130 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.1e-06
                             PIN_4   1 fVlDTnvlLhd..pealksfkeehdvviPitVleELdklKkgsserelarlarqanrlldellekesgrlkvqtsae 75 
                                       fV+DT+v+ +    + l+ ++e+ +vviP  V+ E++++ ++ +   +++   + ++ l++l e+e   l +  ++ 
  gi|242399381|ref|YP_002994805.1|   7 FVVDTSVIVDGrlTQYLDGINEKVKVVIPEAVVAEIEHQANEGK--AIGHTGLEELKKLRNLAENERILLEFYGERP 81 
                                       8*******986224567777*****************9999998..9999999999999999999888888888877 PP

                             PIN_4  76 elpee.eseseknDnrIlavalelkeekpdrkvvLvskDinlrikAkalg 124
                                       +l +   ++s + D+ I +va el+ +       L++ D+  r  A a+g
  gi|242399381|ref|YP_002994805.1|  82 DLWQIrRAKSGEIDHIIREVARELNAT-------LITGDQVQRDVAIAKG 124
                                       777654444778999999999888764.......4555555555555555 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       1.2   7.6e+02      75     139 ..     128     193 ..     100     198 .. 0.66
   2 !   17.7   0.0   3.3e-06    0.0021      22      73 ..     250     299 ..     241     395 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.2
                            AAA_25  75 lyvsaEdsedelrrRlravgeal....rddarllvldlagv.eslpLfakdrggtlltadvdaleaaiee 139
                                       +y  +E +  e++ Rl+  + ++     ++++   l  +g+ ++ +L+ ++r+++l+++++++++++i e
  gi|242399381|ref|YP_002994805.1| 128 IY--LEAKK-EIKHRLEDFFDEYtmsvHLKGGIMPLAKKGKpGQWRLV-PIRDEALVDEELEKIADDIVE 193
                                       33..44555.88888888888886666555555555556666666765.588888899999999888876 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 3.3e-06
                            AAA_25  22 rrwlvkgllpagelallaGapgtGKttlaldlalava.tGkpwlgpvapeqgk 73 
                                       +++l+++l  + e +++aGapg GKtt+a  la  +a tGk   + +  e+ +
  gi|242399381|ref|YP_002994805.1| 250 PEKLLERLTDKAEGIIIAGAPGEGKTTFAQALAEYYAsTGK-IVKTM--EKPR 299
                                       57899999999**********************99998887.33322..5555 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 ?    2.3   0.0      0.14        88     152     182 ..      89     119 ..      79     124 .. 0.85
   2 !   14.6   0.0   2.5e-05     0.016      19      58 ..     261     297 ..     251     348 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.14
                                       HHHHHHHHHHHHHHHHCTSXEEEEEEXSGGG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C 152 qevseisrsLkalakelnvpvialsqLsrav 182
                                        +  ei + ++++a+eln  +i+  q++r+v
  gi|242399381|ref|YP_002994805.1|  89 AKSGEIDHIIREVARELNATLITGDQVQRDV 119
                                       556788888999****************987 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 2.5e-05
                                       TXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C  19 gdliiiAarpsmGktalalniaenaavkeklpvavfslem 58 
                                       ++ iiiA+ p+ Gkt++a  +ae  a + k   +v  +e 
  gi|242399381|ref|YP_002994805.1| 261 AEGIIIAGAPGEGKTTFAQALAEYYASTGK---IVKTMEK 297
                                       5669*******************9997444...4455555 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 !   16.9   0.0   6.7e-06    0.0041      44      85 ..     258     299 ..     245     348 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 6.7e-06
                         IstB_IS21  44 iekkenivllGpsGvGKshlaialgveavraglsvlfvrved 85 
                                       ++k+e+i++ G +G GK+ +a al+   + +g+ v  +  ++
  gi|242399381|ref|YP_002994805.1| 258 TDKAEGIIIAGAPGEGKTTFAQALAEYYASTGKIVKTMEKPR 299
                                       7899*********************99999998886655543 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.8e-05     0.011       1      35 [.     264     299 ..     264     326 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.8e-05
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf.gvnlrdvaken 35 
                                       I+++G+pG GKtt+a++L++  ++ g +++ + k +
  gi|242399381|ref|YP_002994805.1| 264 IIIAGAPGEGKTTFAQALAEYYAStGKIVKTMEKPR 299
                                       9*****************987433555555555444 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.2      0.18   1.1e+02      15      57 ..      29      70 ..      19      75 .. 0.79
   2 !   17.5   1.3   4.4e-06    0.0027       7      59 ..     465     519 ..     461     545 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.18
                                      EEEEEEECCSCEEEEEEEESCHHHHHTGGG.HHHHHHHHHHHHH CS
                              KH_2 15 vskveIertanrviiviresqpgivIGkgG.snikkigkelrkd 57
                                      + kv+I  ++  v  +++ ++ g +IG+ G +++kk++  ++++
  gi|242399381|ref|YP_002994805.1| 29 KVKVVI--PEAVVAEIEHQANEGKAIGHTGlEELKKLRNLAENE 70
                                      556666..4456667899***********978899999999875 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 4.4e-06
                                       HHHT.ECET..EEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHH CS
                              KH_2   7 avei.kkag..vskveIertanrviiviresqpgivIGkgGsnikkigkelrkdie 59 
                                       ++ei k+    +++ve+  +++++ii   e     +IGk+G++i +i+k+l+  i+
  gi|242399381|ref|YP_002994805.1| 465 KQEIkKFLPdvYAEVEL-ASPHKAIIYADEFDIPTIIGKKGKRITEIEKKLGISID 519
                                       55664444455667777.35799999*************************98774 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.2   6.3e-05     0.039       3      50 ..     268     315 ..     266     330 .. 0.81
   2 ?   -1.3   0.0       2.3   1.4e+03     113     127 ..     322     338 ..     313     344 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.3e-05
                                       ESTTSSHHHHHHHHHHHHHHTTE.EEEESSSTTSHHHHHHHHHHHTCS CS
                   Thymidylate_kin   3 GlDGaGKttqaellkerlkeegikvvltrepggteiGekirelllkee 50 
                                       G  G GKtt+a++l+e++ + g+ v +   p++ ++ e i ++     
  gi|242399381|ref|YP_002994805.1| 268 GAPGEGKTTFAQALAEYYASTGKIVKTMEKPRDLQVSEEITQYTALGG 315
                                       77799*****************65777777999*****9999976444 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.3
                                       GTTS..E-SEEEEEESS CS
                   Thymidylate_kin 113 dvll..kPdltflldvd 127
                                       dvll  +Pd+t++ ++ 
  gi|242399381|ref|YP_002994805.1| 322 DVLLlvRPDYTIFDEMR 338
                                       566668*******9865 PP

>> KH_5  NusA-like KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.2   4.9e-05      0.03      19      53 ..     496     529 ..     486     537 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.9e-05
                              KH_5  19 vGaivgkkGsrikavsseLkgekidvvewseDlae 53 
                                       + +i+gkkG+ri +++++L g  idv  ++e +ae
  gi|242399381|ref|YP_002994805.1| 496 IPTIIGKKGKRITEIEKKL-GISIDVRSFDEKMAE 529
                                       569****************.*****9999988877 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       4.6   2.8e+03      53      75 ..     126     149 ..      64     169 .. 0.56
   2 ?   13.0   0.0   0.00012     0.077       5      80 ..     264     344 ..     260     349 .. 0.74
   3 ?   -1.9   0.0       5.2   3.2e+03      85      85 ..     506     506 ..     450     590 .. 0.61

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 4.6
                            AAA_14  53 lelileklke.ekktylflDEiqe 75 
                                       + ++le  ke +++   f+DE  +
  gi|242399381|ref|YP_002994805.1| 126 EVIYLEAKKEiKHRLEDFFDEYTM 149
                                       333333211112222234454444 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00012
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklke.......ekktylflDEiq 74 
                                       ++i Ga   GKTt+++ l++ +   +   +  +++++rd + +++ + ++++  ++++        +  y ++DE+ 
  gi|242399381|ref|YP_002994805.1| 264 IIIAGAPGEGKTTFAQALAEYYA--STGKIVKTMEKPRDLQVSEEITQYTALGGRMEKtgdvlllVRPDYTIFDEMR 338
                                       7999**********999985555..66777778999999877755333333333332246788888899*******9 PP

                            AAA_14  75 evpewe 80 
                                       + ++++
  gi|242399381|ref|YP_002994805.1| 339 KTSDFK 344
                                       998875 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 5.2
                            AAA_14  85 s 85 
                                       +
  gi|242399381|ref|YP_002994805.1| 506 R 506
                                       1 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   8.9e-05     0.055       2      22 ..     264     284 ..     263     306 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8.9e-05
                            AAA_28   2 ivitGgestGKTtlleaLaar 22 
                                       i+i G+++ GKTt ++aLa+ 
  gi|242399381|ref|YP_002994805.1| 264 IIIAGAPGEGKTTFAQALAEY 284
                                       89*****************86 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0    0.0001     0.063      15      63 ..     253     301 ..     247     376 .. 0.81
   2 ?   -2.5   0.0       9.2   5.7e+03     116     131 ..     453     477 ..     407     495 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.0001
                            AAA_16  15 alervrsgrpelvllsGesGvGKsslvrellralekdggif.lrgkcdql 63 
                                       +ler+ +   e +++ G++G GK++ +++l++++  +g i+ + +k ++l
  gi|242399381|ref|YP_002994805.1| 253 LLERLTDKA-EGIIIAGAPGEGKTTFAQALAEYYASTGKIVkTMEKPRDL 301
                                       677777666.8999*****************9988886555466666665 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 9.2
                            AAA_16 116 a........srllellkrll.alls 131
                                       +        +rl +++k++l + ++
  gi|242399381|ref|YP_002994805.1| 453 KppamklaeKRLKQEIKKFLpDVYA 477
                                       2333336668888888888875544 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 ?   -2.7   0.0         9   5.5e+03      66      83 ..     176     193 ..     147     195 .. 0.79
   2 ?   12.5   0.0   0.00017      0.11       2      45 ..     264     310 ..     263     343 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 9
                                       -SEEEEESGGG--HHHHH CS
                             AAA_5  66 geilvlDEveraesevln 83 
                                        e lv++E+e++ +++++
  gi|242399381|ref|YP_002994805.1| 176 DEALVDEELEKIADDIVE 193
                                       567899999999999876 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00017
                                       EEEE--SSSSHHHHHHHGGGGB...S--EEEEE--TT--HHHHH--B CS
                             AAA_5   2 vlLvGppGtgKselaerlaaal...nreveyvqltrdtteedlkgrr 45 
                                       +++ G+pG gK+++a+ la+ +   ++ v ++  +rd++ ++ + ++
  gi|242399381|ref|YP_002994805.1| 264 IIIAGAPGEGKTTFAQALAEYYastGKIVKTMEKPRDLQVSEEITQY 310
                                       7999*****************98888888888888888755433333 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   9.3e-05     0.058       3      25 ..     264     286 ..     262     294 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.3e-05
                                       EEEEC-TTTCHHHHHHHHHHHHC CS
                             NACHT   3 vilqGeaGsGKTtLlqklalawa 25 
                                       +i+ G++G GKTt++q la+  a
  gi|242399381|ref|YP_002994805.1| 264 IIIAGAPGEGKTTFAQALAEYYA 286
                                       79****************98766 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00035      0.22       2      31 ..     264     293 ..     263     302 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00035
                                       EEEE--TTSSHHHHHHHHHHHH...GGGEE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvg 31 
                                       ++i G pG GKtT+ + ++e  +s g  v+
  gi|242399381|ref|YP_002994805.1| 264 IIIAGAPGEGKTTFAQALAEYYASTGKIVK 293
                                       89******************9999987775 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    0.0002      0.13       1      26 [.     264     289 ..     264     348 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.0002
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl 26 
                                       i++ G++geGK+t+a+ La+  +++ 
  gi|242399381|ref|YP_002994805.1| 264 IIIAGAPGEGKTTFAQALAEYYASTG 289
                                       6899**************99887554 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00016       0.1      15      49 ..     258     292 ..     251     318 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00016
                            AAA_30  15 tsgdrvavltGpAGtGKttalkalreaweaaggrv 49 
                                       t+++   ++ G++G GKtt  +al+e +++ g+ v
  gi|242399381|ref|YP_002994805.1| 258 TDKAEGIIIAGAPGEGKTTFAQALAEYYASTGKIV 292
                                       44555789*********************998654 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1    0.0003      0.18       1      23 [.     264     286 ..     264     327 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0003
                                       EEEESSTTSSHHHHHHHHHHHHT CS
                               AAA   1 vllyGppGtGKTllakavakelg 23 
                                       +++ G pG GKT++a+a+a+   
  gi|242399381|ref|YP_002994805.1| 264 IIIAGAPGEGKTTFAQALAEYYA 286
                                       5789***************9853 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 ?   -2.3   0.0         5   3.1e+03     126     157 ..       5      34 ..       2     105 .. 0.71
   2 ?   10.9   0.1   0.00045      0.28       1      28 [.     266     293 ..     266     296 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 5
                        ATP_bind_1 126 vvyLvDsqrltd..ptkfisgllsalsamlrlel 157
                                        v++vD+ ++ d   t++++g    ++  +++ +
  gi|242399381|ref|YP_002994805.1|   5 KVFVVDTSVIVDgrLTQYLDG----INEKVKVVI 34 
                                       588899998888777788877....344444444 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00045
                        ATP_bind_1   1 vvGpaGsGKttfvgalseilelrgrsva 28 
                                       ++G +G GKttf +al+e++ ++g+ v+
  gi|242399381|ref|YP_002994805.1| 266 IAGAPGEGKTTFAQALAEYYASTGKIVK 293
                                       68******************99987665 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00024      0.15      19      48 ..     264     293 ..     251     296 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00024
                        Zeta_toxin  19 illgGqpGAGKselaellkdelerqgnvvr 48 
                                       i+++G+pG GK++ a++l+++ +++g++v+
  gi|242399381|ref|YP_002994805.1| 264 IIIAGAPGEGKTTFAQALAEYYASTGKIVK 293
                                       89*******************999999985 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0       1.3   7.9e+02      16      62 ..      98     143 ..      95     150 .. 0.66
   2 ?   10.2   0.0     0.001      0.62       2      21 ..     264     283 ..     264     313 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.3
                            AAA_33  16 aerllkklgavllssdtlrrrlfg.tdqqsktdytrvldrlyqilnel 62 
                                       +++++++l a+l++ d++ r ++  ++++    y +++++++ +l+++
  gi|242399381|ref|YP_002994805.1|  98 IREVARELNATLITGDQVQRDVAIaKGVE--VIYLEAKKEIKHRLEDF 143
                                       67888999999999999888877633332..23566666666666555 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.001
                            AAA_33   2 vllvGlpGsGKstlaerllk 21 
                                       +++ G+pG GK+t+a+ l++
  gi|242399381|ref|YP_002994805.1| 264 IIIAGAPGEGKTTFAQALAE 283
                                       6889************9985 PP

>> Hydin_ADK  Hydin Adenylate kinase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.4   0.00027      0.17       2      24 ..     264     286 ..     263     293 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00027
                         Hydin_ADK   2 iivhGaPlsGKtatavtLakkYe 24 
                                       ii+ GaP  GKt+ a +La +Y 
  gi|242399381|ref|YP_002994805.1| 264 IIIAGAPGEGKTTFAQALAEYYA 286
                                       9*********************6 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00032       0.2       4      35 ..     264     295 ..     263     313 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00032
                                       EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE CS
                             KTI12   4 vvltGlPssGKstrakeLakaleeekrsvvvi 35 
                                       +++ G P  GK+t+a+ La++ +++++ v  +
  gi|242399381|ref|YP_002994805.1| 264 IIIAGAPGEGKTTFAQALAEYYASTGKIVKTM 295
                                       89*******************99988776655 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00065       0.4      12      50 ..     262     299 ..     258     368 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00065
                                       SEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  12 ekvaivGenGaGKStLlkllagllkpteGeilldgkdlk 50 
                                       e + i G  G GK+t++++la+ +    G+i   +++ +
  gi|242399381|ref|YP_002994805.1| 262 EGIIIAGAPGEGKTTFAQALAEYYA-STGKIVKTMEKPR 299
                                       66889***************99887.6788833333333 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      0.92   5.7e+02      25      71 ..      63     118 ..      38     153 .. 0.68
   2 ?    8.3   0.0    0.0042       2.6       6      29 ..     262     285 ..     257     312 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.92
                            AAA_22  25 lleqldeeakaee.......erpevvfvtlpsstsskdllrellralglelka......e 71 
                                       l++ +++e    +       erp++  +  ++s++ + + re++r+l+  l +       
  gi|242399381|ref|YP_002994805.1|  63 LRNLAENE----RillefygERPDLWQIRRAKSGEIDHIIREVARELNATLITgdqvqrD 118
                                       33333333....133346888888888888899999999999999998877774444440 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0042
                            AAA_22   6 gilvvtGesGtGKTtllrrlleql 29 
                                         +++ G +G GKTt ++ l+e +
  gi|242399381|ref|YP_002994805.1| 262 EGIIIAGAPGEGKTTFAQALAEYY 285
                                       5689***************99876 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0     0.001      0.63      14      54 ..     252     291 ..     234     297 .. 0.86
   2 ?   -2.1   0.1       5.3   3.3e+03      68      96 ..     462     496 ..     458     550 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.001
                                       HHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.... CS
                            ResIII  14 nlleklkskrdkrglikmaTGtGKTlvaaklierllkkgke 54 
                                       +lle l+ ++ + ++i+ a G GKT  a +l+e++++ gk+
  gi|242399381|ref|YP_002994805.1| 252 KLLERLT-DKAEGIIIAGAPGEGKTTFAQALAEYYASTGKI 291
                                       5677777.8899999********************998775 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 5.3
                                       HHHHHHGGGGTGG..........GEEEESSS-B-- CS
                            ResIII  68 eqtleefkkflseayke......igkkvsgdkkka 96 
                                       +++++e+kkfl++ y+e      ++ ++  d+ ++
  gi|242399381|ref|YP_002994805.1| 462 KRLKQEIKKFLPDVYAEvelaspHKAIIYADEFDI 496
                                       56778888888888876666665333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (605 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       752  (0.0419432); expected 358.6 (0.02)
Passed bias filter:                      628  (0.0350271); expected 358.6 (0.02)
Passed Vit filter:                       110  (0.00613531); 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: 0.74u 0.35s 00:00:01.08 Elapsed: 00:00:00.49
# Mc/sec: 3678.46
//
Query:       gi|242399382|ref|YP_002994806.1|  [L=237]
Description: Cell division inhibitor minD like protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      2e-25   89.8   0.1    8.7e-25   87.7   0.1    1.8  2  AAA_31       AAA domain
    1.2e-23   83.6   0.0    1.6e-23   83.2   0.0    1.1  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    5.4e-23   81.7   0.4      5e-22   78.6   0.4    2.3  1  ParA         NUBPL iron-transfer P-loop NTPase
    8.1e-16   58.2   0.0    4.1e-15   55.9   0.0    1.8  1  CBP_BcsQ     Cellulose biosynthesis protein BcsQ
    4.4e-11   42.7   0.1    0.00026   20.5   0.0    2.2  2  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
    5.1e-09   35.8   0.0      1e-08   34.8   0.0    1.5  1  MipZ         ATPase MipZ
      2e-05   24.5   0.0    4.8e-05   23.3   0.0    1.7  1  AAA_26       AAA domain
      5e-05   22.6   0.9    0.00052   19.3   1.0    2.4  2  ArsA_ATPase  Anion-transporting ATPase
     0.0024   17.5   0.0     0.0034   17.0   0.0    1.3  1  AAA_25       AAA domain
  ------ inclusion threshold ------
      0.023   14.4   0.0      0.041   13.6   0.0    1.5  2  AAA_30       AAA domain
      0.032   13.5   1.0       0.05   12.9   1.0    1.4  1  VirC1        VirC1 protein
      0.062   13.0   0.7       0.13   12.0   0.7    1.5  1  AAA_24       AAA domain
      0.074   13.0   0.0       0.42   10.6   0.0    2.1  2  KH_7         KH domain
       0.27   11.0   0.9        1.2    8.8   0.9    1.9  1  ATP_bind_1   Conserved hypothetical ATP binding protein


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 !   87.7   0.1   6.8e-28   8.7e-25       2     160 ..       3     154 ..       2     166 .. 0.87
   2 ?    0.7   0.0      0.34   4.3e+02      19      34 ..     151     166 ..     149     208 .. 0.87

  Alignments for each domain:
  == domain 1  score: 87.7 bits;  conditional E-value: 6.8e-28
                            AAA_31   2 kvIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlD.pQanattglgiekneiektlyevlieeknikeaiiktk 77 
                                       ++Ia+a  KGG GKTT ++nl+ al  lgkkv  vD+D + an+t ++++  ++++ktl+++l+ e++i+eai +t+
  gi|242399382|ref|YP_002994806.1|   3 RIIAVASGKGGTGKTTLVCNLSIALGLLGKKVCAVDADlTMANLTLYFRL--EDTSKTLHDALMGEIEINEAIHTTR 77 
                                       89************************************446899999986..77789******************** PP

                            AAA_31  78 venldlipssidLaeaeielvelekkeeilkellekvkdeYDyiiiDcpPsLglltenaLvasdsviipvqaeayal 154
                                       +e ++lip+ +d  ++ +         + + e++ k+kd++Dy+iiDcp  L++ + + ++  ++++ +++++  ++
  gi|242399382|ref|YP_002994806.1|  78 YEFVYLIPGALDWEHVAK------ADPRNFPEIIPKIKDDFDYVIIDCPAGLQMDALSVIFGGEEIVLVTNPDITSI 148
                                       **********99887643......3344568*****************************99999999999988887 PP

                            AAA_31 155 eGleql 160
                                         ++++
  gi|242399382|ref|YP_002994806.1| 149 GDAMKV 154
                                       666655 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.34
                            AAA_31  19 svnlaaalaklgkkvL 34 
                                       +++++a l k+gkkvL
  gi|242399382|ref|YP_002994806.1| 151 AMKVGAILKKAGKKVL 166
                                       678999*********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 !   83.2   0.0   1.2e-26   1.6e-23       1     128 []       5     213 ..       5     213 .. 0.94

  Alignments for each domain:
  == domain 1  score: 83.2 bits;  conditional E-value: 1.2e-26
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH....................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................... RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep....................... 54 
                                       ia+as+kGG+GKTtl++nL +al   g++V +vDaD  + nl++++ le   ++                       
  gi|242399382|ref|YP_002994806.1|   5 IAVASGKGGTGKTTLVCNLSIALGLLGKKVCAVDADLTMANLTLYFRLEDTSKTlhdalmgeieineaihttryefv 81 
                                       89*****************************************9888888888899999****************** PP

                                       ....................................................................CCHCCCHHH CS
                                       ....................................................................xxxxxxxxx RF
                              CbiA  55 ....................................................................dlkrllell 63 
                                                                                                           d+ +++ +l
  gi|242399382|ref|YP_002994806.1|  82 ylipgaldwehvakadprnfpeiipkikddfdyviidcpaglqmdalsvifggeeivlvtnpditsigDAMKVGAIL 158
                                       **************************************************************888888777777777 PP

                                       HHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHHTS-H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  64 ealgkkkalllkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeavaeapargepv 128
                                       ++ gkk      ++g+++nr++++  ++ ++  l+e +   + p+lgvip+d+ v ea  +g pv
  gi|242399382|ref|YP_002994806.1| 159 KKAGKK------VLGFIFNRYESQ--KNGISPELTEDLM--EFPLLGVIPEDSTVREATLEGVPV 213
                                       777766......9***********..9999999999775..******************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 !   78.6   0.4   3.9e-25     5e-22       3     244 ..       2     232 ..       1     234 [. 0.87

  Alignments for each domain:
  == domain 1  score: 78.6 bits;  conditional E-value: 3.9e-25
                              ParA   3 kkviavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeekpeqsekkliPvea.kgikvmSi 78 
                                       +++iav+SgKGG GK+t+ +nl++aL   g+kv+ +DaD++  ++   + +e+++ + +++ +  +e  + i++   
  gi|242399382|ref|YP_002994806.1|   2 RRIIAVASGKGGTGKTTLVCNLSIALGLLGKKVCAVDADLTMANLTLYFRLEDTSKTLHDALMGEIEInEAIHTTRY 78 
                                       689**************************************************988888878889998788999999 PP

                              ParA  79 gfllesedeavvwrGpmks..kaikqllkdvewgelDyLiiDlPPGtgDeqltvaqklplagaviVttpqevaladv 153
                                       +f+      a+ w    k+  +   +++ +++ ++ Dy+iiD+P G    +l+v+     +++v+Vt p   ++ d+
  gi|242399382|ref|YP_002994806.1|  79 EFVYL-IPGALDWEHVAKAdpRNFPEIIPKIK-DDFDYVIIDCPAGLQMDALSVIFG--GEEIVLVTNPDITSIGDA 151
                                       99887.77999**9887762246777888776.89***********99999999865..579*************** PP

                              ParA 154 kkaiemfkkvkvkvlGvveNmsgfvcpkcgekteifgkgggeklaeelgvpllgeipldpeireasdegkplvlkep 230
                                        k  +++kk+  kvlG + N      +k g      +    e + + +++pllg ip d+++rea+ eg p+v+ +p
  gi|242399382|ref|YP_002994806.1| 152 MKVGAILKKAGKKVLGFIFNRYE--SQKNG-----IS---PELTEDLMEFPLLGVIPEDSTVREATLEGVPVVIYNP 218
                                       *****************988433..33222.....22...2334456899*************************** PP

                              ParA 231 eseaakaleeiaek 244
                                       +++a++a+ e+a++
  gi|242399382|ref|YP_002994806.1| 219 KAKASQAIIELAQR 232
                                       ********999986 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.9   0.0   3.2e-18   4.1e-15       3     232 ..       4     232 ..       2     233 .. 0.83

  Alignments for each domain:
  == domain 1  score: 55.9 bits;  conditional E-value: 3.2e-18
                          CBP_BcsQ   3 vlalqGvRGGvGttsllaaLawalhelgesvlviDls.pdnlLrlhFnvdieqregwaraeldgapwrqaaleyapg 78 
                                       ++a+   +GG+G+t+l+  L++al  lg++v ++D+  +   L+l+F ++ ++++++  a++ + ++++a+   + +
  gi|242399382|ref|YP_002994806.1|   4 IIAVASGKGGTGKTTLVCNLSIALGLLGKKVCAVDADlTMANLTLYFRLE-DTSKTLHDALMGEIEINEAIHTTRYE 79 
                                       67777789**************************985234569******9.9*******************999999 PP

                          CBP_BcsQ  79 ldllPfGelnveekenlqqlaekaeallaalkelkeqyrwillDlpagasaltrellaladlvllvvepdanc...h 152
                                       +  l  G+l  e  +     ++++ ++ + + ++k +++++++D+pag +  + +++   +  +lv++pd  +    
  gi|242399382|ref|YP_002994806.1|  80 FVYLIPGALDWEHVA-----KADPRNFPEIIPKIKDDFDYVIIDCPAGLQMDALSVIFGGEEIVLVTNPDITSigdA 151
                                       887777**9998877.....679999********************************************9874334 PP

                          CBP_BcsQ 153 vrLhqqalpaaellLiNqfeaasqlqqDllqlWlqslrrllPl..vihrDealaEalaakqPlgeyrpdslaaeevk 227
                                       ++      +a + +L   f+     ++ +     + l +  Pl  vi +D ++ Ea +   P+  y p++ a++++ 
  gi|242399382|ref|YP_002994806.1| 152 MKVGAILKKAGKKVLGFIFNRYESQKNGISPELTEDLME-FPLlgVIPEDSTVREATLEGVPVVIYNPKAKASQAII 227
                                       566665555666665555544444444454444444433.3544689****************************** PP

                          CBP_BcsQ 228 tLanw 232
                                        La++
  gi|242399382|ref|YP_002994806.1| 228 ELAQR 232
                                       **986 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.1   2.2e-07   0.00029       3      39 ..       5      42 ..       3      79 .. 0.77
   2 !   20.5   0.0     2e-07   0.00026     142     243 ..     135     232 ..     105     236 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.2e-07
                         Fer4_NifH  3 iai.yGkGGiGksttsqnlsaalaemgkkvlivGCDPk 39
                                      ia+  GkGG Gk+t ++nls+al   gkkv  v  D  
  gi|242399382|ref|YP_002994806.1|  5 IAVaSGKGGTGKTTLVCNLSIALGLLGKKVCAVDADLT 42
                                      55425*************************99988754 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 2e-07
                         Fer4_NifH 142 qevyivtsgelmalyaanniakgiekyaksggvrlgGliinsrkvddereliekfaeel.gtkvlevvPrdeivrka 217
                                       +e+++vt+ +++++  a ++ + ++k  k    ++ G i n r  ++++++  +++e+l + ++l v+P d +vr+a
  gi|242399382|ref|YP_002994806.1| 135 EEIVLVTNPDITSIGDAMKVGAILKKAGK----KVLGFIFN-RYESQKNGISPELTEDLmEFPLLGVIPEDSTVREA 206
                                       78999999999999999999876655444....678*****.88999999999**9986379*************** PP

                         Fer4_NifH 218 elrkktvieyapeseqakeyrelark 243
                                        l+   v+ y+p+++ ++   ela++
  gi|242399382|ref|YP_002994806.1| 207 TLEGVPVVIYNPKAKASQAIIELAQR 232
                                       ***********************987 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   0.0   7.9e-12     1e-08       2     110 ..       4     122 ..       3     142 .. 0.73

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 7.9e-12
                                       EEEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHHHH..HHHHHHHHHH...T------EEE-.... CS
                              MipZ   2 vivlgnekGGsGksttavhvavaLlkkGarvaaidldlrqrtlaryl..enraataerk...glsLplpeala.... 69 
                                       +i ++  kGG+Gk+t    + +aL   G++v a+d dl  + l+ y+  e+ ++t +     +++++++ +++    
  gi|242399382|ref|YP_002994806.1|   4 IIAVASGKGGTGKTTLVCNLSIALGLLGKKVCAVDADLTMANLTLYFrlEDTSKTLHDAlmgEIEINEAIHTTryef 80 
                                       899******************************************98335555554433112444444333220011 PP

                                       SSS.-HHHHTTS-HHHHHHHHHHHHHHHHHH-SEEEEE--SS CS
                              MipZ  70 lse.aeeaeveeeeeaevaeleelvadleaeldfividtPGs 110
                                       +     + + e+ ++a+ +++ e++ +++ ++d+++id+P  
  gi|242399382|ref|YP_002994806.1|  81 VYLiPGALDWEHVAKADPRNFPEIIPKIKDDFDYVIIDCPAG 122
                                       11111244556666777789********************75 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   3.7e-08   4.8e-05     130     197 ..     136     206 ..     102     207 .. 0.92

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 3.7e-08
                            AAA_26 130 pvilVargglgtinqllltiealrqknvrvlGvilNkvrnpe...nvetlekksgipvlGvvPylpdleap 197
                                       +++lV++++  +i +++   ++l++ +++vlG i+N+  +++     e  e   + p+lGv+P +++++++
  gi|242399382|ref|YP_002994806.1| 136 EIVLVTNPDITSIGDAMKVGAILKKAGKKVLGFIFNRYESQKngiSPELTEDLMEFPLLGVIPEDSTVREA 206
                                       8************************************9888667788999999999*********999876 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   1.0   4.1e-07   0.00052       5      78 ..       7      78 ..       2     131 .. 0.75
   2 ?   -0.1   0.0      0.32   4.1e+02     209     245 ..     137     173 ..     124     180 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 4.1e-07
                                      EEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STT.THHHHHHTS--BSS-EEETSSEEEEE--HHHHHHHHHC CS
                       ArsA_ATPase  5 lvgGKGGVGKttvsaatavklsekgkkvllistDPA.hslsDsfdqklgkeptkvkeNLsavEidpeveleeakq 78
                                      + +GKGG GKtt+ + +++ l   gkkv  +  D    +l   f    + + + +++ L+  Ei+++++++ ++ 
  gi|242399382|ref|YP_002994806.1|  7 VASGKGGTGKTTLVCNLSIALGLLGKKVCAVDADLTmANLTLYFRL--EDTSKTLHDALM-GEIEINEAIHTTRY 78
                                      458*************************999999542566666655..444455555554.46666666655555 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.32
                                       EEEEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEEEE CS
                       ArsA_ATPase 209 frlVvipEklslkEteRaikeLkkygikvdavivNkl 245
                                       ++lV++p+  s+ + ++  + Lkk g kv   i N++
  gi|242399382|ref|YP_002994806.1| 137 IVLVTNPDITSIGDAMKVGAILKKAGKKVLGFIFNRY 173
                                       689*********************9999999999986 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   2.6e-06    0.0034      35      90 ..       5      63 ..       1     120 [. 0.68

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.6e-06
                            AAA_25 35 lallaGapgtGKttlaldlalava.tGkpwlg...pvapeqgkVlyvsaEdsedelrrRl 90
                                      +a+  G +gtGKttl+++l++a+  +Gk++     ++ +    +ly  +Ed+ ++l+  l
  gi|242399382|ref|YP_002994806.1|  5 IAVASGKGGTGKTTLVCNLSIALGlLGKKVCAvdaDL-TMANLTLYFRLEDTSKTLHDAL 63
                                      57789****************9988999887787644.3455578999999988888655 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   3.2e-05     0.041      19      77 ..       4      63 ..       1     118 [. 0.84
   2 ?   -3.1   0.0       4.2   5.4e+03      45      61 ..     209     225 ..     202     229 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.2e-05
                            AAA_30 19 rvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkv.Laeelgieastiakll 77
                                       +av+ G  GtGKtt++  l  a+   g++v+++    ++A+  L   l+ +++t++  l
  gi|242399382|ref|YP_002994806.1|  4 IIAVASGKGGTGKTTLVCNLSIALGLLGKKVCAVDADLTMANLtLYFRLEDTSKTLHDAL 63
                                      57899********************99****99877777777669999999999999887 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 4.2
                            AAA_30  45 aggrviglAptgkaAkv 61 
                                       +g +v+++ p++ka+++
  gi|242399382|ref|YP_002994806.1| 209 EGVPVVIYNPKAKASQA 225
                                       58899999999999987 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   1.0   3.9e-05      0.05       3      39 ..       4      40 ..       1      82 [. 0.90

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.9e-05
                             VirC1  3 litfcslkGGaGkttalmglcsalasdgkrvalfead 39
                                      +i+++s kGG+Gktt +  l  al   gk+v+  +ad
  gi|242399382|ref|YP_002994806.1|  4 IIAVASGKGGTGKTTLVCNLSIALGLLGKKVCAVDAD 40
                                      7999*******************************99 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.7    0.0001      0.13       8      72 ..       9     118 ..       2     128 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0001
                            AAA_24   8 yGpsgiGKTtlakel....................gpkplfidtekGlksldadkfpdie...swedfldevvel.. 59 
                                        G+ g+GKTtl+ +l                     + +l++ +e+ +k l ++ + +ie   ++ + + e+v+l  
  gi|242399382|ref|YP_002994806.1|   9 SGKGGTGKTTLVCNLsialgllgkkvcavdadltmANLTLYFRLEDTSKTLHDALMGEIEineAIHTTRYEFVYLip 85 
                                       69*************88889887777777777776666777799999999999999999888888888888888899 PP

                            AAA_24  60 ....................aaeladyktlviD 72 
                                                           ++ ++d++ ++iD
  gi|242399382|ref|YP_002994806.1|  86 galdwehvakadprnfpeiiPKIKDDFDYVIID 118
                                       99999999999999999999************9 PP

>> KH_7  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       1.2   1.5e+03      23      38 ..     129     143 ..     117     161 .. 0.77
   2 ?   10.6   0.0   0.00033      0.42      14      53 ..     196     231 ..     186     235 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.2
                              KH_7  23 dveFEGPelViYtknp 38 
                                       +v F G e+V+ t np
  gi|242399382|ref|YP_002994806.1| 129 SVIFGGEEIVLVT-NP 143
                                       6889999999865.44 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00033
                              KH_7  14 klPkevkitdveFEGPelViYtknpklfaengdlirklAk 53 
                                        +P++ ++ + + EG  +ViY  npk+ a  ++ i +lA+
  gi|242399382|ref|YP_002994806.1| 196 VIPEDSTVREATLEGVPVVIY--NPKAKA--SQAIIELAQ 231
                                       69*******************..555444..556666666 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.9   0.00095       1.2       3      99 ..      10     120 ..       8     130 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00095
                        ATP_bind_1   3 GpaGsGKttfvgalseilelrgrsvavvNLDPAaeelp.Yeaavdirelitledvmedlglgpngalvva.le.... 73 
                                       G  G GKtt+v +ls  l l g++v  v  D    +l+ Y    d+ ++++ + +m +  ++ n a+ +  +e    
  gi|242399382|ref|YP_002994806.1|  10 GKGGTGKTTLVCNLSIALGLLGKKVCAVDADLTMANLTlYFRLEDTSKTLHDA-LMGE--IEINEAIHTTrYEfvyl 83 
                                       888*************************9998777766366667888888765.4555..46666664431445555 PP

                        ATP_bind_1  74 ............flresldwldeeleke.ed.dyllfDtP 99 
                                                          ++ e + k  +d dy+++D+P
  gi|242399382|ref|YP_002994806.1|  84 ipgaldwehvakA---DPRNFPEIIPKIkDDfDYVIIDCP 120
                                       5555555543221...222223333444344688888888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 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:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.57u 0.34s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 1418.64
//
Query:       gi|242399383|ref|YP_002994807.1|  [L=509]
Description: Asparagine synthetase [Thermococcus sibiricus MM 739]
Scores for 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-53  181.7   0.1    6.2e-31  108.3   0.0    2.1  2  Asn_synthase     Asparagine synthase
    7.4e-26   90.5   0.0    1.5e-25   89.5   0.0    1.6  1  GATase_7         Glutamine amidotransferase domain
    3.1e-21   76.0   0.0      9e-21   74.5   0.0    1.7  2  GATase_6         Glutamine amidotransferase domain
     0.0011   18.5   0.0      0.002   17.7   0.0    1.3  1  QueC             Queuosine biosynthesis protein QueC
  ------ inclusion threshold ------
      0.015   14.5   0.0      0.029   13.5   0.0    1.5  1  NAD_synthase     NAD synthase
       0.02   14.2   0.0      0.076   12.3   0.0    1.8  2  Arginosuc_synth  Arginosuccinate synthase


Domain annotation for each model (and alignments):
>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.3   0.0   2.1e-34   6.2e-31      13     139 ..     264     388 ..     255     399 .. 0.93
   2 !   71.9   0.0   2.6e-23   7.7e-20     211     298 ..     395     483 ..     390     505 .. 0.88

  Alignments for each domain:
  == domain 1  score: 108.3 bits;  conditional E-value: 2.1e-34
                      Asn_synthase  13 rlradvpvGalLSGGlDSSliaalaarqsksplktFsigfeekgsdeakyakevaehlgtehtelvlteeelldalp 89 
                                        lr+  +v +l+SGGlDSSlia la+++sk ++  +++g   +gs+++++a++v+e+l +   e+v++ ee+ +al 
  gi|242399383|ref|YP_002994807.1| 264 KLRSSKRVRVLFSGGLDSSLIALLAKKYSK-EVILYTAGA--EGSPDLEWARKVSEQLDLTLKEYVFDLEEVKEALY 337
                                       589999***********************9.9********..*********************************** PP

                      Asn_synthase  90 dviyhlee..pfadrsaiplyllsrlakrkgvkvvLsGeGaDElfgGYpyfy 139
                                        v+ ++ee   +  +  ip+y++ +la ++ +k++LsG+GaDElfgGY   y
  gi|242399383|ref|YP_002994807.1| 338 PVMFAIEEpnAMNLAIGIPMYFATKLAAEDRIKILLSGQGADELFGGYA-KY 388
                                       ********887888999*******************************8.33 PP

  == domain 2  score: 71.9 bits;  conditional E-value: 2.6e-23
                      Asn_synthase 211 lyldlktllpgdllrkDrasmahglEaRvPflDhrlvevalrlppelklrggieKyiLRealegy.lPeeileRpKe 286
                                       +  dl ++ + +l r D+++m +g+E+R+PflD +lv++ lr+p ++k+++g+ K+iLRe++  + lP+e+++R+K+
  gi|242399383|ref|YP_002994807.1| 395 MEKDLIKMGEKNLARDDKIAMLNGVEGRFPFLDLNLVRAGLRVPKKYKINNGTRKAILREVALELgLPKEVAYREKK 471
                                       56788889999*************************************************998888*********** PP

                      Asn_synthase 287 gfsapvgewklk 298
                                       + ++++ ++kl 
  gi|242399383|ref|YP_002994807.1| 472 ACQYGTNAQKLL 483
                                       ***988887554 PP

>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.5   0.0     5e-29   1.5e-25       2     121 ..      89     207 ..      88     209 .. 0.96

  Alignments for each domain:
  == domain 1  score: 89.5 bits;  conditional E-value: 5e-29
                          GATase_7   2 rrlsiidseagaQPmvssedgrlvivfnGeiyNykelreeLeakghrfrtksDtevllallea.........ewgee 69 
                                        rl++  s++  QP+++    ++++++nGeiyN+k++r  Le+kg++f+++ Dtev+l+ le          + + e
  gi|242399383|ref|YP_002994807.1|  89 CRLAMTGSKSFTQPFYN----EFILIHNGEIYNHKQMRGFLESKGVEFESDVDTEVILRFLEFliemnkpisQAVSE 161
                                       69999999********5....8***************************************99*********99*** PP

                          GATase_7  70 alerlnGmfAfaiwdeeekrlllaRDrlGikPLyygedkgdallfaSelkal 121
                                       ++  lnG +A+a  d+e+  ++l RD++Gi+PLyy  + g   +faSe k l
  gi|242399383|ref|YP_002994807.1| 162 LMIALNGDYAVAFSDKEN--IYLFRDPMGIRPLYYSPN-G---FFASEKKVL 207
                                       *****************9..******************.8...9****9988 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.5   0.0     3e-24     9e-21       2     131 ..      72     200 ..      71     204 .. 0.86
   2 ?   -2.7   0.0       2.1   6.3e+03      59      89 ..     264     296 ..     255     305 .. 0.73

  Alignments for each domain:
  == domain 1  score: 74.5 bits;  conditional E-value: 3e-24
                          GATase_6   2 dasglaslvedevalaHvRlaivglaeeegaqPfpsedgrlllvhNGeiynykelreelpalkglafrsrsDtevll 78 
                                       d+s++ ++ +++++l+  Rla++g +  +  qPf   + +++l+hNGeiyn+k++r  l++ kg++f+s++Dtev+l
  gi|242399383|ref|YP_002994807.1|  72 DFSEVNEIPDGDIGLLQCRLAMTGSK--SFTQPF---YNEFILIHNGEIYNHKQMRGFLES-KGVEFESDVDTEVIL 142
                                       88999999999**************8..777***...999*********************.*************** PP

                          GATase_6  79 all.....eelG.....eevlerlrGmfafaiwdkrentlilardrlgvkplyyavdesglaf 131
                                       + l      + +     +e++ +l+G++a+a+ d  ++++ l rd +g++plyy+    +  f
  gi|242399383|ref|YP_002994807.1| 143 RFLeflieMNKPisqavSELMIALNGDYAVAFSD--KENIYLFRDPMGIRPLYYSP---NGFF 200
                                       *998998744446444477777********9887..6789999***********93...4445 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.1
                          GATase_6  59 elpalkgla..frsrsDtevllalleelGeevl 89 
                                       +l++ k+++  f +  D+ +++ l++++ +ev+
  gi|242399383|ref|YP_002994807.1| 264 KLRSSKRVRvlFSGGLDSSLIALLAKKYSKEVI 296
                                       566656666668889999999999988888776 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   6.7e-07     0.002       4      62 ..     273     330 ..     270     345 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 6.7e-07
                                       EE--SSHHHHHHHHHHHHH-SEEEEEEEESS-TTSHHHHHHHHHHHHT--..-EEEEE-G CS
                              QueC   4 vllSGGlDSttvlalakkegkevealtfdYgqrhkkeleaakkiakelgve.ehkildld 62 
                                       vl+SGGlDS+ +++lakk  kev++ t   g   + +le a+k++++l+++ ++ ++dl+
  gi|242399383|ref|YP_002994807.1| 273 VLFSGGLDSSLIALLAKKYSKEVILYTA--GAEGSPDLEWARKVSEQLDLTlKEYVFDLE 330
                                       89********************988665..888899999999999999974244455555 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   9.6e-06     0.029      17     116 ..     267     363 ..     254     390 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.6e-06
                                       TTSEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--.SSSTTHHHHHHHHHHHHHHTSEEEE..---HHHHHHHHH CS
                      NAD_synthase  17 gakgvvlGlSGGvDSslvaalavkalgkenvlalllP.ssvsseedvedalalaenlgievkt..idikpivrafeq 90 
                                        +k v +  SGG+DSsl+a la+k    +    ++l     +   d+e a+++ e+l++  k+  +d++++ +a+  
  gi|242399383|ref|YP_002994807.1| 267 SSKRVRVLFSGGLDSSLIALLAKKYS--K---EVILYtAGAEGSPDLEWARKVSEQLDLTLKEyvFDLEEVKEALYP 338
                                       456666778*************9987..2...233332667778899999999999877655411677777777655 PP

                                       HHHHHH-HHHHHHHHHHHHHHHHHHH CS
                      NAD_synthase  91 elkeakedlakgNlkaRiRmailyai 116
                                        +  a e+ ++ Nl   i m +  + 
  gi|242399383|ref|YP_002994807.1| 339 VMF-AIEEPNAMNLAIGIPMYFATKL 363
                                       322.2224555566655555555555 PP

>> Arginosuc_synth  Arginosuccinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.37   1.1e+03     341     383 ..      89     131 ..      83     134 .. 0.74
   2 ?   12.3   0.0   2.6e-05     0.076       4      70 ..     275     338 ..     273     350 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.37
                   Arginosuc_synth 341 GsvvvlgResees.lYdeelasydeedefdqkeaeGfikihglq 383
                                        +++++g +s ++ +Y+e +   +  + +++k+++Gf++ +g++
  gi|242399383|ref|YP_002994807.1|  89 CRLAMTGSKSFTQpFYNEFILIHN-GEIYNHKQMRGFLESKGVE 131
                                       566778888877746666555555.999**********999876 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 2.6e-05
                   Arginosuc_synth   4 ysGGlDtsviikllkeklgeeviavavdvGqeeedldevkekalklg.avksvvvDakeefvedyifp 70 
                                       +sGGlD s  i+ll++k+++evi +++    ++ dl+ +++ +++l  ++k +v D +e  v++ ++p
  gi|242399383|ref|YP_002994807.1| 275 FSGGLDSSL-IALLAKKYSKEVILYTAGAE-GSPDLEWARKVSEQLDlTLKEYVFDLEE--VKEALYP 338
                                       9*****885.89***********9999763.3479999999999887346889999755..5666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (509 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.68u 0.31s 00:00:00.99 Elapsed: 00:00:00.51
# Mc/sec: 2974.82
//
Query:       gi|242399384|ref|YP_002994808.1|  [L=387]
Description: hypothetical protein TSIB_1408 [Thermococcus sibiricus MM 739]
Scores for complete 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   25.8   2.2       0.15   12.8   0.0    3.4  3  CW_binding_2   Putative cell wall binding repeat 2
  ------ inclusion threshold ------
      0.011   15.7  11.4      0.035   14.0  11.4    1.9  1  YfdX           YfdX protein
      0.021   14.8   0.9      0.041   13.9   0.9    1.5  1  DUF3858        Domain of Unknown Function with PDB structure 
      0.026   14.6   6.2      0.053   13.6   0.9    2.8  2  DUF4363        Domain of unknown function (DUF4363)
      0.038   12.6   2.6      0.031   12.9   1.0    1.6  2  Zw10           Centromere/kinetochore Zw10
      0.073   13.5   5.4       0.52   10.7   0.0    2.4  2  DUF1771        Domain of unknown function (DUF1771)
      0.093   12.9   7.3        2.8    8.1   5.1    3.1  2  HEPN           HEPN domain
       0.11   13.1  11.6       0.31   11.7   0.4    2.9  3  DUF4398        Domain of unknown function (DUF4398)
       0.13   13.1   2.6         27    5.7   0.0    3.6  3  DUF2624        Protein of unknown function (DUF2624)
       0.14   11.8   1.3       0.24   11.1   1.3    1.3  1  Thioredoxin_5  Thioredoxin
       0.15   12.4   0.8         10    6.5   0.6    2.7  2  DUF3813        Protein of unknown function (DUF3813)
       0.18   12.2   3.8        3.8    8.0   0.2    2.6  2  DUF2564        Protein of unknown function (DUF2564)
       0.32    9.9   5.1       0.46    9.4   3.6    1.8  2  SBP_bac_5      Bacterial extracellular solute-binding protein
       0.35   10.5   4.9       0.55    9.8   4.9    1.2  1  BAR            BAR domain
       0.37   10.9   6.6        1.7    8.7   5.5    2.6  2  EIF_2_alpha    Eukaryotic translation initiation factor 2 alp
       0.41   10.7   1.9       0.49   10.4   0.2    2.0  2  CbiG_N         Cobalamin synthesis G N-terminal
       0.49    8.9   6.0       0.56    8.7   6.0    1.1  1  Macoilin       Macoilin family
        1.3    9.1   6.0        1.8    8.7   0.4    2.9  2  PTS_IIA        PTS system, Lactose/Cellobiose specific IIA su
        1.7    8.9   8.2        6.4    7.0   2.3    2.9  2  PIN_2          PIN domain
        7.5    6.8  11.6          1    9.6   0.2    2.8  3  SMBP           Small metal-binding protein


Domain annotation for each model (and alignments):
>> CW_binding_2  Putative cell wall binding repeat 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.1   0.00091      0.82      19      69 ..      34      91 ..      15      93 .. 0.66
   2 !   12.8   0.0   0.00016      0.15       1      46 [.     105     167 ..     105     187 .. 0.69
   3 ?    0.0   0.0       1.6   1.4e+03       6      31 ..     231     284 ..     229     316 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00091
                                      EET.THHHHHHHHHHHHHT--EEEE-.TS..SS.-HHHHHHH..........EEEES-TTTS-HH CS
                      CW_binding_2 19 atg.faDALsaaalaakknaPiLLtd.kl..dtalkalksat..........vyilGGegvvsds 69
                                      ++   aD+  a  la  +na ++ t  +        ++   t          v+i+GG  +v+ +
  gi|242399384|ref|YP_002994808.1| 34 VSDnEADSALAEELATLLNASVVVTTwGVydP----NV---TaeimiygpdkVIIIGGPDAVPRD 91
                                      44446888888888888888888887522211....12...1334777777899*******9865 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00016
                                       EE--SSHHHHHHHHHH.H..............EEETTHHHHHHHHHHHHHT.--EEEE-.TS.S CS
                      CW_binding_2   1 RiaGaDRyeTaaaiak.a..............latgfaDALsaaalaakkn.aPiLLtd.kl.d 46 
                                       R++G DRy T++ +++ a              +a g  D  ++  + + ++ + i+++d +l +
  gi|242399384|ref|YP_002994808.1| 105 RWYGGDRYRTNLDVIQnAleeypelfenvkiiIAHG-RDLGAIKLAKGIEGkKFIIYVDnNLtN 167
                                       99**************65999999999988765888.774444433444443788888743233 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 1.6
                                       SHHHHHHHHHHH..................EEE........T..THHHHHHHHH CS
                      CW_binding_2   6 DRyeTaaaiaka..................lat........g..faDALsaaal 31 
                                       +R eTa + +++                  +a+        g  +  A++a a 
  gi|242399384|ref|YP_002994808.1| 231 NRTETAKEMLDNltipaatkllelaeekiqIANesynegnyGkaYGQAIAAKAH 284
                                       788888888874476655555554444444233333332221233334444333 PP

>> YfdX  YfdX protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0  11.4   3.9e-05     0.035       1     144 [.     229     363 ..     229     367 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.9e-05
                                       HHHHHHHHHHHHCTT-HHHHHHHHHHHHHHHTS-HHHHHCCB-S--SSSS-EEEEEEEEEEE------HHHHHHHHH CS
                              YfdX   1 AlrdiqkArlaldqgdtkeAkkllekAqgkleaaladdpklvkkapasadalvPvdaevividdladtpekkaaikk 77 
                                       A++ ++ A   ld+  + +A+klle A++k+++a + +++          ++  ++++ i++    +   +k a k+
  gi|242399384|ref|YP_002994808.1| 229 AINRTETAKEMLDNLTIPAATKLLELAEEKIQIANESYNEG---------NYGKAYGQAIAAKAH-AEAIIKLASKE 295
                                       7899*************************************.........555555555555553.33344555555 PP

                                       HHHHHHTT-HHHHHHHHHHTT-EEEEEE.EEEEHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHT-E CS
                              YfdX  78 anellkkgdtqaArelLkllgseiditt.allPLatypaavkkAaelleegkyyeAkeaLkealntlv 144
                                        ++ l+++ + +  ++ + l++ i + + a +++ ++++ +  A +++++ +y+ Ake+++ea n l+
  gi|242399384|ref|YP_002994808.1| 296 WKNVLHARVNTQLEREIHKLEVKIKVLEkAGIDVTEIKTRLESAKNAIQSADYETAKELIEEAKNMLR 363
                                       55555555555555566666666655541346666666666666666666666666666666655544 PP

>> DUF3858  Domain of Unknown Function with PDB structure (DUF3858)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.9   4.6e-05     0.041      46     112 ..     294     364 ..     250     367 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.6e-05
                                       -TT-EE-S--S-EEEEETTEEEEEEEEEETTE....EEEEEEEEE--SEE-HHHHHHHHHHHHHHH-GGGG CS
                           DUF3858  46 peglklvtkpvekkisnkvGsveitvkkegnk....veivrslklkkqlitpaeYkafrsLmtewkdanek 112
                                       +e  ++    v+ +++ ++ ++e+++k  ++     +ei+  l+  k+ i+ a+Y+  ++L+ e k++ + 
  gi|242399384|ref|YP_002994808.1| 294 KEWKNVLHARVNTQLEREIHKLEVKIKVLEKAgidvTEIKTRLESAKNAIQSADYETAKELIEEAKNMLRD 364
                                       4455566677889999999999999886554322237999************************9998765 PP

>> DUF4363  Domain of unknown function (DUF4363)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.4      0.16   1.5e+02      60     107 .]     252     299 ..     228     299 .. 0.80
   2 ?   13.6   0.9   5.9e-05     0.053      11      45 ..     329     363 ..     328     365 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.16
                           DUF4363  60 ldeietslaklkayietedkeealaelaelkfllehikekeklsleNI 107
                                       l+  e+++  +++  +++++  a+++  ++k   e i +  +  ++N+
  gi|242399384|ref|YP_002994808.1| 252 LELAEEKIQIANESYNEGNYGKAYGQAIAAKAHAEAIIKLASKEWKNV 299
                                       566677888888888999999999999999999999999888888886 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 5.9e-05
                           DUF4363  11 tdelsekleeleeaienedweeakekleelekeWe 45 
                                       ++e++++le +++ai++ d+e+ake +ee++++ +
  gi|242399384|ref|YP_002994808.1| 329 VTEIKTRLESAKNAIQSADYETAKELIEEAKNMLR 363
                                       67999*************************99865 PP

>> Zw10  Centromere/kinetochore Zw10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.1     1e+03     121     153 ..     224     254 ..     187     275 .. 0.68
   2 ?   12.9   1.0   3.4e-05     0.031      84     138 ..     305     363 ..     276     376 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.1
                              Zw10 121 kaflvaadlleelkslldlekvekafq.lkilka 153
                                       +a+ +a ++ e++k++ld + ++ a++ l+   +
  gi|242399384|ref|YP_002994808.1| 224 QAIEFAINRTETAKEMLDNLTIPAATKlLE---L 254
                                       367777788888888888777775554333...2 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 3.4e-05
                              Zw10  84 laelkqqlkekevvlellea....lkkieealeelkealknkaflvaadlleelkslld 138
                                        ++l++++ + ev +++le+    + +i++ le  k+a+++ ++ +a++l+ee+k++l 
  gi|242399384|ref|YP_002994808.1| 305 NTQLEREIHKLEVKIKVLEKagidVTEIKTRLESAKNAIQSADYETAKELIEEAKNMLR 363
                                       37899999*********986444479*****************************9983 PP

>> DUF1771  Domain of unknown function (DUF1771)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   2.5      0.17   1.5e+02       8      48 ..     248     288 ..     247     295 .. 0.82
   2 ?   10.7   0.0   0.00058      0.52      19      46 ..     336     363 ..     329     365 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.17
                           DUF1771   8 AdeharkrnelfekAaeAyrrGdgaaAkelseqGkehgekm 48 
                                       A ++ ++  e  + A e y++G+ ++A   +  +k h e +
  gi|242399384|ref|YP_002994808.1| 248 ATKLLELAEEKIQIANESYNEGNYGKAYGQAIAAKAHAEAI 288
                                       66778888888999*********999999888888888876 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00058
                           DUF1771  19 fekAaeAyrrGdgaaAkelseqGkehge 46 
                                       +e A++A ++ d + Akel e++k   +
  gi|242399384|ref|YP_002994808.1| 336 LESAKNAIQSADYETAKELIEEAKNMLR 363
                                       689*********************8766 PP

>> HEPN  HEPN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.9     0.016        14      67     108 ..     249     292 ..     177     302 .. 0.78
   2 ?    8.1   5.1    0.0031       2.8       3     108 ..     250     365 ..     248     366 .. 0.59

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.016
                                       ...-HHHHHHHHHHHCCCHHCCCTSS--S..--HHHHHHHHHHH CS
                              HEPN  67 lkeseelreeleeLekayiesrYpdakee..yteedaeealkda 108
                                       +k  e  +e+++ +++ y e  Y+ a+ +    +  ae ++k a
  gi|242399384|ref|YP_002994808.1| 249 TKLLELAEEKIQIANESYNEGNYGKAYGQaiAAKAHAEAIIKLA 292
                                       33367777778888888888888887776666666666666655 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0031
                                       HHHHHHHHHHHHHHHHHHTT-HHHH...HHHHHHHHHHHHH.......HHHHH..TT--.SSCCHHHHHHCCHHHT. CS
                              HEPN   3 ewlrrAeedleaAellleegdydla...cfhaqqaaekalK.......Alllk..kggeppkthdlreLleelkkel 67 
                                       ++l+ Aee+++ A+++++eg y  a   + +a   ae ++K        +l +  +++   + h l   ++ l+k +
  gi|242399384|ref|YP_002994808.1| 250 KLLELAEEKIQIANESYNEGNYGKAygqAIAAKAHAEAIIKlaskewkNVLHArvNTQLEREIHKLEVKIKVLEKAG 326
                                       67888999999999999999887662223344444444444000011122222223333445555555555555555 PP

                                       ..-HHHHHHHHHHHCCCHHCCCTSS--S--HHHHHHHHHHH CS
                              HEPN  68 keseelreeleeLekayiesrYpdakeeyteedaeealkda 108
                                       ++  e+++ le + +a + ++Y+ ake    e+a+++l+da
  gi|242399384|ref|YP_002994808.1| 327 IDVTEIKTRLESAKNAIQSADYETAKE--LIEEAKNMLRDA 365
                                       558888888888888888888888888..788888888766 PP

>> DUF4398  Domain of unknown function (DUF4398)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1       6.4   5.7e+03      42      66 ..      38      48 ..      22      53 .. 0.53
   2 ?    6.9   2.3     0.011       9.5      22      60 ..     248     286 ..     224     297 .. 0.86
   3 ?   11.7   0.4   0.00035      0.31      26      57 ..     329     360 ..     322     368 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 6.4
                           DUF4398 42 ekdyeeAdhlaylAerdaelAearA 66
                                      e              +d +lAe+ A
  gi|242399384|ref|YP_002994808.1| 38 E--------------ADSALAEELA 48
                                      2..............2333444433 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.011
                           DUF4398  22 ApaeleeAreaLaqAeaamaekdyeeAdhlaylAerdae 60 
                                       A++ le A+e+++ A++  +e++y +A   a  A+++ae
  gi|242399384|ref|YP_002994808.1| 248 ATKLLELAEEKIQIANESYNEGNYGKAYGQAIAAKAHAE 286
                                       56669************999****************998 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.00035
                           DUF4398  26 leeAreaLaqAeaamaekdyeeAdhlaylAer 57 
                                        +e +  L+ A+ a + +dye+A++l ++A+ 
  gi|242399384|ref|YP_002994808.1| 329 VTEIKTRLESAKNAIQSADYETAKELIEEAKN 360
                                       6788999***********************97 PP

>> DUF2624  Protein of unknown function (DUF2624)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0      0.03        27      29      62 ..      20      53 ..      18      64 .. 0.89
   2 ?    4.0   0.2       0.1        93      23      65 ..     271     314 ..     269     325 .. 0.82
   3 ?    0.7   0.1       1.1     1e+03      41      75 ..     320     354 ..     316     363 .. 0.66

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.03
                           DUF2624 29 veltksqAekivkilrekkidifnkeerkkllke 62
                                      ++l+++q + iv ++++++ d   +ee + ll+ 
  gi|242399384|ref|YP_002994808.1| 20 IPLSQAQSTSIVILVSDNEADSALAEELATLLNA 53
                                      89*********************99999999986 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.1
                           DUF2624  23 yakqygvelt.ksqAekivkilrekkidifnkeerkkllkelak 65 
                                       y+k yg  +  k+ Ae+i+k+ +++  ++  +    +l +e++k
  gi|242399384|ref|YP_002994808.1| 271 YGKAYGQAIAaKAHAEAIIKLASKEWKNVLHARVNTQLEREIHK 314
                                       99999999962679***********9999888777777776665 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 1.1
                           DUF2624  41 kilrekkidifnkeerkkllkelakitspqtakkv 75 
                                       k+l +  id+ + + r +  k+  ++++ +tak++
  gi|242399384|ref|YP_002994808.1| 320 KVLEKAGIDVTEIKTRLESAKNAIQSADYETAKEL 354
                                       67777777777666666666666666666666653 PP

>> Thioredoxin_5  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.3   0.00026      0.24      54     153 ..     254     354 ..     212     357 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00026
                     Thioredoxin_5  54 asrtgmsidgdvlleellsssYlaslaiKA.AelQgkkkgrkFLrklqealfle.kkniskeellleiaekaglDve 128
                                         + +++i ++++ e    + Y  ++a KA Ae   k +++++ + l   +  + +++i k e+ ++++ekag+Dv+
  gi|242399384|ref|YP_002994808.1| 254 LAEEKIQIANESYNEGNYGKAYGQAIAAKAhAEAIIKLASKEWKNVLHARVNTQlEREIHKLEVKIKVLEKAGIDVT 330
                                       4556778888889999999999999****98888889999999999999887764689******************* PP

                     Thioredoxin_5 129 efkeDlesklakkafq.cDlklakem 153
                                       e k+ les   k+a q +D ++ake+
  gi|242399384|ref|YP_002994808.1| 331 EIKTRLESA--KNAIQsADYETAKEL 354
                                       ******998..666552699999986 PP

>> DUF3813  Protein of unknown function (DUF3813)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.6     0.011        10      26      41 ..     331     346 ..     320     353 .. 0.75
   2 ?    6.4   1.0     0.012        11      16      43 ..     339     367 ..     337     370 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.011
                           DUF3813  26 eqqeaiqrAKnAlssA 41 
                                       e ++ ++ AKnA++sA
  gi|242399384|ref|YP_002994808.1| 331 EIKTRLESAKNAIQSA 346
                                       55566899*******9 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.012
                           DUF3813  16 akeaaaasee.eqqeaiqrAKnAlssAYa 43 
                                       ak+a ++++   ++e i+ AKn l  A+ 
  gi|242399384|ref|YP_002994808.1| 339 AKNAIQSADYeTAKELIEEAKNMLRDAFI 367
                                       44444444332555668888888888885 PP

>> DUF2564  Protein of unknown function (DUF2564)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.5     0.045        40       8      47 ..     226     268 ..     222     293 .. 0.84
   2 ?    8.0   0.2    0.0042       3.8       4      41 ..     328     365 ..     310     370 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.045
                           DUF2564   8 velav...etAqkmvGqATmsmdpdqlesAtqAiedAreqlss 47 
                                       +e+a+   etA+ m  + T+    ++le A++ i+ A e +++
  gi|242399384|ref|YP_002994808.1| 226 IEFAInrtETAKEMLDNLTIPAATKLLELAEEKIQIANESYNE 268
                                       5666544479999999999999999999999999999998876 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0042
                           DUF2564   4 dlkqvelavetAqkmvGqATmsmdpdqlesAtqAiedA 41 
                                       d+ +++ + e+A+ ++ +A  +  ++++e+A++ + dA
  gi|242399384|ref|YP_002994808.1| 328 DVTEIKTRLESAKNAIQSADYETAKELIEEAKNMLRDA 365
                                       56778888888888888888888888888888888887 PP

>> SBP_bac_5  Bacterial extracellular solute-binding proteins, family 5 Middle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   3.6   0.00051      0.46     225     330 ..     224     331 ..     223     351 .. 0.69
   2 ?   -0.1   0.1      0.39   3.5e+02     269     288 ..     345     364 ..     334     370 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00051
                                       HHHHHHS-HHHHHHHCTTTSSEEESSSSTTTSTTCCSCHCCCSHH......SHHHHHHHHHHHTT-BCSSTSCEETC CS
                         SBP_bac_5 225 qAlsyAiDreeivkavlegyatpansllppsspgadeeykpayka......ydpekAkklLkeaGykdgdggglrek 295
                                       qA+  Ai+r+e +k++l ++ +pa++ l +      ++ ++ y++      y  + A k  +ea +k   +++    
  gi|242399384|ref|YP_002994808.1| 224 QAIEFAINRTETAKEMLDNLTIPAATKLLELAEEKIQIANESYNEgnygkaYGQAIAAKAHAEAIIKLASKEWK--- 297
                                       9**********************999766555544444444444456668888999999999999999998773... PP

                                       EEEEEEEEETTSHHHHHHHHHHHHHHHHTTEEEEE CS
                         SBP_bac_5 296 klkltlllasgspaekaiaeliqqqlkkiGikvev 330
                                         +l   ++++ + e   +e+  + l+k+Gi+v+ 
  gi|242399384|ref|YP_002994808.1| 298 -NVLHARVNTQLEREIHKLEVKIKVLEKAGIDVTE 331
                                       .3333333333333335578889999999999863 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.39
                                       HSHHHHHHHHHHHTT-BCSS CS
                         SBP_bac_5 269 aydpekAkklLkeaGykdgd 288
                                         d e Ak+l++ea +  +d
  gi|242399384|ref|YP_002994808.1| 345 SADYETAKELIEEAKNMLRD 364
                                       35899999999999887765 PP

>> BAR  BAR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   4.9   0.00061      0.55      56     186 ..     231     361 ..     212     366 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00061
                               BAR  56 npgarakqivlekl...keqplelLaesmieagkelgedssfgkalekygeavkklaqteeelekrvetnfldplre 129
                                       n++ +ak++ l++l       l +Lae  i++  e  ++ ++gka+ +  +a        +   k+ ++ +   +++
  gi|242399384|ref|YP_002994808.1| 231 NRTETAKEM-LDNLtipAATKLLELAEEKIQIANESYNEGNYGKAYGQAIAAKAHAEAIIKLASKEWKNVLHARVNT 306
                                       445555555.5555555555666788888888888888888999999888888888888888888888888899*** PP

                               BAR 130 llekefkeiqkerkklehkrlDyDaakarlkklktkkskkakdeekaeeelrkAqqk 186
                                        le e+ +++ ++k le+  +D    k+rl+++k++ +  + d e+a+e +++A+++
  gi|242399384|ref|YP_002994808.1| 307 QLEREIHKLEVKIKVLEKAGIDVTEIKTRLESAKNAIQ--SADYETAKELIEEAKNM 361
                                       ********************************994333..33447777777777765 PP

>> 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 ?   -1.9   0.0       3.7   3.3e+03      29      51 ..     183     205 ..     117     218 .. 0.60
   2 ?    8.7   5.5    0.0019       1.7      12      87 ..     270     344 ..     209     365 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3.7
                                       HHHHTTS-TTTHHHHHHCTHHHH CS
                       EIF_2_alpha  29 vldkleipeeveeaLveiikkkl 51 
                                       +l++  +++ ++e + e i++++
  gi|242399384|ref|YP_002994808.1| 183 ILKSQLMNNGTAERIRERIRERV 205
                                       23333344445555555555554 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0019
                                       TTS-HHHHHHHHHSTTHHHHHTTS-TTTHHHHHHCTHHHHHHT-EEEEEEEEEEE-STTHHH..HHHHHHHHHST.S CS
                       EIF_2_alpha  12 kyghaydaFklaitdeevldkleipeeveeaLveiikkklkpqkvkiradieltcftkdGve..aIkeaLkageeas 86 
                                       +yg+ay    +a  + e++ kl  ++e++++L   ++++l+ + +k++ +i++   +k G++  +Ik+ L+++++a 
  gi|242399384|ref|YP_002994808.1| 270 NYGKAYGQAIAAKAHAEAIIKL-ASKEWKNVLHARVNTQLEREIHKLEVKIKVL--EKAGIDvtEIKTRLESAKNAI 343
                                       4777777776666666777776.689*********************9988886..566654228*****9666633 PP

                                       . CS
                       EIF_2_alpha  87 n 87 
                                       +
  gi|242399384|ref|YP_002994808.1| 344 Q 344
                                       2 PP

>> CbiG_N  Cobalamin synthesis G N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.2   0.00055      0.49      40      79 ..      20      59 ..      17      61 .. 0.80
   2 ?   -2.6   0.1       6.6   5.9e+03      64      79 ..     276     291 ..     272     293 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00055
                                      EEE-TT--EEEEEE-TT.TTHHHHHHHHHHHTT-EE-XXX CS
                            CbiG_N 40 vvvdeagrfvisllsGhlggAnelAeeiaallgaepviTt 79
                                      + +++a++  i +l    +   +lAee+a+ll+a  v+Tt
  gi|242399384|ref|YP_002994808.1| 20 IPLSQAQSTSIVILVSDNEADSALAEELATLLNASVVVTT 59
                                      55667777777777777577789****************9 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 6.6
                                       HHHHHHHTT-EE-XXX CS
                            CbiG_N  64 AeeiaallgaepviTt 79 
                                        + iaa  +ae++i  
  gi|242399384|ref|YP_002994808.1| 276 GQAIAAKAHAEAIIKL 291
                                       5678888899988865 PP

>> Macoilin  Macoilin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   6.0   0.00063      0.56     475     558 ..     252     334 ..     165     362 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00063
                          Macoilin 475 LkeekearaslekqLaeekkrkkeeeetaaravalaaasr..secteslksk.kreleaeikkLekelklkeeq.ir 547
                                       L+  +e+ + +++  +e    k   ++ aa+a a a+ +   +e  ++l+ + +++le ei+kLe ++k+ e+  i+
  gi|242399384|ref|YP_002994808.1| 252 LELAEEKIQIANESYNEGNYGKAYGQAIAAKAHAEAIIKLasKEWKNVLHARvNTQLEREIHKLEVKIKVLEKAgID 328
                                       444444444555555555556666778888888888765444999****9883579*************99986133 PP

                          Macoilin 548 elelkvqelrk 558
                                              e++ 
  gi|242399384|ref|YP_002994808.1| 329 VT-----EIKT 334
                                       33.....3333 PP

>> PTS_IIA  PTS system, Lactose/Cellobiose specific IIA subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.9      0.26   2.4e+02      26      46 ..     249     269 ..     234     322 .. 0.76
   2 ?    8.7   0.4     0.002       1.8      17      46 ..     336     365 ..     328     368 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.26
                           PTS_IIA  26 egdfeeaeellkeAeeelkeA 46 
                                       ++ +e aee+++ A+e+++e+
  gi|242399384|ref|YP_002994808.1| 249 TKLLELAEEKIQIANESYNEG 269
                                       444566666666666666665 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.002
                           PTS_IIA  17 ameAlkaakegdfeeaeellkeAeeelkeA 46 
                                       +  A +a+++ d+e+a+el++eA++ l++A
  gi|242399384|ref|YP_002994808.1| 336 LESAKNAIQSADYETAKELIEEAKNMLRDA 365
                                       556788999****************99987 PP

>> PIN_2  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.2     0.056        50      22      83 ..     216     274 ..     197     283 .. 0.67
   2 ?    7.0   2.3    0.0071       6.4      38      89 ..     311     364 ..     285     366 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.056
                             PIN_2  22 lvekaleliapeeaveeiekhkealvkksklseeeleellelletkikiveeslyeskikeA 83 
                                        v++++   a e+a++  e  ke ++   +l+  ++ +llel+e+ki+i +es+ e +  +A
  gi|242399384|ref|YP_002994808.1| 216 EVTPEMAWQAIEFAINRTETAKE-ML--DNLTIPAATKLLELAEEKIQIANESYNEGNYGKA 274
                                       44444444455555554444444.44..57788889999**************988666666 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0071
                             PIN_2  38 eiekhke..alvkksklseeeleellelletkikiveeslyeskikeAkeriar 89 
                                       ei+k +   ++++k +++  e+++ le ++++i++ + ++ ++ i+eAk+++++
  gi|242399384|ref|YP_002994808.1| 311 EIHKLEVkiKVLEKAGIDVTEIKTRLESAKNAIQSADYETAKELIEEAKNMLRD 364
                                       55554431146899************************************9986 PP

>> SMBP  Small metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   2.0       1.5   1.3e+03      30      64 ..     229     273 ..     217     291 .. 0.50
   2 ?   -0.1   5.2       1.1     1e+03      35      85 ..     279     325 ..     242     328 .. 0.56
   3 ?    9.6   0.2    0.0012         1      31      60 ..     336     365 ..     327     372 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.5
                                       HHHHHHHHHHHHHT...T-HHHHHHHHHHHHHHHHHH........ CS
                              SMBP  30 AiehaeaAvahgka...ghakalveHaeealkhakaa.......a 64 
                                       Ai+ +e A++  ++     a++l+e aee ++ a+++       +
  gi|242399384|ref|YP_002994808.1| 229 AINRTETAKEMLDNltiPAATKLLELAEEKIQIANESynegnygK 273
                                       566666665555541113466666666666666666644433331 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.1
                                       HHHHHHHHTT-HHHHHHHHHHHHHHHHHH....-------HHHHHHHHHHHH CS
                              SMBP  35 eaAvahgkaghakalveHaeealkhakaa.aekakeeekehldegikhLeeA 85 
                                        aA+a     ha+a+++ a +  k +  a  + + e e ++l+  ik Le+A
  gi|242399384|ref|YP_002994808.1| 279 IAAKA-----HAEAIIKLASKEWKNVLHArVNTQLEREIHKLEVKIKVLEKA 325
                                       22222.....333455555555555444444455555556666666666665 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.0012
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                              SMBP  31 iehaeaAvahgkaghakalveHaeealkha 60 
                                       +e a++A+++++ ++ak+l+e+a++ l  a
  gi|242399384|ref|YP_002994808.1| 336 LESAKNAIQSADYETAKELIEEAKNMLRDA 365
                                       789*********************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1489  (0.0830498); expected 358.6 (0.02)
Passed bias filter:                      838  (0.0467399); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); 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: 0.75u 0.37s 00:00:01.12 Elapsed: 00:00:00.56
# Mc/sec: 2097.95
//
Query:       gi|242399385|ref|YP_002994809.1|  [L=367]
Description: Glycosyltransferase, family 4 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-31  109.1   0.1    3.6e-31  108.4   0.1    1.3  1  Glyco_transf_4   Glycosyltransferase Family 4
    5.8e-29  100.8   0.8    4.5e-28   97.9   0.2    2.6  3  Glycos_transf_1  Glycosyl transferases group 1
    2.2e-25   89.7   0.1    2.7e-23   82.9   0.0    2.9  3  Glyco_trans_1_4  Glycosyl transferases group 1
    2.1e-21   76.4   1.5    4.8e-21   75.3   0.9    1.8  2  Glyco_trans_4_2  Glycosyl transferase 4-like
    8.5e-20   71.8   0.0    1.1e-19   71.4   0.0    1.2  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
      3e-06   27.5   0.0    5.5e-06   26.7   0.0    1.4  1  Glyco_trans_1_2  Glycosyl transferases group 1
    1.2e-05   25.2   1.8     0.0018   18.0   0.2    3.0  4  DUF3492          Domain of unknown function (DUF3492)
      0.001   18.8   0.2       0.19   11.4   0.0    2.6  2  Glyco_transf_5   Starch synthase catalytic domain
  ------ inclusion threshold ------
      0.039   13.1   0.0      0.061   12.5   0.0    1.3  1  TMEM173          Transmembrane protein 173
      0.097   12.4   0.3        9.6    6.0   0.0    3.1  3  PEP-utilizers    PEP-utilising enzyme, mobile 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 !  108.4   0.1     2e-34   3.6e-31       2     167 ..      14     169 ..      13     171 .. 0.96

  Alignments for each domain:
  == domain 1  score: 108.4 bits;  conditional E-value: 2e-34
                    Glyco_transf_4   2 GGverhvleLaraLarrGheVtvvtpgddgpleeevelvvrvprvplpllkrllrslaflrrlrrllkrekpDvvHa 78 
                                       GGv+ h+ +La++L+++ heV+++t g+ +p   e+e v++++ + +++l++ l++l +++++ +l kr k+Dv+Ha
  gi|242399385|ref|YP_002994809.1|  14 GGVASHTNNLAKELRKK-HEVHILTYGPIKPRKFEREFVHQIKVPQIFGLRGILFTLLAALKIIKLQKRIKFDVIHA 89 
                                       9****************.**********999999999**************************************** PP

                    Glyco_transf_4  79 hspaalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrllrradrviavSeatadelrerygvp 155
                                       h+ ++  +a++ ++ +l +p+++t+Hg++         +   +l r++ ++ l+++d viavS+++++  ++ +g  
  gi|242399385|ref|YP_002994809.1|  90 HYVGTTSYAGILAKEKLSVPVIVTAHGSD------LDFMSNLPLGRYFVKKSLSKSDLVIAVSHHLQKKAIS-MG-- 157
                                       *****************************......6778888999***************************.99.. PP

                    Glyco_transf_4 156 pekitVipnGvD 167
                                       + ki+Vipn + 
  gi|242399385|ref|YP_002994809.1| 158 ATKIRVIPNSIK 169
                                       689******986 PP

>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       0.4   7.2e+02      49      82 ..       2      40 ..       1      46 [. 0.82
   2 ?   -1.8   0.0         1   1.9e+03     115     132 ..     106     123 ..     105     156 .. 0.72
   3 !   97.9   0.2   2.5e-31   4.5e-28       8     170 ..     171     318 ..     165     320 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.4
                                      EEEEES......STTHHHHHHHHHHHCTTCGGGEEECCH CS
                   Glycos_transf_1 49 klviaG.....ngeeekelkklaeelelsdnviflgevs 82
                                      k++i+G     +g       +la+el  +++v++l + +
  gi|242399385|ref|YP_002994809.1|  2 KILIIGhypphKGGVASHTNNLAKELRKKHEVHILTYGP 40
                                      667888888888888888999999999999999987765 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1
                                       TT--EEEETTTTHCHHCH CS
                   Glycos_transf_1 115 aglpviasnaggpaevvk 132
                                       + +pvi++++g  ++   
  gi|242399385|ref|YP_002994809.1| 106 LSVPVIVTAHGSDLDFMS 123
                                       578999999987666555 PP

  == domain 3  score: 97.9 bits;  conditional E-value: 2.5e-31
                                       HTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSS CS
                   Glycos_transf_1   8 klgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsre 84 
                                        ++++ k+++i ++g+l+++K+++++ik+++++     p  k++++G+g+ +  l+k+       +nv+flg+++  
  gi|242399385|ref|YP_002994809.1| 171 IKKEDAKREYITFIGALTPYKDPQTFIKLAKQF-----PHEKFLVVGDGPLRMDLEKQ-----APKNVKFLGYKE-- 235
                                       55677899***********************75.....666*********97777776.....789********9.. PP

                                       SHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHH CS
                   Glycos_transf_1  85 dleellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeel 161
                                       d+  +l++ +++v+ps +EgfG+v++EA ++g+pvi  ++gg++e++++g++G+ +k+   e+l+e+++ ll+++ +
  gi|242399385|ref|YP_002994809.1| 236 DVGGILSKTKLLVVPSLREGFGLVIIEANSLGVPVIGRAVGGIKELIREGKNGYTFKTF--EELVEKVEILLSNK-K 309
                                       ***********************************************************..*************7.7 PP

                                       HHHHHHHHH CS
                   Glycos_transf_1 162 rerlgenar 170
                                       + ++g+ ++
  gi|242399385|ref|YP_002994809.1| 310 ALKMGKIGK 318
                                       777777765 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.084   1.5e+02       3      50 ..       2      50 ..       1      75 [. 0.75
   2 ?    0.2   0.0      0.51   9.2e+02      57      98 ..     119     164 ..      61     174 .. 0.53
   3 !   82.9   0.0   1.5e-26   2.7e-23       2     134 .]     179     307 ..     178     307 .. 0.94

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.084
                                      EEEEES---GG.GTHHHHHHHH.HHHH.HH.EEEEEES---...HHHHHHH CS
                   Glyco_trans_1_4  3 vilfvGrleenvkgvdllleav.pllrkkd.vrlvivGdgp.rpeeleela 50
                                      +il +G + +++ gv    +++ ++lrkk+ v+++ +G  p +p+++e++ 
  gi|242399385|ref|YP_002994809.1|  2 KILIIGHYPPHKGGVASHTNNLaKELRKKHeVHILTYG--PiKPRKFEREF 50
                                      5888999955667889999999999**88559999999..66776777533 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.51
                                       EEEE---..TH..HHHHHHH-SEEEE-----SHHHHHHHHTT-EEE CS
                   Glyco_trans_1_4  57 veftGfv..ed..laellaaadvfvaPsegfglkllEamaaglpvV 98 
                                         f+  +      +++ l+++d+++a s  ++ k++ + a ++ v+
  gi|242399385|ref|YP_002994809.1| 119 LDFMSNLplGRyfVKKSLSKSDLVIAVSHHLQKKAISMGATKIRVI 164
                                       4444444221123666677777777777666666666666666555 PP

  == domain 3  score: 82.9 bits;  conditional E-value: 1.5e-26
                                       EEEEEES---GG.GTHHHHHHHHHHHH.HHEEEEEES---...HHHHHHHTT-T.TEEEE---THHHHHHHH-SEEE CS
                   Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkkdvrlvivGdgp.rpeeleelaagleerveftGfvedlaellaaadvfv 77 
                                         i f+G+l  ++k  + +++ +++  ++  ++++vGdgp r  +le++a    ++v+f+G+ ed+  +l++ +++v
  gi|242399385|ref|YP_002994809.1| 179 EYITFIGAL-TPYKDPQTFIKLAKQFPHE--KFLVVGDGPlR-MDLEKQAP---KNVKFLGYKEDVGGILSKTKLLV 248
                                       5799*****.567**************89..9********65.59*98885...79********************* PP

                                       E--..---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHHHH- CS
                   Glyco_trans_1_4  78 aPs..egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailrLled 134
                                       +Ps  egfgl+++Ea ++g+pv+  +vggi+e++  g+ng+ ++    e+l+e+++ Ll++
  gi|242399385|ref|YP_002994809.1| 249 VPSlrEGFGLVIIEANSLGVPVIGRAVGGIKELIreGKNGYTFK--TFEELVEKVEILLSN 307
                                       ****99*****************************99******9..99********99986 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 !   75.3   0.9   2.7e-24   4.8e-21      11     138 ..      18     145 ..       2     146 .. 0.80
   2 ?   -1.4   0.0       1.2   2.2e+03       8      44 ..     285     319 ..     281     335 .. 0.72

  Alignments for each domain:
  == domain 1  score: 75.3 bits;  conditional E-value: 2.7e-24
                   Glyco_trans_4_2  11 vhtlrlakeLakrgyeVhvitpkkgakdeleaegihvhrlkvd.....rkgpleylkafklkklikkikPDvvhahy 82 
                                        ht++lakeL+k  +eVh++t ++ + ++ e+e +h +++  +     r + +++l+a+k++kl k+ik+Dv+hahy
  gi|242399385|ref|YP_002994809.1|  18 SHTNNLAKELRK-KHEVHILTYGPIKPRKFEREFVHQIKV--PqifglRGILFTLLAALKIIKLQKRIKFDVIHAHY 91 
                                       49**********.9********999655444666655555..546885555************************** PP

                   Glyco_trans_4_2  83 akpygllgslaarlsgvipvvlsvwGldv.lkfpkksklkklllklalkkatkvist 138
                                       +    ++g la+ ++  +pv+++++G+d  + ++ +    ++ +k +l+k+++vi+ 
  gi|242399385|ref|YP_002994809.1|  92 VGTTSYAGILAKEKLS-VPVIVTAHGSDLdFMSNLPL--GRYFVKKSLSKSDLVIAV 145
                                       9776666666655666.**********9877777777..***************986 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.2
                   Glyco_trans_4_2   8 lssvhtlrlakeLakrgyeVhvitpkkga.kdeleaeg 44 
                                        ++++t +  +eL +   +V+++ ++k+a k  ++ + 
  gi|242399385|ref|YP_002994809.1| 285 GKNGYTFKTFEELVE---KVEILLSNKKAlKMGKIGKT 319
                                       567888888899988...88888888877666555554 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 !   71.4   0.0   6.4e-23   1.1e-19       1     159 [.      14     166 ..      14     167 .. 0.86

  Alignments for each domain:
  == domain 1  score: 71.4 bits;  conditional E-value: 6.4e-23
                   Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvltpapapgapeleedgvrvhrlpvprrpspladlaalralrrll....rqrrer 73 
                                       gG++ ++++la++L++  heV++lt +p  ++     ++  vh ++vp     ++    l+ l ++l     q+r +
  gi|242399385|ref|YP_002994809.1|  14 GGVASHTNNLAKELRKK-HEVHILTYGPIKPRK---FEREFVHQIKVPQI---FGLRGILFTLLAALkiikLQKRIK 83 
                                       8****************.*******86644444...45568999999955...56666778888887777999**** PP

                   Glyco_trans_4_4  74 pdvvhahs.ptaglaarlarrrrgiplvvtlhglllrrgsgavrrlyralerrllrradavlvvseaeaeelralgv 149
                                       +dv+hah+  t+++a+ la+ + ++p++vt+hg +l+       +l r + + +l+  d+v++vs+++ ++++ +g+
  gi|242399385|ref|YP_002994809.1|  84 FDVIHAHYvGTTSYAGILAKEKLSVPVIVTAHGSDLDFM--SNLPLGRYFVKKSLSKSDLVIAVSHHLQKKAISMGA 158
                                       ********66899*******889*********9887644..455677788**************************9 PP

                   Glyco_trans_4_4 150 padrvvvvpn 159
                                          +++v+pn
  gi|242399385|ref|YP_002994809.1| 159 T--KIRVIPN 166
                                       8..9*****9 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0   3.1e-09   5.5e-06       4      69 ..     249     313 ..     245     335 .. 0.84

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 3.1e-09
                   Glyco_trans_1_2   4 npsrsespnlrlfEaaacGafaltddaegleelftpgkevilfedleelaekiryllanpeerrai 69 
                                        ps +e++ l++ Ea   G++++  +  g+ el+++gk + +f++ eel+ek++ ll+n +   ++
  gi|242399385|ref|YP_002994809.1| 249 VPSLREGFGLVIIEANSLGVPVIGRAVGGIKELIREGKNGYTFKTFEELVEKVEILLSNKKA-LKM 313
                                       488999*******************99***************************88877654.444 PP

>> DUF3492  Domain of unknown function (DUF3492)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.1   0.0    0.0088        16       6      30 ..       4      28 ..       1      54 [. 0.78
   2 !   18.0   0.2     1e-06    0.0018     165     205 ..      73     116 ..      44     117 .. 0.82
   3 ?   -2.4   0.0       1.8   3.1e+03     245     266 ..     138     159 ..     132     160 .. 0.88
   4 ?   -1.9   0.0       1.2   2.2e+03     115     144 ..     308     338 ..     278     341 .. 0.61

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0088
                           DUF3492  6 llEGTYPyvsGGVSsWvhqlitklp 30
                                      l+ G YP  +GGV+s  ++l ++l 
  gi|242399385|ref|YP_002994809.1|  4 LIIGHYPPHKGGVASHTNNLAKELR 28
                                      55599***************99875 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 1e-06
                           DUF3492 165 l...laeelpkadvyHavstGyAgllgallkerkgtpllltEHG 205
                                       l     ++ +k dv+Ha+  G  ++ g+l+ke+ ++p+++t HG
  gi|242399385|ref|YP_002994809.1|  73 LkiiKLQKRIKFDVIHAHYVGTTSYAGILAKEKLSVPVIVTAHG 116
                                       23234566799********************************9 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.8
                           DUF3492 245 aadkiitlyeknrerqiedGAd 266
                                       ++d +i+++++ ++ +i++GA 
  gi|242399385|ref|YP_002994809.1| 138 KSDLVIAVSHHLQKKAISMGAT 159
                                       7899****************96 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 1.2
                           DUF3492 115 eke.kklsledflkskeawdlileayeelle 144
                                       +k+ k  +  + ++s+ +w++i + +ee ++
  gi|242399385|ref|YP_002994809.1| 308 KKAlKMGKIGKTISSQYSWERIRHLIEESYR 338
                                       2234556667778888889988888777655 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 !   11.4   0.0    0.0001      0.19      15      59 ..      13      54 ..       3      65 .. 0.84
   2 ?    4.7   0.1     0.012        21     121     171 ..      71     116 ..      60     158 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0001
                    Glyco_transf_5 15 tGGLadvvgaLpkaLaklghdvrvilPrygaikeekkeleevael 59
                                       GG+a ++  L+k+L+k+ h+v++++  yg ik +k+e e v+++
  gi|242399385|ref|YP_002994809.1| 13 KGGVASHTNNLAKELRKK-HEVHILT--YGPIKPRKFEREFVHQI 54
                                      59*************997.8*****9..88899988777777665 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.012
                    Glyco_transf_5 121 aalelleklgw.kpdvihahDW.htalvpallkelykerglfkkiktvftiHN 171
                                       aal++++  +  k+dvihah    t+ +++l+ke          +++++t H 
  gi|242399385|ref|YP_002994809.1|  71 AALKIIKLQKRiKFDVIHAHYVgTTSYAGILAKEKL-------SVPVIVTAHG 116
                                       444444443333799999997514556666666653.......2888888885 PP

>> TMEM173  Transmembrane protein 173
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   3.4e-05     0.061     162     214 ..     131     183 ..     125     201 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.4e-05
                                       S--STCCCCCTTEEEEEE---EEEEETTCEEEEE--EEEEEEETTCEEEEEEE CS
                           TMEM173 162 evsdkleeadeniefleeLeeeeidrAGvkgRvykhsvYkikdednkavycvv 214
                                       +v+++l+++d  i+  ++L+++ i ++  k Rv  +s+ +ik+ed k  y+  
  gi|242399385|ref|YP_002994809.1| 131 FVKKSLSKSDLVIAVSHHLQKKAISMGATKIRVIPNSIKTIKKEDAKREYITF 183
                                       799**************************************999999887755 PP

>> PEP-utilizers  PEP-utilising enzyme, mobile domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.079   1.4e+02      31      46 ..      13      28 ..      12      30 .. 0.90
   2 ?    6.0   0.0    0.0054       9.6      33      56 ..      93     117 ..      86     143 .. 0.86
   3 ?   -0.7   0.0      0.69   1.2e+03      40      53 ..     261     274 ..     259     289 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.079
                                      --TTHHHHHHHHHHTT CS
                     PEP-utilizers 31 rGGmtSHaAivArelg 46
                                      +GG  SH+  +A+el 
  gi|242399385|ref|YP_002994809.1| 13 KGGVASHTNNLAKELR 28
                                      79***********997 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0054
                                       TTHHHHHHHHHH.TT--EEE--SSH CS
                     PEP-utilizers  33 GmtSHaAivAre.lgiPaVvgvgea 56 
                                       G tS a i+A+e l +P++v +++ 
  gi|242399385|ref|YP_002994809.1|  93 GTTSYAGILAKEkLSVPVIVTAHGS 117
                                       99********9669******98765 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.69
                                       HHHHHTT--EEE-- CS
                     PEP-utilizers  40 ivArelgiPaVvgv 53 
                                       i A +lg+P++  +
  gi|242399385|ref|YP_002994809.1| 261 IEANSLGVPVIGRA 274
                                       66999****99754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 2731.01
//
Query:       gi|242399386|ref|YP_002994810.1|  [L=341]
Description: Sua5 superfamily-related protein [Thermococcus sibiricus MM 739]
Scores for 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-61  204.5   0.0    1.8e-60  203.5   0.0    1.5  2  Sua5_yciO_yrdC   Telomere recombination
    3.2e-36  124.8   0.2      5e-36  124.2   0.2    1.3  1  SUA5             Putative GTP-binding controlling metal-bindi
  ------ inclusion threshold ------
      0.028   14.8   0.2        1.6    9.1   0.0    2.4  2  RuvX             Holliday junction resolvase
       0.14   12.4   0.6          8    6.6   0.0    2.6  2  Isochorismatase  Isochorismatase family


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 !  203.5   0.0     4e-64   1.8e-60       2     179 .]      22     197 ..      21     197 .. 0.98
   2 ?   -3.4   0.0       1.3     6e+03      82     103 ..     252     272 ..     236     274 .. 0.67

  Alignments for each domain:
  == domain 1  score: 203.5 bits;  conditional E-value: 4e-64
                                       HHHTTSEEEEE-SSSEEEEEETTSHHHHHHHHHHHTSHCCC--EEEESSCCCCCCCC-TC--HHHHHHHHCT-SSSC CS
                    Sua5_yciO_yrdC   2 alrkGgivaiptetvYgLacdatneeaverlreiKgrpsdkplavlvasledlkklaeseveeealkllerfwPGpi 78 
                                       ++++ ++va+ptetvYgL++da ne+av++++++Kgrp d+pl++++a++e++ +la+ ev+e a  l++rfwPGp+
  gi|242399386|ref|YP_002994810.1|  22 FIKESKLVAFPTETVYGLGADALNEDAVRKIFQAKGRPPDNPLIIHIANFEQIYELAR-EVPETAKILAQRFWPGPL 97 
                                       68999****************************************************9.****************** PP

                                       EEEEE..E-TS-HHHHTTTTEEEEEE-SSHHHHHHHHHCTS-EEEEES-STTS-S-SSHHHHHHHC-TTSECB-SS- CS
                    Sua5_yciO_yrdC  79 tlllkrskeklpkevapglktvGvrlPdtplarlLlealgeplvaTSanlsgepsitdaeeveeelgeivdlildgg 155
                                       tl+l++++e +p + ++gl+tv++r+Pd+++a++L++  ++p++a+San+sg+ps+t ae+v +++ +++++i+dgg
  gi|242399386|ref|YP_002994810.1|  98 TLVLPKKDE-VPYVTTGGLETVAIRMPDHEIALALIQSSDRPIAAPSANISGKPSPTLAEHVVDDFYGKIECIIDGG 173
                                       *****8555.******************************************************************* PP

                                       --SSS---EEEETTSSTSSECEXX CS
                    Sua5_yciO_yrdC 156 eiavgvdstVvdltegkpkilRrG 179
                                       e+++gv+stVvdlt ++p +lR+G
  gi|242399386|ref|YP_002994810.1| 174 ETKIGVESTVVDLTTHPPMLLRPG 197
                                       **********************98 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.3
                                       EE..E-TS-HHHHTTTTEEEEE CS
                    Sua5_yciO_yrdC  82 lkrskeklpkevapglktvGvr 103
                                       +k+ ke l ke  +++ +vGv+
  gi|242399386|ref|YP_002994810.1| 252 TKKIKE-LIKEYKKQKIRVGVM 272
                                       343333.666667777788887 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 !  124.2   0.2   1.1e-39     5e-36       3     134 .]     201     335 ..     199     335 .. 0.85

  Alignments for each domain:
  == domain 1  score: 124.2 bits;  conditional E-value: 1.1e-39
                                       HHHHHHHS-..-.-.....---....----------S-SSEEEEE--GGGHHHH......HHHHHTTS-EEEEEEGG CS
                              SUA5   3 leeleevld..a.vek.keekp....raPGmkyrHYaPkapvvlveaeeeeeaake.ekleekkksgkkvgvlatse 70 
                                       lee+++v++  + +    + kp    +aPGmky+HYaP+a+v+++e+e e+ ++k+ e ++e+kk++ +vgv+at++
  gi|242399386|ref|YP_002994810.1| 201 LEEIKKVIGkvNvH-PaVKGKPiklaKAPGMKYKHYAPEAQVIVIEGEREQVTKKIkELIKEYKKQKIRVGVMATGD 276
                                       699****9533222.23344445667***********************99998888999**************988 PP

                                       GTGGTSEEEEE..E-TT-HHHHHHHHHHHHHHHHHS--SEEEEE----STTHHHHHHHHHHHTT CS
                              SUA5  71 skeaassvlslslgsrsdleeaarnLFaaLrelDeegvdlilvegvpeeglglAvmnRLrkAAg 134
                                         ea +   ++  g  +++ee+arnLF+aLrelD++gv++il+eg++e+glglAvmnRL+kAAg
  gi|242399386|ref|YP_002994810.1| 277 FYEA-DAYFNI--G--ENEEEIARNLFKALRELDKSGVNVILAEGIEERGLGLAVMNRLKKAAG 335
                                       8874.334444..4..9**********************************************7 PP

>> RuvX  Holliday junction resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1     0.013        60       6      72 ..     170     233 ..     168     242 .. 0.80
   2 ?    9.1   0.0   0.00035       1.6      27      84 ..     238     296 ..     227     334 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.013
                                       EEESSSEEEEEEE-S--SS---EEEEE---HHHHHHHHHHHHHHTT--EEEEE------SSS---SS CS
                              RuvX   6 lDvGtkriGvAvsdplgilaspletierkskekdleelkelvkeeeveeiVvGlPlnldgsegesak 72 
                                       +D G+ +iGv  +  + ++ +p   ++ +     lee+k+++ + +v+  V G P++l +  g + k
  gi|242399386|ref|YP_002994810.1| 170 IDGGETKIGVESTVVDLTT-HPPMLLRPG--GLPLEEIKKVIGKVNVHPAVKGKPIKLAKAPGMKYK 233
                                       7999999999877777664.666666655..5789********************999887776655 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00035
                                       -EEEEE.---HHHHHHHHHHHHHHTT--EEEEE------SSS---SSTTHHHHHHHHHT CS
                              RuvX  27 pletie.rkskekdleelkelvkeeeveeiVvGlPlnldgsegesakkvrkfaeeLakr 84 
                                         ++i  ++++e+  +++kel+ke++ ++i vG+  + d  e+++  ++ +  ee+a++
  gi|242399386|ref|YP_002994810.1| 238 EAQVIViEGEREQVTKKIKELIKEYKKQKIRVGVMATGDFYEADAYFNIGENEEEIARN 296
                                       4555554666799********************99666666655555554444444444 PP

>> Isochorismatase  Isochorismatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1     0.019        83     115     135 ..     167     187 ..     153     189 .. 0.87
   2 ?    6.6   0.0    0.0018         8      20      52 ..     245     277 ..     235     312 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.019
                   Isochorismatase 115 tivlaGiatdvCVeatardal 135
                                       ++++ G +t ++Ve+t++d+ 
  gi|242399386|ref|YP_002994810.1| 167 ECIIDGGETKIGVESTVVDLT 187
                                       57888*************986 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0018
                   Isochorismatase  20 seeisavveninkllkaarkagipviftrdvhe 52 
                                       + e ++v ++i++l+k+++k++i+v ++   + 
  gi|242399386|ref|YP_002994810.1| 245 EGEREQVTKKIKELIKEYKKQKIRVGVMATGDF 277
                                       5678999****************9877766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       879  (0.0490267); expected 358.6 (0.02)
Passed bias filter:                      710  (0.0396006); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 2361.04
//
Query:       gi|242399387|ref|YP_002994811.1|  [L=394]
Description: hypothetical protein TSIB_1411 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0023   17.4  15.1      0.012   15.1   1.5    4.6  2  SNAP       Soluble NSF attachment protein, SNAP
  ------ inclusion threshold ------
       0.29   11.0   2.2        3.3    7.6   0.1    2.5  2  LBR_tudor  Lamin-B receptor of TUDOR domain
        1.1    9.6   6.5        6.5    7.1   0.0    4.3  5  TPR_12     Tetratricopeptide repeat
        7.2    6.6  10.3        2.8    7.9   0.1    4.4  4  TPR_1      Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> SNAP  Soluble NSF attachment protein, SNAP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   1.5   2.6e-06     0.012      32     180 ..      27     200 ..      19     202 .. 0.73
   2 ?   -1.5   6.4      0.29   1.3e+03      51     124 ..     219     293 ..     213     379 .. 0.58

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.6e-06
                                       HHHHHHHHHHHHHHHHTT-THHHHHHHHHHHHHHHHTT..-HHHHHHHHHHHHHHHHHT........-HH.....HH CS
                              SNAP  32 eeAadlyeqAAnayklakkweeAgeaflkaAecqeklk..ekdeaanayveAakcykkv........spe.....eA 93 
                                       ++  +l+++ A++y  +k++ +A++++  + ++  +++  + ++a   ++++a  y           +p+     e 
  gi|242399387|ref|YP_002994811.1|  27 KKGINLLIKSAREYEFQKRFLDAARMYRYIGDLILNVNpqDLKDARPFLLKSAYHYLDIlereieadNPNlelldEF 103
                                       56677889999999999999999999999999988865114456666666666555444454455553323344456 PP

                                       HHHHHHHHHHHHHTT-HHHHHH....HHHHHHHHHHHTT--HHHHHHHHHHHHHHHH....H...TT-HHHHHHHHH CS
                              SNAP  94 vealekAieiytekgrfrraAk....lkkeiaelyekelgdlekAieaYekAaelye....q...eeakalankcll 159
                                       ++ + + +ei+ ek++f++ Ak    ++k++++   ke ++++ Ai +Ye+A  +y+    +   ee  +    ++ 
  gi|242399387|ref|YP_002994811.1| 104 CSNVLRVFEILGEKEKFEKYAKefgvMYKNLGDTKLKE-KNIQTAIMSYETARRYYKiihyKegiEETVSILLDLFG 179
                                       66677889999******999985555799*****9999.*****************844442222444555567788 PP

                                       HHHHHHHHTT-HHHHHHHHHH CS
                              SNAP 160 kvAelsaelekyekAieiyek 180
                                       k Ae+  ++++y+kA + + k
  gi|242399387|ref|YP_002994811.1| 180 KGAEIFVSKKEYQKAGDTFFK 200
                                       999999999999999998866 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.29
                                       THHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHT-HHHHHHHHH.HHHHHHHHTT-HHHHHHHHHHHHHHH CS
                              SNAP  51 weeAgeaflkaAecqeklkekdeaanayveAakcykkvspeeAveale.kAieiytekgrfrraAklkkeiaely 124
                                       +e+Ag+ +++a++   + ++  ++a+++++A  +y   ++++ v+ +  +A +++ +     r A++ +e++e +
  gi|242399387|ref|YP_002994811.1| 219 MENAGRNYERASKEWYSKGDLYTTAKMLLNAEYSYLLADNAKRVKLVGlNASKMFYQLVEEYRRARFVNELGEAL 293
                                       567777777777776667777777777777777777766666666553266667666666666667777777654 PP

>> LBR_tudor  Lamin-B receptor of TUDOR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.2     0.022        99      30      54 ..     120     144 ..     117     145 .. 0.90
   2 ?    7.6   0.1   0.00073       3.3      26      48 ..     147     170 ..     144     173 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.022
                         LBR_tudor  30 fdekkqlYtVkykDGTelelkesdi 54 
                                       f++  +++ V yk   + +lke++i
  gi|242399387|ref|YP_002994811.1| 120 FEKYAKEFGVMYKNLGDTKLKEKNI 144
                                       7888899***************998 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00073
                         LBR_tudor  26 kvlsfdekkqlYtV.kykDGTele 48 
                                        ++s++++ + Y++ +yk G e+ 
  gi|242399387|ref|YP_002994811.1| 147 AIMSYETARRYYKIiHYKEGIEET 170
                                       69**********9636****9986 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       0.4   1.8e+03      47      69 ..      32      54 ..      23      59 .. 0.73
   2 ?    7.1   0.0    0.0014       6.5       5      33 ..     130     158 ..     126     167 .. 0.65
   3 ?    0.1   0.1      0.23     1e+03      16      50 ..     216     248 ..     212     260 .. 0.74
   4 ?   -2.5   0.0       1.5   6.5e+03      60      70 ..     288     298 ..     269     302 .. 0.58
   5 ?    1.4   0.1     0.091   4.1e+02      24      41 ..     361     378 ..     355     382 .. 0.65

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.4
                            TPR_12 47 tlrnLgrlyralgryeeAlelle 69
                                       l+  +r y+ ++r+ +A ++++
  gi|242399387|ref|YP_002994811.1| 32 LLIKSAREYEFQKRFLDAARMYR 54
                                      56666777777777777777775 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0014
                            TPR_12   5 alnnlaavlrrlgrydeAlellekaleia 33 
                                       ++ nl+++ ++ ++ + A+  +e+a++ +
  gi|242399387|ref|YP_002994811.1| 130 MYKNLGDTKLKEKNIQTAIMSYETARRYY 158
                                       55566666666666666666666665443 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.23
                            TPR_12  16 lgrydeAlellekaleiarrllGpdhpltattlrn 50 
                                       ++ ++ A +++e+a   + +   +d + ta  l n
  gi|242399387|ref|YP_002994811.1| 216 MELMENAGRNYERASKEWYSK--GDLYTTAKMLLN 248
                                       566889999999998888666..666677776666 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 1.5
                            TPR_12  60 ryeeAlellee 70 
                                       ++ eAl +l e
  gi|242399387|ref|YP_002994811.1| 288 ELGEALLMLSE 298
                                       33444444444 PP

  == domain 5  score: 1.4 bits;  conditional E-value: 0.091
                            TPR_12  24 ellekaleiarrllGpdh 41 
                                       e + +a+eia+ ++++ +
  gi|242399387|ref|YP_002994811.1| 361 EAYAQAIEIAELVFETRY 378
                                       556677777776666655 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.1   0.00062       2.8       4      27 ..     131     154 ..     129     158 .. 0.94
   2 ?   -1.2   0.0      0.49   2.2e+03      10      20 ..     184     194 ..     182     200 .. 0.73
   3 ?    1.7   0.3     0.056   2.5e+02       2      24 ..     231     253 ..     230     256 .. 0.81
   4 ?   -0.2   0.3      0.22     1e+03      14      29 ..     360     368 ..     356     371 .. 0.56

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00062
                                       HHHHHHHHHHTT-HHHHHHHHHHH CS
                             TPR_1   4 lynlGnayfklgkydeAleyyekA 27 
                                       ++nlG + +k ++ + A+  ye A
  gi|242399387|ref|YP_002994811.1| 131 YKNLGDTKLKEKNIQTAIMSYETA 154
                                       99********************98 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.49
                                       HHHHTT-HHHH CS
                             TPR_1  10 ayfklgkydeA 20 
                                       ++ ++++y++A
  gi|242399387|ref|YP_002994811.1| 184 IFVSKKEYQKA 194
                                       66678999999 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.056
                                       HHHHHHHHHHHHTT-HHHHHHHH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyy 24 
                                       k +y +G +y   +++  A+  y
  gi|242399387|ref|YP_002994811.1| 231 KEWYSKGDLYTTAKMLLNAEYSY 253
                                       68********9988887777666 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 0.22
                                       TT-HHHHHHHHHHHHH CS
                             TPR_1  14 lgkydeAleyyekALe 29 
                                        + y +A       +e
  gi|242399387|ref|YP_002994811.1| 360 REAYAQA-------IE 368
                                       5555555.......55 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       756  (0.0421663); 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:                         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 0.32s 00:00:00.98 Elapsed: 00:00:00.51
# Mc/sec: 2308.64
//
Query:       gi|242399388|ref|YP_002994812.1|  [L=68]
Description: hypothetical protein TSIB_1412 [Thermococcus sibiricus MM 739]
Scores for complete 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   31.4   0.2    1.7e-07   31.0   0.2    1.2  1  HTH_11           HTH domain
    1.6e-07   31.3   0.1      2e-07   31.0   0.1    1.1  1  HTH_20           Helix-turn-helix domain
    1.3e-06   27.8   0.1    1.6e-06   27.6   0.1    1.2  1  HTH_24           Winged helix-turn-helix DNA-binding
    9.1e-06   25.5   0.4    1.9e-05   24.5   0.4    1.7  1  HTH_12           Ribonuclease R winged-helix domain
    1.3e-05   25.0   0.1    1.7e-05   24.6   0.1    1.2  1  HTH_5            Bacterial regulatory protein, arsR family
    5.6e-05   22.9   0.2    6.6e-05   22.7   0.2    1.1  1  MarR_2           MarR family
     0.0018   18.6   0.1     0.0023   18.2   0.1    1.1  1  Rrf2             Transcriptional regulator
     0.0051   16.3   0.0     0.0065   15.9   0.0    1.1  1  RepL             Firmicute plasmid replication protein (RepL)
     0.0093   16.0   0.1      0.013   15.5   0.1    1.1  1  HTH_Mga          M protein trans-acting positive regulator (M
     0.0097   15.7   0.0      0.016   15.0   0.0    1.4  1  HTH_AsnC-type    AsnC-type helix-turn-helix domain
  ------ inclusion threshold ------
       0.01   15.5   0.1      0.013   15.1   0.1    1.2  1  GntR             Bacterial regulatory proteins, gntR family
      0.013   15.1   0.0      0.017   14.8   0.0    1.2  1  HrcA_DNA-bdg     Winged helix-turn-helix transcription repres
       0.02   15.1   0.0      0.025   14.7   0.0    1.3  1  DUF2582          Winged helix-turn-helix domain (DUF2582)
       0.02   14.9   0.1      0.036   14.1   0.1    1.5  1  Put_DNA-bind_N   Putative DNA-binding protein N-terminus
      0.027   14.3   0.0      0.036   13.8   0.0    1.2  1  HTH_IclR         IclR helix-turn-helix domain
      0.029   14.0   0.7      0.053   13.2   0.1    1.7  2  Sigma70_r4_2     Sigma-70, region 4
      0.031   14.8   0.2      0.035   14.6   0.1    1.2  1  HTH_27           Winged helix DNA-binding domain
      0.033   14.6   0.0      0.047   14.1   0.0    1.3  1  HTH_26           Cro/C1-type HTH DNA-binding domain
      0.049   13.6   0.0      0.056   13.4   0.0    1.2  1  MarR             MarR family
      0.054   13.2   0.0      0.069   12.9   0.0    1.2  1  HTH_41           Helix-turn-helix domain
      0.063   13.1   0.1      0.063   13.1   0.1    1.7  2  MerR             MerR family regulatory protein
      0.087   12.6   0.1       0.75    9.6   0.1    2.0  2  HTH_10           HTH DNA binding domain
       0.09   12.4   0.0      0.094   12.3   0.0    1.0  1  ArsR             ArsR transcriptional regulator
      0.092   12.8   0.1       0.11   12.6   0.1    1.1  1  Replic_Relax     Replication-relaxation
       0.11   12.4   0.0       0.12   12.3   0.0    1.2  1  Phage_rep_org_N  N-terminal phage replisome organiser (Phage_
       0.12   12.0   0.1       0.17   11.5   0.1    1.2  1  GerE             Bacterial regulatory proteins, luxR family
       0.15   12.2   0.0        0.2   11.8   0.0    1.2  1  HTH_9            RNA polymerase III subunit RPC82 helix-turn-
       0.16   11.9   0.1       0.23   11.5   0.1    1.2  1  HTH_36           Helix-turn-helix 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 !   31.0   0.2   2.7e-10   1.7e-07       6      55 .]       6      61 ..       3      61 .. 0.80

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 2.7e-10
                            HTH_11  6 lelLleargp.isgeeLAeeLnvSrrtvrrdIkaLeelg.....vpIesepgrGYr 55
                                      l+ +++ ++  is++eLA+++++S+rtvr  +k+L+e       + +   ++rGYr
  gi|242399388|ref|YP_002994812.1|  6 LQVFRALDDRpISSKELARKTSLSERTVRYALKILKENElveeiFFLRDARKRGYR 61
                                      66666666666************************988777777666666666776 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.1   3.1e-10     2e-07      13      56 ..       6      48 ..       3      50 .. 0.95

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 3.1e-10
                                      HHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20 13 rrilraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56
                                      + ++raL ++++ + +ela+  +ls  t++y L++L e +Lve 
  gi|242399388|ref|YP_002994812.1|  6 LQVFRAL-DDRPISSKELARKTSLSERTVRYALKILKENELVEE 48
                                      789****.**********************************96 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.1   2.4e-09   1.6e-06      14      48 .]      13      47 ..       3      47 .. 0.87

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 2.4e-09
                            HTH_24 14 knprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      ++  is +eLA+++ lS  tv++ lk L+e++l++
  gi|242399388|ref|YP_002994812.1| 13 DDRPISSKELARKTSLSERTVRYALKILKENELVE 47
                                      3555****************************996 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.4     3e-08   1.9e-05      10      49 ..      13      47 ..       6      61 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 3e-08
                            HTH_12 10 sdkpigakeiaeeLkkrgydigeravRyrLrkleergltr 49
                                       d+pi++ke+a         ++er+vRy L++l e++l++
  gi|242399388|ref|YP_002994812.1| 13 DDRPISSKELAR-----KTSLSERTVRYALKILKENELVE 47
                                      589*******95.....5689****************997 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.1   2.7e-08   1.7e-05       5      46 ..       6      47 ..       4      48 .. 0.94

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 2.7e-08
                                      HHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  5 lkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      l++ ++L +++ ++ ela+++ ls+ tv++ Lk+L+e  LVe
  gi|242399388|ref|YP_002994812.1|  6 LQVFRALDDRPISSKELARKTSLSERTVRYALKILKENELVE 47
                                      67789999*********************************8 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.2     1e-07   6.6e-05       3      61 ..       1      56 [.       1      58 [. 0.91

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1e-07
                                      --HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSSS CS
                            MarR_2  3 ltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeDkR 61
                                      ++++ ++v  aL +rp   ++ +elar++ ls  +v ++lk L +  Lve+   ++D+R
  gi|242399388|ref|YP_002994812.1|  1 MPRSALQVFRALDDRP---ISSKELARKTSLSERTVRYALKILKENELVEEIFFLRDAR 56
                                      6788899********9...*******************************976666666 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   3.6e-06    0.0023      22      56 ..      13      47 ..       4      49 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.6e-06
                                      TCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2 22 eeepvsseeiaerqnispsylekilakLrkaglvk 56
                                      +++p+ss+e+a+++++s++ ++  l+ L++++lv+
  gi|242399388|ref|YP_002994812.1| 13 DDRPISSKELARKTSLSERTVRYALKILKENELVE 47
                                      5678*****************************98 PP

>> RepL  Firmicute plasmid replication protein (RepL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0     1e-05    0.0065      78     106 ..      19      47 ..      14      50 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1e-05
                              RepL  78 nRelaeetgislktvsetlkileeanilk 106
                                       ++ela++t +s +tv+  lkil+e +++ 
  gi|242399388|ref|YP_002994812.1|  19 SKELARKTSLSERTVRYALKILKENELVE 47 
                                       689*********************99875 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 !   15.5   0.1     2e-05     0.013      16      49 ..      13      46 ..      12      52 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2e-05
                           HTH_Mga 16 eneksltldelakeLglseltlqsdiseLnel.Fp 49
                                      + ++ ++ +ela +++lse+t++  +  L+e  + 
  gi|242399388|ref|YP_002994812.1| 13 D-DRPISSKELARKTSLSERTVRYALKILKENeLV 46
                                      5.778999*******************99975444 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   2.5e-05     0.016      15      39 ..      14      38 ..      12      41 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.5e-05
                     HTH_AsnC-type 15 daRisyaeLAervGlSestvlrRvr 39
                                      d  is +eLA+++ lSe tv+  ++
  gi|242399388|ref|YP_002994812.1| 14 DRPISSKELARKTSLSERTVRYALK 38
                                      56799***************97665 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.1     2e-05     0.013      26      55 ..      18      47 ..       7      49 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2e-05
                                      -HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              GntR 26 sereLaaefgVsrttvReALrrLeaeglve 55
                                      s +eLa +   s  tvR AL+ L++  lve
  gi|242399388|ref|YP_002994812.1| 18 SSKELARKTSLSERTVRYALKILKENELVE 47
                                      679*************************97 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 ?   14.8   0.0   2.6e-05     0.017      20      55 ..      13      48 ..       3      50 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.6e-05
                      HrcA_DNA-bdg 20 kkravKgeeiAevlkrneGtvRNqlqsLkalgLveg 55
                                      ++r++ ++e+A + +  e tvR  l++Lk  +Lve 
  gi|242399388|ref|YP_002994812.1| 13 DDRPISSKELARKTSLSERTVRYALKILKENELVEE 48
                                      4899*****************************985 PP

>> DUF2582  Winged helix-turn-helix domain (DUF2582)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0     4e-05     0.025      12      43 ..       7      37 ..       3      56 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4e-05
                                      HHHHHHCCSSSEEHHHHHHHCT-SCHHHHHHH CS
                           DUF2582 12 kvwhlLnengeislkelkrktglsdkelalAi 43
                                      +v+++L++ + is kel+rkt+ls++ +  A+
  gi|242399388|ref|YP_002994812.1|  7 QVFRALDD-RPISSKELARKTSLSERTVRYAL 37
                                      89******.******************99997 PP

>> Put_DNA-bind_N  Putative DNA-binding protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   5.7e-05     0.036      19      45 ..       8      34 ..       3      35 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.7e-05
                                      HHHHTT--EE-HHHHHHHCTS-HHHHH CS
                    Put_DNA-bind_N 19 elkeegveriSSteLaealgvtaaqvR 45
                                       +++ +   iSS+eLa+++ +++ +vR
  gi|242399388|ref|YP_002994812.1|  8 VFRALDDRPISSKELARKTSLSERTVR 34
                                      555556667*****************9 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   5.7e-05     0.036       5      49 ..       5      47 ..       4      49 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.7e-05
                                      HHHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR  5 alaiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                      al++ +al  +  + + +elAr+t l+  tv+  L+ L e  +ve
  gi|242399388|ref|YP_002994812.1|  5 ALQVFRALDDR--PISSKELARKTSLSERTVRYALKILKENELVE 47
                                      56666666544..4579*********************9999998 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   0.1   8.2e-05     0.053      28      47 ..      18      37 ..      17      38 .. 0.93
   2 ?   -2.6   0.0       7.4   4.7e+03      16      23 ..      47      54 ..      44      57 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.2e-05
                                      -HHHHHHHHT--HHHHHHHH CS
                      Sigma70_r4_2 28 sykEIAellgisegtVksrl 47
                                      s kE A+++ +se+tV+++l
  gi|242399388|ref|YP_002994812.1| 18 SSKELARKTSLSERTVRYAL 37
                                      89***************988 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 7.4
                                      HHHHHHHH CS
                      Sigma70_r4_2 16 reifllry 23
                                       eif lr+
  gi|242399388|ref|YP_002994812.1| 47 EEIFFLRD 54
                                      57888875 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   5.5e-05     0.035      12      50 ..      12      48 ..       1      62 [. 0.79

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.5e-05
                            HTH_27 12 irhrrrrkkladlcgrlnvedshisyslkkLtekGLver 50
                                      +   +r+ + ++l++++ ++  ++ y+lk L e++Lve+
  gi|242399388|ref|YP_002994812.1| 12 LD--DRPISSKELARKTSLSERTVRYALKILKENELVEE 48
                                      33..556666***************************87 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   7.3e-05     0.047       5      27 ..      11      33 ..       9      45 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7.3e-05
                            HTH_26  5 lmadrgitkseLargtgisaatl 27
                                      ++ dr i+++eLar+t +s+ t+
  gi|242399388|ref|YP_002994812.1| 11 ALDDRPISSKELARKTSLSERTV 33
                                      6899****************998 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   8.7e-05     0.056      16      48 ..      15      47 ..       8      57 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.7e-05
                                      TTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR 16 gplsvseLakklgvskstvtrvldrLekkGlie 48
                                       p+s +eLa+k ++s  tv  +l+ L +++l+e
  gi|242399388|ref|YP_002994812.1| 15 RPISSKELARKTSLSERTVRYALKILKENELVE 47
                                      58999**************************98 PP

>> HTH_41  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00011     0.069      10      36 ..      20      46 ..      14      49 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
                            HTH_41 10 eelakeleLSvGlvQkALklLeddkai 36
                                      +ela + +LS  +v  ALk L+++  +
  gi|242399388|ref|YP_002994812.1| 20 KELARKTSLSERTVRYALKILKENELV 46
                                      69********************99877 PP

>> MerR  MerR family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   9.9e-05     0.063       2      18 ..      19      35 ..      18      35 .. 0.93
   2 ?   -2.5   1.0       7.2   4.6e+03      33      37 ..      58      62 ..      53      62 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.9e-05
                                      HHHHHHHHTTTHHHHHH CS
                              MerR  2 IgevAeltGvsprtLRy 18
                                       +e+A++t +s rt+Ry
  gi|242399388|ref|YP_002994812.1| 19 SKELARKTSLSERTVRY 35
                                      58**************9 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 7.2
                                      TSSEE CS
                              MerR 33 gGyRl 37
                                       GyR+
  gi|242399388|ref|YP_002994812.1| 58 RGYRR 62
                                      59997 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1    0.0012      0.75      21      46 ..      14      39 ..      13      45 .. 0.89
   2 ?    1.0   0.0      0.61   3.9e+02       8      17 ..      51      60 ..      47      61 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0012
                            HTH_10 21 PRrvtlkeLAkelGIskstlsehLrk 46
                                      +R +++keLA +  +s+ t+ + L+ 
  gi|242399388|ref|YP_002994812.1| 14 DRPISSKELARKTSLSERTVRYALKI 39
                                      5889******************9985 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.61
                            HTH_10  8 vlklAyemGY 17
                                      +l+ A + GY
  gi|242399388|ref|YP_002994812.1| 51 FLRDARKRGY 60
                                      7999*****9 PP

>> ArsR  ArsR transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00015     0.094      21      59 ..       7      48 ..       2      62 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00015
                              ArsR 21 kvyeelskeWlteeeleeklgee...veealklLkkikliEs 59
                                      +v+++l ++ ++ +el+ k+  +   v+ alk+Lk+ +l+E+
  gi|242399388|ref|YP_002994812.1|  7 QVFRALDDRPISSKELARKTSLSertVRYALKILKENELVEE 48
                                      89**************998754334699*************8 PP

>> Replic_Relax  Replication-relaxation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   0.00017      0.11       8      52 ..      15      59 ..      10      65 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00017
                      Replic_Relax  8 rvlTtrqiarllfashratarrrLarLrelgllsr.lrkrvggarg 52
                                      r+ +++ +ar +  s+r+ +r +L++L+e++l++  +  r+ ++rg
  gi|242399388|ref|YP_002994812.1| 15 RPISSKELARKTSLSERT-VRYALKILKENELVEEiFFLRDARKRG 59
                                      78999*************.***************987666444444 PP

>> Phage_rep_org_N  N-terminal phage replisome organiser (Phage_rep_org_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00019      0.12      53      85 ..      16      48 ..       4      57 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00019
                   Phage_rep_org_N 53 pytaemlalifnreletvrlaLkvlkdleliei 85
                                      p   ++la  ++    tvr aLk+lk+ el+e 
  gi|242399388|ref|YP_002994812.1| 16 PISSKELARKTSLSERTVRYALKILKENELVEE 48
                                      6678999************************96 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00026      0.17      19      39 ..      18      38 ..      17      42 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00026
                                      -HHHHHHHHTS-HHHHHHHHH CS
                              GerE 19 snkeIAeelniSekTVkvhks 39
                                      s+ke A++ ++Se+TV++ ++
  gi|242399388|ref|YP_002994812.1| 18 SSKELARKTSLSERTVRYALK 38
                                      78**************98765 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 ?   11.8   0.0   0.00032       0.2      29      57 ..      18      46 ..      12      50 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00032
                                      EHHHHHHHHSSTHHHHHHHHHHHHHTTSE CS
                             HTH_9 29 tlrelvkktkLsldqVkksLvvLiqhrlV 57
                                      +++el++kt+Ls + V+ +L +L  + lV
  gi|242399388|ref|YP_002994812.1| 18 SSKELARKTSLSERTVRYALKILKENELV 46
                                      789*****************999877777 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00035      0.23      29      52 ..      20      43 ..      16      46 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00035
                            HTH_36 29 etlakrlglsknTvsraikeLeql 52
                                      + la+++ ls++Tv+ a+k L + 
  gi|242399388|ref|YP_002994812.1| 20 KELARKTSLSERTVRYALKILKEN 43
                                      78*****************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); 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: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 431.71
//
Query:       gi|242399389|ref|YP_002994813.1|  [L=236]
Description: hypothetical protein TSIB_1413 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.17   11.8   0.8       0.44   10.5   0.8    1.7  1  YqbF      YqbF, hypothetical protein domain


Domain annotation for each model (and alignments):
>> YqbF  YqbF, hypothetical protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.8   2.4e-05      0.44      17      36 ..     133     152 ..     129     161 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 2.4e-05
                                       -EEEE-HHHHHHHHHSTTEE CS
                              YqbF  17 veedVekeiynYLqdnefFe 36 
                                       +e+ +ek i ++L++n fF 
  gi|242399389|ref|YP_002994813.1| 133 KEKSIEKQITEILRKNFFFR 152
                                       7999**************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); 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 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1715.55
//
Query:       gi|242399390|ref|YP_002994814.1|  [L=143]
Description: hypothetical protein TSIB_1414 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.53
# Mc/sec: 813.63
//
Query:       gi|242399391|ref|YP_002994815.1|  [L=137]
Description: hypothetical protein TSIB_1415 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); 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 0.33s 00:00:00.85 Elapsed: 00:00:00.52
# Mc/sec: 790.82
//
Query:       gi|242399392|ref|YP_002994816.1|  [L=235]
Description: Nucleotidyltransferase [Thermococcus sibiricus MM 739]
Scores for complete 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   34.6   0.1    4.3e-08   33.3   0.1    1.9  1  NTP_transf_2  Nucleotidyltransferase domain
    3.8e-05   23.7   0.1    0.00013   22.0   0.1    1.9  1  Polbeta       Polymerase beta, Nucleotidyltransferase
    0.00035   20.9   0.0    0.00068   19.9   0.0    1.4  1  DUF4269       Domain of unknown function (DUF4269)


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 !   33.3   0.1   7.2e-12   4.3e-08       3      64 ..      31      86 ..      29     187 .. 0.85

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 7.2e-12
                                      HHHHHHHHHTTTSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEE CS
                      NTP_transf_2  3 klleelkelepvakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfle 64
                                      k+l+++k+l    + +++GS+arG+ +k+SDiD+++ ++ ++       ++ +l  +++  +
  gi|242399392|ref|YP_002994816.1| 31 KALQIMKKLA-QFDPHVYGSVARGDVRKDSDIDIVIPYKVPSF-----LIEHALENMPFQKK 86
                                      7888999888.99999*************************54.....45555554444444 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.1   2.1e-08   0.00013      18      41 ..      46      69 ..      30      88 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 2.1e-08
                                      EEEEEE-S------EEEEEEEESS CS
                           Polbeta 18 lFGSrakgkareeSDiDlavllke 41
                                      ++GS+a+g+ r++SDiD+ + +k 
  gi|242399392|ref|YP_002994816.1| 46 VYGSVARGDVRKDSDIDIVIPYKV 69
                                      8*****************998775 PP

>> DUF4269  Domain of unknown function (DUF4269)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   1.1e-07   0.00068       5      50 ..      32      77 ..      29      92 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.1e-07
                           DUF4269  5 elkvlekLkefepvlvgtipididveesDlDiicevedleafkaal 50
                                       l++++kL++f+p++ g+++ +  +++sD+Di++ ++ ++ + +++
  gi|242399392|ref|YP_002994816.1| 32 ALQIMKKLAQFDPHVYGSVARGDVRKDSDIDIVIPYKVPSFLIEHA 77
                                      689*******************99**********999888776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); 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: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1690.08
//
Query:       gi|242399393|ref|YP_002994817.1|  [L=502]
Description: hypothetical protein TSIB_1417 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-15   56.5  16.8    0.00098   19.4   0.9    6.7  6  DUF5122         Domain of unknown function (DUF5122) beta-pro
    1.2e-05   24.4   1.6     0.0015   17.5   0.3    3.0  2  Arylsulfotrans  Arylsulfotransferase (ASST)
     0.0048   17.2   3.6         12    6.3   0.0    4.1  3  Kelch_3         Galactose oxidase, central domain
     0.0071   16.3   3.6        4.5    7.3   0.0    4.2  4  Peptidase_S24   Peptidase S24-like
  ------ inclusion threshold ------
      0.093   12.8  20.2        8.3    6.7   0.1    6.2  6  NHL             NHL repeat
       0.11   13.1  16.6       0.28   11.7   0.3    5.1  5  PQQ_3           PQQ-like domain
        0.4   11.0   1.5         16    5.8   0.1    3.0  3  TonB_2          TonB C terminal
       0.81    9.7   0.0       0.81    9.7   0.0    4.0  4  Kelch_4         Galactose oxidase, central domain
        3.5    7.6   6.5         28    4.7   0.4    3.3  3  DUF5643         Family of unknown function (DUF5643)


Domain annotation for each model (and alignments):
>> DUF5122  Domain of unknown function (DUF5122) beta-propeller
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   6.1e-05      0.12       2      32 ..      56      86 ..      55      86 .. 0.87
   2 ?    1.4   0.0       0.2     4e+02       2      30 ..     105     135 ..     104     136 .. 0.78
   3 !   19.4   0.9   4.9e-07   0.00098       2      32 ..     213     242 ..     212     242 .. 0.95
   4 !   14.3   0.2   1.9e-05     0.039       2      32 ..     263     292 ..     262     292 .. 0.92
   5 !    7.1   0.1    0.0034       6.7       2      16 ..     313     327 ..     312     337 .. 0.83
   6 !    7.8   0.3     0.002         4       2      13 ..     365     376 ..     364     380 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.1e-05
                           DUF5122  2 pDGKIlVaGsftsyngssdfalvRLnaDGsl 32
                                      pDG I+VaG ++ +   s+f + + + +G+l
  gi|242399393|ref|YP_002994817.1| 56 PDGEIIVAGHTYFDWWHSNFLIFKTDENGTL 86
                                      9***********7788888888888888887 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.2
                           DUF5122   2 pDGKIlVaGsftsy..ngssdfalvRLnaDG 30 
                                       p+G  l++G+++     ++ +  + R+++ G
  gi|242399393|ref|YP_002994817.1| 105 PNGDTLAVGYSYAFmgLYPDSLTISRFDSEG 135
                                       788899******5568888888888888777 PP

  == domain 3  score: 19.4 bits;  conditional E-value: 4.9e-07
                           DUF5122   2 pDGKIlVaGsftsyngssdfalvRLnaDGsl 32 
                                       ++G I+VaG+++ +++  df ++RL+ +G+l
  gi|242399393|ref|YP_002994817.1| 213 SNGDIIVAGDSG-NDYAKDFLVLRLDENGNL 242
                                       7899********.99**************97 PP

  == domain 4  score: 14.3 bits;  conditional E-value: 1.9e-05
                           DUF5122   2 pDGKIlVaGsftsyngssdfalvRLnaDGsl 32 
                                       p+G I+VaG +  ++  +d  ++RL+++G++
  gi|242399393|ref|YP_002994817.1| 263 PNGDIVVAGQTE-NGEYNDAWVIRLDSNGNI 292
                                       89**********.88999999********85 PP

  == domain 5  score: 7.1 bits;  conditional E-value: 0.0034
                           DUF5122   2 pDGKIlVaGsftsyn 16 
                                       +DG I+++G+++s +
  gi|242399393|ref|YP_002994817.1| 313 SDGGIVLVGYTNSFG 327
                                       8***********763 PP

  == domain 6  score: 7.8 bits;  conditional E-value: 0.002
                           DUF5122   2 pDGKIlVaGsft 13 
                                       p+G I+VaG+++
  gi|242399393|ref|YP_002994817.1| 365 PNGNIVVAGWSG 376
                                       89********98 PP

>> Arylsulfotrans  Arylsulfotransferase (ASST)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.019        37      29     105 ..      76     152 ..      53     174 .. 0.74
   2 !   17.5   0.3   7.7e-07    0.0015      27     107 ..     280     373 ..     209     378 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.019
                    Arylsulfotrans  29 nnlivDtkGevrWyldqdkisdnk.lkrlkngkllilsgqklaefdllGr...vikeyrlpggyidlhHdivelpng 101
                                         + +D++G ++W  +   +  +  +k l ng+ l++     +++ ++G     ++  r++ + +dl H ++  p+ 
  gi|242399393|ref|YP_002994817.1|  76 LIFKTDENGTLKWNRTLTYSDVAYaVKVLPNGDTLAV----GYSYAFMGLypdSLTISRFDSEGNDLEHYYYSVPDA 148
                                       4567899999999876655444335999999999954....355555555444777778888889999999999998 PP

                    Arylsulfotrans 102 nllv 105
                                       n+++
  gi|242399393|ref|YP_002994817.1| 149 NVVL 152
                                       8876 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 7.7e-07
                    Arylsulfotrans  27 kknnlivDtkGevrWyldqdkisdnk...lkrlkngkllilsg..........qklaefdllGrvikeyrlpggyid 90 
                                       ++ ++ +D +G+++W  +   + ++    ++ l++g ++++              +  +d  G+v  +y  +gg +d
  gi|242399393|ref|YP_002994817.1| 280 DAWVIRLDSNGNIIWQKQFGGSGEDGvnsITVLSDGGIVLVGYtnsfgasnmdAWVLVLDSSGNVKWNYIYDGGSYD 356
                                       4455668999999999988888876677799999998887766899***9986667889****************** PP

                    Arylsulfotrans  91 lhHdivelpngnllvlv 107
                                       + H++++ pngn++v++
  gi|242399393|ref|YP_002994817.1| 357 AAHSVDVVPNGNIVVAG 373
                                       *************9975 PP

>> Kelch_3  Galactose oxidase, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.049        97      16      30 ..     176     190 ..     171     208 .. 0.75
   2 !    6.3   0.0     0.006        12      11      34 ..     221     247 ..     217     256 .. 0.87
   3 ?    5.2   0.4     0.013        26       9      32 ..     271     295 ..     267     308 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.049
                           Kelch_3  16 drlndvyvydldtnt 30 
                                        ++ dv+v+ ld+n 
  gi|242399393|ref|YP_002994817.1| 176 LPEEDVWVLKLDKNA 190
                                       67789********94 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.006
                           Kelch_3  11 gddgqdrlndvyvydldtn...tWaei 34 
                                       gd+g+d+ +d++v+ ld n   +W+++
  gi|242399393|ref|YP_002994817.1| 221 GDSGNDYAKDFLVLRLDENgnlKWQKT 247
                                       567*************99999999986 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.013
                           Kelch_3   9 Glgddgqdrlndvyvydldtn...tWa 32 
                                       G +   +  +nd +v+ ld+n    W+
  gi|242399393|ref|YP_002994817.1| 271 GQT--ENGEYNDAWVIRLDSNgniIWQ 295
                                       555..68889**********9877776 PP

>> Peptidase_S24  Peptidase S24-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       2.2   4.3e+03       4      18 ..      48      62 ..      47      67 .. 0.76
   2 !    6.1   0.1    0.0053        11      24      46 ..     211     231 ..     156     255 .. 0.69
   3 !    7.3   0.0    0.0023       4.5      12      55 ..     263     307 ..     260     318 .. 0.90
   4 ?   -0.3   0.0      0.52     1e+03      26      39 ..     365     378 ..     348     385 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.2
                                      SSTTCCTXXTTXEEE CS
                     Peptidase_S24  4 GdSMeptlldGdlil 18
                                      G+S  +  +dG++i+
  gi|242399393|ref|YP_002994817.1| 48 GGSLVDVTPDGEIIV 62
                                      778888888888887 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0053
                                       ---TTSEEEEEETTCE-EEEEEE CS
                     Peptidase_S24  24 epkrGdivvfrlpgeeeayiKrv 46 
                                        + +Gdi+v+ + g+  +y K +
  gi|242399393|ref|YP_002994817.1| 211 MASNGDIIVAGDSGN--DYAKDF 231
                                       6789******99999..677765 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0023
                                       XTTXEEEEECTS---TTSEEEEEETTCE.-EEEEEEEEETTEEEE CS
                     Peptidase_S24  12 ldGdlilVdkfsepkrGdivvfrlpgee.eayiKrviglpgdrvl 55 
                                       ++Gd+++  ++++ +  d  v+rl+ +  +++ K++ g ++d v 
  gi|242399393|ref|YP_002994817.1| 263 PNGDIVVAGQTENGEYNDAWVIRLDSNGnIIWQKQFGGSGEDGVN 307
                                       689999999999999999999999999989999999999999886 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 0.52
                                       -TTSEEEEEETTCE CS
                     Peptidase_S24  26 krGdivvfrlpgee 39 
                                        +G ivv+ + g++
  gi|242399393|ref|YP_002994817.1| 365 PNGNIVVAGWSGGD 378
                                       5899****999986 PP

>> NHL  NHL repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1     0.062   1.2e+02       7      18 ..      52      63 ..      52      63 .. 0.92
   2 ?    6.7   0.1    0.0042       8.3       4      18 ..     206     220 ..     204     225 .. 0.86
   3 ?    6.2   0.1     0.006        12       7      18 ..     259     270 ..     258     276 .. 0.88
   4 ?   -1.5   0.1       1.6   3.3e+03       7      16 ..     284     293 ..     279     293 .. 0.79
   5 ?   -0.2   0.4      0.63   1.3e+03       6      16 ..     308     318 ..     305     321 .. 0.71
   6 ?    6.4   0.6     0.005       9.9       5      18 ..     359     372 ..     357     372 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.062
                                      EEEETTTEEEEE CS
                               NHL  7 vavdsnGdiyVa 18
                                      v v+++G+i+Va
  gi|242399393|ref|YP_002994817.1| 52 VDVTPDGEIIVA 63
                                      7899*******8 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0042
                                       EEEEEEETTTEEEEE CS
                               NHL   4 PhGvavdsnGdiyVa 18 
                                       ++ va+ snGdi+Va
  gi|242399393|ref|YP_002994817.1| 206 AWAVAMASNGDIIVA 220
                                       688***********8 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.006
                                       EEEETTTEEEEE CS
                               NHL   7 vavdsnGdiyVa 18 
                                       vav +nGdi+Va
  gi|242399393|ref|YP_002994817.1| 259 VAVAPNGDIVVA 270
                                       89*********9 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 1.6
                                       EEEETTTEEE CS
                               NHL   7 vavdsnGdiy 16 
                                       +++dsnG+i+
  gi|242399393|ref|YP_002994817.1| 284 IRLDSNGNII 293
                                       8899***996 PP

  == domain 5  score: -0.2 bits;  conditional E-value: 0.63
                                       EEEEETTTEEE CS
                               NHL   6 GvavdsnGdiy 16 
                                       +++v+s+G i+
  gi|242399393|ref|YP_002994817.1| 308 SITVLSDGGIV 318
                                       68999777665 PP

  == domain 6  score: 6.4 bits;  conditional E-value: 0.005
                                       EEEEEETTTEEEEE CS
                               NHL   5 hGvavdsnGdiyVa 18 
                                       h+v v++nG+i+Va
  gi|242399393|ref|YP_002994817.1| 359 HSVDVVPNGNIVVA 372
                                       99***********8 PP

>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1       0.1     2e+02       1      18 [.      84     111 ..      84     127 .. 0.68
   2 ?   -1.8   0.0       2.6   5.1e+03      17      31 ..     211     224 ..     202     227 .. 0.61
   3 ?    3.9   0.0      0.04        80       1      27 [.     240     271 ..     240     288 .. 0.72
   4 ?   11.7   0.3   0.00014      0.28       1      31 [.     290     333 ..     290     341 .. 0.65
   5 ?    2.1   1.9      0.15   3.1e+02       1      31 [.     342     376 ..     342     379 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.1
                             PQQ_3   1 GevlWsvqlpg.pvnssp.........a 18 
                                       G+++W+++l + +v +++         a
  gi|242399393|ref|YP_002994817.1|  84 GTLKWNRTLTYsDVAYAVkvlpngdtlA 111
                                       99*****999888877776433333333 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.6
                             PQQ_3  17 pavdgglvyvgtgdG 31 
                                       +a  g+++++g++ G
  gi|242399393|ref|YP_002994817.1| 211 MASNGDIIVAGDS-G 224
                                       3555677777765.4 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.04
                             PQQ_3   1 GevlWsvqlpg...pvnsspavd..gglvyvg 27 
                                       G ++W+++++    ++ +++av+  g++v++g
  gi|242399393|ref|YP_002994817.1| 240 GNLKWQKTFDKnneDIAYAVAVApnGDIVVAG 271
                                       889****8865556999999998646666655 PP

  == domain 4  score: 11.7 bits;  conditional E-value: 0.00014
                             PQQ_3   1 GevlWsvqlpgpvnssp....av.dgglvyvgtg........dG 31 
                                       G ++W++q++g +  ++    ++ dgg+v vg +        d 
  gi|242399393|ref|YP_002994817.1| 290 GNIIWQKQFGGSGEDGVnsitVLsDGGIVLVGYTnsfgasnmDA 333
                                       889*******9777777777855255666665445555555555 PP

  == domain 5  score: 2.1 bits;  conditional E-value: 0.15
                             PQQ_3   1 GevlWsv..qlpg.pvnssp.avdgglvyvgtgdG 31 
                                       G v+W++  + ++ ++  s+ +v +g ++v+++ G
  gi|242399393|ref|YP_002994817.1| 342 GNVKWNYiyDGGSyDAAHSVdVVPNGNIVVAGWSG 376
                                       889****774444477677788899*****99966 PP

>> TonB_2  TonB C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.0         9   1.8e+04      32      41 ..      52      61 ..      52      63 .. 0.78
   2 ?    3.1   0.1     0.058   1.2e+02      15      48 ..     243     276 ..     232     283 .. 0.69
   3 ?    5.8   0.1    0.0081        16      16      58 ..     294     335 ..     279     338 .. 0.82

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 9
                            TonB_2 32 itidpdGeiv 41
                                      + ++pdGei+
  gi|242399393|ref|YP_002994817.1| 52 VDVTPDGEII 61
                                      5689****84 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.058
                            TonB_2  15 nwafpsqisgnleavveitidpdGeiv.svrlvks 48 
                                       +w++ ++ ++n      + ++p+G iv + + ++ 
  gi|242399393|ref|YP_002994817.1| 243 KWQKTFD-KNNEDIAYAVAVAPNGDIVvAGQTENG 276
                                       3955555.99999************9545555554 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.0081
                            TonB_2  16 wafpsqisgnleavveitidpdGeivsvrlvksSgneafDkav 58 
                                       w+++++  ++   v +it+  dG iv v  ++s g + +D+ v
  gi|242399393|ref|YP_002994817.1| 294 WQKQFG-GSGEDGVNSITVLSDGGIVLVGYTNSFGASNMDAWV 335
                                       866666.88899999*********************9999866 PP

>> Kelch_4  Galactose oxidase, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1         2   3.9e+03       8      19 ..      52      64 ..      48      64 .. 0.76
   2 ?    9.7   0.0   0.00041      0.81       7      39 ..     258     289 ..     256     296 .. 0.81
   3 ?    1.5   0.3      0.15     3e+02      18      30 ..     298     314 ..     298     321 .. 0.82
   4 ?   -2.1   0.1         2   3.9e+03       5      19 ..     359     373 ..     358     373 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2
                           Kelch_4  8 tsi.pdgtiylfG 19
                                      + + pdg+i++ G
  gi|242399393|ref|YP_002994817.1| 52 VDVtPDGEIIVAG 64
                                      55559*****998 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00041
                           Kelch_4   7 atsi.pdgtiylfGGrgedgtllndlylldlstn 39 
                                       a+++ p+g+i+ + G++e+g  +nd++++ l +n
  gi|242399393|ref|YP_002994817.1| 258 AVAVaPNGDIV-VAGQTENG-EYNDAWVIRLDSN 289
                                       77887889999.9******6.*******988776 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.15
                           Kelch_4  18 fGGrgedg....tllnd 30 
                                       fGG gedg    t+l+d
  gi|242399393|ref|YP_002994817.1| 298 FGGSGEDGvnsiTVLSD 314
                                       89999999777777776 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 2
                           Kelch_4   5 hsatsipdgtiylfG 19 
                                       hs+ ++p+g+i++ G
  gi|242399393|ref|YP_002994817.1| 359 HSVDVVPNGNIVVAG 373
                                       5555789*****998 PP

>> DUF5643  Family of unknown function (DUF5643)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.2     0.043        86      46      88 ..     208     255 ..     188     267 .. 0.70
   2 ?    4.7   0.4     0.014        28      44      72 ..     275     305 ..     266     313 .. 0.64
   3 ?    0.9   0.0      0.21   4.3e+02      47      71 ..     330     357 ..     320     365 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.043
                           DUF5643  46 k.....sldfevvDdkGnelegisgggsgtgkkefeyeitfepldenp 88 
                                             + d+ v  d Gn + +       + +++ ++ +tf++++e++
  gi|242399393|ref|YP_002994817.1| 208 AvamasNGDIIVAGDSGNDYAKDFLVLRLDENGNLKWQKTFDKNNEDI 255
                                       256665666888899999999655577777799***********8875 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.014
                           DUF5643  44 keksld.fevv.DdkGnelegisgggsgtgk 72 
                                       ++++ d + +  D +Gn++ +++ ggsg+++
  gi|242399393|ref|YP_002994817.1| 275 NGEYNDaWVIRlDSNGNIIWQKQFGGSGEDG 305
                                       333233255545******8878999999993 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.21
                           DUF5643  47 sld.f.evvDdkGne.legisgggsgtg 71 
                                       ++d +  v D  Gn+ +++i  ggs + 
  gi|242399393|ref|YP_002994817.1| 330 NMDaWvLVLDSSGNVkWNYIYDGGSYDA 357
                                       455552567****999**9888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (502 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.65u 0.28s 00:00:00.93 Elapsed: 00:00:00.48
# Mc/sec: 3151.98
//
Query:       gi|242399394|ref|YP_002994818.1|  [L=108]
Description: Mannose-6-phosphate isomerase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-10   40.4   0.1    2.3e-10   40.0   0.1    1.1  1  Cupin_2       Cupin domain
    6.1e-06   25.9   0.0    6.1e-06   25.9   0.0    1.2  1  3-HAO         3-hydroxyanthranilic acid dioxygenase
     0.0082   15.8   0.0      0.012   15.2   0.0    1.3  1  Cupin_1       Cupin
  ------ inclusion threshold ------
      0.013   15.2   0.0      0.017   14.8   0.0    1.2  1  Cupin_3       Protein of unknown function (DUF861)
      0.018   14.8   0.0      0.019   14.7   0.0    1.1  1  Cupin_6       Cupin
       0.11   12.7   0.0       0.21   11.8   0.0    1.5  2  CENP-C_C      Mif2/CENP-C like
       0.11   12.4   0.1       0.14   12.1   0.1    1.1  1  AraC_binding  AraC-like ligand binding domain
       0.13   11.7   0.1       0.16   11.4   0.1    1.2  1  Cupin_4       Cupin superfamily protein


Domain annotation for each model (and alignments):
>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   0.1     1e-13   2.3e-10      12      61 ..      41      91 ..      33      99 .. 0.88

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 1e-13
                                      EEECSSSEEEEEEEEESEEEEE.ECTEEEEEETTEEEEE-TT-EEEEEE-S CS
                           Cupin_2 12 pshrHpgedeffyVleGegelt.vdgeeveleaGdsvyfpagtpHrfrNtg 61
                                       +h H++ede+fyV +G ++++  d  +++l++G+++++p+g++H  +  +
  gi|242399394|ref|YP_002994818.1| 41 HWHKHTNEDELFYVYRGSIVIQlRDFPDIVLHEGEMALVPRGVEHCPKALE 91
                                      59********************88899******************987655 PP

>> 3-HAO  3-hydroxyanthranilic acid dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   2.7e-09   6.1e-06      46     107 ..      40      99 ..       1     108 [] 0.71

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 2.7e-09
                                       S-EEE.-SS-EEEEEEES-EEEEEEETTCCCEEEE-TTEEEEE-TT--EEEEE-TT-EEEEEE CS
                             3-HAO  46 kdyhl.eegeeffyqkkGdmvlkvldegkardivireGeifllParvphsPqrfadsvGlvve 107
                                         +h   + +e+fy  +G++v+++ d     div++eGe+ l+P  v+h P+ +  s  l+ e
  gi|242399394|ref|YP_002994818.1|  40 YHWHKhTNEDELFYVYRGSIVIQLRD---FPDIVLHEGEMALVPRGVEHCPKALEPSYVLMFE 99 
                                       23333134579*********998875...78********************988777666655 PP

>> Cupin_1  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   5.6e-06     0.012      47     103 ..      41      91 ..      29     100 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.6e-06
                                       EEEEESSS-EEEEEEESEEEEEEEETTSS.EEEEEE.EETTEEEEE-TT-EEEEEEES CS
                           Cupin_1  47 lPhyhpnateiayvlqGegrvgfvvpgngnrdfhkk.lreGdvfvvPaglvhfqynsg 103
                                         h h+n  e++yv  G+  +++        df    l+eG++  vP+g+ h+ ++ +
  gi|242399394|ref|YP_002994818.1|  41 HWHKHTNEDELFYVYRGSIVIQLR-------DFPDIvLHEGEMALVPRGVEHCPKALE 91 
                                       557789************994333.......444444***************988874 PP

>> Cupin_3  Protein of unknown function (DUF861)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   7.5e-06     0.017      17      61 ..      38      84 ..      33      95 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 7.5e-06
                                      EEEEECESS..EEEEEEEECEEEEEETTTEEEEEETTEEEEE-TTEE CS
                           Cupin_3 17 Gkfrltyee..dEfcyileGevkvtpeggetvelraGDlvvlpkgls 61
                                      G+++++  +  dE++y+ +G + +   +  ++ l +G ++ +p g +
  gi|242399394|ref|YP_002994818.1| 38 GEYHWHKHTneDELFYVYRGSIVIQLRDFPDIVLHEGEMALVPRGVE 84
                                      66666654434********************************9986 PP

>> Cupin_6  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   8.4e-06     0.019      33      72 ..      48      86 ..      21     103 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 8.4e-06
                           Cupin_6 33 glalhvvlrGscwlidpasgepvrLsagdvvllpggephv 72
                                      + +l+ v rGs+ +++ +    + L++g+++l+p+g +h+
  gi|242399394|ref|YP_002994818.1| 48 EDELFYVYRGSIVIQLRD-FPDIVLHEGEMALVPRGVEHC 86
                                      357999*********666.567****************97 PP

>> CENP-C_C  Mif2/CENP-C like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       2.1   4.8e+03      63      72 ..      23      32 ..      20      42 .. 0.79
   2 ?   11.8   0.0   9.5e-05      0.21      31      70 ..      47      86 ..      32      98 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.1
                                      E-TT-EEEEE CS
                          CENP-C_C 63 vPagneysie 72
                                      v + ney i+
  gi|242399394|ref|YP_002994818.1| 23 VARINEYVIR 32
                                      6788999886 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 9.5e-05
                                      -SEEEEEEEEESEEEEEETTEE.EEEETT-EEEE-TT-EEE CS
                          CENP-C_C 31 kkatlvFyViqGrvevtvskts.fvigkgsvFqvPagneys 70
                                      +++   FyV++G + +++ +    v+ +g + +vP+g e +
  gi|242399394|ref|YP_002994818.1| 47 NED-ELFYVYRGSIVIQLRDFPdIVLHEGEMALVPRGVEHC 86
                                      444.46*************975278899********98765 PP

>> AraC_binding  AraC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   6.1e-05      0.14      15      59 ..      40      85 ..      31     102 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.1e-05
                                      SEEEETT-SEEEEEEEEE-EEEEETTEE.EEE-TT-EEEE-TTS-E CS
                      AraC_binding 15 sfpphvhdeyvihyvteGtgrlrlngrt.ydlgpGdlfLlppgepH 59
                                       ++ ++ +e ++ yv +G+  ++l++     l++G++ L+p+g+ H
  gi|242399394|ref|YP_002994818.1| 40 YHWHKHTNEDELFYVYRGSIVIQLRDFPdIVLHEGEMALVPRGVEH 85
                                      3333344499************8888777***************99 PP

>> Cupin_4  Cupin superfamily protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   7.1e-05      0.16     174     202 ..      65      93 ..      36      98 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7.1e-05
                                       -SEEEEE-TT-EEEE-TT-EEEEEBBT-C CS
                           Cupin_4 174 pvedfvLepGDlLYlPrgviHqgvaedes 202
                                          d+vL  G +  +Prgv H+++a+++s
  gi|242399394|ref|YP_002994818.1|  65 DFPDIVLHEGEMALVPRGVEHCPKALEPS 93 
                                       4559*********************9977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       267  (0.0148921); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 796.17
//
Query:       gi|242399395|ref|YP_002994819.1|  [L=278]
Description: Purine-nucleoside phosphorylase [Thermococcus sibiricus MM 739]
Scores for complete 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-52  178.4   0.0    1.4e-52  178.3   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 !  178.3   0.0   7.9e-57   1.4e-52       1     233 [.      15     258 ..      15     259 .. 0.96

  Alignments for each domain:
  == domain 1  score: 178.3 bits;  conditional E-value: 7.9e-57
                                       CEEEEESSH....HHHHHHHHHEEEEEEEEEE.TTEEEEEEEETTEEE.EEEE--....SSHHHHHHHHHHHHHHHC CS
                         PNP_UDP_1   1 kiaiivgsp....gevellaespleetpfgregrgfkfvtGtlkgkpv.vivstG....iGkpnaavvaeirllkef 68 
                                       +iaii+gs+      +e+l+e+   +tp+g+     k+ +Gt+kg+++ +++++G    + ++ ++++a+i+ l+e+
  gi|242399395|ref|YP_002994819.1|  15 RIAIIGGSGvydpRLLENLREE-MIKTPYGNI----KVKIGTYKGEEIaFLARHGekhsVPPHKINYRANIWGLHEL 86 
                                       69*******9885556666666.*********....*******9999879*************************** PP

                                       --SEEEEEEEEEESSTTT-TT-EEEEEEEEESSSCCGCCTHHCC.......TCCCCTTSSEE--HHHHHHHHHCHHT CS
                         PNP_UDP_1  69 gvkaiiriGtaGglnpdlkvGDvvipddainfdgrsplygpkee.......gqyfpdsydapadpelrallkeaaea 138
                                       gv++i++++++G++n+++k+GD+vi d++i+f+  +++++++ e       ++ ++d++d+ ++pelr+ l +aa++
  gi|242399395|ref|YP_002994819.1|  87 GVERILATSAVGSVNEAMKPGDFVILDQLIDFTKNRTYTFYDGEdaphernFVAHVDFTDP-YCPELRDSLIRAARE 162
                                       *************************************************************.*************** PP

                                       TTTTEEE.EEEEEESESS-CHHHHHHHHHHTC-CEEESSHHHHHHHHHHTT--EEEEEEEEETTTBETTCTCH.HCC CS
                         PNP_UDP_1 139 lgikvhr.GvvatadgfyaeteaelrllrrlgadaveMEtaavaqlArelgipfaairvvsdlaaggadaeatheev 214
                                       lg  +h  G++a+++g+++et+ae+r+lr lgad+v+M+ +++a+lArel++++a++++v+++ ag+   + th ev
  gi|242399395|ref|YP_002994819.1| 163 LGFSYHPrGTYAAMEGPRFETRAEIRALRILGADVVGMTQSPEAILARELEMCYASVAIVTNYGAGISKTKLTHSEV 239
                                       **999999********************************************************************* PP

                                       CHHHHHHHHHHHHHHHHHH CS
                         PNP_UDP_1 215 eefaqeaaknaaalllall 233
                                        e +q+ ++ ++ ll++++
  gi|242399395|ref|YP_002994819.1| 240 VELMQQKSEEIKLLLMKAV 258
                                       ***********99998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1754.39
//
Query:       gi|242399396|ref|YP_002994820.1|  [L=348]
Description: hypothetical protein TSIB_1420 [Thermococcus sibiricus MM 739]
Scores for complete 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   21.4   0.0        1.6    8.4   0.0    3.6  4  RPN7          26S proteasome subunit RPN7
     0.0021   18.3   2.3      0.052   13.8   0.1    3.2  4  TPR_12        Tetratricopeptide repeat
  ------ inclusion threshold ------
       0.11   12.5   0.1       0.35   10.8   0.1    1.9  2  pRN1_helical  Primase helical domain
       0.13   12.9   0.2          5    7.9   0.0    3.3  4  CdiI_2        CdiI immunity protein
       0.16   11.5   0.2        3.3    7.2   0.0    2.7  3  Foie-gras_1   Foie gras liver health family 1
       0.69   10.2   4.8        1.5    9.1   0.0    4.1  6  TPR_2         Tetratricopeptide repeat
       0.99    9.3   0.0       0.99    9.3   0.0    3.5  6  TPR_1         Tetratricopeptide repeat
        1.3    9.0   3.5        8.1    6.4   0.5    2.9  3  LcrG          LcrG protein


Domain annotation for each model (and alignments):
>> RPN7  26S proteasome subunit RPN7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.013        29      38      76 ..     135     173 ..     127     178 .. 0.87
   2 ?    1.9   0.0     0.072   1.6e+02      36      62 ..     166     192 ..     144     199 .. 0.77
   3 ?    3.9   0.0     0.017        39      39      66 ..     262     289 ..     250     300 .. 0.85
   4 !    8.4   0.0    0.0007       1.6      42      85 ..     298     341 ..     291     343 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.013
                                       HHHHHHHHHHHCT-HHHHHHHHHTCCCC--SHHHHHHHH CS
                              RPN7  38 akldlaehYlkigdleeAlkaysrireyctslkhkidml 76 
                                       + l + + Yl++g l+ A++  ++++++  s+k+k ++l
  gi|242399396|ref|YP_002994820.1| 135 TLLSILKAYLSAGILKDAIQISKELLDEPWSSKAKSEIL 173
                                       56788999*************************998876 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.072
                                       HHHHHHHHHHHHHCT-HHHHHHHHHTC CS
                              RPN7  36 rrakldlaehYlkigdleeAlkaysri 62 
                                        +ak ++ ++++k  ++e+Al+ ++ i
  gi|242399396|ref|YP_002994820.1| 166 SKAKSEILKFHIKREEIENALEIFNTI 192
                                       578889999999999999999999877 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.017
                                       HHHHHHHHHHCT-HHHHHHHHHTCCCC- CS
                              RPN7  39 kldlaehYlkigdleeAlkaysrireyc 66 
                                       + +   ++ +ig +e+A++  s+i ++ 
  gi|242399396|ref|YP_002994820.1| 262 QVKVVAFFNRIGRREKAIEQASKIKDDY 289
                                       5677899****************98764 PP

  == domain 4  score: 8.4 bits;  conditional E-value: 0.0007
                                       HHHHHHHCT-HHHHHHHHHTCCCC--SHHHHHHHHHHHHHHHHH CS
                              RPN7  42 laehYlkigdleeAlkaysrireyctslkhkidmllnlirvaif 85 
                                       +a  Yl+ gdl++A+ a++ + ++  ++    ++l++++r+ai+
  gi|242399396|ref|YP_002994820.1| 298 IAMGYLRQGDLDKAIDAVMNVKDPKWNSRLLEEILVKILRLAIE 341
                                       5667*************************************995 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.08   1.8e+02      23      73 ..      42      89 ..      42      92 .. 0.75
   2 ?   -3.2   0.0       4.9   1.1e+04      53      71 ..     141     159 ..     134     161 .. 0.58
   3 ?   -2.5   0.0         3   6.7e+03      27      40 ..     183     195 ..     179     200 .. 0.64
   4 !   13.8   0.1   2.3e-05     0.052      27      66 ..     276     313 ..     273     315 .. 0.95

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.08
                            TPR_12 23 lellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeala 73
                                      le ++k+l+ a+++  +d ++++  l+n g++   + +   A + + ++++
  gi|242399396|ref|YP_002994820.1| 42 LEAFRKSLAGAEAI--EDLDELVDLLINVGTYIGGA-NKNSAARVFARVVE 89
                                      578999*****999..99999999999999885555.66666666666655 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 4.9
                            TPR_12  53 rlyralgryeeAlelleea 71 
                                        +y+ +g +++A+++ +e 
  gi|242399396|ref|YP_002994820.1| 141 KAYLSAGILKDAIQISKEL 159
                                       5566666666666666655 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 3
                            TPR_12  27 ekaleiarrllGpd 40 
                                       e alei++ + G d
  gi|242399396|ref|YP_002994820.1| 183 ENALEIFNTIEG-D 195
                                       678888866644.4 PP

  == domain 4  score: 13.8 bits;  conditional E-value: 2.3e-05
                            TPR_12  27 ekaleiarrllGpdhpltattlrnLgrlyralgryeeAle 66 
                                       eka+e+a+++  +d +l++ +   +++ y+++g++++A++
  gi|242399396|ref|YP_002994820.1| 276 EKAIEQASKI--KDDYLASLAFGEIAMGYLRQGDLDKAID 313
                                       89********..9999**********************98 PP

>> pRN1_helical  Primase helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       2.9   6.5e+03      70      81 ..      24      35 ..       4      64 .. 0.73
   2 ?   10.8   0.1   0.00016      0.35       9      43 ..     201     235 ..     192     262 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.9
                      pRN1_helical 70 ktyaeigidrsr 81
                                       tya ig++  r
  gi|242399396|ref|YP_002994820.1| 24 LTYARIGLELYR 35
                                      578888877655 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00016
                      pRN1_helical   9 eklkeemakydrykgktleaireelckeikkklee 43 
                                         + e++ k+  y  k l+a+ree  k+++++l  
  gi|242399396|ref|YP_002994820.1| 201 MEIAEDLMKFPEYLSKFLDALREEELKAVSRELLG 235
                                       4578999***********************99855 PP

>> CdiI_2  CdiI immunity protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.84   1.9e+03      28      61 ..      68     101 ..      56     113 .. 0.79
   2 ?   -1.7   0.0       2.2   4.9e+03      16      57 ..     128     166 ..     120     189 .. 0.67
   3 ?    7.9   0.0    0.0022         5      24      89 ..     210     274 ..     200     275 .. 0.89
   4 ?   -1.0   0.0       1.3   2.9e+03      22      47 ..     306     331 ..     302     347 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.84
                            CdiI_2  28 ledYvssespeevaelideieellassldeelee 61 
                                       +  Y+  ++++  a++ + + ell+  + ++ ++
  gi|242399396|ref|YP_002994820.1|  68 VGTYIGGANKNSAARVFARVVELLEGAPPQSRDR 101
                                       5679999999999999999999999777554444 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.2
                            CdiI_2  16 DydlegdsieeiledYvssespeevaelideieellasslde 57 
                                       D  + ++++  il++Y+s    + ++++i+  +ell+++ ++
  gi|242399396|ref|YP_002994820.1| 128 DSRIRNETLLSILKAYLSA---GILKDAIQISKELLDEPWSS 166
                                       6666677777777777773...46666666666666665544 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0022
                            CdiI_2  24 ieeiledYvssespeevaelideieellassldeeleeaflaelgaefdpeawgltarefLeevae 89 
                                       + e l+++++   +ee++++ +e+  ll +s++   ++++++++ +++  e+ + ++  f++++ +
  gi|242399396|ref|YP_002994820.1| 210 FPEYLSKFLDALREEELKAVSRELLGLLIESPSG-EYADLVEKIAEKVPDENVQVKVVAFFNRIGR 274
                                       77999***************************88.78888899999999999********999866 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 1.3
                            CdiI_2  22 dsieeiledYvssespeevaelidei 47 
                                       +++++++++ ++  +p++  +l++ei
  gi|242399396|ref|YP_002994820.1| 306 GDLDKAIDAVMNVKDPKWNSRLLEEI 331
                                       56888999999999999999999997 PP

>> Foie-gras_1  Foie gras liver health family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.15   3.3e+02     186     256 ..     129     159 ..      85     163 .. 0.62
   2 ?   -1.2   0.0      0.55   1.2e+03     189     207 ..     196     214 ..     180     223 .. 0.76
   3 ?    7.2   0.0    0.0015       3.3     174     216 ..     276     318 ..     248     343 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.15
                       Foie-gras_1 186 tRlaeelsleiAeeylrlgdwkkalellqpltlsyrkegWwsLleevlwalrecalkvqdvkdvlavdleL 256
                                        R+++e  l i ++yl +g                                          kd+++++ eL
  gi|242399396|ref|YP_002994820.1| 129 SRIRNETLLSILKAYLSAGI----------------------------------------LKDAIQISKEL 159
                                       55555555555555555555........................................55555555554 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.55
                       Foie-gras_1 189 aeelsleiAeeylrlgdwk 207
                                       +e+l +eiAe++++  ++ 
  gi|242399396|ref|YP_002994820.1| 196 REKLIMEIAEDLMKFPEYL 214
                                       489999*******998875 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0015
                       Foie-gras_1 174 ekaleeFskrkqtRlaeelsleiAeeylrlgdwkkalellqpl 216
                                       eka+e++sk k + la+    eiA  ylr gd +ka++    +
  gi|242399396|ref|YP_002994820.1| 276 EKAIEQASKIKDDYLASLAFGEIAMGYLRQGDLDKAIDAVMNV 318
                                       89**************99999***************9876444 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       6.7   1.5e+04       2      13 ..      24      35 ..      23      38 .. 0.67
   2 ?   -1.3   0.1       1.4   3.2e+03      18      30 ..      52      64 ..      52      65 .. 0.85
   3 ?   -2.5   0.0       3.6     8e+03      18      30 ..      78      90 ..      76      93 .. 0.81
   4 ?   -2.9   0.0       4.6     1e+04      14      24 ..     179     189 ..     176     191 .. 0.54
   5 ?   -1.8   0.0       2.2   4.8e+03      15      24 ..     273     282 ..     271     285 .. 0.74
   6 ?    9.1   0.0   0.00069       1.5       6      23 ..     297     314 ..     292     315 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 6.7
                             TPR_2  2 ealynlGlayyk 13
                                        + ++Gl +y+
  gi|242399396|ref|YP_002994820.1| 24 LTYARIGLELYR 35
                                      457777877776 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.4
                             TPR_2 18 eeAleafekAlel 30
                                      +eA+e++++ + l
  gi|242399396|ref|YP_002994820.1| 52 AEAIEDLDELVDL 64
                                      69*****998876 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 3.6
                             TPR_2 18 eeAleafekAlel 30
                                      + A++ f +++el
  gi|242399396|ref|YP_002994820.1| 78 NSAARVFARVVEL 90
                                      6799999999998 PP

  == domain 4  score: -2.9 bits;  conditional E-value: 4.6
                             TPR_2  14 lgdyeeAleaf 24 
                                       + + e Ale f
  gi|242399396|ref|YP_002994820.1| 179 REEIENALEIF 189
                                       45555555554 PP

  == domain 5  score: -1.8 bits;  conditional E-value: 2.2
                             TPR_2  15 gdyeeAleaf 24 
                                       g+ e+A+e  
  gi|242399396|ref|YP_002994820.1| 273 GRREKAIEQA 282
                                       7889999865 PP

  == domain 6  score: 9.1 bits;  conditional E-value: 0.00069
                             TPR_2   6 nlGlayyklgdyeeAlea 23 
                                       ++++ y+++gd+++A++a
  gi|242399396|ref|YP_002994820.1| 297 EIAMGYLRQGDLDKAIDA 314
                                       68999**********986 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.1   2.4e+03       1      16 [.      23      38 ..      23      40 .. 0.79
   2 ?   -3.3   0.1       4.5     1e+04      19      25 ..      53      59 ..      52      60 .. 0.78
   3 ?   -2.7   0.1       2.7   6.1e+03      10      22 ..     142     154 ..     141     154 .. 0.86
   4 ?   -2.7   0.0       2.8   6.4e+03      13      23 ..     178     188 ..     176     190 .. 0.69
   5 ?   -3.3   0.0       4.3   9.6e+03      16      22 ..     274     280 ..     271     282 .. 0.68
   6 ?    9.3   0.0   0.00044      0.99       3      23 ..     294     314 ..     292     315 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.1
                                      HHHHHHHHHHHHHTT- CS
                             TPR_1  1 akalynlGnayfklgk 16
                                      a ++ ++G+ +++ ++
  gi|242399396|ref|YP_002994820.1| 23 ALTYARIGLELYRIED 38
                                      5689999*99998766 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 4.5
                                      HHHHHHH CS
                             TPR_1 19 eAleyye 25
                                      eA+e+ +
  gi|242399396|ref|YP_002994820.1| 53 EAIEDLD 59
                                      8999976 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 2.7
                                       HHHHTT-HHHHHH CS
                             TPR_1  10 ayfklgkydeAle 22 
                                       ay++ g +++A++
  gi|242399396|ref|YP_002994820.1| 142 AYLSAGILKDAIQ 154
                                       7999999999996 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 2.8
                                       HTT-HHHHHHH CS
                             TPR_1  13 klgkydeAley 23 
                                       k ++ + Ale 
  gi|242399396|ref|YP_002994820.1| 178 KREEIENALEI 188
                                       66778888875 PP

  == domain 5  score: -3.3 bits;  conditional E-value: 4.3
                                       -HHHHHH CS
                             TPR_1  16 kydeAle 22 
                                       + ++A+e
  gi|242399396|ref|YP_002994820.1| 274 RREKAIE 280
                                       5577776 PP

  == domain 6  score: 9.3 bits;  conditional E-value: 0.00044
                                       HHHHHHHHHHHTT-HHHHHHH CS
                             TPR_1   3 alynlGnayfklgkydeAley 23 
                                       a+  +++ y+++g++d+A+++
  gi|242399396|ref|YP_002994820.1| 294 AFGEIAMGYLRQGDLDKAIDA 314
                                       66778999***********96 PP

>> LcrG  LcrG protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.075   1.7e+02       4      44 ..      44      84 ..      41     105 .. 0.78
   2 ?    6.4   0.5    0.0036       8.1      20      60 ..     194     234 ..     176     240 .. 0.89
   3 ?   -3.1   0.0       3.3   7.4e+03      12      31 ..     314     333 ..     307     341 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.075
                              LcrG  4 efaktlkaaelairdsdeRakllqelleglGla.peageklf 44
                                       f+k l  ae ai+d de  +ll ++   +G a  + + ++f
  gi|242399396|ref|YP_002994820.1| 44 AFRKSLAGAE-AIEDLDELVDLLINVGTYIGGAnKNSAARVF 84
                                      6899999999.8***********9998888744044444454 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0036
                              LcrG  20 deRakllqelleglGlapeageklfggleaelvkaaeqeLl 60 
                                        +R+kl+ e+ e+l   pe   k++ +l  e++ka  +eLl
  gi|242399396|ref|YP_002994820.1| 194 GDREKLIMEIAEDLMKFPEYLSKFLDALREEELKAVSRELL 234
                                       479*************************************8 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 3.3
                              LcrG  12 aelairdsdeRakllqelle 31 
                                       a + ++d    ++ll+e+l 
  gi|242399396|ref|YP_002994820.1| 314 AVMNVKDPKWNSRLLEEILV 333
                                       45677888888888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 2137.94
//
Query:       gi|242399397|ref|YP_002994821.1|  [L=69]
Description: hypothetical protein TSIB_1421 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.082   13.2   0.0      0.088   13.1   0.0    1.1  1  Ycf54          Protein of unknown function (DUF2488)
       0.13   12.7   0.1       0.42   11.1   0.1    1.7  2  ribosomal_L24  Ribosomal proteins 50S L24/mitochondrial 39S L


Domain annotation for each model (and alignments):
>> Ycf54  Protein of unknown function (DUF2488)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   9.8e-06     0.088      23      72 ..       5      57 ..       1      64 [. 0.74

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.8e-06
                                      HHHHHHHHHHTT-..---EEEEESBGGGGSGGGHHHHHHS-SS.EEEEEES-H CS
                             Ycf54 23 Lkerarnykeknk..eidfwlvkePaFleapelkeikkklpkp.aaAivstdk 72
                                      +k+  r++ ++ k    d+w v + ++l++p++  +  k+ k   +  vs d+
  gi|242399397|ref|YP_002994821.1|  5 IKKDLRKFMKELKlhYDDVWHVPSSEYLKNPDFVVVDPKTGKKmKVSFVSLDD 57
                                      555566655544411579*****************998886542788898875 PP

>> ribosomal_L24  Ribosomal proteins 50S L24/mitochondrial 39S L24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.28   2.5e+03      21      34 ..      13      26 ..      10      34 .. 0.78
   2 ?   11.1   0.1   4.6e-05      0.42      33      54 ..      39      60 ..      37      64 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.28
                     ribosomal_L24 21 ekEapIhvSnVmlv 34
                                       kE  +h+  V +v
  gi|242399397|ref|YP_002994821.1| 13 MKELKLHYDDVWHV 26
                                      58889999988766 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 4.6e-05
                     ribosomal_L24 33 lvdpkcgkptrvgfrlkedgkk 54
                                      +vdpk+gk+ +v+f   +dg+ 
  gi|242399397|ref|YP_002994821.1| 39 VVDPKTGKKMKVSFVSLDDGEV 60
                                      79************55588874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); 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: 0.47u 0.33s 00:00:00.80 Elapsed: 00:00:00.51
# Mc/sec: 408.98
//
Query:       gi|242399398|ref|YP_002994822.1|  [L=281]
Description: hypothetical protein TSIB_1422 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.9e-50  170.2   0.5    6.7e-50  170.0   0.5    1.0  1  DUF89     Protein of unknown function DUF89


Domain annotation for each model (and alignments):
>> DUF89  Protein of unknown function DUF89
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.0   0.5   3.7e-54   6.7e-50       2     352 ..       4     278 ..       3     279 .. 0.95

  Alignments for each domain:
  == domain 1  score: 170.0 bits;  conditional E-value: 3.7e-54
                                       HHTHHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHCTTCGHHH-HHHHT-BTTBSBHHHHHHHHHHHHHH CS
                             DUF89   2 leerlpciltqviddlekakdekeeelkkiieelselkeelqtdkpltpledeeekrswfnapwlfaecylyrrlle 78 
                                       ++e++ ci +q+++ +e+++d+  e++k ++   ++l+ +l++d+    +                 ++++  +l++
  gi|242399398|ref|YP_002994822.1|   4 HYECFMCIANQCQRIIEMTTDD-LEKRKTAAVFSAKLMGKLKEDSISGIV-----------------ASEIISELYK 62 
                                       78********************.9999999999999**999988766555.................********** PP

                                       HHTHSGGGTTS-TTHHHHHHHHHHHHHHHHHHHHHHHHCCSHHHHHHHHHHHHHHHCG--CCCHTSHHCHHHHHHHH CS
                             DUF89  79 lfglskelknyDpFkeqKeesnksalkaveelakrleeledekelfkellkislwGNaiDlsllateediqkdqeee 155
                                       ++g       +DpFke+Ke+sn+ a+k +e+++k l   e   +++k++lk++++GN+iD+++      ++++ e +
  gi|242399398|ref|YP_002994822.1|  63 FLG------IEDPFKEYKERSNEIAKKILENITKNL---E---IDLKTALKLAIVGNIIDFAVGY----SPEKIERD 123
                                       ***......************************983...3...56999*****************....99999*** PP

                                       HHHHHHCTESEE-HHHHHHHHCTCHTSEEEEE--BTTHHHHHHHHHHHHHHHCTTTSEEEEEEBSS--TTTB-BHHH CS
                             DUF89 156 arkaleknilvddleklweklkkkkakrvdivlDNaGfElvfDlllaeeLlesglatkVvlhvkaiPwfvsDvtpeD 232
                                       +    +++++vd++e+l++ l  k+a+ +++++DN+G E++fD l++++++es +  ++++++k+ P  ++D+t+++
  gi|242399398|ref|YP_002994822.1| 124 IIHLINEDLYVDNSEELFKTL--KNARVLLYLTDNCG-EIYFDKLFLKKIKESFPDLEIYIAGKEQP-LINDATVNE 196
                                       *********************..**************.*****************************.********* PP

                                       HHHHHHHHH-TTTSHHHHCHTTHHHHHHTSEEEEESSCGGSSS--CCGSSSHHHHHHHHHC-SEEEEEHHHHHHHHT CS
                             DUF89 233 fewlleqladsksfelsalgagldellkegklvlrgssfwttglsysempeapelyeelekadLvifKGdlNyrkLt 309
                                       ++                  agl+e   +g+++++g     +g++++++  +  + e +++ad++i+KG++N+++L 
  gi|242399398|ref|YP_002994822.1| 197 LR-----------------VAGLQE---VGEIISTGFG--VVGVPLDRI--SGRFKEIFDSADVIIAKGQANFETLN 249
                                       **.................******...*******988..*********..*************************8 PP

                                       TSCTTTTTSEHHHHTGTSS--EEEEEE--SHHHHHHH.STTTHE CS
                             DUF89 310 gdrkwppttpfttalgfspvpvlaLrtvKadvvagll.egegek 352
                                       + ++ +               +++L+++K+ +++++l +++g++
  gi|242399398|ref|YP_002994822.1| 250 ESNDRR---------------IFYLLKAKCMPISRELrVPQGAM 278
                                       887777...............**************999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       766  (0.0427241); expected 358.6 (0.02)
Passed bias filter:                      570  (0.0317921); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2064.22
//
Query:       gi|242399399|ref|YP_002994823.1|  [L=40]
Description: hypothetical protein TSIB_1423 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.035   14.0   0.2      0.043   13.7   0.2    1.2  1  DUF3198   Protein of unknown function (DUF3198)


Domain annotation for each model (and alignments):
>> DUF3198  Protein of unknown function (DUF3198)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2   2.4e-06     0.043      22      46 ..       3      27 ..       1      30 [. 0.94

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.4e-06
                                      HHHHHHHHHHH-SHHHHHHHHHHHH CS
                           DUF3198 22 lkeLekiarklGssYqqrLeeakek 46
                                      ++e+e+i+r ++  Y   +e +k+k
  gi|242399399|ref|YP_002994823.1|  3 VREMEIISRLYDYLYLREFERKKKK 27
                                      69*********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      196  (0.010932); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.39
# Mc/sec: 307.27
//
Query:       gi|242399400|ref|YP_002994824.1|  [L=453]
Description: Signal recognition 54 kDa protein [Thermococcus sibiricus MM 739]
Scores for complete 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-75  251.4   0.0      1e-74  250.4   0.0    1.5  1  SRP54            SRP54-type protein, GTPase domain
    7.1e-34  116.4   4.5    1.6e-33  115.3   3.4    2.2  1  SRP_SPB          Signal peptide binding domain
    1.8e-19   69.7   2.8    1.8e-19   69.7   2.8    2.5  2  SRP54_N          SRP54-type protein, helical bundle domain
    4.6e-05   23.5   0.0    0.00015   21.8   0.0    1.9  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
    5.9e-05   23.4   0.1    0.00024   21.4   0.0    2.0  1  AAA_22           AAA domain
     0.0002   21.0   1.2      0.011   15.3   0.7    2.6  2  cobW             CobW/HypB/UreG, nucleotide-binding domain
    0.00062   19.7   0.6     0.0019   18.1   0.1    2.0  2  MobB             Molybdopterin guanine dinucleotide synthesis
     0.0013   17.7   0.4       0.01   14.9   0.1    2.3  3  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
     0.0014   19.1   0.1     0.0014   19.1   0.1    2.3  2  AAA_17           AAA domain
     0.0026   17.9   0.0     0.0057   16.8   0.0    1.6  1  AAA_33           AAA domain
     0.0031   17.3   0.0     0.0093   15.7   0.0    1.8  1  AAA_30           AAA domain
     0.0033   16.5   0.3     0.0063   15.6   0.3    1.4  1  IMPDH            IMP dehydrogenase / GMP reductase domain
     0.0036   16.7   0.0       0.01   15.2   0.0    1.8  1  6PF2K            6-phosphofructo-2-kinase
     0.0055   15.6   0.0      0.011   14.6   0.0    1.5  1  Fe-ADH           Iron-containing alcohol dehydrogenase
     0.0064   16.3   2.0     0.0085   15.9   0.1    2.1  3  ATP_bind_1       Conserved hypothetical ATP binding protein
     0.0076   16.3   0.0      0.027   14.5   0.0    1.9  2  Glyco_transf_4   Glycosyltransferase Family 4
     0.0078   16.6   0.0      0.028   14.8   0.0    1.9  2  AAA_16           AAA ATPase domain
     0.0095   15.9   1.2      0.053   13.4   0.1    2.4  2  NTPase_1         NTPase
     0.0099   15.2   0.2      0.028   13.7   0.0    1.9  2  Zeta_toxin       Zeta toxin
  ------ inclusion threshold ------
      0.016   15.0   0.3        1.4    8.7   0.0    2.7  3  RNase_Zc3h12a    Zc3h12a-like Ribonuclease NYN domain
      0.017   15.0   0.5      0.083   12.8   0.0    2.3  3  APS_kinase       Adenylylsulphate kinase
      0.019   14.4   0.5      0.029   13.7   0.5    1.2  1  Beach            Beige/BEACH domain
      0.021   14.3   2.1      0.074   12.5   0.0    2.6  3  KTI12            Chromatin associated protein KTI12
      0.026   13.6   0.2      0.067   12.3   0.2    1.6  2  LpxK             Tetraacyldisaccharide-1-P 4'-kinase
      0.038   14.1   1.1          1    9.4   0.0    2.8  2  tRNA_lig_kinase  tRNA ligase kinase domain
      0.048   13.8   0.3       0.22   11.7   0.3    2.1  1  Bromo_TP_like    Histone-fold protein
      0.048   13.4   0.0       0.11   12.2   0.0    1.6  1  VirE             Virulence-associated protein E
      0.059   13.1   1.7      0.081   12.6   0.1    2.0  1  Thymidylate_kin  Thymidylate kinase
      0.096   12.8   1.2        1.4    9.0   0.3    2.4  2  Mod_r            Modifier of rudimentary (Mod(r)) protein
       0.28   10.4   2.9        1.7    7.9   2.9    2.0  1  DUF4763          Domain of unknown function (DUF4763)
       0.52   10.4   3.7        9.5    6.4   0.3    3.4  3  ASL_C            Adenylosuccinate lyase C-terminal


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 !  250.4   0.0   1.8e-77     1e-74       1     196 []     105     300 ..     105     300 .. 0.99

  Alignments for each domain:
  == domain 1  score: 250.4 bits;  conditional E-value: 1.8e-77
                                       SEEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEESSTTSCHHHHHHHHHH CS
                             SRP54   1 pnvillvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvikkkeeadpaavakeave 77 
                                       p+v+l vG+qG+GKTt++aKL+++++k+g+kv +v+ Dt+R++A++QLk+l e +g++v+++ ee++++++ake+ve
  gi|242399400|ref|YP_002994824.1| 105 PTVLLTVGIQGSGKTTSVAKLSRYFQKHGYKVGVVCSDTWRPGAYQQLKQLIEPYGIEVFGNPEEKNAIKLAKEGVE 181
                                       5799************************************************************************* PP

                                       HHHHTTSSEEEEEE--SSTTHHHHHHHHHHHHHHHSSSEEEEEEETTBHTHHHHHHHHHHHHSSCSEEEEESTTSSS CS
                             SRP54  78 kakeekidvvlvDTaGrlqndkelmeelkkikkvvkpdevllvldattgqeavkqakaFkeavgitgviltklDgda 154
                                        +k++++dv++vD+aGr++++k l+ee+++i+++++p+ev+l++d+t+gq+a++qa aFkea+ i+++i+tklDg+a
  gi|242399400|ref|YP_002994824.1| 182 YFKKKGVDVIIVDSAGRHKEEKGLIEEMRQISNTINPHEVILIIDGTIGQQAYNQALAFKEATPIGSIIVTKLDGSA 258
                                       ***************************************************************************** PP

                                       STTHHHHHHHHHTS-EEEEE-SSSTTGEEE--HHHHHHHHHT CS
                             SRP54 155 kgGaalsiaaelklPikfigvGekiedleefdperlvsrllg 196
                                       kgG+als++ +++ PikfigvGeki+dle+fdp+r+vsrllg
  gi|242399400|ref|YP_002994824.1| 259 KGGGALSAVVATGAPIKFIGVGEKIDDLEPFDPKRFVSRLLG 300
                                       ****************************************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 !  115.3   3.4   2.8e-36   1.6e-33       1      98 [.     332     430 ..     332     431 .. 0.94

  Alignments for each domain:
  == domain 1  score: 115.3 bits;  conditional E-value: 2.8e-36
                                       SSCTHHHHHHHHHHHCCCCCCHHHHCCC.......H...CCCCCHHHHHHHHHTTSBHHHHHSGCG-..HHHHHHHH CS
                           SRP_SPB   1 eftlrdlleqlqqikkmGplskllsmiPgmsae..akaeeeaekklkrieaiidSMTkeErdspekllkesRkrRiA 75 
                                       +f+l+d++ ql+ +kkmGpl+++l+miPgm+ +   +  +++e +lk++++i+dSMT+eE+++pe +++ sR++RiA
  gi|242399400|ref|YP_002994824.1| 332 KFNLKDMYAQLEAMKKMGPLQQILKMIPGMGYSlpDEMVRMSEVRLKKFKVIMDSMTEEELENPE-IINYSRIKRIA 407
                                       69***************************998876433478899*********************.9999******* PP

                                       HHTTS-HHHHHHHHHHHHHHHHH CS
                           SRP_SPB  76 rGsGtsvqevnellkqfeqmkkm 98 
                                       rGsGt++++v+el++q++qmkk+
  gi|242399400|ref|YP_002994824.1| 408 RGSGTTTKDVKELINQYNQMKKF 430
                                       *********************96 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 !   69.7   2.8   3.2e-22   1.8e-19       1      75 []      11      88 ..      11      88 .. 0.96
   2 ?   -1.6   0.2       5.8   3.4e+03       5      28 ..     307     330 ..     304     331 .. 0.71

  Alignments for each domain:
  == domain 1  score: 69.7 bits;  conditional E-value: 3.2e-22
                                      HHHHHHHHHHHHCCSSCGHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHCTTS...S-HHHHHHHHHHHHH CS
                           SRP54_N  1 LgkklnsalkklsgkskideedleealkeleeaLleaDVgvkvvkklienvkkkavgekk...lkpkqqvkkivkdeL 75
                                      Lg++ln+alkkl ++s++de+++ ++++++++aL+++DV+v++v +l+++++k+a++ek    +++k++++kiv++eL
  gi|242399400|ref|YP_002994824.1| 11 LGQSLNNALKKLARASTVDEALVRDVVRDIQRALITSDVNVRLVLDLTKKIEKRALEEKPpagVSKKEHIVKIVYEEL 88
                                      899************************************************999999555*****************8 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 5.8
                                       HHHHHHHHCCSSCGHHHHHHHHHH CS
                           SRP54_N   5 lnsalkklsgkskideedleealk 28 
                                       l + +  ls+  + +eed+e +lk
  gi|242399400|ref|YP_002994824.1| 307 LLEKFEELSKEVEFKEEDMEKFLK 330
                                       555566777777888888888776 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 !   21.8   0.0   2.7e-07   0.00015       9      92 ..     115     341 ..     108     361 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 2.7e-07
                                       TSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH............................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................... RF
                              CbiA   9 GvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep............................... 54 
                                       G+GKTt +a+L r+++++g++V +v  D+ ++ +   ++l++ iep                               
  gi|242399400|ref|YP_002994824.1| 115 GSGKTTSVAKLSRYFQKHGYKVGVVCSDTWRPGAY--QQLKQLIEPygievfgnpeeknaiklakegveyfkkkgvd 189
                                       99***************************999986..7778888888889999999999999999999999999999 PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|242399400|ref|YP_002994824.1| 190 viivdsagrhkeekglieemrqisntinpheviliidgtigqqaynqalafkeatpigsiivtkldgsakgggalsa 266
                                       99999999999999999999999999999999999999999999999999999999999999999998888888888 PP

                                       ....................................CCHCCCHHHHHHCHCHHHH...EEEEEEEEESS...-TT CS
                                       ....................................xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx RF
                              CbiA  55 ....................................dlkrllellealgkkkall.lkiagvvlnrvdgeneetl 92 
                                                                           d++ lle +e+l+k+++ +  ++  ++  +++ ++++++
  gi|242399400|ref|YP_002994824.1| 267 vvatgapikfigvgekiddlepfdpkrfvsrllglgDIQGLLEKFEELSKEVEFKeEDMEKFLKGKFNLKDMYAQ 341
                                       888888888888888888888888888888888888888888888888887666576666666666666655554 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   4.1e-07   0.00024       6     126 ..     106     224 ..     101     232 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 4.1e-07
                            AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka..erlsseelle 80 
                                       ++l+ +G  G+GKTt++++l + ++++      +++vv  +   ++  ++l ++l + +g e  +  e+++   l +
  gi|242399400|ref|YP_002994824.1| 106 TVLLTVGIQGSGKTTSVAKLSRYFQKHG----YKVGVVCSDTWRPGAYQQL-KQLIEPYGIEVFGnpEEKNAIKLAK 177
                                       678889****************997654....4999998888888844444.666666666666666668999999* PP

                            AAA_22  81 aleqalraravielliiDEaqhlr.seealeeLrsllnl.srkgvqli 126
                                          +++++++v  ++i+D a +   ++ ++ee r+++n  + + v li
  gi|242399400|ref|YP_002994824.1| 178 EGVEYFKKKGV-DVIIVDSAGRHKeEKGLIEEMRQISNTiNPHEVILI 224
                                       ***********.**********965599********995555555444 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 !   15.3   0.7   1.9e-05     0.011       3     152 ..     108     256 ..     106     270 .. 0.70
   2 ?   -2.6   0.0       6.2   3.6e+03      28      79 ..     379     427 ..     372     433 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.9e-05
                                       EEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SSCHCCC...CCCHCCCT.EEEETTTTECCHCTT-HHHHHH CS
                              cobW   3 tvltGflGsGKTtLlnhll..enraglklavivNefgevsiDa...ellretgveivelenGciCctlredllkele 74 
                                       ++ +G  GsGKTt + +l    +++g+k+ v+  +    +  +   +l++  g e++   + +     + +l ke  
  gi|242399400|ref|YP_002994824.1| 108 LLTVGIQGSGKTTSVAKLSryFQKHGYKVGVVCSDTWRPGAYQqlkQLIEPYGIEVFGNPEEK----NAIKLAKEGV 180
                                       5668999***********988788***********9864444400034444444444333333....3444555555 PP

                                       HHHHHHTT-SEEEEEECT.TTTHHHHHTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-H CS
                              cobW  75 aleereerldviliEttG.laePapvafteeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnKt 150
                                       ++ +++  +dvi++ + G   e + ++ + +++++ ++   v+ ++D+  +  ++  ++ +a ++ +    ++++K 
  gi|242399400|ref|YP_002994824.1| 181 EYFKKK-GVDVIIVDSAGrHKEEKGLIEEMRQISNTINPHEVILIIDG-TI-GQQAYNQALAFKEATPIGSIIVTKL 254
                                       566666.6**********666777777779******************.44.4555555566666666667788888 PP

                                       HH CS
                              cobW 151 Dl 152
                                       D 
  gi|242399400|ref|YP_002994824.1| 255 DG 256
                                       86 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 6.2
                                       -EEEEESS-SSCHCCCCCCHCCCT.EEEETTTTECCHCTT-HHHHHHHHHHH CS
                              cobW  28 klavivNefgevsiDaellretgveivelenGciCctlredllkelealeer 79 
                                       k  vi+  + e ++++  + +  + i  ++ G    t  +d+ + ++++ ++
  gi|242399400|ref|YP_002994824.1| 379 KFKVIMDSMTEEELENPEIINY-SRIKRIARGSGTTT--KDVKELINQYNQM 427
                                       6667777777766666555555.35777777777666..5555555555554 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 !   18.1   0.1   3.3e-06    0.0019       2      33 ..     108     139 ..     107     145 .. 0.91
   2 ?   -1.7   0.1       4.3   2.5e+03      40      56 ..     180     197 ..     168     222 .. 0.54

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 3.3e-06
                              MobB   2 lgivgksgsGKTtLleklipelkarglrvgti 33 
                                       l  vg +gsGKTt + kl + ++++g++vg++
  gi|242399400|ref|YP_002994824.1| 108 LLTVGIQGSGKTTSVAKLSRYFQKHGYKVGVV 139
                                       6789**************************98 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 4.3
                              MobB  40 fd.vdkpgkDsyrhrkAG 56 
                                       ++ ++k+g D   + +AG
  gi|242399400|ref|YP_002994824.1| 180 VEyFKKKGVDVIIVDSAG 197
                                       333333333333333333 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 !   14.9   0.1   1.7e-05      0.01      31      66 ..     107     142 ..      98     148 .. 0.87
   2 ?   -0.5   0.0      0.86     5e+02     110     140 ..     176     206 ..     172     218 .. 0.79
   3 ?   -2.6   0.0       3.6   2.1e+03     206     235 ..     405     434 ..     385     446 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.7e-05
                                       EEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE- CS
                              MeaB  31 vvGltGvPGaGkstlvealglelrrrGkrvavlavD 66 
                                       v+   G+ G+Gk t v +l   ++++G++v+v+  D
  gi|242399400|ref|YP_002994824.1| 107 VLLTVGIQGSGKTTSVAKLSRYFQKHGYKVGVVCSD 142
                                       455579**************************9877 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.86
                                       HHHHHHHHHHTT-SEEEEEEESSTTHHHHHH CS
                              MeaB 110 trevvllleaaGfDvvlietvGvGqsevdva 140
                                       ++e v+ +   G Dv++++  G  + e  ++
  gi|242399400|ref|YP_002994824.1| 176 AKEGVEYFKKKGVDVIIVDSAGRHKEEKGLI 206
                                       567788889999******9999887776665 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 3.6
                                       EEEEEBCCCTBSHHHHHHHHHHHHHHHHHT CS
                              MeaB 206 kvlktsavegeGidelvdaieehrevlkkt 235
                                       ++ + s+++ + ++el+++ ++ +++ ++ 
  gi|242399400|ref|YP_002994824.1| 405 RIARGSGTTTKDVKELINQYNQMKKFFRSM 434
                                       567778888888888887766665555443 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       8.2   4.7e+03      49      69 ..      49      69 ..      13      99 .. 0.61
   2 !   19.1   0.1   2.4e-06    0.0014       1     108 [.     111     224 ..     111     229 .. 0.69

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 8.2
                                      SHHHHHHHHHHHHHHHHHHHH CS
                            AAA_17 49 lpleekkelqkeaaekiaeea 69
                                      ++ +   +l+k+++++  ee+
  gi|242399400|ref|YP_002994824.1| 49 VNVRLVLDLTKKIEKRALEEK 69
                                      333444445555555555554 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 2.4e-06
                                       EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSHHHHC....TS.HHHHHHHHHHHHHHHHHHHH..H CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrgglakardemr....kl.pleekkelqkeaaekiaeea..k 70 
                                       +G+ GsGK+t ++kl + ++ + +  G +  ++ ++g  ++ ++ ++    ++  + e+k   k+a+e ++  +  +
  gi|242399400|ref|YP_002994824.1| 111 VGIQGSGKTTSVAKLSRYFQKHGYKVGVVCSDTWRPGAYQQLKQLIEpygiEVfGNPEEKNAIKLAKEGVEYFKkkG 187
                                       79**************8777777777777777766665544444444544432233334444566666554433114 PP

                                       SSEEEEEE-SEEEETTEEEESSHHHHHHHH..SEEEEE CS
                            AAA_17  71 kkgvlvdghprikeqagfldglpkevleelkpdaiill 108
                                        + ++vd   r ke++g+++++  ++ ++++p+ +il+
  gi|242399400|ref|YP_002994824.1| 188 VDVIIVDSAGRHKEEKGLIEEMR-QISNTINPHEVILI 224
                                       4558*************999988.599*****999986 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   9.9e-06    0.0057       1      75 [.     107     192 ..     107     225 .. 0.61

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 9.9e-06
                            AAA_33   1 lvllvGlpGsGKstlaerl...lkklg..avllssdtlrrrlfgtdqqskt..........dytrvldrlyqilnel 62 
                                       ++l+vG +GsGK+t + +l    +k+g  + ++ sdt+r   + + +q ++          +    ++++++  +e 
  gi|242399400|ref|YP_002994824.1| 107 VLLTVGIQGSGKTTSVAKLsryFQKHGykVGVVCSDTWRPGAYQQLKQLIEpygievfgnpE----EKNAIKLAKEG 179
                                       789************999877799999777779****9998887666644433333322211....22244444444 PP

                            AAA_33  63 arkalsagrnvil 75 
                                       ++   ++g +vi+
  gi|242399400|ref|YP_002994824.1| 180 VEYFKKKGVDVII 192
                                       4555566666555 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.6e-05    0.0093      19      54 ..     106     141 ..      99     226 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.6e-05
                            AAA_30  19 rvavltGpAGtGKttalkalreaweaaggrviglAp 54 
                                        v + +G  G+GKtt++++l + ++++g++v ++ +
  gi|242399400|ref|YP_002994824.1| 106 TVLLTVGIQGSGKTTSVAKLSRYFQKHGYKVGVVCS 141
                                       488999************************965433 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.3   1.1e-05    0.0063     106     169 ..     177     245 ..     170     278 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.1e-05
                                       HHHHHHHHHTT-SEEEEE-STSS..SHHHHHHHHHHHHHTTT...SEEEEEEE-SHHHHHHHHHTT-SE CS
                                       xxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 106 lervkalveagvdvlvvdsahgh..sekvleavkeikkkvee...veviaGnvataegakaLieagada 169
                                       +e v+ + ++gvdv++vdsa  h  +++ +e +++i +++++   + +i G + +++  +aL+  +a  
  gi|242399400|ref|YP_002994824.1| 177 KEGVEYFKKKGVDVIIVDSAGRHkeEKGLIEEMRQISNTINPhevILIIDGTIGQQAYNQALAFKEATP 245
                                       577889999***********6661156899*******99975234566799999999999988776654 PP

>> 6PF2K  6-phosphofructo-2-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.7e-05      0.01       9     122 ..     101     213 ..      93     233 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.7e-05
                                       T..S-EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHHHHHHSS....---GGGGSTT-HHHHHHHHHHH CS
                             6PF2K   9 lknsklvivlvGLpargKtyiskkltrylkwlgvrtkvFnvgkyrreaska....lsdaeffrpdneealklrekla 81 
                                        k++++v++ vG+   gKt+   kl+ry +  g++  v      r  a ++     + + ++ + n+e     ek a
  gi|242399400|ref|YP_002994824.1| 101 IKAKPTVLLTVGIQGSGKTTSVAKLSRYFQKHGYKVGVVCSDTWRPGAYQQlkqlIEPYGIEVFGNPE-----EKNA 172
                                       578999************************99999999888888877776632223344444444444.....5566 PP

                                       HHHHHHHHHHHHTS--SEEEEES---SHHHHHHHHHHHHHT CS
                             6PF2K  82 laalkdllaylneeegqvaifDAtNttrerRklilefveen 122
                                        +  k+ ++y+++++ +v i D     +e++ li e+ +  
  gi|242399400|ref|YP_002994824.1| 173 IKLAKEGVEYFKKKGVDVIIVDSAGRHKEEKGLIEEMRQIS 213
                                       777788999***************99999999998876544 PP

>> Fe-ADH  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   1.9e-05     0.011      10      86 ..     121     192 ..     113     193 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.9e-05
                                       GGGGHHHHHTTT-..EEEEEEEHHHH.HH.THHHHHHHHHCTT-EEEE.EEE-S---HHHHHHHHTTS-TT.--EEE CS
                            Fe-ADH  10 aleelgellkklgakralivtdkgslkksglldkvlesleeagievtvfdgvepnptleeveeaaalareegadvvi 86 
                                       ++++l ++++k+g+ ++ +v++   + + g+++++++ +e  gie  vf++ e+   ++  +e+++ ++++g+dv+i
  gi|242399400|ref|YP_002994824.1| 121 SVAKLSRYFQKHGY-KVGVVCSDT-W-RPGAYQQLKQLIEPYGIE--VFGNPEEKNAIKLAKEGVEYFKKKGVDVII 192
                                       6789999******5.******999.7.89**********888776..5699999999*******************8 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   1.5e-05    0.0085       2      31 ..     111     140 ..     110     146 .. 0.93
   2 ?   -2.6   0.1       6.6   3.8e+03     174     205 ..     339     370 ..     307     401 .. 0.55
   3 ?   -2.5   0.1         6   3.5e+03     200     216 ..     413     429 ..     368     439 .. 0.60

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.5e-05
                        ATP_bind_1   2 vGpaGsGKttfvgalseilelrgrsvavvN 31 
                                       vG  GsGKtt v +ls ++++ g++v vv 
  gi|242399400|ref|YP_002994824.1| 111 VGIQGSGKTTSVAKLSRYFQKHGYKVGVVC 140
                                       799************************996 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 6.6
                        ATP_bind_1 174 ekeleffedvealslllekeeekykklaeaia 205
                                         +le ++ +  l+++l+   +   +l+ +++
  gi|242399400|ref|YP_002994824.1| 339 YAQLEAMKKMGPLQQILKMIPGMGYSLPDEMV 370
                                       23344444444444444444444444444444 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 6
                        ATP_bind_1 200 laeaiaelleefalvlr 216
                                        +++++el+++++ + +
  gi|242399400|ref|YP_002994824.1| 413 TTKDVKELINQYNQMKK 429
                                       44444444444444433 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       4.3   2.5e+03       7      37 ..      36      69 ..      33      96 .. 0.70
   2 !   14.5   0.0   4.7e-05     0.027       3      81 ..     117     196 ..     115     200 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 4.3
                    Glyco_transf_4  7 hvleLaraLarrGheVtvv...tpgddgpleeev 37
                                      +v+++ raL    ++V++v   t + ++++ ee 
  gi|242399400|ref|YP_002994824.1| 36 VVRDIQRALITSDVNVRLVldlTKKIEKRALEEK 69
                                      6899999999999999999777666666666664 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 4.7e-05
                    Glyco_transf_4   3 GverhvleLaraLarrGheVtvvtpgddgpleeev.elvvrvprvplpllkrllrslaflrrlrrllkrekpDvvHa 78 
                                       G  ++v  L+r+++++G++V vv++++ +p ++++ + ++++ ++  ++++  ++ +  ++   + +k+ ++Dv+ +
  gi|242399400|ref|YP_002994824.1| 117 GKTTSVAKLSRYFQKHGYKVGVVCSDTWRPGAYQQlKQLIEPYGIEVFGNPEEKNAIKLAKEGVEYFKKKGVDVIIV 193
                                       567899*****************988877777777799999999999****************************98 PP

                    Glyco_transf_4  79 hsp 81 
                                        s+
  gi|242399400|ref|YP_002994824.1| 194 DSA 196
                                       775 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0         4   2.3e+03      81      81 ..      36      36 ..       7     109 .. 0.51
   2 !   14.8   0.0   4.8e-05     0.028      24     142 ..     105     226 ..      86     228 .. 0.59

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 4
                            AAA_16 81 l 81
                                      +
  gi|242399400|ref|YP_002994824.1| 36 V 36
                                      1 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 4.8e-05
                            AAA_16  24 pelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrek 100
                                       p ++l +G +G+GK++ v +l r+++k+ g+ +   c +  +  +y++l q+++   +  ++  ++e++++   +++
  gi|242399400|ref|YP_002994824.1| 105 PTVLLTVGIQGSGKTTSVAKLSRYFQKH-GYKVGVVCSDTWRPGAYQQLKQLIEP--YGIEVFGNPEEKNAIKLAKE 178
                                       4677778***************999999.44444444444222245555555533..22222222344344444444 PP

                            AAA_16 101 leeala.......avpelagaea..srllellkrllallsrderplvlvlD 142
                                         e ++       +v+++ +  +  + l e+++++ + + + ++ ++l++D
  gi|242399400|ref|YP_002994824.1| 179 GVEYFKkkgvdviIVDSAGRH-KeeKGLIEEMRQISNTINP-HE-VILIID 226
                                       444444666655323222222.2357777777777766665.33.788877 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.1   9.2e-05     0.053       4      36 ..     109     141 ..     106     151 .. 0.80
   2 ?    0.4   0.1      0.95   5.5e+02      90     129 ..     184     223 ..     168     240 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.2e-05
                                       EE.--TTSSHHHHHHHHHHHH...GGGEEEEEEE CS
                          NTPase_1   4 iT.GppGvGKtTlvkkvlellkssgvkvgGfyte 36 
                                       +T G +G+GKtT v k+++  +++g+kvg ++++
  gi|242399400|ref|YP_002994824.1| 109 LTvGIQGSGKTTSVAKLSRYFQKHGYKVG-VVCS 141
                                       444899*********************95.5554 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.95
                                       HHHHHHH-EEEE---STTGGG-HHHHH...HHHHHHTTTSEEE CS
                          NTPase_1  90 rkalseadviviDEiGkmElkskkfke...aveevLksekpvl 129
                                       +k  ++ dvi++D  G+   + k ++e   ++ +++++++++l
  gi|242399400|ref|YP_002994824.1| 184 KK--KGVDVIIVDSAGRHKEE-KGLIEemrQISNTINPHEVIL 223
                                       33..67899999999986433.333330114555555555444 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   4.9e-05     0.028      10      98 ..      99     190 ..      90     212 .. 0.63
   2 ?   -3.3   0.0         8   4.6e+03     157     179 ..     418     440 ..     414     447 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.9e-05
                        Zeta_toxin  10 ypsqerPklillgGqpGAGKselaellkdelerqgnvv.rldpDdlRelh.Peyeeilka.dpkkaseltqkdasel 83 
                                       +  + +P+++l +G +G+GK++  ++l ++++++g  v ++  D+ R+    + +++++    + + +  +k a +l
  gi|242399400|ref|YP_002994824.1|  99 VEIKAKPTVLLTVGIQGSGKTTSVAKLSRYFQKHGYKVgVVCSDTWRPGAyQQLKQLIEPyGIEVFGNPEEKNAIKL 175
                                       555689*************************9777665256677777643022333333212222233334555666 PP

                        Zeta_toxin  84 vekllqeaiengyni 98 
                                       +++ +++  ++g+++
  gi|242399400|ref|YP_002994824.1| 176 AKEGVEYFKKKGVDV 190
                                       666666666666664 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 8
                        Zeta_toxin 157 eehdeafeglresvealeeekql 179
                                       +e +++++++++ ++ ++++k++
  gi|242399400|ref|YP_002994824.1| 418 KELINQYNQMKKFFRSMDKRKLA 440
                                       56677888888888888877765 PP

>> RNase_Zc3h12a  Zc3h12a-like Ribonuclease NYN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.096        56      25      53 ..     120     148 ..     106     160 .. 0.78
   2 ?    8.7   0.0    0.0024       1.4      28     108 ..     177     252 ..     160     255 .. 0.75
   3 ?   -2.6   0.1       7.2   4.2e+03      75      99 ..     419     443 ..     378     447 .. 0.46

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.096
                     RNase_Zc3h12a  25 rglaiaveyFvkrgheeitvfvpkfrkea 53 
                                         +a + +yF k g+++ +v + ++r  a
  gi|242399400|ref|YP_002994824.1| 120 TSVAKLSRYFQKHGYKVGVVCSDTWRPGA 148
                                       56677889*****************8655 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0024
                     RNase_Zc3h12a  28 aiaveyFvkrgheeitvfvpkfrkealkkekvsdkealeeLekenlivltpskyldgkksvsyddrlilelAeekdG 104
                                       ++ veyF+k+g+++i+v ++   +++ +k  +++ +++++ ++ + ++l   +++    +++y   l+ + A     
  gi|242399400|ref|YP_002994824.1| 177 KEGVEYFKKKGVDVIIVDSAGR-HKE-EKGLIEEMRQISNTINPHEVILIIDGTIG---QQAYNQALAFKEATPIGS 248
                                       5679********6666655544.444.5899*******998886665555555665...588999999999999999 PP

                     RNase_Zc3h12a 105 vivs 108
                                       +iv+
  gi|242399400|ref|YP_002994824.1| 249 IIVT 252
                                       9998 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 7.2
                     RNase_Zc3h12a  75 vltpskyldgkksvsyddrlilelA 99 
                                       +l +++++ +k  +s d r + ++A
  gi|242399400|ref|YP_002994824.1| 419 ELINQYNQMKKFFRSMDKRKLAKMA 443
                                       2333334444444555555555555 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       9.3   5.4e+03      92     130 ..      37      74 ..      24      87 .. 0.53
   2 ?   12.8   0.0   0.00014     0.083       2      49 ..     105     152 ..     104     157 .. 0.89
   3 ?   -2.0   0.0       4.9   2.9e+03      55      72 ..     431     448 ..     416     451 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 9.3
                                       HHHHHHCHTEEEEEEEE--HHHHHHHTTTSHHHHHHTTS CS
                        APS_kinase  92 arelleealkfievfvdtplevceerDpkglYkkareGe 130
                                       +r++ + al   +v v+  l+ +++ +++ l +k  +G 
  gi|242399400|ref|YP_002994824.1|  37 VRDIQR-ALITSDVNVRLVLDLTKKIEKRALEEKPPAGV 74 
                                       333333.23334555555555555555555555555554 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00014
                                       -EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT- CS
                        APS_kinase   2 gvvvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdL 49 
                                       ++v++  G+ gsGK+t   +l+++ +++g++v ++  d+ R g +++L
  gi|242399400|ref|YP_002994824.1| 105 PTVLLTVGIQGSGKTTSVAKLSRYFQKHGYKVGVVCSDTWRPGAYQQL 152
                                       5677778*******************************9999888877 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 4.9
                                       HHHHHHHHHHHHHHHHHH CS
                        APS_kinase  55 dRkenirrvaevakllad 72 
                                        R+++ r++a++ak+++ 
  gi|242399400|ref|YP_002994824.1| 431 FRSMDKRKLAKMAKRFNM 448
                                       588999999999999975 PP

>> Beach  Beige/BEACH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.5   5.1e-05     0.029      56     169 ..     313     442 ..     303     448 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.1e-05
                             Beach  56 dLskpigalneerleklkeryeelee..............eepkflygshyssa.aivlyylvRlePftelalelqs 117
                                       +Lsk +   +e+ ++ lk +++ ++               ++ k++ g  ys +  +v +  vRl+ f  ++ ++ +
  gi|242399400|ref|YP_002994824.1| 313 ELSKEVEFKEEDMEKFLKGKFNLKDMyaqleamkkmgplqQILKMIPGMGYSLPdEMVRMSEVRLKKFKVIMDSMTE 389
                                       55666655555555555555554211233334455666667778888999997746788899*************** PP

                             Beach 118 gkfdvadrl.fksieeawesvtesesdvkEliPeffylpefllnsnnldlglk 169
                                       ++ ++++ + ++ i++  + + ++++dvkEli ++  +++f+++ ++ +l ++
  gi|242399400|ref|YP_002994824.1| 390 EELENPEIInYSRIKRIARGSGTTTKDVKELINQYNQMKKFFRSMDKRKLAKM 442
                                       ******98735679999999999*********************999888754 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00013     0.074       5      40 ..     109     144 ..     105     156 .. 0.84
   2 ?   -1.9   0.0       3.2   1.8e+03      17      41 ..     175     199 ..     165     213 .. 0.79
   3 ?   -0.2   0.3      0.92   5.3e+02     212     266 ..     385     442 ..     304     446 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00013
                                       EEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHH CS
                             KTI12   5 vltGlPssGKstrakeLakaleeekrsvvviddesl 40 
                                       +  G+  sGK+t +++L++++++++++v v+ +++ 
  gi|242399400|ref|YP_002994824.1| 109 LTVGIQGSGKTTSVAKLSRYFQKHGYKVGVVCSDTW 144
                                       3459999*********************99988876 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.2
                                       HHHHHHHHHHHTT--EEEE-THHHH CS
                             KTI12  17 rakeLakaleeekrsvvviddeslg 41 
                                       +ake  +++++++ +v+++d++  +
  gi|242399400|ref|YP_002994824.1| 175 LAKEGVEYFKKKGVDVIIVDSAGRH 199
                                       5677778999999999999987666 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.92
                                       .HTT--HHH....................HHHHHHHHHHHHHHHT.TSSS--HHHHHHH CS
                             KTI12 212 savaidkltlpgsseslelpak....kltlaeLsrlrrqFvklnkaklenvdeekiakl 266
                                        ++  ++l++p+  ++ ++++       t + +++l  q+ +++k   +++d+ k+ak+
  gi|242399400|ref|YP_002994824.1| 385 DSMTEEELENPEIINYSRIKRIargsGTTTKDVKELINQYNQMKK-FFRSMDKRKLAKM 442
                                       344444455554444444443333345677788888888888888.7777777777665 PP

>> LpxK  Tetraacyldisaccharide-1-P 4'-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   0.00012     0.067      46      71 ..     114     139 ..     105     141 .. 0.89
   2 ?   -3.7   0.0       8.6     5e+03     125     137 ..     184     196 ..     178     203 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00012
                                       S-HSHHHHHHHHHHHTTTS..-EEEE CS
                              LpxK  46 GGtGKTPlvialvkllqarglkvgvl 71 
                                        G+GKT  v+ l +++q++g+kvgv+
  gi|242399400|ref|YP_002994824.1| 114 QGSGKTTSVAKLSRYFQKHGYKVGVV 139
                                       49***********************8 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 8.6
                                       HHC--SEEEEET- CS
                              LpxK 125 akaeldviilDDG 137
                                       +k+++dvii+D +
  gi|242399400|ref|YP_002994824.1| 184 KKKGVDVIIVDSA 196
                                       4466889998865 PP

>> tRNA_lig_kinase  tRNA ligase kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.23   1.3e+02       1      25 [.     107     131 ..     107     156 .. 0.87
   2 ?    9.4   0.0    0.0018         1      33      82 ..     166     214 ..     147     225 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.23
                                       EEEEE--TTSSHHHHHHHHHHH-TT CS
                   tRNA_lig_kinase   1 llvpiatiGCGkttvaltlenlfge 25 
                                       +l+++ + G Gktt    l++ f +
  gi|242399400|ref|YP_002994824.1| 107 VLLTVGIQGSGKTTSVAKLSRYFQK 131
                                       6899999*********999999975 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0018
                                       GS-TT-SS-HHHHHHHTTSSTT--EEEEES---SHHHHHHHHHHHHHHHH CS
                   tRNA_lig_kinase  33 nitgkdkkklvkealellkkdeskvvlvDrnnhqkreRkqlfeeidelke 82 
                                       n ++k+  kl+ke +e +kk++  v++vD    +k e k l+ee+ ++ +
  gi|242399400|ref|YP_002994824.1| 166 NPEEKNAIKLAKEGVEYFKKKGVDVIIVDSAGRHK-EEKGLIEEMRQISN 214
                                       55678899*********************987665.55788888887765 PP

>> Bromo_TP_like  Histone-fold protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.3   0.00038      0.22      61     108 ..     312     359 ..     304     364 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00038
                     Bromo_TP_like  61 eeslgedsYkrnELlsFLkyqlnlkkqlktkeaveedeslleiLkvlp 108
                                       ee + e ++k++++ +FLk + nlk+   + ea+++   l +iLk++p
  gi|242399400|ref|YP_002994824.1| 312 EELSKEVEFKEEDMEKFLKGKFNLKDMYAQLEAMKKMGPLQQILKMIP 359
                                       56778999**************************************98 PP

>> VirE  Virulence-associated protein E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00019      0.11      21      76 ..      72     129 ..      52     136 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00019
                              VirE  21 lGaedstytravsklflvaavarvleP.giKfD.fvlvLvGkqgsgKstfleklgeew 76 
                                        G++++++  ++    l+   ++  +P  iK+  +vl  vG qgsgK+t+++kl+ ++
  gi|242399400|ref|YP_002994824.1|  72 AGVSKKEHIVKIVYEELTNFLGKEAKPvEIKAKpTVLLTVGIQGSGKTTSVAKLSRYF 129
                                       5888888888888889999999999998888762677779**************9988 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   0.00014     0.081       3      27 ..     112     136 ..     112     142 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00014
                                       ESTTSSHHHHHHHHHHHHHHTTE.E CS
                   Thymidylate_kin   3 GlDGaGKttqaellkerlkeegikv 27 
                                       G+ G+GKtt +++l +++++ g+kv
  gi|242399400|ref|YP_002994824.1| 112 GIQGSGKTTSVAKLSRYFQKHGYKV 136
                                       99********************994 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 ?    9.0   0.3    0.0025       1.4      63     102 ..     304     344 ..     301     348 .. 0.92
   2 ?    1.8   0.0      0.41   2.4e+02       4      29 ..     413     438 ..     410     447 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0025
                             Mod_r  63 lqekleelkelekefeekeqeldell.qkfspdallarLqt 102
                                       +q  le+++el+ke+e ke+++++ l  kf+++ ++a+L++
  gi|242399400|ref|YP_002994824.1| 304 IQGLLEKFEELSKEVEFKEEDMEKFLkGKFNLKDMYAQLEA 344
                                       788899******************9999**********986 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.41
                             Mod_r   4 SkeeLqelledeeklealvktlpevk 29 
                                       ++++ +el+++  ++++++ ++++ k
  gi|242399400|ref|YP_002994824.1| 413 TTKDVKELINQYNQMKKFFRSMDKRK 438
                                       78889999999999999998887644 PP

>> DUF4763  Domain of unknown function (DUF4763)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   2.9    0.0029       1.7      30     148 ..     312     435 ..     303     444 .. 0.58

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0029
                           DUF4763  30 eeisseselpaeqe..eeeeeldLdeiydelekiKqrvlelrskLalnvp....ecPeidecvdedle.lellt..s 97 
                                       ee+s+e e+++e      +++++L+++y++le++K ++ +l++ L++  p      P  de+v +++  l++++  +
  gi|242399400|ref|YP_002994824.1| 312 EELSKEVEFKEEDMekFLKGKFNLKDMYAQLEAMK-KMGPLQQILKMI-PgmgySLP--DEMVRMSEVrLKKFKviM 384
                                       5566666655543225899**************98.578888888743.32333333..444444332023333112 PP

                           DUF4763  98 eqpeileLqrnnhkLrqqlaelqqhlkasrkslkelreslcqekkrlrklq 148
                                       ++    eL   +     +++++++   +++k++kel +++ q kk+ r++ 
  gi|242399400|ref|YP_002994824.1| 385 DSMTEEELENPEIINYSRIKRIARGSGTTTKDVKELINQYNQMKKFFRSMD 435
                                       333334444445555556666666666666666666666666666666665 PP

>> ASL_C  Adenylosuccinate lyase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0       1.3   7.5e+02      73      97 ..      17      41 ..       9      58 .. 0.81
   2 ?    2.1   0.1      0.34     2e+02      73     110 ..     309     346 ..     299     352 .. 0.80
   3 ?    6.4   0.3     0.016       9.5      71     101 ..     399     429 ..     368     444 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.3
                                      HHHHHHHTTS---HHHHHHHHHCS- CS
                             ASL_C 73 eklkeltrgkkitkeslkefiesle 97
                                      ++lk+l r ++++++ +++++++++
  gi|242399400|ref|YP_002994824.1| 17 NALKKLARASTVDEALVRDVVRDIQ 41
                                      5799********9999999998764 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.34
                                       HHHHHHHTTS---HHHHHHHHHCS-S-HHHHHHHHC-- CS
                             ASL_C  73 eklkeltrgkkitkeslkefieslevseeakeeLkalt 110
                                       ek  el ++ + ++e++++f+++    +++ ++L+a++
  gi|242399400|ref|YP_002994824.1| 309 EKFEELSKEVEFKEEDMEKFLKGKFNLKDMYAQLEAMK 346
                                       7889999999***********99865566667777665 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.016
                                       HHHHHHHHHTTS---HHHHHHHHHCS-S-HH CS
                             ASL_C  71 pYeklkeltrgkkitkeslkefieslevsee 101
                                        Y ++k++ rg+ +t++++ke+i++ +  ++
  gi|242399400|ref|YP_002994824.1| 399 NYSRIKRIARGSGTTTKDVKELINQYNQMKK 429
                                       39*********************99864443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (453 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1148  (0.0640303); expected 358.6 (0.02)
Passed bias filter:                      784  (0.043728); expected 358.6 (0.02)
Passed Vit filter:                       122  (0.00680462); expected 17.9 (0.001)
Passed Fwd filter:                        31  (0.00172904); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              31  [number of targets reported over threshold]
# CPU time: 0.63u 0.32s 00:00:00.95 Elapsed: 00:00:00.46
# Mc/sec: 2988.90
//
Query:       gi|242399401|ref|YP_002994825.1|  [L=79]
Description: transcription regulator, Lrp/AsnC family [Thermococcus sibiricus MM 739]
Scores for complete 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-18   64.2   0.2    8.9e-18   64.0   0.2    1.0  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
  ------ inclusion threshold ------
      0.027   14.5   0.2      0.093   12.8   0.2    1.7  1  NapD            NapD protein
      0.066   14.0   0.0      0.071   13.9   0.0    1.1  1  GARS_N          Phosphoribosylglycinamide synthetase, N domai


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 !   64.0   0.2   1.5e-21   8.9e-18       1      72 [.       6      74 ..       6      76 .. 0.96

  Alignments for each domain:
  == domain 1  score: 64.0 bits;  conditional E-value: 1.5e-21
                                      EEEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEE CS
                    AsnC_trans_reg  1 vlvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsiv 72
                                      vl+ ++pg+    +++ e+l +lp+V+e+y+v G+yd++++v v++++ l++f+++ l+++++++ tet+i+
  gi|242399401|ref|YP_002994825.1|  6 VLIIVKPGN---EDVVYEKLSKLPQVKEVYKVYGEYDIIIRVEVENIKGLDEFHDNVLRRINEIEMTETLIA 74
                                      678899999...9*********************************************************97 PP

>> NapD  NapD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   1.6e-05     0.093       6      50 ..       6      58 ..       6      76 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.6e-05
                              NapD  6 lvVqarperlaavkaalaalpgv.EvhasdeegklVvviEaesed.......e 50
                                      +++ ++p++ + v ++l +lp+v Ev+ + +e  +++ +E e+ +       +
  gi|242399401|ref|YP_002994825.1|  6 VLIIVKPGNEDVVYEKLSKLPQVkEVYKVYGEYDIIIRVEVENIKgldefhdN 58
                                      57999*****************999***************9998844433333 PP

>> GARS_N  Phosphoribosylglycinamide synthetase, N 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     0.071       3      38 ..       6      53 ..       4      75 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.2e-05
                                      EEEEESSHHHHHHHHHHTTSTTESEEEEEE--CGG............T CS
                            GARS_N  3 vLvvGsGGRehalawklaqspkvekvyvapgNagt............e 38
                                      vL++ + G e  + +kl++ p+v++vy + g   +            +
  gi|242399401|ref|YP_002994825.1|  6 VLIIVKPGNEDVVYEKLSKLPQVKEVYKVYGEYDIiirvevenikglD 53
                                      89***************************9998887777764333331 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); 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: 0.47u 0.33s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 474.77
//
Query:       gi|242399402|ref|YP_002994826.1|  [L=174]
Description: Fe-S-cluster oxidoreductase [Thermococcus sibiricus MM 739]
Scores for complete 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   56.5   0.8    4.5e-15   56.1   0.8    1.2  1  CxxCxxCC       Putative zinc- or iron-chelating domain
  ------ inclusion threshold ------
       0.02   14.7   0.9        2.5    7.9   0.1    2.1  2  DUF3109        Protein of unknown function (DUF3109)
      0.068   13.2   0.1       0.11   12.6   0.1    1.3  1  Nit_Regul_Hom  Uncharacterized protein, homolog of nitrogen r


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 !   56.1   0.8   7.5e-19   4.5e-15       2      84 ..      26     129 ..      25     130 .. 0.87

  Alignments for each domain:
  == domain 1  score: 56.1 bits;  conditional E-value: 7.5e-19
                          CxxCxxCC   2 Cke.CgaCCkelkvklteedlerlkaaevaeeeeeskkiak.................adgrCvfldeetklCkiYe 60 
                                       C   C+ CC e ++ l++ed++++++ +++  e+   +  k                  d  Cvfl ++  +CkiY+
  gi|242399402|ref|YP_002994826.1|  26 CLPkCARCCIEFDIPLRDEDIAKIEELDYNAWEFVDYE--KmfyrgdkflgyglkkrpFDDGCVFLGDDY-KCKIYS 99 
                                       7777*************************665555444..44588***********************96.****** PP

                          CxxCxxCC  61 eRpkicrlfpas......ekeellaraetC 84 
                                       +Rp++crl+p++      + e + + +++C
  gi|242399402|ref|YP_002994826.1| 100 HRPLACRLYPFVlirhgmNLEIYVKEDSFC 129
                                       ***********9998888777788888888 PP

>> DUF3109  Protein of unknown function (DUF3109)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.1    0.0018        11      17      60 ..      23      62 ..      11      70 .. 0.81
   2 ?    7.9   0.1   0.00042       2.5     113     147 ..      96     130 ..      86     156 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0018
                           DUF3109 17 kFvCdleaCkGaCCvegdaGapleeeElekleeilekvkealse 60
                                      kF+C l +C   CC+e d   pl++e+++k+ee+  + +e+++ 
  gi|242399402|ref|YP_002994826.1| 23 KFTC-LPKCA-RCCIEFD--IPLRDEDIAKIEELDYNAWEFVDY 62
                                      6777.77885.8999877..59*********9998888887765 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00042
                           DUF3109 113 kikfkKPisChlyPirvkklselealnyerweiCk 147
                                       ki  ++P+ C+lyP  + ++    ++  ++ + Ck
  gi|242399402|ref|YP_002994826.1|  96 KIYSHRPLACRLYPFVLIRHGMNLEIYVKEDSFCK 130
                                       667789********988877776666666666776 PP

>> Nit_Regul_Hom  Uncharacterized protein, homolog of nitrogen regulatory protein PII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   1.8e-05      0.11       4      42 ..     118     156 ..     115     168 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.8e-05
                     Nit_Regul_Hom   4 llklfvesenlgkvinalseagitGfylieYkGlsPqew 42 
                                        l+++v ++   k in    + itG ++i+Y G   +e+
  gi|242399402|ref|YP_002994826.1| 118 NLEIYVKEDSFCKGINNPNGESITGNFIIQYFGNVIEEY 156
                                       699****************************99776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); expected 358.6 (0.02)
Passed bias filter:                      201  (0.0112109); 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: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1241.88
//
Query:       gi|242399403|ref|YP_002994827.1|  [L=237]
Description: Adenine phosphoribosyltransferase, fused to N-terminal DNA-binding domain, partial [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-11   44.5   0.2    1.6e-11   44.0   0.2    1.3  1  Pribosyltran    Phosphoribosyl transferase domain
    1.2e-05   25.3   0.3    2.3e-05   24.3   0.3    1.5  1  HTH_3           Helix-turn-helix
  ------ inclusion threshold ------
       0.02   14.4   0.1       0.18   11.4   0.1    2.5  2  HTH_24          Winged helix-turn-helix DNA-binding
      0.027   14.9   0.0      0.058   13.8   0.0    1.5  1  HTH_26          Cro/C1-type HTH DNA-binding domain
      0.036   14.6   0.4       0.14   12.7   0.0    2.2  3  PepSY_like      Putative beta-lactamase-inhibitor-like, PepSY
       0.11   12.6   0.1       0.35   11.0   0.1    1.8  1  Trp_repressor   Trp repressor protein
       0.14   12.3   0.1       0.31   11.1   0.1    1.6  1  MqsA_antitoxin  Antitoxin component of bacterial toxin-antito


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 !   44.0   0.2   6.2e-15   1.6e-11       5     124 ..      89     214 ..      85     233 .. 0.87

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 6.2e-15
                                       TTT---EEEEEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE.......... CS
                      Pribosyltran   5 llenpaildavarlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdes.. 79 
                                       +l+   +++ +a+ +a+++++   k+d +++ a+ G+p+a ++ +eL+  +++v+++k+r+ g e++ +++ ++s  
  gi|242399403|ref|YP_002994827.1|  89 ILSDNDLMNLIAESIASKYRD--KKIDKILTAATDGIPLAIHIGNELG--VDVVYAKKKREVGVEKFYEVNYVSSss 161
                                       555566788888888888888..9***********************9..789999999999999999888888899 PP

                                       ........EE----TTSEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEE CS
                      Pribosyltran  80 ........rlledpagkkVliVDDildtGgTllaalelLkekgpeevriavlv 124
                                                  ++++g+ +liVDD++ +G T +a le  k ++ + v+   l+
  gi|242399403|ref|YP_002994827.1| 162 gsimtlylPHWAIKKGENILIVDDVVRSGETQKALLEMCKQANTTPVGMFFLI 214
                                       ********999**************************9999998877776666 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.3     9e-09   2.3e-05       1      47 [.      14      61 ..      14      63 .. 0.88

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 9e-09
                                      HHHHHH.HTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHH CS
                             HTH_3  1 lkelRk.qlglsqeeLAeklGvsrstisriEnGernPsletlkklaka 47
                                      ++ lR+ +++++ eeL++ +G++ + ++r+ +G+  Ps ++  +l k 
  gi|242399403|ref|YP_002994827.1| 14 IRVLRLlKKNYTYEELSRITGLPITVLNRYVRGKVLPSTQRTRELIKI 61
                                      5667888******************************99876666665 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   7.2e-05      0.18       7      39 ..      15      45 ..      10      45 .. 0.82
   2 ?   -0.6   0.0      0.39   9.9e+02      29      40 ..     214     225 ..     213     225 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7.2e-05
                            HTH_24  7 kILelLqknprisqreLAerlglSpstvnrrlk 39
                                      ++L+lL+k  + ++ eL++ +gl+++ +nr+++
  gi|242399403|ref|YP_002994827.1| 15 RVLRLLKK--NYTYEELSRITGLPITVLNRYVR 45
                                      55555555..78*******************97 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.39
                            HTH_24  29 lSpstvnrrlkr 40 
                                       +S+++v  r+k+
  gi|242399403|ref|YP_002994827.1| 214 ISVGNVIDRIKE 225
                                       8*********96 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.3e-05     0.058       8      46 ..      21      61 ..      16      63 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.3e-05
                            HTH_26  8 drgitkseLargtgisaatlsrlvkgk..pervsldtLdki 46
                                      ++++t+ eL+r tg+  + l+r+v gk  p++ ++ +L ki
  gi|242399403|ref|YP_002994827.1| 21 KKNYTYEELSRITGLPITVLNRYVRGKvlPSTQRTRELIKI 61
                                      8999***********************55577777777777 PP

>> PepSY_like  Putative beta-lactamase-inhibitor-like, PepSY-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0         3   7.8e+03      40      57 ..      16      33 ..      15      39 .. 0.80
   2 ?   12.7   0.0   5.4e-05      0.14      11      69 ..      74     131 ..      66     145 .. 0.79
   3 ?   -3.6   0.0       6.6   1.7e+04      56      65 ..     220     229 ..     217     233 .. 0.53

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 3
                                      HHHHHHHHTTTEEEEEEE CS
                        PepSY_like 40 vlkaiknsypdekvtkie 57
                                      vl+ +k++y+ e+  +i+
  gi|242399403|ref|YP_002994827.1| 16 VLRLLKKNYTYEELSRIT 33
                                      667789999998887775 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 5.4e-05
                                       EEEEE-TTS-EEEEE-TTSEESGGGS-HHHHHHHHHHTTTEEEEEEEECS...SEEEEEETT CS
                        PepSY_like  11 teveFdkkGeWkeiegkkteiplsilpkavlkaiknsypdekvtkierkk...keyeielen 69 
                                         + Fdk G +  ++     ++ ++l + ++++i+++y d+k++ki  +        i + n
  gi|242399403|ref|YP_002994827.1|  74 RRIIFDKHGLFDNLK----ILSDNDLMNLIAESIASKYRDKKIDKILTAAtdgIPLAIHIGN 131
                                       5799*********99....88************************98776433444555555 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 6.6
                                       EEECSSEEEE CS
                        PepSY_like  56 ierkkkeyei 65 
                                       i+r k+ey+i
  gi|242399403|ref|YP_002994827.1| 220 IDRIKEEYKI 229
                                       4444455555 PP

>> Trp_repressor  Trp repressor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00013      0.35      31      68 ..       3      42 ..       1      47 [. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00013
                     Trp_repressor 31 ErealaqRlqvvk..eLLkeelsqreIaeelgvSiAtItR 68
                                       +e++ + l+v++  +LLk++++++e++  +g  i+   R
  gi|242399403|ref|YP_002994827.1|  3 QIESVKEKLRVIRvlRLLKKNYTYEELSRITGLPITVLNR 42
                                      57888888888763349***************99998777 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 ?   11.1   0.1   0.00012      0.31      74     130 ..      13      72 ..       2      73 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00012
                    MqsA_antitoxin  74 iarvrk..kleldqreaaeifGgGvnafsryekGkvrppla.lvkllklldrhPelleei 130
                                       ++rv +  k + + +e+++i G  +  ++ry +Gkv p++  + +l+k+l  + +l ee+
  gi|242399403|ref|YP_002994827.1|  13 VIRVLRllKKNYTYEELSRITGLPITVLNRYVRGKVLPSTQrTRELIKILSPYMNLEEEV 72 
                                       444444124467889**********************98762557999999999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1461.05
//
Query:       gi|242399404|ref|YP_002994828.1|  [L=116]
Description: hypothetical protein TSIB_1428 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score 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   0.1      0.014   15.6   0.1    1.1  1  zf-C2H2_aberr  Aberrant zinc-finger
        0.2   11.8   1.7        2.7    8.2   0.4    2.4  2  zf-RAG1        Recombination-activating protein 1 zinc-finger


Domain annotation for each model (and alignments):
>> zf-C2H2_aberr  Aberrant zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.1   1.5e-06     0.014      29      91 ..      26      97 ..      13     112 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.5e-06
                     zf-C2H2_aberr 29 lytnsefslkCpvrkCses........ivelen.telleehlekehaakllellkeleieikkteetekvny 91
                                       y n++f++ Cp+++C e         iv le  +++l+e ++k+   +++++l+ + + ++ t + ++v+ 
  gi|242399404|ref|YP_002994828.1| 26 TYLNEKFKFICPIEECGENieiegvikIVSLEEyKQVLKETVKKNKEFEVIKTLNPTPLIFDGTVNGKRVKL 97
                                      69**************98888899888777765156677888888888999988888777777766666665 PP

>> zf-RAG1  Recombination-activating protein 1 zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.4   0.00031       2.7       5      17 ..      36      48 ..      34      49 .. 0.87
   2 ?    2.4   0.0      0.02   1.8e+02      14      21 ..      54      61 ..      52      64 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00031
                           zf-RAG1  5 CPaKdCdEeVsLE 17
                                      CP+ +C E++  E
  gi|242399404|ref|YP_002994828.1| 36 CPIEECGENIEIE 48
                                      *********9876 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.02
                           zf-RAG1 14 VsLEkYnq 21
                                      VsLE+Y q
  gi|242399404|ref|YP_002994828.1| 54 VSLEEYKQ 61
                                      9*****87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       846  (0.0471861); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); 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: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 745.69
//
Query:       gi|242399405|ref|YP_002994829.1|  [L=151]
Description: Transcription regulator, Lrp/AsnC family [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-19   68.2   0.6    6.7e-19   67.2   0.6    1.5  1  HTH_24           Winged helix-turn-helix DNA-binding
    1.5e-16   59.9   0.1    2.5e-16   59.2   0.1    1.4  1  HTH_AsnC-type    AsnC-type helix-turn-helix domain
    5.6e-14   51.9   0.1    8.6e-14   51.3   0.1    1.3  1  AsnC_trans_reg   Lrp/AsnC ligand binding domain
    2.2e-07   30.5   0.1    3.9e-07   29.7   0.1    1.4  1  HTH_23           Homeodomain-like domain
    2.4e-07   30.6   0.1    4.1e-07   29.8   0.1    1.5  1  HTH_11           HTH domain
    1.3e-06   28.4   0.0      2e-06   27.8   0.0    1.3  1  HTH_20           Helix-turn-helix domain
    1.5e-06   28.2   0.0    2.9e-06   27.3   0.0    1.4  1  HTH_28           Helix-turn-helix domain
    2.4e-06   27.3   0.0    3.9e-06   26.6   0.0    1.3  1  HTH_5            Bacterial regulatory protein, arsR family
      7e-06   25.6   0.0    1.4e-05   24.7   0.0    1.5  1  Sigma70_r4_2     Sigma-70, region 4
    4.5e-05   23.1   0.2     0.0001   22.0   0.1    1.7  1  HTH_38           Helix-turn-helix domain
    0.00024   20.6   0.1    0.00064   19.3   0.1    1.7  1  HTH_50           Helix-turn-helix domain
    0.00025   20.9   0.1    0.00056   19.8   0.1    1.5  1  MarR             MarR family
    0.00049   19.7   0.0     0.0013   18.4   0.0    1.7  1  HTH_41           Helix-turn-helix domain
     0.0005   19.9   0.5     0.0014   18.5   0.1    1.8  2  TrmB             Sugar-specific transcriptional regulator Trm
    0.00074   19.3   0.0     0.0012   18.6   0.0    1.2  1  HTH_IclR         IclR helix-turn-helix domain
    0.00088   19.0   0.0     0.0016   18.2   0.0    1.4  1  HTH_30           PucR C-terminal helix-turn-helix domain
    0.00098   18.8   0.1     0.0026   17.5   0.1    1.7  1  HTH_DeoR         DeoR-like helix-turn-helix domain
      0.001   18.7   0.1     0.0019   17.8   0.1    1.4  1  GntR             Bacterial regulatory proteins, gntR family
     0.0016   18.4   0.0     0.0031   17.5   0.0    1.5  1  HTH_Crp_2        Crp-like helix-turn-helix domain
     0.0039   16.8   0.0     0.0073   15.9   0.0    1.4  1  Crp              Bacterial regulatory proteins, crp family
     0.0048   16.9   0.0      0.009   16.0   0.0    1.4  1  HTH_29           Winged helix-turn helix
     0.0051   17.2   0.1      0.012   16.0   0.1    1.7  1  HTH_40           Helix-turn-helix domain
     0.0064   16.0   0.0      0.014   14.9   0.0    1.6  1  HTH_CodY         CodY helix-turn-helix domain
     0.0073   15.3   0.1      0.011   14.8   0.1    1.1  1  TnsD             Tn7-like transposition protein D
     0.0085   15.9   0.1      0.017   14.9   0.1    1.5  1  HTH_10           HTH DNA binding domain
     0.0098   15.4   0.0      0.019   14.5   0.0    1.4  1  Sigma70_r4       Sigma-70, region 4
       0.01   16.0   0.1      0.028   14.6   0.0    1.7  1  HTH_34           Winged helix DNA-binding domain
       0.01   15.6   0.0      0.025   14.3   0.0    1.6  1  TetR_N           Bacterial regulatory proteins, tetR family
  ------ inclusion threshold ------
       0.01   15.8   0.1      0.016   15.2   0.1    1.3  1  HTH_36           Helix-turn-helix domain
      0.012   15.5   0.0      0.019   14.9   0.0    1.3  1  MarR_2           MarR family
      0.023   14.8   0.0      0.041   14.0   0.0    1.4  1  AsnC_trans_reg2  AsnC-like ligand binding domain
      0.024   14.4   0.0      0.041   13.7   0.0    1.3  1  LexA_DNA_bind    LexA DNA binding domain
      0.026   14.6   0.0      0.047   13.7   0.0    1.4  1  HTH_Mga          M protein trans-acting positive regulator (M
      0.029   14.5   0.0      0.049   13.8   0.0    1.5  1  FUR              Ferric uptake regulator family
      0.046   13.1   0.0      0.073   12.5   0.0    1.3  1  RepL             Firmicute plasmid replication protein (RepL)
      0.047   13.9   0.0       0.16   12.2   0.0    1.9  1  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
      0.055   13.4   0.1       0.13   12.2   0.1    1.7  1  PadR             Transcriptional regulator PadR-like family
      0.064   12.9   0.1        0.1   12.2   0.1    1.2  1  DDRGK            DDRGK domain
      0.075   13.0   0.4       0.19   11.7   0.4    1.7  1  HTH_12           Ribonuclease R winged-helix domain
      0.077   13.0   0.1       0.21   11.6   0.0    1.7  2  GYD              GYD domain
      0.087   12.9   0.0       0.19   11.8   0.0    1.7  1  HTH_22           HTH domain
      0.088   13.4   0.0       0.29   11.8   0.0    1.8  2  HTH_32           Homeodomain-like domain
       0.12   12.7   0.1        2.4    8.5   0.0    2.4  2  NUMOD1           NUMOD1 domain
       0.13   12.5   0.1       0.32   11.3   0.1    1.6  1  HTH_Tnp_Tc3_2    Transposase
       0.18   11.3   0.0       0.28   10.6   0.0    1.3  1  HTH_Tnp_ISL3     Helix-turn-helix domain of transposase famil


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 !   67.2   0.6   1.7e-21   6.7e-19       2      47 ..       7      52 ..       6      52 .. 0.99

  Alignments for each domain:
  == domain 1  score: 67.2 bits;  conditional E-value: 1.7e-21
                            HTH_24  2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      de+drkI+++Lqk++r+s+re+A++lg+ ++tv  rlk+LeeeG+I
  gi|242399405|ref|YP_002994829.1|  7 DELDRKIISILQKDARLSYREIAKKLGIAVGTVYNRLKKLEEEGVI 52
                                      89*******************************************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 !   59.2   0.1   6.4e-19   2.5e-16       2      42 .]       7      47 ..       5      47 .. 0.98

  Alignments for each domain:
  == domain 1  score: 59.2 bits;  conditional E-value: 6.4e-19
                     HTH_AsnC-type  2 DeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrLe 42
                                      De+DrkI+++Lq+daR+sy+e+A+++G++  tv +R+++Le
  gi|242399405|ref|YP_002994829.1|  7 DELDRKIISILQKDARLSYREIAKKLGIAVGTVYNRLKKLE 47
                                      ****************************************8 PP

>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.3   0.1   2.2e-16   8.6e-14       1      74 [.      72     141 ..      72     142 .. 0.94

  Alignments for each domain:
  == domain 1  score: 51.3 bits;  conditional E-value: 2.2e-16
                                       EEEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEE CS
                    AsnC_trans_reg   1 vlvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivle 74 
                                       ++v+ ++++   + e+e+++a  p V  +y vtG+yd+++++++r  e++++f+++ l +++gv++t t++++ 
  gi|242399405|ref|YP_002994829.1|  72 IGVRAQGKR---IIEIEKEIASDPHVACVYDVTGEYDIIVIAKFRGREDMNKFVKK-LLRIDGVEKTYTHVAMD 141
                                       578888777...99***************************************988.**************995 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.1   9.8e-10   3.9e-07       6      46 ..      11      51 ..       7      53 .. 0.87

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 9.8e-10
                            HTH_23  6 eRlrillllaeGlsvreIAreLgvsrrTvyrwlkryreeGl 46
                                      +++  +l  + +ls+reIA++Lg+   Tvy+ lk+ +eeG+
  gi|242399405|ref|YP_002994829.1| 11 RKIISILQKDARLSYREIAKKLGIAVGTVYNRLKKLEEEGV 51
                                      56666777788*************************99996 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.1     1e-09   4.1e-07       3      45 ..      11      52 ..      10      78 .. 0.93

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 1e-09
                            HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvp 45
                                      ++i+ +L +++  +s  e+A++L++   tv++++k+Lee gv 
  gi|242399405|ref|YP_002994829.1| 11 RKIISIL-QKDARLSYREIAKKLGIAVGTVYNRLKKLEEEGVI 52
                                      699****.99999****************************75 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.0     5e-09     2e-06      10      54 ..       8      52 ..       5      54 .. 0.92

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 5e-09
                                      HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTE CS
                            HTH_20 10 PvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLv 54
                                      +  r+i + L  ++ l+  e+a+ l+++  t++++L++Lee g +
  gi|242399405|ref|YP_002994829.1|  8 ELDRKIISILQKDARLSYREIAKKLGIAVGTVYNRLKKLEEEGVI 52
                                      56699************************************9987 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   7.2e-09   2.9e-06       6      41 ..      16      51 ..      11      59 .. 0.79

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 7.2e-09
                            HTH_28  6 ikllaaGhsvreaArelgisrrtvyrWikryeegGi 41
                                      i++  a  s+re+A++lgi   tvy  +k++ee+G+
  gi|242399405|ref|YP_002994829.1| 16 ILQKDARLSYREIAKKLGIAVGTVYNRLKKLEEEGV 51
                                      55555666***************************5 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 !   26.6   0.0   9.7e-09   3.9e-06       5      45 ..      11      52 ..       7      52 .. 0.94

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 9.7e-09
                                      HHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5  5 lkILklLae.gelcvcelaeelglsqstvShHLkkLreaGLV 45
                                      +kI+++L++   l+  e+a++lg+  +tv   LkkL+e+G++
  gi|242399405|ref|YP_002994829.1| 11 RKIISILQKdARLSYREIAKKLGIAVGTVYNRLKKLEEEGVI 52
                                      69*******888****************************87 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 !   24.7   0.0   3.5e-08   1.4e-05      27      49 ..      23      45 ..       8      47 .. 0.93

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 3.5e-08
                                      --HHHHHHHHT--HHHHHHHHHH CS
                      Sigma70_r4_2 27 lsykEIAellgisegtVksrlsR 49
                                      lsy+EIA++lgi +gtV++rl++
  gi|242399405|ref|YP_002994829.1| 23 LSYREIAKKLGIAVGTVYNRLKK 45
                                      8*******************986 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.1   2.6e-07    0.0001       9      42 ..      10      44 ..       6      46 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 2.6e-07
                            HTH_38  9 eReeIerl.laeGlslreIArrLgrspsTIsRElk 42
                                      +R  I +l  ++ ls+reIA++Lg + +T+++ lk
  gi|242399405|ref|YP_002994829.1| 10 DRKIISILqKDARLSYREIAKKLGIAVGTVYNRLK 44
                                      899*****55688******************9888 PP

>> HTH_50  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1   1.6e-06   0.00064       7      46 ..       5      45 ..       4      47 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.6e-06
                            HTH_50  7 yveefErelikkayek.YpStRklAkrLGvShtaianklrk 46
                                      +v+e +r++i  + +    S R +Ak+LG+   ++ n+l+k
  gi|242399405|ref|YP_002994829.1|  5 MVDELDRKIISILQKDaRLSYREIAKKLGIAVGTVYNRLKK 45
                                      7899999999887765146********************98 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.1   1.4e-06   0.00056      10      47 ..      15      52 ..      11      53 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.4e-06
                                      HHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                              MarR 10 rilyeqgplsvseLakklgvskstvtrvldrLekkGli 47
                                       il     ls  e+akklg+  +tv + l++Le++G i
  gi|242399405|ref|YP_002994829.1| 15 SILQKDARLSYREIAKKLGIAVGTVYNRLKKLEEEGVI 52
                                      555555567888************************87 PP

>> HTH_41  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   3.3e-06    0.0013      11      36 ..      27      52 ..      22      53 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 3.3e-06
                            HTH_41 11 elakeleLSvGlvQkALklLeddkai 36
                                      e+ak+l++ vG+v   Lk+Le++++i
  gi|242399405|ref|YP_002994829.1| 27 EIAKKLGIAVGTVYNRLKKLEEEGVI 52
                                      899*********************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 !   18.5   0.1   3.5e-06    0.0014      17      52 ..      17      52 ..       7      53 .. 0.87
   2 ?   -1.7   0.0       6.8   2.7e+03      37      55 ..     116     134 ..     113     138 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 3.5e-06
                                      HHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSE CS
                              TrmB 17 LlklgpatadeiaeelgvprskvYevLrsLedkGlV 52
                                      L k  +++ +eia++lg+   +vY+ L++Le+ G++
  gi|242399405|ref|YP_002994829.1| 17 LQKDARLSYREIAKKLGIAVGTVYNRLKKLEEEGVI 52
                                      447778899************************986 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 6.8
                                       HCHHHHHHHHHHCTSEEEE CS
                              TrmB  37 skvYevLrsLedkGlVere 55 
                                          ++ +++L++ + Ve+ 
  gi|242399405|ref|YP_002994829.1| 116 EDMNKFVKKLLRIDGVEKT 134
                                       5667889999998888875 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0     3e-06    0.0012      13      47 ..      18      51 ..      12      52 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 3e-06
                                      CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTS CS
                          HTH_IclR 13 aeapqeltlselArrtglpkStvhRlLqtLvelGy 47
                                       + + +l+ +e+A+++g++  tv++ L+ L+e+G 
  gi|242399405|ref|YP_002994829.1| 18 QK-DARLSYREIAKKLGIAVGTVYNRLKKLEEEGV 51
                                      44.44599*************************96 PP

>> HTH_30  PucR C-terminal helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0     4e-06    0.0016      11      38 ..      21      48 ..      19      54 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 4e-06
                                      TTT-HHHHHHHHTS-HHHHHHHHHHHHH CS
                            HTH_30 11 nggnisatAkaLhvHrnTlryRLrriee 38
                                      +  ++++ Ak+L++ + T+++RL+++ee
  gi|242399405|ref|YP_002994829.1| 21 ARLSYREIAKKLGIAVGTVYNRLKKLEE 48
                                      567999********************98 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   6.4e-06    0.0026       4      44 ..      12      52 ..      10      54 .. 0.95

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 6.4e-06
                          HTH_DeoR  4 qilellkqqgklsveelvellgvSeaTiRRDLneLeeqgll 44
                                      +i+  l+++  ls  e++  lg++  T+ + L++Lee+g++
  gi|242399405|ref|YP_002994829.1| 12 KIISILQKDARLSYREIAKKLGIAVGTVYNRLKKLEEEGVI 52
                                      89*************************************97 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   4.8e-06    0.0019       6      54 ..       6      52 ..       3      54 .. 0.95

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 4.8e-06
                                      HHHHHHHHHTTSS-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                              GntR  6 yerLredIlsgelrpGdkLPsereLaaefgVsrttvReALrrLeaeglv 54
                                      +++L+++I+s  l+  ++L s re+a+++g+   tv   L++Le+eg++
  gi|242399405|ref|YP_002994829.1|  6 VDELDRKIIS-ILQKDARL-SYREIAKKLGIAVGTVYNRLKKLEEEGVI 52
                                      689*******.********.***************************97 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   7.7e-06    0.0031      19      51 ..      20      52 ..       6      59 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 7.7e-06
                                      EEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSE CS
                         HTH_Crp_2 19 elpltqeelAsmlGltretvsrilseLkregli 51
                                      + +l+ +e+A  lG+   tv   l++L++eg+i
  gi|242399405|ref|YP_002994829.1| 20 DARLSYREIAKKLGIAVGTVYNRLKKLEEEGVI 52
                                      4689****************************9 PP

>> Crp  Bacterial regulatory proteins, crp family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.8e-05    0.0073       2      32 .]      22      52 ..      22      52 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.8e-05
                                      E--HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                               Crp  2 pmSRqdIAdylGlTrETVSRlLtrLrekGLI 32
                                      ++S  +IA+ lG ++ TV   L++L+e+G+I
  gi|242399405|ref|YP_002994829.1| 22 RLSYREIAKKLGIAVGTVYNRLKKLEEEGVI 52
                                      68999*************8889********9 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   2.2e-05     0.009      12      41 ..      23      51 ..      14      57 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.2e-05
                            HTH_29 12 vstvsqiAkllglsrrtvyrwlkrfeegGl 41
                                      + + ++iAk lg+   tvy+ lk  ee+G+
  gi|242399405|ref|YP_002994829.1| 23 L-SYREIAKKLGIAVGTVYNRLKKLEEEGV 51
                                      4.499************************5 PP

>> HTH_40  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     3e-05     0.012      12      48 ..      22      64 ..      12      99 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3e-05
                            HTH_40 12 glsieeIAkerglkesTIegHLaelieeg......eeidlerl 48
                                       ls  eIAk+ g++++T+++ L +l eeg       ++d+++l
  gi|242399405|ref|YP_002994829.1| 22 RLSYREIAKKLGIAVGTVYNRLKKLEEEGvilgfaPKLDYNKL 64
                                      58999***********************866666655666665 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 !   14.9   0.0   3.5e-05     0.014       3      34 ..      21      52 ..      19      55 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.5e-05
                          HTH_CodY  3 GrLtaskiaDriGitrsvivnaLrkLesaGii 34
                                       rL   +ia ++Gi+   + n L+kLe  G+i
  gi|242399405|ref|YP_002994829.1| 21 ARLSYREIAKKLGIAVGTVYNRLKKLEEEGVI 52
                                      5888899************************9 PP

>> TnsD  Tn7-like transposition protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1   2.7e-05     0.011     192     226 ..      15      49 ..       8      51 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.7e-05
                              TnsD 192 keLveeeglslkeiAkelgvdiktVlryakklgll 226
                                        +L +++ ls++eiAk lg+ ++tV+  +kkl+++
  gi|242399405|ref|YP_002994829.1|  15 SILQKDARLSYREIAKKLGIAVGTVYNRLKKLEEE 49 
                                       5788889***********************99876 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   4.4e-05     0.017      23      49 ..      22      48 ..      18      49 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.4e-05
                            HTH_10 23 rvtlkeLAkelGIskstlsehLrkaes 49
                                      r + +e+Ak+lGI+  t++++L+k e+
  gi|242399405|ref|YP_002994829.1| 22 RLSYREIAKKLGIAVGTVYNRLKKLEE 48
                                      77899******************9875 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   4.7e-05     0.019       8      43 ..       9      45 ..       6      46 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.7e-05
                                      HHHHHHHHHH.TTT--HHHHHHHHTS-HHHHHHHHHH CS
                        Sigma70_r4  8 rerevlelrf.geglTleEIgerlgiSrerVrqiekr 43
                                       +r++++    +  l++ EI+++lgi  ++V  ++k+
  gi|242399405|ref|YP_002994829.1|  9 LDRKIISILQkDARLSYREIAKKLGIAVGTVYNRLKK 45
                                      56777777777999*****************888775 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0     7e-05     0.028       4      44 ..      12      52 ..      10      54 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 7e-05
                            HTH_34  4 avlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYi 44
                                      +++s+L ++ + +++e+ ++l++  g  +  lkkLe+ g i
  gi|242399405|ref|YP_002994829.1| 12 KIISILQKDARLSYREIAKKLGIAVGTVYNRLKKLEEEGVI 52
                                      699**********************************9966 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 !   14.3   0.0   6.4e-05     0.025      16      35 ..      22      41 ..      20      43 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.4e-05
                                      T--HHHHHHHHTSSHHHHHH CS
                            TetR_N 16 attvreIAkrAGvskgalYr 35
                                      +++ reIAk++G++ g++Y 
  gi|242399405|ref|YP_002994829.1| 22 RLSYREIAKKLGIAVGTVYN 41
                                      6899***************7 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.1     4e-05     0.016      27      55 .]      24      52 ..      13      52 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4e-05
                            HTH_36 27 sqetlakrlglsknTvsraikeLeqlGyi 55
                                      s++ +ak+lg+ + Tv++ +k+Le+ G i
  gi|242399405|ref|YP_002994829.1| 24 SYREIAKKLGIAVGTVYNRLKKLEEEGVI 52
                                      99**********************98865 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   4.7e-05     0.019      18      51 ..      20      52 ..      10      70 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.7e-05
                                      TTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSE CS
                            MarR_2 18 pgrdltvgelarrlglsksavsrilkrLvaaGLv 51
                                      +  +l+ +e+a++lg+  ++v ++lk+L++ G +
  gi|242399405|ref|YP_002994829.1| 20 DA-RLSYREIAKKLGIAVGTVYNRLKKLEEEGVI 52
                                      33.4999*************************87 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    0.0001     0.041       1      73 [.      63     135 ..      63     144 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 0.0001
                   AsnC_trans_reg2   1 klGfkanalvawkvpeerveevaevvaelpevtHcYeRewpynlyfmvharseeeveevlaeiaaatgledye 73 
                                       klG+  ++ + ++++ +r+ e+ + +a+ p+v+ +Y    +y + ++   r +e+++++++++ +  g+e+++
  gi|242399405|ref|YP_002994829.1|  63 KLGYDLTTIIGVRAQGKRIIEIEKEIASDPHVACVYDVTGEYDIIVIAKFRGREDMNKFVKKLLRIDGVEKTY 135
                                       799999999999***************************************************9999998655 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 ?   13.7   0.0    0.0001     0.041      27      56 ..      24      52 ..      14      55 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.0001
                                      -HHHHHHHHTS-.HHHHHHHHHHHHHTTSE CS
                     LexA_DNA_bind 27 sireiaralglkSpsaveehLkaLerKGyi 56
                                      s reia++lg++   +v ++Lk+Le  G+i
  gi|242399405|ref|YP_002994829.1| 24 SYREIAKKLGIA-VGTVYNRLKKLEEEGVI 52
                                      78**********.99*************98 PP

>> HTH_Mga  M protein trans-acting positive regulator (MGA) HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   0.00012     0.047       8      45 ..      11      47 ..       7      51 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00012
                           HTH_Mga  8 lkLlelLteneksltldelakeLglseltlqsdiseLn 45
                                       k++++L + + +l++ e+ak+Lg+   t+ +++ +L 
  gi|242399405|ref|YP_002994829.1| 11 RKIISILQK-DARLSYREIAKKLGIAVGTVYNRLKKLE 47
                                      589******.***************9999998888886 PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   0.00012     0.049      36      61 ..      30      55 ..       9      91 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00012
                                      TTTT--HHHHHHHHHHHHHTTSEEEE CS
                               FUR 36 edpeislaTVYrtLklleeaglvkel 61
                                      ++  i + TVY+ Lk lee+g++  +
  gi|242399405|ref|YP_002994829.1| 30 KKLGIAVGTVYNRLKKLEEEGVILGF 55
                                      4457999**************99755 PP

>> RepL  Firmicute plasmid replication protein (RepL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00018     0.073      77     105 ..      24      52 ..       3      56 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00018
                              RepL  77 tnRelaeetgislktvsetlkileeanil 105
                                         Re+a++ gi++ tv + lk lee +++
  gi|242399405|ref|YP_002994829.1|  24 SYREIAKKLGIAVGTVYNRLKKLEEEGVI 52 
                                       57**********************99887 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00039      0.16      23      50 ..      23      50 ..      11      53 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00039
                                      B-HHHHHHHHTS-HHHHHHHHHHHHHTT CS
                    Fe_dep_repress 23 vktkdlaerLnvspssVsemlkkLekdG 50
                                       +  ++a+ L+++  +V   lkkLe++G
  gi|242399405|ref|YP_002994829.1| 23 LSYREIAKKLGIAVGTVYNRLKKLEEEG 50
                                      56789**********************9 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00034      0.13      29      48 ..      34      53 ..      24      71 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00034
                                      TTHHHHHHHHHHHHHTTSEE CS
                              PadR 29 lseGslYpaLkrLekeglve 48
                                      +  G++Y  Lk+Le+eg++ 
  gi|242399405|ref|YP_002994829.1| 34 IAVGTVYNRLKKLEEEGVIL 53
                                      568**************996 PP

>> DDRGK  DDRGK domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00025       0.1     100     145 ..       9      54 ..       3      56 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00025
                                       HHHHHHHHHHH-SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS-E CS
                             DDRGK 100 lleefinyikekKvvlleelavkfklktqevierikeLeeqgsltG 145
                                       l +++i  +++       e+a k+++    v +r+k+Lee+g + G
  gi|242399405|ref|YP_002994829.1|   9 LDRKIISILQKDARLSYREIAKKLGIAVGTVYNRLKKLEEEGVILG 54 
                                       567788888888888899*************************998 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.4   0.00048      0.19       2      54 ..      12      62 ..      11      71 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00048
                            HTH_12  2 eILkilaesdkpigakeiaeeLkkrgydigeravRyrLrkleerg....ltrrvgya 54
                                      +I++il++  + ++ +eia++L     ++   +v  rL+klee+g    +  +  y+
  gi|242399405|ref|YP_002994829.1| 12 KIISILQKDAR-LSYREIAKKLG---IAV--GTVYNRLKKLEEEGvilgFAPKLDYN 62
                                      59999999888.*******9995...444..66779********9776666676666 PP

>> GYD  GYD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0         8   3.2e+03      26      41 ..      25      40 ..      14      43 .. 0.69
   2 ?   11.6   0.0   0.00052      0.21      16      83 ..      75     141 ..      66     146 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 8
                               GYD 26 kealveslGgklesly 41
                                       ++++++lG+ + ++y
  gi|242399405|ref|YP_002994829.1| 25 YREIAKKLGIAVGTVY 40
                                      3455599999888777 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00052
                               GYD  16 kdsperreeakealveslGgkleslyatlGeyDvvvivEapDdetaaalslal.aasGtvrtetlraft 83 
                                       + +++r+ e+++++  + +  +  +y ++GeyD++vi  +  +e + ++  +l +  G  +t t+ a++
  gi|242399405|ref|YP_002994829.1|  75 RAQGKRIIEIEKEI--ASDPHVACVYDVTGEYDIIVIAKFRGREDMNKFVKKLlRIDGVEKTYTHVAMD 141
                                       56677888888888..778889999*********************99875541455655556666665 PP

>> HTH_22  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00047      0.19      43      63 .]      24      44 ..       5      44 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00047
                            HTH_22 43 avekvAekLgiSraTvYryLr 63
                                      +  ++A+kLgi   TvY+ L+
  gi|242399405|ref|YP_002994829.1| 24 SYREIAKKLGIAVGTVYNRLK 44
                                      6678**************996 PP

>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00073      0.29      31      73 .]       7      43 ..       3      43 .. 0.87
   2 ?    1.5   0.0       1.2   4.7e+02       1      20 [.      38      58 ..      38      60 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00073
                            HTH_32 31 devrariiallreeprWsprqlaarlaeregvkvShstvyriL 73
                                      de+ ++ii +l+++ r+s+r++a++l       ++  tvy+ L
  gi|242399405|ref|YP_002994829.1|  7 DELDRKIISILQKDARLSYREIAKKL------GIAVGTVYNRL 43
                                      89999******7788***********......79999999765 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 1.2
                            HTH_32  1 TvsrwlkRyneeGle.gLkdr 20
                                      Tv++ lk+ +eeG+  g++++
  gi|242399405|ref|YP_002994829.1| 38 TVYNRLKKLEEEGVIlGFAPK 58
                                      9************88888775 PP

>> NUMOD1  NUMOD1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0    0.0061       2.4      18      35 ..      24      41 ..      24      43 .. 0.91
   2 ?    1.7   0.0      0.81   3.2e+02       5      26 ..      97     122 ..      96     124 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0061
                            NUMOD1 18 SireAakyLgishntInk 35
                                      S+re ak+Lgi   t+++
  gi|242399405|ref|YP_002994829.1| 24 SYREIAKKLGIAVGTVYN 41
                                      89************9975 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.81
                            NUMOD1   5 vYDlntkt....igkFsSireAakyL 26 
                                       vYD+++ +    i kF+   ++ k++
  gi|242399405|ref|YP_002994829.1|  97 VYDVTGEYdiivIAKFRGREDMNKFV 122
                                       9*****99987778888777776665 PP

>> HTH_Tnp_Tc3_2  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1    0.0008      0.32       1      41 [.      10      45 ..      10      48 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0008
                     HTH_Tnp_Tc3_2  1 krrIvrlvrkdPritlreLanelkeeGksvsreTirrrLrk 41
                                      +r+I+++ +kd r ++re+a++l   G+     T+ +rL+k
  gi|242399405|ref|YP_002994829.1| 10 DRKIISILQKDARLSYREIAKKL---GI--AVGTVYNRLKK 45
                                      79*********************...55..55799999987 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00071      0.28      16      49 ..       9      44 ..       7      46 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00071
                      HTH_Tnp_ISL3 16 leayilellles..rsvkavArqlgvSwtTVwrild 49
                                      l+++i+  l+++   s +++A+ lg+   TV ++l+
  gi|242399405|ref|YP_002994829.1|  9 LDRKIISILQKDarLSYREIAKKLGIAVGTVYNRLK 44
                                      778888888888889******************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); expected 358.6 (0.02)
Passed bias filter:                      573  (0.0319594); expected 358.6 (0.02)
Passed Vit filter:                       121  (0.00674884); expected 17.9 (0.001)
Passed Fwd filter:                        45  (0.0025099); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              45  [number of targets reported over threshold]
# CPU time: 0.49u 0.32s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 923.54
//
Query:       gi|242399406|ref|YP_002994831.1|  [L=75]
Description: Sulfur carrier protein ThiS [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-10   40.9   0.2    2.9e-10   40.6   0.2    1.1  1  ThiS      ThiS family
     0.0021   18.1   0.1     0.0027   17.7   0.1    1.2  1  TGS       TGS domain
     0.0036   17.1   0.1     0.0042   16.9   0.1    1.1  1  Ub-Mut7C  Mut7-C ubiquitin
  ------ inclusion threshold ------
      0.072   13.4   0.3      0.091   13.1   0.3    1.4  1  FERM_f0   N-terminal or F0 domain of Talin-head FERM


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 !   40.6   0.2   6.5e-14   2.9e-10      12      77 .]      18      75 .]      11      75 .] 0.93

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 6.5e-14
                                      T.CEEEEESSTSBHHHHHHHHHHHTCHHGTTTTEEEEETTEEEGCCTTTSB--TTCEEEEEESTTC- CS
                              ThiS 12 g.eeelelaegstvaelleaLgerypelalerrvavavNgeivprlwldtelkdgDevailppVaGG 77
                                      + e+ele + g++v+++l+a+g++       +  ++ vNg+++ +   d ++kd+D v+++p+V+GG
  gi|242399406|ref|YP_002994831.1| 18 KiEKELEYQKGMKVKDILKAVGFNT------ESAIAKVNGKVALE---DDPIKDNDYVEVIPVVSGG 75
                                      157899*******************......**************...******************9 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1     6e-07    0.0027      11      59 ..      23      69 ..      13      70 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 6e-07
                                      EEEETTB-HHHHHHHHSTTHHHHEEEEEECSEEEETTSBB-SSEEEEEE CS
                               TGS 11 pdlprgatveDfAykIhrslakkfiyAlVnGqrvgldhvLedgdvveIv 59
                                       ++++g  v+D+ ++++  +  +  +A+VnG+    d +++d+d ve++
  gi|242399406|ref|YP_002994831.1| 23 LEYQKGMKVKDILKAVG--FNTESAIAKVNGKVALEDDPIKDNDYVEVI 69
                                      45778888888888887..666669**********************97 PP

>> Ub-Mut7C  Mut7-C ubiquitin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   9.4e-07    0.0042      27      77 ..      23      72 ..      12      74 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 9.4e-07
                          Ub-Mut7C 27 vafdeaatvkhviEalGVPhtEVelilvnGesvgfshiledGdrvavypvf 77
                                       + +++  vk+++ a+G   tE  + +vnG+ +  +  ++d d v+v pv 
  gi|242399406|ref|YP_002994831.1| 23 LEYQKGMKVKDILKAVGF-NTESAIAKVNGKVALEDDPIKDNDYVEVIPVV 72
                                      566778889********8.7*****************************85 PP

>> FERM_f0  N-terminal or F0 domain of Talin-head FERM
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.3     2e-05     0.091       1      31 [.       8      38 ..       8      65 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2e-05
                           FERM_f0  1 LslkislveknvtktiqFdpettVydackli 31
                                      L +ki++ + ++ k +++++ + V+d++k +
  gi|242399406|ref|YP_002994831.1|  8 LMIKIKVIGRKIEKELEYQKGMKVKDILKAV 38
                                      789************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.33s 00:00:00.80 Elapsed: 00:00:00.51
# Mc/sec: 445.57
//
Query:       gi|242399407|ref|YP_002994832.1|  [L=40]
Description: hypothetical protein TSIB_1432 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       177  (0.00987227); expected 358.6 (0.02)
Passed bias filter:                      162  (0.00903564); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.27s 00:00:00.61 Elapsed: 00:00:00.42
# Mc/sec: 288.38
//
Query:       gi|242399408|ref|YP_002994833.1|  [L=412]
Description: Alanine aminotransferase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.4e-56  189.9   0.0    8.9e-56  189.6   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    2.1e-05   24.0   0.0    6.3e-05   22.4   0.0    1.6  2  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    2.5e-05   23.7   0.0    0.00012   21.5   0.0    1.9  2  Beta_elim_lyase  Beta-eliminating lyase
  ------ inclusion threshold ------
      0.054   12.4   0.0       0.43    9.5   0.0    2.1  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 !  189.6   0.0     2e-59   8.9e-56       2     345 ..      46     386 ..      45     401 .. 0.94

  Alignments for each domain:
  == domain 1  score: 189.6 bits;  conditional E-value: 2e-59
                                       EEEESSSSSTTSTTSS.HHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHH CS
                     Aminotran_1_2   2 dvinLgsneylgdsgk.ptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGa 77 
                                       ++i+L+++++        ++++ +ka  e  + +++ n yg+++g +el+ea+ +  ++++++++++e  v+v+   
  gi|242399408|ref|YP_002994833.1|  46 KIIKLNIGDPVKF--DfQPPEHMKKAYCE--AIMEGHNYYGDSEGDKELREAIVEREKKKNGVDITPE-DVQVTAAV 117
                                       789******9888..43588888888877..99***********************************.******** PP

                                       HHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEE CS
                     Aminotran_1_2  78 galiealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilv 154
                                       +++++ ++ +l ++ g+eil+p p+y++y   ++ +gg    y++ +ee+++ d++++ +++++      ktk i+v
  gi|242399408|ref|YP_002994833.1| 118 TEALQFIFGAL-IDGGEEILIPGPSYPPYVGLVKFYGGVPKAYKTIEEEGWQPDVDDMRRKVTD------KTKAIAV 187
                                       ***********.****************************************************......******* PP

                                       ESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EE CS
                     Aminotran_1_2 155 esphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvG 231
                                        +p+NPtG+++ +++l++++dla +y l +++De+Y  + ++ + +v+  + + +++ ++++++lsK + ++G+R+G
  gi|242399408|ref|YP_002994833.1| 188 INPNNPTGALYEKKTLQEIIDLAGEYDLPIISDEIYDFMTYEGK-HVS-PSSLTKDVPVIVMNGLSKIYFATGWRLG 262
                                       *****************************************965.456.89************************** PP

                                       EEEE.EH.....HHHHHHHHHHHHHTS.SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS.TEEEE CS
                     Aminotran_1_2 232 yilg.na.....avvsqlrklsrpfls.ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLael.glkvl 300
                                       y +  ++     +v++++ kl+r  l   +++q+a+ a l+ + +   +lee  ++l++rr++++++L+e  g++  
  gi|242399408|ref|YP_002994833.1| 263 YMCFiDPenklaEVREAIGKLARIRLCpNTPAQKAAIAGLRGPMD---YLEEYMAKLKERRDYIYKRLNEMpGISTQ 336
                                       ***9666****************99999**************997...9**************************** PP

                                       CCSCSSEEEEEETHH...CHHHHHHHHHHTCTEEEEEGGGGTS..TTEEE CS
                     Aminotran_1_2 301 asqsgmflltdlsae...takelskkLleevgvyvtpgtsftv..pgrlR 345
                                       ++q++++ +  +++    ++ke+    l + +v+ ++g+ f+   + ++R
  gi|242399408|ref|YP_002994833.1| 337 KPQGAFYIFPKIEEGpwkSDKEFVLDVLHNAHVLFVHGSGFGEggEMHFR 386
                                       ************9989999999999988888********99976655555 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   1.4e-08   6.3e-05      44     144 ..     114     220 ..      92     234 .. 0.84
   2 ?   -1.9   0.0      0.35   1.6e+03     231     264 ..     303     336 ..     295     345 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.4e-08
                                       ESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EE.EEE-B-TTTSSB-GGGCGGG--TTEEEEEEB- CS
                   DegT_DnrJ_EryC1  44 vssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakp.vfvDvdpdtynidpaaieaaitertkaIlpVh 119
                                       ++  t+Al+ +  al    g+e+++p  ++   +  v   g +p  +  ++++ +++d++++++++t +tkaI +++
  gi|242399408|ref|YP_002994833.1| 114 TAAVTEALQFIFGALID-GGEEILIPGPSYPPYVGLVKFYGGVPkAYKTIEEEGWQPDVDDMRRKVTDKTKAIAVIN 189
                                       44557788888887754.59**********************99446789**********************99886 PP

                                       ...GGGB--...-HHHHHHHHHHCT-EEEEE CS
                   DegT_DnrJ_EryC1 120 ...lyGqva...dmdalkaiaakhglkvieD 144
                                            G+      ++++ ++a +++l++i+D
  gi|242399408|ref|YP_002994833.1| 190 pnnPTGALYekkTLQEIIDLAGEYDLPIISD 220
                                       2224677663336999999**********99 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.35
                                       HHHHCTHHHHHHHHHHHHHHHHHHHHTCCCCEES CS
                   DegT_DnrJ_EryC1 231 laqLerldelvarRreiaelykeeLaelegtael 264
                                       +  +++l+e +a+ +e  +++ ++L+e++g++++
  gi|242399408|ref|YP_002994833.1| 303 RGPMDYLEEYMAKLKERRDYIYKRLNEMPGISTQ 336
                                       5568899999999999999999999999986443 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.17   7.7e+02     205     241 ..      12      48 ..      10      52 .. 0.93
   2 !   21.5   0.0   2.6e-08   0.00012      11     167 ..      63     220 ..      59     222 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.17
                                       -EEEEE-HH....HHHHHHHHHHHHT---SSTHHHHH CS
                   Beta_elim_lyase 205 Ggvlafrddeledylaerveqrkylggglrqagvlaa 241
                                       Ggv+++r ++    ++++++ +   + +l+++g+++ 
  gi|242399408|ref|YP_002994833.1|  12 GGVVMIRPSNRAMGIEYAIRDVVLPARELEKQGIKII 48 
                                       99*******99999*******************9985 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 2.6e-08
                                       -HHHHHHH.HCS----CCCT--HHHHHHHHHHHHHTT-SEEEE........ES-HHHHHHHHHHHH--TTEEEEEET CS
                   Beta_elim_lyase  11 teamsdaq.aaamlGdesYgedktvnrLedavaelfgkeaalf........vpqGtaAnsillkillqrgeevivte 78 
                                        e m +a   a+m G++ Yg++++ ++L +a+ e   k+ ++         ++  t A ++ + +l+  gee+++  
  gi|242399408|ref|YP_002994833.1|  63 PEHMKKAYcEAIMEGHNYYGDSEGDKELREAIVEREKKKNGVDitpedvqvTAAVTEALQFIFGALIDGGEEILIP- 138
                                       578999998999**********************88888888556677776888999999999****999999865. PP

                                       T-HHHHSSTTHHHHCC--EEEEE-.EBTT.TBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHH CS
                   Beta_elim_lyase  79 pahihfdetgaiaelagvklrdlk.nkea.GkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrev 153
                                        +  +    g +++++gv ++  k ++e+  + d++++++++++      k+k+i + + nn   G  ++ + l+e+
  gi|242399408|ref|YP_002994833.1| 139 -GPSYPPYVGLVKFYGGV-PKAYKtIEEEgWQPDVDDMRRKVTD------KTKAIAVINPNNP-TGALYEKKTLQEI 206
                                       .55688889********9.55555234432699******99999......689*********5.9************ PP

                                       HHHHHHCT-EEEEE CS
                   Beta_elim_lyase 154 aaiakkygiplhlD 167
                                        ++a +y++p++ D
  gi|242399408|ref|YP_002994833.1| 207 IDLAGEYDLPIISD 220
                                       **********9988 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   9.6e-05      0.43     122     168 ..     164     213 ..      97     228 .. 0.84
   2 ?    0.4   0.0     0.054   2.4e+02     260     301 ..     301     337 ..     292     342 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 9.6e-05
                                       ETTSCBEGGGHHHH--TTEEEEEEESBETTTTEB--...HHHHHHHHHHT CS
                       Aminotran_5 122 deegeldldelekllnektklvaithvsnvtGtiqp...veeigklakkk 168
                                       +e+++ d+d+++ ++++ktk++a+   +n tG + +   ++ei++la ++
  gi|242399408|ref|YP_002994833.1| 164 EEGWQPDVDDMRRKVTDKTKAIAVINPNNPTGALYEkktLQEIIDLAGEY 213
                                       467899**************************975511156666666555 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.054
                                       HHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES CS
                       Aminotran_5 260 glgaaleyleeigleaiekhekelaeyllerlkslpgvrlyg 301
                                       gl+  ++yl     e+ +++ ke ++y+++rl+++pg+ + +
  gi|242399408|ref|YP_002994833.1| 301 GLRGPMDYL-----EEYMAKLKERRDYIYKRLNEMPGISTQK 337
                                       555555555.....67778889999************99844 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      561  (0.0312901); 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: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 3030.67
//
Query:       gi|242399409|ref|YP_002994834.1|  [L=369]
Description: Ni-Fe hydrogenase maturation protein HypD [Thermococcus sibiricus MM 739]
Scores for complete 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-133  445.7   0.0   1.3e-133  445.5   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 !  445.5   0.0  7.2e-138  1.3e-133       2     351 .]      11     366 ..      10     366 .. 0.97

  Alignments for each domain:
  == domain 1  score: 445.5 bits;  conditional E-value: 7.2e-138
                                       HHHHHHHHHHHHHHT.SS-EEEEE--HHHHHHHHHTTHHHHS-TTEEEEE-S--TTTTS-HHHHHHHHHHHHH.... CS
                              HypD   2 lakkllekikkeakk.erelkimevCGghthaivryglrslLpenielisGPGCpVCvtpeeeidkaielaek.... 73 
                                       la+++l+ i++ea+k  re+k+m+vCG+h+ +++r+g+rslLpen++++sGPGCpVC+tp+e+i  ++e++++    
  gi|242399409|ref|YP_002994834.1|  11 LAQRILQGIRREAEKiGREVKLMHVCGTHEDTVTRSGIRSLLPENVKVMSGPGCPVCITPAEDIAVMMEIMRRaree 87 
                                       688999*******999******************************************************9875666 PP

                                       .--EEEEE-CCHHG---TT--HHHHHHTT-EEEE-SSHHHHHHHHHH-TTSEEEEEEEE-HHHHHHHHHHHHHHHHH CS
                              HypD  74 .eevilatfgDmlrvpgskksLleakaegadvrivyspldalkiakenpdkevvflavGFEttapatalalleakke 149
                                        ee+il+tfgDm+++p+  +s++++k+e  dvr+vys+ d++k+a +++++ vv+++ GFEtt+++ a +l+e+ ++
  gi|242399409|ref|YP_002994834.1|  88 gEEIILTTFGDMYKIPTAIGSFADLKSEDFDVRVVYSIYDSYKMALKENNHLVVHFSPGFETTTAPAAGVLKEVIEK 164
                                       679************************************************************************** PP

                                       T-SSEEEEEEEE-HHHHHHHHHHTT.---SEEEEEHHHHHHHTTHHHHHHHHHH---EEEE-SSHHHHHHHHHHHHH CS
                              HypD 150 glknfsvlsshklvppalealleseelkidgfiapghvstviGlkayeelaeeykvpvvvaGFepldilqailmlvk 226
                                       +++nf+++s+h+l+ppa+eal+++  + +dg+i pghvst+iG+k +e +++ey+vp+vvaGFep+d l+a++ml++
  gi|242399409|ref|YP_002994834.1| 165 DVSNFKIYSVHRLTPPAVEALIKQG-TVFDGLIDPGHVSTIIGVKGWEYITKEYGVPQVVAGFEPVDFLMAVFMLLR 240
                                       **********************998.68************************************************* PP

                                       HHHTT---EEETTTTT--TT--HHHHHHHHHHEEEEEEEETTTEEEEEEEEEE-GGGGGGBGGGT---.-S---SS- CS
                              HypD 227 qleegeaeveneYkrvvkeegnkkaqklieevfevrdaewRglgvipksglklreeyaefdaekkfel.ekeeekek 302
                                        +++ge+++en+Y+rvvk egn++aqk++e +f+++da+wR+lg ipksgl++++ey++f++++ +++ + e  + +
  gi|242399409|ref|YP_002994834.1| 241 IIRKGETKIENQYTRVVKYEGNVEAQKTMEMLFDTVDAKWRALGIIPKSGLEIKDEYKDFEIRTFYKVePPELPDLE 317
                                       ********************************************************************555667789 PP

                                       TT--HHHHHTTS--GGGSTTBTTTB-SSS-SSHHHHSTT-HHHHHHHTT CS
                              HypD 303 kackcgevlkGkakPedCklFgkaCtpenpvGacmvSsEGaCaayykyg 351
                                       k+c+cg+vl+G a P++C+lFgk+Ctp+npvG+cmvS EG+C+++ykyg
  gi|242399409|ref|YP_002994834.1| 318 KGCICGAVLRGLALPTQCPLFGKKCTPRNPVGPCMVSYEGTCQIFYKYG 366
                                       99*********************************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); expected 358.6 (0.02)
Passed Vit filter:                        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 0.26s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2612.87
//
Query:       gi|242399410|ref|YP_002994835.1|  [L=77]
Description: Ni-Fe hydrogenase maturation protein HypC [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.3e-29  100.8   0.2    3.8e-29  100.6   0.2    1.1  1  HupF_HypC  HupF/HypC family
  ------ inclusion threshold ------
       0.11   12.8   0.0       0.11   12.7   0.0    1.1  1  AHSA1      Activator of Hsp90 ATPase homolog 1-like protein


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 !  100.6   0.2   4.3e-33   3.8e-29       1      65 []       4      68 ..       4      68 .. 0.99

  Alignments for each domain:
  == domain 1  score: 100.6 bits;  conditional E-value: 4.3e-33
                                      CCEEEEEEEEEEETTEEEEECTTEEEEEEGTTCTTB-TT-EEEEETTEEEEEE-HHHHHHHHHHH CS
                         HupF_HypC  1 MCLaiPgkvveiedelAlvdvgGvrrevslalveevkvGdyVLvhvGfAiekideeeaeetlell 65
                                      MCLaiP+k++ei+d++A+vd+gGv+rev++++v+++kvGdyV+vh GfAiek+de+ a e+l+++
  gi|242399410|ref|YP_002994835.1|  4 MCLAIPAKIIEIKDNVAMVDFGGVKREVRIDFVPHAKVGDYVIVHTGFAIEKMDEKAALESLKAW 68
                                      **************************************************************997 PP

>> AHSA1  Activator of Hsp90 ATPase homolog 1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.2e-05      0.11      74     121 ..      26      76 ..       7      77 .] 0.79

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.2e-05
                                       EEEEEEEEEEEEETTEEEEEEEEEEEEHCHHHHHH...HHHHHHHHHHHHH CS
                             AHSA1  74 eeestvtieleeegggTrltlthtglprkqkeeeg...veeGweqsldqLk 121
                                       + + +v+i + ++ +   ++++htg++ ++++e++     + we++++ ++
  gi|242399410|ref|YP_002994835.1|  26 GVKREVRIDFVPHAKVGDYVIVHTGFAIEKMDEKAaleSLKAWEEVMKAME 76 
                                       66779****************************988777788888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 512.96
//
Query:       gi|242399411|ref|YP_002994836.1|  [L=291]
Description: dihidrodipicolinate synthase [Thermococcus sibiricus MM 739]
Scores for 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-70  234.6   0.0      1e-69  234.4   0.0    1.0  1  DHDPS     Dihydrodipicolinate synthetase family
  ------ inclusion threshold ------
      0.025   14.1   0.0      0.069   12.7   0.0    1.7  1  WHIM1     WSTF, HB1, Itc1p, MBD9 motif 1
       0.19   12.0   0.0       0.47   10.7   0.0    1.7  2  Fer4_12   4Fe-4S single cluster domain


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 !  234.4   0.0   1.7e-73     1e-69       2     286 ..       2     285 ..       1     288 [. 0.97

  Alignments for each domain:
  == domain 1  score: 234.4 bits;  conditional E-value: 1.7e-73
                                       -SEEEEE----B-TTSSB-HHHHHHHHHHHHHCT-SEEEESSCCCTGGGS-HHHHHHHHHHHHHHHTTSSEEEEE-- CS
                             DHDPS   2 fsgiitalvtpfdedgkldkealrklieflinkgvdglvvaGttGEsatlsteekeqlveiaveaakgripviagvG 78 
                                       ++g++++ +tpfde+ k+++e lr+l+++ +++ ++glv +G+ GE++ l+ eek ++++i++e+   + pviagv 
  gi|242399411|ref|YP_002994836.1|   2 IEGVFVPHITPFDEEEKINEEMLRELVHYFVDAKLNGLVTLGSNGEFPYLNFEEKLKVLKIVREE--SSLPVIAGVA 76 
                                       5799***********************************************************97..68******** PP

                                       -SSHHHHHHHHHCCCCCT-SEEEEE---SS---HHHHHHHHHHHHHCHSS-EEEEE-HHHHSHHHHHHHHHHHHT.S CS
                             DHDPS  79 snstseaiklakkaeeaGadgvlavtPYYnkpsqeglyqhfkaiieatdlpvilYnvpsrtgadlspetvkrLae.l 154
                                        nst+e iklak+a + G+dg+l+ +PYY kp+ ++l  h+  i+ + + p++lYnvp+ t  ++ +++v++L+e  
  gi|242399411|ref|YP_002994836.1|  77 ENSTRETIKLAKEAWDIGVDGLLIAPPYYFKPNVRELFAHYSRIAYEVEAPILLYNVPKFTTINIDIDVVEKLVEeH 153
                                       *********************************************8888*************************99* PP

                                       TTEEEEEE-SS-CTHHHHHHCCCSTTSEEEES-GGGHHHHHHTT-SEEEESCHHCHHHHHHHHHHHHHTT-HHHHHH CS
                             DHDPS 155 enivgvKeavgdleevikikkevgkdlviysGddelllsalslGadGvisvtsniagermrqlikalkeGdlaeaae 231
                                       +nivg+K+ +g++ ++ +++++vg +++i++G  +l+ + + lGa+G++ + +n+a+++  +l++a +e + + a+ 
  gi|242399411|ref|YP_002994836.1| 154 SNIVGIKDSSGSIGRIAELIRRVGGKISILAGTADLMYPSWVLGAHGAVVAVANVAPRLCVELYNAFREQKYERARR 230
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHCCCC.SCCHHHHHHHHCTTSSSBB.--TTS--S-HHHHHHHHHHH CS
                             DHDPS 232 lnekllplikilfae.pnvilvktalellGlvveatlrkPltpleeeekeeleall 286
                                       l+  ++ l++ ++++   ++ +k+a+++ Gl+v++  r P +pl+e++ e +e++l
  gi|242399411|ref|YP_002994836.1| 231 LQLMVNYLNEVVVKKyNQISAIKEAMRMRGLEVGY-PRMPALPLDEKALEDIEKTL 285
                                       ***************455679**************.**************999987 PP

>> WHIM1  WSTF, HB1, Itc1p, MBD9 motif 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.2e-05     0.069      13      30 ..      45      62 ..      39      63 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.2e-05
                                      CSTCCCS-HHHHHHHHHH CS
                             WHIM1 13 kggYyeLspeeklkiLki 30
                                      +g+++ L++eeklk+Lki
  gi|242399411|ref|YP_002994836.1| 45 NGEFPYLNFEEKLKVLKI 62
                                      799**************8 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   7.9e-05      0.47      21      84 ..       4      68 ..       3      98 .. 0.87
   2 ?   -3.4   0.0       1.8   1.1e+04      85     102 ..     125     142 ..     107     157 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 7.9e-05
                           Fer4_12 21 gCfnketwsfksgkeftkelleeiiedlkkesiegltllG..GE.Pllpenaeallelvkevkeekp 84
                                      g f + +  f++++++++e+l+e+++ + + + +gl+ lG  GE P l  n e+ l+++k v+ee +
  gi|242399411|ref|YP_002994836.1|  4 GVFVPHITPFDEEEKINEEMLRELVHYFVDAKLNGLVTLGsnGEfPYL--NFEEKLKVLKIVREESS 68
                                      567788899*******************************77886777..99********9999976 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.8
                           Fer4_12  85 ekdiwlytgytleelskk 102
                                       e  i+ly++ ++ +++ +
  gi|242399411|ref|YP_002994836.1| 125 EAPILLYNVPKFTTINID 142
                                       455667777766666544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.49
# Mc/sec: 1778.46
//
Query:       gi|242399412|ref|YP_002994837.1|  [L=280]
Description: Carbohydrate/pyrimidine kinase, PfkB family [Thermococcus sibiricus MM 739]
Scores for 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-10   38.3   0.0    6.3e-06   25.7   0.0    2.1  2  PfkB      pfkB family carbohydrate kinase


Domain annotation for each model (and alignments):
>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0   1.3e-05      0.23      33     107 ..      18      87 ..       3     124 .. 0.81
   2 !   25.7   0.0   3.5e-10   6.3e-06     210     293 ..     169     250 ..     152     258 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 1.3e-05
                                       EEEESHHHHHHHHHHHTT-EEEEEEEEESSHHHHHHHHHHHHTTEEETTEEEESSSEEEEEEEEETTTSEEEEEE CS
                              PfkB  33 ksaGGagaNvAvalarlgadvafigavGdDnfGeflleelkkegvdtdyvkidedtrtglalivvdedgertivf 107
                                        +aGG +  +A al++  + v ++++vG+++   + leel+++gv +  ++i  +++t  +l  ++e+g rt+  
  gi|242399412|ref|YP_002994837.1|  18 ERAGGGAYYSALALSKFCN-VLVLTKVGKSF-PISWLEELEARGVSV--IIIPSEKSTVYKLHYTSENG-RTLEL 87 
                                       5789999999999999876.***********.*************88..88889999999999999987.55544 PP

  == domain 2  score: 25.7 bits;  conditional E-value: 3.5e-10
                                       HHHHHHHHTTSSEEEEEEGGGEEEEEETTEEEEEEE.SSSS-SBGTTHHHHHHHHHHHHHHTTHHHHHHHHHHHHHH CS
                              PfkB 210 aalhklkakgaktvvvtlGkeGalvvekdgelkvpavpkvkvvDttGAGDsfvggflaallegksleealrfanavA 286
                                       ++l+++++k  ++++++ G e  ++++++++++ ++  k+k+  +tGAGD f + f + l +  s+ +al++ n++ 
  gi|242399412|ref|YP_002994837.1| 169 QRLKNMNPKEFEVLLISNGPESGIAYHRGDKYIYKP-LKKKIKESTGAGDVFLAVFSY-LYKKYSFIQALKMTNTFT 243
                                       46678888888*************************.57***************9977.556688888888888887 PP

                                       HHHHTSS CS
                              PfkB 287 alvvqkk 293
                                       a  ++k+
  gi|242399412|ref|YP_002994837.1| 244 ATFLEKR 250
                                       7776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1884.57
//
Query:       gi|242399413|ref|YP_002994838.1|  [L=183]
Description: ADP-ribose pyrophosphatase [Thermococcus sibiricus MM 739]
Scores for complete 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   80.5   0.0    1.5e-22   80.0   0.0    1.2  1  NUDIX     NUDIX domain


Domain annotation for each model (and alignments):
>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.0   0.0   8.5e-27   1.5e-22       6     129 ..      52     169 ..      49     171 .. 0.86

  Alignments for each domain:
  == domain 1  score: 80.0 bits;  conditional E-value: 8.5e-27
                                       EEEEEEETTSEEEEEEESSSSTTT.EESSEEECBTTSHHHHHHHHHHHHHHSEEEEEEEEEEEEEEEEEEEEEEEEE CS
                             NUDIX   6 vgvvllnekgevLlvrrskkpfpg.WelPgGkvepgEtpeeAArREleEEtGleaellellgrlhylapydgpygde 81 
                                       v +v+l + g ++l++r++ p ++ W+lPgG+ve+gE++e+AA+RE++EEtGl++el++l+g    ++++++++++ 
  gi|242399413|ref|YP_002994838.1|  52 VDLVILYKGG-IVLIKRFNEPYKDyWALPGGFVEYGEKVENAAIREAKEETGLDVELIKLIG----VYSDPKRDPRG 123
                                       5556444444.*******8888889*************************************....77788888889 PP

                                       EEEEEEEEEEECSGCSSTSTTTEEEEEEEEHHHHHHHHTHCTHHHHHH CS
                             NUDIX  82 heilyvfleevegelepndenevsevrwvpleellkeklaaesrkllp 129
                                       h ++  fl++ +g l+ +  ++  e+r +++ee+++ kla ++ k+++
  gi|242399413|ref|YP_002994838.1| 124 HTVTTAFLAKGKGVLRGG--DDAGEARVFSFEEIKEIKLAFDHGKIIK 169
                                       ********9999998888..55568999******99999999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); 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: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1235.26
//
Query:       gi|242399414|ref|YP_002994839.1|  [L=117]
Description: hypothetical protein TSIB_1439 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.2e-13   49.0   0.0    6.2e-13   48.8   0.0    1.1  1  DUF498    Protein of unknown function (DUF498/DUF598)


Domain annotation for each model (and alignments):
>> DUF498  Protein of unknown function (DUF498/DUF598)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.8   0.0   3.5e-17   6.2e-13       1     109 []       2     114 ..       2     114 .. 0.87

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 3.5e-17
                                       EEEEESSEEEETTEEESSEEEE-SSSEEE-T.......HCS.TTCEECHHHHHHCT..T..SEEEEE-TTS.----- CS
                            DUF498   1 idaygeggfelngvkysgsllvlpeeafawd.......vak.aedlteeslellellepkpellilGtGkr.qlpls 68 
                                       i+++++g + +ng+ky+++++++p++  + +       +++ +++l++++l+++  l++++++l++GtG + +l l 
  gi|242399414|ref|YP_002994839.1|   2 IEGIEFGRIIINGQKYKHDIVIYPSGKIEKRkkwlskkKHGtSHKLDPDELREY--LKEDFDVLLVGTGIYgLLSLL 76 
                                       7899*******************99886663355777645669***********..99*************999999 PP

                                       HHHHHHHHCCTSEEEEE-HHHHHHHHHHHHHHT--EEEEEE CS
                            DUF498  69 pevrealnelgigvevmdtraAartyNllaaegrrVaaaLi 109
                                        e ++ ++++  ++   +t++Aa+ +N l +++ rV+a+++
  gi|242399414|ref|YP_002994839.1|  77 SESKALVRDK--EILEKPTKEAAELFNELKSKK-RVLAIFH 114
                                       9999999988..56789************8865.5888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       772  (0.0430587); expected 358.6 (0.02)
Passed bias filter:                      564  (0.0314574); 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: 0.42u 0.31s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 775.55
//
Query:       gi|242399415|ref|YP_002994840.1|  [L=491]
Description: hypothetical protein TSIB_1440 [Thermococcus sibiricus MM 739]
Scores for complete 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  208.6  53.3    2.1e-61  208.4  53.3    1.0  1  12TM_1    Membrane protein of 12 TMs


Domain annotation for each model (and alignments):
>> 12TM_1  Membrane protein of 12 TMs
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  208.4  53.3   1.2e-65   2.1e-61       5     445 ..      40     485 ..      36     490 .. 0.87

  Alignments for each domain:
  == domain 1  score: 208.4 bits;  conditional E-value: 1.2e-65
                            12TM_1   5 svllqsimftvlglvlvgp.sliseras...flSslliLlfvlslfitalnslyfassldllepLrsLPvkfkdrvl 77 
                                        +  q++ f+ +gl++++   + ++r +    + sl++L+fv+++++ta   +y++s   l++pL  LP+++  ++l
  gi|242399415|ref|YP_002994840.1|  40 GLGVQTFGFIPFGLLMASTfVFTNDRLVlasLMVSLALLPFVFAMYVTAIQASYVLSI-GLFKPLEALPIRLGSKYL 115
                                       567899*******98876426778888844444567789***************9998.****************** PP

                            12TM_1  78 avfllieslsvlaFlvsillavllvgnltagllglLwailaillGfslvlllfilfGsri...sgrkslskallria 151
                                       + +l++e  ++l  +  + + v++ + +  g l lLw ++ + lG+ l+l+++  f  ++    g+   +k+l++++
  gi|242399415|ref|YP_002994840.1| 116 SGLLFLEISPALGVIL-PSVFVIMAKYPLEGTLALLWVFIGLFLGHALGLVIVNFFALKVhqrAGKGHTLKSLVKAV 191
                                       ****************.88889999999************************9999876522257777788888888 PP

                            12TM_1 152 glilflvlifglyliiqyaanilylvikeipeaykyifPffflsIeepffslllsllYtallsfaykyslkrlfkrl 228
                                        ++lf+ +++++ ++ qy ++  ++ +++i  +y++++Pf++ sI ep+ s+ l+++Y+a++  +y++ l+ ++k++
  gi|242399415|ref|YP_002994840.1| 192 FFLLFIGMFMAMNYL-QYYIREHSEEVARIIGKYFIAYPFSVASIFEPSRSAGLLMVYVAIIAPVYYLTLRAVWKKI 267
                                       888866666666555.5555555****************************************************** PP

                            12TM_1 229 ..eeiakvkgrvktkykikvrspltamliKDfkillRksqalvlllvPivivlpnvfsivseaqpvlltifiialii 303
                                         +  +  k  v+ k k+k  ++l+a+  KDf++ +Rk+ +lv +l+P+++vlp+++  + ++q +ll + ++ ++i
  gi|242399415|ref|YP_002994840.1| 268 lePPVVSEKIFVS-KFKAKITNKLLALTLKDFRMFVRKPAMLVAFLIPLYMVLPTIVDAFRKGQLSLLNVLVVLFMI 343
                                       8755666666666.9****************************************************7766666654 PP

                            12TM_1 304 .vlSsvylilllaievsgfsllkaLPlerreillsKlltilliylvvsvvlvllvliykgsnalylliilpspilvv 379
                                        + S+   + +l++e+++++llk LP+ +re++lsK+l +++++++++v +v+ +  y   ++l+l+ +++ p+++ 
  gi|242399415|ref|YP_002994840.1| 344 gLFSVAGADAVLKVEGNVLELLKTLPIRKREFMLSKILSMTIVPITIGVLIVIFGARYDVDSLLLLPYAFMLPLISA 420
                                       27899999********************************************************************* PP

                            12TM_1 380 liallislnrlgaetinlpsfgvlktivlfilslvivgivaipsli.lseplsflvslvitliiall 445
                                       +i +l+ ++  ++e i +p++  l +i + i+++++++++a p  + l+ ++     ++++++++l+
  gi|242399415|ref|YP_002994840.1| 421 SITMLYLFRY-TGEDIGIPELSWLYMIFMIIIVGIVFALIAAPLVFgLKHLFV-SQGIALGILFILF 485
                                       *********8.***************************999987762444433.2333444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (491 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1073  (0.0598472); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.46
# Mc/sec: 3192.57
//
Query:       gi|242399416|ref|YP_002994841.1|  [L=253]
Description: ATP-binding transport protein [Thermococcus sibiricus MM 739]
Scores for complete 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-29  101.6   0.0    8.3e-29  100.9   0.0    1.4  1  ABC_tran   ABC transporter
    6.7e-14   52.4   3.4    9.6e-09   35.5   0.5    2.2  2  AAA_21     AAA domain, putative AbiEii toxin, Type IV TA syst
    0.00084   18.4   0.0     0.0017   17.3   0.0    1.4  1  AAA_10     AAA-like domain
     0.0035   17.6   0.3        3.8    7.8   0.0    2.4  2  AAA_22     AAA domain
  ------ inclusion threshold ------
      0.013   15.2   0.0       0.12   12.1   0.0    2.0  2  AAA_30     AAA domain
      0.017   14.6   0.8        1.2    8.5   0.3    2.2  2  SMC_N      RecF/RecN/SMC N terminal domain
      0.019   14.7   0.2      0.035   13.8   0.2    1.4  1  AAA_29     P-loop containing region of AAA domain
      0.023   14.2   0.0       0.04   13.4   0.0    1.4  1  Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/
      0.026   15.1   0.2       0.68   10.5   0.2    2.3  1  AAA_18     AAA domain
       0.11   12.7   0.0       0.23   11.7   0.0    1.6  1  SbcCD_C    Putative exonuclease SbcCD, C subunit
       0.12   12.4   0.5       0.56   10.3   0.5    2.1  1  DUF87      Helicase HerA, central domain
       0.31   10.7   3.1        1.5    8.4   0.1    2.6  3  AAA_15     AAA ATPase domain
       0.66   10.4   5.8       0.21   12.1   1.0    2.1  2  AAA_23     AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.9   0.0     6e-32   8.3e-29       1     137 []      17     161 ..      17     161 .. 0.97

  Alignments for each domain:
  == domain 1  score: 100.9 bits;  conditional E-value: 6e-32
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l+ + + +++ge+++++G+nG+GKSt +k+l g ++pt+G++l+dg d ++ +  ++++ +g++p+ p l + lt +
  gi|242399416|ref|YP_002994841.1|  17 LNGIGFRVNNGEIYGLLGPNGSGKSTTMKILVGIVRPTSGQVLVDGVDPTR-DSIKVKEMVGYVPEIPVLYESLTPG 92 
                                       68899*********************************************9.7788999****************** PP

                                       HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       e              e +e+++++++ +g++e  d+ +     +LS G +q+v+l  all +p++l+lDE+++
  gi|242399416|ref|YP_002994841.1|  93 EFfnfigsvrgipkeELEERVSQFVEAFGIEEYLDQFI----GTLSFGTQQKVSLISALLHDPQVLILDEAMN 161
                                       *99***********999999******************....****************************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 !   18.2   0.3   1.3e-06    0.0018       2      23 ..      30      51 ..      29     129 .. 0.78
   2 !   35.5   0.5     7e-12   9.6e-09     235     297 ..     127     190 ..      82     195 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.3e-06
                            AAA_21  2 nvliGpNgsGKSnLLdaldlla 23
                                       +l GpNgsGKS+ +++l ++ 
  gi|242399416|ref|YP_002994841.1| 30 YGLLGPNGSGKSTTMKILVGIV 51
                                      689***************8874 PP

  == domain 2  score: 35.5 bits;  conditional E-value: 7e-12
                            AAA_21 235 rel....SdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                       +++    S Gt++   l++all ++    +l++DE  ngL+Pk  r l ell e +++g  +i++TH
  gi|242399416|ref|YP_002994841.1| 127 DQFigtlSFGTQQKVSLISALLHDP---QVLILDEAMNGLDPKSARILRELLLEFKKEGRSIIFSTH 190
                                       4444444****************99...9***********************999999********* PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.2e-06    0.0017      18      70 ..      23      81 ..      18     101 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.2e-06
                            AAA_10 18 ktnasas.liiGdlGnGKSvlakllvlyisllggkali..iDpkkerekfketl...pe 70
                                      + n+ +   ++G+ G GKS ++k+lv  ++   g++l+  +Dp+++  k ke +   pe
  gi|242399416|ref|YP_002994841.1| 23 RVNNGEIyGLLGPNGSGKSTTMKILVGIVRPTSGQVLVdgVDPTRDSIKVKEMVgyvPE 81
                                      56777665799**************************999******9988887755555 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    0.0028       3.8       9      25 ..      31      47 ..      24      69 .. 0.87
   2 !    7.8   0.0    0.0028       3.9      91     126 ..     149     186 ..     114     198 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0028
                            AAA_22  9 vvtGesGtGKTtllrrl 25
                                       + G+ G+GK+t+++ l
  gi|242399416|ref|YP_002994841.1| 31 GLLGPNGSGKSTTMKIL 47
                                      578**********9976 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0028
                            AAA_22  91 v.ielliiDEaqh.lr..seealeeLrsllnlsrkgvqli 126
                                         +++li+DEa + l+  s+++l+eL  ll++++ g ++i
  gi|242399416|ref|YP_002994841.1| 149 HdPQVLILDEAMNgLDpkSARILREL--LLEFKKEGRSII 186
                                       14689**********88779999998..444335554444 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   8.4e-05      0.12      20      50 ..      29      59 ..      22      78 .. 0.83
   2 ?    1.0   0.0      0.22     3e+02      84     108 ..     146     174 ..      88     188 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.4e-05
                            AAA_30 20 vavltGpAGtGKttalkalreaweaaggrvi 50
                                      +  l Gp G+GK+t++k l+ +++   g+v+
  gi|242399416|ref|YP_002994841.1| 29 IYGLLGPNGSGKSTTMKILVGIVRPTSGQVL 59
                                      67789***************99998866665 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.22
                            AAA_30  84 arlepgtllivDEagmv....dtkqlaal 108
                                       a l++ ++li DEa       +++ l++l
  gi|242399416|ref|YP_002994841.1| 146 ALLHDPQVLILDEAMNGldpkSARILREL 174
                                       4456679******9654333344444444 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 ?    8.5   0.3   0.00089       1.2      28      41 ..      31      44 ..      22      50 .. 0.83
   2 ?    4.5   0.0     0.015        21     161     197 ..     153     189 ..     109     209 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00089
                                      EEEESTTSSHHHHH CS
                                      xxxxxxxxxxxxxx RF
                             SMC_N 28 aivGpNGSGKsnll 41
                                       ++GpNGSGKs  +
  gi|242399416|ref|YP_002994841.1| 31 GLLGPNGSGKSTTM 44
                                      689********876 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.015
                                       EEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 161 lyllDeidaaLDeknvkkvaellkeksknaQfivisl 197
                                       + +lDe    LD k  +++ ell e +k+   i+ s 
  gi|242399416|ref|YP_002994841.1| 153 VLILDEAMNGLDPKSARILRELLLEFKKEGRSIIFST 189
                                       4689*********************999988888775 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   2.6e-05     0.035      19      39 ..      24      44 ..      17      55 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.6e-05
                            AAA_29 19 idlkgatlltGpsGsGKSTll 39
                                      ++  +++ l Gp+GsGKST +
  gi|242399416|ref|YP_002994841.1| 24 VNNGEIYGLLGPNGSGKSTTM 44
                                      553348889**********76 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 ?   13.4   0.0   2.9e-05      0.04       6      44 ..      33      71 ..      28      81 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.9e-05
                         Fer4_NifH  6 yGkGGiGksttsqnlsaalaemgkkvlivGCDPkaDstr 44
                                       G  G+Gkstt++ l+  +  +  +vl+ G DP  Ds +
  gi|242399416|ref|YP_002994841.1| 33 LGPNGSGKSTTMKILVGIVRPTSGQVLVDGVDPTRDSIK 71
                                      5778********************************986 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.2   0.00049      0.68       3      80 ..      32     157 ..      31     232 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00049
                            AAA_18   3 ltGtpGvGKttlakeL........................skrlgf..................gvnlrdvakengl 37 
                                       l G+ G+GK+t  k L                                                g+  +++ + +g+
  gi|242399416|ref|YP_002994841.1|  32 LLGPNGSGKSTTMKILvgivrptsgqvlvdgvdptrdsikV----KemvgyvpeipvlyesltpGEFFNFIGSVRGI 104
                                       78************996666555544444444444443332....03334366666666666666666666666666 PP

                            AAA_18  38 llevdpealdeskrldedkldklldaleenss............aleegknlvid 80 
                                         e+ +e  + s+ ++    ++ ld++ +  s             l+++++l++d
  gi|242399416|ref|YP_002994841.1| 105 PKEELEE--RVSQFVEAFGIEEYLDQFIGTLSfgtqqkvslisaLLHDPQVLILD 157
                                       6666666..5555555556666666666655566666666666644444444444 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 ?   11.7   0.0   0.00016      0.23      62      88 ..     149     175 ..     121     177 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00016
                           SbcCD_C  62 palrlvfLDEAFsklDeesiatllell 88 
                                       +++++++LDEA ++lD++s++ l ell
  gi|242399416|ref|YP_002994841.1| 149 HDPQVLILDEAMNGLDPKSARILRELL 175
                                       56899**************99887765 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.5    0.0004      0.56      27      44 ..      31      48 ..      29     188 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0004
                             DUF87 27 AilgsTGsGKSntvavLl 44
                                      + lg  GsGKS+t+++L+
  gi|242399416|ref|YP_002994841.1| 31 GLLGPNGSGKSTTMKILV 48
                                      678999*********987 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.1    0.0011       1.5      28      43 ..      32      47 ..      22      57 .. 0.88
   2 ?    2.1   0.0     0.095   1.3e+02     299     364 ..     135     190 ..      71     191 .. 0.77
   3 ?   -1.5   0.1       1.1   1.6e+03     148     254 ..     219     244 ..     203     252 .. 0.48

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0011
                            AAA_15 28 liGkNnsGKSsileal 43
                                      l G+N+sGKS+ +++l
  gi|242399416|ref|YP_002994841.1| 32 LLGPNGSGKSTTMKIL 47
                                      78************98 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.095
                            AAA_15 299 sGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                       +G+q+ ++li  +l+         ++ +l+++E  + L p+  ++l +ll+e  ++++  +i++TH
  gi|242399416|ref|YP_002994841.1| 135 FGTQQKVSLISALLH---------DPQVLILDEAMNGLDPKSARILRELLLEFKKEGR-SIIFSTH 190
                                       555555555554443.........346688899999999999***********99999.9*****9 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1.1
                            AAA_15 148 pkekeeklekekeelkidkedlkklikkleeslkkeeelknvlksaiiklllisakRnvsdedsekkssllgklkek 224
                                        ke+ +                                                                       
  gi|242399416|ref|YP_002994841.1| 219 LKERAH----------------------------------------------------------------------- 224
                                       222222....................................................................... PP

                            AAA_15 225 ileealqekleeelteklkeiqeklkeidk 254
                                                 ee+l++++ ++ e+ +e ++
  gi|242399416|ref|YP_002994841.1| 225 ----------EENLEDIFLKLTESKDEVYN 244
                                       ..........33333333333333333333 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.0   0.00015      0.21      18      37 ..      26      45 ..       9      50 .. 0.79
   2 ?    0.6   0.3      0.48   6.6e+02     153     192 ..     181     235 ..      98     252 .. 0.42

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00015
                            AAA_23 18 skgltlItGpNGaGKTTild 37
                                      +  ++ + GpNG+GK+T + 
  gi|242399416|ref|YP_002994841.1| 26 NGEIYGLLGPNGSGKSTTMK 45
                                      4568899**********875 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.48
                            AAA_23 153 e.............................rleelekeleeledekkllekleqekekekeleeleeel 192
                                       e                              +e   +el+e                 e++le++  +l
  gi|242399416|ref|YP_002994841.1| 181 EgrsiifsthilplaemicdrigliykgeiIVEGTMEELKERAH--------------EENLEDIFLKL 235
                                       13333333333333333333333333333322222233333333..............33333333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       662  (0.0369234); expected 358.6 (0.02)
Passed bias filter:                      589  (0.0328518); expected 358.6 (0.02)
Passed Vit filter:                       104  (0.00580066); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 1761.89
//
Query:       gi|242399417|ref|YP_002994842.1|  [L=517]
Description: Pterin-binding protein [Thermococcus sibiricus MM 739]
Scores for complete 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   0.1    0.00026   21.0   0.0    2.2  2  DUF4346      Domain of unknown function (DUF4346)
     0.0001   22.1   0.0    0.00022   21.0   0.0    1.6  1  Pterin_bind  Pterin binding enzyme
     0.0051   17.2   0.4       0.33   11.3   0.0    2.8  3  Radical_SAM  Radical SAM superfamily
  ------ inclusion threshold ------
       0.03   14.8   0.0      0.092   13.2   0.0    1.8  1  DUF4830      Domain of unknown function (DUF4830)


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 ?   -0.8   0.0      0.33   1.5e+03      91     102 ..     311     322 ..     293     327 .. 0.81
   2 !   21.0   0.0   5.9e-08   0.00026      72     117 ..     456     508 ..     427     509 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.33
                           DUF4346  91 kldhaaYlGRel 102
                                        l+h  YlGR +
  gi|242399417|ref|YP_002994842.1| 311 ILEHVPYLGRSI 322
                                       589*******76 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 5.9e-08
                           DUF4346  72 takelcvkileeeeelpvtkld.......haaYlGRelqraeaaLlsgkeYiq 117
                                         k++ + + e+ +    t l+       ha YlGRel +a++aL+ +++Y+q
  gi|242399417|ref|YP_002994842.1| 456 GTKQVLTMVGENPDAIIDTILEhfeisprHAFYLGRELEKAKTALKLKRRYLQ 508
                                       55666666666655555455544446666***********************9 PP

>> Pterin_bind  Pterin binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   4.9e-08   0.00022      18     104 ..     178     258 ..     172     312 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 4.9e-08
                                       THHHHHHHHHHHHHHTT-SEEEEESS-TSTT--CCHHHHHHHHHHHHHH.HHHHHC.TSEEEEE-S-HHHHHHHHHT CS
                       Pterin_bind  18 edldkalaqarkmveeGAdilDiggestrPgaervdeeeelervvpvle.alrdea.dvpisiDttkaevaeaAlka 92 
                                       +++++++++a   +++GAd++Dig+ s+       +e+ +   ++p ++ +++++  dvpis D+ + + +e+ +++
  gi|242399417|ref|YP_002994842.1| 178 LSVEEIVNKALYYLKSGADVIDIGMISG-------EENLDFIDLLPEIReKIKENGfDVPISFDSLNEKELER-VSE 246
                                       6899************************.......4444444555555414556666********99887776.445 PP

                                       TSEEEEETTTTS CS
                       Pterin_bind  93 gadivNdvsgee 104
                                        ad++ ++ g +
  gi|242399417|ref|YP_002994842.1| 247 HADLLLSIDGSN 258
                                       566666666655 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   7.3e-05      0.33      24     143 ..     173     300 ..     159     309 .. 0.77
   2 ?   -1.2   0.0      0.52   2.3e+03      61      92 ..     400     428 ..     389     444 .. 0.79
   3 ?    2.4   0.0     0.041   1.9e+02      41      73 ..     450     484 ..     429     503 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 7.3e-05
                                       HHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHG..HHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxx RF
                       Radical_SAM  24 grgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritvetngtlpd..eeklerll 98 
                                       +++  lsveei++++ ++  + g++++ +g+     + df++ll +++++     ++ + ++   ++  e+ ler  
  gi|242399417|ref|YP_002994842.1| 173 VDAPKLSVEEIVNKALYY-LKSGADVIDIGMISGEENLDFIDLLPEIREK---IKENGFDVPISFDSlnEKELERVS 245
                                       667889************.6888777777755555555788888888887...455555554444445599999999 PP

                                       HTT-SEEEEEEBSSSHH...........HHHHHHT.CTSHHHHHHHHHHHHHHTTSE CS
                                       xxxxxxxxxxxxxxxxx...........xxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  99 elgvdrvslgleaadde...........kvlklmn.rghtfeevlealeklreagik 143
                                       e     + l+++  + e           ++ ++++  ++ +e +++ lekl+e+ i 
  gi|242399417|ref|YP_002994842.1| 246 EH--ADLLLSIDGSNLEklvtktpvvliPTNQKTGyFPQKPENRVKFLEKLKENAIQ 300
                                       94..589999999999999*****88887777777877888***********99775 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.52
                                       TTHHHHHHHHHHTCCCTEEEEEEECSSCHGHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  61 pdfvellerlaklavpgiritvetngtlpdee 92 
                                       +d+ ++l+ l+++  +  +it+e+n + ++  
  gi|242399417|ref|YP_002994842.1| 400 KDLGFDLLILKEK--KREEITYEINSPILE-A 428
                                       6788888899998..79999**99999984.3 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.041
                                       HH.HHTT.SEEEEEESSTGGGSTTHHHHHHHHHHT CS
                                       xx.xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  41 lk.aekg.vkevilgggepllypdfvellerlakl 73 
                                          a++g + +++++g +p++  d + + ++++ +
  gi|242399417|ref|YP_002994842.1| 450 WViAHRGtKQVLTMVGENPDAIIDTILEHFEISPR 484
                                       444788989****************9999998876 PP

>> DUF4830  Domain of unknown function (DUF4830)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.1e-05     0.092      35      79 ..     398     449 ..     385     452 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.1e-05
                           DUF4830  35 lqkdiGldLekykgkevtrytYelk.......nypkeenevranllvkegki 79 
                                       + kd G+dL  +k+k+ +++tYe++       +++ + ++++  +++kegki
  gi|242399417|ref|YP_002994842.1| 398 IPKDLGFDLLILKEKKREEITYEINspileakQREIKLEDIYFRIFIKEGKI 449
                                       679**********************999987766667777999999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (517 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       705  (0.0393218); 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):               4  [number of targets reported over threshold]
# CPU time: 0.71u 0.36s 00:00:01.06 Elapsed: 00:00:00.57
# Mc/sec: 2723.07
//
Query:       gi|242399418|ref|YP_002994843.1|  [L=98]
Description: Methlytransferase, [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-27   95.0   2.6    2.6e-27   94.9   2.6    1.0  1  DUF3216   Protein of unknown function (DUF3216)


Domain annotation for each model (and alignments):
>> DUF3216  Protein of unknown function (DUF3216)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.9   2.6   1.4e-31   2.6e-27       2      91 .]       5      95 ..       4      95 .. 0.96

  Alignments for each domain:
  == domain 1  score: 94.9 bits;  conditional E-value: 1.4e-31
                                      HHHHHHHHCTT-HHHHHHHHHHHHHTTTHHHHH-HHHHHHHHHHHHHHHHHHHTTT-.--HHHHHHHHHHHHHHHHHH- CS
                           DUF3216  2 eklkellleleeenllkaleafvrltgGlekkrGedfikvsilGfleGlltvlkeky.deekvkellekvkakreelee 79
                                      ek+k+l+ +l+e++ll++++ f+ l+  l  k+Gedf+ v+ilGfleG+l  l++ky +++ ++ lle +++kr+elee
  gi|242399418|ref|YP_002994843.1|  5 EKVKALCEKLGEKDLLRTIDSFIILQRELSTKKGEDFVNVAILGFLEGMLVSLRKKYpQNQDIQGLLELIRTKRAELEE 83
                                      9********************************************************55778***************** PP

                                      ---XXXXXXXXX CS
                           DUF3216 80 llrkpripllve 91
                                      ++rkp i l++e
  gi|242399418|ref|YP_002994843.1| 84 KFRKPEIHLFEE 95
                                      ******998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       643  (0.0358637); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); 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 0.35s 00:00:00.88 Elapsed: 00:00:00.56
# Mc/sec: 529.37
//
Query:       gi|242399419|ref|YP_002994844.1|  [L=260]
Description: TatD-related deoxyribonuclease [Thermococcus sibiricus MM 739]
Scores for 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-54  184.7   0.0    2.3e-54  184.5   0.0    1.0  1  TatD_DNase    TatD related DNase
    0.00012   21.5   0.2    0.00049   19.5   0.2    1.9  1  Amidohydro_1  Amidohydrolase family
     0.0038   17.1   0.1       0.42   10.3   0.0    2.8  3  Amidohydro_2  Amidohydrolase


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 !  184.5   0.0   3.8e-58   2.3e-54       1     254 [.       9     255 ..       9     256 .. 0.94

  Alignments for each domain:
  == domain 1  score: 184.5 bits;  conditional E-value: 3.8e-58
                                       EEEEE-TTSCCCTTTHHHHHHHHHHTTEEEEEEE-SSGGGHH..HHHHHHTT.TTTEEEEE---GGGGGCC.CCHHH CS
                        TatD_DNase   1 iDaHcHldskefeedreeileraeeagvaavvvvgtsskdsk..avlelakkypnkvyavlGiHPnevdeasedlle 75 
                                       iDaH+H++   f+++ + i+e+ + ++++a+v   t+  +++  +  el + y + ++++lG+ Pne+++ + + ++
  gi|242399419|ref|YP_002994844.1|   9 IDAHAHVEM--FKKNVPLIVEESK-KELKAIVDSITEYRKFRvwKSWELLEPYFGFIFPTLGFAPNEAKRGNWERVK 82 
                                       8********..99999*9999887.6888888887877788878889999999999********************* PP

                                       HHHHHHHCCCTSEEEEEEEEEET.-CCCCCGHHHHHHHHHHHHHHHHHTTEEEEEEEES-HHHHHHHHHHCGGCCSE CS
                        TatD_DNase  76 elkelanvkhskvvaiGeiGLDy.ysreestkeaqeevFeeqlrlAkelklplviHlrkaeedlleilkeaaeakak 151
                                       +++e+  +k++++vaiGeiGLDy y   e+++e q+++F+++l lA++l+lp+viH+r+ae++  e++++++ +   
  gi|242399419|ref|YP_002994844.1|  83 KVEEFIWAKKDEIVAIGEIGLDYyYAGTEKERENQKAIFDHFLTLAEDLNLPVVIHARDAEREAFEMVQRKGLVA-- 157
                                       *****99****************5588999****************************************98655.. PP

                                       EEETT--S-HHHHHHHHHTTEEEEE-GGGGTTTTHHHHHHHHHS-GGGEEE---TTSSEECCCTTSE--GGGHHHHH CS
                        TatD_DNase 152 vvlHsfsgsaeeakkflklgyyislsglltfknakelrelvkavpldrlLiETDaPyltpkpyrgkrnepanvayvv 228
                                         +Hs+sg++e+ak++++    ++++  +tf    e+  ++k ++ +++L+ETDaPy++p  ++g++n+p +v+  v
  gi|242399419|ref|YP_002994844.1| 158 -YFHSYSGDVETAKEIVENSHLVGINTGVTF--IPEVETVAKVLDIENILVETDAPYMSP--FKGEKNKPTYVRVAV 229
                                       .8*****************************..55899999*******************..999************ PP

                                       HHHHHHHTS-HHHHHHHHHHHHHHHH CS
                        TatD_DNase 229 eklaelkaltleelaeitaeNakrlf 254
                                       ek+a++k++ +ee++ +t +N++ +f
  gi|242399419|ref|YP_002994844.1| 230 EKIAAIKGVGVEEVESVTDKNTLMFF 255
                                       ***********************999 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.2   8.2e-08   0.00049      88     247 ..      63     258 ..       7     259 .. 0.64

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 8.2e-08
                                       S.....GCCCSHHHHHHHHHHHHHHHHHHCTTTCEE.EEEEECGTCCSHHH.......HHHHHHHHHHHHTTEEEEE CS
                      Amidohydro_1  88 r.....gsaetskasreklkagaaetikgkadgvvk.valapheapafsde.......elkealkeakkrdlpvaiH 151
                                               +e  + ++e++k+  +e+i++k+d++v   +++    +a ++          ++ l +a++ +lpv+iH
  gi|242399419|ref|YP_002994844.1|  63 FptlgfAPNEAKRGNWERVKKV-EEFIWAKKDEIVAiGEIGLDYYYAGTEKerenqkaIFDHFLTLAEDLNLPVVIH 138
                                       03335577889999*****998.8***********988777665555554455555548888888************ PP

                                       E..TSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEE.HH......HHHHHHHHHHHHCEE... CS
                      Amidohydro_1 152 a..letkgevedaeaafgetiehgthlevaeslglldeiklilahgvhlt.pt......eaellkerlkeagva... 216
                                       a  +e +++ e++++++      +++ ++ +     +++k i++   ++   t      e+e++++ l+  ++    
  gi|242399419|ref|YP_002994844.1| 139 ArdAEREAF-EMVQRKGL----VAYFHSYSG---DVETAKEIVENSHLVGiNTgvtfipEVETVAKVLDIENILvet 207
                                       *74443333.45555555....333333323...3455555554444444522444666788877777766666666 PP

                                       ....................HHHHHHHHSEHHHHHHHHHHHHTSCEEEEEE CS
                      Amidohydro_1 217 ....................hcpfsnsilrsgrealrkaldeGvkvglgtD 247
                                                            + +   i + g+e ++ + d+++ +++g D
  gi|242399419|ref|YP_002994844.1| 208 dapymspfkgeknkptyvrvAVEKIAAIKGVGVEEVESVTDKNTLMFFGID 258
                                       666644444444444444444444444477777777777666666777666 PP

>> Amidohydro_2  Amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       0.2   1.2e+03       1       7 [.       9      15 ..       9      98 .. 0.67
   2 !   10.3   0.0   7.1e-05      0.42     123     179 ..     113     159 ..     104     169 .. 0.83
   3 !    3.4   0.0    0.0091        54     223     260 ..     181     218 ..     167     257 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.2
                                      EEEEEEE CS
                      Amidohydro_2  1 iDvHaHl 7 
                                      iD+HaH+
  gi|242399419|ref|YP_002994844.1|  9 IDAHAHV 15
                                      7888884 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 7.1e-05
                                       CCTTTCGGHHHHHHHHHHHT-EEEEE....CHHHCHHHHHHHHHHHHHHHCCHHHHC CS
                      Amidohydro_2 123 ddllgdrldrpifealeelglpvdihtGpspewlfggpqettraiqplllsgvarkf 179
                                       ++ ++ + +++++ ++e+l+lpv ih           ++++ +a+ ++++ g+++ f
  gi|242399419|ref|YP_002994844.1| 113 ERENQKAIFDHFLTLAEDLNLPVVIH----------ARDAEREAFEMVQRKGLVAYF 159
                                       5567777789****************..........688888888888888888766 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.0091
                                       EECCHHCHHHHHHHHHHH-GGGEEEE--BTSTTSTSCT CS
                      Amidohydro_2 223 fdspladppalarlieavgpdrilfGsDyPhptleaep 260
                                         + +++ p ++++ ++++ ++il  +D P+ +++   
  gi|242399419|ref|YP_002994844.1| 181 INTGVTFIPEVETVAKVLDIENILVETDAPYMSPFKGE 218
                                       57889999**********************99887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       660  (0.0368119); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); 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: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1683.93
//
Query:       gi|242399420|ref|YP_002994845.1|  [L=87]
Description: hypothetical protein TSIB_1445 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-14   53.9   0.4    2.4e-14   53.8   0.4    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 !   53.8   0.4   1.3e-18   2.4e-14       4      76 .]       6      78 ..       1      78 [. 0.88

  Alignments for each domain:
  == domain 1  score: 53.8 bits;  conditional E-value: 1.3e-18
                            MJ1316  4 aqdvlnRirWdkeldkskfvvgyldR..fkgikevpleeiswiedflleeeegelaIPlHRiryikrk.gevvWdR 76
                                      +++vl++i++d++ +++++ + +++R   ++ik++p++ i+    ++++e++    IP+HRi  + +k g+vvW++
  gi|242399420|ref|YP_002994845.1|  6 VKEVLSKIKYDARENEEDYYIVIEHRgtYGNIKKIPVKMITLGHGYFFIEDT---QIPYHRILAVIKKdGKVVWKK 78
                                      589************************999********99998885555555...4******9987755*****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 549.48
//
Query:       gi|242399421|ref|YP_002994846.1|  [L=237]
Description: Hydrolase, metallo-beta-lactamase superfamily [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.5e-29  100.8   0.3    1.7e-28  100.0   0.3    1.3  1  Lactamase_B    Metallo-beta-lactamase superfamily
    1.7e-06   27.7   0.0    2.1e-06   27.4   0.0    1.2  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 !  100.0   0.3   1.9e-32   1.7e-28       6     197 .]      28     215 ..      24     215 .. 0.92

  Alignments for each domain:
  == domain 1  score: 100.0 bits;  conditional E-value: 1.9e-32
                                       SEEEEEEETTCEEEES--SCHHHHHHHH.HHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHC CS
                       Lactamase_B   6 vnsyliegdggviLiDtGtsteaaraal.elaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapa 81 
                                       +n+yl +++++ +++DtGt+  + r ++ + + ++l++++  ++++TH H+DH+Gg++ ++e      + v  + + 
  gi|242399421|ref|YP_002994846.1|  28 SNIYLFRDENEGLIVDTGTGVYWHRYFEiLERENYLEGLEKVTILNTHEHFDHVGGNKRFKEFLEKMGVSVIFASHR 104
                                       8***************************889999****************************999998888888888 PP

                                       CHCHHHHHHHHHCCHH...TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSH CS
                       Lactamase_B  82 lfmeeaddaasrkgll...lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallag 155
                                          + ++++  +  l    ++++ ++ ++ ++e++d    gr+ l+v+++pgh++g+++++ +++++lftGD+++++
  gi|242399421|ref|YP_002994846.1| 105 IAADVLEKGDDYVVLSyayGRRFEPQTVELKLEDGDKLQIGRKKLKVIHTPGHTAGSICLYEPEERILFTGDTVFNR 181
                                       8888888888888777888999999999999999999**************************************** PP

                                       HCCCCCC.TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEESS CS
                       Lactamase_B 156 etgridltlrgaevrdpsdaekyldsllklaglkaevlvpgH 197
                                         gr+dl        +++  e++++s+  l + +++v + gH
  gi|242399421|ref|YP_002994846.1| 182 TVGRTDL--------PTGNFEELINSINVLSTFEVDVALSGH 215
                                       *******........888888888888888888888888887 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0   2.3e-10   2.1e-06       4     144 ..      41     178 ..      39     232 .. 0.69

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 2.3e-10
                                       EES--TTHHHH.HTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCC.C--EEEEEE.EEHHHHH.HCCTTCGH CS
                     Lactamase_B_2   4 LiDagpdlrqq.alralqPvelrdelppidaVllthaHyDHlaglltlre.lrpkklply.apkgvla.vleanfvy 76 
                                       ++D+g+++  +     l++ + ++ l+++  +l th+H+DH+ g   ++e l++  + ++ a+ +++a vle++ +y
  gi|242399421|ref|YP_002994846.1|  41 IVDTGTGVYWHrYFEILERENYLEGLEKVT-ILNTHEHFDHVGGNKRFKEfLEKMGVSVIfASHRIAAdVLEKGDDY 116
                                       677888844442222223333678899999.*******************655555886668877766267777777 PP

                                       HHCHTT....TTEEEEEE-..TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S CS
                     Lactamase_B_2  77 laleee....pavnvheld..wgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtg 144
                                        +l  +    ++ +++el+   g+++++g  +  ++++  ++           ++ + ++ ++++r++++gDt 
  gi|242399421|ref|YP_002994846.1| 117 VVLSYAygrrFEPQTVELKleDGDKLQIGRKK--LKVIHTPGH----------TAGSICLYEPEERILFTGDTV 178
                                       77777766664444444442255666666443..444433333..........34578899999********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1560.37
//
Query:       gi|242399422|ref|YP_002994847.1|  [L=39]
Description: hypothetical protein TSIB_1447 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.085   12.0   0.0      0.085   12.0   0.0    1.0  1  GSP_synth  Glutathionylspermidine synthase preATP-grasp
       0.17   10.5   0.0       0.17   10.5   0.0    1.0  1  GDA1_CD39  GDA1/CD39 (nucleoside phosphatase) family


Domain annotation for each model (and alignments):
>> GSP_synth  Glutathionylspermidine synthase preATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   9.5e-06     0.085     236     269 ..       7      38 ..       1      39 [] 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9.5e-06
                         GSP_synth 236 eelaeallevrllePawklllsnKalLallWely 269
                                       ++l ++    r leP  k+++ nK l a+l++ y
  gi|242399422|ref|YP_002994847.1|   7 PKLSKSV--RRHLEPDEKVVVKNKWLVAILHDGY 38 
                                       5666666..899******************9977 PP

>> GDA1_CD39  GDA1/CD39 (nucleoside phosphatase) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   1.9e-05      0.17     352     380 ..      10      38 ..       2      39 .] 0.85

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 1.9e-05
                         GDA1_CD39 352 skkskeksiseeeaCfkgayvlslLhdGf 380
                                       sk+++ + +++e++ +k ++ +++LhdG+
  gi|242399422|ref|YP_002994847.1|  10 SKSVRRHLEPDEKVVVKNKWLVAILHDGY 38 
                                       566777888999****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 280.25
//
Query:       gi|242399423|ref|YP_002994848.1|  [L=974]
Description: kinase domain protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-20   73.7  71.3     0.0099   16.2   0.5   13.4 13  DUF5122        Domain of unknown function (DUF5122) beta-prop
    6.2e-07   29.1  29.2          4    7.7   0.1   10.4 10  NHL            NHL repeat
    8.1e-05   22.5   0.0         32    4.6   0.0    7.2  9  DUF2103        Predicted metal-binding protein (DUF2103)
     0.0001   22.0  32.6        1.5    8.7   0.3   10.8 10  RHS            RHS protein
    0.00049   19.8   2.0        6.9    6.6   0.0    5.2  5  RCC1_2         Regulator of chromosome condensation (RCC1) re
     0.0063   16.4  43.5        4.8    7.3   0.1   12.0 12  PQQ            PQQ enzyme repeat
     0.0081   16.1   3.8       0.48   10.4   0.0    5.4  7  Peptidase_S24  Peptidase S24-like
     0.0095   16.0   1.5        1.8    8.6   0.2    2.3  2  Laminin_II     Laminin Domain II
  ------ inclusion threshold ------
      0.022   15.3   0.1         25    5.5   0.0    4.9  5  Laminin_G_2    Laminin G domain
      0.056   13.9   0.0         77    3.8   0.0    4.2  4  Usp            Universal stress protein family
       0.06   13.5   3.8         13    6.0   0.1    5.3  5  Tox-HDC        Toxin with a H, D/N and C signature
       0.15   12.9  10.3         13    6.9   0.0    7.6  8  WD40           WD domain, G-beta repeat
       0.36   10.7   4.2         63    3.5   0.0    5.6  5  DUF1508        Domain of unknown function (DUF1508)
          2    8.3  10.4         36    4.2   0.1    5.0  6  Flavi_NS2B     Flavivirus non-structural protein NS2B


Domain annotation for each model (and alignments):
>> DUF5122  Domain of unknown function (DUF5122) beta-propeller
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.5   0.00017      0.22       2      31 ..      63      94 ..      62      95 .. 0.93
   2 !   10.1   0.8    0.0006      0.77       3      31 ..     117     146 ..     115     147 .. 0.83
   3 !   14.5   0.5   2.6e-05     0.033       2      31 ..     168     198 ..     167     199 .. 0.92
   4 !   10.0   0.7   0.00065      0.84       3      31 ..     221     250 ..     220     251 .. 0.92
   5 ?    2.3   0.3      0.17   2.2e+02       2      21 ..     272     290 ..     271     301 .. 0.72
   6 ?    2.8   0.0      0.12   1.5e+02       2      31 ..     330     349 ..     329     350 .. 0.82
   7 ?   -0.4   0.3       1.1   1.5e+03       2      28 ..     504     531 ..     504     535 .. 0.65
   8 !    6.6   1.5    0.0077       9.8       7      31 ..     561     586 ..     555     587 .. 0.87
   9 !   15.2   0.4   1.5e-05     0.019       2      31 ..     608     638 ..     607     639 .. 0.93
  10 !   14.5   0.4   2.6e-05     0.033       2      31 ..     660     690 ..     659     691 .. 0.93
  11 !   16.2   0.5   7.7e-06    0.0099       3      32 ..     713     743 ..     712     743 .. 0.91
  12 !   12.2   0.5   0.00014      0.17       3      31 ..     765     794 ..     764     795 .. 0.91
  13 ?    2.5   0.0      0.14   1.8e+02       6      32 ..     821     848 ..     819     848 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00017
                           DUF5122  2 pDGKIlVaGsftsy..ngssdfalvRLnaDGs 31
                                      p+G ++VaG++ s   ++++d  ++RL+a+G+
  gi|242399423|ref|YP_002994848.1| 63 PNGDLIVAGYTQSFsdSDWGDVWVLRLDANGN 94
                                      8999********7799***************8 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0006
                           DUF5122   3 DGKIlVaGsftsy.ngssdfalvRLnaDGs 31 
                                       +G I+VaG+++s  +g sd  +++L+  G+
  gi|242399423|ref|YP_002994848.1| 117 NGNIVVAGYTNSFsDGYSDVWVLCLDGSGN 146
                                       79*********6679999988888887776 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 2.6e-05
                           DUF5122   2 pDGKIlVaGsftsy.ngssdfalvRLnaDGs 31 
                                       p+G ++V+G + s  +gssdf ++RL+ +G+
  gi|242399423|ref|YP_002994848.1| 168 PNGDVIVVGFTVSFgAGSSDFWVLRLDENGN 198
                                       8999********667***************8 PP

  == domain 4  score: 10.0 bits;  conditional E-value: 0.00065
                           DUF5122   3 DGKIlVaGsftsy.ngssdfalvRLnaDGs 31 
                                       DG I+V G+++s  +g  d+ ++RL++ G+
  gi|242399423|ref|YP_002994848.1| 221 DGDIIVTGWTNSFgAGYEDIWILRLDSGGN 250
                                       9**********667************9997 PP

  == domain 5  score: 2.3 bits;  conditional E-value: 0.17
                           DUF5122   2 pDGKIlVaGsftsyngssdf 21 
                                       p+G I+Va +++s   ++df
  gi|242399423|ref|YP_002994848.1| 272 PNGDIIVASYTGSF-ENGDF 290
                                       899********965.55555 PP

  == domain 6  score: 2.8 bits;  conditional E-value: 0.12
                           DUF5122   2 pDGKIlVaGsftsyngssdfalvRLnaDGs 31 
                                       p+G Il+aG+            +RL ++G 
  gi|242399423|ref|YP_002994848.1| 330 PNGDILLAGWDL----------LRLSPNGE 349
                                       899999999976..........88888885 PP

  == domain 7  score: -0.4 bits;  conditional E-value: 1.1
                           DUF5122   2 pDGKIlVaGsftsy.ngssdfalvRLna 28 
                                       p+G ++VaG + s   g  df +++L+ 
  gi|242399423|ref|YP_002994848.1| 504 PNGDVIVAGGTESFgVGYEDFWVLKLDK 531
                                       6777888887774447777777777665 PP

  == domain 8  score: 6.6 bits;  conditional E-value: 0.0077
                           DUF5122   7 lVaGsftsy.ngssdfalvRLnaDGs 31 
                                       +VaG ++s  +g  d  ++RL+a+G+
  gi|242399423|ref|YP_002994848.1| 561 IVAGFTNSFgAGYDDAWVLRLDANGN 586
                                       8******6679999999********8 PP

  == domain 9  score: 15.2 bits;  conditional E-value: 1.5e-05
                           DUF5122   2 pDGKIlVaGsftsy.ngssdfalvRLnaDGs 31 
                                       p+G I++ G+++s  +g sdf ++RL+ +G+
  gi|242399423|ref|YP_002994848.1| 608 PNGDIIATGYTYSFgAGYSDFWVLRLDENGN 638
                                       89**********667***************8 PP

  == domain 10  score: 14.5 bits;  conditional E-value: 2.6e-05
                           DUF5122   2 pDGKIlVaGsftsy.ngssdfalvRLnaDGs 31 
                                       p+G I+V G + s  +g++d  ++RL+a+G+
  gi|242399423|ref|YP_002994848.1| 660 PNGEIIVTGATLSFgAGGTDVWVLRLDANGN 690
                                       89**********667***************8 PP

  == domain 11  score: 16.2 bits;  conditional E-value: 7.7e-06
                           DUF5122   3 DGKIlVaGsftsy.ngssdfalvRLnaDGsl 32 
                                       +G I+VaG+++s  +g+ df ++RL+a+G++
  gi|242399423|ref|YP_002994848.1| 713 NGDIIVAGDTMSFgAGGADFWVLRLDANGNI 743
                                       588********667***************85 PP

  == domain 12  score: 12.2 bits;  conditional E-value: 0.00014
                           DUF5122   3 DGKIlVaGsftsy.ngssdfalvRLnaDGs 31 
                                       +G I+V G+++s  +g +d  l+RL+a+G+
  gi|242399423|ref|YP_002994848.1| 765 NGDIIVTGESNSFgAGYYDAWLLRLDANGN 794
                                       588********667***************8 PP

  == domain 13  score: 2.5 bits;  conditional E-value: 0.14
                           DUF5122   6 IlVaGsftsy.ngssdfalvRLnaDGsl 32 
                                       ++VaG ++s   +  d  ++RL +DG+l
  gi|242399423|ref|YP_002994848.1| 821 LIVAGATYSFsVSEADGWVLRLPPDGNL 848
                                       6899999966688888889999999987 PP

>> NHL  NHL repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.1     0.016        21       3      18 ..      55      70 ..      53      70 .. 0.92
   2 !    6.3   0.2    0.0082        10       3      18 ..     108     123 ..     107     128 .. 0.89
   3 ?    1.2   0.1      0.35   4.5e+02       7      17 ..     164     174 ..     161     175 .. 0.91
   4 ?   -1.8   0.1       3.1     4e+03       7      18 ..     216     227 ..     213     227 .. 0.78
   5 !    6.4   0.0     0.008        10       3      18 ..     264     279 ..     263     292 .. 0.92
   6 !    7.6   0.0    0.0034       4.3       3      18 ..     322     337 ..     321     337 .. 0.91
   7 ?   -1.0   0.1       1.7   2.2e+03      11      18 ..     504     511 ..     502     511 .. 0.88
   8 !    7.7   0.1    0.0031         4       3      18 ..     652     667 ..     651     667 .. 0.94
   9 ?    2.6   0.3      0.13   1.7e+02       7      18 ..     708     719 ..     707     719 .. 0.93
  10 ?    4.1   0.1      0.04        52       4      18 ..     757     771 ..     756     776 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.016
                                      SEEEEEEETTTEEEEE CS
                               NHL  3 yPhGvavdsnGdiyVa 18
                                      y++ va+ +nGd++Va
  gi|242399423|ref|YP_002994848.1| 55 YAWPVAIAPNGDLIVA 70
                                      7899***********8 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0082
                                       SEEEEEEETTTEEEEE CS
                               NHL   3 yPhGvavdsnGdiyVa 18 
                                       +P  va+++nG+i+Va
  gi|242399423|ref|YP_002994848.1| 108 SPVAVAITQNGNIVVA 123
                                       6999***********9 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.35
                                       EEEETTTEEEE CS
                               NHL   7 vavdsnGdiyV 17 
                                       +a+++nGd++V
  gi|242399423|ref|YP_002994848.1| 164 IALTPNGDVIV 174
                                       7999******9 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 3.1
                                       EEEETTTEEEEE CS
                               NHL   7 vavdsnGdiyVa 18 
                                       va++ +Gdi+V+
  gi|242399423|ref|YP_002994848.1| 216 VAITLDGDIIVT 227
                                       666669****97 PP

  == domain 5  score: 6.4 bits;  conditional E-value: 0.008
                                       SEEEEEEETTTEEEEE CS
                               NHL   3 yPhGvavdsnGdiyVa 18 
                                       +P  v++d+nGdi+Va
  gi|242399423|ref|YP_002994848.1| 264 RPDAVTIDPNGDIIVA 279
                                       57789**********8 PP

  == domain 6  score: 7.6 bits;  conditional E-value: 0.0034
                                       SEEEEEEETTTEEEEE CS
                               NHL   3 yPhGvavdsnGdiyVa 18 
                                       +P+G+a+ +nGdi+ a
  gi|242399423|ref|YP_002994848.1| 322 SPNGIAIAPNGDILLA 337
                                       6************976 PP

  == domain 7  score: -1.0 bits;  conditional E-value: 1.7
                                       TTTEEEEE CS
                               NHL  11 snGdiyVa 18 
                                       +nGd++Va
  gi|242399423|ref|YP_002994848.1| 504 PNGDVIVA 511
                                       8******8 PP

  == domain 8  score: 7.7 bits;  conditional E-value: 0.0031
                                       SEEEEEEETTTEEEEE CS
                               NHL   3 yPhGvavdsnGdiyVa 18 
                                       yP  +av +nG+i+V+
  gi|242399423|ref|YP_002994848.1| 652 YPVAIAVAPNGEIIVT 667
                                       89*************8 PP

  == domain 9  score: 2.6 bits;  conditional E-value: 0.13
                                       EEEETTTEEEEE CS
                               NHL   7 vavdsnGdiyVa 18 
                                       vav  nGdi+Va
  gi|242399423|ref|YP_002994848.1| 708 VAVAENGDIIVA 719
                                       899********8 PP

  == domain 10  score: 4.1 bits;  conditional E-value: 0.04
                                       EEEEEEETTTEEEEE CS
                               NHL   4 PhGvavdsnGdiyVa 18 
                                       ++ +a++ nGdi+V+
  gi|242399423|ref|YP_002994848.1| 757 AWAIAIVENGDIIVT 771
                                       5889**********8 PP

>> DUF2103  Predicted metal-binding protein (DUF2103)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.75   9.6e+02      53      73 ..      84     104 ..      73     117 .. 0.85
   2 ?    1.3   0.0      0.26   3.3e+02      53      74 ..     188     209 ..     173     217 .. 0.85
   3 ?   -2.3   0.0       3.5   4.5e+03      54      73 ..     241     260 ..     235     263 .. 0.83
   4 ?   -0.1   0.0      0.71   9.1e+02      54      83 ..     525     555 ..     504     565 .. 0.77
   5 ?    0.6   0.0      0.45   5.8e+02      54      84 ..     577     608 ..     571     613 .. 0.79
   6 ?    1.3   0.0      0.26   3.3e+02      54      72 ..     629     647 ..     612     659 .. 0.86
   7 ?    4.6   0.0     0.025        32      48      76 ..     675     703 ..     656     717 .. 0.78
   8 ?    0.5   0.0      0.47     6e+02      49      73 ..     728     752 ..     714     763 .. 0.81
   9 ?   -2.6   0.0       4.5   5.7e+03      53      67 ..     784     798 ..     769     803 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.75
                           DUF2103  53 vkvtraderGnlrlllrdgss 73 
                                       v v+r d +Gn++   + g s
  gi|242399423|ref|YP_002994848.1|  84 VWVLRLDANGNVKWQKTYGGS 104
                                       5699*********98887776 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.26
                           DUF2103  53 vkvtraderGnlrlllrdgssv 74 
                                       + v+r de+Gn++   + g s 
  gi|242399423|ref|YP_002994848.1| 188 FWVLRLDENGNVKWQKTYGGSG 209
                                       5699*********998888875 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 3.5
                           DUF2103  54 kvtraderGnlrlllrdgss 73 
                                        ++r d+ Gn++   + g s
  gi|242399423|ref|YP_002994848.1| 241 WILRLDSGGNIKWQKTYGGS 260
                                       58899*******98888876 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 0.71
                           DUF2103  54 kvtraderGnlrlllrdgssvQevfi.vtta 83 
                                        v++ d+ Gn++   + g s  e  i v ta
  gi|242399423|ref|YP_002994848.1| 525 WVLKLDKGGNVKWQKIYGGSGSEWAIsVATA 555
                                       58899*********99999999887733333 PP

  == domain 5  score: 0.6 bits;  conditional E-value: 0.45
                           DUF2103  54 kvtraderGnlrlllrdgssvQe.vfivttak 84 
                                        v+r d +Gn++   + g    + ++ vtta 
  gi|242399423|ref|YP_002994848.1| 577 WVLRLDANGNVKWQKTYGGNDDDlIRAVTTAP 608
                                       589*********99988876655367788775 PP

  == domain 6  score: 1.3 bits;  conditional E-value: 0.26
                           DUF2103  54 kvtraderGnlrlllrdgs 72 
                                        v+r de+Gn++  ++ g 
  gi|242399423|ref|YP_002994848.1| 629 WVLRLDENGNVKWQMTYGG 647
                                       589*********9998875 PP

  == domain 7  score: 4.6 bits;  conditional E-value: 0.025
                           DUF2103  48 ggglrvkvtraderGnlrlllrdgssvQe 76 
                                        gg +v v+r d +Gn++   + g s+ e
  gi|242399423|ref|YP_002994848.1| 675 AGGTDVWVLRLDANGNVKWQKTYGGSADE 703
                                       5778899**************99999876 PP

  == domain 8  score: 0.5 bits;  conditional E-value: 0.47
                           DUF2103  49 gglrvkvtraderGnlrlllrdgss 73 
                                       gg ++ v+r d +Gn++     g s
  gi|242399423|ref|YP_002994848.1| 728 GGADFWVLRLDANGNIKWQKAYGGS 752
                                       56677899*********98887776 PP

  == domain 9  score: -2.6 bits;  conditional E-value: 4.5
                           DUF2103  53 vkvtraderGnlrll 67 
                                       + ++r d +Gn++  
  gi|242399423|ref|YP_002994848.1| 784 AWLLRLDANGNVKWQ 798
                                       567899******975 PP

>> RHS  RHS protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1     0.066        85      17      28 ..      90     101 ..      89     103 .. 0.89
   2 ?    5.0   0.4     0.016        21      17      32 ..     142     157 ..     140     159 .. 0.92
   3 ?    3.5   0.1     0.046        59      17      29 ..     194     206 ..     193     212 .. 0.88
   4 ?   -0.3   0.0      0.71   9.1e+02      17      28 ..     246     257 ..     245     259 .. 0.87
   5 !    8.7   0.3    0.0011       1.5      17      33 ..     296     312 ..     295     315 .. 0.91
   6 ?    3.0   0.1     0.066        85      17      28 ..     582     593 ..     581     595 .. 0.89
   7 ?    4.2   0.0     0.028        36      17      28 ..     634     645 ..     633     647 .. 0.90
   8 ?    3.0   0.1     0.066        85      17      28 ..     686     697 ..     685     699 .. 0.89
   9 ?    2.5   0.1     0.099   1.3e+02      17      28 ..     738     749 ..     737     754 .. 0.86
  10 ?    3.0   0.1     0.066        85      17      28 ..     790     801 ..     789     803 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.066
                               RHS  17 DanGeivWaaey 28 
                                       DanG++ W+ +y
  gi|242399423|ref|YP_002994848.1|  90 DANGNVKWQKTY 101
                                       9********888 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.016
                               RHS  17 DanGeivWaaeydaWG 32 
                                       D +G++ W+ +y +W+
  gi|242399423|ref|YP_002994848.1| 142 DGSGNVKWQKSYGDWH 157
                                       889************7 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.046
                               RHS  17 DanGeivWaaeyd 29 
                                       D+nG++ W+ +y 
  gi|242399423|ref|YP_002994848.1| 194 DENGNVKWQKTYG 206
                                       9********9986 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 0.71
                               RHS  17 DanGeivWaaey 28 
                                       D+ G+i W+ +y
  gi|242399423|ref|YP_002994848.1| 246 DSGGNIKWQKTY 257
                                       899******888 PP

  == domain 5  score: 8.7 bits;  conditional E-value: 0.0011
                               RHS  17 DanGeivWaaeydaWGn 33 
                                       D +G+i W+ +y  WG 
  gi|242399423|ref|YP_002994848.1| 296 DGSGNIKWQKTYGLWGD 312
                                       889*************7 PP

  == domain 6  score: 3.0 bits;  conditional E-value: 0.066
                               RHS  17 DanGeivWaaey 28 
                                       DanG++ W+ +y
  gi|242399423|ref|YP_002994848.1| 582 DANGNVKWQKTY 593
                                       9********888 PP

  == domain 7  score: 4.2 bits;  conditional E-value: 0.028
                               RHS  17 DanGeivWaaey 28 
                                       D+nG++ W+ +y
  gi|242399423|ref|YP_002994848.1| 634 DENGNVKWQMTY 645
                                       9********999 PP

  == domain 8  score: 3.0 bits;  conditional E-value: 0.066
                               RHS  17 DanGeivWaaey 28 
                                       DanG++ W+ +y
  gi|242399423|ref|YP_002994848.1| 686 DANGNVKWQKTY 697
                                       9********888 PP

  == domain 9  score: 2.5 bits;  conditional E-value: 0.099
                               RHS  17 DanGeivWaaey 28 
                                       DanG+i W+  y
  gi|242399423|ref|YP_002994848.1| 738 DANGNIKWQKAY 749
                                       9*******9777 PP

  == domain 10  score: 3.0 bits;  conditional E-value: 0.066
                               RHS  17 DanGeivWaaey 28 
                                       DanG++ W+ +y
  gi|242399423|ref|YP_002994848.1| 790 DANGNVKWQKTY 801
                                       9********888 PP

>> RCC1_2  Regulator of chromosome condensation (RCC1) repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.51   6.6e+02      11      27 ..     111     128 ..     111     132 .. 0.82
   2 ?    0.1   0.0      0.61   7.8e+02       6      22 ..     153     174 ..     152     176 .. 0.82
   3 !    6.3   0.0    0.0066       8.5      11      29 ..     215     234 ..     215     235 .. 0.93
   4 ?   -2.3   0.0       3.4   4.4e+03      11      25 ..     707     721 ..     707     726 .. 0.79
   5 !    6.6   0.0    0.0054       6.9      11      29 ..     759     778 ..     759     779 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.51
                            RCC1_2  11 scaLtedGeVlcWGs.Ns 27 
                                       ++a+t +G+++  G  Ns
  gi|242399423|ref|YP_002994848.1| 111 AVAITQNGNIVVAGYtNS 128
                                       68*******999996565 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.61
                            RCC1_2   6 aGdyH.....scaLtedGeVlc 22 
                                        Gd H      +aLt +G+V  
  gi|242399423|ref|YP_002994848.1| 153 YGDWHddeatMIALTPNGDVIV 174
                                       688899999899*******976 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.0066
                            RCC1_2  11 scaLtedGeVlcWGs.NsdG 29 
                                       ++a+t dG++  +G+ Ns+G
  gi|242399423|ref|YP_002994848.1| 215 AVAITLDGDIIVTGWtNSFG 234
                                       68************99**99 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 3.4
                            RCC1_2  11 scaLtedGeVlcWGs 25 
                                       ++a+ e+G++   G+
  gi|242399423|ref|YP_002994848.1| 707 AVAVAENGDIIVAGD 721
                                       589999***998887 PP

  == domain 5  score: 6.6 bits;  conditional E-value: 0.0054
                            RCC1_2  11 scaLtedGeVlcWG.sNsdG 29 
                                       ++a++e+G++  +G sNs+G
  gi|242399423|ref|YP_002994848.1| 759 AIAIVENGDIIVTGeSNSFG 778
                                       689***********88**99 PP

>> PQQ  PQQ enzyme repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1   0.8    0.0088        11      15      37 ..      89     110 ..      79     111 .. 0.88
   2 ?    1.0   0.1      0.36   4.6e+02      15      29 ..     141     154 ..     138     156 .. 0.76
   3 ?    3.0   0.1     0.084   1.1e+02      15      30 ..     193     207 ..     191     208 .. 0.85
   4 ?    2.5   0.1      0.12   1.6e+02      20      37 ..     249     266 ..     245     267 .. 0.86
   5 ?   -0.1   0.1      0.84   1.1e+03      15      27 ..     295     306 ..     292     309 .. 0.76
   6 ?    1.5   0.1      0.25   3.3e+02      19      30 ..     347     358 ..     345     359 .. 0.88
   7 ?   -2.0   0.1       3.4   4.3e+03      20      27 ..     533     540 ..     529     544 .. 0.81
   8 !    6.3   0.1    0.0079        10      15      33 ..     581     598 ..     578     601 .. 0.88
   9 !    7.3   0.1    0.0037       4.8      15      37 ..     633     654 ..     631     655 .. 0.89
  10 ?    3.1   0.1     0.078     1e+02      15      30 ..     685     699 ..     683     703 .. 0.84
  11 ?    1.5   0.1      0.25   3.2e+02      15      30 ..     737     751 ..     736     754 .. 0.83
  12 ?    5.2   0.1     0.017        22      15      34 ..     789     807 ..     786     810 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0088
                                       EETTTCCEEEEEESSSCGSSESE CS
                               PQQ  15 lDadTGkvlWrfktggpvlslpi 37 
                                       lD ++G+v+W++  gg ++ +p+
  gi|242399423|ref|YP_002994848.1|  89 LD-ANGNVKWQKTYGGSDVDSPV 110
                                       56.79***********9999986 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.36
                                       EETTTCCEEEEEESS CS
                               PQQ  15 lDadTGkvlWrfktg 29 
                                       lD  +G+v+W++  g
  gi|242399423|ref|YP_002994848.1| 141 LD-GSGNVKWQKSYG 154
                                       66.78*****98766 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.084
                                       EETTTCCEEEEEESSS CS
                               PQQ  15 lDadTGkvlWrfktgg 30 
                                       lD ++G+v+W++  gg
  gi|242399423|ref|YP_002994848.1| 193 LD-ENGNVKWQKTYGG 207
                                       67.89******98775 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.12
                                       CCEEEEEESSSCGSSESE CS
                               PQQ  20 GkvlWrfktggpvlslpi 37 
                                       G+++W++  gg ++ +p+
  gi|242399423|ref|YP_002994848.1| 249 GNIKWQKTYGGSDDERPD 266
                                       9**********9998886 PP

  == domain 5  score: -0.1 bits;  conditional E-value: 0.84
                                       EETTTCCEEEEEE CS
                               PQQ  15 lDadTGkvlWrfk 27 
                                       lD  +G+++W++ 
  gi|242399423|ref|YP_002994848.1| 295 LD-GSGNIKWQKT 306
                                       66.78*****975 PP

  == domain 6  score: 1.5 bits;  conditional E-value: 0.25
                                       TCCEEEEEESSS CS
                               PQQ  19 TGkvlWrfktgg 30 
                                       +G+v+W +++gg
  gi|242399423|ref|YP_002994848.1| 347 NGEVKWAKDIGG 358
                                       8******99987 PP

  == domain 7  score: -2.0 bits;  conditional E-value: 3.4
                                       CCEEEEEE CS
                               PQQ  20 GkvlWrfk 27 
                                       G+v+W++ 
  gi|242399423|ref|YP_002994848.1| 533 GNVKWQKI 540
                                       99***975 PP

  == domain 8  score: 6.3 bits;  conditional E-value: 0.0079
                                       EETTTCCEEEEEESSSCGS CS
                               PQQ  15 lDadTGkvlWrfktggpvl 33 
                                       lD ++G+v+W++  gg+++
  gi|242399423|ref|YP_002994848.1| 581 LD-ANGNVKWQKTYGGNDD 598
                                       56.89***********997 PP

  == domain 9  score: 7.3 bits;  conditional E-value: 0.0037
                                       EETTTCCEEEEEESSSCGSSESE CS
                               PQQ  15 lDadTGkvlWrfktggpvlslpi 37 
                                       lD ++G+v+W+   gg++  +p+
  gi|242399423|ref|YP_002994848.1| 633 LD-ENGNVKWQMTYGGNDEDYPV 654
                                       67.89************998886 PP

  == domain 10  score: 3.1 bits;  conditional E-value: 0.078
                                       EETTTCCEEEEEESSS CS
                               PQQ  15 lDadTGkvlWrfktgg 30 
                                       lD ++G+v+W++  gg
  gi|242399423|ref|YP_002994848.1| 685 LD-ANGNVKWQKTYGG 699
                                       56.89******98887 PP

  == domain 11  score: 1.5 bits;  conditional E-value: 0.25
                                       EETTTCCEEEEEESSS CS
                               PQQ  15 lDadTGkvlWrfktgg 30 
                                       lD ++G+++W++  gg
  gi|242399423|ref|YP_002994848.1| 737 LD-ANGNIKWQKAYGG 751
                                       56.89******87765 PP

  == domain 12  score: 5.2 bits;  conditional E-value: 0.017
                                       EETTTCCEEEEEESSSCGSS CS
                               PQQ  15 lDadTGkvlWrfktggpvls 34 
                                       lD ++G+v+W++  gg ++ 
  gi|242399423|ref|YP_002994848.1| 789 LD-ANGNVKWQKTYGGIDND 807
                                       56.89*********999875 PP

>> Peptidase_S24  Peptidase S24-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       1.2   1.5e+03      13      39 ..      64      93 ..      62     103 .. 0.75
   2 ?   -3.3   0.0       7.2   9.2e+03      26      36 ..     116     126 ..     115     128 .. 0.80
   3 ?   -0.7   0.1       1.1   1.5e+03      11      38 ..     167     196 ..     163     232 .. 0.56
   4 !   10.4   0.0   0.00038      0.48      12      39 ..     272     299 ..     272     321 .. 0.87
   5 ?   -1.1   0.0       1.5   1.9e+03      23      34 ..     533     564 ..     502     594 .. 0.53
   6 ?   -0.7   0.0       1.1   1.4e+03      25      34 ..     711     720 ..     701     730 .. 0.87
   7 ?   -2.5   0.0         4   5.1e+03      25      33 ..     763     771 ..     761     776 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.2
                                      TTXEEEEE...CTS---TTSEEEEEETTCE CS
                     Peptidase_S24 13 dGdlilVd...kfsepkrGdivvfrlpgee 39
                                      +Gdli+      fs+ + Gd+ v rl+ + 
  gi|242399423|ref|YP_002994848.1| 64 NGDLIVAGytqSFSDSDWGDVWVLRLDANG 93
                                      788888775556668899999999998875 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 7.2
                                       -TTSEEEEEET CS
                     Peptidase_S24  26 krGdivvfrlp 36 
                                       ++G ivv+ + 
  gi|242399423|ref|YP_002994848.1| 116 QNGNIVVAGYT 126
                                       79*****9776 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.1
                                       XXTTXEEEEECTS..---TTSEEEEEETTC CS
                     Peptidase_S24  11 lldGdlilVdkfs..epkrGdivvfrlpge 38 
                                        ++Gd+i+V  ++   + + d+ v rl+++
  gi|242399423|ref|YP_002994848.1| 167 TPNGDVIVVGFTVsfGAGSSDFWVLRLDEN 196
                                       567777777533333333333444444444 PP

  == domain 4  score: 10.4 bits;  conditional E-value: 0.00038
                                       XTTXEEEEECTS---TTSEEEEEETTCE CS
                     Peptidase_S24  12 ldGdlilVdkfsepkrGdivvfrlpgee 39 
                                       ++Gd+i+ + + + ++Gd+ vf+l+g  
  gi|242399423|ref|YP_002994848.1| 272 PNGDIIVASYTGSFENGDFWVFKLDGSG 299
                                       58************************96 PP

  == domain 5  score: -1.1 bits;  conditional E-value: 1.5
                                       S....................---TTSEEEEE CS
                     Peptidase_S24  23 s....................epkrGdivvfr 34 
                                                            ++++Gd +v+ 
  gi|242399423|ref|YP_002994848.1| 533 GnvkwqkiyggsgsewaisvaTADNGDSIVAG 564
                                       03333334444444444444466666666665 PP

  == domain 6  score: -0.7 bits;  conditional E-value: 1.1
                                       --TTSEEEEE CS
                     Peptidase_S24  25 pkrGdivvfr 34 
                                       +++Gdi+v+ 
  gi|242399423|ref|YP_002994848.1| 711 AENGDIIVAG 720
                                       689****995 PP

  == domain 7  score: -2.5 bits;  conditional E-value: 4
                                       --TTSEEEE CS
                     Peptidase_S24  25 pkrGdivvf 33 
                                       +++Gdi+v 
  gi|242399423|ref|YP_002994848.1| 763 VENGDIIVT 771
                                       578888886 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.2    0.0014       1.8      33      72 ..     414     453 ..     408     464 .. 0.87
   2 !    6.2   0.1    0.0078        10      23      69 ..     858     904 ..     852     905 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0014
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTG CS
                        Laminin_II  33 lseinrsveetnekvkdankairdArrsvkkLeklapqLl 72 
                                       + ein+ v+ tn+ vkd+n  i+d +  v + + +++ L 
  gi|242399423|ref|YP_002994848.1| 414 VYEINAVVQTTNAAVKDSNAKIQDTNADVYDTNAEVETLW 453
                                       5689999999*******************99999999886 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0078
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTT CS
                        Laminin_II  23 sqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklap 69 
                                       ++++++t++++s+ ++ v + n++vkd    i d + +vk+L   ap
  gi|242399423|ref|YP_002994848.1| 858 NAQVSETSAEVSTSAAVVGQSNAVVKDTIAEIYDTNANVKTLLAYAP 904
                                       6799*************************************976665 PP

>> Laminin_G_2  Laminin G domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.82   1.1e+03      47      99 ..      73     125 ..      63     137 .. 0.72
   2 ?    0.8   0.0      0.53   6.8e+02      14      42 ..     182     211 ..     167     223 .. 0.80
   3 ?    5.5   0.0      0.02        25       3      42 ..     605     651 ..     604     658 .. 0.89
   4 ?   -0.3   0.0       1.2   1.5e+03       5      40 ..     659     701 ..     655     713 .. 0.85
   5 ?   -0.9   0.0       1.9   2.4e+03       7      40 ..     713     753 ..     709     767 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.82
                                       SSS-ESSSSEEEEEEECTTEEEEEECTS--CCCE-CSS.......S.EEES-- CS
                       Laminin_G_2  47 gkklndgewHsveverkgknltlsvDggetseanepgesqgldleeslylGGl 99 
                                       +++++d +w +v v r + n +++  +    +   ++    +++++++++ G+
  gi|242399423|ref|YP_002994848.1|  73 TQSFSDSDWGDVWVLRLDANGNVKWQKTYGGSDVDSPVAVAITQNGNIVVAGY 125
                                       78899999999999999888887776666666666666666677777777666 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.53
                                       EESTTEEEEEEEE.TTEEEEEEESSS-EEE CS
                       Laminin_G_2  14 gdeksdflalelk.dgklvltynlgsgdte 42 
                                       g ++sdf+ l l+ +g+++ +  +g++ +e
  gi|242399423|ref|YP_002994848.1| 182 GAGSSDFWVLRLDeNGNVKWQKTYGGSGEE 211
                                       4478*********9*****99999876655 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.02
                                       E--SSEEEEEEEE......STTEEEEEEEE.TTEEEEEEESSS-EEE CS
                       Laminin_G_2   3 TrqpdGlLlyagd......eksdflalelk.dgklvltynlgsgdte 42 
                                       T+ p+G ++ +g       + sdf+ l l+ +g+++ ++ +g++d+ 
  gi|242399423|ref|YP_002994848.1| 605 TTAPNGDIIATGYtysfgaGYSDFWVLRLDeNGNVKWQMTYGGNDED 651
                                       78888989888888889999**********************99875 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 1.2
                                       -SSEEEEEEEE......STTEEEEEEEE.TTEEEEEEESSS-E CS
                       Laminin_G_2   5 qpdGlLlyagd......eksdflalelk.dgklvltynlgsgd 40 
                                        p+G ++ +g       +++d + l l+ +g+++ +  +g++ 
  gi|242399423|ref|YP_002994848.1| 659 APNGEIIVTGAtlsfgaGGTDVWVLRLDaNGNVKWQKTYGGSA 701
                                       5889998888888888899*********9****9999988765 PP

  == domain 5  score: -0.9 bits;  conditional E-value: 1.9
                                       SEEEEEEEE......STTEEEEEEEE.TTEEEEEEESSS-E CS
                       Laminin_G_2   7 dGlLlyagd......eksdflalelk.dgklvltynlgsgd 40 
                                       +G ++ agd      ++ df+ l l+ +g+++ +  +g++ 
  gi|242399423|ref|YP_002994848.1| 713 NGDIIVAGDtmsfgaGGADFWVLRLDaNGNIKWQKAYGGSG 753
                                       555666666666666899********99*999988887655 PP

>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0      0.06        77      75     113 ..     193     231 ..     187     237 .. 0.89
   2 ?    2.3   0.0      0.17   2.2e+02      76     112 ..     530     566 ..     526     572 .. 0.88
   3 ?    1.4   0.0      0.32   4.1e+02      75     110 ..     685     720 ..     679     728 .. 0.89
   4 ?   -2.6   0.0       5.7   7.3e+03      76     111 ..     738     773 ..     735     777 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.06
                                       HHCTTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCC CS
                               Usp  75 aeaggvkvevvveegdpaeeilevaeeedadliVvGsrg 113
                                       +++ g +   ++ +g++ ee   va  +d d+iV+G++ 
  gi|242399423|ref|YP_002994848.1| 193 LDENGNVKWQKTYGGSGEEEAEAVAITLDGDIIVTGWTN 231
                                       567788888999************************985 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.17
                                       HCTTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESC CS
                               Usp  76 eaggvkvevvveegdpaeeilevaeeedadliVvGsr 112
                                       ++gg +   ++ +g+++e  + va + + d iV G +
  gi|242399423|ref|YP_002994848.1| 530 DKGGNVKWQKIYGGSGSEWAISVATADNGDSIVAGFT 566
                                       6678888999***********************9965 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.32
                                       HHCTTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEE CS
                               Usp  75 aeaggvkvevvveegdpaeeilevaeeedadliVvG 110
                                       ++a g +   ++ +g+++ee   va +e+ d+iV G
  gi|242399423|ref|YP_002994848.1| 685 LDANGNVKWQKTYGGSADEEAYAVAVAENGDIIVAG 720
                                       5677888889999*********************98 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 5.7
                                       HCTTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEES CS
                               Usp  76 eaggvkvevvveegdpaeeilevaeeedadliVvGs 111
                                       +a g +   +  +g+++e    +a  e+ d+iV+G 
  gi|242399423|ref|YP_002994848.1| 738 DANGNIKWQKAYGGSGDEDAWAIAIVENGDIIVTGE 773
                                       56667777788899999999999999*******996 PP

>> Tox-HDC  Toxin with a H, D/N and C signature
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.55     7e+02      25      56 ..     164     197 ..     158     205 .. 0.74
   2 ?    6.0   0.1      0.01        13      23      57 ..     266     300 ..     254     316 .. 0.80
   3 ?   -0.5   0.1         1   1.3e+03      29      57 ..     504     534 ..     501     541 .. 0.74
   4 ?    1.3   0.0      0.29   3.7e+02      21      64 ..     600     645 ..     584     652 .. 0.75
   5 ?   -0.3   0.0      0.86   1.1e+03      24      56 ..     655     689 ..     642     723 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.55
                           Tox-HDC  25 iskkPngdivil..sGshGsnlgenwlpngkreg 56 
                                       i+  Pngd+ ++  + s G+   + w+     +g
  gi|242399423|ref|YP_002994848.1| 164 IALTPNGDVIVVgfTVSFGAGSSDFWVLRLDENG 197
                                       6678****99864467899999999996555444 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.01
                           Tox-HDC  23 ekiskkPngdivilsGshGsnlgenwlpngkrege 57 
                                       ++++  Pngdi + s +   ++g+ w+      g+
  gi|242399423|ref|YP_002994848.1| 266 DAVTIDPNGDIIVASYTGSFENGDFWVFKLDGSGN 300
                                       678889********999999*******55444454 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 1
                           Tox-HDC  29 PngdivilsG..shGsnlgenwlpngkrege 57 
                                       Pngd+ +  G  s G+   + w+    + g+
  gi|242399423|ref|YP_002994848.1| 504 PNGDVIVAGGteSFGVGYEDFWVLKLDKGGN 534
                                       9****99998334688777899976666555 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 0.29
                           Tox-HDC  21 vlekiskkPngdivil..sGshGsnlgenwlpngkregelrlefkf 64 
                                       ++ +++  Pngdi     + s G+   + w+     +g+++ ++ +
  gi|242399423|ref|YP_002994848.1| 600 LIRAVTTAPNGDIIATgyTYSFGAGYSDFWVLRLDENGNVKWQMTY 645
                                       47788999****9653224588999999999887777777766665 PP

  == domain 5  score: -0.3 bits;  conditional E-value: 0.86
                           Tox-HDC  24 kiskkPngdivilsG...shGsnlgenwlpngkreg 56 
                                       +i+  Png+i +  G   s G+   + w+     +g
  gi|242399423|ref|YP_002994848.1| 655 AIAVAPNGEIIVT-GatlSFGAGGTDVWVLRLDANG 689
                                       68889****9664.4233678766779995544444 PP

>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       1.7   2.2e+03      16      29 ..      59      72 ..      45      80 .. 0.74
   2 ?    1.1   0.0      0.69   8.8e+02       4      29 ..      98     125 ..      96     138 .. 0.73
   3 ?   -0.8   0.0       2.6   3.3e+03      15      28 ..     267     280 ..     253     293 .. 0.74
   4 ?   -0.8   0.0       2.7   3.4e+03      14      29 ..     324     338 ..     314     341 .. 0.81
   5 ?   -1.4   0.1       4.1   5.3e+03       5      28 ..     539     564 ..     536     574 .. 0.76
   6 ?    6.9   0.0    0.0098        13       4      29 ..     590     617 ..     588     625 .. 0.88
   7 ?    1.1   0.0      0.68   8.8e+02       5      29 ..     643     669 ..     640     678 .. 0.82
   8 ?   -2.3   0.0       7.9     1e+04      13      29 ..     705     721 ..     693     723 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.7
                                      EEEETTSSEEEEEE CS
                              WD40 16 lafspdgawlasGs 29
                                      +a  p+g+++++G 
  gi|242399423|ref|YP_002994848.1| 59 VAIAPNGDLIVAGY 72
                                      3459******9994 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.69
                                       EEEEESS...SSEEEEEEETTSSEEEEEE CS
                              WD40   4 lrtltGH...ssvtslafspdgawlasGs 29 
                                       ++t+ G    s+v ++a  ++g+ +++G 
  gi|242399423|ref|YP_002994848.1|  98 QKTYGGSdvdSPV-AVAITQNGNIVVAGY 125
                                       6788888653447.9999********994 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 2.6
                                       EEEEETTSSEEEEE CS
                              WD40  15 slafspdgawlasG 28 
                                       ++  +p+g+ ++++
  gi|242399423|ref|YP_002994848.1| 267 AVTIDPNGDIIVAS 280
                                       56679*****9854 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 2.7
                                       EEEEEETTSSEEEEEE CS
                              WD40  14 tslafspdgawlasGs 29 
                                       +++a  p+g+ l++ +
  gi|242399423|ref|YP_002994848.1| 324 NGIAIAPNGDILLA-G 338
                                       567899*****996.5 PP

  == domain 5  score: -1.4 bits;  conditional E-value: 4.1
                                       EEEESS.SS..EEEEEEETTSSEEEEE CS
                              WD40   5 rtltGH.ss..vtslafspdgawlasG 28 
                                       +++ G  s   + s+a+ ++g+ +++G
  gi|242399423|ref|YP_002994848.1| 539 KIYGGSgSEwaI-SVATADNGDSIVAG 564
                                       567666433678.99999999999998 PP

  == domain 6  score: 6.9 bits;  conditional E-value: 0.0098
                                       EEEEESS.SS.EEEEEEETTSSEEEEEE CS
                              WD40   4 lrtltGH.ss.vtslafspdgawlasGs 29 
                                       ++t+ G  ++ ++++ + p+g+ +a+G 
  gi|242399423|ref|YP_002994848.1| 590 QKTYGGNdDDlIRAVTTAPNGDIIATGY 617
                                       78999**65599**************94 PP

  == domain 7  score: 1.1 bits;  conditional E-value: 0.68
                                       EEEESS.SS..EEEEEEETTSSEEEEEE CS
                              WD40   5 rtltGH.ss..vtslafspdgawlasGs 29 
                                        t+ G   +  v ++a+ p+g  +++G 
  gi|242399423|ref|YP_002994848.1| 643 MTYGGNdEDypV-AIAVAPNGEIIVTGA 669
                                       678888544777.999*********994 PP

  == domain 8  score: -2.3 bits;  conditional E-value: 7.9
                                       EEEEEEETTSSEEEEEE CS
                              WD40  13 vtslafspdgawlasGs 29 
                                        +++a+  +g+ +++G+
  gi|242399423|ref|YP_002994848.1| 705 AYAVAVAENGDIIVAGD 721
                                       578899999**999874 PP

>> DUF1508  Domain of unknown function (DUF1508)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.049        63      12      25 ..     607     620 ..     602     624 .. 0.91
   2 ?    0.1   0.0      0.59   7.5e+02      12      21 ..     659     668 ..     658     670 .. 0.85
   3 ?   -0.6   0.0      0.96   1.2e+03       3      21 ..     702     720 ..     700     722 .. 0.76
   4 ?   -2.0   0.1       2.7   3.5e+03      13      22 ..     764     773 ..     763     774 .. 0.89
   5 ?    1.9   0.0      0.16   2.1e+02       1      25 [.     805     829 ..     805     834 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.049
                                       -TTS-EEEEEEEBS CS
                           DUF1508  12 aaNgevIatsegYs 25 
                                       a Ng +Iat+ +Ys
  gi|242399423|ref|YP_002994848.1| 607 APNGDIIATGYTYS 620
                                       78*********997 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.59
                                       -TTS-EEEEE CS
                           DUF1508  12 aaNgevIats 21 
                                       a Nge+I t+
  gi|242399423|ref|YP_002994848.1| 659 APNGEIIVTG 668
                                       89*****997 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.96
                                       TTEEEEEEE-TTS-EEEEE CS
                           DUF1508   3 nGefrFrLkaaNgevIats 21 
                                       ++e + + +a+Ng +I ++
  gi|242399423|ref|YP_002994848.1| 702 DEEAYAVAVAENGDIIVAG 720
                                       5666667789******876 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 2.7
                                       TTS-EEEEEE CS
                           DUF1508  13 aNgevIatse 22 
                                       +Ng +I t+e
  gi|242399423|ref|YP_002994848.1| 764 ENGDIIVTGE 773
                                       6*******98 PP

  == domain 5  score: 1.9 bits;  conditional E-value: 0.16
                                       ETTTEEEEEEE-TTS-EEEEEEEBS CS
                           DUF1508   1 DknGefrFrLkaaNgevIatsegYs 25 
                                       D+++  r +L a+N   I ++ +Ys
  gi|242399423|ref|YP_002994848.1| 805 DNDDIARAVLIAENSDLIVAGATYS 829
                                       566667999**************97 PP

>> Flavi_NS2B  Flavivirus non-structural protein NS2B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       8.7   1.1e+04      82     104 ..       6      28 ..       4      43 .. 0.81
   2 ?   -1.3   0.0       1.5   1.9e+03      43      81 ..      82     120 ..      63     124 .. 0.81
   3 ?    1.6   0.1      0.18   2.3e+02      30      81 ..     173     224 ..     163     228 .. 0.75
   4 ?    4.2   0.1     0.028        36      48      80 ..     527     559 ..     509     563 .. 0.93
   5 ?    4.1   0.1      0.03        39      27      83 ..     662     718 ..     655     724 .. 0.83
   6 ?   -0.1   0.0       0.6   7.7e+02      48      86 ..     735     773 ..     716     776 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 8.7
                        Flavi_NS2B  82 klkdeekvdtdtvllkalllvia 104
                                       k+k eek +   ++l  +ll +a
  gi|242399423|ref|YP_002994848.1|   6 KVKFEEKIKSPVIILWIVLLFGA 28 
                                       88999999999999888887765 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.5
                        Flavi_NS2B  43 GrvddlelkklaevsweeeaeisGasaridvelsedGel 81 
                                       G v  l l+  ++v w++    s   + + v++ ++G++
  gi|242399423|ref|YP_002994848.1|  82 GDVWVLRLDANGNVKWQKTYGGSDVDSPVAVAITQNGNI 120
                                       66677999999******9999999999999999999987 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.18
                        Flavi_NS2B  30 ivGGllialvvvaGrvd..dlelkklaevsweeeaeisGasaridvelsedGel 81 
                                       iv G+ +     aG++d   l l+  ++v w++    sG  +   v++  dG++
  gi|242399423|ref|YP_002994848.1| 173 IVVGFTVSFG--AGSSDfwVLRLDENGNVKWQKTYGGSGEEEAEAVAITLDGDI 224
                                       4445444443..4555522699999*********99999999999999999986 PP

  == domain 4  score: 4.2 bits;  conditional E-value: 0.028
                        Flavi_NS2B  48 lelkklaevsweeeaeisGasaridvelsedGe 80 
                                       l+l+k ++v w++    sG+   i v+  ++G+
  gi|242399423|ref|YP_002994848.1| 527 LKLDKGGNVKWQKIYGGSGSEWAISVATADNGD 559
                                       89****************************997 PP

  == domain 5  score: 4.1 bits;  conditional E-value: 0.03
                        Flavi_NS2B  27 GPlivGGllialvvvaGrvddlelkklaevsweeeaeisGasaridvelsedGelkl 83 
                                       G +iv G  +   +    v  l l+  ++v w++    s   + + v++ e+G++ +
  gi|242399423|ref|YP_002994848.1| 662 GEIIVTGATLSFGAGGTDVWVLRLDANGNVKWQKTYGGSADEEAYAVAVAENGDIIV 718
                                       66777777666666666677899*************99*99************9865 PP

  == domain 6  score: -0.1 bits;  conditional E-value: 0.6
                        Flavi_NS2B  48 lelkklaevsweeeaeisGasaridvelsedGelklkde 86 
                                       l l+  +++ w++    sG    + +++ e+G++ +  e
  gi|242399423|ref|YP_002994848.1| 735 LRLDANGNIKWQKAYGGSGDEDAWAIAIVENGDIIVTGE 773
                                       7899999*************************9987766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (974 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       837  (0.0466841); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); 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):              14  [number of targets reported over threshold]
# CPU time: 0.76u 0.25s 00:00:01.01 Elapsed: 00:00:00.45
# Mc/sec: 6524.59
//
Query:       gi|242399424|ref|YP_002994849.1|  [L=150]
Description: hypothetical protein TSIB_1449 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       890  (0.0496402); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.32s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 921.08
//
Query:       gi|242399425|ref|YP_002994850.1|  [L=689]
Description: hypothetical protein TSIB_1450 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.11   12.4   0.0        1.1    9.3   0.0    2.6  3  Rib       Rib/alpha-like repeat


Domain annotation for each model (and alignments):
>> Rib  Rib/alpha-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   6.2e-05       1.1      33      56 ..     282     305 ..     265     309 .. 0.87
   2 ?   -2.6   0.0      0.31   5.5e+03      17      30 ..     588     600 ..     580     612 .. 0.69
   3 ?   -1.4   0.0      0.13   2.3e+03       3      28 ..     606     637 ..     604     661 .. 0.57

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 6.2e-05
                               Rib  33 pdttksGekeavvvVtYPDGskde 56 
                                        d+  sG ++   vVt PDGsk +
  gi|242399425|ref|YP_002994850.1| 282 ADVDGSGAENLYAVVTLPDGSKKR 305
                                       588999***************986 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.31
                               Rib  17 NksdlPdGTkytWk 30 
                                       N  +lP+ T+++ +
  gi|242399425|ref|YP_002994850.1| 588 N-MNLPENTRVSIV 600
                                       4.489999998755 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.13
                               Rib   3 vkvGevpdatdgikNksdlPdGTky......t 28 
                                       +k G++ d+t   +N++d   G  +      +
  gi|242399425|ref|YP_002994850.1| 606 TKIGKLLDPTGYFGNMADATVGALIdlrkkiE 637
                                       67788888888888877766666553333330 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (689 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); 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 0.24s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 4828.26
//
Query:       gi|242399426|ref|YP_002994851.1|  [L=402]
Description: calcium-binding protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.18   10.6   0.0       0.26   10.1   0.0    1.1  1  DUF1015      Protein of unknown function (DUF1015)


Domain annotation for each model (and alignments):
>> DUF1015  Protein of unknown function (DUF1015)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   1.4e-05      0.26      19      85 ..     217     284 ..     209     299 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 1.4e-05
                           DUF1015  19 asppYD.viseeearelakknpysflrlilpeadledeedeedryekaaetleewleegvlvqdekpa 85 
                                       +s  ++  +s+eea el+++  ++++ l+ ++a++e++e+++++y +a++ +e+ l++g+ +  +k++
  gi|242399426|ref|YP_002994851.1| 217 TSESFTcPPSQEEAYELFVQAYNNVTSLMGSNASQEEQEEAYAKYLEAKACYESSLNSGTSISPPKEG 284
                                       4556666679**************************9999999***************9988877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       665  (0.0370907); 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:                         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: 0.69u 0.33s 00:00:01.02 Elapsed: 00:00:00.55
# Mc/sec: 2201.62
//
Query:       gi|242399427|ref|YP_002994852.1|  [L=129]
Description: hypothetical protein TSIB_1452 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       910  (0.0507558); expected 358.6 (0.02)
Passed bias filter:                      651  (0.0363099); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 801.50
//
Query:       gi|242399428|ref|YP_002994853.1|  [L=350]
Description: ArgE/DapE-related deacylase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.4e-26   91.0   0.1    1.1e-25   90.5   0.1    1.2  1  Peptidase_M20  Peptidase family M20/M25/M40
    9.8e-09   34.6   0.0    0.00013   21.1   0.0    2.1  2  Peptidase_M42  M42 glutamyl aminopeptidase
    2.3e-08   33.9   0.0    3.3e-07   30.2   0.0    2.3  1  M20_dimer      Peptidase dimerisation domain
    2.4e-07   30.6   0.0    3.6e-06   26.8   0.0    2.0  2  Peptidase_M28  Peptidase family M28


Domain annotation for each model (and alignments):
>> Peptidase_M20  Peptidase family M20/M25/M40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.5   0.1   2.6e-29   1.1e-25       2     204 ..      62     343 ..      61     345 .. 0.88

  Alignments for each domain:
  == domain 1  score: 90.5 bits;  conditional E-value: 2.6e-29
                                       EEEES-BSSTTCGGGSSSTTSEEETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTTTHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20   2 lgsHlDvVpeeetdgwttpfslteedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggrgGa 78 
                                       +  H+D+     +     pf      + +yG Ga+d kgg++++l  +++lk+ ++++  ++ ++f+ dEE g++G+
  gi|242399428|ref|YP_002994853.1|  62 FEVHMDTIDIRAE-----PFVRG---NIVYGTGASDVKGGLASVLLMMESLKRGNQNL--NVGVVFVSDEEKGGMGS 128
                                       678******3333.....66666...99**************************9655..***********888*** PP

                                       HHHHHHHHTTTCESEEEEEEEESSSBTCHSTETEEEE........................................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................................ RF
                     Peptidase_M20  79 kallegleerekvdavfelhieepgileagklaigvv........................................ 115
                                       + ++e    r+k++    +++ ep+ le +                                               
  gi|242399428|ref|YP_002994853.1| 129 ALFME----RYKPKM---AIVIEPTDLEVHI-----Ahagnieayfevdgkeahgacpesginaidqtykmieelks 193
                                       *****....999**9...44677*****444.....3445679********************************** PP

                                       ...............................................................EEEEEEEEEESHEE CS
                                       ...............................................................xxxxxxxxxxxxxx RF
                     Peptidase_M20 116 ...............................................................kvevelleggapvt 129
                                                                                                      k+e++++++g+   
  gi|242399428|ref|YP_002994853.1| 194 lepfkqkgkyfdayiglqelicenpyylipalckgrlearllptqevedildliepileeytlKYEYTEIWDGYELD 270
                                       *************************************************************9889999778877655 PP

                                       ECCHHHHHHHHHHHHHHHTSCEEEEEES.SSBHTHHHH..TTTEEEEEEESSG.GCTTSTTTEEEHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx..xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20 130 lndsplvkalaeaaeelfgekvelivsg.pggtdarff..agiptvmifgpgs.glaHspnEyvdledlekgikvla 202
                                        + +++v+++++a++e+ g +  +   g + +tda  f  +g+   ++fgpg+ +++H+  E++d++d++++ ++l+
  gi|242399428|ref|YP_002994853.1| 271 ED-EEIVQLAKKAMDEV-GIE--D-FGGmRSWTDAINFmyNGT-KTIVFGPGNlDISHTKSERIDVRDVVEASEFLK 341
                                       55.*************9.944..3.344557888877779999.5558****99********************998 PP

                                       HH CS
                                       xx RF
                     Peptidase_M20 203 rl 204
                                       ++
  gi|242399428|ref|YP_002994853.1| 342 KI 343
                                       75 PP

>> Peptidase_M42  M42 glutamyl aminopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   2.9e-08   0.00013     112     192 ..      67     147 ..      33     161 .. 0.86
   2 !   11.6   0.0   2.3e-05       0.1     227     290 ..     273     337 ..     267     339 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2.9e-08
                                       -EEEES---EEETTECEEETTHHHHHHHHHHHHHHHHHCTSS-SSEEEEEEESTCTTTSHHHHHHHHHH--SEEEEE CS
                     Peptidase_M42 112 divvfdkefvelangkivskalDdragvavllellkelkeeeleatvylvatvqEEvGlrGaktsaekikpdiaiav 188
                                       d++ ++ e+ + +n  + + a D + g+a +l ++++lk+ + + +v +v+   EE G +G++ + e++kp++ai++
  gi|242399428|ref|YP_002994853.1|  67 DTIDIRAEPFVRGNIVYGTGASDVKGGLASVLLMMESLKRGNQNLNVGVVFVSDEEKGGMGSALFMERYKPKMAIVI 143
                                       666777777777777777889999***************************************************** PP

                                       EEEE CS
                     Peptidase_M42 189 Dvta 192
                                       + t 
  gi|242399428|ref|YP_002994853.1| 144 EPTD 147
                                       9775 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 2.3e-05
                                       HHHHHHHHHTT--EEEEEESSSSSTHHHHHTSTTTSEEEEEEEE.EBSTTSTTEEEEHHHHHHHH CS
                     Peptidase_M42 227 kkllelAkknnipyqlevlsgggtDAgaihltgegvptalisip.tryiHspvevahlddleatv 290
                                       +++++lAkk+  ++ +e + g+ + ++ai +  +g++t++ +++ ++ +H+++e+++++d+ ++ 
  gi|242399428|ref|YP_002994853.1| 273 EEIVQLAKKAMDEVGIEDFGGMRSWTDAINFMYNGTKTIVFGPGnLDISHTKSERIDVRDVVEAS 337
                                       5789999999999999999999999999999999*********835899************9886 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0   7.3e-11   3.3e-07       1     108 [.     152     258 ..     152     259 .. 0.79

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 7.3e-11
                                       SEB-EEEEEEEEEE-B-EEGG-TTTTB-HHHHHHHHHHCSCTTEEC.....TCCTCCCCCEECCE-CCCC...EESS CS
                         M20_dimer   1 ighkGlaggkitvkgkagHsgapgagaNAieklarllaeledeegdiaeerslprttlnvtgiegGsakn...vipd 74 
                                       i+h G +++  +v+gk +H++ p+ g+NAi +  ++++el+++e  +   +  ++    ++ +++    n    ip+
  gi|242399428|ref|YP_002994853.1| 152 IAHAGNIEAYFEVDGKEAHGACPESGINAIDQTYKMIEELKSLEPFK---QKGKYFDAYIG-LQELICENpyyLIPA 224
                                       6899*************************************993322...22222332222.23333445555**** PP

                                       EEEEEEEEEHHHHHHHHHHHHHHHHHHTSCCSTT CS
                         M20_dimer  75 eaeakidiRllpgedpeevleeieeilekeaped 108
                                        ++  ++ Rllp++++e++l+ ie ile+   ++
  gi|242399428|ref|YP_002994853.1| 225 LCKGRLEARLLPTQEVEDILDLIEPILEEYTLKY 258
                                       ***************************9987665 PP

>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.0     8e-10   3.6e-06      15      98 ..      60     165 ..      51     204 .. 0.74
   2 ?    1.7   0.0      0.04   1.8e+02     113     180 ..     269     329 ..     245     343 .. 0.71

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 8e-10
                                       EEEEEE--B-TTT.....TCC..T---TTTTHHHHHHHHHHHHHCHHGGCCSSEEEEEEEESSCSGSSHHHHHHHH. CS
                     Peptidase_M28  15 lllgAHyDsvgvg.....rgp..ifvGAdDnAsgvaalLelarvlaasgsrpkrgvrflffdaEEagllGSkafak. 83 
                                       l +  H+D++ +      rg+     GA D   g a++L +++ l++ g + + +v ++f++ EE+g +GS  f++ 
  gi|242399428|ref|YP_002994853.1|  60 LFFEVHMDTIDIRaepfvRGNivYGTGASDVKGGLASVLLMMESLKR-G-NQNLNVGVVFVSDEEKGGMGSALFMEr 134
                                       666779****9987777755565557********************8.4.789999999****************85 PP

                                       HHCCCTTE.................EEEEEEC CS
                     Peptidase_M28  84 akpelkki.................aavlnlD 98 
                                        kp+++ i                 +a++++D
  gi|242399428|ref|YP_002994853.1| 135 YKPKMA-IvieptdlevhiahagniEAYFEVD 165
                                       444322.2233333333333333336666666 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.04
                                       HHHCHHHHHHHHHHHHHTT-TTSCCEEEEESSTT-STTHHHHTTT--EEEECTSSS-TTTTSTTSSGG CS
                     Peptidase_M28 113 dkssselekelkalakpvgraaaedpfdersgrgrsDhspflkagvpvldlaetgfpevyHtprDtld 180
                                        ++++e+ + +k+++++vg +   d    +++r+ +D++ f  +g +++ +   g+ +  Ht++ ++d
  gi|242399428|ref|YP_002994853.1| 269 LDEDEEIVQLAKKAMDEVGIE---D---FGGMRSWTDAINFMYNGTKTIVF-GPGNLDISHTKSERID 329
                                       455555555666666666553...3...3457778***********99999.6666666688877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2351.19
//
Query:       gi|242399429|ref|YP_002994854.1|  [L=309]
Description: carboxylesterase, alpha/beta hydrolase superfamily [Thermococcus sibiricus MM 739]
Scores for complete 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   86.9   0.0    9.1e-24   84.5   0.0    1.8  1  Abhydrolase_1  alpha/beta hydrolase fold
    3.9e-23   83.2   0.0    4.6e-23   83.0   0.0    1.1  1  Abhydrolase_6  Alpha/beta hydrolase family
    3.6e-15   55.9   0.0    1.4e-14   54.0   0.0    1.9  1  Hydrolase_4    Serine aminopeptidase, S33
      2e-07   30.0   0.0    4.4e-07   28.9   0.0    1.4  1  Ndr            Ndr family
    2.2e-06   27.6   0.0     0.0039   17.1   0.0    2.3  2  Ser_hydrolase  Serine hydrolase
    4.9e-06   26.5   0.2     0.0022   17.9   0.0    2.9  3  Abhydrolase_2  Phospholipase/Carboxylesterase
    0.00036   20.6   0.0    0.00075   19.6   0.0    1.5  1  Abhydrolase_4  TAP-like protein
    0.00073   19.3   0.0      0.029   14.1   0.0    2.1  2  Abhydrolase_5  Alpha/beta hydrolase family
     0.0023   17.6   0.5      0.018   14.7   0.1    2.5  2  FSH1           Serine hydrolase (FSH1)
     0.0078   15.8   0.0      0.022   14.3   0.0    1.7  2  LIDHydrolase   Lipid-droplet associated hydrolase
     0.0092   15.4   0.0      0.018   14.5   0.0    1.4  1  DUF3530        Protein of unknown function (DUF3530)
  ------ inclusion threshold ------
      0.013   15.0   0.0       0.62    9.5   0.0    2.1  2  Peptidase_S9   Prolyl oligopeptidase family
      0.014   15.1   0.0      0.021   14.4   0.0    1.2  1  Esterase       Putative esterase
       0.03   14.2   0.0      0.051   13.4   0.0    1.3  1  Lipase_3       Lipase (class 3)
      0.038   13.8   0.0      0.055   13.3   0.0    1.2  1  Abhydrolase_3  alpha/beta hydrolase fold
       0.16   11.3   0.0          2    7.7   0.0    2.2  2  DUF915         Alpha/beta hydrolase of unknown function (DUF9


Domain annotation for each model (and alignments):
>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.5   0.0   8.1e-27   9.1e-24       3     257 .]      59     296 ..      57     296 .. 0.89

  Alignments for each domain:
  == domain 1  score: 84.5 bits;  conditional E-value: 8.1e-27
                                       EEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB...CHHSHHHHHHHHHHHHHHCTTSSEEE CS
                     Abhydrolase_1   3 lvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacin..ddygtasvaddldrildalgddkltl 77 
                                       l++lhG+++s  +w+   l ++      +v+++D +G+g +++   +    + y+    a+   +++d +g +k tl
  gi|242399429|ref|YP_002994854.1|  59 LLLLHGFGASTFSWRY--LLEGNL--SERVVAFDRPGFGLTERKNPKGLlcNPYSPEGAAELTLKLMDEFGMEKATL 131
                                       9***************..666666..569***********999988766888899998999999************* PP

                                       EEETHHHHHHHHHHHHHGGGEEEEEEESECSSCCHHHHHHHHHHHHHHCHHCHHHHHHHHHHHHHHHHCCSCHHHHH CS
                     Abhydrolase_1  78 vGhSmGGmialayaaeyperVkalvllgaidpaaslieaqrqqaksfpdffdgyaadcarnpagplladelaaleqr 154
                                       vGhS G  +al +  ++perV +l+l+++ ++ +   ++ +  ++s+p++   +       ++ + +  e+a+++q+
  gi|242399429|ref|YP_002994854.1| 132 VGHSAGAGVALLVSIKAPERVEKLILVAP-AWGSRNQSTFQKLIFSLPWTEKYFPLILRFSVGRLEGILENAWYNQS 207
                                       *****************************.*******************99999999999999999999******** PP

                                       HHHHHHHHHHCHHHCCHHHHHHHCHHHHHHHHHHHHHHHHCCHHHHHHHHHCTHHHHSEEEEEEETTCSSSCHHHHH CS
                     Abhydrolase_1 155 hrlvdalkfpdkskrfpssgsdnasslatgalksieqwpttdsaklllrlrelknvlaptlvisgtsDplvppkale 231
                                                ++++   +  +++    +  ++l+++  + ++++    l+     n ++ptl+++ ++D++vp +++ 
  gi|242399429|ref|YP_002994854.1| 208 ---------KLTEEVWEGYKRPLKAKDWDKGLFWVTKYGEYPNITEELK-----NLNIPTLIVHCRQDKIVPLESGK 270
                                       .........6666666666678888888888888888888888765544.....5557******************* PP

                                       HHHHCHTSEEEEEEETCSSSHHHHSH CS
                     Abhydrolase_1 232 dlaqllpkkrlvvisdagHlaflegp 257
                                       +l q +p+++l + + +gHl + e+p
  gi|242399429|ref|YP_002994854.1| 271 KLHQIIPNSQLAIMEECGHLPHEEKP 296
                                       *********************99986 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.0   0.0   4.1e-26   4.6e-23       1     217 [.      59     299 ..      59     302 .. 0.71

  Alignments for each domain:
  == domain 1  score: 83.0 bits;  conditional E-value: 4.1e-26
                                       EEEE--GC.....G.CHHHHHHHHCCTCEEEEE--TTST........S-GGCS--HHHCHHH.HHHHCCTT..TTSE CS
                     Abhydrolase_6   1 vlllHGagssassW.lvapLaallaagvhvlapDlpGhG........rsdpppldledladl.aalldelaagggpv 67 
                                       +lllHG+g+s  sW +   L   l+++v  +a+D+pG+G        +  + p++ e +a+l + l de++    ++
  gi|242399429|ref|YP_002994854.1|  59 LLLLHGFGASTFSWrY--LLEGNLSERV--VAFDRPGFGlterknpkGLLCNPYSPEGAAELtLKLMDEFG--MEKA 129
                                       79*******9999964..4455558899..*********55544333225566888889999999*****6..9*** PP

                                       EEEEETCHHHHHHHHHHCC....EE.EEES-..----TTT......S----TTHHHHHHTT-CCCCHCCH.S-HSCC CS
                     Abhydrolase_6  68 vlvGHSlGGalalaaapla..lvvg.vlldppptalpagl......laaalelllallallrllawlsre.plprlf 134
                                        lvGHS G+ +al++   a  +v++ +l++p   a++ ++      l + l++ +++ +l  ++   ++e +l   +
  gi|242399429|ref|YP_002994854.1| 130 TLVGHSAGAGVALLVSIKApeRVEKlILVAP---AWGSRNqstfqkLIFSLPWTEKYFPLILRFSVGRLEgILENAW 203
                                       **************555558776779*****...9999997666665555555555555444433333336666688 PP

                                       CCHHH.CCCCHCHCCCGHH..HHCCHHCHTT........CCHHTT-TTGCEEE.CTT-CHHHHCHHCCCH..STTEE CS
                     Abhydrolase_6 135 laded.adaawrarlarla..allaglgllp........aaawadlpvpllvl.ggeDplvprllerlla..qagar 197
                                       +++   +++ w  + ++l   + ++gl++ +         ++++ l  p+l++ + +D++vp    + l+  ++  +
  gi|242399429|ref|YP_002994854.1| 204 YNQSKlTEEVWEGYKRPLKakDWDKGLFWVTkygeypniTEELKNLNIPTLIVhCRQDKIVPLESGKKLHqiIPNSQ 280
                                       8877744688888888888763333444332211111335566666666688889*******77666666799**** PP

                                       ETCE...SSS-HHHHSHHHH CS
                     Abhydrolase_6 198 lpvvlpgaGHlphleepdev 217
                                       l  +++ +GHlph+e+p e+
  gi|242399429|ref|YP_002994854.1| 281 L-AIMEECGHLPHEEKPSEF 299
                                       *.***************776 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.0   0.0   1.2e-17   1.4e-14      33     238 ..      83     295 ..      54     296 .. 0.78

  Alignments for each domain:
  == domain 1  score: 54.0 bits;  conditional E-value: 1.2e-17
                       Hydrolase_4  33 avyalDhrGhGrse...gkrghvpsfddyvdDlaafvekvkeehpelplfllGhSmGGliallyllrypdkvaglil 106
                                        v+a+D  G+G +e   +k   +++++   + +a+++ k+ +e + ++ +l+GhS G+ +all+  + p++v++lil
  gi|242399429|ref|YP_002994854.1|  83 RVVAFDRPGFGLTErknPKGLLCNPYS--PEGAAELTLKLMDEFGMEKATLVGHSAGAGVALLVSIKAPERVEKLIL 157
                                       599999999999997744444455544..588999999999************************************ PP

                       Hydrolase_4 107 saPalkikaklkappllklllkllgkllpklqv........snnlkadslsrdpevvaayeadplvhgkitvr.lll 174
                                       +aPa + +++  +++l    l ++ k +p +            +      s+ +e+v +  + pl  ++   + +++
  gi|242399429|ref|YP_002994854.1| 158 VAPAWGSRNQSTFQKLIF-SLPWTEKYFPLILRfsvgrlegILENAWYNQSKLTEEVWEGYKRPLKAKDWDKGlFWV 233
                                       ****99998864333333.4666777777665567688755333345556777888889999999966665551566 PP

                       Hydrolase_4 175 elldamkrleeraakitlPllllhGeaDkvvdpeasrelyerlgskdktlklypglyHellnEp 238
                                       + +    +++e+ +++++P+l++h  +Dk+v+ e  ++l++ ++  + +l++++++ H  + E+
  gi|242399429|ref|YP_002994854.1| 234 TKYGEYPNITEELKNLNIPTLIVHCRQDKIVPLESGKKLHQIIP--NSQLAIMEECGHLPHEEK 295
                                       7788899*************************************..79***********99997 PP

>> Ndr  Ndr family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0     4e-10   4.4e-07      85     276 ..     113     307 ..     106     308 .. 0.72

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 4e-10
                                       HHTTHHHHHHHHT---EEEEEETHHHHHHHHHHHHSGGGEEEEEEES---S---HHHHHHHHHH.......TTTS-H CS
                               Ndr  85 ladqllavldhfklksviglGvgaGAyilarfalkhperveglvLinitskaagwvewakeKlsskllkkvgltdll 161
                                        a+  l+++d f ++++  +G  aGA + ++ ++k perve l+L+ +     + ++++ +Kl+     +  +t+  
  gi|242399429|ref|YP_002994854.1| 113 AAELTLKLMDEFGMEKATLVGHSAGAGVALLVSIKAPERVEKLILVAPAWG--SRNQSTFQKLIF----SLPWTEKY 183
                                       567778899*************************************87643..444555555552....23333333 PP

                                       HHHHHHHHS-HHHHHH..........T-HHHHHHHHHHHT-TTHHHHHHHHHHHHT-------TTSSSS-EEEEEET CS
                               Ndr 162 kdlllahkFgkeekse..........nsdlvreyrkllkerlnsknlelyleaynkRrdleierkklevkvllvvGd 228
                                         l+l    g+ e              +++ + y++ lk+++  k l  +++ y +  ++++e+k+l++++l+v   
  gi|242399429|ref|YP_002994854.1| 184 FPLILRFSVGRLEGILenawynqsklTEEVWEGYKRPLKAKDWDKGL-FWVTKYGEYPNITEELKNLNIPTLIVHCR 259
                                       33333333333221111222333333568999*********997776.47789*********************988 PP

                                       TSTTH..HHHHHHHHHS-TTTEEEEEETT-TT-HHHH-HHHHHHHHHHHH CS
                               Ndr 229 kspfv..devvevnskldkkkttllkvadsgglvleeqPdklaeslklfl 276
                                       +   v  ++  ++++ +   +++l  ++++g l+ ee+P   ++ l  fl
  gi|242399429|ref|YP_002994854.1| 260 QDKIVplESGKKLHQIIP--NSQLAIMEECGHLPHEEKPSEFLQILSDFL 307
                                       766541155566666654..56777799*************999998887 PP

>> Ser_hydrolase  Serine hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   3.4e-06    0.0039      55     101 ..     127     172 ..     113     187 .. 0.84
   2 !    8.2   0.0    0.0019       2.1     111     160 ..     247     297 ..     238     306 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.4e-06
                                       TTEEEEEETCHHHHHHHHHHHTTSSSEEEEEEET--SGGS..TT.GG CS
                     Ser_hydrolase  55 ekvvlvAHSlgclavlhaaelqlakkvagalLVapadveeeaaklae 101
                                       ek++lv HS g+ ++l +   +++++v++ +LVapa  ++++++ ++
  gi|242399429|ref|YP_002994854.1| 127 EKATLVGHSAGAGVALLVS-IKAPERVEKLILVAPAWGSRNQSTFQK 172
                                       5789********9999988.9***************98766666555 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0019
                                       SHHCCHCEEEEETTBTTC-HHHHHHHHHHC.T-EEEEETT-TTSSGGGT-S CS
                     Ser_hydrolase 111 eklpfpslvvaSenDpyvsfeeaeelaeaw.gaelvdlgeaGHinadsgfg 160
                                       ++l++p+l+v  + D++v+ e  ++l + + +++l  ++e GH+  ++  +
  gi|242399429|ref|YP_002994854.1| 247 KNLNIPTLIVHCRQDKIVPLESGKKLHQIIpNSQLAIMEECGHLPHEEKPS 297
                                       6899************************9867899999*****98887655 PP

>> Abhydrolase_2  Phospholipase/Carboxylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.025        28      10      31 ..      52      73 ..      45      87 .. 0.80
   2 ?    0.3   0.0      0.46   5.1e+02     106     132 ..     128     154 ..     118     173 .. 0.81
   3 !   17.9   0.0   1.9e-06    0.0022     150     214 ..     246     308 ..     237     309 .] 0.80

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.025
                                      SS---EEEEEE--TT--SHHHH CS
                     Abhydrolase_2 10 kdkaqavviflHGlGdsghawa 31
                                      +++ +  +++lHG G+s  +w 
  gi|242399429|ref|YP_002994854.1| 52 EKPGEGNLLLLHGFGASTFSWR 73
                                      67778889*********98886 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.46
                                       GEEEEEETHHHHHHHHHHHT-SS--SE CS
                     Abhydrolase_2 106 riiigGFSqGaalalylaltlpkklgg 132
                                       +  ++G S Ga +al  +++ p+++  
  gi|242399429|ref|YP_002994854.1| 128 KATLVGHSAGAGVALLVSIKAPERVEK 154
                                       55689**********999999887655 PP

  == domain 3  score: 17.9 bits;  conditional E-value: 1.9e-06
                                       S-GGGGG-EEEEEEETT-SSS-HHHHHHHHHHHHTTS-GEEEEEETT--SS-.-HHHHHHHHHHHH CS
                     Abhydrolase_2 150 atavtkklpilqiHgeeDpvvplalgkaakevlkkllkkvelksyeglaHsi.deeemqdikeflk 214
                                         +++  +p l +H+ +D++vpl  gk++++++ +++     ++ + l H++ ++e++q +++fl+
  gi|242399429|ref|YP_002994854.1| 246 LKNLN--IPTLIVHCRQDKIVPLESGKKLHQIIPNSQLAIMEECGH-LPHEEkPSEFLQILSDFLN 308
                                       44455..9***************************99966666666.7787615677899999986 PP

>> Abhydrolase_4  TAP-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   6.7e-07   0.00075      25      74 ..     241     290 ..     219     308 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 6.7e-07
                     Abhydrolase_4  25 prdestakgaapvLllqnerDpaTPyegakklakalggavlvtvegeGHg 74 
                                       ++ e+ ++ ++p+L++  ++D ++P+e++kkl++ +++++l + e+ GH 
  gi|242399429|ref|YP_002994854.1| 241 NITEELKNLNIPTLIVHCRQDKIVPLESGKKLHQIIPNSQLAIMEECGHL 290
                                       3333333447***********************************99996 PP

>> Abhydrolase_5  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.067        75      55      91 ..     125     162 ..     113     182 .. 0.68
   2 !   14.1   0.0   2.6e-05     0.029      87     133 ..     236     283 ..     222     292 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.067
                     Abhydrolase_5  55 klekfvvgGhslGGvvasrfaaee.ekiegvvflasYP 91 
                                       ++ek  + Ghs G  va  ++ +  e++e ++++a   
  gi|242399429|ref|YP_002994854.1| 125 GMEKATLVGHSAGAGVALLVSIKApERVEKLILVAPAW 162
                                       47899999*****77777766655489***99998433 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 2.6e-05
                     Abhydrolase_5  87 lasYPe.kdelselskkvlsivgteDgvlnvkslekakkflpkdtkvv 133
                                       ++ YP+  +el++l++++l +   +D +++ +s +k ++ +p+    +
  gi|242399429|ref|YP_002994854.1| 236 YGEYPNiTEELKNLNIPTLIVHCRQDKIVPLESGKKLHQIIPNSQLAI 283
                                       467999999******************************999765444 PP

>> FSH1  Serine hydrolase (FSH1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0         1   1.1e+03       6      19 ..      58      71 ..      55      78 .. 0.79
   2 !   14.7   0.1   1.6e-05     0.018     151     200 ..     239     289 ..     109     298 .. 0.67

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1
                              FSH1  6 kiLcLhGytqsgei 19
                                      ++L LhG++ s+  
  gi|242399429|ref|YP_002994854.1| 58 NLLLLHGFGASTFS 71
                                      78******998765 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 1.6e-05
                              FSH1 151 yeeyy.eedkiqtptLhvlGelDtvvdeerseaLaeafknsskvlkHpggH 200
                                       y +   e +++++ptL v+ ++D++v+ e  ++L++ + ns+  +  + gH
  gi|242399429|ref|YP_002994854.1| 239 YPNITeELKNLNIPTLIVHCRQDKIVPLESGKKLHQIIPNSQLAIMEECGH 289
                                       44444566788*****************************76666666666 PP

>> LIDHydrolase  Lipid-droplet associated hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0     2e-05     0.022      85     148 ..     127     189 ..      80     213 .. 0.83
   2 ?   -1.2   0.0       1.1   1.2e+03     230     263 ..     257     292 ..     241     293 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2e-05
                      LIDHydrolase  85 vklilvGHSvGaYialevlkrlsersikkvvlLfPtiediakSpngkkltkllaylpflalvvg 148
                                        k  lvGHS Ga +al v  +++er ++k++l+ P     ++S+ +k+++ l    +++ l++ 
  gi|242399429|ref|YP_002994854.1| 127 EKATLVGHSAGAGVALLVSIKAPER-VEKLILVAPAWGSRNQSTFQKLIFSLPWTEKYFPLILR 189
                                       6889********************9.**********9999999999988888444444444444 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.1
                      LIDHydrolase 230 fgkkDhWvpeetrdelkellgeeklevde..kgipH 263
                                         ++D+ vp e  ++l + +++++l + e   ++pH
  gi|242399429|ref|YP_002994854.1| 257 HCRQDKIVPLESGKKLHQIIPNSQLAIMEecGHLPH 292
                                       5689999**************988887332455555 PP

>> DUF3530  Protein of unknown function (DUF3530)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   1.6e-05     0.018     189     246 ..     119     174 ..     115     180 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.6e-05
                           DUF3530 189 aflnqrgaenivllghgtgAywaarylaekksakvdaLvlvdarepaeaaekqLaeql 246
                                       +++++ g e+ +l+gh  gA+ a+ +++ k ++ v++L+lv++ + +++ ++ +++ +
  gi|242399429|ref|YP_002994854.1| 119 KLMDEFGMEKATLVGHSAGAGVAL-LVSIKAPERVEKLILVAPAWGSRN-QSTFQKLI 174
                                       667788999************887.78889****************999.77666655 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     0.038        43      63     116 ..     126     181 ..     113     185 .. 0.83
   2 ?    9.5   0.0   0.00055      0.62     111     169 ..     209     276 ..     196     309 .] 0.71

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.038
                                       GGGEEEEEETHHHHHHHHHHHH-GGG-SEEEEESE---CCCHHCSTTS.THH.HCC CS
                      Peptidase_S9  63 serlaitGgSyGGyltgaalnqrpdlFkaavaevpvvdvlrydsdtdl.lte.eym 116
                                        e+  + G+S+G  +++ +  ++p++ + ++ ++p    +++ ++++l +   +++
  gi|242399429|ref|YP_002994854.1| 126 MEKATLVGHSAGAGVALLVSIKAPERVEKLILVAPAWGSRNQSTFQKLiFSLpWTE 181
                                       578899******9999999999******9999999999999999988886664444 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00055
                                       THH.HCCCC--TTT...CHHHHHHHHHH-CGGG--.....---EEEEEEETT-SSS-THHHHHHHHHH CS
                      Peptidase_S9 111 lte.eymewgnpee...neegykelspyspldnvk.....aypplLlihGlaDdrvppaealklvaaL 169
                                       lte  ++++  p +     +g  ++ +y  + n++      + p+L++h  +D+ vp++++ kl +  
  gi|242399429|ref|YP_002994854.1| 209 LTEeVWEGYKRPLKakdWDKGLFWVTKYGEYPNITeelknLNIPTLIVHCRQDKIVPLESGKKLHQII 276
                                       55557777777766444345566999999999999999999*******************99987655 PP

>> Esterase  Putative esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.9e-05     0.021     108     166 ..     122     171 ..     113     179 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.9e-05
                                       HHCSEECCCEEEEEETHHHHHHHHHHHCSTTTCCEEEEES--S-CCHCHHHCTTCCHHH CS
                          Esterase 108 anfrtapdgravaGqSmGGlgALilalkhpdrFgsvssfSpivnpsnamWgqeekeawq 166
                                       ++f  ++   +++G+S G+ +AL++ +k+p+r    +  +p        Wg  +++++q
  gi|242399429|ref|YP_002994854.1| 122 DEFGMEKA--TLVGHSAGAGVALLVSIKAPERVEKLILVAPA-------WGSRNQSTFQ 171
                                       55555555..9*****************************77.......9998888777 PP

>> Lipase_3  Lipase (class 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   4.5e-05     0.051      58      89 ..     120     151 ..     111     167 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.5e-05
                                       HHHHTT-EEEEEEEETHHHHHHHHHHHHHHHT CS
                          Lipase_3  58 llekypeysivvtGHSLGgalAlLaaldlven 89 
                                       l++++   + +++GHS G+++AlL+++   e+
  gi|242399429|ref|YP_002994854.1| 120 LMDEFGMEKATLVGHSAGAGVALLVSIKAPER 151
                                       67777778899**************9987666 PP

>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   4.9e-05     0.055      70     114 ..     126     165 ..     108     206 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.9e-05
                                       TCEEEEEEETHHHHHHHHHHHHHHHTT---EEEEEEESE.-SSTSS CS
                     Abhydrolase_3  70 psrivlaGdSaGGnlaaavalrardegepkvagqvliyP.vtdler 114
                                        ++ +l+G SaG+  a+ v+++a ++    v+ ++l+ P +    r
  gi|242399429|ref|YP_002994854.1| 126 MEKATLVGHSAGAGVALLVSIKAPER----VEKLILVAPaWG-S-R 165
                                       57789********************8....999999999532.2.2 PP

>> DUF915  Alpha/beta hydrolase of unknown function (DUF915)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0018         2      95     116 ..     119     140 ..     111     151 .. 0.85
   2 ?    0.9   0.0      0.21   2.4e+02     198     225 ..     258     285 ..     237     293 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0018
                            DUF915  95 eLkkkYnikkfnavGhSmGgla 116
                                       +L  +++++k+ +vGhS+G+  
  gi|242399429|ref|YP_002994854.1| 119 KLMDEFGMEKATLVGHSAGAGV 140
                                       7999***************864 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.21
                            DUF915 198 kqsDgivplasseslkyllkknaksyte 225
                                          D+ivpl+s + l++++ ++   ++e
  gi|242399429|ref|YP_002994854.1| 258 CRQDKIVPLESGKKLHQIIPNSQLAIME 285
                                       567****************998766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 2080.57
//
Query:       gi|242399430|ref|YP_002994855.1|  [L=916]
Description: Large helicase-related protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.2e-31  107.1   0.0    7.8e-29  100.7   0.0    2.3  2  DEAD            DEAD/DEAH box helicase
    4.2e-19   68.9   0.0    1.4e-18   67.2   0.0    2.0  1  Helicase_C      Helicase conserved C-terminal domain
    3.8e-18   66.0   1.7    4.4e-17   62.5   0.8    2.6  2  DEAD_assoc      DEAD/H associated
    1.6e-07   31.5   0.0    1.4e-06   28.4   0.0    2.2  2  ResIII          Type III restriction enzyme, res subunit
  ------ inclusion threshold ------
      0.011   15.4   0.7      0.021   14.5   0.2    1.7  2  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal
      0.022   14.3   0.3      0.092   12.3   0.0    2.2  2  AAA_25          AAA domain
      0.057   13.8   0.0          1    9.7   0.0    2.5  2  AAA_19          AAA domain
      0.068   13.2   0.0       0.17   11.9   0.0    1.7  1  HypA            Hydrogenase/urease nickel incorporation, meta
       0.17   11.6   0.0        0.4   10.4   0.0    1.6  1  AAA_30          AAA domain


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.7   0.0   3.9e-32   7.8e-29       2     170 ..      18     182 ..      17     189 .. 0.93
   2 ?    4.1   0.0     0.018        36      46     105 ..     244     303 ..     231     318 .. 0.76

  Alignments for each domain:
  == domain 1  score: 100.7 bits;  conditional E-value: 3.9e-32
                                       HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   2 diQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrv 78 
                                       + Q +a++++ +g++vl+ a+TGsGKT+a+l+pv+++++e +g +   al+++P+++L ++ l++l  ++++++l+v
  gi|242399430|ref|YP_002994855.1|  18 ELQMKAFEEVSSGKSVLIVAPTGSGKTEAALLPVFNAILE-DGLKPISALYIAPLKALNRDLLDRLLWWGEKLNLNV 93 
                                       579************************************9.99999******************************* PP

                                       EEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSH..CTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  79 lliiggvaardqlskldngvdivvgtpgrlddllstgkln..lsqvrflVlDEadrlldqgfsdfinrilnqlpqit 153
                                       ++  g+++a ++ +++++ +++++ tp+ l  +l+ ++l+  +s+v+f+V+DE+ +l d++++ +++  l++l++i 
  gi|242399430|ref|YP_002994855.1|  94 EVRHGDTSAYRKAQQVKKPPHVLIITPETLGIILTMKSLRkaISNVKFVVVDEIVELVDNKRGAQLSLALERLAEIA 170
                                       ****************788*************9966666666*******************************7664 PP

                                       TTSTTTSEEEEEESSBS CS
                                       xxxxxxxxxxxxxxxxx RF
                              DEAD 154 cdgklqrqvivlSATlp 170
                                            + q + lSAT+ 
  gi|242399430|ref|YP_002994855.1| 171 -----EFQRVGLSATVG 182
                                       .....4569******97 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.018
                                       TS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSHHHHHHHHHTT.CSEEEEEH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx RF
                              DEAD  46 tgpkalivePtreLaeqtlnnlkkfkkyidlrvlliiggvaardqlskldng.vdivvgtp 105
                                       +  +al+ + tr+ ae  ++++k ++k++++     ++++a+ +  ++l++g ++ +v t 
  gi|242399430|ref|YP_002994855.1| 244 KYERALVFTNTRQFAEILAHRFKAWGKPVEVHHG-SLSKEARVQAEKALKEGsIKALVCTS 303
                                       4569***********************9664433.44555555555666655788888886 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 !   67.2   0.0   7.2e-22   1.4e-18       5     107 ..     237     336 ..     233     341 .. 0.91

  Alignments for each domain:
  == domain 1  score: 67.2 bits;  conditional E-value: 7.2e-22
                                       HHHHHHHHTTTTSEEEEEESSHHHHHHHHHHHHHT...TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTS CS
                        Helicase_C   5 allellkleeeggkilifvntidrlekvklllekk...gikvavlhgelpqnereeileqfnkgesdvLiatdvaer 78 
                                        l e++   e+ +++l+f+nt++ +   ++l +++   g  v v+hg+l+++ r ++ ++ ++g+++ L++t+ +e 
  gi|242399430|ref|YP_002994855.1| 237 VLWEII---EKYERALVFTNTRQFA---EILAHRFkawGKPVEVHHGSLSKEARVQAEKALKEGSIKALVCTSSMEL 307
                                       555666...8999**********99...77777777789************************************** PP

                                       SSTSTTESEEEESSSSSSHHHHHHHHTTS CS
                        Helicase_C  79 GidipkvnlVinfdlprnvtsyiqriGRt 107
                                       Gidi +v++Vi++  pr+v ++iqriGR 
  gi|242399430|ref|YP_002994855.1| 308 GIDIGDVDVVIQYMSPRQVNRLIQRIGRS 336
                                       ****************************5 PP

>> DEAD_assoc  DEAD/H associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   0.0         6   1.2e+04      34      64 ..     122     151 ..     120     171 .. 0.63
   2 !   62.5   0.8   2.2e-20   4.4e-17       4     191 .]     587     752 ..     584     752 .. 0.85

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 6
                        DEAD_assoc  34 alalllaarlsrrfgidvqvaanDdgivlll 64 
                                       +l+ +l+    r+  ++v++++ D+ ++l +
  gi|242399430|ref|YP_002994855.1| 122 TLGIILTMKSLRKAISNVKFVVVDEIVEL-V 151
                                       67777777777777777888888877777.3 PP

  == domain 2  score: 62.5 bits;  conditional E-value: 2.2e-20
                        DEAD_assoc   4 drtllvErfrdelgdwrlvvhspfGrrvnealalllaarlsrrfgidvqvaanDdgivlllpleerlpllldellel 80 
                                       dr +  E++ +      l++h+ fG ++nea+++ l a l++++g  + + a+  +iv+ +p +    ++ +e+ e+
  gi|242399430|ref|YP_002994855.1| 587 DRDIGLESVPK-----ALIIHADFGNQANEAIGRFLMAFLAAKYGKVFVMKAQAHAIVIRTPFQ----VNPKEVKEY 654
                                       55555666644.....68*****************************************66443....334566666 PP

                        DEAD_assoc  81 lspd..eleedleaalnaselfkrrFrevAaralllprrypgkrkplwqqrlraaqLldvareypdfpllleavrev 155
                                       l +d   le ++ + l +s+ +++r+ +vA+r+++l r+ +                 +v r ++++++ +e+++e 
  gi|242399430|ref|YP_002994855.1| 655 LLQDhrVLEFVISRGLRGSSPYRWRMLNVAKRMGALRREAKI---------------RKVERLFEGTVIEKETLNEL 716
                                       65552258889999**********************999765...............44555556999********* PP

                        DEAD_assoc 156 ledqlDlerlaellrriaageirvvevetprpSpfA 191
                                       ++d++D+er++e+lr +++g++r+++v  ++pSp+A
  gi|242399430|ref|YP_002994855.1| 717 FHDKIDVERAEEVLRLLKEGRVRIKAVLRKEPSPLA 752
                                       **********************************98 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 !   28.4   0.0   7.1e-10   1.4e-06      15     169 ..      27     181 ..       6     183 .. 0.77
   2 ?    0.2   0.0      0.33   6.5e+02      42      93 ..     235     284 ..     232     310 .. 0.68

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 7.1e-10
                                       HT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.......-EEEEESSHHHHHHHHHHGGGGTGG....GEEEE CS
                            ResIII  15 lleklkskrdkrglikmaTGtGKTlvaaklierllkkgkee..kflflvprkslleqtleefkkflseaykeigkkv 89 
                                       +         k +li+++TG+GKT  a+  + +   + + +   +l ++p k+l   +l+++  + ++ + +  ++ 
  gi|242399430|ref|YP_002994855.1|  27 V------SSGKSVLIVAPTGSGKTEAALLPVFNAILEDGLKpiSALYIAPLKALNRDLLDRLLWWGEKLNLN-VEVR 96 
                                       3......466899**************7766666666666679*******************8888877653.3333 PP

                                       SSS-B--.........-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T.......TTHHHHHT- CS
                            ResIII  90 sgdkkka..kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk.......swreilekf 157
                                       +gd+      ++ ++  ++l++t ++l  ++   + +s ++  ++ +++++DE   l ++k       + ++ l  +
  gi|242399430|ref|YP_002994855.1|  97 HGDTSAYrkAQQVKKPPHVLIITPETLGIIL---TMKSLRKAISNVKFVVVDEIVELVDNKrgaqlslALER-LAEI 169
                                       33333333344678899**************...8899999999999************9755544445555.5556 PP

                                       --SEEEEEESS- CS
                            ResIII 158 keavllglTATp 169
                                        e+ ++gl+AT 
  gi|242399430|ref|YP_002994855.1| 170 AEFQRVGLSATV 181
                                       88*********6 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.33
                                       HHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS- CS
                            ResIII  42 aklierllkkgkeekflflvprkslleqtleefkkflseaykeigkkvsgdk 93 
                                       +++ +++ +k++  ++l++ ++++  e + ++fk + ++    +g   ++ +
  gi|242399430|ref|YP_002994855.1| 235 LRVLWEIIEKYE--RALVFTNTRQFAEILAHRFKAWGKPVEVHHGSLSKEAR 284
                                       567899999855..9******************9998876554333333333 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 ?   -3.4   0.0       4.3   8.6e+03      19      26 ..     295     302 ..     292     303 .. 0.80
   2 ?   14.5   0.2   1.1e-05     0.021      16      53 ..     781     819 ..     772     820 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 4.3
                    zinc_ribbon_10  19 nryalICs 26 
                                       +++al+C+
  gi|242399430|ref|YP_002994855.1| 295 SIKALVCT 302
                                       789****7 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 1.1e-05
                    zinc_ribbon_10  16 saknryalICskChshnGlap.keeleevkyrCpkCgal 53 
                                       + ++ +alIC++C +++ +   + +++    +CpkC +l
  gi|242399430|ref|YP_002994855.1| 781 LLNTEVALICTNCGWKSTTRVsRLKNRLEHLQCPKCSSL 819
                                       567889***********998745555555899****886 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   4.6e-05     0.092      32     176 ..      29     170 ..      22     182 .. 0.68
   2 ?   -2.4   0.1       1.5   2.9e+03      55      97 ..     229     272 ..     225     294 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.6e-05
                            AAA_25  32 agelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEds.edelrrRlravgeal......rdda 101
                                        g+ +l+++++g+GKt +al  ++   + +   g +  +++  ly++   + + +l  Rl ++ge+l      r+ +
  gi|242399430|ref|YP_002994855.1|  29 SGKSVLIVAPTGSGKTEAALLPVFNAILED---G-L--KPISALYIAPLKAlNRDLLDRLLWWGEKLnlnvevRHGD 99 
                                       58899*************999999888766...3.3..799******9999788*************6666643333 PP

                            AAA_25 102 rllvldlagveslpLfakdrggtlltadvdaleaaieeveg....vrlvviDplsralggdensnsdvgalvealer 174
                                       + +  ++++v++ p +        +t+++  ++ ++++  +    v++vv+D + +++++  ++ ++ + ++e+l++
  gi|242399430|ref|YP_002994855.1| 100 TSAYRKAQQVKKPPHVLI------ITPETLGIILTMKSLRKaisnVKFVVVDEIVELVDN--KRGAQLSLALERLAE 168
                                       333333444433333333......55555555555554433444499*****99998754..344555666666666 PP

                            AAA_25 175 ia 176
                                       ia
  gi|242399430|ref|YP_002994855.1| 169 IA 170
                                       55 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.5
                            AAA_25  55 lavatGkpwlg.pvapeqgkVlyvsaEdsedelrrRlravgeal 97 
                                       l+vat   +l+ +++   ++ ++ ++ + ++ l+ R++a+g+ +
  gi|242399430|ref|YP_002994855.1| 229 LDVATRLRVLWeIIEKYERALVFTNTRQFAEILAHRFKAWGKPV 272
                                       56777677777666668888899999999999999999999765 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0    0.0005         1       1      69 [.      20      98 ..      20     165 .. 0.64
   2 ?    0.9   0.0      0.27   5.4e+02      33      92 ..     237     292 ..     231     364 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0005
                            AAA_19  1 qreave.alkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae.........a 69
                                      q +a e  ++ k +l++a+ G+GKT+     v  ++ + g+kp + l +a+ +   + l +rl   g++          
  gi|242399430|ref|YP_002994855.1| 20 QMKAFEeVSSGKSVLIVAPTGSGKTEAALLPVFNAILEDGLKPISALYIAPLKALNRDLLDRLLWWGEKlnlnvevrhG 98
                                      6678876788999************998888888888888999999999998777777777775555445555444441 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.27
                            AAA_19  33 llvelggvkpeeillvaftgrAakelrerlaalgaeatTiHrlalldfddlltealelle 92 
                                       +l e+  +k e+ l+ + t++ a+ l+ r +a g++ +  H+   l  + ++ +a ++l+
  gi|242399430|ref|YP_002994855.1| 237 VLWEII-EKYERALVFTNTRQFAEILAHRFKAWGKPVEVHHGS--LSKEARV-QAEKALK 292
                                       555555.3468999**********************9999977..6555555.3444444 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   8.4e-05      0.17      65     100 ..     782     824 ..     706     836 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.4e-05
                                       EEE--EEEETTTS-EEECHH.HHH.......S-TTTSSS-EEEE CS
                              HypA  65 eevpvkvrCreCgkefelee.kal.......rCpkCgsadveiv 100
                                        +++v + C++Cg + +++  + l       +CpkC+s  v++ 
  gi|242399430|ref|YP_002994855.1| 782 LNTEVALICTNCGWKSTTRVsR-LknrlehlQCPKCSSLMVTVA 824
                                       5678999******776654431.23455666*******999886 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0    0.0002       0.4       3     106 ..      17     157 ..      15     171 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0002
                            AAA_30   3 naeQaaavealltsgdrvavltGpAGtGKtta..lkalreaweaag..grviglAptgkaAkvLa.......eelgi 68 
                                       n+ Q +a+e++ +++   +++++p G+GKt a  l + ++++e+     + + +Ap ++  ++L        e+l++
  gi|242399430|ref|YP_002994855.1|  17 NELQMKAFEEVSSGK--SVLIVAPTGSGKTEAalLPVFNAILEDGLkpISALYIAPLKALNRDLLdrllwwgEKLNL 91 
                                       7889*****997777..69***********74214455555555523466668888888888877344444423332 PP

                            AAA_30  69 eastiakllkrlk...........................grarlepgtllivDEag.mvdtkqla 106
                                       + +  +  +++++                            r+++++ + ++vDE+  +vd+k  a
  gi|242399430|ref|YP_002994855.1|  92 NVEVRHGDTSAYRkaqqvkkpphvliitpetlgiiltmksLRKAISNVKFVVVDEIVeLVDNKRGA 157
                                       222222222222222334456666677777888888777644556666888888864144555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (916 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.79u 0.29s 00:00:01.08 Elapsed: 00:00:00.47
# Mc/sec: 5879.00
//
Query:       gi|242399431|ref|YP_002994856.1|  [L=399]
Description: Fe-containing alcohol dehydrogenase [Thermococcus sibiricus MM 739]
Scores for complete 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-92  307.8   0.0    9.4e-92  307.6   0.0    1.0  1  Fe-ADH    Iron-containing alcohol dehydrogenase
    4.4e-12   46.2   0.1    3.7e-07   30.1   0.0    2.1  2  Fe-ADH_2  Iron-containing alcohol dehydrogenase
  ------ inclusion threshold ------
      0.039   14.0   0.0       0.35   10.9   0.0    2.1  2  DUF1638   Protein of unknown function (DUF1638)


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 !  307.6   0.0   1.6e-95   9.4e-92       2     364 .]      27     388 ..      26     388 .. 0.93

  Alignments for each domain:
  == domain 1  score: 307.6 bits;  conditional E-value: 1.6e-95
                                       SEEEEETTGGGGHHHHHTTT-..EEEEEEEHHHH.HH.THHHHHHHHHCTT-EEEE.EEE-S---HHHHHHHHTTS- CS
                            Fe-ADH   2 trivfgkgaleelgellkklgakralivtdkgslkksglldkvlesleeagievtvfdgvepnptleeveeaaalar 78 
                                       tri++g+g+l+++++ ++++   r++++ +k++    g+l++v +  eeag ev+ ++g + +p +e+vee++ ++r
  gi|242399431|ref|YP_002994856.1|  27 TRIIMGEGSLRYVESVARNYE--RVMVLSSKSMR-IHGFLNEVMDYAEEAGAEVDAIEGLPAEPAYEDVEEILPRIR 100
                                       79******************6..*********87.999*************************************** PP

                                       TT.--EEEEEESHHHHHHHHHHHHHTT..........................--EEEEESS-S-S-TT-SEEEEE. CS
                            Fe-ADH  79 eegadvviavGGGsviDtAKaialllanpe..vedyl......gegkakkkkalpliaiPTtaGtGsevtplavitd 147
                                       e+ +d++ia+GGGsviD+ Kai ++++ p+  +e++       +  +  +k + pli+iP+t+G Gsev++++v+  
  gi|242399431|ref|YP_002994856.1| 101 EFSPDLLIALGGGSVIDITKAIKVFYEVPDlrFEEVAfldrftKPVRIIPKLKTPLITIPSTSGAGSEVSAASVLK- 176
                                       ***************************98778555556674445555667777***********************. PP

                                       -TTSEEEEE-..SS--SEEEEEHHHHHHS-HHHHHHHHHHHHHHHHHHHHHHT---TTSSB--HHHHHHHHHHHHHH CS
                            Fe-ADH 148 eeegeklsifdpellPdlaivDpeltltlPkrvtaatglDalahalEayvskkanplsdalaleairliaknlerav 224
                                        ++g+k+ ++++e+ P++ai+Dp+l  t+  +++ ++glD+l+h +Eay++k a+p+sda+al ai++++k+l+ +v
  gi|242399431|ref|YP_002994856.1| 177 -KDGAKYNLVSYEIAPEYAILDPRLPRTMSEKIARNSGLDVLVHGIEAYTTKVATPFSDAMALGAIKTVFKWLPLSV 252
                                       .6779************************************************************************ PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHSS---HHHHHHHHHHC.CGGGGGS-HHHHHHHHH............HHHHHHT CS
                            Fe-ADH 225 adgedleareqmllastlaglafsnaglgavHalahalgalfgiphglanaillpavlrfnaeaa.p.erlaqlara 299
                                       +   d +are++++a+t+ag+af na+lg++H+l+h+       phgl+nai+lp+v+ fn++++   +++ ++ar+
  gi|242399431|ref|YP_002994856.1| 253 KG--DGKAREKIHYAATMAGIAFLNARLGICHSLSHKAAW--IGPHGLLNAIFLPYVIHFNMKDEgTrKKYTKIARE 325
                                       66..89********************************99..358*****************888877********* PP

                                       .......T--HHHHHHHHHHHHHTT---SHHHHT-TT-....HHHHHHHHHT-TSGGGGSSS---HHHH CS
                            Fe-ADH 300 lggesdeeaaeeliealrellkelglptsLselgvdee....dldklaeaalkdrslannpreltaedv 364
                                       +g     +  eel+e ++e+++ lg+p +L+el v ee    +ld++ae+a++d+ ++ np+e++ ed+
  gi|242399431|ref|YP_002994856.1| 326 IG----FNTSEELLEVIKEFNEMLGVP-KLNEL-VGEEtflsKLDEMAEKAYNDPLINFNPVEPSIEDI 388
                                       95....5799*****************.9***9.7776477778*********************9997 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 !   30.1   0.0   6.2e-11   3.7e-07      14      96 ..      43     124 ..      30     149 .. 0.85
   2 !   14.2   0.2   4.3e-06     0.026      97     234 ..     151     287 ..     146     297 .. 0.86

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 6.2e-11
                          Fe-ADH_2  14 lkelelkkvllvadentkka.agekveeslkeagikvevveeveeeadleeveklvealreketdlvvavGgGtiiD 89 
                                        +  ++++v++++++ +  +   ++v ++ +eag +v+++e   +e+  e+ve+++ ++re + dl++a+GgG++iD
  gi|242399431|ref|YP_002994856.1|  43 AR--NYERVMVLSSKSMRIHgFLNEVMDYAEEAGAEVDAIEGLPAEPAYEDVEEILPRIREFSPDLLIALGGGSVID 117
                                       32..46789999999988776899***************************************************** PP

                          Fe-ADH_2  90 iakyvsa 96 
                                       i+k +  
  gi|242399431|ref|YP_002994856.1| 118 ITKAIKV 124
                                       ***9865 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 4.3e-06
                          Fe-ADH_2  97 klnvpyvsvpTaaSvDGfaspgaslvvdgkkrtv.akaaaPlaviaDldvlaeAPrrllasGvGDllgkytaladwk 172
                                       kl+ p++ +p +    +  s  + l++dg+k  +     aP   i+D  + ++  +++ +    D+l   +  ++ k
  gi|242399431|ref|YP_002994856.1| 151 KLKTPLITIPSTSGAGSEVSAASVLKKDGAKYNLvSYEIAPEYAILDPRLPRTMSEKIARNSGLDVLVHGIEAYTTK 227
                                       567888888888777778888888999999999876666888888999999999999987544599999999999** PP

                          Fe-ADH_2 173 lanevseplaklsaamvqeaaeklvedkketealeellealalsgigisrpaSGsEHliSHa 234
                                       +a+ +s+ +a+ ++++v++ +   v  k++ +a e++  a +++gi++ ++  G +H +SH 
  gi|242399431|ref|YP_002994856.1| 228 VATPFSDAMALGAIKTVFKWLPLSV--KGDGKAREKIHYAATMAGIAFLNARLGICHSLSHK 287
                                       *****************99998888..699999****************************6 PP

>> DUF1638  Protein of unknown function (DUF1638)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   5.9e-05      0.35      84     152 ..      15      82 ..       5      86 .. 0.80
   2 ?    0.4   0.0       0.1   6.1e+02     113     146 ..     316     348 ..     306     363 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 5.9e-05
                           DUF1638  84 ltpgwvkewdrlvleky.geelarmifgkllkgYkrlvyidtgltddpeleeraeefaarlglelevipg 152
                                       +  ++++ +  l + ++   e   ++++ + ++Y+r++++ ++++  + + +++ ++a++ g e+++i+g
  gi|242399431|ref|YP_002994856.1|  15 FLVMLMRFF-SL-KTRIiMGEGSLRYVESVARNYERVMVLSSKSMRIHGFLNEVMDYAEEAGAEVDAIEG 82 
                                       445555444.33.566645777778889999*********************************999887 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.1
                           DUF1638 113 lkgYkrlvyidtgltddpeleeraeefaarlgle 146
                                        k+Y++++    g++  +el e ++ef + lg++
  gi|242399431|ref|YP_002994856.1| 316 RKKYTKIARE-IGFNTSEELLEVIKEFNEMLGVP 348
                                       4567777764.59999999999999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2506.12
//
Query:       gi|242399432|ref|YP_002994857.1|  [L=354]
Description: Translation initiation factor eIF-2B, beta subunit [Thermococcus sibiricus MM 739]
Scores for complete 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-82  275.9   0.0    4.1e-82  275.6   0.0    1.1  1  IF-2B     Initiation factor 2 subunit family
  ------ inclusion threshold ------
        0.2   11.4   0.1       0.47   10.2   0.1    1.5  1  DEAD      DEAD/DEAH box helicase
       0.21   11.9   0.1       0.32   11.3   0.1    1.2  1  DUF737    Protein of unknown function (DUF737)


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 !  275.6   0.0   6.9e-86   4.1e-82       1     282 []      55     343 ..      55     343 .. 0.98

  Alignments for each domain:
  == domain 1  score: 275.6 bits;  conditional E-value: 6.9e-86
                                       SS-SHHHHHHHHHHHHHHHHHHCCCSTHHHHHHHHHHHHHHHHTSSTS-HHHHHHHHHHHHHHHCCTTTSSHHHHHH CS
                             IF-2B   1 kvrGspaiaiaalevllevikdaktskvaeLkeelrkaidlLkkarPtavslgnairrllkeiselksssdvkeakk 77 
                                       +vrG+pai+ +a+++l+  ++++++++ +++  e  ka + Lk++rPtav+l++a++r+++ ++e +++++++ +kk
  gi|242399432|ref|YP_002994857.1|  55 QVRGAPAIGATAAYGLALLAEKSNAKTKEKFFDEFYKAFEILKNTRPTAVNLFWALNRVKR-LLEEHKENNLDTIKK 130
                                       79***********************************************************.899************ PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHTTC-TTEEEEEES--SH........HHHHHHHHHHTTEEEEEEEEEXTTTTH CS
                             IF-2B  78 sliekikelikeieeadekigdiaaelikdgdtilTicnskt........vlevlraaakekkkfkVivvEsrPrlq 146
                                        +ie+++++++e++ea+  +g+++ae + +g ++lT+cn+++        v + lr  ++e+k    +v E+rP lq
  gi|242399432|ref|YP_002994857.1| 131 LIIEEAHKIADEDVEANLRMGHYGAEILPEG-NVLTHCNAGSlatvhlgtVGAALRVMHREGKLKLLWVDETRPVLQ 206
                                       ****************************777.68***************99999*********************** PP

                                       H.HTHHHHHHHTTXEEEEEEGGGHHHHHHC.TESEEEEEXSEEETTSEEEEETTHHHHHHHHHHTTXEEEEEXXGGG CS
                             IF-2B 147 G.rltakeLvqagipvtlitdsavayvmse.evdkvivGAdrilenGaiankiGTsslAvlAkefnipvlvvaeslk 221
                                       G rl a+e  ++gip +li d+++++vm++ +vd++ivGAdri++nG+ ankiGT+slAvlAke++ip++++a+ ++
  gi|242399432|ref|YP_002994857.1| 207 GaRLSAWEYHYDGIPLKLISDNMAGFVMQQgKVDAIIVGADRIVANGDFANKIGTYSLAVLAKEHKIPFFTIAPIST 283
                                       ***************************************************************************** PP

                                       BESTSSSGGGSSXXBEXTHHHHEETTEESSTTTEEEEEBSEEEEEGGGXSEEEETTEEEXC CS
                             IF-2B 222 fservqldedifieerdpeellnitgeriaeeelkvvnpafDvtPpelItliITevGvlpp 282
                                       ++ +++ +++i ieer++ee+l + g +ia+ +++v+npafDvtP++++t+iIT+ Gv+ p
  gi|242399432|ref|YP_002994857.1| 284 VDMNLKSGKEIPIEERPKEEVLTCGGCKIAP-DVDVYNPAFDVTPHKYLTAIITDRGVVYP 343
                                       ******************************9.**************************976 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   7.9e-05      0.47     106     144 ..     111     150 ..      70     179 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 7.9e-05
                                       HHHHHHH.HCTSSHCTTEEEEEEETHHHHHHTTTHHHHHH CS
                                       xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 106 grlddll.stgklnlsqvrflVlDEadrlldqgfsdfinr 144
                                        r+ +ll + ++ nl+ ++ l++ Ea+++ d++ +  ++ 
  gi|242399432|ref|YP_002994857.1| 111 NRVKRLLeEHKENNLDTIKKLIIEEAHKIADEDVEANLRM 150
                                       45666664455567******************98887765 PP

>> DUF737  Protein of unknown function (DUF737)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   5.4e-05      0.32      77     144 ..      76     149 ..      45     157 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.4e-05
                            DUF737  77 veeeelrkkikeelqkrleeeqakaea......vqeelakllerEreaaqeelteailrerlstedErlkaqll 144
                                        ++ + ++k  +e++k +e  + ++ +        + +++lle+ +e + +++++ i+ e  ++ dE  +a+l 
  gi|242399432|ref|YP_002994857.1|  76 KSNAKTKEKFFDEFYKAFEILKNTRPTavnlfwALNRVKRLLEEHKENNLDTIKKLIIEEAHKIADEDVEANLR 149
                                       55678899999******9998888766677777678*******************************9999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2402.92
//
Query:       gi|242399433|ref|YP_002994858.1|  [L=171]
Description: Translation initiation factor eIF-2B, beta subunit [Thermococcus sibiricus MM 739]
Scores for 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-57  191.6   3.5      1e-56  191.5   3.5    1.0  1  NTPase_1         NTPase
    5.5e-09   35.8   0.1    1.7e-08   34.2   0.1    1.7  1  DUF2478          Protein of unknown function (DUF2478)
    3.7e-07   30.6   0.8    6.9e-07   29.8   0.8    1.5  1  AAA              ATPase family associated with various cellul
    4.5e-06   27.2   0.7    1.2e-05   25.9   0.5    2.0  1  AAA_18           AAA domain
    1.4e-05   25.4   0.1    4.8e-05   23.7   0.1    1.9  1  AAA_22           AAA domain
    1.8e-05   24.5   1.1      0.046   13.3   0.2    2.1  2  SRP54            SRP54-type protein, GTPase domain
    0.00014   21.6   0.5    0.00036   20.3   0.5    1.6  1  AAA_30           AAA domain
    0.00015   21.6   1.6    0.00027   20.7   1.6    1.5  1  AAA_24           AAA domain
    0.00028   21.3   3.0    0.00094   19.6   1.9    2.2  2  AAA_17           AAA domain
    0.00034   20.7   2.3     0.0038   17.3   2.3    2.1  1  MMR_HSR1         50S ribosome-binding GTPase
    0.00096   18.7   0.8     0.0021   17.6   0.8    1.7  1  KdpD             Osmosensitive K+ channel His kinase sensor d
      0.001   19.0   0.1     0.0026   17.7   0.1    1.7  1  APS_kinase       Adenylylsulphate kinase
     0.0013   19.0   1.3      0.012   15.9   1.0    2.3  1  AAA_19           AAA domain
     0.0015   17.6   1.1     0.0022   17.0   0.3    1.8  2  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
     0.0016   18.3   0.9     0.0055   16.6   0.4    2.0  2  MobB             Molybdopterin guanine dinucleotide synthesis
     0.0017   18.8   0.1      0.005   17.2   0.1    2.0  1  AAA_16           AAA ATPase domain
     0.0017   18.1   0.8       0.48   10.2   0.1    2.2  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
     0.0031   17.3   0.2      0.056   13.2   0.1    2.1  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
     0.0034   17.4   2.7       0.19   11.8   0.2    2.4  2  AAA_14           AAA domain
     0.0037   17.2   0.8        2.6    8.0   0.1    2.3  2  AAA_5            AAA domain (dynein-related subfamily)
     0.0048   16.2   1.7       0.02   14.1   1.6    1.8  1  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.005   16.5   2.3       0.05   13.2   2.2    2.1  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
  ------ inclusion threshold ------
      0.011   15.7   2.1      0.024   14.6   2.1    1.7  1  ATPase_2         ATPase domain predominantly from Archaea
      0.011   15.2   2.1       0.16   11.4   0.1    2.3  2  KTI12            Chromatin associated protein KTI12
      0.013   15.4   0.7      0.095   12.5   0.1    2.1  2  Bac_DnaA         Bacterial dnaA  protein
      0.014   15.1   0.1        3.5    7.3   0.0    2.2  2  IstB_IS21        IstB-like ATP binding protein
      0.022   14.0   0.3       0.09   12.0   0.0    1.9  2  DUF1611          Domain of unknown function (DUF1611_C) P-loo
      0.024   13.8   0.7      0.045   12.9   0.2    1.7  2  NB-ARC           NB-ARC domain
      0.024   15.0   0.1        1.4    9.3   0.0    2.3  2  RNA_helicase     RNA helicase
      0.037   14.2   0.1      0.051   13.7   0.1    1.4  1  AAA_33           AAA domain
       0.04   14.0   0.8      0.084   13.0   0.1    1.8  2  ADK              Adenylate kinase
       0.04   13.4   0.2      0.061   12.8   0.2    1.4  1  Arf              ADP-ribosylation factor family
      0.042   13.2   0.1        3.9    6.7   0.0    2.1  2  DnaB_C           DnaB-like helicase C terminal domain
      0.053   13.8   0.6       0.16   12.2   0.6    1.9  1  AAA_28           AAA domain
      0.054   13.5   0.5        4.6    7.2   0.2    2.2  2  ResIII           Type III restriction enzyme, res subunit
      0.083   12.8   0.3       0.28   11.1   0.2    1.8  2  NACHT            NACHT domain
       0.12   12.1   4.2        0.6    9.9   0.1    2.7  3  AAA_11           AAA domain
       0.42   10.2   1.9        6.8    6.2   0.0    2.5  3  AAA_25           AAA domain
       0.63    9.7   4.6        1.3    8.7   0.6    2.3  2  Thymidylate_kin  Thymidylate kinase


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 !  191.5   3.5   2.2e-59     1e-56       1     167 [.       2     161 ..       2     162 .. 0.99

  Alignments for each domain:
  == domain 1  score: 191.5 bits;  conditional E-value: 2.2e-59
                                       EEEEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE-------EEEEEET.T--EEEEEETT---SSEETTEEE- CS
                          NTPase_1   1 kvfiTGppGvGKtTlvkkvlellkssgvkvgGfyteevreggrrigFkivdlasgeegiLarveakreprvgkyvvd 77 
                                       k+fiTG pGvGKtT++ kv+++lk++++kvgGf+t+e+re+g+r+gFki +l++geegiLa  + +  prvgkyvv+
  gi|242399433|ref|YP_002994858.1|   2 KIFITGLPGVGKTTIILKVTKELKNHDLKVGGFVTQEIREKGKRVGFKIKALDTGEEGILAWAG-NGYPRVGKYVVN 77 
                                       69**************************************************************.9*********** PP

                                       HHHHHHHHHHHHHHHHHHH-EEEE---STTGGG-HHHHHHHHHHHTTTSEEEEE--SS--SHHHHHHHT-TT-EEEE CS
                          NTPase_1  78 vesfeelalealrkalseadviviDEiGkmElkskkfkeaveevLksekpvlavihrrkdlalveeirerkdvkvfe 154
                                       +++++++a++a+r+a+++advi+iDEiG mE+ks++f+++++ev+ksek++la++hrr     v++++    ++v+ 
  gi|242399433|ref|YP_002994858.1|  78 LKDINNIAVSAIRRAVENADVIIIDEIGAMEYKSREFAKSIDEVIKSEKVLLATVHRR----YVDKFKTL--GRVYV 148
                                       **********************************************************....8******9..***** PP

                                       --TTTTTTHHHHH CS
                          NTPase_1 155 vteenrdalleei 167
                                       +t+enr+++ +ei
  gi|242399433|ref|YP_002994858.1| 149 LTPENREQIRQEI 161
                                       ***********99 PP

>> DUF2478  Protein of unknown function (DUF2478)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.1   3.7e-11   1.7e-08      13     141 ..      14     143 ..       4     159 .. 0.81

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 3.7e-11
                           DUF2478  13 dalLaafaerlraeGlrvaGvvqenaeeaegkkcdmeledlatgeririsqdlg..sgsqgCrLdpeaLae.aaaav 86 
                                        +++ ++ ++l++++l+v+G+v ++ +e +gk+   +++ l+tge+  +       ++     ++ + +++ a+ a+
  gi|242399433|ref|YP_002994858.1|  14 TTIILKVTKELKNHDLKVGGFVTQEIRE-KGKRVGFKIKALDTGEEGILAWAGNgyPRVGKYVVNLKDINNiAVSAI 89 
                                       56777899**************888875.57889**********997666443311344446789999988356677 PP

                           DUF2478  87 eralaegadlvivnkFGkqEaeGrGlreeiaaalaagiPvltaVseklleaWraF 141
                                       +ra+ e+ad++i+   G  E + r +++ i ++++++  +l +V++++++++++ 
  gi|242399433|ref|YP_002994858.1|  90 RRAV-ENADVIIIDEIGAMEYKSREFAKSIDEVIKSEKVLLATVHRRYVDKFKTL 143
                                       8888.99*********************************************875 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.8   1.5e-09   6.9e-07       2      95 ..       4     134 ..       3     168 .. 0.61

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 1.5e-09
                                       EEESSTTSSHHHHHHHHHHHHTHE.............EEEEETTTCSSS............................ CS
                               AAA   2 llyGppGtGKTllakavakelgve.............fleisgsellsk............................ 37 
                                        ++G pG+GKT+++  v kel+ +                        k                            
  gi|242399433|ref|YP_002994858.1|   4 FITGLPGVGKTTIILKVTKELKNHdlkvggfvtqeirE----------Kgkrvgfkikaldtgeegilawagngypr 70 
                                       579*****************975533333433333330..........24445555555555556999977777775 PP

                                       ...STTHHHHHHHHHHHHHHHTS..TSEEEEEETGGGHHHHH..TTCCCHHHHHHHHHHHHHHHH CS
                               AAA  38 ...yvgesekkirelfkeakeka..kpsilfiDEidalaksr..sgseseeeervvnqLlteldg 95 
                                          y   + k+i+++  +a + a  +  +++iDEi a+  ++    ++ +e  +  ++Ll+ + +
  gi|242399433|ref|YP_002994858.1|  71 vgkY-VVNLKDINNIAVSAIRRAveNADVIIIDEIGAMEYKSreFAKSIDEVIKSEKVLLATVHR 134
                                       5532.2333444444444333337556***********877745444555555556666655444 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.5   2.6e-08   1.2e-05       1      88 [.       3     110 ..       3     133 .. 0.67

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 2.6e-08
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf....................gvnlrdvakenglllevdpealdeskrldedkl 57 
                                       I++tG pGvGKtt+   + k+l++                    g++++ + + ++  l +  + +++  + + +  
  gi|242399433|ref|YP_002994858.1|   3 IFITGLPGVGKTTIILKVTKELKNhdlkvggfvtqeirekgkrvGFKIKALDTGEEGILAWAGNGYPRVGKYVVNLK 79 
                                       9*************999999996679999666666666665555444444444444444444443444444444444 PP

                            AAA_18  58 dklldaleenssaleegknlvidghlaeles 88 
                                       d +  a+ ++++a e++++++id + a  ++
  gi|242399433|ref|YP_002994858.1|  80 DINNIAVSAIRRAVENADVIIIDEIGAMEYK 110
                                       4444444444448899999999998776665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.1     1e-07   4.8e-05       8     113 ..       3     116 ..       2     157 .. 0.65

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1e-07
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee........erpevvfvtlpsst.sskdllrellralglelka..erl 73 
                                       +++tG +G+GKTt + +++++l+++             e+ + v ++++++  + + +l +  + + + +k+  + +
  gi|242399433|ref|YP_002994858.1|   3 IFITGLPGVGKTTIILKVTKELKNHDLKVGgfvtqeirEKGKRVGFKIKALDtGEEGILAWAGNGYPRVGKYvvNLK 79 
                                       689*******************8765555599999999666666555555554899999999999999999944333 PP

                            AAA_22  74 sseell.ealeqalraravielliiDEaqhlr..seealeeLr 113
                                       +   +  +a+++a+++     ++iiDE+  +   s    e+ +
  gi|242399433|ref|YP_002994858.1|  80 DINNIAvSAIRRAVEN---ADVIIIDEIGAMEykS---REFAK 116
                                       3333333444444444...567******9995542...22222 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.2    0.0001     0.046       4      32 ..       3      31 ..       1      41 [. 0.89
   2 !   10.2   0.1   0.00091      0.42      67     119 ..      80     129 ..      67     141 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.0001
                                      EEEEESTTSSHHHHHHHHHHHHHHTTS-E CS
                             SRP54  4 illvGlqGaGKTttlaKLaallkkegkkv 32
                                      i + Gl G+GKTt + K+ + lk++  kv
  gi|242399433|ref|YP_002994858.1|  3 IFITGLPGVGKTTIILKVTKELKNHDLKV 31
                                      7899*******************998887 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00091
                                       CHHHHHHHHHHHHHHTTSSEEEEEE--SSTTHHHHHHHHHHHHHHHSSSEEEE CS
                             SRP54  67 dpaavakeavekakeekidvvlvDTaGrlqndkelmeelkkikkvvkpdevll 119
                                       d  ++a  a+++a e ++dv+++D  G ++++++ ++  k+i +v+k+++vll
  gi|242399433|ref|YP_002994858.1|  80 DINNIAVSAIRRAVE-NADVIIIDEIGAMEYKSREFA--KSIDEVIKSEKVLL 129
                                       667899999999988.78***********99988765..67888888887776 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.5   7.9e-07   0.00036      22     109 ..       4     118 ..       2     132 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 7.9e-07
                            AAA_30  22 vltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelgiea.stiak.llkrlk............... 81 
                                       ++tG +G GKtt++ ++++ ++++  +v g+  ++   k  + ++ i+a +t ++ +l + +               
  gi|242399433|ref|YP_002994858.1|   4 FITGLPGVGKTTIILKVTKELKNHDLKVGGFVTQEIREKGKRVGFKIKAlDTGEEgILAW-Agngyprvgkyvvnlk 79 
                                       69*****************9**9*99**99988876666555444454413333313433.3488899999999999 PP

                            AAA_30  82 .........grarlepgtllivDEagmv..dtkqlaall 109
                                                 r ++e+++++i+DE+g +   ++++a+ +
  gi|242399433|ref|YP_002994858.1|  80 dinniavsaIRRAVENADVIIIDEIGAMeyKSREFAKSI 118
                                       9*****99844577888*********9944444444444 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   1.6   5.8e-07   0.00027       4     128 ..       2     150 ..       1     171 [] 0.82

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 5.8e-07
                            AAA_24   4 kiliyGpsgiGKTtlakel....gpkplfi.......................dtekGlksldadkfpdieswedfl 53 
                                       ki+i+G +g+GKTt++++     +++ l +                         e+G  +  ++ +p++ ++   l
  gi|242399433|ref|YP_002994858.1|   2 KIFITGLPGVGKTTIILKVtkelKNHDLKVggfvtqeirekgkrvgfkikaldTGEEGILAWAGNGYPRVGKYVVNL 78 
                                       89*****************7776555555588889999999999999999995557799999999999999888888 PP

                            AAA_24  54 devvel.....aaeladyktlviDtideleelclaevirqnekaeskedkgdgkGygelaeefrrllkklqelrknv 125
                                       ++++ +     +++ ++ ++++iD i+ +e   ++ ++  +e+ +s+ +       ++la+ +rr+++k++ l+   
  gi|242399433|ref|YP_002994858.1|  79 KDINNIavsaiRRAVENADVIIIDEIGAMEYKSREFAKSIDEVIKSE-K-------VLLATVHRRYVDKFKTLGRVY 147
                                       888888898899999999***********999999999999998776.2.......688888888888888888755 PP

                            AAA_24 126 ifi 128
                                       +++
  gi|242399433|ref|YP_002994858.1| 148 VLT 150
                                       555 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   1.9   2.1e-06   0.00094       1      39 [.       6      49 ..       6     136 .. 0.67
   2 ?   -1.2   0.0       5.4   2.5e+03      32      65 ..     130     165 ..     120     168 .. 0.53

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.1e-06
                                      EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTT.....S CS
                            AAA_17  1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrgg.....l 39
                                      +G+PG+GK+t++ k+ ++++ + l  G  + +e++++g      
  gi|242399433|ref|YP_002994858.1|  6 TGLPGVGKTTIILKVTKELKNHDLKVGGFVTQEIREKGkrvgfK 49
                                      7*********************************9998443331 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 5.4
                                       HHHHTTTSHSSHHHHC..TSHHHHHHHHHHHHHHHH CS
                            AAA_17  32 eeakrgglakardemr..klpleekkelqkeaaeki 65 
                                       +++ r+  +k +   r   l  e ++++++e++e++
  gi|242399433|ref|YP_002994858.1| 130 ATVHRRYVDKFKTLGRvyVLTPENREQIRQEIIENL 165
                                       555555543333333322455566666666666655 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   2.3   8.2e-06    0.0038       1      84 [.       2     133 ..       2     171 .] 0.58

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 8.2e-06
                                       EEEEEESTTSSHHHHHHHHHTS..TEEESSSTTSSSSEEEEEEEETTEE............................ CS
                          MMR_HSR1   1 evaivGrpNvGKStLinaltge..kaivsdkpgtTrdinegrvklkgke............................ 47 
                                       ++ i G p vGK+t+i + t+e  +   +   ++T++i+e+  ++ g +                            
  gi|242399433|ref|YP_002994858.1|   2 KIFITGLPGVGKTTIILKVTKElkNHDLKVGGFVTQEIREKGKRV-GFKikaldtgeegilawagngyprvgkyvvn 77 
                                       589******************964456666779****97663331.2231122233344445555555555555555 PP

                                       ....................EEEEECGGCSSHHHHHHHHHHHHHHHHCT.SEEEEEEE CS
                          MMR_HSR1  48 ....................ielvDtpGliegaseekglgkaflaleea.dlillvvd 84 
                                                           ++++D  G +e   ++++++k++ +++++ +++l  v 
  gi|242399433|ref|YP_002994858.1|  78 lkdinniavsairravenadVIIIDEIGAME--YKSREFAKSIDEVIKSeKVLLATVH 133
                                       5555555555555555555577777777554..4444566666666665355555554 PP

>> KdpD  Osmosensitive K+ channel His kinase sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.8   4.6e-06    0.0021       5     104 ..       1     117 [.       1     164 [. 0.76

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4.6e-06
                              KdpD   5 lkiflGaapGvGktyamLeeaqelkeegvdvviglvethgrketealleglevi...............pr.kevey 65 
                                       +kif+   pGvGkt  +L+  +elk++  +v  g+v ++ r++ +++  +++ +               pr  ++ +
  gi|242399433|ref|YP_002994858.1|   1 MKIFITGLPGVGKTTIILKVTKELKNHDLKVG-GFVTQEIREKGKRVGFKIKALdtgeegilawagngyPRvGKYVV 76 
                                       59**********************99998864.89999999999888878877777788888888887744134445 PP

                              KdpD  66 kgkeleeldldaila..rkpevvlvDelahtnapgsrhekr 104
                                       + k ++++ + ai +  ++ +v+++De++  + ++ + +k 
  gi|242399433|ref|YP_002994858.1|  77 NLKDINNIAVSAIRRavENADVIIIDEIGAMEYKSREFAKS 117
                                       55666666666665533567888888888877666665554 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   5.6e-06    0.0026       5      44 ..       3      42 ..       1      55 [. 0.88

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 5.6e-06
                                      EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTT CS
                        APS_kinase  5 vwltGlsgsGKstianalekkLvekgisvylLdGdnvRhg 44
                                      +++tGl g GK+ti  ++ k+L+++  +v     +++R++
  gi|242399433|ref|YP_002994858.1|  3 IFITGLPGVGKTTIILKVTKELKNHDLKVGGFVTQEIREK 42
                                      9***************************999999999976 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   1.0   2.6e-05     0.012      13     118 ..       3     111 ..       1     130 [. 0.63

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.6e-05
                            AAA_19  13 llvtaGpGtGKTrvlkhivallvelggvkp.........eeillvaftgrAakelrerlaalgaeatTiHrlal... 77 
                                       +++t+ pG GKT+++ ++ ++l++   +k+         e+   v f  +A +  +e +              l   
  gi|242399433|ref|YP_002994858.1|   3 IFITGLPGVGKTTIILKVTKELKNHD-LKVggfvtqeirEKGKRVGFKIKALDTGEEGI--------------Lawa 64 
                                       689**************999998877.44434444444444444444444444444444..............0333 PP

                            AAA_19  78 ...........ldfddlltealelleeaeeekklqeeellivDEfqdvdelq 118
                                                  ++++d+++ a+++++     + +++++++i+DE+  ++   
  gi|242399433|ref|YP_002994858.1|  65 gngyprvgkyvVNLKDINNIAVSAIR-----RAVENADVIIIDEIGAMEYKS 111
                                       34444444455788888866776655.....466566689999987776555 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 !   17.0   0.3   4.8e-06    0.0022      32      61 ..       3      32 ..       1      55 [. 0.93
   2 ?   -1.7   0.0       2.5   1.2e+03     124     131 ..      98     105 ..      74     164 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.8e-06
                                      EEEEE-TTSSHHHHHHHHHHHHHCTT--EE CS
                              MeaB 32 vGltGvPGaGkstlvealglelrrrGkrva 61
                                      + +tG+PG+Gk t++ +++ el+++  +v+
  gi|242399433|ref|YP_002994858.1|  3 IFITGLPGVGKTTIILKVTKELKNHDLKVG 32
                                      679*********************999986 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.5
                                       EEEEEEES CS
                              MeaB 124 vvlietvG 131
                                       v++i+ +G
  gi|242399433|ref|YP_002994858.1|  98 VIIIDEIG 105
                                       33333322 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.4   1.2e-05    0.0055       2      31 ..       3      32 ..       2      47 .. 0.92
   2 ?    0.0   0.0       1.6   7.4e+02      23      43 ..      79     102 ..      59     142 .. 0.61

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.2e-05
                              MobB  2 lgivgksgsGKTtLleklipelkarglrvg 31
                                      + i+g  g GKTt++ k+ +elk+++l+vg
  gi|242399433|ref|YP_002994858.1|  3 IFITGLPGVGKTTIILKVTKELKNHDLKVG 32
                                      67999************************8 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1.6
                              MobB  23 lkarglrvgtiKhahhgfd...vd 43 
                                          +++ v++i+ a+++ d   +d
  gi|242399433|ref|YP_002994858.1|  79 KDINNIAVSAIRRAVENADviiID 102
                                       444556666666666666533334 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   1.1e-05     0.005      27      58 ..       3      37 ..       2     149 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.1e-05
                            AAA_16 27 vllsGesGvGKsslvrellralekd....ggiflrg 58
                                      ++++G +GvGK++++ ++ ++l+ +    g  f+++
  gi|242399433|ref|YP_002994858.1|  3 IFITGLPGVGKTTIILKVTKELKNHdlkvG-GFVTQ 37
                                      68******************9999977642.33333 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.1     0.001      0.48      36      60 ..       3      27 ..       1      43 [. 0.84
   2 ?    6.7   0.1     0.012       5.5      75     103 ..      86     114 ..      77     131 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.001
                            RuvB_N 36 vllyGpPGlGkttlakiiakelgvk 60
                                      ++++G PG+Gktt+   ++kel+ +
  gi|242399433|ref|YP_002994858.1|  3 IFITGLPGVGKTTIILKVTKELKNH 27
                                      7899****************99864 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.012
                            RuvB_N  75 laalltnleekdvlfideihrlsraveev 103
                                       ++a+   +e+ dv+ idei  ++ +  e+
  gi|242399433|ref|YP_002994858.1|  86 VSAIRRAVENADVIIIDEIGAMEYKSREF 114
                                       6789999************9998877765 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 !   13.2   0.1   0.00012     0.056       1      25 [.       3      29 ..       3      57 .. 0.79
   2 ?    2.4   0.0      0.24   1.1e+02      55      75 ..      90     108 ..      71     124 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00012
                   Viral_helicase1  1 ivvhGvpGcGKStlirkllrts..lil 25
                                      i + G pG GK+t+i k+ ++   ++l
  gi|242399433|ref|YP_002994858.1|  3 IFITGLPGVGKTTIILKVTKELknHDL 29
                                      5799**************999555444 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.24
                   Viral_helicase1  55 malvkstkgkililDEylllh 75 
                                         +v+  +++++i+DE+++++
  gi|242399433|ref|YP_002994858.1|  90 RRAVE--NADVIIIDEIGAME 108
                                       44444..499*******9987 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.2   0.00041      0.19       5      27 ..       3      25 ..       1      62 [. 0.85
   2 ?    5.9   0.2     0.027        12      54      89 ..      87     124 ..      73     166 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00041
                            AAA_14  5 lvitGaRrvGKTtllkqlikell 27
                                      ++itG+  vGKTt++ ++ kel 
  gi|242399433|ref|YP_002994858.1|  3 IFITGLPGVGKTTIILKVTKELK 25
                                      689***************99987 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.027
                            AAA_14  54 elileklkeekktylflDEiqev....pewekalkslvde 89 
                                       ++i++ +  e+  ++++DEi  +    +e+ k + +++++
  gi|242399433|ref|YP_002994858.1|  87 SAIRRAV--ENADVIIIDEIGAMeyksREFAKSIDEVIKS 124
                                       2333332..5678999999988755554555555554444 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.1    0.0058       2.6       2      23 ..       3      24 ..       2      31 .. 0.83
   2 !    8.0   0.1    0.0057       2.6      53      97 ..      83     130 ..      71     167 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0058
                                      EEEE--SSSSHHHHHHHGGGGB CS
                             AAA_5  2 vlLvGppGtgKselaerlaaal 23
                                      +++ G pG+gK++++ ++ + l
  gi|242399433|ref|YP_002994858.1|  3 IFITGLPGVGKTTIILKVTKEL 24
                                      7899**********99888766 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0057
                                       ....--------G-SEEEEESGGG--...HHHHHHHHHHHHSSEEE.. CS
                             AAA_5  53 slvdsplvraaregeilvlDEverae...sevlnsLlslleerrllle 97 
                                           s++ ra+++++++++DE+  +e   +e ++s   ++  +++ll+
  gi|242399433|ref|YP_002994858.1|  83 NIAVSAIRRAVENADVIIIDEIGAMEyksREFAKSIDEVIKSEKVLLA 130
                                       556678899999**********87654345666666666666666644 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   1.6   4.4e-05      0.02       4     124 ..       3     126 ..       2     137 .. 0.54

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.4e-05
                           DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvl....vlrealakke..ekkkkkeafeklssfinnl 74 
                                       +++tG +G GKt + l++  el++++++    ++++  ++         +al+  e       ++   ++ +++ nl
  gi|242399433|ref|YP_002994858.1|   3 IFITGLPGVGKTTIILKVTKELKNHDLKV-GGFVTQEIREKGkrvgFKIKALDTGEegILAWAGNGYPRVGKYVVNL 78 
                                       79********************4444322.22222211111111112222222222233344566666666666666 PP

                           DUF2075  75 sef...kkaeekkeepkedvvivDEAhrlltksdqaekqseenqlkelmkrak 124
                                       +        + +++ +++dv+i+DE   +  ks+        + ++e++k +k
  gi|242399433|ref|YP_002994858.1|  79 KDInniAVSAIRRAVENADVIIIDEIGAMEYKSRE-----FAKSIDEVIKSEK 126
                                       66655545555677777888888886555553332.....2344555555555 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 !   13.2   2.2   0.00011      0.05       3      37 ..       3      40 ..       1     133 [. 0.58

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00011
                                      EEEEESTTCCHHHHHHHHH..CT--SS-EE.EEESS-S CS
                              cobW  3 tvltGflGsGKTtLlnhll..enraglkla.vivNefg 37
                                      + +tG +G GKTt++ +++   ++++lk+   ++ e+ 
  gi|242399433|ref|YP_002994858.1|  3 IFITGLPGVGKTTIILKVTkeLKNHDLKVGgFVTQEIR 40
                                      679****************5534444444313444444 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   2.1   5.1e-05     0.024      23     136 ..       3     112 ..       1     150 [. 0.63

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.1e-05
                          ATPase_2  23 yfiYGpegsGKtaLlkeiienledkdkyv.iyyialreesiskldefie..eeeekkklekalgiavpkaeleeilk 96 
                                       +fi+G  g+GKt+++ ++ ++l+++d +v  ++++  +e+ +++  +i+  ++ e+  +   +g+  p++    + +
  gi|242399433|ref|YP_002994858.1|   3 IFITGLPGVGKTTIILKVTKELKNHDLKVgGFVTQEIREKGKRVGFKIKalDTGEEG-ILAWAGNGYPRVGKYVV-N 77 
                                       7*********************98886552577666666666666665564443333.55566777777665322.2 PP

                          ATPase_2  97 .eksklvfkaielllekikkkgkkiiiiiDelqklidlgln 136
                                        + +++   a++++ +++++     +iiiDe+  +  ++++
  gi|242399433|ref|YP_002994858.1|  78 lKDINN--IAVSAIRRAVENA---DVIIIDEIGAME-YKSR 112
                                       222222..2333333333333...588899987666.5555 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00035      0.16       4      32 ..       3      31 ..       1      52 [. 0.88
   2 ?    3.6   0.4     0.084        38      54      79 ..      79     104 ..      73     167 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00035
                                      EEEE--TTSSHHHHHHHHHHHHHHTT--E CS
                             KTI12  4 vvltGlPssGKstrakeLakaleeekrsv 32
                                      + +tGlP +GK+t+  ++ k+l++++ +v
  gi|242399433|ref|YP_002994858.1|  3 IFITGLPGVGKTTIILKVTKELKNHDLKV 31
                                      789********************998887 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.084
                                       HHHHHHHHHHHHHHHTT.SEEEE-S- CS
                             KTI12  54 kalRsslrsavkrdLskekvVIvDsl 79 
                                       k++ +   sa++r++++ +v+I+D++
  gi|242399433|ref|YP_002994858.1|  79 KDINNIAVSAIRRAVENADVIIIDEI 104
                                       6677778899**************86 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.62   2.9e+02      37      63 ..       3      27 ..       2      41 .. 0.77
   2 ?   12.5   0.1   0.00021     0.095      83     139 ..      81     134 ..      71     145 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.62
                                      EEEE-SSSSSHHHHHHHHHHHHHHHSS CS
                          Bac_DnaA 37 lfiygevGlGktHLlkaignevlenap 63
                                      +fi g  G+Gkt ++  +++e+++  +
  gi|242399433|ref|YP_002994858.1|  3 IFITGLPGVGKTTIILKVTKELKN--H 27
                                      6999999*****998887776654..3 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00021
                                       HHTT-HHHHHHHHTT-SEEEEE-GGGGTT-HHHHHHHHHHHHHHHTTT-EEEEEESS CS
                          Bac_DnaA  83 lrdkkaeefkeklrkvDvLliDDiqflagkektqeelfhtfnalleegkqvvlssDr 139
                                       +++ +++++++ + ++Dv++iD+i  +++k+    e+ + ++++++++k ++ +  r
  gi|242399433|ref|YP_002994858.1|  81 INNIAVSAIRRAVENADVIIIDEIGAMEYKS---REFAKSIDEVIKSEKVLLATVHR 134
                                       555677899*********************9...89999999999999988877665 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   0.0     0.019       8.6      50      79 ..       3      32 ..       1      45 [. 0.83
   2 ?    7.3   0.0    0.0076       3.5     103     134 ..      90     122 ..      67     134 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.019
                         IstB_IS21 50 ivllGpsGvGKshlaialgveavraglsvl 79
                                      i ++G +GvGK+ +   + +e  +++l+v 
  gi|242399433|ref|YP_002994858.1|  3 IFITGLPGVGKTTIILKVTKELKNHDLKVG 32
                                      789**********99999999988888885 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0076
                         IstB_IS21 103 lkrllkvdllilDdlgllpld.qaeaellfevi 134
                                        +++ ++d++i+D++g  + + ++ a+ + evi
  gi|242399433|ref|YP_002994858.1|  90 RRAVENADVIIIDEIGAMEYKsREFAKSIDEVI 122
                                       3456678*********88765044566666666 PP

>> DUF1611  Domain of unknown function (DUF1611_C) P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.1      0.29   1.3e+02      24      50 ..      11      37 ..       6      39 .. 0.89
   2 ?   12.0   0.0    0.0002      0.09      24      95 ..      31     103 ..      27     118 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.29
                           DUF1611 24 vGKrttaleleealeerGlkaafvaTg 50
                                      vGK t  l+++++l++  lk++ + T 
  gi|242399433|ref|YP_002994858.1| 11 VGKTTIILKVTKELKNHDLKVGGFVTQ 37
                                      8****************9999877775 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.0002
                           DUF1611  24 vGKrttaleleealeerGlkaafvaTgqtgili.agegvv.ld..avvvdfvaGaveglvkkaaeeeepdlilveG 95 
                                       vG ++ + e++e+ ++ G+k++ + Tg+ gil  ag+g + ++  +v  +++   + +++ +a e  ++d+i+++ 
  gi|242399433|ref|YP_002994858.1|  31 VGGFV-TQEIREKGKRVGFKIKALDTGEEGILAwAGNGYPrVGkyVVNLKDINNIAVSAIRRAVE--NADVIIIDE 103
                                       55554.46899999***********************9863332267789999999999999996..559999975 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   0.2   9.7e-05     0.045      23      46 ..       3      26 ..       1      42 [. 0.87
   2 ?   -1.5   0.0       2.5   1.1e+03      50      77 ..     139     166 ..     108     169 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.7e-05
                                      EEEEESTTSSHHHHHHHHCCSHCC CS
                            NB-ARC 23 valvGmgGvGKttlakqilnksde 46
                                      +++ G +GvGKtt++ ++ +++++
  gi|242399433|ref|YP_002994858.1|  3 IFITGLPGVGKTTIILKVTKELKN 26
                                      89****************998654 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.5
                                       CBTEEEEEEEESXXHHHHHHHXXHHHHH CS
                            NB-ARC  50 rFdsvawvvvsktdkseeiletilkeLs 77 
                                       +F  +  v v    + e+i ++i+++L 
  gi|242399433|ref|YP_002994858.1| 139 KFKTLGRVYVLTPENREQIRQEIIENLR 166
                                       5556666666666677777777777775 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0    0.0031       1.4       1      25 [.       3      27 ..       3      45 .. 0.85
   2 ?    3.8   0.0      0.16        72      48      84 ..      94     129 ..      79     149 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0031
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakallkk 25
                                      i+++G +g+GK+t++ +++k+l ++
  gi|242399433|ref|YP_002994858.1|  3 IFITGLPGVGKTTIILKVTKELKNH 27
                                      789**************99999866 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.16
                      RNA_helicase  48 tgqevvvidDfgqvkdeenpsdlaelirlvsstpypl 84 
                                       ++ +v++id++g+++ + + +  + + ++++s ++ l
  gi|242399433|ref|YP_002994858.1|  94 ENADVIIIDEIGAMEYK-SREFAKSIDEVIKSEKVLL 129
                                       57899********9955.4558888888888887765 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   0.00011     0.051       2      32 ..       3      39 ..       3     135 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00011
                            AAA_33  2 vllvGlpGsGKstlaerllkklg......avllssdt 32
                                      +++ GlpG+GK+t + ++ k+l+      + ++++ +
  gi|242399433|ref|YP_002994858.1|  3 IFITGLPGVGKTTIILKVTKELKnhdlkvGGFVTQEI 39
                                      5789**************9998866666655555555 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   0.00018     0.084       1      47 [.       5      52 ..       5      60 .. 0.87
   2 ?   -0.7   0.0         3   1.4e+03     130     130 ..     109     109 ..      63     164 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00018
                                      EEESTTSSHHHHHHHHHHHHTSEEEEHHHHHHHHH.HCT-HHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx RF
                               ADK  1 llGaPgaGKGtqaeklvkkyglahlstGdllRaev.ksgtelGkeake 47
                                      + G Pg GK t   k++k+++   l  G ++ +e+ ++g ++G ++k+
  gi|242399433|ref|YP_002994858.1|  5 ITGLPGVGKTTIILKVTKELKNHDLKVGGFVTQEIrEKGKRVGFKIKA 52
                                      679*******************************94567788999986 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 3
                                       H CS
                                       x RF
                               ADK 130 k 130
                                        
  gi|242399433|ref|YP_002994858.1| 109 Y 109
                                       1 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   0.00013     0.061      15      57 ..       1      43 [.       1      83 [. 0.81

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00013
                                      EEEEEEESTTSSHHHHHHHHHHSSCEECSSSSSEEEEEEEETT CS
                               Arf 15 lrilllGLDnaGKtTilkklkleelvttvPTigfnveeleikn 57
                                      ++i + GL + GKtTi+ k+++e  ++     gf ++e++ k+
  gi|242399433|ref|YP_002994858.1|  1 MKIFITGLPGVGKTTIILKVTKELKNHDLKVGGFVTQEIREKG 43
                                      79*****************999888888888889888887753 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 ?    6.7   0.0    0.0085       3.9      22      51 ..       3      31 ..       2      45 .. 0.79
   2 ?    4.6   0.1     0.039        18     114     156 ..      86     120 ..      66     133 .. 0.63

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0085
                                      EEEEEXTTSSHHHHHHHHHHHHHHCSTSEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C 22 iiiAarpsmGktalalniaenaavkeklpv 51
                                      i i + p++Gkt++ l++ ++  + ++l+v
  gi|242399433|ref|YP_002994858.1|  3 IFITGLPGVGKTTIILKVTKELKN-HDLKV 31
                                      57899*************998775.55555 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.039
                                       HHHHHHHHHHHHHHTTEEEEEEEEGGGTBTSCSSSCCCHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C 114 vseirskarrlkkekglgliviDyLqlmegseekenreqevse 156
                                       vs     +rr    ++ ++i+iD +  me ++  ++  + + e
  gi|242399433|ref|YP_002994858.1|  86 VSA----IRRA--VENADVIIIDEIGAMEYKS--REFAKSIDE 120
                                       222....3333..25789**********9653..233334444 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.6   0.00035      0.16       1      23 [.       2      33 ..       2     169 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00035
                            AAA_28  1 kivitGgestGKTtll....eaLaar.....g 23
                                      ki itG ++ GKTt++    ++L+++     g
  gi|242399433|ref|YP_002994858.1|  2 KIFITGLPGVGKTTIIlkvtKELKNHdlkvgG 33
                                      799***********996666777777555543 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.2    0.0099       4.6      29      51 ..       5      27 ..       1      45 [. 0.85
   2 ?    5.0   0.0     0.047        22     125     163 ..      88     128 ..      54     161 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0099
                                      EEESTTSTHHHHHHHHHHHH-S. CS
                            ResIII 29 ikmaTGtGKTlvaaklierllkk 51
                                      i    G+GKT +++k++++l+++
  gi|242399433|ref|YP_002994858.1|  5 ITGLPGVGKTTIILKVTKELKNH 27
                                      66667**************9985 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.047
                                       ..HHHTTT-SEEEEETGGGTTS...TTTHHHHHT---SEEE CS
                            ResIII 125 seellrdrfdviiiDEaHrlgak..kswreilekfkeavll 163
                                         +   ++ dviiiDE   + +k  ++ ++i e +k+ ++l
  gi|242399433|ref|YP_002994858.1|  88 AIRRAVENADVIIIDEIGAMEYKsrEFAKSIDEVIKSEKVL 128
                                       5566678889******9888886433555577666654444 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   0.00061      0.28       3      30 ..       3      30 ..       1      36 [. 0.89
   2 ?   -0.7   0.0       2.5   1.1e+03      85     131 ..      99     136 ..      77     165 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00061
                                      EEEEC-TTTCHHHHHHHHHHHHCTS-SC CS
                             NACHT  3 vilqGeaGsGKTtLlqklalawaegklp 30
                                      ++++G +G+GKTt + k+  +++  +l+
  gi|242399433|ref|YP_002994858.1|  3 IFITGLPGVGKTTIILKVTKELKNHDLK 30
                                      799*******************998876 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.5
                                       EEEE-STT-SS-TCH.........HHHHHCTTTTT--EEEEEEECCC CS
                             NACHT  85 lilDglDelvtdlgqkekqpvrtlLselirkkllpeasllltvrpra 131
                                       +i+D +  ++ + ++         +++ i + + +e  ll+tv+ r 
  gi|242399433|ref|YP_002994858.1|  99 IIIDEIGAMEYKSRE---------FAKSIDEVIKSEKVLLATVHRRY 136
                                       555555555554444.........44444444444555555554444 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1    0.0013       0.6      21      45 ..       4      35 ..       2      53 .. 0.71
   2 ?    2.5   0.3      0.23     1e+02     209     226 ..      87     104 ..      81     111 .. 0.79
   3 ?   -0.5   0.0       1.9   8.7e+02     182     213 ..     112     142 ..     105     149 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0013
                            AAA_11 21 liqGPPGtgKTktivellsqllsr.......r 45
                                       i G PG gKT+ i+++ ++l ++        
  gi|242399433|ref|YP_002994858.1|  4 FITGLPGVGKTTIILKVTKELKNHdlkvggfV 35
                                      58999****************65455444431 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.23
                            AAA_11 209 klleklakkfdvviIDEA 226
                                       ++++++ ++ dv+iIDE 
  gi|242399433|ref|YP_002994858.1|  87 SAIRRAVENADVIIIDEI 104
                                       5677777899*******5 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 1.9
                            AAA_11 182 eeaeesleeevldeaeivltTlsgagskllek 213
                                       +e+ +s+ +ev+++ ++ l+T++    +++++
  gi|242399433|ref|YP_002994858.1| 112 REFAKSI-DEVIKSEKVLLATVHRRYVDKFKT 142
                                       4455555.999999999999998776666665 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.015       6.8      37      52 ..       4      19 ..       2      28 .. 0.88
   2 ?    2.7   0.2      0.17        79     134     158 ..      90     111 ..      69     128 .. 0.72
   3 ?   -1.6   0.0       3.7   1.7e+03      86     111 ..     132     154 ..     121     168 .. 0.58

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.015
                            AAA_25 37 llaGapgtGKttlald 52
                                       ++G pg+GKtt+ l 
  gi|242399433|ref|YP_002994858.1|  4 FITGLPGVGKTTIILK 19
                                      689*********9986 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.17
                            AAA_25 134 eaaieevegvrlvviDplsralggd 158
                                       +   ++ve++++++iD + ++   +
  gi|242399433|ref|YP_002994858.1|  90 R---RAVENADVIIIDEIGAMEYKS 111
                                       3...456679******998875555 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 3.7
                            AAA_25  86 lrrRlravgealrddarllvldlagv 111
                                       ++rR+   +++l   +r++vl+ +++
  gi|242399433|ref|YP_002994858.1| 132 VHRRYVDKFKTL---GRVYVLTPENR 154
                                       555555555555...55555554333 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.6    0.0028       1.3       2      42 ..       6      50 ..       5      60 .. 0.74
   2 ?    2.6   0.2       0.2        92     120     185 .]      98     161 ..      79     162 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0028
                                      EESTTSSHHHHHHHHHHHHHHTTE...EEEESS..STTSHHHHHH CS
                   Thymidylate_kin  2 EGlDGaGKttqaellkerlkeegik..vvltre..pggteiGeki 42
                                       Gl G+GKtt++ ++ + lk+  +k   ++t+e  ++g ++G ki
  gi|242399433|ref|YP_002994858.1|  6 TGLPGVGKTTIILKVTKELKNHDLKvgGFVTQEirEKGKRVGFKI 50
                                      6999*****************999855466666333445555555 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.2
                                       EEEEEESSHHHHHTSCCTTSSTTTSHHHHHHHHHHHHHHHHHHHHTTSTEEEEETTS-HHHHHHHH CS
                   Thymidylate_kin 120 ltflldvdpevalkRlakrdeldeeeeeqldflrkvrerylelakederiliidasksieevheeI 185
                                       ++++ ++   +   R  +++  de ++ ++  l +v++ry + +k+ +r++++ + ++ e++++eI
  gi|242399433|ref|YP_002994858.1|  98 VIIIDEIGAMEYKSREFAKSI-DEVIKSEKVLLATVHRRYVDKFKTLGRVYVL-TPENREQIRQEI 161
                                       555555555555555555555.4555555555778888888888877777777.555566666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       795  (0.0443416); expected 358.6 (0.02)
Passed bias filter:                      567  (0.0316247); expected 358.6 (0.02)
Passed Vit filter:                       110  (0.00613531); expected 17.9 (0.001)
Passed Fwd filter:                        39  (0.00217525); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              39  [number of targets reported over threshold]
# CPU time: 0.65u 0.30s 00:00:00.95 Elapsed: 00:00:00.48
# Mc/sec: 1074.27
//
Query:       gi|242399434|ref|YP_002994859.1|  [L=243]
Description: iron ABC transporter ATPase [Thermococcus sibiricus MM 739]
Scores for complete 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-30  104.0   0.0    1.4e-29  103.3   0.0    1.3  1  ABC_tran        ABC transporter
    3.7e-09   36.8   0.2    8.5e-06   25.8   0.0    2.1  2  AAA_21          AAA domain, putative AbiEii toxin, Type IV TA
    1.1e-08   34.8   0.6     0.0012   18.4   0.1    2.1  2  SMC_N           RecF/RecN/SMC N terminal domain
    9.4e-06   26.3   0.0    1.3e-05   25.8   0.0    1.6  1  AAA_23          AAA domain
    4.5e-05   23.5   0.0     0.0001   22.3   0.0    1.7  1  Rad17           Rad17 P-loop domain
    4.5e-05   23.1   0.1    8.8e-05   22.2   0.1    1.4  1  AAA_29          P-loop containing region of AAA domain
    0.00022   21.5   0.0    0.00048   20.4   0.0    1.6  1  AAA_22          AAA domain
     0.0003   20.6   0.0    0.00094   19.0   0.0    1.6  1  AAA_15          AAA ATPase domain
    0.00036   19.5   0.0       0.32    9.8   0.0    2.1  2  ABC_ATPase      Predicted ATPase of the ABC class
    0.00047   19.8   0.0     0.0008   19.1   0.0    1.3  1  AAA_27          AAA domain
    0.00053   19.8   0.0     0.0014   18.4   0.0    1.7  1  AAA_30          AAA domain
    0.00067   19.6   0.1     0.0015   18.5   0.1    1.6  1  RsgA_GTPase     RsgA GTPase
    0.00081   19.3   0.2       0.11   12.4   0.0    2.2  2  NTPase_1        NTPase
     0.0034   17.6   0.1      0.024   14.8   0.1    2.4  1  AAA_33          AAA domain
     0.0055   15.9   0.0     0.0085   15.3   0.0    1.2  1  PIF1            PIF1-like helicase
  ------ inclusion threshold ------
      0.016   15.6   0.0      0.022   15.1   0.0    1.5  1  AAA_16          AAA ATPase domain
      0.021   14.2   0.0      0.039   13.3   0.0    1.5  2  Mg_chelatase    Magnesium chelatase, subunit ChlI
      0.035   14.2   0.4      0.077   13.1   0.1    1.7  2  MMR_HSR1        50S ribosome-binding GTPase
      0.037   14.1   0.0       0.26   11.3   0.0    2.1  2  AAA_14          AAA domain
      0.044   13.7   0.1      0.095   12.6   0.1    1.5  1  MobB            Molybdopterin guanine dinucleotide synthesis 
      0.045   13.7   0.1      0.098   12.6   0.1    1.6  1  NACHT           NACHT domain
      0.053   13.4   0.1       0.11   12.5   0.1    1.5  1  Thioredoxin_13  Thioredoxin-like domain
      0.067   13.6   0.2       0.18   12.2   0.1    1.9  2  AAA             ATPase family associated with various cellula
      0.075   12.9   0.0      0.096   12.6   0.0    1.5  1  ATPase_2        ATPase domain predominantly from Archaea
      0.097   11.6   0.0       0.16   10.9   0.0    1.3  1  MeaB            Methylmalonyl Co-A mutase-associated GTPase M
      0.099   11.5   0.1       0.34    9.7   0.0    1.7  2  AFG1_ATPase     AFG1-like ATPase
       0.13   12.5   0.2       0.29   11.4   0.2    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 !  103.3   0.0   2.1e-32   1.4e-29       1     137 []      21     158 ..      21     158 .. 0.95

  Alignments for each domain:
  == domain 1  score: 103.3 bits;  conditional E-value: 2.1e-32
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       lknvs++ keg ++aivG+nGaGKStLlk+l g+lkp +G  +l+g +l + + ++  k i+++pq +      tv+
  gi|242399434|ref|YP_002994859.1|  21 LKNVSFSAKEGDLLAIVGPNGAGKSTLLKCLVGMLKP-KGYAKLNGINLLNLKPKERAKYISYVPQSSYPEFAFTVE 96 
                                       79**********************************8.9************999*************8888888899 PP

                                       HH......HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en......esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       e       +    +e+al+++g+ e k++ v    ++LSgG+ q v +aral++ ++++llDEpt+
  gi|242399434|ref|YP_002994859.1|  97 EFvelgsyATGGSVEDALKTVGMWERKHELV----TKLSGGEYQLVLVARALAQGSNVMLLDEPTS 158
                                       9999988777778************999999....*****************************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 !   25.8   0.0   1.3e-08   8.5e-06       2      66 ..      34      99 ..      33     129 .. 0.79
   2 !    9.5   0.0    0.0012      0.79     244     290 ..     137     178 ..     117     184 .. 0.70

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 1.3e-08
                            AAA_21  2 nvliGpNgsGKSnLLdaldllarl.....drdvegltdelsggggirkipslldlydpeipfefeieefl 66
                                       +++GpNg+GKS+LL++l ++        ++ ++ l+ ++    ++r    ++ + +  ++f+f++eef+
  gi|242399434|ref|YP_002994859.1| 34 LAIVGPNGAGKSTLLKCLVGMLKPkgyakLNGINLLNLKP----KERAKYISYVPQSSYPEFAFTVEEFV 99
                                      58****************9998778877777777777777....77777777777777777777777665 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0012
                            AAA_21 244 llalltallralkkgsllliDEpEngLHPkllrrllellkelsrnga 290
                                       l   ++   ++++ + + l+DEp ++L+     r++ llk l++   
  gi|242399434|ref|YP_002994859.1| 137 L---VLVARALAQGSNVMLLDEPTSHLDINHALRIMNLLKTLKK--E 178
                                       4...444444444459************9666667777765554..4 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   1.9e-05     0.013      24      45 ..      31      52 ..       3      78 .. 0.71
   2 !   18.4   0.1   1.8e-06    0.0012     136     198 ..     129     187 ..     102     205 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.9e-05
                                      SSEEEEEESTTSSHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 24 ksftaivGpNGSGKsnlldAil 45
                                        + aivGpNG+GKs ll  + 
  gi|242399434|ref|YP_002994859.1| 31 GDLLAIVGPNGAGKSTLLKCLV 52
                                      34679************99875 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 1.8e-06
                                       CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislr 198
                                        LSgGe +Lv +a  +A    + + ++llDe  ++LD ++  ++ +llk+ +k+  ++ + ++
  gi|242399434|ref|YP_002994859.1| 129 KLSGGEYQLVLVARALA----QGSNVMLLDEPTSHLDINHALRIMNLLKTLKKEKIVVTVMHD 187
                                       79*******98776665....78899*************************977655544444 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   1.9e-08   1.3e-05      15      43 ..      24      55 ..       7     237 .. 0.82

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 1.9e-08
                            AAA_23 15 idF...skgltlItGpNGaGKTTildAiklaL 43
                                      + F   +  l +I+GpNGaGK+T+l ++  +L
  gi|242399434|ref|YP_002994859.1| 24 VSFsakEGDLLAIVGPNGAGKSTLLKCLVGML 55
                                      56655556799****************97666 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   1.5e-07    0.0001      32      90 ..      18      76 ..       9     118 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.5e-07
                             Rad17 32 kewlkadvLesrkkriLLisGPsGCgkstvvkvLskelgiklrewlnpvslkepdnqks 90
                                      ke lk  +   ++  +L i GP G gkst +k L   l +k    ln+++l + + ++ 
  gi|242399434|ref|YP_002994859.1| 18 KEVLKNVSFSAKEGDLLAIVGPNGAGKSTLLKCLVGMLKPKGYAKLNGINLLNLKPKER 76
                                      678888888888889**********************************9876555433 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.1   1.3e-07   8.8e-05      17      55 ..      26      64 ..      18      67 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.3e-07
                            AAA_29 17 ieidlkgatlltGpsGsGKSTllDAiqalLvpakkvrfN 55
                                      ++ ++ +   ++Gp+G+GKSTll  +  +L p+  ++ N
  gi|242399434|ref|YP_002994859.1| 26 FSAKEGDLLAIVGPNGAGKSTLLKCLVGMLKPKGYAKLN 64
                                      4444444899***************99999999988888 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   7.2e-07   0.00048       5     114 ..      31     174 ..      27     193 .. 0.61

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 7.2e-07
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaee...........erpevvfvtlpsstsskdllrellralglelka 70 
                                         +l+++G+ G+GK+tll+ l+  l+   +a+            er++++++ ++ss    +++  + ++++l+  a
  gi|242399434|ref|YP_002994859.1|  31 GDLLAIVGPNGAGKSTLLKCLVGMLKPKGYAKLnginllnlkpkERAKYISYVPQSS--YPEFAFTVEEFVELGSYA 105
                                       6789*********************98888888999999998665555555555544..466666666666666666 PP

                            AAA_22  71 ......................erlsseell.ealeqalraravielliiDEaqh.lr..s.eealeeLrs 114
                                                               ls  e+   ++++al +     ++++DE    l+  +  ++++ L++
  gi|242399434|ref|YP_002994859.1| 106 tggsvedalktvgmwerkhelvTKLSGGEYQlVLVARALAQG--SNVMLLDEPTShLDinHaLRIMNLLKT 174
                                       566666455555544444433322222222223333333333..346666665554655413444444444 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   1.4e-06   0.00094      24      54 ..      29      62 ..      20      98 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.4e-06
                            AAA_15 24 e...ltvliGkNnsGKSsilealdlFlnnkekkn 54
                                      +   l  ++G+N++GKS++l+ l  +l+ k + +
  gi|242399434|ref|YP_002994859.1| 29 KegdLLAIVGPNGAGKSTLLKCLVGMLKPKGYAK 62
                                      334699**********************994433 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0   0.00048      0.32     242     264 ..      28      51 ..       6      55 .. 0.80
   2 !    7.7   0.0     0.002       1.3     322     373 ..     129     180 ..     121     202 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00048
                                       E-SS.EEEEEE-TTSSHHHHHHHH CS
                        ABC_ATPase 242 ipkG.vtlIvGggfhGKsTLLeAl 264
                                        ++G + +IvG++  GKsTLL+ l
  gi|242399434|ref|YP_002994859.1|  28 AKEGdLLAIVGPNGAGKSTLLKCL 51 
                                       5778899**************988 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.002
                                       S--HHHHHHHHHHHHHHTT-SEEEEEGGGS-HHHH---HHHHHHS-GGG--B CS
                        ABC_ATPase 322 dASGStsqAanimealeagakllLiDEDtsAtNlmirDermqelvskekepi 373
                                       + SG  +q + +++al  g++++L+DE ts   + +  + m+ l   +ke i
  gi|242399434|ref|YP_002994859.1| 129 KLSGGEYQLVLVARALAQGSNVMLLDEPTSHLDINHALRIMNLLKTLKKEKI 180
                                       569999***********************98777666666666665555554 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   1.2e-06    0.0008      18      47 ..      23      52 ..      20      55 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.2e-06
                            AAA_27 18 sldfsaeeadlhliyGpNEAGKstalrAis 47
                                      +++fsa+e dl  i+GpN AGKst+l+ + 
  gi|242399434|ref|YP_002994859.1| 23 NVSFSAKEGDLLAIVGPNGAGKSTLLKCLV 52
                                      689***********************9876 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   2.1e-06    0.0014       4      47 ..      15      66 ..      12     187 .. 0.57

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.1e-06
                            AAA_30  4 aeQaaaveall..tsgdrvavltGpAGtGKttalkalreaweaag......g 47
                                       +Q+++++++   +++  + +++Gp G+GK+t+lk l+ +++ +g       
  gi|242399434|ref|YP_002994859.1| 15 YDQKEVLKNVSfsAKEGDLLAIVGPNGAGKSTLLKCLVGMLKPKGyaklngI 66
                                      578888877641133445999*****************99999986565552 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1   2.2e-06    0.0015      79     122 ..      11      54 ..       1      64 [. 0.82

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.2e-06
                                       EEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase  79 vllvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallpe 122
                                       v + s ++ke l++++   k+ ++ ++vG+ G+GKStL++ l++ 
  gi|242399434|ref|YP_002994859.1|  11 VSF-SYDQKEVLKNVSFSAKEgDLLAIVGPNGAGKSTLLKCLVGM 54 
                                       444.567789999999999988******************99886 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   0.00017      0.11       3      33 ..      35      66 ..      33      80 .. 0.85
   2 ?    5.2   0.0     0.027        18      89     153 ..     140     207 ..     113     224 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00017
                                      EEE--TTSSHHHHHHHHHHHH...GG.GEEEE CS
                          NTPase_1  3 fiTGppGvGKtTlvkkvlellkssgv.kvgGf 33
                                      +i Gp G GK+Tl+k ++ +lk +g+ k++G+
  gi|242399434|ref|YP_002994859.1| 35 AIVGPNGAGKSTLLKCLVGMLKPKGYaKLNGI 66
                                      789*******************9997345665 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.027
                                       HHHHH.HHH-EEEE--.-STTGGG-HHHHHHHHHHHTTTSEEEEE--SS-.-SHHHHHHHT-TT-EEE CS
                          NTPase_1  89 lrkal.seadviviDE.iGkmElkskkfkeaveevLksekpvlavihrrk.dlalveeirerkdvkvf 153
                                       + +al ++++v+++DE    +  + +  +  + ++Lk+ek+v++v+h  +  l+  +++    +++v 
  gi|242399434|ref|YP_002994859.1| 140 VARALaQGSNVMLLDEpTSHLDINHALRIMNLLKTLKKEKIVVTVMHDLNlALNYADNLLILDKGEVR 207
                                       344444788899999955678888888899999**************987666666666666555555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1   3.6e-05     0.024       1      33 [.      33     113 ..      33     192 .. 0.52

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.6e-05
                            AAA_33   1 lvllvGlpGsGKstlaerllkklg...avllssdt.......................................... 32 
                                       l+ +vG++G+GKstl++ l+  l+   +  l+  +                                          
  gi|242399434|ref|YP_002994859.1|  33 LLAIVGPNGAGKSTLLKCLVGMLKpkgYAKLNGINllnlkpkerakyisyvpqssypefaftveefvelgsyatggs 109
                                       5678*************996555544465555554444444555555555555555555444444444444444444 PP

                            AAA_33  33 ...l 33 
                                          +
  gi|242399434|ref|YP_002994859.1| 110 vedA 113
                                       4443 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.3e-05    0.0085       3      51 ..      14      60 ..      12      66 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.3e-05
                                      -HHHHHHHHHH......HCTS-EEEEESTTSSCHHHHHHHHHHCHCTCC CS
                              PIF1  3 neeQkkvfdaiieavlnekgklfFvtGsgGtgKtflwkallkklrsegk 51
                                      + +Qk+v++++  + ++++g l+ + G  G+gK+ l+k l+ +l+++g 
  gi|242399434|ref|YP_002994859.1| 14 SYDQKEVLKNV--SFSAKEGDLLAIVGPNGAGKSTLLKCLVGMLKPKGY 60
                                      679********..999****************************99875 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   3.3e-05     0.022      21      53 ..      28      59 ..      17     184 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.3e-05
                            AAA_16 21 sgrpelvllsGesGvGKsslvrellralekdgg 53
                                      + ++ l+ ++G+ G GKs+l+++l   l+ + g
  gi|242399434|ref|YP_002994859.1| 28 AKEGDLLAIVGPNGAGKSTLLKCLVGMLKPK-G 59
                                      34457999***************98666665.3 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   5.9e-05     0.039       8      52 ..      17      61 ..      12     119 .. 0.79
   2 ?   -3.1   0.0       6.3   4.2e+03      25      51 ..     150     177 ..     130     188 .. 0.52

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.9e-05
                      Mg_chelatase  8 qeeakraleiaaaGgHnlllvGppGsGKtmlakrlpsllpplsee 52
                                      q+e  + +  +a  g  l +vGp G+GK+ l k+l ++l p   +
  gi|242399434|ref|YP_002994859.1| 17 QKEVLKNVSFSAKEGDLLAIVGPNGAGKSTLLKCLVGMLKPKGYA 61
                                      55666667777778888999******************9887655 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 6.3
                      Mg_chelatase  25 lllvGppGsGKtm.lakrlpsllpplse 51 
                                       ++l+  p s   +  a r+++ll  l++
  gi|242399434|ref|YP_002994859.1| 150 VMLLDEPTSHLDInHALRIMNLLKTLKK 177
                                       3333333333222134455555555544 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   0.00012     0.077       3      22 ..      35      54 ..      33      78 .. 0.87
   2 ?   -2.0   0.0       5.5   3.6e+03      70      70 ..     172     172 ..     126     207 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00012
                                      EEEESTTSSHHHHHHHHHTS CS
                          MMR_HSR1  3 aivGrpNvGKStLinaltge 22
                                      aivG   +GKStL++ l+g 
  gi|242399434|ref|YP_002994859.1| 35 AIVGPNGAGKSTLLKCLVGM 54
                                      8****************984 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 5.5
                                       H CS
                          MMR_HSR1  70 f 70 
                                       +
  gi|242399434|ref|YP_002994859.1| 172 L 172
                                       1 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0    0.0004      0.26       4      46 ..      33      73 ..      30     100 .. 0.70
   2 ?    0.4   0.0      0.95   6.3e+02      61      86 ..     145     169 ..     121     199 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0004
                            AAA_14  4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkl 46
                                      +l+i+G+  +GK+tllk l+  l   ++ +  +n  +  + k 
  gi|242399434|ref|YP_002994859.1| 33 LLAIVGPNGAGKSTLLKCLVGMLK--PKGYAKLNGINLLNLKP 73
                                      689**************9997666..55555555554444433 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.95
                            AAA_14  61 keekktylflDEiqevpewekalksl 86 
                                         ++ ++++lDE     ++ +al+ +
  gi|242399434|ref|YP_002994859.1| 145 A-QGSNVMLLDEPTSHLDINHALRIM 169
                                       3.478889999988877777766643 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   0.00014     0.095       2      28 ..      34      60 ..      33      64 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00014
                              MobB  2 lgivgksgsGKTtLleklipelkargl 28
                                      l+ivg +g+GK tLl+ l+ +lk +g+
  gi|242399434|ref|YP_002994859.1| 34 LAIVGPNGAGKSTLLKCLVGMLKPKGY 60
                                      89*********************9998 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   0.00015     0.098       2      28 ..      33      59 ..      32      78 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00015
                                      CEEEEC-TTTCHHHHHHHHHHHHCTS- CS
                             NACHT  2 lvilqGeaGsGKTtLlqklalawaegk 28
                                      l+++ G++G GK+tLl+ l+  ++ + 
  gi|242399434|ref|YP_002994859.1| 33 LLAIVGPNGAGKSTLLKCLVGMLKPKG 59
                                      789**************9998877665 PP

>> Thioredoxin_13  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   0.00016      0.11      70     122 ..     144     199 ..     122     219 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00016
                                       --TT--EEEETTEEE-GGG...-SHHHHHHHHHHHHHHHHHHGGGS--HHHHHHHH CS
                    Thioredoxin_13  70 vqpgqnalwlNGvaldesd...idpfsLldlLrkErkllnslkklglsseqaskll 122
                                       + +g+n+++l+  +   +    + +++Ll++L+kE+ +++ +++l+l  + a +ll
  gi|242399434|ref|YP_002994859.1| 144 LAQGSNVMLLDEPTSHLDInhaLRIMNLLKTLKKEKIVVTVMHDLNLALNYADNLL 199
                                       56788888888765544333348999*********************999999998 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00028      0.18       3      46 ..      36      80 ..      34     155 .. 0.82
   2 ?   -0.9   0.0       3.1     2e+03      53      53 ..     175     175 ..     138     236 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00028
                                      EESSTTSSHHHHHHHHHHHHT.HEEEEEETTTCSSSSTTHHHHHH CS
                               AAA  3 lyGppGtGKTllakavakelg.vefleisgsellskyvgesekki 46
                                      ++Gp G GK++l k ++  l+   + +++g +ll+   +e++k i
  gi|242399434|ref|YP_002994859.1| 36 IVGPNGAGKSTLLKCLVGMLKpKGYAKLNGINLLNLKPKERAKYI 80
                                      79*****************98544666776666655444444444 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 3.1
                                       H CS
                               AAA  53 a 53 
                                       +
  gi|242399434|ref|YP_002994859.1| 175 L 175
                                       2 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00015     0.096      20      57 ..      31      68 ..      15     197 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00015
                          ATPase_2 20 neiyfiYGpegsGKtaLlkeiienledkdkyviyyial 57
                                       + + i Gp g GK++Llk ++  l+ k++ ++  i+l
  gi|242399434|ref|YP_002994859.1| 31 GDLLAIVGPNGAGKSTLLKCLVGMLKPKGYAKLNGINL 68
                                      5678899*****************99999855544444 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00024      0.16      14      58 ..      16      60 ..       4      66 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00024
                                      HHHHHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT- CS
                              MeaB 14 eakellerllakaGraqvvGltGvPGaGkstlvealglelrrrGk 58
                                      + ke+l++++ +a +   + + G  GaGkstl++ l+  l+ +G+
  gi|242399434|ref|YP_002994859.1| 16 DQKEVLKNVSFSAKEGDLLAIVGPNGAGKSTLLKCLVGMLKPKGY 60
                                      5689999**999************************999998885 PP

>> AFG1_ATPase  AFG1-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0         1   6.9e+02      65      80 ..      34      49 ..       7      57 .. 0.79
   2 ?    9.7   0.0   0.00051      0.34     101     161 ..     121     182 ..     110     188 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1
                       AFG1_ATPase 65 lYlwGgvGrGKtylmd 80
                                      l + G+ G GK+ l+ 
  gi|242399434|ref|YP_002994859.1| 34 LAIVGPNGAGKSTLLK 49
                                      67889*******9986 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00051
                       AFG1_ATPase 101 arvhdeltklrkekdplaivadrlaeearvlCfDEfevs.DiadamllsrLleaLfargvtl 161
                                        r h+ +tkl++++  l  va +la+ ++v+ +DE + + Di  a+ +  Ll+ L + ++++
  gi|242399434|ref|YP_002994859.1| 121 ERKHELVTKLSGGEYQLVLVARALAQGSNVMLLDEPTSHlDINHALRIMNLLKTLKKEKIVV 182
                                       5779999****************************76655*******************997 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   0.00044      0.29       8      48 ..      29      69 ..      22     189 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00044
                            AAA_19  8 lkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillv 48
                                       + ++l+++++ G GK+++lk+ v +l+  g  k++ i l+
  gi|242399434|ref|YP_002994859.1| 29 KEGDLLAIVGPNGAGKSTLLKCLVGMLKPKGYAKLNGINLL 69
                                      56778999*******************99998888777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); expected 358.6 (0.02)
Passed bias filter:                      550  (0.0306766); expected 358.6 (0.02)
Passed Vit filter:                       103  (0.00574488); 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: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 1542.59
//
Query:       gi|242399435|ref|YP_002994860.1|  [L=332]
Description: iron ABC transporter [Thermococcus sibiricus MM 739]
Scores for complete 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-90  302.4  28.6    3.8e-90  302.1  28.6    1.0  1  FecCD            FecCD transport family
  ------ inclusion threshold ------
        3.3    8.2   7.6    3.9e+02    1.5   7.6    2.7  1  Phage_holin_3_1  Phage holin family (Lysis protein S)


Domain annotation for each model (and alignments):
>> FecCD  FecCD transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  302.1  28.6   4.3e-94   3.8e-90       3     312 .]      12     324 ..       9     324 .. 0.96

  Alignments for each domain:
  == domain 1  score: 302.1 bits;  conditional E-value: 4.3e-94
                             FecCD   3 llllllslllgavkispsevfeallgka..........dsleaeivlelrlprvlaallvGaaLavaGallQtvtrN 69 
                                       +ll+ll +++g+vkis+s+++++++ ++           + +a i+l++rlpr+++a lvG++La aG+  Q++++N
  gi|242399435|ref|YP_002994860.1|  12 ILLILLGIAVGPVKISLSDILASFSLENikiafsrpnmLKGNAYIILQIRLPRIILAYLVGVSLASAGTASQALFKN 88 
                                       6899******************9887777777777655444445********************************* PP

                             FecCD  70 pLadPsilGissgaalgavlalllllgslslfalplaaflgallalllvlllarkrkgasplkliLaGiavsallsa 146
                                       pLadP+i+Gis gaa+ga la+l++      ++++++a++ga+la++ v+ +a+ ++++   +l+LaGia+++++sa
  gi|242399435|ref|YP_002994860.1|  89 PLADPYIIGISGGAAVGASLAALYF-----PQYMSIFALFGAVLAVFTVYKIAKVNGHIPVDTLLLAGIALGFFTSA 160
                                       ***********************98.....67899****************************************** PP

                             FecCD 147 ltsllllllneealesilfwllGslsgaswskvllllvllllllllllllarkldllalgdetAkslGvnvervrll 223
                                       lts+ll++  +ea+++++fwl+G+++g +w++v l+l  ++l++++l++  ++l+ll lg+e + s+G++++ +r l
  gi|242399435|ref|YP_002994860.1| 161 LTSYLLYV-RKEAIHNAIFWLMGTFNGSEWDDVKLVLFSSILGVFFLFFTWKELNLLLLGEE-SVSMGLDINLYRKL 235
                                       ******99.99*************************************************97.689*********** PP

                             FecCD 224 llllvalltavavalvGpigFvGLivPhiarllvgadhrkllplsallGallllladllarlllsptelpvgivtal 300
                                       ++ +++llt+ ava +G+igFvGLi Ph +r+l+g++h++llp+sal+G+ l+++ad+lar+ll+p+e+pvgi+tal
  gi|242399435|ref|YP_002994860.1| 236 IIGVISLLTSFAVATSGIIGFVGLISPHAMRILFGPNHKRLLPASALFGGSLMVFADILARVLLRPSEIPVGIITAL 312
                                       ***************************************************************************** PP

                             FecCD 301 iGapffiylllr 312
                                       +Gapffiyll++
  gi|242399435|ref|YP_002994860.1| 313 FGAPFFIYLLMK 324
                                       **********97 PP

>> Phage_holin_3_1  Phage holin family (Lysis protein S)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   7.6     0.044   3.9e+02      63      85 ..     237     259 ..     102     269 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.044
                   Phage_holin_3_1  63 lellglpaslavviggliGflGv 85 
                                       + +++l +s+av+++g+iGf+G 
  gi|242399435|ref|YP_002994860.1| 237 IGVISLLTSFAVATSGIIGFVGL 259
                                       45567779999999999999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       768  (0.0428356); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); 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):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2022.98
//
Query:       gi|242399436|ref|YP_002994861.1|  [L=333]
Description: Met-10+ like protein [Thermococcus sibiricus MM 739]
Scores for complete 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-71  237.8   1.3    1.3e-70  237.2   1.3    1.3  1  Met_10           Met-10+ like-protein
    8.5e-19   67.2   1.5    2.8e-18   65.6   1.5    1.9  1  Trm5_N           tRNA methyltransferase 5 N-terminal domain
    5.6e-07   29.2   0.0    1.4e-06   27.9   0.0    1.6  2  PrmA             Ribosomal protein L11 methyltransferase (Prm
    7.5e-06   25.6   0.0    1.6e-05   24.5   0.0    1.5  1  MTS              Methyltransferase small domain
    4.8e-05   23.0   0.0    7.5e-05   22.4   0.0    1.4  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
    0.00012   21.3   0.0    0.00019   20.7   0.0    1.4  1  TRM              N2,N2-dimethylguanosine tRNA methyltransfera
    0.00025   20.7   0.0     0.0093   15.6   0.0    2.3  2  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
    0.00052   20.7   0.0     0.0017   19.0   0.0    1.9  1  Methyltransf_25  Methyltransferase domain
     0.0044   16.8   0.0      0.053   13.3   0.0    2.1  2  Methyltransf_31  Methyltransferase domain
  ------ inclusion threshold ------
       0.05   12.6   0.0      0.092   11.7   0.0    1.4  1  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase


Domain annotation for each model (and alignments):
>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  237.2   1.3   7.5e-74   1.3e-70       2     199 .]      85     280 ..      84     280 .. 0.99

  Alignments for each domain:
  == domain 1  score: 237.2 bits;  conditional E-value: 7.5e-74
                                       EEEEETTEEEEEB-TTSSHHHHHHHHHHHHHS.S-SCEEEE-S-SBTTTTB--EEEEEES-.SEEEEEETTEEEEEE CS
                            Met_10   2 kfeiiGdvvilnlreelkeykkvigevildkt.kvktvlrkvsevegefRtfelevlaGsdstetihkEngcrfklD 77 
                                       +f+iiGd++i++l+eel  + k ig++il+++ ++k+v+ k s+v+ge+R++el +laG+++te ih+Eng+r+klD
  gi|242399436|ref|YP_002994861.1|  85 SFDIIGDIAIIELPEELISHGKNIGKAILKVHkHIKAVFAKGSKVSGEYRVRELLHLAGENRTEAIHRENGIRLKLD 161
                                       79******************************9******************************************** PP

                                       TTTS---GGGHHHHHHHHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEE CS
                            Met_10  78 vskvyfsskleaErerlaklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvk 154
                                       v+kvyfs++l++Er+r+ + ++egevV d+fAG+Gp++i +ak  k k+v+a d+nP +++yl+en klNkve+ + 
  gi|242399436|ref|YP_002994861.1| 162 VAKVYFSPRLATERMRVFERAKEGEVVFDMFAGVGPYSILLAK--KVKMVFACDVNPIAIRYLEENKKLNKVENLI- 235
                                       *******************************************..*******************************. PP

                                       EEES-GGG---TT-EEEEEE--TTTGGGGHHHHHHHEEEEEEEEE CS
                            Met_10 155 pileDgrevireqladrvvmnlpksaieFldkvlaalkdggvihy 199
                                       pil+D+r+v+ + +adrv+mnlpk a+eFl++++  +++ggvihy
  gi|242399436|ref|YP_002994861.1| 236 PILGDVRKVAGQVKADRVIMNLPKFAHEFLKEAMISVRKGGVIHY 280
                                       ********************************************9 PP

>> Trm5_N  tRNA methyltransferase 5 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.6   1.5   1.5e-21   2.8e-18       1      47 []       6      52 ..       6      52 .. 0.97

  Alignments for each domain:
  == domain 1  score: 65.6 bits;  conditional E-value: 1.5e-21
                                      EEEEEGGGHHHHHHHHHHTT-B-TTS--EEETTEEEEEB-S--HHHH CS
                            Trm5_N  1 cikVpkkegEkvRkkLlekglLdrnyKIksdddylyIPvkeepegye 47
                                      +ikVpkke+Ek+Rk Lle++lLd n+KIk+++d++++P+ke ++g+e
  gi|242399436|ref|YP_002994861.1|  6 GIKVPKKEAEKIRKQLLELNLLDVNFKIKHQNDFVIFPIKERIKGFE 52
                                      7*****************************************99976 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.1     2e+03       7      65 ..       7      61 ..       4      78 .. 0.67
   2 !   27.9   0.0     8e-10   1.4e-06     159     261 ..     182     283 ..     172     311 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.1
                              PrmA  7 vttkkeaeeavsniLeelgakgvaiedsklleeedifepaleeeelkeevkvkalfkee 65
                                      +++ k+++e++ + L el+   v ++ ++ +++  if   + +e++k    +++ f++ 
  gi|242399436|ref|YP_002994861.1|  7 IKVPKKEAEKIRKQLLELNLLDVNFKIKH-QNDFVIF---PIKERIKGFEIIETTFEKA 61
                                      77888888889888888888888887666.4444444...4555555555566666554 PP

  == domain 2  score: 27.9 bits;  conditional E-value: 8e-10
                              PrmA 159 vkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseellk...eekadviva 232
                                        kege v+D+ +G G  +i  ak   k v+a D++++A++  +eN +lNkve+ + +   +++ k   + kad ++ 
  gi|242399436|ref|YP_002994861.1| 182 AKEGEVVFDMFAGVGPYSILLAK-KVKMVFACDVNPIAIRYLEENKKLNKVENLIPIL--GDVRKvagQVKADRVIM 255
                                       688999*************9888.6899*************************99774..44443335799****** PP

                              PrmA 233 NILaevlielaedikklvkeggllilSGi 261
                                       N L +   e++++++  v++gg++   G 
  gi|242399436|ref|YP_002994861.1| 256 N-LPKFAHEFLKEAMISVRKGGVIHYYGF 283
                                       *.789999999999999999999877775 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   8.9e-09   1.6e-05      31     128 ..     184     271 ..     169     310 .. 0.79

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 8.9e-09
                                       TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTSTTS-EEEEEE--- CS
                               MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvleeveekkfdlivsNPP 106
                                       + + v D+ +G+G+ ++ lak+ +   v ++dv+  A++  +en + nk+e +  +  dv + + + k d +++N P
  gi|242399436|ref|YP_002994861.1| 184 EGEVVFDMFAGVGPYSILLAKKVKM--VFACDVNPIAIRYLEENKKLNKVEnLIPILGDVRKVAGQVKADRVIMNLP 258
                                       445588***************9988..9***********************9888999****9999*********87 PP

                                       STTTCHCHHHHHHHHHHHHHHH CS
                               MTS 107 fhagkatelavaeeliaeAkea 128
                                                  a+e+++eA   
  gi|242399436|ref|YP_002994861.1| 259 K---------FAHEFLKEAMIS 271
                                       2.........344455555555 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 !   22.4   0.0   4.2e-08   7.5e-05       2      71 ..     186     254 ..     185     310 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 4.2e-08
                   Methyltransf_15   2 rvilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklklekik 71 
                                       +v+ D+f+G G  +i +a++ + v+a ++n+  +   ++N ++  v++ i ++lgdv ++  ++k +++ 
  gi|242399436|ref|YP_002994861.1| 186 EVVFDMFAGVGPYSILLAKKVKMVFACDVNPIAIRYLEENKKLNKVENLI-PILGDVRKVAGQVKADRVI 254
                                       5899****************************************998766.899****987777766653 PP

>> TRM  N2,N2-dimethylguanosine tRNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   1.1e-07   0.00019      52     149 ..     187     278 ..     125     280 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.1e-07
                                       EEEESS-TTSHHHHHHHHH-S-EEEEEEE-S-HHHHHHHHHHHHHTT--GGEEEE-S-HHHHHC--SS-EEEEEE-- CS
                               TRM  52 kvldaLsasGlRaiRfalEvpgvkevlaNDisekAvelikeNvklneveeivvineddAnvllaekkkrfdviDlDP 128
                                        v+d +++ G  +i  a+    vk v+a D+++ A+  ++eN kln+ve+++ i   d + +  ++k    ++ l  
  gi|242399436|ref|YP_002994861.1| 187 VVFDMFAGVGPYSILLAKK---VKMVFACDVNPIAIRYLEENKKLNKVENLIPILG-DVRKVAGQVKADRVIMNLPK 259
                                       5889999999999988887...999*************************776666.99999988888888888888 PP

                                       SS--GGGHHHHHHHEEEEEEE CS
                               TRM 129 fGspapfldsavqsvkekglL 149
                                       f  + +fl  a+ sv+++g++
  gi|242399436|ref|YP_002994861.1| 260 F--AHEFLKEAMISVRKGGVI 278
                                       8..689999999999999876 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 !   15.6   0.0   5.2e-06    0.0093       7      88 ..     183     258 ..     178     262 .. 0.87
   2 !    6.3   0.0    0.0038       6.8     106     152 ..     250     299 ..     248     317 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 5.2e-06
                                       -TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC..EEEE CS
                   Methyltr_RsmB-F   7 qeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlggelfDri 83 
                                       +e+e ++D+ a+ G    ++    k+ + v+A d+n   ++ ++en k   v+n+i + +D+rk+    g+ + Dr+
  gi|242399436|ref|YP_002994861.1| 183 KEGEVVFDMFAGVGPYSILL---AKKVKMVFACDVNPIAIRYLEENKKLNKVENLIPILGDVRKVA---GQVKADRV 253
                                       7999*******999866555...56799*******************9999************995...55557*** PP

                                       EEEE- CS
                   Methyltr_RsmB-F  84 LlDaP 88 
                                       ++  P
  gi|242399436|ref|YP_002994861.1| 254 IMNLP 258
                                       99887 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0038
                                       -HHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEES--S...TTTTHHHHHH CS
                   Methyltr_RsmB-F 106 kekdiaqlaklqkellsaaidllkkgGvlvYsTCsvl...veEneeviee 152
                                        ++ i++l k  +e l+ a+ +++kgGv+ Y   s +    eE  e ie+
  gi|242399436|ref|YP_002994861.1| 250 ADRVIMNLPKFAHEFLKEAMISVRKGGVIHYYGFSHEenlFEEHLEKIEK 299
                                       677899999**********************8887641114555555554 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   9.6e-07    0.0017       1      97 []     188     276 ..     188     276 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 9.6e-07
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEEEST.GG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvssga.lh 75 
                                       v d+ +G G +++ lak++  + v ++D+++ ++++ +e+ + +++ n+  + gd++++  +  + D v+++   + 
  gi|242399436|ref|YP_002994861.1| 188 VFDMFAGVGPYSILLAKKV--KMVFACDVNPIAIRYLEENKKLNKVeNLIPILGDVRKVAGQ-VKADRVIMNLPkFA 261
                                       78999*************9..9*******************999999***********9865.59999999643333 PP

                                       GSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  76 hlsdedlekalkeiarvLkpgG 97 
                                              +++lke+   +++gG
  gi|242399436|ref|YP_002994861.1| 262 -------HEFLKEAMISVRKGG 276
                                       .......356777666666666 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.15   2.7e+02      31     102 ..      48     117 ..      38     159 .. 0.67
   2 !   13.3   0.0   2.9e-05     0.053       3     119 ..     184     290 ..     182     325 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.15
                   Methyltransf_31  31 vvGiDiseeaielArenaqklgldnveFeqgdiee.leklledekfDlilsnevl....naladpdkileeiervlk 102
                                       + G++i e+  e+A+++   + + +v    ++ +  l+     ++fD+i + +++     ++++ ++i + i +v k
  gi|242399436|ref|YP_002994861.1|  48 IKGFEIIETTFEKATKR--PHSYREVVNIPSELQPlLP-----SSFDIIGDIAIIelpeELISHGKNIGKAILKVHK 117
                                       66777777777777775..7777766666666666555.....7899999987777777555555555554444433 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 2.9e-05
                   Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlil 79 
                                       +g +v D  +G G +++ la+++ +   v+  D ++ ai++ +en + ++++n+    gd+ +   +    k D ++
  gi|242399436|ref|YP_002994861.1| 184 EGEVVFDMFAGVGPYSILLAKKVKM---VFACDVNPIAIRYLEENKKLNKVENLIPILGDVRKVAGQ---VKADRVI 254
                                       678999**************88755...***********************************5533...5688888 PP

                   Methyltransf_31  80 snevlnaladpdkileeiervlkpggilliedprllaelp 119
                                        n +    ++  ++l+e+   +++gg++    ++++++l 
  gi|242399436|ref|YP_002994861.1| 255 MNLP----KFAHEFLKEAMISVRKGGVIHYYGFSHEENLF 290
                                       8644....34445555555555666666655555444444 PP

>> tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   5.2e-05     0.092     204     251 ..     187     234 ..     170     254 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.2e-05
                   tRNA_U5-meth_tr 204 dllelycGnGnfslalarnfekvlateiakssveaaqyniaankidnv 251
                                        +++++ G G +s+ la++++ v+a ++   ++     n + nk++n+
  gi|242399436|ref|YP_002994861.1| 187 VVFDMFAGVGPYSILLAKKVKMVFACDVNPIAIRYLEENKKLNKVENL 234
                                       46799******************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       928  (0.0517597); expected 358.6 (0.02)
Passed bias filter:                      704  (0.039266); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.63u 0.32s 00:00:00.95 Elapsed: 00:00:00.51
# Mc/sec: 1983.10
//
Query:       gi|242399437|ref|YP_002994862.1|  [L=230]
Description: nucleotidyltransferase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.3e-08   33.3   2.2    9.1e-08   32.3   2.2    1.7  1  NTP_transf_2  Nucleotidyltransferase domain
    4.2e-05   23.6   0.7    9.3e-05   22.4   0.3    1.8  2  Polbeta       Polymerase beta, Nucleotidyltransferase
  ------ inclusion threshold ------
      0.032   14.4   0.0      0.061   13.5   0.0    1.4  1  FANC_SAP      Fanconi anemia-associated nuclease SAP 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 !   32.3   2.2   1.5e-11   9.1e-08       9      75 ..      14      90 ..       6     140 .. 0.76

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 1.5e-11
                                      HHHTT....TSEEEEEHHHHCTTSCTT.SSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEEEEE........ CS
                      NTP_transf_2  9 kelep....vakvvlfGSyarGtalkg.SDiDllvvlpeevsrekkeegleklaeiikfleellglevdlv........ 74
                                      +++e+     +++vl+GS++rG++ kg SD+D++ v++ e +          +   +k+++ + ++evd+         
  gi|242399437|ref|YP_002994862.1| 14 EKNEKlkdeLYSLVLYGSAVRGDFIKGvSDLDFFAVVKTEDK-----ILPSLKEILEKCTKDIDAVEVDVAweflknld 87
                                      3333334468******************************76.....44466777888999999*****9976655555 PP

                                      ..C CS
                      NTP_transf_2 75 ..t 75
                                        +
  gi|242399437|ref|YP_002994862.1| 88 glF 90
                                      552 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.3   1.6e-08   9.3e-05       1      72 [.      11      79 ..       7      95 .. 0.73
   2 ?   -2.3   0.0       0.8   4.8e+03      85      91 ..     111     117 ..      96     147 .. 0.68

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.6e-08
                                      -STTTTHHHHHHHHSTTEEEEEE-S----.--EEEEEEEESS---HHHHHHHHHHHHHH.SSSEEEEEETTTS CS
                           Polbeta  1 ekikeilekekeielaylFGSrakgkare.eSDiDlavllkekldleeelelaaelediklgkkvDlvdlnea 72
                                      +ki++  + ++e+  ++l+GS ++g++ +  SD+D++ ++k++   ++ l   +e+ +    k++D v+++ a
  gi|242399437|ref|YP_002994862.1| 11 NKIEKNEKLKDELYSLVLYGSAVRGDFIKgVSDLDFFAVVKTE---DKILPSLKEILEK-CTKDIDAVEVDVA 79
                                      45666666667999************99769**********99...4444444444444.5677777766655 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.8
                                       EEEES-S CS
                           Polbeta  85 kllyskd 91 
                                        ++y +d
  gi|242399437|ref|YP_002994862.1| 111 VVIYGED 117
                                       4444433 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 ?   13.5   0.0     1e-05     0.061      15      42 ..     158     185 ..     156     195 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1e-05
                          FANC_SAP  15 ELlqaFaavlaaksarKaelleaLrdrs 42 
                                       E+++++a+   aks++K + le+Lr+  
  gi|242399437|ref|YP_002994862.1| 158 EVARLLALINGAKSLKKEDILETLRTLG 185
                                       88888888555**************865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1404.74
//
Query:       gi|242399438|ref|YP_002994863.1|  [L=154]
Description: hypothetical protein TSIB_1463 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-18   65.6   0.0    4.3e-18   65.3   0.0    1.1  1  DUF192    Uncharacterized ACR, COG1430


Domain annotation for each model (and alignments):
>> DUF192  Uncharacterized ACR, COG1430
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.3   0.0   2.4e-22   4.3e-18       2      96 .]      14     114 ..      13     114 .. 0.90

  Alignments for each domain:
  == domain 1  score: 65.3 bits;  conditional E-value: 2.4e-22
                                       EEEEE-SHHHHHHTTTT-----TTEEEEEEECCEE..EEEE--TT--S-EEEEEE-TTSBEEEEEEEE-TT...... CS
                            DUF192   2 tvevAdteeerarGLmgreslpedegmlfvfdker..ehsfwMkntripLdiifldadgriveieealkpq...... 70 
                                       +v++Adt+ +r+rGLm + ++  +++++f++++e+  + s++M++++ ++d+ifld+++++v++++a  p+      
  gi|242399438|ref|YP_002994863.1|  14 RVKIADTFFKRFRGLMLTPNV--NYALVFILPSETrlNASIHMFFMLQSIDVIFLDSSREVVDLKRAR-PWrfyvpk 87 
                                       699***************865..799****999984569**************************866.**666655 PP

                                       .-ECEEEEEETTHHHHHT--TT-EEE. CS
                            DUF192  71 .svryvLElpaGaakklgikpGdrlei 96 
                                         ++y++E p G+++ l+ + Gd++++
  gi|242399438|ref|YP_002994863.1|  88 gGAKYIIETPVGVIDYLNAEIGDEIDW 114
                                       449*********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 997.95
//
Query:       gi|242399439|ref|YP_002994864.1|  [L=282]
Description: Ferredoxin:NADP+ oxidoreductase, subunit beta [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-12   46.5   1.4    3.7e-12   45.8   1.4    1.4  1  DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydr
  ------ inclusion threshold ------
      0.037   14.0   0.1      0.092   12.8   0.1    1.6  1  Fer2_3           2Fe-2S iron-sulfur cluster binding domain
       0.09   13.5   0.1        0.3   11.8   0.1    1.9  1  TPR_6            Tetratricopeptide repeat
       0.11   11.4   0.0       0.17   10.8   0.0    1.2  1  Alk_phosphatase  Alkaline phosphatase


Domain annotation for each model (and alignments):
>> DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydroorotate dehydrogenase B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   1.4   8.2e-16   3.7e-12       2      42 .]     214     250 ..     213     250 .. 0.92

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 8.2e-16
                                       ---SSSSSSS-TTEEEETTCTT.CEEETTTT-CEEECCCB. CS
                   DHODB_Fe-S_bind   2 erMaCGvGaClgCvvktkggdggeykrvCkdGPvFdadevd 42 
                                       ++M++G+G+C++C+v ++g    e k++C+dGP+Fda+++d
  gi|242399439|ref|YP_002994864.1| 214 QIMVDGTGMCGSCRVLYDG----EVKFACRDGPMFDAHKID 250
                                       68***************77....59*************985 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 ?   12.8   0.1     2e-05     0.092      54      73 ..     220     239 ..     213     252 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2e-05
                            Fer2_3  54 egiCGscavainGkptlaCt 73 
                                        g+CGsc v  +G+++ aC+
  gi|242399439|ref|YP_002994864.1| 220 TGMCGSCRVLYDGEVKFACR 239
                                       79*****************7 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   6.7e-05       0.3       9      32 ..     120     143 ..     111     144 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.7e-05
                                       HHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   9 syrklgdtdkAlealerlikeYPd 32 
                                       +++++g+++ A++++e+  + YP+
  gi|242399439|ref|YP_002994864.1| 120 AMKEAGNYTIAIQTFENAANTYPE 143
                                       567779*****************6 PP

>> Alk_phosphatase  Alkaline phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   3.8e-05      0.17      71     163 ..      95     190 ..      92     199 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3.8e-05
                                       SBTBTT-BSB-TTS..T-B---HHHHHHHTT-EEEEEEEEE.TTSHHHHTTTTTBSSTTSSSHHHSTCCCHHTTS-S CS
                   Alk_phosphatase  71 vktyngaigvdaaa..gkevksvleaAkkaGkstGlVtTtr.itdAtPaalvahvesRkwkedaavpaealeegkkd 144
                                       vk y +++ v+ a+  + e  + l+a k+aG  t  + T +  ++  P  + a+++  + +  ++  + + ++   d
  gi|242399439|ref|YP_002994864.1|  95 VKHYGNVVFVSDAVcaQAESYATLKAMKEAGNYTIAIQTFEnAANTYPEKYLAKSVADEHYLTTEDGSIGIKGHYLD 171
                                       789999999999987677888899********999999977145666*******9999888888856667789999* PP

                                       HHHHHHHCST-SEEEEESC CS
                   Alk_phosphatase 145 iaeqlikakkidvllGGGr 163
                                       + ++li++ k+d+++GGG+
  gi|242399439|ref|YP_002994864.1| 172 VLKELIEKDKVDIVFGGGK 190
                                       ******************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1803.22
//
Query:       gi|242399440|ref|YP_002994865.1|  [L=480]
Description: Ferredoxin:NADP+ oxidoreductase, subunit alpha [Thermococcus sibiricus MM 739]
Scores for complete 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-40  139.0   2.4    2.7e-40  138.5   2.4    1.2  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    1.5e-38  131.0   0.7    2.4e-38  130.4   0.7    1.3  1  Fer4_20        Dihydroprymidine dehydrogenase domain II, 4Fe-
    1.9e-13   50.7   4.6    3.6e-06   27.4   0.4    3.2  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    3.5e-12   46.2   4.1    1.6e-08   34.2   0.2    2.8  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    2.5e-08   34.0   1.0    7.1e-08   32.6   0.1    2.1  2  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    3.6e-08   33.0   0.7     0.0042   16.4   0.1    2.4  2  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
    1.1e-06   28.1   1.2    2.4e-06   27.0   0.1    1.9  2  Thi4           Thi4 family
    1.9e-06   27.5   6.9    0.00023   20.6   0.1    3.0  3  FAD_oxidored   FAD dependent oxidoreductase
    2.3e-06   26.9   2.9    0.00046   19.4   0.1    2.7  3  GIDA           Glucose inhibited division protein A
    1.1e-05   24.3   4.8    7.8e-05   21.5   0.9    2.5  2  HI0933_like    HI0933-like protein
    3.5e-05   23.2   1.0    4.8e-05   22.8   0.2    1.6  2  FAD_binding_3  FAD binding domain
    7.4e-05   22.0   0.5    7.4e-05   22.0   0.5    2.7  3  FAD_binding_2  FAD binding domain
    0.00012   22.4   1.2       0.15   12.5   0.3    2.7  2  NAD_binding_7  Putative NAD(P)-binding
    0.00015   21.8   0.7          2    8.5   0.0    3.8  4  Shikimate_DH   Shikimate / quinate 5-dehydrogenase
    0.00031   20.1   1.0       0.25   10.7   0.1    2.8  3  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
    0.00063   18.3   0.0     0.0045   15.5   0.0    1.9  2  FMO-like       Flavin-binding monooxygenase-like
    0.00085   19.0   3.0     0.0068   16.0   0.2    3.1  4  DAO            FAD dependent oxidoreductase
    0.00096   18.5   0.4     0.0068   15.7   0.0    2.3  3  Amino_oxidase  Flavin containing amine oxidoreductase
     0.0015   19.0   0.1        1.4    9.4   0.0    2.5  2  XdhC_C         XdhC Rossmann domain
     0.0033   18.0   4.1       0.41   11.3   1.2    3.8  2  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
  ------ inclusion threshold ------
      0.015   14.7   0.0        2.6    7.4   0.0    2.4  2  PALP           Pyridoxal-phosphate dependent enzyme
      0.028   13.5   0.2       0.06   12.4   0.2    1.5  1  Lycopene_cycl  Lycopene cyclase protein
      0.058   13.3   0.9       0.83    9.5   0.1    2.3  2  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
      0.089   12.4   0.7         13    5.3   0.0    2.7  2  IlvN           Acetohydroxy acid isomeroreductase, NADPH-bind
       0.26   11.3   4.4       0.51   10.3   0.2    2.8  3  NAD_binding_9  FAD-NAD(P)-binding
        1.3    9.2   6.6        3.1    8.0   6.6    1.7  1  Fer4_10        4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.5   2.4   3.8e-43   2.7e-40       2     290 ..     158     458 ..     157     468 .. 0.82

  Alignments for each domain:
  == domain 1  score: 138.5 bits;  conditional E-value: 3.8e-43
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHHHHHHCHHHHCCCCHCCTCEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeiasevvkklnqgielllgeevvki 78 
                                       +v+v+G+GpAGl+aa +la+ g+kvt++   ++++  g +l + + +++ ++ei+ ++       i +l +  +v+i
  gi|242399440|ref|YP_002994865.1| 158 KVAVVGSGPAGLTAAGELAKMGYKVTIF---EALHKPGGVLIYGIPEFRLPKEILDKE-------IAKLIE-LGVEI 223
                                       89**************************...88889999999***********99975.......666666.55555 PP

                                       EESC...EEEEETEEECTCEEEEEESEEEE---E.EE-BCTCTTC.........TTBEECCSECHHHHHHCCSS-T. CS
                                       xxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxx. RF
                       Pyr_redox_2  79 dpgk...kkvklekkkegdeekiaydklvlAtGs.sprdlgipGv........aenvgklvrtldsaealklkllp. 142
                                        p+    k+++le      e   +yd++++ tG+ +p++l+ipG         +   +    +l++a ++ +  +p 
  gi|242399440|ref|YP_002994865.1| 224 KPNYvigKTLTLE------ELLEEYDAVFIGTGAgTPKLLNIPGIlldgiytaN--EFLTRINLMKAYEFPKYDTPl 292
                                       5444111255554......45569*********7689999*****988887433..33333477777777777777* PP

                                       ...SEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTE.. CS
                                       ...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                       Pyr_redox_2 143 ...krivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgnge.. 214
                                          kr+vv+G+G+++++ A  + ++g+ev + ++r r    +  +++++  ++ e+eGv++ +  ++ e++g+++  
  gi|242399440|ref|YP_002994865.1| 293 tigKRTVVIGAGNTAMDAARSALRMGSEVIIAYRRGRE--DMTARIEEI--HHAEEEGVKFEFFLNPIEFIGDENgk 365
                                       **********************************9987..477888877..888999******************96 PP

                                       .......EEEEEETTSCE....................EEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTS CS
                                       .......xxxxxxxxxxx....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 215 .......klevvledgee....................idadlvvvavGvrpstelleeklglelderggivvdefl 264
                                              k        +                     ++ad+vv+a+G++p++ + ee+ gl+++++g +vvde+l
  gi|242399440|ref|YP_002994865.1| 366 vkavkfeK-------MKAleekdakgkrkivgtgeyilLEADTVVIAIGLEPNKVISEEATGLKTNPNGTLVVDERL 435
                                       66553332.......333334445668899************************9988******************* PP

                                       BESSTTEEE-GGGCTECCSS--HHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 265 rtnvpgiyaiGDvaggkggpelaqaA 290
                                        t++ g++a GD +   +g +++  A
  gi|242399440|ref|YP_002994865.1| 436 MTSISGVFAGGDAI---RGEATVILA 458
                                       ************99...555555544 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 !  130.4   0.7   3.5e-41   2.4e-38       1     112 [.      21     139 ..      21     140 .. 0.93

  Alignments for each domain:
  == domain 1  score: 130.4 bits;  conditional E-value: 3.5e-41
                                       HTTS-S-SB----HHHHHHHHTT----T..T-HHHHCSTT---HHHHHHHHHTT-......HHHHHHHHHHH-S-HH CS
                           Fer4_20   1 raknfkevalglteeealeeAsRClqCk..kapcvkgCPveidipefikkiaegn......leeaakiiketnslpa 69 
                                       r+k+f ev+lg++  +a++eA+RC+qC    apc+kgCPv+i+ip+fik+++e+       +++a+++i+++n+lpa
  gi|242399440|ref|YP_002994865.1|  21 RTKSFVEVNLGYDFASAIKEAERCIQCPpeYAPCIKGCPVHINIPGFIKALRENSnnsneaVKNALRVIWNDNTLPA 97 
                                       5788***********************644899******************9987677777999************* PP

                                       HHHHHS-GGGTGCCS-GGGTTB.----HHHHHHHHHHHHHHT- CS
                           Fer4_20  70 vcgrvCpqeelCegaCvlekkgkepvaigklerfvadaareeg 112
                                       ++grvCpqe++Ce+ Cv++k g +p++igklerfvad+ar+++
  gi|242399440|ref|YP_002994865.1|  98 ITGRVCPQEDQCEAPCVMGKVG-DPINIGKLERFVADYARKHN 139
                                       ******************9888.****************9986 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.4   9.2e-08   6.4e-05       1      35 [.     158     192 ..     158     232 .. 0.91
   2 !   27.4   0.4   5.3e-09   3.6e-06       1      79 [.     297     372 ..     297     380 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 9.2e-08
                                       EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                         Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkll 35 
                                       kv+vvG+G  gl +Ag+la++g kVt++e+  k+ 
  gi|242399440|ref|YP_002994865.1| 158 KVAVVGSGPAGLTAAGELAKMGYKVTIFEALHKPG 192
                                       79***************************998876 PP

  == domain 2  score: 27.4 bits;  conditional E-value: 5.3e-09
                                       EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTS.EEEE CS
                         Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedg.vesv 76 
                                       + vv+G+G++++++A  + ++g++V +  r+ +       +a+ +   + e++g+++ +  ++ e+ g+e+g v++v
  gi|242399440|ref|YP_002994865.1| 297 RTVVIGAGNTAMDAARSALRMGSEVIIAYRRGRED----MTARIEEIHHAEEEGVKFEFFLNPIEFIGDENGkVKAV 369
                                       579***************************97655....44444445566888************************ PP

                                       EEE CS
                         Pyr_redox  77 klk 79 
                                       k++
  gi|242399440|ref|YP_002994865.1| 370 KFE 372
                                       *97 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.4   0.00012     0.084       2      29 ..     161     187 ..     160     197 .. 0.91
   2 !   34.2   0.2   2.3e-11   1.6e-08     163     305 .]     294     446 ..     239     446 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00012
                       Pyr_redox_3   2 IiGaGPaGlaaaielkkagledylilEk 29 
                                       ++G GPaGl+aa el k+g  +++i E 
  gi|242399440|ref|YP_002994865.1| 161 VVGSGPAGLTAAGELAKMGY-KVTIFEA 187
                                       8*******************.6999885 PP

  == domain 2  score: 34.2 bits;  conditional E-value: 2.3e-11
                       Pyr_redox_3 163 agqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvke.............ek 226
                                        g++ vViG++n+a+DaA    r+g+eV +++r+  +e++     ++++ + + + e +  e             +k
  gi|242399440|ref|YP_002994865.1| 294 IGKRTVVIGAGNTAMDAARSALRMGSEVIIAYRRG-REDMT----ARIEEIHHAEEEGVKFEfflnpiefigdenGK 365
                                       3899*****************************96.33333....33333333222222222233345555656888 PP

                       Pyr_redox_3 227 ikvlfnaevkeikekeeeykvk.tedgkk.vevkddvvlatGykpdlsflkk.slfeldedgrpvlteeteetnvpg 300
                                       +k+++ +++k+++ek+ + k k   +g+  + + d vv+a+G +p+  + ++  +++++ +g+ v++e  + + ++g
  gi|242399440|ref|YP_002994865.1| 366 VKAVKFEKMKALEEKDAKGKRKiVGTGEYiLLEADTVVIAIGLEPNKVISEEaTGLKTNPNGTLVVDERLMTS-ISG 441
                                       9988888999998888776655333333304447889999******988888899************999965.899 PP

                       Pyr_redox_3 301 lflaG 305
                                       +f  G
  gi|242399440|ref|YP_002994865.1| 442 VFAGG 446
                                       99766 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 !   32.6   0.1     1e-10   7.1e-08       1      33 [.     161     193 ..     161     205 .. 0.96
   2 ?   -0.9   0.1       2.9     2e+03       1      21 [.     300     320 ..     300     326 .. 0.79

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 1e-10
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSG CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrlGG 33 
                                       +vG+G +Gl+aA +Lak g++v+++e+ +++GG
  gi|242399440|ref|YP_002994865.1| 161 VVGSGPAGLTAAGELAKMGYKVTIFEALHKPGG 193
                                       8*******************************9 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.9
                                       EE--SHHHHHHHHHHHCCTEE CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfd 21 
                                       ++GaG +++ aA+ + + g +
  gi|242399440|ref|YP_002994865.1| 300 VIGAGNTAMDAARSALRMGSE 320
                                       8******99999876666555 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 !   16.4   0.1   6.1e-06    0.0042      28      59 ..     156     187 ..     148     191 .. 0.91
   2 !   14.9   0.0   1.8e-05     0.012      30      60 ..     297     327 ..     267     431 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6.1e-06
                                       --EEEEESTSHHHHHHHHHHHHTT-EEEEEES CS
                       AlaDh_PNT_C  28 pakvlviGgGvaGlqAiatakglgakVtvlDv 59 
                                       ++kv v+G G aGl A+   +++g kVt+++ 
  gi|242399440|ref|YP_002994865.1| 156 KGKVAVVGSGPAGLTAAGELAKMGYKVTIFEA 187
                                       79***************************985 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 1.8e-05
                                       EEEEESTSHHHHHHHHHHHHTT-EEEEEESS CS
                       AlaDh_PNT_C  30 kvlviGgGvaGlqAiatakglgakVtvlDvr 60 
                                       +++viG+G   + A++ a ++g +V +   r
  gi|242399440|ref|YP_002994865.1| 297 RTVVIGAGNTAMDAARSALRMGSEVIIAYRR 327
                                       789**********************987554 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.1   3.5e-09   2.4e-06      15      73 ..     154     213 ..     142     231 .. 0.76
   2 ?   -1.2   0.1       1.5     1e+03      20      37 ..     298     315 ..     293     326 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 3.5e-09
                                       HTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTTBS..EEEEETTT CS
                              Thi4  15 yaesDvvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGqlfs..aivvrkpa 73 
                                        ++  v++vG+G++GLtaa  lak  + kv+i+e+   pGG    G   f   + ++ k+ 
  gi|242399440|ref|YP_002994865.1| 154 NMKGKVAVVGSGPAGLTAAGELAKM-GYKVTIFEALHKPGGVLIYGIPEFRlpKEILDKEI 213
                                       567789*******************.**************988888666632244555554 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.5
                                       EEEE--SHHHHHHHHHHH CS
                              Thi4  20 vvivGaGssGLtaayyla 37 
                                        v++GaG + + aa+   
  gi|242399440|ref|YP_002994865.1| 298 TVVIGAGNTAMDAARSAL 315
                                       5899******99998754 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.1   3.4e-07   0.00023       2      41 ..     159     198 ..     158     208 .. 0.94
   2 !    8.1   0.8    0.0021       1.4       3      31 ..     299     327 ..     298     329 .. 0.92
   3 ?    1.0   0.1      0.31   2.2e+02     114     171 ..     359     419 ..     332     476 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 3.4e-07
                      FAD_oxidored   2 vvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsg 41 
                                       v VvG+gpaG++AA   a++G kv + e     GG l  g
  gi|242399440|ref|YP_002994865.1| 159 VAVVGSGPAGLTAAGELAKMGYKVTIFEALHKPGGVLIYG 198
                                       89*********************************98766 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0021
                      FAD_oxidored   3 vVvGGgpaGvaAAiaAaraGakvlLveer 31 
                                       vV+G+g   + AA +A r+G +v++  +r
  gi|242399440|ref|YP_002994865.1| 299 VVIGAGNTAMDAARSALRMGSEVIIAYRR 327
                                       8***********************98776 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.31
                      FAD_oxidored 114 eke.gkriesvtveske.g.rktirAkvfiDATgdGdlaalaGvpyrvGresreetgepaa 171
                                       + + ++++++v++e+ +   +k  ++k+ i +Tg+  l+++  v + +G e ++   e a 
  gi|242399440|ref|YP_002994865.1| 359 IGDeNGKVKAVKFEKMKaLeEKDAKGKRKIVGTGEYILLEADTVVIAIGLEPNKVISEEAT 419
                                       4432568******9988636999*****************999999999999998888743 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.1   6.7e-07   0.00046       1      29 [.     158     188 ..     158     219 .. 0.86
   2 !    7.4   0.1    0.0028         2       3      28 ..     299     324 ..     297     343 .. 0.82
   3 ?   -2.1   0.1       2.2   1.5e+03     114     114 ..     414     414 ..     361     473 .. 0.58

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 6.7e-07
                                       CEEEE-SSHHHHHHHHHHHHTT--EEEE..E CS
                              GIDA   1 dviViGgGhAGceAAlaaarlGakvlLi..t 29 
                                       +v V+G G AG+ AA ++a++G+kv+++   
  gi|242399440|ref|YP_002994865.1| 158 KVAVVGSGPAGLTAAGELAKMGYKVTIFeaL 188
                                       699***********************99432 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0028
                                       EEE-SSHHHHHHHHHHHHTT--EEEE CS
                              GIDA   3 iViGgGhAGceAAlaaarlGakvlLi 28 
                                       +ViG+G   + AA  a r+G +v++ 
  gi|242399440|ref|YP_002994865.1| 299 VVIGAGNTAMDAARSALRMGSEVIIA 324
                                       8**********************987 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 2.2
                                       E CS
                              GIDA 114 i 114
                                       i
  gi|242399440|ref|YP_002994865.1| 414 I 414
                                       2 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.9   1.1e-07   7.8e-05       2      36 ..     158     192 ..     157     198 .. 0.94
   2 ?    3.8   0.2     0.028        19       2      28 ..     297     323 ..     296     329 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.1e-07
                                       SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                       HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakklg 36 
                                       +v+v+G G+AGl aA ++ak g +V+++e+ +k+g
  gi|242399440|ref|YP_002994865.1| 158 KVAVVGSGPAGLTAAGELAKMGYKVTIFEALHKPG 192
                                       69****************************99988 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.028
                                       SEEEE--SHHHHHHHHHHHHTT--EEE CS
                       HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVll 28 
                                       +++viG+G   + aA sa + g++V++
  gi|242399440|ref|YP_002994865.1| 297 RTVVIGAGNTAMDAARSALRMGSEVII 323
                                       689*********************997 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.2     7e-08   4.8e-05       3      34 ..     158     189 ..     156     192 .. 0.91
   2 ?   -2.5   0.0       3.4   2.3e+03       5      35 ..     299     329 ..     297     341 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 7e-08
                                       EEEEE--SHHHHHHHHHHHHTTHHEEEEESSS CS
                     FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekrs 34 
                                       +V++VG+GpaGl++a +L++ G +v++ e   
  gi|242399440|ref|YP_002994865.1| 158 KVAVVGSGPAGLTAAGELAKMGYKVTIFEALH 189
                                       79*************************99765 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.4
                                       EEE--SHHHHHHHHHHHHTTHHEEEEESSSS CS
                     FAD_binding_3   5 lIVGaGpaGlmlallLseaGvrvvlvekrst 35 
                                       +++GaG + + +a+   + G +v++  +r +
  gi|242399440|ref|YP_002994865.1| 299 VVIGAGNTAMDAARSALRMGSEVIIAYRRGR 329
                                       7999999999999998888888888776655 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.5   1.1e-07   7.4e-05       2      35 ..     159     192 ..     158     197 .. 0.90
   2 ?    2.7   0.1      0.08        55       3      28 ..     299     324 ..     297     334 .. 0.91
   3 ?   -1.8   0.1       1.8   1.2e+03     374     402 ..     419     449 ..     417     456 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.1e-07
                                       EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGG CS
                     FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavvekeqefg 35 
                                       v V+GsG AGL+AA e+a+ G kv++ e  ++ g
  gi|242399440|ref|YP_002994865.1| 159 VAVVGSGPAGLTAAGELAKMGYKVTIFEALHKPG 192
                                       89*************************9887655 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.08
                                       EEE--SHHHHHHHHHHHHTTT-EEEE CS
                     FAD_binding_2   3 iViGsGlAGLaAAleaaeaGlkvavv 28 
                                       +ViG+G   + AA +a + G +v++ 
  gi|242399440|ref|YP_002994865.1| 299 VVIGAGNTAMDAARSALRMGSEVIIA 324
                                       9**********************985 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 1.8
                                       -EEEBETTSBE..STTEEESSBTEEE-STCE CS
                     FAD_binding_2 374 gGvetdengrv..ldadgqpipGLYAaGeva 402
                                        G++t++ng    +++  + i+G +A G ++
  gi|242399440|ref|YP_002994865.1| 419 TGLKTNPNGTLvvDERLMTSISGVFAGGDAI 449
                                       6999999998666888889*******99887 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 !    8.1   0.0    0.0052       3.6       9      36 ..     158     185 ..     154     250 .. 0.82
   2 !   12.5   0.3   0.00022      0.15       7      79 ..     295     415 ..     293     477 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0052
                     NAD_binding_7   9 kvlvvGgGevAarkvrklleagakvtvv 36 
                                       kv vvG G+ +++ +  l++ g kvt+ 
  gi|242399440|ref|YP_002994865.1| 158 KVAVVGSGPAGLTAAGELAKMGYKVTIF 185
                                       799***********************96 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00022
                     NAD_binding_7   7 gkkvlvvGgGevAarkvrklleagakvtvvapevkeele....elvklaeee......................... 54 
                                       gk+ +v+G+G+ A+  +r+ l+ g +v++   +  e +     e +++aeee                         
  gi|242399440|ref|YP_002994865.1| 295 GKRTVVIGAGNTAMDAARSALRMGSEVIIAYRRGREDMTarieE-IHHAEEEgvkfefflnpiefigdengkvkavk 370
                                       799************************99655532222223312.22222223444444444444444444444444 PP

                     NAD_binding_7  55 ......l.ekd..............legadlviaatddrelneria 79 
                                             l ekd              l +ad+v++a+   e n+ i 
  gi|242399440|ref|YP_002994865.1| 371 fekmkaLeEKDakgkrkivgtgeyiLLEADTVVIAIG-LEPNKVIS 415
                                       3333331222244444444444454555777777773.44444444 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1      0.11        78      12      42 ..     156     185 ..     143     187 .. 0.84
   2 ?    5.6   0.0     0.022        15      45      88 ..     212     254 ..     207     258 .. 0.75
   3 !    8.5   0.0    0.0029         2      12      55 ..     295     338 ..     288     354 .. 0.76
   4 ?   -1.9   0.0       4.6   3.2e+03      72      91 ..     395     414 ..     371     432 .. 0.58

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.11
                                       T-EEEEES-SHHHHHHHHHHHCCT-CEEEEE CS
                      Shikimate_DH  12 ekkvlliGaGemaelvakhLlakgvkkvvva 42 
                                       + kv ++G G  +  +a  L++ g+k v+++
  gi|242399440|ref|YP_002994865.1| 156 KGKVAVVGSGPAGLTAAGELAKMGYK-VTIF 185
                                       569*******************9999.8885 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.022
                                       SHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SSSSS- CS
                      Shikimate_DH  45 tlerakelaeelkgeeiealkleelkellaeadvvisataseep 88 
                                       ++++  el  e+k + + + k   l+ell+e+d v++ t++ +p
  gi|242399440|ref|YP_002994865.1| 212 EIAKLIELGVEIKPN-YVIGKTLTLEELLEEYDAVFIGTGAGTP 254
                                       566666677777655.666666789***************9887 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0029
                                       T-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHH CS
                      Shikimate_DH  12 ekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaee 55 
                                       +k+ ++iGaG++a  +a+  l+ g + ++   R +e + +  ee
  gi|242399440|ref|YP_002994865.1| 295 GKRTVVIGAGNTAMDAARSALRMGSEVIIAYRRGREDMTARIEE 338
                                       6899*****************99999555555556655555555 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 4.6
                                       HHHT-SEEEE-SSSSS-SB- CS
                      Shikimate_DH  72 llaeadvvisataseepile 91 
                                       +l ead v++a++ e + + 
  gi|242399440|ref|YP_002994865.1| 395 ILLEADTVVIAIGLEPNKVI 414
                                       45567777777765544444 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 !    7.1   0.0    0.0046       3.2      31      69 ..     152     189 ..     126     204 .. 0.77
   2 ?   -3.6   0.0       8.6   5.9e+03      82      97 ..     232     247 ..     226     249 .. 0.81
   3 !   10.7   0.1   0.00037      0.25      35      76 ..     294     335 ..     270     377 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0046
                                       BS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSH CS
                      2-Hacid_dh_C  31 gkelsgktvGiiGlGrIGqavakrlkafgmkviaydrsk 69 
                                       g e  + +v+++G G  G ++a  l+++g kv++++  +
  gi|242399440|ref|YP_002994865.1| 152 G-ENMKGKVAVVGSGPAGLTAAGELAKMGYKVTIFEALH 189
                                       3.4445579***********************9987765 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 8.6
                                       ECSHHHHHHH-SEEEE CS
                      2-Hacid_dh_C  82 lvsleellaesDivsl 97 
                                         +leell+e D v++
  gi|242399440|ref|YP_002994865.1| 232 TLTLEELLEEYDAVFI 247
                                       56899*****999976 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00037
                                       TTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHH CS
                      2-Hacid_dh_C  35 sgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeee 76 
                                        gk+  +iG+G+ +  +a+ +  +g +vi+  r+ +++ +++
  gi|242399440|ref|YP_002994865.1| 294 IGKRTVVIGAGNTAMDAARSALRMGSEVIIAYRRGREDMTAR 335
                                       589999**********************99988888555232 PP

>> FMO-like  Flavin-binding monooxygenase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.28   1.9e+02       3      38 ..     158     193 ..     154     198 .. 0.80
   2 !   15.5   0.0   6.5e-06    0.0045     139     218 ..     242     330 ..     236     344 .. 0.70

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.28
                          FMO-like   3 kvaviGaGvsGlasikccleegleptcfersddiGG 38 
                                       kvav+G+G +Gl++     + g + t fe  +  GG
  gi|242399440|ref|YP_002994865.1| 158 KVAVVGSGPAGLTAAGELAKMGYKVTIFEALHKPGG 193
                                       899999999999998888888888888887766666 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 6.5e-06
                          FMO-like 139 fdavmvctGhhv.....nphlplesfpGiekfkGqyfhsrdykepev....fkgkrvlviGlGnsggdiavelsrta 206
                                       +dav + tG  +      p + l+     ++f  ++   + y  p+       gkr +viG Gn++ d a  + r+ 
  gi|242399440|ref|YP_002994865.1| 242 YDAVFIGTGAGTpkllnIPGILLDGIYTANEFLTRINLMKAYEFPKYdtplTIGKRTVVIGAGNTAMDAARSALRMG 318
                                       677777776544111112334455555567788887777777777641121459*********************** PP

                          FMO-like 207 eqvllstrsGsw 218
                                        +v+++ r+G  
  gi|242399440|ref|YP_002994865.1| 319 SEVIIAYRRGRE 330
                                       ********9965 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.2   9.9e-06    0.0068       1      33 [.     158     192 ..     158     194 .. 0.91
   2 ?   -0.5   0.0         1   7.1e+02     180     343 ..     233     260 ..     205     270 .. 0.55
   3 ?   -2.1   0.1       3.3   2.2e+03       2      25 ..     298     323 ..     297     330 .. 0.78
   4 ?    0.9   0.0      0.39   2.7e+02     161     205 ..     366     411 ..     339     438 .. 0.63

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 9.9e-06
                                       EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
                               DAO   1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiag 33 
                                       +v+++G+G +Gl++A eLa+ g  Vt++e+ + +g
  gi|242399440|ref|YP_002994865.1| 158 KVAVVGSGPAGLTAAGELAKMGykVTIFEALHKPG 192
                                       59*****************99********977666 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1
                                       EEEEEECTEEE.EEEEEEEE--GGGHHHHHTTCTTTSEEEEEEEEEEEEEECCTHSTGSGCSEEEEEEEETTTTEEE CS
                               DAO 180 wgverttpgen.daadavVnaaGawsdllgllkeldlpispvrgqvlvlkplseklvspaailpvpetdddgrgvyv 255
                                        ++     +e  +++dav + +Ga++                                                   
  gi|242399440|ref|YP_002994865.1| 233 LTL-----EELlEEYDAVFIGTGAGTP-------------------------------------------------- 254
                                       222.....1122235666666666655.................................................. PP

                                       EEETTSEEEEEESSEEETTCSSTSCSHHHHHHHHHHHHHHSGGGCGEEEEEEEEEEETTSSEEEEEEETEEEEEEEE CS
                               DAO 256 tprkdgrvlvGgtadeesgdddpevdeedidellealrklfPqlgdvlrkwaGlrplpdglpligetpgvkglylat 332
                                                                                                                    
  gi|242399440|ref|YP_002994865.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                                       ECTTTHHHHHH CS
                               DAO 333 GhsghGltlap 343
                                             l + p
  gi|242399440|ref|YP_002994865.1| 255 -----KLLNIP 260
                                       .....444444 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 3.3
                                       EEEECTSHHHHHHHHHHHHTT..EEE CS
                               DAO   2 vviiGGGiiGlstAyeLarrg..Vtl 25 
                                        v+iG+G + + +A+ + r g  V++
  gi|242399440|ref|YP_002994865.1| 298 TVVIGAGNTAMDAARSALRMGseVII 323
                                       69*****9999999988776777665 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 0.39
                                       -EEEESECEEEEEEEE..TCEEEEEEECTEEEE..EEEEEEE--GGGHH CS
                               DAO 161 veilegtevtgleeed..gkvwgverttpgend..aadavVnaaGawsd 205
                                       v+ ++ ++ ++lee+d  gk + v   t ge    +ad+vV+a G+  +
  gi|242399440|ref|YP_002994865.1| 366 VKAVKFEKMKALEEKDakGKRKIV--GT-GEYIllEADTVVIAIGLEPN 411
                                       444444566666665543332223..33.333256779******99866 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   9.9e-06    0.0068       2      28 ..     167     193 ..     166     195 .. 0.97
   2 ?   -0.2   0.0      0.67   4.6e+02     241     266 ..     385     412 ..     363     427 .. 0.72
   3 ?   -2.0   0.0       2.4   1.6e+03     415     451 ..     436     469 ..     418     470 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 9.9e-06
                                       HHHHHHHHHHHTTEEEEEEESSSSSBT CS
                     Amino_oxidase   2 aGLaaArqLlsaGfdVtvlEardrvGG 28 
                                       aGL+aA +L+  G++Vt++Ea   +GG
  gi|242399440|ref|YP_002994865.1| 167 AGLTAAGELAKMGYKVTIFEALHKPGG 193
                                       9*************************9 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.67
                                       EEEEETTSTEE..EESEEEE-S-HHHHH CS
                     Amino_oxidase 241 vtvtledgevv..eaDaVvvTvplgvlk 266
                                        +  + +ge +  eaD Vv+++ l   k
  gi|242399440|ref|YP_002994865.1| 385 KRKIVGTGEYIllEADTVVIAIGLEPNK 412
                                       3334557777799*********987666 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 2.4
                                       CHHCSTTEEE.SGGGCTTTTTSHHHHHHHHHHHHHHH CS
                     Amino_oxidase 415 kpegdprlffAGehtsreypgtvegAilSGlraAari 451
                                       ++  ++++f  G+++     +tv  A+  G++aA  i
  gi|242399440|ref|YP_002994865.1| 436 MT-SISGVFAGGDAIR--GEATVILAMGDGKKAAKSI 469
                                       33.58999999***99..9999***********9877 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0     0.002       1.4      39     109 ..     103     196 ..      78     204 .. 0.76
   2 ?    7.0   0.0     0.011       7.9       2      40 ..     299     337 ..     298     405 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.002
                                       -TT-SE....................-EEEE--S-HHHHHHHHHHHSSS-...-SEEEESS-HHHHHHHCTTS.--. CS
                            XdhC_C  39 fpeade....................tavvvlthdhklDaealeaalrkk...aayigllGSrkkaarrlerlraag 92 
                                        p++d+                     +v+   ++h++D+e+l++  ++     + ++++GS     +   +l++ g
  gi|242399440|ref|YP_002994865.1| 103 CPQEDQceapcvmgkvgdpinigkleRFVADYARKHNIDEELLQEFANNGenmKGKVAVVGSGPAGLTAAGELAKMG 179
                                       4544445556666666666667777677777899*************83335455******************999* PP

                                       ......TTEESS-S--S CS
                            XdhC_C  93 lseeelarlhaPiGldi 109
                                       ++ + ++ lh P G+ i
  gi|242399440|ref|YP_002994865.1| 180 YKVTIFEALHKPGGVLI 196
                                       ************99876 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.011
                                       EEE--STTHHHHHHHHHHHTEEEEEEES-GGGG-GGG-T CS
                            XdhC_C   2 vifGaghvaqalarlaaalgfrvtvvdpreefatkerfp 40 
                                       v++Gag+ a   ar a ++g +v+++  r +   ++r++
  gi|242399440|ref|YP_002994865.1| 299 VVIGAGNTAMDAARSALRMGSEVIIAYRRGREDMTARIE 337
                                       79***********************99998545444444 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 ?    2.3   0.1      0.37   2.5e+02       1      30 [.     158     184 ..     158     190 .. 0.91
   2 !   11.3   1.2   0.00059      0.41       3      47 ..     299     340 ..     297     433 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.37
                                       EEEEETTSHHHHHHHHHHHHTTS-GGCEEE CS
                     F420_oxidored   1 kigiiGaGnmgealasgllaagaqpheivv 30 
                                       k++++G+G  g + a  l++ g   +++++
  gi|242399440|ref|YP_002994865.1| 158 KVAVVGSGPAGLTAAGELAKMG---YKVTI 184
                                       79********************...88886 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00059
                                       EEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC CS
                     F420_oxidored   3 giiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg 47 
                                        +iGaGn +   a+ +l+ g   +e+++a +r  e +++  ee+ 
  gi|242399440|ref|YP_002994865.1| 299 VVIGAGNTAMDAARSALRMG---SEVIIAYRRGREDMTARIEEIH 340
                                       58******************...***********99988777765 PP

>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.024        16      53     101 ..     154     220 ..     137     255 .. 0.68
   2 ?    7.4   0.0    0.0038       2.6      55      90 ..     295     330 ..     276     387 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.024
                                       TTTSEEEEEBSSHHHHHHHHHHHHHT-EEEEE..................EETTS-HHHHHHHHHTT CS
                              PALP  53 tgaktvveassGNhgralAaaaallGlkvtiv..................vpadaspekvallrllG 101
                                       + +  v++ +sG +g+ +A   a++G+kvti+                  +p+      +a+l +lG
  gi|242399440|ref|YP_002994865.1| 154 NMKGKVAVVGSGPAGLTAAGELAKMGYKVTIFealhkpggvliygipefrLPKEILDKEIAKLIELG 220
                                       45667899999********************955555555444444444444444445555555555 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0038
                                       TSEEEEEBSSHHHHHHHHHHHHHT-EEEEEEETTS- CS
                              PALP  55 aktvveassGNhgralAaaaallGlkvtivvpadas 90 
                                       +k+ v+ ++GN+++ +A  a ++G +v+i   ++  
  gi|242399440|ref|YP_002994865.1| 295 GKRTVVIGAGNTAMDAARSALRMGSEVIIAYRRGRE 330
                                       67789999*********************9877766 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   8.6e-05      0.06       2      33 ..     159     188 ..     158     193 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.6e-05
                     Lycopene_cycl   2 vvviGaGpAglslAarlteakpglkvvlieas 33 
                                       v+v+G+GpAgl  A +l  ak+g kv++ ea 
  gi|242399440|ref|YP_002994865.1| 159 VAVVGSGPAGLTAAGEL--AKMGYKVTIFEAL 188
                                       89***************..*********9985 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1    0.0012      0.83       1      29 [.     158     186 ..     158     191 .. 0.93
   2 ?    1.9   0.1      0.25   1.7e+02       3      40 ..     299     337 ..     297     351 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0012
                                       EEEEE--SCCHHHHHHHHHHTT-EEEEE- CS
                           3HCDH_N   1 kvaviGaGtmGagiaavfasagleVvlvd 29 
                                       kvav+G+G  G   a  +a+ g++V++++
  gi|242399440|ref|YP_002994865.1| 158 KVAVVGSGPAGLTAAGELAKMGYKVTIFE 186
                                       79************************987 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.25
                                       EEE--SCCHHHHHHHHHHTT-EEEEE-S.-HHHHHHHHH CS
                           3HCDH_N   3 aviGaGtmGagiaavfasagleVvlvdi.seealekale 40 
                                        viGaG      a  +++ g eV +  +  +e +++  e
  gi|242399440|ref|YP_002994865.1| 299 VVIGAGNTAMDAARSALRMGSEVIIAYRrGREDMTARIE 337
                                       59*********************9977623334444444 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 ?    4.5   0.0     0.034        23       6      32 ..     158     184 ..     154     192 .. 0.90
   2 ?    5.3   0.0     0.019        13       4      42 ..     295     333 ..     293     350 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.034
                                       -EEEES-SHHHHHHHHHHHHTT--EEE CS
                              IlvN   6 kiaviGyGsqGhaqalnlrdsgldvvv 32 
                                       k+av+G G  G + a +l   g +v++
  gi|242399440|ref|YP_002994865.1| 158 KVAVVGSGPAGLTAAGELAKMGYKVTI 184
                                       8***********************998 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.019
                                       TS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHH CS
                              IlvN   4 gkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvk 42 
                                       gk+ +viG G+ +   a+     g +v+++ r+g++ ++
  gi|242399440|ref|YP_002994865.1| 295 GKRTVVIGAGNTAMDAARSALRMGSEVIIAYRRGREDMT 333
                                       68899**********9999999***********995443 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 ?   10.3   0.2   0.00074      0.51       1      39 [.     160     193 ..     160     200 .. 0.88
   2 ?    1.5   0.0      0.37   2.6e+02     117     154 ..     369     407 ..     359     409 .. 0.69
   3 ?   -3.0   0.0       9.3   6.4e+03     118     138 ..     412     432 ..     411     437 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00074
                     NAD_binding_9   1 aivGaGprGlavlerLlarakkkspleitlfdp.sepgag 39 
                                       a+vG Gp+Gl+++ +L++        ++t+f+  ++pg g
  gi|242399440|ref|YP_002994865.1| 160 AVVGSGPAGLTAAGELAKM-----GYKVTIFEAlHKPG-G 193
                                       89***************99.....599******99998.4 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.37
                     NAD_binding_9 117 vevhraevvdleeradgqavlladgasl.aadaVvLAlG 154
                                       v++ + ++++ ++++++++++ +++  l +ad Vv+A+G
  gi|242399440|ref|YP_002994865.1| 369 VKFEKMKALEEKDAKGKRKIVGTGEYILlEADTVVIAIG 407
                                       44555555555556666778777776644********99 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 9.3
                     NAD_binding_9 118 evhraevvdleeradgqavll 138
                                       +v+++e++ l+++++g  v+ 
  gi|242399440|ref|YP_002994865.1| 412 KVISEEATGLKTNPNGTLVVD 432
                                       578999*******99987765 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   6.6    0.0045       3.1       3      24 ..      38      80 ..      36     114 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0045
                           Fer4_10  3 vidddtCirCg....kCvkaCPadl.................t 24
                                      ++++++Ci+C      C k CP+++                 +
  gi|242399440|ref|YP_002994865.1| 38 IKEAERCIQCPpeyaPCIKGCPVHInipgfikalrensnnsnE 80
                                      67899*****988889*******99888887777654444331 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (480 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); 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: 0.74u 0.31s 00:00:01.05 Elapsed: 00:00:00.52
# Mc/sec: 2777.76
//
Query:       gi|242399441|ref|YP_002994866.1|  [L=186]
Description: 2-oxoglutarate ferredoxin oxidoreductase 2 (KGOR), subunit gamma [Thermococcus sibiricus MM 739]
Scores for complete 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  123.2   0.0    1.4e-35  123.0   0.0    1.0  1  POR        Pyruvate ferredoxin/flavodoxin oxidoreductase
  ------ inclusion threshold ------
      0.093   13.4   0.0       0.16   12.6   0.0    1.4  1  GTP-bdg_N  GTP-binding GTPase N-terminal
        0.1   12.8   0.0       0.19   11.9   0.0    1.4  1  CDC37_C    Cdc37 C 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 !  123.0   0.0   2.3e-39   1.4e-35       1     177 []      11     176 ..      11     176 .. 0.97

  Alignments for each domain:
  == domain 1  score: 123.0 bits;  conditional E-value: 2.3e-39
                                       CTSTHHHHHHHHHHHH.HHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHHHHGGGE CS
                               POR   1 GGqGvvtagkilakaa.araGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetlsehldgl 76 
                                       GGqGv++ + il++aa +++G+y +++++yg+e rGg+s ++v isd+  +++++  ++d+ + l +++++++l+ +
  gi|242399441|ref|YP_002994866.1|  11 GGQGVILSSVILGRAAaVYEGLYSVQTQSYGPESRGGASKAEVIISDD-LIDYPKALNPDYAILLSQQAYEKYLSLV 86 
                                       9***************9*******************************.8999999********************* PP

                                       EEEEEEEEECTCGTT-CCHHHCTS-HHHHHHHT-EEEEE-HHHHHHHCCC.CCHHHHHHHHHHHHHHT.S-HHHHHH CS
                               POR  77 kpggiiiynseelkpdelkkakeeerelkerlgvrvygvdatkiakeiggneraaNtvmlGalaallg.lplealee 152
                                       k+ggi+i+ ++ +++++++ +k            +vy++++tk+a+e+ g ++++N++ lG+l++l+g +++ea+e+
  gi|242399441|ref|YP_002994866.1|  87 KEGGIVIVEKDLIPNRNEELEKN----------FKVYVLPFTKLAEESTGLSLTMNILTLGFLVRLTGiVSEEAIEK 153
                                       ********************996..........479***************************************** PP

                                       HHHCCS-CH.HHHHHHHHHHHHHHH CS
                               POR 153 aikkrfpkkkeviekNlkafragye 177
                                       a+ +++pk      +Nlka+++g+e
  gi|242399441|ref|YP_002994866.1| 154 AVLDSIPKG--TEHLNLKALKKGFE 176
                                       *******96..889*********86 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 ?   12.6   0.0   2.7e-05      0.16      28      79 ..      67     116 ..      48     121 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.7e-05
                         GTP-bdg_N  28 kpdpatyiGkGkveeikelveeeeadlvifddeLspsqqrnLekelevkViD 79 
                                       +pd a+++ +   e+  +lv+e    +vi++++L p+  ++Lek+++v V+ 
  gi|242399441|ref|YP_002994866.1|  67 NPDYAILLSQQAYEKYLSLVKEG--GIVIVEKDLIPNRNEELEKNFKVYVLP 116
                                       67788888899999999999996..89*********************9985 PP

>> CDC37_C  Cdc37 C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   3.2e-05      0.19      50      82 ..      79     111 ..      73     116 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.2e-05
                           CDC37_C  50 Aeeilellgeagilsleellvdatteegekelk 82 
                                        e++l+l++e+gi+ +e+ l+++ +ee ek++k
  gi|242399441|ref|YP_002994866.1|  79 YEKYLSLVKEGGIVIVEKDLIPNRNEELEKNFK 111
                                       499***************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1138.14
//
Query:       gi|242399442|ref|YP_002994867.1|  [L=281]
Description: 2-ketoglutarate ferredoxin oxidoreductase 2 (KGOR), subunit beta [Thermococcus sibiricus MM 739]
Scores for complete 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-37  128.1   0.2    3.5e-37  127.5   0.2    1.2  1  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
  ------ inclusion threshold ------
       0.03   13.1   0.1      0.046   12.5   0.1    1.2  1  XFP_N         XFP N-terminal domain


Domain annotation for each model (and alignments):
>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.5   0.2   3.9e-41   3.5e-37       2     152 ..      56     202 ..      50     203 .. 0.95

  Alignments for each domain:
  == domain 1  score: 127.5 bits;  conditional E-value: 3.9e-41
                                       SSHHHHHHHHHHTTSSSSEEEC.ETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEE CS
                      TPP_enzyme_C   2 iGcltlwaarllkvkrprsylt.sgglgtmGyglpaAiGaklakpdrevvaivGDGgflmi.lqelatavrrnlpit 76 
                                       iGc+++           + y++ +g+++t+G++l++A+G+k+a+pd +v+a++GDG+ + i +++l++a+rrnl+it
  gi|242399442|ref|YP_002994867.1|  56 IGCSSR----------VPGYVNfDGLHTTHGRALAFATGIKMANPDLKVIAFMGDGDAAAIgGNHLIHAIRRNLDIT 122
                                       566666..........6678888****************************************************** PP

                                       EEEEE-SBCCCHHHH...HHHHTCCTTTTSBB.BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHHHHCSSSEE CS
                      TPP_enzyme_C  77 vvvlnNegygmtggq...qepfggkrksgpagkdlkpvdfaklaealGak.garvekadveeleealkealekkgpa 149
                                       v+++nN +ygmtggq   ++p+g + +++p+g+ ++p+d+a+la  +Ga+ +ar ++ +  +  + +k+al+k+g++
  gi|242399442|ref|YP_002994867.1| 123 VILINNFTYGMTGGQvapTTPKGLRGTTAPYGSFENPFDIAELAVVAGANyVARWSVFNYLQGINSIKKALQKEGFT 199
                                       **************************************************9999999999***************** PP

                                       EEE CS
                      TPP_enzyme_C 150 lie 152
                                       l+e
  gi|242399442|ref|YP_002994867.1| 200 LVE 202
                                       **8 PP

>> XFP_N  XFP N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   5.2e-06     0.046     129     171 ..      59     104 ..      48     116 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.2e-06
                             XFP_N 129 aaetPGsiheGG...elGyalshayGavldnPdlivacvvGdGeae 171
                                       ++ +PG ++  G     G al+ a+G  + nPdl v++ +GdG+a 
  gi|242399442|ref|YP_002994867.1|  59 SSRVPGYVNFDGlhtTHGRALAFATGIKMANPDLKVIAFMGDGDAA 104
                                       5678888876653335699************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); 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 0.27s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1890.78
//
Query:       gi|242399443|ref|YP_002994868.1|  [L=379]
Description: 2-ketoglutarate:ferredoxin oxidoreductase 2 (KGOR), subunit alpha [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-79  267.4   0.3    1.5e-79  267.0   0.3    1.2  1  POR_N            Pyruvate flavodoxin/ferredoxin oxidoreductas
    3.1e-22   78.8   0.2    5.3e-21   74.9   0.2    2.3  2  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
    1.4e-09   37.9   0.0    2.9e-09   36.9   0.0    1.5  1  Transketolase_C  Transketolase, C-terminal domain
    1.2e-05   25.0   0.3    1.8e-05   24.4   0.3    1.3  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 !  267.0   0.3   3.4e-83   1.5e-79       2     229 ..      16     251 ..      15     253 .. 0.96

  Alignments for each domain:
  == domain 1  score: 267.0 bits;  conditional E-value: 3.4e-83
                                       HHHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCC CS
                             POR_N   2 aaiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmien 78 
                                       aai ag++++a+YPITP+sei+e+++ +++ ++    + +qme+Eig+i+aviGA+++Ga+++TaTSg+G++Lm+en
  gi|242399443|ref|YP_002994868.1|  16 AAILAGCRFYAGYPITPASEIFEAMSVYMPLVDG---VNIQMEDEIGSIAAVIGASWTGAKSMTATSGPGFSLMMEN 89 
                                       89*******************************5...9*************************************** PP

                                       HHHHHHTT--EEEEEEEEE-STTBEEEEE--TTCHHHH.....S---EEEE-SSHHHHHHHHHHHHHHHHHCTSEEE CS
                             POR_N  79 lglaageelPvvivvvaRalpstglsirtdqsDlmaar.....dtglivlasenvqeafdlalvAfnlAekvrvPvi 150
                                       lg+a+++e+P+v+v+v+R++pstg+++  +q+Dlm+a+     d+ livl +++vqeafd++++AfnlAek+r+Pvi
  gi|242399443|ref|YP_002994868.1|  90 LGYAIMTETPLVLVNVQRSGPSTGQPTLAAQGDLMQAIwgthgDHSLIVLTPATVQEAFDMTIKAFNLAEKYRTPVI 166
                                       ***************************************************************************** PP

                                       EEEEHHHH.HEEEEEEC-SGG.GS-----SBXXXXXXXX........SXXXBXXTXXTSSXXEEESBXBXTTSXBXX CS
                             POR_N 151 vlfDgfllshevekvelpdeedelklikekleeyerkey........aldpekpiargtaanpdtglehrekgneae 219
                                       +l+D+ ++ h++e+v+ p  + el+li +kl+++e++++        +l p +p++ ++  +++tgl+h+ekg++++
  gi|242399443|ref|YP_002994868.1| 167 LLTDAEVG-HMRERVYAPHPD-ELELIYRKLPANEEEAKypfgdvhgDLIPPMPVFGKGHHTYVTGLTHDEKGRPQT 241
                                       ********.*********999.8889988888887766678************************************ PP

                                       XXHHHHHHHH CS
                             POR_N 220 daaekvveev 229
                                        + e +++ +
  gi|242399443|ref|YP_002994868.1| 242 VQSEIHEKLI 251
                                       9888888766 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 ?    1.4   0.0     0.088   3.9e+02      27      43 ..     171     187 ..     165     197 .. 0.89
   2 !   74.9   0.2   1.2e-24   5.3e-21       1     102 []     276     370 ..     276     370 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.088
                                       --EEEEEES--BS--HH CS
                           PFOR_II  27 ikvGllrlrtlrPFPee 43 
                                        +vG +r r++ P P e
  gi|242399443|ref|YP_002994868.1| 171 AEVGHMRERVYAPHPDE 187
                                       58*************86 PP

  == domain 2  score: 74.9 bits;  conditional E-value: 1.2e-24
                                       -SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHHHHHHH CS
                           PFOR_II   1 AevvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlveevkaa 77 
                                       Ae++i+ +G+va++a +av+elR++gik+Gll+  +++PF  e +++++++v+k+ v+++n      Gql++ vk+ 
  gi|242399443|ref|YP_002994868.1| 276 AEIAIISFGIVARSAMRAVKELRKKGIKAGLLKFNVVWPFDFELIERIAEGVEKIYVVEMNL-----GQLYHMVKEG 347
                                       9*************************************************************.....********** PP

                                       TGGGTSEEEEEE--GGG----HHHH CS
                           PFOR_II  78 lkkskvkvvnfvaglgGrditvedi 102
                                        +++  ++v++++++gG+++t+++i
  gi|242399443|ref|YP_002994868.1| 348 ANGK--APVELISKIGGEVHTPKEI 370
                                       *999..****************997 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.0   6.4e-13   2.9e-09       8      68 ..     274     334 ..     269     340 .. 0.94

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 6.4e-13
                                       TTSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEE CS
                   Transketolase_C   8 egkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvve 68 
                                       e  +++++++G   + a++A++eL+k+gi+a ++    v+p+D+e+i+ +++  +++ vve
  gi|242399443|ref|YP_002994868.1| 274 EDAEIAIISFGIVARSAMRAVKELRKKGIKAGLLKFNVVWPFDFELIERIAEGVEKIYVVE 334
                                       6789*******************************************************98 PP

>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.3     4e-09   1.8e-05       3     159 ..       9     169 ..       7     178 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 4e-09
                                       HHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT.TSEEEE-SS...HHHHHHHHHHHHHHHTS-EEEEE-CHHHH CS
                      TPP_enzyme_N   3 vaealvraLkalgvehvfgvpGsrilplldalseeqgirvvlarh...EqgaafaAdgyaratgkpgvvlvtsgpGa 76 
                                       + ea++ra   +g + + g+p +   ++++a+s    +++v  ++   E   + +A  +  +        +tsgpG+
  gi|242399443|ref|YP_002994868.1|   9 GDEAIARAAILAGCRFYAGYPITPASEIFEAMSVY--MPLVDGVNiqmEDEIGSIAAVIGASWTGAKSMTATSGPGF 83 
                                       678899999999999999**************999..66665554444777777777666654446666677***** PP

                                       HHCHHHHHHHHHHT--EEEEEEE--CCCHHS..TC--T-.CCHHHCCCSSEEEE-SSGGGHHHHHH...HHHHHHHS CS
                      TPP_enzyme_N  77 tnaltalaeAkvdriPllvlsgdrptslrgqgvlqqeld.qlalfrpvtkyaervtspeelpealr...rAirtals 149
                                         ++ +l  A  + +Pl+++  +r+  ++gq++l  + d  +a+   +  ++  v +p++++ea++   +A+  a +
  gi|242399443|ref|YP_002994868.1|  84 SLMMENLGYAIMTETPLVLVNVQRSGPSTGQPTLAAQGDlMQAIWGTHGDHSLIVLTPATVQEAFDmtiKAFNLA-E 159
                                       ******************************888886666234456688899999999999999999788888888.9 PP

                                       SS--EEEEEE CS
                      TPP_enzyme_N 150 grpgPvylel 159
                                       + ++Pv l  
  gi|242399443|ref|YP_002994868.1| 160 KYRTPVILLT 169
                                       9999*99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       750  (0.0418317); expected 358.6 (0.02)
Passed bias filter:                      613  (0.0341904); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.49
# Mc/sec: 2311.70
//
Query:       gi|242399444|ref|YP_002994869.1|  [L=170]
Description: 2-ketoglutarate:ferredoxin oxidoreductase (KGOR), subunit gamma [Thermococcus sibiricus MM 739]
Scores for complete 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-38  130.6   0.5      1e-37  129.9   0.5    1.3  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 !  129.9   0.5   5.7e-42     1e-37       1     177 []       9     166 ..       9     166 .. 0.96

  Alignments for each domain:
  == domain 1  score: 129.9 bits;  conditional E-value: 5.7e-42
                                       CTSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHHHHGGGEE CS
                               POR   1 GGqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetlsehldglk 77 
                                       GGqGv++ag il++aaa++G++v+++++ygs+ rGghs++++ is++pi++ i   +ad+l+al +  ++   + lk
  gi|242399444|ref|YP_002994869.1|   9 GGQGVILAGVILGDAAAIEGLNVVQTQDYGSQSRGGHSIADLIISKDPIYDLIV-TKADVLLALAQLGYESTKESLK 84 
                                       9**********************************************9999999.********************** PP

                                       EEEEEEEECTCGTT-CCHHHCTS-HHHHHHHT-EEEEE-HHHHHHHCCC.CCHHHHHHHHHHHHHHT.S-HHHHHHH CS
                               POR  78 pggiiiynseelkpdelkkakeeerelkerlgvrvygvdatkiakeiggneraaNtvmlGalaallg.lplealeea 153
                                       +gg++i++++ ++pd +                   g ++t+ia+e+ g ++++N+v+lG+l+a ++ ++ e++e+a
  gi|242399444|ref|YP_002994869.1|  85 EGGLLIVDTGLVQPDKEFT-----------------GAPFTRIAEEKVGLALTVNMVALGYLVAKTNvVKKESVEKA 144
                                       *********9877776655.................789****************************99******** PP

                                       HHCCS-CH.HHHHHHHHHHHHHHH CS
                               POR 154 ikkrfpkkkeviekNlkafragye 177
                                       i++r+pk     e Nlkafr gye
  gi|242399444|ref|YP_002994869.1| 145 IRRRVPKG--TEEINLKAFRTGYE 166
                                       ******96..89***********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); 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: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1269.85
//
Query:       gi|242399445|ref|YP_002994870.1|  [L=287]
Description: 2-ketoglutarate:ferredoxin oxidoreductase (KGOR), subunit beta [Thermococcus sibiricus MM 739]
Scores for complete 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-37  128.1   0.1    3.4e-37  127.6   0.1    1.2  1  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b


Domain annotation for each model (and alignments):
>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.6   0.1   1.9e-41   3.4e-37       2     152 ..      57     204 ..      56     205 .. 0.94

  Alignments for each domain:
  == domain 1  score: 127.6 bits;  conditional E-value: 1.9e-41
                                       SSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEEE CS
                      TPP_enzyme_C   2 iGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGaklakpdrevvaivGDGgflmi.lqelatavrrnlpitv 77 
                                       iGc+         +++ + +l +++++t+G+++++A+G+k+  pd++vv+i+GDG+++ i +++l++a+rrn++itv
  gi|242399445|ref|YP_002994870.1|  57 IGCSAW-------IAS-PYFLADTLHTTHGRAIAYATGVKVGLPDKKVVVISGDGDLAGIgGNHLIHAARRNIDITV 125
                                       677775.......333.3688899*****************99********************************** PP

                                       EEEE-SBCCCHHHH...HHHHTCCTTTTSBB.BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHHHHCSSSEEE CS
                      TPP_enzyme_C  78 vvlnNegygmtggq...qepfggkrksgpagkdlkpvdfaklaealGak.garvekadveeleealkealekkgpal 150
                                       +++nN +ygmtggq   ++pfg+ ++++p+++ ++p+++ + ++++Ga+ +ar ++ +v  l e +k+al+ kg+al
  gi|242399445|ref|YP_002994870.1| 126 ILVNNFIYGMTGGQvapTTPFGAITTTSPYRNVEHPLNISETVASAGASyVARWTTFHVYPLIESIKRALSVKGFAL 202
                                       *************************************************999************************* PP

                                       EE CS
                      TPP_enzyme_C 151 ie 152
                                       +e
  gi|242399445|ref|YP_002994870.1| 203 VE 204
                                       *8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1871.94
//
Query:       gi|242399446|ref|YP_002994871.1|  [L=405]
Description: 2-ketoglutarate:ferredoxin oxidoreductase (KGOR), subunit alpha [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-75  252.9   0.0    3.8e-75  252.6   0.0    1.1  1  POR_N            Pyruvate flavodoxin/ferredoxin oxidoreductas
    4.5e-19   68.6   0.3    7.2e-19   68.0   0.3    1.3  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
    2.1e-05   24.4   0.1    4.5e-05   23.3   0.0    1.6  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 !  252.6   0.0   6.4e-79   3.8e-75       2     230 ..      34     270 ..      33     271 .. 0.96

  Alignments for each domain:
  == domain 1  score: 252.6 bits;  conditional E-value: 6.4e-79
                                       HHHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCC CS
                             POR_N   2 aaiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmien 78 
                                       +a+ ag++++a+YPITP+seiae++a+ l+k +    +++qme+Eig+i+av+GA+++G +++TaTSg+G++Lm+en
  gi|242399446|ref|YP_002994871.1|  34 GALFAGCRFYAGYPITPASEIAETMARELPKLKG---YYIQMEDEIGSIAAVVGASWTGFKSMTATSGPGFSLMQEN 107
                                       7899*****************************5...**************************************** PP

                                       HHHHHHTT--EEEEEEEEE-STTBEEEEE--TTCHHHH.....S---EEEE-SSHHHHHHHHHHHHHHHHHCTSEEE CS
                             POR_N  79 lglaageelPvvivvvaRalpstglsirtdqsDlmaar.....dtglivlasenvqeafdlalvAfnlAekvrvPvi 150
                                       lg+a+ +e+P+v+v+v+R++pstg++++++q+D+++ar     d+++i++++ +v++ f+ +++Afnl+ek+r+Pv+
  gi|242399446|ref|YP_002994871.1| 108 LGYAIFTETPLVLVDVQRSGPSTGQATKGAQGDFFQARwgthgDHPIIAISPTSVEDSFWETIRAFNLSEKFRIPVL 184
                                       ***************************************************************************** PP

                                       EEEEHHHH.HEEEEEEC-SGG.GS-----SBXXXXXXXX........SXXXBXXTXXTSSXXEEESBXBXTTSXBXX CS
                             POR_N 151 vlfDgfllshevekvelpdeedelklikekleeyerkey........aldpekpiargtaanpdtglehrekgneae 219
                                       vl Dg+++ h++e++++pd e e++++ +kl+ ++++++        +l p +p++  ++++++tg++h+e+g +++
  gi|242399446|ref|YP_002994871.1| 185 VLADGIIG-HTREQINIPDPE-EVEIVYRKLPTSDEEAKypfgdvhgDLIPPMPLFGHGYFTHVTGSTHKENGLRDV 259
                                       ********.************.8888888887776665568************************************ PP

                                       XXHHHHHHHHH CS
                             POR_N 220 daaekvveeve 230
                                        + e++++ v+
  gi|242399446|ref|YP_002994871.1| 260 YTPEVHDRLVR 270
                                       *9999998876 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 !   68.0   0.3   1.2e-22   7.2e-19       1     102 []     294     388 ..     294     388 .. 0.98

  Alignments for each domain:
  == domain 1  score: 68.0 bits;  conditional E-value: 1.2e-22
                                       -SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHHHHHHH CS
                           PFOR_II   1 AevvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlveevkaa 77 
                                       Ae+++v  G +a+    av+++R++gikvGl+ ++t+ PFP e++kel k+v+ ++v ++n      Gq++ ev++ 
  gi|242399446|ref|YP_002994871.1| 294 AEILLVSWGVSARPSLGAVMKARKKGIKVGLFVPKTVHPFPGERIKELSKNVQLIIVPEMNL-----GQVILEVQRF 365
                                       9*************************************************************.....********** PP

                                       TGGGTSEEEEEE--GGG----HHHH CS
                           PFOR_II  78 lkkskvkvvnfvaglgGrditvedi 102
                                       + ++   +v  v+++gG  +tve+i
  gi|242399446|ref|YP_002994871.1| 366 VRDE--VPVIGVNKIGGVPLTVEEI 388
                                       **99..999999**********997 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       1.6   9.5e+03      54      86 ..      59      89 ..      53      95 .. 0.68
   2 !   23.3   0.0   7.6e-09   4.5e-05       7      68 ..     291     352 ..     285     397 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 1.6
                                      HHHHHHHHSEEEEEEEEESTTSHHHHHHHHHHH CS
                   Transketolase_C 54 ilesvkktgrlvvveeavkrgGigsevaaalae 86
                                       +e+ k +g ++ +e+  ++g+i++ v a ++ 
  gi|242399446|ref|YP_002994871.1| 59 ARELPKLKGYYIQMED--EIGSIAAVVGASWTG 89
                                      5566666677777777..678888888887776 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 7.6e-09
                                       ETTSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEE CS
                   Transketolase_C   7 regkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvve 68 
                                        e  +++lv++G   + +l A+ +++k+gi++ +  + tv p+  e i+e+ k+ + ++v e
  gi|242399446|ref|YP_002994871.1| 291 VEDAEILLVSWGVSARPSLGAVMKARKKGIKVGLFVPKTVHPFPGERIKELSKNVQLIIVPE 352
                                       57889********************************************9999988888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); 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: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 2446.16
//
Query:       gi|242399447|ref|YP_002994872.1|  [L=112]
Description: 2-ketoglutarate:ferredoxin oxidoreductase and 2-oxoglutarate ferredoxin oxidoreductase 2 (KGOR), subunit delta [Thermococcus sibiricus MM 739]
Scores for 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-11   41.3  11.2    3.4e-05   23.5   3.2    2.2  2  Fer4        4Fe-4S binding domain
    2.2e-10   40.9   4.9    3.5e-10   40.3   4.9    1.3  1  Fer4_7      4Fe-4S dicluster domain
    5.1e-08   32.9   5.8      0.001   19.2   0.9    2.2  2  Fer4_21     4Fe-4S dicluster domain
    3.1e-07   30.5  15.7    6.6e-05   23.0   9.1    2.1  2  Fer4_9      4Fe-4S dicluster domain
      2e-06   27.6  10.8     0.0031   17.5   1.1    2.3  2  Fer4_2      4Fe-4S binding domain
    5.9e-06   26.4   0.2      7e-06   26.1   0.2    1.2  1  ETF_QO      Electron transfer flavoprotein-ubiquinone oxidore
    8.2e-06   25.7  10.3     0.0074   16.3   2.7    2.3  2  Fer4_6      4Fe-4S binding domain
    8.3e-06   26.3   5.3      0.049   14.2   1.5    2.2  2  Fer4_13     4Fe-4S single cluster domain of Ferredoxin I
    1.9e-05   25.1   8.1     0.0085   16.6  10.0    2.2  2  Fer4_17     4Fe-4S dicluster domain
    2.2e-05   25.3   7.7      0.011   16.6   0.3    2.3  2  Fer4_16     4Fe-4S double cluster binding domain
    8.9e-05   22.5   9.4    0.00097   19.2   9.7    2.1  2  Fer4_10     4Fe-4S dicluster domain
    0.00014   22.6   3.4      0.024   15.5   0.2    2.2  2  Fer4_22     4Fe-4S dicluster domain
    0.00091   19.9   6.4      0.015   16.0   0.3    2.4  2  Fer4_15     4Fe-4S single cluster domain
     0.0048   17.3  10.0       0.06   13.9   2.2    2.4  2  Fer4_4      4Fe-4S binding domain
     0.0072   15.8   0.1       0.01   15.3   0.1    1.2  1  DUF3343     Protein of unknown function (DUF3343)
  ------ inclusion threshold ------
      0.016   15.6  10.1       0.88   10.1   1.2    2.2  2  Fer4_8      4Fe-4S dicluster domain
       0.13   13.3  14.4        0.7   11.0   3.5    2.5  2  Fer4_3      4Fe-4S binding domain
        3.3    7.9   8.3        9.7    6.4   1.6    2.1  2  Fer4_18     4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   1.1   5.1e-08     5e-05       2      22 ..      50      70 ..      49      72 .. 0.88
   2 !   23.5   3.2   3.4e-08   3.4e-05       1      23 [.      86     108 ..      86     109 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 5.1e-08
                                      EEETTTSSS-THHHHHSTTTE CS
                              Fer4  2 videekCigCGaCvevCPvgA 22
                                       +d+ +C gCG+C e CP  +
  gi|242399447|ref|YP_002994872.1| 50 SVDTFLCKGCGICLELCPRKV 70
                                      68999*************865 PP

  == domain 2  score: 23.5 bits;  conditional E-value: 3.4e-08
                                       EEEETTTSSS-THHHHHSTTTEE CS
                              Fer4   1 vvideekCigCGaCvevCPvgAI 23 
                                       + ++ +kC++C++C+  CP  AI
  gi|242399447|ref|YP_002994872.1|  86 IPVNADKCVKCKLCELLCPDFAI 108
                                       579****************9988 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   4.9   3.5e-13   3.5e-10       2      49 ..      56     104 ..      55     107 .. 0.92

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 3.5e-13
                            Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekv.eidpekClgCgaCvavCP 49 
                                       C gCg C + Cp k++e+ +e +ekg++++  ++++kC+ C+ C+  CP
  gi|242399447|ref|YP_002994872.1|  56 CKGCGICLELCPRKVFEWSKELSEKGVHYPiPVNADKCVKCKLCELLCP 104
                                       **************************97763689*************** PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.3   6.7e-06    0.0067      27      52 ..      42      67 ..      31      72 .. 0.78
   2 !   19.2   0.9     1e-06     0.001      34      54 ..      86     105 ..      75     110 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.7e-06
                           Fer4_21 27 eidaktvlkvvedeCvGCnlCssvCP 52
                                       ++++  + v +  C GC +C++ CP
  gi|242399447|ref|YP_002994872.1| 42 GKTEAVEISVDTFLCKGCGICLELCP 67
                                      45555566788889************ PP

  == domain 2  score: 19.2 bits;  conditional E-value: 1e-06
                           Fer4_21  34 lkvvedeCvGCnlCssvCPve 54 
                                       ++v +d+Cv C+lC   CP +
  gi|242399447|ref|YP_002994872.1|  86 IPVNADKCVKCKLCELLCP-D 105
                                       4788999999999999999.4 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.5   3.1e-06    0.0031      33      49 ..      46      69 ..      23      71 .. 0.71
   2 !   23.0   9.1   6.7e-08   6.6e-05       2      50 ..      56     107 ..      55     108 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.1e-06
                            Fer4_9 33 e.......eaCigCgaCveaCpkg 49
                                      +         C gCg C+e Cp++
  gi|242399447|ref|YP_002994872.1| 46 AveisvdtFLCKGCGICLELCPRK 69
                                      2444555568************98 PP

  == domain 2  score: 23.0 bits;  conditional E-value: 6.7e-08
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraase...eaCigCgaCveaCpkga 50 
                                       C gCg C e Cp +v++ ++   +  ++       ++C++C+ C+  Cp  a
  gi|242399447|ref|YP_002994872.1|  56 CKGCGICLELCPRKVFEWSKELSEKGVHYPIPvnaDKCVKCKLCELLCPDFA 107
                                       ***************9777665555544333356799************855 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   1.1   3.1e-06    0.0031       4      21 ..      50      67 ..      46      68 .. 0.87
   2 !   15.0   2.8     2e-05      0.02       2      21 ..      85     104 ..      84     105 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.1e-06
                            Fer4_2  4 vvdtdrCigCgaCvsaCP 21
                                       vdt  C gCg+C+  CP
  gi|242399447|ref|YP_002994872.1| 50 SVDTFLCKGCGICLELCP 67
                                      578889************ PP

  == domain 2  score: 15.0 bits;  conditional E-value: 2e-05
                            Fer4_2   2 pvvvdtdrCigCgaCvsaCP 21 
                                       p+ v++d+C+ C+ C   CP
  gi|242399447|ref|YP_002994872.1|  85 PIPVNADKCVKCKLCELLCP 104
                                       6789*************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 !   26.1   0.2     7e-09     7e-06      38      90 ..      54     108 ..      19     112 .] 0.70

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 7e-09
                                       HHHHHS-THHHH-TTS-EEEEETTTTSSEE..EEE-CCC--S--HHHHH-TT--E CS
                            ETF_QO  38 nlekyagpeqryCPagvyeivedeeakekk..lqinaqnCvhCktCdikdpsqni 90 
                                        l k  g++   CP  v+e+ ++ ++k+++  + +na  Cv Ck C++  p+  i
  gi|242399447|ref|YP_002994872.1|  54 FLCKGCGICLELCPRKVFEWSKELSEKGVHypIPVNADKCVKCKLCELLCPDFAI 108
                                       344445778899*********98766666511678************98887665 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.9   4.8e-05     0.048       8      21 ..      55      68 ..      48      71 .. 0.81
   2 !   16.3   2.7   7.4e-06    0.0074       4      24 .]      88     108 ..      88     108 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.8e-05
                            Fer4_6  8 kCigCgdCvrvCPe 21
                                      +C gCg C   CP 
  gi|242399447|ref|YP_002994872.1| 55 LCKGCGICLELCPR 68
                                      8************6 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 7.4e-06
                            Fer4_6   4 idpdkCigCgdCvrvCPegai 24 
                                       +++dkC+ C  C+  CP  ai
  gi|242399447|ref|YP_002994872.1|  88 VNADKCVKCKLCELLCPDFAI 108
                                       799**************8665 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.1   6.9e-05     0.068       1      24 [.      51      75 ..      51      83 .. 0.83
   2 !   14.2   1.5   4.9e-05     0.049       1      19 [.      88     106 ..      88     106 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.9e-05
                           Fer4_13  1 VDrdtCiacgaCvelaP.dvFeedd 24
                                      VD   C +cg+C el+P +vFe  +
  gi|242399447|ref|YP_002994872.1| 51 VDTFLCKGCGICLELCPrKVFEWSK 75
                                      78889************55887665 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 4.9e-05
                           Fer4_13   1 VDrdtCiacgaCvelaPdv 19 
                                       V+ d+C+ c++C  l+Pd+
  gi|242399447|ref|YP_002994872.1|  88 VNADKCVKCKLCELLCPDF 106
                                       899**************96 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.4   2.1e-05     0.021      32      59 ..      42      69 ..      11      71 .. 0.66
   2 !   16.6  10.0   8.6e-06    0.0085       2      57 ..      56     104 ..      55     106 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.1e-05
                           Fer4_17 32 glleeaekeekaslCieCgeCerkCPqg 59
                                      g++e++e +    lC +Cg C + CP +
  gi|242399447|ref|YP_002994872.1| 42 GKTEAVEISVDTFLCKGCGICLELCPRK 69
                                      6666677777888899999999999876 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 8.6e-06
                           Fer4_17   2 CiqCgyClpeCpsyea...ydnepkkllraaklglleeaekeekaslCieCgeCerkCP 57 
                                       C +Cg Cl+ Cp+       +  +k + + + +          +a++C++C++Ce  CP
  gi|242399447|ref|YP_002994872.1|  56 CKGCGICLELCPRKVFewsKELSEKGVHYPIPV----------NADKCVKCKLCELLCP 104
                                       ************955422244456666666555..........699************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 !   16.6   0.3   1.1e-05     0.011       2      20 ..      56      74 ..      55      84 .. 0.84
   2 !   11.5   2.3   0.00044      0.43       1      18 [.      92     109 ..      92     111 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.1e-05
                           Fer4_16  2 CgtCgkCaevCPtnaikek 20
                                      C++Cg C+e CP ++++  
  gi|242399447|ref|YP_002994872.1| 56 CKGCGICLELCPRKVFEWS 74
                                      ************9998755 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00044
                           Fer4_16   1 rCgtCgkCaevCPtnaik 18 
                                       +C++C+ C   CP  ai 
  gi|242399447|ref|YP_002994872.1|  92 KCVKCKLCELLCPDFAIA 109
                                       6*************9996 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   9.7   9.8e-07   0.00097       3      56 .]      50     104 ..      48     104 .. 0.93
   2 !   11.4   3.0   0.00028      0.27       4      21 ..      88     105 ..      85     111 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 9.8e-07
                           Fer4_10   3 vidddtCirCgkCvkaCPadl.tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                        +d+  C +Cg C + CP ++ + ++   e+  + ++ ++ +kC +c  C   CP
  gi|242399447|ref|YP_002994872.1|  50 SVDTFLCKGCGICLELCPRKVfEWSKELSEKGVHYPIPVNADKCVKCKLCELLCP 104
                                       678899*************999889999999999********************9 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00028
                           Fer4_10   4 idddtCirCgkCvkaCPa 21 
                                       +++d+C++C+ C   CP 
  gi|242399447|ref|YP_002994872.1|  88 VNADKCVKCKLCELLCPD 105
                                       5899************96 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.2   2.4e-05     0.024      67      95 ..      41      69 ..       7      70 .. 0.84
   2 !    8.4   0.3    0.0039       3.9       1      13 [.      92     104 ..      74     108 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.4e-05
                           Fer4_22 67 lhklsefkekfgesgCvGCgRCieacpvk 95
                                      + k++ ++ ++++  C GCg C e cp k
  gi|242399447|ref|YP_002994872.1| 41 IGKTEAVEISVDTFLCKGCGICLELCPRK 69
                                      557788888999**************987 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0039
                           Fer4_22   1 rClsCgaCtlvCp 13 
                                       +C++C  C l+Cp
  gi|242399447|ref|YP_002994872.1|  92 KCVKCKLCELLCP 104
                                       5888888888887 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.3   1.5e-05     0.015       1      23 [.      49      72 ..      49      80 .. 0.83
   2 ?    6.6   1.2     0.013        13       3      21 ..      88     106 ..      86     108 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.5e-05
                           Fer4_15  1 VvvDrdaCigcglCvaeap.evfe 23
                                      + vD  +C gcg C++++p +vfe
  gi|242399447|ref|YP_002994872.1| 49 ISVDTFLCKGCGICLELCPrKVFE 72
                                      689***************625665 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.013
                           Fer4_15   3 vDrdaCigcglCvaeapev 21 
                                       v+ d+C  c lC  ++p++
  gi|242399447|ref|YP_002994872.1|  88 VNADKCVKCKLCELLCPDF 106
                                       789**************86 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   1.1    0.0054       5.4       4      16 ..      56      68 ..      52      75 .. 0.91
   2 !   13.9   2.2   6.1e-05      0.06       2      15 ..      91     104 ..      90     106 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0054
                            Fer4_4  4 CigCgsCvaaCPq 16
                                      C gCg C   CP 
  gi|242399447|ref|YP_002994872.1| 56 CKGCGICLELCPR 68
                                      9**********95 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 6.1e-05
                            Fer4_4   2 erCigCgsCvaaCP 15 
                                       ++C+ C+ C+  CP
  gi|242399447|ref|YP_002994872.1|  91 DKCVKCKLCELLCP 104
                                       89***********9 PP

>> DUF3343  Protein of unknown function (DUF3343)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1     1e-05      0.01      19      64 ..      39      84 ..      29      85 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1e-05
                           DUF3343 19 lkeggiearliplPreisagCGlalrvneedieeasrllseaeipy 64
                                      l+ g++ea  i++   + +gCG++l++ ++++ e+s+ lse++++y
  gi|242399447|ref|YP_002994872.1| 39 LSIGKTEAVEISVDTFLCKGCGICLELCPRKVFEWSKELSEKGVHY 84
                                      5556777777777777889************************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 ?   10.1   1.2   0.00088      0.88      48      65 .]      53      70 ..      28      70 .. 0.76
   2 ?    9.3   2.7    0.0016       1.6       2      16 ..      90     104 ..      89     110 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00088
                            Fer4_8 48 lwsCttcgaCtevCpvgi 65
                                       + C +cg C e Cp ++
  gi|242399447|ref|YP_002994872.1| 53 TFLCKGCGICLELCPRKV 70
                                      567999999999998875 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0016
                            Fer4_8   2 lekCieCgaCqsaCp 16 
                                       ++kC++C +C+  Cp
  gi|242399447|ref|YP_002994872.1|  90 ADKCVKCKLCELLCP 104
                                       567888888877777 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   3.5   0.00071       0.7       1      14 [.      56      69 ..      56      70 .. 0.93
   2 ?    7.6   3.1    0.0084       8.4       1      12 [.      93     104 ..      93     106 .. 0.97

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00071
                            Fer4_3  1 CtgCgaCvevCPvg 14
                                      C gCg C+e CP +
  gi|242399447|ref|YP_002994872.1| 56 CKGCGICLELCPRK 69
                                      9***********76 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0084
                            Fer4_3   1 CtgCgaCvevCP 12 
                                       C+ C +C+  CP
  gi|242399447|ref|YP_002994872.1|  93 CVKCKLCELLCP 104
                                       9**********9 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.6     0.014        14      58      75 ..      53      70 ..      30      74 .. 0.78
   2 ?    6.4   1.6    0.0098       9.7      57      72 ..      89     104 ..      72     111 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.014
                           Fer4_18 58 agdcidcescvkvcPtgi 75
                                      +  c  c+ c+++cP ++
  gi|242399447|ref|YP_002994872.1| 53 TFLCKGCGICLELCPRKV 70
                                      556999*********876 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0098
                           Fer4_18  57 gagdcidcescvkvcP 72 
                                       +a +c++c+ c  +cP
  gi|242399447|ref|YP_002994872.1|  89 NADKCVKCKLCELLCP 104
                                       5678***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 775.86
//
Query:       gi|242399448|ref|YP_002994873.1|  [L=328]
Description: Fe-S oxidoreductase [Thermococcus sibiricus MM 739]
Scores for complete 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   33.6   0.1      2e-07   31.6   0.0    1.8  2  Radical_SAM  Radical SAM superfamily
  ------ inclusion threshold ------
      0.038   13.2   0.2      0.069   12.4   0.2    1.4  1  DUF3834      Protein of unknown function (DUF3834)


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 !   31.6   0.0   2.2e-11     2e-07      10     144 ..      40     182 ..      26     197 .. 0.79
   2 ?   -0.5   0.0      0.16   1.4e+03     126     142 ..     198     213 ..     189     262 .. 0.55

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 2.2e-11
                                       --TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGS.......TTHHHHHHHHHHTCCCTE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  10 rCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggeplly.......pdfvellerlaklavpgi 78 
                                       +C  C+ p    +++  +   +e+ ++ +k++  +kg + + i+++g  +++       +++++ l++++   ++  
  gi|242399448|ref|YP_002994873.1|  40 ACYMCSYPAEAPKTPWTQRDLIEYFKKALKKIEGKKGpISVRIFTSGSFFDDgevkpttRKEIFSLLAEI---EDVK 113
                                       49******99899999999999999999999996777799999998888888777754433334444444...459* PP

                                       EEEEEECSSCHGHHHHHHHHHTT...-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET CS
                                       xxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  79 ritvetngtlpdeeklerllelg...vdrvslgleaaddekvlklmnrghtfeevlealeklreagikr 144
                                       +i+vet   l++ e +++l++l       v++gle+a+d+     +n+g+tfee++ a + ++eag  +
  gi|242399448|ref|YP_002994873.1| 114 EIVVETRSELVRFETVKELVDLVegkHFEVAIGLETANDDIADVGINKGNTFEEFITASKVIKEAGAYV 182
                                       ************99999999999988999***********5555566******************9663 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.16
                                       HHHHHHHHHHHHHHTTS CS
                                       xxxxxxxxxxxxxxxxx RF
                       Radical_SAM 126 tfeevlealeklreagi 142
                                       ++e+++e+++k++ +  
  gi|242399448|ref|YP_002994873.1| 198 GIEDIKESIKKAAPY-T 213
                                       445555555554433.2 PP

>> DUF3834  Protein of unknown function (DUF3834)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   7.7e-06     0.069      92     178 ..     118     213 ..     108     232 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.7e-06
                           DUF3834  92 kikaevvyaddpeevlkllnegevdsav........va.selkkgeafedllkklgvyvpGsCgaavken...eeef 156
                                       + ++e+v  ++++e+++l++ ++ + a+        +a   ++kg++fe++++  +v +  + ga+vk++   +  f
  gi|242399448|ref|YP_002994873.1| 118 ETRSELVRFETVKELVDLVEGKHFEVAIgletanddIAdVGINKGNTFEEFITASKV-IK-EAGAYVKTYlllKPAF 192
                                       5689999999999999999999988775433333333325689**********4444.44.79******98755567 PP

                           DUF3834 157 idaYeeGIelikedpeeaaeyi 178
                                       +++ ++GIe ike  ++aa y 
  gi|242399448|ref|YP_002994873.1| 193 LNE-RDGIEDIKESIKKAAPYT 213
                                       666.89*************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       773  (0.0431145); expected 358.6 (0.02)
Passed bias filter:                      622  (0.0346924); 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 0.24s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2436.21
//
Query:       gi|242399449|ref|YP_002994874.1|  [L=194]
Description: hypothetical protein TSIB_1474 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-27   96.4  14.5    2.5e-27   95.8  14.5    1.3  1  DUF996         Protein of unknown function (DUF996)
     0.0045   16.9  13.9       0.24   11.3   6.0    2.5  2  DUF2975        Protein of unknown function (DUF2975)
  ------ inclusion threshold ------
      0.011   15.2   9.9      0.015   14.8   9.9    1.1  1  DUF373         Domain of unknown function (DUF373)
      0.068   13.0   5.5          2    8.3   0.3    2.5  2  DUF1418        Protein of unknown function (DUF1418)
       0.68   10.1  10.7      0.053   13.6   2.1    2.1  2  MpPF26         M penetrans paralogue family 26
       0.76   10.0   5.3       0.34   11.2   0.4    2.2  2  DUF3522        Protein of unknown function (DUF3522)
       0.82    9.8   6.8        1.7    8.7   0.9    2.1  2  DHHC           DHHC palmitoyltransferase
        1.4    8.2   9.5      0.033   13.5   1.2    2.3  3  NicO           High-affinity nickel-transport protein
        1.5    7.8  15.9       0.35    9.9  10.9    2.1  2  DUF973         Protein of unknown function (DUF973)
        3.1    8.3   8.1        2.3    8.7   0.4    2.8  2  MerC           MerC mercury resistance protein
        4.7    7.1  10.0        3.2    7.6   1.9    2.3  2  DUF1461        Protein of unknown function (DUF1461)
        5.8    7.4  10.3         10    6.6   0.6    2.7  2  DUF3262        Protein of unknown function (DUF3262)
        9.1    6.0   5.8        4.6    7.0   3.3    1.7  2  FA_desaturase  Fatty acid desaturase


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 !   95.8  14.5   1.8e-30   2.5e-27       2     135 .]      31     170 ..      30     170 .. 0.89

  Alignments for each domain:
  == domain 1  score: 95.8 bits;  conditional E-value: 1.8e-30
                            DUF996   2 sivGliLvlvalkeiskavndekifsnaliafilsiialvvailalllvlga.latalelpgleeaas....lilll 73 
                                        ++Gl+L+l a+kei++++++e+if+++l+ +il + al+v+ila+ l++g+ ++ +  ++g+ee+++    li+ +
  gi|242399449|ref|YP_002994874.1|  31 MLLGLVLLLFAVKEIADEIEREDIFRDYLVGVILRFGALIVIILAFFLAMGFaVLKGAPFKGMEEGFEgmrmLIAPI 107
                                       689************************************99988887777651556778888888888666666667 PP

                            DUF996  74 llvliiayvlliisavflkksyellgkrtgvklFetagllyfiGaiLtivl.vGliilliaei 135
                                       l+  ++a++l++i +++ +ksye++++++ v++F+t+g lyf+G iL+i l +Gl++lli++i
  gi|242399449|ref|YP_002994874.1| 108 LVGALLAWILFVIGTYYTRKSYEKISSEVQVDTFKTVGFLYFVGGILVIALgIGLLVLLIGKI 170
                                       77779********************************************************98 PP

>> DUF2975  Protein of unknown function (DUF2975)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   6.0   0.00017      0.24      25     113 ..      29     117 ..      22     126 .. 0.70
   2 !    9.0   5.0    0.0009       1.2      64     120 ..     109     174 ..     104     187 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00017
                           DUF2975  25 vlallafvvalvqlwkLlrsirkgevFspanvrrLrriglaliaaalllaagivalallaelelapgvvllllgvaf 101
                                       ++ ll +v+ l+++  +   i+++++F +  v  + r g +++++ + ++a+++a+   a ++     + ++ +++ 
  gi|242399449|ref|YP_002994874.1|  29 LVMLLGLVLLLFAVKEIADEIEREDIFRDYLVGVILRFGALIVIILAFFLAMGFAVLKGAPFKGMEEGFEGMRMLIA 105
                                       5556667788899999*****************************88888888888777774444433333333333 PP

                           DUF2975 102 aslvigllvlvl 113
                                         lv +ll+++l
  gi|242399449|ref|YP_002994874.1| 106 PILVGALLAWIL 117
                                       333333333332 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0009
                           DUF2975  64 laliaaalllaagivalallae.lelap........gvvllllgvafaslvigllvlvlaellaeA 120
                                       + +++a++l+++g  ++  + e ++ +         g + +++g+ +++l+igllvl++ ++l++ 
  gi|242399449|ref|YP_002994874.1| 109 VGALLAWILFVIGTYYTRKSYEkISSEVqvdtfktvGFLYFVGGILVIALGIGLLVLLIGKILEIV 174
                                       566777899999999999888866655588889999999999999999***************985 PP

>> DUF373  Domain of unknown function (DUF373)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   9.9   1.1e-05     0.015     158     286 ..      30     171 ..      25     184 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.1e-05
                            DUF373 158 LvplGlllliyallll..............lglpelalaiillllGlylllrGfgldelleelleklkesleegrit 220
                                       +++lGl+ll++a+  +              +g+  l ++++++++ +++l  Gf + +     ++ ++e +e  r+ 
  gi|242399449|ref|YP_002994874.1|  30 VMLLGLVLLLFAVKEIadeieredifrdylVGV-ILRFGALIVIILAFFLAMGFAVLK--GAPFKGMEEGFEGMRML 103
                                       5689******************99997654333.234556677777888999999888..77899************ PP

                            DUF373 221 fvtyvvallllligiisgyislesvss..asvssglltlilafiygavewlalailtaslgkiideyl 286
                                       +  ++v++ll+ i ++ g++ + ++++  +s  +  + +++ f+y +  +l++a+ + +l+ +i ++l
  gi|242399449|ref|YP_002994874.1| 104 IAPILVGALLAWILFVIGTYYTRKSYEkiSSEVQVDTFKTVGFLYFVGGILVIALGIGLLVLLIGKIL 171
                                       *****999997776666666556666545333333344455577775555555544444444444333 PP

>> DUF1418  Protein of unknown function (DUF1418)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.9    0.0056       7.7       6      60 ..      22      76 ..      17      96 .. 0.81
   2 ?    8.3   0.3    0.0014         2      12      44 ..     155     188 ..     142     190 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0056
                           DUF1418  6 klPrsvlilevlGliLLvlayLsvndylsLPgplsskeaaivmiflGvllllPaa 60
                                       +Pr+  ++ +lGl+LL  a   + d ++  + +    + +++ f  +++++ a 
  gi|242399449|ref|YP_002994874.1| 22 FVPRAWSLVMLLGLVLLLFAVKEIADEIEREDIFRDYLVGVILRFGALIVIILAF 76
                                      57888888999*****************999999999999999998887777664 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0014
                           DUF1418  12 lilevlGl.iLLvlayLsvndylsLPgplsskea 44 
                                       +i+  +Gl +LL+  +L +  y sLP+ ++++e+
  gi|242399449|ref|YP_002994874.1| 155 VIALGIGLlVLLIGKILEIVAYFSLPESIKKEEV 188
                                       5556678625666789***********9988765 PP

>> MpPF26  M penetrans paralogue family 26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   2.1   3.9e-05     0.053      25     121 ..      27     122 ..      13     133 .. 0.86
   2 ?    2.4   6.5      0.12   1.6e+02      22      80 ..     112     173 ..     100     191 .. 0.53

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.9e-05
                            MpPF26  25 lllvsllayivllskskllskeyeeesslleaelligvllillidifyivnfileiiLiiKvselkkkhpefkkvkl 101
                                        +lv+ll ++ ll + k    e+e e  + ++ +++++ + +li i +++ f+++ + ++K   +k+ +  f+ +++
  gi|242399449|ref|YP_002994874.1|  27 WSLVMLLGLVLLLFAVKEIADEIEREDIFRDYLVGVILRFGALIVI-ILAFFLAMGFAVLKGAPFKGMEEGFEGMRM 102
                                       6788888888888888888889899999999988888888888888.9999************************** PP

                            MpPF26 102 htvLliigifilpifsiidc 121
                                       ++   ++g ++ +i+ +i +
  gi|242399449|ref|YP_002994874.1| 103 LIAPILVGALLAWILFVIGT 122
                                       **************999965 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.12
                            MpPF26  22 atvlllvsllayivllskskllskeyeeesslleaelligvllillidi...fyivnfilei 80 
                                       + + +l+++ +y++  s +k++s+   +  + +     +g +l+++ +i   ++++  ilei
  gi|242399449|ref|YP_002994874.1| 112 LLAWILFVIGTYYTRKSYEKISSEVQVDTFKTVGFLYFVGGILVIALGIgllVLLIGKILEI 173
                                       22233444445555555555555555555555555555555555555554444444444444 PP

>> DUF3522  Protein of unknown function (DUF3522)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.57   7.9e+02     149     168 ..      24      45 ..      12      58 .. 0.74
   2 ?   11.2   0.4   0.00025      0.34     110     167 ..      99     160 ..      90     172 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.57
                           DUF3522 149 krlnlqqllpgllllalAl..f 168
                                       +r +   +l gl+ll++A+  +
  gi|242399449|ref|YP_002994874.1|  24 PRAWSLVMLLGLVLLLFAVkeI 45 
                                       6788888899999999888533 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00025
                           DUF3522 110 slantiipilvgllillvswliecvkkrklypsllr....rrlkrlnlqqllpgllllalAl 167
                                       +++ +i+pilvg+l+  + ++i ++ +rk+y ++ +     + k++   +++ g+l++al++
  gi|242399449|ref|YP_002994874.1|  99 GMRMLIAPILVGALLAWILFVIGTYYTRKSYEKISSevqvDTFKTVGFLYFVGGILVIALGI 160
                                       67899***************************955576666667777777777788777777 PP

>> DHHC  DHHC palmitoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.6     0.028        38      59     109 ..      31      81 ..      15      88 .. 0.53
   2 ?    8.7   0.9    0.0012       1.7      47     116 ..      99     165 ..      96     185 .. 0.61

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.028
                              DHHC  59 llllilalvlllialvklveeekkseflavtllkkllsilllvlsllflll 109
                                       +ll ++ l++++  + +++e e+ ++ + v  +  ++++++++l++++++ 
  gi|242399449|ref|YP_002994874.1|  31 MLLGLVLLLFAVKEIADEIEREDIFRDYLVGVILRFGALIVIILAFFLAMG 81 
                                       222233333344444444444444444444444446666666665555443 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0012
                              DHHC  47 NykyFllfllylllllilalvlllialvklveeekkseflavtllkkllsilllvlsllfllllgllllf 116
                                        +++ ++ +l+ +ll+++ +v+  ++ +k +e+ + +    v+++k+ + +l++v  +l+++l + ll+ 
  gi|242399449|ref|YP_002994874.1|  99 GMRMLIAPILVGALLAWILFVIGTYYTRKSYEKISSE--VQVDTFKT-VGFLYFVGGILVIALGIGLLVL 165
                                       5666777777888888888888888887777777665..44555654.3344444444444444444433 PP

>> NicO  High-affinity nickel-transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1      0.63   8.6e+02      39      65 ..      12      38 ..       3      56 .. 0.57
   2 ?   13.5   1.2   2.4e-05     0.033      38     110 ..      59     132 ..      52     148 .. 0.76
   3 ?   -0.4   0.3      0.41   5.6e+02     209     229 ..     146     165 ..     132     187 .. 0.60

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.63
                              NicO 39 rGillslgsslvvvlvavllvvaavlv 65
                                       G +lsl+s  v  + ++++ +++vl+
  gi|242399449|ref|YP_002994874.1| 12 IGAILSLLSGFVPRAWSLVMLLGLVLL 38
                                      566666666666554444444333333 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 2.4e-05
                              NicO  38 krGillslgsslvvvlvavllvvaavlvlrltslsetgaaigtei.asFllvilllnllllrkl.rklfrklerl 110
                                        +G++l +g +l+v+++a +l+++ ++++  +   + +++ g+ + ++ +lv +ll+++l++   + +++++e++
  gi|242399449|ref|YP_002994874.1|  59 LVGVILRFG-ALIVIILAFFLAMGFAVLKGAPFKGMEEGFEGMRMlIAPILVGALLAWILFVIGtYYTRKSYEKI 132
                                       589999998.699999**************9999***********888888888888888764303333334333 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.41
                              NicO 209 waflggrklvyamsitgtsit 229
                                        +++ g +lv a+ i g+ ++
  gi|242399449|ref|YP_002994874.1| 146 FLYFVGGILVIALGI-GLLVL 165
                                       455555555555555.33333 PP

>> DUF973  Protein of unknown function (DUF973)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1      0.28   3.8e+02     173     198 ..      13      46 ..       4      58 .. 0.53
   2 ?    9.9  10.9   0.00025      0.35      22     126 ..      68     170 ..      56     186 .. 0.64

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.28
                            DUF973 173 liiipvi........dilsfIGyilsyiglgnvl 198
                                         i++++        +++ + G++l  ++++++ 
  gi|242399449|ref|YP_002994874.1|  13 GAILSLLsgfvprawSLVMLLGLVLLLFAVKEIA 46 
                                       3333333222333333555555555555555555 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00025
                            DUF973  22 aliliilvlvvlft.aissglsqliqssasilssvlllliaaiiliiiasvllilgllkirsgfsiLsstgrdvgiG 97 
                                       ali+iil + +++  a+ +  ++  + + + ++++ +l+ ++++ +++a +l ++g + +r+ ++++ s + +v   
  gi|242399449|ref|YP_002994874.1|  68 ALIVIILAFFLAMGfAVLK--GAPFKGMEEGFEGMRMLIAPILVGALLAWILFVIGTYYTRKSYEKI-SSEVQVDTF 141
                                       3344444333222233333..567778888999999*******************************.667788888 PP

                            DUF973  98 itgltliligaiiiiigvilaivsllsli 126
                                       +t  +l+ +g i++i   i ++v l+  i
  gi|242399449|ref|YP_002994874.1| 142 KTVGFLYFVGGILVIALGIGLLVLLIGKI 170
                                       88888888888775432232222333222 PP

>> MerC  MerC mercury resistance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.4    0.0017       2.3      50     112 ..      14      75 ..       9      79 .. 0.80
   2 ?    0.3   5.1      0.68   9.3e+02      66      81 ..     107     122 ..      56     191 .. 0.55

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0017
                              MerC  50 gllalvvgyrrhrktsvlvlgalGllillvalflgteaeetllfgslwqvltvlGaalLaiah 112
                                       ++l+l++g    r +s+++l+ l ll+++v+ ++   + e +  + l+ v+  +Ga++++i  
  gi|242399449|ref|YP_002994874.1|  14 AILSLLSG-FVPRAWSLVMLLGLVLLLFAVKEIADEIEREDIFRDYLVGVILRFGALIVIILA 75 
                                       45566666.55899********************9555566668889999999**99999865 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.68
                              MerC  66 vlvlgalGllillval 81 
                                       +lv ++l+++++++++
  gi|242399449|ref|YP_002994874.1| 107 ILVGALLAWILFVIGT 122
                                       2333333333333333 PP

>> DUF1461  Protein of unknown function (DUF1461)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   1.9    0.0023       3.2      99     154 ..      24      82 ..      17      85 .. 0.66
   2 ?    4.3   0.9     0.024        34      99     146 ..     107     160 ..      95     168 .. 0.42

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0023
                           DUF1461  99 vrlvtlillvllllllivlkkkkkkirllk.skslllavillllil..iilgllalidF 154
                                        r+ +l++l+ l+lll+  k+  ++i+    ++++l++vil +  l  iil+++++++F
  gi|242399449|ref|YP_002994874.1|  24 PRAWSLVMLLGLVLLLFAVKEIADEIEREDiFRDYLVGVILRFGALivIILAFFLAMGF 82 
                                       56667777767777777777776666666688899999999876551155555666666 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.024
                           DUF1461  99 vrlvtlillvllllllivlkkkkkkir......llkskslllavilllliliil 146
                                       +++ +l++++l+++ +++++k+ +ki+       +k+ ++l+ v+ +l+i + +
  gi|242399449|ref|YP_002994874.1| 107 ILVGALLAWILFVIGTYYTRKSYEKISsevqvdTFKTVGFLYFVGGILVIALGI 160
                                       333344444444444444444433333222222222444444444444444444 PP

>> DUF3262  Protein of unknown function (DUF3262)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   2.6     0.022        31      28      76 .]      30      78 ..      19      78 .. 0.84
   2 ?    6.6   0.6    0.0074        10      19      55 ..      99     135 ..      95     159 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.022
                           DUF3262 28 llvvllLwaaWalvsvYkgWaeekiseadllslviRavvlllvlgflfl 76
                                      ++ + l+++ +a+ +      +e+i ++ l  +++R+ +l+++++ +fl
  gi|242399449|ref|YP_002994874.1| 30 VMLLGLVLLLFAVKEIADEIEREDIFRDYLVGVILRFGALIVIILAFFL 78
                                      55566677778888888899999999999*************9999996 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0074
                           DUF3262  19 alklliagillvvllLwaaWalvsvYkgWaeekisea 55 
                                        + +lia il+  ll w  +++ + Y + + ekis  
  gi|242399449|ref|YP_002994874.1|  99 GMRMLIAPILVGALLAWILFVIGTYYTRKSYEKISSE 135
                                       5778899999999999999999999998888888754 PP

>> FA_desaturase  Fatty acid desaturase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   3.3    0.0033       4.6      94     209 ..      21     145 ..       9     153 .. 0.59
   2 ?    1.2   0.7      0.19   2.7e+02     117     127 ..     123     133 ..      97     179 .. 0.39

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0033
                     FA_desaturase  94 ryllrlllgllvlgwllalvlglwlrrlarrrapsksrrrk....wrllawlllllawlglwlalllllglall... 163
                                        +++r ++++++lg++l l         ++ ++++ +++r      +l+++ l + a+++++la++l+ g+a+l   
  gi|242399449|ref|YP_002994874.1|  21 GFVPRAWSLVMLLGLVLLL---------FAVKEIADEIEREdifrDYLVGVILRFGALIVIILAFFLAMGFAVLkga 88 
                                       4566666666666643333.........3333333333333344444444444444444444455554455544555 PP

                     FA_desaturase 164 ............lwlvplllllfllalvlnyveHyggdwgerqvetsasirsaswlln 209
                                                    +l++ +l+++lla++l+++  y+++  +  +    +++ + + ++
  gi|242399449|ref|YP_002994874.1|  89 pfkgmeegfegmRMLIAPILVGALLAWILFVIGTYYTRKSYEKISSEVQVD-TFKTVG 145
                                       788999999999778888888889999999999999665555555555554.555555 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.19
                     FA_desaturase 117 wlrrlarrrap 127
                                       + +r  + + +
  gi|242399449|ref|YP_002994874.1| 123 YYTRKSYEKIS 133
                                       22222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1103  (0.0615204); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.43
# Mc/sec: 1356.58
//
Query:       gi|242399450|ref|YP_002994875.1|  [L=261]
Description: 5'-nucleotidase surE [Thermococcus sibiricus MM 739]
Scores for complete 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-54  183.5   0.0    4.4e-54  183.2   0.0    1.1  1  SurE      Survival protein SurE


Domain annotation for each model (and alignments):
>> SurE  Survival protein SurE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.2   0.0   2.4e-58   4.4e-54       1     193 [.       4     194 ..       4     196 .. 0.90

  Alignments for each domain:
  == domain 1  score: 183.2 bits;  conditional E-value: 2.4e-58
                                       EEEE-SS-TT-HHHHHHHHHHTTTTSEEEEEEESSS-TTCTTS--SSSEEEEEEEECSTTTCEEEESS-HHHHHHHH CS
                              SurE   1 iLltNDDGieapgiralvealaaaghevvvvaPdserSgigkaltleeplrveseeeeeeeeeyavsGtPadcvkla 77 
                                       iL+tNDDGi+++gi+a veal++ g ev+vvaP  +rS++g+a+tl++plrv++ + ++++ +ya++G P+dcv +a
  gi|242399450|ref|YP_002994875.1|   4 ILVTNDDGIHSRGIKAAVEALQDLG-EVYVVAPMFQRSASGRAMTLHRPLRVKRINLKGTKVAYALDGMPVDCVIFA 79 
                                       8*********************888.***************************777779****************** PP

                                       HHTTTTTS.SSEEEEEEEES---GGGGGG-HHHHHHHHHHHTTSEEEEEEEESSS...SS-SSS---HHHHHHHHHH CS
                              SurE  78 leellkekkpdlVvSGiNhGaNlgtdvlySGTvgAaleaalegipaiAvSlaskk...eeekkeedtfeaaakvaak 151
                                       +  +    k dl vSGiN G+N++t+++ SGT +Aa+eaa+++ip+iA+Sl++++   +  + ee +f+ a++++++
  gi|242399450|ref|YP_002994875.1|  80 MARFG---KFDLAVSGINLGENMSTEITISGTASAAIEAATHDIPSIAMSLEVNRekhKFGEGEEIDFSVAKSFLKR 153
                                       *6665...46******************************************998776333445667********** PP

                                       HHTTETTS-...SS-EEEEEEESS.GCG-SEEEE-B--CCSC CS
                              SurE 152 lveklieklllekvellnvNvPeleeeeikgvkvtrlgrrry 193
                                       +++ ++++ + ++v++ln+NvP   ++e + +++t+l++r+y
  gi|242399450|ref|YP_002994875.1| 154 ISNAILSNGMPKSVDMLNINVPYD-AHENTPIELTKLAKRMY 194
                                       **********************43.44445577*****9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1604.14
//
Query:       gi|242399451|ref|YP_002994876.1|  [L=284]
Description: hypothetical protein TSIB_1476 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.9e-37  126.9  10.8    2.9e-10   40.4   0.5    4.2  4  CBS         CBS domain
  ------ inclusion threshold ------
      0.019   15.1   0.4        8.7    6.5   0.0    3.4  4  sCache_3_2  Single cache domain 3
      0.022   14.8   5.0        2.6    8.2   0.1    3.6  4  PRC         PRC-barrel domain


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.1   7.4e-11   4.4e-07       1      52 [.       5      57 ..       5      61 .. 0.90
   2 !   40.4   0.5   4.8e-14   2.9e-10       6      54 ..      70     118 ..      64     121 .. 0.91
   3 !   24.5   0.0   4.6e-09   2.8e-05      11      53 ..     141     183 ..     130     184 .. 0.87
   4 !   36.6   0.2   7.6e-13   4.6e-09       1      56 [.     226     281 ..     226     282 .. 0.96

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 7.4e-11
                                      HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTT..BEEEEEEHHHHH CS
                               CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedg..klvGivtlrDll 52
                                      V+ +mt+d+v++   +t   al+l+++++v+++PVV + g  ++vGiv+ + +l
  gi|242399451|ref|YP_002994876.1|  5 VKNLMTPDPVVIELPATRNYALDLFKRYKVRSFPVV-KRGtkEIVGIVSIKSVL 57
                                      7899*********************9999*******.455548*******9887 PP

  == domain 2  score: 40.4 bits;  conditional E-value: 4.8e-14
                                       BSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                               CBS   6 trdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54 
                                        rdv+ v+p++ l++a++l+ +++++r+ VVd+++++vGi+t  D++r 
  gi|242399451|ref|YP_002994876.1|  70 KRDVPLVTPNDALKKAVKLILKNKYRRVVVVDKENHVVGILTVGDIIRR 118
                                       68999**************87989****889****************97 PP

  == domain 3  score: 24.5 bits;  conditional E-value: 4.6e-09
                                       EEETTSBHHHHHHH.HHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                               CBS  11 tvppdttleealel.mrekgvsrlPVVdedgklvGivtlrDllr 53 
                                       +v   t+l+ al+  + +++   lPV+d+dg l+Gi+ ++Dll+
  gi|242399451|ref|YP_002994876.1| 141 VVWKGTPLKAALKAlLLSNAM-VLPVIDDDGSLIGIIDETDLLK 183
                                       7888999*****995558888.99******************96 PP

  == domain 4  score: 36.6 bits;  conditional E-value: 7.6e-13
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                       V ++mt+++  ++p +++ e++++m+++++ +lPV+ ++g+++G++ + Dl++a++
  gi|242399451|ref|YP_002994876.1| 226 VQELMTTELKLATPHMSVYEVANIMTQEHIEQLPVIKGEGEIIGLIRDIDLVKAIV 281
                                       789**********************9999*************************97 PP

>> sCache_3_2  Single cache domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.63   3.7e+03     108     124 ..      36      53 ..       8      53 .. 0.74
   2 ?    1.8   0.0     0.041   2.5e+02      65     125 ..      56     113 ..      52     118 .. 0.77
   3 ?    6.5   0.0    0.0015       8.7     106     122 ..     160     176 ..     151     177 .. 0.89
   4 ?    2.3   0.0     0.027   1.6e+02     108     123 ..     257     272 ..     226     272 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.63
                        sCache_3_2 108 klPvfda.dgrviGivsv 124
                                         Pv+++   +++Givs+
  gi|242399451|ref|YP_002994876.1|  36 SFPVVKRgTKEIVGIVSI 53 
                                       568777757789999997 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.041
                        sCache_3_2  65 vlahpdpaevgrklsgpataaalkagrayvgtv.tgtlgpslrvklPvfdadgrviGivsvG 125
                                       vl hpd +++   +    + ++++ + a  + v +++++++ rv+  v+d+++ v+Gi+ vG
  gi|242399451|ref|YP_002994876.1|  56 VLLHPDEDQLAMLI--KRDVPLVTPNDALKKAVkLILKNKYRRVV--VVDKENHVVGILTVG 113
                                       66677777776666..67777777777777777678889999998..579999*****9999 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.0015
                        sCache_3_2 106 rvklPvfdadgrviGiv 122
                                        ++lPv+d+dg++iGi+
  gi|242399451|ref|YP_002994876.1| 160 AMVLPVIDDDGSLIGII 176
                                       689************98 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.027
                        sCache_3_2 108 klPvfdadgrviGivs 123
                                       +lPv++++g++iG+++
  gi|242399451|ref|YP_002994876.1| 257 QLPVIKGEGEIIGLIR 272
                                       89***********985 PP

>> PRC  PRC-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.021   1.2e+02       4      42 ..      29      70 ..      26      81 .. 0.87
   2 ?   -2.9   0.2       1.3   7.5e+03      28      40 ..      98     109 ..      96     115 .. 0.63
   3 ?    4.0   0.0    0.0086        52      12      29 ..     163     180 ..     154     202 .. 0.80
   4 ?    8.2   0.1   0.00043       2.6       9      28 ..     255     274 ..     248     278 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.021
                                      CCS---TT-EEEETT.SSEEEEE..EEEEEETTTTEEEEEEE CS
                               PRC  4 frasdliGkeVyted.GeklGkV..kDvvidekegrvralvv 42
                                      f   +++  +V+ +   e++G V  k v+++++e ++  l+ 
  gi|242399451|ref|YP_002994876.1| 29 FKRYKVRSFPVVKRGtKEIVGIVsiKSVLLHPDEDQLAMLIK 70
                                      67788899999999989*****999********999998875 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.3
                                       EEEETTTTEEEEE CS
                               PRC  28 vvidekegrvral 40 
                                       vv+d+ e++v+++
  gi|242399451|ref|YP_002994876.1|  98 VVVDK-ENHVVGI 109
                                       67776.5555554 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.0086
                                       -EEEETTSSEEEEEEEEE CS
                               PRC  12 keVytedGeklGkVkDvv 29 
                                       ++V+++dG  +G + +  
  gi|242399451|ref|YP_002994876.1| 163 LPVIDDDGSLIGIIDETD 180
                                       79**********996544 PP

  == domain 4  score: 8.2 bits;  conditional E-value: 0.00043
                                       -TT-EEEETTSSEEEEEEEE CS
                               PRC   9 liGkeVytedGeklGkVkDv 28 
                                       ++ ++V+ ++Ge++G + D+
  gi|242399451|ref|YP_002994876.1| 255 IEQLPVIKGEGEIIGLIRDI 274
                                       7889***************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1866.76
//
Query:       gi|242399452|ref|YP_002994877.1|  [L=337]
Description: Homoserine dehydrogenase [Thermococcus sibiricus MM 739]
Scores for 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-52  176.3   0.1    7.3e-52  175.8   0.1    1.2  1  Homoserine_dh    Homoserine dehydrogenase
    7.7e-09   36.2   0.0    2.1e-08   34.9   0.0    1.8  1  NAD_binding_3    Homoserine dehydrogenase, NAD binding domain
    0.00037   20.3   0.2     0.0028   17.4   0.1    2.4  3  ELFV_dehydrog    Glutamate/Leucine/Phenylalanine/Valine dehyd
  ------ inclusion threshold ------
      0.089   13.1   0.1       0.17   12.1   0.1    1.7  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma


Domain annotation for each model (and alignments):
>> Homoserine_dh  Homoserine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.8   0.1   1.6e-55   7.3e-52       1     173 []     156     327 ..     156     327 .. 0.97

  Alignments for each domain:
  == domain 1  score: 175.8 bits;  conditional E-value: 1.6e-55
                                       --HHHHHHTCTTSEEEEEEEE--HHHHHHHHHHHCHTT-HHHHHHHHHHTTSS-SSTHHHHTTHHHHHHHHHHHHHH CS
                     Homoserine_dh   1 PiiktlkeilsgdritrieGilngtlnyiltemeeegasfsevlkeaqelGyaeaDptdDveGlDaarKlailarla 77 
                                       Pii+ lke   +d ++ri+G++ngt+ +ilt +e+ g++f+e+lk+aq  G+ae+Dp++D++G+Daa+K++il  la
  gi|242399452|ref|YP_002994877.1| 156 PIINLLKEEILADSVKRISGVFNGTTTFILTSIET-GMTFKEALKQAQTAGIAERDPSNDLKGIDAAYKATILHHLA 231
                                       9*****99999***********************7.999************************************** PP

                                       CTTT--GGGSEE--STTS-HHHHHHHHCTTEEEEEEEEE..CEEEEEEEEEETTSGGGHSSST-EEEEEEESSSEEE CS
                     Homoserine_dh  78 fgleveledvevegiskltaedikeakeegkvlklvasa..vearVkpelvpkshplasvkgsenavlvetdrlgel 152
                                         +++++++v++egi++l++e+i+eak+eg  ++lva++   ++++kp++v ++ pla v+g+ n+ ++etd lgel
  gi|242399452|ref|YP_002994877.1| 232 -FYPIDFKEVHIEGIENLSEEEIREAKKEGTPFRLVATVeeGKVEIKPKKVYENGPLA-VSGTSNVAVIETDLLGEL 306
                                       .69***********************************65449***************.****************** PP

                                       EEEES-SSHHHHHHHHHHHHH CS
                     Homoserine_dh 153 viqGpgaGaepTAsavlsDll 173
                                       +++G+gaG ++TAs+v++D++
  gi|242399452|ref|YP_002994877.1| 307 MLKGSGAGIKETASGVVGDII 327
                                       *******************97 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 !   34.9   0.0   4.6e-12   2.1e-08       1     116 [.      10     147 ..      10     148 .. 0.80

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 4.6e-12
                                       --SHHHHHHHHHHHH---S......SEEEEEEEEESS.EEE-TT...............HHHHHT--CB---HHHHH CS
                     NAD_binding_3   1 GlGaiGsavleqlkrqqse......ielelvavadrd.sllskd...............rkallasealtldlddli 55 
                                       G+G++G++v+e l  +         i++++v ++d + +  +++                +++ ++e ++ +l    
  gi|242399452|ref|YP_002994877.1|  10 GFGNVGRGVAEVLYTKMPHfkkkygINIKVVSITDTSaTIWDQEainlreaietknhfgSLKFWGNEYEVYKL---- 82 
                                       99***********99888889999*************666666678888888855555533344444444333.... PP

                                       HHH........S-EEEEE-S--HHHHTTHHHHHHTTEEEE-S--CGGG-HHHHHHHTSSSTTS--.EE- CS
                     NAD_binding_3  56 ahl........dpdvvVEcasseavaelvlkaLkagkdvvtankgaladealyeeLreaaeangakiyv 116
                                                  d+dv+++++ ++ + +  l+aLk+gk vvt nk  ++    y+eL+++a++++  +++
  gi|242399452|ref|YP_002994877.1|  83 --DpmevvkeiDADVIIDVTNDKNASKWHLEALKRGKGVVTSNKPPVV--FDYKELVDLANSKNLPYLF 147
                                       ..144444555*************************************..99********999877766 PP

>> ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   6.2e-07    0.0028      35     118 ..       6      97 ..       1     107 [. 0.75
   2 ?   -1.7   0.0      0.42   1.9e+03      19      55 ..     224     260 ..     220     273 .. 0.80
   3 ?   -1.4   0.0      0.36   1.6e+03      30      53 ..     282     305 ..     253     310 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 6.2e-07
                                       EEEE--SHHHHHHHHHHHH..........CT-EEEEEEESSEEEEETTEE-HHHHHHHHHCSSSSTTHSHHSTSTSE CS
                     ELFV_dehydrog  35 vaisGsGnvgsyaalllte..........lgakvvavsDssGviydpeGldieellelkeerksvkeykkssekkae 101
                                       + i G+Gnvg  +a+ l +           + kvv++ D s +i d+e ++++e +e k++ +s+k   ++   ++ 
  gi|242399452|ref|YP_002994877.1|   6 LSIIGFGNVGRGVAEVLYTkmphfkkkygINIKVVSITDTSATIWDQEAINLREAIETKNHFGSLKFWGNEY--EVY 80 
                                       678899999999988765422222222225899*******************************98887543..344 PP

                                       EESHHSHHHHSS-SEEE CS
                     ELFV_dehydrog 102 yieneeellelkvdilv 118
                                       +++  e + e+++d+++
  gi|242399452|ref|YP_002994877.1|  81 KLDPMEVVKEIDADVII 97 
                                       55555566777777765 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.42
                                       HHHHHHTTTS-STTEEEEEE--SHHHHHHHHHHHHCT CS
                     ELFV_dehydrog  19 eemlkklkldslegkrvaisGsGnvgsyaallltelg 55 
                                         +l++l++  ++ k+v i G  n+   +++ +++ g
  gi|242399452|ref|YP_002994877.1| 224 ATILHHLAFYPIDFKEVHIEGIENLSEEEIREAKKEG 260
                                       5678888888888899999999999999999887766 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.36
                                       STTEEEEEE--SHHHHHHHHHHHH CS
                     ELFV_dehydrog  30 legkrvaisGsGnvgsyaalllte 53 
                                       +e+  +a+sG  nv+  +  ll e
  gi|242399452|ref|YP_002994877.1| 282 YENGPLAVSGTSNVAVIETDLLGE 305
                                       456678999999999999888755 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   3.9e-05      0.17       3      40 ..       8      48 ..       6     146 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.9e-05
                                      EE--SHHHHHHHHHHHCTCCT-G.....EEEEEESSHHHHHHH CS
                   Sacchrp_dh_NADP  3 iiGaGsvGqavaellarhfdvda.....eitvadrskekleal 40
                                      iiG+G+vG++vae+l  + ++++     +i v++ ++++  a+
  gi|242399452|ref|YP_002994877.1|  8 IIGFGNVGRGVAEVLYTKMPHFKkkygiNIKVVSITDTS--AT 48
                                      9*************9887766666778888888888887..33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       659  (0.0367561); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); 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: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 2443.03
//
Query:       gi|242399453|ref|YP_002994878.1|  [L=175]
Description: hypothetical protein TSIB_1478 [Thermococcus sibiricus MM 739]
Scores for complete 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   21.8   0.0    0.00031   21.3   0.0    1.4  1  ASCH      ASCH domain


Domain annotation for each model (and alignments):
>> ASCH  ASCH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   1.7e-08   0.00031       2      64 ..       6      87 ..       5     131 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.7e-08
                                      EE-TTHHHHHHTTS--EEEESSTTTGGGT-CEEEEEECCC......................CTSEEEEEEEEEEEEEE CS
                              ASCH  2 sfhqelaslivsGkKtaeirvwdeelpkvrgdllilaalk......................ptgralgivevtkvevk 58
                                      ++hq + +li++G K +eir+ +    + +gd+  l+ ++                      ++g ++g +ev +v   
  gi|242399453|ref|YP_002994878.1|  6 ALHQVYGELIFRGLKFHEIRKAPIV--R-EGDVVFLYIARgnpvvlkrtlkklglseeqaltQRGSIAGGFEVGEVIRA 81
                                      79******************55555..4.58999987777999999999999999999999999999999999999888 PP

                                      HHHHHH CS
                              ASCH 59 pfeevt 64
                                      +fe++ 
  gi|242399453|ref|YP_002994878.1| 82 DFENLW 87
                                      998873 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1296.98
//
Query:       gi|242399454|ref|YP_002994879.1|  [L=201]
Description: Zn-finger, ZPR1 type:Zn-finger, ZPR1-related type [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-40  138.9   0.1    1.5e-40  138.6   0.1    1.1  1  zf-ZPR1          ZPR1 zinc-finger domain
    4.6e-05   23.7   0.1    9.8e-05   22.7   0.1    1.5  1  Lar_restr_allev  Restriction alleviation protein Lar
  ------ inclusion threshold ------
      0.031   13.8   1.5       0.17   11.4   1.5    2.2  1  TF_Zn_Ribbon     TFIIB zinc-binding
       0.04   14.2   3.2       0.43   10.9   3.2    2.1  1  Prim_Zn_Ribbon   Zinc-binding domain of primase-helicase
      0.052   13.5   0.2      0.093   12.7   0.2    1.3  1  PhnA_Zn_Ribbon   PhnA Zinc-Ribbon
      0.069   12.9   0.2         14    5.5   0.1    2.2  2  Rubredoxin_2     Rubredoxin metal binding domain
      0.076   13.3   0.0       0.18   12.1   0.0    1.6  1  Cobl             Cordon-bleu ubiquitin-like domain


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 !  138.6   0.1     6e-44   1.5e-40       2     157 ..      11     167 ..      10     169 .. 0.93

  Alignments for each domain:
  == domain 1  score: 138.6 bits;  conditional E-value: 6e-44
                           zf-ZPR1   2 lCpsCgkengetrlllt.kiPyfkeviimsfeCehCgyknnevksageieekGkritlkveseedlnrqvlkSetat 77 
                                       +Cp Cg++n+ + l ++ +iPyf++v+ +++ Ce+Cgy+n +v+ ++e+e+  k +t+kve+e+dl ++v++S+++t
  gi|242399454|ref|YP_002994879.1|  11 DCPICGGKNTLKALNYLhEIPYFGKVMESTIICEKCGYRNADVMLLEEKEP--KMYTVKVEEEKDLFTRVVRSKSGT 85 
                                       6********999998888*********************************..************************ PP

                           zf-ZPR1  78 veipeleleippg.tlegrlttvEGlLeqikeele.keegdqaeredeekekieeflekleeliegeepftlildDp 152
                                       +e++e++++i+pg +++g++t+vEG+Le+++e l   ++ +++e+++e+ +kiee+l+ +e ++eg++p+t+ + Dp
  gi|242399454|ref|YP_002994879.1|  86 IELEEIGIKIEPGpASQGFVTNVEGVLERARETLLmAKNFKKEENDEESIKKIEEILNYIEGVKEGKKPLTVRIMDP 162
                                       **********************************852234444444489**************************** PP

                           zf-ZPR1 153 agnSf 157
                                       +gnS+
  gi|242399454|ref|YP_002994879.1| 163 FGNSA 167
                                       ****7 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.1   3.8e-08   9.8e-05       3      41 ..       9      53 ..       8      73 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 3.8e-08
                   Lar_restr_allev  3 LkpCPfCggravlersqrvvaeigq.......cvyCadCgastpwf 41
                                      L +CP Cgg+++l+  ++ ++ i +       +++C++Cg+ + ++
  gi|242399454|ref|YP_002994879.1|  9 LGDCPICGGKNTLKALNYLHE-IPYfgkvmesTIICEKCGYRNADV 53
                                      568*************99996.6667***************44443 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.5   6.8e-05      0.17       3      27 ..      12      48 ..      10      49 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.8e-05
                                      ETTTTCEE.C...........HEETSTTCEEESSSSB CS
                      TF_Zn_Ribbon  3 CPnCgstn.l...........veDpergelvCtdCGl 27
                                      CP+Cg++n l               ++ +++C++CG+
  gi|242399454|ref|YP_002994879.1| 12 CPICGGKNtLkalnylheipyFGKVMESTIICEKCGY 48
                                      ********55****9997775445999********96 PP

>> Prim_Zn_Ribbon  Zinc-binding domain of primase-helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   3.2   0.00017      0.43       4      37 ..      10      53 ..       8      54 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00017
                                      E--TTTT-TTTEE.ETT.............S-EEETTTTB..XXXX CS
                    Prim_Zn_Ribbon  4 spCPvCGGrDrFr.fddkdgr.........GtwfCrqCgg..ggdg 37
                                      + CP+CGG+   +                 +t +C +C g  ++d+
  gi|242399454|ref|YP_002994879.1| 10 GDCPICGGKNTLKaLNYLH-EipyfgkvmeSTIICEKC-GyrNADV 53
                                      68******98777444433.3699999999********.6577776 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   3.6e-05     0.093       2      27 ..       9      48 ..       8      48 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.6e-05
                    PhnA_Zn_Ribbon  2 lpkCplCaSeytY..............edgallvCpeCah 27
                                      l+ Cp C+  +t+              +  +  +C++C++
  gi|242399454|ref|YP_002994879.1|  9 LGDCPICGGKNTLkalnylheipyfgkVMESTIICEKCGY 48
                                      678***********************************96 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0    0.0055        14      14      27 ..       9      22 ..       5      23 .. 0.87
   2 ?    5.5   0.1    0.0054        14       2      12 ..      42      52 ..      42      54 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0055
                      Rubredoxin_2 14 fGrCpsCgsWntlk 27
                                      +G Cp Cg  ntlk
  gi|242399454|ref|YP_002994879.1|  9 LGDCPICGGKNTLK 22
                                      799*****999987 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0054
                      Rubredoxin_2  2 vCsqCGfesak 12
                                      +C++CG++ a 
  gi|242399454|ref|YP_002994879.1| 42 ICEKCGYRNAD 52
                                      5******9765 PP

>> Cobl  Cordon-bleu ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   7.2e-05      0.18      39      59 ..      40      60 ..      32      75 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.2e-05
                                      HHHHHHTT--TTSEEEES-SS CS
                              Cobl 39 pvicekcefdpehvlllkdsi 59
                                      ++icekc +  ++v+ll ++ 
  gi|242399454|ref|YP_002994879.1| 40 TIICEKCGYRNADVMLLEEKE 60
                                      69***************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1213  (0.0676558); expected 358.6 (0.02)
Passed bias filter:                      861  (0.0480228); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 1196.30
//
Query:       gi|242399455|ref|YP_002994880.1|  [L=129]
Description: hypothetical protein TSIB_1480 [Thermococcus sibiricus MM 739]
Scores for complete 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   55.2   0.4    8.3e-15   54.8   0.4    1.2  1  SepF      Cell division protein SepF


Domain annotation for each model (and alignments):
>> SepF  Cell division protein SepF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.8   0.4   4.6e-19   8.3e-15       1      72 []      51     126 ..      51     126 .. 0.96

  Alignments for each domain:
  == domain 1  score: 54.8 bits;  conditional E-value: 4.6e-19
                                       EEEEE-SSGGGHHHHHHHHHTT-EEEEE-CCCTC..HHHHHHHHHHHHHHHHCT-EEEEECTT..EEEEE-TT-EE CS
                              SepF   1 vvvveprsfedaqeiadalkegkiVilnledldk..eeakrivdflsgvvyaldGdiqkvgkk..vflitPknvdi 72 
                                       ++ + ++s++d ++i +++++g+i+i +l+ l++  e++ ++v+ ++g+++al+G+ +k++k+   +litP++++i
  gi|242399455|ref|YP_002994880.1|  51 IKKIVVTSYSDLEKISEEVQAGNIIIADLTPLESkpEVLAKVVEQIKGITQALGGETAKIAKHeiKILITPPDIKI 126
                                       567889*******************************************************9789*********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       702  (0.0391544); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 787.34
//
Query:       gi|242399456|ref|YP_002994881.1|  [L=67]
Description: Archaeal histone A [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-20   73.7   0.7    1.2e-20   73.6   0.7    1.0  1  CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) a
    3.8e-10   40.2   0.3    4.1e-10   40.1   0.3    1.1  1  Histone        Core histone H2A/H2B/H3/H4
    2.9e-07   30.6   0.1    2.9e-07   30.6   0.1    1.0  1  CENP-T_C       Centromere kinetochore component CENP-T histon
      5e-07   30.0   0.1    5.2e-07   30.0   0.1    1.1  1  CENP-S         CENP-S protein
    1.3e-06   28.5   0.3    1.3e-06   28.4   0.3    1.1  1  TAF            TATA box binding protein associated factor (TA
    2.4e-06   27.6   0.0    2.7e-06   27.5   0.0    1.0  1  TFIID-31kDa    Transcription initiation factor IID, 31kD subu
      3e-05   24.4   0.1    3.4e-05   24.2   0.1    1.1  1  TFIID_20kDa    Transcription initiation factor TFIID subunit 
    0.00017   21.5   0.0    0.00019   21.4   0.0    1.0  1  Bromo_TP       Bromodomain associated
    0.00058   19.8   0.0    0.00062   19.7   0.0    1.1  1  TFIID-18kDa    Transcription initiation factor IID, 18kD subu
     0.0043   17.3   1.2     0.0052   17.1   1.2    1.1  1  CENP-X         CENP-S associating Centromere protein X


Domain annotation for each model (and alignments):
>> CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) and archaeal histone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.6   0.7   6.5e-24   1.2e-20       1      65 []       2      65 ..       2      65 .. 0.99

  Alignments for each domain:
  == domain 1  score: 73.6 bits;  conditional E-value: 6.5e-24
                                      XXXXHHHHHHHHHCCTTXS-B-HHHHHHHHHHHHHHHHHHHHHHHHHHCCTTSSCE-HHHHHHHH CS
                     CBFD_NFYB_HMF  1 aeLPiarvkkImksdpdarkiakdAkeliaecveefieelaseAaeickkekrKtikaehiklAv 65
                                      aeLPia+++++++++ +a+++++dA +++ae +ee++ e+a++++e + +++rKt+kae+iklAv
  gi|242399456|ref|YP_002994881.1|  2 AELPIAPIDRLIRKA-GAERVSEDAAKVLAEYLEEYAVEVAKKSVEFARHAGRKTVKAEDIKLAV 65
                                      69*************.************************************************8 PP

>> Histone  Core histone H2A/H2B/H3/H4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.1   0.3   2.3e-13   4.1e-10      63     129 ..       5      66 ..       1      67 [] 0.90

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 2.3e-13
                                       XHHHHHHHHHHHH.TTSSSXEEXHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTXSEEXHHHHHHHHH CS
                           Histone  63 qklpfaRvvreivksekedlrisaeavlalqealEallvelfeeAnllakhaKRvTitpkDiqlArr 129
                                       + +p++R++r+         r+s +a  +l+e lE + ve+++ +   a+ha R+T+ ++Di+lA++
  gi|242399456|ref|YP_002994881.1|   5 PIAPIDRLIRKAGA-----ERVSEDAAKVLAEYLEEYAVEVAKKSVEFARHAGRKTVKAEDIKLAVK 66 
                                       56788887777665.....9*********************************************98 PP

>> CENP-T_C  Centromere kinetochore component CENP-T histone fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.1   1.6e-10   2.9e-07       9      75 ..       5      66 ..       1      67 [] 0.84

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 1.6e-10
                          CENP-T_C  9 PaavvkklakrfakasgskaklekealkalekasdkffeqvgeDLeayakHagRKtidesDvilLmk 75
                                      P a + +l +++       ++++++a k+l + ++++   v++    +a+HagRKt++++D+ l +k
  gi|242399456|ref|YP_002994881.1|  5 PIAPIDRLIRKA-----GAERVSEDAAKVLAEYLEEYAVEVAKKSVEFARHAGRKTVKAEDIKLAVK 66
                                      555555555544.....6679****************************************987665 PP

>> CENP-S  CENP-S protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.1   2.9e-10   5.2e-07      24      71 ..      19      66 ..       6      67 .] 0.88

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 2.9e-10
                            CENP-S 24 veatkqfiaaltelvykqlenlakDLeaFakHAkRstittdDvlLlaR 71
                                       ++++++ + l+e   + + ++ak    Fa+HA+R+t++++D++L ++
  gi|242399456|ref|YP_002994881.1| 19 ERVSEDAAKVLAEYLEEYAVEVAKKSVEFARHAGRKTVKAEDIKLAVK 66
                                      5688899999999999999**************************876 PP

>> TAF  TATA box binding protein associated factor (TAF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.3   7.5e-10   1.3e-06      17      66 .]      17      66 ..       2      66 .. 0.93

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 7.5e-10
                                      T---B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH- CS
                               TAF 17 GitnLsdeaaalLaedveyrlkeivqeaakfmrhskRqkLtvaDvdsALr 66
                                      G + +s++aa++Lae +e+   e++++++ f rh+ R++  ++D+  A++
  gi|242399456|ref|YP_002994881.1| 17 GAERVSEDAAKVLAEYLEEYAVEVAKKSVEFARHAGRKTVKAEDIKLAVK 66
                                      88899****************************************99976 PP

>> TFIID-31kDa  Transcription initiation factor IID, 31kD subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.0   1.5e-09   2.7e-06      11      68 ..       9      66 ..       5      67 .] 0.95

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 1.5e-09
                       TFIID-31kDa 11 ihliLaslgvteyeerVvlqLldfayrytssvLedAkvlaehakkkevslddvrlAiq 68
                                      i  ++++ g + ++e+  + L +    y ++v + +  +a+ha++k+v+++d++lA++
  gi|242399456|ref|YP_002994881.1|  9 IDRLIRKAGAERVSEDAAKVLAEYLEEYAVEVAKKSVEFARHAGRKTVKAEDIKLAVK 66
                                      7789999*************************************************97 PP

>> TFIID_20kDa  Transcription initiation factor TFIID subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.1   1.9e-08   3.4e-05      14      63 ..      17      66 ..       8      67 .] 0.88

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 1.9e-08
                                      SS----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHH CS
                       TFIID_20kDa 14 setkldedvedlLleiaddFvesvtkfacklakhRksdklevrDiqlhle 63
                                      + +++ ed   +L+e+ +++  +v k+++++a+h   +++ + Di+l ++
  gi|242399456|ref|YP_002994881.1| 17 GAERVSEDAAKVLAEYLEEYAVEVAKKSVEFARHAGRKTVKAEDIKLAVK 66
                                      45678999***************************************886 PP

>> Bromo_TP  Bromodomain associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   1.1e-07   0.00019      16      67 ..      13      64 ..       9      67 .] 0.93

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.1e-07
                                      HHHHT-SEE-HHHHHHHHHHHHHHHHHHHHHHHHHHTTSS-SS--HHHHHHH CS
                          Bromo_TP 16 leeaGfdsaeesaLEtLteiaqkYirelgeqaksfaehagRseptlkDvvlt 67
                                       ++aG +++ e a   L e +++Y  e++++  +fa hagR +++ +D+ l+
  gi|242399456|ref|YP_002994881.1| 13 IRKAGAERVSEDAAKVLAEYLEEYAVEVAKKSVEFARHAGRKTVKAEDIKLA 64
                                      689999*******************************************987 PP

>> TFIID-18kDa  Transcription initiation factor IID, 18kD subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   3.5e-07   0.00062      22      64 ..      23      65 ..      10      67 .] 0.90

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 3.5e-07
                                      HHHHHHHHHHHHHHHHHHHHHHHC-XXXX...XXXXXXXXXXX CS
                       TFIID-18kDa 22 qetvqlledlvrgyliellqqaakvaklrgsrkitlEDllfli 64
                                      ++++++l + +++y +e+ +++++ a++ g++ ++ ED++ ++
  gi|242399456|ref|YP_002994881.1| 23 EDAAKVLAEYLEEYAVEVAKKSVEFARHAGRKTVKAEDIKLAV 65
                                      57789999*******************************9876 PP

>> CENP-X  CENP-S associating Centromere protein X
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   1.2   2.9e-06    0.0052      17      64 ..      19      61 ..       9      65 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.9e-06
                                      -EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SE.....EECHHH CS
                            CENP-X 17 tkItkdalelvaeylklFvrEavaRaaeeaeeegkeeseksklevedL 64
                                       ++++da +++aeyl+ + +E +  ++e a+  g ++     +  ed+
  gi|242399456|ref|YP_002994881.1| 19 ERVSEDAAKVLAEYLEEYAVEVAKKSVEFARHAGRKT-----VKAEDI 61
                                      59***************************99999888.....555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       715  (0.0398795); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); 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):              10  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 468.90
//
Query:       gi|242399457|ref|YP_002994882.1|  [L=424]
Description: Fe-S oxidoreductase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.5e-27   94.7   0.4    1.4e-25   90.6   0.0    2.6  3  Radical_SAM  Radical SAM superfamily
    1.1e-09   38.3   0.0    2.3e-09   37.3   0.0    1.5  1  B12-binding  B12 binding domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.16   1.4e+03      33      59 ..      61      85 ..      57      95 .. 0.80
   2 ?    0.4   0.0     0.084   7.5e+02     124     154 ..     103     132 ..      81     135 .. 0.82
   3 !   90.6   0.0   1.6e-29   1.4e-25       1     166 [.     168     339 ..     168     340 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.16
                                      HHHHHHHHHHHHTTSEEEEEESSTGGG CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 33 eileevkelkaekgvkevilgggepll 59
                                      +i++evk+l +ek ++ +++ gg  + 
  gi|242399457|ref|YP_002994882.1| 61 DIEKEVKIL-KEK-TNALLIAGGYHTT 85
                                      699999999.577.8999888887665 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.084
                                       TSHHHHHHHHHHHHHHTTSETEEEEEEEBTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 124 ghtfeevlealeklreagikrvvdrivglpG 154
                                       g++ e +  +l++l+e++++ ++  ++g++G
  gi|242399457|ref|YP_002994882.1| 103 GEGEEVIFHLLKTLTENNFR-ITKELLGIKG 132
                                       566699999***********.9999999998 PP

  == domain 3  score: 90.6 bits;  conditional E-value: 1.6e-29
                                       EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTC.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                       Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlakla.. 74 
                                       ++++rgC+++C +C++p+   ++ r r++++++i++  k++ ++++ +    +  g p    ++ +l + l++l+  
  gi|242399457|ref|YP_002994882.1| 168 IEISRGCPFGCYYCQTPYV--KGFRMRHRPIDQIVKYSKRM-KDMRyITPNAFAYGSPGGILNLNKLEALLKALQpi 241
                                       6899**************7..********************.69999999999999999999999999999999999 PP

                                       .CCTEEEEEEECSSCHG.....HHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET CS
                                       .xxxxxxxxxxxxxxxx.....xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  75 .vpgiritvetngtlpd.....eeklerllelg.vdrvslgleaaddekvlklmnrghtfeevlealeklreagikr 144
                                        ++g+r+++ t +  ++     +e le+ll++    r+++g++++dde+++ ++ r+ht e v +a+e++ e++i++
  gi|242399457|ref|YP_002994882.1| 242 rKEGRRLFYGTFPSEVRpefikPETLELLLKYAdNRRLAIGAQSGDDEMFKAMH-RMHTTENVRQAVEYMLEYDIEP 317
                                       9**************99*******************************888888.********************** PP

                                       EEEEEEEBTTTSHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 145 vvdrivglpGendeeleellel 166
                                       vvd+ivglp+e++e  ++ +e+
  gi|242399457|ref|YP_002994882.1| 318 VVDFIVGLPNETKESQRKSIEF 339
                                       *************997777776 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.0   2.5e-13   2.3e-09      22     116 ..      21     108 ..       6     113 .. 0.78

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 2.5e-13
                       B12-binding  22 aalrdagfeVqllganven..........edivaairaekpdvvglSalltsqleavkelvellkrirprvkvvvGG 88 
                                       +al+              +          +d+ + i + +  vv+ S+ +t +++++++ v+ lk++  ++ +++GG
  gi|242399457|ref|YP_002994882.1|  21 GALES-------------QgfdigellitKDFSE-ILKARSKVVLYSF-FTEEIWDIEKEVKILKEK-TNALLIAGG 81 
                                       33444.............3333333444355555.5555699******.***************998.679****** PP

                       B12-binding  89 ahpsldpeetleaklgiddvvvgegeda 116
                                        h +++p+ tl++ lg+d++ +gege+ 
  gi|242399457|ref|YP_002994882.1|  82 YHTTAMPKHTLNK-LGFDIATIGEGEEV 108
                                       ***********98.************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (424 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       678  (0.0378158); expected 358.6 (0.02)
Passed bias filter:                      637  (0.035529); 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: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.46
# Mc/sec: 2778.44
//
Query:       gi|242399458|ref|YP_002994883.1|  [L=231]
Description: Metallophosphoesterase, calcineurin superfamily [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-32  113.1   0.0    1.8e-32  112.8   0.0    1.1  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    2.1e-15   57.8   0.1    2.7e-15   57.4   0.1    1.2  1  Metallophos    Calcineurin-like phosphoesterase
     0.0023   17.3   0.0        1.8    7.8   0.0    2.5  3  Metallophos_3  Metallophosphoesterase, calcineurin superfamil
  ------ inclusion threshold ------
      0.034   13.9   0.0      0.083   12.7   0.0    1.7  2  NAGLU_N        Alpha-N-acetylglucosaminidase (NAGLU) N-termin


Domain annotation for each model (and alignments):
>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.8   0.0     4e-36   1.8e-32       1     165 []       1     196 [.       1     196 [. 0.92

  Alignments for each domain:
  == domain 1  score: 112.8 bits;  conditional E-value: 4e-36
                     Metallophos_2   1 MklaiiSDlHsnldaleavlealkevgvdaiihaGDl..eeeepevleellela....pvlaVrGNnD......... 62 
                                       M +++iSD+Hsnl+al+av + +k++  d i++ GDl  ++++p+ + e+++      ++l VrGN+D         
  gi|242399458|ref|YP_002994883.1|   1 MLIGLISDIHSNLEALKAVWKNVKRA--DVIFCIGDLvgYGANPNEVVEFFRKQmekrQILCVRGNHDnaiafgitw 75 
                                       99************************..********99******977777776679********************* PP

                     Metallophos_2  63 .......eev..veedvlreaaelgtdlpeeaelelagekvlliHgdpl..........gvkdalaellkeaeegsd 120
                                              e +  +e+ + +e+ e+ ++lp ++ +e+++e++l+iHg+p             + ++ e lk+   +++
  gi|242399458|ref|YP_002994883.1|  76 gfnpyarEAIkwHEKVMTAENLEFIRKLPVKELFEVDNETFLIIHGSPRapldeyifpwLPDSEFVEILKY--FREK 150
                                       ***9997444788999999999*************************98********98888888888888..4555 PP

                     Metallophos_2 121 vvvcGHtHvpevekeggvlvvnPGsvgeprdgdpe.tyaildtdek 165
                                        +v+GHtH++ ++++gg++++nPG vg+prdgd +  ya +dtd++
  gi|242399458|ref|YP_002994883.1| 151 NLVLGHTHMQMLKEIGGRRIINPGGVGQPRDGDWRaAYAFIDTDND 196
                                       699******************************999*******985 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.4   0.1   5.9e-19   2.7e-15       3     172 ..       3     160 ..       1     199 [. 0.74

  Alignments for each domain:
  == domain 1  score: 57.4 bits;  conditional E-value: 5.9e-19
                                       EEEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHHTSEEEEEC-TTS...C CS
                       Metallophos   3 ilvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrgdlekellellaalvkypipvylllGNHe...g 76 
                                       i +i+D+H      +l++l++++++++r    d++++ GDlv  g  ++e++e++++  + + ++ +++GNH+   +
  gi|242399458|ref|YP_002994883.1|   3 IGLISDIH-----SNLEALKAVWKNVKRA---DVIFCIGDLVGYGANPNEVVEFFRKQME-KRQILCVRGNHDnaiA 70 
                                       789*****.....*************666...*************99999****877777.699*********9996 PP

                                       HHH.HHHHHHHHHHHH...HHHHEHHHCEEETSEEEEEETTE.EEEEEEESECEEETHHHHHHHHHHHSCHHHHCC. CS
                       Metallophos  77 fee.ellnkygylgif...sepwrsdaevfnnlplaslgsgs.lkvlllhGgspellvsldklgslnleleapepg. 147
                                       f +   +n+y+ ++i    +     + e+   lp+ +l +    ++l++hG                 ++ + ++  
  gi|242399458|ref|YP_002994883.1|  71 FGItWGFNPYAREAIKwheKVMTAENLEFIRKLPVKELFEVDnETFLIIHGS----------------PRAPLDEYi 131
                                       66666677777666665554444455899999999999999999*******9................222222223 PP

                                       HHHHHH....HHHHTTCSEEEEEESSESS CS
                       Metallophos 148 dewlkd....lekrekadwvivlgHsply 172
                                         wl d       +  ++  +vlgH  + 
  gi|242399458|ref|YP_002994883.1| 132 FPWLPDsefvEILKYFREKNLVLGHTHMQ 160
                                       55555555553344444466666666555 PP

>> Metallophos_3  Metallophosphoesterase, calcineurin superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0   0.00068       3.1      11      65 ..       6      56 ..       3      70 .. 0.71
   2 ?   -1.6   0.0      0.31   1.4e+03      83     107 ..     106     131 ..      81     137 .. 0.68
   3 !    7.8   0.0   0.00041       1.8     201     257 .]     139     203 ..      93     203 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00068
                                      EE--TT-GGGHHHHHHHHHHH--SEEEEES-----HHHHHHHHHHHHTT----TH CS
                     Metallophos_3 11 isdlkgevellerlveviedkdpDllvlvGdlvkaeakadeyesaqeerrepdkk 65
                                      isd++ + e l+ + + +  k +D++  +Gdlv+ +a+ +e    +  r++ +k+
  gi|242399458|ref|YP_002994883.1|  6 ISDIHSNLEALKAVWKNV--KRADVIFCIGDLVGYGANPNEVV--EFFRKQMEKR 56
                                      667777777777777666..689***********999988765..3333333343 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.31
                                       HHHHTT-SEEE.EE--TTS--HHHHH CS
                     Metallophos_3  83 relgeldvpaf.vvPGkrDaPlevfl 107
                                       +el e+d ++f ++ G   aPl++++
  gi|242399458|ref|YP_002994883.1| 106 KELFEVDNETFlIIHGSPRAPLDEYI 131
                                       56666666666256899999999986 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.00041
                                       HHHHHHHHH--SEEEE-SS--EE.EEETTEEEEE--BG...GGTE....EEEEETTTTEEEEEE- CS
                     Metallophos_3 201 vvaelvktlnPevvvvghavkeh.eelgktlvvnPGal...eeGd....favvdleekkveleqv 257
                                       +  e++k ++ +  v gh++ +   e+g   ++nPG +   ++Gd    +a++d+++ +v +e+v
  gi|242399458|ref|YP_002994883.1| 139 EFVEILKYFREKNLVLGHTHMQMlKEIGGRRIINPGGVgqpRDGDwraaYAFIDTDNDEVMFERV 203
                                       5668899999999999***9999999*********988333456666669**********99986 PP

>> NAGLU_N  Alpha-N-acetylglucosaminidase (NAGLU) N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.8e-05     0.083      30      70 ..      47      93 ..      34     105 .. 0.75
   2 ?   -2.2   0.0      0.82   3.7e+03      27      38 ..     104     115 ..      93     122 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.8e-05
                                      -EEEEE-SSS.-EEEEESSHHHHHHHHHHHHHHHS--B--T.....T CS
                           NAGLU_N 30 dvFeisskgg.kilIrGnsgvalasGlnwYLkyycgvhisw.....n 70
                                      ++F+ + ++   +++rGn  +a+a G+ w  + y+   i w     +
  gi|242399458|ref|YP_002994883.1| 47 EFFRKQMEKRqILCVRGNHDNAIAFGITWGFNPYAREAIKWhekvmT 93
                                      66666655553668***************************543333 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.82
                                       TTB-EEEEE-SS CS
                           NAGLU_N  27 sgkdvFeisskg 38 
                                         k+ Fe++++ 
  gi|242399458|ref|YP_002994883.1| 104 PVKELFEVDNET 115
                                       567889998764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); 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: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1418.08
//
Query:       gi|242399459|ref|YP_002994884.1|  [L=43]
Description: hypothetical protein TSIB_1484 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 280.82
//
Query:       gi|242399460|ref|YP_002994885.1|  [L=37]
Description: hypothetical protein TSIB_1485 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       291  (0.0162307); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.46
# Mc/sec: 239.52
//
Query:       gi|242399461|ref|YP_002994886.1|  [L=213]
Description: hypothetical protein TSIB_1486 [Thermococcus sibiricus MM 739]
Scores for complete 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  122.1   0.1    3.1e-35  121.9   0.1    1.1  1  Cas_Cas6  CRISPR associated protein Cas6


Domain annotation for each model (and alignments):
>> Cas_Cas6  CRISPR associated protein Cas6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.9   0.1   1.8e-39   3.1e-35       1     146 []      57     201 ..      57     201 .. 0.93

  Alignments for each domain:
  == domain 1  score: 121.9 bits;  conditional E-value: 1.8e-39
                                       HHHCS-EEEETTEEEEEEEEEE----S--TCEE.EEESS-BBEEEEEEETTCCEEEEE-TTSTTHHHHHHHHHHHHH CS
                          Cas_Cas6   1 gllknkeirlgnnefkveevellkepeitssevvfktlSPivvrstkkengkkktyylspddeeFsellkenlkkky 77 
                                       gll+++ ++l +++f+veev++l+ep  +s+++  +tlSPi v + k e g+ k+y+lsp +++F+e+l+enlk+ky
  gi|242399461|ref|YP_002994886.1|  57 GLLQEPDVELWGEKFYVEEVKALAEPSSYSGRT-YSTLSPIAVTTLKPELGRLKQYDLSPMEDKFYENLRENLKEKY 132
                                       699************************999966.**********88******************************* PP

                                       HHHHSS..SS---EEEEE.EEEE.......TEEEEEEEEEEEEEE-HHHHHHHHHC-SCS-CCCT-S-EEE CS
                          Cas_Cas6  78 kalygeekeeklsikpdk.kvkkivvkkk.etyirGylgrfelegdpellklaydaGlGeknsqGFGmvev 146
                                        +lyg+++  ++++k+ k + k++ v  k +++ r+++  f+ +gd++l++++y+aG+Gekns+GFGmv+v
  gi|242399461|ref|YP_002994886.1| 133 VLLYGKKSPDDFEVKVFKaRPKRFEV--KpGIFQRAWHLVFKAYGDEDLMRVGYQAGFGEKNSLGFGMVKV 201
                                       *******8888888888855666444..2599*************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1648.69
//
Query:       gi|242399462|ref|YP_002994887.1|  [L=454]
Description: hypothetical protein TSIB_1487 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.14   12.0   0.1       0.53   10.1   0.1    2.0  1  ScsC_N    Copper resistance protein ScsC N-terminal domain


Domain annotation for each model (and alignments):
>> ScsC_N  Copper resistance protein ScsC N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1     3e-05      0.53       5      14 ..     148     157 ..     146     158 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 3e-05
                            ScsC_N   5 iekivrdYLl 14 
                                       ieki+rdYLl
  gi|242399462|ref|YP_002994887.1| 148 IEKIIRDYLL 157
                                       9********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       785  (0.0437838); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); 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 0.28s 00:00:00.89 Elapsed: 00:00:00.45
# Mc/sec: 3058.81
//
Query:       gi|242399463|ref|YP_002994888.1|  [L=294]
Description: hypothetical protein TSIB_1488 [Thermococcus sibiricus MM 739]
Scores for complete 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   33.4   0.0    7.3e-08   31.8   0.0    1.5  2  DevR        CRISPR-associated negative auto-regulator DevR/Cs
  ------ inclusion threshold ------
       0.26   10.6   0.0       0.42    9.9   0.0    1.2  1  Thiolase_N  Thiolase, N-terminal domain


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 ?   -2.4   0.0      0.22   1.9e+03      15      57 ..      19      56 ..      14      61 .. 0.66
   2 !   31.8   0.0   8.1e-12   7.3e-08     103     257 ..      81     240 ..      76     252 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.22
                                      -----------EEEEEE--TT--EEEEEE-THHHHHHHHHHHH CS
                              DevR 15 desvGNytehrkvpvvlkeeykvrtvpaiSgeslkHayfetlv 57
                                      +e  G  ++++k+      +   +++p++S  ++k ++ e l+
  gi|242399463|ref|YP_002994888.1| 19 NEVDGDRIRIKKLV-----STSGEVYPFVSARAVKRGIREKLT 56
                                      44455555555554.....378889999999988877776665 PP

  == domain 2  score: 31.8 bits;  conditional E-value: 8.1e-12
                                       H-HHHHHH-EEEGGGT..EEE--SEEE--BEE-TTTTTTT-----------------------------HHHHHSSE CS
                              DevR 103 ecvveDvfGfLitekeksvkRkspvkfsyavpveesekavvdaqfharydllenrarkkgeeeekqnifqvEehsal 179
                                       ++v +D+fG+L+ + +++  R++pv +s ++ ve +    ++  f  r+ +        + +++++++f+ E++  +
  gi|242399463|ref|YP_002994888.1|  81 KYVDNDLFGYLYIKGNEQKPRQAPVSLSPIIAVEHTP---IQIDFGGRFPR--------EMGSTNPTPFETEVADFI 146
                                       6899*********************************...9*********7........55799*********9866 PP

                                       EEEEEEEEGGGTTS-TT...................S--EE---S-HHHHHHHHHHHHHTHHHHHH----------- CS
                              DevR 180 YalsfvlDldriGkpev...................kkskieyvleeeerkkRikaalkallnlLsgsfgakrarll 237
                                         + +v+ ++r+G  +                     k+ ++y l+e+er +R+ a+l+ lln  +g +  +r+ ++
  gi|242399463|ref|YP_002994888.1| 147 GLMKIVI-TERVGIFSEnektdqvkkwdeyakegkiTKQGTTYILPEKERIRRVSALLEILLN--EGWAYPRRTNYF 220
                                       6666655.799999888899***************999999*********************9..777778888888 PP

                                       ---EEEEEEEE--SSS---- CS
                              DevR 238 Pvfeveslvaavskkpfpvf 257
                                        + e  s ++ + +  +pv 
  gi|242399463|ref|YP_002994888.1| 221 AMAEHISTIIYAGERLYPVW 240
                                       88888887777777666665 PP

>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   4.7e-05      0.42     185     228 ..     240     284 ..     237     289 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 4.7e-05
                                       HHHHHTTTTTTTBE-EEEEESSSE.EEE-S-TTS-TT--HHHHHT CS
                        Thiolase_N 185 aaaqkagkFkdeivPvkvkgkkgk.ktvdkdeairsevtaekLak 228
                                       ++a ++ +Fk+e vP ++++ k+  +t d  +++ ++  +ekLa+
  gi|242399463|ref|YP_002994888.1| 240 WKAFEEYHFKKELVPYQITEGKEFlETYDLKKGLVPKKDIEKLAT 284
                                       5899999*****************99****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1809.18
//
Query:       gi|242399464|ref|YP_002994889.1|  [L=218]
Description: hypothetical protein TSIB_1489 [Thermococcus sibiricus MM 739]
Scores for complete 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   20.8   0.0    0.00041   20.3   0.0    1.4  1  Cas_Cas5d  CRISPR-associated protein (Cas_Cas5)


Domain annotation for each model (and alignments):
>> Cas_Cas5d  CRISPR-associated protein (Cas_Cas5)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   2.3e-08   0.00041       5      51 ..       8      54 ..       4     120 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2.3e-08
                                      EEECCEE-EB-TTCCSCCCBESS--HHHHHHHHHHHHT--TTS--CC CS
                         Cas_Cas5d  5 rlegplasfgrpsrkveretydvPtkSavlGllaaalGirrdddlee 51
                                       + ++la f+  ++ ++r +y +P +++vlG+  ++lG+ r+  l+e
  gi|242399464|ref|YP_002994889.1|  8 DVLFDLAHFKVHTTMKGRTSYLIPLPTTVLGFFFSILGKGREAYLRE 54
                                      566899***********************************987555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       269  (0.0150036); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1349.94
//
Query:       gi|242399465|ref|YP_002994890.1|  [L=733]
Description: hypothetical protein TSIB_1490 [Thermococcus sibiricus MM 739]
Scores for complete 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   39.5   0.0    2.4e-09   37.2   0.0    2.2  2  DEAD        DEAD/DEAH box helicase
    3.9e-07   30.2   0.3    3.9e-07   30.2   0.3    2.7  3  ResIII      Type III restriction enzyme, res subunit
      5e-07   30.0   0.1    1.8e-06   28.3   0.0    2.0  2  Helicase_C  Helicase conserved C-terminal domain
    0.00023   21.4   0.1    0.00066   19.9   0.1    1.9  1  HD          HD domain
  ------ inclusion threshold ------
      0.036   14.2   0.1      0.075   13.2   0.1    1.5  1  HD_6        HD domain
        0.2   11.4   1.4       0.43   10.4   0.5    2.0  2  FixP_N      N-terminal domain of cytochrome oxidase-cbb3, Fix


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 !   37.2   0.0   7.9e-13   2.4e-09       9     175 ..     224     395 ..     216     396 .. 0.65
   2 ?   -3.1   0.0         2   5.9e+03      38      72 ..     435     467 ..     428     501 .. 0.54

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 7.9e-13
                                       HHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTT.ST.....SEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx.....xxxx RF
                              DEAD   9 plilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkky.id.....lrvl 79 
                                       + + +g+++l +a+TG GKT a l  +        +kt + +++v Pt   ++++ +++kk++k  ++         
  gi|242399465|ref|YP_002994890.1| 224 NMANSGENILFSAPTGWGKTFASLTIAS-------TKTPTHIIYVLPTITSIRKMKETIKKILKMkVEdnyyfAD-- 291
                                       445589***************9555444.......688889***********************43332222222.. PP

                                       EEETTSSHHHHHHHH.......HTT...CSEEEEEHHHHHH.HHHCTSSHCTTEEE....EEEETHHHHHHTTTHHH CS
                                       xxxxxxxxxxxxxxx.......xxx...xxxxxxxxxxxxx.xxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxx RF
                              DEAD  80 liiggvaardqlskl.......dng...vdivvgtpgrldd.llstgklnlsqvrf....lVlDEadrlldqgfsdf 141
                                         +++va+++++++        + +     ++++t ++++  +l+ gk  l+++ f    +++DE + +  +g    
  gi|242399465|ref|YP_002994890.1| 292 --VEKVAKQKDYERSvdwelfiS-RsfmSPVTLTTLDQIVLtFLHVGKYFLKRFHFrnsiFIFDEFHLYPISGLYIL 365
                                       ..333333333333222223332.324555666665555552447888777777544455*********99976665 PP

                                       HHHHHHHSHHHCTTSTTTSEEEEEESSBSHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 142 inrilnqlpqitcdgklqrqvivlSATlpkdvkk 175
                                       ++ i +      ++   + +++++SAT++  +++
  gi|242399465|ref|YP_002994890.1| 366 LKFIQKYN----QEFDYNIKTVFMSATVHPALEN 395
                                       55533333....23334566*********87765 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2
                                       HHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  38 ivyetkgktgpkalivePtreLaeqtlnnlkkfkk 72 
                                       +++  k+ +   +l+++ t e a + +  lk+  k
  gi|242399465|ref|YP_002994890.1| 435 EIA--KKAQDGNVLVICNTVEKAIKLYLLLKRHYK 467
                                       333..345555666666666666666666665555 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.3   1.3e-10   3.9e-07      14     169 ..     224     389 ..     193     390 .. 0.69
   2 ?   -1.1   0.0      0.54   1.6e+03      43      65 ..     431     453 ..     427     504 .. 0.71
   3 ?   -2.4   0.2       1.4   4.1e+03      66      94 ..     571     599 ..     566     650 .. 0.44

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 1.3e-10
                                       HHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG.......... CS
                            ResIII  14 nlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseayke...... 84 
                                       n++     +  +++l+ ++TG GKT+ ++ ++   +      +++ + p+++ + +++e++kk+l+ ++++      
  gi|242399465|ref|YP_002994890.1| 224 NMA-----NSGENILFSAPTGWGKTFASLTIASTKTPT----HIIYVLPTITSIRKMKETIKKILKMKVEDnyyfad 291
                                       333.....67789*****************99998886....9*******************999999999898884 PP

                                       GEEEESSS-B--.......-SEEEEEHHHHHHTH....................HHHTTT-SEEEEETGGGTTS... CS
                            ResIII  85 igkkvsgdkkkakekdstnkkilvttiqsldadseee............eeeseellrdrfdviiiDEaHrlgak.. 147
                                       ++k+ +++ +++    s +++++++   +    +  +             ++  +  + r+ ++i+DE H +  +  
  gi|242399465|ref|YP_002994890.1| 292 VEKVAKQKDYER----SVDWELFISRSFMSPVTL--TtldqivltflhvGKYFLKRFHFRNSIFIFDEFHLYPISgl 362
                                       444444444444....777777776544444444..23455555555444444455555555********9999755 PP

                                       ....TTTHHHHHT---.SEEEEEESS- CS
                            ResIII 148 ....kswreilekfke.avllglTATp 169
                                           k++++ ++ f+   + + ++AT 
  gi|242399465|ref|YP_002994890.1| 363 yillKFIQKYNQEFDYnIKTVFMSATV 389
                                       555534444444443336677888885 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.54
                                       HHHHHH-S.....-EEEEESSHH CS
                            ResIII  43 klierllkkgkeekflflvprks 65 
                                       ++ e+++kk++  ++l+++++ +
  gi|242399465|ref|YP_002994890.1| 431 AILEEIAKKAQDGNVLVICNTVE 453
                                       67788888888889999998863 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.4
                                       HHHHHHHHGGGGTGG....GEEEESSS-B CS
                            ResIII  66 lleqtleefkkflseaykeigkkvsgdkk 94 
                                       l +  leef   ++++++ i++++++  k
  gi|242399465|ref|YP_002994890.1| 571 LAKTILEEFDGNIKTEFELIEQFKESSLK 599
                                       55555566655555444332222111111 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 ?   -3.9   0.0         6   1.8e+04      15      33 ..     254     273 ..     247     288 .. 0.60
   2 !   28.3   0.0     6e-10   1.8e-06       6     110 ..     432     539 ..     429     540 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 6
                                       TTSEEEEEESSHHHHHH.HH CS
                        Helicase_C  15 eggkilifvntidrlek.vk 33 
                                           i+ +++ti+++ k  +
  gi|242399465|ref|YP_002994890.1| 254 TPTHIIYVLPTITSIRKmKE 273
                                       55667777788887754322 PP

  == domain 2  score: 28.3 bits;  conditional E-value: 6e-10
                                       HHHHHHHTTTTSEEEEEESSHHHHHHHHHHHHHT..TSTEEEESTTSTHHHHHHHHHHHH....TTSSSEEEESGGG CS
                        Helicase_C   6 llellkleeeggkilifvntidrlekvklllekk..gikvavlhgelpqnereeileqfn....kgesdvLiatdva 76 
                                       +le++ +++++g++l+++nt++++ k+ lll+++    k++ lh++ + ++r+e  +q        +  v ++t+va
  gi|242399465|ref|YP_002994890.1| 432 ILEEIAKKAQDGNVLVICNTVEKAIKLYLLLKRHykIKKTLLLHSRFTYKDRKEKETQLEwlsrIPKGFVFVSTQVA 508
                                       444456899*************77555555555564578999***********999998776543556699****** PP

                                       TSSSTSTTESEEEESSSSSSHHHHHHHHTTSSST CS
                        Helicase_C  77 erGidipkvnlVinfdlprnvtsyiqriGRtgRa 110
                                       e ++d+   ++++   +p  ++s+iqr GR+ R+
  gi|242399465|ref|YP_002994890.1| 509 EVSLDMS-FDYLFTELAP--LSSLIQRFGRVNRY 539
                                       ******4.7777777766..78*********996 PP

>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.1   2.2e-07   0.00066       3      97 ..      31     118 ..      29     180 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2.2e-07
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHHHHHHHHH CS
                                HD   3 eHsleVaklarrlaedlgeeedrellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevekrlgldle 79 
                                       +H+ eV ++++ la+++g++e + +l++ a  HD+Gk  +          ++k + H+  +a++  ++ + ++    
  gi|242399465|ref|YP_002994890.1|  31 QHIEEVIRVSKSLAKKHGLQEYEKVLKTLAWWHDLGKLNPKW-DIT----KKKKPPHSALSAYLFLRHSNIKDP--R 100
                                       7**************************************775.333....335688******998888777755..5 PP

                                       HHHHHHHTTCCHHHHHHH CS
                                HD  80 dvaklirehheswegkkr 97 
                                       +++ + r+h++  ++   
  gi|242399465|ref|YP_002994890.1| 101 IFYFILRHHSHLTPILSH 118
                                       777777777776665554 PP

>> HD_6  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   2.5e-05     0.075      23      77 ..      36      79 ..      16     168 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.5e-05
                                      HHHHHHHHHHHTS-HHHHHC..TS-HHHHHHHHHHHHHCCCGGGSSHHHHTTS--- CS
                              HD_6 23 vaavaealldkwlsllarll.rgleeealrrllaflaalHDlGKaspaFqakvpel 77
                                      v              ++++l ++   ++ +++l  la +HDlGK++p+    ++++
  gi|242399465|ref|YP_002994890.1| 36 VIR------------VSKSLaKKHGLQEYEKVLKTLAWWHDLGKLNPKWDITKKKK 79
                                      333............3344433445578899****************998776433 PP

>> FixP_N  N-terminal domain of cytochrome oxidase-cbb3, FixP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0         3     9e+03      20      32 ..     237     249 ..     236     251 .. 0.79
   2 ?   10.4   0.5   0.00014      0.43      12      25 ..     670     683 ..     668     684 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 3
                            FixP_N  20 PrWWlylFyativ 32 
                                       P++W  +F  + +
  gi|242399465|ref|YP_002994890.1| 237 PTGWGKTFASLTI 249
                                       99**999987665 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00014
                            FixP_N  12 IrElnnplPrWWly 25 
                                       I+E+ +p+P WWl+
  gi|242399465|ref|YP_002994890.1| 670 IKEYLTPIPIWWLF 683
                                       9***********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (733 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1165  (0.0649785); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); 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: 0.75u 0.32s 00:00:01.07 Elapsed: 00:00:00.49
# Mc/sec: 4490.37
//
Query:       gi|242399466|ref|YP_002994891.1|  [L=173]
Description: exonuclease, RecB family [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-54  185.0   1.6    1.2e-54  184.8   1.6    1.0  1  Cas_Cas4  Domain of unknown function DUF83
     0.0004   20.4   0.8     0.0014   18.6   0.4    1.6  2  PDDEXK_1  PD-(D/E)XK nuclease superfamily
  ------ inclusion threshold ------
      0.011   16.1   0.6      0.018   15.4   0.6    1.4  1  PDDEXK_3  PD-(D/E)XK nuclease superfamily
      0.026   14.3   0.3      0.044   13.6   0.3    1.3  1  HycI      Hydrogenase maturation protease


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 !  184.8   1.6   2.7e-58   1.2e-54       2     161 ..      17     172 ..      16     173 .] 0.98

  Alignments for each domain:
  == domain 1  score: 184.8 bits;  conditional E-value: 2.7e-58
                          Cas_Cas4   2 gtkiqyyliCkrklwlisheitleensetvelGkllheesyerekkevelsesikiDvvekekeklvvvEvKkskkk 78 
                                       gt+i+y++iC++klw++s++it+e++se v+lGk+lhe+sy  e+kev++ +sikiD+++ ++++++v+EvKk+k++
  gi|242399466|ref|YP_002994891.1|  17 GTEINYLFICPTKLWYFSKGITMEQESEYVDLGKFLHERSYFGEEKEVQI-GSIKIDFIK-RGNTIEVHEVKKGKSM 91 
                                       89************************************************.*********.**************** PP

                          Cas_Cas4  79 eeaaklQllyYlllLekkgveikeGvleypkekkreevelteelreelekaikeieeiissekppkvkkkkiCkkCa 155
                                       e+a+++Q lyYl++L+  g+++k ++l+ypk ++++e+ l+  ++ee+e+ai+e+e+i s ++pp+++k+++CkkCa
  gi|242399466|ref|YP_002994891.1|  92 EKAHEMQALYYLYYLKVLGIRAK-AILNYPKLRETKEIILD-GHEEEVEEAINEAERIKSLSAPPSPVKSRKCKKCA 166
                                       ***********************.****************5.67899****************************** PP

                          Cas_Cas4 156 yaelCl 161
                                       y++lC+
  gi|242399466|ref|YP_002994891.1| 167 YYDLCW 172
                                       *****9 PP

>> PDDEXK_1  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.24   1.1e+03       7      42 ..      20      54 ..      18      65 .. 0.73
   2 !   18.6   0.4   3.2e-07    0.0014     133     254 ..      70     171 ..      54     172 .. 0.65

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.24
                          PDDEXK_1  7 letfleCplr.fflryllglreeeeleapdlGtlvHa 42
                                      ++ +  Cp + ++++++  +  e+e e  dlG ++H+
  gi|242399466|ref|YP_002994891.1| 20 INYLFICPTKlWYFSKGITM--EQESEYVDLGKFLHE 54
                                      55666688774666544444..777777799999996 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 3.2e-07
                          PDDEXK_1 133 riDrvddkegelriiDyKtgsappkskelaelkeglQlllYllalaegeelkeegepagalylrleepkvkdeevvk 209
                                       +iD + + +  +++ + K g+     ++    ++++Q l Yl++l+          +a+a++         + +++k
  gi|242399466|ref|YP_002994891.1|  70 KIDFIKRGNT-IEVHEVKKGK---SMEK----AHEMQALYYLYYLKVLGI------RAKAILNYP------KLRETK 126
                                       5899876666.*******999...4444....5669*********99832......566665555......333333 PP

                          PDDEXK_1 210 km..alteeeleallqeleelaeeilagefparpskk..CeyCpyksvC 254
                                       ++  +  eee e++ +e+    e+i++   p++p k   C+ C+y ++C
  gi|242399466|ref|YP_002994891.1| 127 EIilDGHEEEVEEAINEA----ERIKSLSAPPSPVKSrkCKKCAYYDLC 171
                                       330023444444444444....45554455555554455********99 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 ?   15.4   0.6     4e-06     0.018      54     114 ..      63     127 ..      50     130 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 4e-06
                          PDDEXK_3  54 gkevgeeyrlDllveekv..ivElKaveelkeeheaqlln...YlkltklklGlliNFnkkklkee 114
                                       + ++g+ + +D++ + +   + E+K  ++++++he+q l    Ylk+++++   ++N+ k ++++e
  gi|242399466|ref|YP_002994891.1|  63 EVQIGS-IKIDFIKRGNTieVHEVKKGKSMEKAHEMQALYylyYLKVLGIRAKAILNYPKLRETKE 127
                                       556666.788888854431267***************976111578888*********99665555 PP

>> HycI  Hydrogenase maturation protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.3   9.7e-06     0.044      56     124 ..      79     145 ..      64     148 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.7e-06
                                       EEECCHHHHHHTTC.CGCCCHCHHHHHHHHHHCCS--SEEEEEEE--S-BST..CCS--HHHHCCHHHHH CS
                              HycI  56 iikddevpkklkakkmsaHqlplaevlklleekgeipkevillgvqpesled.vgielseevkkavekav 124
                                       +i++ ev k ++ +   aH++   + l +l+  g i++++il   +  ++ + +  + +eev++a+++a 
  gi|242399466|ref|YP_002994891.1|  79 TIEVHEVKKGKSME--KAHEMQALYYLYYLKVLG-IRAKAILNYPKLRETKEiILDGHEEEVEEAINEAE 145
                                       68999999866666..9****************7.78888888888777777466688999****99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); 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: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1052.92
//
Query:       gi|242399467|ref|YP_002994892.1|  [L=322]
Description: CRISPR-associated protein Cas1 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-83  279.8   0.7    2.5e-83  279.5   0.7    1.1  1  Cas_Cas1  CRISPR associated protein Cas1
  ------ inclusion threshold ------
      0.068   13.1   0.4        2.4    8.1   0.1    2.6  2  DUF4041   Domain of unknown function (DUF4041)


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 !  279.5   0.7   2.8e-87   2.5e-83       3     283 .]       8     277 ..       6     277 .. 0.96

  Alignments for each domain:
  == domain 1  score: 279.5 bits;  conditional E-value: 2.8e-87
                                       EESTEEEEEEETTEEEEEESSEEEEEEECCCEEEEEEESTEEEEHHHHHHHHHTT-EEEEE-TTS-EEEEEEE.SSS CS
                          Cas_Cas1   3 vteqgaylrkkgerlvvekegeekkeiplediesivifgevslstkalrllaekgipvvflsengkylgrlep.ees 78 
                                       + ++g+ l++++++l++e+ +  k+ + +e i +i+i+g+v+++++ l++la+kgi+v+f++++g+y g+++p e+ 
  gi|242399467|ref|YP_002994892.1|   8 LLSDGT-LSRRENTLYFENAQG-KRPLAVEGIYDIYIYGHVNITSQSLHFLAQKGIAVHFFNHYGYYDGSFYPrESL 82 
                                       678899.*************88.9*************************************************9999 PP

                                       STHHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHCCHHCTTHHHHCHCHHHHHHHHHHHH-HSHHHHHHHH CS
                          Cas_Cas1  79 gnvelrraQyraaddeekrlelakkivagklenqrkvlrrlkrdreeeeleeaieeleelleklekaesleeLrgiE 155
                                       ++++l+++Q++++ d+ekrl+lak +v g ++n++k+l+++  +    +++e        l++le++e+++e++++E
  gi|242399467|ref|YP_002994892.1|  83 NSGDLLIKQAKHYLDREKRLKLAKLFVVGGVKNMEKNLKKWGMKV---SFNEF-------LNELEAVEKISEVMNVE 149
                                       ****************************************99999...45555.......55566699********* PP

                                       HHHHHHHHHHHHHHCSCGGS-SS-SSSS-SSHHHHHHHHHHHHHHHHHHHHHHTSS--TT--SSS--TTSS-HHHHH CS
                          Cas_Cas1 156 GeaakaYfeafdkllkeefefegRsrrppkDpvNalLsfgYtllysevlsaieavgLdPyiGfLHedrpgrpsLalD 232
                                       ++++++Y++ +d+ l+e+f++ +R+rrpp++++Nal+sf+++ +y++++s++++++L P+i++LHe+ ++r+sLalD
  gi|242399467|ref|YP_002994892.1| 150 ARVRQEYYASWDETLPEDFKIVKRTRRPPQNEINALISFLNSRIYATIVSELYNTQLSPTISYLHEPGERRFSLALD 226
                                       ***************************************************************************** PP

                                       HHHHHHHHHCHHHHHHHHHTTSS-GGGEEEETTEEEE-HHHHHHHHHHHHH CS
                          Cas_Cas1 233 LmEefRpllvDrlvlslinkrqlkekdFekeengvlLteegrkkfleafee 283
                                       L E+f+p+++Dr+  +l++++++k+++F ++ ngvlL+++g+k++l+af+e
  gi|242399467|ref|YP_002994892.1| 227 LSEIFKPIIADRITNRLVKQGIIKKEHFRNDLNGVLLNDKGKKIVLKAFNE 277
                                       *************************************************86 PP

>> DUF4041  Domain of unknown function (DUF4041)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.016   1.4e+02      35      53 ..     137     157 ..     134     159 .. 0.79
   2 ?    8.1   0.1   0.00027       2.4       1      31 [.     269     298 ..     269     314 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.016
                           DUF4041  35 eainklgktm..nirItpeYl 53 
                                       ea++k+ ++m  ++r+ +eY+
  gi|242399467|ref|YP_002994892.1| 137 EAVEKISEVMnvEARVRQEYY 157
                                       899*******55567888886 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00027
                           DUF4041   1 KlmlrAFNgEcdaaiskVkynnietlekRIe 31 
                                       K++l+AFN+E    +++ + ++ + +++R++
  gi|242399467|ref|YP_002994892.1| 269 KIVLKAFNEEMQKSVRHPRLKK-NVTKQRLI 298
                                       89********999999877765.34455555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       836  (0.0466284); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); 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: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2020.81
//
Query:       gi|242399468|ref|YP_002994893.1|  [L=231]
Description: hypothetical protein TSIB_1493 [Thermococcus sibiricus MM 739]
Scores for 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   32.1   0.0    2.1e-07   31.1   0.0    1.5  1  PDDEXK_1  PD-(D/E)XK nuclease superfamily
  ------ inclusion threshold ------
      0.032   14.3   0.0       0.16   12.0   0.0    2.0  1  Cas_Cas4  Domain of unknown function DUF83
      0.072   12.9   0.0       0.17   11.7   0.0    1.6  2  Dna2      DNA replication factor Dna2


Domain annotation for each model (and alignments):
>> PDDEXK_1  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.0   3.5e-11   2.1e-07     104     254 ..      78     229 ..      36     230 .. 0.73

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 3.5e-11
                          PDDEXK_1 104 laeeleakrg.frpvalelefggekvrLkGriDrvd..dkegelriiDyKtgsappkskelaelkegl.......Ql 170
                                       l+   ea ++  ++v++el+ g     L+GriD+v   +  +   + D+  + + p++++  e+ e+        Ql
  gi|242399468|ref|YP_002994893.1|  78 LQGDIEATPEiEKEVSYELGDG---WLLTGRIDLVIgeHVFEFKFLSDWS-YEKIPENLD--EVDEESvlnayteQL 148
                                       4444444444566677776666...99*******9965555566777775.777778888..777777568888888 PP

                          PDDEXK_1 171 llYllalaegeelkeegepagalylrleepkvk.deevvkkmalteeeleallqeleel...aeeilagefparpsk 243
                                        +Yl +l           + g l+++ +++ +  ++ ++k    +++ +  +l++++ +   +e+i++ge p +p++
  gi|242399468|ref|YP_002994893.1| 149 NAYLNILPDA--------EFGHLWIFRHNELIPwKKLEIK---KDSKAFKGFLKRAKGIvklIESIENGELPKDPEP 214
                                       8888888888........8899998888877772333333...3566666665555555555**************9 PP

                          PDDEXK_1 244 k....CeyCpyksvC 254
                                       +    C++C +ks+C
  gi|242399468|ref|YP_002994893.1| 215 RfeweCKNCIFKSIC 229
                                       999************ PP

>> Cas_Cas4  Domain of unknown function DUF83
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.7e-05      0.16       4     160 ..      28     229 ..      25     231 .] 0.65

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.7e-05
                          Cas_Cas4   4 kiqyyliCkrklwlish...eitleensetvelGkllhe.................esyerekkevelse....... 53 
                                        + ++ +C+ k++l  +   ++  e+n+e++  G++lh                  e+  + +kev++ e       
  gi|242399468|ref|YP_002994893.1|  28 SVTSVSFCPLKAALTTRydvRFFGEKNKERIL-GQVLHMgllglikdswsylqgdiEATPEIEKEVSY-Elgdgwll 102
                                       67788889999988776544677788888887.99999999988888877776654333334488888.34578998 PP

                          Cas_Cas4  54 sikiDvvekekeklvvvEvKkskkk.................eeaaklQllyYlllLekkgveikeGvleypkekkr 113
                                       +++iD+v     +  v+E+K  +                    +a + Ql +Yl +L     +++ G l++   ++ 
  gi|242399468|ref|YP_002994893.1| 103 TGRIDLVI----GEHVFEFKFLSDWsyekipenldevdeesvLNAYTEQLNAYLNILP----DAEFGHLWIFRHNEL 171
                                       99999998....4444444433333333344444444444436677888999988888....455577777777766 PP

                          Cas_Cas4 114 ee...velteelr......eelekaikeieeiisse..kppkvkkkkiCkkCayaelC 160
                                            +e++++ +      ++++ ++k ie+i + e  k p++  +  Ck+C ++++C
  gi|242399468|ref|YP_002994893.1| 172 IPwkkLEIKKDSKafkgflKRAKGIVKLIESIENGElpKDPEPRFEWECKNCIFKSIC 229
                                       44444666655542222225677777778888777755678889999*********** PP

>> Dna2  DNA replication factor Dna2
   #    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      55      94 ..      27      65 ..      19      97 .. 0.83
   2 ?   -2.2   0.0      0.52   3.1e+03     103     126 ..     121     144 ..     100     151 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.9e-05
                              Dna2 55 vsaTsvanslsClRravLqerl..kvsgesskamliGtilHe 94
                                      +s Tsv    +C+ +a L +r+  +++ge++k+ ++G++lH 
  gi|242399468|ref|YP_002994893.1| 27 ISVTSV---SFCPLKAALTTRYdvRFFGEKNKERILGQVLHM 65
                                      555555...69**********9999****************6 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.52
                              Dna2 103 eeldkekleelldklleknleely 126
                                       ++++ ek+ e+ld++ e+++ + y
  gi|242399468|ref|YP_002994893.1| 121 SDWSYEKIPENLDEVDEESVLNAY 144
                                       368888888888888887776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 1464.45
//
Query:       gi|242399469|ref|YP_002994894.1|  [L=85]
Description: CRISPR-associated protein Cas2 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.4e-23   82.1   1.1    2.7e-23   81.9   1.1    1.0  1  CRISPR_Cas2  CRISPR associated protein Cas2
  ------ inclusion threshold ------
      0.073   13.5   0.1      0.096   13.1   0.1    1.2  1  DUF1040      Protein of unknown function (DUF1040)


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 !   81.9   1.1     3e-27   2.7e-23       1      74 [.       1      71 [.       1      73 [. 0.96

  Alignments for each domain:
  == domain 1  score: 81.9 bits;  conditional E-value: 3e-27
                                      EEEEEEEECHCHHHHHHHHHHHHHHTTEEEEETTEEEEEESHHHHHHHHHHHHHHSHTTTCEEEEEEEETCHHH CS
                       CRISPR_Cas2  1 mlvlvvYDikedrkrrrkvakilkkyGfqrvQySVFegelseaqleklkkrlkkiidpeedsiriykltekqfe 74
                                      m+++vvYD+  +  r++kv+k+l+++ +++vQ+SVFege++ a++e++kk +k++id++eds++iy+l+++ ++
  gi|242399469|ref|YP_002994894.1|  1 MYIIVVYDV--NVSRVNKVKKFLRQH-LIWVQNSVFEGEVTLAEYERIKKGIKELIDENEDSVIIYRLRARPKR 71
                                      9********..***************.*****************************************988766 PP

>> DUF1040  Protein of unknown function (DUF1040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   1.1e-05     0.096       4      74 ..      12      82 ..       9      84 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.1e-05
                           DUF1040  4 hrinellellqpe..Wkkekdlnllqllqkla.eeagfegeleeltddvliyhlkmresdkeemiPGlkkdyee 74
                                       r+n++ ++l+++  W +++ ++   +l++      g+++ ++e +d v+iy+l+ r + k+    G++k+ +e
  gi|242399469|ref|YP_002994894.1| 12 SRVNKVKKFLRQHliWVQNSVFEGEVTLAEYErIKKGIKELIDENEDSVIIYRLRARPKRKNL---GIEKNPVE 82
                                      688888888876444777777665555544431456888888999999*******99888774...56666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       648  (0.0361426); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); 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: 00:00:00.49
# Mc/sec: 517.42
//
Query:       gi|242399470|ref|YP_002994895.1|  [L=773]
Description: Hydrogenase maturation protein HypF [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.1e-46  155.6   0.0    1.4e-45  155.0   0.0    1.3  1  Sua5_yciO_yrdC   Telomere recombination
    8.7e-32  108.6  19.5    4.3e-16   58.4   3.6    2.4  2  zf-HYPF          HypF finger
    1.4e-28   99.6   0.2    3.1e-28   98.4   0.2    1.5  1  HypF_C           HypF Kae1-like domain
    2.8e-26   91.7   0.0    7.2e-25   87.2   0.0    2.7  2  Acylphosphatase  Acylphosphatase
    8.3e-06   25.7   0.1    6.2e-05   22.8   0.0    2.0  2  Peptidase_M22    Glycoprotease family
    0.00095   18.9   0.1      0.042   13.5   0.0    2.2  2  Carbam_trans_N   Carbamoyltransferase N-terminus
  ------ inclusion threshold ------
      0.027   14.0   0.0      0.063   12.8   0.0    1.6  1  BcrAD_BadFG      BadF/BadG/BcrA/BcrD ATPase family
       0.11   11.9   0.0       0.53    9.7   0.0    2.0  2  ROK              ROK family
        2.7    7.4   5.1        3.4    7.1   0.2    2.3  2  NMD3             NMD3 family


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 !  155.0   0.0   7.2e-49   1.4e-45       1     178 [.     211     386 ..     211     387 .. 0.98

  Alignments for each domain:
  == domain 1  score: 155.0 bits;  conditional E-value: 7.2e-49
                                       HHHHTTSEEEEE-SSSEEEEEETTSHHHHHHHHHHHTSHCCC--EEEESSCCCCCCCC-.TC--HHHHHHHHCT-SS CS
                    Sua5_yciO_yrdC   1 ealrkGgivaiptetvYgLacdatneeaverlreiKgrpsdkplavlvasledlkklae.seveeealkllerfwPG 76 
                                       e+++kG+ivai+++++ ++acdatnee+ ++lr++  rp ++p+a+++++le+++++a  se+e+e l++ ++    
  gi|242399470|ref|YP_002994895.1| 211 ELIDKGHIVAIKGIGGIHIACDATNEETLRELRKRILRP-EQPFAIMAKDLETIENFAIvSEIEREELTSYRK---- 282
                                       5799***********************************.*********************************.... PP

                                       SCEEEEE..E-TS-HHHHTTTTEEEEEE-SSHHHHHHHHHCTS-.EEEEES-STTS-S-SSHHHHHHHC-TTSECB- CS
                    Sua5_yciO_yrdC  77 pitlllkrskeklpkevapglktvGvrlPdtplarlLlealgep.lvaTSanlsgepsitdaeeveeelgeivdlil 152
                                       pi+ l+k++  +lp+ +apgl t+Gv+lP+  +++ L+++ ++p  v+TSan +g p+++d+e + +el+  +d++l
  gi|242399470|ref|YP_002994895.1| 283 PIVALRKKEPFPLPETLAPGLPTIGVMLPYAGTHYILFHYSKSPvYVMTSANYPGMPMVIDNETALKELKTLADYFL 359
                                       *******88888*****************************99988******************************* PP

                                       SS-.--SSS---EEEETTSSTSSECEX CS
                    Sua5_yciO_yrdC 153 dgg.eiavgvdstVvdltegkpkilRr 178
                                        ++ +i +++d++V+++++gk  ++Rr
  gi|242399470|ref|YP_002994895.1| 360 LHNrKILNRTDDSVIRFVDGKRAVIRR 386
                                       **************************8 PP

>> zf-HYPF  HypF finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.4   3.6   2.1e-19   4.3e-16       1      34 []     111     144 ..     111     144 .. 0.98
   2 !   55.8   8.1   1.4e-18   2.7e-15       1      34 []     161     194 ..     161     194 .. 0.98

  Alignments for each domain:
  == domain 1  score: 58.4 bits;  conditional E-value: 2.1e-19
                                       --HHHHHHHC-TTSTTTT-TT---TTTS--EEEE CS
                           zf-HYPF   1 lCedClrEykdpldRRfhaqfisCtnCGPrlsli 34 
                                       +C+dClrE++dp d+R+ ++fi CtnCGPr+++i
  gi|242399470|ref|YP_002994895.1| 111 ICDDCLRELFDPRDKRYMYPFIVCTNCGPRFTII 144
                                       7*******************************97 PP

  == domain 2  score: 55.8 bits;  conditional E-value: 1.4e-18
                                       --HHHHHHHC-TTSTTTT-TT---TTTS--EEEE CS
                           zf-HYPF   1 lCedClrEykdpldRRfhaqfisCtnCGPrlsli 34 
                                       +C+ C+ Eykdpl+RR+ha++++C+ CGP ++l+
  gi|242399470|ref|YP_002994895.1| 161 MCDYCESEYKDPLNRRYHAEPVCCPVCGPSYRLY 194
                                       9******************************996 PP

>> HypF_C  HypF Kae1-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.4   0.2   1.6e-31   3.1e-28       7     102 .]     404     500 ..     400     500 .. 0.97

  Alignments for each domain:
  == domain 1  score: 98.4 bits;  conditional E-value: 1.6e-31
                            HypF_C   7 LAlGaelkntfalakggqallsqhlGdlenletleayeealeeleklleik.pevivcDlhpdylstklaeelaeke 82 
                                       L +Gael n+f +ak+++++ sq++G+ +++e le+++ a+++++k+l+++  ++iv+D+hp y++tkla e+ae+e
  gi|242399470|ref|YP_002994895.1| 404 LTVGAELMNAFGIAKNSKVYPSQYIGNTSKVEVLEFMRGAISHFKKILRVQnLDLIVADMHPLYNTTKLAMEIAEEE 480
                                       89************************************************7589*********************** PP

                            HypF_C  83 klelievqHHhAHllavlae 102
                                       ++e+++vqHH+AH+++v+ae
  gi|242399470|ref|YP_002994895.1| 481 GVEFLQVQHHYAHVASVMAE 500
                                       *******************8 PP

>> Acylphosphatase  Acylphosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.2   0.0   3.6e-28   7.2e-25       1      84 [.       7      90 ..       7      91 .. 0.94
   2 ?    1.3   0.0      0.23   4.6e+02      26      66 ..     640     682 ..     633     687 .. 0.73

  Alignments for each domain:
  == domain 1  score: 87.2 bits;  conditional E-value: 3.6e-28
                   Acylphosphatase  1 vrllvtGrVQgvgFRkfvrrlAkelglkGyvrNlsdgsVeivaegeeekvekfleelksgppk.arvdeveveeleeee 78
                                      +++ v+G+VQgvgFR+f++r+A+e+ l+Gyv+Nl d  Veiv+eg+ee++++fl++lk + p+ arv++++++el+ ++
  gi|242399470|ref|YP_002994895.1|  7 YHIHVEGIVQGVGFRPFIYRIAHEHSLRGYVKNLGDAGVEIVVEGKEEDIRAFLKALKDKAPPlARVEKIKTKELPLQG 85
                                      6899*******************************************************77767***********9999 PP

                   Acylphosphatase 79 efkdFe 84
                                        ++F 
  gi|242399470|ref|YP_002994895.1| 86 F-DRFY 90
                                      8.8886 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.23
                   Acylphosphatase  26 glkGyvrNlsdg.sVeivaegeeekvekfleelksgppk.arv 66 
                                       +l+G + + +++   ++ +egee kve++ +++ ++ ++ a +
  gi|242399470|ref|YP_002994895.1| 640 KLEGVAFRGKNDlGFRVPVEGEELKVEELFRQVLESRTNpADI 682
                                       566664433333368999**********999998865554665 PP

>> Peptidase_M22  Glycoprotease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.27   5.4e+02      73     103 ..     473     503 ..     465     513 .. 0.78
   2 !   22.8   0.0   3.1e-08   6.2e-05     134     258 ..     611     741 ..     596     753 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.27
                                       HHHHHHHCT--EEEEEHHHHHHHCCHCTSEC CS
                     Peptidase_M22  73 AkglalalnkPlvgVnhleahalaarleeke 103
                                       A  +a   ++++++V+h  ah+++++ e+k 
  gi|242399470|ref|YP_002994895.1| 473 AMEIAEEEGVEFLQVQHHYAHVASVMAENKL 503
                                       66677788999*************9877544 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 3.1e-08
                                       SSEHHHHHHHHHHHHT..SSCCHHHHHHHC.TCS.......EET...TEEE.CHHHHHHHHHHST..T....HHHHH CS
                     Peptidase_M22 134 ddaagealdkvarllglpypggpkieklak.egkkiefprplkg...ldfsfsGlktavlkelek..e....vedla 200
                                          +g  ld++a ll++ y+   + e ++k eg +++     k+   + +   G++ +v +++++  e     +d+a
  gi|242399470|ref|YP_002994895.1| 611 ASSTGRVLDAFAVLLNVAYKRTYEGEPAMKlEGVAFR---G-KNdlgFRVPVEGEELKVEELFRQvlEsrtnPADIA 683
                                       566899999******9999555555544443442222...1.112347788889999999999555436788***** PP

                                       HHHHHHHHHHHHHHHHHHHHHCTBSEEEEESGGGGXHHHHHCHCCHHHHTTSEEEXXX CS
                     Peptidase_M22 201 asfqeavvdhlvekteralklpkakelvilGGvaankrLrealeeeaeelglkliiPp 258
                                       +s+  a  +   e++ + +k+ ++k+++++GGva n+++ ++++++ e  +l+++ ++
  gi|242399470|ref|YP_002994895.1| 684 YSVHLALGRAFGEIAVEKAKEFDIKNVALSGGVAYNELIVKTIRKIVESNNLRFYTTH 741
                                       ********************************************99988999999876 PP

>> Carbam_trans_N  Carbamoyltransferase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.031        62     120     157 ..     480     515 ..     437     529 .. 0.73
   2 !   13.5   0.0   2.1e-05     0.042     248     308 ..     666     722 ..     605     754 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.031
                    Carbam_trans_N 120 drkdvslyeHhlsHaaSaystSpFakkeklvlcldgdG 157
                                       +  + + ++Hh +H+aS+        +e   ++ldg+G
  gi|242399470|ref|YP_002994895.1| 480 EGVEFLQVQHHYAHVASVMAENKL--DEVIGIALDGVG 515
                                       334567799********9887776..666667777776 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 2.1e-05
                    Carbam_trans_N 248 hdffeasalrlkearekdedlaAsiqvflErlvvevlnivyeklkirnLclaGGvalNikl 308
                                       +++f + +    e r++  d+a s++ +l r   e      ++++i+n +l+GGva N  +
  gi|242399470|ref|YP_002994895.1| 666 EELFRQVL----ESRTNPADIAYSVHLALGRAFGEIAVEKAKEFDIKNVALSGGVAYNELI 722
                                       34444333....5555567*****************9999999**************9555 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 ?   12.8   0.0   3.2e-05     0.063     190     248 ..     678     738 ..     661     753 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.2e-05
                                       -HHHHHHHHHHHHHHHHHHHHHTT---SS...EEEESGGGG-HHHHHHH.....HHHH-S- CS
                       BcrAD_BadFG 190 kaedIlaglhraialrvialisrsggvtde..vtltGGvakneaavkelrklvkenygevk 248
                                          dI   +h a+ +   +++ + + + d   v l GGva ne +vk++rk v++n+++ +
  gi|242399470|ref|YP_002994895.1| 678 NPADIAYSVHLALGRAFGEIAVEKAKEFDIknVALSGGVAYNELIVKTIRKIVESNNLRFY 738
                                       44555555555555555555544444444444************************99864 PP

>> ROK  ROK family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.58   1.2e+03       3      49 ..     403     450 ..     401     459 .. 0.86
   2 ?    9.7   0.0   0.00027      0.53     191     261 ..     659     733 ..     640     757 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.58
                                       EEEE-SSEEEEEEEETTS-EEEEEEE.EEHCCHHCCHHHHHHHHHHCC CS
                               ROK   3 gidiGgtkialalvdeegeilarekv.etptetteetlvdaiaelvde 49 
                                       g+ +G++ +++  +++++++  ++++ +t++ ++ e ++ ai+++++ 
  gi|242399470|ref|YP_002994895.1| 403 GLTVGAELMNAFGIAKNSKVYPSQYIgNTSKVEVLEFMRGAISHFKKI 450
                                       78899999999999999999999999888999999*******999875 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00027
                                       CGTTS-HHHHHHHHCTT-HHHHHHHHHHHHHHHHHHHHH....HHHH--SEEEEEHCCCTSTTHHHHHHHHHHHC CS
                               ROK 191 kgekleakeiiklaekgdevaeevverlaeylakaiadl....inlfdpqaivlgGgvseadklleairklvkky 261
                                       +ge+l+++e+++++ ++  + +++  ++  +l++a  ++    +  fd++ + l Ggv   + ++++irk v++ 
  gi|242399470|ref|YP_002994895.1| 659 EGEELKVEELFRQVLESRTNPADIAYSVHLALGRAFGEIavekAKEFDIKNVALSGGVAYNELIVKTIRKIVESN 733
                                       7889999999999998888777777776666666655551111678************************99875 PP

>> NMD3  NMD3 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.2    0.0017       3.4      10      43 ..     106     139 ..      99     146 .. 0.82
   2 ?    1.1   4.9      0.11   2.3e+02       1      45 [.     134     191 ..     134     222 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0017
                              NMD3  10 elinglCedCllkevditegiekievevCkeCgr 43 
                                       ++  ++C+dCl++ +d  ++   + + vC +Cg 
  gi|242399470|ref|YP_002994895.1| 106 PPDVSICDDCLRELFDPRDKRYMYPFIVCTNCGP 139
                                       454559**********9998888*********95 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.11
                              NMD3   1 CcrCGkei...........eeling......lCedCllkevditegiekievevCkeCgryl 45 
                                       C +CG +            +    +      +C+ C  + +d ++   ++e  +C+ Cg  +
  gi|242399470|ref|YP_002994895.1| 134 CTNCGPRFtiiedlpydriN----TtmrefdMCDYCESEYKDPLNRRYHAEPVCCPVCGPSY 191
                                       89999998667666653331....3666788****************99*********9655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (773 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.77u 0.33s 00:00:01.10 Elapsed: 00:00:00.54
# Mc/sec: 4348.60
//
Query:       gi|242399471|ref|YP_002994896.1|  [L=156]
Description: hypothetical protein TSIB_1496 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.089   12.8   1.4       0.16   12.0   1.4    1.4  1  DUF2933   Protein of unknown function (DUF2933)


Domain annotation for each model (and alignments):
>> DUF2933  Protein of unknown function (DUF2933)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.4   9.1e-06      0.16      19      34 ..       9      24 ..       5      26 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9.1e-06
                           DUF2933 19 llgllPfllLLlCPlm 34
                                      +l+++ f+lLLlCPl+
  gi|242399471|ref|YP_002994896.1|  9 ILAFMIFILLLLCPLA 24
                                      7899**********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:                      469  (0.0261587); 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: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1112.96
//
Query:       gi|242399472|ref|YP_002994897.1|  [L=138]
Description: hypothetical protein TSIB_1497 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 1029.56
//
Query:       gi|242399473|ref|YP_002994898.1|  [L=162]
Description: Peptidase S26B, signal peptidase [Thermococcus sibiricus MM 739]
Scores for complete 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-07   29.7   0.9    7.3e-07   29.1   0.9    1.4  1  Peptidase_S24  Peptidase S24-like


Domain annotation for each model (and alignments):
>> Peptidase_S24  Peptidase S24-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.9   4.1e-11   7.3e-07       2      55 ..      33      91 ..      32     109 .. 0.78

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 4.1e-11
                                      XXSSTTCCTXXTTXEEEEECTS---TTSEEEEEETTCE..-EEEEEEE...EETTEEEE CS
                     Peptidase_S24  2 vpGdSMeptlldGdlilVdkfsepkrGdivvfrlpgee..eayiKrvi...glpgdrvl 55
                                      v  dSMep++ + +l++V+++s++k Gd++   ++  +      +rvi   +++g++v 
  gi|242399473|ref|YP_002994898.1| 33 VLTDSMEPEITPFSLVIVSPESDIKIGDVILYEVELSKkkYKVLHRVIdikERKGQIVY 91
                                      778****************************9988888889999999977644444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       787  (0.0438954); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); 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: 00:00:00.47
# Mc/sec: 1033.36
//
Query:       gi|242399474|ref|YP_002994899.1|  [L=336]
Description: HypE hydrogenase expression/formation protein [Thermococcus sibiricus MM 739]
Scores for complete 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  105.9   0.8    3.1e-30  105.4   0.8    1.2  1  AIRS_C    AIR synthase related protein, C-terminal domain
    4.9e-17   62.4   0.2    9.9e-17   61.4   0.2    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 !  105.4   0.8   3.5e-34   3.1e-30       1     149 [.     160     308 ..     160     314 .. 0.93

  Alignments for each domain:
  == domain 1  score: 105.4 bits;  conditional E-value: 3.5e-34
                                       STTEEEEEEETSSCTCCHHHHHHHCHHHCTSHTTTSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHHHHH CS
                            AIRS_C   1 kpGdvliltgslGlggagtslkrkileeeglddsavqlgdvlleptliyvkralaalkglvkaahDvTgGGLlgala 77 
                                       k Gdv++  g+ G +g++++++r+++ +e++      ++dv   + +++ +++ +   ++++a++D T+GGL++al+
  gi|242399474|ref|YP_002994899.1| 160 KIGDVVLISGTVGDHGIALMSHREGIGFETEL-----KSDVTPIWEVVKSVAKVIGW-EHIHAMKDPTRGGLSNALN 230
                                       57****************************99.....9******************9.******************* PP

                                       HHHHTTTEEEEEECGTHHHHHHHHHHHHHHHC.....STTTEEEEEEEHGGHHHHHHHHHHTTC.CCEEEEEEEEES CS
                            AIRS_C  78 emapasgvgaeidldkvpifdelesplemlls.....ensGrllvavppeeadavlaileeegl.peaavIGevtak 148
                                       e+a++s+vg+ + ++++p++ e++ +++ml +     +n+G+++++v++e a+ +l+++++  l  eaa+IGevt++
  gi|242399474|ref|YP_002994899.1| 231 EIARKSNVGILVRESDIPVRPEVRAASDMLGInpyevANEGKVVMIVEREFAEDALEAMRKTKLgREAAIIGEVTDQ 307
                                       ************************6666666666666****************************99********97 PP

                                       S CS
                            AIRS_C 149 e 149
                                        
  gi|242399474|ref|YP_002994899.1| 308 Y 308
                                       5 PP

>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.4   0.2   1.1e-20   9.9e-17       1      93 [.      40     149 ..      40     150 .. 0.86

  Alignments for each domain:
  == domain 1  score: 61.4 bits;  conditional E-value: 1.1e-20
                                       SSSE........EEEEEEEEE.EECCTCCCC....HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC......HHHHHH CS
                              AIRS   1 dDaa........vvvttdshnrpvlvepvhf....iGakavavnlsDlaamGArPlalllslalp......wleevv 59 
                                       dD a        +v+t+d       v+p  f    +G++av ++++Dla+mGA+Plal +s++++      ++e+++
  gi|242399474|ref|YP_002994899.1|  40 DDGAtipfgnkhLVFTID----GHTVKPLFFpggdVGRLAVSGTVNDLAVMGAEPLALANSMIIQegfdgeDFERIL 112
                                       677755555555699999....66777777788889***************************************** PP

                                       HHHHHHHHHTT-EEEEEEEEEESS...EEEEEEEEEE CS
                              AIRS  60 rglaeaaeelgvplvgGdtsfsne...ptisvtavGl 93 
                                       +++ e a+e+ vp+v+Gdt++ ++   +++ ++ +G+
  gi|242399474|ref|YP_002994899.1| 113 KSMDETAREVPVPIVTGDTKVVEDkigIFVITAGIGI 149
                                       ********************99777776666677776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 2045.06
//
Query:       gi|242399475|ref|YP_002994900.1|  [L=37]
Description: hypothetical protein TSIB_1500 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       171  (0.00953762); expected 358.6 (0.02)
Passed bias filter:                      155  (0.00864521); 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: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.44
# Mc/sec: 254.61
//
Query:       gi|242399476|ref|YP_002994901.1|  [L=215]
Description: hypothetical protein TSIB_1501 [Thermococcus sibiricus MM 739]
Scores for complete 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-55  186.2   4.9    7.1e-55  186.0   4.9    1.0  1  DUF257    Pyrococcus protein of unknown function, DUF257


Domain annotation for each model (and alignments):
>> DUF257  Pyrococcus protein of unknown function, DUF257
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  186.0   4.9     4e-59   7.1e-55       2     204 ..      10     212 ..       9     213 .. 0.98

  Alignments for each domain:
  == domain 1  score: 186.0 bits;  conditional E-value: 4e-59
                            DUF257   2 lletlrpGetvLiEyssssvpevllyliakyskeknvPllvdDvlDtllivlkhlkllGldvpe.esikviKigGtk 77 
                                       ll++l+ GetvL+E++s +     ly i+k s e n P++vdD lDt++++ +h+kl+G+++++ +++kviK gG+ 
  gi|242399476|ref|YP_002994901.1|  10 LLDSLKWGETVLLEHDSLTSSVQGLYYIIKWSMERNYPVVVDDFLDTFYLYATHMKLAGFNTSIlNNVKVIKLGGKL 86 
                                       799************************************************************************** PP

                            DUF257  78 evgnvvkkidfdkdpsiylskykravekvsveetvinlvlglerllllldnrrdlyklvksikkylgnknRkafyli 154
                                       +vg +v+++++++ p++y +ky   +  + ++ +vin+vlg erll++ + ++++   ++++ +y+gn++R+afy+i
  gi|242399476|ref|YP_002994901.1|  87 KVGDIVTRLPVNE-PEVYEKKYAEVTGSLFKQGKVINPVLGFERLLMFTNSNQEILMELNAVLEYIGNEKRIAFYII 162
                                       **********998.***************998999****************************************** PP

                            DUF257 155 nrnllesikPellplLEeiassvieiesekealivrilKslnldivgtti 204
                                       n +++e+++P + +lL e+a++vi+i+++++  ++ il+s+n +i g++i
  gi|242399476|ref|YP_002994901.1| 163 NEEVIEKSNPCIEFLLREMATTVIKISKKESRTVFSILRSVNNEIDGKEI 212
                                       ********************************************999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1553.68
//
Query:       gi|242399477|ref|YP_002994902.1|  [L=40]
Description: hypothetical protein TSIB_1502 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       201  (0.0112109); expected 358.6 (0.02)
Passed bias filter:                      160  (0.00892409); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 282.05
//
Query:       gi|242399478|ref|YP_002994903.1|  [L=298]
Description: Methionine aminopeptidase [Thermococcus sibiricus MM 739]
Scores for complete 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-42  145.8   0.0    1.7e-42  145.5   0.0    1.1  1  Peptidase_M24  Metallopeptidase family M24
     0.0075   16.8   0.2        2.7    8.6   0.1    2.4  2  ATP-cone       ATP cone 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 !  145.5   0.0   1.8e-46   1.7e-42       2     209 .]       9     291 ..       8     291 .. 0.84

  Alignments for each domain:
  == domain 1  score: 145.5 bits;  conditional E-value: 1.8e-46
                                       HHHHHHHHHHHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHTTTCEESSSSEEEEGGGGGSTTTBC...SSSB--TTE CS
                     Peptidase_M24   2 lirkaariasaaleavleaikpgvterelaaeieattlkrhgarglafppivasgenaavlhytp...ndrvlkegd 75 
                                       ++ ka++i++++ ++vl+ ikpg++ +e+a+++e++t++   ++++afp  + +++n+ ++hytp   ++ vlkegd
  gi|242399478|ref|YP_002994903.1|   9 KLLKAGKITKEIKKEVLHLIKPGTSLYEIAEFVEKRTVE--LGGKPAFP--CNLSINEIAAHYTPydgDKVVLKEGD 81 
                                       6789******************************88443..46789***..9999999999****8755666***** PP

                                       EEEEEEEEEETTEEEEEEEEEECSSGSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHHHHHTTBCCGBSSC CS
                     Peptidase_M24  76 lvlidagaeydgyasDitrTvlvGkftpeqrelyeavleaqeaaikavkpGvtlseidaaarevlesaglakffphg 152
                                        +++d+g+++dgy++D+++Tv vG    e+++l+ea +ea+e+ai+ +k+Gv+++ei+++++e+++ +g+  ++ ++
  gi|242399478|ref|YP_002994903.1|  82 YLKVDLGVHVDGYIADTAFTVRVG--M-EEDDLIEASKEALENAIAVIKAGVKINEIGKVIEETIRGHGF-NPIVNL 154
                                       *********************999..3.4677**********************************99**.999*** PP

                                       SEEEESS.SSSEE..EEEESSSTTCSSB--TTBEEEEEE......EEEEETTT........................ CS
                     Peptidase_M24 153 lGHgvGl.evhde..gpsvsresndgrkleeGmvftiEp......giyfapge........................ 196
                                        GH + + ++h +   p+++r ++d+ +l+eG++++iEp      g      +                        
  gi|242399478|ref|YP_002994903.1| 155 SGHVIERyKLHTGisIPNIYR-PHDNYELKEGDIVAIEPfattgaG------Qvietpptliymyirdrpvrlpqar 224
                                       ******99***9855566665.999**************6555441......2333444445555555667777777 PP

                                       .....................................................E.EEEEBEEEEEES CS
                     Peptidase_M24 197 .....................................................g.gvriedtvlvte 209
                                                                                            g + + e+tv+v e
  gi|242399478|ref|YP_002994903.1| 225 tllsyvkknfstlpfayrwvqnlmpevqlklaliqlekvgafygypilkeikgGiVSQAEHTVIVEE 291
                                       7777888888888888888999999999999999999999999999999999867889999999875 PP

>> ATP-cone  ATP cone domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.8   0.0    0.0023        21      32      64 ..      12      44 ..       2      68 .. 0.84
   2 !    8.6   0.1    0.0003       2.7      31      70 ..     109     148 ..      97     154 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0023
                                      HHHHHHHHHHHHHHHHHIIT-BHHHHHHHHHHH CS
                          ATP-cone 32 eideiaeeveaevrkrlrdgisteeIqdlvekt 64
                                      ++ +i++e+ +ev   ++ g s  eI ++vek 
  gi|242399478|ref|YP_002994903.1| 12 KAGKITKEIKKEVLHLIKPGTSLYEIAEFVEKR 44
                                      4678999***********************986 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0003
                                       HHHHHHHHHHHHHHHHHHIIT-BHHHHHHHHHHHHHHSS- CS
                          ATP-cone  31 eeideiaeeveaevrkrlrdgisteeIqdlvektliehpd 70 
                                       +++ e ++e  +++   +++g+++ eI++++e+t++ h+ 
  gi|242399478|ref|YP_002994903.1| 109 DDLIEASKEALENAIAVIKAGVKINEIGKVIEETIRGHGF 148
                                       4555556677778889999***************998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1808.51
//
Query:       gi|242399479|ref|YP_002994904.1|  [L=494]
Description: Trk-type pottasium transport system, membrane componen [Thermococcus sibiricus MM 739]
Scores for complete 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-62  209.9  26.2    4.3e-61  206.9  26.2    1.9  1  TrkH      Cation transport protein


Domain annotation for each model (and alignments):
>> TrkH  Cation transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  206.9  26.2   2.4e-65   4.3e-61      12     489 ..      59     479 ..      51     484 .. 0.90

  Alignments for each domain:
  == domain 1  score: 206.9 bits;  conditional E-value: 2.4e-65
                              TrkH  12 tialgavllfldkeskyplalkddfqivkaaeialsvdgtlklllesaslafldalfeavsgltttglsvivveesl 88 
                                       + ++g++ l++ +e+   ++l+++++ +   ++  s+ + ++ + + a + f d+ fe++s++t tgl+++ ++es+
  gi|242399479|ref|YP_002994904.1|  59 C-IIGGAWLARHSERVEDVNLRQAMISAAFVWLFASFVSVIPFM-KIAGMSFVDSYFESMSAWTGTGLTMMRNLESY 133
                                       3.44444455556666889999999999999**99*99999976.999999************************** PP

                              TrkH  89 prsgltlraqlqqiGglgvvvlaylslptlgrgsaflylseaqkeelggkelrslselikilvvyyvgleilafvll 165
                                       p  +l++ra +q++Gg+g+v +a  +l+++g   a ly++ea    + +  l++l  ++ki+  +y ++++l++ l+
  gi|242399479|ref|YP_002994904.1| 134 PHVILFWRAWMQWLGGIGIVLVALTILIRPGVAAARLYKAEA----RTERILPNLVNTSKIIFQIYTVITLLGIYLY 206
                                       ******************************************....9999*************************** PP

                              TrkH 166 vvliytakaysevvdstgvsplwwaffhsmSafnnlGfsltpnSlasfnknivillvaiifiilGnigFpillrvii 242
                                                y++++       l++a  hsm ++ ++G+s ++ S + fn+  +i++++i+++i+G+++F+++++++ 
  gi|242399479|ref|YP_002994904.1| 207 ---------YTNGM------GLFDATIHSMVGVGTGGMSSHDLSVGFFNS-LSIEAITIFLMIMGATNFTVHYKMFK 267
                                       .........*****......******************************.**********************9884 PP

                              TrkH 243 aikkkilrdlkqikeslsflldlprr.cftLllasgfvwllllelavlnvtdnilfilldegslvvksipkgsrvlk 318
                                        +    ++        +sf++d++++ +f+ l++  +++ ++l+                      + +  + ++++
  gi|242399479|ref|YP_002994904.1| 268 EK----SP--------VSFFRDIQVKyMFFFLTPAVALIGYALTT--------------------QAGLTIAHSFRE 312
                                       32....23........68*******95466777777777777762....................24455668999* PP

                              TrkH 319 alFqsvstrta.GFsvvdlsnlhpaikvllvlmmyigglpgStaggIrrtnvyeefslgkyeieqekepk.avskks 393
                                       a+F ++s+ t+ GFs+ dls+ +   k+l+ + m++gg +gStaggI+ +++   f+++k+ ieq   pk av k++
  gi|242399479|ref|YP_002994904.1| 313 AIFHAASAVTCtGFSITDLSKYPELAKLLIGFLMVVGGGAGSTAGGIKLIRITLTFQSLKWTIEQAILPKgAVIKRK 389
                                       ***************************************************************************** PP

                              TrkH 394 idgkhlerqllvdlwslflvlliilileglklsdvqepdfsffdiLfevvSaygtvGLSlGaknaslsaqlttiskl 470
                                       i+    +++ l ++ ++ + + i+l+l+g + ++v     s++d++fev+Sa+g+vGLS+G    ++s  l+   k+
  gi|242399479|ref|YP_002994904.1| 390 IGEYVFTEEDLQEVLGFTMTY-IALLLTGTVWTMVR-VGASLADAFFEVASAQGNVGLSVG----ITSTALPIDVKI 460
                                       ****************87776.56667778877777.589*********************....8888888889** PP

                              TrkH 471 vlialmirGrlrglpvlld 489
                                       +li+ m++Grl++++ l++
  gi|242399479|ref|YP_002994904.1| 461 LLILHMWIGRLEIFSTLVF 479
                                       ***************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (494 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       742  (0.0413855); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 3498.46
//
Query:       gi|242399480|ref|YP_002994905.1|  [L=279]
Description: ABC transporter ATP-binding protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      3e-27   95.8   0.0    4.7e-27   95.2   0.0    1.3  1  ABC_tran     ABC transporter
    2.9e-07   30.2   0.5    1.7e-05   24.4   0.5    2.1  1  SMC_N        RecF/RecN/SMC N terminal domain
    6.2e-05   22.5   0.3     0.0055   16.1   0.0    2.8  3  TniB         Bacterial TniB protein
    0.00034   20.5   6.2     0.0028   17.5   0.4    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    0.00092   19.5   0.5     0.0086   16.4   0.4    2.3  2  AAA_22       AAA domain
     0.0067   16.1   0.7      0.013   15.3   0.2    1.7  2  AAA_29       P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.014   15.8   0.0      0.023   15.1   0.0    1.5  1  AAA_16       AAA ATPase domain
      0.059   12.7   1.1        3.1    7.1   0.1    2.4  2  ATPase       KaiC
      0.092   11.9   0.0       0.15   11.2   0.0    1.3  1  NB-ARC       NB-ARC domain
       0.12   12.6   0.0        2.4    8.4   0.0    2.3  1  SbcCD_C      Putative exonuclease SbcCD, C subunit
       0.13   12.1   0.3        0.4   10.6   0.1    1.8  2  RsgA_GTPase  RsgA GTPase
       0.19   11.4   0.2        1.3    8.7   0.1    2.0  2  AAA_24       AAA domain
        0.2   10.2   0.4        3.1    6.3   0.1    2.0  2  AAA_13       AAA domain
       0.59   10.2   2.6        1.7    8.7   0.3    2.4  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 !   95.2   0.0   3.7e-30   4.7e-27       1     137 []      19     170 ..      19     170 .. 0.95

  Alignments for each domain:
  == domain 1  score: 95.2 bits;  conditional E-value: 3.7e-30
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--.....SEEEEEETTCEGGGB-HHHCCHCEEEE-SS..--S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp.....teGeilldgkdlkeqeleslrkeigvlpqe..pql 70 
                                       lkn++lk+k+ge ++i+G +G+GKStL+ ++ g          +G++ ++g ++ke +  +l+k +g + q+  +ql
  gi|242399480|ref|YP_002994905.1|  19 LKNINLKVKKGEFLGILGASGSGKSTLCLTFNGIIPHsikgeFNGNVFVQGYNTKEASVAELSKLVGLVLQNpdSQL 95 
                                       79*******************************99888878789999*************************97777 PP

                                       -TTSBHHHH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEES CS
                                       xxxxxxxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  71 fpeltvren.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDE 134
                                       f+ + v+e+             e +++++  l+  gl++l+++       +LSgGqkqr+++a +l+ kp++l+lDE
  gi|242399480|ref|YP_002994905.1|  96 FNMT-VEEEvafslenlgldveEIRRRVYWSLKITGLEGLENEFP----PNLSGGQKQRLVIASVLAMKPQILVLDE 167
                                       7777.99999***********999999************999998....**************************** PP

                                       TTT CS
                                       xxx RF
                          ABC_tran 135 pta 137
                                       pt+
  gi|242399480|ref|YP_002994905.1| 168 PTS 170
                                       *96 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.5   1.3e-08   1.7e-05       9     200 ..      13     203 ..       6     219 .. 0.68

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 1.3e-08
                                       SETTEECEEEEEETTS.SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEE....EE CS
                                       xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xx RF
                             SMC_N   9 nFksyagktvilpfsk.sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkae....ve 80 
                                       + k y  k++ l+++k +f  i+G+ GSGKs l+     ++     ++++ e   ++  +  + ++++ ae    v 
  gi|242399480|ref|YP_002994905.1|  13 GAKEYSLKNINLKVKKgEFLGILGASGSGKSTLCLTFNGIIP----HSIKGEFNGNVFVQGYNTKEASVAElsklVG 85 
                                       668888888888887735899999999999999877655555....3677777766666634444444444111144 PP

                                       EEEEETTEESSSSSSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  81 itfdnedkklkiekeevsisrrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvk 157
                                       ++++n+d++l   + e ++  ++++ g    +i ++   + +++ l   ++  + +LSgG+k+ + +a ++A+   k
  gi|242399480|ref|YP_002994905.1|  86 LVLQNPDSQLFNMTVEEEVAFSLENLGLDVEEIRRRVYWSLKITGLEGLENEFPPNLSGGQKQRLVIASVLAM---K 159
                                       5558888887666666677777777776666777777777777776666666677********9999988876...4 PP

                                       --SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxx RF
                             SMC_N 158 paplyllDeidaaLDeknvkkvaellkekskn..aQfivislree 200
                                       p+ + +lDe  ++LD   +++v +l+   +k+    +i + +++e
  gi|242399480|ref|YP_002994905.1| 160 PQ-ILVLDEPTSQLDPLGREQVLSLITLLNKEqsITIILVEHNTE 203
                                       55.789********************9666541134444444433 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.056        71      38      56 ..      32      50 ..      19      84 .. 0.84
   2 !   16.1   0.0   4.3e-06    0.0055      91     160 ..     131     198 ..     121     206 .. 0.93
   3 ?    0.2   0.0      0.34   4.4e+02     113     153 ..     203     243 ..     198     252 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.056
                              TniB 38 lllvGdsnnGKtmivekFa 56
                                      l ++G s  GK++++  F 
  gi|242399480|ref|YP_002994905.1| 32 LGILGASGSGKSTLCLTFN 50
                                      6799***********9997 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 4.3e-06
                              TniB  91 LealgaplkararvskleqqvlrllrelkvrvLiiDEihnllagsarkqreflnalksLgnelkipivlv 160
                                       Le l+ ++ ++ +  ++++ v++   ++k+++L++DE  + l      ++++l ++  L+ e +i+i+lv
  gi|242399480|ref|YP_002994905.1| 131 LEGLENEFPPNLSGGQKQRLVIASVLAMKPQILVLDEPTSQL--DPLGREQVLSLITLLNKEQSITIILV 198
                                       7889999999*****************************999..7888999*****************98 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.34
                              TniB 113 rllrelkvrvLiiDEihnllagsarkqreflnalksLgnel 153
                                       ++l ++  r++++D  + +++g+ r+  e   +l++Lg ++
  gi|242399480|ref|YP_002994905.1| 203 EYLFDFADRLIVLDKGELVMEGKPREVFEEAGFLRNLGIKI 243
                                       566677889******************99999999998665 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.8   1.0    0.0083        11       2      22 ..      32      52 ..      31      70 .. 0.80
   2 !   17.5   0.4   2.2e-06    0.0028     235     297 ..     140     200 ..      64     207 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0083
                            AAA_21  2 nvliGpNgsGKSnLLdaldll 22
                                       ++ G+ gsGKS+L  ++ ++
  gi|242399480|ref|YP_002994905.1| 32 LGILGASGSGKSTLCLTFNGI 52
                                      5799*********97777666 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 2.2e-06
                            AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEngLHP...kllrrllellkelsrngaQviltTH 297
                                        +lS G+k+   +++++l+  +   +l++DEp + L+P   + + +l++ll+++++  + +il+ H
  gi|242399480|ref|YP_002994905.1| 140 PNLSGGQKQR-LVIASVLAMKP--QILVLDEPTSQLDPlgrEQVLSLITLLNKEQS--ITIILVEH 200
                                       4679******.99999998777..9*************777777777788888888..88887655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.4   6.7e-06    0.0086       5     128 ..      29     198 ..      24     205 .. 0.65
   2 ?   -2.7   0.0         5   6.5e+03      93     112 ..     211     233 ..     198     248 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6.7e-06
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka........... 70 
                                         +l + G sG+GK+tl+ ++    +  +k e ++  +v  + +++ s ++l + +   l+++ +            
  gi|242399480|ref|YP_002994905.1|  29 GEFLGILGASGSGKSTLCLTFNGIIPHSIKGEFNGNVFVQGYNTKEASVAELSKLVGLVLQNPDSQlfnmtveeeva 105
                                       5678899*****************99877777766666644444444444444444444444444444488888888 PP

                            AAA_22  71 .....erlsseellealeqalrarav............................ielliiDEaqh.lr..seealee 111
                                             +l+ ee++++++  l+ ++                             +++l++DE    l+    e++  
  gi|242399480|ref|YP_002994905.1| 106 fslenLGLDVEEIRRRVYWSLKITGLeglenefppnlsggqkqrlviasvlamkPQILVLDEPTSqLDplGREQVLS 182
                                       88888555555555555555555555555555555555555555555555566679******999898665777777 PP

                            AAA_22 112 LrsllnlsrkgvqliLv 128
                                       L +lln +++++++iLv
  gi|242399480|ref|YP_002994905.1| 183 LITLLN-KEQSITIILV 198
                                       778888.8999999998 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5
                            AAA_22  93 elliiDEaqhlr...seealeeL 112
                                       +l+++D  + ++   + e++ee 
  gi|242399480|ref|YP_002994905.1| 211 RLIVLDKGELVMegkPREVFEEA 233
                                       68888888886655436666665 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 !   15.3   0.2   9.8e-06     0.013      17      38 ..      24      45 ..      15      63 .. 0.75
   2 ?   -3.6   0.0       7.6   9.7e+03      38      46 ..     269     277 ..     269     278 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 9.8e-06
                            AAA_29 17 ieidlkg.atlltGpsGsGKSTl 38
                                      ++++  g +  + G+sGsGKSTl
  gi|242399480|ref|YP_002994905.1| 24 LKVKK-GeFLGILGASGSGKSTL 45
                                      55553.34778***********9 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 7.6
                            AAA_29  38 llDAiqalL 46 
                                       l+DAi + L
  gi|242399480|ref|YP_002994905.1| 269 LVDAIRTFL 277
                                       79**99876 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   1.8e-05     0.023      22      91 ..      29      93 ..      19     200 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.8e-05
                            AAA_16 22 grpelvllsGesGvGKsslvrellralekd......ggiflrgkcdqlesaipysalaqalareellrqlldeaes 91
                                      g  e + + G+sG+GKs+l  ++   +  +      g +f++g +++          a++++ ++l+  +l++++s
  gi|242399480|ref|YP_002994905.1| 29 G--EFLGILGASGSGKSTLCLTFNGIIPHSikgefnGNVFVQGYNTKE---------ASVAELSKLVGLVLQNPDS 93
                                      4..567799***********9999877777555576667777777777.........3333333455555555333 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.1    0.0025       3.1      18      39 ..      28      49 ..      22      65 .. 0.90
   2 ?    4.3   0.1     0.017        22     136     163 ..     172     200 ..      98     211 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0025
                            ATPase 18 egrvvlitGepGtGKtifalqF 39
                                      +g+   i G +G+GK++++l+F
  gi|242399480|ref|YP_002994905.1| 28 KGEFLGILGASGSGKSTLCLTF 49
                                      6777889*************99 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.017
                            ATPase 136 keavaReilrqlvrvl.kklgvTailvse 163
                                        + + Re++  l++ l k+  +T ilv+ 
  gi|242399480|ref|YP_002994905.1| 172 LDPLGREQVLSLITLLnKEQSITIILVEH 200
                                       35578***********7778888888765 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00012      0.15      21      89 ..      30     101 ..      16     120 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00012
                                       EEEEEEESTTSSHHHHHHHHCCSH.CCCCCCBTEEEEE..EEESXXHHHHHHHXXHHHHHCCCTTSSSS-ST CS
                            NB-ARC  21 lvvalvGmgGvGKttlakqilnks.devegrFdsvawv..vvsktdkseeiletilkeLslseddleekeev 89 
                                        ++++ G  G+GK+tl    +    ++++g+F++ ++v    +k+ +  e+ + +  +L++ +++l +++ +
  gi|242399480|ref|YP_002994905.1|  30 EFLGILGASGSGKSTLCLTFNGIIpHSIKGEFNGNVFVqgYNTKEASVAELSKLVGLVLQNPDSQLFNMTVE 101
                                       489*************86655443137888999888773345677777777777777777666666666554 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0    0.0019       2.4      63      88 ..     159     184 ..     139     185 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0019
                           SbcCD_C  63 alrlvfLDEAFsklDeesiatllell 88 
                                       ++++++LDE  s+lD+  ++++l+l+
  gi|242399480|ref|YP_002994905.1| 159 KPQILVLDEPTSQLDPLGREQVLSLI 184
                                       58899**********99999999886 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00031       0.4      87     118 ..      16      48 ..       4      83 .. 0.80
   2 ?   -1.4   0.0       1.5   1.9e+03      49      78 ..     211     242 ..     182     255 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00031
                                       HTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHH CS
                       RsgA_GTPase  87 kegleelkellkd.ktsvlvGqSGvGKStLina 118
                                       + +l++++ ++k+ ++  ++G SG GKStL  +
  gi|242399480|ref|YP_002994905.1|  16 EYSLKNINLKVKKgEFLGILGASGSGKSTLCLT 48 
                                       456777777777779999************744 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.5
                                       EEEEEE-GGG--HHH..HHHHHHHHHHHTTSE CS
                       RsgA_GTPase  49 pvivlnKiDlleeee..eleelkeelealgye 78 
                                        +ivl K +l+ e +  e+ e +  l++lg++
  gi|242399480|ref|YP_002994905.1| 211 RLIVLDKGELVMEGKprEVFEEAGFLRNLGIK 242
                                       57899999999888755555555556666665 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.1     0.001       1.3       6      22 ..      33      49 ..      29      67 .. 0.87
   2 ?    0.3   0.0      0.39     5e+02     108     152 ..     177     222 ..     175     237 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.001
                            AAA_24  6 liyGpsgiGKTtlakel 22
                                       i G sg+GK+tl++++
  gi|242399480|ref|YP_002994905.1| 33 GILGASGSGKSTLCLTF 49
                                      699************99 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.39
                            AAA_24 108 aeefrrllkklqelrk.nvifiahektrkdedpegeakytrlepkl 152
                                       +e++ +l++ l++ +  ++i++ h ++  +++ ++    ++ e+ +
  gi|242399480|ref|YP_002994905.1| 177 REQVLSLITLLNKEQSiTIILVEHNTEYLFDFADRLIVLDKGELVM 222
                                       57889999999999999*******9999988887765555555555 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.1    0.0024       3.1      21      54 ..      34      71 ..      20     112 .. 0.78
   2 ?    2.2   0.0     0.044        56     526     574 ..     159     205 ..     152     219 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0024
                            AAA_13 21 iYGwNGaGKTtLSrllrslelgetepkfangsi....e 54
                                      i G+ G+GK+tL+  ++ +  ++++ +f+   +    +
  gi|242399480|ref|YP_002994905.1| 34 ILGASGSGKSTLCLTFNGIIPHSIKGEFNGNVFvqgyN 71
                                      67999**************9999999996665554441 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.044
                            AAA_13 526 kdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleff 574
                                       k +i v+D P S LD      v sli      k++   +++  Hn+e++
  gi|242399480|ref|YP_002994905.1| 159 KPQILVLDEPTSQLDPLGREQVLSLITLLN--KEQSITIILVEHNTEYL 205
                                       899**********************98774..78888899999999987 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.3    0.0013       1.7      26      39 ..      32      45 ..      18      49 .. 0.87
   2 ?   -0.3   0.1      0.76   9.7e+02     156     156 ..     144     144 ..      70     205 .. 0.51
   3 ?    0.2   0.1      0.51   6.5e+02      42      81 ..     182     217 ..     178     243 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0013
                             DUF87 26 lAilgsTGsGKSnt 39
                                      l+ilg +GsGKS++
  gi|242399480|ref|YP_002994905.1| 32 LGILGASGSGKSTL 45
                                      79**********97 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.76
                             DUF87 156 e 156
                                       +
  gi|242399480|ref|YP_002994905.1| 144 G 144
                                       2 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.51
                             DUF87  42 vLleellekkgatililDpHGEYgkalekllsekvkvitp 81 
                                       +L+  l +++++ti+++ ++ EY   +    ++++ v+++
  gi|242399480|ref|YP_002994905.1| 182 SLITLLNKEQSITIILVEHNTEYLFDF----ADRLIVLDK 217
                                       678888889999999999999999888....777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); 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: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 1857.82
//
Query:       gi|242399481|ref|YP_002994906.1|  [L=183]
Description: Adenylate cyclase 2 [Thermococcus sibiricus MM 739]
Scores for complete 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-31  107.9   4.8    6.2e-31  107.7   4.8    1.0  1  CYTH      CYTH domain
     0.0023   17.8   0.4     0.0077   16.2   0.1    2.2  2  PUB       PUB domain


Domain annotation for each model (and alignments):
>> CYTH  CYTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.7   4.8   6.9e-35   6.2e-31       1     172 [.       1     164 [.       1     169 [. 0.88

  Alignments for each domain:
  == domain 1  score: 107.7 bits;  conditional E-value: 6.9e-35
                                       EEEEEEEEEE-HHHHHHHHHHHHHCTCEEEEEEEEEEEEEE-TTTHHHHTTEEEEEE..EETTTEEE.EEEEEECSS CS
                              CYTH   1 miEvEvKflvsaaeyedlelrlaelrakeettveqrdtYydtpdrdlartdeaLRiR..raegdgee.ltlKgpgvd 74 
                                       miE+E+K   +   +++    ++e+ ++  +++  +d+Y+ +p+rd+++tdeaLRiR  r++g+ e  lt+Kgp+ d
  gi|242399481|ref|YP_002994906.1|   1 MIEIELKGYADDRVFRN----IREA-FEFMRKEIHEDMYFSHPCRDFSKTDEALRIRikRFNGHFEAlLTYKGPKID 72 
                                       89*******95444444....4555.89999999***********************9999999999********99 PP

                                       ST...EEEEEEEECCCEEECCCCHHHHHHHHHHHTT-EEEEEEEEEEEEEEE.TTEEEEEEEETTTTEEEEEEEEEE CS
                              CYTH  75 ge...reevegevsreEyeeplsdaaeaaelldglglepvasvkklRrkykl.egvevalDaveflegeevEiElev 147
                                       +    r         +E e++++++++ +ell +lg+++v +vkk R+ky + +gv+++lD+ e+l g++vEiE  +
  gi|242399481|ref|YP_002994906.1|  73 NIsktR---------KEIEVTIDNVDAYIELLHALGFREVLTVKKSREKYYVeKGVTITLDEIEGL-GKFVEIEKLE 139
                                       944444.........566666669****************************666***********.********** PP

                                       SSHHHHHHHHHHHHHHHHHTTEEGG CS
                              CYTH 148 edeeevkeaaekllallrelglssa 172
                                        de+  ++ ++ ll++l+ lg++  
  gi|242399481|ref|YP_002994906.1| 140 TDERNIENEVKRLLKILESLGVKQF 164
                                       *********************9874 PP

>> PUB  PUB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   8.5e-07    0.0077      25      68 ..      69     115 ..      12     128 .. 0.88
   2 ?   -2.4   0.0      0.54   4.8e+03      48      52 ..     153     157 ..     138     178 .. 0.62

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 8.5e-07
                               PUB  25 ekyrrIrleNkafkekvlplegavelLealGFeekne...eeeeflv 68 
                                       +k   I+++ k ++ ++++++  +elL+alGF+e      + e+++v
  gi|242399481|ref|YP_002994906.1|  69 PKIDNISKTRKEIEVTIDNVDAYIELLHALGFREVLTvkkSREKYYV 115
                                       788899**************************985446644444554 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.54
                               PUB  48 velLe 52 
                                       +++Le
  gi|242399481|ref|YP_002994906.1| 153 LKILE 157
                                       22222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       945  (0.0527079); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); 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: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1438.81
//
Query:       gi|242399482|ref|YP_002994907.1|  [L=189]
Description: Archaemetzincin [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.9e-30  104.7   0.0      1e-29  104.0   0.0    1.5  1  Peptidase_M54  Peptidase family M54
    0.00068   19.5   0.0    0.00093   19.1   0.0    1.2  1  Peptidase_M10  Matrixin
      0.004   15.8   0.1      0.005   15.5   0.1    1.1  1  Metallopep     Putative peptidase family
  ------ inclusion threshold ------
      0.013   16.0   0.0      0.014   15.9   0.0    1.3  1  Reprolysin_3   Metallo-peptidase family M12B Reprolysin-like
      0.035   13.0   0.1       0.05   12.6   0.1    1.1  1  Peptidase_M66  Peptidase M66
      0.045   13.9   0.0       0.06   13.5   0.0    1.3  1  Reprolysin_5   Metallo-peptidase family M12
       0.13   12.2   0.1       0.19   11.6   0.1    1.2  1  Peptidase_M43  Pregnancy-associated plasma protein-A


Domain annotation for each model (and alignments):
>> Peptidase_M54  Peptidase family M54
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.0   0.0   3.9e-33     1e-29      76     194 .]      66     180 ..       8     180 .. 0.84

  Alignments for each domain:
  == domain 1  score: 104.0 bits;  conditional E-value: 3.9e-33
                                       HHHT--S--..SEE.........EEEESS-EE-TT-S-BSEEE-SSSSEEEEE-T..--......SHHHHHHHHHHH CS
                     Peptidase_M54  76 kLkemkddvndDsitkifgi.ttlplgsrdqyidiykkvlGievsiGnyavlals..ikefyte.dkeLflervvke 148
                                       k+ e++          i gi  +l++++ d y +++++++G++    + a+++l+  + efy e +k L  +r +ke
  gi|242399482|ref|YP_002994907.1|  66 KIAEIR---------GIEGIsVALGITDADLYEEGMNFIFGLANPYLRSAIISLArlRPEFYGEeNKGLLKNRAIKE 133
                                       444444.........3344423799******************************98889**886999********* PP

                                       HHHHHHHHTT----S-.TSTTS--SSHHHHHHS-SS--HHHHHHHHH CS
                     Peptidase_M54 149 vlhelGhlyGLshCke.dCvmnfsndlkdvDrkapkyCksCleklkr 194
                                        +helGh++GL hC++  Cvm fsn++ d D k  +yC++Cleklkr
  gi|242399482|ref|YP_002994907.1| 134 AMHELGHVFGLEHCPNpRCVMHFSNSIIDTDYKGNTYCETCLEKLKR 180
                                       *********************************************97 PP

>> Peptidase_M10  Matrixin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   3.6e-07   0.00093     113     135 ..     134     156 ..     116     167 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 3.6e-07
                                       HHHHHHHHTTBESXSSTTSTTSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M10 113 aaHEiGHalGLeHssdkdalmyp 135
                                       a+HE+GH+ GLeH  +++ +m+ 
  gi|242399482|ref|YP_002994907.1| 134 AMHELGHVFGLEHCPNPRCVMHF 156
                                       89*******************85 PP

>> Metallopep  Putative peptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1     2e-06     0.005     318     337 ..     134     155 ..     128     178 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2e-06
                        Metallopep 318 flHEiGHllglpHqed..Gvml 337
                                       ++HE+GH++gl H+++   vm 
  gi|242399482|ref|YP_002994907.1| 134 AMHELGHVFGLEHCPNprCVMH 155
                                       6*************99777875 PP

>> Reprolysin_3  Metallo-peptidase family M12B Reprolysin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.9   0.0   5.5e-06     0.014     108     123 ..     127     146 ..      28     147 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5.5e-06
                      Reprolysin_3 108 a....dtvaHEiGHnfganH 123
                                       +    + ++HE+GH fg++H
  gi|242399482|ref|YP_002994907.1| 127 KnraiKEAMHELGHVFGLEH 146
                                       03444889************ PP

>> Peptidase_M66  Peptidase M66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   1.9e-05      0.05     184     210 ..     124     148 ..     118     162 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.9e-05
                     Peptidase_M66 184 GivtgdatltgefiHEqGHalGLpHyl 210
                                       G   + ++  +e +HE+GH +GL H +
  gi|242399482|ref|YP_002994907.1| 124 G--LLKNRAIKEAMHELGHVFGLEHCP 148
                                       5..6788899999************76 PP

>> Reprolysin_5  Metallo-peptidase family M12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.3e-05      0.06     144     164 ..     132     152 ..      84     176 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.3e-05
                      Reprolysin_5 144 qvvaHElGHnfGavHDcdsss 164
                                       +  +HElGH fG +H ++  +
  gi|242399482|ref|YP_002994907.1| 132 KEAMHELGHVFGLEHCPNPRC 152
                                       5578***********887654 PP

>> Peptidase_M43  Pregnancy-associated plasma protein-A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   7.3e-05      0.19      73     107 ..     135     169 ..     119     183 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.3e-05
                     Peptidase_M43  73 thelGhfLgLihtfeggCerGegDkvsDtpsedgk 107
                                        helGh +gL+h  +  C    ++ + Dt+ + ++
  gi|242399482|ref|YP_002994907.1| 135 MHELGHVFGLEHCPNPRCVMHFSNSIIDTDYKGNT 169
                                       6*****************99999999999987444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 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:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.51u 0.33s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1162.74
//
Query:       gi|242399483|ref|YP_002994908.1|  [L=140]
Description: hypothetical protein TSIB_1508 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-12   46.8   0.2      3e-12   46.5   0.2    1.1  1  DUF86     Protein of unknown function DUF86
     0.0025   17.9   0.5        0.6   10.3   0.0    3.2  3  UBA_2     Ubiquitin associated domain (UBA)
     0.0075   16.0   0.2      0.054   13.2   0.0    2.5  3  CUE       CUE domain


Domain annotation for each model (and alignments):
>> DUF86  Protein of unknown function DUF86
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.5   0.2     5e-16     3e-12       3     114 ..      15     127 ..      13     136 .. 0.93

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 5e-16
                                       HHHHHHCCHH...TSTSCCGSHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----SSC..HHHHHHHTTSS-HHHHH CS
                             DUF86   3 ealeklkefteeldeeeflsdeleydavernlqvigEaaidiakhlakklgikkpgdy..ifeilaekgviaeepee 77 
                                       +++e++k+ +   + +efl+  l +d +++ l+ ++++++d  ++++ +l +++   y  i+e+l+++++i++  +e
  gi|242399483|ref|YP_002994908.1|  15 DSVERIKDAF-PETPDEFLRMGLAKDGIYKRLEFAIQNILDSFNEIIVALELGPSIGYkdIVETLHKNKIIDDRLKE 90 
                                       6788999998.8999*********************************99999888888****************** PP

                                       HHHHHHCCHHHHHT-CCCTTHHHHHHHHHHTCHHHHH CS
                             DUF86  78 pwrkmiglRNrLvHgYlgidpeivwsiikenlpdlee 114
                                       ++  +++lR++L+ +Y  i++e  ++  +e+l+++e+
  gi|242399483|ref|YP_002994908.1|  91 KLEFLVQLRDVLIYDYDLISDEMAFQNMEEYLRFVED 127
                                       ******************************9988775 PP

>> UBA_2  Ubiquitin associated domain (UBA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.014        84      17      40 ..       3      24 ..       1      25 [. 0.84
   2 !   10.3   0.0    0.0001       0.6      12      39 ..      33      62 ..      32      65 .. 0.92
   3 ?    1.7   0.1     0.048   2.9e+02      12      27 ..      68      81 ..      57      92 .. 0.69

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.014
                             UBA_2 17 kdeIieaLekaekskssneIkDAY 40
                                      k eI   Le ae+s  ++ IkDA+
  gi|242399483|ref|YP_002994908.1|  3 KGEIEYKLELAEDS--VERIKDAF 24
                                      66888888999999..9******8 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0001
                             UBA_2 12 tMGYdkdeIieaLekaeks..kssneIkDA 39
                                      +MG  kd I+  Le a ++  +s neI  A
  gi|242399483|ref|YP_002994908.1| 33 RMGLAKDGIYKRLEFAIQNilDSFNEIIVA 62
                                      7******************9999***9998 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.048
                             UBA_2 12 tMGYdkdeIieaLeka 27
                                      + GY   +I+e L+k+
  gi|242399483|ref|YP_002994908.1| 68 SIGY--KDIVETLHKN 81
                                      3444..6999999987 PP

>> CUE  CUE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0     9e-06     0.054       3      23 ..      15      35 ..      13      40 .. 0.84
   2 ?   -1.5   0.0      0.36   2.2e+03      13      28 ..      67      81 ..      67      85 .. 0.75
   3 ?   -1.4   0.1      0.33     2e+03      19      30 ..      97     107 ..      95     108 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9e-06
                                      HHHHHHHHHSTTS-HHHHHHH CS
                               CUE  3 qmletLkemFPdldeevIrav 23
                                      + +e +k++FP+ ++e++r+ 
  gi|242399483|ref|YP_002994908.1| 15 DSVERIKDAFPETPDEFLRMG 35
                                      779***************975 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.36
                                      TTS-HHHHHHHHHHCT CS
                               CUE 13 PdldeevIravLrasn 28
                                      P+++  +I+  L  +n
  gi|242399483|ref|YP_002994908.1| 67 PSIGYKDIVETL-HKN 81
                                      888899999888.554 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.33
                                       HHHHHHHHCTTT CS
                               CUE  19 vIravLrasngn 30 
                                       ++r+vL  ++++
  gi|242399483|ref|YP_002994908.1|  97 QLRDVL-IYDYD 107
                                       789999.88887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 948.38
//
Query:       gi|242399484|ref|YP_002994909.1|  [L=348]
Description: Deblocking aminopeptidase [Thermococcus sibiricus MM 739]
Scores for complete 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-101  336.9   0.7   9.4e-101  336.7   0.7    1.1  1  Peptidase_M42  M42 glutamyl aminopeptidase
    3.8e-08   33.3   0.2      1e-07   31.9   0.2    1.7  1  Peptidase_M20  Peptidase family M20/M25/M40
    8.3e-06   24.8   0.1    0.00031   19.6   0.0    2.4  3  Peptidase_M18  Aminopeptidase I zinc metalloprotease (M18)
     0.0012   18.6   0.2      0.074   12.7   0.0    2.3  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 !  336.7   0.7  2.1e-104  9.4e-101       1     292 []      48     333 ..      48     333 .. 0.97

  Alignments for each domain:
  == domain 1  score: 336.7 bits;  conditional E-value: 2.1e-104
                                       S-EEEEEESSTTSSEEEEEEE--B-EEEEEEEETTSEEEEEEESS--GGGTTTEEEEEEETTEEEEEEEEE--CGGC CS
                     Peptidase_M42   1 GnliakkkgkekepkvmiaAHmDeiGfmVkeIkedGflrfekvGGvdpkvlegqrvkiltkkgkisGvigskppHll 77 
                                       Gn+ia+kkg  ++p++miaAHmD+iG+mV++I+e+G l++ +vGGvdp++l +qrv+i+++kg+++Gv+g+ ppHl+
  gi|242399484|ref|YP_002994909.1|  48 GNVIAHKKG--DGPRIMIAAHMDKIGLMVNHIDEKGYLHVVSVGGVDPRTLVAQRVRIFGEKGDVYGVVGHIPPHLT 122
                                       9********..****************************************************************** PP

                                       HHHHHHCT--GCGEEEEGSGSSHHHHHHTTS-TT-EEEES---EEETTECEEETTHHHHHHHHHHHHHHHHHCTSS- CS
                     Peptidase_M42  78 keeerkkaleikelfiDigakskeeaeelGisvGdivvfdkefvelangkivskalDdragvavllellkelkeeel 154
                                       k+eer+ka +++ ++iD+ga+skee+e++Gi++G+i+ f + f++l+++++++ +lDdr+++++++e++++l+e++ 
  gi|242399484|ref|YP_002994909.1| 123 KPEERTKAADWDTIVIDVGADSKEEVEKMGIKIGTIMEFAPAFTRLNENRFTTPYLDDRICLYAMIEVARALEEHQ- 198
                                       ************************************************************************9987. PP

                                       SSEEEEEEESTCTTTSHHHHHHHHHH--SEEEEEEEEEE-CSTTSTTTTSS.TTS-CEEEEEETTCCSHHHHHHHHH CS
                     Peptidase_M42 155 eatvylvatvqEEvGlrGaktsaekikpdiaiavDvtaagdtpgskekeak.lgkGpvirvkDasgiyhpklrkkll 230
                                        a++y+va+vqEEvGlrGa+++++ i+p+i ia+Dvt+a ++pg+k k    lgkGpv+ v    ++++pk+r + +
  gi|242399484|ref|YP_002994909.1| 199 -ADIYFVASVQEEVGLRGARVASYAIDPEIGIAMDVTFA-KQPGDKGKIVPeLGKGPVMDVG---PNINPKVRAFAE 270
                                       .*************************************9.556666666566*****99888...************ PP

                                       HHHHHTT--EEEE.EESSSSSTHHHHHTSTTTSEEEEEEEEEBSTTSTTEEEEHHHHHHHHHH CS
                     Peptidase_M42 231 elAkknnipyqle.vlsgggtDAgaihltgegvptalisiptryiHspvevahlddleatvkL 292
                                       e+Akk++ip+q+e   + +gtDA+ +++++egv ta++sip++y+Hs+ve+++ +d+++t+kL
  gi|242399484|ref|YP_002994909.1| 271 EVAKKHEIPLQIEpSPRPTGTDANIMQINREGVATAVLSIPIKYMHSQVELTDARDVDNTIKL 333
                                       *************999*********************************************98 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 !   31.9   0.2   2.3e-11     1e-07      37     206 ..     179     339 ..     177     340 .. 0.71

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 2.3e-11
                                       TTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTTTHHHHHHHHHHTTTCESEEEEEEEESSSBTCHSTETEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20  37 dmkggvlaalealralkdegikpkgtivllfqpdEEggrgGakallegleerekvdavfelhieepgileagklaig 113
                                       d+   + a++e++ral+++    + +i +++ + EE+g +Ga+     +    ++  ++++     ++ + gk+++ 
  gi|242399484|ref|YP_002994909.1| 179 DDRICLYAMIEVARALEEH----QADIYFVASVQEEVGLRGARVASYAID--PEIGIAMDVTFAKQPGDK-GKIVPE 248
                                       6666789999999999999....68***********88788844444222..333333333333333333.343333 PP

                                       EEEEEEEEEEEESHEEECCHHHHHHHHHHHHHHHTSCEEEEEES.SSBHTHHHH....TTTEEEEEEESSGGCTTST CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx....xxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20 114 vvkvevelleggapvtlndsplvkalaeaaeelfgekvelivsg.pggtdarff....agiptvmifgpgsglaHsp 185
                                       ++k  v        + + +++++++++e+a++      + ++s+ p gtda+++    +g+ t+++  p  + +Hs 
  gi|242399484|ref|YP_002994909.1| 249 LGKGPVM----DVGPNI-NPKVRAFAEEVAKKH-EIPLQIEPSPrPTGTDANIMqinrEGVATAVLSIPI-KYMHSQ 318
                                       3332222....223444.599999999999995.555677788899********8877777677666699.9***** PP

                                       TTEEEHHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20 186 nEyvdledlekgikvlarlle 206
                                        E +d +d+ + ik+ +++le
  gi|242399484|ref|YP_002994909.1| 319 VELTDARDVDNTIKLAKHFLE 339
                                       ****************99997 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 ?   -3.4   0.1       0.7   3.1e+03      64      82 ..      59      77 ..      50      87 .. 0.67
   2 !    2.8   0.0    0.0093        42     225     278 ..     169     217 ..     118     227 .. 0.72
   3 !   19.6   0.0     7e-08   0.00031     334     431 ..     246     337 ..     218     338 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 0.7
                                      --EEEEEE---SEEEEECC CS
                     Peptidase_M18 64 gfsiigaHtDsptlrvKpk 82
                                      +  +i+aH D   l v ++
  gi|242399484|ref|YP_002994909.1| 59 PRIMIAAHMDKIGLMVNHI 77
                                      4446899999999888655 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.0093
                                       TT-EEEESSHHHHHHHHHHHHHHCCCCHT-TTTS-SEEEEEEESSCCGTS-STT CS
                     Peptidase_M18 225 ekeflfaprlDnkvscfaaleallesaedsleeedkvrivalfDnEEvGStsaq 278
                                       +++  ++p lD++++ +a +e   +++e+    +  +  va++ +EEvG  +a+
  gi|242399484|ref|YP_002994909.1| 169 NENRFTTPYLDDRICLYAMIEVARALEEH----QADIYFVASV-QEEVGLRGAR 217
                                       555667899********988876666554....3345555555.7889977776 PP

  == domain 3  score: 19.6 bits;  conditional E-value: 7e-08
                                       S--TTSEEEEEEETTSSSTT-HHHHHHHHHHHHHHC-EEEEEEE-TTS----HCHHHHHHHHT-EEEEEE-EEBSTT CS
                     Peptidase_M18 334 apllnkGvvikvnanqryatnsagaallkevaqkanvklQelvvrndspcGstigpilaaktGirtiDlGaaqlsmH 410
                                        p+l+kG+v+ v +n       +  a  +eva+k +++lQ       +p+G+    +   + G+ t  l +++  mH
  gi|242399484|ref|YP_002994909.1| 246 VPELGKGPVMDVGPNIN----PKVRAFAEEVAKKHEIPLQIE--PSPRPTGTDANIMQINREGVATAVLSIPIKYMH 316
                                       689999***99999975....55567889***********64..5789*******9********************* PP

                                       SSSEEEECCHHHHHHHHHHHC CS
                     Peptidase_M18 411 SireltgskdveeavklfkaF 431
                                       S  elt++ dv +++kl k F
  gi|242399484|ref|YP_002994909.1| 317 SQVELTDARDVDNTIKLAKHF 337
                                       *****************9998 PP

>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.8   0.2    0.0091        41       1      26 [.      49      72 ..      49      92 .. 0.80
   2 !   12.7   0.0   1.6e-05     0.074      37      82 ..     179     220 ..     176     338 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.0091
                                      EEEEEESTTCESEEEEEEEE--B-TT CS
                     Peptidase_M28  1 NviatlegkatdevlllgAHyDsvgv 26
                                      Nvia  +g+    +++++AH+D +g 
  gi|242399484|ref|YP_002994909.1| 49 NVIAHKKGDG--PRIMIAAHMDKIGL 72
                                      8898888888..58********9886 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 1.6e-05
                                       TTHHHHHHHHHHHHHCHHGGCCSSEEEEEEEESSCSGSSHHHHHHH CS
                     Peptidase_M28  37 DnAsgvaalLelarvlaasgsrpkrgvrflffdaEEagllGSkafa 82 
                                       D+  +  a++e+ar+l++     + ++ f++   EE gl G++   
  gi|242399484|ref|YP_002994909.1| 179 DDRICLYAMIEVARALEE----HQADIYFVASVQEEVGLRGARVAS 220
                                       66678899*********7....589*****************8654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 2206.69
//
Query:       gi|242399485|ref|YP_002994910.1|  [L=520]
Description: hypothetical protein TSIB_1510 [Thermococcus sibiricus MM 739]
Scores for complete 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   32.9   5.6     0.0028   17.9   0.2    3.0  3  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
    6.1e-06   26.2   1.1     0.0016   18.4   0.3    3.9  5  Big_1            Bacterial Ig-like domain (group 1)
    7.3e-06   26.0   1.0      0.033   14.3   0.1    3.4  3  MG4              Macroglobulin domain MG4
    0.00012   22.3   2.7     0.0057   16.9   0.1    3.2  3  Invasin_D3       Invasin, domain 3
  ------ inclusion threshold ------
      0.017   15.4   0.0      0.076   13.3   0.0    2.2  2  CARDB            CARDB
      0.046   13.6   0.6         15    5.5   0.1    3.4  3  DUF824           Salmonella repeat of unknown function (DUF82
      0.069   13.4   1.1       0.81    9.9   0.1    2.7  2  Cohesin          Cohesin domain
      0.083   13.2   0.0        0.3   11.4   0.0    2.1  1  NPCBM_assoc      NPCBM-associated, NEW3 domain of alpha-galac
       0.12   12.2   0.2        4.6    7.1   0.0    2.6  2  fn3_3            Polysaccharide lyase family 4, domain II
       0.17   12.2   2.4         11    6.5   0.0    3.7  4  SpaA             Prealbumin-like fold 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 ?   -3.8   0.0       9.3   1.7e+04      48      56 ..     209     217 ..     206     227 .. 0.50
   2 !   16.6   0.4   3.9e-06    0.0069       2      58 ..     248     298 ..     247     308 .. 0.90
   3 !   17.9   0.2   1.6e-06    0.0028       4      71 ..     323     389 ..     320     397 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 9.3
                   CarboxypepD_reg  48 gtysvtvsa 56 
                                       g+y+v +++
  gi|242399485|ref|YP_002994910.1| 209 GNYTVIMRS 217
                                       555555443 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 3.9e-06
                   CarboxypepD_reg   2 isGrVtdasgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapG 58 
                                       is rVtd++g+++ g  V ++       ++ +t++ G+  +++ +pgty++t   +G
  gi|242399485|ref|YP_002994910.1| 248 ISVRVTDEHGNGVGGIPVNIE------GTQLQTNSYGTAFIEANKPGTYRITLNLDG 298
                                       899******************......788999*****************9988777 PP

  == domain 3  score: 17.9 bits;  conditional E-value: 1.6e-06
                   CarboxypepD_reg   4 GrVtdasgapiagatVtvtnadtgtvastttdadGafrlrglpp...gtysvtvsapGyatatreevtlta 71 
                                        +V+d+sg +++ a+V++   +   +++ ttd++G+  ++ l     g+++++++ + y  a+   v++++
  gi|242399485|ref|YP_002994910.1| 323 IYVRDSSGVGVPKASVEAI--GPLGKSYGTTDENGTALIN-LNEtgfGSIRIKAENDAYIGAEA-VVEVEK 389
                                       68*****************..56679999**********7.65559999999999999988885.577765 PP

>> Big_1  Bacterial Ig-like domain (group 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1       1.2   2.1e+03       6      29 ..      44      67 ..      42      70 .. 0.86
   2 !   18.4   0.3   8.9e-07    0.0016       9      52 ..     248     294 ..     245     296 .. 0.89
   3 !   14.6   0.0   1.3e-05     0.024       8      64 .]     320     373 ..     316     373 .. 0.87
   4 ?   -6.0   2.9        10   1.8e+04      50      59 ..     403     412 ..     401     415 .. 0.44
   5 ?   -2.7   0.0       3.4   6.1e+03      39      52 ..     492     505 ..     483     512 .. 0.66

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.2
                             Big_1  6 tntltatvkDangnpvagatVtfs 29
                                      t+ + +t+++  +  ++++t+++s
  gi|242399485|ref|YP_002994910.1| 44 TVSVPVTLVNIGNESIENITIHVS 67
                                      778889999999999***999887 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 8.9e-07
                             Big_1   9 ltatvkDangnpvagatVtfsvsg.gals..assgtTdanGkatvtl 52 
                                       ++++v+D++gn v g++V+++ ++ +++s  ++    ++ G++++tl
  gi|242399485|ref|YP_002994910.1| 248 ISVRVTDEHGNGVGGIPVNIEGTQlQTNSygTAFIEANKPGTYRITL 294
                                       89**********************87777888888899999998887 PP

  == domain 3  score: 14.6 bits;  conditional E-value: 1.3e-05
                             Big_1   8 tltatvkDangnpvagatVtfsvsggalsassgtTdanGkatvtltstkagtvtvtA 64 
                                       tl + v+D++g  v+ a+V    +      s gtTd+nG+a ++l  t  g+  ++A
  gi|242399485|ref|YP_002994910.1| 320 TLLIYVRDSSGVGVPKASVEAIGPL---GKSYGTTDENGTALINLNETGFGSIRIKA 373
                                       78899************99988555...55689*************99999998876 PP

  == domain 4  score: -6.0 bits;  conditional E-value: 10
                             Big_1  50 vtltstkagt 59 
                                       ++ tst a +
  gi|242399485|ref|YP_002994910.1| 403 TSSTSTSANQ 412
                                       3444444443 PP

  == domain 5  score: -2.7 bits;  conditional E-value: 3.4
                             Big_1  39 sgtTdanGkatvtl 52 
                                         +T +nGk+  ++
  gi|242399485|ref|YP_002994910.1| 492 GEVTIENGKVIWKI 505
                                       45777888876665 PP

>> MG4  Macroglobulin domain MG4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0       0.2   3.6e+02      11      39 ..      40      68 ..      29     111 .. 0.83
   2 !   14.3   0.1   1.9e-05     0.033      18      74 ..     248     306 ..     247     321 .. 0.70
   3 !    7.0   0.0    0.0037       6.6      20      66 ..     323     365 ..     320     389 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.2
                               MG4 11 KpGlPfsikVlvkdpdgspaknvpVkiea 39
                                      KpG   s+ V +++  ++ ++n+++ ++ 
  gi|242399485|ref|YP_002994910.1| 40 KPGETVSVPVTLVNIGNESIENITIHVSG 68
                                      999999*******************9987 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 1.9e-05
                               MG4  18 ikVlvkdpdgspaknvpVkiealk..seteekeslttdedGtakfsintpedaksltit 74 
                                       i V+v+d+ g+ ++++pV ie ++  +++     ++ ++ Gt ++++n+ ++  +  ++
  gi|242399485|ref|YP_002994910.1| 248 ISVRVTDEHGNGVGGIPVNIEGTQlqTNSYGTAFIEANKPGTYRITLNLDGKIVETFVE 306
                                       78********************4422333333334466777777777776665555555 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0037
                               MG4  20 VlvkdpdgspaknvpVkiea.lkseteekeslttdedGtakfsintpe 66 
                                       ++v d+ g  +++  V     l+     k+  ttde+Gta +++n ++
  gi|242399485|ref|YP_002994910.1| 323 IYVRDSSGVGVPKASVEAIGpLG-----KSYGTTDENGTALINLNETG 365
                                       67888888888888888776454.....6889***********99665 PP

>> Invasin_D3  Invasin, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       1.6   2.8e+03      23      46 ..      46      69 ..      39     119 .. 0.62
   2 !   16.9   0.1   3.2e-06    0.0057      23      87 ..     247     303 ..     243     310 .. 0.82
   3 ?    3.7   0.1     0.042        75      21      91 ..     318     385 ..     314     389 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.6
                        Invasin_D3 23 tltvtlkDangnpvsgltvtfstt 46
                                       + vtl +  ++ + + t+++s  
  gi|242399485|ref|YP_002994910.1| 46 SVPVTLVNIGNESIENITIHVSGP 69
                                      566777777777777777666643 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 3.2e-06
                        Invasin_D3  23 tltvtlkDangnpvsgltvtfsttsagtlsavtdngdGtytatLtattagtatitptvnGvaiaa 87 
                                       +++v ++D++gn v+g  v++  t      ++++n++Gt  a + a++ gt+ it  ++G++ ++
  gi|242399485|ref|YP_002994910.1| 247 VISVRVTDEHGNGVGGIPVNIEGT------QLQTNSYGT--AFIEANKPGTYRITLNLDGKIVET 303
                                       799*******************77......677888885..778889999999999999966554 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.042
                        Invasin_D3  21 tstltvtlkDangnpvsgltvtfsttsagtlsavtdngdGtytatLtattagtatitptvnGvaiaatatv 91 
                                       + tl + ++D +g  v  ++v+      g+ s  t++++Gt    L  t  g++ i+++ +   i+a+a v
  gi|242399485|ref|YP_002994910.1| 318 NETLLIYVRDSSGVGVPKASVEAIGP-LGK-SYGTTDENGTALINLNETGFGSIRIKAENDA-YIGAEAVV 385
                                       66788899999999999999999988.885.44478889*******9999999999998774.55666555 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   4.3e-05     0.076      13      84 ..      37     112 ..      27     121 .. 0.85
   2 ?   -3.9   0.0       9.2   1.6e+04      72      86 ..     283     298 ..     270     302 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.3e-05
                                       SEEETTSEEEEEEEEEE-SSS-EEEEEEEE...EETTEEEEEEEESEE-CTEEEEEEEEEE-S.-S-CEEEEEEEE CS
                             CARDB  13 seafvgeentitvtvkNqGtaasgatkval...yldgelvgtvtvpsLaagesttvsftwtte.ategevtltvvv 84 
                                        ea +ge++++ vt+ N G+++ +++++ +   ++ g l g+ ++++L++ e+ + ++++ ++   +g ++l++ +
  gi|242399485|ref|YP_002994910.1|  37 FEAKPGETVSVPVTLVNIGNESIENITIHVsgpIVKGLLYGQEYIKKLEPAETMDKTLSIYVQdVRAGVYDLKIIA 112
                                       57899********************999984445777777*******************99998999999988766 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 9.2
                                       S.-S-CEEEEEEEEST CS
                             CARDB  72 e.ategevtltvvvDp 86 
                                       e  ++g++ +t++ D 
  gi|242399485|ref|YP_002994910.1| 283 EaNKPGTYRITLNLDG 298
                                       3347788888888775 PP

>> DUF824  Salmonella repeat of unknown function (DUF824)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1    0.0085        15       9      36 ..      39      66 ..      37      67 .. 0.91
   2 ?    1.7   0.0      0.13   2.3e+02      19      36 ..     250     267 ..     248     271 .. 0.90
   3 ?    2.1   0.0     0.097   1.7e+02      16      34 ..     320     338 ..     320     339 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0085
                            DUF824  9 aKkGEsipltitvkDasGnPvpnapftl 36
                                      aK GE++ + +t ++  ++++ n ++ +
  gi|242399485|ref|YP_002994910.1| 39 AKPGETVSVPVTLVNIGNESIENITIHV 66
                                      9*******************99988766 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.13
                            DUF824  19 itvkDasGnPvpnapftl 36 
                                       + v+D  Gn v+  p+++
  gi|242399485|ref|YP_002994910.1| 250 VRVTDEHGNGVGGIPVNI 267
                                       88*************998 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.097
                            DUF824  16 pltitvkDasGnPvpnapf 34 
                                       +l i v+D+sG  vp a++
  gi|242399485|ref|YP_002994910.1| 320 TLLIYVRDSSGVGVPKASV 338
                                       58999******99999886 PP

>> Cohesin  Cohesin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   0.00045      0.81       9      34 ..      38      64 ..      32      68 .. 0.85
   2 ?    0.8   0.1      0.29   5.2e+02      19      75 ..     249     293 ..     245     310 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00045
                                      EE-TTSEEEEEEEEESECTT.EEEEEE CS
                           Cohesin  9 sakvGdtvtvpvtvsnvskk.vaaaqf 34
                                      +ak+G+tv+vpvt+ n+ +  +  + +
  gi|242399485|ref|YP_002994910.1| 38 EAKPGETVSVPVTLVNIGNEsIENITI 64
                                      689**************9987776665 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.29
                                       EEEEESECTT.EEEEEEEEEE.TTTEEEEEEEE-TTSSSGGHCEEEEEECGTTEEEEE CS
                           Cohesin  19 pvtvsnvskk.vaaaqftikYDpavlevvsvkaGsivknssvnfgsnlleepgkikfl 75 
                                        v+v++  ++ v+++ ++i+   ++l+ +s+  G+++ +++         +pg+++++
  gi|242399485|ref|YP_002994910.1| 249 SVRVTDEHGNgVGGIPVNIEG--TQLQTNSY--GTAFIEAN---------KPGTYRIT 293
                                       578888888889999999987..89999955..55554444.........44444444 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 ?   11.4   0.0   0.00017       0.3       2      31 ..      40      69 ..      39     114 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00017
                       NPCBM_assoc  2 epGetvtltltvtndgtaaatnvslslslP 31
                                      +pGetv++ +t++n g+++++n+ + +s+P
  gi|242399485|ref|YP_002994910.1| 40 KPGETVSVPVTLVNIGNESIENITIHVSGP 69
                                      89**************************99 PP

>> fn3_3  Polysaccharide lyase family 4, domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.099   1.8e+02      32      51 ..      91     110 ..      87     117 .. 0.80
   2 ?    7.1   0.0    0.0026       4.6      31      60 ..     274     303 ..     269     309 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.099
                             fn3_3  32 dssgsftipnVkpGtYrltv 51 
                                       d++ s+ +++V++G Y l +
  gi|242399485|ref|YP_002994910.1|  91 DKTLSIYVQDVRAGVYDLKI 110
                                       566788899********987 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0026
                             fn3_3  31 adssgsftipnVkpGtYrltvYadglfgdy 60 
                                       ++s g+  i++ kpGtYr t+  dg ++++
  gi|242399485|ref|YP_002994910.1| 274 TNSYGTAFIEANKPGTYRITLNLDGKIVET 303
                                       55669999************9999888776 PP

>> SpaA  Prealbumin-like fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0     0.006        11      32      58 ..     266     292 ..     164     293 .. 0.73
   2 ?    2.8   0.1     0.082   1.5e+02      36      49 ..     347     360 ..     316     415 .. 0.81
   3 ?   -1.0   0.0       1.3   2.3e+03      54      64 ..     458     468 ..     426     486 .. 0.86
   4 ?   -1.0   0.0       1.2   2.2e+03      37      54 ..     492     511 ..     472     512 .. 0.64

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.006
                                       CCEESEEE-BTTSEEEEEEEESEEEEE CS
                              SpaA  32 gtevttlttdenGkatfegLplGtYll 58 
                                       + e t+l t++ G+a +e+ ++GtY +
  gi|242399485|ref|YP_002994910.1| 266 NIEGTQLQTNSYGTAFIEANKPGTYRI 292
                                       33458999*****************87 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.082
                                       SEEE-BTTSEEEEE CS
                              SpaA  36 ttlttdenGkatfe 49 
                                        + ttdenG+a ++
  gi|242399485|ref|YP_002994910.1| 347 SYGTTDENGTALIN 360
                                       5689******9876 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 1.3
                                       EEEEEEEEE-S CS
                              SpaA  54 GtYllvEtkaP 64 
                                        +Y++v +kaP
  gi|242399485|ref|YP_002994910.1| 458 DKYYFVKIKAP 468
                                       58999999999 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 1.2
                                       EEE-BTTSEEEEE..EEESE CS
                              SpaA  37 tlttdenGkatfe..gLplG 54 
                                         +t enGk+ ++  +L++G
  gi|242399485|ref|YP_002994910.1| 492 GEVTIENGKVIWKieKLEPG 511
                                       34567799875543388877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (520 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       652  (0.0363657); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.48
# Mc/sec: 3239.88
//
Query:       gi|242399486|ref|YP_002994911.1|  [L=136]
Description: Archaeal type Holliday junction resolvase [Thermococcus sibiricus MM 739]
Scores for 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  101.4   0.1    3.4e-29  100.7   0.1    1.4  1  Hjc         Archaeal holliday junction resolvase (hjc)
    0.00027   21.1   0.0    0.00052   20.2   0.0    1.5  1  UPF0102     Uncharacterised protein family UPF0102
     0.0029   17.6   0.0     0.0068   16.4   0.0    1.6  1  HicA_toxin  HicA toxin of bacterial toxin-antitoxin,
  ------ inclusion threshold ------
       0.06   12.9   0.0       0.16   11.5   0.0    1.8  1  AHJR-like   REase_AHJR-like


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 !  100.7   0.1   7.5e-33   3.4e-29       1      91 [.      10      95 ..      10      97 .. 0.98

  Alignments for each domain:
  == domain 1  score: 100.7 bits;  conditional E-value: 7.5e-33
                                      HHHHHHHHHHHHTT-EEEEBSCSSSSSSSS-SEEEEETTEEEEEEEEEESSSEEEEEHHHHHHHHHHHHHHTCEEEEEE CS
                               Hjc  1 tyERelvkiLrergfavvRsagSggatkplpDviAirgdvvlviEvKsskkeriylkkeqvekllefarkaggelllav 79
                                      t+ERel+k+L+++gfavvRsagS+++     D+iA++g+++l+iEvK+++ +++yl++e++ k+ +f++ +gg+ ++av
  gi|242399486|ref|YP_002994911.1| 10 TAERELIKMLEKEGFAVVRSAGSKKV-----DIIAGNGKTYLCIEVKTTRSDKLYLSEEDMLKIKSFSKAFGGKGVIAV 83
                                      58************************.....************************************************ PP

                                      EETTTEEEEEEG CS
                               Hjc 80 klqgkewkllvv 91
                                      k+ ++ w+++ v
  gi|242399486|ref|YP_002994911.1| 84 KFINNGWYFFDV 95
                                      **********88 PP

>> UPF0102  Uncharacterised protein family UPF0102
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   1.1e-07   0.00052       2      49 ..      12      59 ..      11      76 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.1e-07
                                      HHHHHHHHHHTT-EEEEEEEEETTEEEEEEE..TTEEEEEEEEE.-..... CS
                           UPF0102  2 EelaaeyLekkgyeilernwrcragEiDiia..tevlvfvEVKt.Rssekf 49
                                      E+   ++Lek+g+ ++    +     +Diia  +++++ +EVKt Rs++ +
  gi|242399486|ref|YP_002994911.1| 12 ERELIKMLEKEGFAVVRSAGS---KKVDIIAgnGKTYLCIEVKTtRSDKLY 59
                                      7888899********999885...68*******889********5544433 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 !   16.4   0.0   1.5e-06    0.0068       2      21 ..      13      32 ..      13      48 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.5e-06
                                      HCHHHHHHHTT-EEEEEETT CS
                        HicA_toxin  2 reviklLeklGfevvrqkGS 21
                                      re+ik Lek Gf vvr+ GS
  gi|242399486|ref|YP_002994911.1| 13 RELIKMLEKEGFAVVRSAGS 32
                                      8******************9 PP

>> AHJR-like  REase_AHJR-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   3.5e-05      0.16      44      69 ..      34      62 ..       9      74 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.5e-05
                         AHJR-like 44 rpDliarkdeeaviiEvksrrs...sase 69
                                      + D+ia +++ ++ iEvk+ rs     se
  gi|242399486|ref|YP_002994911.1| 34 KVDIIAGNGKTYLCIEVKTTRSdklYLSE 62
                                      67*****************9996554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 976.67
//
Query:       gi|242399487|ref|YP_002994912.1|  [L=174]
Description: Ferripyochelin binding protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.4e-18   64.6  14.5    2.1e-08   33.6   7.0    4.2  4  Hexapep    Bacterial transferase hexapeptide (six repeats)
    0.00096   18.9  18.7     0.0048   16.6   3.5    3.7  4  Hexapep_2  Hexapeptide repeat of succinyl-transferase


Domain annotation for each model (and alignments):
>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.4e-07    0.0012       2      36 .]      11      45 ..      10      45 .. 0.95
   2 !    4.4   0.1    0.0038        34      21      34 ..      51      64 ..      47      66 .. 0.55
   3 !   10.4   0.3   4.8e-05      0.43      20      36 .]      72      88 ..      71      88 .. 0.76
   4 !   33.6   7.0   2.3e-12   2.1e-08       1      34 [.      88     121 ..      88     123 .. 0.95

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.4e-07
                                      EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEES CS
                           Hexapep  2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvigg 36
                                      ++I++ ++++ +a+i g+V++ + + I++ +v++g
  gi|242399487|ref|YP_002994912.1| 11 PKIHETAFVDENAYIIGDVVLEEKSSIWPSAVLRG 45
                                      68******************************986 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0038
                                      EE-TTEEEETTEEE CS
                           Hexapep 21 kIGdnvkIgagvvi 34
                                       IG+++ I  +v +
  gi|242399487|ref|YP_002994912.1| 51 YIGKGSNIQDNVSV 64
                                      45555555555544 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 4.8e-05
                                      EEE-TTEEEETTEEEES CS
                           Hexapep 20 VkIGdnvkIgagvvigg 36
                                      +++G++v++g+++vi+g
  gi|242399487|ref|YP_002994912.1| 72 TILGEYVTVGHNAVIHG 88
                                      57888888888888875 PP

  == domain 4  score: 33.6 bits;  conditional E-value: 2.3e-12
                                       TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEE CS
                           Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvi 34 
                                       +++IG++v+Ig++a++++++kIG++v++gag+ i
  gi|242399487|ref|YP_002994912.1|  88 GAKIGNHVIIGMGAIVLDGAKIGNHVIVGAGALI 121
                                       589*****************************98 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       0.1     9e+02      13      24 ..      22      35 ..      18      37 .. 0.73
   2 !    5.4   0.5    0.0017        16       6      32 ..      60      86 ..      49      87 .. 0.62
   3 !   16.6   3.5   5.3e-07    0.0048       1      32 [.      71     103 ..      71     105 .. 0.94
   4 !   14.7   7.4   2.2e-06     0.019       3      31 ..      90     120 ..      88     123 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.1
                                      T-EE.S.EEE-TT- CS
                         Hexapep_2 13 nagi.G.vslGdnc 24
                                      na+i G v l++++
  gi|242399487|ref|YP_002994912.1| 22 NAYIiGdVVLEEKS 35
                                      88955558888775 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0017
                                      TT-EE-TT-EESEEE-TT-EE-TT-EE CS
                         Hexapep_2  6 dnCliGanagiGvslGdncvvgaGvvi 32
                                      dn+ ++ + g++++lG+ ++vg + vi
  gi|242399487|ref|YP_002994912.1| 60 DNVSVHTSHGMPTILGEYVTVGHNAVI 86
                                      333344444457999999999888887 PP

  == domain 3  score: 16.6 bits;  conditional E-value: 5.3e-07
                                       .EEE-TT-EE-TT-EE.SEEE-TT-EE-TT-EE CS
                         Hexapep_2   1 pviIGdnCliGanagi.GvslGdncvvgaGvvi 32 
                                       p+i G+ + +G na+i G ++G+ +++g+G ++
  gi|242399487|ref|YP_002994912.1|  71 PTILGEYVTVGHNAVIhGAKIGNHVIIGMGAIV 103
                                       8999**************************887 PP

  == domain 4  score: 14.7 bits;  conditional E-value: 2.2e-06
                                       EE-TT-EE-TT-EE..SEEE-TT-EE-TT-E CS
                         Hexapep_2   3 iIGdnCliGanagi..GvslGdncvvgaGvv 31 
                                       +IG+ ++iG  a++  G ++G+ ++vgaG  
  gi|242399487|ref|YP_002994912.1|  90 KIGNHVIIGMGAIVldGAKIGNHVIVGAGAL 120
                                       8************99**************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1158.91
//
Query:       gi|242399488|ref|YP_002994913.1|  [L=268]
Description: Undecaprenyl pyrophosphate synthetase [Thermococcus sibiricus MM 739]
Scores for complete 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-80  270.1   0.1    1.6e-80  269.9   0.1    1.0  1  Prenyltransf   Putative undecaprenyl diphosphate synthase
     0.0031   17.7   0.8     0.0053   17.0   0.4    1.6  1  Seryl_tRNA_N   Seryl-tRNA synthetase N-terminal domain
  ------ inclusion threshold ------
       0.15   11.6   0.2       0.49    9.9   0.1    1.8  2  Glyco_hydro_4  Family 4 glycosyl hydrolase


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 !  269.9   0.1   2.6e-84   1.6e-80       1     224 []      45     267 ..      45     267 .. 0.93

  Alignments for each domain:
  == domain 1  score: 269.9 bits;  conditional E-value: 2.6e-84
                                       EE--HHHHHHHTT.S-HHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEEGGGGGS-HHHHHHHHHHHH...HHHHHH CS
                      Prenyltransf   1 imDGNrRwAkkrgleereeGhkaGaealkeilelclelgvkvvtvYafSteNfkRskeevdalmellk...eellke 74 
                                       imDGNrRwA+  + ++  +Gh  G ++l+eile+c +lg++++tvYafSteNf+Rskeev++lm+l++   +el+++
  gi|242399488|ref|YP_002994913.1|  45 IMDGNRRWARILN-KPPWYGHLFGSKKLEEILEWCRDLGIRTLTVYAFSTENFNRSKEEVKMLMDLFEkkfKELIHD 120
                                       9************.88888************************************************8666666665 PP

                                       HHHHHHHTTEEEEEESSGGGS-HHHHHHHHHHHHHHT.TTTSEEEEEEEEE-HHHHHHHHHHHHHHTT..SSSG.GG CS
                      Prenyltransf  75 elkellkegvrvrviGdlellpedvlealekaeeatkknnkklvlniavnYgsrdeiveavrelvkekseekkk.ee 150
                                       +  +++k g+rv+v+G++ellpe+v++a+e+ae+atkk n+ ++lnia++Yg+r+eiv+av+++v++ +  k + +e
  gi|242399488|ref|YP_002994913.1| 121 R--RVHKYGIRVNVLGRKELLPENVRKAAEEAEQATKKYNN-YNLNIAIAYGGRSEIVDAVKRIVDDIQVGKLNkNE 194
                                       5..89999*****************************8887.**********************9998755554367 PP

                                       HSHHHHHCTSTT..TSSS-SEEEEESS--S-TTSSTTTTTT-EEEEESSSGGG--HHHHHHHHHHHHHCHHHTT CS
                      Prenyltransf 151 ideetlekhlytakalpdpDlliRtsGeeRlSnFllwqlayselyfldvlWPdfskedllealleyqkrerrfg 224
                                       ide+ l+++ly+  ++ dpD++iRt+Ge R+SnFl++q+aysel+f+dv++P+f+k d+l++++eyqkr+rrfg
  gi|242399488|ref|YP_002994913.1| 195 IDEKLLKRYLYV-PNMTDPDIVIRTGGEVRISNFLIYQIAYSELFFVDVYFPEFRKIDFLRIIREYQKRDRRFG 267
                                       89*********8.557********************************************************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 !   17.0   0.4   8.9e-07    0.0053      35     107 ..     140     209 ..     120     210 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 8.9e-07
                                       HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCTS--- CS
                      Seryl_tRNA_N  35 dekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaeleklllaiPNi 107
                                        e+ r++  e+e++ ++ N+ + +I+ a      ++e+++ vk + ++++  + + +e++++l k  l +PN+
  gi|242399488|ref|YP_002994913.1| 140 PENVRKAAEEAEQATKKYNNYNLNIAIAYG---GRSEIVDAVKRIVDDIQVGKLNKNEIDEKLLKRYLYVPNM 209
                                       57899************************6...58*************************************8 PP

>> Glyco_hydro_4  Family 4 glycosyl hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       0.2   1.2e+03      13      54 ..      68     109 ..      63     123 .. 0.76
   2 ?    9.9   0.1   8.1e-05      0.49      50     102 ..     155     206 ..     136     221 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.2
                                       HHHHHHHHHTTTTCTEEEEEEE-SSHHHHHHHHHHHHHHHHH CS
                     Glyco_hydro_4  13 aklllgdlkkteelsvselaLvDideerldaiqtlakklvee 54 
                                       +k+l+  l+   +l +++l+ +    e  +++++ +k l++ 
  gi|242399488|ref|YP_002994913.1|  68 SKKLEEILEWCRDLGIRTLTVYAFSTENFNRSKEEVKMLMDL 109
                                       567777777788888899999998888888888888887765 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 8.1e-05
                                       HHHHHCTTTCEEEEESSHHHHHTT-SEEEE---TTHHHHHHHHHHCCHTTTTT CS
                     Glyco_hydro_4  50 klveeagadlkieattdrkealkdadfVitairvGlekareidekiplryGie 102
                                       k  ++++ +++i a+  r e + ++  ++  i+vG+++  eidek+ +ry ++
  gi|242399488|ref|YP_002994913.1| 155 KKYNNYNLNIAI-AYGGRSEIVDAVKRIVDDIQVGKLNKNEIDEKLLKRYLYV 206
                                       333445555555.45678899999999*******************9998655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1121  (0.0625244); expected 358.6 (0.02)
Passed bias filter:                      760  (0.0423894); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 1651.23
//
Query:       gi|242399489|ref|YP_002994914.1|  [L=732]
Description: Elongation factor 2 [Thermococcus sibiricus MM 739]
Scores for complete 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-64  215.3   0.1    8.3e-64  214.7   0.1    1.3  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    2.3e-26   91.9   0.1    1.8e-25   89.0   0.0    2.5  3  EFG_IV       Elongation factor G, domain IV
    1.4e-25   89.1   0.3      3e-25   88.1   0.3    1.6  1  EFG_II       Elongation Factor G, domain II
    2.7e-23   81.8   0.1      1e-22   79.9   0.1    2.1  1  EFG_C        Elongation factor G C-terminus
    3.1e-15   56.3   1.2      7e-15   55.2   1.2    1.7  1  GTP_EFTU_D2  Elongation factor Tu domain 2
     0.0026   17.8   0.0     0.0072   16.4   0.0    1.8  1  MMR_HSR1     50S ribosome-binding GTPase
     0.0067   16.3   0.0      0.016   15.0   0.0    1.6  1  RF3_C        Class II release factor RF3, C-terminal domain
  ------ inclusion threshold ------
       0.12   12.7   0.0       0.41   10.9   0.0    2.0  1  DUF2283      Protein of unknown function (DUF2283)


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 !  214.7   0.1   3.7e-67   8.3e-64       2     193 ..      20     257 ..      19     258 .. 0.90

  Alignments for each domain:
  == domain 1  score: 214.7 bits;  conditional E-value: 3.7e-67
                                       CEEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEET..TCSSEEEEEEE CS
                          GTP_EFTU   2 rirnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaislek..etkkylinliD 76 
                                       rirn+gi++h+DhGKtTL+d+Ll+ +g+is+  e a+++ vlD+ ++E++rgiTi++a++s+ +    +kyl+nliD
  gi|242399489|ref|YP_002994914.1|  20 RIRNMGIAAHIDHGKTTLSDNLLAGAGMISE--ELAGKQLVLDFDEQEQARGITINAANVSMIHeyGDQKYLVNLID 94 
                                       89*****************************..889999***********************9435899******** PP

                                       ESSSGGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGSTHHHHHHHHHHHHHHHHHH CS
                          GTP_EFTU  77 tPGHvdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrlkaelkeiveevkqklsrk 153
                                       tPGHvdF  +v+r++r++Dga++vvdaveGv+pqte+vlr+al+e v++++fiNK+Drl++elk  ++++++++ r+
  gi|242399489|ref|YP_002994914.1|  95 TPGHVDFGGDVTRAMRAIDGAIIVVDAVEGVMPQTETVLRQALREYVKPVLFINKVDRLIKELKLNPQQMQERFVRV 171
                                       **************************************************************************888 PP

                                       .............HHHHHHHHHTTT.........TTEEEEEEBTTTTBTHH.......................... CS
                          GTP_EFTU 154 .............eeklekygekge.........kevpvvfgSalkgegvk.......................... 182
                                                               e         ++ +v+fgSa+ +++++                          
  gi|242399489|ref|YP_002994914.1| 172 itdvnrlirkyapA----------EfknkwlvnvNDGSVAFGSAYYNWALSvpymkktgvsfkdiidltnagdlktl 238
                                       77776666555531..........03334455557889**********88888888888889999999999999999 PP

                                       ........HHHHHHHHHSH CS
                          GTP_EFTU 183 ........tllealvellp 193
                                                +l+++v++lp
  gi|242399489|ref|YP_002994914.1| 239 rkkaplhvVVLDMVVRHLP 257
                                       9999999899******998 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 ?   -2.4   0.0       1.7   3.8e+03       3      14 ..     463     474 ..     461     502 .. 0.77
   2 !   89.0   0.0   8.2e-29   1.8e-25      11     120 ..     513     618 ..     506     619 .. 0.95
   3 ?   -1.3   0.0      0.81   1.8e+03      27      61 ..     655     689 ..     636     700 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.7
                                       CESCEE.SS-CC CS
                            EFG_IV   3 VayrEtirkpvk 14 
                                       V yrE+i+k++ 
  gi|242399489|ref|YP_002994914.1| 463 VVYRESITKQSP 474
                                       889999999876 PP

  == domain 2  score: 89.0 bits;  conditional E-value: 8.2e-29
                                       S-CCHCCCCCCCHTSSSHCCCCCEEEECCTTTTSSEEEEE--STCCCHCCCCHHHHCCCCCCTTS-TTTS--EESEE CS
                            EFG_IV  11 kpvkereeklkkqsggdgqyakvileiePleegsgnefvdetkggqvpkeyieavekGfqealkeGplagepvtdvk 87 
                                       k++k +++kl++  g+d + a+ i++i+      gn+f d+tkg q+++e++++ ++Gf++a++eGpla+epv+ v 
  gi|242399489|ref|YP_002994914.1| 513 KDTKVVAKKLAE-LGMDYEIARGIVDIYN-----GNMFLDNTKGLQYLNEVMDLLVDGFHQAMDEGPLAREPVMKVI 583
                                       788888899999.9***************.....9****************************************** PP

                                       EEEEEEE--T..TTC-HHHHHHHHCHHHHHHHHCC CS
                            EFG_IV  88 vtLldgslhe..vdsseaafkpaarralkeallkA 120
                                       v+L+d+++he  v++++a++ pa r a++ a++k+
  gi|242399489|ref|YP_002994914.1| 584 VRLVDAKIHEdnVHRGPAQIYPAIRTAIHCAMMKS 618
                                       ********************************998 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.81
                                       SHCCCCCEEEECCTTTTSSEEEEE--STCCCHCCC CS
                            EFG_IV  27 dgqyakvileiePleegsgnefvdetkggqvpkey 61 
                                        +q+++v++ i +++  + + f  +++g    +  
  gi|242399489|ref|YP_002994914.1| 655 MRQEGEVMIIISEAPVAEMFGFAGAIRGATSGRAL 689
                                       4899*********9999999999988887655555 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 !   88.1   0.3   1.3e-28     3e-25       2      74 ..     387     459 ..     386     460 .. 0.98

  Alignments for each domain:
  == domain 1  score: 88.1 bits;  conditional E-value: 1.3e-28
                            EFG_II   2 PePvislaiepkskadedklskaLarlleEDptlrverdeeTketilsGmGelHleivverlkreykvevelg 74 
                                       +ePv+++aie+k+ +d  +l +aL++l++EDptl+v+ deeT++ +lsGmGelHle+ +  lk++ +v+v+++
  gi|242399489|ref|YP_002994914.1| 387 SEPVVTVAIEAKNVKDLPRLIEALRQLAKEDPTLHVKIDEETGQHLLSGMGELHLEVKLVHLKEQWGVDVDVS 459
                                       69********************************************************************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 !   79.9   0.1   4.6e-26     1e-22       1      85 [.     621     704 ..     621     708 .. 0.97

  Alignments for each domain:
  == domain 1  score: 79.9 bits;  conditional E-value: 4.6e-26
                                       EEEEEEEEEEEEEECCCCCCHHHHHHHCT-EEEEEEEE.TTEEEEEEEEEGGG-TTHHHCHHHCTTTS-EEEEEEEE CS
                             EFG_C   1 vllEPivkveievpeeyvgkvisdlssrrGeiedmeqdasgrviieaeiPlaeligfateLrslTkGegsfsmefsg 77 
                                       vl+EP++kv i+vp ey+g v  ++++rrG+++dm+q+ ++ +ii  e+P+ae++gfa ++r +T+G++ +s+e +g
  gi|242399489|ref|YP_002994914.1| 621 VLYEPYQKVVINVPYEYMGSVSREMNQRRGQLIDMRQE-GEVMIIISEAPVAEMFGFAGAIRGATSGRALWSTEHAG 696
                                       589***********************************.************************************** PP

                                       EEE--HHH CS
                             EFG_C  78 Yeevpgdk 85 
                                       ++ vp ++
  gi|242399489|ref|YP_002994914.1| 697 FKRVPTEL 704
                                       ****9875 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 !   55.2   1.2   3.1e-18     7e-15       1      73 [.     306     372 ..     306     373 .. 0.97

  Alignments for each domain:
  == domain 1  score: 55.2 bits;  conditional E-value: 3.1e-18
                                       EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEE CS
                       GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtl 73 
                                       G+va+grv+sGt+k+G+ev+i   + ++k    ri+++   +++e++ ++ ++aG+iva+ gl da ++G+t+
  gi|242399489|ref|YP_002994914.1| 306 GEVATGRVWSGTVKTGQEVHI--ITAKRK---ARIQQVGIYMGPERINMEAVPAGNIVAVTGLRDA-MAGETV 372
                                       89*******************..988899...*********************************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 !   16.4   0.0   3.2e-06    0.0072      10     111 ..      32     146 ..      23     149 .. 0.53

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.2e-06
                                       SSHHHHHHHHHT................STEEESSSTTSSSSEEEEEEE....ETTEEEEEEECGGCSSHHHHHHHH CS
                          MMR_HSR1  10 vGKStLinaltg................ekaivsdkpgtTrdinegrvk....lkgkeielvDtpGliegaseekgl 66 
                                        GK+tL   l+                 +  + ++  g T++     +      ++  ++l+DtpG ++    + ++
  gi|242399489|ref|YP_002994914.1|  32 HGKTTLSDNLLAgagmiseelagkqlvlDFDEQEQARGITINAANVSMIheygDQKYLVNLIDTPGHVD---FGGDV 105
                                       68888887777434444444433322222234455556666663333323432223559*******665...22234 PP

                                       HHHHHHHHCTSEEEEEEETTTTCSHHHHHHHHHH.HHHTTSEEEEE CS
                          MMR_HSR1  67 gkaflaleeadlillvvdaseeklkpldeeleel.leeakkplilv 111
                                       ++a++     d +++vvda  e++ p+ e++ +  l+e  kp+ l 
  gi|242399489|ref|YP_002994914.1| 106 TRAMR---AIDGAIIVVDAV-EGVMPQTETVLRQaLREYVKPV-LF 146
                                       44444...479*******99.6577776665544044455554.33 PP

>> RF3_C  Class II release factor RF3, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   7.3e-06     0.016      14      89 ..     394     469 ..     385     492 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 7.3e-06
                                       EEEESSGGGHHHHHHHHHHHHHCTSSEEEEET.TSS-EEEEESSTHHHHHHHHHHHHHH---EEEEE-S--EEEEE CS
                             RF3_C  14 rvrlkdplkrkqlrkgleqLaeEGavqvfkeeeageelilgaVGqLQfeVveeRlknEYgvevrleslpyslarwv 89 
                                        +++k++    +l ++l+qLa+E  +   k +e++ + +l+ +G+L +eV    lk+ +gv+v++++  + +   +
  gi|242399489|ref|YP_002994914.1| 394 AIEAKNVKDLPRLIEALRQLAKEDPTLHVKIDEETGQHLLSGMGELHLEVKLVHLKEQWGVDVDVSEPIVVYRESI 469
                                       57788888888999***********9999999999****************************9987555555555 PP

>> DUF2283  Protein of unknown function (DUF2283)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00018      0.41      23      48 ..      49      75 ..      41      76 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00018
                           DUF2283 23 seev.dddiilDfDedGrlvGIEiLnA 48
                                      see+ + +++lDfDe+ +  GI+i  A
  gi|242399489|ref|YP_002994914.1| 49 SEELaGKQLVLDFDEQEQARGITINAA 75
                                      5666255*****************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (732 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); 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: 0.66u 0.28s 00:00:00.94 Elapsed: 00:00:00.46
# Mc/sec: 4771.96
//
Query:       gi|242399490|ref|YP_002994915.1|  [L=305]
Description: Asparaginyl-tRNA synthetase-related protein [Thermococcus sibiricus MM 739]
Scores for complete 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  149.4   0.0    1.5e-43  149.1   0.0    1.0  1  tRNA-synt_2   tRNA synthetases class II (D, K and N)
  ------ inclusion threshold ------
      0.085   12.3   0.7        2.6    7.5   0.0    3.0  4  tRNA-synt_2d  tRNA synthetases class II core domain (F)


Domain annotation for each model (and alignments):
>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.1   0.0   1.7e-47   1.5e-43      11     313 ..       8     298 ..       3     299 .. 0.90

  Alignments for each domain:
  == domain 1  score: 149.1 bits;  conditional E-value: 1.7e-47
                                       HHCCSHHHHHHHHHHHHHHHHHHHHHHHTT-EE----SEESS--SSSS--EEEEETTT.TEEE....-E-S-SHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxx RF
                       tRNA-synt_2  11 ldlrtekvskvlrlrstvtkavrkyleengfieietPiLsksdteegarlFkvksrekekeff....aLtqspqlyl 83 
                                       ++l +++++k++r+++++++++ +++ ++gf    + +Ls+ + +    +   k r+ e + +     L  s+ l++
  gi|242399490|ref|YP_002994915.1|   8 VQLISRDIEKTIRVQTKLIDYLTDFFVKKGFKWLLPVMLSSITDPLWPDPASSKMRAPEIDAYgtrlKLMHSMILHK 84 
                                       677788999*************************9999999977777777777777765566668889********* PP

                                       HHHHHCTHSEEEEEEEEE--S--BTT..B-S-CEEEEEEEEET-SCHHHHHHHHHHHHHHHHHHHHCSCCCCCHTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2  84 ellivagidrvfqiaraFRaEdsrtd..rhlaEFtqieaemsfieeedimqvleelikslvkevlessakdiefvir 158
                                       ++ i+ g++++f ++++ R E+ + d  rh  EFtqi++e+++++++d+m+++eeli  l+ke+ ++     e+  +
  gi|242399490|ref|YP_002994915.1|  85 QFAIAMGLEKIFVLSPNIRLEERDRDdgRHAYEFTQIDFEIAYATMDDVMSLIEELIVGLFKEA-RTW----EELGE 156
                                       *********************88754449***********************************.555....44555 PP

                                       TTSEE-SSS-EEEEHHHHHHHHHTS-SS--HHHHHHHHHHS--SEEEEEEEBGGGSTTCBBBSTTSTTBBSEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 159 rnskdlkkpfkrltykeaieklneigkdldkaderalvkkeknepvfvtdfPaelkpFyarkeeddkkltesyDlli 235
                                       r   ++k pfkr+t++e  e+      + d++  ra+ +     p+++td     + Fy r++ +++   ++yDl++
  gi|242399490|ref|YP_002994915.1| 157 RDLPKVKVPFKRFTMAEIEEE-----FGDDEEASRAMEE-----PFWITDIS---REFYDREDPKRPGHFRNYDLIL 220
                                       555689***********9999.....8889999999977.....******86...67******************** PP

                                       T.TE.EEEEEEEB--SHHHHHHHHHHCCHHSSSGGGGHHHHHHHHCT.--SEEEEEEEHHHHHHHHCT-SSGGGCSS CS
                                       x.xx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 236 n.gv.ElvgGslRiedpeeleeklkskgldeeaeekfswylealeyG.apphgGlglGldRlvmlllgsesIrdvia 309
                                       + g+ E+ +G  R++++e   +klk+ gl+      f  yle+ + G + p +G g+G++Rlv +++g+++I +v++
  gi|242399490|ref|YP_002994915.1| 221 PeGYgEVSSGGEREWEYEAILRKLKESGLS---LRAFRPYLEVAKAGkLKPSAGAGIGIERLVRYIVGAKHIAEVQP 294
                                       9889**************************...*************93469************************** PP

                                       S-XX CS
                                       xxxx RF
                       tRNA-synt_2 310 FPkl 313
                                       FP++
  gi|242399490|ref|YP_002994915.1| 295 FPRV 298
                                       **95 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 ?   -0.7   0.0     0.092   8.2e+02      13      36 ..      16      39 ..       7      42 .. 0.82
   2 ?    7.5   0.0   0.00029       2.6     113     156 ..     107     148 ..      89     154 .. 0.88
   3 ?   -3.3   0.0      0.55   4.9e+03      57      71 ..     181     195 ..     160     204 .. 0.70
   4 ?    1.1   0.0     0.026   2.3e+02     209     231 ..     267     289 ..     255     293 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.092
                                      HSB-SHHHHHHHHHHHHHHCTTCE CS
                      tRNA-synt_2d 13 agklhpltkvleeikeiflelgfe 36
                                      + ++++ tk+++ ++++f++ gf+
  gi|242399490|ref|YP_002994915.1| 16 EKTIRVQTKLIDYLTDFFVKKGFK 39
                                      4567888999************97 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00029
                                       SST-SSSB-SEEEEEEEEEEETT--HHHHHHHHHHHHHHHCTST CS
                      tRNA-synt_2d 113 rdavDathlaeFhqveglvvdenvsladlkgvleellkklfgae 156
                                       rd +D +h +eF+q+++ ++    +++d++ ++eel+  lf + 
  gi|242399490|ref|YP_002994915.1| 107 RDRDDGRHAYEFTQIDFEIAY--ATMDDVMSLIEELIVGLFKEA 148
                                       68899***********99875..89************9998765 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 0.55
                                       TTSHHHCHTTSEBTC CS
                      tRNA-synt_2d  57 qdhpaRdmqdtFylk 71 
                                       ++++ R+m++ F+++
  gi|242399490|ref|YP_002994915.1| 181 DEEASRAMEEPFWIT 195
                                       456677777777774 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 0.026
                                       SEEEEEEEEHHHHHHHHHT-SSG CS
                      tRNA-synt_2d 209 vsgfafGlGveRlamlkygieDi 231
                                       ++ ++ G+G+eRl    +g + i
  gi|242399490|ref|YP_002994915.1| 267 KPSAGAGIGIERLVRYIVGAKHI 289
                                       5567889*****99988888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2114.75
//
Query:       gi|242399491|ref|YP_002994916.1|  [L=215]
Description: NAD(P)H oxidase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-32  112.8   0.7    3.4e-17   63.0   0.2    2.1  2  Nitroreductase  Nitroreductase family
    1.3e-16   60.9   1.2    5.5e-06   26.1   0.0    3.3  3  TM1586_NiRdase  Putative TM nitroreductase


Domain annotation for each model (and alignments):
>> Nitroreductase  Nitroreductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.0   0.2   3.8e-21   3.4e-17       1      54 [.      44      97 ..      44     100 .. 0.94
   2 !   48.7   0.0   9.8e-17   8.8e-13      82     170 .]     101     187 ..      97     187 .. 0.86

  Alignments for each domain:
  == domain 1  score: 63.0 bits;  conditional E-value: 3.8e-21
                                      HHH--B---B-S----HHHHHHHHHHHHTS--GGG---EEEEEE.-CCCHHHHH CS
                    Nitroreductase  1 irkRrSiRkFddepvpkeelekileaarraPsagnlqpwrfvvvqdkelrykla 54
                                      ++kRrSiRk++d++vp+e +ekile a ++Ps++n++pw+fvvv+ +e+++kla
  gi|242399491|ref|YP_002994916.1| 44 VKKRRSIRKYQDRKVPREYVEKILEVAFYSPSSMNRRPWHFVVVEGREIIKKLA 97
                                      589*****************************************9888888887 PP

  == domain 2  score: 48.7 bits;  conditional E-value: 9.8e-17
                                       HHHHHHHHSSEEEEE---TTS---HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE-GGG......GGHH...H CS
                    Nitroreductase  82 kaqkalagapvlivivatldkserkaaerayryalldagaaaqnllLaAtalGlgscpiggfd......eaae...e 149
                                       +a  +l++ap+ iv+           +e+  +  ++da++aa+ ++LaAtalGlg+c+ + +d      +  +    
  gi|242399491|ref|YP_002994916.1| 101 GALRFLETAPLAIVV---------CGDEKISSAWVFDASIAAEHIQLAATALGLGACWGHVLDrqhseeK--SaedY 166
                                       567899*********.........777777788889***************************6666541..15568 PP

                                       HHHHHT-S..SEEEEEEEEE- CS
                    Nitroreductase 150 vrkllglpdeeeivvliavGy 170
                                       vr+llg+p++ +i+++i++Gy
  gi|242399491|ref|YP_002994916.1| 167 VRELLGIPEHVRILCVIGIGY 187
                                       ********99**********9 PP

>> TM1586_NiRdase  Putative TM nitroreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.8   3.4e-06      0.03       2      28 ..      40      66 ..      39      66 .. 0.90
   2 !   26.1   0.0   6.2e-10   5.5e-06     158     191 ..      61      94 ..      59     117 .. 0.81
   3 !   21.2   0.0   1.9e-08   0.00017      87     145 ..     132     200 ..     102     206 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.4e-06
                                      HHHHHHH--B---B--S---HHHHHHH CS
                    TM1586_NiRdase  2 lyeaiekRhsvRkYkdealeeelleel 28
                                       +e ++kR+s+RkY+d++++ e +e++
  gi|242399491|ref|YP_002994916.1| 40 FFEVVKKRRSIRKYQDRKVPREYVEKI 66
                                      6799*****************999875 PP

  == domain 2  score: 26.1 bits;  conditional E-value: 6.2e-10
                                       HHHHHHHHHHHTS--GGG----EEE.E-SSEE.. CS
                    TM1586_NiRdase 158 ewfkeileaarlAPsAlNqqpwrfelkdddeiki 191
                                       e++++ile+a ++Ps++N++pw+f +++  ei  
  gi|242399491|ref|YP_002994916.1|  61 EYVEKILEVAFYSPSSMNRRPWHFVVVEGREIIK 94 
                                       7899*********************999877754 PP

  == domain 3  score: 21.2 bits;  conditional E-value: 1.9e-08
                                       HHHHHHHHHHHTT-EEEEES--SST.....................T-S-EEEEE-BS----.-----H CS
                    TM1586_NiRdase  87 ygeqlvLkltalGlgtcWvggtykk..........kkakvelkkgeklvivIalGyaktklveakrkpl 145
                                         e++ L +talGlg cW      +          +++ + +++  ++++vI +Gy+ +++ e+++k++
  gi|242399491|ref|YP_002994916.1| 132 AAEHIQLAATALGLGACWGHVLDRQhseeksaedyVRELLGIPEHVRILCVIGIGYPVEQKLEHDEKEI 200
                                       679***************654333322233444444555778999********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1459.70
//
Query:       gi|242399492|ref|YP_002994917.1|  [L=963]
Description: Glutamate synthase beta chain-related oxidoreductase, containing 2Fe- 2S and 4Fe-4S clusters [Thermococcus sibiricus MM 739]
Scores for 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-41  140.9   2.3      1e-40  139.9   2.3    1.5  1  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
      5e-24   84.3   3.5      1e-18   67.1   0.1    2.7  2  Fer4_20          Dihydroprymidine dehydrogenase domain II, 4F
    1.4e-19   70.4   1.5    1.7e-14   53.8   0.1    2.4  2  Pyr_redox_3      Pyridine nucleotide-disulphide oxidoreductas
    7.1e-18   64.9   8.2    2.7e-10   40.7   1.2    4.1  3  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
    1.1e-12   48.0   0.0      1e-10   41.7   0.0    2.9  2  NAD_binding_8    NAD(P)-binding Rossmann-like domain
    6.1e-09   35.8   0.0    1.6e-08   34.5   0.0    1.8  1  Fer2_4           2Fe-2S iron-sulfur cluster binding domain
    8.6e-09   35.8   0.1    3.8e-05   24.1   0.1    2.8  2  NAD_binding_7    Putative NAD(P)-binding
    1.9e-08   33.8   0.4     0.0014   18.0   0.2    2.5  2  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
    9.7e-08   31.8   2.4    8.2e-06   25.4   0.0    2.2  2  FAD_oxidored     FAD dependent oxidoreductase
    3.2e-07   30.2   3.8      6e-05   22.8   0.1    4.2  4  DAO              FAD dependent oxidoreductase
      2e-06   26.8   0.7    3.6e-05   22.6   0.1    2.2  2  HI0933_like      HI0933-like protein
    6.8e-06   25.7   0.0      0.047   13.1   0.0    2.7  2  PALP             Pyridoxal-phosphate dependent enzyme
    7.8e-06   25.2   1.1    0.00068   18.8   0.0    2.8  3  FAD_binding_2    FAD binding domain
    1.3e-05   24.5   0.5      0.016   14.3   0.0    3.2  3  GIDA             Glucose inhibited division protein A
    6.5e-05   23.4   0.0      0.076   13.5   0.0    2.5  2  XdhC_C           XdhC Rossmann domain
    9.8e-05   21.8   0.1       0.23   10.8   0.1    2.4  2  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
    0.00011   21.1   0.2       0.19   10.4   0.1    3.1  3  Oxidored_nitro   Nitrogenase component 1 type Oxidoreductase
    0.00024   20.5   0.0    0.00057   19.3   0.0    1.6  2  Amino_oxidase    Flavin containing amine oxidoreductase
     0.0003   20.1   1.0      0.015   14.5   0.1    2.2  2  FAD_binding_3    FAD binding domain
      0.001   18.3   0.0      0.013   14.6   0.0    2.1  2  K_oxygenase      L-lysine 6-monooxygenase (NADPH-requiring)
     0.0019   18.4   0.2        5.8    7.2   0.1    3.5  3  TrkA_N           TrkA-N domain
     0.0022   17.3   0.5      0.005   16.1   0.0    1.8  2  Thi4             Thi4 family
     0.0076   14.7   0.0       0.46    8.9   0.0    2.1  2  FMO-like         Flavin-binding monooxygenase-like
     0.0078   15.7   3.6      0.013   15.1   0.0    2.6  2  NADH-G_4Fe-4S_3  NADH-ubiquinone oxidoreductase-G iron-sulfur
  ------ inclusion threshold ------
       0.02   14.7   0.9       0.02   14.7   0.9    4.6  3  Fer4             4Fe-4S binding domain
       0.02   14.5   0.1        1.2    8.7   0.0    2.4  2  IlvN             Acetohydroxy acid isomeroreductase, NADPH-bi
      0.024   14.5   0.2        1.7    8.5   0.0    2.3  2  YjeF_N           YjeF-related protein N-terminus
      0.055   13.5   4.9      0.041   13.9   1.6    2.5  2  Molybdop_Fe4S4   Molybdopterin oxidoreductase Fe4S4 domain
      0.059   12.9   0.0       0.12   11.9   0.0    1.5  1  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
      0.092   11.7   0.0       0.25   10.3   0.0    1.6  2  Molybdopterin    Molybdopterin oxidoreductase
       0.11   13.1   0.1        9.9    6.8   0.1    3.5  2  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
       0.14   11.2   0.2       0.88    8.5   0.1    2.0  2  Lycopene_cycl    Lycopene cyclase protein
       0.19   11.6   2.0          6    6.7   0.3    2.5  2  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
       0.21   11.4   0.6          1    9.2   0.1    2.3  2  DFP              DNA / pantothenate metabolism flavoprotein
       0.31   11.0   0.6        1.2    9.1   0.1    2.2  2  NAD_binding_9    FAD-NAD(P)-binding
        3.3    8.5   6.4       0.93   10.3   1.3    2.8  1  Fer4_15          4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.9   2.3     2e-43     1e-40       1     290 [.     196     489 ..     196     493 .. 0.86

  Alignments for each domain:
  == domain 1  score: 139.9 bits;  conditional E-value: 2e-43
                                       CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH.HHHHCHHHHCCCCHCCTCE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias.evvkklnqgielllgeevv 76 
                                       k+++v+GgGpAGla+a +l++ g++vt++   +++++ g ++ + +  ++ +++++  +  + +n+gie+ ++   +
  gi|242399492|ref|YP_002994917.1| 196 KRIAVVGGGPAGLACAYYLRTMGHDVTIF---DAMPHLGGMMRYGIPPYRLPKDVLDkDIATVINTGIEVKTN---T 266
                                       589**************************...88999999*************99997555556667776666...3 PP

                                       EEEESCEEEEETEEECTCEEEEEESEEEE---E.EE-BCTCTTC..TTBEECCSECHHHHHHCCSS-TSEEEEES-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  77 kidpgkkkvklekkkegdeekiaydklvlAtGs.sprdlgipGv.aenvgklvrtldsaealklkllpkrivvvGgG 151
                                       +   gk ++ le+++       +yd+++l  G+ ++r++gi+G+  ++v+++ + l++++  ++ +l kr++vvGgG
  gi|242399492|ref|YP_002994917.1| 267 A--LGK-DIALEELR------EQYDAVFLGVGAwKSRKMGIEGEdLDGVIHGTEFLRKVNMGEKVELGKRVIVVGGG 334
                                       3..355.77776655......59*********9788999***998999***************************** PP

                                       HHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTE.....EEEEEETTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxx RF
                       Pyr_redox_2 152 yiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgnge.....klevvledg 223
                                       ++++++A ++ +lg++vt+v++r++    ++ +   +  e+ e+eGv++++ t++++i+g+++      ++++l++ 
  gi|242399492|ref|YP_002994917.1| 335 NTAMDVARTALRLGADVTVVYRRSKSE--MPANS--REVEEAEEEGVKFMFLTNPVKIIGKEKveeveLIKMKLGEP 407
                                       ***********************9996..44333..334677888******************99554444888887 PP

                                       CE...............EEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTS.BESSTTEEE-GGGC.TECCS CS
                                       xx...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx.xxxxx RF
                       Pyr_redox_2 224 ee...............idadlvvvavGvrpstelleeklglelderggivvdefl.rtnvpgiyaiGDva.ggkgg 283
                                       +                +++d v++a+G   + e+l +++g+e  +rg+++vde   +tn +g++a GD + g+ ++
  gi|242399492|ref|YP_002994917.1| 408 DAsgrrrpmpiegsefrVKVDNVILAIGQYCDEEFL-RTIGIEA-KRGRVLVDEVTlQTNKEGVFAGGDLVlGPSTV 482
                                       779999******************************.*******.********9655**************555566 PP

                                       S--HHHH CS
                                       xxxxxxx RF
                       Pyr_redox_2 284 pelaqaA 290
                                       +e++ + 
  gi|242399492|ref|YP_002994917.1| 483 IESIATG 489
                                       6555554 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 !   67.1   0.1   2.1e-21     1e-18      30     111 ..     105     183 ..     101     185 .. 0.94
   2 !   16.6   1.0     1e-05     0.005       1      30 [.     567     596 ..     567     613 .. 0.87

  Alignments for each domain:
  == domain 1  score: 67.1 bits;  conditional E-value: 2.1e-21
                                       -HHHHCSTT---HHHHHHHHHTT-HHHHHHHHHHH-S-HHHHHHHS-GGGTGCCS-GGGTTB.----HHHHHHHHHH CS
                           Fer4_20  30 apcvkgCPveidipefikkiaegnleeaakiiketnslpavcgrvCpqeelCegaCvlekkgkepvaigklerfvad 106
                                        pc++gCP++ d+++++  ia g+++ea+k++ke+ +lpav grvCp    Ce++C ++  + ep+ai++l+rf+ad
  gi|242399492|ref|YP_002994917.1| 105 GPCQNGCPAHSDVQGYLALIAMGRYHEAVKLMKEKYILPAVLGRVCPAF--CEEECRRNLVE-EPLAIRQLKRFAAD 178
                                       58*********************************************87..*******8666.9************* PP

                                       HHHHT CS
                           Fer4_20 107 aaree 111
                                       +  e+
  gi|242399492|ref|YP_002994917.1| 179 YDLEN 183
                                       *9887 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 1e-05
                                       HTTS-S-SB----HHHHHHHHTT----TT- CS
                           Fer4_20   1 raknfkevalglteeealeeAsRClqCkka 30 
                                       r++nfkev+ +++ee++l+eA+RC++C   
  gi|242399492|ref|YP_002994917.1| 567 RKSNFKEVEPTMDEETVLTEAQRCMSCGCM 596
                                       5789***********************644 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   1.7e-05    0.0085       2      30 ..     200     227 ..     199     239 .. 0.84
   2 !   53.8   0.1   3.4e-17   1.7e-14     122     305 .]     280     473 ..     250     473 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.7e-05
                       Pyr_redox_3   2 IiGaGPaGlaaaielkkagledylilEkg 30 
                                       ++G+GPaGla+a+ l+ +g  d++i +  
  gi|242399492|ref|YP_002994917.1| 200 VVGGGPAGLACAYYLRTMGH-DVTIFDAM 227
                                       8******************9.79998876 PP

  == domain 2  score: 53.8 bits;  conditional E-value: 3.4e-17
                       Pyr_redox_3 122 tyeAkkviiAtGefdkPnklnipGeek.lvkhyskv....kefhkya.gqkvvViGgknSavDaAlelvrkgaeVtv 192
                                       +y A  v++  G + k +k++i+Ge+   v+h  ++    +  +k++ g++v+V+Gg+n+a+D+A    r ga+Vtv
  gi|242399492|ref|YP_002994917.1| 280 QYDA--VFLGVGAW-KSRKMGIEGEDLdGVIHGTEFlrkvNMGEKVElGKRVIVVGGGNTAMDVARTALRLGADVTV 353
                                       5544..67777775.46778999999534555443322116667777899*************************** PP

                       Pyr_redox_3 193 vtrgseiekeesdpsyslkpdienrleelvkeekikvlfnaevkeikekeeeykvktedgkkvev..........kd 259
                                       v+r+s+ e      s +++   e+ ++ +  ++ +k++ +++v+e++  + +     ++g++              d
  gi|242399492|ref|YP_002994917.1| 354 VYRRSKSEM--PANSREVEEAEEEGVKFMFLTNPVKIIGKEKVEEVELIKMKLGEPDASGRRRPMpiegsefrvkVD 428
                                       ****96444..578999***********999999*********9998654443222222222221223333333568 PP

                       Pyr_redox_3 260 dvvlatGykpdlsflkkslfeldedgrpvlteeteetnvpglflaG 305
                                       +v+la+G  +d +fl+  ++e  + gr++++e t +tn +g+f  G
  gi|242399492|ref|YP_002994917.1| 429 NVILAIGQYCDEEFLRTIGIEA-KRGRVLVDEVTLQTNKEGVFAGG 473
                                       899*************999987.99******************876 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.1   9.5e-08   4.7e-05       1      35 [.     197     231 ..     197     238 .. 0.93
   2 !   40.7   1.2   5.5e-13   2.7e-10       1      78 [.     327     399 ..     327     403 .. 0.92
   3 ?    1.8   0.0      0.73   3.6e+02      25      47 ..     548     571 ..     540     578 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 9.5e-08
                                       EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                         Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkll 35 
                                       +++vvGgG  gl +A +l+ +g++Vt+++++++l 
  gi|242399492|ref|YP_002994917.1| 197 RIAVVGGGPAGLACAYYLRTMGHDVTIFDAMPHLG 231
                                       79*****************************9997 PP

  == domain 2  score: 40.7 bits;  conditional E-value: 5.5e-13
                                       EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEE CS
                         Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedgvesvk 77 
                                       +v+vvGgG++++++A ++ +lg++Vtvv r++k        a ++  e+ e++g+++++ t++++i g+e+ ve+v+
  gi|242399492|ref|YP_002994917.1| 327 RVIVVGGGNTAMDVARTALRLGADVTVVYRRSKSE----MPANSREVEEAEEEGVKFMFLTNPVKIIGKEK-VEEVE 398
                                       79*******************************99....5566666899********************99.99998 PP

                                       E CS
                         Pyr_redox  78 l 78 
                                       l
  gi|242399492|ref|YP_002994917.1| 399 L 399
                                       6 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.73
                                       EEEEESSSSSS.TTSSHHHHHHHH CS
                         Pyr_redox  25 Vtvversdkll.rllDeeaskilq 47 
                                          ver++++  +llD+e++k   
  gi|242399492|ref|YP_002994917.1| 548 YEHVERKPRVKvKLLDPEIRKSNF 571
                                       5669***************99655 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 !   41.7   0.0     2e-13     1e-10       1      37 [.     200     236 ..     200     259 .. 0.90
   2 ?    3.0   0.0      0.25   1.2e+02       1      28 [.     330     357 ..     330     375 .. 0.90

  Alignments for each domain:
  == domain 1  score: 41.7 bits;  conditional E-value: 2e-13
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-E CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraas 37 
                                       +vG+G +Gl++Ay+L+  g+dv+++++ ++lGG ++ 
  gi|242399492|ref|YP_002994917.1| 200 VVGGGPAGLACAYYLRTMGHDVTIFDAMPHLGGMMRY 236
                                       8********************************9975 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.25
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SS CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekr 28 
                                       +vG+G +++  A+++ + g+dv+++ +r
  gi|242399492|ref|YP_002994917.1| 330 VVGGGNTAMDVARTALRLGADVTVVYRR 357
                                       8**********************98655 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 !   34.5   0.0   3.2e-11   1.6e-08       2      80 ..       8      80 ..       7      82 .. 0.91

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 3.2e-11
                            Fer2_4  2 rpvtltfDGkevtvpeGdtvasAllangvdvprsckygrprgelcaggeCrnClVevegepnvracstpvedGlkvetq 80
                                      ++v++t++Gke+++p+++++++ l +   +vp  c++    + + + g+Cr ClV++   + + +c+ +  +Gl++et 
  gi|242399492|ref|YP_002994917.1|  8 EMVKITVNGKEFEAPKDKSLIEFLREI-THVPGFCYT----EAFDPYGSCRLCLVQTPR-GITTSCTLKPMEGLSIETL 80
                                      79********************87765.789******....9**************974.558*************995 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 !    8.6   0.0    0.0051       2.6       6      39 ..     194     227 ..     192     275 .. 0.85
   2 !   24.1   0.1   7.6e-08   3.8e-05       7      93 ..     325     461 ..     324     471 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0051
                     NAD_binding_7   6 kgkkvlvvGgGevAarkvrklleagakvtvvape 39 
                                       +gk++ vvGgG+ ++  ++ l   g +vt+ +  
  gi|242399492|ref|YP_002994917.1| 194 TGKRIAVVGGGPAGLACAYYLRTMGHDVTIFDAM 227
                                       699**************************98755 PP

  == domain 2  score: 24.1 bits;  conditional E-value: 7.6e-08
                     NAD_binding_7   7 gkkvlvvGgGevAarkvrklleagakvtvvapevkeele...........elvklaeee.................. 54 
                                       gk+v+vvGgG+ A+  +r+ l+ ga+vtvv  ++k+e++           e                          
  gi|242399492|ref|YP_002994917.1| 325 GKRVIVVGGGNTAMDVARTALRLGADVTVVYRRSKSEMPansreveeaeeE-------Gvkfmfltnpvkiigkekv 394
                                       79****************************999755555544433344440.......1444444444444444444 PP

                     NAD_binding_7  55 ............................lekdlegadlviaatddrelneriaeaakarrilvnvad 93 
                                                                   ++ +++++ l+i    d+e  + i  +ak+ r+lv  ++
  gi|242399492|ref|YP_002994917.1| 395 eevelikmklgepdasgrrrpmpiegseFRVKVDNVILAIGQYCDEEFLRTIGIEAKRGRVLVDEVT 461
                                       4444444444444444444444444444555577777777777788888888888888888887665 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 !   13.3   0.0   7.4e-05     0.037      29      61 ..     196     228 ..     184     233 .. 0.88
   2 !   18.0   0.2   2.8e-06    0.0014       2      64 ..     306     361 ..     305     401 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.4e-05
                                       -EEEEESTSHHHHHHHHHHHHTT-EEEEEESSH CS
                       AlaDh_PNT_C  29 akvlviGgGvaGlqAiatakglgakVtvlDvrp 61 
                                        ++ v+GgG aGl+ +   + +g +Vt++D  p
  gi|242399492|ref|YP_002994917.1| 196 KRIAVVGGGPAGLACAYYLRTMGHDVTIFDAMP 228
                                       5899**************************865 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 2.8e-06
                                       HHHHHHHCSCGCTSEEETTCEETCB---EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHH CS
                       AlaDh_PNT_C   2 vleaakalekffggkgtlaGgvpgvepakvlviGgGvaGlqAiatakglgakVtvlDvrparl 64 
                                       v+++ ++l k ++g+ + +G+       +v+v+GgG   +  ++ta +lga+Vtv+  r++  
  gi|242399492|ref|YP_002994917.1| 306 VIHGTEFLRKVNMGEKVELGK-------RVIVVGGGNTAMDVARTALRLGADVTVVYRRSKSE 361
                                       567777777777777777775.......78*************************98887654 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0   1.6e-08   8.2e-06       2      42 ..     198     238 ..     197     260 .. 0.92
   2 ?    5.8   0.8     0.015       7.3       2      31 ..     328     357 ..     327     359 .. 0.94

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 1.6e-08
                      FAD_oxidored   2 vvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsgl 42 
                                       + VvGGgpaG+a+A+    +G  v + +  ++lGG++  g+
  gi|242399492|ref|YP_002994917.1| 198 IAVVGGGPAGLACAYYLRTMGHDVTIFDAMPHLGGMMRYGI 238
                                       78**********************************97765 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.015
                      FAD_oxidored   2 vvVvGGgpaGvaAAiaAaraGakvlLveer 31 
                                       v+VvGGg   +  A +A r Ga v +v +r
  gi|242399492|ref|YP_002994917.1| 328 VIVVGGGNTAMDVARTALRLGADVTVVYRR 357
                                       9*************************9876 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.1   1.2e-07     6e-05       2      33 ..     198     231 ..     197     235 .. 0.87
   2 ?    3.4   0.4     0.093        46       1      30 [.     327     358 ..     327     370 .. 0.89
   3 ?    0.7   0.0      0.63   3.1e+02     154     226 ..     370     457 ..     368     471 .. 0.66
   4 ?   -0.8   0.0       1.8   8.9e+02     247     309 ..     625     684 ..     601     726 .. 0.70

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.2e-07
                                       EEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
                               DAO   2 vviiGGGiiGlstAyeLarrg..Vtllekgdiag 33 
                                       ++++GGG +Gl++Ay+L + g  Vt++++ + +g
  gi|242399492|ref|YP_002994917.1| 198 IAVVGGGPAGLACAYYLRTMGhdVTIFDAMPHLG 231
                                       9****************655889*****987766 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.093
                                       EEEEECTSHHHHHHHHHHHHTT..EEEEESSS CS
                               DAO   1 dvviiGGGiiGlstAyeLarrg..Vtllekgd 30 
                                       +v+++GGG + + +A+ + r g  Vt++ +++
  gi|242399492|ref|YP_002994917.1| 327 RVIVVGGGNTAMDVARTALRLGadVTVVYRRS 358
                                       59****************99999****99885 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.63
                                       HHHHHTT-EEEESECEEEEEEEETCEEEEE...........EECTEEEE...........EEEEEEE--GGGHH..H CS
                               DAO 154 raaealGveilegtevtgleeedgkvwgve...........rttpgend...........aadavVnaaGawsd..l 206
                                       ++ae+ Gv++ + t+ +++    +kv +ve               g+++           ++d v++a G + d  +
  gi|242399492|ref|YP_002994917.1| 370 EEAEEEGVKFMFLTNPVKIIG-KEKVEEVElikmklgepdaS---GRRRpmpiegsefrvKVDNVILAIGQYCDeeF 442
                                       578899998888888777622.23677777766666543220...3322667777777666788********99844 PP

                                       HHTTCTTTSEEEEEEEEEEE CS
                               DAO 207 lgllkeldlpispvrgqvlv 226
                                       l   +++   i++ rg vlv
  gi|242399492|ref|YP_002994917.1| 443 L---RTI--GIEAKRGRVLV 457
                                       4...444..66777777665 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 1.8
                                       EETTTTEEEEEETTSEEEEEESSEEETTCSSTSCSHHHHHHHHHHHHHHS.GGGCGEEEEEEEE CS
                               DAO 247 dddgrgvyvtprkdgrvlvGgtadeesgdddpevdeedidellealrklf.PqlgdvlrkwaGl 309
                                         d++++ v+ + +++ +++g      ++++  + e  +d+l +  ++++ Pqlg+ l+ + G+
  gi|242399492|ref|YP_002994917.1| 625 EIDETHPNVVLD-NNKCVLCGQ---CVNFTHEIAREGIVDYLFRGFKTYIgPQLGERLEDQKGV 684
                                       455667777777.577888885...5788888889999999*********99998877677664 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   0.1   7.3e-08   3.6e-05       2      36 ..     197     231 ..     196     236 .. 0.93
   2 ?    2.4   0.1     0.099        49       2      30 ..     327     355 ..     326     361 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 7.3e-08
                                       SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                       HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakklg 36 
                                       +++v+GgG+AGl +A  +++ g++V++++++++lg
  gi|242399492|ref|YP_002994917.1| 197 RIAVVGGGPAGLACAYYLRTMGHDVTIFDAMPHLG 231
                                       689****************************9998 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.099
                                       SEEEE--SHHHHHHHHHHHHTT--EEEE- CS
                       HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVllle 30 
                                       +viv+GgG   +  A +a + g++V+++ 
  gi|242399492|ref|YP_002994917.1| 327 RVIVVGGGNTAMDVARTALRLGADVTVVY 355
                                       79***********************9985 PP

>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0    0.0011      0.57      54      86 ..     194     228 ..     169     286 .. 0.82
   2 !   13.1   0.0   9.5e-05     0.047      54      91 ..     324     361 ..     309     396 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0011
                                       TTSEEEEEBSSHHHHHHHHHHHHHT-EEEEE..EE CS
                              PALP  54 gaktvveassGNhgralAaaaallGlkvtiv..vp 86 
                                        +k++++ ++G +g+a+A++ + +G +vti+  +p
  gi|242399492|ref|YP_002994917.1| 194 TGKRIAVVGGGPAGLACAYYLRTMGHDVTIFdaMP 228
                                       6889999************************7744 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 9.5e-05
                                       TTSEEEEEBSSHHHHHHHHHHHHHT-EEEEEEETTS-H CS
                              PALP  54 gaktvveassGNhgralAaaaallGlkvtivvpadasp 91 
                                        +k+v++ ++GN+++ +A  a +lG +vt+v  +++s+
  gi|242399492|ref|YP_002994917.1| 324 LGKRVIVVGGGNTAMDVARTALRLGADVTVVYRRSKSE 361
                                       5789***************************7777662 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.4e-06   0.00068       2      36 ..     198     232 ..     197     237 .. 0.92
   2 ?    3.9   0.1     0.048        24       2      30 ..     328     356 ..     327     364 .. 0.91
   3 ?   -0.8   0.0       1.3   6.4e+02     149     204 ..     370     439 ..     366     457 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.4e-06
                                       EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS CS
                     FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavvekeqefgg 36 
                                       + V+G+G AGLa+A+ ++  G++v++ + ++  gg
  gi|242399492|ref|YP_002994917.1| 198 IAVVGGGPAGLACAYYLRTMGHDVTIFDAMPHLGG 232
                                       68***************************999887 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.048
                                       EEEE--SHHHHHHHHHHHHTTT-EEEEES CS
                     FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavvek 30 
                                       viV+G+G   +  A +a + G++v+vv  
  gi|242399492|ref|YP_002994917.1| 328 VIVVGGGNTAMDVARTALRLGADVTVVYR 356
                                       9*************************965 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 1.3
                                       HHHHTCTEEEEESEEEEEEEECTTEEEEEEEEET...............TTTCEEEEEESEEEE-----GG CS
                     FAD_binding_2 149 esarkagvdfqerteadeLivedgrvtGavvenp...............esgrevrirakavvlatgGfgr 204
                                       e+a++ gv+f++ t+ +++i  +++v  +++ ++                +g+e+r++ ++v+la g +  
  gi|242399492|ref|YP_002994917.1| 370 EEAEEEGVKFMFLTNPVKIIG-KEKVEEVELIKMklgepdasgrrrpmpIEGSEFRVKVDNVILAIGQYCD 439
                                       666777778888888888765.66677776666666777777777777799999*************9987 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   3.2e-05     0.016       2      29 ..     198     227 ..     197     262 .. 0.88
   2 ?    4.8   0.0     0.025        12       2      28 ..     328     354 ..     327     372 .. 0.87
   3 ?    1.9   0.0      0.19        95     348     391 ..     459     503 ..     453     504 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.2e-05
                                       EEEE-SSHHHHHHHHHHHHTT--EEEE..E CS
                              GIDA   2 viViGgGhAGceAAlaaarlGakvlLi..t 29 
                                       + V+GgG AG+++A+ +  +G++v+++   
  gi|242399492|ref|YP_002994917.1| 198 IAVVGGGPAGLACAYYLRTMGHDVTIFdaM 227
                                       78**********************998432 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.025
                                       EEEE-SSHHHHHHHHHHHHTT--EEEE CS
                              GIDA   2 viViGgGhAGceAAlaaarlGakvlLi 28 
                                       viV+GgG   +  A +a rlGa+v+ +
  gi|242399492|ref|YP_002994917.1| 328 VIVVGGGNTAMDVARTALRLGADVTVV 354
                                       9***********************988 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.19
                                       T.TSBBSSSBTEEE-CG.GGTB-SHHHHHHHHHHHHHHHHHHHCTS CS
                              GIDA 348 n.tLetkkvkgLflAGq.inGteGYeEaaaqGllAGinaarkakgk 391
                                       + tL+t+ ++g+f+ G+ + G +  +E++a+G  A+i + +++kgk
  gi|242399492|ref|YP_002994917.1| 459 EvTLQTN-KEGVFAGGDlVLGPSTVIESIATGRRAAIMIDLYLKGK 503
                                       4589998.89******94469999*****************99986 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0     0.013       6.3       2      33 ..     199     230 ..     198     285 .. 0.84
   2 !   13.5   0.0   0.00015     0.076       1      41 [.     328     371 ..     328     427 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.013
                                       EEE--STTHHHHHHHHHHHTEEEEEEES-GGG CS
                            XdhC_C   2 vifGaghvaqalarlaaalgfrvtvvdpreef 33 
                                       +++G+g+ + a+a +++++g +vt++d+ +++
  gi|242399492|ref|YP_002994917.1| 199 AVVGGGPAGLACAYYLRTMGHDVTIFDAMPHL 230
                                       79*************************98875 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.00015
                                       EEEE--STTHHHHHHHHHHHTEEEEEEES-GGGG...-GGG-TT CS
                            XdhC_C   1 lvifGaghvaqalarlaaalgfrvtvvdpreefa...tkerfpe 41 
                                       ++++G+g+ a  +ar a +lg +vtvv  r++ +   + ++++e
  gi|242399492|ref|YP_002994917.1| 328 VIVVGGGNTAMDVARTALRLGADVTVVYRRSKSEmpaNSREVEE 371
                                       689***************************98663333333333 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0    0.0026       1.3      15      70 ..     178     229 ..     167     260 .. 0.81
   2 !   10.8   0.1   0.00046      0.23      36      78 ..     325     367 ..     305     403 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0026
                                       HHHHHTTCCHTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHH CS
                      2-Hacid_dh_C  15 deevregewksekallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskk 70 
                                       d ++++g w       +   +gk+++++G G  G a a +l+ +g +v+++d  ++
  gi|242399492|ref|YP_002994917.1| 178 DYDLENGPW----MPEIPPSTGKRIAVVGGGPAGLACAYYLRTMGHDVTIFDAMPH 229
                                       444566667....33444568******************************98865 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00046
                                       TSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHH CS
                      2-Hacid_dh_C  36 gktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeel 78 
                                       gk+v ++G G+ +  va+++  +g++v+++ r+ k+e  +++ 
  gi|242399492|ref|YP_002994917.1| 325 GKRVIVVGGGNTAMDVARTALRLGADVTVVYRRSKSEMPANSR 367
                                       89*************************9998887766533333 PP

>> Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.26   1.3e+02     271     299 ..     194     222 ..     172     224 .. 0.92
   2 !   10.4   0.1   0.00039      0.19     272     312 ..     325     366 ..     310     403 .. 0.75
   3 ?    5.4   0.0     0.013       6.4     144     198 ..     785     839 ..     737     855 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.26
                                       TT-EEEEECSSHHHHHHHHHHHHHT-EEE CS
                    Oxidored_nitro 271 agkrvaiygdpdrvvalarllkelGmevv 299
                                        gkr+a++g++   +a a +l+ +G +v 
  gi|242399492|ref|YP_002994917.1| 194 TGKRIAVVGGGPAGLACAYYLRTMGHDVT 222
                                       69***********************9886 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00039
                                       T-EEEEECSSHHHHHHHHHHHHHT-EEEEEEESSS-HHHH.H CS
                    Oxidored_nitro 272 gkrvaiygdpdrvvalarllkelGmevvaagtetahrdde.e 312
                                       gkrv+++g++ +++ +ar    lG++v ++  +++++     
  gi|242399492|ref|YP_002994917.1| 325 GKRVIVVGGGNTAMDVARTALRLGADVTVVYRRSKSEMPAnS 366
                                       9**************************999877766544433 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.013
                                       -SSEEEEEEETTCGHGHHHHHHHHHHHHTEEEEEEECTSB-HHHHGGGGG-SEEE CS
                    Oxidored_nitro 144 eprkvnilgeynlgpgdlrelkelleklGlevnavftggtsleelraagraklnl 198
                                       e++  +++  ++l+ +++  lkel e+ G+ +  ++ g+ s + l+++ +ak +l
  gi|242399492|ref|YP_002994917.1| 785 EEKECALILTPSLTNEEIMFLKELAERKGIPIGSTIDGEGSTATLEDIRNAKRVL 839
                                       566888999999999**********************************999776 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   1.1e-06   0.00057       2      29 ..     206     233 ..     205     236 .. 0.94
   2 ?   -3.4   0.0       8.9   4.4e+03     418     448 ..     465     493 ..     458     493 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.1e-06
                                       HHHHHHHHHHHTTEEEEEEESSSSSBTT CS
                     Amino_oxidase   2 aGLaaArqLlsaGfdVtvlEardrvGGR 29 
                                       aGLa+A++L + G+dVt++ a +++GG 
  gi|242399492|ref|YP_002994917.1| 206 AGLACAYYLRTMGHDVTIFDAMPHLGGM 233
                                       9**************************5 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 8.9
                                       CSTTEEE.SGGGCTTTTTSHHHHHHHHHHHH CS
                     Amino_oxidase 418 gdprlffAGehtsreypgtvegAilSGlraA 448
                                       +  ++f  G+ +    p+tv   i +G+raA
  gi|242399492|ref|YP_002994917.1| 465 NKEGVFAGGDLVL--GPSTVIESIATGRRAA 493
                                       5778888888888..9**************9 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   3.1e-05     0.015       4      33 ..     198     227 ..     196     232 .. 0.92
   2 ?    4.0   0.1     0.048        24       4      36 ..     328     360 ..     326     372 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.1e-05
                                       EEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                     FAD_binding_3   4 VlIVGaGpaGlmlallLseaGvrvvlvekr 33 
                                       +++VG+GpaGl  a  L++ G +v++ + +
  gi|242399492|ref|YP_002994917.1| 198 IAVVGGGPAGLACAYYLRTMGHDVTIFDAM 227
                                       689**********************99876 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.048
                                       EEEE--SHHHHHHHHHHHHTTHHEEEEESSSSS CS
                     FAD_binding_3   4 VlIVGaGpaGlmlallLseaGvrvvlvekrstt 36 
                                       V++VG+G + +  a+   + G +v++v +rs+ 
  gi|242399492|ref|YP_002994917.1| 328 VIVVGGGNTAMDVARTALRLGADVTVVYRRSKS 360
                                       9****************************9976 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0       0.4     2e+02     190     213 ..     194     217 ..     182     228 .. 0.78
   2 !   14.6   0.0   2.7e-05     0.013     170     234 ..     302     366 ..     268     377 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.4
                       K_oxygenase 190 akkriaVvGsGqSaaeifedllrr 213
                                       ++kriaVvG+G  +   ++ l + 
  gi|242399492|ref|YP_002994917.1| 194 TGKRIAVVGGGPAGLACAYYLRTM 217
                                       689999***998887776666555 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 2.7e-05
                       K_oxygenase 170 egkervvHsseylerkee...llakkriaVvGsGqSaaeifedllrrqkkvelklvtrsealepldds 234
                                       +  + v+H  e+l++ +     + +kr++VvG+G +a ++++ +lr  +  ++++v r+++ e   +s
  gi|242399492|ref|YP_002994917.1| 302 D-LDGVIHGTEFLRKVNMgekVELGKRVIVVGGGNTAMDVARTALRLGA--DVTVVYRRSKSEMPANS 366
                                       3.36799*****9998766657779********************9987..78888888876655555 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0      0.03        15       1      30 [.     198     227 ..     198     230 .. 0.89
   2 ?    7.2   0.1     0.012       5.8       1      42 [.     328     377 ..     328     389 .. 0.73
   3 ?    0.5   0.0       1.4   6.9e+02      45      63 ..     433     451 ..     422     463 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.03
                                       EEEES-SHHHHHHHHHHHH.TTEEEEEEESS CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLse.ggkdvvvidkd 30 
                                       i+++G G  G + a +L++ g+ dv++ d  
  gi|242399492|ref|YP_002994917.1| 198 IAVVGGGPAGLACAYYLRTmGH-DVTIFDAM 227
                                       79*****************777.7***9975 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.012
                                       EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHH........HHHHHHTTS CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeer........veelreegl 42 
                                       +i++G G++++ +a++  + g  dv+v+ ++ +         vee++eeg+
  gi|242399492|ref|YP_002994917.1| 328 VIVVGGGNTAMDVARTALRlGA-DVTVVYRRSKSempansreVEEAEEEGV 377
                                       79*****************777.7***987764422333333556565555 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 1.4
                                       EES-TTSHHHHHHTTGGGE CS
                            TrkA_N  45 vvgdatdeevLeeagieka 63 
                                        +g++ dee+L+ +gie  
  gi|242399492|ref|YP_002994917.1| 433 AIGQYCDEEFLRTIGIEAK 451
                                       5799************975 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0     1e-05     0.005      20      60 ..     198     237 ..     193     265 .. 0.88
   2 ?   -2.8   0.1       6.1     3e+03      20      38 ..     328     346 ..     324     357 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1e-05
                                       EEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTT CS
                              Thi4  20 vvivGaGssGLtaayylakkpdlkvailersvspGGGawlG 60 
                                       +++vG+G++GL++ayyl +  +  v+i+++   +GG +  G
  gi|242399492|ref|YP_002994917.1| 198 IAVVGGGPAGLACAYYLRTM-GHDVTIFDAMPHLGGMMRYG 237
                                       89***************999.999****9999998876655 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 6.1
                                       EEEE--SHHHHHHHHHHHH CS
                              Thi4  20 vvivGaGssGLtaayylak 38 
                                       v++vG+G + +  a++  +
  gi|242399492|ref|YP_002994917.1| 328 VIVVGGGNTAMDVARTALR 346
                                       99******99999987554 PP

>> FMO-like  Flavin-binding monooxygenase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.035        17       2      42 ..     196     236 ..     195     240 .. 0.94
   2 !    8.9   0.0   0.00091      0.46     180     214 ..     322     356 ..     275     368 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.035
                          FMO-like   2 kkvaviGaGvsGlasikccleegleptcfersddiGGlwrf 42 
                                       k++av+G+G +Gla        g + t f+    +GG+ r+
  gi|242399492|ref|YP_002994917.1| 196 KRIAVVGGGPAGLACAYYLRTMGHDVTIFDAMPHLGGMMRY 236
                                       9**************9999999***************9987 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00091
                          FMO-like 180 vfkgkrvlviGlGnsggdiavelsrtaeqvllstr 214
                                       v  gkrv+v+G Gn++ d+a  + r  ++v +  r
  gi|242399492|ref|YP_002994917.1| 322 VELGKRVIVVGGGNTAMDVARTALRLGADVTVVYR 356
                                       4569****************999999998877665 PP

>> NADH-G_4Fe-4S_3  NADH-ubiquinone oxidoreductase-G iron-sulfur binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   2.5e-05     0.013       1      16 [.      88     103 ..      88     109 .. 0.95
   2 ?   -0.6   1.5       1.9   9.6e+02      16      35 ..     590     611 ..     586     615 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.5e-05
                   NADH-G_4Fe-4S_3   1 RktilellLanHpldC 16 
                                       Rkt+lel+L++H  dC
  gi|242399492|ref|YP_002994917.1|  88 RKTALELILSDHYGDC 103
                                       9*************** PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.9
                   NADH-G_4Fe-4S_3  16 CltCdkn..GnCeLQdlayelg 35 
                                       C++C      +C+L ++a  + 
  gi|242399492|ref|YP_002994917.1| 590 CMSCGCMevFRCKLREYATLYD 611
                                       77766553368*****998886 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.9     4e-05      0.02       1      16 [.     633     648 ..     633     649 .. 0.90
   2 ?    5.4   0.1     0.036        18      16      24 .]     691     699 ..     690     699 .. 0.89
   3 ?   -2.1   1.2         8     4e+03      11      19 ..     719     727 ..     717     730 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4e-05
                                       EEEETTTSSS-THHHH CS
                              Fer4   1 vvideekCigCGaCve 16 
                                       vv d +kC+ CG+Cv+
  gi|242399492|ref|YP_002994917.1| 633 VVLDNNKCVLCGQCVN 648
                                       5789**********96 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.036
                                       HHSTTTEEE CS
                              Fer4  16 evCPvgAIt 24 
                                       ++CPvgAIt
  gi|242399492|ref|YP_002994917.1| 691 DICPVGAIT 699
                                       79******7 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 8
                                       -THHHHHST CS
                              Fer4  11 CGaCvevCP 19 
                                       C+ C  +C 
  gi|242399492|ref|YP_002994917.1| 719 CNGCSFACE 727
                                       788888885 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 ?    8.7   0.0    0.0024       1.2       4      32 ..     195     223 ..     193     227 .. 0.94
   2 ?    3.0   0.0      0.14        68       4      52 ..     325     380 ..     323     389 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0024
                                       TS-EEEES-SHHHHHHHHHHHHTT--EEE CS
                              IlvN   4 gkkiaviGyGsqGhaqalnlrdsgldvvv 32 
                                       gk+iav+G G  G a a  lr  g dv++
  gi|242399492|ref|YP_002994917.1| 195 GKRIAVVGGGPAGLACAYYLRTMGHDVTI 223
                                       89*************************97 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.14
                                       TS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-.......HHHHHHHHTT-EEE CS
                              IlvN   4 gkkiaviGyGsqGhaqalnlrdsgldvvvglregs.......ksvkkAkeegfevl 52 
                                       gk++ v+G G+ +   a+     g dv+v  r+++       + v++A+eeg++ +
  gi|242399492|ref|YP_002994917.1| 325 GKRVIVVGGGNTAMDVARTALRLGADVTVVYRRSKsempansREVEEAEEEGVKFM 380
                                       799**************999999*****9999887566665456777888877766 PP

>> YjeF_N  YjeF-related protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0      0.13        63      39      59 ..     204     224 ..     194     243 .. 0.86
   2 ?    8.5   0.0    0.0033       1.7      28      94 ..     326     388 ..     309     400 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.13
                            YjeF_N  39 GgdglaaArhLaqegakVtvl 59 
                                       G  gla+A +L+ +g++Vt++
  gi|242399492|ref|YP_002994917.1| 204 GPAGLACAYYLRTMGHDVTIF 224
                                       899***************995 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0033
                            YjeF_N  28 kvlvlvGsgnnGgdglaaArhLaqegakVtvllleeeekldedaeralellkkaggkvveekpeedl 94 
                                       k +++vG+gn+   ++ +Ar  ++ ga+Vtv+ ++++++    + r++e++++ g+k+   +++ + 
  gi|242399492|ref|YP_002994917.1| 326 KRVIVVGGGNT---AMDVARTALRLGADVTVV-YRRSKSEMPANSREVEEAEEEGVKFMFLTNPVKI 388
                                       55788999887...55589999999******5.66666666789999********999887776655 PP

>> Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1         4     2e+03       7      19 ..     149     162 ..     148     173 .. 0.79
   2 ?   13.9   1.6   8.3e-05     0.041       4      34 ..     715     745 ..     712     756 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 4
                                       E-S.SBTT--EEEE CS
                    Molybdop_Fe4S4   7 aCp.yCgvgCglev 19 
                                       +Cp +C   C  ++
  gi|242399492|ref|YP_002994917.1| 149 VCPaFCEEECRRNL 162
                                       7******9997555 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 8.3e-05
                                       EEEE-SSBTT--EEEEEEETTEEEEEEE-TT CS
                    Molybdop_Fe4S4   4 vktaCpyCgvgCglevhvkdgkivkvegdpd 34 
                                       vkt+C  C+  C ++++v ++  v++   +d
  gi|242399492|ref|YP_002994917.1| 715 VKTVCNGCSFACEMNIEVYNDILVRASSRKD 745
                                       9*****************9998887777665 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00025      0.12       2     129 ..     197     335 ..     196     358 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00025
                                       EEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-S......S--TTHHHHHHHHCHTTT...EEEES- CS
                    UDPG_MGDP_dh_N   2 kisviGlGYvGlvtaavlaeighevigvDideekvdklnsgkip......iyepgLeelvkkavesgr...lsfttd 69 
                                       +i+v+G G  Gl +a  l  +gh+v++ D   +   +++ g  p      + ++++++++++ +e +    l     
  gi|242399492|ref|YP_002994917.1| 197 RIAVVGGGPAGLACAYYLRTMGHDVTIFDAMPHLGGMMRYGIPPyrlpkdVLDKDIATVINTGIEVKTntaLGKDIA 273
                                       8****************************999988888888765333333566777777776654332000333444 PP

                                       HHHHHHC-SEEEE-----B-T..TTTCB-THHHHHHHHHHHHHHHCEEEEEE-S---TTHHH CS
                    UDPG_MGDP_dh_N  70 vekaveeadvifiaVgTPskk..kgkaaDlkyvesaarsiaealkkgkvvvvkSTvpvgtae 129
                                       +e+  e+ d++f+ Vg   ++    +  Dl+ v + ++ + ++   +kv   k  ++vg  +
  gi|242399492|ref|YP_002994917.1| 274 LEELREQYDAVFLGVGAWKSRkmGIEGEDLDGVIHGTEFLRKVNMGEKVELGKRVIVVGGGN 335
                                       56666777888888887665544233347777777777776666666666666666666555 PP

>> Molybdopterin  Molybdopterin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       6.9   3.4e+03      50      80 ..     793     823 ..     779     829 .. 0.82
   2 ?   10.3   0.0    0.0005      0.25     385     422 ..     923     960 ..     919     962 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 6.9
                                       BTSSCSHHHHHHHHHHHHHTT-EEE-BEECC CS
                     Molybdopterin  50 sgplmsmeslaslkkllsllggknlsfydwy 80 
                                         p + +e+++ lk+l+++ g +++s++d  
  gi|242399492|ref|YP_002994917.1| 793 LTPSLTNEEIMFLKELAERKGIPIGSTIDGE 823
                                       4567789****************99999875 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0005
                                       EEEEBE-CCGSEEEEE-TTSEEEEEEESSS-STT-BEH CS
                     Molybdopterin 385 iiLPaatwyEkedlytndegrfqhlkqavsppgeaksd 422
                                       +iLP+  w Eke+++tn++g   + k+a ++ ++ ks 
  gi|242399492|ref|YP_002994917.1| 923 LILPSGLWAEKEGTVTNAFGMDLKVKKARKAHYDVKSL 960
                                       69******************************999985 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 ?    1.5   0.0      0.88   4.4e+02       1      30 [.     197     223 ..     197     229 .. 0.90
   2 ?    6.8   0.1      0.02       9.9       2      47 ..     328     370 ..     327     460 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.88
                                       EEEEETTSHHHHHHHHHHHHTTS-GGCEEE CS
                     F420_oxidored   1 kigiiGaGnmgealasgllaagaqpheivv 30 
                                       +i+++G+G  g a a  l + g   h++++
  gi|242399492|ref|YP_002994917.1| 197 RIAVVGGGPAGLACAYYLRTMG---HDVTI 223
                                       79********************...99996 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.02
                                       EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC CS
                     F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg 47 
                                       + ++G+Gn +  +a+ +l+ g    +++v+ +r+++++ +  +e++
  gi|242399492|ref|YP_002994917.1| 328 VIVVGGGNTAMDVARTALRLG---ADVTVVYRRSKSEMPANSREVE 370
                                       5578*****************...9**9999999887766665554 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.1    0.0018      0.88       2      36 ..     198     230 ..     197     235 .. 0.90
   2 ?    0.1   0.0      0.65   3.2e+02       2      39 ..     328     363 ..     327     380 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0018
                     Lycopene_cycl   2 vvviGaGpAglslAarlteakpglkvvlieaspsl 36 
                                       ++v+G+GpAgl+ A  l    +g  v++ +a p+l
  gi|242399492|ref|YP_002994917.1| 198 IAVVGGGPAGLACAYYL--RTMGHDVTIFDAMPHL 230
                                       78***************..9999999999998865 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.65
                     Lycopene_cycl   2 vvviGaGpAglslAarlteakpglkvvlieaspsllfp 39 
                                       v+v+G+G   + +A      + g  v+++    ++ +p
  gi|242399492|ref|YP_002994917.1| 328 VIVVGGGNTAMDVARTA--LRLGADVTVVYRRSKSEMP 363
                                       89************998..6666666666443333333 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 ?    6.7   0.3     0.012         6       2      31 ..     198     227 ..     197     238 .. 0.93
   2 ?    3.8   0.1     0.097        48       2      34 ..     328     360 ..     327     396 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.012
                                       EEEE--SCCHHHHHHHHHHTT-EEEEE-S- CS
                           3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdis 31 
                                       +av+G G  G   a+ +   g++V+++d  
  gi|242399492|ref|YP_002994917.1| 198 IAVVGGGPAGLACAYYLRTMGHDVTIFDAM 227
                                       9**************************986 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.097
                                       EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHH CS
                           3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdiseea 34 
                                       v v+G G     +a  +++ g +V++v +++++
  gi|242399492|ref|YP_002994917.1| 328 VIVVGGGNTAMDVARTALRLGADVTVVYRRSKS 360
                                       88***********************99885543 PP

>> DFP  DNA / pantothenate metabolism flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.1     0.002         1      29      71 ..     334     374 ..     331     380 .. 0.85
   2 ?   -1.8   0.0       4.8   2.4e+03      38      58 ..     858     879 ..     856     908 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.002
                                       -HHHHHHHHHHHHTT-EEEEEE-S-SS---TT-EEEE--SHHH CS
                               DFP  29 GkmGyalAeaaaarGaeVtlvsgpvsletpegvevvkvesaee 71 
                                       G +++ +A+ a++ Ga+Vt+v   ++ e p  ++  +ve+aee
  gi|242399492|ref|YP_002994917.1| 334 GNTAMDVARTALRLGADVTVVYRRSKSEMP--ANSREVEEAEE 374
                                       89999*****************99888878..56667777765 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.8
                                       HHHHTT-EEEEEE-S-.SS--- CS
                               DFP  38 aaaarGaeVtlvsgpv.sletp 58 
                                       +++++G eV ++ gp   ++ p
  gi|242399492|ref|YP_002994917.1| 858 EIVEEGYEVAIIEGPAePMDVP 879
                                       67899**********6244444 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1    0.0024       1.2       1      40 [.     199     233 ..     199     243 .. 0.82
   2 ?   -1.8   0.0       5.4   2.7e+03     143     155 ..     424     436 ..     409     436 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0024
                     NAD_binding_9   1 aivGaGprGlavlerLlarakkkspleitlfdpsep.gagr 40 
                                       a+vG+Gp+Gla++  L         +++t+fd  ++ g g+
  gi|242399492|ref|YP_002994917.1| 199 AVVGGGPAGLACAYYLRTM-----GHDVTIFDAMPHlG-GM 233
                                       89************99877.....699*****987735.44 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 5.4
                     NAD_binding_9 143 slaadaVvLAlGh 155
                                       ++++d+V+LA+G+
  gi|242399492|ref|YP_002994917.1| 424 RVKVDNVILAIGQ 436
                                       689********95 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   1.3    0.0019      0.93       1      64 [.     633     698 ..     633     699 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0019
                           Fer4_15   1 VvvDrdaCigcglCvaea.....pevfeldedglasvllddgeiaeg...evpddeeeaaqeAaraCPvdAI 64 
                                       Vv+D ++C  cg+Cv        + ++    +g+++ ++       +   +++d++   + e  + CPv+AI
  gi|242399492|ref|YP_002994917.1| 633 VVLDNNKCVLCGQCVNFTheiarEGIVDYLFRGFKTYIGP------QlgeRLEDQKGVFIGELTDICPVGAI 698
                                       89*************9872222222222222333333322......12236666666666666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (963 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      513  (0.0286129); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); 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):              36  [number of targets reported over threshold]
# CPU time: 0.88u 0.35s 00:00:01.23 Elapsed: 00:00:00.51
# Mc/sec: 5660.27
//
Query:       gi|242399493|ref|YP_002994918.1|  [L=602]
Description: NADH:ubiquinone oxidoreductase, NADH-binding subunit F [Thermococcus sibiricus MM 739]
Scores for complete 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-51  172.0   0.0    1.6e-50  170.9   0.0    1.6  1  Complex1_51K     Respiratory-chain NADH dehydrogenase 51 Kd s
      2e-30  104.7   0.0      2e-30  104.7   0.0    3.1  3  NADH_4Fe-4S      NADH-ubiquinone oxidoreductase-F iron-sulfur
    1.1e-11   44.0  14.1    2.5e-07   30.2   1.9    3.9  4  Fer4             4Fe-4S binding domain
    9.1e-09   35.1   0.7    1.7e-08   34.2   0.7    1.5  1  SLBB             SLBB domain
    8.8e-07   29.0  12.1    8.8e-07   29.0  12.1    2.7  2  Fer4_9           4Fe-4S dicluster domain
    1.4e-06   28.3  12.0    1.4e-06   28.3  12.0    2.9  2  Fer4_10          4Fe-4S dicluster domain
    4.2e-06   27.3  25.0      2e-05   25.1  14.6    3.5  4  Fer4_7           4Fe-4S dicluster domain
    6.3e-05   22.9  14.1    0.00012   22.0   2.4    4.4  4  Fer4_6           4Fe-4S binding domain
    7.1e-05   22.9  26.9      0.002   18.2   2.7    3.7  4  Fer4_21          4Fe-4S dicluster domain
    0.00025   20.9  23.0     0.0076   16.3   1.5    4.3  3  Fer4_2           4Fe-4S binding domain
    0.00035   20.5   0.0    0.00086   19.2   0.0    1.7  1  2Fe-2S_thioredx  Thioredoxin-like [2Fe-2S] ferredoxin
     0.0028   18.6  21.0     0.0053   17.7   2.3    3.5  3  Fer4_16          4Fe-4S double cluster binding domain
     0.0052   16.7   0.1     0.0092   15.9   0.1    1.3  1  Suc_Fer-like     Sucrase/ferredoxin-like
  ------ inclusion threshold ------
      0.029   14.8  16.7       0.28   11.7   2.1    3.4  3  Fer4_8           4Fe-4S dicluster domain
        2.1    9.1  23.5       0.58   10.8   4.1    3.5  3  Fer4_4           4Fe-4S binding domain
        4.7    7.3  14.7       0.76    9.8   0.6    3.3  3  zf-CXXC          CXXC zinc finger domain
        6.4    8.0  26.7       0.28   12.2   2.9    3.5  2  Fer4_3           4Fe-4S binding domain
        7.5    7.2  21.7       0.49   11.0   2.2    3.3  3  Fer4_13          4Fe-4S single cluster domain of Ferredoxin I
        8.5    7.0  19.2        2.7    8.6   2.7    3.3  4  Fer4_17          4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Complex1_51K  Respiratory-chain NADH dehydrogenase 51 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.9   0.0   1.7e-53   1.6e-50       1     151 [.     158     329 ..     158     330 .. 0.97

  Alignments for each domain:
  == domain 1  score: 170.9 bits;  conditional E-value: 1.7e-53
                      Complex1_51K   1 vkeagivGrGGagfPthvKlkakakkkk..kylivNaaEcEPgltkDrllmreepheileGlkiaaealgaekgvig 75 
                                       ++++g++GrGGagfPt++K+k+++++    ky+++Na+E++Pg ++Dr +++ +ph+++eG++i a+a+ga+kg+i+
  gi|242399493|ref|YP_002994918.1| 158 ITKSGLRGRGGAGFPTGLKWKFTRDAPGdeKYIVCNADEGDPGAFMDRNVLEGDPHRVIEGMIIGAYAIGATKGFIY 234
                                       689*********************965599*********************************************** PP

                      Complex1_51K  76 vrdekpeaiealekalaeakaagl...........ldievvklagkYpaGeekaLiesltgr.evprgkpp..advg 138
                                       vr+e+p ai++l+ al++a+++g+           ++i ++++ag++++Gee+aLi+s++g+ ++pr +pp  a++g
  gi|242399493|ref|YP_002994918.1| 235 VRAEYPLAIKRLRIALKQAREKGFlgenilgsgfsFEIVIKEGAGAFVCGEETALIASIEGKrGMPRPRPPypAQKG 311
                                       *********************************************************************9999**** PP

                      Complex1_51K 139 v.....vvnNveTlaavy 151
                                       +      +nNveT+a+v+
  gi|242399493|ref|YP_002994918.1| 312 LwgrptNINNVETWANVP 329
                                       *****************8 PP

>> NADH_4Fe-4S  NADH-ubiquinone oxidoreductase-F iron-sulfur binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.7   0.0   2.1e-33     2e-30       1      85 []     440     524 ..     440     524 .. 0.99
   2 ?   -2.4   1.8       5.7   5.4e+03      12      22 ..     544     554 ..     538     557 .. 0.82
   3 ?    2.2   1.1      0.21   1.9e+02      10      23 ..     572     585 ..     569     592 .. 0.87

  Alignments for each domain:
  == domain 1  score: 104.7 bits;  conditional E-value: 2.1e-33
                                       HHHHHHHHHHHHH--S--HHHHIIIIHHHHHHHHHTBT---HHHHHHHHHHHHHHSS--SSTHHHHHHHHHHHHHHH CS
                       NADH_4Fe-4S   1 dvarrllefyaaesCGkCtpCreGtkrllelleriaagegteedldlleelaetikgtslCalgdsaanpvlsalrk 77 
                                       dva+++l+f+ +esCGkCt Cr Gtkr+ ell++i++geg  ed+++le+la  +k++slC+lg++a+npvl++l++
  gi|242399493|ref|YP_002994918.1| 440 DVAKFFLDFTVKESCGKCTFCRLGTKRMWELLDKITKGEGALEDIEKLEKLAPLVKTGSLCGLGQTAPNPVLTTLKY 516
                                       689************************************************************************** PP

                                       HHHHHHH. CS
                       NADH_4Fe-4S  78 Freefeah 85 
                                       F++e+ ah
  gi|242399493|ref|YP_002994918.1| 517 FKDEYLAH 524
                                       *****998 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5.7
                                       HH--S--HHHH CS
                       NADH_4Fe-4S  12 aesCGkCtpCr 22 
                                        e C  Ct C 
  gi|242399493|ref|YP_002994918.1| 544 TEKCTGCTACA 554
                                       68899999996 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.21
                                       HHHH--S--HHHHI CS
                       NADH_4Fe-4S  10 yaaesCGkCtpCre 23 
                                       +++e C kC+ C e
  gi|242399493|ref|YP_002994918.1| 572 INQEACIKCGTCYE 585
                                       789*********86 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1       8.1   7.6e+03       2       9 ..     431     438 ..     430     438 .. 0.80
   2 ?   -0.8   1.4       1.7   1.6e+03       7      11 ..     456     460 ..     451     462 .. 0.60
   3 !   27.6   4.7   1.7e-09   1.6e-06       1      24 []     540     563 ..     540     563 .. 0.95
   4 !   30.2   1.9   2.6e-10   2.5e-07       3      24 .]     572     593 ..     570     593 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 8.1
                                       EEETTTSS CS
                              Fer4   2 videekCi 9  
                                       v de+ C+
  gi|242399493|ref|YP_002994918.1| 431 VMDEDTCM 438
                                       779***95 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.7
                                       TSSS- CS
                              Fer4   7 kCigC 11 
                                       kC++C
  gi|242399493|ref|YP_002994918.1| 456 KCTFC 460
                                       55555 PP

  == domain 3  score: 27.6 bits;  conditional E-value: 1.7e-09
                                       EEEETTTSSS-THHHHHSTTTEEE CS
                              Fer4   1 vvideekCigCGaCvevCPvgAIt 24 
                                       +vi++ekC+gC aC+ +CPv AI+
  gi|242399493|ref|YP_002994918.1| 540 YVIITEKCTGCTACAIMCPVKAIS 563
                                       689*******************96 PP

  == domain 4  score: 30.2 bits;  conditional E-value: 2.6e-10
                                       EETTTSSS-THHHHHSTTTEEE CS
                              Fer4   3 ideekCigCGaCvevCPvgAIt 24 
                                       i++e Ci+CG+C+evC ++AI+
  gi|242399493|ref|YP_002994918.1| 572 INQEACIKCGTCYEVCRFNAIE 593
                                       99*******************6 PP

>> SLBB  SLBB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.7   1.8e-11   1.7e-08       2      56 ..     353     401 ..     352     403 .. 0.94

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 1.8e-11
                                       EEEESSBSS-EEEEEETT-BHHHHHHTTT-SBSS.........-E.EEE-SSSSS- CS
                              SLBB   2 VtVtGeVkrPgnyevpigttlsdlieqaGGltddadlksvnLarl.avipgGpmmg 56 
                                       + ++G++k+ gn+evp+g+tl++++++ GG+t+++        +  av +gGp+ g
  gi|242399493|ref|YP_002994918.1| 353 FALSGKIKHGGNVEVPMGITLREILYEIGGGTKTGK-------KIkAVQLGGPSGG 401
                                       678*********************************.......9999******977 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.4       1.2   1.1e+03      35      42 ..     453     460 ..     427     465 .. 0.67
   2 !   29.0  12.1   9.3e-10   8.8e-07       1      51 []     546     592 ..     546     592 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.2
                            Fer4_9  35 aCigCgaC 42 
                                       +C +C  C
  gi|242399493|ref|YP_002994918.1| 453 SCGKCTFC 460
                                       34444444 PP

  == domain 2  score: 29.0 bits;  conditional E-value: 9.3e-10
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                       kCtgC+aC  +Cp +++++++++    +++    aCi+Cg+C+e+C  +ai
  gi|242399493|ref|YP_002994918.1| 546 KCTGCTACAIMCPVKAISGERGKPHLINQE----ACIKCGTCYEVCRFNAI 592
                                       7**********************9999876....6***********98876 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   2.8       1.7   1.6e+03      38      48 ..     450     460 ..     436     465 .. 0.71
   2 !   28.3  12.0   1.5e-09   1.4e-06       2      55 ..     540     587 ..     539     588 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.7
                           Fer4_10  38 vrkkvekCtgc 48 
                                       v++ ++kCt+c
  gi|242399493|ref|YP_002994918.1| 450 VKESCGKCTFC 460
                                       44556666666 PP

  == domain 2  score: 28.3 bits;  conditional E-value: 1.5e-09
                           Fer4_10   2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaC 55 
                                        vi +++C++C++C  +CP+      +    +++++  ++ e+C++cg C+e+C
  gi|242399493|ref|YP_002994918.1| 540 YVIITEKCTGCTACAIMCPV------KAISGERGKPHLINQEACIKCGTCYEVC 587
                                       57889***************......6666777788888*************** PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.2      0.53     5e+02       2       8 ..     454     460 ..     411     465 .. 0.70
   2 !   14.2   5.9   5.3e-05      0.05      30      52 .]     539     561 ..     517     561 .. 0.84
   3 !   25.1  14.6   2.1e-08     2e-05       1      52 []     546     591 ..     546     591 .. 0.88
   4 !   16.3   2.6   1.2e-05     0.011       1      24 [.     576     599 ..     576     602 .] 0.88

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.53
                            Fer4_7   2 CigCgaC 8  
                                       C +C +C
  gi|242399493|ref|YP_002994918.1| 454 CGKCTFC 460
                                       4444444 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 5.3e-05
                            Fer4_7  30 kveidpekClgCgaCvavCPtga 52 
                                       k++i  ekC+gC+aC+  CP++a
  gi|242399493|ref|YP_002994918.1| 539 KYVIITEKCTGCTACAIMCPVKA 561
                                       67788999999999999999986 PP

  == domain 3  score: 25.1 bits;  conditional E-value: 2.1e-08
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                       +C+gC aC+ +Cpvkai+ +      g +   i++e C+ Cg C +vC ++a
  gi|242399493|ref|YP_002994918.1| 546 KCTGCTACAIMCPVKAISGER-----G-KPHLINQEACIKCGTCYEVCRFNA 591
                                       7*****************955.....3.235689**************9987 PP

  == domain 4  score: 16.3 bits;  conditional E-value: 1.2e-05
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeen 24 
                                       +Ci+Cg C ++C  +aie++++++
  gi|242399493|ref|YP_002994918.1| 576 ACIKCGTCYEVCRFNAIEITDAKK 599
                                       5*****************998754 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.8       3.4   3.2e+03      10      17 ..      43      51 ..      43      52 .. 0.83
   2 ?    1.9   1.4      0.29   2.7e+02       2      16 ..     430     458 ..     429     460 .. 0.79
   3 !   14.8   4.1   2.3e-05     0.022       4      24 .]     542     562 ..     541     562 .. 0.92
   4 !   22.0   2.4   1.3e-07   0.00012       4      24 .]     572     592 ..     571     592 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 3.4
                            Fer4_6 10 igC.gdCvr 17
                                      +gC g C+r
  gi|242399493|ref|YP_002994918.1| 43 VGCvGMCYR 51
                                      589999997 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.29
                            Fer4_6   2 veidpdkCi..............gCgdCv 16 
                                       v+ d+d C               +Cg+C+
  gi|242399493|ref|YP_002994918.1| 430 VVMDEDTCMvdvakffldftvkeSCGKCT 458
                                       78899999668888888888777899996 PP

  == domain 3  score: 14.8 bits;  conditional E-value: 2.3e-05
                            Fer4_6   4 idpdkCigCgdCvrvCPegai 24 
                                       i  +kC+gC +C++ CP +ai
  gi|242399493|ref|YP_002994918.1| 542 IITEKCTGCTACAIMCPVKAI 562
                                       7789**************998 PP

  == domain 4  score: 22.0 bits;  conditional E-value: 1.3e-07
                            Fer4_6   4 idpdkCigCgdCvrvCPegai 24 
                                       i++++Ci Cg C+ vC ++ai
  gi|242399493|ref|YP_002994918.1| 572 INQEACIKCGTCYEVCRFNAI 592
                                       89***************9998 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1       9.3   8.8e+03      21      44 ..      22      45 ..       9      52 .. 0.53
   2 ?    0.2   0.4       0.9   8.5e+02      37      47 ..     450     460 ..     429     464 .. 0.72
   3 !   17.1   6.0   4.6e-06    0.0044      35      57 ..     541     562 ..     525     563 .. 0.84
   4 !   18.2   2.7   2.1e-06     0.002       3      31 ..     572     597 ..     570     601 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 9.3
                           Fer4_21 21 tshqaieidaktvlkvvedeCvGC 44
                                      ++++a++ + +++   ++ + vGC
  gi|242399493|ref|YP_002994918.1| 22 ETYEAVKEELEKRNLDIKLKIVGC 45
                                      456666555444444445555666 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.9
                           Fer4_21  37 vedeCvGCnlC 47 
                                       v+++C  C+ C
  gi|242399493|ref|YP_002994918.1| 450 VKESCGKCTFC 460
                                       45666666666 PP

  == domain 3  score: 17.1 bits;  conditional E-value: 4.6e-06
                           Fer4_21  35 kvvedeCvGCnlCssvCPvedci 57 
                                        +++++C+GC+ C+++CPv ++i
  gi|242399493|ref|YP_002994918.1| 541 VIITEKCTGCTACAIMCPV-KAI 562
                                       5679**************9.665 PP

  == domain 4  score: 18.2 bits;  conditional E-value: 2.1e-06
                           Fer4_21   3 idedkCigCgkCliaCedtshqaieidak 31 
                                       i+++ Ci+Cg C+ +C+    +aiei+++
  gi|242399493|ref|YP_002994918.1| 572 INQEACIKCGTCYEVCR---FNAIEITDA 597
                                       99***************...677766544 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   3.5       1.1     1e+03      12      20 ..     453     460 ..     428     461 .. 0.64
   2 !   13.9   3.0   4.5e-05     0.042       3      21 ..     540     558 ..     539     559 .. 0.90
   3 !   16.3   1.5   8.1e-06    0.0076       4      20 ..     571     587 ..     568     589 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.1
                            Fer4_2  12 gCgaCvsaC 20 
                                       +Cg+C + C
  gi|242399493|ref|YP_002994918.1| 453 SCGKC-TFC 460
                                       39999.666 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 4.5e-05
                            Fer4_2   3 vvvdtdrCigCgaCvsaCP 21 
                                       +v+ t++C+gC aC   CP
  gi|242399493|ref|YP_002994918.1| 540 YVIITEKCTGCTACAIMCP 558
                                       7899**********999*9 PP

  == domain 3  score: 16.3 bits;  conditional E-value: 8.1e-06
                            Fer4_2   4 vvdtdrCigCgaCvsaC 20 
                                        ++ ++Ci Cg+C+ +C
  gi|242399493|ref|YP_002994918.1| 571 LINQEACIKCGTCYEVC 587
                                       689************** PP

>> 2Fe-2S_thioredx  Thioredoxin-like [2Fe-2S] ferredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   9.1e-07   0.00086      70     143 ..       9      80 ..       4      82 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 9.1e-07
                                       EE-SHHHHTTTHHHHHHHHHHHHT--TT-B-TTSSEEEEEES--S-GGGSSEEEESSS....SEEES-HHHHHHHHH CS
                   2Fe-2S_thioredx  70 vCtttpCalrgseeilealekklgikagettadgkftleeveClGaCanaPvvqinde....vyedltpekveeile 142
                                       v ++ +  ++g++e +ea++++l+      +++  ++l+ v C+G+C + P + i  +    +y+++tp++v +i+e
  gi|242399493|ref|YP_002994918.1|   9 VGMNSCGIAAGARETYEAVKEELE------KRNLDIKLKIVGCVGMCYREPLLDIITDneiiTYGHVTPDRVPRIIE 79 
                                       556666677899999999999985......5678899****************9944223459*************9 PP

                                       H CS
                   2Fe-2S_thioredx 143 k 143
                                       +
  gi|242399493|ref|YP_002994918.1|  80 E 80 
                                       7 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   1.7       8.3   7.8e+03       2       8 ..     454     460 ..     451     462 .. 0.69
   2 !   17.7   2.3   5.7e-06    0.0053       1      20 [.     546     565 ..     546     575 .. 0.88
   3 !   12.5   2.2   0.00023      0.22       2      20 ..     577     595 ..     576     601 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 8.3
                           Fer4_16   2 CgtCgkC 8  
                                       Cg+C+ C
  gi|242399493|ref|YP_002994918.1| 454 CGKCTFC 460
                                       6666666 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 5.7e-06
                           Fer4_16   1 rCgtCgkCaevCPtnaikek 20 
                                       +C++C++Ca +CP++ai+++
  gi|242399493|ref|YP_002994918.1| 546 KCTGCTACAIMCPVKAISGE 565
                                       5****************988 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 0.00023
                           Fer4_16   2 CgtCgkCaevCPtnaikek 20 
                                       C++Cg C evC  nai+ +
  gi|242399493|ref|YP_002994918.1| 577 CIKCGTCYEVCRFNAIEIT 595
                                       ****************865 PP

>> Suc_Fer-like  Sucrase/ferredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   9.7e-06    0.0092     160     191 ..      54      90 ..      41      95 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 9.7e-06
                      Suc_Fer-like 160 k.....agqgiwygrvepedvegiveetilkgkvvke 191
                                             ++++i yg+v+p+ v++i+ee++ +gk +++
  gi|242399493|ref|YP_002994918.1|  54 LldiitDNEIITYGHVTPDRVPRIIEEHVINGKPIED 90 
                                       4555556789***********************9987 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.3      0.86   8.1e+02       3      12 ..     452     461 ..     450     471 .. 0.85
   2 ?   11.7   2.1    0.0003      0.28       3      17 ..     545     559 ..     520     571 .. 0.79
   3 ?   10.6   1.5   0.00065      0.61       3      16 ..     575     588 ..     573     600 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.86
                            Fer4_8   3 ekCieCgaCq 12 
                                       e+C++C +C+
  gi|242399493|ref|YP_002994918.1| 452 ESCGKCTFCR 461
                                       5799999996 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.0003
                            Fer4_8   3 ekCieCgaCqsaCpv 17 
                                       ekC++C aC  +Cpv
  gi|242399493|ref|YP_002994918.1| 545 EKCTGCTACAIMCPV 559
                                       456666666666664 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00065
                            Fer4_8   3 ekCieCgaCqsaCp 16 
                                       e+Ci+Cg C + C 
  gi|242399493|ref|YP_002994918.1| 575 EACIKCGTCYEVCR 588
                                       78999999999995 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.9       3.2     3e+03       7      11 ..     454     458 ..     435     460 .. 0.85
   2 ?    8.9   3.8    0.0025       2.4       2      16 ..     545     559 ..     544     560 .. 0.92
   3 ?   10.8   4.1   0.00062      0.58       1      16 [.     574     589 ..     574     590 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 3.2
                            Fer4_4   7 CgsCv 11 
                                       Cg+C+
  gi|242399493|ref|YP_002994918.1| 454 CGKCT 458
                                       99997 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0025
                            Fer4_4   2 erCigCgsCvaaCPq 16 
                                       e+C+gC +C + CP+
  gi|242399493|ref|YP_002994918.1| 545 EKCTGCTACAIMCPV 559
                                       89************7 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00062
                            Fer4_4   1 qerCigCgsCvaaCPq 16 
                                       qe Ci Cg C+ +C +
  gi|242399493|ref|YP_002994918.1| 574 QEACIKCGTCYEVCRF 589
                                       799***********76 PP

>> zf-CXXC  CXXC zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.6    0.0008      0.76      18      31 ..     451     464 ..     449     469 .. 0.79
   2 ?    3.3   0.8      0.09        85      18      30 ..     544     556 ..     542     567 .. 0.76
   3 ?    2.0   1.1      0.22   2.1e+02      18      34 ..     574     590 ..     572     598 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0008
                                       --.BS-SCCCCTSC CS
                           zf-CXXC  18 tedCgkCsaCrdkk 31 
                                       +e CgkC++Cr  +
  gi|242399493|ref|YP_002994918.1| 451 KESCGKCTFCRLGT 464
                                       678*******9755 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.09
                                       --.BS-SCCCCTS CS
                           zf-CXXC  18 tedCgkCsaCrdk 30 
                                       te C  C+aC  +
  gi|242399493|ref|YP_002994918.1| 544 TEKCTGCTACAIM 556
                                       5668889998776 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.22
                                       --.BS-SCCCCTSCCCT CS
                           zf-CXXC  18 tedCgkCsaCrdkkkfg 34 
                                       +e C kC +C +  +f+
  gi|242399493|ref|YP_002994918.1| 574 QEACIKCGTCYEVCRFN 590
                                       45577777777766666 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   6.7    0.0041       3.9       1      15 []     547     561 ..     547     561 .. 0.98
   2 ?   12.2   2.9   0.00029      0.28       1      15 []     577     591 ..     577     591 .. 0.96

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0041
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       CtgC aC   CPv+A
  gi|242399493|ref|YP_002994918.1| 547 CTGCTACAIMCPVKA 561
                                       *************98 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00029
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C+ Cg+C evC+ +A
  gi|242399493|ref|YP_002994918.1| 577 CIKCGTCYEVCRFNA 591
                                       ************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 ?   -1.8   0.6       5.1   4.9e+03       4      13 ..     452     461 ..     450     464 .. 0.85
   2 ?    6.4   4.9     0.014        13       4      17 ..     545     558 ..     543     559 .. 0.93
   3 ?   11.0   2.2   0.00051      0.49       1      16 [.     572     587 ..     572     589 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 5.1
                           Fer4_13   4 dtCiacgaCv 13 
                                       ++C  c+ C+
  gi|242399493|ref|YP_002994918.1| 452 ESCGKCTFCR 461
                                       8899999997 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.014
                           Fer4_13   4 dtCiacgaCvelaP 17 
                                       ++C++c+aC+ ++P
  gi|242399493|ref|YP_002994918.1| 545 EKCTGCTACAIMCP 558
                                       89***********9 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00051
                           Fer4_13   1 VDrdtCiacgaCvela 16 
                                       ++++ Ci cg+C+e++
  gi|242399493|ref|YP_002994918.1| 572 INQEACIKCGTCYEVC 587
                                       799***********99 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.2       2.6   2.5e+03       2       8 ..     454     460 ..     451     473 .. 0.68
   2 ?    8.6   2.7    0.0029       2.7       1      20 [.     546     565 ..     546     576 .. 0.75
   3 ?    6.9   2.8      0.01       9.5      45      56 ..     576     587 ..     560     591 .. 0.71
   4 ?    6.6   3.4     0.012        11       1      17 [.     576     592 ..     576     600 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 2.6
                           Fer4_17   2 CiqCgyC 8  
                                       C +C +C
  gi|242399493|ref|YP_002994918.1| 454 CGKCTFC 460
                                       4444444 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0029
                           Fer4_17   1 rCiqCgyClpeCpsyeaydn 20 
                                       +C++C +C+ +Cp  ++ ++
  gi|242399493|ref|YP_002994918.1| 546 KCTGCTACAIMCPVKAISGE 565
                                       69999999999998776544 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.01
                           Fer4_17  45 lCieCgeCerkC 56 
                                        Ci+Cg C ++C
  gi|242399493|ref|YP_002994918.1| 576 ACIKCGTCYEVC 587
                                       566666666666 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.012
                           Fer4_17   1 rCiqCgyClpeCpsyea 17 
                                       +Ci+Cg C ++C ++++
  gi|242399493|ref|YP_002994918.1| 576 ACIKCGTCYEVCRFNAI 592
                                       59999999999987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (602 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); 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):              19  [number of targets reported over threshold]
# CPU time: 0.66u 0.29s 00:00:00.95 Elapsed: 00:00:00.50
# Mc/sec: 3647.09
//
Query:       gi|242399494|ref|YP_002994919.1|  [L=154]
Description: NADH:ubiquinone oxidoreductase, subunit E [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-53  180.3   0.0    2.1e-53  180.1   0.0    1.0  1  2Fe-2S_thioredx  Thioredoxin-like [2Fe-2S] ferredoxin


Domain annotation for each model (and alignments):
>> 2Fe-2S_thioredx  Thioredoxin-like [2Fe-2S] ferredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.1   0.0   1.2e-57   2.1e-53       4     145 .]       7     148 ..       5     148 .. 0.98

  Alignments for each domain:
  == domain 1  score: 180.1 bits;  conditional E-value: 1.2e-57
                                       HHTTS--GGGGHHHHHHHHHHHHSS--HHHHHHHHHHHTS-HHHHHHHHTTSSSS-SS---SEEEEEE-SHHHHTTT CS
                   2Fe-2S_thioredx   4 iiakypekrsaliplLklvQeeegwlpeealeevaellgvppaevyevatFYsmfnlkpvgkyviqvCtttpCalrg 80 
                                       +i +y+ + s+liplL+++Qe++g+lp+ealee++++l+vp ++vy+vatFY++f+ +p gkyvi++C++t+C+++g
  gi|242399494|ref|YP_002994919.1|   7 YIYHYEPNPSSLIPLLQKTQETFGYLPKEALEEISRYLKVPLSRVYGVATFYAQFRFEPLGKYVIKICHGTACHVNG 83 
                                       67789999********************************************************************* PP

                                       HHHHHHHHHHHHT--TT-B-TTSSEEEEEES--S-GGGSSEEEESSSSEEES-HHHHHHHHHHHH CS
                   2Fe-2S_thioredx  81 seeilealekklgikagettadgkftleeveClGaCanaPvvqindevyedltpekveeileklk 145
                                       + +i +a+++++gi++g+tt dg +tle+v ClG+C+ aPv++in++vy++ltp+kv++i+++lk
  gi|242399494|ref|YP_002994919.1|  84 AVNISQAIREEVGIEEGQTTVDGLITLERVACLGCCSLAPVIMINEKVYGKLTPDKVRKIIRNLK 148
                                       *************************************************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); 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 0.29s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 986.48
//
Query:       gi|242399495|ref|YP_002994920.1|  [L=337]
Description: NiFe hydrogenase II, subunit beta [Thermococcus sibiricus MM 739]
Scores for complete 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-24   85.0  14.2    4.8e-24   85.0  14.2    1.6  1  Fer4_22   4Fe-4S dicluster domain
    2.6e-05   24.3  16.2    0.00099   19.2   0.2    2.7  2  Fer4_10   4Fe-4S dicluster domain
    0.00026   20.9  10.5     0.0047   17.0   1.9    3.2  2  Fer4_2    4Fe-4S binding domain
    0.00031   20.8  15.7      0.099   12.8  16.4    2.8  2  Fer4_9    4Fe-4S dicluster domain
    0.00038   20.9  13.8     0.0035   17.7  14.4    2.2  2  Fer4_8    4Fe-4S dicluster domain
    0.00052   20.5  17.0      0.033   14.8   2.7    2.8  3  Fer4_7    4Fe-4S dicluster domain
      0.009   16.9  17.6      0.089   13.7   2.1    2.8  2  Fer4_16   4Fe-4S double cluster binding domain
  ------ inclusion threshold ------
      0.019   14.7   3.4      0.019   14.7   3.4    3.2  3  Fer4      4Fe-4S binding domain
      0.035   14.2  18.2       0.34   11.1   1.9    2.6  2  Fer4_21   4Fe-4S dicluster domain
       0.15   12.2  21.6      0.098   12.8   4.5    3.4  3  Fer4_6    4Fe-4S binding domain
       0.21   12.2  20.4        4.1    8.0  20.7    2.4  2  Fer4_17   4Fe-4S dicluster domain
        1.4   10.0  22.8        2.8    9.1   3.5    3.6  3  Fer4_3    4Fe-4S binding domain
        1.5    9.5  19.8       0.25   11.9   2.3    3.1  2  Fer4_4    4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.0  14.2   3.5e-27   4.8e-24       2      96 .]     232     323 ..     231     323 .. 0.92

  Alignments for each domain:
  == domain 1  score: 85.0 bits;  conditional E-value: 3.5e-27
                           Fer4_22   2 ClsCgaCtlvCptCsCfdvedetkeeskegervrvwdsClleeftkvaggenvrkekkerlrqrllhklsefkekfg 78 
                                       Cl+Cg+C++vCptC C++v d    ++ e+ rvr++dsC++e++  vagg+n+r+++ +r+r+r++ k   + +  +
  gi|242399495|ref|YP_002994920.1| 232 CLGCGNCNMVCPTCRCYEVCDLWV-NAYEAVRVRRYDSCFMETHGLVAGGHNFRATRLDRFRHRYYCKN--YFDPES 305
                                       ***********************4.57899*************************************94..344455 PP

                           Fer4_22  79 esgCvGCgRCieacpvki 96 
                                          CvGCgRC+e cp+ki
  gi|242399495|ref|YP_002994920.1| 306 GFNCVGCGRCDEFCPAKI 323
                                       678************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 !    7.3  10.6    0.0036         5       6      23 ..     229     246 ..     225     274 .. 0.74
   2 !   19.2   0.2   7.2e-07   0.00099       8      29 ..     308     329 ..     301     336 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0036
                           Fer4_10   6 ddtCirCgkCvkaCPadl 23 
                                       +  C++Cg+C+ +CP++ 
  gi|242399495|ref|YP_002994920.1| 229 ERICLGCGNCNMVCPTCR 246
                                       578************965 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 7.2e-07
                           Fer4_10   8 tCirCgkCvkaCPadltsvgak 29 
                                        C++Cg+C ++CPa++++v++ 
  gi|242399495|ref|YP_002994920.1| 308 NCVGCGRCDEFCPAKIEHVKVL 329
                                       6*************88777654 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   1.9   3.4e-06    0.0047       7      22 .]     229     244 ..     222     244 .. 0.83
   2 !   16.5   1.7   4.8e-06    0.0066       4      22 .]     300     321 ..     298     321 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.4e-06
                            Fer4_2   7 tdrCigCgaCvsaCPa 22 
                                       +++C+gCg C  +CP+
  gi|242399495|ref|YP_002994920.1| 229 ERICLGCGNCNMVCPT 244
                                       679************7 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 4.8e-06
                            Fer4_2   4 vvdtd...rCigCgaCvsaCPa 22 
                                       ++d++   +C+gCg C   CPa
  gi|242399495|ref|YP_002994920.1| 300 YFDPEsgfNCVGCGRCDEFCPA 321
                                       577788889************8 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   3.7    0.0011       1.5      35      48 ..     231     244 ..     189     246 .. 0.74
   2 !   12.8  16.4   7.2e-05     0.099       2      49 ..     232     322 ..     231     324 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0011
                            Fer4_9  35 aCigCgaCveaCpk 48 
                                        C+gCg C  +Cp+
  gi|242399495|ref|YP_002994920.1| 231 ICLGCGNCNMVCPT 244
                                       46666666666664 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 7.2e-05
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraase...........................................ea 35 
                                       C gCg+C  +Cp++ + e +    ++++a +                                             +
  gi|242399495|ref|YP_002994920.1| 232 CLGCGNCNMVCPTCRCYEVCDLWVNAYEAVRVrrydscfmethglvagghnfratrldrfrhryycknyfdpesgFN 308
                                       99999999999888887777766666666655666778888999999999999999999****************99 PP

                            Fer4_9  36 CigCgaCveaCpkg 49 
                                       C+gCg+C e Cp +
  gi|242399495|ref|YP_002994920.1| 309 CVGCGRCDEFCPAK 322
                                       ************87 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   3.1   0.00057      0.78      45      63 ..     226     244 ..     183     246 .. 0.62
   2 !   17.7  14.4   2.6e-06    0.0035       5      65 .]     232     323 ..     229     323 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00057
                            Fer4_8  45 eealwsCttcgaCtevCpv 63 
                                       +++   C++cg+C+ vCp+
  gi|242399495|ref|YP_002994920.1| 226 KKYERICLGCGNCNMVCPT 244
                                       5556668888888888885 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 2.6e-06
                            Fer4_8   5 CieCgaCqsaCpvlrr.......................tkkhlldargeaaedvqeeqvlee............ee 46 
                                       C +Cg C+  Cp++r+                       +  h l a g +   + + +                 e
  gi|242399495|ref|YP_002994920.1| 232 CLGCGNCNMVCPTCRCyevcdlwvnayeavrvrrydscfMETHGLVAGGHNFR-ATRLD---RfrhryycknyfdPE 304
                                       ************88886666666666665555555555322222222222222.22222...033356666777789 PP

                            Fer4_8  47 alwsCttcgaCtevCpvgi 65 
                                       + ++C++cg+C+e Cp +i
  gi|242399495|ref|YP_002994920.1| 305 SGFNCVGCGRCDEFCPAKI 323
                                       99**************997 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   2.7   2.4e-05     0.033      30      50 ..     224     244 ..     187     245 .. 0.74
   2 !   10.7  18.8   0.00044       0.6       2      51 ..     232     322 ..     231     323 .. 0.54
   3 !   12.1   3.3   0.00016      0.22       2      16 ..     309     323 ..     308     333 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.4e-05
                            Fer4_7  30 kveidpekClgCgaCvavCPt 50 
                                        ++  ++ ClgCg+C  vCPt
  gi|242399495|ref|YP_002994920.1| 224 VWKKYERICLGCGNCNMVCPT 244
                                       55666677***********97 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00044
                            Fer4_7   2 CigCgaCvaaC..................................pvkaieldeeenekgtekv............. 31 
                                       C gCg+C  +C                                                    +             
  gi|242399495|ref|YP_002994920.1| 232 CLGCGNCNMVCptcrcyevcdlwvnayeavrvrrydscfmethglV-----------------Agghnfratrldrf 291
                                       ***********44444444444444333333333333333333220.................02333333333333 PP

                            Fer4_7  32 ........eidpe...kClgCgaCvavCPtg 51 
                                               ++dpe   +C+gCg+C + CP++
  gi|242399495|ref|YP_002994920.1| 292 rhryycknYFDPEsgfNCVGCGRCDEFCPAK 322
                                       44444555999985566************86 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 0.00016
                            Fer4_7   2 CigCgaCvaaCpvka 16 
                                       C+gCg+C + Cp+k 
  gi|242399495|ref|YP_002994920.1| 309 CVGCGRCDEFCPAKI 323
                                       999999999999775 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   2.1   6.5e-05     0.089      42      65 ..     219     243 ..     184     245 .. 0.70
   2 !    7.0   8.9    0.0082        11      38      66 ..     293     321 ..     244     322 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.5e-05
                           Fer4_16  42 aedeekckkqeai.tgCdiCqdvCP 65 
                                       a d+   kk+e+i  gC++C++vCP
  gi|242399495|ref|YP_002994920.1| 219 AFDSPVWKKYERIcLGCGNCNMVCP 243
                                       445544454444449*********9 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0082
                           Fer4_16  38 kkdlaedeekckkqeaitgCdiCqdvCPa 66 
                                       ++ + ++++  +++ ++ gC++C + CPa
  gi|242399495|ref|YP_002994920.1| 293 HRYYCKNYFDPESGFNCVGCGRCDEFCPA 321
                                       45556677778888999999999999997 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   3.4   1.4e-05     0.019       7      20 ..     231     244 ..     226     244 .. 0.89
   2 ?   -2.5   2.9       3.8   5.2e+03      13      18 ..     246     251 ..     245     252 .. 0.90
   3 ?   12.6   5.2   6.5e-05     0.089       8      20 ..     309     321 ..     308     323 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.4e-05
                                       TSSS-THHHHHSTT CS
                              Fer4   7 kCigCGaCvevCPv 20 
                                        C gCG+C +vCP+
  gi|242399495|ref|YP_002994920.1| 231 ICLGCGNCNMVCPT 244
                                       6************7 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.8
                                       HHHHHS CS
                              Fer4  13 aCvevC 18 
                                       +C+evC
  gi|242399495|ref|YP_002994920.1| 246 RCYEVC 251
                                       6***** PP

  == domain 3  score: 12.6 bits;  conditional E-value: 6.5e-05
                                       SSS-THHHHHSTT CS
                              Fer4   8 CigCGaCvevCPv 20 
                                       C+gCG+C e CP 
  gi|242399495|ref|YP_002994920.1| 309 CVGCGRCDEFCPA 321
                                       ************7 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   7.2   0.00083       1.2      34      56 ..     225     247 ..     213     250 .. 0.82
   2 ?   11.1   1.9   0.00025      0.34      40      53 ..     308     321 ..     296     327 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00083
                           Fer4_21  34 lkvvedeCvGCnlCssvCPvedc 56 
                                       +k  e  C GC  C  vCP+  c
  gi|242399495|ref|YP_002994920.1| 225 WKKYERICLGCGNCNMVCPTCRC 247
                                       4566788************9877 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00025
                           Fer4_21  40 eCvGCnlCssvCPv 53 
                                       +CvGC  C + CP 
  gi|242399495|ref|YP_002994920.1| 308 NCVGCGRCDEFCPA 321
                                       79999999999995 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   4.5   7.1e-05     0.098       8      21 ..     231     244 ..     229     244 .. 0.92
   2 ?    0.7   0.2      0.48   6.6e+02      14      19 ..     246     251 ..     246     258 .. 0.86
   3 ?    7.0   4.2    0.0049       6.7       8      22 ..     308     322 ..     308     324 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.1e-05
                            Fer4_6   8 kCigCgdCvrvCPe 21 
                                        C+gCg+C +vCP+
  gi|242399495|ref|YP_002994920.1| 231 ICLGCGNCNMVCPT 244
                                       6************7 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.48
                            Fer4_6  14 dCvrvC 19 
                                       +C+ vC
  gi|242399495|ref|YP_002994920.1| 246 RCYEVC 251
                                       7***** PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0049
                            Fer4_6   8 kCigCgdCvrvCPeg 22 
                                       +C+gCg+C   CP++
  gi|242399495|ref|YP_002994920.1| 308 NCVGCGRCDEFCPAK 322
                                       6*******9999985 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   5.2     0.003       4.1      44      57 ..     230     243 ..     200     245 .. 0.86
   2 ?    8.0  20.7     0.003       4.1       2      60 ..     232     323 ..     231     324 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.003
                           Fer4_17  44 slCieCgeCerkCP 57 
                                         C++Cg+C+++CP
  gi|242399495|ref|YP_002994920.1| 230 RICLGCGNCNMVCP 243
                                       569**********9 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.003
                           Fer4_17   2 CiqCgyClpeCpsyeaydn.......epkkllraakl....................glleeaeke........... 40 
                                       C +Cg C  +Cp++++y+        +++  +r++ +                            +           
  gi|242399495|ref|YP_002994920.1| 232 CLGCGNCNMVCPTCRCYEVcdlwvnaYEAVRVRRYDScfmethglvagghnfratrlD-------Rfrhryycknyf 301
                                       ****************777333333234444444444777888777777555553331.......023334555567 PP

                           Fer4_17  41 ..ekaslCieCgeCerkCPqgl 60 
                                         e   +C++Cg+C++ CP+++
  gi|242399495|ref|YP_002994920.1| 302 dpESGFNCVGCGRCDEFCPAKI 323
                                       76799**************987 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   5.2    0.0039       5.4       1      13 [.     232     244 ..     232     245 .. 0.95
   2 ?    1.7   1.3      0.45   6.2e+02       4      11 ..     245     251 ..     244     257 .. 0.82
   3 ?    9.1   3.5     0.002       2.8       1      13 [.     309     321 ..     309     323 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0039
                            Fer4_3   1 CtgCgaCvevCPv 13 
                                       C+gCg C  vCP+
  gi|242399495|ref|YP_002994920.1| 232 CLGCGNCNMVCPT 244
                                       ************6 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.45
                            Fer4_3   4 CgaCvevC 11 
                                       C +C evC
  gi|242399495|ref|YP_002994920.1| 245 C-RCYEVC 251
                                       8.5***** PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.002
                            Fer4_3   1 CtgCgaCvevCPv 13 
                                       C+gCg+C e CP 
  gi|242399495|ref|YP_002994920.1| 309 CVGCGRCDEFCPA 321
                                       ************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 ?    1.4   9.8      0.43   5.9e+02       4      16 ..     232     244 ..     226     252 .. 0.89
   2 ?   11.9   2.3   0.00018      0.25       3      16 ..     308     321 ..     304     326 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.43
                            Fer4_4   4 CigCgsCvaaCPq 16 
                                       C+gCg C  +CP+
  gi|242399495|ref|YP_002994920.1| 232 CLGCGNCNMVCPT 244
                                       ************6 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00018
                            Fer4_4   3 rCigCgsCvaaCPq 16 
                                       +C+gCg+C  +CP 
  gi|242399495|ref|YP_002994920.1| 308 NCVGCGRCDEFCPA 321
                                       6************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       921  (0.0513693); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.49
# Mc/sec: 2054.30
//
Query:       gi|242399496|ref|YP_002994921.1|  [L=288]
Description: NiFe hydrogenase II, subunit gamma [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.9e-14   50.9   2.1    3.2e-13   49.2   2.1    1.9  1  DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydr
    2.1e-13   50.8   0.0    3.8e-13   50.0   0.0    1.4  1  NAD_binding_1    Oxidoreductase NAD-binding domain
    2.7e-09   37.3   0.0    4.6e-09   36.5   0.0    1.4  1  FAD_binding_6    Oxidoreductase FAD-binding domain
  ------ inclusion threshold ------
      0.015   15.4   0.0      0.033   14.3   0.0    1.6  1  FAD_binding_8    FAD-binding domain
       0.15   12.1   0.0       0.37   10.8   0.0    1.6  1  tRNA_anti-codon  OB-fold nucleic acid 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 !   49.2   2.1   8.9e-17   3.2e-13       1      39 [.     245     279 ..     245     281 .. 0.93

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 8.9e-17
                                       ----SSSSSSS-TTEEEETTCTT.CEEETTTT-CEEECC CS
                   DHODB_Fe-S_bind   1 eerMaCGvGaClgCvvktkggdggeykrvCkdGPvFdad 39 
                                       e+rM CGvG C++C v t+++     k+vCkdGPvF+++
  gi|242399496|ref|YP_002994921.1| 245 ERRMRCGVGKCGHCIVGTSTS----IKYVCKDGPVFTYW 279
                                       89****************875....9**********986 PP

>> NAD_binding_1  Oxidoreductase NAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.0   0.0   1.1e-16   3.8e-13       1     107 [.     113     226 ..     113     228 .. 0.80

  Alignments for each domain:
  == domain 1  score: 50.0 bits;  conditional E-value: 1.1e-16
                                       EEEEGGGGHHHHHHHHHHHHHCTTCSEEEEEEEESSGCGSTTHHHHHHHHHHCTT.EEEEEEE.........ESSCT CS
                     NAD_binding_1   1 miagGtGiaPvrsvlraileeakdktkvvlvyGnrteedllyreeleelakklpg.rlkvvav.........vsree 67 
                                       ++agG G+aP+rsvl+ +l+   +  +++l+yG++  ed+l+ree+  l k  ++ +++v  +           ++ 
  gi|242399496|ref|YP_002994921.1| 113 LVAGGLGMAPLRSVLWYALDT-GKYENIYLFYGTKAYEDILFREEVIHLLKHGEDmKCHVKLAyevespsciYLEKG 188
                                       79******************8.888************************9999999998887765555444433444 PP

                                       TTSSSEESSHHHHHHHHHHHHSSTTEEEEEECSHHHHHHH CS
                     NAD_binding_1  68 agweggkgrvqdalleellslkkeethvyvCGppgMikav 107
                                        +++  kg v+d ++ e  +   e+t +++CGpp M k+v
  gi|242399496|ref|YP_002994921.1| 189 YSPRVCKGVVTDLFRGENFD--VENTYALICGPPVMYKFV 226
                                       44445555555555555555..9*************9987 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 !   36.5   0.0   1.3e-12   4.6e-09       5      96 ..      11      99 ..       7     101 .. 0.84

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 1.3e-12
                                      EEEEECCTTEEEEEEEE..STTTS-----TT-EEEEEECETTCCEEEEEE.BSSTTECCEEEEEEE--TT-HHHHHHHC CS
                     FAD_binding_6  5 tekeevsedtrifrfkl..psekqklglpvGqhvflrlkikgeaviRsYtpissenekGelellvkvypgGkmsqaLde 81
                                       e++e+++  + f++++  p+ + ++++ +Gq+v+++++  ge    + +++s+++ +G+++l v+++  G+m+++++e
  gi|242399496|ref|YP_002994921.1| 11 LEVKELTPREKLFTLRFvdPEINRNFKYKPGQFVIVDIRGFGE---FPISLCSTPTREGYFQLCVRRV--GRMTKYMQE 84
                                      56666666666666655115567899*************8888...688999**************98..********* PP

                                      S-TT-EEEEEEEE-S CS
                     FAD_binding_6 82 lkigdtleikGPlGk 96
                                      lk gd + i+GP+G+
  gi|242399496|ref|YP_002994921.1| 85 LKEGDIVGIRGPYGN 99
                                      *************97 PP

>> FAD_binding_8  FAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   9.2e-06     0.033      24      80 ..      32      84 ..       7     100 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 9.2e-06
                     FAD_binding_8 24 pkkslkykaGqyvyinipslsklfwqsHPFtiasape.ddklslvikvksgltkklak 80
                                       ++ +kyk+Gq+v + i+   ++     P ++ s+p  + + +l+++  + +tk +++
  gi|242399496|ref|YP_002994921.1| 32 INRNFKYKPGQFVIVDIRGFGEF-----PISLCSTPTrEGYFQLCVRRVGRMTKYMQE 84
                                      3456*****************99.....********9999************998875 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 ?   10.8   0.0    0.0001      0.37      27      56 ..      65      95 ..      62     100 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0001
                                      TEEEEEEEET.HHHHHHHTTS-TTSEEEEEE CS
                   tRNA_anti-codon 27 tgriqvvlfr.eeatklaenlkeGdvvrvtG 56
                                      +g +q+ + r + +tk++++lkeGd+v+++G
  gi|242399496|ref|YP_002994921.1| 65 EGYFQLCVRRvGRMTKYMQELKEGDIVGIRG 95
                                      5778888888999****************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 2309.32
//
Query:       gi|242399497|ref|YP_002994922.1|  [L=246]
Description: NiFe hydrogenase II, subunit delta [Thermococcus sibiricus MM 739]
Scores for complete 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-23   81.3   0.0    7.7e-23   80.8   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 !   80.8   0.0   4.3e-27   7.7e-23       1     131 []      13     149 ..      13     149 .. 0.84

  Alignments for each domain:
  == domain 1  score: 80.8 bits;  conditional E-value: 4.3e-27
                                       -SHHHHHHT-TTTTHHHHHHTEEEEEETTT-S--HHHHHHTHTTTSEEEEEESBE...EEEHHHHHHHHGGGSSEEE CS
                       Oxidored_q6   1 CtGcsisllaleedlldllelielryhetlladskeeeieakekeadvlvveGavtrkpkealellkelaekakavi 77 
                                       C+Gc +++l l+e+l+dlle+ e++    ++++ k      ++   d+++v+G+v  +++ +l+ll+ ++++++++i
  gi|242399497|ref|YP_002994922.1|  13 CGGCALNILFLYEKLFDLLEFYEIKE-FHMASSFK------EHDTLDIAIVTGSV--STQRDLDLLHYARNHSNYLI 80 
                                       *******************9998877.44434444......4459**********..******************** PP

                                       EESHHHHH-TGGGSTT-TEE...............-HHHHHHHC.S-E.EEE-SSS--HHHHHHHHHHH CS
                       Oxidored_q6  78 avGtCAafGGipaaannpsv...............geevgellevvpvdinipGCPphpeailetllal 131
                                       a+GtCA++G ++a  +   +                 +++++ ++v vd+ +pGCP ++++i+++l++l
  gi|242399497|ref|YP_002994922.1|  81 ALGTCATHGDVQASVEGKIRdklekvygtkanpmkALDSTPIVQHVAVDYAMPGCPYDKDEIYQVLMNL 149
                                       ************887765224567777776665542566899999********************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); 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: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1649.12
//
Query:       gi|242399498|ref|YP_002994923.1|  [L=416]
Description: NiFe hydrogenase II, catalytic subunit alpha [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-34  120.2   0.0    3.4e-18   65.8   0.0    2.6  3  NiFeSe_Hases  Nickel-dependent hydrogenase


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 !   51.2   0.0   5.2e-18   9.4e-14       2      90 ..      40     128 ..      39     144 .. 0.90
   2 ?   -0.7   0.0     0.029   5.2e+02     165     205 ..     145     182 ..     134     214 .. 0.80
   3 !   65.8   0.0   1.9e-22   3.4e-18     303     505 .]     226     412 ..     196     412 .. 0.80

  Alignments for each domain:
  == domain 1  score: 51.2 bits;  conditional E-value: 5.2e-18
                                       -HHHHTTTS-GGGHHHHHHTT-SSSTTHHHHHHHHHHHHHHT----HHHHHHHHHHHHHHHHHHHHHHHHHTTGGGT CS
                      NiFeSe_Hases   2 GlElilkgrdprdawalvqRiCGVCttvHalasvravedAlgikipknarlirnliaaalllhdhivhFYhLhalDw 78 
                                        +El+  gr   d+  l  RiC +C  +H++asv  +e+Alg+++p++ +l+r+l    +l+++h +h+Y L a D 
  gi|242399498|ref|YP_002994923.1|  40 FFELLTLGRHYWDVPDLEARICAICYLSHSVASVLGIERALGVNVPEEITLLRELGLLGELIESHALHLYLLVAPDL 116
                                       5799999*********************************************************************8 PP

                                       S-THGGGGS-HH CS
                      NiFeSe_Hases  79 vdvvsalkadpk 90 
                                          ++a++   k
  gi|242399498|ref|YP_002994923.1| 117 FGYADAIRMASK 128
                                       887777766544 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.029
                                       HHHHHHHSSSSS--.EBTTBESSGBGSBSHHHHHHHHHHHH CS
                      NiFeSe_Hases 165 kivaifggknPhpqslvvGGvtcaidllnaerlaevkslik 205
                                        i  ++gg++ h  ++  GG   +   +++e+l++++s ++
  gi|242399498|ref|YP_002994923.1| 145 YIRELLGGREIHGINIKPGGFGRY---PTIEELEQIESQCE 182
                                       567789******999*****9999...66777776666544 PP

  == domain 3  score: 65.8 bits;  conditional E-value: 1.9e-22
                                       -EB---EEE--TTSB-BSS-EEEETTB--BESHHHHHHHHHHTT-HHHHHHHHHHHHHHT-HGGGGSSHHHHHHHHH CS
                      NiFeSe_Hases 303 tepkytleeldeegkYswikaPrykgkamevGplarvlvayakgkeevkelvdkllkklglkvealfstlGRtaaRa 379
                                       ++ +y  +  +++  Ys+ k  rykg+ + vG+l rv+++    ++ +k++ ++  +kl     ++      ++a a
  gi|242399498|ref|YP_002994923.1| 226 EKFDYLEHIEEKTLPYSFAKQSRYKGNIFMVGALPRVMLKHDMLTPMAKHFYEEHKEKLASGYVSF-----NNLAQA 297
                                       445565444445669***********************9988777777777777666666555333.....4799** PP

                                       HHHHHHHHHHHHHHHHHHHHHHTTB---B--TT-SGGGS-SEEEEEEEEEETTEEEEEEEEE.ETTEEEEEEEE-HH CS
                      NiFeSe_Hases 380 leakliaellkewldelvenikkgdtetaneekldkkevpkeakGvglveapRGaLsHwiki.kdgkienYqavvPs 455
                                       +e  ++ e++ke  ++l ++  +g++  +          p+e +G+g+veapRG+L H+ +i ++g+i+  +++ P+
  gi|242399498|ref|YP_002994923.1| 298 IELLYALEKAKEVAKTLLDKGIEGENVPI---------EPQEGEGIGYVEAPRGVLVHHYRIdEKGNIAYSNIITPT 365
                                       ******************99999833322.........2578********************5567999999999** PP

                                       HHHH--S-TT----HHHHHHTT-B-SSTTS-HHHH.HHHHHT--BHHHHH- CS
                      NiFeSe_Hases 456 TWnasPrdakgqkgayEaaLigtpvadpekPleil.rtihSfDPClACavH 505
                                         n +      + + yE+a      +d++  l+ l  t+++fDPC++C+vH
  gi|242399498|ref|YP_002994923.1| 366 AFNHGIM----ELSLYEEARKRYGSSDETTFLQKLeETVRAFDPCISCSVH 412
                                       ***9975....678999999999999999999876369************* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); 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 0.26s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 3082.66
//
Query:       gi|242399499|ref|YP_002994924.1|  [L=223]
Description: hypothetical protein TSIB_1524 [Thermococcus sibiricus MM 739]
Scores for complete 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-59  200.4   0.7    3.1e-59  200.2   0.7    1.0  1  DUF257    Pyrococcus protein of unknown function, DUF257


Domain annotation for each model (and alignments):
>> DUF257  Pyrococcus protein of unknown function, DUF257
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  200.2   0.7   1.7e-63   3.1e-59       2     204 ..      10     213 ..       9     214 .. 0.97

  Alignments for each domain:
  == domain 1  score: 200.2 bits;  conditional E-value: 1.7e-63
                            DUF257   2 lletlrpGetvLiEyssssvpevllyliakyskeknvPllvdDvlDtllivlkhlkllGldvpeesikviKigGtke 78 
                                       l++++++GetvL+Ey  s++pe++ + ++ y++  ++P+++dD++D l+i+ khl+++G+d++  ++ v+K+gG+++
  gi|242399499|ref|YP_002994924.1|  10 LVDKIKFGETVLVEYYHSFIPEITTLGLLYYGRTRGLPVIIDDNFDFLYIIQKHLEFVGIDEDFGDALVVKTGGKRD 86 
                                       799************************************************************************** PP

                            DUF257  79 vgnvvkkidfdkdpsiylskykravekvsveetv.inlvlglerllllldnrrdlyklvksikkylgnknRkafyli 154
                                       vgnvv+k++f  +p iy+++y+ +++    + ++ in+vlglerl+ ++    ++y  v +i+++lgn++Rk+fyl+
  gi|242399499|ref|YP_002994924.1|  87 VGNVVAKLKFSGEPIIYMRNYEESSKATFSKVEKsINIVLGLERLFSFVSSISEFYTFVIAIQSFLGNEKRKSFYLV 163
                                       *************************9998885555****************************************** PP

                            DUF257 155 nrnllesikPellplLEeiassvieiesekealivrilKslnldivgtti 204
                                       n++++ si  ++lp+LE+ias+vie   +++  +++++K+ +l+++g++i
  gi|242399499|ref|YP_002994924.1| 164 NKEIASSIPFNPLPELERIASTVIEGVPTPTSGVFTFKKTTSLNLLGKKI 213
                                       ********999************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); 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 0.26s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1470.62
//
Query:       gi|242399500|ref|YP_002994925.1|  [L=223]
Description: hypothetical protein TSIB_1525 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.5e-51  172.7   1.6      1e-50  172.4   1.6    1.0  1  DUF257    Pyrococcus protein of unknown function, DUF257
  ------ inclusion threshold ------
       0.33   10.7   1.2       0.56   10.0   0.1    2.1  2  DUF4408   Domain of unknown function (DUF4408)


Domain annotation for each model (and alignments):
>> DUF257  Pyrococcus protein of unknown function, DUF257
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.4   1.6   1.1e-54     1e-50       2     193 ..      11     202 ..      10     211 .. 0.96

  Alignments for each domain:
  == domain 1  score: 172.4 bits;  conditional E-value: 1.1e-54
                            DUF257   2 lletlrpGetvLiEyssssvpevllyliakyskeknvPllvdDvlDtllivlkhlkllGldvpeesikviKigGtke 78 
                                        +++  +G++vLiE ++s++  ++ y+++ y++e ++ +++dD+lD+l +v+khl++ G++++  ++ viK+gG+ +
  gi|242399500|ref|YP_002994925.1|  11 VMDKTPFGDLVLIEDETSYGSVLVAYALLRYARERGMKIMIDDILDSLFLVKKHLEFFGIREDFSNAIVIKTGGKMD 87 
                                       688999*********************************************************************** PP

                            DUF257  79 vgnvvkkidfdkdpsiylskykravekvsveetvinlvlglerllllldnrrdlyklvksikkylgnknRkafylin 155
                                       vgnv++ki+ + +  iyls+y+  ++++    + in++l++erl+ +++++++ly +++ i+ +lgnk Rkafy+i+
  gi|242399500|ref|YP_002994925.1|  88 VGNVIRKIPLEPELVIYLSRYESLINEIFSIGEYINIILNPERLFAFVEKPTELYMVINFIQGFLGNKSRKAFYIID 164
                                       ****************************887888******************************************* PP

                            DUF257 156 rnllesikPellplLEeiassvieiesekealivrilK 193
                                       +n++ + k ++ p+LE ia++v  i+ e+ +  v++ K
  gi|242399500|ref|YP_002994925.1| 165 KNIASTLKFNPIPELEGIATTVAYIRGENGKGKVTFGK 202
                                       *************************9999887777776 PP

>> DUF4408  Domain of unknown function (DUF4408)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.2      0.38   3.4e+03      19      25 ..      74      80 ..      74      80 .. 0.88
   2 ?   10.0   0.1   6.2e-05      0.56       7      32 ..     132     157 ..     122     157 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.38
                           DUF4408 19 vlNlIIv 25
                                      ++N I++
  gi|242399500|ref|YP_002994925.1| 74 FSNAIVI 80
                                      79***97 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 6.2e-05
                           DUF4408   7 tvswlkPpyLFvvlNlIIvtIvaeSk 32 
                                       ++++ kP+ L+ v+N+I +++  +S+
  gi|242399500|ref|YP_002994925.1| 132 FAFVEKPTELYMVINFIQGFLGNKSR 157
                                       567779***********999988887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); 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: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1356.67
//
Query:       gi|242399501|ref|YP_002994926.1|  [L=102]
Description: hypothetical protein TSIB_1526 [Thermococcus sibiricus MM 739]
Scores for complete 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-10   38.4   0.5    1.2e-09   38.0   0.5    1.2  1  GTP_EFTU_D4  Elongation factor Tu domain 4


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 !   38.0   0.5   6.5e-14   1.2e-09       6      82 ..      25      94 ..      20      99 .. 0.88

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 6.5e-14
                                      EEEEEEEEETCCCEEEEEEEEEEEEETT-EEEETTE.EEEEEEEEEETTEEESEEETT-EEEEEEESS-TTTS--TT CS
                       GTP_EFTU_D4  6 kilpgvvfrrsdpaivGvevlgGvikpgvklikedGrevGeilqiqdkgkkleeakaGqevaisiegkivGrqikeg 82
                                      + ++++ ++  ++++vG ev++Gvi+pg+k+   +G++   i++iq+ ++++++a + ++va+ ++gk    + k g
  gi|242399501|ref|YP_002994926.1| 25 FKVEKTFKIFGKEVLVG-EVIEGVIYPGYKI---KGERAALIREIQRDRQEVDFALEYDKVALVLDGKL---NPKVG 94
                                      56788889999******.*************...99*******************************98...44444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.31s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 644.62
//
Query:       gi|242399502|ref|YP_002994927.1|  [L=281]
Description: metal-dependent hydrolase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.1e-30  104.2   0.3    8.3e-30  104.0   0.3    1.0  1  TatD_DNase    TatD related DNase
  ------ inclusion threshold ------
      0.024   14.8   0.0       0.19   12.0   0.0    2.3  2  Cas_VVA1548   Putative CRISPR-associated protein (Cas_VVA1548
      0.091   12.2   0.1       0.17   11.3   0.1    1.4  1  AP_endonuc_2  Xylose isomerase-like TIM barrel


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 !  104.0   0.3   1.4e-33   8.3e-30       1     254 [.       4     275 ..       4     276 .. 0.87

  Alignments for each domain:
  == domain 1  score: 104.0 bits;  conditional E-value: 1.4e-33
                                       EEEEE-TTSCCCTTTHHHHHHHHHHTTEEEEEEE-SSG..................GGHHHHHHHHTT.TTTEEEEE CS
                        TatD_DNase   1 iDaHcHldskefeedreeileraeeagvaavvvvgtss..................kdskavlelakkypnkvyavl 59 
                                       +D+H H+d   f+    e+++++++ag++++  v  s                    +++ v+++ ++ + k +av+
  gi|242399502|ref|YP_002994927.1|   4 FDNHFHVDP--FKGLFLEAVKQFHRAGGTHLNIVYKSAhdygfngaraedfmkamnFHIELVEKINRETSVKAFAVI 78 
                                       7********..6666****************755555568888888888888877458889**************** PP

                                       ---GGGGGC.........C.CCHHHHHHHH.HHCCCTSEEEEEEEEEET-CCCCCGHHHHHHHHHHHHHHHHHTTEE CS
                        TatD_DNase  60 GiHPnevde.........asedlleelkel.anvkhskvvaiGeiGLDyysreestkeaqeevFeeqlrlAkelklp 126
                                       G+HP+e +          a+++++++l+ + + + ++k++aiGeiG+++y ++++ + +  e++++ ++lAke +++
  gi|242399502|ref|YP_002994927.1|  79 GVHPAEFAYlaekkgveyAKNEVMKALDYAqKLCFEKKAIAIGEIGRPHYEVSKEIWNESIELMKYGMELAKEADCA 155
                                       ****888888889999987788889999998889******************************************* PP

                                       EEEEEES....-HHHHHHHHHHCGGCCSEEEETT--S-HHHHHHHHHTTEEEEE-GGGGTTTTHHHHHHH.HHS-GG CS
                        TatD_DNase 127 lviHlrk....aeedlleilkeaaeakakvvlHsfsgsaeeakkflklgyyislsglltfknakelrelv.kavpld 198
                                       +++H+++     +++l ei+k+++ ++ kvv H  s    ++++ +  g++ s+ +          ++l+ + ++ d
  gi|242399502|ref|YP_002994927.1| 156 VQLHTESfneeKFRELGEIVKKVGIKPYKVVKHY-SPPLIKVAEEV--GVFPSILAS--------KKALIeALMQGD 221
                                       *******75555559*********7777*****8.66666666666..9*****992........234446899*** PP

                                       GEEE---TTSSEECCCTTSE--GGGHHHHHHHHHHHHTS-HHHHHHHHHHHHHHHH CS
                        TatD_DNase 199 rlLiETDaPyltpkpyrgkrnepanvayvveklaelkaltleelaeitaeNakrlf 254
                                       r+L+ETD  y+++k+  g++  p++v++   +  ++  +++e+  +i+ eN k ++
  gi|242399502|ref|YP_002994927.1| 222 RFLMETD--YIDDKQRPGAVLGPKTVPKRTLAFIQQGLMSEETAHKIHVENPKNVY 275
                                       *******..9***77767*****************999**************9998 PP

>> Cas_VVA1548  Putative CRISPR-associated protein (Cas_VVA1548)
   #    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       9      59 ..      49      98 ..      45     110 .. 0.91
   2 ?   -0.6   0.0      0.26   1.6e+03      11      47 ..     173     208 ..     166     213 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.2e-05
                       Cas_VVA1548  9 avewlreqglevdevvkhldseeiekGdkViGtLPvhlaaevcekgarylh 59
                                      a +++++ +++++  v+ ++ e+  k   ViG+ P + a    +kg++y +
  gi|242399502|ref|YP_002994927.1| 49 AEDFMKAMNFHIE-LVEKINRETSVKAFAVIGVHPAEFAYLAEKKGVEYAK 98
                                      67999*******9.**************************999******86 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.26
                       Cas_VVA1548  11 ewlreqglevdevvkhldseeiekGdkViGtLPvhla 47 
                                       e +++ g++  +vvkh ++  i+  ++V G+ P  la
  gi|242399502|ref|YP_002994927.1| 173 EIVKKVGIKPYKVVKHYSPPLIKVAEEV-GVFPSILA 208
                                       6678889999999999999999888876.88887666 PP

>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   2.9e-05      0.17      61     155 ..      89     182 ..      59     186 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.9e-05
                                       TTCS.HHHHHHHHHHHHHHHHHHTBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSEEEEE--TTTT CS
                      AP_endonuc_2  61 rear.reesvdalkraielaaaLGapllvlhpGtagagpkgseeeawerlaeslneladyaekegvklalEtlagsg 136
                                        e++  e +++++ +a+++a++L  +   + +G  g+++ +  +e w+  +e ++   + a++++   a++ +++s+
  gi|242399502|ref|YP_002994927.1|  89 AEKKgVEYAKNEVMKALDYAQKLCFEKKAIAIGEIGRPHYEVSKEIWNESIELMKYGMELAKEAD--CAVQLHTESF 163
                                       334478999**************877777777777788888888999999999999999977555..5777777788 PP

                                       SSSTCHHHHHHHHHHTTTT CS
                      AP_endonuc_2 137 velgdeelarlldavdspn 155
                                       +e + +el +++++v+ + 
  gi|242399502|ref|YP_002994927.1| 164 NEEKFRELGEIVKKVGIKP 182
                                       778889********99665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); 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: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1682.93
//
Query:       gi|242399503|ref|YP_002994928.1|  [L=350]
Description: Probable RNA 3'-terminal phosphate cyclase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.7e-75  253.1   0.0    1.9e-75  252.9   0.0    1.0  1  RTC         RNA 3'-terminal phosphate cyclase
    2.8e-23   82.4   0.0    5.3e-23   81.5   0.0    1.5  1  RTC_insert  RNA 3'-terminal phosphate cyclase (RTC), insert d


Domain annotation for each model (and alignments):
>> RTC  RNA 3'-terminal phosphate cyclase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  252.9   0.0   2.1e-79   1.9e-75       1     222 []       8     332 ..       8     332 .. 0.97

  Alignments for each domain:
  == domain 1  score: 252.9 bits;  conditional E-value: 2.1e-79
                                       STTTSTHHHHHHHHHHHHH---EEEESTTTTSSS-S--HHHHHHHHHHHHHHT-EEE--STT-SEEEEE------SE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               RTC   1 lgegGgqiLRtalaLsaltgkpvrIenIRanRkkPGLraqhltavrllakitnaevegaeigsteleFkPgeikage 77 
                                       +gegGgqiLRta+aLs++tg+p++I nIRa+R++PGLr+qhl+++ +l+++++a+v+ga+ gsteleF P++++ ++
  gi|242399503|ref|YP_002994928.1|   8 YGEGGGQILRTAVALSVITGEPIKIINIRAKRSNPGLRPQHLHGILALKELSDAKVKGAKEGSTELEFYPKSTRVRH 84 
                                       69*********************************************************************999*** PP

                                       EEEEEESSEBHHHHHHHHHHHHTTSSS-EEEEEEEBSBBTTS--HHHHHHTHHHHHHHHT.-EEEEEEEE--BTTTB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               RTC  78 yevdigtAGsitlllqtllplllfakkpseltlkGgTnvsaapsvdylktvllpllkrfgvlelelelkkrGfypkG 154
                                       ++v i+tAGsi+l+lq+llp+++fa+++++ +++GgT+v ++p+vdylk+++l +l+++g +++e+e+++rG+yp+G
  gi|242399503|ref|YP_002994928.1|  85 VKVLIKTAGSISLVLQALLPAMVFAEEEVTFEITGGTDVAWSPPVDYLKHITLYALEKLG-IKVEIEIRRRGHYPRG 160
                                       ************************************************************.7*************** PP

                                       -EEEEEEEE-.-S---EB........................................................... CS
                                       xxxxxxxxxxxxxxxxxx........................................................... RF
                               RTC 155 gGevelevepskklkpie........................................................... 172
                                       gG v  +v p  + +p+                                                            
  gi|242399503|ref|YP_002994928.1| 161 GGFVIGKVYPWGTKRPLVartfdkiysfegishavrlpshvairqakaakealervypsipikiheeyyeqgkdphf 237
                                       ********776544444456689****************************************************** PP

                                       ...............................................BSS-HHHHHHHHHHHHHHT.-EEEEESS-- CS
                                       ...............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               RTC 173 ...............................................acvDehlqdqlilfmaLakgksrirvaelt 202
                                                                                       +vD++l dqli+f+++a g   i v+e+t
  gi|242399503|ref|YP_002994928.1| 238 gpgsgiviwantdvlrlggdalgergkpaeivgreaakalieqlgprHAVDKFLGDQLIPFLTFAGG--DIWVSEVT 312
                                       *****************************************************************98..7******* PP

                                       HHHHHHHHHHHHHSS-EEEE CS
                                       xxxxxxxxxxxxxxxxxxxx RF
                               RTC 203 lhtetairvieqflgvkfkv 222
                                       +h++t+++v+eqf+g  f++
  gi|242399503|ref|YP_002994928.1| 313 KHLITNVWVVEQFFGRVFEM 332
                                       ***************99985 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 !   81.5   0.0   5.9e-27   5.3e-23       4     102 ..     183     281 ..     180     282 .. 0.91

  Alignments for each domain:
  == domain 1  score: 81.5 bits;  conditional E-value: 5.9e-27
                                       ---SEEEEEEEEESS-THHHHHHHHHHHHHHTTTSS..EEEEEEE.EE-CGGC-SS-EEEEEEEEE-T.TS-EEEEE CS
                        RTC_insert   4 GrvkrirGvafaarvspsvanrmveaargvLnkllp..dvyiytdvvkegkesgkspGfgisLvaetttegvllgae 78 
                                        ++ + +G+++a+r++++va r+++aa++ L++ +p   ++i+ + +++gk+ + +pG+gi+++a t+    +lg++
  gi|242399503|ref|YP_002994928.1| 183 DKIYSFEGISHAVRLPSHVAIRQAKAAKEALERVYPsiPIKIHEEYYEQGKDPHFGPGSGIVIWANTD--VLRLGGD 257
                                       689999******************************6656666666889999***************6..5****** PP

                                       EEE-TT--HHHHHHHHHHHHHHHH CS
                        RTC_insert  79 algekgvppedvGeeaaeeLleei 102
                                       alge+g+p+e vG+eaa++L+e++
  gi|242399503|ref|YP_002994928.1| 258 ALGERGKPAEIVGREAAKALIEQL 281
                                       ********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       253  (0.0141112); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 2242.71
//
Query:       gi|242399504|ref|YP_002994929.1|  [L=392]
Description: hypothetical protein TSIB_1529 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score 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   14.2   0.1       0.11   12.9   0.1    1.7  1  DUF3662   Protein of unknown function (DUF2662)
      0.091   12.8   0.4         19    5.3   0.0    3.0  3  DUF2420   Protein of unknown function (DUF2420)


Domain annotation for each model (and alignments):
>> DUF3662  Protein of unknown function (DUF2662)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   1.2e-05      0.11      26      70 ..     264     308 ..     259     332 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.2e-05
                           DUF3662  26 pvEiakaLrremddnarvvsrgrvlaPneYtveLspeDyerlasl 70 
                                       p+E+ k+L +  ++++++++++++ +P e+t+ + ++  e+ +++
  gi|242399504|ref|YP_002994929.1| 264 PIELVKRLLKIKEKRIMRIDERKIRIPTEFTIIVETQNAEKYEKI 308
                                       99**********************************999998875 PP

>> DUF2420  Protein of unknown function (DUF2420)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0    0.0058        52      42      64 ..      36      58 ..      27      83 .. 0.89
   2 ?    5.3   0.0    0.0021        19      13      46 ..     114     146 ..     107     147 .. 0.88
   3 ?   -1.7   0.0      0.33     3e+03      60      74 ..     354     368 ..     329     379 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.0058
                           DUF2420 42 peLdltltEdnvynkdislndil 64
                                      +eL  tl Ed +y+k+i  +d++
  gi|242399504|ref|YP_002994929.1| 36 EELAKTLLEDFLYAKEIHPSDFV 58
                                      678889***************98 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0021
                           DUF2420  13 selfaalRsfleekegelvsaekElvLeipeLdl 46 
                                       ++l+a +Rs  e++ ++   +e+ ++L++ +Ldl
  gi|242399504|ref|YP_002994929.1| 114 KDLLAEIRSIKEKE-KHVKLKEEPILLDFTNLDL 146
                                       689******99998.777899999********98 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.33
                           DUF2420  60 lndilsifkiLkens 74 
                                       ++ ++++f++L+++ 
  gi|242399504|ref|YP_002994929.1| 354 VSLLVKLFQQLQAKE 368
                                       455788888888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); 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: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2490.78
//
Query:       gi|242399505|ref|YP_002994930.1|  [L=170]
Description: Metallophosphoesterase, calcineurin superfamily [Thermococcus sibiricus MM 739]
Scores for 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-32  110.5   0.0    1.1e-31  110.3   0.0    1.0  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    1.7e-10   41.7   1.3    6.5e-08   33.3   0.2    2.2  2  Metallophos    Calcineurin-like phosphoesterase
     0.0013   18.1   0.3      0.043   13.1   0.1    2.0  2  Metallophos_3  Metallophosphoesterase, calcineurin superfamil


Domain annotation for each model (and alignments):
>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.3   0.0   1.8e-35   1.1e-31       1     164 [.       1     151 [.       1     152 [. 0.88

  Alignments for each domain:
  == domain 1  score: 110.3 bits;  conditional E-value: 1.8e-35
                     Metallophos_2   1 MklaiiSDlHsnldaleavlealkevgvdaiihaGDleeeepevleellela.pvlaVrGNnDeevveedvlreaae 76 
                                       M ++i+SD+H+nl a+ +++e +++++vd++ihaGD+  ++p v +e+ +l+ p++ V+GNnD          e+++
  gi|242399505|ref|YP_002994930.1|   1 MLIGIMSDTHDNLPAISKAIEFFNSENVDLVIHAGDY--VAPFVKKEFSKLKaPLRGVFGNND---------GEKEG 66 
                                       9************************************..************9***********.........45555 PP

                     Metallophos_2  77 lgtdlp...eeaelelagekvlliHgdplgvkdalaellkeaeegsdvvvcGHtHvpevekeggvlvvnPGsvgepr 150
                                       l++ +    e  ele++g ++ ++Hg+    ++++ e++ + ++  dvv+ GHtH+ e++++g  +v+nPG+v++  
  gi|242399505|ref|YP_002994930.1|  67 LKNTVGvedEILELEVDGLRIVVLHGT----NEKIVEAFAK-SQLYDVVIRGHTHKYEIRERGRSIVLNPGEVCGYV 138
                                       5555544034456666**********9....7888888877.66668*****************************9 PP

                     Metallophos_2 151 dgdpetyaildtde 164
                                        g + ++a+ldt++
  gi|242399505|ref|YP_002994930.1| 139 SGVK-SVALLDTRK 151
                                       9998.******997 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.2   1.1e-11   6.5e-08       3      76 ..       3      68 ..       1      97 [. 0.77
   2 !    8.1   0.3   0.00059       3.5     171     204 .]      94     118 ..      74     118 .. 0.72

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 1.1e-11
                                      EEEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHHTSEEEEEC-TTS...... CS
                       Metallophos  3 ilvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrgdlekellellaalvkypipvylllGNHe...... 75
                                      i +++D+H      +l+++ k+++ +++e ++dlv++aGD+v        + + +++l +   p+  + GN +      
  gi|242399505|ref|YP_002994930.1|  3 IGIMSDTH-----DNLPAISKAIEFFNSE-NVDLVIHAGDYVAPF-----VKKEFSKLKA---PLRGVFGNNDgekegl 67
                                      889*****.....*************999.**************9.....7777888888...9999******333322 PP

                                      C CS
                       Metallophos 76 g 76
                                       
  gi|242399505|ref|YP_002994930.1| 68 K 68
                                      0 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00059
                                       SSCSSSCSCCHHHHHHHHHHTTESEEEEESSSSE CS
                       Metallophos 171 lyrgsgylfgdealedllkkygvdlvisGHtHvy 204
                                       ++         + +e + k    d+vi+GHtH+y
  gi|242399505|ref|YP_002994930.1|  94 NE---------KIVEAFAKSQLYDVVIRGHTHKY 118
                                       44.........555666666668*********97 PP

>> Metallophos_3  Metallophosphoesterase, calcineurin superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.5   0.0    0.0062        37      12      53 ..       7      47 ..       2      88 .. 0.71
   2 !   13.1   0.1   7.2e-06     0.043     197     254 ..      93     156 ..      86     159 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.0062
                                      E--TT-GGGHHHHHHHHHHH--SEEEEES-----HHHHHHHH CS
                     Metallophos_3 12 sdlkgevellerlveviedkdpDllvlvGdlvkaeakadeye 53
                                      sd +++   + + +e  +  ++Dl++  Gd v +  k +e+ 
  gi|242399505|ref|YP_002994930.1|  7 SDTHDNLPAISKAIEFFNSENVDLVIHAGDYVAPFVK-KEFS 47
                                      56666666777777788899**********9877654.4555 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 7.2e-06
                                       -S-HHHHHHHHHH--SEEEE-SS--EE.EEETTEEEEE--BGG...GT..EEEEEETTTTEEEE CS
                     Metallophos_3 197 kgsevvaelvktlnPevvvvghavkeh.eelgktlvvnPGale...eG..dfavvdleekkvel 254
                                         +++v  + k+   +vv+ gh++k +  e g+++v nPG++     G    a++d+++++v++
  gi|242399505|ref|YP_002994930.1|  93 TNEKIVEAFAKSQLYDVVIRGHTHKYEiRERGRSIVLNPGEVCgyvSGvkSVALLDTRKREVKI 156
                                       567788899999999**********999899*********974222343356778888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1236.98
//
Query:       gi|242399506|ref|YP_002994931.1|  [L=162]
Description: hypothetical protein TSIB_1531 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-05   25.9   1.9    1.4e-05   25.5   1.9    1.2  1  Sld5           GINS complex protein
  ------ inclusion threshold ------
       0.12   12.5   1.2         14    5.8   0.0    2.1  2  Kinesin_assoc  Kinesin-associated


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 !   25.5   1.9   1.5e-09   1.4e-05       3     109 .]      25     145 ..      23     145 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 1.5e-09
                                       EEHHHHHHHHHTTSCCCHHCHHHCHHHHHHCCCHHTTSSSSTTTTTTHHHHHHHHHHHHT................. CS
                              Sld5   3 LPlWlaelLkrqrrveieppewlspesleailedetkssdlpslpphflelavkllelard................ 63 
                                       L  W a++L++++ vei ++    + +l++++++e+++++   lp   +  a+ ++   ++                
  gi|242399506|ref|YP_002994931.1|  25 LEDWKAKELWESGIVEIIDESEKIISELDQVIAEERANEPIMPLPTGLYSRAEFYIYYLENyvrkkteieidvlnak 101
                                       778***********************************999999999999998766666666666777788888899 PP

                                       ...HCHHHHHHHHHHHHHHHHHHHTHCHHHHHHHTS-TCCHCCS-HHHH CS
                              Sld5  64 ...ldelkrllrdllevRlakirkfaenledaagggggellsglseeEk 109
                                          l++lk+  + l ++R +ki +  +   +++     e+l++l +eEk
  gi|242399506|ref|YP_002994931.1| 102 mtkLSNLKKKYEHLKKLRFKKILNAIMFRPGSL-----EILNRLAPEEK 145
                                       8899999999****************9999999.....********996 PP

>> Kinesin_assoc  Kinesin-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.7    0.0019        17      99     119 ..      38      58 ..      23      66 .. 0.83
   2 ?    5.8   0.0    0.0016        14      75     110 ..     112     147 ..      70     160 .. 0.65

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0019
                     Kinesin_assoc  99 aierlketekiiaelnetWee 119
                                        +e + e+ekii+el++   e
  gi|242399506|ref|YP_002994931.1|  38 IVEIIDESEKIISELDQVIAE 58 
                                       689999*********997655 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0016
                     Kinesin_assoc  75 alssraesvssleerivfspaseeaierlketekii 110
                                        ++ ++  + ++ + i+f p+s e ++rl   ek i
  gi|242399506|ref|YP_002994931.1| 112 YEHLKKLRFKKILNAIMFRPGSLEILNRLAPEEKKI 147
                                       2222334788999****************9888754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1179  (0.0657594); expected 358.6 (0.02)
Passed bias filter:                      596  (0.0332422); 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: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1133.76
//
Query:       gi|242399507|ref|YP_002994932.1|  [L=1076]
Description: Cell division control protein [Thermococcus sibiricus MM 739]
Scores for complete 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-85  286.2   0.2    8.8e-56  188.5   0.0    3.3  3  MCM              MCM P-loop domain
    6.1e-44  149.2   5.5    3.6e-26   91.7   0.3    3.2  2  Intein_splicing  Intein splicing domain
    1.1e-35  122.2   0.0    2.2e-35  121.2   0.0    1.4  1  MCM_OB           MCM OB domain
    1.2e-30  105.8   1.2    3.5e-30  104.3   1.2    1.9  1  MCM_lid          MCM AAA-lid domain
    1.7e-13   51.0   0.3      7e-13   49.1   0.3    2.1  1  MCM_N            MCM N-terminal domain
    2.2e-07   30.5   0.0    1.8e-06   27.5   0.0    2.1  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    1.1e-05   25.4   0.0    3.1e-05   23.9   0.0    1.8  1  HTH_3            Helix-turn-helix
    0.00021   21.1   0.1     0.0027   17.6   0.0    2.5  2  AAA_3            ATPase family associated with various cellul
    0.00031   20.8   0.5      0.022   14.7   0.0    3.1  3  AAA_5            AAA domain (dynein-related subfamily)
    0.00053   19.7   0.2     0.0076   16.0   0.0    2.4  2  Sigma54_activat  Sigma-54 interaction domain
    0.00083   19.4   0.4     0.0018   18.3   0.4    1.5  1  Zn-ribbon_8      Zinc ribbon domain
     0.0012   18.8   0.2      0.007   16.4   0.0    2.4  2  HTH_19           Helix-turn-helix domain
  ------ inclusion threshold ------
      0.024   15.0   0.0      0.079   13.3   0.0    1.9  1  HTH_31           Helix-turn-helix domain
      0.027   14.5   0.1      0.077   13.0   0.1    1.7  1  HypA             Hydrogenase/urease nickel incorporation, met
      0.051   13.7   0.1      0.051   13.7   0.1    3.3  2  DUF2540          Protein of unknown function (DUF2540)
      0.053   13.5   0.5        3.2    7.8   0.0    2.4  2  PhnA_Zn_Ribbon   PhnA Zinc-Ribbon
       0.14   11.9   0.1        0.5   10.1   0.1    1.9  1  DEAD             DEAD/DEAH box helicase
       0.33   10.5   2.0        4.2    7.0   0.3    2.6  2  TF_Zn_Ribbon     TFIIB zinc-binding


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 !   68.8   0.0   3.4e-22   3.4e-19       1      71 [.     265     335 ..     265     351 .. 0.97
   2 !   25.0   0.0   8.7e-09   8.7e-06      62     101 ..     580     619 ..     573     638 .. 0.81
   3 !  188.5   0.0   8.8e-59   8.8e-56      98     223 ..     757     882 ..     734     883 .. 0.97

  Alignments for each domain:
  == domain 1  score: 68.8 bits;  conditional E-value: 3.4e-22
                                       HHHHHHHHHTSSTHHHHHHHHSSTTSSS-HHHHHHHHHHHH---EBBBSSSSBBCSS-EEEEEESSTSTHH CS
                               MCM   1 eveeikelakekdiieklvksiapsiyghedvkkaillqlfggvkkkledktklrgdinvllvgdpgtaKs 71 
                                       ++++ikelak+kd+++ +v+siap+iyg+++ k +i+l+lfgg +++l+d+t+lrg+ ++llvgdpg+aK 
  gi|242399507|ref|YP_002994932.1| 265 DEQKIKELAKRKDVVDVIVESIAPAIYGMKKEKLGIALALFGGRTQQLPDGTRLRGESHILLVGDPGVAKC 335
                                       5799*****************************************************************96 PP

  == domain 2  score: 25.0 bits;  conditional E-value: 8.7e-09
                                       EEESSTSTHHHHHHHHHHHSSSEEEEESSSSSSSHSSSEE CS
                               MCM  62 lvgdpgtaKsqlLkyveklapravytsgkgssaagLtaav 101
                                       +  d  +  sqlL+yv++lapra+ytsgk+ssaagL +a 
  gi|242399507|ref|YP_002994932.1| 580 IANDIFVHNSQLLRYVSNLAPRAIYTSGKSSSAAGLCVAP 619
                                       566777889***************************8775 PP

  == domain 3  score: 188.5 bits;  conditional E-value: 8.8e-59
                                       SSEEEEESSSSSEEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEESSSCEEEEE--EEEEEEE--S CS
                               MCM  98 taavvrdeetgefvleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisiaKaGivatLnartsvlaAanpk 174
                                       taa vrde tg +vleaG lvlad Gv++iDe+dkm+++drs++hEa+Eqqt+si+KaGi+atLnart+v+aAanpk
  gi|242399507|ref|YP_002994932.1| 757 TAAAVRDELTGSWVLEAGVLVLADMGVALIDEIDKMSDRDRSSIHEALEQQTVSISKAGITATLNARTTVIAAANPK 833
                                       9**************************************************************************** PP

                                       SSSCCTTS-HHHHSSSSHHHHHHSSEEEEE-SSTTHHHHHHHHHHHHHH CS
                               MCM 175 agrydkkksvaeninlsaalLsrFDlifvllDkvdeekDeelaehivsl 223
                                       +gr+++ ks+ e+++l+++lLsrFDlifvllD++de+ D+e+aehi+++
  gi|242399507|ref|YP_002994932.1| 834 YGRFNRMKSLPEQLDLPPTLLSRFDLIFVLLDEPDEKFDSEVAEHILKV 882
                                       **********************************************986 PP

>> Intein_splicing  Intein splicing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.7   0.3   3.6e-29   3.6e-26       2     134 .]     343     588 ..     342     588 .. 0.94
   2 !   59.0   0.0   4.4e-19   4.4e-16      11     134 .]     631     756 ..     622     756 .. 0.81

  Alignments for each domain:
  == domain 1  score: 91.7 bits;  conditional E-value: 3.6e-29
                                       EECTTCEEEEHHHHCC.....................ECTTEEEEEETTTTEEEEEEEEEEEEEEEE.EEEEEEETT CS
                                       xxxxxxxxxxxxxxxx.....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                   Intein_splicing   2 iledgeekvkieelve.....................kegeevlslnledlklevksvkkliklklk.elyeikles 56 
                                       +l+dg+++ ki+++ve                       + ++ +l+  +lk+ +++ + ++k k+  +++ +k++ 
  gi|242399507|ref|YP_002994932.1| 343 LLADGSIE-KIGKIVEeaikraeengtlgkvddgfyaPINLSIFALDTRTLKVTKARANIAWKRKTPgKMFIVKTKT 418
                                       68888888.9999999999888888888888777776667788899999999999999999*999999********* PP

                                       S-EEEEETT-EEEECCTTEEEEEECCC--TT-EEEEE........................................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................................ RF
                   Intein_splicing  57 grkikaTpeHkllvvrdegivEkradeLkegdliavp........................................ 93 
                                       g++ik+Tp H+++++++++   ++a++L+++dliavp                                        
  gi|242399507|ref|YP_002994932.1| 419 GKEIKVTPTHPFFTFENGEFKTRSAKDLTAEDLIAVPrgfhhfgeeqslnsdalpslgnvlreirevlglsqfevgi 495
                                       ***************9988888******************************************************* PP

                                       ...................................................HSCEEEEEEEEEEE.EECEEEEEEEE CS
                                       ...................................................xxxxxxxxxxxxxx.xxxxxxxxxxx RF
                   Intein_splicing  94 ...................................................dadvvwdkvksiev.edeeeyVYdlt 118
                                                                                          ++d+ wd +++i+v + ++e VYdl+
  gi|242399507|ref|YP_002994932.1| 496 npstylhyerneerptrehlmkivetfervaisekideavirkiellkllaNSDIFWDGIEDIKVyTPKDEWVYDLQ 572
                                       ****************************************************************83556999***** PP

                                       ETTT-EEEECTTEEE- CS
                                       xxxxxxxxxxxxxxxx RF
                   Intein_splicing 119 vednhNFvangiivHN 134
                                       v+++hNF+an+i+vHN
  gi|242399507|ref|YP_002994932.1| 573 VPEHHNFIANDIFVHN 588
                                       ***************9 PP

  == domain 2  score: 59.0 bits;  conditional E-value: 4.4e-19
                                       EHHHHCC....ECTTEEEEEETTTTEEEEEE......EEEEEEEEEE.EEEEEEETTS-EEEEETT-EEEECCTTEE CS
                                       xxxxxxx....xxxxxxxxxxxxxxxxxxxx......xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Intein_splicing  11 kieelve....kegeevlslnledlklevks......vkkliklklk.elyeiklesgrkikaTpeHkllvvrdegi 76 
                                       +i++lve    ++ ee  s++ e+l+l vk+      v kl+klk   +l++i++++g +i++Tpe kll+    g+
  gi|242399507|ref|YP_002994932.1| 631 RIGNLVEkvipHKVEEYESVDAEKLGLAVKTqngyqkVLKLWKLKAPeKLVRITTSNGASIIVTPETKLLTP--SGW 705
                                       67888888887555555667888888888888888889*****99988************************..9** PP

                                       EEEECCC--TT-EEEEEHSCEEEEEEEEEEEEEC.EEEEEEEEETTT-EEEECTTEEE- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx RF
                   Intein_splicing  77 vEkradeLkegdliavpdadvvwdkvksievede.eeyVYdltvednhNFvangiivHN 134
                                         + a++Lk g++++v+  +      +s+e  ++  eyVYdltve+ h F+ang+ivHN
  gi|242399507|ref|YP_002994932.1| 706 --VPAEKLK-GEVLTVAGPQ-----SVSVELIQSpYEYVYDLTVENSHSFIANGFIVHN 756
                                       ..8*****8.6777766655.....2344444433789********************9 PP

>> MCM_OB  MCM OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.2   0.0   2.2e-38   2.2e-35       3     124 ..     105     229 ..     103     231 .. 0.91

  Alignments for each domain:
  == domain 1  score: 121.2 bits;  conditional E-value: 2.2e-38
                                       GG--GGGTTSEEEEEEEEEEE---EEEEEEEEEEETTT-.-EEES---.......-SB-..TTT-HHH-EEE-GGGS CS
                            MCM_OB   3 RdlrsehigklvkveGivtrasevkpklkkavfeckkcgktvevelee.......PrkCeekeCeskdpfkleteks 72 
                                       ++l sehi+kl++veGi+tr++evkp +++av+ ck+cg+++  +l++       P+kC  ++C+ +++++l+++ks
  gi|242399507|ref|YP_002994932.1| 105 KELGSEHINKLIQVEGIITRITEVKPFVSRAVYLCKDCGHEMV-RLQKpfaslikPNKC--ENCG-SRNVELDVDKS 177
                                       799************************************9655.5555444455599**..89**.79********* PP

                                       EEEEEEEEEEE-------------EEEEEEEGGGTT---TT-EEEEEEEEEE CS
                            MCM_OB  73 kfvdfqklklQEspeevpaGelPrslevileddlvdkvkPGdrvevtGiyra 124
                                       +f +fq+ +lQ++pe++  G++Pr ++vil ddlvd + PGdrv +tG++r+
  gi|242399507|ref|YP_002994932.1| 178 TFLNFQSFRLQDRPESLRGGQMPRFVDVILLDDLVDIALPGDRVIITGVLRV 229
                                       *************************************************997 PP

>> MCM_lid  MCM AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.3   1.2   3.5e-33   3.5e-30       1      84 [.     897     984 ..     897     987 .. 0.93

  Alignments for each domain:
  == domain 1  score: 104.3 bits;  conditional E-value: 3.5e-33
                                       HHHHHHHHHHHHTT--BETCHHHHHHHHHHHHHHHHH....TSSTSSSST--HHHHHHHHHHHHHHHHHHTSSSE-H CS
                           MCM_lid   1 ellrkYiayarekikPklseeakeklseaYvelRkee....edskrksipitvRqLesliRLseAlAklrlsevvte 73 
                                       +ll+kYiayar++i+P+l+ ea+e+++++Y+++Rk+     e++  k ipit+RqLe+liRLseA+A++rlsev+t+
  gi|242399507|ref|YP_002994932.1| 897 DLLKKYIAYARKNIHPTLTREAMEEIKRYYIRMRKTIgkgaENEGIKPIPITPRQLEALIRLSEAHARMRLSEVITR 973
                                       58*********************************888775444899****************************** PP

                                       HHHHHHHHHHH CS
                           MCM_lid  74 edveeairllk 84 
                                       ed++ ai+l++
  gi|242399507|ref|YP_002994932.1| 974 EDAKVAIELVE 984
                                       *********97 PP

>> MCM_N  MCM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.1   0.3   7.1e-16     7e-13       2      80 ..       8      83 ..       7     115 .. 0.90

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 7.1e-16
                             MCM_N  2 ekFedFLeefkddsededgekkYrdqlqemaer.ekttLevdlddLaafdeeLaeailenpkeylplleealkevvkkl 79
                                      e+F +FL+++    +d++g+++Y+++++++++   k+++++++++L+afd+eLae++++ p+e++ + e+a++ v+++ 
  gi|242399507|ref|YP_002994932.1|  8 ERFVKFLKDY----TDDEGNRVYLNKIRDILTVtPKRSITISWEHLNAFDPELAEELTTTPEEVISAAEDAIQIVLQEE 82
                                      79********....78899**********9965389*************************************999875 PP

                             MCM_N 80 e 80
                                      +
  gi|242399507|ref|YP_002994932.1| 83 F 83
                                      4 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.51   5.1e+02      21      37 ..     320     336 ..     317     353 .. 0.86
   2 !   27.5   0.0   1.8e-09   1.8e-06      93     158 ..     767     832 ..     736     844 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.51
                      Mg_chelatase  21 GgHnlllvGppGsGKtm 37 
                                       G+ ++llvG pG  K +
  gi|242399507|ref|YP_002994932.1| 320 GESHILLVGDPGVAKCV 336
                                       899*********99975 PP

  == domain 2  score: 27.5 bits;  conditional E-value: 1.8e-09
                      Mg_chelatase  93 ggskpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNp 158
                                       g+   + G + la  Gv ++DE+ +++ +   ++ e le+++v+is+a  +++  ar++++aa+Np
  gi|242399507|ref|YP_002994932.1| 767 GSWVLEAGVLVLADMGVALIDEIDKMSDRDRSSIHEALEQQTVSISKAGITATLNARTTVIAAANP 832
                                       455678999********************************************************9 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   3.1e-08   3.1e-05       1      49 [.     479     523 ..     479     529 .. 0.93

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 3.1e-08
                                       HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHT CS
                             HTH_3   1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLg 49 
                                       l+e+R+ lglsq     ++G+ +st+ ++E++e +P+ e l k+ +++ 
  gi|242399507|ref|YP_002994932.1| 479 LREIREVLGLSQ----FEVGINPSTYLHYERNEERPTREHLMKIVETFE 523
                                       89**********....****************999***********997 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 ?    0.2   0.0      0.62   6.2e+02       1      17 [.     323     339 ..     323     353 .. 0.80
   2 !   17.6   0.0   2.7e-06    0.0027      64     113 ..     782     833 ..     754     848 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.62
                             AAA_3   1 hvllegvPGlaktllvk 17 
                                       h+ll g PG+ak +  +
  gi|242399507|ref|YP_002994932.1| 323 HILLVGDPGVAKCVEYN 339
                                       9***********87655 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 2.7e-06
                             AAA_3  64 nllladeinrappktqsalleameerqvtve..gethklpepflvlatqnPi 113
                                        + l dei++ + + +s++ ea+e+++v+++  g t +l+   +v+a+ nP 
  gi|242399507|ref|YP_002994932.1| 782 GVALIDEIDKMSDRDRSSIHEALEQQTVSISkaGITATLNARTTVIAAANPK 833
                                       36899**********************99862256999************94 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 ?    2.4   0.0      0.14   1.4e+02       1      12 [.     323     334 ..     323     336 .. 0.93
   2 ?   -1.2   0.0       1.9   1.9e+03      76     134 ..     466     535 ..     445     538 .. 0.78
   3 !   14.7   0.0   2.3e-05     0.022      25     130 ..     749     840 ..     709     857 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.14
                                       EEEEE--SSSSH CS
                             AAA_5   1 dvlLvGppGtgK 12 
                                       ++lLvG+pG++K
  gi|242399507|ref|YP_002994932.1| 323 HILLVGDPGVAK 334
                                       79*********9 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.9
                                       G--HHHHHHHHHHHHSSEEE..-SSSEEE---..................-EEEEEESS--.-TT-TTHHH CS
                             AAA_5  76 raesevlnsLlslleerrllleeggelvkakndd.ller...........frviatanpldrslnelspal 134
                                        ++s++l+sL ++l e r  l  ++++v+ ++ + l ++           + ++ t +++   ++++++a+
  gi|242399507|ref|YP_002994932.1| 466 SLNSDALPSLGNVLREIREVLGLSQFEVGINPSTyLHYErneerptrehlMKIVETFERVA-ISEKIDEAV 535
                                       5789999*******99999999999999999988766666777787777766666666666.566666665 PP

  == domain 3  score: 14.7 bits;  conditional E-value: 2.3e-05
                                       --EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG--HHHHHHHHHHHHSSEEE..-SSS CS
                             AAA_5  25 reveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEveraesevlnsLlslleerrllleegge 101
                                       ++ ++v +t+   +++l+g++ +       + ++lv       ++++DE++++++   +s +  le++++++ + g 
  gi|242399507|ref|YP_002994932.1| 749 ANGFIVHNTAAAVRDELTGSWVL-------EAGVLV--LADMGVALIDEIDKMSDRDRSSIHEALEQQTVSISKAGI 816
                                       56788899999999999999995.......889999..77889****************************999988 PP

                                       EEE---......-EEEEEESS--.-TT-T CS
                             AAA_5 102 lvkaknddllerfrviatanpldrslnel 130
                                           ++      ++via+anp +++ n++
  gi|242399507|ref|YP_002994932.1| 817 TATLNAR-----TTVIAAANPKYGRFNRM 840
                                       8888775.....9*********9555444 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.41   4.1e+02     136     159 ..      66      89 ..      58      94 .. 0.89
   2 !   16.0   0.0   7.6e-06    0.0076      79     146 ..     766     835 ..     759     848 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.41
                                       EEEEEESS-HHHHHHTTSS-HHHH CS
                   Sigma54_activat 136 riiaatnedleeaveegkfredLy 159
                                        +i+a++  ++  ++e+ fr++L+
  gi|242399507|ref|YP_002994932.1|  66 EVISAAEDAIQIVLQEEFFRKELF 89 
                                       699*******************98 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 7.6e-06
                                       TTTSS-BEHHHHHTTTSEEEEETGGGS-HHHHHHHHHHHHHSE..EESBTSSSEEE--EEEEEEESS-HH CS
                   Sigma54_activat  79 tGAekekkGlfekadgGtlfLDeigelplelQekLlrvlqege..vervGsskeikvdvriiaatnedle 146
                                       tG+   ++G +  ad G+ ++Dei +++ +  + + ++l++++  +++ G +++ ++ + +iaa+n +  
  gi|242399507|ref|YP_002994932.1| 766 TGSWVLEAGVLVLADMGVALIDEIDKMSDRDRSSIHEALEQQTvsISKAGITATLNARTTVIAAANPKYG 835
                                       67777789*******************************999722579****************997765 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.4   1.8e-06    0.0018       6      37 ..     137     171 ..     136     172 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.8e-06
                       Zn-ribbon_8   6 YrCeeCghefevlqsis.daplta.CPeCgs.evr 37 
                                       Y C++Cghe  +lq+ +    ++  C +Cgs +v+
  gi|242399507|ref|YP_002994932.1| 137 YLCKDCGHEMVRLQKPFaSLIKPNkCENCGSrNVE 171
                                       99************99965557778******8875 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       3.1   3.1e+03      37      60 ..      81     104 ..      55     108 .. 0.64
   2 !   16.4   0.0   7.1e-06     0.007       1      53 [.     476     523 ..     476     525 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3.1
                            HTH_19  37 kdvpsaelllkiaealgidleyll 60 
                                        + +  el++  a++++++ +yl 
  gi|242399507|ref|YP_002994932.1|  81 EEFFRKELFKIHARFFELPKTYLV 104
                                       445556777778999999999996 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 7.1e-06
                            HTH_19   1 GerLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealg 53 
                                       G  L+e+Re lgl+q     ++gi++s + ++E ++   p++e l ki+e+++
  gi|242399507|ref|YP_002994932.1| 476 GNVLREIREVLGLSQ----FEVGINPSTYLHYERNEE-RPTREHLMKIVETFE 523
                                       6679**********8....668*************88.************997 PP

>> HTH_31  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   7.9e-05     0.079       2      51 ..     475     519 ..     474     524 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.9e-05
                            HTH_31   2 LGalLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavleala 51 
                                       LG  Lr+ Re  GLsq ev    g+ +st+ ++E+ ++ rp+++ l +++
  gi|242399507|ref|YP_002994932.1| 475 LGNVLREIREVLGLSQFEV----GINPSTYLHYERNEE-RPTREHLMKIV 519
                                       9*****************7....***************.8***9887665 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 ?   13.0   0.1   7.7e-05     0.077      68     100 ..     134     173 ..     114     182 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.7e-05
                                       --EEEETTTS-EEE.CHHHHH.......S-TTTSSS-EEEE CS
                              HypA  68 pvkvrCreCgkefe.leekal.......rCpkCgsadveiv 100
                                       ++++ C++Cg+e+  l++  +       +C++Cgs++ve+ 
  gi|242399507|ref|YP_002994932.1| 134 RAVYLCKDCGHEMVrLQKP-FaslikpnKCENCGSRNVELD 173
                                       67889*******9955543.13468888*********9975 PP

>> DUF2540  Protein of unknown function (DUF2540)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.2       7.5   7.5e+03      19      49 ..     518     549 ..     503     550 .. 0.68
   2 ?   13.7   0.1   5.1e-05     0.051      17      47 ..     641     671 ..     632     682 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 7.5
                                       HGGG-----H.HHHHHHHHS---EEEEEE--H CS
                           DUF2540  19 klenlenvdv.etlkkakeaekktkktltLsd 49 
                                        +e  e v++ e++ +a  ++  + k+l  sd
  gi|242399507|ref|YP_002994932.1| 518 IVETFERVAIsEKIDEAVIRKIELLKLLANSD 549
                                       36778888875788888888877777777666 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 5.1e-05
                                       HHHGGG-----HHHHHHHHHS---EEEEEE- CS
                           DUF2540  17 lHklenlenvdvetlkkakeaekktkktltL 47 
                                        Hk+e+ e+vd e+l+ a +++  ++k l+L
  gi|242399507|ref|YP_002994932.1| 641 PHKVEEYESVDAEKLGLAVKTQNGYQKVLKL 671
                                       5****************************98 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0    0.0032       3.2      15      28 ..     132     145 ..     108     147 .. 0.92
   2 ?    3.4   0.2     0.073        73       4      10 ..     161     167 ..     155     173 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0032
                    PhnA_Zn_Ribbon  15 edgallvCpeCahE 28 
                                       + +a+++C +C+hE
  gi|242399507|ref|YP_002994932.1| 132 VSRAVYLCKDCGHE 145
                                       6789*********9 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.073
                    PhnA_Zn_Ribbon   4 kCplCaS 10 
                                       kC++C+S
  gi|242399507|ref|YP_002994932.1| 161 KCENCGS 167
                                       9****99 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1    0.0005       0.5     101     171 ..     754     823 ..     736     827 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0005
                                       EEEEHHHHHHHH......HCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSEEEEEESSBS. CS
                                       xxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                              DEAD 101 vvgtpgrlddll......stgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqrqvivlSATlp. 170
                                       v  t   + d l      + g l l ++ +  +DE+d+++d ++s      +++l+q+t + +       ++ATl+ 
  gi|242399507|ref|YP_002994932.1| 754 VHNTAAAVRDELtgswvlEAGVLVLADMGVALIDEIDKMSDRDRSSI----HEALEQQTVSIS----KAGITATLNa 822
                                       555666666644466666889999*****************955554....444544445444....7899999984 PP

                                       H CS
                                       x RF
                              DEAD 171 k 171
                                       +
  gi|242399507|ref|YP_002994932.1| 823 R 823
                                       4 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1      0.13   1.3e+02      20      27 ..     137     144 ..     133     147 .. 0.77
   2 ?    7.0   0.3    0.0042       4.2       2      20 ..     161     179 ..     160     180 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.13
                                       EEESSSSB CS
                      TF_Zn_Ribbon  20 lvCtdCGl 27 
                                       ++C+dCG 
  gi|242399507|ref|YP_002994932.1| 137 YLCKDCGH 144
                                       78999996 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0042
                                       EETTTTCEECHEETSTTCE CS
                      TF_Zn_Ribbon   2 kCPnCgstnlveDpergel 20 
                                       kC nCgs+n+++D +  ++
  gi|242399507|ref|YP_002994932.1| 161 KCENCGSRNVELDVDKSTF 179
                                       8************887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1076 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1094  (0.0610185); expected 358.6 (0.02)
Passed bias filter:                      838  (0.0467399); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); 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: 0.87u 0.30s 00:00:01.17 Elapsed: 00:00:00.48
# Mc/sec: 6776.15
//
Query:       gi|242399508|ref|YP_002994933.1|  [L=143]
Description: Translation initiation factor 2 subunit beta [Thermococcus sibiricus MM 739]
Scores for complete 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  128.8   0.0      1e-37  128.6   0.0    1.1  1  eIF-5_eIF-2B     Domain found in IF2B/IF5
      0.002   17.3   0.0     0.0021   17.2   0.0    1.1  1  Tmemb_55A        Transmembrane protein 55A
      0.002   18.5   0.8     0.0036   17.7   0.8    1.4  1  Lar_restr_allev  Restriction alleviation protein Lar
     0.0036   17.3   0.3     0.0062   16.6   0.3    1.3  1  Elf1             Transcription elongation factor Elf1 like
     0.0074   16.2   0.0     0.0085   16.0   0.0    1.3  1  FdhE             Protein involved in formate dehydrogenase fo
  ------ inclusion threshold ------
      0.016   15.3   0.3        1.5    9.0   0.0    2.6  2  Zn-ribbon_8      Zinc ribbon domain
      0.024   14.6   0.4      0.041   13.8   0.4    1.4  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
      0.025   14.3   1.1        7.1    6.5   0.1    2.5  2  zinc_ribbon_2    zinc-ribbon domain
      0.055   12.8   1.2      0.055   12.8   1.2    2.0  2  zf-TFIIB         Transcription factor zinc-finger
       0.12   12.3   0.2         15    5.5   0.1    2.4  2  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
       0.14   11.6   1.3       0.29   10.6   1.3    1.6  1  Vps36-NZF-N      Vacuolar protein sorting 36 NZF-N zinc-finge
       0.21   11.0   2.6        0.8    9.2   0.2    2.2  2  zf-ribbon_3      zinc-ribbon domain
       0.34   10.5   2.8        1.2    8.7   2.8    2.0  1  TF_Zn_Ribbon     TFIIB zinc-binding
       0.81    9.3   4.3        1.6    8.4   0.2    2.6  3  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 !  128.6   0.0   8.1e-41     1e-37       2     116 ..      24     136 ..      23     137 .. 0.97

  Alignments for each domain:
  == domain 1  score: 128.6 bits;  conditional E-value: 8.1e-41
                                       .CCCSSSS--SSTT--EEEETT.EEEETTHHHHHHHHTTSHHHHHHHHHHHHTSEEEESETTEEEESSSSSCCHHHH CS
                      eIF-5_eIF-2B   2 eekedkkerykmpklqvkvegkkktvivNfeeiakaLnrdpehvlkyllkelgtqgsidengrlilngkfeakklek 78 
                                       e+++++++r+++p++ v++eg+ kt+i+Nf++ia+a+nrdp+h+lk++l+e++t+g + e++r++l+g+f+   + +
  gi|242399508|ref|YP_002994933.1|  24 ENVKHHDSRFEVPTAVVTIEGN-KTLIENFRDIAEAMNRDPNHLLKFILREVATAGAL-EGRRVVLQGRFTPYMIAN 98 
                                       56678899**************.***********************************.99**************** PP

                                       HHHHHHHHHTSTSSSTSTCEEECCSSSCEEEEESSSTC CS
                      eIF-5_eIF-2B  79 lldkyieeyVlCkeCkspetelekeerllvlkCkaCga 116
                                       +l+ky++eyV+C+ C+sp+t+++k++r ++lkC+aCga
  gi|242399508|ref|YP_002994933.1|  99 KLKKYLKEYVICPVCGSPDTKIIKKDRFHFLKCEACGA 136
                                       *************************************8 PP

>> Tmemb_55A  Transmembrane protein 55A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   1.7e-06    0.0021      42      91 ..      91     141 ..      56     143 .] 0.84

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.7e-06
                         Tmemb_55A  42 PPpYsplaseesgsapvitCrvCqsl.idvegkleqhvvkCevCneatpik 91 
                                         pY   ++ ++  +  + C vC+s   ++ +k   h +kCe+C   tpi 
  gi|242399508|ref|YP_002994933.1|  91 FTPYMIANKLKKYLKEYVICPVCGSPdTKIIKKDRFHFLKCEACGAETPIT 141
                                       5577777777777788999*****9647899999***************96 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.8   2.8e-06    0.0036       6      38 ..     110     138 ..     105     142 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.8e-06
                   Lar_restr_allev   6 CPfCggravlersqrvvaeigqcvyCadCgast 38 
                                       CP Cg++++++  +++      +  C+ Cga t
  gi|242399508|ref|YP_002994933.1| 110 CPVCGSPDTKIIKKDRFH----FLKCEACGAET 138
                                       *************99998....*********43 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.3   4.9e-06    0.0062      12      55 ..      98     138 ..      88     142 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 4.9e-06
                              Elf1  12 kkkkkklptkFdCpfCnheksvevkldkkekiaevsCkvCgesf 55 
                                       +k kk+l+++  Cp+C++    + k+ kk++   ++C+ Cg+++
  gi|242399508|ref|YP_002994933.1|  98 NKLKKYLKEYVICPVCGSP---DTKIIKKDRFHFLKCEACGAET 138
                                       455566999999*******...89****************9876 PP

>> FdhE  Protein involved in formate dehydrogenase formation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   6.7e-06    0.0085     156     203 ..      95     137 ..      41     141 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 6.7e-06
                                       --TTSSS-.-TT-SS-TTT---EEEEEEE-------EEEEEETTT--E CS
                              FdhE 156 ldakalaelaeekglCPvCgsaPvasvvriggeaeglRylhCslCete 203
                                       + a++l+++ +e  +CPvCgs P + +++    +++  +l+C  C +e
  gi|242399508|ref|YP_002994933.1|  95 MIANKLKKYLKEYVICPVCGS-PDTKIIK----KDRFHFLKCEACGAE 137
                                       45788899999*********9.5677883....56799*******876 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0    0.0012       1.5      28      40 .]     108     121 ..      95     121 .. 0.79
   2 ?    3.8   0.1     0.048        61       7      14 ..     130     137 ..     125     141 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0012
                       Zn-ribbon_8  28 a.CPeCgsevrrvi 40 
                                       + CP Cgs+ +++i
  gi|242399508|ref|YP_002994933.1| 108 ViCPVCGSPDTKII 121
                                       55******777765 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.048
                       Zn-ribbon_8   7 rCeeCghe 14 
                                       +Ce+Cg e
  gi|242399508|ref|YP_002994933.1| 130 KCEACGAE 137
                                       57777754 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 ?   13.8   0.4   3.2e-05     0.041      19      45 ..     108     136 ..     100     137 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.2e-05
                     Zn_Tnp_IS1595  19 fvCPhCgsr..kayriktrglfqCkeCrk 45 
                                       ++CP Cgs   k+++  +   ++C++C++
  gi|242399508|ref|YP_002994933.1| 108 VICPVCGSPdtKIIKKDRFHFLKCEACGA 136
                                       68******97777777779999*****96 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1    0.0055       7.1      13      22 ..     107     116 ..     101     116 .. 0.73
   2 ?    6.3   0.1    0.0062       7.9      15      22 ..     128     137 ..     118     138 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0055
                     zinc_ribbon_2  13 akFCpyCGtp 22 
                                        + Cp CG+p
  gi|242399508|ref|YP_002994933.1| 107 YVICPVCGSP 116
                                       5679999987 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0062
                     zinc_ribbon_2  15 F..CpyCGtp 22 
                                       F  C+ CG++
  gi|242399508|ref|YP_002994933.1| 128 FlkCEACGAE 137
                                       3778888876 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1      0.45   5.8e+02      31      40 ..       7      16 ..       7      17 .. 0.86
   2 ?   12.8   1.2   4.3e-05     0.055       2      26 ..     110     135 ..     109     135 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.45
                          zf-TFIIB 31 drgeleklle 40
                                      d+ ++eklle
  gi|242399508|ref|YP_002994933.1|  7 DYYDYEKLLE 16
                                      7889*****8 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 4.3e-05
                          zf-TFIIB   2 CPkCqd.eleeserggveidyCpqCr 26 
                                       CP+C++ + ++++++ +++ +C++C+
  gi|242399508|ref|YP_002994933.1| 110 CPVCGSpDTKIIKKDRFHFLKCEACG 135
                                       ******77999999***********7 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 ?    5.5   0.1     0.012        15      27      35 ..     109     117 ..     104     118 .. 0.86
   2 ?    4.3   0.0     0.028        36       8      19 ..     125     136 ..     120     139 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.012
                           DUF35_N  27 vCphCgsdd 35 
                                       +Cp Cgs d
  gi|242399508|ref|YP_002994933.1| 109 ICPVCGSPD 117
                                       8*****986 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.028
                           DUF35_N   8 rLvgqrCpdCGt 19 
                                       r+ + +C +CG+
  gi|242399508|ref|YP_002994933.1| 125 RFHFLKCEACGA 136
                                       777889****97 PP

>> Vps36-NZF-N  Vacuolar protein sorting 36 NZF-N zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   1.3   0.00022      0.29      11      47 ..     109     142 ..     101     143 .] 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00022
                       Vps36-NZF-N  11 vCpICsfsNevpsnfdpnastplPpClaCGvkpdlel 47 
                                       +Cp+C    +  + ++ +++  + +C+aCG + ++++
  gi|242399508|ref|YP_002994933.1| 109 ICPVCGSPDT--KIIK-KDRFHFLKCEACGAETPITH 142
                                       7999998653..3355.789***********999987 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.2   0.00063       0.8       2      13 ..     107     117 ..     106     119 .. 0.82
   2 ?    1.7   0.2      0.14   1.8e+02      19      24 ..     131     136 ..     129     139 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00063
                       zf-ribbon_3   2 tvrCPnCGapls 13 
                                       +v CP CG+p +
  gi|242399508|ref|YP_002994933.1| 107 YVICPVCGSP-D 117
                                       689*****98.4 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.14
                       zf-ribbon_3  19 CpyCGt 24 
                                       C  CG+
  gi|242399508|ref|YP_002994933.1| 131 CEACGA 136
                                       555664 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   2.8   0.00094       1.2       2      27 ..     109     136 ..     108     140 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00094
                                       EETTTTCEEC.HEETSTTCE.EESSSSB CS
                      TF_Zn_Ribbon   2 kCPnCgstnl.veDpergel.vCtdCGl 27 
                                       +CP+Cgs+++ +   +r  +  C++CG+
  gi|242399508|ref|YP_002994933.1| 109 ICPVCGSPDTkIIKKDRFHFlKCEACGA 136
                                       7******874455555666658999996 PP

>> zf_C2H2_13  Zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       3.8   4.9e+03       3       9 ..      45      51 ..      43      54 .. 0.79
   2 ?    8.4   0.2    0.0012       1.6       6      26 ..      95     116 ..      93     122 .. 0.90
   3 ?    2.1   0.2      0.11   1.4e+02      17      25 ..     128     136 ..     116     142 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3.8
                        zf_C2H2_13  3 ntrlied 9 
                                      n +lie+
  gi|242399508|ref|YP_002994933.1| 45 NKTLIEN 51
                                      8889998 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0012
                        zf_C2H2_13   6 liedpLdtn.lnYRvCnkCGkP 26 
                                       +i + L +   +Y +C  CG P
  gi|242399508|ref|YP_002994933.1|  95 MIANKLKKYlKEYVICPVCGSP 116
                                       688999999889********99 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.11
                        zf_C2H2_13  17 YRvCnkCGk 25 
                                       +  C++CG 
  gi|242399508|ref|YP_002994933.1| 128 FLKCEACGA 136
                                       556*****5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       802  (0.044732); expected 358.6 (0.02)
Passed bias filter:                      705  (0.0393218); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.52
# Mc/sec: 825.77
//
Query:       gi|242399509|ref|YP_002994934.1|  [L=527]
Description: Methylmalonyl-CoA decarboxylase, subunit alpha [Thermococcus sibiricus MM 739]
Scores for 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-204  678.5   0.3   5.8e-204  678.3   0.3    1.0  1  Carboxyl_trans  Carboxyl transferase domain
    3.6e-07   29.9   0.3      8e-07   28.8   0.1    1.6  2  MdcE            Malonate decarboxylase gamma subunit (MdcE)
  ------ inclusion threshold ------
       0.17   12.3   0.3       0.44   10.9   0.3    1.7  1  FlgM            Anti-sigma-28 factor, FlgM


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 !  678.3   0.3  9.6e-208  5.8e-204       1     494 []      33     525 ..      33     525 .. 0.99

  Alignments for each domain:
  == domain 1  score: 678.3 bits;  conditional E-value: 9.6e-208
                                       SSCTTCEEEEEEEEHTTSGGGEBEHHHHHHHHHHHHHHH.HHT..EEEEEEEESBETTEEHHHHTTEEEEESSTTSG CS
                    Carboxyl_trans   1 kehprGkltareridllldpgsFgeledlffhrvtelgr.kkklprdgvvtgsGaviGravevvaqdktvlggslgp 76 
                                       k+h++Gkltareri++lldpgsF+el ++++hr te+g+ k +lp+dgv+tg+G+++Gr v+v+aqd+tv+ggslg+
  gi|242399509|ref|YP_002994934.1|  33 KQHEKGKLTARERIEKLLDPGSFVELGAFVKHRNTEFGLdKMELPADGVITGYGTIDGRLVFVFAQDFTVMGGSLGE 109
                                       69*************************************999*********************************** PP

                                       GGCEEECHHHHHHHHHTEEEEEEEEE-ESSSGHHSSHHHHHHHHHHHHHHHHHHHCS-EEEEESSEEETHHHHHHHH CS
                    Carboxyl_trans  77 akgekllkaqeeaikagepligindsgGaegriqegveslrgsGkifgenskasgeIpqislvtgrcaGggaYlpal 153
                                       +++ k+ +++e+a++ag+p+ig+ndsgGa  riqegv++l+g+G+if+ n+ +sg++pqi+ ++g+caGg++Y+pa+
  gi|242399509|ref|YP_002994934.1| 110 MHAAKIKRVMELALEAGAPVIGLNDSGGA--RIQEGVDALKGYGEIFKMNTVLSGVVPQITAIMGPCAGGAVYSPAI 184
                                       *****************************..********************************************** PP

                                       TSEEEEETT.EEEEESSTHHHHHHHHSSCC-SSCHHHHSHHHHTTTTSSSEEESSHHHHHHHHHHHHTTS-SSTTSG CS
                    Carboxyl_trans 154 gdrvimvee.tskifltGpdvikkvlgreevtseelgGatqhmtksGvahltaeddeealelirkllsylPkkasnn 229
                                       gd+++mv++    +f+tGp+v+k+v+g  ev+s +lgG+++h++ksG ahl+ ++dee+l+lir+l++ylP   +nn
  gi|242399509|ref|YP_002994934.1| 185 GDFILMVDNpATFMFITGPQVVKAVTG-VEVSSTQLGGGMVHAQKSGQAHLIGKSDEEVLMLIRRLIGYLP---PNN 257
                                       *********99****************.*******************************************...*** PP

                                       GSS----ECSSGSSSH.....HCS-CTTTS---HHHHHHCEEC.....TTC-EEESTTSSTTEEEEEEEETTEEEEE CS
                    Carboxyl_trans 230 resaPivetadepdrd...lieivPdnakkpyDvreviarlvd.....egeFlEikegyAktvVvGfArlgGipvGv 298
                                       +e++P+ +t+d+p r+   l+eivPd+++k yDvr+vi ++vd     + +FlEi++ +A++ +vGf+r++G++vG+
  gi|242399509|ref|YP_002994934.1| 258 MEKPPKFPTTDPPFRKsdkLYEIVPDDPNKGYDVRQVIYEIVDrdangNPDFLEILPYFAPNAIVGFGRMNGQTVGI 334
                                       ***************999999**************************999*************************** PP

                                       EEE--SEEETTEE-HHHHHHHHHHHHHHHHTT--EEEEE-BSEE--SHHHHHTTHHHHHHHHHHHHHT--S-EEEEE CS
                    Carboxyl_trans 299 vAnetrveaGqvlfidsavKaarfirlcdaenlPlviladvrGflvGqrqeyggilkhGaklvdalaeakvPkitvi 375
                                       +An++ + aG vl+ids++K arf+r+cda+n+P+v+l+dv+G+l+G +qeyggi++hGak+++a++ea+vP++tvi
  gi|242399509|ref|YP_002994934.1| 335 IANNPIHLAG-VLDIDSSDKIARFVRTCDAFNIPIVTLVDVPGYLPGVQQEYGGIIRHGAKVLYAYSEATVPMVTVI 410
                                       **********.****************************************************************** PP

                                       -TEEEHHHHHTTTGGGSTTTTEEETTT-EEESS-HHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    Carboxyl_trans 376 lrkayGGayvvmdskingadlvaawptariaVlgpegaveilfrkekaaaemerkdlaaerkkklkeyeeellnpyv 452
                                       lrkayGGay++m+sk++gad+v+awpta+iaV+gpega++i+frke+a+ae    ++++ r++k++ey+e+++npyv
  gi|242399509|ref|YP_002994934.1| 411 LRKAYGGAYLAMGSKHLGADFVFAWPTAEIAVMGPEGAANIIFRKEIAKAE----NPEEVRQEKIREYREKFANPYV 483
                                       **************************************************9....99******************** PP

                                       HHHHHHHHTTSSHHHHHHTTSSSEEEHGGGHHHHHHHHHHHH CS
                    Carboxyl_trans 453 aaargfaDavidpsetraklvialelewkkarklparkrrni 494
                                       aa+rg++D+vidp+etr+k+++ale++++k++klp++k++ni
  gi|242399509|ref|YP_002994934.1| 484 AASRGYIDDVIDPAETRGKIIMALEALESKRVKLPPKKHGNI 525
                                       ****************************************97 PP

>> MdcE  Malonate decarboxylase gamma subunit (MdcE)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0      0.59   3.5e+03      93     111 ..     114     132 ..      91     143 .. 0.80
   2 !   28.8   0.1   1.3e-10     8e-07      22     151 ..     325     452 ..     315     461 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.59
                                       HHHHHHHHHHHHT--EEEE CS
                              MdcE  93 hlakalarArlaGhpvigl 111
                                        +  ++ +A  aG+pvigl
  gi|242399509|ref|YP_002994934.1| 114 KIKRVMELALEAGAPVIGL 132
                                       4445677788889999997 PP

  == domain 2  score: 28.8 bits;  conditional E-value: 1.3e-10
                                       EEETTEEEEEEEE---TTSS-B-HHHHHHHHHHHHHHHTSSS--EEEEEEEE--B--SHHHHHHTHHHHHHHHHHHH CS
                              MdcE  22 gsltlesvrfvaVigdankgevGvdealaLaaaVleaieraekrpilvlvDvasQrlgrrdEllGihealahlakal 98 
                                       g+++++ v+ +a  ++   g + +d + ++a  V      a + pi+ lvDv++   g ++E  Gi    a +  a+
  gi|242399509|ref|YP_002994934.1| 325 GRMNGQTVGIIANNPIHLAGVLDIDSSDKIARFVRTC--DAFNIPIVTLVDVPGYLPGVQQEYGGIIRHGAKVLYAY 399
                                       5556666666666666666666666666666666544..36678**********************88877777777 PP

                                       HHHHHHT--EEEEEEEEEEHHHHHHTT...TT-SEEEEEET-EEESS-HHHHHHHH CS
                              MdcE  99 arArlaGhpvigllvGkavsGaflahg...lqanrlialpgvqvavmdkasaArvT 151
                                         A     p+++++  ka  Ga+la+g   l a+ + a p +++avm+   aA + 
  gi|242399509|ref|YP_002994934.1| 400 SEAT---VPMVTVILRKAYGGAYLAMGskhLGADFVFAWPTAEIAVMGPEGAANII 452
                                       7776...5*****************9966567******************999985 PP

>> FlgM  Anti-sigma-28 factor, FlgM
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.3   7.4e-05      0.44      12      39 ..     457     480 ..     448     482 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 7.4e-05
                              FlgM  12 lqkakqaaaaap.evreekVaelKeaIas 39 
                                       ++k     a++p evr+ek+ e +e+ a+
  gi|242399509|ref|YP_002994934.1| 457 IAK-----AENPeEVRQEKIREYREKFAN 480
                                       333.....455856************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (527 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:                        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: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.48
# Mc/sec: 3299.03
//
Query:       gi|242399510|ref|YP_002994935.1|  [L=137]
Description: Methylmalonyl-CoA decarboxylase, delta subunit [Thermococcus sibiricus MM 739]
Scores for 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-14   51.8   0.5    1.2e-13   51.4   0.5    1.1  1  OAD_gamma   Oxaloacetate decarboxylase, gamma chain


Domain annotation for each model (and alignments):
>> OAD_gamma  Oxaloacetate decarboxylase, gamma chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.4   0.5   6.7e-18   1.2e-13       2      76 ..      19      94 ..      18      95 .. 0.90

  Alignments for each domain:
  == domain 1  score: 51.4 bits;  conditional E-value: 6.7e-18
                         OAD_gamma  2 egllltllGmgvVFvvLilLslvislfskiikkkakkkkkkakaaaaaaaaaaaaa.eldddeelvAvIaaAiaay 76
                                      egl +t+lG++vVF+vL +L l+++ ++++ ++  +++k+ ++a+++++++++ ++ + + +++ +AvI+aAi ay
  gi|242399510|ref|YP_002994935.1| 19 EGLYITILGVTVVFLVLSILALAMYGIGYLERALIERAKPVEAAPKPKEEKEKYVEeKPSIEPKKLAVITAAILAY 94
                                      79*****************************9998888888888888887776666899**************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       761  (0.0424452); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 956.07
//
Query:       gi|242399511|ref|YP_002994936.1|  [L=157]
Description: Methylmalonyl-CoA decarboxylase, gamma subunit [Thermococcus sibiricus MM 739]
Scores for complete 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   88.5   2.4    4.7e-25   87.2   2.4    1.7  1  Biotin_lipoyl    Biotin-requiring enzyme
    3.2e-15   55.7   1.6    6.5e-07   29.1   0.0    2.3  2  Biotin_lipoyl_2  Biotin-lipoyl like
    3.1e-06   27.8   0.9      0.055   14.2   0.0    2.7  3  HlyD_3           HlyD family secretion protein
    3.1e-05   23.3   0.2       0.06   12.6   0.0    2.2  2  HlyD_D23         Barrel-sandwich domain of CusB or HlyD membr
    0.00033   20.5   0.7      0.041   13.8   0.1    2.3  2  RnfC_N           RnfC Barrel sandwich hybrid domain
    0.00049   19.8   0.1       0.27   11.0   0.0    2.4  2  PTS_EIIA_1       phosphoenolpyruvate-dependent sugar phosphot
     0.0015   18.0   0.9      0.053   12.9   0.2    2.1  2  NQRA             Na(+)-translocating NADH-quinone reductase s
  ------ inclusion threshold ------
      0.084   12.8   0.2       0.15   11.9   0.2    1.4  1  GCV_H            Glycine cleavage H-protein
       0.17   12.1   1.2        2.7    8.3   1.2    2.7  1  Peptidase_M23    Peptidase family M23
        2.5    6.9   7.1       0.42    9.4   0.3    2.3  3  YqfD             Putative stage IV sporulation protein YqfD


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 !   87.2   2.4   2.6e-28   4.7e-25       2      73 .]      90     156 ..      89     156 .. 0.97

  Alignments for each domain:
  == domain 1  score: 87.2 bits;  conditional E-value: 2.6e-28
                                       EEEESSSEEEEEE.ECSESSSTTCEE-TTSEEEEEECTTEEEEEEBSSSEEEEEESSTTTEEE-TTCEEEEE CS
                     Biotin_lipoyl   2 eiksPmiGesveegvvevlvkvGdkVkagqvlaeveamKmemeieapkaGvvkeilvkeGdtvevgdllaki 73 
                                        +++Pm+G++ +     vlv +Gd+Vk gq l+++eamKme+ei++pk+Gvvk+ilvkeGdtv++g+ l+++
  gi|242399511|ref|YP_002994936.1|  90 VVTAPMPGKILR-----VLVREGDQVKVGQGLLVLEAMKMENEIPSPKDGVVKKILVKEGDTVDTGQALIEL 156
                                       699*********.....****************************************************986 PP

>> Biotin_lipoyl_2  Biotin-lipoyl like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0   3.6e-10   6.5e-07       5      41 ..      91     127 ..      90     129 .. 0.91
   2 !   26.0   0.3   3.2e-09   5.8e-06       5      33 ..     128     156 ..     125     156 .. 0.94

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 3.6e-10
                   Biotin_lipoyl_2   5 IaapvsGrVaqlnVkdGqrVkaGdvLaelDsralqla 41 
                                       ++ap +G++ +++V++G++Vk G+ L++l+  + +++
  gi|242399511|ref|YP_002994936.1|  91 VTAPMPGKILRVLVREGDQVKVGQGLLVLEAMKMENE 127
                                       789**************************99887775 PP

  == domain 2  score: 26.0 bits;  conditional E-value: 3.2e-09
                   Biotin_lipoyl_2   5 IaapvsGrVaqlnVkdGqrVkaGdvLael 33 
                                       I +p +G+V++++Vk+G+ V +G+ L+el
  gi|242399511|ref|YP_002994936.1| 128 IPSPKDGVVKKILVKEGDTVDTGQALIEL 156
                                       67899*********************997 PP

>> HlyD_3  HlyD family secretion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       4.3   7.8e+03      74      74 ..      19      19 ..       2      40 .. 0.48
   2 !   11.7   0.0   0.00018      0.32       1      30 [.      90     119 ..      90     126 .. 0.91
   3 !   14.2   0.0   3.1e-05     0.055       2      30 ..     128     156 ..     127     157 .] 0.92

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 4.3
                            HlyD_3 74 e 74
                                      e
  gi|242399511|ref|YP_002994936.1| 19 E 19
                                      2 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00018
                            HlyD_3   1 tlrApvdGvvvelnveegevvqagdellei 30 
                                       +++Ap  G++  + v+eg+ v  g+ ll +
  gi|242399511|ref|YP_002994936.1|  90 VVTAPMPGKILRVLVREGDQVKVGQGLLVL 119
                                       69***********************99876 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 3.1e-05
                            HlyD_3   2 lrApvdGvvvelnveegevvqagdellei 30 
                                       + +p dGvv+++ v+eg+ v  g++l e+
  gi|242399511|ref|YP_002994936.1| 128 IPSPKDGVVKKILVKEGDTVDTGQALIEL 156
                                       569**********************9885 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 !    9.6   0.0   0.00028       0.5      21      55 ..      90     123 ..      84     127 .. 0.77
   2 !   12.6   0.0   3.3e-05      0.06     109     138 ..     126     155 ..     119     157 .] 0.84

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00028
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          HlyD_D23  21 rvsarveGwveklyvnatgdkVkkGqpLaelyspe 55 
                                       +v+a + G + ++ v+ +gd+Vk Gq L+ l++ +
  gi|242399511|ref|YP_002994936.1|  90 VVTAPMPGKILRVLVR-EGDQVKVGQGLLVLEAMK 123
                                       6778888888888888.888888888888877655 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 3.3e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          HlyD_D23 109 vtvkapisGvVteknvreGqyvqpgdtlft 138
                                        ++ +p +GvV +  v eG++v++g++l++
  gi|242399511|ref|YP_002994936.1| 126 NEIPSPKDGVVKKILVKEGDTVDTGQALIE 155
                                       578899999**99999***99999999987 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 !   13.8   0.1   2.3e-05     0.041      39      80 ..      97     139 ..      82     140 .. 0.85
   2 !    8.1   0.2    0.0014       2.5      40      58 ..     135     153 ..     132     157 .] 0.85

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.3e-05
                            RnfC_N  39 GapakplvkvgdkVlkGqkiaeaeg.fvsapvhasvsGtVkai 80 
                                       G+  ++lv +gd+V+ Gq +   e+  +  ++ ++  G Vk+i
  gi|242399511|ref|YP_002994936.1|  97 GKILRVLVREGDQVKVGQGLLVLEAmKMENEIPSPKDGVVKKI 139
                                       666789************8877766456999**********98 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0014
                            RnfC_N  40 apakplvkvgdkVlkGqki 58 
                                          k+lvk+gd+V +Gq +
  gi|242399511|ref|YP_002994936.1| 135 VVKKILVKEGDTVDTGQAL 153
                                       56799************87 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 !   11.0   0.0   0.00015      0.27      76     112 ..      92     128 ..      88     137 .. 0.85
   2 !    6.9   0.0    0.0028       5.1      85     102 ..     138     155 ..     130     157 .] 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00015
                                       TTTTTTTTEEES----SEE-SEEEEEEE-HHHHGGGS CS
                        PTS_EIIA_1  76 tvklkgegFellvkegdkVkagdklvevdleaikkag 112
                                       t  + g+  ++lv+egd+Vk g+ l+ ++  +++++ 
  gi|242399511|ref|YP_002994936.1|  92 TAPMPGKILRVLVREGDQVKVGQGLLVLEAMKMENEI 128
                                       56688999******************99998888765 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0028
                                       EES----SEE-SEEEEEE CS
                        PTS_EIIA_1  85 ellvkegdkVkagdklve 102
                                       ++lvkegd+V +g+ l+e
  gi|242399511|ref|YP_002994936.1| 138 KILVKEGDTVDTGQALIE 155
                                       789*************98 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 !   12.9   0.2     3e-05     0.053      35      79 ..      94     139 ..      77     140 .. 0.80
   2 !    7.5   0.1    0.0014       2.5      38      59 ..     134     155 ..     129     156 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3e-05
                              NQRA  35 dyvglkpklkvkegdkVkkGqvlfe.dKknpgvlftspasGevvei 79 
                                       +  g  ++++v+egd+Vk Gq l+  +  + +  + sp +G+v++i
  gi|242399511|ref|YP_002994936.1|  94 PMPGKILRVLVREGDQVKVGQGLLVlEAMKMENEIPSPKDGVVKKI 139
                                       556667899************876515556688899*******998 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0014
                              NQRA  38 glkpklkvkegdkVkkGqvlfe 59 
                                       g+  k++vkegd+V +Gq+l+e
  gi|242399511|ref|YP_002994936.1| 134 GVVKKILVKEGDTVDTGQALIE 155
                                       67789**************986 PP

>> GCV_H  Glycine cleavage H-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   8.6e-05      0.15      31      73 ..      97     138 ..      87     149 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.6e-05
                                       -SEEEEE---TT-EE-TT-EEEEEEESS-EEEEE-SSSEEEEE CS
                             GCV_H  31 gdvvfvelpevgtkvkkgeslaavEsvKaasevyapvsGevve 73 
                                       g+++ v +  +g++vk g+ l ++E+ K+  e+++p +G v +
  gi|242399511|ref|YP_002994936.1|  97 GKILRVLV-REGDQVKVGQGLLVLEAMKMENEIPSPKDGVVKK 138
                                       56666644.579***************************9865 PP

>> Peptidase_M23  Peptidase family M23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   1.2    0.0015       2.7      14      69 ..      89     153 ..      83     157 .] 0.62

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0015
                                       -EEEESSSEEE....EEEEEETTTEEEEEEEECTCEEEEEEE.....ESEESS-TTEEE-TTCEE CS
                     Peptidase_M23  14 tpVlAaadGtV....vfagkkegyGnvviidhgdgystlyah.....lskisvkegqkVkaGqvI 69 
                                       + V+A++ G++    v  g++ ++G+ +++  + +++  +       ++ki vkeg++V++Gq +
  gi|242399511|ref|YP_002994936.1|  89 NVVTAPMPGKIlrvlVREGDQVKVGQGLLVLEAMKMENEIPSpkdgvVKKILVKEGDTVDTGQAL 153
                                       447888888886644444444466666666665555555544233337788899********986 PP

>> YqfD  Putative stage IV sporulation protein YqfD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1       1.6   2.9e+03     158     171 ..       7      20 ..       5      38 .. 0.66
   2 ?    2.0   0.1      0.04        73     205     219 ..     102     116 ..      81     131 .. 0.79
   3 ?    9.4   0.3   0.00024      0.42     190     221 ..     131     155 ..     119     156 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.6
                              YqfD 158 veikGtrlivevve 171
                                       v ++G+ ++vev+e
  gi|242399511|ref|YP_002994936.1|   7 VIVDGVPYEVEVEE 20 
                                       66666666666666 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.04
                              YqfD 205 plvkegdtVkkGdvL 219
                                        lv+egd Vk G+ L
  gi|242399511|ref|YP_002994936.1| 102 VLVREGDQVKVGQGL 116
                                       468888888888854 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.00024
                              YqfD 190 kkdGvItkvivesGeplvkegdtVkkGdvLIs 221
                                        kdGv++k+       lvkegdtV +G+ LI+
  gi|242399511|ref|YP_002994936.1| 131 PKDGVVKKI-------LVKEGDTVDTGQALIE 155
                                       567777776.......6799999*****9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); 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: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1116.16
//
Query:       gi|242399512|ref|YP_002994937.1|  [L=377]
Description: Ion gradient-generating decarboxylase subunit beta [Thermococcus sibiricus MM 739]
Scores for complete 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-158  526.3  29.6   3.6e-158  526.1  29.6    1.0  1  OAD_beta  Na+-transporting oxaloacetate decarboxylase beta su
  ------ inclusion threshold ------
       0.43   10.4   1.7        1.1    9.0   0.1    2.2  2  TMEM40    Transmembrane protein 40 family


Domain annotation for each model (and alignments):
>> OAD_beta  Na+-transporting oxaloacetate decarboxylase beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  526.1  29.6    4e-162  3.6e-158       2     348 ..      23     375 ..      22     376 .. 0.99

  Alignments for each domain:
  == domain 1  score: 526.1 bits;  conditional E-value: 4e-162
                          OAD_beta   2 nlvmiliglvllyLaikkkleplllvpigfgallvNlpeaglle......gllellyegavksellplliFlgiGal 72 
                                       n++mil+g++l+yLai+ ++eplll+pig++a+lvNlp +g+l+      gl++l+ +  +++e++plliF+g+Ga+
  gi|242399512|ref|YP_002994937.1|  23 NIIMILVGFTLMYLAIRYEMEPLLLLPIGVSAVLVNLPLTGILSadphhpGLFYLIKHYLIDTEVVPLLIFFGLGAM 99 
                                       79*************************************9999999999**************************** PP

                          OAD_beta  73 tDfgpllanpkslllgaaaqlGifvtllvalllgftlkeaasigiiGgaDGptaifvasklapellgaiavaaYsYm 149
                                       tDfgp++a+pk+ llgaaaq+G+f+++l+a++lgf+l+eaasigiiGgaDGpt+i++++klap+llga avaaYsYm
  gi|242399512|ref|YP_002994937.1| 100 TDFGPMIADPKTALLGAAAQIGVFIAMLTAVALGFNLQEAASIGIIGGADGPTTIYLTTKLAPHLLGATAVAAYSYM 176
                                       ***************************************************************************** PP

                          OAD_beta 150 aLvpiiqppiikllttkkerkikmeklrkvskkekilfpivvtivvallvpsaapLigmlmlGnllresgvverlsk 226
                                       +Lvpiiqpp+i++ltt kerki+me+lr+vsk+ek++fpi+ +i+++llvpsaapL+gmlm+Gnl+resgvverlsk
  gi|242399512|ref|YP_002994937.1| 177 SLVPIIQPPVIRALTTPKERKIRMEQLRPVSKREKVIFPIASMIIIGLLVPSAAPLVGMLMIGNLFRESGVVERLSK 253
                                       ***************************************************************************** PP

                          OAD_beta 227 taqnellnivtillgltvgatmeaekflkletllilvlGlvafvlstagGvllaklmnllskkkiNPliGaaGvsav 303
                                       +a++el+nivti+lgl vg+tm+ae+fl+++tl+il lG+vaf+ +tagGvll+klm++ls++kiNP+iGaaGvsav
  gi|242399512|ref|YP_002994937.1| 254 AAREELMNIVTIFLGLGVGSTMQAESFLTVKTLMILGLGVVAFASATAGGVLLGKLMMKLSGGKINPMIGAAGVSAV 330
                                       ***************************************************************************** PP

                          OAD_beta 304 PmaarvvqkvgqkedpsnflLmhamgpnvaGvigsavaagvllal 348
                                       Pm+arvvqk+++kedp nf+LmhamgpnvaGvig+avaagvll++
  gi|242399512|ref|YP_002994937.1| 331 PMSARVVQKLAAKEDPGNFILMHAMGPNVAGVIGTAVAAGVLLSV 375
                                       *******************************************97 PP

>> TMEM40  Transmembrane protein 40 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.3      0.11     1e+03      70      96 ..       9      35 ..       5      48 .. 0.74
   2 ?    9.0   0.1   0.00012       1.1      38      94 ..     249     308 ..     240     315 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.11
                            TMEM40 70 dwfmslgvglltfasletvgiyfglvy 96
                                      d+f  +g+  lt+  +  + + f l+y
  gi|242399512|ref|YP_002994937.1|  9 DFFTNIGIFHLTIGNIIMILVGFTLMY 35
                                      777777777777777777777777776 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00012
                            TMEM40  38 rrlnikkddeffhfv..llcfaigallvsyhyy.adwfmslgvglltfasletvgiyfgl 94 
                                       +rl     +e++ +v  +l +++g+ + +  +     +m lg+g+++fas  + g+ +g 
  gi|242399512|ref|YP_002994937.1| 249 ERLSKAAREELMNIVtiFLGLGVGSTMQAESFLtVKTLMILGLGVVAFASATAGGVLLGK 308
                                       56666666777776622567788999888777525789**************99999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 2423.89
//
Query:       gi|242399513|ref|YP_002994938.1|  [L=550]
Description: Thermosome beta subunit [Thermococcus sibiricus MM 739]
Scores for 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-184  612.0  27.1     8e-184  611.8  27.1    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 !  611.8  27.1  4.4e-188    8e-184       1     490 [.      36     526 ..      36     527 .. 0.99

  Alignments for each domain:
  == domain 1  score: 611.8 bits;  conditional E-value: 4.4e-188
                                       HHHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHH CS
                        Cpn60_TCP1   1 ladivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleea 77 
                                       +a++v+ttlGPkGmdKmlv++ g++v+TnDGatil++++++hPaak+++e+a++qd+e+GDGTtt+v++ageLl +a
  gi|242399513|ref|YP_002994938.1|  36 IAETVRTTLGPKGMDKMLVDSLGDIVITNDGATILEQIDVQHPAAKMIIEVAKTQDKEAGDGTTTAVVIAGELLAKA 112
                                       799************************************************************************** PP

                                       HHHHHCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHH.HCH CS
                        Cpn60_TCP1  78 ekliaagvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAv.kli 153
                                       e+l+++++hp+ +i+gy  a+eka e+ ++i  +is+e +++e+L k+a+ts+++k  ++++e l+kl+v+Av ++ 
  gi|242399513|ref|YP_002994938.1| 113 EELLDQNIHPSIVIKGYTLAAEKAQEIVDSI--AISVEPDNEETLTKIASTSITGKNAESHKELLAKLAVEAVkQVA 187
                                       *******************************..8888899*********************************8877 PP

                                       CCCS..EECSCCCEECCCCEECECTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HHCCHHHCCCCSCC CS
                        Cpn60_TCP1 154 eene..keldlgrikvvkieggsledselveGlvldkgvlspdmpkklenakvllldvsLeiektetkttvvlsdae 228
                                       e+ +  + +d+++ik++k+eggs++d++l++G+v+dk+ ++p mpkk+ nak++l++  Le +ktet++++++++++
  gi|242399513|ref|YP_002994938.1| 188 EKVNgtYVVDIDNIKLEKKEGGSVRDTQLIKGVVIDKERVHPRMPKKVINAKIALINDALEVKKTETDAKINITSPD 264
                                       77779999********************************************************************* PP

                                       HHHHHHHHHHHHHHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCGGGGG CS
                        Cpn60_TCP1 229 eleklekaeekqleellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatGatavssledlt 305
                                       +l +++++eek+l+e++e+++++g+nv++cqkgiddla+h+lak+gila+rrvkk+d+e+lakatGa++v++++dlt
  gi|242399513|ref|YP_002994938.1| 265 QLYAFLEQEEKMLQEMVEQVAATGANVLFCQKGIDDLAQHYLAKHGILAVRRVKKSDMEKLAKATGAKVVTNVKDLT 341
                                       ***************************************************************************** PP

                                       CGC-EEEEEEEECCETTCCEEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHHH CS
                        Cpn60_TCP1 306 peelGtakkveeekigsekttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatele 382
                                       +e+lG+a+ vee+k+  e+++++e++k++k++til+rg t++v+de+era+edA++v k ++ed+ ++pGGGatel 
  gi|242399513|ref|YP_002994938.1| 342 SEDLGYAEVVEERKVAGENMIFVEGCKNPKAVTILIRGGTEHVVDEVERALEDAIKVSKDVMEDGAILPGGGATELD 418
                                       ***************************************************************************** PP

                                       HHHHHHCCCCTSXCCHHHHHHHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHHHTTXTTEEEETTTTCEEECCCCTX CS
                        Cpn60_TCP1 383 lakklkeyaksvsgeeqlaieafakALevipktLaeNaGldpievlaklraahnkgekelgidvesgeiidlveagv 459
                                       l+ +l+e+ak+v g+eqla+eafa+AL+vipktLaeNaGld+i+vl k  ++h+++ k  g+dv  ge+ d++e+gv
  gi|242399513|ref|YP_002994938.1| 419 LSIRLDEFAKKVGGKEQLAVEAFAEALKVIPKTLAENAGLDTIDVLVKAISEHKNKGKAIGVDVFAGEPADMLERGV 495
                                       *****************************************************99999******************* PP

                                       EEEHHHHHHHHHHHHHHHHHHHCEEEEEXXX CS
                        Cpn60_TCP1 460 vDplkvkrqalksAteaastiLrideiikak 490
                                       ++p++vkrqa+ksA+e+a +iLrid++i ak
  gi|242399513|ref|YP_002994938.1| 496 IEPARVKRQAIKSASEVAIMILRIDDVIAAK 526
                                       ****************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (550 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       810  (0.0451782); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); 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: 0.70u 0.34s 00:00:01.04 Elapsed: 00:00:00.54
# Mc/sec: 3063.49
//
Query:       gi|242399514|ref|YP_002994939.1|  [L=203]
Description: hypothetical protein TSIB_1539 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-31  108.9   0.0    2.2e-31  108.3   0.0    1.3  1  UPF0029   Uncharacterized protein family UPF0029
    7.3e-09   35.4   0.0    1.2e-08   34.6   0.0    1.4  1  DUF1949   Domain of unknown function (DUF1949)


Domain annotation for each model (and alignments):
>> UPF0029  Uncharacterized protein family UPF0029
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.3   0.0   2.4e-35   2.2e-31       2     105 .]      19     124 ..      18     124 .. 0.96

  Alignments for each domain:
  == domain 1  score: 108.3 bits;  conditional E-value: 2.4e-35
                                       TEEEEEEEEE-SSHHHHHHHHHHH--..TTSSEEEEEE....EE....TTEE-TTSST..SHHHHHHHHHHTTB-SE CS
                           UPF0029   2 kSrFiavlaaveseeevkaileelkkenkkathniyAyrlrqkvekvnedsdddgEpa..AGkkllelLekeklenv 76 
                                       +S Fi+++++v+se+e+k++++++k  +++athn++Ayr+r+ ++ +   +dddgEp+  AG+++ ++Le ++lenv
  gi|242399514|ref|YP_002994939.1|  19 DSLFIGYAMSVNSEKEAKEFIRNVKGAHSDATHNVSAYRVREGNT-LLVYYDDDGEPRgsAGRPVFKVLEYKGLENV 94 
                                       599***********************************9988884.6777*************************** PP

                                       EEEEEEE--SS--HHHHH.HHHHHHHHHHH CS
                           UPF0029  77 lvvvtRwfGGikLGpgrl.raiseaareaL 105
                                       +vvvtR+fGG+kLG g+l +a+se+a+eaL
  gi|242399514|ref|YP_002994939.1|  95 VVVVTRYFGGTKLGYGGLvKAYSETASEAL 124
                                       ***************************997 PP

>> DUF1949  Domain of unknown function (DUF1949)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   0.0   1.4e-12   1.2e-08       2      56 .]     141     195 ..     140     195 .. 0.97

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 1.4e-12
                           DUF1949   2 tvdYadlgkverlLeqfgativdteYtddVtltlavpeeeveafkaaLtdltsGr 56 
                                        ++Y++++ +e  +e+f+a+i++ +++  V +++ + +e+ ++f++ ++++t Gr
  gi|242399514|ref|YP_002994939.1| 141 VFPYNLYSVIEKAIEKFEAEILERNFSVEVRFVVGIIPEQKDEFIKYVNEITKGR 195
                                       689***************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       752  (0.0419432); expected 358.6 (0.02)
Passed bias filter:                      575  (0.0320709); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.33s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1283.41
//
Query:       gi|242399515|ref|YP_002994940.1|  [L=130]
Description: hypothetical protein TSIB_1540 [Thermococcus sibiricus MM 739]
Scores for 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   0.3    0.00013   21.6   0.3    1.3  1  Sigma70_r4_2  Sigma-70, region 4
    0.00011   21.9   0.2    0.00045   20.0   0.3    1.9  2  HTH_10        HTH DNA binding domain
    0.00099   19.0   0.0     0.0016   18.3   0.0    1.4  1  HTH_11        HTH domain
     0.0032   17.0   0.0     0.0062   16.1   0.0    1.5  1  HTH_24        Winged helix-turn-helix DNA-binding
      0.005   16.3   0.1     0.0074   15.8   0.1    1.4  1  Sigma70_r4    Sigma-70, region 4
     0.0093   15.6   0.3      0.022   14.4   0.1    1.6  2  GntR          Bacterial regulatory proteins, gntR family
  ------ inclusion threshold ------
      0.011   15.6   0.1       0.02   14.8   0.1    1.4  1  MarR_2        MarR family
      0.017   15.1   0.3      0.033   14.2   0.0    1.6  2  HTH_Crp_2     Crp-like helix-turn-helix domain
      0.029   14.4   0.6       0.13   12.4   0.1    2.0  2  HTH_3         Helix-turn-helix
      0.043   13.9   0.2      0.066   13.3   0.2    1.3  1  Sigma70_r3    Sigma-70 region 3
      0.048   13.9   0.1      0.086   13.1   0.1    1.5  1  KORA          TrfB plasmid transcriptional repressor
      0.051   13.6   0.0      0.085   12.9   0.0    1.3  1  HTH_29        Winged helix-turn helix
      0.052   14.1   0.1       0.08   13.5   0.1    1.2  1  DUF134        Protein of unknown function  DUF134
       0.07   13.0   0.2       0.12   12.3   0.2    1.4  1  Sigma70_ECF   ECF sigma factor
      0.091   13.0   0.0       0.14   12.4   0.0    1.3  1  UPF0122       Putative helix-turn-helix protein, YlxM / p13 l
      0.098   12.2   0.2       0.15   11.6   0.2    1.3  1  GerE          Bacterial regulatory proteins, luxR family
        0.1   12.4   0.0       0.19   11.6   0.0    1.4  1  HTH_23        Homeodomain-like domain
       0.11   12.3   0.0       0.16   11.8   0.0    1.2  1  EssA          WXG100 protein secretion system (Wss), protein 
       0.16   11.9   0.1       0.32   10.9   0.1    1.5  1  TrmB          Sugar-specific transcriptional regulator TrmB


Domain annotation for each model (and alignments):
>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.3   1.3e-07   0.00013      10      54 .]       3      46 ..       1      46 [. 0.90

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.3e-07
                                      TS-HHHHHHHHHHHTS---HHHHHHHHT--HHHHHHHHHHHHHHH CS
                      Sigma70_r4_2 10 eLperqreifllryleglsykEIAellgisegtVksrlsRArkkL 54
                                      +Lpe   +i ++ + +++   EIAe lgis ++V+++l+ A++kL
  gi|242399515|ref|YP_002994940.1|  3 RLPESMEKIWTM-RAKEMREIEIAESLGISRQAVNKALKDAKAKL 46
                                      688888888888.57999999**********************98 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.3   4.7e-07   0.00045      28      53 .]      23      48 ..      15      48 .. 0.89
   2 ?   -1.6   0.0       2.6   2.4e+03       8      16 ..     106     114 ..     105     120 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 4.7e-07
                            HTH_10 28 eLAkelGIskstlsehLrkaesklie 53
                                      e+A+ lGIs++++ + L+ a+ kl+e
  gi|242399515|ref|YP_002994940.1| 23 EIAESLGISRQAVNKALKDAKAKLFE 48
                                      8**********************985 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.6
                            HTH_10   8 vlklAyemG 16 
                                       +l++A+e+G
  gi|242399515|ref|YP_002994940.1| 106 ILQHALELG 114
                                       688888887 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.7e-06    0.0016      20      44 ..      23      47 ..      22      69 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.7e-06
                            HTH_11 20 eLAeeLnvSrrtvrrdIkaLeelgv 44
                                      e+Ae L++Sr++v + +k+ +++++
  gi|242399515|ref|YP_002994940.1| 23 EIAESLGISRQAVNKALKDAKAKLF 47
                                      89*****************999984 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   6.6e-06    0.0062      22      40 ..      23      41 ..      21      45 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 6.6e-06
                            HTH_24 22 eLAerlglSpstvnrrlkr 40
                                      e+Ae lg+S+++vn+ lk 
  gi|242399515|ref|YP_002994940.1| 23 EIAESLGISRQAVNKALKD 41
                                      9****************97 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   7.8e-06    0.0074      25      48 ..      23      46 ..       3      48 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 7.8e-06
                                      HHHHHHTS-HHHHHHHHHHHHHHH CS
                        Sigma70_r4 25 EIgerlgiSrerVrqiekrAlrkL 48
                                      EI+e lgiSr +V   +k+A  kL
  gi|242399515|ref|YP_002994940.1| 23 EIAESLGISRQAVNKALKDAKAKL 46
                                      9*******************9999 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.1   2.4e-05     0.022      26      50 ..      20      44 ..      13      46 .. 0.89
   2 ?   -2.4   0.0       4.2     4e+03      49      64 .]      57      72 ..      52      72 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.4e-05
                                      -HHHHHHHHTS-HHHHHHHHHHHHH CS
                              GntR 26 sereLaaefgVsrttvReALrrLea 50
                                      +e e+a+ +g+sr+ v++AL+  +a
  gi|242399515|ref|YP_002994940.1| 20 REIEIAESLGISRQAVNKALKDAKA 44
                                      788*****************98876 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.2
                                      HHTTSEEEETTCEEEE CS
                              GntR 49 eaeglverrqgrGtfV 64
                                       ++ +v ++  +G+ V
  gi|242399515|ref|YP_002994940.1| 57 FSWEIVRVNAEKGFMV 72
                                      4677888888888876 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1   2.1e-05      0.02      26      47 ..      23      44 ..      14      45 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.1e-05
                                      HHHHHHTSSHHHHHHHHHHHHH CS
                            MarR_2 26 elarrlglsksavsrilkrLva 47
                                      e+a+ lg+s++av+++lk++ a
  gi|242399515|ref|YP_002994940.1| 23 EIAESLGISRQAVNKALKDAKA 44
                                      9*****************9987 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   3.5e-05     0.033      25      45 ..      22      42 ..       8      45 .. 0.88
   2 ?   -2.1   0.1       4.3     4e+03      47      60 ..     112     128 ..     106     130 .] 0.59

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.5e-05
                                      HHHHHHTTSSHHHHHHHHHHH CS
                         HTH_Crp_2 25 eelAsmlGltretvsrilseL 45
                                       e+A+ lG++r+ v+++l++ 
  gi|242399515|ref|YP_002994940.1| 22 IEIAESLGISRQAVNKALKDA 42
                                      59****************985 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.3
                                       HTTSEEE..TEE.EEES CS
                         HTH_Crp_2  47 reglisr..grr.iril 60 
                                       + g+i+r  +++ i++l
  gi|242399515|ref|YP_002994940.1| 112 ELGIIKRpdKKElIKVL 128
                                       56888843234466666 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00013      0.13      12      48 ..      21      57 ..      14      58 .. 0.82
   2 ?    0.1   0.1      0.93   8.8e+02      29      46 ..     111     129 ..     110     130 .] 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00013
                                      HHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHH CS
                             HTH_3 12 qeeLAeklGvsrstisriEnGernPsletlkklakaL 48
                                        e+Ae lG+sr+++++  ++  +   e  ++la+++
  gi|242399515|ref|YP_002994940.1| 21 EIEIAESLGISRQAVNKALKDAKAKLFEAFFALAETF 57
                                      5799*************99997778888888888765 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.93
                                       HHTT.SSCSBHHHHHHHHH CS
                             HTH_3  29 iEnG.ernPsletlkklak 46 
                                       +E G + +P+ + l+k+++
  gi|242399515|ref|YP_002994940.1| 111 LELGiIKRPDKKELIKVLE 129
                                       67788778******99875 PP

>> Sigma70_r3  Sigma-70 region 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2     7e-05     0.066      23      45 ..      21      43 ..       6      46 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7e-05
                                      HHHHHHHHTXXHHHHHHHHHHHX CS
                        Sigma70_r3 23 peEiAeeLglseekVrevleaar 45
                                      + EiAe+Lg+s + V ++l++a+
  gi|242399515|ref|YP_002994940.1| 21 EIEIAESLGISRQAVNKALKDAK 43
                                      67*******************98 PP

>> KORA  TrfB plasmid transcriptional repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   9.1e-05     0.086      29      57 ..      16      44 ..       5      72 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.1e-05
                              KORA 29 Vegkkqadvatelgltkqavsqavkrvwa 57
                                       ++ +  ++a+ lg+++qav++a k + a
  gi|242399515|ref|YP_002994940.1| 16 AKEMREIEIAESLGISRQAVNKALKDAKA 44
                                      56778889**************9886543 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0     9e-05     0.085      14      36 ..      20      42 ..      11      45 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9e-05
                            HTH_29 14 tvsqiAkllglsrrtvyrwlkrf 36
                                      +  +iA+ lg+sr+ v+++lk+ 
  gi|242399515|ref|YP_002994940.1| 20 REIEIAESLGISRQAVNKALKDA 42
                                      5569****************975 PP

>> DUF134  Protein of unknown function  DUF134
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   8.5e-05      0.08      41      83 ..       9      51 ..       2      55 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.5e-05
                            DUF134 41 eairlvdyedlkqeeaaklmGiskatlwrlltearkkiakalv 83
                                      e i  +  ++++  e a+ +Gis++++ + l++a+ k+ +a +
  gi|242399515|ref|YP_002994940.1|  9 EKIWTMRAKEMREIEIAESLGISRQAVNKALKDAKAKLFEAFF 51
                                      556666678999999***********************99986 PP

>> Sigma70_ECF  ECF sigma factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   0.00012      0.12     140     182 ..       7      49 ..       3      52 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00012
                       Sigma70_ECF 140 qarlvelrkleGlsveEiAeklgvskrtverrlalaRawlere 182
                                       +++++  ++ + +   EiAe lg+s+++v++ l+ a+a+l ++
  gi|242399515|ref|YP_002994940.1|   7 SMEKIWTMRAKEMREIEIAESLGISRQAVNKALKDAKAKLFEA 49 
                                       5556666666666777**********************99876 PP

>> UPF0122  Putative helix-turn-helix protein, YlxM / p13 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00014      0.14      38      62 ..      23      47 ..      13      60 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00014
                           UPF0122 38 EiAeefnvsrqavydnikrteklle 62
                                      EiAe   +srqav   +k +++ l+
  gi|242399515|ref|YP_002994940.1| 23 EIAESLGISRQAVNKALKDAKAKLF 47
                                      9*****************9987664 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   0.00016      0.15      15      45 ..      16      46 ..      10      47 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00016
                                      CTTS-HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                              GerE 15 aeGksnkeIAeelniSekTVkvhksnimkKL 45
                                      a+ +   eIAe+l+iS + V+  ++ +  KL
  gi|242399515|ref|YP_002994940.1| 16 AKEMREIEIAESLGISRQAVNKALKDAKAKL 46
                                      5566778**************9999999998 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0    0.0002      0.19      21      40 ..      22      41 ..      13      46 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0002
                            HTH_23 21 reIAreLgvsrrTvyrwlkr 40
                                       eIA+ Lg+sr+ v + lk 
  gi|242399515|ref|YP_002994940.1| 22 IEIAESLGISRQAVNKALKD 41
                                      59*************99986 PP

>> EssA  WXG100 protein secretion system (Wss), protein EssA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00017      0.16      52      94 ..       8      49 ..       4      66 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00017
                              EssA 52 eeeinkkkkaEkkeieelkdsLFeeekesneavkdtkesLFss 94
                                       e+i   +++E  eie + +sL +  +  n+a+kd k +LF+ 
  gi|242399515|ref|YP_002994940.1|  8 MEKIWTMRAKEMREIE-IAESLGISRQAVNKALKDAKAKLFEA 49
                                      5788889999999996.99**********************86 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00033      0.32      21      44 ..      17      40 ..      14      45 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00033
                                      CCCHHCHHCCCTTSSCHCHHHHHH CS
                              TrmB 21 gpatadeiaeelgvprskvYevLr 44
                                      ++++  eiae lg++r+ v+++L+
  gi|242399515|ref|YP_002994940.1| 17 KEMREIEIAESLGISRQAVNKALK 40
                                      6778889***************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       765  (0.0426683); expected 358.6 (0.02)
Passed bias filter:                      645  (0.0359752); expected 358.6 (0.02)
Passed Vit filter:                       110  (0.00613531); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.47u 0.34s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 808.99
//
Query:       gi|242399516|ref|YP_002994941.1|  [L=235]
Description: hypothetical protein TSIB_1541 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       836  (0.0466284); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.37s 00:00:00.91 Elapsed: 00:00:00.52
# Mc/sec: 1363.54
//
Query:       gi|242399517|ref|YP_002994942.1|  [L=231]
Description: hypothetical protein TSIB_1542 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score 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   0.0      0.023   14.8   0.0    1.4  1  bPH_5     Bacterial PH domain
      0.088   12.9   0.0       0.18   11.9   0.0    1.4  1  bPH_4     Bacterial PH domain


Domain annotation for each model (and alignments):
>> bPH_5  Bacterial PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   2.5e-06     0.023       3      49 ..      59     104 ..      57     107 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.5e-06
                             bPH_5   3 yildeeglvIrwifgkeeIplseIeavrvsegvikgvrlfgtskpgy 49 
                                       + ++e+ lv++ +f  ++Ip++eI++v   +++ kgv+lf + +++ 
  gi|242399517|ref|YP_002994942.1|  59 VEIKENMLVLKYPFWSVKIPFEEIREVMLANEL-KGVKLFRYAWKNA 104
                                       6789999**************************.6999998888776 PP

>> bPH_4  Bacterial PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0     2e-05      0.18       4      30 ..      60      86 ..      59      95 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2e-05
                             bPH_4  4 eitegvLliksGfirkkIpiedIkkir 30
                                      ei+e+ L+ k+ f++ kIp+e+I+++ 
  gi|242399517|ref|YP_002994942.1| 60 EIKENMLVLKYPFWSVKIPFEEIREVM 86
                                      699*********************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1029  (0.0573931); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1392.13
//
Query:       gi|242399518|ref|YP_002994943.1|  [L=104]
Description: hypothetical protein TSIB_1543 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score 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   14.4   0.9       0.03   14.0   0.6    1.4  1  Drf_FH3   Diaphanous FH3 Domain


Domain annotation for each model (and alignments):
>> Drf_FH3  Diaphanous FH3 Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.6   1.6e-06      0.03      76     125 ..      38      98 ..      24     101 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.6e-06
                                       HHHHHCTSCSHHHHHHHHHHHHHHHHHHHHHHHHHT...........XXXXXXXXXXXXXX CS
                           Drf_FH3  76 iidklreleneeLddqlqafeeerneDeeellerae...........dktvdlddpeelfe 125
                                        +d + e+++e+L+ ++++fee+  +D++ +l+ ++           + +  ++d++++ +
  gi|242399518|ref|YP_002994943.1|  38 FLDDMLESKDEKLKYAMKKFEENGVDDAKLVLKGNNavlvlkiedviSIRFVFEDVQSIAQ 98 
                                       6899*************************99988886666666666677777777777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1245  (0.0694406); expected 358.6 (0.02)
Passed bias filter:                      683  (0.0380947); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 654.78
//
Query:       gi|242399519|ref|YP_002994944.1|  [L=224]
Description: Serine/threonine protein kinase, RIO1 family [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-15   56.7   0.2    2.7e-15   56.4   0.2    1.2  1  RIO1            RIO1 family
    1.3e-13   50.9   0.5    1.7e-13   50.6   0.5    1.1  1  Pkinase         Protein kinase domain
    3.9e-13   49.3   0.4    4.8e-13   49.0   0.4    1.1  1  Pkinase_Tyr     Protein tyrosine kinase
    1.7e-11   43.9   0.2    2.5e-11   43.3   0.2    1.3  1  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family
    8.8e-10   38.9   0.2      7e-05   22.9   0.1    2.3  2  APH             Phosphotransferase enzyme family
     0.0002   21.1   0.3    0.00033   20.3   0.3    1.4  1  WaaY            Lipopolysaccharide core biosynthesis protein 
     0.0039   16.8   0.0       0.53    9.8   0.0    2.1  2  Choline_kinase  Choline/ethanolamine kinase
  ------ inclusion threshold ------
      0.048   13.0   0.0      0.092   12.0   0.0    1.5  1  EcKinase        Ecdysteroid kinase
      0.081   12.5   0.0        0.2   11.2   0.0    1.5  1  FTA2            Kinetochore Sim4 complex subunit FTA2


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 !   56.4   0.2   1.4e-18   2.7e-15      42     150 ..      43     150 ..       4     184 .. 0.82

  Alignments for each domain:
  == domain 1  score: 56.4 bits;  conditional E-value: 1.4e-18
                                       --GS-HHHHHHHHHHHHHHHHHHHHHTT--S--EEEE..ETTEEEEE--EETTEEGGBHHHCG-HHHHHHHHHHHHH CS
                              RIO1  42 ksktnprklvklwaekEfrnLkrleeagvpvPkpiel..krhvlvmefigedgvaapklkdveeeeeaeelyeevle 116
                                       + k    kl k  + +E r+L+r++e gv++P ++e+  k+  +vme+i+  g ++++  ++ + ee  +l +e+ +
  gi|242399519|ref|YP_002994944.1|  43 RIKEIDEKLRKERTVREARILHRAKEFGVNAPYVYEVdlKDMKIVMEYIE--GERLKEYLEAVSMEERLKLCREIGK 117
                                       345556778889999******************9865227889*******..777776555554668888******* PP

                                       HHHHHHHTSTEEESS-STTSEEEETTEEEE--GT CS
                              RIO1 117 emrklykeaglvHaDLSeyNvlvdedkvviIDvs 150
                                       +m kl  eag+vH+DL   N+++  +k+++ID++
  gi|242399519|ref|YP_002994944.1| 118 QMGKLH-EAGIVHGDLTTSNMILRGGKIYFIDFG 150
                                       *99998.*************************96 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.6   0.5   8.4e-17   1.7e-13      28     147 ..      43     154 ..      25     177 .. 0.86

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 8.4e-17
                                       EEEEEECHCHCHHHHHHHHHHHHHHHHHSCTTB--EEEEEEESSEEEEEEE--TTEBHHHHHHHHSS--HHHHHHHH CS
                           Pkinase  28 AvKkikkekakkkkekkvlrEikilkklkhpnivrlyevfeekdelylvleyveggeladllerkgslseeeakkia 104
                                        +K+i+++ +k    ++++rE +il++ k   +   y +  + +++ +v+ey+eg+ l+++le   ++s+ee  k++
  gi|242399519|ref|YP_002994944.1|  43 RIKEIDEKLRK----ERTVREARILHRAKEFGVNAPYVYEVDLKDMKIVMEYIEGERLKEYLE---AVSMEERLKLC 112
                                       34444433333....6789**********99999999999999*******************9...599******** PP

                                       HHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSEE CS
                           Pkinase 105 kqilegleylHskgiiHrDlKpeNiLidekgelKitDFGlake 147
                                       ++i + +  lH++gi+H Dl ++N+++   g++  +DFGla+ 
  gi|242399519|ref|YP_002994944.1| 113 REIGKQMGKLHEAGIVHGDLTTSNMILR-GGKIYFIDFGLAEF 154
                                       ****************************.9***********86 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.0   0.4   2.4e-16   4.8e-13       2     153 ..       2     155 ..       1     182 [. 0.80

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 2.4e-16
                                       EEEEEEEEESSEEEEEEEEET.TTTSSEEEEEEEEE.......STTSSHHHHHHHHHHHHHHHTS-BTTB--EEEEE CS
                       Pkinase_Tyr   2 elgkklGeGafGkVvegtlkg.ekekkevkVavKtl.......keeateeekeelleeakimkklkhpnivkllgvc 70 
                                       ++ k + +Ga +k++ ++ ++     +e+kV++K         ke  ++ +ke+ ++ea+i+++ k   + + +   
  gi|242399519|ref|YP_002994944.1|   2 KVMKLIKQGAEAKIYLASFEElYFPFNEEKVIIKHRipkryriKEIDEKLRKERTVREARILHRAKEFGVNAPYVYE 78 
                                       567889999*********9998777788999999753211111344444458889999****999999998888888 PP

                                       ESSSSEEEEEE--TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEETTEEEE-ST CS
                       Pkinase_Tyr  71 tkeepllivteyvkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLlsenkvvkisDf 147
                                       ++ + + iv+ey++g  L+++L++      ++++ l+++ ++ k m  L++  +vH dl++ N++l+ + ++   Df
  gi|242399519|ref|YP_002994944.1|  79 VDLKDMKIVMEYIEGERLKEYLEAV-----SMEERLKLCREIGKQMGKLHEAGIVHGDLTTSNMILR-GGKIYFIDF 149
                                       89999*****************986.....9*********************************999.6677788** PP

                                       TTHEET CS
                       Pkinase_Tyr 148 GLardi 153
                                       GLa+  
  gi|242399519|ref|YP_002994944.1| 150 GLAEFD 155
                                       **9854 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.3   0.2   1.3e-14   2.5e-11      52     207 .]      50     191 ..      34     191 .. 0.90

  Alignments for each domain:
  == domain 1  score: 43.3 bits;  conditional E-value: 1.3e-14
                               Kdo  52 klgrtravrEfrllkrLeeagvavpkpvaagavkvgleyrAlllterlegaqdLedllakwaelaeelkrallkavg 128
                                       kl + r vrE r+l+r +e gv++p+      + +       +++e +eg + L+++l+    ++ e + +l +++g
  gi|242399519|ref|YP_002994944.1|  50 KLRKERTVREARILHRAKEFGVNAPYVYEVDLKDM------KIVMEYIEG-ERLKEYLEA---VSMEERLKLCREIG 116
                                       577889*******************9766665555......59******9.56******8...88899999****** PP

                               Kdo 129 rliaklhragvnHadlyaknillqqeeeeeaeiwliDldkarlrlradrwrekdLarLkrsfl..kielteadweal 203
                                       + + klh+ag+ H+dl   n+ l+ ++     i++iD+  a+  +    ++  dL+ L r ++  + ++ e+ +e++
  gi|242399519|ref|YP_002994944.1| 117 KQMGKLHEAGIVHGDLTTSNMILRGGK-----IYFIDFGLAEFDS-SLEAQGVDLHLLRRAMEstHYKWFEKGFEEV 187
                                       ************************996.....**********999.999*******999987798999********* PP

                               Kdo 204 lraY 207
                                       l++Y
  gi|242399519|ref|YP_002994944.1| 188 LKGY 191
                                       **99 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   4.6e-06    0.0091      32     108 ..      51     125 ..      31     126 .. 0.80
   2 !   22.9   0.1   3.5e-08     7e-05     165     197 ..     124     153 ..     123     210 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4.6e-06
                                       S-HHHHHHHHHHHHHHHHTT-B--B-CTTBS-EEETTEEEEEEE----EE-SS...HHHHHHHHHHHHHHHHHHCCH CS
                               APH  32 raaeeirrevallrlLakagvpvPevlagdtddeeigllfalieyvpgrsllr...klsaaqlpellealgeflaal 105
                                         +e++ re+++l+   + gv +P v+  d  d  i      +ey++g+ l +   + s++++ +l++++g   ++l
  gi|242399519|ref|YP_002994944.1|  51 LRKERTVREARILHRAKEFGVNAPYVYEVDLKDMKIV-----MEYIEGERLKEyleAVSMEERLKLCREIGKQMGKL 122
                                       467788899999999999999*****99655555555.....7777777777777799******************* PP

                                       HCH CS
                               APH 106 hqv 108
                                       h++
  gi|242399519|ref|YP_002994944.1| 123 HEA 125
                                       *97 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 3.5e-08
                                       -EEEE-SS-SGGGEEEC..TTEEEEE---TT-E CS
                               APH 165 ptvllHgDlhpgNllvdpddgrvtGviDfedag 197
                                       +++++HgDl + N++++  +g++ ++iDf++a 
  gi|242399519|ref|YP_002994944.1| 124 EAGIVHGDLTTSNMILR--GGKI-YFIDFGLAE 153
                                       5789*************..9**9.******985 PP

>> WaaY  Lipopolysaccharide core biosynthesis protein (WaaY)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.3   1.7e-07   0.00033     119     179 ..      85     150 ..      31     170 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.7e-07
                              WaaY 119 imiieyiegielvdm...peiddevk..akikqsieklhqlgmvsgdphrgnfivkkdevriidls 179
                                        +++eyieg  l +     ++++ +k   +i + + klh+ g+v gd    n+i++++++  id+ 
  gi|242399519|ref|YP_002994944.1|  85 KIVMEYIEGERLKEYleaVSMEERLKlcREIGKQMGKLHEAGIVHGDLTTSNMILRGGKIYFIDFG 150
                                       46789999987765411145667666447999*******************************974 PP

>> Choline_kinase  Choline/ethanolamine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0      0.01        21      48      81 ..      87     125 ..      49     128 .. 0.60
   2 !    9.8   0.0   0.00026      0.53     149     174 ..     129     152 ..     124     166 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.01
                                       EEE--TCEE--T..TGGGCH...HHHHHHHHHHHHHTTC CS
                    Choline_kinase  48 ieefiesrtlst..edlrep...eiskkiAkklaelHsl 81 
                                       + e+ie+++l+   e ++ +   ++ ++i+k++++lH+ 
  gi|242399519|ref|YP_002994944.1|  87 VMEYIEGERLKEylEAVSMEerlKLCREIGKQMGKLHEA 125
                                       4577777766532233333211256889*********85 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00026
                                       -S--SGGGEEE.-CTTEEEE--GTT- CS
                    Choline_kinase 149 HnDlqegNillnkeekklvlIDFEYa 174
                                       H Dl  +N++l    +k+++IDF  a
  gi|242399519|ref|YP_002994944.1| 129 HGDLTTSNMIL--RGGKIYFIDFGLA 152
                                       9**********..**********655 PP

>> EcKinase  Ecdysteroid kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   4.6e-05     0.092     211     252 ..     121     156 ..      63     194 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.6e-05
                          EcKinase 211 eeefnvlnHGDlwvnNimfkydeegepedvilvDFQlsrygS 252
                                       + + + ++HGDl ++N++++        +++++DF l+++ S
  gi|242399519|ref|YP_002994944.1| 121 KLHEAGIVHGDLTTSNMILRGG------KIYFIDFGLAEFDS 156
                                       3344679************886......79*******99988 PP

>> FTA2  Kinetochore Sim4 complex subunit FTA2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0    0.0001       0.2     165     208 ..      99     144 ..      81     152 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0001
                              FTA2 165 ellkeqeelevsqlpkllrdlkklhklgIvvrDlkeenyi..dgkL 208
                                       +l   + e + +  +++ +++ klh++gIv+ Dl ++n+i  +gk+
  gi|242399519|ref|YP_002994944.1|  99 YLEAVSMEERLKLCREIGKQMGKLHEAGIVHGDLTTSNMIlrGGKI 144
                                       66666677778889999*******************9986547775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       652  (0.0363657); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 1486.67
//
Query:       gi|242399520|ref|YP_002994945.1|  [L=565]
Description: MutS-like DNA mismatch repair ATPase [Thermococcus sibiricus MM 739]
Scores for complete 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      3e-07   30.7   0.0    1.4  1  MutS_V     MutS domain V
    0.00038   20.5   0.2     0.0024   17.9   0.0    2.4  2  AAA_14     AAA domain
     0.0018   18.7   0.9        8.8    6.7   0.1    3.6  3  AAA_16     AAA ATPase domain
     0.0055   16.6  10.6      0.046   13.5   0.4    3.8  4  AAA_21     AAA domain, putative AbiEii toxin, Type IV TA syst
     0.0064   16.9   1.8      0.026   15.0   0.0    2.4  2  AAA        ATPase family associated with various cellular act
     0.0078   16.8   1.1       0.11   13.2   0.2    3.2  3  CdiI_2     CdiI immunity protein
     0.0083   16.0   0.0      0.046   13.6   0.0    2.2  3  CPT        Chloramphenicol phosphotransferase-like protein
  ------ inclusion threshold ------
      0.015   15.5   0.1       0.04   14.2   0.0    1.8  1  AAA_28     AAA domain
      0.045   13.9   1.5       0.33   11.1   0.2    2.7  2  Gp49       Phage derived protein Gp49-like (DUF891)
       0.35   10.9   3.8        3.8    7.6   0.1    3.1  2  CARD_2     Caspase recruitment domain
        0.4   11.2   2.6        1.7    9.2   0.4    2.7  2  ABC_tran   ABC transporter
       0.45   10.6   4.9        1.6    8.8   4.6    2.1  1  7TMR-HDED  7TM-HD extracellular
        0.9    9.8   4.7        2.1    8.6   0.6    2.6  2  MRP-L51    Mitochondrial ribosomal subunit
        5.6    7.7   6.9         37    5.1   0.0    3.3  3  DUF2203    Uncharacterized conserved protein (DUF2203)
        8.5    6.9   7.0        6.9    7.2   4.0    2.4  2  DUF2779    Domain of unknown function(DUF2779)


Domain annotation for each model (and alignments):
>> MutS_V  MutS domain V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.0   2.5e-10     3e-07       1      86 [.     379     461 ..     379     522 .. 0.88

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 2.5e-10
                                       EEEE-STTSSHHHHHHHHHHHHHHHHHT--BSSSEEEEE--SEEEEEE--------SS-HHHHHHHHHHHHHTT--T CS
                            MutS_V   1 llitGpnmaGkstylrqvalivllaqiGsfvpaekaeisivdkiftRvgasDdlakgkstFmvEmlEtasilknate 77 
                                       +++tG+n +Gk ++l  ++ iv+l+++G  vpaeka ++++d++f       + + g  tF + +   a+ l +  +
  gi|242399520|ref|YP_002994945.1| 379 VILTGANSGGKTSLLELISQIVILTHMGFPVPAEKAWVEPLDELFFFR--RKRSSYGAGTFETALRSFARSLAKEGK 453
                                       599****************************************98643..567788999*******99999998765 PP

                                       TSEEEEEST CS
                            MutS_V  78 kslvilDEl 86 
                                         l+++DE 
  gi|242399520|ref|YP_002994945.1| 454 -KLILIDEF 461
                                       .59999997 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.2       1.2   1.4e+03      57      99 ..     172     212 ..     143     231 .. 0.57
   2 !   17.9   0.0     2e-06    0.0024       3      86 ..     377     474 ..     375     548 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.2
                            AAA_14  57 leklkeekktylflDEiqevpewekalkslvdeg.knldvivtG 99 
                                        + +++++k +  lDEi +    ek l++ ++e  k++ + +tG
  gi|242399520|ref|YP_002994945.1| 172 EK-VMKKRKLLSELDEIVRE--EEKRLNERIEELlKEFSLTLTG 212
                                       22.33356777778888554..2333333333333344555555 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 2e-06
                            AAA_14   3 kilvitGaRrvGKTtllkqlikell.......vkkesilyinldderdkkladpe.......kllelileklkeekk 65 
                                       +++++tGa   GKT ll+ + +  +       v++e+     ld+  + +++ ++       + l+ + ++l +e+k
  gi|242399520|ref|YP_002994945.1| 377 RVVILTGANSGGKTSLLELISQIVIlthmgfpVPAEKAWVEPLDELFFFRRKRSSygagtfeTALRSFARSLAKEGK 453
                                       79**************97765544488899*98989988888998777443322223342226677777776567** PP

                            AAA_14  66 tylflDEiqevpewekalksl 86 
                                       +++++DE   ++e   a+k +
  gi|242399520|ref|YP_002994945.1| 454 KLILIDEFEAITEPGAAVKII 474
                                       ***********8888777765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1      0.14   1.7e+02      80     129 ..     150     206 ..     129     230 .. 0.79
   2 !    6.7   0.1    0.0073       8.8      23      47 ..     375     399 ..     367     413 .. 0.83
   3 ?    5.6   0.0     0.016        19     115     164 ..     433     483 ..     411     491 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.14
                            AAA_16  80 ellrqlldeaesaeleawrekleeala......avpelagaeasrllellkrll.al 129
                                        + + l++++ s+e   + +++e++++      + +e+ ++e++rl+e + +ll ++
  gi|242399520|ref|YP_002994945.1| 150 NIKALLGEDSVSNEILVHLREIEKVMKkrkllsELDEIVREEEKRLNERIEELLkEF 206
                                       344555566888888888888888888999999899999999999999999998443 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0073
                            AAA_16  23 rpelvllsGesGvGKsslvrellra 47 
                                       ++++v+l+G+   GK+sl++ + + 
  gi|242399520|ref|YP_002994945.1| 375 GERVVILTGANSGGKTSLLELISQI 399
                                       3489***************998864 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.016
                            AAA_16 115 easrllellkrllallsrderplvlvlDdlqwade..aslqllaaLlrlles 164
                                       +a  +  +l+++++ l+++++  ++++D+++ + e  a  +++ +Ll+ +  
  gi|242399520|ref|YP_002994945.1| 433 GAGTFETALRSFARSLAKEGK-KLILIDEFEAITEpgAAVKIIGELLKIAHE 483
                                       45678899*****77777455.7999*****999977777778887776544 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.3   1.6e+03      95     156 ..      18      79 ..       6     127 .. 0.68
   2 ?    0.9   0.1      0.27   3.3e+02     126     197 ..     276     352 ..     250     361 .. 0.81
   3 !   13.5   0.4   3.9e-05     0.046       2      22 ..     379     399 ..     378     405 .. 0.90
   4 !    6.1   0.1    0.0072       8.5     255     297 ..     451     493 ..     431     494 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.3
                            AAA_21  95 esgllldkrsleeedvfnpeargirggvsvfslkelsvsepndlqfgkaltditsrawslll 156
                                        + l++ k+sl    +f+p+   + ++++ ++lk  ++++  +l+ + a ++ +++ +++l+
  gi|242399520|ref|YP_002994945.1|  18 IKNLIQLKESLVYLEKFFPTNNKEEIIRRQEYLKKNLPKIRPELKEFLAKIKPIRFRRDYLH 79 
                                       55555555555555666666666666666666666666666666666666666666666655 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.27
                            AAA_21 126 slkelsvsepndlqfgkaltditsrawsllllldglrke.....rigllnifadyfgfakekrllqrlvrslklvei 197
                                       +++e  +se +++++++ ++++++ ++++++l   lr+e     +  +l+++ ++  +   ++l+++ ++ ++ +++
  gi|242399520|ref|YP_002994945.1| 276 ERIEAMRSELEREIKMEIYLKSREVLRKIRPLIPQLREElkrayELEFLRAVSEFTQGFAFPELIEGGIGFINGRHL 352
                                       678888999999*********************99999999888777777777777777777777777777666655 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 3.9e-05
                            AAA_21   2 nvliGpNgsGKSnLLdaldll 22 
                                        +l+G+N+ GK++LL++++ +
  gi|242399520|ref|YP_002994945.1| 379 VILTGANSGGKTSLLELISQI 399
                                       69****************865 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.0072
                            AAA_21 255 lkkgsllliDEpEngLHPkllrrll.ellkelsrngaQviltTH 297
                                        +k +l+liDE+E+  +P +  +++ ellk+++++   v++++H
  gi|242399520|ref|YP_002994945.1| 451 EGK-KLILIDEFEAITEPGAAVKIIgELLKIAHEREFYVVIVSH 493
                                       233.9*************66655555999***999999999998 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 ?    0.3   0.7      0.73   8.7e+02      61      75 ..     165     188 ..     138     258 .. 0.64
   2 !   15.0   0.0   2.1e-05     0.026       1     117 [.     379     500 ..     379     513 .. 0.70

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.73
                                       EEEEETGGGHHHHH.........T CS
                               AAA  61 ilfiDEidalaksr.........s 75 
                                        + + Ei++++k+r          
  gi|242399520|ref|YP_002994945.1| 165 LVHLREIEKVMKKRkllseldeiV 188
                                       444555555555553322221111 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 2.1e-05
                                       EEEESSTTSSHHHHHHHHHHHH.....THE...............EEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS CS
                               AAA   1 vllyGppGtGKTllakavakel.....gve...............fleisgsellskyvgesekkirelfkeakeka 57 
                                       v+l+G    GKT+l + + + +     g++               f++ + s+      g  e  +r + +++ ++ 
  gi|242399520|ref|YP_002994945.1| 379 VILTGANSGGKTSLLELISQIVilthmGFPvpaekawvepldelfFFRRKRSSYG---AGTFETALRSFARSLAKEG 452
                                       689999999***********95444443334445555555555557888888887...9999******999966665 PP

                                       TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTH CS
                               AAA  58 kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldp 117
                                        ++ ++iDE++a+++         + +++ +Ll+   + +     + v+++++  ++l++
  gi|242399520|ref|YP_002994945.1| 453 -KKLILIDEFEAITEPG------AAVKIIGELLKIAHERE-----FYVVIVSHLGEDLKR 500
                                       .6***********8777......66777777777665543.....455555655555555 PP

>> CdiI_2  CdiI immunity protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.99   1.2e+03      39      70 ..      10      42 ..       3      68 .. 0.79
   2 !   13.2   0.2   8.8e-05      0.11      25      89 ..     162     224 ..     153     225 .. 0.86
   3 ?   -2.6   0.0       7.5     9e+03      24      49 ..     437     463 ..     434     486 .. 0.53

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.99
                            CdiI_2 39 evaelideieellassldee.leeaflaelgae 70
                                        + ++dei++l++++++   le+ f ++ ++e
  gi|242399520|ref|YP_002994945.1| 10 IYKGIRDEIKNLIQLKESLVyLEKFFPTNNKEE 42
                                      567889999999999988778888886666555 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 8.8e-05
                            CdiI_2  25 eeiledYvssespeevaelideieellassldeeleeaflaelgaefdpeawgltarefLeevae 89 
                                       +eil   ++ e+ ++ ++l++e++e+++++++  l+e + +el +ef+ ++ g    +fL++++e
  gi|242399520|ref|YP_002994945.1| 162 NEILVHLREIEKVMKKRKLLSELDEIVREEEKR-LNERI-EELLKEFSLTLTGKDLLDFLKKLKE 224
                                       56666667778888999***********98865.*****.99*******************9985 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 7.5
                            CdiI_2  24 ieeiledYvssespe.evaelideiee 49 
                                       +e +l+++ +s  +e +   lide+e+
  gi|242399520|ref|YP_002994945.1| 437 FETALRSFARSLAKEgKKLILIDEFEA 463
                                       555666665554332033334444444 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       3.9   4.7e+03      89     115 ..     185     212 ..     184     218 .. 0.85
   2 ?   -1.5   0.0       1.7     2e+03      65     103 ..     219     257 ..     193     288 .. 0.68
   3 !   13.6   0.0   3.9e-05     0.046       2     106 ..     377     478 ..     376     517 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 3.9
                                       EE--TTTHH.HHHHHHHHHTTS-EEEEE CS
                               CPT  89 Ddvilekew.lvdllrrllsgldvllVG 115
                                       D+++ e+e+ l +++++ll+++ + l G
  gi|242399520|ref|YP_002994945.1| 185 DEIVREEEKrLNERIEELLKEFSLTLTG 212
                                       888888888899*******999888776 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.7
                                       HHHHHHHHHHHHHHHHHTT-EEEEEE--TTTHHHHHHHH CS
                               CPT  65 ldlllaalyeavaamaraGnnvivDdvilekewlvdllr 103
                                       l++l ++ ye++ ++  +  n i+ +++ ++e l++ll+
  gi|242399520|ref|YP_002994945.1| 219 LKKLKEGDYESIFSHFSQVENEILEEMVKSEERLSNLLE 257
                                       566777888888888888888888888888888777663 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 3.9e-05
                                       -EEEEEE-TTSSHHHHHHHHHHHSSS-EEEEEHHHHHHHS-GGGGTSTTSEEEETTSEEE-HHHHHHHHHHHHHHHH CS
                               CPT   2 riilLnGgsssGKsslaralqevldepwlhlgvDafvealppkrqdeadglefeteleeigpeldlllaalyeavaa 78 
                                       r+++L G+ s GK+sl + + +++  +++ ++v a      ++ +++ d+l f+  ++ +     ++++al+   ++
  gi|242399520|ref|YP_002994945.1| 377 RVVILTGANSGGKTSLLELISQIVILTHMGFPVPAE-----KAWVEPLDELFFF-RRKRSSYGAGTFETALRSFARS 447
                                       79**********************999999988653.....3455566677555.4444555556666666666677 PP

                                       HHHTT-EEE.EE..E--TTTHHHHHHHHHHH CS
                               CPT  79 maraGnnvi.vD..dvilekewlvdllrrll 106
                                        a++G+++i +D  ++i+e+ ++v+++ +ll
  gi|242399520|ref|YP_002994945.1| 448 LAKEGKKLIlIDefEAITEPGAAVKIIGELL 478
                                       7888888762455555666665666665655 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   3.3e-05      0.04       2      29 ..     379     412 ..     378     460 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.3e-05
                            AAA_28   2 ivitGgestGKTtlleaLa.....ar.gypvvpE 29 
                                       +++tG+ s+GKT+lle ++      + g+pv +E
  gi|242399520|ref|YP_002994945.1| 379 VILTGANSGGKTSLLELISqivilTHmGFPVPAE 412
                                       89**************999444443368887754 PP

>> Gp49  Phage derived protein Gp49-like (DUF891)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   0.00028      0.33       6      57 ..      35      85 ..      30      91 .. 0.92
   2 ?    0.5   0.1      0.57   6.9e+02       1      43 [.     217     258 ..     217     261 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00028
                              Gp49  6 lpkkarakilaaldlleeggpdlgkplvkkledglwElrpksaggiiRvlya 57
                                      +p++ +++i++  ++l+++ p+++++l+++l  +++ +r++++  + R+l +
  gi|242399520|ref|YP_002994945.1| 35 FPTNNKEEIIRRQEYLKKNLPKIRPELKEFLA-KIKPIRFRRDYLHDRLLVV 85
                                      699****************************9.***************9976 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.57
                              Gp49   1 eeldalpkkarakilaaldlleeggpdlgkplvkkle..dglwEl 43 
                                       ++l++l +  +++i+ +++++e++     +++vk  e  ++l E+
  gi|242399520|ref|YP_002994945.1| 217 DFLKKLKEGDYESIFSHFSQVENEI---LEEMVKSEErlSNLLEI 258
                                       6999*****************9985...45555554444566665 PP

>> CARD_2  Caspase recruitment domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.1    0.0031       3.8      10      45 ..      12      47 ..       4      55 .. 0.87
   2 ?    2.3   1.2      0.14   1.7e+02      12      68 ..     167     225 ..     158     249 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0031
                                      HHTHHHH.TT--HHHHGGG-T.TS-HHHHHHHHHHH CS
                            CARD_2 10 rllrprlketikpseilphltecLteedkeeIraee 45
                                      + +r+++k+ i+ +e l +l++++ ++ keeI +++
  gi|242399520|ref|YP_002994945.1| 12 KGIRDEIKNLIQLKESLVYLEKFFPTNNKEEIIRRQ 47
                                      67899**************************98765 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.14
                                       THHHH.TT--HHHHGGG-T.TS-HHH...HHHHHHHHHHHHHHHHHHHHHHHHCT..STT CS
                            CARD_2  12 lrprlketikpseilphltecLteed...keeIraeeenkGniaaaeeLldrllrsekeg 68 
                                       + +++++ +k +++l++l+e+ +ee+    e+I+   ++ + + + + Lld l++  keg
  gi|242399520|ref|YP_002994945.1| 167 HLREIEKVMKKRKLLSELDEIVREEEkrlNERIEELLKEFSLTLTGKDLLDFLKK-LKEG 225
                                       5677888888888888888888888855557888777777777777777777777.4444 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1      0.57   6.9e+02      52     100 ..     162     214 ..     143     253 .. 0.69
   2 ?    9.2   0.4    0.0014       1.7      10      35 ..     375     400 ..     368     406 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.57
                                       B-HHHCCHCEEEE-SS--S-TTSB..HHHH..HHHTCHHHHHHHSTTGGTTCB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx..xxxx..xxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  52 qeleslrkeigvlpqepqlfpelt..vren..esdeeiekalsklglkelkdt 100
                                       +e+ +  +ei+ + ++ +l +el   vre+    +e+ie++l++++l+ + ++
  gi|242399520|ref|YP_002994945.1| 162 NEILVHLREIEKVMKKRKLLSELDeiVREEekRLNERIEELLKEFSLTLTGKD 214
                                       44555556777777776666666554555566777788888888887764444 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0014
                                       TTSEEEEEESTTSSHHHHHHHHTTSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  10 egekvaivGenGaGKStLlkllagll 35 
                                         ++v ++G n  GK++Ll+l+++ +
  gi|242399520|ref|YP_002994945.1| 375 GERVVILTGANSGGKTSLLELISQIV 400
                                       45667789**************9876 PP

>> 7TMR-HDED  7TM-HD extracellular
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   4.6    0.0013       1.6      54     131 ..     178     279 ..       8     313 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0013
                         7TMR-HDED  54 enlleeleelratseenlselieqlkqarekyaqagaelsdeelr.allelsdeeleelqqgieqilerilsqgipe 129
                                       ++ll+el+e+ +++e+ l+e+ie+l ++++ +      l+  +l  +l +l++++ e + +  +q+ ++il++ +++
  gi|242399520|ref|YP_002994945.1| 178 RKLLSELDEIVREEEKRLNERIEELLKEFSLT------LTGKDLLdFLKKLKEGDYESIFSHFSQVENEILEEMVKS 248
                                       45666666655599***************999......766666669*9**********************997777 PP

                         7TMR-HDED 130 d.............................e 131
                                       +                             e
  gi|242399520|ref|YP_002994945.1| 249 EerlsnlleidveifsreslypvevpteriE 279
                                       7555555555555555555555555543433 PP

>> MRP-L51  Mitochondrial ribosomal subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.3       0.2   2.4e+02      45      88 ..      12      54 ..       4      69 .. 0.74
   2 ?    8.6   0.6    0.0018       2.1      50      88 ..     169     206 ..     160     209 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.2
                           MRP-L51 45 rgvkgnElqrllrkrklvaeklkeaepek.wkelekrikyLykkl 88
                                      +g++ +E++ l++ ++ +   l++++p++  +e+ +r++yL k+l
  gi|242399520|ref|YP_002994945.1| 12 KGIR-DEIKNLIQLKESLVY-LEKFFPTNnKEEIIRRQEYLKKNL 54
                                      4555.788888888877766.677777651556788888987765 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0018
                           MRP-L51  50 nElqrllrkrklvaeklkeaepekwkelekrikyLykkl 88 
                                        E++++++krkl++e l+e   e+ k+l+ ri+ L+k++
  gi|242399520|ref|YP_002994945.1| 169 REIEKVMKKRKLLSE-LDEIVREEEKRLNERIEELLKEF 206
                                       5999***********.99*****************9976 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.031        37       7      71 ..       6      70 ..       4      80 .. 0.91
   2 ?    3.2   2.1      0.11   1.4e+02      30      91 ..     165     223 ..     138     268 .. 0.62
   3 ?   -2.2   0.0       5.5   6.5e+03      19      39 ..     242     262 ..     228     303 .. 0.48

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.031
                           DUF2203  7 eAnalLpllkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeiee 71
                                      eA+a+   +++ +++l++l++ l  le+   ++++e+  + +++l+++l +++ e++e++++i+ 
  gi|242399520|ref|YP_002994945.1|  6 EAKAIYKGIRDEIKNLIQLKESLVYLEKFFPTNNKEEIIRRQEYLKKNLPKIRPELKEFLAKIKP 70
                                      89999999*****************999999988888888899*****************99975 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.11
                           DUF2203  30 eeleeeleeakaeaekse.....aaeleaeleeleaeieelveeieelGvevkdleaglvDFpakld 91 
                                            +l+e+++ ++k++      +  ++e+++l+++ieel++e+      + + +  l+DF  kl+
  gi|242399520|ref|YP_002994945.1| 165 LV---HLREIEKVMKKRKllselDEIVREEEKRLNERIEELLKEF---SLTLTGKD--LLDFLKKLK 223
                                       22...3333333333333322345555556666666666665555...34444443..467766655 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 5.5
                           DUF2203  19 leelralrkeleeleeeleea 39 
                                       lee+++ +++l +l e   e+
  gi|242399520|ref|YP_002994945.1| 242 LEEMVKSEERLSNLLEIDVEI 262
                                       444444444444443322222 PP

>> DUF2779  Domain of unknown function(DUF2779)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       8.5     1e+04      43      43 ..      48      48 ..      12      73 .. 0.51
   2 ?    7.2   4.0    0.0058       6.9      51      98 ..     174     256 ..     155     323 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 8.5
                           DUF2779 43 e 43
                                      e
  gi|242399520|ref|YP_002994945.1| 48 E 48
                                      2 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0058
                           DUF2779  51 tdpreelieeLikiieke....................................gsvvvynksfEksrlkelaqlfp 91 
                                       + ++++l++eL +i+++e                                     s++ ++++ E+++l+e+ +  +
  gi|242399520|ref|YP_002994945.1| 174 VMKKRKLLSELDEIVREEekrlnerieellkefsltltgkdlldflkklkegdyESIFSHFSQVENEILEEMVKSEE 250
                                       455666666666666555566666666666666666889999999999999999*******************8544 PP

                           DUF2779  92 eykeelk 98 
                                       +++ +l 
  gi|242399520|ref|YP_002994945.1| 251 RLS-NLL 256
                                       444.333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (565 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1073  (0.0598472); expected 358.6 (0.02)
Passed bias filter:                      613  (0.0341904); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); 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: 0.80u 0.37s 00:00:01.17 Elapsed: 00:00:00.53
# Mc/sec: 3203.12
//
Query:       gi|242399521|ref|YP_002994946.1|  [L=157]
Description: Probable molybdenum cofactor biosynthesis protein C [Thermococcus sibiricus MM 739]
Scores for complete 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-52  175.8   0.4    5.6e-52  175.4   0.4    1.0  1  MoaC      MoaC family


Domain annotation for each model (and alignments):
>> MoaC  MoaC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.4   0.4   3.1e-56   5.6e-52       1     134 [.      17     155 ..      17     156 .. 0.98

  Alignments for each domain:
  == domain 1  score: 175.4 bits;  conditional E-value: 3.1e-56
                                       E---TTS--EEEEEEEEEEEEE-HHHHHHHHTTSSTTB-HHHHHHHHHHHHHHHHHHHSTT-----EEEEEEEEEEE CS
                              MoaC   1 mvdvsekeetkrtAvAegrvklseetlelikekklkkGdvlavariagimaaKktseliplcHplpltkvevelele 77 
                                       mv+v++ke++ r+A+A+gr+kl++et++li+e+k+kkG+v+a a+iagi+a+K+t+e+iplcHp+plt v++ +e  
  gi|242399521|ref|YP_002994946.1|  17 MVEVGQKEVVFRKAIAKGRIKLKPETIRLIQEGKTKKGNVIASAQIAGILAVKRTWEIIPLCHPIPLTGVDIAFEFG 93 
                                       9*************************************************************************876 PP

                                       TTTTEEEEEEEEEEEESS--HHHHHHHHHHHHHHHHHHHTTTHTT.......-EEEEEEEEEEE CS
                              MoaC  78 eeeesveieatvktegktGvemEALtavsvaaltvyDmvKavdke.......mvieevrlveKs 134
                                         ++ +e +++v++  ktGvemEALt+vsva+lt++DmvKav+k+       ++ie++r+veK 
  gi|242399521|ref|YP_002994946.1|  94 --KDYIEATCEVRAYYKTGVEMEALTGVSVALLTIWDMVKAVEKDekgqypfTRIEDIRVVEKI 155
                                       ..8*****************************************99****************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1095.55
//
Query:       gi|242399522|ref|YP_002994947.1|  [L=116]
Description: hypothetical protein TSIB_1547 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-36  125.4   2.6    1.4e-36  125.2   2.6    1.0  1  YbjQ_1           Putative heavy-metal-binding
     0.0022   18.4   1.3        1.8    9.0   0.3    2.2  2  SeleniumBinding  Selenium binding protein


Domain annotation for each model (and alignments):
>> YbjQ_1  Putative heavy-metal-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.2   2.6   1.6e-40   1.4e-36       2     103 ..      12     112 ..      11     113 .. 0.98

  Alignments for each domain:
  == domain 1  score: 125.2 bits;  conditional E-value: 1.6e-40
                            YbjQ_1   2 ivtttesiegkeivevlgivtgetvrsrnvlkdilaglrslvGGelkayeeeleeareeAlerlkeeAeelGAnAvv 78 
                                       i++tte+++g+++v+vlg+ +g tvr+++++kdilaglr+++GGe+k+y+e+l+eare Aler+ ++A++ GAn ++
  gi|242399522|ref|YP_002994947.1|  12 IISTTENVPGYKVVKVLGLARGATVRAKHLGKDILAGLRNIAGGEVKEYTEMLAEAREVALERMIQDAKKRGANGII 88 
                                       89*************************************************************************** PP

                            YbjQ_1  79 gvrldtseigekgmlevlayGTAVk 103
                                       gvr+ ts +++ g++e++ayGTAV+
  gi|242399522|ref|YP_002994947.1|  89 GVRFMTSAVAS-GAAEIFAYGTAVI 112
                                       *********88.************8 PP

>> SeleniumBinding  Selenium binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0   0.00029       2.6       5      20 ..       9      24 ..       5      46 .. 0.83
   2 !    9.0   0.3   0.00021       1.8      39      73 ..      72     111 ..      51     115 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00029
                   SeleniumBinding  5 dkfiittaneiPGvel 20
                                      ++fii t++++PG ++
  gi|242399522|ref|YP_002994947.1|  9 EEFIISTTENVPGYKV 24
                                      68***********875 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00021
                   SeleniumBinding  39 lkaleekvkekkglaligfkl..tai.dg..kllGyGtav 73 
                                       l+ + + +k++++ ++ig +    a+  g  +++ yGtav
  gi|242399522|ref|YP_002994947.1|  72 LERMIQDAKKRGANGIIGVRFmtSAVaSGaaEIFAYGTAV 111
                                       5667788999999999997651144434478********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 771.69
//
Query:       gi|242399523|ref|YP_002994948.1|  [L=323]
Description: hypothetical protein TSIB_1548 [Thermococcus sibiricus MM 739]
Scores for complete 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-34  117.8  18.2      1e-33  116.9  18.2    1.4  1  ABC2_membrane_2  ABC-2 family transporter protein
    1.6e-13   50.5  30.1    1.6e-13   50.5  30.1    2.0  2  ABC2_membrane_3  ABC-2 family transporter protein
    1.5e-08   34.8  21.7    1.5e-08   34.8  21.7    2.3  3  ABC2_membrane_4  ABC-2 family transporter protein
    8.5e-07   28.6  24.9    8.5e-07   28.6  24.9    2.3  2  ABC2_membrane    ABC-2 type transporter
    0.00089   18.9  31.3    0.00089   18.9  31.3    2.8  2  ABC2_membrane_5  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 !  116.9  18.2   2.8e-37     1e-33       2     288 .]       5     322 ..       4     322 .. 0.89

  Alignments for each domain:
  == domain 1  score: 116.9 bits;  conditional E-value: 2.8e-37
                   ABC2_membrane_2   2 aiakkEfrdlvrsrrfllltvllplidvalaylkdlgsslqseakaikeatlaleyveaasasdeaedtdqdlkvvs 78 
                                        ia k+f  +vr ++f  ++ l+++i +al y++++ + +++++k+ ++     +++                    
  gi|242399523|ref|YP_002994948.1|   5 KIALKDFEVSVRTKKFQSTVGLFIIIAMALIYYSKILGISEESYKSPFQMVFLSSFSN------------------- 62 
                                       699***********************99999999999999999998887665533332................... PP

                   ABC2_membrane_2  79 timavlipviaalfgadaiagEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvllalaiilalgiv 155
                                        +++  i ++++lfga++i+ E e+gT+k+l +kP++R++i+lgK++g+++i   i   l++ + l++a+ l+ g +
  gi|242399523|ref|YP_002994948.1|  63 -AFTYSISLLGLLFGATSISNEIENGTMKILGTKPIYRSQIILGKLLGSSLI---IFAGLVIFYTLTVAFALIIGFP 135
                                       .688899*********************************************...4444444455567778888888 PP

                   ABC2_membrane_2 156 laledllllvvasvlllllv.vflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavp..... 226
                                       +  ed++++++ + +++l++  f ++gll+S+++r+s++ + +a+++f+++++l + ++  va + ag  +      
  gi|242399523|ref|YP_002994948.1| 136 FYQEDFVRFLITFPFSFLYGlIFSSFGLLISVFIRKSKNVLIMAIFIFIFFNVLLSTIAGVVALAIAGLPPVpelpe 212
                                       89999999999999999999999******************************99998866555555443335566* PP

                   ABC2_membrane_2 227 ...........................qeindflsllsptsayntllneilagsdlna................... 257
                                                                   + + +++++ p  +y+ + + ++ g+++ +                   
  gi|242399523|ref|YP_002994948.1| 213 nalnlteeeledlilkdpsyqawltelVNTTEKILYIAPNYHYQEIMRLLFGGKPQISevvsaitynemvvedrslg 289
                                       ***************************999************************9888******************* PP

                   ABC2_membrane_2 258 ..lgstatnllilllllavllvlgyvlFkrkDl 288
                                         lg+   n+++l ++ + +l ++y  F r+Dl
  gi|242399523|ref|YP_002994948.1| 290 esLGLILQNVIMLMIMFLLPLPVSYIKFIRADL 322
                                       ******************************997 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   1.6      0.16   5.7e+02     157     186 ..      18      46 ..       4      61 .. 0.57
   2 !   50.5  30.1   4.4e-17   1.6e-13     159     338 ..      56     308 ..      41     315 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.16
                   ABC2_membrane_3 157 snvasflvgliliilifitasfiavsiveE 186
                                       ++++s++  +i+i +++i++s i+ +i eE
  gi|242399523|ref|YP_002994948.1|  18 KKFQSTVGLFIIIAMALIYYSKIL-GISEE 46 
                                       444444444555555555555444.44444 PP

  == domain 2  score: 50.5 bits;  conditional E-value: 4.4e-17
                   ABC2_membrane_3 159 vasflvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilll..afgl.. 231
                                       + s +  ++ + +++++++f a+si +E e+++++++ + ++ ++q++l+k+lg+ l+ +  l+++  l  af+l  
  gi|242399523|ref|YP_002994948.1|  56 FLSSFSNAFTYSISLLGLLFGATSISNEIENGTMKILGTKPIYRSQIILGKLLGSSLIIFAGLVIFYTLtvAFALii 132
                                       5566777999**************************************************99887766444555566 PP

                   ABC2_membrane_3 232 gipfg.....nlglllllfllfglayialgyllsslfknsetaqilifivil....llsgffgglfp.ledlp.... 294
                                       g+pf+      +++++ +++l+gl+++++g+l+s+++++s+++ i+++++++    lls + g++ + +  lp    
  gi|242399523|ref|YP_002994948.1| 133 GFPFYqedfvRFLITFPFSFLYGLIFSSFGLLISVFIRKSKNVLIMAIFIFIffnvLLSTIAGVVALaIAGLPpvpe 209
                                       4777766466778888************************9988775555555776444444444334333333556 PP

                   ABC2_membrane_3 295 ...............................salkwifsiiPffapglgllrlitgd..plwe.............. 324
                                                                      +++ +i++i P++++ + + rl++g   +++e              
  gi|242399523|ref|YP_002994948.1| 210 lpenalnlteeeledlilkdpsyqawltelvNTTEKILYIAPNYHYQEIM-RLLFGGkpQISEvvsaitynemvved 285
                                       669999999**********99999999999999*************9999.6665552444448888999999999* PP

                   ABC2_membrane_3 325 .........illsliilalfavv 338
                                                il+++i+l +++++
  gi|242399523|ref|YP_002994948.1| 286 rslgeslglILQNVIMLMIMFLL 308
                                       ********999*********997 PP

>> ABC2_membrane_4  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8  21.7   4.3e-12   1.5e-08      15     175 ..      25     186 ..      16     189 .. 0.68
   2 ?    1.5   7.8     0.071   2.6e+02      99     155 ..     144     189 ..     140     207 .. 0.48
   3 ?   -1.0   0.2      0.41   1.5e+03     142     153 ..     296     307 ..     272     319 .. 0.51

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 4.3e-12
                   ABC2_membrane_4  15 vwllvlaallvpllallyfnllgktgldpaefyslsvfgftlllllplilgiiasylifrEeqndtlknLltiPvsr 91 
                                        +++++a++l+ +  +l +   ++++ +p +++ ls+f++ ++  + l+  ++++++i++E +n+t+k L t P+ r
  gi|242399523|ref|YP_002994948.1|  25 GLFIIIAMALIYYSKILGI--SEESYKSPFQMVFLSSFSNAFTYSISLLGLLFGATSISNEIENGTMKILGTKPIYR 99 
                                       3444444444444444443..356778889999999***9999888888889************************* PP

                   ABC2_membrane_4  92 tklllaKlivllllsvllmlvtflitvlfallsgfvgfsvklvlellkkclelgllvffavlpiial...vl.lkks 164
                                        +++l+Kl+   l++++ +++++++tv+fal++gf+ ++ + ++++l  +   +l+ +++++  +++   +   k+ 
  gi|242399523|ref|YP_002994948.1| 100 SQIILGKLLGSSLIIFAGLVIFYTLTVAFALIIGFPFYQ-EDFVRFLITFPFSFLYGLIFSSFGLLIsvfIRkSKNV 175
                                       **********************************99765.4555555444333333333333333331003203333 PP

                   ABC2_membrane_4 165 yvlpliltlvy 175
                                        ++++ + +++
  gi|242399523|ref|YP_002994948.1| 176 LIMAIFIFIFF 186
                                       34444444444 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.071
                   ABC2_membrane_4  99 livllllsvllmlvtflitvlfallsgfvgfsvklvlellkkclelgllvffavlpi 155
                                       +           l+tf +++l +l++ ++g+ ++ ++++ k +l++++++f+++ ++
  gi|242399523|ref|YP_002994948.1| 144 F-----------LITFPFSFLYGLIFSSFGLLISVFIRKSKNVLIMAIFIFIFFNVL 189
                                       3...........445555555555555555555555555555555555444433222 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.41
                   ABC2_membrane_4 142 lelgllvffavl 153
                                       l+ ++++++++l
  gi|242399523|ref|YP_002994948.1| 296 LQNVIMLMIMFL 307
                                       322222222211 PP

>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6  24.9   2.4e-10   8.5e-07      16     176 ..      16     190 ..       5     201 .. 0.79
   2 ?    1.1   0.2      0.06   2.2e+02     102     128 ..     288     313 ..     271     320 .. 0.74

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 2.4e-10
                     ABC2_membrane  16 rdpslgllwrliqplllalvfgtvfgnlg..nsedglnr......pgllffsvlflafsaltsvapvferergvler 84 
                                       r++     + l+ ++ +al++ + + ++   + ++ +++       +++  s+  l+ +++ +++++ e+e+g+++ 
  gi|242399523|ref|YP_002994948.1|  16 RTKKFQSTVGLFIIIAMALIYYSKILGISeeSYKSPFQMvflssfSNAFTYSISLLG-LLFGATSISNEIENGTMKI 91 
                                       444333367889999999999999998666532222233577888889999999999.78888889*********** PP

                     ABC2_membrane  85 elvsplyslsayvlakvlvelpvsllqalifllivyf...lvgldls.....rfflflllllltalaasslgllisa 153
                                       + + p+  +s ++l+k+l++ +++++  +if ++++    ++g++       rf++ +++ +l++l++ss+gllis+
  gi|242399523|ref|YP_002994948.1|  92 LGTKPI-YRSQIILGKLLGSSLIIFAGLVIFYTLTVAfalIIGFPFYqedfvRFLITFPFSFLYGLIFSSFGLLISV 167
                                       ******.8899*********7777777777766444413335777777799999*********************** PP

                     ABC2_membrane 154 lapsfedasqlaslvllplllls 176
                                       + ++ +++ ++a ++++++++l 
  gi|242399523|ref|YP_002994948.1| 168 FIRKSKNVLIMAIFIFIFFNVLL 190
                                       *****************999875 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.06
                     ABC2_membrane 102 lvelpvsllqalifllivyflvgldls 128
                                       l+e +  +lq +i+l+i+++l  l++s
  gi|242399523|ref|YP_002994948.1| 288 LGESLGLILQNVIMLMIMFLL-PLPVS 313
                                       566666777777888787777.77776 PP

>> ABC2_membrane_5  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9  31.3   2.5e-07   0.00089      29     167 ..      54     193 ..       8     217 .. 0.72
   2 ?    0.3   0.9      0.12   4.4e+02     110     139 ..     286     314 ..     269     318 .. 0.63

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.5e-07
                   ABC2_membrane_5  29 liflndsvllifsilslvisiililttlsyDekskwnkylltLPvtrkeiVksKYlfvlililiailitlllliiav 105
                                       ++fl+ s++  f++ + ++  +   t++s++  ++++k+l t P+ r++i+  K l++ ++i+++++i++ l++   
  gi|242399523|ref|YP_002994948.1|  54 MVFLS-SFSNAFTYSISLLGLLFGATSISNEIENGTMKILGTKPIYRSQIILGKLLGSSLIIFAGLVIFYTLTVAFA 129
                                       34443.34444555555555555779******************************999888888777766665555 PP

                   ABC2_membrane_5 106 likgn....vtisevllsiliglvialiflaivlPlyfkfgvekgrivliiiifgiifllvaifsl 167
                                       li g      ++  +l+++ ++++++lif+++ l +       k++ vli++if++if+ v ++ +
  gi|242399523|ref|YP_002994948.1| 130 LIIGFpfyqEDFVRFLITFPFSFLYGLIFSSFGLLISVFIR--KSKNVLIMAIFIFIFFNVLLSTI 193
                                       55555344455556777777777788888998888888887..44444444444444443333333 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.12
                   ABC2_membrane_5 110 nvtisevllsiliglvialiflaivlPlyf 139
                                       +  + e+l  il  +++ +i++ + lP+ +
  gi|242399523|ref|YP_002994948.1| 286 R-SLGESLGLILQNVIMLMIMFLLPLPVSY 314
                                       3.3567777777778888888888888777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1115  (0.0621897); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.71u 0.30s 00:00:01.01 Elapsed: 00:00:00.50
# Mc/sec: 1927.98
//
Query:       gi|242399524|ref|YP_002994949.1|  [L=308]
Description: ABC transporter [Thermococcus sibiricus MM 739]
Scores for complete 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-32  111.2   0.0    1.1e-31  110.2   0.0    1.5  1  ABC_tran        ABC transporter
    1.1e-10   42.1   1.4    2.2e-10   41.1   1.4    1.5  1  DUF4162         Domain of unknown function (DUF4162)
    3.9e-10   40.0   6.5    1.4e-07   31.6   0.0    3.0  3  AAA_21          AAA domain, putative AbiEii toxin, Type IV TA
  ------ inclusion threshold ------
      0.017   15.6   1.1      0.017   15.6   1.1    2.3  2  AAA_23          AAA domain
      0.019   14.8   0.2       0.05   13.4   0.0    1.7  2  MukB            MukB N-terminal
      0.042   13.6   0.1      0.074   12.8   0.1    1.3  1  AAA_29          P-loop containing region of AAA domain
      0.044   13.4   0.0       0.12   12.0   0.0    1.7  1  SRP54           SRP54-type protein, GTPase domain
       0.07   12.6   0.1         10    5.5   0.0    2.3  2  SMC_N           RecF/RecN/SMC N terminal domain
       0.15   11.4   0.0       0.23   10.8   0.0    1.2  1  Glyco_hydro_20  Glycosyl hydrolase family 20, catalytic domai


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.2   0.0   5.4e-35   1.1e-31       1     137 []      19     163 ..      19     163 .. 0.97

  Alignments for each domain:
  == domain 1  score: 110.2 bits;  conditional E-value: 5.4e-35
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       ++n++l++++g + +++G+nGaGK+t +  ++gl  p++G+i++ g+d+ + +  ++++ +g+lp++++l +elt+ 
  gi|242399524|ref|YP_002994949.1|  19 VDNLTLNIEKGIIFGFLGPNGAGKTTTILSMLGLIIPDNGKIQIMGHDVLK-SPIKAKNLLGYLPENATLYEELTAW 94 
                                       589************************************************.55567899***************** PP

                                       HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       +n             e++++ie++l+ +gl e++ ++v    +++S+G+kqr+ la+al+++p++l+lDEpt+
  gi|242399524|ref|YP_002994949.1|  95 RNleffasfyripnrEKEKRIEELLKLVGLWEVRYKRV----KNFSKGMKQRLLLAKALVNDPDVLILDEPTS 163
                                       **************999*********************....*****************************96 PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   1.4   1.1e-13   2.2e-10       1      81 []     216     301 ..     216     301 .. 0.90

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 1.1e-13
                                       E-HHHHHTTS.-SSEEEEE...-------..---EEEE-TTS-EEEEE-------------.----EEEEEEEE--- CS
                           DUF4162   1 GtleeiKrsy.gknrieve...adaeelleepgveeveeeggelelkledeeaanellkal.tsgveirsFeeeePs 72 
                                       G+l+ iK+++   + +e++   ++    l+++g+  ve+ +++ ++  ++e+ + ++ ++l ++g++i+s++ eePs
  gi|242399524|ref|YP_002994949.1| 216 GPLNHIKKQFmELEGYEIKietKQRMPELNVDGIIRVERIDERKSIIFTKEDIRAQISDYLtNKGITIVSLKIEEPS 292
                                       899*******888888888767778888899******999988888888889*********88************** PP

                                       HHHHHHHHH CS
                           DUF4162  73 LndIFiekv 81 
                                       L+d+F+++v
  gi|242399524|ref|YP_002994949.1| 293 LEDVFLKTV 301
                                       *******98 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.7   0.00041      0.82       2      22 ..      32      52 ..      31      68 .. 0.73
   2 !   31.6   0.0   7.2e-11   1.4e-07     236     298 ..     134     193 ..      70     198 .. 0.73
   3 ?    1.0   0.2      0.15     3e+02      27     110 ..     213     295 ..     206     307 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00041
                            AAA_21  2 nvliGpNgsGKSnLLdaldll 22
                                       ++ GpNg+GK++ +  + +l
  gi|242399524|ref|YP_002994949.1| 32 FGFLGPNGAGKTTTILSMLGL 52
                                      6789*********98777655 PP

  == domain 2  score: 31.6 bits;  conditional E-value: 7.2e-11
                            AAA_21 236 elSdGtkrllalltallralkkgsllliDEpEngLHP...kllrrllellkelsrngaQviltTHS 298
                                       ++S G+k+ l l+ al  ++   ++l++DEp +gL+P   +l+++++   ke++++g  v++++H 
  gi|242399524|ref|YP_002994949.1| 134 NFSKGMKQRLLLAKALVNDP---DVLILDEPTSGLDPegaHLVKSIV---KEEAKTGKTVFFSSHI 193
                                       34*******9*******999...9*************7777777777...***************5 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.15
                            AAA_21  27 rdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglrlersqveeklssvetllesgllldkr 103
                                       r + +l++++  + ++ +++ ++ +++  ++ +   +    + ++ r ++ + ++++++ +s++ t++++++ + k 
  gi|242399524|ref|YP_002994949.1| 213 RAIGPLNHIKKQFMELEGYEIKIETKQRMPELNVDGI-IRVERIDERKSIIFTKEDIRAQISDYLTNKGITIVSLKI 288
                                       5567888888888889999999999999999999999.999999999999999999988888888888888887777 PP

                            AAA_21 104 sleeedv 110
                                        +++  +
  gi|242399524|ref|YP_002994949.1| 289 EEPSLED 295
                                       6666555 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   1.1   8.5e-06     0.017      10      36 ..      16      46 ..       3      52 .. 0.77
   2 ?    0.6   0.7      0.35     7e+02     153     195 ..     205     275 ..     108     280 .. 0.59

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 8.5e-06
                            AAA_23 10 f...rdqeidFskg.ltlItGpNGaGKTTil 36
                                      f   ++ +++ +kg ++ + GpNGaGKTT +
  gi|242399524|ref|YP_002994949.1| 16 FiavDNLTLNIEKGiIFGFLGPNGAGKTTTI 46
                                      366688999998864899**********976 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.35
                            AAA_23 153 e.....................rleelekeleeledekkllekl..........eqekekekeleeleeeleei 195
                                                             +le +e ++e+++ + +l   +           ++k+   + e+++ ++ ++
  gi|242399524|ref|YP_002994949.1| 205 GiivrgrlraigplnhikkqfmELEGYEIKIETKQRMPEL---NvdgiirveriDERKSIIFTKEDIRAQISDY 275
                                       3444444444443333333333566666666555555543...0223333322233444444666666666665 PP

>> MukB  MukB N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.5e-05      0.05      31      58 ..      34      61 ..      21      88 .. 0.88
   2 ?   -2.2   0.0       1.4   2.9e+03     141     165 ..     210     234 ..     175     240 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.5e-05
                                      HHS--SHHHHHHHHHHHHHHS--TTT-- CS
                              MukB 31 lsGgnGaGksttmaafvtaliPdlsllh 58
                                      + G nGaGk+tt+ +++  +iPd  +++
  gi|242399524|ref|YP_002994949.1| 34 FLGPNGAGKTTTILSMLGLIIPDNGKIQ 61
                                      5699*******************98776 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.4
                                       SS--EE--HHHHHHHHHTSTT-EEE CS
                              MukB 141 dkkarvrelnelkekleelegvrlk 165
                                        +   + +ln++k+++ eleg ++k
  gi|242399524|ref|YP_002994949.1| 210 GRLRAIGPLNHIKKQFMELEGYEIK 234
                                       3344677899999999999987766 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 ?   12.8   0.1   3.7e-05     0.074      15      50 ..      22      57 ..      15      62 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.7e-05
                            AAA_29 15 htieidlkg.atlltGpsGsGKSTllDAiqalLvpak 50
                                       t++i+ kg ++ + Gp+G+GK+T + ++  l++p++
  gi|242399524|ref|YP_002994949.1| 22 LTLNIE-KGiIFGFLGPNGAGKTTTILSMLGLIIPDN 57
                                      566676.6778889**********9999999999987 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   5.9e-05      0.12       6      39 ..      34      67 ..      30      72 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.9e-05
                                      EEESTTSSHHHHHHHHHHHHHHTTS-EEEEEEST CS
                             SRP54  6 lvGlqGaGKTttlaKLaallkkegkkvllvaaDt 39
                                      ++G++GaGKTtt+  +  l+  ++ k+ ++  D+
  gi|242399524|ref|YP_002994949.1| 34 FLGPNGAGKTTTILSMLGLIIPDNGKIQIMGHDV 67
                                      89***********999999999998998888886 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1    0.0083        17      20      44 ..      24      49 ..       4      54 .. 0.75
   2 ?    5.5   0.0    0.0051        10     148     211 ..     142     206 ..     100     212 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0083
                                      EETTSSEEE.EEESTTSSHHHHHHHH CS
                                      xxxxxxxxx.xxxxxxxxxxxxxxxx RF
                             SMC_N 20 lpfsksfta.ivGpNGSGKsnlldAi 44
                                      l+++k++ +  +GpNG+GK+  + ++
  gi|242399524|ref|YP_002994949.1| 24 LNIEKGIIFgFLGPNGAGKTTTILSM 49
                                      555555543368*******9877665 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0051
                                       HHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-SCEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 148 aLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislreemlekadklvgv 211
                                        Ll+A   v+   + +lDe  + LD +  + v +++ke+ k+   ++  s+    +e+ +  vg+
  gi|242399524|ref|YP_002994949.1| 142 RLLLAKALVNDPDVLILDEPTSGLDPEGAHLVKSIVKEEAKTgKTVFFSSHILSEVEELSDKVGI 206
                                       578888888888899**********************9988745566666666666666555555 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 ?   10.8   0.0   0.00012      0.23      33      96 ..     219     285 ..     214     299 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00012
                    Glyco_hydro_20  33 NvlHwHltDdqgwrlei...kkyPeLtekgakreskeseeelsgfYtkedir.eiveYAaergieVip 96 
                                       N +    ++ +g+ ++i   +++PeL   g  r ++  +e++s ++tkedir +i +Y  ++gi+++ 
  gi|242399524|ref|YP_002994949.1| 219 NHIKKQFMELEGYEIKIetkQRMPELNVDGIIRVER-IDERKSIIFTKEDIRaQISDYLTNKGITIVS 285
                                       55555667778999999666689********99976.7788888*******85799*********984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 1892.13
//
Query:       gi|242399525|ref|YP_002994950.1|  [L=717]
Description: hypothetical protein TSIB_1550 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-25   88.1   0.0    3.3e-14   52.9   0.2    4.8  4  NPCBM_assoc      NPCBM-associated, NEW3 domain of alpha-galac
    3.4e-12   46.5   3.7    2.1e-08   34.3   0.0    4.8  6  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
    1.1e-10   41.8   0.3     0.0045   17.4   0.1    5.3  5  MG2              MG2 domain
    9.8e-10   38.7   7.0       0.13   12.5   1.0    6.6  7  FixG_C           IG-like fold at C-terminal of FixG, putative
    4.8e-07   30.1   1.2      0.025   14.8   0.1    4.7  4  DUF4625          Domain of unknown function (DUF4625)
    1.1e-06   28.4   2.3    1.6e-05   24.7   0.3    3.6  3  PEGA             PEGA domain
    1.6e-05   25.0   9.7      0.079   13.0   0.1    6.4  6  DUF916           Bacterial protein of unknown function (DUF91
    1.8e-05   24.6   0.5    1.8e-05   24.6   0.5    3.8  5  CarbopepD_reg_2  CarboxypepD_reg-like domain
     0.0015   19.2   1.7        4.2    8.1   0.0    4.6  4  fn3_5            Fn3-like domain
     0.0017   18.7   2.3        5.2    7.3   0.0    4.1  4  CBM_4_9          Carbohydrate binding domain
     0.0032   17.6   0.9      0.032   14.4   0.4    2.9  2  fn3_6            Fibronectin type-III domain
     0.0033   17.7   0.3      0.043   14.1   0.1    2.9  3  Alpha_adaptinC2  Adaptin C-terminal domain
     0.0034   17.7   0.4        8.9    6.7   0.3    3.6  3  DUF11            Domain of unknown function DUF11
  ------ inclusion threshold ------
      0.011   16.1   0.2        3.8    7.9   0.0    3.8  4  Transglut_N      Transglutaminase family
      0.016   15.2   0.1       0.19   11.8   0.0    2.8  2  CooC_C           CS1-pili formation C-terminal
      0.016   15.0   6.0      0.081   12.8   0.6    3.7  4  DUF4832          Domain of unknown function (DUF4832)
      0.063   14.2   0.2       0.68   10.9   0.1    2.8  2  DUF756           Domain of unknown function (DUF756)
      0.069   13.3  13.7        1.5    9.0   1.0    4.8  5  DUF4469          Domain of unknown function (DUF4469) with IG
       0.16   12.0   0.5        1.1    9.4   0.1    2.7  2  I-set            Immunoglobulin I-set domain
       0.17   11.8   3.5      0.096   12.6   0.3    2.3  2  Peptidase_S55    SpoIVB peptidase S55
       0.36   11.0   2.2          7    6.9   0.1    3.8  4  Ig_GlcNase       Exo-beta-D-glucosaminidase Ig-fold domain
       0.51   10.3   8.8        9.6    6.2   0.2    4.7  4  DUF1533          Protein of unknown function (DUF1533)
          6    7.5   6.7         68    4.1   0.0    4.5  5  MBG              MBG domain


Domain annotation for each model (and alignments):
>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   0.00019      0.15       3      76 ..     193     270 ..     191     271 .. 0.79
   2 !    9.7   0.0    0.0013      0.99      24      77 ..     319     374 ..     309     375 .. 0.74
   3 !    6.9   0.0    0.0095       7.4      46      77 ..     535     566 ..     507     568 .. 0.75
   4 !   52.9   0.2   4.2e-17   3.3e-14       2      77 ..     599     672 ..     598     674 .. 0.96

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00019
                       NPCBM_assoc   3 pGetvtltltvtndgtaaatnvslslslPeGWt...vvevspasaa..slapGetveatvkVtppagaaaGdyevta 74 
                                        G++ t+ +t+tn+g++ +      +s+P++W+     e+   +++  +l+p ++v+  + +  p+ga+ G  ++t+
  gi|242399525|ref|YP_002994950.1| 193 SGAELTIPITITNNGNDDIILPLDIISAPAEWRiefLGESNNYEVSeiTLPPEDSVTIFLHINTPEGAK-GPNNITF 268
                                       79999**********776654444589******444334444555589********************9.8889888 PP

                       NPCBM_assoc  75 ka 76 
                                       ++
  gi|242399525|ref|YP_002994950.1| 269 SV 270
                                       75 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0013
                       NPCBM_assoc  24 vslslsl.PeGWtvvevspasaa..slapGetveatvkVtppagaaaGdyevtakar 77 
                                       v l+++  P +W  v ++ + ++  s   +   e+++ V++p++++ G+y+++++a+
  gi|242399525|ref|YP_002994950.1| 319 VFLEITEkPLNWD-VYFTLNGLRitSFLLNSNKEVNLIVKIPQNIELGTYPIKFTAN 374
                                       5555555577777.44444433333777888999********************996 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0095
                       NPCBM_assoc  46 slapGetveatvkVtppagaaaGdyevtakar 77 
                                       ++    ++ + +k+ pp +a++G y+ t++++
  gi|242399525|ref|YP_002994950.1| 535 KVSSESSQIVHLKIIPPLNAKPGVYNATLRVK 566
                                       566777888999****************9987 PP

  == domain 4  score: 52.9 bits;  conditional E-value: 4.2e-17
                       NPCBM_assoc   2 epGetvtltltvtndgtaaatnvslslslPeGWtvvevspasaaslapGetveatvkVtppagaaaGdyevtakar 77 
                                       +pGe+ +++lt+ n+g+ a+tnv++++ +P GW+ vev+p+++a+l+ + + ++ +++++++++ aG+y+v +ka+
  gi|242399525|ref|YP_002994950.1| 599 KPGEKREVKLTLRNSGN-AITNVNIEVNTPNGWE-VEVEPQKLAKLESNSAKTVILRIKVSETTPAGEYKVSIKAK 672
                                       79************996.79**************.**************************************998 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       7.8   6.1e+03      47      60 ..      41      54 ..      29      59 .. 0.70
   2 ?   -1.9   0.0       5.4   4.2e+03      45      63 ..     362     380 ..     360     387 .. 0.78
   3 !   34.3   0.0   2.7e-11   2.1e-08       4      82 .]     397     467 ..     394     467 .. 0.94
   4 ?    2.5   0.1      0.22   1.7e+02      14      79 ..     558     622 ..     553     625 .. 0.68
   5 ?   -0.1   0.0       1.5   1.2e+03       9      28 ..     612     630 ..     605     636 .. 0.75
   6 ?    6.2   0.2     0.016        13      45      76 ..     660     691 ..     655     698 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 7.8
                   CarboxypepD_reg 47 pgtysvtvsapGya 60
                                       g+y+++++ + y 
  gi|242399525|ref|YP_002994950.1| 41 VGNYQIEITQEKYS 54
                                      37777777777664 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 5.4
                   CarboxypepD_reg  45 lppgtysvtvsapGyatat 63 
                                       ++ gty ++++a+G + a 
  gi|242399525|ref|YP_002994950.1| 362 IELGTYPIKFTANGIEKAI 380
                                       5669********9987765 PP

  == domain 3  score: 34.3 bits;  conditional E-value: 2.7e-11
                   CarboxypepD_reg   4 GrVtdasgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatreevtltagqtttldit 80 
                                        +V d++g+pi+  +V +       + +  t+ dG+   + +p g+y++tvs++Gy+ +  + + l++g++++++it
  gi|242399525|ref|YP_002994950.1| 397 LSVIDENGTPIPKTKVQIG------NETYITNIDGSLE-KEMPKGNYNITVSKEGYENHQLT-LNLEDGEERDVTIT 465
                                       57*****************......7999*********.56*******************95.************** PP

                   CarboxypepD_reg  81 Le 82 
                                       L+
  gi|242399525|ref|YP_002994950.1| 466 LK 467
                                       95 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.22
                   CarboxypepD_reg  14 iagatVtvtnadt.gtvastttdadGafrlrglppgtysvtvsapGyatatreevtltagqt..ttldi 79 
                                       + +at++v+++++ +  ++ + +  G++  + l++ +y +   +pG +   +  +tl++ ++  t+++i
  gi|242399525|ref|YP_002994950.1| 558 VYNATLRVKASSGeEIAKNIQVEVIGRYEAS-LETSNYLLSL-KPGEKREVK--LTLRNSGNaiTNVNI 622
                                       6689999987544045799999999999975.9999999998.666666653..556655441244555 PP

  == domain 5  score: -0.1 bits;  conditional E-value: 1.5
                   CarboxypepD_reg   9 asgapiagatVtvtnadtgt 28 
                                        sg++i++++++v  +++g 
  gi|242399525|ref|YP_002994950.1| 612 NSGNAITNVNIEVN-TPNGW 630
                                       4899*******998.45554 PP

  == domain 6  score: 6.2 bits;  conditional E-value: 0.016
                   CarboxypepD_reg  45 lppgtysvtvsapGyatatreevtltagqttt 76 
                                        p+g+y+v + a+  +t + + +t+++ q+++
  gi|242399525|ref|YP_002994950.1| 660 TPAGEYKVSIKAKADQTESETRLTVRVRQNSN 691
                                       577*********9999999999**99999876 PP

>> MG2  MG2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0       1.3     1e+03      60      82 ..      28      50 ..      21      60 .. 0.82
   2 ?    4.1   0.0     0.081        64      49      84 ..     342     375 ..     332     384 .. 0.73
   3 !    9.2   0.0    0.0021       1.6      34      87 ..     393     447 ..     378     455 .. 0.83
   4 ?    3.0   0.0      0.18   1.4e+02      47      92 ..     530     575 ..     514     581 .. 0.76
   5 !   17.4   0.1   5.7e-06    0.0045      12      91 ..     599     679 ..     597     686 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.3
                                      EEEEEEE--TT--SEEEEEEEEE CS
                               MG2 60 gaesefalpeaaklGeysvelsa 82
                                      ++e+++++ e    G+y++e+ +
  gi|242399525|ref|YP_002994950.1| 28 VFEGRVQIGEILIVGNYQIEITQ 50
                                      58999999999*********922 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.081
                                       EEEEEEE-CTTEEEEEEE--TT--SEEEEEEEEECS CS
                               MG2  49 kelplatdetggaesefalpeaaklGeysvelsads 84 
                                        ++ l+++++  ++  +++p++ +lG+y +++ a++
  gi|242399525|ref|YP_002994950.1| 342 TSFLLNSNKE--VNLIVKIPQNIELGTYPIKFTANG 375
                                       5555555555..88899*************995554 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0021
                                       EEEEEEEE-TTSSEEEEEEE.EE-CTTEEEEEEE--TT--SEEEEEEEEECSTTT CS
                               MG2  34 lplkltirdpdgkevkelpl.atdetggaesefalpeaaklGeysvelsadsaee 87 
                                       ++l+l++ d++g  + ++++   +et + + +  l ++ + G+y++++s+++ e+
  gi|242399525|ref|YP_002994950.1| 393 AKLHLSVIDENGTPIPKTKVqIGNETYITNIDGSLEKEMPKGNYNITVSKEGYEN 447
                                       6899************9999677888889*******************6655544 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.18
                                       EEEEEEEEE-CTTEEEEEEE--TT--SEEEEEEEEECSTTT-EEEE CS
                               MG2  47 evkelplatdetggaesefalpeaaklGeysvelsadsaeeslssg 92 
                                       evk+l++ ++++++++ ++  p +ak G y+++l+ +  +++   +
  gi|242399525|ref|YP_002994950.1| 530 EVKSLKVSSESSQIVHLKIIPPLNAKPGVYNATLRVKASSGEEIAK 575
                                       788888999999999999999**********999444444444333 PP

  == domain 5  score: 17.4 bits;  conditional E-value: 5.7e-06
                                       -TT-EEEEEEEEESTTCSB---EEEEEEEE-TTSSEEEEEEE.....EE-CTTEEEEEEE--TT--SEEEEEEEEEC CS
                               MG2  12 rPgetVslkallrdetlqglaklplkltirdpdgkevkelpl.....atdetggaesefalpeaaklGeysvelsad 83 
                                       +Pge+ ++k  lr+ +++++++  + +++++p+g ev+ +p      +++++ ++  +++++e+++ Gey+v+++a+
  gi|242399525|ref|YP_002994950.1| 599 KPGEKREVKLTLRN-SGNAITN--VNIEVNTPNGWEVEVEPQklaklESNSAKTVILRIKVSETTPAGEYKVSIKAK 672
                                       89999999999975.5566666..9999999999988888776655556666668899****************555 PP

                                       STTT-EEE CS
                               MG2  84 saeeslss 91 
                                        +++++ +
  gi|242399525|ref|YP_002994950.1| 673 ADQTES-E 679
                                       444433.2 PP

>> FixG_C  IG-like fold at C-terminal of FixG, putative oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0    0.0042       3.3      39     105 ..     203     274 ..     198     292 .. 0.69
   2 ?    1.4   0.0      0.46   3.6e+02      49      89 ..     277     316 ..     272     343 .. 0.79
   3 ?    0.9   0.0      0.67   5.2e+02      76     111 ..     349     383 ..     346     388 .. 0.77
   4 ?    0.4   0.0      0.94   7.3e+02      48      84 ..     435     467 ..     427     483 .. 0.78
   5 !   10.9   0.0    0.0005      0.39      34     107 ..     491     571 ..     481     581 .. 0.65
   6 ?    5.0   0.0     0.034        27      47      86 ..     575     613 ..     570     619 .. 0.84
   7 !   12.5   1.0   0.00017      0.13      37     111 ..     608     680 ..     606     690 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0042
                                       EEE-SSS-EEEEEEEES-S.S-EE.......E.S--EEEE-TT-EEEEEEEEEE-GGG-SSSEEEEEEEEEEGG CS
                            FixG_C  39 ilNktekprrytlsveglp.glel......agraekeitvapgekrkvpvfvrvpaealkkkstpitfkvtddd 105
                                       i+N  +++  + l++ + p + ++      ++++ +eit++p+ ++++ + + +p++a  k+ ++itf v d+ 
  gi|242399525|ref|YP_002994950.1| 203 ITNNGNDDIILPLDIISAPaEWRIeflgesNNYEVSEITLPPEDSVTIFLHINTPEGA--KGPNNITFSVGDKI 274
                                       6666667766677776543333334465543355699******999999999999998..77889999995333 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.46
                                       EEEEEES-SS-EE.E.S--EEEE-TT-EEEEEEEEEE-GGG CS
                            FixG_C  49 ytlsveglpglelagraekeitvapgekrkvpvfvrvpaea 89 
                                       +t++v +++++e+   +   i+v++g+  ++pv+   p+ +
  gi|242399525|ref|YP_002994950.1| 277 ITVDVVDKEEIEI-ITPLLGIEVEAGSLISLPVYFIGPETK 316
                                       6777888889999.778999*************99888776 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.67
                                       EEEEEEEEEE-GGG-SSSEEEEEEEEEEG.GGTEEEE CS
                            FixG_C  76 krkvpvfvrvpaealkkkstpitfkvtdd.deketve 111
                                       +++v ++v++p++  + ++ pi+f+++ + ++++tv+
  gi|242399525|ref|YP_002994950.1| 349 NKEVNLIVKIPQNI-ELGTYPIKFTAN-GiEKAITVS 383
                                       679999****9986.77888******7.436666654 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 0.94
                                       EEEEEEES-SS-EE.E.S--EEEE-TT-EEEEEEEEE CS
                            FixG_C  48 rytlsveglpglelagraekeitvapgekrkvpvfvr 84 
                                       +y+++v+ ++g e     + +++++ ge+r+v+++++
  gi|242399525|ref|YP_002994950.1| 435 NYNITVS-KEGYEN-H--QLTLNLEDGEERDVTITLK 467
                                       5788888.467777.3..4789999999999999886 PP

  == domain 5  score: 10.9 bits;  conditional E-value: 0.0005
                                       EEEEEEEE-SSS-EEEEEEEES-S...S-EE......E.S--EEEE-TT-EEEEEEEEEE.-GGG-SSSEEEEEEEE CS
                            FixG_C  34 sYtlkilNktekprrytlsveglp...glel.....agraekeitvapgekrkvpvfvrv.paealkkkstpitfkv 101
                                       sY +++ N  +++ +y ls+eglp    +++     ++ + k+++v +++  +++v +++ p+ ++k++  + t++v
  gi|242399525|ref|YP_002994950.1| 491 SYKIQLENLGKEDDEYFLSLEGLPsewAIRFlkdiqSNLEVKSLKVSSES--SQIVHLKIiPPLNAKPGVYNATLRV 565
                                       7*********************9887755554332212223455555554..4555555544445577777888888 PP

                                       EEGGGT CS
                            FixG_C 102 tdddek 107
                                       + ++++
  gi|242399525|ref|YP_002994950.1| 566 KASSGE 571
                                       733322 PP

  == domain 6  score: 5.0 bits;  conditional E-value: 0.034
                                       EEEEEEEES-SS-EE.E.S--EEEE-TT-EEEEEEEEEE- CS
                            FixG_C  47 rrytlsveglpglelagraekeitvapgekrkvpvfvrvp 86 
                                       ++++++v g  +++l + ++  ++++pgekr+v++++r  
  gi|242399525|ref|YP_002994950.1| 575 KNIQVEVIGRYEASL-ETSNYLLSLKPGEKREVKLTLRNS 613
                                       568999999989999.55689***************9865 PP

  == domain 7  score: 12.5 bits;  conditional E-value: 0.00017
                                       EEEEE-SSS-EEEEEEEES-SS-EE.E.S--EEEE-TT-EEEEEEEEEE-GGG-SSSEEEEEEEEEEGGGTEEEE CS
                            FixG_C  37 lkilNktekprrytlsveglpglelagraekeitvapgekrkvpvfvrvpaealkkkstpitfkvtdddeketve 111
                                       l+++N  +   +++++v+  +g e++ +++k  ++++++ ++v+++++v +   ++++ ++++k++ d+ +e+++
  gi|242399525|ref|YP_002994950.1| 608 LTLRNSGNAITNVNIEVNTPNGWEVEVEPQKLAKLESNSAKTVILRIKVSETT-PAGEYKVSIKAKADQ-TESET 680
                                       789***************99999998899999********9999999998887.66777******8333.23332 PP

>> DUF4625  Domain of unknown function (DUF4625)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       7.3   5.7e+03      98     123 ..     254     278 ..     237     289 .. 0.61
   2 ?    5.6   0.0     0.022        17      89     115 ..     347     373 ..     329     385 .. 0.86
   3 !   14.8   0.1   3.2e-05     0.025      87     131 ..     537     581 ..     397     582 .. 0.91
   4 ?    4.1   0.0     0.067        52      33     116 ..     643     672 ..     614     694 .. 0.58

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 7.3
                           DUF4625  98 ieiPadaeaGdYhlvirvtDasGnet 123
                                       i+ P+ a +G  +++++v D+ G +t
  gi|242399525|ref|YP_002994950.1| 254 INTPEGA-KGPNNITFSVGDKIGEIT 278
                                       5555444.355555555555555544 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.022
                           DUF4625  89 kkeyelheeieiPadaeaGdYhlvirv 115
                                       ++++e++  ++iP+++e G Y + +++
  gi|242399525|ref|YP_002994950.1| 347 NSNKEVNLIVKIPQNIELGTYPIKFTA 373
                                       468999***************988774 PP

  == domain 3  score: 14.8 bits;  conditional E-value: 3.2e-05
                           DUF4625  87 gskkeyelheeieiPadaeaGdYhlvirvtDasGneteesreiki 131
                                        s++++++h +i +P +a++G Y+ ++rv   sG e  +++++++
  gi|242399525|ref|YP_002994950.1| 537 SSESSQIVHLKIIPPLNAKPGVYNATLRVKASSGEEIAKNIQVEV 581
                                       344699****************************99998888776 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.067
                           DUF4625  33 kiGetlhfeaklsdnealasykvdihnnfDhhshsseakegekewsfeksydlsgskkeyelheeieiPadaeaGdY 109
                                       +                                                      s++++++   i++ ++ +aG+Y
  gi|242399525|ref|YP_002994950.1| 643 E------------------------------------------------------SNSAKTVILRIKVSETTPAGEY 665
                                       3......................................................3344445555555555555555 PP

                           DUF4625 110 hlvirvt 116
                                        + i++ 
  gi|242399525|ref|YP_002994950.1| 666 KVSIKAK 672
                                       5555442 PP

>> PEGA  PEGA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.76   5.9e+02      33      45 ..      41      53 ..      37      57 .. 0.88
   2 !   24.7   0.3     2e-08   1.6e-05      28      68 ..     428     468 ..     410     470 .. 0.89
   3 ?   -2.6   0.0       6.8   5.3e+03      31      42 ..     660     671 ..     656     690 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.76
                              PEGA 33 aGnyslrvekeGY 45
                                       Gny++++ +e Y
  gi|242399525|ref|YP_002994950.1| 41 VGNYQIEITQEKY 53
                                      7**********99 PP

  == domain 2  score: 24.7 bits;  conditional E-value: 2e-08
                              PEGA  28 tlsleaGnyslrvekeGYedlektvtvtagetvklnltLek 68 
                                       + ++++Gny ++v+keGYe+   t ++++ge+  +++tL+k
  gi|242399525|ref|YP_002994950.1| 428 EKEMPKGNYNITVSKEGYENHQLTLNLEDGEERDVTITLKK 468
                                       56689*********************************997 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 6.8
                              PEGA  31 leaGnyslrvek 42 
                                        +aG+y++ +++
  gi|242399525|ref|YP_002994950.1| 660 TPAGEYKVSIKA 671
                                       688999998875 PP

>> DUF916  Bacterial protein of unknown function (DUF916)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.26     2e+02      20      49 ..     188     217 ..     164     223 .. 0.73
   2 ?    3.2   0.0      0.11        85      82     106 ..     234     259 ..     225     264 .. 0.84
   3 ?    1.7   0.3      0.32   2.5e+02      43     102 ..     410     467 ..     374     470 .. 0.77
   4 ?    3.6   0.0     0.088        68      74     119 ..     519     566 ..     450     567 .. 0.65
   5 !   13.0   0.1    0.0001     0.079      16      51 ..     591     626 ..     580     631 .. 0.90
   6 ?    1.2   0.1      0.45   3.5e+02      82     114 ..     635     667 ..     628     673 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.26
                            DUF916  20 dLkvkpgqeqelevkikNssdkeitveitv 49 
                                        L+ k g+e ++ ++i+N+ + +i + +++
  gi|242399525|ref|YP_002994950.1| 188 SLRTKSGAELTIPITITNNGNDDIILPLDI 217
                                       477888889999999999988887766555 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.11
                            DUF916  82 kip.keitlpakesktvklkikmPke 106
                                       + + +eitlp++ s+t+ l+i++P+ 
  gi|242399525|ref|YP_002994950.1| 234 NYEvSEITLPPEDSVTIFLHINTPEG 259
                                       556689******************85 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.32
                            DUF916  43 itveitvntAvTndnGvidYskskekkdkslkvslselvkipkeitlpakesktvklkik 102
                                       ++v+i  +t +Tn +G ++ +  k +++   +vs + + + + +++l+ +e+++v++++k
  gi|242399525|ref|YP_002994950.1| 410 TKVQIGNETYITNIDGSLEKEMPKGNYNI--TVSKEGYENHQLTLNLEDGEERDVTITLK 467
                                       57888888888999998886666666555..56777777888999999999999999987 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.088
                            DUF916  74 kvslselvkip..keitlpakesktvklkikmPkeefdGvilGGiyve 119
                                          l++++++   k++++  ++s++v+lki  P ++  Gv+   ++v+
  gi|242399525|ref|YP_002994950.1| 519 IRFLKDIQSNLevKSLKVSSESSQIVHLKIIPPLNAKPGVYNATLRVK 566
                                       446777777667899******************999999998888775 PP

  == domain 5  score: 13.0 bits;  conditional E-value: 0.0001
                            DUF916  16 ksYFdLkvkpgqeqelevkikNssdkeitveitvnt 51 
                                       +s + L +kpg+++e++++++Ns +  ++v+i+vnt
  gi|242399525|ref|YP_002994950.1| 591 TSNYLLSLKPGEKREVKLTLRNSGNAITNVNIEVNT 626
                                       56689*****************************97 PP

  == domain 6  score: 1.2 bits;  conditional E-value: 0.45
                            DUF916  82 kipkeitlpakesktvklkikmPkeefdGvilG 114
                                       +++k  +l+ ++ ktv l ik+ ++   G +  
  gi|242399525|ref|YP_002994950.1| 635 EPQKLAKLESNSAKTVILRIKVSETTPAGEYKV 667
                                       44577899**************99998887655 PP

>> CarbopepD_reg_2  CarboxypepD_reg-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       8.8   6.9e+03      34      49 ..      42      56 ..      41      58 .. 0.84
   2 ?   -1.6   0.0       3.4   2.7e+03      13      28 ..     135     150 ..     126     151 .. 0.78
   3 ?   -2.3   0.0       5.9   4.6e+03      40      64 ..     361     384 ..     360     393 .. 0.70
   4 !   24.6   0.5   2.3e-08   1.8e-05       5      78 ..     399     468 ..     398     476 .. 0.90
   5 ?   -2.3   0.1       5.8   4.5e+03      46      62 ..     606     622 ..     565     644 .. 0.61

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 8.8
                   CarbopepD_reg_2 34 GnFelknlpagkytLv 49
                                      Gn++++ ++++ky L+
  gi|242399525|ref|YP_002994950.1| 42 GNYQIE-ITQEKYSLK 56
                                      99**96.888999885 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.4
                   CarbopepD_reg_2  13 plpgatVyvkgtkkgt 28 
                                       ++ g+ Vyvk+++  t
  gi|242399525|ref|YP_002994950.1| 135 SVNGVEVYVKENSSRT 150
                                       6899******998776 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 5.9
                   CarbopepD_reg_2  40 nlpagkytLvvsyvGyktqekkvtv 64 
                                       n++ g+y +++++ G +++ ++v++
  gi|242399525|ref|YP_002994950.1| 361 NIELGTYPIKFTANGIEKA-ITVSI 384
                                       5667899999999998884.55555 PP

  == domain 4  score: 24.6 bits;  conditional E-value: 2.3e-08
                   CarbopepD_reg_2   5 VvdketkeplpgatVyvkgtkkgtvTdenGnFelknlpagkytLvvsyvGyktqekkvtvskektldvnillke 78 
                                       V+d++ ++p+p  +V++ + +   +T+ +G+ e  ++p+g+y ++vs  Gy++ + +++++++++ dv+i+lk+
  gi|242399525|ref|YP_002994950.1| 399 VIDEN-GTPIPKTKVQIGNET--YITNIDGSLEK-EMPKGNYNITVSKEGYENHQLTLNLEDGEERDVTITLKK 468
                                       88876.69*********6655..68********6.6*********************************99985 PP

  == domain 5  score: -2.3 bits;  conditional E-value: 5.8
                   CarbopepD_reg_2  46 ytLvvsyvGyktqekkv 62 
                                       ++L+ +  G    ++++
  gi|242399525|ref|YP_002994950.1| 606 VKLTLRNSGNAITNVNI 622
                                       33333333333333333 PP

>> fn3_5  Fn3-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0    0.0054       4.2      57      91 ..     231     265 ..     187     272 .. 0.86
   2 ?   -1.3   0.0       4.4   3.4e+03      11      45 ..     437     470 ..     427     488 .. 0.60
   3 ?    4.7   0.1      0.06        47      37      81 ..     564     611 ..     481     633 .. 0.67
   4 ?    2.0   0.1       0.4   3.2e+02       7      38 ..     601     632 ..     596     692 .. 0.55

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0054
                             fn3_5  57 aaltfetskvtvpAnssktvtvtldlpsdakkkng 91 
                                        +++ e s++t+p++ s+t+ + ++ p++ak +n+
  gi|242399525|ref|YP_002994950.1| 231 ESNNYEVSEITLPPEDSVTIFLHINTPEGAKGPNN 265
                                       6889999*********************9998776 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 4.4
                             fn3_5  11 sftltlkNtsnkaltykvsandvlTdladkeegkl 45 
                                       ++t++ + + n++lt+++++    +d++ + ++ l
  gi|242399525|ref|YP_002994950.1| 437 NITVSKEGYENHQLTLNLEDG-EERDVTITLKKLL 470
                                       555555666666666666666.5555555555444 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.06
                             fn3_5  37 ladkeegklilkaaspeike...aaltfetskvtvpAnssktvtvtld 81 
                                       ++ + +g+ i k ++ e  +   a+l+++   + ++++++++v++tl 
  gi|242399525|ref|YP_002994950.1| 564 RVKASSGEEIAKNIQVEVIGryeASLETSNYLLSLKPGEKREVKLTLR 611
                                       344455555555555555446777777777778888888888777775 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.4
                             fn3_5   7 gdkfsftltlkNtsnkaltykvsandvlTdla 38 
                                       g+k++++ltl+N +n     +++ n+ +  ++
  gi|242399525|ref|YP_002994950.1| 601 GEKREVKLTLRNSGNAITNVNIEVNTPNGWEV 632
                                       56778888888888887777777774333333 PP

>> CBM_4_9  Carbohydrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       1.7   1.3e+03      64     101 ..     366     402 ..     353     430 .. 0.68
   2 ?    0.1   0.0       1.2   9.2e+02      29      65 ..     427     472 ..     415     506 .. 0.71
   3 !    7.3   0.0    0.0067       5.2      64     133 ..     558     627 ..     525     638 .. 0.81
   4 !    7.0   0.1    0.0087       6.8      63      95 ..     663     692 ..     643     702 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.7
                                       EEEEEEEEEESSTSEEEEEEEEEESSTTS..CTCEEEEEE CS
                           CBM_4_9  64 tYtvsfwvkassgksrtikvkigdtdadg..anydevade 101
                                       tY ++f++ + ++    i+v+i++t+  +  +    v+de
  gi|242399525|ref|YP_002994950.1| 366 TYPIKFTANGIEK---AITVSIYKTHRGElaKLHLSVIDE 402
                                       7999999999555...999999999985465555555555 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.2
                                       ECGC.SSSSEEEEEESCSS........TTCEEEEEEECCS-TT-EE CS
                           CBM_4_9  29 vdvs.yngtyslkvsgrge........twdgqaiditirlekgktY 65 
                                       ++++ ++g+y+++vs+ g           dg ++d+ti+l+k   Y
  gi|242399525|ref|YP_002994950.1| 427 LEKEmPKGNYNITVSKEGYenhqltlnLEDGEERDVTITLKKLLHY 472
                                       5555667777777777765433343333467777777777776666 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0067
                                       EEEEEEEEEESSTS..EEEEEEEEEESSTTSCTCEEEEEEEEEESTSEEEEEEEEE-SSCSCCEEEEEEEEC CS
                           CBM_4_9  64 tYtvsfwvkassgk..srtikvkigdtdadganydevadekvelkgewktlegtFtipkstdenvelyvelg 133
                                        Y+  + vkassg+   ++i v++ ++++ + +++++     + +ge  +++ t   + + ++nv ++v+++
  gi|242399525|ref|YP_002994950.1| 558 VYNATLRVKASSGEeiAKNIQVEVIGRYEASLETSNYL--LSLKPGEKREVKLTLRNSGNAITNVNIEVNTP 627
                                       59999********9999999999999999774444444..56888*************9***********94 PP

  == domain 4  score: 7.0 bits;  conditional E-value: 0.0087
                                       -EEEEEEEEEESSTS.EEEEEEEEEESSTTSCTC CS
                           CBM_4_9  63 ktYtvsfwvkassgk.srtikvkigdtdadgany 95 
                                        +Y+vs+++ka++ + +++++v ++++++    y
  gi|242399525|ref|YP_002994950.1| 663 GEYKVSIKAKADQTEsETRLTVRVRQNSN----Y 692
                                       58***********9888888888888776....3 PP

>> fn3_6  Fibronectin type-III domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       2.2   1.8e+03      44      70 ..     435     467 ..     410     483 .. 0.56
   2 !   14.4   0.4   4.2e-05     0.032      16      76 ..     601     661 ..     588     688 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 2.2
                             fn3_6  44 gvkvtVeP.......seLefsekgekksftvtvt 70 
                                       ++++tV+         +L+++  ge++++t+t++
  gi|242399525|ref|YP_002994950.1| 435 NYNITVSKegyenhqLTLNLE-DGEERDVTITLK 467
                                       355555555555522233333.566666666665 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 4.2e-05
                             fn3_6  16 kgtvtvtRtvtnVgsseatYkakveapegvkvtVePseLefsekgekksftvtvtakksae 76 
                                        ++++v+ t++n g++ ++ +++v++p+g +v+VeP++L+  e++  k++ +++++++++ 
  gi|242399525|ref|YP_002994950.1| 601 GEKREVKLTLRNSGNAITNVNIEVNTPNGWEVEVEPQKLAKLESNSAKTVILRIKVSETTP 661
                                       56788999999****99*******************9999888999999988888887544 PP

>> Alpha_adaptinC2  Adaptin C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0         6   4.7e+03       9      38 ..     178     209 ..     174     211 .. 0.71
   2 ?   -1.6   0.0       4.3   3.4e+03      60      94 ..     237     269 ..     231     280 .. 0.77
   3 !   14.1   0.1   5.5e-05     0.043      29      96 ..     607     670 ..     595     684 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 6
                                       TTEEEEEEEEE..TTSTTEEEEEEEEEE-SSS CS
                   Alpha_adaptinC2   9 ddlqIgfkfek..perpgqiritlsftNkssq 38 
                                       +d+++++ f++  ++++ +++i +++tN+ + 
  gi|242399525|ref|YP_002994950.1| 178 KDYELYYPFKSlrTKSGAELTIPITITNNGND 209
                                       56666666777656677779999999998765 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 4.3
                                       ES-S-B-TTCEEEEEEEEEEESCTTS-EEEEEEEE CS
                   Alpha_adaptinC2  60 psstvlppnpggqitqvllienpskkplrmrlris 94 
                                        s+ +lpp   +++t  l i++p + + ++++ +s
  gi|242399525|ref|YP_002994950.1| 237 VSEITLPP--EDSVTIFLHINTPEGAKGPNNITFS 269
                                       57778888..99********997766666666555 PP

  == domain 3  score: 14.1 bits;  conditional E-value: 5.5e-05
                                       EEEEEE-SSS-EEEEEEEEEEBTTCEEEEEEES-S-B-TTCEEEEEEEEEEESCTTS-EEEEEEEEEE CS
                   Alpha_adaptinC2  29 tlsftNkssqpisnfsfqaavpkslklqlqppsstvlppnpggqitqvllienpskkplrmrlrisyk 96 
                                       +l++ N s + i+n++++++ p++++++++p++  +l    +   t +l+i   s+ ++   +++s k
  gi|242399525|ref|YP_002994950.1| 607 KLTLRN-SGNAITNVNIEVNTPNGWEVEVEPQKLAKLES--NSAKTVILRIKV-SETTPAGEYKVSIK 670
                                       666777.669****************************7..666666666655.56666666777666 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.021        16       9      29 ..     190     210 ..     175     215 .. 0.85
   2 ?   -0.0   0.0       1.4   1.1e+03      40      76 ..     432     466 ..     370     469 .. 0.79
   3 ?    6.7   0.3     0.011       8.9      10      51 ..     598     637 ..     586     695 .. 0.59

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.021
                             DUF11   9 evrpGdtvtytltvtNtgpas 29 
                                       + ++G+++t  +t tN+g+++
  gi|242399525|ref|YP_002994950.1| 190 RTKSGAELTIPITITNNGNDD 210
                                       6689**************986 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1.4
                             DUF11  40 PaglayvsvsasqgtasaltsvgsLeagesatlsftv 76 
                                       P g   ++vs   g  + + +  +Le ge++ +++t+
  gi|242399525|ref|YP_002994950.1| 432 PKGNYNITVSKE-GYENHQLT-LNLEDGEERDVTITL 466
                                       555554555555.33333333.688999998888887 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.011
                             DUF11  10 vrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsas 51 
                                       ++pG++ ++ lt++N+g+a   +v ++   P g + v+v  +
  gi|242399525|ref|YP_002994950.1| 598 LKPGEKREVKLTLRNSGNAIT-NVNIEVNTPNGWE-VEVEPQ 637
                                       689*************99988.7777766666665.444333 PP

>> Transglut_N  Transglutaminase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       8.4   6.6e+03      68     105 ..     208     245 ..     185     251 .. 0.65
   2 ?   -2.2   0.0       6.5     5e+03      91     114 ..     347     370 ..     312     373 .. 0.63
   3 ?    3.4   0.0      0.12        96      85     117 ..     533     565 ..     513     566 .. 0.83
   4 ?    7.9   0.0    0.0049       3.8      68     117 ..     617     671 ..     578     672 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 8.4
                       Transglut_N  68 gtkvvlplsseedeskWsaeveessgnsltvs.itspan 105
                                       +  ++lpl+  +++ +W++e+   ++n+++vs it p++
  gi|242399525|ref|YP_002994950.1| 208 NDDIILPLDIISAPAEWRIEFL-GESNNYEVSeITLPPE 245
                                       5566777777778889999988.4444444433666665 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 6.5
                       Transglut_N  91 ssgnsltvsitspanaivgrykls 114
                                       +s++++++ +++p n   g y ++
  gi|242399525|ref|YP_002994950.1| 347 NSNKEVNLIVKIPQNIELGTYPIK 370
                                       555688888999999888888766 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.12
                       Transglut_N  85 saeveessgnsltvsitspanaivgryklsvet 117
                                       s +v+++s++ + ++i +p na  g y+ ++++
  gi|242399525|ref|YP_002994950.1| 533 SLKVSSESSQIVHLKIIPPLNAKPGVYNATLRV 565
                                       45667566699****************999987 PP

  == domain 4  score: 7.9 bits;  conditional E-value: 0.0049
                       Transglut_N  68 gtkvvlplsseedeskWsaevee.......ssg.nsltvsitspanaivgryklsvet 117
                                        t+v +++   +++++W++eve        s++ +++ + i+++ +++ g+yk+s++ 
  gi|242399525|ref|YP_002994950.1| 617 ITNVNIEV---NTPNGWEVEVEPqklakleSNSaKTVILRIKVSETTPAGEYKVSIKA 671
                                       34444444...4788999999964566654333369*******************986 PP

>> CooC_C  CS1-pili formation C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00025      0.19      24      83 ..     400     462 ..     397     470 .. 0.85
   2 ?   -1.2   0.0       2.7   2.1e+03      43      62 ..     657     676 ..     639     695 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00025
                            CooC_C  24 vdedgqplanakilnhagvavteedGvFtlevdakapsltvengdt.lyeveldlert..rde 83 
                                       +de+g+p+ + k+  +  + +t+ dG    e+ +++ ++tv++++    +++l+le+   rd+
  gi|242399525|ref|YP_002994950.1| 400 IDENGTPIPKTKVQIGNETYITNIDGSLEKEMPKGNYNITVSKEGYeNHQLTLNLEDGeeRDV 462
                                       79****************************************999888888888876542444 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.7
                            CooC_C  43 avteedGvFtlevdakapsl 62 
                                       + t   G+++++++aka ++
  gi|242399525|ref|YP_002994950.1| 657 SETTPAGEYKVSIKAKADQT 676
                                       33444677777777666554 PP

>> DUF4832  Domain of unknown function (DUF4832)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       2.3   1.8e+03     167     193 ..     343     369 ..     316     380 .. 0.79
   2 ?    2.0   0.0       0.2   1.6e+02     167     195 ..     411     440 ..     377     460 .. 0.74
   3 ?   -1.3   0.0       2.1   1.6e+03     166     203 ..     532     571 ..     521     582 .. 0.65
   4 ?   12.8   0.6    0.0001     0.081     109     207 ..     589     679 ..     582     688 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 2.3
                           DUF4832 167 kwlpgttttitiklklpselakGkykv 193
                                       ++l ++++++++ +k+p++++ G+y +
  gi|242399525|ref|YP_002994950.1| 343 SFLLNSNKEVNLIVKIPQNIELGTYPI 369
                                       55556777788889*********9976 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.2
                           DUF4832 167 kwlp.gttttitiklklpselakGkykvyL 195
                                       k++  ++t+  +i+ +l++e++kG+y++ +
  gi|242399525|ref|YP_002994950.1| 411 KVQIgNETYITNIDGSLEKEMPKGNYNITV 440
                                       3333144444777899********999876 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 2.1
                           DUF4832 166 rkwlpgtttt..itiklklpselakGkykvyLnlpdpseg 203
                                       ++++ +++ +  +++k+  p + + G y+  L+++  s +
  gi|242399525|ref|YP_002994950.1| 532 KSLKVSSESSqiVHLKIIPPLNAKPGVYNATLRVKASSGE 571
                                       44444333332366777677************99988766 PP

  == domain 4  score: 12.8 bits;  conditional E-value: 0.0001
                           DUF4832 109 lessslskkvkaggtlsleltlkNeGfAalynerkvelvlrdeegeekyklkldadprkwlpgttttitiklklpse 185
                                       le s++  + k+g++ +++ltl+N+G A  + +  v++ +   +g e    ++ + + k+ +++ +t+ + +k+ ++
  gi|242399525|ref|YP_002994950.1| 589 LETSNYLLSLKPGEKREVKLTLRNSGNA--ITN--VNIEVNTPNGWE--VEVEPQKLAKLESNSAKTVILRIKVSET 659
                                       5566666677889999999999999976..444..444444444444..123555555555566666777799**** PP

                           DUF4832 186 lakGkykvyLnlpdpseglkdr 207
                                       +++G+ykv+++ +  +++  ++
  gi|242399525|ref|YP_002994950.1| 660 TPAGEYKVSIKAKADQTE--SE 679
                                       **********99988887..33 PP

>> DUF756  Domain of unknown function (DUF756)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       4.1   3.2e+03      12      33 ..     448     469 ..     389     512 .. 0.70
   2 ?   10.9   0.1   0.00087      0.68      12      53 ..     604     645 ..     572     674 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 4.1
                            DUF756  12 gnlrltlrNtgkaaarftVydn 33 
                                        +l+l l + +++ +++t+++ 
  gi|242399525|ref|YP_002994950.1| 448 HQLTLNLEDGEERDVTITLKKL 469
                                       4455555555555555555554 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00087
                            DUF756  12 gnlrltlrNtgkaaarftVydnaka..pwtytveagdqledhwk 53 
                                       ++++ltlrN+g+a   ++++ n  +   w++ ve+ +  +++ +
  gi|242399525|ref|YP_002994950.1| 604 REVKLTLRNSGNAITNVNIEVN--TpnGWEVEVEPQKLAKLESN 645
                                       89**********9999999998..4459*****99976665544 PP

>> DUF4469  Domain of unknown function (DUF4469) with IG-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       8.8   6.8e+03      18      36 ..     112     130 ..     108     151 .. 0.81
   2 ?    8.5   0.1    0.0029       2.3      54      84 ..     342     372 ..     321     382 .. 0.84
   3 ?   -0.2   0.1       1.4   1.1e+03      70      84 ..     427     441 ..     400     454 .. 0.72
   4 ?    0.7   0.0      0.77     6e+02      53      83 ..     568     598 ..     525     613 .. 0.67
   5 ?    9.0   1.0    0.0019       1.5      39      97 ..     616     684 ..     602     687 .. 0.67

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 8.8
                                       TTSEEEEEEES-----SST CS
                           DUF4469  18 aggnveikGkklkiagedp 36 
                                        g+ ++i+G  +k+ + d+
  gi|242399525|ref|YP_002994950.1| 112 EGDLFNIEGYVIKVLEVDK 130
                                       5778999999999988775 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0029
                                       -GGGEEEEETTEEEEE--TT--SEEEEEEEE CS
                           DUF4469  54 kaekivrNkpseLifllPasleaGeYtlevt 84 
                                       ++  +  Nk  +Li+++P+++e G+Y ++ t
  gi|242399525|ref|YP_002994950.1| 342 TSFLLNSNKEVNLIVKIPQNIELGTYPIKFT 372
                                       555677899*****************99876 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 1.4
                                       --TT--SEEEEEEEE CS
                           DUF4469  70 lPasleaGeYtlevt 84 
                                       l +++++G+Y+++v 
  gi|242399525|ref|YP_002994950.1| 427 LEKEMPKGNYNITVS 441
                                       5566777*****996 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.77
                                       E-GGGEEEEETTEEEEE--TT--SEEEEEEE CS
                           DUF4469  53 vkaekivrNkpseLifllPasleaGeYtlev 83 
                                        + e+i++N   e+i    asle+++Y l++
  gi|242399525|ref|YP_002994950.1| 568 SSGEEIAKNIQVEVIGRYEASLETSNYLLSL 598
                                       3345566666666666666666666666655 PP

  == domain 5  score: 9.0 bits;  conditional E-value: 0.0019
                                       EEEEEETT.......T--EEEE-GGGEEEEETTEEE..EE--TT--SEEEEEEEEE--.SSSSS--SS- CS
                           DUF4469  39 Giffvsee.......egestkvkaekivrNkpseLi..fllPasleaGeYtlevtTqy.ssskkllkep 97 
                                        i+ v+ e       e e+++ k +k+  N+ +++i  ++++++ +aGeY+++++ ++ +++++++ ++
  gi|242399525|ref|YP_002994950.1| 616 AITNVNIEvntpngwEVEVEPQKLAKLESNSAKTVIlrIKVSETTPAGEYKVSIKAKAdQTESETRLTV 684
                                       55555555555544444447777888999999987722567899*************965555555555 PP

>> I-set  Immunoglobulin I-set domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       4.8   3.7e+03      68      88 ..     433     454 ..     411     455 .. 0.79
   2 ?    9.4   0.1    0.0014       1.1      47      90 .]     640     684 ..     619     684 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 4.8
                                       GEEEEEEEEET.SEEEEEEEEE CS
                             I-set  68 eGkYtckatns.agkaeakaeL 88 
                                       +G+Y+++++ + +++ + +++L
  gi|242399525|ref|YP_002994950.1| 433 KGNYNITVSKEgYENHQLTLNL 454
                                       6889999888866666666665 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0014
                                       EEEEEET.TEEEEEESSB-GGGGEEEEEEEEETSEEEEEEEEEEE CS
                             I-set  47 vkvtvee.aeytLtIsnvevsDeGkYtckatnsagkaeakaeLkV 90 
                                        k++ ++ ++  L+I+  e+  +G+Y++ ++ +a + e++++L+V
  gi|242399525|ref|YP_002994950.1| 640 AKLESNSaKTVILRIKVSETTPAGEYKVSIKAKADQTESETRLTV 684
                                       455555558889*******************************98 PP

>> Peptidase_S55  SpoIVB peptidase S55
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1         3   2.4e+03      46      69 ..     386     409 ..     349     471 .. 0.53
   2 ?   12.6   0.3   0.00012     0.096      59     160 ..     547     655 ..     522     664 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3
                     Peptidase_S55  46 eikeGeiveaeilsikkgkkgkpG 69 
                                       ++++Ge+ + +++ i++  +  p 
  gi|242399525|ref|YP_002994950.1| 386 KTHRGELAKLHLSVIDENGTPIPK 409
                                       444444444444444333332222 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00012
                     Peptidase_S55  59 sikkgkkgkpGelkgvieeeekvlGeiekntelGifGklekeekkkkkkeklevalkeevk.....egkakiltvle 130
                                       +i    + kpG  +++++ +++   ei kn ++ ++G++e++ +++++  +l+ + k+evk     +g+a   +++e
  gi|242399525|ref|YP_002994950.1| 547 KIIPPLNAKPGVYNATLRVKASSGEEIAKNIQVEVIGRYEASLETSNYLLSLKPGEKREVKltlrnSGNAITNVNIE 623
                                       556677899************88889*************99999988899999999999974444469999999999 PP

                     Peptidase_S55 131 deeveeyeieie..kikkeskekeknlvikvt 160
                                        ++++ +e+e+e  k+ k ++++ k+++++++
  gi|242399525|ref|YP_002994950.1| 624 VNTPNGWEVEVEpqKLAKLESNSAKTVILRIK 655
                                       99999999999633777888888999998886 PP

>> Ig_GlcNase  Exo-beta-D-glucosaminidase Ig-fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0        10   7.8e+03      72      92 ..     240     260 ..     234     269 .. 0.72
   2 ?   -1.0   0.0       2.4   1.9e+03      39      78 ..     452     458 ..     427     480 .. 0.52
   3 ?    6.9   0.1    0.0089         7      70     103 ..     593     627 ..     530     632 .. 0.84
   4 ?    0.4   0.1      0.94   7.3e+02      35      55 ..     665     685 ..     634     697 .. 0.56

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 10
                        Ig_GlcNase  72 vtLlPgEsltltveypaaalk 92 
                                       +tL P++s+t+ +++++ + +
  gi|242399525|ref|YP_002994950.1| 240 ITLPPEDSVTIFLHINTPEGA 260
                                       899999999998777665554 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.4
                        Ig_GlcNase  39 LenkssvpAffvrlnlvdaageevlPvlwsDNyvtLlPgE 78 
                                       L                                 +L  gE
  gi|242399525|ref|YP_002994950.1| 452 L---------------------------------NLEDGE 458
                                       2.................................223334 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0089
                        Ig_GlcNase  70 Ny.vtLlPgEsltltveypaaalkgkkpkvevsGw 103
                                       Ny ++L PgE+++++++ +++ ++ ++ ++ev+  
  gi|242399525|ref|YP_002994950.1| 593 NYlLSLKPGEKREVKLTLRNSGNAITNVNIEVNTP 627
                                       552699************99999988889988755 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 0.94
                        Ig_GlcNase  35 vtvtLenkssvpAffvrlnlv 55 
                                       ++v ++ k+++    +rl+++
  gi|242399525|ref|YP_002994950.1| 665 YKVSIKAKADQTESETRLTVR 685
                                       333333333333333333332 PP

>> DUF1533  Protein of unknown function (DUF1533)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1       1.1   8.9e+02      37      53 ..      39      53 ..      29      54 .. 0.77
   2 ?   -0.8   0.1       1.9   1.5e+03      38      53 ..     362     376 ..     335     382 .. 0.77
   3 ?    6.2   0.2     0.012       9.6      41      59 ..     433     451 ..     402     452 .. 0.76
   4 ?    5.3   0.1     0.024        19      11      53 ..     632     674 ..     615     678 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.1
                           DUF1533 37 vfnkaGentIvIkakGY 53
                                      ++  +G+++I+I   +Y
  gi|242399525|ref|YP_002994950.1| 39 LI--VGNYQIEITQEKY 53
                                      44..89******99999 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.9
                           DUF1533  38 fnkaGentIvIkakGY 53 
                                       + + G++ I++ a+G 
  gi|242399525|ref|YP_002994950.1| 362 I-ELGTYPIKFTANGI 376
                                       4.78999999999995 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.012
                           DUF1533  41 aGentIvIkakGYeDvtit 59 
                                        G+++I+++  GYe+ ++t
  gi|242399525|ref|YP_002994950.1| 433 KGNYNITVSKEGYENHQLT 451
                                       69************98776 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.024
                           DUF1533  11 vtvNGkklennkyslssigk..LklkasvfnkaGentIvIkakGY 53 
                                       v+v  +kl  +k + +s++   L +k s  + aGe+++ Ikak +
  gi|242399525|ref|YP_002994950.1| 632 VEVEPQKL--AKLESNSAKTviLRIKVSETTPAGEYKVSIKAKAD 674
                                       55555555..3333333333348888888889**********966 PP

>> MBG  MBG domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       8.7   6.7e+03      56      66 ..      41      51 ..      39      54 .. 0.85
   2 ?   -1.6   0.0       5.5   4.3e+03       3      40 ..     234     272 ..     232     273 .. 0.76
   3 ?    4.1   0.0     0.088        68      50      70 ..     358     378 ..     334     383 .. 0.81
   4 ?    0.4   0.1       1.3     1e+03      43      68 ..     420     445 ..     386     465 .. 0.69
   5 ?    2.1   0.2      0.38   2.9e+02      24      68 ..     626     674 ..     605     698 .. 0.61

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 8.7
                               MBG 56 vGtYtvkLtaa 66
                                      vG+Y+++ t+ 
  gi|242399525|ref|YP_002994950.1| 41 VGNYQIEITQE 51
                                      899***99986 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 5.5
                               MBG   3 tYdGqaatlddsnsnnkitti.ttngkdatktytltagD 40 
                                        Y  +++tl++++s++   +i t++g++++++ t++ gD
  gi|242399525|ref|YP_002994950.1| 234 NYEVSEITLPPEDSVTIFLHInTPEGAKGPNNITFSVGD 272
                                       566677888887777755555799999999999998887 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.088
                               MBG  50 ttaptnvGtYtvkLtaaglak 70 
                                       + ++++ GtY +k ta+g++k
  gi|242399525|ref|YP_002994950.1| 358 IPQNIELGTYPIKFTANGIEK 378
                                       5566888***********987 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 1.3
                               MBG  43 wktadgnttaptnvGtYtvkLtaagl 68 
                                       +++ dg+ ++    G+Y+++ ++ g 
  gi|242399525|ref|YP_002994950.1| 420 ITNIDGSLEKEMPKGNYNITVSKEGY 445
                                       34666666666677888888888775 PP

  == domain 5  score: 2.1 bits;  conditional E-value: 0.38
                               MBG  24 ttngkdatktytltagDfewktadgn.....ttaptnvGtYtvkLtaagl 68 
                                       t+ng  + +    + + +e ++a++      +++ t +G Y+v+ +a+  
  gi|242399525|ref|YP_002994950.1| 626 TPNGWEVEVEP-QKLAKLESNSAKTVilrikVSETTPAGEYKVSIKAKAD 674
                                       56665555444.33344444334333666668889999****99998764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (717 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       589  (0.0328518); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); 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: 0.76u 0.30s 00:00:01.06 Elapsed: 00:00:00.46
# Mc/sec: 4685.92
//
Query:       gi|242399526|ref|YP_002994951.1|  [L=326]
Description: hypothetical protein TSIB_1551 [Thermococcus sibiricus MM 739]
Scores for complete 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-44  151.0  12.0    4.8e-44  150.8  12.0    1.0  1  ABC2_membrane_2  ABC-2 family transporter protein
    7.6e-09   35.8  14.3    4.8e-08   33.2  14.3    2.1  1  ABC2_membrane_4  ABC-2 family transporter protein
      1e-07   31.6  15.6    1.8e-07   30.8  15.6    1.3  1  ABC2_membrane    ABC-2 type transporter
    1.1e-06   28.3  11.9    1.1e-06   28.3  11.9    2.2  2  ABC2_membrane_5  ABC-2 family transporter protein
    0.00044   19.5  25.5     0.0039   16.4  25.5    2.3  1  ABC2_membrane_3  ABC-2 family transporter protein
  ------ inclusion threshold ------
      0.041   14.2   2.2       0.77   10.1   0.7    2.7  2  DUF3382          Domain of unknown function (DUF3382)
       0.54   10.8   2.0        1.1    9.8   0.1    2.3  2  DUF4179          Domain of unknown function (DUF4179)


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 !  150.8  12.0   1.9e-47   4.8e-44       1     288 []      12     325 ..      12     325 .. 0.90

  Alignments for each domain:
  == domain 1  score: 150.8 bits;  conditional E-value: 1.9e-47
                   ABC2_membrane_2   1 laiakkEfrdlvrsrrfllltvllpli..dvalaylkdlgsslqseakaikeatlaleyveaasasdeaedtdqdlk 75 
                                       ++ia +Ef  ++rs+rf+++ + ++++  ++   + ++l ++ ++ ++a  ++ l+   + + + +  ++ t+  + 
  gi|242399526|ref|YP_002994951.1|  12 INIALREFHSSIRSKRFVITLASYLFMifFFTYSIRDELIQRAGQTEVAYTSLPLTGVDGNIVITPLSLSTTSNLS- 87 
                                       58***************99877655552245555556666666677777777777766666766666666666666. PP

                   ABC2_membrane_2  76 vvstimavlipviaalfgadaiagEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvllalaiilal 152
                                            + +++ ++++++gad+i++E e+gT+k+lLs+P +Rd +++gKf+g++++   + +++ +++++++ + l l
  gi|242399526|ref|YP_002994951.1|  88 ----TILIFGSILGITLGADSINREIEDGTIKVLLSHPLYRDHLITGKFLGNALS---LGLMISVGFVFSIDYLLLL 157
                                       ....88899**********************************************...******************* PP

                   ABC2_membrane_2 153 givlaledllllvvasvlllllv.vflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavp.. 226
                                       gi++++++l++ ++a+ ++l+++  fl++g+++Ss+++ s+ ++++a++++++l +++p+v+ ++a++l g+++   
  gi|242399526|ref|YP_002994951.1| 158 GIPIDGSSLIRSLIAAFVTLVYTtIFLSMGIAFSSLLKRSEISTLVAIVFVIFLILVYPLVSPTLASKLVGEKPYcp 234
                                       ***********99998888888889*********************************************99999** PP

                   ABC2_membrane_2 227 .....................qeindflsllsptsayntllneilagsdlna........lgstatnllilllllav 274
                                                              ++  l++l+pt +y  l+  +++g++l +        l + +t+lli+l  l+ 
  gi|242399526|ref|YP_002994951.1| 235 seynenkidsciamkewekkrLLWKKRLLTLTPTYHYGSLITYVFSGDELTQdyipleesLSLGVTSLLIFLNELIL 311
                                       *******************9999*************************9999*******9999************** PP

                   ABC2_membrane_2 275 llvlgyvlFkrkDl 288
                                       +l+l+y +F ++Dl
  gi|242399526|ref|YP_002994951.1| 312 PLALAYIRFATMDL 325
                                       ************97 PP

>> ABC2_membrane_4  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2  14.3   1.9e-11   4.8e-08      11     177 ..      24     209 ..      18     214 .. 0.70

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 1.9e-11
                   ABC2_membrane_4  11 rskivwllvlaallvpllallyfn...............llgktgldpaefys....lsvfgftlllllplilgi.i 67 
                                       rsk + +++++ l++ ++ +  ++                l  tg+d + + +     ++++++++l++  ilgi +
  gi|242399526|ref|YP_002994951.1|  24 RSKRFVITLASYLFMIFFFTYSIRdeliqragqtevaytSLPLTGVDGNIVITplslSTTSNLSTILIFGSILGItL 100
                                       5666666666666555543333335555544444444432222333333322222213466788999********77 PP

                   ABC2_membrane_4  68 asylifrEeqndtlknLltiPvsrtklllaKlivllllsvllmlvtflitvlfallsgfvgfsvklvlellkkclel 144
                                       ++ +i+rE +++t+k Ll  P  r +l+ +K++  +l   l++ v f++++   ll+g +++++++++++l   +++
  gi|242399526|ref|YP_002994951.1| 101 GADSINREIEDGTIKVLLSHPLYRDHLITGKFLGNALSLGLMISVGFVFSIDYLLLLG-IPIDGSSLIRSLIAAFVT 176
                                       9********************************9999888888899999888877777.77*******999999999 PP

                   ABC2_membrane_4 145 gllvffavlpiialvllkksyvlpliltlvyti 177
                                        ++++++++  ia+++l k + ++ ++++v++i
  gi|242399526|ref|YP_002994951.1| 177 LVYTTIFLSMGIAFSSLLKRSEISTLVAIVFVI 209
                                       998888888889887655555555555655555 PP

>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8  15.6   6.9e-11   1.8e-07       8     179 ..      16     218 ..      12     223 .. 0.83

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 6.9e-11
                     ABC2_membrane   8 kreflqrwrdpslgllwrliqplllalvfgtvfgn..lgnsedglnr.............................. 52 
                                        ref + +r++  + +  l++ l+++++f++ + +  +       +r                              
  gi|242399526|ref|YP_002994951.1|  16 LREFHSSIRSK-RF-VITLASYLFMIFFFTYSIRDelI-------QRagqtevaytslpltgvdgnivitplslstt 83 
                                       68999999999.55.679****************6442.......33334445558899999999************ PP

                     ABC2_membrane  53 ....pgllffsvlflafsaltsvapvferergvlerelvsplyslsayvlakvlve.lpvsllqalifll.ivyfl. 122
                                             l+f+s+l ++   l + ++++e+e g+++ +l++pl  +   +++k+l++ l ++l++++ f++ i y+l 
  gi|242399526|ref|YP_002994951.1|  84 snlsTILIFGSILGIT---LGADSINREIEDGTIKVLLSHPL-YRDHLITGKFLGNaLSLGLMISVGFVFsIDYLLl 156
                                       **99999999999999...555668*****************.5667778888888788888888888886655542 PP

                     ABC2_membrane 123 vgldls.....rfflflllllltalaasslgllisalapsfedasqlaslvllpllllsGff 179
                                       +g++++     r +++ +++l+++ +++s+g+++s+l++  e  +++a +++++l+l+ + +
  gi|242399526|ref|YP_002994951.1| 157 LGIPIDgssliRSLIAAFVTLVYTTIFLSMGIAFSSLLKRSEISTLVAIVFVIFLILVYPLV 218
                                       6*****9876666********************************99999999999876665 PP

>> ABC2_membrane_5  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1      0.12   3.2e+02      42      53 ..      32      43 ..      15      67 .. 0.56
   2 !   28.3  11.9   4.4e-10   1.1e-06      30     164 ..      79     217 ..      72     232 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.12
                   ABC2_membrane_5 42 ilslvisiilil 53
                                      ++s +++i+  +
  gi|242399526|ref|YP_002994951.1| 32 LASYLFMIFFFT 43
                                      111111111112 PP

  == domain 2  score: 28.3 bits;  conditional E-value: 4.4e-10
                   ABC2_membrane_5  30 iflndsvllifsilslvisiililttlsyDekskwnkylltLPvtrkeiVksKYlfvlililiailitlllliiavl 106
                                        ++++s l +++i+  ++ i+l   ++  +  +++ k+ll+ P+ r  ++  K+l+ ++   ++i ++++++i + l
  gi|242399526|ref|YP_002994951.1|  79 SLSTTSNLSTILIFGSILGITLGADSINREIEDGTIKVLLSHPLYRDHLITGKFLGNALSLGLMISVGFVFSIDYLL 155
                                       3445667788899999*******************************************************987777 PP

                   ABC2_membrane_5 107 ikgn....vtisevllsiliglvialiflaivlPlyfkfgvekgrivliiiifgiifllvai 164
                                       + g       +  +l+++++ lv+++ifl++ + +  +++ +++ +++ i+++++ +l++ +
  gi|242399526|ref|YP_002994951.1| 156 LLGIpidgSSLIRSLIAAFVTLVYTTIFLSMGIAFSSLLKRSEISTLVAIVFVIFLILVYPL 217
                                       77777666555667777777888889999999999999997777766666666555555544 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 !   16.4  25.5   1.5e-06    0.0039     154     320 ..      76     282 ..       6     318 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.5e-06
                   ABC2_membrane_3 154 eelsnvasflvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllill..l. 227
                                        +ls ++   ++ ili+ ++++++  a si +E e ++++++l+ ++ +  ++++k+lg +l   l++ + ++  + 
  gi|242399526|ref|YP_002994951.1|  76 TPLSLSTTSNLSTILIFGSILGITLGADSINREIEDGTIKVLLSHPLYRDHLITGKFLGNALSLGLMISVGFVfsId 152
                                       3344444446678999999999999************************************9888777665552423 PP

                   ABC2_membrane_3 228 ...afglgipfg..nlgl.ll..llfllfglayialgyllsslfknsetaqilifivilllsgffgglfpledlp.. 294
                                          ++g  ip++  +l+  l+  ++ l++  +++++g ++ssl k+se   + + iv++++++++++l++    +  
  gi|242399526|ref|YP_002994951.1| 153 yllLLG--IPIDgsSLIRsLIaaFVTLVYTTIFLSMGIAFSSLLKRSEISTL-VAIVFVIFLILVYPLVSPTLASkl 226
                                       345888..888854444323356999999****************9977544.333334344444444442222233 PP

                   ABC2_membrane_3 295 ..............................salkwifsiiPffapglgllrlitgd 320
                                                                      + k ++ + P++++g +++ + +gd
  gi|242399526|ref|YP_002994951.1| 227 vgekpycpseynenkidsciamkewekkrlLWKKRLLTLTPTYHYGSLITYVFSGD 282
                                       33444455555555555555554444433333334555666666666666665555 PP

>> DUF3382  Domain of unknown function (DUF3382)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.065   1.7e+02       8      35 ..      83     110 ..      77     119 .. 0.80
   2 ?   10.1   0.7    0.0003      0.77       2      55 ..     165     213 ..     164     235 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.065
                           DUF3382   8 iaallalvlfvpilGlqleldgtrlvle 35 
                                       ++ l ++++f+ ilG++l  d+++ ++e
  gi|242399526|ref|YP_002994951.1|  83 TSNLSTILIFGSILGITLGADSINREIE 110
                                       6667899***********9999887766 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0003
                           DUF3382   2 aLknAliaallalvlfvpilGlqleldgtrlvleprwglvaiavavvfvgqLlr 55 
                                       +L+ +liaa+++lv ++ +l +     g+ +    +   + ++va+vfv  L++
  gi|242399526|ref|YP_002994951.1| 165 SLIRSLIAAFVTLVYTTIFLSM-----GIAFSSLLKRSEISTLVAIVFVIFLIL 213
                                       6899******************.....544444444466777777777665543 PP

>> DUF4179  Domain of unknown function (DUF4179)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.2      0.79     2e+03      13      31 ..     171     189 ..     165     200 .. 0.59
   2 ?    9.8   0.1   0.00042       1.1       4      37 ..     196     232 ..     194     255 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.79
                                       XXXXXXXXXXXXXXXXXXX CS
                           DUF4179  13 aaalvllllssrllspalA 31 
                                       +aa+v+l++++++ls  +A
  gi|242399526|ref|YP_002994951.1| 171 IAAFVTLVYTTIFLSMGIA 189
                                       4555555456666655555 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00042
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....-- CS
                           DUF4179   4 rrikkvaaaaaalvllllssrllspalAsal..n.pv 37 
                                       r+  ++ +a++ +++l+l+  l+sp+lAs l  + p+
  gi|242399526|ref|YP_002994951.1| 196 RSEISTLVAIVFVIFLILVYPLVSPTLASKLvgEkPY 232
                                       44456677777777778***********998773344 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       976  (0.0544369); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 2099.96
//
Query:       gi|242399527|ref|YP_002994952.1|  [L=938]
Description: hypothetical protein TSIB_1552 [Thermococcus sibiricus MM 739]
Scores for complete 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-178  593.3   0.0   3.3e-178  593.1   0.0    1.0  1  RtcB             tRNA-splicing ligase RtcB
    9.2e-17   61.1   6.2    2.5e-12   46.9   0.1    3.0  3  LAGLIDADG_3      LAGLIDADG-like domain
    1.3e-15   57.5   0.0    3.1e-15   56.3   0.0    1.7  1  Intein_splicing  Intein splicing domain


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 !  593.1   0.0  5.5e-182  3.3e-178       1     412 []      46     938 .]      46     938 .] 1.00

  Alignments for each domain:
  == domain 1  score: 593.1 bits;  conditional E-value: 5.5e-182
                                       HHHHHTTSTTB-S-EEEEEEEE--SSS-EEEEEEE-...-EE-HHHC-SST.......................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxx.......................... RF
                              RtcB   1 qlknvaslpgivkhvaamPDvHlGkgapiGsViatk...gviiPaaVGvDI.......................... 48 
                                       q++nva+lpgi+k++++mPD H+G+g+piG+V+a++   gvi+P++VG+D+                          
  gi|242399527|ref|YP_002994952.1|  46 QAANVAMLPGIYKYSIVMPDGHQGYGFPIGGVAAFDvkeGVISPGGVGYDVnclhedtevisdlgfrikvrelpkkf 122
                                       89*************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              RtcB  49 ............................................................................. 48 
                                                                                                                    
  gi|242399527|ref|YP_002994952.1| 123 kriplkvynveeghndssrimlvaerdseeeiyeihlssgrilkasgdhpiltedgyklteelkpgdlvaiypfegp 199
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              RtcB  49 ............................................................................. 48 
                                                                                                                    
  gi|242399527|ref|YP_002994952.1| 200 eyeeppneillsyedfegedrqiirylenrgllslsfrdlrigilarilgyfigdgsfdvykekngrkrlvtvfygd 276
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              RtcB  49 ............................................................................. 48 
                                                                                                                    
  gi|242399527|ref|YP_002994952.1| 277 reglealrndlefyfnirasrvysrkrkqkvktawgefktegteysikvtskafallliklgapvgkksdvefdvpd 353
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              RtcB  49 ............................................................................. 48 
                                                                                                                    
  gi|242399527|ref|YP_002994952.1| 354 wiknaplwikrnflaglfgadgtkptfltekhkytpnsisltvvkskeleenlrdylesiknmlsefgvtshiwkvq 430
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              RtcB  49 ............................................................................. 48 
                                                                                                                    
  gi|242399527|ref|YP_002994952.1| 431 eydgrvmyrltiysntlelyqflshigyeytskkpyalifaeylrrkllvaskikeksivkrnqrlakllpdferfa 507
                                       ***************************************************************************** PP

                                       ................................................-EEEEEEEEEEHHHHGGGHHHHHHHHHHH CS
                                       ................................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              RtcB  49 ................................................CGvrllktnltaeeleeklkelvkeleka 77 
                                                                                       CGvrl++tnlt++e+++++kelv++l+k+
  gi|242399527|ref|YP_002994952.1| 508 kvygleggfvldpvvevrkvksdskllydigvyhsahnfiangiivhnCGVRLIRTNLTEKEVRPRIKELVDTLFKN 584
                                       ***************************************************************************** PP

                                       S-------------HHHHHHHHHHTHHHHHHTTSS-GGGGGGBGGGG--TT--GGGS-HHHHHHHGGGTT---STT- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              RtcB  78 vpvglgskkkvklskkeleevleegakwaveeglgeeedlekieeegalkeadlekvskkakerarkqlGtlGsGNH 154
                                       vp+glgsk++v+l++++le+vl++gakwav++g+g++edle++ee+g++++a++++vs++ak+r+++qlG+lGsGNH
  gi|242399527|ref|YP_002994952.1| 585 VPSGLGSKGRVRLHWTQLEDVLSDGAKWAVDNGYGWKEDLEHLEENGRMEGANSDAVSQTAKQRGAPQLGSLGSGNH 661
                                       ***************************************************************************** PP

                                       EEEEEEEEEES-HHHHHHHT--TTEEEEEEEE--HHHHHHHHHHHHHHHHCCHHHCT---SSGGG--EETTSHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              RtcB 155 FiEvqlveeildeeaakalgleegqvvvmlHsGSRglGhqiaedylkiakkalkkkgiklpdrdLaylpagseegqa 231
                                       F+Evq+v+ei++e++ak +gl egq+vvm+H+GSRglGhq+a+dyl+i++ka +k+++ +pdr+L+ +p+++eegq+
  gi|242399527|ref|YP_002994952.1| 662 FLEVQVVDEIFNEQIAKVYGLFEGQIVVMVHTGSRGLGHQVASDYLRIMEKANRKYNVPWPDRELVSVPFQTEEGQR 738
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHT.T--HHHH--EEEEEEESEEEEEEEE..T...EEEEEEEES-EE-.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x...xxxxxxxxxxxxx.. RF
                              RtcB 232 YlkamqaaanyAkaNRqvitervreilekvlkkekedlelelvvdvaHNiakkEehe.d...ekvlVhRKGAtrA.. 302
                                       Y++am+ aan+A+aNRq+it++vre++e+v+k+++edle+++v+dvaHNiak Eehe d    kv+VhRKGAtrA  
  gi|242399527|ref|YP_002994952.1| 739 YFSAMKGAANFAWANRQMITHWVRESFEEVFKQKAEDLEMNVVYDVAHNIAKVEEHEvDgrkVKVVVHRKGATRAfp 815
                                       *********************************99**********************966889************** PP

                                       ...........TT--EEEE--STTS-EEEEE--HHHH..SSSEE---S-----------------TTTTTCCCT-EE CS
                                       ...........xxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              RtcB 303 ...........kvgqpviipGsmgtkSyivkGkgnae..sfgStsHGAGRlmsRakakkkfkleevkkdleeqgigv 366
                                                  +vgqpv+ipGsmgt+Sy+++G + ++  +fgSt+HGAGR++sR++a+++f++++++++l ++gi++
  gi|242399527|ref|YP_002994952.1| 816 agheavprayrNVGQPVLIPGSMGTASYVLAGAEGSMreTFGSTCHGAGRVLSRHAATRQFRGDRLRNELMQRGIYI 892
                                       **********************************99999************************************** PP

                                       EE------------------HHHHHHHHCTS-EEEEEEEEEEEEE- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              RtcB 367 earkkegvleEapeaYKdideVveaqaeaglvevvarlkpvlvvkg 412
                                       +a+++++v+eEap+aYK++d+Vv+++++ag+++ var++p++v+kg
  gi|242399527|ref|YP_002994952.1| 893 KAASMRVVAEEAPGAYKNVDNVVQVVHDAGIANLVARMRPIGVAKG 938
                                       ********************************************97 PP

>> LAGLIDADG_3  LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.3   1.3e-06    0.0078       4      65 ..     244     311 ..     242     337 .. 0.78
   2 !   46.9   0.1   4.2e-16   2.5e-12       1      83 []     361     457 ..     361     457 .. 0.87
   3 ?   -2.1   0.1      0.84     5e+03      31      62 ..     461     493 ..     459     500 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.3e-06
                                       HHHHHHHHHHCCECCECSTTTTS...EEEEES-HHHHHHHHHHHH.HCT.HSCEEEE..EEE-SCCCC CS
                       LAGLIDADG_3   4 aafLrGlfdaDGsvskskkkgvs...isltssskelledvqrlLl.rlGIestiyek..kkakgrgvy 65 
                                       +a + G+f +DGs+++ k+k+++   +++   ++e le +++ L+  ++I ++   +  +k+k ++ +
  gi|242399527|ref|YP_002994952.1| 244 LARILGYFIGDGSFDVYKEKNGRkrlVTVFYGDREGLEALRNDLEfYFNIRASRVYSrkRKQKVKTAW 311
                                       6899***************9999999999999************999999765555525555555555 PP

  == domain 2  score: 46.9 bits;  conditional E-value: 4.2e-16
                                       HHHHHHHHHHHHHCCECCECSTTTTS.....EEEEES-........HHHHHHHHHHHHHCT.HSCEEEEEEE-SCCC CS
                       LAGLIDADG_3   1 evkaafLrGlfdaDGsvskskkkgvs.....isltsss........kelledvqrlLlrlGIestiyekkkakgrgv 64 
                                       + k++fL+Glf aDG+  ++ + + +     islt  +        +++le ++++L+++G++s i + ++ +gr++
  gi|242399527|ref|YP_002994952.1| 361 WIKRNFLAGLFGADGTKPTFLTEKHKytpnsISLTVVKskeleenlRDYLESIKNMLSEFGVTSHIWKVQEYDGRVM 437
                                       679*************9877655554456698888888999************************************ PP

                                       CECCCHCHC.TTCGGGTTTX CS
                       LAGLIDADG_3  65 yrlliisge.nlkrFlekig 83 
                                       yrl+i+s+  +l  Fl++ig
  gi|242399527|ref|YP_002994952.1| 438 YRLTIYSNTlELYQFLSHIG 457
                                       *9999987537899999887 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.84
                                       ES-HHHHHHHHHHHH.HCT.HSCEEEEEEE-SC CS
                       LAGLIDADG_3  31 ssskelledvqrlLl.rlGIestiyekkkakgr 62 
                                       +s+k ++  ++++L  +l + s+i+ek + k++
  gi|242399527|ref|YP_002994952.1| 461 TSKKPYALIFAEYLRrKLLVASKIKEKSIVKRN 493
                                       455555555666666589999999999444443 PP

>> Intein_splicing  Intein splicing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.3   0.0   5.2e-19   3.1e-15      25     134 .]     129     555 ..     105     555 .. 0.96

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 5.2e-19
                                       EEETTTTEEEEEEEEEEEEEEEE.EEEEEEETTS-EEEEETT-EEEECCTTEEEEEECCC--TT-EEEEE....... CS
                                       xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....... RF
                   Intein_splicing  25 slnledlklevksvkkliklklk.elyeiklesgrkikaTpeHkllvvrdegivEkradeLkegdliavp....... 93 
                                       ++n+e+ +   +++  +++ + + e+yei+l+sgr +ka+++H++l+   +g   k  +eLk+gdl+a+        
  gi|242399527|ref|YP_002994952.1| 129 VYNVEEGHNDSSRIMLVAERDSEeEIYEIHLSSGRILKASGDHPILTE--DGY--KLTEELKPGDLVAIYpfegpey 201
                                       578888888888899999998889***********************9..788..889**********989****** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                   Intein_splicing  94 ............................................................................. 93 
                                                                                                                    
  gi|242399527|ref|YP_002994952.1| 202 eeppneillsyedfegedrqiirylenrgllslsfrdlrigilarilgyfigdgsfdvykekngrkrlvtvfygdre 278
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                   Intein_splicing  94 ............................................................................. 93 
                                                                                                                    
  gi|242399527|ref|YP_002994952.1| 279 glealrndlefyfnirasrvysrkrkqkvktawgefktegteysikvtskafallliklgapvgkksdvefdvpdwi 355
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                   Intein_splicing  94 ............................................................................. 93 
                                                                                                                    
  gi|242399527|ref|YP_002994952.1| 356 knaplwikrnflaglfgadgtkptfltekhkytpnsisltvvkskeleenlrdylesiknmlsefgvtshiwkvqey 432
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                   Intein_splicing  94 ............................................................................. 93 
                                                                                                                    
  gi|242399527|ref|YP_002994952.1| 433 dgrvmyrltiysntlelyqflshigyeytskkpyalifaeylrrkllvaskikeksivkrnqrlakllpdferfakv 509
                                       ***************************************************************************** PP

                                       ...HSCEEEEEEEEEEEEEC.EEEEEEEEETT.T-EEEECTTEEE- CS
                                       ...xxxxxxxxxxxxxxxxx.xxxxxxxxxxx.xxxxxxxxxxxxx RF
                   Intein_splicing  94 ...dadvvwdkvksievede.eeyVYdltved.nhNFvangiivHN 134
                                          ++  v+d v+++++ ++  +  Yd+ v +  hNF+angiivHN
  gi|242399527|ref|YP_002994952.1| 510 yglEGGFVLDPVVEVRKVKSdSKLLYDIGVYHsAHNFIANGIIVHN 555
                                       **9999*********8766538889*****7527***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (938 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.81u 0.35s 00:00:01.16 Elapsed: 00:00:00.51
# Mc/sec: 5530.42
//
Query:       gi|242399528|ref|YP_002994953.1|  [L=134]
Description: hypothetical protein TSIB_1553 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-12   47.7   1.0    1.8e-12   47.0   1.0    1.4  1  Methyltranf_PUA  RNA-binding PUA-like domain of methyltransfe


Domain annotation for each model (and alignments):
>> Methyltranf_PUA  RNA-binding PUA-like domain of methyltransferase RsmF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.0   1.0     1e-16   1.8e-12       1      50 []      83     131 ..      83     131 .. 0.97

  Alignments for each domain:
  == domain 1  score: 47.0 bits;  conditional E-value: 1e-16
                   Methyltranf_PUA   1 alrYlkGetielepdlkkGwvlVcydgyplGwgKlvggrlKNkyPkglRr 50 
                                       a+ +l G+++ ++++ + Gwv+++++ y lG+g++++g +KN++Pk++R+
  gi|242399528|ref|YP_002994953.1|  83 AKLWLSGKDLKTSTEMR-GWVILKWGLYYLGCGRAKDGIIKNYVPKERRI 131
                                       6779************9.******************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       188  (0.0104858); expected 358.6 (0.02)
Passed bias filter:                      184  (0.0102627); 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 0.27s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 911.96
//
Query:       gi|242399529|ref|YP_002994954.1|  [L=304]
Description: nucleolar protein I [Thermococcus sibiricus MM 739]
Scores for 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  182.0   0.0    1.3e-53  181.6   0.0    1.2  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
    9.2e-17   61.3   0.1    2.2e-16   60.1   0.0    1.7  2  Methyltr_RsmF_N  N-terminal domain of 16S rRNA methyltransfer
    1.4e-05   24.9   0.0    1.9e-05   24.5   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
     0.0023   17.7   0.0     0.0033   17.2   0.0    1.3  1  Met_10           Met-10+ like-protein
     0.0048   17.6   0.0      0.089   13.5   0.0    2.4  3  Methyltransf_25  Methyltransferase domain
  ------ inclusion threshold ------
      0.018   15.2   0.0      0.035   14.2   0.0    1.4  1  FtsJ             FtsJ-like methyltransferase
      0.071   12.8   0.0       0.11   12.2   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl


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 !  181.6   0.0   5.2e-57   1.3e-53       2     199 ..      98     301 ..      97     302 .. 0.90

  Alignments for each domain:
  == domain 1  score: 181.6 bits;  conditional E-value: 5.2e-57
                                       HHH---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC. CS
                   Methyltr_RsmB-F   2 llLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlgge 78 
                                       ++L+pq++e +lD++aaPG+KTt ia+ m+nkg+++A+d++k+R++ +++nl+r+gv nt v+  D++++ ++    
  gi|242399529|ref|YP_002994954.1|  98 VVLDPQPGELVLDMAAAPGAKTTQIAQYMENKGCIIANDMKKWRVNVLIANLNRFGVLNTRVTVKDGTYFGRFEN-- 172
                                       68********************************************************************87766.. PP

                                       .EEEEEEEE--CCGGGTTT-TCHHHH--HHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEES--STTTTHHHHHHHHH CS
                   Methyltr_RsmB-F  79 lfDriLlDaPCsgtgvirrdpdvklrrkekdiaqlaklqkellsaaidllkkgGvlvYsTCsvlveEneevieeaLk 155
                                       +fD+iLlDaPCs+ g++r+  +  ++ + k ++++++ qk+l+ aa + lk+ GvlvYsTC++ + Ene v++++L 
  gi|242399529|ref|YP_002994954.1| 173 TFDKILLDAPCSSVGMVRKSFKFLFSWSMKKVITYSNIQKKLIMAAYKALKPRGVLVYSTCTIDPLENEGVVDYLLL 249
                                       6*************************************************************************976 PP

                                       H-.TTEEEESSBST......TSTTSSECEEC.TSEEE-TTTTSS-SEEEEEE CS
                   Methyltr_RsmB-F 156 kr.edvelvetels......epkglklgeea.gtlrllPhtenkdgffiakl 199
                                       k+ +++e ++++l+      e++g+k++ee  + lr+ P+ +n+++ff+ak+
  gi|242399529|ref|YP_002994954.1| 250 KTdAKIEKIDLPLHstppvlEFDGMKYSEEVrKCLRIHPQDNNTEAFFVAKI 301
                                       65155665555544212222778888888876789***************97 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 !   60.1   0.0   8.5e-20   2.2e-16       2      90 .]       8      94 ..       7      94 .. 0.93
   2 ?   -3.7   0.0       6.9   1.8e+04      24      39 ..     276     291 ..     274     297 .. 0.67

  Alignments for each domain:
  == domain 1  score: 60.1 bits;  conditional E-value: 8.5e-20
                                      -HHHHHHHHHHHGGGHHHHHHHHH-----EEE--TTS..TTHHHHHHH.-SS--B-TT-TTEEES---...TTSHHHHT CS
                   Methyltr_RsmF_N  2 PeeFiekmkellgeeaeaflaaleeprkkglRvNtlKisveeleklse.efelepvpwceeGfyleeeerpgkhplhea 79
                                      +++F e+++el   + e+f++ + +p+k+++R+NtlK+  + +++  e + elep+pw++eGf+++ + ++g   ++  
  gi|242399529|ref|YP_002994954.1|  8 NKAFYERYSELD--NSEEFWNLMVAPMKQSIRINTLKAPLDYIKERLEeRYELEPIPWVKEGFFINTR-EFGDMIEYSL 83
                                      689999999985..56899*99***************9999999877779****************99.9********* PP

                                      TS-EE--TTTH CS
                   Methyltr_RsmF_N 80 GlyYiQEpSam 90
                                      Gl++ QE+S+m
  gi|242399529|ref|YP_002994954.1| 84 GLVFPQEASSM 94
                                      **********9 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 6.9
                                       HH-----EEE--TTS. CS
                   Methyltr_RsmF_N  24 leeprkkglRvNtlKi 39 
                                       ++e+ +k lR+ +   
  gi|242399529|ref|YP_002994954.1| 276 YSEEVRKCLRIHPQDN 291
                                       6677788888877654 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   7.5e-09   1.9e-05       5     113 ..     106     234 ..     102     279 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 7.5e-09
                   Methyltransf_31   5 lrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsn 81 
                                         vlD +++ G++t ++a+ +  k+ ++  D+++  +++  +n+ + g+ n ++ + d + +   +e ++fD il +
  gi|242399529|ref|YP_002994954.1| 106 ELVLDMAAAPGAKTTQIAQYMENKGCIIANDMKKWRVNVLIANLNRFGVLNTRVTVKDGTYFGR-FE-NTFDKILLD 180
                                       569****************99999********************************99999876.77.9******** PP

                   Methyltransf_31  82 ......................evlnaladpdkileeiervlkpggilliedpr 113
                                                              v+ + + ++k ++ + ++lkp g+l+ +++ 
  gi|242399529|ref|YP_002994954.1| 181 apcssvgmvrksfkflfswsmkKVITYSNIQKKLIMAAYKALKPRGVLVYSTCT 234
                                       888888888887777777777777799999*********************998 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   1.3e-06    0.0033      99     189 ..     103     194 ..      90     230 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.3e-06
                                       -TT-EEEETT-TTTCCHHHCCHHTTSS.EEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG---.TT-EEEEE CS
                            Met_10  99 eegevVvdvfAGiGpfaipiakyskak.rvlaidlnPesvkylkeniklNkvekvvkpileDgrevir.eqladrvv 173
                                       ++ge+V+d+ A  G  +  ia+y ++k  ++a+d+    v+ l  n+++  v ++  +  +Dg  + r e+++d+++
  gi|242399529|ref|YP_002994954.1| 103 QPGELVLDMAAAPGAKTTQIAQYMENKgCIIANDMKKWRVNVLIANLNRFGVLNTR-VTVKDGTYFGRfENTFDKIL 178
                                       89********************97654389*******************9998875.7899*****999*****988 PP

                                       E--TTTGGGGHHHHHH CS
                            Met_10 174 mnlpksaieFldkvla 189
                                       +++p s++  + k ++
  gi|242399529|ref|YP_002994954.1| 179 LDAPCSSVGMVRKSFK 194
                                       8888777766666444 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       5.1   1.3e+04      22      49 ..      13      39 ..       5      53 .. 0.62
   2 !   13.5   0.0   3.5e-05     0.089       1      70 [.     108     179 ..     108     191 .. 0.93
   3 ?    1.5   0.0      0.19     5e+02      62      97 .]     190     226 ..     179     226 .. 0.72

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 5.1
                                      SEEEEEESSHHHHHHHHHHHHHTTTTEE CS
                   Methyltransf_25 22 akvtgvDiseemleaareraeeeglnve 49
                                      +++  +D see+++ + + +++ +++++
  gi|242399529|ref|YP_002994954.1| 13 ERYSELDNSEEFWNLMVAPMKQ-SIRIN 39
                                      5566677788777776665533.34444 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 3.5e-05
                                       EEEET-TTSHHHHHHHCTS.TSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEE CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrl.gkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvs 70 
                                       vLd+++ +G  t ++a+ + +k+ +++ D+ +  ++   +++++ g+ n ++ ++d + +   +++fD +++
  gi|242399529|ref|YP_002994954.1| 108 VLDMAAAPGAKTTQIAQYMeNKGCIIANDMKKWRVNVLIANLNRFGVlNTRVTVKDGTYFGRFENTFDKILL 179
                                       9*****************9769********************999999************99999***9986 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.19
                                       TTTEEEEEEESTGGGSSH.HHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  62 dgsfDlvvssgalhhlsd.edlekalkeiarvLkpgG 97 
                                        +sf + +s+ +  +++  + ++k++  ++++Lkp G
  gi|242399529|ref|YP_002994954.1| 190 RKSFKFLFSWSMKKVITYsNIQKKLIMAAYKALKPRG 226
                                       5688888887664444440445789**********98 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.4e-05     0.035      21      95 ..     104     181 ..      89     251 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.4e-05
                                       TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS......HHHTTEEEECS-CCCSSHHHHHCHCHHHSSEEEE CS
                              FtsJ  21 pgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm......aplpgvttiqgditdpetiekikealserkvdlv 91 
                                       pg+ v+D +aaPG+ +  ++q +++kg ++a D+++       a+l++  ++++ +t ++     +  + e+ +d +
  gi|242399529|ref|YP_002994954.1| 104 PGELVLDMAAAPGAKTTQIAQYMENKGCIIANDMKKWrvnvliANLNRFGVLNTRVTVKDGTYFGR--F-ENTFDKI 177
                                       7788*******************999********99866666555566666666665554433222..1.2345555 PP

                                       EE-- CS
                              FtsJ  92 vsDg 95 
                                       + D 
  gi|242399529|ref|YP_002994954.1| 178 LLDA 181
                                       5554 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   4.4e-05      0.11      72     151 ..     103     182 ..      88     188 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.4e-05
                                       -TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGGTTGGG-SEEEEEE CS
                              PCMT  72 kkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGrkGyeekaPYdaihv 148
                                       ++g+ vL++ +  G +t  +a+++++kg +++ +  k  v+   +nl++ ++ n  v+v DG++    +  +d+i++
  gi|242399529|ref|YP_002994954.1| 103 QPGELVLDMAAAPGAKTTQIAQYMENKGCIIANDMKKWRVNVLIANLNRFGVLNTRVTVKDGTYFGRFENTFDKILL 179
                                       78999*****************************99999***********************997777788999988 PP

                                       SSB CS
                              PCMT 149 gaa 151
                                        a 
  gi|242399529|ref|YP_002994954.1| 180 DAP 182
                                       775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 2032.10
//
Query:       gi|242399530|ref|YP_002994955.1|  [L=144]
Description: hypothetical protein TSIB_1555 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.7e-45  152.9   0.6    6.4e-45  152.8   0.6    1.0  1  Archease  Archease protein family (MTH1598/TM1083)


Domain annotation for each model (and alignments):
>> Archease  Archease protein family (MTH1598/TM1083)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.8   0.6   3.5e-49   6.4e-45       1     138 []       7     144 .]       7     144 .] 0.97

  Alignments for each domain:
  == domain 1  score: 152.8 bits;  conditional E-value: 3.5e-49
                                       EEE---SSEEEEEEE-SSSHHHHHHHHHHHHHHHS--TT---S-EEEEEEEESSSHHHHHHHHHHHHHHHHHT--S- CS
                          Archease   1 yeyldhtADviieawGksleeafesaalalfeymtdlskvepkeekeieveaedledlLfdfLdellylfdteyfvf 77 
                                       +e+ +htAD++i+++G++leeafe++a alf++m+d+ kv+ ke +eieve+edl +lL++fL+ell+l+dte +vf
  gi|242399530|ref|YP_002994955.1|   7 WEHYEHTADIGIRGYGDTLEEAFEAVATALFDVMVDVRKVDRKEMREIEVEGEDLYALLYSFLEELLILHDTEGLVF 83 
                                       899************************************************************************** PP

                                       ---EEEE.E-SSSEEEEEEEE----.-TT--------B--S---EEEE.ETTEEEEEEEEE- CS
                          Archease  78 kevkvdeeeeeeeleleaeargekfdkekhevqtevKAvTyhelriee.eddgweayvvvDi 138
                                        +++v+ e+++e+++l+a+a+ge++ +ekhe ++evKA+Tyhe++i++ ed++w  ++v Di
  gi|242399530|ref|YP_002994955.1|  84 GDFEVKIEKTKEGYKLKAKAYGEPL-SEKHEPKEEVKAITYHEMNIKQfEDGTWMTQLVPDI 144
                                       ***99888999**************.778*999*************9978899****99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 970.25
//
Query:       gi|242399531|ref|YP_002994956.1|  [L=288]
Description: 3-methyl-2-oxobutanoate hydroxymethyltransferase [Thermococcus sibiricus MM 739]
Scores for complete 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-109  364.3   0.2   3.7e-109  364.1   0.2    1.0  1  Pantoate_transf  Ketopantoate hydroxymethyltransferase
    3.3e-08   33.3   0.9    1.5e-06   27.9   0.2    2.3  2  PEP_mutase       Phosphoenolpyruvate phosphomutase
     0.0026   17.0   0.5        2.4    7.3   0.0    3.1  3  NanE             Putative N-acetylmannosamine-6-phosphate epi
     0.0059   16.2   0.4       0.11   12.1   0.1    2.3  2  Amdase           Arylmalonate decarboxylase
  ------ inclusion threshold ------
      0.015   14.8   0.4        2.4    7.6   0.1    2.2  2  ComA             (2R)-phospho-3-sulfolactate synthase (ComA)
       0.04   13.4   0.9        2.9    7.3   0.1    2.5  2  BtpA             BtpA family
      0.076   12.2   0.1       0.15   11.2   0.1    1.5  1  Peptidase_U32    Peptidase family U32


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 !  364.1   0.2  1.5e-112  3.7e-109       2     258 ..       4     257 ..       3     258 .. 0.99

  Alignments for each domain:
  == domain 1  score: 364.1 bits;  conditional E-value: 1.5e-112
                   Pantoate_transf   2 vtvkdlrkmkeegekiamlTaydattAklvdeagvdviLVGDslgmvvlgyestlpvtleemiyhtkaVargakral 78 
                                       +t+k++ +mk + eki+m+Tayd++++ ++d+ag+d+i VGDslgmvv+g+e+tl+vt+++m+yht+aVa+++kr l
  gi|242399531|ref|YP_002994956.1|   4 ITTKRIMEMKGK-EKITMVTAYDYPSGLIADKAGIDIIFVGDSLGMVVYGDENTLNVTMDQMVYHTRAVAKAVKRGL 79 
                                       78999*****87.**************************************************************** PP

                   Pantoate_transf  79 vvadlPfgsyeaskeqalenAarllkeggadavKleggaevaetvkalveagipVmgHiGltPqsvnalggykvqgk 155
                                       v+ad+Pf+sye+s e+ ++nAarl+++ gadavK+egg ++ ++vk+lv++gipVmgH GltPq+  +lggy++ g+
  gi|242399531|ref|YP_002994956.1|  80 VLADMPFMSYETSVEEGIKNAARLVQA-GADAVKIEGGYDHKKLVKKLVRSGIPVMGHTGLTPQRYLRLGGYHITGE 155
                                       **************************9.************************************************* PP

                   Pantoate_transf 156 teeeaeklledakaleeaGafalvlEavpaelakeiteklsiptIGIGAGaacdGqvlvlhDllgltekfkpkfvkk 232
                                       teee e++++dakale+aGafa+vlE v +++ak +te+++iptIGIG+G++cdGqvlv+hDllg++ +++p fvkk
  gi|242399531|ref|YP_002994956.1| 156 TEEEIEEIIRDAKALEKAGAFAVVLEFVLSDVAKLVTEEVKIPTIGIGSGPYCDGQVLVWHDLLGFY-EHTPPFVKK 231
                                       *******************************************************************.789****** PP

                   Pantoate_transf 233 yaelaesieeavkaYaeevkegsFPa 258
                                       ya+l+++i+ a+++Y+eevk+g+FP+
  gi|242399531|ref|YP_002994956.1| 232 YADLRNIIQLALENYKEEVKDGKFPS 257
                                       *************************7 PP

>> PEP_mutase  Phosphoenolpyruvate phosphomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.2   5.8e-10   1.5e-06       6     107 ..      14     116 ..       9     130 .. 0.88
   2 ?    3.6   0.0     0.015        38     151     178 ..     156     183 ..     146     201 .. 0.71

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 5.8e-10
                        PEP_mutase   6 akgeplvlpnawDalsakiveeagfkalatsSlavaaslGvpDgeelpleellaavraiaevvslPl.ivDle.dGy 80 
                                        k e + ++ a+D  s  i+ +ag++ + ++      ++G + + ++++++++ ++ra+a++v+  l ++D+    y
  gi|242399531|ref|YP_002994956.1|  14 GK-EKITMVTAYDYPSGLIADKAGIDIIFVGDSLGMVVYGDENTLNVTMDQMVYHTRAVAKAVKRGLvLADMPfMSY 89 
                                       44.7899************************999999**************************7654399*97479* PP

                        PEP_mutase  81 gespeevaetvrrliaaGvvgvniEDk 107
                                       + s+ee  ++ +rl++aG+ +v iE  
  gi|242399531|ref|YP_002994956.1|  90 ETSVEEGIKNAARLVQAGADAVKIEGG 116
                                       *************************77 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.015
                        PEP_mutase 151 agagleeaieRaraYaeAGAdgvfvpgl 178
                                        ++++ee i+ a+a  +AGA +v+   +
  gi|242399531|ref|YP_002994956.1| 156 TEEEIEEIIRDAKALEKAGAFAVVLEFV 183
                                       5567778888888888888877766554 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 !    5.0   0.1    0.0046        12      85     116 ..       9      40 ..       1      83 [. 0.79
   2 ?    1.4   0.0     0.061   1.6e+02       9      31 ..     104     127 ..      85     142 .. 0.61
   3 !    7.3   0.0   0.00095       2.4       5      45 ..     167     209 ..     163     217 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0046
                                       HHHHHHH--EEEEE-SSHHHHHHHHHTT-SEE CS
                              NanE  85 ikkikekyqllmaDistleeglvakklGvdiv 116
                                       i ++k k ++ m     +  gl+a+k+G+di+
  gi|242399531|ref|YP_002994956.1|   9 IMEMKGKEKITMVTAYDYPSGLIADKAGIDII 40 
                                       44677788999*999***************86 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.061
                                       HHHT-SEEEEESHHHHHH.HHTT- CS
                              NanE   9 eqaGavgiriegvedika.ikavv 31 
                                       +qaGa +++ieg  d k+ +k+ v
  gi|242399531|ref|YP_002994956.1| 104 VQAGADAVKIEGGYDHKKlVKKLV 127
                                       456666666665544433134443 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.00095
                                       HHHHHHHT-SEEEEESH.HHHHH.HHTT--S-EEEE-B---TT CS
                              NanE   5 akaaeqaGavgiriegv.edika.ikavvdlPiiGivkrdlpd 45 
                                       aka e+aGa ++  e v +d+++ + ++v++P iGi    + d
  gi|242399531|ref|YP_002994956.1| 167 AKALEKAGAFAVVLEFVlSDVAKlVTEEVKIPTIGIGSGPYCD 209
                                       99*************8756776537899*******97666655 PP

>> Amdase  Arylmalonate decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.1   4.3e-05      0.11      16      55 ..      76     115 ..      62     117 .. 0.90
   2 ?    1.8   0.0     0.061   1.6e+02      31      53 ..     158     180 ..     147     182 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.3e-05
                            Amdase  16 AeGLglkelskegydevidrvveaArelaerGaqavslmG 55 
                                        +GL l+++   +y++ +++ ++ A++l ++Ga+av + G
  gi|242399531|ref|YP_002994956.1|  76 KRGLVLADMPFMSYETSVEEGIKNAARLVQAGADAVKIEG 115
                                       58**********************************9866 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.061
                            Amdase  31 evidrvveaArelaerGaqavsl 53 
                                       e i++++  A++l+++Ga av+l
  gi|242399531|ref|YP_002994956.1| 158 EEIEEIIRDAKALEKAGAFAVVL 180
                                       56899***************987 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 ?    7.6   0.1   0.00094       2.4     138     167 ..      87     116 ..      49     131 .. 0.69
   2 ?    6.0   0.0    0.0028       7.3     114     171 ..     120     187 ..     117     197 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00094
                                       HHTT--CCHHHHHHHHHHHHTECEEEE--T CS
                              ComA 138 lesesdveklieeakrdleaGaekviiEar 167
                                        + e++ve+ i++a+r ++aGa++v iE+ 
  gi|242399531|ref|YP_002994956.1|  87 MSYETSVEEGIKNAARLVQAGADAVKIEGG 116
                                       3667999********************986 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0028
                                       HHHHHHHCCTTSEEEEEES-SSH..........HHHTT--CCHHHHHHHHHHHHTECEEEE--TTT-- CS
                              ComA 114 lrliekakkeglkvlpevgkkdg..........elesesdveklieeakrdleaGaekviiEaresGi 171
                                       ++l++k+ ++g+ v+ ++g   +          + e e+++e++i+ ak+  +aGa +v++E   s+ 
  gi|242399531|ref|YP_002994956.1| 120 KKLVKKLVRSGIPVMGHTGLTPQrylrlggyhiTGETEEEIEEIIRDAKALEKAGAFAVVLEFVLSDV 187
                                       567778888888888777776666677777777778889*********************99765555 PP

>> BtpA  BtpA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1    0.0076        20      25      54 ..      90     119 ..      77     137 .. 0.80
   2 ?    7.3   0.1    0.0011       2.9      18      50 ..     150     182 ..     131     200 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0076
                              BtpA  25 eevidkAvkeakaleegGvDavilenygda 54 
                                       e+ +++ +k+a  l ++G+Dav +e  +d 
  gi|242399531|ref|YP_002994956.1|  90 ETSVEEGIKNAARLVQAGADAVKIEGGYDH 119
                                       5678999***************99976663 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0011
                              BtpA  18 aeykanleevidkAvkeakaleegGvDavilen 50 
                                       ++ +++ ee i++ +++akale++G+ av+le 
  gi|242399531|ref|YP_002994956.1| 150 YHITGETEEEIEEIIRDAKALEKAGAFAVVLEF 182
                                       5566788899********************995 PP

>> Peptidase_U32  Peptidase family U32
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   5.7e-05      0.15     158     190 ..      96     128 ..      64     129 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5.7e-05
                     Peptidase_U32 158 lieelpelleaGvdslKIeGRmkspeyvatvvr 190
                                       +i++  +l++aG d++KIeG + +++ v++ vr
  gi|242399531|ref|YP_002994956.1|  96 GIKNAARLVQAGADAVKIEGGYDHKKLVKKLVR 128
                                       6788899********************999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       663  (0.0369792); expected 358.6 (0.02)
Passed bias filter:                      513  (0.0286129); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 1701.65
//
Query:       gi|242399532|ref|YP_002994957.1|  [L=354]
Description: hypothetical protein TSIB_1557 [Thermococcus sibiricus MM 739]
Scores for complete 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-46  158.0   0.0      4e-46  157.8   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    6.9e-05   21.6   0.0    8.4e-05   21.3   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    0.00019   20.1   0.1    0.00025   19.7   0.1    1.2  1  Met_gamma_lyase  Methionine gamma-lyase
    0.00054   19.0   0.0     0.0018   17.2   0.0    1.8  2  Alliinase_C      Allinase
  ------ inclusion threshold ------
      0.016   14.5   0.0      0.024   13.9   0.0    1.3  1  Beta_elim_lyase  Beta-eliminating lyase
      0.022   13.7   0.1      0.035   13.1   0.1    1.2  1  Aminotran_5      Aminotransferase class-V
       0.16   12.3   0.0        1.8    8.9   0.0    2.3  3  DUF5616          Domain of unknown function (DUF5616)


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 !  157.8   0.0   1.6e-49     4e-46       7     358 ..      34     352 ..      28     354 .] 0.92

  Alignments for each domain:
  == domain 1  score: 157.8 bits;  conditional E-value: 1.6e-49
                                       SSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHH CS
                     Aminotran_1_2   7 gsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagaliea 83 
                                       + + ++++    t+p+v+++ k       ++ +y++ + + el++al +++g      ++++ ++ +g G+  + e 
  gi|242399532|ref|YP_002994957.1|  34 SLGTNPFG----TSPRVKQKLKN---LEIEISKYPDVH-YTELRNALSDYWG------IDKN-SIFFGYGSMGCFEK 95 
                                       66778888....99999999976...777899******.*************......9999.************** PP

                                       HHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TT CS
                     Aminotran_1_2  84 lifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNP 160
                                       ++ ++ +  g ++l  +p y+ y+ ++  +gg   ++ l+ e++f++d+ ++++  ++      ++ ++++ +phNP
  gi|242399532|ref|YP_002994957.1|  96 VNKFA-IKNGAKVLGISPQYTRYISDVIVMGGIYESVLLKAENNFKIDIGEIINSMTS------EHTLFYLDNPHNP 165
                                       *9999.99**************************************************......999********** PP

                                       T--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEE.E CS
                     Aminotran_1_2 161 tGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilg.n 236
                                       tG++ tl+e+e++++ ak++++l+++DeaY++fv ++++      n+++ +nl++++s+sK fGla  RvGy+++ n
  gi|242399532|ref|YP_002994957.1| 166 TGQLVTLKEIEEIVEEAKQKGVLVLIDEAYGDFVDKKQS----AINLNA-DNLIVLRSFSKGFGLASMRVGYAVIrN 237
                                       ************************************665....788988.699**********************9* PP

                                       HHHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS.TEEEECCSCSSEEEEEE CS
                     Aminotran_1_2 237 aavvsqlrklsrpflsssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLael.glkvlasqsgmflltdl 312
                                        ++++  +k+  pf +++ + a+++aal+d++    +le++r+++++  +++  +L++   ++ + +++ + l+ ++
  gi|242399532|ref|YP_002994957.1| 238 RELRELYKKVDLPFPITATGEALAVAALRDQE----FLEKSRKQIATIKERIIHNLKKMfQIPETHPKTPIMLV-GG 309
                                       ******************************99....89******************999999999998887766.55 PP

                                       THHCHHHHHHHHHHTCTEEEEEGGGGTS..TTEEEEECTTS-HHHHHH CS
                     Aminotran_1_2 313 saetakelskkLleevgvyvtpgtsftv..pgrlRitvAglteeelee 358
                                       +       ++  l++ gv+ ++g+ f     + +R+ v+   ee l++
  gi|242399532|ref|YP_002994957.1| 310 EGD----TYDYFLKR-GVLTVAGSAFKPldNSYVRLRVPKNEEELLRR 352
                                       555....5899****.**********9999999999997666666665 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   3.3e-08   8.4e-05     126     207 ..     142     230 ..     101     287 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 3.3e-08
                                       SHHHHHHHCCTTEEEEEEESS-TTTT---...-HHHHHHHHHHTT-EEEEEGTTTHT..TTS-GGGGT-S..EEEEE CS
                   Cys_Met_Meta_PP 126 dleelekaikentklvylEtptnpllkvv...DiekiaklakkagvlvvvDntfasp..llqrplklgaD..ivvhS 195
                                       d+ e+ + ++++  l+yl+ p np+ ++v    ie+i++ ak++gvlv++D ++       q +++l+aD  iv++S
  gi|242399532|ref|YP_002994957.1| 142 DIGEIINSMTSEHTLFYLDNPHNPTGQLVtlkEIEEIVEEAKQKGVLVLIDEAYGDFvdKKQSAINLNADnlIVLRS 218
                                       55677788889999**********977652237889999999999********9876336799*******9999999 PP

                                       TTTTTTCSSS-- CS
                   Cys_Met_Meta_PP 196 aTKylgGhsdvv 207
                                        +K  g  s  v
  gi|242399532|ref|YP_002994957.1| 219 FSKGFGLASMRV 230
                                       999665544444 PP

>> Met_gamma_lyase  Methionine gamma-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.1   9.9e-08   0.00025     131     227 ..     127     225 ..     104     264 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 9.9e-08
                   Met_gamma_lyase 131 kykevdlleeg..kvdieavkeaikektkliliqrskGyserkslsieeieeiiklvkeinedvivfvdncyGefve 205
                                        y++v l++e+  k+di ++ ++++++  l  +   +   + + ++++eieei++  k+  + v+v++d+ yG+fv+
  gi|242399532|ref|YP_002994957.1| 127 IYESVLLKAENnfKIDIGEIINSMTSEHTLFYLDNPHNP-TGQLVTLKEIEEIVEEAKQ--KGVLVLIDEAYGDFVD 200
                                       588888876542379999*******99999999987764.567899*********9885..78************** PP

                   Met_gamma_lyase 206 eke.PtevGad..liaGsliknpGG 227
                                       +k+  +++ ad  ++  s+ k  G 
  gi|242399532|ref|YP_002994957.1| 201 KKQsAINLNADnlIVLRSFSKGFGL 225
                                       9862567788743344555555444 PP

>> Alliinase_C  Allinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   7.2e-07    0.0018     123     214 ..     139     241 ..      89     291 .. 0.75
   2 ?   -0.9   0.0      0.22   5.6e+02     315     349 ..     311     346 ..     303     351 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 7.2e-07
                                       EEEESTT-.--S..S-EEEEEESS-TTT---...-..----...-TT-EEEEEE-TT...-STTTS---S-B--SEE CS
                       Alliinase_C 123 weGdaaayvkkknpeefielvtsPnnPdgll...r..eavv...kgseakviyDlay...YWPhytpitskadedim 188
                                       ++ d  + +++ ++e+ +     P nP g+l   +  e++v   k++ + v+ D ay      + ++i+ +ad+ i+
  gi|242399532|ref|YP_002994957.1| 139 FKIDIGEIINSMTSEHTLFYLDNPHNPTGQLvtlKeiEEIVeeaKQKGVLVLIDEAYgdfVDKKQSAINLNADNLIV 215
                                       5555555556666666666777899999987333333578854333444578899984422467899********** PP

                                       EEEHHHHHS-GGG-EEEEEES-HHHH CS
                       Alliinase_C 189 LftlskltGhaGsrlGWalvkdkeva 214
                                       L ++sk  G a  r+G+a+++++e+ 
  gi|242399532|ref|YP_002994957.1| 216 LRSFSKGFGLASMRVGYAVIRNRELR 241
                                       *********************98753 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.22
                                       .-HHHHHHTTTEEEEEGGGGT.S-TTEEEEESSS-H CS
                       Alliinase_C 315 edcaevlrekkiltrsGevfe.aesryvrlsllkrd 349
                                        d ++ + ++++lt +G+ f+  +++yvrl + k++
  gi|242399532|ref|YP_002994957.1| 311 GDTYDYFLKRGVLTVAGSAFKpLDNSYVRLRVPKNE 346
                                       688999999**********9835999***9887766 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   9.4e-06     0.024     126     169 ..     152     194 ..      80     195 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9.4e-06
                                       -EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEET CS
                   Beta_elim_lyase 126 ekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgA 169
                                        +  l +l + +n   Gq v+l+e++e+ + ak++g+ +++D A
  gi|242399532|ref|YP_002994957.1| 152 SEHTLFYLDNPHNP-TGQLVTLKEIEEIVEEAKQKGVLVLIDEA 194
                                       4677899999***5.9**************************76 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   1.4e-05     0.035     119     177 ..     133     194 ..     128     214 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.4e-05
                                       EEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTE...B--HHHHHHHHHHTT-EEEEE-T CS
                       Aminotran_5 119 ipldeegeldldelekllnektklvaithvsnvtGt...iqpveeigklakkkgalvlvDaa 177
                                       ++++++ ++d+ e+ + ++ +  l ++    n tG    ++++eei++ ak+kg+lvl+D a
  gi|242399532|ref|YP_002994957.1| 133 LKAENNFKIDIGEIINSMTSEHTLFYLDNPHNPTGQlvtLKEIEEIVEEAKQKGVLVLIDEA 194
                                       678889999**************************6444789999***************87 PP

>> DUF5616  Domain of unknown function (DUF5616)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       2.7     7e+03      99     130 ..      51      80 ..      45      84 .. 0.77
   2 ?    8.9   0.0   0.00071       1.8      60     128 ..     143     215 ..     126     227 .. 0.80
   3 ?    0.3   0.0      0.32   8.1e+02     111     138 ..     269     296 ..     256     298 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.7
                           DUF5616  99 legevelvknvDkeLkeseeivatsDsvildk 130
                                        ++e+e++k +D   +e+++  a sD + +dk
  gi|242399532|ref|YP_002994957.1|  51 KNLEIEISKYPDVHYTELRN--ALSDYWGIDK 80 
                                       46889999999999998888..7888877775 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00071
                           DUF5616  60 ilellkelkvkkvifllDkpvSnSgela..klireileeaglegevelvknvDkeLk..eseeivatsDsvil 128
                                       i+e+++++  +++ f+lD+p   +g+l   k i+ei+eea+ +g   l +++  + +  ++++i   +D  i+
  gi|242399532|ref|YP_002994957.1| 143 IGEIINSMTSEHTLFYLDNPHNPTGQLVtlKEIEEIVEEAKQKGVLVLIDEAYGDFVdkKQSAINLNADNLIV 215
                                       78999*********************9733679********99999999888666552144447777787664 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.32
                           DUF5616 111 keLkeseeivatsDsvildkvksvldla 138
                                       + L++s++ +at    i+++ k+++ ++
  gi|242399532|ref|YP_002994957.1| 269 EFLEKSRKQIATIKERIIHNLKKMFQIP 296
                                       4567777789999999999999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      560  (0.0312343); 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: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.51
# Mc/sec: 2102.02
//
Query:       gi|242399533|ref|YP_002994958.1|  [L=282]
Description: Permease, drug/metabolite transporter (DMT) superfamily [Thermococcus sibiricus MM 739]
Scores for complete 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-38  130.5  31.5    3.9e-23   82.1  13.6    2.1  2  EamA       EamA-like transporter family
     0.0037   16.3   5.5     0.0077   15.2   0.7    2.2  2  CRT-like   CRT-like, chloroquine-resistance transporter-like
     0.0037   16.5   3.1     0.0037   16.5   3.1    2.2  2  PUNUT      Purine nucleobase transmembrane transport
  ------ inclusion threshold ------
       0.23   11.3   0.0       0.34   10.8   0.0    1.2  1  Cas_Cas5d  CRISPR-associated protein (Cas_Cas5)
        1.6    8.3  15.1      0.032   13.8   6.1    2.6  3  EmrE       Putative multidrug resistance efflux transporter


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 !   82.1  13.6   1.1e-26   3.9e-23       3     137 .]       7     140 ..       5     140 .. 0.97
   2 !   54.6   9.9   3.4e-18   1.2e-14       2     136 ..     149     272 ..     148     273 .. 0.92

  Alignments for each domain:
  == domain 1  score: 82.1 bits;  conditional E-value: 1.1e-26
                              EamA   3 gillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegkl.aklslkdwllllllgllgtvla 78 
                                       g +la+l++++++i +v++k+  + ++p+++++++ +ia+++l +i + + +++ a+ s++ +   +l+g++gt+la
  gi|242399533|ref|YP_002994958.1|   7 GTFLAFLGMFLYGIEPVVIKA--NPTNPMSFAAFSAIIASLILWPIVFSTSSWKeARESPQYIPKAALVGVFGTALA 81 
                                       789*****************9..69*************************999988899999*************** PP

                              EamA  79 fllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllill 137
                                       ++++ y+ + ++a naslit+ e++f+ +ls+++l+ek+t+ q+l  +lillG+ l+++
  gi|242399533|ref|YP_002994958.1|  82 YIAYSYGAQLSTAINASLITRAEVLFSFVLSYIILREKITKNQILWSILILLGLTLVIT 140
                                       ********************************************************985 PP

  == domain 2  score: 54.6 bits;  conditional E-value: 3.4e-18
                              EamA   2 lgillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvla 78 
                                       +g+ll+ll+ lfw ++ v++k+l   ++p+ ++++r +++gilll++al+++  +   s+ +++  l+l+     l+
  gi|242399533|ref|YP_002994958.1| 149 KGDLLLLLVPLFWQSGHVIAKRL--PYNPFLIAAFRNTFGGILLLLLALPRGLEF---SKFAIAEALILS-----LG 215
                                       799*******************9..9************************99999...555555555555.....8* PP

                              EamA  79 fllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                       +++++ ++k+++ s+a+ i++ +P++++  +++l ge++t+++++g++li +G+l+++
  gi|242399533|ref|YP_002994958.1| 216 QVVWYLSIKRINLSKATAIITPAPAVAIGVAIVL-GETFTSYHMIGFILITVGTLVVS 272
                                       *****************************99988.********************997 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 !   15.2   0.7   2.1e-06    0.0077      42     151 ..      39     151 ..      27     162 .. 0.83
   2 !    3.3   0.3     0.009        32     110     144 ..     243     278 ..     226     282 .] 0.73

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.1e-06
                          CRT-like  42 vpiffavvlykllltndipketrsfpkr..kFaimgaLDavsgilvvigavstsGslq.vllnqaiipitllaslll 115
                                         i  +++l+ ++++ +  ke r++p++  k a++g+  +  ++++   + ++s  +  +l++ a + +++++s ++
  gi|242399533|ref|YP_002994958.1|  39 SAIIASLILWPIVFSTSSWKEARESPQYipKAALVGVFGTALAYIAYSYGAQLSTAINaSLITRAEVLFSFVLSYII 115
                                       45566677888999999999*******9778999***9999999998888888877752799*************** PP

                          CRT-like 116 lkerysliqylGAlviilgvvvvlipsllgessegn 151
                                       l+e+    q+l  ++i+lg+ +v+++  +    +g+
  gi|242399533|ref|YP_002994958.1| 116 LREKITKNQILWSILILLGLTLVITQGKAIVPRKGD 151
                                       ********************9998877666666555 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.009
                          CRT-like 110 lasllllkerysliqylGAlviilgvvvv.lipsll 144
                                       +   ++l e +  ++++G ++i++g +vv  i s l
  gi|242399533|ref|YP_002994958.1| 243 IGVAIVLGETFTSYHMIGFILITVGTLVVsRIKSEL 278
                                       5567899999999*****998887765540454444 PP

>> PUNUT  Purine nucleobase transmembrane transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   3.1     1e-06    0.0037      69     147 ..      61     140 ..      32     150 .. 0.71
   2 ?    0.9   0.8     0.058   2.1e+02      95     145 ..     222     271 ..     200     281 .. 0.54

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1e-06
                             PUNUT  69 lslkklvllyivlGll.vavdnllyslgllylpvstfslilatqLaFtaifsalinkqkftrfiinsvvlltisaal 144
                                         + + +  + ++G+  +a+  + ys+g +   +  +sli+ +  +F+ ++s++i + k+t   i+  +l+ ++ +l
  gi|242399533|ref|YP_002994958.1|  61 RESPQYIPKAALVGVFgTALAYIAYSYGAQLSTAINASLITRAEVLFSFVLSYIILREKITKNQILWSILILLGLTL 137
                                       3445555566677776244455669****9999999*************************9887766666666665 PP

                             PUNUT 145 lal 147
                                       + +
  gi|242399533|ref|YP_002994958.1| 138 VIT 140
                                       554 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.058
                             PUNUT  95 gllylpvstfslilatqLaFtaifsalinkqkftrfiinsvvlltisaall 145
                                         + +++s ++ i++   a  ai  a++    ft + ++  +l+t+++ ++
  gi|242399533|ref|YP_002994958.1| 222 SIKRINLSKATAIITPAPA-VAIGVAIVLGETFTSYHMIGFILITVGTLVV 271
                                       4444444444444444333.2444555556666666666666666666555 PP

>> Cas_Cas5d  CRISPR-associated protein (Cas_Cas5)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   9.5e-05      0.34      13      43 ..      52      82 ..      50     113 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 9.5e-05
                                      EB-TTCCSCCCBESS--HHHHHHHHHHHHT- CS
                         Cas_Cas5d 13 fgrpsrkveretydvPtkSavlGllaaalGi 43
                                      f + s k+ re+ ++++k a++G+ + al++
  gi|242399533|ref|YP_002994958.1| 52 FSTSSWKEARESPQYIPKAALVGVFGTALAY 82
                                      788999999********************54 PP

>> EmrE  Putative multidrug resistance efflux transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1      0.22   7.8e+02      93     131 ..       9      50 ..       6      56 .. 0.68
   2 ?   13.8   6.1     9e-06     0.032      28     110 ..      64     146 ..      37     187 .. 0.78
   3 ?   -1.1   0.5      0.32   1.1e+03     228     255 ..     242     269 ..     223     271 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.22
                              EmrE  93 llillGvvlvqlee..akelslkelllgvlpvlvaaf.aYPl 131
                                       +l +lG++l  +e   +k+ +++ + ++++++++a++  +P+
  gi|242399533|ref|YP_002994958.1|   9 FLAFLGMFLYGIEPvvIKANPTNPMSFAAFSAIIASLiLWPI 50 
                                       566777777777764456667777777778777777414665 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 9e-06
                              EmrE  28 kkkplfwllwgsiGfglfYallcfaaayapgWlvAatwqitivagllllplfkrkkiplkalllsllillGvvlvql 104
                                        + + +  l+g +G +l Y   +++a+ + +   + + +  ++ + +l+ ++ r+ki ++++l+s+lillG +lv +
  gi|242399533|ref|YP_002994958.1|  64 PQYIPKAALVGVFGTALAYIAYSYGAQLSTAINASLITRAEVLFSFVLSYIILREKITKNQILWSILILLGLTLVIT 140
                                       344445567899999999*********99998888888999*********999*********************988 PP

                              EmrE 105 eeakel 110
                                       +    +
  gi|242399533|ref|YP_002994958.1| 141 QGKAIV 146
                                       876555 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.32
                              EmrE 228 igeilllnaalpsllglvGialiilGlv 255
                                       + ++ ++ +++ + + ++G++li +G +
  gi|242399533|ref|YP_002994958.1| 242 AIGVAIVLGETFTSYHMIGFILITVGTL 269
                                       4444444455556678899999988865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); 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):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2136.26
//
Query:       gi|242399534|ref|YP_002994959.1|  [L=112]
Description: hypothetical protein TSIB_1559 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.8e-15   55.1   0.0    7.7e-15   55.0   0.0    1.2  1  PqqD      Coenzyme PQQ synthesis protein D (PqqD)
  ------ inclusion threshold ------
      0.016   14.4   0.0      0.088   12.0   0.0    1.8  2  DUF4317   Domain of unknown function (DUF4317)


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 !   55.0   0.0   8.6e-19   7.7e-15      10      67 .]      43     102 ..       8     102 .. 0.86

  Alignments for each domain:
  == domain 1  score: 55.0 bits;  conditional E-value: 8.6e-19
                                       ..E..EE--CHHHHHHHH-SSSS-HHHHHHHHHHHCT--HHHHHHHHHHHHHHHHCTT-- CS
                              PqqD  10 gky..isLnetgafiWklldgersveeivaalaeeydvdeeeaeadvlafldqLrekgli 67 
                                       g+y  ++L+e g+f+W+l+dg+r++e+i ++++e++++++e++++++  f+ +L +++li
  gi|242399534|ref|YP_002994959.1|  43 GEYrrLELDELGTFVWDLCDGTRTIEQIGKKVKERFGEEAEPLYERLVTFILELYKRNLI 102
                                       4454469*****************************9999******************98 PP

>> DUF4317  Domain of unknown function (DUF4317)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   9.8e-06     0.088     338     365 ..       6      33 ..       2      36 .. 0.87
   2 ?    0.1   0.0     0.039   3.5e+02     299     323 ..      66      90 ..      61      97 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9.8e-06
                           DUF4317 338 kvkpekldlvktqvidGkkclvIeidee 365
                                       ++ p++ d+++ + i+Gk++l+I+++ +
  gi|242399534|ref|YP_002994959.1|   6 TLIPKRNDEIELREINGKHYLLIPMKSK 33 
                                       567999******************9765 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.039
                           DUF4317 299 klekiekafeeafgedtelkaenli 323
                                       ++e+i k+ +e fge++e++ e l+
  gi|242399534|ref|YP_002994959.1|  66 TIEQIGKKVKERFGEEAEPLYERLV 90 
                                       689999999****999999988886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.34s 00:00:00.86 Elapsed: 00:00:00.53
# Mc/sec: 637.25
//
Query:       gi|242399535|ref|YP_002994960.1|  [L=112]
Description: 30S ribosomal protein S10P [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.8e-28   97.3   0.1    5.6e-28   97.0   0.1    1.1  1  Ribosomal_S10  Ribosomal protein S10p/S20e
  ------ inclusion threshold ------
      0.031   15.1   0.0      0.056   14.3   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 !   97.0   0.1   6.3e-32   5.6e-28       1      97 [.      15     108 ..      15     109 .. 0.98

  Alignments for each domain:
  == domain 1  score: 97.0 bits;  conditional E-value: 6.3e-32
                                       EEEEEESSHHHHHHHHHHHHHHTTSSS-EE---EEEEEEEEEEEEE--SS--.S--EEEEEEEEEEEEEEEE.E-HH CS
                     Ribosomal_S10   1 rirlkSydsklLekavkkivraakelgikvkgpvplPtkrkrvtvlksphvd.kksreqfeirthkRlidisdatke 76 
                                       ri+l S+d ++L++++++i+++a+++g++++gp+plPtkr r+t++ksp ++ + + ++fe+r+hkRlidi +a+++
  gi|242399535|ref|YP_002994960.1|  15 RIKLASTDISALNDVTDQIKQIAERTGVRMSGPIPLPTKRIRITTRKSPDGEgSATFDKFELRVHKRLIDI-EADER 90 
                                       8**********************************************************************.6**** PP

                                       HHHHHS-...S---SS-EEEE CS
                     Ribosomal_S10  77 tidtllkllqlnlpegVsvev 97 
                                        ++++++   +++pe V +e+
  gi|242399535|ref|YP_002994960.1|  91 AMRQIMR---IRVPEDVTIEI 108
                                       *******...*********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 ?   14.3   0.0   6.3e-06     0.056       6      55 ..      14      59 ..      11      62 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.3e-06
                            PriA_C  6 alirvsgkdeekveeaaeelaellkealkleeveilgpapapiakikgry 55
                                      a+i++ ++d ++++++ ++++++ ++    ++v++ gp+p p ++i+   
  gi|242399535|ref|YP_002994960.1| 14 ARIKLASTDISALNDVTDQIKQIAER----TGVRMSGPIPLPTKRIRITT 59
                                      799999***************99999....6799************9655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 800.73
//
Query:       gi|242399536|ref|YP_002994961.1|  [L=428]
Description: Elongation factor 1-alpha [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.3e-58  196.9   0.1    3.2e-58  196.5   0.1    1.1  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    4.8e-39  133.1   0.1      1e-38  132.0   0.1    1.6  1  GTP_EFTU_D3  Elongation factor Tu C-terminal domain
    5.4e-18   65.1   2.8    9.1e-17   61.2   0.5    2.9  3  GTP_EFTU_D2  Elongation factor Tu domain 2
      4e-05   23.7   0.1    0.00016   21.7   0.1    1.9  1  MMR_HSR1     50S ribosome-binding GTPase
  ------ inclusion threshold ------
      0.013   15.0   0.3        0.1   12.1   0.1    2.4  2  FeoB_N       Ferrous iron transport protein B
      0.073   13.1   0.1         11    6.1   0.0    2.8  3  Dynamin_N    Dynamin family
      0.084   12.8   0.4       0.25   11.2   0.4    1.8  1  GTP_EFTU_D4  Elongation factor Tu domain 4


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 !  196.5   0.1   1.3e-61   3.2e-58       1     190 [.       5     209 ..       5     213 .. 0.91

  Alignments for each domain:
  == domain 1  score: 196.5 bits;  conditional E-value: 1.3e-61
                                       TCEEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHST...........HCHSHHHHHHTSCSSCEEEEEETT CS
                          GTP_EFTU   1 krirnigiighvDhGKtTLtdrLlyktgaiskkgekaeeerv...........lDtlkeErergiTiksaaisleke 66 
                                       k+++ni++ighvDhGK+T+++rLl++t +i ++  k+ ee+            +D+lkeErergiTi++a++++e  
  gi|242399536|ref|YP_002994961.1|   5 KPHVNIVFIGHVDHGKSTTIGRLLFDTANIPEQIIKKFEEMGekgksfkfawvMDRLKEERERGITIDVAHTKFE-- 79 
                                       579*****************************998884333355678899*************************.. PP

                                       CSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTE.EEEEEESCGST...HHHH CS
                          GTP_EFTU  67 tkkylinliDtPGHvdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvp.iivfiNKmDrl...kael 139
                                       t ++ i++iD+PGH+dF+k++i+g++++D avl+v+a++Gv+pqt+e++ la+++g++ iiv +NKmD +   ++++
  gi|242399536|ref|YP_002994961.1|  80 TPHRYITIIDAPGHRDFVKNMITGASQADAAVLIVAATDGVMPQTKEHAFLARTLGINhIIVGVNKMDAVkydEKRF 156
                                       **********************************************************9***********9999999 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHH............HHHHHHHH CS
                          GTP_EFTU 140 keiveevkqklsrkeeklekygekgekevpvvfgSalkgegvk............tllealve 190
                                       ke++++v  kl      l+  g+k+   +pv+++Sa++g++v             tl+eal++
  gi|242399536|ref|YP_002994961.1| 157 KEVATQVT-KL------LQMLGYKN---FPVIPISAWEGDNVVkksdkmpwyngpTLIEALDQ 209
                                       99999999.55......57788885...8***********98877777777777778888776 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 !  132.0   0.1   4.1e-42     1e-38       2     111 ..     317     424 ..     316     425 .. 0.98

  Alignments for each domain:
  == domain 1  score: 132.0 bits;  conditional E-value: 4.1e-42
                                       -EEECCEEEEEEESSS..SS-BSTT-EEEEESSS-EEEEEEEEEEECCSSTTSB-BSS-SSCCSTT-CEEEEEEECC CS
                       GTP_EFTU_D3   2 ikphtkfeAqvyilekerhtpitagYrpvlyirtadvtgkvveLlskldkktekvsekkpefvkpGdnvivevelik 78 
                                       ++p ++f+Aq+++l++  +t+it gY+pvl+++t++v++++++Ll+kld++t++v+e++p+f+k+Gd++iv ++++k
  gi|242399536|ref|YP_002994961.1| 317 VRPRDTFKAQIIVLNH--PTAITIGYTPVLHAHTTQVAVRFEQLLAKLDPRTGNVVEENPQFIKTGDSAIVVLRPTK 391
                                       568899**********..*********************************************************** PP

                                       EEEE--TTTHCCCCEEEEECTTCEEEEEEEEEE CS
                       GTP_EFTU_D3  79 pialekgseypqlGrFaiReggrTvaaGvvtei 111
                                       p+++e ++e pqlGrFaiR++g+TvaaG+v +i
  gi|242399536|ref|YP_002994961.1| 392 PMVIEPVKELPQLGRFAIRDMGQTVAAGMVISI 424
                                       ******************************998 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.052   1.3e+02      19      48 ..      10      37 ..       5      71 .. 0.72
   2 ?   -3.5   0.0       5.8   1.5e+04      26      41 ..     154     169 ..     146     171 .. 0.69
   3 !   61.2   0.5   3.6e-20   9.1e-17       1      72 [.     235     306 ..     235     308 .. 0.95

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.052
                                      EEEEC.TCTTSEEEEEEEEEEEEETEEESEE CS
                       GTP_EFTU_D2 19 vrilg.ndtskkeivtrissletfhededea 48
                                      ++++g +d +k+   t+i++l+   ++  e+
  gi|242399536|ref|YP_002994961.1| 10 IVFIGhVDHGKS---TTIGRLLFDTANIPEQ 37
                                      667787999999...*******999888777 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 5.8
                                       TTSEEEEEEEEEEEEE CS
                       GTP_EFTU_D2  26 tskkeivtrissletf 41 
                                       +  ke  t++++l+ +
  gi|242399536|ref|YP_002994961.1| 154 KRFKEVATQVTKLLQM 169
                                       4455678899999876 PP

  == domain 3  score: 61.2 bits;  conditional E-value: 3.6e-20
                                       EEEEEEEEEESEEETTEEEEEEC.TCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCE CS
                       GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilg.ndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdt 72 
                                       Gtv  grv++G+lk+Gd + + + ++   k+i+++++s+e++he + ea +g+n+G++v+++g +d i++Gd+
  gi|242399536|ref|YP_002994961.1| 235 GTVPVGRVETGVLKVGDVIIFEPaSTIFHKPIQGEVKSIEMHHESMPEALPGDNIGFNVRGVGKND-IKRGDV 306
                                       99*********************77777777***********************************.*****9 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.1   6.3e-08   0.00016       1     104 [.       9     134 ..       9     145 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 6.3e-08
                                       EEEEEESTTSSHHHHHHHHH...................T..........STEEESSSTTSSSSEEEEEEEETTEEE CS
                          MMR_HSR1   1 evaivGrpNvGKStLinalt...................g..........ekaivsdkpgtTrdinegrvklkgkei 48 
                                       +++++G+   GKSt i +l+                   +          ++ + +++ g T+d+ + ++++ ++ i
  gi|242399536|ref|YP_002994961.1|   9 NIVFIGHVDHGKSTTIGRLLfdtanipeqiikkfeemgeKgksfkfawvmDRLKEERERGITIDVAHTKFETPHRYI 85 
                                       589****************988887777777766666550566666665468999999*************88899* PP

                                       EEEECGGCSSHHHHHHHHHHHHHHHHCTSEEEEEEETTTTCSHHHHHHHHHHHHHT CS
                          MMR_HSR1  49 elvDtpGliegaseekglgkaflaleeadlillvvdaseeklkpldeeleelleea 104
                                       +++D pG  +    +  +++ +    +ad+++l+v a+ +++ p+ +e + l +  
  gi|242399536|ref|YP_002994961.1|  86 TIIDAPG--H----RDFVKNMITGASQADAAVLIVAAT-DGVMPQTKEHAFLARTL 134
                                       *******..3....223555556666789988888866.66777777766555444 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 ?   -1.4   0.0       0.6   1.5e+03       2      20 ..       9      27 ..       8      35 .. 0.84
   2 ?   12.1   0.1   4.1e-05       0.1      32     149 ..      68     188 ..      65     195 .. 0.65

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.6
                                      EEEEEESTTSSHHHHHHHH CS
                            FeoB_N  2 tvalvGnpnvGkttlfnal 20
                                      +++++G  + Gk+t + +l
  gi|242399536|ref|YP_002994961.1|  9 NIVFIGHVDHGKSTTIGRL 27
                                      6899*********998776 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 4.1e-05
                                       TSSSEEEEEEEEETTEEEEEEE----SSS..SSSSHHHHHHHHHHHCTSSSEEE.EEEEGGGHHHHHHHHHHHHHTT CS
                            FeoB_N  32 GvtvekkegklklkgkeveivDlPGiYsl..sayseeekvardflleeepdvvv.nvvdatnlernLyLtlqllelg 105
                                       G+t++ +++k+++ ++ ++i+D PG  ++  + ++   +    +l+   +d v+ +  + + l r+L +        
  gi|242399536|ref|YP_002994961.1|  68 GITIDVAHTKFETPHRYITIIDAPGHRDFvkNMITGASQADAAVLIVAATDGVMpQTKEHAFLARTLGIN------- 137
                                       99***********************977733444445555555555555554441333444444444443....... PP

                                       SSEEEEEETHHHHHH.....TTEEE-HHHHHHHHT...S-EEEEBTTTTBTH CS
                            FeoB_N 106 vpvvlalnmideaek.....kgieidlkkLsekLg...vpvvktsakkkegi 149
                                        ++++ +n++d+++      k++  +++kL ++Lg   +pv+++sa +++++
  gi|242399536|ref|YP_002994961.1| 138 -HIIVGVNKMDAVKYdekrfKEVATQVTKLLQMLGyknFPVIPISAWEGDNV 188
                                       .456666666666541111156677889999999855569999999998877 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.012        31       1      19 [.      10      28 ..      10      39 .. 0.87
   2 ?    6.1   0.0    0.0042        11      68     154 ..      34     134 ..      25     147 .. 0.62
   3 ?   -1.5   0.0      0.91   2.3e+03      29      88 ..     308     378 ..     306     399 .. 0.57

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.012
                                      EEEEEBTTTTHHHHHHHHH CS
                         Dynamin_N  1 iavvGsqSsGKSSvlnaLl 19
                                      i+++G++ +GKS+ +  Ll
  gi|242399536|ref|YP_002994961.1| 10 IVFIGHVDHGKSTTIGRLL 28
                                      89***********998887 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0042
                                       HHHHHHHHHHHHHTSSSS--SS.................-EEEEEEETTS-SEEEEE---B-SSSGTTSHHHHHHHS CS
                         Dynamin_N  68 vreeieketekiagankgiskk.................villkilsllvkgltlvDlPGldsvnkrdqelvkeyik 127
                                       + e+i k++e+  +++k+++                   v + ++++     +t++D PG  +  k   ++++ + +
  gi|242399536|ref|YP_002994961.1|  34 IPEQIIKKFEEMGEKGKSFKFAwvmdrlkeerergitidVAH-TKFETPHRYITIIDAPGHRDFVK---NMITGASQ 106
                                       555566666665555555543366666666666666553444.44444456799******988433...47887777 PP

                                       TTEEEEEEEETTS-CCC-.CHHHHHHHH CS
                         Dynamin_N 128 kadiilavtsanhdlsns.ealflarev 154
                                         +++l v + +  + ++ e  flar +
  gi|242399536|ref|YP_002994961.1| 107 ADAAVLIVAATDGVMPQTkEHAFLARTL 134
                                       7777777777776666654777777654 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.91
                                       SS---S-EEEEECCT---C...........CS...SSEEEET-EB--CHHHHHHHHHHHHHHHTSSSS--S CS
                         Dynamin_N  29 nptTrrplelqlgeeeeas...........eravkeelkekekkledfsevreeieketekiagankgisk 88 
                                       ++tT  p++++ +++ +a+            +   +     ++    f+++  +++ +t ++ ++n ++ k
  gi|242399536|ref|YP_002994961.1| 308 GHTTNPPTVVRPRDTFKAQiivlnhptaitIGYTPVLHAHTTQVAVRFEQLLAKLDPRTGNVVEENPQFIK 378
                                       56777777777777777665555433333333333333333555666666666666666666666555554 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 ?   11.2   0.4    0.0001      0.25      21      84 ..     239     306 ..     220     307 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0001
                                       EEEEEEEEEEETT-EEEETTE.EE......EEEEEEEETTEEESEEETT-EEEEEEESS-TTT.S--TT-E CS
                       GTP_EFTU_D4  21 vGvevlgGvikpgvklikedGrev......GeilqiqdkgkkleeakaGqevaisiegkivGr.qikegdi 84 
                                       vG +v +Gv+k+g  +i e  +++      Ge+++i+ +++++ ea  G++++  ++g  vG+ +ik gd+
  gi|242399536|ref|YP_002994961.1| 239 VG-RVETGVLKVGDVIIFEPASTIfhkpiqGEVKSIEMHHESMPEALPGDNIGFNVRG--VGKnDIKRGDV 306
                                       77.899999999988888888877777778**************************99..56526888885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      574  (0.0320152); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.67u 0.29s 00:00:00.96 Elapsed: 00:00:00.49
# Mc/sec: 2640.47
//
Query:       gi|242399537|ref|YP_002994962.1|  [L=161]
Description: hypothetical protein TSIB_1562 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
       0.01   16.3   0.0      0.014   15.9   0.0    1.2  1  Transglut_core   Transglutaminase-like superfamily
  ------ inclusion threshold ------
       0.11   12.0   0.1       0.14   11.7   0.1    1.2  1  DUF553           Transglutaminase-like domain
       0.13   12.6   0.5        7.3    7.0   0.0    2.7  3  HV_small_capsid  Small capsid protein of Herpesviridae


Domain annotation for each model (and alignments):
>> Transglut_core  Transglutaminase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   2.3e-06     0.014      11      98 ..      20     106 ..      10     120 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.3e-06
                    Transglut_core  11 akdplekakaiyewvrknveysaprrtpgsrd...aeavletgkGncedfaslfvallRalGipaRvvtgylsgeee 84 
                                       + ++++ ++++++ + k++ y  p+ t ++++   + +++ ++ Gnc +++ l +++lR lG   R v+ +l  ++ 
  gi|242399537|ref|YP_002994962.1|  20 KLNDKKGLQKLHRDLLKEICYI-PTITIKDNNelhPLNTIGQRCGNCLQISILEASILRGLGFSEREVYVFLLLHKG 95 
                                       4566788999999999999999.555555555555889999******************************998865 PP

                    Transglut_core  85 keqsvasedaHawv 98 
                                       +      e +Ha+ 
  gi|242399537|ref|YP_002994962.1|  96 E---SVFEASHAVC 106
                                       4...4444556555 PP

>> DUF553  Transglutaminase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   2.3e-05      0.14      54     136 ..      28     128 ..      13     148 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.3e-05
                            DUF553  54 skvdskilklie.............tpkeilktkkgiCrDYaiLTaalLlnlnisk..vylvsvtfenskvg...Ha 112
                                       +k   + lk+i               p +++ ++ g C   +iL a +L  l+ s+  vy++    ++++v    Ha
  gi|242399537|ref|YP_002994962.1|  28 QKLHRDLLKEICyiptitikdnnelHPLNTIGQRCGNCLQISILEASILRGLGFSEreVYVFLLLHKGESVFeasHA 104
                                       555555555555666666667777799**********************9999874338998888888888777899 PP

                            DUF553 113 avavkidgtyfvlDqklpiikide 136
                                       +  v  + +   l  +  i+++++
  gi|242399537|ref|YP_002994962.1| 105 VCGVFLEKKEICLENEVIILDPSN 128
                                       999999888888877777777765 PP

>> HV_small_capsid  Small capsid protein of Herpesviridae
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.59   3.5e+03       7      28 ..      18      39 ..      12      49 .. 0.69
   2 ?    7.0   0.0    0.0012       7.3      33      48 ..      97     112 ..      83     120 .. 0.82
   3 ?    3.9   0.1     0.011        66      32      67 ..     127     160 ..     111     161 .] 0.64

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.59
                   HV_small_capsid  7 qisvaskkeeekkkrqvltvvL 28
                                      +i   +kk  +k +r++l+ + 
  gi|242399537|ref|YP_002994962.1| 18 NIKLNDKKGLQKLHRDLLKEIC 39
                                      5556677777777887777665 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0012
                   HV_small_capsid  33 eiseashPvLavlLsk 48 
                                        + eash v +v+L k
  gi|242399537|ref|YP_002994962.1|  97 SVFEASHAVCGVFLEK 112
                                       577***********98 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.011
                   HV_small_capsid  32 teiseashPvLavlLskYakqsslfvDktafkLDLl 67 
                                       +++   s   L  lL+      + f+Dk af +++l
  gi|242399537|ref|YP_002994962.1| 127 SNLKTCSISLLKLLLTH--NIHTFFNDKIAFLVEIL 160
                                       46666666666666665..45689*******88876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.44
# Mc/sec: 1089.01
//
Query:       gi|242399538|ref|YP_002994963.1|  [L=391]
Description: major facilitator superfamily MFS_1 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-32  112.9  30.5    1.6e-32  112.9  30.5    1.8  2  MFS_1           Major Facilitator Superfamily
    1.7e-07   30.4  11.1    1.7e-07   30.4  11.1    2.2  2  Sugar_tr        Sugar (and other) transporter
  ------ inclusion threshold ------
       0.13   12.4   6.3       0.14   12.4   1.7    3.2  2  DUF2985         Protein of unknown function (DUF2985)


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 !  112.9  30.5   2.6e-36   1.6e-32       1     353 []      10     357 ..      10     357 .. 0.87
   2 ?    1.8   3.9     0.015        89     251     295 ..     347     387 ..     344     390 .. 0.70

  Alignments for each domain:
  == domain 1  score: 112.9 bits;  conditional E-value: 2.6e-36
                             MFS_1   1 lllaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalg.l 76 
                                       +l+++f + + r+ +++ lp++++++  +  se+ l +++ +++++++s+ +G ++d +Gr+++ +l++++++ + +
  gi|242399538|ref|YP_002994963.1|  10 ILITGFPINMVRAYFFIYLPILVNNQ--AGSSELALSMSIAGALSLIFSFSGGLIADSLGRKPMAVLSVFSMIPTlG 84 
                                       578999999***********766666..5689999999*************************************33 PP

                             MFS_1  77 llllfasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWra 152
                                       lll +  +   ++l l ++ ++g  ++ p+  alia+ + ++ rgr+++l+ +++ ++ i+gp+l  +++  lg+ +
  gi|242399538|ref|YP_002994963.1|  85 LLL-M-KNPLaIMLSLILFHSIGI-FFSPGTTALIAESTEEKIRGRVFSLVHVSSTVAWIIGPMLTNWIIKKLGFVY 158
                                       333.4.665559999999999995.**************************************************** PP

                             MFS_1 153 vfyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvp.....awkallkdpvlwillialllfffgfs 224
                                       v y++ ++++++ + f l l+e+ p++++ ++++ e    ++++++      +++ll+ p     l+ l++ ++++s
  gi|242399538|ref|YP_002994963.1| 159 VLYVVLVMLFILSL-FRLMLVETLPKKRPLNGVTSE---IKKNIISsiknsDFRKLLNTPLA--PLALLFCLSAFIS 229
                                       ***********988.677777888888888888886...44444444555899999999956..6666666655555 PP

                             MFS_1 225 g.lltllplylqevlgls.glllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtss 299
                                       + + t+l  yl + ++l+  ++ ++  ++++ ++++++ ++ag+++d l+++++ ++ +l+ +++  ++all+ +  
  gi|242399538|ref|YP_002994963.1| 230 ScFNTFLYPYLDSWMKLDsDVIVNV--FSASRFFVLVAYFVAGFMVDYLSPKKTFIVDILGDSITMTLFALLSKY-A 303
                                       56****************9888999..99999999999*************************************.9 PP

                             MFS_1 300 avllllvlvliGf.glgfvfpsllalasdlappeeagtasglfntagslggalgp 353
                                       ++ +l++l+l G+ g ++ ++++ +++s++  +e+ +ta+g  nt+ +l g+++p
  gi|242399538|ref|YP_002994963.1| 304 PTYSLIFLALSGLfGEALSNIAYSVYTSKHQ-KEYLATAYGTLNTLPGLIGIFAP 357
                                       999999*******888887777777777775.8*******************998 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.015
                             MFS_1 251 allalvgailallagrlsdrlgrrrrlllallllllaalglalla 295
                                        l++l+g+++ +++g+l + +    ++l +l++ +++++gl+++ 
  gi|242399538|ref|YP_002994963.1| 347 TLPGLIGIFAPVIWGALWR-V---DPWLTILAASMMTFVGLFFAI 387
                                       5789999999999999984.3...456666666666666666654 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4  11.1   2.9e-11   1.7e-07     272     436 ..      23     175 ..       8     187 .. 0.79
   2 !    5.2   8.4    0.0014       8.2     241     438 ..     206     390 ..     178     391 .] 0.63

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 2.9e-11
                                       HHHHHTTT.HHHHSS-THHHHHHHHHHHHHHHHHHHHHHHHHHS-SHHHHHHHHHHHHHHHHHHH..HHHHTTSS.. CS
                          Sugar_tr 272 aimyyspt.ifenlglsksllvtiivgvvnfvatfvaiflvdrfGRRtllllGaagmaicfvilgivalllvakska 347
                                       ++++y p  + +++g s+ +l   i g++  +++f + ++ d +GR+++ +l+++ m+  + +l      l ++   
  gi|242399538|ref|YP_002994963.1|  23 YFFIYLPIlVNNQAGSSELALSMSIAGALSLIFSFSGGLIADSLGRKPMAVLSVFSMIPTLGLL------LMKNP-- 91 
                                       455555550556788889899999*************************999999987655444......33443.. PP

                                       .CHHHHHHHHHHHHHHHTTTTHHHHHHHHHHSHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHT-HHHHHHHH CS
                          Sugar_tr 348 asivaivfialfialfalgwgpvpwvlvsElfpqsvRskalaiavavnwlanflisllfpiiteaigggyvflvfag 424
                                          +++ +i++  +   +++g++   l++E   +++R+ + +++ +++ +a ++  +l+ +i +++g  +v++++++
  gi|242399538|ref|YP_002994963.1|  92 -LAIMLSLILFHSIGIFFSPGTTA--LIAESTEEKIRGRVFSLVHVSSTVAWIIGPMLTNWIIKKLG--FVYVLYVV 163
                                       .34455555555555555666666..88***************************************..99999999 PP

                                       HHHHHHHHHHHH CS
                          Sugar_tr 425 lavlfiifvfff 436
                                       l++lfi+  f  
  gi|242399538|ref|YP_002994963.1| 164 LVMLFILSLFRL 175
                                       999999988854 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0014
                                       .HTTHHHHSH...HHHHHHHHHHHHHHTTHHHHHHHTTTHHHHSS-THHHHHHHHHHHHHH..HHHHHHHHHHHHS- CS
                          Sugar_tr 241 swkellssktvrqrlligvvlqifqqltGinaimyysptifenlglsksllvtiivgvvnf..vatfvaiflvdrfG 315
                                       + ++ll +     +l   ++l ++  +    +++++ p++ + + l+ +++v++      f  va fva f+vd+++
  gi|242399538|ref|YP_002994963.1| 206 DFRKLLNT-----PLAPLALLFCLSAFISSCFNTFLYPYLDSWMKLDSDVIVNVFSASRFFvlVAYFVAGFMVDYLS 277
                                       45555555.....5666666666666666666666677777777777777777766554441145677778888888 PP

                                       SHHHHHHHHHHHHHHHHHHH..HHHHTTSS...CHHHHHHHHHHHHHHHTTTTHHHHHHHHHHSHTTTHHHHHHHHH CS
                          Sugar_tr 316 RRtllllGaagmaicfvilgivalllvakskaasivaivfialfialfalgwgpvpwvlvsElfpqsvRskalaiav 392
                                        ++++++ ++g +i +++++     l +k   a   +++f+al   + +  +  + + +    ++++  +  la a+
  gi|242399538|ref|YP_002994963.1| 278 PKKTFIVDILGDSITMTLFA-----LLSK--YAPTYSLIFLALSGLFGE-ALSNIAYSV----YTSKHQKEYLATAY 342
                                       88888888888888888776.....3333..134555556665544444.555555444....67777777777888 PP

                                       HHHHHHHHHHHHHHHHHHCHHH..T-HHHHHHHHHHHHHHHHHHHHS- CS
                          Sugar_tr 393 avnwlanflisllfpiiteaig..ggyvflvfaglavlfiifvfffvp 438
                                        + ++   li+++ p+i +a++   ++  ++ a+++ ++ +f  + v 
  gi|242399538|ref|YP_002994963.1| 343 GTLNTLPGLIGIFAPVIWGALWrvDPWLTILAASMMTFVGLFFAIMVK 390
                                       888888888888888888888866677777777777777777766665 PP

>> DUF2985  Protein of unknown function (DUF2985)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   1.7   2.3e-05      0.14       1      38 [.     148     198 ..     148     229 .. 0.71
   2 ?    0.5   0.1      0.12   7.1e+02      44      62 ..     282     301 ..     243     358 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.3e-05
                           DUF2985   1 kfvktplgflvtiYglnvvawgamlf.LlLlgaapamn............i 38 
                                       +++ + lgf+ ++Y+++v+++ + lf L+L++ +p+              i
  gi|242399538|ref|YP_002994963.1| 148 NWIIKKLGFVYVLYVVLVMLFILSLFrLMLVETLPKKRplngvtseikknI 198
                                       69*****************99988886888999998555444333333330 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.12
                           DUF2985  44 kwieid.sqilnALFcvtgf 62 
                                       ++++i  + i   LF++ + 
  gi|242399538|ref|YP_002994963.1| 282 FIVDILgDSITMTLFALLSK 301
                                       33444325666666666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       947  (0.0528195); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.73u 0.31s 00:00:01.04 Elapsed: 00:00:00.52
# Mc/sec: 2277.18
//
Query:       gi|242399539|ref|YP_002994964.1|  [L=355]
Description: hypothetical protein TSIB_1564 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.7e-20   74.1   0.0    2.5e-20   73.5   0.0    1.2  1  Radical_SAM  Radical SAM superfamily
    1.9e-07   31.5   0.1    5.7e-07   30.0   0.1    1.9  1  SPASM        Iron-sulfur cluster-binding domain
    4.3e-06   27.1   1.3    2.4e-05   24.6   0.0    2.3  2  Fer4_12      4Fe-4S single cluster domain
    8.7e-06   25.9   0.0    1.8e-05   24.9   0.0    1.5  1  Fer4_14      4Fe-4S single cluster domain
  ------ inclusion threshold ------
        7.7    6.8   6.4        6.2    7.1   1.4    2.4  2  Fer4_2       4Fe-4S 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 !   73.5   0.0   6.9e-24   2.5e-20       3     150 ..      13     154 ..      11     159 .. 0.95

  Alignments for each domain:
  == domain 1  score: 73.5 bits;  conditional E-value: 6.9e-24
                                       EESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   3 vtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgir 79 
                                        tr Cnl+C +C+++ +  r+++  +l   + l+ + e+  + g ++++++ggepll++d++  l + a +  ++++
  gi|242399539|ref|YP_002994964.1|  13 LTRSCNLQCEHCWINAS--RTYPMVELEDKYFLNAFNEA-LDLGLDTLFISGGEPLLRSDLAITLIKVANN--SKVK 84 
                                       699************97..********************.8*****************************9..9*** PP

                                       EEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  80 itvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdriv 150
                                       +++etngtl+++  l++l++++   +sl+l+ +++ ++    +++  + +vl+++ klr++gi++vv++ v
  gi|242399539|ref|YP_002994964.1|  85 TVLETNGTLITPPLLKELAKYE-IDISLSLDFPSEVEFNAFRHGKRVYRRVLDVIPKLRDLGIPPVVVVSV 154
                                       **********************.99***********9999999*********************9776654 PP

>> SPASM  Iron-sulfur cluster-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.1   1.6e-10   5.7e-07       4      67 ..     244     307 ..     242     308 .. 0.76

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 1.6e-10
                             SPASM   4 psrslfInsdGdVvpCcvdkktyvee.lklGnireesleeIwnse..eyqefrkskkfplielCrnC 67 
                                        +++l I +dG V++C +    ++ +  ++Gni+eesl++Iw s    + e+r+ k ++ + +C+ C
  gi|242399539|ref|YP_002994964.1| 244 YTKMLGILPDGGVSLCGIG---IEYPeTVIGNIKEESLRDIWYSGrgFLGELRRVKPDEFQGICSGC 307
                                       568899**********444...33345***************5554556668856677788899999 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 !   24.6   0.0   6.8e-09   2.4e-05      11      97 ..      13      95 ..       6     123 .. 0.78
   2 ?   -0.1   0.8      0.28   9.9e+02      10      42 ..     308     340 ..     301     348 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 6.8e-09
                           Fer4_12 11 fvsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpekdiw 89
                                      ++  Cnl+C+ C  ++ +     +  +k  l+   e l +   + l ++GGEPll    +  + l+k   + k+ k+++
  gi|242399539|ref|YP_002994964.1| 13 LTRSCNLQCEHCWINASRTYPMVELEDKYFLNAFNEAL-DLGLDTLFISGGEPLL--RSDLAITLIKVANNSKV-KTVL 87
                                      4778********97766666655555555555555444.7788************..999999****9999999.89** PP

                           Fer4_12 90 lytgytle 97
                                      +++g+ + 
  gi|242399539|ref|YP_002994964.1| 88 ETNGTLIT 95
                                      ****9865 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.28
                           Fer4_12  10 lfvsgCnlsCkgCfnketwsfksgkeftkelle 42 
                                       ++ s C   C+ +  +e +sf+++ ++ ++l e
  gi|242399539|ref|YP_002994964.1| 308 ILRSYCANICPAFAYEEYKSFTASFPVCQKLFE 340
                                       55678999****999*******99999887765 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   4.9e-09   1.8e-05       5      92 ..      14      94 ..      11     114 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 4.9e-09
                           Fer4_14  5 lsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekki 83
                                      + +Cnl+C  C  +++    + + +++  l + +   ++ +   + l ++GGePL   + +  ++l+k   +++  +k 
  gi|242399539|ref|YP_002994964.1| 14 TRSCNLQCEHCWINASRTYPMVELEDKYFL-NAF--NEALDLGLDTLFISGGEPL--LRSDLAITLIKVANNSK--VKT 85
                                      679*********888788888888888888.666..4556666699*********..78999999999888888..999 PP

                           Fer4_14 84 wletngtle 92
                                       letngtl 
  gi|242399539|ref|YP_002994964.1| 86 VLETNGTLI 94
                                      9*****975 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.3     0.087   3.1e+02       5      16 ..      12      24 ..       9      28 .. 0.81
   2 ?    7.1   1.4    0.0017       6.2       9      22 .]     303     319 ..     295     319 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.087
                            Fer4_2  5 vdtdrCi.gCgaC 16
                                      + t++C+ +C+ C
  gi|242399539|ref|YP_002994964.1| 12 YLTRSCNlQCEHC 24
                                      66889*769*999 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0017
                            Fer4_2   9 rCigC...gaCvsaCPa 22 
                                       +C gC   + C + CPa
  gi|242399539|ref|YP_002994964.1| 303 ICSGCilrSYCANICPA 319
                                       7*****988*******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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 0.26s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2439.28
//
Query:       gi|242399540|ref|YP_002994965.1|  [L=60]
Description: hypothetical protein TSIB_1565 [Thermococcus sibiricus MM 739]
Scores for complete 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   21.8   0.1    0.00019   21.6   0.1    1.1  1  PqqD      Coenzyme PQQ synthesis protein D (PqqD)


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 !   21.6   0.1   1.1e-08   0.00019      18      67 .]       1      52 [.       1      52 [. 0.91

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.1e-08
                                      HHHHHHHH-SSSS-HHHHHHHHHHHCT--..HHHHHHHHHHHHHHHHCTT-- CS
                              PqqD 18 tgafiWklldgersveeivaalaeeydvd..eeeaeadvlafldqLrekgli 67
                                      +g +++k+ +g  ++ ei+  +++  d++   e + +d+l+f+++L + gl+
  gi|242399540|ref|YP_002994965.1|  1 MGELVLKYSNGSLTIKEIANYVKKDIDEEidIEIITKDILEFIKHLSKLGLL 52
                                      6899*******999**********9987765678****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       952  (0.0530983); expected 358.6 (0.02)
Passed bias filter:                      552  (0.0307881); 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: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 415.69
//
Query:       gi|242399541|ref|YP_002994966.1|  [L=38]
Description: hypothetical protein TSIB_1566 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 246.81
//
Query:       gi|242399542|ref|YP_002994967.1|  [L=290]
Description: hypothetical protein TSIB_1567 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score 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   0.0       0.26   11.4   0.0    1.4  1  YrhC      YrhC-like protein


Domain annotation for each model (and alignments):
>> YrhC  YrhC-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   1.5e-05      0.26      37      63 ..      11      37 ..       3      44 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1.5e-05
                              YrhC 37 tlkksillgaivvfLllaflflrrskk 63
                                         k++llga++v+L++a++f r +++
  gi|242399542|ref|YP_002994967.1| 11 MRPKKYLLGAVLVLLIYAVFFSRAIII 37
                                      56799*************999876654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); 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 0.25s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2050.04
//
Query:       gi|242399543|ref|YP_002994968.1|  [L=197]
Description: ATPase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.6e-08   32.8   0.1    4.9e-08   32.4   0.1    1.1  1  T2SSE           Type II/IV secretion system protein
    0.00089   19.7   0.0     0.0012   19.3   0.0    1.3  1  AAA_16          AAA ATPase domain
     0.0019   18.0   0.9        0.5   10.1   0.1    2.1  2  Kinase-PPPase   Kinase/pyrophosphorylase
     0.0025   17.4   0.6      0.047   13.3   0.0    2.1  2  AAA_25          AAA domain
      0.003   17.4   0.0     0.0047   16.8   0.0    1.3  1  CPT             Chloramphenicol phosphotransferase-like prote
     0.0053   17.3   0.0     0.0087   16.6   0.0    1.3  1  ABC_tran        ABC transporter
     0.0082   16.2   0.2      0.015   15.4   0.2    1.5  1  Creatinase_N_2  Creatinase/Prolidase N-terminal domain
  ------ inclusion threshold ------
      0.018   15.0   0.0      0.033   14.2   0.0    1.4  1  AAA_5           AAA domain (dynein-related subfamily)
      0.019   15.2   0.0      0.044   14.1   0.0    1.6  1  AAA_22          AAA domain
      0.031   14.1   0.0      0.054   13.3   0.0    1.5  1  DMRL_synthase   6,7-dimethyl-8-ribityllumazine synthase
      0.047   14.2   0.3       0.11   13.1   0.3    1.7  1  AAA_18          AAA domain
      0.048   13.7   0.8       0.11   12.5   0.8    1.8  1  AAA_14          AAA domain
      0.075   13.1   0.2       0.16   12.1   0.2    1.8  1  MMR_HSR1        50S ribosome-binding GTPase
      0.078   13.3   0.3        1.6    9.1   0.1    2.6  2  CooT            CO dehydrogenase accessory protein CooT
      0.082   12.6   0.0       0.15   11.8   0.0    1.4  1  DUF4423         Domain of unknown function (DUF4423)
      0.092   12.1   0.0       0.19   11.0   0.0    1.5  1  FtsK_SpoIIIE    FtsK/SpoIIIE family
      0.093   12.5   0.0       0.21   11.4   0.0    1.5  1  AAA_29          P-loop containing region of AAA domain
      0.095   12.2   0.3        1.8    8.0   0.0    2.6  3  AAA_7           P-loop containing dynein motor region


Domain annotation for each model (and alignments):
>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.1   4.9e-11   4.9e-08     104     205 ..       7     111 ..       3     115 .. 0.91

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 4.9e-11
                             T2SSE 104 tlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeinksderivtvEDpvEiqleganqvqln 180
                                       t +dl   e+ ++++ ev++ a+ ++g ilv G+   GKt l+ a+++ i+++  +iv+v    E ++ ++n   + 
  gi|242399543|ref|YP_002994968.1|   7 TPEDLLRYETITKDQLEVIKDAILKKGDILVVGTSRAGKTKLIEAMIHLIPDE-WEIVVVTAYGEFKPFKKNIHVID 82 
                                       56799999********************************************9.99***********9877777666 PP

                             T2SSE 181 ak....kakvtfadllraaLRlrPDrimv 205
                                       ++    ++k  ++++++++  l+PD +++
  gi|242399543|ref|YP_002994968.1|  83 TEfnekSTKQRTEEVIEEIKKLNPDYVVI 111
                                       666666899999*************9997 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   1.2e-06    0.0012      25     107 ..      33     126 ..      18     173 .. 0.61

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.2e-06
                            AAA_16  25 elvllsGesGvGKsslvrellralekd...ggif..lrgkcdqlesaipy.sa.laqalareellrqlldeaesael 94 
                                       + +l++G s  GK++l+++  + + ++      +  ++g+++ ++++i+  ++ + +  ++ +  +++ +e   ++l
  gi|242399543|ref|YP_002994968.1|  33 GDILVVGTSRAGKTKLIEAMIHLIPDEweiV--VvtAYGEFKPFKKNIHViDTeFNEKSTK-QRTEEVIEE--IKKL 104
                                       459******************8888878433..336********99977642234444433.333333333..4455 PP

                            AAA_16  95 eawrekleeala.........a 107
                                       +++   +++  +         +
  gi|242399543|ref|YP_002994968.1| 105 NPDYVVIDTLHTvdipylldkI 126
                                       5555555555554444444442 PP

>> Kinase-PPPase  Kinase/pyrophosphorylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.1   0.00051       0.5     134     151 ..      29      46 ..      17      49 .. 0.89
   2 !    6.9   0.0    0.0049       4.9      18     126 ..      66     187 ..      53     196 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00051
                     Kinase-PPPase 134 klkeADivLvGvSRtsKT 151
                                        lk+ Di++vG SR++KT
  gi|242399543|ref|YP_002994968.1|  29 ILKKGDILVVGTSRAGKT 46 
                                       5899*************9 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0049
                     Kinase-PPPase  18 aalaqF....eevevelevlpfvkteekleevleeakeee..aivvyTlvdeelrealeeaaeekgvea..vdllgp 86 
                                       +a  +F    ++++v  + ++  +t+++ eev+ee+k+ +   +v+ Tl + ++   l++  +++ + +  + l ++
  gi|242399543|ref|YP_002994968.1|  66 TAYGEFkpfkKNIHVIDTEFNEKSTKQRTEEVIEEIKKLNpdYVVIDTLHTVDIPYLLDKIIDDYPLIIssLVLSRD 142
                                       5555565545557777777888899999********7744459999*******999999999987654400445577 PP

                     Kinase-PPPase  87 llealeeelgvkpke..epgllhkl...dedYfkrieAieFalkh 126
                                       lle++++ l+ + k+  + +l+ +l    ++  +r++Ai   ++ 
  gi|242399543|ref|YP_002994968.1| 143 LLEEIKHWLRIDDKTlaRFELVIELyrdIKSGLRRVNAIYRVVQK 187
                                       888888877776555333333333322234445677777555544 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1     0.097        97      25      49 ..      24      48 ..      15      60 .. 0.87
   2 !   13.3   0.0   4.7e-05     0.047     112     153 ..      76     116 ..      49     119 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.097
                            AAA_25 25 lvkgllpagelallaGapgtGKttl 49
                                      ++k+ + +++ +l++G + +GKt l
  gi|242399543|ref|YP_002994968.1| 24 VIKDAILKKGDILVVGTSRAGKTKL 48
                                      68888999999************76 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 4.7e-05
                            AAA_25 112 eslpLfakdrggtlltadvdaleaaieevegvrlvviDplsr 153
                                       +++++++++++++ +++ +++++++i++  +++ vviD+l  
  gi|242399543|ref|YP_002994968.1|  76 KNIHVIDTEFNEKSTKQRTEEVIEEIKKL-NPDYVVIDTLHT 116
                                       67899999999999**************5.6********975 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   4.7e-06    0.0047       4      60 ..      35      91 ..      33     110 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 4.7e-06
                                      EEEEE-TTSSHHHHHHHHHHHSSS-EEEEEHHHHHHHS-GGGGTSTTSEEEETTSEE CS
                               CPT  4 ilLnGgsssGKsslaralqevldepwlhlgvDafvealppkrqdeadglefetelee 60
                                      il  G+s++GK+ l +a+ +++++ w  + v a+ e  p k+  + ++ ef+ +  +
  gi|242399543|ref|YP_002994968.1| 35 ILVVGTSRAGKTKLIEAMIHLIPDEWEIVVVTAYGEFKPFKKNIHVIDTEFNEKSTK 91
                                      7889********************************999999999999888854443 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   8.7e-06    0.0087      14     106 ..      35     131 ..      26     151 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 8.7e-06
                                       EEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH........HHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxx RF
                          ABC_tran  14 vaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren........esd 82 
                                       + +vG + aGK+ L++++++l  ++ + + +    + + e + ++k+i v+  e + +++++  e+        + d
  gi|242399543|ref|YP_002994968.1|  35 ILVVGTSRAGKTKLIEAMIHLIPDEWEIVVV----TAYGEFKPFKKNIHVIDTEFNEKSTKQRTEEvieeikklNPD 107
                                       5689*****************8766555533....35567899********99955555554333357667777777 PP

                                       TCHHHHHHHSTTGGTTCBGESTTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  83 eeiekalsklglkelkdtvvkssp 106
                                         + + l+++++++l d+++++ p
  gi|242399543|ref|YP_002994968.1| 108 YVVIDTLHTVDIPYLLDKIIDDYP 131
                                       779999******999999998876 PP

>> Creatinase_N_2  Creatinase/Prolidase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.2   1.5e-05     0.015       7      54 ..      75     124 ..      71     192 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.5e-05
                                       ----EE--HHHHSS-HHHHHHHHHHHHHHTT-SEEEE-SHH..HHHHHTT CS
                    Creatinase_N_2   7 kepvfvlpeeyaGesvaeKlerlrkelkkkkadalvlsald..eiAWllN 54 
                                       k+++ v ++e++ +s++++ e++ +e+kk + d++v+ +l+  +i +ll 
  gi|242399543|ref|YP_002994968.1|  75 KKNIHVIDTEFNEKSTKQRTEEVIEEIKKLNPDYVVIDTLHtvDIPYLLD 124
                                       7899*********************************9997335666665 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 ?   14.2   0.0   3.3e-05     0.033       1      85 [.      34     114 ..      34     127 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.3e-05
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG- CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEvera 77 
                                       d+l+vG +  gK++l+e + +++ +e+e+v  t++ + + +k  +++   +t++ +++ ++  +e    v++E++++
  gi|242399543|ref|YP_002994968.1|  34 DILVVGTSRAGKTKLIEAMIHLIPDEWEIVVVTAYGEFKPFKKNIHVI--DTEFNEKSTKQRTEE----VIEEIKKL 104
                                       578999999*************************************94..444444444433322....44555555 PP

                                       -HH..HHHHH CS
                             AAA_5  78 ese..vlnsL 85 
                                       +++  v+++L
  gi|242399543|ref|YP_002994968.1| 105 NPDyvVIDTL 114
                                       5432233333 PP

>> AAA_22  AAA 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     0.044       6     118 ..      33     153 ..      29     167 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.4e-05
                            AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.sskdllrellralglelkaerlsseellea 81 
                                       g ++v+G s +GKT l++ + +  +        + e+v vt+ ++    k+  + +  ++++      +s+++  e 
  gi|242399543|ref|YP_002994968.1|  33 GDILVVGTSRAGKTKLIEAMIHLIPD-------EWEIVVVTAYGEFkPFKKNIHVIDTEFNE------KSTKQRTEE 96 
                                       5589*******************963.......66677777777775666667888888885......366666677 PP

                            AAA_22  82 leqalraravielliiDEaqhlr......s...............eealeeLrsllnl 118
                                       + + +++      ++iD  + ++      +                ++lee++++l +
  gi|242399543|ref|YP_002994968.1|  97 VIEEIKKLNP-DYVVIDTLHTVDipylldKiiddypliisslvlsRDLLEEIKHWLRI 153
                                       7777777777.77777777777655444413333444444555557777777776665 PP

>> DMRL_synthase  6,7-dimethyl-8-ribityllumazine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   5.4e-05     0.054       3      58 ..      77     129 ..      75     165 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.4e-05
                                       EEEEEEESTTHHHHHHHHHHHHHHHHHCTTSSCCEEEEEESSCCCHHHHHHHHCTS CS
                     DMRL_synthase   3 riaiVvarfneeitdkllegaldelkeagvaeenidvvtVPGafElplaakklaes 58 
                                       +i ++ ++fne+ t++  e++++e+k+++    +++v++   ++++p+ ++k++++
  gi|242399543|ref|YP_002994968.1|  77 NIHVIDTEFNEKSTKQRTEEVIEEIKKLN---PDYVVIDTLHTVDIPYLLDKIIDD 129
                                       789**************************...489***************999984 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.3   0.00011      0.11       1      94 [.      35     126 ..      35     160 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00011
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf...gvnlrdvakenglllevdpe..aldeskrldedkldklldaleenssale 72 
                                       Il+ Gt+++GKt l ++   +  +   ++++  +a+ +   +  + +  +++ +++  +++++++++++++ +    
  gi|242399543|ref|YP_002994968.1|  35 ILVVGTSRAGKTKLIEAMIHL--IpdeWEIVVVTAYGEFKPFKKNIHviDTEFNEKSTKQRTEEVIEEIKKLNP--- 106
                                       99***************9444..344455555555555555555555777788888889999999999999986... PP

                            AAA_18  73 egknlvidghlaeleseaakdi 94 
                                         + +vid ++   +++ + +i
  gi|242399543|ref|YP_002994968.1| 107 --DYVVIDTLHTVDIPYLLDKI 126
                                       ..999**999998888877665 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.8   0.00011      0.11       5      76 ..      35     117 ..      31     169 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
                            AAA_14   5 lvitGaRrvGKTtllkqlikell................vkkesilyinldderdkkladpekllelileklkeekk 65 
                                       ++++G  r+GKT l++ +i +l+                  k++i  i+ + +++++++ +e+++e+i++     + 
  gi|242399543|ref|YP_002994968.1|  35 ILVVGTSRAGKTKLIEAMI-HLIpdeweivvvtaygefkPFKKNIHVIDTEFNEKSTKQRTEEVIEEIKK----LNP 106
                                       6899**************9.55546666666666555542234444444444444333333334444444....366 PP

                            AAA_14  66 tylflDEiqev 76 
                                        y+++D  + v
  gi|242399543|ref|YP_002994968.1| 107 DYVVIDTLHTV 117
                                       89999988776 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   0.00016      0.16       2      57 ..      35      86 ..      34     187 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00016
                                      EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCS CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGli 57
                                      +++vG + +GK+ Li a++       ++  +T   +++ +k   k+i+++Dt    
  gi|242399543|ref|YP_002994968.1| 35 ILVVGTSRAGKTKLIEAMIHLIPDEWEIVVVTAYGEFKPFK---KNIHVIDTEF-N 86
                                      89*****************7444444444444444444443...3445555433.2 PP

>> CooT  CO dehydrogenase accessory protein CooT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1    0.0016       1.6      14      53 ..      44      83 ..      32      87 .. 0.86
   2 ?    1.5   0.0      0.38   3.8e+02      21      37 ..     180     196 ..     176     197 .] 0.86

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0016
                              CooT 14 eeelvmedVdkiepeedgvvltdifGeekevegkIkeidL 53
                                       +++++e+ +++ p+e ++v+++ +Ge k ++  I+ id 
  gi|242399543|ref|YP_002994968.1| 44 GKTKLIEAMIHLIPDEWEIVVVTAYGEFKPFKKNIHVIDT 83
                                      4589********************************9996 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.38
                              CooT  21 dVdkiepeedgvvltdi 37 
                                       ++ ++  ++++++l+ i
  gi|242399543|ref|YP_002994968.1| 180 AIYRVVQKDGKIELEKI 196
                                       68899********9977 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00015      0.15      17      66 ..      56     105 ..      41     106 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00015
                           DUF4423  17 yfssWyypvirellplkdfkadpeelakrlrpkisaeevekalefLlklg 66 
                                       + ++W ++v+ +  + k+fk++++ +   +++k +++++e+ +e  +kl+
  gi|242399543|ref|YP_002994968.1|  56 IPDEWEIVVVTAYGEFKPFKKNIHVIDTEFNEKSTKQRTEEVIEEIKKLN 105
                                       6689***************************************9888875 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00019      0.19      39      60 ..      31      53 ..      10      56 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00019
                                      -..SEEEE--TTSSHHHHHHHHH CS
                      FtsK_SpoIIIE 39 a.shllvaGatgsGKStalntLi 60
                                        + +lv+G++  GK+  + ++i
  gi|242399543|ref|YP_002994968.1| 31 KkGDILVVGTSRAGKTKLIEAMI 53
                                      2489******************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 ?   11.4   0.0   0.00021      0.21      22      46 ..      32      56 ..      21      61 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00021
                            AAA_29 22 kgatlltGpsGsGKSTllDAiqalL 46
                                      kg +l++G+s +GK+ l+ A++ l+
  gi|242399543|ref|YP_002994968.1| 32 KGDILVVGTSRAGKTKLIEAMIHLI 56
                                      5679*****************9874 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0    0.0018       1.8      26      67 ..      25      65 ..      14      91 .. 0.81
   2 ?    0.3   0.1      0.43   4.3e+02      59      84 ..      75     100 ..      63     104 .. 0.85
   3 ?    0.7   0.0      0.32   3.1e+02       9      31 ..     106     128 ..      99     134 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0018
                             AAA_7 26 lelllknkkpvllvGptGtGKtviikdllkkldkekylslti 67
                                      ++  + +k  +l+vG++  GKt +i+ +++ ++ +++ ++++
  gi|242399543|ref|YP_002994968.1| 25 IKDAILKKGDILVVGTSRAGKTKLIEAMIHLIP-DEWEIVVV 65
                                      4555667778*****************999988.77777665 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.43
                             AAA_7  59 kekylsltinfsaqtsanqlqdiies 84 
                                       k+++ ++  +f+ + + +++ ++ie+
  gi|242399543|ref|YP_002994968.1|  75 KKNIHVIDTEFNEKSTKQRTEEVIEE 100
                                       478889999**************996 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.32
                             AAA_7   9 fseilVptvdtvrysyllelllk 31 
                                        + +++ t  tv + yll+++++
  gi|242399543|ref|YP_002994968.1| 106 PDYVVIDTLHTVDIPYLLDKIID 128
                                       567899*************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1255  (0.0699983); expected 358.6 (0.02)
Passed bias filter:                      841  (0.0469072); expected 358.6 (0.02)
Passed Vit filter:                       130  (0.00725082); 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: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 1274.88
//
Query:       gi|242399544|ref|YP_002994969.1|  [L=381]
Description: transaminase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-36  126.1   0.0    1.8e-36  125.9   0.0    1.0  1  Aminotran_5      Aminotransferase class-V
    6.8e-08   32.1   0.0    1.2e-07   31.3   0.0    1.3  1  Aminotran_1_2    Aminotransferase class I and II
    3.4e-07   29.1   0.0    5.1e-07   28.6   0.0    1.1  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    9.4e-06   24.7   0.0    1.4e-05   24.2   0.0    1.2  1  GDC-P            Glycine cleavage system P-protein
    0.00087   18.6   0.0     0.0023   17.2   0.0    1.8  1  Beta_elim_lyase  Beta-eliminating lyase


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 !  125.9   0.0   5.1e-40   1.8e-36      33     370 ..      40     365 ..      19     366 .. 0.91

  Alignments for each domain:
  == domain 1  score: 125.9 bits;  conditional E-value: 5.1e-40
                                       SSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHH CS
                       Aminotran_5  33 svhhlgkeatkaveearekvaelinaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqela 109
                                       + +h++ke +++  ++ e++++++++e+ e ++f s++t  +++ +++    +++g +++vt ++  +++   +++ 
  gi|242399544|ref|YP_002994969.1|  40 MFSHRAKEYKQMHVDTVERLKKFLEVEKGEVLLFPSSGTGVMEASIRNG---ISKGGKVLVTIIGAFGKR--YKQVV 111
                                       789*************************9999*******9999999998...9*****************..9**** PP

                                       HHHTEEEEEEEBETTSCBEGGGHHHH-..-TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTTTS- CS
                       Aminotran_5 110 krtgakvkvipldeegeldldelekll..nektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqavghip 184
                                       ++ g k + ++ ++++ +++++l+++l  n+++++v+it ++++tG+++p++e++k+ak+++ lv+vDa++a+g + 
  gi|242399544|ref|YP_002994969.1| 112 ETNGRKAVTLEYEPGKAVKPEDLDEALkkNPDVEAVTITYNETSTGVLNPLPELAKVAKEHDKLVFVDAVSAMGGAD 188
                                       ***************************55589999****************************************** PP

                                       --HHHHTESEEEEETTTTTS.STT-EEEEEEHHHHHTS..SS.STTSEEEEET..TEEEEHCTTGGGS.SS--HHHH CS
                       Aminotran_5 185 idvkklgvDflafsghKllg.PtGiGvlyvrkellekleplllggemveevsl..eettfaeapskfeaGTpnvagi 258
                                       i++ k+g+D+++ s++K +g P+G+ v  +++e +e +++++  g +++ +++   ++  +++ps     Tp +++ 
  gi|242399544|ref|YP_002994969.1| 189 IKFTKWGIDVVFGSSQKAFGvPPGLAVGAFSEEFIEIAHKMEERGWYFDIPRYikVQKEKQGPPS-----TPAMPQE 260
                                       *****************5555*****************************999633444677777.....******* PP

                                       HHHHHHHHHH.HCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-CTCBSEEEEEE.TTCSHHHHHHHHHHTTE CS
                       Aminotran_5 259 iglgaaleyl.eeigleaiekhekelaeyllerlkslpgvrlygpdkaerrasivsfnf.kgvhaedvatlLdeegI 333
                                        gl+ +l+++ + +g e+  +  ++ +e++++++++++   l  +++  ++++i+++ + +g++ ++v ++++e+g 
  gi|242399544|ref|YP_002994969.1| 261 FGLNVVLRIIeKMGGKEKWLEMYRKRSEMIRNGVREIGLDIL--AEPGYESPTITAVLTpEGIKGDQVYNAMRERGF 335
                                       **********66667888999999*************98777..46799********9989**************** PP

                                       EEEEE-TTTHHHHHHTT.S-EEEEE--TTS-HHHHHH CS
                       Aminotran_5 334 avrsGhhcaqplmkrlalegtvRaSlyiynteeevdr 370
                                       ++  G             e+t+R++ + y+t e+++ 
  gi|242399544|ref|YP_002994969.1| 336 ELAKGYGEG-------IKEKTFRIGNMGYMTFEDIEE 365
                                       ****87777.......4579*****999******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 !   31.3   0.0   3.3e-11   1.2e-07      44     252 ..      52     235 ..      27     246 .. 0.78

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 3.3e-11
                                       THHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEE.ESS-.THHHHHHHHTTSEEE CS
                     Aminotran_1_2  44 dglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvp.dpty.asyknilrlsggevv 118
                                       +   +  e+l kfl       +k e+ +  +sG+g + + +   +   +g ++lv     +   yk++++ +g + v
  gi|242399544|ref|YP_002994969.1|  52 H--VDTVERLKKFLE-----VEKGEVLLFPSSGTGVMEASIRNGI--SKGGKVLVTiIGAFgKRYKQVVETNGRKAV 119
                                       3..666777777777.....3334434455555555555555555..34444444303345257************* PP

                                       EEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBS CS
                     Aminotran_1_2 119 ryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfvf 195
                                       + +++  ++  +  e+l+ealk++p     +  + ++     tG++ +l+el k+   ak++  l+fvD + a +  
  gi|242399544|ref|YP_002994969.1| 120 TLEYE--PGKAVKPEDLDEALKKNP----DVEAVTITYNETSTGVLNPLPELAKV---AKEHDKLVFVDAVSAMGGA 187
                                       ***98..999*************77....6778**********************...***********99988888 PP

                                       SSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEE..EHHHHHHHHHHHHHHTS CS
                     Aminotran_1_2 196 gsldavatranveeepnllivgslsKafGlaGeRvGyilg..naavvsqlrklsrpfls 252
                                       +       + + + +++ ++ gs  KafG++    G ++g  ++++++ + k+  ++++
  gi|242399544|ref|YP_002994969.1| 188 D-------IKFTKWGID-VVFGSSQKAFGVPP---GLAVGafSEEFIEIAHKMEERGWY 235
                                       8.......999999999.************97...666665588999999999877765 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 !   28.6   0.0   1.4e-10   5.1e-07      42     198 ..      44     205 ..      33     209 .. 0.80

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 1.4e-10
                                       SS-SBTTT--HHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHTTS-TTEEE.EEESTSSHHHHHHHHHTHHHTTC CS
                   Cys_Met_Meta_PP  42 kgyeYsRsgnptrsvleeriaaLeggeaalavssGmaAiaaailallkaGdei.vvsddlYggtqrllkkvlkklgi 117
                                       ++ eY  +   t++ l++   ++e+ge  l  ssG++ ++a+i++ +++G ++ v+   ++g+ ++++ ++  +  +
  gi|242399544|ref|YP_002994969.1|  44 RAKEYKQMHVDTVERLKK-FLEVEKGEVLLFPSSGTGVMEASIRNGISKGGKVlVTIIGAFGKRYKQVVETNGRKAV 119
                                       556788888888888866.5589**********************99997775155678***********9999888 PP

                                       EEEEEST..TSHHHHHHHCCT.....TEEEEEEESS-TTTT----HHHHHHHHHHTT-EEEEEGTT.THTTTS-GGG CS
                   Cys_Met_Meta_PP 118 evkfvdt..sdleelekaike.....ntklvylEtptnpllkvvDiekiaklakkagvlvvvDntf.aspllqrplk 186
                                       + ++      ++e+l +a+k+      + + y Et t  l     ++++ak+ak+++ lv+vD++  + ++ ++  k
  gi|242399544|ref|YP_002994969.1| 120 TLEYEPGkaVKPEDLDEALKKnpdveAVTITYNETSTGVLNP---LPELAKVAKEHDKLVFVDAVSaMGGADIKFTK 193
                                       888876633688999999998332222445677887777655...56778899**********98615569****** PP

                                       GT-SEEEEETTT CS
                   Cys_Met_Meta_PP 187 lgaDivvhSaTK 198
                                       +g+D+v  S  K
  gi|242399544|ref|YP_002994969.1| 194 WGIDVVFGSSQK 205
                                       *******99877 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 !   24.2   0.0   3.8e-09   1.4e-05     162     265 ..     102     212 ..      75     232 .. 0.70

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 3.8e-09
                                       TS-HHHHHHHHHHHGGGT-EEEEE-GGG--S-.........S-EEEEEEEES-T.TSB----HHHHHHHHHTT-EEE CS
                             GDC-P 162 kvhpqtlevlktrakglgieivevdlteekvtd......kekevagvlvqypnt.eGriedlkelvekakkkkslvv 231
                                       +  +++++v++t  ++  + ++ ++ ++ k +d      k+ +v +v + y +t +G +++l el++ ak+++ lv 
  gi|242399544|ref|YP_002994969.1| 102 AFGKRYKQVVETNGRKA-VTLEYEPGKAVKPEDldealkKNPDVEAVTITYNETsTGVLNPLPELAKVAKEHDKLVF 177
                                       55566777777765432.22333333333333333555589**********9983588999***********99988 PP

                                       E.EE-TTGGGTB--HHHHT-SEEEEE-TT.TT---G CS
                             GDC-P 232 v.aadllaLtllkpPgelgaDivvGsaqr.fGvPlg 265
                                       v a+  +  + +k  +++g D+v+Gs+q+ fGvP g
  gi|242399544|ref|YP_002994969.1| 178 VdAVSAMGGADIK-FTKWGIDVVFGSSQKaFGVPPG 212
                                       7245666666665.68************77****76 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   6.5e-07    0.0023      49     225 ..      70     229 ..      30     379 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 6.5e-07
                                       EEEEES-HHHHHHHHHHHH--TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTTTBE-HHHHHHHS--S-TTS CS
                   Beta_elim_lyase  49 aalfvpqGtaAnsillkillqrgeevivtepahihfdetgaiaelagvklrdlknkeaGkmdlekleaaikevgahe 125
                                         lf  +Gt+  + +++  + +g +v+vt+ + +  +  ++++e +g k+++l+ +    +++e+l +a+k+  +  
  gi|242399544|ref|YP_002994969.1|  70 VLLFPSSGTGVMEASIRNGISKGGKVLVTIIGAF-GKRYKQVVETNGRKAVTLEYEPGKAVKPEDLDEALKK--N-- 141
                                       3456667888888888888888888888887543.3445788999************888************..5.. PP

                                       -EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHHTS-CHHHHTTSSEEEEESSSTT-- CS
                   Beta_elim_lyase 126 ekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaakslgeivkemfsyvDsvtmslkKdlla 202
                                       ++++++++t   +t+ G       l e+a++ak+++  +++D+      ++  g+++k    ++D+v  s  K  ++
  gi|242399544|ref|YP_002994969.1| 142 PDVEAVTITYN-ETSTGVLN---PLPELAKVAKEHDKLVFVDAV-----SAMGGADIKFTKWGIDVVFGSSQKAFGV 209
                                       77888877764.44456555...566778899**********85.....34477889988899************** PP

                                       SS-.EEEEE-HH....HHHHHHHH CS
                   Beta_elim_lyase 203 nvG.gvlafrddeledylaerveq 225
                                       + G +v af+++    +++ ++++
  gi|242399544|ref|YP_002994969.1| 210 PPGlAVGAFSEE----FIEIAHKM 229
                                       ***999999999....77777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       859  (0.0479112); expected 358.6 (0.02)
Passed bias filter:                      745  (0.0415528); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 2600.95
//
Query:       gi|242399545|ref|YP_002994970.1|  [L=242]
Description: Peptidase C26 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.1e-46  157.8   0.0    3.7e-46  157.6   0.0    1.0  1  Peptidase_C26  Peptidase C26
    3.8e-18   65.9   0.0    7.9e-18   64.9   0.0    1.5  1  GATase         Glutamine amidotransferase class-I
    0.00038   20.1   0.0     0.0009   18.9   0.0    1.8  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
  ------ inclusion threshold ------
        1.4    9.5   3.9         11    6.6   2.1    2.1  2  Ccdc124        Coiled-coil domain-containing protein 124 /Oxs


Domain annotation for each model (and alignments):
>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.6   0.0   8.2e-50   3.7e-46       1     216 []       3     216 ..       3     216 .. 0.90

  Alignments for each domain:
  == domain 1  score: 157.6 bits;  conditional E-value: 8.2e-50
                     Peptidase_C26   1 pvigitanees.lkkeavqdaeesylaasyveavekagglpvllpieedeedvk....aildkldgllltGgqdveP 72 
                                       p+igit+  +  +  ++ ++ ++ y+ + y  av k+gglp+++p+ +++  +k    +i++kld++l++Gg d  +
  gi|242399545|ref|YP_002994970.1|   3 PMIGITGAWSVeTWGHSEEHGGYFYVGSYYSTAVSKSGGLPFIIPLPHKNAILKeftvEIVSKLDAILFSGGGD--A 77 
                                       89*****99884556666777789*********************988765554222279**************..8 PP

                     Peptidase_C26  73 slygeepsekeeeadpeRdalelaLiraalergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhrehe.qsaas 148
                                       + +++e+ ++  e +p R ++e  L+ +a +r++PilgiCrG+q+l  ++ G+l+ +  +      h+++   +++ 
  gi|242399545|ref|YP_002994970.1|  78 KKFKKEELPTLYEQQPLRYSFEKELLLEAWKRDLPILGICRGYQMLVEVFDGRLMDETID-----GHKQNLpGYEPW 149
                                       9999999***********************************************998875.....333333259*** PP

                     Peptidase_C26 149 havkvekgsllaellgseeievnslHhqaikelaeelrveAvaeDgviEaieseeakafvlgvQwHPE 216
                                       h+++++++s +++l+g++e++vns+H qa++++ ++++ + +++Dg+iEaie++++ +fv+gvQ+HPE
  gi|242399545|ref|YP_002994970.1| 150 HSLRIKENSKFENLVGTREMKVNSFHIQAVEKVPKGFEAVGWSDDGIIEAIEAIDK-EFVFGVQFHPE 216
                                       *******************************************************5.5*********9 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.9   0.0   1.8e-21   7.9e-18      39     184 ..      62     230 ..      45     236 .. 0.71

  Alignments for each domain:
  == domain 1  score: 64.9 bits;  conditional E-value: 1.8e-21
                                       THHSTSEEEEEEESSCTT................TTTHHHHHHHHCTSTS-EEEETHHHHHHHHHTTTEEEEEECEE CS
                            GATase  39 llknpdgilvsgGpgspg................vegkieaikearenkiPiLGICLGmQllaiefgrkvvkekeke 99 
                                       + ++ d+il+sgG  +++                +  + e++ ea ++++PiLGIC G Q+l++ f + +  e+  +
  gi|242399545|ref|YP_002994970.1|  62 IVSKLDAILFSGGGDAKKfkkeelptlyeqqplrYSFEKELLLEAWKRDLPILGICRGYQMLVEVFDGRLMDET-ID 137
                                       367788888888877777777778877666666666666777777889********************888555.33 PP

                                       EEEEEEEEEETTT............CGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEEEEEEEETTT. CS
                            GATase 100 hhggtmrlgddet............allyglknevierhrHryevnpkelepaglevtakseddeelmeiiekknp. 163
                                        h+++ +   +e             + l g+ +e+++   H  +v++   +p+g+e +++s+d+  +++i   ++  
  gi|242399545|ref|YP_002994970.1| 138 GHKQNLP--GYEPwhslrikenskfENLVGT-REMKVNSFHIQAVEK---VPKGFEAVGWSDDG-IIEAIEAIDKEf 207
                                       3333333..3333345556666557777777.889999999999999...***********776.899999999988 PP

                                       EEEESSBTTSTT..STTHHHHHH CS
                            GATase 164 fvgvQFHPEsts..tpegpellf 184
                                       ++gvQFHPE +    p+ ++++ 
  gi|242399545|ref|YP_002994970.1| 208 VFGVQFHPEERYdvDPHAKAIFD 230
                                       *********65411455444444 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 !   18.9   0.0     2e-07    0.0009      53     100 ..      88     135 ..      45     188 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2e-07
                          GATase_3  53 iqdlallresgldeaikeaaeaggpvlgiCGGlqmLGeeiedpegveg 100
                                       + +++ lr s  +e + ea +++ p+lgiC G+qmL e +      e+
  gi|242399545|ref|YP_002994970.1|  88 LYEQQPLRYSFEKELLLEAWKRDLPILGICRGYQMLVEVFDGRLMDET 135
                                       44455555555677789999****************998766555544 PP

>> Ccdc124  Coiled-coil domain-containing protein 124 /Oxs1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   2.1    0.0025        11      89     121 ..      78     109 ..      77     111 .. 0.93
   2 ?    2.4   0.0     0.048   2.1e+02      58      96 ..     193     237 ..     147     241 .. 0.64

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0025
                           Ccdc124  89 kafeeeeLprlkeenpgLrlsQlkqllkkewkk 121
                                       k+f++eeLp+l e++p Lr s  k+ll ++wk+
  gi|242399545|ref|YP_002994970.1|  78 KKFKKEELPTLYEQQP-LRYSFEKELLLEAWKR 109
                                       79*********99987.**************98 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.048
                           Ccdc124  58 AsgideaiaaLsvkk.eekldrhpekr......lkAaYkafeeeeL 96 
                                         gi eai+a+++ +   +++ hpe r      +kA + +f e+ +
  gi|242399545|ref|YP_002994970.1| 193 DDGIIEAIEAIDK-EfVFGVQFHPEERydvdphAKAIFDHFVEKAI 237
                                       5678899999999.44677788888773333335788888877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.34s 00:00:00.94 Elapsed: 00:00:00.55
# Mc/sec: 1321.40
//
Query:       gi|242399546|ref|YP_002994971.1|  [L=457]
Description: hypothetical protein TSIB_1571 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-31  109.3   0.0      2e-31  109.0   0.0    1.2  1  AtuA      Acyclic terpene utilisation family protein AtuA


Domain annotation for each model (and alignments):
>> AtuA  Acyclic terpene utilisation family protein AtuA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.0   0.0   1.1e-35     2e-31      84     340 ..      96     344 ..      17     356 .. 0.85

  Alignments for each domain:
  == domain 1  score: 109.0 bits;  conditional E-value: 1.1e-35
                              AtuA  84 kalaekvaelakelglkkelkvavveGDdvlekveelleege....lleege...........elvsanaYlGaegI 145
                                       ++ a+ +++l k++glk   k a++  D   e++ + le+g+    l    +           +     a++G+e+ 
  gi|242399546|ref|YP_002994971.1|  96 NQFARIIKNLTKKHGLK-PFKMATIYADVQKETLLKRLEKGDviegL----HgrpplnkeilnRTNHIVAVMGVEPY 167
                                       467899999*******6.6*********9999999999999955550....344555555556899999******** PP

                              AtuA 146 veALeagAdiVitGRvaDaslvlapaawefgWkeddydelAgalvaGhllECgaqvtGGnfagfkevedlanlgfPi 222
                                       ++ALe+gAd++i+GR++D ++++apa+    W+         a++aG++lEC+++v++++    k          ++
  gi|242399546|ref|YP_002994971.1| 168 IKALEEGADVIIAGRSSDVAVFAAPAL----WSGIPE---DIAFYAGKVLECASFVAEPFAG--K---------ESV 226
                                       ***************************....665542...259***************9877..3.........489 PP

                              AtuA 223 aeisadGevvitkeegtgGlvtvdtvkeqllYEiqgpalYlnpDvvadlseveleqvgedrVrvsgvkgepppptlk 299
                                       + i ++ ev+i+ ++ + ++ t+++v+++ +YE  +p+++  p+  +d++ + +e+++e r rv+g k+  ++p++k
  gi|242399546|ref|YP_002994971.1| 227 LGILREDEVIIEPMS-NYQRATPESVASHAMYERIDPFIEWLPGGYIDMRGCVYEAIDEKRTRVRGSKFY-RTPEYK 301
                                       **************9.77899************************************************9.9999** PP

                              AtuA 300 vavtykggyqaeaelslaG...ldaeekaelaeeqvrerlekka 340
                                       ++++  +g  +e +++++G   + + +  + + e+ r+++++k+
  gi|242399546|ref|YP_002994971.1| 302 IKLEG-SGKVGERCFMIVGirdPYLIANLDKVIEWSRKKVKEKF 344
                                       ****9.9************6664455566666666666666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (457 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       284  (0.0158403); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2925.67
//
Query:       gi|242399547|ref|YP_002994972.1|  [L=120]
Description: hypothetical protein TSIB_1572 [Thermococcus sibiricus MM 739]
Scores for complete 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  121.6   0.0    1.9e-35  121.4   0.0    1.0  1  DUF4387   Domain of unknown function (DUF4387)


Domain annotation for each model (and alignments):
>> DUF4387  Domain of unknown function (DUF4387)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.4   0.0   1.1e-39   1.9e-35       1      97 [.       6     102 ..       6     103 .. 0.98

  Alignments for each domain:
  == domain 1  score: 121.4 bits;  conditional E-value: 1.1e-39
                           DUF4387   1 LsdlakviRsKnaGpfeitlDilfkdkeaYervkesklltkeliaklykieeedivkivefdpalaiKvtikRpvas 77 
                                       L +lak+iRsKnaG+ +it+Di+fkd+++Ye +k+++l+tkelia++y++ +e+iv +v+fdpa+aiK+ti+R  +s
  gi|242399547|ref|YP_002994972.1|   6 LVELAKTIRSKNAGVDHITFDIIFKDRAVYEYIKQNHLITKELIAQIYHMPPERIVLFVYFDPAKAIKFTIRRFKPS 82 
                                       689************************************************************************** PP

                           DUF4387  78 GslgerDvygaqqhapLlkl 97 
                                       Gs+ge+Dv gaqq+ pL+++
  gi|242399547|ref|YP_002994972.1|  83 GSPGETDVMGAQQYPPLFEI 102
                                       *****************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 838.27
//
Query:       gi|242399548|ref|YP_002994973.1|  [L=465]
Description: C4-dicarboxylate anaerobic carrier [Thermococcus sibiricus MM 739]
Scores for complete 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-88  297.7  18.7    1.4e-88  297.4  18.7    1.0  1  DcuC             C4-dicarboxylate anaerobic carrier
    1.3e-10   40.2  16.1    3.2e-08   32.3   5.3    2.3  2  ABG_transport    AbgT putative transporter family
    2.3e-08   33.6  27.5      1e-07   31.5  14.4    2.2  2  Na_H_antiporter  Na+/H+ antiporter family
    4.1e-07   29.4   7.4    4.1e-07   29.4   7.4    2.1  2  SCFA_trans       Short chain fatty acid transporter
  ------ inclusion threshold ------
      0.031   12.6   0.1       0.06   11.6   0.1    1.5  1  OATP             Organic Anion Transporter Polypeptide (OATP)
      0.096   12.6   7.0        1.4    8.8   0.1    3.7  4  Claudin_3        Tight junction protein, Claudin-like


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 !  297.4  18.7   4.7e-92   1.4e-88       2     463 ..      12     457 ..      12     459 .. 0.95

  Alignments for each domain:
  == domain 1  score: 297.4 bits;  conditional E-value: 4.7e-92
                              DcuC   2 pslltilfiiivlaailtwvipagayekagkiiilgilegvlekpevlpdtlkstgqlmldleiielvkveltsrav 78 
                                       p+ + i+f++i++a+++tw  pag+y++ +    + ++ + +  pe++  +  +++  +  l++i      + ++a+
  gi|242399548|ref|YP_002994973.1|  12 PHGYFIIFVLILIATLATWTLPAGEYDRFK----DPNSGKTIVDPESFHYVDPNPVDPFEMLQAIPT----GFKQAA 80 
                                       67799***********************88....999999999999999997777776666666666....9***** PP

                              DcuC  79 dvglfilvvGGfagvvnrtGaidagvkalvkklkgrekllilllvvlfvlggtvlgiseetvafypiLvPvlvalGy 155
                                       ++++f++++ G+++++  tGa+dag+ a+v klkgr+ +l+l+++++f+l g v+g  eet+ ++p+ v + +alGy
  gi|242399548|ref|YP_002994973.1|  81 GIIAFVFIIAGAIQIIRSTGALDAGIIAMVNKLKGRDTPLLLAIMFVFALLGSVFGFAEETIPLIPLGVAMALALGY 157
                                       ***************************************************************************** PP

                              DcuC 156 dsivavaaillatqvgilastinPfavviAaeiAgvsiadgivlrllvlviltlisiaflyfYakkikkdp....vy 228
                                       d++v+  ++ +a+ vg++++++nPf++++A++iA++++++g+  r++   ++ +i+ +f+  Ya+ ++kdp    +y
  gi|242399548|ref|YP_002994973.1| 158 DRVVGFHIVRTAAWVGFAGAMLNPFTIGVAQSIAELPLYSGLWYRIICFLVFFAIGAVFILKYARDVRKDPkksiLY 234
                                       ***********************************************************************999988 PP

                              DcuC 229 sekdeskelfskekseseesfskrqkvvlilfvlplilvllglafvivngewylpeiavlflamgilvefiaklngl 305
                                         + e+++ fs + +++e   +  +k++l++++  + l ++g    +++  wy  ei +lfl +gi+ ++ia   ++
  gi|242399548|ref|YP_002994973.1| 235 GYEGEDRAEFSLNYEQQEL--TPTRKLILLVLFGGILLQIYG----VIEYGWYTTEISALFLGLGIIAGLIA---KM 302
                                       8888888888888887554..5889999999999*******9....66667*********************...89 PP

                              DcuC 306 kekeiveafveGaaellgvalvvglargveviaeggmiidtilnlisnalsglsgivfilvmlliqallafvvpSgs 382
                                       +  + +  fv Ga+ +   al++g+ar++ vi+ +g ++dti++ +++ l +l  + + + m li  +++f+++Sgs
  gi|242399548|ref|YP_002994973.1| 303 NPSKLFGEFVSGAKGVTYGALIIGFARAIVVILSEGRVLDTIIHGLATPLGSLGPATAGVAMFLIHSIINFFIGSGS 379
                                       999999********************************************999999999****************** PP

                              DcuC 383 glavltmplmapLAdlvgvpralvvlafqlasgllniisPtsgvvvatlglarvsfgtwvkfvakllavllvvsill 459
                                       g+a++tmp+m pLAdl+gv+r+++vlafq+++g++n+ +P    ++  l  a + +++wv+ ++kl++ l + +++l
  gi|242399548|ref|YP_002994973.1| 380 GQAAATMPIMTPLADLIGVTRQTAVLAFQFGDGITNMFYPA---MIYYLVFADIPYDRWVRHIWKLVVYLTIAGAIL 453
                                       ****************************************9...89999********************99999998 PP

                              DcuC 460 liva 463
                                       + +a
  gi|242399548|ref|YP_002994973.1| 454 VAIA 457
                                       8765 PP

>> ABG_transport  AbgT putative transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   3.0     5e-06     0.015      15     174 ..      13     180 ..       6     226 .. 0.69
   2 !   32.3   5.3   1.1e-11   3.2e-08     352     449 ..     332     427 ..     283     456 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5e-06
                     ABG_transport  15 dPvllfiilivvllvasailsalglsv.knpraegek....etievknllseeglallltelvknftsfapLGlvLv 86 
                                       +  ++ ++li++  +a++ l a +++  k+p ++g++    e ++ ++    + +  +l+ +++ f + a + + + 
  gi|242399548|ref|YP_002994973.1|  13 HGYFIIFVLILIATLATWTLPAGEYDRfKDP-NSGKTivdpESFHYVDPNPVDPF-EMLQAIPTGFKQAAGIIAFVF 87 
                                       4444545555555566666666666541444.33333222222222222222333.356677777777766544444 PP

                     ABG_transport  87 vllG.vgvaersGllsallkklvrkapkk...litptvvligilshtasdaa.yvvliPlaallfialGrhPlaGla 158
                                       ++ G + +  ++G l+a + ++v+k   +   l++ ++++ ++l+++ + a  ++ liPl+  + +alG+  + G+ 
  gi|242399548|ref|YP_002994973.1|  88 IIAGaIQIIRSTGALDAGIIAMVNKLKGRdtpLLLAIMFVFALLGSVFGFAEeTIPLIPLGVAMALALGYDRVVGFH 164
                                       4444368999*************998644333777777888999998887752677********************* PP

                     ABG_transport 159 aafagvsggfsanlll 174
                                       +   ++  gf++ +l 
  gi|242399548|ref|YP_002994973.1| 165 IVRTAAWVGFAGAMLN 180
                                       **999999**998874 PP

  == domain 2  score: 32.3 bits;  conditional E-value: 1.1e-11
                     ABG_transport 352 valfnwsnlGkilavkgaelLkeigltgillllglillsalinlligsasakWavlaPifvPmlmllgisPeltqaa 428
                                       v ++++ ++   +    a+ L ++     ++ +++ l+ ++in++igs+s + a++ Pi+ P+  l+g++ + + +a
  gi|242399548|ref|YP_002994973.1| 332 VVILSEGRVLDTIIHGLATPLGSL--GPATAGVAMFLIHSIINFFIGSGSGQAAATMPIMTPLADLIGVTRQTAVLA 406
                                       555555555555544555555544..44556799******************************************* PP

                     ABG_transport 429 yRigDsvtniitPlmsyfplv 449
                                       +  gD +tn+  P m y+ ++
  gi|242399548|ref|YP_002994973.1| 407 FQFGDGITNMFYPAMIYYLVF 427
                                       *************99997554 PP

>> Na_H_antiporter  Na+/H+ antiporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   7.5    0.0018       5.4     151     255 ..      70     180 ..      65     183 .. 0.80
   2 !   31.5  14.4   3.4e-11     1e-07      35     296 ..     194     456 ..     166     462 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0018
                   Na_H_antiporter 151 kllnrGiksmlgaililllAwgiggvlealgvteslvsslakgv..vskgllplilflvallvafatGtswgtigIi 225
                                       + + +G+k  +g+i+ +++ +g  ++++ +g++++ +  +++++      ll +i+f+ all +++ G    ti++i
  gi|242399548|ref|YP_002994973.1|  70 QAIPTGFKQAAGIIAFVFIIAGAIQIIRSTGALDAGIIAMVNKLkgRDTPLLLAIMFVFALLGSVF-GFAEETIPLI 145
                                       56789****************************9866666666657778999999****9998876.5555678876 PP

                   Na_H_antiporter 226 lpiavplaaklgisl......lalvraveaggtlgd 255
                                        p+ v +a +lg+++       ++++ v+ +g++ +
  gi|242399548|ref|YP_002994973.1| 146 -PLGVAMALALGYDRvvgfhiVRTAAWVGFAGAMLN 180
                                       .89999999999999777666677777777777665 PP

  == domain 2  score: 31.5 bits;  conditional E-value: 3.4e-11
                   Na_H_antiporter  35 mlvqsipanvysifallvvglvvl..llrdigamlraeaear.............eleekeltklpiavliiltlsk 96 
                                        l++ + ++++++++++++g+v+   ++rd+ +  ++                  ++e +elt  p   li+l l++
  gi|242399548|ref|YP_002994973.1| 194 PLYSGLWYRIICFLVFFAIGAVFIlkYARDVRKDPKK-SI-LygyegedraefslNYEQQELT--PTRKLILLVLFG 266
                                       4566677899999999999999997766666662222.33.2477777778888888888888..666666555543 PP

                   Na_H_antiporter  97 mpytgalalvaivkafivalafqntdvatalvvgalaglivatllelaslseidkllnrGiksmlgaililllAwgi 173
                                        +++ +         +i ++ ++   +a  l +g+ agli +++ +      + + ++ G+k++ +  li+ +A +i
  gi|242399548|ref|YP_002994973.1| 267 GILLQIYG-------VIEYGWYTTEISALFLGLGIIAGLIAKMNPSK-----LFGEFVSGAKGVTYGALIIGFARAI 331
                                       33332222.......23333333333344455677777777777665.....************************* PP

                   Na_H_antiporter 174 ggvlealgvteslvsslakgvvs..kgllplilflvallvafatGtswgtigIilpiavplaaklgisllalvrave 248
                                         +l +  v+++++++la+ + s  ++ + +++fl+  +++f++G+  g  + ++pi+ pla+ +g+++   v a  
  gi|242399548|ref|YP_002994973.1| 332 VVILSEGRVLDTIIHGLATPLGSlgPATAGVAMFLIHSIINFFIGSGSGQAAATMPIMTPLADLIGVTRQTAVLAFQ 408
                                       *******************98555599999***************************************99999999 PP

                   Na_H_antiporter 249 aggtlgdhlsPisdttilsstglnad.hidhvsytqlpyallvapitai 296
                                        g  +++ + P+    ++ + +   d  + h++ ++++  +  a+++ai
  gi|242399548|ref|YP_002994973.1| 409 FGDGITNMFYPAMIYYLVFADIP-YDrWVRHIWKLVVYLTIAGAILVAI 456
                                       9999********99999999999.5779*****6666555555544444 PP

>> SCFA_trans  Short chain fatty acid transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.5     0.085   2.5e+02      87     154 ..      69     137 ..      64     154 .. 0.67
   2 !   29.4   7.4   1.4e-10   4.1e-07     260     415 ..     264     420 ..     186     458 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.085
                        SCFA_trans  87 iaslakdtksavvlvtllaliaavinw..GlGlvvgailakevarrvkgldyalliaaayi.glltwhgGl 154
                                       + +++ + k+a+ +++++ +ia  i      G + + i+a  +  + kg d +ll+a  ++ +ll    G+
  gi|242399548|ref|YP_002994973.1|  69 LQAIPTGFKQAAGIIAFVFIIAGAIQIirSTGALDAGIIA--MVNKLKGRDTPLLLAIMFVfALLGSVFGF 137
                                       5678888888999999988888776641145555555555..56788888888888887752445555555 PP

  == domain 2  score: 29.4 bits;  conditional E-value: 1.4e-10
                        SCFA_trans 260 ilGiaylgvy.fyekGfn.ltlnsvnl.ifllvGlllhktPlaymraitr.aarsvaGilvqfPfyaGimgmmessa 332
                                       ++G + l +y   e G +  ++ ++ l + +++Gl+  ++P          a + + G l+   f   i  ++    
  gi|242399548|ref|YP_002994973.1| 264 LFGGILLQIYgVIEYGWYtTEISALFLgLGIIAGLIAKMNPSKLFGEFVSgAKGVTYGALI-IGFARAIVVILSEG- 338
                                       3333444444244555543334444442347888888888887665544404445556655.56666666666543. PP

                        SCFA_trans 333 lGGpslatliaeafinva..nkktfplltlfsaalinifiPsGGGewaiqgpilipaaqalGvdlGksvlaiayGda 407
                                          + l t+i    + +    + t  +  +++ ++in+fi sG G+ a+  pi+ p a+ +Gv    +vla+ +Gd 
  gi|242399548|ref|YP_002994973.1| 339 ---RVLDTIIHGLATPLGslGPATAGVAMFLIHSIINFFIGSGSGQAAATMPIMTPLADLIGVTRQTAVLAFQFGDG 412
                                       ...3444444444433331136677788899********************************************** PP

                        SCFA_trans 408 wtnliqPf 415
                                        tn++ P 
  gi|242399548|ref|YP_002994973.1| 413 ITNMFYPA 420
                                       *****995 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 ?   11.6   0.1     2e-05      0.06     131     186 ..      83     138 ..      13     141 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2e-05
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP 131 lvllfflaqlllGiGatpiytlGisYidDnvkkknsplylgilyalrilGpalGfl 186
                                       + ++f++a  ++ i +t     Gi  + +  k +++pl+l+i++++++lG ++Gf+
  gi|242399548|ref|YP_002994973.1|  83 IAFVFIIAGAIQIIRSTGALDAGIIAMVNKLKGRDTPLLLAIMFVFALLGSVFGFA 138
                                       45599999999999999999***********************************6 PP

>> Claudin_3  Tight junction protein, Claudin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.37   1.1e+03      99     124 ..      17      42 ..      10      51 .. 0.82
   2 ?    4.9   0.4    0.0074        22      36      71 ..     186     219 ..     159     224 .. 0.75
   3 ?    8.8   0.1   0.00048       1.4       6      34 ..     258     286 ..     250     307 .. 0.82
   4 ?   -3.0   0.2       2.1   6.3e+03     137     149 ..     444     456 ..     434     460 .. 0.60

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.37
                         Claudin_3  99 llslliviltviaviliavnvskfnd 124
                                       ++++li i t+++ +l a ++++f+d
  gi|242399548|ref|YP_002994973.1|  17 IIFVLILIATLATWTLPAGEYDRFKD 42 
                                       67889999999999999999998876 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0074
                         Claudin_3  36 keksiGivPfssteagwleaasimmyislalflvvi 71 
                                         +si+ +P +s  + w+ + +++++++++ ++++ 
  gi|242399548|ref|YP_002994973.1| 186 VAQSIAELPLYS--GLWYRIICFLVFFAIGAVFILK 219
                                       455666678888..88*************9998875 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.00048
                         Claudin_3   6 kalgvlvvisfilnivglftpaWiteest 34 
                                       k ++++++++++l+i+g+  ++W t e  
  gi|242399548|ref|YP_002994973.1| 258 KLILLVLFGGILLQIYGVIEYGWYTTEIS 286
                                       5677779*****************99876 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 2.1
                         Claudin_3 137 awlsvisailsli 149
                                       ++l+++ ail++i
  gi|242399548|ref|YP_002994973.1| 444 VYLTIAGAILVAI 456
                                       3455555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (465 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       679  (0.0378716); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.47
# Mc/sec: 2975.80
//
Query:       gi|242399549|ref|YP_002994974.1|  [L=354]
Description: Alanine racemase, N-terminal, partial [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-19   70.8   0.0    1.5e-19   70.5   0.0    1.1  1  Ala_racemase_N  Alanine racemase, N-terminal domain
  ------ inclusion threshold ------
       0.14   12.0   0.1       0.39   10.5   0.0    1.6  2  GEP5            Genetic interactor of prohibitin 5


Domain annotation for each model (and alignments):
>> Ala_racemase_N  Alanine racemase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.5   0.0   1.7e-23   1.5e-19       1     212 [.       7     221 ..       7     228 .. 0.89

  Alignments for each domain:
  == domain 1  score: 70.5 bits;  conditional E-value: 1.7e-23
                                       EEHHHHHHHHHHHHHHS.CTTSEEEEE-HHHHHTTHHHHHHHHHHHTTESEEEESSHHHHHHHHHTTSCSEEEEESC CS
                    Ala_racemase_N   1 idldalrhNlrrlrala.gpgaklmavvKanayghgavevaralaeggadgfgvatleEalelreagitapilvleg 76 
                                       i+l+a+++N+rr+ + + + g +++ ++K      g  +va+a ++gg++ +g ++++  ++++e+ ++a+ ++++ 
  gi|242399549|ref|YP_002994974.1|   7 INLSAIEDNVRRVVEFCtSYGINVVGITKG---ACGEPKVAKAILRGGVQILGDSRIQNIIKMKESNVKAEFMLIRS 80 
                                       89***************666999*******...5666679999999******************************* PP

                                       STGGGHHHHHHTTEEEEESSHHHHHHHHHHHHHTTS-EEEEEEBESSSSSSSBSCHHHHHHHHHHHHTTTEEEEEEE CS
                    Ala_racemase_N  77 fspeelaalaeydltvtvdsleqlealaaaareagkplrvhlkidtgmgRlGftpeeleellealaalpglrleglm 153
                                          +e++++++y    + + l+ le+l++a  e g++++  +++d+g  R G+ p+e+  +l+++++l+g++++g+ 
  gi|242399549|ref|YP_002994974.1|  81 PMISEVESVVKYAEYSLNSELKVLEQLSKASLEYGRRHKAIIMVDVGDRREGIMPNEFVPFLKEAKKLKGVEIVGVG 157
                                       99*********9666666667888***************************************************** PP

                                       -S-SSTTSTSHHHHHHHHHHHHHHHHHHHTT.GGGSEEEEESHHHHHHS..GGG....TTEEEESG CS
                    Ala_racemase_N 154 tHfasadepdeeteaqlarfeealeelekag.lrppvvslanSaailla..aah....fdmvRpGi 212
                                       t +++      +t ++++ +++++e+++    +++p++s +++  + l   + +     + +R+G 
  gi|242399549|ref|YP_002994974.1| 158 TNLGCFGGVL-PTPRNHEMLKKLTEKVKYILgIENPIISSGGTVVLNLLerE-QssygINQLRIGE 221
                                       ******9988.9***************9877899999999998877666431.2234677777775 PP

>> GEP5  Genetic interactor of prohibitin 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.32   2.9e+03     187     212 ..      58      84 ..      55     116 .. 0.69
   2 ?   10.5   0.0   4.3e-05      0.39     155     213 ..     141     196 ..     134     203 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.32
                              GEP5 187 vridnLlkkkvayvkk.vLaiekPiLs 212
                                        ri+n  k k + vk   + i +P++s
  gi|242399549|ref|YP_002994974.1|  58 SRIQNIIKMKESNVKAeFMLIRSPMIS 84 
                                       677777777777776413445555543 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 4.3e-05
                              GEP5 155 FlksnptlcsnkklkipivEiplnplGldipavridnLlkkkvayvkkvLaiekPiLsr 213
                                       Flk+ ++l   k ++i  v   l  +G  +p  r  ++lkk +++vk +L ie+Pi+s 
  gi|242399549|ref|YP_002994974.1| 141 FLKEAKKL---KGVEIVGVGTNLGCFGGVLPTPRNHEMLKKLTEKVKYILGIENPIISS 196
                                       88888888...8998888888899********************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2432.68
//
Query:       gi|242399550|ref|YP_002994975.1|  [L=350]
Description: hypothetical protein TSIB_1575 [Thermococcus sibiricus MM 739]
Scores for complete 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-56  189.5   2.5    7.5e-56  189.1   2.5    1.2  1  NRD1_2    NrpR regulatory domains NRD1 and 2
    3.7e-16   58.8   1.6      1e-15   57.4   0.2    2.4  2  HTH_12    Ribonuclease R winged-helix domain
    0.00049   20.1   0.0     0.0011   19.0   0.0    1.6  1  HTH_20    Helix-turn-helix domain
     0.0016   18.3   0.0      0.012   15.6   0.0    2.6  2  MarR      MarR family


Domain annotation for each model (and alignments):
>> NRD1_2  NrpR regulatory domains NRD1 and 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.1   2.5   1.7e-59   7.5e-56       6     237 ..     109     343 ..     104     344 .. 0.97

  Alignments for each domain:
  == domain 1  score: 189.1 bits;  conditional E-value: 1.7e-59
                                       HHHHHHHCC---BTTTTB-EEEEEEEEEEGGGHHHHHHHHHHHHHTT-SSSSEEEEEE-SSE..........EEEEE CS
                            NRD1_2   6 skieelaykvtfdpetgkGkVivNlslidkedleealeilkeviksglsvsdrvkileegek..elevpegkvgiat 80 
                                         ie+l++ +++d++++kGk++vN  +++k++++ ++ +l ++ k+++++s++++il+e+++  ++ev+eg vgi  
  gi|242399550|ref|YP_002994975.1| 109 IEIEKLITDSDYDINKNKGKIMVNAIMVPKDKYDAVVPLLLDISKTNVITSPLLAILDEKDSiwHFEVKEGYVGILG 185
                                       579************************************************************************** PP

                                       E-CHHHHHHHHCTT--EEEEEEEEEEE-SS.-EEEEEEEESTT-SS-HHHHCGGG.........--SSSEEEEEEEE CS
                            NRD1_2  81 vCSitidgvLlknGIpvkpkyGGlleiedkepvrFtelIsYegtsidPlevfiskklTsvlevietgegkilAnlRe 157
                                       ++S t+d +++k+GI ++++ +Gl ++e++ p++F+e+Is+ gt+i+P e++i+ ++Tsv++v++tg+g+++A++++
  gi|242399550|ref|YP_002994975.1| 186 ISSRTYDIIFQKSGICLQSTATGLYHLENNIPKGFVEIISHLGTTISPGELLIRGGYTSVHKVASTGSGYVTAAIKT 262
                                       ***************************************************************************** PP

                                       EETTTHHHHHHHHHHH...T-TTEEEE--..TT--BTTB---TTEEEEEEE-TTHHHHHHHHTT---EEEEEEEEEE CS
                            NRD1_2 158 ipvsarekveeileklkkagisgvleige..pneevlgvpveeekvgivvvgGlnpiaalkeagikveikalsglid 232
                                       +    ++++ +ileklkk++isgv e +   p+++ ++v  +++k  +vv+gG n++a+++e gi+ +++++ +l++
  gi|242399550|ref|YP_002994975.1| 263 FSSFRYDDTLRILEKLKKNNISGVAEHSSiiPENKRVNVM-DKNKGYLVVYGGANYFAPIVETGISKKLEIARDLYE 338
                                       ***************************9966777777775.77999******************************* PP

                                       GGGSE CS
                            NRD1_2 233 iselk 237
                                       i+++k
  gi|242399550|ref|YP_002994975.1| 339 IQKMK 343
                                       ****8 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.4   0.2   2.3e-19     1e-15       2      66 .]      31      95 ..      30      95 .. 0.98
   2 ?   -1.0   0.1       0.4   1.8e+03      16      31 ..     108     123 ..     100     125 .. 0.84

  Alignments for each domain:
  == domain 1  score: 57.4 bits;  conditional E-value: 2.3e-19
                            HTH_12  2 eILkilaesdkpigakeiaeeLkkrgydigeravRyrLrkleergltrrvgyagreltEkGleeL 66
                                      eIL+il  s+ p  + e+a+ Lk+rg d+  r+vRy+L  leerg+++r g+ g++ltE+G++e+
  gi|242399550|ref|YP_002994975.1| 31 EILRILYFSEGPKTSIELAKFLKNRGIDVDPRTVRYHLFHLEERGFIKRLGRKGAKLTERGVNEI 95
                                      8************************************************************9985 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.4
                            HTH_12  16 akeiaeeLkkrgydig 31 
                                       + ei++ + + +ydi 
  gi|242399550|ref|YP_002994975.1| 108 SIEIEKLITDSDYDIN 123
                                       6689999*******95 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   2.5e-07    0.0011      13      56 ..      30      79 ..      20      83 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.5e-07
                                      HHHHHHH.STCTTB-HHHHHHHH.....TS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20 13 rrilraL.araegltaselaerl.....dlskntlsyHLrvLeeagLvev 56
                                      ++ilr L  ++++ t  ela+ l     d+++ t++yHL  Lee g++++
  gi|242399550|ref|YP_002994975.1| 30 LEILRILyFSEGPKTSIELAKFLknrgiDVDPRTVRYHLFHLEERGFIKR 79
                                      678888899**************998888*******************86 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   2.6e-06     0.012       3      50 ..      27      80 ..      25      84 .. 0.85
   2 ?   -2.7   0.0       1.4   6.1e+03       9      31 ..     209     231 ..     207     232 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.6e-06
                                      HHHHHHHHHHHHSTTEEHH.HHHHHHT.....S-HHHHHHHHHHHHHTTSEEEE CS
                              MarR  3 ltqfviLrilyeqgplsvs.eLakklg.....vskstvtrvldrLekkGlieRs 50
                                      +t ++iLrily +++++ s eLak+l+     v++ tv   l +Le++G+i+R 
  gi|242399550|ref|YP_002994975.1| 27 MTVLEILRILYFSEGPKTSiELAKFLKnrgidVDPRTVRYHLFHLEERGFIKRL 80
                                      56689******999988888*****8544444********************96 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.4
                                       HHHHHHSTTEEHHHHHHHHTS-H CS
                              MarR   9 LrilyeqgplsvseLakklgvsk 31 
                                       L+ l+++ p    e+ ++lg+++
  gi|242399550|ref|YP_002994975.1| 209 LYHLENNIPKGFVEIISHLGTTI 231
                                       67788888888889999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.52
# Mc/sec: 2011.80
//
Query:       gi|242399551|ref|YP_002994976.1|  [L=180]
Description: 50S ribosomal protein L10e [Thermococcus sibiricus MM 739]
Scores for complete 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  110.4   0.1    7.9e-32  110.0   0.1    1.1  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 !  110.0   0.1   4.4e-36   7.9e-32       3     129 ..      14     160 ..      12     162 .. 0.95

  Alignments for each domain:
  == domain 1  score: 110.0 bits;  conditional E-value: 4.4e-36
                                       SSXXBSSSXXSSTSXX.XSXXXXXESX........EEEEESSXEEEEHHHHHHHHHHHCTCCCCTSXC...EEXXSX CS
                     Ribosomal_L16   3 rkkyrKsrkryirgvs.tkgtklefgd........ygLvalekgqltaealeaariainrylkkkrgk...klwirv 67 
                                       +++y++++  yirg++ +++t++++g+        ++L + e+ q++++aleaar  +nryl+k+ g+   + +irv
  gi|242399551|ref|YP_002994976.1|  14 KPAYTRRE--YIRGAPgPRITIFDMGNpagdfefeVSLHTAEPVQIRQNALEAARTQLNRYLSKNVGRsnfHYKIRV 88 
                                       689***99..***********************9999****************************99999******* PP

                                       XXXEEEEE-.....SS-TTTSSSS....XEEEEEEEEEXSSCEEEEE...TTXXXSHHHHHHHHHHHHTSSSXE CS
                     Ribosomal_L16  68 fphhpvtkk.....agedRmgkGk....Gkpegwvarvkigqiifei...kagvneeiakealrraasKlpikt 129
                                       +p+++++++      ++dR g+G+    Gkp g +ar k++q i+++   k   + + a  a++ra++K+p+k+
  gi|242399551|ref|YP_002994976.1|  89 YPFQVLRENpmatgRKADRYGNGMrrpfGKPIGLAARLKKDQKILTVrvnK--QHLKFALAAMKRASMKFPCKC 160
                                       *********88888889******************************7532..4999***************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 1113.96
//
Query:       gi|242399552|ref|YP_002994977.1|  [L=370]
Description: hypothetical protein TSIB_1577 [Thermococcus sibiricus MM 739]
Scores for complete 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-43  148.7   0.1    2.4e-43  148.4   0.1    1.1  1  Peripla_BP_2  Periplasmic binding protein


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.4   0.1   1.4e-47   2.4e-43       1     236 [.     111     329 ..     111     330 .. 0.95

  Alignments for each domain:
  == domain 1  score: 148.4 bits;  conditional E-value: 1.4e-47
                                       EEE-SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT..TS-BSBESSSB-HHHHHHH--SEEEE-GGG...GGGHH CS
                      Peripla_BP_2   1 iaslspsvteillalGatdkvvgvdtttsdpldadkleeaivevgadgeidvEklaalkPDlvilskglgltdedee 77 
                                       ++sl+ps+te+l+ +Ga+dkvvg+ +++++p+  +    +  +v +d+e+++E +a lkPDl+i+ k++    + ++
  gi|242399552|ref|YP_002994977.1| 111 VVSLAPSITETLYFIGALDKVVGITKWDNYPNNVQ----EGRTVVGDMEPNIEIIASLKPDLIIGLKYH---LKYID 180
                                       89********************************9....8889999********************999...89999 PP

                                       HHHHHS-EEE----TTSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT.-EEEEEEEETTE..EEEE CS
                      Peripla_BP_2  78 llksgiptvivessntgeslkeqiralgellgledeaeklvaeidsklaaaksaidsekpkpvlvfggadeggyvva 154
                                       +l++++p++ive++++ e+++e ++ lg +++++++a++++  +++k+++++++++ + +++v++  ++d+   + a
  gi|242399552|ref|YP_002994977.1| 181 QLEKIAPVLIVEPQSV-EEIYEALELLGNVTNRPEQAQEVIIGMKNKIEDIQKKVEGKRKPKVFYIVWGDP--LMTA 254
                                       9**************8.*****************************************7788888887777..**** PP

                                       -TTSTTTHHHHTS--EESTTT--STT-EEE-HHHHHHH--SEEEEEEHHHHT-S--HHHHT-SHHHHTSHHHHTT-E CS
                      Peripla_BP_2 155 gsnsyigdlldalgieniaaeskkseyeeisaEqilasdpdvifvsgraeadnktgleflkenpllaelpAvkngrV 231
                                       g++++ig+l+   g+eni+a+  ++++ ++s E++ a++p++i+  ++    +   + +l ++pl+ +++AvkngrV
  gi|242399552|ref|YP_002994977.1| 255 GNGTFIGELITLGGGENIFAD--TQGWPQVSVEEVIARNPEIIILPPS----AGITANELCNSPLA-NTEAVKNGRV 324
                                       *********************..8************************....77778889999887.********** PP

                                       EEE-H CS
                      Peripla_BP_2 232 yalds 236
                                       y+l s
  gi|242399552|ref|YP_002994977.1| 325 YTLSS 329
                                       **965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 2610.60
//
Query:       gi|242399553|ref|YP_002994978.1|  [L=55]
Description: hypothetical protein TSIB_1578 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.25    9.7   2.4       0.28    9.5   2.4    1.0  1  Mem_trans    Membrane transport protein
       0.62    9.9   2.8       0.64    9.8   2.8    1.0  1  PhoQ_Sensor  PhoQ Sensor
        1.1    7.9   4.4        1.1    8.0   4.4    1.0  1  DUF2207      Predicted membrane protein (DUF2207)


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 ?    9.5   2.4   4.7e-05      0.28     109     153 ..      10      54 ..       9      55 .] 0.95

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 4.7e-05
                         Mem_trans 109 vlgipllkalygeygvslmvqvvvlqciiiytlllflfeyrgakl 153
                                        l+++ll al ++ g+  +v ++v + i+i  ++lf+f  ++a++
  gi|242399553|ref|YP_002994978.1|  10 LLPLVLLLALLYTLGLVGVVPFMVSYYITIFLIFLFIFLRWEARF 54 
                                       59*************************************999975 PP

>> PhoQ_Sensor  PhoQ Sensor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   2.8   0.00011      0.64       7      42 ..       8      42 ..       3      50 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00011
                       PhoQ_Sensor  7 rfllataavvlalslsyGlvavvGylvsfdkttyrl 42
                                      rfll   +++lal  + Glv vv ++vs+  t + +
  gi|242399553|ref|YP_002994978.1|  8 RFLLP-LVLLLALLYTLGLVGVVPFMVSYYITIFLI 42
                                      77775.44566666777************9999976 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   4.4   0.00018       1.1     381     428 ..       4      48 ..       1      55 [] 0.46

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00018
                           DUF2207 381 kklsalglgliilglilillallllvlllvfllilllillliaiivll 428
                                       k+l  ++  l +++l+++l++l+l+++ + f++ + + ++li+++++l
  gi|242399553|ref|YP_002994978.1|   4 KRLYRFL--LPLVLLLALLYTLGLVGV-VPFMVSYYITIFLIFLFIFL 48 
                                       3444444..444444444444444444.45555555555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       936  (0.0522059); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 374.88
//
Query:       gi|242399554|ref|YP_002994979.1|  [L=270]
Description: Uracil-DNA glycosylase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.1e-21   75.3   0.0    7.9e-21   74.7   0.0    1.3  1  UDG       Uracil DNA glycosylase superfamily
  ------ inclusion threshold ------
      0.051   13.1   0.0       0.11   12.0   0.0    1.5  1  DUF4918   Domain of unknown function (DUF4918)


Domain annotation for each model (and alignments):
>> UDG  Uracil DNA glycosylase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.7   0.0   8.8e-25   7.9e-21       7     117 ..     110     205 ..     104     238 .. 0.86

  Alignments for each domain:
  == domain 1  score: 74.7 bits;  conditional E-value: 8.8e-25
                                       T-SEEEEESSTCHH.HHHHSSSS.-.STT--HHHHHHHCCCCCCCHHGCTEEEEESSS....SEC.GCTTCCCCTCC CS
                               UDG   7 dakvvivGeaPgae.edatglpFsg.ragnllrkllneaglkrdleseqgvyitnvvkcrppgnr.dtptsaeikac 80 
                                        +++v+vGeaPg++ +  tg++F   ++g llrk+l ++g+++     + vyitnvvkc pp+n+ +  +++e    
  gi|242399554|ref|YP_002994979.1| 110 GSRIVLVGEAPGRKgCGLTGICFYRdASGMLLRKMLFSLGVNP-----DFVYITNVVKCNPPENKfKGFSKKE---- 177
                                       689***********999******778999**************.....*****************999*****.... PP

                                       HHHHHHHHHHHHSSEEEEESHHHHHH..HHHHSCESC CS
                               UDG  81 aplleeeiellkprlivllGktaakallgeklgklrg 117
                                         lle+e+++++p+ i ++G+ta+kal         +
  gi|242399554|ref|YP_002994979.1| 178 LSLLEKELKIVQPKGIFAIGRTAYKAL---------K 205
                                       599***********************8.........1 PP

>> DUF4918  Domain of unknown function (DUF4918)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.3e-05      0.11      52      74 ..     111     133 ..     104     145 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.3e-05
                                       -EEEEE-S---SSGGGGTSSTT- CS
                           DUF4918  52 kRklilginPgRfgagvtgvpFt 74 
                                       +R++++g  PgR g g+tg+ F 
  gi|242399554|ref|YP_002994979.1| 111 SRIVLVGEAPGRKGCGLTGICFY 133
                                       6999*****************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1799.11
//
Query:       gi|242399555|ref|YP_002994980.1|  [L=410]
Description: 2-Phosphoglycerate mutase (PGM) [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.3e-54  182.4   0.0    1.1e-53  181.6   0.0    1.4  1  PhosphMutase     2,3-bisphosphoglycerate-independent phosphog
    7.1e-49  166.4   0.0    8.4e-49  166.2   0.0    1.0  1  Metalloenzyme    Metalloenzyme superfamily
    1.2e-10   41.5   0.0    1.2e-08   35.0   0.0    2.1  2  Phosphodiest     Type I phosphodiesterase / nucleotide pyroph
    0.00086   18.8   0.0      0.097   12.0   0.0    2.3  2  Sulfatase        Sulfatase
     0.0034   16.4   0.1     0.0063   15.5   0.1    1.5  1  Alk_phosphatase  Alkaline phosphatase
  ------ inclusion threshold ------
       0.11   12.0   0.1       0.42   10.2   0.0    1.8  2  EF_TS            Elongation factor TS


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 !  181.6   0.0   3.8e-57   1.1e-53       1     170 []      39     207 ..      39     207 .. 0.98

  Alignments for each domain:
  == domain 1  score: 181.6 bits;  conditional E-value: 3.8e-57
                                       HHTSEEEEEE-----------TCHHHHTT--HHCH---HHHHHHHHTT----TT-EEEEEEEEEEC..TTCEEETTG CS
                      PhosphMutase   1 AkkGetGlldtvpegiapgSdvAnlsilGydpkkyytGRGplEAlgiGlelkpgdvafRcnlvtvdeedgiiidrra 77 
                                       Ak+G++G  d++++g ++gSd+A+l+i+Gydp + y+GRG +EAlg+Gl+l+++d+afR+n++t+  e+gii+drra
  gi|242399555|ref|YP_002994980.1|  39 AKMGILGQQDPIAPGKPAGSDTAHLAIFGYDPYQTYRGRGFFEALGVGLDLDEDDLAFRVNFATI--ENGIITDRRA 113
                                       89***************************************************************..69******** PP

                                       GG-.-TTHHHHHHHT-EEE.TTEEEEEEE-STTEEEEEE....--S-B--S--..SSTTS------BS.SGGGHHHH CS
                      PhosphMutase  78 gristeeakeLikalneeleegvevkfypgveyrhllvl....lsdkitdtdpphdkegkeikellplkseeaketa 150
                                       gristeea+eL+ka++e+++  ve+ f  ++++r++lvl    ++ k+ + dp  ++ gk++++     +ee+k+ a
  gi|242399555|ref|YP_002994980.1| 114 GRISTEEAHELAKAIQENVKLPVEFIFVGATGHRAVLVLkgmaNGYKVGENDP--HEAGKPPHKFEY-ADEESKKVA 187
                                       *******************7789********************999*******..99**********.589****** PP

                                       HHHHHHHHHHHHHHHHSHHH CS
                      PhosphMutase 151 ellnelieksqeiLedhpvN 170
                                       e+l+e+++k++e+Le hp+N
  gi|242399555|ref|YP_002994980.1| 188 EILEEFVKKAHEVLERHPIN 207
                                       *******************9 PP

>> Metalloenzyme  Metalloenzyme superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.2   0.0   2.8e-52   8.4e-49       2     246 ..       4     399 ..       3     401 .. 0.98

  Alignments for each domain:
  == domain 1  score: 166.2 bits;  conditional E-value: 2.8e-52
                                       EEEEEEETTBB----GGGTT...HHHS--HHHHHHHHH.......SEEEEEESSSTT----HHHHHHHH........ CS
                                       xxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........ RF
                     Metalloenzyme   2 kvvlvvlDGlGeapadelna...ihvAktPtldkLkkeaPerwlikahgtavglpeddmgnsevgHlel........ 67 
                                       k +l++lDGlG++  +el++   +++A+tP++d+L+k+       ++ g++ +++ ++ ++s+++Hl++        
  gi|242399555|ref|YP_002994980.1|   4 KGILIILDGLGDRLIKELGGktpLEYANTPNMDELAKM-------GILGQQDPIAPGKPAGSDTAHLAIfgydpyqt 73 
                                       5689**********************************.......99****************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                     Metalloenzyme  68 ............................................................................. 67 
                                                                                                                    
  gi|242399555|ref|YP_002994980.1|  74 yrgrgffealgvgldldeddlafrvnfatiengiitdrragristeeahelakaiqenvklpvefifvgatghravl 150
                                       ***************************************************************************** PP

                                       ..........................................................HHHHTT-----EEEEEEEE CS
                                       ..........................................................xxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme  68 ..........................................................lrisetvkfahvtffwngg 86 
                                                                                                 +r++e++ +a++++++++g
  gi|242399555|ref|YP_002994980.1| 151 vlkgmangykvgendpheagkpphkfeyadeeskkvaeileefvkkahevlerhpineKRRKEGKPVANYLLIRGAG 227
                                       **********************************************************9****************** PP

                                       -S---SS.HHHHHT--EEEE--SHH....................STT--HHHHHHHHHHHH.CC.-SEEEEEE-HH CS
                                       xxxxxxx.xxxxxxxxxxxxxxxxx....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme  87 rsgyfnp.leereeipsdtvitfdl....................qpemkavevaekaldailsgkfdlvvvnikna 142
                                       ++++++  + e ++++++ v+++ l                    + +++ +++a+ka++ +  +++d+v++++k +
  gi|242399555|ref|YP_002994980.1| 228 TYPNIPMkFTEEWKVKAAAVVATALvkgvaraigfdvytpegatgEYNTDPMAKAKKAVELL--EEYDFVFLHFKPT 302
                                       *************************************************************9..55*********** PP

                                       HHHHHTT-HHHHHHHHHHHHHHHHHHHTTS-TTTEEEEEE-SSB--TTTSS........-----EEEEEESTT---- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme 143 DmvGHtgdleatiaaieaaDeavkeildaieqvdgilvvtADHgnaedmvkrdkqplTsHtlepVPilivgkglapd 219
                                       D++GH++++ +++++ie+aDe+++ i+++i+ +++++++t+DH+++ ++++        H+ +pVP+livg g+++d
  gi|242399555|ref|YP_002994980.1| 303 DAAGHDNNPMKKVEMIEKADEMIGYIMENIDLEKTVIAITGDHSTPCEVKN--------HSGDPVPLLIVGGGVRTD 371
                                       ***************************************************........*****************9 PP

                                       S--S.SHHHHTT-TTEEEEGGGHHHHHH CS
                                       xxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme 220 kvke.gakfrekggLanvaatllnllgl 246
                                       + ++ +++++ +gg+++v+++ +  + +
  gi|242399555|ref|YP_002994980.1| 372 DRETfSERECMRGGIGRVRGKYIVPMIM 399
                                       99999999999********998876665 PP

>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.4   0.0    0.0077        23       2      42 ..       6      52 ..       6      65 .. 0.84
   2 !   35.0   0.0     4e-12   1.2e-08      86     234 ..     193     347 ..     169     377 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0077
                                      EEEEETT-BTTHHHHHG.S......TSHHHHHHHHHSEEESEEE-SSS CS
                      Phosphodiest  2 lvislDGlradlldrla.e......llpnlaaLakegvsapnlrpvfP 42
                                      ++i+lDGl  +l+++l  +       +pn+++Lak g+ +   +p++P
  gi|242399555|ref|YP_002994980.1|  6 ILIILDGLGDRLIKELGgKtpleyaNTPNMDELAKMGILGQ-QDPIAP 52
                                      79*******99999988767888889**********99988.555554 PP

  == domain 2  score: 35.0 bits;  conditional E-value: 4e-12
                                       G....GGGCTTS-HHHHHHHTHTTCEEEESE...TTTTSEBTTCT.SC......TBHHSBTCT.CSTTSCHHHHHHH CS
                      Phosphodiest  86 a....prwwqgepiwdtaakarglkaaalfw...pgsevdystyyylvs.....etppryleddfnakvpledkvdk 150
                                       +    ++++   pi ++  k+ g+ +a++     +g++++++++ +++       + ++ l + ++ + +++    +
  gi|242399555|ref|YP_002994980.1| 193 FvkkaHEVLERHPINEKRRKE-GKPVANYLLirgAGTYPNIPMKFTEEWkvkaaAVVATALVKGVARAIGFDVYTPE 268
                                       033334556669999999999.***9999999999999999987555555555555555555566666688875555 PP

                                       HHHHHHHHCHTHSHHHHHCT.SSESEEEEEECCCHHHHHHH-TTSHHHHHHHHHHHHHHHHHHHHHHHTTGTTTEEE CS
                      Phosphodiest 151 avlqtwldaafakvvlekel.ekpdlllvyleetDtvgHkfGpdspevedalrrvDkaigdLlealderglsaetni 226
                                        +++++ ++++ak+  + el e++d++++++  tD++gH   p  ++  + ++++D++ig+++e +d +    +t i
  gi|242399555|ref|YP_002994980.1| 269 GATGEYNTDPMAKAKKAVELlEEYDFVFLHFKPTDAAGHDNNP--MKKVEMIEKADEMIGYIMENIDLE----KTVI 339
                                       58899******997777777*******************8866..3345799***************99....999* PP

                                       EEEES--- CS
                      Phosphodiest 227 ilvSDHGm 234
                                        +++DH  
  gi|242399555|ref|YP_002994980.1| 340 AITGDHST 347
                                       ******75 PP

>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.1   0.0    0.0041        12       4      38 ..       6      44 ..       3      47 .. 0.86
   2 !   12.0   0.0   3.2e-05     0.097     209     258 ..     309     354 ..     113     399 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0041
                                      EEEEESSE-TTGSGGGTTTSCS....SHHHHHHHHTSEE CS
                         Sulfatase  4 vliladdlgagdlglyggktat....tpnldrlaeeglr 38
                                      +li++d lg+  ++  ggkt+     tpn+d+la+ g++
  gi|242399555|ref|YP_002994980.1|  6 ILIILDGLGDRLIKELGGKTPLeyanTPNMDELAKMGIL 44
                                      89*********999999999555555*********9986 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 3.2e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHTTTGGGEEEEEEESSSSCCCGHHT CS
                         Sulfatase 209 qlleaylnsveyvDdligrvlaaLeenglldntlvvftSDhgasleesng 258
                                       ++  +   ++e +D++ig +++ +     l++t++ +t+Dh    e +n+
  gi|242399555|ref|YP_002994980.1| 309 NNPMKKVEMIEKADEMIGYIMENI----DLEKTVIAITGDHSTPCEVKNH 354
                                       555566789***************....*************988876444 PP

>> Alk_phosphatase  Alkaline phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   2.1e-06    0.0063     261     316 ..     301     355 ..     241     377 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.1e-06
                                       CHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHCHHCTTEEEEEEESSEESEEEESTT CS
                   Alk_phosphatase 261 rIDhaaHendavgalsEvvefdeAvkaalefakkeketlvvvTaDHshvfsfggyt 316
                                         D a+H+n+++++++ + + de + + +e  +  ++t++  T DHs+ +++  ++
  gi|242399555|ref|YP_002994980.1| 301 PTDAAGHDNNPMKKVEMIEKADEMIGYIMENID-LEKTVIAITGDHSTPCEVKNHS 355
                                       569******************************.999***********87776665 PP

>> EF_TS  Elongation factor TS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1      0.42   1.2e+03     127     151 ..     187     216 ..     177     247 .. 0.71
   2 ?   10.2   0.0   0.00014      0.42       9      76 ..     275     343 ..     273     382 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.42
                             EF_TS 127 devdaevlekekei.....lkeqakeegkp 151
                                       +e+ +e+++k +e+     ++e+ ++egkp
  gi|242399555|ref|YP_002994980.1| 187 AEILEEFVKKAHEVlerhpINEKRRKEGKP 216
                                       455566666666664444444455555665 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00014
                             EF_TS   9 ETDFVAknekFqelvkkvaeaaleekakdleellalkledetveealkekiakigEkielrrf.aklea 76 
                                       +TD  Ak +k +el ++     l+ k++d++   + ++++ ++ e+ +e+i  i E+i l++    +++
  gi|242399555|ref|YP_002994980.1| 275 NTDPMAKAKKAVELLEEYDFVFLHFKPTDAAGHDNNPMKKVEMIEKADEMIGYIMENIDLEKTvIAITG 343
                                       6999********************************************************996244554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       771  (0.043003); expected 358.6 (0.02)
Passed bias filter:                      713  (0.039768); 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: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 2625.75
//
Query:       gi|242399556|ref|YP_002994981.1|  [L=42]
Description: bis(5'-adenosyl)-triphosphatase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.061   13.3   0.0      0.061   13.3   0.0    1.1  1  Wx5_PLAF3D7  Protein of unknown function (Wx5_PLAF3D7)
       0.12   12.2   0.9       0.12   12.3   0.9    1.0  1  DER1         Der1-like family


Domain annotation for each model (and alignments):
>> Wx5_PLAF3D7  Protein of unknown function (Wx5_PLAF3D7)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   6.8e-06     0.061      83     109 ..      16      42 .]       4      42 .] 0.92

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.8e-06
                       Wx5_PLAF3D7  83 WrdkmWnkkWakYlenvhklinkkLnd 109
                                       W +++ +  W+ Y+ +v+++i +kL+d
  gi|242399556|ref|YP_002994981.1|  16 WGSYVFDAPWCPYVIHVFTSIGEKLED 42 
                                       99999*******************986 PP

>> DER1  Der1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.9   1.3e-05      0.12     118     152 ..       3      36 ..       1      41 [. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.3e-05
                              DER1 118 YvwskknkdvqvsFfgvlrvkakylPlvllafsfl 152
                                       + w +  k + v F+g   + a++ P+v+ +f  +
  gi|242399556|ref|YP_002994981.1|   3 FFWEI-TKYTAVVFWGSYVFDAPWCPYVIHVFTSI 36 
                                       55654.4678899*****************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       233  (0.0129957); expected 358.6 (0.02)
Passed bias filter:                      184  (0.0102627); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.28s 00:00:00.65 Elapsed: 00:00:00.44
# Mc/sec: 284.94
//
Query:       gi|242399557|ref|YP_002994982.1|  [L=163]
Description: bis(5'-adenosyl)-triphosphatase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-14   54.3   0.0    2.8e-14   53.6   0.0    1.3  1  HIT       HIT domain
    7.6e-07   29.6   0.1    1.3e-06   28.8   0.0    1.4  2  DcpS_C    Scavenger mRNA decapping enzyme C-term binding
    0.00042   20.2   0.0    0.00069   19.5   0.0    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 !   53.6   0.0   4.6e-18   2.8e-14       6      95 ..      35     125 ..      30     128 .. 0.95

  Alignments for each domain:
  == domain 1  score: 53.6 bits;  conditional E-value: 4.6e-18
                                       CCEEEE-SSEEEEE-SS-SSSSEEEEEESSTGCSGGGCCHHHHHHHHHHHHHHHHHHHTCTTCCCEEEEEEESGGGT CS
                               HIT   6 stvvyeddlvlafldidpkapghlLvipkkhlselhdlteeelakllsavkkvakalqkkfknkglrvvinngahag 82 
                                         ++y+ ++++++ ++ p  pgh+ + p +h+ e+++lt+eel +++++++   k+l++ +k +g+++ +n g  ag
  gi|242399557|ref|YP_002994982.1|  35 RLILYRGKHAFIIMNNYPYNPGHVMIAPYRHVGEWEKLTDEELLDIMKLSQLTIKVLKRAMKPQGFNMGVNIGCVAG 111
                                       5689999********************************************************************** PP

                                       -SSS.S-EEEEEEC CS
                               HIT  83 qsva.hlHiHvipr 95 
                                         v+ h+H+H++pr
  gi|242399557|ref|YP_002994982.1| 112 AGVKdHVHLHIVPR 125
                                       *9965*******98 PP

>> DcpS_C  Scavenger mRNA decapping enzyme C-term binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.0   2.2e-10   1.3e-06       2     100 ..      21     123 ..      20     131 .. 0.83
   2 ?   -2.9   0.0       1.6   9.4e+03      59      72 ..     146     159 ..     141     163 .] 0.49

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 2.2e-10
                                       -HHHHHHTTSS.-B-E.EEE-SSEEEEE-SS-SSSEEEEEEESS---SGGG--TTTTTHHHHHHHHHHHHHHHTT-T CS
                            DcpS_C   2 wvfnilakgke.perv.vyedekfvvlkDikpkaklhllvipkrdikslrdLtkehlpllkemrekakkvieekyne 76 
                                       ++f+++ k++  +er+ +y+ +++ ++   +p ++ h+++ p+r++ + ++Lt+e+l  + ++ +   kv+++ +  
  gi|242399557|ref|YP_002994982.1|  21 CIFCDFPKENHdEERLiLYRGKHAFIIMNNYPYNPGHVMIAPYRHVGEWEKLTDEELLDIMKLSQLTIKVLKRAM-- 95 
                                       889998887774444448899***********************************999999*********9988.. PP

                                       -EEEEE--SCCCT-.....-S-S--EEEE CS
                            DcpS_C  77 vdaeelrvgvhyqP.....svyhlHlHvi 100
                                        +++ +++gv++         +h+HlH++
  gi|242399557|ref|YP_002994982.1|  96 -KPQGFNMGVNIGCvagagVKDHVHLHIV 123
                                       .456666666665555557778*****98 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.6
                                       HHHHHHHHHHHHHH CS
                            DcpS_C  59 lkemrekakkviee 72 
                                       l+e ++++kk+++e
  gi|242399557|ref|YP_002994982.1| 146 LEEAYKELKKALQE 159
                                       44444444444444 PP

>> CwfJ_C_1  Protein similar to CwfJ C-terminus 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   1.2e-07   0.00069      11      75 ..      18      84 ..      11     124 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.2e-07
                                      HHH-S--.--SS--.-SS--S-B-SSEEEE---S-SSTT-EEEEESS--SSTTSS-HHHHHHHHHHH CS
                          CwfJ_C_1 11 ldsClfC.lsnpkl.ekhlivsignkvYlalpkgpLssgHvliipieHisallsldeevldeirkfr 75
                                       + C fC + +++  e++li+  g+++++ + + p + gHv+i p  H+ +  +l +e+l +i k  
  gi|242399557|ref|YP_002994982.1| 18 HNGCIFCdFPKENHdEERLILYRGKHAFIIMNNYPYNPGHVMIAPYRHVGEWEKLTDEELLDIMKLS 84
                                      57799*97666555167889999****************************9888777666665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       985  (0.0549389); expected 358.6 (0.02)
Passed bias filter:                      852  (0.0475208); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1182.13
//
Query:       gi|242399558|ref|YP_002994983.1|  [L=560]
Description: Na+/H+ antiporter, , NhaC family [Thermococcus sibiricus MM 739]
Scores for complete 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-77  258.3  29.9    8.8e-77  258.3  29.9    2.2  2  Na_H_antiporter  Na+/H+ antiporter family


Domain annotation for each model (and alignments):
>> Na_H_antiporter  Na+/H+ antiporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   1.0     0.017     3e+02     169     240 ..      86     153 ..      12     165 .. 0.75
   2 !  258.3  29.9   4.9e-81   8.8e-77       1     302 [.     167     496 ..     167     497 .. 0.96

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.017
                   Na_H_antiporter 169 lAwgiggvlealgvteslvsslakgvvskgllplilflvallvafatGtswgtigIilpiavplaaklgisl 240
                                       +++g + + +a g  +++ + +++++ + + + l+  + + l+ f     +   +I++ +++p+ ++  +s+
  gi|242399558|ref|YP_002994983.1|  86 IGAGVALIYKAGG-MNAIAKAVTRKIRTSKAASLMAAIFGTLIFF---DDYTNTIIVGNTMRPITDRARVSR 153
                                       4556666666666.8888888888885555555554444444444...556666666666666666666665 PP

  == domain 2  score: 258.3 bits;  conditional E-value: 4.9e-81
                   Na_H_antiporter   1 vavfgdkssplsdtvgliagilktdlieeiaalgmlvqsipanvysifallvvglvvlllrdigamlraeaear... 74 
                                       vav+  +s++++++ gl + ++ + + e i+a+++++ s p+++y i+a+++v lv+ + +++g+ml+ae +ar   
  gi|242399558|ref|YP_002994983.1| 167 VAVLAVVSTWIGYELGLLKDAI-ASVGESISAYSAWFASWPYRFYPILAIILVYLVAITHKHYGPMLKAEYRARkeg 242
                                       6788889***************.899999999********************************************* PP

                   Na_H_antiporter  75 .......................eleekeltklpiavliiltlskmpytgalalvaivkafivalafqntdvatalv 128
                                                              + +++++  lp+++l++lt+ + ++tg+++  a+ ++  ++ ++ n+d+++alv
  gi|242399558|ref|YP_002994983.1| 243 kvlrdgaqpmmttevdvgmpiegKESVWVFV-LPVLTLVALTFLGLWVTGGGS--ATYAEGGFQAVLSNADSTWALV 316
                                       *****99999999998888887777777777.9********************..7788999*************** PP

                   Na_H_antiporter 129 vgalaglivatllela....slseidkllnrGiksmlgaililllAwgiggvlealgvteslvsslakgvvskgllp 201
                                       +g++ +++va++l +     sl+e+++++++G+k m +a++il+lAw+i+++ +a+g t+++v s+a+ v s+gl+p
  gi|242399558|ref|YP_002994983.1| 317 WGSFGMVVVAMALVIGmkimSLKEVEETVVAGMKQMHFAMMILILAWSIKSACDAVG-TADYVVSVASNVLSPGLVP 392
                                       ***********99988899**************************************.******************* PP

                   Na_H_antiporter 202 lilflvallvafatGtswgtigIilpiavplaaklgisl....lalvraveaggtlgdhlsPisdttilsstglnad 274
                                       l++f+va++++f+tGtswgt++I++piavpla +l+ s     +a ++ v+agg++gdh+sPisdtti+ss++ ++d
  gi|242399558|ref|YP_002994983.1| 393 LVVFIVAAFISFTTGTSWGTFAIMMPIAVPLAYQLSGSFgsvvYASIASVFAGGVFGDHCSPISDTTIMSSMFSGCD 469
                                       **************************************9999*********************************** PP

                   Na_H_antiporter 275 hidhvsytqlpyallvapitailllvfG 302
                                       hidhvs tq+pya ++a+i a++l++f+
  gi|242399558|ref|YP_002994983.1| 470 HIDHVS-TQIPYAVTAAAIGALMLVLFA 496
                                       ******.******************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (560 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       805  (0.0448993); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); 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: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.46
# Mc/sec: 3635.42
//
Query:       gi|242399559|ref|YP_002994984.1|  [L=258]
Description: Thymidylate synthase thyX [Thermococcus sibiricus MM 739]
Scores for complete 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-61  207.0   1.2    2.8e-61  206.6   1.2    1.0  1  Thy1      Thymidylate synthase complementing protein


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 !  206.6   1.2   1.5e-65   2.8e-61       1     185 [.      21     212 ..      21     213 .. 0.94

  Alignments for each domain:
  == domain 1  score: 206.6 bits;  conditional E-value: 1.5e-65
                                       EEEEEE.CHHHHHHHHHHHHHTTCSSHHHH..S.GCCHHHHHHHHHHTTGGGGGGG-EEEEEEEEEEHHHHHHHTT- CS
                              Thy1   1 kLldyt.dpeklvaaaarvcygsseeaeele.e.eekkeklikkllkhghgsplehasftfeiegvSravlrqlvrH 74 
                                       kL++yt  p +++  aa ++y  + e+e  e   +++ e+ + ++l++gh+s+leha ftf+ieg+Sr +++qlvrH
  gi|242399559|ref|YP_002994984.1|  21 KLINYTpRPLETITWAALISYWDKWESEAFErItKDDVENHLPRVLSYGHESILEHAIFTFAIEGCSRTCSHQLVRH 97 
                                       69*******************877444444442468889************************************** PP

                                       TTSEEEE--TTTSGCCCTC....BS--GGGCC.HHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHGGGSBTTBEEEEE CS
                              Thy1  75 RiasfsqqSqRYvesskea....fvippeieqkeeleelyeeamekaleaykelleagvarEdaryvLPlatktklv 147
                                       R+as++qqS+RY +  +e+    fvip+++++++el e++++ me++++ y+e  ++g+ +Edar++LP+a++tk+v
  gi|242399559|ref|YP_002994984.1|  98 RLASYTQQSMRYIKINPEEveetFVIPESVKKDPELYEKWKKLMEETIKLYEESYAKGIHQEDARFILPQAVRTKIV 174
                                       **************99977899*********99******************************************** PP

                                       EEEEHHHHHHHHHHHSSTTS-HHHHHHHHHHHHHHHHH CS
                              Thy1 148 vtmNlrsLlhflelracsrAqwEirelaeemleelkkv 185
                                       vtmNlr+L+hfl  rac rAqwEi ++a++mlee++k+
  gi|242399559|ref|YP_002994984.1| 175 VTMNLRELKHFLGFRACARAQWEINHIAWKMLEEIAKI 212
                                       **********************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       789  (0.0440069); expected 358.6 (0.02)
Passed bias filter:                      573  (0.0319594); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 1506.78
//
Query:       gi|242399560|ref|YP_002994985.1|  [L=315]
Description: Ornithine carbamoyltransferase [Thermococcus sibiricus MM 739]
Scores for complete 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-65  217.6   0.2    1.2e-64  217.2   0.2    1.2  1  OTCace    Aspartate/ornithine carbamoyltransferase, Asp/Orn b
    4.2e-51  172.9   0.0    1.2e-50  171.4   0.0    1.7  2  OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl


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 !  217.2   0.2   1.3e-68   1.2e-64       1     156 [.     154     308 ..     154     309 .. 0.99

  Alignments for each domain:
  == domain 1  score: 217.2 bits;  conditional E-value: 1.3e-68
                                       CC.EEEEESSTTSHHHHHHHHHHHHCT-EEEEES-TTSSH-HHHHHHHHHHHHHHT-EEEEESSCHHHHTT-SEEEE CS
                            OTCace   1 kglkiafvGdkknnvanslikllarlgmdvvlvaPkglepdkevleeakknakksggsititedleeavkgaDvvyt 77 
                                       +g+k+++vGd+ nnva+sl+++ ++lg++vv+++P+g+epd  v++ a++na++sggs+++ +d+ +avk+aDv+yt
  gi|242399560|ref|YP_002994985.1| 154 EGIKVVYVGDG-NNVAHSLMIAGTKLGANVVVATPEGYEPDARVIKWAEENAAESGGSFELLHDPVQAVKDADVIYT 229
                                       69*********.***************************************************************** PP

                                       --SSETTCCGGHHHHHHHHCCCSB-HHHHHHS-TT-EEEE-S---BTTTB-HHHHTSTTBHHHHHHHHHHHHHHHHH CS
                            OTCace  78 dvwvsmgeekereerlkklkdyqvteellklakkdaivlHcLPakrgeEvtdeVfdsprsvvfeqaeNrlhtikAll 154
                                       dvw+smg+e+e eer k ++++qv+++l+k+akkd i++HcLPa+rgeEvtd+V+dsp+svvf++aeNrlh++kA +
  gi|242399560|ref|YP_002994985.1| 230 DVWASMGQEAEAEERRKVFMPFQVNKDLVKHAKKDYIFMHCLPAHRGEEVTDDVVDSPNSVVFDEAENRLHAQKAAM 306
                                       ***************************************************************************** PP

                                       HH CS
                            OTCace 155 vl 156
                                       +l
  gi|242399560|ref|YP_002994985.1| 307 AL 308
                                       97 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 !  171.4   0.0   1.3e-54   1.2e-50       1     148 []       8     148 ..       8     148 .. 0.97
   2 ?   -1.9   0.0      0.34     3e+03      56      74 ..     170     187 ..     168     206 .. 0.80

  Alignments for each domain:
  == domain 1  score: 171.4 bits;  conditional E-value: 1.3e-54
                                       S-BSSGGGS-HHHHHHHHHHHHHHHHHHHTTT-STTTTT-EEEEEESS--HHHHHHHHHHHHHTTSEEEEEESTTTS CS
                          OTCace_N   1 rhllsledlskeeieelldlaaelkekvkkekkekllkgktlallFeepStRTrvSfevAakrlGgkvlslseaedi 77 
                                       r++l l+d+++eeie++l++a+ +k  +k  k ++ l+gktla++F++pStRTr+Sfev++++lGg  l+l+ a+d+
  gi|242399560|ref|YP_002994985.1|   8 RDILCLQDFTREEIETILKTAEMMKIWNKIGKPHRVLEGKTLAMIFQKPSTRTRISFEVGIYQLGGYGLYLN-AQDL 83 
                                       7899*********************87777******************************************.87** PP

                                       CTTTGGSTTSSCHHHHHHHHHHHTSEEEEEESSHHHHHHHHHHHSSEEEEEEETSSB-HHHHHHHHHHHHH CS
                          OTCace_N  78 qlssvskgrkEsleDtarvlsryvdaiviRhpgaeeleelakyasvpviNagdgdgeHPtQaLaDlltire 148
                                       ql      r+E+++Dtarvlsryvd+i++R+++++++ +laky svpviN++ +d +HP+QaLaD +ti+e
  gi|242399560|ref|YP_002994985.1|  84 QLR-----RGETIADTARVLSRYVDGIMARVFDHQDVVDLAKYGSVPVINGL-SDFSHPCQALADYMTIKE 148
                                       **9.....77******************************************.****************97 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.34
                                       HHHHHHHHTTSEEEEEEST CS
                          OTCace_N  56 SfevAakrlGgkvlslsea 74 
                                       S  +A ++lG++v++ + +
  gi|242399560|ref|YP_002994985.1| 170 SLMIAGTKLGANVVVAT-P 187
                                       7788999****999987.4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2107.42
//
Query:       gi|242399561|ref|YP_002994986.1|  [L=301]
Description: Hydrolase, HAD superfamily [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-15   57.3   0.2      3e-15   56.7   0.2    1.2  1  HAD_2           Haloacid dehalogenase-like hydrolase
    3.1e-10   40.7   0.1    4.2e-10   40.3   0.1    1.2  1  Hydrolase       haloacid dehalogenase-like hydrolase
    2.2e-05   24.5   0.0      4e-05   23.6   0.0    1.4  1  Hydrolase_like  HAD-hyrolase-like
  ------ inclusion threshold ------
      0.035   13.3   0.2      0.048   12.8   0.2    1.1  1  dCache_2        Cache domain
       0.11   12.5   0.4       0.17   11.9   0.4    1.3  1  DUF1451         Zinc-ribbon containing domain


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 !   56.7   0.2   8.4e-19     3e-15       3     178 .]      79     271 ..      77     271 .. 0.76

  Alignments for each domain:
  == domain 1  score: 56.7 bits;  conditional E-value: 8.4e-19
                             HAD_2   3 FDlDgTlldteeliiqafnelleey........glselseeelrkliglslrellrklgeseeeee........... 60 
                                       FD+ +Tlld + +i + ++ l e          +    ++ee++k+    + +  + l+      e           
  gi|242399561|ref|YP_002994986.1|  79 FDVWNTLLDINVMIENLVKALSELLkvpeeeiaEKTIKTREEIKKIRKSRSGDPEKALE------Esqellaralev 149
                                       9999******9999999998887774444444322244444444444444444444444......155555698888 PP

                             HAD_2  61 kieellrkyneekkk.kevkpydgvkelLeeLkeagyklgivTsk...sreaveekleqlgiesyFdvivtsedvek 133
                                       ++e + r + +     +e  ++++vke+L++L + +y +    +     +  ++  le++g+ +y+++   s++++ 
  gi|242399561|ref|YP_002994986.1| 150 DVEIVKRAVAKATLSvDERIVLPEVKETLKKL-HGKYIITTTGNVmfwPSTYTRLILEKFGLADYITKQFYSDEIKA 225
                                       777777777777776888999***********.77775544444333347889999********************* PP

                             HAD_2 134 kKPdpeviekaleklklkkeeviyvGDsp.tDieaakkagikviav 178
                                        KP  e +++ l+ +++ +ee+i +GD++  D+e+a ++g++++++
  gi|242399561|ref|YP_002994986.1| 226 YKPMKEAFLAPLRYFNVPPEEAIHIGDTKaEDFEGALNTGMHACWI 271
                                       *******************************************996 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   0.1   1.2e-13   4.2e-10       1     204 [.      74     259 ..      74     265 .. 0.73

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 1.2e-13
                                       SSEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHH...HHHHHHHHHETTTEHHHHTHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase   1 iktvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakar...sgaltgfatfigrgayaigkp 74 
                                       i+++ fD+ +TL++ +  +e +++ +    ++ l +  e  i+++ ++  +++   + + +g  +     ++++ ++
  gi|242399561|ref|YP_002994986.1|  74 IRLISFDVWNTLLDINVMIENLVKAL----SELLKVP-EEEIAEKTIKTREEIkkiRKSRSGDPE-----KALEESQ 140
                                       78999***********6666666666....2222222.222333333333333222444455555.....9999999 PP

                                       HHHHHHHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHH.HTHHBHTTHHHHHHHHHHTTEEEEEEESSEH....H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....x RF
                         Hydrolase  75 ewltaldippdlgaaigsaqsqgrtvallqaralavftia.dplkvkpeaaeavasLkaagievvlltgdnp....e 146
                                       e+l++                +   ++++  ra+a  t++ d++ v pe++e++++L+  g   ++ t +n     +
  gi|242399561|ref|YP_002994986.1| 141 ELLARA--------------LEVDVEIVK--RAVAKATLSvDERIVLPEVKETLKKLH--GK-YIITTTGNVmfwpS 198
                                       999988..............778888888..9999999999*****************..66.55666666668877 PP

                                       HHH.HHHHHTT.GGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHH.HHH CS
                                       xxx.xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx RF
                         Hydrolase 147 tae.raanqlG.ddyfdaviasdietvakpspegkvaaireLqgkpeevamVGDgvn.Daa 204
                                       t+   +++++G +dy+   + sd+ +  kp +e+++a +r ++++pee +++GD+   D +
  gi|242399561|ref|YP_002994986.1| 199 TYTrLILEKFGlADYITKQFYSDEIKAYKPMKEAFLAPLRYFNVPPEEAIHIGDTKAeDFE 259
                                       777355555***999977777777778***************************9776665 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   1.1e-08     4e-05       4      53 ..     227     276 ..     225     294 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 1.1e-08
                                       TTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESSSSS CS
                    Hydrolase_like   4 KPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVltGvt 53 
                                       KP +e++ + l+ ++++pee + iGD+ a D +gA n G++ + +    +
  gi|242399561|ref|YP_002994986.1| 227 KPMKEAFLAPLRYFNVPPEEAIHIGDTKAEDFEGALNTGMHACWIDPETE 276
                                       9*****************************************98865555 PP

>> dCache_2  Cache domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   1.3e-05     0.048       8     147 ..     101     234 ..      97     246 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.3e-05
                          dCache_2   8 eiekleeetikerkellksevdsaielieyeknsleeslkesLksrveeaysiaeeiyekyknelseeeakklikea 84 
                                       e+ k+ ee+i e++ + ++e++++ ++   + +++ e+ +e L    e  ++i++   +k    ++e  +  ++ke+
  gi|242399561|ref|YP_002994986.1| 101 ELLKVPEEEIAEKTIKTREEIKKIRKSRSGDPEKALEESQELLARALEVDVEIVKRAVAKATLSVDERIVLPEVKET 177
                                       67788899****************************************************777899999******** PP

                          dCache_2  85 lrsirydggegyyfiidskgtlilhpds...psleGknlldlkdkdGryiiremiklakkkgeGfv 147
                                       l++++     g  +ii+++g++++ p +     le   l d+ +k+   ++ ++ik++k  +e f+
  gi|242399561|ref|YP_002994986.1| 178 LKKLH-----GK-YIITTTGNVMFWPSTytrLILEKFGLADYITKQ---FYSDEIKAYKPMKEAFL 234
                                       *****.....55.568888999999998655345554466665555...88899998888888776 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.4   4.7e-05      0.17      11      98 ..      96     181 ..      74     195 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.7e-05
                           DUF1451  11 eeeleelvekakeklseaeeltkeelelvaeylkrDleeaarsleeskeeleewlsldlelieesllealasiaDkt 87 
                                        ++l+el++  +e+++e+   t+ee++++++  + D e+a    ees+e l+  l++d+e++++ + +a +s+ ++ 
  gi|242399561|ref|YP_002994986.1|  96 VKALSELLKVPEEEIAEKTIKTREEIKKIRKSRSGDPEKAL---EESQELLARALEVDVEIVKRAVAKATLSVDERI 169
                                       6789999***********************99999888765...566666678********************9886 PP

                           DUF1451  88 qv.elaelaedl 98 
                                        + e++e  ++l
  gi|242399561|ref|YP_002994986.1| 170 VLpEVKETLKKL 181
                                       542444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1025  (0.0571699); expected 358.6 (0.02)
Passed bias filter:                      644  (0.0359195); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2061.08
//
Query:       gi|242399562|ref|YP_002994987.1|  [L=227]
Description: hypothetical protein TSIB_1587 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.052   13.5   0.5      0.081   12.9   0.5    1.2  1  Prok-RING_1    Prokaryotic RING finger family 1
      0.088   12.5   1.3       0.15   11.8   1.3    1.4  1  A2L_zn_ribbon  A2L zinc ribbon domain
       0.11   12.3   0.2        0.7    9.8   0.0    2.1  2  zf-C2H2_3      zinc-finger of acetyl-transferase ESCO
       0.17   11.9   1.0        8.2    6.5   0.3    2.4  2  Rubredoxin     Rubredoxin


Domain annotation for each model (and alignments):
>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.5   1.8e-05     0.081       3      30 ..     176     203 ..     174     205 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.8e-05
                       Prok-RING_1   3 tgkkCpvCgkelkeedDiVvCpeCgtpy 30 
                                       ++ +CpvC  el+ ed    C +Cg +y
  gi|242399562|ref|YP_002994987.1| 176 NEYRCPVCFSELSVEDGYLKCHTCGFVY 203
                                       6789*********************776 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   1.3   3.4e-05      0.15       2      31 ..     176     203 ..     175     204 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.4e-05
                     A2L_zn_ribbon   2 nlkvCsvCggngilnseqgylvCieCgasf 31 
                                       n++ C vC ++  +  e+gyl C  Cg+++
  gi|242399562|ref|YP_002994987.1| 176 NEYRCPVCFSELSV--EDGYLKCHTCGFVY 203
                                       678899******99..************98 PP

>> zf-C2H2_3  zinc-finger of acetyl-transferase ESCO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.16   7.2e+02      12      19 ..     176     183 ..     170     184 .. 0.74
   2 ?    9.8   0.0   0.00016       0.7      15      28 ..     195     208 ..     186     213 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.16
                         zf-C2H2_3  12 gasqCkeC 19 
                                       ++ +C++C
  gi|242399562|ref|YP_002994987.1| 176 NEYRCPVC 183
                                       4578**** PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00016
                         zf-C2H2_3  15 qCkeCgMvYnpgsp 28 
                                       +C++Cg vY+  s 
  gi|242399562|ref|YP_002994987.1| 195 KCHTCGFVYTGESD 208
                                       6********97665 PP

>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.016        72      34      40 ..     177     183 ..     170     189 .. 0.81
   2 ?    6.5   0.3    0.0018       8.2       3      12 ..     195     204 ..     193     210 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.016
                                       T-BBTTT CS
                        Rubredoxin  34 dWvCPdC 40 
                                       +++CP+C
  gi|242399562|ref|YP_002994987.1| 177 EYRCPVC 183
                                       7999999 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0018
                                       EETTT-BEEE CS
                        Rubredoxin   3 eCkvCgyvYd 12 
                                       +C++Cg+vY 
  gi|242399562|ref|YP_002994987.1| 195 KCHTCGFVYT 204
                                       8********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 1330.37
//
Query:       gi|242399563|ref|YP_002994988.1|  [L=1442]
Description: DNA polymerase II large subunit [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
          0 1232.3   0.1          0 1231.3   0.1    1.5  1  PolC_DP2         DNA polymerase II large subunit DP2
    1.1e-09   38.3   2.4    1.1e-09   38.3   2.4    2.7  2  Intein_splicing  Intein splicing domain
    0.00063   19.7  11.1       0.36   10.8   4.5    3.3  3  zinc-ribbons_6   zinc-ribbons
  ------ inclusion threshold ------
       0.12   12.4  15.8       0.91    9.6   8.6    2.6  2  DZR              Double zinc ribbon
        0.3   11.1  12.9        2.6    8.1   0.1    3.6  2  HypA             Hydrogenase/urease nickel incorporation, met
        1.1    9.9   9.5         16    6.1   5.6    2.7  2  zf-CHY           CHY zinc finger
        2.3    8.4  23.3        2.7    8.2   1.8    3.9  3  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 ! 1231.3   0.1         0         0       1     864 []      10     948 ..      10     948 .. 0.97

  Alignments for each domain:
  == domain 1  score: 1231.3 bits;  conditional E-value: 0
                          PolC_DP2   1 eYfeklekeleeayeiaekarskgldpkeevEiplAkdladRvekllgikgvaerirelekelsreevalkiakeia 77 
                                       +Yfe l++e+++ayeiaekars+g+dp++e+E+p A+d+a Rve+l+g+kgvaerir+l ke+++e +alk+++ei+
  gi|242399563|ref|YP_002994988.1|  10 KYFEFLQREIDKAYEIAEKARSQGKDPTQEIEVPQATDMAGRVESLVGPKGVAERIRSLVKEYGKELAALKVVDEII 86 
                                       6**************************************************************************** PP

                          PolC_DP2  78 egkvgeaeskeeavdkavrtalalltegvvaAPleGiakvkikknddgteylkvyyaGPiRsaGGtaqalsvLvaDy 154
                                       egk++++e+ke+ +d+ vrtala+lteg+v+APleGia+vkikkn+dgt+yl+vyyaGPiRs+GGtaqalsvLv+Dy
  gi|242399563|ref|YP_002994988.1|  87 EGKFKKFENKEQLADQCVRTALAILTEGIVSAPLEGIADVKIKKNEDGTNYLAVYYAGPIRSSGGTAQALSVLVGDY 163
                                       ***************************************************************************** PP

                          PolC_DP2 155 vrkklgldrykpreeeieRyveEielYer.vaslqyspsdeeirlivknipveidGeatedeevsgyrdlervetnr 230
                                       vrkklgldr+k +ee++eRyveEi+lY+r v++lqy ps++e+rl+v+nip+ei+Ge+t+++evs +r+++ vetn 
  gi|242399563|ref|YP_002994988.1| 164 VRKKLGLDRFKLTEEHVERYVEEIDLYHRaVTRLQYYPSPDEVRLAVRNIPIEITGETTDNVEVS-HRNVPGVETNY 239
                                       *****************************************************************.*********** PP

                          PolC_DP2 231 vRGGmllvlaeGialkakKikkkvkklklegWewleelikaekeekkeeeeek........................ 283
                                       +RGG++lv+aeG+++ka+K+ k+++k++++gWewl+e+++a+++ k++e+eek                        
  gi|242399563|ref|YP_002994988.1| 240 LRGGAILVIAEGVLQKANKLVKYIDKMGIDGWEWLKEFVEAKEKGKSDEKEEKaleesktetavgettkikkgfyhe 316
                                       *****************************************99999999999999********************** PP

                          PolC_DP2 284 ......kevkpkekylrdliaGRpvlshpsrkGGfRLrYGRsrntglatagihPatmelldeflavGtqlkverPgK 354
                                             ++++p++ky +++i+GRp+++ ps++GGfRLrYGRsr +g+at++i+Pa+m ++deflavGtq+k+erPgK
  gi|242399563|ref|YP_002994988.1| 317 lyeklkATISPNAKYTKEIIGGRPLFAEPSTNGGFRLRYGRSRVSGFATWSINPAVMIMVDEFLAVGTQMKTERPGK 393
                                       *****999********************************************************************* PP

                          PolC_DP2 355 aaavvpvdsiegPtvklknGdvvriddveealeikkeveeildlGeiLvayGeflennhpLvpasyveewwiqelek 431
                                       +++v+p ++iegP+vklk+G+vvr+dd ++ale+k++veeil+lG+ L+a+G+f+enn++L+pa+yveewwiqel +
  gi|242399563|ref|YP_002994988.1| 394 GCIVTPASTIEGPIVKLKDGSVVRVDDYHKALELKDRVEEILYLGDALIAFGDFVENNQTLLPANYVEEWWIQELVE 470
                                       ***************************************************************************** PP

                          PolC_DP2 432 aaakkeaee....................................kpsaeealelseeldvpLhPkytylwhdisve 472
                                       +++++ + e                                    kp++eeal+ls+ l++pLhP yt++w++++ve
  gi|242399563|ref|YP_002994988.1| 471 TVNDVYELElrpfqenerdsveeaadyldiepetlakllydplvtKPTIEEALHLSNILKIPLHPYYTLYWNTLTVE 547
                                       ****99999******************************************************************** PP

                          PolC_DP2 473 elekLaeavaekkkl..........eeeklvleleeevkeiLekllvehkvkeekivi..eealallkslgldleee 537
                                       el kL++a+ ++++           ++ ++ le+   +k++Le l+veh ++++++++    a+a+l+ l   +  +
  gi|242399563|ref|YP_002994988.1| 548 ELIKLQNALVNATIEwgeyrgfryaKRLEISLETLGGAKRYLELLGVEHIIEGDTVIVdyPWAAAVLTPLANLE--K 622
                                       **********999779999888854333444444445*********************5433444555554433..4 PP

                          PolC_DP2 538 klekeeekdalelvnelsglevrekaptrigaRmGRPeKskeRkmkpavhvLfpigeaggkrrsvkeaakkkgeiev 614
                                       k+e +e +++++l+ne+s++++r++  + ig+RmGRPeK+keRkmkp+vhvLfpig agg++r++ +aa++ ++ +v
  gi|242399563|ref|YP_002994988.1| 623 KIEFKEFHTPIDLINEISDIKLRDRGISWIGSRMGRPEKAKERKMKPPVHVLFPIGLAGGNSRDIYKAAQEGKTSDV 699
                                       555567789*************************************************************66666** PP

                          PolC_DP2 615 eiarrkCkkCgketlearCeeCgekteeklvCkkceeeve.eekcekcekeakavkkkkidlkellekaleklgere 690
                                       eia+ kC++Cg+  +  +C+eCge+ +  ++C+kc+ e+  + +c+kc+ e+k +k+++i  +ell++a++++g+  
  gi|242399563|ref|YP_002994988.1| 700 EIAHFKCTSCGHVDIFPTCPECGEEAKLLYHCPKCGFESIlDTRCPKCDIEMKPYKRRRISPSELLNSAMQNVGI-- 774
                                       ************************************98886899*******************************.. PP

                          PolC_DP2 691 ekleelkgvkgltskekipEpleKgilRakhdvsvfkdgtvRyDmtdlplthfrpkeigvsveklrelGYteDieGk 767
                                        +l++lkgv+g+ s +ki+EpleKgilRa++dv+vfkdgt+R+D+td+p+thf+pkeigvs+ekl+elGYt+D+eGk
  gi|242399563|ref|YP_002994988.1| 775 YTLDKLKGVMGMSSAHKIAEPLEKGILRARNDVYVFKDGTIRFDATDAPITHFKPKEIGVSIEKLKELGYTHDFEGK 851
                                       78*************************************************************************** PP

                          PolC_DP2 768 plesedqivelkvqDivlsedaaeyllkvakfvDdlLeklyglerfYnvekkedLiGklviglaPHtsagvlgRiiG 844
                                       pl+s dqi+elkvqDi+ls++a++yl+kvakfvDdlL+k+ygl+rfYnvek+edLiG+lviglaPHtsag++gRiiG
  gi|242399563|ref|YP_002994988.1| 852 PLVSGDQILELKVQDIILSKEAGRYLVKVAKFVDDLLDKVYGLPRFYNVEKMEDLIGHLVIGLAPHTSAGIIGRIIG 928
                                       ***************************************************************************** PP

                          PolC_DP2 845 ftkasvgyahPyfHaakRRn 864
                                       f++a vgyahPy+HaakRRn
  gi|242399563|ref|YP_002994988.1| 929 FVDALVGYAHPYYHAAKRRN 948
                                       *******************9 PP

>> Intein_splicing  Intein splicing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.2   0.5       5.8   1.5e+04      14      50 ..     276     318 ..     272     326 .. 0.54
   2 !   38.3   2.4   4.5e-13   1.1e-09      12     133 ..     969    1113 ..     961    1114 .. 0.82

  Alignments for each domain:
  == domain 1  score: -4.2 bits;  conditional E-value: 5.8
                                       HHCC......ECTTEEEEEETTTTEEEEEEEEEEEEEEEEEEE CS
                                       xxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Intein_splicing  14 elve......kegeevlslnledlklevksvkkliklklkely 50 
                                       e+ve      ++++e+ +l++++ +  v + +k+ k  ++ely
  gi|242399563|ref|YP_002994988.1| 276 EFVEakekgkSDEKEEKALEESKTETAVGETTKIKKGFYHELY 318
                                       5555444444555566666666665555554444444444444 PP

  == domain 2  score: 38.3 bits;  conditional E-value: 4.5e-13
                                        HHHHCC.................ECTTEEEEEETTTTEEEEEEEEEEEEEEEE.EEEEEEETTS-EEEEETT-EE CS
                                        xxxxxx.................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                   Intein_splicing   12 ieelve.................kegeevlslnledlklevksvkkliklklk.elyeiklesgrkikaTpeHkl 68  
                                        ++el+e                 k + +v s + e+ k+    ++ +ik  ++ +l++ +le gr+  +T +H++
  gi|242399563|ref|YP_002994988.1|  969 LKELYElfedehyenmvyvrkkpKADIKVYSFDPETGKVVLTDIEDVIKAPITdHLIRFELELGRSFETTIDHPV 1043
                                        5555555556666677777777788889999999999999999**********9********************* PP

                                        EECCTTEEEEEECCC--TT-EEEEE...HSCEEEEEEEEEEEEEC.EEEEEEEEETTT-EEEE.CTTEEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx.xxxxxx RF
                   Intein_splicing   69 lvvrdegivEkradeLkegdliavp...dadvvwdkvksievede.eeyVYdltvednhNFva.ngiivH 133 
                                        lv+++++   kra e+ke+d+++v    d+  +   +k+ie  +   + V++l+ +++hN +  ++i+ H
  gi|242399563|ref|YP_002994988.1| 1044 LVYENGKFFKKRAFEVKESDIMVVIdesDSKPLKITIKKIEFVKPtGDFVFSLNAKNYHNVLInENIVTH 1113
                                        ***99***************999874333335667788888665525679***********997888899 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   4.5   0.00014      0.36      15      49 ..     702     735 ..     688     736 .. 0.80
   2 !    7.5   1.5    0.0016         4      17      40 ..     729     752 ..     724     756 .. 0.87
   3 !    7.6   0.0    0.0014       3.6      14      63 ..    1278    1330 ..    1263    1333 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00014
                                       SEEE-TTT--EEEEEEE-SSS-S---EEEETTEEE CS
                    zinc-ribbons_6  15 eqyhCeaCqedlkkealCpeCeqelevlkaCgavd 49 
                                       ++++C +C  +++  ++CpeC++e + l  C + +
  gi|242399563|ref|YP_002994988.1| 702 AHFKCTSCG-HVDIFPTCPECGEEAKLLYHCPKCG 735
                                       7999****7.6999************999997755 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0016
                                       EE-TTT--EEEEEEE-SSS-S--- CS
                    zinc-ribbons_6  17 yhCeaCqedlkkealCpeCeqele 40 
                                       yhC +C  +    + Cp+C+ e++
  gi|242399563|ref|YP_002994988.1| 729 YHCPKCGFESILDTRCPKCDIEMK 752
                                       9******************98776 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0014
                                        SSEEE-TTT--EEEE...EEE-SSS-S---EEEETTEEEE--TTTT----TTS CS
                    zinc-ribbons_6   14 geqyhCeaCqedlkk...ealCpeCeqelevlkaCgavdyfCnkcneLiSkkr 63  
                                         ++++C +C++++++      C +C+ ++      ga++ +  +++ L +k +
  gi|242399563|ref|YP_002994988.1| 1278 RQEFRCVKCNTKYRRpplRGKCTKCGGKIVLTVSKGAIEKYLPTAKMLVAKYN 1330
                                        4799*******998722245799**9999888888887766666666666655 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   8.6   0.00036      0.91       1      48 [.     706     747 ..     703     756 .. 0.84
   2 ?    6.6   0.7    0.0031       8.1      12      37 ..    1280    1305 ..    1274    1310 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00036
                               DZR   1 CpqCgeelppdarfCseCgtklkavaaedrCpsCgekvdpearfCpeC 48 
                                       C +Cg+   +   +C+eCg++ k     ++Cp+Cg +  +++r Cp+C
  gi|242399563|ref|YP_002994988.1| 706 CTSCGHV--DIFPTCPECGEEAKL---LYHCPKCGFESILDTR-CPKC 747
                                       8888887..77889*****99774...7999999999999855.8888 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0031
                               DZR   12 arfCseCgtklkavaaedrCpsCgek 37  
                                           C +C+tk ++++   +C +Cg k
  gi|242399563|ref|YP_002994988.1| 1280 EFRCVKCNTKYRRPPLRGKCTKCGGK 1305
                                        55699*****9999999******966 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   9.6      0.52   1.3e+03      72      95 ..     717     737 ..     690     755 .. 0.64
   2 ?    8.1   0.1     0.001       2.6      68      97 ..    1278    1307 ..    1226    1316 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.52
                                       EETTTS-EEECHHHHHS-TTTSSS CS
                              HypA  72 rCreCgkefeleekalrCpkCgsa 95 
                                       +C eCg+e +l    ++CpkCg +
  gi|242399563|ref|YP_002994988.1| 717 TCPECGEEAKLL---YHCPKCGFE 737
                                       566666555544...346666544 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.001
                                        --EEEETTTS-EEECHHHHHS-TTTSSS-E CS
                              HypA   68 pvkvrCreCgkefeleekalrCpkCgsadv 97  
                                        + ++rC +C+++++    + +C kCg++ v
  gi|242399563|ref|YP_002994988.1| 1278 RQEFRCVKCNTKYRRPPLRGKCTKCGGKIV 1307
                                        568999999999996653678999998744 PP

>> zf-CHY  CHY zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   5.6    0.0061        16      33      73 ..     695     735 ..     687     749 .. 0.81
   2 ?    4.4   0.1     0.021        55      34      62 ..    1273    1304 ..    1264    1324 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0061
                            zf-CHY  33 elerlevkevlcllCeteqekavlCkkCkkefa.eyfCpiCk 73 
                                       +++ +e+ +++c+ C ++ ++  +C +C++e++  y+Cp+C 
  gi|242399563|ref|YP_002994988.1| 695 KTSDVEIAHFKCTSCGHV-DIFPTCPECGEEAKlLYHCPKCG 735
                                       66778889999****998.77889****997662577**996 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.021
                            zf-CHY   34 lerlevkevlcllCeteq...ekavlCkkCkk 62  
                                        l+ ++ +e+ c++C+t+    +   +C+kC+ 
  gi|242399563|ref|YP_002994988.1| 1273 LRSFTRQEFRCVKCNTKYrrpPLRGKCTKCGG 1304
                                        56677889999999997633344556999976 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   5.1    0.0087        22       6      36 ..     704     725 ..     703     727 .. 0.80
   2 ?    8.2   1.8     0.001       2.7       6      33 ..     729     748 ..     728     752 .. 0.86
   3 ?    4.9   1.6     0.011        29       5      35 ..    1280    1305 ..    1280    1307 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0087
                       Zn-ribbon_8   6 YrCeeCghefevlqsisdapltaCPeCgsev 36 
                                       ++C++Cg   +++        ++CPeCg+e+
  gi|242399563|ref|YP_002994988.1| 704 FKCTSCG-HVDIF--------PTCPECGEEA 725
                                       89*****.66644........67*****976 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.001
                       Zn-ribbon_8   6 YrCeeCghefevlqsisdapltaCPeCg 33 
                                       Y+C +Cg  fe +       +t CP+C 
  gi|242399563|ref|YP_002994988.1| 729 YHCPKCG--FESIL------DTRCPKCD 748
                                       9******..99776......788****5 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.011
                       Zn-ribbon_8    5 eYrCeeCghefevlqsisdaplta.CPeCgse 35  
                                        e+rC +C++++       ++pl   C +Cg++
  gi|242399563|ref|YP_002994988.1| 1280 EFRCVKCNTKYR------RPPLRGkCTKCGGK 1305
                                        8*******7777......5677777****985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1442 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1356  (0.0756317); expected 358.6 (0.02)
Passed bias filter:                      706  (0.0393775); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 1.20u 0.36s 00:00:01.56 Elapsed: 00:00:00.59
# Mc/sec: 7358.59
//
Query:       gi|242399564|ref|YP_002994989.1|  [L=660]
Description: DNA polymerase II, small subunit [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-15   56.7   0.0    3.5e-15   55.9   0.0    1.3  1  DNA_pol_E_B    DNA polymerase alpha/epsilon subunit B
    1.9e-11   44.9   0.3    3.5e-11   44.0   0.3    1.4  1  Metallophos    Calcineurin-like phosphoesterase
    4.6e-06   26.9   0.0    1.2e-05   25.6   0.0    1.6  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
  ------ inclusion threshold ------
      0.071   13.1   0.3        2.5    8.2   0.0    3.0  3  DUF4974        Domain of unknown function (DUF4974)
        3.8    7.8   6.6         13    6.0   6.6    2.0  1  DUF2072        Zn-ribbon containing protein


Domain annotation for each model (and alignments):
>> DNA_pol_E_B  DNA polymerase alpha/epsilon subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.9   0.0   9.7e-19   3.5e-15       3     203 ..     396     598 ..     394     602 .. 0.86

  Alignments for each domain:
  == domain 1  score: 55.9 bits;  conditional E-value: 9.7e-19
                                       EEES--S-TT---...-HHHHHHHHHHH.......HTT--SEEEEES-SSBTTSHHHHHT---S--SSHHHHHHHHT CS
                       DNA_pol_E_B   3 ivsglnldndnrs...leaLrkiLqgya......peesppdvlilaGnfvdaahkaiasskvstdekkenfdalall 70 
                                       ++s++++ +d++    + ++ ++L+g+       +  s+++ li+aG  vd        ++ ++ +  + fd  ++l
  gi|242399564|ref|YP_002994989.1| 396 LISDIHVGSDKFCekaFMKFIEWLNGHVnskaeeEIVSRIKYLIIAGDVVDGIGIYP--GQYNELSIPDIFDQYEAL 470
                                       78888888777775555555555555558887655568999**********444333..44446899999******* PP

                                       HHHHTTS-TTSEEEEE--TTBTT-S-SBSB----TTTTT--TTT...EEE--BSEEEEETTEEEEE--S-HHHH--- CS
                       DNA_pol_E_B  71 lsilesllekttvvlvPgpnDpanstvlPqqPlprlllsrikrvfkelklvtNPsrielnsvevvltsddivkdlkr 147
                                        + l+++  ++t+++ Pg  D+a   +lPq+ + r + + + +  k++++++NP  i+l + e++++ +  ++d+  
  gi|242399564|ref|YP_002994989.1| 471 ANLLSNVPDHITMFIGPGNHDAARM-ALPQPEFYRDYAKPLYEL-KNAVIISNPAVIDLHGREFLIVHGRGIEDVVS 545
                                       *************************.**********88888885.89****************************** PP

                                       EEESHHHHHS-HHHHHHHHHHHHTBS---SS--B-GGGGGGGB-GGG---SEEE-- CS
                       DNA_pol_E_B 148 eslkesntdverlrklvktildqrhlaPlaptlrpvswdkddalvleplPdvlvlp 203
                                       ++ + s+   ++  k +  +l+ rh+aP++   +p+  d  d lv+e++Pd++ ++
  gi|242399564|ref|YP_002994989.1| 546 YVPNMSH---HQPVKPMVELLKLRHVAPTFGGKVPIAPDSEDLLVIESVPDLVQMG 598
                                       *******...688888889********************************98766 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.0   0.3   9.7e-15   3.5e-11       4     203 ..     395     602 ..     394     603 .. 0.63

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 9.7e-15
                                       EEEESBTB...TTCCTHHHHHHHHHHHH......HHH.....TTESEEEEESTSSSSS................HHH CS
                       Metallophos   4 lvigDlHl...algggqlddllkllddl......lre.....ekpdlvllaGDlvdrg................dle 50 
                                       ++i+D+H+   +    +  +++k++++l      +       +++ ++++aGD+vd+                 d  
  gi|242399564|ref|YP_002994989.1| 395 ALISDIHVgsdK---FCEKAFMKFIEWLnghvnsK-AeeeivSRIKYLIIAGDVVDGIgiypgqynelsipdifDQY 467
                                       689*****5555...55555555555553335541.04566778899999*******88999999999777655444 PP

                                       HHHHHHHHHHHHHTSEEEEEC-TTS.........CHHH.HHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEE CS
                       Metallophos  51 kellellaalvkypipvylllGNHe.........gfee.ellnkygylgifsepwrsdaevfnnlplaslgsgslkv 117
                                       ++l++ll+ + + +i  ++ +GNH+          f+    +         +    ++a   +n+ +++l++   ++
  gi|242399564|ref|YP_002994989.1| 468 EALANLLSNVPD-HITMFIGPGNHDaarmalpqpEFYRdYAK---------PLYELKNAVIISNPAVIDLHGR--EF 532
                                       445555555555.5777********55444333333332222.........2222334889999999999999..** PP

                                       EEEESECEEETHHHHHHHHHHHSCHHHHCCHHHHHHHHHHTTCSEEEEEESSESSCSSSCSCCHHHHHHH.HHHTTE CS
                       Metallophos 118 lllhGgspellvsldklgslnleleapepgdewlkdlekrekadwvivlgHsplyrgsgylfgdealedl.lkkygv 193
                                       l++hG  +e+   ++ + + +++++++    e+lk               H+ ++  +g++   +  edl   +  +
  gi|242399564|ref|YP_002994989.1| 533 LIVHGRGIED--VVSYVPNMSHHQPVKPM-VELLKL-------------RHVAPT-FGGKVPIAPDSEDLlVIESVP 592
                                       ******5444..44444444444444333.444444.............677777.555555555555563777779 PP

                                       SEEEEESSSS CS
                       Metallophos 194 dlvisGHtHv 203
                                       dlv +GH+Hv
  gi|242399564|ref|YP_002994989.1| 593 DLVQMGHVHV 602
                                       *********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 !   25.6   0.0   3.3e-09   1.2e-05       4     149 ..     395     622 ..     393     644 .. 0.75

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 3.3e-09
                     Metallophos_2   4 aiiSDlH.................snldaleavlealkevgvdaiihaGD...........leeeep.......... 42 
                                       a+iSD+H                  n++   ++ e++ +  + ++i aGD           +               
  gi|242399564|ref|YP_002994989.1| 395 ALISDIHvgsdkfcekafmkfiewLNGHVNSKAEEEIVSR-IKYLIIAGDvvdgigiypgqY----Nelsipdifdq 466
                                       789*****99999998777777776666677778888888.99*******666666555551....04444444433 PP

                     Metallophos_2  43 .evleellela....pvlaVrGNnDeevveedvlreaaelgtdl.............peeaelelagekvlliHgdp 101
                                        e+l++ll+       + + +GN+D   ++++ l +++++++ +              + a+++l g+++l++Hg  
  gi|242399564|ref|YP_002994989.1| 467 yEALANLLSNVpdhiTMFIGPGNHD---AARMALPQPEFYRD-YakplyelknaviiSNPAVIDLHGREFLIVHGRG 539
                                       334444444337666888889****...44444444444443.3377777777778879999999**********98 PP

                     Metallophos_2 102 l....................................gvkdalaellkeaeegsdvvvcGHtHvpevekeggvlvvn 142
                                                                              + + ++ll   e++ d+v +GH Hv   +  +gv ++n
  gi|242399564|ref|YP_002994989.1| 540 IedvvsyvpnmshhqpvkpmvellklrhvaptfggkvPIAPDSEDLLVI-ESVPDLVQMGHVHVLDYQIYRGVFLIN 615
                                       8********************************6655444445555544.88899********************** PP

                     Metallophos_2 143 PGsvgep 149
                                        G  + +
  gi|242399564|ref|YP_002994989.1| 616 SGTWQAQ 622
                                       **98776 PP

>> DUF4974  Domain of unknown function (DUF4974)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.23   8.3e+02      16      51 ..      23      58 ..      22      59 .. 0.82
   2 ?    0.0   0.1      0.24   8.8e+02      20      40 ..     193     213 ..     187     220 .. 0.81
   3 ?    8.2   0.0   0.00069       2.5       8      29 ..     224     245 ..     221     255 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.23
                                      HHHHHT--EEE-TTS----EEEEEE.S-.-.HHHHHH CS
                           DUF4974 16 LerwYnveivieneelknyrftgtf.srnesleevLe 51
                                      L+ +Yn ++ +  e +k  + +gtf  ++ + ee+L+
  gi|242399564|ref|YP_002994989.1| 23 LSEHYNKDFALP-ELIKFAKARGTFvIDQITAEEFLK 58
                                      899********9.889999999999666668888776 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.24
                                       HT--EEE-TTS----EEEEEE CS
                           DUF4974  20 Ynveivieneelknyrftgtf 40 
                                       Y+v iv e ee+ +++ t ++
  gi|242399564|ref|YP_002994989.1| 193 YGVPIVAEEEEIPEEKKTYSV 213
                                       ********9999999866654 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.00069
                                       EHHHHHHHHHHHHT--EEE-TT CS
                           DUF4974   8 sLeeilkkLerwYnveiviene 29 
                                        +e i+k +e +Yn++++++n 
  gi|242399564|ref|YP_002994989.1| 224 GFEFIAKSIESKYNIKFDVRNV 245
                                       5889**************9985 PP

>> DUF2072  Zn-ribbon containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   6.6    0.0038        13      28      96 ..      70     136 ..      68     192 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0038
                           DUF2072  28 kkFlyvkeeekkedvseekeelvaeaeeeieevldaeeteeeklekkekekaekekeeedrvesvrile 96 
                                       +kFl+v+++ek+e  +ee e+   e+++++  v  a e  ee   ++e++k+++ +ee++ ve  ++le
  gi|242399564|ref|YP_002994989.1|  70 EKFLFVEKSEKAEGITEEAEQRALETSGTVGAVETATEIVEES--VEESSKTSTISEETEVVEKAQVLE 136
                                       79***********999999988888887766664444444443..334566666677777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (660 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       870  (0.0485247); expected 358.6 (0.02)
Passed bias filter:                      574  (0.0320152); 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: 0.87u 0.33s 00:00:01.20 Elapsed: 00:00:00.58
# Mc/sec: 3418.11
//
Query:       gi|242399565|ref|YP_002994990.1|  [L=420]
Description: Cell division control like protein [Thermococcus sibiricus MM 739]
Scores for complete 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   88.7   0.1    4.6e-25   87.4   0.1    1.7  1  Cdc6_C           CDC6, C terminal winged helix domain
    1.2e-09   38.8   0.0    1.5e-08   35.2   0.0    2.4  1  AAA_16           AAA ATPase domain
    5.2e-09   36.6   0.1    2.1e-08   34.7   0.0    2.0  2  AAA              ATPase family associated with various cellul
    3.1e-08   34.0   0.0    2.1e-07   31.3   0.0    2.1  2  AAA_22           AAA domain
    5.2e-05   22.7   0.0    0.00013   21.4   0.0    1.7  1  TniB             Bacterial TniB protein
    0.00022   20.5   0.1    0.00046   19.5   0.1    1.5  1  NB-ARC           NB-ARC domain
    0.00033   20.6   3.2     0.0017   18.3   3.2    2.1  1  ATPase_2         ATPase domain predominantly from Archaea
     0.0021   17.1   0.0     0.0033   16.4   0.0    1.3  1  Kinesin          Kinesin motor domain
     0.0046   16.7   0.9        1.1    9.0   0.0    2.4  2  DEAD             DEAD/DEAH box helicase
     0.0058   15.5   0.6      0.032   13.0   0.0    2.0  2  AAA_32           AAA domain
     0.0092   15.3   0.0      0.014   14.7   0.0    1.3  1  DUF2075          Uncharacterized conserved protein (DUF2075)
     0.0097   15.8   0.0      0.026   14.5   0.0    1.8  1  Microtub_bd      Microtubule binding
  ------ inclusion threshold ------
      0.011   15.4   0.5      0.024   14.4   0.5    1.6  1  AAA_24           AAA domain
      0.011   15.8   0.0      0.066   13.3   0.0    2.2  2  AAA_2            AAA domain (Cdc48 subfamily)
      0.012   14.8   0.0      0.047   12.8   0.0    1.9  2  DUF815           Protein of unknown function (DUF815)
      0.017   15.4   0.3      0.071   13.5   0.0    2.1  2  AAA_assoc_2      AAA C-terminal domain
       0.03   14.3   0.0      0.091   12.7   0.0    1.9  1  NACHT            NACHT domain
      0.035   14.2   0.1       0.15   12.1   0.0    2.1  2  DUF87            Helicase HerA, central domain
      0.036   13.8   0.0       0.13   11.9   0.0    1.9  2  Sigma54_activat  Sigma-54 interaction domain
      0.036   13.2   0.0      0.072   12.3   0.0    1.4  1  PIF1             PIF1-like helicase
      0.083   13.3   0.0       0.19   12.1   0.0    1.6  1  RNA_helicase     RNA helicase
       0.11   12.0   0.0        0.2   11.1   0.0    1.3  1  AAA_7            P-loop containing dynein motor region
       0.12   12.9   0.4        1.2    9.7   0.1    2.5  2  AAA_18           AAA domain


Domain annotation for each model (and alignments):
>> Cdc6_C  CDC6, C terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.4   0.1   5.9e-28   4.6e-25       1      82 [.     315     394 ..     315     396 .. 0.97

  Alignments for each domain:
  == domain 1  score: 87.4 bits;  conditional E-value: 5.9e-28
                                       HHHHHHHHCHCSSS-EEHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEESSS CS
                            Cdc6_C   1 LcalvlllrksgkeevttgevyevYkslCesegvdpltqrevsdllseLemlgileleksskGrregrtrkisLnvd 77 
                                       L+a+vll + +g+ ++ tg+vy  Y++lCe ++++pltqr++sdl++eL+mlgi++++++skGr +grt++i+Ln+ 
  gi|242399565|ref|YP_002994990.1| 315 LYAIVLLDE-NGELPANTGDVYSIYRELCEYLDLEPLTQRRISDLINELDMLGIVNAKVVSKGR-YGRTKEIRLNIT 389
                                       89*****99.*****************************************************9.***********9 PP

                                       CHHHH CS
                            Cdc6_C  78 pddvl 82 
                                       p +v+
  gi|242399565|ref|YP_002994990.1| 390 PYKVK 394
                                       98887 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.0     2e-11   1.5e-08       2     161 ..      38     178 ..      37     190 .. 0.65

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 2e-11
                            AAA_16   2 lvGReeeleqLlsalervrsgrp.elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqala 77 
                                       l+ R+e++e+L ++l +v +g++ ++++++G  G+GK+  vr + + l k     +++k+d           ++++ 
  gi|242399565|ref|YP_002994990.1|  38 LPHRREQVETLVHILVPVLRGETpSNIFVYGKTGTGKTVTVRYVTEDLIK-----ISQKYDIP---------VDVIY 100
                                       889******************************************96665.....45555555.........22221 PP

                            AAA_16  78 .reellrqlldeaesaeleawrekleealaavpelagaeasrllellkrllallsrderplvlvlDdlqwadeaslq 153
                                        + e++    +   ++ ++++re+   ++     l g     ++++lk++++    +er l++vlD+++++   s +
  gi|242399565|ref|YP_002994990.1| 101 lNCEIIDTQYRV-LANIVNYFREESGVEVP----LVGWPTDEVYAQLKKAVD---MKERFLIIVLDEIDKLVKKSGD 169
                                       011233333222.22244444444333333....333333778888899883...2366899999999966554444 PP

                            AAA_16 154 l.laaLlrl 161
                                         l++L r 
  gi|242399565|ref|YP_002994990.1| 170 DvLYSLTRI 178
                                       438888775 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 !   34.7   0.0   2.7e-11   2.1e-08       2     120 ..      65     207 ..      64     218 .. 0.78
   2 ?   -1.9   0.0       5.4   4.2e+03      38      70 ..     295     327 ..     273     346 .. 0.59

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 2.7e-11
                                       EEESSTTSSHHHHHHHHHHHH.......T..HEEEEEETTTCSSS....................STTHHHHHHHHH CS
                               AAA   2 llyGppGtGKTllakavakel.......g..vefleisgsellsk....................yvgesekkirel 49 
                                        +yG  GtGKT +++ v ++l       +  v+++ +++  +  +                    +vg   +++ + 
  gi|242399565|ref|YP_002994990.1|  65 FVYGKTGTGKTVTVRYVTEDLikisqkyDipVDVIYLNCEIIDTQyrvlanivnyfreesgvevpLVGWPTDEVYAQ 141
                                       69******************765554431336677777766665567777788888888888888888888888888 PP

                                       HHHHHHTS.TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS...GGGSTHHHH CS
                               AAA  50 fkeakeka.kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnr...pdkldpall 120
                                       +k+a  ++ +  i+++DEid+l+k++       +++v+  L +   ++k+  +kv +ig++n+    + ldp +l
  gi|242399565|ref|YP_002994990.1| 142 LKKAVDMKeRFLIIVLDEIDKLVKKS-------GDDVLYSLTRINTELKN--AKVSIIGISNDlrfKEYLDPRVL 207
                                       88887777445***************.......99999999999999988..69********9776666777666 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 5.4
                                       STTHHHHHHHHHHHHHHHTSTS.EEEEEETGGGH CS
                               AAA  38 yvgesekkirelfkeakekakp.silfiDEidal 70 
                                       + +++++++ +++   ++      i+++DE  +l
  gi|242399565|ref|YP_002994990.1| 295 IEQDTMEEVIKTLPLHSKIL-LyAIVLLDENGEL 327
                                       34444444444443333333.3388888886665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.0   2.6e-10   2.1e-07       4     131 ..      60     193 ..      57     199 .. 0.82
   2 ?   -0.4   0.0       1.7   1.3e+03      49      79 ..     329     359 ..     309     368 .. 0.79

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 2.6e-10
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee.erpevvfvtlpsstsskdllrellralglelka....erlss 75 
                                       t + ++v+G +GtGKT+++r ++e l + +++++  +++v++ ++    ++  +l ++++ + +e        +  +
  gi|242399565|ref|YP_002994990.1|  60 TPSNIFVYGKTGTGKTVTVRYVTEDL-IKISQKYdIPVDVIYLNCEIIDTQYRVLANIVNYFREESGVevplVGWPT 135
                                       66789*******************98.667777699***********************999976666888877889 PP

                            AAA_22  76 eellealeqalraravielliiDEaqhlr..s.eealeeLrsllnlsrkgvqliLvGtp 131
                                       +e++++l +a++ + +  ++++DE+++l   s +++l  L ++ n + k+ ++ ++G  
  gi|242399565|ref|YP_002994990.1| 136 DEVYAQLKKAVDMKERFLIIVLDEIDKLVkkSgDDVLYSLTRI-NTELKNAKVSIIGIS 193
                                       999999999999999999*********9876368888888333.335777777777765 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.7
                            AAA_22  49 sst.sskdllrellralglelkaerlsseell 79 
                                       + t +  +++rel++ l+le  +   + ++l+
  gi|242399565|ref|YP_002994990.1| 329 ANTgDVYSIYRELCEYLDLEPLT-QRRISDLI 359
                                       44458899999999999998888.55555555 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   1.7e-07   0.00013      24     159 ..      50     191 ..      37     198 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.7e-07
                              TniB  24 eeLleypkrkrmpnlllvGdsnnGKtmivekFarlhppekdedaekvpvlvvqappkpdekrlyaaiLealgaplka 100
                                       + L+ + + + ++n+ ++G++ +GKt+ v+  +++  + +++ +  v+v+++++    ++ r  a+i++ ++++   
  gi|242399565|ref|YP_002994990.1|  50 HILVPVLRGETPSNIFVYGKTGTGKTVTVRYVTEDLIKISQKYDIPVDVIYLNCEIIDTQYRVLANIVNYFREESGV 126
                                       4455566777889****************9999999999999999***************************99888 PP

                              TniB 101 ra.....rvskleqqvlrllrelkvr..vLiiDEihnllagsarkqreflnalksLgnelkipivl 159
                                       +       +++ ++q  +   ++k r  ++++DEi++l++ s ++    l  + +   + k++i++
  gi|242399565|ref|YP_002994990.1| 127 EVplvgwPTDEVYAQLKKAV-DMKERflIIVLDEIDKLVKKSGDDVLYSLTRINTELKNAKVSIIG 191
                                       86322224444444443333.34555225667*******888777666666666655556666665 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.1   5.9e-07   0.00046      18     112 ..      61     160 ..      42     175 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 5.9e-07
                                       SCSEEEEEEESTTSSHHHHHHHHCCSHCCCCCCBT...EEEEEEEESXXHHHHHHHXXHHHHHCCCTTSSSS-STTS CS
                            NB-ARC  18 lqslvvalvGmgGvGKttlakqilnksdevegrFd...svawvvvsktdkseeiletilkeLslseddleekeeves 91 
                                       +    ++++G+ G GKt+ ++ + +++ ++ +++d    v+++     d+++++l +i++ + ++ +  e    + +
  gi|242399565|ref|YP_002994990.1|  61 PS--NIFVYGKTGTGKTVTVRYVTEDLIKISQKYDipvDVIYLNCEIIDTQYRVLANIVNYFREE-SGVEVPLVGWP 134
                                       44..699****************************433356667778899999999999999555.55554433332 PP

                                       ...HHHHHHHHCCCT.TEEE.EEEEE CS
                            NB-ARC  92 ...lkrklvrlLltk.rfll.vlDDV 112
                                             +l ++   k rfl+ vlD +
  gi|242399565|ref|YP_002994990.1| 135 tdeVYAQLKKAVDMKeRFLIiVLDEI 160
                                       34478888888888888875256655 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   3.2   2.2e-06    0.0017      13     154 ..      54     184 ..      41     238 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.2e-06
                          ATPase_2  13 eilerepneiyfiYGpegsGKtaLlkeiienledkdk......yviyyialreesiskldefieeeeekkklekalg 83 
                                        +l+ e+ + +f+YG  g GKt  ++ + e l + ++      +viy  + + +++++        + ++++++  g
  gi|242399565|ref|YP_002994990.1|  54 PVLRGETPSNIFVYGKTGTGKTVTVRYVTEDLIKISQkydipvDVIY-LNCEIIDTQYRVLA----NIVNYFREESG 125
                                       5788999999********************99544433454534444.33444444333333....45555555555 PP

                          ATPase_2  84 iavpkaeleeilkeksklvfkaielllekikkkgkkiiiiiDelqklidlglngaellvkeLlnliesltk 154
                                        +vp +             ++  ++l++++  k + +ii++De+ kl+  + ++  +++++L ++  +l +
  gi|242399565|ref|YP_002994990.1| 126 VEVPLVGW---------PTDEVYAQLKKAVDMKERFLIIVLDEIDKLV--K-KSGDDVLYSLTRINTELKN 184
                                       55555554.........3456666777777777777999999999999..4.5577888888887666433 PP

>> Kinesin  Kinesin motor 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    0.0033      39      93 ..      19      79 ..       3      92 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 4.2e-06
                                      SCEEEEESEEEETTS-.....HHHHHHHHHHHHHHHHHTTSE.EEEEEEESTTSSHHHHHT CS
                           Kinesin 39 eekkfkFdkvfdeeat.....qeevyeetakplvesvleGyn.atifaYGqtgsGKTyTme 93
                                      +e+ fk + v+ ++ t     +++ + et  +++  vl+G   + if YG+tg+GKT T+ 
  gi|242399565|ref|YP_002994990.1| 19 NERIFKNKDVLRHSYTpkelpHRREQVETLVHILVPVLRGETpSNIFVYGKTGTGKTVTVR 79
                                      555555566666655555555333333344566667777765378************9986 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.2     0.015        12      14      30 ..      61      77 ..      41      92 .. 0.74
   2 !    9.0   0.0    0.0014       1.1     122     166 ..     152     193 ..     130     201 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.015
                                      TCEEEEEESTTSSHHHH CS
                                      xxxxxxxxxxxxxxxxx RF
                              DEAD 14 ggdvlvaaeTGsGKTla 30
                                        +++v ++TG+GKT  
  gi|242399565|ref|YP_002994990.1| 61 PSNIFVYGKTGTGKTVT 77
                                      3699***********86 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0014
                                       EEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 122 vrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqrqvivlS 166
                                       + ++VlDE+d+l ++  +d++   l+++++  ++ k    +i +S
  gi|242399565|ref|YP_002994990.1| 152 FLIIVLDEIDKLVKK-SGDDVLYSLTRINTELKNAK--VSIIGIS 193
                                       4579**********9.77777777999966655555..4477776 PP

>> AAA_32  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   4.2e-05     0.032      32      68 ..      63     102 ..      59     107 .. 0.83
   2 ?    0.2   0.1      0.32   2.5e+02     479     510 ..     263     294 ..     256     297 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.2e-05
                            AAA_32  32 NifvlGesgtGrttlvkrlle...eiakkeptpdDwcYvn 68 
                                       Nifv G++gtG+t +v+ + e   +i++k + p D++Y+n
  gi|242399565|ref|YP_002994990.1|  63 NIFVYGKTGTGKTVTVRYVTEdliKISQKYDIPVDVIYLN 102
                                       9************988877662225688999999****86 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.32
                            AAA_32 479 eiadllrEAdywakkegaevveaehVekAlee 510
                                       +  dllr +  +a++e +  v+++hV kA e+
  gi|242399565|ref|YP_002994990.1| 263 RALDLLRVSGEIAEREMSPKVTEKHVWKAQEK 294
                                       67899***********************9875 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.8e-05     0.014       3     127 ..      63     189 ..      61     226 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.8e-05
                           DUF2075   3 vvlVtGvaGtGKtvvllnllael..eddeeertavylsvNhplvlvlrealakkeekkkkkeafeklssfinnlsef 77 
                                        ++V G++GtGKtv    +  +l   +++ +  + +++ N + +++ ++ la+   ++ ++e+  ++  +  +++e 
  gi|242399565|ref|YP_002994990.1|  63 NIFVYGKTGTGKTVTVRYVTEDLikISQKYDIPVDVIYLNCEIIDTQYRVLANIV-NYFREESGVEVPLVGWPTDEV 138
                                       69*************999999996555666667889999*********9999988.555555555555555666655 PP

                           DUF2075  78 ..kkaeekkeepkedvvivDEAhrlltksdqaekqseenqlkelmkrakvvv 127
                                         + +++ ++++++ +++ DE  +l +ks  +  +     +++ +k+akv++
  gi|242399565|ref|YP_002994990.1| 139 yaQLKKAVDMKERFLIIVLDEIDKLVKKSGDDVLY-SLTRINTELKNAKVSI 189
                                       77777888999999999999999999966664443.4455555556566655 PP

>> Microtub_bd  Microtubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   3.3e-05     0.026      80     105 ..      58      83 ..       8     118 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.3e-05
                                       TT--EEEEEEES.............. CS
                       Microtub_bd  80 dgynvcifaygqTGsGKtyTmegeee 105
                                        ++  +if yg+TG GKt T+   +e
  gi|242399565|ref|YP_002994990.1|  58 GETPSNIFVYGKTGTGKTVTVRYVTE 83 
                                       566789**************987444 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.5     3e-05     0.024       3      85 ..      62     171 ..      60     186 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3e-05
                            AAA_24   3 lkiliyGpsgiGKTtlakel.............gpkplfidtekGlksldadkfpdie................swe 50 
                                        +i++yG+ g+GKT +++               + +++++++e     ++ + + +i                   +
  gi|242399565|ref|YP_002994990.1|  62 SNIFVYGKTGTGKTVTVRYVtedlikisqkydiPVDVIYLNCEIID--TQYRVLANIVnyfreesgvevplvgwPTD 136
                                       5899****************88888888888888888888888722..22222222223556888999999977778 PP

                            AAA_24  51 dfldevvelaaeladyktlviDtideleelclaev 85 
                                       +++ ++++  + ++++ ++v+D id+l++   ++v
  gi|242399565|ref|YP_002994990.1| 137 EVYAQLKKAVDMKERFLIIVLDEIDKLVKKSGDDV 171
                                       88999999999999*************99887776 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   8.5e-05     0.066       4      99 ..      62     175 ..      59     186 .. 0.67
   2 ?   -2.4   0.0       5.9   4.6e+03      39      56 ..     290     307 ..     270     323 .. 0.46

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.5e-05
                                       --EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHH..HTTS........ CS
                             AAA_2   4 isilllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvga..eegG........ 70 
                                       ++i + g+tg+Gkt + + + e l   ++k  i +d   l       ++++        +v++  ee+G        
  gi|242399565|ref|YP_002994990.1|  62 SNIFVYGKTGTGKTVTVRYVTEDLIKISQKYDIPVDVIYLNC-----EIIDTQYRVLANIVNYfrEESGvevplvgw 133
                                       678888999999999555544443322333444445544444.....444444443333333322777778888888 PP

                                       ....................EEEEETGGG-------------HHHHHHH CS
                             AAA_2  71 ....................ivllDEidKihpkessgadvSregVqrdL 99 
                                                           i+ lDEidK  +        S+++V+  L
  gi|242399565|ref|YP_002994990.1| 134 ptdevyaqlkkavdmkerflIIVLDEIDKLVK-------KSGDDVLYSL 175
                                       8999999999999999999************9.......5666666555 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5.9
                                       EGGG-------THHHHHH CS
                             AAA_2  39 daselleeeevehlvsrl 56 
                                        a+e +e++ +e++++ l
  gi|242399565|ref|YP_002994990.1| 290 KAQEKIEQDTMEEVIKTL 307
                                       344444433333333333 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     6e-05     0.047      30      78 ..      38      86 ..      21     123 .. 0.81
   2 ?   -1.2   0.1       1.2     9e+02      91     120 ..     171     200 ..     157     212 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6e-05
                            DUF815 30 LvgidkqkealventeqfleglpannvLLwGarGtGKSslvkallneya 78
                                      L    +q e+lv+     l+g++ +n++++G+ GtGK  +v+ +++++ 
  gi|242399565|ref|YP_002994990.1| 38 LPHRREQVETLVHILVPVLRGETPSNIFVYGKTGTGKTVTVRYVTEDLI 86
                                      5556678888888889999***********************9988765 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.2
                            DUF815  91 dlkelpklvellrerperfilfvDDLsFee 120
                                        l +l ++ ++l++++  +i    DL F+e
  gi|242399565|ref|YP_002994990.1| 171 VLYSLTRINTELKNAKVSIIGISNDLRFKE 200
                                       4789999*******************9987 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 ?   -1.4   0.0         4   3.1e+03      56      71 ..     224     239 ..     154     241 .. 0.56
   2 ?   13.5   0.0     9e-05     0.071      13      56 ..     251     305 ..     243     312 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 4
                                       XXXXXXXXXXXXXHHH CS
                       AAA_assoc_2  56 qrkalryDkagdehYd 71 
                                       q + +++ +a++++Yd
  gi|242399565|ref|YP_002994990.1| 224 QLRDILMQRAQEAFYD 239
                                       3334455556666665 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 9e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXX............XXXXXXXXXXXXXXXX CS
                       AAA_assoc_2  13 ealaeladGDaRkaLnlLElaaeaaeak...........egkieitledleealq 56 
                                       +ala+  +GDaR+aL lL +  e ae++           + +++i+++++ee+++
  gi|242399565|ref|YP_002994990.1| 251 SALAAREHGDARRALDLLRVSGEIAEREmspkvtekhvwKAQEKIEQDTMEEVIK 305
                                       67888899***********999999887777888888888888888888888875 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00012     0.091       3     112 ..      64     175 ..      62     215 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00012
                                       EEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-...-HCHHHCCCCTS--SSS-C........ CS
                             NACHT   3 vilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgnarsladllfsqlpepaapvse........ 71 
                                       +++ G+ G GKT+ ++ + +++ +  ++ +    v++l++  + ++   r la+++     e++ +v+         
  gi|242399565|ref|YP_002994990.1|  64 IFVYGKTGTGKTVTVRYVTEDLIKISQKYDIPVDVIYLNCEIIDTQY--RVLANIVNYFREESGVEVPLvgwptdev 138
                                       799******************999998887544599******99986..5577777776777777776688877777 PP

                                       ..CHHHHCCSCCCEE.EEEE-STT-SS-TCH.........HHHH CS
                             NACHT  72 ..vwavllelperlL.lilDglDelvtdlgqkekqpvrtlLsel 112
                                           +  +  +er L ++lD +D+lv++ g        ++L +l
  gi|242399565|ref|YP_002994990.1| 139 yaQLKKAVDMKERFLiIVLDEIDKLVKKSGD-------DVLYSL 175
                                       6666677888888886789******997777.......444444 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0    0.0002      0.15      28      50 ..      66      89 ..      63      99 .. 0.85
   2 ?   -2.3   0.0       5.1     4e+03     161     181 ..     149     169 ..     106     197 .. 0.51

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0002
                             DUF87 28 ilgsTGsGKSntvavLleelle.k 50
                                      + g+TG+GK+ tv++  e l++ +
  gi|242399565|ref|YP_002994990.1| 66 VYGKTGTGKTVTVRYVTEDLIKiS 89
                                      89******************9763 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 5.1
                             DUF87 161 knqaiarlldkledllrkggs 181
                                       k++    +ld +++l +k g+
  gi|242399565|ref|YP_002994990.1| 149 KERFLIIVLDEIDKLVKKSGD 169
                                       333333334444444444444 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00017      0.13      20      59 ..      59     104 ..      39     114 .. 0.67
   2 ?   -2.5   0.0       4.7   3.6e+03      96     117 ..     154     175 ..     153     181 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00017
                                       TSSS-EEEECSTTSSHHHHHHHHHH....HSTTTTS..-EEEEETT CS
                   Sigma54_activat  20 ktdlsvlitGesGtGKellaraihe....askrkek..pfvavnca 59 
                                       +t++++++ G++GtGK++  r + e     s++ +    ++ +nc 
  gi|242399565|ref|YP_002994990.1|  59 ETPSNIFVYGKTGTGKTVTVRYVTEdlikISQKYDIpvDVIYLNCE 104
                                       56799**************999988544333333331234566665 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.7
                                       EEEEETGGGS-HHHHHHHHHHH CS
                   Sigma54_activat  96 tlfLDeigelplelQekLlrvl 117
                                       ++ LDei +l  +    +l+ l
  gi|242399565|ref|YP_002994990.1| 154 IIVLDEIDKLVKKSGDDVLYSL 175
                                       5789****99988877777766 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   9.2e-05     0.072       5      45 ..      43      84 ..      41      96 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9.2e-05
                                      HHHHHHHHH.......HCTS-EEEEESTTSSCHHHHHHHHHH CS
                              PIF1  5 eQkkvfdaiieavln.ekgklfFvtGsgGtgKtflwkallkk 45
                                      eQ + + +i+  vl+ e + ++Fv+G  GtgKt   + +++ 
  gi|242399565|ref|YP_002994990.1| 43 EQVETLVHILVPVLRgETPSNIFVYGKTGTGKTVTVRYVTED 84
                                      5666666666666655999**************988877665 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   0.00024      0.19       1      26 [.      64      89 ..      64     105 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00024
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakallkkl 26
                                      i++yG++g+GK++++++++++l k +
  gi|242399565|ref|YP_002994990.1| 64 IFVYGKTGTGKTVTVRYVTEDLIKIS 89
                                      79*****************9998433 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00026       0.2      34      57 ..      62      85 ..      45      96 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00026
                             AAA_7 34 kpvllvGptGtGKtviikdllkkl 57
                                       +++++G+tGtGKtv+++ +++ l
  gi|242399565|ref|YP_002994990.1| 62 SNIFVYGKTGTGKTVTVRYVTEDL 85
                                      57899************9988776 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1    0.0016       1.2       1      25 [.      64      98 ..      64     172 .. 0.74
   2 ?    0.3   0.0       1.2   9.7e+02      28      69 ..     270     312 ..     249     327 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0016
                            AAA_18  1 IlltGtpGvGKttlakeLskrl.gf.........g 25
                                      I++ G+ G+GKt   +++ + l ++         +
  gi|242399565|ref|YP_002994990.1| 64 IFVYGKTGTGKTVTVRYVTEDLiKIsqkydipvdV 98
                                      99****************99874445443333331 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.2
                            AAA_18  28 lrdvakenglllevdpe.aldeskrldedkldklldaleenss 69 
                                       ++  ++e++++  v+++  ++ ++++++d +++++++l  +s+
  gi|242399565|ref|YP_002994990.1| 270 VSGEIAEREMSPKVTEKhVWKAQEKIEQDTMEEVIKTLPLHSK 312
                                       3444455555555555569999999999999999999877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (420 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       925  (0.0515924); expected 358.6 (0.02)
Passed bias filter:                      742  (0.0413855); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); 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: 0.82u 0.39s 00:00:01.21 Elapsed: 00:00:00.59
# Mc/sec: 2160.37
//
Query:       gi|242399566|ref|YP_002994991.1|  [L=441]
Description: Tbp-interacting protein tip49 [Thermococcus sibiricus MM 739]
Scores for complete 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-139  463.3   1.3   6.5e-139  463.0   1.3    1.1  1  TIP49            TIP49 P-loop domain
    1.8e-19   69.6   0.1    6.6e-19   67.8   0.1    2.1  1  TIP49_C          TIP49 AAA-lid domain
    1.3e-11   45.0   0.1    3.7e-07   30.6   0.0    2.4  2  AAA              ATPase family associated with various cellul
      1e-08   35.1   0.3    1.8e-05   24.5   0.1    2.3  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    7.8e-05   23.0   0.0       0.21   11.9   0.0    2.4  2  AAA_22           AAA domain
    0.00011   22.6   0.2    0.00067   20.1   0.2    2.2  1  AAA_16           AAA ATPase domain
     0.0002   21.4   0.1     0.0046   17.0   0.0    2.4  2  AAA_5            AAA domain (dynein-related subfamily)
    0.00044   20.3   0.1      0.027   14.5   0.1    2.3  2  ResIII           Type III restriction enzyme, res subunit
    0.00096   18.6   1.0      0.025   14.0   0.3    2.3  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0011   18.5   0.1     0.0034   16.9   0.0    1.7  2  AAA_7            P-loop containing dynein motor region
     0.0016   18.2   0.2      0.099   12.3   0.1    2.5  2  Sigma54_activat  Sigma-54 interaction domain
     0.0022   18.4   0.6      0.022   15.1   0.6    2.1  1  AAA_19           AAA domain
     0.0081   15.5   0.2      0.017   14.4   0.2    1.4  1  Zeta_toxin       Zeta toxin
  ------ inclusion threshold ------
       0.01   15.8   1.0      0.022   14.7   0.4    1.8  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.011   16.2   2.0      0.014   15.9   0.5    1.9  1  AAA_23           AAA domain
      0.012   15.8   0.0      0.023   14.9   0.0    1.5  1  AAA_33           AAA domain
      0.013   16.0   0.1      0.027   15.0   0.1    1.5  1  ABC_tran         ABC transporter
      0.017   14.7   0.0      0.035   13.7   0.0    1.7  1  AAA_25           AAA domain
      0.028   14.8   0.0      0.055   13.9   0.0    1.5  1  RNA_helicase     RNA helicase
      0.038   13.7   0.1      0.076   12.7   0.1    1.5  1  IstB_IS21        IstB-like ATP binding protein
      0.038   13.0   1.3       0.16   11.0   0.3    2.1  2  T2SSE            Type II/IV secretion system protein
      0.039   14.4   1.8       0.13   12.7   0.1    2.7  2  AAA_17           AAA domain
      0.041   13.2   0.0      0.096   12.0   0.0    1.6  1  DnaB_C           DnaB-like helicase C terminal domain
      0.043   13.7   0.3        0.9    9.3   0.1    2.4  2  Bac_DnaA         Bacterial dnaA  protein
      0.054   13.4   0.1        0.1   12.5   0.1    1.4  1  NACHT            NACHT domain
      0.059   13.9   0.1       0.22   12.0   0.0    2.0  2  AAA_18           AAA domain
      0.073   12.8   3.0       0.38   10.5   1.2    2.5  2  DEAD             DEAD/DEAH box helicase
      0.081   12.3   0.0       0.18   11.2   0.0    1.5  1  IPT              Isopentenyl transferase
       0.11   12.3   0.1       0.28   11.0   0.0    1.6  1  DNA_pol3_delta   DNA polymerase III, delta subunit
       0.13   12.6   0.0       0.29   11.5   0.0    1.5  1  zf-H3C2          Zinc-finger like, probable DNA-binding
       0.14   12.1   0.0        0.5   10.3   0.0    1.8  2  Rad17            Rad17 P-loop domain
       0.35   10.6   1.1       0.76    9.6   1.1    1.5  1  AAA_29           P-loop containing region of 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 !  463.0   1.3  1.2e-141  6.5e-139       1     351 []      14     358 ..      14     358 .. 0.99

  Alignments for each domain:
  == domain 1  score: 463.0 bits;  conditional E-value: 1.2e-141
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49   1 rislhshikgLGldedgeaekeeeglvGqkkareaagvivelikekklaGravLlaGpsgtGktalaiaiskelged 77 
                                       ri+ hshi+gLGlde+g+a+ +++g+vGq+kareaag+ v+lik++klaG+++Ll+Gp+g+Gkta+a++i+kelged
  gi|242399566|ref|YP_002994991.1|  14 RIGSHSHIRGLGLDENGKAKFVADGMVGQTKAREAAGIAVKLIKKGKLAGKGILLVGPTGSGKTAIAMGIAKELGED 90 
                                       799************************************************************************** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-S-EEEEEEEEEEE...-SSS-...TTS--EEEEEE-SS-E CS
                             TIP49  78 vpfvalsgsevyslevkktevltqalrksigvrikeekevleGevveleveeaenpls.kekkikevkitlktakee 153
                                       vpfv++sgse+ys+e+kkte l qalr++igvri ee+ v+eG+v  ++++++++p++ + +  ++v+itlkt++ e
  gi|242399566|ref|YP_002994991.1|  91 VPFVQISGSEIYSAEIKKTEFLKQALRRAIGVRISEERRVYEGKVERIQINKTKHPFNpYVEVPESVTITLKTKDDE 167
                                       **********************************************************9999*************** PP

                                       EEEEE-HHHHHHHHHHT--TT-EEEEETTT--EEE-SSS-SS------S--------S---S----XXXXXXXXXXX CS
                             TIP49 154 kklklgskiaeellkekvkegDviviekesGkvkklGrsearakefDiekdefvelPkGevekkkevvqevtLhdlD 230
                                       k+++ g +ia +ll+  ++egDv+++++e+G+v klG+++ ++  f    +++ve+P+G v k ke++ +v+L dlD
  gi|242399566|ref|YP_002994991.1| 168 KTIRAGREIAYQLLEMGIEEGDVVQLDAETGRVSKLGTTKGEEGLF---FKKVVEVPSGPVLKIKEFTYTVSLSDLD 241
                                       ***************************************9999855...89************************** PP

                                       XXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49 231 vanarpqdllslllqllkskkteiteklreeinkkvakyveegkaeivpGvlfiDevhmlDiecfsylnralesela 307
                                       ++n+r+ +++s++     +   eit+++re+++++v+++veegka +vpGvlfiDe hmlDie+fs+l ra+e+el+
  gi|242399566|ref|YP_002994991.1| 242 LVNSRAGGIFSVF----FGGGLEITDEIREKVDETVKQWVEEGKAVLVPGVLFIDECHMLDIEAFSFLARAMENELS 314
                                       *************....89999******************************************************* PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49 308 PivilatnrgiakirGtdiisphGipvDlldrlliiktekytke 351
                                       Pi+ilatnrg++kirGtd+++phGip+D+ldrllii+te+y++e
  gi|242399566|ref|YP_002994991.1| 315 PILILATNRGVTKIRGTDLEAPHGIPIDMLDRLLIINTEPYKRE 358
                                       *****************************************985 PP

>> TIP49_C  TIP49 AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.8   0.1   1.2e-21   6.6e-19       1      66 []     363     425 ..     363     425 .. 0.96

  Alignments for each domain:
  == domain 1  score: 67.8 bits;  conditional E-value: 1.2e-21
                           TIP49_C   1 IlkiRakeEgvkldeeAldlLakigtetSLRYaiqLltpasilakkrkkkevevedveeveeLFlD 66 
                                       I+kiRa eEg++++e+A+d++a++g++tSLRYa+qLl+pas+la    ++ev+ e++e++e  F D
  gi|242399566|ref|YP_002994991.1| 363 IVKIRAIEEGIEISEDAIDYIAELGEKTSLRYAVQLLAPASVLA---TGGEVKREHIEKAEGYFSD 425
                                       89*****************************************6...5788**********99988 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.0   6.7e-10   3.7e-07       1      42 [.      66     109 ..      66     132 .. 0.84
   2 !   12.1   0.0   0.00036       0.2      33     115 ..     260     328 ..     230     334 .. 0.75

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 6.7e-10
                                       EEEESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCSSSSTTHH CS
                               AAA   1 vllyGppGtGKTllakavakelg..vefleisgsellskyvges 42 
                                       +ll+Gp G GKT++a  +akelg  v+f++isgse+ s  ++++
  gi|242399566|ref|YP_002994991.1|  66 ILLVGPTGSGKTAIAMGIAKELGedVPFVQISGSEIYSAEIKKT 109
                                       69********************777***********96654444 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00036
                                       TCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEE CS
                               AAA  33 ellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigat 109
                                       e+++++ ++  + +++ ++e k+   p +lfiDE + l  +             + L ++++++ +     i+i+at
  gi|242399566|ref|YP_002994991.1| 260 EITDEIREKVDETVKQWVEEGKAVLVPGVLFIDECHMLDIEA-----------FSFLARAMENELS----PILILAT 321
                                       455555555566666666665555589***********6555...........9********9999....3999999 PP

                                       SS.GGGS CS
                               AAA 110 nr.pdkl 115
                                       nr + k+
  gi|242399566|ref|YP_002994991.1| 322 NRgVTKI 328
                                       9966555 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 !   24.5   0.1   3.2e-08   1.8e-05       8      61 ..      38      91 ..      33     108 .. 0.89
   2 !    8.3   0.0    0.0033       1.8      86     117 ..     287     318 ..     281     333 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 3.2e-08
                            RuvB_N  8 eyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakelgvkl 61
                                        +gq+k +e   i+++  kk + a   +ll+Gp G Gkt++a+ iakelg ++
  gi|242399566|ref|YP_002994991.1| 38 GMVGQTKAREAAGIAVKLIKKGKLAGKGILLVGPTGSGKTAIAMGIAKELGEDV 91
                                      579***********************************************9765 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0033
                            RuvB_N  86 dvlfideihrlsraveevlysamedfrldivi 117
                                        vlfide h l+ ++  +l  ame+    i+i
  gi|242399566|ref|YP_002994991.1| 287 GVLFIDECHMLDIEAFSFLARAMENELSPILI 318
                                       59**********************87666655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   0.00037      0.21       8      56 ..      66     111 ..      62     165 .. 0.75
   2 !    8.8   0.0    0.0033       1.9      80     121 ..     271     313 ..     217     329 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00037
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst......sskdl 56 
                                       ++++G++G+GKT  +  ++++l         + +v fv++++s+      + +++
  gi|242399566|ref|YP_002994991.1|  66 ILLVGPTGSGKTAIAMGIAKEL---------GEDVPFVQISGSEiysaeiKKTEF 111
                                       799************9999999.........566666666655554444555555 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0033
                            AAA_22  80 ealeqalrarav...ielliiDEaqhlrseealeeL.rsllnlsrk 121
                                       e++ q +++ ++   +++l iDE + l   ea+++L r + n  + 
  gi|242399566|ref|YP_002994991.1| 271 ETVKQWVEEGKAvlvPGVLFIDECHML-DIEAFSFLaRAMEN--EL 313
                                       4455555555556779***********.89999999444444..32 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.2   1.2e-06   0.00067      25      89 ..      64     119 ..      46     319 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.2e-06
                            AAA_16  25 elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldea 89 
                                         +ll+G+ G+GK++++  ++++l +d + f++    +         +   +++ e+l+q l++a
  gi|242399566|ref|YP_002994991.1|  64 KGILLVGPTGSGKTAIAMGIAKELGED-VPFVQISGSEI--------YSAEIKKTEFLKQALRRA 119
                                       789************************.55544444444........222233334444444442 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   8.2e-06    0.0046       2      33 ..      66      97 ..      65     133 .. 0.88
   2 ?    1.9   0.0      0.38   2.1e+02      51      92 ..     265     312 ..     255     329 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 8.2e-06
                                      EEEE--SSSSHHHHHHHGGGGBS--EEEEE-- CS
                             AAA_5  2 vlLvGppGtgKselaerlaaalnreveyvqlt 33
                                      +lLvGp+G+gK+ +a+ +a+ l+  v  vq++
  gi|242399566|ref|YP_002994991.1| 66 ILLVGPTGSGKTAIAMGIAKELGEDVPFVQIS 97
                                      89********************8877777765 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.38
                                       ......--------......G-SEEEEESGGG--HHHHHHHHHHHHSS CS
                             AAA_5  51 ttslvdsplvraar......egeilvlDEveraesevlnsLlslleer 92 
                                        ++ vd  +++ ++       + +l++DE ++++ e+++ L + +e++
  gi|242399566|ref|YP_002994991.1| 265 IREKVDETVKQWVEegkavlVPGVLFIDECHMLDIEAFSFLARAMENE 312
                                       4555555555444444445578899********999999999988875 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 !   14.5   0.1   4.9e-05     0.027      24      50 ..      63      89 ..      41     169 .. 0.88
   2 ?    3.6   0.0       0.1        58     134     147 ..     283     300 ..     255     321 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.9e-05
                                      TSEEEEEESTTSTHHHHHHHHHHHH-S CS
                            ResIII 24 dkrglikmaTGtGKTlvaaklierllk 50
                                       k +l++ +TG+GKT +a+ ++++l +
  gi|242399566|ref|YP_002994991.1| 63 GKGILLVGPTGSGKTAIAMGIAKELGE 89
                                      45788*****************99865 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.1
                                       S....EEEEETGGGTTS. CS
                            ResIII 134 d....viiiDEaHrlgak 147
                                            v++iDE+H l  +
  gi|242399566|ref|YP_002994991.1| 283 VlvpgVLFIDECHMLDIE 300
                                       145559*******98774 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.3   4.4e-05     0.025       5      64 ..      39     105 ..      36     120 .. 0.71
   2 ?    2.7   0.0      0.12        68     107     133 ..     286     312 ..     275     324 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.4e-05
                      Mg_chelatase   5 vkGqeeakraleiaa.......aGgHnlllvGppGsGKtmlakrlpsllpplseeealevakiasva 64 
                                       ++Gq++a++a  ia+         g  +llvGp GsGKt +a  +++ l +     ++  ++i+s  
  gi|242399566|ref|YP_002994991.1|  39 MVGQTKAREAAGIAVklikkgkLAGKGILLVGPTGSGKTAIAMGIAKELGEDVPFVQISGSEIYSAE 105
                                       5789999998888863333222235689**************9998877776666666666666655 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.12
                      Mg_chelatase 107 nGvLfLDElpefkrkvlevLRePledg 133
                                        GvLf+DE+  ++ +++  L + +e++
  gi|242399566|ref|YP_002994991.1| 286 PGVLFIDECHMLDIEAFSFLARAMENE 312
                                       59**********999999999999875 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   0.0   6.1e-06    0.0034      32      75 ..      62     104 ..      52     121 .. 0.80
   2 ?   -2.1   0.0       4.1   2.3e+03     103     117 ..     288     302 ..     279     304 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 6.1e-06
                             AAA_7  32 nkkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsa 75 
                                       ++k +llvGptG+GKt+i++ + k+l  e++ +++i+ s   sa
  gi|242399566|ref|YP_002994991.1|  62 AGKGILLVGPTGSGKTAIAMGIAKELG-EDVPFVQISGSEIYSA 104
                                       57899********************99.7777777776665555 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.1
                             AAA_7 103 vvFvDDlnmpakeky 117
                                       v+F+D+ +m   e +
  gi|242399566|ref|YP_002994991.1| 288 VLFIDECHMLDIEAF 302
                                       79*******998876 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.1   0.00018     0.099      11      61 ..      52     101 ..      40     114 .. 0.78
   2 ?    3.1   0.0      0.12        67      95     119 ..     287     311 ..     280     316 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00018
                                       HHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS CS
                   Sigma54_activat  11 lleqikkvaktdlsvlitGesGtGKellaraiheaskrkekpfvavncaai 61 
                                       +++ ikk       +l++G +G+GK+ +a  i ++   ++ pfv++  ++i
  gi|242399566|ref|YP_002994991.1|  52 AVKLIKKGKLAGKGILLVGPTGSGKTAIAMGIAKELG-EDVPFVQISGSEI 101
                                       45666777777789*****************988766.7889999987766 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.12
                                       SEEEEETGGGS-HHHHHHHHHHHHH CS
                   Sigma54_activat  95 GtlfLDeigelplelQekLlrvlqe 119
                                       G+lf+De + l++e+ + L r++++
  gi|242399566|ref|YP_002994991.1| 287 GVLFIDECHMLDIEAFSFLARAMEN 311
                                       99************99999999886 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.6   3.9e-05     0.022       7     128 ..      60     311 ..      54     319 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.9e-05
                            AAA_19   7 alkekvllvtaGpGtGKTrvlkhivallvelg.gvkp............eeillvaftgrAakelrerlaalgae.. 68 
                                       +l+ k +l++++ G+GKT + ++i ++l e    v+              e+l  a+ +    +++e+ ++++++  
  gi|242399566|ref|YP_002994991.1|  60 KLAGKGILLVGPTGSGKTAIAMGIAKELGEDVpFVQIsgseiysaeikkTEFLKQALRRAIGVRISEERRVYEGKve 136
                                       56778899*****************9997755134446666666555444444444433333456665555555589 PP

                            AAA_19  69 ....atTiHrlal................................................................ 77 
                                            +T H + +                                                                
  gi|242399566|ref|YP_002994991.1| 137 riqiNKTKHPF-Npyvevpesvtitlktkddektiragreiayqllemgieegdvvqldaetgrvsklgttkgeegl 212
                                       99987788877.3588889999999999999999999999999********************************** PP

                            AAA_19  78 ..............................................ldfddllteal.elle.eaeeekklqeeell 106
                                                                                     l+++d++ e++ e ++   ee k +    +l
  gi|242399566|ref|YP_002994991.1| 213 ffkkvvevpsgpvlkikeftytvslsdldlvnsraggifsvffgggLEITDEIREKVdETVKqWVEEGKAVLVPGVL 289
                                       **********************************************55544443333033444233455555777** PP

                            AAA_19 107 ivDEfqdvdelqyrLlkallge 128
                                       ++DE  ++d  ++++l + +++
  gi|242399566|ref|YP_002994991.1| 290 FIDECHMLDIEAFSFLARAMEN 311
                                       *********7777777666544 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.2     3e-05     0.017      18      52 ..      65      99 ..      55     105 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3e-05
                        Zeta_toxin 18 lillgGqpGAGKselaellkdelerqgnvvrldpD 52
                                       ill+G +G+GK+++a  +++el+++  +v++++ 
  gi|242399566|ref|YP_002994991.1| 65 GILLVGPTGSGKTAIAMGIAKELGEDVPFVQISGS 99
                                      599********************999999999875 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.4     4e-05     0.022      10      45 ..      51      89 ..      42      98 .. 0.74
   2 ?   -2.5   0.0       8.4   4.7e+03       2      29 ..     164     198 ..     163     199 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4e-05
                                      HHHHHHHCH...TEEEEEEESTTSSHHHHHHHHHHHTT- CS
                              TsaE 10 lgkklakal...gdvilLeGdLGaGKTtlvrglakalgv 45
                                      ++ kl k+    g+ ilL G+ G+GKT+++ g+ak+lg 
  gi|242399566|ref|YP_002994991.1| 51 IAVKLIKKGklaGKGILLVGPTGSGKTAIAMGIAKELGE 89
                                      444444433344667*********************985 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 8.4
                                       SSHHHHHHHHHHHHHCH.......TEEEEEEESTT CS
                              TsaE   2 kseeetealgkklakal.......gdvilLeGdLG 29 
                                       k+ e+t ++g+++a +l       gdv+ L+ + G
  gi|242399566|ref|YP_002994991.1| 164 KDDEKTIRAGREIAYQLlemgieeGDVVQLDAETG 198
                                       57788999999999877777777667788877655 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.9   0.5   2.4e-05     0.014      23      69 ..      67     144 ..      61     218 .. 0.57

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.4e-05
                            AAA_23  23 lItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdve.iese.............................. 68 
                                       l++Gp+G+GKT+i   i   L++++p     sg+ + +++++    e                              
  gi|242399566|ref|YP_002994991.1|  67 LLVGPTGSGKTAIAMGIAKELGEDVPFV-QISGSEIYSAEIKkT--Eflkqalrraigvriseerrvyegkveriqi 140
                                       89********************999754.445555555555521..1233333333333333333222222222222 PP

                            AAA_23  69 ...g 69 
                                          +
  gi|242399566|ref|YP_002994991.1| 141 nktK 144
                                       2220 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   4.1e-05     0.023       2      32 ..      66     100 ..      66     162 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.1e-05
                            AAA_33   2 vllvGlpGsGKstlaerllkklg....avllssdt 32 
                                       +llvG+ GsGK+  a +++k+lg    +v +s  +
  gi|242399566|ref|YP_002994991.1|  66 ILLVGPTGSGKTAIAMGIAKELGedvpFVQISGSE 100
                                       689*******************9988777777665 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.1   4.8e-05     0.027      11      60 ..      63     108 ..      57     195 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.8e-05
                                       TSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG...B-HHHCCHC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxx RF
                          ABC_tran  11 gekvaivGenGaGKStLlkllagllkpteGeilldgkdlke...qeleslrke 60 
                                       g+ + +vG++G+GK+ +++ +a++l  +   +++ g ++ +   +       +
  gi|242399566|ref|YP_002994991.1|  63 GKGILLVGPTGSGKTAIAMGIAKELGEDVPFVQISGSEIYSaeiK-------K 108
                                       77899********************99999999988888884442.......2 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   6.3e-05     0.035      28      65 ..      59      95 ..      46     196 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.3e-05
                            AAA_25 28 gllpagelallaGapgtGKttlaldlalavatGkpwlg 65
                                      g l ag+ +ll+G++g+GKt++a+ +a ++ ++ p+  
  gi|242399566|ref|YP_002994991.1| 59 GKL-AGKGILLVGPTGSGKTAIAMGIAKELGEDVPFVQ 95
                                      665.79999*****************999888888765 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   9.8e-05     0.055       1      45 [.      66     113 ..      66     123 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9.8e-05
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl..klkkkdsvys.rnpeddfwd 45 
                                       i+l+Gp+g GK+ +a  +ak+l +++   +++ +++ys   ++++f++
  gi|242399566|ref|YP_002994991.1|  66 ILLVGPTGSGKTAIAMGIAKELGEDVpfVQISGSEIYSaEIKKTEFLK 113
                                       689********************9987777778999997777777765 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   0.00014     0.076      48      71 ..      64      87 ..      32     107 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00014
                         IstB_IS21 48 enivllGpsGvGKshlaialgvea 71
                                      ++i+l+Gp+G GK+ +a+ +++e 
  gi|242399566|ref|YP_002994991.1| 64 KGILLVGPTGSGKTAIAMGIAKEL 87
                                      689***********9999888764 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 ?   11.0   0.3   0.00028      0.16     130     156 ..      64      90 ..      44     100 .. 0.81
   2 ?   -0.3   0.0      0.81   4.5e+02      37      87 ..      99     150 ..      91     179 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00028
                             T2SSE 130 glilvsGgTgsGKttllyallkeinks 156
                                       + il+ G+TgsGKt ++  + ke+ ++
  gi|242399566|ref|YP_002994991.1|  64 KGILLVGPTGSGKTAIAMGIAKELGED 90 
                                       568999********9998888887765 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.81
                             T2SSE  37 reveelekaalerlisriaalakldiseerplqdarlp.ekgvrlrvvllPv 87 
                                       +e+ + e +++e+l + +  + + +iseer + +++++  +  + +  + P 
  gi|242399566|ref|YP_002994991.1|  99 SEIYSAEIKKTEFLKQALRRAIGVRISEERRVYEGKVErIQINKTKHPFNPY 150
                                       5777888899999999999999999999999999999843334444444444 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   0.00023      0.13       1      65 [.      69     138 ..      69     148 .. 0.74
   2 ?   -1.0   0.0       3.8   2.1e+03      50      83 ..     258     292 ..     245     319 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00023
                                       EE-TTSSHHHHHHHHHHHH....TEEEEEHHHHHHHHHHTTTS.HSSHHHHCTSHHHHHHHHHHHHHHHH CS
                            AAA_17   1 lGgPGsGKgtqceklveky....gfthlsaGdllreeakrggl.akardemrklpleekkelqkeaaeki 65 
                                       +G+ GsGK+ ++  +++++     f  +s +++  +e+k+ +  ++a  +   + ++e++++ +   e+i
  gi|242399566|ref|YP_002994991.1|  69 VGPTGSGKTAIAMGIAKELgedvPFVQISGSEIYSAEIKKTEFlKQALRRAIGVRISEERRVYEGKVERI 138
                                       799*************9885544688899888888*****995376666666677777666666555555 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3.8
                                       HHHHHHHHHHHHHHHHHHHH.HSSEEEEEE-SEEE CS
                            AAA_17  50 pleekkelqkeaaekiaeea.kkkgvlvdghprik 83 
                                        le+++e+++++ e++++   + k vlv g   i+
  gi|242399566|ref|YP_002994991.1| 258 GLEITDEIREKVDETVKQWVeEGKAVLVPGVLFID 292
                                       56777888888888887765244557777776654 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 ?   12.0   0.0   0.00017     0.096      19      96 ..      63     147 ..      54     179 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00017
                                       TXEEEEEEXTTSSHHHHHHHHHHHHHH....CSTSEEEEEESSSXHHHHHHHHHHHHHTXX...HHHHHHTTSXHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxx RF
                            DnaB_C  19 gdliiiAarpsmGktalalniaenaav....keklpvavfslemsaeqlvqRllsseaeid...skklrtgklkeed 88 
                                       g+ i++ +  + Gkta+a+ ia++  +     +  +  ++s e ++++ +++ l    +++   ++++++gk+++ +
  gi|242399566|ref|YP_002994991.1|  63 GKGILLVGPTGSGKTAIAMGIAKELGEdvpfVQISGSEIYSAEIKKTEFLKQALRRAIGVRiseERRVYEGKVERIQ 139
                                       5568889999************9988633322333589****************99988873334566778888877 PP

                                       HHHHHHHH CS
                                       xxxxxxxx RF
                            DnaB_C  89 weklteai 96 
                                       ++k ++ +
  gi|242399566|ref|YP_002994991.1| 140 INKTKHPF 147
                                       77777655 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.27   1.5e+02      10      64 ..      39      93 ..      31     142 .. 0.80
   2 ?    9.3   0.1    0.0016       0.9      82     197 ..     264     386 ..     259     399 .. 0.71

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.27
                                      ----TTTHHHHHHHHHHHHSTTT.S--EEEE-SSSSSHHHHHHHHHHHHHHHSSS CS
                          Bac_DnaA 10 FviGasnrlAlaaalkvaeapgkkynPlfiygevGlGktHLlkaignevlenape 64
                                       v  +  r A  +a+k+ ++ + +   +++ g++G Gkt +   i++e+ e+ p 
  gi|242399566|ref|YP_002994991.1| 39 MVGQTKAREAAGIAVKLIKKGKLAGKGILLVGPTGSGKTAIAMGIAKELGEDVPF 93
                                      55555566677777778888888888999**********9999999888777665 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0016
                                       HHHTT-HHHHHHHHTT-SEEEEE-GGGGTT-HHHHHHHHHHHHHHHTTT-E..EEEEESS-TTT-SS--HHH..... CS
                          Bac_DnaA  82 alrdkkaeefkeklrkvDvLliDDiqflagkektqeelfhtfnalleegkq..vvlssDrsPkeleeledrl..... 151
                                        +r+k  e+ k+ + +  ++l+  + f+ + +  + e f  +   +e++    ++l+++r  ++++  +        
  gi|242399566|ref|YP_002994991.1| 264 EIREKVDETVKQWVEEGKAVLVPGVLFIDECHMLDIEAFSFLARAMENELSpiLILATNRGVTKIRGTDLEAphgip 340
                                       56666666677777777777777777777777777777777776666653322666777777777654433211112 PP

                                       HHHHHSSEEEE-----HHHHHHHHHHHHHHTT----TTHHHHHHHH CS
                          Bac_DnaA 152 rsrfeaGlvvdieppdletrlailkkkieaeklevpeevlefiaer 197
                                          +++ l+++ ep  +e   +i+k ++ +e++e+ e+++ +iae 
  gi|242399566|ref|YP_002994991.1| 341 IDMLDRLLIINTEPYKREEIKEIVKIRAIEEGIEISEDAIDYIAEL 386
                                       45678889************************************85 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   0.00018       0.1       3      29 ..      66      92 ..      64      97 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00018
                                      EEEEC-TTTCHHHHHHHHHHHHCTS-S CS
                             NACHT  3 vilqGeaGsGKTtLlqklalawaegkl 29
                                      ++l G+ GsGKT+ + ++a ++ e+ +
  gi|242399566|ref|YP_002994991.1| 66 ILLVGPTGSGKTAIAMGIAKELGEDVP 92
                                      789******************998765 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0    0.0004      0.22       1      26 [.      66      89 ..      66     141 .. 0.82
   2 ?   -2.1   0.0       9.4   5.3e+03      51      82 ..     260     288 ..     256     301 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0004
                            AAA_18  1 IlltGtpGvGKttlakeLskrlgfgv 26
                                      Ill G+ G+GKt +a  ++k+l  g+
  gi|242399566|ref|YP_002994991.1| 66 ILLVGPTGSGKTAIAMGIAKEL--GE 89
                                      99****************9998..33 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 9.4
                            AAA_18  51 rldedkldklldaleenssaleegknlvidgh 82 
                                       ++ ++ ++k+ ++++++    eegk +++ g+
  gi|242399566|ref|YP_002994991.1| 260 EITDEIREKVDETVKQWV---EEGKAVLVPGV 288
                                       567778888888888885...57777766555 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.2   0.00068      0.38      12      32 ..      61      81 ..      50     166 .. 0.87
   2 ?    1.2   0.0       0.5   2.8e+02     123     149 ..     287     313 ..     260     322 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00068
                                      HTTCEEEEEESTTSSHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 12 lgggdvlvaaeTGsGKTlafl 32
                                      l g+ +l+ ++TGsGKT++++
  gi|242399566|ref|YP_002994991.1| 61 LAGKGILLVGPTGSGKTAIAM 81
                                      46899************9976 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.5
                                       EEEEEETHHHHHHTTTHHHHHHHHHHS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 123 rflVlDEadrlldqgfsdfinrilnql 149
                                        +l +DE+++l  + fs   +++ n+l
  gi|242399566|ref|YP_002994991.1| 287 GVLFIDECHMLDIEAFSFLARAMENEL 313
                                       56889*******999999999888887 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00032      0.18       5      28 ..      67      90 ..      64      96 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00032
                               IPT  5 lifGatttGKtaeaiklaketgap 28
                                      l++G+t++GKta a+ +ake g  
  gi|242399566|ref|YP_002994991.1| 67 LLVGPTGSGKTAIAMGIAKELGED 90
                                      89*****************98865 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 ?   11.0   0.0   0.00049      0.28     119     159 ..     348     388 ..     340     398 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00049
                                       EEEEE----TTTHHHHHHHHHHHTT-EE-HHHHHHHHHHHT CS
                    DNA_pol3_delta 119 tvveaktlkeeelkkwiqkraqelglkiekealelLlelve 159
                                        +++ ++ k ee+k+ ++ ra e+g++i+++a+++++el e
  gi|242399566|ref|YP_002994991.1| 348 LIINTEPYKREEIKEIVKIRAIEEGIEISEDAIDYIAELGE 388
                                       57888999****************************99866 PP

>> zf-H3C2  Zinc-finger like, probable DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00052      0.29      20      83 ..     269     330 ..     260     335 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00052
                                       EETTTTEEEETTEEEE-HHHHHHHHHHHHHHH---HHHHHHHHHTST-SSEETTHHHHHHHHHH CS
                           zf-H3C2  20 ydktkkywvyqgkpvmpdqftfelldflhqlthlsfskmkallershspyymlnrdrtlknite 83 
                                        d+t k wv +gk v+   + f  +d  h l   +fs +   +e   sp  +l  +r + +i  
  gi|242399566|ref|YP_002994991.1| 269 VDETVKQWVEEGKAVLVPGVLF--IDECHMLDIEAFSFLARAMENELSPILILATNRGVTKIRG 330
                                       6899***********9887766..899****************************999988865 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00089       0.5      48      94 ..      66     113 ..      52     120 .. 0.83
   2 ?   -1.7   0.0       4.3   2.4e+03     151     178 ..     268     297 ..     263     301 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00089
                             Rad17  48 LLisGPsGCgkstvvkvLskelgiklr.ewlnpvslkepdnqksdfkg 94 
                                       +L+ GP+G gk+ +   ++kelg ++    + + ++ +++ +k++f+ 
  gi|242399566|ref|YP_002994991.1|  66 ILLVGPTGSGKTAIAMGIAKELGEDVPfVQISGSEIYSAEIKKTEFLK 113
                                       5788*******************9985256888888899999998865 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 4.3
                             Rad17 151 alrevirkylrsseal..plilviteiesl 178
                                       ++ e +++++  ++a+  p +l i e+  l
  gi|242399566|ref|YP_002994991.1| 268 KVDETVKQWVEEGKAVlvPGVLFIDECHML 297
                                       567889999999999878889999999876 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 ?    9.6   1.1    0.0014      0.76      23      38 ..      63      79 ..      56      83 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0014
                            AAA_29 23 g.atlltGpsGsGKSTl 38
                                      g  +ll+Gp+GsGK+++
  gi|242399566|ref|YP_002994991.1| 63 GkGILLVGPTGSGKTAI 79
                                      4449**********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       609  (0.0339673); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); expected 358.6 (0.02)
Passed Vit filter:                       107  (0.00596798); expected 17.9 (0.001)
Passed Fwd filter:                        32  (0.00178482); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              32  [number of targets reported over threshold]
# CPU time: 0.68u 0.33s 00:00:01.01 Elapsed: 00:00:00.51
# Mc/sec: 2624.28
//
Query:       gi|242399567|ref|YP_002994992.1|  [L=104]
Description: H/ACA RNA-protein complex component Gar1 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-09   38.1   0.0    1.4e-09   37.9   0.0    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 !   37.9   0.0   7.8e-14   1.4e-09      22     102 ..       3      75 ..       1     102 [. 0.78

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 7.8e-14
                                       EEEEEEEEETT.EEEEEE---S--B--BTT-EEEETT--EEEE--EEES-SSS-EEEEE--GGHHHHHHHTTTTSEE CS
                              Gar1  22 eiGtvssiven.evviksttsgekkvldfnsilflenktqiGkVdEifGpvnepyysVklnsseeikaksfkvgdkv 97 
                                        +G+vs   ++  ++ +st      ++  n ++ ++n ++iG V ++fGpv++py+++k+     ik+ +  +g+ +
  gi|242399567|ref|YP_002994992.1|   3 RLGKVSTYAKQgFLILRST-----SIPALNDRVVDKNLQVIGIVKDVFGPVESPYVAIKPR----IKNPEKYIGEVL 70 
                                       6788888777724455555.....69**********************************9....88877889**** PP

                                       EEE-X CS
                              Gar1  98 yiapd 102
                                       yi+ +
  gi|242399567|ref|YP_002994992.1|  71 YIDKR 75 
                                       **998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); 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: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 666.61
//
Query:       gi|242399568|ref|YP_002994993.1|  [L=272]
Description: Transcription initiation factor IIB 2 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.7e-37  125.9   1.1    6.4e-18   64.6   0.2    2.2  2  TFIIB          Transcription factor TFIIB repeat
    0.00025   20.5   0.8     0.0013   18.2   0.1    2.6  2  Sigma70_r4     Sigma-70, region 4
    0.00068   19.4   0.0       0.31   10.8   0.0    2.2  2  Cyclin_N       Cyclin, N-terminal domain
  ------ inclusion threshold ------
       0.02   14.3   0.2      0.072   12.5   0.2    2.0  1  HTH_Tnp_ISL3   Helix-turn-helix domain of transposase family 
      0.045   13.8   0.3       0.45   10.6   0.1    2.4  2  HTH_3          Helix-turn-helix
      0.073   12.8   0.7       0.23   11.2   0.1    2.2  2  Sigma70_r4_2   Sigma-70, region 4
      0.093   12.8   0.0        0.2   11.7   0.0    1.6  1  RB_B           Retinoblastoma-associated protein B domain
        0.1   12.7   0.0          7    6.8   0.0    2.2  2  Cyclin_C       Cyclin, C-terminal domain
       0.12   11.9   0.0       0.18   11.3   0.0    1.2  1  UMPH-1         Pyrimidine 5'-nucleotidase (UMPH-1)
       0.21   11.5   3.5       0.26   11.2   0.1    2.9  3  HTH_AsnC-type  AsnC-type helix-turn-helix 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 !   60.3   0.1   7.7e-20   1.4e-16       2      71 .]      92     161 ..      91     161 .. 0.98
   2 !   64.6   0.2   3.6e-21   6.4e-18       2      71 .]     186     255 ..     185     255 .. 0.98

  Alignments for each domain:
  == domain 1  score: 60.3 bits;  conditional E-value: 7.7e-20
                                       HHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                             TFIIB   2 krfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                        r+ ++++Lp  +++ A  l+++a+ ++++ Grs +g+++Acly Acr ++  rt+ ei + ++V +k+i
  gi|242399568|ref|YP_002994993.1|  92 DRMGSQIGLPRNIREIAALLYRKAVINRLVRGRSIEGMVSACLYAACRIANAPRTLDEIEDFSKVDKKEI 161
                                       58999***************************************************************98 PP

  == domain 2  score: 64.6 bits;  conditional E-value: 3.6e-21
                                       HHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                             TFIIB   2 krfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                        rf d+l+  ek +++A  ++++a ++++++G+ p+giaAA++yiA+++e++k tq+e+++v++V+e+t+
  gi|242399568|ref|YP_002994993.1| 186 VRFGDQLGVTEKTKRRAMRIVNQAIKMGLTSGKGPTGIAAAAIYIASLLEGEKMTQREVAEVARVTEVTV 255
                                       5899****************************************************************97 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.1   1.9e+03      27      38 ..     189     200 ..     189     211 .. 0.61
   2 !   18.2   0.1   7.4e-07    0.0013      18      48 ..     236     266 ..     227     267 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.1
                                       HHHHTS-HHHHH CS
                        Sigma70_r4  27 gerlgiSrerVr 38 
                                       g++lg+++ + r
  gi|242399568|ref|YP_002994993.1| 189 GDQLGVTEKTKR 200
                                       678888876533 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 7.4e-07
                                       TTT--HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                        Sigma70_r4  18 geglTleEIgerlgiSrerVrqiekrAlrkL 48 
                                       ge++T+ E++e+  +++ +Vr + k+ ++kL
  gi|242399568|ref|YP_002994993.1| 236 GEKMTQREVAEVARVTEVTVRNRYKELVDKL 266
                                       89************************99998 PP

>> Cyclin_N  Cyclin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   0.00017      0.31      45     126 ..      98     176 ..      81     177 .. 0.84
   2 !    7.3   0.0    0.0021       3.8      33     103 ..     180     252 ..     171     270 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00017
                                       TT--TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHHHHHSSS---HHHHHHHTTTSS-HHHHHHHHHHHHHH CS
                          Cyclin_N  45 fkltpetlflavnyldRflskksvpkdklqlvgatcLllAaKveeisppkledlvyitdeafteeeilemErliLet 121
                                         l +++  +a+ ++ + + ++ v+ + ++ ++ +cL+ A+++ ++ p +l+++   ++  ++++ei +  r+++++
  gi|242399568|ref|YP_002994993.1|  98 IGLPRNIREIAALLYRKAVINRLVRGRSIEGMVSACLYAACRIANA-PRTLDEIEDFSK--VDKKEIGRSYRYLVRE 171
                                       556666666788888888889999999999*************999.999999998865..9999999999999999 PP

                                       TTT-- CS
                          Cyclin_N 122 Lnfdl 126
                                       Ln +l
  gi|242399568|ref|YP_002994993.1| 172 LNLKL 176
                                       99877 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0021
                                       HHHHHHHHHHHHTT--TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHHHHHSSS..---HHHHHHHTT CS
                          Cyclin_N  33 ilidwlvevaekfkltpetlflavnyldRflskksvpkdklqlvgatcLllAaKveeis..ppkledlvyitd 103
                                       + +d++v+   ++ +t++t   a++++++ ++   ++ +    ++a+++++A+ +e  +    ++ +++ +t+
  gi|242399568|ref|YP_002994993.1| 180 NPVDYVVRFGDQLGVTEKTKRRAMRIVNQAIKMGLTSGKGPTGIAAAAIYIASLLEGEKmtQREVAEVARVTE 252
                                       45899***************************9999999**************99554311444444444443 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2     4e-05     0.072      18      52 .]     228     263 ..     224     263 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4e-05
                      HTH_Tnp_ISL3  18 ayilellles.rsvkavArqlgvSwtTVwrildryv 52 
                                        yi+ ll    ++ ++vA+  +v++ TV+++++++v
  gi|242399568|ref|YP_002994993.1| 228 IYIASLLEGEkMTQREVAEVARVTEVTVRNRYKELV 263
                                       58999999999********************99876 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.36   6.5e+02      13      34 ..     105     125 ..      97     128 .. 0.79
   2 ?   10.6   0.1   0.00025      0.45       1      27 [.     230     256 ..     230     258 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.36
                                       HHHHHHHTSSHHHHHHHHTTSS CS
                             HTH_3  13 eeLAeklGvsrstisriEnGer 34 
                                       +e+A++l   ++ i+r+ +G++
  gi|242399568|ref|YP_002994993.1| 105 REIAALL-YRKAVINRLVRGRS 125
                                       6777777.68999*******65 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00025
                                       HHHHHHHTTHHHHHHHHHHTSSHHHHH CS
                             HTH_3   1 lkelRkqlglsqeeLAeklGvsrstis 27 
                                       ++ l++  +++q+e+Ae++ v+  t++
  gi|242399568|ref|YP_002994993.1| 230 IASLLEGEKMTQREVAEVARVTEVTVR 256
                                       56788899**************99986 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       2.4   4.3e+03      31      36 ..     106     111 ..     104     125 .. 0.54
   2 ?   11.2   0.1   0.00013      0.23      25      48 ..     237     260 ..     230     266 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.4
                                       HHHHHH CS
                      Sigma70_r4_2  31 EIAell 36 
                                       EIA+ll
  gi|242399568|ref|YP_002994993.1| 106 EIAALL 111
                                       666655 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00013
                                       S---HHHHHHHHT--HHHHHHHHH CS
                      Sigma70_r4_2  25 eglsykEIAellgisegtVksrls 48 
                                       e ++++E+Ae+  ++e+tV++r++
  gi|242399568|ref|YP_002994993.1| 237 EKMTQREVAEVARVTEVTVRNRYK 260
                                       779*******************96 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 ?   11.7   0.0   0.00011       0.2      12      88 ..      86     160 ..      75     180 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00011
                              RB_B  12 laavrlrdLcerLklsselrekiwtlfehvlveetellkdRhlDqillcavYvvakvtkeelsFkeiikaYrkqpqa 88 
                                        a + l ++ +++ l +++re +  l ++++++  +l++ R ++ ++ +++Y+ +++ ++ +++ ei +  +  +++
  gi|242399568|ref|YP_002994993.1|  86 FALSELDRMGSQIGLPRNIREIAALLYRKAVIN--RLVRGRSIEGMVSACLYAACRIANAPRTLDEIEDFSKVDKKE 160
                                       556666667777777777777666666666665..69***************************9997766655554 PP

>> Cyclin_C  Cyclin, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.028        50      49      87 ..     131     169 ..     129     182 .. 0.87
   2 ?    6.8   0.0    0.0039         7      43      90 ..     219     266 ..     178     271 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.028
                                       HHHHHHCCHHHHS--S-HHHHHHC---HHHHHHHHHHHH CS
                          Cyclin_C  49 aaalllarstlnspewtetlehytgyskedlkpcvelil 87 
                                       +a+l++a+++ n p   +++e +++++k+++   ++ ++
  gi|242399568|ref|YP_002994993.1| 131 SACLYAACRIANAPRTLDEIEDFSKVDKKEIGRSYRYLV 169
                                       699**************************9987777665 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0039
                                       -HHHHHHHHHHHCCHHHHS--S-HHHHHHC---HHHHHHHHHHHHHHH CS
                          Cyclin_C  43 ppSliAaaalllarstlnspewtetlehytgyskedlkpcvelilell 90 
                                        p  iAaaa+++a+   +++  ++++ ++ ++++  +++ ++ +++ l
  gi|242399568|ref|YP_002994993.1| 219 GPTGIAAAAIYIASLLEGEKMTQREVAEVARVTEVTVRNRYKELVDKL 266
                                       56779********99988888999999999999999999999988765 PP

>> UMPH-1  Pyrimidine 5'-nucleotidase (UMPH-1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   9.9e-05      0.18      68     103 ..     232     267 ..     229     272 .] 0.91

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 9.9e-05
                            UMPH-1  68 aLlieqklkkeeiaevvkeskialrdgveelfekle 103
                                       +Ll ++k+++ e+aev++ +++++r++++el++kl+
  gi|242399568|ref|YP_002994993.1| 232 SLLEGEKMTQREVAEVARVTEVTVRNRYKELVDKLN 267
                                       6999******************************97 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1       1.9   3.4e+03       2      12 ..      78      88 ..      78      93 .. 0.75
   2 ?   -1.4   0.0       1.2   2.1e+03      24      36 ..     189     201 ..     186     204 .. 0.78
   3 ?   11.2   0.1   0.00014      0.26      12      41 ..     233     262 ..     230     263 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.9
                     HTH_AsnC-type  2 DeiDrkILeaL 12
                                      D+iDr +  aL
  gi|242399568|ref|YP_002994993.1| 78 DAIDRNLAFAL 88
                                      89999875555 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.2
                     HTH_AsnC-type  24 AervGlSestvlr 36 
                                       ++++G++e t +r
  gi|242399568|ref|YP_002994993.1| 189 GDQLGVTEKTKRR 201
                                       899****988555 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.00014
                     HTH_AsnC-type  12 LqedaRisyaeLAervGlSestvlrRvrrL 41 
                                       L e  +++ +e+Ae   ++e tv++R++ L
  gi|242399568|ref|YP_002994993.1| 233 LLEGEKMTQREVAEVARVTEVTVRNRYKEL 262
                                       55666899*******************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1654.14
//
Query:       gi|242399569|ref|YP_002994994.1|  [L=175]
Description: Metallophosphoesterase, calcineurin superfamily [Thermococcus sibiricus MM 739]
Scores for complete 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  100.2   0.0    1.5e-28  100.0   0.0    1.0  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    2.9e-07   31.2   0.9    0.00043   20.8   0.1    2.5  3  Metallophos    Calcineurin-like phosphoesterase
     0.0075   15.9   0.0       0.01   15.5   0.0    1.2  1  DUF4940        Domain of unknown function (DUF4940)


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 !  100.0   0.0   2.6e-32   1.5e-28       2     164 ..       6     157 ..       5     158 .. 0.92

  Alignments for each domain:
  == domain 1  score: 100.0 bits;  conditional E-value: 2.6e-32
                     Metallophos_2   2 klaiiSDlH...snldaleavlealkevgvdaiihaGDleeeepevleellelapvlaVrGNnDeevveedvlreaa 75 
                                       kl+i+ D+H   +  ++++ +++ +k+++vd+i+h+GDl  ++pevle+l e+ p +aV+GN D             
  gi|242399569|ref|YP_002994994.1|   6 KLGILGDTHypdKTSHLPDLIFNVFKSEKVDLILHTGDL--TAPEVLERLTEISPTIAVKGNLD------------- 67 
                                       89*********9999999999*****************9..***********************............. PP

                     Metallophos_2  76 elgtdlpeeaelelagekvlliHgdpl..gvkdalaellkeaeegsdvvvcGHtHvpeveke....ggvlvvnPGsv 146
                                         +t lpee+ le+++ k++liHg++    +++ l++ + e  +g+d++++GHtH+    k     ++v++ nPGs+
  gi|242399569|ref|YP_002994994.1|  68 --QTTLPEEKILEINNLKIGLIHGHQFlsLDEQILKYKALE--MGVDILIFGHTHRFFYNKYeymgKEVILFNPGSP 140
                                       ..99*********************9997778888888888..9*************777773444488999***** PP

                     Metallophos_2 147 geprdgdpetyaildtde 164
                                       + pr +dp t+++ +++e
  gi|242399569|ref|YP_002994994.1| 141 TVPRMSDP-TFVVGEITE 157
                                       ********.******997 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.1   7.3e-08   0.00043       2      76 ..       6      71 ..       5     106 .. 0.65
   2 !    9.0   0.3    0.0003       1.8     167     203 ..      89     119 ..      78     120 .. 0.78
   3 ?   -2.6   0.0         1   6.3e+03      32      53 ..     146     172 ..     135     174 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 7.3e-08
                                      EEEEEESBTBTTCCTHHHHHHHHH.HHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHHTSEEEEEC-TTS...C CS
                       Metallophos  2 rilvigDlHlalgggqlddllkll.ddllreekpdlvllaGDlvdrgdlekellellaalvkypipvylllGNHe...g 76
                                      ++ ++gD+H    +   + l +l+ + +++e k+dl+l++GDl+   +le  l e          p ++++GN +    
  gi|242399569|ref|YP_002994994.1|  6 KLGILGDTH---YPDKTSHLPDLIfNVFKSE-KVDLILHTGDLTAPEVLER-LTEI----S----PTIAVKGNLDqttL 71
                                      66799****...4455555555552445555.**********999986666.4444....3....46888999885431 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0003
                                       ESSESSCSSSCSCCHHHHHHH.HHHTTESEEEEESSSS CS
                       Metallophos 167 gHsplyrgsgylfgdealedl.lkkygvdlvisGHtHv 203
                                       gH  l+        de++ ++   + gvd+ i+GHtH+
  gi|242399569|ref|YP_002994994.1|  89 GHQFLS-------LDEQILKYkALEMGVDILIFGHTHR 119
                                       444444.......67788888889999**********6 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 1
                                       TTESEEEEESTSSSSS.......HHHHHH CS
                       Metallophos  32 ekpdlvllaGDlvdrg.......dlekel 53 
                                       ++p +v+  G +++r        ++e+ +
  gi|242399569|ref|YP_002994994.1| 146 SDPTFVV--GEITERKfkfrifkPWETQW 172
                                       4777888..88888888888787777766 PP

>> DUF4940  Domain of unknown function (DUF4940)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.7e-06      0.01      36     115 ..       7      85 ..       1      91 [. 0.88

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.7e-06
                           DUF4940  36 qlllkkklYpeeikklskvlksdwkkekvvviletkeeekrlsyResLSkvaldvvnlgekDlyvlpantleikkea 112
                                         +l    Yp++ ++l +++++ +k ekv  il+t ++ +  +  e+L +++  +   g++D   lp  ++  +++ 
  gi|242399569|ref|YP_002994994.1|   7 LGILGDTHYPDKTSHLPDLIFNVFKSEKVDLILHTGDLTAP-EVLERLTEISPTIAVKGNLDQTTLPEEKILEINNL 82 
                                       55788899*****************************9875.4579*********************9999888888 PP

                           DUF4940 113 klS 115
                                       k+ 
  gi|242399569|ref|YP_002994994.1|  83 KIG 85 
                                       765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       244  (0.0136092); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); 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 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1217.80
//
Query:       gi|242399570|ref|YP_002994995.1|  [L=70]
Description: Archaeal histone B [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.1e-20   71.8   2.9    4.5e-20   71.7   2.9    1.0  1  CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) a
    5.1e-10   39.8   0.4    6.5e-10   39.5   0.4    1.1  1  Histone        Core histone H2A/H2B/H3/H4
    1.5e-07   31.5   0.6    1.6e-07   31.4   0.6    1.2  1  TAF            TATA box binding protein associated factor (TA
    1.4e-05   25.2   0.1    1.5e-05   25.1   0.1    1.1  1  CENP-T_C       Centromere kinetochore component CENP-T histon
    1.8e-05   25.1   0.1      2e-05   24.9   0.1    1.1  1  CENP-S         CENP-S protein
    0.00023   21.2   0.0    0.00026   21.1   0.0    1.1  1  TFIID-31kDa    Transcription initiation factor IID, 31kD subu
    0.00049   20.1   0.0    0.00053   19.9   0.0    1.1  1  TFIID-18kDa    Transcription initiation factor IID, 18kD subu
     0.0011   19.4   0.1     0.0013   19.2   0.1    1.1  1  TFIID_20kDa    Transcription initiation factor TFIID subunit 
     0.0017   18.5   0.6     0.0021   18.2   0.6    1.1  1  DUF1931        Domain of unknown function (DUF1931)
  ------ inclusion threshold ------
       0.13   12.3   0.0       0.15   12.1   0.0    1.1  1  Bromo_TP       Bromodomain associated
       0.43   10.7   0.4       0.43   10.7   0.4    2.1  2  CaM_bdg_C0     Calmodulin-binding domain C0 of NMDA receptor 


Domain annotation for each model (and alignments):
>> CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) and archaeal histone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.7   2.9   2.8e-23   4.5e-20       1      65 []       5      68 ..       5      68 .. 0.98

  Alignments for each domain:
  == domain 1  score: 71.7 bits;  conditional E-value: 2.8e-23
                                      XXXXHHHHHHHHHCCTTXS-B-HHHHHHHHHHHHHHHHHHHHHHHHHHCCTTSSCE-HHHHHHHH CS
                     CBFD_NFYB_HMF  1 aeLPiarvkkImksdpdarkiakdAkeliaecveefieelaseAaeickkekrKtikaehiklAv 65
                                      aeLPia+++++++++ +a +++++A +++ae++ee + e+a++A++++k+++rKt+kae+iklA+
  gi|242399570|ref|YP_002994995.1|  5 AELPIAPIDRLVRKA-GAPRVSEEAAKVLAEHLEEKAMEIAKKAVDLAKHAGRKTVKAEDIKLAI 68
                                      69*************.***********************************************97 PP

>> Histone  Core histone H2A/H2B/H3/H4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.5   0.4     4e-13   6.5e-10      63     129 ..       8      69 ..       4      70 .] 0.92

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 4e-13
                                       XHHHHHHHHHHHH.TTSSSXEEXHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTXSEEXHHHHHHHHH CS
                           Histone  63 qklpfaRvvreivksekedlrisaeavlalqealEallvelfeeAnllakhaKRvTitpkDiqlArr 129
                                       + +p++R+vr+         r+s ea  +l+e lE   +e+++ A  lakha R+T+ ++Di+lA++
  gi|242399570|ref|YP_002994995.1|   8 PIAPIDRLVRKAGA-----PRVSEEAAKVLAEHLEEKAMEIAKKAVDLAKHAGRKTVKAEDIKLAIK 69 
                                       66899999888776.....9*********************************************98 PP

>> TAF  TATA box binding protein associated factor (TAF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.6   9.9e-11   1.6e-07      17      66 .]      20      69 ..       1      69 [. 0.92

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 9.9e-11
                                      T---B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH- CS
                               TAF 17 GitnLsdeaaalLaedveyrlkeivqeaakfmrhskRqkLtvaDvdsALr 66
                                      G   +s+eaa++Lae +e++  ei+++a+   +h+ R++  ++D+  A++
  gi|242399570|ref|YP_002994995.1| 20 GAPRVSEEAAKVLAEHLEEKAMEIAKKAVDLAKHAGRKTVKAEDIKLAIK 69
                                      666789****************************************9997 PP

>> CENP-T_C  Centromere kinetochore component CENP-T histone fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.1   9.2e-09   1.5e-05       8      75 ..       7      69 ..       2      70 .] 0.86

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 9.2e-09
                          CENP-T_C  8 lPaavvkklakrfakasgskaklekealkalekasdkffeqvgeDLeayakHagRKtidesDvilLmk 75
                                      lP a + +l++++        ++++ea k+l + +++    +++     akHagRKt++++D+ l +k
  gi|242399570|ref|YP_002994995.1|  7 LPIAPIDRLVRKA-----GAPRVSEEAAKVLAEHLEEKAMEIAKKAVDLAKHAGRKTVKAEDIKLAIK 69
                                      6777777777665.....6789************99999999999999**************988766 PP

>> CENP-S  CENP-S protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.1   1.2e-08     2e-05      25      70 ..      23      68 ..      11      70 .] 0.88

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1.2e-08
                            CENP-S 25 eatkqfiaaltelvykqlenlakDLeaFakHAkRstittdDvlLla 70
                                      ++++++ + l+e   +++ ++ak     akHA+R+t++++D++L  
  gi|242399570|ref|YP_002994995.1| 23 RVSEEAAKVLAEHLEEKAMEIAKKAVDLAKHAGRKTVKAEDIKLAI 68
                                      578888899999999999999999999****************986 PP

>> TFIID-31kDa  Transcription initiation factor IID, 31kD subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   1.6e-07   0.00026      11      68 ..      12      69 ..       8      70 .] 0.90

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.6e-07
                       TFIID-31kDa 11 ihliLaslgvteyeerVvlqLldfayrytssvLedAkvlaehakkkevslddvrlAiq 68
                                      i  + ++ g   ++e+  + L +      +++ + A  la+ha++k+v+++d++lAi+
  gi|242399570|ref|YP_002994995.1| 12 IDRLVRKAGAPRVSEEAAKVLAEHLEEKAMEIAKKAVDLAKHAGRKTVKAEDIKLAIK 69
                                      56778888888999999999999999999****************************8 PP

>> TFIID-18kDa  Transcription initiation factor IID, 18kD subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   3.3e-07   0.00053      21      65 ..      25      69 ..      14      70 .] 0.91

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 3.3e-07
                                      -HHHHHHHHHHHHHHHHHHHHHHHC-XXXX...XXXXXXXXXXXX CS
                       TFIID-18kDa 21 lqetvqlledlvrgyliellqqaakvaklrgsrkitlEDllfliR 65
                                       +e++++l + +++  +e+ ++a+++ak+ g++ ++ ED++ +i+
  gi|242399570|ref|YP_002994995.1| 25 SEEAAKVLAEHLEEKAMEIAKKAVDLAKHAGRKTVKAEDIKLAIK 69
                                      5789999999*******************************9986 PP

>> TFIID_20kDa  Transcription initiation factor TFIID subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   7.9e-07    0.0013      17      63 ..      23      69 ..      11      70 .] 0.86

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 7.9e-07
                                      ---HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHH CS
                       TFIID_20kDa 17 kldedvedlLleiaddFvesvtkfacklakhRksdklevrDiqlhle 63
                                      ++ e+   +L+e  ++   ++ k+a+ lakh   +++ + Di+l ++
  gi|242399570|ref|YP_002994995.1| 23 RVSEEAAKVLAEHLEEKAMEIAKKAVDLAKHAGRKTVKAEDIKLAIK 69
                                      567888999***********************************886 PP

>> DUF1931  Domain of unknown function (DUF1931)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.6   1.3e-06    0.0021       1      55 [.      12      66 ..      12      68 .. 0.96

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.3e-06
                                      HHHHHHHHHS----HHHHHHHHHHHHHHHHHCCCCHHHHHHHTT-SEE-GGGS-- CS
                           DUF1931  1 lerlfreaagLdvdkedlkrisdfVekklydLllvaeenAkangrdviepaDLPi 55
                                      ++rl r+a    v +e +k + + +e+k  +++ +a + Ak  gr++++ +D+ +
  gi|242399570|ref|YP_002994995.1| 12 IDRLVRKAGAPRVSEEAAKVLAEHLEEKAMEIAKKAVDLAKHAGRKTVKAEDIKL 66
                                      6899************************************************976 PP

>> Bromo_TP  Bromodomain associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   8.9e-05      0.15      26      69 ..      26      69 ..      13      70 .] 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.9e-05
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHTTSS-SS--HHHHHHHHH CS
                          Bromo_TP 26 esaLEtLteiaqkYirelgeqaksfaehagRseptlkDvvltLq 69
                                      e+a   L e +++   e++++a   a hagR +++ +D+ l+++
  gi|242399570|ref|YP_002994995.1| 26 EEAAKVLAEHLEEKAMEIAKKAVDLAKHAGRKTVKAEDIKLAIK 69
                                      55555566666666699**********************99875 PP

>> CaM_bdg_C0  Calmodulin-binding domain C0 of NMDA receptor NR1 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.4   0.00026      0.43      11      22 ..      38      49 ..      35      50 .. 0.92
   2 ?   -0.8   0.2         1   1.7e+03       5      11 ..      52      58 ..      51      62 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00026
                        CaM_bdg_C0 11 qKqlELArhAaD 22
                                      +K +E+A++A+D
  gi|242399570|ref|YP_002994995.1| 38 EKAMEIAKKAVD 49
                                      799********9 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1
                        CaM_bdg_C0  5 KHqirkq 11
                                      KH +rk 
  gi|242399570|ref|YP_002994995.1| 52 KHAGRKT 58
                                      7888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1083  (0.0604049); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.48u 0.32s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 419.81
//
Query:       gi|242399571|ref|YP_002994996.1|  [L=447]
Description: Ribulose bisphosphate carboxylase [Thermococcus sibiricus MM 739]
Scores for complete 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-97  324.7   0.0    6.2e-97  324.4   0.0    1.1  1  RuBisCO_large    Ribulose bisphosphate carboxylase large chai
    2.9e-44  150.1   0.1    9.2e-44  148.5   0.0    1.8  2  RuBisCO_large_N  Ribulose bisphosphate carboxylase large chai
     0.0087   15.8   0.1       0.13   12.0   0.0    2.1  2  DUF697           Domain of unknown function (DUF697)
  ------ inclusion threshold ------
      0.012   15.7   0.1       0.61   10.3   0.0    2.5  2  LigA             Aromatic-ring-opening dioxygenase LigAB, Lig
      0.058   13.1   0.0       0.13   12.0   0.0    1.5  1  4HFCP_synth      4-HFC-P synthase


Domain annotation for each model (and alignments):
>> RuBisCO_large  Ribulose bisphosphate carboxylase large chain, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  324.4   0.0  1.7e-100   6.2e-97       1     299 []     145     441 ..     145     441 .. 0.98

  Alignments for each domain:
  == domain 1  score: 324.4 bits;  conditional E-value: 1.7e-100
                                       .HHHHHHHH...T--EEEEE-SSSS---HHHHHHHHHHHHTT-.SEEE--TT-SSBTTB-HHHHHHHHHHHHHHHHH CS
                     RuBisCO_large   1 giaverevlnkegrpilGtiiKPklGLspknyarvvyelllgglDfiKdDEnlnsqpfarlkdrieavaeaikraqd 77 
                                       gi++ re+l+ ++rpi G + KPk+G sp++++++ yell++g D+iKdDEnl+ + ++r+++r++++a++i+r ++
  gi|242399571|ref|YP_002994996.1| 145 GIKGVRETLEIKDRPIYGVVPKPKVGYSPEELEKLSYELLSAGADYIKDDENLTGPWYNRFEERADVMARVIDRVEA 221
                                       7999************************************************************************* PP

                                       HHSS--EEEEE---SSHHHHHHHHHHHHHHHGGEEEEEHHHH-HHHHHHHHHHSTTS..EEEEE-TTTHHHHST--S CS
                     RuBisCO_large  78 etGekklyalnitaddleemlrraefvketggeivlvdvlviGfaaitslrkafrknelllHlHraghgaltrqskh 154
                                       etGekk++ +nit +d++em++r e+++e g   ++vdv+ +G+a+++++r  +++ +++lH+Hra+h+++tr++ h
  gi|242399571|ref|YP_002994996.1| 222 ETGEKKTWFANIT-ADIREMENRLEILAEYGLPHAMVDVVIVGWASLEYIRDLAEDYDIALHAHRAMHATFTRNHYH 297
                                       *************.578************************************************************ PP

                                       EE-HHHHHHHHHHHT-SEEE---TTSSSBS--GG......GHHHHHHHHSSEEE-SS-EEE-TT----EEEEESS-- CS
                     RuBisCO_large 155 GisfrvlakllRLlGvdhlhtgtvgvgklegdesvvkgfkdtlrekmleedeaegiffeqdlaslkavlpvasgGih 231
                                       Gis++vlakl R++G d+lh+gt+g gkleg++  v      lre++ + d+++  +++q+++++k+++p  sgG+h
  gi|242399571|ref|YP_002994996.1| 298 GISMFVLAKLYRIIGLDQLHVGTAGAGKLEGEKWDVIQNARILREEHYKPDKNDVFHLDQKFYHIKPAFPTSSGGLH 374
                                       ********************************9766666669*********************************** PP

                                       TTTHHHHHHHHS---SEEE-HHHHHTSTT-HHHHHHHHHHHHHHHHHT--HHHHHTT-HHHHHHHHHX CS
                     RuBisCO_large 232 agqlpellenlgesdvilqaGGGilgHpdgaaaGakalrqaleaaveGadleeyAkehkeLarAlesw 299
                                        g+lp+++++lg+ d++lq GGG+lgHpdg+aaGaka+rqal+a+++G++l eyAk+hkeLarAle+w
  gi|242399571|ref|YP_002994996.1| 375 PGNLPQVINALGS-DIVLQLGGGTLGHPDGPAAGAKAVRQALDAIMQGISLDEYAKTHKELARALEKW 441
                                       ************9.*****************************************************9 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 !  148.5   0.0   2.6e-47   9.2e-44       2     118 ..      15     133 ..      14     135 .. 0.98
   2 ?   -2.0   0.0         1   3.8e+03       4      22 ..     342     364 ..     340     369 .. 0.63

  Alignments for each domain:
  == domain 1  score: 148.5 bits;  conditional E-value: 2.6e-47
                   RuBisCO_large_N   2 yvdedyepk.etdllaafrvePaegvsveeaaaavAaeSStgtwtevsttkd.ellkklkakvyeieeveeekelvk 76 
                                       yvd++yep+ ++d++a+fr++P +g+++e+aa+avAaeSStgtwt+++ +++ e++++l+ak+y+++++ +++++v+
  gi|242399571|ref|YP_002994996.1|  15 YVDKNYEPNfKRDIVAVFRITPTDGYTIEQAAGAVAAESSTGTWTTLYPWYEeERWSDLSAKAYYFHDMGDGSWIVR 91 
                                       99*******9****************************************9879*********************** PP

                   RuBisCO_large_N  77 iAYplelFeegsipqllssiaGnifgmkavkalrleDirlPk 118
                                       +AYp + Fee ++p ll+siaGn+fgmk+vk lrleD++lP+
  gi|242399571|ref|YP_002994996.1|  92 VAYPAHAFEEWNLPGLLASIAGNVFGMKRVKGLRLEDLYLPE 133
                                       *****************************************7 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1
                   RuBisCO_large_N   4 dedyepketdllaa....frveP 22 
                                       +e+y+p+++d+  +    ++++P
  gi|242399571|ref|YP_002994996.1| 342 EEHYKPDKNDVFHLdqkfYHIKP 364
                                       77899999888642222255555 PP

>> DUF697  Domain of unknown function (DUF697)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   3.6e-05      0.13      41      74 ..     253     286 ..     252     300 .. 0.93
   2 ?    1.4   0.0     0.064   2.3e+02      86     143 ..     382     443 ..     378     446 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.6e-05
                            DUF697  41 PlalvDllavaavnlrlirelaelYgielgyega 74 
                                       P a+vD+++v ++ l+ ir+lae Y+i l  ++a
  gi|242399571|ref|YP_002994996.1| 253 PHAMVDVVIVGWASLEYIRDLAEDYDIALHAHRA 286
                                       99*************************9988776 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.064
                            DUF697  86 aglGlvelgtdllkqllsl....nlatklsaraaQGvvagllTarvGlsaieylrplaswgd 143
                                       + +  + ++ +l++++l++       +k++++a+ +++ g++     +  +e+ r l++wg+
  gi|242399571|ref|YP_002994996.1| 382 INALGSDIVLQLGGGTLGHpdgpAAGAKAVRQALDAIMQGISLDEYAKTHKELARALEKWGH 443
                                       556678899999999999999999999999999999*9999999999999999999999987 PP

>> LigA  Aromatic-ring-opening dioxygenase LigAB, LigA subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00017      0.61      49      76 ..     297     324 ..     271     336 .. 0.83
   2 ?    2.8   0.0     0.036   1.3e+02      67      85 ..     412     430 ..     405     432 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00017
                                       HT--HHHHHHHHHHTT--HHHHHHHHTT CS
                              LigA  49 lGgniyyLaKlaavlglsmqeigaamtG 76 
                                       +G ++++LaKl +++gl+ +++g a  G
  gi|242399571|ref|YP_002994996.1| 297 HGISMFVLAKLYRIIGLDQLHVGTAGAG 324
                                       699*******************987655 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.036
                                       HHHHHHHHTTS-HHHHHTT CS
                              LigA  67 mqeigaamtGmsleeFqat 85 
                                        q + a m+G+sl+e+ +t
  gi|242399571|ref|YP_002994996.1| 412 RQALDAIMQGISLDEYAKT 430
                                       57889***********997 PP

>> 4HFCP_synth  4-HFC-P synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   3.6e-05      0.13      62     151 ..     171     260 ..     168     287 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.6e-05
                                       S-HHHHHHHHHHHHHTT-SEEEEE..E-S..--SHHHHHHHHHHHHHHHHHH-TTS.EEEEEEETTGGGTT---GGG CS
                       4HFCP_synth  62 ekpgtvslaalgaaaagvdyvKvG..lag..lkkeeealealkavvkavkeedkek.kvvavlyaDaervasvsple 133
                                       ++p+ + +  +++ +ag+dy+K    l g   ++ ee ++++++v+ +v++e+ ek ++ a + aD +     +  +
  gi|242399571|ref|YP_002994996.1| 171 YSPEELEKLSYELLSAGADYIKDDenLTGpwYNRFEERADVMARVIDRVEAETGEKkTWFANITADIR-----EMEN 242
                                       56777788889999********765555555899***************99986655**********8.....4444 PP

                                       HHHHHHHHT-SEEEEE-S CS
                       4HFCP_synth 134 llelaaeagaagvmlDTa 151
                                        le++ae g+  +m+D +
  gi|242399571|ref|YP_002994996.1| 243 RLEILAEYGLPHAMVDVV 260
                                       999999*********976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 3073.51
//
Query:       gi|242399572|ref|YP_002994997.1|  [L=196]
Description: Thymidine kinase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.6e-53  181.2   0.0    1.8e-53  181.0   0.0    1.0  1  TK          Thymidine kinase
     0.0071   16.4   0.1      0.014   15.4   0.1    1.5  1  AAA_14      AAA domain
  ------ inclusion threshold ------
      0.019   14.8   0.0      0.045   13.6   0.0    1.6  1  zf-C4_ClpX  ClpX C4-type zinc finger


Domain annotation for each model (and alignments):
>> TK  Thymidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.0   0.0   3.1e-57   1.8e-53       2     177 .]      10     193 ..       9     193 .. 0.96

  Alignments for each domain:
  == domain 1  score: 181.0 bits;  conditional E-value: 3.1e-57
                                TK   2 sielilgpmfaGKsteLlrrvkryqlaekkvvvikaakdnRysegkvvthdgisleak..ksktssleeikeeleee 76 
                                        +e+i+gpmfaGK++eL++r++r   a+ k  ++k+++dnRyse+k+v+h+g+s ea    +  + ++ i++++++e
  gi|242399572|ref|YP_002994997.1|  10 FLEVITGPMFAGKTSELIKRIERQIFAKRKAALFKPSIDNRYSEDKLVAHNGLSYEAFviPTTEEGVKMIYQKTKKE 86 
                                       799*******************************************************54444456899999***** PP

                                TK  77 dvdvvlvDEaqFfeqdivelseklanegkivivagLdtdFerklFenilkllalaekvkklkavCmkCgkkAsftkr 153
                                        ++v+++DE+qFf+  ive+ +kla+eg+ vi+ gL+ dF+++ Fe  ++lla+a+++++l+a+C++Cg++A+ t+r
  gi|242399572|ref|YP_002994997.1|  87 GFEVIGIDEVQFFPMSIVEILDKLADEGIYVIASGLNLDFKGDAFEVTKELLAMADNIVYLTAICSVCGREATRTQR 163
                                       ***************************************************************************** PP

                                TK 154 ln......kekeviliGgkekYvsvCrkcy 177
                                       l       +++  il+Gg e Y++ Crk++
  gi|242399572|ref|YP_002994997.1| 164 LIngkpapRDSPRILVGGMEAYEARCRKHH 193
                                       *99999999*******************97 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   2.3e-06     0.014       6     101 ..      13     123 ..       9     138 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.3e-06
                            AAA_14   6 vitGaRrvGKTtllkqlikell.vkkesilyinldderd............kkladpe........kllelileklk 61 
                                       vitG+  +GKT  l + i++++ +k++  l+    d+r+            +     e        +  ++i +k k
  gi|242399572|ref|YP_002994997.1|  13 VITGPMFAGKTSELIKRIERQIfAKRKAALFKPSIDNRYsedklvahnglsY-----EafviptteEGVKMIYQKTK 84 
                                       89*********99999998888755555555544444553444444444331.....13334433344566666655 PP

                            AAA_14  62 eekktylflDEiqevpe.wekalkslvdegknldvivtGSn 101
                                       +e+ +++ +DE+q  p  + ++l +l deg  + vi++G n
  gi|242399572|ref|YP_002994997.1|  85 KEGFEVIGIDEVQFFPMsIVEILDKLADEG--IYVIASGLN 123
                                       578999*********964889999999998..778888755 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 ?   13.6   0.0   7.5e-06     0.045       3      20 ..     151     168 ..     149     170 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.5e-06
                        zf-C4_ClpX   3 CSFCgksesevkklIagp 20 
                                       CS Cg++++  ++lI g 
  gi|242399572|ref|YP_002994997.1| 151 CSVCGREATRTQRLINGK 168
                                       ***************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      584  (0.0325729); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.55
# Mc/sec: 1082.37
//
Query:       gi|242399573|ref|YP_002994998.1|  [L=148]
Description: alanyl-tRNA synthetase-like protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00052   20.1   0.1      0.001   19.1   0.1    1.5  1  tRNA_SAD  Threonyl and Alanyl tRNA synthetase second addition


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 !   19.1   0.1   5.7e-08     0.001       2      31 ..     101     130 ..     100     139 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 5.7e-08
                                       EEEEETT.EEEEESS---SBGGGC-SEEEE CS
                          tRNA_SAD   2 rvvsiGdisvelCgGtHvpnTgeIgafkil 31 
                                        vv i+d+ +++C   H + TgeIg +ki 
  gi|242399573|ref|YP_002994998.1| 101 KVVVIEDWNINACNKEHTKTTGEIGQIKIR 130
                                       6999*************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1031.23
//
Query:       gi|242399574|ref|YP_002994999.1|  [L=335]
Description: Aspartate-semialdehyde dehydrogenase [Thermococcus sibiricus MM 739]
Scores for complete 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  104.5   0.0    8.1e-30  103.8   0.0    1.4  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
    1.3e-28  100.3   0.0    1.9e-28   99.8   0.0    1.3  1  Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation dom
     0.0067   16.5   0.0      0.012   15.8   0.0    1.4  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
  ------ inclusion threshold ------
      0.019   15.2   0.0      0.033   14.5   0.0    1.4  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
      0.028   14.0   0.1      0.077   12.6   0.0    1.7  2  Gp_dh_C          Glyceraldehyde 3-phosphate dehydrogenase, C-
      0.044   14.6   0.0      0.079   13.8   0.0    1.4  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
      0.073   13.8   0.0       0.18   12.6   0.0    1.7  1  DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomer


Domain annotation for each model (and alignments):
>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.8   0.0   3.1e-33   8.1e-30       2     119 ..       3     120 ..       2     122 .. 0.95

  Alignments for each domain:
  == domain 1  score: 103.8 bits;  conditional E-value: 3.1e-33
                                       EEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSG..GGTTTECEBEEEGGGGGC.TT-SEEEE-SC CS
                    Semialdhyde_dh   2 vaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavk..aleegkdlkvedvdeeel.kevdivflalp 75 
                                       vai+GatG vGq ++rlLe+hp++++ +l++s+rs+G+k++e++     ee+ ++++e+   ee+  +vd+vf+alp
  gi|242399574|ref|YP_002994999.1|   3 VAILGATGLVGQSFVRLLENHPWFDVKYLIASQRSKGRKFRELATweVSEEIGEMRIES--LEEFdGNVDLVFSALP 77 
                                       9******************************************9998899999999999..666768********** PP

                                       HHHHHHHHHHHHHTTSEEEESSSTTTTSTTSEBE-HHHHGGGGG CS
                    Semialdhyde_dh  76 agvskelapklaeagvkviDlssdfRlkddavyvlpevnreaik 119
                                       ++++ ++++kl ++++ v++++s +R++ d+++ +pevn e+++
  gi|242399574|ref|YP_002994999.1|  78 SSIAGNVEEKL-AEKIPVFSNASSHRYEGDVPILVPEVNGEHLS 120
                                       ***********.889**************************986 PP

>> Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.8   0.0   7.5e-32   1.9e-28       1     183 [.     150     315 ..     150     316 .. 0.86

  Alignments for each domain:
  == domain 1  score: 99.8 bits;  conditional E-value: 7.5e-32
                                       HHHHHHCTT.EEEEEEEEEEEGGGCHHHHHHHHHHHHHHHHHSTTS.CTTTSSHHTTSEESTCSTBTTTTCHCBHHH CS
                   Semialdhyde_dhC   1 LkPLldalgelervivatyqavSGaGkkgvreLlkqvaelqrsdeakpgvfgvpiagNlipyidkeedkgepetree 77 
                                       Lk+L +  ++++rv+v+t+qa+SGaG                      g + ++i +N+ipyi kee k e+e+r++
  gi|242399574|ref|YP_002994999.1| 150 LKALSK--FGIQRVNVVTMQAISGAGF--------------------SGLSAMQIFDNVIPYIEKEEWKVENESRKI 204
                                       667777..67*****************....................6***************************** PP

                                       HHHHHHHHHHCTESCSEEEEEEEESBSSEEEEEEEEEESSSHHHHHHHHHHHHCS...........TTEEEEESSHC CS
                   Semialdhyde_dhC  78 lkavaetkkileftekvsatcvrVPvlrGhseavtiklklkdveveeveellaaa...........pevkvvvneee 143
                                       l+++++ k   + +e +s + +rVPv  Gh+eav+++l+ +d +vee ++ +++             ++ ++     
  gi|242399574|ref|YP_002994999.1| 205 LGKLENNKITPASFE-ISVITTRVPVSHGHTEAVFVELE-EDPTVEELKKSFESFdplgslklpsyAKPLLYK---- 275
                                       ******999999997.**********************5.888888888888888877887776544444444.... PP

                                       HHSSHH..HHTTCSSSEEEEEEEEETTCTTEEEEEEEEETTT CS
                   Semialdhyde_dhC 144 drPtpa..avaggtnsvsVGRirkdemgdeglklvvvgDNll 183
                                       ++P+p+   + gg+++v+ GR++k e+g+  +k++++g+Nl+
  gi|242399574|ref|YP_002994999.1| 276 EIPQPKfhRDFGGGMTVTFGRMEKIEEGK--FKYITLGHNLI 315
                                       4566651166667*************999..**********8 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   4.5e-06     0.012       1      92 [.       1      92 [.       1      97 [. 0.74

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4.5e-06
                                      EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEBSSHHHHHHH-SEEEE..-S.- CS
                            DapB_N  1 ikvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglgklgvavtddleevlekadvliD..FT.t 76
                                      ++va++Ga+G +G++ v+++e+++ + +   + +++   +g+++ el+   +++ ++ +   e le++d  +D  F+  
  gi|242399574|ref|YP_002994999.1|  1 MEVAILGATGLVGQSFVRLLENHPWFDVKYLIASQR--SKGRKFRELATW-EVSEEIGEMRIESLEEFDGNVDlvFSaL 76
                                      78*****************************99988..577888877766.4445555555566666776666334435 PP

                                      HHHHHHHHHHHHHTT- CS
                            DapB_N 77 peavlenlklalekgv 92
                                      p+++  n++  l++++
  gi|242399574|ref|YP_002994999.1| 77 PSSIAGNVEEKLAEKI 92
                                      7777777776666665 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.3e-05     0.033       1      42 [.       3      43 ..       3      89 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.3e-05
                                      EEEE--.SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHC CS
                   Sacchrp_dh_NADP  1 vliiGa.GsvGqavaellarhfdvdaeitvadrskeklealaa 42
                                      v i+Ga G vGq++++ll++h  +d +  +a++  ++  + + 
  gi|242399574|ref|YP_002994999.1|  3 VAILGAtGLVGQSFVRLLENHPWFDVKYLIASQRSKG--RKFR 43
                                      689******************9887799999988776..3333 PP

>> Gp_dh_C  Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.2   3.1e+03      10      24 ..     154     168 ..     147     171 .. 0.82
   2 ?   12.6   0.0     3e-05     0.077      71     107 ..     219     255 ..     211     267 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.2
                                       HHHEEEEEEEEEEEE CS
                           Gp_dh_C  10 dkfgikkglmttvha 24 
                                       +kfgi+++ ++t  a
  gi|242399574|ref|YP_002994999.1| 154 SKFGIQRVNVVTMQA 168
                                       589***999999876 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 3e-05
                                       TEEEEEEEESSSSEEEEEEEEEESSTS-HHHHHHHHH CS
                           Gp_dh_C  71 kldglAvrVPtpnvsvvdlvvelekevtveevnaalk 107
                                       +++ +  rVP+  ++   + vele++ tvee ++ ++
  gi|242399574|ref|YP_002994999.1| 219 EISVITTRVPVSHGHTEAVFVELEEDPTVEELKKSFE 255
                                       5677889*************************99987 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.1e-05     0.079       2      85 ..       2      91 ..       1      96 [. 0.80

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.1e-05
                                      EEEEETT.SHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESS........HHHHHTCT.TESEEEE-S CS
                      GFO_IDH_MocA  2 rvaiiGa.Gkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysd........leelladp.eidavivat 70
                                       vai Ga G +g+ ++  l e++++ +v  l+ ++ ++ ++++e   +e+ ++        lee    + ++d+v+ a 
  gi|242399574|ref|YP_002994999.1|  2 EVAILGAtGLVGQSFV-RLLENHPWFDVKYLIASQRSKGRKFRELATWEVSEEigemriesLEEF---DgNVDLVFSAL 76
                                      79*****8888*****.555555*******************99999998888555553323333...258******** PP

                                      -GGGHHHHHHHHHHT CS
                      GFO_IDH_MocA 71 pngtheelakaalea 85
                                      p++   +++++++e+
  gi|242399574|ref|YP_002994999.1| 77 PSSIAGNVEEKLAEK 91
                                      999999999988775 PP

>> DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   6.8e-05      0.18       1      35 [.       3      36 ..       3      52 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.8e-05
                                      EEEESTTSHHHHHHHHHHHHCTTTEEEEEEEESST CS
                   DXP_reductoisom  1 vviLGsTGSIGtqtLdvieenpdkfevvalaagsn 35
                                      v+iLG+TG +G++ + ++e++p  f+v  l a+++
  gi|242399574|ref|YP_002994999.1|  3 VAILGATGLVGQSFVRLLENHP-WFDVKYLIASQR 36
                                      79********************.999999998655 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:                      532  (0.0296726); 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: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2116.21
//
Query:       gi|242399575|ref|YP_002995000.1|  [L=390]
Description: Threonine synthase [Thermococcus sibiricus MM 739]
Scores for complete 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-81  271.9   0.0    7.6e-81  271.7   0.0    1.0  1  PALP           Pyridoxal-phosphate dependent enzyme
     0.0048   17.0   0.0         17    5.6   0.0    3.2  3  ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthas


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  271.7   0.0   8.4e-85   7.6e-81       2     294 .]      61     360 ..      60     360 .. 0.95

  Alignments for each domain:
  == domain 1  score: 271.7 bits;  conditional E-value: 8.4e-85
                                       GGCSSS--EEEECCTCCCCCCE.EEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHH CS
                              PALP   2 tlgigpTPlvrlprlskelgvp.lflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaall 77 
                                       +l +g+TP+ rl++l+ elg + l++K+E+ nptgSfKdRg++  ++++ e  g + v++as+GN+ ++lAa+aa+ 
  gi|242399575|ref|YP_002995000.1|  61 SLNEGGTPIYRLENLQTELGMKeLYVKNEGANPTGSFKDRGMTVGVSKALEL-GMDKVICASTGNTSASLAAYAAKS 136
                                       6789************************************************.************************ PP

                                       T-EEEEEEETTS-H.HHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHHHTHHHHHHHH CS
                              PALP  78 Glkvtivvpadasp.ekvallrllGaevvevggdydeavaaaaelaaegegaylvsqfdnptviegygtiglEileq 153
                                       ++k++++vp+++ + +k+a+   +Ga+vv v g++d+a++++ e+ +e  g+y++++  np + eg++ti++Ei +q
  gi|242399575|ref|YP_002995000.1| 137 NIKAYVLVPSGKIAlGKLAQAIVYGAKVVPVRGNFDDALNVVVEASSE-LGVYMLNSI-NPFRLEGQKTIAFEIFDQ 211
                                       *************88*********************************.*********.9***************** PP

                                       TTTTEEEEEEE-SSSHHHHHHHHHHHH....HSTT..-EEEEEEECTTCGGTTCCS..S..SS..B.SSS.CCSTCS CS
                              PALP 154 lggkpdavvvpvGgGgliaGiaaglke....rrpd..vrvigvepegsdalarslragrr.vtvpvsdtiadglavg 223
                                       lg +pd v++pvG++g+i++i++g++e    ++ d  +++ig+++eg+++lar++++ r  +++++++tia+++++g
  gi|242399575|ref|YP_002995000.1| 212 LGFVPDKVILPVGNAGNISAIWKGFRElyeaGFIDklPKMIGIQAEGASPLARAWKERRDfKPLEKPETIATAIRIG 288
                                       ***************************8776444488******************555541456666********** PP

                                       ..CGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHHHHHHHHCCTTCEEEEEEE-B CS
                              PALP 224 ..spselafelldrlvdeivtvsdeealeamrllarregivvepssaaalaalklreagelkegdrvvviltg 294
                                         ++ ++a+++++++++   +v+dee+l+a++ la++egi+vep+sa +la+l ++ ++e++e+++vv+i tg
  gi|242399575|ref|YP_002995000.1| 289 npANWPKAWRVVEESGGVLESVTDEEILKAQKMLASKEGIFVEPASASSLAGL-MKLRNEIEEDESVVLITTG 360
                                       8888899**********************************************.****************997 PP

>> ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1     0.011        97      27      65 ..     106     142 ..      98     165 .. 0.73
   2 !    5.6   0.0    0.0019        17      23      50 ..     204     231 ..     199     246 .. 0.89
   3 !    4.0   0.0    0.0061        55      50      81 ..     334     363 ..     332     370 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.011
                                       HHHHHT--GGGB--THHHH-B-GGGHHHHHHHHHHHTTS CS
                     ACP_syn_III_C  27 vakklglpeekvvvnldeyGntsaasiplaLdeaveegk 65 
                                       v k l+l ++kv  + + +Gntsa+   +a +  ++   
  gi|242399575|ref|YP_002995000.1| 106 VSKALELGMDKV--ICASTGNTSASLAAYAAKSNIKAYV 142
                                       678889999998..7899******987777776666555 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0019
                                       HHHHHHHHHT--GGGB--THHHH-B-GG CS
                     ACP_syn_III_C  23 iidavakklglpeekvvvnldeyGntsa 50 
                                       i  ++ ++lg+ ++kv+  + + Gn+sa
  gi|242399575|ref|YP_002995000.1| 204 IAFEIFDQLGFVPDKVILPVGNAGNISA 231
                                       555699*********************9 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.0061
                                       GGHHHHHHHHHHHTTSS-TT-EEEEEEEETTT CS
                     ACP_syn_III_C  50 aasiplaLdeaveegklkpgdlvllvgfGaGl 81 
                                       +as++  L ++ +  ++++ + v+l+++G Gl
  gi|242399575|ref|YP_002995000.1| 334 SASSLAGLMKLRN--EIEEDESVVLITTGHGL 363
                                       8999999999999..9***************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); 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: 00:00:00.47
# Mc/sec: 2482.79
//
Query:       gi|242399576|ref|YP_002995001.1|  [L=291]
Description: Homoserine kinase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-14   53.8   0.0    4.5e-14   52.6   0.0    1.7  1  GHMP_kinases_C  GHMP kinases C terminal
    1.8e-13   50.5   0.2    4.4e-13   49.2   0.2    1.7  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 !   52.6   0.0     5e-18   4.5e-14       3      75 ..     200     267 ..     198     274 .. 0.90

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 5e-18
                    GHMP_kinases_C   3 ealergdlellgellnlsqrselkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkdeaeqv 75 
                                        ale+gd+e++g+ll +  +   + ++++l p+++++ +a++e+Ga+g+++sG+  Gp+vfal+++ de  ++
  gi|242399576|ref|YP_002995001.1| 200 LALENGDIEEVGKLLDDYLA---MPYRKPLIPWFDKIRKAALENGAYGVSISGS--GPAVFALGENLDEIGRA 267
                                       589*************8888...66*****************************..********999985444 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 !   49.2   0.2     5e-17   4.4e-13       2      66 .]      75     140 ..      74     140 .. 0.94

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 5e-17
                                       EEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHHHH..HHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
                    GHMP_kinases_N   2 ivikseiPvgaGLGSSAAlavalvaAllallglslee..aklaleaerlaqggngsggDvaasvyGg 66 
                                       ++ik+ i +++GLGSS+A a+++++A+++ll+++ +e  ++ ale+e+ a  g+++g+++ ++++Gg
  gi|242399576|ref|YP_002995001.1|  75 MKIKKGIRPKSGLGSSGASALGGALAVARLLDIDDKEiiLRAALEGEKVAS-GSPHGDNIVPALFGG 140
                                       6899***************************98875579********9998.**************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1858.73
//
Query:       gi|242399577|ref|YP_002995002.1|  [L=351]
Description: Aspartate kinase [Thermococcus sibiricus MM 739]
Scores for complete 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-46  157.5   0.0      5e-46  157.3   0.0    1.1  1  AA_kinase  Amino acid kinase family


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.3   0.0   2.8e-50     5e-46       2     239 ..      10     273 ..       9     275 .. 0.87

  Alignments for each domain:
  == domain 1  score: 157.3 bits;  conditional E-value: 2.8e-50
                                       EEEEEE-TTCCCCTCCHHHHHHHHHHHHHHHHTTEEEEEE--.HHHHHHHHHHTCCCCCHHHC.............. CS
                         AA_kinase   2 rvVvKlGGssltdkeeaslrrlaeqiaalkesgnklvvVhGg.gsftdgllalksglssgelaa............. 64 
                                       rvV+K+GGss+     +s+ ++++ +++l  +gn++v+V ++ +++td ll+l+   s+++l++             
  gi|242399577|ref|YP_002995002.1|  10 RVVIKFGGSSVR----DSFSEALRLVQKL-YEGNEVVIVLSAlKGVTDLLLKLAESKSPEFLKEfeeiylrtierlg 81 
                                       89**********....4599*********.***********************777777777767777775555443 PP

                                       ......E..HHHHHHHHH........................HHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCC CS
                         AA_kinase  65 ...glrstleeagevatr........................dalaslgerlvaallaaglpavglsaaaldateag 114
                                                                                 d ++s+gerl+ +l++++l++ g+++ ++da+   
  gi|242399577|ref|YP_002995002.1|  82 ielS-------------IeneirelkfilrnekafpsrkayiDHVLSFGERLSVKLFSKALEDEGIKSTPVDAFYLI 145
                                       3331.............02334455667777999999999********************************99988 PP

                                       E........HHHTTTCEEECCHHHHHHHTT-EEEEESEEEEETTTE...EEEE-HHHHHHHHHHHCTSSEEEEEESS CS
                         AA_kinase 115 r......degsdgnvesvdaeaieelleagvvpvltgfigldeege...lgrgssDtiaallAealgAdkliiltdV 182
                                              + + d + ++ ++  +ee+l++g vpv+tgf   + +g    lgrg+sD++a+ l+ +l+A+ ++i++dV
  gi|242399577|ref|YP_002995002.1| 146 EtngsfgNAKVDLKKTKDKIWIVEEILKRGRVPVITGFL-GNFNGFrttLGRGGSDYTASVLGRLLNARAVLIMSDV 221
                                       89996666666666666667778**************98.7777778999*************************** PP

                                       SSCESSTTTTCCTTCECCEEEHHHCHHCSSS.TTTHHHHCHHHHHHHHHCTT-EEEE CS
                         AA_kinase 183 dGVydadpkkvpdarllpeisvdeaeesaselatgGmkvkhpaalaaarrggipvvI 239
                                        G+y+adpk+v da+l+p  s++e+       ++ Gmk++h++a+++++++ ip+++
  gi|242399577|ref|YP_002995002.1| 222 KGIYTADPKIVRDAKLIPFASYEEVST----ASMLGMKALHERAVEPVKGK-IPIIL 273
                                       ***************************....*****************998.**986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); 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 0.29s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2295.58
//
Query:       gi|242399578|ref|YP_002995003.1|  [L=78]
Description: hypothetical protein TSIB_1603 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0084   16.0   0.0     0.0097   15.8   0.0    1.2  1  Phage_rep_org_N  N-terminal phage replisome organiser (Phage_
     0.0093   16.0   0.0      0.012   15.7   0.0    1.3  1  HisKA            His Kinase A (phospho-acceptor) domain


Domain annotation for each model (and alignments):
>> 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 !   15.8   0.0   1.1e-06    0.0097      51      98 ..      18      65 ..       7      70 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.1e-06
                   Phage_rep_org_N 51 nipytaemlalifnreletvrlaLkvlkdlelieisedkvikiknwek 98
                                      +++ + e+++  ++++++t++l  k+lk+l+li+  e++  k  ++ k
  gi|242399578|ref|YP_002995003.1| 18 SLNAFLEEISKDTRKPISTLKLNAKILKKLGLIDYGEKNHPKPIELTK 65
                                      567789****************************98887766555555 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.3e-06     0.012       1      31 [.      18      50 ..      18      74 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.3e-06
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHC.... CS
                             HisKA  1 slgrflagvaHELrtPLsailgnaeaLkre..g 31
                                      sl+ fl  ++ + r P+s++++na++Lk+   +
  gi|242399578|ref|YP_002995003.1| 18 SLNAFLEEISKDTRKPISTLKLNAKILKKLglI 50
                                      6889***********************986662 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.50
# Mc/sec: 472.09
//
Query:       gi|242399579|ref|YP_002995004.1|  [L=109]
Description: Transketolase, N-terminal section, partial [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.019   14.8   0.1      0.031   14.1   0.1    1.3  1  DUF1533          Protein of unknown function (DUF1533)
       0.12   11.3   0.0       0.18   10.7   0.0    1.2  1  Transketolase_N  Transketolase, thiamine diphosphate binding 


Domain annotation for each model (and alignments):
>> DUF1533  Protein of unknown function (DUF1533)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   3.5e-06     0.031      21      52 ..      22      54 ..       9      59 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.5e-06
                           DUF1533 21 nkyslssigk.LklkasvfnkaGentIvIkakG 52
                                      n + l+s+   L++ + v+ k Gen + I +kG
  gi|242399579|ref|YP_002995004.1| 22 NNFHLNSSITcLEILKAVIAKKGENDVIILSKG 54
                                      66677777777*********************9 PP

>> Transketolase_N  Transketolase, thiamine diphosphate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0     2e-05      0.18      55     117 ..      46     100 ..      40     106 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 2e-05
                                       S-EEEESSGGGHHHHHHHHHHTTSS--HHHHTTTTSTT-SS-SS--TTTSTT--S---STTHH CS
                   Transketolase_N  55 RDRfvLsnGhaslllYsllhLtGydlsledlksfrqlgsktpGhPelghtagvevttGPLGqG 117
                                        D  +Ls Gh++   Y++l  +G+ ls e+lksf ++         l++   + +tt P GqG
  gi|242399579|ref|YP_002995004.1|  46 NDVIILSKGHSAPAFYVILSELGL-LSEEELKSFTKMAK-------LSKLIQLSITTYPEGQG 100
                                       6889****************9998.8889*****98754.......33444555666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 773.29
//
Query:       gi|242399580|ref|YP_002995005.1|  [L=446]
Description: glycerate kinase [Thermococcus sibiricus MM 739]
Scores for complete 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-81  272.5   0.1    3.5e-81  272.1   0.1    1.2  1  DUF4147         Domain of unknown function (DUF4147)
    8.9e-36  122.4   0.4    1.9e-35  121.3   0.4    1.6  1  MOFRL           MOFRL family
  ------ inclusion threshold ------
      0.045   14.3   0.1       0.25   11.8   0.0    2.2  3  NBD_C           Nucleotide-binding C-terminal domain
       0.11   12.8   0.1        2.4    8.6   0.0    2.7  2  GHMP_kinases_C  GHMP kinases C terminal


Domain annotation for each model (and alignments):
>> DUF4147  Domain of unknown function (DUF4147)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  272.1   0.1   7.9e-85   3.5e-81       3     229 .]      20     253 ..      18     253 .. 0.94

  Alignments for each domain:
  == domain 1  score: 272.1 bits;  conditional E-value: 7.9e-85
                                       HHHHHHHHHTTSHHHHHHTTHHHH--..............-SEEEEEESTTHHHHHHHHH....HHHGEEEEEEETT CS
                           DUF4147   3 raifeaaveavdpeklvkralslkee.......eldlskkkrvvvvgaGKAaaamaaalee...ealksgvvvvkkg 69 
                                        +++e++++++dp++++kral+++++       e+    k++++v+++GKAa++ma+a+ee   +++++g+ v+k+g
  gi|242399580|ref|YP_002995005.1|  20 LNLMEETIKSADPYEAIKRALKVEDNrliikerEFP--IKGKIYVLAFGKAACSMAQAVEEildDKIAEGIAVTKYG 94 
                                       6799*****************995554544422455..55********************88888888********* PP

                                       -----TT-EEEEE-SSS--HHHHHHHHHHHHHHSS--TT-EEEEEE-TTHHHHS--B-TT--HHHHHHHHHHHHHCT CS
                           DUF4147  70 haeekerievleaahplPdeesveaarkilelaeklkeddlvlvliSGGgSAllaaPaegitledkqaltkaLlasG 146
                                       ++ + ++i+v+ea+hp+Pde+s+++a+  +ela+k++e+d++lvliSGGgSAl+ +P++gi+ledk +++++Ll+sG
  gi|242399580|ref|YP_002995005.1|  95 YSLPLKKIKVIEAGHPIPDESSMKGAHLGVELAKKVGENDILLVLISGGGSALFMLPEDGISLEDKMKTNELLLKSG 171
                                       ***************************************************************************** PP

                                       --HHHHHHHHHTTBSSTTTHHHHHHTTSEEEEEEE--STT--TTTGGG-TTS-----HHHHHHHHHHTT---..-HH CS
                           DUF4147 147 asIqelNtVRkhlsaikGGrLaraaaparvvsLilSDVvgddldvIASGPtvpdsstfadalailekykleeklpes 223
                                       a+I e+NtVRkh+s++kGG+La++++  +++sL+lSDVvgd+l++IASGPtv+d++tf+da ++l+ y+++eklp+s
  gi|242399580|ref|YP_002995005.1| 172 AKIYEINTVRKHISKVKGGKLAKLVKG-TLISLVLSDVVGDPLEAIASGPTVKDPTTFQDAYRLLKLYNVWEKLPQS 247
                                       *************************98.************************************************* PP

                                       HHHHH. CS
                           DUF4147 224 vrelLe 229
                                       v++++e
  gi|242399580|ref|YP_002995005.1| 248 VKRHIE 253
                                       ***985 PP

>> MOFRL  MOFRL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.3   0.4   4.3e-39   1.9e-35       1     108 [.     333     438 ..     333     439 .. 0.96

  Alignments for each domain:
  == domain 1  score: 121.3 bits;  conditional E-value: 4.3e-39
                                       EEEEEEE--B----S-.----HHHHHHHHHHH...HTTT-TTEEEEEEETTS--SSSS--EEEEETTHHHHHHHTT- CS
                             MOFRL   1 vvllsgGEttvtvkgk.GkGGrnqelalalalelkelegaeevvllsagtDGiDGptdaaGaivdaetleraeaagl 76 
                                       +vl++gGEttvt++g+ G GG+nqe+al++a++++ l   ++v++l+++tDG+DGptdaaG++vd+ tle+++++++
  gi|242399580|ref|YP_002995005.1| 333 CVLIAGGETTVTIEGEpGLGGPNQEFALSIARKIAGL---KGVAVLAMDTDGTDGPTDAAGGLVDSYTLETLKKRDI 406
                                       689**********9989***************66666...9************************************ PP

                                       -HHHHHHTT-HHHHHHHTT-EE-----S---- CS
                             MOFRL  77 dakeaLanndsyeffeklgallktgpTgtNVn 108
                                       d++e+L+++++ye++++++all tgpT+tNVn
  gi|242399580|ref|YP_002995005.1| 407 DVEEFLKAHNAYEALKEVNALLLTGPTRTNVN 438
                                       *******************************8 PP

>> NBD_C  Nucleotide-binding C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0         1   4.5e+03      78     119 ..     101     143 ..      65     150 .. 0.58
   2 ?   11.8   0.0   5.6e-05      0.25      84     124 ..     300     344 ..     254     350 .. 0.71
   3 ?   -2.7   0.0       1.6   7.1e+03      29      48 ..     405     423 ..     395     433 .. 0.57

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1
                                       H---HHCCC-HHHH.HHHHHHHHHHHHHHHHHCTECEEEEESH CS
                             NBD_C  78 aleslqaelglera.geriaaalaeiarrlvergvrrlviaGG 119
                                       +++ ++a + + ++ + + a++ +e+a+++ e+ +  ++i+GG
  gi|242399580|ref|YP_002995005.1| 101 KIKVIEAGHPIPDEsSMKGAHLGVELAKKVGENDILLVLISGG 143
                                       4455555555555544455566667777776666777777766 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 5.6e-05
                                       CCC-HHHHHHHHHHHHHHHHHHHH..HCTECE..EEEESHHHHHH CS
                             NBD_C  84 aelglerageriaaalaeiarrlv..ergvrr..lviaGGdtssa 124
                                        ++ le +++++a a+++i+++++  er+++r  ++iaGG+t+  
  gi|242399580|ref|YP_002995005.1| 300 LTTTLEGEAREVAIAFGSIIEEIYhrERPFKRpcVLIAGGETTVT 344
                                       3334455599**************75555555599*******975 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 1.6
                                       EEEHHHHHSCCTCHHHHHHH CS
                             NBD_C  29 eldvealledeesaeaeier 48 
                                       ++dve++l+ +++a +++++
  gi|242399580|ref|YP_002995005.1| 405 DIDVEEFLK-AHNAYEALKE 423
                                       789999994.3333333333 PP

>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.15   6.6e+02       3      41 ..       6      41 ..       5      42 .. 0.82
   2 ?    8.6   0.0   0.00054       2.4      41      68 ..     125     153 ..     124     165 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.15
                    GHMP_kinases_C  3 ealergdlellgellnlsqrselkavvgilppeleelle 41
                                      e+l +gd+++ + +lnl+ +   +   +  +++++++l+
  gi|242399580|ref|YP_002995005.1|  6 ELLSQGDIKSKEIALNLMEE---TIKSADPYEAIKRALK 41
                                      78899***********9999...7778888888877765 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00054
                    GHMP_kinases_C  41 ealselG...algaklsGaGgGptvfalfkd 68 
                                       e+++++G   +l + +sG   G+++f+l +d
  gi|242399580|ref|YP_002995005.1| 125 ELAKKVGendILLVLISGG--GSALFMLPED 153
                                       45566666669********..*******965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); 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: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 2740.01
//
Query:       gi|242399581|ref|YP_002995006.1|  [L=139]
Description: hypothetical protein TSIB_1606 [Thermococcus sibiricus MM 739]
Scores for 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-51  171.3   1.6      1e-50  171.1   1.6    1.0  1  DUF371    Domain of unknown function (DUF371)
  ------ inclusion threshold ------
      0.072   13.2   0.0       0.11   12.7   0.0    1.4  1  OapA      Opacity-associated protein A LysM-like domain


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 !  171.1   1.6   1.2e-54     1e-50       1     132 [.       6     137 ..       6     138 .. 0.98

  Alignments for each domain:
  == domain 1  score: 171.1 bits;  conditional E-value: 1.2e-54
                                       EEEE--TT-----SSEEEEES-S---TT-TTEEEBS-S--GGGS-HHHHHHHS----EEEEEEE-SS-EEEEEEE-- CS
                            DUF371   1 ikarGHenvkaehksTleitkddeltprgdCIigveadkaaadlseelkealkeeeatitvtlevgeledeitgrGs 77 
                                       ++++GHenvka+h+sTleitk+d+ltprgdCIi+v+a+k++++ls+e+kealk+ + ++++++++++++de+++ G+
  gi|242399581|ref|YP_002995006.1|   6 VTCYGHENVKATHRSTLEITKEDYLTPRGDCIICVKANKGLKELSDEIKEALKSGR-KVKIRITADGIVDELEAVGD 81 
                                       689***************************************************99.******************** PP

                                       TT-----SSEEEEESSS---TTEEEBS-S--GGGS-HHHHHHHHT.T-EEEEEEEE CS
                            DUF371  78 pkltlenerdlvvRkSdyvddrTllvkadkaaadldrelveaLkk.gaeltvelev 132
                                       ++lt+ene ++v+RkS+yvd+rTl+++a+kaa+d++relv++L++ +++++ve++v
  gi|242399581|ref|YP_002995006.1|  82 ERLTFENEISMVIRKSEYVDGRTLAIRANKAARDIKRELVKKLRNpEQRVVVEIIV 137
                                       *********************************************999****9998 PP

>> OapA  Opacity-associated protein A LysM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.2e-05      0.11      41      68 ..      55      82 ..      28      98 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.2e-05
                              OapA 41 SnlksGqkvriklnaqgkvdelqlekga 68
                                        lksG kv+i+++a+g vdel+   ++
  gi|242399581|ref|YP_002995006.1| 55 EALKSGRKVKIRITADGIVDELEAVGDE 82
                                      579******************9865554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       742  (0.0413855); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 908.53
//
Query:       gi|242399582|ref|YP_002995007.1|  [L=67]
Description: 30S ribosomal protein S17e [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-16   60.5   0.4    1.6e-16   60.3   0.4    1.0  1  Ribosomal_S17e  Ribosomal S17


Domain annotation for each model (and alignments):
>> Ribosomal_S17e  Ribosomal S17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.3   0.4     9e-21   1.6e-16       1      64 [.       1      64 [.       1      66 [. 0.94

  Alignments for each domain:
  == domain 1  score: 60.3 bits;  conditional E-value: 9e-21
                                      XX----HHHHHHHHHHHHS-TTT--S-HHHHHHHHHHHS----SHHHHHHHHHHHHHHHHTTSS CS
                    Ribosomal_S17e  1 mgrvrtktvKkaarviiekyyskltndFhtnkkvceevaiipskklrnkiaGyvthlmkriqkg 64
                                      mg++++  +K++ar++ ++y +++t+dF++nkk +ee + i sk +rn+iaGyvt+l++  ++g
  gi|242399582|ref|YP_002995007.1|  1 MGNIKQGFIKRTARELFDRYPNEFTRDFEHNKKKVEELTNITSKTMRNRIAGYVTRLVRLKEEG 64
                                      8999999**************************************************9876666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       860  (0.047967); 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: 0.47u 0.34s 00:00:00.81 Elapsed: 00:00:00.51
# Mc/sec: 394.54
//
Query:       gi|242399583|ref|YP_002995008.1|  [L=206]
Description: Archaeal heat shock regulator, ArsR family [Thermococcus sibiricus MM 739]
Scores for complete 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-14   51.7   0.2    1.4e-13   50.5   0.2    1.6  1  HTH_5           Bacterial regulatory protein, arsR family
      4e-11   42.8   0.2    9.9e-11   41.5   0.2    1.7  1  HTH_20          Helix-turn-helix domain
    0.00022   20.9   0.1      0.039   13.5   0.0    2.3  2  ArsR            ArsR transcriptional regulator
     0.0003   20.7   0.2      0.025   14.5   0.1    2.4  2  HTH_11          HTH domain
    0.00042   20.2   2.4    0.00062   19.7   0.1    2.5  2  PadR            Transcriptional regulator PadR-like family
    0.00059   19.7   0.1     0.0016   18.3   0.1    1.7  1  TrmB            Sugar-specific transcriptional regulator TrmB
    0.00065   19.6   1.3     0.0009   19.2   1.3    1.2  1  Apolipoprotein  Apolipoprotein A1/A4/E domain
     0.0022   17.5   4.4     0.0051   16.3   1.5    3.0  3  HTH_24          Winged helix-turn-helix DNA-binding
     0.0029   17.4   0.1      0.016   15.0   0.1    2.2  2  MarR_2          MarR family
  ------ inclusion threshold ------
      0.012   15.6   0.1       0.15   12.0   0.0    2.3  2  MarR            MarR family
      0.013   15.4   3.5      0.088   12.7   0.1    2.7  3  HxlR            HxlR-like helix-turn-helix
      0.022   14.8   0.0      0.037   14.1   0.0    1.3  1  SRP1_TIP1       Seripauperin and TIP1 family
      0.027   15.0   0.0      0.062   13.8   0.0    1.6  1  HTH_27          Winged helix DNA-binding domain
       0.04   13.7   0.1        0.2   11.5   0.0    2.2  3  HTH_10          HTH DNA binding domain
      0.049   13.5   3.4       0.23   11.3   0.1    3.1  3  IF2_N           Translation initiation factor IF-2, N-termina
      0.052   13.7   0.4       0.09   12.9   0.4    1.4  1  DUF613          Protein of unknown function (DUF613)
      0.064   13.0   5.5       0.11   12.3   5.5    1.3  1  Geminin         Geminin
       0.11   11.8   0.7       0.16   11.2   0.7    1.2  1  Topoisom_I      Eukaryotic DNA topoisomerase I, catalytic cor
        0.2   11.5   5.1       0.28   11.0   5.1    1.2  1  PCRF            PCRF domain
        0.2   10.4   1.9       0.27   10.0   1.9    1.1  1  Mgr1            Mgr1-like, i-AAA protease complex subunit
       0.25   10.9   8.5          1    8.9   0.1    3.0  3  DDRGK           DDRGK domain
       0.44   10.6   8.7        3.6    7.7   0.7    2.9  3  NYD-SP28        Sperm tail
          2    9.1  10.9        1.9    9.1   8.6    1.7  1  Com_YlbF        Control of competence regulator ComK, YlbF/Ym
        3.9    7.2   6.9       0.87    9.3   0.5    2.7  2  TFA2_Winged_2   TFA2 Winged helix domain 2


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 !   50.5   0.2   1.9e-16   1.4e-13       1      46 [.      18      63 ..      18      63 .. 0.97

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 1.9e-16
                                      SHHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  1 dptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      ++tR++IL lL ++++ ++el++el++ q +v +HL++L+ aGL+e
  gi|242399583|ref|YP_002995008.1| 18 NETRRRILLLLTKRPYFISELSKELNVGQKAVLEHLRILEGAGLIE 63
                                      68******************************************96 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.5   0.2   1.3e-13   9.9e-11       3      59 ..      12      67 ..      10      68 .. 0.96

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 1.3e-13
                                      HHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECT CS
                            HTH_20  3 iaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvre 59
                                      ++++L++++Rrril +L ++++   sel ++l + ++ +  HLr+Le agL+e++ e
  gi|242399583|ref|YP_002995008.1| 12 LLDVLGNETRRRILLLL-TKRPYFISELSKELNVGQKAVLEHLRILEGAGLIEGRVE 67
                                      789**************.***********************************9976 PP

>> ArsR  ArsR transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   5.3e-05     0.039      10      75 ..      12      79 ..       8      83 .. 0.84
   2 ?    5.1   0.3     0.021        16     103     146 ..     128     171 ..     106     197 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.3e-05
                              ArsR 10 llqvfdsetkkkvyeelskeWlteeeleekl..gee.veealklLkkikliEsqWrmpepgekpekeYh 75
                                      ll v+++et ++++  l+k+ +  +el+++l  g++ v e l++L+ ++liE + +   p   p+k Y+
  gi|242399583|ref|YP_002995008.1| 12 LLDVLGNETRRRILLLLTKRPYFISELSKELnvGQKaVLEHLRILEGAGLIEGRVEKI-PRGRPRKYYQ 79
                                      8999***********************99762255579999***********986543.5688998886 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.021
                              ArsR 103 deeleelvekiekeveegntsisdlsrklglsplfiralakrse 146
                                        +el ++ ++ie+ +ee  ++ s+l +   l ++++r l+ r  
  gi|242399583|ref|YP_002995008.1| 128 VKELADFLNEIEERIEEYMKMKSELEEVRMLAETYMRNLMMRVA 171
                                       46888899999999999999999999999999999998887765 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   3.3e-05     0.025       3      48 ..      22      64 ..      20      78 .. 0.81
   2 ?    3.9   0.0      0.07        53       6      26 ..     114     136 ..     109     136 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.3e-05
                            HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvpIes 48
                                      + il lL  +r+   ++eL++eLnv  ++v  ++++Le +g  Ie+
  gi|242399583|ref|YP_002995008.1| 22 RRILLLL-TKRP-YFISELSKELNVGQKAVLEHLRILEGAG-LIEG 64
                                      6677777.5555.5788***********************9.4444 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.07
                            HTH_11   6 lelLleargp..isgeeLAeeLn 26 
                                       +++L+++rgp  i  +eLA+ Ln
  gi|242399583|ref|YP_002995008.1| 114 VKQLIKSRGPveIKVKELADFLN 136
                                       689999999989999****9886 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.1   8.3e-07   0.00062      27      65 ..      42      80 ..      24      85 .. 0.78
   2 ?   -2.0   0.0       4.8   3.6e+03       4      22 ..     170     188 ..     167     202 .. 0.68

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 8.3e-07
                                      CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEE CS
                              PadR 27 lelseGslYpaLkrLekeglveseweesgegpprkyYrl 65
                                      l++ +  +   L+ Le  gl+e++ e+  +g+prkyY++
  gi|242399583|ref|YP_002995008.1| 42 LNVGQKAVLEHLRILEGAGLIEGRVEKIPRGRPRKYYQI 80
                                      455566677889**************99*********98 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.8
                                       HHCCS-EEHHHHHHHHHCC CS
                              PadR   4 lleeqpsyGyeiikeleel 22 
                                       +++e++ +  e+ +e+ee 
  gi|242399583|ref|YP_002995008.1| 170 VAKESEDHFDELLEEFEEI 188
                                       5566666767777777765 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1   2.1e-06    0.0016      16      64 ..      26      79 ..      23      82 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.1e-06
                                      HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.....TTEEEE CS
                              TrmB 16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.....pklYra 64
                                       Ll++ p  ++e+++el+v +  v e Lr Le +Gl+e + ++     p++Y  
  gi|242399583|ref|YP_002995008.1| 26 LLLTKRPYFISELSKELNVGQKAVLEHLRILEGAGLIEGRVEKiprgrPRKYYQ 79
                                      578999999*****************************9988888889888865 PP

>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   1.3   1.2e-06    0.0009      27     104 ..     103     188 ..      86     204 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.2e-06
                                       HHHHHHHHHHHHHHHH.........HHHHHHHHHHCCCCHHHHHHCCCHHHHHHHHHCCHHHHHHHHHHHHCHHCCH CS
                    Apolipoprotein  27 lrdrlskeleelrarl.........raeleevrarlepyrdevqeqlgqnleelrqrlapyteelrerlaadaeelq 94 
                                        ++r +ke ee+++ +          +el +  + +e++++e   +++++lee+r   ++y ++l+ r+a+++e+  
  gi|242399583|ref|YP_002995008.1| 103 KAPRTTKEYEEVKQLIksrgpveikVKELADFLNEIEERIEEY-MKMKSELEEVRMLAETYMRNLMMRVAKESEDHF 178
                                       67899999999999999999999999****************9.789************************999988 PP

                                       HCHCCHCHHH CS
                    Apolipoprotein  95 eqlavyaeel 104
                                       + l +  ee+
  gi|242399583|ref|YP_002995008.1| 179 DELLEEFEEI 188
                                       8888888873 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   1.5   6.8e-06    0.0051       2      48 .]      18      63 ..      17      63 .. 0.94
   2 ?   -1.2   0.0       2.1   1.6e+03      18      28 ..     126     136 ..     124     136 .. 0.85
   3 ?   -2.7   0.1         6   4.5e+03      12      27 ..     182     197 ..     180     198 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 6.8e-06
                            HTH_24  2 detdrkILelLqknpr.isqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      +et+r+IL lL k p  is  eL+++l++ + +v+++l+ Le +GlI+
  gi|242399583|ref|YP_002995008.1| 18 NETRRRILLLLTKRPYfIS--ELSKELNVGQKAVLEHLRILEGAGLIE 63
                                      799**********888776..*************************97 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.1
                            HTH_24  18 isqreLAerlg 28 
                                       i  +eLA+ l+
  gi|242399583|ref|YP_002995008.1| 126 IKVKELADFLN 136
                                       7789***9987 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 6
                            HTH_24  12 LqknprisqreLAerl 27 
                                       L++   i  reL e+l
  gi|242399583|ref|YP_002995008.1| 182 LEEFEEILPRELIEEL 197
                                       5566667778888876 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   2.2e-05     0.016       6      54 ..      20      65 ..       8      71 .. 0.87
   2 ?   -1.4   0.0       2.9   2.2e+03      16      31 ..     120     135 ..     117     136 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.2e-05
                                      HHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2  6 aqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                      + +r+L+ L  rp     ++el ++l++ + av  +l+ L+ aGL+e r
  gi|242399583|ref|YP_002995008.1| 20 TRRRILLLLTKRP---YFISELSKELNVGQKAVLEHLRILEGAGLIEGR 65
                                      5678888888888...6*****************************965 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.9
                                       CTTTSEEEHHHHHHHH CS
                            MarR_2  16 rrpgrdltvgelarrl 31 
                                        r++ ++ v+ela+ l
  gi|242399583|ref|YP_002995008.1| 120 SRGPVEIKVKELADFL 135
                                       56666889*****987 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0    0.0002      0.15      18      48 ..      33      63 ..      18      65 .. 0.86
   2 ?    0.9   0.0       0.6   4.5e+02      12      28 ..     118     136 ..     116     136 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0002
                                      EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR 18 lsvseLakklgvskstvtrvldrLekkGlie 48
                                        +seL k l+v + +v + l+ Le +Glie
  gi|242399583|ref|YP_002995008.1| 33 YFISELSKELNVGQKAVLEHLRILEGAGLIE 63
                                      5589**************************7 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.6
                                       HHHSTT..EEHHHHHHHHT CS
                              MarR  12 lyeqgp..lsvseLakklg 28 
                                       ++++gp  ++v+eLa++l+
  gi|242399583|ref|YP_002995008.1| 118 IKSRGPveIKVKELADFLN 136
                                       677777336666***9986 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   0.00012     0.088       3      72 ..      17      86 ..      15     103 .. 0.75
   2 ?   -2.0   0.0       4.5   3.3e+03      70      88 ..     129     147 ..     124     150 .. 0.71
   3 ?    3.2   0.1      0.11        82       9      46 ..     166     203 ..     158     206 .] 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00012
                                      HSTTHHHHHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEE..SSSS-EEEEEE-TCGGGG CS
                              HxlR  3 ggkWkllilvellkgkkRfselkralpkisqkmLaqrLreLeqdglierevy..pevPpkveYsltekGrsl 72
                                      g+  +  il  l+k +   sel+++l ++ qk   ++Lr Le  glie +v   p+  p+  Y+  ++G  l
  gi|242399583|ref|YP_002995008.1| 17 GNETRRRILLLLTKRPYFISELSKEL-NVGQKAVLEHLRILEGAGLIEGRVEkiPRGRPRKYYQ-IKRGIRL 86
                                      555566799999999999********.********************97664114444544444.3555555 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.5
                                       GGGHHHHHHHHHHHHHHHH CS
                              HxlR  70 rslepvlqelkkwgeeyle 88 
                                       ++l++ l+e+++ +eey++
  gi|242399583|ref|YP_002995008.1| 129 KELADFLNEIEERIEEYMK 147
                                       5677777777777777776 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.11
                                       HHHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHT CS
                              HxlR   9 lilvellkgkkRfselkralpkisqkmLaqrLreLeqd 46 
                                       l+++   + +  f el +++ +i  + L+++L++++++
  gi|242399583|ref|YP_002995008.1| 166 LMMRVAKESEDHFDELLEEFEEILPRELIEELKRIKKE 203
                                       566777788999*********************99876 PP

>> SRP1_TIP1  Seripauperin and TIP1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0     5e-05     0.037      10      67 ..     126     185 ..     118     196 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5e-05
                         SRP1_TIP1  10 aevaelevllnDvksnlkeYlslakansgfs..lPsgvlsvyaalatatddsYttllsei 67 
                                        +v+el+ +ln +++ ++eY+++ ++ +++     + + ++++ +a++++d +  ll+e+
  gi|242399583|ref|YP_002995008.1| 126 IKVKELADFLNEIEERIEEYMKMKSELEEVRmlAETYMRNLMMRVAKESEDHFDELLEEF 185
                                       6899*********************96666643456678899999999999999998875 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   8.3e-05     0.062      16      52 ..      30      66 ..      22      81 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.3e-05
                            HTH_27 16 rrrkkladlcgrlnvedshisyslkkLtekGLvertg 52
                                       r+  +++l++ lnv++ ++ + l+ L+ +GL+e   
  gi|242399583|ref|YP_002995008.1| 30 KRPYFISELSKELNVGQKAVLEHLRILEGAGLIEGRV 66
                                      5666689**************************4333 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00026       0.2      26      47 ..      35      56 ..      29      59 .. 0.87
   2 ?   -2.7   0.0       7.4   5.6e+03      17      29 ..      77      89 ..      77      89 .. 0.86
   3 ?   -1.9   0.0       4.1     3e+03      23      33 ..     125     135 ..     123     144 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00026
                            HTH_10 26 lkeLAkelGIskstlsehLrka 47
                                      ++eL+kel++ + +++ehLr  
  gi|242399583|ref|YP_002995008.1| 35 ISELSKELNVGQKAVLEHLRIL 56
                                      78******************75 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 7.4
                            HTH_10 17 YFdyPRrvtlkeL 29
                                      Y+   R ++l+ L
  gi|242399583|ref|YP_002995008.1| 77 YYQIKRGIRLEVL 89
                                      9999999999865 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 4.1
                            HTH_10  23 rvtlkeLAkel 33 
                                       ++++keLA+ l
  gi|242399583|ref|YP_002995008.1| 125 EIKVKELADFL 135
                                       56777777654 PP

>> IF2_N  Translation initiation factor IF-2, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00031      0.23       6      24 ..      35      53 ..      34      56 .. 0.94
   2 ?    1.1   0.1      0.48   3.6e+02       4      14 ..     126     136 ..     123     148 .. 0.72
   3 ?   -1.4   0.1       2.9   2.2e+03      17      26 ..     190     198 ..     175     199 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00031
                             IF2_N  6 VyeLAkeLgvkskevikkL 24
                                      ++eL keL+v  k v+++L
  gi|242399583|ref|YP_002995008.1| 35 ISELSKELNVGQKAVLEHL 53
                                      79***************99 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.48
                             IF2_N   4 irVyeLAkeLg 14 
                                       i V+eLA+ L+
  gi|242399583|ref|YP_002995008.1| 126 IKVKELADFLN 136
                                       67777776555 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 2.9
                             IF2_N  17 skevikkLfk 26 
                                       + e+i++L k
  gi|242399583|ref|YP_002995008.1| 190 PRELIEEL-K 198
                                       56888888.4 PP

>> DUF613  Protein of unknown function (DUF613)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.4   0.00012      0.09      49      89 ..     122     163 ..     107     189 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00012
                            DUF613  49 GPlkikvseyekitkiikkrtkrykkllee.kkikginiifq 89 
                                       GP++ikv+e+    + i++r ++y+k+ +e ++++ +  ++ 
  gi|242399583|ref|YP_002995008.1| 122 GPVEIKVKELADFLNEIEERIEEYMKMKSElEEVRMLAETYM 163
                                       9**************************988787776554444 PP

>> Geminin  Geminin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   5.5   0.00014      0.11     136     185 ..     136     183 ..     126     191 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00014
                           Geminin 136 keiEqkdeeiarLkeENeeLaelAeHVqymadmieRLtgkspdnleelke 185
                                        eiE++ ee  ++k+E ee++ lAe   ym +++ R+ ++s d ++el e
  gi|242399583|ref|YP_002995008.1| 136 NEIEERIEEYMKMKSELEEVRMLAE--TYMRNLMMRVAKESEDHFDELLE 183
                                       69**********************9..6*****************99855 PP

>> Topoisom_I  Eukaryotic DNA topoisomerase I, catalytic core
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.7   0.00022      0.16      15      64 ..     127     176 ..     126     181 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00022
                                       HHHHHHHHHHHHHHHHHHHTT-S-HHHHHHHHHHHHHHHH---------T CS
                        Topoisom_I  15 karkLkkvvekiredykkklkskeilekqlatavylidklaLrvGnekee 64 
                                       k+++L++++++i e++++ +k k+ le+++ +a   + +l++rv +e e+
  gi|242399583|ref|YP_002995008.1| 127 KVKELADFLNEIEERIEEYMKMKSELEEVRMLAETYMRNLMMRVAKESED 176
                                       6899*****************************************99765 PP

>> PCRF  PCRF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   5.1   0.00037      0.28       2      91 ..     108     194 ..     107     205 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00037
                                       HHHHTTTTTST.-GGGTTTGGGSSSTTHHHHHTHHHHHHHHHHHHHTTTHHH...HT....-S-..-GGGTHHHHHH CS
                              PCRF   2 eeeleelekklsdpevwedqekakklskelaeleeivealeeleealedleeakelleedeelaelaeeeleeleke 78 
                                       ++e+ee+++ +++   +e   k+k+l+  l+e+ee +e++ +++++le+++ + e +   + + ++a+e  +++++ 
  gi|242399583|ref|YP_002995008.1| 108 TKEYEEVKQLIKSRGPVE--IKVKELADFLNEIEERIEEYMKMKSELEEVRMLAETY-MRNLMMRVAKESEDHFDEL 181
                                       579999999999988876..5889999999999999999999999999999988877.3334444566655666666 PP

                                       HHHH..HHHHHT- CS
                              PCRF  79 leeleeelkklLl 91 
                                       lee+ee l + L+
  gi|242399583|ref|YP_002995008.1| 182 LEEFEEILPRELI 194
                                       6666555666555 PP

>> Mgr1  Mgr1-like, i-AAA protease complex subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   1.9   0.00036      0.27     245     313 ..     113     187 ..     106     203 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00036
                              Mgr1 245 aenpiikWfGPleykPmsfseyLd....rleyhLdmlellqekr..kskeaskellekikhteeeleelieknke 313
                                           +ik  GP+e+k    +++L+    r+e +++m   l+e r  +++ + + +++  k++e++ +el e+ +e
  gi|242399583|ref|YP_002995008.1| 113 EVKQLIKSRGPVEIKVKELADFLNeieeRIEEYMKMKSELEEVRmlAETYMRNLMMRVAKESEDHFDELLEEFEE 187
                                       456799*****************7333356667788888888883233344556677777899999999887665 PP

>> DDRGK  DDRGK domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.015        11     114     145 ..      33      64 ..      21      73 .. 0.89
   2 ?    8.9   0.1    0.0014         1     157     186 ..     107     138 ..     106     140 .. 0.89
   3 ?   -2.0   4.0       3.1   2.3e+03      41      79 ..     144     182 ..     135     206 .] 0.34

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.015
                                       E-HHHHHHHH-S-HHHHHHHHHHHHHHSSS-E CS
                             DDRGK 114 vlleelavkfklktqevierikeLeeqgsltG 145
                                         + el+ ++++  + v e ++ Le  g ++G
  gi|242399583|ref|YP_002995008.1|  33 YFISELSKELNVGQKAVLEHLRILEGAGLIEG 64 
                                       5699**************************99 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0014
                                       --XXXXXXXXXXXXXXXX..XXXXXXXXXXXX CS
                             DDRGK 157 tdeEleavakyikkkGrv..siselveesnkl 186
                                       t +E+e v++ ik++G v  + +el+ + n++
  gi|242399583|ref|YP_002995008.1| 107 TTKEYEEVKQLIKSRGPVeiKVKELADFLNEI 138
                                       679*************9977889***999975 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 3.1
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             DDRGK  41 erkekeekeeekekkkeeeerkkeeekerkeqeeyeklk 79 
                                       e+ + + + ee +  +e  +r+     +++ ++ +++l 
  gi|242399583|ref|YP_002995008.1| 144 EYMKMKSELEEVRMLAETYMRNLMMRVAKESEDHFDELL 182
                                       222222222222222222222222222222222222222 PP

>> NYD-SP28  Sperm tail
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       1.2   9.3e+02      64      91 ..      23      50 ..      13      55 .. 0.70
   2 ?    5.8   1.3     0.019        14      48      75 ..     125     152 ..      95     157 .. 0.76
   3 ?    7.7   0.7    0.0049       3.6      16      56 ..     159     199 ..     153     204 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.2
                          NYD-SP28 64 aceelideKdklikelqeeLkekdeqyv 91
                                      ++  l+ ++  +i+el +eL+  ++   
  gi|242399583|ref|YP_002995008.1| 23 RILLLLTKRPYFISELSKELNVGQKAVL 50
                                      5555666667789999999987766555 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.019
                          NYD-SP28  48 knkpqeLrkeleeqkqaceelideKdkl 75 
                                       + k +eL + l+e ++++ee ++ K +l
  gi|242399583|ref|YP_002995008.1| 125 EIKVKELADFLNEIEERIEEYMKMKSEL 152
                                       6799********************9886 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0049
                          NYD-SP28  16 lrqerkekleeeaksseekfeeinekWreilrknkpqeLrk 56 
                                       + +++++ + + ak+se+ f+e+ e+++eil ++  +eL++
  gi|242399583|ref|YP_002995008.1| 159 AETYMRNLMMRVAKESEDHFDELLEEFEEILPRELIEELKR 199
                                       667899999999*******************9999999975 PP

>> Com_YlbF  Control of competence regulator ComK, YlbF/YmcA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   8.6    0.0026       1.9      19     100 ..     109     189 ..     103     193 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0026
                                       HHHHHHHHHHHCSHHHHHHHHHHHHHHHHHHHHHHTT----HHHHHHHHHHHHHHHTSHHHHHHHHHHHHHHHHHHH CS
                          Com_YlbF  19 keykeaeealeedeelqklikefkklqkelqekqmkgeelkeeekkelqelkeeldknplvkeyleaeqelnellqe 95 
                                       key+e ++ +++   +  ++ke+ +  +e++e  + + ++k e + e++ l e ++ n  ++  +e+e+ ++ell+e
  gi|242399583|ref|YP_002995008.1| 109 KEYEEVKQLIKSRGPVEIKVKELADFLNEIEERIEEYMKMKSELE-EVRMLAETYMRNLMMRVAKESEDHFDELLEE 184
                                       788888888888888888888888888888887777777788888.9****************************** PP

                                       HHHHH CS
                          Com_YlbF  96 vnkii 100
                                         +i+
  gi|242399583|ref|YP_002995008.1| 185 FEEIL 189
                                       99997 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 ?    0.8   0.0      0.52   3.9e+02      22      42 ..      40      60 ..      19      69 .. 0.74
   2 ?    9.3   0.5    0.0012      0.87       4      37 ..     112     144 ..     109     155 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.52
                     TFA2_Winged_2 22 kdLkdswpdveealeeLeaeg 42
                                      k+L+ + + v e+l+ Le+ g
  gi|242399583|ref|YP_002995008.1| 40 KELNVGQKAVLEHLRILEGAG 60
                                      788888888999999998866 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0012
                     TFA2_Winged_2   4 eeLlalLkkrpkaeGikvkdLkdswpdveealee 37 
                                       ee ++l+k+r +++ ikvk+L d     ee +ee
  gi|242399583|ref|YP_002995008.1| 112 EEVKQLIKSR-GPVEIKVKELADFLNEIEERIEE 144
                                       899*******.9***********99999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1914  (0.106754); expected 358.6 (0.02)
Passed bias filter:                     1063  (0.0592894); expected 358.6 (0.02)
Passed Vit filter:                       149  (0.00831056); 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 0.29s 00:00:00.92 Elapsed: 00:00:00.48
# Mc/sec: 1302.74
//
Query:       gi|242399584|ref|YP_002995009.1|  [L=227]
Description: Glyoxalase II family member [Thermococcus sibiricus MM 739]
Scores for 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-30  104.3   0.8    9.4e-30  104.1   0.8    1.1  1  Lactamase_B    Metallo-beta-lactamase superfamily
    1.9e-11   43.9   0.0    2.6e-11   43.4   0.0    1.2  1  Lactamase_B_5  Metallo-beta-lactamase superfamily
    3.2e-06   26.8   0.1    4.2e-06   26.4   0.1    1.2  1  Lactamase_B_2  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.051   13.0   0.0       0.08   12.4   0.0    1.2  1  Lactamase_B_6  Metallo-beta-lactamase superfamily domain
       0.11   12.6   0.0         16    5.6   0.0    2.3  2  DUF3683        Protein of unknown function (DUF3683)


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 !  104.1   0.8   2.6e-33   9.4e-30       4     183 ..      31     195 ..      28     206 .. 0.90

  Alignments for each domain:
  == domain 1  score: 104.1 bits;  conditional E-value: 2.6e-33
                                       CSSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHH CS
                       Lactamase_B   4 dpvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeap 80 
                                       +++n+yli+ +++ i iD+G+++e+++ ++ + +l++ p++v+++i+TH+H+DH+G l++l++at+++v+a++ee p
  gi|242399584|ref|YP_002995009.1|  31 TFANVYLIVRKDKIIAIDAGLPEEYEKVLEYIDSLRRFPEEVETIIVTHAHYDHVGSLKDLKDATGANVAAHEEEIP 107
                                       578************************************************************************** PP

                                       CCHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHC CS
                       Lactamase_B  81 alfmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallaget 157
                                       +l++e               +++  + v  e+   +++++++l+v++ pgh++g++++ + + k lf+GD++ +++ 
  gi|242399584|ref|YP_002995009.1| 108 YLTGEKT-------------FRRTINPVEVEISLKDGDEIHGLKVIHSPGHTPGSICLLDLETKALFVGDLVMEENG 171
                                       *******.............7788889*********************************************96655 PP

                                       CCCCC.TTCEEE-SHCHHHHHHHHHH CS
                       Lactamase_B 158 gridltlrgaevrdpsdaekyldsll 183
                                        + +      + +dp  +++++++ll
  gi|242399584|ref|YP_002995009.1| 172 KLKEI--PHQYSLDPMKNREAIRRLL 195
                                       55555..4466666666666666655 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 !   43.4   0.0   7.1e-15   2.6e-11      55     197 ..      71     223 ..      27     225 .. 0.78

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 7.1e-15
                     Lactamase_B_5  55 gvawivltns..dhlraakeiaeltyakiagp.......aaeketf.....piacdrwlsdgdelvsglkvlelkgs 117
                                        v+ i++t +  dh+ + k++ + t+a++a+        ++ek  f     p++ +  l+dgde + glkv++  g 
  gi|242399584|ref|YP_002995009.1|  71 EVETIIVTHAhyDHVGSLKDLKDATGANVAAHeeeipylTGEKT-FrrtinPVEVEISLKDGDE-IHGLKVIHSPG- 144
                                       5788999975449*****************96222223235553.2233349************.58*****9877. PP

                     Lactamase_B_5 118 ktpgelall.leettlitgdlvrakkagsltllpdekllnreeavasvrrlaalekieavlvgdgwsvfrdgsdrlk 193
                                       +tpg ++ll le ++l  gdlv  ++ g l  +p++  l+  +   ++rrl +++ ++ +l   g +++ +g+++l+
  gi|242399584|ref|YP_002995009.1| 145 HTPGSICLLdLETKALFVGDLVM-EENGKLKEIPHQYSLDPMKNREAIRRLLDVDFVH-LLPSHGQPILNEGKEKLR 219
                                       699999988799**********7.568***************************9996.7899************** PP

                     Lactamase_B_5 194 elaa 197
                                       el+ 
  gi|242399584|ref|YP_002995009.1| 220 ELVG 223
                                       **86 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 !   26.4   0.1   1.2e-09   4.2e-06      24     116 ..      65     145 ..      44     181 .. 0.66

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 1.2e-09
                                       SS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTTTTEEEEEE-TTSEEEECS CS
                     Lactamase_B_2  24 lrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleeepavnvheldwgesfelgd 100
                                       lr+ +++++ +++thaHyDH+  l +l+  ++  +++ a+++ + +l+ +  +         ++++++ + s++ g 
  gi|242399584|ref|YP_002995009.1|  65 LRRFPEEVETIIVTHAHYDHVGSLKDLKDATG--ANVAAHEEEIPYLTGEKTFR-------RTINPVEVEISLKDG- 131
                                       5667889**********************544..67889988888888884333.......333444444444444. PP

                                       TTEEEEEEEE-EE--C CS
                     Lactamase_B_2 101 ggleitatparhksgr 116
                                        + ei+   + h+ g 
  gi|242399584|ref|YP_002995009.1| 132 -D-EIHGLKVIHSPGH 145
                                       .3.4555555555555 PP

>> Lactamase_B_6  Metallo-beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   2.2e-05      0.08       9      55 ..      45      91 ..      38     102 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.2e-05
                     Lactamase_B_6  9 iLlDvGwdeskvslesalkelekviptvdliLLshatlehlGayall 55
                                      i +D G  e+  ++ + ++ l++  ++v+ i+++ha  +h+G++  l
  gi|242399584|ref|YP_002995009.1| 45 IAIDAGLPEEYEKVLEYIDSLRRFPEEVETIIVTHAHYDHVGSLKDL 91
                                      7799999998777778888888899*****************98655 PP

>> DUF3683  Protein of unknown function (DUF3683)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0    0.0091        33      40     102 ..      11      76 ..       4      88 .. 0.64
   2 ?    5.6   0.0    0.0045        16       2      31 ..     172     203 ..     171     208 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0091
                           DUF3683  40 tgrsarllyevlGdiwvvrRnpylqddlldnkkr....rkalvealehrleeiekrrereekveell 102
                                         +   ++++v+Gdi++v+ n + +  l+  k +     + l e+ e+ le i++ r+  e+ve+++
  gi|242399584|ref|YP_002995009.1|  11 QCKNGDFIMKVIGDIHLVD-NTFANVYLIVRKDKiiaiDAGLPEEYEKVLEYIDSLRRFPEEVETII 76 
                                       55667789********997.55555555544444111134466666666777777666666666665 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0045
                           DUF3683   2 rlReiPynyt..sfsDreivirllgeeawell 31 
                                       +l+eiP+ y    +++re++ rll+ + ++ll
  gi|242399584|ref|YP_002995009.1| 172 KLKEIPHQYSldPMKNREAIRRLLDVDFVHLL 203
                                       579***999743699***********999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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 0.33s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 1305.20
//
Query:       gi|242399585|ref|YP_002995010.1|  [L=841]
Description: type III restriction enzyme, res subunit [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.1e-38  132.0   0.0    4.4e-38  131.0   0.0    1.6  1  ResIII      Type III restriction enzyme, res subunit
    7.1e-21   74.9   0.0    1.4e-20   74.0   0.0    1.5  1  SWI2_SNF2   SWI2/SNF2 ATPase
    2.7e-17   63.4   0.8    6.6e-17   62.1   0.8    1.7  1  EcoEI_R_C   EcoEI R protein C-terminal
    4.8e-11   42.6   0.0    1.4e-10   41.1   0.0    1.8  1  HSDR_N_2    Type I restriction enzyme R protein N terminus (H
    1.6e-09   38.0   0.0    4.2e-07   30.1   0.0    2.7  1  HSDR_N      Type I restriction enzyme R protein N terminus (H
    1.8e-07   31.5   0.0    4.6e-07   30.2   0.0    1.7  1  Helicase_C  Helicase conserved C-terminal domain
    2.8e-07   30.5   0.0    6.9e-06   25.9   0.0    2.8  3  DEAD        DEAD/DEAH box helicase
     0.0019   17.0   0.0     0.0052   15.5   0.0    1.6  2  SNF2_N      SNF2 family N-terminal domain
  ------ inclusion threshold ------
      0.027   13.7   0.0      0.054   12.7   0.0    1.4  1  DUF2075     Uncharacterized conserved protein (DUF2075)
       0.04   13.4   0.0      0.096   12.1   0.0    1.5  2  PhoH        PhoH-like protein
      0.097   11.5   0.0       0.16   10.9   0.0    1.2  1  AAA_34      P-loop containing NTP hydrolase pore-1
      0.099   11.7   0.0       0.22   10.5   0.0    1.5  1  T2SSE       Type II/IV secretion system protein


Domain annotation for each model (and alignments):
>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.0   0.0     3e-41   4.4e-38       2     171 .]     160     315 ..     159     315 .. 0.97

  Alignments for each domain:
  == domain 1  score: 131.0 bits;  conditional E-value: 3e-41
                                       -EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGT CS
                            ResIII   2 lelreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkfl 78 
                                       +++r+yQ  a+++ le++   ++kr+l+ maTG+GKT+va++++++l+k++  +k+lf+v+r  l +q++++f+ f 
  gi|242399585|ref|YP_002995010.1| 160 KKPRYYQDVAVRRALEEIL-LGRKRLLLTMATGSGKTYVAFQIAWKLRKSNFLKKILFIVDRVYLRNQAYNAFEAFG 235
                                       689***************9.********************************************************* PP

                                       GG....GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.TTTHHHHH CS
                            ResIII  79 seaykeigkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakkswreile 155
                                       ++       +++gd+ ++       k+++++t+q+l++++ ++++  + +++d+fd++iiDE+Hr+g  + w  il 
  gi|242399585|ref|YP_002995010.1| 236 NSR-----WELKGDNFNF------AKDVYFATYQTLYSEK-NGKRVYQYFDPDYFDLVIIDECHRSGW-NRWHDILG 299
                                       987.....589*******......9***************.779************************.******** PP

                                       T---SEEEEEESS-S- CS
                            ResIII 156 kfkeavllglTATper 171
                                       +f++a+ lglTATp+r
  gi|242399585|ref|YP_002995010.1| 300 YFNNAIHLGLTATPKR 315
                                       **************96 PP

>> SWI2_SNF2  SWI2/SNF2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.0   0.0   9.3e-24   1.4e-20       1     189 [.     165     345 ..     165     375 .. 0.85

  Alignments for each domain:
  == domain 1  score: 74.0 bits;  conditional E-value: 9.3e-24
                         SWI2_SNF2   1 qQyravekavervkegdrkgGviWHtqGSGKsltmvflakklleeelknpkvvvvtDRkdLdkQlsktfakageekp 77 
                                       +Q +av++a+e++  g rk  ++   +GSGK++  + +a kl++ +   +k+++++DR  L +Q ++ f+++g+++ 
  gi|242399585|ref|YP_002995010.1| 165 YQDVAVRRALEEILLG-RKRLLLTMATGSGKTYVAFQIAWKLRK-SNFLKKILFIVDRVYLRNQAYNAFEAFGNSRW 239
                                       5889999999999997.788899999******************.88899********************9987764 PP

                         SWI2_SNF2  78 kqaesrkeLkellekesekiifttiqKfe.ee.ekeklevlsereniivlvDEaHRsqygelakklrkalpnaafig 152
                                              eLk    + +++++f+t q +  e+  k+ ++ ++ +   +v++DE+HRs  ++ ++ l   ++na ++g
  gi|242399585|ref|YP_002995010.1| 240 -------ELKGDNFNFAKDVYFATYQTLYsEKnGKRVYQYFDPDYFDLVIIDECHRSGWNRWHDIL-GYFNNAIHLG 308
                                       .......4554443457899******9973332334568888888889*************99865.789******* PP

                         SWI2_SNF2 153 FTGTPilkkdkktkevFgeyidkYtikeaveDgavvp 189
                                       +T TP  +++ +  + Fg+ + +Y++++ +eDg   p
  gi|242399585|ref|YP_002995010.1| 309 LTATPKRSDNVDVYKYFGDPVYEYKLAQGIEDGYLAP 345
                                       *********************************9876 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 !   62.1   0.8   4.4e-20   6.6e-17       2     169 .]     679     835 ..     678     835 .. 0.92

  Alignments for each domain:
  == domain 1  score: 62.1 bits;  conditional E-value: 4.4e-20
                         EcoEI_R_C   2 eyvekfrkfieenkdsidaLqiiwsdreltkellkeLeekLkepppgitpealweayellekkvspqltdlidlirk 78 
                                       eyv+++++++++  +s+++L++iw +r+++ +  +eL+++      gi+ + +    +  e       +d +dl++ 
  gi|242399585|ref|YP_002995010.1| 679 EYVKYSQEQVRKRVASLEDLKKIWLNRQVRLRFKEELKKA------GIDLKMISLIKKVSE-------ADEFDLLAN 742
                                       8***************************************......****99988885553.......3******** PP

                         EcoEI_R_C  79 iagldeeletrserverafkrwikekkft....eeqrewLelildhiaangviel..ddldeapefkqkgglgkayk 149
                                       ++++ +++++r+er++ +++     k+f+    e+ re++  ++dh+   g  e+   ++ ++p+f+ +ggl+ +++
  gi|242399585|ref|YP_002995010.1| 743 LLFQ-APIVSRDERAKLFMEVK---KEFLdrfgERGREIILDLIDHYRLYGLSEIedPKVFNLPNFQIYGGLKGIAR 815
                                       ****.89*********999983...34444555**********************9989999999************ PP

                         EcoEI_R_C 150 lFGgkqeldeileelneely 169
                                       +FGg + l++ilee+++ ly
  gi|242399585|ref|YP_002995010.1| 816 IFGGARGLKKILEEIEKGLY 835
                                       ****************9887 PP

>> HSDR_N_2  Type I restriction enzyme R protein N terminus (HSDR_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   0.0   9.3e-14   1.4e-10       4     105 ..      10     122 ..       7     125 .. 0.87

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 9.3e-14
                          HSDR_N_2   4 wvRqklikyLveelgypkeliavekelqlg.........skkkraDivvykkd..kkpllivecKapsvkiseevle 69 
                                        +R kli   +++ g ++++i++e+ ++lg         ++ kraD+v++  d  ++++ +ve+K+ s+   + +le
  gi|242399585|ref|YP_002995010.1|  10 DTRAKLIDPKLHDAGWNENRIKREYVISLGrilnndgsrTSPKRADYVLFYPDiqGHIIAVVEAKKASEDPYK-GLE 85 
                                       5788889999999***************999999999888999*******9998788999*********9985.*** PP

                          HSDR_N_2  70 qlksYlealkaeylvvtNglehivykvdkkkk.kfee 105
                                       q+k+Y+++l a+++  tNgl++  y+  +k+  +f e
  gi|242399585|ref|YP_002995010.1|  86 QAKRYAKTLDAPFAYSTNGLKIVEYDFLTKQSnEFSE 122
                                       *********************9999975544325554 PP

>> HSDR_N  Type I restriction enzyme R protein N terminus (HSDR_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.0   2.8e-10   4.2e-07      92     191 ..      10     115 ..       5     118 .. 0.78

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 2.8e-10
                                       EEEEESS-SSSGGG..S-EEEEE----S..........SSS---EEEEEEET...TEEEEEEEE--TT-HHHHHHHH CS
                            HSDR_N  92 kknikLiDkknlen..NrfqvvnQvtvt..........gnqkrrpDivlfvn...glplvviElKrpgtieeAinQi 153
                                       + + kLiD k   +  N+  + ++++++          +++++r+D+vlf     g +++v+E+K++          
  gi|242399585|ref|YP_002995010.1|  10 DTRAKLIDPKLHDAgwNENRIKREYVISlgrilnndgsRTSPKRADYVLFYPdiqGHIIAVVEAKKA---------- 76 
                                       4567788877555555888999999999999999999999**********65555***********4.......... PP

                                       TSS---.---S..SSGGGGG-.....-EEEEE-SS-EEEEE--SS CS
                            HSDR_N 154 kryrkeksdvs..ipqlfrYl.....qfgvisngketrfyaktkr 191
                                             ++d    ++q+ rY+     +f +++ng ++  y+  ++
  gi|242399585|ref|YP_002995010.1|  77 ------SEDPYkgLEQAKRYAktldaPFAYSTNGLKIVEYDFLTK 115
                                       ......333334688888888888889999999999888887766 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 !   30.2   0.0   3.1e-10   4.6e-07       5     110 ..     407     521 ..     403     522 .. 0.70

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 3.1e-10
                                       HHHHHHHHTTTTSEEEEEESSHHHHHH.HHHHHHHT.......TSTEEEESTTSTHHHHHHHHHHHH..TTSSSEE. CS
                        Helicase_C   5 allellkleeeggkilifvntidrlek.vklllekk.......gikvavlhgelpqnereeileqfn..kgesdvL. 70 
                                        + ++l++++   k+++f++t++++ + + ll++++       ++ + ++  +   +  +   ++f   ++ + v+ 
  gi|242399585|ref|YP_002995010.1| 407 WIAQFLESTNPFAKTVVFCPTQRHAREvAALLNNHFnnkfnvdNYAYPIISDD--PEAHQVLKNSFAsnDEIFPVVa 481
                                       567788999999***********887754555333344346555555555554..4444445556653144455442 PP

                                       EESGGGTSSSTSTTESEEEESSSSSSHHHHHHHHTTSSST CS
                        Helicase_C  71 iatdvaerGidipkvnlVinfdlprnvtsyiqriGRtgRa 110
                                        + dv+++Gid+p ++++i++    +  +++q iGR+ R 
  gi|242399585|ref|YP_002995010.1| 482 TTVDVLSTGIDVPPIKNIIFLKHIGSKVEFHQIIGRASRL 521
                                       44588********************************995 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   4.6e-09   6.9e-06       7     170 ..     173     314 ..     168     320 .. 0.75
   2 ?   -2.1   0.0       1.8   2.7e+03      48     118 ..     419     447 ..     401     487 .. 0.54
   3 ?    0.4   0.0      0.33   4.9e+02      59      96 ..     703     742 ..     700     782 .. 0.78

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 4.6e-09
                                       HHHHHH.TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEE CS
                                       xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   7 aiplil.gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvllii 82 
                                       a+++il g + +l+ ++TGsGKT +++  + +     k++  +k+l+++    L +q +n ++ f++    r++  +
  gi|242399585|ref|YP_002995010.1| 173 ALEEILlGRKRLLLTMATGSGKTYVAFQIAWKLR---KSNFLKKILFIVDRVYLRNQAYNAFEAFGNS---RWE--L 241
                                       5556664778**************9887777444...678888************************4...554..6 PP

                                       TTSSHHHHHHHHHTTCSEEEEEHHHHHHHH....HCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  83 ggvaardqlskldngvdivvgtpgrlddll....stgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcd 155
                                       +g++ +          d++++t + l +        ++++ + + ++++DE++r   +   d +    n++      
  gi|242399585|ref|YP_002995010.1| 242 KGDNFNFA-------KDVYFATYQTLYSEKngkrVYQYFDPDYFDLVIIDECHRSGWNRWHDILGYFNNAI------ 305
                                       67666333.......5666777777777553322223466888999********99998888888877777...... PP

                                       STTTSEEEEEESSBS CS
                                       xxxxxxxxxxxxxxx RF
                              DEAD 156 gklqrqvivlSATlp 170
                                              + l+AT++
  gi|242399585|ref|YP_002995010.1| 306 ------HLGLTATPK 314
                                       ......566777765 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.8
                                       -EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  48 pkalivePtreLaeqtlnnlkkfkkyidlrvlliiggvaardqlskldngvdivvgtpgrlddllstgkln 118
                                        k+++ +Pt+  a++++  l++ ++                                          +k+n
  gi|242399585|ref|YP_002995010.1| 419 AKTVVFCPTQRHAREVAALLNNHFN------------------------------------------NKFN 447
                                       5666666666666655555544444..........................................2223 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.33
                                       HHHHHHHHHHHHTTT..STSEEEEEETTSSHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  59 Laeqtlnnlkkfkky..idlrvlliiggvaardqlskldn 96 
                                       L +q+  ++k+ +k+  idl++ ++i++v++ d+ + l n
  gi|242399585|ref|YP_002995010.1| 703 LNRQVRLRFKEELKKagIDLKMISLIKKVSEADEFDLLAN 742
                                       5667777887777754688****9*******999998843 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 !   15.5   0.0   3.5e-06    0.0052     142     223 ..     242     321 ..     203     325 .. 0.84
   2 ?   -2.5   0.0       1.1   1.6e+03     109     161 ..     405     488 ..     395     509 .. 0.53

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.5e-06
                                       ----------EEEE-HHHHHHHT......TTS-S-S-SEEEES-GGGT--TTSHHHHHHHH---S-EEEE-S--SSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N 142 vapklladydvvittYdvlsreaelqkkrsvlkqvewkrvvlDEghtlknstskaaeavskLstsnrwiltGTPiqn 218
                                         +++  ++dv + tY++l +e++ + +++ +     + v++DE+h+  ++ ++ + ++  +++   + lt+TP   
  gi|242399585|ref|YP_002995010.1| 242 KGDNFNFAKDVYFATYQTLYSEKNGKRVYQYFDPDYFDLVIIDECHR--SGWNRWHDILGYFNNAIHLGLTATPKRS 316
                                       556777899*************************************6..6678888888888888889999998766 PP

                                       -HHHH CS
                                       xxxxx RF
                            SNF2_N 219 sledl 223
                                       +  d+
  gi|242399585|ref|YP_002995010.1| 317 DNVDV 321
                                       66665 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.1
                                       HHHHHHHHHH-TTS-EEE--SSHHHH...............................-----------------... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx...............................xxxxxxxxxxxxxxxxx... RF
                            SNF2_N 109 dqWeneierhvsssalrvlvyggqkk...............................mkkkntkvapklladyd... 151
                                        +W  ++ + +++ a +v+    q++                                    ++v+++ +a  d   
  gi|242399585|ref|YP_002995010.1| 405 VNWIAQFLESTNPFAKTVVFCPTQRHarevaallnnhfnnkfnvdnyaypiisddpeA----HQVLKNSFASNDeif 477
                                       5666666666666655555555544445555555555555555555555555543331....222222222222122 PP

                                       .EEEE-HHHHH CS
                                       .xxxxxxxxxx RF
                            SNF2_N 152 .vvittYdvls 161
                                        vv tt dvls
  gi|242399585|ref|YP_002995010.1| 478 pVVATTVDVLS 488
                                       25666666655 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.6e-05     0.054       9      99 ..     189     288 ..     182     307 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.6e-05
                           DUF2075   9 vaGtGKtvvllnllaeleddeeertavylsvNhplvlvlrealakke..ekkkkkeafe.....klssfinnlsef. 77 
                                       ++G+GKt+v+++++ +l++++  ++  +++    l++  ++a++     + + k+++f+     +++++ + +se+ 
  gi|242399585|ref|YP_002995010.1| 189 ATGSGKTYVAFQIAWKLRKSNFLKKILFIVDRVYLRNQAYNAFEAFGnsRWELKGDNFNfakdvYFATYQTLYSEKn 265
                                       57***************555544444555555568888888876555553444444444100012333333344337 PP

                           DUF2075  78 .kkaeekkeepkedvvivDEAhr 99 
                                        k+ ++  + + +d+vi+DE hr
  gi|242399585|ref|YP_002995010.1| 266 gKRVYQYFDPDYFDLVIIDECHR 288
                                       799999999*************9 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   6.4e-05     0.096      24      55 ..     186     217 ..     168     232 .. 0.82
   2 ?   -4.2   0.0       6.2   9.3e+03     133     152 ..     760     779 ..     752     781 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.4e-05
                                       EE--TTSSTTHHHHHHHHHHHHTTS-SEEEEE CS
                              PhoH  24 aiGpaGtGKtylavalavealkkkkvkriilt 55 
                                        +  +G+GKty+a ++a ++ k++ +k+i+++
  gi|242399585|ref|YP_002995010.1| 186 LTMATGSGKTYVAFQIAWKLRKSNFLKKILFI 217
                                       45579***********************9876 PP

  == domain 2  score: -4.2 bits;  conditional E-value: 6.2
                                       HHHHHHHHTTB-TT-EEEEE CS
                              PhoH 133 keqmkmfltRlGenskvvvt 152
                                        e  k+fl R+Ge  + +++
  gi|242399585|ref|YP_002995010.1| 760 MEVKKEFLDRFGERGREIIL 779
                                       5667899*****99998875 PP

>> AAA_34  P-loop containing NTP hydrolase pore-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00011      0.16     134     183 ..     245     288 ..     178     293 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00011
                            AAA_34 134 seelkeGvlFvtYstliseskkkkksrleqlveWlgedfdGvivfDEchk 183
                                       + ++ + v F+tY+tl se++       +++ ++++ d+  +++ DEch+
  gi|242399585|ref|YP_002995010.1| 245 NFNFAKDVYFATYQTLYSEKNG------KRVYQYFDPDYFDLVIIDECHR 288
                                       5578889**********99877......3467789955555999*****8 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00015      0.22     114     171 ..     166     225 ..     138     236 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00015
                             T2SSE 114 lkekiaevlrkavrerglilvsGgTgsGKttllyallkeinks..derivtvEDpvEiql 171
                                       ++ +++++l++ +  r+ +l++ +TgsGKt ++  +  ++ ks   ++i+ + D v ++ 
  gi|242399585|ref|YP_002995010.1| 166 QDVAVRRALEEILLGRKRLLLTMATGSGKTYVAFQIAWKLRKSnfLKKILFIVDRVYLRN 225
                                       456788999999999****************99998888888855577777777766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (841 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       771  (0.043003); expected 358.6 (0.02)
Passed bias filter:                      605  (0.0337442); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        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 0.31s 00:00:01.14 Elapsed: 00:00:00.53
# Mc/sec: 4742.88
//
Query:       gi|242399586|ref|YP_002995011.1|  [L=498]
Description: Type I restriction-modification system methyltransferase subunit [Thermococcus sibiricus MM 739]
Scores for complete 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-64  217.4   0.0    3.7e-64  216.9   0.0    1.1  1  N6_Mtase         N-6 DNA Methylase
    2.8e-12   46.8   0.0    7.8e-12   45.3   0.0    1.7  2  UPF0020          Putative RNA methylase family UPF0020
    6.7e-11   43.0   0.2    6.7e-11   43.0   0.2    2.4  3  HsdM_N           HsdM N-terminal domain
     0.0011   18.5   0.1     0.0049   16.4   0.0    2.1  2  MTS              Methyltransferase small domain
     0.0045   16.6   0.0       0.02   14.6   0.0    2.0  1  Cons_hypoth95    Conserved hypothetical protein 95
     0.0055   16.4   0.4      0.015   15.0   0.0    2.1  3  N6_N4_Mtase      DNA methylase
  ------ inclusion threshold ------
      0.045   13.5   0.0       0.14   11.9   0.0    1.8  2  Methyltransf_31  Methyltransferase domain
      0.072   12.7   0.1       0.19   11.3   0.1    1.8  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase


Domain annotation for each model (and alignments):
>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  216.9   0.0   1.7e-67   3.7e-64       2     303 ..     146     458 ..     145     465 .. 0.90

  Alignments for each domain:
  == domain 1  score: 216.9 bits;  conditional E-value: 1.7e-67
                          N6_Mtase   2 skdllGdvYEyllrkfaeeegksgGeffTPrevsklivellepksgesvyDpacGsggllvqaekvlkee.....dg 73 
                                       ++++++++YE +l      eg  +Ge++TPr +++++v++++p+ g++v+Dp cGsgg+lv+a ++++e+     d 
  gi|242399586|ref|YP_002995011.1| 146 DTHIMSQLYEETLMLM-GREGGAAGEYYTPRPIVRFMVKVVDPRIGQTVFDPFCGSGGFLVEAYNHMYEQaktaeDL 221
                                       5799********9888.6677788********************************************997776666 PP

                          N6_Mtase  74 ktkelsiyGqeknettyrLakmNlllhgieykkvkirlgdtlekpkfekdkkfdvvvaNppfnqkewkektlekder 150
                                        + ++ +yGqe+++++y +a+mN llh+++ k       dt++++ ++  +  dv+++Nppf+ k        k++ 
  gi|242399586|ref|YP_002995011.1| 222 RKLDKAFYGQELKTQAYLIANMNTLLHNVNAK---LVKTDTFSEDLHNPGELYDVILTNPPFGGK-I------KESN 288
                                       677889************************99...7889*********99***************.3......3333 PP

                          N6_Mtase 151 freavapksnadlafllhiieslkpkGraavvlangvLfr.ggkegkIrkalvekdlveavialpeklFynts.... 222
                                       +++ + ++++ +la l+h+++++kp+G++++vl++gvL++ + +  k+rk+l+ek++v a+++lp+++F n s    
  gi|242399586|ref|YP_002995011.1| 289 LQNLIVKTRSTELAALQHVMKKAKPGGKVGIVLPDGVLSNvTKAYVKVRKELLEKNNVFAIVSLPQGVFANISpkgg 365
                                       4556899*********************************899999************************9762222 PP

                          N6_Mtase 223 ..iptcilvlkkekaerkgkvlfidaseefkkkdrkknklteediekildtykek............skevdkfskv 285
                                          +t++l+++++k   + +v+ ++      k+ ++ n++++ed++  l+ ++++            +k  ++ s+v
  gi|242399586|ref|YP_002995011.1| 366 sgPKTSLLFFERGK--PTREVWYYELIPPNGKNYTRANPIKDEDLSDALKKFEAWkkyletddeewkKKALSENSWV 440
                                       22579*********..79********99999999*********************99998887777777777***** PP

                          N6_Mtase 286 veleeiaendynlnvgry 303
                                       v++eei+e dy+l+  ++
  gi|242399586|ref|YP_002995011.1| 441 VSVEEIKEMDYDLSARNP 458
                                       *************98765 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       3.1   6.9e+03     129     151 ..      98     120 ..      79     131 .. 0.62
   2 !   45.3   0.0   3.5e-15   7.8e-12      18     139 ..     179     288 ..     175     312 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 3.1
                                       ---------HHHHHHHHHHHHHH CS
                           UPF0020 129 pPYGerlgskkalekLYseflre 151
                                        PY  +lg + +l+k+ + f++ 
  gi|242399586|ref|YP_002995011.1|  98 WPYLSSLGGTDELNKIGEIFSNV 120
                                       48888888777777766666555 PP

  == domain 2  score: 45.3 bits;  conditional E-value: 3.5e-15
                                       HHHHHHTT--TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH--EEEEES-HHHHHHHHH CS
                           UPF0020  18 aalvrlagwkpgepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelklygsDldrrvvqgare 94 
                                       + +v++ + + g++ +DP+CGsG++l+Ea     + a            ++ae   + +  +yg +l+ ++   a+ 
  gi|242399586|ref|YP_002995011.1| 179 RFMVKVVDPRIGQTVFDPFCGSGGFLVEAYNHMYEQA------------KTAEDLRKLDKAFYGQELKTQAYLIANM 243
                                       569**************************87777777............345555556666**************** PP

                                       HHHHTT-GGGEEEEE--GGG--STTS---EEEE----------HH CS
                           UPF0020  95 NaekagvgdliefsqadaakLrlkegevdvivtnpPYGerlgskk 139
                                       N    +v+ +    +    +L+++ + +dvi+tnpP+G ++++ +
  gi|242399586|ref|YP_002995011.1| 244 NTLLHNVNAKLVKTDTFSEDLHNPGELYDVILTNPPFGGKIKESN 288
                                       ********999999999*****88889*************99764 PP

>> HsdM_N  HsdM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.0   0.2     3e-14   6.7e-11       1     130 [.       6     130 ..       6     137 .. 0.76
   2 ?   -2.7   0.0       3.7   8.4e+03     102     102 ..     244     244 ..     209     276 .. 0.46
   3 ?   -1.7   0.1       1.9   4.2e+03      32      49 ..     420     442 ..     399     468 .. 0.62

  Alignments for each domain:
  == domain 1  score: 43.0 bits;  conditional E-value: 3e-14
                                       HHHHHHHHHHHHHHS.-SHHHHHHHHHHHHHHHHHHHHHHHHHHCC.......--..--------....S-CCCSHH CS
                            HsdM_N   1 lesklwkaadiLRgk.vdaseykeyilgLlFlKrlddveeereeklleeykenaleeleeklkskeafyipeelrWk 76 
                                       l+sk+  + +i+R + +  ++y+e++ ++lFlK l+d+eeer+ ++       +   ++ek+  +    i+ee+ ++
  gi|242399586|ref|YP_002995011.1|   6 LASKIEHIYEIMRAEgLTILDYVEQLSWMLFLKILSDREEERKLEA-------E--VKGEKYVPI----IKEEYLFH 69 
                                       6899*********8899*************************9999.......3..356655555....99****** PP

                                       HHHHS.........--HHHHHHHHHH.CHHHHCT--S....THHHHHHHS......S-----SSHHHH CS
                            HsdM_N  77 elakk.........kdddelgenlnk.afpaleelnk....slkgvfmkddfnafalgeitkkspalL 130
                                       ++ k+         kd + + +++++ ++p+l++l      + +g+++++     +  +    +p++L
  gi|242399586|ref|YP_002995011.1|  70 NWPKRfgvdslkkvKDVKTFYDFITNeLWPYLSSLGGtdelNKIGEIFSN-----VTVK--VHDPHNL 130
                                       *9888888888777777788999988999999999765443356666544.....2222..2455555 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.7
                                       - CS
                            HsdM_N 102 n 102
                                       n
  gi|242399586|ref|YP_002995011.1| 244 N 244
                                       1 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 1.9
                                       HHHHHHHHHHHHCC......... CS
                            HsdM_N  32 Krlddveeereekllee.....y 49 
                                       K+l+   ee ++k+l+e      
  gi|242399586|ref|YP_002995011.1| 420 KYLETDDEEWKKKALSEnswvvS 442
                                       55555555555555444444331 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       2.4   5.3e+03     129     162 ..     110     143 ..     107     145 .. 0.76
   2 !   16.4   0.0   2.2e-06    0.0049      61     122 ..     231     293 ..     178     310 .. 0.65

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.4
                                       EEEEEEEEEEEETTSCHHHHHHHHHS--EEEEEE CS
                               MTS 129 LkegGeLliVanrklgyeslleelfgnvevvakt 162
                                       L++ Ge++  +  k++ ++ l e+f+n+e + k+
  gi|242399586|ref|YP_002995011.1| 110 LNKIGEIFSNVTVKVHDPHNLLEIFQNIEDIHKD 143
                                       7777888777777777888899999999888776 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 2.2e-06
                                       EESBHHHHHHHHHHHHHTTGCEEEEE-STTTTST...TS-EEEEEE---STTTCHCHHHHHHHHH CS
                               MTS  61 vdvdarAlesakenleanklevevvasdvleeve...ekkfdlivsNPPfhagkatelavaeeli 122
                                        + +++A  +a+ n   +++++++v++d ++e      + +d+i++NPPf  + +  ++  ++li
  gi|242399586|ref|YP_002995011.1| 231 QELKTQAYLIANMNTLLHNVNAKLVKTDTFSEDLhnpGELYDVILTNPPFGGKIK--ESNLQNLI 293
                                       3556788888889999999999999888887643122468**********76655..44444444 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   8.7e-06      0.02      41     136 ..     190     292 ..     180     312 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 8.7e-06
                                       CC-EEEETT-TTSHHHHHHHHTT-SEEEEEE...........S-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCT CS
                     Cons_hypoth95  41 egarvLDlfaGsGalglEAlSRgakkavlve...........kdkeavkilkenleelkleeetaelkedaleallk 106
                                         ++v D f+GsG+  +EA     ++a   e           ++ ++++ l +n+++l  + +++ +k d +++ l+
  gi|242399586|ref|YP_002995011.1| 190 G-QTVFDPFCGSGGFLVEAYNHMYEQAKTAEdlrkldkafygQELKTQAYLIANMNTLLHNVNAKLVKTDTFSEDLH 265
                                       4.4599*************9987777766652221111111144556666777777776565788888888877777 PP

                                       S--SS-EEEEEEE--SSSTTCH.HHHHHHH CS
                     Cons_hypoth95 107 lakkkeefdivflDPPyakellieevlell 136
                                       +   +e +d++  +PP+  +   e  l+ l
  gi|242399586|ref|YP_002995011.1| 266 N--PGELYDVILTNPPFGGKIK-ESNLQNL 292
                                       7..57789*********98854.5555544 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   6.7e-06     0.015     173     210 ..     170     208 ..      44     243 .. 0.69
   2 ?   -2.2   0.0       1.2   2.8e+03       2      16 ..     272     286 ..     271     312 .. 0.79
   3 ?   -2.9   0.2         2   4.4e+03     145     165 ..     378     398 ..     374     447 .. 0.57

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 6.7e-06
                                       SS---HHHHHHHHHHHS-T.T-EEEETT-TTTHHHHHHH CS
                       N6_N4_Mtase 173 paqkPvallerlIklstkk.gdivlDpFaGSGtTavaak 210
                                       ++  P+ ++++++k   +  g++v+DpF+GSG  +v+a 
  gi|242399586|ref|YP_002995011.1| 170 EYYTPRPIVRFMVKVVDPRiGQTVFDPFCGSGGFLVEAY 208
                                       55679999999999999989***********65444443 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.2
                                       EEEEE--SSSSSCS. CS
                       N6_N4_Mtase   2 dlivtdpPYntgkdy 16 
                                       d+i+t pP++ + ++
  gi|242399586|ref|YP_002995011.1| 272 DVILTNPPFGGKIKE 286
                                       789999**9999884 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 2
                                       -B--BSEEE-SCCCTTSTTS- CS
                       N6_N4_Mtase 145 gkkiediWdlseiqsnekksk 165
                                       gk++ ++W  + i++n k+ +
  gi|242399586|ref|YP_002995011.1| 378 GKPTREVWYYELIPPNGKNYT 398
                                       566666663333333333322 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       4.6     1e+04      93     126 ..       9      44 ..       6      63 .. 0.64
   2 ?   11.9   0.0   6.3e-05      0.14       6     119 ..     192     330 ..     188     370 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 4.6
                   Methyltransf_31  93 ileeiervlkpggilliedprllaelp..akveees 126
                                        +e i + ++ +g  +++++  l++++  +++++ +
  gi|242399586|ref|YP_002995011.1|   9 KIEHIYEIMRAEGLTILDYVEQLSWMLflKILSDRE 44 
                                       567777888888888888888666655544444433 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 6.3e-05
                   Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkae...........vvGiDiseeaielArenaqklgldnveFeqgdieeleklle 71 
                                       +v D+ CG+G ++ e++  ++++a+           ++G + + +a   A+ n+  +++ n+++ + d ++ + +  
  gi|242399586|ref|YP_002995011.1| 192 TVFDPFCGSGGFLVEAYNHMYEQAKtaedlrkldkaFYGQELKTQAYLIANMNTLLHNV-NAKLVKTDTFSEDLH-- 265
                                       799***************888888888899999999**********9999999888888.89999***9998844.. PP

                   Methyltransf_31  72 d..ekfDlilsn.............evl..naladpdkileeiervlkpggilliedpr.llaelp 119
                                          e +D+il+n             + l   + +   ++l+ + +  kpgg + i  p+ +l+++ 
  gi|242399586|ref|YP_002995011.1| 266 NpgELYDVILTNppfggkikesnlqN-LivKTRSTELAALQHVMKKAKPGGKVGIVLPDgVLSNVT 330
                                       34499*******66665555544431.144555666677889999999999999888886444444 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   8.6e-05      0.19       3     105 ..     192     303 ..     190     355 .. 0.52

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8.6e-05
                   Methyltransf_15   3 vilDlfsGaGGnviqfalv..............fekviaieinleklacaqhNaevYgvsdkitlvlgdvfellakl 65 
                                       ++ D+f+G+GG  ++  ++               +  ++ e +++   +a+ N+ + +v+ k  lv+ d f+  + l
  gi|242399586|ref|YP_002995011.1| 192 TVFDPFCGSGGFLVEAYNHmyeqaktaedlrklDKAFYGQELKTQAYLIANMNTLLHNVNAK--LVKTDTFS--EDL 264
                                       789********988765553222333333222212223333333333333333333333222..23333333..333 PP

                   Methyltransf_15  66 klekikvdlvflSpPwGGpsYkkqekfdlkkklkplkleq 105
                                       +     +d++++ pP GG   k+ +  +l  k +  +l  
  gi|242399586|ref|YP_002995011.1| 265 HNPGELYDVILTNPPFGGKI-KESNLQNLIVKTRSTELAA 303
                                       3333369***********53.3333334433443333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (498 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       785  (0.0437838); expected 358.6 (0.02)
Passed bias filter:                      566  (0.031569); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.67u 0.32s 00:00:00.99 Elapsed: 00:00:00.51
# Mc/sec: 2931.52
//
Query:       gi|242399587|ref|YP_002995012.1|  [L=434]
Description: type I specificity subunit HsdS [Thermococcus sibiricus MM 739]
Scores for complete 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  171.6   0.3    9.7e-32  110.5   0.0    2.1  2  Methylase_S   Type I restriction modification DNA specificity
  ------ inclusion threshold ------
      0.029   14.6   0.6      0.059   13.6   0.6    1.4  1  Metal_resist  Heavy-metal resistance
      0.036   14.5   0.0      0.088   13.2   0.0    1.7  1  RAMA          Restriction Enzyme Adenine Methylase Associated
       0.18   12.0   4.5        9.6    6.5   0.9    2.6  2  MRPL52        Mitoribosomal protein mL52
          6    6.6   9.8        6.4    6.5   4.6    2.1  2  ERM           Ezrin/radixin/moesin family


Domain annotation for each model (and alignments):
>> Methylase_S  Type I restriction modification DNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.5   0.0   2.7e-35   9.7e-32       1     162 [.      36     205 ..      36     209 .. 0.95
   2 !   59.5   0.1   1.3e-19   4.6e-16       3     154 ..     234     402 ..     232     420 .. 0.82

  Alignments for each domain:
  == domain 1  score: 110.5 bits;  conditional E-value: 2.7e-35
                                       ETT-EEEEHHHHEEEEE-----TT..GGTTT--EEEE-HHHCCT.........EE-HHHHCCTT---B-TT-EEEE- CS
                       Methylase_S   1 pedwevvkLgdvfeikkgktpkkk..elkengkypyiragilnn.........kvvkdglgykkkyilpkgdiliss 66 
                                       pe+w  v+Lgd++e+k g tp++   e++eng++p++++++ ++         k+++ gl+++++++l  g+il+s+
  gi|242399587|ref|YP_002995012.1|  36 PEGWRWVRLGDIAELKAGGTPSRRvkEYWENGTIPWVKISDIPDsglvekteeKITELGLKNSSAKLLSPGTILFSI 112
                                       89*********************999**************77777******************************** PP

                                       SSSTT-EEEESS-BEE-TTEEEEEESTTT--HHHHHHHHHHCHHHHHHHCCSSTTT---HHHHCC-EEEE--HHHHH CS
                       Methylase_S  67 ratiGkvayrdkkyylnqsvivlipknkkkineflylylllklkklkslsvgstqpkltkenlkkikIplPpleeQk 143
                                        ati+kv + + ++ +nq +  +ipk +++   +l++ l+++ ++l  + +g+ q ++++  l+k+kIplPp eeQk
  gi|242399587|ref|YP_002995012.1| 113 FATISKVGILKIPAATNQAIVGIIPKISIDR-GYLFYSLKYFGQELVYQGRGGVQDNINMRILSKLKIPLPPIEEQK 188
                                       *************************965555.9******************************************** PP

                                       HHHHHHHHHHHHHHHHHHH CS
                       Methylase_S 144 kIakiLsqldntielekki 162
                                       +I+  L+ + +   le+++
  gi|242399587|ref|YP_002995012.1| 189 RIVAKLDEVHR--RLEEAK 205
                                       **********9..888844 PP

  == domain 2  score: 59.5 bits;  conditional E-value: 1.3e-19
                                       T-EEEEHHHHEEE.EE-----TTGGTTT--EEEE-HHHCCT.........EE-HHHHCCTT---B-TT-EEEE-S.. CS
                       Methylase_S   3 dwevvkLgdvfei.kkgktpkkkelkengkypyiragilnn.........kvvkdglgykkkyilpkgdilissr.. 67 
                                       +we  ++g v    k g + +kk +  +g+ p +r++ ++          kv+ d + ++++y+l+kgd+l++    
  gi|242399587|ref|YP_002995012.1| 234 GWEWTTIGKVSREmKPGFARNKKHISRDGV-PHLRPNNVDVgrlnlkkivKVTLDDKINIEEYYLKKGDVLFNNTns 309
                                       566666666654435555555555555555.77777722225777798999999999****************889* PP

                                       .SSTT-EEEESS..-BEE-TTEEEEEESTTT--HHHHHHHHHHCHHHHHHH.....CCSSTTT---HHHHCC-EEEE CS
                       Methylase_S  68 .atiGkvayrdk..kyylnqsvivlipknkkkineflylylllklkklksl.....svgstqpkltkenlkkikIpl 136
                                        + +G++a+ ++  ky +++++ ++++k k+ i  +++l l+ ++ +++ +     ++ ++q+ +++ +l+k  Ipl
  gi|242399587|ref|YP_002995012.1| 310 fELVGRAAIVPEdlKYGYSNHITRIRVK-KEVI-LPEWLTLAINYLWMQGYfrevcTRWVGQAGVNMNTLAKTRIPL 384
                                       ************6669***********9.8999.****************999**9********************* PP

                                       --HHHHHHHHHHHHHHHH CS
                       Methylase_S 137 PpleeQkkIakiLsqldn 154
                                       P+leeQk+I+++L+++ +
  gi|242399587|ref|YP_002995012.1| 385 PSLEEQKRIVSYLDSIQE 402
                                       **************9987 PP

>> Metal_resist  Heavy-metal resistance
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.6   1.6e-05     0.059      46      81 ..     185     220 ..     157     222 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.6e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                      Metal_resist  46 eqraelraalrdharelralrrelraarrelaalla 81 
                                       e++++  a l++ +r+l+++ r +r+ar+e+++l+a
  gi|242399587|ref|YP_002995012.1| 185 EEQKRIVAKLDEVHRRLEEAKRLAREAREEAERLMA 220
                                       8999******************************98 PP

>> RAMA  Restriction Enzyme Adenine Methylase Associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.5e-05     0.088      24      74 ..      66     125 ..      37     159 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.5e-05
                              RAMA  24 r.....vtlkdLleagllepGekllieykg.rthkAdlladGkIkgqefgspsaaa....k 74 
                                       +     v+++d+ ++gl+e  e+ +  ++g ++ +A+ll+ G+I    f+++s+++     
  gi|242399587|ref|YP_002995012.1|  66 NgtipwVKISDIPDSGLVEKTEEKI-TELGlKNSSAKLLSPGTILFSIFATISKVGilkiP 125
                                       1345679***************999.888845667******************98755442 PP

>> MRPL52  Mitoribosomal protein mL52
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.9    0.0027       9.6      48      87 ..     184     223 ..     176     225 .. 0.91
   2 ?    5.9   0.1    0.0041        15      49      81 ..     388     420 ..     379     427 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0027
                            MRPL52  48 eelakkivkllsEideaeerykkkqeeeeeeeqkiieskl 87 
                                       +e +k+iv  l+E++   e  k+  +e+ ee +++ +s l
  gi|242399587|ref|YP_002995012.1| 184 IEEQKRIVAKLDEVHRRLEEAKRLAREAREEAERLMASAL 223
                                       5789*****************************9998877 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0041
                            MRPL52  49 elakkivkllsEideaeerykkkqeeeeeeeqk 81 
                                       e +k+iv +l+ i+e  ++  k  ee+e+e +k
  gi|242399587|ref|YP_002995012.1| 388 EEQKRIVSYLDSIQERAQKLVKLYEEREKELEK 420
                                       6789****************9999999998776 PP

>> ERM  Ezrin/radixin/moesin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   4.6    0.0018       6.4      29      77 ..     185     233 ..     183     248 .. 0.86
   2 ?    2.8   0.2     0.025        88      74     108 ..     387     421 ..     369     428 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0018
                               ERM  29 reseetaelLaekarraeeeaelLeqkaaeaeeeiqrlkesaekeeeek 77 
                                       +e+++ + +L+e  rr+ee+++l  + ++eae+ ++   ++   ++eek
  gi|242399587|ref|YP_002995012.1| 185 EEQKRIVAKLDEVHRRLEEAKRLAREAREEAERLMASALHEVFSKAEEK 233
                                       6889999999999999999999999999999999988888877777777 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.025
                               ERM  74 eeekeklerklreaeleaarleeeserkeeeaerL 108
                                        ee++++   l+  +++a++l++  e++e+e e+L
  gi|242399587|ref|YP_002995012.1| 387 LEEQKRIVSYLDSIQERAQKLVKLYEEREKELEKL 421
                                       57888888899999999999999999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1005  (0.0560544); expected 358.6 (0.02)
Passed bias filter:                      711  (0.0396564); 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):               5  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 2826.50
//
Query:       gi|242399588|ref|YP_002995013.1|  [L=371]
Description: hypothetical protein TSIB_1613 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       842  (0.046963); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 2315.50
//
Query:       gi|242399589|ref|YP_002995014.1|  [L=438]
Description: hypothetical protein TSIB_1614 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (438 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.31s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 2725.56
//
Query:       gi|242399590|ref|YP_002995015.1|  [L=144]
Description: hypothetical protein TSIB_1615 [Thermococcus sibiricus MM 739]
Scores for complete 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-27   94.3   0.9    7.4e-27   94.1   0.9    1.0  1  EVE             EVE domain
    7.7e-06   25.8   0.0    9.5e-06   25.5   0.0    1.2  1  Dev_Cell_Death  Development and cell death domain


Domain annotation for each model (and alignments):
>> EVE  EVE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.1   0.9   8.3e-31   7.4e-27       1     144 [.       2     141 ..       2     142 .. 0.84

  Alignments for each domain:
  == domain 1  score: 94.1 bits;  conditional E-value: 8.3e-31
                                       -EEEEEEBHHTSHHHHHCHHHCEEE-EE-GHHHHHHHCC--TT-EEEEE....ETSSS..S-EEEEEEEEECEEEE- CS
                               EVE   1 ayWllksepdefsiddlkrkkeegWdgvrnyqarnllramkkGDlvlfY....hsgek..lqaivgiaeVvseaypd 71 
                                       ayWl+++++d  +++ +  k++++W gv++ +++n++ ++k+GD++l+Y     ++++  +++ivgi+eVvse+y+d
  gi|242399590|ref|YP_002995015.1|   2 AYWLCITNRD--NWKVI--KEKNVW-GVPK-RHKNTIAKVKPGDKLLIYvkqeRKDKQilEPKIVGIFEVVSEPYED 72 
                                       6*********..*****..9*****.****.99****************887544444999**************** PP

                                       GGGG-TTSTT--TTTBTTS--EEEEEEEE.......EEEEEEEEHHHHTTHGTCTTSHHHHCCT-SEEEE-HHHHHH CS
                               EVE  72 etqfdpkskyydpkskkekpwlrvdvkpv.......kklkrplslkelkaepelegmkllrkgrlsvrpvteedwel 141
                                       ++ + ++     p  ++e+ +lrv++kpv       k+l ++l++ ++k+  +++g  +      ++r+++eed++l
  gi|242399590|ref|YP_002995015.1|  73 SKRIFKS-----PPHSNETYPLRVKIKPVklgevdfKPLIPKLRFITNKK--KWSGHLM----GKAMREIPEEDYKL 138
                                       ***9554.....3333233379*******888888888888888888888..5677777....999*********** PP

                                       HHH CS
                               EVE 142 ile 144
                                       i +
  gi|242399590|ref|YP_002995015.1| 139 IKK 141
                                       976 PP

>> Dev_Cell_Death  Development and cell death domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   1.1e-09   9.5e-06       7      91 ..       8     106 ..       4     137 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 1.1e-09
                    Dev_Cell_Death   7 cnketkkecfrkklfglpaeklslvkkikpglkLfLfdyderkLyGvfeAasdGglniepkafts..........ek 73 
                                        n++  k   +k++ g+p+++++++ k+kpg kL+++  +erk   + e +  G +++ ++ +++          ++
  gi|242399590|ref|YP_002995015.1|   8 TNRDNWKVIKEKNVWGVPKRHKNTIAKVKPGDKLLIYVKQERKDKQILEPKIVGIFEVVSEPYEDskrifkspphSN 84 
                                       566667777899******************************99999999999999999999977788888899999 PP

                    Dev_Cell_Death  74 skfpaQvrfk....ikkkckPL 91 
                                       +++p  v++k     ++++kPL
  gi|242399590|ref|YP_002995015.1|  85 ETYPLRVKIKpvklGEVDFKPL 106
                                       9999999999444444556665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1032.78
//
Query:       gi|242399591|ref|YP_002995016.1|  [L=362]
Description: archaeal ATPase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-17   64.8   0.2    3.2e-17   63.2   0.0    1.7  2  ATPase_2  ATPase domain predominantly from Archaea
      3e-08   33.7   0.0      0.001   19.1   0.0    2.6  2  AAA_14    AAA domain
    1.5e-05   25.4   0.0    5.9e-05   23.5   0.0    1.9  1  AAA_16    AAA ATPase domain
     0.0001   22.6   0.0    0.00045   20.5   0.0    2.0  1  AAA_22    AAA domain
     0.0026   16.9   0.0     0.0044   16.1   0.0    1.3  1  T2SSE     Type II/IV secretion system protein
  ------ inclusion threshold ------
      0.027   14.4   0.2      0.067   13.1   0.2    1.7  1  HTH_12    Ribonuclease R winged-helix domain
      0.071   13.9   0.0       0.47   11.3   0.0    2.2  2  DUF4373   Domain of unknown function (DUF4373)
      0.096   13.0   0.3        8.6    6.8   0.0    2.5  2  Rrf2      Transcriptional regulator
       0.14   12.1   1.6       0.92    9.5   0.2    2.7  2  HTH_45    Winged helix-turn-helix


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 !   63.2   0.0   1.6e-20   3.2e-17       5     231 ..      19     247 ..      15     249 .. 0.77
   2 ?   -1.1   0.0      0.72   1.4e+03     138     163 ..     270     295 ..     258     347 .. 0.50

  Alignments for each domain:
  == domain 1  score: 63.2 bits;  conditional E-value: 1.6e-20
                          ATPase_2   5 ekelkeleeilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkkleka 81 
                                        + l+ +e + +  ++++  i+Gp+++GKt++l  ++++le+ ++ + y   +  ++ ++++++    + ++ +++ 
  gi|242399591|ref|YP_002995016.1|  19 AEYLSFIEAVEK--RRNFFIITGPRRIGKTSFLYASLNELEK-EYGIPY-AVVDARAATSINSK----YPQRIISER 87 
                                       555566665544..59999*********************44.444444.33444444444444....334444444 PP

                          ATPase_2  82 l..........giavpkaeleeilk..eksklvfkaielllekikkkgkkiiiiiDelqklidlglngaellvkeLl 146
                                       l          g +v k ++ +i     ++ + +  i ++l +i++     ii +De+q+l+   +n  e+l k ++
  gi|242399591|ref|YP_002995016.1|  88 LykalvsrgfvGGVVSKIKGIKIGGieIETDEHNIDIVDILSAINEGNELAIIAFDEAQYLR--FSN--EDLTKLFA 160
                                       44444555567555555555555555456667789999********9999************..666..9******9 PP

                          ATPase_2 147 nliesltkekhlcvviclsSeglfie...rvyneselegrhky.ilvddldketalnflkegfkel.eelskedfee 218
                                        +++sl+   ++++v+ +s  g++ +   + + +++l gr +  i++  ++  ++l+fl++gf+e  +  ++ ++  
  gi|242399591|ref|YP_002995016.1| 161 WVLDSLP---NVILVFTGSQVGVLENflrLEDGKAPLFGRYEVrINLPRFNPSESLEFLRRGFEEYsIRVNERELLP 234
                                       9999976...78***********8877768999*********************************8888******* PP

                          ATPase_2 219 iyryvGGkPkalv 231
                                       +++ ++G P+ lv
  gi|242399591|ref|YP_002995016.1| 235 VVNTLDGVPGWLV 247
                                       *********9876 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.72
                          ATPase_2 138 aellvkeLlnliesltkekhlcvvic 163
                                       a ++v+  ++ +++l+ ++++++ i+
  gi|242399591|ref|YP_002995016.1| 270 AMKYVETEFEELDKLSPRYKIIMRIV 295
                                       44444444444444444444443322 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   5.1e-07     0.001       3      48 ..      33      77 ..      31      98 .. 0.71
   2 !   12.0   0.0   7.8e-05      0.16      51     107 ..     123     183 ..     103     213 .. 0.68

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 5.1e-07
                            AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkklad 48
                                      +  +itG+Rr+GKT +l+  ++el  k+  i y  +d    ++++ 
  gi|242399591|ref|YP_002995016.1| 33 NFFIITGPRRIGKTSFLYASLNELE-KEYGIPYAVVDARAATSINS 77
                                      6789****************98888.77777777777766655442 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 7.8e-05
                            AAA_14  51 kllelileklkeekktylflDEiqev....pewekalkslvdegknldvivtGSnskllsk 107
                                       ++ +++ +  ++++  ++ +DE+q++    +++ k    ++d+ +n+ +++tGS+ ++l +
  gi|242399591|ref|YP_002995016.1| 123 DIVDILSAINEGNELAIIAFDEAQYLrfsnEDLTKLFAWVLDSLPNVILVFTGSQVGVLEN 183
                                       34444444333367888*********665556666666666677***********999865 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   2.9e-08   5.9e-05       1     169 [.      13     171 ..      13     172 .. 0.65

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 2.9e-08
                            AAA_16   1 rlvGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekd....ggif.lrgkcdqlesaipysal 72 
                                       +l+GR++e    ls +e+v + r +  +++G++ +GK+s + + l++lek+    ++++ +r+ +  +      s +
  gi|242399591|ref|YP_002995016.1|  13 ELFGRRAEY---LSFIEAVEKRR-NFFIITGPRRIGKTSFLYASLNELEKEygipYAVVdARAATSIN------SKY 79 
                                       599******...99999998888.9****************999999**9976665555555555555......557 PP

                            AAA_16  73 aqalareellrqlldeaesaeleawrekleealaavpelagaeasrllellkrllallsrderplvlvlDdlqwade 149
                                        q +  e+l+++l ++     ++    k+++    + e++       +  + ++l+ + ++ +  ++ +D++q +++
  gi|242399591|ref|YP_002995016.1|  80 PQRIISERLYKALVSR---GFVGGVVSKIKGIKIGGIEIET---DEHNIDIVDILSAINEGNELAIIAFDEAQYLRF 150
                                       7777788888888888...3333333333333221222222...223333334443333333337888888888888 PP

                            AAA_16 150 aslqllaaLlrllesk.pllv 169
                                       +  +l ++++  l+s  ++++
  gi|242399591|ref|YP_002995016.1| 151 SNEDLTKLFAWVLDSLpNVIL 171
                                       888887777777776446665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   2.3e-07   0.00045       3     130 ..      30     174 ..      27     182 .. 0.70

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.3e-07
                            AAA_22   3 ktagilvvtGesGtGKTtllrrlleqldeeakaee..............erpevvfvtlpsstsskdllrellralg 65 
                                       k++++ ++tG+  +GKT  l   l++l++e+ + +                             ++ + ++l +al 
  gi|242399591|ref|YP_002995016.1|  30 KRRNFFIITGPRRIGKTSFLYASLNELEKEYGIPYavvdaraatsinskY-------------PQRIISERLYKALV 93 
                                       6899**************99999999988776655554443333333322.............23333444444444 PP

                            AAA_22  66 lelka.................erlsseellealeqalraravielliiDEaqhlr.seealeeLrsllnlsrkgvq 124
                                       +++                   e+++    +  +  a+++    +++  DEaq+lr s+e l++L  ++   +++  
  gi|242399591|ref|YP_002995016.1|  94 SRGFVggvvskikgikiggieiETDEHNIDIVDILSAINEGNELAIIAFDEAQYLRfSNEDLTKLFAWVL--DSLPN 168
                                       333336666667777777*997777777777999999999888899*********999****99988887..66666 PP

                            AAA_22 125 liLvGt 130
                                       +iLv t
  gi|242399591|ref|YP_002995016.1| 169 VILVFT 174
                                       666655 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 !   16.1   0.0   2.2e-06    0.0044     117     156 ..      20      59 ..       8      71 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.2e-06
                             T2SSE 117 kiaevlrkavrerglilvsGgTgsGKttllyallkeinks 156
                                       ++ +++++  ++r  ++++G+   GKt +lya l+e++k+
  gi|242399591|ref|YP_002995016.1|  20 EYLSFIEAVEKRRNFFIITGPRRIGKTSFLYASLNELEKE 59 
                                       5677887777789999*********************987 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.2   3.4e-05     0.067      19      60 ..     310     352 ..     290     354 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.4e-05
                            HTH_12  19 iaeeLkkr.gydigeravRyrLrkleergltrrvgyagreltE 60 
                                       i +  ++  +++i e+++R  L kl + g+ +  gy++ ++++
  gi|242399591|ref|YP_002995016.1| 310 IKNLAEEElEENIDEKSMRKYLSKLVDYGFLETIGYGKYRIPD 352
                                       5555666679****************************99997 PP

>> DUF4373  Domain of unknown function (DUF4373)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.9   3.7e+03      41      77 ..     222     273 ..     214     281 .. 0.70
   2 ?   11.3   0.0   0.00024      0.47      26      89 ..     288     349 ..     285     350 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.9
                           DUF4373  41 gyyiewdeeqlllladka...............klevdeeevkeiveacvey 77 
                                       +y i+++e++ll +++ +               +  + +e ++++++++++y
  gi|242399591|ref|YP_002995016.1| 222 EYSIRVNERELLPVVNTLdgvpgwlvhygarriDGLTHDEAIERVLNEAMKY 273
                                       6777777777777777666666666666666665556677888888877665 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00024
                           DUF4373  26 ygvyvkllekiykekgyyiewdeeqlllladkaklevdeeevkeiveacveyglFdkelfeedg 89 
                                       y +++ ++  + +  g+  +wd+ + l+  + ++ ++de+++++ ++++v+yg+++   + ++ 
  gi|242399591|ref|YP_002995016.1| 288 YKIIMRIVARLSEGRGH-ARWDRIKNLAEEE-LEENIDEKSMRKYLSKLVDYGFLETIGYGKYR 349
                                       679999********999.9999998887777.799********************988777765 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.2     0.039        77      53      83 .]     100     131 ..      66     131 .. 0.83
   2 ?    6.8   0.0    0.0043       8.6       3      57 ..     284     342 ..     283     349 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.039
                                       TSEEEETTT-.TCEEESSHCCCSBHHHHHHHH CS
                              Rrf2  53 glvksvrGkg.GGyrLakppeeItlldvvrav 83 
                                       g+v  ++G + GG+ +  + ++I + d++ a+
  gi|242399591|ref|YP_002995016.1| 100 GVVSKIKGIKiGGIEIETDEHNIDIVDILSAI 131
                                       56777889554*****************9986 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0043
                                       --HHHHHHHHHHHHHHHSSTCC-.B-HHHHHH...HHTS-HHHHHHHHHHHHHTTSEEE CS
                              Rrf2   3 lsskteyalhallyLakeeeeep.vsseeiae...rqnispsylekilakLrkaglvks 57 
                                       ls + ++ +++++ L++ +++    +++++ae   + ni ++ ++k l+kL   g++++
  gi|242399591|ref|YP_002995016.1| 284 LSPRYKIIMRIVARLSEGRGHARwDRIKNLAEeelEENIDEKSMRKYLSKLVDYGFLET 342
                                       66677788889999988655544389999**966567******************9987 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1      0.39   7.7e+02       8      19 ..     124     135 ..     120     142 .. 0.83
   2 ?    9.5   0.2   0.00046      0.92      28      58 ..     319     350 ..     286     352 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.39
                            HTH_45   8 iadILeaisege 19 
                                       i+dIL+ai+eg+
  gi|242399591|ref|YP_002995016.1| 124 IVDILSAINEGN 135
                                       79******7664 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00046
                            HTH_45  28 kanLsykllnkYLdmLvekglikk.skekYvl 58 
                                       + n++ k ++kYL++Lv+ g++++   +kY++
  gi|242399591|ref|YP_002995016.1| 319 EENIDEKSMRKYLSKLVDYGFLETiGYGKYRI 350
                                       56999*****************8767788876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      565  (0.0315132); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); 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: 00:00:00.46
# Mc/sec: 2350.35
//
Query:       gi|242399592|ref|YP_002995017.1|  [L=395]
Description: hypothetical protein TSIB_1617 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.045   14.2   0.2      0.091   13.2   0.2    1.5  1  Phage_holin_6_1  Bacteriophage holin of superfamily 6 (Holin_


Domain annotation for each model (and alignments):
>> Phage_holin_6_1  Bacteriophage holin of superfamily 6 (Holin_LLH)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   5.1e-06     0.091      66      95 ..     278     308 ..     276     311 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.1e-06
                   Phage_holin_6_1  66 eeAleklkellkekgi.sitddeleglIEaa 95 
                                       +eAl+  +e+lkekgi +i+d+++e+++E a
  gi|242399592|ref|YP_002995017.1| 278 KEALRVELEWLKEKGIiNISDEDIEAIVEVA 308
                                       67888889*********************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       633  (0.0353059); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); 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: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 2430.40
//
Query:       gi|242399593|ref|YP_002995018.1|  [L=90]
Description: hypothetical protein TSIB_1618 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.1e-12   47.5   0.1    2.4e-12   47.3   0.1    1.0  1  ThiS        ThiS family
     0.0059   16.9   0.1     0.0085   16.4   0.1    1.6  1  Urm1        Urm1 (Ubiquitin related modifier)
  ------ inclusion threshold ------
      0.029   14.2   0.0      0.032   14.0   0.0    1.1  1  Collectrin  Renal amino acid transporter


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 !   47.3   0.1     4e-16   2.4e-12       1      77 []       9      90 .]       9      90 .] 0.93

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 4e-16
                                      EEETTCCHHHHT..CEEEEESSTSBHHHHHHHHHHHTCHHG...TTTTEEEEETTEEEGC.CTTTSB--TTCEEEEEES CS
                              ThiS  1 vllfaelrelag..eeelelaegstvaelleaLgerypela...lerrvavavNgeivpr.lwldtelkdgDevailpp 73
                                      v+l a++ e  +  e  + l+e+st+++ll++L+ +  +++    +r++++++Ng+ +++  + +++lkd D+++i+p+
  gi|242399593|ref|YP_002995018.1|  9 VKLIAQVAEGIErlEFWVFLEENSTLGDLLKKLELER-KIKiewDKRNIVILINGRSAEFlGGVKAKLKDMDKIVIMPV 86
                                      789999999999999999****************888.56678*99**************66***************** PP

                                      TTC- CS
                              ThiS 74 VaGG 77
                                       aGG
  gi|242399593|ref|YP_002995018.1| 87 AAGG 90
                                      ***9 PP

>> Urm1  Urm1 (Ubiquitin related modifier)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   1.4e-06    0.0085      60      96 .]      54      90 .]       1      90 [] 0.83

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.4e-06
                                      TTEEEEETTCEHHHCTCCCSB--TTEEEEEEETTT-- CS
                              Urm1 60 PGilvLindaDwellgekdyelkdkDkivFistlhGG 96
                                        i++Lin    e lg  + +lkd Dkiv +    GG
  gi|242399593|ref|YP_002995018.1| 54 RNIVILINGRSAEFLGGVKAKLKDMDKIVIMPVAAGG 90
                                      569*************************998877776 PP

>> Collectrin  Renal amino acid transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   5.3e-06     0.032      56     110 ..      15      69 ..       3      83 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.3e-06
                        Collectrin  56 vlnetqrvSfwfvvtspknesklvpkeeveeairksrnrineaflLddktLeflg 110
                                       v +  +r  fw+++ + ++  +l++k e+e++i+ + ++ n + l++ ++ eflg
  gi|242399593|ref|YP_002995018.1|  15 VAEGIERLEFWVFLEENSTLGDLLKKLELERKIKIEWDKRNIVILINGRSAEFLG 69 
                                       667789***********************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.30s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 563.57
//
Query:       gi|242399594|ref|YP_002995019.1|  [L=612]
Description: Aldehyde ferredoxin oxidoreductase (AOR) [Thermococcus sibiricus MM 739]
Scores for complete 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-121  404.2   0.0     7e-121  403.8   0.0    1.1  1  AFOR_C    Aldehyde ferredoxin oxidoreductase, domains 2 & 3
    5.4e-80  267.9   0.4    2.1e-79  266.0   0.3    1.9  2  AFOR_N    Aldehyde ferredoxin oxidoreductase, N-terminal doma


Domain annotation for each model (and alignments):
>> AFOR_C  Aldehyde ferredoxin oxidoreductase, domains 2 & 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  403.8   0.0  7.8e-125    7e-121       4     382 .]     222     605 ..     219     605 .. 0.95

  Alignments for each domain:
  == domain 1  score: 403.8 bits;  conditional E-value: 7.8e-125
                                       HHHHHHHHHSH.HHHHHHHH-GGGHHHHHHHTT---BTTTTBS--TTGGGGSHHHHHHHTEEEE.E-TT-SS--EEE CS
                            AFOR_C   4 kkiqkeiksspqvtaelrkyGTaelvnianetgalptknfqegtfekaekisgealeekylvknegCfsCpiaCgre 80 
                                       k+  + +ks+p+   +++++GT+  v +  + g +pt+nf+++   +ae  + e l++ y vk++gC++C i+Cg++
  gi|242399594|ref|YP_002995019.1| 222 KEQVESYKSNPAFE-GFHNLGTNFAVYPFYTLGHFPTYNFKQKELYGAEIFQPEILSQ-YVVKHSGCWGCMIRCGKV 296
                                       67788999***666.***************************6655566555577776.*****99*********** PP

                                       EE.......ET.EE---HHHHHHHTGGGT---HHHHHHHHHHHHHHTB-HHHHHHHHHHHHHHHHTTSS-HHHHTS- CS
                            AFOR_C  81 vkveegkk.vk.vegpeyetlaalGsnlgiddleailklnelcdelGlDtisaGntiafamelyekGllkkedtdgl 155
                                       +k ++g++ ++  + peyet +++G nlg+ ++e+i+++n lcd +GlDtis+G +i+fa+elyekG++ k++tdgl
  gi|242399594|ref|YP_002995019.1| 297 FKLTKGPYaGTvWDFPEYETHWSFGGNLGNINVETIVYANMLCDFYGLDTISTGVAIGFAIELYEKGIIGKSETDGL 373
                                       *******9666999*************************************************************** PP

                                       ---TT-THHHHHHHHHHHTT-TTHHHHTT-HHHHHHCTT..-GGG--EETTEE--SS-GGG-HHHHHHHHH-TTSS- CS
                            AFOR_C 156 elefgdaeallellekiAkregigdllAeGvkrlaeklg..aeelamhvkGlelpaydprgakgmalaYatsnrGac 230
                                       el++gd++ + el+++iA r gigdllAeG++++aek+g  ae++a+hvkGle+paydpr ak+++l++ats+ Ga+
  gi|242399594|ref|YP_002995019.1| 374 ELRWGDPDIIPELVKRIALRIGIGDLLAEGTRKAAEKIGrgAEKYAIHVKGLEFPAYDPRSAKAHGLNFATSPIGAS 450
                                       ***************************************************************************** PP

                                       SGGG-THHHH....S---TT--HHHHHHHHHHHHHHHHHHHHT--GGGG-HHH......HHHHHHHHHT--..--HH CS
                            AFOR_C 231 Hlrayliale....ekvdpletegkaelvkwfqdltalvdslglCkftseaeerldlelyakllsavtGid..vtee 301
                                       H  ++  +      +k dp++tegk+e++k+ qd ta+ + +++C f+  + e++++++yak+l+a+tGi+   +++
  gi|242399594|ref|YP_002995019.1| 451 HCIGWNKFEImgipRKADPFATEGKGEITKYVQDETAIAETAIFCIFPF-NMEMVTIDMYAKMLYAATGIEefKDPK 526
                                       **9886555579**99*********************************.8999****************87789** PP

                                       HHHHHHHHHHHHHHHHHHHHT--HHHS---HHHHHS---SSTTTT---..-HHHHHHHHHHHHT--TTS---HHHHH CS
                            AFOR_C 302 ellkaGeRiynleRlfnlreGltrkddtlperlleeplkegpakgkvledeleemldeyYelrGWdetGvPtketlk 378
                                        l+ aGeRi+nleR++n+reG++ k d++per+++ep    p+kg+    e e +l++yY++rGWde+GvPt+e+l+
  gi|242399594|ref|YP_002995019.1| 527 HLWLAGERIFNLERAINIREGIDGKYDKMPERIVKEPVLREPSKGQIF--EEEILLKDYYKVRGWDENGVPTREKLR 601
                                       ***********************************************9..77999********************** PP

                                       HCT- CS
                            AFOR_C 379 rLgL 382
                                       +L+L
  gi|242399594|ref|YP_002995019.1| 602 ELEL 605
                                       **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 !  266.0   0.3   2.4e-83   2.1e-79       1     197 [.       6     205 ..       6     206 .. 0.98
   2 ?   -0.8   0.0      0.13   1.2e+03      27      76 ..     411     462 ..     401     471 .. 0.76

  Alignments for each domain:
  == domain 1  score: 266.0 bits;  conditional E-value: 2.4e-83
                                       SEEEEEETTTTEEEEEE--HHHHHHH-SCHHHHHHHHHHHS-TTS-TTSTTS-EEEEE-TTTTSSSTTB-EEEEEEE CS
                            AFOR_N   1 gkilrvdLstgkieveelpeelaekylGgrglaakllldevppgvdplspenplvfatGpltgtpapgsgrlvvvak 77 
                                       gkilr+dL+++k++ve+l+ee+++k++Ggrg++ak+l+de++pg+ plspen+lv+++Gpltgt++ +++r+++ +k
  gi|242399594|ref|YP_002995019.1|   6 GKILRIDLTNKKATVEPLKEEVLKKFIGGRGIGAKILWDELKPGICPLSPENKLVLTVGPLTGTKVQSASRWMAQFK 82 
                                       79*************************************************************************** PP

                                       -TTTSSEEEEEEETCHHHHHHHCT-SEEEEES--SS-EEEEEETTEEEEEE-TTTTTS-HHHHHHHHHHHHTS..EE CS
                            AFOR_N  78 sPltgtlgesnaGgrfgaelkraGydaivieGkaekpvylvieddkveiedaedlwgldtyettealkeelgd..kv 152
                                       sPltgt+ +s  Gg+fgaelk+aGy+ai++eGkaekp+y++i+d++ve++dae +wg++t +t e lkee+++  ++
  gi|242399594|ref|YP_002995019.1|  83 SPLTGTYFRSVGGGFFGAELKFAGYEAIIVEGKAEKPTYVYINDENVEFRDAERIWGMNTLATREFLKEETDKnaHM 159
                                       *********************************************************************88887788 PP

                                       EEE-HHHHTT-TTB-E.EE.TTEEE-SSSHHHHHHHTTEEEEEEE- CS
                            AFOR_N 153 aviGpaGenlvrfAsisvd.dgraagrgGlGavmgsKnlkaivvrg 197
                                       ++iGpaGenlv+f++i++d d+r a+rgG GavmgsKnlkaivv+g
  gi|242399594|ref|YP_002995019.1| 160 VMIGPAGENLVKFSAIVTDgDFRTAARGGGGAVMGSKNLKAIVVKG 205
                                       8***************777*************************99 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.13
                                       -SCHHHHHHHHHHHS-.TTS-TTSTT.S-EEEEE-TTTTSSSTTB-EEEEEE CS
                            AFOR_N  27 lGgrglaakllldevp.pgvdplspe.nplvfatGpltgtpapgsgrlvvva 76 
                                       +G  +  ++++ + ++ p +dp s +   l fat+p+  + + g ++++++ 
  gi|242399594|ref|YP_002995019.1| 411 IGRGAEKYAIHVKGLEfPAYDPRSAKaHGLNFATSPIGASHCIGWNKFEIMG 462
                                       5555556677777777788999977615699******999999999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (612 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 3939.25
//
Query:       gi|242399595|ref|YP_002995020.1|  [L=170]
Description: hypothetical protein TSIB_1620 [Thermococcus sibiricus MM 739]
Scores for complete 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-11   45.0   0.0    2.4e-11   44.6   0.0    1.1  1  Methyltransf_24  Methyltransferase domain
    8.8e-05   21.8   0.0    0.00015   21.0   0.0    1.3  1  Methyltransf_3   O-methyltransferase


Domain annotation for each model (and alignments):
>> Methyltransf_24  Methyltransferase 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   2.4e-11       1     106 []      23     134 ..      23     134 .. 0.90

  Alignments for each domain:
  == domain 1  score: 44.6 bits;  conditional E-value: 2.7e-15
                   Methyltransf_24   1 vEiGvysGvstlwllralrrnga...grlvavdhdpgaeeaaalare.aglddrvrlikadseealasla..agsiD 71 
                                       +EiGvy G  +  + +a+++n      +++ +d +++++ ++++ ++ ++    ++l ++ds+ +l+++      +D
  gi|242399595|ref|YP_002995020.1|  23 MEIGVYDGENARSMIEAAKENFSpeeIEYYGFDYFEDEWLYQRIYKKlEETGCKFKLFRGDSRVTLPQHVdeLPIMD 99 
                                       59*******************9999999********877788888886666667*************888544458* PP

                   Methyltransf_24  72 llfiDgghaaeavledleallprlapggvvlfdDi 106
                                       l+fiDgg ++e+++ d e++++++ +++vv+++++
  gi|242399595|ref|YP_002995020.1| 100 LIFIDGGKSYETAKSDWENCRKLMGKHTVVFVHNY 134
                                       *********************************98 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   1.6e-08   0.00015      37     162 ..       8     138 ..       3     156 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.6e-08
                                       HHHHHHHHHHT--EEEEE--TTSHHHHHHHTTS.....-TT-EEEEEES-HHHHHHHHHHHHHTT-GGGEEEEES-H CS
                    Methyltransf_3  37 qfLslLvklvnakrvleiGvftGyslLatalal.....PeDGkilaididreayeialkfiqkagvaekieliegda 108
                                        fL+  +k    kr +eiGv+ G  + ++  a      Pe+ +    d  +++    + + +    + k +l +gd+
  gi|242399595|ref|YP_002995020.1|   8 AFLNDHIKRNKCKRLMEIGVYDGENARSMIEAAkenfsPEEIEYYGFDYFEDEWLYQRIYKKLEETGCKFKLFRGDS 84 
                                       5899999999*************8777766554122337777777777766666556666666678899******** PP

                                       HHHHHHHHTSSS---EEEEEE-S-GG..GHHHHHHHHHHTEEEEEEEEEE-TTGGG CS
                    Methyltransf_3 109 lkvLeelvkdkklpefDfifvDaDks..syvnyyeklleLvkvGgliaiDntLWeG 162
                                       + +L + v++   p +D+if+D  ks  + +  +e++ +L+ +  ++ + n  + G
  gi|242399595|ref|YP_002995020.1|  85 RVTLPQHVDEL--PIMDLIFIDGGKSyeTAKSDWENCRKLMGKHTVVFVHNYEFPG 138
                                       ******99887..89********997223355678888888888877777766666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.44
# Mc/sec: 1162.75
//
Query:       gi|242399596|ref|YP_002995021.1|  [L=433]
Description: Acetamidase/formamidase [Thermococcus sibiricus MM 739]
Scores for 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-57  192.6   0.0    2.4e-55  187.9   0.0    2.0  1  FmdA_AmdA       Acetamidase/Formamidase family
  ------ inclusion threshold ------
       0.05   12.4   0.0      0.096   11.4   0.0    1.4  1  tRNA-synt_1g    tRNA synthetases class I (M)
      0.069   12.8   0.9       0.14   11.8   0.9    1.6  1  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
      0.089   12.7   1.0       0.16   11.9   1.0    1.4  1  Prok-RING_1     Prokaryotic RING finger family 1
       0.16   12.0   0.3       0.29   11.2   0.3    1.3  1  DZR             Double zinc ribbon
       0.24   10.9   2.8          6    6.4   0.2    2.3  2  zf-ribbon_3     zinc-ribbon domain
        1.2    9.3   3.7        5.5    7.2   3.8    1.9  2  Zn-ribbon_8     Zinc ribbon domain


Domain annotation for each model (and alignments):
>> FmdA_AmdA  Acetamidase/Formamidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.9   0.0   9.4e-59   2.4e-55      56     372 ..      45     417 ..      41     418 .. 0.89

  Alignments for each domain:
  == domain 1  score: 187.9 bits;  conditional E-value: 9.4e-59
                         FmdA_AmdA  56 vrtvdlkkvHeltgPvevegAepGDllvveildievl........................................ 92 
                                       ++t++l+++He+  Pv+vegA++ D lv++i++i+vl                                        
  gi|242399596|ref|YP_002995021.1|  45 MITPTLRGGHEVNVPVAVEGAKVSDGLVMKIKSIKVLskaassgvdtvregafvgdpfvakkcptcnepwpefevvg 121
                                       7899*********************************8888888888888888888888777777777777777777 PP

                         FmdA_AmdA  93 .............eea.....ewGytgifdkenggGfl..kdafpeaakaiwdlegiyassrq..........ipgv 139
                                                    + a      +Gyt++fd++ g+G++  k++++ +ak++w+ ++++++s+q          i+gv
  gi|242399596|ref|YP_002995021.1| 122 igedavrckhcgsP-AspfkmVNGYTMVFDHNLGVGVTvnKETAEMIAKDAWEWHSLPKNSKQvpilifakadIVGV 197
                                       77666666555551.0566669****************99************************************* PP

                         FmdA_AmdA 140 rfrglphpGllGtapskelldswnareeeliekralallpepkeallgkleeeaekvaaegartvpprengGnmDik 216
                                         r++p++G++Gt+p+ +++ds+na +        l  +p+p   +  +                  + ++G++Di+
  gi|242399596|ref|YP_002995021.1| 198 PSRIIPFLGQFGTVPAVNIPDSHNAGDFGS----FLIDAPHPYAITKEEY---------------DTKLTDGHLDID 255
                                       ************************965433....2334577665554432...............23679******* PP

                         FmdA_AmdA 217 nlsrGskvylPVkveGaklsvGDlHfsqGDGEisfcg.aiemsgvvtlkvevikggmeklgiknpiflp........ 284
                                       ++++G+++++PVkv+G++++ GD H++qGDGE+  +g ++++s+  +++v+vik++    ++++p++lp        
  gi|242399596|ref|YP_002995021.1| 256 AVKEGAIIIAPVKVDGGGVYAGDAHAMQGDGEV--AGhTTDVSAESEIEVSVIKNL----NLDGPLLLPleedlppl 326
                                       *********************************..********************9....***************** PP

                         FmdA_AmdA 285 .......................eevepryseylsfeGisvdesgkqhyldltvAyrnallraieyLkkfGytkeqa 338
                                                              e+v+p     ++++G     sg     +++ A+ ++++ra++++          
  gi|242399596|ref|YP_002995021.1| 327 akpwrkdewervqtlakkfgiepEPVAP-----IQIIG-----SGP----TINEAAMRGFERAAKLFG--------- 380
                                       ******************9999999999.....9****.....999....9*****************......... PP

                         FmdA_AmdA 339 ylllsvapvegr..isgivdi...Pnvva.tlalPldiFd 372
                                          +s+++v++r  isg+v+i   P++v+ ++ +Pldi +
  gi|242399596|ref|YP_002995021.1| 381 ---MSIEEVKNRvtISGAVEIgrlPGIVQvSMQVPLDILE 417
                                       ...*********999***********9973689****986 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   3.8e-05     0.096      99     173 ..      67     150 ..      62     161 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.8e-05
                                       HHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GGG-EE.................-TTS-EE-TTSSB-E...... CS
                      tRNA-synt_1g  99 lvqeifkklkekgliyekeieqlycpkderflpdryvegtCPkckse.........eargdqceecgkkleptelin 166
                                       ++  ++ k+k+ + +++ +++++  ++++ f  d +v  +CP+c++            ++ +c++cg+  +p +++n
  gi|242399596|ref|YP_002995021.1|  67 VSDGLVMKIKSIKVLSKAASSGVDTVREGAFVGDPFVAKKCPTCNEPwpefevvgiGEDAVRCKHCGSPASPFKMVN 143
                                       666778889999999999999999********************975333333333567889**************9 PP

                                       ....... CS
                      tRNA-synt_1g 167 pksaisg 173
                                         +++ +
  gi|242399596|ref|YP_002995021.1| 144 GYTMVFD 150
                                       9988766 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 ?   11.8   0.9   5.6e-05      0.14      14      25 ..     123     134 ..     106     135 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.6e-05
                                       SSS----SSS-- CS
                    DNA_RNApol_7kD  14 kgdpiRCkeCGh 25 
                                        +d++RCk+CG+
  gi|242399596|ref|YP_002995021.1| 123 GEDAVRCKHCGS 134
                                       589********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 ?   11.9   1.0   6.4e-05      0.16       4      29 ..     104     135 ..     101     136 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.4e-05
                       Prok-RING_1   4 gkkCpvCgkelkee......dDiVvCpeCgtp 29 
                                        kkCp C+++  e       +D+V C +Cg+p
  gi|242399596|ref|YP_002995021.1| 104 AKKCPTCNEPWPEFevvgigEDAVRCKHCGSP 135
                                       689*****987664455677**********98 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.3   0.00011      0.29      12      40 ..     104     138 ..     101     142 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00011
                               DZR  12 arfCseCgtklkavaa......edrCpsCgekvdp 40 
                                       a+ C++C+++ ++ +       + rC +Cg++++p
  gi|242399596|ref|YP_002995021.1| 104 AKKCPTCNEPWPEFEVvgigedAVRCKHCGSPASP 138
                                       57788888887654447788888888888888776 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.2    0.0093        24       3      11 ..     105     113 ..     103     119 .. 0.84
   2 ?    6.4   0.2    0.0023         6      14      25 ..     124     135 ..     120     138 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0093
                       zf-ribbon_3   3 vrCPnCGap 11 
                                       ++CP C++p
  gi|242399596|ref|YP_002995021.1| 105 KKCPTCNEP 113
                                       79****987 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0023
                       zf-ribbon_3  14 sddnvCpyCGtk 25 
                                       +d++ C++CG++
  gi|242399596|ref|YP_002995021.1| 124 EDAVRCKHCGSP 135
                                       677778888865 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.6      0.11   2.7e+02      27      34 ..     105     112 ..      97     117 .. 0.77
   2 ?    7.2   3.8    0.0021       5.5       7      36 ..     106     136 ..     104     138 .. 0.69

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.11
                       Zn-ribbon_8  27 taCPeCgs 34 
                                       ++CP+C++
  gi|242399596|ref|YP_002995021.1| 105 KKCPTCNE 112
                                       45****86 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0021
                       Zn-ribbon_8   7 rCeeCghefevlqsisdaplta.CPeCgsev 36 
                                       +C  C++   ++  +   ++ + C++Cgs++
  gi|242399596|ref|YP_002995021.1| 106 KCPTCNEPWPEFEVVGIGEDAVrCKHCGSPA 136
                                       69999987665554444445566*****965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); 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: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 2583.27
//
Query:       gi|242399597|ref|YP_002995022.1|  [L=175]
Description: hypothetical protein TSIB_1622 [Thermococcus sibiricus MM 739]
Scores for complete 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   34.6  30.2    2.6e-08   34.1  30.2    1.2  1  DUF1097   Protein of unknown function (DUF1097)
  ------ inclusion threshold ------
       0.14   12.3   4.5       0.22   11.6   0.7    2.3  2  YrhC      YrhC-like protein
       0.17   12.0   5.4       0.29   11.3   5.4    1.4  1  Popeye    Popeye protein conserved region


Domain annotation for each model (and alignments):
>> DUF1097  Protein of unknown function (DUF1097)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1  30.2   4.3e-12   2.6e-08       3     141 ..      13     160 ..      11     168 .. 0.80

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 4.3e-12
                           DUF1097   3 svgvlaglwallaatlg..elpvWagFigwasffaaGggkkgllkslltnllGvvwAllaillisllggnlgl.lal 76 
                                       ++ + +++++ +a  lg  +lpvW+ Fi wa +f +G+++++l+++   +l G ++ ++ +  + +l++++++ +a+
  gi|242399597|ref|YP_002995022.1|  13 ATPITVAVATPFATRLGtwGLPVWISFIVWAEYFVLGANMEALKMIGYGFLYGCLMTAFWLASSVALTSAMAFdIAF 89 
                                       67788888888888888889************************************998888877777766652344 PP

                           DUF1097  77 llvvgivaflmvllakipll.sfiPaiflGlastfatllktava......lsnpllavivslllGavfGyls 141
                                       +++ +i ++l+v+  k p l ++++ if+G+++t+a+++++a +         ++ ++++ +l++ +fG+  
  gi|242399597|ref|YP_002995022.1|  90 IITNFIWIGLIVYSFKNPSLgKAVLPIFNGVSMTLAVYFTGALPpvevgaY-SATFVAAFWTLIAGYFGAFL 160
                                       4499***************99*********************99**99963.44444444444444444433 PP

>> YrhC  YrhC-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.2     0.042   2.5e+02      38      61 ..      54      77 ..      47      86 .. 0.79
   2 ?   11.6   0.7   3.7e-05      0.22      18      58 ..      89     129 ..      84     132 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.042
                              YrhC 38 lkksillgaivvfLllaflflrrs 61
                                      + k+i +g+  ++L+ af +++ +
  gi|242399597|ref|YP_002995022.1| 54 ALKMIGYGFLYGCLMTAFWLASSV 77
                                      567888899999999999887765 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 3.7e-05
                              YrhC  18 LalsaFLyiGlviPseaketlkksillgaivvfLllaflfl 58 
                                       ++++ F++iGl++ s++   l k++l  + +v ++la++f 
  gi|242399597|ref|YP_002995022.1|  89 FIITNFIWIGLIVYSFKNPSLGKAVLPIFNGVSMTLAVYFT 129
                                       78899**********************************96 PP

>> Popeye  Popeye protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   5.4   4.9e-05      0.29      10      96 ..      39     125 ..      32     129 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.9e-05
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            Popeye  10 nillllaflapsgvlgllvlrsllvlGflllalwawlvvCaldiflWnlllvlinlaqllyllyklrpvkfekelee 86 
                                       +i+ +  f+ + ++  l ++    + G+l+ a w    v  + ++   +++++ n++ +  ++y +++ ++ k +  
  gi|242399597|ref|YP_002995022.1|  39 FIVWAEYFVLGANMEALKMIGYGFLYGCLMTAFWLASSVALTSAMAFDIAFIITNFIWIGLIVYSFKNPSLGKAVLP 115
                                       55666667777777777777777889*********************************************999999 PP

                                       xxxxxxxxxx RF
                            Popeye  87 lYkklFqplk 96 
                                       +++ +  +l 
  gi|242399597|ref|YP_002995022.1| 116 IFNGVSMTLA 125
                                       9987766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      210  (0.0117129); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.28s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 1096.01
//
Query:       gi|242399598|ref|YP_002995023.1|  [L=348]
Description: phosphoenolpyruvate synthase [Thermococcus sibiricus MM 739]
Scores for complete 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-113  378.5   0.7   3.3e-113  378.3   0.7    1.0  1  PPDK_N    Pyruvate phosphate dikinase, PEP/pyruvate binding d


Domain annotation for each model (and alignments):
>> PPDK_N  Pyruvate phosphate dikinase, PEP/pyruvate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  378.3   0.7  1.9e-117  3.3e-113       2     318 ..      23     340 ..      22     347 .. 0.97

  Alignments for each domain:
  == domain 1  score: 378.3 bits;  conditional E-value: 1.9e-117
                            PPDK_N   2 elvGGKganLaellneagipvPpgfaitadafrefleengleekideelke.ldvddvdelrkaskeirelilsael 77 
                                       ++vGGKganL+el  ++g++vP+gf++t++af+ef+ e+g+ ++++ +l++  ++++v+e+++++k+i+++i+sa+l
  gi|242399598|ref|YP_002995023.1|  23 NIVGGKGANLGEL-VSIGVRVPEGFVVTSTAFKEFMRESGIWDELQTLLDKtKNITKVSEIQETAKRIQNMIISAHL 98 
                                       79***********.55*********************************9956899********************* PP

                            PPDK_N  78 PeeleeaikeayeelgkkfgdeelpvaVRSSataEDlpkasfaGqqdtyLnvggeeevleaikavfaSlfnerAilY 154
                                        ++le++i eaye+l++  ++++++va+RSSataEDlp asfaG+qdtyL v++ e+v+e++k+++aSl+++rAi+Y
  gi|242399598|ref|YP_002995023.1|  99 NKDLEREIIEAYEKLCEIKNEKNTKVAIRSSATAEDLPSASFAGMQDTYLYVSTPESVIEHVKKCWASLYTPRAIVY 175
                                       ****************988888******************************************************* PP

                            PPDK_N 155 rkekgldheevalavvvqkmvnsdlgasGVafsldpetGfkdevlinasyGlGeaVVaGrvtpdefvvekstrkile 231
                                       r++ +++h +v +avvvq+mv+s+  a+GV+f+++p tG+++e++i+ ++GlGeaVV+Grv pd+fvv+k+t+k+l+
  gi|242399598|ref|YP_002995023.1| 176 RNQMDIPHRNVYMAVVVQAMVRSK--AAGVMFTVNPITGNENEIVIEGTWGLGEAVVSGRVIPDHFVVDKNTKKVLK 250
                                       ************************..*************************************************** PP

                            PPDK_N 232 kkigekeikivydekeegtkevevpeeereklaLsdeeveeLaeiakkiekhygtpmdiEfaid...eeegklyllQ 305
                                       k+++ek+i++  d+++ ++ke +v  + r++++Ls +e+e L ++a kiekhyg  mdiE+aid   +  +k+ ++Q
  gi|242399598|ref|YP_002995023.1| 251 KQLAEKDIRMDWDPSTGTVKELPVFPQFRKRPSLSTAEIEVLVDYALKIEKHYGIFMDIEWAIDkyeGFPEKIKIVQ 327
                                       ***************988******777*************************************999999******* PP

                            PPDK_N 306 aRpetrtsekkek 318
                                       aR et+++ kk k
  gi|242399598|ref|YP_002995023.1| 328 ARAETVWNVKKGK 340
                                       *******998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       938  (0.0523175); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); 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: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 2851.44
//
Query:       gi|242399599|ref|YP_002995024.1|  [L=96]
Description: hypothetical protein TSIB_1624 [Thermococcus sibiricus MM 739]
Scores for complete 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   0.0    1.9e-06   28.4   0.0    1.1  1  ThiS         ThiS family
  ------ inclusion threshold ------
      0.028   14.8   1.1       0.37   11.2   1.1    2.0  1  Urm1         Urm1 (Ubiquitin related modifier)
      0.075   12.8   0.1       0.11   12.2   0.1    1.2  1  XPC-binding  XPC-binding domain
       0.11   12.0   0.0       0.13   11.7   0.0    1.1  1  DUF5017      Domain of unknown function (DUF5017)


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 !   28.4   0.0   4.3e-10   1.9e-06       5      77 .]       9      94 ..       5      94 .. 0.90

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 4.3e-10
                                      TCCHHHHT...CEEEEESSTSBHHHHHHHHHHHTCHHG.........TTTTEEEEETTEEEGC.CTTTSB--TTCEEEE CS
                              ThiS  5 aelrelag...eeelelaegstvaelleaLgerypela.........lerrvavavNgeivpr.lwldtelkdgDevai 70
                                      +  +e+++   e  +++++  tv+el++ L e+ypela           ++  + v g+++ + +     l+dg ev +
  gi|242399599|ref|YP_002995024.1|  9 GPFYEKTKkhkEIIELDKNSITVQELVKFLFEQYPELAqffennpekIFEFSTIIVRGRVLIPqDLPRVHLSDGEEVFF 87
                                      55667777777777889999*************************997799**********9977************** PP

                                      EESTTC- CS
                              ThiS 71 lppVaGG 77
                                      lp+V GG
  gi|242399599|ref|YP_002995024.1| 88 LPVVHGG 94
                                      ******9 PP

>> Urm1  Urm1 (Ubiquitin related modifier)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.1   8.2e-05      0.37      14      96 .]      12      94 ..       2      94 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 8.2e-05
                                      CTT-SEEEEEE-SSSSS-BHHHHHHHHCCCC-SSGHHHCBS.TTSB-TTEEEEETTCEHHHCTCCCSB--TTEEEEEEE CS
                              Urm1 14 lekkkkhkveleieseevnleeliayikknlikerkevFle.kdkvrPGilvLindaDwellgekdyelkdkDkivFis 91
                                      +ek+kkhk  +e ++++++++el++++ ++  +   + F +  +k+     +++       ++    +l d++++ F+ 
  gi|242399599|ref|YP_002995024.1| 12 YEKTKKHKEIIELDKNSITVQELVKFLFEQYPE-LAQFFENnPEKIFEFSTIIVRGRVLIPQDLPRVHLSDGEEVFFLP 89
                                      57788888889999*************998755.556665545566555555555555555566678888888888888 PP

                                      TTT-- CS
                              Urm1 92 tlhGG 96
                                       +hGG
  gi|242399599|ref|YP_002995024.1| 90 VVHGG 94
                                      88888 PP

>> XPC-binding  XPC-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   2.5e-05      0.11      22      50 ..      29      57 ..      24      60 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.5e-05
                       XPC-binding 22 qlLqplLqqlaqsnPqllqlIqqnqeeFl 50
                                         q+l++ l ++ P+l+q +++n+e+  
  gi|242399599|ref|YP_002995024.1| 29 ITVQELVKFLFEQYPELAQFFENNPEKIF 57
                                      5679999999****************876 PP

>> DUF5017  Domain of unknown function (DUF5017)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   2.9e-05      0.13      14      53 ..      22      61 ..      13      70 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.9e-05
                           DUF5017 14 VstekttykvgdtvtFkftGnpdlisfYsGevgkdYeykd 53
                                      ++ +k++++v + v+F f+ +p+l  f+  ++ k +e++ 
  gi|242399599|ref|YP_002995024.1| 22 IELDKNSITVQELVKFLFEQYPELAQFFENNPEKIFEFST 61
                                      6789********************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       773  (0.0431145); expected 358.6 (0.02)
Passed bias filter:                      638  (0.0355848); 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: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 581.07
//
Query:       gi|242399600|ref|YP_002995025.1|  [L=272]
Description: Cyclase [Thermococcus sibiricus MM 739]
Scores for complete 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-42  143.1   0.0      8e-42  142.7   0.0    1.2  1  Cyclase   Putative cyclase
  ------ inclusion threshold ------
        0.1   12.4   0.0       0.19   11.5   0.0    1.4  1  DUF348    G5-linked-Ubiquitin-like domain


Domain annotation for each model (and alignments):
>> Cyclase  Putative cyclase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.7   0.0     9e-46     8e-42       1     135 [.      14     197 ..      14     198 .. 0.81

  Alignments for each domain:
  == domain 1  score: 142.7 bits;  conditional E-value: 9e-46
                           Cyclase   1 idLshplsedtpvw.pdp.........................................islsehtGTHlDapgHfa 35 
                                       idL++p+++ +p   ++                                          ++l++h+GTHlDap+Hf+
  gi|242399600|ref|YP_002995025.1|  14 IDLTLPIQPFMPDIvGHVkmakwnheqgarlnsvptgidpidfppgppfyeyhsqaweeLTLTTHIGTHLDAPWHFF 90 
                                       79999995555444331123334455566666666666667777777777777777777*****************9 PP

                           Cyclase  36 e.........ktidelpleelvgpavvldvsakaaaedyeiitaedleaalakqgveikpgdivlirTgwskrledk 103
                                       +         ktide+ple+++g++vvldv++    ++  +it++d+++al+k++++i+p divli+Tgw+k+ +++
  gi|242399600|ref|YP_002995025.1|  91 PttengkmkaKTIDEVPLEWCIGNGVVLDVRHVG--PGG-LITEDDVKEALKKINYKIQPWDIVLIQTGWDKK-WGT 163
                                       98776666555*******************9984..455.78*******************************.566 PP

                           Cyclase 104 eky..rnpglseeaaewlaekgvkavGvDtlsvD 135
                                       ++y  ++pg+s+ea+ +l+e+gvk++G+D++++D
  gi|242399600|ref|YP_002995025.1| 164 KEYfeNHPGMSREATLYLIEQGVKVMGIDAFGFD 197
                                       7777999*************************99 PP

>> DUF348  G5-linked-Ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   2.1e-05      0.19      15      36 ..     130     151 ..     128     153 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.1e-05
                                       --SSHHHHHHHTT----TT-EE CS
                            DUF348  15 aadTVgdlLeeagitlgeqDkV 36 
                                       ++d+V+++L++ + ++++ D+V
  gi|242399600|ref|YP_002995025.1| 130 TEDDVKEALKKINYKIQPWDIV 151
                                       89******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        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 0.26s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1805.78
//
Query:       gi|242399601|ref|YP_002995026.1|  [L=639]
Description: Tungsten-containing aldehyde ferredoxin oxidoreductase (AOR) [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-90  304.4   0.0    1.5e-90  304.0   0.0    1.2  1  AFOR_C    Aldehyde ferredoxin oxidoreductase, domains 2 & 3
    1.9e-77  259.6   0.1    2.7e-77  259.1   0.1    1.2  1  AFOR_N    Aldehyde ferredoxin oxidoreductase, N-terminal doma


Domain annotation for each model (and alignments):
>> AFOR_C  Aldehyde ferredoxin oxidoreductase, domains 2 & 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  304.0   0.0   1.7e-94   1.5e-90       4     382 .]     226     621 ..     223     621 .. 0.92

  Alignments for each domain:
  == domain 1  score: 304.0 bits;  conditional E-value: 1.7e-94
                                       HHHHHHHHHSH.HHHHHHHH-GGGHHHHHHHTT---BTTTTBS-..-TTGGGGSHHHHHHHTEEEE.E-TT-SS--E CS
                            AFOR_C   4 kkiqkeiksspqvtaelrkyGTaelvnianetgalptknfqegt..fekaekisgealeekylvknegCfsCpiaCg 78 
                                       +++ +++ ++p++++  r +G++ l  +  ++g l ++n  +g+   e+ ek+s+e + + y+vk ++C+ CpiaC 
  gi|242399601|ref|YP_002995026.1| 226 EELLQVFLDDPMTSQVGRLLGSNFLHRVHSSHGTLIVENGHRGYatEEELEKVSAESILK-YHVKGRSCYLCPIACT 301
                                       56677888899888888999**********************99866666**********.*****99********* PP

                                       EEEE.......ET.EE---HHHHHHHTGGGT---HHHHHHHHHHHHHHTB-HHHHHHHHHHHHHHHHTTSS-HHHHT CS
                            AFOR_C  79 revkveegkk.vk.vegpeyetlaalGsnlgiddleailklnelcdelGlDtisaGntiafamelyekGllkkedtd 153
                                       r v +e++k+ v  + gpey ++ +l+   g  d ea ++ln+lcd +G+D  ++ + iafa++lye+G+++ke+++
  gi|242399601|ref|YP_002995026.1| 302 RSVYMESEKYgVIkGRGPEYYSMQSLTYRAGGWDTEAGIYLNKLCDAYGIDATTLPSNIAFAIDLYENGIITKEQVG 378
                                       *********97668*************************************************************** PP

                                       S----TT-THHHHHHHHHHHTT-T.THHHHTT-HHHHHHCTT..-GGG--EETTEE--SS-GGG-HHHHHHHHH-TT CS
                            AFOR_C 154 glelefgdaeallellekiAkreg.igdllAeGvkrlaeklg..aeelamhvkGlelpaydprgakgmalaYatsnr 227
                                       glel++g+ +a++e+++ +A+r+g ig+l A+ +k+l +++g  +e +a +vkGl +p  dpr+   + + Ya+++r
  gi|242399601|ref|YP_002995026.1| 379 GLELTWGNFDAMEEIIKSVAYRKGkIGELFAKSTKELIKEFGpeSEWYALEVKGLTMPSNDPRAGNVYNMRYAIATR 455
                                       *******************************************99999***************************** PP

                                       SS-SGGG-THHHH..S---TT--HHHHHHHHHHHHHHHHHHHHT--GGGG.......-HHH......HHHHHHHHHT CS
                            AFOR_C 228 GacHlrayliale..ekvdpletegkaelvkwfqdltalvdslglCkfts.......eaeerldlelyakllsavtG 295
                                       Ga+Hlr  + +     k d+l++ +  e+++ f+ + +lv+ + +C+++        e    ++++ + k+++a+tG
  gi|242399601|ref|YP_002995026.1| 456 GADHLRVSVLSSGrsLKWDELPEYEAMEVFVRFETYVTLVNLFNVCNWAYssytstpE-IAEIKEKGMFKVYNAATG 531
                                       ******5555555598888898879999999*******************9***9953.45589999********** PP

                                       ----HHHHHHHHHHHHHHHHHHHHHHT--HHHS---HHHHHS---SSTTT.T---...-HHHHHHHHHHHHT--T.T CS
                            AFOR_C 296 idvteeellkaGeRiynleRlfnlreGltrkddtlperlleeplkegpak.gkvl.edeleemldeyYelrGWde.t 369
                                       +++t+e++ ka+ R +  eR+ n+r Gl+r++d lp+r++eepl+  ++  +k   ++++e++ld+yY+lrG d+ t
  gi|242399601|ref|YP_002995026.1| 532 LNLTPEDFAKAAHRTIITERAENVRYGLRREHDYLPRRVFEEPLPVNEKGdTKIFpREKFEKLLDAYYALRGLDPkT 608
                                       ********************************************644444133444666****************** PP

                                       S---HHHHHHCT- CS
                            AFOR_C 370 GvPtketlkrLgL 382
                                        vP+++ l++LgL
  gi|242399601|ref|YP_002995026.1| 609 TVPKPSVLRELGL 621
                                       ************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 !  259.1   0.1     3e-81   2.7e-77       1     198 []      11     210 ..      11     210 .. 0.98

  Alignments for each domain:
  == domain 1  score: 259.1 bits;  conditional E-value: 3e-81
                                       SEEEEEETTTTEEEEEE--HHHHHHH-SCHHHHHHHHHHHS-TTS-TTSTTS-EEEEE-TTTTSSSTTB-EEEEEEE CS
                            AFOR_N   1 gkilrvdLstgkieveelpeelaekylGgrglaakllldevppgvdplspenplvfatGpltgtpapgsgrlvvvak 77 
                                       gk l+vdLs++ki +++l++ela +y+Ggrg+ akll+d v+p+ dpl+p+nplvfatGpl+g+ ap+sgr++v+a+
  gi|242399601|ref|YP_002995026.1|  11 GKTLWVDLSKNKILIKDLDPELAVNYIGGRGFVAKLLFDLVDPEKDPLDPQNPLVFATGPLSGI-APASGRFTVGAR 86 
                                       689************************************************************9.************ PP

                                       -TTTSSEEEEEEETCHHHHHHHCT-SEEEEES--SS-EEEEEETTEEEEEE-TTTTTS-HHHHHHHHHHHHTS...E CS
                            AFOR_N  78 sPltgtlgesnaGgrfgaelkraGydaivieGkaekpvylvieddkveiedaedlwgldtyettealkeelgd...k 151
                                       sP tg  g+sn+Gg f++elk+aGyd+iv++G+ae+pvy++i+d++vei++a+dlwgl+t+et ++l+e++gd   k
  gi|242399601|ref|YP_002995026.1|  87 SPATGIHGDSNSGGDFAMELKHAGYDFIVVTGRAEEPVYISIQDENVEIKSAKDLWGLTTHETFDRLREKEGDrniK 163
                                       *********************************************************************99999999 PP

                                       EEEE-HHHHTT-TTB-E.EETTEEE-SSSHHHHHHHTTEEEEEEE-- CS
                            AFOR_N 152 vaviGpaGenlvrfAsisvddgraagrgGlGavmgsKnlkaivvrgt 198
                                       +++iGpaGenlv+ A+++ +++raa+r G+GavmgsKnlkai vrgt
  gi|242399601|ref|YP_002995026.1| 164 AVTIGPAGENLVATAAVIETESRAAARAGMGAVMGSKNLKAISVRGT 210
                                       99***************555*************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (639 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); 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: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 4446.42
//
Query:       gi|242399602|ref|YP_002995027.1|  [L=160]
Description: Fe-S cluster-containing protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-16   58.8  27.9      3e-07   30.0   2.5    5.1  5  Fer4      4Fe-4S binding domain
      4e-13   48.8  30.9    2.5e-05   24.1   2.4    4.3  4  Fer4_6    4Fe-4S binding domain
    8.4e-13   48.3  46.4    5.1e-06   26.6  12.4    2.6  3  Fer4_9    4Fe-4S dicluster domain
    1.6e-12   47.8  27.6    9.2e-08   32.6  11.3    3.2  4  Fer4_7    4Fe-4S dicluster domain
    6.6e-12   45.4  13.4    6.6e-12   45.4  13.4    2.3  2  Fer4_11   4Fe-4S dicluster domain
    2.5e-11   43.0  29.4    0.00012   22.0   2.9    4.4  4  Fer4_2    4Fe-4S binding domain
      8e-11   41.9  28.5    2.2e-07   30.9  10.9    3.2  3  Fer4_21   4Fe-4S dicluster domain
    1.3e-09   38.0  29.3    0.00048   20.2  14.0    3.6  4  Fer4_10   4Fe-4S dicluster domain
      3e-09   37.7  25.4      0.093   13.7   5.7    4.4  4  Fer4_16   4Fe-4S double cluster binding domain
    8.5e-05   23.2  36.3      0.021   15.7   3.2    4.3  4  Fer4_3    4Fe-4S binding domain
    0.00041   20.6  32.6     0.0066   16.9   3.5    4.3  4  Fer4_4    4Fe-4S binding domain
     0.0012   19.3  28.4      0.007   16.8   7.4    3.2  2  Fer4_8    4Fe-4S dicluster domain
     0.0019   18.7  30.9        0.1   13.1   2.8    3.7  5  Fer4_17   4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.016   15.9  21.1       0.33   11.7   1.2    4.0  3  Fer4_15   4Fe-4S single cluster domain
       0.12   12.9   2.8       0.12   12.9   2.8    4.2  4  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
       0.75    9.6  27.1       0.11   12.3   1.9    3.8  4  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 !   18.3   1.9   1.3e-06    0.0014       2      18 ..       6      22 ..       5      23 .. 0.93
   2 ?   -0.6   0.2       1.2   1.3e+03       7      12 ..      52      57 ..      50      58 .. 0.75
   3 !   12.2   0.1   0.00011      0.12      13      23 ..      60      70 ..      59      71 .. 0.89
   4 !   30.0   2.5   2.7e-10     3e-07       2      23 ..      80     101 ..      79     102 .. 0.93
   5 !   14.0   0.7     3e-05     0.034       6      24 .]     114     132 ..     114     132 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.3e-06
                                      EEETTTSSS-THHHHHS CS
                              Fer4  2 videekCigCGaCvevC 18
                                      v+ +ekC gC++C  vC
  gi|242399602|ref|YP_002995027.1|  6 VFYPEKCSGCNICSTVC 22
                                      688************** PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.2
                                      TSSS-T CS
                              Fer4  7 kCigCG 12
                                       C+ C 
  gi|242399602|ref|YP_002995027.1| 52 VCVQCE 57
                                      599995 PP

  == domain 3  score: 12.2 bits;  conditional E-value: 0.00011
                                      HHHHHSTTTEE CS
                              Fer4 13 aCvevCPvgAI 23
                                       C+++CP++A+
  gi|242399602|ref|YP_002995027.1| 60 FCIQACPFDAL 70
                                      5*********8 PP

  == domain 4  score: 30.0 bits;  conditional E-value: 2.7e-10
                                       EEETTTSSS-THHHHHSTTTEE CS
                              Fer4   2 videekCigCGaCvevCPvgAI 23 
                                       v+d ekC++C +C+++CP++ I
  gi|242399602|ref|YP_002995027.1|  80 VVDHEKCTRCRLCIKACPYNGI 101
                                       89*****************976 PP

  == domain 5  score: 14.0 bits;  conditional E-value: 3e-05
                                       TTSSS-THHHHHSTTTEEE CS
                              Fer4   6 ekCigCGaCvevCPvgAIt 24 
                                       ++C g  +C++ CP++AI+
  gi|242399602|ref|YP_002995027.1| 114 DLCDGDPQCAKYCPTEAIQ 132
                                       56777779*********95 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.9   1.6e-06    0.0018       6      22 ..       9      25 ..       5      27 .. 0.88
   2 !   12.5   2.3   0.00011      0.12       9      24 .]      53      70 ..      50      70 .. 0.91
   3 !   24.1   2.4   2.3e-08   2.5e-05       3      22 ..      80      99 ..      79     102 .. 0.89
   4 !   10.7   3.3    0.0004      0.45       8      24 .]     112     131 ..     109     131 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.6e-06
                            Fer4_6  6 pdkCigCgdCvrvCPeg 22
                                      p+kC gC+ C +vC ++
  gi|242399602|ref|YP_002995027.1|  9 PEKCSGCNICSTVCSAY 25
                                      89************986 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00011
                            Fer4_6  9 CigCgd..CvrvCPegai 24
                                      C++C++  C+ +CP++a+
  gi|242399602|ref|YP_002995027.1| 53 CVQCEEkfCIQACPFDAL 70
                                      ****888********996 PP

  == domain 3  score: 24.1 bits;  conditional E-value: 2.3e-08
                            Fer4_6  3 eidpdkCigCgdCvrvCPeg 22
                                      ++d +kC+ C+ C+++CP++
  gi|242399602|ref|YP_002995027.1| 80 VVDHEKCTRCRLCIKACPYN 99
                                      69****************95 PP

  == domain 4  score: 10.7 bits;  conditional E-value: 0.0004
                            Fer4_6   8 kCigC.gd..CvrvCPegai 24 
                                        C+ C gd  C++ CP+ ai
  gi|242399602|ref|YP_002995027.1| 112 ICDLCdGDpqCAKYCPTEAI 131
                                       6999*8889********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 !   26.5   7.4   4.6e-09   5.2e-06       1      50 [.      11      69 ..      11      70 .. 0.74
   2 !   26.6  12.4   4.5e-09   5.1e-06       2      49 ..      53      99 ..      52     102 .. 0.88
   3 !   20.1  10.7   4.6e-07   0.00052       1      51 []      85     131 ..      85     131 .. 0.89

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 4.6e-09
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraase.......eaCigCga..CveaCpkga 50
                                      kC gC+ C ++C a +    +  r +    ++e       + C++C++  C++aCp +a
  gi|242399602|ref|YP_002995027.1| 11 KCSGCNICSTVCSAYHLGVVNPDRSRIRVLRKEqenldvvNVCVQCEEkfCIQACPFDA 69
                                      7***********777664444443333333333357****99**************886 PP

  == domain 2  score: 26.6 bits;  conditional E-value: 4.5e-09
                            Fer4_9  2 CtgCga..CveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkg 49
                                      C++C +  C++aCp+++ +    ++   ++++   +C+ C+ C++aCp +
  gi|242399602|ref|YP_002995027.1| 53 CVQCEEkfCIQACPFDALSVNPETGATVVDHE---KCTRCRLCIKACPYN 99
                                      ****8778**********99999999998764...8************85 PP

  == domain 3  score: 20.1 bits;  conditional E-value: 4.6e-07
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCga...CveaCpkgai 51 
                                       kCt+C+ C++aCp++ ++ d   + +++       C  C     C++ Cp++ai
  gi|242399602|ref|YP_002995027.1|  85 KCTRCRLCIKACPYNGIILDPMLNQIKI-------CDLCDGdpqCAKYCPTEAI 131
                                       7*****************9999999887.......777776666*******987 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   3.7   0.00053      0.59      34      49 ..       8      23 ..       4      25 .. 0.79
   2 !   21.4  12.1   2.6e-07   0.00029       1      52 []      11      69 ..      11      69 .. 0.78
   3 !   32.6  11.3   8.2e-11   9.2e-08       2      51 ..      53      99 ..      52     100 .. 0.91
   4 !   12.1   0.4    0.0002      0.22       2      22 ..     113     136 ..     112     155 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00053
                            Fer4_7 34 dpekClgCgaCvavCP 49
                                       pekC+gC+ C +vC 
  gi|242399602|ref|YP_002995027.1|  8 YPEKCSGCNICSTVCS 23
                                      5788999999999994 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 2.6e-07
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeeenek....gtekveid.pekClgCga..CvavCPtga 52
                                      +C gC+ C  +C+++ + + + ++ +    ++e+ ++d  + C++C++  C+++CP++a
  gi|242399602|ref|YP_002995027.1| 11 KCSGCNICSTVCSAYHLGVVNPDRSRirvlRKEQENLDvVNVCVQCEEkfCIQACPFDA 69
                                      7************88888876655544455446667763567**************997 PP

  == domain 3  score: 32.6 bits;  conditional E-value: 8.2e-11
                            Fer4_7  2 CigC..gaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtg 51
                                      C++C  ++C +aCp +a+++++e     t  +++d+ekC+ C+ C+++CP++
  gi|242399602|ref|YP_002995027.1| 53 CVQCeeKFCIQACPFDALSVNPE-----TGATVVDHEKCTRCRLCIKACPYN 99
                                      ****555*************998.....56899*****************86 PP

  == domain 4  score: 12.1 bits;  conditional E-value: 0.0002
                            Fer4_7   2 CigCg...aCvaaCpvkaieldee 22 
                                       C  C    +C+++Cp++ai++  +
  gi|242399602|ref|YP_002995027.1| 113 CDLCDgdpQCAKYCPTEAIQFVHS 136
                                       666755559***********9753 PP

>> Fer4_11  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   1.0     0.095   1.1e+02       4      26 ..       6      28 ..       4      52 .. 0.68
   2 !   45.4  13.4   5.9e-15   6.6e-12       8      98 ..      51     134 ..      44     136 .. 0.94

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.095
                           Fer4_11  4 lflpeqCrhCleppCvasapse..a 26
                                      +f pe+C  C    C +++ ++   
  gi|242399602|ref|YP_002995027.1|  6 VFYPEKCSGCN--ICSTVCSAYhlG 28
                                      799*******6..577777766443 PP

  == domain 2  score: 45.4 bits;  conditional E-value: 5.9e-15
                           Fer4_11   8 eqCrhCleppCvasapseaivkdeetGaVlldektkkeevrevveacPykivrkneetgkvekCdmcldrveaGllp 84 
                                       + C +C+e+ C++++p +a+  ++etGa ++d++++  ++r +++acPy+ +  +   ++++ Cd+c         p
  gi|242399602|ref|YP_002995027.1|  51 NVCVQCEEKFCIQACPFDALSVNPETGATVVDHEKCT-RCRLCIKACPYNGIILDPMLNQIKICDLCDG------DP 120
                                       68**********************************8.*****************************53......69 PP

                           Fer4_11  85 acvescptgalnfg 98 
                                       +c + cpt+a++f 
  gi|242399602|ref|YP_002995027.1| 121 QCAKYCPTEAIQFV 134
                                       9*********9996 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   1.5   4.3e-07   0.00048       4      21 ..       6      23 ..       3      24 .. 0.88
   2 !   13.0   1.6   7.7e-05     0.086       7      21 ..      50      66 ..      47      67 .. 0.85
   3 !   22.0   2.9   1.1e-07   0.00012       4      22 .]      80      98 ..      77      98 .. 0.91
   4 ?    4.7   1.5     0.032        36       9      22 .]     112     128 ..     107     128 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 4.3e-07
                            Fer4_2  4 vvdtdrCigCgaCvsaCP 21
                                      v+ +++C gC++C ++C 
  gi|242399602|ref|YP_002995027.1|  6 VFYPEKCSGCNICSTVCS 23
                                      7889*************6 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 7.7e-05
                            Fer4_2  7 tdrCigCg..aCvsaCP 21
                                       + C++C+   C++aCP
  gi|242399602|ref|YP_002995027.1| 50 VNVCVQCEekFCIQACP 66
                                      578****667******* PP

  == domain 3  score: 22.0 bits;  conditional E-value: 1.1e-07
                            Fer4_2  4 vvdtdrCigCgaCvsaCPa 22
                                      vvd ++C++C+ C++aCP+
  gi|242399602|ref|YP_002995027.1| 80 VVDHEKCTRCRLCIKACPY 98
                                      7899**************5 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.032
                            Fer4_2   9 rCigCg...aCvsaCPa 22 
                                       +C  C     C + CP+
  gi|242399602|ref|YP_002995027.1| 112 ICDLCDgdpQCAKYCPT 128
                                       6999955889******7 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   1.2   5.8e-06    0.0065      36      51 ..       7      22 ..       1      26 [. 0.83
   2 !   30.9  10.9     2e-10   2.2e-07       6      57 ..      51     102 ..      49     106 .. 0.89
   3 ?    5.4   1.8     0.018        20      37      58 ..     112     132 ..     101     133 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.8e-06
                           Fer4_21 36 vvedeCvGCnlCssvC 51
                                         ++C GCn+Cs+vC
  gi|242399602|ref|YP_002995027.1|  7 FYPEKCSGCNICSTVC 22
                                      5579************ PP

  == domain 2  score: 30.9 bits;  conditional E-value: 2e-10
                           Fer4_21   6 dkCigCgk..CliaCedtshqaieidaktvlkvv.edeCvGCnlCssvCPvedci 57 
                                       + C++C++  C++aC+    +a++++++t ++vv +++C+ C lC++ CP ++ i
  gi|242399602|ref|YP_002995027.1|  51 NVCVQCEEkfCIQACP---FDALSVNPETGATVVdHEKCTRCRLCIKACPYNGII 102
                                       57****7555******...8*********99997689*************87766 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.018
                           Fer4_21  37 vedeCvGCnlCssvCPvedcie 58 
                                       + d C G   C++ CP+ ++i+
  gi|242399602|ref|YP_002995027.1| 112 ICDLCDGDPQCAKYCPT-EAIQ 132
                                       468899999*******7.8886 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  10.9     4e-06    0.0044       3      56 .]       6      66 ..       4      66 .. 0.77
   2 !   20.2  14.0   4.3e-07   0.00048       7      56 .]      51      97 ..      46      97 .. 0.91
   3 !   19.0  12.6     1e-06    0.0011       3      56 .]      80     127 ..      78     127 .. 0.68
   4 !    9.0   1.3    0.0013       1.5       8      24 ..     112     139 ..     105     157 .. 0.64

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4e-06
                           Fer4_10  3 vidddtCirCgkCvkaCPadl......tsvgakgeaseeeavrkkvekCtgcg..aCveaCP 56
                                      v+ +++C +C+ C ++C a++      ++++ +  ++e+e  + +v  C +c+   C++aCP
  gi|242399602|ref|YP_002995027.1|  6 VFYPEKCSGCNICSTVCSAYHlgvvnpDRSRIRVLRKEQENLD-VVNVCVQCEekFCIQACP 66
                                      56689************66669**9876666666655555544.5889****7669*****9 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 4.3e-07
                           Fer4_10  7 dtCirCg..kCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      + C++C+   C +aCP+     +a   + e +a  ++ ekCt+c  C++aCP
  gi|242399602|ref|YP_002995027.1| 51 NVCVQCEekFCIQACPF-----DALSVNPETGATVVDHEKCTRCRLCIKACP 97
                                      68*****666*******.....9999999999999999*************9 PP

  == domain 3  score: 19.0 bits;  conditional E-value: 1e-06
                           Fer4_10   3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       v+d ++C+rC+ C kaCP+     +++  +   +++ k ++ C+g  +C++ CP
  gi|242399602|ref|YP_002995027.1|  80 VVDHEKCTRCRLCIKACPY-----NGIILDPMLNQI-KICDLCDGDPQCAKYCP 127
                                       7899***************.....333333333333.3455555555******9 PP

  == domain 4  score: 9.0 bits;  conditional E-value: 0.0013
                           Fer4_10   8 tCirCg...kCvkaCPadl........t 24 
                                        C  C    +C k CP+ +        +
  gi|242399602|ref|YP_002995027.1| 112 ICDLCDgdpQCAKYCPTEAiqfvhslaS 139
                                       566665555********77555444431 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 !   11.3   0.4   0.00044       0.5      53      65 ..      11      23 ..       6      44 .. 0.84
   2 !   13.2   1.1   0.00012      0.13       2      21 ..      53      74 ..      52      84 .. 0.85
   3 !   13.7   5.7   8.3e-05     0.093       1      20 [.      85     104 ..      85     118 .. 0.83
   4 !   10.8   1.9   0.00068      0.76       6      20 ..     120     134 ..     112     158 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00044
                           Fer4_16 53 aitgCdiCqdvCP 65
                                      ++ gC+iC +vC 
  gi|242399602|ref|YP_002995027.1| 11 KCSGCNICSTVCS 23
                                      6788888888885 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00012
                           Fer4_16  2 CgtCgk..CaevCPtnaikekk 21
                                      C++C++  C+++CP +a++ + 
  gi|242399602|ref|YP_002995027.1| 53 CVQCEEkfCIQACPFDALSVNP 74
                                      ****9999*********99774 PP

  == domain 3  score: 13.7 bits;  conditional E-value: 8.3e-05
                           Fer4_16   1 rCgtCgkCaevCPtnaikek 20 
                                       +C++C+ C+++CP n i  +
  gi|242399602|ref|YP_002995027.1|  85 KCTRCRLCIKACPYNGIILD 104
                                       6*************998776 PP

  == domain 4  score: 10.8 bits;  conditional E-value: 0.00068
                           Fer4_16   6 gkCaevCPtnaikek 20 
                                        +Ca+ CPt+ai+  
  gi|242399602|ref|YP_002995027.1| 120 PQCAKYCPTEAIQFV 134
                                       58**********977 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   4.2      0.09     1e+02       1      11 [.      12      22 ..      12      25 .. 0.95
   2 !   11.8   2.9   0.00035      0.39       1      15 []      53      69 ..      53      69 .. 0.88
   3 !   15.7   3.2   1.9e-05     0.021       1      14 [.      86      99 ..      86     100 .. 0.94
   4 !    9.8   2.8    0.0015       1.7       1      15 []     113     130 ..     113     130 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.09
                            Fer4_3  1 CtgCgaCvevC 11
                                      C gC+ C  vC
  gi|242399602|ref|YP_002995027.1| 12 CSGCNICSTVC 22
                                      99********* PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00035
                            Fer4_3  1 CtgCga..CvevCPvgA 15
                                      C++C+   C ++CP +A
  gi|242399602|ref|YP_002995027.1| 53 CVQCEEkfCIQACPFDA 69
                                      9***8557******998 PP

  == domain 3  score: 15.7 bits;  conditional E-value: 1.9e-05
                            Fer4_3  1 CtgCgaCvevCPvg 14
                                      Ct C++C ++CP++
  gi|242399602|ref|YP_002995027.1| 86 CTRCRLCIKACPYN 99
                                      ************97 PP

  == domain 4  score: 9.8 bits;  conditional E-value: 0.0015
                            Fer4_3   1 CtgCg...aCvevCPvgA 15 
                                       C+ C    +C + CP+ A
  gi|242399602|ref|YP_002995027.1| 113 CDLCDgdpQCAKYCPTEA 130
                                       9***66999******876 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   1.7      0.01        12       1      15 [.       9      23 ..       9      31 .. 0.91
   2 !    9.1   1.7    0.0018         2       3      16 ..      52      67 ..      44      69 .. 0.86
   3 !   16.9   3.5   5.9e-06    0.0066       2      17 .]      84      99 ..      83      99 .. 0.93
   4 ?    5.2   3.0     0.032        36       6      16 ..     115     128 ..     111     130 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.01
                            Fer4_4  1 qerCigCgsCvaaCP 15
                                      +e+C gC  C  +C+
  gi|242399602|ref|YP_002995027.1|  9 PEKCSGCNICSTVCS 23
                                      69********99997 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0018
                            Fer4_4  3 rCigCgs..CvaaCPq 16
                                       C++C    C+ aCP+
  gi|242399602|ref|YP_002995027.1| 52 VCVQCEEkfCIQACPF 67
                                      5*****667******7 PP

  == domain 3  score: 16.9 bits;  conditional E-value: 5.9e-06
                            Fer4_4  2 erCigCgsCvaaCPqg 17
                                      e+C++C+ C+ aCP++
  gi|242399602|ref|YP_002995027.1| 84 EKCTRCRLCIKACPYN 99
                                      89************86 PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.032
                            Fer4_4   6 gCg...sCvaaCPq 16 
                                        C+   +C  +CP+
  gi|242399602|ref|YP_002995027.1| 115 LCDgdpQCAKYCPT 128
                                       4444449******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 !   16.8   7.4   6.3e-06     0.007       3      63 ..      10      67 ..       9      69 .. 0.79
   2 ?    3.4   1.8     0.095   1.1e+02      46      64 ..     111     129 ..     102     130 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 6.3e-06
                            Fer4_8  3 ekCieCgaCqsaCpvlrrtkkhlldargeaaed.vqeeqvleeeealwsCttcga..CtevCpv 63
                                      ekC +C  C + C +++     +  +r ++  + +++ +       ++ C++c++  C ++Cp 
  gi|242399602|ref|YP_002995027.1| 10 EKCSGCNICSTVCSAYHLGVVNPDRSRIRVLRKeQENLD------VVNVCVQCEEkfCIQACPF 67
                                      69***********99999876666666666662044444......5********999******6 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.095
                            Fer4_8  46 ealwsCttcgaCtevCpvg 64 
                                       ++ + C +  +C++ Cp++
  gi|242399602|ref|YP_002995027.1| 111 KICDLCDGDPQCAKYCPTE 129
                                       56778888888******85 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7  10.0   0.00026       0.3       1      58 [.      11      67 ..      11      70 .. 0.78
   2 ?    5.8   2.1     0.018        20       2      16 ..      53      69 ..      52      83 .. 0.77
   3 !   13.1   2.8   9.2e-05       0.1       1      15 [.      85      99 ..      70     104 .. 0.77
   4 !   12.8   3.2   0.00012      0.13       1      17 [.      85     101 ..      85     111 .. 0.80
   5 ?    5.7   1.7      0.02        22      41      59 ..     111     129 ..     100     130 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00026
                           Fer4_17  1 rCiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCge..CerkCPq 58
                                      +C++C  C  +C+ y     +p++ + ++     +e+e+ ++++ C++C+e  C ++CP 
  gi|242399602|ref|YP_002995027.1| 11 KCSGCNICSTVCSAYHLGVVNPDRSRIRVLR---KEQENLDVVNVCVQCEEkfCIQACPF 67
                                      6*************99977777766666333...3334459********8777*****96 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.018
                           Fer4_17  2 CiqCgy..ClpeCpsye 16
                                      C qC+   C+++Cp+ +
  gi|242399602|ref|YP_002995027.1| 53 CVQCEEkfCIQACPFDA 69
                                      99**9555******855 PP

  == domain 3  score: 13.1 bits;  conditional E-value: 9.2e-05
                           Fer4_17  1 rCiqCgyClpeCpsy 15
                                      +C++C+ C+++Cp++
  gi|242399602|ref|YP_002995027.1| 85 KCTRCRLCIKACPYN 99
                                      467777777777665 PP

  == domain 4  score: 12.8 bits;  conditional E-value: 0.00012
                           Fer4_17   1 rCiqCgyClpeCpsyea 17 
                                       +C++C+ C+++Cp++ +
  gi|242399602|ref|YP_002995027.1|  85 KCTRCRLCIKACPYNGI 101
                                       69999999999998765 PP

  == domain 5  score: 5.7 bits;  conditional E-value: 0.02
                           Fer4_17  41 ekaslCieCgeCerkCPqg 59 
                                       + ++lC +  +C+++CP +
  gi|242399602|ref|YP_002995027.1| 111 KICDLCDGDPQCAKYCPTE 129
                                       457899999********75 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 ?    4.4   7.0     0.058        65       6      66 .]      10      72 ..       7      72 .. 0.66
   2 ?   11.7   1.2    0.0003      0.33       2      19 ..      80      97 ..      79     101 .. 0.94
   3 ?    7.5   0.3     0.006       6.7       6      20 ..     114     128 ..     113     156 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.058
                           Fer4_15  6 daCigcglCvaeapevfelded.glasvllddgeiaeg.evpddeeeaaqeAaraCPvdAIrv 66
                                      ++C gc+ C ++++ +     + + +++++ ++e++    v+     + ++  +aCP dA++v
  gi|242399602|ref|YP_002995027.1| 10 EKCSGCNICSTVCSAYHLGVVNpDRSRIRVLRKEQENLdVVNVCVQCEEKFCIQACPFDALSV 72
                                      68***********88766555336777776665533333333344444556778999999876 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.0003
                           Fer4_15  2 vvDrdaCigcglCvaeap 19
                                      vvD+++C+ c lC++++p
  gi|242399602|ref|YP_002995027.1| 80 VVDHEKCTRCRLCIKACP 97
                                      79**************98 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.006
                           Fer4_15   6 daCigcglCvaeape 20 
                                       d+C+g+ +C++ +p+
  gi|242399602|ref|YP_002995027.1| 114 DLCDGDPQCAKYCPT 128
                                       789999999999974 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7  11.6       3.9   4.4e+03       4      37 ..      10      45 ..       9      72 .. 0.60
   2 ?    1.3   1.7      0.45   5.1e+02       6      29 ..      53      79 ..      47      81 .. 0.65
   3 ?   12.9   2.8   0.00011      0.12       1      17 [.      81      97 ..      81      99 .. 0.96
   4 ?    3.8   0.3     0.074        83      48      57 ..     123     132 ..     114     133 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3.9
                           Fer4_13  4 dtCiacgaCvelaPdvF..eeddeggasvvaeqpts 37
                                      ++C++c++C  ++        +++ ++ +v ++++ 
  gi|242399602|ref|YP_002995027.1| 10 EKCSGCNICSTVCSAYHlgVVNPDRSRIRVLRKEQE 45
                                      79***********87653346777777777766554 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.45
                           Fer4_13  6 Ciacga..CvelaP.dvFeeddeggas 29
                                      C+ c+   C +++P d    ++e ga 
  gi|242399602|ref|YP_002995027.1| 53 CVQCEEkfCIQACPfDALSVNPETGAT 79
                                      666653338888886666666666665 PP

  == domain 3  score: 12.9 bits;  conditional E-value: 0.00011
                           Fer4_13  1 VDrdtCiacgaCvelaP 17
                                      VD ++C+ c +C +++P
  gi|242399602|ref|YP_002995027.1| 81 VDHEKCTRCRLCIKACP 97
                                      9***************9 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.074
                           Fer4_13  48 adaCPvesIg 57 
                                       a+ CP+e+I+
  gi|242399602|ref|YP_002995027.1| 123 AKYCPTEAIQ 132
                                       5679999986 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 ?   -1.2   1.0       1.5   1.7e+03      27      76 ..      15      23 ..       8      29 .. 0.55
   2 ?   12.3   1.9   9.6e-05      0.11      14      39 ..      43      68 ..      34      73 .. 0.82
   3 ?    6.7   1.6    0.0054         6      16      41 ..      78     101 ..      67     112 .. 0.78
   4 ?    8.8   0.8    0.0012       1.4      21      61 ..     110     149 ..     104     156 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.5
                                      -TT-HHHHCSTT---HHHHHHHHHTT-HHHHHHHHHHH-S-HHHHHHHS- CS
                           Fer4_20 27 CkkapcvkgCPveidipefikkiaegnleeaakiiketnslpavcgrvCp 76
                                      C                                         ++c+ vC+
  gi|242399602|ref|YP_002995027.1| 15 C-----------------------------------------NICSTVCS 23
                                      3.........................................34444444 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 9.6e-05
                                      HHHHHHHHTT----TT-HHHHCSTT- CS
                           Fer4_20 14 eeealeeAsRClqCkkapcvkgCPve 39
                                      e+e l+  + C+qC+++ c+++CP +
  gi|242399602|ref|YP_002995027.1| 43 EQENLDVVNVCVQCEEKFCIQACPFD 68
                                      5566777788**************75 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0054
                                       HHHHHHTT----TT-HHHHCSTT--- CS
                           Fer4_20  16 ealeeAsRClqCkkapcvkgCPveid 41 
                                       +++ + ++C +C  + c+k+CP +  
  gi|242399602|ref|YP_002995027.1|  78 ATVVDHEKCTRC--RLCIKACPYNGI 101
                                       56678899****..89******9755 PP

  == domain 4  score: 8.8 bits;  conditional E-value: 0.0012
                                       HTT----T.T-HHHHCSTT---HHHHHHHHHTT-HHHHHHHH CS
                           Fer4_20  21 AsRClqCk.kapcvkgCPveidipefikkiaegnleeaakii 61 
                                        + C  C  +++c k CP+e    +f++++a++  +e  ++i
  gi|242399602|ref|YP_002995027.1| 110 IKICDLCDgDPQCAKYCPTEA--IQFVHSLASKVAHEQNRTI 149
                                       566999976999******975..5888888887776666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       953  (0.0531541); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); 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):              16  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.53
# Mc/sec: 911.14
//
Query:       gi|242399603|ref|YP_002995028.1|  [L=604]
Description: Aldehyde ferredoxin oxidoreductase (AOR) [Thermococcus sibiricus MM 739]
Scores for complete 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-112  376.9   0.0   1.7e-112  376.2   0.0    1.3  1  AFOR_C    Aldehyde ferredoxin oxidoreductase, domains 2 & 3
    1.2e-65  221.1   0.8    1.7e-65  220.6   0.8    1.2  1  AFOR_N    Aldehyde ferredoxin oxidoreductase, N-terminal doma
  ------ inclusion threshold ------
       0.18   10.2   0.0       0.27    9.6   0.0    1.1  1  DUF3688   Protein of unknown function (DUF3688)


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 !  376.2   0.0  2.8e-116  1.7e-112      16     372 ..     235     600 ..     220     603 .. 0.90

  Alignments for each domain:
  == domain 1  score: 376.2 bits;  conditional E-value: 2.8e-116
                                       HHHHHHHH-GGGHHHHHHHTT---BTTTTBS-..-TTGGGGSHHHHHHHTEEEE.E-TT-SS--EEEEE.......E CS
                            AFOR_C  16 vtaelrkyGTaelvnianetgalptknfqegt..fekaekisgealeekylvknegCfsCpiaCgrevkveegkk.v 89 
                                          +lr+yG+a+ v+++++ g lp++nf +g    ek+ kisg+++ ekyl++  +C+ CpiaC+r v+v++gk+  
  gi|242399603|ref|YP_002995028.1| 235 GGTGLRNYGSAGGVKAYHALGNLPIRNFLWGKwdDEKVAKISGDTMTEKYLKSPFACTLCPIACKRLVEVKNGKYfK 311
                                       2239**************************994445559***************99*******************77 PP

                                       T..EE---HHHHHHHTGGGT---HHHHHHHHHHHHHHTB-HHHHHHHHHHHHHHHHTTSS-HHHHTS----TT-THH CS
                            AFOR_C  90 k..vegpeyetlaalGsnlgiddleailklnelcdelGlDtisaGntiafamelyekGllkkedtdglelefgdaea 164
                                       +  + gpeyet+++lGsnl  ddleai+k+n++cd+lGlDtisaGn+i+f++++ ekG+++k +++gl+le+gdae+
  gi|242399603|ref|YP_002995028.1| 312 EftGLGPEYETVGLLGSNLLLDDLEAIIKANNICDRLGLDTISAGNVIGFLFDAAEKGIVDK-NIEGLNLEWGDAET 387
                                       7**99*******************************************************98.789*********** PP

                                       HHHHHHHHHTT-TTHHHHTT-HHHHHHCTT-GGG--EETTEE--SS-GGG-HHHHHHHHH-TTSS-SGG.G-THHHH CS
                            AFOR_C 165 llellekiAkregigdllAeGvkrlaeklgaeelamhvkGlelpaydprgakgmalaYatsnrGacHlr.ayliale 240
                                       + +llekiA+regigd+lAeGv+++a+klga+ela+++kGle+pa+d r+ ++++l+Yat+nrGa+Hl   ++ +  
  gi|242399603|ref|YP_002995028.1| 388 VHKLLEKIAYREGIGDILAEGVRKAAQKLGAPELAVEIKGLEMPAHDGRAYWSHGLSYATMNRGADHLGwPHMPFKG 464
                                       ********************************************************************854444444 PP

                                       .........S---TT--.HHHHHHHHHHHHHHHHHHHHT--GGGG-HHH......HHHHHHHHHT----HHHHHHHH CS
                            AFOR_C 241 .........ekvdplet.egkaelvkwfqdltalvdslglCkftseaeerldlelyakllsavtGidvteeellkaG 307
                                                   +++   ++  e v+ +q+l+ ++dsl+lCk++      l+++++ kll+ vtG ++t+e+l+++G
  gi|242399603|ref|YP_002995028.1| 465 vsvpelgitAFENRYIDgDELIETVIKMQNLMIIYDSLILCKYAF--SAGLTVTDIIKLLYFVTGKEYTPEKLMEIG 539
                                       9999999985556776668*************************9..56789************************* PP

                                       HHHHHHHHHHHHHHT--HHHS---HHHHHS---SSTTTT---..-HHHHHHHHHHHHT--TTS-- CS
                            AFOR_C 308 eRiynleRlfnlreGltrkddtlperlleeplkegpakgkvledeleemldeyYelrGWdetGvP 372
                                       +Ri+  +R +n+ +Glt kdd+lp+r+   p     +++kv+   +e+ l++yYelrG +++G +
  gi|242399603|ref|YP_002995028.1| 540 NRIWKTQRKINNELGLTSKDDKLPPRMA-LPHA-NRDDTKVP--PVEKWLPRYYELRGINPDGTV 600
                                       ***************************9.3442.23333455..5******************87 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 !  220.6   0.8   2.9e-69   1.7e-65       1     198 []      11     210 ..      11     210 .. 0.97

  Alignments for each domain:
  == domain 1  score: 220.6 bits;  conditional E-value: 2.9e-69
                                       SEEEEEETTTTEEEEEE--HHHHHHH-SCHHHHHHHHHHHS-TTS-TTSTTS-EEEEE-TTTTSSSTTB-EEEEEEE CS
                            AFOR_N   1 gkilrvdLstgkieveelpeelaekylGgrglaakllldevppgvdplspenplvfatGpltgtpapgsgrlvvvak 77 
                                       gkil+vdLs++k e+ e ++e+++ky+Gg g+a++++++e+++   p +++n +vfa+Gplt  ++p+ gr++v+++
  gi|242399603|ref|YP_002995028.1|  11 GKILNVDLSENKLEILEANPEVYDKYMGGAGYAVHVIHKELKKIKSPEDESNIMVFAVGPLTIDGIPNGGRVTVGSI 87 
                                       79*************************************************************************** PP

                                       -TTTSSEEEEEEETCHHHHHHHCT-SEEEEES--SS-EEEEEETTEEEEEE-TTTTTS-HHHHHHHHHHHHTS...E CS
                            AFOR_N  78 sPltgtlgesnaGgrfgaelkraGydaivieGkaekpvylvieddkveiedaedlwgldtyettealkeelgd...k 151
                                       sP tg +ge+++G rf+ e+k+aG+dai+++Gkaekpvyl+++d+++ei+da+++wg+d++et + l+++l+d   k
  gi|242399603|ref|YP_002995028.1|  88 SPETGVWGETHIGTRFAIEMKKAGFDAIIVKGKAEKPVYLYLNDGEAEIRDASKYWGKDIHETINSLRSDLNDptvK 164
                                       *********************************************************************99998888 PP

                                       EEEE-HHHHTT-TTB-E.EETTEEE-SSSHHHHHHHTTEEEEEEE-- CS
                            AFOR_N 152 vaviGpaGenlvrfAsisvddgraagrgGlGavmgsKnlkaivvrgt 198
                                       +++iGpaGe++v++++i  +++   gr+GlGavmgsKnlkaiv++gt
  gi|242399603|ref|YP_002995028.1| 165 ALAIGPAGEKKVKISII-ANEEGFGGRCGLGAVMGSKNLKAIVAKGT 210
                                       88***************.6656668*******************996 PP

>> DUF3688  Protein of unknown function (DUF3688)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   4.5e-05      0.27     392     466 ..     273     353 ..     263     365 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 4.5e-05
                           DUF3688 392 qqfsgqfdlskflqsffasalvpvfqnrslfieng.yidnl.....qydtvlvnffalklqnfnnillienindklq 462
                                        ++sg+    k+l+s fa +l p+  +r + ++ng y  ++     +y+tv +    l l++++ i+ ++ni d+l 
  gi|242399603|ref|YP_002995028.1| 273 AKISGDTMTEKYLKSPFACTLCPIACKRLVEVKNGkYFKEFtglgpEYETVGLLGSNLLLDDLEAIIKANNICDRLG 349
                                       578999999*************************9666665333447****99999********************9 PP

                           DUF3688 463 fdkl 466
                                       +d +
  gi|242399603|ref|YP_002995028.1| 350 LDTI 353
                                       9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (604 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.67u 0.30s 00:00:00.97 Elapsed: 00:00:00.48
# Mc/sec: 3797.51
//
Query:       gi|242399604|ref|YP_002995029.1|  [L=256]
Description: hypothetical protein TSIB_1629 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.4e-27   95.1   0.0    6.1e-27   94.9   0.0    1.0  1  DUF169    Uncharacterised ArCR, COG2043


Domain annotation for each model (and alignments):
>> DUF169  Uncharacterised ArCR, COG2043
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.9   0.0   3.4e-31   6.1e-27       2     204 ..      13     219 ..      12     221 .. 0.90

  Alignments for each domain:
  == domain 1  score: 94.9 bits;  conditional E-value: 3.4e-31
                            DUF169   2 LaealrlktePVavkfsdekpelpekke..kieekkrlCqmvalarakgktvvftaetlg.CpgGaaalGfkelpek 75 
                                       ++  +++k  P+a k+++e++ +pe k+  k+++k +lCq+ +l++ ++kt  ++ ++l+ C+ G ++lGf+elpek
  gi|242399604|ref|YP_002995029.1|  13 IEYRIKPKGAPIAFKMVEEDK-IPEYKNikKMRRKLTLCQVLKLVAIHEKTYRVDSKSLAgCVFGPYILGFEELPEK 88 
                                       6677899***********988.88877765767777******************9999988**************99 PP

                            DUF169  76 lksg..egylkspeaakkfveslprleagevkyvvvapLekaefe...PdvvvffanpeqlmrLvqlalydrgggrl 147
                                       lk     g+  ++e  +k+++++  l++g+++  ++ pL+++++    Pd +++++np q++ L+ ++   + + + 
  gi|242399604|ref|YP_002995029.1|  89 LKAKwlSGKEYTEEGYEKMIQDIVHLPQGKYQEAIFGPLKDFHELkidPDGIILIVNPTQAYLLLGGYYDSEFK-KP 164
                                       999998777779**********9999*************998887788*******************9877767.99 PP

                            DUF169 148 nvsfpgngaaCadivaypykegepniglgdpgarkfaklkddelafgiPyelleemv 204
                                        ++f g  aaC+ iva     + p + +++ gar++a+++dde+ +g+ +e+le+ +
  gi|242399604|ref|YP_002995029.1| 165 YSNFNG-HAACE-IVATLTLGNHPWLNIPCGGARAMAHVQDDEIWLGMDVEELEKAL 219
                                       9*****.8***9.777777777888****************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 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:                        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: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1546.94
//
Query:       gi|242399605|ref|YP_002995030.1|  [L=418]
Description: 2-isopropylmalate synthase 1 [Thermococcus sibiricus MM 739]
Scores for complete 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-49  169.2   0.0    1.8e-49  168.7   0.0    1.2  1  HMGL-like  HMGL-like


Domain annotation for each model (and alignments):
>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.7   0.0   9.8e-54   1.8e-49       2     264 .]      40     297 ..      39     297 .. 0.98

  Alignments for each domain:
  == domain 1  score: 168.7 bits;  conditional E-value: 9.8e-54
                                       -EEEE-TTTHHHHTSSS---HHHHHHHHHHHHHHT-SEE--TSGGGT.THHHHHHHS---TT-B..--EE-SSHHHH CS
                         HMGL-like   2 vkivdttLRDGeqalkaalsveeklaiakaLdeagvdeiEvgfpaaseddfevvraiakavkkarilalvrarekdi 78 
                                       v + d t R+G+q +++a++ +e + iakaLde+g+d iE+ +p++s+dd e+ +++++ + +a++l+ v  +++d 
  gi|242399605|ref|YP_002995030.1|  40 VVLHDATIREGQQMPGVAFKRDEIVMIAKALDELGIDRIEL-IPFLSKDDEEAAKELVDMGLNAKLLSFVSWKKEDT 115
                                       6789************************************7.9********************************** PP

                                       HHHHH....TT-SEEEEEEES-HHHHHHHHSSTHHHHHHHHHHHHHHHHHTT-ETTT-BTTTBS--HHHHHHHHHHH CS
                         HMGL-like  79 kaavealkgagakrvhvfiatselhlkaklkkdreevakkaeeavkaarslgkdvelsledasrtdleflaevveaa 155
                                       + a +       + v +    +  + k+  +   ee++++ ++a  +a+++g  v+  + d  +++l+f+ + v+a+
  gi|242399605|ref|YP_002995030.1| 116 DLALK----LDLEGVVLDFVGNPWQGKVFWNLKPEEIIERGVNAALYAKDHGLYVVAMPWDDFKAPLDFVEQNVKAL 188
                                       *****....99999999999999999*************************************************** PP

                                       HHHT-SEEEEEETTS---HHHHHHHHHHHHHHS-.GGGEEEEEB-TTS-HHHHHHHHHHTT--EEEEBTTS--SSBB CS
                         HMGL-like 156 eeaGatriniaDtvGvltPneaaelisalkervkdkvilsvHcHndlGlAvantlaAveaGadrvdgtvnGlGeraG 232
                                        ea ++ri i Dt G + P ++  ++++lk+  + k++l++H Hnd+GlA+a +l+Av  G++ + +tvnGlGer G
  gi|242399605|ref|YP_002995030.1| 189 TEAHVDRITICDTYGDALPWAMEYVMKRLKKAAD-KTPLELHIHNDFGLATAGALVAVASGVEGLHVTVNGLGERVG 264
                                       *********************************9.****************************************** PP

                                       B-BHHHHHHHHHHTT.-B----HHHHHHHHHHH CS
                         HMGL-like 233 naaleelvaalealg.vdtgldlqklrsiaalv 264
                                        ++lee+++ale l  v+t+++l+kl++i+++v
  gi|242399605|ref|YP_002995030.1| 265 LLSLEEIAVALEFLLgVKTNINLEKLYEISKIV 297
                                       ************8755*************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       678  (0.0378158); expected 358.6 (0.02)
Passed bias filter:                      586  (0.0326845); 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: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 2748.89
//
Query:       gi|242399606|ref|YP_002995031.1|  [L=296]
Description: hypothetical protein TSIB_1631 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 1859.46
//
Query:       gi|242399607|ref|YP_002995032.1|  [L=133]
Description: hypothetical protein TSIB_1632 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.3e-17   61.1   0.4    8.6e-17   60.6   0.4    1.3  1  Cupin_2          Cupin domain
    1.7e-06   28.0   0.0    2.1e-06   27.7   0.0    1.1  1  AraC_binding     AraC-like ligand binding domain
    0.00012   22.3   0.1    0.00015   22.0   0.1    1.2  1  Ectoine_synth    Ectoine synthase
    0.00019   21.1   0.3    0.00025   20.7   0.3    1.1  1  DMSP_lyase       Dimethlysulfonioproprionate lyase
    0.00024   20.7   0.1    0.00039   20.0   0.1    1.3  1  Cupin_3          Protein of unknown function (DUF861)
     0.0011   18.6   0.0     0.0013   18.4   0.0    1.1  1  Cupin_1          Cupin
  ------ inclusion threshold ------
       0.03   14.2   0.0      0.037   13.9   0.0    1.1  1  MannoseP_isomer  Mannose-6-phosphate isomerase
      0.043   13.5   0.1      0.071   12.8   0.1    1.4  1  Auxin_BP         Auxin binding protein


Domain annotation for each model (and alignments):
>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.6   0.4   3.8e-20   8.6e-17       5      71 .]      42     108 ..      29     108 .. 0.95

  Alignments for each domain:
  == domain 1  score: 60.6 bits;  conditional E-value: 3.8e-20
                                       EETTEEEEEECSSSEEEEEEEEESEEEEE.ECTEEEEEETTEEEEE-TT-EEEEEE-SSS-EEEEEEE CS
                           Cupin_2   5 lppGesapshrHpgedeffyVleGegelt.vdgeeveleaGdsvyfpagtpHrfrNtgdeparllvvy 71 
                                       + p+ +++ h+H+   e+ y+ +G+g+ +  dgeeve++++ +vy pag+ H+++Nt+de ++l++vy
  gi|242399607|ref|YP_002995032.1|  42 IYPHSTTGLHTHDVD-EYMYIASGHGVAIsEDGEEVEVHPDMLVYAPAGVKHEMKNTSDETLKLICVY 108
                                       66888999******8.*********88888************************************97 PP

>> AraC_binding  AraC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.0   9.5e-10   2.1e-06      11      93 ..      43     126 ..      37     131 .. 0.90

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 9.5e-10
                                       STT-SEEEETT-SEEEEEEEEE-EEE.EETTEEEEE-TT-EEEE-TTS-EEEEE-TTSEEEEEEEEE---GGGGGGG CS
                      AraC_binding  11 ypdhsfpphvhdeyvihyvteGtgrl.rlngrtydlgpGdlfLlppgepHdyesdsedgweyrwlyfegellerile 86 
                                       yp   ++ h+hd  + +y+++G+g   + +g++++++p+ l+  p g+ H++   s++ +++ ++y+++  +  + e
  gi|242399607|ref|YP_002995032.1|  43 YPHSTTGLHTHDVDEYMYIASGHGVAiSEDGEEVEVHPDMLVYAPAGVKHEMKNTSDETLKLICVYVPALRASGYFE 119
                                       66667799****9999****************************************************999988888 PP

                                       ---EEET CS
                      AraC_binding  87 dssilag 93 
                                       +++  a+
  gi|242399607|ref|YP_002995032.1| 120 EAEKKAK 126
                                       8876655 PP

>> Ectoine_synth  Ectoine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.1   6.6e-08   0.00015      40     114 ..      40     115 ..      21     126 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 6.6e-08
                                       EEE-TT--EEEE-TT-EEEEEEEE--EEEEETTT--EEEE-TTEEEEETTT-EEEEEESS..-EEEEEEEES--XSS CS
                     Ectoine_synth  40 ttikagtetelkYknHleavycieGegeveeledgevyeikpgtlYlldkhdkHllrakk..elrlvcvFnPpltGk 114
                                         i+  ++t l+ ++  e +y+ +G+g     edge+ e++p +l       kH ++ ++   l+l+cv+ P+l  +
  gi|242399607|ref|YP_002995032.1|  40 SLIYPHSTTGLHTHDVDEYMYIASGHGVAI-SEDGEEVEVHPDMLVYAPAGVKHEMKNTSdeTLKLICVYVPALRAS 115
                                       567888888889888899********9655.579*********99888888999999877568**********9865 PP

>> DMSP_lyase  Dimethlysulfonioproprionate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.3   1.1e-07   0.00025      92     159 ..      32      99 ..      27     103 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.1e-07
                        DMSP_lyase  92 rddvalGlvllaPkvrYPdHhhaa.eelYlvlsggaefrqgeaewlsrgiGevifnepgikhamrsaee 159
                                       +++++l ++l+ P+ +   H h   e +Y++  +g+ ++++++e ++++ + +++++ g+kh m+ +++
  gi|242399607|ref|YP_002995032.1|  32 NKELTLLVSLIYPHSTTGLHTHDVdEYMYIASGHGVAISEDGEE-VEVHPDMLVYAPAGVKHEMKNTSD 99 
                                       67888889**************994668999999*999999998.9******************98765 PP

>> Cupin_3  Protein of unknown function (DUF861)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.1   1.7e-07   0.00039      24      63 ..      54      93 ..      46     103 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.7e-07
                                      SSEEEEEEEECEEEEEETTTEEEEEETTEEEEE-TTEEEC CS
                           Cupin_3 24 eedEfcyileGevkvtpeggetvelraGDlvvlpkglsgt 63
                                      + dE++yi +G+     e+ge+ve+ +  lv+ p+g + +
  gi|242399607|ref|YP_002995032.1| 54 DVDEYMYIASGHGVAISEDGEEVEVHPDMLVYAPAGVKHE 93
                                      67**********************************9654 PP

>> Cupin_1  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   5.8e-07    0.0013      38     114 ..      39     108 ..      16     130 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 5.8e-07
                                       EEE..TTEEEEEEEESSS-EEEEEEESEEEEEEEETTSS.EEEEEE.EETTEEEEE-TT-EEEEEEESSSSEEEEEE CS
                           Cupin_1  38 vdl.epgglllPhyhpnateiayvlqGegrvgfvvpgngnrdfhkk.lreGdvfvvPaglvhfqynsgdepavaivv 112
                                       v l +p++   +h+h    e  y+  G g    +++++     + + +++  +++ Pag+ h ++n+ d +++ +++
  gi|242399607|ref|YP_002995032.1|  39 VSLiYPHSTTGLHTH-DVDEYMYIASGHGV---AISED----GEEVeVHPDMLVYAPAGVKHEMKNTSD-ETLKLIC 106
                                       33337**********.************99...55653....44555********************85.5555555 PP

                                       EE CS
                           Cupin_1 113 fd 114
                                       + 
  gi|242399607|ref|YP_002995032.1| 107 VY 108
                                       44 PP

>> MannoseP_isomer  Mannose-6-phosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.6e-05     0.037      81     136 ..      51     108 ..      35     122 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.6e-05
                   MannoseP_isomer  81 hhhraehWvvv.kGt.akvtvddevlllkenestyiplgaihrlenpGkiplelievq 136
                                       h h  + ++ + +G    ++ d e+++++ +  +y p+g+ h ++n    +l+li v 
  gi|242399607|ref|YP_002995032.1|  51 HTHDVDEYMYIaSGHgVAISEDGEEVEVHPDMLVYAPAGVKHEMKNTSDETLKLICVY 108
                                       555555544441444246888999*******************************885 PP

>> Auxin_BP  Auxin binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   3.2e-05     0.071      35     123 ..      26     105 ..       5     117 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.2e-05
                                       -HHHH--SSEEEEEEEE-TT-B--EEEESS-EEEEEEE--EEEEE--SSSSS--S-EEEEE-TTEEEEE-TT--EEE CS
                          Auxin_BP  35 gsvlhgmkevevwlqtlapgsrtpihrhsceevfvvlkgkgtlylasssskypgkpqelpifanstlsipvndahqv 111
                                        s + g ke+ + +  + p s t +h h ++e + +  g+g  +          +  e+++ ++  +  p    h++
  gi|242399607|ref|YP_002995032.1|  26 FSPNVGNKELTLLVSLIYPHSTTGLHTHDVDEYMYIASGHGVAIS--------EDGEEVEVHPDMLVYAPAGVKHEM 94 
                                       5667899**************************999999996542........234566677777788888888888 PP

                                       E---SSS-EEEE CS
                          Auxin_BP 112 kntgehedlqvl 123
                                       knt+  e l+++
  gi|242399607|ref|YP_002995032.1|  95 KNTS-DETLKLI 105
                                       8877.5666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); 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: 0.55u 0.33s 00:00:00.88 Elapsed: 00:00:00.54
# Mc/sec: 745.12
//
Query:       gi|242399608|ref|YP_002995033.1|  [L=309]
Description: Malate dehydrogenase [Thermococcus sibiricus MM 739]
Scores for 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-41  139.2   0.1    1.4e-40  138.6   0.1    1.2  1  Ldh_1_N          lactate/malate dehydrogenase, NAD binding do
    3.7e-24   85.5   0.0    5.6e-24   84.9   0.0    1.3  1  Ldh_1_C          lactate/malate dehydrogenase, alpha/beta C-t
    2.9e-05   23.7   2.1    0.00044   19.8   0.1    2.5  3  Glyco_hydro_4    Family 4 glycosyl hydrolase
  ------ inclusion threshold ------
      0.043   13.2   0.1      0.089   12.1   0.1    1.6  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
      0.057   13.7   0.1       0.58   10.4   0.1    2.3  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
      0.059   12.7   0.0        0.1   11.9   0.0    1.3  1  ThiF             ThiF family
      0.066   13.3   0.0       0.15   12.2   0.0    1.6  1  Glyco_hydro_4C   Family 4 glycosyl hydrolase C-terminal domai
        0.2   12.3   1.4       0.98   10.0   0.4    2.6  3  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent


Domain annotation for each model (and alignments):
>> Ldh_1_N  lactate/malate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.6   0.1   6.3e-44   1.4e-40       1     141 []      15     155 ..      15     155 .. 0.95

  Alignments for each domain:
  == domain 1  score: 138.6 bits;  conditional E-value: 6.3e-44
                                       EEEEEETTTSHHHHHHHHHHHHTTSSSEEEEE-SSHHHHHHHHHHHHHCHCCSTS.-EEEEESSGGGGTTESEEEE- CS
                           Ldh_1_N   1 vkvavvGaaGgiGqslalllankkladelaLlDiakekleGvaldlshistflsv.kvkvsekeeealkdadvvvit 76 
                                       +k+  vGa G +G+++a++ +++  ++e+aL+Di ++ + G+a+dl h+++ l   + +v+++++++l+++d+vv+t
  gi|242399608|ref|YP_002995033.1|  15 MKIGFVGA-GRVGSTIAFTCLQQLDVEEIALVDIMENLAIGEAMDLAHAAAGLGKyPEIVGGSDYSILEGSDIVVVT 90 
                                       6999****.**************88888**********************998651666677*************** PP

                                       -S-SS-TTTTHHHHHHHHHHHHHHHHHHHHHHTTTSEEEE-SSSHHHHHHHHHHHHTS-GGGEEE CS
                           Ldh_1_N  77 agvprkpGetRddLlkvNakIvkeiveaiakvapnaivlvvsNPvdiltevlkkasglpkkrvig 141
                                       ag  rkpG++R+dL  +Na+I+k+++++i++++p+ ++lv++NPvd++t+v++k sg ++++v+g
  gi|242399608|ref|YP_002995033.1|  91 AGSARKPGMSRLDLAMKNAGIIKDVARKIMESSPESKILVITNPVDLMTYVMWKESGKSRNEVFG 155
                                       ***************************************************************98 PP

>> Ldh_1_C  lactate/malate dehydrogenase, alpha/beta C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.9   0.0   2.5e-27   5.6e-24       3     162 ..     160     306 ..     158     308 .. 0.91

  Alignments for each domain:
  == domain 1  score: 84.9 bits;  conditional E-value: 2.5e-27
                                       HHHHHHHHHHHHHHTS-GGGEE--EEBSSSTETTEEHHHHHTTSTTSTHHHHHHHHHHHHHHHHHHHHHHTTSSSS- CS
                           Ldh_1_C   3 LDivRaktflaekagvtprsvkvtViGgHsgvtiipllsqvkellklsekqleeliervqnggdevvkakkGagsat 79 
                                       LD++R+k  l e  gv ++ +k+ ++G+H++   i      +  +  +  +le+   +v++ ++ev+k+k   g+++
  gi|242399608|ref|YP_002995033.1| 160 LDSMRLKRTLHEL-GV-KNINKAWILGEHGDSMFISR----TLIDAENVPELEKVLSEVRFVAAEVIKRK---GATF 227
                                       9999999999764.55.46789*********998888....3334456789999****************...9*** PP

                                       HHHHHHHHHHHHHHHTTHTEEEEEEEEEESCCCECCSSEEEEEEEEEEETTEEEEE-------HHHHHHHHHHHHHH CS
                           Ldh_1_C  80 lsmAvAgakfveallrdtkeilsagvyldgevglkdqeieyfsvPvvlgknGvekvleilklndfeeekleksvkeL 156
                                       ++ A A++++++a+l++tke+++a+v+l+ge g++d   + ++vP+++gknGvek++e  +l+++ +e+l++svk L
  gi|242399608|ref|YP_002995033.1| 228 YGPAIAAYRMINAVLNNTKEEMPASVILKGEFGFSD---VSVGVPAIIGKNGVEKIVE-YPLDPQDMENLRNSVKLL 300
                                       ************************************...89*****************.****************** PP

                                       HHHHHH CS
                           Ldh_1_C 157 kkeiek 162
                                       k+ +++
  gi|242399608|ref|YP_002995033.1| 301 KERLKE 306
                                       *98875 PP

>> Glyco_hydro_4  Family 4 glycosyl hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1     0.024        54       1      42 [.      16      50 ..      16     103 .. 0.65
   2 !   19.8   0.1     2e-07   0.00044     117     162 ..     105     150 ..      97     166 .. 0.88
   3 ?   -3.7   0.0       3.2   7.2e+03      62      80 ..     200     218 ..     196     221 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.024
                                      EEEEETTTSSSHHHHHHHHHHTTTTCTEEEEEEE-SSHHHHH CS
                     Glyco_hydro_4  1 kiviiGgGStifaklllgdlkkteelsvselaLvDideerld 42
                                      ki+++G+G      + +++ +  ++l+v+e+aLvDi e   +
  gi|242399608|ref|YP_002995033.1| 16 KIGFVGAGRVG---STIAFTC-LQQLDVEEIALVDIME---N 50
                                      68888887543...2333333.5689*********988...3 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 2e-07
                                       HHHHHHHHHHHHHHHHHH-TTSEEEE-SSSHHHHHHHHHHHSTTSE CS
                     Glyco_hydro_4 117 glrtipvlleIakdieelcPdawvlnytNPaavvteallrlvpnik 162
                                       ++++ +++ ++a++i e +P++ +l  tNP+  +t ++ + +++++
  gi|242399608|ref|YP_002995033.1| 105 AMKNAGIIKDVARKIMESSPESKILVITNPVDLMTYVMWKESGKSR 150
                                       6788899********************************9988765 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 3.2
                                       EEESSHHHHHTT-SEEEE- CS
                     Glyco_hydro_4  62 eattdrkealkdadfVita 80 
                                       e + +++++l+++ fV ++
  gi|242399608|ref|YP_002995033.1| 200 ENVPELEKVLSEVRFVAAE 218
                                       5667789999999999775 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 ?   12.1   0.1     4e-05     0.089      31      68 ..       9      48 ..       4      91 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4e-05
                                      BS-GTTSEEEEES-SHHHHHHHHH.HHHTT-.EEEEESSS CS
                      2-Hacid_dh_C 31 gkelsgktvGiiGlGrIGqavakr.lkafgm.kviaydrs 68
                                      ++e++++++G +G+Gr+G+++a + l+++++ ++  +d  
  gi|242399608|ref|YP_002995033.1|  9 QSEVAKMKIGFVGAGRVGSTIAFTcLQQLDVeEIALVDIM 48
                                      57999****************9751558888555555655 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 ?   10.4   0.1   0.00026      0.58       1      33 [.      17      48 ..      17      64 .. 0.88
   2 ?    0.4   0.0      0.34   7.5e+02      54      73 ..     197     215 ..     179     222 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00026
                                      EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESS CS
                   Sacchrp_dh_NADP  1 vliiGaGsvGqavaellarhfdvdaeitvadrs 33
                                      + ++GaG+vG+ +a  ++++ dv+ ei+++d  
  gi|242399608|ref|YP_002995033.1| 17 IGFVGAGRVGSTIAFTCLQQLDVE-EIALVDIM 48
                                      5689*******************6.99998865 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.34
                                       --TTTHHHHHHHHHTTSSEE CS
                   Sacchrp_dh_NADP  54 ldaenyeavLaallkegdlv 73 
                                       +daen+++ L+++l+e  +v
  gi|242399608|ref|YP_002995033.1| 197 IDAENVPE-LEKVLSEVRFV 215
                                       799*****.*****999887 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   4.6e-05       0.1      11      49 ..       7      46 ..       1      48 [. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.6e-05
                                      HHHHHHHTSEEEEE--SHHHHHHHHHHHH.HTTTEEEEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                              ThiF 11 dgqekLrdskvllvGaGglGsellknLal.sGvgkltlvD 49
                                      + q +++++k+  vGaG +Gs ++ +    + v+++ lvD
  gi|242399608|ref|YP_002995033.1|  7 KEQSEVAKMKIGFVGAGRVGSTIAFTCLQqLDVEEIALVD 46
                                      78999*****************998866559******999 PP

>> Glyco_hydro_4C  Family 4 glycosyl hydrolase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   6.5e-05      0.15     104     180 ..     216     298 ..     162     304 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.5e-05
                                       HHHSSCHTS-S.......HHHHHHHHHHTS-EEEEEEEE-TTSSTTS-TTSEEEEEEEEETTEEEEB--CS-.HHHH CS
                    Glyco_hydro_4C 104 klelekrsgey.......avdiieaivtdkprrlvvnvpNnglIpnLpddavVEvpclvdkngirpvavgel.peql 172
                                       + e+ kr+g+        a ++i+a+++++++++   v  +g      +d+ V vp++++kng++ +   +l p+ +
  gi|242399608|ref|YP_002995033.1| 216 AAEVIKRKGATfygpaiaAYRMINAVLNNTKEEMPASVILKGEFGF--SDVSVGVPAIIGKNGVEKIVEYPLdPQDM 290
                                       33355666666789999899*********************98765..89*****************9999977777 PP

                                       HHCHHHHH CS
                    Glyco_hydro_4C 173 aallrtni 180
                                       + l ++++
  gi|242399608|ref|YP_002995033.1| 291 ENLRNSVK 298
                                       77766655 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 ?   10.0   0.4   0.00044      0.98       1      67 [.      16      89 ..      16      94 .. 0.60
   2 ?   -1.0   0.0       1.2   2.7e+03      74      92 ..     112     130 ..     104     134 .. 0.79
   3 ?   -2.5   0.0       3.6   8.1e+03      41      50 ..     167     176 ..     145     211 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00044
                                      EEEEETTSHHHHHHHHHHHHTTS-GGCEEEE...EESSCCCHHHHHHHHC.....-EEECECHHHHHHH-SEEEE CS
                     F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivva...nsrnpekaeelaeelg.....vkvtavdneeaaeeadvvvl 67
                                      kig++GaG++g+++a  +l++  + +ei ++    +    +a  la ++      +++ +++    +e +d+vv+
  gi|242399608|ref|YP_002995033.1| 16 KIGFVGAGRVGSTIAFTCLQQL-DVEEIALVdimENLAIGEAMDLAHAAAglgkyPEIVGGSDYSILEGSDIVVV 89
                                      7**************9988874.5555554300022222222222222224556667777777777777777776 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.2
                                       HHHHHHHCGHHHHTTSEEE CS
                     F420_oxidored  74 veevlselakdalkgklvi 92 
                                       +++v++++++++ + k+++
  gi|242399608|ref|YP_002995033.1| 112 IKDVARKIMESSPESKILV 130
                                       6889999999988888887 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 3.6
                                       HHHHHHC-EE CS
                     F420_oxidored  41 elaeelgvkv 50 
                                        +  elgvk 
  gi|242399608|ref|YP_002995033.1| 167 RTLHELGVKN 176
                                       3333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.64u 0.37s 00:00:01.01 Elapsed: 00:00:00.56
# Mc/sec: 1646.96
//
Query:       gi|242399609|ref|YP_002995034.1|  [L=476]
Description: hypothetical protein TSIB_1634 [Thermococcus sibiricus MM 739]
Scores for complete 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-95  320.9   0.0    7.5e-90  301.8   0.0    2.0  2  UPF0261        Uncharacterised protein family (UPF0261)
  ------ inclusion threshold ------
      0.036   13.3   0.0      0.056   12.7   0.0    1.2  1  Acyl_transf_2  Acyl transferase


Domain annotation for each model (and alignments):
>> UPF0261  Uncharacterised protein family (UPF0261)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  301.8   0.0   8.4e-94   7.5e-90       2     351 ..       5     358 ..       4     361 .. 0.94
   2 !   17.3   0.0     2e-07    0.0018     349     402 ..     378     433 ..     375     435 .. 0.90

  Alignments for each domain:
  == domain 1  score: 301.8 bits;  conditional E-value: 8.4e-94
                           UPF0261   2 tvlligtlDTKleellflrelieeegvevlliDvgtree..ekeaidisreevleaagkeaeeelesldrgeaieam 76 
                                       tv+++gt+DTK+ e+++l+e+ie  g + +liD++ r+   +  ++d++++ v+++ g+++e e+++++r+ea e+m
  gi|242399609|ref|YP_002995034.1|   5 TVCIMGTFDTKGIEAKYLKEKIELYGGTPFLIDISLRKYnpTIITPDVPNHIVAQEGGSTIE-EVSKKNRKEAQEIM 80 
                                       89*********************************998854555889******999999855.588*********** PP

                           UPF0261  77 seaaaklvkely.eekidgvislGGsggtslataamralpiGlPKlivSTvAsgdvspyvgesDitlmysvvDiaG. 151
                                       +++a k++++l  e+k+ g+i++GGs g+ +at+++++lp+ +PK+++ST+   +vsp++  sDi +  s+ D+aG 
  gi|242399609|ref|YP_002995034.1|  81 IKGAVKILSNLLtEKKLGGIIAFGGSVGSGMATRILKTLPLFVPKYLISTLPQ-EVSPIIVGSDIKVWWSISDMAGg 156
                                       ************8888***********************************98.9*********************8 PP

                           UPF0261 152 ..lNsilrkvLsnAaaaiaGmakaeekskeekeeeeekplvaitmfGvttpavdairelLeeegyevlvFhAtG.tG 225
                                         +Nsi  +vL++ aaai+G  ka+        +  +kp++ +t fG+ttp     +e +e++g+ev+ FhA G +G
  gi|242399609|ref|YP_002995034.1| 157 nkINSIEATVLNQIAAAIMGELKAKPV------DIPKKPIIVATQFGTTTPHLLMSKEIIENKGFEVISFHAVGlSG 227
                                       88889999****************995......6789*************************************779 PP

                           UPF0261 226 GramErLir.eglldavlDltttEladelvggvlsagpd...RleaaaekgiPqvvsvGalDmvnfgaletvpekfk 298
                                       G +mE+ ir e+ + +v Dltt+E++de++gg+l a ++   Rl+aa+e+++P+++ +G+lD v fg+ et+p+k++
  gi|242399609|ref|YP_002995034.1| 228 GYTMEEFIRsEERVVGVYDLTTHEIVDEIAGGILIASHEgrlRLRAAIERKLPYIILPGGLDQVVFGPPETIPKKYR 304
                                       9*******835689*******************8776666669********************************** PP

                           UPF0261 299 grklyehnp.qvtlvrtsaeenrelgefiaeklnkakgpvrvllPkkGvsalda 351
                                       +r +yeh +  vtl+r ++ee+ + g++iae++n+a++pv +++P +G+sa+d+
  gi|242399609|ref|YP_002995034.1| 305 KRFFYEHSKgMVTLMRSNEEEMYRSGKLIAERINDAESPVIIIIPIHGFSAYDK 358
                                       *******98359***************************************997 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 2e-07
                           UPF0261 349 ldaeggpfedpeadealfealeeelkese..ievvevdahindeeFaeavaealle 402
                                       l++++ p++dp+ad +l++ ++++++ ++  ++++ vdahind+e  + v++ l++
  gi|242399609|ref|YP_002995034.1| 378 LEMTDIPWWDPSADMMLWKGIQDHVDLTNpnVTIIPVDAHINDPELVHFVIQILIK 433
                                       5677889*****************9988888***************9999988776 PP

>> Acyl_transf_2  Acyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   6.2e-06     0.056      28     128 ..     185     283 ..     169     291 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.2e-06
                                       --S-EEEEE-TT-GGGGGGHHHHHHHHTTT--EEEE---B-------.------HHHHHHHHHHHHHHHHHTT---E CS
                     Acyl_transf_2  28 krnntiviasgfarrmdhfaglaeylsengfhvirydslnhvglssg.eidefsmsvgkkslltvidwlkekkinni 103
                                         ++ i++a+ f     h+    e + ++gf+vi   s++ vgls g +++ef  s   + ++ v+d   ++ +++i
  gi|242399609|ref|YP_002995034.1| 185 IPKKPIIVATQFGTTTPHLLMSKEIIENKGFEVI---SFHAVGLSGGyTMEEFIRS--EERVVGVYDLTTHEIVDEI 256
                                       557789***************************9...6799****99567888776..5678999999888888998 PP

                                       ..EEEEETTHHHHHHHHTTTS--SEEE CS
                     Acyl_transf_2 104 ..gliasslsariayevvaeielsfli 128
                                         g++ +s   r+    + e +l ++i
  gi|242399609|ref|YP_002995034.1| 257 agGILIASHEGRLRLRAAIERKLPYII 283
                                       777888998888888777777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (476 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); 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: 0.71u 0.36s 00:00:01.06 Elapsed: 00:00:00.57
# Mc/sec: 2525.25
//
Query:       gi|242399610|ref|YP_002995035.1|  [L=607]
Description: PEP-utilising enzyme, mobile region [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-22   79.4   0.1      2e-22   78.7   0.1    1.4  1  PEP-utilizers   PEP-utilising enzyme, mobile domain
  ------ inclusion threshold ------
      0.041   13.8   0.0      0.077   12.9   0.0    1.5  1  SspB            Stringent starvation protein B
      0.061   13.5   1.7       0.37   11.0   0.7    2.6  2  CAF1A           Chromatin assembly factor 1 subunit A


Domain annotation for each model (and alignments):
>> PEP-utilizers  PEP-utilising enzyme, mobile domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.7   0.1   3.3e-26     2e-22       1      73 []     527     599 ..     527     599 .. 0.98

  Alignments for each domain:
  == domain 1  score: 78.7 bits;  conditional E-value: 3.3e-26
                                       G--S-EEEEES---HHHHTTS-GEEEEEES--TTHHHHHHHHHHTT--EEE--SSHH.HH--TEEEEEETTTT CS
                     PEP-utilizers   1 kleegvILvaeetspsdiagldkaaGivterGGmtSHaAivArelgiPaVvgvgeatielkegdlitvDgstG 73 
                                       k+eeg+ILv++ tsp++i  ++k++G++t+ GG  SH Aiv+re+giP++vg++ at+ lk+g  + +Dg +G
  gi|242399610|ref|YP_002995035.1| 527 KVEEGDILVCDITSPAWISVYPKVKGVITNSGGLSSHPAIVSREFGIPCIVGTRIATKMLKDGMKVRLDGVKG 599
                                       5799******************************************************************998 PP

>> SspB  Stringent starvation protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.3e-05     0.077       8      54 ..     360     407 ..     353     424 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.3e-05
                                       HHHHHHHHHHHCCCTT.-ET..EEEEEETTSTT-BS-HHHHGGGSBTT CS
                              SspB   8 Ravvrwvldevaeene.lpehhFyitvdtdapgVkvperLreeypeem 54 
                                       ++vv++ ++++ +    +p+hhFyi  +t+a    v ++L +++++e+
  gi|242399610|ref|YP_002995035.1| 360 KEVVKEQMERAIKMAPlTPNHHFYIDQQTNAAAKYVLRELGRKFVKEG 407
                                       5667777777777777688******************9*******997 PP

>> CAF1A  Chromatin assembly factor 1 subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.7   6.2e-05      0.37      34      68 ..     326     361 ..     311     369 .. 0.66
   2 ?   -0.4   0.0      0.22   1.3e+03      12      21 ..     456     465 ..     452     487 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6.2e-05
                             CAF1A  34 ekeldYdyDSdaEWeeeeeeeg.edleseedeeeee 68 
                                        +++dYd+  d+EW   +++e+ e+l +   e+++e
  gi|242399610|ref|YP_002995035.1| 326 YLSMDYDFYADKEWIATDQQEAiEKLMEMIPEDKKE 361
                                       5679**********9876544447776544433333 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.22
                             CAF1A  12 pYyGTwtkks 21 
                                       pY+GT+t+ s
  gi|242399610|ref|YP_002995035.1| 456 PYVGTITEWS 465
                                       8*****9744 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (607 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1011  (0.0563891); expected 358.6 (0.02)
Passed bias filter:                      608  (0.0339115); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.78u 0.33s 00:00:01.11 Elapsed: 00:00:00.53
# Mc/sec: 3450.82
//
Query:       gi|242399611|ref|YP_002995036.1|  [L=140]
Description: DNA-binding protein [Thermococcus sibiricus MM 739]
Scores for complete 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   80.3   0.0    1.5e-22   79.9   0.0    1.1  1  DUF296    Plants and Prokaryotes Conserved (PCC) domain


Domain annotation for each model (and alignments):
>> DUF296  Plants and Prokaryotes Conserved (PCC) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.9   0.0   8.6e-27   1.5e-22       3      94 ..      10     108 ..       8     118 .. 0.90

  Alignments for each domain:
  == domain 1  score: 79.9 bits;  conditional E-value: 8.6e-27
                                       EEEEE-TTSBHHHHHHHHHHHHT-SSEEEEEEEEEEEEEE.EEECTTT....EE-S-EEEEEEEEEEEETT..EEEE CS
                            DUF296   3 hvlrlepGediveaieefarkrgiraacvlsaiGavsnvt.rladgee....kllgrfeilslsGtilpdg..lHlh 72 
                                       +v++le++ed+ve+++++a++++i+a++++s+iG++++ + ++++g+     kl+g +e++s++G + ++   +H+h
  gi|242399611|ref|YP_002995036.1|  10 IVVKLEKNEDLVEKLTQLAQEENIKAGMIVSGIGMLRDPEiGYYTGTGyeqkKLEGVYELVSITGYLQETTprVHIH 86 
                                       79***************************************99999999998889**********99986689**** PP

                                       EEEEETTSEEEEEEEEEE.EEE CS
                            DUF296  73 vslagedgqvvgGhlaegplva 94 
                                       +s+a+++ +v+gGhl++g++  
  gi|242399611|ref|YP_002995036.1|  87 ISIADKNNKVYGGHLLSGKCDP 108
                                       ******************7763 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); 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: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 805.59
//
Query:       gi|242399612|ref|YP_002995037.1|  [L=102]
Description: hypothetical protein TSIB_1637 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score 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   14.7   0.1      0.018   14.5   0.1    1.2  1  Aldolase  KDPG and KHG aldolase


Domain annotation for each model (and alignments):
>> Aldolase  KDPG and KHG aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1     1e-06     0.018      11      58 ..      31      80 ..      21      87 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1e-06
                                      EEEE--SSGGGHHHHHHHHHHTT--EEEEE..TTSTTHHHHHHHHHHH-T CS
                          Aldolase 11 vpvivikdkedalplaeaLvagGlrvlevt..lrteaaldairvlrkerp 58
                                      + v+ +kd e+a+++a+ Lv++G+ ++e+   +  ++ +++++++  ++p
  gi|242399612|ref|YP_002995037.1| 31 LHVVGVKDYEEACKIAKELVNDGIGAIELCggFGHKGVAKIVEAVEGKVP 80
                                      46999***********************9533666777777776665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 576.96
//
Query:       gi|242399613|ref|YP_002995038.1|  [L=327]
Description: Pyruvate dehydrogenase, beta subunit [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-53  181.4   0.0    1.7e-53  180.9   0.0    1.2  1  Transket_pyr     Transketolase, pyrimidine binding domain
    1.9e-41  140.8   0.2    5.1e-41  139.4   0.1    1.8  2  Transketolase_C  Transketolase, C-terminal domain
     0.0089   16.3   0.1      0.022   15.0   0.1    1.7  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
  ------ inclusion threshold ------
       0.09   13.1   0.0         14    6.1   0.0    2.4  2  Ribosomal_S22    30S ribosomal protein subunit S22 family
       0.12   12.3   0.0       0.22   11.5   0.0    1.4  1  Rpp20            Rpp20 subunit of nuclear RNase MRP and P


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 !  180.9   0.0   4.8e-57   1.7e-53       2     176 ..       6     182 ..       5     184 .. 0.98

  Alignments for each domain:
  == domain 1  score: 180.9 bits;  conditional E-value: 4.8e-57
                                       EEEHHHHHHHHHHHHHCTTTTEEEEESSTH..HHHTTCHCCHHEGGTTEGEEE--S-HHHHHHHHHHHHHHCTTEEE CS
                      Transket_pyr   2 kiawrkaeaealaellkedpevvligaDva..ggtfsvrkgllhdqgegrvidsgisEqavlgfavGaalagpllvi 76 
                                       +i++++a++eal+ ++ +dp+vv++g+Dv+  gg f+v+kgll++ ge+rv d++i+E++++g+ vGaa++g l+++
  gi|242399613|ref|YP_002995038.1|   6 EITFAQALNEALDYEMSKDPKVVVMGEDVGqyGGIFGVTKGLLEKYGEERVKDTPIAESGFIGTGVGAAASGLLRPV 82 
                                       6899********************************************************************999** PP

                                       EEEEEHHHHGGG..HHGGHHHHHCHHHHHT--EEEEESBSGGGSTTGTTTSBSSHHHHHHTSTTEEEE--SSHHHHH CS
                      Transket_pyr  77 veaqFgdFangA..qiyadqairsgeakgklkvgvvtrlpigvgedGpehqsaeleaflrlipglkvvrPsdpaetk 151
                                       ve++F dF+ +A  qiy+++a+++++++gk+k+++v+r+  g+g ++++++s++l a++ ++pglkvv+Ps+p+++k
  gi|242399613|ref|YP_002995038.1|  83 VELMFIDFLGVAydQIYNQAAKIRYMFGGKAKIPIVIRTVSGAGASAAAQHSQSLHALFVHVPGLKVVYPSTPYDAK 159
                                       ***************************************************************************** PP

                                       HHHHHHHHSSS.SEEEEEE-SSEEC CS
                      Transket_pyr 152 hllrrairredrkPvvlrlpksllr 176
                                       +ll   i+  d++Pvv++++k+l+ 
  gi|242399613|ref|YP_002995038.1| 160 GLLISSIE--DDDPVVFIEHKMLYG 182
                                       ********..899**********96 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       2.1   7.6e+03      57      75 ..      21      39 ..       7      51 .. 0.62
   2 !  139.4   0.1   1.4e-44   5.1e-41       1     124 []     197     319 ..     197     319 .. 0.99

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.1
                                      HHHHHSEEEEEEEEESTTS CS
                   Transketolase_C 57 svkktgrlvvveeavkrgG 75
                                      + k  + +v+ e+  + gG
  gi|242399613|ref|YP_002995038.1| 21 MSKDPKVVVMGEDVGQYGG 39
                                      4445555555555555555 PP

  == domain 2  score: 139.4 bits;  conditional E-value: 1.4e-44
                                       TEEEEEETTSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEESTTSHH CS
                   Transketolase_C   1 gkaeilregkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeavkrgGig 77 
                                       g+a+i++egkdvt+va+  mv++ale+ae+Le+egis+eV+d+r++ plD+etil+s+kktgrlv+v+ea++r++++
  gi|242399613|ref|YP_002995038.1| 197 GEADIKKEGKDVTVVATALMVYRALEVAEKLEEEGISVEVIDPRSLVPLDEETILNSIKKTGRLVIVDEAYPRCSFA 273
                                       899************************************************************************** PP

                                       HHHHHHHHHCCCTTCSSEEEEEEE-SSSSSSGHHHHHHHTT-SHHHH CS
                   Transketolase_C  78 sevaaalaeeafdgldapvkrvggpdviepgsaeelekafgldaeki 124
                                       +++aa+   +afd+l+apvk v++p +++p+s ++lek++ +++eki
  gi|242399613|ref|YP_002995038.1| 274 TDIAALAVSKAFDSLKAPVKLVTAPSTPVPFS-PALEKEWVPSTEKI 319
                                       ********************************.99*********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 !   15.0   0.1   6.2e-06     0.022       2      76 ..     207     278 ..     206     295 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 6.2e-06
                                       SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHHHHHH CS
                           PFOR_II   2 evvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlveevka 76 
                                       +v +va++ ++  a +++++l eegi+v ++ +r+l P  ee + + +kk+ ++v +d ++    +   +++++a
  gi|242399613|ref|YP_002995038.1| 207 DVTVVATALMVYRALEVAEKLEEEGISVEVIDPRSLVPLDEETILNSIKKTGRLVIVDEAY---PRCSFATDIAA 278
                                       7899999999************************************************999...34666666665 PP

>> Ribosomal_S22  30S ribosomal protein subunit S22 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.014        52      13      28 ..      17      32 ..      15      35 .. 0.90
   2 ?    6.1   0.0    0.0039        14      28      41 ..     246     259 ..     243     260 .. 0.96

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.014
                     Ribosomal_S22 13 LdyKlSrQkKvVlEGD 28
                                      Ldy +S+  KvV+ G+
  gi|242399613|ref|YP_002995038.1| 17 LDYEMSKDPKVVVMGE 32
                                      9***********9986 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0039
                     Ribosomal_S22  28 DkesvvNhinaTGR 41 
                                       D+e+++N i+ TGR
  gi|242399613|ref|YP_002995038.1| 246 DEETILNSIKKTGR 259
                                       9************9 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 ?   11.5   0.0   6.2e-05      0.22      54      93 ..     198     236 ..     191     248 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.2e-05
                             Rpp20  54 kkeeelkkeeVfvkatGrAiekalsvgrwfqekeeykvrv 93 
                                       + + +++ ++V+v at   + +al+v+++++e+ ++ v+v
  gi|242399613|ref|YP_002995038.1| 198 EADIKKEGKDVTVVATALMVYRALEVAEKLEEE-GISVEV 236
                                       67788999**********************988.444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 1963.35
//
Query:       gi|242399614|ref|YP_002995039.1|  [L=332]
Description: Pyruvate dehydrogenase [Thermococcus sibiricus MM 739]
Scores for 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-97  324.8   0.0    4.7e-97  324.6   0.0    1.0  1  E1_dh            Dehydrogenase E1 component
    7.8e-07   29.0   6.2    2.1e-06   27.6   2.8    2.5  2  TPP_enzyme_C     Thiamine pyrophosphate enzyme, C-terminal TP
     0.0045   16.0   0.0     0.0073   15.3   0.0    1.3  1  Transketolase_N  Transketolase, thiamine diphosphate binding 
  ------ inclusion threshold ------
      0.028   14.5   0.2      0.049   13.7   0.2    1.3  1  DUF1451          Zinc-ribbon containing domain
      0.028   13.6   0.0      0.069   12.3   0.0    1.6  1  DXP_synthase_N   1-deoxy-D-xylulose-5-phosphate synthase


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 !  324.6   0.0  1.3e-100   4.7e-97       2     300 .]      15     313 ..      14     313 .. 0.98

  Alignments for each domain:
  == domain 1  score: 324.6 bits;  conditional E-value: 1.3e-100
                                       HHHHHHHHHHHHHHHHHTTSS-S-----TT-HHHHHHHHHTS-TTSEEEESS--HHHHHHTT--HHHHHHHHTT-T. CS
                             E1_dh   2 klvllrrvedaldalykrkkrigfyhlsagqealkvgiaaalekeDliiteYReagvllarglsleeilaeltgkv. 77 
                                       ++v +r+ e++++ l+ + k+ gf+hl++g+ea+++g+ a+l keD+i +++R++g+++a+g ++++ +ael gk+ 
  gi|242399614|ref|YP_002995039.1|  15 TMVKIREHEERVAELFAQGKIPGFVHLYIGEEAVATGVMAHLRKEDFITSTHRGHGHFIAKGGNIKASMAELFGKAt 91 
                                       6899999********************************************************************** PP

                                       ...TTSSGTT-.-E..BTT..BEEE-SSTTTHHHHHHHHHHHHHHHTS---EEEEEEGGGTT-HHHHHHHHHHHHTT CS
                             E1_dh  78 ...kgkggsrhelmyaekesrilggngivgaqvplvaGialaakiegkkevailliGDgAanqGdvyealnlaalwk 151
                                          kgkggs+h +++   +   lg+ngivg   p++ G+al  k +g ++va++++GDgA+nq +++ea+nlaa+wk
  gi|242399614|ref|YP_002995039.1|  92 gicKGKGGSMH-IADLDVG--ELGANGIVGGGIPHAVGAALGIKLNGLDNVAVAFFGDGASNQQNFHEAINLAAIWK 165
                                       ***********.8877666..8******************************************************* PP

                                       --EEEEEEEESEETTEEHHHH-S---GGG..TTTTS-EEEEETTSHHHHHHHHHHHHHHHHTTT--EEEEEEE--SS CS
                             E1_dh 152 lpvifvveNNkygisTeaekasaskeladrargvgipglrVdgnDplavyeAvkfAaeraregkgpllielvtYRyg 228
                                       lpv+fv+eNN y is +++k++a k++a+ra+++gipg+ Vdg+D++avye++k+A+erar+g+gp++ie++tYRy 
  gi|242399614|ref|YP_002995039.1| 166 LPVVFVCENNLYQISLPYSKQQAIKSVAERAVAYGIPGVSVDGQDVFAVYEVAKEAIERARNGEGPTIIEAKTYRYR 242
                                       ***************************************************************************** PP

                                       -SSTTSHSHSSSHHHHHHHHHHHH-HHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHHHHHHHHHHS----GG CS
                             E1_dh 229 gHsesDdpstyrtreeveevrkkkdpiqrlkelLvkkgvvseeelkeiekevrkeveeavkkaeskkelepe 300
                                       gH+e D p++yr++ee+e ++++kdpi+++++ + +kg++++eel++++++v+ke+eea+k ae+++ ++pe
  gi|242399614|ref|YP_002995039.1| 243 GHFEGD-PQIYRSKEEIEWWKNNKDPITIFEKTVLEKGLLTKEELDAVREKVKKEIEEAIKFAEESPWPKPE 313
                                       ******.9***********************************************************99885 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 !   27.6   2.8   5.9e-10   2.1e-06      27     152 ..     114     235 ..     107     236 .. 0.69
   2 ?   -3.1   0.1       1.7     6e+03     128     142 ..     292     304 ..     279     308 .. 0.60

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 5.9e-10
                                       TS-TTTHHHHHHHHHH...HST.TSEEEEEEEHHHHHHT.GGGHHHHHHT.T-SEEEEEEE-SBCCCHHHHHHHHTC CS
                      TPP_enzyme_C  27 lgtmGyglpaAiGakl...akp.drevvaivGDGgflmi.lqelatavrr.nlpitvvvlnNegygmtggqqepfgg 97 
                                        g  G g+p A+Ga+l   ++  d+  va+ GDG+     ++e ++ +   +lp+++v+ nN +       + p+ +
  gi|242399614|ref|YP_002995039.1| 114 NGIVGGGIPHAVGAALgikLNGlDNVAVAFFGDGASNQQnFHEAINLAAIwKLPVVFVCENNLYQI-----SLPYSK 185
                                       57788888888888886653445889********96555477777766653779988888886652.....223222 PP

                                       CTTTTSBB.BS----HHHHHHHTTSEEEEESSH.HHHHHHHHHHHH....CSSSEEEEE CS
                      TPP_enzyme_C  98 krksgpagkdlkpvdfaklaealGakgarvekadveeleealkeal....ekkgpalie 152
                                                 +  +++a+ a a+G++g++v+ +dv  + e+ kea+    + +gp++ie
  gi|242399614|ref|YP_002995039.1| 186 -Q--------QAIKSVAERAVAYGIPGVSVDGQDVFAVYEVAKEAIerarNGEGPTIIE 235
                                       .2........233479999*******998888877776555555544444*******98 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.7
                                       SSH.HHHHHHHHHHH CS
                      TPP_enzyme_C 128 ekadveeleealkea 142
                                       +++  +e+eea+k a
  gi|242399614|ref|YP_002995039.1| 292 KVK--KEIEEAIKFA 304
                                       333..6666666655 PP

>> Transketolase_N  Transketolase, thiamine diphosphate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0     2e-06    0.0073     143     243 ..     136     238 ..     109     247 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2e-06
                                       ----EEEEEEHHHHHSHHHHHHHHHHHHTT-TTEEEEEEES..SEETTEEGGGT--S-HHHHHHHTT-EEEEETTTT CS
                   Transketolase_N 143 vdhytyvilgDgclmeGvsseasslagtlkLgkLivlyDdn..kisidGeteisftedvakrfeaygWhvievedge 217
                                       +d+   ++ gDg  +    +ea++la+  kL  +  + ++n  +is+  + +++  ++va+r  ayg   ++v dg+
  gi|242399614|ref|YP_002995039.1| 136 LDNVAVAFFGDGASNQQNFHEAINLAAIWKLPVV-FVCENNlyQISLPYS-KQQAIKSVAERAVAYGIPGVSV-DGQ 209
                                       6888999************************854.444555336777655.5556689*********988875.556 PP

                                       -HHHH....HHHHHHHHH-TTS-EEEEEE- CS
                   Transketolase_N 218 dveai....kaaieeakaekdkPsliklrt 243
                                       dv a+    k+aie+a++  + P++i+ +t
  gi|242399614|ref|YP_002995039.1| 210 DVFAVyevaKEAIERARNG-EGPTIIEAKT 238
                                       6544422236899999998.89*****999 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2   1.4e-05     0.049      11      57 ..     261     307 ..     253     317 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.4e-05
                           DUF1451  11 eeeleelvekakeklseaeeltkeelelvaeylkrDleeaarslees 57 
                                       +++ ++ ++  ++ + e++ ltkeel+ v+e +k+++eea ++ ees
  gi|242399614|ref|YP_002995039.1| 261 WKNNKDPITIFEKTVLEKGLLTKEELDAVREKVKKEIEEAIKFAEES 307
                                       55556678889999***************************999886 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 ?   12.3   0.0   1.9e-05     0.069     116     179 ..     120     183 ..     113     271 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.9e-05
                    DXP_synthase_N 116 sisaalGlavardlkgekkkvvaviGDgaltgGmafealnnigelkkkllvilNdNemsisknv 179
                                        i  a+G a   +l+g ++ +va  GDga      +ea+n ++  k  ++ +  +N   is + 
  gi|242399614|ref|YP_002995039.1| 120 GIPHAVGAALGIKLNGLDNVAVAFFGDGASNQQNFHEAINLAAIWKLPVVFVCENNLYQISLPY 183
                                       577899************************************************9999888654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       910  (0.0507558); expected 358.6 (0.02)
Passed bias filter:                      742  (0.0413855); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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 0.34s 00:00:00.94 Elapsed: 00:00:00.48
# Mc/sec: 2084.27
//
Query:       gi|242399615|ref|YP_002995040.1|  [L=86]
Description: branched-chain alpha-keto acid dehydrogenase subunit E2 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-18   65.3   7.1    3.6e-18   65.2   7.1    1.0  1  Biotin_lipoyl    Biotin-requiring enzyme
    1.2e-06   28.4   3.9    2.1e-06   27.6   1.8    1.9  2  GCV_H            Glycine cleavage H-protein
    1.9e-06   27.6   0.6     0.0055   16.5   0.2    2.1  2  Biotin_lipoyl_2  Biotin-lipoyl like
     0.0017   18.3   0.8      0.022   14.7   0.1    2.0  2  RnfC_N           RnfC Barrel sandwich hybrid domain
     0.0054   17.4   1.6       0.26   12.0   0.2    2.1  2  HlyD_3           HlyD family secretion protein
  ------ inclusion threshold ------
      0.015   15.0   2.4       0.32   10.7   0.2    2.3  2  PYNP_C           Pyrimidine nucleoside phosphorylase C-termin
      0.027   14.5   0.6       0.27   11.3   0.1    2.0  2  QRPTase_N        Quinolinate phosphoribosyl transferase, N-te
       0.08   13.3   0.1      0.093   13.1   0.1    1.1  1  DUF3634          Protein of unknown function (DUF3634)


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 !   65.2   7.1   1.6e-21   3.6e-18       3      73 .]      10      81 ..       8      81 .. 0.97

  Alignments for each domain:
  == domain 1  score: 65.2 bits;  conditional E-value: 1.6e-21
                                      EEESSSEEEEEE..ECSESSSTTCEE-TTSEEEEEECTTEEEEEEBSSSEEEEEESSTTTEEE-TTCEEEEE CS
                     Biotin_lipoyl  3 iksPmiGesveeg.vvevlvkvGdkVkagqvlaeveamKmemeieapkaGvvkeilvkeGdtvevgdllaki 73
                                      + +P++G ++++g +ve+++k G+ V++++v+a+ve+ K++ e++ap +G+++eil+++Gd+v vg+++ +i
  gi|242399615|ref|YP_002995040.1| 10 VIMPKLGMTMKKGtIVEWKKKRGERVEKEEVVAIVESEKLTGEVKAPTSGILVEILHDVGDEVPVGEVIGVI 81
                                      779******************************************************************887 PP

>> GCV_H  Glycine cleavage H-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   1.8   9.4e-10   2.1e-06      33      80 ..      24      70 ..       9      72 .. 0.85
   2 ?    3.5   0.1     0.029        65      38      56 ..      65      83 ..      64      86 .] 0.91

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 9.4e-10
                                      EEEEE---TT-EE-TT-EEEEEEESS-EEEEE-SSSEEEEEE-GGGTT CS
                             GCV_H 33 vvfvelpevgtkvkkgeslaavEsvKaasevyapvsGevvevNeklee 80
                                      +v  + ++ g++v+k+e +a+vEs K ++ev ap sG +ve+ +++ +
  gi|242399615|ref|YP_002995040.1| 24 IVEWK-KKRGERVEKEEVVAIVESEKLTGEVKAPTSGILVEILHDVGD 70
                                      44443.678********************************9888876 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.029
                                      ---TT-EE-TT-EEEEEEE CS
                             GCV_H 38 lpevgtkvkkgeslaavEs 56
                                      l +vg++v  ge ++++Es
  gi|242399615|ref|YP_002995040.1| 65 LHDVGDEVPVGEVIGVIES 83
                                      6799**************9 PP

>> Biotin_lipoyl_2  Biotin-lipoyl like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0   0.00018      0.41      10      39 ..      21      50 ..      11      54 .. 0.88
   2 !   16.5   0.2   2.5e-06    0.0055       5      37 ..      53      85 ..      50      86 .] 0.94

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00018
                   Biotin_lipoyl_2 10 sGrVaqlnVkdGqrVkaGdvLaelDsralq 39
                                       G+++++  k G rV++  v a+ +s++l 
  gi|242399615|ref|YP_002995040.1| 21 KGTIVEWKKKRGERVEKEEVVAIVESEKLT 50
                                      59***********************99986 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 2.5e-06
                   Biotin_lipoyl_2  5 IaapvsGrVaqlnVkdGqrVkaGdvLaelDsra 37
                                      ++ap+sG +++++   G++V  G v+ +++s++
  gi|242399615|ref|YP_002995040.1| 53 VKAPTSGILVEILHDVGDEVPVGEVIGVIESEE 85
                                      89****************************986 PP

>> RnfC_N  RnfC Barrel sandwich hybrid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1     1e-05     0.022      39      80 ..      22      64 ..       9      68 .. 0.80
   2 ?    3.9   0.1     0.023        51      44      60 ..      64      80 ..      62      85 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1e-05
                            RnfC_N 39 GapakplvkvgdkVlkGqkiaeaeg.fvsapvhasvsGtVkai 80
                                      G+  +   k g++V+k +++a  e+  ++ +v a++sG  ++i
  gi|242399615|ref|YP_002995040.1| 22 GTIVEWKKKRGERVEKEEVVAIVESeKLTGEVKAPTSGILVEI 64
                                      6666677799*********997765566***********9998 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.023
                            RnfC_N 44 plvkvgdkVlkGqkiae 60
                                      +l +vgd+V  G++i+ 
  gi|242399615|ref|YP_002995040.1| 64 ILHDVGDEVPVGEVIGV 80
                                      67789**********95 PP

>> HlyD_3  HlyD family secretion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.8   0.1    0.0096        21       7      34 ..      21      47 ..      18      54 .. 0.76
   2 !   12.0   0.2   0.00012      0.26       2      32 ..      53      83 ..      52      86 .] 0.91

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0096
                            HlyD_3  7 dGvvvelnveegevvqagdelleiippd 34
                                       G++ve++ + ge v++ ++++ +   +
  gi|242399615|ref|YP_002995040.1| 21 KGTIVEWKKKRGERVEKEEVVAIVE-SE 47
                                      69***************77776554.44 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00012
                            HlyD_3  2 lrApvdGvvvelnveegevvqagdelleiip 32
                                      ++Ap +G++ve+ + +g+ v+ g+++  i  
  gi|242399615|ref|YP_002995040.1| 53 VKAPTSGILVEILHDVGDEVPVGEVIGVIES 83
                                      89************************99965 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 ?   10.7   0.2   0.00014      0.32      34      53 ..      25      44 ..       6      57 .. 0.84
   2 ?    4.9   0.2    0.0091        20      35      53 ..      63      81 ..      48      86 .] 0.82

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00014
                                      EEES--TT-EEBTTSEEEEE CS
                            PYNP_C 34 ielhkklGdkVkkGeplati 53
                                      +e +kk G++V+k+e++a +
  gi|242399615|ref|YP_002995040.1| 25 VEWKKKRGERVEKEEVVAIV 44
                                      7889*************987 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0091
                                      EES--TT-EEBTTSEEEEE CS
                            PYNP_C 35 elhkklGdkVkkGeplati 53
                                      e+   +Gd+V  Ge++ +i
  gi|242399615|ref|YP_002995040.1| 63 EILHDVGDEVPVGEVIGVI 81
                                      56778**********9877 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 ?   11.3   0.1   0.00012      0.27      44      68 ..      21      45 ..       8      49 .. 0.84
   2 ?    1.9   0.0       0.1   2.3e+02      45      68 ..      59      82 ..      47      85 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00012
                                      TTTEEEESS-TT-EEETTEEEEEEE CS
                         QRPTase_N 44 pglevellvkDGervekgdvlleie 68
                                      +g+ ve+++k Gervek++v++ +e
  gi|242399615|ref|YP_002995040.1| 21 KGTIVEWKKKRGERVEKEEVVAIVE 45
                                      67889*****************987 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.1
                                      TTEEEESS-TT-EEETTEEEEEEE CS
                         QRPTase_N 45 glevellvkDGervekgdvlleie 68
                                      g+ ve+l + G++v  g+v+  ie
  gi|242399615|ref|YP_002995040.1| 59 GILVEILHDVGDEVPVGEVIGVIE 82
                                      7889999999*********99887 PP

>> DUF3634  Protein of unknown function (DUF3634)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   4.2e-05     0.093      19      79 ..       7      71 ..       1      73 [. 0.78

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.2e-05
                           DUF3634 19 r.....evlevkfkdgklasvkGkiPekfk.kdlrdiakaeklsgevrvekerggvrlhvskdvpkk 79
                                      r     + l + +k g++ + k k  e+ + +++ +i ++ekl+gev++    +g+ + + +dv+++
  gi|242399615|ref|YP_002995040.1|  7 RinvimPKLGMTMKKGTIVEWKKKRGERVEkEEVVAIVESEKLTGEVKAPT--SGILVEILHDVGDE 71
                                      4444446688999****9999999999996257***************988..77778888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.34s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 489.28
//
Query:       gi|242399616|ref|YP_002995041.1|  [L=272]
Description: Dihydrolipoyllysine-residue acetyltransferase component of pyruvatedehydrogenase complex (E2) [Thermococcus sibiricus MM 739]
Scores for complete 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-79  266.2   0.3    2.6e-79  266.0   0.3    1.1  1  2-oxoacid_dh  2-oxoacid dehydrogenases acyltransferase (catal
    2.9e-06   27.5   0.0    7.2e-06   26.2   0.0    1.7  1  E3_binding    e3 binding domain
    5.1e-05   23.3   0.0     0.0001   22.3   0.0    1.5  1  CAT           Chloramphenicol acetyltransferase
  ------ inclusion threshold ------
      0.016   13.2   0.1       0.02   12.9   0.1    1.0  1  TssR          Type VI secretion system, TssR


Domain annotation for each model (and alignments):
>> 2-oxoacid_dh  2-oxoacid dehydrogenases acyltransferase (catalytic domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  266.0   0.3   5.7e-83   2.6e-79       5     232 ..      48     269 ..      44     270 .. 0.97

  Alignments for each domain:
  == domain 1  score: 266.0 bits;  conditional E-value: 5.7e-83
                                       XXXXXXXXXXXXXXXXXXXX.XXXEEEEEEEEE-HHHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHHH-GGGG CS
                      2-oxoacid_dh   5 ervplsgirkaiakrlteskqeiphftlsdevdvtallelrkelkekeakeekakltlldflikavalAlkefPeln 81 
                                       e+ ++ girk+ia+rl++s +e+ h+tl +e ++++l+++rk+l ek+      k++++ +++k++a+A++ef e+n
  gi|242399616|ref|YP_002995041.1|  48 EERKVFGIRKVIADRLSKSYREAVHVTLNMETEIDNLIQMRKKLTEKLG----EKPSYTVLMLKCIAKAIREFIEIN 120
                                       5668889***************************************996....39********************** PP

                                       -EE.EESEEEE--SS--EEEE--------EEEE--GGG--HHHHHHHHHHHHHHHTTT---GGGTSS-SEEEE---- CS
                      2-oxoacid_dh  82 asvdeeekeivvkkhvniGvAvatprGLlvPviknadkkslleiakelkelaekaregklkpedleggtftisNlGm 158
                                       a++++e+  iv++++vni vAv++p GL++Pvi+n+dkk+l e+ k++++++e+a++g+lk++d+ ggtfti+NlGm
  gi|242399616|ref|YP_002995041.1| 121 ATMEKEK--IVIYDNVNINVAVDSPIGLITPVIRNVDKKNLKELLKDYADIVERAKKGSLKEKDFVGGTFTITNLGM 195
                                       ***9999..******************************************************************** PP

                                       -----------TT-SEEEEE---.B--TTSTT-HT---EEEEEEEEETTT--HHHHHHHHHHHHHTT-HHXXXX CS
                      2-oxoacid_dh 159 lGvtsftPiinppqvaIlgvgrikerpvvkegelvvrkvmtlslsaDHRvidGaeaarFlntlkkllenpeell 232
                                       +Gv+sftPiinppq aIlg++ri+++pv+k+ge +v++vm lsl++DHR+idGa aarFl+++k +le+pe+++
  gi|242399616|ref|YP_002995041.1| 196 FGVDSFTPIINPPQIAILGLNRITQKPVIKNGETKVASVMVLSLTFDHRAIDGAPAARFLERVKYYLEHPEKVF 269
                                       **********************************************************************9976 PP

>> E3_binding  e3 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   1.6e-09   7.2e-06       8      36 .]       7      35 ..       6      35 .. 0.95

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 1.6e-09
                                      HHHHHHCT--TTTS---CTTTBE-HHHHC CS
                        E3_binding  8 RklAkelGidLsdvkGtGpgGRItkeDVl 36
                                      R++A+++ i+Ls++kG+G +G +t eD +
  gi|242399616|ref|YP_002995041.1|  7 RMIAEQYDINLSKIKGSGVNGEVTLEDLE 35
                                      99*************************86 PP

>> CAT  Chloramphenicol acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   2.3e-08    0.0001      16     202 ..      65     258 ..      56     259 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 2.3e-08
                               CAT  16 ehylkvvkctysltveld.italkkeikkk..klkvypa.liyllarvvnkhkefrmalkdeelvvWdsvnPaytvf 88 
                                       + y++ v++t ++ +e+d + +++k++++k  ++ +y + ++  +a+++ ++ e   ++++e++v++d+vn   +v 
  gi|242399616|ref|YP_002995041.1|  65 KSYREAVHVTLNMETEIDnLIQMRKKLTEKlgEKPSYTVlMLKCIAKAIREFIEINATMEKEKIVIYDNVNINVAVD 141
                                       5799*************8667888888877323446776145689*******************************9 PP

                               CAT  89 nketetfssiwteydedfaeflktyaediaeysektklfPksdllentlnvsslPWvsftsfnlnvaneedyllPif 165
                                        +      +i    +++++e+lk+ya+ +++ ++    + ++d++  t++++ l     +sf+  ++  +  +l + 
  gi|242399616|ref|YP_002995041.1| 142 SPIGLITPVIRNVDKKNLKELLKDYADIVERAKK-G-SLKEKDFVGGTFTITNLGMFGVDSFTPIINPPQIAILGLN 216
                                       99999999999999***********988876544.4.455667*******************998888777776665 PP

                               CAT 166 tigk...ykkeedkv..llPvaiqvhhavcdGfhaarllnel 202
                                        i++    k+ e kv  ++ +++   h + dG  aar+l+ +
  gi|242399616|ref|YP_002995041.1| 217 RITQkpvIKNGETKVasVMVLSLTFDHRAIDGAPAARFLERV 258
                                       5543222344566774468999999***********999876 PP

>> TssR  Type VI secretion system, TssR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   4.4e-06      0.02     575     693 ..      33     206 ..      22     230 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.4e-06
                              TssR 575 qekekvpaesakkllqekypllveaylpkdvkealedleyglLLseeEleqlrefleelagkevdkk.......... 641
                                         ++++ +  + k+ +e + + +++ +   +++++++  ++ L  e+E+++l+++ ++l++k  +k           
  gi|242399616|ref|YP_002995041.1|  33 DLEKYIREHFFPKVREERKVFGIRKVIADRLSKSYREAVHVTLNMETEIDNLIQMRKKLTEKLGEKPsytvlmlkci 109
                                       55677888888999999999999999999******99999*********************9999889********* PP

                              TssR 642 .............................................tkkerkkliknyvkelkklnllklskkkikkl 673
                                                                                     kk++k+l+k+y ++++  ++ +l+ k+    
  gi|242399616|ref|YP_002995041.1| 110 akairefieinatmekekiviydnvninvavdspiglitpvirnvDKKNLKELLKDYADIVERAKKGSLKEKDFVGG 186
                                       **************************************************************999888888887777 PP

                              TssR 674 slsealelitglpsssellk 693
                                       +   +    +g++s++++++
  gi|242399616|ref|YP_002995041.1| 187 TFTITNLGMFGVDSFTPIIN 206
                                       77777777777777666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       839  (0.0467957); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); 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: 0.63u 0.36s 00:00:00.99 Elapsed: 00:00:00.54
# Mc/sec: 1503.24
//
Query:       gi|242399617|ref|YP_002995042.1|  [L=110]
Description: hypothetical protein TSIB_1642 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      1e-32  112.6   0.2    1.1e-32  112.4   0.2    1.0  1  Lin0512_fam  Conserved hypothetical protein (Lin0512_fam)


Domain annotation for each model (and alignments):
>> Lin0512_fam  Conserved hypothetical protein (Lin0512_fam)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.4   0.2   6.3e-37   1.1e-32       8     114 .]       1     106 [.       1     106 [. 0.96

  Alignments for each domain:
  == domain 1  score: 112.4 bits;  conditional E-value: 6.3e-37
                       Lin0512_fam   8 mGvdlhgqdvtkAAvrAvkdAisrnslpglaeilglpkedldemkvevklavpkpekvdleavkavlPy.gevevev 83 
                                       mGvd+hgqd+tkAA++AvkdAi+r + +gl e+++l+ e  ++mkvev ++vp p+kvd+e+vk+++P+  ++ ++v
  gi|242399617|ref|YP_002995042.1|   1 MGVDQHGQDPTKAAIKAVKDAITRICAVGLLELFELEFE--KDMKVEVIIGVPYPQKVDVEKVKEAIPLpCKKVIKV 75 
                                       8*********************************99966..9***************************667799** PP

                       Lin0512_fam  84 veGGldvsgialeelgdkndeivianaavtv 114
                                       veGGl+  gial+e+gdk++ei+ia+a +t+
  gi|242399617|ref|YP_002995042.1|  76 VEGGLKGPGIALKEFGDKTNEILIAIAFITI 106
                                       ***************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); 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 0.36s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 624.53
//
Query:       gi|242399618|ref|YP_002995043.1|  [L=329]
Description: ATP-NAD/AcoX kinase [Thermococcus sibiricus MM 739]
Scores for complete 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   0.2    4.4e-12   45.8   0.1    2.1  2  NAD_kinase  ATP-NAD kinase
    3.5e-06   26.6   0.5    2.2e-05   24.1   0.3    2.1  2  DAGK_cat    Diacylglycerol kinase catalytic domain


Domain annotation for each model (and alignments):
>> NAD_kinase  ATP-NAD kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   0.1   4.9e-16   4.4e-12       1     149 [.       8     174 ..       8     210 .. 0.71
   2 !    2.1   0.0      0.01        89     246     280 ..     273     304 ..     253     313 .. 0.71

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 4.9e-16
                                       .EEEEESSC................GGTCSHHHHHHHHHHHCT-..EEEEECCGGCCSSSTT--HHHHTTTT--... CS
                        NAD_kinase   1 kvgivvnpi................kkeaieraeevarwLldalsrvlevtveeklgeslaeaaefrsevisvlkkv 61 
                                       +vgi++np                 + e ++++++++ ++++    v++v+   ++ +++ +a+    e + ++   
  gi|242399618|ref|YP_002995043.1|   8 TVGIIANPEsgrdirrliahasvfdNMEKVNIVKRLLLIMQEL--GVEKVLAMPETFGIVPAALHAIGEHVVME--- 79 
                                       5899999998888888888777776555566666666655555..56666655555555555433322222222... PP

                                       ................EEECCC-TTTTTSSSEEEEEE-HHHHHHHHHHHHHCT-EEEEEESSS--SS-SE.EGGGHH CS
                        NAD_kinase  62 kttd............dtrkaleafadagvdliivvGGDGTaldvarllqkaeiPvlgvnaGvkgfltef.epeaaa 125
                                                       dt+ka+e + +++v +iiv+GGDGT + va++    +iP++ +++G+++  + + e   a+
  gi|242399618|ref|YP_002995043.1|  80 ---VemlpikvfgdwrDTLKATELM-KDKVNVIIVIGGDGTNRVVAKASG--DIPIMPISTGTNNVFPYMiEATIAG 150
                                       ...1233344668676777777666.99**********************..8***************997777778 PP

                                       HHHHHHHHT-SEEEEEEEEEEEEE CS
                        NAD_kinase 126 ellekllegeirvekrevldavim 149
                                        + +++ +g +++e+ +  +  i 
  gi|242399618|ref|YP_002995043.1| 151 ATVSAIATGMVKPEEGTYKTKRIE 174
                                       888888889999998876555554 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.01
                                       TT-EEEEEE-SS--EEEEETTTEEEEE-TT-EEEE CS
                        NAD_kinase 246 sssklrirvasrseallaldGseelelspgdevrv 280
                                        ++++++   ++s  llaldG++e+e++ + + ++
  gi|242399618|ref|YP_002995043.1| 273 LNEEVEL---KTSPSLLALDGERETEMKGRITAKI 304
                                       3344443...49*************9986655555 PP

>> DAGK_cat  Diacylglycerol kinase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0     0.057   5.1e+02       3      20 ..      10      26 ..       8      46 .. 0.72
   2 !   24.1   0.3   2.5e-09   2.2e-05      48     102 ..      97     146 ..      64     166 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.057
                                      EEEE-TTCTTTTHHHHHH CS
                          DAGK_cat  3 lvivNpksGkgkgekllr 20
                                       +i Np+sG +++++l+ 
  gi|242399618|ref|YP_002995043.1| 10 GIIANPESG-RDIRRLIA 26
                                      689*****9.55555554 PP

  == domain 2  score: 24.1 bits;  conditional E-value: 2.5e-09
                                       HHHHHHCC-SEEEEEESHHHHHHHHHHHCTHHCTTSEEEEEE-SS--HHHHHCT- CS
                          DAGK_cat  48 akeakeegvdlivvaGGDGtvsevlnglleelatkpplgiiPlGtgNdlaralgi 102
                                       a+e+ +++v++i+v+GGDGt + v+++  +     +p+  i +Gt N + + ++ 
  gi|242399618|ref|YP_002995043.1|  97 ATELMKDKVNVIIVIGGDGTNRVVAKASGD-----IPIMPISTGTNNVFPYMIEA 146
                                       566777899***********8777776666.....**************998844 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); 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: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 1961.12
//
Query:       gi|242399619|ref|YP_002995044.1|  [L=261]
Description: Biotin/lipoate A/B protein ligase [Thermococcus sibiricus MM 739]
Scores for complete 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-10   38.9   0.0    1.5e-09   37.9   0.0    1.5  1  BPL_LplA_LipB  Biotin/lipoate A/B protein ligase family
  ------ inclusion threshold ------
      0.037   13.9   0.3       0.24   11.2   0.1    1.9  2  Peptidase_M10  Matrixin


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 !   37.9   0.0   1.6e-13   1.5e-09       2     131 .]      48     160 ..      47     160 .. 0.89

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 1.6e-13
                                       EEEES-HHHHHH..GCGGG--TT-EEEEEEESS-B-B--B-TTSEEEEEEEEESS...-CCGTHHHHHHHHHHHHHH CS
                     BPL_LplA_LipB   2 gevikstntllkeslnsselesgglvvvrrqtgGrnvwhspkgeltyslllspeqktfqnrvlelyvsllvlavlea 78 
                                       g+++k +     e++n+++ ++ +  ++rr tgG  v+h+ +g+++ysl+++ +   ++ ++l  + +   l +l++
  gi|242399619|ref|YP_002995044.1|  48 GRFVKVE-----EDINLENANKFRFPIIRRFTGGGTVYHD-EGCVNYSLIIKRDV-RYPLDYLYAHLLKGTLLALKK 117
                                       6777775.....9***************************.***********775.888899999999999999999 PP

                                       H......HHTT-TTEEEETTTEEEETTEEEEEEEEEEEETTS-EEEEEEEEEE CS
                     BPL_LplA_LipB  79 lgyrdskpgiegipvfikwpnDlyvngrKlaGiavtstrgktlhhivigvgvn 131
                                       l          g   + k  nD++vn rK++G a   + ++   h++i+v+ +
  gi|242399619|ref|YP_002995044.1| 118 L----------GLRPYLKNTNDIVVNERKVSGTAAGLRWEVLFLHGSILVDSD 160
                                       9..........444455569****************************99865 PP

>> Peptidase_M10  Matrixin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0     0.062   5.6e+02      21      56 ..      26      61 ..      16      78 .. 0.83
   2 ?   11.2   0.1   2.7e-05      0.24       6      70 ..     178     245 ..     172     250 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.062
                                      HHHHHHHHHHHHHHHTTSSSEEEEESSSCESEEEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M10 21 eevrkairrAfkvwsevtplkFtevkkgeadikieF 56
                                       +  +ai++ ++ w+++ +l   +  k e di++e 
  gi|242399619|ref|YP_002995044.1| 26 VRGVDAISDTLRIWKNKNSLILGRFVKVEEDINLEN 61
                                      5556899999*******9999999999999998875 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 2.7e-05
                                       EEEEEESSSXTTSXHHHHHHHHHHHHHHHHTTS..SSEEEEESSSCESE.EEEEESSSSSSSSSXBSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx RF
                     Peptidase_M10   6 nltyrilnetpdleeeevrkairrAfkvwsevt..plkFtevkkgeadi.kieFgrgehgdgypfdgk 70 
                                        ++yr+ n t+ +++ ++++ ++     +s+v   pl+F+e  ++e+ i +i ++++  +d+++f+g+
  gi|242399619|ref|YP_002995044.1| 178 PVKYRVANLTSFIKNVSMDHIVEALIWGYSRVFsaPLTFEEPAEEESKItEILYKEKYSKDEWNFEGS 245
                                       689******999999998888888888888887558******988888846***************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.36s 00:00:00.95 Elapsed: 00:00:00.54
# Mc/sec: 1442.70
//
Query:       gi|242399620|ref|YP_002995045.1|  [L=78]
Description: 2-oxoglutarate dehydrogenase, E2 component, dihydrolipoamide succinyltransferase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-14   53.0   8.5    3.1e-14   52.6   8.5    1.2  1  Biotin_lipoyl    Biotin-requiring enzyme
    9.4e-08   31.8   5.5     0.0025   17.6   0.2    2.2  2  Biotin_lipoyl_2  Biotin-lipoyl like
     0.0023   18.6   2.4      0.027   15.2   0.2    2.1  2  HlyD_3           HlyD family secretion protein
     0.0041   17.1   0.5      0.094   12.8   0.1    2.1  2  QRPTase_N        Quinolinate phosphoribosyl transferase, N-te
  ------ inclusion threshold ------
      0.015   15.2   1.4      0.029   14.3   1.4    1.5  1  RnfC_N           RnfC Barrel sandwich hybrid domain
      0.024   14.5   0.2      0.045   13.6   0.2    1.4  1  DUF2154          Cell wall-active antibiotics response 4TMS Y
      0.054   12.9   0.1      0.063   12.7   0.1    1.0  1  SBP_bac_6        Bacterial extracellular solute-binding prote
      0.096   12.8   0.2        0.4   10.8   0.3    1.8  2  TetR_C_21        Tetracyclin repressor-like, C-terminal domai
       0.11   12.7   0.9         10    6.4   0.1    2.2  2  Peptidase_M23    Peptidase family M23


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 !   52.6   8.5   1.5e-17   3.1e-14       2      72 ..       4      74 ..       3      77 .. 0.95

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 1.5e-17
                                      EEEESSSEEEEEE..ECSESSSTTCEE-TTSEEEEEECTTEEEEEEBSSSEEEEEESSTTTEEE-TTCEEEE CS
                     Biotin_lipoyl  2 eiksPmiGesveeg.vvevlvkvGdkVkagqvlaeveamKmemeieapkaGvvkeilvkeGdtvevgdllak 72
                                      e+k+P+i++  ++g v ++++k+Gd Vk+g+ +aev   K+++ i+a+++G++k ilv+e+ +v++gd++a+
  gi|242399620|ref|YP_002995045.1|  4 EVKVPTISQEDKKGvVNQWYKKDGDVVKEGEEIAEVMIEKVTVIIKAQASGKLK-ILVPENGEVSQGDVIAV 74
                                      79**************************************************96.88888999*******97 PP

>> Biotin_lipoyl_2  Biotin-lipoyl like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.2   1.3e-06    0.0025      10      32 ..      16      38 ..       9      43 .. 0.90
   2 !   16.8   1.2   2.2e-06    0.0044       3      34 ..      46      76 ..      38      78 .] 0.89

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.3e-06
                   Biotin_lipoyl_2 10 sGrVaqlnVkdGqrVkaGdvLae 32
                                       G+V q++ kdG++Vk+G  +ae
  gi|242399620|ref|YP_002995045.1| 16 KGVVNQWYKKDGDVVKEGEEIAE 38
                                      69****************99987 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 2.2e-06
                   Biotin_lipoyl_2  3 vsIaapvsGrVaqlnVkdGqrVkaGdvLaelD 34
                                      v I+a+ sG++ +++V ++ +V +Gdv+a+ +
  gi|242399620|ref|YP_002995045.1| 46 VIIKAQASGKL-KILVPENGEVSQGDVIAVVE 76
                                      889*******9.59***************976 PP

>> HlyD_3  HlyD family secretion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.2   1.3e-05     0.027       7      41 ..      16      51 ..      14      57 .. 0.83
   2 !    6.1   0.2    0.0089        18       2      30 ..      48      75 ..      47      77 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.3e-05
                            HlyD_3  7 dGvvvelnveegevvqagdelleiippd.tllveak 41
                                       Gvv+++  + g+vv +g+e++e++ ++ t++++a+
  gi|242399620|ref|YP_002995045.1| 16 KGVVNQWYKKDGDVVKEGEEIAEVMIEKvTVIIKAQ 51
                                      69**********************976436666665 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0089
                            HlyD_3  2 lrApvdGvvvelnveegevvqagdellei 30
                                      ++A  +G+++ l  e+ge v++gd+++ +
  gi|242399620|ref|YP_002995045.1| 48 IKAQASGKLKILVPENGE-VSQGDVIAVV 75
                                      8999******9999****.******9987 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 !   12.8   0.1   4.7e-05     0.094      44      67 ..      16      39 ..       4      47 .. 0.87
   2 ?    3.4   0.0     0.041        81      45      68 ..      53      76 ..      40      78 .] 0.76

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.7e-05
                                      TTTEEEESS-TT-EEETTEEEEEE CS
                         QRPTase_N 44 pglevellvkDGervekgdvllei 67
                                      +g+  ++++kDG+ v++g+ ++e+
  gi|242399620|ref|YP_002995045.1| 16 KGVVNQWYKKDGDVVKEGEEIAEV 39
                                      467788***************997 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.041
                                      TTEEEESS-TT-EEETTEEEEEEE CS
                         QRPTase_N 45 glevellvkDGervekgdvlleie 68
                                      + + ++lv++  +v++gdv++ +e
  gi|242399620|ref|YP_002995045.1| 53 SGKLKILVPENGEVSQGDVIAVVE 76
                                      557788999999999999999886 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 ?   14.3   1.4   1.4e-05     0.029      39      86 ..      17      65 ..       6      78 .] 0.76

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.4e-05
                            RnfC_N 39 GapakplvkvgdkVlkGqkiaeaeg.fvsapvhasvsGtVkaiekrlva 86
                                      G  ++   k gd V++G+ iae     v++ + a  sG+ k + + +  
  gi|242399620|ref|YP_002995045.1| 17 GVVNQWYKKDGDVVKEGEEIAEVMIeKVTVIIKAQASGKLKILVPENGE 65
                                      6666777899************964477***********9877665554 PP

>> DUF2154  Cell wall-active antibiotics response 4TMS YvqF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2   2.3e-05     0.045      35      62 ..      40      67 ..      36      73 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.3e-05
                           DUF2154 35 lpegetvivirkliGdvkilVPedvevs 62
                                      + e+ tvi+  +  G++kilVPe+ evs
  gi|242399620|ref|YP_002995045.1| 40 MIEKVTVIIKAQASGKLKILVPENGEVS 67
                                      5678999******************997 PP

>> SBP_bac_6  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   3.1e-05     0.063     129     185 ..      20      75 ..      12      77 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.1e-05
                         SBP_bac_6 129 paqmvkaagslesgepavsvvpyffadilpekkkgknlkvvwPedGalvspifmlvk 185
                                       + +  k  + +++ge+ + v++   + i++++   ++lk+++Pe+G +   ++++v+
  gi|242399620|ref|YP_002995045.1|  20 NQWYKKDGDVVKEGEEIAEVMIEKVTVIIKAQA-SGKLKILVPENGEVSQGDVIAVV 75 
                                       55556666778899999***************7.779*************9999987 PP

>> TetR_C_21  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.25   4.9e+02      45      63 ..       3      21 ..       1      26 [. 0.84
   2 ?   10.8   0.3    0.0002       0.4      33      62 ..      28      57 ..      11      63 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.25
                         TetR_C_21 45 leekvaairaaQraGtvda 63
                                      +e kv +i+++ ++G v++
  gi|242399620|ref|YP_002995045.1|  3 IEVKVPTISQEDKKGVVNQ 21
                                      68899**********9986 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0002
                         TetR_C_21 33 eeleeeeeraesleekvaairaaQraGtvd 62
                                      + ++e ee ae++ ekv+ i +aQ++G+++
  gi|242399620|ref|YP_002995045.1| 28 DVVKEGEEIAEVMIEKVTVIIKAQASGKLK 57
                                      5788889999*****************986 PP

>> Peptidase_M23  Peptidase family M23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.1    0.0051        10      57      73 ..      24      40 ..      15      52 .. 0.85
   2 ?    5.5   0.1    0.0099        20      54      73 ..      57      76 ..      42      78 .] 0.81

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0051
                                      S-TTEEE-TTCEEEEEB CS
                     Peptidase_M23 57 vkegqkVkaGqvIGtvg 73
                                       k g+ Vk+G+ I++v 
  gi|242399620|ref|YP_002995045.1| 24 KKDGDVVKEGEEIAEVM 40
                                      589***********986 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0099
                                      EESS-TTEEE-TTCEEEEEB CS
                     Peptidase_M23 54 kisvkegqkVkaGqvIGtvg 73
                                      ki v e+ +V++G+vI+ v 
  gi|242399620|ref|YP_002995045.1| 57 KILVPENGEVSQGDVIAVVE 76
                                      45688999********9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       739  (0.0412181); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 447.58
//
Query:       gi|242399621|ref|YP_002995046.1|  [L=335]
Description: Thiamine pyrophosphate-dependent dehydrogenase, E1 component beta subunit [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-47  161.6   0.0    2.8e-47  160.7   0.0    1.4  1  Transket_pyr     Transketolase, pyrimidine binding domain
    8.7e-37  125.8   0.2    1.3e-36  125.2   0.2    1.3  1  Transketolase_C  Transketolase, C-terminal domain


Domain annotation for each model (and alignments):
>> Transket_pyr  Transketolase, pyrimidine binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.7   0.0   3.1e-51   2.8e-47       2     175 ..       7     181 ..       6     183 .. 0.98

  Alignments for each domain:
  == domain 1  score: 160.7 bits;  conditional E-value: 3.1e-51
                                       EEEHHHHHHHHHHHHHCTTTTEEEEESSTH..HHHTTCHCCHHEGGTTEGEEE--S-HHHHHHHHHHHHHHCTTEEE CS
                      Transket_pyr   2 kiawrkaeaealaellkedpevvligaDva..ggtfsvrkgllhdqgegrvidsgisEqavlgfavGaalagpllvi 76 
                                       k+ + ka+ ea+a+++++d++v+++g+D++  gg f++++gll+++g++rv d++isE+a++g+a+Gaa +g +++i
  gi|242399621|ref|YP_002995046.1|   7 KLPMYKAISEAIAQEMERDENVFVMGEDIGayGGIFGATSGLLEKFGPERVRDTPISESAFIGAALGAASKG-MRPI 82 
                                       567889******************************************************************.8*** PP

                                       EEEEEHHHHGGG..HHGGHHHHHCHHHHHT--EEEEESBSGGGSTTGTTTSBSSHHHHHHTSTTEEEE--SSHHHHH CS
                      Transket_pyr  77 veaqFgdFangA..qiyadqairsgeakgklkvgvvtrlpigvgedGpehqsaeleaflrlipglkvvrPsdpaetk 151
                                       ve++F+dF+ +A  qiy++ a+  ++++g+lk+++v+ + ig g + ++++s+ l+ +++++pglk+v Ps+ +++k
  gi|242399621|ref|YP_002995046.1|  83 VELMFVDFFGVAmdQIYNHIAKAYYMSGGQLKMPIVITTAIGGGYSDAAQHSQCLYGLFAHVPGLKIVIPSNSYDAK 159
                                       ***************************************************************************** PP

                                       HHHHHHHHSSS.SEEEEEE-SSEE CS
                      Transket_pyr 152 hllrrairredrkPvvlrlpksll 175
                                       +l+  air  d++Pv+ +++k+l+
  gi|242399621|ref|YP_002995046.1| 160 GLMISAIR--DDNPVMYFFHKGLM 181
                                       ********..89*********986 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.2   0.2   1.5e-40   1.3e-36       1     124 []     206     327 ..     206     327 .. 0.98

  Alignments for each domain:
  == domain 1  score: 125.2 bits;  conditional E-value: 1.5e-40
                                       TEEEEEETTSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEESTTSHH CS
                   Transketolase_C   1 gkaeilregkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeavkrgGig 77 
                                       g+a+++reg+dvt+v++ ++v+e + AaeeLekegisaeV+dlr++ plDk+t+l+svkktgrlv+ +e++++ G++
  gi|242399621|ref|YP_002995046.1| 206 GEAKVVREGSDVTIVGVAKTVHEGIWAAEELEKEGISAEVIDLRSLVPLDKKTLLDSVKKTGRLVIADEDYRSYGMS 282
                                       89*************************************************************************** PP

                                       HHHHHHHHHCCCTTCSSEEEEEEE-SSSSSSGHHHHHHHTT-SHHHH CS
                   Transketolase_C  78 sevaaalaeeafdgldapvkrvggpdviepgsaeelekafgldaeki 124
                                        e++a++ e++  +l+ap +rv+ pdv++p+s   lek++++d+eki
  gi|242399621|ref|YP_002995046.1| 283 GEIIATVVENG-ISLEAPPVRVAYPDVPVPYS-RVLEKYVLPDKEKI 327
                                       *********87.58******************.99**********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 2065.25
//
Query:       gi|242399622|ref|YP_002995047.1|  [L=335]
Description: Thiamine pyrophosphate-dependent dehydrogenase, E1 component alpha subunit [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-85  287.2   0.0    1.4e-85  286.9   0.0    1.0  1  E1_dh            Dehydrogenase E1 component
      3e-09   36.5   0.1      7e-09   35.3   0.1    1.6  1  DXP_synthase_N   1-deoxy-D-xylulose-5-phosphate synthase
    8.3e-08   32.2   4.6      6e-07   29.4   1.2    3.1  3  TPP_enzyme_C     Thiamine pyrophosphate enzyme, C-terminal TP
    0.00013   21.1   0.0    0.00023   20.3   0.0    1.4  1  Transketolase_N  Transketolase, thiamine diphosphate binding 
  ------ inclusion threshold ------
      0.091   12.5   0.8       0.26   11.0   0.3    2.0  2  SpoVS            Stage V sporulation protein S (SpoVS)


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 !  286.9   0.0     4e-89   1.4e-85      22     300 .]      48     324 ..      40     324 .. 0.96

  Alignments for each domain:
  == domain 1  score: 286.9 bits;  conditional E-value: 4e-89
                                       S-S-----TT-HHHHHHHHHTS-TTSEEEESS--HHHHHHTT--HHHHHHHHTT-T....TTSSGTT-.-E..BTT. CS
                             E1_dh  22 rigfyhlsagqealkvgiaaalekeDliiteYReagvllarglsleeilaeltgkv....kgkggsrhelmyaekes 94 
                                       + g  hls gqe ++vg+  +l++eD+++ ++R + + +a+g++l+++ ae+ gk+     gkgg +h l +a ++ 
  gi|242399622|ref|YP_002995047.1|  48 IPGELHLSSGQESAAVGVCLHLKPEDAVVGTHRAHHFAIAKGVDLKKMTAEIFGKAtglsGGKGGHMH-LFDAYQN- 122
                                       667789**************************************************888788888888.8878888. PP

                                       .BEEE-SSTTTHHHHHHHHHHHHHHHTS---EEEEEEGGGTT-HHHHHHHHHHHHTT--EEEEEEEESEETTEEHHH CS
                             E1_dh  95 rilggngivgaqvplvaGialaakiegkkevailliGDgAanqGdvyealnlaalwklpvifvveNNkygisTeaek 171
                                         +  +givga  p++ G+ +aak +g++ va+++ GDgAanqG+++ealnlaa+wklpvifv+e N ++is++++k
  gi|242399622|ref|YP_002995047.1| 123 --FSCSGIVGASFPQAVGVGIAAKLKGEDYVAVAVGGDGAANQGTFHEALNLAAIWKLPVIFVIEDNSWAISVPKDK 197
                                       ..99************************************************************************* PP

                                       H-S---GGG..TTTTS-EEEEETTSHHHHHHHHHHHHHHHHTTT--EEEEEEE--SS-SSTTSHSHSSSHHHHHHHH CS
                             E1_dh 172 asaskeladrargvgipglrVdgnDplavyeAvkfAaeraregkgpllielvtYRyggHsesDdpstyrtreeveev 248
                                       ++a+ + ++ra+++gipg+ Vdg+D++avye++k+A+erar+g+gp+lie++ YR+ gH+e D p+ yr ++e  e 
  gi|242399622|ref|YP_002995047.1| 198 STAVSKNSERAAAYGIPGVSVDGTDVIAVYEVAKEAVERARRGEGPSLIEIKVYRLRGHFEGD-PQHYR-PKEDFEL 272
                                       ***************************************************************.9****.7777788 PP

                                       HHHH-HHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHHHHHHHHHHS----GG CS
                             E1_dh 249 rkkkdpiqrlkelLvkkgvvseeelkeiekevrkeveeavkkaeskkelepe 300
                                        k+kdp+  +++lL +kg+++eeel++i++e  kev+ea++ a +++++epe
  gi|242399622|ref|YP_002995047.1| 273 AKQKDPLLNFEKLLLEKGIATEEELNKIKEENVKEVQEAIDFAVNSPYPEPE 324
                                       8888********************************************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 !   35.3   0.1     2e-12     7e-09     109     177 ..     125     193 ..      71     211 .. 0.83

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 2e-12
                    DXP_synthase_N 109 eagHsstsisaalGlavardlkgekkkvvaviGDgaltgGmafealnnigelkkkllvilNdNemsisk 177
                                        +g  ++s  +a+G+ +a++lkge++ +vav GDga   G  +ealn ++  k  ++ ++ dN+++is 
  gi|242399622|ref|YP_002995047.1| 125 CSGIVGASFPQAVGVGIAAKLKGEDYVAVAVGGDGAANQGTFHEALNLAAIWKLPVIFVIEDNSWAISV 193
                                       24556788999******************************************************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 ?   -3.7   0.0       2.5   8.9e+03      36      50 ..      61      76 ..      60      77 .. 0.78
   2 !   29.4   1.2   1.7e-10     6e-07      22     153 .]     121     248 ..     110     248 .. 0.70
   3 ?    1.4   0.0      0.07   2.5e+02     107     145 ..     276     318 ..     255     322 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 2.5
                                      HHHHHHH.HSTTSEEE CS
                      TPP_enzyme_C 36 aAiGakl.akpdrevv 50
                                      aA+G++l +kp+  vv
  gi|242399622|ref|YP_002995047.1| 61 AAVGVCLhLKPEDAVV 76
                                      899***9778876766 PP

  == domain 2  score: 29.4 bits;  conditional E-value: 1.7e-10
                                       ECETTTS-TTTHHHHHHHHHHH....STTSEEEEEEEHHH.HHHT.GGGHHHHHHTT-SEEEEEEE-SBCCCHHHHH CS
                      TPP_enzyme_C  22 ltsgglgtmGyglpaAiGakla....kpdrevvaivGDGg.flmi.lqelatavrrnlpitvvvlnNegygmtggqq 92 
                                       ++ +  g  G ++p A+G+ +a     +d   va+ GDG+  + + +++l  a+  +lp+++v+ +N++   + + +
  gi|242399622|ref|YP_002995047.1| 121 QNFSCSGIVGASFPQAVGVGIAaklkGEDYVAVAVGGDGAaNQGTfHEALNLAAIWKLPVIFVIEDNSWAISVPKDK 197
                                       455567889999999999999534423478999*******445556677777888899*********9986555543 PP

                                       HHHTCCTTTTSBB.BS----HHHHHHHTTSEEEEESSH.HHHHHHHHHHHH....CSSSEEEEEE CS
                      TPP_enzyme_C  93 epfggkrksgpagkdlkpvdfaklaealGakgarvekadveeleealkeal....ekkgpaliev 153
                                       + + +           k+    + a+a+G++g++v+ +dv  + e+ kea+    + +gp+lie+
  gi|242399622|ref|YP_002995047.1| 198 STAVS-----------KN---SERAAAYGIPGVSVDGTDVIAVYEVAKEAVerarRGEGPSLIEI 248
                                       33332...........22...35699999999977777776665555555444449*******97 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.07
                                       BS----HHHHHHHTTSEEE....EESSH.HHHHHHHHHHHHCS CS
                      TPP_enzyme_C 107 dlkpvdfaklaealGakga....rvekadveeleealkealek 145
                                       +++ ++f+kl    G+       ++++++v+e++ea++ a+++
  gi|242399622|ref|YP_002995047.1| 276 KDPLLNFEKLLLEKGIATEeelnKIKEENVKEVQEAIDFAVNS 318
                                       566778999999999995558999999**********999876 PP

>> Transketolase_N  Transketolase, thiamine diphosphate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   6.3e-08   0.00023     148     242 ..     153     249 ..     127     262 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 6.3e-08
                                       EEEEEHHHHHSHHHHHHHHHHHHTT-TTEEEEEEES.SEETTEEGGGT--S-HHHHHHHTT-EEEEETTTT-HHHH. CS
                   Transketolase_N 148 yvilgDgclmeGvsseasslagtlkLgkLivlyDdn.kisidGeteisftedvakrfeaygWhvievedgedveai. 222
                                        ++ gDg  + G  +ea +la+  kL  + v+ D+   is+  + +++++   ++r +ayg   ++  dg+dv a+ 
  gi|242399622|ref|YP_002995047.1| 153 VAVGGDGAANQGTFHEALNLAAIWKLPVIFVIEDNSwAISVPKDKSTAVS-KNSERAAAYGIPGVS-VDGTDVIAVy 227
                                       34568*********************987777665435666555555444.557899999988777.5666665552 PP

                                       ...HHHHHHHHH-TTS-EEEEEE CS
                   Transketolase_N 223 ...kaaieeakaekdkPsliklr 242
                                          k+a+e+a++  + Psli+++
  gi|242399622|ref|YP_002995047.1| 228 evaKEAVERARRG-EGPSLIEIK 249
                                       2236789999888.88****998 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 ?   -2.3   0.0       1.1   3.8e+03      40      60 ..      73      93 ..      58      97 .. 0.80
   2 ?   11.0   0.3   7.4e-05      0.26       7      41 ..     130     164 ..     127     173 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.1
                                      HHHHHHHHHHHHHGGGTEEEE CS
                             SpoVS 40 qavkAiaiargflapegidlv 60
                                       av +   a +f   +g+dl 
  gi|242399622|ref|YP_002995047.1| 73 DAVVGTHRAHHFAIAKGVDLK 93
                                      577777788889999999986 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 7.4e-05
                                       TT--HHHHHHHHHHHHHHTSEEEEEE-SHHHHHHH CS
                             SpoVS   7 sksnpnkvagAiagvlrekgkvevqaiGagAvnqa 41 
                                       ++s p++v+  ia++l+ ++ v+v + G gA+nq 
  gi|242399622|ref|YP_002995047.1| 130 GASFPQAVGVGIAAKLKGEDYVAVAVGGDGAANQG 164
                                       6799*****************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       725  (0.0404373); expected 358.6 (0.02)
Passed bias filter:                      593  (0.0330749); 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: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2224.83
//
Query:       gi|242399623|ref|YP_002995048.1|  [L=262]
Description: hypothetical protein TSIB_1648 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.038   13.6   0.0       0.11   12.2   0.0    1.8  2  SH3_1     SH3 domain


Domain annotation for each model (and alignments):
>> SH3_1  SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       0.5   8.9e+03       1       7 [.      41      47 ..      41      48 .. 0.85
   2 ?   12.2   0.0   5.9e-06      0.11      15      47 ..     146     177 ..     143     178 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 0.5
                                      EESSSBE CS
                             SH3_1  1 iAlYDYe 7 
                                      +Al+++e
  gi|242399623|ref|YP_002995048.1| 41 KALFPFE 47
                                      79***97 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 5.9e-06
                                       EBSTTEEEEEEEECSS.SEEEEEETTSTEEEEEE CS
                             SH3_1  15 sfkkGDviivleksed.gWwkgrlkgtgkeGliP 47 
                                       ++ kG++++v+ek+e   W+k  +k++  +G+ P
  gi|242399623|ref|YP_002995048.1| 146 PIAKGETFEVIEKEERyIWLKSLRKSG--KGMTP 177
                                       678******************999974..78766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); 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: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.54
# Mc/sec: 1463.34
//
Query:       gi|242399624|ref|YP_002995049.1|  [L=265]
Description: radical SAM domain protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.3e-11   43.8   0.1    1.1e-10   42.2   0.0    1.7  2  Radical_SAM  Radical SAM superfamily
  ------ inclusion threshold ------
      0.055   13.7   0.3       0.63   10.3   0.0    2.2  2  Fer4_12      4Fe-4S single cluster domain
        6.5    6.4  10.0         50    3.5   6.0    2.9  3  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 !   42.2   0.0   1.8e-14   1.1e-10       5     159 ..      28     183 ..      24     188 .. 0.86
   2 ?   -1.1   0.0      0.35   2.1e+03     120     143 ..     225     248 ..     202     255 .. 0.60

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 1.8e-14
                                       SEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTC...CCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxx RF
                       Radical_SAM   5 rgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlakla...vpg 77 
                                        gC ++C++C+ ++  ++ ++g   ++ e++  + el a+k+  +ev++++   + y +++++l+  +k     ++ 
  gi|242399624|ref|YP_002995049.1|  28 VGCQFACKYCYAKFICKWKPYGDWGTWVEVKTNAPEL-ARKRvHGEVFMSSL-SDPYQPIERELKLTRKTLqmmDKR 102
                                       79***********************************.79995666666666.55555566666666665579999* PP

                                       EEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEEEBT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  78 iritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvdrivglp 153
                                        ++++ t  +l+  + +++++      v l+++++  +  +++++  +++ + ++eal++l++ gik+  ++ +++p
  gi|242399624|ref|YP_002995049.1| 103 NKLSILTKSPLV-VRDIDLFKLFDDIEVGLTINSFEGK-EKQIIEpFTPSQKLRIEALKTLKDEGIKNYGFISPIIP 177
                                       ***********9.9999999999999999999999999.888888889***************************** PP

                                       TTSHHH CS
                                       xxxxxx RF
                       Radical_SAM 154 Gendee 159
                                       G +d e
  gi|242399624|ref|YP_002995049.1| 178 GITDIE 183
                                       ***964 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.35
                                       HHTCTSHHHHHHHHHHHHHHTTSE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 120 lmnrghtfeevlealeklreagik 143
                                       ++n  + +e v+e++ +++ ++ik
  gi|242399624|ref|YP_002995049.1| 225 MINEDKFWEFVKELIALIKHLDIK 248
                                       344444555555555555554444 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00011      0.63      12      30 ..      27      45 ..      17     107 .. 0.77
   2 ?    1.2   0.0     0.067     4e+02      73     115 ..     208     249 ..     199     257 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00011
                           Fer4_12 12 vsgCnlsCkgCfnketwsf 30
                                        gC+++Ck+C++k + + 
  gi|242399624|ref|YP_002995049.1| 27 YVGCQFACKYCYAKFICKW 45
                                      569*********9866544 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.067
                           Fer4_12  73 lelvkevkeekpekdiwlytgytleelskkekeellkeidvlv 115
                                        ++v+ +ke++pe   ++ +  ++ e+ k e   l+k +d+  
  gi|242399624|ref|YP_002995049.1| 208 RKFVEILKENFPESYEIMINEDKFWEFVK-ELIALIKHLDIKA 249
                                       68999999999999999999999999987.5888888888755 PP

>> DUF1848  Domain of unknown function (DUF1848)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   6.0    0.0083        50     252     265 .]      26      39 ..      21      39 .. 0.92
   2 ?    0.3   0.0     0.077   4.6e+02     149     183 ..      73     108 ..      58     120 .. 0.70
   3 ?    1.9   0.0     0.025   1.5e+02      85     107 ..     140     163 ..     126     169 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.0083
                           DUF1848 252 ayntClhgCvYCYA 265
                                       +y  C+  C+YCYA
  gi|242399624|ref|YP_002995049.1|  26 QYVGCQFACKYCYA 39 
                                       7999*********9 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.077
                           DUF1848 149 kvviSfvdlykkvkrnlkk.klelrelseeekeela 183
                                        ++ S+ d+y+ ++r+lk  + +l+ +++++k +++
  gi|242399624|ref|YP_002995049.1|  73 VFMSSLSDPYQPIERELKLtRKTLQMMDKRNKLSIL 108
                                       456788999999999996423556666666655555 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.025
                           DUF1848  85 eke.lepnvpsleerietfkelse 107
                                       ek+ +ep +ps + rie++k+l +
  gi|242399624|ref|YP_002995049.1| 140 EKQiIEPFTPSQKLRIEALKTLKD 163
                                       34459****************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       738  (0.0411624); expected 358.6 (0.02)
Passed bias filter:                      582  (0.0324614); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.33s 00:00:00.95 Elapsed: 00:00:00.52
# Mc/sec: 1528.67
//
Query:       gi|242399625|ref|YP_002995050.1|  [L=246]
Description: hypothetical protein TSIB_1650 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-68  230.7  12.9    1.7e-68  230.5  12.9    1.0  1  DUF1624   Protein of unknown function (DUF1624)
  ------ inclusion threshold ------
      0.078   11.8  12.7       0.09   11.6   5.4    3.0  3  OpgC_C    OpgC protein


Domain annotation for each model (and alignments):
>> DUF1624  Protein of unknown function (DUF1624)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  230.5  12.9   1.9e-72   1.7e-68       1     223 []      10     228 ..      10     228 .. 0.97

  Alignments for each domain:
  == domain 1  score: 230.5 bits;  conditional E-value: 1.9e-72
                           DUF1624   1 RieeiDalRGiAlilMiifHflfdLeffgylavslatsglwvvfarliaslFlfiaGvslvlahskslrw.rkflkR 76 
                                       R++eiD++RGiAli+M+i +f++dL+ff  ++ + +   +w++fa+++aslF+ i+G+sl+++h+++++  rk+l+R
  gi|242399625|ref|YP_002995050.1|  10 RFWEIDFARGIALIMMLISNFVTDLQFFLDYSEHKL---FWRIFAYATASLFVSISGLSLWISHARGKKNiRKYLQR 83 
                                       9***************************99997766...***************************99888****** PP

                           DUF1624  77 glkilaaallitaatylllpdsfivFGiLhlialalllallflrlpkalllllallilalglllreaifdlplllwl 153
                                       + k+++++llit+ ty+ll++++i+FG+Lh++++a+ll+++f++l+++++++ a l+l+++ ++re   ++  ll+l
  gi|242399625|ref|YP_002995050.1|  84 FTKLFGLGLLITLSTYILLKRGTIYFGVLHFLGVASLLVIPFYQLGWKNIFI-APLFLLGHEIVREIHAESLFLLPL 159
                                       ***************************************************9.9999999***************** PP

                           DUF1624 154 glssekfetndYvplfPWfgvvllGialgkllyekgkrrlklpslpkaklvrplallGrhsLliYlihqp 223
                                       g+++++f+t+dY+p+fPWfgv+llG a+g +ly++g+r+++l +l++ +++ +++++Gr++L iYlihqp
  gi|242399625|ref|YP_002995050.1| 160 GITPHQFFTLDYFPIFPWFGVFLLGTAVGGILYPHGQRKFNLNNLDN-PVIDVICFIGRNTLKIYLIHQP 228
                                       *****************************************876666.8********************9 PP

>> OpgC_C  OpgC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   5.4     1e-05      0.09       1      93 [.      10     102 ..      10     143 .. 0.73
   2 ?   -1.9   3.0      0.13   1.1e+03     178     207 ..     157     188 ..      94     201 .. 0.62
   3 ?    3.4   0.0    0.0033        29     290     315 ..     202     227 ..     190     240 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1e-05
                            OpgC_C   1 RdlrlDlfRGlalvlivvdHi.......pgsvlskltlrnfGfsdaAevFVflSGlavglvYgraaeregalaaaar 70 
                                       R +++D+ RG+al+++++           +    kl  r f++   A +FV +SGl++ + ++r       ++  ++
  gi|242399625|ref|YP_002995050.1|  10 RFWEIDFARGIALIMMLISNFvtdlqffLDYSEHKLFWRIFAYA-TASLFVSISGLSLWISHARG------KKNIRK 79 
                                       6799************9966536433322222335666667766.578**********9998887......345667 PP

                            OpgC_C  71 ilrRawelYvahiallvlvlali 93 
                                        l+R ++l+   +++++ +++l+
  gi|242399625|ref|YP_002995050.1|  80 YLQRFTKLFGLGLLITLSTYILL 102
                                       77777777777776666666655 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.13
                            OpgC_C 178 lnlpalpsgf..ewfFnpfaWQllFvlGlllg 207
                                       l l  +p +f   ++F++f W  +F+lG ++g
  gi|242399625|ref|YP_002995050.1| 157 LPLGITPHQFftLDYFPIFPWFGVFLLGTAVG 188
                                       44444443331147888888888888887765 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.0033
                            OpgC_C 290 ralraavlrplillGrhsLavFvvgv 315
                                       ++l+++v  +++ +Gr++L+++ ++ 
  gi|242399625|ref|YP_002995050.1| 202 NNLDNPVIDVICFIGRNTLKIYLIHQ 227
                                       567789999**************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.34s 00:00:00.96 Elapsed: 00:00:00.56
# Mc/sec: 1333.90
//
Query:       gi|242399626|ref|YP_002995051.1|  [L=129]
Description: Membrane protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.9e-14   53.2   1.0    2.9e-14   53.2   1.0    1.5  2  NfeD         NfeD-like C-terminal, partner-binding
  ------ inclusion threshold ------
       0.09   13.2   0.4        1.8    9.0   0.4    2.4  1  GTP_EFTU_D2  Elongation factor Tu domain 2


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 ?   -2.3   0.1      0.65   5.9e+03       4      15 ..      20      30 ..      19      39 .. 0.58
   2 !   53.2   1.0   3.3e-18   2.9e-14       5      83 ..      45     126 ..      40     126 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.65
                                      XXXXXXXXXXXX CS
                              NfeD  4 vvsvlllvllrp 15
                                      vv  ++l+++ p
  gi|242399626|ref|YP_002995051.1| 20 VV-GIFLFFILP 30
                                      34.445555444 PP

  == domain 2  score: 53.2 bits;  conditional E-value: 3.3e-18
                                       XXXXXX..XXXXXXS---SSS--S.S---GGTTSEEEEEE-BS.-EEEEETTEEEEEE-.SS.B-TT-EEEEEEE-S CS
                              NfeD   5 vsvlll..vllrplllkklkkkekktnaealiGkegvvledig.tGrvkvdGeeWsarsege.iekgerVrVveveG 77 
                                       +++l++  v+ +++l+  ++k+ +  + ealiG  ++v+e+++ +G vkv++e W a++ ++  +kge+V+++e++G
  gi|242399626|ref|YP_002995051.1|  45 IGFLIFkdVIAVKFLWEVFDKRVE-VGPEALIGNDAIVVEELNpKGVVKVGNELWIAECLSGtAKKGEKVEIIEIRG 120
                                       333333344455888888866555.8999*************558**************7666************** PP

                                       SSEEEE CS
                              NfeD  78 ltliVe 83 
                                       ++l V+
  gi|242399626|ref|YP_002995051.1| 121 TKLLVK 126
                                       ****97 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 ?    9.0   0.4    0.0002       1.8       9      26 ..     103     121 ..      88     128 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0002
                                       EESEEETTEEEEEEC.TCT CS
                       GTP_EFTU_D2   9 ysGtlkkGdevrilg.ndt 26 
                                        sGt kkG++v+i+   +t
  gi|242399626|ref|YP_002995051.1| 103 LSGTAKKGEKVEIIEiRGT 121
                                       6899999999999776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); 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: 0.50u 0.34s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 776.85
//
Query:       gi|242399627|ref|YP_002995052.1|  [L=392]
Description: threonine synthase [Thermococcus sibiricus MM 739]
Scores for complete 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-68  229.8   0.8    5.6e-68  229.5   0.8    1.1  1  PALP            Pyridoxal-phosphate dependent enzyme
  ------ inclusion threshold ------
      0.044   13.8   0.2      0.077   13.0   0.2    1.4  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.062   13.0   2.1       0.13   12.0   2.1    1.4  1  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
       0.12   12.4   0.8       0.29   11.2   0.8    1.6  1  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
       0.24   11.1   3.2       0.94    9.3   3.3    1.9  1  zinc_ribbon_2   zinc-ribbon domain
       0.36   10.6   5.3       0.84    9.4   0.4    2.3  2  zf-C2H2_11      zinc-finger C2H2-type


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 !  229.5   0.8   1.9e-71   5.6e-68       2     294 .]      77     377 ..      76     377 .. 0.97

  Alignments for each domain:
  == domain 1  score: 229.5 bits;  conditional E-value: 1.9e-71
                                       GGCSSS--EEEECCTCCCCCCE.EEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHH CS
                              PALP   2 tlgigpTPlvrlprlskelgvp.lflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaall 77 
                                       +l +g+T+l r ++l+k+lg   l++K+E+ nptg+fKdRg +  ++++ e   a+ vv+as+GN++++++a+++++
  gi|242399627|ref|YP_002995052.1|  77 SLNEGGTRLYRMKNLEKKLGFGkLYIKNEGENPTGAFKDRGSSVEITKALEF-HARKVVVASTGNMAASISAYGSKA 152
                                       6789************************************************.************************ PP

                                       T-EEEEEEETTS-HHHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHHHTHHHHHHHHT CS
                              PALP  78 GlkvtivvpadaspekvallrllGaevvevggdydeavaaaaelaaegegaylvsqfdnptviegygtiglEileql 154
                                       Gl+vtivvp++++ +k+ +   +Ga++   g++ydea+a  +++a+e e++yl+  +   +++eg++++g+Ei +ql
  gi|242399627|ref|YP_002995052.1| 153 GLEVTIVVPEGTPIGKLVQAVVYGAKIKIHGTTYDEALAESERMAKE-EDYYLTGNY--HYRVEGQKSTGFEIFDQL 226
                                       ***********************************************.*********..5***************** PP

                                       T.TTEEEEEEE-SSSHHHHHHHHHHHH......HSTT..-EEEEEEECTTCGGTTCCS..S.SS..B...SSS.CCS CS
                              PALP 155 g.gkpdavvvpvGgGgliaGiaaglke......rrpd..vrvigvepegsdalarslragrrvtvpvs..dtiadgl 220
                                         ++pd++vvp+G G  + +i+++ ke         +  +++ gv++eg da+ +++++g + +  ++  +t a+++
  gi|242399627|ref|YP_002995052.1| 227 RfDSPDWIVVPIGAGTHLRAIWKAAKEfykvglI--ErlPKIAGVQVEGYDAIVKAWKEGMPIKPRKEkkPTVASAI 301
                                       ***************************9877432..367*********************9998887788******* PP

                                       TCS..CGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHH.HHHHHHCCTTCEEEEEEE-B CS
                              PALP 221 avg..spselafelldrlvdeivtvsdeealeamrllarregivvepssaaalaal.klreagelkegdrvvviltg 294
                                       av+  +++e ++++++++ +    v++eea+ a  ll  +eg++vepss +ala + ++re g +++++r+vvi tg
  gi|242399627|ref|YP_002995052.1| 302 AVKapVDGENVLRAIEESKGHLGVVTNEEAMNAGLLLG-KEGLFVEPSSSTALALArQMREEGIIDKDERIVVIATG 377
                                       **************************************.************************************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 ?   13.0   0.2   2.6e-05     0.077      66      95 ..       4      33 ..       1      42 [. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.6e-05
                                      EE--EEEETTTS-EEECHHHHHS-TTTSSS CS
                              HypA 66 evpvkvrCreCgkefeleekalrCpkCgsa 95
                                        + +++C++Cg e++l++  ++C +Cg+ 
  gi|242399627|ref|YP_002995052.1|  4 MFETTLKCTKCGIEYSLASGVYKCRECGAP 33
                                      567889**********9975789****985 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   2.1   4.3e-05      0.13       2      24 ..      10      31 ..      10      33 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.3e-05
                                      B-SSS--B----SSS----SSS- CS
                    DNA_RNApol_7kD  2 iCgeCgaevslkkgdpiRCkeCG 24
                                      +C +Cg e sl +g + +C+eCG
  gi|242399627|ref|YP_002995052.1| 10 KCTKCGIEYSLASG-VYKCRECG 31
                                      6*************.99****** 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 ?   11.2   0.8   9.6e-05      0.29      18      44 ..       8      31 ..       3      32 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 9.6e-05
                     Zn_Tnp_IS1595 18 gfvCPhCgsrkayriktrglfqCkeCr 44
                                      +  C +Cg    y++++ g+++C+eC+
  gi|242399627|ref|YP_002995052.1|  8 TLKCTKCG--IEYSLAS-GVYKCRECG 31
                                      568*****..5699999.********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 ?    9.3   3.3   0.00032      0.94       1      23 []      10      34 ..      10      34 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00032
                     zinc_ribbon_2  1 fCpnCGaelq.d.nakFCpyCGtpl 23
                                      +C++CG e +   ++  C +CG+pl
  gi|242399627|ref|YP_002995052.1| 10 KCTKCGIEYSlAsGVYKCRECGAPL 34
                                      8*******965438888******98 PP

>> zf-C2H2_11  zinc-finger C2H2-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.4   0.00028      0.84       2      15 ..       6      19 ..       6      23 .. 0.90
   2 ?    3.3   0.5     0.023        68       5      12 ..      25      32 ..      21      33 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00028
                        zf-C2H2_11  2 estcqCleCGlcft 15
                                      e+t++C++CG  ++
  gi|242399627|ref|YP_002995052.1|  6 ETTLKCTKCGIEYS 19
                                      589********998 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.023
                        zf-C2H2_11  5 cqCleCGl 12
                                      ++C+eCG 
  gi|242399627|ref|YP_002995052.1| 25 YKCRECGA 32
                                      79****95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); expected 358.6 (0.02)
Passed bias filter:                      603  (0.0336327); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.61u 0.38s 00:00:00.99 Elapsed: 00:00:00.55
# Mc/sec: 2131.76
//
Query:       gi|242399628|ref|YP_002995053.1|  [L=363]
Description: DNA methylase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-13   50.3   0.0    1.3e-11   44.6   0.0    3.2  2  UPF0020          Putative RNA methylase family UPF0020
    1.1e-05   25.2   0.0    3.5e-05   23.6   0.0    1.7  1  N6_N4_Mtase      DNA methylase
    6.9e-05   22.7   0.0     0.0001   22.2   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
    0.00049   19.9   0.0    0.00074   19.3   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
  ------ inclusion threshold ------
      0.031   13.8   0.0      0.052   13.1   0.0    1.3  1  MTS              Methyltransferase small domain
      0.033   13.8   0.0      0.051   13.2   0.0    1.3  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
      0.069   12.8   0.0       0.15   11.7   0.0    1.5  1  Cons_hypoth95    Conserved hypothetical protein 95


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 ?   -1.4   0.0      0.63   1.6e+03     141     160 ..      88     107 ..      85     118 .. 0.84
   2 !   44.6   0.0     5e-15   1.3e-11      12     171 ..     173     320 ..     164     342 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.63
                                       HHHHHHHHHHHHHHH-TT.. CS
                           UPF0020 141 lekLYseflrelkrvlrggg 160
                                        +kL++++++e+k+ ++++g
  gi|242399628|ref|YP_002995053.1|  88 DWKLWRKLGSEIKKTFKSHG 107
                                       589*************9977 PP

  == domain 2  score: 44.6 bits;  conditional E-value: 5e-15
                                       S-HHHHHHHHHHTT--TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH--EEEEES-HHH CS
                           UPF0020  12 LketLAaalvrlagwkpgepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelklygsDldrrv 88 
                                       + ++LA+ +++l+++++g+ +lDP+CG Gti  E  l+g n++                          gsD+++r+
  gi|242399628|ref|YP_002995053.1| 173 IPPRLARIMINLTEIRQGN-FLDPFCGIGTIVQEFVLQGLNAY--------------------------GSDSNPRA 222
                                       6789***********9985.99*******************99..........................******** PP

                                       HHHHHHHHH....HTT-GGGEEEEE--GGG--.STTS---EEEE----..........------HHHHHHHHHHHHH CS
                           UPF0020  89 vqgareNae....kagvgdliefsqadaakLr.lkegevdvivtnpPY..........GerlgskkalekLYseflr 150
                                       ++ga+eN++    + + +++ +++  d++kL+   + ++d+ivt+p            Ge+++ +++l+++Y ++ +
  gi|242399628|ref|YP_002995053.1| 223 IHGAKENLKwlkkEFRTKGSAHLEICDVRKLKrCFRVKFDAIVTEPYMgkplkyhpttGEAIKLANELDRFYFSVFD 299
                                       *******963333677889999**********544449******97432222335555778888889999******* PP

                                       HHHHH-TT..-EEEEEESSHH CS
                           UPF0020 151 elkrvlrgggrlvlltsenka 171
                                       ++  vl+++gr v+++++++ 
  gi|242399628|ref|YP_002995053.1| 300 SFGDVLKRHGRVVFVFPAYRL 320
                                       ****************98875 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   1.4e-08   3.5e-05     176     230 ..     173     227 ..     170     228 .. 0.93

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 1.4e-08
                                       --HHHHHHHHHHHS-TT-EEEETT-TTTHHHHHHHHTT-EEEEEESSHHHHHHHH CS
                       N6_N4_Mtase 176 kPvallerlIklstkkgdivlDpFaGSGtTavaakelgrkfiGieieeeyvelae 230
                                        P  l++ +I+l+    ++ lDpF+G Gt++++   +g +++G + +++++  a+
  gi|242399628|ref|YP_002995053.1| 173 IPPRLARIMINLTEIRQGNFLDPFCGIGTIVQEFVLQGLNAYGSDSNPRAIHGAK 227
                                       799********************************************99987665 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     4e-08    0.0001      20     153 ..     186     355 ..     159     363 .] 0.78

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 4e-08
                   Methyltransf_23  20 lraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiaekakkaqkdqfdeqeaaepqg............... 81 
                                       + ++g+ Ld  cG G+  +++  +g + +g D +p+a++ a++  k+ k+ f    +++  g               
  gi|242399628|ref|YP_002995053.1| 186 EIRQGNFLDPFCGIGTIVQEFVLQGLNAYGSDSNPRAIHGAKENLKWLKKEF----RTK--Gsahleicdvrklkrc 256
                                       67788*************************************7777777777....222..2335555666666789 PP

                   Methyltransf_23  82 ...kfdlIvlrevlehvp.dpp.................ellrqiatllkpgGylllseplasl.......kedrll 130
                                          kfd Iv   +++    ++p                 ++++++++ lk  G++++  p+ +l       ke+++l
  gi|242399628|ref|YP_002995053.1| 257 frvKFDAIVTEPYMGKPLkYHPttgeaiklaneldrfyfSVFDSFGDVLKRHGRVVFVFPAYRLndgriyrKERKWL 333
                                       999********999987724448************************************99888999*998899999 PP

                   Methyltransf_23 131 ldwlylvpagrhisffsarslke 153
                                       ++ +++v a r   f  ++ + +
  gi|242399628|ref|YP_002995053.1| 334 EKLGFEVMA-RYTDFEERHRIVR 355
                                       998888766.6666666655555 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   2.9e-07   0.00074       6     108 ..     191     312 ..     188     347 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 2.9e-07
                   Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.....nveFeqgdieeleklledekfDl 77 
                                       ++lD+ CG G+++ e+     ++ + +G D +++ai  A+en++ l+ +      +++e++d+ +l+  +   kfD 
  gi|242399628|ref|YP_002995053.1| 191 NFLDPFCGIGTIVQEFV---LQGLNAYGSDSNPRAIHGAKENLKWLKKEfrtkgSAHLEICDVRKLKRCFR-VKFDA 263
                                       78**************9...3567899**************98865555447888999*******885466.89*** PP

                   Methyltransf_31  78 ilsn..............evlnaladpdkile....eiervlkpggill 108
                                       i++               e++ + +++d ++     +  +vlk +g+++
  gi|242399628|ref|YP_002995053.1| 264 IVTEpymgkplkyhpttgEAIKLANELDRFYFsvfdSFGDVLKRHGRVV 312
                                       **98666655555554443333333333322233336666666666666 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0     2e-05     0.052      26     112 ..     183     275 ..     178     289 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2e-05
                                       HCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC......EEEEE-ST..TTTST CS
                               MTS  26 tlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle......vevvasdv..leeve 94 
                                       +l++ ++g+ lD  cG+G +  ++  +   ++    d + rA++ akenl+  k e      +++  +dv  l+   
  gi|242399628|ref|YP_002995053.1| 183 NLTEIRQGNFLDPFCGIGTIVQEFVLQG--LNAYGSDSNPRAIHGAKENLKWLKKEfrtkgsAHLEICDVrkLKRCF 257
                                       67777999***********999887755..4589****************987777667777666666662255666 PP

                                       TS-EEEEEE---STTTCH CS
                               MTS  95 ekkfdlivsNPPfhagka 112
                                         kfd+iv+ P + +  +
  gi|242399628|ref|YP_002995053.1| 258 RVKFDAIVTEPYMGKPLK 275
                                       899999999996655555 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 ?   13.2   0.0     2e-05     0.051       4      82 ..     192     271 ..     189     297 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2e-05
                   Methyltransf_15   4 ilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklkleki...kvdlvfl 77 
                                        lD+f+G G  v +f l++ + +++++n++ +  a++N +    +++  ++    +e+    kl+++   k+d +++
  gi|242399628|ref|YP_002995053.1| 192 FLDPFCGIGTIVQEFVLQGLNAYGSDSNPRAIHGAKENLKWL--KKEFRTKGSAHLEICDVRKLKRCfrvKFDAIVT 266
                                       69*************************************987..444444444444444444444433335667776 PP

                   Methyltransf_15  78 SpPwG 82 
                                        p +G
  gi|242399628|ref|YP_002995053.1| 267 EPYMG 271
                                       66666 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   5.8e-05      0.15      39     100 ..     186     246 ..     179     286 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.8e-05
                                       CHCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES- CS
                     Cons_hypoth95  39 eiegarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkeda 100
                                       ei++ ++LD f+G G++  E +  g  +a+  +++++a++  kenl+ lk e +t+   + +
  gi|242399628|ref|YP_002995053.1| 186 EIRQGNFLDPFCGIGTIVQEFVLQG-LNAYGSDSNPRAIHGAKENLKWLKKEFRTKGSAHLE 246
                                       59999******************99.67899******************9665444333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); 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: 0.72u 0.37s 00:00:01.08 Elapsed: 00:00:00.62
# Mc/sec: 1767.32
//
Query:       gi|242399629|ref|YP_002995054.1|  [L=133]
Description: hypothetical protein TSIB_1654 [Thermococcus sibiricus MM 739]
Scores for complete 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-38  130.3   0.0    3.9e-38  130.1   0.0    1.0  1  UPF0047    Uncharacterised protein family UPF0047
  ------ inclusion threshold ------
      0.028   14.7   0.0      0.032   14.5   0.0    1.2  1  TetR_C_10  Tetracyclin repressor-like, C-terminal domain


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 !  130.1   0.0   4.4e-42   3.9e-38       1     114 [.      17     129 ..      17     130 .. 0.96

  Alignments for each domain:
  == domain 1  score: 130.1 bits;  conditional E-value: 4.4e-42
                                       E-HHHHHHHHHHHT.SEEEEEEEESSSSEEEEEEESSSHHHHHHHHHHHHHHSTTT.T-GGGTTS..THHHHHHHHH CS
                           UPF0047   1 diteeveeavkesgvkeGlvlvfsrhttasltinEnadpdvqeDleealeklvpee.eYrhnaegpdnadaHlkssl 76 
                                       di + +e+ ++es++keGl+++f++htt++l+inEn ++++ eD++ +l++lvp+   Y+h+   ++na++Hl+s+l
  gi|242399629|ref|YP_002995054.1|  17 DIAHLIEQKIRESKIKEGLAVIFTQHTTTALFINEN-ENGLLEDVKGFLQTLVPKGkGYKHD-RIDRNAHSHLRSIL 91 
                                       688899******************************.******************99*****.5668********** PP

                                       H-SEEEEEEETTEE---TTEEEEEEESS-SSEEEEEEE CS
                           UPF0047  77 lgssltipvedgklalGtwqsiylveldgpreRkvvvq 114
                                       l++sl ip++dg+l lGtwqs+++veldgpr+R+v+++
  gi|242399629|ref|YP_002995054.1|  92 LNPSLAIPIKDGTLLLGTWQSVIFVELDGPRRRRVFIK 129
                                       ***********************************997 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 ?   14.5   0.0   3.5e-06     0.032      38      79 ..      31      72 ..       3      98 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.5e-06
                         TetR_C_10 38 keneqaflflethkdakyLdeeskelfeelmdfltdliekGk 79
                                       ++  a++f++  + a +++e+ + l+e++ +fl++l+ kGk
  gi|242399629|ref|YP_002995054.1| 31 IKEGLAVIFTQHTTTALFINENENGLLEDVKGFLQTLVPKGK 72
                                      4556799********************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.34s 00:00:00.82 Elapsed: 00:00:00.52
# Mc/sec: 771.91
//
Query:       gi|242399630|ref|YP_002995055.1|  [L=213]
Description: hypothetical protein TSIB_1655 [Thermococcus sibiricus MM 739]
Scores for complete 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   0.2    1.2e-30  106.9   0.2    1.0  1  DUF257    Pyrococcus protein of unknown function, DUF257


Domain annotation for each model (and alignments):
>> DUF257  Pyrococcus protein of unknown function, DUF257
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.9   0.2   6.7e-35   1.2e-30       1     200 [.      11     207 ..      11     212 .. 0.91

  Alignments for each domain:
  == domain 1  score: 106.9 bits;  conditional E-value: 6.7e-35
                            DUF257   1 elletlrpGetvLiEyssssvpevllyliakyskeknvPllvdDvlDtllivlkhlkllGldvpeesikviKigG.t 76 
                                       e+ ++l+pGe vL+Eyss   p +   +ia  +++k   llv D + t+ ++lk+ ++ G + + +++k i ig  +
  gi|242399630|ref|YP_002995055.1|  11 EFFDKLKPGEIVLVEYSSRDDPTLFVAEIARWADAKKYQLLVTDLFNTVELYLKRANFRGSHCELKKAKFIEIGFrK 87 
                                       799**********************************************************************9844 PP

                            DUF257  77 kevgnvvkkidfdkdpsiylskykravekvsveetvinlvlglerllllldnrrdlyklvksikkylgnknRkafyl 153
                                           n++  +  d++    +s+y+++++k++ e+ ++ l++g+er ++  ++++ +   v+ + ++lg+  R+afy+
  gi|242399630|ref|YP_002995055.1|  88 IPEVNMIGFLRGDRELPALVSEYRQIFDKMLSEKFTVVLLFGIERWFIKRNEKIPF---VNVLTSFLGDTPRIAFYI 161
                                       455699************************998888**********9876666655...589999************ PP

                            DUF257 154 inrnllesikPellplLEeiassvieiesekealivrilKslnldiv 200
                                       +nr++l+   P   +lLE+ a+++ie+++     i  i K+ln +++
  gi|242399630|ref|YP_002995055.1| 162 VNRDILNIASPGAFALLEDLATTIIEFKKGVRRKI-VITKALNRELE 207
                                       ***************************99885555.58899998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.34s 00:00:00.87 Elapsed: 00:00:00.53
# Mc/sec: 1204.78
//
Query:       gi|242399631|ref|YP_002995056.1|  [L=37]
Description: hypothetical protein TSIB_1656 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.33s 00:00:00.79 Elapsed: 00:00:00.51
# Mc/sec: 216.96
//
Query:       gi|242399632|ref|YP_002995057.1|  [L=148]
Description: transcription regulator, ArsR family [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0013   18.6   2.2     0.0024   17.8   0.6    2.2  2  HTH_11           HTH domain
     0.0017   18.0   0.1     0.0038   16.9   0.1    1.6  1  HrcA_DNA-bdg     Winged helix-turn-helix transcription repres
     0.0036   17.1   0.1      0.065   13.1   0.0    2.3  2  HTH_5            Bacterial regulatory protein, arsR family
     0.0061   16.9   0.2      0.013   15.9   0.0    1.6  2  Penicillinase_R  Penicillinase repressor
  ------ inclusion threshold ------
      0.025   14.9   0.5       0.17   12.3   0.1    2.1  2  Rrf2             Transcriptional regulator
      0.092   12.9   0.0       0.19   11.9   0.0    1.5  1  FUR              Ferric uptake regulator family
       0.13   12.2   0.8        0.3   11.1   0.8    1.6  1  DASH_Dad4        DASH complex subunit Dad4
        1.9    8.9   6.9       0.56   10.6   2.7    2.1  2  FlaC_arch        Flagella accessory protein C (FlaC)


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 ?   -0.9   0.0      0.73   1.6e+03       7      17 ..      15      26 ..       6      35 .. 0.52
   2 !   17.8   0.6   1.1e-06    0.0024       3      54 ..      67     124 ..      66     125 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.73
                            HTH_11  7 elLleargp.is 17
                                      ++L+++ +  ++
  gi|242399632|ref|YP_002995057.1| 15 KILRKTLNElMT 26
                                      444444444444 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 1.1e-06
                            HTH_11   3 lqilelLleargp.is..geeLAeeLnv.SrrtvrrdIkaLeelg..vpIesepgrGY 54 
                                       + i+++L++ ++  is   +eL+++ +  Sr tvr  I+ L++l    ++++e+g+GY
  gi|242399632|ref|YP_002995057.1|  67 REIVRILFDLKSAnISqiTQELKKRRGKaSRNTVREKIQYLSSLNvvEEVDGEKGKGY 124
                                       56888888888877773348888888877***************************** 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 !   16.9   0.1   1.7e-06    0.0038       5      63 ..      65     124 ..      63     132 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.7e-06
                      HrcA_DNA-bdg   5 vqkeilqaLielyrkkkravKgeeiAevlkrneGtvRNqlqsLkalgLvegvpGPkG.GY 63 
                                       + +ei++ L +l   + +++  e      k    tvR  +q L +l++ve v G kG GY
  gi|242399632|ref|YP_002995057.1|  65 IAREIVRILFDLKSANISQITQELKKRRGKASRNTVREKIQYLSSLNVVEEVDGEKGkGY 124
                                       56777777777777777666544444444556679*********************9777 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.12   2.7e+02      15      32 ..       4      21 ..       2      23 .. 0.85
   2 !   13.1   0.0   2.9e-05     0.065       1      34 [.      63      97 ..      63      97 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.12
                                      SEEHHHHHHHHTS-HHHH CS
                             HTH_5 15 elcvcelaeelglsqstv 32
                                      e+ v  l+ee+++ + t+
  gi|242399632|ref|YP_002995057.1|  4 EQDVEKLSEEVKILRKTL 21
                                      789999******998886 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 2.9e-05
                                      SHHHHHHHHHHTT.SSEEHHHHHHHHTS-HHHHHH CS
                             HTH_5  1 dptRlkILklLae.gelcvcelaeelglsqstvSh 34
                                      dp  ++I+++L + +++ +++++ el++ +++ S+
  gi|242399632|ref|YP_002995057.1| 63 DPIAREIVRILFDlKSANISQITQELKKRRGKASR 97
                                      7999************************9998775 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       2.6   5.8e+03      33      42 ..      16      25 ..       6      38 .. 0.50
   2 !   15.9   0.0   5.6e-06     0.013       6      57 ..      67     119 ..      64     129 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.6
                                      --HHHHHHHH CS
                   Penicillinase_R 33 laysTVktll 42
                                        ++T   l+
  gi|242399632|ref|YP_002995057.1| 16 ILRKTLNELM 25
                                      3333333333 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 5.6e-06
                                       SHHHHHHHHHS-EEHHHHHHT--GGG--.-HHHHHHHHHHHHHTTS-EEEEET CS
                   Penicillinase_R   6 aevmeilwekgeatvkevveeleeekel.aysTVktllrrLvkKgllsrekeg 57 
                                       +e+ +il ++++a+++++ +el++++   +++TV+  ++ L   +++++   +
  gi|242399632|ref|YP_002995057.1|  67 REIVRILFDLKSANISQITQELKKRRGKaSRNTVREKIQYLSSLNVVEEVDGE 119
                                       69***********************76659******99999999888876654 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.38   8.5e+02      27      47 ..       6      26 ..       2      30 .. 0.79
   2 ?   12.3   0.1   7.5e-05      0.17      12      70 ..      71     129 ..      66     132 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.38
                                      -HHHHHHHHTS-HHHHHHHHH CS
                              Rrf2 27 sseeiaerqnispsylekila 47
                                       +e+++e+++i ++ l  +++
  gi|242399632|ref|YP_002995057.1|  6 DVEKLSEEVKILRKTLNELMT 26
                                      678899999999998888886 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 7.5e-05
                                       HHHHHHHHSSTCC-B-HHHHHH.HHTS-HHHHHHHHHHHHHTTSEEEETTT-T.CEEESSH CS
                              Rrf2  12 hallyLakeeeeepvsseeiae.rqnispsylekilakLrkaglvksvrGkgG.GyrLakp 70 
                                       ++l +L++ + ++ + ++e+ + r + s++ ++  ++ L+  ++v+ v G +G Gy+L+k+
  gi|242399632|ref|YP_002995057.1|  71 RILFDLKSANISQ-I-TQELKKrRGKASRNTVREKIQYLSSLNVVEEVDGEKGkGYALKKE 129
                                       6666666666655.3.44555525689***********************99989***997 PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   8.3e-05      0.19      24      70 ..      79     124 ..      60     134 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.3e-05
                                       BEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEETTSEEEE CS
                               FUR  24 lsaeevykelkeedpeislaTVYrtLklleeaglvkelefedgesry 70 
                                        ++ ++++elk+++ + s  TV   ++ l+++++v+e++ e+g + y
  gi|242399632|ref|YP_002995057.1|  79 ANISQITQELKKRRGKASRNTVREKIQYLSSLNVVEEVDGEKG-KGY 124
                                       57789*********************************98855.445 PP

>> DASH_Dad4  DASH complex subunit Dad4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.8   0.00013       0.3      19      58 ..       6      42 ..       5      48 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00013
                         DASH_Dad4 19 nvekLnesvvelnkeleeinkkNknvelvsqlwenYqrnv 58
                                       vekL+e v+ l k+l+e  +   + elvs l enY + +
  gi|242399632|ref|YP_002995057.1|  6 DVEKLSEEVKILRKTLNELMT---SFELVSRLAENYLKLM 42
                                      69**************99986...699*********8765 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   2.7   0.00025      0.56       6      44 ..       4      45 ..       3      47 .. 0.84
   2 ?   -0.5   0.1      0.76   1.7e+03      15      27 ..      96     108 ..      80     118 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00025
                         FlaC_arch  6 Enklsklsteletvkkeneelsks...veelkenVkdllsLY 44
                                      E++++kls e++ ++k+++el +s   v +l en  +l+++Y
  gi|242399632|ref|YP_002995057.1|  4 EQDVEKLSEEVKILRKTLNELMTSfelVSRLAENYLKLMNIY 45
                                      899999999999999999999988444557888889999999 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.76
                         FlaC_arch  15 eletvkkeneels 27 
                                       + +tv+++++ ls
  gi|242399632|ref|YP_002995057.1|  96 SRNTVREKIQYLS 108
                                       5567777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1235  (0.0688828); expected 358.6 (0.02)
Passed bias filter:                      813  (0.0453455); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.63u 0.39s 00:00:01.02 Elapsed: 00:00:00.59
# Mc/sec: 755.23
//
Query:       gi|242399633|ref|YP_002995058.1|  [L=198]
Description: hypothetical protein TSIB_1658 [Thermococcus sibiricus MM 739]
Scores for complete 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   18.0   3.2      0.003   17.2   3.2    1.3  1  GCIP          Grap2 and cyclin-D-interacting
  ------ inclusion threshold ------
      0.064   12.8   1.0       0.13   11.8   1.1    1.4  1  CobU          Cobinamide kinase / cobinamide phosphate guanyl
      0.077   12.8   3.5      0.036   13.9   1.0    1.6  2  Bacillus_HBL  Bacillus haemolytic enterotoxin (HBL)
       0.15   12.4   4.5       0.39   11.0   0.1    3.0  4  GAT           GAT domain
       0.17   10.9   2.0       0.24   10.4   2.0    1.2  1  Atg14         Vacuolar sorting 38 and autophagy-related subun
       0.18   11.4  14.2        1.1    8.9   3.6    2.4  2  DUF4795       Domain of unknown function (DUF4795)
       0.31   11.6   5.9        6.8    7.2   5.0    2.4  2  Carbpep_Y_N   Carboxypeptidase Y pro-peptide
       0.31   10.7   0.8         13    5.3   0.0    2.2  2  TMP_2         Prophage tail length tape measure protein
       0.64    8.1   9.2       0.98    7.5   9.2    1.2  1  HSP70         Hsp70 protein
        2.3    9.1   9.8        7.4    7.4   6.0    3.0  2  Csm2_III-A    Csm2 Type III-A
        2.3    8.4   7.2        1.5    9.0   4.7    1.9  2  Fib_alpha     Fibrinogen alpha/beta chain family
        3.3    8.0  16.6        5.4    7.3  16.5    1.6  1  zf-C4H2       Zinc finger-containing protein


Domain annotation for each model (and alignments):
>> GCIP  Grap2 and cyclin-D-interacting
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   3.2     2e-06     0.003     136     254 ..      12     129 ..      10     134 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2e-06
                                       HHHHHHHHH....S------------------TTS--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--TT...-H CS
                              GCIP 136 eEmkelleeedeeedededdldddedeergnqdrklseeekevikavlkllkatvallkklsrsiteegkkdskeqv 212
                                       eEmk+  e+  e+e  ++ ++++  +e +++  +  seee+e+i++  ++l++++   +k  +s +  + ++  e +
  gi|242399633|ref|YP_002995058.1|  12 EEMKKKIEKAIESEAGAKKFIEETIKELTKELREAKSEEEIELIEKKIEMLEDMLYATSKKKESKE--DVEELGEVL 86 
                                       79999999988899999999999999999999999****************999999988754444..333333444 PP

                                       HH.HHHHHHHHHHHHHHHHHHHHHHSSS--HHHHHHHHHHHHH CS
                              GCIP 213 aq.ldklldlskeiseqvDdLaaslYPpqnisavkaqvekLas 254
                                        +  ++l +++++i   + +L  ++Y p +++++ ++v+++ +
  gi|242399633|ref|YP_002995058.1|  87 STvSEHLPKIMDSIFGPIKELLNDVYDPEKAEKFGKNVASFYK 129
                                       4458**************************9999999988765 PP

>> CobU  Cobinamide kinase / cobinamide phosphate guanyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   1.1   8.9e-05      0.13      35     116 ..      10      90 ..       6     100 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.9e-05
                              CobU  35 lDeemaeRiarHrerRpaeWetveep.ldlaealkeeek.kevvLvDcltlwltnllleeeaekveekleeeveell 109
                                       + eem+++i++  e+     + +ee+ ++l++ l+e+++ +e+ L++    +l+ +l++++++   ++ +e+veel 
  gi|242399633|ref|YP_002995058.1|  10 FGEEMKKKIEKAIESEAGAKKFIEETiKELTKELREAKSeEEIELIEKKIEMLEDMLYATSKK---KESKEDVEELG 83 
                                       578********999997777777775379*****9988879*****************98866...56666666666 PP

                              CobU 110 ealkelk 116
                                       e+l++++
  gi|242399633|ref|YP_002995058.1|  84 EVLSTVS 90 
                                       6655544 PP

>> Bacillus_HBL  Bacillus haemolytic enterotoxin (HBL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   1.0   2.4e-05     0.036      78     166 ..       4      99 ..       3     106 .. 0.74
   2 ?   -2.3   0.1       2.2   3.3e+03      92     112 ..     159     178 ..     138     189 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.4e-05
                      Bacillus_HBL  78 igYstkF.qsyyktlveav..dkkdkaellellekLqeeiqqnqke.....vkqlikeLkklklklakdsknFktdv 146
                                       +++++kF ++ +k++++a+  ++++k+ + e +++L +e+ + + e     ++++i++L+++  ++ k++ + k+dv
  gi|242399633|ref|YP_002995058.1|   4 MEFDEKFgEEMKKKIEKAIesEAGAKKFIEETIKELTKELREAKSEeeielIEKKIEMLEDMLYATSKKK-ESKEDV 79 
                                       6788999556788899999887888888999999999998765433122224566777777777666655.559*** PP

                      Bacillus_HBL 147 deltsilagdsgvisqlqne 166
                                       +el ++l++ s +++++   
  gi|242399633|ref|YP_002995058.1|  80 EELGEVLSTVSEHLPKIMDS 99 
                                       **********9999998665 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.2
                      Bacillus_HBL  92 veavdkkdkaellellekLqe 112
                                       v a   kdk + le+ ++Lq+
  gi|242399633|ref|YP_002995058.1| 159 VGAF-MKDKMGKLEGFKELQN 178
                                       3333.4555555555555554 PP

>> GAT  GAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1       1.3     2e+03      35      55 ..      13      33 ..      12      41 .. 0.60
   2 ?    1.6   0.1      0.23   3.4e+02      23      37 ..      33      47 ..      24      55 .. 0.85
   3 ?   11.0   0.1   0.00026      0.39       2      43 ..      57      99 ..      56     113 .. 0.71
   4 ?   -2.0   0.0       3.2   4.7e+03      10      36 ..     158     183 ..     149     188 .. 0.63

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.3
                               GAT 35 amqpriqklieetadeedlla 55
                                      +m+++i k ie+ a  ++ ++
  gi|242399633|ref|YP_002995058.1| 13 EMKKKIEKAIESEAGAKKFIE 33
                                      678888888887644443333 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.23
                               GAT 23 nellkeLyetckamq 37
                                      +e++keL +++++++
  gi|242399633|ref|YP_002995058.1| 33 EETIKELTKELREAK 47
                                      699999999999886 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00026
                               GAT  2 nnaklLsemLsstepd.eellenellkeLyetckamqpriqkl 43
                                      +++++L++mL +t+++ e+ ++ e l e  +t+ +  p+i++ 
  gi|242399633|ref|YP_002995058.1| 57 KKIEMLEDMLYATSKKkESKEDVEELGEVLSTVSEHLPKIMDS 99
                                      799**********855455556666666666666666666654 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 3.2
                               GAT  10 mLsstepdeellenellkeLyetckam 36 
                                       ++ ++ +d ++ + e +keL +  k+ 
  gi|242399633|ref|YP_002995058.1| 158 LVGAFMKD-KMGKLEGFKELQNLGKKK 183
                                       55555555.677888888887766655 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   2.0   0.00016      0.24      39     109 ..      12      78 ..       8     114 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00016
                             Atg14  39 eslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsd 109
                                       e++kkkieka+e++      ++k   ++ k  ++  + a+++e+++++++k++ l + + +++kk +++ d
  gi|242399633|ref|YP_002995058.1|  12 EEMKKKIEKAIESEA----GAKKFIEETIKELTKELREAKSEEEIELIEKKIEMLEDMLYATSKKKESKED 78 
                                       688999***999999....5677777777777788888888999999999999999999888888666554 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   3.6   0.00072       1.1     116     156 ..       8      50 ..       3      54 .. 0.78
   2 ?    7.2   5.6    0.0024       3.5      33     153 ..      48     163 ..      44     196 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00072
                           DUF4795 116 dtLqeelkekld.rlele.pLkeqleerlkelqkelqeameke 156
                                       ++  ee+k+k++ ++e e   k+++ee++kel kel+ea + e
  gi|242399633|ref|YP_002995058.1|   8 EKFGEEMKKKIEkAIESEaGAKKFIEETIKELTKELREAKSEE 50 
                                       56679999999985666525899************99876655 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0024
                           DUF4795  33 lekrledkekklealkkqieelekvkadkeeveeelaekadkeaLatkvsrdqfDeakkeLekmleelle..kleeq 107
                                        e+++e  ekk+e+l++ + ++ k+k+ ke+vee  ++ +  +    k+    +D+ +  +++ l+++++  k e+ 
  gi|242399633|ref|YP_002995058.1|  48 SEEEIELIEKKIEMLEDMLYATSKKKESKEDVEELGEVLSTVSEHLPKI----MDSIFGPIKELLNDVYDpeKAEKF 120
                                       5778888999**********************99988877777777777....899999999999888852278899 PP

                           DUF4795 108 eealkkaldtLqeelkekld.rlelepLkeqleerlkelqkelqeam 153
                                        +++ +++++L    +  +d  + +e  ke++e  ++++++ +   m
  gi|242399633|ref|YP_002995058.1| 121 GKNVASFYKELV---GAGMDpDKAFELTKEYME-SMNIIKTLVGAFM 163
                                       999999999998...777886555555556655.3444443333222 PP

>> Carbpep_Y_N  Carboxypeptidase Y pro-peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   5.0    0.0046       6.8      37      99 ..       3      66 ..       1      79 [. 0.65
   2 ?    4.7   0.2     0.028        43      38      84 ..      65     111 ..      54     132 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0046
                       Carbpep_Y_N 37 elnydtkklskllee.eekknnvfekiskvlneplkeltseakkiWsemelkf.Pdavsklkfkt 99
                                      e+++d +k+++ +++  ek  +  + ++k+++e +kelt+e++++ se e++   ++++ l+  +
  gi|242399633|ref|YP_002995058.1|  3 EMEFD-EKFGEEMKKkIEKAIESEAGAKKFIEETIKELTKELREAKSEEEIELiEKKIEMLEDML 66
                                      67777.66777776667788888899*****************9988755543133444444333 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.028
                       Carbpep_Y_N  38 lnydtkklsklleeeekknnvfekiskvlneplkeltseakkiWsem 84 
                                       + y+t+k++++ e+ e+ ++v++++s++l   ++++   +k++ +++
  gi|242399633|ref|YP_002995058.1|  65 MLYATSKKKESKEDVEELGEVLSTVSEHLPKIMDSIFGPIKELLNDV 111
                                       4456777777777799999**********999999988888877766 PP

>> TMP_2  Prophage tail length tape measure protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.3     0.029        43     148     182 ..      12      46 ..       8      69 .. 0.61
   2 ?    5.3   0.0     0.009        13     161     193 ..     117     149 ..     114     156 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.029
                             TMP_2 148 eqlervakaaaelekatGqsvdetakelaklakdP 182
                                       e++++ ++ a+e e+   + ++et+kel k   ++
  gi|242399633|ref|YP_002995058.1|  12 EEMKKKIEKAIESEAGAKKFIEETIKELTKELREA 46 
                                       55777777777777777777777777777644333 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.009
                             TMP_2 161 ekatGqsvdetakelaklakdPvkaaeklneql 193
                                       ++  G++v+  +kel  ++ dP ka e  +e +
  gi|242399633|ref|YP_002995058.1| 117 AEKFGKNVASFYKELVGAGMDPDKAFELTKEYM 149
                                       5678*********************97666655 PP

>> HSP70  Hsp70 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   9.2   0.00066      0.98     513     596 ..       7      92 ..       2      95 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00066
                                       HHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.GGGSTHHHHHHHHHHHHHHHCHTTSSC.HHHHHHHHHHHH CS
                             HSP70 513 daeesaeedkkkkeaieakneaeelvyslekkleee.aekvseaekekvesaieeLkeeleeee.keeieakteelk 587
                                       d++  +e  kk ++aie+++ a+++++++ k+l++e +e+ se+e e +e++ie L++ l +++ k+e ++++eel 
  gi|242399633|ref|YP_002995058.1|   7 DEKFGEEMKKKIEKAIESEAGAKKFIEETIKELTKElREAKSEEEIELIEKKIEMLEDMLYATSkKKESKEDVEELG 83 
                                       44445566677788999999999999999999999966677777779999999999999855443889999999999 PP

                                       HHHHHHHHH CS
                             HSP70 588 kvvekiaek 596
                                       +v++++ e+
  gi|242399633|ref|YP_002995058.1|  84 EVLSTVSEH 92 
                                       998887765 PP

>> Csm2_III-A  Csm2 Type III-A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   6.0     0.005       7.4      34      90 ..      35      91 ..       7     109 .. 0.74
   2 ?    1.4   0.0      0.38   5.7e+02      74     104 ..     121     151 ..     107     155 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.005
                                      HHHHHHHHHHHTHHHH.HHHTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--S CS
                        Csm2_III-A 34 evkrieekikkkkeee.seeilrklkllkpklaYaagreeavkelsevlkkaidkvkk 90
                                      ++k++ +++++ k+ee  e i++k+++l   ++Ya +++++ ke +e+l +++ +v++
  gi|242399633|ref|YP_002995058.1| 35 TIKELTKELREAKSEEeIELIEKKIEMLE-DMLYATSKKKESKEDVEELGEVLSTVSE 91
                                      68999999999999997888999999997.5677777765555555555555555544 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.38
                                       HHHHHHHHHHHHHH--SH.HHHHHHHHHHHH CS
                        Csm2_III-A  74 vkelsevlkkaidkvkkskekfkrfvdffEA 104
                                        k+ ++  k+++ +  ++++ f++ ++++E+
  gi|242399633|ref|YP_002995058.1| 121 GKNVASFYKELVGAGMDPDKAFELTKEYMES 151
                                       3555566778888888888999999999998 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 ?    9.0   4.7   0.00099       1.5      39     121 ..      13      96 ..       4     106 .. 0.70
   2 ?   -0.5   0.0      0.85   1.3e+03      97      97 ..     159     159 ..      91     194 .. 0.55

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00099
                                       CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH..HHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHH CS
                         Fib_alpha  39 kleneleeisnstkeaeelvkeikdslrekqkskkdn..dnvikksskeleeeilrlketidaqesnirvLqnvles 113
                                       ++++++e++ +s+  a++ ++e+ + l+++ +++k +   ++i+k  ++le ++l+   + ++  + +++L +vl++
  gi|242399633|ref|YP_002995058.1|  13 EMKKKIEKAIESEAGAKKFIEETIKELTKELREAKSEeeIELIEKKIEMLE-DMLYATSKKKESKEDVEELGEVLST 88 
                                       555666666666666666555555555555554444322678999999999.9999999999999999999999998 PP

                                       HHHHHHHH CS
                         Fib_alpha 114 neqkiqkL 121
                                        ++++ k+
  gi|242399633|ref|YP_002995058.1|  89 VSEHLPKI 96 
                                       88877666 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.85
                                       H CS
                         Fib_alpha  97 i 97 
                                       +
  gi|242399633|ref|YP_002995058.1| 159 V 159
                                       1 PP

>> zf-C4H2  Zinc finger-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3  16.5    0.0036       5.4      13     102 ..      12      99 ..       8     196 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0036
                           zf-C4H2  13 eklknklakevealekeekcleeykkelelLeqEkmaHveeLrlIhaDinalEsvikeaeeekekslekakklyeey 89 
                                       e++k+k+ k++e+    +k++ee+ kel++  +E ++  ee+ lI++ i+ lE+++  +  +k++s+e +++l e +
  gi|242399633|ref|YP_002995058.1|  12 EEMKKKIEKAIESEAGAKKFIEETIKELTKELREAKS-EEEIELIEKKIEMLEDMLYATS-KKKESKEDVEELGEVL 86 
                                       6799*******************99888765555444.599*************998665.4556677777777777 PP

                           zf-C4H2  90 kklkeevnelrse 102
                                       + + e++ ++  +
  gi|242399633|ref|YP_002995058.1|  87 STVSEHLPKIMDS 99 
                                       7777777766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2809  (0.156674); expected 358.6 (0.02)
Passed bias filter:                     1004  (0.0559987); expected 358.6 (0.02)
Passed Vit filter:                       125  (0.00697194); 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: 0.74u 0.39s 00:00:01.12 Elapsed: 00:00:00.56
# Mc/sec: 1061.86
//
Query:       gi|242399634|ref|YP_002995059.1|  [L=188]
Description: GTP-binding protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.2e-22   78.4   0.1    6.8e-22   77.7   0.1    1.3  1  MMR_HSR1      50S ribosome-binding GTPase
    6.8e-13   48.4   0.9    1.3e-12   47.5   0.9    1.4  1  FeoB_N        Ferrous iron transport protein B
    3.8e-10   39.6   0.3    1.2e-06   28.2   0.0    2.3  2  GTP_EFTU      Elongation factor Tu GTP binding domain
    2.8e-08   34.0   0.3    2.9e-05   24.2   0.2    2.5  3  Dynamin_N     Dynamin family
    1.9e-07   31.1   3.1     0.0071   16.3   0.2    2.6  2  RsgA_GTPase   RsgA GTPase
    4.9e-07   29.5   0.5    6.7e-06   25.8   0.0    2.0  2  cobW          CobW/HypB/UreG, nucleotide-binding domain
    1.3e-06   28.0   2.1      0.024   14.1   0.2    2.2  2  Arf           ADP-ribosylation factor family
    2.4e-06   27.4   0.7     0.0041   16.9   0.0    2.2  2  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
    5.1e-06   26.7   0.2     0.0029   17.8   0.1    2.3  2  Roc           Ras of Complex, Roc, domain of DAPkinase
    2.2e-05   24.4   0.4    3.7e-05   23.7   0.4    1.4  1  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
     0.0001   21.7   3.2     0.0024   17.2   0.0    2.4  2  Septin        Septin
    0.00048   19.5   0.0    0.00088   18.6   0.0    1.4  1  GBP           Guanylate-binding protein, N-terminal domain
     0.0006   19.4   0.3     0.0055   16.3   0.3    2.2  1  Ras           Ras family
     0.0017   18.2   0.1      0.044   13.6   0.0    2.3  2  ATP_bind_1    Conserved hypothetical ATP binding protein
  ------ inclusion threshold ------
      0.012   15.0   0.1      0.019   14.3   0.1    1.5  1  AIG1          AIG1 family
      0.015   15.6   0.2      0.031   14.5   0.2    1.6  1  AAA_28        AAA domain
      0.022   15.0   0.3      0.091   13.0   0.3    1.9  1  AAA_22        AAA domain
      0.036   13.4   0.8      0.049   13.0   0.8    1.5  1  Gtr1_RagA     Gtr1/RagA G protein conserved region
      0.042   14.4   1.5      0.072   13.6   1.5    1.7  1  ABC_tran      ABC transporter
      0.085   12.6   0.1       0.17   11.7   0.1    1.4  1  AAA_29        P-loop containing region of AAA domain
       0.11   12.2   2.3       0.29   10.9   0.3    2.5  2  NOG1          Nucleolar GTP-binding protein 1 (NOG1)


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 !   77.7   0.1     8e-25   6.8e-22       1     114 []       3     136 ..       3     136 .. 0.69

  Alignments for each domain:
  == domain 1  score: 77.7 bits;  conditional E-value: 8e-25
                                       EEEEEESTTSSHHHHHHHHHTS.TEEESSSTTSSSSEEEEEEE...........ETT.EEEEEEECGGCSS...... CS
                          MMR_HSR1   1 evaivGrpNvGKStLinaltge.kaivsdkpgtTrdinegrvk...........lkg.keielvDtpGlie...... 58 
                                       +vai+G  NvGKStL+nal+g+ +++++ +pgtT+ i+++ +            ++g +e++l+Dt+Gl++      
  gi|242399634|ref|YP_002995059.1|   3 KVAIIGAENVGKSTLMNALLGKkVSETQPIPGTTKGIIKRAFGtvkipktmknpFGGaDELVLIDTAGLYDpqyelr 79 
                                       69*******************9678************99987654465555454334577********974333233 PP

                                       HHHHHH.HHHHHHHHHHCTSEEEEEEETT...TTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                          MMR_HSR1  59 gaseek.glgkaflaleeadlillvvdas...eeklkpldeeleelleeakkplilvlnk 114
                                       g+  ++ ++++ + ++ +ad+i+ ++da+   ++++++l +++ +++   +kp+i+v+nk
  gi|242399634|ref|YP_002995059.1|  80 GKVLSEeKFKELLNEIASADVIINMIDAQyglHRGMEKL-HHILKFR--YEKPIIVVVNK 136
                                       2222221333333345559********885442334333.4444554..78********8 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.5   0.9   1.6e-15   1.3e-12       1     155 [.       2     177 ..       2     178 .. 0.83

  Alignments for each domain:
  == domain 1  score: 47.5 bits;  conditional E-value: 1.6e-15
                                       EEEEEEESTTSSHHHHHHHHHTTS.EEEEESTTSS...SEEEEEEEEE.........TTEEEEEEE----....SSS CS
                            FeoB_N   1 itvalvGnpnvGkttlfnaltgak.qkvgNwpGvt...vekkegklkl.........kgkeveivDlPGi....Ysl 60 
                                       i+va++G  nvGk+tl+nal g+k ++    pG+t   ++++ g++k+           +e+ ++D  G     Y+l
  gi|242399634|ref|YP_002995059.1|   2 IKVAIIGAENVGKSTLMNALLGKKvSETQPIPGTTkgiIKRAFGTVKIpktmknpfgGADELVLIDTAGLydpqYEL 78 
                                       589*******************994578889***955556667777768888777755699********94444567 PP

                                       SSSSHHHHHHHHHHHC.TSSSEEEEEEEGG.GHHHHHHHHHHHHHTT..SSEEEEEETHHHHHHTTEEE-HHHHHHH CS
                            FeoB_N  61 sayseeekvardflle.eepdvvvnvvdat.nlernLyLtlqllelg..vpvvlalnmideaekkgieidlkkLsek 133
                                             e+  +++l e  ++dv++n++da+  l+r +  +  +l ++  +p+++++n+id + k+++e   + ++++
  gi|242399634|ref|YP_002995059.1|  79 RGKVLSEEKFKELLNEiASADVIINMIDAQyGLHRGMEKLHHILKFRyeKPIIVVVNKIDLIPKEKVEELREIIKKR 155
                                       76666666667777642789*********835*****99999998754499************************** PP

                                       HTS-EEEEBTTTTBTHHHHHHH CS
                            FeoB_N 134 Lgvpvvktsakkkegieellka 155
                                       L+ + + +s  + eg++ell++
  gi|242399634|ref|YP_002995059.1| 156 LEQEPIMLSLVTYEGFNELLEK 177
                                       ******************9986 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 !    9.4   0.1    0.0008      0.69       4      27 ..       2      25 ..       1      40 [. 0.85
   2 !   28.2   0.0   1.5e-09   1.2e-06      85     188 ..      89     178 ..      86     185 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0008
                                      EEEEEEESTTSSHHHHHHHHHHHT CS
                          GTP_EFTU  4 rnigiighvDhGKtTLtdrLlykt 27
                                      ++++iig  + GK+TL+ +Ll k+
  gi|242399634|ref|YP_002995059.1|  2 IKVAIIGAENVGKSTLMNALLGKK 25
                                      6899****************9654 PP

  == domain 2  score: 28.2 bits;  conditional E-value: 1.5e-09
                                       HHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHH.HTTTEEEEEEESCGST.HHHHHHHHHHHHHHHHHHHHHHHH CS
                          GTP_EFTU  85 kevirglrvlDgavlvvdaveGvepqteevlrlal.kegvpiivfiNKmDrl.kaelkeiveevkqklsrkeeklek 159
                                       ke  + ++ +D+ + ++da+ G     e++ ++++ +++ piiv++NK+D + k++++e+ e +k++l+++      
  gi|242399634|ref|YP_002995059.1|  89 KELLNEIASADVIINMIDAQYGLHRGMEKLHHILKfRYEKPIIVVVNKIDLIpKEKVEELREIIKKRLEQE------ 159
                                       566777899*************9999988776664277888***********9999999999999999433...... PP

                                       HHHTTTTTEEEEEEBTTTTBTHHHHHHHH CS
                          GTP_EFTU 160 ygekgekevpvvfgSalkgegvktlleal 188
                                                  ++ S ++ eg+++lle l
  gi|242399634|ref|YP_002995059.1| 160 ----------PIMLSLVTYEGFNELLEKL 178
                                       ..........3444445555555554444 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.2   3.4e-08   2.9e-05       1      34 [.       4      37 ..       4      48 .. 0.93
   2 !    7.3   0.0    0.0053       4.5      99     167 ..      59     136 ..      44     137 .. 0.79
   3 ?   -2.2   0.0       4.3   3.6e+03      65     132 ..     145     162 ..     141     170 .. 0.51

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 3.4e-08
                                      EEEEEBTTTTHHHHHHHHHTS--S---SSS---S CS
                         Dynamin_N  1 iavvGsqSsGKSSvlnaLlgedilprgpnptTrr 34
                                      +a++G+ + GKS+++naLlg+++  ++p+p T +
  gi|242399634|ref|YP_002995059.1|  4 VAIIGAENVGKSTLMNALLGKKVSETQPIPGTTK 37
                                      79***************************99965 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0053
                                       TS-SEEEEE---B-SSSGTTS.........HHHHHHHSTTEEEEEEEETTS-CCC-CHHHHHHHHSTTBTT.EEEEE CS
                         Dynamin_N  99 lvkgltlvDlPGldsvnkrdq.........elvkeyikkadiilavtsanhdlsnsealflarevdpkgkr.tivvl 165
                                         ++l+l+D+ Gl + + +           + + + i +ad+i+ + +a+  l     ++l++ ++ + ++ +ivv+
  gi|242399634|ref|YP_002995059.1|  59 GADELVLIDTAGLYDPQYELRgkvlseekfKELLNEIASADVIINMIDAQYGLH-RGMEKLHHILKFRYEKpIIVVV 134
                                       56789**********99999899****99988888899***********99888.5566666666665555466666 PP

                                       E- CS
                         Dynamin_N 166 tk 167
                                       +k
  gi|242399634|ref|YP_002995059.1| 135 NK 136
                                       66 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 4.3
                                       CHHHHHHHHHHHHHHHTSSSS--SS-EEEEEEETTS-SEEEEE---B-SSSGTTSHHHHHHHSTTEEE CS
                         Dynamin_N  65 fsevreeieketekiagankgiskkvillkilsllvkgltlvDlPGldsvnkrdqelvkeyikkadii 132
                                       ++e+re                                                   +k+ ++++ i+
  gi|242399634|ref|YP_002995059.1| 145 VEELREI--------------------------------------------------IKKRLEQEPIM 162
                                       4444444..................................................44444444444 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.2   8.4e-06    0.0071     103     132 ..       5      34 ..       3      77 .. 0.80
   2 !   15.0   0.2     2e-05     0.017      47      97 ..     128     178 ..      94     183 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 8.4e-06
                                       EEECSTTSSHHHHHHHHCTT-----S---- CS
                       RsgA_GTPase 103 vlvGqSGvGKStLinallpelelktgevse 132
                                       +++G   vGKStL+nall+++  +t+ +  
  gi|242399634|ref|YP_002995059.1|   5 AIIGAENVGKSTLMNALLGKKVSETQPIPG 34 
                                       6899999*************9999998865 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 2e-05
                                       -EEEEEEE-GGG--HHHHHHHHHHHH.HHTTSEEEE--TTTHTTHHHHHHHC CS
                       RsgA_GTPase  47 iepvivlnKiDlleeeeeleelkeel.ealgyevllvsaktkegleelkell 97 
                                        ++++v+nKiDl+ +e+ +eel+e + ++l+ e++++s  t eg++el e+l
  gi|242399634|ref|YP_002995059.1| 128 KPIIVVVNKIDLIPKEK-VEELREIIkKRLEQEPIMLSLVTYEGFNELLEKL 178
                                       467899***********.77777665167999**************999877 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1      0.13   1.1e+02      11      24 ..      12      25 ..       3      53 .. 0.76
   2 !   25.8   0.0   7.9e-09   6.7e-06      84     171 ..      62     157 ..      42     162 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.13
                                      CCHHHHHHHHH.CT- CS
                              cobW 11 sGKTtLlnhll.enr 24
                                       GK+tL+n+ll + +
  gi|242399634|ref|YP_002995059.1| 12 VGKSTLMNALLgK-K 25
                                      6*********952.3 PP

  == domain 2  score: 25.8 bits;  conditional E-value: 7.9e-09
                                       SEEEEEECTTTTHHHH....HTT....SHHHHHCCCECEEEEEEETTTH..CCHCCHHHHHHHHHHTSSEEEEE-HH CS
                              cobW  84 dviliEttGlaePapv....aft....eeelksdltldavvavvDaknl.eaeeekieekaedqlaaadllvlnKtD 151
                                       +++li t Gl +P+      +++    +e l++ + +d+++ ++Da+   ++  ek ++ ++   ++  ++v+nK+D
  gi|242399634|ref|YP_002995059.1|  62 ELVLIDTAGLYDPQYElrgkVLSeekfKELLNEIASADVIINMIDAQYGlHRGMEKLHHILKFRYEKPIIVVVNKID 138
                                       6799*********98767654446776777788999**********65467888999******************** PP

                                       HHCHC..HHHHHHHHHHHHT CS
                              cobW 152 lldeeallekleerlrqlnp 171
                                       l+++e+ +e+l+e++++  +
  gi|242399634|ref|YP_002995059.1| 139 LIPKEK-VEELREIIKKRLE 157
                                       *****5.5999998887554 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.1   3.4e-05     0.029      15      49 ..       2      36 ..       1      49 [. 0.89
   2 !   14.1   0.2   2.8e-05     0.024      82     172 ..      98     179 ..      85     182 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.4e-05
                                      EEEEEEESTTSSHHHHHHHHHHSSCEECSSSSSEE CS
                               Arf 15 lrilllGLDnaGKtTilkklkleelvttvPTigfn 49
                                      +++ ++G +n GK+T+++ l  +++++t+P  g +
  gi|242399634|ref|YP_002995059.1|  2 IKVAIIGAENVGKSTLMNALLGKKVSETQPIPGTT 36
                                      6899**************************88766 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 2.8e-05
                                       ESEEEEEEETT-CTTHHHHHHHHHHHCTSGCCTTSEEEEEEE-TTSTTSS-HHHHHHHTTGGGSSSSSSEEEEEEBT CS
                               Arf  82 tdavifvvDsadreRleeakeeLkalleeeelkevallvlaNKqDlpealseeelrellgleelkgkrkleiqkcsa 158
                                        d++i ++D++    l+   e+L+++l+ +   e +++v+ NK+Dl    + eelre+++ ++l+ +++   ++ s 
  gi|242399634|ref|YP_002995059.1|  98 ADVIINMIDAQ--YGLHRGMEKLHHILKFRY--EKPIIVVVNKIDLIPKEKVEELREIIK-KRLE-QEP---IMLSL 165
                                       57777777765..357778888999998764..56899999********99999999876.4566.455...46688 PP

                                       TTTBTHHHHHHHHH CS
                               Arf 159 vkgeglkeglewls 172
                                       v+ eg++e le+l+
  gi|242399634|ref|YP_002995059.1| 166 VTYEGFNELLEKLV 179
                                       99999999999987 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   0.1    0.0011      0.98       1      27 [.       1      27 [.       1      39 [. 0.86
   2 !   16.9   0.0   4.8e-06    0.0041      49     141 ..      84     178 ..      65     180 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0011
                         PduV-EutP  1 mkkilliGkvgsGKttLtqalkgeelk 27
                                      m k+ +iG+ ++GK tL++al g++++
  gi|242399634|ref|YP_002995059.1|  1 MIKVAIIGAENVGKSTLMNALLGKKVS 27
                                      67999****************999875 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 4.8e-06
                         PduV-EutP  49 enrklysalivtsaeadvialvqdateeesvfppgfasvf....nkeviGiitkidlaedeenieaveelLksaGae 121
                                        ++k+ + l+ + a+advi  + da+   +   +++ +++    +k++i ++ kidl   +e++e  +e +k+   +
  gi|242399634|ref|YP_002995059.1|  84 SEEKFKELLNEI-ASADVIINMIDAQYGLHRGMEKLHHILkfryEKPIIVVVNKIDLI-PKEKVEELREIIKKRLEQ 158
                                       555555555444.56888887777776555544444444311228*************.8999************** PP

                         PduV-EutP 122 kifevsavekegieellkyl 141
                                       + + +s v+ eg++ell+ l
  gi|242399634|ref|YP_002995059.1| 159 EPIMLSLVTYEGFNELLEKL 178
                                       ****************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 !   17.8   0.1   3.4e-06    0.0029       1      29 [.       3      31 ..       3      73 .. 0.76
   2 !    7.1   0.0    0.0072       6.1      80     120 .]      98     139 ..      84     139 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.4e-06
                                      EEEEESSTTSSHHHHHHCHCT-CCC-EEE CS
                               Roc  1 KvvlvGdsgvGKtsllkrfvedkfsekek 29
                                      Kv ++G ++vGK++l++ ++ +k+se++ 
  gi|242399634|ref|YP_002995059.1|  3 KVAIIGAENVGKSTLMNALLGKKVSETQP 31
                                      89*********************998764 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0072
                                       SCEEEEEEEGHHH.HCHHHHHHHHHHHCSSS-EEEEEE-TTT CS
                               Roc  80 aalailvydsrss.enlkeWlkelkkvagkspvilvgnkiDl 120
                                       a+++i ++d++   ++  e l+++ k + ++p+i+v+nkiDl
  gi|242399634|ref|YP_002995059.1|  98 ADVIINMIDAQYGlHRGMEKLHHILKFRYEKPIIVVVNKIDL 139
                                       55666666655432455567788889999***********95 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 !   23.7   0.4   4.3e-08   3.7e-05      15     100 ..      83     178 ..      75     183 .. 0.74

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 4.3e-08
                      MMR_HSR1_Xtn  15 ldeetvkkilkeykihnaevlir.edvt......vDdlidviegnrvYipclyvlNKiDlisleeldelare..... 79 
                                       l+ee+ k++l+e  i +a+v+i+  d++      +++l  ++ + r  +p ++v+NKiDli +e+++el++      
  gi|242399634|ref|YP_002995059.1|  83 LSEEKFKELLNE--IASADVIINmIDAQyglhrgMEKLHHIL-KFRYEKPIIVVVNKIDLIPKEKVEELREIikkrl 156
                                       566667777765..7788888874344455555555555444.334448999****************999556777 PP

                      MMR_HSR1_Xtn  80 .pnsvviSaekelnldeLkeki 100
                                        ++ +++S  +  +++eL+ek+
  gi|242399634|ref|YP_002995059.1| 157 eQEPIMLSLVTYEGFNELLEKL 178
                                       6799**************9986 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   2.8e-06    0.0024       6      92 ..       3     108 ..       1     120 [. 0.59
   2 ?    4.2   1.2     0.026        22     143     177 ..     129     163 ..     113     177 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.8e-06
                                       EEEEEEBTTSSCCCCCCTTSSSS----.....................--------------S-E.EEEEEEEETTC CS
                            Septin   6 tlmvvGesglGkttlintlfetdliee.....................ekleeasekkkktveik.kkkvvieedgv 60 
                                        + ++G++ +Gk+tl+n+l+ +++ e+                     ++++++   +    e+    ++ + + + 
  gi|242399634|ref|YP_002995059.1|   3 KVAIIGAENVGKSTLMNALLGKKVSETqpipgttkgiikrafgtvkipKTMKNPFGGA---DELVlIDTAGLYDPQY 76 
                                       6789**********************95555555555555554442222222222222...2222133344444455 PP

                                       EEEEEEEE---BSSSSSHHCCCHHHHHHHHHH CS
                            Septin  61 klnltviDtpgfGdavdnskswepiveyideq 92 
                                       +l+  v+  + f + ++   s ++i+++id q
  gi|242399634|ref|YP_002995059.1|  77 ELRGKVLSEEKFKELLNEIASADVIINMIDAQ 108
                                       55555555555555555555555555555555 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.026
                                       -EEEEESSGGGS-HHHHHHHHHHHHHHHHHTT--- CS
                            Septin 143 nliPviaKaDtltkeElkefKkkireeleeeeiki 177
                                        +i v+ K D + ke ++e+++ i+++le+e i +
  gi|242399634|ref|YP_002995059.1| 129 PIIVVVNKIDLIPKEKVEELREIIKKRLEQEPIML 163
                                       5899**************************98865 PP

>> GBP  Guanylate-binding protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0     1e-06   0.00088      22      87 ..       2      74 ..       1      84 [. 0.78

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1e-06
                                      EEEEEEEBTTSSHHHHHHHHHTBSSSSESSSCSSST-SSEEEESCE.........-SSSTCEEEEEEEEECBTTT CS
                               GBP 22 vvvaivGlyRkGksfLlnklarkkkGFslrstvesetkGiliWcep.........hpkkekvalvLlDteGlgDv 87
                                      + vai+G+   Gks L+n l++kk   s    +   tkGi   +           +p +    lvL+Dt Gl D 
  gi|242399634|ref|YP_002995059.1|  2 IKVAIIGAENVGKSTLMNALLGKKV--SETQPIPGTTKGIIKRAFGtvkipktmkNPFGGADELVLIDTAGLYDP 74
                                      679*******************885..566677778888865433233566766788888999**********94 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.3   6.5e-06    0.0055       1     124 [.       3     147 ..       3     182 .. 0.63

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 6.5e-06
                                       EEEEEESTTSSHHHHHHHHHHSSCSSSCT...TTSSEE.EEEEEEEET.......TEEEEEEEEEETTSGG.GHHHH CS
                               Ras   1 KlvlvGdsavGKtslllrfvkdkFkeeye...sTigvd.fytkeievd.......gkevkleiwDTAGqee.fkslr 65 
                                       K+ ++G ++vGK++l++    +k +e++    +T g+      ++++        g   +l + DTAG  +   +lr
  gi|242399634|ref|YP_002995059.1|   3 KVAIIGAENVGKSTLMNALLGKKVSETQPipgTTKGIIkRAFGTVKIPktmknpfGGADELVLIDTAGLYDpQYELR 79 
                                       899*****************9999887532223444322333333333556677888889********533133566 PP

                                       HHHHTTESEEEEEEETTBHHHHHTHHHHHHHHHHHST.........TTSEEEEEEETTTGGGG-SS-H CS
                               Ras  66 elyyrdaegillvyditsresfenvkkwveeikrvae.........envpivLvGnKvDleekravst 124
                                        +++++ +   l+ +i s++   n+ +    ++r +e          + pi++v nK+Dl  k++v++
  gi|242399634|ref|YP_002995059.1|  80 GKVLSEEKFKELLNEIASADVIINMIDAQYGLHRGMEklhhilkfrYEKPIIVVVNKIDLIPKEKVEE 147
                                       6666666666666666665555544333222222222222233355458999999****999998875 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      0.12   1.1e+02       1      16 [.       6      21 ..       6      30 .. 0.89
   2 !   13.6   0.0   5.1e-05     0.044      91     181 ..      61     149 ..      44     184 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.12
                        ATP_bind_1  1 vvGpaGsGKttfvgal 16
                                      ++G   +GK+t+++al
  gi|242399634|ref|YP_002995059.1|  6 IIGAENVGKSTLMNAL 21
                                      689999*******998 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 5.1e-05
                        ATP_bind_1  91 ddyllfDtPG....QielfthseslakiveeLes.efalvvvyLvDsqrltd.ptkfisgllsalsamlrlelPhvv 161
                                       d+++l+Dt G    Q el   + s  k+ e L++   a v+++++D+q+     ++ +++        +r+e P +v
  gi|242399634|ref|YP_002995059.1|  61 DELVLIDTAGlydpQYELRGKVLSEEKFKELLNEiASADVIINMIDAQYGLHrGMEKLHH-----ILKFRYEKPIIV 132
                                       578899998888889999988888889999999999999999999999966635555555.....56799******* PP

                        ATP_bind_1 162 vlnkfDllkeklekeleffe 181
                                       v+nk+Dl+ ++   ++e + 
  gi|242399634|ref|YP_002995059.1| 133 VVNKIDLIPKE---KVEELR 149
                                       *******9854...222222 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   2.3e-05     0.019       3      88 ..       4     102 ..       2     158 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.3e-05
                                       EEEESSTTSSHHHHHHHHHTS--SS--...TTTS---SS-EEEEEEETT........EEEEEEE--SCCCTTCC..H CS
                              AIG1   3 ivlvGktgnGkSaTgNsilgkkaFesk...lsaqsvtkkcqkksrtwdg........kkinViDTPglfdlsvs..a 66 
                                       + ++G   +GkS+  N++lgkk+ e++    ++++++k+    ++ ++          +++ iDT gl d +++   
  gi|242399634|ref|YP_002995059.1|   4 VAIIGAENVGKSTLMNALLGKKVSETQpipGTTKGIIKRAFGTVKIPKTmknpfggaDELVLIDTAGLYDPQYElrG 80 
                                       6789*******************66552223344444443222221111112233458999*******999985325 PP

                                       HCHHHHHHHHHHHCTT-ESEEE CS
                              AIG1  67 dkiskeivrclllseegihall 88 
                                       + +s+e  + ll    + ++++
  gi|242399634|ref|YP_002995059.1|  81 KVLSEEKFKELLNEIASADVII 102
                                       5566666666665556666665 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.2   3.6e-05     0.031       1      21 [.       3      23 ..       3      52 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.6e-05
                            AAA_28  1 kivitGgestGKTtlleaLaa 21
                                      k++i+G+e  GK+tl++aL  
  gi|242399634|ref|YP_002995059.1|  3 KVAIIGAENVGKSTLMNALLG 23
                                      79****************974 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.3   0.00011     0.091       9     133 ..       5     171 ..       4     175 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00011
                            AAA_22   9 vvtGesGtGKTtllrrlleqldeeakaee.........................erpevvfvtlpsst.sskdllre 59 
                                       +++G   +GK+tl++ ll +++ e ++                             +e+v+++ +++   + +l+ +
  gi|242399634|ref|YP_002995059.1|   5 AIIGAENVGKSTLMNALLGKKVSETQPIPgttkgiikrafgtvkipktmknpfgGADELVLIDTAGLYdPQYELRGK 81 
                                       79******************988877777999999997777777777777777744455555555555444444444 PP

                            AAA_22  60 llra..lglelka............erlsseellealeqalrarav.ielliiDEaqhlrseealeeLrsllnl..s 119
                                       +l++  +++ l++            +   +++ +e+l++ l+ r+  + ++++  ++ + ++e +eeLr++ +   +
  gi|242399634|ref|YP_002995059.1|  82 VLSEekFKELLNEiasadviinmidAQYGLHRGMEKLHHILKFRYEkPIIVVVNKIDLI-PKEKVEELREIIKKrlE 157
                                       44321133333336666677777777777777788888888777778888889999999.88888888777665555 PP

                            AAA_22 120 rkgvqliLvGtpel 133
                                       + ++ l Lv  +++
  gi|242399634|ref|YP_002995059.1| 158 QEPIMLSLVTYEGF 171
                                       77776666655555 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 ?   13.0   0.8   5.7e-05     0.049      76     143 ..      97     159 ..       3     172 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.7e-05
                         Gtr1_RagA  76 nvgvliyVfDvesreleedletlkeilealrqyspeakvfvlihKmDliqedereeifeerkeeiree 143
                                       + +v+i ++D++       l++  e l+++ ++  e  + v ++K+Dli +++ ee+ e +k+++++e
  gi|242399634|ref|YP_002995059.1|  97 SADVIINMIDAQ-----YGLHRGMEKLHHILKFRYEKPIIVVVNKIDLIPKEKVEELREIIKKRLEQE 159
                                       345889999998.....45555566667777778888999****************999999998876 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   1.5   8.4e-05     0.072      13      38 ..       3      28 ..       2     165 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.4e-05
                                      EEEEEESTTSSHHHHHHHHTTSS--S CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 13 kvaivGenGaGKStLlkllagllkpt 38
                                      kvai+G    GKStL+++l+g+   +
  gi|242399634|ref|YP_002995059.1|  3 KVAIIGAENVGKSTLMNALLGKKVSE 28
                                      69******************986553 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1    0.0002      0.17      25      42 ..       4      21 ..       2      24 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0002
                            AAA_29 25 tlltGpsGsGKSTllDAi 42
                                      + ++G+  +GKSTl+ A+
  gi|242399634|ref|YP_002995059.1|  4 VAIIGAENVGKSTLMNAL 21
                                      579************997 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 ?   10.9   0.3   0.00034      0.29      41      58 .]     121     138 ..      92     138 .. 0.73
   2 ?    0.1   0.1       0.8   6.9e+02      36      51 ..     147     162 ..     143     166 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00034
                              NOG1  41 ikelfankpvivvlnKiD 58 
                                       i +   +kp+ivv+nKiD
  gi|242399634|ref|YP_002995059.1| 121 ILKFRYEKPIIVVVNKID 138
                                       33333459*********9 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.8
                              NOG1  36 sLleeikelfankpvi 51 
                                       +L+e ik++++++p++
  gi|242399634|ref|YP_002995059.1| 147 ELREIIKKRLEQEPIM 162
                                       69999*****999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       824  (0.0459591); expected 358.6 (0.02)
Passed bias filter:                      606  (0.0338); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); 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: 0.68u 0.38s 00:00:01.06 Elapsed: 00:00:00.56
# Mc/sec: 1002.04
//
Query:       gi|242399635|ref|YP_002995060.1|  [L=153]
Description: GTP-binding protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.14   12.2   1.8       0.34   10.9   0.2    2.2  2  KOW       KOW motif


Domain annotation for each model (and alignments):
>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.2   1.9e-05      0.34       8      29 ..      70      91 ..      68      93 .. 0.89
   2 ?    0.1   0.1     0.047   8.5e+02       2       7 ..     123     128 ..     122     134 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 1.9e-05
                                      SSSTTTTCEEEEEEEETTTTEE CS
                               KOW  8 vsGphkGktGkVvkvdqhkvrV 29
                                       +G ++G+  +++ + ++kv+V
  gi|242399635|ref|YP_002995060.1| 70 KRGEFRGRNVMIEGIVEDKVTV 91
                                      58*****************777 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.047
                                       TSEEEE CS
                               KOW   2 GdhVkV 7  
                                       Gd+VkV
  gi|242399635|ref|YP_002995060.1| 123 GDIVKV 128
                                       777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.32s 00:00:00.81 Elapsed: 00:00:00.51
# Mc/sec: 904.13
//
Query:       gi|242399636|ref|YP_002995061.1|  [L=179]
Description: Metal-dependent phosphohydrolase, HD superfamily [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-26   92.3   0.1    3.6e-26   92.1   0.1    1.1  1  HD_3      HD domain
    1.4e-14   54.3   0.5    3.9e-14   52.8   0.5    1.7  1  HD_2      HD containing hydrolase-like enzyme
    2.5e-06   27.7   0.6    3.8e-05   23.9   0.6    2.2  1  HD        HD domain
  ------ inclusion threshold ------
      0.093   13.4   0.1       0.13   13.0   0.1    1.3  1  HOCHOB    Homeobox-cysteine loop-homeobox


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 !   92.1   0.1     8e-30   3.6e-26       2     150 ..       9     155 ..       8     174 .. 0.83

  Alignments for each domain:
  == domain 1  score: 92.1 bits;  conditional E-value: 8e-30
                              HD_3   2 ekLKfqkRqgwlqtgrvreesvaeHmwrvalmalllseelk...ekvdiarvikmfLiHDlvEiltgDiispdelak 75 
                                       +kLK+ +R gwl  g+ ++esva+H ++v l++l+l++el     +++++r++k +++HDl+E+   D++  d+   
  gi|242399636|ref|YP_002995061.1|   9 GKLKKLPRMGWLLRGIPKPESVADHAFCVTLITLFLADELRkkgININVERALKIAILHDLAEARITDLPL-DAQIY 84 
                                       79*************************************984444699*********************66.54556 PP

                              HD_3  76 eekeeeekeaaerilkllpeelaeellalweEFeeretkeakfakdlDklepllqalekegdslaafeaklsqvy 150
                                        +k++ ek+ + +il+    e + e+ +l++++ee+ + e+k++k  Dkle++lqa+e+e+   + +e + + v 
  gi|242399636|ref|YP_002995061.1|  85 IDKKKAEKKSMIDILGA---E-KVEYFELFQDYEEERSIEGKLVKFADKLEMVLQAWEYEKAGFKGLEEFWNAVD 155
                                       66667777776677665...3.678***********************************988777755544444 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 !   52.8   0.5   8.7e-18   3.9e-14      15     153 ..      19     148 ..       9     176 .. 0.77

  Alignments for each domain:
  == domain 1  score: 52.8 bits;  conditional E-value: 8.7e-18
                              HD_2  15 walmrntreenvaeHslevaliahalalienkkfggkldaerlallalyHDasEiitGDlptpvKyanpeireayke 91 
                                       w l    ++e+va+H++ v+li+ +la   +kk g ++++er++++a++HD++E+ + Dlp +      +i    k+
  gi|242399636|ref|YP_002995061.1|  19 WLLRGIPKPESVADHAFCVTLITLFLADELRKK-GININVERALKIAILHDLAEARITDLPLD-----AQIYIDKKK 89 
                                       455556789******************955545.67*************************76.....455555566 PP

                              HD_2  92 vEeeaeekllelLpeelreeyeelladeeaeeeekklvkaaDklsalikcleelkagnkeFe 153
                                        E+   +++++ L +e  e +e +   ee+++ e+klvk aDkl+ ++++ e +kag k  e
  gi|242399636|ref|YP_002995061.1|  90 AEK---KSMIDILGAEKVEYFELFQDYEEERSIEGKLVKFADKLEMVLQAWEYEKAGFKGLE 148
                                       665...678888888866655555446666677**********************9987533 PP

>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.6   8.4e-09   3.8e-05       2     121 ..      31     132 ..      30     133 .. 0.70

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 8.4e-09
                                       HHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHHHHH CS
                                HD   2 leHsleVaklarrlaedlge...eedrellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevekrlg 75 
                                       ++H + V  ++  la++l +   + ++e++l++a+lHD+++ ++ d  +            +++   + ++++k+  
  gi|242399636|ref|YP_002995061.1|  31 ADHAFCVTLITLFLADELRKkgiNINVERALKIAILHDLAEARITDLPL-----------DAQIYIDKKKAEKKSMI 96 
                                       689999999999******99*************************9333...........33333333333333331 PP

                                       HHHHHHHHHHHTTCCHHHHHHHHHHHHCCTSCHHHHHHHHHHHHHH CS
                                HD  76 ldledvaklirehheswegkkrprglaerqlslearivklaDrlaa 121
                                       +   + a+ +++     +        +e++ s+e ++vk aD+l++
  gi|242399636|ref|YP_002995061.1|  97 D--ILGAEKVEYFELFQD--------YEEERSIEGKLVKFADKLEM 132
                                       1..233444444444444........66788888899999998875 PP

>> HOCHOB  Homeobox-cysteine loop-homeobox
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   2.8e-05      0.13       1      69 [.      80     149 ..      80     178 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.8e-05
                            HOCHOB   1 DlelfeknrHPsiqemikiseetgvkYeqvfkRfselRllkkekCeknDtCekvakyfeske.kydglld 69 
                                       D +++   +    + mi+i    +v+Y ++f+ ++e R+++ +  +  D+ e v++  e ++  ++gl++
  gi|242399636|ref|YP_002995061.1|  80 DAQIYIDKKKAEKKSMIDILGAEKVEYFELFQDYEEERSIEGKLVKFADKLEMVLQAWEYEKaGFKGLEE 149
                                       67788888888889*************************************9999876654314555443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 1017.26
//
Query:       gi|242399637|ref|YP_002995062.1|  [L=293]
Description: Zinc-dependent hydrolase, glyoxylase II family [Thermococcus sibiricus MM 739]
Scores for 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-16   59.6   0.0    6.2e-16   59.0   0.0    1.2  1  Lactamase_B    Metallo-beta-lactamase superfamily
    0.00019   21.0   0.0    0.00025   20.6   0.0    1.3  1  Lactamase_B_2  Beta-lactamase superfamily domain
    0.00033   20.6   0.0    0.00063   19.7   0.0    1.6  2  Lactamase_B_3  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.0   0.0     1e-19   6.2e-16       6     183 ..      19     189 ..      17     202 .. 0.85

  Alignments for each domain:
  == domain 1  score: 59.0 bits;  conditional E-value: 1e-19
                                       SEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCC CS
                       Lactamase_B   6 vnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapal 82 
                                       + s+ i +++++++iD+G ++ ++++++  + l++ + ++ ++i TH+H+DH++ +++l +   ++ ++ ++++  l
  gi|242399637|ref|YP_002995062.1|  19 SPSTMIKTGEKTVIIDPGNGSKRPKELR--RELRKIGVEINYIIATHAHADHVAIVPKLDKPLFIHRYEFSIAETPL 93 
                                       6799**********************97..99999999*************************************** PP

                                       HCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCC CS
                       Lactamase_B  83 fmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallagetgr 159
                                       ++e + +++ + ++    v+ ++++v  +   +  ++  +l +   pgh++g   + +++  vl++GD ++ +  ++
  gi|242399637|ref|YP_002995062.1|  94 NRELLTFGSKAPKG--FLVYQFPSEVRVHAIFDWSDELFGLRALELPGHSPGMTGFLDEENAVLYAGDSFFGERVIE 168
                                       *****888888774..8888888888888888888888899999999***********************9665555 PP

                                       CCC.TTCEEE-SHCHHHHHHHHHH CS
                       Lactamase_B 160 idltlrgaevrdpsdaekyldsll 183
                                       +      ++ + p + ++++++l 
  gi|242399637|ref|YP_002995062.1| 169 GVG---LPYLIEPNLFKESIKRLV 189
                                       544...556666666666655555 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   4.2e-08   0.00025       2      55 ..      30      83 ..      29     168 .. 0.70

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 4.2e-08
                                      EEEES--TTHHHH.HTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCC...C-- CS
                     Lactamase_B_2  2 riLiDagpdlrqq.alralqPvelrdelppidaVllthaHyDHlaglltlre...lrp 55
                                       ++iD+g +   + +lr+    elr+   +i+ ++ thaH+DH+a ++ l +   ++ 
  gi|242399637|ref|YP_002995062.1| 30 TVIIDPGNGSKRPkELRR----ELRKIGVEINYIIATHAHADHVAIVPKLDKplfIHR 83
                                      589******666632322....25666679**************98888888765443 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0     1e-07   0.00063       4      52 ..      16      71 ..      15     162 .. 0.83
   2 ?   -2.7   0.0       0.8   4.8e+03     120     145 ..     185     210 ..     166     217 .. 0.66

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1e-07
                     Lactamase_B_3  4 wlghnsflletagarilvDPfkanlgyeppa..........eeaDlvlisqaledHahl 52
                                      + g+ s +++t+++++++DP+++    ++p+          +e++ ++ ++a++dH ++
  gi|242399637|ref|YP_002995062.1| 16 YPGSPSTMIKTGEKTVIIDPGNG---SKRPKelrrelrkigVEINYIIATHAHADHVAI 71
                                      5688899**************63...333333444566666***************976 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.8
                     Lactamase_B_3 120 seelkelgrvDvvltPvggpltlgqe 145
                                        + l + ++  v+l+P +g+ ++g e
  gi|242399637|ref|YP_002995062.1| 185 IKRLVNYAEEGVLLIPSHGKSVKGEE 210
                                       45555556666888888887666544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.37s 00:00:00.96 Elapsed: 00:00:00.55
# Mc/sec: 1602.21
//
Query:       gi|242399638|ref|YP_002995063.1|  [L=206]
Description: exonuclease, RecB family [Thermococcus sibiricus MM 739]
Scores for complete 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-05   23.3   0.3     0.0012   18.9   0.2    2.0  2  PDDEXK_1  PD-(D/E)XK nuclease superfamily
     0.0029   17.7   0.1      0.029   14.5   0.1    2.2  1  Cas_Cas4  Domain of unknown function DUF83


Domain annotation for each model (and alignments):
>> PDDEXK_1  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.011        96      10      49 ..      12      53 ..       9      64 .. 0.73
   2 !   18.9   0.2   1.3e-07    0.0012     128     254 ..      73     199 ..      51     200 .. 0.61

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.011
                          PDDEXK_1 10 fleCplrfflryllglre......eeeleapdlGtlvHaaleefye 49
                                       ++Cp+r ++ +l g++e        +l   + G   H +l ++ +
  gi|242399638|ref|YP_002995063.1| 12 AMTCPRRIYF-RLKGYKEkwpdfvRVRL---EQGINTHNVLGDILK 53
                                      689*******.68888555554444444...66******9998877 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 1.3e-07
                          PDDEXK_1 128 vrLkGriDrvddkegelriiDyKtgsappkskelaelkegl.QlllYllalaegeelkeegepagalylrlee.pkv 202
                                       ++++GriD      +  + i+ K g++  ++       ++l Ql +Yl +++ +         + ++y++l+e pk+
  gi|242399638|ref|YP_002995063.1|  73 FEIHGRIDAYK---N--YPIEIK-GKTSLPRIP---YDYHLaQLNIYLRWAESE--------YGYLYYVKLQErPKK 132
                                       56888888853...3..557777.663334443...566778***********9........8899*****997777 PP

                          PDDEXK_1 203 k.......deevvkkmalteeel...eallqeleel...aeeilagefparpskk..CeyCpyksvC 254
                                               + +vvk    ++ e+   e+l +e  ++   +++ ++  +p++   +  C++Cpy  +C
  gi|242399638|ref|YP_002995063.1| 133 VldgidfsKFPVVKGKNFKAFEIpydEKLFRETVKQfyvIKKHYERGIPPKGWNDytCRFCPYYYIC 199
                                       799999994444444433333332223333333333255444444445555444478********99 PP

>> Cas_Cas4  Domain of unknown function DUF83
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   3.3e-06     0.029     109     160 ..     148     199 ..      10     201 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.3e-06
                          Cas_Cas4 109 kekkreevelteelreelekaikeieeiissekppkvkkkkiCkkCayaelC 160
                                       k+ k  e+ ++e+l +e+ k    i++  ++  ppk  +   C+ C y+ +C
  gi|242399638|ref|YP_002995063.1| 148 KNFKAFEIPYDEKLFRETVKQFYVIKKHYERGIPPKGWNDYTCRFCPYYYIC 199
                                       4445667999****************************************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.37s 00:00:00.93 Elapsed: 00:00:00.54
# Mc/sec: 1150.41
//
Query:       gi|242399639|ref|YP_002995064.1|  [L=114]
Description: hypothetical protein TSIB_1664 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); 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: 0.55u 0.35s 00:00:00.90 Elapsed: 00:00:00.54
# Mc/sec: 638.19
//
Query:       gi|242399640|ref|YP_002995065.1|  [L=280]
Description: Met-10+ like protein [Thermococcus sibiricus MM 739]
Scores for complete 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-69  231.5   1.1    8.7e-69  231.3   1.1    1.1  1  Met_10           Met-10+ like-protein
    0.00013   21.5   0.0    0.00024   20.6   0.0    1.4  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    0.00017   20.7   0.0    0.00022   20.4   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase
    0.00035   20.3   0.0    0.00063   19.4   0.0    1.4  1  Cons_hypoth95    Conserved hypothetical protein 95
    0.00092   18.8   0.0     0.0015   18.1   0.0    1.4  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
     0.0039   16.7   0.0     0.0084   15.7   0.0    1.6  2  MTS              Methyltransferase small domain
     0.0086   15.0   0.1      0.012   14.5   0.1    1.2  1  Pox_A51          Poxvirus A51 protein
     0.0094   15.9   0.0      0.019   14.9   0.0    1.5  1  ADH_zinc_N       Zinc-binding dehydrogenase
  ------ inclusion threshold ------
      0.011   16.4   0.0      0.024   15.3   0.0    1.6  1  Methyltransf_25  Methyltransferase domain
      0.043   13.2   0.0      0.069   12.5   0.0    1.3  1  DNA_methylase    C-5 cytosine-specific DNA methylase


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 !  231.3   1.1   4.9e-72   8.7e-69       2     199 .]      31     225 ..      30     225 .. 0.98

  Alignments for each domain:
  == domain 1  score: 231.3 bits;  conditional E-value: 4.9e-72
                                       EEEEETTEEEEEB-TTSSHHHHHHHHHHHHHSS-SCEEEE-S-SBTTTTB--EEEEEES-.SEEEEEETTEEEEEET CS
                            Met_10   2 kfeiiGdvvilnlreelkeykkvigevildktkvktvlrkvsevegefRtfelevlaGsdstetihkEngcrfklDv 78 
                                       ++ + Gdv+il lreel +yk++i++v++++  vktvlrk +   gefR++++e+++G+d  +tihkEng+ +k+D 
  gi|242399640|ref|YP_002995065.1|  31 HWVQLGDVLILPLREELLPYKEEIAKVYAEILGVKTVLRKGKI-GGEFRETNYEIIYGND-PITIHKENGILYKFDA 105
                                       58899*********************************99765.****************.9*************** PP

                                       TTS---GGGHHHHHHHHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEE CS
                            Met_10  79 skvyfsskleaErerlaklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkp 155
                                       skv+fs+++ +Er r+a++++++e+Vvd+fAGiG+++ipiak++ a+ v+ai++ P+++k+l eni+lNkv++++++
  gi|242399640|ref|YP_002995065.1| 106 SKVMFSPANVKERVRMARVAKPNELVVDMFAGIGHLSIPIAKHCGAR-VIAIEKSPYTFKFLVENIELNKVQERMTA 181
                                       ******************************************99887.***************************** PP

                                       EES-GGG---TT-EEEEEE--TTTGGGGHHHHHHHEEEEEEEEE CS
                            Met_10 156 ileDgrevireqladrvvmnlpksaieFldkvlaalkdggvihy 199
                                       ++ D+re+  e++a+r++m+++ +++eF+ k+l+++kd+++ihy
  gi|242399640|ref|YP_002995065.1| 182 YNIDNREFKGENMANRILMGYVVKTHEFIPKALEIAKDEAIIHY 225
                                       *******************************************9 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   1.4e-07   0.00024     157     220 ..     123     186 ..     119     225 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.4e-07
                              PrmA 157 klvkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalsee 220
                                       ++ k++e v+D+ +G G L+i  ak   ++v+a+   + + k   eN+elNkv+++++ ++ ++
  gi|242399640|ref|YP_002995065.1| 123 RVAKPNELVVDMFAGIGHLSIPIAKHCGARVIAIEKSPYTFKFLVENIELNKVQERMTAYNIDN 186
                                       678999*************************************************998765333 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   1.2e-07   0.00022      23      96 ..     119     196 ..     100     274 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.2e-07
                                       HHHH-GG.TTSEEEEES-TTTCCHHHHHCC-.SEEEEE-S-HHHHHHHHCHTT...TCCCEEEE-S-CCGHHHHHHH CS
                            RrnaAD  23 ldklnle.ekltvleigpGkGilTeeLakra.kqvvvlElderLakllqkkls...kdeklkvvhqDflkfetpeev 94 
                                       ++ + +  ++  v+++ +G G+l+ ++ak +   v ++E+ +  +k+l ++++    +e+++ ++ D  +f+  + +
  gi|242399640|ref|YP_002995065.1| 119 VRMARVAkPNELVVDMFAGIGHLSIPIAKHCgARVIAIEKSPYTFKFLVENIElnkVQERMTAYNIDNREFKGEN-M 194
                                       444444468999**************************************999888999********99998766.4 PP

                                       CT CS
                            RrnaAD  95 te 96 
                                        +
  gi|242399640|ref|YP_002995065.1| 195 AN 196
                                       44 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   3.5e-07   0.00063      41     103 ..     127     189 ..     112     206 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 3.5e-07
                                       CC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHH CS
                     Cons_hypoth95  41 egarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedalea 103
                                        ++ v+D+faG G l++  +    ++++++ek++ ++k l en+e  k++e++++++ d+ e 
  gi|242399640|ref|YP_002995065.1| 127 PNELVVDMFAGIGHLSIPIAKHCGARVIAIEKSPYTFKFLVENIELNKVQERMTAYNIDNREF 189
                                       56679************99999999**************************999999888765 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 !   18.1   0.0   8.3e-07    0.0015       2      60 ..     129     188 ..     128     225 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 8.3e-07
                   Methyltransf_15   2 rvilDlfsGaGGnviqfalv.fekviaieinleklacaqhNaevYgvsdkitlvlgdvfe 60 
                                       ++++D+f+G G  +i +a++ + +viaie+++ + +   +N e+  v++++t    d  e
  gi|242399640|ref|YP_002995065.1| 129 ELVVDMFAGIGHLSIPIAKHcGARVIAIEKSPYTFKFLVENIELNKVQERMTAYNIDNRE 188
                                       579***************99899***************************9998877666 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       3.2   5.8e+03      90     111 ..      74      95 ..      55      99 .. 0.71
   2 !   15.7   0.0   4.7e-06    0.0084      31      91 ..     127     186 ..     100     200 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 3.2
                                       TTTSTTS-EEEEEE---STTTC CS
                               MTS  90 leeveekkfdlivsNPPfhagk 111
                                         e+ e ++++i  N P+  +k
  gi|242399640|ref|YP_002995065.1|  74 GGEFRETNYEIIYGNDPITIHK 95 
                                       5566778888888888886655 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 4.7e-06
                                       TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTT CS
                               MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvle 91 
                                        ++ v+D+ +G+G l++ +ak++   +v +++++ +  ++  en+e nk++ +++a ++ +
  gi|242399640|ref|YP_002995065.1| 127 PNELVVDMFAGIGHLSIPIAKHCGA-RVIAIEKSPYTFKFLVENIELNKVQERMTAYNIDN 186
                                       55679****************9987.899**********************7777766654 PP

>> Pox_A51  Poxvirus A51 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   6.6e-06     0.012     131     211 ..     167     249 ..     140     257 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.6e-06
                           Pox_A51 131 lkcielneqkvailaknsd.ilvkGknisilill.fdekiypliPlirsisdndvlisrhnrlheeiPnknWfkfyv 205
                                       +++ieln+ +  + a n d    kG+n+   il+ +  k++ +iP    i++++ +i  hn + e +  ++ fk + 
  gi|242399640|ref|YP_002995065.1| 167 VENIELNKVQERMTAYNIDnREFKGENMANRILMgYVVKTHEFIPKALEIAKDEAIIHYHNTVPEKLMPEEPFKTFQ 243
                                       57899998776555555441456*******99997789****************************99999999998 PP

                           Pox_A51 206 elkhey 211
                                       e   ey
  gi|242399640|ref|YP_002995065.1| 244 ETAREY 249
                                       888777 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.1e-05     0.019       1      28 [.     137     164 ..     137     181 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.1e-05
                                       HHHHHHHHHHHHTT-EEEEEESSHHHHH CS
                        ADH_zinc_N   1 gvGlaavqlAkalGaeviavdsseekle 28 
                                       g+G++ + +Ak++Ga+via+  s+  ++
  gi|242399640|ref|YP_002995065.1| 137 GIGHLSIPIAKHCGARVIAIEKSPYTFK 164
                                       8********************9987665 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.0   1.4e-05     0.024       1      61 [.     131     190 ..     131     219 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.4e-05
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSS CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfe 61 
                                       v+d+ +G G+l++ +ak++g a+v++++ s+   +   e++e ++++ ++   ++++ +f+
  gi|242399640|ref|YP_002995065.1| 131 VVDMFAGIGHLSIPIAKHCG-ARVIAIEKSPYTFKFLVENIELNKVQERMTAYNIDNREFK 190
                                       899****************8.********************88888544444444444443 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 ?   12.5   0.0   3.9e-05     0.069       3      59 ..     131     190 ..     130     202 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.9e-05
                                       EEEES-TT-HHHHHHHHTT-EEEEEEE--TTTHHHHHHH-..-SEEEES-TTTS-..GS- CS
                     DNA_methylase   3 fidLfaGiGGfrlgleaagfecvaaseidkkaaktYeanfk.kvsigDitkidkk..klp 59 
                                       ++d+faGiG +++  ++  +  v+a+e+ ++ +k++  n++ +++++ +t  +++  +++
  gi|242399640|ref|YP_002995065.1| 131 VVDMFAGIGHLSIPIAKHCGARVIAIEKSPYTFKFLVENIElNKVQERMTAYNIDnrEFK 190
                                       69**************************************98777766666555544555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.53
# Mc/sec: 1598.53
//
Query:       gi|242399641|ref|YP_002995066.1|  [L=53]
Description: hypothetical protein TSIB_1666 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); 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 0.32s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 323.48
//
Query:       gi|242399642|ref|YP_002995067.1|  [L=310]
Description: Radical SAM family protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.6e-14   53.2   4.4    9.2e-13   48.9   2.3    2.5  2  Radical_SAM  Radical SAM superfamily
     0.0011   19.1   0.6      0.061   13.5   0.6    2.8  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 !   48.9   2.3     1e-16   9.2e-13       2     166 ..      60     209 ..      59     210 .. 0.82
   2 ?   -2.8   0.0      0.81   7.3e+03     123     140 ..     242     259 ..     223     267 .. 0.60

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 1e-16
                                       EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgi 78 
                                       + t+ Cn++C+fC+ +           l + +  +   ++ +e+     ++  gepl  p++ve+ ++l+++  p+ 
  gi|242399642|ref|YP_002995067.1|  60 ELTPSCNHDCIFCYSKV---A------LKLKKAPQPGYYG-WENPYAITVSQYGEPLISPKIVEANKMLRERF-PDA 125
                                       67999***********7...3......3333333333334.666577888889******************95.*** PP

                                       EEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHH.HTTSETEEEEEEEBTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                       Radical_SAM  79 ritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklr.eagikrvvdrivglpG 154
                                       r+ + tng l+++e +++l+    d v ++l+aa+ ek++ ++   +tf+ v++al++   ++ ++ +v+r++ +pG
  gi|242399642|ref|YP_002995067.1| 126 RLDLQTNGSLLTKELWQKLDF---DLVMISLDAASREKHKMIT-NANTFDNVVNALKIVGiDKSVR-SVVRTIFMPG 197
                                       ***********8877777776...*************666666.88******99999875255566.9********* PP

                                       TSHHHHHHHHHH CS
                                       xxxxxxxxxxxx RF
                       Radical_SAM 155 endeeleellel 166
                                        nd+++ +++el
  gi|242399642|ref|YP_002995067.1| 198 INDDDIPKIAEL 209
                                       ******999987 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.81
                                       CTSHHHHHHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 123 rghtfeevlealeklrea 140
                                       r +++ e+l+a   ++++
  gi|242399642|ref|YP_002995067.1| 242 RAESIREYLKAAMEAKKY 259
                                       445555566655555555 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 !   13.5   0.6   6.8e-06     0.061       6      92 ..      63     136 ..      59     157 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.8e-06
                           Fer4_14   6 sgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltG.GePLhyenkkellklvkrlkeeypek 81 
                                        +Cn+ C +C+ k + k +  ++  +   e+              ++++  GePL+    +++++  k+l+e++p+ 
  gi|242399642|ref|YP_002995067.1|  63 PSCNHDCIFCYSKVALKLKKAPQPGYYGWENPY------A-----ITVSQyGEPLIS---PKIVEANKMLRERFPDA 125
                                       68*********9997776555544444442222......1.....3333339***76...999************** PP

                           Fer4_14  82 kiwletngtle 92 
                                       +  l+tng+l 
  gi|242399642|ref|YP_002995067.1| 126 RLDLQTNGSLL 136
                                       *******9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); 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:                         2  (0.000111551); expected 0.2 (1e-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 0.33s 00:00:00.95 Elapsed: 00:00:00.53
# Mc/sec: 1769.16
//
Query:       gi|242399643|ref|YP_002995068.1|  [L=275]
Description: ATPase of the PP-loop superfamily [Thermococcus sibiricus MM 739]
Scores for complete 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   0.0    2.2e-09   37.1   0.0    1.4  1  QueC             Queuosine biosynthesis protein QueC
    6.3e-07   29.3   0.1    1.6e-06   28.0   0.0    1.7  2  ATP_bind_3       PP-loop family
    1.1e-05   24.4   0.1    2.2e-05   23.5   0.1    1.4  1  tRNA_Me_trans    tRNA methyl transferase
    2.3e-05   24.5   0.0    3.3e-05   24.0   0.0    1.3  1  PAPS_reduct      Phosphoadenosine phosphosulfate reductase fa
    0.00011   21.8   0.0    0.00021   20.9   0.0    1.4  1  Diphthami_syn_2  Diphthamide synthase
    0.00012   21.3   0.0    0.00019   20.6   0.0    1.3  1  NAD_synthase     NAD synthase
     0.0022   17.6   0.1     0.0055   16.3   0.1    1.7  1  ThiI             Thiamine biosynthesis protein (ThiI)
     0.0038   16.6   0.0     0.0063   15.9   0.0    1.3  1  Arginosuc_synth  Arginosuccinate synthase
  ------ inclusion threshold ------
      0.014   15.5   0.1       0.24   11.6   0.1    2.7  3  DNA_pol_B_thumb  DNA polymerase beta thumb
      0.019   15.4   0.0        1.9    8.9   0.0    2.7  2  Enkurin          Calmodulin-binding
       0.15   11.7   0.0       0.21   11.2   0.0    1.1  1  Asn_synthase     Asparagine synthase
       0.21   11.7   2.5       0.87    9.7   0.5    2.3  2  zf-RRPl_C4       Putative ribonucleoprotein zinc-finger pf C4
       0.23   11.4   9.7      0.054   13.4   3.0    2.4  2  DUF4428          Domain of unknown function (DUF4428)


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 !   37.1   0.0   1.6e-12   2.2e-09       1      80 [.      56     134 ..      56     150 .. 0.89

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 1.6e-12
                                       EEEEE--SSHHHHHHHHHHHHH-S.EEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEEE-GGGGGGSCGGG---- CS
                              QueC   1 kavvllSGGlDSttvlalakkegk.evealtfdYgqrhkkeleaakkiakelgveehkildldllkelggsaLtdee 76 
                                       ka+  +SGG DSt++l+lak+++k  vea+ +d g  +k+ +e ak+i+++l+v   ++l  d ++++ + aL++ +
  gi|242399643|ref|YP_002995068.1|  56 KAIAAFSGGKDSTVALYLAKEKYKvDVEAVMIDHGFMAKEAIENAKRITEHLDV-PLTVLRYD-YSNIFRGALLKVK 130
                                       799*******************9648****************************.*******9.7888888888876 PP

                                       ---- CS
                              QueC  77 ievp 80 
                                          +
  gi|242399643|ref|YP_002995068.1| 131 SPCK 134
                                       6555 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0   1.1e-09   1.6e-06       2     104 ..      57     160 ..      56     163 .. 0.70
   2 ?   -3.0   0.0       3.7   5.1e+03      21      43 ..     224     246 ..     217     255 .. 0.54

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 1.1e-09
                                       EEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE--H......HHCT CS
                        ATP_bind_3   2 vlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvkelckklnikleiekvdv......akkk 72 
                                       +++A+SgG DS++ l+l++++    ++++ a+++dhg+   +ke  e  k++ ++l+++l++ + d       a  k
  gi|242399643|ref|YP_002995068.1|  57 AIAAFSGGKDSTVALYLAKEKY---KVDVEAVMIDHGFM--AKEAIENAKRITEHLDVPLTVLRYDYsnifrgALLK 128
                                       689**************99985...58**********97..456677788999999999999999986555432222 PP

                                       TSTCCCHHHHHHHHHHHHCHHCCT.CEEE--- CS
                        ATP_bind_3  73 gknleeaARelRYevlkealkkegievlllAh 104
                                        k+  ++        lke++ k+g+++++++h
  gi|242399643|ref|YP_002995068.1| 129 VKSPCKKCSSRTMGGLKEYALKKGVKFIITGH 160
                                       22222222222234577777777777777777 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.7
                                       HHCTTTTTEEEEEEEE-SSSTCH CS
                        ATP_bind_3  21 klkkklgiklvaihvdhglrees 43 
                                       k+  +++i+ +a+ v ++l ++ 
  gi|242399643|ref|YP_002995068.1| 224 KHGYSFEIRRIAALVRYRLINTE 246
                                       44445555555666666555443 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.1   1.6e-08   2.2e-05       2     124 ..      56     160 ..      55     165 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.6e-08
                     tRNA_Me_trans   2 kvvvalSgGVDSsvaaallkeqg.yevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdfekeykek 77 
                                       k ++a+SgG DS+va++l ke++  +v++v++           +  a+e +++a+r+ e+l++pl+v+ +   y ++
  gi|242399643|ref|YP_002995068.1|  56 KAIAAFSGGKDSTVALYLAKEKYkVDVEAVMIDH---------GFMAKEAIENAKRITEHLDVPLTVLRYD--Y-SN 120
                                       66899****************9944566665532.........4568899****************99875..3.56 PP

                     tRNA_Me_trans  78 vfeefleeyeeGrTPnPdvlCNkeiKfgallekakeelgadalatGH 124
                                       +f   l + +     +P+ +C  +  +g l e+a + +g++ + tGH
  gi|242399643|ref|YP_002995068.1| 121 IFRGALLKVK-----SPCKKCSSRT-MGGLKEYALK-KGVKFIITGH 160
                                       7777776665.....5888888876.5668888887.8888888888 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   2.4e-08   3.3e-05       3      59 ..      58     115 ..      56     160 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 2.4e-08
                                       EEE--SSCTCHHHHHHHHHH.CTTHEEEEEE-STB-HHHHHHHHHHHHHTT-EEEEEE CS
                       PAPS_reduct   3 vvsvsgGkdslVllhLalka.fkpvpvvfvdtghefpetiefvdeleeryglrlkvye 59 
                                       + ++sgGkds+V l La +  +++v+ v +d g   +e ie  ++++e++++ l v +
  gi|242399643|ref|YP_002995068.1|  58 IAAFSGGKDSTVALYLAKEKyKVDVEAVMIDHGFMAKEAIENAKRITEHLDVPLTVLR 115
                                       679**************865155689************************99988765 PP

>> Diphthami_syn_2  Diphthamide synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   1.5e-07   0.00021       2      36 ..      56      90 ..      55     118 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.5e-07
                   Diphthami_syn_2  2 kvavlysGGkDsilaLykalkesevesLvsvisen 36
                                      k+++ +sGGkDs++aLy a ++++v+    +i+++
  gi|242399643|ref|YP_002995068.1| 56 KAIAAFSGGKDSTVALYLAKEKYKVDVEAVMIDHG 90
                                      78999*******************99988888876 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   1.4e-07   0.00019      16      78 ..      52     113 ..      37     134 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.4e-07
                                       CTTSEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE CS
                      NAD_synthase  16 agakgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievkt 78 
                                       ++ ++++   SGG DS+++ +la++   k  v a+++ + +  +e +e+a+ + e+l++  ++
  gi|242399643|ref|YP_002995068.1|  52 SKVDKAIAAFSGGKDSTVALYLAKEKY-KVDVEAVMIDHGFMAKEAIENAKRITEHLDVPLTV 113
                                       3457999********************.99**************************9987654 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1     4e-06    0.0055       4     118 ..      55     162 ..      52     164 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4e-06
                              ThiI   4 gkvlaLlSgGiDSpVaaylllkR.Gcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdfkevlkei 79 
                                       +k++a  SgG DS Va yl+ ++  + v++v++ ++ ++++eaie  ++++e l        +++  +d+ ++ +  
  gi|242399643|ref|YP_002995068.1|  55 DKAIAAFSGGKDSTVALYLAKEKyKVDVEAVMI-DHGFMAKEAIENAKRITEHLDV-----PLTVLRYDYSNIFRGA 125
                                       689999*************97652677888877.5999999999999999998854.....5567788999999888 PP

                              ThiI  80 lekvkekltivllkrkmlriAekvaeeegakalvtGesL 118
                                       l kvk + +     r+m  + e +a ++g+k ++tG  L
  gi|242399643|ref|YP_002995068.1| 126 LLKVKSPCKKCS-SRTMGGLKE-YALKKGVKFIITGHEL 162
                                       888888777654.456666666.8999999999999876 PP

>> Arginosuc_synth  Arginosuccinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   4.5e-06    0.0063       2      44 ..      59     102 ..      58     118 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4.5e-06
                   Arginosuc_synth   2 LaysGGlDtsviikllkeklgeeviavavdvGqe.eedldevke 44 
                                        a+sGG D +v++ l kek++ +v av++d G   +e ++++k+
  gi|242399643|ref|YP_002995068.1|  59 AAFSGGKDSTVALYLAKEKYKVDVEAVMIDHGFMaKEAIENAKR 102
                                       59******************************761445555554 PP

>> DNA_pol_B_thumb  DNA polymerase beta thumb
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       1.6   2.2e+03       4      32 ..      60      86 ..      57     111 .. 0.48
   2 ?   -0.8   0.0       1.2   1.7e+03      15      26 ..     144     155 ..     143     163 .. 0.87
   3 ?   11.6   0.1   0.00017      0.24      14      62 ..     217     272 ..     216     274 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.6
                                      HHHS-HHHHHHHHHHHHCTTEEEETTEEE CS
                   DNA_pol_B_thumb  4 yfTGsktFnrdlRrlakkkglkLnssglr 32
                                       f+G+k+  ++l  + +k+++k + + ++
  gi|242399643|ref|YP_002995068.1| 60 AFSGGKDSTVAL--YLAKEKYKVDVEAVM 86
                                      566666544443..555556666655555 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.2
                                       HHHHHHCTTEEE CS
                   DNA_pol_B_thumb  15 lRrlakkkglkL 26 
                                       l+++a kkg+k+
  gi|242399643|ref|YP_002995068.1| 144 LKEYALKKGVKF 155
                                       789*******98 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.00017
                                       HHHHHHHCTTEEEETTEEE..............ETCCCEEEC-SSHHHHHHHCTS- CS
                   DNA_pol_B_thumb  14 dlRrlakkkglkLnssglrd...ek....gkaeddddgelvevetErdvfelLglp 62 
                                       +lR++ +k+g++++ + +      +    +ka ++ ++  +  e Er+v++ Lg++
  gi|242399643|ref|YP_002995068.1| 217 ALRQYYEKHGYSFEIRRIAAlvrYRlintEKALKKVSKPEISEEIEREVYKRLGIE 272
                                       59****************976551155556666667777887799*********97 PP

>> Enkurin  Calmodulin-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0    0.0014       1.9      68      95 ..      35      62 ..      29      65 .. 0.86
   2 ?    3.4   0.0     0.077   1.1e+02      35      50 ..     182     197 ..     161     204 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0014
                           Enkurin 68 idtlskrqrKeklEkeLkqlEkdiklle 95
                                      +  ++k + K++lE+ +++++k+i+ ++
  gi|242399643|ref|YP_002995068.1| 35 AHKPNKEKIKAELEELMSKVDKAIAAFS 62
                                      5678999******************998 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.077
                           Enkurin  35 mrllseeerqellegL 50 
                                       ++l+se+er ++le+L
  gi|242399643|ref|YP_002995068.1| 182 LSLMSEKERFKILEKL 197
                                       579***********99 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00016      0.21      22     125 ..      59     159 ..      43     161 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00016
                      Asn_synthase  22 alLSGGlDSSliaalaarqsksplktFsigfeekgsdeakyakevaehlgtehtelvlteeelldalpdviyhleep 98 
                                       a +SGG DS++  +la+++ k ++ ++ i+    + + ++ ak++ ehl ++   l + + +  ++++ ++  +  p
  gi|242399643|ref|YP_002995068.1|  59 AAFSGGKDSTVALYLAKEKYKVDVEAVMIDHGFMAKEAIENAKRITEHLDVP---LTVLRYDYSNIFRGALLKVKSP 132
                                       568*****************99999999987337777789************...6777777777788888878888 PP

                      Asn_synthase  99 fadrsaiplyllsrlakrkgvkvvLsG 125
                                           s+  +  l ++a +kgvk +++G
  gi|242399643|ref|YP_002995068.1| 133 CKKCSSRTMGGLKEYALKKGVKFIITG 159
                                       788888888888888888888888877 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 ?    9.7   0.5   0.00063      0.87       1      38 [.       3      44 ..       3      58 .. 0.77
   2 ?    1.3   0.1      0.25   3.5e+02      79     100 ..     128     150 ..     113     155 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00063
                        zf-RRPl_C4  1 mkkCkyClsk....klknlnetvyCeaCeiyfkvknekqkve 38
                                      m kC+ C++     k+k ++    C++C  y+  k +k+k++
  gi|242399643|ref|YP_002995068.1|  3 MLKCSLCINDektaKIKIVDGRPLCKECMNYLAHKPNKEKIK 44
                                      689****8642222899999************9887776543 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.25
                        zf-RRPl_C4  79 klk.lCkeCkervekvlkndfvk 100
                                       k+k  Ck+C +r+   lk+   k
  gi|242399643|ref|YP_002995068.1| 128 KVKsPCKKCSSRTMGGLKEYALK 150
                                       44435888888888877776555 PP

>> DUF4428  Domain of unknown function (DUF4428)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   3.0   3.9e-05     0.054       1      40 [.       5      44 ..       5      52 .. 0.78
   2 ?    1.5   0.6      0.21   2.9e+02      23      39 ..     133     149 ..     133     154 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.9e-05
                           DUF4428  1 iCaiCgkKigllkrlkleDg.yvCkdClkKlseflsdvkik 40
                                      +C++C +  +  k +k+ Dg  +Ck+C++ l   + + kik
  gi|242399643|ref|YP_002995068.1|  5 KCSLCINDEKTAK-IKIVDGrPLCKECMNYLAHKPNKEKIK 44
                                      6999988888877.88****77*******986666666664 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.21
                           DUF4428  23 CkdClkKlseflsdvki 39 
                                       Ck+C ++  ++l+++  
  gi|242399643|ref|YP_002995068.1| 133 CKKCSSRTMGGLKEYAL 149
                                       ******98777777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       893  (0.0498076); expected 358.6 (0.02)
Passed bias filter:                      633  (0.0353059); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.66u 0.33s 00:00:00.99 Elapsed: 00:00:00.54
# Mc/sec: 1530.42
//
Query:       gi|242399644|ref|YP_002995069.1|  [L=328]
Description: permease [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.1e-40  137.0  30.9    1.2e-39  136.4  30.9    1.2  1  AI-2E_transport  AI-2E family transporter


Domain annotation for each model (and alignments):
>> AI-2E_transport  AI-2E family transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.4  30.9   6.6e-44   1.2e-39       6     326 ..      11     322 ..       6     323 .. 0.90

  Alignments for each domain:
  == domain 1  score: 136.4 bits;  conditional E-value: 6.6e-44
                   AI-2E_transport   6 vllllllalypfiselllplliAlvlayllnpvvkfLkkrgvkrvlavllvlllllvllvllvlllvplliaqltql 82 
                                       v+l++++++++ i++ll  +++A++lay++ p+ k+L ++++    ++l+++lll++l  ++ + lv     ++++l
  gi|242399644|ref|YP_002995069.1|  11 VTLIIAYLAWKTIAPLLSAIFFAAILAYAVLPLHKRL-TTRIDNKKSALILTLLLIGLSSIFTVELVL----IIKNL 82 
                                       667788888888889**********************.889999899999999999998888888884....45555 PP

                   AI-2E_transport  83 vkslpayidslqnilnelpslleelenliqalkqslskilsnilssilnsllsllasllglilslvlvllllfflll 159
                                       + s+  y d  + i+ +l+ +l++       +++ l+k  s+ ++++++++ s++ s+++++l+lv++l +++ +l+
  gi|242399644|ref|YP_002995069.1|  83 IASF--YEDIMNFIYWSLTIELPFG------IHDVLQKLYSQSTPKLAEYVQSYAFSIPKYLLQLVIFLAMFYTFLV 151
                                       5554..3444566666777777777......788889999999999******************************* PP

                   AI-2E_transport 160 dgeklrqgilkllpervrervkailrelektlsgylrgqvlvaliigvlvfigllilg...vpyalllailvglanl 233
                                       + +++++ i+ l+p++ ++  +++l++++ tl++++r+ +l+ ++ g l   g++ +g   +p all ++l++l+++
  gi|242399644|ref|YP_002995069.1| 152 NSDRIKKQIYLLIPRGHEDLGEKLLKRADVTLQALIRAWLLLNIAKGALMTLGFWGFGitdIPTALLAGLLTMLFSF 228
                                       **********************************************999888888666222799************* PP

                   AI-2E_transport 234 iPyiGavivlipiaiialltgg.ikevlivlivvllvqliegnilePklmgkrlglhplvillsllaggklfGlvGl 309
                                       iP++ ++++++++ai++l  g+  k++ i +++++lv+ + + +++Pkl+ k+++l+++++l+ +++g++ fG+ Gl
  gi|242399644|ref|YP_002995069.1| 229 IPLFEGWMIWVVAAIFLLKQGDvLKAIAISIYGAVLVSPLPDFTIRPKLVAKEAKLDEIMVLIGMIGGVWAFGVKGL 305
                                       ************999999999988999999*********************************************** PP

                   AI-2E_transport 310 ilavpltavikaileay 326
                                       i++++++ ++ a+l+++
  gi|242399644|ref|YP_002995069.1| 306 IIGPIILNLVSALLKEW 322
                                       *************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1003  (0.0559429); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.68u 0.35s 00:00:01.03 Elapsed: 00:00:00.55
# Mc/sec: 1794.03
//
Query:       gi|242399645|ref|YP_002995070.1|  [L=181]
Description: Pyrazinamidase/nicotinamidase pxnc [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.2e-45  153.8   0.0    5.8e-45  153.6   0.0    1.0  1  Isochorismatase  Isochorismatase family
     0.0052   16.8   0.2      0.016   15.2   0.1    1.9  2  Put_DNA-bind_N   Putative DNA-binding protein N-terminus
  ------ inclusion threshold ------
      0.023   14.7   1.3       0.04   14.0   0.1    1.9  2  Exog_C           Endo/exonuclease (EXOG) C-terminal domain
       0.19   12.3   1.0         11    6.7   0.2    2.5  3  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas


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 !  153.6   0.0   1.3e-48   5.8e-45       2     174 ..       3     179 ..       2     180 .. 0.94

  Alignments for each domain:
  == domain 1  score: 153.6 bits;  conditional E-value: 1.3e-48
                   Isochorismatase   2 alvviDmqndfveegvkeseeisavveninkllkaarkagipviftrdvheleevkgdlderkaaphfkpgttgael 78 
                                       alv++Dmq+df+++g+  ++e +++++ i++l+k++++++  +++trd h+ ++ +   + +++++h++++t+gae+
  gi|242399645|ref|YP_002995070.1|   3 ALVIVDMQRDFMPGGALPVPEGDKIIPTIEELIKQFKRKDALIVATRDWHPHNHISFRERGGPWPKHCVQNTNGAEI 79 
                                       9**************************************************9999999999**************** PP

                   Isochorismatase  79 vpelaplegdvvvd.......KtrfsafagtdldeiLkelgiktivlaGiatdvCVeatardaldlGyevvvvsDAv 148
                                       v  l+ +   v++        K+ +s+f+gt+l eiLke+g+k+++++G+at++CV+ata+dal++++ev++v++Av
  gi|242399645|ref|YP_002995070.1|  80 VVKLPDD---VIIIskadepdKEAYSGFEGTNLAEILKEKGVKKVYICGVATEYCVRATALDALKHDFEVYLVKNAV 153
                                       ****954...4444455555599****************************************************** PP

                   Isochorismatase 149 aalspelhdaalkrlkqafatvitte 174
                                        ++ pe++++ l++lk++++++++++
  gi|242399645|ref|YP_002995070.1| 154 KGIRPEDEEKVLRELKEKGVEIVSST 179
                                       ********************999876 PP

>> Put_DNA-bind_N  Putative DNA-binding protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.75   3.3e+03      19      28 ..     112     121 ..     108     134 .. 0.79
   2 !   15.2   0.1   3.6e-06     0.016      15      33 ..     163     181 .]     162     181 .] 0.94

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.75
                                       HHHHTT--EE CS
                    Put_DNA-bind_N  19 elkeegveri 28 
                                        lke+gv+++
  gi|242399645|ref|YP_002995070.1| 112 ILKEKGVKKV 121
                                       5899999887 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 3.6e-06
                                       HHHHHHHHTT--EE-HHHH CS
                    Put_DNA-bind_N  15 ryLeelkeegveriSSteL 33 
                                       ++L+elke+gve++SSteL
  gi|242399645|ref|YP_002995070.1| 163 KVLRELKEKGVEIVSSTEL 181
                                       68***************98 PP

>> Exog_C  Endo/exonuclease (EXOG) C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1      0.98   4.4e+03      31      38 ..     113     120 ..     109     120 .. 0.79
   2 ?   14.0   0.1   8.9e-06      0.04       4      37 ..     142     174 ..     140     175 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.98
                            Exog_C  31 Lkeagiep 38 
                                       Lke+g+++
  gi|242399645|ref|YP_002995070.1| 113 LKEKGVKK 120
                                       89999985 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 8.9e-06
                            Exog_C   4 keFtlYlsgRKvesArtlkRLekvmkeLkeagie 37 
                                       ++F+ Yl++  v++ r     ekv+ eLke+g+e
  gi|242399645|ref|YP_002995070.1| 142 HDFEVYLVKNAVKGIRPEDE-EKVLRELKEKGVE 174
                                       79**************9776.***********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 ?    2.2   0.1     0.063   2.8e+02       8      55 ..     103     118 ..      75     121 .. 0.54
   2 ?    4.1   0.1     0.015        69       7      30 ..     102     126 ..     102     142 .. 0.82
   3 ?    6.7   0.2    0.0024        11      15      62 ..     134     180 ..     120     181 .] 0.72

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.063
                                       SHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTE CS
                         Pyr_redox   8 GyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngi 55 
                                       G+ g                                 +l+e l+++g+
  gi|242399645|ref|YP_002995070.1| 103 GFEGT--------------------------------NLAEILKEKGV 118
                                       44444................................55555555554 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.015
                                       SSHHHHHHHHHHHHTT.SEEEEEES CS
                         Pyr_redox   7 gGyiglElAgalaelg.kkVtvver 30 
                                       +G+ g  lA++l+e g kkV+++  
  gi|242399645|ref|YP_002995070.1| 102 SGFEGTNLAEILKEKGvKKVYICGV 126
                                       5999**********99779988765 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0024
                                       HHHHHHTTS..EEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEE CS
                         Pyr_redox  15 Agalaelgk..kVtvversdkllrllDeeaskilqeklekngievllntk 62 
                                       A+al +l++  +V++v ++ k  r +Dee    + ++l+++g+e++ +t+
  gi|242399645|ref|YP_002995070.1| 134 ATALDALKHdfEVYLVKNAVKGIRPEDEE---KVLRELKEKGVEIVSSTE 180
                                       66666666522555555555555555555...999**********98886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      568  (0.0316805); 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: 0.55u 0.33s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 1072.25
//
Query:       gi|242399646|ref|YP_002995071.1|  [L=135]
Description: hypothetical protein TSIB_1671 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.9e-09   36.7   0.0    0.00026   20.6   0.0    2.0  2  DUF2240    Uncharacterized protein conserved in archaea (DUF2
  ------ inclusion threshold ------
      0.051   13.5   0.1      0.075   12.9   0.1    1.5  1  OAM_alpha  D-ornithine 4,5-aminomutase alpha-subunit


Domain annotation for each model (and alignments):
>> DUF2240  Uncharacterized protein conserved in archaea (DUF2240)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   2.9e-08   0.00026      13      63 ..      14      64 ..       6      70 .. 0.90
   2 !   15.6   0.0     1e-06    0.0092      78     143 ..      64     132 ..      61     133 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.9e-08
                           DUF2240 13 krkdklsesdfvfalsldrkwlspdqakklldraeeegLlekkdgdlvpnf 63
                                      k+ ++ s+ +++  + l++ +++  +ak+l+++a ++g++e+k+++l+++ 
  gi|242399646|ref|YP_002995071.1| 14 KGSNEFSKPELIGTIVLRLGLMNYMEAKNLIEEAIKRGIIEQKGDRLIIRE 64
                                      567788999**************************************9875 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 1e-06
                           DUF2240  78 eell....kekstferildaiaastgiekkevvaeinelqeelkglvdveaaalvvakkegvdvddliee 143
                                       ee+l    ++++ f ++++ ia++ g +  ev  e+n+  e+ +  +d +++a ++  ++g+d++ + ++
  gi|242399646|ref|YP_002995071.1|  64 EEMLkkeeQQEDLFGEMINYIAKQLGWSHFEVLEELNKFSERYG-ELDKKVIAYLYGLDKGIDMSKFKDK 132
                                       777887778999********************************.99******************99876 PP

>> OAM_alpha  D-ornithine 4,5-aminomutase alpha-subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   8.4e-06     0.075      44      86 ..      20      63 ..       2      97 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.4e-06
                                      E-HHHHHHHHHHTT-.-HHHHHHHHHHHHHTTGGGG-HHHHHHH CS
                         OAM_alpha 44 tspsiersvLLrmGl.ssleakaivekvlekgllgkGaGhvvyr 86
                                        p +  +++Lr+Gl + +eak+++e+++++g++++   +++ r
  gi|242399646|ref|YP_002995071.1| 20 SKPELIGTIVLRLGLmNYMEAKNLIEEAIKRGIIEQKGDRLIIR 63
                                      5566777899****6478***************98655555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 788.25
//
Query:       gi|242399647|ref|YP_002995072.1|  [L=211]
Description: hypothetical protein TSIB_1672 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        1.4    8.7   4.6       0.39   10.5   0.6    1.9  2  DUF5353   Family of unknown function (DUF5353)


Domain annotation for each model (and alignments):
>> DUF5353  Family of unknown function (DUF5353)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.2     0.098   1.7e+03      44      62 ..      23      41 ..      16      45 .. 0.59
   2 ?   10.5   0.6   2.2e-05      0.39      34      61 ..      61      88 ..      56      92 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.098
                           DUF5353 44 gavGafavgdyyvskylfk 62
                                      g ++++  g y   +yl+k
  gi|242399647|ref|YP_002995072.1| 23 GGLAIILYGAYLNRNYLLK 41
                                      4555555555666666665 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 2.2e-05
                           DUF5353 34 LtwkvvglwagavGafavgdyyvskylf 61
                                      L w ++gl    + +f + dyy+s y f
  gi|242399647|ref|YP_002995072.1| 61 LPWLLIGLLVWSISVFKATDYYLSLYSF 88
                                      88**********************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); 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 0.35s 00:00:00.88 Elapsed: 00:00:00.54
# Mc/sec: 1180.94
//
Query:       gi|242399648|ref|YP_002995073.1|  [L=128]
Description: PaaI related protein, phenylacetic acid degradation-related [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.9e-09   36.4   0.0    8.3e-09   35.7   0.0    1.4  1  4HBT             Thioesterase superfamily
      3e-05   23.6   0.1    4.1e-05   23.1   0.1    1.2  1  MaoC_dehydratas  MaoC like domain
  ------ inclusion threshold ------
      0.011   16.0   0.0      0.012   15.9   0.0    1.0  1  4HBT_3           Thioesterase-like superfamily
      0.037   14.2   0.0      0.062   13.4   0.0    1.3  1  DUF4442          Domain of unknown function (DUF4442)


Domain annotation for each model (and alignments):
>> 4HBT  Thioesterase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.0   1.8e-12   8.3e-09       1      78 [.      40     112 ..      40     113 .. 0.95

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 1.8e-12
                                       TSSB-HHHHHHHHHHHHHHHHHHTTSTTEEEEEEEEEEEESS-BBTTCEEEEEEEEEEEESSEEEEEEEEEETTSCE CS
                              4HBT   1 gGvvhgGvylallDeaagaalrslggrgilvvvvelsidflrpvrlgdeltvearvlrlgrtsavvevevrdedgrl 77 
                                       +G vhgG ++ l+D aa +a++++       v    +++f +pv++ del+++a++++  ++  vv ve++++++++
  gi|242399648|ref|YP_002995073.1|  40 YGLVHGGFTFGLADYAAMLAVNEPTV-----VLGKAEVKFTKPVKVRDELLAKAEIVEDQGRKKVVFVEIFNQKDEK 111
                                       699******************99986.....9******************************************987 PP

                                       E CS
                              4HBT  78 v 78 
                                       v
  gi|242399648|ref|YP_002995073.1| 112 V 112
                                       5 PP

>> MaoC_dehydratas  MaoC like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.1   9.1e-09   4.1e-05      53     120 ..      43     109 ..      39     112 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 9.1e-09
                                       --HHHHHHHHHHHHHHHHSTTEGGGEEEEEEEE-S--BTTCEEEEEEEEEEEEEEEEEEEEEEEEEEE CS
                   MaoC_dehydratas  53 ahGmltlaivaklveeelgdnvvarvgeikvrFtkpVlpgdtlkvelevvgkrdvrktkkvevtkevt 120
                                       +hG +t++++  + +  + +     +g  +v+FtkpV + d+l +++e v+ + ++k++ ve  ++ +
  gi|242399648|ref|YP_002995073.1|  43 VHGGFTFGLADYAAMLAVNE-PTVVLGKAEVKFTKPVKVRDELLAKAEIVEDQGRKKVVFVEIFNQKD 109
                                       8*******998887777766.6689**************************99999999998777655 PP

>> 4HBT_3  Thioesterase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.9   0.0   2.7e-06     0.012      11      77 ..      43     113 ..      31     123 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.7e-06
                                       .-HHHHHHHHHHHHHHT.-S.SS..EEEEEEE-S---SE.EEEEEEEEEE--SS-EEEEEEE.EETTEEEE CS
                            4HBT_3  11 gyGGyvlAlalraaqrtvpdprl..hslhvyFlrpgdag.pviyhvervrdGrsfstrtvel.sqggrpif 77 
                                       ++GG++ +la  aa+ +v +p++    + v F +p+++  +++ ++e v d  +  ++ ve+  q++++++
  gi|242399648|ref|YP_002995073.1|  43 VHGGFTFGLADYAAMLAVNEPTVvlGKAEVKFTKPVKVRdELLAKAEIVEDQGRKKVVFVEIfNQKDEKVL 113
                                       4*****************7774457**************************99999999999556676665 PP

>> DUF4442  Domain of unknown function (DUF4442)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.4e-05     0.062      26     132 .]      20     121 ..      17     121 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.4e-05
                                       EETTEEEEEE---GGGB.-TTSSB-HHHHHHHHHHHHHHHHHHHS-TTEEEEEEEEEEEE-S-..--S-EEEEEE-T CS
                           DUF4442  26 lepgraevrlkkrrrvr.NhigtvHAiAicnlaElamGllaeatlpdthrwipkgmevdYlak..atgdltavaele 99 
                                       +e g+aev+lk r +++    g vH++  + la+ a++l +++       ++  ++ev+++++   + +l a ae+ 
  gi|242399648|ref|YP_002995073.1|  20 IEDGYAEVKLKTREEMKvDEYGLVHGGFTFGLADYAAMLAVNEP----T-VVLGKAEVKFTKPvkVRDELLAKAEIV 91 
                                       78999******999887478999*************98876543....3.455668*****9833567899999988 PP

                                       TS-TT--EEEEEEEEEEETTE.EEEEEEEEEEE CS
                           DUF4442 100 pedvgekeelvvevevrdekgeevvraeitlwv 132
                                       +++ +   + vv ve+ ++k+e+v ++++  +v
  gi|242399648|ref|YP_002995073.1|  92 EDQGR---KKVVFVEIFNQKDEKVLEGNFYCYV 121
                                       77655...678999**********999987776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.33s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 736.96
//
Query:       gi|242399649|ref|YP_002995074.1|  [L=101]
Description: Transcriptional regulator, padR-like family [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-16   60.2   0.3    1.7e-16   59.9   0.3    1.1  1  PadR      Transcriptional regulator PadR-like family
    1.4e-07   32.1   0.1    1.8e-07   31.8   0.1    1.0  1  RTP       Replication terminator protein
    0.00013   22.0   0.2    0.00024   21.2   0.2    1.3  1  HTH_34    Winged helix DNA-binding domain
     0.0058   16.8   0.0     0.0073   16.4   0.0    1.2  1  FUR       Ferric uptake regulator family
  ------ inclusion threshold ------
      0.019   13.4   0.1       0.02   13.3   0.1    1.1  1  DUF505    Protein of unknown function (DUF505)
      0.043   13.8   0.0      0.082   12.9   0.0    1.5  1  HTH_12    Ribonuclease R winged-helix domain


Domain annotation for each model (and alignments):
>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.9   0.3   5.6e-20   1.7e-16       1      75 []      14      84 ..      14      84 .. 0.96

  Alignments for each domain:
  == domain 1  score: 59.9 bits;  conditional E-value: 5.6e-20
                                      HHHHHCCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHHHH CS
                              PadR  1 iLalleeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrelae 75
                                      iL++++++   G+ ++kele++  g +++s+G++Yp+L+ +ek gl++s+w+  ++g++ ++Y++T++G + l+e
  gi|242399649|ref|YP_002995074.1| 14 ILHHASKEAITGTFMMKELENH--G-YKVSPGTIYPLLQNMEKLGLLKSTWKI-KDGRRIRTYQITQEGIKVLEE 84
                                      89********************..9.9*************************9.59*************999875 PP

>> RTP  Replication terminator protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.1     6e-11   1.8e-07       9      98 ..       9      91 ..       2      99 .. 0.90

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 6e-11
                                      HHHHHHHHHHHTT-EBCTCHHHHHHHHHTTTT----HHHHHHHHHHHHHTTSEEEEEEEBTSSSSSEEEEEEESS..HH CS
                               RTP  9 FlklylitlvekkklyglklldelkkeFkelgykPnhseiyralhelvedgilkrrkelkekaklqevviYsltdeGke 87
                                      F+ l++++ + k+   g+ ++ el     + gyk ++ +iy  l+++ + g+lk + ++k   + + + +Y++t+eG  
  gi|242399649|ref|YP_002995074.1|  9 FMGLHILHHASKEAITGTFMMKEL----ENHGYKVSPGTIYPLLQNMEKLGLLKSTWKIK---DGRRIRTYQITQEGIK 80
                                      899999******999999999877....578*****************************...6678999********* PP

                                      HHHHHHHHHHH CS
                               RTP 88 kaklykkqvki 98
                                       ++  kk+vk 
  gi|242399649|ref|YP_002995074.1| 81 VLEESKKKVKE 91
                                      *********95 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 !   21.2   0.2   8.1e-08   0.00024      25      79 ..      38      92 ..      29      93 .. 0.94

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 8.1e-08
                            HTH_34 25 eatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreafkkyvkaLksl 79
                                      +++ g ++  l+ +ek g ++ + + k++++  +++iT+eG +  ++ +k +k+l
  gi|242399649|ref|YP_002995074.1| 38 KVSPGTIYPLLQNMEKLGLLKSTWKIKDGRRIRTYQITQEGIKVLEESKKKVKEL 92
                                      67899*********************************************99987 PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   2.4e-06    0.0073      28      68 ..      27      68 ..       3      99 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.4e-06
                                      HHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEE.EETTSEE CS
                               FUR 28 evykelkeedpeislaTVYrtLklleeaglvkel.efedges 68
                                       ++kel++++ ++s  T+Y  L+ +e++gl+k++ +++dg++
  gi|242399649|ref|YP_002995074.1| 27 FMMKELENHGYKVSPGTIYPLLQNMEKLGLLKSTwKIKDGRR 68
                                      45789999***********************98624444443 PP

>> DUF505  Protein of unknown function (DUF505)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   6.6e-06      0.02     365     410 ..      43      91 ..      14      95 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.6e-06
                            DUF505 365 dlreaLysLesfeLiesev.eekg..kevyvlTeyGekvledqekklre 410
                                       ++   L ++e  +L++s+   ++g   ++y++T++G kvle+ +kk++e
  gi|242399649|ref|YP_002995074.1|  43 TIYPLLQNMEKLGLLKSTWkIKDGrrIRTYQITQEGIKVLEESKKKVKE 91 
                                       5666799***********95466733468*************9998876 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.7e-05     0.082       5      51 ..      13      60 ..      10      82 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.7e-05
                            HTH_12  5 kilae.sdkpigakeiaeeLkkrgydigeravRyrLrkleergltrrv 51
                                      +il+  s++ i    + +eL++ gy+++  ++   L+ +e+ gl +  
  gi|242399649|ref|YP_002995074.1| 13 HILHHaSKEAITGTFMMKELENHGYKVSPGTIYPLLQNMEKLGLLKST 60
                                      56654145678889999**************************98754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       883  (0.0492498); expected 358.6 (0.02)
Passed bias filter:                      632  (0.0352502); 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: 0.56u 0.35s 00:00:00.91 Elapsed: 00:00:00.53
# Mc/sec: 570.65
//
Query:       gi|242399650|ref|YP_002995075.1|  [L=393]
Description: Permease of the major facilitator family, related [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    7.2e-54  183.0  42.5      8e-42  143.4  15.9    2.0  2  MFS_1       Major Facilitator Superfamily
    3.3e-10   39.4  24.0      4e-07   29.3   2.1    3.4  3  Sugar_tr    Sugar (and other) transporter
    4.6e-05   22.2  18.8    9.9e-05   21.1  18.8    1.6  1  MFS_2       MFS/sugar transport protein
    5.5e-05   22.2  19.5    0.00037   19.5  19.4    1.9  1  MFS_1_like  MFS_1 like family
     0.0084   15.2  14.6      0.032   13.2   3.5    3.2  4  PUCC        PUCC protein
  ------ inclusion threshold ------
       0.04   14.1   0.2       0.67   10.2   0.0    3.0  2  DUF2964     Protein of unknown function (DUF2964)
       0.14   12.1   1.5        1.1    9.2   1.1    2.4  2  Ferlin_C    Ferlin C-terminus


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 !  143.4  15.9   3.1e-45     8e-42       2     347 ..      19     351 ..      18     352 .. 0.91
   2 !   53.4  18.6   7.4e-18   1.9e-14       2     172 ..     223     391 ..     222     393 .] 0.90

  Alignments for each domain:
  == domain 1  score: 143.4 bits;  conditional E-value: 3.1e-45
                             MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalg.l 76 
                                        l+ fl+ +++ +++p++p +l++ lgi +   g +++l   +++++ +++G++sd f  r+ ++ lg+ll+ ++ +
  gi|242399650|ref|YP_002995075.1|  19 GLVSFLNDMSSEMIAPIVPTYLTDVLGIGKVISGSIMGLIESLSSLFKVLFGYVSDVFRKRKvFVTLGYLLSTISkG 95 
                                       6899***********************9999999999999999999************999999999********76 PP

                             MFS_1  77 llllfasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg.... 149
                                       +l++ ++s+w +l lrvl  +g g+ ++   alia+ + k + g+ +g+  ++  lGa+ gpl++  l+++l     
  gi|242399650|ref|YP_002995075.1|  96 ALAF-THSWWDFLTLRVLDRIGKGVRTAPRDALIAESSEKGKSGKSFGFHRMMDTLGAVAGPLVAIGLLALLKnypi 171
                                       6666.688889**********************************************************99999*** PP

                             MFS_1 150 ...Wravfyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgf 223
                                          +r++f++ ai + l++++  ++++++++ ++ k++++             ++al++++  + +l++++l+++g 
  gi|242399650|ref|YP_002995075.1| 172 kvaYRYIFLLSAIPGTLGILV--VVFLVRDKGEEVKKKIKG------------ISALKSRNLRL-FLVIVALAALGR 233
                                       ******************886..555556666666656666............89999999554.444444444577 PP

                             MFS_1 224 sglltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssa 300
                                       +++ ++l     + lg+s ++++++++a++ ++ a++a  +g++sd+++++ ++++++++++la+l++a+  +    
  gi|242399650|ref|YP_002995075.1| 234 YSYAFTLWK--AKELGYS-VVQGLGFYAIFNAIYAFSAYPIGYYSDKVSKKGIITIGFGIAALASLLFAYSKTL--- 304
                                       777777777..9******.*******************************************************... PP

                             MFS_1 301 vllllvlvliGfglgfvfpsllalasdlappeeagtasglfntagsl 347
                                       ++ll+++v++G+  ++  ++  a+++dla + e gt++g++ t++++
  gi|242399650|ref|YP_002995075.1| 305 PMLLMAFVFYGIYIAIEDTIPRAYMADLAKEFEKGTIIGAYHTVFGI 351
                                       99999*************************************99876 PP

  == domain 2  score: 53.4 bits;  conditional E-value: 7.4e-18
                             MFS_1   2 llaaflsalarsilgpalplalaedlgispse.igllltlyalgaavaslplGrlsdrfGrrrvlllglllfalgll 77 
                                       l++++l+al+r+ ++++l+   a++lg+s+ + +g  ++++ + +a++++p+G+ sd+++ + ++ +g+ + al++l
  gi|242399650|ref|YP_002995075.1| 223 LVIVALAALGRYSYAFTLW--KAKELGYSVVQgLG-FYAIFNAIYAFSAYPIGYYSDKVSKKGIITIGFGIAALASL 296
                                       5677888889998888885..69****99998334.6889999****************5555************77 PP

                             MFS_1  78 lllfasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravf 154
                                       l++++ +l++ll + v+ G+  ++  ++  a++ad++++ e+g  ig + + f++ +  + ++ g+l + ++    f
  gi|242399650|ref|YP_002995075.1| 297 LFAYSKTLPMLLMAFVFYGIYIAIEDTIPRAYMADLAKEFEKGTIIGAYHTVFGIFVFPASIIVGYLWQEYSLKIGF 373
                                       777867777******************************************************************** PP

                             MFS_1 155 yilaivsllafvlfllll 172
                                       + +a++ l+ + l++ll+
  gi|242399650|ref|YP_002995075.1| 374 LYAAVINLITMFLMALLV 391
                                       **********88777665 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1     0.095   2.4e+02     103     126 ..      42      65 ..      29      66 .. 0.87
   2 !   29.3   2.1   1.6e-10     4e-07      64     191 ..      67     196 ..      48     199 .. 0.91
   3 !   14.0  12.5   6.8e-06     0.017      21     185 ..     227     388 ..     222     392 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.095
                                       TGGGGGHHHHHHHHHHHHHHHHHH CS
                          Sugar_tr 103 evlivgRvlvGigvGlasvlvPmy 126
                                        vl +g+v++G  +Gl+  l++++
  gi|242399650|ref|YP_002995075.1|  42 DVLGIGKVISGSIMGLIESLSSLF 65 
                                       68889***************9986 PP

  == domain 2  score: 29.3 bits;  conditional E-value: 1.6e-10
                                       HHHHHHHHHTTHHHHHHH.HHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHH CS
                          Sugar_tr  64 lfagllgdrfGRkkslli.aavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgal 139
                                       +++g+++d+f ++k++++ + +l+ i+    a+++   s++ +++ Rvl  ig G+ ++    +i+E + k + g+ 
  gi|242399650|ref|YP_002995075.1|  67 VLFGYVSDVFRKRKVFVTlGYLLSTISKGALAFTH---SWWDFLTLRVLDRIGKGVRTAPRDALIAESSEKGKSGKS 140
                                       579**************97889999**********...*************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHH.HTSS-...TTHHHHHHHCCHHHHHHHHHHGGGS CS
                          Sugar_tr 140 vslyqlaitfGilvaaifglgl.nktsn...adgwrillglqlvpallllilllfl 191
                                        +++ ++ t+G + +  +  gl +  +n   ++ +r+ + l+++p  l +++++fl
  gi|242399650|ref|YP_002995075.1| 141 FGFHRMMDTLGAVAGPLVAIGLlALLKNypiKVAYRYIFLLSAIPGTLGILVVVFL 196
                                       ****999999999999999998888888899**********************997 PP

  == domain 3  score: 14.0 bits;  conditional E-value: 6.8e-06
                                       GTHHHHHHHHTSTT--SHHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TT CS
                          Sugar_tr  21 afltllkfaknfglsksksskeessvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaak 97 
                                       a ++l  + + f+l k+k+  + s v+   + +if+++ +++++ +g+ +d++++k ++ i+  ++  +++l a +k
  gi|242399650|ref|YP_002995075.1| 227 ALAALGRYSYAFTLWKAKELGY-SVVQGLGFYAIFNAIYAFSAYPIGYYSDKVSKKGIITIGFGIAALASLLFAYSK 302
                                       5566667778888888888666.588888899********************************************* PP

                                       TTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHH...HHHHHHHHHTSS-TTHHH CS
                          Sugar_tr  98 gknsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgalvslyqlaitfGilv...aaifglglnktsnadgwr 171
                                          ++ +l+++ v+ Gi++ ++ ++   y++ +A++   g++++ y +  +fGi+v   ++i+g+  +++s + g+ 
  gi|242399650|ref|YP_002995075.1| 303 ---TLPMLLMAFVFYGIYIAIEDTIPRAYMADLAKEFEKGTIIGAYHT--VFGIFVfpaSIIVGYLWQEYSLKIGFL 374
                                       ...9********************************999998887764..455554332777788888888755555 PP

                                       HHHHCCHHHHHHHH CS
                          Sugar_tr 172 illglqlvpallll 185
                                       +   ++l+   l++
  gi|242399650|ref|YP_002995075.1| 375 YAAVINLITMFLMA 388
                                       55555555444444 PP

>> MFS_2  MFS/sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1  18.8   3.9e-08   9.9e-05       3     371 ..      19     361 ..      17     362 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 3.9e-08
                             MFS_2   3 glgalaanilsvllatylliFytdvlglsaalvglvllvarlvDaitDpivGtlidktstrwGrrrPwlllsaiila 79 
                                       gl ++  +++s ++a    +++tdvlg+  +  g ++ ++  ++ ++  ++G+++d  +     r+ ++ l+ ++ +
  gi|242399650|ref|YP_002995075.1|  19 GLVSFLNDMSSEMIAPIVPTYLTDVLGIGKVISGSIMGLIESLSSLFKVLFGYVSDVFRK----RKVFVTLGYLLST 91 
                                       6777888899999999999***************************************98....799********** PP

                             MFS_2  80 vsiillftppelsqsakfiwllvtyill.rilytlfeipyvslvpvltkdydeRtsltsvrsflsvlggvlaailaf 155
                                       +s  +l +++++       w ++t+ +l ri   + + p  +l+++ +++ +   s +++ +++ +lg v++ ++a+
  gi|242399650|ref|YP_002995075.1|  92 ISKGALAFTHSW-------WDFLTLRVLdRIGKGVRTAPRDALIAESSEKGKSGKS-FGFHRMMDTLGAVAGPLVAI 160
                                       ***********7.......666666555599999************9888877555.67888889999999999999 PP

                             MFS_2 156 llvlilgglkserkgylifaliialLmllgviivvlgtkervemrkkekteqkeklslleqlkevfrnraflillll 232
                                        l++ l+     + +y+++ l+ a+  +lg+++vv+ ++++ e+        k+k++ + +lk    +r ++++l++
  gi|242399650|ref|YP_002995075.1| 161 GLLALLKN-YPIKVAYRYIFLLSAIPGTLGILVVVFLVRDKGEE-------VKKKIKGISALK----SRNLRLFLVI 225
                                       99999998.78899*************************99655.......777877777665....4667777777 PP

                             MFS_2 233 fllaalalgvlnglllYyltyvlg.ngsaasvfllvvtisallgiplwqplakrlgkkntyllgalltivllvlvll 308
                                       + laal  g +  ++ +   + lg +  +   f++++ +  + ++  + +   + +kk ++ +g+   i+ l+ +l+
  gi|242399650|ref|YP_002995075.1| 226 VALAAL--GRYSYAFTLWKAKELGySVVQGLGFYAIFNAIYAFSAYPIGYYSDKVSKKGIITIGFG--IAALASLLF 298
                                       766666..666666777777777766666666777675555577777889999*****99998865..556666677 PP

                             MFS_2 309 lqpsnlllflvllviagfgvgv.aallpwsmladvvDygelktGkrregvffavlsfisklatg 371
                                       +  s++l++l+++++++ ++++   ++p + +ad++ ++e  t   +++++f++++f   +++g
  gi|242399650|ref|YP_002995075.1| 299 A-YSKTLPMLLMAFVFYGIYIAiEDTIPRAYMADLAKEFEKGTIIGAYHTVFGIFVFPASIIVG 361
                                       7.67777777777776666555378*********************************999987 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 !   19.5  19.4   1.4e-07   0.00037      19     384 ..      33     374 ..      23     375 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.4e-07
                        MFS_1_like  19 lPYltiylk.skglkaseigiitlilpltsilsppiwgvlaDrfgkrkkvvilslllsavlflsllfippskerqee 94 
                                        P +  yl+   g+   ++g i+ ++  +s l + ++g ++D f+krk  v l+ lls+++  +l            
  gi|242399650|ref|YP_002995075.1|  33 APIVPTYLTdVLGIGKVISGSIMGLIESLSSLFKVLFGYVSDVFRKRKVFVTLGYLLSTISKGALA----------- 98 
                                       5667778884468999999********************************************999........... PP

                        MFS_1_like  95 sklevsvaqdvdaektfwilfllvvlasfflaailvlldaatlkel..gedrkdyGrqrlf...GsvGyaifafitG 166
                                                   ++++ w +++l+vl  +      +  da++ +    g+  k +G  r+    G+v   ++a+ + 
  gi|242399650|ref|YP_002995075.1|  99 ------------FTHSWWDFLTLRVLDRIGKGVRTAPRDALIAESSekGKSGKSFGFHRMMdtlGAVAGPLVAIGLL 163
                                       ............678889999999999988888888999999888866777888*****863337777778999999 PP

                        MFS_1_like 167 ilidhysvnllpysallyvlaallvisllvvlilnetekesklkvtkslqvllnilknpeviifllvalilgmswgi 243
                                       +l+  y +++  y++++++ a+  ++ +lvv+ l  ++     + +k + + +  lk +++ +fl++++ l ++   
  gi|242399650|ref|YP_002995075.1| 164 ALLKNYPIKV-AYRYIFLLSAIPGTLGILVVVFLVRDK----GEEVKKKIKGISALKSRNLRLFLVIVA-LAALGRY 234
                                       9999999987.577788888776655555533333332....222322345788899998887776665.5566778 PP

                        MFS_1_like 244 ienFlflYLkelgasntl.lGslvalgvvaeiplfffaeklleklGhvklliiallayilrfllyaiienawlvlpi 319
                                        ++F  +  kelg+s    lG + ++ ++     + ++ +  +k++   +++i++ + +l  ll a+ + + ++l++
  gi|242399650|ref|YP_002995075.1| 235 SYAFTLWKAKELGYSVVQgLGFYAIFNAIYAFSAYPIG-YYSDKVSKKGIITIGFGIAALASLLFAYSKTLPMLLMA 310
                                       899999999******86549*********999999876.668*********************************** PP

                        MFS_1_like 320 evLhgisfgllwaaaveyvskiapksleatgqgllsglyfglGralGsliGGllwdlksaiflFr 384
                                        v++gi +++   +   y++++a +  ++t++g ++++ fg+  +  s+i G+lw+++s+++ F 
  gi|242399650|ref|YP_002995075.1| 311 FVFYGIYIAIEDTIPRAYMADLAKEFEKGTIIGAYHTV-FGIFVFPASIIVGYLWQEYSLKIGFL 374
                                       ***********99999********************98.9*******************998886 PP

>> PUCC  PUCC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.77     2e+03     122     138 ..       5      21 ..       2      51 .. 0.66
   2 !    8.7   0.2    0.0003      0.77      13      63 ..      47      94 ..      38     107 .. 0.80
   3 ?   -0.9   0.2      0.24   6.1e+02     348     398 ..     151     198 ..     115     201 .. 0.64
   4 !   13.2   3.5   1.2e-05     0.032      86     156 ..     302     372 ..     280     392 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.77
                              PUCC 122 rpkvvgllyvmlligiv 138
                                         ++ g+ + ++l+g+v
  gi|242399650|ref|YP_002995075.1|   5 EKRILGISWNVFLLGLV 21 
                                       45789999999999986 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0003
                              PUCC 13 pavvvavlial.pllvapfraliGfrSDtkralGwkRvpyiwlGslalalgl 63
                                        v+++ ++ l + l + f++l+G+ SD  r    kR  ++ lG l+ ++  
  gi|242399650|ref|YP_002995075.1| 47 GKVISGSIMGLiESLSSLFKVLFGYVSDVFR----KRKVFVTLGYLLSTISK 94
                                      55666666654278999**************....**********9988765 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.24
                              PUCC 348 aaglavllggalrdllkalaandaalayglVfaleavlliisilvlnklvr 398
                                        a  + l++ +l+ llk  +     +ay  +f+l a+   + ilv++ lvr
  gi|242399650|ref|YP_002995075.1| 151 GAVAGPLVAIGLLALLKNYP---IKVAYRYIFLLSAIPGTLGILVVVFLVR 198
                                       33333333333333333333...5688999999888877777777776666 PP

  == domain 4  score: 13.2 bits;  conditional E-value: 1.2e-05
                              PUCC  86 aglilaavafllvGlgvslsqTallALladlaeeeerpkvvgllyvmlligivvsaivvgallkdytearL 156
                                        +l ++ +af+ +G+ + +  T   A +adla+e e+  ++g  + ++ i +  ++i+vg l ++y+ +  
  gi|242399650|ref|YP_002995075.1| 302 KTLPMLLMAFVFYGIYIAIEDTIPRAYMADLAKEFEKGTIIGAYHTVFGIFVFPASIIVGYLWQEYSLKIG 372
                                       45567899***************************************9999999**********9865432 PP

>> DUF2964  Protein of unknown function (DUF2964)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       0.7   1.8e+03      15      26 ..      81      92 ..      75     100 .. 0.82
   2 ?   10.2   0.0   0.00026      0.67      31      55 ..     273     297 ..     269     302 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.7
                           DUF2964 15 vFiaLagiaaai 26
                                      vF++L+ ++ +i
  gi|242399650|ref|YP_002995075.1| 81 VFVTLGYLLSTI 92
                                      9****9998887 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00026
                           DUF2964  31 fdedavlrygvialliGiaafVvlL 55 
                                       ++ d+v + g+i++ +Giaa+++lL
  gi|242399650|ref|YP_002995075.1| 273 YYSDKVSKKGIITIGFGIAALASLL 297
                                       78999*****************998 PP

>> Ferlin_C  Ferlin C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.38   9.8e+02      13      34 ..     102     130 ..      99     147 .. 0.71
   2 ?    9.2   1.1   0.00044       1.1     101     143 ..     346     390 ..     331     392 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.38
                          Ferlin_C  13 GWWPliklkeqediereerea.......k 34 
                                        WW +++l+  + i +  r a       +
  gi|242399650|ref|YP_002995075.1| 102 SWWDFLTLRVLDRIGKGVRTAprdaliaE 130
                                       6******9999998888888744444332 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00044
                          Ferlin_C 101 ktsfswlvnrlKtfiffiWkkyk.ky.iiallilallalflvlll 143
                                       +t f  +v ++  ++ ++W++y  k+  ++  ++ l+++fl++ll
  gi|242399650|ref|YP_002995075.1| 346 HTVFGIFVFPASIIVGYLWQEYSlKIgFLYAAVINLITMFLMALL 390
                                       578999****************966545677889999****9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       758  (0.0422779); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.74u 0.32s 00:00:01.06 Elapsed: 00:00:00.53
# Mc/sec: 2212.91
//
Query:       gi|242399651|ref|YP_002995076.1|  [L=331]
Description: L-asparaginase [Thermococcus sibiricus MM 739]
Scores for complete 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-59  200.8   0.0    2.4e-59  200.1   0.0    1.3  1  Asparaginase    Asparaginase, N-terminal
    1.5e-31  108.9   0.1    5.2e-31  107.2   0.0    1.9  2  Asparaginase_C  Glutaminase/Asparaginase C-terminal domain
  ------ inclusion threshold ------
      0.078   12.5   0.5       0.17   11.4   0.1    1.8  2  Proteasome      Proteasome subunit


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 !  200.1   0.0   4.1e-63   2.4e-59       1     186 [.       3     185 ..       3     190 .. 0.96

  Alignments for each domain:
  == domain 1  score: 200.1 bits;  conditional E-value: 4.1e-63
                                       EEEEEEEESGGGEEECTTS--CCEES-HHHHHCCTT.TCCCCSEEEEEEEEEE-GGG--HHHHHHHHHHHHHHCCT- CS
                      Asparaginase   1 kvlvlatGGTiasekdesggalapalsaeellealp.elekiaeleseqlanidSsnmtpadwlklaeaieealeey 76 
                                       k+l+++tGGTias+k+e+g  ++  l+++e+l+  + +le+ ++++s +++nidS+ ++p+dw+ +a+++ +al++y
  gi|242399651|ref|YP_002995076.1|   3 KLLIIGTGGTIASAKTEQG--YKSVLKIDEILKLAKiKLENGYKIDSTNIMNIDSTLIHPEDWEIIAKEVFKALDDY 77 
                                       689****************..99999******888779*************************************** PP

                                       SEEEEE--STTHHHHHHHHHHHEES.SSEEEEE--SS-TTSTT-SHHHHHHHHHHHHHCGGTTSECEEEETTEEEET CS
                      Asparaginase  77 dgfVvlhGTDTlaytAsaLslmlknldkpvvltGsqrplselrsDgpeNlldAllvaasseriagvlvvfngkllra 153
                                       dg++++hGTDTlaytAs+Ls+m+kn +kp+vltGs++p++e +sD+p+N+ +A+++a+++   agv+v+f +k++ +
  gi|242399651|ref|YP_002995076.1|  78 DGIIITHGTDTLAYTASMLSFMIKNPNKPIVLTGSMLPITENGSDAPRNIRTAIKFAMED--VAGVFVAFMDKIMLG 152
                                       **********************************************************87..*************** PP

                                       TTEEE-BSSSSS-EEETTT--SEEEETTEEEES CS
                      Asparaginase 154 nrvtKvhtssldaFespnlgplaevegskvkvn 186
                                       +r++Kv+t  l+aF s+n++ +a+v+g+k+ +n
  gi|242399651|ref|YP_002995076.1| 153 CRTSKVRTLGLNAFMSINYPDVAYVKGEKILYN 185
                                       *************************99888665 PP

>> Asparaginase_C  Glutaminase/Asparaginase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.44   2.6e+03      14      31 ..      69      84 ..      53     111 .. 0.69
   2 !  107.2   0.0   8.6e-35   5.2e-31       1     114 []     206     321 ..     206     321 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.44
                                      HHHHHHHHTT--EEEEEE CS
                    Asparaginase_C 14 kvlkallkkgakGvvleg 31
                                      +v+kal    ++G+++  
  gi|242399651|ref|YP_002995076.1| 69 EVFKAL--DDYDGIIITH 84
                                      444444..3788888764 PP

  == domain 2  score: 107.2 bits;  conditional E-value: 8.6e-35
                                       -EEEEE--TT--HHHHHHHHHTT--EEEEEEBTTTB--H...HHHHHHHHHHTTT-EEEEEESSSBS-----H.... CS
                    Asparaginase_C   1 rVvvlklhpgmdtkvlkallkkgakGvvlegtGvGnlps...allealkeakargivvvatsqcpsgsvsnseyeag 74 
                                       rVvvl+++pg+ +++++a+l++g+kG+vleg+G+G+lp    +ll  +ke+   +i+v++t+q ++ +v++ +ye+g
  gi|242399651|ref|YP_002995076.1| 206 RVVVLRVTPGLGGEIIDAVLDAGYKGIVLEGYGAGGLPYrksNLLSKIKEI-TPKIPVIMTTQALYDGVDMRKYEVG 281
                                       8*************************************6444888888887.779********************** PP

                                       .HHHHHTEEE-TT--HHHHHHHHHHHCTT---HHHHHHHH CS
                    Asparaginase_C  75 kelerlgvisaddmtpeaarikLmlllgkgldpaevrklf 114
                                       +++ + g+i a+dmt ea  +kLm++lg+++d +++r+++
  gi|242399651|ref|YP_002995076.1| 282 RKALETGIIPAKDMTKEATITKLMWALGHTKDVEKIREIM 321
                                       **************************************98 PP

>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   2.8e-05      0.17     136     186 ..       4      54 ..       1      58 [. 0.92
   2 ?   -2.8   0.0      0.64   3.8e+03     156     179 ..     293     316 ..     282     323 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.8e-05
                                       EEEESTTHHHHHHHHHHHHSTTBSHHHHHHHHHHHHHHHHHHBTTSCSSEE CS
                        Proteasome 136 avaiGsgseaaktalekeykedltleeavelavkalkealerdklsgknie 186
                                          iG+g + a +  e+ yk+ l+ +e+++la+  l+++++ d+++  ni+
  gi|242399651|ref|YP_002995076.1|   4 LLIIGTGGTIASAKTEQGYKSVLKIDEILKLAKIKLENGYKIDSTNIMNID 54 
                                       678******************************************999997 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.64
                                       TTBSHHHHHHHHHHHHHHHHHHBT CS
                        Proteasome 156 edltleeavelavkalkealerdk 179
                                       +d+t+e +++    al ++ + +k
  gi|242399651|ref|YP_002995076.1| 293 KDMTKEATITKLMWALGHTKDVEK 316
                                       667777776666666666655444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.35s 00:00:00.97 Elapsed: 00:00:00.55
# Mc/sec: 1820.63
//
Query:       gi|242399652|ref|YP_002995077.1|  [L=70]
Description: hypothetical protein TSIB_1677 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.033   14.6   0.6        0.1   13.1   0.6    1.8  1  DUF4288   Domain of unknown function (DUF4288)
      0.042   14.1   0.3      0.052   13.8   0.1    1.5  2  KIX       KIX domain
      0.048   13.1   0.2      0.057   12.9   0.1    1.3  1  DUF3829   Protein of unknown function (DUF3829)


Domain annotation for each model (and alignments):
>> DUF4288  Domain of unknown function (DUF4288)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.6   1.7e-05       0.1      27      57 ..      17      40 ..      15      68 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.7e-05
                           DUF4288 27 vLvkAdseeeAyekaeklgkeeeepyknadg 57
                                      ++v+Ads+e+A+e ae + k         ++
  gi|242399652|ref|YP_002995077.1| 17 RIVEADSFEKAKELAEHYVKA-------INK 40
                                      69***************8764.......344 PP

>> KIX  KIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   8.7e-06     0.052      39      69 ..       7      38 ..       2      57 .. 0.82
   2 ?   -2.6   0.0       1.2   6.9e+03      18      23 ..      63      68 ..      58      70 .] 0.48

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.7e-06
                               KIX 39 Rmeelieyark.vEkeafekakdrdeYYhlla 69
                                      R  e++ y+r+ vE+++fekak+ +e Y  + 
  gi|242399652|ref|YP_002995077.1|  7 RYGEMKWYVRRiVEADSFEKAKELAEHYVKAI 38
                                      5567777876438***************8765 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.2
                               KIX 18 lvdKlv 23
                                      lv+Kl 
  gi|242399652|ref|YP_002995077.1| 63 LVEKLE 68
                                      444443 PP

>> DUF3829  Protein of unknown function (DUF3829)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   9.6e-06     0.057      92     123 ..      10      40 ..       1      49 [. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.6e-06
                           DUF3829  92 eadaYYkqkdYkdDdfakgkelhaklltayka 123
                                       e++  Y ++  ++D f+k+kel++ +++a+++
  gi|242399652|ref|YP_002995077.1|  10 EMK-WYVRRIVEADSFEKAKELAEHYVKAINK 40 
                                       554.577888*******************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       710  (0.0396006); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 411.86
//
Query:       gi|242399653|ref|YP_002995078.1|  [L=740]
Description: RecJ-like exonuclease, containing OB-fold nucleic acid-binding domains [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-09   37.2   2.1    6.8e-09   35.9   2.1    1.7  1  S1               S1 RNA binding domain
    1.3e-08   34.7   0.2    3.3e-08   33.4   0.2    1.8  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
    1.1e-07   32.0  14.1     0.0017   18.7   1.1    2.5  2  DnaJ_CXXCXGXG    DnaJ central domain
    0.00047   20.3   0.1     0.0018   18.5   0.0    1.9  2  DHH              DHH family
      0.003   17.2   0.6      0.003   17.2   0.6    1.8  2  TackOD1          Thaumarchaeal output domain 1
  ------ inclusion threshold ------
      0.011   15.7  20.5      0.048   13.6   1.7    3.8  4  Anti-TRAP        Tryptophan RNA-binding attenuator protein in
      0.031   14.5   0.0       0.12   12.6   0.0    2.0  1  tRNA_anti_2      OB-fold nucleic acid binding domain
      0.043   14.2   0.0       0.12   12.7   0.0    1.8  1  Rep_fac-A_3      Replication factor A protein 3
      0.054   13.9   0.0       0.22   11.9   0.0    2.1  1  DHHA1            DHHA1 domain
      0.074   12.0   0.0       0.12   11.4   0.0    1.2  1  DUF2851          Protein of unknown function (DUF2851)
        2.3    7.4   4.4        2.6    7.2   0.2    2.5  3  DUF1356          Protein of unknown function (DUF1356)


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 !   35.9   2.1   4.2e-12   6.8e-09       2      72 ..     130     193 ..     129     194 .. 0.96

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 4.2e-12
                                       STTTCEEEEEEEEEETTEEEEEETTTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEEETTTTEEEE CS
                                S1   2 pekgevveGeVtsvtkgGafVelgngvegfvpaselsrdarvedpdevlkvGdevkvkvlkvdkdrrriil 72 
                                       +e+g+v++G + +v+++G+fV l  +v+g++ +++l          +++k+G+e+ v+vl+v+ ++++++l
  gi|242399653|ref|YP_002995078.1| 130 VEVGKVYKGAIDRVERFGVFVSLNPHVTGLIKKKDLLG-------RREYKPGEEILVQVLDVRPEKKEVDL 193
                                       689**********************************5.......5*********************9987 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 !   33.4   0.2     2e-11   3.3e-08       2      72 ..     228     295 ..     227     299 .. 0.93

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 2e-11
                                       EEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEEEEEEECTTSSEEEEEEE CS
                   tRNA_anti-codon   2 tvaGrvtsisdrsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvtGrvkrrpggelelkvee 72 
                                       +++G++t+i  + +g+   ++++Dgtg   + +f +   + + n+++Gd+v++ G+v++  g+ +++  ++
  gi|242399653|ref|YP_002995078.1| 228 RIRGKITQI--QVTGGPTVFTVTDGTGVTWAAAFEAPGVRAYPNIEVGDIVEIIGKVSFHAGE-IQIETSD 295
                                       79*******..************************************************9988.9987666 PP

>> DnaJ_CXXCXGXG  DnaJ central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   1.1     1e-06    0.0017      42      66 ..       4      28 ..       1      35 [. 0.80
   2 !   17.8   5.9     2e-06    0.0033       1      54 [.      61     118 ..      51     127 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1e-06
                     DnaJ_CXXCXGXG 42 stCpeCeGtGkvikekdkCkkCkGk 66
                                      ++CpeC GtGk+ + +++C+ C+G 
  gi|242399653|ref|YP_002995078.1|  4 KECPECYGTGKIKSGEKECEVCNGW 28
                                      6799999999988888889999884 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 2e-06
                     DnaJ_CXXCXGXG   1 CkkCkGsgakkgkkktCktCkGsG.vvree.....qkt.lgpfvqqsqstCpeCeGtGkvi 54 
                                       C++C+G+g  +   +tC+tC+GsG v         + +  +p + +++  C+eCe + kv+
  gi|242399653|ref|YP_002995078.1|  61 CPECHGRGVVP-VYDTCPTCGGSGrVLACDicgriK-EsWEPGM-ETSWVCSECEKKYKVV 118
                                       99999999844.367899999999442222333322.2255533.4677999999887776 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.1e-06    0.0018       3      57 ..     358     481 ..     356     524 .. 0.74
   2 ?   -1.6   0.0         2   3.3e+03      40      52 ..     551     563 ..     540     568 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.1e-06
                                       EEE-ECSSSHHHHHHHHHHHH........................................................ CS
                                       xxxxxxxxxxxxxxxxxxxxx........................................................ RF
                               DHH   3 livghknpDtDsigSaialan........................................................ 23 
                                       ++   ++ DtD+ ++ +al++                                                        
  gi|242399653|ref|YP_002995078.1| 358 IV--RHHADTDGYTAGLALEYaivplleelspdpqakwkffkrrpsrapfyeledvlkdiifmledherfgdplpll 432
                                       44..7899*******99999988888888888888888888888888887777777777777777777777777777 PP

                                       CECS--TCGGCGCCH..HCCCSEEEEEEE-S---S.............S CS
                                       xxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxx.............x RF
                               DHH  24 llvDhneksqavege..akeeaedviiiDHHrlge.............e 57 
                                       ++vD++ + ++  ++  +++ ++ ++++DHH + e             +
  gi|242399653|ref|YP_002995078.1| 433 VIVDNGGTVEDIPAYkrIRAYGVPIVVVDHHDPREfisedraavdeyvD 481
                                       7*****99988776666999*************9766666655555532 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2
                                       CCCSEEEEEEE-S CS
                                       xxxxxxxxxxxxx RF
                               DHH  40 keeaedviiiDHH 52 
                                       ++ +++ ++iDH 
  gi|242399653|ref|YP_002995078.1| 551 EDLKKIAEVIDHE 563
                                       5678999*****5 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.8         3     5e+03      75      81 ..       5      11 ..       2      28 .. 0.41
   2 !   17.2   0.6   1.8e-06     0.003      74     132 ..      59     114 ..      35     120 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3
                           TackOD1 75 lCpsCks 81
                                       Cp+C +
  gi|242399653|ref|YP_002995078.1|  5 ECPECYG 11
                                      3444433 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 1.8e-06
                           TackOD1  74 rlCpsCksg.hlnvrevCpkCkSidieeqelihhftCgnvgpeeeflkegkleCpkCktk 132
                                         Cp+C++   + v ++Cp C+     +  ++ +  Cg++++  e   e++ +C++C++k
  gi|242399653|ref|YP_002995078.1|  59 IPCPECHGRgVVPVYDTCPTCGG----SGRVLACDICGRIKESWEPGMETSWVCSECEKK 114
                                       46*****961567999*****96....5799**************************997 PP

>> Anti-TRAP  Tryptophan RNA-binding attenuator protein inhibitory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   1.7     3e-05     0.048      12      44 ..       5      33 ..       2      43 .. 0.88
   2 ?   11.4   0.3   0.00014      0.23      27      43 ..      55      71 ..      50      74 .. 0.82
   3 ?    4.7   8.4     0.017        28      10      43 ..      58      86 ..      58      93 .. 0.78
   4 ?   -0.9   5.4         1   1.7e+03      13      42 ..      76      85 ..      73     117 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3e-05
                                      E-TTTTTTSEETTE......E-TTTTTSSEEE- CS
                         Anti-TRAP 12 kCdaCngsGkiepeeprasleCPkCsGkglipT 44
                                      +C++C g+Gki++       eC  C+G g +p 
  gi|242399653|ref|YP_002995078.1|  5 ECPECYGTGKIKSG----EKECEVCNGWGYVPA 33
                                      7***********99....569********9996 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00014
                                      .....E-TTTTTSSEEE CS
                         Anti-TRAP 27 prasleCPkCsGkglip 43
                                      +   ++CP+C G+g++p
  gi|242399653|ref|YP_002995078.1| 55 EVDEIPCPECHGRGVVP 71
                                      45679**********99 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.017
                                      EEE-TTTTTTSEETTE......E-TTTTTSSEEE CS
                         Anti-TRAP 10 EtkCdaCngsGkiepeeprasleCPkCsGkglip 43
                                      E +C++C+g G ++  +      CP C+G g ++
  gi|242399653|ref|YP_002995078.1| 58 EIPCPECHGRGVVPVYD-----TCPTCGGSGRVL 86
                                      67888888888888873.....688888888766 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 1
                                      -TTTTTTSEETTE......E-TTTTTSSEE CS
                         Anti-TRAP 13 CdaCngsGkiepeeprasleCPkCsGkgli 42
                                      C++C gsG+                    +
  gi|242399653|ref|YP_002995078.1| 76 CPTCGGSGR--------------------V 85
                                      555555554....................4 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 ?   12.6   0.0   7.3e-05      0.12      17      90 ..     222     292 ..     210     297 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.3e-05
                       tRNA_anti_2  17 elkkavwvrGeisnlkrkasghvYftLkDekakisavifrsraaklkft....ledGmkVlvkgrlsvYeprGsyql 89 
                                          +++ +rG i+++ + + g + ft +D +     v ++ ++++  ++    +e G+ V + g++s+++  G++q+
  gi|242399653|ref|YP_002995078.1| 222 MAGRTIRIRGKITQI-QVTGGPTVFTVTDGTG----VTWAAAFEAPGVRaypnIEVGDIVEIIGKVSFHA--GEIQI 291
                                       334789*********.445899*******885....444444444443333449**************97..44555 PP

                       tRNA_anti_2  90 i 90 
                                        
  gi|242399653|ref|YP_002995078.1| 292 E 292
                                       5 PP

>> Rep_fac-A_3  Replication factor A protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   7.5e-05      0.12      14      76 ..     220     291 ..     216     307 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.5e-05
                                       GGGTTSEEEEEEEEEEE.TTSSEEEEE-TTS-E.........EEEEESS--SS---SEEEEEEEE-T.TS-EEE CS
                       Rep_fac-A_3  14 sqfvgrtvrivgkvesv.psgktlilqstdggs.........vtvrlsedstleiskwvEvvGkvsd.dlgirl 76 
                                       +++ grt+ri gk++++  +g   + + tdg             vr  +  ++e++ +vE++Gkvs  + +i++
  gi|242399653|ref|YP_002995078.1| 220 KEMAGRTIRIRGKITQIqVTGGPTVFTVTDGTGvtwaaafeaPGVRAYP--NIEVGDIVEIIGKVSFhAGEIQI 291
                                       56789***********987776555544444443488776555556555..7*************986555554 PP

>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00013      0.22      39     137 ..     630     733 ..     585     734 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00013
                                       TCEEEEEECHCCHHHHHHHHHHHHHHTHG.BT.TCEEEEEEEECTEEEEEEEESSH....SS-HH...HHHHHHHHH CS
                             DHHA1  39 gvkvlvaevgeewdagalgiaadklkskl.kk.pvivfvakeegdkvkvsarskkd....gvdag...elakeaaak 106
                                       +  +++ +++  +  +  g + d++k+++ ++ p+ +++++ +    + ++r++++    ++d++   ++++e  ++
  gi|242399653|ref|YP_002995078.1| 630 DIELYAPKFEYPAPGKLSGLIHDYFKEQHgEDnPILTLAYGPD---FA-VVRASDGmqvyNFDLNliiKVLQEKLPD 702
                                       5555555663333336666678999998864456666666543...44.4455545589977777335555668999 PP

                                       TTCCEEEETCEEEEEEEHCHHHHHHHHHHHH CS
                             DHHA1 107 lgggGGGHdlAaGagipaekleealealeea 137
                                        g  GGGH +A   +  ++k +e+le++ + 
  gi|242399653|ref|YP_002995078.1| 703 AGVEGGGHSFAGSIKFFEGKRKEVLEEFAKQ 733
                                       9**********98888778888888888776 PP

>> DUF2851  Protein of unknown function (DUF2851)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   7.2e-05      0.12     217     275 ..     350     409 ..     324     420 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7.2e-05
                           DUF2851 217 alllGqaglLe.eeledeyfkklkkeyeflqkkfslkeleasewkflrlRPanfPtiRla 275
                                       a++ G   +++ ++ +d y++ l  ey+ +    +l++ ++++wkf++ RP+  P   l 
  gi|242399653|ref|YP_002995078.1| 350 AIFEGRPIIVRhHADTDGYTAGLALEYAIVPLLEELSPDPQAKWKFFKRRPSRAPFYELE 409
                                       455555555543456699***********************************9988775 PP

>> DUF1356  Protein of unknown function (DUF1356)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.7       0.2   3.2e+02      35      48 ..       6      19 ..       2      25 .. 0.82
   2 ?   -3.0   0.0       2.1   3.4e+03      35      47 ..      22      34 ..      20      36 .. 0.89
   3 ?    7.2   0.2    0.0016       2.6      15      44 ..      52      85 ..      42      88 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.2
                           DUF1356 35 CptCqGtGeiPreq 48
                                      Cp C GtG+i ++ 
  gi|242399653|ref|YP_002995078.1|  6 CPECYGTGKIKSGE 19
                                      **********8764 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.1
                           DUF1356 35 CptCqGtGeiPre 47
                                      C  C G G++P +
  gi|242399653|ref|YP_002995078.1| 22 CEVCNGWGYVPAD 34
                                      99*********87 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0016
                           DUF1356 15 skedvsqvpyveatgrdsv....tCptCqGtGei 44
                                       +e+v ++p+ e  gr+ v    tCptC G+G++
  gi|242399653|ref|YP_002995078.1| 52 VEEEVDEIPCPECHGRGVVpvydTCPTCGGSGRV 85
                                      567888999999999998877889********87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (740 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      561  (0.0312901); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); 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):              11  [number of targets reported over threshold]
# CPU time: 0.79u 0.32s 00:00:01.11 Elapsed: 00:00:00.52
# Mc/sec: 4283.11
//
Query:       gi|242399654|ref|YP_002995079.1|  [L=160]
Description: membrane protein [Thermococcus sibiricus MM 739]
Scores for complete 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-14   51.6   0.4      1e-13   51.2   0.4    1.0  1  DUF2391       Putative integral membrane protein (DUF2391)
  ------ inclusion threshold ------
      0.059   13.6   0.5        1.9    8.7   0.3    2.1  2  THOC7         Tho complex subunit 7
       0.19   12.2   6.1       0.47   10.9   0.2    2.5  2  DUF2663       Protein of unknown function (DUF2663)
        0.2   12.0   2.9        1.2    9.4   0.7    2.2  2  ABC_tran_CTD  ABC transporter C-terminal domain
        5.5    6.9  10.7       0.41   10.5   3.4    2.2  2  DUF2721       Protein of unknown function (DUF2721)


Domain annotation for each model (and alignments):
>> DUF2391  Putative integral membrane protein (DUF2391)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.2   0.4   2.9e-17     1e-13     122     266 ..      16     158 ..      10     159 .. 0.87

  Alignments for each domain:
  == domain 1  score: 51.2 bits;  conditional E-value: 2.9e-17
                           DUF2391 122 ggdeeeeeeeekeeeee.aatladlgltliGAlllafniAPTeEvvllaaavspvqllalillsLlisylivfeagf 197
                                       +++  e +ee ++++++ +  + d++  +iG++ ++++   TeE+  +a +++ +++l++ l++L ++yl++ +a++
  gi|242399654|ref|YP_002995079.1|  16 SKQMGEIQEELDRKNKPdKLGWDDVVQEIIGSITFSLPFLFTEEIWDIAKTLNMWRTLVIFLMTLFMAYLFISKAKL 92 
                                       444444455544433332567899***************************************************** PP

                           DUF2391 198 tgqekreeqrgifqrflsetvvsYlvsLlvslllLwffgrldgdplsevlsatvvLglpaaiGaaaaRl 266
                                       ++ ek e +r i +r+l+ tvvsY+ s l  l+ L+ ++ +++ +l + +sat++ +  a iGa a  l
  gi|242399654|ref|YP_002995079.1|  93 SNIEKEEWHR-IPKRLLTVTVVSYMTSTL--LIYLYGINNIANFSLGQYISATIIVSTFAVIGAIAVDL 158
                                       ***9998887.88999*********9976..789******************************88665 PP

>> THOC7  Tho complex subunit 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.3   0.00054       1.9      80     114 ..       1      35 [.       1      36 [. 0.93
   2 ?    3.1   0.0      0.03   1.1e+02       4      28 ..      88     112 ..      87     138 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00054
                             THOC7  80 ieseieavreeieelkaqLeearatranrkeydel 114
                                       +ese++++ e+ ++l +q+ e +++++++ + d+l
  gi|242399654|ref|YP_002995079.1|   1 MESELKKLNENVAKLSKQMGEIQEELDRKNKPDKL 35 
                                       58999************************999986 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.03
                             THOC7   4 iksRLlnveerplkrltkrllkllt 28 
                                        k +L n e+ +  r+ krll+++ 
  gi|242399654|ref|YP_002995079.1|  88 SKAKLSNIEKEEWHRIPKRLLTVTV 112
                                       6899*****************9543 PP

>> DUF2663  Protein of unknown function (DUF2663)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.8     0.018        66      15      44 ..      63      92 ..      57      97 .. 0.75
   2 ?   10.9   0.2   0.00013      0.47       8      69 ..      96     152 ..      92     159 .. 0.69

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.018
                           DUF2663 15 lekrllllsllallvlllfliyvliksssl 44
                                      ++k l+++++l +++++lf+ y+ i + +l
  gi|242399654|ref|YP_002995079.1| 63 IAKTLNMWRTLVIFLMTLFMAYLFISKAKL 92
                                      567888999999999999999997765554 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00013
                           DUF2663   8 rKkkweklekrllllsllallvlllfliyvlikssslssllsallessvlllllllvallyv 69 
                                        K++w ++ krll++++++ ++++l liy+    ++++++ ++ l++ ++ ++++ +++++ 
  gi|242399654|ref|YP_002995079.1|  96 EKEEWHRIPKRLLTVTVVSYMTSTL-LIYL----YGINNIANFSLGQYISATIIVSTFAVIG 152
                                       59***********999998765544.4455....4566666666666666666666655554 PP

>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.7   0.00035       1.2      13      60 ..       8      29 ..       1      34 [. 0.63
   2 ?    2.6   0.1     0.046   1.6e+02       1      17 [.      91     107 ..      91     110 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00035
                      ABC_tran_CTD 13 leaeIeaLEeeiaeleaeladpelysdpeklaelsaeleeleaeLeel 60
                                      l                           e +a+ls+++ e+++eL+++
  gi|242399654|ref|YP_002995079.1|  8 LN--------------------------ENVAKLSKQMGEIQEELDRK 29
                                      33..........................55667777777777777665 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.046
                      ABC_tran_CTD   1 klsykeqreleeleaeI 17 
                                       kls+ e+ e+ ++++++
  gi|242399654|ref|YP_002995079.1|  91 KLSNIEKEEWHRIPKRL 107
                                       89************986 PP

>> DUF2721  Protein of unknown function (DUF2721)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.7      0.17   6.1e+02      71      88 ..      72      89 ..      62     100 .. 0.74
   2 ?   10.5   3.4   0.00011      0.41      62     115 ..     103     156 ..      98     159 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.17
                           DUF2721 71 vlsallvvlvvlllflsa 88
                                      +l ++l++l ++ lf+s+
  gi|242399654|ref|YP_002995079.1| 72 TLVIFLMTLFMAYLFISK 89
                                      677888888888888854 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00011
                           DUF2721  62 lirrailllvlsallvvlvvlllflsallsldlsllaailfvlalllllvslll 115
                                       + +r +++ v+s ++++l++ l+ ++++ +++l ++++++ +++ +++++++++
  gi|242399654|ref|YP_002995079.1| 103 IPKRLLTVTVVSYMTSTLLIYLYGINNIANFSLGQYISATIIVSTFAVIGAIAV 156
                                       56788999*****************************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1815  (0.101233); expected 358.6 (0.02)
Passed bias filter:                     1085  (0.0605165); expected 358.6 (0.02)
Passed Vit filter:                       203  (0.0113224); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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 0.36s 00:00:01.03 Elapsed: 00:00:00.56
# Mc/sec: 861.95
//
Query:       gi|242399655|ref|YP_002995080.1|  [L=341]
Description: hypothetical protein TSIB_1680 [Thermococcus sibiricus MM 739]
Scores for 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-56  190.0   3.0      5e-56  190.0   3.0    1.5  2  DUF3226    Protein of unknown function (DUF3226)
  ------ inclusion threshold ------
      0.052   13.5   0.2       0.13   12.2   0.2    1.6  1  ApoB100_C  Apolipoprotein B100 C terminal
      0.078   12.7   0.2       0.13   12.0   0.2    1.3  1  DUF2913    Protein of unknown function (DUF2913)


Domain annotation for each model (and alignments):
>> DUF3226  Protein of unknown function (DUF3226)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1      0.36   2.1e+03     218     233 ..      29      44 ..       8      81 .. 0.59
   2 !  190.0   3.0   8.4e-60     5e-56       1     229 [.     104     331 ..     104     338 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.36
                                       SHHHHHHHHHHTT-HH CS
                           DUF3226 218 nrekvlrllslvelle 233
                                       n+ek++++++++++ e
  gi|242399655|ref|YP_002995080.1|  29 NKEKLKKFVNKLNGNE 44 
                                       3333333333333333 PP

  == domain 2  score: 190.0 bits;  conditional E-value: 8.4e-60
                                       EEEEE-SSHHHHHHHHHHHHHTT--EE--S------CCC-TT-..--EEEEETTEEEEEE-S--TTTHHHHHHHHHH CS
                           DUF3226   1 vrllllEGktDvsFFkallkkLygFrEakklceelkvlekvgelskaivLekddvklvvihseGksklkkaLkavlk 77 
                                       v++l+ EGktD++FFka  kk++gF+E+k l+++lk++e ++e+++  +++++d ++++i+seG+ +++++L+++l+
  gi|242399655|ref|YP_002995080.1| 104 VSVLFCEGKTDSKFFKASYKKVFGFKETKDLPPNLKLIETLFERDNYELIKNEDGYIAIIPSEGNAGVIRNLENFLR 180
                                       689************************************************************************** PP

                                       HHHC--.-EEEEEEEEETTSSS-HHHHHHTT-TTS..--EEETTEEEETTEEEEEEEET-S---.-TTB----.SHH CS
                           DUF3226  78 aiklllsnveiigvarDvDeeedvlnwaksilkeagfevrkkddfllienvkivplgignldfn.eelidlkk.elE 152
                                       a++++++ v++igva+D+De e++  + ++ +k ++f  +++++ + +  + i+pl ig  +++  + ++++k ++E
  gi|242399655|ref|YP_002995080.1| 181 AMEVFNFYVQKIGVAIDIDESEEA-VMQSIKGKLSSFRYKVSKKGFKVGSTEIIPLLIG-TKIDlGPCVEWQKpTVE 255
                                       ***********************9.899*******************************.55552599*****9*** PP

                                       HHHHHHHHHTTHHHH-SHHHHHHHHHHTS-B-HHHHHHHHHHHTT--SSBHHHHHHHHHHHHHHHSHHHHHHHHHHT CS
                           DUF3226 153 lllallakkesileklrgslealsedlgrkLkPkdvmhllaiAknytGdslsGlYekfieklihrnrekvlrllslv 229
                                       + ++ + + +  ++kl  +++ l  dl rkLkPk+v++l++ Ak+++G+ l+G+Ye  i+++ + + ek+l+   l 
  gi|242399655|ref|YP_002995080.1| 256 DFMLAILEGDRTFKKLDRTINILCLDLKRKLKPKEVIYLAMAAKKFWGN-LEGFYEMSIMRTPKWKVEKILKESRLY 331
                                       *************************************************.**********99886666665544444 PP

>> ApoB100_C  Apolipoprotein B100 C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   2.2e-05      0.13       3      36 ..      30      62 ..      29      71 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.2e-05
                         ApoB100_C  3 kakLqefsdqlsdyyEkliaeskrLiDLsIekYh 36
                                      k+kL+ f ++l   +E +++ s  LiDL  e+++
  gi|242399655|ref|YP_002995080.1| 30 KEKLKKFVNKLN-GNEMIVTASLELIDLILEEFQ 62
                                      79*********9.89****************995 PP

>> DUF2913  Protein of unknown function (DUF2913)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   2.2e-05      0.13      88     166 ..      22     101 ..       7     123 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.2e-05
                           DUF2913  88 vaeeekeldskleallaeleekewvvitdeevvd.klkldsdgqeslvvcakqleqhfdeegelikpislyvrgdea 163
                                       +++e  ++++kl++++++l+ +e +v+++ e+ d  l+ ++ +++ l+ +++  e  f+e  el k + + +rg+e 
  gi|242399655|ref|YP_002995080.1|  22 LFPEYGKNKEKLKKFVNKLNGNEMIVTASLELIDlILEEFQGEEHFLIYSNTGKELTFKETYELRKYLDFDLRGTET 98 
                                       4556666799************************55666777777777788888899*************9999998 PP

                           DUF2913 164 efv 166
                                       +  
  gi|242399655|ref|YP_002995080.1|  99 KET 101
                                       744 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); 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:                         3  (0.000167327); expected 0.2 (1e-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 0.35s 00:00:00.99 Elapsed: 00:00:00.56
# Mc/sec: 1830.09
//
Query:       gi|242399656|ref|YP_002995081.1|  [L=384]
Description: glycosyltransferase [Thermococcus sibiricus MM 739]
Scores for complete 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   37.7   0.0    2.8e-09   37.0   0.0    1.3  1  Glycos_transf_2  Glycosyl transferase family 2
     0.0016   18.4   0.0     0.0033   17.3   0.0    1.4  1  Glyco_tranf_2_3  Glycosyltransferase like family 2


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   0.0   3.2e-13   2.8e-09       2     124 ..       9     138 ..       8     169 .. 0.83

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 3.2e-13
                                       EEEEESS-TTTHHHHHHHHHHH..GGCCEEEEEEEEES-SSCHHHHHGGGCH...C-TTEEEEEESSS-HHHHHHHH CS
                   Glycos_transf_2   2 vviptyNeektlletlesllaq..dpypdfeiivvDDgStDetveileelak...edprvrvirreenvGkagalna 73 
                                       v ip+yN ++t++ +++ +++   ++     ii  D gS+D+t++i+ +       + r +v++ +   Gk++a+ +
  gi|242399656|ref|YP_002995081.1|   9 VGIPSYNNAETIEYVVKQAAEGlkKYFNGGLIINSDGGSNDGTRDIVMKTPVpdgVEVRSTVYKWPIP-GKGSAMKE 84 
                                       679****************99995555555566666669**********9778777888889999999.******** PP

                                       HHHH--SS...EEEEEESSE.EE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCC CS
                   Glycos_transf_2  74 glraatgd...yilflDaDd.epdpdwleklvealekdgadvvlgqrprifgetd 124
                                        l+ a+ +    ++f+D+D+  ++p+w+ k+++++e+ g+  v++   r++++ +
  gi|242399656|ref|YP_002995081.1|  85 VLEIARDEgadAVVFVDSDLrSITPEWVYKFAKPIEE-GYHFVAPLYLRHKYDGT 138
                                       *******************9558999***********.88777777666666554 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 !   17.3   0.0   3.7e-07    0.0033       4     120 ..       7     126 ..       5     145 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.7e-07
                   Glyco_tranf_2_3   4 lavlVptfneedvlgevlesllaq.e.y.prvevvvvvdesdaetlevaeelaaalp.dvrvrvvvnarnlgstgks 76 
                                       ++v +p++n++++++ v+ +++   + y     ++  + +s ++t++ ++ +  + p +v+vr  ++++ + + gk 
  gi|242399656|ref|YP_002995081.1|   7 VIVGIPSYNNAETIEYVVKQAAEGlKkYfNGGLIINSDGGSNDGTRDIVMKT--PVPdGVEVRS-TVYKWPIP-GKG 79 
                                       89********************77445845566677777799*******986..6662334553.33566666.888 PP

                   Glyco_tranf_2_3  77 ralnealravk...sdlvllvDdDtvv.ePdtlkrllqffltpkvgav 120
                                        a++e+l++++    d v++vD+D +   P+ + +++  +  +++++v
  gi|242399656|ref|YP_002995081.1|  80 SAMKEVLEIARdegADAVVFVDSDLRSiTPEWVYKFAKPI-EEGYHFV 126
                                       8888999998866688********9987888888877776.6666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       862  (0.0480785); expected 358.6 (0.02)
Passed bias filter:                      596  (0.0332422); 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: 0.69u 0.35s 00:00:01.04 Elapsed: 00:00:00.54
# Mc/sec: 2126.55
//
Query:       gi|242399657|ref|YP_002995082.1|  [L=341]
Description: NADH dependent dyhydrogenase [Thermococcus sibiricus MM 739]
Scores for complete 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   0.4    1.1e-28  100.5   0.2    2.0  2  GFO_IDH_MocA    Oxidoreductase family, NAD-binding Rossmann f
    6.9e-07   29.9   0.2    1.2e-06   29.1   0.2    1.4  1  NAD_binding_3   Homoserine dehydrogenase, NAD binding domain
    8.3e-07   29.0   0.0    1.8e-06   28.0   0.0    1.6  1  GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta 
  ------ inclusion threshold ------
       0.02   15.4   0.2      0.065   13.8   0.2    1.9  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent


Domain annotation for each model (and alignments):
>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.5   0.2   2.4e-32   1.1e-28       1     120 []       4     122 ..       4     122 .. 0.94
   2 ?    0.3   0.0      0.26   1.2e+03       5      42 ..     195     231 ..     193     276 .. 0.71

  Alignments for each domain:
  == domain 1  score: 100.5 bits;  conditional E-value: 2.4e-32
                                       EEEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTTESEEEE-S-GGGHHH CS
                      GFO_IDH_MocA   1 lrvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysdleelladpeidavivatpngthee 77 
                                       l+v+iiG+G+i    +++  ++ ++ +vv  +d++a+ra+++a++f+++ y++l++ l+  + d++ + tp++th+e
  gi|242399657|ref|YP_002995082.1|   4 LKVGIIGCGNIFNLAHKNALKNIKEVKVVSCMDIKAKRAKEAAKEFNAKPYTNLDKFLD-LDLDVIEILTPTYTHAE 79 
                                       68*********666666666666999*******************************99.67*************** PP

                                       HHHHHHHTT-EEEEESSS-SSHHHHHHHHHHHHHHTS-EEEE- CS
                      GFO_IDH_MocA  78 lakaaleagkhvllEKPlattveeakelvelaekkgklvsvgy 120
                                       la++al+ gkhv++EKP+a+t eea++++++aek+g  + vg+
  gi|242399657|ref|YP_002995082.1|  80 LAIKALKSGKHVIVEKPIALTSEEAQKMIKTAEKEGLWLLVGH 122
                                       ************************************9999986 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.26
                                       EETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHH CS
                      GFO_IDH_MocA   5 iiGaGkigskhlrplnesqrleevvalldpdaeraeav 42 
                                       i G+Gk+ +k++ ++n+++++  ++  +++++    +v
  gi|242399657|ref|YP_002995082.1| 195 ILGIGKAIRKEA-KINNTHDHFLMMIQFEENKTGLAEV 231
                                       8899***99999.7777767665555555555555544 PP

>> NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.2   2.7e-10   1.2e-06       6     111 ..      10     115 ..       6     120 .. 0.76

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 2.7e-10
                                       HHHHHHHHHH---S...SEEEEEEEEESSEEE-TTHHHHHT--CB---HHHHHHHHS-EEEEE-.S--HHHHTTHHH CS
                     NAD_binding_3   6 Gsavleqlkrqqse...ielelvavadrdsllskdrkallasealtldlddliahldpdvvVEc.asseavaelvlk 78 
                                       G + +  l+ +++     e+++v ++d + +++++ +a+  +++ +++ld++++ ld dv +E  ++    ael+ k
  gi|242399657|ref|YP_002995082.1|  10 GCGNIFNLAHKNALkniKEVKVVSCMDIK-AKRAKEAAKEFNAKPYTNLDKFLD-LDLDV-IEIlTPTYTHAELAIK 83 
                                       43333333333333344579999999999.7777788888889999*****999.77775.6888************ PP

                                       HHHTTEEEE-S--CGGG-HHHHHHHTSSSTTS- CS
                     NAD_binding_3  79 aLkagkdvvtankgaladealyeeLreaaeang 111
                                       aLk+gk+v++    al+ ++  +++++ ae+ g
  gi|242399657|ref|YP_002995082.1|  84 ALKSGKHVIVEKPIALT-SEEAQKMIKTAEKEG 115
                                       *****************.667777777777766 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 !   28.0   0.0     4e-10   1.8e-06      19     111 ..     149     241 ..     134     246 .. 0.75

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 4e-10
                                       EECBEEECHHHHCCGGSHHCSTSHHHHTCHHHHHHHHHHHTSEEEEEEEEE.SEEESCTCCSCSEEE..EEEEEEEE CS
                    GFO_IDH_MocA_C  19 tldtragaeakkrwkrrkkksgGvlgdlgiHdiDllqwLfGqppsvvaalgrmrqnaeaaededaav..msvlnlek 93 
                                         +  + +++++ w + ++k+gGv++dlg+H  D+l+w f ++p+++  +g  + +++ a+++ + +  +   ++e 
  gi|242399657|ref|YP_002995082.1| 149 KAEVQRLPFSESAWYWKPNKGGGVAIDLGVHVTDFLRWYFKSEPIKILGIG--KAIRKEAKINNTHDhfLMMIQFEE 223
                                       567788899999999999******************************998..677666666665555544556666 PP

                                       TTEEEEEEEECCTSSSEE CS
                    GFO_IDH_MocA_C  94 gsgevitlesgvskglsi 111
                                       ++  ++  ++++s ++++
  gi|242399657|ref|YP_002995082.1| 224 NKTGLAEVSWAYSYPARY 241
                                       666666666666666655 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   1.5e-05     0.065       1      90 [.       5      90 ..       5      95 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.5e-05
                                      EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHH.H-SEEEE-S-HHHHHHHH CS
                     F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaae.eadvvvlavkpedveevl 78
                                      k+giiG+Gn+     +++l++  ++ ++v   + + ++a+e+a+e+++k  + +  + ++ + dv+ +  +++ ++e++
  gi|242399657|ref|YP_002995082.1|  5 KVGIIGCGNIFNLAHKNALKN-IKEVKVVSCMDIKAKRAKEAAKEFNAKPYT-NLDKFLDlDLDVIEILTPTYTHAELA 81
                                      79*******976666666666.6666666677999999*******9988888.66667777888997777777777766 PP

                                      HHCGHHHHTTSE CS
                     F420_oxidored 79 selakdalkgkl 90
                                       ++   +++gk 
  gi|242399657|ref|YP_002995082.1| 82 IKA---LKSGKH 90
                                      444...344444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); 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: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.54
# Mc/sec: 1910.66
//
Query:       gi|242399658|ref|YP_002995083.1|  [L=333]
Description: NADH-dependent dyhydrogenase related protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.5e-22   79.5   0.1    5.2e-22   78.9   0.1    1.2  1  GFO_IDH_MocA    Oxidoreductase family, NAD-binding Rossmann f
    0.00019   21.4   0.0    0.00063   19.7   0.0    2.0  1  GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta 


Domain annotation for each model (and alignments):
>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.9   0.1   5.8e-26   5.2e-22      16     118 ..      18     121 ..       2     123 .. 0.84

  Alignments for each domain:
  == domain 1  score: 78.9 bits;  conditional E-value: 5.8e-26
                                       HHHHHHTTTTEEEEEEECSSHHHHHHH..HHHTTHEEESSHHHHHTCTTESEEEE-S-GGGHHHHHHHHHHTT-EEE CS
                      GFO_IDH_MocA  16 lrplnesqrleevvalldpdaeraeav..aesfgveaysdleelladpeidavivatpngtheelakaaleagkhvl 90 
                                       + +  +s++++++ a+   +a+   a+  a+++++++ys++e ll+d+++dav++a+ ++ h+e+a++a+e gkh+l
  gi|242399658|ref|YP_002995083.1|  18 G-KTFASNPKAKLYAISGDGANTDVAIaeAQKMKAKFYSNYESLLKDEKVDAVYIAIETYRHKEIAIRAAEEGKHIL 93 
                                       4.3344557778888887777776666778888888***************************************** PP

                                       EESSS-SSHHHHHHHHHHHHHHTS-EEE CS
                      GFO_IDH_MocA  91 lEKPlattveeakelvelaekkgklvsv 118
                                       lEKP+a+t+e+a+e++++++k+g++++v
  gi|242399658|ref|YP_002995083.1|  94 LEKPIALTLEDADEIIRAVKKAGVKLMV 121
                                       *************************998 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 !   19.7   0.0     7e-08   0.00063       1     111 [.     135     246 ..     135     251 .. 0.64

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 7e-08
                                       HHHHHTTTTSSEEEEEEEEECBEEECHHHHCCGGSH.......HCSTSHHHHTCHHHHHHHHHHHTSEEEEEE.EEE CS
                    GFO_IDH_MocA_C   1 KelIengklGevvsvdvwtldtragaeakkrwkrrk.......kksgGvlgdlgiHdiDllqwLfGqppsvva.alg 69 
                                       K++I++g++G+  ++   + +  + +++ + +  ++       k +gG ++d + H iD l wL + +p +++ ++g
  gi|242399658|ref|YP_002995083.1| 135 KAMIDSGEIGNLEYI---YAISEYVKPPIFLEGLDMswfldknKSGGGGFMDTAPHGIDSLLWLINDEPKSIYaNIG 208
                                       678888888888888...34444444443333333334444489999******************988877763665 PP

                                       .SEEESCTCCSCSEEEEEEEEEEETTEEEEEEEECCTSSSEE CS
                    GFO_IDH_MocA_C  70 rmrqnaeaaededaavmsvlnlekgsgevitlesgvskglsi 111
                                        + +     +d ++a   vl +  g+++v +++++  kg+s+
  gi|242399658|ref|YP_002995083.1| 209 PKIFGF-PVDDIGTA---VLEFKNGVVAVLNAGWANPKGYSY 246
                                       433322.22233333...577777777777777777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); 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: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 2017.96
//
Query:       gi|242399659|ref|YP_002995084.1|  [L=338]
Description: Transcriptional regulator TrmB [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-45  154.5   0.5    3.2e-45  154.1   0.5    1.1  1  Regulator_TrmB   Archaeal transcriptional regulator TrmB
    7.4e-23   80.2   0.1    9.3e-22   76.7   0.1    2.5  2  TrmB             Sugar-specific transcriptional regulator Trm
  ------ inclusion threshold ------
      0.011   15.6   0.0      0.023   14.6   0.0    1.6  1  MarR_2           MarR family
      0.016   15.1   0.0      0.034   14.1   0.0    1.4  1  MarR             MarR family
      0.037   14.1   0.0       0.16   12.1   0.0    2.0  2  HTH_9            RNA polymerase III subunit RPC82 helix-turn-
      0.089   12.7   2.6       0.47   10.4   1.0    2.5  2  ADH_N_assoc      Alcohol dehydrogenase GroES-associated
      0.097   13.0   0.1        5.3    7.5   0.0    2.4  2  Rrf2             Transcriptional regulator
       0.12   12.4   0.3       0.26   11.3   0.1    1.7  2  Coatomer_b_Cpla  Coatomer beta subunit appendage platform
       0.17   10.8   0.0       0.24   10.3   0.0    1.1  1  DUF3533          Protein of unknown function (DUF3533)
       0.21   11.4   0.0        0.5   10.2   0.0    1.6  1  HTH_IclR         IclR helix-turn-helix domain
       0.25   11.5   1.0         27    5.0   0.1    2.4  2  CRIC_ras_sig     Connector enhancer of kinase suppressor of r


Domain annotation for each model (and alignments):
>> Regulator_TrmB  Archaeal transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.1   0.5   1.9e-48   3.2e-45       2     231 ..     111     337 ..     110     338 .] 0.92

  Alignments for each domain:
  == domain 1  score: 154.1 bits;  conditional E-value: 1.9e-48
                                       EEEESSHHHHHHHHHHHHHH-SSEEEEEE-GGGHHHHHHHHHHHHHTT-EEEEEESS----GGGSSSSEEEEEE-S- CS
                    Regulator_TrmB   2 vwvvksretvierieelIesAenelivslpselLeelreeliaaaergvtVllliypdedleeldleevatevrvrr 78 
                                       v vvks++t+ ++i+e I++ ++ l +++ps++Le++ + l+++++  +tV l +y+     ++d  +va+++rvr+
  gi|242399659|ref|YP_002995084.1| 111 VIVVKSKTTLENYIKEAIKNVKYHLSLAIPSNFLEKVVSLLKEKNK-EITVDLFVYG-----NEDVPKVADKIRVRE 181
                                       899**************************************88865.**********.....4445569999***** PP

                                       --S.EEEEETTTEEEEE-SSS-...EEEE--HHHHHHHHHHHHHH........HHH-EEEEE.EES-TT-EEES-HH CS
                    Regulator_TrmB  79 sgapllvivDrkrgvvaprevl...rdkeeeyaiifkekelihvlshyFlttlWktsevikt.depvekpitfssir 151
                                         +p+++i D++ g++ap e++    +  + ya+i+++k+l ++l  yF++ lW t++ i++ + + ++p ++ +ir
  gi|242399659|ref|YP_002995084.1| 182 VEDPIILIQDKALGIYAPPEAFktrGQTIRGYALIIRDKNLLFMLDRYFYHALWPTGKLIYEkKGKLKLPKSYIHIR 258
                                       ********************99873344567*******************************99999********** PP

                                       HHHHHHHHHT.TTS-EEEEEEEEETTT--EEEEEEEEEEEEEETTTTEEEEEEEETTE.EEEEE-TT--SSSEEEEE CS
                    Regulator_TrmB 152 lavedikkllraglkveaeveGrdtetgeevtieGrvveatlnstpgvaslvvetedg.evtVGGlgAvlEDieaee 227
                                        +vedi++   +    e+ev+G+ ++tg++v ++G++v  + ++ + v +++vete+g ++ +GG++A lEDieae 
  gi|242399659|ref|YP_002995084.1| 259 SLVEDIRNY--NLIGNEIEVYGKFVKTGGPVHLTGKIVAFFESEGKVVSNITVETEKGeKYVIGGWNASLEDIEAEL 333
                                       ********7..44557899********************76777777****************************** PP

                                       EEEE CS
                    Regulator_TrmB 228 itle 231
                                       i+le
  gi|242399659|ref|YP_002995084.1| 334 IILE 337
                                       9986 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.7   0.1   5.7e-25   9.3e-22       1      68 []      10      77 ..      10      77 .. 0.98
   2 ?    0.3   0.0      0.39   6.4e+02       3      21 ..     266     284 ..     264     287 .. 0.84

  Alignments for each domain:
  == domain 1  score: 76.7 bits;  conditional E-value: 5.7e-25
                                      HHHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE--HH CS
                              TrmB  1 LqklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYravdpe 68
                                      L++lGL++yE+ +Y++L+k+gp+ta e+a+ ++vp++++Y+v+rsL++kG+V +  +rpk+ +++dp+
  gi|242399659|ref|YP_002995084.1| 10 LKELGLNKYEVNAYFTLIKQGPLTAGELASLSKVPQPRIYDVVRSLMSKGFVAVTSERPKKIVPLDPK 77
                                      899***************************************************************95 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.39
                                       HCHHHHHCCCHCHHHHHHC CS
                              TrmB   3 klGLseyEakvYlaLlklg 21 
                                        ++L  +E++vY + +k g
  gi|242399659|ref|YP_002995084.1| 266 NYNLIGNEIEVYGKFVKTG 284
                                       578889******9999876 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   1.4e-05     0.023      14      54 ..      26      64 ..       8      70 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.4e-05
                                      HHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2 14 LgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                      L   ++  lt+gela   +++++++  +++ L ++G+v  +
  gi|242399659|ref|YP_002995084.1| 26 LIKQGP--LTAGELASLSKVPQPRIYDVVRSLMSKGFVAVT 64
                                      566677..******************************765 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.1e-05     0.034      11      48 ..      25      62 ..      19      66 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.1e-05
                                      HHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR 11 ilyeqgplsvseLakklgvskstvtrvldrLekkGlie 48
                                      +l  qgpl+  eLa+ ++v ++ +  v++ L  kG++ 
  gi|242399659|ref|YP_002995084.1| 25 TLIKQGPLTAGELASLSKVPQPRIYDVVRSLMSKGFVA 62
                                      56689*******************************97 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 ?   12.1   0.0   9.7e-05      0.16      21      57 ..      25      61 ..      21      64 .. 0.94
   2 ?   -2.4   0.0       3.3   5.4e+03      16      27 ..     145     156 ..     144     163 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.7e-05
                                      HHHHHSSBEHHHHHHHHSSTHHHHHHHHHHHHHTTSE CS
                             HTH_9 21 tLlrkgrltlrelvkktkLsldqVkksLvvLiqhrlV 57
                                      tL+++g lt+ el++++k++   + +++ +L+  ++V
  gi|242399659|ref|YP_002995084.1| 25 TLIKQGPLTAGELASLSKVPQPRIYDVVRSLMSKGFV 61
                                      8******************************998887 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.3
                                       HHHHHHHHHHSS CS
                             HTH_9  16 akVvetLlrkgr 27 
                                       +kVv++L +k++
  gi|242399659|ref|YP_002995084.1| 145 EKVVSLLKEKNK 156
                                       689999999876 PP

>> ADH_N_assoc  Alcohol dehydrogenase GroES-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.35   5.6e+02      16      22 ..      42      48 ..      40      48 .. 0.89
   2 ?   10.4   1.0   0.00029      0.47      11      23 .]     176     188 ..     175     188 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.35
                       ADH_N_assoc 16 eVPDPkI 22
                                       VP P+I
  gi|242399659|ref|YP_002995084.1| 42 KVPQPRI 48
                                      6*****9 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00029
                       ADH_N_assoc  11 dVrVeeVPDPkIe 23 
                                       ++rV eV+DP I+
  gi|242399659|ref|YP_002995084.1| 176 KIRVREVEDPIIL 188
                                       79********995 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0033       5.3      23      57 ..      29      63 ..      20      66 .. 0.90
   2 ?    2.8   0.0     0.093   1.5e+02      34      52 ..     136     154 ..     118     156 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0033
                                      CC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              Rrf2 23 eepvsseeiaerqnispsylekilakLrkaglvks 57
                                      ++p+++ e+a+  +++++ +  +++ L  +g+v +
  gi|242399659|ref|YP_002995084.1| 29 QGPLTAGELASLSKVPQPRIYDVVRSLMSKGFVAV 63
                                      5689****************************976 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.093
                                       HHTS-HHHHHHHHHHHHHT CS
                              Rrf2  34 rqnispsylekilakLrka 52 
                                       +  i+ ++lek+++ L+++
  gi|242399659|ref|YP_002995084.1| 136 SLAIPSNFLEKVVSLLKEK 154
                                       5689************986 PP

>> Coatomer_b_Cpla  Coatomer beta subunit appendage platform
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00016      0.26      15      65 ..      85     135 ..      78     186 .. 0.90
   2 ?   -3.7   0.0       6.8   1.1e+04      93     104 ..     303     315 ..     294     321 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00016
                   Coatomer_b_Cpla  15 mdyikpakiseeeFremWaefeWEnkiavktkltdlkeyleelvkktnmkl 65 
                                        +yik++++ ++e + m++  e   ++ v  ++t+l++y++e +k+++ +l
  gi|242399659|ref|YP_002995084.1|  85 KNYIKKMELAKRELKAMYTPHESNREVIVVKSKTTLENYIKEAIKNVKYHL 135
                                       58******************************************9998765 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 6.8
                   Coatomer_b_Cpla  93 alanvsiekee.e 104
                                       ++ n+++e+e+ e
  gi|242399659|ref|YP_002995084.1| 303 VVSNITVETEKgE 315
                                       5667777777633 PP

>> DUF3533  Protein of unknown function (DUF3533)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00015      0.24      74     117 ..     116     160 ..      73     168 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00015
                           DUF3533  74 efkeseeeveelvhkekywgaivvkenateklyaal.sangassy 117
                                       + ++ e+ ++e++ + ky +++ +++n+ ek++++l ++n++ ++
  gi|242399659|ref|YP_002995084.1| 116 SKTTLENYIKEAIKNVKYHLSLAIPSNFLEKVVSLLkEKNKEITV 160
                                       22337899****************************777766554 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00031       0.5      16      49 ..      29      62 ..      27      64 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00031
                                      BSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR 16 pqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                      +++lt  elA  + +p +  +  +++L+  G+v 
  gi|242399659|ref|YP_002995084.1| 29 QGPLTAGELASLSKVPQPRIYDVVRSLMSKGFVA 62
                                      5789****************************95 PP

>> CRIC_ras_sig  Connector enhancer of kinase suppressor of ras
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1     0.019        31      14      52 ..     118     154 ..     113     160 .. 0.87
   2 ?    5.0   0.1     0.017        27      48      63 ..     215     230 ..     213     235 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.019
                      CRIC_ras_sig  14 rslqnaiqsrrrsnsydgsssrklpndvLsavvelitaa 52 
                                        +l+n+i++  ++ +y    s ++p+++L+ vv l+++ 
  gi|242399659|ref|YP_002995084.1| 118 TTLENYIKEAIKNVKY--HLSLAIPSNFLEKVVSLLKEK 154
                                       6899999999999998..88999************9875 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.017
                      CRIC_ras_sig  48 litaakallswLdRyp 63 
                                       li   k+ll++LdRy 
  gi|242399659|ref|YP_002995084.1| 215 LIIRDKNLLFMLDRYF 230
                                       89999*********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1145  (0.063863); expected 358.6 (0.02)
Passed bias filter:                      805  (0.0448993); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.73u 0.37s 00:00:01.10 Elapsed: 00:00:00.58
# Mc/sec: 1766.71
//
Query:       gi|242399660|ref|YP_002995085.1|  [L=224]
Description: Triosephosphate isomerase (TIM) [Thermococcus sibiricus MM 739]
Scores for complete 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   0.1    1.5e-10   40.9   0.0    1.8  2  TIM            Triosephosphate isomerase
    4.6e-06   26.1   0.1    4.6e-06   26.1   0.1    1.9  3  ThiG           Thiazole biosynthesis protein ThiG
    0.00043   19.5   0.0     0.0011   18.2   0.0    1.6  1  IGPS           Indole-3-glycerol phosphate synthase
      0.002   17.2   0.5     0.0033   16.5   0.1    1.5  2  FMN_dh         FMN-dependent dehydrogenase
  ------ inclusion threshold ------
      0.026   14.0   0.4      0.095   12.1   0.1    2.0  3  His_biosynth   Histidine biosynthesis protein
      0.036   13.5   2.2      0.039   13.3   0.8    1.6  2  NMO            Nitronate monooxygenase
       0.12   11.5   1.9       0.21   10.8   0.3    2.0  2  NanE           Putative N-acetylmannosamine-6-phosphate epime
        0.7    9.7   3.5        1.7    8.5   0.0    2.7  3  RNA_pol_inhib  RNA polymerase inhibitor


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 !   40.9   0.0   6.5e-14   1.5e-10       2     106 ..       6     109 ..       5     123 .. 0.86
   2 ?    0.1   0.0      0.19   4.2e+02     159     188 ..     138     170 ..     122     177 .. 0.72

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 6.5e-14
                                       EEEEE-TBTS..-HHHHHHHHHHHHHHCHGCTSEEEEE--GGGHHHHHHHHTTSSECEEES--BSSSSBS-TT--BH CS
                               TIM   2 liagNwKmnk..tleeakellkklkaklkeekvevviappflylekvkklleesklklgaqnvsaeksGafTGevsa 76 
                                       +ia N+K++   t + a +++k++++ +ke+ v++v+ap++  l ++++ +e   + + aq ++  k G++TG v  
  gi|242399660|ref|YP_002995085.1|   6 VIAINFKTYIeaTGKRALKIAKAAEEVYKETGVTIVVAPQLADLYRIAQEVE---IPVFAQHIDPIKPGSHTGHVLP 79 
                                       7999***998446677888888899999999**************9888886...********************** PP

                                       HHHHHTT-SEEEES-HHHHHHST--HHHHH CS
                               TIM  77 emlkdlgvkyviiGHsErrqlfkEtdelva 106
                                       e +k++g+  +++ HsE r ++ + ++ ++
  gi|242399660|ref|YP_002995085.1|  80 EAVKEAGAVGTLLNHSENRMILADLEAAIR 109
                                       ********************9998766654 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.19
                                       EEEE--GGGSSSS...----HHHHHHHHHHHHH CS
                               TIM 159 viAYePvWAiGtg...ktatpeqaqevhaairk 188
                                       ++A eP   iGtg   ++a+pe + ++++ ++k
  gi|242399660|ref|YP_002995085.1| 138 YVAVEPPELIGTGipvSKAKPEVITNTVNLVKK 170
                                       789999999***933334566667777766665 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1      0.91     2e+03      74     100 ..      18      44 ..      16      59 .. 0.75
   2 ?   -2.6   0.1       1.2   2.7e+03     218     229 ..     106     117 ..      72     134 .. 0.50
   3 !   26.1   0.1   2.1e-09   4.6e-06     168     215 ..     166     214 ..     145     221 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.91
                                       SHHHHHHHHHHHHHTTS-SEEEE--BC CS
                              ThiG  74 taeeAvriarlarevletdliklEvia 100
                                       t + A++ia+ a ev +   + + v +
  gi|242399660|ref|YP_002995085.1|  18 TGKRALKIAKAAEEVYKETGVTIVVAP 44 
                                       567788888888888887777666655 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHH CS
                              ThiG 218 rafklaveaGrl 229
                                       +a++ a e G +
  gi|242399660|ref|YP_002995085.1| 106 AAIRRAEEVGLM 117
                                       233333333333 PP

  == domain 3  score: 26.1 bits;  conditional E-value: 2.1e-09
                                       HHHHHH-..SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSHHH CS
                              ThiG 168 kiiieea..kvPvivDAGigspsdaaqamelGadavllntavaeakdpva 215
                                       +++ +++  kv v+  AGi + +d+ +a+elG+ +vll++ v++akdp +
  gi|242399660|ref|YP_002995085.1| 166 NLV-KKInpKVGVLTGAGISTGEDVKKALELGTVGVLLASGVTKAKDPEK 214
                                       333.3333699*************************************76 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   4.8e-07    0.0011     197     254 .]     162     219 ..     158     219 .. 0.96

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 4.8e-07
                                       HHHHHHCHCC-TTSEEEEESSS-SHHHHHHHCCTT-SEEEESHHHHC-TTHHHHHHHH CS
                              IGPS 197 ntteeLaklvpkdvllvaeSGiktredveklkeegvnafLvGeslmrqedvekairel 254
                                        +t +L+k+++ +v + +  Gi+t edv+k  e g  ++L  + +++++d ekair+l
  gi|242399660|ref|YP_002995085.1| 162 TNTVNLVKKINPKVGVLTGAGISTGEDVKKALELGTVGVLLASGVTKAKDPEKAIRDL 219
                                       68999**************************************************987 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.1       1.8   4.1e+03      80      95 ..     107     122 ..      97     135 .. 0.56
   2 !   16.5   0.1   1.5e-06    0.0033     262     301 ..     165     204 ..     154     217 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.8
                                       HHHHHHHHTS-EEEET CS
                            FMN_dh  80 laraaakagipfvlst 95 
                                       + r a++ g++ ++ +
  gi|242399660|ref|YP_002995085.1| 107 AIRRAEEVGLMTMICS 122
                                       3344555555444433 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 1.5e-06
                                       HHHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESH CS
                            FMN_dh 262 peiveavggrievlvDgGirrGsDvlkAlalGAdavllGR 301
                                        ++v++++ ++ vl   Gi++G+Dv kAl lG  +vll+ 
  gi|242399660|ref|YP_002995085.1| 165 VNLVKKINPKVGVLTGAGISTGEDVKKALELGTVGVLLAS 204
                                       445778888999************************9875 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       2.6   5.8e+03      64      76 ..      48      60 ..      44      62 .. 0.68
   2 ?   -2.1   0.0      0.94   2.1e+03      45      59 ..      98     112 ..      93     125 .. 0.67
   3 ?   12.1   0.1   4.2e-05     0.095      60     109 ..     163     210 ..     153     221 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2.6
                                      HHHHHHHH-SSEE CS
                      His_biosynth 64 lveeiaeevfipv 76
                                       + +ia+ev+ipv
  gi|242399660|ref|YP_002995085.1| 48 DLYRIAQEVEIPV 60
                                      4667888888776 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.94
                                       EEEEEEHHHHCTTHH CS
                      His_biosynth  45 elhvvDldaakegre 59 
                                       +++++Dl+aa +  e
  gi|242399660|ref|YP_002995085.1|  98 RMILADLEAAIRRAE 112
                                       677888888874433 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 4.2e-05
                                       HHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-T CS
                      His_biosynth  60 anldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavknp 109
                                       +  +lv++i  +  + v  G GI++ edv+++le+g   v +++ + k +
  gi|242399660|ref|YP_002995085.1| 163 NTVNLVKKINPK--VGVLTGAGISTGEDVKKALELGTVGVLLASGVTKAK 210
                                       456788888888..88999*****************99999998876654 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1      0.49   1.1e+03      23      41 ..      74      92 ..      55     115 .. 0.68
   2 ?   13.3   0.8   1.7e-05     0.039     128     225 ..     107     206 ..      99     216 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.49
                               NMO 23 skarLaaavsnaGgLGvla 41
                                      ++  L  av +aG+ G l 
  gi|242399660|ref|YP_002995085.1| 74 TGHVLPEAVKEAGAVGTLL 92
                                      5556777999999999885 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 1.7e-05
                               NMO 128 vvarlkeagvvliptissvkearkvearGaDalivqGpeaGGh.qGtpevgd.kglfaLvpqvldavd.iPviAaGG 201
                                       ++ r +e+g++ ++     k   +v+a+ +D + v+ pe  G  ++ +++++ +  ++ v+ v++    + v+   G
  gi|242399660|ref|YP_002995085.1| 107 AIRRAEEVGLMTMICSNNPKVSAAVAALSPDYVAVEPPELIGTgIP-VSKAKpEVITNTVNLVKKINPkVGVLTGAG 182
                                       6677777777777777777778888999999999999987554144.4444444555556666665545999***** PP

                               NMO 202 iidrrgvaaaLalGAsgvqigtrf 225
                                       i ++++v+ aL lG  gv +++  
  gi|242399660|ref|YP_002995085.1| 183 ISTGEDVKKALELGTVGVLLASGV 206
                                       ******************999865 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1      0.35   7.8e+02       9      35 ..      34      60 ..      23      69 .. 0.71
   2 ?   10.8   0.3   9.2e-05      0.21     114     180 ..     145     210 ..      87     218 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.35
                                      HHHT-SEEEEESHHHHHHHHTT--S-E CS
                              NanE  9 eqaGavgiriegvedikaikavvdlPi 35
                                      +++G + + +  ++d+  i ++v++P+
  gi|242399660|ref|YP_002995085.1| 34 KETGVTIVVAPQLADLYRIAQEVEIPV 60
                                      346666677778888888888888887 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 9.2e-05
                                       SEEE-TTTTSSTTS-.SS--HHHHHHHHHTT--EEEES---SHHHHHHHHTT--SEEEE-HHHH-HH CS
                              NanE 114 divGttlsGytkeeekaepDfalvkalseaglkviaeGrintPekakkaieiGvdavvvGsaitrle 180
                                       +++Gt +     + e   + ++lvk+++  ++ v++   i t e  kka+e+G + v + s +t+ +
  gi|242399660|ref|YP_002995085.1| 145 ELIGTGIPVSKAKPEVITNTVNLVKKIN-PKVGVLTGAGISTGEDVKKALELGTVGVLLASGVTKAK 210
                                       5677776655555555788999**9985.6899999999************************9976 PP

>> RNA_pol_inhib  RNA polymerase inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.16   3.6e+02      28      39 ..      27      38 ..      24      42 .. 0.82
   2 ?    8.5   0.0   0.00074       1.7      11      24 ..      53      66 ..      46      67 .. 0.86
   3 ?   -2.7   0.3       2.3   5.2e+03      22      32 ..     103     113 ..     102     114 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.16
                     RNA_pol_inhib 28 elAeeeYeeaGf 39
                                       +Aee Y+e G 
  gi|242399660|ref|YP_002995085.1| 27 KAAEEVYKETGV 38
                                      689******994 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00074
                     RNA_pol_inhib 11 eesfEVPvyAesld 24
                                       +++E+Pv+A+ +d
  gi|242399660|ref|YP_002995085.1| 53 AQEVEIPVFAQHID 66
                                      5799*******998 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 2.3
                     RNA_pol_inhib  22 sldeAlelAee 32 
                                       +l+ A   Aee
  gi|242399660|ref|YP_002995085.1| 103 DLEAAIRRAEE 113
                                       89999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.62u 0.34s 00:00:00.96 Elapsed: 00:00:00.55
# Mc/sec: 1226.05
//
Query:       gi|242399661|ref|YP_002995086.1|  [L=654]
Description: Glyceraldehyde-3-phosphate:ferredoxin oxidoreductase (GAPOR) [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-38  132.7   0.2    4.3e-38  131.2   0.0    1.9  3  AFOR_N         Aldehyde ferredoxin oxidoreductase, N-terminal
    2.1e-22   79.7   0.0    4.6e-22   78.6   0.0    1.5  1  AFOR_C         Aldehyde ferredoxin oxidoreductase, domains 2 
  ------ inclusion threshold ------
       0.02   14.1   0.0      0.036   13.2   0.0    1.3  1  Peptidase_M19  Membrane dipeptidase (Peptidase family M19)


Domain annotation for each model (and alignments):
>> 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 !  131.2   0.0   7.1e-42   4.3e-38       3     197 ..       5     228 ..       3     229 .. 0.90
   2 ?   -2.9   0.0      0.88   5.2e+03     106     133 ..     248     275 ..     241     280 .. 0.80
   3 ?   -3.3   0.0       1.1   6.8e+03      59      92 ..     360     391 ..     358     399 .. 0.51

  Alignments for each domain:
  == domain 1  score: 131.2 bits;  conditional E-value: 7.1e-42
                                       EEEEETTTTEEEEEE--HHHHHHH-SCHHHHHHHHHHHS-..TTS-TTSTTS-EEEEE-TTTTSSSTTB-EEEEEEE CS
                            AFOR_N   3 ilrvdLstgkieveelpeelaekylGgrglaakllldevp..pgvdplspenplvfatGpltgtpapgsgrlvvvak 77 
                                       +l+v+L++++i+ e++++e +    G   +a++l+ + ++  +  d ++p+n++vf+ Gp++g+ +pg++r+++v +
  gi|242399661|ref|YP_002995086.1|   5 VLKVNLNEKSINLEDFEREGI---YGIIDYALYLHDEVYKtyEAEDHYDPKNVMVFGKGPFAGSILPGAHRMTFVYR 78 
                                       89***************6554...7**********99443336679******************************* PP

                                       -TTTSSEEEEEEETCHHHHHHHCT-SEEEEES--SS-EEEEEETT.........EEEEEE-TTTTT.....S-HHHH CS
                            AFOR_N  78 sPltgtlgesnaGgrfgaelkraGydaivieGkaekpvylviedd.........kveiedaedlwg.....ldtyet 140
                                       sP+ g++  s++Gg ++++++r+G+d++v+eGk ekp++l++++d         ++++e++ ++w       ++y++
  gi|242399661|ref|YP_002995086.1|  79 SPQYGGVFPSTMGG-AAYQFQRVGIDFVVLEGKREKPTVLILTNDgeklnvelhEIDFEKVIEIWRgykgeEGVYAL 154
                                       **************.***************************888899977777788888888888999988***** PP

                                       HHHHHHHHTS.......EEEEE-HHHHTT-TTB-E.EE.........TTEEE-SSSHHHHHH.HTTEEEEEEE- CS
                            AFOR_N 141 tealkeelgd.......kvaviGpaGenlvrfAsisvd.........dgraagrgGlGavmg.sKnlkaivvrg 197
                                       t++l ++++d       ++a++Gpa  n+  +A++s +         ++  a+rgG+G+v+  ++n+ ai++ g
  gi|242399661|ref|YP_002995086.1| 155 TQYLIDNFNDkfegmeyRIACVGPASLNTNMGAIFSQTlrngkrivgSEDWAARGGTGSVLLrAHNVIAIIFGG 228
                                       ****9988778888999999**************977799988887544467*********99********998 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.88
                                       EEES--SS-EEEEEETTEEEEEE-TTTT CS
                            AFOR_N 106 vieGkaekpvylvieddkveiedaedlw 133
                                       ++eG ++kp+  vi++++v+ +   +l+
  gi|242399661|ref|YP_002995086.1| 248 IVEGVHKKPMNEVISENTVKYKYNPKLK 275
                                       7999999999999999999988777766 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 1.1
                                       -TTTTSSSTTB-EEEEEEE-TTTSSEEEEEEETC CS
                            AFOR_N  59 GpltgtpapgsgrlvvvaksPltgtlgesnaGgr 92 
                                       Gpl+g+    ++ ++v a+     ++   ++Gg+
  gi|242399661|ref|YP_002995086.1| 360 GPLSGVITLRASDVSVHAVDA--MGFDAISFGGT 391
                                       555555555555555555442..33444444444 PP

>> 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 !   78.6   0.0   7.6e-26   4.6e-22       8     300 ..     259     575 ..     253     588 .. 0.76

  Alignments for each domain:
  == domain 1  score: 78.6 bits;  conditional E-value: 7.6e-26
                                       HHHHHSH.HHH...HHHHH-GGGHHHHHHHTT---BTTTTBS--TTGGGGSH.........HHHHHH.TEEEE.E.- CS
                            AFOR_C   8 keiksspqvta...elrkyGTaelvnianetgalptknfqegtfekaekisg.........ealeek.ylvkneg.C 70 
                                       ++i ++ + ++   +l++ GT +   +  e + +p+ n+q  + +k e+++          e ++++ +++kn   C
  gi|242399661|ref|YP_002995086.1| 259 EVISENTVKYKynpKLKTGGTFGGN-YPAEGDFVPILNWQMPYIPKEERVKIhenimkyywEPFNKEaIETKNWTnC 334
                                       5555555444444477888886655.6789999********995555444333255545555555555999998899 PP

                                       TT.-SS--EEEEE......ETEE---HHHHHHHTGGGT---HHHHHHHHHHHHHHTB-HHHHHHHHHHHHHHHHTTS CS
                            AFOR_C  71 fs.CpiaCgrevkveegkkvkvegpeyetlaalGsnlgiddleailklnelcdelGlDtisaGntiafamelyekGl 146
                                          Cp+ C+++ +        ++  eye   a G+  g+  l a     + +d +G+D is+G+t+a++ el+ +Gl
  gi|242399661|ref|YP_002995086.1| 335 GEpCPVVCKKYAN--------GHHIEYEPREANGPLSGVITLRASDVSVHAVDAMGFDAISFGGTVAWVLELVYRGL 403
                                       989********99........4568**************************************************** PP

                                       S-HHHH...............TS----TT-THHHHHHHHHHHTT-T.THHHHTT-HHHHHHCTT.....-GGG--EE CS
                            AFOR_C 147 lkkedt...............dglelefgdaeallellekiAkreg.igdllAeGvkrlaeklg.....aeelamhv 202
                                       lk +++               + +e +  +a+ + el +++A  e+ i+++++eG++r+ae l+        +  + 
  gi|242399661|ref|YP_002995086.1| 404 LKPDEVglsdkpefdkdslimKPVETSEKNAKLVAELAHRVAFAENeIAKIIGEGIRRAAEILDekfkdRLSYGESF 480
                                       ***999***************999************************************88886653433333333 PP

                                       TTEE--SS-GGG-HHHHH........HHHH-TTSS-SGGG-THHHHS---TT--HHHHHHHHHHHHHHHHHHHHT-- CS
                            AFOR_C 203 kGlelpaydprgakgmal........aYatsnrGacHlraylialeekvdpletegkaelvkwfqdltalvdslglC 271
                                       k  ++  y p g+ g  +        +Y + +  +++   y + +       e+e+ a+ ++ +  +  ++d +g C
  gi|242399661|ref|YP_002995086.1| 481 K--DYGVYTPIGISGEMVptmywaigNYIPLPIQGRYWTFYQFGVFL-----EPEELANRIIASALYEYWYDNVGWC 550
                                       3..36666666666544444444444899888866665544444443.....5579999999*************** PP

                                       GGGG-HHH......HHHHHHHHHT----H CS
                            AFOR_C 272 kftseaeerldlelyakllsavtGidvte 300
                                       +f +++ +++  +l+ +++    G++v+ 
  gi|242399661|ref|YP_002995086.1| 551 RFHRGWAKPVLKALFMEAY----GENVDM 575
                                       ****777755555555544....444443 PP

>> Peptidase_M19  Membrane dipeptidase (Peptidase family M19)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   6.1e-06     0.036     256     315 ..     376     461 ..     371     464 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.1e-06
                                       HHHHHT-GGGEEE---TTTTSS-.........................BBTBSSGGGHHHHHHHHHH.TTS-HHHHH CS
                     Peptidase_M19 256 yivelaGidhVGlGsDfdgggel.........................pegledvsklpnltaeLlr.rgyseadie 306
                                       + v+ +G d++ +G+   +  el                         ++ +e+ +k  +l+aeL++   ++e++i+
  gi|242399661|ref|YP_002995086.1| 376 HAVDAMGFDAISFGGTVAWVLELvyrgllkpdevglsdkpefdkdsliMKPVETSEKNAKLVAELAHrVAFAENEIA 452
                                       556666666666666665555555666666666666666666666666******************9458******* PP

                                       HHHTHHHHH CS
                     Peptidase_M19 307 kilggNflr 315
                                       ki+g+ + r
  gi|242399661|ref|YP_002995086.1| 453 KIIGEGIRR 461
                                       ***987666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (654 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      596  (0.0332422); 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: 0.82u 0.36s 00:00:01.18 Elapsed: 00:00:00.58
# Mc/sec: 3412.70
//
Query:       gi|242399662|ref|YP_002995087.1|  [L=374]
Description: fructose-1,6-bisphosphatase (FBP) [Thermococcus sibiricus MM 739]
Scores for complete 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-186  617.8   0.0   7.2e-186  617.6   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 !  617.6   0.0    4e-190  7.2e-186       1     361 []       6     372 ..       6     372 .. 0.99

  Alignments for each domain:
  == domain 1  score: 617.6 bits;  conditional E-value: 4e-190
                          FBPase_3   1 kvtlsvikaDvGslaGhtkvheellekveevleeakkkgllidfyvtkvGDDielimthtkgvdneevhklawdafk 77 
                                       k+t+svikaD+G+++Gh+kvh++l+ek++e l++ak++g++idf+ t++GDD++limth++gvd+e++h+lawd+fk
  gi|242399662|ref|YP_002995087.1|   6 KITISVIKADIGGWPGHCKVHPALIEKANELLNKAKEEGIIIDFHATYCGDDLQLIMTHKHGVDSEKIHGLAWDIFK 82 
                                       89*************************************************************************** PP

                          FBPase_3  78 eatevakelklygaGqDlLkdafsGnvkGlGPgvaelefeeRksepvvvfaaDktepgafnlplykifadpfntaGl 154
                                       eate+akel+lygaGqDlLkdafsGn++G+GPg+ae+e++ Rksep+v+f +Dktepgafnlp++++f dpfntaGl
  gi|242399662|ref|YP_002995087.1|  83 EATEIAKELGLYGAGQDLLKDAFSGNIRGMGPGIAEMEITLRKSEPIVTFHMDKTEPGAFNLPIFRMFGDPFNTAGL 159
                                       ***************************************************************************** PP

                          FBPase_3 155 vidpklheGfkfevlDvieekkillsapeelydllallgakeryvikrvysk.....kdeeiaavvsterlsliaGk 226
                                       vidp++h+Gf+fev+D++e+kk++l++peelyd+lal+gak+ryvikrvy k      ++e++avvste+l +iaG+
  gi|242399662|ref|YP_002995087.1| 160 VIDPNMHMGFRFEVWDIKEHKKVILNSPEELYDILALIGAKSRYVIKRVYPKkghklPEDEPVAVVSTEKLYEIAGE 236
                                       **************************************************99777777889**************** PP

                          FBPase_3 227 YvGkDDPvaivRaqsglPavgevlepfalphlvaGwmrGshngplmPvslkdakptrfdgpprvvalgfqlk.egkl 302
                                       YvGkDDPvaivRaqsglPa+gevlepfa+ph+v+GwmrGshngp+mPv+lk a+p+rfdgpprvvalg+q++ +gkl
  gi|242399662|ref|YP_002995087.1| 237 YVGKDDPVAIVRAQSGLPALGEVLEPFAFPHIVSGWMRGSHNGPIMPVPLKYATPSRFDGPPRVVALGWQINkDGKL 313
                                       ***********************************************************************879*** PP

                          FBPase_3 303 vgpvDlfddpafdeaRekaaeiadelRrqGpfephrlpeeeleYttlpevleklkerfe 361
                                       vgpvDlf+d afdeaR+ka eiad++Rr+Gpfephrlp e++eYttlp+vl+kl+erfe
  gi|242399662|ref|YP_002995087.1| 314 VGPVDLFEDVAFDEARKKALEIADYMRRHGPFEPHRLPLEDMEYTTLPSVLKKLEERFE 372
                                       *********************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.65u 0.34s 00:00:00.99 Elapsed: 00:00:00.55
# Mc/sec: 2044.77
//
Query:       gi|242399663|ref|YP_002995088.1|  [L=79]
Description: hypothetical protein TSIB_1688 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
       0.11   13.1   1.9       0.91   10.1   0.6    2.0  2  Syntaxin-6_N  Syntaxin 6, N-terminal


Domain annotation for each model (and alignments):
>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.6   5.1e-05      0.91      70      98 ..      10      38 ..       2      39 .. 0.84
   2 ?    2.5   0.0     0.012   2.2e+02      48      69 ..      50      71 ..      44      77 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 5.1e-05
                      Syntaxin-6_N 70 npskfkidekelsrrrafveevreevkem 98
                                       ++kf+i+e+e++rr+  v+++++ v ++
  gi|242399663|ref|YP_002995088.1| 10 GEDKFRITEEEVARRELKVTKINDDVIQV 38
                                      5689*******************999765 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.012
                      Syntaxin-6_N 48 kalrsiewdledLeetvrivek 69
                                       a+++i+ + e+L+e ++++++
  gi|242399663|ref|YP_002995088.1| 50 GAVSTINIKKEELKELIKVARE 71
                                      6788999999999999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1163  (0.064867); expected 358.6 (0.02)
Passed bias filter:                      659  (0.0367561); 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 0.35s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 452.69
//
Query:       gi|242399664|ref|YP_002995089.1|  [L=199]
Description: hypothetical protein TSIB_1689 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        1.8    8.6   8.5         17    5.4   8.5    2.3  1  NdhL      NADH dehydrogenase transmembrane subunit


Domain annotation for each model (and alignments):
>> NdhL  NADH dehydrogenase transmembrane subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   8.5   0.00096        17      15      65 ..      12      69 ..       6      78 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.00096
                              NdhL 15 aylalsvlYllviPlilylw.......lrkRWyvaskiErlliymlvflfFPGlllla 65
                                      ++++  vlY ++iP++l++w       ++kR y+ +++  l++  ++   F G+ +l 
  gi|242399664|ref|YP_002995089.1| 12 TFGTFFVLYYVIIPAVLLTWfwkyyvyIKKRQYKLKQLGVLILLAFILTSFSGFKVLE 69
                                      56777899*******9965522222227899999999999999999999998876665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       693  (0.0386525); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); 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: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.53
# Mc/sec: 1136.68
//
Query:       gi|242399665|ref|YP_002995090.1|  [L=38]
Description: hypothetical protein TSIB_1690 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); 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 0.30s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 244.65
//
Query:       gi|242399666|ref|YP_002995091.1|  [L=133]
Description: Iron-molybdenum cofactor-binding protein [Thermococcus sibiricus MM 739]
Scores for 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-22   77.2   2.4    9.1e-22   77.2   0.3    1.8  2  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 !   77.2   0.3   5.1e-26   9.1e-22       2      94 ..      14     103 ..      13     104 .. 0.96
   2 ?   -0.3   0.1     0.078   1.4e+03      17      36 ..     106     127 ..     105     132 .. 0.59

  Alignments for each domain:
  == domain 1  score: 77.2 bits;  conditional E-value: 5.1e-26
                                       TSCB-STCCC-SEEEEEEESSSCEEEEEEEE.GCCCTSSCSSTHHHHHHHHTT-SEEEESSSCHHHHHHHCTTTSEE CS
                     Nitro_FeMo-Co   2 gsrvdqhFGrapyFaiyeveegevkivenrveeaadaegggggklaqllaeegvdvvivgkiGpralakleaagiev 78 
                                       +s v++hFGra+yF++++ve++++k  e+    + + e++g+g l+++++e+g +vv++ ++G+ra+  +++ giev
  gi|242399666|ref|YP_002995091.1|  14 ESNVSGHFGRAKYFVFVDVEDNKIKNAEVV---EVPFEEHGPGDLPNFIKEHGGEVVLAYGMGRRAIDYFNQLGIEV 87 
                                       799*******************99999999...9999**************************************** PP

                                       EES-SSBHHHHHHHHH CS
                     Nitro_FeMo-Co  79 ykgaggtveealkevl 94 
                                       ++ga g++e+++++++
  gi|242399666|ref|YP_002995091.1|  88 VTGAYGKIEDVVDAFI 103
                                       ************9985 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.078
                                       EEEESSSCEEEEEEE..E.GCC CS
                     Nitro_FeMo-Co  17 iyeveegevkivenr..veeaa 36 
                                       + ev+++ ++ +e +   ee++
  gi|242399666|ref|YP_002995091.1| 106 VLEVDPHWKEKIEREkeKEEHC 127
                                       6789999777777773333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.34s 00:00:00.93 Elapsed: 00:00:00.56
# Mc/sec: 720.71
//
Query:       gi|242399667|ref|YP_002995092.1|  [L=316]
Description: iron ABC transporter [Thermococcus sibiricus MM 739]
Scores for complete 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-32  110.6   2.2    1.1e-31  110.2   2.2    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 !  110.2   2.2   6.3e-36   1.1e-31       6     217 ..      95     312 ..      90     313 .. 0.87

  Alignments for each domain:
  == domain 1  score: 110.2 bits;  conditional E-value: 6.3e-36
                           UPF0051   6 tlivveegaevtiieeyagc...........gvveifvgenAklkyvkvqnwsedavnlstkraeegrdaklelttv 71 
                                        +i v++g++v+++   ++c           +  +i + e+A++ y   + ++e++  +s +++e++r+ +++    
  gi|242399667|ref|YP_002995092.1|  95 FDITVGKGSKVKFL---SHCifpyakdfthdAYAKIRIDEGASVIYEDEHVHGEGVRMISITEVEVRRKGRYTGKFS 168
                                       4699**********...55555555555556****************999999999999999998888777766655 PP

                           UPF0051  72 slggkltrk..epsvelkgegaeaelnglylakgkqhldtrtkvdhngpntssrilskgvlkdearavfrgkikvrk 146
                                        ++ +      e++++++ + a +el++++ a +++ ++++  + + g ++++++++  ++ d+a+a +  +     
  gi|242399667|ref|YP_002995092.1| 169 LIKHRAKELklEMKADID-DYAVTELSSKVKAVKDDSVEIKEVAYLTGAHSRANLKTTVIAFDNAKANVVNEA--YG 242
                                       555553333114455554.9***********************************************999999..78 PP

                           UPF0051 147 gaqktdahqenrnLllsdkaradtiPeleidaddvkasHgAtvGkideeqlfYLmsRGlseeeArrlivrg 217
                                         + +++h+e++ ++ ++ a ++t+P l +++d+++++H+A++G+i+e ql+ Lm++Gl+eeeA +li++g
  gi|242399667|ref|YP_002995092.1| 243 LGEYSKGHIECHEIVKGE-ADVQTVPLLRVKNDKAELTHEASIGRINEAQLMQLMAKGLTEEEAAELIIKG 312
                                       89***************7.**************************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       633  (0.0353059); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); 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 0.31s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 1903.04
//
Query:       gi|242399668|ref|YP_002995093.1|  [L=247]
Description: ABC transporter, ATP-binding protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-27   97.1   0.0    1.6e-27   96.7   0.0    1.2  1  ABC_tran       ABC transporter
    6.8e-09   35.9   1.0     0.0016   18.3   0.2    2.1  2  AAA_21         AAA domain, putative AbiEii toxin, Type IV TA 
    1.4e-07   31.2   0.1     0.0031   17.0   0.0    2.1  2  SMC_N          RecF/RecN/SMC N terminal domain
     0.0048   16.6   0.0     0.0081   15.9   0.0    1.4  1  AAA_29         P-loop containing region of AAA domain
     0.0082   16.7   0.4      0.016   15.7   0.2    1.5  1  AAA_23         AAA domain
  ------ inclusion threshold ------
      0.032   13.9   0.1      0.087   12.5   0.0    1.6  2  AAA_15         AAA ATPase domain
      0.041   13.0   0.0      0.054   12.6   0.0    1.2  1  T2SSE          Type II/IV secretion system protein
      0.049   13.5   0.0       0.24   11.3   0.0    1.9  2  RsgA_GTPase    RsgA GTPase
      0.052   14.2   0.0       0.21   12.2   0.0    1.8  1  PIG-L          GlcNAc-PI de-N-acetylase
      0.067   13.2   0.0       0.13   12.3   0.0    1.4  1  AAA_5          AAA domain (dynein-related subfamily)
      0.085   12.6   0.5        1.9    8.1   0.0    2.1  2  AAA_24         AAA domain
      0.089   12.2   0.0       0.13   11.7   0.0    1.2  1  Peptidase_C3G  Tungro spherical virus-type peptidase
       0.12   11.7   0.8        8.4    5.7   0.1    2.3  2  ATPase         KaiC


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.7   0.0   1.2e-30   1.6e-27       1     136 [.      17     160 ..      17     161 .. 0.90

  Alignments for each domain:
  == domain 1  score: 96.7 bits;  conditional E-value: 1.2e-30
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltv 76 
                                       l+++++ +keg  + i+G+nGaGKSt++ +l+g  kp eG+i + +kd++e + +e++r  i+ l qep   +++tv
  gi|242399668|ref|YP_002995093.1|  17 LEKINMRFKEGMSYSILGPNGAGKSTIAYILMGVIKPSEGRIFMGDKDITElNITERARLGISLLWQEPARYDGITV 93 
                                       6789***************************************99******9999********************** PP

                                       HHH........HHHTCHHHHHHHSTTGGTTCBGESTTS..GGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxx........xxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  77 ren........esdeeiekalsklglkelkdtvvkssp..ssLSgGqkqrvalarallkkpkllllDEpt 136
                                       +e          ++ee++++l+ +gl++   +  +s+   +sLSgG+++rv+la +ll kpk  +lDEp 
  gi|242399668|ref|YP_002995093.1|  94 EEYltlggklnVDKEELKEVLEIVGLPY---ELYHSRFvdKSLSGGERKRVELASILLLKPKYAILDEPD 160
                                       **9*****77767777777777777777...444444445****************************95 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   4.3e-06    0.0059       4      78 ..      32      94 ..      30     117 .. 0.70
   2 !   18.3   0.2   1.1e-06    0.0016     237     298 ..     133     191 ..     125     195 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 4.3e-06
                            AAA_21  4 liGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglrl 78
                                      + GpNg+GKS++ ++l ++            ++++ g i + ++ +++ +++++++++i+++ ++  ry+++   
  gi|242399668|ref|YP_002995093.1| 32 ILGPNGAGKSTIAYILMGV------------IKPSEGRIFMGDKDITELNITERARLGISLLWQEPARYDGITVE 94
                                      89**************555............67777777777777777777777777777555555555555555 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 1.1e-06
                            AAA_21 237 lSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHS 298
                                       lS G ++   l+++ll  +k     ++DEp++gL+  +++ + ++l++l+r g+ +il TH 
  gi|242399668|ref|YP_002995093.1| 133 LSGGERKRVELASILLLKPKY---AILDEPDSGLDITVTELIDRILDYLKRIGTTIILITHH 191
                                       677887777888999988855...8***********777777788888888799*******6 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.1   6.3e-05     0.087      16      42 ..      18      45 ..       9      60 .. 0.83
   2 !   17.0   0.0   2.3e-06    0.0031     118     208 ..     105     201 ..      87     210 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.3e-05
                                      EEEEEETTSSEE.EEEESTTSSHHHHHH CS
                                      xxxxxxxxxxxx.xxxxxxxxxxxxxxx RF
                             SMC_N 16 ktvilpfsksft.aivGpNGSGKsnlld 42
                                      +++ ++f+++++ +i+GpNG+GKs +  
  gi|242399668|ref|YP_002995093.1| 18 EKINMRFKEGMSySILGPNGAGKSTIAY 45
                                      67888899988747**********9975 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 2.3e-06
                                       E-HHHHHHHHHCTT-STT.........CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 118 vtkkevsellesagiske.........lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellke 185
                                       v k+e++e+le +g+  e         +LSgGe++ v la ++ +   kp+   +lDe d+ LD + ++ + ++l+ 
  gi|242399668|ref|YP_002995093.1| 105 VDKEELKEVLEIVGLPYElyhsrfvdkSLSGGERKRVELASILLL---KPK-YAILDEPDSGLDITVTELIDRILDY 177
                                       555666666666666555666666666************988654...444.469**********999988888885 PP

                                       HCTT.SEEEEE-SSHHHCCC-SCE CS
                                       xxxx.xxxxxxxxxxxxxxxxxxx RF
                             SMC_N 186 kskn.aQfivislreemlekadkl 208
                                        +   + +i i+++e++ +k +  
  gi|242399668|ref|YP_002995093.1| 178 LKRIgTTIILITHHEDIAKKTEFS 201
                                       5544399999*****999988755 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   5.9e-06    0.0081      17      39 ..      22      44 ..      15      59 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5.9e-06
                            AAA_29 17 ieidlkg.atlltGpsGsGKSTll 39
                                      ++++ +g ++ + Gp+G+GKST+ 
  gi|242399668|ref|YP_002995093.1| 22 MRFK-EGmSYSILGPNGAGKSTIA 44
                                      5666.556999***********95 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.2   1.2e-05     0.016      22      36 ..      30      44 ..      12      72 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.2e-05
                            AAA_23 22 tlItGpNGaGKTTil 36
                                      + I GpNGaGK+Ti 
  gi|242399668|ref|YP_002995093.1| 30 YSILGPNGAGKSTIA 44
                                      57***********96 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   6.3e-05     0.087      14      63 ..      17      63 ..      14     113 .. 0.76
   2 ?   -1.2   0.0      0.93   1.3e+03     235     256 ..     164     185 ..     105     223 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.3e-05
                            AAA_15 14 lkdveidlseelt.vliGkNnsGKSsilealdlFlnnkekknkkvikieke 63
                                      l+++ + ++e ++  + G+N++GKS+i+++l   ++ +    +  i+  ++
  gi|242399668|ref|YP_002995093.1| 17 LEKINMRFKEGMSySILGPNGAGKSTIAYILMGVIKPS----EGRIFMGDK 63
                                      56677778887444799**************8888877....344444444 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.93
                            AAA_15 235 eeelteklkeiqeklkeidkkl 256
                                       ++ +te +++i++ lk i  ++
  gi|242399668|ref|YP_002995093.1| 164 DITVTELIDRILDYLKRIGTTI 185
                                       5666666666666666666655 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   3.9e-05     0.054     127     174 ..      25      73 ..       4      97 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.9e-05
                             T2SSE 127 rerglilvsGgTgsGKttllyallkeinksderivtvE.DpvEiqlega 174
                                       +e ++  + G+ g GK+t++y+l+  i+ s+ ri +   D  E+++ + 
  gi|242399668|ref|YP_002995093.1|  25 KEGMSYSILGPNGAGKSTIAYILMGVIKPSEGRIFMGDkDITELNITER 73 
                                       555555677*********************9999764337777777655 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00017      0.24      81     121 ..       8      49 ..       3      63 .. 0.82
   2 ?   -0.3   0.0      0.62   8.6e+02      32      62 ..     168     198 ..     112     210 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00017
                                       E--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  81 lvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallp 121
                                       + sa+ ++ le+++ ++k+     ++G+ G+GKSt+   l++
  gi|242399668|ref|YP_002995093.1|   8 TYSANGRKILEKINMRFKEgMSYSILGPNGAGKSTIAYILMG 49 
                                       667888889999*999999667789**********9887776 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.62
                                       HHHHHHHHHHHHHTT-EEEEEEE-GGG--HH CS
                       RsgA_GTPase  32 lnlldrfLvlaeekgiepvivlnKiDlleee 62 
                                       ++l+dr+L  +++ g +++++    D+++++
  gi|242399668|ref|YP_002995093.1| 168 TELIDRILDYLKRIGTTIILITHHEDIAKKT 198
                                       4566666666666666666655555555554 PP

>> PIG-L  GlcNAc-PI de-N-acetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00015      0.21      53     115 ..     104     194 ..      84     199 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00015
                                       HHHHHHHHHHHHHCTE..EEEEECCCBTT-STT.............................S-CHHHHHHHHHHHH CS
                             PIG-L  53 eiRekEaraaakhlgvadedvffldfpDgsles.............................ydedellddlaklie 100
                                       ++ ++E++++++++g+   ++++ +f D+sl+                               + +el+d++ ++++
  gi|242399668|ref|YP_002995093.1| 104 NVDKEELKEVLEIVGL-PYELYHSRFVDKSLSGgerkrvelasilllkpkyaildepdsgldITVTELIDRILDYLK 179
                                       56899***********.7789999999999999999999999999999999999999999999************** PP

                                       HH--SEEEEE-TTTT CS
                             PIG-L 101 ryrPdvvltldpegd 115
                                       r+  +++l+++ e++
  gi|242399668|ref|YP_002995093.1| 180 RIGTTIILITHHEDI 194
                                       **9999888877765 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 ?   12.3   0.0   9.4e-05      0.13       4      47 ..      32      76 ..      30      97 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9.4e-05
                                      EE--SSSSHHHHHHHGGGGB.S--EEEEE--TT--HHHHH--B-- CS
                             AAA_5  4 LvGppGtgKselaerlaaal.nreveyvqltrdtteedlkgrrei 47
                                      ++Gp G gKs++a  l  ++  +e  + ++ +d+te +++ r ++
  gi|242399668|ref|YP_002995093.1| 32 ILGPNGAGKSTIAYILMGVIkPSEGRIFMGDKDITELNITERARL 76
                                      68***********************************99998776 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0    0.0014       1.9       3      22 ..      28      47 ..      26      73 .. 0.78
   2 ?    2.7   0.1     0.065        89     107     133 ..     167     193 ..     165     204 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0014
                            AAA_24  3 lkiliyGpsgiGKTtlakel 22
                                      +++ i Gp+g+GK+t+a+ l
  gi|242399668|ref|YP_002995093.1| 28 MSYSILGPNGAGKSTIAYIL 47
                                      56779************977 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.065
                            AAA_24 107 laeefrrllkklqelrknvifiahekt 133
                                       ++e + r+l++l+  + ++i+i h + 
  gi|242399668|ref|YP_002995093.1| 167 VTELIDRILDYLKRIGTTIILITHHED 193
                                       567788999999*******99999775 PP

>> Peptidase_C3G  Tungro spherical virus-type peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   9.7e-05      0.13      26      78 ..     165     217 ..     158     223 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.7e-05
                     Peptidase_C3G  26 vnvlpnrtaylnvlrliGtyvvlpahylealeeedtlyficfslviklrlerd 78 
                                       ++v+    + l+ l+ iGt ++l +h+ +  ++ +  yf+c  ++++  +  +
  gi|242399668|ref|YP_002995093.1| 165 ITVTELIDRILDYLKRIGTTIILITHHEDIAKKTEFSYFVCSGKIVRKGFSDE 217
                                       66777788999****************9999999999********99877665 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1    0.0061       8.4      12      36 ..      20      44 ..      13      80 .. 0.85
   2 ?    4.4   0.1     0.015        20     142     186 ..     169     210 ..     161     221 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0061
                            ATPase 12 lkgGipegrvvlitGepGtGKtifa 36
                                      ++  + eg ++ i G  G+GK+++a
  gi|242399668|ref|YP_002995093.1| 20 INMRFKEGMSYSILGPNGAGKSTIA 44
                                      457899****************997 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.015
                            ATPase 142 eilrqlvrvlkklgvTailvsekssseeaaggygveefivdgviv 186
                                       e +++++  lk +g+T il++    +e+ a++ + + f+++g iv
  gi|242399668|ref|YP_002995093.1| 169 ELIDRILDYLKRIGTTIILITH---HEDIAKKTEFSYFVCSGKIV 210
                                       67899999*************9...67777888888888888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      565  (0.0315132); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); 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 0.38s 00:00:01.01 Elapsed: 00:00:00.55
# Mc/sec: 1344.81
//
Query:       gi|242399669|ref|YP_002995094.1|  [L=121]
Description: Heterodisulfide reductase subunit A-like protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       666  (0.0371465); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); 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: 0.52u 0.35s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 702.53
//
Query:       gi|242399670|ref|YP_002995095.1|  [L=70]
Description: Ferredoxin [Thermococcus sibiricus MM 739]
Scores for 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-10   38.5  16.3    8.3e-08   31.7   2.3    3.0  2  Fer4      4Fe-4S binding domain
    6.9e-10   38.4  13.6    7.4e-07   28.9   2.1    2.3  2  Fer4_2    4Fe-4S binding domain
    9.7e-10   38.1  13.1      8e-05   22.5   1.8    2.3  2  Fer4_6    4Fe-4S binding domain
    2.5e-09   37.2   9.5      3e-09   36.9   9.5    1.1  1  Fer4_9    4Fe-4S dicluster domain
    4.9e-08   33.4  12.5    6.5e-08   33.1  12.5    1.2  1  Fer4_7    4Fe-4S dicluster domain
    1.8e-07   31.2  12.1    4.1e-07   30.0  12.3    1.5  2  Fer4_10   4Fe-4S dicluster domain
    2.2e-07   30.9  19.8    7.5e-05   22.8  10.7    1.7  2  Fer4_21   4Fe-4S dicluster domain
    6.1e-05   23.2  13.4    0.00035   20.8   1.6    2.5  2  Fer4_4    4Fe-4S binding domain
    0.00024   21.6  11.3     0.0031   18.0  11.3    2.0  1  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
     0.0014   19.5  12.9       0.17   12.9   3.0    2.2  4  Fer4_16   4Fe-4S double cluster binding domain
     0.0072   16.4   6.2      0.039   14.1   6.6    1.8  2  ETF_QO    Electron transfer flavoprotein-ubiquinone oxidoredu
  ------ inclusion threshold ------
      0.023   15.2  12.2      0.047   14.2   2.2    2.1  2  Fer4_17   4Fe-4S dicluster domain
      0.036   14.9   6.5      0.051   14.4   0.5    2.1  2  Fer4_22   4Fe-4S dicluster domain
      0.094   13.5   7.3       0.94   10.3   7.3    2.1  1  Fer4_15   4Fe-4S single cluster domain
      0.097   13.7  17.3       0.79   10.8   5.6    2.8  2  Fer4_3    4Fe-4S binding domain
       0.32   11.5  13.7       0.34   11.4   3.6    2.1  2  Fer4_8    4Fe-4S dicluster domain
        2.1    8.6  10.1        1.1    9.5   2.0    2.0  2  Fer4_18   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   2.3   7.9e-11   8.3e-08       2      22 ..      10      30 ..       9      32 .. 0.91
   2 !   10.2   6.3   0.00051      0.54       2      23 ..      42      64 ..      41      65 .. 0.85

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 7.9e-11
                                      EEETTTSSS-THHHHHSTTTE CS
                              Fer4  2 videekCigCGaCvevCPvgA 22
                                       id+ekC+gC +Cv+ CP+++
  gi|242399670|ref|YP_002995095.1| 10 MIDYEKCTGCLTCVNFCPHEV 30
                                      69****************987 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00051
                                      EEETTTSS.S-THHHHHSTTTEE CS
                              Fer4  2 videekCi.gCGaCvevCPvgAI 23
                                      v+++e C+ +C  C  +CP gAI
  gi|242399670|ref|YP_002995095.1| 42 VVNPENCVeFCRGCQRICPAGAI 64
                                      5778888747************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 !   28.9   2.1     7e-10   7.4e-07       1      22 []       7      28 ..       7      28 .. 0.95
   2 !   15.0   4.0   1.8e-05     0.019       3      22 .]      41      61 ..      39      61 .. 0.92

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 7e-10
                            Fer4_2  1 apvvvdtdrCigCgaCvsaCPa 22
                                      +++ +d ++C+gC +Cv+ CP+
  gi|242399670|ref|YP_002995095.1|  7 WYPMIDYEKCTGCLTCVNFCPH 28
                                      6899*****************7 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 1.8e-05
                            Fer4_2  3 vvvdtdrCig.CgaCvsaCPa 22
                                       vv++++C++ C+ C+  CPa
  gi|242399670|ref|YP_002995095.1| 41 RVVNPENCVEfCRGCQRICPA 61
                                      589*****************8 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   1.8   7.6e-08     8e-05       4      23 ..      11      30 ..       9      31 .. 0.93
   2 !   20.9   3.9   2.5e-07   0.00026       3      24 .]      42      64 ..      42      64 .. 0.96

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 7.6e-08
                            Fer4_6  4 idpdkCigCgdCvrvCPega 23
                                      id++kC+gC  Cv+ CP+ +
  gi|242399670|ref|YP_002995095.1| 11 IDYEKCTGCLTCVNFCPHEV 30
                                      89***************986 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 2.5e-07
                            Fer4_6  3 eidpdkCig.CgdCvrvCPegai 24
                                      +++p++C+  C+ C r+CP+gai
  gi|242399670|ref|YP_002995095.1| 42 VVNPENCVEfCRGCQRICPAGAI 64
                                      69******99************8 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   9.5   2.9e-12     3e-09       1      51 []      15      64 ..      15      64 .. 0.93

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 2.9e-12
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCig.CgaCveaCpkgai 51
                                      kCtgC +Cv+ Cp++v++ d +++k r+ + +  +C++ C+ C  +Cp gai
  gi|242399670|ref|YP_002995095.1| 15 KCTGCLTCVNFCPHEVYEVDPNPGKPRVVNPE--NCVEfCRGCQRICPAGAI 64
                                      7**************************98875..6*766**********997 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1  12.5   6.1e-11   6.5e-08       1      52 []      15      63 ..      15      63 .. 0.87

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 6.1e-11
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekCl.gCgaCvavCPtga 52
                                      +C+gC  Cv+ Cp+++ e+d+   +++    +++pe+C+ +C+ C++ CP+ga
  gi|242399670|ref|YP_002995095.1| 15 KCTGCLTCVNFCPHEVYEVDPNPGKPR----VVNPENCVeFCRGCQRICPAGA 63
                                      7*******************9844444....679****737**********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 !   30.0  12.3   3.9e-10   4.1e-07       3      56 .]      10      60 ..       8      60 .. 0.87
   2 !   12.2   3.2   0.00014      0.15       3      21 ..      42      61 ..      40      66 .. 0.81

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 3.9e-10
                           Fer4_10  3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtg.cgaCveaCP 56
                                       id ++C++C +Cv++CP      +++   +++++  +++e+C + c  C+++CP
  gi|242399670|ref|YP_002995095.1| 10 MIDYEKCTGCLTCVNFCPH----EVYEVDPNPGKPRVVNPENCVEfCRGCQRICP 60
                                      699****************....677777777777777*****988********9 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00014
                           Fer4_10  3 vidddtCi.rCgkCvkaCPa 21
                                      v++++ C+  C+ C++ CPa
  gi|242399670|ref|YP_002995095.1| 42 VVNPENCVeFCRGCQRICPA 61
                                      5788999757********99 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   1.7   1.1e-06    0.0012      33      53 ..       7      28 ..       1      33 [. 0.72
   2 !   22.8  10.7   7.1e-08   7.5e-05       2      58 ..      10      65 ..       9      66 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.1e-06
                           Fer4_21 33 vlkvv.edeCvGCnlCssvCPv 53
                                       ++++  ++C+GC  C++ CP 
  gi|242399670|ref|YP_002995095.1|  7 WYPMIdYEKCTGCLTCVNFCPH 28
                                      44444279*************4 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 7.1e-08
                           Fer4_21  2 ridedkCigCgkCliaCedtshqaieidaktvl..kvvedeCvG.CnlCssvCPvedcie 58
                                      +id +kC gC  C+  C+   h+  e+d++      v  ++Cv  C  C  +CP  ++i+
  gi|242399670|ref|YP_002995095.1| 10 MIDYEKCTGCLTCVNFCP---HEVYEVDPNPGKprVVNPENCVEfCRGCQRICPA-GAIN 65
                                      69****************...777788877544115568****66*********5.8885 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   1.6   3.3e-07   0.00035       1      15 [.      13      27 ..      13      39 .. 0.91
   2 !    7.4   4.5    0.0069       7.3       2      17 .]      46      62 ..      45      62 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 3.3e-07
                            Fer4_4  1 qerCigCgsCvaaCP 15
                                      +e+C+gC  Cv++CP
  gi|242399670|ref|YP_002995095.1| 13 YEKCTGCLTCVNFCP 27
                                      59************* PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0069
                            Fer4_4  2 erCi.gCgsCvaaCPqg 17
                                      e+C+  C+ C ++CP g
  gi|242399670|ref|YP_002995095.1| 46 ENCVeFCRGCQRICPAG 62
                                      677745*********75 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 !   18.0  11.3   2.9e-06    0.0031       1      56 [.      11      64 ..      11      65 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.9e-06
                           Fer4_13  1 VDrdtCiacgaCvelaP.dvFeeddeggasvvaeqptseeekadaeeAadaCPvesI 56
                                      +D ++C++c +Cv+++P +v+e d++ g+ +v++ ++     + ++     CP  +I
  gi|242399670|ref|YP_002995095.1| 11 IDYEKCTGCLTCVNFCPhEVYEVDPNPGKPRVVNPENC---VEFCRGCQRICPAGAI 64
                                      799**************77**********999764443...4556777777777777 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 !   12.9   3.0   0.00016      0.17      51      66 ..      13      28 ..       2      29 .. 0.71
   2 !   11.2   5.2   0.00052      0.55       1      20 [.      15      34 ..      15      50 .. 0.73
   3 !    9.2   3.1    0.0022       2.4      53      66 ..      47      61 ..      36      62 .. 0.76
   4 !   10.8   2.8   0.00072      0.76       2      18 ..      48      65 ..      47      68 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00016
                           Fer4_16 51 qeaitgCdiCqdvCPa 66
                                      +e++tgC +C++ CP+
  gi|242399670|ref|YP_002995095.1| 13 YEKCTGCLTCVNFCPH 28
                                      4668999999999986 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00052
                           Fer4_16  1 rCgtCgkCaevCPtnaikek 20
                                      +C++C  C++ CP+++ + +
  gi|242399670|ref|YP_002995095.1| 15 KCTGCLTCVNFCPHEVYEVD 34
                                      59999999999999987755 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0022
                           Fer4_16 53 ai.tgCdiCqdvCPa 66
                                      ++  +C+ Cq++CPa
  gi|242399670|ref|YP_002995095.1| 47 NCvEFCRGCQRICPA 61
                                      44499*********8 PP

  == domain 4  score: 10.8 bits;  conditional E-value: 0.00072
                           Fer4_16  2 Cgt.CgkCaevCPtnaik 18
                                      C++ C+ C  +CP++ai+
  gi|242399670|ref|YP_002995095.1| 48 CVEfCRGCQRICPAGAIN 65
                                      666699999999999986 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 ?    0.2   0.3      0.76     8e+02      70      81 ..      11      22 ..       3      24 .. 0.82
   2 !   14.1   6.6   3.7e-05     0.039      47      92 ..      23      66 ..      13      69 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.76
                                      E-CCC--S--HH CS
                            ETF_QO 70 inaqnCvhCktC 81
                                      i+ + C  C tC
  gi|242399670|ref|YP_002995095.1| 11 IDYEKCTGCLTC 22
                                      77889999*999 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 3.7e-05
                                      HHH-TTS-EEEEETTTTSSEEEEE-CCC--.S--HHHHH-TT--EEE CS
                            ETF_QO 47 qryCPagvyeivedeeakekklqinaqnCv.hCktCdikdpsqniew 92
                                        +CP  vye+  +    ++  ++n +nCv  C+ C+   p   i++
  gi|242399670|ref|YP_002995095.1| 23 VNFCPHEVYEVDPNP--GKP-RVVNPENCVeFCRGCQRICPAGAINY 66
                                      68********98766..445.579******56*****9999999997 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   2.2   4.5e-05     0.047      42      60 ..      12      30 ..       1      31 [. 0.79
   2 ?    6.9   2.6    0.0088       9.2      44      59 ..      46      62 ..      32      63 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.5e-05
                           Fer4_17 42 kaslCieCgeCerkCPqgl 60
                                        ++C++C  C+  CP+++
  gi|242399670|ref|YP_002995095.1| 12 DYEKCTGCLTCVNFCPHEV 30
                                      5789************986 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0088
                           Fer4_17 44 slCie.CgeCerkCPqg 59
                                      ++C+e C++C+r CP+g
  gi|242399670|ref|YP_002995095.1| 46 ENCVEfCRGCQRICPAG 62
                                      678877*********86 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.5   4.8e-05     0.051      70      95 ..       4      29 ..       1      30 [. 0.85
   2 ?    4.0   1.0     0.086        91       2      14 ..      48      61 ..      41      67 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.8e-05
                           Fer4_22 70 lsefkekfgesgCvGCgRCieacpvk 95
                                       +++   ++ ++C+GC  C++ cp++
  gi|242399670|ref|YP_002995095.1|  4 AKNWYPMIDYEKCTGCLTCVNFCPHE 29
                                      467888999***************87 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.086
                           Fer4_22  2 Cls.CgaCtlvCpt 14
                                      C++ C  C+ +Cp+
  gi|242399670|ref|YP_002995095.1| 48 CVEfCRGCQRICPA 61
                                      44336666666664 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   7.3    0.0009      0.94       3      33 ..      11      43 ..      10      66 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0009
                           Fer4_15  3 vDrdaCigcglCvaea.pevfelded.glasvl 33
                                      +D ++C+gc  Cv  +  ev e d + g+++v+
  gi|242399670|ref|YP_002995095.1| 11 IDYEKCTGCLTCVNFCpHEVYEVDPNpGKPRVV 43
                                      9***************44677777755888766 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   5.6   0.00075      0.79       1      13 [.      16      28 ..      16      30 .. 0.93
   2 ?    7.7   3.9    0.0072       7.6       1      15 []      48      63 ..      46      63 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00075
                            Fer4_3  1 CtgCgaCvevCPv 13
                                      CtgC +Cv+ CP 
  gi|242399670|ref|YP_002995095.1| 16 CTGCLTCVNFCPH 28
                                      ****99******5 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0072
                            Fer4_3  1 Ct.gCgaCvevCPvgA 15
                                      C+  C+ C + CP gA
  gi|242399670|ref|YP_002995095.1| 48 CVeFCRGCQRICPAGA 63
                                      6646988******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 ?   11.4   3.6   0.00032      0.34      49      64 ..      14      29 ..       3      30 .. 0.82
   2 ?    5.5   2.7     0.021        23      53      64 ..      51      62 ..      39      63 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00032
                            Fer4_8 49 wsCttcgaCtevCpvg 64
                                      ++Ct+c  C++ Cp +
  gi|242399670|ref|YP_002995095.1| 14 EKCTGCLTCVNFCPHE 29
                                      6899999999999976 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.021
                            Fer4_8 53 tcgaCtevCpvg 64
                                       c+ C++ Cp g
  gi|242399670|ref|YP_002995095.1| 51 FCRGCQRICPAG 62
                                      378888888865 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   2.0    0.0011       1.1      59      75 ..      14      30 ..       3      36 .. 0.87
   2 ?    4.3   1.3     0.041        43      59      74 ..      46      62 ..      36      66 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0011
                           Fer4_18 59 gdcidcescvkvcPtgi 75
                                       +c+ c +cv+ cP ++
  gi|242399670|ref|YP_002995095.1| 14 EKCTGCLTCVNFCPHEV 30
                                      68************876 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.041
                           Fer4_18 59 gdcid.cescvkvcPtg 74
                                       +c++ c+ c ++cP g
  gi|242399670|ref|YP_002995095.1| 46 ENCVEfCRGCQRICPAG 62
                                      6788669********87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      188  (0.0104858); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); 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: 0.54u 0.34s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 402.34
//
Query:       gi|242399671|ref|YP_002995096.1|  [L=110]
Description: Iron-molybdenum cofactor-binding protein [Thermococcus sibiricus MM 739]
Scores for complete 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-13   50.6   0.0      2e-13   50.5   0.0    1.0  1  Nitro_FeMo-Co   Dinitrogenase iron-molybdenum cofactor
  ------ inclusion threshold ------
      0.069   13.4   0.0       0.09   13.0   0.0    1.4  1  baeRF_family10  Bacterial archaeo-eukaryotic release factor f


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 !   50.5   0.0   2.2e-17     2e-13       2      94 ..      14     107 ..      13     108 .. 0.91

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 2.2e-17
                                       TSCB-STCCC-SEEEEEEESSSCEEEEEEEE.GCCCTSSCSSTHHHHHHHHTT-SEEEESSSCHHHHHHHCTTTSEE CS
                     Nitro_FeMo-Co   2 gsrvdqhFGrapyFaiyeveegevkivenrveeaadaegggggklaqllaeegvdvvivgkiGpralakleaagiev 78 
                                       ++rv +   ra++F+++e++ g++k v++ ++++ ++++g+g k+a +l + gvdv+++    p+ +  lea g+++
  gi|242399671|ref|YP_002995096.1|  14 DDRVHESLVRAETFTVVELDGGNIKEVQVIENPYRGEPHGAGPKVALFLVNLGVDVLLTPMECPKGKPILEAGGVRI 90 
                                       78999***************9988844444555******************************************** PP

                                       EES.-SSBHHHHHHHHH CS
                     Nitro_FeMo-Co  79 ykg.aggtveealkevl 94 
                                       +k+ ag+ veeal+ ++
  gi|242399671|ref|YP_002995096.1|  91 VKVkAGKRVEEALRSLR 107
                                       *************9875 PP

>> baeRF_family10  Bacterial archaeo-eukaryotic release factor family 10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0     1e-05      0.09      20      56 ..      21      57 ..      15     107 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1e-05
                    baeRF_family10 20 lvdreraRlfevylgeleeveevegevpgrtktggwk 56
                                      lv++e + + e  +g ++ev+++e+++ g ++++g+k
  gi|242399671|ref|YP_002995096.1| 21 LVRAETFTVVELDGGNIKEVQVIENPYRGEPHGAGPK 57
                                      89*******************************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       225  (0.0125495); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.33s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 632.60
//
Query:       gi|242399672|ref|YP_002995097.1|  [L=296]
Description: Cobalt/zinc/cadmium cation efflux pump protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-44  152.0  12.8    1.9e-44  151.8  12.8    1.0  1  Cation_efflux  Cation efflux family
    8.4e-12   45.1   1.7    1.5e-11   44.2   1.7    1.4  1  ZT_dimer       Dimerisation domain of Zinc Transporter
  ------ inclusion threshold ------
       0.19   12.2   0.0       0.33   11.4   0.0    1.4  1  Lipocalin_8    Lipocalin-like domain


Domain annotation for each model (and alignments):
>> Cation_efflux  Cation efflux family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.8  12.8   3.1e-48   1.9e-44       2     199 .]      14     203 ..      13     203 .. 0.97

  Alignments for each domain:
  == domain 1  score: 151.8 bits;  conditional E-value: 3.1e-48
                     Cation_efflux   2 ilsllanlilalvelivglltnSlalladafhslsdlvsllllllalklsrkppderfpfGygrlevlgalvsglll 78 
                                       + s+++n+i++++e+++gll++Slall+d++h++ d +sll +++a+++  ++++e+++fGy r+e l+a++++++l
  gi|242399672|ref|YP_002995097.1|  14 LFSFALNIIITIAEVVGGLLSGSLALLSDSLHNFGDSMSLLASYFAIRIGERKANEKYTFGYRRVEILVAFMNSAVL 90 
                                       6799************************************************************************* PP

                     Cation_efflux  79 lglavfllleaiqklikegereihaglalvvalvslvvnlalllilrragrklrsaalkaaalhvlgDaltslgvlv 155
                                       +g+ + ll+ea+ ++   +++ i+ +l+l+val++l+ nl+++l+l++++   +  ++++a+lh l+D+l+s++v+ 
  gi|242399672|ref|YP_002995097.1|  91 VGVSLLLLVEAYRRFK--NPEPIDGPLMLGVALIGLFANLFSVLLLHEHA---HGLNVRSAYLHLLTDTLSSVAVVA 162
                                       ***************9..*****************************998...89*********************9 PP

                     Cation_efflux 156 salvillfnlksgplaDpvaslligliilysalkllkeslseLl 199
                                       + + i+ +n     ++Dp+++++i+l+il  a+++l+es+ +L+
  gi|242399672|ref|YP_002995097.1| 163 GGIAIMKWNI---LWIDPLVTVFISLYILREAYEILRESIEVLM 203
                                       9999988755...48***************************97 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 !   44.2   1.7   2.5e-15   1.5e-11       5      77 ..     210     280 ..     206     282 .. 0.92

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 2.5e-15
                                       HHHHHHHHHTT-SS-EEEEEEEEE-S-.---EEEEEEEE-TTS-HHHHHHHHHHHHHHHHHH-TT--EEEEEEE CS
                          ZT_dimer   5 eeeeireiiksvpgvkgvhdlrtrksG.skifvdlhievdgdlsvkeaHeiadevekrikeefpgvadvliHve 77 
                                       ++e++++ i+++pgvk+ h++++ ++G ++++ ++h+evd d+++ ea +i+de+e+r++ +f g+++v++ +e
  gi|242399672|ref|YP_002995097.1| 210 DLEAVKREIEAIPGVKNAHHFHAWRIGeDEVHFECHVEVD-DMPLGEAQRIIDEIEERLR-KF-GITHVTVQLE 280
                                       67899999*******************88**********6.68****************8.89.99*****987 PP

>> Lipocalin_8  Lipocalin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   5.5e-05      0.33      88     121 ..     256     289 ..     229     295 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.5e-05
                       Lipocalin_8  88 gdkkvddtveeLepyGinsleetFeveklsgskm 121
                                        +  +d+ +e L+++Gi+++  ++ev +++g+++
  gi|242399672|ref|YP_002995097.1| 256 AQRIIDEIEERLRKFGITHVTVQLEVDRCDGKNL 289
                                       567899999***********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); 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 0.35s 00:00:00.94 Elapsed: 00:00:00.51
# Mc/sec: 1734.95
//
Query:       gi|242399673|ref|YP_002995098.1|  [L=146]
Description: stress-inducible protein, OsmC/Ohr family [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-19   70.7   0.0    1.8e-19   70.1   0.0    1.3  1  OsmC      OsmC-like protein
  ------ inclusion threshold ------
      0.082   13.2   0.1       0.21   11.8   0.2    1.7  1  MecA_N    NTF2-like N-terminal transpeptidase domain


Domain annotation for each model (and alignments):
>> OsmC  OsmC-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.1   0.0     2e-23   1.8e-19       1      97 [.      37     131 ..      35     134 .. 0.91

  Alignments for each domain:
  == domain 1  score: 70.1 bits;  conditional E-value: 2e-23
                                       TTXSSB-HHHHHHHHHHHHHHHHHHHHTCCCT---SCEEEEEEEEEECCECTCEEEEEEEEEEE-SS-H..HHHHHH CS
                              OsmC   1 gdgsgpsPeelllaalasCfaitlravakkkgikledleveveaerdpegakgiteirlkvevkipgadseeklkkl 77 
                                       g + gp+P+e+llaa+++C++++  ++ kk+++k+++++v v++ rd+e ++ ++ei++kv++  ++++ e+k+ ++
  gi|242399673|ref|YP_002995098.1|  37 GRNAGPNPTEYLLAAIGGCLTVNWGRLIKKMRLKVDEMHVIVSGWRDQEEPR-LKEITYKVRIV-TEEP-EKKVLRV 110
                                       5677*********************************************999.**********5.5556.6****** PP

                                       HHHHHHHSHHHHHH.CT-SSS CS
                              OsmC  78 lekaekrCpvsntl.kngvkv 97 
                                        e+aek+ +v nt+ ++ +k 
  gi|242399673|ref|YP_002995098.1| 111 KELAEKYGTVFNTVgAEKIKG 131
                                       **************7777765 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 ?   11.8   0.2   2.4e-05      0.21      23      63 ..      98     138 ..      89     145 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.4e-05
                                       CTB--BSSBSS-HHHHHHHHHHHCCCTT-EEEEEEEEEEEE CS
                            MecA_N  23 sllseqskkeisekeavekyqaiydglqvkklkieakkvkk 63 
                                        +++e++kk +  ke+ eky ++++ ++++k+k e + v k
  gi|242399673|ref|YP_002995098.1|  98 IVTEEPEKKVLRVKELAEKYGTVFNTVGAEKIKGEVEIVRK 138
                                       5788999*************************977666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.35s 00:00:00.91 Elapsed: 00:00:00.55
# Mc/sec: 803.47
//
Query:       gi|242399674|ref|YP_002995099.1|  [L=149]
Description: Trx-linked arsenate reductase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-26   93.8   0.0    2.1e-26   93.0   0.0    1.4  1  LMWPc            Low molecular weight phosphotyrosine protein
  ------ inclusion threshold ------
      0.068   13.8   0.1       0.11   13.1   0.1    1.3  1  DUF5398          Family of unknown function (DUF5398)
       0.11   12.5   0.0       0.13   12.2   0.0    1.1  1  Peptidase_M16_C  Peptidase M16 inactive domain


Domain annotation for each model (and alignments):
>> LMWPc  Low molecular weight phosphotyrosine protein phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.0   0.0   3.5e-30   2.1e-26       1     141 [.       6     127 ..       6     128 .. 0.93

  Alignments for each domain:
  == domain 1  score: 93.0 bits;  conditional E-value: 3.5e-30
                                       EEEEESSSSSHHHHHHHHHHHHHHHTT-CCCEEEEEEESTSTTT-B--HHHHHHHHHTTS--TT-BB-BS-HHHHHH CS
                             LMWPc   1 vlfvClgNicRSpmAealfrkelekagleekvevdSaGtgalvgkradpravevlkekgislsghvarqlskeelae 77 
                                       +lfvC++N++RS+mAea+f++  ++     +++v SaGt+  +++++dp a +v++e gisl+g++++  ++e++++
  gi|242399674|ref|YP_002995099.1|   6 ILFVCVKNSARSQMAEAFFNHFNDD----PRFKVMSAGTE--PAEEIDPLARKVMEEIGISLEGQYPKLYTEEMAEK 76 
                                       89********************776....79*********..*********************************** PP

                                       SSEEEESSHHHHHHHHHHCCTTGGGGEEEGGGGSSTSS---HTTSSHHHHHHHHHHHHHHHHHH CS
                             LMWPc  78 lDlilamdeenkreleslapekekakvkllgeyteqldieDPyygeieafeevldeieeavkkl 141
                                       + ++++m      + ++ ap  e       + +  ++ +eDPy++ ie+++ev+dei+++v kl
  gi|242399674|ref|YP_002995099.1|  77 AYIVITMGCL---DRCPYAPP-E-------KTW--DWGLEDPYGKPIEKYREVRDEIKRRVIKL 127
                                       *******644...55899999.4.......357..*************************9987 PP

>> DUF5398  Family of unknown function (DUF5398)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   1.8e-05      0.11      27      56 ..     110     139 ..      96     146 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.8e-05
                           DUF5398  27 vkkakeikqkvesriqkikeaLReGenkee 56 
                                       + k +e++ +++ r+ k+ e L+ G++kee
  gi|242399674|ref|YP_002995099.1| 110 IEKYREVRDEIKRRVIKLIEDLKAGKSKEE 139
                                       5799*************************8 PP

>> Peptidase_M16_C  Peptidase M16 inactive domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.2e-05      0.13       9      71 ..      21     114 ..      15     141 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.2e-05
                                       HHHHHHSSGG.GEEEEEEESS-HHHHHHHHHHHHTTSTHHSH..............................CSGSC CS
                   Peptidase_M16_C   9 efykkfYrpe.nmvlaivGdvdheelvkliekyfgdlkaska..............................ppakp 54 
                                       e + ++++ + ++++  +G  + ee+  l++k++ +++ s +                              pp+k 
  gi|242399674|ref|YP_002995099.1|  21 EAFFNHFNDDpRFKVMSAGTEPAEEIDPLARKVMEEIGISLEgqypklyteemaekayivitmgcldrcpyaPPEKT 97 
                                       45555666666***************************998899999999999999999999999999999955555 PP

                                       TSSSSSGGGSSEEEEEE CS
                   Peptidase_M16_C  55 tgepltpatlkkppvvl 71 
                                       ++  l+++  k+ ++++
  gi|242399674|ref|YP_002995099.1|  98 WDWGLEDPYGKPIEKYR 114
                                       55555522222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); 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 0.35s 00:00:00.92 Elapsed: 00:00:00.54
# Mc/sec: 825.61
//
Query:       gi|242399675|ref|YP_002995100.1|  [L=364]
Description: Arsenical-resistance membrane protein [Thermococcus sibiricus MM 739]
Scores for complete 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-47  160.6  15.9    3.6e-47  160.6  15.9    2.3  3  SBF       Sodium Bile acid symporter family
    5.3e-12   45.7  23.4    1.4e-11   44.3  23.4    1.6  1  SBF_like  SBF-like CPA transporter family (DUF4137)


Domain annotation for each model (and alignments):
>> SBF  Sodium Bile acid symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1      0.44     4e+03     136     154 ..      15      33 ..      11      48 .. 0.65
   2 !  160.6  15.9     4e-51   3.6e-47       2     194 ..      52     253 ..      51     254 .. 0.95
   3 ?   -0.3   0.3     0.079   7.1e+02      60      94 ..     304     338 ..     258     348 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.44
                               SBF 136 ivviiPliaGillryillk 154
                                       i v + +iaGi l ++++ 
  gi|242399675|ref|YP_002995100.1|  15 IWVALCIIAGIALGKFMPS 33 
                                       5566667788887777776 PP

  == domain 2  score: 160.6 bits;  conditional E-value: 4e-51
                               SBF   2 ilLilmmfpmglkveveklkellkr..pkalllglvlqwvikPllmfilakillrdl..........klepelavGl 66 
                                       +l+  m++pm++kv+++++k++ k    k l+++ v +w+ikP+ mf+++ ++++ l          +l++e+++G 
  gi|242399675|ref|YP_002995100.1|  52 VLIWAMIYPMMVKVDFSAIKNVHKGqmLKGLIVTWVTNWLIKPFSMFLISSFFIGILfsaklglidvSLAKEYIAGA 128
                                       67889******************98789*************************99999******************* PP

                               SBF  67 ilvglapggamsnvwtylakGdlelsvvlvalstllailltPlllyllaksleqttlkvpieeivksvlivviiPli 143
                                       il+g+ap++am+ vw+yla+Gd  +++v va++ ++ ++ ++ ++ +l++++   +++vp+e++++sv+++v+iPl+
  gi|242399675|ref|YP_002995100.1| 129 ILLGAAPCTAMVFVWSYLADGDPLYTLVQVATNDIIILFAFAPIVGFLMGLN---KIPVPYETLLISVVLFVVIPLT 202
                                       ***************************************9966666666777...7********************* PP

                               SBF 144 aGillryillkhkGrewfeskllpavspisligllltivvifalkgelive 194
                                       aG+++r+ +l++kG ewfe+ +lp++s +s++glllt+++if+++g++i+e
  gi|242399675|ref|YP_002995100.1| 203 AGYISRRHILRTKGPEWFEKNFLPKLSTVSIVGLLLTLILIFSFQGNIILE 253
                                       ************************************************987 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.079
                               SBF  60 pelavGlilvglapggamsnvwtylakGdlelsvv 94 
                                         +av++ l gl +g+a+++v++ l +    ls+v
  gi|242399675|ref|YP_002995100.1| 304 LAVAVAIALFGLESGAALATVVGVLEEVPIMLSLV 338
                                       45677888888888888888888777665555555 PP

>> SBF_like  SBF-like CPA transporter family (DUF4137)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.3  23.4   1.5e-15   1.4e-11       3     294 ..      17     327 ..      15     344 .. 0.77

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 1.5e-15
                          SBF_like   3 fllllilvillAslvPvfakaggtikaeyvikyg.ValiFllsGl....slsteellanlrnwrlhllvllisfllt 74 
                                         l++i+ i+l+ ++P++ +a +++ + +v+  + V +  +++ +     +s  + +++ +  +  +++ +++ l+ 
  gi|242399675|ref|YP_002995100.1|  17 VALCIIAGIALGKFMPSVSQALSKFTVANVNIPIaVLIWAMIYPMmvkvDFSAIKNVHKGQMLKGLIVTWVTNWLIK 93 
                                       56677777777777777777766666654432221433333333311003444444455555555666666666666 PP

                          SBF_like  75 plivlalvsllkaald............pelliGllllaalPtTvssnvvmtsqAgGnealalceavignllGvflt 139
                                       p  ++ ++s++  +l             +e ++G +ll a+P+T ++  v    A+G+ + +l++++   ++  f+ 
  gi|242399675|ref|YP_002995100.1|  94 PFSMFLISSFFIGILFsaklglidvslaKEYIAGAILLGAAPCT-AMVFVWSYLADGDPLYTLVQVATNDIIILFAF 169
                                       666666666666544444556666666588**************.56778999************************ PP

                          SBF_like 140 PalvqlllsgssvsvdyaevlkklllsvllPlvvGqvlqkifp..klvkrl.kkllkkvdslvlllivyts.fstaf 212
                                       +++v++l++ ++++v y+++l +++l v++Pl +G + ++ +   k  +++ k++l k+++++++ +  t  +  +f
  gi|242399675|ref|YP_002995100.1| 170 APIVGFLMGLNKIPVPYETLLISVVLFVVIPLTAGYISRRHILrtKGPEWFeKNFLPKLSTVSIVGLLLTLiLIFSF 246
                                       ***************************************76543589999967888888888877555554144568 PP

                          SBF_like 213 aqgaftsvshiillvifnvallLllvvlvillllarllklskedeiavlfcgsaKslalgvplisvlfgsnpqlgll 289
                                       + +++ + +  i+l+ + +++  ++++ +i++ +a l+kl+++ +  + f+g+     l+v ++  lfg ++ ++l+
  gi|242399675|ref|YP_002995100.1| 247 QGNIILENPLHIVLIAIPLTIQTYFIF-AIAYGWAWLWKLPHKVAAPASFIGASNFFELAVAVAIALFGLESGAALA 322
                                       999999999999999999999999988.7999*************************************99888887 PP

                          SBF_like 290 llPll 294
                                       ++  +
  gi|242399675|ref|YP_002995100.1| 323 TVVGV 327
                                       77655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       760  (0.0423894); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.68u 0.33s 00:00:01.01 Elapsed: 00:00:00.55
# Mc/sec: 1996.35
//
Query:       gi|242399676|ref|YP_002995101.1|  [L=207]
Description: NAD(P)H-flavin oxidoreductase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-33  115.4   0.0    3.1e-33  115.2   0.0    1.0  1  Nitroreductase  Nitroreductase family
    6.6e-08   32.4   0.0      0.004   16.7   0.0    2.1  2  TM1586_NiRdase  Putative TM nitroreductase


Domain annotation for each model (and alignments):
>> Nitroreductase  Nitroreductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.2   0.0   3.5e-37   3.1e-33       4     169 ..      34     203 ..      31     204 .. 0.94

  Alignments for each domain:
  == domain 1  score: 115.2 bits;  conditional E-value: 3.5e-37
                                       --B---B-S----HHHHHHHHHHH........HTS--GGG---EEEEEE..-CCCH....HHHHHHHHHHHHHHHTT CS
                    Nitroreductase   4 RrSiRkFddepvpkeelekileaa........rraPsagnlqpwrfvvv.qdkelr....yklaeaalelllkaeaq 67 
                                       R+SiR +++ep+++e++++il+aa        r++Psag  +p++++v+ ++ e +    y +  ++++l l +e +
  gi|242399676|ref|YP_002995101.1|  34 RKSIRRYKAEPLTLEQVSQILWAAyginahgkRTSPSAGACYPFEVYVAvSNVEGLepgfYHYDGKNHALELIREGN 110
                                       9***********************************************************77777766666666667 PP

                                       -SS-GGGGGGHHHHHHHHHHHHSSEEEEE---TTS---HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE-GGG CS
                    Nitroreductase  68 aelaqryrkeelklkaqkalagapvlivivatldkserkaaerayryalldagaaaqnllLaAtalGlgscpiggfd 144
                                       +     ++      ++q +++ ap+ i+iva++++ +r+++er+yry ++dag++ qn++L  talGlg++ +g+f 
  gi|242399676|ref|YP_002995101.1| 111 LNGPLAKA-----CLNQRHVEIAPINIIIVAHYERTTRRYGERGYRYVHIDAGHMGQNIYLQVTALGLGTVAVGAFR 182
                                       77777766.....9*************************************************************** PP

                                       GGHHHHHHHHT-S..SEEEEEEEEE CS
                    Nitroreductase 145 eaaeevrkllglpdeeeivvliavG 169
                                       +++  v+k++++p   +++++++vG
  gi|242399676|ref|YP_002995101.1| 183 DKE--VKKVIDVP--GDPLYIFPVG 203
                                       ***..********..9********9 PP

>> TM1586_NiRdase  Putative TM nitroreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   3.6e-06     0.032       3      36 ..      28      61 ..      26      69 .. 0.86
   2 !   16.7   0.0   4.5e-07     0.004      80     121 ..     153     195 ..     143     207 .] 0.75

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.6e-06
                                      HHHHHH--B---B--S---HHHHHHHHH-----S CS
                    TM1586_NiRdase  3 yeaiekRhsvRkYkdealeeelleelkeaieein 36
                                       eai+ R+s+R+Yk e+l+ e+++++  a+  in
  gi|242399676|ref|YP_002995101.1| 28 EEAINLRKSIRRYKAEPLTLEQVSQILWAAYGIN 61
                                      69*****************999999987777776 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 4.5e-07
                                       HHHHHHHHHHHHHHHHHHTT-EEEEES--SST........... CS
                    TM1586_NiRdase  80 leekaGYygeqlvLkltalGlgtcWvggtykk.kkakvelkkg 121
                                       ++  aG +g+++ L++talGlgt  vg+  +k +k+ ++++ +
  gi|242399676|ref|YP_002995101.1| 153 VHIDAGHMGQNIYLQVTALGLGTVAVGAFRDKeVKKVIDVPGD 195
                                       56789**********************9998844444554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); 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: 0.57u 0.34s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 1187.81
//
Query:       gi|242399677|ref|YP_002995102.1|  [L=117]
Description: hypothetical protein TSIB_1702 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.089   13.0   0.1       0.18   12.0   0.1    1.6  1  NusG_II   NusG domain II


Domain annotation for each model (and alignments):
>> NusG_II  NusG domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1     1e-05      0.18       3      63 ..      10      72 ..       4     115 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1e-05
                                      XXXXXXXXXX................EEEEEETTEEEEEEEE-TT--EEEEEEE-TTS..EEEEEEE CS
                           NusG_II  3 llllllslll....lllaakkkkeaktavitvdgkvvktisLskedeektieiegeeg..tnvieik 63
                                      ++ll ++  +    l l+++ +  a++a  +  g v+k+++L+ ++   ++e +g     t+ ie k
  gi|242399677|ref|YP_002995102.1| 10 VVLLGVA--GgiyvLGLKETGSYVALKATFRMGGAVYKEYQLEGDTLVFKFERNG--DffTQAIETK 72
                                      3333333..244666677788888899***************7777666666333..2335555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       718  (0.0400469); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); 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: 0.57u 0.33s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 655.22
//
Query:       gi|242399678|ref|YP_002995103.1|  [L=101]
Description: Thioredoxin [Thermococcus sibiricus MM 739]
Scores for complete 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-13   48.7   0.0      7e-13   48.5   0.0    1.0  1  Thioredoxin    Thioredoxin
    0.00016   21.7   0.0     0.0002   21.3   0.0    1.3  1  Thioredoxin_3  Thioredoxin domain
    0.00024   21.5   0.0     0.0045   17.4   0.0    2.0  1  Thioredoxin_2  Thioredoxin-like domain
     0.0019   18.2   0.0     0.0021   18.0   0.0    1.2  1  HyaE           Hydrogenase-1 expression protein HyaE
  ------ inclusion threshold ------
      0.011   16.0   0.1       0.57   10.5   0.1    2.0  2  Thioredoxin_8  Thioredoxin-like
       0.13   11.6   0.0       0.15   11.3   0.0    1.1  1  OST3_OST6      OST3 / OST6 family, transporter family
       0.13   12.1   0.0       0.17   11.8   0.0    1.2  1  AhpC-TSA       AhpC/TSA family


Domain annotation for each model (and alignments):
>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.5   0.0   2.7e-16     7e-13       9     102 ..       4      96 ..       2      97 .. 0.94

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 2.7e-16
                                       HHHHHHTTTSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEEETTEEE CS
                       Thioredoxin   9 nFeeevakekklvlveFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlklfkngkev 85 
                                       +++ ++  ++ +v++ F  + C++C+ +++++e+++ee++ ++++++v ++++++++k++ev ++Ptl+ +k+gkev
  gi|242399678|ref|YP_002995103.1|   4 EYDGKIDFNRGKVVLWFSIQGCPPCRLVESFMEEVSEEFS-EIRFIHVGAEKWSNIVKRFEVLNVPTLVYLKDGKEV 79 
                                       677888888999****************************.************************************ PP

                                       EEEESS-HHHHHHHHHH CS
                       Thioredoxin  86 kkyegarekeklaaflk 102
                                       ++ +  r+ke++ a+++
  gi|242399678|ref|YP_002995103.1|  80 ARQNLIRSKEEVLAKIE 96 
                                       ****9999999998886 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   7.8e-08    0.0002       8      55 ..      23      72 ..      15      96 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 7.8e-08
                                      SSSTTCHHHHHHHHHHCHCC.TCECEEECCTTHHHH.HHCT-SSSSEEEC CS
                     Thioredoxin_3  8 pgCakCpklekavkeaaaek.gikaevekvtdfeei.ekygVmsvPalvi 55
                                      +gC+ C+ +e++++e+ +e  +i +  + +++ ++i ++++V  vP+lv+
  gi|242399678|ref|YP_002995103.1| 23 QGCPPCRLVESFMEEVSEEFsEIRFIHVGAEKWSNIvKRFEVLNVPTLVY 72
                                      58*****************967**************************86 PP

>> Thioredoxin_2  Thioredoxin-like 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    0.0045       5      95 ..      13      81 ..      10      95 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.8e-06
                     Thioredoxin_2  5 gkpvlvvftdpdCpyCkklkkelkel.ddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgtP 82
                                        +v+++f+  +Cp C++ +  ++e+ +            + +e+ ++++  +k  +            +++++v  +P
  gi|242399678|ref|YP_002995103.1| 13 RGKVVLWFSIQGCPPCRLVESFMEEVsE------------EFSEIRFIHVGAEKWSN-----------IVKRFEVLNVP 68
                                      5689*******************99922............22555666666666655...........77888888888 PP

                     Thioredoxin_2 83 tiv.fldgkeivar 95
                                      t+v + dgk +var
  gi|242399678|ref|YP_002995103.1| 69 TLVyLKDGK-EVAR 81
                                      877677777.5554 PP

>> HyaE  Hydrogenase-1 expression protein HyaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   8.4e-07    0.0021      49     103 ..      34      86 ..      16      91 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 8.4e-07
                                       HHHHHHCT-TTS-EEEEEETHHHHHHHHHCCT-TSSSEEEEEETTEEEEEEESSS CS
                              HyaE  49 vlpEllkaFpnalraavvadreqeealaerfgvlktPsllflrdgeylgvlakir 103
                                        + E+ ++F +   + v a  e+ +++ +rf+vl +P+l++l+dg+ ++  + ir
  gi|242399678|ref|YP_002995103.1|  34 FMEEVSEEFSEIRFIHVGA--EKWSNIVKRFEVLNVPTLVYLKDGKEVARQNLIR 86 
                                       5779999999999988888..9999********************9887666555 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00022      0.57       4      45 ..      16      54 ..      14      67 .. 0.84
   2 ?    5.8   0.0     0.007        18      68      94 ..      52      78 ..      46      79 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00022
                                      EEEEE--SSSHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-SS CS
                     Thioredoxin_8  4 vlLyfgaswcppckaftpklkelyeklkkkkkveivyvsldk 45
                                      v+L f+   cppc+ + + + e++e+++    +++++v   k
  gi|242399678|ref|YP_002995103.1| 16 VVLWFSIQGCPPCRLVESFMEEVSEEFS---EIRFIHVGAEK 54
                                      78999999*******************8...89999988655 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.007
                                      TT-HHHHTT-S--TT-SEEEEE-TT-B CS
                     Thioredoxin_8 68 dkkrnklkkkynvkaiPtlvvldknge 94
                                       +k + + k+++v ++Ptlv l+  +e
  gi|242399678|ref|YP_002995103.1| 52 AEKWSNIVKRFEVLNVPTLVYLKDGKE 78
                                      5555678899**********9987665 PP

>> OST3_OST6  OST3 / OST6 family, transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0     6e-05      0.15      45     108 ..      24      79 ..      18      99 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 6e-05
                         OST3_OST6  45 kCelCrefepefelvakswrkdekskskklfFakvdfdegkdvFqklglnsaPhlllfppkkgp 108
                                       +C +Cr +e+ +e v++ + +          F++v  ++ +++++++++ ++P l++ +  k+ 
  gi|242399678|ref|YP_002995103.1|  24 GCPPCRLVESFMEEVSEEFSEI--------RFIHVGAEKWSNIVKRFEVLNVPTLVYLKDGKEV 79 
                                       6777777777777777776555........7**************************9985543 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   6.6e-05      0.17      23      96 ..      11      81 ..       7      94 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.6e-05
                                      H.TTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHHHH-H.SSEEEE-TTSHHHH CS
                          AhpC-TSA 23 y.kgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfiekeslnfpllsDeegkvak 96
                                      + +gk+v+ f ++   cp+C+   + ++++ eef    +  i v +++  ++ k  e  +++  + +   ++va+
  gi|242399678|ref|YP_002995103.1| 11 FnRGKVVLWFSIQ--GCPPCRLVESFMEEVSEEFS--EIRFIHVGAEKWSNIVKRFEVLNVPTLVYLKDGKEVAR 81
                                      5466444444444..6******************9..56667777777776666666666555555555666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       708  (0.0394891); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.58u 0.34s 00:00:00.92 Elapsed: 00:00:00.54
# Mc/sec: 559.73
//
Query:       gi|242399679|ref|YP_002995104.1|  [L=799]
Description: Heavy-metal transporting P-type ATPase [Thermococcus sibiricus MM 739]
Scores for 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-58  195.4   1.1      6e-58  195.4   1.1    2.0  2  E1-E2_ATPase  E1-E2 ATPase
    1.1e-46  159.7   6.0    1.1e-46  159.7   6.0    1.8  2  Hydrolase     haloacid dehalogenase-like hydrolase
    2.4e-34  117.6   9.0    2.5e-18   66.3   0.3    3.5  3  HMA           Heavy-metal-associated domain
    1.3e-07   31.6   3.3    6.7e-06   26.0   0.8    2.5  2  Hydrolase_3   haloacid dehalogenase-like hydrolase
    1.8e-05   25.3   0.1    5.9e-05   23.6   0.1    2.1  1  HAD           haloacid dehalogenase-like hydrolase
      3e-05   24.2   1.7    5.6e-05   23.3   0.4    2.2  2  HAD_2         Haloacid dehalogenase-like hydrolase
     0.0025   17.2   0.1     0.0068   15.7   0.1    1.7  1  DUF1538       Protein of unknown function (DUF1538)
  ------ inclusion threshold ------
      0.017   14.6   0.2      0.038   13.5   0.2    1.5  1  CPSase_L_D2   Carbamoyl-phosphate synthase L chain, ATP bindi
      0.022   14.9   0.0       0.13   12.4   0.0    2.4  2  Hydrolase_6   Haloacid dehalogenase-like hydrolase
      0.025   14.6   3.8        8.4    6.5   0.1    3.9  2  B12-binding   B12 binding domain


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.4   1.1   3.3e-61     6e-58       2     180 ..     287     466 ..     286     467 .. 0.98
   2 ?   -2.1   0.1       1.3   2.3e+03      97     143 ..     727     773 ..     713     789 .. 0.58

  Alignments for each domain:
  == domain 1  score: 195.4 bits;  conditional E-value: 3.3e-61
                                       SS--EEEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-SEEE-TTTS---S-EE-G-TTEE-TT-EEEE CS
                      E1-E2_ATPase   2 llpptakvirdgteeeidakelvpGDivllkagdrvpaDgrivegsaevdesaLTGEslpvekekgdmvfsGtvvvs 78 
                                       l++++a+v+rdg+e e++++e+++GDiv++k+g ++p+Dg+++eg++ vdes++TGE  p  k+ gd+v++Gt++++
  gi|242399679|ref|YP_002995104.1| 287 LQAKKATVVRDGKEIEVPISEVKVGDIVIVKPGGKIPVDGVVIEGESYVDESMITGEPIPSLKKFGDKVIGGTINKN 363
                                       7899************************************************************************* PP

                                       -EEEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTT.HHHHHHHHH CS
                      E1-E2_ATPase  79 geakavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgksla.eallralal 154
                                         +k+++ ++g+dt l++i++lveea+++++p+q+ +d ++ +++p+vl+iall f++++++ +++  + ++  l++
  gi|242399679|ref|YP_002995104.1| 364 SVLKIKAEKVGRDTLLAQIIKLVEEAQNTRPPVQRLADTVVTYFIPAVLVIALLSFAYWYFIAGKPLvFGFTTLLSV 440
                                       *************************************************************9888888********* PP

                                       HHHHS-TTHHHHHHHHHHHHHHHHHH CS
                      E1-E2_ATPase 155 lvaaiPcaLplavplalalgarrlak 180
                                       lv+a+Pca++la+p+al++g+++ a+
  gi|242399679|ref|YP_002995104.1| 441 LVIACPCAFGLATPTALTVGIGKGAE 466
                                       **********************9885 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.3
                                       TSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSS CS
                      E1-E2_ATPase  97 iarlveeakskktplqkkldklgkvlvpvvlliallvflialllgks 143
                                       ++++++ ++++  ++++++   + + ++++ ++a l+fl++ +++++
  gi|242399679|ref|YP_002995104.1| 727 VVKAIKLSQKTIGKIKQNIFWAMFYNTILIPFAAGLAFLLFEITFQP 773
                                       55566666666666666666666666666666666666655554444 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.7   6.0   6.3e-50   1.1e-46       3     210 .]     485     699 ..     483     699 .. 0.96
   2 ?   -4.0   0.0       8.2   1.5e+04     168     188 ..     716     736 ..     706     742 .. 0.65

  Alignments for each domain:
  == domain 1  score: 159.7 bits;  conditional E-value: 6.3e-50
                                       EEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHH......HHCHHHHHHHHHHHHHHHHH...HHHHHETTTE... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxx...xxxxxxxxxx... RF
                         Hydrolase   3 tvvfDkdGTLttgepsvedvivsaalalaaaletg......sehpigkalvaaakarsgal...tgfatfigrg... 67 
                                       +v+fDk+GTLt+g+p+v+dvi    +++++ l+++      sehp+g+alv++ +++s  l   ++f++++g+g   
  gi|242399679|ref|YP_002995104.1| 485 VVLFDKTGTLTKGRPEVTDVITFG-MDEKELLRLVasaekrSEHPLGEALVKKVQEMSLGLeepEEFEAITGKGvra 560
                                       89**********************.999999999999********************5555557************* PP

                                       .....HHHHTHHHHHHHH.HCHHHHHHHHHHHHHHCHHHHHH..TTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEE CS
                                       .....xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  68 .....ayaigkpewltal.dippdlgaaigsaqsqgrtvall..qaralavftiadplkvkpeaaeavasLkaagie 136
                                            +++ g+++++t++    +d++++ ++++++++t++++  ++++++++ iad+  +k++a+e++++L+++  +
  gi|242399679|ref|YP_002995104.1| 561 vvgggEVLAGNRKLMTEQgYSVEDVEEELQKLEDEAKTAIIVaiDGKIVGIIGIADT--IKEGAKEVIEELHRMDKK 635
                                       *******************9999***************99999999***********..****************** PP

                                       EEEEESSEHHHHHHHHHHTTGGGESEEEEHHCES.STTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 137 vvlltgdnpetaeraanqlGddyfdaviasdiet.vakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                       v+++tgdn++ta+++a+qlG           ++   a+++p++k   +++Lq+k+e v++VGDg+nDa+ala+A+
  gi|242399679|ref|YP_002995104.1| 636 VGMITGDNKRTANAIAKQLG-----------VDYvLAEVLPQDKAGEVKKLQEKGEIVIFVGDGINDAPALAQAD 699
                                       ********************...........7777***************************************8 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 8.2
                                       CESSTTTSHHHHHHHHHHHTS CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 168 ietvakpspegkvaaireLqg 188
                                       + +  k +p+++v+ai+  q 
  gi|242399679|ref|YP_002995104.1| 716 DIVLVKNDPKDVVKAIKLSQK 736
                                       444667888888888887774 PP

>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.0   0.9   4.6e-18   8.3e-15       1      62 []       4      65 ..       4      65 .. 0.98
   2 !   66.3   0.3   1.4e-21   2.5e-18       1      62 []      74     135 ..      74     135 .. 0.98
   3 ?   -2.8   0.1       5.1   9.1e+03      13      25 ..     582     594 ..     581     601 .. 0.85

  Alignments for each domain:
  == domain 1  score: 55.0 bits;  conditional E-value: 4.6e-18
                               HMA  1 tvrvsgmhCagCaakvekvLselpgVesvkvdlatktvtVegdaestklrkiieaiekagyk 62
                                      t++v gm+Ca C++++e +Ls l+gV+++k +l++ tv V++d+++++l+kii+aie+ gy+
  gi|242399679|ref|YP_002995104.1|  4 TLKVNGMTCAMCVKTIEIALSQLEGVKTAKANLNSETVFVDFDESKVSLNKIIQAIEDVGYE 65
                                      689*********************************************************96 PP

  == domain 2  score: 66.3 bits;  conditional E-value: 1.4e-21
                               HMA   1 tvrvsgmhCagCaakvekvLselpgVesvkvdlatktvtVegdaestklrkiieaiekagyk 62 
                                       +v+v gm+Ca Ca++vek++ elpgV +v+v+lat t+ ++++++s+++++i++aie  gy+
  gi|242399679|ref|YP_002995104.1|  74 VVKVGGMTCAMCAKTVEKAIDELPGVLDVSVNLATETARISYNPSSVDVEDIRRAIEGVGYD 135
                                       689*********************************************************96 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 5.1
                               HMA  13 aakvekvLselpg 25 
                                       + +ve+ L++l++
  gi|242399679|ref|YP_002995104.1| 582 VEDVEEELQKLED 594
                                       6789999999975 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.4   0.1    0.0073        13      14      59 ..     616     660 ..     579     663 .. 0.92
   2 !   26.0   0.8   3.7e-09   6.7e-06     197     255 .]     673     731 ..     668     731 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0073
                                       S---HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEEE CS
                       Hydrolase_3  14 kkisektkeaikklkekgikvviATGRslravlpvleelgldlpvi 59 
                                        +i+e +ke+i++l+  + kv   TG + r++  ++++lg+d +v+
  gi|242399679|ref|YP_002995104.1| 616 DTIKEGAKEVIEELHRMDKKVGMITGDNKRTANAIAKQLGVD-YVL 660
                                       579999**********************************99.654 PP

  == domain 2  score: 26.0 bits;  conditional E-value: 3.7e-09
                                       HHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE--GGGTHHHHHH CS
                       Hydrolase_3 197 kelnisleeviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtksnnedGVakal 255
                                       k+l+ + e vi +GDg ND + L +a++g+A+gna++ + +  d v  +n+   V+ka+
  gi|242399679|ref|YP_002995104.1| 673 KKLQEKGEIVIFVGDGINDAPALAQADVGIAVGNATDIAMESGDIVLVKNDPKDVVKAI 731
                                       567778889**************************************999986666665 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.1   3.3e-08   5.9e-05      64     187 ..     579     695 ..     486     696 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 3.3e-08
                               HAD  64 gls.eelaaelerfvaevirpk................lldpgalellaahraaGdrvvvvSgglrplvepllaelg 123
                                       g+s e++++el+++ +e+++                  ++++ga+e++++ ++   +v +++g +++ + +++++lg
  gi|242399679|ref|YP_002995104.1| 579 GYSvEDVEEELQKLEDEAKTAIivaidgkivgiigiadTIKEGAKEVIEELHRMDKKVGMITGDNKRTANAIAKQLG 655
                                       555555555555555544444455555556665555455889*******9999999********************* PP

                               HAD 124 adevlatelevddrltgelglegkpvrgegkvaalrewlaaegegidleevvayGDspsDlpll 187
                                       +d+vla+      +l            ++g v++l+e         + e v+++GD+++D p+l
  gi|242399679|ref|YP_002995104.1| 656 VDYVLAE------VLPQD---------KAGEVKKLQE---------KGEIVIFVGDGINDAPAL 695
                                       *******......44444.........4456777777.........33449***********98 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       3.3   5.9e+03      80     101 ..     581     601 ..     572     605 .. 0.77
   2 !   23.3   0.4   3.1e-08   5.6e-05      81     173 ..     619     700 ..     615     704 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3.3
                             HAD_2  80 pydgvkelLeeLkeagyklgiv 101
                                        +++v+e L++L e + k +i+
  gi|242399679|ref|YP_002995104.1| 581 SVEDVEEELQKL-EDEAKTAII 601
                                       568999999999.667777776 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 3.1e-08
                             HAD_2  81 ydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekkKPdpeviekaleklklkkeeviy 157
                                        +g+ke++eeL++++ k+g +T  ++++++   +qlg++ ++  ++ ++++++ K           kl+ k e vi+
  gi|242399679|ref|YP_002995104.1| 619 KEGAKEVIEELHRMDKKVGMITGDNKRTANAIAKQLGVDYVLAEVLPQDKAGEVK-----------KLQEKGEIVIF 684
                                       689*************************************************996...........999999***** PP

                             HAD_2 158 vGDsptDieaakkagi 173
                                       vGD ++D  a  +a +
  gi|242399679|ref|YP_002995104.1| 685 VGDGINDAPALAQADV 700
                                       ******9988666655 PP

>> DUF1538  Protein of unknown function (DUF1538)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   3.8e-06    0.0068      91     194 ..     149     246 ..     144     262 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.8e-06
                           DUF1538  91 eevsagaikkkvlilavaiGvglaialgvlrillgislkylllpgyllvllltllvpkefvaiafDsgGvttgpitv 167
                                       +ev + ++k++   l +a Gvg+ + l++    +gi+++ l+++ ++l+ + ++++ + +++ a+ s    t    +
  gi|242399679|ref|YP_002995104.1| 149 KEVRERHLKEMKRNLLIAWGVGIPLFLSMQLKRFGIHIENLIYVQFILATMAIAYAGRGIFKKAYSSLKHKTL--NM 223
                                       4677888888888999*************************************************88776665..55 PP

                           DUF1538 168 plilalglGvasalegknalvdgFGlv 194
                                        ++ alg+G a  ++    +   FGlv
  gi|242399679|ref|YP_002995104.1| 224 EVMYALGIGSAYLTS----VLATFGLV 246
                                       568999999998887....88899988 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 ?   13.5   0.2   2.1e-05     0.038      75     129 ..      42      97 ..      20     104 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.1e-05
                                       HHHHSTS-EEEEE--SSSEEEEEEEEEETTS-EEEEEEEEECCEC.TCCCCEEEES CS
                       CPSase_L_D2  75 kaafgnkqvlvekslkgpkeiEvevlrDakgnvitvcerenslql.rtqkvievAP 129
                                        + f +++v ++k ++   ++ +ev+r +k+ v+ v+ + + +     +k i + P
  gi|242399679|ref|YP_002995104.1|  42 FVDFDESKVSLNKIIQAIEDVGYEVIRERKNVVVKVGGMTCAMCAkTVEKAIDELP 97 
                                       457999***********************************998844566776666 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       3.4   6.1e+03       1      14 [.     486     499 ..     486     545 .. 0.75
   2 ?   12.4   0.0   7.2e-05      0.13      11      51 ..     614     654 ..     579     686 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3.4
                                       EEEESTTTSEETTE CS
                       Hydrolase_6   1 flfDidGvLwrgdk 14 
                                       +lfD  G+L +g+ 
  gi|242399679|ref|YP_002995104.1| 486 VLFDKTGTLTKGRP 499
                                       68999999998864 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 7.2e-05
                                       ETTEE-TTHHHHHHHHHHTT-EEEEEE---SS-HHHHHHHH CS
                       Hydrolase_6  11 rgdkaipgaaealnalraagkpvvllTNnsskseeeyakkl 51 
                                         d++ +ga+e+++ l+++ k+v ++T  ++++ +++ak+l
  gi|242399679|ref|YP_002995104.1| 614 IADTIKEGAKEVIEELHRMDKKVGMITGDNKRTANAIAKQL 654
                                       4677889**************************99999987 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1    0.0047       8.4      35      87 ..     117     168 ..      40     186 .. 0.82
   2 ?    5.5   0.4    0.0092        17      25     108 ..     576     659 ..     572     663 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0047
                       B12-binding  35 ganvenedivaairaekpdvvglSalltsqleavkelvel.lkrirprvkvvvG 87 
                                          v++edi +ai+   +d++g+      + +  ke+ e+ lk++++++ +++G
  gi|242399679|ref|YP_002995104.1| 117 PSSVDVEDIRRAIEGVGYDFLGVEG--EETRDIEKEVRERhLKEMKRNLLIAWG 168
                                       4456679999999999999999987..777777788888899999999999999 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0092
                       B12-binding  25 rdagfeVqllganven...edivaairaekpdvvglSalltsqleavkelvellkrirprvkvvvGGahpsldpeet 98 
                                        ++g++V++++ + ++   e+  a i a +  +vg+  +  +  e++ke++e+l+r++++v  ++G    +++ +  
  gi|242399679|ref|YP_002995104.1| 576 TEQGYSVEDVEEELQKledEAKTAIIVAIDGKIVGIIGIADTIKEGAKEVIEELHRMDKKVGMITGDNK-RTANAI- 650
                                       56799999997777777555555566666777799999999999*********************9876.444444. PP

                       B12-binding  99 leak.lgiddv 108
                                         ak lg+d+v
  gi|242399679|ref|YP_002995104.1| 651 --AKqLGVDYV 659
                                       ..333888885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (799 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1133  (0.0631937); expected 358.6 (0.02)
Passed bias filter:                      745  (0.0415528); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); 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: 0.86u 0.38s 00:00:01.24 Elapsed: 00:00:00.53
# Mc/sec: 4516.42
//
Query:       gi|242399680|ref|YP_002995105.1|  [L=200]
Description: Transcriptional regulatory protein, asnC family [Thermococcus sibiricus MM 739]
Scores for complete 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   68.9   8.7    3.7e-19   68.7   7.4    1.7  1  Arc_trans_TRASH  Archaeal TRASH domain
      5e-17   61.2   1.6    8.1e-17   60.5   1.6    1.4  1  HTH_24           Winged helix-turn-helix DNA-binding
    1.3e-13   50.5   1.8      2e-13   49.9   1.8    1.3  1  HTH_AsnC-type    AsnC-type helix-turn-helix domain
    3.6e-08   33.2   0.7    1.3e-07   31.5   0.2    2.0  2  HTH_11           HTH domain
      1e-07   31.7   1.0    1.6e-07   31.1   0.3    1.7  1  HTH_5            Bacterial regulatory protein, arsR family
    1.2e-07   31.5   0.1      2e-07   30.8   0.1    1.4  1  MarR_2           MarR family
    2.8e-07   30.5   0.4    5.5e-07   29.5   0.4    1.5  1  HTH_Mga          M protein trans-acting positive regulator (M
    5.8e-07   29.4   0.2    1.1e-06   28.5   0.2    1.5  1  HTH_Crp_2        Crp-like helix-turn-helix domain
      1e-06   28.5   0.8      9e-06   25.5   0.2    2.2  2  TrmB             Sugar-specific transcriptional regulator Trm
    1.1e-06   28.5   0.1    2.3e-06   27.4   0.1    1.5  1  MarR             MarR family
      3e-06   27.2   0.1    4.9e-06   26.5   0.1    1.3  1  HTH_20           Helix-turn-helix domain
    4.6e-06   26.7   0.0    1.3e-05   25.3   0.0    1.7  1  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
    1.7e-05   24.4   0.0    3.1e-05   23.6   0.0    1.4  1  HTH_23           Homeodomain-like domain
    3.2e-05   24.4   0.7    0.00051   20.6   0.0    2.6  2  Mga              Mga helix-turn-helix domain
    3.4e-05   23.6   0.1    5.8e-05   22.8   0.1    1.3  1  HTH_IclR         IclR helix-turn-helix domain
    3.4e-05   23.5   0.2     0.0001   22.0   0.1    1.9  1  HTH_DeoR         DeoR-like helix-turn-helix domain
    3.4e-05   23.9   0.0    5.7e-05   23.2   0.0    1.4  1  HTH_28           Helix-turn-helix domain
    6.9e-05   22.4   0.0    0.00012   21.7   0.0    1.4  1  Sigma70_r4_2     Sigma-70, region 4
    9.8e-05   22.1   0.0    0.00017   21.3   0.0    1.4  1  HTH_30           PucR C-terminal helix-turn-helix domain
     0.0001   21.9   0.3    0.00023   20.7   0.3    1.6  1  GntR             Bacterial regulatory proteins, gntR family
    0.00016   21.1   0.0    0.00029   20.3   0.0    1.5  1  Sigma70_r4       Sigma-70, region 4
    0.00021   20.9   0.1     0.0014   18.3   0.0    2.2  2  HTH_41           Helix-turn-helix domain
    0.00029   20.6   0.1    0.00067   19.4   0.1    1.5  1  HTH_10           HTH DNA binding domain
    0.00043   20.0   0.1    0.00086   19.0   0.1    1.6  1  HTH_8            Bacterial regulatory protein, Fis family
    0.00043   20.2   0.0    0.00075   19.5   0.0    1.4  1  HTH_29           Winged helix-turn helix
    0.00094   19.1   4.9     0.0016   18.3   4.9    1.4  1  zf-FCS           MYM-type Zinc finger with FCS sequence motif
     0.0011   18.9   0.4     0.0021   18.0   0.0    1.7  1  HTH_36           Helix-turn-helix domain
     0.0011   19.2   0.2     0.0029   17.9   0.0    1.7  1  Rrf2             Transcriptional regulator
     0.0014   18.2   0.0     0.0027   17.2   0.0    1.5  1  HTH_CodY         CodY helix-turn-helix domain
     0.0017   18.4   2.1     0.0021   18.1   0.1    2.3  1  DUF2089          Protein of unknown function (DUF2089)
     0.0043   17.0   0.2     0.0091   16.0   0.2    1.7  1  HTH_19           Helix-turn-helix domain
     0.0053   16.8   2.6      0.011   15.8   2.2    1.8  1  YHS              YHS domain
      0.006   16.3   0.1      0.013   15.3   0.1    1.5  1  LexA_DNA_bind    LexA DNA binding domain
     0.0091   16.0   0.1      0.019   15.0   0.1    1.6  1  HTH_3            Helix-turn-helix
     0.0093   16.1   0.0      0.024   14.8   0.0    1.8  1  HTH_17           Helix-turn-helix domain
  ------ inclusion threshold ------
      0.012   15.9   0.5      0.012   15.9   0.5    2.4  2  HTH_WhiA         WhiA C-terminal HTH domain
      0.013   15.4   0.0      0.025   14.5   0.0    1.5  1  HTH_1            Bacterial regulatory helix-turn-helix protei
      0.014   15.5   0.0      0.044   13.9   0.0    1.9  1  HTH_22           HTH domain
      0.017   15.0   0.1      0.041   13.9   0.1    1.6  1  AsnC_trans_reg   Lrp/AsnC ligand binding domain
      0.018   15.0   0.1       0.04   13.8   0.0    1.6  1  DUF1441          Protein of unknown function (DUF1441)
      0.019   15.0   0.1      0.054   13.6   0.1    1.7  1  HTH_9            RNA polymerase III subunit RPC82 helix-turn-
      0.023   14.8   0.0      0.073   13.2   0.0    1.9  1  HTH_7            Helix-turn-helix domain of resolvase
       0.03   14.7   0.0      0.066   13.6   0.0    1.5  1  FaeA             FaeA-like protein
       0.03   14.3   0.0       0.09   12.7   0.0    1.8  1  HTH_37           Helix-turn-helix domain
      0.042   13.7   0.2       0.13   12.1   0.1    1.9  1  HxlR             HxlR-like helix-turn-helix
      0.053   12.9   0.0      0.093   12.2   0.0    1.3  1  HTH_Tnp_ISL3     Helix-turn-helix domain of transposase famil
      0.061   13.2   4.7       0.11   12.3   4.7    1.4  1  VATC             Vms1-associating treble clef domain
      0.068   13.4   3.3       0.11   12.7   3.3    1.4  1  LIM              LIM domain
      0.079   13.2   0.0       0.29   11.4   0.0    1.9  1  NUMOD1           NUMOD1 domain
      0.084   13.0   0.1       0.31   11.1   0.0    1.9  1  FeoC             FeoC like transcriptional regulator
      0.085   13.5   0.0       0.16   12.7   0.0    1.4  1  RPA_C            Replication protein A C terminal
      0.094   13.2   0.1       0.33   11.4   0.0    1.9  1  HTH_26           Cro/C1-type HTH DNA-binding domain
       0.14   11.9   0.1       0.28   10.9   0.1    1.5  1  Crp              Bacterial regulatory proteins, crp family
       0.15   11.6   4.2        5.1    6.8   0.9    2.6  2  Sgf11            Sgf11 (transcriptional regulation protein)
       0.59   10.4   3.8        1.1    9.5   1.8    2.4  2  Ta0938           Ta0938
        1.9    8.6  11.2        5.5    7.1   0.9    2.4  2  zf-C2H2_6        C2H2-type zinc finger
        2.7    8.6  14.9        4.8    7.8   1.1    2.4  2  zf-H2C2_2        Zinc-finger double domain


Domain annotation for each model (and alignments):
>> Arc_trans_TRASH  Archaeal TRASH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.7   7.4   1.2e-21   3.7e-19       1      36 [.     144     179 ..     144     180 .. 0.97

  Alignments for each domain:
  == domain 1  score: 68.7 bits;  conditional E-value: 1.2e-21
                   Arc_trans_TRASH   1 CDYCGkeivgePivyklknkvYyvCCktCkselkkk 36 
                                       CDYCGkei gePiv k++nkvY++CC+tC++e+k++
  gi|242399680|ref|YP_002995105.1| 144 CDYCGKEIIGEPIVHKYHNKVYFFCCPTCLREFKRT 179
                                       **********************************87 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 !   60.5   1.6   2.6e-19   8.1e-17       1      48 []       4      51 ..       4      51 .. 0.98

  Alignments for each domain:
  == domain 1  score: 60.5 bits;  conditional E-value: 2.6e-19
                            HTH_24  1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      ld++d+k++ lL +n+r+s++eLAerlg+S++tv+ rl++Le+eG+I+
  gi|242399680|ref|YP_002995105.1|  4 LDDLDLKLIYLLLDNARLSISELAERLGISRPTVKSRLEKLEKEGVIR 51
                                      79*********************************************7 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.9   1.8   6.4e-16     2e-13       1      42 []       4      45 ..       4      45 .. 0.99

  Alignments for each domain:
  == domain 1  score: 49.9 bits;  conditional E-value: 6.4e-16
                     HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrLe 42
                                      LD++D+k++ +L  +aR+s +eLAer+G+S++tv  R+++Le
  gi|242399680|ref|YP_002995105.1|  4 LDDLDLKLIYLLLDNARLSISELAERLGISRPTVKSRLEKLE 45
                                      8****************************************8 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.2     4e-10   1.3e-07       4      44 ..      10      53 ..       8      60 .. 0.83
   2 ?   -1.1   0.0       5.9   1.9e+03       1      29 [.      63      91 ..      63      94 .. 0.80

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 4e-10
                            HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg....v 44
                                      +++ lLl++   +s++eLAe+L++Sr tv  ++++Le+ g    +
  gi|242399680|ref|YP_002995105.1| 10 KLIYLLLDNAR-LSISELAERLGISRPTVKSRLEKLEKEGvirgY 53
                                      67777766665.****************************55554 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 5.9
                            HTH_11  1 RllqilelLleargpisgeeLAeeLnvSr 29
                                      R+  ++ l+ ++++p   +eL e +++ r
  gi|242399680|ref|YP_002995105.1| 63 RAHNVVALIVKTEKPEKMDELEEIIEINR 91
                                      56667888888888889999999999887 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 !   31.1   0.3     5e-10   1.6e-07       5      45 ..       9      50 ..       5      51 .. 0.94

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 5e-10
                                      HHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5  5 lkILklLae.gelcvcelaeelglsqstvShHLkkLreaGLV 45
                                      lk+++lL +   l+++elae lg+s++tv   L kL+++G++
  gi|242399680|ref|YP_002995105.1|  9 LKLIYLLLDnARLSISELAERLGISRPTVKSRLEKLEKEGVI 50
                                      799******666****************************98 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.1   6.4e-10     2e-07      10      52 ..      11      51 ..       4      63 .. 0.90

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 6.4e-10
                                      HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                            MarR_2 10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                                      +++ L ++ +  l+++ela+rlg+s+++v  +l++L++ G ++
  gi|242399680|ref|YP_002995105.1| 11 LIYLLLDNAR--LSISELAERLGISRPTVKSRLEKLEKEGVIR 51
                                      5667788887..****************************997 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 !   29.5   0.4   1.7e-09   5.5e-07       5      45 ..       6      45 ..       2      58 .. 0.87

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 1.7e-09
                           HTH_Mga  5 krklkLlelLteneksltldelakeLglseltlqsdiseLn 45
                                        +lkL+ lL++ + +l+++ela++Lg+s+ t++s++++L 
  gi|242399680|ref|YP_002995105.1|  6 DLDLKLIYLLLD-NARLSISELAERLGISRPTVKSRLEKLE 45
                                      5689********.*************************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 !   28.5   0.2   3.6e-09   1.1e-06      21      67 ..      20      64 ..       7      65 .. 0.85

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 3.6e-09
                                      EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETEEEEES-HHHHHH CS
                         HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglisrgrririldleaLra 67
                                      +l+  elA++lG++r tv   l +L++eg+i+     + l++e Lra
  gi|242399680|ref|YP_002995105.1| 20 RLSISELAERLGISRPTVKSRLEKLEKEGVIRGY--TIKLNPELLRA 64
                                      78999**************************944..45578888886 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.2   2.9e-08     9e-06      10      53 ..       8      51 ..       3      68 .. 0.82
   2 ?    1.2   0.0       1.1   3.5e+02      18      37 ..      72      92 ..      67     102 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 2.9e-08
                                      CCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEE CS
                              TrmB 10 EakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVe 53
                                      + k    Ll + +++++e+ae+lg++r++v + L++Le+ G+++
  gi|242399680|ref|YP_002995105.1|  8 DLKLIYLLLDNARLSISELAERLGISRPTVKSRLEKLEKEGVIR 51
                                      555556788********************************997 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 1.1
                                      H.HHCCCHHCHHCCCTTSSCH CS
                              TrmB 18 l.klgpatadeiaeelgvprs 37
                                      + +++p ++de+ e++++ r 
  gi|242399680|ref|YP_002995105.1| 72 VkTEKPEKMDELEEIIEINRF 92
                                      3578999**********9985 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.1   7.3e-09   2.3e-06       7      48 ..      10      51 ..       6      55 .. 0.92

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 7.3e-09
                                      HHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR  7 viLrilyeqgplsvseLakklgvskstvtrvldrLekkGlie 48
                                      +++++l ++  ls+seLa++lg+s++tv   l +Lek+G i+
  gi|242399680|ref|YP_002995105.1| 10 KLIYLLLDNARLSISELAERLGISRPTVKSRLEKLEKEGVIR 51
                                      67888999999****************************997 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.1   1.6e-08   4.9e-06      16      57 ..      13      53 ..       9      56 .. 0.90

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 1.6e-08
                                      HHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                            HTH_20 16 lraLaraegltaselaerldlskntlsyHLrvLeeagLvevv 57
                                      + +L +++ l+ selaerl++s+ t+  +L++Le+ g +++ 
  gi|242399680|ref|YP_002995105.1| 13 YLLL-DNARLSISELAERLGISRPTVKSRLEKLEKEGVIRGY 53
                                      5556.9999*****************************9975 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   4.1e-08   1.3e-05      10      51 ..       9      49 ..       6      52 .. 0.93

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 4.1e-08
                                      HHHHHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTS CS
                    Fe_dep_repress 10 LetIYtlseekkvvktkdlaerLnvspssVsemlkkLekdGy 51
                                      L+ IY l  +++  + ++laerL++s ++V   l+kLek+G 
  gi|242399680|ref|YP_002995105.1|  9 LKLIYLLL-DNARLSISELAERLGISRPTVKSRLEKLEKEGV 49
                                      78999999.888999*************************95 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   9.7e-08   3.1e-05       9      46 ..      10      49 ..       9      51 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 9.7e-08
                            HTH_23  9 rillllae..GlsvreIAreLgvsrrTvyrwlkryreeGl 46
                                      + ++ll++  +ls++e A++Lg+sr Tv   l++ ++eG+
  gi|242399680|ref|YP_002995105.1| 10 KLIYLLLDnaRLSISELAERLGISRPTVKSRLEKLEKEGV 49
                                      5788888889*******************88777777886 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   1.6e-06   0.00051      16      65 ..       6      57 ..       3      66 .. 0.87
   2 ?    1.0   0.0         2   6.4e+02      36      65 ..      98     120 ..      77     136 .. 0.54

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.6e-06
                                      SHHHHHHHHHHHHSEEEHHHHHHHCT--HHHHHHHHHHHHH..HCHCCT-EE CS
                               Mga 16 slkyqllkflfeeeevsieelaqelyiSestlkrkikelnk..lLkefdlel 65
                                      +l+++l+ +l+ ++++si ela++l iS+ t+k  +++l+k  +++ + ++l
  gi|242399680|ref|YP_002995105.1|  6 DLDLKLIYLLLDNARLSISELAERLGISRPTVKSRLEKLEKegVIRGYTIKL 57
                                      57899**********************************9844588888887 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 2
                                       HHHHCT--HHHHHHHHHHHHHHCHCCT-EE CS
                               Mga  36 laqelyiSestlkrkikelnklLkefdlel 65 
                                       l++  + S          l+ +++e   e+
  gi|242399680|ref|YP_002995105.1|  98 LIKVAVNSMED-------LKRVIEETSVEV 120
                                       44444444444.......444444444444 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.1   1.8e-07   5.8e-05      16      49 ..      18      51 ..      11      52 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.8e-07
                                      BSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR 16 pqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                      + +l++selA+r+g++++tv   L  L+++G ++
  gi|242399680|ref|YP_002995105.1| 18 NARLSISELAERLGISRPTVKSRLEKLEKEGVIR 51
                                      5679***************************876 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 !   22.0   0.1   3.2e-07    0.0001       4      46 ..      10      51 ..       8      54 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 3.2e-07
                          HTH_DeoR  4 qilellkqqgklsveelvellgvSeaTiRRDLneLeeqglltR 46
                                      +++ ll +   ls+ el+e+lg+S  T+   L++Le++g++ R
  gi|242399680|ref|YP_002995105.1| 10 KLIYLLLDNARLSISELAERLGISRPTVKSRLEKLEKEGVI-R 51
                                      67889999*******************************95.4 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   1.8e-07   5.7e-05      11      41 ..      18      49 ..       9      56 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1.8e-07
                            HTH_28 11 aGh.svreaArelgisrrtvyrWikryeegGi 41
                                      + + s++e+A++lgisr tv++ + ++e++G+
  gi|242399680|ref|YP_002995105.1| 18 NARlSISELAERLGISRPTVKSRLEKLEKEGV 49
                                      33579**************************5 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   3.8e-07   0.00012      18      49 ..      12      43 ..       8      47 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 3.8e-07
                                      HHHHHHTS---HHHHHHHHT--HHHHHHHHHH CS
                      Sigma70_r4_2 18 ifllryleglsykEIAellgisegtVksrlsR 49
                                      i+ll +   ls+ E Ae+lgis  tVksrl +
  gi|242399680|ref|YP_002995105.1| 12 IYLLLDNARLSISELAERLGISRPTVKSRLEK 43
                                      778888889********************976 PP

>> HTH_30  PucR C-terminal helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   5.3e-07   0.00017      11      37 ..      19      45 ..       9      47 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 5.3e-07
                                      TTT-HHHHHHHHTS-HHHHHHHHHHHH CS
                            HTH_30 11 nggnisatAkaLhvHrnTlryRLrrie 37
                                      +  +is+ A++L+++r T++ RL+++e
  gi|242399680|ref|YP_002995105.1| 19 ARLSISELAERLGISRPTVKSRLEKLE 45
                                      3489*********************98 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.3   7.4e-07   0.00023      22      54 ..      19      50 ..      14      52 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 7.4e-07
                                      SB---HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                              GntR 22 dkLPsereLaaefgVsrttvReALrrLeaeglv 54
                                      ++L s +eLa+++g+sr+tv   L +Le eg++
  gi|242399680|ref|YP_002995105.1| 19 ARL-SISELAERLGISRPTVKSRLEKLEKEGVI 50
                                      689.9**************************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 !   20.3   0.0   9.3e-07   0.00029      10      42 ..       9      42 ..       1      44 [. 0.78

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 9.3e-07
                                      HHHHHHHH.TTT--HHHHHHHHTS-HHHHHHHHH CS
                        Sigma70_r4 10 revlelrf.geglTleEIgerlgiSrerVrqiek 42
                                       + ++l      l+ +E++erlgiSr +V++++ 
  gi|242399680|ref|YP_002995105.1|  9 LKLIYLLLdNARLSISELAERLGISRPTVKSRLE 42
                                      4444444478899******************986 PP

>> HTH_41  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   4.4e-06    0.0014       8      36 ..      22      50 ..      19      52 .. 0.95
   2 ?   -0.7   0.0       3.8   1.2e+03      22      35 ..      98     111 ..      79     115 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 4.4e-06
                            HTH_41  8 tIeelakeleLSvGlvQkALklLeddkai 36
                                      +I+ela+ l++S+ +v + L++Le++++i
  gi|242399680|ref|YP_002995105.1| 22 SISELAERLGISRPTVKSRLEKLEKEGVI 50
                                      7**************************99 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 3.8
                            HTH_41  22 lvQkALklLeddka 35 
                                       l+  A++++ed k 
  gi|242399680|ref|YP_002995105.1|  98 LIKVAVNSMEDLKR 111
                                       67789999999775 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.1   2.1e-06   0.00067      23      49 ..      20      46 ..      17      47 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 2.1e-06
                            HTH_10 23 rvtlkeLAkelGIskstlsehLrkaes 49
                                      r +++eLA++lGIs++t++ +L+k e+
  gi|242399680|ref|YP_002995105.1| 20 RLSISELAERLGISRPTVKSRLEKLEK 46
                                      7899*******************9886 PP

>> HTH_8  Bacterial regulatory protein, Fis family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.1   2.7e-06   0.00086       4      42 .]       6      44 ..       3      44 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.7e-06
                                      HHHHHHHHHHHHHTTT-HHHHHHHHTS-HHHHHHHHHHT CS
                             HTH_8  4 evEkelIeaALertgGnkskAArlLGisRrtLyrKLkkY 42
                                      +++ +lI   L+ ++  +s+ A++LGisR t+  +L+k+
  gi|242399680|ref|YP_002995105.1|  6 DLDLKLIYLLLDNARLSISELAERLGISRPTVKSRLEKL 44
                                      55556666678888899*******************996 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   2.4e-06   0.00075       2      41 ..      10      49 ..      10      63 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 2.4e-06
                            HTH_29  2 aqallllaeGvstvsqiAkllglsrrtvyrwlkrfeegGl 41
                                      +++ lll+ +  ++s++A++lg+sr+tv   l+  e++G+
  gi|242399680|ref|YP_002995105.1| 10 KLIYLLLDNARLSISELAERLGISRPTVKSRLEKLEKEGV 49
                                      6789999999999***********************9994 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 !   18.3   4.9   5.2e-06    0.0016       2      41 .]     140     176 ..     139     176 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 5.2e-06
                            zf-FCS   2 vkkrCwfCkkyikgkpeftyvlendgvvgqFCStsCldsY 41 
                                       v ++C++C+k+i g p    v  + ++v+ FC+ +Cl ++
  gi|242399680|ref|YP_002995105.1| 140 VPFKCDYCGKEIIGEPI---VHKYHNKVYFFCCPTCLREF 176
                                       5689************8...99999***********9877 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   6.6e-06    0.0021      27      55 .]      22      50 ..      17      50 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 6.6e-06
                            HTH_36 27 sqetlakrlglsknTvsraikeLeqlGyi 55
                                      s + la+rlg+s+ Tv + + +Le+ G i
  gi|242399680|ref|YP_002995105.1| 22 SISELAERLGISRPTVKSRLEKLEKEGVI 50
                                      7899********************98865 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   9.1e-06    0.0029      18      56 ..      15      51 ..       9      54 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 9.1e-06
                                      HHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2 18 akeeeeepvsseeiaerqnispsylekilakLrkaglvk 56
                                       + +    +s++e+aer +is++ ++  l+kL+k+g+++
  gi|242399680|ref|YP_002995105.1| 15 LLDNA--RLSISELAERLGISRPTVKSRLEKLEKEGVIR 51
                                      44444..49****************************97 PP

>> HTH_CodY  CodY helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   8.7e-06    0.0027       3      35 ..      19      51 ..      17      65 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 8.7e-06
                          HTH_CodY  3 GrLtaskiaDriGitrsvivnaLrkLesaGiie 35
                                       rL  s++a+r+Gi r  +   L kLe  G+i 
  gi|242399680|ref|YP_002995105.1| 19 ARLSISELAERLGISRPTVKSRLEKLEKEGVIR 51
                                      6999***************************96 PP

>> DUF2089  Protein of unknown function (DUF2089)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1   6.7e-06    0.0021      33      75 ..       3      46 ..       1      85 [. 0.86

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 6.7e-06
                           DUF2089 33 rLskeqlefvelfika.rGnlkevekelgisYpTvrnrldeile 75
                                      +L++ +l+++ l++ + r +++e++++lgis pTv++rl+++ +
  gi|242399680|ref|YP_002995105.1|  3 KLDDLDLKLIYLLLDNaRLSISELAERLGISRPTVKSRLEKLEK 46
                                      67777888888888642789********************9865 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.2   2.9e-05    0.0091       4      36 ..      12      51 ..      10      79 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.9e-05
                            HTH_19  4 LkeaReelgltqeelaerlgis....rskisaiEng...k 36
                                      +  +  ++ l++ elaerlgis    +s++ ++E++   +
  gi|242399680|ref|YP_002995105.1| 12 IYLLLDNARLSISELAERLGISrptvKSRLEKLEKEgviR 51
                                      56688999**************************876552 PP

>> YHS  YHS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   2.2   3.5e-05     0.011      20      40 ..     159     179 ..     146     182 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.5e-05
                               YHS  20 eYkGkeYyFcSegCkdkFede 40 
                                       +Y+ k Y+Fc++ C+ +F++ 
  gi|242399680|ref|YP_002995105.1| 159 KYHNKVYFFCCPTCLREFKRT 179
                                       6999**************975 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1     4e-05     0.013      27      57 ..      22      51 ..      21      56 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4e-05
                                      -HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE CS
                     LexA_DNA_bind 27 sireiaralglkSpsaveehLkaLerKGyie 57
                                      si e+a++lg++   +v+++L++Le+ G+i+
  gi|242399680|ref|YP_002995105.1| 22 SISELAERLGIS-RPTVKSRLEKLEKEGVIR 51
                                      899********8.779**************8 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   6.1e-05     0.019       4      26 ..      15      37 ..      12      45 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 6.1e-05
                                      HHHHTTHHHHHHHHHHTSSHHHH CS
                             HTH_3  4 lRkqlglsqeeLAeklGvsrsti 26
                                      l++ + ls+ eLAe+lG+sr t+
  gi|242399680|ref|YP_002995105.1| 15 LLDNARLSISELAERLGISRPTV 37
                                      5567779***************9 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   7.6e-05     0.024       2      19 ..      21      38 ..      20      57 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 7.6e-05
                            HTH_17  2 ltveEaAelLgvsrstvy 19
                                      l+++E+Ae Lg+sr tv 
  gi|242399680|ref|YP_002995105.1| 21 LSISELAERLGISRPTVK 38
                                      89**************98 PP

>> HTH_WhiA  WhiA C-terminal HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.9   0.5   3.9e-05     0.012      37      82 ..       3      46 ..       1      47 [. 0.89
   2 ?   -1.2   0.1       8.6   2.7e+03      61      64 ..      84      87 ..      62     116 .. 0.58

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3.9e-05
                                      GS-HHHHHHHHHHHH-TTS-HHHHHHTT..T--HHHHHHHHHHHHH CS
                          HTH_WhiA 37 klpeklkevaelRlenpdaSLkeLgelleppisKSgvnhrlrklke 82
                                      kl++   +++ l l+n  +S++eL+e l   is+ +v+ rl+kl++
  gi|242399680|ref|YP_002995105.1|  3 KLDDLDLKLIYLLLDNARLSISELAERL--GISRPTVKSRLEKLEK 46
                                      5666667888999***************..9*************97 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 8.6
                                      HHTT CS
                          HTH_WhiA 61 gell 64
                                       e++
  gi|242399680|ref|YP_002995105.1| 84 EEII 87
                                      3332 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   7.9e-05     0.025      15      40 ..      22      47 ..       9      48 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 7.9e-05
                                      SHHHHHHHHTS-HHHHHHHHHHHHHH CS
                             HTH_1 15 sftrAAeeLglsqpavsrqikrLEee 40
                                      s+++ Ae+Lg+s p+v  ++ +LE+e
  gi|242399680|ref|YP_002995105.1| 22 SISELAERLGISRPTVKSRLEKLEKE 47
                                      89999*******************86 PP

>> HTH_22  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   0.00014     0.044      41      58 ..      20      37 ..      18      42 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00014
                            HTH_22 41 kgavekvAekLgiSraTv 58
                                      + +++++Ae+LgiSr+Tv
  gi|242399680|ref|YP_002995105.1| 20 RLSISELAERLGISRPTV 37
                                      5699*************9 PP

>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   0.00013     0.041      19      57 ..      79     116 ..      73     127 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00013
                                       HHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHT CS
                    AsnC_trans_reg  19 alaelpeVvecyrvtGdydyllkvvvrdlealerflrek 57 
                                       ++ el+e++e+ r t +  yl+kv+v ++e+l r+++e+
  gi|242399680|ref|YP_002995105.1|  79 KMDELEEIIEINRFT-STKYLIKVAVNSMEDLKRVIEET 116
                                       677899999999999.789****************9884 PP

>> DUF1441  Protein of unknown function (DUF1441)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   0.00013      0.04       2      48 ..      21      66 ..      20      85 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00013
                           DUF1441  2 lnitqlaeitglhRqtvkkRlkgvepaagsnkknkvYaltdviaall 48
                                      l+i++lae  g+ R tvk+Rl+++e  +   ++ ++    ++++a  
  gi|242399680|ref|YP_002995105.1| 21 LSISELAERLGISRPTVKSRLEKLEKEG-VIRGYTIKLNPELLRAHN 66
                                      79*********************99543.234444433333333333 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   0.00017     0.054      17      48 ..      10      41 ..       4      48 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00017
                                      HHHHHHHHHSSBEHHHHHHHHSSTHHHHHHHH CS
                             HTH_9 17 kVvetLlrkgrltlrelvkktkLsldqVkksL 48
                                      k + +Ll+++rl+++el++++++s+  Vk+ L
  gi|242399680|ref|YP_002995105.1| 10 KLIYLLLDNARLSISELAERLGISRPTVKSRL 41
                                      56779************************977 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   0.00023     0.073      10      39 ..       8      38 ..       2      44 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00023
                                      HHGGGGSSTTTT.--STTTSSSS---SSSS- CS
                             HTH_7 10 dinrvvkLleeG.isiskIAkevnisRsTvY 39
                                      d+  +  Ll++   sis++A++++isR Tv+
  gi|242399680|ref|YP_002995105.1|  8 DLKLIYLLLDNArLSISELAERLGISRPTVK 38
                                      55667778888889***************96 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   0.00021     0.066      14      46 ..      19      51 ..       9      56 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00021
                                      ----HHHHHHHHTS-HHHHHHHHHHHHHHSSEE CS
                              FaeA 14 apckTreiAdalglsaYQaRyYLeqLekegkik 46
                                      a    +e+A+ lg+s   +++ Le+Lekeg i+
  gi|242399680|ref|YP_002995105.1| 19 ARLSISELAERLGISRPTVKSRLEKLEKEGVIR 51
                                      555678************************997 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00029      0.09      22      50 ..      11      39 ..       7      48 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00029
                                      HHHHHHHHCT--HHHHHHHHT--HHHHHH CS
                            HTH_37 22 aiaeliekrelsqseaaqllgiaqPkvsr 50
                                       i+ l++  +ls se+a++lgi++P v +
  gi|242399680|ref|YP_002995105.1| 11 LIYLLLDNARLSISELAERLGISRPTVKS 39
                                      5888999******************9954 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00041      0.13      13      58 ..      15      59 ..       8      64 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00041
                                      HHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS CS
                              HxlR 13 ellkgkkRfselkralpkisqkmLaqrLreLeqdglierevypevP 58
                                       l + +   sel+++l +is+ +  +rL +Le++g+i   +++  P
  gi|242399680|ref|YP_002995105.1| 15 LLDNARLSISELAERL-GISRPTVKSRLEKLEKEGVIRGYTIKLNP 59
                                      3444666789******.9*******************877776666 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0    0.0003     0.093      20      49 ..      12      42 ..       9      44 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0003
                      HTH_Tnp_ISL3 20 ilellles.rsvkavArqlgvSwtTVwrild 49
                                      i+ ll +   s+++ A++lg+S  TV+ +l 
  gi|242399680|ref|YP_002995105.1| 12 IYLLLDNArLSISELAERLGISRPTVKSRLE 42
                                      5666667789*****************9885 PP

>> VATC  Vms1-associating treble clef domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   4.7   0.00035      0.11       5      39 ..     143     180 ..     140     183 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00035
                              VATC   5 rCsiCgesleg....kvyFekfdfrYCstkClraHRran 39 
                                       +C+ Cg+++ g    ++y +k  + +C   Clr+ +r++
  gi|242399680|ref|YP_002995105.1| 143 KCDYCGKEIIGepivHKYHNKV-YFFCCPTCLREFKRTR 180
                                       7********9877655677776.77********998876 PP

>> LIM  LIM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   3.3   0.00036      0.11       1      40 [.     144     180 ..     144     193 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00036
                                       -TTT--BE-TTTEEEEETTEEEETTTSB-TTT-SB-CTT. CS
                               LIM   1 CagCnkkiadrelvlkaldkvwHeeCFtCsdCqkeLkegs 40 
                                       C  C+k+i+ + +v k  +kv+    F+C +C +e+k+++
  gi|242399680|ref|YP_002995105.1| 144 CDYCGKEIIGEPIVHKYHNKVY---FFCCPTCLREFKRTR 180
                                       99************88888888...588889988888765 PP

>> NUMOD1  NUMOD1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00092      0.29      18      34 ..      22      38 ..      22      40 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00092
                            NUMOD1 18 SireAakyLgishntIn 34
                                      Si+e+a+ Lgis++t++
  gi|242399680|ref|YP_002995105.1| 22 SISELAERLGISRPTVK 38
                                      9**************97 PP

>> FeoC  FeoC like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00099      0.31      11      45 ..      17      51 ..      10      56 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00099
                              FeoC 11 ergrvslkeLsrhfkaspealeamLeqwvrkGrve 45
                                       + r s++eL+ ++ +s  ++++ Le +++ G ++
  gi|242399680|ref|YP_002995105.1| 17 DNARLSISELAERLGISRPTVKSRLEKLEKEGVIR 51
                                      67899*************************99876 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 ?   12.7   0.0    0.0005      0.16      68      97 ..      21      50 ..       9      54 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.0005
                                      EEHHHHHHHSTSXHHHHHHHHHHHHHTTSE CS
                             RPA_C 68 vhvdeiaqklrlsvndvkqavdeLsneGii 97
                                      ++++e+a++l++s  +vk+ +++L++eG+i
  gi|242399680|ref|YP_002995105.1| 21 LSISELAERLGISRPTVKSRLEKLEKEGVI 50
                                      799*************************99 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0    0.0011      0.33       5      28 ..      15      38 ..      12      49 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0011
                            HTH_26  5 lmadrgitkseLargtgisaatls 28
                                      l+   ++++seLa+++gis++t++
  gi|242399680|ref|YP_002995105.1| 15 LLDNARLSISELAERLGISRPTVK 38
                                      56677889**************95 PP

>> Crp  Bacterial regulatory proteins, crp family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1    0.0009      0.28       2      32 .]      20      50 ..      20      50 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0009
                                      E--HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                               Crp  2 pmSRqdIAdylGlTrETVSRlLtrLrekGLI 32
                                      ++S  ++A+ lG +r TV   L +L+++G+I
  gi|242399680|ref|YP_002995105.1| 20 RLSISELAERLGISRPTVKSRLEKLEKEGVI 50
                                      57888*************7779********9 PP

>> Sgf11  Sgf11 (transcriptional regulation protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.1     0.041        13       5      14 ..     142     151 ..     139     153 .. 0.88
   2 ?    6.8   0.9     0.016       5.1       3      18 ..     165     180 ..     163     180 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.041
                                       EE-TTTSSEE CS
                             Sgf11   5 vtCpnCgRqi 14 
                                       ++C++Cg++i
  gi|242399680|ref|YP_002995105.1| 142 FKCDYCGKEI 151
                                       89******98 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.016
                                       -EEE-TTTSSEEEGGG CS
                             Sgf11   3 eyvtCpnCgRqiaasR 18 
                                        +++Cp C R+ + +R
  gi|242399680|ref|YP_002995105.1| 165 YFFCCPTCLREFKRTR 180
                                       68********977665 PP

>> Ta0938  Ta0938
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       7.6   2.4e+03      56      67 ..      73      84 ..      62     124 .. 0.49
   2 ?    9.5   1.8    0.0036       1.1      31      57 ..     160     186 ..     138     198 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 7.6
                                      HHHHHHHS---E CS
                            Ta0938 56 krtglskidele 67
                                      k  + +k+dele
  gi|242399680|ref|YP_002995105.1| 73 KTEKPEKMDELE 84
                                      444444444442 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0036
                                       -TT--BSSS--SSSS-TTS-THHHHHH CS
                            Ta0938  31 vdgeklffccdicakefvnllnevkkr 57 
                                        + +  ffcc  c +ef+   +++ k 
  gi|242399680|ref|YP_002995105.1| 160 YHNKVYFFCCPTCLREFKRTRENIEKF 186
                                       455568***********9987777653 PP

>> zf-C2H2_6  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.9     0.018       5.5       2      10 ..     142     150 ..     142     150 .. 0.91
   2 ?    5.8   3.5     0.044        14       2      12 ..     167     177 ..     166     178 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.018
                         zf-C2H2_6   2 heCsvCsks 10 
                                       ++C++C+k+
  gi|242399680|ref|YP_002995105.1| 142 FKCDYCGKE 150
                                       89*****95 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.044
                         zf-C2H2_6   2 heCsvCsksFp 12 
                                       ++C++C+++F+
  gi|242399680|ref|YP_002995105.1| 167 FCCPTCLREFK 177
                                       9*********7 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 ?    7.8   1.1     0.015       4.8      14      22 ..     141     149 ..     131     150 .. 0.77
   2 ?    5.4   6.8     0.085        27       7      26 .]     159     178 ..     158     178 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.015
                         zf-H2C2_2  14 pyeCplCdk 22 
                                       p++C++C+k
  gi|242399680|ref|YP_002995105.1| 141 PFKCDYCGK 149
                                       8******99 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.085
                         zf-H2C2_2   7 rkHtgekpyeCplCdkaFkt 26 
                                       + H +  +++Cp C   Fk+
  gi|242399680|ref|YP_002995105.1| 159 KYHNKVYFFCCPTCLREFKR 178
                                       56889999**********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1278  (0.0712812); expected 358.6 (0.02)
Passed bias filter:                      747  (0.0416643); expected 358.6 (0.02)
Passed Vit filter:                       170  (0.00948185); 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: 0.67u 0.35s 00:00:01.02 Elapsed: 00:00:00.56
# Mc/sec: 1080.91
//
Query:       gi|242399681|ref|YP_002995106.1|  [L=236]
Description: cytochrome C-type biogenesis protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-05   23.2  15.0    6.7e-05   22.4  15.0    1.3  1  SfLAP     Sap, sulfolipid-1-addressing protein


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 !   22.4  15.0   3.7e-09   6.7e-05       1     207 [.      24     230 ..      24     233 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 3.7e-09
                             SfLAP   1 llvlAlvvalsPlrlgvavlllsr......prpvlnllaFlvgwlvvlvalglivlfvlrsllsgasaapssaikal 71 
                                       +++l+++ al P    ++v+lls       +r +  ++ F++g+++++ +++ +++ + +++l ++     +++ a+
  gi|242399681|ref|YP_002995106.1|  24 VIALGILNALRPSIFLMIVFLLSMialvdeNRVLKVGFSFTAGAFLGYSVIASALMSLHGKFL-FL----RHFVVAF 95 
                                       689*******************988888889***************************99999.88....7889999 PP

                             SfLAP  72 qivlGvlllllaaveavrrpkassrselprllsrleslleggalwvAlvlgllsakplllylaalaaigasgasvgt 148
                                        i++G+  +l ++  ++ + ++  r+++ r l++  +++++ a++v++v+  ls + +l+  + ++ +++ g s + 
  gi|242399681|ref|YP_002995106.1|  96 GIAVGLYKILSSLGYVKISTSNPLREKSNRILEK--ATSPASAFLVGGVMSFLSLSCVLPSYLLVTSLLSDGFSFSI 170
                                       9999999998776665555457777777777775..6789************************************* PP

                             SfLAP 149 qvvalvvFvvvalavveipllaylvap..ertqavlerlkdwlrsnrrlilavilgvvGll 207
                                         ++l +Fv ++++++++  l++      +++  ++++l   +  + +l+++++l++v +l
  gi|242399681|ref|YP_002995106.1| 171 RAALLGMFVGISVLPLALVTLGFHYGNkyGKLSGAVNKLS-KMSGRGDLAMGLVLVLVSVL 230
                                       ******************9999877652268888888885.46777888888888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       713  (0.039768); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); 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: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.54
# Mc/sec: 1315.28
//
Query:       gi|242399682|ref|YP_002995107.1|  [L=117]
Description: hypothetical protein TSIB_1707 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.33s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 696.27
//
Query:       gi|242399683|ref|YP_002995108.1|  [L=117]
Description: hypothetical protein TSIB_1708 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score 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   0.0        0.2   11.9   0.0    1.2  1  DUF1269   Protein of unknown function (DUF1269)


Domain annotation for each model (and alignments):
>> DUF1269  Protein of unknown function (DUF1269)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   1.1e-05       0.2       6      60 ..       7      77 ..       4     104 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.1e-05
                           DUF1269  6 lwGllvGllflnPllGaa................vGAaaGAlvgals.dvgidddflkelgeklkpgtsalf 60
                                      l+G+++G+++  P  ++a                +G ++G ++g +  +  +dd++ +e +e++  g  a +
  gi|242399683|ref|YP_002995108.1|  7 LIGFIIGVIIAIP-YSLAhsgapdqserdslwngFGPMTGHIQGGMMvHGMMDDEMYQETEEHMASGDFAEM 77
                                      689**********.55555778999999999999********999661666789999********9998855 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       838  (0.0467399); expected 358.6 (0.02)
Passed bias filter:                      607  (0.0338558); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 702.70
//
Query:       gi|242399684|ref|YP_002995109.1|  [L=203]
Description: Ubiquinone/menaquinone biosynthesis methyltransferase [Thermococcus sibiricus MM 739]
Scores for complete 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-24   85.4   0.0    5.6e-24   84.6   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    2.9e-22   79.1   0.1    1.9e-21   76.5   0.0    1.9  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    3.5e-22   78.9   0.0    8.2e-22   77.7   0.0    1.6  2  Methyltransf_25  Methyltransferase domain
    2.8e-21   75.9   0.0    3.9e-21   75.4   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    1.3e-18   67.4   0.0    1.6e-18   67.1   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
    1.9e-17   63.8   0.0      3e-17   63.2   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
    1.5e-06   27.8   0.0      2e-06   27.4   0.0    1.2  1  TehB             Tellurite resistance protein TehB
    2.1e-06   27.3   0.0    3.5e-06   26.6   0.0    1.3  1  Methyltransf_4   Putative methyltransferase
      4e-06   26.3   0.0    5.4e-06   25.9   0.0    1.3  1  CMAS             Mycolic acid cyclopropane synthetase
    0.00012   21.9   0.0    0.00019   21.3   0.0    1.3  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
     0.0019   17.8   0.0     0.0029   17.2   0.0    1.2  1  MetW             Methionine biosynthesis protein MetW
      0.005   15.8   0.0     0.0096   14.9   0.0    1.4  1  Methyltransf_9   Protein of unknown function (DUF1698)
     0.0066   16.3   0.0      0.017   15.0   0.0    1.7  2  Methyltransf_8   Hypothetical methyltransferase
  ------ inclusion threshold ------
      0.041   12.3   0.1      0.041   12.3   0.1    1.1  1  DUF2194          Uncharacterised protein conserved in bacteri


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 !   84.6   0.0   4.4e-27   5.6e-24       1      96 []      45     140 ..      45     140 .. 0.97

  Alignments for each domain:
  == domain 1  score: 84.6 bits;  conditional E-value: 4.4e-27
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-TT-EEEEEEES-CCC-CC CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl.kvefvvadaeklpfednsfDlvvssevlhhved 76 
                                       L++G+GtG+++ ++   + +vvg+D+s  ml+ a+ek +e gl +v+++ +d +++ f dn+fD vvs++v+++v+d
  gi|242399684|ref|YP_002995109.1|  45 LEIGVGTGKNLLYYPPDV-EVVGIDFSSGMLEKAEEKRKELGLkNVKLLLMDTQNMEFDDNTFDTVVSTFVFCTVPD 120
                                       89*************777.***********************9********************************** PP

                                       HHHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  77 pekalkeiaRvLkpgGllvi 96 
                                       p k lke++RvLkpgG+ ++
  gi|242399684|ref|YP_002995109.1| 121 PVKGLKEAYRVLKPGGRTIF 140
                                       ****************9886 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.5   0.0   1.4e-24   1.9e-21      13     168 ..      10     157 ..       4     175 .. 0.85
   2 ?    0.7   0.0      0.22   2.8e+02     205     232 ..     175     202 ..     167     203 .] 0.80

  Alignments for each domain:
  == domain 1  score: 76.5 bits;  conditional E-value: 1.4e-24
                                       XX-HHHHHHHHHHHHHTTTHHHHHHHHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHH CS
                   Ubie_methyltran  13 fesvaskyDlmndvlslgihrlWkkfveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvge 89 
                                       +++ ++ yD   + + +    +++k+   lv +    kvl++  Gtg   +          +vv++D+++ mL+ +e
  gi|242399684|ref|YP_002995109.1|  10 YDKFSKIYDIFESPMEMMAFSKYRKKALSLVKG----KVLEIGVGTGKNLLYY----PPDVEVVGIDFSSGMLEKAE 78 
                                       567777788888888888888888877766544....6899999999766554....456689************** PP

                                       HHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEEEEE----SHHHHHHH CS
                   Ubie_methyltran  90 kklkeegkinieflqanaeeLpfeddsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvvlefskvelpllsqay 166
                                       +k ke g +n+++l  ++++++f+d++fD+v  +f +  v+D  k+LkeayrvlkpGGr + le  k + +ll+++ 
  gi|242399684|ref|YP_002995109.1|  79 EKRKELGLKNVKLLLMDTQNMEFDDNTFDTVVSTFVFCTVPDPVKGLKEAYRVLKPGGRTIFLEHMKSQSKLLNVPL 155
                                       *********************************************************************99999886 PP

                                       HH CS
                   Ubie_methyltran 167 el 168
                                        l
  gi|242399684|ref|YP_002995109.1| 156 YL 157
                                       54 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.22
                                       HHHHHHTTEEEEEEEEEGGGTEEEEEEE CS
                   Ubie_methyltran 205 keliedaGfksveyesltgGvvaihigv 232
                                       ++ ie+aGfk  + e+l + +v + +++
  gi|242399684|ref|YP_002995109.1| 175 QKNIEKAGFKIEKVENLFFDIVRLIVAT 202
                                       556899****999999999988776665 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.7   0.0   6.4e-25   8.2e-22       1      97 []      44     136 ..      44     136 .. 0.94
   2 ?   -2.5   0.0       6.9   8.8e+03      33      50 ..     170     187 ..     168     195 .. 0.71

  Alignments for each domain:
  == domain 1  score: 77.7 bits;  conditional E-value: 6.4e-25
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEEESTGGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvssgalhh 76 
                                       vL++G GtG+++l+        +v+g+D+s++mle+a+e+ +e gl nv+++ +d ++++f+d++fD vvs+++++ 
  gi|242399684|ref|YP_002995109.1|  44 VLEIGVGTGKNLLYYPPD---VEVVGIDFSSGMLEKAEEKRKELGLkNVKLLLMDTQNMEFDDNTFDTVVSTFVFCT 117
                                       9**************977...69**********************9*************************877665 PP

                                       SSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  77 lsdedlekalkeiarvLkpgG 97 
                                       +  +d  k lke++rvLkpgG
  gi|242399684|ref|YP_002995109.1| 118 V--PDPVKGLKEAYRVLKPGG 136
                                       5..5788*************9 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 6.9
                                       HHHHHHHHHHHTTTTEEE CS
                   Methyltransf_25  33 mleaareraeeeglnvef 50 
                                       +l+++++++e++g+++e 
  gi|242399684|ref|YP_002995109.1| 170 LLRETQKNIEKAGFKIEK 187
                                       577888888888876664 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.4   0.0   3.1e-24   3.9e-21       6     113 ..      43     144 ..      40     192 .. 0.83

  Alignments for each domain:
  == domain 1  score: 75.4 bits;  conditional E-value: 3.1e-24
                   Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsne 82 
                                       +vl++G GtG+ ++       p+ evvGiD+s  ++e+A+e++++lgl+nv++   d +++e  + d++fD ++s  
  gi|242399684|ref|YP_002995109.1|  43 KVLEIGVGTGKNLLY----YPPDVEVVGIDFSSGMLEKAEEKRKELGLKNVKLLLMDTQNME--FDDNTFDTVVSTF 113
                                       799999999775543....569****************************************..************* PP

                   Methyltransf_31  83 vlnaladpdkileeiervlkpggilliedpr 113
                                       v+++++dp k l+e+ rvlkpgg+ +  ++ 
  gi|242399684|ref|YP_002995109.1| 114 VFCTVPDPVKGLKEAYRVLKPGGRTIFLEHM 144
                                       ************************9988776 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.1   0.0   1.2e-21   1.6e-18      20     133 ..      38     153 ..      20     188 .. 0.79

  Alignments for each domain:
  == domain 1  score: 67.1 bits;  conditional E-value: 1.2e-21
                   Methyltransf_23  20 lraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae......kakkaqkdqfdeqeaaepqgkfdlIvlre 90 
                                          +g+vL+iG GtG +l ++ +  ++v+g+D s+ + e+ae      + k+ +   +d q+ ++++++fd++v+++
  gi|242399684|ref|YP_002995109.1|  38 SLVKGKVLEIGVGTGKNLLYYPPD-VEVVGIDFSSGMLEKAEekrkelGLKNVKLLLMDTQNMEFDDNTFDTVVSTF 113
                                       34578**************88554.7**********************888888888889999************** PP

                   Methyltransf_23  91 vlehvpdppellrqiatllkpgGylllseplaslkedrllldw 133
                                       v+++vpdp + l+ +++ lkpgG+ +++e+ +s    ++ll++
  gi|242399684|ref|YP_002995109.1| 114 VFCTVPDPVKGLKEAYRVLKPGGRTIFLEHMKS---QSKLLNV 153
                                       ******************************766...4445544 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.2   0.0   2.4e-20     3e-17       1      98 [.      45     137 ..      45     138 .. 0.95

  Alignments for each domain:
  == domain 1  score: 63.2 bits;  conditional E-value: 2.4e-20
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlh 77 
                                       LeiG GtG +l +  ++   +e++g+D+s+ ++e+a+ek ++ + +n++ +  ++++ + +d   +fD+vv+ +v++
  gi|242399684|ref|YP_002995109.1|  45 LEIGVGTGKNLLYYPPD---VEVVGIDFSSGMLEKAEEKRKELGLKNVKLLLMDTQNMEFDDN--TFDTVVSTFVFC 116
                                       8********99999777...******************************9999999887776..************ PP

                   Methyltransf_12  78 hlkdirevldnirklLkpgGr 98 
                                        ++d+ + l++++++LkpgGr
  gi|242399684|ref|YP_002995109.1| 117 TVPDPVKGLKEAYRVLKPGGR 137
                                       ********************7 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0   1.5e-09     2e-06       9     141 ..      20     149 ..       7     163 .. 0.76

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 1.5e-09
                                       HHHHHT-----HHHHHHCCCS-S-EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE- CS
                              TehB   9 fskkynltathsevveavkivkpgkvldlgcgqgrnslylsllgydvtawdknensiafleeikekenlknistaly 85 
                                       f+   ++ a     ++a  +vk gkvl++g g g+n ly      +v  +d  +  ++  ee ++   lkn++  l+
  gi|242399684|ref|YP_002995109.1|  20 FESPMEMMAFSKYRKKALSLVK-GKVLEIGVGTGKNLLYYPP-DVEVVGIDFSSGMLEKAEEKRKELGLKNVKLLLM 94 
                                       4444444444444455555555.9***************975.6799999999999999999999999********* PP

                                       -GGG----S-.EEEEEEESSGGGS-GGGHHHHHHHHHHTEEEEEEEEEEEEB--SSS CS
                              TehB  86 dineaklder.ydfilstvvlmfleaeripsiienmqectkvggynlivaamstddv 141
                                       d +++++d++ +d ++st v+  + ++ +  + ++  +  k+gg  + +  m+++  
  gi|242399684|ref|YP_002995109.1|  95 DTQNMEFDDNtFDTVVSTFVFCTV-PDPVKGL-KEAYRVLKPGGRTIFLEHMKSQSK 149
                                       *******87549******999765.5556655.445567788988888888877665 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0   2.8e-09   3.5e-06       5     108 ..      44     145 ..      41     154 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 2.8e-09
                                       EEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-C..CCHHHHCS-TTSEEEEEEE CS
                    Methyltransf_4   5 vleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgda..lkvllelledgslekifil 79 
                                       vleiG+G G+ l+      Pd++++Gi+ ++ +++k+ +k ++l+lkN+++l  d   +++  + + +   + +f  
  gi|242399684|ref|YP_002995109.1|  44 VLEIGVGTGKNLLY---YPPDVEVVGIDFSSGMLEKAEEKRKELGLKNVKLLLMDTqnMEFDDNTFDTVVSTFVFCT 117
                                       79********9996...58***********************************99666677777777777777777 PP

                                       S-----SGGGGGGSTTSHHHHHHHHHHEE CS
                    Methyltransf_4  80 FPDPwfKkrhhKrRllqpellkelarvLk 108
                                        PDP  K  ++  R+l+p   + + + +k
  gi|242399684|ref|YP_002995109.1| 118 VPDP-VKGLKEAYRVLKPGGRTIFLEHMK 145
                                       8999.577777888887766665555555 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   4.2e-09   5.4e-06      57     218 ..      36     191 ..       8     199 .. 0.76

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 4.2e-09
                                       TTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG..---.--SE CS
                              CMAS  57 klelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyed..lde.kvdr 130
                                        l+l +G ++L+iG G G+ + +     dv+vvg+ +S+   ++a+++ +el+l++ v+++l+d ++  +d+  +d 
  gi|242399684|ref|YP_002995109.1|  36 ALSLVKG-KVLEIGVGTGKNLLYYPP--DVEVVGIDFSSGMLEKAEEKRKELGLKN-VKLLLMDTQNmeFDDnTFDT 108
                                       4667777.699********9998765..6************************765.66777776651155579*** PP

                                       EEEES-GGGTSGGGHHHHHHHHHHHS-TT-EEEEEEEEE--HHHHHC.TTCCCHHHHHHTSTTS---BHHHHHHHHH CS
                              CMAS 131 vvsvgafehvgkenydtffkklkkllkedGllllhtitslhkkelae.rglklkfidkeiFPgGelpsieeieeeis 206
                                       vvs  +f  v      +  k+++++lk++G+ +    ++ ++k l+    l   fi++ +  g     ++e +++i+
  gi|242399684|ref|YP_002995109.1| 109 VVSTFVFCTVPDP--VKGLKEAYRVLKPGGRTIFLEHMKSQSKLLNVpLYLMEPFIKTLL--GT--SLLRETQKNIE 179
                                       ***9999888644..566899*********865544444444444420333337777654..22..33567788999 PP

                                       HTT-EEEEEEE- CS
                              CMAS 207 eagftvvdvesl 218
                                       +agf++++ve+l
  gi|242399684|ref|YP_002995109.1| 180 KAGFKIEKVENL 191
                                       99****999998 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   1.5e-07   0.00019      69     170 ..      37     139 ..      10     152 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.5e-07
                                       TT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGGTTGGG-SEEE CS
                              PCMT  69 lelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGrkGyeekaPYda 145
                                       l+l kg +vLe+G G+G +      +  ++  vv+i+ +  + e+a+++ k+l+l+nv++   D ++   +   +d+
  gi|242399684|ref|YP_002995109.1|  37 LSLVKG-KVLEIGVGTGKNLL----YYPPDVEVVGIDFSSGMLEKAEEKRKELGLKNVKLLLMDTQNMEFDDNTFDT 108
                                       446555.8*********9854....5678899********************************99887788889*9 PP

                                       EEESSBBSS--HHH......HHTEEEEEEEE CS
                              PCMT 146 ihvgaaapeiPeal......idQLkeGGrlv 170
                                       ++ +     +P++        + Lk+GGr +
  gi|242399684|ref|YP_002995109.1| 109 VVSTFVFCTVPDPVkglkeaYRVLKPGGRTI 139
                                       9999999999976411111144556666554 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   2.3e-06    0.0029      14     102 ..      41     132 ..      34     140 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.3e-06
                              MetW  14 gsrvldlGcGdGellellkeekqvdgrGleldeegvaecvak....Glsviq.gdldkdlenfedksfdyvvlsqtl 85 
                                       + +vl++G G G+ l +     +v+  G++ ++  + ++ +k    Gl+ ++   +d++  +f+d++fd vv +  +
  gi|242399684|ref|YP_002995109.1|  41 KGKVLEIGVGTGKNLLYY--PPDVEVVGIDFSSGMLEKAEEKrkelGLKNVKlLLMDTQNMEFDDNTFDTVVSTFVF 115
                                       579*********966555..56899999**9999998887664455675444145799999**************** PP

                              MetW  86 qatrnpkevldellrig 102
                                        ++ +p + l+e  r+ 
  gi|242399684|ref|YP_002995109.1| 116 CTVPDPVKGLKEAYRVL 132
                                       ************99985 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 !   14.9   0.0   7.5e-06    0.0096     111     217 ..      37     140 ..      26     153 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 7.5e-06
                                       S.--TT-EEEEET-TTSHHHHHHHHCT-SEEEEE---HHHHHHHHHHHCCTTTTSSEEEE---GGGS-T.---EEEE CS
                    Methyltransf_9 111 lsdlkgrtildvGcgnGyhlwrmvgegaklvvGidPselfliqfeavrkllgedqrahllplgieqlpe.leafdtv 186
                                       ls +kg ++l++G g+G  l          vvGid s+  l + e  rk lg ++ + ll +  ++++   ++fdtv
  gi|242399684|ref|YP_002995109.1|  37 LSLVKG-KVLEIGVGTGKNLLYYP--PDVEVVGIDFSSGMLEKAEEKRKELGLKNVKLLL-MDTQNMEFdDNTFDTV 109
                                       444444.58999999999886554..34579*********************99988888.99999998789***** PP

                                       EEES-GGG-S-HHHHHHHHHCTEEEEEEEEE CS
                    Methyltransf_9 187 fsmGvlyhrrsPldhllqlkdqlvkgGelvl 217
                                        s  v+     P+  l +    l+ gG  ++
  gi|242399684|ref|YP_002995109.1| 110 VSTFVFCTVPDPVKGLKEAYRVLKPGGRTIF 140
                                       **************************98663 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.3e-05     0.017     106     158 ..      89     142 ..      67     191 .. 0.78
   2 ?   -1.2   0.0       1.2   1.6e+03     169     184 ..     174     189 ..     168     198 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.3e-05
                                       TTEEES-TTS-S--TT-EEEEEEES--.-SS-HHHHHHHHHHHEEEEEEEEEEE CS
                    Methyltransf_8 106 ervvacdlakvPledesvdvavfclsl.mgtnladflkeanrvlkvGGllkvae 158
                                        ++   d +++  +d++ d +v  + +  + +  + lkea+rvlk+GG     e
  gi|242399684|ref|YP_002995109.1|  89 VKLLLMDTQNMEFDDNTFDTVVSTFVFcTVPDPVKGLKEAYRVLKPGGRTIFLE 142
                                       55667799999********99987765146789999************755433 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.2
                                       HHHHHHCTTEEEEEEE CS
                    Methyltransf_8 169 faraltklGfevkskd 184
                                        +++++k Gf++++++
  gi|242399684|ref|YP_002995109.1| 174 TQKNIEKAGFKIEKVE 189
                                       5789999999998765 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 ?   12.3   0.1   3.2e-05     0.041      41     106 ..      87     149 ..      24     190 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.2e-05
                           DUF2194  41 lkieyelkdveklnfskidlekYetVivtyyseeldklkeyLkqlvefvengGklffannlgastd 106
                                        +++  l+d ++++f   d + ++tV++t+   +++++ + Lk+ ++ ++ gG+ +f++ ++ +++
  gi|242399684|ref|YP_002995109.1|  87 KNVKLLLMDTQNMEF---DDNTFDTVVSTFVFCTVPDPVKGLKEAYRVLKPGGRTIFLEHMKSQSK 149
                                       456666778888655...4577*************************************9988774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); 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:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 1213.73
//
Query:       gi|242399685|ref|YP_002995110.1|  [L=97]
Description: Membrane protein-like protein [Thermococcus sibiricus MM 739]
Scores for complete 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   39.8   6.9    3.3e-10   39.3   6.9    1.2  1  SHOCT     Short C-terminal domain
    6.1e-05   23.0   0.2    8.4e-05   22.6   0.2    1.2  1  DUF1707   Domain of unknown function (DUF1707)
     0.0038   17.2   0.6     0.0068   16.4   0.6    1.4  1  GvpG      Gas vesicle protein G
     0.0049   16.8   0.0     0.0065   16.4   0.0    1.1  1  DUF4083   Domain of unknown function (DUF4083)
  ------ inclusion threshold ------
      0.016   15.1   0.4      0.022   14.6   0.4    1.3  1  VbhA      Antitoxin VbhA
       0.17   11.6   0.0        0.2   11.3   0.0    1.1  1  DUF21     Cyclin M transmembrane N-terminal domain
        7.8    6.5   9.9         11    6.1   9.9    1.2  1  Apq12     Nuclear pore assembly and biogenesis


Domain annotation for each model (and alignments):
>> SHOCT  Short C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3   6.9   1.3e-13   3.3e-10       2      28 .]      69      95 ..      68      95 .. 0.97

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 1.3e-13
                             SHOCT  2 aLekLkeLyarGeIteEEFeakKakLL 28
                                      aLe+L+e yarGeI+++E+e++K+kLL
  gi|242399685|ref|YP_002995110.1| 69 ALEILDEKYARGEIDDDEYERRKRKLL 95
                                      9*************************8 PP

>> DUF1707  Domain of unknown function (DUF1707)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.2   3.3e-08   8.4e-05       8      35 ..      66      93 ..      62      96 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 3.3e-08
                           DUF1707  8 ReravelLrealaeGrLtldEfdeRlea 35
                                       +ra+e+L+e +a+G ++ dE+++R  +
  gi|242399685|ref|YP_002995110.1| 66 KKRALEILDEKYARGEIDDDEYERRKRK 93
                                      579**********************776 PP

>> GvpG  Gas vesicle protein G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.6   2.6e-06    0.0068       9      62 ..      46      95 ..      37      96 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.6e-06
                              GvpG  9 vrgviWiaeqvqeraeeqlddqenlrkeLaaLqqeLdaGeIdeeeFdrrEeelL 62
                                      + gv+W ++ + ++      ++++    L  L+ +  +GeId++e++rr  +lL
  gi|242399685|ref|YP_002995110.1| 46 IAGVAWFIRWILDQSSGSTSKKRA----LEILDEKYARGEIDDDEYERRKRKLL 95
                                      678888888888877766666654....678******************99998 PP

>> DUF4083  Domain of unknown function (DUF4083)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   2.5e-06    0.0065       5      44 ..      32      71 ..      29      75 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.5e-06
                           DUF4083  5 liyliivivLilllvfsftlfiRrvvsrsaakkkkskele 44
                                      +   i++++  ++++ ++  fiR ++ +s+ + +k+  le
  gi|242399685|ref|YP_002995110.1| 32 WFGAILMLLFWGAIIAGVAWFIRWILDQSSGSTSKKRALE 71
                                      55579999***********************999999887 PP

>> VbhA  Antitoxin VbhA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.4   8.6e-06     0.022      28      43 ..      75      90 ..      64      93 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 8.6e-06
                              VbhA 28 eayvrGeIdadElvrr 43
                                      e+y+rGeId dE+ rr
  gi|242399685|ref|YP_002995110.1| 75 EKYARGEIDDDEYERR 90
                                      79***********998 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 ?   11.3   0.0     8e-05       0.2     122     176 .]      32      86 ..      25      86 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8e-05
                             DUF21 122 pplrvlmvllyPlv.wllskllnlilesesepavseeelkklveeseeegvieeee 176
                                       ++  +lm l++ ++ + + +++++il ++s+  +s++   ++++e++++g+i+ +e
  gi|242399685|ref|YP_002995110.1|  32 WFGAILMLLFWGAIiAGVAWFIRWIL-DQSSGSTSKKRALEILDEKYARGEIDDDE 86 
                                       55567888886555156*********.899999999999*************9987 PP

>> Apq12  Nuclear pore assembly and biogenesis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   9.9    0.0042        11      28      50 ..      29      51 ..      24      54 .. 0.94

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0042
                             Apq12 28 vlfwvrllvrlvfwlavvlvgay 50
                                      ++ w+ +++ l+fw+a+++ +a+
  gi|242399685|ref|YP_002995110.1| 29 WFGWFGAILMLLFWGAIIAGVAW 51
                                      999*****************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       788  (0.0439511); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.50u 0.34s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 568.85
//
Query:       gi|242399686|ref|YP_002995111.1|  [L=300]
Description: hypothetical protein TSIB_1711 [Thermococcus sibiricus MM 739]
Scores for complete 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-43  145.9  40.2      4e-26   91.8  10.6    2.1  2  EamA      EamA-like transporter family
    3.4e-05   23.6  12.1    4.5e-05   23.2  10.3    2.2  1  EmrE      Putative multidrug resistance efflux transporter
     0.0075   15.5   4.3     0.0075   15.5   4.3    2.5  3  PUNUT     Purine nucleobase transmembrane transport
  ------ inclusion threshold ------
       0.03   14.3   1.1       0.03   14.3   1.1    3.4  2  TMEM234   Putative transmembrane family 234


Domain annotation for each model (and alignments):
>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.8  10.6     9e-30     4e-26       2     137 .]       5     152 ..       4     152 .. 0.92
   2 !   60.4  21.6   4.4e-20     2e-16       2     136 ..     165     298 ..     164     299 .. 0.98

  Alignments for each domain:
  == domain 1  score: 91.8 bits;  conditional E-value: 9e-30
                              EamA   2 lgillallaalfwaiyfvlskillrkvspltltfvrfliagilllii........allkegkl..........akls 60 
                                        g++ a+laa++++i+ +l ki+lr+v+p+ +++  +l agi+l+++        +      l          +++s
  gi|242399686|ref|YP_002995111.1|   5 YGYVSAVLAAFLFGISSTLNKIALRDVHPMVVAGSVYLTAGIVLMLLrftpvkerI------LkkfesgvktqESFS 75 
                                       6999****************************************999776666651......24444445788999* PP

                              EamA  61 lkdwllllllgllgtvlafllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllill 137
                                        +d+ +l+++ l+g++l++l f+ +l++t+a nasl++++e +ft++++ l+++ek + ++ +gi+lil+G+++i++
  gi|242399686|ref|YP_002995111.1|  76 GRDIVILAFVVLFGSFLGPLSFMFGLNNTTAVNASLLLNTETLFTVLIALLVFKEKASRRSGIGILLILIGTVVIST 152
                                       **************************************************************************986 PP

  == domain 2  score: 60.4 bits;  conditional E-value: 4.4e-20
                              EamA   2 lgillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvla 78 
                                       lg +l+lla l+wai   lsk l+ k + + +t +  l++g++lli+a l e +l   +l+++ +++ +g++++ + 
  gi|242399686|ref|YP_002995111.1| 165 LGNILILLAGLSWAIDNNLSKLLSVKRDLFLVTSLKGLFGGAALLILASLVEVSL-HVPLQSIPYVFTVGAFSIGFS 240
                                       799****************************************************.********************* PP

                              EamA  79 fllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                        +lf+ al++++a + + i+s++ ++ +i+++l+lge++t  + +  vl+++Gv++++
  gi|242399686|ref|YP_002995111.1| 241 LVLFLFALREIGAMKTGAIFSTSSLVGAIFAFLVLGESFTTVKAFFGVLMFIGVYILS 298
                                       *******************************************************987 PP

>> EmrE  Putative multidrug resistance efflux transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2  10.3     1e-08   4.5e-05      40     232 ..      86     279 ..      46     299 .. 0.66

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1e-08
                              EmrE  40 iGfglfYallcfaaayapgWlvAatwq..itivagllllplfkrkkiplkalllsllillGvvlvqleeakelslke 114
                                       + fg f  +l+f     ++  v a     +  + ++l+++l+ ++k   ++ +  llil+G v++ +e+ +e++l++
  gi|242399686|ref|YP_002995111.1|  86 VLFGSFLGPLSFMFGLNNTTAVNASLLlnTETLFTVLIALLVFKEKASRRSGIGILLILIGTVVISTENFREVELSK 162
                                       45666666666655555555444443301335666777766669********************************* PP

                              EmrE 115 lllgvlpvlvaafaYPlGnrkvleassgk...............................ldafqrvllmtlgslPf 160
                                        llg + +l+a +++ + n +   +s ++                               l+++  v+ +   s+ f
  gi|242399686|ref|YP_002995111.1| 163 GLLGNILILLAGLSWAIDNNLSKLLSVKRdlflvtslkglfggaallilaslvevslhvpLQSIPYVFTVGAFSIGF 239
                                       *******************9766555555445655666666666666665555555555555555555555555555 PP

                              EmrE 161 wlilaligliqpglpsasqvlqt..llvAllsgviAtvlFlkAtdlakkdsselaaveatQasevifaligeil 232
                                        l+l l++l + g+ +++ +++t  l+ A+++ +                                  ++ge +
  gi|242399686|ref|YP_002995111.1| 240 SLVLFLFALREIGAMKTGAIFSTssLVGAIFAFL----------------------------------VLGESF 279
                                       5555555555555555555554311223444433..................................334444 PP

>> PUNUT  Purine nucleobase transmembrane transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1      0.41   1.8e+03     164     189 ..       5      30 ..       3      52 .. 0.70
   2 !   15.5   4.3   1.7e-06    0.0075      47     174 ..      48     175 ..      36     190 .. 0.69
   3 ?    1.1   6.8     0.042   1.9e+02      83     147 ..     235     299 ..     211     300 .] 0.85

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.41
                             PUNUT 164 igfiltlaasllfaLlLslvellfek 189
                                       +g++ ++ a+ lf+++  l +++ + 
  gi|242399686|ref|YP_002995111.1|   5 YGYVSAVLAAFLFGISSTLNKIALRD 30 
                                       67777788888887776666555554 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.7e-06
                             PUNUT  47 llpllllllskkrkq....kettssslslkklvllyivlGllvavdnllyslgllylpvstfslilatqLaFtaifs 119
                                       l++l +++ +++  +      +t++s+s + +v+l+ v+ + +++  l + +gl++  +  +sl+l t  +Ft +++
  gi|242399686|ref|YP_002995111.1|  48 LMLLRFTPVKERILKkfesGVKTQESFSGRDIVILAFVVLFGSFLGPLSFMFGLNNTTAVNASLLLNTETLFTVLIA 124
                                       33334443333322224445677777777777777665544444444445567777777789*************** PP

                             PUNUT 120 alinkqkftrfiinsvvlltisaallalssssdkpaeeskkkyvigfiltlaasl 174
                                        l+ k k  r + + ++l+ i++++++++++ +     + +k + g il l a+l
  gi|242399686|ref|YP_002995111.1| 125 LLVFKEKASRRSGIGILLILIGTVVISTENFREV----ELSKGLLGNILILLAGL 175
                                       **************************97766543....33344566666666655 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.042
                             PUNUT  83 llvavdnllyslgllylpvstfslilatqLaFtaifsalinkqkftrfiinsvvlltisaallal 147
                                       + ++++ +l+ ++l ++ +     i++t+ +  aif++l+    ft + ++  vl+ i+ ++l+l
  gi|242399686|ref|YP_002995111.1| 235 FSIGFSLVLFLFALREIGAMKTGAIFSTSSLVGAIFAFLVLGESFTTVKAFFGVLMFIGVYILSL 299
                                       56788999999999999999999999999999****************99999999999999986 PP

>> TMEM234  Putative transmembrane family 234
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   1.1   6.7e-06      0.03      56     115 ..      92     150 ..      56     151 .. 0.87
   2 ?   -1.3   6.3      0.47   2.1e+03      59     114 ..     242     296 ..     170     298 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.7e-06
                           TMEM234  56 sgSvlfflllgkadlslavpiaNslafvfTvltelllgekvlkkktvlgmllvvvgialc 115
                                       +g + f++ l+++    a+ + N+ + +fTvl++ll+ ++  ++++ +g+ll+++g++++
  gi|242399686|ref|YP_002995111.1|  92 LGPLSFMFGLNNTTAVNASLLLNT-ETLFTVLIALLVFKEKASRRSGIGILLILIGTVVI 150
                                       577889999999999999999997.6799*****999999999**************987 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.47
                           TMEM234  59 vlfflllgkadlslavpiaNslafvfTvltelllgekvlkkktvlgmllvvvgial 114
                                       vlf ++l+++    + +i  + + v  +   l+lge +++ k++ g+l+ ++g+++
  gi|242399686|ref|YP_002995111.1| 242 VLFLFALREIGAMKTGAIFSTSSLVGAIFAFLVLGESFTTVKAFFGVLM-FIGVYI 296
                                       6777788877776666666555555555566999999999999999866.456555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       797  (0.0444531); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.66u 0.33s 00:00:00.99 Elapsed: 00:00:00.55
# Mc/sec: 1648.53
//
Query:       gi|242399687|ref|YP_002995112.1|  [L=74]
Description: Mercury ion binding protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.7e-11   43.0   0.9    8.2e-11   42.2   0.9    1.4  1  HMA       Heavy-metal-associated domain
     0.0062   16.3   0.1       0.01   15.7   0.1    1.4  1  TusA      Sulfurtransferase TusA
  ------ inclusion threshold ------
      0.025   14.9   0.3          2    8.8   0.1    2.4  2  Fer2_BFD  BFD-like [2Fe-2S] binding domain


Domain annotation for each model (and alignments):
>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.2   0.9   1.4e-14   8.2e-11       1      62 []       7      66 ..       7      66 .. 0.94

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 1.4e-14
                               HMA  1 tvrvsgmhCagCaakvekvLselpgVesvkvdlatktvtVegdaestklrkiieaiekagyk 62
                                      ++++++m C +C+ +++k+++++ g  + +v l++k+++Ve+d+ +++l +ii+ai+  gy+
  gi|242399687|ref|YP_002995112.1|  7 VLKIPNMSCKHCVMRITKAIERV-GA-KGEVTLEEKKAVVEFDPGKVTLDDIINAIKRYGYE 66
                                      589*****************887.55.9999***************999***********97 PP

>> TusA  Sulfurtransferase TusA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   1.7e-06      0.01       7      57 ..      12      69 ..       6      73 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.7e-06
                                      T-STTCCHHHHHHHHCCC.GCT-EEE......EEESSCHHH.HHHHHHHHHHTEEEEEE CS
                              TusA  7 GlvCPePllklkkalekl.eegevle......vladdpaat.ediprfakklghelvev 57
                                      +++C  +++++ ka+e++ + gev        v +d    t  di +  k+ g+e ve+
  gi|242399687|ref|YP_002995112.1| 12 NMSCKHCVMRITKAIERVgAKGEVTLeekkavVEFDPGKVTlDDIINAIKRYGYE-VEI 69
                                      799***************888877745677779999988888*************.666 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 ?    8.8   0.1   0.00033         2      27      50 ..       3      27 ..       1      38 [. 0.89
   2 ?    4.6   0.0    0.0072        43       7      20 ..      50      63 ..      49      71 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00033
                          Fer2_BFD 27 evkrrtkagtg.CggCrpaieeiLa 50
                                       vk+ +k ++  C+ C+ +i + ++
  gi|242399687|ref|YP_002995112.1|  3 MVKAVLKIPNMsCKHCVMRITKAIE 27
                                      589999999999********99876 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0072
                          Fer2_BFD  7 gvtegeIrdairra 20
                                      +vt ++I++ai+r 
  gi|242399687|ref|YP_002995112.1| 50 KVTLDDIINAIKRY 63
                                      6999*******885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       821  (0.0457917); expected 358.6 (0.02)
Passed bias filter:                      644  (0.0359195); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 425.77
//
Query:       gi|242399688|ref|YP_002995113.1|  [L=38]
Description: hypothetical protein TSIB_1713 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       248  (0.0138323); expected 358.6 (0.02)
Passed bias filter:                      190  (0.0105974); 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 0.30s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 242.13
//
Query:       gi|242399689|ref|YP_002995114.1|  [L=124]
Description: hypothetical protein TSIB_1714 [Thermococcus sibiricus MM 739]
Scores for complete 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   23.2   0.0    9.6e-05   22.2   0.0    1.6  2  DUF302    Domain of unknown function DUF302


Domain annotation for each model (and alignments):
>> DUF302  Domain of unknown function DUF302
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   5.4e-09   9.6e-05      16      54 ..      48      87 ..      36      94 .. 0.88
   2 ?   -3.0   0.0       0.4   7.2e+03      51      63 .]     100     112 ..      97     112 .. 0.72

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 5.4e-09
                                      S-EEEEEEE-HHHHHHHHCC-GGGGGG-SEEEEEEE.ETT CS
                            DUF302 16 rpykilgaCnPklatealqadpeiglllPcrvvVye.kdg 54
                                       +y++l +C+ +l +e+++ dp ig+l Pc    y+ +dg
  gi|242399689|ref|YP_002995114.1| 48 ADYHLLFICDKELVAELVKIDPNIGALFPCTGFGYRrEDG 87
                                      68****************************9888887776 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.4
                                       EETTEEEEEEE-H CS
                            DUF302  51 ekdgkttvsyvdP 63 
                                       + +g+ +v+ ++P
  gi|242399689|ref|YP_002995114.1| 100 KIAGERVVELMRP 112
                                       5567888898887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        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: 734.85
//
Query:       gi|242399690|ref|YP_002995115.1|  [L=140]
Description: CoA-binding domain protein [Thermococcus sibiricus MM 739]
Scores for complete 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-34  116.5   0.0    9.8e-34  116.3   0.0    1.0  1  CoA_binding_2   CoA binding domain
    4.2e-12   46.6   0.0    5.9e-12   46.1   0.0    1.1  1  CoA_binding     CoA binding domain
     0.0023   17.5   0.1     0.0042   16.6   0.1    1.5  1  ABC_transp_aux  ABC-type uncharacterized transport system
  ------ inclusion threshold ------
      0.039   14.4   0.1        0.1   13.0   0.1    1.7  1  Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domai
      0.048   14.5   0.0      0.084   13.7   0.0    1.6  1  GFO_IDH_MocA    Oxidoreductase family, NAD-binding Rossmann f
      0.052   13.8   0.1       0.16   12.2   0.0    1.8  2  SpoU_sub_bind   RNA 2'-O ribose methyltransferase substrate b
       0.09   12.9   0.0       0.16   12.1   0.0    1.5  1  DpaA_N          Dipicolinate synthase subunit A N-terminal do


Domain annotation for each model (and alignments):
>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.3   0.0   3.8e-37   9.8e-34       1     114 [.      17     130 ..      17     132 .. 0.98

  Alignments for each domain:
  == domain 1  score: 116.3 bits;  conditional E-value: 3.8e-37
                                       --EEEET--S-TTSHHHHHHHHHHHHT--EEEESSS-SEETTEES----T....T--EEEE-S-HHHHGGGHHHHHH CS
                     CoA_binding_2   1 rtiaVvGasdnpgkfgykvlryllehglpvvpVnpkeeeilgekvyaslaedpepvdlvdvftppeatpeivkeala 77 
                                       ++ia+vGa +n++k+g+ +l+ l ++g++v+pVnp+++ei+g k+y+s++e p++vd++++++pp++  +++kea++
  gi|242399690|ref|YP_002995115.1|  17 KKIALVGATKNSTKYGNIILKDLINKGFEVLPVNPNYDEIEGLKCYRSVKEIPKEVDVIVFVLPPKVGIQVAKEAVE 93 
                                       68************************************************968************************ PP

                                       H--SEEEE-TT---HHHHHHHHHTT-EEE.ES-HHHH CS
                     CoA_binding_2  78 lgakavwlqpgsedeeaaelaeeagirvvgdrCilve 114
                                       +g k +w+qpg+e+ee+ e++e+ag+++   rCi+ve
  gi|242399690|ref|YP_002995115.1|  94 AGFKKLWFQPGAESEEIREFLEKAGVEYSFGRCIMVE 130
                                       ************************************9 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.1   0.0   2.3e-15   5.9e-12       4      91 ..      17     100 ..      14     102 .. 0.91

  Alignments for each domain:
  == domain 1  score: 46.1 bits;  conditional E-value: 2.3e-15
                                       EEEEEETTTSHHHHHHHHHHHHHHECEEEEEEC-TTTTTCEETTEEEESCHHHHHHHCTTTEEEEES-HHHHHHHHH CS
                       CoA_binding   4 tkviviGagglgiaglyhfkeklkygikavfgvnprkvgtevlglpvyksvdeleektevdvavitvPaesaqeavd 80 
                                       +k++++Ga+++ ++ +  + ++l  +  +v +vnp+  ++e++gl++y sv+e++++  vdv v ++P++   ++++
  gi|242399690|ref|YP_002995115.1|  17 KKIALVGATKNSTKYGNIILKDLINKGFEVLPVNPN--YDEIEGLKCYRSVKEIPKE--VDVIVFVLPPKVGIQVAK 89 
                                       79**************55555555577789******..*******************..****************** PP

                                       HHHHTT-SEEE CS
                       CoA_binding  81 elveagikgiv 91 
                                       e+veag k  +
  gi|242399690|ref|YP_002995115.1|  90 EAVEAGFKKLW 100
                                       ******99876 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 !   16.6   0.1   1.6e-06    0.0042     138     204 ..       7      82 ..       5     125 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.6e-06
                    ABC_transp_aux 138 airkltdkkkpkvgfltghgelslsspse.adfleeleenYnveevdldsedi...........lpedidvlviakp 202
                                       ++rk+++k+ +k++++ g  + s++  +    ++++++++++v +v+++ ++i           +p+++dv+v + p
  gi|242399690|ref|YP_002995115.1|   7 LVRKMNHKEFKKIALV-GATKNSTK--YGnIILKDLINKGFEVLPVNPNYDEIeglkcyrsvkeIPKEVDVIVFVLP 80 
                                       799*************.34433333..343678899999**********************9999*********988 PP

                    ABC_transp_aux 203 tk 204
                                       +k
  gi|242399690|ref|YP_002995115.1|  81 PK 82 
                                       86 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   4.1e-05       0.1      47      92 ..      52      97 ..       5     101 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.1e-05
                                      GGTTTECEBEEEGGGGGCTT-SEEEE-SCHHHHHHHHHHHHHTTSE CS
                    Semialdhyde_dh 47 aleegkdlkvedvdeeelkevdivflalpagvskelapklaeagvk 92
                                      + +e++ lk+    +e+ kevd++++ lp +v  ++a++++eag+k
  gi|242399690|ref|YP_002995115.1| 52 NYDEIEGLKCYRSVKEIPKEVDVIVFVLPPKVGIQVAKEAVEAGFK 97
                                      667777777777777788*************************985 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   3.3e-05     0.084      46      88 ..      57      97 ..      17     124 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.3e-05
                                      TTHEEESSHHHHHTCTTESEEEE-S-GGGHHHHHHHHHHTT-E CS
                      GFO_IDH_MocA 46 fgveaysdleelladpeidavivatpngtheelakaaleagkh 88
                                       g+++y +++e+++  e+d+++ + p++ + ++ak+a+eag +
  gi|242399690|ref|YP_002995115.1| 57 EGLKCYRSVKEIPK--EVDVIVFVLPPKVGIQVAKEAVEAGFK 97
                                      4778**********..************************975 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 ?   -1.4   0.0       1.1   2.9e+03      15      32 ..      13      31 ..       8      52 .. 0.51
   2 ?   12.2   0.0   6.4e-05      0.16       4      46 ..      84     121 ..      83     123 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.1
                     SpoU_sub_bind 15 grriekl.lvtegradkrl 32
                                      +++++k+ lv  +++  ++
  gi|242399690|ref|YP_002995115.1| 13 HKEFKKIaLVGATKNSTKY 31
                                      4555665444444555554 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 6.4e-05
                     SpoU_sub_bind   4 GlhaVleaLksgrriekllvtegradkrleellklakkrgikv 46 
                                       G++   ea ++g  ++kl++++g++ +   e+ + ++k+g+++
  gi|242399690|ref|YP_002995115.1|  84 GIQVAKEAVEAG--FKKLWFQPGAESE---EIREFLEKAGVEY 121
                                       888889999999..*********4444...6777777778877 PP

>> DpaA_N  Dipicolinate synthase subunit A N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   6.2e-05      0.16      14      60 ..      35      80 ..      33      99 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.2e-05
                                      HHHHHHHTT-EEEEES-TSSS-BTTEEEE-GGGS-GGG-SEEE--TT CS
                            DpaA_N 14 larkLaekgakvslygleleekiegvekaesleealedadviilPvp 60
                                      + + L++kg++v  +   + ++ieg++++ s++e  +++dvi++ +p
  gi|242399690|ref|YP_002995115.1| 35 ILKDLINKGFEVLPVNP-NYDEIEGLKCYRSVKEIPKEVDVIVFVLP 80
                                      568899******99988.99**********************98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 845.83
//
Query:       gi|242399691|ref|YP_002995116.1|  [L=285]
Description: FTR1 family protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-63  214.8  19.8    1.9e-63  214.5  19.8    1.0  1  FTR1          Iron permease FTR1 family
     0.0075   16.6   0.3     0.0075   16.6   0.3    2.5  3  DUF2919       Protein of unknown function (DUF2919)
  ------ inclusion threshold ------
      0.012   14.9   3.1      0.012   14.9   3.1    2.5  2  Peptidase_U4  Sporulation factor SpoIIGA


Domain annotation for each model (and alignments):
>> FTR1  Iron permease FTR1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  214.5  19.8   3.1e-67   1.9e-63       2     303 ..       3     263 ..       2     267 .. 0.98

  Alignments for each domain:
  == domain 1  score: 214.5 bits;  conditional E-value: 3.1e-67
                              FTR1   2 faiflvvlregleaslivsvllallkqtqretdklqvwagialavllalaigqafasitaalqkdkalieeellegv 78 
                                       ++ fl+++re+lea++iv++++ +l +t+re++ + vw+g+ l+vl ++ +g+ + +++++l+      e+el+eg+
  gi|242399691|ref|YP_002995116.1|   3 VGAFLITFREALEAAIIVAIIIVYLRRTGREKQIKDVWTGVGLSVLVSIVLGAVILKLYGGLA------EKELFEGI 73 
                                       678************************************************************......9******* PP

                              FTR1  79 lsliavvviswmilwmrrvgkklkeeveqklakavaeiknrekaaqkgekgsekwalfilsFlivlREGlEavLfva 155
                                       +s++av+v++ mi+wm+++gk+lk+e+e+k+ +a+++i                 al++++F++v+REGlE+vLf++
  gi|242399691|ref|YP_002995116.1|  74 ASYLAVIVLTSMIYWMATKGKNLKAEIERKVGEAISSI-----------------ALIVFTFVVVFREGLETVLFLT 133
                                       ***********************************966.................********************** PP

                              FTR1 156 aivaytvkrvsalilgvvlGaliavvlglliyrglvklslqsffilegflLllvaagLfsvgtlellekaeacngkd 232
                                       ++ +++      +++g +lG + a++l++liy ++++++l++ff+++++lL+lvaagL ++gt+el e+ae+ +g  
  gi|242399691|ref|YP_002995116.1| 134 PFATQDL---GGTLAGLLLGSISALILAYLIYGVGMRINLRTFFYYSSILLVLVAAGLAGYGTHELIEWAEE-EGMH 206
                                       *******...89************************************************************.**** PP

                              FTR1 233 yiefkkskslskisllslllvaflaveregleivlaliGwantgplglivyaavwlvvlillgllliklgv 303
                                        + ++  ++ + i++ s+ ++   ++++++  i+ +l+G++++         ++w +vl+++g+ll++l +
  gi|242399691|ref|YP_002995116.1| 207 LGFIEEPAYDLGIPKDSVFHH---KGAIGS--IFAVLFGYSVK---------MEWGRVLVQFGYLLVALYL 263
                                       *********************...******..***********.........**************99755 PP

>> DUF2919  Protein of unknown function (DUF2919)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.3   1.3e-06    0.0075      64     137 ..      17      91 ..       9      99 .. 0.81
   2 ?   -0.1   0.3      0.17     1e+03      59      96 ..     146     183 ..     107     203 .. 0.54
   3 ?   -1.8   0.0       0.6   3.6e+03      79     100 ..     244     265 ..     229     271 .. 0.54

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.3e-06
                           DUF2919  64 vpalllllligrrkkssewleklwragrplllllllv.dlllqlyrlalsheafswltaltlllllwvllyllks 137
                                       ++++ ++++  rr  +++ ++ +w+     +l+++++  ++l+ly    ++e f+ ++   ++++l +++y++  
  gi|242399691|ref|YP_002995116.1|  17 AIIVAIIIVYLRRTGREKQIKDVWTGVGLSVLVSIVLgAVILKLYGGLAEKELFEGIASYLAVIVLTSMIYWMAT 91 
                                       4455566888899999999999999877555555555499999*************************9999865 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.17
                           DUF2919  59 gLalgvpallll..lligrrkkssewleklwragrpllll 96 
                                       gL+lg ++ l+l  l+ g     +  l++ + +   ll+l
  gi|242399691|ref|YP_002995116.1| 146 GLLLGSISALILayLIYGVG--MRINLRTFFYYSSILLVL 183
                                       44444444333322333222..233344444444444444 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.6
                           DUF2919  79 ssewleklwragrplllllllv 100
                                       + ew + l++ g+ l+ l+l++
  gi|242399691|ref|YP_002995116.1| 244 KMEWGRVLVQFGYLLVALYLVL 265
                                       3556666666666555555554 PP

>> Peptidase_U4  Sporulation factor SpoIIGA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   3.1     2e-06     0.012      64     131 ..      16      92 ..       3     115 .. 0.78
   2 ?   -3.2   6.7      0.67     4e+03      59     136 ..     148     199 ..     104     272 .. 0.53

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2e-06
                      Peptidase_U4  64 lkilvsllmvli..afgpkslkeflkalllfylvsfllgGilfalsylllkskn........llvlllgalvaylll 130
                                       + i+v++++v++  + + k++k+++ +++l +lvs++lg +++ l+   l+ k+        l+v++l+ ++ ++ +
  gi|242399691|ref|YP_002995116.1|  16 AAIIVAIIIVYLrrTGREKQIKDVWTGVGLSVLVSIVLGAVILKLYG-GLAEKElfegiasyLAVIVLTSMIYWMAT 91 
                                       45788888887766688999**************************9.55555567788887888888888888888 PP

                      Peptidase_U4 131 k 131
                                       k
  gi|242399691|ref|YP_002995116.1|  92 K 92 
                                       7 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 0.67
                      Peptidase_U4  59 llsillkilvsllmvliafgpkslkeflkalllfylvsfllgGilfalsylllksknllvlllgalvaylllkllvk 135
                                       ll  ++ +++++l+  + ++++  + f                              +l++l++a++a ++++ l++
  gi|242399691|ref|YP_002995116.1| 148 LLGSISALILAYLIYGVGMRINLRTFFYYSS--------------------------ILLVLVAAGLAGYGTHELIE 198
                                       2222333333333333333333333333333..........................33344444444433333333 PP

                      Peptidase_U4 136 i 136
                                       +
  gi|242399691|ref|YP_002995116.1| 199 W 199
                                       3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       851  (0.047465); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); 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):               3  [number of targets reported over threshold]
# CPU time: 0.65u 0.36s 00:00:01.01 Elapsed: 00:00:00.56
# Mc/sec: 1528.37
//
Query:       gi|242399692|ref|YP_002995117.1|  [L=192]
Description: Alkyl hydroperoxide reductase subunit c [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.6e-40  135.7   0.0    9.3e-40  135.4   0.0    1.1  1  AhpC-TSA       AhpC/TSA family
    9.9e-20   70.8   0.0    1.2e-19   70.5   0.0    1.1  1  Redoxin        Redoxin
    1.3e-05   24.9   0.0    2.8e-05   23.9   0.0    1.6  1  1-cysPrx_C     C-terminal domain of 1-Cys peroxiredoxin
    0.00067   19.6   0.0     0.0013   18.7   0.0    1.5  1  SCO1-SenC      SCO1/SenC
     0.0034   17.5   0.0     0.0052   16.9   0.0    1.3  1  AhpC-TSA_2     AhpC/TSA antioxidant enzyme
     0.0071   16.7   0.0      0.012   15.9   0.0    1.4  1  Thioredoxin_8  Thioredoxin-like
  ------ inclusion threshold ------
      0.027   15.0   0.0      0.069   13.6   0.0    1.9  1  DUF3471        Domain of unknown function (DUF3471)
       0.12   12.4   0.2       0.24   11.5   0.2    1.4  1  UvsW           ATP-dependant DNA helicase UvsW


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 !  135.4   0.0   4.2e-43   9.3e-40       1     122 [.       7     137 ..       7     139 .. 0.97

  Alignments for each domain:
  == domain 1  score: 135.4 bits;  conditional E-value: 4.2e-43
                                       TTSB----EEE.....STTCEEEECHHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHH CS
                          AhpC-TSA   1 vgdkapdfelk.....nadgetvslsdykgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspes 72 
                                       vg+ +pdfe++     + + ++ ++sdy+gk+v+l fyp+d+++vC+tel++lak+yeefk++g+e+i vs+d+ + 
  gi|242399692|ref|YP_002995117.1|   7 VGETVPDFEANayfpeKDEIGKLRFSDYRGKWVILAFYPADFTFVCPTELEELAKYYEEFKKEGAEIISVSTDTAYV 83 
                                       799**********9988889********************************************************* PP

                                       HHHHHHH-H.....SSEEEE-TTSHHHHHTT-EETTTTECSCEEEEE-TTSBEE CS
                          AhpC-TSA  73 hkkfiekes....lnfpllsDeegkvakaygvlkeekglalratfvidkegkir 122
                                       hk+++++      +++p+l+D+ gk+++ +g + e++g+ +ratf+id++gk++
  gi|242399692|ref|YP_002995117.1|  84 HKAWHDTSPsikkIKYPMLADPAGKISRLFGTYIEDEGVSWRATFIIDPDGKVV 137
                                       *******999999***************************************97 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.5   0.0   5.2e-23   1.2e-19       2     138 ..       7     147 ..       6     157 .. 0.90

  Alignments for each domain:
  == domain 1  score: 70.5 bits;  conditional E-value: 5.2e-23
                                       TTSBB---E....CCEETTCEEEEEHHHHTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSH CS
                           Redoxin   2 agdkaPdft....lplaatdgnsvslsefkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadnda 74 
                                       +g+++Pdf+    +p+ +++  ++  s+++gk v++ f+p+ f+ +C +e+ +l+k++e++k++g +++ v++d+ a
  gi|242399692|ref|YP_002995117.1|   7 VGETVPDFEanayFPE-KDEIGKLRFSDYRGKWVILAFYPADFTFVCPTELEELAKYYEEFKKEGAEIISVSTDT-A 81 
                                       7999*****9999777.6788899********************************************9998876.7 PP

                                       HHHHHHHH.....TT-TSEEEE-TTSHHHHHTT-TTEEE.GGGEEE-EEEEEEETTEEEEEEESSSCHT CS
                           Redoxin  75 fvkefwgk.....eglkfpvlsDgsaaftkalGlrleedaseglrtpryavidedgkvvylevepepet 138
                                       +v ++w +     +++k+p+l+D+ +++++ +G ++e    eg+  +++++id dgkvv ++ ++++ +
  gi|242399692|ref|YP_002995117.1|  82 YVHKAWHDtspsiKKIKYPMLADPAGKISRLFGTYIED---EGVSWRATFIIDPDGKVVSMHIHDNSIG 147
                                       9********************************99764...56899******************99854 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 !   23.9   0.0   1.2e-08   2.8e-05       3      31 ..     161     187 ..     159     191 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 1.2e-08
                                       HHHHHH.T-BB-TTT.TBT-EEE---SSHH CS
                        1-cysPrx_C   3 Qladkh.gvatPAnWkpGdkvivpPpatee 31 
                                       +++ +h g ++PA W pG++++   +++ +
  gi|242399692|ref|YP_002995117.1| 161 KYVREHpGQVCPASWEPGKETL---KVSLD 187
                                       68999*999*************...98876 PP

>> SCO1-SenC  SCO1/SenC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   5.6e-07    0.0013      17      67 ..      32      80 ..      22      96 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 5.6e-07
                         SCO1-SenC 17 edlegkpslvffgFthCpdvCpttlanmaevldalgeeaekvqplfiTvDP 67
                                      +d++gk++++ f  +  + vCpt+l+++a++++++++e+   ++++++ D 
  gi|242399692|ref|YP_002995117.1| 32 SDYRGKWVILAFYPADFTFVCPTELEELAKYYEEFKKEG--AEIISVSTDT 80
                                      799***********************************5..5667777775 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 !   16.9   0.0   2.3e-06    0.0052       2      80 ..      59     160 ..      58     174 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.3e-06
                        AhpC-TSA_2   2 Lsrdkpeldaagvklvaigigdp.sakkFvkl....tgfpfelyvDpsaklyqalglk..................r 55 
                                       L+++ +e++++g +++ ++ +++   k++ +      ++++++++Dp +k+ +++g +                  +
  gi|242399692|ref|YP_002995117.1|  59 LAKYYEEFKKEGAEIISVSTDTAyVHKAWHDTspsiKKIKYPMLADPAGKISRLFGTYiedegvswratfiidpdgK 135
                                       8999*******************55*****999999999*******************9999999999999999888 PP

                        AhpC-TSA_2  56 glklklaplslqkalenllkrlkei 80 
                                         +++++ +s+ +  +++l++l++ 
  gi|242399692|ref|YP_002995117.1| 136 VVSMHIHDNSIGRSAKEILRMLRAS 160
                                       8888888888888888888888776 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   5.5e-06     0.012       1      95 []      36     136 ..      36     136 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5.5e-06
                                       .SEEEEEE-.-SSSHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-SS-..HHHHHHHGGGS-TTSEE.EE-TT-HHHH CS
                     Thioredoxin_8   1 gkvvlLyfg.aswcppckaftpklkelyeklkkkkkveivyvsldkk..eeefekylkknkkpwlsvpfddkkrnkl 74 
                                       gk+v+L f+ a++   c + +++l ++ye++k k + ei++vs d     ++++++  +   + + +p   +   k+
  gi|242399692|ref|YP_002995117.1|  36 GKWVILAFYpADFTFVCPTELEELAKYYEEFK-KEGAEIISVSTDTAyvHKAWHDTSPSI--KKIKYPMLADPAGKI 109
                                       5788887764778889***************9.7***********753368888888888..788888777777777 PP

                                       TT-S--TT......-SEEEEE-TT-BE CS
                     Thioredoxin_8  75 kkkynvka......iPtlvvldkngev 95 
                                        + +++        +  ++++d++g+v
  gi|242399692|ref|YP_002995117.1| 110 SRLFGTYIedegvsWRATFIIDPDGKV 136
                                       777775444566667777777777765 PP

>> DUF3471  Domain of unknown function (DUF3471)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   3.1e-05     0.069      68      89 ..     121     142 ..      65     153 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.1e-05
                           DUF3471  68 eadakveFeldedgkvtrltlk 89 
                                        ++++++F++d+dgkv +++++
  gi|242399692|ref|YP_002995117.1| 121 GVSWRATFIIDPDGKVVSMHIH 142
                                       56899****************9 PP

>> UvsW  ATP-dependant DNA helicase UvsW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   0.00011      0.24      10      29 ..      56      74 ..      51      81 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00011
                                      HHHHHHHHHHHTTT..S--T CS
                              UvsW 10 lvElEklYkkkkKElGaelk 29
                                      l+El k+Y   kKE Gae+ 
  gi|242399692|ref|YP_002995117.1| 56 LEELAKYYEEFKKE-GAEII 74
                                      89************.***95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); 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: 0.58u 0.34s 00:00:00.92 Elapsed: 00:00:00.52
# Mc/sec: 1105.18
//
Query:       gi|242399693|ref|YP_002995118.1|  [L=188]
Description: NADPH-dependent FMN reductase, [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-27   96.5   0.0    1.7e-27   96.1   0.0    1.2  1  FMN_red       NADPH-dependent FMN reductase
    5.7e-08   32.7   0.0    1.3e-07   31.5   0.0    1.7  1  Flavodoxin_2  Flavodoxin-like fold
  ------ inclusion threshold ------
      0.031   14.5   0.0       0.12   12.6   0.0    2.0  1  Flavodoxin_5  Flavodoxin domain
      0.059   13.6   0.0       0.89    9.8   0.0    2.3  1  Flavodoxin_1  Flavodoxin
       0.17   11.9   0.0       0.35   10.9   0.0    1.5  1  Lin0512_fam   Conserved hypothetical protein (Lin0512_fam)
          2    9.0   3.9       0.69   10.4   0.4    2.0  2  COMP          Cartilage oligomeric matrix protein


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 !   96.1   0.0   5.5e-31   1.7e-27       1     148 [.       1     135 [.       1     140 [. 0.94

  Alignments for each domain:
  == domain 1  score: 96.1 bits;  conditional E-value: 5.5e-31
                                       -EEEEEES--STT-HHHHHHHHHHCCT-T.T-CEEEEETTTS.--..---HCHGHTCGGSHHHHHHHHHHHH-SCEE CS
                           FMN_red   1 mkilvisGSlrkgsntrklaewaaealkeagaevelidladlilpcalcdkdlesegqtsddvaellekiaaadali 77 
                                       mk+ vi G++r+ ++++k+a+++ + ++e ++++elid++d+ l   +++  +    +  +++++ ++ki +ad li
  gi|242399693|ref|YP_002995118.1|   1 MKLKVILGTARESRKSEKVANYIVRKAQELDLKTELIDVKDY-LL--AYTHRW----KITPEMERYRKKIIEADSLI 70 
                                       8999*************************************9.66..788777....49****************** PP

                                       EEEEECTTCE-HHHHHHHHCHT-.SSCHCCTT-EEEEEEE-SSTTTTHHHHHHHHHHHHHTT-EEEECSEE CS
                           FMN_red  78 ivtPeYngsysgllKnalDrlsrtrgkkelrgKpvalvavgggrrgglraeeqlrqvlaelgaivvpraav 148
                                       iv PeYngsy+g lK +lD +     ++e ++ pv++v+v+  + gg+r+ ++lr ++ + ++ +v+++ +
  gi|242399693|ref|YP_002995118.1|  71 IVAPEYNGSYPGELKILLDTI-----YDEYEALPVGIVTVS-VVTGGMRLLQELRLAALNYKMLPVGQVLF 135
                                       *********************.....9***********888.78*********************998655 PP

>> Flavodoxin_2  Flavodoxin-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.0   4.3e-11   1.3e-07       1     109 [.       1      97 [.       1     160 [. 0.89

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 4.3e-11
                                       -EEEEEE--TTGGCCHHHCHHHHHHHHHCCCTTTEEEEEEHHCCT-----CCCCHCCHHHHTT.CHHHHHHH.HHHH CS
                      Flavodoxin_2   1 mkiLiinahprpeksfssalaqafvealekagphevtvrdLyadflpvlttrdlaaklayeek.padveseq.iekl 75 
                                       mk+ +i +  r+ + +s ++a+ +v+++++ +  + + +d+ +          l   lay +  ++  e+e+  +k+
  gi|242399693|ref|YP_002995118.1|   1 MKLKVILGTARE-SRKSEKVANYIVRKAQELD-LKTELIDVKDY---------L---LAYTHRwKITPEMERyRKKI 63 
                                       888899999999.5888***************.99*******94.........2...36666656899999999*** PP

                                       HCSSEEEEEEE-BTTB--HHHHHHHHHHS-TTTS CS
                      Flavodoxin_2  76 laadaivlqfPlwwfgvPailKgwiDrvltagfa 109
                                        +ad +++++P ++ ++P  lK  +D ++    a
  gi|242399693|ref|YP_002995118.1|  64 IEADSLIIVAPEYNGSYPGELKILLDTIYDEYEA 97 
                                       **************************99876655 PP

>> Flavodoxin_5  Flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   4.1e-05      0.12      38      87 ..      60     109 ..      15     119 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.1e-05
                      Flavodoxin_5  38 sedlesydavvigasvyygkllpelakFvekhreaLstkpvalfsvslta 87 
                                       ++++ ++d  +i+a+ y+g+ ++el+ ++++  ++ ++ pv +++vs+++
  gi|242399693|ref|YP_002995118.1|  60 RKKIIEADSLIIVAPEYNGSYPGELKILLDTIYDEYEALPVGIVTVSVVT 109
                                       5788899****************************************985 PP

>> Flavodoxin_1  Flavodoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0    0.0003      0.89       9      90 ..      15     105 ..      10     152 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0003
                                       HHHHHHHHHHHHHHHTTTEEEEEEEEGTTSC..............GGGGGTHSEEEEEEEEETTTBEEGGGHHHHHH CS
                      Flavodoxin_1   9 nteklAkqlaeelgehgfnadvvslsdydes..............lseieeealllvvtsTfgnGdppengesffqd 71 
                                       ++ek+A+ + ++++e ++++++++++dy  +               ++i e + l++v++  +nG+ p + +   + 
  gi|242399693|ref|YP_002995118.1|  15 KSEKVANYIVRKAQELDLKTELIDVKDYLLAythrwkitpemeryRKKIIEADSLIIVAP-EYNGSYPGELKILLDT 90 
                                       799999999999999999999999999976666777776777777667777777777777.5558888766644444 PP

                                       HHHHHCHHGCCSTTTTEEE CS
                      Flavodoxin_1  72 llelkgdeledgdlsgvrf 90 
                                        ++++    e+ +   v++
  gi|242399693|ref|YP_002995118.1|  91 IYDEY----EALPVGIVTV 105
                                       44444....4455555555 PP

>> Lin0512_fam  Conserved hypothetical protein (Lin0512_fam)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00012      0.35      72      98 ..      96     123 ..      88     133 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00012
                       Lin0512_fam  72 avlPygevevevveGGldv.sgialeel 98 
                                       ++lP+g v+v+vv+GG++  + + l++l
  gi|242399693|ref|YP_002995118.1|  96 EALPVGIVTVSVVTGGMRLlQELRLAAL 123
                                       689**************99777666655 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       1.5   4.6e+03      14      21 ..     112     119 ..     112     120 .. 0.85
   2 ?   10.4   0.4   0.00023      0.69       4      30 ..     157     183 ..     154     186 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.5
                              COMP  14 tqllkeLr 21 
                                       ++ll+eLr
  gi|242399693|ref|YP_002995118.1| 112 MRLLQELR 119
                                       68999998 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00023
                              COMP   4 kqLlrqLseltqllkeLreelrqQvkE 30 
                                       + Llr L    ++lk +r+e+r+  +E
  gi|242399693|ref|YP_002995118.1| 157 ERLLRALEKYAKALKPIRDEVREKLRE 183
                                       789********************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1229  (0.0685482); expected 358.6 (0.02)
Passed bias filter:                      736  (0.0410508); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
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: 00:00:00.50
# Mc/sec: 1122.27
//
Query:       gi|242399694|ref|YP_002995119.1|  [L=377]
Description: SufBD protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-33  115.8   0.1      3e-33  115.4   0.1    1.2  1  UPF0051   Uncharacterized protein family (UPF0051)
  ------ inclusion threshold ------
       0.12   13.1   0.2        2.2    8.9   0.0    2.4  2  RHH_6     Ribbon-helix-helix domain


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 !  115.4   0.1   3.3e-37     3e-33      11     217 ..     141     349 ..     119     350 .. 0.87

  Alignments for each domain:
  == domain 1  score: 115.4 bits;  conditional E-value: 3.3e-37
                           UPF0051  11 eegaevtiieey..agcgvveifvg...enAklkyvkvqnwse.davnlstkraeegrdaklelttvslggkltrke 81 
                                        e+ +v ii  y  + +gv  ++++   ++A+l++++v ++++ + +     ra +g+  +++ +t+  ggk++ ++
  gi|242399694|ref|YP_002995119.1| 141 AENVKVPII-IYdmTEEGVKSFVIElkaRKAELELLTVGKHKSlSHYL---LRASLGGGTRVKAFTIISGGKMSHHR 213
                                       355666666.33544459999999866677889999888774423332...356789999***************** PP

                           UPF0051  82 psvelkgegaeaelnglylakgkqhldtrtkvdhngpntssrilskgvlkdearavfrgkikvrkgaqktdahqenr 158
                                        +  l+g+g+e+ l+g+ ++ g + +d+ t+v   g++t ++  ++g + +++ +v rg  kv +ga +++++++++
  gi|242399694|ref|YP_002995119.1| 214 EDYSLEGKGSELVLRGMPIGIG-SAVDYLTNVLQYGERTVGETRVHGFAYQNGWTVHRGVAKVFEGARGSSSEVSSH 289
                                       *********************9.78**************************************************** PP

                           UPF0051 159 nLllsdkaradtiPeleidaddvk.asHgAtvGkideeqlfYLmsRGlseeeArrlivrg 217
                                       ++ +++++   ++P+le+d++d++ asH ++v+++de++lfYL++RGl+++eA +l v+g
  gi|242399694|ref|YP_002995119.1| 290 VITMDKGSLGVSVPMLEVDTGDIEaASHSSSVSQFDEDALFYLRARGLTRKEALSLFVHG 349
                                       *********************************************************998 PP

>> RHH_6  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0     0.051   4.6e+02      36      54 ..     154     172 ..     151     184 .. 0.84
   2 ?    8.9   0.0   0.00025       2.2      11      54 ..     322     367 ..     316     377 .] 0.73

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.051
                             RHH_6  36 ieeAVrayllelaveeaka 54 
                                        ee V+++++el++ +a+ 
  gi|242399694|ref|YP_002995119.1| 154 TEEGVKSFVIELKARKAEL 172
                                       699**********998875 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00025
                             RHH_6  11 petdqavrafLAsqGggrkGdLSrfie...eAVrayllelaveeaka 54 
                                       +++d+    +L ++G  rk +LS f+    eA + +l  l+  +a++
  gi|242399694|ref|YP_002995119.1| 322 SQFDEDALFYLRARGLTRKEALSLFVHgigEALSDHLEKLR-SKARS 367
                                       47999999*****************7533378888775444.44455 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.64u 0.34s 00:00:00.98 Elapsed: 00:00:00.57
# Mc/sec: 2007.69
//
Query:       gi|242399695|ref|YP_002995120.1|  [L=475]
Description: SufB; FeS assembly protein SufB [Thermococcus sibiricus MM 739]
Scores for complete 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-62  208.9   0.1    9.2e-62  208.6   0.1    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 !  208.6   0.1   5.1e-66   9.2e-62       2     218 .]     219     444 ..     218     444 .. 0.97

  Alignments for each domain:
  == domain 1  score: 208.6 bits;  conditional E-value: 5.1e-66
                           UPF0051   2 qfertlivveegaevtiieeyagc............gvveifvgenAklkyvkvqnwsedavnlstkraeegrdakl 66 
                                       qfe+tl+v++eg+ v++i   +gc            g+vei++++nA++k++++qnws++++n+++kra  + +a +
  gi|242399695|ref|YP_002995120.1| 219 QFEHTLLVADEGSYVHFI---EGCsapmykgfsfhdGMVEIYAHKNATVKFTTIQNWSRNVINFNNKRAIIEDNAYV 292
                                       89****************...666666666777777*********************************9999**** PP

                           UPF0051  67 elttvslggkltrkepsvelkgegaeaelnglylakgkqhldtrtkvdhngpntssrilskgvlkdearavfrgkik 143
                                       e++++s+g+ +t+++ps++lkg+ +++  + + l++g    dt+ k  h g+ntss+i+sk+++++++ +++rg ++
  gi|242399695|ref|YP_002995120.1| 293 EWIEGSIGSMITYTYPSSVLKGDYSRTAQYVVSLSNGPFMKDTGAKSFHVGKNTSSKIVSKSISANGGINIYRGLVR 369
                                       ***************************************************************************** PP

                           UPF0051 144 vrkgaqktdahqenrnLllsdkaradtiPeleidaddvkasHgAtvGkideeqlfYLmsRGlseeeArrlivrgf 218
                                       +++ga+++ a +++++L+l+ ++ra+t P+ + d+  + + H+At+Gk++e++lfYL++RG++eeeA++liv gf
  gi|242399695|ref|YP_002995120.1| 370 IARGAENSTATVSCDSLILDGESRAYTYPHNQNDEPSASIIHEATTGKLSEDKLFYLNARGIKEEEAKSLIVLGF 444
                                       *************************************************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.68u 0.32s 00:00:01.00 Elapsed: 00:00:00.55
# Mc/sec: 2587.41
//
Query:       gi|242399696|ref|YP_002995121.1|  [L=243]
Description: ABC transporter ATPase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.6e-21   75.5   0.0    7.5e-21   75.1   0.0    1.2  1  ABC_tran        ABC transporter
    1.1e-10   41.8   0.2    1.2e-05   25.3   0.0    2.1  2  AAA_21          AAA domain, putative AbiEii toxin, Type IV TA
    1.5e-05   24.6   0.1      0.058   12.8   0.0    2.2  2  SMC_N           RecF/RecN/SMC N terminal domain
    0.00056   20.2   0.1     0.0055   17.0   0.1    2.2  1  AAA_22          AAA domain
    0.00061   19.7   0.1      0.002   18.1   0.0    1.8  2  RsgA_GTPase     RsgA GTPase
     0.0021   17.7   0.0     0.0046   16.6   0.0    1.6  2  AAA_25          AAA domain
     0.0033   17.5   0.0      0.014   15.4   0.0    2.0  2  AAA_14          AAA domain
     0.0035   17.1   0.0       0.39   10.4   0.0    2.3  2  IstB_IS21       IstB-like ATP binding protein
     0.0063   16.2   0.0      0.012   15.3   0.0    1.4  1  AAA_29          P-loop containing region of AAA domain
     0.0075   15.9   0.0      0.014   15.0   0.0    1.4  1  AAA_27          AAA domain
     0.0086   16.2   0.0      0.012   15.8   0.0    1.3  1  AAA_33          AAA domain
  ------ inclusion threshold ------
      0.011   14.4   0.0        1.2    7.7   0.0    2.2  2  AAA_13          AAA domain
      0.022   15.2   0.1      0.051   14.1   0.0    1.6  2  AAA_23          AAA domain
      0.034   13.9   0.1       0.11   12.2   0.0    1.8  2  AAA_24          AAA domain
      0.039   14.4   0.2       0.32   11.4   0.2    2.5  2  AAA             ATPase family associated with various cellula
      0.045   13.7   0.0       0.34   10.8   0.0    2.0  2  ATPase_2        ATPase domain predominantly from Archaea
       0.05   13.5   0.2       0.63    9.9   0.0    2.1  2  NACHT           NACHT domain
      0.056   13.8   0.0       0.12   12.7   0.0    1.9  1  AAA_16          AAA ATPase domain
      0.059   12.4   0.0      0.087   11.9   0.0    1.3  1  T2SSE           Type II/IV secretion system protein
      0.069   12.9   0.0        0.1   12.3   0.0    1.4  1  Cytidylate_kin  Cytidylate kinase
      0.074   13.6   0.0       0.15   12.6   0.0    1.7  1  AAA_18          AAA domain
      0.077   12.4   0.0       0.16   11.4   0.0    1.5  1  PhoH            PhoH-like protein
       0.15   12.1   0.2          9    6.3   0.0    2.3  2  MutS_V          MutS domain V
       0.17   12.1   0.0       0.27   11.5   0.0    1.3  1  AAA_28          AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.1   0.0     1e-23   7.5e-21       1     136 [.      19     169 ..      19     170 .. 0.84

  Alignments for each domain:
  == domain 1  score: 75.1 bits;  conditional E-value: 1e-23
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--..SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp..teGeilldgkdlke.qeleslrkeigvlpqepqlfpel 74 
                                       lk+++l +  ge+++++G+nG+GKStL+ ++ag+ k     G+i +d +d+++  ++e++r+ +   +q+p   +++
  gi|242399696|ref|YP_002995121.1|  19 LKDINLIVDDGELHVVMGPNGSGKSTLALTIAGHPKYqvIDGRIIFDVEDITNlPPEERVRRGVFLSFQHPVEVEGV 95 
                                       799******************************87665599************99***************9999999 PP

                                       BHHHH...........HHHTCHHHHHHHSTTGGTTCBGESTTS.GGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  75 tvren...........esdeeiekalsklglkelkdtvvkssp.ssLSgGqkqrvalarallkkpkllllDEpt 136
                                       +v +            ++ +  e + + ++  +l+d+++++     +SgG+++++++ +a l kpkll+lDEp 
  gi|242399696|ref|YP_002995121.1|  96 KVIQFlqrvlknlknlDEIQAYEIIFAAVQELGLDDSILTRFLnVGFSGGERKKLEMLQAYLVKPKLLILDEPD 169
                                       8887788898888775333334445555666666666665444699**************************95 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   2.4e-05     0.018       2      49 ..      32      73 ..      31      93 .. 0.68
   2 !   25.3   0.0   1.6e-08   1.2e-05     235     297 ..     140     199 ..      98     205 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.4e-05
                            AAA_21  2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipsll 49
                                       v+ GpNgsGKS+L  ++      +++ +   ++ + +++  +i++l+
  gi|242399696|ref|YP_002995121.1| 32 HVVMGPNGSGKSTLALTI------AGHPKYQVIDGRIIFDVEDITNLP 73
                                      6899**********9999......555555555555555555555555 PP

  == domain 2  score: 25.3 bits;  conditional E-value: 1.6e-08
                            AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                         +S G ++ l +l a+l  +   +ll++DEp++g +   l+ ++ ++++l+++g+ ++l TH
  gi|242399696|ref|YP_002995121.1| 140 VGFSGGERKKLEMLQAYLVKP---KLLILDEPDSGVDVDSLKMIASVINKLHEGGTSILLITH 199
                                       4569**************988...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 !   12.8   0.0   7.8e-05     0.058      25      41 ..      30      46 ..       5      51 .. 0.84
   2 !   10.1   0.0   0.00054       0.4     137     205 ..     142     207 ..      67     221 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.8e-05
                                      SEEEEEESTTSSHHHHH CS
                                      xxxxxxxxxxxxxxxxx RF
                             SMC_N 25 sftaivGpNGSGKsnll 41
                                      ++ +++GpNGSGKs l 
  gi|242399696|ref|YP_002995121.1| 30 ELHVVMGPNGSGKSTLA 46
                                      5789**********986 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00054
                                       S-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                             SMC_N 137 LSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislreemleka 205
                                       +SgGe++   l +l A + vkp+ l +lDe d+  D    k +a+++++ ++  + ++ i++  ++le+ 
  gi|242399696|ref|YP_002995121.1| 142 FSGGERK--KLEMLQA-YLVKPK-LLILDEPDSGVDVDSLKMIASVINKLHEGgTSILLITHYGRILEHL 207
                                       6788765..2333322.335554.789*********************9988768999999988888765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   7.4e-06    0.0055       7     131 ..      31     200 ..      25     207 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 7.4e-06
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaee..................erpevv.fvtlpsst...sskdllrell 61 
                                       + vv+G+ G+GK+tl+ +++    +++ ++                   +r   + +++ p++    +  ++l+++l
  gi|242399696|ref|YP_002995121.1|  31 LHVVMGPNGSGKSTLALTIAGHP-KYQVIDGriifdveditnlppeervRRGV-FlSFQHPVEVegvKVIQFLQRVL 105
                                       569****************9985.565666599*9999999999998643333.24555555556678889999999 PP

                            AAA_22  62 ralglelka............................erlsseellealeqalrarav............ielliiD 98 
                                       ++l++   +                              + +               +            ++lli+D
  gi|242399696|ref|YP_002995121.1| 106 KNLKNLD-EiqayeiifaavqelglddsiltrflnvgFSGGE---------------RkklemlqaylvkPKLLILD 166
                                       9999644.4477777777777755555555444443322222...............2455555555556678**** PP

                            AAA_22  99 Eaqh.lrseealeeLrsllnl.srkgvqliLvGtp 131
                                       E +  +   + l+ + s  n  ++ g++++L+ ++
  gi|242399696|ref|YP_002995121.1| 167 EPDSgV-DVDSLKMIASVINKlHEGGTSILLITHY 200
                                       *99999.7777777777777777999999998776 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   2.6e-06     0.002      77     126 ..       6      56 ..       2      62 .. 0.88
   2 ?   -1.9   0.0       3.7   2.7e+03      20      40 ..     119     139 ..     104     165 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.6e-06
                                       SEEEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT---- CS
                       RsgA_GTPase  77 yevllvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallpelelk 126
                                       +e l+v+a++ke l++++  ++d ++ v++G+ G GKStL  +++++ + +
  gi|242399696|ref|YP_002995121.1|   6 VENLKVKAEDKEILKDINLIVDDgELHVVMGPNGSGKSTLALTIAGHPKYQ 56 
                                       67789999*************999****************99999876665 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.7
                                       EEEEESTTTT--HHHHHHHHH CS
                       RsgA_GTPase  20 livvslkepelslnlldrfLv 40 
                                       +i  +++e  l+ ++l+rfL 
  gi|242399696|ref|YP_002995121.1| 119 IIFAAVQELGLDDSILTRFLN 139
                                       444556666788888888885 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   6.2e-06    0.0046      29      55 ..      25      51 ..       4      93 .. 0.85
   2 ?   -2.3   0.0       3.7   2.8e+03     164     189 ..     179     200 ..     148     202 .. 0.52

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 6.2e-06
                            AAA_25 29 llpagelallaGapgtGKttlaldlal 55
                                      ++  gel++++G+ g+GK+tlal +a 
  gi|242399696|ref|YP_002995121.1| 25 IVDDGELHVVMGPNGSGKSTLALTIAG 51
                                      67889******************9885 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.7
                            AAA_25 164 dvgalvealeriarrtgaavllvhHv 189
                                        +++++   +++ ++ g  +ll+ H 
  gi|242399696|ref|YP_002995121.1| 179 MIASVI---NKL-HEGGTSILLITHY 200
                                       223333...333.4456667777775 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.9e-05     0.014       4      86 ..      31     127 ..      28     151 .. 0.69
   2 ?   -1.1   0.0       2.4   1.8e+03      64      73 ..     159     168 ..     128     196 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.9e-05
                            AAA_14   4 ilvitGaRrvGKTtllkqlikell.vkkesilyinldderd............kkladpe........kllelilek 59 
                                       + v++G+  +GK+tl+ +++ +      +  + ++++d ++             ++   +        k+++++++ 
  gi|242399696|ref|YP_002995121.1|  31 LHVVMGPNGSGKSTLALTIAGHPKyQVIDGRIIFDVEDITNlppeervrrgvfLSF---QhpvevegvKVIQFLQRV 104
                                       6799***************9887774556777788888888666655554444222...133333344444444443 PP

                            AAA_14  60 lkeekktylflDEiqevpewekalksl 86 
                                            k++  lDEiq ++ ++ a+++l
  gi|242399696|ref|YP_002995121.1| 105 ----LKNLKNLDEIQAYEIIFAAVQEL 127
                                       ....455677********999999987 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.4
                            AAA_14  64 kktylflDEi 73 
                                       k ++l+lDE 
  gi|242399696|ref|YP_002995121.1| 159 KPKLLILDEP 168
                                       5688999994 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 !   10.4   0.0   0.00052      0.39      44      68 ..      26      50 ..       7      64 .. 0.85
   2 ?    4.4   0.0     0.036        27      97     139 ..     148     189 ..     140     202 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00052
                         IstB_IS21 44 iekkenivllGpsGvGKshlaialg 68
                                      +++ e  v++Gp G GKs la +++
  gi|242399696|ref|YP_002995121.1| 26 VDDGELHVVMGPNGSGKSTLALTIA 50
                                      67788899*************9987 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.036
                         IstB_IS21  97 gklaralkrllkvdllilDdlgllpldqaeaellfeviekrye 139
                                        kl+  ++ l+k++llilD+     +d ++ +++  vi+k  e
  gi|242399696|ref|YP_002995121.1| 148 KKLEMLQAYLVKPKLLILDEPD-SGVDVDSLKMIASVINKLHE 189
                                       5788888999*********964.45677777777777777766 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 !   15.3   0.0   1.6e-05     0.012      23      38 ..      29      45 ..      20      50 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.6e-05
                            AAA_29 23 g.atlltGpsGsGKSTl 38
                                      g  ++++Gp+GsGKSTl
  gi|242399696|ref|YP_002995121.1| 29 GeLHVVMGPNGSGKSTL 45
                                      447899**********9 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.9e-05     0.014      20      43 ..      23      46 ..      12      51 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.9e-05
                            AAA_27 20 dfsaeeadlhliyGpNEAGKstal 43
                                      ++  ++ +lh+++GpN +GKst+ 
  gi|242399696|ref|YP_002995121.1| 23 NLIVDDGELHVVMGPNGSGKSTLA 46
                                      45556889**************85 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.6e-05     0.012       1      32 [.      31      62 ..      31     126 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.6e-05
                            AAA_33  1 lvllvGlpGsGKstlaerllkklgavllssdt 32
                                      l ++ G++GsGKstla  ++ + ++++++  +
  gi|242399696|ref|YP_002995121.1| 31 LHVVMGPNGSGKSTLALTIAGHPKYQVIDGRI 62
                                      57899***************999999998665 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0016       1.2      20      38 ..      33      51 ..      19      81 .. 0.84
   2 ?    4.6   0.0     0.014        10     524     578 ..     157     208 ..     148     220 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0016
                            AAA_13 20 liYGwNGaGKTtLSrllrs 38
                                      ++ G NG+GK+tL+  ++ 
  gi|242399696|ref|YP_002995121.1| 33 VVMGPNGSGKSTLALTIAG 51
                                      788**********999886 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.014
                            AAA_13 524 igkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleffkevk 578
                                       + k k  ++D P S  D +sl +++s i++     +    +++ TH    +  +k
  gi|242399696|ref|YP_002995121.1| 157 LVKPKLLILDEPDSGVDVDSLKMIASVINKLH---EGGTSILLITHYGRILEHLK 208
                                       458999*************************8...99999999999766666665 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   6.8e-05     0.051      15      35 ..      22      45 ..       4      50 .. 0.81
   2 ?   -2.2   0.0       6.7     5e+03     182     186 ..     111     115 ..      84     157 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.8e-05
                            AAA_23 15 idF...skgltlItGpNGaGKTTi 35
                                      i++   +  l ++ GpNG+GK+T+
  gi|242399696|ref|YP_002995121.1| 22 INLivdDGELHVVMGPNGSGKSTL 45
                                      6667766679999**********9 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 6.7
                            AAA_23 182 ekele 186
                                        +e++
  gi|242399696|ref|YP_002995121.1| 111 LDEIQ 115
                                       22222 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00015      0.11       6      29 ..      33      58 ..      31      72 .. 0.83
   2 ?   -2.0   0.0       3.4   2.5e+03     113     132 ..     103     126 ..      96     139 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00015
                            AAA_24  6 liyGpsgiGKTtlakel..gpkplfi 29
                                      +++Gp+g+GK+tla+++   pk  +i
  gi|242399696|ref|YP_002995121.1| 33 VVMGPNGSGKSTLALTIagHPKYQVI 58
                                      79**************9765555555 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.4
                            AAA_24 113 rllkklqelrk....nvifiahek 132
                                       r+lk+l++l++     +if a ++
  gi|242399696|ref|YP_002995121.1| 103 RVLKNLKNLDEiqayEIIFAAVQE 126
                                       556666666666668999988765 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 ?   11.4   0.2   0.00043      0.32       3      26 ..      34      57 ..      32     189 .. 0.80
   2 ?    0.0   0.0       1.4   1.1e+03      58      72 ..     159     173 ..     147     213 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00043
                                      EESSTTSSHHHHHHHHHHHHTHEE CS
                               AAA  3 lyGppGtGKTllakavakelgvef 26
                                      ++Gp G GK++la  +a + + ++
  gi|242399696|ref|YP_002995121.1| 34 VMGPNGSGKSTLALTIAGHPKYQV 57
                                      79***************9966553 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1.4
                                       TSEEEEEETGGGHHH CS
                               AAA  58 kpsilfiDEidalak 72 
                                       kp+ l++DE d+ + 
  gi|242399696|ref|YP_002995121.1| 159 KPKLLILDEPDSGVD 173
                                       567777777776544 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 ?   10.8   0.0   0.00045      0.34       8      41 ..      19      50 ..      15      67 .. 0.83
   2 ?    0.5   0.0      0.61   4.6e+02      36     123 ..     100     197 ..      98     199 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00045
                          ATPase_2  8 lkeleeilerepneiyfiYGpegsGKtaLlkeii 41
                                      lk+++ i++    e  ++ Gp gsGK++L   i+
  gi|242399696|ref|YP_002995121.1| 19 LKDINLIVDD--GELHVVMGPNGSGKSTLALTIA 50
                                      5777777777..68899************98876 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.61
                          ATPase_2  36 Llkeiienledkdkyviyyialreesiskldefie........eeeekkklekalgiavpkaeleeilk..eksklv 102
                                       +l+++++nl+++d+   y i +  +++  ld++i            e+kkle +l+  + k +l  il+  +   +v
  gi|242399696|ref|YP_002995121.1| 100 FLQRVLKNLKNLDEIQAYEIIFAAVQELGLDDSILtrflnvgfSGGERKKLE-MLQAYLVKPKL-LILDepDSGVDV 174
                                       5778888888989888888888888888877776666776775333344333.33333333333.245545444444 PP

                          ATPase_2 103 f..kaielllekikkkgkkiiii 123
                                       +  k i+++++k+ + g+ i +i
  gi|242399696|ref|YP_002995121.1| 175 DslKMIASVINKLHEGGTSILLI 197
                                       42256777777777777766665 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00084      0.63       3      21 ..      32      50 ..      30      64 .. 0.88
   2 ?    1.7   0.0      0.28   2.1e+02      82     129 ..     160     200 ..      97     215 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00084
                                      EEEEC-TTTCHHHHHHHHH CS
                             NACHT  3 vilqGeaGsGKTtLlqkla 21
                                       ++ G++GsGK+tL+  +a
  gi|242399696|ref|YP_002995121.1| 32 HVVMGPNGSGKSTLALTIA 50
                                      5899***********9887 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.28
                                       CEEEEEE-STT-SS-TCH.........HHHHHCTTTTT--EEEEEEEC CS
                             NACHT  82 rlLlilDglDelvtdlgqkekqpvrtlLselirkkllpeasllltvrp 129
                                         LlilD  D  v+ ++        +++++ i+k +  ++s+ll+++ 
  gi|242399696|ref|YP_002995121.1| 160 PKLLILDEPDSGVDVDSL-------KMIASVINKLHEGGTSILLITHY 200
                                       447999999999998877.......89999999988888888888765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00017      0.12      24      51 ..      29      56 ..      15     197 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00017
                            AAA_16 24 pelvllsGesGvGKsslvrellralekd 51
                                      +el ++ G+ G+GKs+l+ +++ + + +
  gi|242399696|ref|YP_002995121.1| 29 GELHVVMGPNGSGKSTLALTIAGHPKYQ 56
                                      46778*************9888766655 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   0.0   0.00012     0.087     107     169 ..       8      72 ..       2     105 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00012
                             T2SSE 107 dlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeinks..deriv.tvEDpvEi 169
                                       +l +++  +++i + ++  v    l +v G+ gsGK+tl+ ++    + +  d ri+  vED   +
  gi|242399696|ref|YP_002995121.1|   8 NLKVKA-EDKEILKDINLIVDDGELHVVMGPNGSGKSTLALTIAGHPKYQviDGRIIfDVEDITNL 72 
                                       555444.4566677788899999999*************988877655555666655158886655 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00014       0.1       5      32 ..      36      63 ..      33     119 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00014
                                      -STTSSHHHHHHHHHHHHT-EEEEHHHH CS
                    Cytidylate_kin  5 GPagsGKssvaralaeklglkyldtgal 32
                                      GP gsGKs++a ++a + +++++d   +
  gi|242399696|ref|YP_002995121.1| 36 GPNGSGKSTLALTIAGHPKYQVIDGRII 63
                                      9******************999997655 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00021      0.15       2      69 ..      33     113 ..      33     167 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00021
                            AAA_18   2 lltGtpGvGKttlakeLskrlgf.............gvnlrdvakenglllevdpe...aldeskrldedkldklld 62 
                                       +++G+ G+GK+tla  ++ + ++              +nl    + ++ ++         ++ + + ++++l+++l+
  gi|242399696|ref|YP_002995121.1|  33 VVMGPNGSGKSTLALTIAGHPKYqvidgriifdvedITNLPPEERVRRGVFL---SfqhPVEVEGVKVIQFLQRVLK 106
                                       589**************98878888885555553333333333333333333...1444788888888888888888 PP

                            AAA_18  63 aleenss 69 
                                       +l++ ++
  gi|242399696|ref|YP_002995121.1| 107 NLKNLDE 113
                                       8888765 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00022      0.16      13      40 ..      22      50 ..      10      65 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00022
                                      HHHHH.H-SEEEEE--TTSSTTHHHHHHH CS
                              PhoH 13 lealk.kndivfaiGpaGtGKtylavala 40
                                      ++ +  + ++ +++Gp G+GK+ la+++a
  gi|242399696|ref|YP_002995121.1| 22 INLIVdDGELHVVMGPNGSGKSTLALTIA 50
                                      44444577899***************998 PP

>> MutS_V  MutS domain V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1     0.068        51       2      14 ..      33      45 ..      32      50 .. 0.85
   2 ?    6.3   0.0     0.012         9      77     126 ..     159     206 ..     115     234 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.068
                                      EEE-STTSSHHHH CS
                            MutS_V  2 litGpnmaGksty 14
                                      ++ Gpn +Gkst+
  gi|242399696|ref|YP_002995121.1| 33 VVMGPNGSGKSTL 45
                                      899********97 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.012
                                       TTSEEEEESTS-SS-HHHHHHHHHHHHHHHHHTT--EEEEEES-GGGGGH CS
                            MutS_V  77 ekslvilDElGRGtstydGlaialavaeyllekikaktlfatHyheltkl 126
                                       +  l+ilDE   G   +d l +  +v++ l+e   +  l+ tHy  + + 
  gi|242399696|ref|YP_002995121.1| 159 KPKLLILDEPDSGVD-VDSLKMIASVINKLHE-GGTSILLITHYGRILEH 206
                                       557999***999976.689999999*****98.68889999***887654 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00036      0.27       2      27 ..      32      58 ..      31      79 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00036
                            AAA_28  2 ivitGgestGKTtlleaLaar.gypvv 27
                                       v++G+ ++GK+tl+  +a + +y+v+
  gi|242399696|ref|YP_002995121.1| 32 HVVMGPNGSGKSTLALTIAGHpKYQVI 58
                                      599****************99999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       662  (0.0369234); expected 358.6 (0.02)
Passed bias filter:                      579  (0.032294); expected 358.6 (0.02)
Passed Vit filter:                       104  (0.00580066); 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: 0.70u 0.38s 00:00:01.08 Elapsed: 00:00:00.57
# Mc/sec: 1284.02
//
Query:       gi|242399697|ref|YP_002995122.1|  [L=173]
Description: ferritin-like protein [Thermococcus sibiricus MM 739]
Scores for complete 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-47  158.7   2.2    9.4e-47  158.5   2.2    1.0  1  Ferritin        Ferritin-like domain
     0.0023   18.3   5.8     0.0035   17.7   5.8    1.4  1  Rubrerythrin    Rubrerythrin
     0.0093   16.4   0.3      0.021   15.2   0.0    1.7  2  Lipoprotein_10  Putative mycoplasma lipoprotein, C-terminal r


Domain annotation for each model (and alignments):
>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.5   2.2   1.6e-50   9.4e-47       1     140 [.       7     142 ..       7     144 .. 0.99

  Alignments for each domain:
  == domain 1  score: 158.5 bits;  conditional E-value: 1.6e-50
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS....SHHHHHHC-SSSS CS
                          Ferritin   1 ikaLneqladeltaayqylamawyvkgpgleglaeffdeqaeeerehadklaerilalGgtpvltraeleeieapke 77 
                                       +kaLneql++e+++ay+y+ama y+++ +leg+a++++ qaeee +ha +++++i +++g     r+el+ei++p++
  gi|242399697|ref|YP_002995122.1|   7 LKALNEQLNKEIYSAYLYFAMAGYFDDLNLEGFANWMKAQAEEEVGHALRFYNYIYDRNG-----RVELSEIPKPPK 78 
                                       589*********************************************************.....************ PP

                                       .CSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Ferritin  78 .fgsveevleaalehekkvteslrelielaeeegDpatadfledfleeqeeheweleallekle 140
                                        +gs+ e++eaa+ehek +++s++el+ laeee+D+ t+ fle+f++eq+e+e+ ++++l+kl+
  gi|242399697|ref|YP_002995122.1|  79 eWGSPIEAFEAAYEHEKFISKSIHELAVLAEEEKDYPTRAFLEWFINEQVEEEASVKKVLDKLK 142
                                       **************************************************************97 PP

>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   5.8   5.9e-07    0.0035       3     124 ..      10     125 ..       4     138 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 5.9e-07
                                       HHHHHHHHHHHHHHHHHHHHCHH.TT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSBBS-------TT CS
                      Rubrerythrin   3 LekAiagEssarrlYkelaekak.egypqiaelFeelAeeEreHakilnklleklepelelevkekvreyaeakpkf 78 
                                       L++ +  E+    lY ++a  ++  +++  a+ +++ AeeE  Ha ++++ + ++++  e        e  ++++++
  gi|242399697|ref|YP_002995122.1|  10 LNEQLNKEIYSAYLYFAMAGYFDdLNLEGFANWMKAQAEEEVGHALRFYNYIYDRNGRVE------LSEIPKPPKEW 80 
                                       55666677777888888888888888999*******************************......5788899**** PP

                                       GGHHHHHHHHHHHHHHHHHCHHHHHHHHHHHTTSHHHHHHHHHHHH CS
                      Rubrerythrin  79 lttaknLeeaiegayaeeeemyrfyeelaekegneeakklfkklae 124
                                        +  +  e+a+e +    + +  +++ lae+e++ +++ ++++ ++
  gi|242399697|ref|YP_002995122.1|  81 GSPIEAFEAAYEHEKFISKSI-HELAVLAEEEKDYPTRAFLEWFIN 125
                                       ********9999888876666.666666776766668888887665 PP

>> Lipoprotein_10  Putative mycoplasma lipoprotein, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1       1.2   6.9e+03      19      32 ..      35      48 ..      31      51 .. 0.70
   2 !   15.2   0.0   3.6e-06     0.021      10      39 ..     106     135 ..     103     153 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.2
                    Lipoprotein_10 19 aTkkFvnWllnske 32
                                      + + F nW+  + e
  gi|242399697|ref|YP_002995122.1| 35 NLEGFANWMKAQAE 48
                                      55679999977655 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 3.6e-06
                    Lipoprotein_10  10 ihaNekedeaTkkFvnWllnskeeweekkk 39 
                                       + a e+ d  T++F++W++n++ e e++ k
  gi|242399697|ref|YP_002995122.1| 106 VLAEEEKDYPTRAFLEWFINEQVEEEASVK 135
                                       668999****************99888733 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.33s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1045.43
//
Query:       gi|242399698|ref|YP_002995123.1|  [L=366]
Description: thiamine biosynthesis protein THII [Thermococcus sibiricus MM 739]
Scores for complete 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-53  179.0   0.0    1.1e-52  178.5   0.0    1.2  1  ThiI           Thiamine biosynthesis protein (ThiI)
    4.6e-21   75.4   1.3    4.6e-21   75.4   1.3    2.1  2  THUMP          THUMP domain
      2e-09   37.3   0.0    3.4e-07   30.0   0.1    2.6  2  QueC           Queuosine biosynthesis protein QueC
    2.7e-05   23.1   0.1    4.3e-05   22.5   0.1    1.3  1  tRNA_Me_trans  tRNA methyl transferase
    0.00026   21.1   0.0    0.00049   20.2   0.0    1.5  1  PAPS_reduct    Phosphoadenosine phosphosulfate reductase fami
  ------ inclusion threshold ------
      0.022   14.8   0.0      0.037   14.1   0.0    1.3  1  QueH           Epoxyqueuosine reductase QueH
      0.022   14.5   0.0        8.1    6.2   0.0    2.2  2  ATP_bind_3     PP-loop family
      0.039   13.6   0.0      0.076   12.7   0.0    1.4  1  Asn_synthase   Asparagine synthase
       0.13   11.3   0.0       0.22   10.6   0.0    1.3  1  NAD_synthase   NAD synthase


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 !  178.5   0.0   5.6e-56   1.1e-52       1     195 [.     166     360 ..     166     362 .. 0.92

  Alignments for each domain:
  == domain 1  score: 178.5 bits;  conditional E-value: 5.6e-56
                              ThiI   1 gtqgkvlaLlSgGiDSpVaaylllkRGcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdfkevlk 77 
                                       gtqgkv+aLlSgGiDSpVaa+l+lkRG +v +vh++    ++++a+++vek++e+l++y+    ++l+v ++ evlk
  gi|242399698|ref|YP_002995123.1| 166 GTQGKVVALLSGGIDSPVAAFLMLKRGAEVIAVHFD----QGKNARKVVEKVVEILSDYSP-EPIELIVENHFEVLK 237
                                       89*********************************7....88999***************7.899**9999877776 PP

                              ThiI  78 eilekv....kekltivllkrkmlriAekvaeeegakalvtGesLgqVaSqtleNlrvisavvnllilrPLigldKe 150
                                         +  +    + + t+v++k  mlr A +va+e+ga  +vtG+sLgqVaSqtl+Nl   + +v+ ++ rPL+g+dKe
  gi|242399698|ref|YP_002995123.1| 238 PYVITLnklnRREWTCVVCKVAMLRRAAEVAKENGALGIVTGDSLGQVASQTLTNLYFETITVDFPVHRPLLGFDKE 314
                                       54433323338899*************************************************************** PP

                              ThiI 151 eiiklAkeigtyeisieke.dkCsvlakhPttkakleevekaeekl 195
                                       ei+ +A++i ty+   e +   C++ +++ +t+ klee e+++ +l
  gi|242399698|ref|YP_002995123.1| 315 EIVSIARKIKTYDAFLEYPyCDCPFRPERVVTQGKLEEFERIRTEL 360
                                       *************998877688****************99988766 PP

>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.4   1.3   2.3e-24   4.6e-21       2     143 ..      29     155 ..      28     156 .. 0.90
   2 ?   -1.5   0.0       1.3   2.5e+03      57      80 ..     199     222 ..     187     250 .. 0.72

  Alignments for each domain:
  == domain 1  score: 75.4 bits;  conditional E-value: 2.3e-24
                                       HHHHHHHHTT.H-SEEEEETTEEEEECTEEEEEETHHHHHHHHHTSTTECEEEEEEEEEESSHHHHHHHHHHHHHHH CS
                             THUMP   2 eieellkegkvnverveagkgrivvelkgekpeedeellkealekargiqrvipvcevceadledileaakeivkkk 78 
                                       +ie++lk+++++ +++   +gri+v+           ++  ++ k++g+++v+p+    +++    l+ a + ++++
  gi|242399698|ref|YP_002995123.1|  29 NIEKILKRKGITGKVKVI-RGRILVDAP--------DKAAWIIAKVPGVVSVSPARVMSYDEAPGYLREALKKFNPR 96 
                                       89*********9996655.699999965........5566699************9999998888888888877777 PP

                                       HHHCT-EEEEEEEESSSTSSSHHHHHHHHHHHHHHCCTT-EE-SSS-SEEEEEEEETTEEEEEEE CS
                             THUMP  79 feeeketFaVrvkrrgkhfeftsreinrevGkaivektglkVdlenPdivvrveiikdkayisid 143
                                             +F+V++ r +k+f  ts+e+nrevG++i +++g+kVdlenP+++v +eii+ kay++ +
  gi|242399698|ref|YP_002995123.1|  97 ------SFRVETQRLDKTFLKTSVEVNREVGAFIAKEFGWKVDLENPELTVGIEIINGKAYVFFE 155
                                       ......9*******************************************************975 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.3
                                       EEEEESSHHHHHHHHHHHHHHHHH CS
                             THUMP  57 cevceadledileaakeivkkkfe 80 
                                         + +++  ++ e+++ei +++  
  gi|242399698|ref|YP_002995123.1| 199 HFDQGKNARKVVEKVVEILSDYSP 222
                                       455666667777777777666554 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.1   1.7e-10   3.4e-07       1      52 [.     170     221 ..     170     279 .. 0.85
   2 !    4.7   0.0    0.0096        19     150     174 ..     300     324 ..     282     335 .. 0.82

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 1.7e-10
                                       EEEEE--SSHHHHHHHHHHHHH-SEEEEEEEESS-TTSHHHHHHHHHHHHT- CS
                              QueC   1 kavvllSGGlDSttvlalakkegkevealtfdYgqrhkkeleaakkiakelg 52 
                                       k+v llSGG+DS ++++l++k+g+ev+a++fd g++++k +e++ +i +++ 
  gi|242399698|ref|YP_002995123.1| 170 KVVALLSGGIDSPVAAFLMLKRGAEVIAVHFDQGKNARKVVEKVVEILSDYS 221
                                       6899***********************************9999999998877 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0096
                                       S--EEE-TTTT--HHHHHHHHHHTT CS
                              QueC 150 kkieieaPlidlsKaeivklgkelg 174
                                        ++ ++ Pl+ ++K+eiv ++ +++
  gi|242399698|ref|YP_002995123.1| 300 VDFPVHRPLLGFDKEEIVSIARKIK 324
                                       57899***************99886 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.1   2.2e-08   4.3e-05       2      38 ..     170     206 ..     169     220 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 2.2e-08
                     tRNA_Me_trans   2 kvvvalSgGVDSsvaaallkeqgyevigvflklweee 38 
                                       kvv++lSgG+DS vaa+l+ ++g evi+v++   +++
  gi|242399698|ref|YP_002995123.1| 170 KVVALLSGGIDSPVAAFLMLKRGAEVIAVHFDQGKNA 206
                                       89****************************9877664 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   2.4e-07   0.00049       2      99 ..     171     269 ..     170     323 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 2.4e-07
                                       EEEE--SSCTCHHHHHHHHHHCTTHEEEEEE-STB-HHHHHHHHHHHHHT...T-EEEEEE-SCHHHHHHHHHH-S- CS
                       PAPS_reduct   2 lvvsvsgGkdslVllhLalkafkpvpvvfvdtghefpetiefvdeleery...glrlkvyepeeevaekinaekhgs 75 
                                       +v + sgG+ds V   L+lk   +v  v+ d+g++ ++++e v e+ + y    ++l+v +  e  +  +++ ++  
  gi|242399698|ref|YP_002995123.1| 171 VVALLSGGIDSPVAAFLMLKRGAEVIAVHFDQGKNARKVVEKVVEILSDYspePIELIVENHFEVLKPYVITLNKLN 247
                                       68899*********************************************988899999999999999888888544 PP

                                       THHHCHHHHHHTHHHHHHHHHCTT CS
                       PAPS_reduct  76 slyeeaaeriaKveplkkaLekld 99 
                                       +  e+  + ++Kv  l++a e  +
  gi|242399698|ref|YP_002995123.1| 248 RR-EW-TCVVCKVAMLRRAAEVAK 269
                                       44.66.789999999999765444 PP

>> QueH  Epoxyqueuosine reductase QueH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.9e-05     0.037      72     171 ..     240     339 ..     200     343 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.9e-05
                              QueH  72 vkglekekekgeRCekCyelrLektaelAkengfdaftttltiSplknaelineigeelaeeygvkflasdfkkkeg 148
                                       v  l+k + ++  C +C    L+++ae+Akeng+  + t  ++ ++ +++l n   e+++ +  v+     f k+e 
  gi|242399698|ref|YP_002995123.1| 240 VITLNKLNRREWTCVVCKVAMLRRAAEVAKENGALGIVTGDSLGQVASQTLTNLYFETITVDFPVHRPLLGFDKEEI 316
                                       3345666777799************************************************************9999 PP

                              QueH 149 ykrsielskelglYrQkYCGCvf 171
                                       ++ + ++     + +  YC C f
  gi|242399698|ref|YP_002995123.1| 317 VSIARKIKTYDAFLEYPYCDCPF 339
                                       9999999999999999*****98 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.004       8.1       3      42 ..     172     207 ..     170     236 .. 0.71
   2 ?    6.1   0.0    0.0044       8.7     138     158 ..     302     322 ..     276     327 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.004
                                       EEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTC CS
                        ATP_bind_3   3 lvAvSgGlDSmaLllllaklkkklgiklvaihvdhglree 42 
                                       ++ +SgG+DS +   l+ k       +++a+h+d g+ ++
  gi|242399698|ref|YP_002995123.1| 172 VALLSGGIDSPVAAFLMLKRGA----EVIAVHFDQGKNAR 207
                                       5558******999999988844....78888888765433 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0044
                                       CCEE-CCCT--HHHHHHHHHH CS
                        ATP_bind_3 138 irlvRPlLkvskeeleeylke 158
                                         + RPlL + kee+ +++++
  gi|242399698|ref|YP_002995123.1| 302 FPVHRPLLGFDKEEIVSIARK 322
                                       6789*************9987 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.8e-05     0.076      18      68 ..     169     215 ..     165     221 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.8e-05
                      Asn_synthase  18 vpvGalLSGGlDSSliaalaarqsksplktFsigfeekgsdeakyakevae 68 
                                        +v alLSGG+DS + a+l+ +     +   +++f ++g + +k+ ++v+e
  gi|242399698|ref|YP_002995123.1| 169 GKVVALLSGGIDSPVAAFLMLKRG---AEVIAVHF-DQGKNARKVVEKVVE 215
                                       67899*********9999999965...68889999.777777777777765 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00011      0.22      20      68 ..     170     216 ..     165     255 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00011
                                       EEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHH CS
                      NAD_synthase  20 gvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalal 68 
                                       +vv  lSGG+DS ++a l  k    ++v+a+ + + ++ ++ ve+ +++
  gi|242399698|ref|YP_002995123.1| 170 KVVALLSGGIDSPVAAFLMLKRG--AEVIAVHFDQGKNARKVVEKVVEI 216
                                       78889************988764..778888876666655555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       647  (0.0360868); expected 358.6 (0.02)
Passed bias filter:                      566  (0.031569); 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: 0.66u 0.37s 00:00:01.03 Elapsed: 00:00:00.56
# Mc/sec: 1962.44
//
Query:       gi|242399699|ref|YP_002995124.1|  [L=326]
Description: Molybdopterin biosynthesis protein moeb [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.3e-44  151.6   0.0    3.8e-44  150.9   0.0    1.2  1  ThiF           ThiF family
    2.2e-06   27.5   0.0    4.4e-06   26.6   0.0    1.5  1  TBP            Transcription factor TFIID (or TATA-binding pr
     0.0014   18.7   0.0     0.0051   16.9   0.0    1.9  2  Shikimate_DH   Shikimate / quinate 5-dehydrogenase
     0.0053   17.2   0.0     0.0098   16.3   0.0    1.3  1  NAD_binding_7  Putative NAD(P)-binding
  ------ inclusion threshold ------
      0.052   14.1   0.1        2.2    8.9   0.1    2.5  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
      0.076   12.4   0.0       0.14   11.6   0.0    1.4  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
       0.14   11.7   0.2       0.33   10.5   0.2    1.6  1  DAO            FAD dependent oxidoreductase
       0.24   11.1   0.0        0.4   10.4   0.0    1.3  1  ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydro


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 !  150.9   0.0   1.7e-47   3.8e-44       2     240 ..      12     230 ..      11     237 .. 0.92

  Alignments for each domain:
  == domain 1  score: 150.9 bits;  conditional E-value: 1.7e-47
                                       HHHHHHHHHHHHHHHHTSEEEEE--SHHHHHHHHHHHHHTTTEEEEEESSB--GGGGGTBTTS-GGGTTSBHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF   2 srqlallgedgqekLrdskvllvGaGglGsellknLalsGvgkltlvDnDkielsNlnRqflfreediGkpKaevaa 78 
                                       sr+  ++g +gq+kL++s+v +vGaG+lGs+ +  L ++Gvgk+ +vD D ++ s+l R ++ ++ed+GkpK+e+++
  gi|242399699|ref|YP_002995124.1|  12 SRHFPIIGIEGQRKLSESTVTVVGAGALGSWEVYFLHKLGVGKIIVVDRDFVDESDLPRTIY-TKEDVGKPKVEALK 87 
                                       677778999**************************************************966.************** PP

                                       HHHHHT-TTSEEEEEES-CCGCCS-HHHHTT-SEEEEESSSHHHHHHHHHHHHHHT-EEEEEEEETTEEEEEEEEEC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF  79 ealqeinpdveveavteritdetvleellesvDlVvdalDniearrlvnracvkkgiplieagtlgfegqvvviipg 155
                                       e+         v  + e+++++t   +ll ++Dl++d++Dni +r  +n+++vk+ +p+i  g+l ++g++++iip 
  gi|242399699|ref|YP_002995124.1|  88 ERFG-------VIGHFEDLNPST--VNLLDEADLIIDGTDNIYTRQVINDYAVKNNKPWIYVGVLSTYGNIMPIIPR 155
                                       9986.......55679*****87..48************************************************** PP

                                       CS-ECTSS-TGGS.EECCCCEEHHHHHHCTE-B-HHHHHHHHHHHHHHHHHHHTTBCGGGCCEEEECCTTTTEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF 156 ktgcyeCldpsstedptekkvplctsiagnipaiatttavvaglaalellkllsgkeklenslltqvdllesrfenv 232
                                       kt+c++Cl+p    + +e+  p+c ++ag   +++ ++++++++a+  + k+l g+e +  +l  ++d+++  fe+v
  gi|242399699|ref|YP_002995124.1| 156 KTACFRCLMP----KLPERPMPTC-AVAG---IMSYVPSLATSIAVGLAAKILLGEE-IKSELI-FFDTKTLEFERV 222
                                       *********9....999999****.****...*********************9999.333333.7*********** PP

                                       CCEEEEEE CS
                                       xxxxxxxx RF
                              ThiF 233 elerakks 240
                                       e+ r +++
  gi|242399699|ref|YP_002995124.1| 223 EVPRREEC 230
                                       **887755 PP

>> TBP  Transcription factor TFIID (or TATA-binding protein, TBP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0     2e-09   4.4e-06      15      78 ..     263     323 ..     254     325 .. 0.90

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 2e-09
                                       SCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHH CS
                               TBP  15 leldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakki 78 
                                       ++++L+++a+++ek ++eY +      +++++++ + +l+F+sG++v+ Ga++e e+++ ++++
  gi|242399699|ref|YP_002995124.1| 263 MNINLDEFAERLEKLGIEYLKTS---QFIQFEDEDYEILVFKSGRMVVRGAEEEREAKNLFARY 323
                                       689******9998999***9776...68899999*************************99986 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   2.3e-06    0.0051       9      56 ..      25      72 ..      20      93 .. 0.83
   2 ?   -0.8   0.0      0.65   1.5e+03      49      84 ..      83     118 ..      76     140 .. 0.61

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.3e-06
                                      ..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHH CS
                      Shikimate_DH  9 slkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeel 56
                                      +l+e++v+++GaG +++  +  L++ gv k++v+ R++   ++l + +
  gi|242399699|ref|YP_002995124.1| 25 KLSESTVTVVGAGALGSWEVYFLHKLGVGKIIVVDRDFVDESDLPRTI 72
                                      6899********************************988777776665 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.65
                                       HHHHHHHHT.ET-EEEEGC.GHHHHHHT-SEEEE-SS CS
                      Shikimate_DH  49 akelaeelkgeeiealkle.elkellaeadvvisata 84 
                                       +++l e+++    ++ +l+ +  +ll+ead++i  t 
  gi|242399699|ref|YP_002995124.1|  83 VEALKERFGVI-GHFEDLNpSTVNLLDEADLIIDGTD 118
                                       56666666333.2233332134578999999998875 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 !   16.3   0.0   4.4e-06    0.0098       4      86 ..      25     134 ..      24     142 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.4e-06
                     NAD_binding_7   4 dlkgkkvlvvGgGevAarkvrklleag.akvtvvapevkeele.............elvklaeeelekd........ 58 
                                       +l++ +v vvG+G ++   v+ l + g  k++vv+ ++ +e++              +v++                
  gi|242399699|ref|YP_002995124.1|  25 KLSESTVTVVGAGALGSWEVYFLHKLGvGKIIVVDRDFVDESDlprtiytkedvgkPKVEA-------Lkerfgvig 94 
                                       57899********************9978********655555655555554444422222.......022333334 PP

                     NAD_binding_7  59 ............legadlviaatddrelneriaeaakarr 86 
                                                   l++adl+i  td+   ++ i ++a +++
  gi|242399699|ref|YP_002995124.1|  95 hfedlnpstvnlLDEADLIIDGTDNIYTRQVINDYAVKNN 134
                                       444456666777999****999999888888888874444 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.1   0.00098       2.2       2      30 ..      31      60 ..      30      74 .. 0.83
   2 ?    2.6   0.0     0.093   2.1e+02      45      70 ..     269     294 ..     266     303 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00098
                                      EEEECSSHHHHHHHHHHHHTTS.EEEEEES CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgk.kVtvver 30
                                      v+vvG+G +g  +  +l++lg  k+ vv+r
  gi|242399699|ref|YP_002995124.1| 31 VTVVGAGALGSWEVYFLHKLGVgKIIVVDR 60
                                      89*******************735555554 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.093
                                       HHHHHHHHTTEEEECSEEEEEEEEET CS
                         Pyr_redox  45 ilqeklekngievllntkveeiegse 70 
                                       +++e+lek+gie l  ++  ++e ++
  gi|242399699|ref|YP_002995124.1| 269 EFAERLEKLGIEYLKTSQFIQFEDED 294
                                       5789*********9999988888554 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0     6e-05      0.14      32     112 ..      24     110 ..      18     113 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6e-05
                                       S-GTTSEEEEES-SHHHHHHHHHHHHTT-.EEEEESSSHHHHH.....CHHHHTCEECSHHHHHHH-SEEEE-S--S CS
                      2-Hacid_dh_C  32 kelsgktvGiiGlGrIGqavakrlkafgm.kviaydrskkkee.....eeeelgvelvsleellaesDivslhlplt 102
                                       ++ls++tv ++G+G++G+     l+++g+ k+i++dr   +e+        ++ v + ++e+l ++  ++     l+
  gi|242399699|ref|YP_002995124.1|  24 RKLSESTVTVVGAGALGSWEVYFLHKLGVgKIIVVDRDFVDESdlprtIYTKEDVGKPKVEALKERFGVIGHFEDLN 100
                                       689**************************9******98776664444322333334445555555555555555566 PP

                                       TTTTTSBSHH CS
                      2-Hacid_dh_C 103 petrhlinae 112
                                       p+t +l++++
  gi|242399699|ref|YP_002995124.1| 101 PSTVNLLDEA 110
                                       6666666665 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.2   0.00015      0.33       2      31 ..      31      62 ..      30      66 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00015
                                      EEEECTSHHHHHHHHHHHHTT...EEEEESSSS CS
                               DAO  2 vviiGGGiiGlstAyeLarrg...Vtllekgdi 31
                                      v ++G+G  G++  y+L + g   +++++++ +
  gi|242399699|ref|YP_002995124.1| 31 VTVVGAGALGSWEVYFLHKLGvgkIIVVDRD-F 62
                                      89***************888788*******9.4 PP

>> ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00018       0.4      28     105 ..      24     109 ..      18     131 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00018
                                       S-STTEEEEEE--SHHHHHHHHHHHHCT-EEEEE........EESSEEEEETTEE-HHHHHHHHHCSSSSTTHSHHS CS
                     ELFV_dehydrog  28 dslegkrvaisGsGnvgsyaallltelgakvvav........sDssGviydpeGldieellelkeerksvkeykkss 96 
                                       ++l++++v++ G G +gs+++ +l++lg   + v        sD   +iy +e + + ++ +lke+ + + ++++ +
  gi|242399699|ref|YP_002995124.1|  24 RKLSESTVTVVGAGALGSWEVYFLHKLGVGKIIVvdrdfvdeSDLPRTIYTKEDVGKPKVEALKERFGVIGHFEDLN 100
                                       378999*********************97666660222222233445788888889999999999998888888665 PP

                                       TSTSEEESH CS
                     ELFV_dehydrog  97 ekkaeyien 105
                                        ++++ +++
  gi|242399699|ref|YP_002995124.1| 101 PSTVNLLDE 109
                                       555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      561  (0.0312901); 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: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.51
# Mc/sec: 1927.71
//
Query:       gi|242399700|ref|YP_002995125.1|  [L=268]
Description: hypothetical protein TSIB_1725 [Thermococcus sibiricus MM 739]
Scores for complete 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-96  322.8  19.8    1.3e-96  322.6  19.8    1.0  1  Heliorhodopsin  Heliorhodopsin
  ------ inclusion threshold ------
       0.02   15.1   0.3        3.3    8.1   0.0    2.8  2  DUF3040         Protein of unknown function (DUF3040)
        0.1   11.9   6.9      0.073   12.3   5.6    1.4  1  SecY            SecY translocase
       0.27   11.2  15.4       0.17   11.8   2.4    2.5  2  Claudin_3       Tight junction protein, Claudin-like
          3    7.7  12.7       0.57   10.1   6.8    2.3  2  DsbD_2          Cytochrome C biogenesis protein transmembrane
        7.7    5.8  11.9        2.6    7.4   7.3    2.4  2  DUF373          Domain of unknown function (DUF373)


Domain annotation for each model (and alignments):
>> Heliorhodopsin  Heliorhodopsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  322.6  19.8  4.4e-100   1.3e-96       1     242 []      14     266 ..      14     266 .. 0.97

  Alignments for each domain:
  == domain 1  score: 322.6 bits;  conditional E-value: 4.4e-100
                    Heliorhodopsin   1 Lrkfnlimgvlhlvqavlllvlan..dfslpvttsylegd......petaalapeteelfeve.lgvlvalFlllsa 68 
                                       Lr++n+i+g+lh++++v +l+l+   +++ +v+t+yl+++      + ++++ pe++++f+++ lgvlvalF l+sa
  gi|242399700|ref|YP_002995125.1|  14 LRRMNIIAGILHAITGVSMLALGFllEWERSVYTFYLKYEiireggKLAFNIYPEPRVFFTLKyLGVLVALFPLMSA 90 
                                       89*********************999***********6665554447788999**********9************* PP

                    Heliorhodopsin  69 lahlliatvlfkrYeenLkkginkfRWveyslsssiMivliallvGvldiaaliaifvlnaamilfGllmEkinqtt 145
                                       +ah+++a + f++Y+enLkkg+n++RW+ey+lsss+Mivlial++Gv+d+++l++if+lna+++l+G+lmE  nq+t
  gi|242399700|ref|YP_002995125.1|  91 VAHFTVAGPKFDKYVENLKKGMNPYRWYEYTLSSSVMIVLIALFIGVVDFWSLVMIFTLNAVTMLLGYLMELLNQYT 167
                                       ***************************************************************************** PP

                    Heliorhodopsin 146 ektnwlpfifGciagivpWivillyllaa..eseeevPaFvyaivvslfvlfnlFalnmllqykkvgkwkdylyGEr 220
                                       ektnw+pfi+G+i+givpWiv+++y++aa   +e+++P+Fvy+i++++f+lfn+F+lnm+lqyk+vgkwkdyl GE+
  gi|242399700|ref|YP_002995125.1| 168 EKTNWSPFIIGWISGIVPWIVLFAYFFAAvsVAEAKPPTFVYLIFFIYFILFNIFPLNMYLQYKRVGKWKDYLHGEK 244
                                       *****************************98899******************************************* PP

                    Heliorhodopsin 221 vYivLSLvaKslLAWqvfagtl 242
                                       vYi+LSLvaK+lLAW+vfag++
  gi|242399700|ref|YP_002995125.1| 245 VYITLSLVAKTLLAWIVFAGVF 266
                                       ********************86 PP

>> DUF3040  Protein of unknown function (DUF3040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0    0.0011       3.3      39      65 ..      13      39 ..       2      49 .. 0.75
   2 ?    4.2   0.0     0.018        53      22      82 ..      98     158 ..      92     160 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0011
                           DUF3040 39 rslrrlavlavllfvaGllllvlGvaa 65
                                      r +r ++++++l +++G+ +l lG+++
  gi|242399700|ref|YP_002995125.1| 13 RLRRMNIIAGILHAITGVSMLALGFLL 39
                                      3346668899999999********765 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.018
                           DUF3040  22 DPklaaalrggaararrrslrrlavlavllfvaGllllvlGvaaaa..vvlgvvGfvvmlagv 82 
                                        Pk+ + +  ++ ++     r++ +     +++ l++l++Gv+     v++  + +v+ml+g 
  gi|242399700|ref|YP_002995125.1|  98 GPKFDKYV--ENLKKGMNPYRWYEYTLSSSVMIVLIALFIGVVDFWslVMIFTLNAVTMLLGY 158
                                       68999999..55555555566666666666666788888886543345778888888888775 PP

>> SecY  SecY translocase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   5.6   2.5e-05     0.073      36     183 ..     110     261 ..      75     267 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.5e-05
                                       HHHHHHHHHHHHHH.HHHHHHHHHHHHHHHCHH.HHHHHHHHHHHHHHHHHHHHHHHHSSTTHHHHHHHHHHHHHHC CS
                              SecY  36 egrkkinqitrylt.vvlalvqalgialslglalllivlqltagtvllmwLgEqitekGiGnGisllifagivarlp 111
                                       +g + +  ++  l+  v++++ al+i + + +  l+++++l a t+ll +L E+++++      s +i+  i+  +p
  gi|242399700|ref|YP_002995125.1| 110 KGMNPYRWYEYTLSsSVMIVLIALFIGV-VDFWSLVMIFTLNAVTMLLGYLMELLNQYTEKTNWSPFIIGWISGIVP 185
                                       4444444444333312333444444332.24789**********************************988888888 PP

                                       ..CHSS-HHHHSS..THHHHHHHHHHHHHHHHHCHHHHBEEEECBBBSTT.........S.S-EEEEETTCCCSCHH CS
                              SecY 112 ..kalsglielalegilallllllvtllvillvvyveeaerripvqyakr..grk...ggqssylPlklnyagviPi 181
                                           ++ +++ +  ++  +    +v+l++++  ++++ +  +  +qy++     k   +g++ y+ l l++   + +
  gi|242399700|ref|YP_002995125.1| 186 wiVLFAYFFAAV--SVAEAKPPTFVYLIFFIYFILFNIFPLNMYLQYKRVgkW-KdylHGEKVYITLSLVAKTLLAW 259
                                       533333344443..334444445555555555566666677777787744322.24678889999999998888888 PP

                                       HH CS
                              SecY 182 If 183
                                       I+
  gi|242399700|ref|YP_002995125.1| 260 IV 261
                                       75 PP

>> Claudin_3  Tight junction protein, Claudin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   2.4   5.8e-05      0.17       5      80 ..      75     148 ..      65     158 .. 0.88
   2 ?    2.7   7.9     0.037   1.1e+02      12      91 ..     154     232 ..     145     267 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.8e-05
                         Claudin_3   5 lkalgvlvvisfilnivglftpaWiteestkkeksiGivPfssteagwleaasimmyislalflvvi.liyivivrk 80 
                                       lk+lgvlv +  ++++v+ ft a   ++++ ++   G +P+     + +++ s +m + +alf+ v+ ++ +v+++ 
  gi|242399700|ref|YP_002995125.1|  75 LKYLGVLVALFPLMSAVAHFTVAGPKFDKYVENLKKGMNPYRW---YEYTLSSSVMIVLIALFIGVVdFWSLVMIFT 148
                                       799********************9999999999*********9...99****************9998666655554 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.037
                         Claudin_3  12 vvisfilnivglftpaWiteestkkeksiGivPfssteagwleaasimmyislalflvviliyivivrkvkkngysk 88 
                                       ++++ +++++  +t++ + ++ + +    GivP+ +  a++++a+s+       ++ ++++iy++ ++++  n y  
  gi|242399700|ref|YP_002995125.1| 154 MLLGYLMELLNQYTEK-TNWSPFIIGWISGIVPWIVLFAYFFAAVSVAEAKPPTFVYLIFFIYFILFNIFPLNMYLQ 229
                                       5555555555555544.333444666789*******99999*****9999888888888888888888888888887 PP

                         Claudin_3  89 svr 91 
                                       ++r
  gi|242399700|ref|YP_002995125.1| 230 YKR 232
                                       776 PP

>> DsbD_2  Cytochrome C biogenesis protein transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.4      0.14     4e+02      68      93 ..      19      44 ..       8      98 .. 0.49
   2 ?   10.1   6.8   0.00019      0.57      71     161 ..     129     214 ..     110     248 .. 0.70

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.14
                            DsbD_2 68 glrallgvllgllllllglklllkkk 93
                                       + ++l+ ++g+ +l+lg+ l ++++
  gi|242399700|ref|YP_002995125.1| 19 IIAGILHAITGVSMLALGFLLEWERS 44
                                      33344444444444444443333333 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00019
                            DsbD_2  71 allgvllgllllllglklllkkkllklerlgkllsrllkklakklkslasalllGllnGllpCglvysalllalasg 147
                                        l+++++g++     ++l++  +l+++  l + l +ll+++++  k+ +s++++G + G++p  ++++ +++a++ +
  gi|242399700|ref|YP_002995125.1| 129 VLIALFIGVVDF---WSLVMIFTLNAVTMLLGYLMELLNQYTE--KTNWSPFIIGWISGIVPWIVLFAYFFAAVSVA 200
                                       222222222222...2333334556666677777777777777..89***************887777777777777 PP

                            DsbD_2 148 saleGalvmlaFgL 161
                                       +a    +v l+F +
  gi|242399700|ref|YP_002995125.1| 201 EAKPPTFVYLIFFI 214
                                       77777777777765 PP

>> DUF373  Domain of unknown function (DUF373)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.2      0.22   6.5e+02     176     200 ..      16      40 ..       9      66 .. 0.71
   2 ?    7.4   7.3   0.00089       2.6     202     327 ..     100     251 ..      70     267 .. 0.66

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.22
                            DUF373 176 lpelalaiillllGlylllrGfgld 200
                                        ++++++i+ ++ G+ +l  Gf l+
  gi|242399700|ref|YP_002995125.1|  16 RMNIIAGILHAITGVSMLALGFLLE 40 
                                       5677888888888888888888775 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.00089
                            DUF373 202 lleelleklkesleegritfvtyvvallllligiisgyislesvssasvssglltlilafiyg.............. 264
                                       ++++++e+lk+ ++ +r    t   +++++li+++ g++ ++s+     + + +t++l ++++              
  gi|242399700|ref|YP_002995125.1| 100 KFDKYVENLKKGMNPYRWYEYTLSSSVMIVLIALFIGVVDFWSLVM-IFTLNAVTMLLGYLMEllnqytektnwspf 175
                                       4667888999999999999999999999999999999999999988.344444444444555555558899999999 PP

                            DUF373 265 avewlalailtaslgkiideylkreekdiarllllpflvlaiglvlygasaylls.............lsilalsl 327
                                       ++ w+   +  ++l   + ++++  e +   +++l+f+++ i + ++ +  yl +               +++lsl
  gi|242399700|ref|YP_002995125.1| 176 IIGWISGIVPWIVLFAYFFAAVSVAEAKPPTFVYLIFFIYFILFNIFPLNMYLQYkrvgkwkdylhgeKVYITLSL 251
                                       5555555555555544444444344445556677777777777777777777733677777777776633344444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1164  (0.0649228); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); 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):               6  [number of targets reported over threshold]
# CPU time: 0.69u 0.38s 00:00:01.06 Elapsed: 00:00:00.58
# Mc/sec: 1396.59
//
Query:       gi|242399701|ref|YP_002995126.1|  [L=149]
Description: Flavodoxin, FldA [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.1e-11   42.5   0.0    9.1e-05   22.7   0.0    2.2  2  Flavodoxin_5  Flavodoxin domain
      1e-07   31.8   0.4      0.011   15.4   0.0    2.1  2  Flavodoxin_3  Flavodoxin domain
     0.0012   18.6   0.1      0.068   12.9   0.1    2.1  1  Flavodoxin_4  Flavodoxin
     0.0013   18.5   0.0      0.002   17.9   0.0    1.5  1  FMN_red       NADPH-dependent FMN reductase
     0.0017   18.6   0.0      0.086   13.1   0.0    2.4  2  Flavodoxin_1  Flavodoxin


Domain annotation for each model (and alignments):
>> Flavodoxin_5  Flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   6.8e-07    0.0024       1      29 [.       4      32 ..       4      42 .. 0.90
   2 !   22.7   0.0   2.5e-08   9.1e-05      34     100 ..      59     122 ..      39     143 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 6.8e-07
                      Flavodoxin_5  1 lilYsSrdGqTkkiaeriaeelreegelv 29
                                      l+++ Sr G+Tk++a++ia++l + +++v
  gi|242399701|ref|YP_002995126.1|  4 LVVFYSRSGTTKRVAQEIAKALNADVDEV 32
                                      799********************998775 PP

  == domain 2  score: 22.7 bits;  conditional E-value: 2.5e-08
                      Flavodoxin_5  34 vekesedlesydavvigasvyygkllpelakFvekhreaLstkpvalfsvsltarkpeksyvrkflk 100
                                       + ++++d ++yd v+ig+sv +g++ p+++ ++ +++++++  + a+f+++  + ++  +++++ l+
  gi|242399701|ref|YP_002995126.1|  59 I-EFEKDPSEYDFVIIGTSVWNGRVTPAIRTYLLQNKDKIK--NAAFFCTCEGRAGKCLEQMEELLE 122
                                       5.47789******************************9886..567777665433332234444444 PP

>> Flavodoxin_3  Flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   3.1e-06     0.011       1      34 [.       4      35 ..       4      58 .. 0.77
   2 !   15.4   0.1   3.2e-06     0.011      28     124 ..      58     147 ..      44     149 .] 0.79

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.1e-06
                      Flavodoxin_3  1 lilysSltGNTkkvAeaikealeeekeivsikea 34
                                      l+++ S++G Tk vA++i++al++  ++ ++ ++
  gi|242399701|ref|YP_002995126.1|  4 LVVFYSRSGTTKRVAQEIAKALNA--DVDEVIDK 35
                                      599********************9..44444333 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 3.2e-06
                      Flavodoxin_3  28 ivsikeakekveeadvvfvGfwvdkgtadeealkfletlknk..killfgTlGagkdseyakkilekvkalleknne 102
                                        +++  +k+  +e+d+v++G+ v  g    +++++l + k+k  + ++f T+        a k+le++++llek+  
  gi|242399701|ref|YP_002995126.1|  58 EIEF--EKD-PSEYDFVIIGTSVWNGRVTPAIRTYLLQNKDKikNAAFFCTCEG-----RAGKCLEQMEELLEKK-P 125
                                       3333..344.569**********************9888774337889999854.....5789*******99875.6 PP

                      Flavodoxin_3 103 vlgeflcqGkisekvrekyekl 124
                                       vl++ l + k++e ++e +e+l
  gi|242399701|ref|YP_002995126.1| 126 VLKKILMRKKLDEGIKELMEEL 147
                                       8899999999999999999887 PP

>> Flavodoxin_4  Flavodoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.1   1.9e-05     0.068       1      32 [.       2      33 ..       2     135 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.9e-05
                                      -EEEEE--SSSHHHHHHHHHHHHHT-EEEE-- CS
                      Flavodoxin_4  1 kilvayfscsgvtkavaeklaaitgadlyeik 32
                                      k lv ++s sg tk va+++a    ad+ e+ 
  gi|242399701|ref|YP_002995126.1|  2 KTLVVFYSRSGTTKRVAQEIAKALNADVDEVI 33
                                      67999****************99999998874 PP

>> FMN_red  NADPH-dependent FMN reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   5.7e-07     0.002       1      94 [.       1      89 [.       1     127 [. 0.77

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 5.7e-07
                                      -EEEEEES--STT-HHHHHHHHHHCCT-T.T-CE.EEEE..TTTS..--..---HCHGHTCGGSHHHHHHHHHHHH-SC CS
                           FMN_red  1 mkilvisGSlrkgsntrklaewaaealkeagaev.elid..ladl.ilpcalcdkdlesegqtsddvaellekiaaada 75
                                      mk lv++ S +  ++t+++a+++a+al   +a+v e+id       il+  ++ ++ +     +    e+ +   + d 
  gi|242399701|ref|YP_002995126.1|  1 MKTLVVFYSRS--GTTKRVAQEIAKAL---NADVdEVIDkkS-RRgILG--FLRAGYDA-TRGKTTEIEFEKDPSEYDF 70
                                      67777777765..9*************...577745667432.223566..66655533.22344447999******** PP

                                      EEEEEEECTTCE-HHHHHH CS
                           FMN_red 76 liivtPeYngsysgllKna 94
                                      +ii+t ++ng +++++ + 
  gi|242399701|ref|YP_002995126.1| 71 VIIGTSVWNGRVTPAIRTY 89
                                      **************98876 PP

>> Flavodoxin_1  Flavodoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0   2.4e-05     0.086       1      26 [.       5      29 ..       5      38 .. 0.86
   2 ?    3.3   0.0     0.025        90      37      73 ..      60      89 ..      43     124 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.4e-05
                                      EEEETSSSHHHHHHHHHHHHHHHTTT CS
                      Flavodoxin_1  1 ilYgSetGnteklAkqlaeelgehgf 26
                                      ++++S  G+t+ +A+++a+ l+ +++
  gi|242399701|ref|YP_002995126.1|  5 VVFYSRSGTTKRVAQEIAKALN-ADV 29
                                      89*******************9.454 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.025
                                      TSCGGGGGTHSEEEEEEEEETTTBEEGGGHHHHHHHH CS
                      Flavodoxin_1 37 deslseieeealllvvtsTfgnGdppengesffqdll 73
                                      +   ++  e+++++++ts ++ G ++     ++ + +
  gi|242399701|ref|YP_002995126.1| 60 EF-EKDPSEYDFVIIGTSVWN-GRVT-----PAIRTY 89
                                      43.3788899********777.7666.....444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       906  (0.0505327); expected 358.6 (0.02)
Passed bias filter:                      666  (0.0371465); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.61u 0.40s 00:00:01.01 Elapsed: 00:00:00.57
# Mc/sec: 782.72
//
Query:       gi|242399702|ref|YP_002995127.1|  [L=138]
Description: Regulatory protein, MarR [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-08   34.8   1.6    1.1e-08   34.8   0.3    1.7  2  TrmB             Sugar-specific transcriptional regulator Trm
    5.1e-08   33.3   1.0    8.4e-08   32.6   0.2    1.7  2  HTH_27           Winged helix DNA-binding domain
    1.4e-07   31.3   0.2    3.4e-07   30.1   0.2    1.6  1  MarR             MarR family
      2e-07   30.8   0.0    3.2e-07   30.1   0.0    1.3  1  MarR_2           MarR family
    6.1e-06   26.0   0.1     0.0091   15.8   0.0    2.4  2  HTH_IclR         IclR helix-turn-helix domain
    3.6e-05   23.7   0.2    6.2e-05   22.9   0.2    1.4  1  HTH_45           Winged helix-turn-helix
    4.2e-05   23.7   1.7    4.5e-05   23.6   0.5    1.7  1  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
    5.3e-05   23.6   1.4    0.00013   22.3   1.3    1.9  1  Penicillinase_R  Penicillinase repressor
    6.7e-05   22.5   0.3    0.00016   21.3   0.1    1.7  1  GntR             Bacterial regulatory proteins, gntR family
    0.00026   21.0   2.1    0.00035   20.5   2.1    1.1  1  CortBP2          Cortactin-binding protein-2
     0.0004   20.3   0.0    0.00061   19.7   0.0    1.4  1  HTH_Crp_2        Crp-like helix-turn-helix domain
    0.00049   19.6   0.2    0.00049   19.6   0.2    2.0  3  HTH_24           Winged helix-turn-helix DNA-binding
    0.00059   19.7   0.3     0.0015   18.4   0.3    1.7  1  HTH_36           Helix-turn-helix domain
     0.0008   19.7   0.1     0.0014   18.9   0.1    1.4  1  Rrf2             Transcriptional regulator
     0.0023   17.7   0.9      0.031   14.1   0.3    2.7  3  HTH_10           HTH DNA binding domain
     0.0024   17.9   0.0     0.0048   16.9   0.0    1.4  1  S10_plectin      Plectin/S10 domain
     0.0029   17.5   0.9     0.0079   16.1   0.4    2.1  2  HTH_11           HTH domain
      0.003   17.6   0.1     0.0081   16.2   0.1    1.8  1  HTH_20           Helix-turn-helix domain
  ------ inclusion threshold ------
      0.014   15.3   0.6      0.037   14.0   0.2    2.0  1  HTH_12           Ribonuclease R winged-helix domain
      0.015   15.1   0.1      0.027   14.2   0.1    1.6  1  DUF4364          Domain of unknown function (DUF4364)
       0.02   14.6   0.5        0.2   11.5   0.2    2.5  2  LexA_DNA_bind    LexA DNA binding domain
      0.024   14.7   0.8      0.033   14.2   0.8    1.4  1  GPP34            Golgi phosphoprotein 3 (GPP34)
      0.025   14.4   0.4      0.052   13.4   0.4    1.6  1  HxlR             HxlR-like helix-turn-helix
      0.032   14.3   0.0      0.039   14.0   0.0    1.1  1  Replic_Relax     Replication-relaxation
      0.041   13.7   0.2       0.15   11.9   0.0    2.1  1  HTH_23           Homeodomain-like domain
      0.044   13.5   1.2      0.081   12.6   0.3    2.0  2  HTH_41           Helix-turn-helix domain
      0.047   13.6   0.3      0.047   13.6   0.3    2.3  2  HTH_5            Bacterial regulatory protein, arsR family
      0.055   13.4   0.1       0.14   12.2   0.1    1.8  1  Cdc6_C           CDC6, C terminal winged helix domain
      0.078   13.0   0.0       0.14   12.2   0.0    1.4  1  HTH_29           Winged helix-turn helix
       0.08   12.7   1.1       0.25   11.1   1.1    1.9  1  LacI             Bacterial regulatory proteins, lacI family
        0.1   12.5   0.3       0.65   10.0   0.1    2.4  1  HTH_1            Bacterial regulatory helix-turn-helix protei
       0.11   12.5   0.6       0.21   11.6   0.1    1.6  2  APAF1_C          APAF-1 helical domain
       0.12   12.7   0.1       0.19   12.0   0.1    1.4  1  PaaX             PaaX-like protein
       0.12   12.3   0.5       0.32   11.0   0.5    1.7  1  TBPIP            TBPIP/Hop2 winged helix domain
       0.15   12.1   0.2       0.15   12.1   0.2    2.2  2  z-alpha          Adenosine deaminase z-alpha 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 !   34.8   0.3   2.2e-11   1.1e-08       3      59 ..      29      83 ..      27      93 .. 0.78
   2 ?   -2.4   0.0       9.2   4.7e+03       7      17 ..     116     126 ..     105     130 .. 0.46

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 2.2e-11
                                      HCHHHHHCCCHCHHHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTT CS
                              TrmB  3 klGLseyEakvYlaLl.klgpatadeiaeelgvprskvYevLrsLedkGlVerekgrp 59
                                      +lG +  E+k+   L+  +  +t +++ +e +v++s++ +vL+sLe+kG+V+re++ +
  gi|242399702|ref|YP_002995127.1| 29 ELGVTFLEFKA---LVhLKSAKTQKDLLKEMNVSKSTASKVLSSLERKGIVKRERRGK 83
                                      55666666555...5544788999******************************9653 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 9.2
                                       HHHCCCHCHHH CS
                              TrmB   7 seyEakvYlaL 17 
                                       ++ E + +l L
  gi|242399702|ref|YP_002995127.1| 116 TSKEKSEFLSL 126
                                       33344444444 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 !   32.6   0.2   1.6e-10   8.4e-08      14      68 .]      42      93 ..      32      93 .. 0.84
   2 ?   -1.6   0.0       7.6   3.9e+03      40      54 ..     105     119 ..      95     129 .. 0.54

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 1.6e-10
                            HTH_27 14 hrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                      h    k+++dl + +nv++s++s++l+ L++kG v+r++    +++  v+lTdkG
  gi|242399702|ref|YP_002995127.1| 42 HLKSAKTQKDLLKEMNVSKSTASKVLSSLERKGIVKRERR---GKAYIVELTDKG 93
                                      44588999***************************55544...699********9 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 7.6
                            HTH_27  40 kkLtekGLvertgde 54 
                                       k+L+ek + ++t +e
  gi|242399702|ref|YP_002995127.1| 105 KELEEKMFAQMTSKE 119
                                       455555555555555 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.2   6.6e-10   3.4e-07      17      51 ..      46      80 ..      33      82 .. 0.88

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 6.6e-10
                                      TEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                              MarR 17 plsvseLakklgvskstvtrvldrLekkGlieRsk 51
                                      + ++++L k ++vskst+++vl  Le+kG ++R++
  gi|242399702|ref|YP_002995127.1| 46 AKTQKDLLKEMNVSKSTASKVLSSLERKGIVKRER 80
                                      56899****************************98 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   6.2e-10   3.2e-07       1      55 [.      30      80 ..      30      84 .. 0.94

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 6.2e-10
                                      TT--HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2  1 lgltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                      lg+t  ++ +L +L  +     t+++l +++++sks++s++l  L+++G v r++
  gi|242399702|ref|YP_002995127.1| 30 LGVTFLEFKALVHLKSAK----TQKDLLKEMNVSKSTASKVLSSLERKGIVKRER 80
                                      699***********9999....*****************************9984 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.8e-05    0.0091      22      51 ..      50      79 ..      38      80 .. 0.88
   2 !    8.2   0.0    0.0042       2.2       3      28 ..      91     116 ..      89     128 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.8e-05
                                      HHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                          HTH_IclR 22 selArrtglpkStvhRlLqtLvelGyveqd 51
                                      ++l ++  ++kSt++  L++L++ G+v+++
  gi|242399702|ref|YP_002995127.1| 50 KDLLKEMNVSKSTASKVLSSLERKGIVKRE 79
                                      678888999******************986 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0042
                                       HHHHHHHCT-CTTBSS-BHHHHHHHH CS
                          HTH_IclR   3 dRalaiLdalaeapqeltlselArrt 28 
                                       d++l++L+a++ea+ el  +  A+ t
  gi|242399702|ref|YP_002995127.1|  91 DKGLEVLKAIEEAGKELEEKMFAQMT 116
                                       8*************997655555555 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.2   1.2e-07   6.2e-05      18      72 ..      45     103 ..      37     108 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.2e-07
                            HTH_45  18 geakkTkimykanLsykllnkYLdmLvekgli..kkskekY..vlTekGlelleklkel 72 
                                       + +++  ++++ n s ++++k L+ L  kg++  + +++ Y  +lT+kGle+l+ ++e 
  gi|242399702|ref|YP_002995127.1|  45 SAKTQKDLLKEMNVSKSTASKVLSSLERKGIVkrERRGKAYivELTDKGLEVLKAIEEA 103
                                       445556799***********************6655788884468**********9986 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.5   8.7e-08   4.5e-05      24      57 ..      48      81 ..      41      84 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 8.7e-08
                                      -HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT CS
                    Fe_dep_repress 24 ktkdlaerLnvspssVsemlkkLekdGyveyeky 57
                                      ++kdl +++nvs+s++s+ l+ Le++G v+ e +
  gi|242399702|ref|YP_002995127.1| 48 TQKDLLKEMNVSKSTASKVLSSLERKGIVKRERR 81
                                      568999***********************98766 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   1.3   2.5e-07   0.00013      19      61 ..      44      86 ..      33     128 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 2.5e-07
                                      EHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEETTEEE CS
                   Penicillinase_R 19 tvkevveeleeekelaysTVktllrrLvkKgllsrekegrafi 61
                                      ++++ ++ l +e+++++sT   +l+ L++Kg+++re+ g+a+i
  gi|242399702|ref|YP_002995127.1| 44 KSAKTQKDLLKEMNVSKSTASKVLSSLERKGIVKRERRGKAYI 86
                                      5566678899999***************************997 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.1     3e-07   0.00016      27      63 ..      49      85 ..      48      86 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 3e-07
                                      HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTCEEE CS
                              GntR 27 ereLaaefgVsrttvReALrrLeaeglverrqgrGtf 63
                                      +++L +e++Vs++t  ++L+ Le++g+v r++++ ++
  gi|242399702|ref|YP_002995127.1| 49 QKDLLKEMNVSKSTASKVLSSLERKGIVKRERRGKAY 85
                                      67899**************************998665 PP

>> CortBP2  Cortactin-binding protein-2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   2.1   6.8e-07   0.00035      28     110 ..      40     121 ..      38     132 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 6.8e-07
                           CortBP2  28 IaaLkaekvkqlllearygskvnlsdplqALqRDselaksketsesevkklyekqlaeLekliekqreaqermleqL 104
                                       + +Lk+ k+++ ll++   sk + s++l++L+R    +k+++  ++ + +l++k l++L+++ e  +e +e+m +q+
  gi|242399702|ref|YP_002995127.1|  40 LVHLKSAKTQKDLLKEMNVSKSTASKVLSSLERKG-IVKRERRGKAYIVELTDKGLEVLKAIEEAGKELEEKMFAQM 115
                                       5689****9999999988888889*********99.556666777777779************************** PP

                           CortBP2 105 aaaekr 110
                                       ++ ek+
  gi|242399702|ref|YP_002995127.1| 116 TSKEKS 121
                                       *99986 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   1.2e-06   0.00061      23      57 ..      48      86 ..      15      96 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.2e-06
                                      HHHHHHHHTTSSHHHHHHHHHHHHHTTSEEE.TEE...E CS
                         HTH_Crp_2 23 tqeelAsmlGltretvsrilseLkreglisr.grr...i 57
                                      tq++l   ++++ +t s++ls L+r+g+++r +r+   i
  gi|242399702|ref|YP_002995127.1| 48 TQKDLLKEMNVSKSTASKVLSSLERKGIVKReRRGkayI 86
                                      89999999**********************523323342 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       9.7     5e+03      40      46 ..      26      32 ..      25      32 .. 0.80
   2 !   19.6   0.2   9.6e-07   0.00049      19      48 .]      48      77 ..      44      77 .. 0.97
   3 ?   -2.1   0.0       5.9     3e+03       3      15 ..      91     103 ..      89     105 .. 0.69

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 9.7
                            HTH_24 40 rLeeeGl 46
                                      rLee G+
  gi|242399702|ref|YP_002995127.1| 26 RLEELGV 32
                                      8999986 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 9.6e-07
                            HTH_24 19 sqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      +q++L ++ ++S+st ++ l  Le++G++k
  gi|242399702|ref|YP_002995127.1| 48 TQKDLLKEMNVSKSTASKVLSSLERKGIVK 77
                                      9***************************97 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 5.9
                            HTH_24   3 etdrkILelLqkn 15 
                                       ++ +++L+++++ 
  gi|242399702|ref|YP_002995127.1|  91 DKGLEVLKAIEEA 103
                                       5567888888875 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.3   2.9e-06    0.0015      27      55 .]      48      76 ..      43      76 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.9e-06
                            HTH_36 27 sqetlakrlglsknTvsraikeLeqlGyi 55
                                      +q++l k +++sk+T+s+ + +Le++G++
  gi|242399702|ref|YP_002995127.1| 48 TQKDLLKEMNVSKSTASKVLSSLERKGIV 76
                                      799************************85 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   2.7e-06    0.0014      13      59 ..      39      80 ..      31      92 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.7e-06
                                      HHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                              Rrf2 13 allyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvr 59
                                      al++L++ +++     +++ +++n+s+s ++k+l+ L+++g+vk +r
  gi|242399702|ref|YP_002995127.1| 39 ALVHLKSAKTQ-----KDLLKEMNVSKSTASKVLSSLERKGIVKRER 80
                                      56666666554.....69*************************8653 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.3     6e-05     0.031      25      50 ..      48      73 ..      43      75 .. 0.91
   2 ?    0.7   0.0      0.88   4.5e+02       1      11 [.      89      99 ..      89     104 .. 0.86
   3 ?   -2.6   0.0       9.8     5e+03      37      48 ..     120     131 ..     119     133 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6e-05
                            HTH_10 25 tlkeLAkelGIskstlsehLrkaesk 50
                                      t k+L ke+++skst+s+ L++ e+k
  gi|242399702|ref|YP_002995127.1| 48 TQKDLLKEMNVSKSTASKVLSSLERK 73
                                      668999****************9998 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.88
                            HTH_10  1 LTdkqlevlkl 11
                                      LTdk levlk+
  gi|242399702|ref|YP_002995127.1| 89 LTDKGLEVLKA 99
                                      9*******985 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 9.8
                            HTH_10  37 kstlsehLrkae 48 
                                       ks ++  L+ka+
  gi|242399702|ref|YP_002995127.1| 120 KSEFLSLLKKAI 131
                                       566777777775 PP

>> S10_plectin  Plectin/S10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   9.3e-06    0.0048      22      76 ..      45      99 ..      28     107 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 9.3e-06
                                      E--SS----SSS---HHHHHHHHHHCCCCTSEEEEEETTEEEEEE-HHHHHHHHH CS
                       S10_plectin 22 kkdfelkkheelnvpnlqvikalqSLksrgyvkeqfaWrhyYytLtneGieylre 76
                                      + +++    +e+nv++    k+l SL+ +g+vk++   + y   Lt++G+e+l+ 
  gi|242399702|ref|YP_002995127.1| 45 SAKTQKDLLKEMNVSKSTASKVLSSLERKGIVKRERRGKAYIVELTDKGLEVLKA 99
                                      445555666889****************************************986 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.4   1.5e-05    0.0079      12      48 ..      43      77 ..      34      96 .. 0.79
   2 ?   -2.1   0.0       7.6   3.9e+03      36      47 ..      97     108 ..      95     111 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.5e-05
                            HTH_11 12 argpisgeeLAeeLnvSrrtvrrdIkaLeelgvpIes 48
                                       ++  + ++L +e+nvS++t  + + +Le +g  I++
  gi|242399702|ref|YP_002995127.1| 43 LKSAKTQKDLLKEMNVSKSTASKVLSSLERKG--IVK 77
                                      45555899************************..333 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 7.6
                            HTH_11  36 IkaLeelgvpIe 47 
                                       +ka+ee+g ++e
  gi|242399702|ref|YP_002995127.1|  97 LKAIEEAGKELE 108
                                       677888886655 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   0.1   1.6e-05    0.0081      12      61 .]      20      83 ..       9      83 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.6e-05
                                      HHHHHHHHSTCTTB-HHHHHHHHT...............S-HHHHHHHHHHHHHCTTEEEECTEE CS
                            HTH_20 12 RrrilraLaraegltaselaerld...............lskntlsyHLrvLeeagLvevvregr 61
                                      R +++  L ++ g+t+ e+++++                +sk+t+s+ L  Le+ g+v+++r g+
  gi|242399702|ref|YP_002995127.1| 20 RKAFEERL-EELGVTFLEFKALVHlksaktqkdllkemnVSKSTASKVLSSLERKGIVKRERRGK 83
                                      66667777.666666666666663333444445555555***********************985 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.2   7.2e-05     0.037      37      66 .]      65      97 ..      45      97 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.2e-05
                            HTH_12 37 yrLrkleergltrrvgyagr...eltEkGleeL 66
                                        L +le++g+++r +++++   elt+kGle L
  gi|242399702|ref|YP_002995127.1| 65 KVLSSLERKGIVKRERRGKAyivELTDKGLEVL 97
                                      56889*************7644489****9986 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   5.3e-05     0.027      35      75 ..      62     102 ..      40     129 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.3e-05
                           DUF4364  35 dlqqalseLvesglieeeekenktlykiTekGketlelfen 75 
                                       + +++ls L+ +g ++ e++ +  + ++T+kG e+l+ +e+
  gi|242399702|ref|YP_002995127.1|  62 TASKVLSSLERKGIVKRERRGKAYIVELTDKGLEVLKAIEE 102
                                       67899*************9999999***********98875 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   0.00039       0.2      30      59 ..      51      79 ..      42      84 .. 0.83
   2 ?    0.2   0.0       1.3   6.6e+02       3      17 ..      88     102 ..      87     113 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00039
                                      HHHHHHTS-.HHHHHHHHHHHHHTTSEE-G CS
                     LexA_DNA_bind 30 eiaralglkSpsaveehLkaLerKGyierd 59
                                      ++ ++++++  s++ + L  LerKG+++r+
  gi|242399702|ref|YP_002995127.1| 51 DLLKEMNVS-KSTASKVLSSLERKGIVKRE 79
                                      556677765.999**************986 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.3
                                       ---HHHHHHHHHHHH CS
                     LexA_DNA_bind   3 kLTerQrevldlika 17 
                                       +LT++  evl+ i++
  gi|242399702|ref|YP_002995127.1|  88 ELTDKGLEVLKAIEE 102
                                       589999999999886 PP

>> GPP34  Golgi phosphoprotein 3 (GPP34)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.8   6.5e-05     0.033      71     115 ..      43      86 ..      24     130 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6.5e-05
                             GPP34  71 ikaserprsvktwvdlls..ksvrervakgLvdkGilrtekrrflgl 115
                                       +k   ++++ k++++ +   ks++ +v+++L++kGi+++e+r +  +
  gi|242399702|ref|YP_002995127.1|  43 LK---SAKTQKDLLKEMNvsKSTASKVLSSLERKGIVKRERRGKAYI 86 
                                       43...4456788888877889*******************9985444 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.4    0.0001     0.052      18      79 ..      46     103 ..      36     116 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.0001
                                       -EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHHHHHHH CS
                              HxlR  18 kkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrslepvlqel 79 
                                        k  ++l +++ ++s+++ ++ L  Le++g+++re   +       +lt+kG ++ ++++e 
  gi|242399702|ref|YP_002995127.1|  46 AKTQKDLLKEM-NVSKSTASKVLSSLERKGIVKRERRGK---AYIVELTDKGLEVLKAIEEA 103
                                       44557888888.9*********************97654...45678999998887777664 PP

>> Replic_Relax  Replication-relaxation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   7.7e-05     0.039      20      75 ..      57     106 ..      39     125 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.7e-05
                      Replic_Relax  20 fashra.tarrrLarLrelgllsrlrkrvggarggsepyvYaLtpkGarllaaqra...e 75 
                                       + s  + ta+++L  L+++g+++r ++r    +   + y+  Lt kG ++l+a ++   e
  gi|242399702|ref|YP_002995127.1|  57 NVS--KsTASKVLSSLERKGIVKR-ERR----G---KAYIVELTDKGLEVLKAIEEagkE 106
                                       333..2469**************9.222....2...489************776655331 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   0.0    0.0003      0.15      10      46 ..      39      75 ..      36      79 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0003
                            HTH_23 10 illllaeGlsvreIAreLgvsrrTvyrwlkryreeGl 46
                                      +l +l+  +++++  +e++vs++T +++l+  +++G+
  gi|242399702|ref|YP_002995127.1| 39 ALVHLKSAKTQKDLLKEMNVSKSTASKVLSSLERKGI 75
                                      6667777799********************9977986 PP

>> HTH_41  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.3   0.00016     0.081       8      43 ..      48      83 ..      38      84 .. 0.94
   2 ?   -2.2   0.0       6.7   3.4e+03       6      15 ..      97     106 ..      92     108 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00016
                            HTH_41  8 tIeelakeleLSvGlvQkALklLeddkaislerrGr 43
                                      t ++l ke+ +S  +  k L +Le +++++ errG+
  gi|242399702|ref|YP_002995127.1| 48 TQKDLLKEMNVSKSTASKVLSSLERKGIVKRERRGK 83
                                      567999*****************************7 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 6.7
                            HTH_41   6 lktIeelake 15 
                                       lk Iee  ke
  gi|242399702|ref|YP_002995127.1|  97 LKAIEEAGKE 106
                                       5566666555 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.3   9.2e-05     0.047      16      46 ..      47      77 ..      39      78 .. 0.90
   2 ?   -2.6   0.0       9.9   5.1e+03      36      43 ..      97     104 ..      94     106 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.2e-05
                                      EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5 16 lcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      ++  +l +e+++s+st S  L+ L+  G+V+
  gi|242399702|ref|YP_002995127.1| 47 KTQKDLLKEMNVSKSTASKVLSSLERKGIVK 77
                                      566899************************7 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 9.9
                                       HHHHHHTT CS
                             HTH_5  36 LkkLreaG 43 
                                       Lk+ +eaG
  gi|242399702|ref|YP_002995127.1|  97 LKAIEEAG 104
                                       55555555 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 ?   12.2   0.1   0.00027      0.14      37      80 ..      58      95 ..      39      99 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00027
                                      --HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEESSSCHH CS
                            Cdc6_C 37 ltqrevsdllseLemlgileleksskGrregrtrkisLnvdpdd 80
                                      ++ ++ s++ls Le +gi+++e++      g+ + ++L+    +
  gi|242399702|ref|YP_002995127.1| 58 VSKSTASKVLSSLERKGIVKRERR------GKAYIVELTDKGLE 95
                                      688999***************976......77777777665555 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00028      0.14       4      50 ..      39      82 ..      38      91 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00028
                            HTH_29  4 allllaeGvstvsqiAkllglsrrtvyrwlkrfeegGlaalldrrrs 50
                                      al +l+ +  t +++ k +++s++t  ++l   e +G+   ++ rr+
  gi|242399702|ref|YP_002995127.1| 39 ALVHLKSAK-TQKDLLKEMNVSKSTASKVLSSLERKGI--VKRERRG 82
                                      677788887.99*************************6..6553333 PP

>> LacI  Bacterial regulatory proteins, lacI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.1    0.0005      0.25       3      23 ..      50      70 ..      48     104 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0005
                                      HHHHHHCTS-HHHHHHHCTTS CS
                              LacI  3 kDVArlAGVSkaTVSrvLnnk 23
                                      kD+ ++ +VSk+T+S+vL++ 
  gi|242399702|ref|YP_002995127.1| 50 KDLLKEMNVSKSTASKVLSSL 70
                                      56667779**********875 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 ?   10.0   0.1    0.0013      0.65      21      59 ..      54      93 ..      54      94 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0013
                                      HHHTS-HHHHHHHHHHHHHHHTS-SEEESSSE....EEE-HHH CS
                             HTH_1 21 eeLglsqpavsrqikrLEeelgvpLfeRtgrg....lrLTeaG 59
                                      +e+++s +++s+ +++LE+     ++ R  rg    ++LT+ G
  gi|242399702|ref|YP_002995127.1| 54 KEMNVSKSTASKVLSSLERKG---IVKRERRGkayiVELTDKG 93
                                      689***************964...4555445455777777777 PP

>> APAF1_C  APAF-1 helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1    0.0004      0.21      45      98 ..       5      58 ..       2      74 .. 0.90
   2 ?   -1.7   0.0       5.2   2.7e+03      79      98 ..     110     129 ..      97     135 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0004
                           APAF1_C 45 veelkallldldwieakvkltgpsslledyvkyrkileendeeeledfeeflsv 98
                                       e+++ l+++l w+ +k+    + +l   + +++++++ + +++ +d+++ ++v
  gi|242399702|ref|YP_002995127.1|  5 SEKACDLISELYWVMRKAFEERLEELGVTFLEFKALVHLKSAKTQKDLLKEMNV 58
                                      6899**************************************999999876655 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 5.2
                           APAF1_C  79 kileendeeeledfeeflsv 98 
                                       k++ +  ++e ++f+++l++
  gi|242399702|ref|YP_002995127.1| 110 KMFAQMTSKEKSEFLSLLKK 129
                                       66666667777777777765 PP

>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00037      0.19      29      70 .]      52      93 ..      45      93 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00037
                              PaaX 29 llaelGiseslvRaalsRlakaGwlvrekegrrsfYrLsdkg 70
                                      ll+e+ +s s+    ls l+++G ++re+ g++ + +L+dkg
  gi|242399702|ref|YP_002995127.1| 52 LLKEMNVSKSTASKVLSSLERKGIVKRERRGKAYIVELTDKG 93
                                      8999***************************99999****97 PP

>> TBPIP  TBPIP/Hop2 winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.5   0.00062      0.32      25      58 ..      52      86 ..      44      88 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00062
                             TBPIP 25 nlqk.klgKtavqkaLdeLvdegkiieKeyGKqki 58
                                       l++ +++K ++ k+L +L+ +g ++    GK+ i
  gi|242399702|ref|YP_002995127.1| 52 LLKEmNVSKSTASKVLSSLERKGIVKRERRGKAYI 86
                                      467789********************999999866 PP

>> z-alpha  Adenosine deaminase z-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2    0.0003      0.15      19      54 ..      44      79 ..      35      82 .. 0.88
   2 ?   -0.9   0.0       3.4   1.7e+03       9      18 ..      96     105 ..      90     129 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0003
                                      TCECCHHHHHHHHCC-HHHHHHHHHHHHHTTSEEEE CS
                           z-alpha 19 kkaatalalergLstpkreiNrvLydlerkgkvyre 54
                                      k+a t+ +l  +++  k  + +vL +lerkg v re
  gi|242399702|ref|YP_002995127.1| 44 KSAKTQKDLLKEMNVSKSTASKVLSSLERKGIVKRE 79
                                      4778999999999999*****************998 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 3.4
                                       HHHHHHHC-T CS
                           z-alpha   9 ilelLeelge 18 
                                       +l+++ee g 
  gi|242399702|ref|YP_002995127.1|  96 VLKAIEEAGK 105
                                       6777777773 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1260  (0.0702772); expected 358.6 (0.02)
Passed bias filter:                      646  (0.036031); 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):              35  [number of targets reported over threshold]
# CPU time: 0.57u 0.33s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 824.48
//
Query:       gi|242399703|ref|YP_002995128.1|  [L=459]
Description: MatE family member protein [Thermococcus sibiricus MM 739]
Scores for complete 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-56  188.2  35.2    4.3e-33  114.3  10.4    2.9  4  MatE             MatE
    5.8e-13   49.1  18.0      5e-12   46.1   5.4    4.8  4  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai
  ------ inclusion threshold ------
       0.06   12.2   0.2      0.097   11.5   0.2    1.2  1  DUF1177          Protein of unknown function (DUF1177)


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 !  114.3  10.4   7.1e-37   4.3e-33       1     161 []      26     186 ..      26     186 .. 0.99
   2 ?   -2.6   0.4      0.65   3.9e+03      75      89 ..     201     215 ..     191     221 .. 0.47
   3 !   87.9  16.7   9.3e-29   5.6e-25       1     161 []     248     413 ..     248     413 .. 0.95
   4 ?   -3.2   0.0      0.94   5.6e+03      44      69 ..     427     452 ..     422     456 .. 0.55

  Alignments for each domain:
  == domain 1  score: 114.3 bits;  conditional E-value: 7.1e-37
                              MatE   1 PialenllesllslidtllvgrlgskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqgli 77 
                                       P+++ + ++++++l+d ++v++lg++alAav++++++++ +++++ gl++++++ +++++Ga+++++a +++++++i
  gi|242399703|ref|YP_002995128.1|  26 PMMIGMSVQTIYNLVDGIWVSGLGPNALAAVGLFFPVFMGIIALAAGLGVGASSAIARRIGARDKEGADNVAVHAII 102
                                       99*************************************************************************** PP

                              MatE  78 lllllsliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislislll 154
                                       l+++l+++i l +l  ++ ++  +++  e + la  y r+l++g+++ ++++v +gilrg g++ +++ ++++++ l
  gi|242399703|ref|YP_002995128.1| 103 LSVILGVAIPLTMLPTIDSLFMSMGARGEAVDLAIAYARVLLIGAFVAVFSNVGNGILRGEGDANRAMLAMVLGSGL 179
                                       ***************************************************************************** PP

                              MatE 155 niplnyl 161
                                       n++l+++
  gi|242399703|ref|YP_002995128.1| 180 NMILDPI 186
                                       ****986 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.65
                              MatE  75 glilllllsliiall 89 
                                       +++l++ + ++++++
  gi|242399703|ref|YP_002995128.1| 201 ATLLSMMVTALFIAY 215
                                       223333333333333 PP

  == domain 3  score: 87.9 bits;  conditional E-value: 9.3e-29
                              MatE   1 Pialenllesllslidtllvgrl.gskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqgl 76 
                                       P+ l++l +s+  ++++ ++ +  g++ +A+ + a+++++l +v++lg++ta+t+++g a+G++n +++++a+ +++
  gi|242399703|ref|YP_002995128.1| 248 PASLSQLSMSIAMFFLNRVAIMAgGENGVAVFTSAWRVTMLGIVPILGMATATTAVTGAAYGERNIEKLETAYLYAI 324
                                       999************************************************************************** PP

                              MatE  77 illlllsliiallvllfseqilslftqdee...vlelakrylrililgipalalqlvlsgilrgagktkvplyisli 150
                                       +l++ + l +++++++f++q ++lft++e+   + +     lr l +++++  + +++s++++g+g+ + +l+++++
  gi|242399703|ref|YP_002995128.1| 325 KLAFMIELGVIAFIMVFAPQVAYLFTYSEAaqvIKPELISALRTLPIFLVLTPFGMMTSAMFQGIGEGEKSLVLTIF 401
                                       ********************************97777777777777777777788********************** PP

                              MatE 151 sl.llniplnyl 161
                                       ++ + ++ ++yl
  gi|242399703|ref|YP_002995128.1| 402 RTlIMQVGFAYL 413
                                       **9999999996 PP

  == domain 4  score: -3.2 bits;  conditional E-value: 0.94
                              MatE  44 fllglstalttlvgqalGaknfkrak 69 
                                       +++ +++ +++l+g  +G  ++k++k
  gi|242399703|ref|YP_002995128.1| 427 IGIVMGNMVAALTGFTWGRLKVKALK 452
                                       44445555556666666666666655 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 ?   -3.2   7.8       1.3   7.7e+03     105     139 ..      33      68 ..       8     121 .. 0.61
   2 !   46.1   5.4   8.4e-16     5e-12       3      85 ..     141     227 ..     139     239 .. 0.87
   3 ?   -4.2   7.4       2.7   1.6e+04      58     134 ..     249     337 ..     242     343 .. 0.60
   4 !   16.9   4.7   8.4e-07     0.005       2      72 ..     366     439 ..     365     452 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.3
                   Polysacc_synt_C 105 vylllllllgllllaal..alllavlvgalvYlllll 139
                                       v ++++l+ g++ +  l  + l+av++   v+++++ 
  gi|242399703|ref|YP_002995128.1|  33 VQTIYNLVDGIWVSG-LgpNALAAVGLFFPVFMGIIA 68 
                                       455666666666555.335555555555555544443 PP

  == domain 2  score: 46.1 bits;  conditional E-value: 8.4e-16
                   Polysacc_synt_C   3 ailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllli..plfgivGaaiatvlallvvavln..ly 75 
                                       ++l ++++++++s+v+++iL g g + +a++a+v+g  +++il  ++i    fg+vGaa+at+l+++v+a+++  + 
  gi|242399703|ref|YP_002995128.1| 141 RVLLIGAFVAVFSNVGNGILRGEGDANRAMLAMVLGSGLNMILDPIFIytLGFGVVGAAYATLLSMMVTALFIayWL 217
                                       7999********************************************555779****************9995556 PP

                   Polysacc_synt_C  76 alrrllgikl 85 
                                       +++r + +++
  gi|242399703|ref|YP_002995128.1| 218 FVKRDTYVDI 227
                                       6777777776 PP

  == domain 3  score: -4.2 bits;  conditional E-value: 2.7
                   Polysacc_synt_C  58 aaiatvlallvvavlnlyalrrllgiklellrrllkpllaalvmgivvylllllllglllla............ala 122
                                       a+++ +   +++++ln +a++      + ++++ +++ ++++v  + + + +  + g+  ++            a+ 
  gi|242399703|ref|YP_002995128.1| 249 ASLSQLSMSIAMFFLNRVAIMAGGENGVAVFTSAWRVTMLGIVPILGMATATTAVTGAAYGErniekletaylyAIK 325
                                       67777778888888888888886655554577777777777776666554555555444444555577776666443 PP

                   Polysacc_synt_C 123 lllavlvgalvY 134
                                       l++ + +g++++
  gi|242399703|ref|YP_002995128.1| 326 LAFMIELGVIAF 337
                                       333333444444 PP

  == domain 4  score: 16.9 bits;  conditional E-value: 8.4e-07
                   Polysacc_synt_C   2 LailalsiiflslstvlssiLqglgrqkialkalvi.galvklilnllli..plfgivGaaiatvlallvvavl 72 
                                       L+ l + ++++ + +++s+++qg+g+  + l+ +++ ++++++++ +l++   +fg+ G+ i++v + +v+a+ 
  gi|242399703|ref|YP_002995128.1| 366 LRTLPIFLVLTPFGMMTSAMFQGIGEGEKSLVLTIFrTLIMQVGFAYLFVhyTSFGLRGVWIGIVMGNMVAALT 439
                                       67777889999999************999999888835679*********77799***********99999875 PP

>> DUF1177  Protein of unknown function (DUF1177)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   1.6e-05     0.097     196     249 ..     285     337 ..     265     340 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 1.6e-05
                           DUF1177 196 PavatkaPvvgvAittetvvpGcatgashledleeaarfviEvakefgkgkvkf 249
                                        ++   +P++g+A+ ++t+v+G a g  ++e+le+a  ++i +a  ++ g ++f
  gi|242399703|ref|YP_002995128.1| 285 VTMLGIVPILGMAT-ATTAVTGAAYGERNIEKLETAYLYAIKLAFMIELGVIAF 337
                                       5566679*****96.5689************************99998887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (459 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       713  (0.039768); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.67u 0.33s 00:00:01.00 Elapsed: 00:00:00.55
# Mc/sec: 2520.83
//
Query:       gi|242399704|ref|YP_002995129.1|  [L=67]
Description: 4-oxalocrotonate tautomerase, [Thermococcus sibiricus MM 739]
Scores for complete 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   33.5   1.6    3.9e-08   33.1   1.6    1.3  1  Tautomerase      Tautomerase enzyme
  ------ inclusion threshold ------
      0.029   14.5   1.0      0.031   14.4   1.0    1.1  1  Spore_YhcN_YlaJ  Sporulation lipoprotein YhcN/YlaJ (Spore_Yhc
       0.11   12.4   0.0        3.7    7.5   0.0    2.2  2  VbhA             Antitoxin VbhA


Domain annotation for each model (and alignments):
>> Tautomerase  Tautomerase enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   1.6   6.6e-12   3.9e-08       1      59 [.       5      60 ..       5      61 .. 0.89

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 6.6e-12
                                      -EEEEEESTCS-HHHHHHHHHHHHHHHHHHHTS-GGG-EEEEEEE-TTSEEETTEEHHH CS
                       Tautomerase  1 PfvnIklvegrsaeqKaeLaervTealvealgaprsaivVvieEvpaenwgvggesved 59
                                      P ++I+ ++    e K+eL++++Te++ e++++    ++V+i+E + en+gv ge ++d
  gi|242399704|ref|YP_002995129.1|  5 PTIIIEGLKAD-VETKRELVKKITEVVREVYKIH--HVTVIIHENELENVGVDGELLSD 60
                                      56667777666.********************96..69*****************9876 PP

>> Spore_YhcN_YlaJ  Sporulation lipoprotein YhcN/YlaJ (Spore_YhcN_YlaJ)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   1.0   5.2e-06     0.031      56      87 ..      17      48 ..      13      65 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.2e-06
                   Spore_YhcN_YlaJ 56 dydgetaqniaqrverlegVedarvlvtgndv 87
                                      ++++e++++i++ v+++ ++++++v++++n++
  gi|242399704|ref|YP_002995129.1| 17 ETKRELVKKITEVVREVYKIHHVTVIIHENEL 48
                                      68899*************************97 PP

>> VbhA  Antitoxin VbhA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.015        89      13      28 ..       8      23 ..       6      33 .. 0.87
   2 ?    7.5   0.0   0.00061       3.7       4      29 ..      38      63 ..      37      67 .] 0.87

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.015
                              VbhA 13 elEGlepsaetvadle 28
                                       +EGl+ + et++ l+
  gi|242399704|ref|YP_002995129.1|  8 IIEGLKADVETKRELV 23
                                      68******99999876 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00061
                              VbhA  4 aVrqAlAsnelEGlepsaetvadlea 29
                                      +V   ++ nelE + ++ e+  d+ a
  gi|242399704|ref|YP_002995129.1| 38 HVTVIIHENELENVGVDGELLSDAIA 63
                                      78899***************999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       945  (0.0527079); expected 358.6 (0.02)
Passed bias filter:                      559  (0.0311785); 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: 0.49u 0.35s 00:00:00.84 Elapsed: 00:00:00.52
# Mc/sec: 390.74
//
Query:       gi|242399705|ref|YP_002995130.1|  [L=72]
Description: hypothetical protein TSIB_1730 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score 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   14.4   3.5      0.026   14.1   3.5    1.1  1  Ac81      Baculoviridae AC81


Domain annotation for each model (and alignments):
>> Ac81  Baculoviridae AC81
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   3.5   1.4e-06     0.026      91     125 ..       8      44 ..       3      53 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.4e-06
                              Ac81  91 vkcdyCvkeeleenvq..kdnnFnilfnNCeklikgv 125
                                        +c+ C+ e+le+ v+  k++nFn+ ++ C +l+ + 
  gi|242399705|ref|YP_002995130.1|   8 KVCKFCAGERLEDIVKrlKERNFNVSVEECIELCAKY 44 
                                       68*************9667***********9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       893  (0.0498076); expected 358.6 (0.02)
Passed bias filter:                      620  (0.0345808); 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 0.36s 00:00:00.88 Elapsed: 00:00:00.54
# Mc/sec: 403.37
//
Query:       gi|242399706|ref|YP_002995131.1|  [L=109]
Description: hypothetical protein TSIB_1731 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       318  (0.0177366); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.33s 00:00:00.87 Elapsed: 00:00:00.53
# Mc/sec: 618.37
//
Query:       gi|242399707|ref|YP_002995132.1|  [L=420]
Description: Cytochrome c-type biogenesis protein [Thermococcus sibiricus MM 739]
Scores for 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-13   48.5  22.8    1.1e-11   45.1  22.8    2.4  1  DsbD           Cytochrome C biogenesis protein transmembrane 
    2.1e-09   37.6  15.7    5.1e-09   36.3  15.5    1.7  2  DsbD_2         Cytochrome C biogenesis protein transmembrane 
    0.00018   21.9   0.0    0.00043   20.7   0.0    1.6  1  Thioredoxin_2  Thioredoxin-like domain
     0.0026   17.6   0.0       0.15   11.9   0.0    2.1  2  TraF           F plasmid transfer operon protein
  ------ inclusion threshold ------
      0.017   15.0   0.0      0.035   14.0   0.0    1.4  1  DUF2847        Protein of unknown function (DUF2847)
       0.02   15.0   0.2       0.28   11.3   0.0    2.1  2  Thioredoxin_4  Thioredoxin
      0.024   14.8   0.7      0.024   14.8   0.7    3.6  3  DUF4040        Domain of unknown function (DUF4040)
      0.047   13.9   0.0      0.081   13.1   0.0    1.4  1  Thioredoxin_7  Thioredoxin-like
        5.7    7.1   6.2         16    5.6   0.8    3.0  2  CytB6-F_Fe-S   Cytochrome B6-F complex Fe-S subunit


Domain annotation for each model (and alignments):
>> DsbD  Cytochrome C biogenesis protein transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.1  22.8   5.3e-15   1.1e-11       1     213 []     197     402 ..     197     402 .. 0.78

  Alignments for each domain:
  == domain 1  score: 45.1 bits;  conditional E-value: 5.3e-15
                              DsbD   1 aflaGllsflsPCilpliPaylsyisgvsvedvktekkkvkvllkallFvlGlslvfvslglsaaflgqllkdvkev 77 
                                       +f aG+ls +sPC+lpli  ++s +           k++v+      + ++Gl++ f++lg+ a+ lg+ +++++ +
  gi|242399707|ref|YP_002995132.1| 197 IFSAGILSVFSPCVLPLIVGTFSLLF---------AKRRVE------VIIVGLVMSFSLLGALAGVLGSYIVQIRGA 258
                                       599***************99999987.........234553......569*************************** PP

                              DsbD  78 irrvaglivillGlhflg.vfkievleklklllkikkkaelsvlgalllGltFalgwsPCigPvlasvlalaaskes 153
                                       +  ++gl  i++G +++   ++ ++  +     +   +++   ++ +llG + ++ w  Ci+P ++  +++aa ++s
  gi|242399707|ref|YP_002995132.1| 259 LYFIGGLGFIFVGASLISdTINQKFTSFIPHPSERVYSKNG-HIYDFLLGSALGVTWIGCIAPYVGFAVITAALSGS 334
                                       **************998525666777777777665555555.79**********************9999******* PP

                              DsbD 154 lakgallllvyvlGlaip..fllvgl.llellkkklk....slkkysk.aveiaggvllvllGvllll 213
                                       ++kg++++ vy lG+++   +ll +  l+e ++kk+     sl++ +k   e++ g++++l+G+l+l+
  gi|242399707|ref|YP_002995132.1| 335 ILKGIIIMSVYGLGIGLTiyLLLSSKdLAEWINKKFLsgkiSLNEGKKaRWEKILGIVIILFGLLMLT 402
                                       ***********98766551055544234444444443111145543331356777899999***9986 PP

>> DsbD_2  Cytochrome C biogenesis protein transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.3       0.2   4.1e+02     120     144 ..     196     220 ..     188     224 .. 0.79
   2 !   36.3  15.5   2.6e-12   5.1e-09       2     198 ..     197     398 ..     196     399 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.2
                            DsbD_2 120 salllGllnGllpCglvysalllal 144
                                       s++ +G+l  + pC l + + +++l
  gi|242399707|ref|YP_002995132.1| 196 SIFSAGILSVFSPCVLPLIVGTFSL 220
                                       78999*********88777666655 PP

  == domain 2  score: 36.3 bits;  conditional E-value: 2.6e-12
                            DsbD_2   2 afllgLlgsl.hClgmCggivlalslskpkralalllynlGRilsYallGalvgllgsvlqlageleglrallgvll 77 
                                       +f +g+l+ + +C++    iv ++sl   kr+++ ++  +G ++s++llGal+g+lgs + ++      r++l ++ 
  gi|242399707|ref|YP_002995132.1| 197 IFSAGILSVFsPCVLP--LIVGTFSLLFAKRRVEVII--VGLVMSFSLLGALAGVLGSYIVQI------RGALYFIG 263
                                       7889999999999998..8889999999999888765..788******************664......56666676 PP

                            DsbD_2  78 gllllllglklllkkkllklerlgkllsrllkklakklkslasalllGllnGllp..C..glvysalllalasgsal 150
                                       gl  +++g++l+     +k+ ++  + s   +++ +k +++   +llG + G+    C  + v +a++ a++sgs+l
  gi|242399707|ref|YP_002995132.1| 264 GLGFIFVGASLISDTINQKFTSFIPHPS---ERVYSK-NGHIYDFLLGSALGVTWigCiaPYVGFAVITAALSGSIL 336
                                       7766777777764443334433333333...333332.4555667777666643333765889************** PP

                            DsbD_2 151 eGalvmlaFgLG...Tlpalllfglllgll...........skklrkkllrlagvllillgl 198
                                       +G+++m ++gLG   T+ +ll    l++++           ++  ++++ +++g+++il+gl
  gi|242399707|ref|YP_002995132.1| 337 KGIIIMSVYGLGiglTIYLLLSSKDLAEWInkkflsgkislNEGKKARWEKILGIVIILFGL 398
                                       ***********988889999999999999944444444444335559*************98 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   2.1e-07   0.00043       3     102 ..      50     163 ..      48     168 .. 0.63

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.1e-07
                     Thioredoxin_2   3 gngkpvlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkd.............. 65 
                                        +g+++lv++++++Cp C  +k+++++ ++ ++      lk  ++ + +++++ +   ++++               
  gi|242399707|ref|YP_002995132.1|  50 HEGEYFLVFYHSETCPACTYMKNNVFPTEKAREV-----LKG-INLITIDVYRVRGL-TNLRYrvygevlviqpdnt 119
                                       57899999999*****************555555.....433.35555555555555.2222255555555555666 PP

                     Thioredoxin_2  66 ...ieenvelarkygvrgtPtivfldgk....eivarlpGyvpa 102
                                            +++  +  +gv gtPt+v++  +        + +G++++
  gi|242399707|ref|YP_002995132.1| 120 gyyRPKERGEVVNVGVPGTPTMVIFKVEngekILKSIAVGALNP 163
                                       65555566666678*******77554333544334455666666 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   7.5e-05      0.15     110     148 ..      33      71 ..      22      80 .. 0.88
   2 ?    3.6   0.0     0.026        51     162     214 ..     111     161 ..      99     167 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.5e-05
                              TraF 110 kvlndarkeekeaalkklakeygLlfFyrgkcpyceaqa 148
                                       k +n  ++ee e+ l+++++ey+L+f ++++cp+c+ + 
  gi|242399707|ref|YP_002995132.1|  33 KFYNPSNEEELEELLSAHEGEYFLVFYHSETCPACTYMK 71 
                                       678889999**************************9775 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.026
                              TraF 162 vraVsvdgrplpelpnarvdkgqaarlgvkrtPalvlvdpksqkvv..pvaaGll 214
                                       v++++ d++   +     +++g   + gv  tP++v+++ ++++ +   +a+G+l
  gi|242399707|ref|YP_002995132.1| 111 VLVIQPDNTGYYR----PKERGEVVNVGVPGTPTMVIFKVENGEKIlkSIAVGAL 161
                                       5556666665532....35899999************999997666568888876 PP

>> DUF2847  Protein of unknown function (DUF2847)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.7e-05     0.035       5      65 ..      39     101 ..      37     104 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.7e-05
                           DUF2847   5 teeqleeileeskekpvlifKhstrcsiSaealkelekeleeeeee..vkvylldviesrevS 65 
                                       +ee+lee+l+ ++ + +l+f hs +c+  + +++++  + +++e    ++++ +dv + r + 
  gi|242399707|ref|YP_002995132.1|  39 NEEELEELLSAHEGEYFLVFYHSETCPACTYMKNNVFPTEKAREVLkgINLITIDVYRVRGLT 101
                                       689************************999888887554444443224888888888888665 PP

>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00014      0.28      16      46 ..      55      86 ..      49     100 .. 0.78
   2 ?    1.4   0.0      0.16   3.2e+02     132     155 ..     129     156 ..     124     163 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00014
                                      EEEEEE-TT-HHHHHHHHHHH.HHHHHHHHTT CS
                     Thioredoxin_4 16 tvieyedlrCphCakfeeeve.klleeyidtG 46
                                      +++ y++ +Cp C+ ++++v+   +++ + +G
  gi|242399707|ref|YP_002995132.1| 55 FLVFYHSETCPACTYMKNNVFpTEKAREVLKG 86
                                      6899****************954555555555 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.16
                                       HHHHHT--SS-EEEE....TTEEE-TT- CS
                     Thioredoxin_4 132 eakkagiestPtfii....ngekveepq 155
                                       e+ + g+ +tPt++i    ngek+ +++
  gi|242399707|ref|YP_002995132.1| 129 EVVNVGVPGTPTMVIfkveNGEKILKSI 156
                                       567789********99999999886665 PP

>> DUF4040  Domain of unknown function (DUF4040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.4      0.92   1.8e+03      17      34 ..     189     206 ..     185     207 .. 0.77
   2 ?    2.1   1.5      0.11   2.2e+02       3      30 ..     213     240 ..     211     247 .. 0.83
   3 ?   14.8   0.7   1.2e-05     0.024       5      43 ..     324     363 ..     321     364 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.92
                           DUF4040  17 laavillgvvGllvallf 34 
                                       ++ v+ll++++ ++  +f
  gi|242399707|ref|YP_002995132.1| 189 ISLVLLLSIFSAGILSVF 206
                                       678999999999886666 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.11
                           DUF4040   3 lvlaalaavlardrlaavillgvvGllv 30 
                                       l+++++ +++a++r+  +i+  v+++ +
  gi|242399707|ref|YP_002995132.1| 213 LIVGTFSLLFAKRRVEVIIVGLVMSFSL 240
                                       68999999*******9999888877754 PP

  == domain 3  score: 14.8 bits;  conditional E-value: 1.2e-05
                           DUF4040   5 laalaavlardrlaavillgvvGllval.lfvllgAPDvA 43 
                                        a+++a+l+ + l+ +i+++v+Gl++ l +++ll+  D+A
  gi|242399707|ref|YP_002995132.1| 324 FAVITAALSGSILKGIIIMSVYGLGIGLtIYLLLSSKDLA 363
                                       58999999******************98468889999988 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   4.1e-05     0.081      17      61 ..      52     101 ..      40     145 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.1e-05
                                       T--EEEEE--TT-HHHHHHHHHHHH-HHHHH.HHHT-EEEEESS......- CS
                     Thioredoxin_7  17 gkpvlvffgaswcftCqalerdflsdeevkaalaekfvllrvdv......t 61 
                                       g   lvf ++++c+ C+ ++ ++  +e+ ++ + + + l ++dv      t
  gi|242399707|ref|YP_002995132.1|  52 GEYFLVFYHSETCPACTYMKNNVFPTEKARE-VLKGINLITIDVyrvrglT 101
                                       566799*************************.8888888888875555441 PP

>> CytB6-F_Fe-S  Cytochrome B6-F complex Fe-S subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.5      0.06   1.2e+02      11      29 ..     235     253 ..     234     262 .. 0.86
   2 ?    5.6   0.8    0.0081        16      14      34 ..     304     324 ..     301     328 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.06
                      CytB6-F_Fe-S  11 llNlllvGaialtaaaaLy 29 
                                       ++++ l+Ga+a++ ++ ++
  gi|242399707|ref|YP_002995132.1| 235 VMSFSLLGALAGVLGSYIV 253
                                       69**********9999876 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0081
                      CytB6-F_Fe-S  14 lllvGaialtaaaaLyPvvkF 34 
                                       +ll+ a+++t  + + P+v F
  gi|242399707|ref|YP_002995132.1| 304 FLLGSALGVTWIGCIAPYVGF 324
                                       99*****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (420 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       944  (0.0526521); expected 358.6 (0.02)
Passed bias filter:                      586  (0.0326845); 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):               9  [number of targets reported over threshold]
# CPU time: 0.69u 0.33s 00:00:01.02 Elapsed: 00:00:00.52
# Mc/sec: 2440.27
//
Query:       gi|242399708|ref|YP_002995133.1|  [L=117]
Description: hypothetical protein TSIB_1733 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.4e-17   60.7   0.3    2.9e-16   59.1   0.1    1.7  2  DUF302    Domain of unknown function DUF302


Domain annotation for each model (and alignments):
>> DUF302  Domain of unknown function DUF302
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0     0.088   1.6e+03      10      20 ..      18      30 ..      13      37 .. 0.51
   2 !   59.1   0.1   1.6e-20   2.9e-16       7      59 ..      40      92 ..      37      95 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.088
                                      TT-S--S-..EEE CS
                            DUF302 10 klgedlrp..yki 20
                                      kl ++l++  yk+
  gi|242399708|ref|YP_002995133.1| 18 KLKAELEKkgYKV 30
                                      4444443223444 PP

  == domain 2  score: 59.1 bits;  conditional E-value: 1.6e-20
                                      HHCTT-S--S-EEEEEEE-HHHHHHHHCC-GGGGGG-SEEEEEEEETTEEEEE CS
                            DUF302  7 lkkklgedlrpykilgaCnPklatealqadpeiglllPcrvvVyekdgkttvs 59
                                      +k+klg+d++pykil +CnPk  +e+ +a+ eig + Pc v++yekd++++++
  gi|242399708|ref|YP_002995133.1| 40 VKAKLGVDMEPYKILYVCNPKKFYEMTKAEYEIGSFAPCPVLLYEKDESVYIA 92
                                      79*************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       951  (0.0530426); expected 358.6 (0.02)
Passed bias filter:                      690  (0.0384851); 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: 0.53u 0.35s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 666.41
//
Query:       gi|242399709|ref|YP_002995134.1|  [L=272]
Description: hypothetical protein TSIB_1734 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.041   14.0   0.4        1.8    8.7   0.2    2.5  3  NAD_binding_2  NAD binding domain of 6-phosphogluconate dehyd
      0.095   12.6   0.0       0.16   11.8   0.0    1.4  1  PDDEXK_1       PD-(D/E)XK nuclease superfamily
      0.099   12.6   0.1       0.16   11.9   0.1    1.3  1  DeoRC          DeoR C terminal sensor domain


Domain annotation for each model (and alignments):
>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.023   1.3e+02      73     107 ..      24      58 ..       5      75 .. 0.73
   2 ?   -2.5   0.0      0.87   5.2e+03      74      92 ..      96     114 ..      83     124 .. 0.74
   3 ?    8.7   0.2    0.0003       1.8     115     148 ..     208     241 ..     189     245 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.023
                                       HHSHCCC--TT-EEEE-S---HHHHHHHHHHHHHT CS
                     NAD_binding_2  73 iegllealkkgdilidgstsspedtrelakelkek 107
                                       +e++ +al++g ++i ++t+++  ++e+ +e  ek
  gi|242399709|ref|YP_002995134.1|  24 LEEVQHALENGFVYIATGTTAAYVAEEILREKIEK 58 
                                       45577888888888888888887777776654444 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.87
                                       HSHCCC--TT-EEEE-S-- CS
                     NAD_binding_2  74 egllealkkgdilidgsts 92 
                                        + l+++ ++d++i g+++
  gi|242399709|ref|YP_002995134.1|  96 LEALKEMGPDDVYIKGANA 114
                                       4577888999999998885 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0003
                                       EEESHHHHHHHT-EEEEEEE-HHHHHHHHHHHHH CS
                     NAD_binding_2 115 PVSGGeegAekGtLsimvGGseeafervkpvlea 148
                                       P+  G +g ++G++++++ G+ee++e++k++ +a
  gi|242399709|ref|YP_002995134.1| 208 PIASGGAGGAEGSVTLVLEGDEEDMEKAKEITKA 241
                                       77555555556777***************99876 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 ?   11.8   0.0   2.7e-05      0.16     225     254 ..     235     265 ..     188     266 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.7e-05
                          PDDEXK_1 225 leelaeeilagefparpskk..CeyCpyksvC 254
                                       ++e + ++ +ge p +p+++  C+ Cp+++vC
  gi|242399709|ref|YP_002995134.1| 235 AKE-ITKAVKGEPPLKPYTEedCSICPFAKVC 265
                                       333.344446899999998889********** PP

>> DeoRC  DeoR C terminal sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   2.7e-05      0.16       4      42 ..      12      55 ..       9      69 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.7e-05
                             DeoRC  4 eeKrrIAkaAael..ie...dgdtifldaGtTtlelaraLaekk 42
                                      e Kr IAka ++l  ++   ++  +++ +GtT++++a+++ ++k
  gi|242399709|ref|YP_002995134.1| 12 ESKRLIAKAIVALeeVQhalENGFVYIATGTTAAYVAEEILREK 55
                                      678888887655411333337999***************98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); 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: 0.61u 0.34s 00:00:00.95 Elapsed: 00:00:00.55
# Mc/sec: 1501.97
//
Query:       gi|242399710|ref|YP_002995135.1|  [L=203]
Description: IS element ISTsi1 orfA, resolvase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-24   86.8   0.4    1.9e-24   86.5   0.4    1.1  1  Resolvase    Resolvase, N terminal domain
    1.9e-13   50.4   0.7      4e-13   49.3   0.5    1.7  2  HTH_17       Helix-turn-helix domain
    0.00018   21.6   0.1    0.00051   20.1   0.1    1.8  1  MerR_1       MerR HTH family regulatory protein
     0.0012   18.6   0.1     0.0025   17.5   0.1    1.6  1  MerR         MerR family regulatory protein
     0.0015   18.3   0.1     0.0053   16.5   0.1    1.9  2  HTH_23       Homeodomain-like domain
  ------ inclusion threshold ------
      0.012   15.6   0.3      0.021   14.8   0.2    1.3  1  DUF2797      Protein of unknown function (DUF2797)
      0.073   13.0   0.5          1    9.2   0.2    2.1  2  Cas_APE2256  CRISPR-associated protein (Cas_APE2256)
      0.094   12.9   0.1       0.32   11.2   0.1    1.9  2  AbiEi_4      Transcriptional regulator, AbiEi antitoxin
       0.15   12.1   0.0       0.76    9.8   0.0    2.1  3  B12-binding  B12 binding domain


Domain annotation for each model (and alignments):
>> Resolvase  Resolvase, N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.5   0.4   9.3e-28   1.9e-24       1     137 [.      57     190 ..      57     199 .. 0.90

  Alignments for each domain:
  == domain 1  score: 86.5 bits;  conditional E-value: 9.3e-28
                                       EEEEEEES-----THHHHHHHHHHHH-S--..SE...EEEE.S-TT-TT-HHHHHHHHHHTT-EE.EEEESSCCCC- CS
                         Resolvase   1 aigYaRvSteeqddslerQkealrayakenglkivkefeDkgvSGakleRpglkrllaalregkgdvlvvekldRLa 77 
                                       +++YaRvS+++q+++lerQ+e l++y+ ++g++++k+++D   SG +++R+glk+l +++++g++  +v++  dRL+
  gi|242399710|ref|YP_002995135.1|  57 VAIYARVSSQNQKEDLERQVEYLKNYCSAKGYQVAKIITDI-SSGLNENRKGLKQLFKLVENGEITKVVITYKDRLT 132
                                       689**************************************.***********************9*********** PP

                                       S...S-HHHHHHHHHTT-EEEESS..SS----HHHHHHHHHHHHHHHHHHHHHCT-TTHH CS
                         Resolvase  78 Rsvrdlltlleelrekgvslvsldegidtstpmgrlllqilaalaeferelirertkegl 137
                                       R  +++l+    ++++gv++ ++ +  +++ ++++l+ ++la++  f  +l  +r+++ +
  gi|242399710|ref|YP_002995135.1| 133 RFGFKYLEQ--YFNSHGVEIEVIFDDEEKTLEEKELVEDLLAIVTSFAGKLYGARSHKKK 190
                                       **9999987..67888888888886456666779*************9999999988754 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.3   0.5     2e-16     4e-13       1      49 [.       3      51 ..       3      53 .. 0.96
   2 ?   -3.2   0.0       5.2     1e+04      21      30 ..     114     123 ..     113     145 .. 0.54

  Alignments for each domain:
  == domain 1  score: 49.3 bits;  conditional E-value: 2e-16
                            HTH_17  1 lltveEaAelLgvsrstvyrlirrgelpaakiGrrwriprsdleewlek 49
                                      l+ + Ea++ Lgvs+ t+ r+i++g+l+a++iG+ +r+p+s++ + le+
  gi|242399710|ref|YP_002995135.1|  3 LYRTGEASKKLGVSKMTILRWIKSGKLKAHRIGKEYRVPESEIKKILEG 51
                                      6999*****************************************9997 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 5.2
                            HTH_17  21 lirrgelpaa 30 
                                       l+ +ge+  +
  gi|242399710|ref|YP_002995135.1| 114 LVENGEITKV 123
                                       6667777554 PP

>> MerR_1  MerR HTH family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.1   2.6e-07   0.00051       1      36 [.       4      39 ..       4      40 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2.6e-07
                                      EEHHHHHHHHTS-HHHHHHHHHHTT-S-EE-TTS-E CS
                            MerR_1  1 ysigevakilgvtthtlrywekegllkpkrteggrr 36
                                      y+ ge++k+lgv++ t+  w k g+lk  r ++ +r
  gi|242399710|ref|YP_002995135.1|  4 YRTGEASKKLGVSKMTILRWIKSGKLKAHRIGKEYR 39
                                      899*************************99777766 PP

>> MerR  MerR family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   1.3e-06    0.0025       1      36 [.       5      39 ..       5      40 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.3e-06
                                      EHHHHHHHHTTTHHHHHHHHHTTSSTSEEETTTSSE CS
                              MerR  1 tIgevAeltGvsprtLRyYEreGLipppeRtegGyR 36
                                      ++ge+++++Gvs  t+ ++ + G++ +++R    yR
  gi|242399710|ref|YP_002995135.1|  5 RTGEASKKLGVSKMTILRWIKSGKL-KAHRIGKEYR 39
                                      58***********************.8888777777 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   2.7e-06    0.0053      18      39 ..       4      25 ..       2      26 .. 0.90
   2 ?   -2.5   0.0       2.4   4.8e+03      22      32 ..      33      43 ..      29      58 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.7e-06
                            HTH_23 18 lsvreIAreLgvsrrTvyrwlk 39
                                      +++ e++++Lgvs++T+ rw+k
  gi|242399710|ref|YP_002995135.1|  4 YRTGEASKKLGVSKMTILRWIK 25
                                      56779***************98 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.4
                            HTH_23 22 eIAreLgvsrr 32
                                      +I +e+ v+++
  gi|242399710|ref|YP_002995135.1| 33 RIGKEYRVPES 43
                                      66677666665 PP

>> DUF2797  Protein of unknown function (DUF2797)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.2     1e-05     0.021      78     169 ..       7      95 ..       2     124 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1e-05
                           DUF2797  78 nssevKVGiTrkeqvptRwidQGAvqaiplaevanRrlaglvevalketvaDktnwrkmlksevedvdlsaeaeela 154
                                        +++ K G+++ +    Rwi  G  +a  + + + R  + ++++ l+ +++D++  ++  +s++++ dl+++ e l+
  gi|242399710|ref|YP_002995135.1|   7 GEASKKLGVSKMT--ILRWIKSGKLKAHRIGK-EYRVPESEIKKILEGKIPDQVAIYARVSSQNQKEDLERQVEYLK 80 
                                       5667899999965..56*************98.678888899999999999************************** PP

                           DUF2797 155 eliaeeselgaeaie 169
                                       ++++++    a++i+
  gi|242399710|ref|YP_002995135.1|  81 NYCSAKGYQVAKIIT 95 
                                       **9994333334443 PP

>> Cas_APE2256  CRISPR-associated protein (Cas_APE2256)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.055   1.1e+02      39      81 ..      76     116 ..      44     130 .. 0.73
   2 ?    9.2   0.2   0.00052         1      39      98 ..     136     195 ..     108     197 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.055
                       Cas_APE2256  39 aeilkeyleeegaevevveieklsdlgreeFreglrnLvekla 81 
                                        e+lk+y + +g++v+ +   ++s    e  r+gl++L++ ++
  gi|242399710|ref|YP_002995135.1|  76 VEYLKNYCSAKGYQVAKII-TDISSGLNE-NRKGLKQLFKLVE 116
                                       5678888888888865433.355544333.4789999888775 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00052
                       Cas_APE2256  39 aeilkeyleeegaevevveieklsdlgreeFreglrnLveklarevknkkregekvlina 98 
                                        ++l++y++++g+e+ev+   + ++l+++e+ e l  +v  +a ++  ++ + +k l+ a
  gi|242399710|ref|YP_002995135.1| 136 FKYLEQYFNSHGVEIEVIFDDEEKTLEEKELVEDLLAIVTSFAGKLYGARSHKKKRLVEA 195
                                       5789*****************************************998888877777765 PP

>> AbiEi_4  Transcriptional regulator, AbiEi antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00016      0.32      15      38 ..       5      29 ..       2      30 .. 0.93
   2 ?   -2.7   0.0       3.4   6.8e+03      31      41 ..     113     123 ..     110     123 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00016
                           AbiEi_4 15 ttrelea.aGispsalrrLvrkGwL 38
                                      +t e+ + +G+s +++ r++++G+L
  gi|242399710|ref|YP_002995135.1|  5 RTGEASKkLGVSKMTILRWIKSGKL 29
                                      89999888***************98 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.4
                           AbiEi_4  31 rLvrkGwLvrl 41 
                                       +Lv+ G+++++
  gi|242399710|ref|YP_002995135.1| 113 KLVENGEITKV 123
                                       69999*99875 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       2.1   4.2e+03      39      65 ..      41      67 ..      37      86 .. 0.67
   2 ?   -0.9   0.0      0.83   1.6e+03      17      32 ..      76      91 ..      72     111 .. 0.81
   3 ?    9.8   0.0   0.00038      0.76       3      48 ..     122     175 ..     120     201 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.1
                       B12-binding 39 enedivaairaekpdvvglSalltsql 65
                                      +  +i + ++   pd v++ a+++sq 
  gi|242399710|ref|YP_002995135.1| 41 PESEIKKILEGKIPDQVAIYARVSSQN 67
                                      556666667777788888777766554 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.83
                       B12-binding 17 lavlaaalrdagfeVq 32
                                      + +l+++++++g++V 
  gi|242399710|ref|YP_002995135.1| 76 VEYLKNYCSAKGYQVA 91
                                      6799999999999997 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.00038
                       B12-binding   3 vllatvggdlhplGlavlaaalrdagfeVqllganven........edivaair 48 
                                        +++t++ +l  +G+++l +++  +g+e++++  + e+        ed++a + 
  gi|242399710|ref|YP_002995135.1| 122 KVVITYKDRLTRFGFKYLEQYFNSHGVEIEVIFDDEEKtleekelvEDLLAIVT 175
                                       68999*************************997777766777555555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1293  (0.0721178); expected 358.6 (0.02)
Passed bias filter:                      788  (0.0439511); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.57u 0.33s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 1199.73
//
Query:       gi|242399711|ref|YP_002995136.1|  [L=393]
Description: IS element ISTsi1 orfB, trasposase [Thermococcus sibiricus MM 739]
Scores for complete 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-25   87.1   0.1    2.4e-24   85.0   0.0    2.1  3  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    3.1e-09   37.1   0.2    3.1e-09   37.1   0.2    1.8  2  OrfB_IS605      Probable transposase
      0.007   16.2   0.1      0.013   15.3   0.1    1.4  1  C1_1            Phorbol esters/diacylglycerol binding domain 
  ------ inclusion threshold ------
      0.015   15.3   0.3      0.026   14.6   0.3    1.3  1  DZR             Double zinc ribbon
      0.035   14.2   0.2      0.061   13.4   0.2    1.3  1  RRT14           Regular of rDNA transcription protein 14
      0.062   13.8   0.0       0.12   12.9   0.0    1.5  1  SCP2            SCP-2 sterol transfer family
      0.077   12.9   1.0        3.8    7.5   0.4    3.1  2  RsgI_N          Anti-sigma factor N-terminus
      0.083   12.6   0.8       0.25   11.1   0.1    2.0  2  CAP_assoc_N     CAP-associated N-terminal
       0.13   12.3   0.2       0.73   10.0   0.8    1.9  2  zf-Mss51        Zinc-finger of mitochondrial splicing suppres
       0.15   11.5   0.3       0.48    9.9   0.3    1.9  1  Vps36-NZF-N     Vacuolar protein sorting 36 NZF-N zinc-finger
       0.17   11.6   2.5       0.61    9.9   2.5    1.9  1  zinc_ribbon_2   zinc-ribbon 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 ?   -1.7   0.0       1.7   2.8e+03       1      19 [.     246     265 ..     246     280 .. 0.73
   2 ?   -2.5   0.0       3.1   5.1e+03       3      17 ..     270     284 ..     268     285 .. 0.85
   3 !   85.0   0.0   1.5e-27   2.4e-24       1      68 [.     290     356 ..     290     357 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.7
                    OrfB_Zn_ribbon   1 frklkeqleykakey.Gikv 19 
                                       ++kl +++ + a++y Gi +
  gi|242399711|ref|YP_002995136.1| 246 YHKLANKIVELAEKYgGIAL 265
                                       67899999999999944555 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.1
                    OrfB_Zn_ribbon   3 klkeqleykakeyGi 17 
                                       ++++ ++y a++ G+
  gi|242399711|ref|YP_002995136.1| 270 EIRNSIRYSAEMNGR 284
                                       68999*****99986 PP

  == domain 3  score: 85.0 bits;  conditional E-value: 1.5e-27
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilk 68 
                                       frkl+ ++eykak +G++v+ v+payTS+ C++Cg+k+++ + +r++kC nCgfeadrDv++++N+  
  gi|242399711|ref|YP_002995136.1| 290 FRKLQSIIEYKAKLKGVEVVFVDPAYTSSLCPVCGEKLSP-NGHRVLKCLNCGFEADRDVVGSWNVRL 356
                                       89**************************************.************************976 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1       2.4     4e+03      47      57 ..      78      88 ..      32      94 .. 0.59
   2 !   37.1   0.2   1.9e-12   3.1e-09       8     105 ..     167     259 ..     160     271 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.4
                        OrfB_IS605 47 ksdykylakei 57
                                       s yk+++k++
  gi|242399711|ref|YP_002995136.1| 78 ASIYKSYRKRK 88
                                      23333333333 PP

  == domain 2  score: 37.1 bits;  conditional E-value: 1.9e-12
                        OrfB_IS605   8 velpkpkgnkaagiDlGinn.Latvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlhrk 83 
                                       +e ++++++  +g+Dl+ nn  +++++++   f+    + k+    +  +++++q+k+k     kk+++ l ++ ++
  gi|242399711|ref|YP_002995136.1| 167 KEVEVKEPEDFVGVDLNENNvTLSLSDGE---FVQIITHEKEIRTGYFVKRRKIQKKVKVG---KKRQELLEKYGER 237
                                       5568899**********887357888888...999999***********************...69999******** PP

                        OrfB_IS605  84 rsrrrkhllhklathliktlke 105
                                        ++r+++l+hkla+++++   +
  gi|242399711|ref|YP_002995136.1| 238 ERNRLNDLYHKLANKIVELAEK 259
                                       ***************9986544 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   8.3e-06     0.013       9      38 ..     315     344 ..     309     347 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 8.3e-06
                                       SS--B-TTT-SB--SSSS-EEEETTT--EE CS
                              C1_1   9 kqptfCkhCgeflwgkekqglkCswCkllv 38 
                                       + ++ C  Cge l+  +++ lkC +C++ +
  gi|242399711|ref|YP_002995136.1| 315 YTSSLCPVCGEKLSPNGHRVLKCLNCGFEA 344
                                       56789********88***********9875 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.3   1.6e-05     0.026      12      39 ..     317     345 ..     311     348 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.6e-05
                               DZR  12 arfCseCgtklkavaa.edrCpsCgekvd 39 
                                       +  C+ Cg+kl++  +   +C +Cg ++d
  gi|242399711|ref|YP_002995136.1| 317 SSLCPVCGEKLSPNGHrVLKCLNCGFEAD 345
                                       56899999999988888999999998776 PP

>> RRT14  Regular of rDNA transcription protein 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   3.7e-05     0.061      82     189 ..     214     322 ..     190     326 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.7e-05
                             RRT14  82 ekklkklakyeiikkkkeeeelteeekkyLnklvkkninalkklskiddleikeeleelkkeiLekteeskrlrkls 158
                                        +k++k++k    ++    e+  e+e++ Ln l +k +n++ +l ++      e+l e++++i  + e + rl++ s
  gi|242399711|ref|YP_002995136.1| 214 RRKIQKKVKVGKKRQE-LLEKYGERERNRLNDLYHKLANKIVELAEKYGGIALEDLTEIRNSIRYSAEMNGRLHRWS 289
                                       4566666665543333.45778899*******************999999999**********************77 PP

                             RRT14 159 kkkkqkkkdFneklkkgsi..sypGLTPGLAPV 189
                                         k q++ +++ klk + +    p+ T  L PV
  gi|242399711|ref|YP_002995136.1| 290 FRKLQSIIEYKAKLKGVEVvfVDPAYTSSLCPV 322
                                       78899********99987766789999999998 PP

>> SCP2  SCP-2 sterol transfer family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   7.2e-05      0.12      25     100 ..     150     231 ..     130     232 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.2e-05
                                       EEEECTC.T.EEEEEETTSTEEE......SSCTTBS-SEEEEEEHHHHHHHHCTSS-HHHHHHTTSSEEEC-HHHHH CS
                              SCP2  25 rfdltdlkg.sltldlkegqldv......aakdegkadvtlslsledllelaegklnpqkafmqgkLkieGDielaq 94 
                                       ++ ++ +kg  + +++++ +++v      +  d  ++ vtlsls+ +++++++ +    + ++ ++ ki+  ++++ 
  gi|242399711|ref|YP_002995136.1| 150 AWLVRTPKGvFINVVFSK-EVEVkepedfVGVDLNENNVTLSLSDGEFVQIITHEKEIRTGYFVKRRKIQKKVKVGK 225
                                       555555655456666766.8888777775444448999*********************************999999 PP

                                       HHHHHH CS
                              SCP2  95 kleall 100
                                       k ++ll
  gi|242399711|ref|YP_002995136.1| 226 KRQELL 231
                                       999887 PP

>> RsgI_N  Anti-sigma factor N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.11   1.7e+02      10      28 ..     153     171 ..     151     171 .. 0.86
   2 ?    7.5   0.4    0.0023       3.8       1      40 [.     180     218 ..     180     228 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.11
                            RsgI_N  10 vlTpdGeFikikrkggmkv 28 
                                       v Tp+G Fi++   ++++v
  gi|242399711|ref|YP_002995136.1| 153 VRTPKGVFINVVFSKEVEV 171
                                       78********988888876 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0023
                            RsgI_N   1 leikkkkaivlTpdGeFikikrkgg.mkvGeEiefpekdii 40 
                                       ++++++ +++  +dGeF+ i ++++  + G    ++ ++i 
  gi|242399711|ref|YP_002995136.1| 180 VDLNENNVTLSLSDGEFVQIITHEKeIRTGY--FVKRRKIQ 218
                                       57899***************99977699999..44433333 PP

>> CAP_assoc_N  CAP-associated N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1      0.83   1.4e+03      92     136 ..      12      57 ..       5      61 .. 0.71
   2 ?   11.1   0.1   0.00015      0.25      33      81 ..     192     240 ..     181     259 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.83
                       CAP_assoc_N  92 felseedlnerplvkvdgtyatlffD.qetnkvtsvryldketllk 136
                                       f+l+e+    ++l++     + + +   ++n++ts   l+ke+ + 
  gi|242399711|ref|YP_002995136.1|  12 FKLKETPEGLNELFSTYRDIVNFLIThAFENNITSFYRLKKEIYKS 57 
                                       6666666666677777666677777778899999988888887655 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00015
                       CAP_assoc_N  33 dykeyiqvgvedgkVvtlytngeeiaikpfkigesleevekklgipeev 81 
                                       ++ e++q+ + +++++t y ++    +k++k+g++++e+ +k+g+ e  
  gi|242399711|ref|YP_002995136.1| 192 SDGEFVQIITHEKEIRTGYFVKRRKIQKKVKVGKKRQELLEKYGERERN 240
                                       6789***************************************998876 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 ?   -2.8   0.0       4.4   7.2e+03      21      37 ..      93     109 ..      90     114 .. 0.82
   2 ?   10.0   0.8   0.00045      0.73       1      24 [.     319     342 ..     319     345 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 4.4
                          zf-Mss51  21 dCGiptycseehwedDy 37 
                                        +G p++  e+ + dD 
  gi|242399711|ref|YP_002995136.1|  93 ASGRPVFKKEAIMLDDH 109
                                       58999999999888885 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00045
                          zf-Mss51   1 lCPvpkhkqtapkhvdfeCpdCGi 24 
                                       lCPv+ +k +++ h  ++C +CG+
  gi|242399711|ref|YP_002995136.1| 319 LCPVCGEKLSPNGHRVLKCLNCGF 342
                                       6**********************7 PP

>> Vps36-NZF-N  Vacuolar protein sorting 36 NZF-N zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.3   0.00029      0.48      25      48 ..     327     349 ..     315     353 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00029
                       Vps36-NZF-N  25 fdpnastplPpClaCGvkpdleli 48 
                                       ++p + + + +Cl+CG ++d++++
  gi|242399711|ref|YP_002995136.1| 327 LSP-NGHRVLKCLNCGFEADRDVV 349
                                       454.678899***********987 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   2.5   0.00038      0.61       2      22 ..     320     343 ..     319     344 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00038
                     zinc_ribbon_2   2 CpnCGael.qdnakF..CpyCGtp 22 
                                       Cp CG++l +++ +   C +CG++
  gi|242399711|ref|YP_002995136.1| 320 CPVCGEKLsPNGHRVlkCLNCGFE 343
                                       ********447888899****985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1153  (0.0643092); expected 358.6 (0.02)
Passed bias filter:                      831  (0.0463495); expected 358.6 (0.02)
Passed Vit filter:                       112  (0.00624686); 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: 0.74u 0.34s 00:00:01.08 Elapsed: 00:00:00.55
# Mc/sec: 2161.01
//
Query:       gi|242399712|ref|YP_002995137.1|  [L=384]
Description: PepQ-1 X-pro dipeptidase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-24   87.2   0.1    1.9e-24   86.5   0.1    1.4  1  Peptidase_M24  Metallopeptidase family M24
      5e-14   53.1   0.0    5.1e-13   49.8   0.0    2.2  2  Creatinase_N   Creatinase/Prolidase N-terminal domain


Domain annotation for each model (and alignments):
>> Peptidase_M24  Metallopeptidase family M24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.5   0.1   2.1e-28   1.9e-24       2     167 ..     150     309 ..     149     352 .. 0.90

  Alignments for each domain:
  == domain 1  score: 86.5 bits;  conditional E-value: 2.1e-28
                                       HHHHHHHHHHHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHTTTCEESSSSEEEEGGGGGSTTTBC.SSSB--TTEEE CS
                     Peptidase_M24   2 lirkaariasaaleavleaikpgvterelaaeieattlkrhgarglafppivasgenaavlhytp.ndrvlkegdlv 77 
                                       +irka++ia++ +e + e+ikpg +e e+aaei ++ l  +g++++   + v++ ++a    ++p  d ++keg++v
  gi|242399712|ref|YP_002995137.1| 150 KIRKAGKIAKKGMEVAEEEIKPGKSELEVAAEIVRE-LMINGSEEPK--VYVSATPRAH---AEPfRDVEIKEGKVV 220
                                       89********************************98.6667888885..4577777776...55533588******* PP

                                       EEEEEEEETTEEEEEEEEEECSSGSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHHHHHTTBCCGBSSCSE CS
                     Peptidase_M24  78 lidagaeydgyasDitrTvlvGkftpeqrelyeavleaqeaaikavkpGvtlseidaaarevlesaglakffphglG 154
                                        + +ga +d+y+ +++r + vG+ +++++ +++a++ea  +a+++ kpG+++ ++ +  +++ +++gl + +  g  
  gi|242399712|ref|YP_002995137.1| 221 TVVIGADWDHYYVNMSRSFPVGNINERAKLALNAMEEAYTKAVELTKPGIKFIAVERELEKIYRERGLIDAYITGYA 297
                                       **************************9****************************************87999***** PP

                                       EEESSSSSEEEEE CS
                     Peptidase_M24 155 HgvGlevhdegps 167
                                       HgvGl + ++ p+
  gi|242399712|ref|YP_002995137.1| 298 HGVGLLIEED-PI 309
                                       *******998.75 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 !   49.8   0.0   5.7e-17   5.1e-13       1     132 []      11     142 ..      11     142 .. 0.87
   2 ?    0.8   0.0     0.082   7.3e+02      26      54 ..     291     315 ..     247     318 .. 0.78

  Alignments for each domain:
  == domain 1  score: 49.8 bits;  conditional E-value: 5.7e-17
                                       HHHHHHHHHHHTT-SEEEEECCHHHHHHHSS...-SSSEEEEEEESSCE.EEEEECTTHHHHHHHH.TTSEEEEEST CS
                      Creatinase_N   1 RlerlralmeekgldallvtspenlrYltGfatetgsrglalvvtadga.lllvdalryteaaeesatveevveydd 76 
                                       R++r+++l++++++d++++   + + Y+tG+      r+ +l ++a+g+ + +v +++ +  +++s + ++v+e+++
  gi|242399712|ref|YP_002995137.1|  11 RVKRFQNLLKRNNIDGAVIRTLSTFVYFTGT---KWLRPSLL-IPAEGEpTVIVAKGEGELFKQRS-WIKNVIEFQK 82 
                                       99*****************************...999999**.************99999999999.*********9 PP

                                       ...HSSHHHHHHHHHHHHT..-EEEE-TTS...SBHHHHHHHHHHCTTSEEEETHHHHHHHHSC CS
                      Creatinase_N  77 ...pvealadllkellese..krvgvelda...ltvafyealkealpdaelvdaselieelRvv 132
                                           +++++ ++k+    +  ++vg+e +        fye +k+  p++e+vd+ +l  elR++
  gi|242399712|ref|YP_002995137.1|  83 teeLMASVTVWIKK----NgfNTVGMEFSIerdAYILFYELFKKLNPGVEIVDVRGLSMELRMI 142
                                       55555555555555....4559999666655445788899999999*****************8 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.082
                                       HHHHSS...-SSSEEEEEEESSCE.EEEEE CS
                      Creatinase_N  26 rYltGfatetgsrglalvvtadga.lllvd 54 
                                        Y+tG+   +  +g+ l++++d+  +++v+
  gi|242399712|ref|YP_002995137.1| 291 AYITGY---A--HGVGLLIEEDPItTIVVP 315
                                       599999...4..444444688877666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); 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: 0.62u 0.35s 00:00:00.97 Elapsed: 00:00:00.53
# Mc/sec: 2197.50
//
Query:       gi|242399713|ref|YP_002995138.1|  [L=103]
Description: carbohydrate-binding protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.2e-15   54.9   0.0    7.9e-15   54.3   0.0    1.3  1  Cupin_2          Cupin domain
    4.1e-08   33.3   0.0    4.6e-08   33.1   0.0    1.1  1  MannoseP_isomer  Mannose-6-phosphate isomerase
      2e-07   31.0   0.0    2.4e-07   30.7   0.0    1.1  1  AraC_binding     AraC-like ligand binding domain
    0.00011   22.5   0.0    0.00017   21.9   0.0    1.3  1  Pirin_C          Pirin C-terminal cupin domain
    0.00022   20.8   0.0    0.00027   20.5   0.0    1.2  1  Cupin_3          Protein of unknown function (DUF861)
     0.0044   16.6   0.0     0.0054   16.4   0.0    1.1  1  Cupin_1          Cupin
  ------ inclusion threshold ------
       0.01   15.7   0.0      0.012   15.5   0.0    1.2  1  Cupin_7          ChrR Cupin-like domain
      0.014   15.0   0.1      0.016   14.9   0.1    1.1  1  3-HAO            3-hydroxyanthranilic acid dioxygenase
      0.028   13.7   0.0      0.028   13.7   0.0    1.1  1  KduI             KduI/IolB family
      0.059   13.1   0.0      0.072   12.8   0.0    1.2  1  Cupin_6          Cupin


Domain annotation for each model (and alignments):
>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.3   0.0   4.4e-18   7.9e-15       2      70 ..      33     100 ..      32     101 .. 0.97

  Alignments for each domain:
  == domain 1  score: 54.3 bits;  conditional E-value: 4.4e-18
                                       EEEEETTEEEEEECSSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEEEE-SSS-EEEEEE CS
                           Cupin_2   2 lvelppGesapshrHpgedeffyVleGegeltvdgeeveleaGdsvyfpagtpHrfrNtgdeparllvv 70 
                                       lv+l+pGe  ++h+ p   +f+y+++G+++++v++e  +++++ +v+ p+  pH+++N+g+  +++lvv
  gi|242399713|ref|YP_002995138.1|  33 LVTLKPGEALERHTTPFD-AFIYIIKGKAVVEVGEENEKVKKDTLVFLPKDIPHAVKNEGNLTLKFLVV 100
                                       89***************8.************************************************98 PP

>> MannoseP_isomer  Mannose-6-phosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.0   2.6e-11   4.6e-08      54     138 ..      20     103 .]       4     103 .] 0.84

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 2.6e-11
                   MannoseP_isomer  54 yevldegeryqvkritvkPgeklslqkhhhraehWv.vvkGtakvtvddevlllkenestyiplgaihrlenpGkip 129
                                        ++l + e+ +v  +t+kPge l   +h    + ++ ++kG a v+v++e  ++k++  +++p++  h+++n G+++
  gi|242399713|ref|YP_002995138.1|  20 VRALLKKENVKVMLVTLKPGEALE--RHTTPFDAFIyIIKGKAVVEVGEENEKVKKDTLVFLPKDIPHAVKNEGNLT 94 
                                       577889999************875..6666666665368************************************** PP

                   MannoseP_isomer 130 lelievqsG 138
                                       l+++ v+ G
  gi|242399713|ref|YP_002995138.1|  95 LKFLVVKLG 103
                                       **9999887 PP

>> AraC_binding  AraC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.0   1.4e-10   2.4e-07      12      75 ..      38     101 ..      36     103 .] 0.91

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 1.4e-10
                                       TT-SEEEETT-SEEEEEEEEE-EEEEETTEEEEE-TT-EEEE-TTS-EEEEE-TTSEEEEEEEE CS
                      AraC_binding  12 pdhsfpphvhdeyvihyvteGtgrlrlngrtydlgpGdlfLlppgepHdyesdsedgweyrwly 75 
                                       p+++ ++h+ ++  ++y+++G++ ++++++   +++++l++lp++ pH    +++  +++ +++
  gi|242399713|ref|YP_002995138.1|  38 PGEALERHTTPFDAFIYIIKGKAVVEVGEENEKVKKDTLVFLPKDIPHAVKNEGNLTLKFLVVK 101
                                       5667789***********************************************8888877766 PP

>> Pirin_C  Pirin C-terminal cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   9.3e-08   0.00017       4      68 ..      34     100 ..      31     101 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 9.3e-08
                                       EEE-TT-EEEEE--TT-EEEEEEEES-E..EESSTTEEE-TTEEEEE-SSSEEEEE--S.S-EEEEEE CS
                           Pirin_C   4 ltleagaelelplpegleaavyvleGel..evggerseieeeqlavlgdgdslvvkaee.kgarvlLl 68 
                                       +tl++g+ le   +  ++a++y+++G++  evg+e++++++++l+ l +     vk e   ++++l++
  gi|242399713|ref|YP_002995138.1|  34 VTLKPGEALERH-TTPFDAFIYIIKGKAvvEVGEENEKVKKDTLVFLPKDIPHAVKNEGnLTLKFLVV 100
                                       89********99.899***********534888999*********99955555554443266777765 PP

>> Cupin_3  Protein of unknown function (DUF861)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   1.5e-07   0.00027      14      67 ..      36      96 ..      24     102 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.5e-07
                                      EECEEE..EECESSEEEEEEEECEEEEEETTTEEEEEETTEEEEE-TTE......EECCCEE CS
                           Cupin_3 14 ctpGkf..rltyeedEfcyileGevkvtpeggetvelraGDlvvlpkgl......sgtwdvs 67
                                       +pG+   r t + d f+yi++G+  v++ g+e  ++++ +lv+lpk+       +g ++ +
  gi|242399713|ref|YP_002995138.1| 36 LKPGEAleRHTTPFDAFIYIIKGKAVVEV-GEENEKVKKDTLVFLPKDIphavknEGNLTLK 96
                                      55665411334455999************.9999*************986666655555555 PP

>> Cupin_1  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0     3e-06    0.0054      20     110 ..      18      97 ..       7     102 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3e-06
                                       ESTTTSTTTHSSTEEEEEEEE.TTEEEEEEEESSS-EEEEEEESEEEEEEEETTSS.EEEEEEEETTEEEEE-TT-E CS
                           Cupin_1  20 ansenlpglntlgisaarvdlepgglllPhyhpnateiayvlqGegrvgfvvpgngnrdfhkklreGdvfvvPaglv 96 
                                       ++++ l  l+++++ +  v l+pg  l+ h++      +y+++G++  + v ++n       k+++ +++ +P+ ++
  gi|242399713|ref|YP_002995138.1|  18 VDVRAL--LKKENVKVMLVTLKPGEALERHTT-PFDAFIYIIKGKAV-VEVGEEN------EKVKKDTLVFLPKDIP 84 
                                       666665..777777777777799999******.89999*********.4455554......89************** PP

                                       EEEEEESSSSEEEE CS
                           Cupin_1  97 hfqynsgdepavai 110
                                       h+++n g + ++ +
  gi|242399713|ref|YP_002995138.1|  85 HAVKNEG-NLTLKF 97 
                                       ******9.544444 PP

>> Cupin_7  ChrR Cupin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.0   6.6e-06     0.012       8      77 ..      16      86 ..      11     102 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 6.6e-06
                                      TTEEEEEEEEESSSS-EEEEEEEE-TTEE---EE-TT-EEEEEEEEEEE....ETTEEEETTEEEEE-TT-EE- CS
                           Cupin_7  8 egvevkpLerdgeekaratslvryapgsafsahkHpggeeilVLeGvfs....deegdypaGsylrnppgssha 77
                                      +gv+v+ L ++++     ++lv ++pg+a+++h+ p    i++++G+      +e+++ ++ + ++ p++  ha
  gi|242399713|ref|YP_002995138.1| 16 HGVDVRALLKKENV---KVMLVTLKPGEALERHTTPFDAFIYIIKGKAVvevgEENEKVKKDTLVFLPKDIPHA 86
                                      68999999977776...9****************************8651111344455666666666666665 PP

>> 3-HAO  3-hydroxyanthranilic acid dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.1   8.8e-06     0.016      27      96 ..      22      88 ..       4     100 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 8.8e-06
                                      EEEEESSEEEEEE-.SSB--S-EEE-SS-EEEEEEES-EEEEEEETTCCCEEEE-TTEEEEE-TT--EEEE CS
                             3-HAO 27 kclhkdglkvlivG.GPnerkdyhleegeeffyqkkGdmvlkvldegkardivireGeifllParvphsPq 96
                                       +l+k+++kv++v   P e  + h  + + f y  kG+ v+ v +e ++    +++  + +lP  +ph+ +
  gi|242399713|ref|YP_002995138.1| 22 ALLKKENVKVMLVTlKPGEALERHTTPFDAFIYIIKGKAVVEVGEENEK----VKKDTLVFLPKDIPHAVK 88
                                      5799********98579***********************999988764....678888889999999865 PP

>> KduI  KduI/IolB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.6e-05     0.028      23      78 ..      25      79 ..       2      95 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.6e-05
                                      CCCCBECCCEEEECHHCHHCHGCSEEEEEEEECCEEEECCTT.EEEEE-TTSSGGG CS
                              KduI 23 gweyvgfsvlkLaagesleletedrEvcvvllaGkvtvevageefeelgeRksvFe 78
                                      + e v++ +++L++ge+le +t+     + +++Gk+ vev gee e++++ + vF 
  gi|242399713|ref|YP_002995138.1| 25 KKENVKVMLVTLKPGEALERHTTPFDAFIYIIKGKAVVEV-GEENEKVKKDTLVFL 79
                                      57789999********************************.558888887777775 PP

>> Cupin_6  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     4e-05     0.072      35      76 ..      51      90 ..      29      98 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4e-05
                           Cupin_6 35 alhvvlrGscwlidpasgepvrLsagdvvllpggephvlads 76
                                      a++ + +G++ +++++  e  ++++  +v+lp++ ph++  +
  gi|242399713|ref|YP_002995138.1| 51 AFIYIIKGKAVVEVGE--ENEKVKKDTLVFLPKDIPHAVKNE 90
                                      7999*********988..78899***************9554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.53u 0.35s 00:00:00.88 Elapsed: 00:00:00.54
# Mc/sec: 574.59
//
Query:       gi|242399714|ref|YP_002995139.1|  [L=446]
Description: Sensory box protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.9e-24   85.4   1.0    4.9e-24   84.0   0.7    2.0  2  DUF438       Family of unknown function (DUF438)
    3.4e-23   82.2   0.0    8.7e-23   80.9   0.0    1.7  1  PAS_10       PAS domain
    6.9e-21   75.2   2.6    7.4e-21   75.1   1.5    1.6  2  Hemerythrin  Hemerythrin HHE cation binding domain
    6.8e-05   23.1   0.0     0.0002   21.6   0.0    1.8  1  PAS_4        PAS fold
  ------ inclusion threshold ------
       0.09   13.2   0.1        0.2   12.1   0.1    1.6  1  sCache_3_3   Single cache domain 3
       0.12   12.0   1.1        1.4    8.7   0.0    3.4  3  EF-hand_1    EF hand
       0.35   11.2   2.6        2.1    8.7   0.0    3.2  3  DUF1947      Domain of unknown function (DUF1947)


Domain annotation for each model (and alignments):
>> DUF438  Family of unknown function (DUF438)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.0   0.7   1.9e-27   4.9e-24       1      66 [.      15      80 ..      15      81 .. 0.98
   2 ?   -3.2   0.0       3.4   8.6e+03      13      24 ..     322     333 ..     319     339 .. 0.75

  Alignments for each domain:
  == domain 1  score: 84.0 bits;  conditional E-value: 1.9e-27
                            DUF438  1 LkellkrLhkgesleevkeefkellkevsaeEIsqaEqeLieeGipveeiqkLCdvHaalfkgale 66
                                      Lk+ll r+h ge+++++keef ++l+++s+ EI+ +EqeL++eGi++++i k+Cd+H++lf++a++
  gi|242399714|ref|YP_002995139.1| 15 LKKLLLRIHGGEDVNKLKEEFRQVLSGISPLEIPIIEQELVKEGISARDIAKMCDLHVELFREAVK 80
                                      8**************************************************************986 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3.4
                            DUF438  13 sleevkeefkel 24 
                                       s+ee+k+ f++l
  gi|242399714|ref|YP_002995139.1| 322 SVEELKAIFEAL 333
                                       678888888765 PP

>> PAS_10  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.9   0.0   3.4e-26   8.7e-23       1     105 [.     326     429 ..     326     430 .. 0.98

  Alignments for each domain:
  == domain 1  score: 80.9 bits;  conditional E-value: 3.4e-26
                            PAS_10   1 lnnlLnstpieltflDdnlqirrFtpaakklfklipadvGrpladihpkkavknveeviealrtgekdevevvvpkn 77 
                                       l+ +++++p+++tf+D+++++r+F+p  +++f+++++ +Grp++ +hp+k+v+ v+++++a+++g+k e +++    
  gi|242399714|ref|YP_002995139.1| 326 LKAIFEALPVDVTFIDKDDRVRFFSPG-ERIFSRTKSVLGRPVQLCHPPKSVQIVNKILKAFKEGRKSEATFWLRIG 401
                                       78999**********************.88*********************************************** PP

                            PAS_10  78 gkwvlvrylpyrdedgeiaGvvetfvDi 105
                                       +k+++++y p+ d++g + G++e+ +Di
  gi|242399714|ref|YP_002995139.1| 402 EKYIYIKYVPLFDKEGTYLGTLEITMDI 429
                                       ***************************9 PP

>> Hemerythrin  Hemerythrin HHE cation binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0         4     1e+04      85     120 ..      30      72 ..      18      74 .. 0.56
   2 !   75.1   1.5   2.9e-24   7.4e-21       1     131 []      94     233 ..      94     233 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 4
                                       HHHHHHHHHCHTCGGSTCHHHHH.......HHHHHHHHHHHHH CS
                       Hemerythrin  85 elleelrellkgleepsaaafae.......lleeladllreHi 120
                                       +l ee+r++l g+++ ++   ++        ++++a++++ H+
  gi|242399714|ref|YP_002995139.1|  30 KLKEEFRQVLSGISPLEIPIIEQelvkegiSARDIAKMCDLHV 72 
                                       4555566666665544444333344444556666666666665 PP

  == domain 2  score: 75.1 bits;  conditional E-value: 2.9e-24
                                       HHHHHHHHHHHHHHHHHHHH....HHHHHH.HHHHCCC.HCCHHHHHHHHHHHHHHHHHHHHHHCHHHHH.CCC.HH CS
                       Hemerythrin   1 aivealdeeHralrallerl....ralada.aaevhga.lrklaelldelvdeleaHhaaEEellfPlledrpggra 71 
                                       +++++l +e++++ + +e+l    r+la++  ++++g+ l  l+el++ l+++  +H+ +EE+l+fP++e r+g +a
  gi|242399714|ref|YP_002995139.1|  94 HPLKTLYLENKEIMKDAEMLnlyaRTLATTkDKRMRGEiLGVLEELVNDLKKVGFTHYNREEMLIFPYIE-RRGLTA 169
                                       68999*************99666555555555555555999999999999999*****************.****** PP

                                       HHHHHHHHHHHHHHHHHHHHHHCHTCGGSTCHHHHH....HHHHHHHHHHHHHHHHHHTHHHHH CS
                       Hemerythrin  72 vldvlereHdeirelleelrellkgleepsaaafae....lleeladllreHiakEesilfpll 131
                                          vl+  Hdeir ++++l+ell++ +e+s+++f e    ++ e a +l +++++E++i++p l
  gi|242399714|ref|YP_002995139.1| 170 IATVLWTKHDEIRFMIKRLAELLRKKDEMSWEEFLErfkeKAGEAAFALSDMVFRENNIFYPTL 233
                                       ************************************999989999999**************86 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   7.8e-08    0.0002       1     105 [.     330     429 ..     330     433 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 7.8e-08
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpge 77 
                                       +++lp+ ++++d+d rv++ ++   e +  + +++lG++++  +p+ + + +  +l++  eg+++  +   l +  +
  gi|242399714|ref|YP_002995139.1| 330 FEALPVDVTFIDKDDRVRFFSPG--ERIFSRTKSVLGRPVQLCHPPKSVQIVNKILKAFKEGRKSEATFW-L-R-IG 401
                                       7899******************8..55677889********99***999999999999999986654444.3.3.47 PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDi 105
                                       e+++ + ++Pl+d +G+ +g+l+i+ Di
  gi|242399714|ref|YP_002995139.1| 402 EKYIYIKYVPLFDKEGTYLGTLEITMDI 429
                                       899***********************99 PP

>> sCache_3_3  Single cache domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   7.8e-05       0.2      68     103 ..     400     435 ..     376     439 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.8e-05
                        sCache_3_3  68 ilgkkyltaYePlkdadgkviGmlfvGlpeeevqal 103
                                       i  k  +  Y+Pl+d++g+ +G l + +++++++++
  gi|242399714|ref|YP_002995139.1| 400 IGEKYIYIKYVPLFDKEGTYLGTLEITMDIAPYKQI 435
                                       455566899**********************99886 PP

>> EF-hand_1  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.89   2.3e+03      20      27 ..      33      40 ..      32      42 .. 0.82
   2 ?   -1.2   0.2      0.77     2e+03      17      27 ..     198     208 ..     194     210 .. 0.80
   3 ?    8.7   0.0   0.00054       1.4      13      28 ..     317     332 ..     317     333 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.89
                                      HHHHHHHH CS
                         EF-hand_1 20 eEfkellk 27
                                      eEf+++l+
  gi|242399714|ref|YP_002995139.1| 33 EEFRQVLS 40
                                      9****986 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.77
                                       EEHHHHHHHHH CS
                         EF-hand_1  17 IdfeEfkellk 27 
                                       +++eEf+e +k
  gi|242399714|ref|YP_002995139.1| 198 MSWEEFLERFK 208
                                       689***99877 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.00054
                                       SSSEEEHHHHHHHHHH CS
                         EF-hand_1  13 gdGkIdfeEfkellkk 28 
                                       g+G+I+ eE+k+++++
  gi|242399714|ref|YP_002995139.1| 317 GTGYISVEELKAIFEA 332
                                       78**********9976 PP

>> DUF1947  Domain of unknown function (DUF1947)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0   0.00082       2.1      10      64 ..     185     237 ..     184     239 .. 0.78
   2 ?   -1.7   0.1       1.5   3.8e+03      15      37 ..     306     327 ..     305     331 .. 0.83
   3 ?    0.2   0.1      0.38   9.7e+02      38      61 ..     401     424 ..     399     428 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00082
                                       HHHHHHHHHTTT---TT--...-EEEE-S.S-EEEEETTEEEEEESSSEEE-HHHHH CS
                           DUF1947  10 akeileklkekyisislesdk.iEieeek.keklYlingvpilfeeekliPtLklLl 64 
                                       +k++ e l++k    ++++++ +E ++ek +e ++  +  +++ e+  ++PtLk+Ll
  gi|242399714|ref|YP_002995139.1| 185 IKRLAELLRKKD---EMSWEEfLERFKEKaGEAAFALS-DMVFRENNIFYPTLKALL 237
                                       589999999999...6777777*******555555555.556777999*******97 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.5
                                       HHHHTTT---TT--..-EEEE-S CS
                           DUF1947  15 eklkekyisislesdkiEieeek 37 
                                       ++lk+++ +i+l +  i +ee k
  gi|242399714|ref|YP_002995139.1| 306 SELKREG-DIDLGTGYISVEELK 327
                                       7899999.999999879999877 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.38
                                       S-EEEEETTEEEEEESSSEEE-HH CS
                           DUF1947  38 keklYlingvpilfeeekliPtLk 61 
                                       +ek+++i  vp++ +e+  + tL+
  gi|242399714|ref|YP_002995139.1| 401 GEKYIYIKYVPLFDKEGTYLGTLE 424
                                       689*********999888877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); 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: 0.68u 0.36s 00:00:01.04 Elapsed: 00:00:00.54
# Mc/sec: 2496.72
//
Query:       gi|242399715|ref|YP_002995140.1|  [L=414]
Description: Flavoprotein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.7e-09   36.0   0.0    1.2e-08   35.2   0.0    1.5  1  Lactamase_B    Metallo-beta-lactamase superfamily
    0.00091   18.8   0.0     0.0017   17.9   0.0    1.4  1  Lactamase_B_2  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.013   15.7   0.0      0.034   14.4   0.0    1.7  1  Flavodoxin_1   Flavodoxin
      0.053   12.9   0.0      0.094   12.1   0.0    1.3  1  Lactamase_B_6  Metallo-beta-lactamase superfamily domain
        0.1   13.2   0.0       0.21   12.1   0.0    1.4  1  OFCC1          Orofacial cleft 1 candidate gene 1 protein


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.0   3.5e-12   1.2e-08       5     154 ..      57     193 ..      54     245 .. 0.82

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 3.5e-12
                                       SSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHC CS
                       Lactamase_B   5 pvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapa 81 
                                       + n+yl++g+++  LiDt  ++ ++ +  +     +++ d+d+++  H+ +DH+G+ ++l+++ + +  +   ++++
  gi|242399715|ref|YP_002995140.1|  57 SYNAYLVVGEEKMALIDTVNPGFEEEFE-NKINDVKNIGDIDYIVMNHAEPDHAGAIPYLMSKNKKALLIATQKGAE 132
                                       569****************999999987.58888899**************************************** PP

                                       CHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSS CS
                       Lactamase_B  82 lfmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDalla 154
                                       + + + d   +r              v+++++++ +gg  +  +    +h +  +  ++ ++k+lf  D++ a
  gi|242399715|ref|YP_002995140.1| 133 MAKTYYDVPDERIM------------VVKDGDTVSLGGKTLRFIEAPWLHWPETMFTYLVEDKILFPCDFFGA 193
                                       ******76666654............777777777777777777777799999999999*******9999874 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 !   17.9   0.0   4.6e-07    0.0017      21     130 ..      86     180 ..      70     198 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 4.6e-07
                                       --SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTTTTEEEEEE-TTSEEE CS
                     Lactamase_B_2  21 PvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleeepavnvheldwgesfe 97 
                                       + + ++++ +id +++ ha+ DH   ++ l    +kk+ l+a+++ ++  ++    +   ++  +++  ++ g++++
  gi|242399715|ref|YP_002995140.1|  86 KINDVKNIGDIDYIVMNHAEPDHAGAIPYLMSK-NKKALLIATQKGAEMAKTYY--D---VP-DERIMVVKDGDTVS 155
                                       223788999**********************95.45566889999988888883..2...33.567999******** PP

                                       ECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEE CS
                     Lactamase_B_2  98 lgdggleitatparhksgrrldrnagdtlGlri 130
                                       lg+   ++++++a+  + +      ++++ +++
  gi|242399715|ref|YP_002995140.1| 156 LGG--KTLRFIEAPWLHWP------ETMFTYLV 180
                                       *94..46777777766666......44555555 PP

>> Flavodoxin_1  Flavodoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   9.4e-06     0.034       1     133 [.     273     393 ..     273     402 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 9.4e-06
                                       EEEETSSSHHHHHHHHHHHHHHHTTTEEEEEEEEGTTSC..GGGGGTHSEEEEEEEEETTTBEEGGGHHHHHHHHHH CS
                      Flavodoxin_1   1 ilYgSetGnteklAkqlaeelgehgfnadvvslsdydes..lseieeealllvvtsTfgnGdppengesffqdllel 75 
                                       i+Y S+ G   ++ ++la +l ++g++++v++l  +d+   ++++ + + ++++++T   G  p       +  +  
  gi|242399715|ref|YP_002995140.1| 273 IVYVSMWGANDAMVRELANLLLAKGVEVRVHNLVGADIGeiAKDLVDSRAIVIGAPTVLAGAHPLA----VYGAYLV 345
                                       89***********************************9999********************99933....2233333 PP

                                       HCHHGCCSTTTTEEEEEEEEECTTSSSTTHHHHHHHHHHHHTTCEEESSSEEEETTST CS
                      Flavodoxin_1  76 kgdeledgdlsgvrfavfglGdsayenFcaagkkldekleelGaerllkllegdednq 133
                                       k            ++av+ lG++++ +     ++l ++l+++  e ++  le+  +++
  gi|242399715|ref|YP_002995140.1| 346 K------ALRPPAKYAVI-LGSYGWHG--RSKDALLQMLSGMKIELVGS-LEVRAKPR 393
                                       3......23345666665.77777777..77777777777777777776.77776665 PP

>> Lactamase_B_6  Metallo-beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.6e-05     0.094      12      63 ..      76     123 ..      65     145 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.6e-05
                     Lactamase_B_6  12 DvGwdeskvslesalkelekviptvdliLLshatlehlGayallyakfkskl 63 
                                       ++G +e   ++e++++++++ i ++d i++ ha+++h Ga ++l+ k k+ l
  gi|242399715|ref|YP_002995140.1|  76 NPGFEE---EFENKINDVKN-IGDIDYIVMNHAEPDHAGAIPYLMSKNKKAL 123
                                       455555...45677887775.789********************98876544 PP

>> OFCC1  Orofacial cleft 1 candidate gene 1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0     6e-05      0.21      20      94 ..      61     142 ..      56     154 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6e-05
                             OFCC1  20 FLmvkeeraaveGienPaFnssstelsakqts....eervirkDrldstLaa...hqqkleleasaeerGnesarny 89 
                                       +L+v ee+ a   + nP+F+ + +++ +  ++    +  v+++ ++d+  a      ++ +    a ++G e+a+ y
  gi|242399715|ref|YP_002995140.1|  61 YLVVGEEKMALIDTVNPGFEEEFENKINDVKNigdiDYIVMNHAEPDHAGAIpylMSKNKKALLIATQKGAEMAKTY 137
                                       89999**************99666555444441111556899999**997752224555666677999********* PP

                             OFCC1  90 fDpla 94 
                                       +D   
  gi|242399715|ref|YP_002995140.1| 138 YDVPD 142
                                       **764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      548  (0.030565); 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: 0.65u 0.34s 00:00:00.99 Elapsed: 00:00:00.52
# Mc/sec: 2391.23
//
Query:       gi|242399716|ref|YP_002995141.1|  [L=157]
Description: hypothetical protein TSIB_1741 [Thermococcus sibiricus MM 739]
Scores for complete 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-18   65.4   0.0      7e-18   64.6   0.0    1.4  1  DUF1858   Domain of unknown function (DUF1858)
    1.5e-08   34.3   0.0    3.5e-08   33.1   0.0    1.6  1  TusA      Sulfurtransferase TusA
    4.7e-06   26.4   0.1    1.1e-05   25.2   0.0    1.8  2  DUF2249   Uncharacterized conserved protein (DUF2249)
  ------ inclusion threshold ------
      0.098   13.2   0.1        1.2    9.7   0.0    2.6  3  HTH_27    Winged helix DNA-binding domain
       0.11   12.9   0.0        0.2   12.1   0.0    1.4  1  SRP9-21   Signal recognition particle 9 kDa protein (SRP9)


Domain annotation for each model (and alignments):
>> DUF1858  Domain of unknown function (DUF1858)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.6   0.0     2e-21     7e-18       1      58 [.      87     144 ..      87     144 .. 0.98

  Alignments for each domain:
  == domain 1  score: 64.6 bits;  conditional E-value: 2e-21
                                       CETTSBHHHHHHH-GGGHHHHHHTTGGGGGSCCHHTTHHHHSBHHHHHHHHT--HHHH CS
                           DUF1858   1 ItkdttIgelleeyPelaevLvelGfhclgcpsllktvakvetleqaakvhgidldeL 58 
                                       It dt++++ll++yPe +++Lv++Gf  l++p+++kt+a+ +tl+qa k+ g++ +++
  gi|242399716|ref|YP_002995141.1|  87 ITGDTNVAKLLKAYPESLKILVKYGFSPLENPVMRKTLARTVTLKQAKKLIGMNDEKF 144
                                       9*****************************************************9986 PP

>> TusA  Sulfurtransferase TusA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.0   9.9e-12   3.5e-08       3      70 .]       2      66 ..       1      66 [. 0.95

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 9.9e-12
                                      EEBTT-STTCCHHHHHHHHCCCGCT-EEEEEESSCHHHHHHHHHHHHHTEEEEEEE-GCC-EEEEEEE CS
                              TusA  3 lDlrGlvCPePllklkkalekleegevlevladdpaatediprfakklghelveveeedgeyrivirk 70
                                      lD+rGl+ P+P + + + l kl+ ge+lev+ d p    di   +++ g+ lve ++ +g ++++++k
  gi|242399716|ref|YP_002995141.1|  2 LDVRGLKPPQPAVIIIESLGKLRVGETLEVIGDKPF--VDIIGKLEEAGY-LVELKDIGGAFVLRVTK 66
                                      9**********************************6..5***********.59**99*******9987 PP

>> DUF2249  Uncharacterized conserved protein (DUF2249)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0     3e-09   1.1e-05       2      34 ..       2      34 ..       1      65 [. 0.95
   2 ?   -3.0   0.0         2   7.2e+03      11      24 ..     142     155 ..     140     156 .. 0.76

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 3e-09
                           DUF2249  2 lDvRelppperhaaIfeafeaLapGetlelvnd 34
                                      lDvR+l+pp++   I e + +L+ Getle++ d
  gi|242399716|ref|YP_002995141.1|  2 LDVRGLKPPQPAVIIIESLGKLRVGETLEVIGD 34
                                      9****************************9976 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2
                           DUF2249  11 erhaaIfeafeaLa 24 
                                       e+++  +e++++L+
  gi|242399716|ref|YP_002995141.1| 142 EKFREMMEELKKLE 155
                                       77888888888886 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00034       1.2      30      65 ..      32      65 ..      24      67 .. 0.84
   2 ?   -1.9   0.0       1.4     5e+03      37      46 ..     102     111 ..      81     112 .. 0.49
   3 ?    0.3   0.0      0.28   9.9e+02      19      44 ..     131     156 ..     114     157 .] 0.79

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00034
                            HTH_27 30 vedshisyslkkLtekGLvertgdeadrrekrvrlT 65
                                      ++d +++ ++ kL+e+G++++ +d   +++  +r+T
  gi|242399716|ref|YP_002995141.1| 32 IGDKPFVDIIGKLEEAGYLVELKDI--GGAFVLRVT 65
                                      56888999***********998887..777777777 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.4
                            HTH_27  37 yslkkLtekG 46 
                                       +slk L+++G
  gi|242399716|ref|YP_002995141.1| 102 ESLKILVKYG 111
                                       5666666665 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.28
                            HTH_27  19 kkladlcgrlnvedshisyslkkLte 44 
                                       k ++ l+g+ +     +++ lkkL++
  gi|242399716|ref|YP_002995141.1| 131 KQAKKLIGMNDEKFREMMEELKKLEK 156
                                       55678899999999999999999987 PP

>> SRP9-21  Signal recognition particle 9 kDa protein (SRP9)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   5.4e-05       0.2      10      41 ..      92     123 ..      90     149 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.4e-05
                           SRP9-21  10 qsslLlearPsttrittkYsikakkkkkkkkk 41 
                                       + ++Ll+a+P++ +i +kY +++ +++  +k+
  gi|242399716|ref|YP_002995141.1|  92 NVAKLLKAYPESLKILVKYGFSPLENPVMRKT 123
                                       5689*****************94444433333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       992  (0.0553294); expected 358.6 (0.02)
Passed bias filter:                      654  (0.0364772); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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: 836.31
//
Query:       gi|242399717|ref|YP_002995142.1|  [L=456]
Description: Prismane-like protein [Thermococcus sibiricus MM 739]
Scores for complete 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-114  382.0   0.0    2.3e-96  323.5   0.0    2.0  2  Prismane  Prismane/CO dehydrogenase family


Domain annotation for each model (and alignments):
>> Prismane  Prismane/CO dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.3   0.0   1.5e-20   2.8e-16       1      78 [.      11      93 ..      11      96 .. 0.97
   2 !  323.5   0.0  1.3e-100   2.3e-96     162     510 ..      90     435 ..      89     436 .. 0.94

  Alignments for each domain:
  == domain 1  score: 59.3 bits;  conditional E-value: 1.5e-20
                                      -EE-SST...CT-ECSCS.SS-TTS-BHHHHHHHHHHHHHHHHHHHHHHHHHHC......HHHHHHHHHCHTSTTTB-S CS
                                      xxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxx RF
                          Prismane  1 mfCrqCe...ngpCritknkrGvCGkdadtavardlliavlkgaaahaaharel......adtliakalfktltnvnfd 70
                                      m+C+qC+    g+C+++    GvCGkd+++  +++ l++ +kg++a+  ha e+      + ++ a+al +tltnvnfd
  gi|242399717|ref|YP_002995142.1| 11 MLCNQCSmslTGGCTVQ----GVCGKDPNLNSLQEALLYGIKGTSAYYYHALEVgyddpkIGHFLAEALYSTLTNVNFD 85
                                      89*****9999******....********************************************************** PP

                                      HHHHHHHH CS
                                      xxxxxxxx RF
                          Prismane 71 dekklkrl 78
                                      ++++l+ +
  gi|242399717|ref|YP_002995142.1| 86 KNRFLELI 93
                                      ****9987 PP

  == domain 2  score: 323.5 bits;  conditional E-value: 1.3e-100
                                       HHHHHHHHHHHHHHHHHHHHHHHHHH-----EEEEECGCG-.SSSEEEEEESS-HHHHHHHHHHHCTTCCC....CC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xx RF
                          Prismane 162 lskalrlGlldlkgmelldeantslfGtPeppltevnlgvldkdkvnIlvsGHdladleelleqtegkgln....vy 234
                                       l+++l+ G + l++m lld+a  ++fG Pep  +ev +g+  ++  +Ilv+GH+ ++l ell+q+++++l+    vy
  gi|242399717|ref|YP_002995142.1|  90 LELILENGRVHLEAMKLLDKAYVETFGRPEP--VEVPTGTA-EG-HGILVTGHSYKALYELLKQIKEMDLEdelkVY 162
                                       678999*************************..********.89.9********************98665111167 PP

                                       CCGCCCCCCHHHHHHHHHCCEEEEECSSGGGHHHHHCCHECEEEESSSS--TTHHHHHHCHCCEEEEECTTB-TTSE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Prismane 235 thgemLpghcctalklkyrhlvgnvGnawqqekaeftgavdaivvdtnCivpplasvaekyktrlittsevakpgak 311
                                       th em p+h++++lk k+++l+gn G +w ++k+ef++++++i+ + nC+++p ++    y++r++t++  + +g+ 
  gi|242399717|ref|YP_002995142.1| 163 THAEMFPAHAYPELK-KFKALYGNWGGSWLHQKKEFAEFPGVILGTSNCVQQPTKA----YQDRIFTVGIAGLEGVP 234
                                       77*************.*************************************777....***************** PP

                                       EE--CTTCHHHHHHHHHHHHCCHCCTTCGG.-.................HHHHHTTSS-EEEEE-B---TTCGCCHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Prismane 312 hieeeekadkdaseiiekAielakareekkve.................idaiksGtIkgvvlvvGCdnakkgrdyy 371
                                       hie     d +++++i++A+e ++ ++ +  +                 +++i+ G+I+++++v+GCd+++kg  yy
  gi|242399717|ref|YP_002995142.1| 235 HIE-----DYNFEPLINRALETPRMKAYDGGKlltgfhhtnvlamkdrlLELIQGGKIRHIFVVGGCDTPHKGMGYY 306
                                       ***.....9****************9774444789999*************************************77 PP

                                       HHHHHHCHHTTEEEEEECHHHHHCCCTTTTECGHHHHSTHCEESEEEEESCCCHHHHHHHHHHHHHHTTSSGGGSSE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Prismane 372 telakelikrdvlvltaGCakyalnklglgtieaaelagegiPrvLdvGsCvdnyrivvialklaealgvdindLpl 448
                                         l+ eli++d l+l+a+C+k+++n  ++gti       +giPr Ld+G+C+  y+i++ia++la++lg+d+n Lp+
  gi|242399717|ref|YP_002995142.1| 307 ERLT-ELIPKDALILSAACGKFRYNARNYGTI-------DGIPRFLDFGQCNNVYSIIEIAIALANELGTDVNSLPV 375
                                       7776.567************************.......59************************************ PP

                                       EEEECC--SHHHHHHHHHHHHTT-.CEEECSS-TTTT-HHHHHHHHCHHHHHHCEEEECHCHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Prismane 449 aalalewyeqKAvailltllalGi.nihlgptlpafgspnvlkvlvedfedriggivtveedp 510
                                        +++l+w+eqKA+ail  ll+lGi  i++gp++p f+++nv +vl ++f  +++ + ++e+d+
  gi|242399717|ref|YP_002995142.1| 376 -SIVLSWMEQKAIAILYSLLYLGIkGIYIGPKPPEFLTSNVFEVLRKQF--DLKLTGDPEKDL 435
                                       .************************************************..888888999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (456 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 2814.74
//
Query:       gi|242399718|ref|YP_002995143.1|  [L=128]
Description: transcriptional regulator [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00028   20.9   0.8     0.0006   19.8   0.2    1.9  2  HTH_3           Helix-turn-helix
    0.00046   20.0   0.2    0.00081   19.2   0.2    1.4  1  HTH_5           Bacterial regulatory protein, arsR family
    0.00047   19.6   0.4     0.0011   18.5   0.4    1.6  1  HTH_24          Winged helix-turn-helix DNA-binding
    0.00059   19.7   0.0     0.0012   18.8   0.0    1.5  1  HTH_37          Helix-turn-helix domain
     0.0022   18.0   0.9     0.0045   17.0   0.9    1.5  1  HTH_19          Helix-turn-helix domain
     0.0091   15.9   0.1      0.015   15.2   0.1    1.3  1  MarR_2          MarR family
  ------ inclusion threshold ------
      0.012   15.6   0.0      0.044   13.7   0.1    1.9  2  MarR            MarR family
       0.03   14.5   0.0       0.08   13.1   0.0    1.6  2  DUF1798         Bacterial domain of unknown function (DUF1798
      0.035   13.9   0.8      0.058   13.2   0.8    1.3  1  HTH_38          Helix-turn-helix domain
      0.081   12.8   0.0       0.17   11.8   0.0    1.6  1  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox
      0.081   13.0   0.0       0.15   12.2   0.0    1.3  1  Sigma70_r3      Sigma-70 region 3
      0.092   12.6   0.0       0.13   12.2   0.0    1.3  1  Sigma70_ECF     ECF sigma factor
      0.096   12.5   0.1       0.16   11.8   0.1    1.3  1  HTH_23          Homeodomain-like domain
       0.11   12.6   0.0       0.16   12.0   0.0    1.3  1  Cro             Cro


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   0.2   4.6e-07    0.0006       3      31 ..      23      51 ..      21      62 .. 0.90
   2 ?   -2.6   0.0       4.7   6.1e+03      12      18 ..      70      76 ..      67      80 .. 0.67

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 4.6e-07
                                      HHHHHTTHHHHHHHHHHTSSHHHHHHHHT CS
                             HTH_3  3 elRkqlglsqeeLAeklGvsrstisriEn 31
                                      e++ ++gl q ++A++l +++s++sr+ +
  gi|242399718|ref|YP_002995143.1| 23 EILREKGLNQLQIAKLLYITQSAVSRYLR 51
                                      56778**********************98 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4.7
                                      HHHHHHH CS
                             HTH_3 12 qeeLAek 18
                                      ++eLAe 
  gi|242399718|ref|YP_002995143.1| 70 LKELAET 76
                                      4677765 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.2   6.4e-07   0.00081       3      37 ..      17      51 ..      15      54 .. 0.95

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 6.4e-07
                                      HHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHH CS
                             HTH_5  3 tRlkILklLaegelcvcelaeelglsqstvShHLk 37
                                       R++++ +L+e+ l   ++a+ l ++qs+vS++L+
  gi|242399718|ref|YP_002995143.1| 17 LRRRLVEILREKGLNQLQIAKLLYITQSAVSRYLR 51
                                      599*******************************9 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.4   8.3e-07    0.0011      11      39 ..      23      51 ..      17      52 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 8.3e-07
                            HTH_24 11 lLqknprisqreLAerlglSpstvnrrlk 39
                                      ++ ++ +++q ++A+ l +++s+v+r+l+
  gi|242399718|ref|YP_002995143.1| 23 EILREKGLNQLQIAKLLYITQSAVSRYLR 51
                                      455669*********************98 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   9.1e-07    0.0012      20      55 ..      18      53 ..       4      61 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 9.1e-07
                                      HHHHHHHHHHCT--HHHHHHHHT--HHHHHHHHTT- CS
                            HTH_37 20 alaiaeliekrelsqseaaqllgiaqPkvsrllrgk 55
                                       +++ e++++++l q ++a+ll i+q+ vsr lr +
  gi|242399718|ref|YP_002995143.1| 18 RRRLVEILREKGLNQLQIAKLLYITQSAVSRYLRMN 53
                                      4668999************************99865 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.9   3.5e-06    0.0045       2      62 ..      19      80 ..      19      83 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.5e-06
                            HTH_19  2 erLkeaReelgltqeelaerlgisrskisaiEngkkdvps..aelllkiaealgidleyllqg 62
                                      +rL e+ +e+gl+q ++a+ l i++s  s +   ++  +    e+++ i ++l+  +e ++++
  gi|242399718|ref|YP_002995143.1| 19 RRLVEILREKGLNQLQIAKLLYITQSAVSRYLRMNR-GALvdVEKFPEIDNKLKELAETIIKK 80
                                      7999****************************9977.55456999999999999999988765 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   1.2e-05     0.015      11      43 ..      21      51 ..      15      52 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.2e-05
                                      HHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHH CS
                            MarR_2 11 LaaLgrrpgrdltvgelarrlglsksavsrilk 43
                                      L ++ r+ g  l++ ++a+ l +++savsr l+
  gi|242399718|ref|YP_002995143.1| 21 LVEILREKG--LNQLQIAKLLYITQSAVSRYLR 51
                                      88999****..*******************886 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   3.4e-05     0.044       9      39 ..      21      51 ..      19      52 .. 0.90
   2 ?   -1.7   0.0       2.2   2.9e+03      39      55 ..      96     112 ..      91     113 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.4e-05
                                      HHHHHHSTTEEHHHHHHHHTS-HHHHHHHHH CS
                              MarR  9 LrilyeqgplsvseLakklgvskstvtrvld 39
                                      L+ + ++ +l++ ++ak l++++s+v+r l+
  gi|242399718|ref|YP_002995143.1| 21 LVEILREKGLNQLQIAKLLYITQSAVSRYLR 51
                                      677888999*******************876 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.2
                                       HHHHHTTSEEEEEETTS CS
                              MarR  39 drLekkGlieRskspeD 55 
                                        ++  kG++ + +s+ D
  gi|242399718|ref|YP_002995143.1|  96 IEMLGKGYVCSFHSKVD 112
                                       57899999988888776 PP

>> DUF1798  Bacterial domain of unknown function (DUF1798)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       2.2   2.8e+03      55      68 ..      24      37 ..       7      54 .. 0.63
   2 ?   13.1   0.0   6.2e-05      0.08      35      85 ..      60     111 ..      58     115 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 2.2
                                      HS--SSS-HHHHHH CS
                           DUF1798 55 kerpkylheeqiea 68
                                        r k l++ qi +
  gi|242399718|ref|YP_002995143.1| 24 ILREKGLNQLQIAK 37
                                      44555555555544 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 6.2e-05
                                       HHHHHHHHHHHHHHHHHHHHHS--S..SS-HHHHHHHHHHHHHHHHHHHH--S CS
                           DUF1798  35 adevkelldewkelalewvkkerpk..ylheeqieataenleklvvqsFfpkt 85 
                                       ++++ e  +++kela+ ++kk rp+  y+h e ++ t+e l k  v sF +k+
  gi|242399718|ref|YP_002995143.1|  60 VEKFPEIDNKLKELAETIIKK-RPDeyYIHGELVKITIEMLGKGYVCSFHSKV 111
                                       6788888899***********.875458*********************9987 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.8   4.5e-05     0.058      10      42 ..      19      51 ..      18      53 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.5e-05
                            HTH_38 10 ReeIerllaeGlslreIArrLgrspsTIsRElk 42
                                      R+  e+l+++Gl++ +IA++L    s +sR l+
  gi|242399718|ref|YP_002995143.1| 19 RRLVEILREKGLNQLQIAKLLYITQSAVSRYLR 51
                                      78889*************************988 PP

>> YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00013      0.17      11      44 ..      32      67 ..      25      75 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00013
                    YdaS_antitoxin 11 qkaLAealgvsqqaVsqWlkgkkq..vpaervpeIe 44
                                      q + A++l ++q+aVs+ l+ +++  v++e  peI 
  gi|242399718|ref|YP_002995143.1| 32 QLQIAKLLYITQSAVSRYLRMNRGalVDVEKFPEID 67
                                      6678****************99999******99995 PP

>> Sigma70_r3  Sigma-70 region 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00011      0.15      26      75 ..      35      83 ..      32      85 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00011
                                      HHHHHTXXHHHHHHHHHHHXXXEETTXBSSSSTTXBSTTTXBXSSSXXHH CS
                        Sigma70_r3 26 iAeeLglseekVrevleaarepvSldlpvgeeedtelgdlleddeaespe 75
                                      iA+ L ++++ V ++l+++r + ++d++ ++e d++l +l e      p+
  gi|242399718|ref|YP_002995143.1| 35 IAKLLYITQSAVSRYLRMNRGA-LVDVEKFPEIDNKLKELAETIIKKRPD 83
                                      9*****************9887.68**************98887555555 PP

>> Sigma70_ECF  ECF sigma factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   9.9e-05      0.13     140     177 ..      18      56 ..       3      64 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.9e-05
                       Sigma70_ECF 140 qarlvelrkleGlsveEiAeklgvskrtverrlalaR.a 177
                                        +rlve+ + +Gl    iA+ l + +++v r l++ R a
  gi|242399718|ref|YP_002995143.1|  18 RRRLVEILREKGLNQLQIAKLLYITQSAVSRYLRMNRgA 56 
                                       5799*******************************9944 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   0.1   0.00012      0.16      10      40 ..      21      52 ..      15      60 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00012
                            HTH_23 10 illllae.GlsvreIAreLgvsrrTvyrwlkr 40
                                       +  l+e Gl++ +IA++L ++++ v+r+l+ 
  gi|242399718|ref|YP_002995143.1| 21 LVEILREkGLNQLQIAKLLYITQSAVSRYLRM 52
                                      44445567*********************986 PP

>> Cro  Cro
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00013      0.16      15      42 ..      32      59 ..      18      63 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00013
                                      HHHHHHHHTS-HHHHHHHHHCT-EEEEE CS
                               Cro 15 QaktAkdlgvkqsaIsKAlkakRnIyli 42
                                      Q + Ak l ++qsa+s+ l+ +R   + 
  gi|242399718|ref|YP_002995143.1| 32 QLQIAKLLYITQSAVSRYLRMNRGALVD 59
                                      999******************9987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       890  (0.0496402); expected 358.6 (0.02)
Passed bias filter:                      759  (0.0423336); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.59u 0.36s 00:00:00.95 Elapsed: 00:00:00.56
# Mc/sec: 692.98
//
Query:       gi|242399719|ref|YP_002995144.1|  [L=433]
Description: Sodium:dicarboxylate symporter [Thermococcus sibiricus MM 739]
Scores for complete 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-107  359.8  31.4     2e-107  359.6  31.4    1.0  1  SDF       Sodium:dicarboxylate symporter family
  ------ inclusion threshold ------
       0.25   11.2   0.6       0.64    9.9   0.6    1.6  1  TIM21     TIM21


Domain annotation for each model (and alignments):
>> SDF  Sodium:dicarboxylate symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  359.6  31.4  2.2e-111    2e-107       3     389 ..      14     427 ..      12     428 .. 0.95

  Alignments for each domain:
  == domain 1  score: 359.6 bits;  conditional E-value: 2.2e-111
                               SDF   3 lqiliglvlGlviGll..........elvkelaalisplgdlfinllkmlivPlvfasiisgiaslgdakklgklgl 69 
                                       +++ ++++lG+++Gl+          +l + +a++isp+g +++++lkm+++P+vf+s+i+g ++l+ +kklg++g+
  gi|242399719|ref|YP_002995144.1|  14 YRVGVAFLLGVAFGLVlwyydmangsNLGERVATYISPFGAVLVRMLKMVVIPIVFFSLIVGSSGLS-PKKLGRVGG 89 
                                       67889**********9*********999**************************************6.********* PP

                               SDF  70 ktllyfllttliAaiiglilalllkpg......selaleassakeaekketdslldlilslipsnifealaegnvla 140
                                       k++l++++t+++Aa+ig+ +a++++pg       e+  ++  +   + +    l+dlil+++ +n+feala+g+ l+
  gi|242399719|ref|YP_002995144.1|  90 KVILWYIFTSFVAAMIGVSIAMFVHPGqgvavdVEKLGSSMGEGGPSITPPSGLTDLILKMF-TNPFEALANGEFLP 165
                                       ***************************99999755556666666777778889*********.8999********** PP

                               SDF 141 vivfailfGialaalgekg.........epllkffeslnevvmkvvkivmklaPigvfaliaslvaskglgalssla 208
                                       +ivfa+lfG+a+  l ++          +++l+f   +n+v++++v+++++++Pigvf+l +  ++ +g +++++++
  gi|242399719|ref|YP_002995144.1| 166 IIVFALLFGLAARVLLDHTqnetekkqiQSILDFAAGANSVMFRIVSWILEYFPIGVFSLAVVNFGLYGPSIIGPYL 242
                                       ************9998877788899999************************************************* PP

                               SDF 209 kflltvylglaihllivlpllllvltkknplkflkkilpalltAfsTaSSaAtLPvtlecaeknlgvsesiasfvlP 285
                                       k +l v+ g++i+++iv+++l+ v+ k np++f+k + ++++t+f T+SSaAtLPvt+++a ++++v+++ a+f lP
  gi|242399719|ref|YP_002995144.1| 243 KAVLGVISGIVIMIFIVYSILVSVFLKENPIDFFKRAKEVMITSFFTRSSAATLPVTIKTAIESFKVKKELAEFSLP 319
                                       ***************************************************************************** PP

                               SDF 286 lGatinmdGtalyeavaaifiaqlfgvelslgqllllvlvatlasiGaagvPgaglvalllvlsalglpveg....i 358
                                       +Gatinm+G ++++ + a+f+a +f+++l++++l++++++++l++iGa gvPg++l++l++vl +lgl        +
  gi|242399719|ref|YP_002995144.1| 320 VGATINMNGVCIHLPMWAVFAADVFNIDLTISSLAIVIITTVLSAIGAGGVPGGSLMLLFIVLGTLGLEPSQiaiiV 396
                                       ********************************************************************954423458 PP

                               SDF 359 alilaidrllDmfrTavNvtGdavaalivak 389
                                       al l++++l+Dmf+T+ NvtGd++++ ivak
  gi|242399719|ref|YP_002995144.1| 397 ALALGVNPLIDMFETMNNVTGDLCCTYIVAK 427
                                       88899************************98 PP

>> TIM21  TIM21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.6   7.1e-05      0.64      15      47 ..     248     280 ..     242     286 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 7.1e-05
                                       XXXXXXXXXXXXXXXXXXXXXXTHHHHHHHHHH CS
                             TIM21  15 vlagvgvtglvlYlilselfspsgdtkifnrAl 47 
                                       v+ g++++  ++Y il ++f ++ +   f+rA 
  gi|242399719|ref|YP_002995144.1| 248 VISGIVIMIFIVYSILVSVFLKENPIDFFKRAK 280
                                       99*****************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       798  (0.0445089); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.67u 0.38s 00:00:01.05 Elapsed: 00:00:00.55
# Mc/sec: 2383.03
//
Query:       gi|242399720|ref|YP_002995145.1|  [L=45]
Description: hypothetical protein TSIB_1745 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       189  (0.0105416); expected 358.6 (0.02)
Passed bias filter:                      167  (0.00931452); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.52
# Mc/sec: 260.73
//
Query:       gi|242399721|ref|YP_002995146.1|  [L=123]
Description: Glutaredoxin/thioredoxin-like protein [Thermococcus sibiricus MM 739]
Scores for complete 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   44.0   0.3    4.1e-11   42.8   0.0    1.7  2  Thioredoxin_3  Thioredoxin domain
    2.3e-05   24.5   0.1    5.9e-05   23.2   0.0    1.7  2  Glutaredoxin   Glutaredoxin
    9.4e-05   22.3   0.3      0.033   14.0   0.0    2.4  3  DSBA           DSBA-like thioredoxin domain
    0.00023   21.3   0.2      0.035   14.2   0.0    2.1  2  Thioredoxin_4  Thioredoxin
     0.0029   17.6   0.0     0.0034   17.3   0.0    1.2  1  Thioredoxin    Thioredoxin
     0.0045   17.4   0.2      0.086   13.3   0.2    2.2  1  Thioredoxin_2  Thioredoxin-like domain
  ------ inclusion threshold ------
      0.025   14.6   0.0       0.17   11.9   0.0    1.9  2  DUF1223        Protein of unknown function (DUF1223)


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 ?   -1.3   0.1      0.92   2.3e+03      31      49 ..      12      31 ..       6      35 .. 0.71
   2 !   42.8   0.0   1.6e-14   4.1e-11       3      73 ..      41     115 ..      39     118 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.92
                                      CEEECCTTHHHH.HHCT-SS CS
                     Thioredoxin_3 31 aevekvtdfeei.ekygVms 49
                                      +e+++ +++ e+ +k g++ 
  gi|242399721|ref|YP_002995146.1| 12 LEMIRRKKMLELmKKAGIIE 31
                                      57777777777767777765 PP

  == domain 2  score: 42.8 bits;  conditional E-value: 1.6e-14
                                       EEE.ESSSSTTCHHHHHHHHHHCHCC.TCEC.EEECC..TTHHHHHHCT-SSSSEEECTTCEEEESS---CCHHHH CS
                     Thioredoxin_3   3 ikv.lgpgCakCpklekavkeaaaek.gika.evekv..tdfeeiekygVmsvPalvidgkvvvsGkvpseeeirk 73 
                                       i+v  +pgC++Cp + ++++e+a +  gi a e+  +  +  ++  ++++m +P+++i+ +v++ G vp+ +e+++
  gi|242399721|ref|YP_002995146.1|  41 IEViTSPGCPYCPIAWAMAQEIARKYdGIIAkEISVAtpEGQRKAREHNIMGTPTILINNRVEFIG-VPNFAEFER 115
                                       89966999*****************97787754444422455666*********************.**9998875 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       3.3   8.4e+03      16      24 ..      21      29 ..      18      36 .. 0.52
   2 !   23.2   0.0   2.3e-08   5.9e-05       1      59 [.      41     102 ..      41     103 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 3.3
                                      HHHHHHTTG CS
                      Glutaredoxin 16 krlLkelgv 24
                                       +l+k+ g+
  gi|242399721|ref|YP_002995146.1| 21 LELMKKAGI 29
                                      455555553 PP

  == domain 2  score: 23.2 bits;  conditional E-value: 2.3e-08
                                       EEEEESTSSHHHHHHHHHH.....HHTTGGEEEEEGCCSHHHHHHHHHHHTSSSSSEEEETTEE CS
                      Glutaredoxin   1 vvlftkptCpyCkkakrlL.....kelgvkfeeidvdkdeeireelkelsgvrtvPqvfidgkh 59 
                                       +++ t+p+CpyC+ a + +     k+ g+  +ei v   +e + + +e  +++  P++ i++++
  gi|242399721|ref|YP_002995146.1|  41 IEVITSPGCPYCPIAWAMAqeiarKYDGIIAKEISVAT-PEGQRKAREH-NIMGTPTILINNRV 102
                                       7899********98777774444444457788888888.5777777777.99*********985 PP

>> DSBA  DSBA-like thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.8   4.6e+03     120     135 ..      15      29 ..       7      36 .. 0.65
   2 !    6.5   0.0    0.0024       6.2       9      29 ..      48      68 ..      40      79 .. 0.79
   3 !   14.0   0.0   1.3e-05     0.033     155     191 ..      80     116 ..      71     118 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.8
                                       TSSHHHHHHHHHHTTS CS
                              DSBA 120 itddqellevaekaGl 135
                                       i++++ +le+++kaG+
  gi|242399721|ref|YP_002995146.1|  15 IRRKK-MLELMKKAGI 29 
                                       44443.7777777777 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0024
                                      TBHHHHHHHHHHHHHHHHCCT CS
                              DSBA  9 lCPyCylgkerleklaarspd 29
                                       CPyC ++++  +++a+++++
  gi|242399721|ref|YP_002995146.1| 48 GCPYCPIAWAMAQEIARKYDG 68
                                      5***************99944 PP

  == domain 3  score: 14.0 bits;  conditional E-value: 1.3e-05
                                       HHHHHHHHTT-SSSSEEEETTCEEEESSSSHHHHHHH CS
                              DSBA 155 entaaaqslgvtGvPtvvvdgkrmvfGadrldtlada 191
                                       e +++a++ ++ G+Pt+++++++ + G++++  ++++
  gi|242399721|ref|YP_002995146.1|  80 EGQRKAREHNIMGTPTILINNRVEFIGVPNFAEFERR 116
                                       66899*****************9*******9999987 PP

>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.5   0.1    0.0069        18      11      46 ..      35      68 ..      32      75 .. 0.75
   2 !   14.2   0.0   1.4e-05     0.035     130     162 ..      82     115 ..      70     119 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0069
                                      TT-SEEEEEEE-TT-HHHHHHHHHHHHHHHHHHHTT CS
                     Thioredoxin_4 11 pdApvtvieyedlrCphCakfeeeveklleeyidtG 46
                                      ++ +v +++ ++  Cp+C       +++ ++y  +G
  gi|242399721|ref|YP_002995146.1| 35 EKPKVIIEVITSPGCPYCPIAWAMAQEIARKY--DG 68
                                      45577777789*******87766667777777..55 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 1.4e-05
                                       HHHHHHHT--SS-EEEETTEE.E-TT--HHHHHH CS
                     Thioredoxin_4 130 skeakkagiestPtfiingek.veepqtyeelka 162
                                       +++a++++i +tPt++in ++ + + ++++e+++
  gi|242399721|ref|YP_002995146.1|  82 QRKAREHNIMGTPTILINNRVeFIGVPNFAEFER 115
                                       6789**************9998888999988876 PP

>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.3e-06    0.0034      13      80 ..      31     100 ..      19     118 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.3e-06
                                       HHTTTSSEEEEEE.E-TTSHHHHCHHHHHHHHHHHCTT.TSEEEEEETTTSHHHHHHTT-SSSSEEEEEE CS
                       Thioredoxin  13 evakekklvlveF.yApwCghCkalaPeleklaeelkd.kvklakvdvdenedlakkyevegiPtlklfk 80 
                                       ev++ek +v++e  ++p C+ C     + +++a+++ +   k + v + e +  a+++++ g Pt+++ +
  gi|242399721|ref|YP_002995146.1|  31 EVKQEKPKVIIEViTSPGCPYCPIAWAMAQEIARKYDGiIAKEISVATPEGQRKAREHNIMGTPTILINN 100
                                       78999999***963689********************866677788889999**************7754 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.2   3.4e-05     0.086       4      99 ..      36     107 ..      32     117 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.4e-05
                     Thioredoxin_2   4 ngkpvlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrg 80 
                                       + k ++ v+t+p+CpyC    +  +e+     +     ++     +a +i+ a+ +          +  ar++++ g
  gi|242399721|ref|YP_002995146.1|  36 KPKVIIEVITSPGCPYCPIAWAMAQEI---ARK-----YDGI---IAKEISVATPEG---------QRKAREHNIMG 92 
                                       4466677999******97633333333...333.....4444...444444444443.........44599999999 PP

                     Thioredoxin_2  81 tPtivfldgkeivarlpGy 99 
                                       tPti++ +      +  G 
  gi|242399721|ref|YP_002995146.1|  93 TPTILINNRV----EFIGV 107
                                       9999988877....45555 PP

>> DUF1223  Protein of unknown function (DUF1223)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   6.7e-05      0.17       1      32 [.      40      71 ..      40      77 .. 0.85
   2 ?    0.6   0.0      0.19   4.8e+02      65      97 ..      86     119 ..      80     123 .] 0.72

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.7e-05
                                      EEEEEE-TT-TT-HHHHHHHHHH.HHHTSSEE CS
                           DUF1223  1 vvELFtSqGCssCPpAdallselaaedkdvva 32
                                      ++E  tS GC  CP A a+ +e+a++ + ++a
  gi|242399721|ref|YP_002995146.1| 40 IIEVITSPGCPYCPIAWAMAQEIARKYDGIIA 71
                                      58999******************888777776 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.19
                                       TT-S---SSEEEETTTEEEETT-.HHHHHHHHHH CS
                           DUF1223  65 lglrsvYTPqvvvnGreevvgsd.eeeleaaisa 97 
                                       ++++ + TP +++n r e++g    +e+e+ +++
  gi|242399721|ref|YP_002995146.1|  86 REHNIMGTPTILINNRVEFIGVPnFAEFERRVRQ 119
                                       4455577*********999986536777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       709  (0.0395449); expected 358.6 (0.02)
Passed bias filter:                      587  (0.0327403); 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: 0.57u 0.36s 00:00:00.93 Elapsed: 00:00:00.54
# Mc/sec: 686.88
//
Query:       gi|242399722|ref|YP_002995147.1|  [L=197]
Description: hypothetical protein TSIB_1747 [Thermococcus sibiricus MM 739]
Scores for complete 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-48  162.7   0.3    9.8e-48  162.3   0.3    1.2  1  TYW3      Methyltransferase TYW3
  ------ inclusion threshold ------
      0.017   14.4   0.1      0.035   13.4   0.1    1.5  2  EAP30     EAP30/Vps36 family


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 !  162.3   0.3   1.1e-51   9.8e-48       2     212 ..      11     193 ..      10     194 .. 0.96

  Alignments for each domain:
  == domain 1  score: 162.3 bits;  conditional E-value: 1.1e-51
                                       HHHHHHHHH....HHHHHCCHC-GGGHHHHHHHHC-SSEEEEEEES-EEEEE............EESSTT-STT-EE CS
                              TYW3   2 rKakiLeeLsvpdtdkspkGsvDekirelideinsledlvTtSSCsGRvsvflegrksaeaeeeaaksggkkgggkw 78 
                                       +K+k+Le+L    +d+ +kG vD++i++l+++insl++++TtSSCsGR+s++            +++  g+k ++ w
  gi|242399722|ref|YP_002995147.1|  11 QKKKALESL----NDALEKGLVDSDIISLLNKINSLKNYFTTSSCSGRISIM------------QMPDLGDKLNAIW 71 
                                       6999*****....9**************************************............677777778889* PP

                                       EEEESS---HHHHHHHHCS--..............SSEEEEEEE--EEEEEESSHHHHHHHHHHHHHCT-TT-EEEE CS
                              TYW3  79 lfvsHdpvkeeellaelfgleeeegsaksseseeeerlilfkfePmILHvlcrslesAqkllsaAleaGfreSGivs 155
                                       l ++H++vk ee+l+++++++               ++++f + ++ILHv +++le+A +ll++A+++Gf++S i+s
  gi|242399722|ref|YP_002995147.1|  72 LGKWHREVKIEEVLDTINKHD--------------GGMLWFMVHSPILHVSAKTLEDAVELLNLAMACGFKHSNIKS 134
                                       ******************997..............79**************************************** PP

                                       ECTTEEEEEEE---EEEEEEE..STS---HHHHHHHHHHHHHHHHHHHHHHHHHHHHC- CS
                              TYW3 156 lkkkkvivairsglklevpig..kellvseeylkllvklanerfeenkkrierfeealk 212
                                       +++kk +v+irs++++++p+g  +el+v+e+yl  +v++an ++++ k++++++e++++
  gi|242399722|ref|YP_002995147.1| 135 VSHKKLVVEIRSTERMDIPLGsdGELWVNESYLVKIVSMANLQLRRTKEKLRKLEDEIQ 193
                                       *********************9755*******************************997 PP

>> EAP30  EAP30/Vps36 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0      0.33     3e+03     211     232 ..       7      28 ..       4      31 .. 0.73
   2 ?   13.4   0.1   3.9e-06     0.035     117     229 ..      79     191 ..      63     192 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.33
                             EAP30 211 nlgwsvarakeaLeelereGll 232
                                       n+ ++++ a e L++++++Gl+
  gi|242399722|ref|YP_002995147.1|   7 NFDLQKKKALESLNDALEKGLV 28 
                                       5667777788888888888876 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 3.9e-06
                             EAP30 117 isleelyalvnrarggva.........lvspdDllraiekl.lvlgsglsvlqvggkkvvrSvptelntdqvevlev 183
                                       +++ee+++ +n+  gg+           vs ++l+ a+e+l l   +g++  +      ++Sv++++   +   ++ 
  gi|242399722|ref|YP_002995147.1|  79 VKIEEVLDTINKHDGGMLwfmvhspilHVSAKTLEDAVELLnLAMACGFKHSN------IKSVSHKKLVVE---IRS 146
                                       67899*******99888679*********************99999****999......888886666666...566 PP

                             EAP30 184 akrlvsllaekssgggvtaselaeeeenlgwsvarakeaLeelere 229
                                        +r+   l + ++   v++s l++  +  +++  r+ke L++le+e
  gi|242399722|ref|YP_002995147.1| 147 TERMDIPLGSDGE-LWVNESYLVKIVSMANLQLRRTKEKLRKLEDE 191
                                       6666544555554.489999999998999*************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1168  (0.0651459); expected 358.6 (0.02)
Passed bias filter:                      676  (0.0377043); 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: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.53
# Mc/sec: 1123.76
//
Query:       gi|242399723|ref|YP_002995148.1|  [L=546]
Description: Thermosome alpha subunit [Thermococcus sibiricus MM 739]
Scores for 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-189  628.1  24.9   1.1e-188  627.9  24.9    1.0  1  Cpn60_TCP1  TCP-1/cpn60 chaperonin family
  ------ inclusion threshold ------
       0.11   12.5   0.1       0.39   10.7   0.1    2.0  1  AAA_5       AAA domain (dynein-related subfamily)
       0.15   11.5   0.9       0.24   10.9   0.1    1.7  2  TrwC        TrwC relaxase


Domain annotation for each model (and alignments):
>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  627.9  24.9  1.8e-192  1.1e-188       1     490 [.      37     527 ..      37     528 .. 0.98

  Alignments for each domain:
  == domain 1  score: 627.9 bits;  conditional E-value: 1.8e-192
                                       HHHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHH CS
                        Cpn60_TCP1   1 ladivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleea 77 
                                       +a++v+ttlGPkGmdKmlv++ g++v+TnDGatil e++i+hPaak++ve+a++qd+e+GDGTtt+v++ageLl++a
  gi|242399723|ref|YP_002995148.1|  37 IAETVRTTLGPKGMDKMLVDSLGDIVITNDGATILDEMDIQHPAAKMMVEVAKTQDKEAGDGTTTAVVIAGELLRRA 113
                                       799************************************************************************** PP

                                       HHHHHCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHHHCHC CS
                        Cpn60_TCP1  78 ekliaagvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAvklie 154
                                       e+l+++++hp++i++gy+ a+eka e+L+ ia+++s    d+e+L+k+a+t++++k  ++e+++l+kl+v+Avkl+ 
  gi|242399723|ref|YP_002995148.1| 114 EELLNQNIHPSVIVKGYNLAAEKAQEILEGIAKDVS--PMDEEILMKAATTAITGKAAEEERDYLAKLAVEAVKLVG 188
                                       *******************************66666..669********************************8887 PP

                                       CCS...EECSCCCEECCCCEECECTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HHCCHHHCCCCSCC CS
                        Cpn60_TCP1 155 ene...keldlgrikvvkieggsledselveGlvldkgvlspdmpkklenakvllldvsLeiektetkttvvlsdae 228
                                       e+    +++d+++ik++k+eggs++d++l++G+v+dk+ ++p mp+k+e+ak++l++  Le ++tet++++++++++
  gi|242399723|ref|YP_002995148.1| 189 EKVgeeYQVDIDNIKLEKKEGGSVRDTQLIKGVVIDKERVHPAMPRKIEDAKIALINEALEVKETETDAEIRITSPD 265
                                       777899*********************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCGGGGG CS
                        Cpn60_TCP1 229 eleklekaeekqleellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatGatavssledlt 305
                                       +l++++++ee++++e+++ki+++g+nvv+cqkgiddla+h+lak+gila+rrvkk+d+e+lakatGa++v+++ dlt
  gi|242399723|ref|YP_002995148.1| 266 QLQAFLEQEERMIKEMVDKIVATGANVVFCQKGIDDLAQHYLAKAGILAVRRVKKSDMEKLAKATGAKIVTNIRDLT 342
                                       ***************************************************************************** PP

                                       CGC-EEEEEEEECCETTCCEEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHHH CS
                        Cpn60_TCP1 306 peelGtakkveeekigsekttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatele 382
                                       +e+lG+a+ vee+k+  e+++++e++k++k++til+rg t++v+de+era+edA++vvk ++ed+k+v+GGGa+e+e
  gi|242399723|ref|YP_002995148.1| 343 SEDLGHAELVEERKVAGENMVFVEGCKNPKAVTILIRGGTEHVVDEVERALEDAIKVVKDIVEDGKIVAGGGASEIE 419
                                       ***************************************************************************** PP

                                       HHHHHHCCCCTSXCCHHHHHHHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHHHTTXTTEEEETTTTCEEECCCCTX CS
                        Cpn60_TCP1 383 lakklkeyaksvsgeeqlaieafakALevipktLaeNaGldpievlaklraahnkgekelgidvesgeiidlveagv 459
                                       la kl+eyak+v g+eqlaie fa+AL++ipktLaeNaGldp +vl k++aah+++  ++g+dv  ge+ d++e+gv
  gi|242399723|ref|YP_002995148.1| 420 LAIKLDEYAKKVGGKEQLAIESFADALKIIPKTLAENAGLDPVDVLVKVTAAHKEKGPTVGVDVFAGEPADMMERGV 496
                                       *****************************************************99999******************* PP

                                       EEEHHHHHHHHHHHHHHHHHHHCEEEEEXXX CS
                        Cpn60_TCP1 460 vDplkvkrqalksAteaastiLrideiikak 490
                                       ++pl+vkrqa+ksA+eaa +iLrid++i a 
  gi|242399723|ref|YP_002995148.1| 497 IEPLRVKRQAIKSASEAAVMILRIDDVIAAS 527
                                       ****************************986 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   6.5e-05      0.39      31      97 ..     341     412 ..     318     427 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 6.5e-05
                                       E--TT--HHHHH--B--.........--------.....G-SEEEEESGGG--HHHHHHHHHHHHSSEEE.. CS
                             AAA_5  31 qltrdtteedlkgrreikngttslvdsplvraar.....egeilvlDEveraesevlnsLlslleerrllle 97 
                                       + ++d+  ++l+ +r++++++ ++v+++   +a       g   v+DEvera  ++++++  + e+ ++   
  gi|242399723|ref|YP_002995148.1| 341 LTSEDLGHAELVEERKVAGENMVFVEGCKNPKAVtilirGGTEHVVDEVERALEDAIKVVKDIVEDGKIVAG 412
                                       34556666677777777777777776665555547888889999**********************998744 PP

>> TrwC  TrwC relaxase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1      0.48   2.9e+03     203     241 ..     173     216 ..     125     269 .. 0.59
   2 ?   10.9   0.1     4e-05      0.24      38     123 ..     310     406 ..     294     419 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.48
                              TrwC 203 aeeleklGyeveer..g...kngvfeiagvpeelleafSkRrqq 241
                                       ++ l+kl +e  +   +   ++ +++i+ ++ e  e  S R +q
  gi|242399723|ref|YP_002995148.1| 173 RDYLAKLAVEAVKLvgEkvgEEYQVDIDNIKLEKKEGGSVRDTQ 216
                                       33344444444333321233556666666666666666666555 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 4e-05
                              TrwC  38 lg.lsg.evteeqfeallegrhpd........tgerlgrakesaererkavagfDltf....saPKSvSllalvgdd 100
                                        g l+  +v++ ++e+l + + ++        t+e lg+a+   e   ++vag  ++f      PK v++l+  g++
  gi|242399723|ref|YP_002995148.1| 310 AGiLAVrRVKKSDMEKLAKATGAKivtnirdlTSEDLGHAELVEE---RKVAGENMVFvegcKNPKAVTILIRGGTE 383
                                       443443489999999999887777789999999999999888654...8899999987444457********99999 PP

                              TrwC 101 erraaieaahdaAvkaalallee 123
                                       ++  ++e+a ++A+k + +++e+
  gi|242399723|ref|YP_002995148.1| 384 HVVDEVERALEDAIKVVKDIVED 406
                                       99899999999998887777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (546 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       732  (0.0408277); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); 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: 0.70u 0.33s 00:00:01.03 Elapsed: 00:00:00.52
# Mc/sec: 3171.37
//
Query:       gi|242399724|ref|YP_002995149.1|  [L=341]
Description: TRP-repeat-containing protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.2e-17   61.9  16.3    2.9e-08   33.9   1.2    4.0  4  TPR_12       Tetratricopeptide repeat
    1.3e-10   41.2   6.6      0.012   16.4   0.0    6.0  6  TPR_14       Tetratricopeptide repeat
    3.5e-10   39.2   2.8    0.00024   20.9   0.0    4.9  4  TPR_7        Tetratricopeptide repeat
    2.7e-09   37.1   0.2     0.0021   18.6   0.0    4.7  4  TPR_6        Tetratricopeptide repeat
    2.9e-08   33.2  17.2    0.00045   20.1   0.4    5.8  6  TPR_2        Tetratricopeptide repeat
    5.1e-08   32.5  20.0    0.00043   20.3   0.3    6.2  5  TPR_8        Tetratricopeptide repeat
    2.5e-07   31.1   9.3     0.0036   17.8   0.3    4.4  4  TPR_19       Tetratricopeptide repeat
    3.9e-07   30.6   1.6       0.02   15.5   0.0    3.7  3  TPR_16       Tetratricopeptide repeat
    1.2e-06   28.2   4.1     0.0035   16.8   0.1    2.6  2  SNAP         Soluble NSF attachment protein, SNAP
    1.2e-05   25.0   2.6       0.13   12.2   0.0    4.6  4  TPR_10       Tetratricopeptide repeat
      4e-05   23.1   0.1    0.00022   20.7   0.0    1.8  2  TPR_MalT     MalT-like TPR region
    9.3e-05   22.2   7.2     0.0024   17.6   2.7    3.5  2  RPN7         26S proteasome subunit RPN7
    0.00019   21.4   5.3        2.5    8.5   0.0    5.4  5  PPR          PPR repeat
    0.00072   19.3   2.3     0.0012   18.6   0.8    2.1  2  TPR_21       Tetratricopeptide repeat-like domain
     0.0016   18.1   0.5     0.0016   18.1   0.5    5.7  7  TPR_1        Tetratricopeptide repeat
     0.0032   16.3   0.2      0.017   14.0   0.1    2.1  2  LppC         LppC putative lipoprotein
     0.0037   17.5   5.4        0.3   11.3   0.1    3.2  2  ANAPC3       Anaphase-promoting complex, cyclosome, subunit 3
     0.0038   17.2   4.1       0.39   10.8   0.1    3.2  3  ANAPC5       Anaphase-promoting complex subunit 5
     0.0087   15.7   7.5        4.1    7.2   0.3    4.6  4  SPOB_a       Sensor_kinase_SpoOB-type, alpha-helical domain
     0.0092   15.8   0.1       0.28   11.0   0.0    2.8  2  ATP13        Mitochondrial ATPase expression
  ------ inclusion threshold ------
      0.015   15.5   0.7         11    6.3   0.0    3.2  3  TPR_5        Tetratrico peptide repeat
      0.046   13.7   1.6       0.41   10.7   0.4    2.9  2  L27_1        L27_1
      0.069   13.2   0.3      0.069   13.2   0.3    4.4  4  MIT          MIT (microtubule interacting and transport) doma
      0.083   12.9   0.6       0.31   11.1   0.6    2.1  1  SapB_1       Saposin-like type B, region 1
       0.12   12.8   0.9         40    4.9   0.1    3.8  3  TPR_17       Tetratricopeptide repeat
       0.15   12.2   0.3       0.15   12.2   0.3    3.6  4  DUF5618      Domain of unknown function (DUF5618)
       0.64    9.7   6.8       0.44   10.2   3.5    2.4  3  DUF2225      Uncharacterized protein conserved in bacteria (D
        1.8    8.9   6.6         26    5.1   0.0    3.9  3  Radical_SAM  Radical SAM superfamily


Domain annotation for each model (and alignments):
>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.9     1e-10   6.6e-08      11      74 ..      64     123 ..      54     126 .. 0.89
   2 !   33.9   1.2   4.6e-11   2.9e-08       4      77 .]      95     166 ..      93     166 .. 0.95
   3 !   19.5   1.1   1.4e-06   0.00088       4      72 ..     135     201 ..     131     205 .. 0.87
   4 ?    0.6   0.1       1.1     7e+02      10      30 ..     218     238 ..     218     251 .. 0.75

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 1e-10
                            TPR_12  11 avlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                       +++++lg++d+ +e+++k +e +++     ++ ++ +l+ L+++y+ +g + +A++ +e+ l++
  gi|242399724|ref|YP_002995149.1|  64 HIYAHLGELDKGIEIYKKLVEKYKEE----REKYLDALYHLADAYEHFGMPNKAIDVYEKLLEL 123
                                       79*****************9999655....6669**************************9997 PP

  == domain 2  score: 33.9 bits;  conditional E-value: 4.6e-11
                            TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiaek 77 
                                        al++la+++ + g   +A++ +ek le+ +++  +++ ++a tl  +++ y++l++ + A+el +ea +++++
  gi|242399724|ref|YP_002995149.1|  95 DALYHLADAYEHFGMPNKAIDVYEKLLELEKKI--GNKREEALTLAHIAINYDELEEVDRAIELMNEASKMFKE 166
                                       5788*****************************..88889*****************************99985 PP

  == domain 3  score: 19.5 bits;  conditional E-value: 1.4e-06
                            TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeal 72 
                                        +l ++a  + +l++ d A+el ++a  ++++l G d  +++ +  +L+  +++ g+y  A+el  e+l
  gi|242399724|ref|YP_002995149.1| 135 LTLAHIAINYDELEEVDRAIELMNEASKMFKEL-G-DERNYLVSILDLAHFHYEVGDYNRAEELILEVL 201
                                       45548999999*******************888.4.4458***********************988877 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 1.1
                            TPR_12  10 aavlrrlgrydeAlellekal 30 
                                       a++ ++++++ +A++ l+ +l
  gi|242399724|ref|YP_002995149.1| 218 AEIKAAQENFKKAFSALRFSL 238
                                       677788888888888887776 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0       3.5   2.2e+03      16      39 ..      15      38 ..       4      44 .. 0.67
   2 !    9.7   0.0    0.0027       1.7       9      35 ..      64      90 ..      57      93 .. 0.86
   3 !   16.4   0.0   1.8e-05     0.012       2      32 ..      95     125 ..      94     137 .. 0.89
   4 ?    2.9   0.1      0.39   2.5e+02       7      29 ..     140     162 ..     131     171 .. 0.76
   5 !    9.0   0.0    0.0042       2.7       5      37 ..     178     209 ..     175     216 .. 0.91
   6 ?   -0.1   0.0       3.8   2.4e+03       8      25 ..     218     235 ..     211     254 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 3.5
                            TPR_14 16 dpdeAiallrralalaPddaeawl 39
                                      d ++ +++l+++l++  +++e++ 
  gi|242399724|ref|YP_002995149.1| 15 DCQKILEILDDYLEKIENEDELRA 38
                                      556678889999997555555544 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0027
                            TPR_14  9 eallalGdpdeAiallrralalaPdda 35
                                      +++++lG++d+ i++++++++++ +++
  gi|242399724|ref|YP_002995149.1| 64 HIYAHLGELDKGIEIYKKLVEKYKEER 90
                                      789******************998765 PP

  == domain 3  score: 16.4 bits;  conditional E-value: 1.8e-05
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaP 32 
                                       +al+ la+a+++ G p +Ai++++++l+l  
  gi|242399724|ref|YP_002995149.1|  95 DALYHLADAYEHFGMPNKAIDVYEKLLELEK 125
                                       699************************9865 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.39
                            TPR_14   7 laeallalGdpdeAiallrrala 29 
                                       +a  + +l++ d+Ai+l ++a +
  gi|242399724|ref|YP_002995149.1| 140 IAINYDELEEVDRAIELMNEASK 162
                                       45557789999******999976 PP

  == domain 5  score: 9.0 bits;  conditional E-value: 0.0042
                            TPR_14   5 lalaeallalGdpdeAiallrralalaPddaea 37 
                                       l+la+++++ Gd+ +A++l  ++l+  P dae+
  gi|242399724|ref|YP_002995149.1| 178 LDLAHFHYEVGDYNRAEELILEVLK-SPRDAEI 209
                                       89*********************99.9998875 PP

  == domain 6  score: -0.1 bits;  conditional E-value: 3.8
                            TPR_14   8 aeallalGdpdeAiallr 25 
                                       ae+ +a++++++A  +lr
  gi|242399724|ref|YP_002995149.1| 218 AEIKAAQENFKKAFSALR 235
                                       567788999999998887 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1      0.26   1.7e+02       4      24 ..      61      81 ..      58      92 .. 0.79
   2 !   20.9   0.0   3.8e-07   0.00024       1      35 [.      96     130 ..      96     131 .. 0.93
   3 ?    1.4   0.0      0.64   4.1e+02       4      23 ..     139     158 ..     136     171 .. 0.73
   4 !   10.3   0.0   0.00091      0.59       2      29 ..     177     204 ..     176     210 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.26
                             TPR_7  4 nLarlysrlGdyeeAielyeq 24
                                       + ++y  lG+ ++ ie+y++
  gi|242399724|ref|YP_002995149.1| 61 EITHIYAHLGELDKGIEIYKK 81
                                      57789999*****99999999 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 3.8e-07
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdpeda 35 
                                       aL+ La++y+  G   +Ai++ye++L+l+k  +++
  gi|242399724|ref|YP_002995149.1|  96 ALYHLADAYEHFGMPNKAIDVYEKLLELEKKIGNK 130
                                       799**************************998876 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.64
                             TPR_7   4 nLarlysrlGdyeeAielye 23 
                                        +a  y +l + ++Aiel  
  gi|242399724|ref|YP_002995149.1| 139 HIAINYDELEEVDRAIELMN 158
                                       555568899999****9865 PP

  == domain 4  score: 10.3 bits;  conditional E-value: 0.00091
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsLalt 29 
                                       +l La+ + ++Gdy +A+el  ++L   
  gi|242399724|ref|YP_002995149.1| 177 ILDLAHFHYEVGDYNRAEELILEVLKSP 204
                                       678*****************99976554 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0    0.0029       1.8      10      30 ..      66      86 ..      61      88 .. 0.91
   2 !   18.6   0.0   3.3e-06    0.0021       1      28 [.      95     122 ..      95     124 .. 0.94
   3 ?    2.3   0.0      0.51   3.3e+02       5      25 ..     139     159 ..     136     164 .. 0.85
   4 ?   -0.4   0.0       3.6   2.3e+03       6      24 ..     180     199 ..     176     203 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0029
                                      HHHHHHHHHHHHHHHHHHHH- CS
                             TPR_6 10 yrklgdtdkAlealerlikeY 30
                                      y  lg+ dk +e++++l+++Y
  gi|242399724|ref|YP_002995149.1| 66 YAHLGELDKGIEIYKKLVEKY 86
                                      77799***************9 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 3.3e-06
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   1 dAlyklalsyrklgdtdkAlealerlik 28 
                                       dAly+la +y+  g + kA++ +e+l++
  gi|242399724|ref|YP_002995149.1|  95 DALYHLADAYEHFGMPNKAIDVYEKLLE 122
                                       8***********66************97 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.51
                                       HHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   5 klalsyrklgdtdkAlealer 25 
                                       ++a  y +l + d+A+e++++
  gi|242399724|ref|YP_002995149.1| 139 HIAINYDELEEVDRAIELMNE 159
                                       6899999988*******9987 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 3.6
                                       HHHHHHHHHHHHHHHH.HHH CS
                             TPR_6   6 lalsyrklgdtdkAle.ale 24 
                                       la  +++ gd+ +A e +le
  gi|242399724|ref|YP_002995149.1| 180 LAHFHYEVGDYNRAEElILE 199
                                       566678856*****994444 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       7.8     5e+03      22      29 ..       5      12 ..       4      13 .. 0.73
   2 ?    7.0   0.2     0.011       7.3      10      32 ..      65      87 ..      64      89 .. 0.91
   3 !   20.1   0.4   7.1e-07   0.00045       2      32 ..      95     125 ..      94     127 .. 0.94
   4 !    7.3   0.1    0.0087       5.6       3      30 ..     136     163 ..     134     167 .. 0.86
   5 !    7.5   0.0    0.0077       4.9       7      29 ..     180     202 ..     177     203 .. 0.91
   6 ?   -1.3   0.2         5   3.2e+03      13      21 ..     223     231 ..     218     235 .. 0.56

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 7.8
                             TPR_2 22 eafekAle 29
                                      e fe+Al+
  gi|242399724|ref|YP_002995149.1|  5 EEFERALK 12
                                      56888886 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.011
                             TPR_2 10 ayyklgdyeeAleafekAleldP 32
                                      +y++lg++++ +e ++k +e + 
  gi|242399724|ref|YP_002995149.1| 65 IYAHLGELDKGIEIYKKLVEKYK 87
                                      79****************99875 PP

  == domain 3  score: 20.1 bits;  conditional E-value: 7.1e-07
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldP 32 
                                       +aly l++ay++ g +++A++ +ek lel+ 
  gi|242399724|ref|YP_002995149.1|  95 DALYHLADAYEHFGMPNKAIDVYEKLLELEK 125
                                       69**************************986 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.0087
                             TPR_2   3 alynlGlayyklgdyeeAleafekAlel 30 
                                        l  ++  y +l + ++A+e++++A + 
  gi|242399724|ref|YP_002995149.1| 136 TLAHIAINYDELEEVDRAIELMNEASKM 163
                                       6778999*****************9775 PP

  == domain 5  score: 7.5 bits;  conditional E-value: 0.0077
                             TPR_2   7 lGlayyklgdyeeAleafekAle 29 
                                       l+  +y+ gdy++A+e+  ++l+
  gi|242399724|ref|YP_002995149.1| 180 LAHFHYEVGDYNRAEELILEVLK 202
                                       7889*************999997 PP

  == domain 6  score: -1.3 bits;  conditional E-value: 5
                             TPR_2  13 klgdyeeAl 21 
                                       ++ ++++A 
  gi|242399724|ref|YP_002995149.1| 223 AQENFKKAF 231
                                       455555554 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.1     0.002       1.3       9      29 ..      64      84 ..      56      84 .. 0.90
   2 !   20.3   0.3   6.8e-07   0.00043       2      33 ..      95     126 ..      94     127 .. 0.95
   3 ?    5.9   0.1     0.027        17       5      30 ..     138     163 ..     134     166 .. 0.86
   4 ?    7.0   0.0     0.012       7.9       6      30 ..     179     203 ..     176     206 .. 0.88
   5 ?   -0.2   0.5       2.5   1.6e+03      17      29 ..     220     232 ..     218     233 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.002
                                      HHHHHTT-HHHHHHHHHHHHH CS
                             TPR_8  9 siylklgdyeeAkeyyekale 29
                                      +iy  lg++++ +e y+k +e
  gi|242399724|ref|YP_002995149.1| 64 HIYAHLGELDKGIEIYKKLVE 84
                                      89****************986 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 6.8e-07
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       +a+y+l+++y+  g  ++A+ +yek lel+++
  gi|242399724|ref|YP_002995149.1|  95 DALYHLADAYEHFGMPNKAIDVYEKLLELEKK 126
                                       79***************************986 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.027
                                       HHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8   5 ynlgsiylklgdyeeAkeyyekalel 30 
                                        +++  y++l++ + A+e +++a ++
  gi|242399724|ref|YP_002995149.1| 138 AHIAINYDELEEVDRAIELMNEASKM 163
                                       567778*****************987 PP

  == domain 4  score: 7.0 bits;  conditional E-value: 0.012
                                       HHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8   6 nlgsiylklgdyeeAkeyyekalel 30 
                                        l++ + + gdy+ A+e + ++l+ 
  gi|242399724|ref|YP_002995149.1| 179 DLAHFHYEVGDYNRAEELILEVLKS 203
                                       699****************999985 PP

  == domain 5  score: -0.2 bits;  conditional E-value: 2.5
                                       HHHHHHHHHHHHH CS
                             TPR_8  17 yeeAkeyyekale 29 
                                       +++A+e ++ka +
  gi|242399724|ref|YP_002995149.1| 220 IKAAQENFKKAFS 232
                                       5799******976 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1      0.42   2.7e+02      33      54 ..      64      85 ..      10      89 .. 0.70
   2 !   17.8   0.3   5.6e-06    0.0036       5      56 ..      70     125 ..      67     129 .. 0.85
   3 ?    2.9   0.2      0.25   1.6e+02      30      55 ..     139     164 ..     117     167 .. 0.75
   4 !   15.3   0.1   3.2e-05     0.021       9      59 ..     159     207 ..     146     213 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.42
                            TPR_19 33 eallalgqldeAealLdalpee 54
                                       ++  lg+ld+ +++ ++l e+
  gi|242399724|ref|YP_002995149.1| 64 HIYAHLGELDKGIEIYKKLVEK 85
                                      4567777777777777777666 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 5.6e-06
                            TPR_19   5 gdyaeAlalleqalqedpk....naearllLAeallalgqldeAealLdalpeedp 56 
                                       g ++  +++++++ +++ +    +++a++ LA+a+   g +++A+++ ++l+e ++
  gi|242399724|ref|YP_002995149.1|  70 GELDKGIEIYKKLVEKYKEerekYLDALYHLADAYEHFGMPNKAIDVYEKLLELEK 125
                                       66777788999988665555556***************************999776 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.25
                            TPR_19  30 lLAeallalgqldeAealLdalpeed 55 
                                         A+ + +l ++d A++l++++ +++
  gi|242399724|ref|YP_002995149.1| 139 HIAINYDELEEVDRAIELMNEASKMF 164
                                       3488899999********99988765 PP

  == domain 4  score: 15.3 bits;  conditional E-value: 3.2e-05
                            TPR_19   9 eAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdda 59 
                                       eA +++++ l ++ +++   l+LA  +++ g+++ Ae+l+ +++++ +d a
  gi|242399724|ref|YP_002995149.1| 159 EASKMFKE-LGDERNYLVSILDLAHFHYEVGDYNRAEELILEVLKSPRD-A 207
                                       44555555.466888****************************999988.5 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   3.1e-05      0.02       6      62 ..      65     122 ..      64     127 .. 0.91
   2 ?    0.8   0.0       1.2   7.9e+02       7      29 ..     144     166 ..     132     174 .. 0.78
   3 !   10.7   0.2     0.001      0.65       1      54 [.     178     231 ..     178     240 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.1e-05
                            TPR_16   6 aalragdyddAaaaleaalkrdpssPd.aaeAllllgdaalrqgrlaeAaalyraalr 62 
                                       +++ +g+ d+ ++ ++ ++++++++ +   +Al++l+da+ ++g   +A+++y+++l+
  gi|242399724|ref|YP_002995149.1|  65 IYAHLGELDKGIEIYKKLVEKYKEEREkYLDALYHLADAYEHFGMPNKAIDVYEKLLE 122
                                       56668999999**************99**************************99875 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 1.2
                            TPR_16   7 alragdyddAaaaleaalkrdps 29 
                                       + ++ + d+A+++ ++a k++++
  gi|242399724|ref|YP_002995149.1| 144 YDELEEVDRAIELMNEASKMFKE 166
                                       56677888899998888888865 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.001
                            TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAa 54 
                                       l+la+ +++ gdy +A+++  ++lk+ ++    + A+   +++ ++q ++++A 
  gi|242399724|ref|YP_002995149.1| 178 LDLAHFHYEVGDYNRAEELILEVLKSPRDAEIEVNARIVDAEIKAAQENFKKAF 231
                                       689999********************9777767777766666666666666665 PP

>> SNAP  Soluble NSF attachment protein, SNAP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.3    0.0001     0.065      64     146 ..      26     108 ..       6     112 .. 0.87
   2 !   16.8   0.1   5.4e-06    0.0035      90     181 ..     110     200 ..     108     211 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.0001
                                       HHHHTT-HHHHHHHHHHHHHHHHHT-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT--HHHHHHHHHH CS
                              SNAP  64 cqeklkekdeaanayveAakcykkvspeeAvealekAieiytekgrfrraAklkkeiaelyekelgdlekAieaYek 140
                                       + ek++++de    + +  + + k++ ++A e  ++  +iy++ g ++++ +++k++ e y++e +++ +A+ + ++
  gi|242399724|ref|YP_002995149.1|  26 YLEKIENEDELRAFLEKVETLILKCEGSDAYELAHEITHIYAHLGELDKGIEIYKKLVEKYKEEREKYLDALYHLAD 102
                                       556777777777777777778889999**********************************************9999 PP

                                       HHHHHH CS
                              SNAP 141 Aaelye 146
                                       A e + 
  gi|242399724|ref|YP_002995149.1| 103 AYEHFG 108
                                       999986 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 5.4e-06
                                       HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                              SNAP  90 peeAvealekAieiytekgrfrraAklkkeiaelyekelgdlekAieaYekAaelyeqeeakalankcllkvAelsa 166
                                       p++A++++ek  e+  + g+ r+ A    +ia  y++ l+++++Aie  ++A++++++ + + +     l++A+++ 
  gi|242399724|ref|YP_002995149.1| 110 PNKAIDVYEKLLELEKKIGNKREEALTLAHIAINYDE-LEEVDRAIELMNEASKMFKELGDERNYLVSILDLAHFHY 185
                                       7899999999999999999999999999999999985.599****************9999999999999******* PP

                                       HTT-HHHHHHHHHHH CS
                              SNAP 167 elekyekAieiyekv 181
                                       e ++y++A e+  +v
  gi|242399724|ref|YP_002995149.1| 186 EVGDYNRAEELILEV 200
                                       *****9998876555 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1      0.13        82       9      34 ..      63      88 ..      58      90 .. 0.86
   2 ?    1.2   0.0      0.56   3.6e+02       4      31 ..      96     123 ..      94     129 .. 0.62
   3 ?    4.4   0.1     0.055        35       2      31 ..     134     163 ..     134     169 .. 0.86
   4 !   12.2   0.0    0.0002      0.13       4      29 ..     176     201 ..     174     203 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.13
                            TPR_10  9 analrqrgrydeAealleealairrr 34
                                       +++ ++g++d+  +++++ ++ +++
  gi|242399724|ref|YP_002995149.1| 63 THIYAHLGELDKGIEIYKKLVEKYKE 88
                                      5789999***********99999997 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.56
                            TPR_10   4 slnNLanalrqrgrydeAealleealai 31 
                                       +l +La a+ + g  ++A + +e+ l++
  gi|242399724|ref|YP_002995149.1|  96 ALYHLADAYEHFGMPNKAIDVYEKLLEL 123
                                       5666666666666666666666666665 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.055
                            TPR_10   2 AsslnNLanalrqrgrydeAealleealai 31 
                                       A +l ++a+ + ++ + d+A +l+ ea  +
  gi|242399724|ref|YP_002995149.1| 134 ALTLAHIAINYDELEEVDRAIELMNEASKM 163
                                       568999******************998655 PP

  == domain 4  score: 12.2 bits;  conditional E-value: 0.0002
                            TPR_10   4 slnNLanalrqrgrydeAealleeal 29 
                                       s  +La+ ++++g+y++Ae+l  e+l
  gi|242399724|ref|YP_002995149.1| 176 SILDLAHFHYEVGDYNRAEELILEVL 201
                                       6678*****************99988 PP

>> TPR_MalT  MalT-like TPR region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       0.8   5.1e+02      65     115 ..      42      91 ..      32      98 .. 0.67
   2 !   20.7   0.0   3.4e-07   0.00022      42     185 ..      96     235 ..      87     245 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.8
                          TPR_MalT  65 eaeklarqadslhvallallqqaeilvaqGrLheAletyeqalqlateqgl 115
                                       ++e+l+++++ ++ a+     ++ i+ + G+L++ +e+y++  + ++e+++
  gi|242399724|ref|YP_002995149.1|  42 KVETLILKCEGSD-AYELAHEITHIYAHLGELDKGIEIYKKLVEKYKEERE 91 
                                       5555555555555.3333334677888899999999999887777777665 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 3.4e-07
                          TPR_MalT  42 atavlGeasllqGdleaAlqalqeaeklarqadslhvallallqqaeilvaqGrLheAletyeqalqlateqglqql 118
                                       a++ l+ a+ + G  ++A ++++++ +l +++++ +  +l+l ++a  + +  + + A+e++++a ++ +e g ++ 
  gi|242399724|ref|YP_002995149.1|  96 ALYHLADAYEHFGMPNKAIDVYEKLLELEKKIGNKREEALTLAHIAINYDELEEVDRAIELMNEASKMFKELGDERN 172
                                       6778899999***99************************************************************99 PP

                          TPR_MalT 119 plvgfllvlladllyEwndLeeAeqhlqeGielleqlepeaaldayvllarialaqGdleeAetlle 185
                                        lv +l   la+ +yE +d  +Ae+  +e ++  ++   e+ + a+++ a+i++aq++ ++A ++l+
  gi|242399724|ref|YP_002995149.1| 173 YLVSIL--DLAHFHYEVGDYNRAEELILEVLKSPRDA--EIEVNARIVDAEIKAAQENFKKAFSALR 235
                                       999999..99******************996666666..9*********************988775 PP

>> RPN7  26S proteasome subunit RPN7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.4     0.045        29      33      66 ..      53      86 ..      27      93 .. 0.74
   2 !   17.6   2.7   3.7e-06    0.0024      33     142 ..      91     203 ..      85     237 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.045
                                      HHHHHHHHHHHHHHHHCT-HHHHHHHHHTCCCC- CS
                              RPN7 33 eeirrakldlaehYlkigdleeAlkaysrireyc 66
                                      ++  ++ +++ + Y+  g+l++ ++ y++++e+ 
  gi|242399724|ref|YP_002995149.1| 53 SDAYELAHEITHIYAHLGELDKGIEIYKKLVEKY 86
                                      555567788999*****************99886 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 3.7e-06
                                       HHHHHHHHHHHHHHHHCT-HHHHHHHHHTCCCC--SHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHCSSS---.. CS
                              RPN7  33 eeirrakldlaehYlkigdleeAlkaysrireyctslkhkidmllnlirvaiffndwdlvskylekakellekggd. 108
                                       e+  +a + la+ Y   g  ++A+  y++++e   + ++k +  l+l ++ai + + + v++ +e ++e  +  ++ 
  gi|242399724|ref|YP_002995149.1|  91 EKYLDALYHLADAYEHFGMPNKAIDVYEKLLELEKKIGNKREEALTLAHIAINYDELEEVDRAIELMNEASKMFKEl 167
                                       566688999****************************************************9988777666665554 PP

                                       HHHHHHHHHHHHHHHHHT..T-HHHHHHHHCTS-GG CS
                              RPN7 109 werknrlkvyeGlallai..rkfkeAaellldilst 142
                                        + +n l  +  la+ ++  +++++A el+l++l +
  gi|242399724|ref|YP_002995149.1| 168 GDERNYLVSILDLAHFHYevGDYNRAEELILEVLKS 203
                                       455666666666665543227888888888887654 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0    0.0061       3.9       9      29 ..      65      85 ..      63      86 .. 0.92
   2 !    8.5   0.0    0.0039       2.5       6      28 ..     100     122 ..      99     124 .. 0.89
   3 ?    1.6   0.2      0.63     4e+02      15      26 ..     156     167 ..     149     171 .. 0.83
   4 ?   -0.6   0.0       3.1     2e+03      14      27 ..     188     201 ..     184     203 .. 0.83
   5 ?   -0.9   0.0       3.9   2.5e+03      18      30 ..     321     333 ..     318     334 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0061
                               PPR  9 gycknGkleeAlelfkeMkek 29
                                       y++ G+l++ +e++k+++ek
  gi|242399724|ref|YP_002995149.1| 65 IYAHLGELDKGIEIYKKLVEK 85
                                      69***************9986 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0039
                               PPR   6 lIsgycknGkleeAlelfkeMke 28 
                                       l ++y + G++ +A++++++++e
  gi|242399724|ref|YP_002995149.1| 100 LADAYEHFGMPNKAIDVYEKLLE 122
                                       5689***************9987 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.63
                               PPR  15 kleeAlelfkeM 26 
                                       ++ eA ++fke+
  gi|242399724|ref|YP_002995149.1| 156 LMNEASKMFKEL 167
                                       578999999997 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 3.1
                               PPR  14 GkleeAlelfkeMk 27 
                                       G++  A+el+ e +
  gi|242399724|ref|YP_002995149.1| 188 GDYNRAEELILEVL 201
                                       9999*****98866 PP

  == domain 5  score: -0.9 bits;  conditional E-value: 3.9
                               PPR  18 eAlelfkeMkekG 30 
                                       e +el++e+k+ G
  gi|242399724|ref|YP_002995149.1| 321 EFKELLDELKKIG 333
                                       6679*****9987 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1       1.9   1.2e+03      43      69 ..      79     104 ..      66     150 .. 0.59
   2 !   18.6   0.8   1.8e-06    0.0012      44     137 ..     145     235 ..     111     256 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.9
                            TPR_21  43 Yqqlqeaveakdaakakeaaeeladey 69 
                                       Y++l+e+ +++ ++   +a  +lad+y
  gi|242399724|ref|YP_002995149.1|  79 YKKLVEKYKEEREK-YLDALYHLADAY 104
                                       44444444443333.333444444433 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 1.8e-06
                            TPR_21  44 qqlqeaveakdaa.kakeaaeeladeyggtaYaalaaLllAkaaveagdlaaAkaqLewvlekakdeelkalarlRL 119
                                       ++l+e     d+a +++++a+++ +e g+     ++ L lA+  +e gd+++A++ + +vl++ +d+e++  ar+  
  gi|242399724|ref|YP_002995149.1| 145 DELEE----VDRAiELMNEASKMFKELGDERNYLVSILDLAHFHYEVGDYNRAEELILEVLKSPRDAEIEVNARIVD 217
                                       44433....333335778888888898888888999***************************************** PP

                            TPR_21 120 arvllaekkydeAlktLe 137
                                       a++ +a++++++A ++L 
  gi|242399724|ref|YP_002995149.1| 218 AEIKAAQENFKKAFSALR 235
                                       *************99985 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       7.1   4.5e+03      15      22 ..       5      12 ..       3      13 .. 0.63
   2 ?   -2.2   0.1       6.7   4.3e+03      23      30 ..      15      22 ..      14      26 .. 0.80
   3 ?    5.1   0.2     0.033        21       9      26 ..      64      81 ..      64      87 .. 0.90
   4 !   18.1   0.5   2.6e-06    0.0016       2      31 ..      95     124 ..      94     126 .. 0.95
   5 ?    0.5   0.0      0.93     6e+02       3      22 ..     136     155 ..     134     162 .. 0.82
   6 ?    4.1   0.1     0.069        44       7      28 ..     180     201 ..     178     202 .. 0.84
   7 ?   -1.8   0.2       5.3   3.4e+03      19      27 ..     222     230 ..     219     233 .. 0.68

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 7.1
                                      T-HHHHHH CS
                             TPR_1 15 gkydeAle 22
                                      ++++ Al+
  gi|242399724|ref|YP_002995149.1|  5 EEFERALK 12
                                      56677765 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 6.7
                                      HHHHHHHH CS
                             TPR_1 23 yyekALel 30
                                      +++k Le+
  gi|242399724|ref|YP_002995149.1| 15 DCQKILEI 22
                                      89****98 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.033
                                      HHHHHTT-HHHHHHHHHH CS
                             TPR_1  9 nayfklgkydeAleyyek 26
                                      ++y +lg++d+ +e y+k
  gi|242399724|ref|YP_002995149.1| 64 HIYAHLGELDKGIEIYKK 81
                                      58**************99 PP

  == domain 4  score: 18.1 bits;  conditional E-value: 2.6e-06
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHS CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALeln 31 
                                       +aly l+ ay + g++++A++ yek Lel+
  gi|242399724|ref|YP_002995149.1|  95 DALYHLADAYEHFGMPNKAIDVYEKLLELE 124
                                       79**************************97 PP

  == domain 5  score: 0.5 bits;  conditional E-value: 0.93
                                       HHHHHHHHHHHTT-HHHHHH CS
                             TPR_1   3 alynlGnayfklgkydeAle 22 
                                       +l  ++  y +l++ d A+e
  gi|242399724|ref|YP_002995149.1| 136 TLAHIAINYDELEEVDRAIE 155
                                       6677888899999*****98 PP

  == domain 6  score: 4.1 bits;  conditional E-value: 0.069
                                       HHHHHHHTT-HHHHHHHHHHHH CS
                             TPR_1   7 lGnayfklgkydeAleyyekAL 28 
                                       l++ +++ g+y+ A+e   ++L
  gi|242399724|ref|YP_002995149.1| 180 LAHFHYEVGDYNRAEELILEVL 201
                                       78999**********9877766 PP

  == domain 7  score: -1.8 bits;  conditional E-value: 5.3
                                       HHHHHHHHH CS
                             TPR_1  19 eAleyyekA 27 
                                        A e ++kA
  gi|242399724|ref|YP_002995149.1| 222 AAQENFKKA 230
                                       566777776 PP

>> LppC  LppC putative lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.37   2.4e+02     372     427 ..     108     162 ..     100     166 .. 0.82
   2 !   14.0   0.1   2.6e-05     0.017      20      93 ..     166     243 ..     148     249 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.37
                                       HSS--EEEEESSGGGHHHHHHHH-.TTTEEEEE---HHHHHHHHHHHHT.T-TTEE CS
                              LppC 372 agtdaaielvdqpadlaqqlkdasrqdidavyivanskelaeikptlanasakdlk 427
                                       +  + ai+++++  +l++++ +++ +  +  +i++n +el e+   ++  +++  k
  gi|242399724|ref|YP_002995149.1| 108 GMPNKAIDVYEKLLELEKKIGNKREEALTLAHIAINYDELEEVDRAIEL-MNEASK 162
                                       556679999************9999999999**********99999988.444445 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 2.6e-05
                                       S.HHHHHHHHHHHHHH...HHTT-HHHHHHHHHT--..S--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHTS-GGGS CS
                              LppC  20 g.eeqntykllAarvl...ieenkiaqaqallrelavqeLtdeqkldkslleaelaaakeqneeAlqqlslqslssL 92 
                                       +  ++++y+++ ++++   +e ++ ++a+ l+ e+ + +   e ++++ ++ ae+ aa+e+ ++A ++l++  l+ L
  gi|242399724|ref|YP_002995149.1| 166 ElGDERNYLVSILDLAhfhYEVGDYNRAEELILEVLKSPRDAEIEVNARIVDAEIKAAQENFKKAFSALRFSLLKAL 242
                                       3556777776665554111688999*********************************************9888877 PP

                                       - CS
                              LppC  93 s 93 
                                        
  gi|242399724|ref|YP_002995149.1| 243 E 243
                                       5 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   1.5     0.012       7.6      13      72 ..      84     147 ..      51     160 .. 0.62
   2 !   11.3   0.1   0.00048       0.3      18      79 ..     169     234 ..     147     237 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.012
                                       HHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-H...HHHHHHHHHHHHTT-H CS
                            ANAPC3  13 erllaaetespedayllAlclylngqykrAyellrka.klnsksl...gcrylfAqcllkLkky 72 
                                       e++ +   + ++++y lA ++ + g  ++A+++++k+ +l++k     + ++++A+ ++ ++++
  gi|242399724|ref|YP_002995149.1|  84 EKYKEEREKYLDALYHLADAYEHFGMPNKAIDVYEKLlELEKKIGnkrEEALTLAHIAINYDEL 147
                                       3333233334445666677777777777777777777444333224445555555555555555 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00048
                                       HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-H...HHHHHHHHHHHHTT-HHHHHHHH CS
                            ANAPC3  18 aetespedayllAlclylngqykrAyellrka.klnsksl...gcrylfAqcllkLkkyeeAiaaL 79 
                                        e++ + +++ lA  +y+ g+y+rA el+ +  k+    +   ++r++ A+   +++++++A +aL
  gi|242399724|ref|YP_002995149.1| 169 DERNYLVSILDLAHFHYEVGDYNRAEELILEVlKSPRDAEievNARIVDAEIKAAQENFKKAFSAL 234
                                       444444455558***************999994444443377889999999999999998888887 PP

>> ANAPC5  Anaphase-promoting complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.3     0.011         7      11      73 ..      13     126 ..       4     150 .. 0.64
   2 !   10.8   0.1   0.00061      0.39      36      70 ..     162     203 ..     134     212 .. 0.79
   3 ?   -2.2   0.1       6.9   4.4e+03      56      73 ..     226     243 ..     213     258 .. 0.51

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.011
                            ANAPC5  11 akdYqqaldsLhryFDyvlsqnessq................................................... 36 
                                       ++d q+ l+ L  y   + +++e ++                                                   
  gi|242399724|ref|YP_002995149.1|  13 SRDCQKILEILDDYLEKIENEDELRAflekvetlilkcegsdayelaheithiyahlgeldkgieiykklvekykee 89 
                                       55555555555555555555555555555566666666666666666666666666666666666666666666666 PP

                            ANAPC5  37 kksyqyalLnlaslhadfghneeAvkaleeairlAre 73 
                                       +++y  al +la    +fg +++A++  e   +l ++
  gi|242399724|ref|YP_002995149.1|  90 REKYLDALYHLADAYEHFGMPNKAIDVYEKLLELEKK 126
                                       899**********************988877665554 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00061
                            ANAPC5  36 q.......kksyqyalLnlaslhadfghneeAvkaleeairl 70 
                                       +       +++y +++L la +h++ g+++ A + + e+ + 
  gi|242399724|ref|YP_002995149.1| 162 KmfkelgdERNYLVSILDLAHFHYEVGDYNRAEELILEVLKS 203
                                       24556666899**********************999998775 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 6.9
                            ANAPC5  56 hneeAvkaleeairlAre 73 
                                       + ++A +al+ +   A e
  gi|242399724|ref|YP_002995149.1| 226 NFKKAFSALRFSLLKALE 243
                                       333444444444444444 PP

>> SPOB_a  Sensor_kinase_SpoOB-type, alpha-helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1       1.9   1.2e+03      39      59 ..      16      36 ..      11      38 .. 0.84
   2 !    7.2   0.3    0.0064       4.1      32      58 ..      65      91 ..      62      95 .. 0.90
   3 !    6.8   0.1    0.0084       5.4      34      57 ..     145     168 ..     143     171 .. 0.89
   4 ?    1.8   0.0       0.3   1.9e+02      35      51 ..     186     202 ..     178     206 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.9
                            SPOB_a 39 ydkaeeyieevvkelkeeski 59
                                      ++k+ e+++++ + +++e ++
  gi|242399724|ref|YP_002995149.1| 16 CQKILEILDDYLEKIENEDEL 36
                                      678999999999999999875 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0064
                            SPOB_a 32 GylqLgkydkaeeyieevvkelkeesk 58
                                       y +Lg++dk  e+ +++v+ +kee++
  gi|242399724|ref|YP_002995149.1| 65 IYAHLGELDKGIEIYKKLVEKYKEERE 91
                                      699*********************965 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0084
                            SPOB_a  34 lqLgkydkaeeyieevvkelkees 57 
                                        +L+++d+a e+++e++k++ke +
  gi|242399724|ref|YP_002995149.1| 145 DELEEVDRAIELMNEASKMFKELG 168
                                       589****************99875 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.3
                            SPOB_a  35 qLgkydkaeeyieevvk 51 
                                       + g y++aee+i ev k
  gi|242399724|ref|YP_002995149.1| 186 EVGDYNRAEELILEVLK 202
                                       7899********99976 PP

>> ATP13  Mitochondrial ATPase expression
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0   0.00044      0.28      55      87 ..      57      92 ..      17     137 .. 0.75
   2 ?    1.5   0.0      0.39   2.5e+02      56      88 ..     136     168 ..     133     186 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00044
                             ATP13 55 elLkaivssfsynneiesAlklvdkfskkYpe...i 87
                                      el   i +++++ +e+++++++ +k+++kY+e    
  gi|242399724|ref|YP_002995149.1| 57 ELAHEITHIYAHLGELDKGIEIYKKLVEKYKEereK 92
                                      566789*************************64441 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.39
                             ATP13  56 lLkaivssfsynneiesAlklvdkfskkYpeie 88 
                                       +L+ i+  +   +e+++A++l+++ sk ++e+ 
  gi|242399724|ref|YP_002995149.1| 136 TLAHIAINYDELEEVDRAIELMNEASKMFKELG 168
                                       6888999999999************99999754 PP

>> TPR_5  Tetratrico peptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0     0.017        11      61     116 ..      23      80 ..      14      85 .. 0.84
   2 ?    5.3   0.0     0.036        23       3      64 ..      96     160 ..      94     180 .. 0.69
   3 ?    0.7   0.1      0.92   5.9e+02      55      79 ..     210     234 ..     145     260 .. 0.58

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.017
                             TPR_5  61 Lraelea..psdelddalaaflaLvLsdlgrereavsivllalaehlprYqRsvtnYa 116
                                       L++ le+  ++del++ l+ +  L+L   g ++  ++  ++ + +hl    + ++ Y 
  gi|242399724|ref|YP_002995149.1|  23 LDDYLEKieNEDELRAFLEKVETLILKCEGSDAYELAHEITHIYAHLGELDKGIEIYK 80 
                                       555555444899***********************************99888888776 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.036
                             TPR_5   3 aaFeragarDstGhedkavplYrraLaeGLagarrrrati...qLassLRnlGeaeealaLLrae 64 
                                       a++  a a +  G ++ka+ +Y++ L+   +  ++r   +    +a     l e+++a++L+++ 
  gi|242399724|ref|YP_002995149.1|  96 ALYHLADAYEHFGMPNKAIDVYEKLLELEKKIGNKREEALtlaHIAINYDELEEVDRAIELMNEA 160
                                       667778899999************98755444444444440023555666677777888887764 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.92
                             TPR_5  55 eealaLLraeleapsdelddalaaf 79 
                                       e   ++++ae++a ++++++a +a+
  gi|242399724|ref|YP_002995149.1| 210 EVNARIVDAEIKAAQENFKKAFSAL 234
                                       2233344444444444444444444 PP

>> L27_1  L27_1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.4   0.00064      0.41       2      36 ..      11      43 ..      10      49 .. 0.87
   2 ?    0.3   0.0       1.1   7.2e+02       5      22 ..     148     165 ..     146     172 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00064
                             L27_1  2 vrkkDaerALelLeeyrakLskeedeeLrqalerv 36
                                      ++++D+++ Le+L++y +k ++  ++eLr  le+v
  gi|242399724|ref|YP_002995149.1| 11 LKSRDCQKILEILDDYLEKIEN--EDELRAFLEKV 43
                                      5899***************766..88999999998 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.1
                             L27_1   5 kDaerALelLeeyrakLs 22 
                                       ++ +rA+el++e  +  +
  gi|242399724|ref|YP_002995149.1| 148 EEVDRAIELMNEASKMFK 165
                                       5678******99776655 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.2      0.41   2.6e+02      32      61 ..       5      31 ..       2      32 .. 0.86
   2 ?   -0.9   1.5       2.7   1.7e+03       3      25 ..      74      98 ..      72     122 .. 0.57
   3 ?   13.2   0.3   0.00011     0.069       3      37 ..     133     167 ..     132     175 .. 0.90
   4 ?   -2.2   0.0       7.3   4.7e+03      27      39 ..     190     202 ..     189     211 .. 0.66

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.41
                               MIT 32 elLlqalkekneerrellrekieeYleRae 61
                                      e +  alk   +++ +++ e +  Yle++e
  gi|242399724|ref|YP_002995149.1|  5 EEFERALK---SRDCQKILEILDDYLEKIE 31
                                      77888998...49999***********998 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.7
                               MIT  3 kAlelvkkAve..eDnagnyeeAle 25
                                      k++e+ kk ve  ++++++y +Al 
  gi|242399724|ref|YP_002995149.1| 74 KGIEIYKKLVEkyKEEREKYLDALY 98
                                      5555555544422244444444444 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 0.00011
                               MIT   3 kAlelvkkAveeDnagnyeeAlelYkealelLlqa 37 
                                       +Al l++ A+++D+ ++ + A+el  ea + ++++
  gi|242399724|ref|YP_002995149.1| 133 EALTLAHIAINYDELEEVDRAIELMNEASKMFKEL 167
                                       79**************************9999876 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 7.3
                               MIT  27 YkealelLlqalk 39 
                                       Y  a el+l++lk
  gi|242399724|ref|YP_002995149.1| 190 YNRAEELILEVLK 202
                                       6667777777777 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 ?   11.1   0.6   0.00049      0.31       5      33 ..      15      43 ..      14      43 .. 0.96

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00049
                                      HHHHHHHHHHHHH-SS--HHHHHHHHHHH CS
                            SapB_1  5 lCefvVkeveklLkdNkTeeeIieaLekv 33
                                      +C+++   ++++L++ ++e+e+ ++Lekv
  gi|242399724|ref|YP_002995149.1| 15 DCQKILEILDDYLEKIENEDELRAFLEKV 43
                                      6*************99***********97 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1     0.062        40      11      33 ..      92     114 ..      78     115 .. 0.77
   2 ?   -1.8   0.0       8.8   5.6e+03       2      10 ..     117     125 ..     116     131 .. 0.82
   3 ?    3.9   0.0      0.13        84      15      34 .]     176     195 ..     170     195 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.062
                            TPR_17  11 nnadaynnLAelllknGdlmtAr 33 
                                       ++ da++ LA ++++ G + +A+
  gi|242399724|ref|YP_002995149.1|  92 KYLDALYHLADAYEHFGMPNKAI 114
                                       5579*************999987 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 8.8
                            TPR_17   2 ylkaleldP 10 
                                       y+k lel++
  gi|242399724|ref|YP_002995149.1| 117 YEKLLELEK 125
                                       999999876 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.13
                            TPR_17  15 aynnLAelllknGdlmtArq 34 
                                       +   LA ++++ Gd+ +A++
  gi|242399724|ref|YP_002995149.1| 176 SILDLAHFHYEVGDYNRAEE 195
                                       66789*************96 PP

>> DUF5618  Domain of unknown function (DUF5618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1      0.57   3.6e+02      45      77 ..      19      53 ..      16      70 .. 0.57
   2 ?    0.9   0.5      0.77   4.9e+02      63      91 ..      72     100 ..      66     109 .. 0.72
   3 ?   12.2   0.3   0.00024      0.15      64     120 ..     111     166 ..     104     169 .. 0.91
   4 ?   -2.4   0.0       7.9   5.1e+03      84      93 ..     226     235 ..     205     276 .. 0.60

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.57
                                      HHHHHHHHH---S.....SS-.--HHHHHHHHHCC CS
                           DUF5618 45 vLlaldellgkkglek..kkrpksvetYkealkkl 77
                                      +L++ld++l+k + e   +   ++vet   + + +
  gi|242399724|ref|YP_002995149.1| 19 ILEILDDYLEKIENEDelRAFLEKVETLILKCEGS 53
                                      8999*****99885542233334555544444444 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.77
                                       -.--HHHHHHHHHCC-HHHHHHHHHHHHH CS
                           DUF5618  63 rpksvetYkealkkldkkllkefnsaydv 91 
                                       + k +e Yk+ ++k+ ++  k ++ +y++
  gi|242399724|ref|YP_002995149.1|  72 LDKGIEIYKKLVEKYKEEREKYLDALYHL 100
                                       56788999999988877777777777743 PP

  == domain 3  score: 12.2 bits;  conditional E-value: 0.00024
                                       .--HHHHHHHHHCC-HHHHHHHHHHHHHHIIIICCT---BHHHHHHHHHHHHHHHHH CS
                           DUF5618  64 pksvetYkealkkldkkllkefnsaydvLhlagyydGiksakvvkeglkaaeklikk 120
                                       +k ++ Y e+l +l+kk+ ++ ++a ++ h+a  yd +++++ + e +++a k+ k 
  gi|242399724|ref|YP_002995149.1| 111 NKAIDVY-EKLLELEKKIGNKREEALTLAHIAINYDELEEVDRAIELMNEASKMFKE 166
                                       4789***.88999****************************************9876 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 7.9
                                       HHHHHHHHHI CS
                           DUF5618  84 efnsaydvLh 93 
                                       +f++a+++L 
  gi|242399724|ref|YP_002995149.1| 226 NFKKAFSALR 235
                                       3333333333 PP

>> DUF2225  Uncharacterized protein conserved in bacteria (DUF2225)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.8     0.083        53     132     186 ..      84     135 ..      45     139 .. 0.56
   2 ?   10.2   3.5   0.00069      0.44      87     175 ..     104     191 ..      75     226 .. 0.74
   3 ?   -1.3   0.1       2.2   1.4e+03     149     149 ..     264     264 ..     215     330 .. 0.57

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.083
                           DUF2225 132 edeekeklflkkAlelykeayekesfpvegideatvlYLiaeLerrlgnkeealr 186
                                       e+ ++e + +  Al+   +aye+   p + id ++    + eLe+++gnk+e   
  gi|242399724|ref|YP_002995149.1|  84 EKYKEEREKYLDALYHLADAYEHFGMPNKAIDVYE---KLLELEKKIGNKREEAL 135
                                       12223333333455555555555555555555444...33467777776666554 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00069
                           DUF2225  87 fskertldeaiesYkLallcyelkkekkskkAklalrlAWlyrdkedeekeklflkkAlelykeayekesfpvegid 163
                                       + +    ++ai  Y   ll  e k  +k + A ++ ++A  y+++e+ +   +++++A +++ke   + ++ v+++d
  gi|242399724|ref|YP_002995149.1| 104 YEHFGMPNKAIDVYEK-LLELEKKIGNKREEALTLAHIAINYDELEEVDRAIELMNEASKMFKELGDERNYLVSILD 179
                                       4444445778888875.55666777788899*********************************9999999888888 PP

                           DUF2225 164 eatvlYLiaeLe 175
                                        a+  Y +++ +
  gi|242399724|ref|YP_002995149.1| 180 LAHFHYEVGDYN 191
                                       777766666544 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 2.2
                           DUF2225 149 k 149
                                       +
  gi|242399724|ref|YP_002995149.1| 264 E 264
                                       1 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   1.2      0.35   2.2e+02     103     140 ..      63     103 ..      20     154 .. 0.64
   2 ?    1.9   0.0      0.39   2.5e+02      96     139 ..     240     280 ..     189     298 .. 0.76
   3 ?    5.1   0.0     0.041        26      61     108 ..     287     340 ..     283     341 .] 0.74

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.35
                                       SEEEEEEBSSSHH..HHHHHHT.CTSHHHHHHHHHHHHHHT CS
                                       xxxxxxxxxxxxx..xxxxxxx.xxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 103 drvslgleaadde..kvlklmn.rghtfeevlealeklrea 140
                                       ++++ +l  +d+    ++kl++  ++++e++l+al  l++a
  gi|242399724|ref|YP_002995149.1|  63 THIYAHLGELDKGieIYKKLVEkYKEEREKYLDALYHLADA 103
                                       55555555555555556666666666667777777666665 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.39
                                       HHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  96 rllelgvdrvslgleaaddekvlklmnrghtfeevlealeklre 139
                                       + le + d ++l  ea+ ++ +  l+   + ++e++e++e l+e
  gi|242399724|ref|YP_002995149.1| 240 KALETE-DLFTLAFEALYEF-ITGLF-EEKLYKEIYENIESLAE 280
                                       334445.999999******9.99999.88999*****9999987 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.041
                                       TTHHHHHHHHHHTC.........CCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEE CS
                                       xxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  61 pdfvellerlakla.........vpgiritvetngtlpdeeklerllelgvdrvslg 108
                                       p+++++  ++ +la          +++ +++e+n+++   e l++l++ g++++ +g
  gi|242399724|ref|YP_002995149.1| 287 PEYTKFFIAIGELAklkegqenrYEEVYTSIEVNEFK---ELLDELKKIGTTVLKIG 340
                                       5555666666666666566666678888888888888...6*********9999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1213  (0.0676558); expected 358.6 (0.02)
Passed bias filter:                      587  (0.0327403); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); 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: 0.79u 0.35s 00:00:01.14 Elapsed: 00:00:00.57
# Mc/sec: 1797.98
//
Query:       gi|242399725|ref|YP_002995150.1|  [L=120]
Description: Elongation factor 1-beta [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-14   54.1   0.0    1.7e-14   53.7   0.0    1.2  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 !   53.7   0.0   9.7e-19   1.7e-14       3      89 ..      34     119 ..      32     120 .] 0.89

  Alignments for each domain:
  == domain 1  score: 53.7 bits;  conditional E-value: 9.7e-19
                                       EEEEEESSS---HHHHHHHHHH.HS-T.....SEE--.--EEE-SSS-EEEEEEEEESSS-G.GGGHHHHHHTTS-S CS
                           EF1_GNE   3 vlevkPeddetdleelekkvksikleg.....lvwgeasklepiafGlkkLqiscvieddkv.stdeleekieeieg 73 
                                       v++v+P d e +l+ele ++k+ +le+     + + + +++epiafGl +L++++  +d ++ s de++++++e+e+
  gi|242399725|ref|YP_002995150.1|  34 VIKVMPTDPEINLDELEGALKK-TLEEkfggkYGLSK-IDREPIAFGLVALKVYVLGKDAEGySFDEVTDAFREVEN 108
                                       89***************99999.55542333566774.99*********************99************** PP

                                       .....SEEEEEEEEEE CS
                           EF1_GNE  74 eledlVqsveivsfnk 89 
                                            V+s+e++ +++
  gi|242399725|ref|YP_002995150.1| 109 -----VESAEVETISR 119
                                       .....*******9987 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:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 716.52
//
Query:       gi|242399726|ref|YP_002995151.1|  [L=48]
Description: hypothetical protein TSIB_1751 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       963  (0.0537119); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.34s 00:00:00.85 Elapsed: 00:00:00.55
# Mc/sec: 263.22
//
Query:       gi|242399727|ref|YP_002995152.1|  [L=813]
Description: ABC-type dipeptide/oligopeptide transport system, probable periplasmic component [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.3e-22   79.5  15.9    6.1e-22   78.1  15.9    1.6  1  SBP_bac_5  Bacterial extracellular solute-binding proteins, f
  ------ inclusion threshold ------
      0.035   14.7   3.6      0.085   13.5   3.6    1.6  1  DUF4690    Small Novel Rich in Cartilage
       0.11   10.6  16.0       0.17   10.1  16.0    1.1  1  SSP160     Special lobe-specific silk protein SSP160
        5.9    6.8   7.9         13    5.7   7.9    1.5  1  TMEM154    TMEM154 protein family


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 !   78.1  15.9   1.4e-25   6.1e-22      29     359 ..     134     597 ..     132     604 .. 0.80

  Alignments for each domain:
  == domain 1  score: 78.1 bits;  conditional E-value: 1.4e-25
                                       B-TTSSB-SHHHHHHH....HHHHHTGGGHCTTHHHHHC...................................... CS
                         SBP_bac_5  29 kFsDGtpltAeDvvfs....ferlldpdtasgyasllee...................................... 63 
                                       +F+DG ++ A+Dv +s    +e++   ++  +y++   e                                      
  gi|242399727|ref|YP_002995152.1| 134 YFHDGHKVSAADVMYSfafeWEWINQDGDDDPYYDAG-Eadwmidfmntilglkfveqtddrmifevyhnyyfpase 209
                                       8**************8665455555555555554444.46********87777777777777777777777777777 PP

                                       ............................................TCTEEEEEEEETTEEEEEESSETT.TTTTHCHH CS
                         SBP_bac_5  64 ............................................dqdikkveavddytvrftlkkpna.lfltllaa 95 
                                                                                   + ++  ++a+++  ++++ + p + ++ +++ +
  gi|242399727|ref|YP_002995152.1| 210 imtaayvvpftgtpwqlwyamselvahnekyswsestetieqvdQINPHHAQAIKESLLQVKNSNPIPeYLKPYIED 286
                                       77777777777777777777777777777777777777777766666666666666666666666655223344443 PP

                                       HHHHHGCCHTCTCTTTTTGTTTSE-BSSSEEEEEEETTT.EEEEEE-TTST.........TTSCSSSSEEEEEE-.S CS
                         SBP_bac_5  96 vpasiakkaaekeddkdkdtnekpvgtGPYklkefkpgq.kivlernpdYw.........gggkpkldriefkvipd 162
                                        +a+   +a++  +++ +++  +++g GPY +++++p++ +++le+++  w         +  +p+++ ie+   ++
  gi|242399727|ref|YP_002995152.1| 287 ENAAK--AAYDSIANFIDQYGHAVIGQGPYYITDYQPENlYVKLEKFDK-WtvpafpepgYDVEPYFETIEIYGLQN 360
                                       33333..588***************************888999******.77999999988899************* PP

                                       HHHHHHHHHTTSSSEEESTTCCTHCHHHHHTTEEE.EEEEEEEEEEEEEETTT................STGGGSHH CS
                         SBP_bac_5 163 sdaraaalqsGeiddvaepppsdieqlkeakglkv.lyespgggvtylafNtk................kppfddkr 222
                                       +d++++++ +G +d+ ++p++++  +   +++++    ++ ++ ++ l+fN                   +pf+  +
  gi|242399727|ref|YP_002995152.1| 361 EDTAILEVAKGTYDVLWYPFAAYRFTGLSEEQKNSiDLYKSTSAFGDLVFNPVhdpdnpyvitvgdkkyFNPFAVRK 437
                                       *********************999999555555555457777777788888888999999999999877669999** PP

                                       HHHHHHHHS-HHHHHHHCTTTSSEEESSSSTTTSTTCCSCHCCCSHH................SHHHHHHHHHHHTT CS
                         SBP_bac_5 223 vRqAlsyAiDreeivkavlegyatpansllppsspgadeeykpayka................ydpekAkklLkeaG 283
                                       vR  l+y i r   v+++++g a++++++  +s  g+++  +  + +                  +++A + L+e G
  gi|242399727|ref|YP_002995152.1| 438 VRFGLQYLISRAHAVQNIFQGSAGAMYTPWVSSETGYNYVQSVVEAYdlseqpdeafalqlieEGMQEAAQELAEMG 514
                                       *****************************88888888777777655589**********999999************ PP

                                       -BCSSTSCEETC.....EEEEEEEEETTSHHHHHHHHHHHHH.HHHTTEEEEEEEECHH....HHHHHHHHCTTESE CS
                         SBP_bac_5 284 ykdgdggglrek.....klkltlllasgspaekaiaeliqqq.lkkiGikvevktvdwa....atylervkdgdfdm 350
                                       yk  + +g   k     +++ ++ l  +   +k+ia +++++ l k+Gi+ e + vd       +y+++ ++ ++++
  gi|242399727|ref|YP_002995152.1| 515 YKLEKVDG---KwyfegEPVKIIGLGRSEDERKDIALYVVNEiLPKVGIESEANIVDRRtasgMVYTSDPSSYQWNF 588
                                       *9875332...34456488888888888888889999999873667**********87779**99999********* PP

                                       EEEEEECTT CS
                         SBP_bac_5 351 illgwgady 359
                                       +  gw +++
  gi|242399727|ref|YP_002995152.1| 589 YTEGWVSST 597
                                       *****9875 PP

>> DUF4690  Small Novel Rich in Cartilage
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   3.6   1.9e-05     0.085      23      77 ..     754     808 ..     741     811 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.9e-05
                           DUF4690  23 plesttkeresdltdlpastselepeDtthlerldeeegslGPGaiaaiviaalL 77 
                                       ++e+t++++++++t+   st ++   +tt +++  +e+g  GP ai a+ +  lL
  gi|242399727|ref|YP_002995152.1| 754 TTETTSSTETTSTTETTSSTETTSTTETTSSTETTTEGGICGPAAILALAVIPLL 808
                                       34555555566666666677777777888888889999********998554444 PP

>> SSP160  Special lobe-specific silk protein SSP160
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1  16.0   3.8e-05      0.17     106     156 ..     747     798 ..     725     808 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 3.8e-05
                            SSP160 106 sssssssatstssststtssssttssnsttttsnstsssnstssg.ltssas 156
                                       s++ ++s+t t+sst tts++ ttss  tt+t+++tss+++t+ g +   a+
  gi|242399727|ref|YP_002995152.1| 747 SAKPTTSTTETTSSTETTSTTETTSSTETTSTTETTSSTETTTEGgICGPAA 798
                                       3344455555555555555555555555555555555555444330333343 PP

>> TMEM154  TMEM154 protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   7.9    0.0028        13      13      52 ..     752     790 ..     743     809 .. 0.54

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0028
                           TMEM154  13 etatleeesadatsaasteseslkqeeakeslssaelsne 52 
                                        ++t ++ s+++ts++ t ++s +++ + e++ss+e+  e
  gi|242399727|ref|YP_002995152.1| 752 TSTTETTSSTETTSTTET-TSSTETTSTTETTSSTETTTE 790
                                       222333333334444444.445556667777777777654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (813 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1263  (0.0704445); expected 358.6 (0.02)
Passed bias filter:                      812  (0.0452898); expected 358.6 (0.02)
Passed Vit filter:                       113  (0.00630264); expected 17.9 (0.001)
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: 0.99u 0.38s 00:00:01.37 Elapsed: 00:00:00.56
# Mc/sec: 4345.88
//
Query:       gi|242399728|ref|YP_002995153.1|  [L=37]
Description: hypothetical protein TSIB_1753 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.33s 00:00:00.86 Elapsed: 00:00:00.55
# Mc/sec: 202.29
//
Query:       gi|242399729|ref|YP_002995154.1|  [L=349]
Description: peptide ABC transporter permease [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-37  129.0  18.8    1.6e-37  129.0  18.8    1.8  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
       0.38   10.4   3.9       0.21   11.2   0.6    2.1  2  HCV_NS2       Hepatitis C virus non-structural protein NS2
         10    6.9  23.1        1.6    9.5   6.2    4.7  4  PrgI          PrgI family protein


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.2       0.5     3e+03     159     168 ..      16      25 ..       6      39 .. 0.50
   2 !  129.0  18.8   2.7e-41   1.6e-37       1     184 [.     139     342 ..     135     343 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.5
                      BPD_transp_1 159 lalviavlll 168
                                       ++l+i++l++
  gi|242399729|ref|YP_002995154.1|  16 VVLAIVTLVM 25 
                                       2222222222 PP

  == domain 2  score: 129.0 bits;  conditional E-value: 2.7e-41
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf.....................vilsilghlilpv 56 
                                       gillG+ aa + ++++d++l++l  v++s+P+ +++++++l+f                      i + l+ + lpv
  gi|242399729|ref|YP_002995154.1| 139 GILLGVKAAQMVGSFFDRALSILALVMSSIPMWWFGMIMLLIFsfkmgwfpsraipdpnltgwpHIVDLLKRMTLPV 215
                                       788888888******************************************************************** PP

                      BPD_transp_1  57 iillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgs 133
                                       ++++++s+++++ +ir+ ++ ++++d++ aara+G++++++++ ++l++a+pp++t +i+++  +lgga+++e +++
  gi|242399729|ref|YP_002995154.1| 216 ATIVIVSFGAWAWVIRNIMIGTMQEDFIMAARAKGVPERKVIYGHALRAAAPPVVTMIIFSLLTSLGGAIITESVFT 292
                                       ***************************************************************************** PP

                      BPD_transp_1 134 wpGlgtllleailgydyseisnggvlalviavlllnlvadilqrlldprvr 184
                                       wpG+g++ + ai+ + +++i+ g++++ v+++l  +++ad+ + +ldprv+
  gi|242399729|ref|YP_002995154.1| 293 WPGMGRVYWIAIETNETNLIM-GLTFVNVLLYLGGVILADVAYGFLDPRVK 342
                                       *********************.***************************97 PP

>> HCV_NS2  Hepatitis C virus non-structural protein NS2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.6   3.5e-05      0.21      27     113 ..      77     165 ..      69     179 .. 0.86
   2 ?   -0.9   0.2      0.18   1.1e+03      68      97 ..     263     291 ..     211     302 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.5e-05
                           HCV_NS2  27 gllakllwylqyliaraearlrvlvpplgarggrdavilltlllaPelv..fevtkiLlailgplylLeasLlrvpy 101
                                         l k  w++    +r  ++ +   ++  + g+ + v+++  ++ P+++  f+ ++i+++ lg l  ++a+ +    
  gi|242399729|ref|YP_002995154.1|  77 YHLDKSYWWRVQYYFRNTLTFNFGKTKNPVFGSEKDVMAILKVAIPRTIqlFTTAQIIIITLGILLGVKAAQMVGSF 153
                                       4577999***99999999**999999999******************973367777888889999888888888899 PP

                           HCV_NS2 102 lvRaaallrlcv 113
                                       + Ra  +l l++
  gi|242399729|ref|YP_002995154.1| 154 FDRALSILALVM 165
                                       999998887766 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.18
                           HCV_NS2  68 lllaPelvfevtkiLlailgplylLeasLl 97 
                                        ++aP +v  +   Ll  lg   +  +s+ 
  gi|242399729|ref|YP_002995154.1| 263 RAAAPPVVTMIIFSLLTSLGGAII-TESVF 291
                                       344577777777777777776544.44444 PP

>> PrgI  PrgI family protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   1.6      0.33     2e+03      66      84 ..      74      92 ..       1      97 [. 0.58
   2 ?    9.5   6.2   0.00026       1.6      17      64 ..     128     176 ..     120     193 .. 0.83
   3 ?    1.9   0.2     0.062   3.7e+02      44      69 ..     209     234 ..     199     258 .. 0.68
   4 ?    4.5   0.0    0.0094        56       8      40 ..     306     338 ..     302     346 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.33
                              PrgI 66 kdglplekylkaiikfklr 84
                                      +++++l+k +++ +++++r
  gi|242399729|ref|YP_002995154.1| 74 RSQYHLDKSYWWRVQYYFR 92
                                      5566677777777777665 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00026
                              PrgI  17 LtlRQliflvlallvaiglylllrafl.eelasvlvillavPvaalgfy 64 
                                       +t  Q+i++ l++l+++ ++ ++ +f+   l+++++++ ++P++ +g++
  gi|242399729|ref|YP_002995154.1| 128 FTTAQIIIITLGILLGVKAAQMVGSFFdRALSILALVMSSIPMWWFGMI 176
                                       9**************************6555555566669**9999886 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.062
                              PrgI  44 eelasvlvillavPvaalgfykkdgl 69 
                                       + ++++++++++v + a++++ ++ +
  gi|242399729|ref|YP_002995154.1| 209 KRMTLPVATIVIVSFGAWAWVIRNIM 234
                                       45668899999999999999955444 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.0094
                              PrgI   8 eyeekiffgLtlRQliflvlallvaiglylllr 40 
                                       + e+ +++gLt+  ++ +++++++a ++y +l 
  gi|242399729|ref|YP_002995154.1| 306 TNETNLIMGLTFVNVLLYLGGVILADVAYGFLD 338
                                       45899******************9888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       804  (0.0448435); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); 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):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.35s 00:00:00.96 Elapsed: 00:00:00.52
# Mc/sec: 2027.14
//
Query:       gi|242399730|ref|YP_002995155.1|  [L=473]
Description: peptide ABC transporter permease [Thermococcus sibiricus MM 739]
Scores for complete 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   96.5  13.6    1.5e-27   96.5  13.6    2.3  3  BPD_transp_1  Binding-protein-dependent transport system inne
    2.3e-05   24.3   0.2    2.3e-05   24.3   0.2    3.2  4  OppC_N        N-terminal TM domain of oligopeptide transport 


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1      0.18   1.6e+03      20      41 ..      25      46 ..      12      84 .. 0.63
   2 ?    2.2   0.4     0.014   1.3e+02     147     177 ..     259     288 ..     239     290 .. 0.72
   3 !   96.5  13.6   1.7e-31   1.5e-27       1     185 []     284     472 ..     280     472 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.18
                      BPD_transp_1 20 lrpliivllslPsfvlaillvl 41
                                      l++l  ++l + + v a++l+ 
  gi|242399730|ref|YP_002995155.1| 25 LLGLLLLFLFIFTAVTAPVLTS 46
                                      4455555555555555555554 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.014
                      BPD_transp_1 147 gydyseisnggvlalviavlllnlvadilqr 177
                                        + + ++s  ++l+++i+v+++++++ i++ 
  gi|242399730|ref|YP_002995155.1| 259 LSGIIWGS-RVSLVIGISVAVFSVIIGIFYG 288
                                       44555555.67899***********999986 PP

  == domain 3  score: 96.5 bits;  conditional E-value: 1.7e-31
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilg.hlilp..viillllsaapyvrlirra 74 
                                       gi+ G+ +a + +++ d++++++ +++ s+Ps+ ++il+        ++g h  l+  v++l+++++++++r+ r++
  gi|242399730|ref|YP_002995155.1| 284 GIFYGVTSA-YLGGWSDEMMMRFQEFMASIPSLPILILMG------AYFGgHIKLWqiVVLLVIFGWVGIARVARSM 353
                                       566677777.************************999999......444444444443899**************** PP

                      BPD_transp_1  75 alrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydys 151
                                       al++ ++ +veaar+lGa++ +i++++++P++lp+++++++l++++++   + l++lg    lg+++  +++g+ ++
  gi|242399730|ref|YP_002995155.1| 354 ALQIKEQVYVEAARVLGAGTGRIIFRHMVPQLLPYAFAQMALSVPSAVLSEASLSYLG----LGDPT-AVTWGQILH 425
                                       **********************************************************....99765.689999999 PP

                      BPD_transp_1 152 eis.............nggvlalviavlllnlvadilqrlldprvrk 185
                                        ++             + + la++++ l ++l+  +l r+l+pr+r+
  gi|242399730|ref|YP_002995155.1| 426 DAQvagaavngywwwvIPPGLAIALVGLTFVLIGTALDRVLNPRLRR 472
                                       99999***************************************995 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 !   24.3   0.2   2.5e-09   2.3e-05       3      44 ..      11      53 ..      10      66 .. 0.76
   2 ?   -0.4   0.3      0.13   1.1e+03      20      35 ..     270     285 ..     266     302 .. 0.58
   3 ?   -2.6   0.1      0.61   5.5e+03      28      32 ..     337     341 ..     332     390 .. 0.66
   4 ?   -2.0   0.1      0.42   3.8e+03      16      25 ..     449     458 ..     448     468 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 2.5e-09
                            OppC_N  3 wqdawrrFkrNklAvvglvilllllliaifaPliaPydp.qdl 44
                                      ++++w+ F+r k  ++gl +l l+++ a+ aP+++ +d  q +
  gi|242399730|ref|YP_002995155.1| 11 LSEFWYDFRRQKSGLLGLLLLFLFIFTAVTAPVLTSPDIpQKW 53
                                      5789******************************755546333 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.13
                            OppC_N  20 lvilllllliaifaPl 35 
                                       lvi + +++++++   
  gi|242399730|ref|YP_002995155.1| 270 LVIGISVAVFSVIIGI 285
                                       5555555555444322 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 0.61
                            OppC_N  28 liaif 32 
                                       l++if
  gi|242399730|ref|YP_002995155.1| 337 LLVIF 341
                                       22222 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 0.42
                            OppC_N  16 Avvglvilll 25 
                                       A+vgl ++l+
  gi|242399730|ref|YP_002995155.1| 449 ALVGLTFVLI 458
                                       8999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (473 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       662  (0.0369234); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.68u 0.31s 00:00:00.99 Elapsed: 00:00:00.52
# Mc/sec: 2722.00
//
Query:       gi|242399731|ref|YP_002995156.1|  [L=322]
Description: ABC-type dipeptide/oligopeptide transport system, ATPase component [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-28  100.5   0.0    1.5e-28  100.0   0.0    1.2  1  ABC_tran     ABC transporter
    4.1e-20   72.1   0.2    6.6e-20   71.4   0.2    1.3  1  oligo_HPY    Oligopeptide/dipeptide transporter, C-terminal r
      1e-05   25.5   0.2    0.00024   21.0   0.0    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
     0.0054   16.6   0.1      0.014   15.3   0.0    1.7  2  RsgA_GTPase  RsgA GTPase
  ------ inclusion threshold ------
      0.018   14.5   0.5       0.14   11.6   0.1    2.0  2  SMC_N        RecF/RecN/SMC N terminal domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.0   0.0   4.2e-32   1.5e-28       2     136 ..      29     185 ..      28     186 .. 0.93

  Alignments for each domain:
  == domain 1  score: 100.0 bits;  conditional E-value: 4.2e-32
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--....SEEEEEETTCEGGG.....B-HHHCCHCEEEE-SS.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxx.. RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkp....teGeilldgkdlke.....qeleslrkeigvlpqe.. 67 
                                       +++s++lk+ge++++ Ge+G+GKS+L  +l+g+ +p      G+i++dg+++        ++e+  ++i++++q   
  gi|242399731|ref|YP_002995156.1|  29 DDISFDLKKGEVLGLAGESGCGKSSLGFTLIGMPTPpgkiVDGSIKIDGREIVGlpenvLRKEIRWQKISMIFQGam 105
                                       89**********************************999999************77776666666678899999988 PP

                                       --S-TTSBHHHH...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEE CS
                                       xxxxxxxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  68 pqlfpeltvren...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllD 133
                                       + l+p +tv+ +           +++e i+ka + l+l++l+ ++v++ p++LSgG+kqrv++a all +p+++++D
  gi|242399731|ref|YP_002995156.1| 106 NALNPVYTVGYQmieplmyqkgmNKEEAINKAQKYLELVGLDPEIVYRYPHELSGGMKQRVVIATALLLEPEVVIAD 182
                                       999999999999*********9999999************************************************* PP

                                       STT CS
                                       xxx RF
                          ABC_tran 134 Ept 136
                                       Ept
  gi|242399731|ref|YP_002995156.1| 183 EPT 185
                                       **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 !   71.4   0.2   1.8e-23   6.6e-20       1      65 []     237     301 ..     237     301 .. 0.99

  Alignments for each domain:
  == domain 1  score: 71.4 bits;  conditional E-value: 1.8e-23
                         oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekdklekikgeapslerldeGCpFapRCpfaleeC 65 
                                       vE+g+s+k+  ep+HPYT++Ll+++prl++  +kle i+g++p+l + ++GC+F+pRCp+ ++ C
  gi|242399731|ref|YP_002995156.1| 237 VEIGDSEKVYYEPAHPYTQKLLAAIPRLHEDLKKLEFIPGQPPNLINPPNGCRFHPRCPYIMQVC 301
                                       8*************************************************************999 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.032   1.2e+02       3      75 ..      42      97 ..      40     104 .. 0.78
   2 !   21.0   0.0   6.6e-08   0.00024     232     303 .]     153     222 ..     143     222 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.032
                            AAA_21  3 vliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryg 75
                                      +l G  g+GKS+L  +l ++                  +++ki   +  +d ++ + +  + +l +++r++ +
  gi|242399731|ref|YP_002995156.1| 42 GLAGESGCGKSSLGFTLIGM----------------PTPPGKIVDGSIKIDGREIVGLPEN-VLRKEIRWQKI 97
                                      6899*********9888665................4588888888888888888888888.88888888765 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 6.6e-08
                            AAA_21 232 lparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSpllld 303
                                       + ++elS G+k+   ++tall  +    +++ DEp + L+  +++ ++ ++k+l++  g   i+ TH+ ++l+
  gi|242399731|ref|YP_002995156.1| 153 RYPHELSGGMKQRVVIATALLLEP---EVVIADEPTTALDVVVQAQIVNMMKKLKKeLGLSMIFITHDLSILA 222
                                       56899*******999999999988...9***********************7777779***********9986 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0     4e-06     0.014      80     119 ..      18      58 ..       2      73 .. 0.80
   2 ?   -2.4   0.0       1.1     4e+03      56      84 ..     188     216 ..     167     232 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4e-06
                                       EE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHH CS
                       RsgA_GTPase  80 llvsaktkegleelkellkd.ktsvlvGqSGvGKStLinal 119
                                       ++++    +++++++  lk+ ++  l+G+SG GKS+L  +l
  gi|242399731|ref|YP_002995156.1|  18 YFTNRGMVRAVDDISFDLKKgEVLGLAGESGCGKSSLGFTL 58 
                                       35566667899*******999***************96666 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.1
                                       GGG--HHHHHHHHHHHHHHTTSEEEE--T CS
                       RsgA_GTPase  56 iDlleeeeeleelkeelealgyevllvsa 84 
                                       +D++ +++ ++ +k+  ++lg++++++  
  gi|242399731|ref|YP_002995156.1| 188 LDVVVQAQIVNMMKKLKKELGLSMIFITH 216
                                       45666666566666667777777777644 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 ?    1.0   0.0     0.066   2.4e+02      27      40 ..      41      54 ..      26      59 .. 0.81
   2 ?   11.6   0.1   3.8e-05      0.14     122     212 ..     136     231 ..      88     238 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.066
                                      EEEEESTTSSHHHH CS
                                      xxxxxxxxxxxxxx RF
                             SMC_N 27 taivGpNGSGKsnl 40
                                        + G+ G+GKs+l
  gi|242399731|ref|YP_002995156.1| 41 LGLAGESGCGKSSL 54
                                      5688********98 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 3.8e-05
                                       HHHHHHHCTT-STT.......CS-HHHHH..HHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT CS
                                       xxxxxxxxxxxxxx.......xxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 122 evsellesagiske.......lLSgGekt..LvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn 189
                                       + ++ le +g+++e       +LSgG k+  ++a aLl      +p+ +++ De   aLD    +++++++k+ +k+
  gi|242399731|ref|YP_002995156.1| 136 KAQKYLELVGLDPEivyryphELSGGMKQrvVIATALL-----LEPE-VVIADEPTTALDVVVQAQIVNMMKKLKKE 206
                                       3344444444444477777779****766115555555.....3454.6789*********************9999 PP

                                       ..SEEEEE-SSHHHCCC-SCEEEEE CS
                                       ..xxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 190 ..aQfivislreemlekadklvgvt 212
                                           +i i+++  +l++ +  + ++
  gi|242399731|ref|YP_002995156.1| 207 lgLSMIFITHDLSILAEISDKIAIM 231
                                       6678899999998888876655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       722  (0.04027); expected 358.6 (0.02)
Passed bias filter:                      629  (0.0350828); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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 0.34s 00:00:00.97 Elapsed: 00:00:00.53
# Mc/sec: 1840.50
//
Query:       gi|242399732|ref|YP_002995157.1|  [L=335]
Description: ABC-type dipeptide/oligopeptide transport system, ATPase component [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      3e-32  112.0   0.0      4e-32  111.6   0.0    1.2  1  ABC_tran      ABC transporter
    1.8e-18   66.8   0.1    3.1e-18   66.1   0.1    1.4  1  oligo_HPY     Oligopeptide/dipeptide transporter, C-terminal 
      6e-05   23.0   0.2     0.0036   17.1   0.0    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
     0.0033   17.2   0.0     0.0049   16.6   0.0    1.2  1  PRK           Phosphoribulokinase / Uridine kinase family
     0.0038   17.5   0.4      0.015   15.6   0.4    1.9  1  AAA_22        AAA domain
     0.0041   16.6   0.0      0.011   15.2   0.0    1.6  1  SMC_N         RecF/RecN/SMC N terminal domain
  ------ inclusion threshold ------
       0.02   14.8   0.0       0.03   14.3   0.0    1.3  1  Rad17         Rad17 P-loop domain
      0.029   14.8   0.0      0.069   13.6   0.0    1.7  2  AAA           ATPase family associated with various cellular 
      0.055   13.2   0.0      0.097   12.4   0.0    1.3  1  AAA_29        P-loop containing region of AAA domain
      0.064   13.7   0.0       0.14   12.5   0.0    1.6  1  RNA_helicase  RNA helicase
       0.15   12.2   0.3       0.29   11.3   0.3    1.5  1  Bombesin      Bombesin-like peptide
       0.15   11.9   0.0       0.26   11.2   0.0    1.4  1  RsgA_GTPase   RsgA GTPase
       0.17   11.6   0.1       0.21   11.2   0.1    1.3  1  AAA_15        AAA ATPase domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.6   0.0   2.9e-35     4e-32       2     136 ..      37     191 ..      36     192 .. 0.94

  Alignments for each domain:
  == domain 1  score: 111.6 bits;  conditional E-value: 2.9e-35
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS..--S-T CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxx..xxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke....qeleslrkeigvlpqe..pqlfp 72 
                                       + +++++++ ++ a+vGe+G+GKSt  kl+ +ll+pt G+i l+g+d+++    +e  ++r+++++++q+  ++l+p
  gi|242399732|ref|YP_002995157.1|  37 DGINFEIYPQQVFALVGESGCGKSTTGKLIVKLLEPTDGKIYLRGQDVTDiktkEEVLEYRRKVQMIFQDpfSSLNP 113
                                       789***********************************************9988888899**********9999*** PP

                                       TSBHHHH...............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEES CS
                                       xxxxxxx...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  73 eltvren...............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDE 134
                                       + ++ +                e++e i+kal+ ++++  +++ ++++p+ LSgGq+qrva+aral+ +p+++++DE
  gi|242399732|ref|YP_002995157.1| 114 RFRIFDVleepllihgigetkaEREELIYKALEMVKIIP-PEDYIGRNPHMLSGGQRQRVAIARALILNPTFIVADE 189
                                       ***999999*********986555555***********9.999999******************************* PP

                                       TT CS
                                       xx RF
                          ABC_tran 135 pt 136
                                       p 
  gi|242399732|ref|YP_002995157.1| 190 PV 191
                                       *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 !   66.1   0.1   2.2e-21   3.1e-18       1      64 [.     243     309 ..     243     311 .. 0.95

  Alignments for each domain:
  == domain 1  score: 66.1 bits;  conditional E-value: 2.2e-21
                         oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekd...klekikgeapslerldeGCpFapRCpfalee 64 
                                       vE+gp++ ++d+p HPYT+aLl++vp++ +e++   k   ikge+ps+ +++ GC+F+pRC +a + 
  gi|242399732|ref|YP_002995157.1| 243 VEMGPAKVVIDNPIHPYTRALLAAVPEPIPERRniiKEIPIKGEVPSAANIPPGCRFHPRCLYAEKG 309
                                       8********************************9999999**********************99876 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 ?    4.7   0.2     0.016        23       2      22 ..      49      69 ..      48     145 .. 0.57
   2 !   17.1   0.0   2.6e-06    0.0036     219     299 ..     139     224 ..      95     227 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.016
                            AAA_21  2 nvliGpNgsGKSnLLdaldll 22
                                       +l+G  g+GKS+  +++  l
  gi|242399732|ref|YP_002995157.1| 49 FALVGESGCGKSTTGKLIVKL 69
                                      68***********99999544 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 2.6e-06
                            AAA_21 219 r.......gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr. 287
                                       +        v +  ++d+  ++++ lS G+++  a++ al+  +   ++++ DEp + L+ ++ +++lel+k+l++ 
  gi|242399732|ref|YP_002995157.1| 139 EliykaleMVKIIPPEDYIGRNPHMLSGGQRQRVAIARALILNP---TFIVADEPVSMLDVSIRAEILELMKDLKEk 212
                                       14444555778889999999*************99999999888...************************777776 PP

                            AAA_21 288 ngaQviltTHSp 299
                                        g+  +  TH+ 
  gi|242399732|ref|YP_002995157.1| 213 MGVTYLYITHDL 224
                                       99999*****96 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   3.5e-06    0.0049       2      84 ..      49     131 ..      48     149 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3.5e-06
                               PRK   2 IgvagsSGaGkttvarklekifgrekvkaaeiegdsflrldraekdleleer.krakekevsflspeandfdllyev 77 
                                        ++ g+SG+Gk+t+ + ++k+++ +  k  +  g+ ++ ++  e+ le +++ +  ++  +s l+p+   fd l+e 
  gi|242399732|ref|YP_002995157.1|  49 FALVGESGCGKSTTGKLIVKLLEPTDGK-IYLRGQDVTDIKTKEEVLEYRRKvQMIFQDPFSSLNPRFRIFDVLEEP 124
                                       6889*******************66666.8889999999999999999987725568999**************998 PP

                               PRK  78 lkelkeg 84 
                                       l+  + g
  gi|242399732|ref|YP_002995157.1| 125 LLIHGIG 131
                                       7655544 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.4   1.1e-05     0.015       5      31 ..      46      72 ..      43     228 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.1e-05
                            AAA_22  5 agilvvtGesGtGKTtllrrlleqlde 31
                                      +++ +++GesG+GK+t+ + +++ l+ 
  gi|242399732|ref|YP_002995157.1| 46 QQVFALVGESGCGKSTTGKLIVKLLEP 72
                                      78899***************9999853 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 !   15.2   0.0   7.9e-06     0.011      24     197 ..      46     222 ..      38     239 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 7.9e-06
                                       SSEEEEEESTTSSHHHHHHHHHHHCTT.TTT.TTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  24 ksftaivGpNGSGKsnlldAilFvLGersak.klrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsi 99 
                                       +++ a+vG+ G+GKs     i  +L  ++ k  lr ++++d+ +k  e+    + +v+++f+++ ++    ++++ i
  gi|242399732|ref|YP_002995157.1|  46 QQVFALVGESGCGKSTTGKLIVKLLEPTDGKiYLRGQDVTDIKTK--EEVLEYRRKVQMIFQDPFSS---LNPRFRI 117
                                       567799***************999987766537999999997665..677777889*****999888...5667777 PP

                                       EEEEETTSEEEEEETTEEE-HHH.HHHHHHCTT-STT.........CS-HHHHHHHHHHHHHHHHCCS--SEEEECT CS
                                       xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 100 srrvkrkgeseykingkevtkke.vsellesagiske.........lLSgGektLvalaLlfAiqkvkpaplyllDe 166
                                          +++     + i +++++++e + + le+++i +          +LSgG+++ va+a  + +       + + De
  gi|242399732|ref|YP_002995157.1| 118 FDVLEEPLL-IHGIGETKAEREElIYKALEMVKIIPPedyigrnphMLSGGQRQRVAIARALIL----NPTFIVADE 189
                                       665544444.556666666664425688888888776788888888********9999866543....3469999** PP

                                       TTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxx RF
                             SMC_N 167 idaaLDeknvkkvaellkekskn..aQfivisl 197
                                         + LD + ++++ el+k  +++  + ++ i++
  gi|242399732|ref|YP_002995157.1| 190 PVSMLDVSIRAEILELMKDLKEKmgVTYLYITH 222
                                       ******************988872234455555 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   2.2e-05      0.03      31      70 ..      32      71 ..      11     122 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.2e-05
                             Rad17 31 vkewlkadvLesrkkriLLisGPsGCgkstvvkvLskelg 70
                                      + ++++    e  ++++  + G sGCgkst+ k + k l 
  gi|242399732|ref|YP_002995157.1| 32 IVHAVDGINFEIYPQQVFALVGESGCGKSTTGKLIVKLLE 71
                                      5566677778888999***************999999875 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0     5e-05     0.069       3      53 ..      51     107 ..      49     145 .. 0.79
   2 ?   -2.2   0.0       3.9   5.3e+03      85     111 ..     198     223 ..     165     227 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5e-05
                                       EESSTTSSHHHHHHHHHHHH.....THEEEEEETTTCS.SSSTTHHHHHHHHHHHHH CS
                               AAA   3 lyGppGtGKTllakavakel.....gvefleisgsell.skyvgesekkirelfkea 53 
                                       l+G  G+GK+++ k ++k l     ++++   +++++  ++ v e  +k++++f++ 
  gi|242399732|ref|YP_002995157.1|  51 LVGESGCGKSTTGKLIVKLLeptdgKIYLRGQDVTDIKtKEEVLEYRRKVQMIFQDP 107
                                       89*****************96665545566666666664556799999999999984 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.9
                                       HHHHHHHHHHHTTTSSSTEEEEEEESS CS
                               AAA  85 vvnqLlteldgvkkkeskvivigatnr 111
                                       + +++l+ ++++k+k + v+ + +t++
  gi|242399732|ref|YP_002995157.1| 198 IRAEILELMKDLKEKMG-VTYLYITHD 223
                                       55677888888888766.777777765 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     7e-05     0.097      12      37 ..      36      61 ..      34      75 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7e-05
                            AAA_29 12 fdghtieidlkgatlltGpsGsGKST 37
                                       dg  +ei +++++ l+G+sG GKST
  gi|242399732|ref|YP_002995157.1| 36 VDGINFEIYPQQVFALVGESGCGKST 61
                                      5667789999999************9 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0    0.0001      0.14       3      40 ..      51      83 ..      49     110 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.0001
                      RNA_helicase  3 lyGpsgeGKStlakeLakallkklklkkkdsvysrnpe 40
                                      l+G+sg+GKSt+ k ++k l+     ++++++y r+ +
  gi|242399732|ref|YP_002995157.1| 51 LVGESGCGKSTTGKLIVKLLE-----PTDGKIYLRGQD 83
                                      79*********9998555554.....778888886644 PP

>> Bombesin  Bombesin-like peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.3   0.00021      0.29       2      12 ..     324     334 ..     323     335 .] 0.97

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00021
                          Bombesin   2 NlWAvGHlMGK 12 
                                       N+WA  Hl GK
  gi|242399732|ref|YP_002995157.1| 324 NHWAECHLIGK 334
                                       9*********9 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   0.00019      0.26      95     117 ..      41      64 ..      14      92 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00019
                                       HHCTT.SEEEEECSTTSSHHHHHH CS
                       RsgA_GTPase  95 ellkd.ktsvlvGqSGvGKStLin 117
                                        ++   ++ +lvG+SG GKSt  +
  gi|242399732|ref|YP_002995157.1|  41 FEIYPqQVFALVGESGCGKSTTGK 64 
                                       555444999***********9433 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00015      0.21      17      70 ..      41      89 ..       6     153 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00015
                            AAA_15 17 veidlseeltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifen 70
                                      +ei  +  +  l+G+ ++GKS+  +++ ++l+ +    + +i++  +d+ + + 
  gi|242399732|ref|YP_002995157.1| 41 FEIYPQQ-VFALVGESGCGKSTTGKLIVKLLEPT----DGKIYLRGQDVTDIKT 89
                                      4444444.999********************988....4444444444443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      618  (0.0344693); expected 358.6 (0.02)
Passed Vit filter:                       101  (0.00563333); 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: 00:00:00.56
# Mc/sec: 1808.86
//
Query:       gi|242399733|ref|YP_002995158.1|  [L=169]
Description: hypothetical protein TSIB_1758 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); 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: 0.54u 0.33s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 984.91
//
Query:       gi|242399734|ref|YP_002995159.1|  [L=254]
Description: NH(3)-dependent NAD(+) synthetase [Thermococcus sibiricus MM 739]
Scores for 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-90  300.0   0.1      1e-89  299.8   0.1    1.0  1  NAD_synthase   NAD synthase
    1.1e-06   27.7   0.2    4.5e-05   22.4   0.2    3.0  3  tRNA_Me_trans  tRNA methyl transferase
    3.7e-06   26.6   0.0    0.00084   18.9   0.0    2.2  2  QueC           Queuosine biosynthesis protein QueC
  ------ inclusion threshold ------
      0.024   14.3   0.0      0.024   14.3   0.0    1.2  1  Asn_synthase   Asparagine synthase
      0.038   13.8   0.0      0.084   12.6   0.0    1.7  1  ATP_bind_3     PP-loop family
      0.088   12.4   0.2        2.1    7.9   0.1    2.3  2  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 !  299.8   0.1   3.4e-93     1e-89       2     242 .]      10     249 ..       9     249 .. 0.98

  Alignments for each domain:
  == domain 1  score: 299.8 bits;  conditional E-value: 3.4e-93
                                       HHHHHHHHHHHHHHCTTSEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE CS
                      NAD_synthase   2 ieelvdflkeyvkkagakgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievkt 78 
                                       i++lv f++e+v++++ kgv+lG+SGGvDS++va+la +a+gke+vl+l++P +   ++dvedal +++nlgi++k+
  gi|242399734|ref|YP_002995159.1|  10 ITKLVSFIQEKVEESNVKGVILGISGGVDSATVAYLAARAIGKEKVLGLVMPYH--INRDVEDALLVCNNLGINYKV 84 
                                       7899***********************************************954..4579***************** PP

                                       ---HHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHTEEEB---BHHHHTTT-S-TTTTT--SBETTTTS- CS
                      NAD_synthase  79 idikpivrafeqelkeakedlakgNlkaRiRmailyaianklnllvlgTgnksElvvGyfTkyGDgaadlapiaell 155
                                       i+ik+iv+ fe++l+ + +++ +gN+ +R+Rm++lya+an+ n+lvlgT+n+sE ++GyfTk+GD a d ap+ +l+
  gi|242399734|ref|YP_002995159.1|  85 INIKSIVNEFEKNLDFELNNVSRGNIMSRTRMILLYAHANSKNYLVLGTSNRSEFLTGYFTKWGDSASDYAPLINLY 161
                                       ***************************************************************************** PP

                                       HHHHHHHHHHTT--HHHHCS--B--SSTT-BHHHHHSS-HHHHHHHHT.HSSSS...HHHHHTTT--HHHHHHHHHH CS
                      NAD_synthase 156 KtevkeLakelnvPervlkkpPsAdLkpgqtDeeeLgikYdelDeiLk.lvekkkspeeiikekelpaevvekiekl 231
                                       Ktev ++a+ l+vP+++++k+PsA+L++gqtDe++Lgi+Y+ lDeiL  lv+ k ++e+i++e+++p ++ve++e+l
  gi|242399734|ref|YP_002995159.1| 162 KTEVWNIARILGVPNEIINKKPSAGLWEGQTDEKDLGITYKLLDEILYrLVDLKMKKENIARELNIPLNKVEYVESL 238
                                       ***********************************************99**************************** PP

                                       HHHTGGGGSSS CS
                      NAD_synthase 232 vkksehKrklp 242
                                       +kksehKrklp
  gi|242399734|ref|YP_002995159.1| 239 IKKSEHKRKLP 249
                                       *********98 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.2   1.5e-08   4.5e-05       3      72 ..      29      89 ..      27      99 .. 0.85
   2 ?   -0.4   0.0      0.13   3.9e+02     167     195 ..     156     186 ..     150     188 .. 0.80
   3 ?    0.6   0.0     0.064   1.9e+02      55      73 ..     219     237 ..     212     242 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.5e-08
                     tRNA_Me_trans  3 vvvalSgGVDSsvaaallkeqg..yevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdfek 72
                                      v+ ++SgGVDS+ +a+l +++    +v g+++  + +           +d++da  v+++lgi+++v+++++
  gi|242399734|ref|YP_002995159.1| 29 VILGISGGVDSATVAYLAARAIgkEKVLGLVMPYHIN-----------RDVEDALLVCNNLGINYKVINIKS 89
                                      899**************99986446788999987765...........799*****************9875 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.13
                     tRNA_Me_trans 167 PlgeltKeevrkiAkeagla..vaekkdSqg 195
                                       Pl +l K+ev +iA+  g++  + +kk S g
  gi|242399734|ref|YP_002995159.1| 156 PLINLYKTEVWNIARILGVPneIINKKPSAG 186
                                       8899999999999999988766778887776 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.064
                     tRNA_Me_trans  55 ervaeklgiplevvdfeke 73 
                                       e++a++l+ipl++v+++++
  gi|242399734|ref|YP_002995159.1| 219 ENIARELNIPLNKVEYVES 237
                                       689************9986 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   2.8e-07   0.00084       3      66 ..      30      92 ..      28     131 .. 0.78
   2 !    5.6   0.0    0.0034        10     156     178 ..     155     177 ..     147     184 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.8e-07
                                      EEE--SSHHHHHHHHHHHHH-..SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEEE-GGGGG CS
                              QueC  3 vvllSGGlDSttvlalakkeg..kevealtfdYgqrhkkeleaakkiakelgveehkildldllke 66
                                      ++ +SGG+DS+tv++la +++  ++v  l + Y+   ++++e a  ++++lg+ + k+++++ + +
  gi|242399734|ref|YP_002995159.1| 30 ILGISGGVDSATVAYLAARAIgkEKVLGLVMPYHI--NRDVEDALLVCNNLGI-NYKVINIKSIVN 92
                                      6779**************99844556666666665..566777889*******.999999986543 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0034
                                       -TTTT--HHHHHHHHHHTTHHHH CS
                              QueC 156 aPlidlsKaeivklgkelgvple 178
                                       aPli+l K+e+++++  lgvp e
  gi|242399734|ref|YP_002995159.1| 155 APLINLYKTEVWNIARILGVPNE 177
                                       9******************9865 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   8.1e-06     0.024      24      73 ..      33      81 ..      18     210 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 8.1e-06
                      Asn_synthase 24 LSGGlDSSliaalaarqsksplktFsigfeekgsdeakyakevaehlgte 73
                                      +SGG+DS+++a+laar    + k   + +  + + +++ a  v++ lg++
  gi|242399734|ref|YP_002995159.1| 33 ISGGVDSATVAYLAARAIG-KEKVLGLVMPYHINRDVEDALLVCNNLGIN 81
                                      6**************9754.333333333226666666666666666666 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.8e-05     0.084       2      59 ..      29      84 ..      28     175 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.8e-05
                                      EEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT- CS
                        ATP_bind_3  2 vlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvkelckklni 59
                                      v++++SgG+DS +  +l+a+   k   k+  +++ +++    ++   ++++l  ++++
  gi|242399734|ref|YP_002995159.1| 29 VILGISGGVDSATVAYLAARAIGK--EKVLGLVMPYHINRDVEDALLVCNNLGINYKV 84
                                      789***************999664..45666777777777777766666666554443 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.1   0.00071       2.1       6      77 ..      29      99 ..      24     134 .. 0.58
   2 ?    2.2   0.0     0.039   1.2e+02     142     161 ..     155     174 ..     150     186 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00071
                              ThiI  6 vlaLlSgGiDSpVaaylllkRGcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdfkevlk 77
                                      v++ +SgG+DS   ayl+ +   + +++ l   p++ ++  e    + + l  +   +++k +v +f++ l+
  gi|242399734|ref|YP_002995159.1| 29 VILGISGGVDSATVAYLAARAIGKEKVLGLV-MPYHINRDVEDALLVCNNLGINYKVINIKSIVNEFEKNLD 99
                                      5566************998765555555553.4554444443333333333333334666666666655543 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.039
                              ThiI 142 rPLigldKeeiiklAkeigt 161
                                        PLi l K e+ ++A+ +g 
  gi|242399734|ref|YP_002995159.1| 155 APLINLYKTEVWNIARILGV 174
                                       6***************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       716  (0.0399353); expected 358.6 (0.02)
Passed bias filter:                      534  (0.0297841); 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: 0.60u 0.37s 00:00:00.97 Elapsed: 00:00:00.54
# Mc/sec: 1419.41
//
Query:       gi|242399735|ref|YP_002995160.1|  [L=279]
Description: Permease, drug/metabolite transporter (DMT) superfamily [Thermococcus sibiricus MM 739]
Scores for complete 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-55  186.2  35.0    4.8e-29  101.3   8.7    2.0  2  EamA       EamA-like transporter family
    1.3e-13   51.0  13.6    5.2e-08   32.6   6.1    2.0  2  TPT        Triose-phosphate Transporter family
    6.8e-07   29.3   8.5     0.0013   18.8   0.2    2.5  2  TMEM234    Putative transmembrane family 234
    0.00022   20.5  22.2     0.0004   19.7   2.2    3.2  2  UAA        UAA transporter family
     0.0073   15.6  17.4      0.033   13.4   1.0    2.5  2  PUNUT      Purine nucleobase transmembrane transport
  ------ inclusion threshold ------
        1.2    9.4  15.5        1.1    9.5   5.0    3.5  2  DMT_YdcZ   Putative inner membrane exporter, YdcZ
        1.5    7.6   6.4       0.35    9.8   2.9    1.7  2  PNTB       NAD(P) transhydrogenase beta subunit
        6.6    6.2  27.0          4    6.9  14.2    3.1  3  SLC35F     Solute carrier family 35


Domain annotation for each model (and alignments):
>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.3  18.3   2.6e-29   5.9e-26       2     135 ..       3     134 ..       2     136 .. 0.95
   2 !  101.3   8.7   2.2e-32   4.8e-29       3     135 ..     146     272 ..     144     274 .. 0.95

  Alignments for each domain:
  == domain 1  score: 91.3 bits;  conditional E-value: 2.6e-29
                              EamA   2 lgillallaalfwaiyfvlskillrkv.spltltfvrfliagillliiallkegklaklslkdwllllllgllgtvl 77 
                                       +g++l++laa +w++ ++++k l+++  +p+t+tf+r+lia+ +ll++   ++ ++   ++  + +++l+g+++++l
  gi|242399735|ref|YP_002995160.1|   3 KGYILIFLAASMWGTLGIFAKLLYQFNlDPFTITFYRTLIAFSILLLYNYSNDFQI---KRHRLPFYALYGFFAVFL 76 
                                       79*********************88655***********99999999988888888...9***************** PP

                              EamA  78 afllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvlli 135
                                       +++l++y +k +s+s+a+l+++ +Pv+++il+++l++ek+t+ ++l+++++++Gv+l+
  gi|242399735|ref|YP_002995160.1|  77 FYILYLYTVKISSVSFAVLLLYSAPVYSTILGYALFKEKITKAKILALIMVIFGVFLV 134
                                       ********************************************************98 PP

  == domain 2  score: 101.3 bits;  conditional E-value: 2.2e-32
                              EamA   3 gillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlaf 79 
                                       + +l ll+ l++a+y++l+ki++++  p +++ +++ +++++l +++ +k       +++++ +l+ l++++tvl++
  gi|242399735|ref|YP_002995160.1| 146 ATVLGLLSGLTYALYGILAKIAVKNEKPEEALLYTIGFGALFLAPFSHFKI------PYESLPYLFGLAFFPTVLGY 216
                                       56899******************************************9955......556***************** PP

                              EamA  80 llffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvlli 135
                                       +l+++al+++++s+as+i+++ePv++lil++l+++e+lt  q++g+v+i+lG l++
  gi|242399735|ref|YP_002995160.1| 217 ILYNKALQEVEVSKASIISTVEPVVALILAYLIFRETLTPQQIVGAVFIILGSLIL 272
                                       ****************************************************9876 PP

>> TPT  Triose-phosphate Transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   6.1   2.3e-11   5.2e-08      19     191 ..      20     188 ..       6     195 .. 0.74
   2 !   23.5   0.8   1.4e-08   3.1e-05      59     138 ..     195     275 ..     189     278 .. 0.89

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 2.3e-11
                               TPT  19 ilnKkilnvfpyPltvsavqllvg.svlilvlwalglkkrpkisseflkailplalvktlghvlavvslskvaVSft 94 
                                       i+ K +++    P+t++  + l+  s+l+l  ++ +++ +++   +f++   + a++ +   +l   +++  +VSf+
  gi|242399735|ref|YP_002995160.1|  20 IFAKLLYQFNLDPFTITFYRTLIAfSILLLYNYSNDFQ-IKRHRLPFYALYGFFAVFLFY--ILYLYTVKISSVSFA 93 
                                       77788888888899999876544404444444444333.333444455544555554444..444455566799*** PP

                               TPT  95 htvKasePiFtvilsrlllgeklsllvylsLlpivgGval.asvtElsFnligfisAlisnltfslrnifsKkllkk 170
                                         +  s+P+++ il   l++ek++ +++l+L+ ++ Gv l a +   + n i+ +  l+s lt +l +i++K ++k+
  gi|242399735|ref|YP_002995160.1|  94 VLLLYSAPVYSTILGYALFKEKITKAKILALIMVIFGVFLvANLDHWDANKIATVLGLLSGLTYALYGILAKIAVKN 170
                                       **************************************86388999*****************************99 PP

                               TPT 171 lkdldalnlfaiitilsllll 191
                                       +k   +  l+  i++ +l+ l
  gi|242399735|ref|YP_002995160.1| 171 EK--PEEALLYTIGFGALF-L 188
                                       65..555566666665554.3 PP

  == domain 2  score: 23.5 bits;  conditional E-value: 1.4e-08
                               TPT  59 kisseflkailplalv.ktlghvlavvslskvaVSfthtvKasePiFtvilsrlllgeklsllvylsLlpivgGval 134
                                       ki +e l +++ la++  +lg +l + +l++v VS + ++ ++eP+ + il+ l+++e+l+ + ++  + i+ G  +
  gi|242399735|ref|YP_002995160.1| 195 KIPYESLPYLFGLAFFpTVLGYILYNKALQEVEVSKASIISTVEPVVALILAYLIFRETLTPQQIVGAVFIILGSLI 271
                                       7888888999999988356899********************************************99999999877 PP

                               TPT 135 asvt 138
                                         + 
  gi|242399735|ref|YP_002995160.1| 272 LHIE 275
                                       6665 PP

>> TMEM234  Putative transmembrane family 234
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   3.2   3.2e-05     0.071      59     115 ..      79     134 ..      66     135 .. 0.88
   2 !   18.8   0.2   5.7e-07    0.0013      47     114 ..     205     271 ..     190     273 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.2e-05
                           TMEM234  59 vlfflllgkadlslavpiaNslafvfTvltelllgekvlkkktvlgmllvvvgialc 115
                                       +l+ ++++  ++s+av +  s  +  T+l   l +ek++k+ ++l +++v++g+ l+
  gi|242399735|ref|YP_002995160.1|  79 ILYLYTVKISSVSFAVLLLYSAPVYSTILGYALFKEKITKA-KILALIMVIFGVFLV 134
                                       89********************9999999888888887665.577899******997 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 5.7e-07
                           TMEM234  47 yliplllNqsgSvlfflllgkadlslavpiaNslafvfTvltelllgekvlkkktvlgmllvvvgial 114
                                       + +++   ++g +l++ +l+++++s a++i+ +++ v+ ++ ++l+ +++l+ ++++g +++++g  +
  gi|242399735|ref|YP_002995160.1| 205 FGLAFFPTVLGYILYNKALQEVEVSKASIIS-TVEPVVALILAYLIFRETLTPQQIVGAVFIILGSLI 271
                                       4456667789***************999886.79999999999999999***************9876 PP

>> UAA  UAA transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5  12.5     0.015        33     155     300 ..       4     136 ..       1     138 [. 0.74
   2 !   19.7   2.2   1.8e-07    0.0004     223     297 ..     200     271 ..     143     275 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.015
                               UAA 155 Giallvlallldavlglvqeklykkygkhskealfyshllslplflllqgellsavkflsesedvallslpsklfyl 231
                                       G++l++la  + + lg++   ly+ ++ +   + fy +l+++ ++ll +    + +++ ++  +++        +y 
  gi|242399735|ref|YP_002995160.1|   4 GYILIFLAASMWGTLGIFAKLLYQ-FNLDPFTITFYRTLIAFSILLLYN--YSNDFQIKRHRLPFY-------ALYG 70 
                                       99*****************99999.999***********9988777664..455555554444444.......4666 PP

                               UAA 232 llnvltqyvcikgVlilisefgaltvtlvltl.RKfvslllSillFknpltlqhlvgtllVflglllysy 300
                                       ++ v + y+     ++ + ++++  +++ l     + s +l + lFk+++t  ++++ ++V++g++l ++
  gi|242399735|ref|YP_002995160.1|  71 FFAVFLFYI----LYLYTVKISSVSFAVLLLYsAPVYSTILGYALFKEKITKAKILALIMVIFGVFLVAN 136
                                       666665554....34444455555555544440445688999***********************99776 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 1.8e-07
                               UAA 223 slpsklfylllnvltqyvcikgVlilisefgaltvtlvltlRKfvslllSillFknpltlqhlvgtllVflglll 297
                                       slp   + +++ ++++y+  +  l  ++ ++a   +++ t+  +v+l+l +l+F++ lt q++vg+++++lg l+
  gi|242399735|ref|YP_002995160.1| 200 SLPYLFGLAFFPTVLGYILYNKALQEVEVSKA---SIISTVEPVVALILAYLIFRETLTPQQIVGAVFIILGSLI 271
                                       45555677777777777766666655555555...677778889**************************99875 PP

>> PUNUT  Purine nucleobase transmembrane transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   8.9    0.0012       2.6      67     147 ..      55     136 ..      40     163 .. 0.78
   2 !   13.4   1.0   1.5e-05     0.033      90     149 ..     217     276 ..     175     278 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0012
                             PUNUT  67 sslslkklvllyivlGll.vavdnllyslgllylpvstfslilatqLaFtaifsalinkqkftrfiinsvvlltisa 142
                                       ++ ++++ + +y + G+  v++  +ly +  +  +vs + l+l +  +++ i+ + + k k+t   i+++++++++ 
  gi|242399735|ref|YP_002995160.1|  55 DFQIKRHRLPFYALYGFFaVFLFYILYLYTVKISSVSFAVLLLYSAPVYSTILGYALFKEKITKAKILALIMVIFGV 131
                                       45556666667777776514455667888888888888999999999************************999998 PP

                             PUNUT 143 allal 147
                                        l+a 
  gi|242399735|ref|YP_002995160.1| 132 FLVAN 136
                                       88774 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 1.5e-05
                             PUNUT  90 llyslgllylpvstfslilatqLaFtaifsalinkqkftrfiinsvvlltisaallalss 149
                                       +ly  +l+++ vs +s+i++   +   i+++li +  +t+  i+  v++++++ +l +++
  gi|242399735|ref|YP_002995160.1| 217 ILYNKALQEVEVSKASIISTVEPVVALILAYLIFRETLTPQQIVGAVFIILGSLILHIEE 276
                                       699**************************************************9998876 PP

>> DMT_YdcZ  Putative inner membrane exporter, YdcZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   5.0   0.00049       1.1      36     139 .]      35     133 ..       7     133 .. 0.78
   2 ?    2.1   2.8     0.096   2.2e+02     119     136 ..     251     268 ..     145     271 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00049
                          DMT_YdcZ  36 vsflvGlivllllllllrksaalaalksvpwwallGGllGavfvtlnillvpklGaaltvvlvllGqllaslliDhf 112
                                       ++f   li++ +lll   ++ +++  ++   ++ l G++ ++  ++ +l + k+  + + vl+l +  + s ++   
  gi|242399735|ref|YP_002995160.1|  35 ITFYRTLIAFSILLLYNYSN-DFQIKRHRLPFYALYGFFAVFLFYILYLYTVKISSVSFAVLLLYSAPVYSTILGY- 109
                                       55555566665555555553.444444444555567899999999999999**********************884. PP

                          DMT_YdcZ 113 GlfgvekrplsltrllGlllllaGvvl 139
                                           + k++++ +++l+l++++ Gv+l
  gi|242399735|ref|YP_002995160.1| 110 ---ALFKEKITKAKILALIMVIFGVFL 133
                                       ...3558999***************96 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.096
                          DMT_YdcZ 119 krplsltrllGlllllaG 136
                                       +++l++++++G++++++G
  gi|242399735|ref|YP_002995160.1| 251 RETLTPQQIVGAVFIILG 268
                                       345566666666666666 PP

>> PNTB  NAD(P) transhydrogenase beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   2.9   0.00015      0.35     175     231 ..      97     163 ..      33     168 .. 0.74
   2 ?   -2.8   0.1         1   2.3e+03      19      47 ..     223     251 ..     209     277 .. 0.44

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00015
                                       X............X.........XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              PNTB 175 l..........vlfvlaasslllllllvlalllGvllvlpiggaDmpvvisllnsysGlaaaaaGfv 231
                                       l           + +++++ + + +l+++ +++Gv+lv++    D + + ++l  +sGl+ a+ G++
  gi|242399735|ref|YP_002995160.1|  97 LysapvystilGYALFKEKITKAKILALIMVIFGVFLVANLDHWDANKIATVLGLLSGLTYALYGIL 163
                                       022333333323333446666678999999*********************************9986 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXX.. CS
                              PNTB  19 lsspktarrgnllgavgmllavvatllll 47 
                                       l++ + ++++++  +  +++ ++a l+  
  gi|242399735|ref|YP_002995160.1| 223 LQEVEVSKASIISTVEPVVALILAYLIFR 251
                                       44444444444444444333333332211 PP

>> SLC35F  Solute carrier family 35
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9  14.2    0.0018         4     228     296 ..      65     133 ..       3     136 .. 0.80
   2 ?    4.7   0.7    0.0082        18     221     298 ..     139     220 ..     134     221 .. 0.61
   3 ?    3.9   0.8     0.014        31      91     142 ..     220     271 ..     215     276 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0018
                            SLC35F 228 llfvgfalvlfllysllpilikktsatsvnlslltsdlyslliglflfhykvswlyllafvviliGlil 296
                                       ++ + +  ++fl+y l    +k +s  +  l l  + +ys ++g  lf++k++   +la+++++ G++l
  gi|242399735|ref|YP_002995160.1|  65 FYALYGFFAVFLFYILYLYTVKISSVSFAVLLLYSAPVYSTILGYALFKEKITKAKILALIMVIFGVFL 133
                                       444445567899***99999*****999999999********************************987 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0082
                            SLC35F 221 hWdaeiallfvgfalvl.fllysllp.ilikktsatsvnlslltsdlyslliglflf....hykvswlyllafvvil 291
                                       hWda+ +   +g   +l ++ly +l+ i +k++     +  l t  + +l++  f +     + + +l+ laf+ ++
  gi|242399735|ref|YP_002995160.1| 139 HWDANKIATVLGLLSGLtYALYGILAkIAVKNEKPE--EALLYTIGFGALFLAPFSHfkipYESLPYLFGLAFFPTV 213
                                       787777777766655442667765441444443322..22355666666666655431111456789999******* PP

                            SLC35F 292 iGlilys 298
                                       +G+ily 
  gi|242399735|ref|YP_002995160.1| 214 LGYILYN 220
                                       *****96 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.014
                            SLC35F  91 vkayqytsltsvqlldcfaipvvlvlswlflkvryrlvkiigvvvcilGvvl 142
                                        ka q  ++  ++++ +   +v l+l++l+++      +i+g v  ilG  +
  gi|242399735|ref|YP_002995160.1| 220 NKALQEVEVSKASIISTVEPVVALILAYLIFRETLTPQQIVGAVFIILGSLI 271
                                       58999999999999999999999*******************9999999655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       916  (0.0510904); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); 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):               8  [number of targets reported over threshold]
# CPU time: 0.67u 0.38s 00:00:01.05 Elapsed: 00:00:00.54
# Mc/sec: 1556.97
//
Query:       gi|242399736|ref|YP_002995161.1|  [L=440]
Description: Glutamine synthetase [Thermococcus sibiricus MM 739]
Scores for complete 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-124  413.5   0.0   7.5e-124  413.2   0.0    1.1  1  Gln-synt_C  Glutamine synthetase, catalytic domain
    2.1e-20   72.2   0.0    4.2e-20   71.3   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 !  413.2   0.0  8.4e-128  7.5e-124       2     338 ..      98     418 ..      97     437 .. 0.94

  Alignments for each domain:
  == domain 1  score: 413.2 bits;  conditional E-value: 8.4e-128
                                       T-HHHHHHHHHHHHHHTTCEEEEEEEEEEEEESEECCCESSEEEEEEE.TB...B.TSS-TTBHCCCCCTCCHHHHH CS
                        Gln-synt_C   2 rdPRsvlkralarlaeeGltvvvgpElEFflfdkeedkeasksllevdseekgrpaekggyfsvapvdeaedlrrei 78 
                                       +dPR++lk + + l++eG+t+++g+E+EF+lf+k+   e              +  + ggyf++  +d+a+++ r i
  gi|242399736|ref|YP_002995161.1|  98 ADPRRILKSVTEDLQKEGITAYIGVEPEFYLFEKNGSWE-------------LKLPDGGGYFDLLGLDKAREIKRAI 161
                                       69*******************************998733.............567899******************* PP

                                       HHHHHHTT--EECCEEECCCTEEEEEE--EECHHHHHHHHHHHHHHHHHHHHTT-EEE-SSSSSTTS---BEEEEEE CS
                        Gln-synt_C  79 vealealgieveashhEvatgQvEinlkfadalkaaDnvvtfKrvvkevArkhgltatFmpKplegdnGsgmHvhlS 155
                                        +++ ++++  e  hhEv++gQ+Ei+++fadal++aDn+v fK++vk+vA+++gl+atFmpKpl+g++G+gmH+h+S
  gi|242399736|ref|YP_002995161.1| 162 AHYMPSFKLIPEVLHHEVGPGQHEIGFRFADALTTADNIVRFKYLVKAVAESYGLYATFMPKPLFGQPGNGMHFHIS 238
                                       ***************************************************************************** PP

                                       EEECTTEESSB-TTSGGGB-HHHHHHHHHHHHHHHHHHHHHS-SCCHHHHCSSSTTSSSBEEEESS-TTCSEEEE-T CS
                        Gln-synt_C 156 lwdkdgknlfadeddeyalselarhfigGllkhakaltaltaptvnSYkRlvpgyeaPvalawgarNRsallRipas 232
                                       lw +dgkn+f +++   ++se a++figG+l+hakalta+t+ptvnSYkRlvpgyeaPv+++wg+ NRsal+Ripa 
  gi|242399736|ref|YP_002995161.1| 239 LW-NDGKNIFVGDN---GVSEEALYFIGGILEHAKALTAITNPTVNSYKRLVPGYEAPVYISWGYANRSALVRIPAY 311
                                       **.**********8...79********************************************************** PP

                                       SGGCSTEEEECEBTTS-HHHHHHHHHHHHHHHHHTT--------S-SSSS-TTTH..TSS-B--SSHHHHHHHHHCS CS
                        Gln-synt_C 233 kekakrvElRlpdasaNPYLalAallaAgldGienklepgepvekdlyelspeer..kgieelPasleeAlealeed 307
                                       k+++ r+E+R+pd+s+NPY a+A++l Ag+dGi++++ep+++ve+++yel+++ r  +g+e+lP++l  Aleal++d
  gi|242399736|ref|YP_002995161.1| 312 KGNSARIEYRAPDPSTNPYFAFATVLKAGMDGIRRQIEPSAHVEENVYELDDKARalLGVETLPSTLAVALEALKKD 388
                                       *****************************************************9999******************** PP

                                       HHHCCSS-HHHHHHHHHHHHHCHHHHHCT-- CS
                        Gln-synt_C 308 ellkevlgeevieaylalkraEleeleeevs 338
                                       +++ke+lg+  +++++++k +E+e+++e+ +
  gi|242399736|ref|YP_002995161.1| 389 KVVKEALGKA-YHNFIKYKTKEWEAYQEYLE 418
                                       ********86.689************55443 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 !   71.3   0.0   4.6e-24   4.2e-20       3      82 ..      16      91 ..      14      92 .. 0.94

  Alignments for each domain:
  == domain 1  score: 71.3 bits;  conditional E-value: 4.6e-24
                                      -EEEEEEE-SSS-EEEEEEEHHHHHHHTTTT-EEEETTSSTTT------EEEEEEEGGGEEE-SS-SS-.EEEEEEEEE CS
                        Gln-synt_N  3 kfvdlqFtDikgklkhvtipadelsedaleegvsFDGSsiegfaeieeSDmlLkPdlstavidPfreekktarvicdvy 81
                                      +f++l F+Di g  k +++p+++  ed+++eg+sFDGSsi gf++ie+SD+  k d++t+v +P++e   +a v+  +y
  gi|242399736|ref|YP_002995161.1| 16 RFLQLVFVDIDGMAKGMEVPIERY-EDVVKEGISFDGSSIPGFQGIEDSDLTFKADPDTYVEVPWEE---VAKVFGYIY 90
                                      79**********************.*****************************************4...778887777 PP

                                      - CS
                        Gln-synt_N 82 d 82
                                      +
  gi|242399736|ref|YP_002995161.1| 91 K 91
                                      5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (440 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); 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: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 2612.05
//
Query:       gi|242399737|ref|YP_002995162.1|  [L=135]
Description: hypothetical protein TSIB_1762 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-35  121.7   3.3    2.1e-35  121.5   3.3    1.0  1  DUF61     Protein of unknown function DUF61


Domain annotation for each model (and alignments):
>> DUF61  Protein of unknown function DUF61
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.5   3.3   1.2e-39   2.1e-35       2     127 .]       6     132 ..       5     132 .. 0.97

  Alignments for each domain:
  == domain 1  score: 121.5 bits;  conditional E-value: 1.2e-39
                                       S---SHHHHHGGGSBSS-EEHHHHHHT--EEEB.TTS-EEE--HHHHHHHHTTS-GGGGGT-EESEEEEE-SSSSE. CS
                             DUF61   2 rilakeiksinkhlPaerktLkelLeeekptivtkdgsehrfdkeeleklkeilpeelwdklkLPIllemdpelges 78 
                                        i+  ei+++n hlP++rk+L +lLeee+p i +++g++h+f+keele+l ++++e+++d l+LPI+le+++    +
  gi|242399737|ref|YP_002995162.1|   6 EIIHREISRLNLHLPKSRKKLGQLLEEEEPKIQLRNGQFHYFKKEELEYLFSLIEENEKDLLYLPIILEITTL-WHG 81 
                                       58999******************************************************************99.688 PP

                                       .EEEES-HHHHHHHHHHT--.....-SSEEEHH.HHHHHHHH-ST...TEE CS
                             DUF61  79 vylvrgkaevkvvskilgke..reeedelviykpevrelrrklptatqliF 127
                                       +++vrg+  vkvv+k+lg     ee++e+++ ++ + ++r+klpt+t+++F
  gi|242399737|ref|YP_002995162.1|  82 YFKVRGRVAVKVVEKVLGSYdmLEEKTEVILPRYLLPKIRKKLPTTTTYAF 132
                                       *******************99999**************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.38s 00:00:00.91 Elapsed: 00:00:00.55
# Mc/sec: 736.03
//
Query:       gi|242399738|ref|YP_002995163.1|  [L=90]
Description: hypothetical protein TSIB_1763 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.022   14.3   0.2      0.022   14.3   0.2    2.2  2  Baculo_11_kDa  Baculovirus 11 kDa family


Domain annotation for each model (and alignments):
>> Baculo_11_kDa  Baculovirus 11 kDa family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.2   1.2e-06     0.022      27      63 ..       4      40 ..       2      46 .. 0.93
   2 ?   -3.7   4.3      0.51   9.2e+03      43      55 ..      77      89 ..      59      90 .] 0.65

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.2e-06
                     Baculo_11_kDa 27 srNrsflrdFvLvicglvvfvvivlfilLlvvilkna 63
                                      ++Nr +l+ +++ i  + vf   vl i+L++ i +++
  gi|242399738|ref|YP_002995163.1|  4 NKNRILLNYYLFTIPQVTVFAGAVLGIMLILDIKTQT 40
                                      89******************************99865 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 0.51
                     Baculo_11_kDa 43 lvvfvvivlfilL 55
                                      +v f+++ +f+lL
  gi|242399738|ref|YP_002995163.1| 77 FVGFMMLGIFLLL 89
                                      4556666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       930  (0.0518713); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.33s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 541.53
//
Query:       gi|242399739|ref|YP_002995164.1|  [L=560]
Description: hypothetical protein TSIB_1764 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score 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   13.3   1.7       0.14   12.0   0.1    2.3  2  DUF4354          Domain of unknown function (DUF4354)
      0.058   13.4   7.6      0.079   12.9   2.4    2.5  2  DUF3439          Domain of unknown function (DUF3439)
       0.15   11.6   0.0       0.28   10.7   0.0    1.4  1  LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region


Domain annotation for each model (and alignments):
>> DUF4354  Domain of unknown function (DUF4354)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   2.3e-05      0.14       1      55 [.      10      65 ..      10      71 .. 0.73
   2 ?   -1.0   0.2      0.24   1.4e+03      44      66 ..     381     403 ..     358     418 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.3e-05
                                      XXX..XXX...XXXXXXXXXXXXXXXXXXSSEEEEEEEEEEEEEEETTEEEEEEEEEE CS
                           DUF4354  1 Mkkifvas...lllagvvllaslefasvpdkvivyatekdkgsvsveekaqytkafkv 55
                                      M+k++v+    l++ +v    +l f++v++k+ v + +  +gs++v ++a   k+f++
  gi|242399739|ref|YP_002995164.1| 10 MRKVLVVFmtlLIISSVACSQTLLFSTVEEKILVISGDYREGSLTVTNNAD--KDFQI 65
                                      7775554400044444445555689**********************9998..99987 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.24
                                       TTEEEEEEEEEEEEEE-SSS-EE CS
                           DUF4354  44 eekaqytkafkvkvvNlsdseid 66 
                                        +k++ + +f v + N+  +e++
  gi|242399739|ref|YP_002995164.1| 381 LNKTTGVFNFSVVIYNANSEEVT 403
                                       46777778999999999999986 PP

>> DUF3439  Domain of unknown function (DUF3439)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.2     0.022   1.3e+02      52      77 ..     325     350 ..     308     363 .. 0.59
   2 ?   12.9   2.4   1.3e-05     0.079      26      74 ..     453     501 ..     438     508 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.022
                           DUF3439  52 tttttttmpttttlptttkmsmvkvp 77 
                                       t  tt t  t   lp  +k  m kv 
  gi|242399739|ref|YP_002995164.1| 325 TRGTTITKTTIPPLPPGSKKVMSKVS 350
                                       22233333333356777776666664 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 1.3e-05
                           DUF3439  26 vdpdsakcsgsgkpvrsiicpttttttttttttmpttttlptttkmsmv 74 
                                       ++++  k s s      i   ttt+t++ttt+   ttt lpt     ++
  gi|242399739|ref|YP_002995164.1| 453 SNNKEQKISDSLEITPPIASNTTTSTSSTTTSITNTTTPLPTPQERNIL 501
                                       56677788888888888999999999999999999999***98766655 PP

>> LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   4.7e-05      0.28     144     196 ..     496     551 ..     483     558 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 4.7e-05
                   LPG_synthase_TM 144 a...vllllalallllavlalllllllrrrlarlarvlkrlarllarfarklasak 196
                                       +   +l ++a+al+++++++l+l+l+   +++r+ r  ++ ++ l rf+r ++ ++
  gi|242399739|ref|YP_002995164.1| 496 QernILKYFAAALVVIFLFLLALYLMPTSPQKRRERPKPKRRSPLGRFKRPKRPET 551
                                       233499*******************************************9998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (560 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       768  (0.0428356); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.32s 00:00:00.95 Elapsed: 00:00:00.49
# Mc/sec: 3403.08
//
Query:       gi|242399740|ref|YP_002995165.1|  [L=285]
Description: Permease, drug/metabolite transporter (DMT) superfamily [Thermococcus sibiricus MM 739]
Scores for complete 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-41  140.0  42.7    5.5e-22   78.4  16.7    2.0  2  EamA      EamA-like transporter family


Domain annotation for each model (and alignments):
>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.8  18.0   5.6e-23     1e-18       6     136 ..       7     138 ..       2     139 .. 0.91
   2 !   78.4  16.7     3e-26   5.5e-22       2     134 ..     151     280 ..     150     281 .. 0.97

  Alignments for each domain:
  == domain 1  score: 67.8 bits;  conditional E-value: 5.6e-23
                              EamA   6 lallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegkl...aklslkdwllllllgllgtvlaf 79 
                                        ++l++l+w++ ++++++  + ++ l+l+f+r l+++++l++++ lk++ +   a l +++ llll +  l  +l +
  gi|242399740|ref|YP_002995165.1|   7 KIILSMLIWGSVGIFARY--SGLDGLRLAFYRVLLGSLVLIFVHSLKDIMWakkAFLAVRHKLLLLCFLGLVLALNW 81 
                                       589*************99..6**********************888888777666677777777777777899999* PP

                              EamA  80 llffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                       ++ff+a+ +t+ ++a+li +l+P+++++ls+++l+e++t k l+ ++l++lG+l+i 
  gi|242399740|ref|YP_002995165.1|  82 VFFFSAVIYTDIAKATLIYYLAPILVVVLSSVFLRERITRKRLFLVFLAFLGALIIG 138
                                       ******************************************************985 PP

  == domain 2  score: 78.4 bits;  conditional E-value: 3e-26
                              EamA   2 lgillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvla 78 
                                       lg+++all+a+f+a+ +vl ++ l++v++  ltf+++l+a+++l+++++  +  +   + ++++++l+++++ tv+a
  gi|242399740|ref|YP_002995165.1| 151 LGVVFALLGAIFYASVTVLGRY-LKDVDSTYLTFFQLLFATLILFPVLVGVGTFH--VTSSSLAIILIIAIFHTVVA 224
                                       699*****************99.7**************************99999..999***************** PP

                              EamA  79 fllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvll 134
                                        ++++ +lk+++a +a+++++l P+ +++++++l+ge +t+k+++g  lil++ ll
  gi|242399740|ref|YP_002995165.1| 225 LFIYMDGLKEVEANEAAILSYLDPLSAIVYAAILFGEIPTFKTVIGGSLILVASLL 280
                                       ***************************************************99775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       993  (0.0553851); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.68u 0.36s 00:00:01.04 Elapsed: 00:00:00.54
# Mc/sec: 1591.49
//
Query:       gi|242399741|ref|YP_002995166.1|  [L=342]
Description: Probable DNA primase small subunit [Thermococcus sibiricus MM 739]
Scores for 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-16   59.0   0.1    1.9e-14   54.1   0.0    2.2  2  DNA_primase_S  DNA primase small subunit


Domain annotation for each model (and alignments):
>> DNA_primase_S  DNA primase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    2.6   0.0     0.007   1.3e+02      16      66 ..      16      67 ..       7      72 .. 0.78
   2 !   54.1   0.0   1.1e-18   1.9e-14       1     175 [.      96     304 ..      96     305 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.007
                                      HHHHHHHHHHHHHHHHHHHH-----GGGEEEEE--SEE.EEEEE--TTEEES CS
                     DNA_primase_S 16 vcekcwkfvsvavkvldellredfgfkdilwvfsgrrG.fHcwvsdkdarpl 66
                                      ++ k w++ +    + ++l   +fgf+++ +  + r+  fH++  ++d + +
  gi|242399741|ref|YP_002995166.1| 16 YYLKEWNVKKIPSFITKTLENREFGFDHTGEGPNDRKNvFHHIKDLEDYVKI 67
                                      5566677777777777777789****************89988888776665 PP

  == domain 2  score: 54.1 bits;  conditional E-value: 1.1e-18
                                       EEEEEETTT-.....TT--HHHHHHHHHHHHHHHHHHHH-----GGGEEEEE--SEEEEEEE--TTEEES-HHHHHH CS
                     DNA_primase_S   1 FDiDmddydd....cseatvcekcwkfvsvavkvldellredfgfkdilwvfsgrrGfHcwvsdkdarpltdeeraa 73 
                                       FDiD++d++      +   vc++c++++++  k     lredfgf++i++++sgr G+H+ v d++a  l+++ r +
  gi|242399741|ref|YP_002995166.1|  96 FDIDAKDLPLkrcnHETGKVCPICLDDAKELTKDTLLILREDFGFENIHLIYSGR-GYHIRVLDDWALGLDSKAREK 171
                                       9***********44444568**********************************5.********************* PP

                                       HHHH..................................................................HCHHHHC CS
                     DNA_primase_S  74 ivnylnly...........................rplhpflsrs.mlki..vkpvveeiileeqdpf..eikkllr 118
                                       i +y++                             +++ + +s    ++i  +k+  e+ii+  + ++  ++kk + 
  gi|242399741|ref|YP_002995166.1| 172 ILSYISSAeeitfedlqerkillssgyyrvfrlrfGYFIKRVSEYhLRNIglNKRQIEQIIDGRDEIYenFVKKAMI 248
                                       ***999889**9*9999999999999999887777444444444333333227788888888888888999999999 PP

                                       T--------..................-----------------....--------- CS
                     DNA_primase_S 119 llpdkslrekkkweakedivlvllyprldeqvtkgikhllkapfcihgktgnvcvpl 175
                                       +++ +  +  k +  + +   +++  ++d  vt ++k+ l+ p ++h k g v++ +
  gi|242399741|ref|YP_002995166.1| 249 SAFSQGVGY-KTLLRLFSLSTTFSKAYFDGRVTVDVKRILRVPSSLHSKVGLVATYI 304
                                       999999999.666667788899999**************************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 2146.59
//
Query:       gi|242399742|ref|YP_002995167.1|  [L=397]
Description: Eukaryotic-type DNA primase, large subunit [Thermococcus sibiricus MM 739]
Scores for 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-32  111.1   0.0    1.5e-31  109.8   0.0    1.5  1  DNA_primase_lrg  Eukaryotic and archaeal DNA primase, large s
     0.0037   17.4   0.1      0.009   16.2   0.1    1.6  1  Lipoprotein_3    Lipoprotein
  ------ inclusion threshold ------
      0.023   14.1   0.1      0.036   13.4   0.1    1.2  1  GCS              Glutamate-cysteine ligase


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 !  109.8   0.0   2.6e-35   1.5e-31       2     197 ..     142     361 ..     141     390 .. 0.89

  Alignments for each domain:
  == domain 1  score: 109.8 bits;  conditional E-value: 2.6e-35
                                       EEEEEHHHHHHHTT..-GGS-EETTEEEE-HHHHHHHHHHHHHHHHHH..........HHGGGSSS---HHHHHHHC CS
                   DNA_primase_lrg   2 fykvpfedvldlvk..rrrvllkkGyaylpkeeleslllekfrkrlekalestkeslpeleeeikederekleelle 76 
                                       +yk++++d+l + +   +  +++kG++yl+k++l++l+++ f+k+lek ++ ++e ++el+e + + + e +e + e
  gi|242399742|ref|YP_002995167.1| 142 QYKMALKDFLIFNEdsLKGFYVRKGHVYLNKSQLITLWKKSFEKNLEKTVNILYEIREELPEYYMKLYSELSEVARE 218
                                       69999999997777544499*******************************************99999999999999 PP

                                       T--.............TTSSTTGGSHHHHTT--HHHHCCHHHHCCCSS--CHHHHHHHHHHH............... CS
                   DNA_primase_lrg  77 alsesyvaedvqeeedskisaknidklakesfPpCmrelleglkknghlkhegrlqltlFlk............... 138
                                       +++          e+ ++++  + + l+ ++fPpC+r +l+g+  +g +++ +++ lt+Fl+               
  gi|242399742|ref|YP_002995167.1| 219 HFK----------EKFERLGSTTAQPLRFHLFPPCIRITLNGV-PSGLRNYGITVLLTSFLSyaricpnppkrdvkv 284
                                       999..........5555666666799*****************.9999***************************** PP

                                       .....HCT--CHHHHCCCHCHST..HHHHHH.HTH..CHCHHHCC..........-STT--------HHHHHHS... CS
                   DNA_primase_lrg 139 .....diglsldeilelwkeaftrteekFdk.eyr..ynirhnyG..........kegkrtnyspysCekiltkppp 197
                                            d+++  +eil+++ +a +r+++++++ +++  +ni+++ G          ++g++t+y+p++Ceki ++ p+
  gi|242399742|ref|YP_002995167.1| 285 kdcikDLKVIKEEILPVIIQAGNRCSPPLFQdQPNeiKNIWYHLGfgytlepnleDSGNSTWYFPPNCEKIRASAPQ 361
                                       ************************9998888899999**********************************666554 PP

>> Lipoprotein_3  Lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   1.5e-06     0.009      21      50 ..     167     196 ..     155     198 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.5e-06
                     Lipoprotein_3  21 elelnKknlitiLkeayesdpkgtvkvLld 50 
                                       ++ lnK +lit+ k+++e++ ++tv++L++
  gi|242399742|ref|YP_002995167.1| 167 HVYLNKSQLITLWKKSFEKNLEKTVNILYE 196
                                       5679***********************986 PP

>> GCS  Glutamate-cysteine ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1     6e-06     0.036      82     181 ..     133     239 ..     116     249 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6e-06
                               GCS  82 lknekkripksrydsvdlylseekrlreey.ndlelpldeevlkklleagvdellakhiahlf.irdpl.....vif 151
                                        +++++ri + +++  d  + +e++l+  y  + ++ l+++ l +l ++ ++++l k +  l+ ir+ l      ++
  gi|242399742|ref|YP_002995167.1| 133 PEEKERRILQYKMALKDFLIFNEDSLKGFYvRKGHVYLNKSQLITLWKKSFEKNLEKTVNILYeIREELpeyymKLY 209
                                       45566778888888888888777777777746678999************************998987622222577 PP

                               GCS 152 eekieqddekstdhFeniqstnWqtlrfKp 181
                                       +e  e   e+ +++Fe + st  q lrf +
  gi|242399742|ref|YP_002995167.1| 210 SELSEVAREHFKEKFERLGSTTAQPLRFHL 239
                                       77778888999999**************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.34s 00:00:01.03 Elapsed: 00:00:00.55
# Mc/sec: 2184.69
//
Query:       gi|242399743|ref|YP_002995168.1|  [L=252]
Description: RecA superfamily ATPase implicated in signal transduction [Thermococcus sibiricus MM 739]
Scores for complete 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-79  266.2   0.2    2.2e-79  266.1   0.2    1.0  1  ATPase           KaiC
    7.4e-10   38.0   0.7    1.4e-09   37.1   0.7    1.3  1  GvpD             GvpD gas vesicle protein
    3.1e-09   36.7   0.0    4.4e-09   36.2   0.0    1.2  1  AAA_25           AAA domain
    0.00041   19.8   0.0    0.00069   19.0   0.0    1.4  1  DnaB_C           DnaB-like helicase C terminal domain
    0.00087   18.4   0.1     0.0014   17.8   0.1    1.3  1  T2SSE            Type II/IV secretion system protein
     0.0011   18.7   0.0     0.0023   17.6   0.0    1.5  1  Sigma54_activat  Sigma-54 interaction domain
     0.0029   17.9   0.1     0.0053   17.0   0.1    1.5  1  AAA_22           AAA domain
      0.004   16.7   0.0      0.006   16.1   0.0    1.2  1  AAA_7            P-loop containing dynein motor region
     0.0042   17.1   0.1     0.0065   16.5   0.1    1.4  1  AAA_14           AAA domain
      0.006   16.6   0.0      0.015   15.3   0.0    1.4  1  ResIII           Type III restriction enzyme, res subunit
     0.0086   15.8   0.0      0.011   15.4   0.0    1.3  1  AAA_24           AAA domain
  ------ inclusion threshold ------
      0.017   15.4   0.0      0.024   15.0   0.0    1.4  1  AAA_19           AAA domain
      0.021   14.6   0.1      0.043   13.6   0.1    1.5  1  AAA_29           P-loop containing region of AAA domain
      0.024   14.6   0.7      0.085   12.8   0.7    1.8  1  ATPase_2         ATPase domain predominantly from Archaea
      0.029   14.3   0.2       0.09   12.7   0.1    1.8  2  NACHT            NACHT domain
      0.029   14.9   0.2      0.085   13.4   0.2    1.8  1  AAA_18           AAA domain
      0.034   14.5   0.0      0.056   13.8   0.0    1.3  1  AAA_16           AAA ATPase domain
      0.049   13.5   0.8       0.08   12.9   0.7    1.5  1  NTPase_1         NTPase
      0.068   13.2   0.0       0.31   11.0   0.0    2.0  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.085   12.6   0.0       0.13   12.0   0.0    1.3  1  AAA_30           AAA domain
      0.086   12.4   0.2       0.19   11.3   0.1    1.6  2  cobW             CobW/HypB/UreG, nucleotide-binding domain
      0.096   12.8   0.0       0.14   12.3   0.0    1.3  1  AAA_33           AAA domain
        0.1   11.5   0.0       0.17   10.8   0.0    1.3  1  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
       0.11   11.8   0.0        0.2   11.0   0.0    1.3  1  FtsK_SpoIIIE     FtsK/SpoIIIE family
       0.17   11.5   0.0       0.26   10.9   0.0    1.3  1  SRP54            SRP54-type protein, GTPase domain
       0.18   12.0   0.1       0.26   11.5   0.1    1.2  1  AAA_28           AAA domain
        2.9    8.4   6.1        1.3    9.5   3.4    1.8  2  AAA_23           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 !  266.1   0.2   3.2e-82   2.2e-79       1     230 [.      13     249 ..      13     250 .. 0.98

  Alignments for each domain:
  == domain 1  score: 266.1 bits;  conditional E-value: 3.2e-82
                            ATPase   1 vktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekl 77 
                                       +k+gI+g+D++++gG+p+++++litG++GtGKt+f++q+++kgae+ygepgv+v++ee+a+d+r++++++Gwdlek+
  gi|242399743|ref|YP_002995168.1|  13 IKSGIPGFDDLIEGGFPDQSTILITGSTGTGKTTFVAQYIYKGAEEYGEPGVLVSLEERAKDIRREMEQFGWDLEKY 89 
                                       699************************************************************************** PP

                            ATPase  78 eeegklaiidasesaeesaee.....kdkedleelieelaeaikeikakrvviDsitgl.ayeekeavaReilrqlv 148
                                       e++g++ai+d ++s +++++e     +d+ +++++++ + +++k+i+akr+ iDsi ++  + ++e ++R+ l +l 
  gi|242399743|ref|YP_002995168.1|  90 EKQGLIAIVDGVSSISGIPSEekfvlEDTLNVDNFLRYIYRVVKSINAKRLAIDSIPSIaFRLQNEGEIRKVLLKLN 166
                                       *****************999999************************************99**************** PP

                            ATPase 149 rvlkklgvTailvsekss.seeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeIteegi 224
                                       ++l ++gvT++l++e+++ + +++++yg+ee+i+ gv+ Ldl+e++ el+R+l ++kmRgtkhs++++pfeIt++g+
  gi|242399743|ref|YP_002995168.1| 167 TILLEMGVTSLLTTEAPDpKGGKISKYGIEEYISRGVVLLDLQEKNIELKRYLLVRKMRGTKHSMRKYPFEITSRGV 243
                                       *****************99889******************************************************* PP

                            ATPase 225 kvleek 230
                                       +v+++ 
  gi|242399743|ref|YP_002995168.1| 244 VVYPSG 249
                                       ***975 PP

>> GvpD  GvpD gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   0.7   2.2e-12   1.4e-09      11     206 ..      32     239 ..      27     245 .. 0.80

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 2.2e-12
                              GvpD  11 ktllikGaPGtGktlftlrgldvlrre..sdvlyvstrvddetv.seay.....fsgeaeldktalldllkdpleld 79 
                                        t+li G  GtGkt+f  +++    +e  ++ + vs     + +  e+      ++   +    a++d +    +++
  gi|242399743|ref|YP_002995168.1|  32 STILITGSTGTGKTTFVAQYIYKGAEEygEPGVLVSLEERAKDIrREMEqfgwdLEKYEKQGLIAIVDGVSSISGIP 108
                                       589**************999876555422567778866655555245545455544444444667889888889999 PP

                              GvpD  80 ldvdvPie.kldlesllefvdeiaaiatkliialdswelvyeylaerydsPediktvkndlvvlaresgvrlvlvle 155
                                        + +  +e +l+++ +l ++  + +  +   +a+ds    +  +a r ++  +i+ v  +l ++  e gv  +l +e
  gi|242399743|ref|YP_002995168.1| 109 SEEKFVLEdTLNVDNFLRYIYRVVKSINAKRLAIDS----IPSIAFRLQNEGEIRKVLLKLNTILLEMGVTSLLTTE 181
                                       8766555439**************999999******....9************************************ PP

                              GvpD 156 taansr..l......eyivdGvvtlnvkeddrgrlrrdlrleklrGvrignrlqPftla 206
                                       +  ++   +      eyi  Gvv l+++e     l+r l + k+rG +   r +Pf ++
  gi|242399743|ref|YP_002995168.1| 182 APDPKGgkIskygieEYISRGVVLLDLQEK-NIELKRYLLVRKMRGTKHSMRKYPFEIT 239
                                       9876421212223349***********999.7799*********************875 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   0.0   6.7e-12   4.4e-09      12     186 ..      10     179 ..       3     182 .. 0.82

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 6.7e-12
                            AAA_25  12 vadlaapppprrwlvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrr 88 
                                         ++++ +p  ++l++g  p ++++l++G +gtGKtt++ +  ++ a+     g       + ++vs+E++++++rr
  gi|242399743|ref|YP_002995168.1|  10 GKRIKSGIPGFDDLIEGGFPDQSTILITGSTGTGKTTFVAQYIYKGAEEY---G------EPGVLVSLEERAKDIRR 77 
                                       56688999999*****999****************************644...4......3779************* PP

                            AAA_25  89 Rlravg...ealrddarllvldlagv.eslpLfakd.rggtl.ltadvdaleaaieevegvrlvviDplsralggde 159
                                        +++ g   e+++ ++  +++d++++   +p  +k   ++tl ++ +++ + +++++++ ++ + iD++ ++     
  gi|242399743|ref|YP_002995168.1|  78 EMEQFGwdlEKYEKQGLIAIVDGVSSiSGIPSEEKFvLEDTLnVDNFLRYIYRVVKSIN-AKRLAIDSIPSIAFRLQ 153
                                       ****9955566687888899998888777776444223445578999999999999986.9********99777644 PP

                            AAA_25 160 nsnsdvgalvealeriarrtgaavllv 186
                                       n + ++++++ +l+ i  + g++ ll+
  gi|242399743|ref|YP_002995168.1| 154 N-EGEIRKVLLKLNTILLEMGVTSLLT 179
                                       4.5889999999999999999998886 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   0.0     1e-06   0.00069       2      66 ..      13      78 ..      12     162 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1e-06
                                      BXSSTHHHHHHC.TSBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHHHHH CS
                                      xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C  2 lstgfkdLDklt.sGlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeqlvqR 66
                                      +++g   +D+l+ +G+ ++  i+i +  ++Gkt+++ + + + a+++  p +++sle  a+++ + 
  gi|242399743|ref|YP_002995168.1| 13 IKSGIPGFDDLIeGGFPDQSTILITGSTGTGKTTFVAQYIYKGAEEYGEPGVLVSLEERAKDIRRE 78
                                      56778888887725799999************************9999999999***999988654 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 !   17.8   0.1   2.1e-06    0.0014     120     148 ..      22      50 ..      13      70 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.1e-06
                             T2SSE 120 evlrkavrerglilvsGgTgsGKttllya 148
                                       ++++     + +il++G Tg+GKtt++  
  gi|242399743|ref|YP_002995168.1|  22 DLIEGGFPDQSTILITGSTGTGKTTFVAQ 50 
                                       556666667899*************9854 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   3.5e-06    0.0023      21      57 ..      30      67 ..      21      86 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.5e-06
                                      SSS-EEEECSTTSSHH.HHHHHHHHHSTTTTS-EEEEE CS
                   Sigma54_activat 21 tdlsvlitGesGtGKe.llaraiheaskrkekpfvavn 57
                                       ++++litG +GtGK+ ++a+ i++  ++  +p v v 
  gi|242399743|ref|YP_002995168.1| 30 DQSTILITGSTGTGKTtFVAQYIYKGAEEYGEPGVLVS 67
                                      5789***********735799***99998888877665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1     8e-06    0.0053       5      33 ..      31      59 ..      29     170 .. 0.63

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 8e-06
                            AAA_22  5 agilvvtGesGtGKTtllrrlleqldeea 33
                                      ++ +++tG +GtGKTt ++++ ++  ee+
  gi|242399743|ref|YP_002995168.1| 31 QSTILITGSTGTGKTTFVAQYIYKGAEEY 59
                                      6789*****************99864333 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 !   16.1   0.0     9e-06     0.006      32      83 ..      30      80 ..      22      96 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 9e-06
                             AAA_7 32 nkkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdiie 83
                                       +  +l++G+tGtGKt+ + +++ k   e+y    + +s    a+++++ +e
  gi|242399743|ref|YP_002995168.1| 30 DQSTILITGSTGTGKTTFVAQYIYKGA-EEYGEPGVLVSLEERAKDIRREME 80
                                      57789****************988877.677766666666666666666665 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   9.8e-06    0.0065       4      93 ..      33     121 ..      30     160 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 9.8e-06
                            AAA_14   4 ilvitGaRrvGKTtllkqlikell.vkkesilyinldderdkkladpekllelileklkeekktylflDEiqevpew 79 
                                        ++itG   +GKTt++ q+i++      e  + ++l++  ++ +++ e+     lek++ ++  + + D ++ ++++
  gi|242399743|ref|YP_002995168.1|  33 TILITGSTGTGKTTFVAQYIYKGAeEYGEPGVLVSLEERAKDIRREMEQ-FGWDLEKYE-KQGLIAIVDGVSSISGI 107
                                       689*****************99887667889999999977765554432.233334344.47888899999999776 PP

                            AAA_14  80 ekalkslvdegknl 93 
                                        +  k +++++ n+
  gi|242399743|ref|YP_002995168.1| 108 PSEEKFVLEDTLNV 121
                                       66666666655444 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 !   15.3   0.0   2.2e-05     0.015      22      59 ..      29      66 ..      10      83 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.2e-05
                                      .TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEE CS
                            ResIII 22 krdkrglikmaTGtGKTlvaaklierllkkgkeekflf 59
                                       ++  +li   TGtGKT   a+ i++ +++++e  +l+
  gi|242399743|ref|YP_002995168.1| 29 PDQSTILITGSTGTGKTTFVAQYIYKGAEEYGEPGVLV 66
                                      678899********************999999887776 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.7e-05     0.011       4      37 ..      33      74 ..      30     134 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.7e-05
                            AAA_24  4 kiliyGpsgiGKTtlakel........gpkplfidtekGlks 37
                                       ili+G+ g+GKTt+++++        g+  +++ +e+ +k+
  gi|242399743|ref|YP_002995168.1| 33 TILITGSTGTGKTTFVAQYiykgaeeyGEPGVLVSLEERAKD 74
                                      69****************977777666555555566665554 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   3.7e-05     0.024      10      56 ..      31      74 ..      28     166 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.7e-05
                            AAA_19 10 ekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAak 56
                                      ++++l+t+  GtGKT+ + + +    e+ g   e+ +lv++ +rA +
  gi|242399743|ref|YP_002995168.1| 31 QSTILITGSTGTGKTTFVAQYIYKGAEEYG---EPGVLVSLEERAKD 74
                                      6789*************9998877777665...46788888888754 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   6.4e-05     0.043      22      39 ..      31      48 ..      20      53 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.4e-05
                            AAA_29 22 kgatlltGpsGsGKSTll 39
                                      ++++l+tG +G+GK+T++
  gi|242399743|ref|YP_002995168.1| 31 QSTILITGSTGTGKTTFV 48
                                      3479************98 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.7   0.00013     0.085      21     124 ..      32     142 ..      28     171 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00013
                          ATPase_2  21 eiyfiYGpegsGKtaLlkeiienl.edkdkyviyyialreesiskldefie......eeeekkklekal.......g 83 
                                       + ++i+G+ g GKt+++ + i +  e++++  +   +l+e++ +  +e+ e      e++ek+ l   +       g
  gi|242399743|ref|YP_002995168.1|  32 STILITGSTGTGKTTFVAQYIYKGaEEYGEPGVL-VSLEERAKDIRREM-EqfgwdlEKYEKQGLIAIVdgvssisG 106
                                       5789***************999985666664443.34444444433333.336699999999988888888777665 PP

                          ATPase_2  84 iavpkaeleeilk..eksklvfkaielllekikkkgkkiiiii 124
                                       i+ +++ +   l+   +  +  ++i ++ ++i+ k+      i
  gi|242399743|ref|YP_002995168.1| 107 IPSEEKFV---LEdtLNVDNFLRYIYRVVKSINAKRL----AI 142
                                       55555444...34355666667777777777777753....44 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   0.00014      0.09       2      27 ..      33      58 ..      32      68 .. 0.83
   2 ?   -1.3   0.0       2.7   1.8e+03      86      99 ..      97     110 ..      68     186 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00014
                                      CEEEEC-TTTCHHHHHHHHHHHHCTS CS
                             NACHT  2 lvilqGeaGsGKTtLlqklalawaeg 27
                                      +++++G  G GKTt++++ + + ae+
  gi|242399743|ref|YP_002995168.1| 33 TILITGSTGTGKTTFVAQYIYKGAEE 58
                                      89**************9987776665 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.7
                                       EEE-STT-SS-TCH CS
                             NACHT  86 ilDglDelvtdlgq 99 
                                       i+Dg+  ++ ++++
  gi|242399743|ref|YP_002995168.1|  97 IVDGVSSISGIPSE 110
                                       56666665555555 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   0.00013     0.085       1      87 [.      34     150 ..      34     170 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00013
                            AAA_18   1 IlltGtpGvGKtt.lakeLskrl.gf...gvnlrdvakenglllevdpealdeskrldedkldklldaleenss... 69 
                                       Il+tG  G+GKtt +a+++ k   ++   gv ++   + ++++ e +++ +d +k  +++ l +++d++  +s    
  gi|242399743|ref|YP_002995168.1|  34 ILITGSTGTGKTTfVAQYIYKGAeEYgepGVLVSLEERAKDIRREMEQFGWDLEK-YEKQGLIAIVDGVSSISGips 109
                                       99***********668999887767788866665555555666666666222222.222222444444444444344 PP

                            AAA_18  70 .......................aleegknlvidghlaele 87 
                                                              ++ ++k l id++++  +
  gi|242399743|ref|YP_002995168.1| 110 eekfvledtlnvdnflryiyrvvKSINAKRLAIDSIPSIAF 150
                                       44444444444444444444477777777777777777766 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   8.4e-05     0.056      24      62 ..      29      74 ..      20     112 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.4e-05
                            AAA_16 24 p..elvllsGesGvGKsslvrel.lr...alekdggif.lrgkcdq 62
                                      p  + +l++G  G+GK++ v +  ++   ++ + g+++ l++++++
  gi|242399743|ref|YP_002995168.1| 29 PdqSTILITGSTGTGKTTFVAQYiYKgaeEYGEPGVLVsLEERAKD 74
                                      25589**************955404422233333555555555555 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.7   0.00012      0.08       2      22 ..      34      54 ..      33     162 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00012
                                      EEEE--TTSSHHHHHHHHHHH CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlel 22
                                      ++iTG+ G+GKtT+v + + +
  gi|242399743|ref|YP_002995168.1| 34 ILITGSTGTGKTTFVAQYIYK 54
                                      89************9886655 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00047      0.31      19      40 ..      31      52 ..      11      60 .. 0.83
   2 ?   -1.6   0.0       3.8   2.5e+03      80     102 ..     190     211 ..     186     231 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00047
                                      TEEEEEEESTTSSHHHHHHHHH CS
                              TsaE 19 gdvilLeGdLGaGKTtlvrgla 40
                                      +++il++G  G+GKTt+v + +
  gi|242399743|ref|YP_002995168.1| 31 QSTILITGSTGTGKTTFVAQYI 52
                                      4579*************97654 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.8
                                       HHHCTTCCCCSTSCEEEEETGGG CS
                              TsaE  80 leelgleeyleeeavvlvEWpek 102
                                       + + g+eey++ ++vvl   +ek
  gi|242399743|ref|YP_002995168.1| 190 ISKYGIEEYIS-RGVVLLDLQEK 211
                                       56789999994.46888888777 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00019      0.13      20      58 ..      33      72 ..      28      97 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00019
                            AAA_30 20 vavltGpAGtGKttalkal.reaweaaggrviglAptgka 58
                                      + ++tG  GtGKtt ++++  + +e+ g++ ++++ +++a
  gi|242399743|ref|YP_002995168.1| 33 TILITGSTGTGKTTFVAQYiYKGAEEYGEPGVLVSLEERA 72
                                      5789************998566666668877777777766 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00028      0.19       2      22 ..      33      54 ..      32      67 .. 0.80
   2 ?   -3.1   0.0       7.5     5e+03     109     122 ..      88     101 ..      86     115 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00028
                                      EEEEEESTTCCHHHHHHHHH.C CS
                              cobW  2 vtvltGflGsGKTtLlnhll.e 22
                                      ++++tG+ G+GKTt++ +++ +
  gi|242399743|ref|YP_002995168.1| 33 TILITGSTGTGKTTFVAQYIyK 54
                                      578**************99952 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 7.5
                                       CCCECEEEEEEETT CS
                              cobW 109 dltldavvavvDak 122
                                       +++ ++++a+vD+ 
  gi|242399743|ref|YP_002995168.1|  88 KYEKQGLIAIVDGV 101
                                       56778999999984 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   0.00021      0.14       2      32 ..      34      70 ..      34     149 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00021
                            AAA_33  2 vllvGlpGsGKstlaerllkklg......avllssdt 32
                                      +l+ G  G+GK+t++ +++ k +      +vl+s  +
  gi|242399743|ref|YP_002995168.1| 34 ILITGSTGTGKTTFVAQYIYKGAeeygepGVLVSLEE 70
                                      5788*************95443334447777777666 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00025      0.17      15      36 ..      31      52 ..      29      66 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00025
                     TrwB_AAD_bind 15 tqhilivGttGsGKtqalekll 36
                                      ++ ili+G+tG+GKt+ + + +
  gi|242399743|ref|YP_002995168.1| 31 QSTILITGSTGTGKTTFVAQYI 52
                                      6789************987754 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00031       0.2      39      58 ..      27      50 ..       8      55 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00031
                                      -.....SEEEE--TTSSHHHHHHH CS
                      FtsK_SpoIIIE 39 a....shllvaGatgsGKStalnt 58
                                           s +l+ G+tg+GK+t++  
  gi|242399743|ref|YP_002995168.1| 27 GfpdqSTILITGSTGTGKTTFVAQ 50
                                      45566789*************965 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00039      0.26       2      25 ..      32      55 ..      31      75 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00039
                                      EEEEEEESTTSSHHHHHHHHHHHH CS
                             SRP54  2 nvillvGlqGaGKTttlaKLaall 25
                                      + il+ G +G+GKTt +a+   + 
  gi|242399743|ref|YP_002995168.1| 32 STILITGSTGTGKTTFVAQYIYKG 55
                                      679**************9876555 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1    0.0004      0.26       2      40 ..      34      72 ..      33      96 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0004
                            AAA_28  2 ivitGgestGKTtlleaLaargypvvpEaareileekla 40
                                      i itG  +tGKTt +++   +g + + E++  +  e+ a
  gi|242399743|ref|YP_002995168.1| 34 ILITGSTGTGKTTFVAQYIYKGAEEYGEPGVLVSLEERA 72
                                      89***********99876655555555555555555554 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   3.4     0.002       1.3      18      36 ..      30      48 ..      20      50 .. 0.86
   2 ?   -1.4   0.0       4.1   2.7e+03     115     138 ..      69      92 ..      50     172 .. 0.54

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.002
                            AAA_23 18 skgltlItGpNGaGKTTil 36
                                      ++   lItG +G+GKTT++
  gi|242399743|ref|YP_002995168.1| 30 DQSTILITGSTGTGKTTFV 48
                                      56678************86 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 4.1
                            AAA_23 115 deleqfisellgskkiilnlilfl 138
                                       +e+ + i+++++++   l+ +  +
  gi|242399743|ref|YP_002995168.1|  69 EERAKDIRREMEQFGWDLEKYEKQ 92 
                                       444444444444444433333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      609  (0.0339673); expected 358.6 (0.02)
Passed Vit filter:                       117  (0.00652574); 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: 0.67u 0.35s 00:00:01.02 Elapsed: 00:00:00.52
# Mc/sec: 1452.07
//
Query:       gi|242399744|ref|YP_002995169.1|  [L=260]
Description: RecA superfamily ATPase implicated in signal transduction [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-27   96.0   0.2      7e-27   94.3   0.2    1.7  1  ATPase        KaiC
    4.4e-05   23.1   0.0    0.00011   21.8   0.0    1.6  2  AAA_25        AAA domain
      7e-05   22.1   0.1     0.0024   17.1   0.0    2.0  2  PAXNEB        PAXNEB protein
      0.001   19.3   0.0      0.026   14.8   0.0    2.3  2  Roc           Ras of Complex, Roc, domain of DAPkinase
     0.0032   17.2   0.1       0.02   14.6   0.0    2.1  2  AAA_24        AAA domain
     0.0052   16.8   0.1       0.01   15.9   0.1    1.8  1  AAA_14        AAA domain
  ------ inclusion threshold ------
      0.014   14.6   0.0      0.028   13.7   0.0    1.5  1  Rad51         Rad51
      0.017   14.6   0.0      0.026   14.0   0.0    1.2  1  RecA          recA bacterial DNA recombination protein
      0.049   12.8   0.6       0.09   11.9   0.6    1.7  1  G-alpha       G-protein alpha subunit
      0.057   12.8   0.0       0.34   10.2   0.0    2.2  3  FtsK_SpoIIIE  FtsK/SpoIIIE family
      0.073   12.5   0.0       0.17   11.3   0.0    1.5  1  TniB          Bacterial TniB protein
      0.093   12.2   0.2        1.2    8.5   0.0    2.1  2  Pox_A32       Poxvirus A32 protein
      0.098   12.7   0.0       0.23   11.5   0.0    1.6  2  TsaE          Threonylcarbamoyl adenosine biosynthesis protei
       0.14   12.4   0.0       0.41   10.9   0.0    1.7  2  AAA_22        AAA domain
       0.15   12.4   0.0        0.2   12.0   0.0    1.6  1  AAA_16        AAA ATPase domain
       0.19   11.9   0.6       0.88    9.8   0.1    2.4  3  PABP          Poly-adenylate binding protein, unique 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 !   94.3   0.2   6.3e-30     7e-27       8     226 ..      25     256 ..      20     260 .] 0.80

  Alignments for each domain:
  == domain 1  score: 94.3 bits;  conditional E-value: 6.3e-30
                            ATPase   8 lDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekleeegkla 84 
                                       +D++l gGip+g+v+l+ G+p +GKt+f  qF+++++ + g +++   ++ p  ++  na  +Gw+l    +e +l+
  gi|242399744|ref|YP_002995169.1|  25 IDHLLMGGIPRGSVILLIGDPKSGKTTFISQFIYNQLIS-GANVISLLIDIPRYEFVSNALDFGWNLITNLNE-RLY 99 
                                       799*********************************999.**************************8666666.6** PP

                            ATPase  85 iidasesaeesaee........kdkedleelieelaeaikeika.........krvviDsitglayeekeavaReil 144
                                       i+da++++++   +         d  d+ ++i+ +++   +i               i sit++  e++++++ + l
  gi|242399744|ref|YP_002995169.1| 100 ILDAYTQRIRGGPKfsfteeaiPDIRDTTHIIDIIKDTTTKILLnnphiedplIVGAISSITPMFFETEKKEIYKFL 176
                                       *******9987666888777773334444444444444444332222344222233588999998899999999*** PP

                            ATPase 145 rqlvrvlkklgvTailvsekssseeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeIte 221
                                         l+ + +k++++ ++ ++  s+ e  +   + + ivdg+i ++l e++ +l+R+l++ +m +t+h    +p++It+
  gi|242399744|ref|YP_002995169.1| 177 EDLKAFSHKNKQVWLIEMN--SGVEDPQVETIIKAIVDGIIEMKLFEENRNLQRYLRVYGMKRTRHVLSWIPYDITD 251
                                       ***********99998777..44444444444444****************************************** PP

                            ATPase 222 egikv 226
                                       +gi  
  gi|242399744|ref|YP_002995169.1| 252 RGILL 256
                                       **965 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   9.9e-08   0.00011      23      53 ..      26      56 ..      10      69 .. 0.88
   2 ?   -3.2   0.0       4.6   5.2e+03     153     182 ..     159     188 ..     152     193 .. 0.64

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 9.9e-08
                            AAA_25 23 rwlvkgllpagelallaGapgtGKttlaldl 53
                                      ++l++g +p+g+++ll+G+p++GKtt+ ++ 
  gi|242399744|ref|YP_002995169.1| 26 DHLLMGGIPRGSVILLIGDPKSGKTTFISQF 56
                                      67889999*******************9986 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 4.6
                            AAA_25 153 ralgg.densnsdvgalvealeriarrtgaa 182
                                       ++++   e++++++ +++e+l+ +++ ++  
  gi|242399744|ref|YP_002995169.1| 159 SITPMfFETEKKEIYKFLEDLKAFSH-KNKQ 188
                                       55555557778888999999999854.4444 PP

>> PAXNEB  PAXNEB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.036        40      26      43 ..      25      42 ..      22      60 .. 0.80
   2 !   17.1   0.0   2.2e-06    0.0024     227     289 ..     165     225 ..     117     236 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.036
                            PAXNEB 26 LDklLgGGLplGsillie 43
                                      +D+lL GG+p Gs++l+ 
  gi|242399744|ref|YP_002995169.1| 25 IDHLLMGGIPRGSVILLI 42
                                      8************98864 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 2.2e-06
                            PAXNEB 227 eeskpedllkFLhsLrallrssnlvalitlplsliarssslvrkieqlvDtvieLesfagsek 289
                                        e+++++++kFL  L+a+  +++ v li + + +   ++++ + i+ +vD++ie++ f++ ++
  gi|242399744|ref|YP_002995169.1| 165 FETEKKEIYKFLEDLKAFSHKNKQVWLIEMNSGVE--DPQVETIIKAIVDGIIEMKLFEENRN 225
                                       478899*************************9998..********************998554 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   2.3e-05     0.026       2      24 ..      39      61 ..      38      77 .. 0.90
   2 ?    2.2   0.0      0.18     2e+02      70     110 ..     158     202 ..     154     212 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.3e-05
                                      EEEESSTTSSHHHHHHCHCT-CC CS
                               Roc  2 vvlvGdsgvGKtsllkrfvedkf 24
                                      ++l+Gd ++GKt+++++f+ ++ 
  gi|242399744|ref|YP_002995169.1| 39 ILLIGDPKSGKTTFISQFIYNQL 61
                                      79*****************9875 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.18
                                       TTT-HHHHCTSC..EEEEEEEGH..HHHCHHHHHHHHHHHCSSS- CS
                               Roc  70 rslhplylreaa..lailvydsr..ssenlkeWlkelkkvagksp 110
                                       +s++p++++ ++  ++ ++ d +  s++n + Wl e+++ +++ +
  gi|242399744|ref|YP_002995169.1| 158 SSITPMFFETEKkeIYKFLEDLKafSHKNKQVWLIEMNSGVEDPQ 202
                                       678899987555114445556441245788899999988766554 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   1.8e-05      0.02       4      27 ..      38      61 ..      35      87 .. 0.85
   2 ?    0.2   0.0      0.48   5.4e+02     151     183 ..     193     230 ..     166     242 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.8e-05
                            AAA_24  4 kiliyGpsgiGKTtlakelgpkpl 27
                                       il++G++++GKTt+++++ ++ l
  gi|242399744|ref|YP_002995169.1| 38 VILLIGDPKSGKTTFISQFIYNQL 61
                                      79****************955554 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.48
                            AAA_24 151 klgkkt.....anelkeevDlvlranlkredkvgervl 183
                                       ++++++        +k +vD +++++l +e  + +r+l
  gi|242399744|ref|YP_002995169.1| 193 EMNSGVedpqvETIIKAIVDGIIEMKLFEENRNLQRYL 230
                                       44444444444677888888888888887775555554 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1     9e-06      0.01       3      71 ..      37     102 ..      35     220 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 9e-06
                            AAA_14   3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflD 71 
                                        ++++ G  ++GKTt++ q+i+++l++  +++ + +d +r++  ++    l++  +++++ ++++ +lD
  gi|242399744|ref|YP_002995169.1|  37 SVILLIGDPKSGKTTFISQFIYNQLISGANVISLLIDIPRYEFVSNA---LDFGWNLITNLNERLYILD 102
                                       5789999999***************9999999999999888655544...3444444444445556666 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.5e-05     0.028      25      57 ..      24      56 ..       6      73 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.5e-05
                                      HHHHHHTSSEESSSEEEEEESTTSSHHHHHHHH CS
                             Rad51 25 klDelLgGGietgsiteifGefrsGktqlchtl 57
                                       +D+lL+GGi+ gs+  ++G+ +sGkt +  ++
  gi|242399744|ref|YP_002995169.1| 24 LIDHLLMGGIPRGSVILLIGDPKSGKTTFISQF 56
                                      58*************************998775 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   2.3e-05     0.026      30      76 ..      16      59 ..       7      81 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.3e-05
                                      ---EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHH CS
                              RecA 30 kvetissGslaldialGiGGlpkGriieiyGpessGkttlalhaiae 76
                                      kve i++    +d  l +GG+p+G +i + G   sGktt+  + i +
  gi|242399744|ref|YP_002995169.1| 16 KVERIPTN--LIDH-LLMGGIPRGSVILLIGDPKSGKTTFISQFIYN 59
                                      55666553..3444.557*********************98887765 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.6   8.1e-05      0.09      25      44 ..      38      57 ..       6     245 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.1e-05
                                      EEEEEESTTSSHHHHHHHHH CS
                           G-alpha 25 kllllGqseSGKsTilkqlk 44
                                       +ll+G  +SGK+T++ q+ 
  gi|242399744|ref|YP_002995169.1| 38 VILLIGDPKSGKTTFISQFI 57
                                      59****************95 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00031      0.34      41      65 ..      38      62 ..      15      83 .. 0.82
   2 ?   -0.8   0.0      0.72   8.1e+02     103     161 ..      81     143 ..      63     162 .. 0.69
   3 ?   -1.4   0.0       1.1   1.2e+03     190     212 ..     203     225 ..     166     237 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00031
                                      SEEEE--TTSSHHHHHHHHHHHHHT CS
                      FtsK_SpoIIIE 41 hllvaGatgsGKStalntLilSlat 65
                                       +l++G ++sGK+t++  +i + + 
  gi|242399744|ref|YP_002995169.1| 38 VILLIGDPKSGKTTFISQFIYNQLI 62
                                      5899****************98765 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.72
                                       HHHHHHHHHHHHHHHHHHHHHHHTT-SSHHH....HHHHHHHHHHTT---B-TT-........ CS
                      FtsK_SpoIIIE 103 eralraleeLvkemeeryalfreagvrsiaa....ydgeiaedpldifgdvflvlDnyddlaa 161
                                        +al +  +L+  ++er  ++++   r + +    + +e+ +d+ d   +++++ D + ++  
  gi|242399744|ref|YP_002995169.1|  81 SNALDFGWNLITNLNERLYILDAYTQRIRGGpkfsFTEEAIPDIRDTTHIIDIIKDTTTKILL 143
                                       566666777788888887777766554444466777788888888888877777777666554 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 1.1
                                       ---EEEEEEC-HHHHHHHHHHH. CS
                      FtsK_SpoIIIE 190 krpslvvivderieLrlaapkds 212
                                        +  + +ivd  ie+ l+ ++ +
  gi|242399744|ref|YP_002995169.1| 203 VETIIKAIVDGIIEMKLFEENRN 225
                                       34456678888888888887775 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00015      0.17      19      59 ..      20      60 ..      14      67 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00015
                              TniB 19 ilerLeeLleypkrkrmpnlllvGdsnnGKtmivekFarlh 59
                                      i ++L + l +    r + +ll+Gd++ GKt+ +++F  ++
  gi|242399744|ref|YP_002995169.1| 20 IPTNLIDHLLMGGIPRGSVILLIGDPKSGKTTFISQFIYNQ 60
                                      55566666666667788899*****************8665 PP

>> Pox_A32  Poxvirus A32 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0    0.0011       1.2      16      85 ..      39     109 ..      36     146 .. 0.76
   2 ?    1.7   0.1      0.13   1.5e+02     169     200 ..     163     194 ..     157     223 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0011
                           Pox_A32  16 lalvGgsGsGktvyLls.LlrtlvkkykhifLltpvknseYdkyvwPdhinkvtseeeleYsLsatkekie 85 
                                       + l+G   sGkt+++ + ++++l+++   i Ll+ +   e+ +       n +t+ +e  Y L a+ ++i+
  gi|242399744|ref|YP_002995169.1|  39 ILLIGDPKSGKTTFISQfIYNQLISGANVISLLIDIPRYEFVSNALDFGWNLITNLNERLYILDAYTQRIR 109
                                       5699***********8735789*************999999888888888888888888888888888886 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.13
                           Pox_A32 169 mslkgskkkllkvlnilrsaeqkkrkvliied 200
                                       m  +++kk++ k+l+ l++ ++k+++v +ie 
  gi|242399744|ref|YP_002995169.1| 163 MFFETEKKEIYKFLEDLKAFSHKNKQVWLIEM 194
                                       5567899**************9*****98874 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00021      0.23       6      44 ..      16      61 ..       9      81 .. 0.75
   2 ?   -3.0   0.0       6.2     7e+03      91     103 ..     186     198 ..     169     215 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00021
                                      HHHHHHHHHHHCH.......TEEEEEEESTTSSHHHHHHHHHHHTT CS
                              TsaE  6 etealgkklakal.......gdvilLeGdLGaGKTtlvrglakalg 44
                                      ++e++ ++l ++l       g+vilL Gd  +GKTt++ +++ +  
  gi|242399744|ref|YP_002995169.1| 16 KVERIPTNLIDHLlmggiprGSVILLIGDPKSGKTTFISQFIYNQL 61
                                      55556666666556666677789***************99876554 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 6.2
                                       TSCEEEEETGGGG CS
                              TsaE  91 eeavvlvEWpekl 103
                                       +++v+l+E  + +
  gi|242399744|ref|YP_002995169.1| 186 NKQVWLIEMNSGV 198
                                       3358888877664 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00037      0.41       5      52 ..      36      82 ..      34     111 .. 0.70
   2 ?   -1.9   0.0       3.3   3.7e+03      52      52 ..     202     202 ..     167     251 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00037
                            AAA_22  5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst...s 52
                                       ++++++G + +GKTt + ++ ++  +      +++  +++++p  +   +
  gi|242399744|ref|YP_002995169.1| 36 GSVILLIGDPKSGKTTFISQFIYNQLIS----GANVISLLIDIPRYEfvsN 82
                                      5789***************999987433....2344444666666555545 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.3
                            AAA_22  52 s 52 
                                        
  gi|242399744|ref|YP_002995169.1| 202 Q 202
                                       1 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00018       0.2       6      45 ..      14      57 ..      12     206 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00018
                            AAA_16  6 eeeleqL.lsalervrsgrp...elvllsGesGvGKsslvrell 45
                                      ee +e++ +++++ + +g+    +++ll+G++ +GK++ + ++ 
  gi|242399744|ref|YP_002995169.1| 14 EEKVERIpTNLIDHLLMGGIprgSVILLIGDPKSGKTTFISQFI 57
                                      66778888888888888877788****************98774 PP

>> PABP  Poly-adenylate binding protein, unique domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       2.7     3e+03      50      62 ..       6      18 ..       2      19 .. 0.79
   2 ?   -2.0   0.0       3.7   4.1e+03      38      48 ..      70      81 ..      49     101 .. 0.65
   3 ?    9.8   0.1   0.00079      0.88      34      60 ..     159     185 ..     118     189 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 2.7
                              PABP 50 llesdeeLrekve 62
                                        +s+ eL+ekve
  gi|242399744|ref|YP_002995169.1|  6 SSSSNSELEEKVE 18
                                      568999*****97 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.7
                              PABP 38 MLLemdnsel.l 48
                                      +L++++ +e   
  gi|242399744|ref|YP_002995169.1| 70 LLIDIPRYEFvS 81
                                      677777777633 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.00079
                              PABP  34 KITGMLLemdnsellellesdeeLrek 60 
                                        IT M  e +++e+ ++le+ +++  k
  gi|242399744|ref|YP_002995169.1| 159 SITPMFFETEKKEIYKFLEDLKAFSHK 185
                                       6*******************9999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       729  (0.0406604); expected 358.6 (0.02)
Passed bias filter:                      628  (0.0350271); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); 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: 0.67u 0.38s 00:00:01.05 Elapsed: 00:00:00.55
# Mc/sec: 1426.48
//
Query:       gi|242399745|ref|YP_002995170.1|  [L=101]
Description: hypothetical protein TSIB_1770 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.32s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 619.00
//
Query:       gi|242399746|ref|YP_002995171.1|  [L=393]
Description: tRNA/rRNA methyltransferase [Thermococcus sibiricus MM 739]
Scores for complete 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   80.1   0.0    1.2  1  Methyltrans_SAM  S-adenosylmethionine-dependent methyltransfe
    1.2e-19   70.8   0.3      2e-19   70.2   0.3    1.4  1  Met_10           Met-10+ like-protein
    4.9e-16   58.3   0.0    1.1e-15   57.2   0.0    1.6  1  PUA_3            PUA-like domain
      2e-15   56.5   0.5    4.9e-15   55.3   0.2    1.9  2  PUA              PUA domain
    5.1e-15   55.6   0.2    9.8e-15   54.7   0.1    1.5  2  Methyltransf_31  Methyltransferase domain
    2.7e-13   50.0   0.0    5.1e-13   49.1   0.0    1.5  1  Cons_hypoth95    Conserved hypothetical protein 95
    3.4e-12   46.4   0.2    5.9e-12   45.6   0.2    1.3  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    3.4e-11   43.0   0.0    6.2e-11   42.1   0.0    1.5  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
    2.4e-09   37.8   0.0    5.3e-09   36.7   0.0    1.6  1  Methyltransf_25  Methyltransferase domain
    1.8e-08   33.9   0.9    3.9e-08   32.7   0.9    1.6  1  Methyltransf_3   O-methyltransferase
    1.4e-06   28.0   0.1    2.5e-06   27.2   0.1    1.4  1  MTS              Methyltransferase small domain
    1.7e-06   27.4   0.1    2.4e-06   27.0   0.1    1.2  1  TRM              N2,N2-dimethylguanosine tRNA methyltransfera
    1.2e-05   25.1   0.1     0.0025   17.5   0.0    2.8  2  UPF0020          Putative RNA methylase family UPF0020
     0.0001   22.3   0.1    0.00026   21.0   0.1    1.7  1  Methyltransf_18  Methyltransferase domain
    0.00011   22.8   0.0    0.00032   21.3   0.0    1.9  1  Methyltransf_11  Methyltransferase domain
    0.00039   20.6   0.1    0.00074   19.7   0.1    1.4  1  FtsJ             FtsJ-like methyltransferase
    0.00097   19.4   0.2     0.0045   17.2   0.1    2.2  1  UPF0113          UPF0113 PUA domain
     0.0048   16.7   0.0     0.0082   16.0   0.0    1.4  1  Methyltransf_23  Methyltransferase domain
     0.0085   15.7   2.1       0.13   11.9   0.0    2.6  2  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
  ------ inclusion threshold ------
      0.019   14.9   0.8      0.054   13.5   0.2    2.1  3  ADH_zinc_N       Zinc-binding dehydrogenase


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 !   80.1   0.0   1.7e-25   1.6e-22      76     237 ..     167     331 ..     103     369 .. 0.83

  Alignments for each domain:
  == domain 1  score: 80.1 bits;  conditional E-value: 1.7e-25
                   Methyltrans_SAM  76 evlvgeldespvvvesglkyqldigrnqnfglfldmrlgrdwvqenak.dknvlnlfaytcgfsvaaiaggaskvvn 151
                                        vl g+ + + +++e   k+ +d+ r q++g+fld r  r  +++  k + +vl++f+yt gf++ a   ga+kv+ 
  gi|242399746|ref|YP_002995171.1| 167 RVLLGKEKYRTIIKEGQAKFIVDM-RGQKTGFFLDQRENRIALEKYIKgGEKVLDVFTYTGGFAIHAAVAGAEKVIA 242
                                       5899*******************8.99**************99999883589************************* PP

                   Methyltrans_SAM 152 vdmargslnkgrdnhrlnghdlrrvsflgydifkswgkikksg.pydlviidppsfqkgsfaltkd...ykkilrrl 224
                                       vd + +++++ ++n +ln+ d ++++fl    f    k++k+g ++d+vi+dpp+f +    l +    y ++  + 
  gi|242399746|ref|YP_002995171.1| 243 VDKSPAAIEQAKENAKLNDVD-GKMDFLVGSAFSIMEKMQKKGeKFDIVILDPPAFVQHEKDLKRGlraYFNVNYQG 318
                                       *******************99.789999999********9888469**********877655544311133333344 PP

                   Methyltrans_SAM 225 pellveggevlac 237
                                        +l+ +gg +++ 
  gi|242399746|ref|YP_002995171.1| 319 LKLVKDGGILVTA 331
                                       4555666665554 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.2   0.3   2.2e-22     2e-19       9     164 ..     117     277 ..     112     370 .. 0.79

  Alignments for each domain:
  == domain 1  score: 70.2 bits;  conditional E-value: 2.2e-22
                                       EEEEEB-TT.SSHHHHHHHHHHHHHS.S-SCEEEE-S-SBTTTTB..--EE.EEEES-.SEEEEEETTEEEEEET.. CS
                            Met_10   9 vvilnlree.lkeykkvigevildkt.kvktvlrkvsevegefRt..fele.vlaGsdstetihkEngcrfklDv.. 78 
                                       ++ +++++  ++++k  ++e+il+++ +++tv++k++  +++ R+  +e+e vl G+++  ti kE   +f +D+  
  gi|242399746|ref|YP_002995171.1| 117 IASIQISSAgMEKFKMNVAEAILEIEpEIETVFEKNTG-RSRRREglPEIErVLLGKEKYRTIIKEGQAKFIVDMrg 192
                                       6666766551566**********************999.777776335554389********************955 PP

                                       TTS---GGGHHHHHHHHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEE CS
                            Met_10  79 skvyfsskleaErerlaklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkp 155
                                       +k  f     + r  l k ++ ge V+dvf   G fai +a+ + a++v+a+d+ P++++  ken klN+v+ ++  
  gi|242399746|ref|YP_002995171.1| 193 QKTGFFLDQRENRIALEKYIKGGEKVLDVFTYTGGFAIHAAV-AGAEKVIAVDKSPAAIEQAKENAKLNDVDGKMDF 268
                                       58999999999999999************************9.77888*************************9976 PP

                                       EES-GGG-- CS
                            Met_10 156 ileDgrevi 164
                                       + + +  ++
  gi|242399746|ref|YP_002995171.1| 269 LVGSAFSIM 277
                                       666555554 PP

>> PUA_3  PUA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.2   0.0   1.2e-18   1.1e-15       3      64 .]       3      64 ..       1      64 [. 0.95

  Alignments for each domain:
  == domain 1  score: 57.2 bits;  conditional E-value: 1.2e-18
                             PUA_3  3 LkkkaekrlrqGhPwvfsneiasvegeledGdvVdvfsekgkflGtGyynpqskiavRilsr 64
                                      +  +a k++ +G   vf++ + ++ege+++GdvV+v+s++gkflG+G+ np+s i +R++++
  gi|242399746|ref|YP_002995171.1|  3 VDAQAYKAIDKGAMIVFKKGVIRTEGEIKPGDVVEVYSRNGKFLGKGFANPNSNIMIRLITK 64
                                      5677889****************************************************996 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.3   0.2   5.4e-18   4.9e-15       4      74 .]       2      74 ..       1      74 [. 0.92
   2 ?   -2.8   0.0       7.1   6.3e+03       2      16 ..     176     190 ..     175     192 .. 0.78

  Alignments for each domain:
  == domain 1  score: 55.3 bits;  conditional E-value: 5.4e-18
                                      EE-HHHHHHHHTT-.EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHH.HCTSEEEEEEEEE CS
                               PUA  4 vvddgAvkallsga.sLlapGvvevegdfeegdvVaivdedgelvavGlanysseelak.ikggksveiervl 74
                                       vd++A+ka+ +ga  ++ +Gv+++eg++++gdvV++++++g+++++G an +s+ + + i+++k v+i+r+l
  gi|242399746|ref|YP_002995171.1|  2 YVDAQAYKAIDKGAmIVFKKGVIRTEGEIKPGDVVEVYSRNGKFLGKGFANPNSNIMIRlITKKKDVKIDREL 74
                                      69************8899*************************************9865166*******9986 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 7.1
                                       EEEE-HHHHHHHHTT CS
                               PUA   2 rvvvddgAvkallsg 16 
                                       r ++++g +k+++ +
  gi|242399746|ref|YP_002995171.1| 176 RTIIKEGQAKFIVDM 190
                                       568999999999875 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       7.9   7.1e+03      39      54 ..      77      93 ..      55     125 .. 0.62
   2 !   54.7   0.1   1.1e-17   9.8e-15       2     122 ..     213     337 ..     212     371 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 7.9
                   Methyltransf_31 39 eaielAre.naqklgld 54
                                      + i++A+e + + lg+d
  gi|242399746|ref|YP_002995171.1| 77 KRIKKANEyRKKILGYD 93
                                      44555555333344444 PP

  == domain 2  score: 54.7 bits;  conditional E-value: 1.1e-17
                   Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdiee.lekl.ledekf 75 
                                       + g +vlD+ + tG +++ +a  +    +v+ +D s+ aie+A+ena+ + +d  + F +g++++ +ek   + ekf
  gi|242399746|ref|YP_002995171.1| 213 KGGEKVLDVFTYTGGFAIHAA--VAGAEKVIAVDKSPAAIEQAKENAKLNDVDgKMDFLVGSAFSiMEKMqKKGEKF 287
                                       67899****************..555678************************************999876666*** PP

                   Methyltransf_31  76 Dlilsnevl..naladpdkile.......eiervlkpggilliedprllaelpakv 122
                                       D+++ + +   ++ +d++  l+       +  +++k+ggil++++++      ++v
  gi|242399746|ref|YP_002995171.1| 288 DIVILDPPAfvQHEKDLKRGLRayfnvnyQGLKLVKDGGILVTASCS------QHV 337
                                       ******55556******************889***************......332 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.1   0.0   5.7e-16   5.1e-13      38     122 ..     210     295 ..     204     355 .. 0.86

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 5.7e-16
                                       CCHC.C-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-E CS
                     Cons_hypoth95  38 aeie.garvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkee 113
                                       ++i+ g++vLD+f  +G+ ++ A+  ga+k+++v+k+++a+++ ken +  +++++++ l+ +a++ ++k  kk+e+
  gi|242399746|ref|YP_002995171.1| 210 KYIKgGEKVLDVFTYTGGFAIHAAVAGAEKVIAVDKSPAAIEQAKENAKLNDVDGKMDFLVGSAFSIMEKMQKKGEK 286
                                       55441578********************************************************************* PP

                                       EEEEEE--S CS
                     Cons_hypoth95 114 fdivflDPP 122
                                       fdiv lDPP
  gi|242399746|ref|YP_002995171.1| 287 FDIVILDPP 295
                                       ********* PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   0.2   6.6e-15   5.9e-12     154     231 ..     207     291 ..     206     293 .. 0.83

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 6.6e-15
                              PrmA 154 aleklvkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklev......alseellk. 223
                                       alek++k+ge+vlDv t +G  ai aa  ga+kv+avD  + A++ akeNa+lN+v+ k++        + e+++k 
  gi|242399746|ref|YP_002995171.1| 207 ALEKYIKGGEKVLDVFTYTGGFAIHAAVAGAEKVIAVDKSPAAIEQAKENAKLNDVDGKMDFlvgsafSIMEKMQKk 283
                                       79*******************************************************98876223322122333324 PP

                              PrmA 224 eekadviv 231
                                        ek+d+++
  gi|242399746|ref|YP_002995171.1| 284 GEKFDIVI 291
                                       78999997 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 !   42.1   0.0     7e-14   6.2e-11       3      81 ..     217     296 ..     215     337 .. 0.95

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 7e-14
                   Methyltransf_15   3 vilDlfsGaGGnviqfalv.fekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklklekikvdlvflS 78 
                                        +lD+f+ +GG +i+ a    ekvia+++++  +++a++Na++ +v+ k+++ +g+ f++++k++ +  k+d+v+l 
  gi|242399746|ref|YP_002995171.1| 217 KVLDVFTYTGGFAIHAAVAgAEKVIAVDKSPAAIEQAKENAKLNDVDGKMDFLVGSAFSIMEKMQKKGEKFDIVILD 293
                                       79***************996789****************************************************** PP

                   Methyltransf_15  79 pPw 81 
                                       pP 
  gi|242399746|ref|YP_002995171.1| 294 PPA 296
                                       *95 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.0     6e-12   5.3e-09       1      92 [.     218     314 ..     218     318 .. 0.89

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 6e-12
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBC....CGBSSSTTTEEEEEEE CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgda....edlpfedgsfDlvvss 71 
                                       vLd+ + tG +++++a + g++kv++vD s++++e+a+e+a+ +++  +++f++g+a    e+++ + ++fD+v++ 
  gi|242399746|ref|YP_002995171.1| 218 VLDVFTYTGGFAIHAAVA-GAEKVIAVDKSPAAIEQAKENAKLNDVdgKMDFLVGSAfsimEKMQKKGEKFDIVIL- 292
                                       89**************99.69********************9999999********9888788999**********. PP

                                       ST.GGGSSHHHHHHHHHHHHHH CS
                   Methyltransf_25  72 ga.lhhlsdedlekalkeiarv 92 
                                            + +++dl++ l+  ++v
  gi|242399746|ref|YP_002995171.1| 293 DPpAFVQHEKDLKRGLRAYFNV 314
                                       4545556788999998877765 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.9   4.4e-11   3.9e-08      45     155 ..     212     330 ..     201     360 .. 0.83

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 4.4e-11
                                       HHT--EEEEE--TTSHHHHHHHTTS-TT-EEEEEES-HHHHHHHHHHHHHTT-GGGEEEEES-HHHHHHHHHTSSS- CS
                    Methyltransf_3  45 lvnakrvleiGvftGyslLatalalPeDGkilaididreayeialkfiqkagvaekieliegdalkvLeelvkdkkl 121
                                       + +  +vl++ ++tG  ++  a a     k++a+d+ + a e a++  +   v+ k+++ +g a +++e++ k+ + 
  gi|242399746|ref|YP_002995171.1| 212 IKGGEKVLDVFTYTGGFAIHAAVAGA--EKVIAVDKSPAAIEQAKENAKLNDVDGKMDFLVGSAFSIMEKMQKKGE- 285
                                       667889********988888887755..59*****************************************99885. PP

                                       --EEEE......EE-S-GG......GHHHHHHHHHHTEEEEEEEEE CS
                    Methyltransf_3 122 pefDfi......fvDaDks......syvnyyeklleLvkvGgliai 155
                                        +fD++      fv  +k+      +y n   ++l+Lvk Gg+++ 
  gi|242399746|ref|YP_002995171.1| 286 -KFDIVildppaFVQHEKDlkrglrAYFNVNYQGLKLVKDGGILVT 330
                                       .89997233333565666433333367777789*********9975 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.1   2.7e-09   2.5e-06      32     116 ..     215     305 ..     204     353 .. 0.74

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 2.7e-09
                                       CSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-S...TTTTST..TS-EEEE CS
                               MTS  32 sgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..vevvasd...vleeve..ekkfdli 101
                                        +kvlD+ + +G  ++++a +  e +v +vd++ +A+e aken++ n+++  ++++  +   ++e+++   +kfd++
  gi|242399746|ref|YP_002995171.1| 215 GEKVLDVFTYTGGFAIHAAVAGAE-KVIAVDKSPAAIEQAKENAKLNDVDgkMDFLVGSafsIMEKMQkkGEKFDIV 290
                                       568**************9998888.8************************88555555400044444422479**** PP

                                       EE---STTTCHCHHH CS
                               MTS 102 vsNPPfhagkatela 116
                                       +  PP   +++++l+
  gi|242399746|ref|YP_002995171.1| 291 ILDPPAFVQHEKDLK 305
                                       *****7666655443 PP

>> TRM  N2,N2-dimethylguanosine tRNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.1   2.6e-09   2.4e-06      51     128 ..     216     294 ..     112     298 .. 0.88

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 2.6e-09
                                       EEEEESS-TTSHHHHHHHHH-S-EEEEEEE-S-HHHHHHHHHHHHHTT--GGEEEE-S-HHHHHC...--SS-EEEE CS
                               TRM  51 ikvldaLsasGlRaiRfalEvpgvkevlaNDisekAvelikeNvklneveeivvineddAnvlla...ekkkrfdvi 124
                                        kvld ++ +G  ai  a+   g+++v+a D s+ A+e  keN+kln+v+  + +  + A  +++   +k ++fd++
  gi|242399746|ref|YP_002995171.1| 216 EKVLDVFTYTGGFAIHAAVA--GAEKVIAVDKSPAAIEQAKENAKLNDVDGKMDFLVGSAFSIMEkmqKKGEKFDIV 290
                                       68999999999999998865..****************************88888888999998876688899**** PP

                                       EE-- CS
                               TRM 125 DlDP 128
                                        lDP
  gi|242399746|ref|YP_002995171.1| 291 ILDP 294
                                       ***9 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0      0.04        36      64      91 ..      65     101 ..      42     121 .. 0.82
   2 !   17.5   0.0   2.8e-06    0.0025      51     130 ..     237     295 ..     211     303 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.04
                                       S.........HHHHHHHHHHHH--EEEEES-HHHHHH CS
                           UPF0020  64 e.........lkaeaeeearaelklygsDldrrvvqg 91 
                                       +         lk++++++++++ k+ g D+  r++ g
  gi|242399746|ref|YP_002995171.1|  65 KkdvkidrelLKKRIKKANEYRKKILGYDKAYRMIYG 101
                                       13334557778999999999*************9965 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 2.8e-06
                                       TT--TTTT----SSHHHHHHHHHHHH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--....STTS--- CS
                           UPF0020  51 aniapgllrefvlelkaeaeeearaelklygsDldrrvvqgareNaekagvgdliefsqadaakLr....lkegevd 123
                                       a                          k++++D+ ++++++a+eNa+   v+++++f +  a ++     +k +++d
  gi|242399746|ref|YP_002995171.1| 237 A-------------------------EKVIAVDKSPAAIEQAKENAKLNDVDGKMDFLVGSAFSIMekmqKKGEKFD 288
                                       3.........................3479******************************999888776444459** PP

                                       EEEE--- CS
                           UPF0020 124 vivtnpP 130
                                       +++ +pP
  gi|242399746|ref|YP_002995171.1| 289 IVILDPP 295
                                       ******9 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.1   2.9e-07   0.00026       8      80 ..     208     279 ..     202     292 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.9e-07
                   Methyltransf_18   8 iaslvekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGleklke 80 
                                       + ++++ g++v+D+ t  g  +i+++  g a+kvia+D ++ ++e+aken++ ++++ k+++ +++ ++ +++
  gi|242399746|ref|YP_002995171.1| 208 LEKYIKGGEKVLDVFTYTGGFAIHAAVAG-AEKVIAVDKSPAAIEQAKENAKLNDVDGKMDFLVGSAFSIMEK 279
                                       5689999*****************99655.78*********************************99987764 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   3.6e-07   0.00032       7      85 ..     225     312 ..     219     330 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 3.6e-07
                                       TSHHHHHHHHTT.SEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECC....CTSS-TT-EEEEEEES..-CCC- CS
                   Methyltransf_11   7 tGrlaealakrg.arvvgvDlskemlklakekaseegl..kvefvvadae....klpfednsfDlvvsse..vlhhv 74 
                                       tG +a + a +g ++v++vD s++++++ake+a+ +++  k++f+v++a     k++ + ++fD+v++    +++h 
  gi|242399746|ref|YP_002995171.1| 225 TGGFAIHAAVAGaEKVIAVDKSPAAIEQAKENAKLNDVdgKMDFLVGSAFsimeKMQKKGEKFDIVILDPpaFVQHE 301
                                       56666666766779**************************9******99833334778889******9866699999 PP

                                       CCHHHHHHHHH CS
                   Methyltransf_11  75 edpekalkeia 85 
                                       +d+++ l+   
  gi|242399746|ref|YP_002995171.1| 302 KDLKRGLRAYF 312
                                       99988887655 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.1   8.3e-07   0.00074      18     146 ..     211     343 ..     178     349 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 8.3e-07
                                       -S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS.....HHHTTEEEE....CS-CCCSSHHHHHCHCH.H CS
                              FtsJ  18 lfkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm.....aplpgvtti....qgditdpetiekikeal.s 84 
                                        +k g++v+D+   +Gg++  ++   ga  kv+avD  p      +  ++ ++     ++d++  ++   ++++  +
  gi|242399746|ref|YP_002995171.1| 211 YIKGGEKVLDVFTYTGGFAIHAAVA-GA-EKVIAVDKSPAaieqaK--ENAKLNdvdgKMDFLVGSAFSIMEKMQkK 283
                                       3577899***************999.87.9*********9665321..33333355889999655555544432204 PP

                                       HSSEEEEEE--S-SS-CHHHHHHHHHCCCCHHHHCCHCCCCECCCEEEECCCHCCCHHHHHH CS
                              FtsJ  85 erkvdlvvsDgapdvsgvhdldeylqsqLllaalelalkllkpggtfvlkifrgeeteallk 146
                                       ++k+d+v+ D   +v+  +dl+  l++  + +    +lkl+k gg++v+  + ++ + +++k
  gi|242399746|ref|YP_002995171.1| 284 GEKFDIVILDPPAFVQHEKDLKRGLRA--YFNVNYQGLKLVKDGGILVTASCSQHVDMQMFK 343
                                       599********9999998888888875..555666677999999999998877666556655 PP

>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1     5e-06    0.0045      18      56 ..      18      60 ..      17      74 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 5e-06
                           UPF0113 18 vlkesilkitesvkenqvvvVlnengeplGiGkirkdt....k 56
                                      v+k+++++ ++++k ++vv V++ ng++lG G ++ ++    +
  gi|242399746|ref|YP_002995171.1| 18 VFKKGVIRTEGEIKPGDVVEVYSRNGKFLGKGFANPNSnimiR 60
                                      8*********************************886654441 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   9.1e-06    0.0082      14      88 ..     206     292 ..     192     355 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 9.1e-06
                   Methyltransf_23  14 erllpklraggrvLdiGcGtGillevlrengf.svtgvDlspeaveiae..........kakkaqkdqfdeq.eaae 78 
                                         l ++ + g +vLd+ + tG ++ +++  g+ +v++vD sp+a+e a+          k ++ + + f  + + ++
  gi|242399746|ref|YP_002995171.1| 206 IALEKYIKGGEKVLDVFTYTGGFAIHAAVAGAeKVIAVDKSPAAIEQAKenaklndvdgKMDFLVGSAFSIMeKMQK 282
                                       44556678889*********************99*************998888888777444444444444422344 PP

                   Methyltransf_23  79 pqgkfdlIvl 88 
                                       + +kfd+++l
  gi|242399746|ref|YP_002995171.1| 283 KGEKFDIVIL 292
                                       5559998875 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 ?   -2.6   0.4       4.1   3.7e+03      95     121 ..      62      90 ..      57      93 .. 0.77
   2 !   11.9   0.0   0.00014      0.13       9     144 ..     215     338 ..     207     361 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 4.1
                                       TTT-TCHHHH--..HHHHHHHHHHHHHHH CS
                   Methyltr_RsmB-F  95 irrdpdvklrrk..ekdiaqlaklqkell 121
                                       i +++dvk+ r+  +k i++ ++ +k++l
  gi|242399746|ref|YP_002995171.1|  62 ITKKKDVKIDREllKKRIKKANEYRKKIL 90 
                                       78889999988755678888888888877 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00014
                                       T-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--.SEEEEES-CTCCHHHHCC....EEE CS
                   Methyltr_RsmB-F   9 eetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvt.ntivleaDarkidkvlgg..elfDr 82 
                                       +e++lD+ +  Gg   h a + + + +v+Avd++   +++ +en k   v  ++  l + a  i + + +  e+fD 
  gi|242399746|ref|YP_002995171.1| 215 GEKVLDVFTYTGGFAIHAA-V-AGAEKVIAVDKSPAAIEQAKENAKLNDVDgKMDFLVGSAFSIMEKMQKkgEKFDI 289
                                       6889999999999887755.3.6888999999999999999999877666654555555444444444333699999 PP

                                       EEEEE--CCGGGTTT-TCHHHH--HHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEES--STT CS
                   Methyltr_RsmB-F  83 iLlDaPCsgtgvirrdpdvklrrkekdiaqlaklqkellsaaidllkkgGvlvYsTCsvlve 144
                                       ++lD P      +         ++ekd+++  +   ++    ++l+k gG+lv + Cs +v+
  gi|242399746|ref|YP_002995171.1| 290 VILDPPA----FV---------QHEKDLKRGLRAYFNVNYQGLKLVKDGGILVTASCSQHVD 338
                                       9999995....33.........4555555555555566666778999999999999999987 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       6.8   6.1e+03      74      87 ..       6      19 ..       5      56 .. 0.73
   2 ?   13.5   0.2     6e-05     0.054       7      63 ..     230     291 ..     225     297 .. 0.76
   3 ?   -3.3   0.0       9.3   8.3e+03      76      90 ..     319     333 ..     317     345 .. 0.63

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 6.8
                                      HHHHCEEEEEEEEE CS
                        ADH_zinc_N 74 aalkllkpgGrlvv 87
                                      +a+k++++g ++v+
  gi|242399746|ref|YP_002995171.1|  6 QAYKAIDKGAMIVF 19
                                      68888888888887 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 6e-05
                                       HHHHHHTT-.EEEEEESSHHHHHHHHHT.......T.ESEEEETTTC.HHHHHHHHHTTTSSEEEEE CS
                        ADH_zinc_N   7 vqlAkalGa.eviavdsseeklelakkl.......G.adevinykea.dlverikeltggegvdvvf 63 
                                       +  A+ +Ga +viavd s+  +e+ak++       G +d+++ +  a ++ e++++    e++d+v+
  gi|242399746|ref|YP_002995171.1| 230 IH-AAVAGAeKVIAVDKSPAAIEQAKENaklndvdGkMDFLVGS--AfSIMEKMQKKG--EKFDIVI 291
                                       44.5567888*****************97888777767777766..446666666655..7899886 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 9.3
                                       HHCEEEEEEEEECSC CS
                        ADH_zinc_N  76 lkllkpgGrlvvvGg 90 
                                       lkl+k gG lv+   
  gi|242399746|ref|YP_002995171.1| 319 LKLVKDGGILVTASC 333
                                       778888888777664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       783  (0.0436723); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); 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: 0.67u 0.34s 00:00:01.01 Elapsed: 00:00:00.52
# Mc/sec: 2290.12
//
Query:       gi|242399747|ref|YP_002995172.1|  [L=248]
Description: SAM-dependent methyltransferase, [Thermococcus sibiricus MM 739]
Scores for complete 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-11   41.8   0.1    2.1e-10   40.4   0.1    1.7  1  Methyltransf_10  RNA methyltransferase
    3.2e-07   30.1   0.0    4.3e-07   29.6   0.0    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    2.8e-06   27.0   0.0    7.9e-05   22.3   0.0    2.1  2  MTS              Methyltransferase small domain
    3.1e-06   27.0   0.0    4.9e-06   26.4   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    5.4e-06   27.0   0.0    1.6e-05   25.5   0.0    1.7  2  Methyltransf_25  Methyltransferase domain
    0.00019   21.4   0.0    0.00036   20.5   0.0    1.4  1  Methyltransf_18  Methyltransferase domain
    0.00021   21.1   0.0     0.0003   20.6   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    0.00028   20.1   0.0    0.00041   19.5   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase
     0.0011   18.5   0.1     0.0019   17.7   0.1    1.4  1  Methyltransf_4   Putative methyltransferase
     0.0031   17.2   0.0     0.0041   16.8   0.0    1.3  1  Cons_hypoth95    Conserved hypothetical protein 95
     0.0033   18.0   0.0      0.009   16.6   0.0    1.7  1  Methyltransf_11  Methyltransferase domain
     0.0049   16.6   0.0     0.0073   16.1   0.0    1.3  1  Methyltransf_16  Lysine methyltransferase
     0.0066   15.8   0.0     0.0095   15.3   0.0    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
  ------ inclusion threshold ------
      0.011   15.6   0.0      0.024   14.5   0.0    1.5  2  Methyltransf_23  Methyltransferase domain
       0.02   14.9   0.1      0.053   13.5   0.1    1.7  1  ADH_zinc_N       Zinc-binding dehydrogenase
      0.022   14.0   0.0      0.038   13.3   0.0    1.3  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
      0.033   14.9   0.0      0.075   13.8   0.0    1.6  1  Methyltransf_12  Methyltransferase domain
      0.056   13.3   0.0      0.096   12.6   0.0    1.4  1  UPF0146          Uncharacterised protein family (UPF0146)


Domain annotation for each model (and alignments):
>> Methyltransf_10  RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4   0.1   2.1e-13   2.1e-10     103     190 ..      82     164 ..      13     168 .. 0.88

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 2.1e-13
                                       --EEEEES-TTTTHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHHT.T-TTTEEEEE--TT-SCCHHSSTTSS-EE CS
                   Methyltransf_10 103 qvraldiGvGanCiyPllGvteyGWrfvgsevddvslasakaivesnsklsdaiklrkqkekkaifdglieeneryd 179
                                         r+l+iG+G   +  ++ ++ +    +++e+dd  +++aka++++n       k++  k + +i++g+i + e++d
  gi|242399747|ref|YP_002995172.1|  82 GERVLEIGTGHTAMMAIMAAKIFKCDVIATEIDDEFFEYAKANISAN-----NSKVQLIKSNGEIINGIIPKREIFD 153
                                       5799*******************************************.....44667778899************** PP

                                       EEEE-S---SS CS
                   Methyltransf_10 180 vtlCnPPfhas 190
                                       v    PP+++ 
  gi|242399747|ref|YP_002995172.1| 154 VIFSAPPYYEK 164
                                       ********975 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0   4.3e-10   4.3e-07     154     231 ..      74     156 ..      65     158 .. 0.84

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 4.3e-10
                              PrmA 154 aleklvkegeevlDvGtG.SGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseell.....ke 224
                                       +l +++++ge+vl +GtG ++++ai aak+   +v+a+ iD+   + ak+N++ N+ + +l ++ ++e++     k+
  gi|242399747|ref|YP_002995172.1|  74 FLKTFLRGGERVLEIGTGhTAMMAIMAAKIFKCDVIATEIDDEFFEYAKANISANNSKVQL-IKSNGEIIngiipKR 149
                                       688999************6689**********************************99988.555555553333358 PP

                              PrmA 225 ekadviv 231
                                       e +dvi+
  gi|242399747|ref|YP_002995172.1| 150 EIFDVIF 156
                                       8899996 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   7.9e-08   7.9e-05      26     110 ..      77     164 ..      70     174 .. 0.83
   2 ?    2.5   0.0     0.094        94     116     149 ..     184     217 ..     177     236 .. 0.68

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 7.9e-08
                                       HCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-S..TTTTST..TS-E CS
                               MTS  26 tlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasd..vleeve..ekkf 98 
                                       t+     ++vl +G+G  ++ a +a++  + +v ++++d +  e ak+n++an+ +v++++s+  +++ +    + f
  gi|242399747|ref|YP_002995172.1|  77 TFLR-GGERVLEIGTGHTAMMAIMAAKIFKCDVIATEIDDEFFEYAKANISANNSKVQLIKSNgeIINGIIpkREIF 152
                                       4444.4678*************************************************999983345665422578* PP

                                       EEEEE---STTT CS
                               MTS  99 dlivsNPPfhag 110
                                       d+i s PP+ ++
  gi|242399747|ref|YP_002995172.1| 153 DVIFSAPPYYEK 164
                                       ********9765 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.094
                                       HHHHHHHHHHHHHEEEEEEEEEEEETTSCHHHHH CS
                               MTS 116 avaeeliaeAkeaLkegGeLliVanrklgyesll 149
                                       + a ++++eA+e+++e+G+  +    k    + +
  gi|242399747|ref|YP_002995172.1| 184 EFAVRILREAREYMTENGKVALFLPDKPSLLKSI 217
                                       67889**************988766555444444 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.0     5e-09   4.9e-06       3     116 ..      81     215 ..      79     242 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 5e-09
                   Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieelekl.ledekfDli 78 
                                        g rvl++G+G  +    +a   ++k++v+  +i+ e  e+A++n + ++++ v++ +++ e ++    ++e fD+i
  gi|242399747|ref|YP_002995172.1|  81 GGERVLEIGTGHTAMMAIMA-AKIFKCDVIATEIDDEFFEYAKANISANNSK-VQLIKSNGEIINGIiPKREIFDVI 155
                                       6889****************.66789*********************99998.888886555555444567****** PP

                   Methyltransf_31  79 lsn.........evl..........naladpdkileeiervlkpggilliedpr...lla 116
                                       +s          +vl          +   +   il+e+ ++++++g +++  p+   ll+
  gi|242399747|ref|YP_002995172.1| 156 FSAppyyekptkGVLtpiegigggvYGEEFAVRILREAREYMTENGKVALFLPDkpsLLK 215
                                       ***99998888844466677788889**********************999999333333 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   1.6e-08   1.6e-05       1      71 [.      85     158 ..      85     171 .. 0.85
   2 ?   -2.2   0.0       7.1     7e+03      26      45 ..     182     201 ..     175     209 .. 0.60

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 1.6e-08
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBS...SSTTTEEEEEEE CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlp...fedgsfDlvvss 71 
                                       vL++G+G+  +++ +a+++ k++v++++i++e+ e+a++++++++ +v++++ + e ++    + + fD+++s+
  gi|242399747|ref|YP_002995172.1|  85 VLEIGTGHTAMMAIMAAKIFKCDVIATEIDDEFFEYAKANISANNSKVQLIKSNGEIINgiiPKREIFDVIFSA 158
                                       8******99888887777647***********************99******999876544368889****995 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 7.1
                                       EEESSHHHHHHHHHHHHHTT CS
                   Methyltransf_25  26 gvDiseemleaareraeeeg 45 
                                       g +++ + l++are + e+g
  gi|242399747|ref|YP_002995172.1| 182 GEEFAVRILREAREYMTENG 201
                                       44555555566665555444 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   3.6e-07   0.00036       9      74 ..      76     139 ..      70     158 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 3.6e-07
                   Methyltransf_18   9 aslvekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdG 74 
                                        ++++ g+rv+ iGt H  + + ++ +     via++i ++ +e ak+ni+ ++   k++++ s+G
  gi|242399747|ref|YP_002995172.1|  76 KTFLRGGERVLEIGTGHTAMMAIMAAKIFKCDVIATEIDDEFFEYAKANISANNS--KVQLIKSNG 139
                                       56788899*********877777776666679******************99875..778877777 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 !   20.6   0.0     3e-07    0.0003      69     134 ..      75     140 ..      63     167 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 3e-07
                                       TT..--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GG CS
                              PCMT  69 le..lkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGr 134
                                       l+  l+ g+rvLe+G+G     a++a  +  k+ v++ e   e+ e ak+n+ +++++ v+++ + G+
  gi|242399747|ref|YP_002995172.1|  75 LKtfLRGGERVLEIGTGHTAMMAIMAAKIF-KCDVIATEIDDEFFEYAKANISANNSK-VQLIKSNGE 140
                                       4456899**********9888888877664.5679*****************988765.555555553 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   4.1e-07   0.00041      22      84 ..      73     138 ..      62     143 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 4.1e-07
                                       HHHHH-GGTTSEEEEES-TTTCCHHHH.HCC-.SEEEEE-S-HHHHHHHHCHTT.TCCCEEEE-S- CS
                            RrnaAD  22 IldklnleekltvleigpGkGilTeeL.akra.kqvvvlElderLakllqkkls.kdeklkvvhqD 84 
                                       I+ k+ l+    vleig+G  ++ +++ ak++   v + E+d ++++  ++++s +++k+++++ +
  gi|242399747|ref|YP_002995172.1|  73 IFLKTFLRGGERVLEIGTGHTAMMAIMaAKIFkCDVIATEIDDEFFEYAKANISaNNSKVQLIKSN 138
                                       666777888899***************899997799*****************99999***99987 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   1.9e-06    0.0019       5      79 ..      85     157 ..      82     167 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.9e-06
                                       EEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCCHHHHCS-TTSEEEEEEE CS
                    Methyltransf_4   5 vleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgdalkvllelledgslekifil 79 
                                       vleiG+G   ++  +A k  ++++++ Ei  +  +++ ++i a++ k +++++++  ++++ +++++++  + + 
  gi|242399747|ref|YP_002995172.1|  85 VLEIGTGHTAMMAIMAAKIFKCDVIATEIDDEFFEYAKANISANNSK-VQLIKSNG-EIINGIIPKREIFDVIFS 157
                                       89***************************************998765.99999998.999999999988777665 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   4.1e-06    0.0041      65     132 ..     106     169 ..      71     214 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 4.1e-06
                                       SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEEEE--SSSTTCH.HHH CS
                     Cons_hypoth95  65 kkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdivflDPPyakellieev 132
                                         +++ e d+e ++  k+n+++ + +    +l++++ e ++    k e fd++f  PPy ++ + + v
  gi|242399747|ref|YP_002995172.1| 106 CDVIATEIDDEFFEYAKANISANNSK---VQLIKSNGEIINGIIPKREIFDVIFSAPPYYEKPT-KGV 169
                                       468999**************999844...7889999999999999**************98865.555 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0     9e-06     0.009       1      67 [.      86     157 ..      86     159 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 9e-06
                                       EEET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTS...S-TT-EEEEEE CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg..arvvgvDlskemlklakekaseeglkvefvvadaeklp...fednsfDlvvs 67 
                                       L++G+G  ++++ +a +   ++v+++++++e+ ++ak+++s ++ kv++++++ e ++    + + fD+++s
  gi|242399747|ref|YP_002995172.1|  86 LEIGTGHTAMMAIMAAKIfkCDVIATEIDDEFFEYAKANISANNSKVQLIKSNGEIINgiiPKREIFDVIFS 157
                                       89****9999999995555************************999******99965334134479999998 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   7.3e-06    0.0073      47     101 ..      82     133 ..      49     170 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 7.3e-06
                   Methyltransf_16  47 klsvlELGsG.tGlvGlavaellpeakviltDlee.llellkknielnknalkskvk 101
                                       + +vlE+G G t ++ +++a+   +++vi t +++   e  k ni +n++    kv+
  gi|242399747|ref|YP_002995172.1|  82 GERVLEIGTGhTAMMAIMAAKI-FKCDVIATEIDDeFFEYAKANISANNS----KVQ 133
                                       679*******566777777776.9*********98799*********873....333 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   9.6e-06    0.0095      54     110 ..      73     130 ..      69     140 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 9.6e-06
                                       HHTTTT--TT-EEEEES-TTSHHHH.HHHHHH--EEEEEES-HHHHHHHHHHHHTS-S CS
                              CMAS  54 ileklelkpGmtlLdiGcGWGslvr.raverydvkvvglTlSkeqaklakkrvdeldl 110
                                       i+ k  l+ G+++L+iG+G  +++   a++ +  +v++  + +e  ++ak+++ + ++
  gi|242399747|ref|YP_002995172.1|  73 IFLKTFLRGGERVLEIGTGHTAMMAiMAAKIFKCDVIATEIDDEFFEYAKANISANNS 130
                                       566788999***********998861566679******************99988764 PP

>> Methyltransf_23  Methyltransferase 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      60 ..      79     121 ..      57     167 .. 0.72
   2 ?   -2.4   0.0       3.6   3.6e+03     101     124 ..     189     212 ..     180     232 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.4e-05
                   Methyltransf_23  20 lraggrvLdiGcGtGillevlrengf..svtgvDlspeaveia 60 
                                       lr g rvL+iG+G+  ++ +++++ f  +v++ ++++e  e a
  gi|242399747|ref|YP_002995172.1|  79 LRGGERVLEIGTGHTAMMAIMAAKIFkcDVIATEIDDEFFEYA 121
                                       78889****************7764434999999987644433 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.6
                   Methyltransf_23 101 llrqiatllkpgGylllseplasl 124
                                        lr +++++ ++G + l  p++++
  gi|242399747|ref|YP_002995172.1| 189 ILREAREYMTENGKVALFLPDKPS 212
                                       566667777777766665555543 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   5.3e-05     0.053       4      32 ..      95     123 ..      93     141 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.3e-05
                                       HHHHHHHHHTT-EEEEEESSHHHHHHHHH CS
                        ADH_zinc_N   4 laavqlAkalGaeviavdsseeklelakk 32 
                                       ++a+++Ak++++ via+ +++e +e+ak 
  gi|242399747|ref|YP_002995172.1|  95 MMAIMAAKIFKCDVIATEIDDEFFEYAKA 123
                                       69************************996 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 ?   13.3   0.0   3.8e-05     0.038      30      94 ..      84     151 ..      77     158 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.8e-05
                                       EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH...TTTCECEEHCHHHHHHHHHHHH-SE CS
                       AlaDh_PNT_C  30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleqles...lgakfvevlksqeellaeavkeadv 94 
                                       +vl iG G   + Ai +ak ++ +V +++++ +  e+ ++    +++ v+++ks+ e ++  + + ++
  gi|242399747|ref|YP_002995172.1|  84 RVLEIGTGHTAMMAIMAAKIFKCDVIATEIDDEFFEYAKAnisANNSKVQLIKSNGEIINGIIPKREI 151
                                       6888*********************************99998766667999****9999999888665 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   7.5e-05     0.075       1      71 [.      86     156 ..      86     159 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.5e-05
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg....ssfDlvv 71 
                                       LeiG+G  ++++ +++k+  +++++++i+ +++e ak+ +++++     +v+l + + +   g     + fD+++
  gi|242399747|ref|YP_002995172.1|  86 LEIGTGHTAMMAIMAAKIFKCDVIATEIDDEFFEYAKANISANNS----KVQLIKSNGEIINGIipkrEIFDVIF 156
                                       8********************************777777666654....44444444322222244556677665 PP

>> UPF0146  Uncharacterised protein family (UPF0146)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   9.6e-05     0.096      14      49 ..      82     123 ..      70     158 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.6e-05
                                       SSEEEEET-TT--HHHHHHHHHS.-EEEEE-SS-S....... CS
                           UPF0146  14 rgkvvEvGiGrkldvaealakrg.vdlvatDikek.....ka 49 
                                        ++v E+G G    +a + ak   +d++at+i+++     ka
  gi|242399747|ref|YP_002995172.1|  82 GERVLEIGTGHTAMMAIMAAKIFkCDVIATEIDDEffeyaKA 123
                                       469************999999877********9984443333 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:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.54
# Mc/sec: 1381.17
//
Query:       gi|242399748|ref|YP_002995173.1|  [L=420]
Description: Succinyl-diaminopimelate desuccinylase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-37  129.3   0.0    1.8e-37  129.0   0.0    1.1  1  Peptidase_M20  Peptidase family M20/M25/M40
      2e-20   72.7   0.0    5.9e-20   71.2   0.0    1.8  2  M20_dimer      Peptidase dimerisation domain
    6.9e-05   22.6   0.0    9.9e-05   22.1   0.0    1.3  1  Peptidase_M28  Peptidase family M28


Domain annotation for each model (and alignments):
>> Peptidase_M20  Peptidase family M20/M25/M40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.0   0.0   3.1e-41   1.8e-37       4     205 ..      95     418 ..      92     420 .] 0.89

  Alignments for each domain:
  == domain 1  score: 129.0 bits;  conditional E-value: 3.1e-41
                                       EES-BSSTTCGGGSSS..TTSEEETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTT.TH CS
                                       xxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx RF
                     Peptidase_M20   4 sHlDvVpeeetdgwtt..pfslteedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggr.gG 77 
                                        HlDvVp+++ ++wt   pf++ ++dGk+yGrG+ d+  +++a l+a++al   gi+pk+ti l+f+ dEE+g+  G
  gi|242399748|ref|YP_002995173.1|  95 THLDVVPPGDLSKWTItkPFEPVVKDGKVYGRGSEDNGQSLVASLYAVKALMNLGIRPKKTIILAFVSDEETGSkHG 171
                                       7******9999****99******************************************************777788 PP

                                       HHHHHH...HHHTTTCESEEEEEEEESSSBTCHSTETEEEE.................................... CS
                                       xxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................................... RF
                     Peptidase_M20  78 akalle...gleerekvdavfelhieepgileagklaigvv.................................... 115
                                        ++l++   +l+  +k d    +++ ++g+ e g+  i +                                     
  gi|242399748|ref|YP_002995173.1| 172 LEWLMKehpELF--RKDDL---VLVPDGGNEE-GT-FIEIAeksilwmkikvkgkqvhasmpglglnahrvaidytk 241
                                       888888433222..24444...4588888887.66.44455678899999999************************ PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                     Peptidase_M20 116 ............................................................................. 115
                                                                                                                    
  gi|242399748|ref|YP_002995173.1| 242 aldgllhkkynardelfdppestfeptmggnpsdapniapgehevvfdcrvlpqykldevlsdaqevaeeikekykk 318
                                       ***************************************************************************** PP

                                       ........EEEEEEE.EEESHEEEC.CHHHHHHHHHHHHHHHTSCEEEEEESSSBHTHHHH..TTTEEEEEEESSGG CS
                                       ........xxxxxxx.xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxx RF
                     Peptidase_M20 116 ........kvevell.eggapvtln.dsplvkalaeaaeelfgekvelivsgpggtdarff..agiptvmifgpgsg 180
                                               +v+ve l +  ap++++ ds++vk+l+++++e+ g++v+    g ggt a++f  ++ip+v++   + +
  gi|242399748|ref|YP_002995173.1| 319 eidgkvlpEVKVEVLqRLDAPAPTPkDSEIVKLLQKVIKEFRGKDVKIGGIG-GGTFAAYFrkLEIPAVVWATLD-E 393
                                       *******9677776666667777778**************769777777777.9999999977777***998877.9 PP

                                       CTTSTTTEEEHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20 181 laHspnEyvdledlekgikvlarll 205
                                       +aH+pnEy ++e++++ +k++a+l+
  gi|242399748|ref|YP_002995173.1| 394 MAHQPNEYAKIENMVEDAKIMAALA 418
                                       *********************9986 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.2   0.0   9.9e-24   5.9e-20       1     108 [.     204     316 ..     204     317 .. 0.95
   2 ?   -2.0   0.0      0.54   3.2e+03      36      67 ..     351     373 ..     346     387 .. 0.71

  Alignments for each domain:
  == domain 1  score: 71.2 bits;  conditional E-value: 9.9e-24
                                       SEB-EEEEEEEEEE-B-EEGG-TTTTB-HHHHHHHHHHCSCTTEEC.........TCCTCCCCCEECCE-C.CCCEE CS
                         M20_dimer   1 ighkGlaggkitvkgkagHsgapgagaNAieklarllaeledeegdia....eerslprttlnvtgiegGs.aknvi 72 
                                       i++k ++++ki+vkgk++H+++pg g NA + +++   +l  + +++     e +++p++t+++t++   s a+n+ 
  gi|242399748|ref|YP_002995173.1| 204 IAEKSILWMKIKVKGKQVHASMPGLGLNAHRVAIDYTKALDGLLHKKYnardELFDPPESTFEPTMGGNPSdAPNIA 280
                                       589*************************************999998889*****************66666****** PP

                                       SSEEEEEEEEEHHHHHHHHHHHHHHHHHHTSCCSTT CS
                         M20_dimer  73 pdeaeakidiRllpgedpeevleeieeilekeaped 108
                                       p+e e+ +d+R+lp+ +++evl + +e++e+ ++++
  gi|242399748|ref|YP_002995173.1| 281 PGEHEVVFDCRVLPQYKLDEVLSDAQEVAEEIKEKY 316
                                       *******************************99987 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.54
                                       HHHCSCTTEEC.....TCCTCCCCCEECCE-C CS
                         M20_dimer  36 llaeledeegdiaeerslprttlnvtgiegGs 67 
                                       ll++  +e         +++  + ++gi gG+
  gi|242399748|ref|YP_002995173.1| 351 LLQKVIKE---------FRGKDVKIGGIGGGT 373
                                       45555554.........677788999999998 PP

>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   1.7e-08   9.9e-05       2      79 ..      76     169 ..      75     224 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.7e-08
                                       EEEEESTTCE..SEEEEEEEE--B-TTT................TCC.T---TTTTHHHHHHHHHHHHHCHHGGCCS CS
                     Peptidase_M28   2 viatlegkat..devlllgAHyDsvgvg................rgp.ifvGAdDnAsgvaalLelarvlaasgsrp 59 
                                       ++a + g++   + +l +  H+D v+ g                +g+    G  Dn+ + +a L+ +++l + g rp
  gi|242399748|ref|YP_002995173.1|  76 ILAYYYGEQGekSPRLWILTHLDVVPPGdlskwtitkpfepvvkDGKvYGRGSEDNGQSLVASLYAVKALMNLGIRP 152
                                       555554444432558999999999999999999999998888875556668*********************999** PP

                                       SEEEEEEEESSCSGSSHHHH CS
                     Peptidase_M28  60 krgvrflffdaEEagllGSk 79 
                                       k++++++f++ EE g   Sk
  gi|242399748|ref|YP_002995173.1| 153 KKTIILAFVSDEETG---SK 169
                                       *************74...33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (420 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       765  (0.0426683); expected 358.6 (0.02)
Passed bias filter:                      704  (0.039266); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.51
# Mc/sec: 2461.63
//
Query:       gi|242399749|ref|YP_002995174.1|  [L=631]
Description: Oligopeptide transporter, OPT family [Thermococcus sibiricus MM 739]
Scores for complete 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-102  343.6  48.2   2.9e-102  343.3  48.2    1.1  1  OPT              OPT oligopeptide transporter protein
  ------ inclusion threshold ------
       0.16   11.2   1.8        1.8    7.8   2.5    2.1  2  Mannosyl_trans2  Mannosyltransferase (PIG-V)
       0.79   10.1   3.1        2.4    8.6   0.9    2.9  2  DUF2839          Protein of unknown function (DUF2839)


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 !  343.3  48.2  4.8e-106  2.9e-102       1     615 [.      18     594 ..      18     595 .. 0.91

  Alignments for each domain:
  == domain 1  score: 343.3 bits;  conditional E-value: 4.8e-106
                               OPT   1 elTlRavvlGillgvlgsavnmyfglrtglvsissipaallafplgkalarilpklslnpgpftikEnvliqtmasa 77 
                                       e+T++a++lG++l++++ a+n+y+g+  g++ ++sipaa+++++++ a+    ++        +i+En+++qt+asa
  gi|242399749|ref|YP_002995174.1|  18 EYTVKAFILGVVLSIIMGAANAYLGMYAGMTVSASIPAAVISMAILMAF----KD-------KNILENNMVQTAASA 83 
                                       57*********************************************98....55.......9************** PP

                               OPT  78 aatlalatglivvipalelygqsag..fgylillslsvqllGvgfagplRkflvypeklifPsglataellkalhkp 152
                                       +++l  a+g+i++ pal++ g+  +  ++ + +++ +++ lG +f++++R++++++e+l++P+g+a+ae+l a++k+
  gi|242399749|ref|YP_002995174.1|  84 GESL--AAGVIFTFPALVVLGTYTEfpYWLVTIIAALGGSLGALFTIVIRRAFIVEERLPYPEGTACAEVLIAGDKG 158
                                       ****..************988877777999999999****************************************9 PP

                               OPT 153 egeeksrlkfflivflgsfvwglfplylfpalssfswltwiapknvvlanlfglgllpltfdwnviaayiGsglivp 229
                                       +       k +++   g++++gl     +++l s + +  ++++++       +g   l +  +++aa++++g+iv+
  gi|242399749|ref|YP_002995174.1| 159 GS----HAKPIFV---GGIFGGL-----YKLLGSSGLWAPAVETAK------FVGRRVLYLGSDLSAALLSVGYIVG 217
                                       96....8999999...*****94.....777999999988888855......33433466889************** PP

                               OPT 230 lwvavnmliGavlswgiliPllyysngwypaylpydvteildedgvldyekyigyglmllaalvallylvqfaaitl 306
                                       l++a+ +++G +++w+i iP+ y  +  +p+ l+   +  l    ++ +++y+g+g+m++++l++l           
  gi|242399749|ref|YP_002995174.1| 218 LNIAFLVFLGGAIAWFIAIPI-YVAKTGNPDGLS---ALDLAWVTWSTKIRYMGVGAMVVGGLWSL----------V 280
                                       *********************.888889999999...555667789********************..........9 PP

                               OPT 307 livhtilkhgkdikaalksarsprteeddrhrrlmrkykdvpmwwylallvlslvigiivvealf..tqlpvwglll 381
                                       ++  +i +++k+  +a + +        +  + + r+++d pm ++l+l+ ++ v ++++++++    ++ + + ++
  gi|242399749|ref|YP_002995174.1| 281 KLRGPISRGIKAGLEATRRK--------QSGELILRTEEDMPMNTVLMLITAFVVPLFLLYAHIIdsIGIAAVMAII 349
                                       ******66666666666665........78999**************99855555444444444456999999**** PP

                               OPT 382 alllafllaivsaiiaGltgl..npvsgigkltqlifgallpg.......rpvanlvfgavvyaaaaqagdfmqDLK 449
                                       +l+++f+ + +++++aG++g+  npvsgi++++ l+ +++l+g       +++a+++++av ++aaa agd mqDL 
  gi|242399749|ref|YP_002995174.1| 350 MLIVGFFGSSIAGYLAGVVGSsnNPVSGITIMSLLFTALVLKGlglsgldGMTATILVAAVICTAAAIAGDTMQDLA 426
                                       **********************************99999999999988988************************** PP

                               OPT 450 tGhllkasPraqfvaqliGtlvgavvniavlkllvkaygdict.adasnaftaPqakvfaavavllvggkkglpwaf 525
                                       tGh+++a+P+ q+v  ++Gt+ +a+v+++vl+ll+kayg+ +t + ++na++aPqa ++a v++ +v+++  l w +
  gi|242399749|ref|YP_002995174.1| 427 TGHIVGATPKRQQVFEVVGTFTAALVMAPVLNLLIKAYGIAGTpTAKENALAAPQAFLMAKVTE-GVFTG-TLEWNM 501
                                       *******************************************99999****************.*****.9***** PP

                               OPT 526 llgavapfilllllkkfpkkstarklplplafavgfylppslsialligglianlwlk...rrdaewakkynyvlaa 599
                                       ++++++++i+l++l+++ + ++ +   +++ +avg+ylp+sl ++++igg++++l+ k   ++  e+    +++ aa
  gi|242399749|ref|YP_002995174.1| 502 VFIGAGIAIALIILDEILAMKNSSFRTPVMPVAVGIYLPLSLGVPIFIGGVLRWLVGKargAKTEEKPTDAGVLGAA 578
                                       ****************9999999999********************************44434444455579***** PP

                               OPT 600 GLiaGealmgviiafl 615
                                       GLiaGealmg++ a l
  gi|242399749|ref|YP_002995174.1| 579 GLIAGEALMGILFAGL 594
                                       ***********99876 PP

>> Mannosyl_trans2  Mannosyltransferase (PIG-V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   2.5    0.0003       1.8      81     177 ..      23     117 ..      14     137 .. 0.87
   2 ?   -0.5   0.0       0.1     6e+02      14      65 ..     457     503 ..     446     509 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0003
                   Mannosyl_trans2  81 aflpllplfvsllskevlaplvgllslravlvlsvfslsillfllaavilsdvsvlvlkareasfkasllfclspaa 157
                                       af+ +  l + +++ + +  ++  +++ a +  +v+s++il+ +  + il ++ v+   +   s  a ++f + pa 
  gi|242399749|ref|YP_002995174.1|  23 AFILGVVLSIIMGAANAYLGMYAGMTVSASIPAAVISMAILMAFKDKNILENNMVQTAASAGESLAAGVIFTF-PAL 98 
                                       8999999999999999999****************************************************99.666 PP

                   Mannosyl_trans2 158 vflasiYseaLfallafsgv 177
                                       v l   Y e  + l+++ + 
  gi|242399749|ref|YP_002995174.1|  99 VVL-GTYTEFPYWLVTIIAA 117
                                       666.5699999999988765 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.1
                   Mannosyl_trans2  14 lvllLviLfrialipddtsealnppcllaspslvdslvekllenlvsWDsvy 65 
                                       l ll+++ + ia  p+ + +al  p     ++l+++++e+++ + + W+ v+
  gi|242399749|ref|YP_002995174.1| 457 LNLLIKA-YGIAGTPTAKENALAAPQ----AFLMAKVTEGVFTGTLEWNMVF 503
                                       4444443.455777888888888887....599***************9998 PP

>> DUF2839  Protein of unknown function (DUF2839)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.9    0.0004       2.4      35      62 ..     256     285 ..     252     288 .. 0.90
   2 ?   -0.9   0.0      0.37   2.2e+03      45      61 ..     340     357 ..     295     361 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0004
                           DUF2839  35 fvklttrgawiGigllvv..lWvvvrfiGp 62 
                                       +v ++t+  ++G+g++vv  lW  v++ Gp
  gi|242399749|ref|YP_002995174.1| 256 WVTWSTKIRYMGVGAMVVggLWSLVKLRGP 285
                                       799**************9778*****9998 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.37
                           DUF2839  45 iGigl.lvvlWvvvrfiG 61 
                                       iGi++ ++++ ++v f G
  gi|242399749|ref|YP_002995174.1| 340 IGIAAvMAIIMLIVGFFG 357
                                       566541455556666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (631 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       891  (0.049696); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.75u 0.35s 00:00:01.10 Elapsed: 00:00:00.55
# Mc/sec: 3458.94
//
Query:       gi|242399750|ref|YP_002995175.1|  [L=271]
Description: Metal dependent hydrolase [Thermococcus sibiricus MM 739]
Scores for complete 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-22   79.4   0.1    3.1e-22   79.1   0.1    1.1  1  Lactamase_B_2  Beta-lactamase superfamily domain
    5.3e-08   32.9   0.0    1.1e-07   31.9   0.0    1.6  1  Lactamase_B_3  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.021   14.8   0.0      0.042   13.8   0.0    1.5  1  Lactamase_B    Metallo-beta-lactamase superfamily
      0.027   14.6   0.0      0.065   13.4   0.0    1.6  2  DUF1525        Protein of unknown function (DUF1525)


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 !   79.1   0.1     7e-26   3.1e-22       1     201 []      32     220 ..      32     220 .. 0.85

  Alignments for each domain:
  == domain 1  score: 79.1 bits;  conditional E-value: 7e-26
                                       SEEEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCC.....C--EEEEEEEEHHHHHHCCT CS
                     Lactamase_B_2   1 rriLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlre.....lrpkklplyapkgvlavlea 72 
                                       rri +D+gp+ +   + +      + ++++id+++++h H DH+++   + e      ++k+  l+ +k+v    e+
  gi|242399750|ref|YP_002995175.1|  32 RRIYVDPGPGALVR-AWRY-----KIDPRKIDVLFVSHRHTDHCNDSEIMVEgmtvgVTKKRGMLITSKSVVYGDED 102
                                       8*********7777.3333.....46799***********************8877544444667788999888888 PP

                                       TCGHHHCHTT.TTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---H CS
                     Lactamase_B_2  73 nfvylaleee.pavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyipe 148
                                       +++++ + +    +++h  ++ge+++lgd   e+t+tp  h+  +        ++G++++++  ++ yi+Dt+y++ 
  gi|242399750|ref|YP_002995175.1| 103 HTPAISKYHLdSLEEIHIPNPGERIQLGDD--EMTITPTIHSDST--------AIGFILKTKLGKIGYIPDTEYFD- 168
                                       88887777768889999999*******985..6888889999999........9**********************. PP

                                       HHHHHHCT-SEEEEE-S-SSTTHHHHHHT---STSHHHHCTTSS..SSEEEEESB CS
                     Lactamase_B_2 149 eigerlggadllllditayeddemirhmgHltpeeaveaaadlg..akrlvliHi 201
                                       ++++ ++g  ll+  + ++++ +m+  ++Hl  e+ + +++d++  ++ l++ Hi
  gi|242399750|ref|YP_002995175.1| 169 DLKKIYEGTRLLI--ASVTRPTNMK-IPYHLCTEDVIYMLKDMKkkPEMLIMSHI 220
                                       5688*********..6666887777.8*****************66667787786 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 !   31.9   0.0   2.5e-11   1.1e-07      16     123 ..      31     173 ..      26     216 .. 0.70

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 2.5e-11
                     Lactamase_B_3  16 garilvDPfka....nlgyeppaeeaDlvlisqaledHahletlkql.............................. 58 
                                         ri+vDP+ +       y+++++++D++ +s++++dH++  ++                                 
  gi|242399750|ref|YP_002995175.1|  31 SRRIYVDPGPGalvrAWRYKIDPRKIDVLFVSHRHTDHCNDSEIMVEgmtvgvtkkrgmlitsksvvygdedhtpai 107
                                       579******44444578899999******************998765668888888888866555555555555544 PP

                     Lactamase_B_3  59 .......aenvkvleegeslevggleiravatshdavggsergenngflleqdgltiyhlGhlahelsseel 123
                                               e++++ ++ge +++g+ e++ ++t h         + +gf+l+ +  +i++ +++ +  + +++
  gi|242399750|ref|YP_002995175.1| 108 skyhldsLEEIHIPNPGERIQLGDDEMTITPTIH------SDSTAIGFILKTKLGKIGYIPDTEYFDDLKKI 173
                                       4444444444444444555666666666666665......44689*******************95444443 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   9.5e-06     0.042      20      59 ..      36      70 ..      26      77 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 9.5e-06
                                      ES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHT CS
                       Lactamase_B 20 iDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiG 59
                                      +D+G ++     +      +++p+++d ++++H H+DH+ 
  gi|242399750|ref|YP_002995175.1| 36 VDPGPGALVRAWR-----YKIDPRKIDVLFVSHRHTDHCN 70
                                      5666655555544.....489*****************85 PP

>> DUF1525  Protein of unknown function (DUF1525)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       2.6   1.2e+04      72      81 ..      42      51 ..      36      53 .. 0.83
   2 ?   13.4   0.0   1.5e-05     0.065      73     109 ..      75     111 ..      62     114 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2.6
                           DUF1525 72 gvadawqlgi 81
                                      +++ aw+++i
  gi|242399750|ref|YP_002995175.1| 42 ALVRAWRYKI 51
                                      7999***998 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 1.5e-05
                           DUF1525  73 vadawqlgikkiPAVvvdrraVvYGeadvaaAlelye 109
                                       +++++++g++k    ++ +++VvYG++d   A++ y+
  gi|242399750|ref|YP_002995175.1|  75 MVEGMTVGVTKKRGMLITSKSVVYGDEDHTPAISKYH 111
                                       7899*****************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.34s 00:00:00.94 Elapsed: 00:00:00.56
# Mc/sec: 1464.95
//
Query:       gi|242399751|ref|YP_002995176.1|  [L=453]
Description: Phosphopentomutase [Thermococcus sibiricus MM 739]
Scores for 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-44  148.9   0.0    1.6e-43  147.8   0.0    1.6  1  PGM_PMM_I    Phosphoglucomutase/phosphomannomutase, alpha/bet
    2.9e-24   85.7   0.0    5.6e-24   84.7   0.0    1.5  1  PGM_PMM_II   Phosphoglucomutase/phosphomannomutase, alpha/bet
    1.1e-12   48.0   0.2    2.7e-12   46.7   0.2    1.7  1  PGM_PMM_IV   Phosphoglucomutase/phosphomannomutase, C-termina
    2.9e-09   37.1   0.0    7.3e-09   35.8   0.0    1.7  1  PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/bet


Domain annotation for each model (and alignments):
>> PGM_PMM_I  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.8   0.0   3.5e-47   1.6e-43       2     135 ..       2     129 ..       1     132 [. 0.96

  Alignments for each domain:
  == domain 1  score: 147.8 bits;  conditional E-value: 3.5e-47
                                       GGBBTTCEEEECCHCTBSCCHHHHHHHHHHHHCHHCSTS-EEEEEE-S-TTHHHHHHHHHHHHHCCT-CEEEEEEB- CS
                         PGM_PMM_I   2 qkfgtsGlRgkvgegeltpelveklgqaiaeylkaeakkkkvvvGrDtRvssrelaealaaglaanGvevillgllp 78 
                                       ++fgt+G+Rg+v   ++tpel++++g+ai++y+      ++vvvGrD+R+ss +l++al++gl+++Gv+vi++gl+p
  gi|242399751|ref|YP_002995176.1|   2 RLFGTAGIRGSVH-SKITPELALNVGKAIGTYIDT----GTVVVGRDARTSSVMLESALVSGLLSTGVDVIRIGLVP 73 
                                       78***********.55******************8....9************************************* PP

                                       HHHHHHHHHHCCECEEEEE--TTS-TTCCCEEEEETTTCE--CHHHHHHHHHHCCT- CS
                         PGM_PMM_I  79 tPavsfairklkadagimitaSHnppeyngiKvylsnGgpispeveekIeaiiekee 135
                                       tP++++a++kl+ +ag+mitaSHnpp++ngiKv++++G+++  e+e+++e+ii++e+
  gi|242399751|ref|YP_002995176.1|  74 TPMLAWATNKLG-NAGVMITASHNPPGDNGIKVFNEKGIEFFLEQEKELENIIFSES 129
                                       **********85.899*************************************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 !   84.7   0.0   1.2e-27   5.6e-24       2     103 .]     149     245 ..     148     245 .. 0.98

  Alignments for each domain:
  == domain 1  score: 84.7 bits;  conditional E-value: 1.2e-27
                                       HHHHHGGGTS-HHHHHHHT-EEEEE-TT-TTHHHHHHHHHHTT-EEEES-----TT-TTSS----TT-TTTTHHHHG CS
                        PGM_PMM_II   2 aYiealkekvdseaikksglkvvidplhGaggeilkellkelgvdvvelnaepdpdfptkapnpeekealkllielv 78 
                                        Yi+++++ vd    ++++lkv++d ++Gag+ i++ ll+e+g++v++ln++ d+ fp++ ++p+  e++++l++lv
  gi|242399751|ref|YP_002995176.1| 149 NYIKEILKYVD----SQTNLKVLLDMGNGAGSLITPYLLREMGAKVITLNSQLDGYFPGRKSEPRY-ENIAYLSNLV 220
                                       69*********....7889***********************************************.********** PP

                                       GGGG-SEEEEE-TTS-BEEEEETTE CS
                        PGM_PMM_II  79 kkegadlglafDgDaDRlgvvderG 103
                                       k+ g dl++a DgDaDR++v+de+G
  gi|242399751|ref|YP_002995176.1| 221 KELGVDLAIAQDGDADRIAVFDEKG 245
                                       ***********************98 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 !   46.7   0.2     6e-16   2.7e-12       1      65 [.     368     434 ..     361     442 .. 0.84

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 6e-16
                                       CCCCCHCC-TT..EECCCCCTTH....HCCCCCCCCGCCEEEE.EEEETTCCEEEEEEEESSHHHHHHH CS
                        PGM_PMM_IV   1 linvrveekakvvaalaallkva....sikeglkilledGrrlavRpSGTepllrvyvEaksdeelarl 65 
                                       +i+ +v ek  v ++l++ll ++     ++ g++  l+dG+++ vRpSGTep++rv+vE+ ++++ ++l
  gi|242399751|ref|YP_002995176.1| 368 EIKYEVVEK--VKERLQDLLRDQveevITISGIRLNLKDGSWVLVRPSGTEPKIRVVVEGITEKRKEEL 434
                                       566666676..56777777777799999999*****************************998888776 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 !   35.8   0.0   1.6e-12   7.3e-09       2     113 ..     250     356 ..     249     357 .. 0.89

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 1.6e-12
                                       HHHHHHHHHHHHHCHCSTTTCEEEEETTS-THHHHHHHHTT-EEEEESSSCHHHHHHHHHTTECEEEETTCEEEETT CS
                       PGM_PMM_III   2 gdqllallakylleeklkpgagvvktvmtslalervakklgiklvetkvGdkyvleemkeegavlGgEeSghiifld 78 
                                        d l+al+a+ + ++++++g  +v ++ ts  +++v+++ g+++++++ G   + + +k+ +a ++ E    +i ++
  gi|242399751|ref|YP_002995176.1| 250 EDTLIALFARLY-AQEHNGG-NIVVSINTSFRIDKVVEEEGGRVYRVPLGQ--LHDGIKRYNAIFASEP-WKFIHPK 321
                                       58999****955.4435555.5****************************8..56999999*****998.789999* PP

                                       TBSS--HHHHHHHHHHHHHHHTS-HHHHHHHHHHH CS
                       PGM_PMM_III  79 eattkDGilaallvleilaetgkslselleellkk 113
                                       +  + D  +++ l+l+i++++gk+lse++++++k 
  gi|242399751|ref|YP_002995176.1| 322 FGLWIDSFVTIGLLLKIITQEGKPLSEIIKDIPKY 356
                                       *****************************888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (453 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       633  (0.0353059); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); 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: 0.68u 0.37s 00:00:01.05 Elapsed: 00:00:00.54
# Mc/sec: 2504.92
//
Query:       gi|242399752|ref|YP_002995177.1|  [L=151]
Description: hypothetical protein TSIB_1777 [Thermococcus sibiricus MM 739]
Scores for complete 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-26   91.7   0.0    4.3e-26   91.3   0.0    1.0  1  UPF0146     Uncharacterised protein family (UPF0146)
  ------ inclusion threshold ------
      0.013   15.5   0.0      0.023   14.7   0.0    1.4  1  ADH_zinc_N  Zinc-binding dehydrogenase
       0.16   12.3   0.0       0.25   11.6   0.0    1.2  1  TrkA_N      TrkA-N domain


Domain annotation for each model (and alignments):
>> UPF0146  Uncharacterised protein family (UPF0146)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.3   0.0   7.3e-30   4.3e-26      11     125 ..      26     142 ..      16     145 .. 0.91

  Alignments for each domain:
  == domain 1  score: 91.3 bits;  conditional E-value: 7.3e-30
                                       HS-SSEEEEET-TT--HHHHHHHHHS-EEEEE-SS-S........STTEE---SSS--HHHHTTEEEEEEES--TTS CS
                           UPF0146  11 enargkvvEvGiGrkldvaealakrgvdlvatDikek...kak.egvrivrDDvtdPnleiYkgadliYslRpPael 83 
                                          +gk+vE+G+G+ ++va +l++ g d++++D + +   kak +g+++++D+++ Pnl +Y+ a++iYs+Rp +e+
  gi|242399752|ref|YP_002995177.1|  26 RHSKGKIVEIGVGFNFKVALKLKELGRDIIVVDWNLEaieKAKeLGLKAYVDNIFTPNLILYRDASVIYSIRPTPEI 102
                                       45678****************************987667889889******************************** PP

                                       HHHHHHHHHHHT-EEEEE-BTTB-----TT-EEEEETTEEEE CS
                           UPF0146  84 qsaildvakkvgAaliikpLlgedvvvekelklvnykgalFy 125
                                        + il++ k+v   ++i p   +++  +k+lkl nykg   y
  gi|242399752|ref|YP_002995177.1| 103 IKPILELGKRVKVPVYIVPFSLDTM--PKSLKLENYKGIPIY 142
                                       ***********************97..**********97555 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   3.9e-06     0.023      11      83 ..      48     138 ..      36     143 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.9e-06
                                       HHTT-EEEEEESSHHHHHHHHHTTESEEEET..................TTC.HHHHHHHHHTTTSSEEEEEESSCS CS
                        ADH_zinc_N  11 kalGaeviavdsseeklelakklGadeviny..................kea.dlverikeltggegvdvvfecvGs 68 
                                       k lG  +i+vd + e +e+ak+lG ++++++                  + + ++ + i el +  +v v++     
  gi|242399752|ref|YP_002995177.1|  48 KELGRDIIVVDWNLEAIEKAKELGLKAYVDNiftpnlilyrdasviysiRPTpEIIKPILELGKRVKVPVYIVPFS- 123
                                       567889*************************999999999888888888666688999999998888888888888. PP

                                       HHHHHHHHHCEEEEE CS
                        ADH_zinc_N  69 gatleaalkllkpgG 83 
                                        +t++ +lkl +++G
  gi|242399752|ref|YP_002995177.1| 124 LDTMPKSLKLENYKG 138
                                       888888888877666 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   4.2e-05      0.25      12      52 ..      42      82 ..      37      87 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.2e-05
                                      HHHHHHHH.TTEEEEEEESSHHHHHHHHHTTSEEEES-TTSH CS
                            TrkA_N 12 slaeeLse.ggkdvvvidkdeerveelreeglevvvgdatde 52
                                      ++a +L+e g  d++v+d + e++e+++e gl+++v +   +
  gi|242399752|ref|YP_002995177.1| 42 KVALKLKElGR-DIIVVDWNLEAIEKAKELGLKAYVDNIFTP 82
                                      58889999555.8********************999887666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.37s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 858.32
//
Query:       gi|242399753|ref|YP_002995178.1|  [L=52]
Description: hypothetical protein TSIB_1778 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       174  (0.00970495); expected 358.6 (0.02)
Passed bias filter:                      163  (0.00909142); 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: 0.50u 0.34s 00:00:00.84 Elapsed: 00:00:00.53
# Mc/sec: 292.64
//
Query:       gi|242399754|ref|YP_002995179.1|  [L=341]
Description: transcription regulator, helix-turn-helix family [Thermococcus sibiricus MM 739]
Scores for 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-47  159.2   0.2    1.2e-46  158.9   0.2    1.1  1  Regulator_TrmB  Archaeal transcriptional regulator TrmB
    3.3e-24   84.5   0.0    6.6e-24   83.6   0.0    1.5  1  TrmB            Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.016   15.3   0.0      0.045   13.9   0.0    1.7  1  HTH_9           RNA polymerase III subunit RPC82 helix-turn-h
       0.12   12.7   0.0       0.33   11.3   0.0    1.7  1  Rrf2            Transcriptional regulator
       0.15   11.8   0.0       0.39   10.5   0.0    1.7  1  LexA_DNA_bind   LexA DNA binding domain
       0.21   11.3   0.0       0.38   10.4   0.0    1.4  1  Prot_ATP_OB_N   Proteasomal ATPase OB N-terminal domain


Domain annotation for each model (and alignments):
>> Regulator_TrmB  Archaeal transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.9   0.2   3.9e-50   1.2e-46       1     230 [.     112     339 ..     112     341 .] 0.96

  Alignments for each domain:
  == domain 1  score: 158.9 bits;  conditional E-value: 3.9e-50
                                       -EEEESSHHHHHHHHHHHHHH-SSEEEEEE-GGGHHHHHHHHHHHHHTT-EEEEEESS----GGGSSSSEEEEEE-S CS
                    Regulator_TrmB   1 avwvvksretvierieelIesAenelivslpselLeelreeliaaaergvtVllliypdedleeldleevatevrvr 77 
                                       ++w+++++e+++er+e +++sA+ e+++++p e+L  l+ee +++++    ++++i + +++e+++++++ +++ + 
  gi|242399754|ref|YP_002995179.1| 112 EIWTIHGFENTLERVEYIVRSARREVLINTPLEFLTLLKEEVRKRKN----IIFVIVS-NFDEIPEWLNKENVILAK 183
                                       69****************************************99988....8888888.8999*******8888888 PP

                                       ---S.EE....EEETTTEEEEE-SSS-.EEEE--HHHHHHHHHHHHHH........HHH-EEEEE..EES-TT-EEE CS
                    Regulator_TrmB  78 rsgapll....vivDrkrgvvaprevl.rdkeeeyaiifkekelihvlshyFlttlWktsevikt..depvekpitf 147
                                       ++gap+l    +i+D ++++++ + ++ r+ke++y+++ k+++li++++h+F+t+++++s+ ik+  +e+ +kp + 
  gi|242399754|ref|YP_002995179.1| 184 SGGAPWLmgtwIIGDIDYALFFGALPKdRRKEKFYSFWGKSPKLIQNYMHWFYTMYFDNSDLIKPveYEKLKKPFEI 260
                                       8889***99999**************9************************************************** PP

                                       S-HHHHHHHHHHHT.TTS-EEEEEEEEETTT--EEEEEEEEEEEEEETTTTEEEEEEEETTE.EEEEE-TT--SSSE CS
                    Regulator_TrmB 148 ssirlavedikkllraglkveaeveGrdtetgeevtieGrvveatlnstpgvaslvvetedg.evtVGGlgAvlEDi 223
                                       ++ir++++ +k+     l+ ++ev G  ++t+ee+ti+G+v++  +++t+ +a++++  e+g e +VGGlg+++ED+
  gi|242399754|ref|YP_002995179.1| 261 ANIRTLITILKQ---TQLPKNIEVIGHFVDTREEATIKGKVID--YEYTSLTANITLVDENGkEWKVGGLGSYFEDV 332
                                       ************...799*************************..**********99999999************** PP

                                       EEEEEEE CS
                    Regulator_TrmB 224 eaeeitl 230
                                       e+e+++l
  gi|242399754|ref|YP_002995179.1| 333 EGEKFIL 339
                                       ****987 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.6   0.0   2.2e-27   6.6e-24       1      68 []      10      77 ..      10      77 .. 0.99

  Alignments for each domain:
  == domain 1  score: 83.6 bits;  conditional E-value: 2.2e-27
                                      HHHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE--HH CS
                              TrmB  1 LqklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYravdpe 68
                                      LqklGL++yE+ +Y++Llklg ++a+++ +e+g+p++++Y+vL+sL +kG+V++ +g+p++Y++v+pe
  gi|242399754|ref|YP_002995179.1| 10 LQKLGLTKYESLAYITLLKLGTSKATDLTKESGIPHTRIYDVLSSLHRKGFVDIMHGTPRMYKPVNPE 77
                                      89****************************************************************97 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.5e-05     0.045      21      58 ..      25      62 ..      23      64 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.5e-05
                                      HHHHHSSBEHHHHHHHHSSTHHHHHHHHHHHHHTTSEE CS
                             HTH_9 21 tLlrkgrltlrelvkktkLsldqVkksLvvLiqhrlVq 58
                                      tLl+ g++ +++l+k+++++++ + ++L++L + ++V+
  gi|242399754|ref|YP_002995179.1| 25 TLLKLGTSKATDLTKESGIPHTRIYDVLSSLHRKGFVD 62
                                      89******************************999995 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00011      0.33      14      60 ..      21      66 ..       9      69 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00011
                                      HHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT CS
                              Rrf2 14 llyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvrG 60
                                      l+y+++ + ++  +++++ ++ +i+++ +  +l+ L ++g+v    G
  gi|242399754|ref|YP_002995179.1| 21 LAYITLLKLGT-SKATDLTKESGIPHTRIYDVLSSLHRKGFVDIMHG 66
                                      66777777665.8999**************************99888 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00013      0.39      46      64 ..      51      69 ..      41      70 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00013
                                      HHHHHHHTTSEE-GGG-CC CS
                     LexA_DNA_bind 46 hLkaLerKGyierdpgkpR 64
                                       L  L+rKG+++++ g+pR
  gi|242399754|ref|YP_002995179.1| 51 VLSSLHRKGFVDIMHGTPR 69
                                      6999**************9 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 ?   10.4   0.0   0.00013      0.38       8      38 ..      55      84 ..      48      85 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00013
                     Prot_ATP_OB_N  8 vnsqdgtadVlvggrrmrVavsPlvdaeeLr 38
                                      ++ + g +d+++g  rm  +v+P++  e+L+
  gi|242399754|ref|YP_002995179.1| 55 LH-RKGFVDIMHGTPRMYKPVNPELVFEKLK 84
                                      55.6899******************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.62u 0.37s 00:00:00.99 Elapsed: 00:00:00.55
# Mc/sec: 1857.51
//
Query:       gi|242399755|ref|YP_002995180.1|  [L=457]
Description: Glycogen synthase [Thermococcus sibiricus MM 739]
Scores for 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  119.4   0.0    2.8e-34  118.9   0.0    1.2  1  Glyco_transf_5   Starch synthase catalytic domain
    8.4e-25   87.3   0.0    1.4e-24   86.5   0.0    1.4  1  Glycos_transf_1  Glycosyl transferases group 1
    4.7e-23   82.1   0.0    9.3e-23   81.1   0.0    1.4  1  Glyco_trans_1_4  Glycosyl transferases group 1
    1.3e-13   51.3   0.6    2.6e-12   47.0   0.5    2.7  2  Glyco_transf_4   Glycosyltransferase Family 4
      7e-07   29.8   0.0    2.5e-06   28.0   0.0    1.8  2  Glyco_trans_4_4  Glycosyl transferase 4-like domain
     0.0069   15.0   0.0        2.8    6.4   0.0    2.8  3  Glycogen_syn     Glycogen synthase
  ------ inclusion threshold ------
      0.024   15.0   0.0      0.084   13.3   0.0    2.0  1  Glyco_trans_1_2  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Glyco_transf_5  Starch synthase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.9   0.0   1.1e-37   2.8e-34       1     233 [.       3     208 ..       3     217 .. 0.86

  Alignments for each domain:
  == domain 1  score: 118.9 bits;  conditional E-value: 1.1e-37
                    Glyco_transf_5   1 kilfvasEvaplaktGGLadvvgaLpkaLaklghdvrvilPrygaikeekkeleevaelskaaedevevev..ekvk 75 
                                       kil+++ E+ p +k+GGLa++++++++ L + g++v v++P++g+i+ ek     ++e++  +          e++k
  gi|242399755|ref|YP_002995180.1|   3 KILMLGFEYLP-VKVGGLAEAITSIAETLTRIGNEVWVFTPSHGHIEGEK-----IFEMNIGIY------GgkERIK 67 
                                       8**********.***********************************986.....555433332......134899* PP

                    Glyco_transf_5  76 vaklkkdgvdvyfldnpeffdreglYgdkgedyednaerfalfsraalellekl...gwkpdvihahDWhtalvpal 149
                                       v++  ++gv+v+ ++    +d + +Yg+   ++e    + + f++a + ll+ l   + kpdv+h hDWht++++ l
  gi|242399755|ref|YP_002995180.1|  68 VYERAQNGVRVFAFSSNL-LDNKDVYGP---GWEGMLGKAVQFGKASVGLLNYLiekEGKPDVLHFHDWHTVFAATL 140
                                       ************999888.56678**87...99999*************99998774447***************** PP

                    Glyco_transf_5 150 lkelykerglfkkiktvftiHNlayqgrfpkdelaalglpaedfekldglefygkvnflkagivyadavttVSptya 226
                                       +k++        + +  ftiH l  + ++p++++++++l         +l  y ++++   g ++ad vttVS++y 
  gi|242399755|ref|YP_002995180.1| 141 IKKYF-------QLPATFTIHRLN-KSKVPAHYFHEAHLR--------ELAPYPDIDPEYVGAYIADVVTTVSRSYL 201
                                       ***85.......3********665.558899999766666........5677899********************** PP

                    Glyco_transf_5 227 kEiltpe 233
                                       +E ++ +
  gi|242399755|ref|YP_002995180.1| 202 WEEWDFY 208
                                       *977655 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 !   86.5   0.0   5.6e-28   1.4e-24      14     172 .]     254     427 ..     242     427 .. 0.90

  Alignments for each domain:
  == domain 1  score: 86.5 bits;  conditional E-value: 5.6e-28
                                       T-EEEEEESS-TTT.TTHHHHHHHHHCCCCC...HCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCH.SSS CS
                   Glycos_transf_1  14 kkkiilsvgrleke.Kgvdllikafallkkq...lnpnvklviaGngeeekelkklaeelelsdnviflgevs.red 85 
                                       +  ++ ++gr++k  Kgvd+l+ka++ + ++   + ++ +++i+G+g+ e e  +++      +n++++ ++  re 
  gi|242399755|ref|YP_002995180.1| 254 DGITFMFIGRFDKGqKGVDTLLKAVENIAENnpsEFSKMRFLIIGKGDPELEKWAHVLGSRYPENIKVITKMLkREF 330
                                       567899******966******************************6666555555555556789****999988999 PP

                                       HHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTT......SEEEE-TT-HHHHHHHHHHHH CS
                   Glycos_transf_1  86 leellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdge......tGllvkpnnaealaeairkll 156
                                         el+ + d +++ps+ E+fG+v +EAm +g + i s++gg+++++ + +      tGllv+p ++ ala ai k+ 
  gi|242399755|ref|YP_002995180.1| 331 TRELYGSVDFVIVPSYFEPFGLVQMEAMCLGAIPIGSAVGGIKDTIISLDedeekaTGLLVPPRDPNALAGAILKMT 407
                                       ************************************************9999************************9 PP

                                       HSH....HHHHHHHHHHHHH CS
                   Glycos_transf_1 157 ede....elrerlgenarkr 172
                                       + +    el  ++++n+++r
  gi|242399755|ref|YP_002995180.1| 408 QLRekdpELLSKMRKNGKRR 427
                                       8887777999******9975 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 !   81.1   0.0   3.6e-26   9.3e-23       3     131 ..     257     406 ..     255     408 .. 0.86

  Alignments for each domain:
  == domain 1  score: 81.1 bits;  conditional E-value: 3.6e-26
                                       EEEEES---GG.GTHHHHHHHHHHHH.HH......EEEEEES---..HHHHHHHT....T-T.TEEEE---..TH.H CS
                   Glyco_trans_1_4   3 vilfvGrleenvkgvdllleavpllrkkd......vrlvivGdgprpeeleelaa....gleerveftGfv..ed.l 66 
                                       +++f+Gr+++ +kgvd ll+av+ +++++      +r++i+G+g +p ele+ a+    ++ e++++  ++   +  
  gi|242399755|ref|YP_002995180.1| 257 TFMFIGRFDKGQKGVDTLLKAVENIAENNpsefskMRFLIIGKG-DP-ELEKWAHvlgsRYPENIKVITKMlkREfT 331
                                       689*****8888**************6634568889******99.65.8988776665555589999999987446* PP

                                       HHHHHH-SEEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--......T..TSSEE--TT-HHHHHHHHHHH CS
                   Glyco_trans_1_4  67 aellaaadvfvaPs..egfglkllEamaaglpvVatdvggiaevv......g..engllvppgdpealaeailrL 131
                                       +el+ ++d +++Ps  e fgl+ +Eam +g   + ++vggi++++      +   +gllvpp+dp+ala ail++
  gi|242399755|ref|YP_002995180.1| 332 RELYGSVDFVIVPSyfEPFGLVQMEAMCLGAIPIGSAVGGIKDTIisldedEekATGLLVPPRDPNALAGAILKM 406
                                       *******************************************99988644144679***************987 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.0   0.5     1e-15   2.6e-12       1     169 [.      16     225 ..      16     226 .. 0.83
   2 ?    0.0   0.0      0.29   7.3e+02     120     142 ..     324     346 ..     307     348 .. 0.75

  Alignments for each domain:
  == domain 1  score: 47.0 bits;  conditional E-value: 1e-15
                    Glyco_transf_4   1 vGGverhvleLaraLarrGheVtvvtpgddgpleeev...................................elvvr 42 
                                       vGG +  +  +a+ L r G eV v+tp++++ ++e+                                       v 
  gi|242399755|ref|YP_002995180.1|  16 VGGLAEAITSIAETLTRIGNEVWVFTPSHGHIEGEKIfemnigiyggkerikvyeraqngvrvfafssnlldNKDVY 92 
                                       79*******************************************************99999999999665533344 PP

                    Glyco_transf_4  43 vprvplpllkrllrslaflrrlrrllkre.kpDvvHahspaalgaallalrrrlgiplVltvHglye.....krllk 113
                                       +p++   l k  ++  a++  l  l+++e kpDv+H h++++++aa l  +   ++p  +t+H l       +++++
  gi|242399755|ref|YP_002995180.1|  93 GPGWEGMLGKAVQFGKASVGLLNYLIEKEgKPDVLHFHDWHTVFAATLIKKY-FQLPATFTIHRLNKskvpaHYFHE 168
                                       455555555555555555666777777779*************999998887.*************99999988888 PP

                    Glyco_transf_4 114 arlkplsrllra.lerrllrradrviavSeatadelrerygvppekitVipnGvDle 169
                                       a+l+ l ++     e+  +  ad v++vS++   e  + y+  + k t ++nG+  +
  gi|242399755|ref|YP_002995180.1| 169 AHLRELAPYPDIdPEYVGAYIADVVTTVSRSYLWEEWDFYRNFEGKATYVYNGIACD 225
                                       88887766655414566699**********988888887886679********9765 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.29
                    Glyco_transf_4 120 srllralerrllrradrviavSe 142
                                       + l r++ r l+ ++d vi++S 
  gi|242399755|ref|YP_002995180.1| 324 KMLKREFTRELYGSVDFVIVPSY 346
                                       45667788889**********96 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 !   28.0   0.0   9.7e-10   2.5e-06       1     139 [.      17     199 ..      17     202 .. 0.69
   2 ?   -1.5   0.0       1.2   3.1e+03     120     137 ..     328     345 ..     319     348 .. 0.86

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 9.7e-10
                   Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvltpapapg....................apeleedgvrvhrlp..vprrps..p 53 
                                       gG +  +  +a+ L + G eV v+tp+                         +e+ ++gvrv  +   +  + +  +
  gi|242399755|ref|YP_002995180.1|  17 GGLAEAITSIAETLTRIGNEVWVFTPSHGHIegekifemnigiyggkerikVYERAQNGVRVFAFSsnLLDNKDvyG 93 
                                       8999999******************5554444555555555555555555577788999999865433333332234 PP

                   Glyco_trans_4_4  54 lad..........laalralrrllrqrrerpdvvhahsptaglaarlarrrrgiplvvtlh........glllrrgs 112
                                       +++           +a+ +l  +l  ++ +pdv+h h++++ +aa l++    +p  +t+h        ++ +++  
  gi|242399755|ref|YP_002995180.1|  94 PGWegmlgkavqfGKASVGLLNYLIEKEGKPDVLHFHDWHTVFAATLIKKYFQLPATFTIHrlnkskvpAHYFHEA- 169
                                       444233222322233445666667569**********************666*********877766555666665. PP

                   Glyco_trans_4_4 113 gavrrly....ralerrllrradavlvvsea 139
                                         +r l+       e+  +  ad+v++vs++
  gi|242399755|ref|YP_002995180.1| 170 -HLRELApypdIDPEYVGAYIADVVTTVSRS 199
                                       .455555435566699************985 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.2
                   Glyco_trans_4_4 120 ralerrllrradavlvvs 137
                                       r++ r l+ ++d v+v+s
  gi|242399755|ref|YP_002995180.1| 328 REFTRELYGSVDFVIVPS 345
                                       678899**********99 PP

>> Glycogen_syn  Glycogen synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.3   0.0    0.0024       6.1      81     174 ..      63     154 ..      47     159 .. 0.80
   2 ?   -1.4   0.0      0.24   6.3e+02     292     317 ..     255     280 ..     250     297 .. 0.78
   3 !    6.4   0.0    0.0011       2.8     469     549 ..     338     419 ..     314     454 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0024
                                       --EEEEE-GGGGSTTHHHHHHHHHHHH-----TT-HHHHHHHHHHHHHHHHHHHHHCT----EEEEEEETGGGHHHH CS
                      Glycogen_syn  81 apkvilfdldsaavkldewkaelwekvkigipeedretndaiilGflvalflkefreleekkavvahfhewlaGvgl 157
                                       + ++ +++     v +  + ++l ++ ++  p  +    +a+ +G   + +l+ + e+e k+ v+ hfh+w +  + 
  gi|242399755|ref|YP_002995180.1|  63 KERIKVYERAQNGVRVFAFSSNLLDNKDVYGPGWEGMLGKAVQFGKASVGLLNYLIEKEGKPDVL-HFHDWHTVFAA 138
                                       5555666666666777788889999999999999999999*************999999999876.*******9999 PP

                                       HHHHHTT-SEEEEEEES CS
                      Glycogen_syn 158 iltrkrkldvatvftth 174
                                       +l++k   ++ + ft h
  gi|242399755|ref|YP_002995180.1| 139 TLIKK-YFQLPATFTIH 154
                                       98875.45666667777 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.24
                                       EEEEEEESSS-TTTTTHHHHHHHHHH CS
                      Glycogen_syn 292 tlyffiaGryefsnkGadifieslar 317
                                        + f+  Gr++   kG+d +++++  
  gi|242399755|ref|YP_002995180.1| 255 GITFMFIGRFDKGQKGVDTLLKAVEN 280
                                       5567777************9988765 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0011
                                       -SEEE---SSBSS-HHHHHHHHTT--EEEETTBHHHHHHHHH-T.TGGGGTEEEE--SSS-HHHHHHHHHHHHHHHH CS
                      Glycogen_syn 469 chlGvfpsyyepwGytpaectvmGipsvttnlsGfGcfmeelie.dakdyGiyivdrrfkslddsveqlaqflyefv 544
                                       + + + psy+ep+G    e   +G   + + + G    +  l e ++k+ G+ +  r  ++l  ++ +++q+ ++  
  gi|242399755|ref|YP_002995180.1| 338 VDFVIVPSYFEPFGLVQMEAMCLGAIPIGSAVGGIKDTIISLDEdEEKATGLLVPPRDPNALAGAILKMTQLREKDP 414
                                       456689******************99999999999877666666255677888888888888888888877766554 PP

                                       T--HH CS
                      Glycogen_syn 545 kksrr 549
                                       +   +
  gi|242399755|ref|YP_002995180.1| 415 ELLSK 419
                                       44444 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 ?   13.3   0.0   3.3e-05     0.084       6      90 ..     345     441 ..     340     443 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.3e-05
                   Glyco_trans_1_2   6 srsespnlrlfEaaacGafaltddaegleelftpgk......evilfe..dleelaekirylla....npeerraia 70 
                                       s  e + l+  Ea+  Ga+ + ++  g+ + +   +      +++l+   d++ la +i ++ +    +pe+ ++++
  gi|242399755|ref|YP_002995180.1| 345 SYFEPFGLVQMEAMCLGAIPIGSAVGGIKDTIISLDedeekaTGLLVPprDPNALAGAILKMTQlrekDPELLSKMR 421
                                       5556677788888888888888877777775544444556667777777887777776655544334899******* PP

                   Glyco_trans_1_2  71 eaarervlaehtydhraeql 90 
                                       +++++r ++++t++++ +++
  gi|242399755|ref|YP_002995180.1| 422 KNGKRRSKEDFTWENACKRY 441
                                       **************998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (457 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.68u 0.32s 00:00:01.00 Elapsed: 00:00:00.53
# Mc/sec: 2604.74
//
Query:       gi|242399756|ref|YP_002995181.1|  [L=90]
Description: Histidine triad (HIT) protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-10   41.7   0.0    1.7e-10   41.5   0.0    1.0  1  HIT       HIT domain
    2.1e-08   34.6   0.0    2.5e-08   34.4   0.0    1.1  1  DcpS_C    Scavenger mRNA decapping enzyme C-term binding
  ------ inclusion threshold ------
       0.08   12.8   0.5       0.13   12.1   0.5    1.5  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 !   41.5   0.0   2.9e-14   1.7e-10       5      76 ..      10      81 ..       7      86 .. 0.96

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 2.9e-14
                                      -CCEEEE-SSEEEEE-SS-SSSSEEEEEESSTGCSGGGCCHHHHHHHHHHHHHHHHHHHTCTTCCCEEEEEE CS
                               HIT  5 pstvvyeddlvlafldidpkapghlLvipkkhlselhdlteeelakllsavkkvakalqkkfknkglrvvin 76
                                      ++ +vye++ + ++ d+ p  +ghlL++pk+h+++l++l+e+e   l++ +++  ++l+k+++ +g+++ +n
  gi|242399756|ref|YP_002995181.1| 10 EDVLVYENEFIRILIDSYPANRGHLLIVPKRHVEKLEELNEKEKLVLIEGIEMAIEKLKKVLEPDGFNIGVN 81
                                      6889****************************************************************9887 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 !   34.4   0.0   4.2e-12   2.5e-08      12      89 ..       9      83 ..       2      86 .. 0.76

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 4.2e-12
                                      S-B-EEEE-SSEEEEE-SS-SSSEEEEEEESS---SGGG--TTTTTHHHHHHHHHHHHHHHTT-T-EEEEE--SCCCT CS
                            DcpS_C 12 epervvyedekfvvlkDikpkaklhllvipkrdikslrdLtkehlpllkemrekakkvieekynevdaeelrvgvhyq 89
                                      +++ +vye+e + +l D +p+++ hll++pkr++++l++L++++  +l e  e a + +++    ++++ +++gv+y+
  gi|242399756|ref|YP_002995181.1|  9 SEDVLVYENEFIRILIDSYPANRGHLLIVPKRHVEKLEELNEKEKLVLIEGIEMAIEKLKK---VLEPDGFNIGVNYP 83
                                      3445699*********************************877655555443333333333...35899999999997 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 ?   12.1   0.5   2.2e-05      0.13      42      67 ..      27      52 ..       1      71 [. 0.75

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.2e-05
                                      S-SSTT-EEEEESS--SSTTSS-HHH CS
                          CwfJ_C_1 42 gpLssgHvliipieHisallsldeev 67
                                       p + gH+li+p  H+++l +l+e++
  gi|242399756|ref|YP_002995181.1| 27 YPANRGHLLIVPKRHVEKLEELNEKE 52
                                      56689***************999965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       663  (0.0369792); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.36s 00:00:00.85 Elapsed: 00:00:00.52
# Mc/sec: 520.68
//
Query:       gi|242399757|ref|YP_002995182.1|  [L=250]
Description: Nucleotide pyrophosphohydrolase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.1e-25   88.2   0.3    1.7e-24   86.3   0.0    1.9  2  tRNA_edit  Aminoacyl-tRNA editing domain
    1.7e-19   69.9   8.3    1.7e-19   69.9   8.3    2.4  3  MazG-like  MazG-like family
    1.7e-05   24.9   5.3    1.7e-05   24.9   5.3    2.0  2  MazG       MazG nucleotide pyrophosphohydrolase domain
  ------ inclusion threshold ------
      0.012   16.0   0.5      0.031   14.7   0.5    1.8  1  PRA-PH     Phosphoribosyl-ATP pyrophosphohydrolase


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 ?   -0.2   0.1      0.23     1e+03      34      70 ..      73     111 ..      47     115 .. 0.80
   2 !   86.3   0.0   3.8e-28   1.7e-24       3     123 .]     125     240 ..     123     240 .. 0.97

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.23
                         tRNA_edit  34 lvlvllpgdreldlkk.lakllga.kklrlaseeelrel 70 
                                        +lvll ++  +dl+k ++++l++  +  +a+e +++el
  gi|242399757|ref|YP_002995182.1|  73 IYLVLLAHELGIDLDKaVREKLKKnEEKYPAKEIRIEEL 111
                                       578888888888886527888887677778888888876 PP

  == domain 2  score: 86.3 bits;  conditional E-value: 3.8e-28
                         tRNA_edit   3 gtktieelaaalgvdpsaiaKtlvlkdkkgelvlvllpgdreldlkklakllgakklrlaseeelrellgvepGgvg 79 
                                       ++kt+ ++++ l + p++i+K+l++ ++++e+vlv++ g+ ++ l kl++ +g  ++r+a+++e+++++g+++Gg++
  gi|242399757|ref|YP_002995182.1| 125 EVKTVRQVVELLSIQPDQIIKSLLFIVNEKEPVLVIVDGSSKASLEKLSRIFG--NIRMAKPKEVEQITGYKVGGIP 199
                                       689**************************************************..********************** PP

                         tRNA_edit  80 PlglkaagvpvllDeslkeyptvvvgagengatlelspedlrkl 123
                                       P+g+    v++++D++++e+  v++g+g+ +++ +l+p+ ++++
  gi|242399757|ref|YP_002995182.1| 200 PVGIP---VKTVIDKKVVEKVFVIGGGGRVDRLSKLDPKKIVEF 240
                                       ****6...*****************************9988765 PP

>> MazG-like  MazG-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0         3   1.3e+04      55      65 ..       2      12 ..       1      15 [. 0.77
   2 !   69.9   8.3   3.7e-23   1.7e-19       1      74 [.      30     105 ..      30     115 .. 0.93
   3 ?   -1.8   0.0      0.85   3.8e+03      53      66 ..     202     216 ..     201     218 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 3
                         MazG-like 55 dfeeideklkk 65
                                      +f+ei+ek  k
  gi|242399757|ref|YP_002995182.1|  2 SFKEIEEKAVK 12
                                      78899998766 PP

  == domain 2  score: 69.9 bits;  conditional E-value: 3.7e-23
                         MazG-like   1 isknlkaiElLkaellksveelfkallk.gseeeildeLAdviiylylLAdrlGidfee.ideklkkklkkypvek 74 
                                       is  ++  ElL+++++++ ee+++ l + + +e+i de+Ad+iiyl+lLA++lGid+++ ++eklkk+++kyp+++
  gi|242399757|ref|YP_002995182.1|  30 ISLAIELGELLEHFQWETNEEILEKLNNtEIKEKIEDEIADIIIYLVLLAHELGIDLDKaVREKLKKNEEKYPAKE 105
                                       7899**********************96599******************************************987 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.85
                         MazG-like  53 Gidfee.ideklkkk 66 
                                       Gi +++ id+k+ +k
  gi|242399757|ref|YP_002995182.1| 202 GIPVKTvIDKKVVEK 216
                                       89999999**99887 PP

>> MazG  MazG nucleotide pyrophosphohydrolase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   5.3   3.8e-09   1.7e-05       5      71 ..      27     102 ..      23     104 .. 0.73
   2 ?   -3.7   0.2       3.2   1.4e+04      27      34 ..     109     116 ..     107     118 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 3.8e-09
                                       HHHHHHHHHHHHHHHHHHTT-HH.............HHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHH CS
                              MazG   5 tllaylleEvgEvaeaIkkedrd.............eleeELGDvLlqvlflaniaeeeggidledvaetileKler 68 
                                       +l+  l+ E gE++e  + e  +             ++e+E++D+++++++la+    e+gidl++++++ l+K e+
  gi|242399757|ref|YP_002995182.1|  27 NLAISLAIELGELLEHFQWETNEeileklnnteikeKIEDEIADIIIYLVLLAH----ELGIDLDKAVREKLKKNEE 99 
                                       555566666666666666633333333444444445******************....5****************99 PP

                                       H-G CS
                              MazG  69 Rhp 71 
                                       ++p
  gi|242399757|ref|YP_002995182.1| 100 KYP 102
                                       988 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 3.2
                                       HHHHHHHH CS
                              MazG  27 deleeELG 34 
                                       +el +ELG
  gi|242399757|ref|YP_002995182.1| 109 EELIKELG 116
                                       57888888 PP

>> PRA-PH  Phosphoribosyl-ATP pyrophosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.5     7e-06     0.031      30      78 ..      43      92 ..      21      98 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 7e-06
                                      HHHHHHHHHHHHT-SC.HHHHHHHHHHHHHHHHHHHHHHCT--CHHHHHH CS
                            PRA-PH 30 ligEEavElleaaseg.dlaeladelaDllYvtygllvllGidldavfee 78
                                      +  E  +E le  ++   ++++ de+aD++  +  l+++lGidld+  +e
  gi|242399757|ref|YP_002995182.1| 43 FQWETNEEILEKLNNTeIKEKIEDEIADIIIYLVLLAHELGIDLDKAVRE 92
                                      44455667777666543788999******99999**********976654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1137  (0.0634168); expected 358.6 (0.02)
Passed bias filter:                      639  (0.0356406); 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: 0.65u 0.36s 00:00:01.01 Elapsed: 00:00:00.57
# Mc/sec: 1322.81
//
Query:       gi|242399758|ref|YP_002995183.1|  [L=95]
Description: hypothetical protein TSIB_1783 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.047   14.0   0.5      0.047   14.0   0.5    2.0  2  dsDNA_bind  Double-stranded DNA-binding domain
       0.11   12.6   0.2       0.19   11.8   0.2    1.4  1  YqzH        YqzH-like protein
       0.12   11.6   0.2       0.11   11.7   0.2    1.1  1  DUF4704     Domain of unknown function (DUF4704)
       0.78    9.8   3.0         17    5.4   0.1    2.0  2  HAD_2       Haloacid dehalogenase-like hydrolase


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 ?    0.8   0.2      0.13     6e+02      89     108 ..       2      21 ..       1      25 [. 0.79
   2 ?   14.0   0.5     1e-05     0.047      63      98 ..      50      85 ..      42      94 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.13
                                       HHHHHHHHHS---XXXXX.. CS
                        dsDNA_bind  89 qLkeLLeqvaekkketkivi 108
                                       ++keLLe v+e   + ki i
  gi|242399758|ref|YP_002995183.1|   2 KIKELLELVDEAIANVKIAI 21 
                                       689*******9777777755 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 1e-05
                                      HHHHHHHHHHHHHHH--SS-----HHHHHHHHHHHS CS
                        dsDNA_bind 63 eraeavenrLiqlaqsGqlrskvteeqLkeLLeqva 98
                                      er +++ ++L q  ++ ++++k +ee+LkeLLe + 
  gi|242399758|ref|YP_002995183.1| 50 ERLNKIRKYLQQFGEEEHVEGKFSEEELKELLEYLR 85
                                      78899***************************9775 PP

>> YqzH  YqzH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   4.3e-05      0.19       9      43 ..      54      89 ..      52      94 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.3e-05
                              YqzH  9 mirkclrqYgrdtelm.plseeeqkeLveriqekkk 43
                                      +irk l+q+g ++ +  + seee keL e++   ++
  gi|242399758|ref|YP_002995183.1| 54 KIRKYLQQFGEEEHVEgKFSEEELKELLEYLRVMRE 89
                                      79*********98875589*********99876655 PP

>> DUF4704  Domain of unknown function (DUF4704)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   2.5e-05      0.11     200     252 ..      40      90 ..       5      94 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.5e-05
                           DUF4704 200 sksldgerpsqeeilklRallLllikqlvlkgsgisedelqallnylltvhed 252
                                       + sl+    + e ++k+R++l ++ ++  + + + se+el+ ll yl  ++e+
  gi|242399758|ref|YP_002995183.1|  40 KRSLK-LEDELERLNKIRKYLQQFGEEEHV-EGKFSEEELKELLEYLRVMREM 90 
                                       44443.36678999*************999.99**************999986 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.1    0.0038        17      84     106 ..       3      27 ..       1      35 [. 0.74
   2 ?    5.2   0.6    0.0044        20      53      92 ..      46      85 ..      30      90 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0038
                             HAD_2  84 vkelLeeLke..agyklgivTsksr 106
                                       +kelLe + e  a++k++iv++k+r
  gi|242399758|ref|YP_002995183.1|   3 IKELLELVDEaiANVKIAIVSNKQR 27 
                                       55666655432279*********87 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0044
                             HAD_2 53 geseeeee..kieellrkyneekkkkevkpydgvkelLeeLk 92
                                      +++ e     ki ++l+++ ee++ +     +++kelLe+L+
  gi|242399758|ref|YP_002995183.1| 46 EDELE--RlnKIRKYLQQFGEEEHVEGKFSEEELKELLEYLR 85
                                      23333..155999999***99999977777789999999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1441  (0.0803726); expected 358.6 (0.02)
Passed bias filter:                      689  (0.0384294); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.36s 00:00:00.95 Elapsed: 00:00:00.55
# Mc/sec: 518.72
//
Query:       gi|242399759|ref|YP_002995184.1|  [L=90]
Description: hypothetical protein TSIB_1784 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.033   14.1   0.5      0.037   13.9   0.5    1.1  1  DUF3487          Protein of unknown function (DUF3487)
      0.041   13.4   0.7      0.068   12.7   0.7    1.4  1  SieB             Super-infection exclusion protein B
       0.15   12.1   6.5       0.18   11.8   6.5    1.1  1  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe
       0.18   11.4   2.3       0.22   11.2   2.3    1.1  1  DUF4131          Domain of unknown function (DUF4131)
       0.58    8.9   4.7       0.67    8.6   4.7    1.0  1  DUF2207          Predicted membrane protein (DUF2207)
       0.83    9.7   0.1       0.83    9.7   0.1    2.1  2  OapA_N           Opacity-associated protein A N-terminal moti
        9.5    5.8   8.9        2.8    7.5   1.2    2.3  2  NapE             Periplasmic nitrate reductase protein NapE


Domain annotation for each model (and alignments):
>> DUF3487  Protein of unknown function (DUF3487)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.5   1.4e-05     0.037      28      83 ..      18      73 ..      10      88 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.4e-05
                           DUF3487 28 laglglvvglvlglllallvgslaliptialllvllvvlvggkllarlKRgkPdty 83
                                       ++lg+++ +++gl++++++g  +li t +l + l++++v++ +  ++ R+  + y
  gi|242399759|ref|YP_002995184.1| 18 KILLGIMAAVIIGLFAIPALGIATLIKTYGLGIGLVFLIVAAAYGFTVWRRSAEAY 73
                                      5789**************************99888888888777666666555555 PP

>> SieB  Super-infection exclusion protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.7   2.7e-05     0.068      19      69 ..      34      83 ..      17      86 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.7e-05
                              SieB 19 leklnlgkfleeyglwiglvflisiayllaqvvskllaeikekikkkreqk 69
                                      + +l+++ ++++ygl iglvfli++a      v++ +ae+++k + k++++
  gi|242399759|ref|YP_002995184.1| 34 IPALGIATLIKTYGLGIGLVFLIVAAAY-GFTVWRRSAEAYAKAHGKYFYD 83
                                      557999*****************96644.5568888889988888887765 PP

>> Phage_holin_3_6  Putative Actinobacterial Holin-X, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   6.5   7.1e-05      0.18      36      91 ..      19      69 ..      12      77 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.1e-05
                   Phage_holin_3_6 36 gagllgaagvlallalllllvala...lalaalwlaalivaavllvlagvlalvglkkl 91
                                       ++ ++aa++++l+a+++l +a +   ++l         +++v+l++a++ ++  +++ 
  gi|242399759|ref|YP_002995184.1| 19 ILLGIMAAVIIGLFAIPALGIATLiktYGL--------GIGLVFLIVAAAYGFTVWRRS 69
                                      455566777777777777777774344555........258888888888888877765 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   2.3   8.6e-05      0.22       6      61 ..      25      75 ..      16      82 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 8.6e-05
                           DUF4131  6 alvllalllllllllllllrrrprrrvllllllllllallgfalrapqpnandlsq 61
                                      a+v+++l+++ +l ++        +++ l+++l++l++++ + +++++++a+ +++
  gi|242399759|ref|YP_002995184.1| 25 AAVIIGLFAIPALGIAT-----LIKTYGLGIGLVFLIVAAAYGFTVWRRSAEAYAK 75
                                      34444444444444444.....468999*******************999987765 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   4.7   0.00026      0.67     385     443 ..      17      74 ..      10      83 .. 0.56

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00026
                           DUF2207 385 alglgliilglilillallllvlllvfllilllillliaiivlllfsrllgrrteeGae 443
                                       + +l++i++++i++l+a+ +l++  +++  ++l+++l+++iv++ +  ++ rr++e ++
  gi|242399759|ref|YP_002995184.1|  17 YKILLGIMAAVIIGLFAIPALGI-ATLIKTYGLGIGLVFLIVAAAYGFTVWRRSAEAYA 74 
                                       34444455555555555555555.66666666666666666666665555566655554 PP

>> OapA_N  Opacity-associated protein A N-terminal motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1   0.00032      0.83       9      27 ..      17      35 ..      15      36 .. 0.94
   2 ?   -0.5   1.0       0.5   1.3e+03      13      24 ..      48      59 ..      47      60 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00032
                            OapA_N  9 HRrlliaLslvvlvlllwP 27
                                      +++ll++ ++v++ l+++P
  gi|242399759|ref|YP_002995184.1| 17 YKILLGIMAAVIIGLFAIP 35
                                      689**************99 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.5
                            OapA_N 13 liaLslvvlvll 24
                                      l++  ++++v++
  gi|242399759|ref|YP_002995184.1| 48 LGIGLVFLIVAA 59
                                      677777777765 PP

>> NapE  Periplasmic nitrate reductase protein NapE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   3.2       0.1   2.6e+02      20      44 ..      27      52 ..      19      57 .. 0.74
   2 ?    7.5   1.2    0.0011       2.8      34      43 ..      57      66 ..      53      70 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.1
                              NapE 20 lfltvvlfPiLsVa.lVggYGfivWm 44
                                      +++ ++ +P+L +a l+  YG+ + +
  gi|242399759|ref|YP_002995184.1| 27 VIIGLFAIPALGIAtLIKTYGLGIGL 52
                                      5666777899999636999*998855 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0011
                              NapE 34 lVggYGfivW 43
                                      + ++YGf+vW
  gi|242399759|ref|YP_002995184.1| 57 VAAAYGFTVW 66
                                      5689****** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       863  (0.0481343); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 552.42
//
Query:       gi|242399760|ref|YP_002995185.1|  [L=632]
Description: Indolepyruvate: ferredoxin oxidoreductase (IOR), subunit alpha [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-32  112.0   0.1    4.3e-32  111.0   0.1    1.5  1  TPP_enzyme_C    Thiamine pyrophosphate enzyme, C-terminal TPP
    2.4e-13   50.4   0.0    3.7e-13   49.8   0.0    1.3  1  POR_N           Pyruvate flavodoxin/ferredoxin oxidoreductase
    1.6e-09   37.2   9.6    8.5e-06   25.4   1.8    2.8  2  Fer4            4Fe-4S binding domain
    8.5e-07   29.0   6.5    2.1e-06   27.8   6.5    1.7  1  Fer4_9          4Fe-4S dicluster domain
    3.9e-06   26.6  15.1    0.00091   19.2   0.6    2.9  2  Fer4_2          4Fe-4S binding domain
    5.6e-06   26.9   6.8    1.8e-05   25.2   6.9    1.9  1  Fer4_7          4Fe-4S dicluster domain
    7.6e-06   25.9   6.7      2e-05   24.6   6.7    1.8  1  Fer4_10         4Fe-4S dicluster domain
    0.00016   21.6  15.1     0.0079   16.2   1.1    2.8  2  Fer4_6          4Fe-4S binding domain
    0.00016   21.7  11.8     0.0031   17.6  10.9    2.6  2  Fer4_21         4Fe-4S dicluster domain
    0.00071   19.2   0.1       0.32   10.6   0.1    2.2  2  TPP_enzyme_N    Thiamine pyrophosphate enzyme, N-terminal TPP
      0.006   17.0  10.2       0.31   11.6   1.2    2.7  2  Fer4_4          4Fe-4S binding domain
  ------ inclusion threshold ------
      0.015   14.9   0.0          2    8.0   0.0    2.5  2  Transket_pyr    Transketolase, pyrimidine binding domain
      0.029   14.8   5.8          1    9.8   0.8    2.5  2  Fer4_8          4Fe-4S dicluster domain
      0.062   13.6   0.1       0.14   12.5   0.1    1.6  1  PFOR_II         Pyruvate:ferredoxin oxidoreductase core domai
      0.069   12.4   0.5        4.8    6.3   0.0    2.2  2  DXP_synthase_N  1-deoxy-D-xylulose-5-phosphate synthase
       0.26   12.2   9.7       0.23   12.4   1.1    2.6  2  Fer4_16         4Fe-4S double cluster binding domain
       0.31   12.1  13.6      0.065   14.2   3.9    2.8  2  Fer4_3          4Fe-4S binding domain
        0.7   10.5   7.1        6.9    7.3   1.1    2.7  2  Fer4_13         4Fe-4S single cluster domain of Ferredoxin I
       0.81   10.3  11.9       0.52   10.9   2.0    2.5  2  Fer4_17         4Fe-4S dicluster domain
       0.83   10.4  11.1        4.1    8.2   2.1    2.6  2  Fer4_15         4Fe-4S single cluster 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 !  111.0   0.1   4.8e-35   4.3e-32       1     152 [.     413     554 ..     413     555 .. 0.96

  Alignments for each domain:
  == domain 1  score: 111.0 bits;  conditional E-value: 4.8e-35
                                       ESSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEE CS
                      TPP_enzyme_C   1 diGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGaklakpdrevvaivGDGgflmi.lqelatavrrnlpit 76 
                                       diGc+ l      ++ +p + +   +   mG +++ A G ++a  +++++a++GD++f+++ lq l+ av++nl+++
  gi|242399760|ref|YP_002995185.1| 413 DIGCYAL------SLLPPLEAIW--TEYVMGASISLANGQSIAM-NKKIIATIGDSTFFHNgLQPLVDAVYKNLDVL 480
                                       8999999......8899999999..8899*************85.67****************************** PP

                                       EEEEE-SBCCCHHHHHHHHTCCTTTTSBB.BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHHHHCSSSEEEEE CS
                      TPP_enzyme_C  77 vvvlnNegygmtggqqepfggkrksgpagkdlkpvdfaklaealGak.garvekadveeleealkealekkgpalie 152
                                       v++l+N++++mtg+q++p +g++++g +   ++++df++l++alG+k +  v+++d++ ++ea+kea++ kgpa+i 
  gi|242399760|ref|YP_002995185.1| 481 VMILDNRTTAMTGHQPHPGTGGSETGRK---FNEIDFEALVRALGVKyVKIVDPYDLKATKEAIKEAMQVKGPAVII 554
                                       ***********************99988...****************888*************************96 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 !   49.8   0.0   4.1e-16   3.7e-13       2     170 ..      34     195 ..      33     238 .. 0.85

  Alignments for each domain:
  == domain 1  score: 49.8 bits;  conditional E-value: 4.1e-16
                                       HHHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCC CS
                             POR_N   2 aaiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmien 78 
                                       +a++ gv ++++YP TPs+e++e++a+l +++         + +E  a + ++  a++G ra+++    Gl  + + 
  gi|242399760|ref|YP_002995185.1|  34 GALESGVSFATGYPGTPSTEVIETIARLNPEVFA-----EWAPNEKVALEEAASVAYTGLRALVTMKCVGLNVAADP 105
                                       789999**********************998885.....57889*****************************9998 PP

                                       HHHHH..HTT--EEEEEEEEE-STTBEEEEE--TTCHHHHS---EEEE-SSHHHHHHHHHHHHHHHHHCTSEEEEEE CS
                             POR_N  79 lglaa..geelPvvivvvaRalpstglsirtdqsDlmaardtglivlasenvqeafdlalvAfnlAekvrvPvivlf 153
                                       l+  a  g e  +vi v+   +p t    +t+q D ++     l vl +++vqea+dl+  A+ l+ek++vPvi  +
  gi|242399760|ref|YP_002995185.1| 106 LMSLAysGVEGGLVILVADDPGPHT---SQTEQDDRYYGKLALLPVLEPADVQEAHDLIKYAYELSEKYKVPVIFRT 179
                                       887652377889*************...89*******************************************9988 PP

                                       EHHHH.HEEEEEEC-SG CS
                             POR_N 154 Dgfllshevekvelpde 170
                                          +  h+  +ve+ + 
  gi|242399760|ref|YP_002995185.1| 180 TTRVN-HTTADVEVGEF 195
                                       77666.99999988653 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   1.2   1.3e-05     0.012       1      15 [.     573     587 ..     573     588 .. 0.92
   2 !   25.4   1.8   9.5e-09   8.5e-06       2      23 ..     605     626 ..     604     627 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.3e-05
                                       EEEETTTSSS-THHH CS
                              Fer4   1 vvideekCigCGaCv 15 
                                       +v++++kC+gC+aC+
  gi|242399760|ref|YP_002995185.1| 573 PVVIKDKCTGCKACA 587
                                       6899**********8 PP

  == domain 2  score: 25.4 bits;  conditional E-value: 9.5e-09
                                       EEETTTSSS-THHHHHSTTTEE CS
                              Fer4   2 videekCigCGaCvevCPvgAI 23 
                                        +d   C+gCG+C++ CP+++I
  gi|242399760|ref|YP_002995185.1| 605 SVDSLICTGCGLCEQLCPFDVI 626
                                       578889**************99 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   6.5   2.3e-09   2.1e-06       1      51 []     579     626 ..     579     627 .. 0.91

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 2.3e-09
                            Fer4_9   1 kCtgCgaC..veaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                       kCtgC+aC   + Cpa v+ e++++  +   +     C+gCg C++ Cp ++i
  gi|242399760|ref|YP_002995185.1| 579 KCTGCKACalLTGCPALVFDEERGKISVDSLI-----CTGCGLCEQLCPFDVI 626
                                       7*******77788**************99866.....************8865 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   2.2   6.9e-06    0.0061       2      22 .]     572     594 ..     571     594 .. 0.85
   2 !   19.2   0.6     1e-06   0.00091       2      21 ..     603     622 ..     602     623 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 6.9e-06
                            Fer4_2   2 pvvvdtdrCigCgaCv..saCPa 22 
                                        +vv  d+C+gC+aC   + CPa
  gi|242399760|ref|YP_002995185.1| 572 IPVVIKDKCTGCKACAllTGCPA 594
                                       589999*********65588**8 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 1e-06
                            Fer4_2   2 pvvvdtdrCigCgaCvsaCP 21 
                                       ++ vd+ +C+gCg C + CP
  gi|242399760|ref|YP_002995185.1| 603 KISVDSLICTGCGLCEQLCP 622
                                       5779**************** PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   6.9   2.1e-08   1.8e-05       1      52 []     579     625 ..     579     625 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 2.1e-08
                            Fer4_7   1 rCigCgaCv..aaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                       +C+gC+aC+    Cp  a+ +dee     + k+ +d+  C+gCg C++ CP+++
  gi|242399760|ref|YP_002995185.1| 579 KCTGCKACAllTGCP--ALVFDEE-----RGKISVDSLICTGCGLCEQLCPFDV 625
                                       7*******9666788..7778776.....569*******************986 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   6.7   2.3e-08     2e-05       3      56 .]     574     622 ..     572     624 .. 0.91

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 2.3e-08
                           Fer4_10   3 vidddtCirCgkCvk..aCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       v+ +d+C++C++C     CPa         +++e +++++++  Ctgcg C + CP
  gi|242399760|ref|YP_002995185.1| 574 VVIKDKCTGCKACALltGCPA-------LVFDEERGKISVDSLICTGCGLCEQLCP 622
                                       56679********97436***.......***************************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 !   14.8   1.7   2.5e-05     0.022       1      21 [.     572     594 ..     572     597 .. 0.86
   2 !   16.2   1.1   8.9e-06    0.0079       1      24 []     603     626 ..     603     626 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.5e-05
                            Fer4_6   1 vveidpdkCigCgdC..vrvCPe 21 
                                       ++++ +dkC+gC +C   + CP+
  gi|242399760|ref|YP_002995185.1| 572 IPVVIKDKCTGCKACalLTGCPA 594
                                       699************76666886 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 8.9e-06
                            Fer4_6   1 vveidpdkCigCgdCvrvCPegai 24 
                                       ++ +d   C+gCg C+  CP+++i
  gi|242399760|ref|YP_002995185.1| 603 KISVDSLICTGCGLCEQLCPFDVI 626
                                       57899999*************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 !   10.1   3.2   0.00074      0.66      33      52 ..     572     593 ..     553     598 .. 0.71
   2 !   17.6  10.9   3.5e-06    0.0031       5      57 ..     577     626 ..     574     628 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00074
                           Fer4_21  33 vlkvvedeCvGCnlCssv..CP 52 
                                       +  v++d+C+GC+ C+    CP
  gi|242399760|ref|YP_002995185.1| 572 IPVVIKDKCTGCKACALLtgCP 593
                                       33467**********8543377 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 3.5e-06
                           Fer4_21   5 edkCigCgkCliaCedtshqaieidakt.vlkvvedeCvGCnlCssvCPvedci 57 
                                       +dkC gC+ C++     +  a+ +d+++ ++ v +  C+GC lC + CP  d+i
  gi|242399760|ref|YP_002995185.1| 577 KDKCTGCKACALLT---GCPALVFDEERgKISVDSLICTGCGLCEQLCPF-DVI 626
                                       69********9863...35599999887356777889************7.655 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 !   10.6   0.1   0.00036      0.32       5     144 ..      29     181 ..      25     188 .. 0.76
   2 !    6.5   0.0    0.0066       5.9      78     159 ..     464     555 ..     441     560 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00036
                                       HHHHHHHHHCT--EEEE---CCCHHHHCCHHCT..TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHH.HHHHC CS
                      TPP_enzyme_N   5 ealvraLkalgvehvfgvpGsrilplldalseeq.girvvlarhEqgaafaAdgyaratgkpgvvlvtsgp.Gatna 79 
                                       ea++    + gv  + g+pG+ ++++++ +++ + ++    a +E +a   A  +a    +  v + ++g   a+  
  gi|242399760|ref|YP_002995185.1|  29 EAIAYGALESGVSFATGYPGTPSTEVIETIARLNpEVFAEWAPNEKVALEEAASVAYTGLRALVTMKCVGLnVAADP 105
                                       6666666677***********************7555556699***********99998777777777788346789 PP

                                       HHHHHHHHHHT--EEEEEEE--CCCHH.............S..TC--T-CCHHHCCCSSEEEE-SSGGGHHHHHHHH CS
                      TPP_enzyme_N  80 ltalaeAkvdriPllvlsgdrptslrg.............qgvlqqeldqlalfrpvtkyaervtspeelpealrrA 143
                                       l++la   v++  +++++ d++ +  +              +vl+++  q+  + ++ kya++++++  +p+++r  
  gi|242399760|ref|YP_002995185.1| 106 LMSLAYSGVEGGLVILVADDPGPHTSQteqddryygklalLPVLEPADVQE--AHDLIKYAYELSEKYKVPVIFRTT 180
                                       999999999998888887777666666667676666555555555333333..358999999999999999888876 PP

                                       H CS
                      TPP_enzyme_N 144 i 144
                                        
  gi|242399760|ref|YP_002995185.1| 181 T 181
                                       5 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0066
                                       HCHHHHHHHHHHT--EEEEEEE--CCCHH.............S..TC--T-CCHHHCCCSSEEEE-SSGGGHHHHHH CS
                      TPP_enzyme_N  78 naltalaeAkvdriPllvlsgdrptslrg.............qgvlqqeldqlalfrpvtkyaervtspeelpealr 141
                                       n+l  l++A + ++ +lv+  d+ t+                   ++ e+d +al+r +    +++ +p +  +a +
  gi|242399760|ref|YP_002995185.1| 464 NGLQPLVDAVYKNLDVLVMILDNRTTAMTghqphpgtggsetGRKFN-EIDFEALVRALGVKYVKIVDPYD-LKATK 538
                                       88889999999999999888888777777689999988998544444.89*********999999999998.56889 PP

                                       HHHHHHHSSS--EEEEEE CS
                      TPP_enzyme_N 142 rAirtalsgrpgPvylel 159
                                       +Ai++a  + +gP+++  
  gi|242399760|ref|YP_002995185.1| 539 EAIKEA-MQVKGPAVIIA 555
                                       999999.78888988865 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   2.2     0.002       1.8       1      11 [.     577     587 ..     577     595 .. 0.84
   2 !   11.6   1.2   0.00035      0.31       4      16 ..     611     623 ..     600     624 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.002
                            Fer4_4   1 qerCigCgsCv 11 
                                       +++C+gC++C 
  gi|242399760|ref|YP_002995185.1| 577 KDKCTGCKACA 587
                                       69********6 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00035
                            Fer4_4   4 CigCgsCvaaCPq 16 
                                       C+gCg C+  CP+
  gi|242399760|ref|YP_002995185.1| 611 CTGCGLCEQLCPF 623
                                       ************7 PP

>> Transket_pyr  Transketolase, pyrimidine binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.034        31     124     171 ..     131     180 ..     122     185 .. 0.86
   2 ?    8.0   0.0    0.0023         2      99     173 ..     481     558 ..     415     560 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.034
                                       TSBSSHHHHHHTSTTEEEE--SSHHHHHHHHHHHHHS..SS.SEEEEEE- CS
                      Transket_pyr 124 hqsaeleaflrlipglkvvrPsdpaetkhllrrairr..edrkPvvlrlp 171
                                        q  ++ +++  ++ l v+ P+d +e+  l++ a++   +++ Pv++r++
  gi|242399760|ref|YP_002995185.1| 131 SQTEQDDRYYGKLALLPVLEPADVQEAHDLIKYAYELseKYKVPVIFRTT 180
                                       45667788999999999*******************9888899***9987 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0023
                                       HHHHHT--EEEEESBSG...GGSTTGTTTSBSSHHHHHHTSTT..EEEE--SSHHHHHHHHHHHHHSSS.SEEEEEE CS
                      Transket_pyr  99 geakgklkvgvvtrlpi...gvgedGpehqsaeleaflrlipg..lkvvrPsdpaetkhllrrairredrkPvvlrl 170
                                        + + ++++ ++ + p+   g  e G   + +  ea+ r++    +k+v P+d   tk+++++a++   ++P v++ 
  gi|242399760|ref|YP_002995185.1| 481 VMILDNRTTAMTGHQPHpgtGGSETGRKFNEIDFEALVRALGVkyVKIVDPYDLKATKEAIKEAMQV--KGPAVIIA 555
                                       4556666666777766643356667777777788888887754779********************5..57****99 PP

                                       -SS CS
                      Transket_pyr 171 pks 173
                                       +++
  gi|242399760|ref|YP_002995185.1| 556 KRE 558
                                       885 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.4    0.0095       8.6       3      17 ..     578     594 ..     573     606 .. 0.76
   2 ?    9.8   0.8    0.0012         1       5      17 ..     611     623 ..     607     630 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0095
                            Fer4_8   3 ekCieCgaCq..saCpv 17 
                                       +kC++C aC   + Cp+
  gi|242399760|ref|YP_002995185.1| 578 DKCTGCKACAllTGCPA 594
                                       57888888877667774 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0012
                            Fer4_8   5 CieCgaCqsaCpv 17 
                                       C++Cg+C++ Cp+
  gi|242399760|ref|YP_002995185.1| 611 CTGCGLCEQLCPF 623
                                       7777777777763 PP

>> PFOR_II  Pyruvate:ferredoxin oxidoreductase core domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   0.00016      0.14       2      81 ..     250     321 ..     249     332 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00016
                                       SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHHHHHHHT CS
                           PFOR_II   2 evvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlveevkaal 78 
                                       e+ i+a G+  + +k++v ++   g k  +l++ t  P P++ + e+lk+vkk +v++  +       l ee+k   
  gi|242399760|ref|YP_002995185.1| 250 EIGIIAEGAPYNYVKEVVPKIG-GGFK--ILKISTPHPLPRKLVVEFLKGVKKAIVVEDGA-----PFLEEEIKIVA 318
                                       6778888888888888888764.3444..7****************************988.....67777777776 PP

                                       GGG CS
                           PFOR_II  79 kks 81 
                                       +++
  gi|242399760|ref|YP_002995185.1| 319 YEE 321
                                       665 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 ?    3.9   0.3      0.03        26     115     174 ..     436     489 ..     431     495 .. 0.81
   2 ?    6.3   0.0    0.0054       4.8     231     269 ..     515     553 ..     500     556 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.03
                    DXP_synthase_N 115 tsisaalGlavardlkgekkkvvaviGDgaltgGmafealnnigelkkkllvilNdNems 174
                                       +sis a G ++a +     kk++a iGD+++     ++ l ++  ++ ++lv++ dN+ +
  gi|242399760|ref|YP_002995185.1| 436 ASISLANGQSIAMN-----KKIIATIGDSTFFH-NGLQPLVDAVYKNLDVLVMILDNRTT 489
                                       68888888888766.....689******99754.34689999999999999999999865 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0054
                    DXP_synthase_N 231 gtlfeelgfkYlGpidGhdleelikvleevkklkgpvll 269
                                       ++l ++lg+kY+  +d  dl++  ++++e+ ++kgp ++
  gi|242399760|ref|YP_002995185.1| 515 EALVRALGVKYVKIVDPYDLKATKEAIKEAMQVKGPAVI 553
                                       468899******************************987 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   2.0      0.16   1.5e+02       1      20 [.     579     600 ..     579     609 .. 0.73
   2 ?   12.4   1.1   0.00026      0.23       2      20 ..     611     629 ..     610     632 .] 0.79

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.16
                           Fer4_16   1 rCgtCgkCa..evCPtnaikek 20 
                                       +C++C++Ca    CP+ +++e+
  gi|242399760|ref|YP_002995185.1| 579 KCTGCKACAllTGCPALVFDEE 600
                                       599*****83356998877776 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00026
                           Fer4_16   2 CgtCgkCaevCPtnaikek 20 
                                       C++Cg C + CP ++i  +
  gi|242399760|ref|YP_002995185.1| 611 CTGCGLCEQLCPFDVIVYP 629
                                       8899999999998888776 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   2.1       0.4   3.6e+02       1       8 [.     580     587 ..     580     589 .. 0.90
   2 ?   14.2   3.9   7.2e-05     0.065       1      14 [.     611     624 ..     611     625 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.4
                            Fer4_3   1 CtgCgaCv 8  
                                       CtgC aC 
  gi|242399760|ref|YP_002995185.1| 580 CTGCKACA 587
                                       *******6 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 7.2e-05
                            Fer4_3   1 CtgCgaCvevCPvg 14 
                                       CtgCg+C++ CP +
  gi|242399760|ref|YP_002995185.1| 611 CTGCGLCEQLCPFD 624
                                       ************75 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.6     0.024        22       3      15 ..     577     589 ..     575     605 .. 0.76
   2 ?    7.3   1.1    0.0077       6.9       1      17 [.     606     622 ..     606     624 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.024
                           Fer4_13   3 rdtCiacgaCvel 15 
                                       +d+C++c+aC+ l
  gi|242399760|ref|YP_002995185.1| 577 KDKCTGCKACALL 589
                                       69********865 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0077
                           Fer4_13   1 VDrdtCiacgaCvelaP 17 
                                       VD   C++cg+C +l+P
  gi|242399760|ref|YP_002995185.1| 606 VDSLICTGCGLCEQLCP 622
                                       67777***********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 ?    4.0   2.4     0.085        76      44      58 ..     578     594 ..     551     597 .. 0.83
   2 ?   10.9   2.0   0.00058      0.52      46      59 ..     611     624 ..     597     626 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.085
                           Fer4_17  44 slCieCgeCe..rkCPq 58 
                                       ++C++C+ C+  + CP+
  gi|242399760|ref|YP_002995185.1| 578 DKCTGCKACAllTGCPA 594
                                       68999999987778885 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00058
                           Fer4_17  46 CieCgeCerkCPqg 59 
                                       C++Cg+Ce+ CP +
  gi|242399760|ref|YP_002995185.1| 611 CTGCGLCEQLCPFD 624
                                       88888888888866 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   2.3    0.0081       7.3       5      32 ..     577     606 ..     574     607 .. 0.79
   2 ?    8.2   2.1    0.0046       4.1       1      19 [.     604     622 ..     604     627 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0081
                           Fer4_15   5 rdaCigcglCvaea..pevfeldedglasv 32 
                                       +d+C+gc +C+ +   p ++  +e+g+ sv
  gi|242399760|ref|YP_002995185.1| 577 KDKCTGCKACALLTgcPALVFDEERGKISV 606
                                       79********98855588887777888655 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0046
                           Fer4_15   1 VvvDrdaCigcglCvaeap 19 
                                       + vD   C+gcglC +++p
  gi|242399760|ref|YP_002995185.1| 604 ISVDSLICTGCGLCEQLCP 622
                                       689999***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (632 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); 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):              20  [number of targets reported over threshold]
# CPU time: 0.78u 0.30s 00:00:01.08 Elapsed: 00:00:00.52
# Mc/sec: 3628.13
//
Query:       gi|242399761|ref|YP_002995186.1|  [L=226]
Description: hypothetical protein TSIB_1786 [Thermococcus sibiricus MM 739]
Scores for complete 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-113  377.0   0.7   2.9e-113  376.8   0.7    1.0  1  DUF4152   Protein of unknown function (DUF4152)


Domain annotation for each model (and alignments):
>> DUF4152  Protein of unknown function (DUF4152)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  376.8   0.7  1.6e-117  2.9e-113       1     224 [.       1     223 [.       1     224 [. 0.99

  Alignments for each domain:
  == domain 1  score: 376.8 bits;  conditional E-value: 1.6e-117
                                       XEEEEEEEEEEEE-TTS-EEEEEEEEEEEEETT-SS-SEEEEEE--STT--TSSHHHHHHHHHHHHHHHHHH--SEE CS
                           DUF4152   1 mrivaadtggalldeayeplgliatvavlvekpyrsakevrvkyadpydydlsgrqairdevllavelarkvkpdvv 77 
                                       mriv+adtggallde y+p+gliat avlve+py++ak++  ky+dp++ydlsgr a++de++la++la+kvkpdv+
  gi|242399761|ref|YP_002995186.1|   1 MRIVSADTGGALLDENYNPIGLIATAAVLVERPYKTAKLSIAKYSDPFKYDLSGRMALKDETFLALKLAKKVKPDVI 77 
                                       9**************************************************************************** PP

                                       EESS-SSS-BGGG--HHHHHTSSS-HHHHHHHHHHHHHHHHHHHHHHHHH--EEE--GGG-HHHHHHHHHHHHHHHH CS
                           DUF4152  78 hldstlggielrkldeptiealgisdkgkevwkelskdlqplakklweetnieivaigkssvpvriaeiyagiysak 154
                                       hldstlggie+rkld+pti+al isd+gk +w+elskdlqplak++weet+iei+aigk sv vriaeiyagiys k
  gi|242399761|ref|YP_002995186.1|  78 HLDSTLGGIEIRKLDDPTIDALRISDRGKAIWHELSKDLQPLAKRFWEETGIEILAIGKESVAVRIAEIYAGIYSVK 154
                                       ***************************************************************************** PP

                                       HHHCTTTTSSEEEEEESTTEEEEEETTEEEEEES-GGGTS-EEEEE----TT-EEEEEE-TTSTTEEEEE CS
                           DUF4152 155 waieyvekegkllvglprymevdikdgkiigesldpregglygkievsvtegvkwelypnplvrrymvle 224
                                       w+iey+ keg + +glprym ++i++ ki+g+sld reg lyg+i     +  +we+ypnp++r +mv+e
  gi|242399761|ref|YP_002995186.1| 155 WGIEYAMKEGFVRIGLPRYMTIEINKEKILGKSLDSREGDLYGEIS-MEGKEFEWEIYPNPIARTFMVFE 223
                                       *********************************************9.667789****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); 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: 0.59u 0.36s 00:00:00.95 Elapsed: 00:00:00.55
# Mc/sec: 1232.63
//
Query:       gi|242399762|ref|YP_002995187.1|  [L=229]
Description: ATP-binding protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-83  279.5   2.1    1.8e-83  279.3   2.1    1.0  1  Diphthami_syn_2  Diphthamide synthase
      2e-06   27.5   0.0    4.5e-06   26.3   0.0    1.6  2  QueC             Queuosine biosynthesis protein QueC
     0.0051   16.4   0.0      0.012   15.2   0.0    1.7  2  ThiI             Thiamine biosynthesis protein (ThiI)
     0.0092   14.8   0.0       0.02   13.7   0.0    1.6  1  tRNA_Me_trans    tRNA methyl transferase
  ------ inclusion threshold ------
      0.076   12.8   0.0        0.7    9.6   0.0    2.1  1  ATP_bind_3       PP-loop family


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 !  279.3   2.1   5.1e-87   1.8e-83       1     217 [.       4     223 ..       4     225 .. 0.97

  Alignments for each domain:
  == domain 1  score: 279.3 bits;  conditional E-value: 5.1e-87
                   Diphthami_syn_2   1 mkvavlysGGkDsilaLykalke.sevesLvsvisenkesymfhvvnvhlvellaesvGiplikletaGeeekeved 76 
                                       m+vavl+sGGkDs++aLy+alk+ +ev++Lvs+ sen+esym+hv+n+hl+el+a ++ ip++k  t+Ge+e eved
  gi|242399762|ref|YP_002995187.1|   4 MRVAVLFSGGKDSTYALYWALKKgFEVKYLVSMYSENDESYMYHVPNIHLTELQAKAINIPFVKGFTKGEKEREVED 80 
                                       89*********************9***************************************************** PP

                   Diphthami_syn_2  77 LkgtlkkldveavviGaieseyqksriervCrelGlksvaPLWkkdpeelleeiveekfevivvavkaegldeslLG 153
                                       Lk  l+ l++e+vv Ga++s+yqk+r+e+v +el + ++ P+Wk dpe+++  i+ee+f+v++v+v+a+glde++LG
  gi|242399762|ref|YP_002995187.1|  81 LKRVLEGLKIEGVVAGALASQYQKERVEKVAKELRINLFTPFWKVDPEKYMRTIIEEGFDVVIVGVSAYGLDEKWLG 157
                                       ***************************************************************************** PP

                   Diphthami_syn_2 154 rridkklidelkklsekygidkagegGeaetlvlDaPlfkkrlevkelekkwde..rrgyldiera 217
                                       rrid k ++elk l++ky ++ agegGe+et+v DaP+fk ++  +++ek wd   + g l +++a
  gi|242399762|ref|YP_002995187.1| 158 RRIDEKALEELKTLNKKYKVHIAGEGGEFETFVRDAPFFKAKVVFDDIEKIWDRytSSGLLIVKKA 223
                                       ****************************************************96224677777776 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   1.3e-09   4.5e-06       3      68 ..       7      70 ..       5      93 .. 0.79
   2 ?   -2.6   0.0      0.87   3.1e+03     143     172 ..     107     136 ..     101     148 .. 0.68

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 1.3e-09
                                      EEE--SSHHHHHHHHHHHHH-SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEEE-GGGGGGS CS
                              QueC  3 vvllSGGlDSttvlalakkegkevealtfdYgqrhkkeleaakkiakelgveehkildldllkelg 68
                                       vl+SGG DSt +l++a+k+g ev+ l   Y ++ ++ +  + +i   +++ + k +++ ++k ++
  gi|242399762|ref|YP_002995187.1|  7 AVLFSGGKDSTYALYWALKKGFEVKYLVSMYSENDESYMYHVPNIH-LTEL-QAKAINIPFVKGFT 70
                                      69******************************99777776666654.3344.45777777777666 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.87
                                       HHHHHHTS--EEE-TTTT--HHHHHHHHHH CS
                              QueC 143 alnlgedkkieieaPlidlsKaeivklgke 172
                                       + +++++ +i++ +P+ +++ ++ +++  e
  gi|242399762|ref|YP_002995187.1| 107 VEKVAKELRINLFTPFWKVDPEKYMRTIIE 136
                                       455667777778888887777766665555 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   3.3e-06     0.012       5      35 ..       5      35 ..       2      85 .. 0.86
   2 ?   -2.9   0.0       1.2   4.3e+03     147     159 ..     102     114 ..      87     120 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.3e-06
                              ThiI  5 kvlaLlSgGiDSpVaaylllkRGcrvvlvhl 35
                                      +v +L SgG DS  a y +lk+G++v+++  
  gi|242399762|ref|YP_002995187.1|  5 RVAVLFSGGKDSTYALYWALKKGFEVKYLVS 35
                                      6789**********************99754 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.2
                              ThiI 147 ldKeeiiklAkei 159
                                       ++Ke + k+Ake+
  gi|242399762|ref|YP_002995187.1| 102 YQKERVEKVAKEL 114
                                       4566666666654 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   5.6e-06      0.02       1      64 [.       4      64 ..       4     116 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.6e-06
                     tRNA_Me_trans  1 kkvvvalSgGVDSsvaaallkeqgyevigvflklweeedeegkeccaeedlkdaervaeklgip 64
                                      ++v+v++SgG DS++a++   ++g+ev+ ++   +e+ de      +  +++  e  a+ ++ip
  gi|242399762|ref|YP_002995187.1|  4 MRVAVLFSGGKDSTYALYWALKKGFEVKYLVSMYSEN-DESY--MYHVPNIHLTELQAKAINIP 64
                                      69************************98655443333.3333..33333444444445555555 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0    0.0002       0.7       2      90 ..       6     121 ..       5     134 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0002
                                       EEEE--SCHHHHHHHHHHHHHCTTTTT........................EEEEEEEE-...SSSTCHHHHHHHHH CS
                        ATP_bind_3   2 vlvAvSgGlDSmaLllllaklkkklgi........................klvaihvdh...glreeskeeaelvk 51 
                                       v+v +SgG DS+  l+++ k+  + +                         ++ ai + +    ++ e+++e e +k
  gi|242399762|ref|YP_002995187.1|   6 VAVLFSGGKDSTYALYWALKKGFEVKYlvsmysendesymyhvpnihltelQAKAINIPFvkgFTKGEKEREVEDLK 82 
                                       56789******965555554443333337778888888888888888877744444444411134456677777777 PP

                                       HHHHHTT-EEEEEE--HHHCTTSTCCCHHHHHHHHHHHH CS
                        ATP_bind_3  52 elckklnikleiekvdvakkkgknleeaARelRYevlke 90 
                                       ++ + l+i+ +++ + +++ +++ +e+ A elR ++++ 
  gi|242399762|ref|YP_002995187.1|  83 RVLEGLKIEGVVAGALASQYQKERVEKVAKELRINLFTP 121
                                       777777777777777777777888888888888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); 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: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.55
# Mc/sec: 1242.61
//
Query:       gi|242399763|ref|YP_002995188.1|  [L=380]
Description: Ino1-like myo-inositol-1-phosphate synthase related [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.6e-19   69.0   0.0    7.7e-19   68.0   0.0    1.6  1  Inos-1-P_synth  Myo-inositol-1-phosphate synthase
    1.1e-13   51.3   0.5    4.9e-13   49.1   0.6    2.0  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 !   68.0   0.0   8.6e-23   7.7e-19       1     109 []     210     315 ..     210     315 .. 0.95

  Alignments for each domain:
  == domain 1  score: 68.0 bits;  conditional E-value: 8.6e-23
                                       SHHHHHHHHHHHHHHTT-EEEEEEEEEEE-HHHHHHTTSHHHHHHHHHHHHHHHHHHHSS--EEE....EEE...EE CS
                    Inos-1-P_synth   1 GqTklksvLaellverglkvksivslNilGnnDgknlseeerfksKkisKssvvddivkanellyvdhevvi...kY 74 
                                       G+T l   ++++l++r+  vk+i+++Ni+Gn D+++l+++er+ksK+ +Kssvv+++++++  +y      i    +
  gi|242399763|ref|YP_002995188.1| 210 GATPLTADILSHLAQRNRYVKDIAQFNIGGNADFLALTDKERNKSKEFTKSSVVKELLGYDAPHY------IkptGF 280
                                       99**********************************************************77654......33369* PP

                                       -GGGTTEEEEEEEEEEEEGGGEEEEEEEEEEEEH. CS
                    Inos-1-P_synth  75 vpylgDsKvaldeieseiflggkntielkleceDS 109
                                       +++lgD+K+  ++ie+  f g+  ++ ++ +++DS
  gi|242399763|ref|YP_002995188.1| 281 LEPLGDKKFIAMHIEYVSFNGAVDELIINGRINDS 315
                                       *********************************98 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 !   49.1   0.6   5.5e-17   4.9e-13      76     293 ..      41     269 ..       4     280 .. 0.75
   2 ?   -2.2   0.0      0.24   2.1e+03     280     299 ..     334     353 ..     318     367 .. 0.66

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 5.5e-17
                                       xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     NAD_binding_5  76 ndl.vfgGwDisslnlaeamerakvldkdlqeqlkpelekikplksvydkdfiaanqeeradnvlkgkskleqleqi 151
                                       +d+ ++g++D+ + ++ +++    v+++   +++ ++l+++  +k++  ++   +n   +a+ +    +++   e +
  gi|242399763|ref|YP_002995188.1|  41 EDIeIVGSYDVDKNKIGKSVY--DVVKNYWENHIPESLKNVIVRKGIHLRSL--RNLPIEAEGLE---DEMTLKEAV 110
                                       555445666666666666554..46666666666666666666666665543..23333333333...667778888 PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx.....xxxxxx RF
                     NAD_binding_5 152 rkdireFkkknkldkvivlwtanTEryievipgvndtlenllkaikeneee.ispstiyavAaile.....gvpyin 222
                                       +k ++e+kk+   +  +++++ +TE +++  ++     e+l kai++n++e + +s++ya+Aa l      g++++n
  gi|242399763|ref|YP_002995188.1| 111 EKLVEEWKKS---TPDVIINVCTTESFTPFGNK-----EKLIKAIEDNNKErLTASQVYAYAAALYakevgGAAFVN 179
                                       8889999985...4568899********99888.....9*******999999*********998633334489**** PP

                                       xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....................xx RF
                     NAD_binding_5 223 gsPqntl.vpglvelAekkgvfiaGdDfKtlLAaPlilDLvllveLaqrvevkk.....................ek 277
                                         P +    p+ velA++++++i GdD  t  A+Pl  D+  l  Laqr ++ k                     +k
  gi|242399763|ref|YP_002995188.1| 180 AIPTLIAnDPAFVELAKENNLVIFGDDGAT-GATPLTADI--LSHLAQRNRYVKdiaqfniggnadflaltdkerNK 253
                                       ******999*******************98.6*******6..78999*99998666666677777777777777788 PP

                                       xxxxxxxxxxxxxxxx RF
                     NAD_binding_5 278 kkefkklesvlsllsy 293
                                       +kef+k + v +ll+y
  gi|242399763|ref|YP_002995188.1| 254 SKEFTKSSVVKELLGY 269
                                       8899988888888876 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.24
                                       xxxxxxxxxxxxxxxxxxxx RF
                     NAD_binding_5 280 efkklesvlsllsyflKaPl 299
                                       + k++ ++ ++ ++++K P 
  gi|242399763|ref|YP_002995188.1| 334 DKKEFGTIYEVNAFYMKNPG 353
                                       33566788888999999984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.40s 00:00:01.08 Elapsed: 00:00:00.59
# Mc/sec: 1946.65
//
Query:       gi|242399764|ref|YP_002995189.1|  [L=409]
Description: Alanyl-tRNA synthetase-related protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.7e-13   50.5   1.2    5.2e-13   49.6   0.8    1.8  2  DHHA1         DHHA1 domain
    1.9e-12   46.5   0.0    3.4e-12   45.7   0.0    1.3  1  tRNA-synt_2c  tRNA synthetases class II (A)
    6.1e-11   42.2   1.1    1.1e-10   41.5   0.1    2.0  2  tRNA_SAD      Threonyl and Alanyl tRNA synthetase second addi
  ------ inclusion threshold ------
      0.028   14.2   0.3      0.048   13.5   0.3    1.3  1  Yuri_gagarin  Yuri gagarin
      0.062   13.3   0.7        1.4    9.0   0.0    2.8  3  CorC_HlyC     Transporter associated domain
        1.3    8.3   5.7        1.8    7.9   0.5    2.4  2  UvrD_C        UvrD-like helicase C-terminal domain


Domain annotation for each model (and alignments):
>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       2.4   7.2e+03      14      37 ..     171     194 ..     160     215 .. 0.64
   2 !   49.6   0.8   1.7e-16   5.2e-13       1     137 [.     277     401 ..     270     406 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.4
                                       HHHCHHHHHHHHHHHHHHHTCEEE CS
                             DHHA1  14 eleelkealaklkaeellekaeev 37 
                                         ee ++al k + ++++ k++ v
  gi|242399764|ref|YP_002995189.1| 171 LPEEVHNALRKDLSKNVQGKIRLV 194
                                       444555666666666665555544 PP

  == domain 2  score: 49.6 bits;  conditional E-value: 1.7e-16
                                       HHHHCHHHHHHHHHHHCHHHHHHHHHHHHHHHTCEEECTCEEEEEECHCCHHHHHHHHHHHHHHTHGBT.TCEEEEE CS
                             DHHA1   1 leslneerkelekeleelkealaklkaeellekaeevkgvkvlvaevgeewdagalgiaadklksklkk.pvivfva 76 
                                       le+l+ e  +l+kel+e+k ++       ll++aee+ +   +++++ ++w++++ +  + ++ +  k+ +++v+++
  gi|242399764|ref|YP_002995189.1| 277 LEELEGEKDQLRKELWEWKSKA-------LLQEAEEI-NGIKIISFL-DTWEMKDAQAFIVYFIE--KNpKTVVLIV 342
                                       3444555555555555555555.......55555555.889999999.9****999999999999..6645555555 PP

                                       EEECTEEEEEEEESSH..SS-HHHHHHHHHHHTTCCEEEE.TCEEEEEEE..HCHHHHHHHHHHHH CS
                             DHHA1  77 keegdkvkvsarskkd..gvdagelakeaaaklgggGGGH.dlAaGagip..aekleealealeea 137
                                       +    ++ + a+ k +  +++++el++e+  ++gggGGG   lA G+g +  +   ee++e ++++
  gi|242399764|ref|YP_002995189.1| 343 GS---NYLLFAKNK-NieRISMNELMREVLNEVGGGGGGSeILARGGGFKrsP---EEVIEIAKKF 401
                                       54...577777777.55********************************8333...5555555544 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 !   45.7   0.0   1.1e-15   3.4e-12     481     551 ..      25      94 ..      10      95 .. 0.83

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 1.1e-15
                                       EEETTEEEESEEXXXXSSSSCSXXXEEEEESSEEEEESEEEEETTEEEEEXSS.XSXXXTTSEEEEEEXHH CS
                      tRNA-synt_2c 481 egeevgvvLdrTpfYaesGGqigDeGliekegaefrvkdvqkakgvvlhkgkleegklkvgdkvkaevdee 551
                                       + ++v + LdrT fY+e+GGq gD G+i+++g +++v++v+ ++ +  h+gk++    +vg++v++e+d+e
  gi|242399764|ref|YP_002995189.1|  25 KDSKVRLKLDRTIFYPEGGGQPGDIGIIKGDGFRVEVEKVEGKEDI-WHEGKVKGRIPEVGEEVELELDWE 94 
                                       334566889****************************999987765.6*****98889***********97 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 !   41.5   0.1   3.6e-14   1.1e-10       1      44 []     191     234 ..     191     234 .. 0.98
   2 ?   -2.8   0.1       2.3   6.9e+03      35      43 ..     350     358 ..     350     359 .. 0.87

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 3.6e-14
                                       EEEEEETT.EEEEESS---SBGGGC-SEEEECCECCCTCEEEEE CS
                          tRNA_SAD   1 vrvvsiGdisvelCgGtHvpnTgeIgafkilseesiakglrRIy 44 
                                       +r+v+i +i+  +CgGtHv+nTge+g +k+l+  ++ k+++RI+
  gi|242399764|ref|YP_002995189.1| 191 IRLVKIPNIDLIPCGGTHVKNTGEVGFIKVLNFYKKTKNIWRIE 234
                                       79****99***********************************7 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.3
                                       CCCTCEEEE CS
                          tRNA_SAD  35 siakglrRI 43 
                                       +++k++ RI
  gi|242399764|ref|YP_002995189.1| 350 AKNKNIERI 358
                                       589*****9 PP

>> Yuri_gagarin  Yuri gagarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.3   1.6e-05     0.048     107     194 ..     210     300 ..     206     308 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.6e-05
                      Yuri_gagarin 107 knceqarkvrelaeelkgeeeqrvelvdkyekll...asfeeqckelkranrrvqslqerlsqveklqeelrterki 180
                                       kn+ ++  ++ l+   k+++  r+e++  y  l+     +e+  + l +  ++ + l er+++ ++l eel  e++ 
  gi|242399764|ref|YP_002995189.1| 210 KNTGEVGFIKVLNFYKKTKNIWRIEFACGYRALIyldKLLEDYWRSLNEMSNKNRPLLERMQEFKQLLEELEGEKDQ 286
                                       56666666666677777788889999999988763325689************************************ PP

                      Yuri_gagarin 181 lreevialkekdak 194
                                       lr+e+   k k   
  gi|242399764|ref|YP_002995189.1| 287 LRKELWEWKSKALL 300
                                       ****9999988655 PP

>> CorC_HlyC  Transporter associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.12   3.7e+02      50      70 ..      47      67 ..      40      68 .. 0.78
   2 ?    9.0   0.0   0.00046       1.4      44      66 ..      78      99 ..      76     114 .. 0.73
   3 ?   -3.5   0.1       3.7   1.1e+04      54      68 ..     155     169 ..     147     170 .. 0.69

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.12
                                      T-EE.EEEETTEEEEEEEEETT CS
                         CorC_HlyC 50 gesv.evdleglrftVlemdgr 70
                                      g+ +  ++ +g+r++V++++g+
  gi|242399764|ref|YP_002995189.1| 47 GD-IgIIKGDGFRVEVEKVEGK 67
                                      55.33667779********986 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00046
                                      -S---TT-EEEEEET.TEEEEEEE CS
                         CorC_HlyC 44 griPkegesvevdle.glrftVle 66
                                      griP++ge+ve++l+ ++r +  +
  gi|242399764|ref|YP_002995189.1| 78 GRIPEVGEEVELELDwEWRYE--N 99
                                      9*******6666666556554..3 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 3.7
                                       EEEETTEEEEEEEEE CS
                         CorC_HlyC  54 evdleglrftVlemd 68 
                                       ev +++l ++V+e +
  gi|242399764|ref|YP_002995189.1| 155 EVVWDNLPVEVEEYE 169
                                       455558889998865 PP

>> UvrD_C  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   1.4     0.018        54     225     277 ..     254     304 ..     166     312 .. 0.78
   2 ?    7.9   0.5    0.0006       1.8      90     154 ..     297     362 ..     296     369 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.018
                                       xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C 225 kekseskrkkee.klenlreLysllkelekkeeeeeveeklneileiatLsese 277
                                       ++ +e + +k++  le+++e+ +ll+ele   e+ + +++l e  ++a L+e e
  gi|242399764|ref|YP_002995189.1| 254 RSLNEMS-NKNRpLLERMQEFKQLLEELEG--EKDQLRKELWEWKSKALLQEAE 304
                                       3333333.344469****************..5555566677776666666555 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0006
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx RF
                            UvrD_C  90 kaLkkegipfnvvdeekfFkreeikdilaylkllankqdkialkrilkrlvlgigkatveri.see 154
                                       kaL +e  ++n ++  +f+++ e+kd+ a++ +++ k+ k+ +  + +++ l+ +++ +eri ++e
  gi|242399764|ref|YP_002995189.1| 297 KALLQEAEEINGIKIISFLDTWEMKDAQAFIVYFIEKNPKTVVLIVGSNYLLFAKNKNIERIsMNE 362
                                       56777777778888999********************9999999999***************5444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1273  (0.0710023); expected 358.6 (0.02)
Passed bias filter:                      794  (0.0442858); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.68u 0.37s 00:00:01.05 Elapsed: 00:00:00.53
# Mc/sec: 2342.85
//
Query:       gi|242399765|ref|YP_002995190.1|  [L=214]
Description: A1A0 ATP synthase, subunit D [Thermococcus sibiricus MM 739]
Scores for 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-61  206.3  13.2    4.6e-61  206.1  13.2    1.0  1  ATP-synt_D  ATP synthase subunit D
  ------ inclusion threshold ------
      0.029   13.5   0.2      0.029   13.5   0.2    1.9  2  Tmemb_cc2   Predicted transmembrane and coiled-coil 2 protein
      0.042   13.6   0.3       0.11   12.3   0.0    1.9  2  CCDC92      Coiled-coil domain of unknown function
      0.071   13.5   3.6         11    6.4   0.1    3.2  3  MutS_IV     MutS family domain IV
       0.13   12.6   2.6        5.5    7.3   0.4    2.7  2  DUF948      Bacterial protein of unknown function (DUF948)
       0.13   11.7   0.2       0.25   10.8   0.2    1.4  1  HNOBA       Heme NO binding associated
       0.18   12.3   0.2       0.18   12.3   0.2    2.2  2  DUF16       Protein of unknown function DUF16
       0.36   10.2  11.3      0.098   12.0   1.0    2.4  2  GAS         Growth-arrest specific micro-tubule binding
       0.77    9.8   7.0       0.23   11.5   1.2    2.3  2  Laminin_II  Laminin Domain II


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 !  206.1  13.2   2.3e-64   4.6e-61       1     196 []      13     206 ..      13     206 .. 0.95

  Alignments for each domain:
  == domain 1  score: 206.1 bits;  conditional E-value: 2.3e-64
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSTSTTSTSHHHHHHHSSS.SS-. CS
                        ATP-synt_D   1 eLirlkkrlklaqrghslLkkKrdaLilefreilkelkelreeleeelkeayfslaeafaaggeediesavlesvkl 77 
                                       eL+rlk+r+kla++gh++Lk+K+daLi+ef++i +e+  lr+e+++++ ea ++l +a +  g  ++++++l svk 
  gi|242399765|ref|YP_002995190.1|  13 ELLRLKRRIKLAEKGHKILKEKQDALIMEFFTIYDEALALRREVNQKIAEAFEQLRLAEIDVGIVKLSEIAL-SVK- 87 
                                       79**********************************************************************.666. PP

                                       .TSS-SEEEEEEBTTSEEEEEEE-..S.SST.SSSSSSSSTCHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        ATP-synt_D  78 akvvkvelktenvaGVkvpvfeleeeksdst.elygllrtgaqldeavealrellellvelasletslelLdeeikk 153
                                        +++++++k +n++GV vp +e e  ++d + + y +++t++++d ++e+++e+lel+ +la++e++l++L++ei+k
  gi|242399765|ref|YP_002995190.1|  88 -SNKEIKIKRRNIMGVPVPLIEAEGFRRDPYeRGYAFVSTSPKVDVTAETFEEVLELVTRLAEIEETLKRLAKEIEK 163
                                       .569*****************8865544443156******************************************* PP

                                       HHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        ATP-synt_D 154 tnrRvNaLekvvIPrleetikyIkseLdEqereeffrlkkvkk 196
                                       t+rRvNaLe+++IPr+ et+kyI++ LdE+ere+ffrlk+vk+
  gi|242399765|ref|YP_002995190.1| 164 TKRRVNALEYIIIPRMAETVKYISQHLDEMERENFFRLKRVKA 206
                                       *****************************************95 PP

>> Tmemb_cc2  Predicted transmembrane and coiled-coil 2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   1.4      0.27   5.5e+02       6      53 ..      16      66 ..      11      71 .. 0.76
   2 ?   13.5   0.2   1.4e-05     0.029     212     272 ..     132     193 ..      84     198 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.27
                         Tmemb_cc2  6 klqqKilkikeqikveqtardenvneYLklasna...DkqQlarIkqvFEk 53
                                      +l+++i   +   k+ ++++d+ + e+ ++  +a    ++  ++I ++FE+
  gi|242399765|ref|YP_002995190.1| 16 RLKRRIKLAEKGHKILKEKQDALIMEFFTIYDEAlalRREVNQKIAEAFEQ 66
                                      567777777777788888888888888888888877777777788888875 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 1.4e-05
                         Tmemb_cc2 212 aesesqeklekileelqeikeeqerleeelerlkeqlkk.elkllkqaLqeeryryerLEeq 272
                                        ++e+ e++ ++++ l+ei+e+ +rl++e+e+ k++++  e+ ++ ++ ++++y +++L e+
  gi|242399765|ref|YP_002995190.1| 132 VTAETFEEVLELVTRLAEIEETLKRLAKEIEKTKRRVNAlEYIIIPRMAETVKYISQHLDEM 193
                                       5667778899999*********************9987559999999999999999999875 PP

>> CCDC92  Coiled-coil domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       2.5     5e+03      29      37 ..      14      22 ..      13      38 .. 0.61
   2 ?   12.3   0.0   5.6e-05      0.11      19      44 ..     151     176 ..     148     187 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.5
                            CCDC92 29 IekLqkenk 37
                                      + +L+++ k
  gi|242399765|ref|YP_002995190.1| 14 LLRLKRRIK 22
                                      556666543 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 5.6e-05
                            CCDC92  19 aatLkgLHkEIekLqkenkdLtfkli 44 
                                       ++tLk L kEIek ++++  L++ +i
  gi|242399765|ref|YP_002995190.1| 151 EETLKRLAKEIEKTKRRVNALEYIII 176
                                       68********************9776 PP

>> MutS_IV  MutS family domain IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.1    0.0098        20       6      36 ..      46      77 ..      41     101 .. 0.76
   2 ?    1.9   0.2      0.14   2.8e+02       5      26 ..     146     167 ..     138     171 .. 0.68
   3 ?    6.4   0.1    0.0057        11      56      85 ..     166     196 ..     160     198 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0098
                                      HHHHHHHHHHHHHHHHHHHCCCCC...CCT-TTB CS
                           MutS_IV  6 Ldelrdrleelekeleeleekere...klgiksl 36
                                      +de+ ++++e++++++e  e++r    + gi  +
  gi|242399765|ref|YP_002995190.1| 46 YDEALALRREVNQKIAEAFEQLRLaeiDVGI--V 77
                                      9*****************9999876444444..3 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.14
                                       HHHHHHHHHHHHHHHHHHHHCC CS
                           MutS_IV   5 eLdelrdrleelekeleeleek 26 
                                       +L e++++l+ l ke+e+ +++
  gi|242399765|ref|YP_002995190.1| 146 RLAEIEETLKRLAKEIEKTKRR 167
                                       5667777777777777776665 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0057
                                       TTT--.SEEEEEECTCEEEEECCCHHHHHHH CS
                           MutS_IV  56 kkvpk.efirlqtlknseryttaelkkleae 85 
                                        +v + e+i++  + + ++y+++ l ++e+e
  gi|242399765|ref|YP_002995190.1| 166 RRVNAlEYIIIPRMAETVKYISQHLDEMERE 196
                                       4555679*********************986 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 ?    4.5   0.1     0.021        41      21      69 ..      14      62 ..      10      72 .. 0.93
   2 ?    7.3   0.4    0.0027       5.5      33      58 ..     145     170 ..     129     212 .. 0.61

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.021
                            DUF948 21 llklkktldeaaatieelekqvdpilkevedllakvnelledvneklek 69
                                      ll+lk+ ++ a++  + l+++ d+++ e  ++ +++ +l  +vn+k+++
  gi|242399765|ref|YP_002995190.1| 14 LLRLKRRIKLAEKGHKILKEKQDALIMEFFTIYDEALALRREVNQKIAE 62
                                      8999*****************************************9975 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0027
                            DUF948  33 atieelekqvdpilkevedllakvne 58 
                                       ++++e+e+ ++ + ke+e++ + vn+
  gi|242399765|ref|YP_002995190.1| 145 TRLAEIEETLKRLAKEIEKTKRRVNA 170
                                       34445555555555555555555555 PP

>> HNOBA  Heme NO binding associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2   0.00012      0.25     177     215 ..     141     178 ..     129     182 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00012
                             HNOBA 177 lelaldqleeksaeLeesmkeleeekkrtdeLLysmiPk 215
                                       lel   +l e  + L++  ke+e+ k+r ++L y +iP+
  gi|242399765|ref|YP_002995190.1| 141 LELVT-RLAEIEETLKRLAKEIEKTKRRVNALEYIIIPR 178
                                       56666.888889999999999*****************8 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.3      0.52     1e+03      61      79 ..      27      43 ..       6      97 .. 0.59
   2 ?   12.3   0.2   8.9e-05      0.18      52      96 ..     142     194 ..     121     206 .. 0.55

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.52
                                      HHHHHHHHHHHHHHHH... CS
                             DUF16 61 gekikelkveqkaqgeeln 79
                                      g+ki  lk++q+a   e+ 
  gi|242399765|ref|YP_002995190.1| 27 GHKI--LKEKQDALIMEFF 43
                                      3333..5555555444332 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 8.9e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHH...............HHHHHHHHHHHHH CS
                             DUF16  52 kleqkvekqgekikelkveqkaqgeeln........kvdetleliletLqkin 96 
                                       +l     + +e +k+l +e+++ ++++n        ++ et++ i + L++++
  gi|242399765|ref|YP_002995190.1| 142 ELVTRLAEIEETLKRLAKEIEKTKRRVNaleyiiipRMAETVKYISQHLDEME 194
                                       22233333344455555555555554553333334566666666666666654 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.0   4.9e-05     0.098      83     144 ..      10      71 ..       3      90 .. 0.91
   2 ?    2.8   3.4     0.031        62      57      88 ..     141     172 ..     130     213 .. 0.52

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.9e-05
                               GAS  83 dkqslknlkarlkelekelkdlkwehevleqrfekvekerdelykkfeaaiqevqqktglkn 144
                                        +++l +lk+r+k +ek  k lk++++ l ++f ++ +e  +l+++ +++i e++++  l +
  gi|242399765|ref|YP_002995190.1|  10 TRMELLRLKRRIKLAEKGHKILKEKQDALIMEFFTIYDEALALRREVNQKIAEAFEQLRLAE 71 
                                       689999***********************************************999887765 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.031
                               GAS  57 krlkepLkkaeeeveeLrkqlknyekdkqslk 88 
                                        +l+  L + ee +++L k++++ ++  ++l+
  gi|242399765|ref|YP_002995190.1| 141 LELVTRLAEIEETLKRLAKEIEKTKRRVNALE 172
                                       44444444444444444444444444444433 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.5      0.16   3.1e+02      41      58 ..      54      71 ..       6      98 .. 0.58
   2 ?   11.5   1.2   0.00011      0.23      11      84 ..     132     210 ..     129     213 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.16
                                      XXXXXXXXXXXXXXXXXX CS
                        Laminin_II 41 eetnekvkdankairdAr 58
                                      +e+n+k+ +a +++r+A+
  gi|242399765|ref|YP_002995190.1| 54 REVNQKIAEAFEQLRLAE 71
                                      235555555555555554 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00011
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXX--TTTTTGG....GHHHHHHHH CS
                        Laminin_II  11 takevleqlaplsqnlentkeklseinrsveetnekvkdankai.rdArrsvkkLeklapqLld....klkelkqle 82 
                                        ++e+ e + +l ++l +++e l+++++++e+t+  v+++  +i     + vk + + +++++     +lk++k l 
  gi|242399765|ref|YP_002995190.1| 132 VTAETFEEVLELVTRLAEIEETLKRLAKEIEKTKRRVNALEYIIiPRMAETVKYISQHLDEMERenffRLKRVKALL 208
                                       57788899999999************************877654245556677777777776432222677777766 PP

                                       HH CS
                        Laminin_II  83 ea 84 
                                       ea
  gi|242399765|ref|YP_002995190.1| 209 EA 210
                                       65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1425  (0.0794802); expected 358.6 (0.02)
Passed bias filter:                      701  (0.0390987); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.69u 0.37s 00:00:01.06 Elapsed: 00:00:00.57
# Mc/sec: 1122.22
//
Query:       gi|242399766|ref|YP_002995191.1|  [L=467]
Description: A1A0 ATP synthase, subunit B [Thermococcus sibiricus MM 739]
Scores for complete 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-69  231.5   0.0    1.1e-68  231.1   0.0    1.2  1  ATP-synt_ab    ATP synthase alpha/beta family, nucleotide-bin
    1.9e-13   50.7   3.1    1.9e-13   50.7   3.1    1.9  2  ATP-synt_ab_N  ATP synthase alpha/beta family, beta-barrel do
    0.00026   21.1   1.1    0.00089   19.4   1.1    1.9  1  HAS-barrel     HAS barrel domain


Domain annotation for each model (and alignments):
>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  231.1   0.0   1.8e-72   1.1e-68       1     213 []     137     355 ..     137     355 .. 0.98

  Alignments for each domain:
  == domain 1  score: 231.1 bits;  conditional E-value: 1.8e-72
                                       SSHHHHHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTS....S.EEEEEEESEEHHHHHHHHHHCHHSSGGGGE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab   1 GirvlDalfpivqGqrtlipgafgvGktvisqslskqsnsd....d.aiiyvgiGergnevaevleefpegtimkrt 72 
                                       Gi+++D + ++v+Gq++ i++++g++++++++++++q++      + a++++++G   +e++ + ++f+e+++++r 
  gi|242399766|ref|YP_002995191.1| 137 GISAIDGMNTLVRGQKLPIFSGSGLPHNMLAAQIARQAKVLgeeeQfAVVFAAMGITYEEANFFKKSFEETGAIERA 213
                                       89***********************************8655888778****************************** PP

                                       EEEEEETTS-HHHHHHHHHHHHHHHHHHHH.TTSEEEEEEETHHHHHHHHHHHHHHTTTSBEGGGSBTTHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  73 vlvantsnepvaareasiytgitlAEyfrd.qgknvlliadslsrwaeAlreislrlgempadqgypaylgaklasl 148
                                       vl++n +++p+++r++++++++t+AEy++   +++vl+i+++++++aeAlreis++ +e+p+++gyp+y++++la++
  gi|242399766|ref|YP_002995191.1| 214 VLFLNLADDPAIERIITPRMALTVAEYLAFdYDMQVLVILTDMTNYAEALREISAAREEVPGRRGYPGYMYTDLATI 290
                                       ****************************9879********************************************* PP

                                       HTTSEEETSSEEEEEEEEEEE-GGCSTTSHHHHHHHHHSSEEEEB-HHHHHTTBSSSBCTTTEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab 149 yERagkapdrtGsvtivaavspaggDfsdpvttatlgitdgfivLdkklaqrkhfPainvlvSvS 213
                                       yERag+++ r+Gs+t++++++++++D+++p+++ t +it+g+ivL+++l++++++P+i+vl S+S
  gi|242399766|ref|YP_002995191.1| 291 YERAGRVRGRKGSITQMPILTMPDDDITHPIPDLTGYITEGQIVLSRDLHRKGIYPPIDVLPSLS 355
                                       ***************************************************************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 !   50.7   3.1   3.2e-17   1.9e-13       1      69 []      14      80 ..      14      80 .. 0.97
   2 ?   -3.7   0.0         3   1.8e+04      49      64 ..     137     152 ..     136     152 .. 0.79

  Alignments for each domain:
  == domain 1  score: 50.7 bits;  conditional E-value: 3.2e-17
                                      EEEEETTEEEEESSTSCETCTTEEEEECCETCSTEEEEEEEEEETTEEEEEESS-STTBBT.TSEEEEES CS
                     ATP-synt_ab_N  1 ivqviGpvvdvefgigrlpgiynalevelvefgtlllgvalnlgedkVrvivmgstdGlsr.GteVkrTG 69
                                      i++++Gp+++v++++g+++g+ + +eve   +g++++g++l+ +ed ++v+v+++t+ l++  t+V++TG
  gi|242399766|ref|YP_002995191.1| 14 ISKIYGPLMIVQGVRGVAYGEVVEIEVE---GGEKRKGQVLEAREDLAIVQVFEGTRDLDVkSTRVRFTG 80
                                      799*************************...699***********************************9 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 3
                                       EEEESS-STTBBTTSE CS
                     ATP-synt_ab_N  49 rvivmgstdGlsrGte 64 
                                       ++ +++++  l+rG++
  gi|242399766|ref|YP_002995191.1| 137 GISAIDGMNTLVRGQK 152
                                       5778889999999975 PP

>> HAS-barrel  HAS barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   1.1   1.5e-07   0.00089       4      88 ..      10      80 ..       8      95 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.5e-07
                        HAS-barrel  4 vigests.sslifrvegskdvkvGeyVeielpdgeivlGmvtdirrgnselsndlalvlsleeleeangddevalated 81
                                      ++++ +  +++++ v g+ +v +Ge Veie ++ge++ G+v+  r+                       d+++++++e+
  gi|242399766|ref|YP_002995191.1| 10 EYSTISKiYGPLMIVQGVRGVAYGEVVEIEVEGGEKRKGQVLEARE-----------------------DLAIVQVFEG 65
                                      57777777**************************************.......................9999999999 PP

                        HAS-barrel 82 t........gvkvlG 88
                                      t        +v+  G
  gi|242399766|ref|YP_002995191.1| 66 TrdldvkstRVRFTG 80
                                      887777777333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (467 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); 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: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.50
# Mc/sec: 2819.70
//
Query:       gi|242399767|ref|YP_002995192.1|  [L=585]
Description: A1A0 ATP synthase, subunit A [Thermococcus sibiricus MM 739]
Scores for complete 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-93  312.3   0.0    2.3e-93  311.8   0.0    1.3  1  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
      5e-49  165.2   0.3    8.9e-49  164.4   0.3    1.4  1  ATP-synt_ab_Xtn  ATPsynthase alpha/beta subunit N-term extens
    1.4e-14   54.3   4.1    4.4e-14   52.8   4.1    1.9  1  ATP-synt_ab_N    ATP synthase alpha/beta family, beta-barrel 
  ------ inclusion threshold ------
      0.033   14.5   0.0      0.071   13.4   0.0    1.5  1  AAA_22           AAA domain


Domain annotation for each model (and alignments):
>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  311.8   0.0     5e-97   2.3e-93       1     213 []     211     434 ..     211     434 .. 0.98

  Alignments for each domain:
  == domain 1  score: 311.8 bits;  conditional E-value: 5e-97
                                       SSHHHHHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSSEEEEEEESEEHHHHHHHHHHCHH......SS.GGG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xx.xxx RF
                       ATP-synt_ab   1 GirvlDalfpivqGqrtlipgafgvGktvisqslskqsnsddaiiyvgiGergnevaevleefpe......gt.imk 70 
                                       G+r++D++fp ++G++ +ipg fg Gktv +++l+k+s+++ +++y+g+Gergne+++vleefp+      g+ +m+
  gi|242399767|ref|YP_002995192.1| 211 GQRTIDTFFPQAKGGTAAIPGPFGSGKTVTQHQLAKWSDAE-VVVYIGCGERGNEMTDVLEEFPKlkdprtGKpLME 286
                                       9************************************9777.***********************998876337*** PP

                                       GEEEEEEETTS-HHHHHHHHHHHHHHHHHHHHTTSEEEEEEETHHHHHHHHHHHHHHTTTSBEGGGSBTTHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  71 rtvlvantsnepvaareasiytgitlAEyfrdqgknvlliadslsrwaeAlreislrlgempadqgypaylgaklas 147
                                       rtvl+antsn+pvaareasiytgit+AEyfrd+g+nv l+ads+srwaeAlreis+rl+emp+++gypayl++k+a+
  gi|242399767|ref|YP_002995192.1| 287 RTVLIANTSNMPVAAREASIYTGITIAEYFRDMGYNVALMADSTSRWAEALREISGRLEEMPGEEGYPAYLASKVAE 363
                                       ***************************************************************************** PP

                                       HHTTSEEE.....TSSEEEEEEEEEEE-GGCSTTSHHHHHHHHHSSEEEEB-HHHHHTTBSSSBCTTTEEE CS
                                       xxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab 148 lyERagka.....pdrtGsvtivaavspaggDfsdpvttatlgitdgfivLdkklaqrkhfPainvlvSvS 213
                                       +yERag++     +dr Gsv+++ avsp+ggD+sdpv ++tl+++++f+ Ld +la+r+hfPain+l+S+S
  gi|242399767|ref|YP_002995192.1| 364 FYERAGRVrtlgsDDRIGSVSVIGAVSPPGGDLSDPVVQNTLRVVKVFWALDADLARRRHFPAINWLTSYS 434
                                       ************9999******************************************************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 !  164.4   0.3     2e-52   8.9e-49       1     121 []      82     202 ..      82     202 .. 0.99

  Alignments for each domain:
  == domain 1  score: 164.4 bits;  conditional E-value: 2e-52
                                       EETTS-BHHHHHHHHTSBE-TT----SS-SSS-EEEEESS-TT-EEETT-EEEEEECTTCEEEEEE--TT-EEEEEE CS
                   ATP-synt_ab_Xtn   1 yDGiqrpLekiaeksgsfierGvkvpaldrekkwefkpkvkvgdkvsggdilGtvqeteliehkimvppkvegkvke 77 
                                       yDGiqrpLe ++++sg+fi rG+++pal+r+kkw+f+pkvkvgdkv ggdi+G+v+et++iehkim+pp++eg++ e
  gi|242399767|ref|YP_002995192.1|  82 YDGIQRPLEILRSQSGDFIGRGLTAPALSRDKKWHFTPKVKVGDKVVGGDIIGVVPETSIIEHKIMIPPEIEGEIIE 158
                                       9**************************************************************************** PP

                                       E--EEEE-TTSECEEECETT.ECEEEESSEEEETTS---ESEEE CS
                   ATP-synt_ab_Xtn  78 iaeegeytvedtiaeveteegkekeltllqkwPvrkprpvkekl 121
                                       i+ eg+yt+e++ia+v+  +g+ ke++++q+wPvr +rp+k+kl
  gi|242399767|ref|YP_002995192.1| 159 IVGEGDYTIEEVIAKVKAPNGEIKEVRMYQRWPVRMKRPYKQKL 202
                                       ******************************************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 !   52.8   4.1   9.7e-18   4.4e-14       1      69 []       4      66 ..       4      66 .. 0.98

  Alignments for each domain:
  == domain 1  score: 52.8 bits;  conditional E-value: 9.7e-18
                                      EEEEETTEEEEESSTSCETCTTEEEEECCETCSTEEEEEEEEEETTEEEEEESS-STTBBTTSEEEEES CS
                     ATP-synt_ab_N  1 ivqviGpvvdvefgigrlpgiynalevelvefgtlllgvalnlgedkVrvivmgstdGlsrGteVkrTG 69
                                      iv+v+Gp+v ++ ++g    +y++++v+  e   +l+g++++l++dk++++v+++t G+++G++V  TG
  gi|242399767|ref|YP_002995192.1|  4 IVRVTGPLVVADEMRG--SRMYEVVRVG--E--LGLIGEIIRLEGDKAVIQVYEETAGIKPGEPVMGTG 66
                                      89**************..**********..9..********************************9998 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   1.6e-05     0.071       6      63 ..     225     275 ..     221     299 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.6e-05
                            AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevv.fvtlpsst.sskdllrellra 63 
                                       g  ++ G+ G+GKT++  +l+++          ++evv ++ + + + + +d+l+e+ + 
  gi|242399767|ref|YP_002995192.1| 225 GTAAIPGPFGSGKTVTQHQLAKWS---------DAEVVvYIGCGERGnEMTDVLEEFPKL 275
                                       67899******************9.........777776999988887777777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (585 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); 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: 0.74u 0.32s 00:00:01.06 Elapsed: 00:00:00.53
# Mc/sec: 3342.27
//
Query:       gi|242399768|ref|YP_002995193.1|  [L=102]
Description: A1A0 ATP synthase, subunit F [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.5e-19   68.0   0.6    1.2e-18   67.2   0.6    1.4  1  ATP-synt_F  ATP synthase (F/14-kDa) subunit


Domain annotation for each model (and alignments):
>> ATP-synt_F  ATP synthase (F/14-kDa) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.2   0.6   6.6e-23   1.2e-18       1      89 [.       3      90 ..       3      93 .. 0.87

  Alignments for each domain:
  == domain 1  score: 67.2 bits;  conditional E-value: 6.6e-23
                                      EEEEESHHHHHHHHHTTCEEEE.....CSSHHHHHHHHHHHHHHTTEEEEEEEHHHHCCCHHHHHHCTCSSSSEEEEES CS
                        ATP-synt_F  1 iavIGdedtvtgfrlaGvgeve.....vtdeeeieealkelleredigiilitekiaeeirelideykeealPaileIP 74
                                      i+v+Gd+dtv+gfrlaGv+e++      ++ e +++++ el+ered+g+ilite++a+++     e+ + a+P+il+IP
  gi|242399768|ref|YP_002995193.1|  3 IVVLGDKDTVLGFRLAGVHETYsfedtTHEIERVRNKIMELIEREDVGVILITERLAQRV-----EIPDVAFPIILQIP 76
                                      89**********************988888999*************************98.....3333478******* PP

                                      CSCCGGSHHCHHHHH CS
                        ATP-synt_F 75 skegpydeekdsvrk 89
                                      +k g+   +++++r+
  gi|242399768|ref|YP_002995193.1| 77 DKYGSL-YGEEQLRE 90
                                      ****76.44556555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); expected 358.6 (0.02)
Passed bias filter:                      580  (0.0323498); 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: 0.58u 0.34s 00:00:00.92 Elapsed: 00:00:00.55
# Mc/sec: 560.17
//
Query:       gi|242399769|ref|YP_002995194.1|  [L=369]
Description: A1A0 ATP synthase, subunit C [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      3e-67  227.5  14.8    3.4e-67  227.3  14.8    1.0  1  vATP-synt_AC39  ATP synthase (C/AC39) subunit
  ------ inclusion threshold ------
      0.088   12.9   0.0       0.21   11.6   0.0    1.6  1  DUF4176         Domain of unknown function (DUF4176)


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 !  227.3  14.8   3.8e-71   3.4e-67       2     335 ..      39     363 ..      38     364 .. 0.96

  Alignments for each domain:
  == domain 1  score: 227.3 bits;  conditional E-value: 3.8e-71
                                       HHHHHHHGGGS--HHHHHHHTTS.-HHHHHHHHHTSGGGGG--.....SSSHHHHHHHHHHHHHHHTTTGGGGS-H. CS
                    vATP-synt_AC39   2 eArvramrsglLteedyenLlqcesledvkryLketdYgnfladelseplsrsdiekalreklarefnklreqapgp 78 
                                       +Ar++am+++l++e+++ +L ++++l+ ++ +L+++dY+ +l + +s  l  ++i++al+++la++++ ++++ p+ 
  gi|242399769|ref|YP_002995194.1|  39 NARIKAMEARLFNEQKLGELSESKTLNNFVMNLEDSDYKPYLGNLPS--LRAETIDRALEASLADTYQLMLKILPKR 113
                                       8****************************************999985..9*************************** PP

                                       .HHHHHHHHHHHHHHHHHHHHHHHHHH.T--GGGS-..--.SSSS-HHHHHHHHHSSSHHHHHHHHHT-HHHHHHHH CS
                    vATP-synt_AC39  79 .srefldyllyrydidNvklllrgklsgdldleeleeklhplgelsaldldklieaksveelyeallgtpyakylee 154
                                        s  f+++ll ++d+ N+  ++++k+sg +     ++++h+lg+l   ++++++eak++ee++ +l+gt+y ++ ++
  gi|242399769|ref|YP_002995194.1| 114 tS-AFFQLLLEEWDVRNISSVVKAKFSG-E---VARDYIHELGTLI-GKVKAMAEAKTLEEILVILEGTEYEDPYQR 184
                                       55.************************6.5...77899*****886.56699************************* PP

                                       .HHCC...--SHHHHHHHHHHHHHHHHHHHHHTSS-HH...HHHHHHHHHHHHHHHHHHHTTTSS......T...-- CS
                    vATP-synt_AC39 155 .aldeleetgdleiienaLdkayledllkfckklggetaeilreilgfeiDlrniniilrskkygelskedrkklli 230
                                        +l+e++     e++e++L+k  +++ll+++++ + e++eil+e++  +iD  n+ +ilr+k  ++ls +++++ li
  gi|242399769|ref|YP_002995194.1| 185 lLLKEISL----EEFETELYKKHYSKLLEYARSRKAEEREILEEFVNLKIDKINLVTILRAKA-HHLSADKIRNSLI 256
                                       88888888....********************99999**************************.99*********** PP

                                       SS-S--HHHHHHHHTT-G.....GG.GGSSTSSTTGGGTT-.-S.HHHHHHHHHHHHHHHHHT.TTSSSTSTHHHHH CS
                    vATP-synt_AC39 231 pggslypeglealaeaedveellaalkyteygelleealee.agslksledaldealvkllkk.afrqqfsvgvfya 305
                                       pgg+++++ +e+l+++ed+e +la l  tey+++l e++e+   +++++e+a+++++ + +++  +++++s+++ ++
  gi|242399769|ref|YP_002995194.1| 257 PGGKMNRKLIETLLNVEDIEMALAELDSTEYSSILREVREKvVVDISAFERAFEKYIQQRMSElTKFYPLSIATPIS 333
                                       *************************************99998444******************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHT--SHHHHG CS
                    vATP-synt_AC39 306 YlklkeqEirnlrwIaegiaqglpkekIre 335
                                       Y++ ke+Eir+l++Ia+ i+ gl +e I++
  gi|242399769|ref|YP_002995194.1| 334 YILQKEWEIRRLKAIAKLIEDGLKPEVIKK 363
                                       ****************************86 PP

>> DUF4176  Domain of unknown function (DUF4176)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   2.4e-05      0.21      14      58 ..      12      55 ..       4      60 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.4e-05
                           DUF4176 14 tkkvmiigrrqieeeekkiydYvgclYPeGildsektllfnhedI 58
                                      t  v+i +    ++++  ++ Y+   YP+  +++ ++ lfn++++
  gi|242399769|ref|YP_002995194.1| 12 TTLVVIFTWVAYKTGQ-ILWKYTPYSYPNARIKAMEARLFNEQKL 55
                                      5567777777777776.5***********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       759  (0.0423336); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.53
# Mc/sec: 2093.14
//
Query:       gi|242399770|ref|YP_002995195.1|  [L=203]
Description: A1A0 ATP synthase, subunit E [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-37  129.3  21.6    1.3e-37  129.2  21.6    1.0  1  vATP-synt_E   ATP synthase (E/31 kDa) subunit
     0.0022   17.9   2.0     0.0039   17.1   2.0    1.3  1  HrpE          HrpE/YscL/FliH and V-type ATPase subunit E
  ------ inclusion threshold ------
      0.028   14.5  12.3      0.028   14.5  12.3    2.6  3  ATP-synt_B    ATP synthase B/B' CF(0)
       0.12   12.2   2.3       0.19   11.6   1.6    1.6  2  DUF3540       Protein of unknown function (DUF3540)
       0.35   11.3  16.7        0.1   13.0  12.7    2.2  2  V-ATPase_G_2  Vacuolar (H+)-ATPase G subunit
       0.47    9.8  26.0        1.2    8.5  10.6    2.8  2  DUF3552       Domain of unknown function (DUF3552)
       0.76    9.1   7.6        1.2    8.4   0.9    2.2  2  NolV          Nodulation protein NolV
        2.9    8.1  12.8        4.1    7.6   0.1    4.7  4  CinA_KH       Damage-inducible protein CinA KH domain
        3.3    8.5   6.3        6.6    7.6   6.3    1.5  1  WBS_methylT   Methyltransferase involved in Williams-Beuren s
        5.2    7.2  23.6        1.6    8.8  12.8    3.6  3  DivIVA        DivIVA protein


Domain annotation for each model (and alignments):
>> vATP-synt_E  ATP synthase (E/31 kDa) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.2  21.6   7.3e-41   1.3e-37       1     199 []      10     202 ..      10     202 .. 0.98

  Alignments for each domain:
  == domain 1  score: 129.2 bits;  conditional E-value: 7.3e-41
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       vATP-synt_E   1 fIrqeAeekAeeIkakaeeefeiekaklveeeeekieeayekkeKqaelqkkiaiSnalnkarlkvLkareevleev 77 
                                       +I++eAe+k + I ++ae+ +e++k++++++++ k + +  k++ qael+k+++i na+++ r+k L  +ee+++ev
  gi|242399770|ref|YP_002995195.1|  10 EINKEAEQKIKYILEEAEQKAEKIKQEAEKKARIKADWIIRKAQTQAELEKQRIIANAKLEVRRKKLVLQEELINEV 86 
                                       699************************************************************************** PP

                                       HHHHHHHHHHHTTSHHCCCCHHHHHHCCCCCCC-SSCEEEEECCCCHHCCCCTHCCCCCCHHCCSSSS--SEEEEES CS
                       vATP-synt_E  78 feeaekkLaeveedkdeYkellkkLivqalvkleepevivrarkeDaelveealdkaaeeykaktkkktvevagdee 154
                                       + +++ +L  ++e +  Y e+lk+Liv ++ +l+e++v+++++ e  +l+++ l++++e +++k +k+ +   g+  
  gi|242399770|ref|YP_002995195.1|  87 IGAIKDRLLSIPEAE--YMEILKDLIVTGIRELGEEKVVLSSNGETLSLLKAHLKEMEESVNEKLGKDITISLGEP- 160
                                       *************99..***************************************************76677777. PP

                                       SEBTTSSSEEEECCSSSCEEECCCHHHCHHHHHHHHHHCCCCCHC CS
                       vATP-synt_E 155 dfledvlGGvvleaadgkikvnnTlearLelvleqllpeirkaLF 199
                                          ++++GGv++++ +  i+++nT+ear+e++  +l+ +i+k LF
  gi|242399770|ref|YP_002995195.1| 161 ---IETIGGVIVQNLEKTIRIDNTFEARMERLQADLRTKIAKILF 202
                                       ...*****************************************9 PP

>> HrpE  HrpE/YscL/FliH and V-type ATPase subunit E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   2.0   2.2e-06    0.0039      27     165 ..      14     155 ..       3     159 .. 0.65

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.2e-06
                              HrpE  27 aeslrarellaeArlqAeqllaqarekaeellevaveqAeaqFWeqAnalLr....glqqeRealeeqlltaveqLL 99 
                                        ++++ + +l+eA ++Ae++ ++a++ka+   +  + +A+ q   + + ++     ++++++  l+e+l+ +v   +
  gi|242399770|ref|YP_002995195.1|  14 EAEQKIKYILEEAEQKAEKIKQEAEKKARIKADWIIRKAQTQAELEKQRIIAnaklEVRRKKLVLQEELINEVIGAI 90 
                                       45677788999999999999999999888777777776666655555555440000345555555666665554444 PP

                              HrpE 100 sdalarlLdetplaeRasALlRqLlks...qqgearatLycHPeaaadvaaWLaehs.dleWklksDeal 165
                                       +d     L  +p+ae ++ +l++L+++     ge +  L+   e+++  +a L+e++ + + kl +D ++
  gi|242399770|ref|YP_002995195.1|  91 KDR----LLSIPEAEYME-ILKDLIVTgirELGEEKVVLSSNGETLSLLKAHLKEMEeSVNEKLGKDITI 155
                                       433....33567777555.455665542325678888999999999999999999987888888888776 PP

>> ATP-synt_B  ATP synthase B/B' CF(0)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   7.4    0.0022       3.9      67     102 ..       4      39 ..       1      40 [. 0.85
   2 ?   14.5  12.3   1.6e-05     0.028      51     107 ..      29      85 ..      28      92 .. 0.88
   3 ?   -2.9   0.1       3.7   6.7e+03     108     117 ..     186     195 ..     172     199 .. 0.51

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0022
                        ATP-synt_B  67 AaeiiknAkkeaeklkeeieaeaeaeaerlkesAaa 102
                                       A+ ii++ +keae+  + i +eae++ae++k++A++
  gi|242399770|ref|YP_002995195.1|   4 ARLIIEEINKEAEQKIKYILEEAEQKAEKIKQEAEK 39 
                                       788999999999999999999999999999999976 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 1.6e-05
                        ATP-synt_B  51 allaeaeqqlkeAraeAaeiiknAkkeaeklkeeieaeaeaeaerlkesAaaeIeqe 107
                                       ++++ ++++ k+Ar +A+ ii++A+ +ae +k+ i+a+a+ e++r k   ++e+  e
  gi|242399770|ref|YP_002995195.1|  29 KAEKIKQEAEKKARIKADWIIRKAQTQAELEKQRIIANAKLEVRRKKLVLQEELINE 85 
                                       67777888999**********************************998888888766 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 3.7
                        ATP-synt_B 108 kdralaeLre 117
                                        +r+ a+Lr 
  gi|242399770|ref|YP_002995195.1| 186 MERLQADLRT 195
                                       2333333333 PP

>> DUF3540  Protein of unknown function (DUF3540)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.6    0.0001      0.19     139     196 ..       6      63 ..       2      64 .. 0.91
   2 ?   -1.9   0.0       1.3   2.4e+03     135     154 ..     159     178 ..     125     197 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0001
                           DUF3540 139 svvdrltqrakrsfRrveeveqvragridyqaeeslrlhakntvitAkelvkidaeqI 196
                                        +++ + + a++ ++++ e  + +a++i+++ae+++r++a+  + +A++++  + ++I
  gi|242399770|ref|YP_002995195.1|   6 LIIEEINKEAEQKIKYILEEAEQKAEKIKQEAEKKARIKADWIIRKAQTQAELEKQRI 63 
                                       678899999**********9**********************9999999998877766 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.3
                           DUF3540 135 ksvesvvdrltqrakrsfRr 154
                                       + +e++ + ++q +++++R+
  gi|242399770|ref|YP_002995195.1| 159 EPIETIGGVIVQNLEKTIRI 178
                                       44555555555555555553 PP

>> V-ATPase_G_2  Vacuolar (H+)-ATPase G subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0  12.7   5.7e-05       0.1      22      91 ..       2      71 ..       1      92 [. 0.83
   2 ?   -1.0   0.1       1.4   2.4e+03      41      61 ..     177     197 ..     170     200 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.7e-05
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCSH CS
                      V-ATPase_G_2 22 EaArkeaereveaAeaeAarilreAeakakalqaeyeqelaeevarireeararaeaeaqavrkraearl 91
                                      E Ar   e+  ++Ae+  + il+eAe+ka+++++e e++ + +   i  +a+++ae e q++ ++a+  +
  gi|242399770|ref|YP_002995195.1|  2 EGARLIIEEINKEAEQKIKYILEEAEQKAEKIKQEAEKKARIKADWIIRKAQTQAELEKQRIIANAKLEV 71
                                      7778888888899999999999999999999999999999999999999999999999998877776544 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.4
                                       HHHHHHHHHHHHHHHHHHHHH CS
                      V-ATPase_G_2  41 rilreAeakakalqaeyeqel 61 
                                       ri +  ea++++lqa+ + ++
  gi|242399770|ref|YP_002995195.1| 177 RIDNTFEARMERLQADLRTKI 197
                                       566667788888888777665 PP

>> DUF3552  Domain of unknown function (DUF3552)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5  10.6   0.00066       1.2      36      74 ..       4      42 ..       1      44 [. 0.76
   2 ?    5.6  10.6    0.0051       9.1      30      73 ..      39      82 ..      38     154 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00066
                           DUF3552 36 AkkiieeAkkeAeakkkealleakeeihklreelekelk 74
                                      A+ iiee +keAe+k k +l ea +++ k+++e+ek  +
  gi|242399770|ref|YP_002995195.1|  4 ARLIIEEINKEAEQKIKYILEEAEQKAEKIKQEAEKKAR 42
                                      777888888888888888888888888888888887765 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0051
                           DUF3552 30 aeAeeeAkkiieeAkkeAeakkkealleakeeihklreelekel 73
                                      ++A+ +A+ ii +A+ +Ae  k+ ++ +ak e+++ +  l +el
  gi|242399770|ref|YP_002995195.1| 39 KKARIKADWIIRKAQTQAELEKQRIIANAKLEVRRKKLVLQEEL 82
                                      58999******************************998888886 PP

>> NolV  Nodulation protein NolV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   2.4    0.0056        10      51      94 ..      18      61 ..      10      63 .. 0.92
   2 ?    8.4   0.9   0.00069       1.2      72     109 ..      59      96 ..      54     140 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0056
                              NolV 51 rlayerelargraeglkagaeemaaliaqavaelarrkavlere 94
                                      ++ y  e a+ +ae +k  ae+ a++ a+ +   a+ +a le++
  gi|242399770|ref|YP_002995195.1| 18 KIKYILEEAEQKAEKIKQEAEKKARIKADWIIRKAQTQAELEKQ 61
                                      5678899***********************************97 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00069
                              NolV  72 emaaliaqavaelarrkavlerelpqlvleilrellga 109
                                       e  ++ia+a  e+ r+k vl++el + v+  +++ l +
  gi|242399770|ref|YP_002995195.1|  59 EKQRIIANAKLEVRRKKLVLQEELINEVIGAIKDRLLS 96 
                                       6679*********************9999999886644 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 ?   -0.1   1.2      0.59   1.1e+03      47      63 ..      25      41 ..       8      49 .. 0.63
   2 ?    4.4   0.4     0.023        42      41      67 ..      68      94 ..      45      97 .. 0.80
   3 ?    7.6   0.1    0.0023       4.1      36      71 ..     118     153 ..      95     153 .. 0.89
   4 ?    0.5   0.0      0.38   6.9e+02      52      73 .]     182     203 .]     170     203 .] 0.82

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.59
                                      EEHHHHHHHHH....HH CS
                           CinA_KH 47 aneeeaealiapveeei 63
                                      + e++ae++ +++e++ 
  gi|242399770|ref|YP_002995195.1| 25 EAEQKAEKIKQEAEKKA 41
                                      34555555555555555 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.023
                                      EEE...EEHHHHHHHHH....HHHHHT CS
                           CinA_KH 41 Rltakaaneeeaealiapveeeirerl 67
                                      +l ++ ++    e+li++v+ +i++rl
  gi|242399770|ref|YP_002995195.1| 68 KLEVRRKKLVLQEELINEVIGAIKDRL 94
                                      5667777777889************98 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0023
                                       TEEEEEEE...EEHHHHHHHHH....HHHHHTTTTE CS
                           CinA_KH  36 gevtvRltakaaneeeaealiapveeeirerlgdyv 71 
                                       ge +v l+ ++++    +a ++++ee + e+lg+ +
  gi|242399770|ref|YP_002995195.1| 118 GEEKVVLSSNGETLSLLKAHLKEMEESVNEKLGKDI 153
                                       678999***************************976 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 0.38
                                       HHHHHH....HHHHHTTTTEEE CS
                           CinA_KH  52 aealiapveeeirerlgdyvyG 73 
                                        ea+++++++ +r ++++ ++G
  gi|242399770|ref|YP_002995195.1| 182 FEARMERLQADLRTKIAKILFG 203
                                       5788999999999999998887 PP

>> WBS_methylT  Methyltransferase involved in Williams-Beuren syndrome
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   6.3    0.0037       6.6      22      62 ..      12      55 ..       5      75 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0037
                       WBS_methylT 22 eseeaeqvkyekrrrkrkkrkkkkkkavk...sreWilkKKerr 62
                                      ++e+++++ky  +++++k++k k++ ++k   + +Wi++K + +
  gi|242399770|ref|YP_002995195.1| 12 NKEAEQKIKYILEEAEQKAEKIKQEAEKKariKADWIIRKAQTQ 55
                                      4557899999999998888866666666656788******8765 PP

>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8  12.8   0.00091       1.6      76     129 ..       8      62 ..       4      63 .. 0.76
   2 ?    1.2   0.1       0.2   3.6e+02      29      68 ..     109     148 ..      98     151 .. 0.79
   3 ?    0.2   0.0      0.42   7.5e+02      30      56 ..     168     194 ..     166     198 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00091
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXX CS
                            DivIVA  76 aeevkanakkeaeliikeAekkaekiveeaeeeak.kiaeeieelkrqarlfrqr 129
                                        ee+ ++a+++ + i++eAe+kaeki +eae++a+ k+   i + + qa+l +qr
  gi|242399770|ref|YP_002995195.1|   8 IEEINKEAEQKIKYILEEAEQKAEKIKQEAEKKARiKADWIIRKAQTQAELEKQR 62 
                                       5899999*******************99999998624444455666666666665 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.2
                                       HHHHHHHHHHHHHHHHHHHHHCCCCTXXXXXXXXXXXXXX CS
                            DivIVA  29 qvakdyeallkeneelkekvkeleeklkeykeleetLkkt 68 
                                        ++  +++l +e+  l ++ ++l    ++ ke+ee++++ 
  gi|242399770|ref|YP_002995195.1| 109 LIVTGIRELGEEKVVLSSNGETLSLLKAHLKEMEESVNEK 148
                                       4666788889999999999999999999999999999876 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.42
                                       HHHHHHHHHHHHHHHHHHHHCCCCTXX CS
                            DivIVA  30 vakdyeallkeneelkekvkeleeklk 56 
                                       +++++e+ ++  ++ ++++++l+ +l 
  gi|242399770|ref|YP_002995195.1| 168 IVQNLEKTIRIDNTFEARMERLQADLR 194
                                       788999999999999999999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2771  (0.154554); expected 358.6 (0.02)
Passed bias filter:                      943  (0.0525964); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.68u 0.34s 00:00:01.02 Elapsed: 00:00:00.51
# Mc/sec: 1208.54
//
Query:       gi|242399771|ref|YP_002995196.1|  [L=161]
Description: A1A0 ATP synthase, subunit c [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.2e-30  104.8  27.7    3.4e-17   62.5  10.6    2.3  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 !   48.2   9.1   5.6e-17     1e-12       1      60 []       9      68 ..       9      68 .. 0.98
   2 !   62.5  10.6   1.9e-21   3.4e-17       1      60 []      96     154 ..      96     154 .. 0.99

  Alignments for each domain:
  == domain 1  score: 48.2 bits;  conditional E-value: 5.6e-17
                                      HHHHHHH.GGGHHHHHHHHHHHHHHHHHHHHSGHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        ATP-synt_C  1 lgaglavGlsalgsGigiGkagsagiravarnpklftksliilafaeaialygLivalil 60
                                      lga+la G+++ +s +g+G+ag+a+++ava++ k f ++l++++++ ++ +ygLi  +++
  gi|242399771|ref|YP_002995196.1|  9 LGAALAAGIAGAASSFGVGIAGAAAAGAVAEDEKNFRNALVLQGLPMTQSIYGLITLFLI 68
                                      7*******************************************************9997 PP

  == domain 2  score: 62.5 bits;  conditional E-value: 1.9e-21
                                       HHHHHHH.GGGHHHHHHHHHHHHHHHHHHHHSGHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        ATP-synt_C   1 lgaglavGlsalgsGigiGkagsagiravarnpklftksliilafaeaialygLivalil 60 
                                       lgagl vGl++l s+i +G+++sagi+a+a+npk ft+s+i++a+ae++a++gL+ alil
  gi|242399771|ref|YP_002995196.1|  96 LGAGLTVGLTGL-SAIPQGIIASAGIGATAKNPKTFTQSIIFAAMAETMAIFGLVGALIL 154
                                       7**********9.*********************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       816  (0.0455129); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.33s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 913.63
//
Query:       gi|242399772|ref|YP_002995197.1|  [L=661]
Description: A1A0 ATP synthase, subunit a [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-32  112.8  19.9    8.3e-22   76.9   1.6    3.0  3  V_ATPase_I       V-type ATPase 116kDa subunit family
     0.0062   16.9   0.0      0.018   15.4   0.0    1.8  1  V_ATPase_I_N     V-type ATPase subunit I, N-terminal domain
  ------ inclusion threshold ------
      0.053   12.3   1.3        0.1   11.3   1.3    1.4  1  Tektin           Tektin family
      0.097   12.7   1.1       0.32   11.1   1.1    1.9  1  DUF1192          Protein of unknown function (DUF1192)
        0.1   13.6   0.3          7    7.7   0.0    3.2  3  AMP-binding_C    AMP-binding enzyme C-terminal domain
       0.12   12.4   2.3       0.31   11.0   0.4    2.4  2  DUF1759          Protein of unknown function (DUF1759)
       0.17   11.2   1.7          5    6.4   0.1    2.2  2  Phlebovirus_NSM  Phlebovirus nonstructural protein NS-M
       0.23   11.0   0.0       0.82    9.2   0.0    1.8  2  EBV-NA3          Epstein-Barr virus nuclear antigen 3 (EBNA-3
       0.25   11.6   1.9       0.25   11.6   0.4    1.7  2  DUF5082          Domain of unknown function (DUF5082)
        1.1    9.4   9.5       0.24   11.5   2.3    2.6  2  UPF0242          Uncharacterised protein family (UPF0242) N-t
        3.8    6.7   8.5        1.9    7.6   0.6    2.8  3  TMPIT            TMPIT-like protein
        6.2    7.6   9.9        2.8    8.7   2.6    2.9  2  RecG_N           RecG N-terminal helical domain


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 !   76.9   1.6   5.6e-25   8.3e-22     104     450 ..      97     435 ..      61     437 .. 0.78
   2 ?   -4.0   1.9       1.6   2.5e+03     516     562 ..     462     509 ..     459     516 .. 0.77
   3 !   48.6   1.8   2.1e-16   3.1e-13     708     812 ..     548     649 ..     544     650 .. 0.75

  Alignments for each domain:
  == domain 1  score: 76.9 bits;  conditional E-value: 5.6e-25
                        V_ATPase_I 104 elkavlekakefleeeeeeeeeeeseeeeeekeeeeeeeseeeeeeelleeeee.................lsfvaG 163
                                         + +++++++fl++ e + +e  +++ ++ ++e e++++e            e                 +++v+G
  gi|242399772|ref|YP_002995197.1|  97 GIEDLIKEIEAFLDKVEPQIKE-MEDKITNLTSEIERKKTEIAIL--------ElltaldleveylkptktVEIVVG 164
                                       4555666666777654222222.1111111122222222211111........011223334556666666888999 PP

                        V_ATPase_I 164 vikrekveaferilwralrgnlflrqaeieepledpetgekveksvfiiffqgeqlkekikkicesfgaklyelpes 240
                                        ++++k+e + + l  +l+  + + +++++              +  ++f+  ++  +k + +   ++ +  e+pe 
  gi|242399772|ref|YP_002995197.1| 165 FVEKDKFEPLIKELNATLQNRVAYVSKDLKG-------------KYLVVFVFLKKDYDKANPLLAKYSLDRLEIPEV 228
                                       9999999999999999998888888887777.............455666666677899****************** PP

                        V_ATPase_I 241 eeereeklkeveeriedlekvleqteealkevleeiakeleewklkvkkekaiyhtLnlfnldvtkkvliaegWvpk 317
                                       + + +e+++++ ++ie  ++ le+ e + +++ +++ +el  ++  ++ e++  ++L  +   +t+ ++   gW+pk
  gi|242399772|ref|YP_002995197.1| 229 KGKPREAIETLWKHIEVKKRELESAEVEARNLAKQYHDELVFYQELMENEREKANMLSNL--VRTNMTFALVGWLPK 303
                                       ***************************************************999999777..4678899999***** PP

                        V_ATPase_I 318 eeleeiqkalkeateessssvpsilneietketpPTyfrtnkfteafQeivdaYGiarYrEvNpalftiitFPFlFa 394
                                       +++++i + lk++t  +   +++ + + e+ ++ P   +  kf e f  + + +G+++Y+E+ p+++   t+ F F+
  gi|242399772|ref|YP_002995197.1| 304 KDVTRIAEGLKKITGGK-VYINTKTPTKEELDEIPIKLKNPKFIEPFEMLTEMFGVPKYNELDPTPVLAFTYSFFFG 379
                                       ************99444.3333333333334789******************************************* PP

                        V_ATPase_I 395 vMFGDiGHGlllllfalllvlkekklkkkkkdeilemlfsgRYiillmGl.fsiYtG 450
                                        M  D+  Gl+++++a ll+  +kkl+   + ++ ++l+   ++ ++mGl f  Y G
  gi|242399772|ref|YP_002995197.1| 380 FMLTDFVYGLIIAVIAYLLIKGHKKLNDG-TYKFSNILVWSAFFTIVMGLlFGSYLG 435
                                       **************************997.578888888888888888853777776 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 1.6
                        V_ATPase_I 516 svilGviqMlfgvllslvNalyfkkkldiilefiPqllf.llsifgYl 562
                                       +  +G+i++++g++l ++  + + +  d ++  +  +l  l ++f+ l
  gi|242399772|ref|YP_002995197.1| 462 ALAIGLIHLFIGYTLGFIVKFRNGEVKDAVFDQLSWMLIiLGVVFIVL 509
                                       6679**************999999999999998876655044455544 PP

  == domain 3  score: 48.6 bits;  conditional E-value: 2.1e-16
                        V_ATPase_I 708 htIEfvLgciSnTASYLRLWALSLAHaqLseVlwemvlkkallksk.svlgvillvilfavfavltvavLllmegls 783
                                        tI    g i n  SY RL AL LA a ++ V+   v    + k +   lg+   v++++vf+   ++    +++l 
  gi|242399772|ref|YP_002995197.1| 548 MTISNFFGFIGNWLSYARLMALALATAGIAMVINIIVQLIWGVKIGpIPLGM---VVGLVVFVGGHIF-STAINALG 620
                                       58888899************************95444433333322133344...4444444443333.34579*** PP

                        V_ATPase_I 784 afLHaLRLhWVEfqsKFykgdGykFepfs 812
                                       af HaLRLh VEf   Fy+g+G kFepf+
  gi|242399772|ref|YP_002995197.1| 621 AFVHALRLHYVEFFGTFYSGEGKKFEPFK 649
                                       ****************************7 PP

>> V_ATPase_I_N  V-type ATPase subunit I, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.2e-05     0.018      32      88 ..     167     223 ..     142     225 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.2e-05
                                       TCCHHHHHHHHHHHHHTTSSEEEEEESSSSEEEEEEEECCCHHHHHHHHHCCT--B- CS
                      V_ATPase_I_N  32 keeeleeleaaLreaLedRyalateavgknrvavvvvlrgeldaaraaLsrvrlgEL 88 
                                       ++++ e l + L+++L++R a  ++ ++++ ++v v l+++ d+a   L++  l  L
  gi|242399772|ref|YP_002995197.1| 167 EKDKFEPLIKELNATLQNRVAYVSKDLKGKYLVVFVFLKKDYDKANPLLAKYSLDRL 223
                                       567899999*****************************************9988655 PP

>> Tektin  Tektin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   1.3     7e-05       0.1     256     296 ..      98     138 ..      90     142 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 7e-05
                            Tektin 256 tedaknkleeqlkkvleeiaeleknieeLekairdkeaplk 296
                                       +ed  +++e  l+kv+ +i+e+e++i++L ++i+ k+  ++
  gi|242399772|ref|YP_002995197.1|  98 IEDLIKEIEAFLDKVEPQIKEMEDKITNLTSEIERKKTEIA 138
                                       6889999****************************998776 PP

>> DUF1192  Protein of unknown function (DUF1192)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.1   0.00022      0.32      22      44 ..     116     138 ..     115     139 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00022
                           DUF1192  22 veELeerIalLeaEIaRleaaia 44 
                                       ++E+e+ I+ L++EI+R +++ia
  gi|242399772|ref|YP_002995197.1| 116 IKEMEDKITNLTSEIERKKTEIA 138
                                       68*****************9996 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.55   8.2e+02      27      71 ..      77     132 ..      69     136 .. 0.64
   2 ?    1.0   0.0      0.59   8.8e+02      25      53 ..     158     185 ..     153     189 .. 0.72
   3 ?    7.7   0.0    0.0047         7      20      62 ..     189     234 ..     170     246 .. 0.71

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.55
                                       ---EEEEEE-.--.---........HHHHHHHHHHHHT-TTT.S-SEEE.E-S---B CS
                     AMP-binding_C  27 ealvafVvlk.dg.sea........leeeLkahvrkelgpya.vpkkvv.fvdelpk 71 
                                         ++af+ +k ++ +          l +e++a++ k  + ++   +k+  +++e+++
  gi|242399772|ref|YP_002995197.1|  77 TGIKAFIFPKlKQkK-RyeyrgiedLIKEIEAFLDKVEPQIKeMEDKITnLTSEIER 132
                                       348999999633321.13446666699999999999888886466677755566655 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.59
                                       TS---EEEEEE----.--HHHHHHHHHHHH CS
                     AMP-binding_C  25 kGealvafVvlkdgs.ealeeeLkahvrke 53 
                                       + e++v+fV    ++ e+l +eL+a +  +
  gi|242399772|ref|YP_002995197.1| 158 TVEIVVGFVEK--DKfEPLIKELNATLQNR 185
                                       56999***986..44477899999888665 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0047
                                       ----TTS---EEEEEE----.--HHHHHHHHH...HHHT-TTT.S-SE CS
                     AMP-binding_C  20 vpdevkGealvafVvlkdgs.ealeeeLkahv...rkelgpya.vpkk 62 
                                       v+ ++kG++lv+fV lk+++ +  ++ L a+    r e+++++ +p++
  gi|242399772|ref|YP_002995197.1| 189 VSKDLKGKYLVVFVFLKKDYdK--ANPLLAKYsldRLEIPEVKgKPRE 234
                                       78999***********987523..356655554544466666656664 PP

>> DUF1759  Protein of unknown function (DUF1759)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.72   1.1e+03     107     139 ..      63      95 ..      59     107 .. 0.87
   2 ?   11.0   0.4   0.00021      0.31      55     118 ..     196     259 ..     168     281 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.72
                           DUF1759 107 ralealgeeadkydailvsllleKldeevrrkw 139
                                       r ++ lg+ ++k ++ +   ++ Kl+++ r ++
  gi|242399772|ref|YP_002995197.1|  63 RLIDFLGNYKEKDETGIKAFIFPKLKQKKRYEY 95 
                                       778899999999999999*********999887 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00021
                           DUF1759  55 nYeaaveaLkkrYdnkrkiirellnelmklpslkeedasqlrrivdavneivralealgeeadk 118
                                        Y +++ +Lkk Yd+ + +++++     ++p++k +  + ++++   ++ + r le++ +ea++
  gi|242399772|ref|YP_002995197.1| 196 KYLVVFVFLKKDYDKANPLLAKYSLDRLEIPEVKGKPREAIETLWKHIEVKKRELESAEVEARN 259
                                       6889999****************99999*****************************9988774 PP

>> Phlebovirus_NSM  Phlebovirus nonstructural protein NS-M
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.3     0.021        31     185     235 ..      89     140 ..      84     145 .. 0.77
   2 ?    6.4   0.1    0.0034         5     196     255 ..     241     298 ..     216     303 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.021
                   Phlebovirus_NSM 185 qkkRndikrgqek..rdakklveesmArvkdlkeelkiltdelsqikseiqil 235
                                       qkkR +  rg e   ++++   +  + ++k++ ++   lt e+++ k+ei il
  gi|242399772|ref|YP_002995197.1|  89 QKKRYE-YRGIEDliKEIEAFLDKVEPQIKEMEDKITNLTSEIERKKTEIAIL 140
                                       677777.6665543367778888888899999999999999999999999876 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0034
                   Phlebovirus_NSM 196 ekrdakklveesmArvkdlkeelkiltdelsqikseiqilrkkikdfetvvpAllsvAll 255
                                       ++ ++kk+  es     + ++  k+  del   ++ ++  r+k  +   +v   +++Al+
  gi|242399772|ref|YP_002995197.1| 241 KHIEVKKRELES--AEVEARNLAKQYHDELVFYQELMENEREKANMLSNLVRTNMTFALV 298
                                       455555544443..3334688899999*******************************96 PP

>> EBV-NA3  Epstein-Barr virus nuclear antigen 3 (EBNA-3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.2   1.8e+03     138     158 ..      64      84 ..      61      94 .. 0.82
   2 ?    9.2   0.0   0.00055      0.82      83     163 ..     242     319 ..     236     341 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.2
                                       S---XXXXXXXXXXXXXXXXX CS
                           EBV-NA3 138 fveflGvlskkdlsaikewfr 158
                                        ++flG  ++kd++ ik ++ 
  gi|242399772|ref|YP_002995197.1|  64 LIDFLGNYKEKDETGIKAFIF 84 
                                       689**************9985 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00055
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-----SS---XXXXXXXXXXXXXXXXXX CS
                           EBV-NA3  83 rispreqkilaaeaevrrlrsksaerYslffDlvelgrsLtkiWeellteenrvsfveflGvlskkdlsaikewfrk 159
                                       +i  ++++ + ae e+r+l +++++    + +l+e  r   ++  +l+ ++  + f   +G+l kkd + i e ++k
  gi|242399772|ref|YP_002995197.1| 242 HIEVKKRELESAEVEARNLAKQYHDELVFYQELMENEREKANMLSNLVRTN--MTF-ALVGWLPKKDVTRIAEGLKK 315
                                       67778999*****************999999****************6444..445.589***************99 PP

                                       XXXX CS
                           EBV-NA3 160 alGr 163
                                        +G 
  gi|242399772|ref|YP_002995197.1| 316 ITGG 319
                                       9985 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.4   0.00017      0.25      67     114 ..      94     140 ..      68     143 .. 0.69
   2 ?   -2.9   0.1       5.2   7.8e+03      86     108 ..     236     258 ..     231     270 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00017
                           DUF5082  67 nydgirsnlessyqtyvdkldelidaieeEIerLenqiseaqgvldtl 114
                                       +y gi+ +l ++++++ dk++  i+++e++I++L ++i+ +++ ++ l
  gi|242399772|ref|YP_002995197.1|  94 EYRGIE-DLIKEIEAFLDKVEPQIKEMEDKITNLTSEIERKKTEIAIL 140
                                       444443.45556777777777777777777777777777777777655 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5.2
                           DUF5082  86 ldelidaieeEIerLenqiseaq 108
                                       +++l ++ie + ++Le+   ea 
  gi|242399772|ref|YP_002995197.1| 236 IETLWKHIEVKKRELESAEVEAR 258
                                       45555555555555555544444 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 ?   11.5   2.3   0.00016      0.24     121     176 ..      86     141 ..      71     151 .. 0.90
   2 ?    1.0   0.8      0.27     4e+02     100     148 ..     238     279 ..     203     295 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00016
                           UPF0242 121 qLqekleaiaedfeelkleleeqLaekqellqeyqetieeqrsvlekrqdqieqLe 176
                                       +L++k+    + +e+l +e+e+ L++ + +++e++ +i+++ s++e+++ +i+ Le
  gi|242399772|ref|YP_002995197.1|  86 KLKQKKRYEYRGIEDLIKEIEAFLDKVEPQIKEMEDKITNLTSEIERKKTEIAILE 141
                                       5777777778899***************************************9998 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.27
                           UPF0242 100 eLkeeldakeeelerlkeenqqLqekleaiaedfeelkleleeqLaekq 148
                                        L ++++ k++ele  + e  +L ++        ++ + +++e +++++
  gi|242399772|ref|YP_002995197.1| 238 TLWKHIEVKKRELESAEVEARNLAKQY-------HDELVFYQELMENER 279
                                       333444444444444444444444333.......333333333333333 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.2      0.03        44      23      60 ..     100     137 ..      84     202 .. 0.52
   2 ?   -1.7   0.1      0.89   1.3e+03      33      81 ..     237     284 ..     205     300 .. 0.59
   3 ?    7.6   0.6    0.0013       1.9     267     313 ..     470     517 ..     446     521 .. 0.67

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.03
                             TMPIT  23 qkleelsklqskcskeikkqkkrlkelksslkklkksv 60 
                                         ++e++++ +k+  +ik+ + ++++l+s++++ k+++
  gi|242399772|ref|YP_002995197.1| 100 DLIKEIEAFLDKVEPQIKEMEDKITNLTSEIERKKTEI 137
                                       23333333444444444444444444444444433332 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.89
                             TMPIT  33 skcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkv 81 
                                       +++ k+i+ +k++l++ + + ++l k+  ++e   ++el e+ +e+ ++
  gi|242399772|ref|YP_002995197.1| 237 ETLWKHIEVKKRELESAEVEARNLAKQY-HDELVFYQELMENEREKANM 284
                                       3444455555555555555555555553.23333444444444444444 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0013
                             TMPIT 267 Lfigqffqlynaltlfklall.eeckewqvlvlgllflilalGNfltt 313
                                       Lfig+   +++ +   ++  +  +   w +++lg++f++la++Nf+++
  gi|242399772|ref|YP_002995197.1| 470 LFIGYTLGFIVKFRNGEVKDAvFDQLSWMLIILGVVFIVLAMANFISM 517
                                       455555555544444444433233449******************976 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 ?    8.7   2.6    0.0019       2.8       2      48 ..     105     149 ..      86     161 .. 0.74
   2 ?    2.1   0.8      0.22   3.3e+02      22      63 ..     235     276 ..     220     289 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0019
                                       HHHHHHHHHHHHTS---TTT........HHHHHHH---.GGGG-HHHH CS
                            RecG_N   2 iEeFLeelekllkkvlsgkleteelieeikkklelidd.plleneevl 48 
                                       iE FL+++e  +k+++ +k  + +l  ei++k  +i+  +ll + +++
  gi|242399772|ref|YP_002995197.1| 105 IEAFLDKVEPQIKEME-DK--ITNLTSEIERKKTEIAIlELLTALDLE 149
                                       8999999999999983.33..368999999977776652344444444 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.22
                                       ........HHHHHHH---GGGG-HHHH.HHHHHHHHHHTTSS CS
                            RecG_N  22 eteelieeikkkleliddplleneevlkeklskfldYikpia 63 
                                        +e l + i+ k  +++  ++e+ +++k++ ++++ Y + ++
  gi|242399772|ref|YP_002995197.1| 235 AIETLWKHIEVKKRELESAEVEARNLAKQYHDELVFYQELME 276
                                       457788888888888888888888888888888888876554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (661 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1969  (0.109822); expected 358.6 (0.02)
Passed bias filter:                     1009  (0.0562775); expected 358.6 (0.02)
Passed Vit filter:                       165  (0.00920297); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 1.08u 0.39s 00:00:01.47 Elapsed: 00:00:00.59
# Mc/sec: 3353.96
//
Query:       gi|242399773|ref|YP_002995198.1|  [L=103]
Description: A1A0 ATP synthase, subunit H [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.7e-06   27.0  24.3    5.4e-06   26.8  24.3    1.1  1  V-ATPase_G_2    Vacuolar (H+)-ATPase G subunit
    1.1e-05   25.6  27.5    7.4e-05   22.9  19.3    2.0  2  ATP-synt_B      ATP synthase B/B' CF(0)
     0.0074   15.7  27.2      0.014   14.8  16.0    2.0  2  DUF3552         Domain of unknown function (DUF3552)
  ------ inclusion threshold ------
      0.012   16.1  24.7      0.018   15.5  24.7    1.2  1  V-ATPase_G      Vacuolar (H+)-ATPase G subunit
      0.081   13.0  22.6        7.6    6.6  22.6    2.2  1  DivIVA          DivIVA protein
      0.092   13.4   9.3       0.58   10.8   3.9    2.1  2  DUF883          Bacterial protein of unknown function (DUF883
       0.11   12.3   9.8       0.08   12.8   7.6    1.7  2  HrpE            HrpE/YscL/FliH and V-type ATPase subunit E
       0.58   10.1  17.1       0.78    9.7  17.1    1.2  1  RRF             Ribosome recycling factor
        1.2    9.3  18.5         19    5.5  18.6    2.0  1  SMBP            Small metal-binding protein
        3.9    6.5   8.5        4.4    6.3   8.5    1.0  1  hDGE_amylase    Glycogen debranching enzyme, glucanotransfera
        4.9    7.3   9.3        5.4    7.1   9.3    1.0  1  DUF262          Protein of unknown function DUF262
        5.2    5.8  20.4          6    5.6  20.4    1.1  1  Mitofilin       Mitochondrial inner membrane protein
        8.5    6.6  11.0         12    6.2  11.0    1.3  1  DUF2072         Zn-ribbon containing protein


Domain annotation for each model (and alignments):
>> V-ATPase_G_2  Vacuolar (H+)-ATPase G subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8  24.3   3.9e-09   5.4e-06       6     100 ..       4      98 ..       1     101 [. 0.95

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 3.9e-09
                                       HTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      V-ATPase_G_2   6 llkeLaerEaeLdqrlEaArkeaereveaAeaeAarilreAeakakalqaeyeqelaeevarireeararaeaeaqa 82 
                                       ++ke+ e E++ ++r+E+A+ ea++ +e+A+ eA++i +e  + a++ ++   +e ++e + ++e++ +++e+e ++
  gi|242399773|ref|YP_002995198.1|   4 IIKEVVEAEKKAEERIEKAKGEAKAILEHAKKEAKQIEEEIINAAQNQANSLIEEKKREGEIEAEKIVKEGEKEIEE 80 
                                       89**************************************9999999999999999*****9*************** PP

                                       HHHHHHCSHHHHHHHHHH CS
                      V-ATPase_G_2  83 vrkraearlqqAvelilk 100
                                       ++ +ae+  ++A+++ +k
  gi|242399773|ref|YP_002995198.1|  81 IKLKAEQNFENAINEAIK 98 
                                       ************998876 PP

>> ATP-synt_B  ATP synthase B/B' CF(0)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9  19.3   5.3e-08   7.4e-05      47     107 ..       6      68 ..       2      69 .. 0.88
   2 !   12.8  10.2     7e-05     0.097      63     117 ..      48     102 ..      47     103 .] 0.95

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 5.3e-08
                        ATP-synt_B  47 keaaallaeaeqqlkeAraeAaeiiknAkkeaeklkeeieaeaeaeaerlkesAaa..eIeqe 107
                                       ke  +++++ae++ ++A+ eA+ i ++Akkea+++ eei+++a+++a++l+e+++   eIe+e
  gi|242399773|ref|YP_002995198.1|   6 KEVVEAEKKAEERIEKAKGEAKAILEHAKKEAKQIEEEIINAAQNQANSLIEEKKRegEIEAE 68 
                                       5677899*******************************************9988651156666 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 7e-05
                        ATP-synt_B  63 AraeAaeiiknAkkeaeklkeeieaeaeaeaerlkesAaaeIeqekdralaeLre 117
                                       A+ +A+ +i++ k+e+e ++e+i++e e+e+e +k +A+++ e + ++a++ +r+
  gi|242399773|ref|YP_002995198.1|  48 AQNQANSLIEEKKREGEIEAEKIVKEGEKEIEEIKLKAEQNFENAINEAIKLIRG 102
                                       999******************************************9999998886 PP

>> DUF3552  Domain of unknown function (DUF3552)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8  16.0     1e-05     0.014      18      68 ..       8      58 ..       3      62 .. 0.87
   2 !    8.9  13.2   0.00066      0.91      22      79 ..      38      95 ..      38     100 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1e-05
                           DUF3552 18 ylvrkkiaekkiaeAeeeAkkiieeAkkeAeakkkealleakeeihklree 68
                                      ++ ++k+ae++i++A+ eAk i+e+AkkeA+++ +e++  a++++  l ee
  gi|242399773|ref|YP_002995198.1|  8 VVEAEKKAEERIEKAKGEAKAILEHAKKEAKQIEEEIINAAQNQANSLIEE 58
                                      5557899************************************99887666 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00066
                           DUF3552 22 kkiaekkiaeAeeeAkkiieeAkkeAeakkkealleakeeihklreelekelkerrne 79
                                      k+i e+ i+ A+++A+++iee k+e e   ++++ e   ei +++ ++e+++++  ne
  gi|242399773|ref|YP_002995198.1| 38 KQIEEEIINAAQNQANSLIEEKKREGEIEAEKIVKEGEKEIEEIKLKAEQNFENAINE 95
                                      6789999*******************************************98876655 PP

>> V-ATPase_G  Vacuolar (H+)-ATPase G subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5  24.7   1.3e-05     0.018       6     101 ..       5     100 ..       2     101 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.3e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHSSHHHHHH CS
                        V-ATPase_G   6 IqqLLqAEkeAaeivkeArkrkakrlkqAkeeAekEieeyrakkekefkekeaeklgseeelekkieketeekikel 82 
                                       I++  +AEk+A+e +++A+ + ++ l  Ak+eA++  ee  +  +++ ++  +ek  + e  ++ki ke e++i+e+
  gi|242399773|ref|YP_002995198.1|   5 IKEVVEAEKKAEERIEKAKGEAKAILEHAKKEAKQIEEEIINAAQNQANSLIEEKKREGEIEAEKIVKEGEKEIEEI 81 
                                       88999****************************87444444444444444444444456777899************ PP

                                       HHHHHHHHHHHHHHHHHHH CS
                        V-ATPase_G  83 kesvkknkeavvkellklv 101
                                       k ++++n e+ ++e +kl+
  gi|242399773|ref|YP_002995198.1|  82 KLKAEQNFENAINEAIKLI 100
                                       ************9988865 PP

>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6  22.6    0.0055       7.6      68     124 ..       7      86 ..       2     102 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0055
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.......................XXXXXXXXXXXXXXXXXX CS
                            DivIVA  68 tlvvaqetaeevkanakkeaeliikeAekkaekive.......................eaeeeakkiaeeieelkr 121
                                        +v a++ aee  ++ak ea+ i++ A+k+a++i e                       eae+ +k+ ++eiee+k 
  gi|242399773|ref|YP_002995198.1|   7 EVVEAEKKAEERIEKAKGEAKAILEHAKKEAKQIEEeiinaaqnqanslieekkregeiEAEKIVKEGEKEIEEIKL 83 
                                       44555555555555555555555555555555555555555555555555599999999999999999999999985 PP

                                       XXX CS
                            DivIVA 122 qar 124
                                       +a+
  gi|242399773|ref|YP_002995198.1|  84 KAE 86 
                                       554 PP

>> DUF883  Bacterial protein of unknown function (DUF883)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   3.9   0.00042      0.58      20      63 ..      10      53 ..       5      58 .. 0.86
   2 ?    9.5   1.2    0.0011       1.5       2      56 ..      39      94 ..      38     101 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00042
                            DUF883 20 eaadeageeaeelRerleerlerarerlrdaeeavaerakeaae 63
                                      ea+++a+e +e+++ ++++ le+a++++++ ee++ + a++ a+
  gi|242399773|ref|YP_002995198.1| 10 EAEKKAEERIEKAKGEAKAILEHAKKEAKQIEEEIINAAQNQAN 53
                                      678999**************************999888887765 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0011
                            DUF883  2 eleael.eslladleellkeaadeageeaeelRerleerlerarerlrdaeeavae 56
                                      ++e+e+ +++ +++++l++e+++e++ eae++ ++ e+++e+ + ++++  e++ +
  gi|242399773|ref|YP_002995198.1| 39 QIEEEIiNAAQNQANSLIEEKKREGEIEAEKIVKEGEKEIEEIKLKAEQNFENAIN 94
                                      5677776899999*****************************99999887766655 PP

>> HrpE  HrpE/YscL/FliH and V-type ATPase subunit E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   7.6   5.8e-05      0.08      19      92 ..       2      71 ..       1      80 [. 0.82
   2 ?    4.2   1.8     0.024        34      19      53 ..      43      77 ..      41     101 .. 0.41

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.8e-05
                              HrpE 19 eilrreqlaeslrarellaeArlqAeqllaqarekaeellevaveqAeaqFWeqAnalLrglqqeRealeeqll 92
                                      ei+ +e + ++++a+e +++A+  A+++l++a++ a+++ e    + +++  +qAn l+++ ++e e   e+++
  gi|242399773|ref|YP_002995198.1|  2 EIIIKEVVEAEKKAEERIEKAKGEAKAILEHAKKEAKQIEE----EIINAAQNQANSLIEEKKREGEIEAEKIV 71
                                      68999*******************************99998....44444447999999999888776555555 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.024
                              HrpE 19 eilrreqlaeslrarellaeArlqAeqllaqarek 53
                                      ei+ + q +++ + +e   e  + Ae+++++ ++ 
  gi|242399773|ref|YP_002995198.1| 43 EIINAAQNQANSLIEEKKREGEIEAEKIVKEGEKE 77
                                      33333333333333333333344444444433333 PP

>> RRF  Ribosome recycling factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7  17.1   0.00057      0.78      84     159 ..      12      87 ..       6      89 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00057
                                       -SSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                               RRF  84 pplTeErrkelvkeakkaaekakvairniRrdankklkklekkiseDdvkkaekeiqkltdkyikeidellkakek 159
                                       ++  eEr ++   eak++ e+ak++ ++i +++ ++ +++++++ e+++++ e e +k++++  kei+e+  ++e+
  gi|242399773|ref|YP_002995198.1|  12 EKKAEERIEKAKGEAKAILEHAKKEAKQIEEEIINAAQNQANSLIEEKKREGEIEAEKIVKEGEKEIEEIKLKAEQ 87 
                                       5667999999999************************99999999************************9888876 PP

>> SMBP  Small metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5  18.6     0.014        19      27     104 ..       8      96 ..       3     100 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.014
                                       HHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH...............-------HHHHHHHHHHHHHHHHHC CS
                              SMBP  27 laeAiehaeaAvahgkaghakalveHaeealkhakaa............aekakeeekehldegikhLeeAIkhgka 91 
                                       + eA ++ae+ ++++k g+aka++eHa++  k+++++            +e++k+e++   ++ +k+ e+ I++ k 
  gi|242399773|ref|YP_002995198.1|   8 VVEAEKKAEERIEKAK-GEAKAILEHAKKEAKQIEEEiinaaqnqanslIEEKKREGEIEAEKIVKEGEKEIEEIKL 83 
                                       56888999999***99.9*******************8777766666654455555555555555555555555555 PP

                                       T-HHHHHHHHHHH CS
                              SMBP  92 ghadvAtkaaeeA 104
                                          +  ++a++eA
  gi|242399773|ref|YP_002995198.1|  84 KAEQNFENAINEA 96 
                                       5555555555555 PP

>> hDGE_amylase  Glycogen debranching enzyme, glucanotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   8.5    0.0032       4.4     207     297 ..      15     101 ..       2     103 .] 0.62

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0032
                                       ..-TT.SHHHHHHHHHHHS-SSTTS--STT---B-HHHHHHHHHHHT-SS.TTT....THHHHHHHHHHHHHHHHHH CS
                      hDGE_amylase 207 eelkeaslkeeaklvkekalkeakkllerfsakidlevaaallkalleeekkeeeeeeevaeklkkildelNlelyk 283
                                       +e + ++ k eak++ e+a keak++ e + +  +++ a +l   ++e++ + e e+e+++++ +k ++e+ l++ +
  gi|242399773|ref|YP_002995198.1|  15 AEERIEKAKGEAKAILEHAKKEAKQIEEEIINAAQNQ-ANSL---IEEKKREGEIEAEKIVKEGEKEIEEIKLKAEQ 87 
                                       1112224555666666666455555554444444333.3333...3344466777899******************* PP

                                       HHHHHHHHHHHHHH CS
                      hDGE_amylase 284 eldedvkaileqll 297
                                       ++++ ++++++ + 
  gi|242399773|ref|YP_002995198.1|  88 NFENAINEAIKLIR 101
                                       ********998776 PP

>> DUF262  Protein of unknown function DUF262
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   9.3    0.0039       5.4      79     165 ..      12     101 ..       3     103 .] 0.71

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0039
                            DUF262  79 keesekriknleaeiek..ekeeededrlkrreresdkellqkllrseklslee.keelaelnsltkkdlakeekrn 152
                                       +++ e+ri++++ e++   e ++++ ++++ ++ + +++  ++l++++k + e  +e+  ++ +++ ++++ + + n
  gi|242399773|ref|YP_002995198.1|  12 EKKAEERIEKAKGEAKAilEHAKKEAKQIEEEIINAAQNQANSLIEEKKREGEIeAEKIVKEGEKEIEEIKLKAEQN 88 
                                       45666677777666666885566666777777777777777777777777666646666666677778888899999 PP

                            DUF262 153 eeknlikayevie 165
                                       +e+ +++a+++i+
  gi|242399773|ref|YP_002995198.1|  89 FENAINEAIKLIR 101
                                       9999999999987 PP

>> Mitofilin  Mitochondrial inner membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6  20.4    0.0044         6     270     362 ..       4      95 ..       1     102 [. 0.74

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0044
                         Mitofilin 270 iipeiitnlkednkkls..kddlnsliahAkteidqlskelaelkkeeekkieralekqkeelekqeealsarleee 344
                                       ii e+    k+ +  ++  k++++++++hAk+e +q+++e++    +++ ++ + +e++k e+e  +e+++++ e+e
  gi|242399773|ref|YP_002995198.1|   4 IIKEVVEAEKKAEERIEkaKGEAKAILEHAKKEAKQIEEEII---NAAQNQANSLIEEKKREGEIEAEKIVKEGEKE 77 
                                       555665555555555551156799999999999999999665...67899999999999999999999999999999 PP

                         Mitofilin 345 rakeerqlrlelerelee 362
                                       +++ + + ++ +e ++ e
  gi|242399773|ref|YP_002995198.1|  78 IEEIKLKAEQNFENAINE 95 
                                       996666666666666554 PP

>> DUF2072  Zn-ribbon containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2  11.0    0.0087        12      43     110 ..      12      86 ..       2      99 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0087
                           DUF2072  43 seekeelvaeaeeeieevldaeeteeeklekk.......ekekaekekeeedrvesvrilepGsYelNlekLler 110
                                       +++ ee + +a++e++ +l+++++e +++e +       ++++  +ek+ e ++e+ +i+++G+ e+   kL  +
  gi|242399773|ref|YP_002995198.1|  12 EKKAEERIEKAKGEAKAILEHAKKEAKQIEEEiinaaqnQANSLIEEKKREGEIEAEKIVKEGEKEIEEIKLKAE 86 
                                       22222445666666777777777777777766777766555666678888899**********999876666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3576  (0.199453); expected 358.6 (0.02)
Passed bias filter:                     1046  (0.0583412); expected 358.6 (0.02)
Passed Vit filter:                       141  (0.00786435); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.68u 0.33s 00:00:01.01 Elapsed: 00:00:00.54
# Mc/sec: 571.12
//
Query:       gi|242399774|ref|YP_002995199.1|  [L=231]
Description: Trk-type pottasium transport system, NAD-binding component [Thermococcus sibiricus MM 739]
Scores for complete 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  109.2   0.7    2.9e-31  108.1   0.4    1.7  2  TrkA_N           TrkA-N domain
    9.1e-10   38.2   0.1      1e-08   34.9   0.1    2.5  2  TrkA_C           TrkA-C domain
    2.1e-07   30.7   0.1    3.5e-07   30.0   0.1    1.4  1  ApbA             Ketopantoate reductase PanE/ApbA
    1.3e-06   28.1   0.1    1.6e-05   24.6   0.0    2.1  2  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
    1.9e-05   24.3   0.5      5e-05   23.0   0.2    1.9  3  NmrA             NmrA-like family
    3.5e-05   24.1   0.3    9.7e-05   22.6   0.2    1.9  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
    6.8e-05   22.3   0.3     0.0001   21.7   0.3    1.4  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
    8.8e-05   22.5   0.1     0.0002   21.3   0.0    1.7  2  NAD_binding_10   NAD(P)H-binding
    0.00021   21.3   0.4    0.00055   20.0   0.3    1.8  2  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
    0.00035   20.5   0.3     0.0008   19.3   0.3    1.7  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
    0.00089   19.7   0.3      0.003   18.0   0.3    2.1  1  NAD_binding_7    Putative NAD(P)-binding
     0.0013   18.7   1.0     0.0022   18.0   1.0    1.4  1  Erp_C            Erp protein C-terminus
     0.0013   19.2   0.0     0.0022   18.5   0.0    1.4  1  XdhC_C           XdhC Rossmann domain
     0.0033   17.9   0.1      0.011   16.3   0.1    1.9  1  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
     0.0059   16.6   0.1       0.02   14.9   0.0    1.9  2  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
     0.0071   16.5   0.8        1.1    9.3   0.3    2.6  2  DapB_N           Dihydrodipicolinate reductase, N-terminus
  ------ inclusion threshold ------
       0.01   15.2   0.0      0.015   14.7   0.0    1.4  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
      0.011   15.3   0.1      0.038   13.5   0.1    1.8  2  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
      0.013   16.1   0.7      0.036   14.6   0.1    2.2  2  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
      0.014   14.7   0.1      0.017   14.4   0.1    1.3  1  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
      0.015   14.6   0.0       0.02   14.1   0.0    1.2  1  FAD_binding_3    FAD binding domain
      0.017   14.6   0.1      0.025   14.0   0.1    1.2  1  Epimerase        NAD dependent epimerase/dehydratase family
      0.017   14.1   0.2      0.026   13.5   0.2    1.2  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
      0.021   15.4   0.1      0.072   13.7   0.1    1.9  1  PglD_N           PglD N-terminal domain
      0.028   14.3   0.1      0.061   13.2   0.1    1.5  1  UPF0146          Uncharacterised protein family (UPF0146)
      0.037   14.2   0.1       0.14   12.3   0.1    2.0  2  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
       0.05   13.5   0.1       0.17   11.7   0.0    1.9  2  Rossmann-like    Rossmann-like domain
      0.051   13.9   0.1       0.12   12.7   0.1    1.7  1  Gp_dh_N          Glyceraldehyde 3-phosphate dehydrogenase, NA
      0.058   13.2   0.3       0.77    9.6   0.0    2.1  2  DFP              DNA / pantothenate metabolism flavoprotein
        0.1   13.2   0.0       0.24   12.0   0.0    1.6  1  Stimulus_sens_1  Stimulus-sensing domain
       0.15   11.5   0.1       0.27   10.7   0.1    1.5  1  adh_short        short chain dehydrogenase
       0.18   12.1   0.0       0.37   11.1   0.0    1.5  1  NAD_binding_8    NAD(P)-binding Rossmann-like domain


Domain annotation for each model (and alignments):
>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.1   0.4   5.1e-34   2.9e-31       1     116 []       3     124 ..       3     124 .. 0.93
   2 ?   -1.7   0.0       5.8   3.2e+03      64      79 ..     177     192 ..     161     217 .. 0.62

  Alignments for each domain:
  == domain 1  score: 108.1 bits;  conditional E-value: 5.1e-34
                                       EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTT.SEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHH CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeg.levvvgdatdeevLeeagiekadaviaatgddean 76 
                                       ++i+G+GrvG+ +a+ L+++g+dv++id d+er++el+      v+ gdatd+++Leea++++ad++ a+tg d+an
  gi|242399774|ref|YP_002995199.1|   3 VVIMGAGRVGYLVAKMLENEGHDVTIIDIDKERAKELSFLVnGLVIEGDATDQKTLEEANLKQADTFAALTGRDDAN 79 
                                       79*****************6558**************9666566********************************* PP

                                       HHHHHHHHHHTSSSEEEEEESSGGGHHHHHHHT.....TSEEEEH CS
                            TrkA_N  77 ilavllakelnpkkkiiaraqdpehaellkklg.....advvisp 116
                                       ila+ lak+lnp++k+i r+++p+++e+++k+      +dvvisp
  gi|242399774|ref|YP_002995199.1|  80 ILACILAKHLNPTIKTILRISKPKNKEVFEKIEdlkkyFDVVISP 124
                                       *******************************87777778999887 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 5.8
                                       SEEEE-SSSHHHHHHH CS
                            TrkA_N  64 daviaatgddeanila 79 
                                       d++i+a+ d + n+++
  gi|242399774|ref|YP_002995199.1| 177 DSLIVAIYDEKGNLVI 192
                                       4455555555555544 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0       1.1   5.9e+02      13      28 ..      54      69 ..      46      98 .. 0.67
   2 !   34.9   0.1   1.8e-11     1e-08       4      69 ..     156     221 ..     153     222 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 1.1
                                      TTSBHHHHTHHHHS-E CS
                            TrkA_C 13 vGktlkelnlrargvl 28
                                      + ktl e+nl++ + +
  gi|242399774|ref|YP_002995199.1| 54 DQKTLEEANLKQADTF 69
                                      5689999998775433 PP

  == domain 2  score: 34.9 bits;  conditional E-value: 1.8e-11
                                       EEEE--GGGTTSBHHHHTHHHHS-EEEEEE-T.-EEES--TT-B--TT-EEEEEEEHHHHHHHHHHH CS
                            TrkA_C   4 vtvpagsplvGktlkelnlrargvlvvairRg.geliipsgdtvLeeGDvllvvgspsdlaelrell 69 
                                       + ++++s +  k +kel l++ + l+vai  + g l+ipsgdt+L +  +++v+++ ++l+++++++
  gi|242399774|ref|YP_002995199.1| 156 FQLSNDSEISEKLVKELSLPK-DSLIVAIYDEkGNLVIPSGDTKLPKKGEVVVFAKNASLKDIKSVF 221
                                       678899***************.*******87779****************************99987 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.1   6.2e-10   3.5e-07       1      95 [.       3     103 ..       3     122 .. 0.87

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 6.2e-10
                                       EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHH..HHHHCEEEEETTCEEEEEECEEECCH...SCCCCS-ESE CS
                              ApbA   1 iailGaGaiGsllaakLakagadvtlilrsr.rlea..lkknGlrltseggeeilrppealsae...ekselepidl 71 
                                       ++i+GaG +G l+a +L + g+dvt+i+ ++ r+++  +  nGl ++++ ++++ +++++l ++   +   +++  +
  gi|242399774|ref|YP_002995199.1|   3 VVIMGAGRVGYLVAKMLENEGHDVTIIDIDKeRAKElsFLVNGLVIEGDATDQKTLEEANLKQAdtfAALTGRDDAN 79 
                                       68*******************************99977889*********777777777777776887777778888 PP

                                       EEE-SSGGGHHHHHHHHGGGECTC CS
                              ApbA  72 vivtvKayqteealeeikplldpn 95 
                                       ++ ++ a ++   +++i ++ +p+
  gi|242399774|ref|YP_002995199.1|  80 ILACILAKHLNPTIKTILRISKPK 103
                                       999999999999999998888776 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   2.8e-08   1.6e-05       2      39 ..       2      39 ..       1      73 [. 0.91
   2 ?    1.4   0.0      0.35     2e+02     133     166 ..     105     137 ..      92     151 .. 0.70

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 2.8e-08
                                      EEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHH CS
                    UDPG_MGDP_dh_N  2 kisviGlGYvGlvtaavlaeighevigvDideekvdkl 39
                                       ++++G+G vG   a +l + gh+v+++Did+e+ ++l
  gi|242399774|ref|YP_002995199.1|  2 FVVIMGAGRVGYLVAKMLENEGHDVTIIDIDKERAKEL 39
                                      589******************************99987 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.35
                                       HHHHHHHCSS-TTCEEEEE------TTSHHHHHH CS
                    UDPG_MGDP_dh_N 133 kkileeaskkkgvdfdvvsnPEflregsavkdll 166
                                       k++ e+ ++  ++ fdvv +PE ++ + + + + 
  gi|242399774|ref|YP_002995199.1| 105 KEVFEKIEDL-KKYFDVVISPEEIAANYIFRSIT 137
                                       4455555554.4889******9988777666655 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.2   8.9e-08     5e-05       2      77 ..       3      78 ..       2      87 .. 0.90
   2 ?   -2.6   0.0       5.7   3.2e+03      42      62 ..     148     169 ..     146     174 .. 0.65
   3 ?   -2.5   0.0       5.3     3e+03     200     222 ..     201     222 ..     155     226 .. 0.53

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 8.9e-08
                                      EESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEE.ES-TT-HHHHHHH.HTT-SEEEE---GGS- CS
                              NmrA  2 lviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelv.kgdlddkeslvea.lkgvdvvfsvtgfysk 77
                                      +vi ++Gr G  v+++l ++gh+v ++  d ++e+ak+l+   + lv +gd+ d++ l+ea lk++d++ + tg  ++
  gi|242399774|ref|YP_002995199.1|  3 VVIMGAGRVGYLVAKMLENEGHDVTII--DIDKERAKELSFLVNGLViEGDATDQKTLEEAnLKQADTFAALTGRDDA 78
                                      588899******************987..9999***********9999***********9989*****9999985544 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 5.7
                                       HSTTEEEES-TT-HHHHH.HHH CS
                              NmrA  42 eaGvelvkgdlddkeslv.eal 62 
                                        +G+e+vk +l +++ ++ +++
  gi|242399774|ref|YP_002995199.1| 148 REGAEIVKFQLSNDSEISeKLV 169
                                       5799999888766555540444 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 5.3
                                       HTTEEEEE-SEEE-HHHHHHHHH CS
                              NmrA 200 lkgkriklagntlsgneivelfe 222
                                        kg+++ +a+n  s+++i ++fe
  gi|242399774|ref|YP_002995199.1| 201 KKGEVVVFAKN-ASLKDIKSVFE 222
                                       24444444444.25555555555 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.2   1.7e-07   9.7e-05       1      73 [.       3      69 ..       3     116 .. 0.82
   2 ?   -1.1   0.0       3.8   2.1e+03      45      69 ..     147     171 ..     105     183 .. 0.64

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.7e-07
                                      EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHH.HTTSSEE CS
                   Sacchrp_dh_NADP  1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaal.lkegdlv 73
                                      v+i GaG+vG  va++l+++++    +t++d +ke++++l   ++g     i+ da +++  L+++ lk++d +
  gi|242399774|ref|YP_002995199.1|  3 VVIMGAGRVGYLVAKMLENEGHD---VTIIDIDKERAKELSFLVNGL---VIEGDATDQKT-LEEAnLKQADTF 69
                                      89******************985...**********99998555554...55566666665.555557777765 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 3.8
                                       TTTCEEEEE--TTTHHHHHHHHHTT CS
                   Sacchrp_dh_NADP  45 lgvrfeaialdaenyeavLaallke 69 
                                        ++ +e+++++ +n++++ ++l+ke
  gi|242399774|ref|YP_002995199.1| 147 PREGAEIVKFQLSNDSEISEKLVKE 171
                                       5566677777777887777777776 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.3   1.8e-07    0.0001      31      94 ..       3      68 ..       2     129 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.8e-07
                                      EEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH.TTTCECEEHCHHHHHHHH.HHHH-SE CS
                       AlaDh_PNT_C 31 vlviGgGvaGlqAiatakglgakVtvlDvrparleqles.lgakfvevlksqeellae.avkeadv 94
                                      v+++G+G +G   +++  + g +Vt++D++++r+++l+  +++ ++e  + ++++l+e ++k+ad 
  gi|242399774|ref|YP_002995199.1|  3 VVIMGAGRVGYLVAKMLENEGHDVTIIDIDKERAKELSFlVNGLVIEGDATDQKTLEEaNLKQADT 68
                                      89************************************9888888888777777776624777774 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   3.6e-07    0.0002       3      73 ..       8      77 ..       7     117 .. 0.82
   2 ?   -2.6   0.0       7.6   4.2e+03      38      58 ..     148     168 ..     144     172 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 3.6e-07
                                      TSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCC CS
                    NAD_binding_10  3 tGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsalggggk 73
                                       G+vG l++k l ++ gh+vt++  ++e+++el+   +  v+egd+td+++l+ea   +   ++al g+++
  gi|242399774|ref|YP_002995199.1|  8 AGRVGYLVAKMLENE-GHDVTIIDIDKERAKELSFLVNGLVIEGDATDQKTLEEANLKQADTFAALTGRDD 77
                                      7********999999.5***************99778888**************97666656777766654 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 7.6
                                       TTTCEEEE--TT-CCHHHHHH CS
                    NAD_binding_10  38 eeglevvegdvtdvedlaeal 58 
                                       +eg+e+v+ ++++ +++ e l
  gi|242399774|ref|YP_002995199.1| 148 REGAEIVKFQLSNDSEISEKL 168
                                       478999999999998888765 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.3   9.8e-07   0.00055      15      59 ..       3      46 ..       1     120 [. 0.69
   2 ?   -1.0   0.0         3   1.7e+03      65      82 ..     107     124 ..      90     139 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 9.8e-07
                                      EEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.E CS
                      Shikimate_DH 15 vlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkge 59
                                      v+++GaG+++ lvak+L ++g + v+++  + erakel   ++g 
  gi|242399774|ref|YP_002995199.1|  3 VVIMGAGRVGYLVAKMLENEGHD-VTIIDIDKERAKELSFLVNGL 46
                                      89****************99998.*************97665544 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3
                                       EGCGHHHHHHT-SEEEE- CS
                      Shikimate_DH  65 kleelkellaeadvvisa 82 
                                        +e++++l + +dvvis 
  gi|242399774|ref|YP_002995199.1| 107 VFEKIEDLKKYFDVVISP 124
                                       466666667778888875 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.3   1.4e-06    0.0008       2      44 ..       3      45 ..       2      82 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.4e-06
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHH CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseealekalekiek 44
                                      v ++GaG +G  +a+++ ++g++V+++di++e++++    ++ 
  gi|242399774|ref|YP_002995199.1|  3 VVIMGAGRVGYLVAKMLENEGHDVTIIDIDKERAKELSFLVNG 45
                                      789*****************************99987655555 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.3   5.3e-06     0.003      10      83 ..       3      87 ..       2     194 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 5.3e-06
                     NAD_binding_7 10 vlvvGgGevAarkvrklleagakvtvvapevkeele..............elvklaeeel.ekdlegadlviaatddre 73
                                      v++ G+G+v++  ++ l ++g +vt+++ + +  ++                    +++l e++l++ad+  a t +++
  gi|242399774|ref|YP_002995199.1|  3 VVIMGAGRVGYLVAKMLENEGHDVTIIDIDKE-RAKelsflvnglviegdA---TDQKTLeEANLKQADTFAALTGRDD 77
                                      79************************999953.333355555544432220...2344454466777777777776666 PP

                     NAD_binding_7 74 lneriaeaak 83
                                       n   + +ak
  gi|242399774|ref|YP_002995199.1| 78 ANILACILAK 87
                                      6655444444 PP

>> Erp_C  Erp protein C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   1.0     4e-06    0.0022       2     125 ..     105     229 ..     104     231 .] 0.80

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 4e-06
                             Erp_C   2 ktltdkideinknidvikeqtsvgakevidkitgpvydd..ftdgnkaiyktwgdledeedeglgkllkelsdtrde 76 
                                       k++ +ki++++k  dv+ +   + a+ +   it p +d   f  +   i k   +l + + e   kl+kels  +d+
  gi|242399774|ref|YP_002995199.1| 105 KEVFEKIEDLKKYFDVVISPEEIAANYIFRSITTPGFDRvlFPREGAEIVK--FQLSN-DSEISEKLVKELSLPKDS 178
                                       56789*********************************8334444455555..45654.456678************ PP

                             Erp_C  77 lrtklnegnkayivlekepkl..kenvnvseikedleklkskleevkkylk 125
                                       l   + ++  + ++   + kl  k +v v   +  l+++ks +e+ k+ ++
  gi|242399774|ref|YP_002995199.1| 179 LIVAIYDEKGNLVIPSGDTKLpkKGEVVVFAKNASLKDIKSVFERKKNNVE 229
                                       ***99888877777666655533667888888999********99998776 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0     4e-06    0.0022       1      80 [.       3      77 ..       3     117 .. 0.62

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 4e-06
                                      EEEE--STTHHHHHHHHHHHTEEEEEEES-GGGG..............-GGG-TT-SE-EEEE--S-HHHHHHHHHHHS CS
                            XdhC_C  1 lvifGaghvaqalarlaaalgfrvtvvdpreefa..............tkerfpeadetavvvlthdhklDaealeaal 65
                                      +vi+Gag v+  +a+++++ g +vt++d ++e a              +                   ++D++ le+a 
  gi|242399774|ref|YP_002995199.1|  3 VVIMGAGRVGYLVAKMLENEGHDVTIIDIDKERAkelsflvnglviegD-------------------ATDQKTLEEAN 62
                                      69*****************************988444454444444440...................44444444444 PP

                                      SS--SEEEESS-HHH CS
                            XdhC_C 66 rkkaayigllGSrkk 80
                                       k+a  +++l  r  
  gi|242399774|ref|YP_002995199.1| 63 LKQADTFAALTGRDD 77
                                      333333333333332 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   1.9e-05     0.011       2      30 ..       3      31 ..       2      39 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.9e-05
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEES CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvver 30
                                      vv++G+G +g  +A++l + g++Vt+++ 
  gi|242399774|ref|YP_002995199.1|  3 VVIMGAGRVGYLVAKMLENEGHDVTIIDI 31
                                      89*************************86 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 !   14.9   0.0   3.6e-05      0.02       2      38 ..       3      39 ..       2      74 .. 0.90
   2 ?   -1.4   0.0       3.5     2e+03      14      59 ..      81     129 ..      78     134 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.6e-05
                                      EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHH CS
                    NAD_Gly3P_dh_N  2 iavlGaGswGtalAkvlaenghevrlwvreeelieei 38
                                      + ++GaG  G  +Ak+l+++gh+v+++  ++e ++e+
  gi|242399774|ref|YP_002995199.1|  3 VVIMGAGRVGYLVAKMLENEGHDVTIIDIDKERAKEL 39
                                      789***************************9998887 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.5
                                       HHHHHHTTT...--EEEE-S-HHHHHHHHHHSSBTTTBTT----TTEEE CS
                    NAD_Gly3P_dh_N  14 lAkvlaeng...hevrlwvreeelieeineehenvkyLpgiklpenlva 59 
                                       lA++la++     ++ l   +++  e++++ +  +ky++ +  pe++ a
  gi|242399774|ref|YP_002995199.1|  81 LACILAKHLnptIKTILRISKPKNKEVFEKIEDLKKYFDVVISPEEIAA 129
                                       5666666553222333444455777777777777888888888877766 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.3    0.0021       1.1       3      29 ..       3      27 ..       1      68 [. 0.72
   2 ?    5.1   0.0     0.041        23      20      72 ..      72     122 ..      66     131 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0021
                                      EEEETTTSHHHHHHHHHHHHSTTEEEE CS
                            DapB_N  3 vavvGasGrmGkevvkaveeaedlelv 29
                                      v+++Ga Gr+G  v+k++e++ ++ ++
  gi|242399774|ref|YP_002995199.1|  3 VVIMGA-GRVGYLVAKMLENE-GHDVT 27
                                      99***9.***********995.33332 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.041
                                       HHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS.--S-BEBSSHHHHHHH-SEEE CS
                            DapB_N  20 veeaedlelvaavdrkeselegkdagellglg.klgvavtddleevlekadvli 72 
                                       ++ ++d+++ a + +k+    +  + ++l ++ + + +v++++e++++ +dv+i
  gi|242399774|ref|YP_002995199.1|  72 LTGRDDANILACILAKH---LNPTIKTILRISkPKNKEVFEKIEDLKKYFDVVI 122
                                       55667777777777776...6777888899988999*****************9 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   2.6e-05     0.015      39      73 ..       3      37 ..       1      74 [. 0.89

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.6e-05
                                      EEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH CS
                      2-Hacid_dh_C 39 vGiiGlGrIGqavakrlkafgmkviaydrskkkee 73
                                      v i+G+Gr+G  vak+l+  g +v+++d  k++ +
  gi|242399774|ref|YP_002995199.1|  3 VVIMGAGRVGYLVAKMLENEGHDVTIIDIDKERAK 37
                                      78*************************99977555 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   6.8e-05     0.038       6      61 ..      11      63 ..       8      77 .. 0.84
   2 ?   -2.4   0.0         5   2.8e+03      14      41 ..     146     172 ..     145     179 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.8e-05
                                      HHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSEEEE--TTSHHHHHHHHH CS
                      adh_short_C2  6 IGraiAkalaeeGaevvltdlneeakkrveelaeelgaevlecDVtdeeqvealve 61
                                      +G+ +Ak l +eG +v + d+++e+   ++el   ++  v+e D+td++++e++  
  gi|242399774|ref|YP_002995199.1| 11 VGYLVAKMLENEGHDVTIIDIDKER---AKELSFLVNGLVIEGDATDQKTLEEANL 63
                                      6899********************9...666766667889**********998755 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5
                                       HHHTT-EEEEEESSGGHHHHHHHHHHHT CS
                      adh_short_C2  14 laeeGaevvltdlneeakkrveelaeel 41 
                                       + +eGae+v  +l++++ +  e+l++el
  gi|242399774|ref|YP_002995199.1| 146 FPREGAEIVKFQLSNDS-EISEKLVKEL 172
                                       56899999999999887.5666666655 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   6.4e-05     0.036       3      53 ..       4      50 ..       2     124 .. 0.87
   2 ?   -1.1   0.0       5.3   2.9e+03      56      68 ..     197     209 ..     160     230 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6.4e-05
                                      EEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECE CS
                     F420_oxidored  3 giiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtav 53
                                       i GaG++g  +a+ l ++g   h+++++ + ++e+a+el   ++  v+++
  gi|242399774|ref|YP_002995199.1|  4 VIMGAGRVGYLVAKMLENEG---HDVTII-DIDKERAKELSFLVNGLVIEG 50
                                      577*****************...****99.********9987777544444 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 5.3
                                       HHHHHH-SEEEE- CS
                     F420_oxidored  56 eeaaeeadvvvla 68 
                                        ++ ++ +vvv+a
  gi|242399774|ref|YP_002995199.1| 197 TKLPKKGEVVVFA 209
                                       3344444444444 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 ?   14.4   0.1     3e-05     0.017       3      72 ..       3      98 ..       1     183 [. 0.66

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3e-05
                                      EEEE--SHHHHHHHHHHHHHTS-EEEEE......TTHCHHHCSHHHHCHHHHHHHHHHHHH.................. CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxx.................. RF
                       Pyr_redox_2  3 vvviGgGpAGlaaaltlaqagakvtlve......legtclnggcllskallgvaedaeias.................. 57
                                      vv+ G+G  G+ +a+ l + g++vt+++      +e  +l +g ++    +g a d+++++                  
  gi|242399774|ref|YP_002995199.1|  3 VVIMGAGRVGYLVAKMLENEGHDVTIIDidkeraKELSFLVNGLVI----EGDATDQKTLEeanlkqadtfaaltgrdd 77
                                      8**************************9654444444444444444....33333333222333455555666666666 PP

                                      .........HHHHCHHHHCCCCHC CS
                                      .........xxxxxxxxxxxxxxx RF
                       Pyr_redox_2 58 .........evvkklnqgielllg 72
                                               +    ln  i+++l+
  gi|242399774|ref|YP_002995199.1| 78 anilacilaK---HLNPTIKTILR 98
                                      6666664432...34444544444 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   3.7e-05      0.02       4      37 ..       3      36 ..       1      62 [. 0.87

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.7e-05
                                      EEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSC CS
                     FAD_binding_3  4 VlIVGaGpaGlmlallLseaGvrvvlvekrsttv 37
                                      V+I GaG +G + a++L + G +v++++  ++++
  gi|242399774|ref|YP_002995199.1|  3 VVIMGAGRVGYLVAKMLENEGHDVTIIDIDKERA 36
                                      99*************************9766554 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   4.5e-05     0.025       3      66 ..       5      67 ..       3      82 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.5e-05
                                      EETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC......EEEE--TT-HHHHHHHHHHHT-S CS
                         Epimerase  3 VtGatGfiGsalvkallekgyevigldrlssasntarledl......elveldltdrsalerlfkeeqpd 66
                                      ++Ga G +G  ++k l+++g++v+ +d ++++ ++     l       ++e+d td++ le++  + q+d
  gi|242399774|ref|YP_002995199.1|  5 IMGA-GRVGYLVAKMLENEGHDVTIIDIDKERAKE-----LsflvngLVIEGDATDQKTLEEANLK-QAD 67
                                      5555.**********************99443332.....2334678999********99997553.555 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.2   4.7e-05     0.026       1      63 [.       3      61 ..       3      77 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.7e-05
                         3Beta_HSD  1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleea 63
                                      vv+ gaG +G  lv ++++ e  ++v ++D++++  + e ++ vn   viegD td+++leea
  gi|242399774|ref|YP_002995199.1|  3 VVIMGAGRVGY-LVAKMLENE-GHDVTIIDIDKERAK-ELSFLVNGL-VIEGDATDQKTLEEA 61
                                      68889999*96.566666655.38*******998877.666666666.9************98 PP

>> PglD_N  PglD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   0.00013     0.072       2      56 ..       3      60 ..       2      72 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00013
                            PglD_N  2 ivIiGaGGhgkvvadiieangeyeiigflDdnkkte....vegypvlgkaiellkslse 56
                                      +vI+GaG  g  va+++e++g    i+ +D++ ++e    v+g+ v++++ +++k l+e
  gi|242399774|ref|YP_002995199.1|  3 VVIMGAGRVGYLVAKMLENEGHDVTIIDIDKERAKElsflVNGL-VIEGDATDQKTLEE 60
                                      79*******************65555566665443312224565.44445555566644 PP

>> UPF0146  Uncharacterised protein family (UPF0146)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   0.00011     0.061      17      52 ..       3      39 ..       2      52 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00011
                                      EEEET-TT--H.HHHHHHHHS-EEEEE-SS-S....S CS
                           UPF0146 17 vvEvGiGrkld.vaealakrgvdlvatDikekkakeg 52
                                      vv +G+Gr  + va++l + g d++++Di++++ake 
  gi|242399774|ref|YP_002995199.1|  3 VVIMGAGRVGYlVAKMLENEGHDVTIIDIDKERAKEL 39
                                      6789999986549********************9975 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00025      0.14       4      39 ..       5      40 ..       3      96 .. 0.84
   2 ?   -1.0   0.0       3.1   1.8e+03      89     101 ..     194     206 ..     149     228 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00025
                                      EE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHH CS
                     NAD_binding_2  4 fiGlGvMGsnmalnllkagykvavynrtkekveelv 39
                                      ++G G  G   a+ l+++g++v++++ +ke+++el 
  gi|242399774|ref|YP_002995199.1|  5 IMGAGRVGYLVAKMLENEGHDVTIIDIDKERAKELS 40
                                      689**************************9999874 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3.1
                                       -S---HHHHHHHH CS
                     NAD_binding_2  89 gstsspedtrela 101
                                       ++ ++  +  e+ 
  gi|242399774|ref|YP_002995199.1| 194 SGDTKLPKKGEVV 206
                                       4433333333332 PP

>> Rossmann-like  Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00031      0.17      13      41 ..       3      31 ..       1      52 [. 0.85
   2 ?   -1.3   0.0       3.4   1.9e+03      72     100 ..     179     206 ..     149     218 .. 0.48

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00031
                     Rossmann-like 13 vGiisaGrvGtalgaaleraghvvvgisa 41
                                      v i++aGrvG  +++ le  gh v+ i  
  gi|242399774|ref|YP_002995199.1|  3 VVIMGAGRVGYLVAKMLENEGHDVTIIDI 31
                                      779*********************98765 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 3.4
                     Rossmann-like  72 lllavPdaelpglvkglaatgavraGtiv 100
                                       l++a+ d +  +lv     t+  ++G++v
  gi|242399774|ref|YP_002995199.1| 179 LIVAIYDEK-GNLVIPSGDTKLPKKGEVV 206
                                       333333322.2233333333344444444 PP

>> Gp_dh_N  Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   0.00022      0.12       3      62 ..       3      62 ..       1      80 [. 0.73

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00022
                                      EEEESTSHHHHHHHHHHHHHT.TCEEEEEE-TS-HHHHHHHHHEETTTEC-SS-EEEETTE CS
                           Gp_dh_N  3 vainGfGRIGrlvlralleek.elevvaindltdletlayllkyDsvhgrfkgeveaeeea 62
                                      v+i G GR+G lv+++l +e  +++++ i +   +++l+ l++   + g  + + + ee++
  gi|242399774|ref|YP_002995199.1|  3 VVIMGAGRVGYLVAKMLENEGhDVTIIDIDK-ERAKELSFLVNGLVIEGDATDQKTLEEAN 62
                                      89*************9995555999999988.66667776666666666655555555555 PP

>> DFP  DNA / pantothenate metabolism flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0    0.0014      0.77      28      54 ..       8      34 ..       5     123 .. 0.76
   2 ?    1.7   0.1      0.34   1.9e+02     115     183 ..     155     228 ..     147     230 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0014
                                      --HHHHHHHHHHHHTT-EEEEEE-S-S CS
                               DFP 28 SGkmGyalAeaaaarGaeVtlvsgpvs 54
                                       G+ Gy +A+ + ++G++Vt++    +
  gi|242399774|ref|YP_002995199.1|  8 AGRVGYLVAKMLENEGHDVTIIDIDKE 34
                                      69********************87643 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.34
                                       ---EEE---HHHHHHHC-S...S-EEEEEEE-S.S-HHHHHHHHHHHTT-SEEEEEEGGGT..TGGG-SS-EEE CS
                               DFP 115 tleleknpdilaelaekkk..kkqllvGFaaet.eellenareklerkgldlivaNdvske..eagfgsdenev 183
                                       + +l++  +i ++l ++ +  k++l+v+   e+ + ++ ++ +kl +kg  ++ a ++s +  +++f++++n+v
  gi|242399774|ref|YP_002995199.1| 155 KFQLSNDSEISEKLVKELSlpKDSLIVAIYDEKgNLVIPSGDTKLPKKGEVVVFAKNASLKdiKSVFERKKNNV 228
                                       556666666666664333332445899999998678899999***99999999998888774566799998876 PP

>> Stimulus_sens_1  Stimulus-sensing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00043      0.24       3      49 ..     162     210 ..     161     230 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00043
                   Stimulus_sens_1   3 perarplLrrLvePtet.RarlYdpdGkLvaDSrtlys.srgeierael 49 
                                        e + +l++ L  P++   + +Yd++G+Lv+ S      ++ge+ +++ 
  gi|242399774|ref|YP_002995199.1| 162 SEISEKLVKELSLPKDSlIVAIYDEKGNLVIPSGDTKLpKKGEVVVFAK 210
                                       588899*********99999***********998665557777777665 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00048      0.27       3      67 ..       3      61 ..       1      73 [. 0.82

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00048
                                      EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHH CS
                         adh_short  3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreeveal 67
                                      v++ Ga++ +G+ +ak l +eG +v+++d+ +e+++e+   ++      l+i++D td++ +e++
  gi|242399774|ref|YP_002995199.1|  3 VVIMGAGR-VGYLVAKMLENEGHDVTIIDIDKERAKELSFLVN-----GLVIEGDATDQKTLEEA 61
                                      78888885.9***********************9977766655.....47888888888877765 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00066      0.37       1      27 [.       5      31 ..       5      34 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00066
                                      EE--SHHHHHHHHHHHCCTEEEEEE-S CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllek 27
                                      I GaG  G + A  L ++g+dv++++ 
  gi|242399774|ref|YP_002995199.1|  5 IMGAGRVGYLVAKMLENEGHDVTIIDI 31
                                      77***********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       817  (0.0455686); expected 358.6 (0.02)
Passed bias filter:                      582  (0.0324614); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                        32  (0.00178482); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              32  [number of targets reported over threshold]
# CPU time: 0.69u 0.37s 00:00:01.06 Elapsed: 00:00:00.57
# Mc/sec: 1219.34
//
Query:       gi|242399775|ref|YP_002995200.1|  [L=506]
Description: SecD protein-export membrane protein [Thermococcus sibiricus MM 739]
Scores for complete 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-15   56.0   7.8      6e-15   55.1   7.8    1.3  1  SecD_SecF  Protein export membrane protein
      6e-05   22.4   0.0    0.00015   21.1   0.0    1.7  1  Sec_GG     SecD/SecF GG Motif
    6.9e-05   21.9   8.7    6.9e-05   21.9   8.7    1.8  2  MMPL       MMPL family
  ------ inclusion threshold ------
      0.036   11.7   8.8      0.059   11.0   8.8    1.2  1  ACR_tran   AcrB/AcrD/AcrF family
       0.12   10.4   7.8        0.2    9.7   7.8    1.3  1  Patched    Patched family


Domain annotation for each model (and alignments):
>> SecD_SecF  Protein export membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.1   7.8   1.7e-18     6e-15      18     173 ..     333     488 ..     325     501 .. 0.88

  Alignments for each domain:
  == domain 1  score: 55.1 bits;  conditional E-value: 1.7e-18
                                       EEEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-H.HHHHHHHHHHHHHHHHHHHHHHHTT----HHHHHHHHHH CS
                         SecD_SecF  18 vetvgpsvskelaekavlallialvliliyvalrFew.rvalaaiialvhDviitvgvlsllgievdlatvaalLti 93 
                                       v+ + p++++++++++++a l+al ++ ++v+l +++ ++a+ ++++ ++ v+ ++gv +l++ ++dl ++a+++  
  gi|242399775|ref|YP_002995200.1| 333 VNYIPPTLGEQFKKQVLQAGLAALFVVGLVVYLHYRKvKIAVPVVLTSLSEVVAILGVAALIKWNLDLPSIAGIIAA 409
                                       56799******************************86389************************************* PP

                                       TTSSSHHHHHHHHHHHHHHHH--SS-HHHHHHHHHHHHHHHHHHTTHHHHHHHHH.HHHHHTTTTHHHHHHHHHHTS CS
                         SecD_SecF  94 iGYSvndtvvvfdrvrenlrkkkratlkeiinlslnqtLtrtiltslttllvvva.llllggdslkdfalallvGli 169
                                       iG  v++++v++d +   ++  k ++   i+++     ++  i +s+tt +v+++ l+ +  + l++fa++ ++G++
  gi|242399775|ref|YP_002995200.1| 410 IGTGVDQQIVITDELLGGIKVGKITKRSGILKRMGRAFFV--IWASATTTIVAMSfLFRFFVGGLRGFAFTTILGVL 484
                                       ******************9887777777777766666665..999999777666516668889************** PP

                                       TTTT CS
                         SecD_SecF 170 vgty 173
                                       +g++
  gi|242399775|ref|YP_002995200.1| 485 IGIL 488
                                       **97 PP

>> Sec_GG  SecD/SecF GG Motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   4.2e-08   0.00015       3      28 .]      26      51 ..      24      51 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 4.2e-08
                                      HHHC--EE-TTTS-EEEEEEEE-TTS CS
                            Sec_GG  3 lftkGlNLGlDFtGGthielqfdqpv 28
                                      ++ +G+++GlD  GG++i+ q + pv
  gi|242399775|ref|YP_002995200.1| 26 IASQGITYGLDISGGVEITTQLERPV 51
                                      7889*******************997 PP

>> MMPL  MMPL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   1.2      0.29     1e+03     171     202 ..      13      46 ..       6      48 .. 0.65
   2 !   21.9   8.7   1.9e-08   6.9e-05      90     292 ..     295     491 ..     258     499 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.29
                              MMPL 171 llplltvvvs..llaalglvlilalllglelstf 202
                                       ll++l++++s   +a++g+++ l    g+e++t+
  gi|242399775|ref|YP_002995200.1|  13 LLLILVILISiiTIASQGITYGLDISGGVEITTQ 46 
                                       3444444444114678999888888888888776 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 1.9e-08
                              MMPL  90 alvtlegdpgsteadesvaairaaveearpleglkvevtGpaatladlrdasdrdlklievvtlvvilviLlivyrS 166
                                       + +++ g++++  a+++++ +  ++++ +   ++kv v G+  +   l + +++++  +++++l v+ ++  + yr 
  gi|242399775|ref|YP_002995200.1| 295 LAISIGGSKEDITAMKQAQVVSVVLRSGS--LPIKVFVEGVNYIPPTLGEQFKKQVLQAGLAALFVVGLVVYLHYRK 369
                                       67888888888888888777766666666..89******************************************** PP

                              MMPL 167 lvaallplltvvvsllaalglvlilalllglelstfvlgllvvl.liavGtDYallLvsRyreelaage.dreeavi 241
                                       + +a+ ++lt + +++a lg++++++       +   ++++ ++ +i++G+D  + ++  +   ++ g+ ++++++ 
  gi|242399775|ref|YP_002995200.1| 370 VKIAVPVVLTSLSEVVAILGVAALIK------WNLDLPSIAGIIaAIGTGVDQQIVITDELLGGIKVGKiTKRSGIL 440
                                       *******9999999999999955444......445555665444279**************99999997245569** PP

                              MMPL 242 ravastgkvvtaaGltvaiamlgLvvarlpvlaqvGvaialGvlvdvlivl 292
                                       + ++++  v+ a++ t ++am  L    ++ l++++++  lGvl+ +li++
  gi|242399775|ref|YP_002995200.1| 441 KRMGRAFFVIWASATTTIVAMSFLFRFFVGGLRGFAFTTILGVLIGILITR 491
                                       ************************************************987 PP

>> ACR_tran  AcrB/AcrD/AcrF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   8.8   1.7e-05     0.059     332     474 ..     347     486 ..     341     501 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 1.7e-05
                                       HHHHHHHHHHHHHHHHHHHHHSSHHHHHHHHHHHHHHHHHHHHHHHH.TT--BCHHHHHHHHHHHHHHHHHHHHHHH CS
                          ACR_tran 332 eVvktLleaivLvvlvvflFLqnlratlipaiavPlsllgtfavlka.lgfslNlltLfgLvlAiGlvvDdAiVvvE 407
                                       +V +  l a+ +v lvv+l  ++++++ +p++   ls ++++  ++a ++  l l ++ g+  AiG  vD+ iV+  
  gi|242399775|ref|YP_002995200.1| 347 QVLQAGLAALFVVGLVVYLHYRKVKIA-VPVVLTSLSEVVAILGVAAlIKWNLDLPSIAGIIAAIGTGVDQQIVITD 422
                                       68888999*****************98.5888888998888877654279999************************ PP

                                       HHHHHHHHHTS-HHHHHHHHHHHHHHHHHHHHHHHHHH..CTGGGGSBHHHHHHHHHHHHHHHHHHHHH CS
                          ACR_tran 408 nierkleeegekpleaalksmkeiqgalvaialvllav..flPilflgGveGklfrqfaltivlaills 474
                                       +    ++  + +++  +lk m+   + + a+a + +++  fl  +f+gG+ G     fa+t +l +l+ 
  gi|242399775|ref|YP_002995200.1| 423 ELLGGIKVGKITKRSGILKRMGRAFFVIWASATTTIVAmsFLFRFFVGGLRG-----FAFTTILGVLIG 486
                                       ***********************99888766554433312777778888877.....555555555544 PP

>> Patched  Patched family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   7.8   5.6e-05       0.2     656     796 ..     345     488 ..     311     490 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 5.6e-05
                           Patched 656 lpstiqnivlallcmfvvallfipelitvlvitlsivsidigviGflslWgvdLDpismitiimsiGfsvdlsaHia 732
                                         +++q  + al+++ +v  l   ++ +++ ++l+ +s  + ++G+ +l   +LD  s++ ii +iG  vd    i+
  gi|242399775|ref|YP_002995200.1| 345 KKQVLQAGLAALFVVGLVVYLHYRKVKIAVPVVLTSLSEVVAILGVAALIKWNLDLPSIAGIIAAIGTGVDQQIVIT 421
                                       5678899999999************************************999************************* PP

                           Patched 733 yafvrsekd...dakeRvvealealgwPvvqgalSTilgvlvLlfvdsymvqvFfktvvLvvvigll 796
                                        +     k    + ++ + + +    + +  +a+ Ti++++ L+       + F+ t +L v+ig+l
  gi|242399775|ref|YP_002995200.1| 422 DELLGGIKVgkiTKRSGILKRMGRAFFVIWASATTTIVAMSFLFRFFVGGLRGFAFTTILGVLIGIL 488
                                       999876665534666668999999999999**************9999999**************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (506 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       955  (0.0532657); expected 358.6 (0.02)
Passed bias filter:                      601  (0.0335211); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.79u 0.34s 00:00:01.13 Elapsed: 00:00:00.56
# Mc/sec: 2724.41
//
Query:       gi|242399776|ref|YP_002995201.1|  [L=286]
Description: Protein-export membrane protein SecF [Thermococcus sibiricus MM 739]
Scores for complete 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  11.5    2.4e-29  102.1  11.5    1.3  1  SecD_SecF  Protein export membrane protein
    1.1e-05   23.8   6.5    1.5e-05   23.4   6.5    1.2  1  Patched    Patched family
     0.0063   16.0   0.2      0.048   13.2   0.1    2.4  2  Sec_GG     SecD/SecF GG Motif
  ------ inclusion threshold ------
      0.011   14.7  11.3      0.016   14.1  11.3    1.2  1  MMPL       MMPL family
      0.017   15.0   0.0      0.029   14.2   0.0    1.4  1  BAT        GAF and HTH_10 associated domain


Domain annotation for each model (and alignments):
>> SecD_SecF  Protein export membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.1  11.5   6.8e-33   2.4e-29       8     188 ..     108     281 ..     101     282 .. 0.89

  Alignments for each domain:
  == domain 1  score: 102.1 bits;  conditional E-value: 6.8e-33
                                       -SSS-EEEEEEEEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-HHHHHHHHHH.HHHHHHHHHHHHHHTT---- CS
                         SecD_SecF   8 evdkdaekisvetvgpsvskelaekavlallialvliliyvalrFewrvalaaiia.lvhDviitvgvlsllgievd 83 
                                       +  +d+ +is    gps+s++ +e+++ a+ +a+++++++v+l F+ ++++  +i  +++D++i+++++s++g+e++
  gi|242399776|ref|YP_002995201.1| 108 SKYPDV-TISQTQFGPSLSRTAQEQSLKAVSMAFIGMAVVVFLFFRIPLPSLTVIFsAFSDMVIALALMSVFGLELT 183
                                       555544.4566677***********************************99887766******************** PP

                                       HHHHHHHHHHTTSSSHHHHHHHHHHHHHHHH--SS-HHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHT.TTTHH CS
                         SecD_SecF  84 latvaalLtiiGYSvndtvvvfdrvrenlrkkkratlkeiinlslnqtLtrtiltslttllvvvallllgg.dslkd 159
                                        at+aalL++iGYSv++++++++++  +    k+ t++ +   ++++ +t++     ttl ++++l++l + +++  
  gi|242399776|ref|YP_002995201.1| 184 QATIAALLMLIGYSVDSNILLTTKLLRR----KEDTIEGAYFSAVSTGFTMST----TTLGALASLWVLSQaEVIDM 252
                                       ***********************99877....578999999999999999764....55667999*99998799*** PP

                                       HHHHHHHHTSTTTTTHHHHHHHHHHHHH- CS
                         SecD_SecF 160 falallvGlivgtyssifiasplllllke 188
                                       +a++l++Gl+++ ++++ +++++l ++ +
  gi|242399776|ref|YP_002995201.1| 253 IATVLIFGLLADFMNTWILNAGVLRWYLQ 281
                                       ************************99875 PP

>> Patched  Patched family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   6.5   4.1e-09   1.5e-05     657     763 ..     130     235 ..     106     259 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 4.1e-09
                           Patched 657 pstiqnivlallcmfvvallfipelitvlvitlsivsidigviGflslWgvdLDpismitiimsiGfsvdlsaHiay 733
                                        + ++ + +a++ m+vv +lf   +  +l +++s  s  +  + ++s+ g +L   ++++++m iG+svd     + 
  gi|242399776|ref|YP_002995201.1| 130 EQSLKAVSMAFIGMAVVVFLFFRIPLPSLTVIFSAFSDMVIALALMSVFGLELTQATIAALLMLIGYSVDSNILLTT 206
                                       566788999****************************9999*****************************9999999 PP

                           Patched 734 afvrsekddakeRvvealealgwPvvqgal 763
                                       +  r ++d+++    +a+++ g+ +    l
  gi|242399776|ref|YP_002995201.1| 207 KLLRRKEDTIEGAYFSAVST-GFTMSTTTL 235
                                       99999997777666666554.666655555 PP

>> Sec_GG  SecD/SecF GG Motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.1   1.4e-05     0.048       9      22 ..      41      54 ..      40      55 .. 0.93
   2 ?   -0.7   0.0       0.3   1.1e+03      18      28 .]      87      97 ..      87      97 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.4e-05
                                      EE-TTTS-EEEEEE CS
                            Sec_GG  9 NLGlDFtGGthiel 22
                                      NLG D++GG++i+l
  gi|242399776|ref|YP_002995201.1| 41 NLGTDLKGGVVITL 54
                                      9***********98 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.3
                                      EEEEEEE-TTS CS
                            Sec_GG 18 thielqfdqpv 28
                                      t+ie++++++v
  gi|242399776|ref|YP_002995201.1| 87 TRIEIKASTDV 97
                                      89******997 PP

>> MMPL  MMPL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1  11.3   4.6e-06     0.016     140     289 ..     127     266 ..      90     271 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.6e-06
                              MMPL 140 asdrdlklievvtlvvilviLlivyrSlvaallplltvvvsllaalglvlilalllglelstfvlgllvvlliavGt 216
                                       ++++++ +++ ++++  +v+ ++ +r ++  l ++ ++  ++++al+l++++    glel+++ +  + ++li+ ++
  gi|242399776|ref|YP_002995201.1| 127 TAQEQSLKAVSMAFIGMAVVVFLFFRIPLPSLTVIFSAFSDMVIALALMSVF----GLELTQA-TIAALLMLIGYSV 198
                                       456666777777777788888999************************5544....4455443.344677899**** PP

                              MMPL 217 DYallLvsRyreelaagedreeaviravastgkvvtaaGltvaiamlgLvvarlpvlaqvGvaialGvlvdvl 289
                                       D ++lL++++   l++ ed+ e+++    stg   t+++ t+ +     v+++ +v+  +++++  G+l d++
  gi|242399776|ref|YP_002995201.1| 199 DSNILLTTKL---LRRKEDTIEGAYFSAVSTG--FTMSTTTLGALASLWVLSQAEVIDMIATVLIFGLLADFM 266
                                       ********98...5666666555555555555..5777777654444457788999999*********99987 PP

>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   8.2e-06     0.029      97     140 ..      74     117 ..      61     131 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 8.2e-06
                               BAT  97 GgtvrsaeaedgrarlvvevPpgadvRsvvealeerypdveLva 140
                                       ++tvr++    g++r+ +  +++++v ++++ ++++ypdv+  +
  gi|242399776|ref|YP_002995201.1|  74 DVTVREIKSITGDTRIEIKASTDVNVQKIISIVKSKYPDVTISQ 117
                                       79**************************************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1075  (0.0599587); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.66u 0.33s 00:00:00.99 Elapsed: 00:00:00.54
# Mc/sec: 1599.86
//
Query:       gi|242399777|ref|YP_002995202.1|  [L=141]
Description: S-adenosylmethionine decarboxylase proenzyme [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.7e-38  129.7   0.0    5.8e-38  129.4   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 !  129.4   0.0   3.2e-42   5.8e-38       1     106 []      10     116 ..      10     116 .. 0.99

  Alignments for each domain:
  == domain 1  score: 129.4 bits;  conditional E-value: 3.2e-42
                                       EEEEEEES--HHHCTSHHHHHHHHHHHHHHCT-EEEEEEEEE-SSS-EEEEEEETTEEEEEEEEGGGTEEEEEEEEE CS
                         AdoMet_dc   1 hllvdlygcdpelledaelleqilteaaeaigatvlsvafhkfepeGvsvvvliaeShlsiHtwpetgyaaiDvftc 77 
                                       h++v++ gcdpe+l+d++++++i+ +aa+  ++++  ++f +f+p Gvs+vv++aeSh+s+Htwpe+gyaa+Dv+tc
  gi|242399777|ref|YP_002995202.1|  10 HYVVEASGCDPEVLKDPNRIREIFMNAAKTGNMEIKASYFFRFSPTGVSGVVIVAESHISVHTWPEEGYAALDVYTC 86 
                                       99*************************************************************************** PP

                                       ST.HHHHHHHHHHHHHHT-SEEEEEEEEEE CS
                         AdoMet_dc  78 ge.ispekaleylieafkadrvtvdelkRG 106
                                       ge ++peka++y+ e+f+a+  +v+e+kRG
  gi|242399777|ref|YP_002995202.1|  87 GEkADPEKAVDYILEKFRAQYAHVSEVKRG 116
                                       *****************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        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 0.36s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 802.11
//
Query:       gi|242399778|ref|YP_002995203.1|  [L=319]
Description: transcription regulator, encoded next to RecA superfamily ATPas [Thermococcus sibiricus MM 739]
Scores for complete 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-06   25.0  51.8     0.0067   15.3  28.5    2.4  2  Spc7             Spc7 kinetochore protein
    1.2e-05   25.4  63.6     0.0041   17.1  24.7    3.8  2  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
     0.0002   21.7  47.5       0.45   10.9   4.1    6.6  7  FlaC_arch        Flagella accessory protein C (FlaC)
    0.00027   20.6   0.3     0.0012   18.6   0.3    2.1  1  HTH_38           Helix-turn-helix domain
    0.00043   19.7  61.7     0.0036   16.7  18.0    3.3  3  GAS              Growth-arrest specific micro-tubule binding
    0.00092   19.2   0.2       0.01   15.9   0.0    2.5  2  HTH_20           Helix-turn-helix domain
    0.00095   19.2   8.8    0.00095   19.2   8.8    6.0  4  bZIP_2           Basic region leucine zipper
     0.0013   18.4   0.1     0.0041   16.9   0.1    1.8  1  HTH_23           Homeodomain-like domain
     0.0025   18.0  55.5     0.0028   17.9  14.7    3.5  3  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
     0.0029   16.9  36.8      0.033   13.5   4.9    3.4  3  DUF3450          Protein of unknown function (DUF3450)
     0.0031   17.4   0.4      0.021   14.7   0.0    2.7  1  HTH_11           HTH domain
     0.0062   16.1   0.4      0.023   14.3   0.1    2.1  1  GerE             Bacterial regulatory proteins, luxR family
     0.0068   16.3   0.5        4.5    7.2   0.0    2.7  2  HTH_5            Bacterial regulatory protein, arsR family
     0.0073   15.8   0.0      0.029   13.9   0.0    2.1  1  HTH_24           Winged helix-turn-helix DNA-binding
     0.0079   16.0  22.6     0.0079   16.0  22.6    2.5  2  TACC_C           Transforming acidic coiled-coil-containing p
     0.0085   13.7  32.3     0.0098   13.5  32.3    1.2  1  DUF3584          Protein of unknown function (DUF3584)
     0.0098   16.0   9.2     0.0098   16.0   9.2    5.5  5  Cep57_CLD_2      Centrosome localisation domain of PPC89
  ------ inclusion threshold ------
      0.016   15.6   1.9      0.095   13.1   0.3    2.6  2  HTH_31           Helix-turn-helix domain
      0.016   15.2  32.0      0.035   14.1  12.4    3.9  4  Laminin_II       Laminin Domain II
      0.019   15.0  51.2      0.068   13.2  35.6    4.0  3  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
      0.023   14.4   3.0      0.037   13.7   3.0    1.4  1  Citrate_ly_lig   Citrate lyase ligase C-terminal domain
      0.026   14.3  51.9       0.06   13.1   7.1    5.5  4  DivIC            Septum formation initiator
      0.038   14.2  41.3       0.17   12.1  27.3    2.6  2  ATG16            Autophagy protein 16 (ATG16)
      0.063   13.3   0.0       0.15   12.1   0.0    1.6  1  HTH_29           Winged helix-turn helix
      0.067   13.2   5.9       0.73    9.9   0.5    3.4  3  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
       0.11   13.0  12.1        3.9    8.0   0.6    4.0  3  NPV_P10          Nucleopolyhedrovirus P10 protein
       0.26    9.4  49.1       0.43    8.7  20.3    2.1  2  EzrA             Septation ring formation regulator, EzrA
       0.28   11.3  54.5      0.077   13.1  27.4    2.9  2  UPF0242          Uncharacterised protein family (UPF0242) N-t
       0.35   10.4  32.1       0.12   11.9  28.0    2.4  1  MscS_porin       Mechanosensitive ion channel porin domain
       0.37    9.1  54.6       0.48    8.7  54.6    1.2  1  MAD              Mitotic checkpoint protein
       0.37   10.5  51.8        6.5    6.4  26.0    3.6  3  DUF4201          Domain of unknown function (DUF4201)
       0.39   10.8  30.9       0.25   11.4   7.0    3.3  3  DUF1664          Protein of unknown function (DUF1664)
        0.4   10.9  48.9      0.085   13.1   4.1    6.6  6  HALZ             Homeobox associated leucine zipper
       0.47   10.8  43.6       0.33   11.3  12.9    4.7  5  BLOC1_2          Biogenesis of lysosome-related organelles co
       0.49   10.8  29.2        1.7    9.1   1.9    3.8  3  Syntaxin_2       Syntaxin-like protein
        0.5   10.2  46.8        1.6    8.5  25.7    3.2  2  Phage_GP20       Phage minor structural protein GP20
       0.51    8.9  47.8        6.2    5.3  27.5    2.4  2  FapA             Flagellar Assembly Protein A
       0.53    9.6  24.5        2.4    7.4  14.2    2.4  2  DUF4407          Domain of unknown function (DUF4407)
       0.54    9.1  36.2     0.0072   15.3  23.7    2.1  2  DNA_topoisoIV    DNA gyrase/topoisomerase IV, subunit A
       0.59   10.4  11.8       0.19   12.0   2.1    3.0  3  Retrotrans_gag   Retrotransposon gag protein
       0.67    9.8  21.2       0.25   11.2   5.9    2.7  2  Bacillus_HBL     Bacillus haemolytic enterotoxin (HBL)
       0.94    9.8   8.3        5.5    7.3   0.2    4.3  3  WXG100           Proteins of 100 residues with WXG
        1.1    9.7  28.5    5.2e+03   -2.0  28.5    4.2  0  HTH_40           Helix-turn-helix domain
        1.2    8.2  36.8       0.23   10.5   5.6    2.6  2  TelA             Toxic anion resistance protein (TelA)
        1.3    9.6  64.0          9    6.8   5.7    5.1  2  ZapB             Cell division protein ZapB
        1.5    9.3  66.1       0.45   11.0  24.7    3.7  3  APG6_N           Apg6 coiled-coil region
        1.5    9.5  44.5        2.5    8.8  12.4    4.4  4  YabA             Initiation control protein YabA
        1.5    8.9   5.7        8.1    6.6   1.6    2.6  2  Flagellin_N      Bacterial flagellin N-terminal helical regio
        1.6    8.8  16.7       0.47   10.5   0.2    4.5  3  Prp19            Prp19/Pso4-like
        1.7    9.6  48.6        9.8    7.2   3.5    4.0  3  PRKG1_interact   cGMP-dependent protein kinase interacting do
        1.7    8.9  44.4       0.05   13.9  15.1    2.8  2  THOC7            Tho complex subunit 7
          2    8.2  45.7       0.43   10.4  18.8    3.3  3  DUF724           Protein of unknown function (DUF724)
        2.4    8.3  55.5       0.89    9.8  24.7    2.9  2  Jnk-SapK_ap_N    JNK_SAPK-associated protein-1
        3.1    5.6  22.6         21    2.9  22.1    2.1  1  Prominin         Prominin
        3.2    6.3  38.4        5.4    5.5  37.7    1.6  2  AAA_13           AAA domain
        3.3    6.9  24.6        3.9    6.7   5.1    3.0  3  HemX             HemX, putative uroporphyrinogen-III C-methyl
        4.3    7.8  34.9       0.12   12.9   7.5    3.6  3  Snapin_Pallidin  Snapin/Pallidin
        4.9    6.7  41.7        5.2    6.6  18.3    2.5  2  HAUS-augmin3     HAUS augmin-like complex subunit 3
        5.5    7.4  44.6        2.5    8.5   4.3    5.0  3  Nnf1             Nnf1
        5.8    7.1  29.3        2.9    8.0   8.8    4.8  5  TolA_bind_tri    TolA binding protein trimerisation
        6.4    6.9  39.6        3.9    7.6  18.3    3.6  3  ADIP             Afadin- and alpha -actinin-Binding
          7    6.8  11.0        2.7    8.2   2.5    2.8  2  MbeD_MobD        MbeD/MobD like
        8.6    5.5  35.8        1.2    8.3   9.5    2.7  2  TMPIT            TMPIT-like protein
        9.9    5.1  42.9         21    4.0  20.8    2.5  2  Atg14            Vacuolar sorting 38 and autophagy-related su


Domain annotation for each model (and alignments):
>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3  28.5   2.4e-05    0.0067     166     275 ..     129     241 ..     105     244 .. 0.65
   2 !   13.8  19.5   6.9e-05     0.019     142     225 ..     235     317 ..     226     319 .] 0.92

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.4e-05
                              Spc7 166 dellpeleeekaeleeeleklqeaaeeles.idkeeLeelreelaelkaeieekkkelaelqeqleeleekieelke 241
                                       +e +++l +e+++l+ e+ek +++ e++++ +d e+Le++  ++++l +e+e+ k+el++ +++ +el+++++e++ 
  gi|242399778|ref|YP_002995203.1| 129 KEEYEKLMQEYENLKLEYEKVKAELEKMKQtVDLESLEKAIGKIERLRKELEAVKAELEKTRKENKELKKELAEARV 205
                                       55566666666666666666666655555556777777777777777777777777777777777777777777777 PP

                              Spc7 242 qkseleeeiaeaervl..eeckgwsesevsrlkeev 275
                                       ++ el+++  e+ +v+  ee+ + +e+e+srl+  v
  gi|242399778|ref|YP_002995203.1| 206 KIMELQSKRIEETKVKelEEKLKAKEEELSRLERLV 241
                                       777777665555555411455566677777777655 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 6.9e-05
                              Spc7 142 egleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieek 218
                                       ++le+ +++++++k +Lek+ ee++ l +el++ek+ele+++++l ++++el++   eeLe+++ ++++l  +ie+ 
  gi|242399778|ref|YP_002995203.1| 235 SRLERLVDEVTREKLELEKKVEEFEGLADELRKEKEELEKKIKELTRENNELKQ-RIEELETYKIRFENLRDKIEKI 310
                                       57899999******************************************9988.7899****************** PP

                              Spc7 219 kkelael 225
                                       k el++l
  gi|242399778|ref|YP_002995203.1| 311 KMELEKL 317
                                       *999987 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 !   17.1  24.7   1.5e-05    0.0041      25     104 ..     131     215 ..     101     220 .. 0.74
   2 !    9.7  31.5    0.0028      0.79       2     101 ..     217     316 ..     216     319 .] 0.78

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.5e-05
                    CENP-F_leu_zip  25 kvenLerelemseenqekvileaEtskaev.....etlkeeieelaeelreleldLvalrsekeeLekelqkkqerv 96 
                                         e+L +e e+++ + ekv+ e E+ k++v     e+   +ie+l++el+  +++L+++r+e++eL+kel + + ++
  gi|242399778|ref|YP_002995203.1| 131 EYEKLMQEYENLKLEYEKVKAELEKMKQTVdleslEKAIGKIERLRKELEAVKAELEKTRKENKELKKELAEARVKI 207
                                       334555555555555555555555555543221115566789*********************************** PP

                    CENP-F_leu_zip  97 seLeslns 104
                                        eL+s + 
  gi|242399778|ref|YP_002995203.1| 208 MELQSKRI 215
                                       ***98765 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0028
                    CENP-F_leu_zip   2 ekkklhvlekLKeserkadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLval 78 
                                       e k ++++ekLK+ e++ + L+  v++  re+ ++e++ e+ +  a++ ++e e+l+++i+el++e +el++ +++l
  gi|242399778|ref|YP_002995203.1| 217 ETKVKELEEKLKAKEEELSRLERLVDEVTREKLELEKKVEEFEGLADELRKEKEELEKKIKELTRENNELKQRIEEL 293
                                       67888999999999999999999999999999999999999999999999999999999999999999999888888 PP

                    CENP-F_leu_zip  79 rsekeeLekelqkkqervs.eLes 101
                                          k    ++l++k e+++ eLe+
  gi|242399778|ref|YP_002995203.1| 294 ETYKIRF-ENLRDKIEKIKmELEK 316
                                       7777555.4455555555435554 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 ?    0.7   0.1       2.6   7.2e+02      22      35 ..     107     120 ..     101     128 .. 0.81
   2 !    9.4   1.2    0.0049       1.4       9      37 ..     132     160 ..     129     167 .. 0.84
   3 !   10.9   4.1    0.0016      0.45       1      32 [.     171     202 ..     161     211 .. 0.67
   4 ?    7.1   5.7     0.026       7.3       1      38 [.     219     256 ..     219     258 .. 0.91
   5 !    8.9   4.8    0.0071         2       4      35 ..     250     281 ..     248     286 .. 0.93
   6 ?    8.1   3.8     0.012       3.4       3      34 ..     263     294 ..     262     296 .. 0.92
   7 ?    8.3   2.6     0.011         3       4      41 ..     285     318 ..     282     319 .] 0.55

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 2.6
                         FlaC_arch  22 eneelsksveelke 35 
                                       +++el k++e++++
  gi|242399778|ref|YP_002995203.1| 107 KLDELIKTIEMIEK 120
                                       68899999999986 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0049
                         FlaC_arch   9 lsklsteletvkkeneelsksveelkenV 37 
                                        +kl  e e++k e e+++ ++e++k++V
  gi|242399778|ref|YP_002995203.1| 132 YEKLMQEYENLKLEYEKVKAELEKMKQTV 160
                                       56777888999999999999999999999 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.0016
                         FlaC_arch   1 ridelEnklsklsteletvkkeneelsksvee 32 
                                       +i+ l ++l+ ++ ele  +ken+el+k++ e
  gi|242399778|ref|YP_002995203.1| 171 KIERLRKELEAVKAELEKTRKENKELKKELAE 202
                                       56666666667777777777777777766654 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.026
                         FlaC_arch   1 ridelEnklsklsteletvkkeneelsksveelkenVk 38 
                                       +++elE+kl+  + el+ +++  +e+  +  el+++V+
  gi|242399778|ref|YP_002995203.1| 219 KVKELEEKLKAKEEELSRLERLVDEVTREKLELEKKVE 256
                                       89***********************9999999999886 PP

  == domain 5  score: 8.9 bits;  conditional E-value: 0.0071
                         FlaC_arch   4 elEnklsklsteletvkkeneelsksveelke 35 
                                       elE+k+++++   + ++ke eel+k+++el +
  gi|242399778|ref|YP_002995203.1| 250 ELEKKVEEFEGLADELRKEKEELEKKIKELTR 281
                                       8***************************9975 PP

  == domain 6  score: 8.1 bits;  conditional E-value: 0.012
                         FlaC_arch   3 delEnklsklsteletvkkeneelsksveelk 34 
                                       del ++ ++l+ +++ + +en+el++ +eel+
  gi|242399778|ref|YP_002995203.1| 263 DELRKEKEELEKKIKELTRENNELKQRIEELE 294
                                       789999999*********************97 PP

  == domain 7  score: 8.3 bits;  conditional E-value: 0.011
                         FlaC_arch   4 elEnklsklsteletvkkeneelsksveelkenVkdll 41 
                                       el ++++    elet k  +e+l++++e++k + ++ll
  gi|242399778|ref|YP_002995203.1| 285 ELKQRIE----ELETYKIRFENLRDKIEKIKMELEKLL 318
                                       3444444....566666666666666666666666655 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.3   4.1e-06    0.0012      18      42 ..      63      87 ..      57      88 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 4.1e-06
                            HTH_38 18 aeGlslreIArrLgrspsTIsRElk 42
                                      ++G++ +eIA +Lgr  +TI ++lk
  gi|242399778|ref|YP_002995203.1| 63 KAGMTTSEIAGELGRTEQTIRKHLK 87
                                      69********************998 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 ?    6.7   8.6     0.015       4.2      67     122 ..     105     160 ..      72     169 .. 0.74
   2 ?    6.1  26.3     0.023       6.4      49     130 ..     172     256 ..     161     257 .. 0.76
   3 !   16.7  18.0   1.3e-05    0.0036      29     104 ..     242     317 ..     239     319 .] 0.92

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.015
                               GAS  67 eeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleqrfekveker 122
                                       + +++eL k ++  ek   +   +k+++++l +e+++lk+e+e ++ ++ek+++  
  gi|242399778|ref|YP_002995203.1| 105 QGKLDELIKTIEMIEKGGLKEVIAKEEYEKLMQEYENLKLEYEKVKAELEKMKQTV 160
                                       44677777788888887777777888888888888888888888888888887754 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.023
                               GAS  49 lseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlk...arlkelekelkdlkwehevleqrfekveker 122
                                       ++ + +e +  k +L+k ++e++eL+k+l++ + + ++l++ +   +++kele++lk+ ++e   le  +++v +e+
  gi|242399778|ref|YP_002995203.1| 172 IERLRKELEAVKAELEKTRKENKELKKELAEARVKIMELQSKRieeTKVKELEEKLKAKEEELSRLERLVDEVTREK 248
                                       55667777788888888888888888888888888887776543337888899999999999999999999999999 PP

                               GAS 123 delykkfe 130
                                        el+kk e
  gi|242399778|ref|YP_002995203.1| 249 LELEKKVE 256
                                       99988876 PP

  == domain 3  score: 16.7 bits;  conditional E-value: 1.3e-05
                               GAS  29 kslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdl 104
                                       ++   e  el+kk e+ e + +e+ +e+++l++++k++++e++eL++++++ e  k +++nl+ ++++ ++el++l
  gi|242399778|ref|YP_002995203.1| 242 DEVTREKLELEKKVEEFEGLADELRKEKEELEKKIKELTRENNELKQRIEELETYKIRFENLRDKIEKIKMELEKL 317
                                       566678899***************************************************************9987 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   3.6e-05      0.01      20      46 ..      61      87 ..      41      96 .. 0.89
   2 ?   -0.1   0.0       3.5   9.9e+02      31      49 ..     277     294 ..     258     295 .. 0.47

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3.6e-05
                                      STCTTB-HHHHHHHHTS-HHHHHHHHH CS
                            HTH_20 20 araegltaselaerldlskntlsyHLr 46
                                      ++++g+t se+a +l+ + +t+++HL+
  gi|242399778|ref|YP_002995203.1| 61 REKAGMTTSEIAGELGRTEQTIRKHLK 87
                                      6789**********************8 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 3.5
                                       HHHHTS-HHHHHHHHHHHH CS
                            HTH_20  31 aerldlskntlsyHLrvLe 49 
                                       +e+     n+l +++++Le
  gi|242399778|ref|YP_002995203.1| 277 KEL-TRENNELKQRIEELE 294
                                       222.133344666666665 PP

>> bZIP_2  Basic region leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.2       1.3   3.7e+02      40      54 .]     171     185 ..     163     185 .. 0.88
   2 ?   -1.2   8.8       8.2   2.3e+03      21      50 ..     225     257 ..     220     260 .. 0.69
   3 !   19.2   8.8   3.4e-06   0.00095      24      53 ..     266     295 ..     263     296 .. 0.95
   4 ?   -0.4   0.6       4.5   1.3e+03      33      51 ..     299     317 ..     297     319 .] 0.69

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 1.3
                                       HHHHHHHHHHHHHHH CS
                            bZIP_2  40 eNaqLrqkveqLeke 54 
                                       ++++Lr+++e++++e
  gi|242399778|ref|YP_002995203.1| 171 KIERLRKELEAVKAE 185
                                       68999****999987 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 8.2
                                       HHHHHHHHH...HHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_2  21 ekkkakeee...leervkeLeeeNaqLrqkveq 50 
                                       ek kakeee   le+ v e+++e+ +L++kve+
  gi|242399778|ref|YP_002995203.1| 225 EKLKAKEEElsrLERLVDEVTREKLELEKKVEE 257
                                       666777776333477888999999999998886 PP

  == domain 3  score: 19.2 bits;  conditional E-value: 3.4e-06
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_2  24 kakeeeleervkeLeeeNaqLrqkveqLek 53 
                                       ++++eele+++keL++eN++L+q++e+Le+
  gi|242399778|ref|YP_002995203.1| 266 RKEKEELEKKIKELTRENNELKQRIEELET 295
                                       7899************************96 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 4.5
                                       HHHHHHHHHHHHHHHHHHH CS
                            bZIP_2  33 rvkeLeeeNaqLrqkveqL 51 
                                       r ++L+ ++++++ ++e+L
  gi|242399778|ref|YP_002995203.1| 299 RFENLRDKIEKIKMELEKL 317
                                       6667777777777777766 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   1.5e-05    0.0041      16      39 ..      62      87 ..      45      92 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.5e-05
                            HTH_23 16 e..GlsvreIAreLgvsrrTvyrwlk 39
                                      e  G++++eIA eLg++++T+++ lk
  gi|242399778|ref|YP_002995203.1| 62 EkaGMTTSEIAGELGRTEQTIRKHLK 87
                                      235******************98766 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   7.3      0.13        37      53      97 ..     109     160 ..      74     166 .. 0.68
   2 ?    7.5  18.4     0.017       4.7      26     100 ..     167     244 ..     163     247 .. 0.85
   3 !   17.9  14.7     1e-05    0.0028      30     101 ..     247     318 ..     239     319 .] 0.94

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.13
                                       HHHHHHCCCCCCTT.......S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  53 NelskeIgkakkkk.......edaeeliaevkelkeelkaleaelkeleael 97 
                                        el k+I+++ k +       e+ e+l++e ++lk e ++++ael+++++ +
  gi|242399778|ref|YP_002995203.1| 109 DELIKTIEMIEKGGlkeviakEEYEKLMQEYENLKLEYEKVKAELEKMKQTV 160
                                       4555666666655544444448888888888888888888888888887765 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.017
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT.S-TCCCCCC..CHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  26 advdelleldekrrelqveleelqaerNelskeIgkakkkk.edaeeliae..vkelkeelkaleaelkeleaelek 99 
                                       + + ++  l ++ +++++ele+ ++e +el ke ++a  k  e  ++ i+e  vkel e+lka+e+el+ le  +++
  gi|242399778|ref|YP_002995203.1| 167 KAIGKIERLRKELEAVKAELEKTRKENKELKKELAEARVKImELQSKRIEEtkVKELEEKLKAKEEELSRLERLVDE 243
                                       56789999*****************************988886666666543389***************9988877 PP

                                       H CS
                      Seryl_tRNA_N 100 l 100
                                       +
  gi|242399778|ref|YP_002995203.1| 244 V 244
                                       6 PP

  == domain 3  score: 17.9 bits;  conditional E-value: 1e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  30 elleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaelekll 101
                                       e lel++k +e +  ++el++e+ el k+I+++ +++++ ++ i+e ++ k ++++l ++ ++++ elekll
  gi|242399778|ref|YP_002995203.1| 247 EKLELEKKVEEFEGLADELRKEKEELEKKIKELTRENNELKQRIEELETYKIRFENLRDKIEKIKMELEKLL 318
                                       6689*****************************************************************997 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   4.9   0.00012     0.033      48      99 ..     127     180 ..     102     182 .. 0.85
   2 ?    6.1  11.3     0.021         6      14      98 ..     182     265 ..     180     267 .. 0.92
   3 !   11.5  13.4   0.00048      0.13      16     103 ..     232     319 .]     219     319 .] 0.86

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00012
                           DUF3450  48 ellaeyralkeeleslevyneqlerlvasqeqe..iasleeqieeieeierelv 99 
                                         ++ey++l +e e+l+++ e++++ +++++q+  ++sle+ i +ie++++el+
  gi|242399778|ref|YP_002995203.1| 127 IAKEEYEKLMQEYENLKLEYEKVKAELEKMKQTvdLESLEKAIGKIERLRKELE 180
                                       5789**********************99988852279**************998 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.021
                           DUF3450  14 laatldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqiee 90 
                                       ++a+l++++ke ++  ++ a++  ki +l+ + +  + ++++l+e+l++ e + ++lerlv+++ +e  +le++ ee
  gi|242399778|ref|YP_002995203.1| 182 VKAELEKTRKENKELKKELAEARVKIMELQSK-RIEETKVKELEEKLKAKEEELSRLERLVDEVTREKLELEKKVEE 257
                                       57899************************875.567899************************************** PP

                           DUF3450  91 ieeierel 98 
                                       +e +++el
  gi|242399778|ref|YP_002995203.1| 258 FEGLADEL 265
                                       **999887 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.00048
                           DUF3450  16 atldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeie 92 
                                       ++l+ ++    + ++++ + +kk+++ +  ++el +e ++l++++++l+ +n++l++ ++++e+   + e+  ++ie
  gi|242399778|ref|YP_002995203.1| 232 EELSRLERLVDEVTREKLELEKKVEEFEGLADELRKEKEELEKKIKELTRENNELKQRIEELETYKIRFENLRDKIE 308
                                       56777778888888899999999999999999999999999999999999999999999999999999999999999 PP

                           DUF3450  93 eierelvplle 103
                                       +i++el+ lle
  gi|242399778|ref|YP_002995203.1| 309 KIKMELEKLLE 319
                                       99999999885 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   7.6e-05     0.021      14      37 ..      63      87 ..      58      93 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 7.6e-05
                            HTH_11 14 gp.isgeeLAeeLnvSrrtvrrdIk 37
                                      +  ++ +e+A eL+++++t+r+++k
  gi|242399778|ref|YP_002995203.1| 63 KAgMTTSEIAGELGRTEQTIRKHLK 87
                                      34499******************98 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.1   8.1e-05     0.023      16      39 ..      64      87 ..      62      88 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 8.1e-05
                                      TTS-HHHHHHHHTS-HHHHHHHHH CS
                              GerE 16 eGksnkeIAeelniSekTVkvhks 39
                                      +G+++ eIA el+  e+T++ h++
  gi|242399778|ref|YP_002995203.1| 64 AGMTTSEIAGELGRTEQTIRKHLK 87
                                      6*******************9986 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0     0.016       4.5      16      37 ..      66      87 ..      59      97 .. 0.92
   2 ?    6.4   0.4     0.029       8.1       2      27 ..     202     229 ..     201     236 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.016
                                      EEHHHHHHHHTS-HHHHHHHHH CS
                             HTH_5 16 lcvcelaeelglsqstvShHLk 37
                                      ++ +e+a elg ++ t++ HLk
  gi|242399778|ref|YP_002995203.1| 66 MTTSEIAGELGRTEQTIRKHLK 87
                                      99*******************8 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.029
                                       HHHHHHHHHHTT..SSEEHHHHHHHHTS CS
                             HTH_5   2 ptRlkILklLae..gelcvcelaeelgl 27 
                                       ++R+kI+ l ++  +e++v el e+l+ 
  gi|242399778|ref|YP_002995203.1| 202 EARVKIMELQSKriEETKVKELEEKLKA 229
                                       68***********************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 !   13.9   0.0    0.0001     0.029      13      39 ..      61      87 ..      58      87 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.0001
                            HTH_24 13 qknprisqreLAerlglSpstvnrrlk 39
                                      +++++++ +e+A +lg + +t++++lk
  gi|242399778|ref|YP_002995203.1| 61 REKAGMTTSEIAGELGRTEQTIRKHLK 87
                                      789**********************98 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 ?    2.5  23.9       0.4   1.1e+02      13     109 ..     128     221 ..     103     228 .. 0.76
   2 !   16.0  22.6   2.8e-05    0.0079       7     107 ..     217     316 ..     211     319 .] 0.84

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.4
                            TACC_C  13 vkeeveekeeeiqelkkkveelkkenqemkkiv..aefektiaqlieekqkqkelakkeiqkvleekeqlladlnsv 87 
                                       +kee e+  +e ++lk ++e+ k+e ++mk++v  ++ ek+i ++ e   k+ e  k+e++k  +e+++l+++l + 
  gi|242399778|ref|YP_002995203.1| 128 AKEEYEKLMQEYENLKLEYEKVKAELEKMKQTVdlESLEKAIGKI-ERLRKELEAVKAELEKTRKENKELKKELAEA 203
                                       677888888888899**************9997335899999886.556689999999****************999 PP

                            TACC_C  88 eksfsdlf.kryekqkevlegyk 109
                                         ++ +l  kr+e  k      k
  gi|242399778|ref|YP_002995203.1| 204 RVKIMELQsKRIEETKV-----K 221
                                       99999985256665554.....4 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 2.8e-05
                            TACC_C   7 daalekvkeeveekeeeiqelkkkveelkkenqemkkivaefektiaqlieekqkqkelakkeiqkvleekeqllad 83 
                                       ++++++++e+ + keee++ l++ v+e ++e++e++k v+efe+   +l +ek ++ e++ ke+ +  +e +q +++
  gi|242399778|ref|YP_002995203.1| 217 ETKVKELEEKLKAKEEELSRLERLVDEVTREKLELEKKVEEFEGLADELRKEK-EELEKKIKELTRENNELKQRIEE 292
                                       567889999999********************************777766666.44456666777777888888899 PP

                            TACC_C  84 lnsveksfsdlfkryekqkevleg 107
                                       l++ +  f++l  ++ek k  le+
  gi|242399778|ref|YP_002995203.1| 293 LETYKIRFENLRDKIEKIKMELEK 316
                                       9999999************99886 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5  32.3   3.5e-05    0.0098     680     875 ..     126     316 ..      16     319 .] 0.72

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.5e-05
                           DUF3584 680 qqaeeqlqkldaqlkqleeqqkaaleelkedlseerlekkakwqevvgeldeqlaelkkaieaartqakarlkelee 756
                                         a+e+ +kl ++ + l+ + +++++el++ +++  le  +k    ++ l ++l+++k+++e+ r+++k+  kel e
  gi|242399778|ref|YP_002995203.1| 126 VIAKEEYEKLMQEYENLKLEYEKVKAELEKMKQTVDLESLEKAIGKIERLRKELEAVKAELEKTRKENKELKKELAE 202
                                       45788899999999999999999999999999999999999999999999999999999999999999999999999 PP

                           DUF3584 757 aykr..eLkskdvDpetvkelkrkieeLekkieriekrreevreYraflqetwlkvdslaeerpalkeqveelesaa 831
                                       a+ +  eL+sk +++ +vkel++k ++ e++++r e+  +ev++ +  l ++    ++  +  ++l +++eele+++
  gi|242399778|ref|YP_002995203.1| 203 ARVKimELQSKRIEETKVKELEEKLKAKEEELSRLERLVDEVTREKLELEKKV---EEFEGLADELRKEKEELEKKI 276
                                       87644499999999999999999999999999999999999998665555544...334444444444444444444 PP

                           DUF3584 832 eeleqeltrliedtklerkklekerkalekqldqldenlrklrd 875
                                       +    eltr ++++k+++++le+ + + e++ d++++ + +l++
  gi|242399778|ref|YP_002995203.1| 277 K----ELTRENNELKQRIEELETYKIRFENLRDKIEKIKMELEK 316
                                       4....444455555555555555555555555555544444443 PP

>> Cep57_CLD_2  Centrosome localisation domain of PPC89
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   5.8       5.9   1.7e+03      44      62 ..     136     154 ..     105     167 .. 0.66
   2 ?    6.2   7.5     0.039        11      35      65 ..     167     197 ..     159     216 .. 0.81
   3 ?    1.7   4.6      0.96   2.7e+02       9      36 ..     217     244 ..     208     249 .. 0.75
   4 !   16.0   9.2   3.5e-05    0.0098      15      58 ..     251     294 ..     246     296 .. 0.94
   5 ?   -1.4   0.3       8.9   2.5e+03      48      64 ..     301     317 ..     298     319 .] 0.61

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 5.9
                       Cep57_CLD_2  44 yeelneLkaevealrkELk 62 
                                        +e ++Lk e e  + EL+
  gi|242399778|ref|YP_002995203.1| 136 MQEYENLKLEYEKVKAELE 154
                                       3444445555555554454 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.039
                       Cep57_CLD_2  35 salrqLgvAyeelneLkaevealrkELkeqr 65 
                                        a+ ++ + + el+  kae+e  rkE+ke +
  gi|242399778|ref|YP_002995203.1| 167 KAIGKIERLRKELEAVKAELEKTRKENKELK 197
                                       5677778888888888888888888877765 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.96
                       Cep57_CLD_2   9 qnrLdsltrklqvheeelkrLnkERdsa 36 
                                       +++ + l++kl + eeel rL ++ d++
  gi|242399778|ref|YP_002995203.1| 217 ETKVKELEEKLKAKEEELSRLERLVDEV 244
                                       5778888888888888888888766654 PP

  == domain 4  score: 16.0 bits;  conditional E-value: 3.5e-05
                       Cep57_CLD_2  15 ltrklqvheeelkrLnkERdsalrqLgvAyeelneLkaevealr 58 
                                       l+ k+++ e++ ++L+kE ++ ++++ +  +e+neLk++ e l+
  gi|242399778|ref|YP_002995203.1| 251 LEKKVEEFEGLADELRKEKEELEKKIKELTRENNELKQRIEELE 294
                                       899**************************************986 PP

  == domain 5  score: -1.4 bits;  conditional E-value: 8.9
                       Cep57_CLD_2  48 neLkaevealrkELkeq 64 
                                       ++L+++ e  + EL+  
  gi|242399778|ref|YP_002995203.1| 301 ENLRDKIEKIKMELEKL 317
                                       45666666666666544 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.3   0.00034     0.095       9      39 ..      60      90 ..      58      97 .. 0.91
   2 ?    0.8   0.1       2.3   6.3e+02      18      48 ..     221     250 ..     188     251 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00034
                            HTH_31  9 lReraGLsqeevAerlgvsestlsrlEqGrr 39
                                      +Re+aG++  e A+ lg +e t+++   G+ 
  gi|242399778|ref|YP_002995203.1| 60 AREKAGMTTSEIAGELGRTEQTIRKHLKGES 90
                                      7***********************9888875 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 2.3
                            HTH_31  18 eevAerlgvsestlsrlEqGrrgrpspavle 48 
                                       +e+ e l   e  lsrlE+    +++++ le
  gi|242399778|ref|YP_002995203.1| 221 KELEEKLKAKEEELSRLERLVD-EVTREKLE 250
                                       5777788888889999999888.68887775 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0         1   2.8e+02      33      69 ..      68     104 ..      58     127 .. 0.66
   2 ?    5.0   2.7     0.083        23      17      67 ..     130     182 ..     123     188 .. 0.79
   3 ?    7.6   9.4     0.013       3.6      25      99 ..     171     241 ..     162     246 .. 0.61
   4 ?   14.1  12.4   0.00013     0.035       4      97 ..     219     312 ..     216     316 .. 0.95

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 1
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTT CS
                        Laminin_II  33 lseinrsveetnekvkdankairdArrsvkkLeklap 69 
                                        sei++++ +t++ +++  k+   A++ v++  +l+ 
  gi|242399778|ref|YP_002995203.1|  68 TSEIAGELGRTEQTIRKHLKGESKAGQLVRETYELIK 104
                                       5778888888888888888888888888876554433 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.083
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXX--T CS
                        Laminin_II  17 eqlaplsqnlentkeklseinrsveetnekvk..dankairdArrsvkkLekl 67 
                                       e  ++l q+ en+k +++++++++e++++ v+  ++ kai   +r  k+Le +
  gi|242399778|ref|YP_002995203.1| 130 EEYEKLMQEYENLKLEYEKVKAELEKMKQTVDleSLEKAIGKIERLRKELEAV 182
                                       56678999999999999999999999999887668888888888888887765 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.013
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGG.GHHHHHHHHHH...HHHHHHHHHHHH CS
                        Laminin_II  25 nlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLld.klkelkqleeassslsdniseikelI 99 
                                       ++e+++++l+ +++++e+t ++ k+++k +++Ar +   +e +  ++++ k+kel+++ +a+    +++s++  l+
  gi|242399778|ref|YP_002995203.1| 171 KIERLRKELEAVKAELEKTRKENKELKKELAEARVK--IMELQSKRIEEtKVKELEEKLKAK---EEELSRLERLV 241
                                       678888888888888888888888888877666544..445555566542555555555553...34555544444 PP

  == domain 4  score: 14.1 bits;  conditional E-value: 0.00013
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHH CS
                        Laminin_II   4 laaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkq 80 
                                       +++e +e++k+ +e l  l+  ++++  +  e++++vee + +++++ k  ++ ++++k+L+++ ++L ++++el++
  gi|242399778|ref|YP_002995203.1| 219 KVKELEEKLKAKEEELSRLERLVDEVTREKLELEKKVEEFEGLADELRKEKEELEKKIKELTRENNELKQRIEELET 295
                                       689999*******************9999999********************************************* PP

                                       HHHH...HHHHHHHHHH CS
                        Laminin_II  81 leeassslsdniseike 97 
                                        +   ++l d+i++ik 
  gi|242399778|ref|YP_002995203.1| 296 YKIRFENLRDKIEKIKM 312
                                       ****9**********95 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   5.7     0.028         8      62      95 ..     128     161 ..      67     174 .. 0.85
   2 ?   13.2  35.6   0.00024     0.068       3     129 .]     165     293 ..     163     293 .. 0.84
   3 ?    3.1   0.5      0.33        94      55      82 ..     289     316 ..     285     319 .] 0.68

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.028
                        TPR_MLP1_2  62 lreelnelkaeiaelkaeaesakaeleeseeswe 95 
                                       ++ee+++l +e+++lk e e++kaele+ ++  +
  gi|242399778|ref|YP_002995203.1| 128 AKEEYEKLMQEYENLKLEYEKVKAELEKMKQTVD 161
                                       5999999999999999999999999999988754 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00024
                        TPR_MLP1_2   3 lksleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkae 79 
                                       l+++  +i++l++e e+ +a+l+k +++ ++ +++++ea  k   el+ +  + +++++l e+l+  ++e++ l+  
  gi|242399778|ref|YP_002995203.1| 165 LEKAIGKIERLRKELEAVKAELEKTRKENKELKKELAEARVKIM-ELQSKRIEETKVKELEEKLKAKEEELSRLERL 240
                                       56777899*********************************986.78888888888999999998888888887776 PP

                        TPR_MLP1_2  80 aesa...kaeleeseesweeqkeelekelselekriedlneqNklLhdQlEsl 129
                                       ++++   k ele++ e+ e   +el+ke++elek+i++l+  N+ L +++E+l
  gi|242399778|ref|YP_002995203.1| 241 VDEVtreKLELEKKVEEFEGLADELRKEKEELEKKIKELTRENNELKQRIEEL 293
                                       666611155566666666667799***************************85 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.33
                        TPR_MLP1_2  55 dvkelqalreelnelkaeiaelkaeaes 82 
                                        ++el++++ ++++l+++i+++k e+e+
  gi|242399778|ref|YP_002995203.1| 289 RIEELETYKIRFENLRDKIEKIKMELEK 316
                                       5677777777777777777777777665 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 ?   13.7   3.0   0.00013     0.037      79     179 ..     146     246 ..      96     249 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00013
                    Citrate_ly_lig  79 flkeqeevaesqaelDlklfkeriakalgitkryvGeeplsevtaaYnqalkevlekaeievveierkekeeelisa 155
                                       + k ++e+++++ ++Dl+  ++ i+k+  ++k         e t++ n++lk+ l +a+++++e++ k+ ee+ +  
  gi|242399778|ref|YP_002995203.1| 146 YEKVKAELEKMKQTVDLESLEKAIGKIERLRKELEAVKAELEKTRKENKELKKELAEARVKIMELQSKRIEETKVKE 222
                                       667889999***********************999999999************************************ PP

                    Citrate_ly_lig 156 skvrkllkeknleklaelvPkttl 179
                                        + +   ke++l++l++lv ++t 
  gi|242399778|ref|YP_002995203.1| 223 LEEKLKAKEEELSRLERLVDEVTR 246
                                       *99999*************99885 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   4.3     0.031       8.8      23      53 ..     129     161 ..     117     168 .. 0.78
   2 ?   13.1   7.1   0.00021      0.06      13      50 ..     166     203 ..     163     217 .. 0.89
   3 ?    1.1   6.9       1.2   3.3e+02      35      72 ..     219     256 ..     206     258 .. 0.62
   4 ?   11.2   9.3   0.00084      0.24      21      51 ..     264     294 ..     262     310 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.031
                                       HHHHHHHHHHHHHHHHHHHHHHHHHCC-XX..X CS
                             DivIC  23 kqeiaalqaelaklkaeneeLeaevkdLks..d 53 
                                       k+e+++l +e+++lk e e+ +ae++++k+  d
  gi|242399778|ref|YP_002995203.1| 129 KEEYEKLMQEYENLKLEYEKVKAELEKMKQtvD 161
                                       788888889999999999999999998877444 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00021
                                       XXXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC- CS
                             DivIC  13 kkgllaykqlkqeiaalqaelaklkaeneeLeaevkdL 50 
                                       +k + ++ +l++e++a +ael+k ++en+eL++e+++ 
  gi|242399778|ref|YP_002995203.1| 166 EKAIGKIERLRKELEAVKAELEKTRKENKELKKELAEA 203
                                       66788999**************************9876 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHHHCC-XXXXXXXXXXXXXXXXXXXXXX CS
                             DivIC  35 klkaeneeLeaevkdLksdedyieerARselglvkpgE 72 
                                       k+k+ +e+L+a+ ++L+  e  ++e+ R++l l k+ E
  gi|242399778|ref|YP_002995203.1| 219 KVKELEEKLKAKEEELSRLERLVDEVTREKLELEKKVE 256
                                       45555555666666665556777777777777766544 PP

  == domain 4  score: 11.2 bits;  conditional E-value: 0.00084
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHCC-X CS
                             DivIC  21 qlkqeiaalqaelaklkaeneeLeaevkdLk 51 
                                       +l++e ++l++++++l+ en+eL++++++L+
  gi|242399778|ref|YP_002995203.1| 264 ELRKEKEELEKKIKELTRENNELKQRIEELE 294
                                       6899999999999999999999999999994 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1  27.3   0.00061      0.17      22     159 ..     130     268 ..     123     268 .. 0.66
   2 ?    7.8  20.6     0.013       3.6      73     166 ..     224     313 ..     221     319 .] 0.77

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00061
                             ATG16  22 qaynrLldrtsaleaenaklekaaasakssksskksakekeasasq.......snskqsakiqsleqklaqlreela 91 
                                       + y +L++  + l+ e +k +++ ++ k+     +++ e++++a         + ++ +a+++++ ++ ++l++ela
  gi|242399778|ref|YP_002995203.1| 130 EEYEKLMQEYENLKLEYEKVKAELEKMKQ-----TVDLESLEKAIGkierlrkELEAVKAELEKTRKENKELKKELA 201
                                       46999999999999999999888887777.....4555555555551111121233455555555555555555555 PP

                             ATG16  92 elyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDE 159
                                       e+  +  el+++ +e ++++++leeklk++ee+l +le+ + +++++  ++e++++e e l ++l+ E
  gi|242399778|ref|YP_002995203.1| 202 EARVKIMELQSKRIE-ETKVKELEEKLKAKEEELSRLERLVDEVTREKLELEKKVEEFEGLADELRKE 268
                                       555555555544333.4678888888888888888888888888888888888888888888888876 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.013
                             ATG16  73 sakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrek 149
                                       ++k+++ e++l++l   + e+ +++ el++++ e +   ++l+++ +e e++++el++e+++l+++++++e      
  gi|242399778|ref|YP_002995203.1| 224 EEKLKAKEEELSRLERLVDEVTREKLELEKKVEEFEGLADELRKEKEELEKKIKELTRENNELKQRIEELET----Y 296
                                       568889999999999999999999999999999999999999999999999999999999999998776654....3 PP

                             ATG16 150 eklvqdlqDElsaLqlq 166
                                       +   ++l+D ++  +++
  gi|242399778|ref|YP_002995203.1| 297 KIRFENLRDKIEKIKME 313
                                       33334444444433333 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00054      0.15       4      34 ..      58      87 ..      56      93 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00054
                            HTH_29  4 allllaeGvstvsqiAkllglsrrtvyrwlk 34
                                      a++  + G+ t+s+iA  lg +++t++++lk
  gi|242399778|ref|YP_002995203.1| 58 AIAREKAGM-TTSEIAGELGRTEQTIRKHLK 87
                                      566778899.9*****************997 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0       2.7   7.4e+02     107     126 ..     107     126 ..      55     138 .. 0.70
   2 ?    3.7   1.1      0.22        61      53      73 ..     171     187 ..     132     250 .. 0.47
   3 ?    9.9   0.5    0.0026      0.73      34     112 ..     235     318 ..     217     319 .] 0.54

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 2.7
                      Baculo_PEP_C 107 tLnnllqalnnldlgalsqe 126
                                        L  l+++++ +++g+l++ 
  gi|242399778|ref|YP_002995203.1| 107 KLDELIKTIEMIEKGGLKEV 126
                                       47778888888888877765 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.22
                      Baculo_PEP_C  53 dlksllaeldtrldtlltnLt 73 
                                       ++++l +    +l+++ ++L+
  gi|242399778|ref|YP_002995203.1| 171 KIERLRK----ELEAVKAELE 187
                                       2222111....1111111111 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.0026
                      Baculo_PEP_C  34 aqlatlldaietqLnalsedlks...llaeldt...rldtlltnLtdalnalqdtlrneLtnlnsiltnLlssvtNi 104
                                       + l++l+d++ ++  +l++++++   l  el++   +l++ +++Lt+  n+l++ ++ eL++ +    nL  ++  i
  gi|242399778|ref|YP_002995203.1| 235 SRLERLVDEVTREKLELEKKVEEfegLADELRKekeELEKKIKELTRENNELKQRIE-ELETYKIRFENLRDKIEKI 310
                                       556666666655444444444430004444444444555555555555555555553.5566666677777777777 PP

                      Baculo_PEP_C 105 nstLnnll 112
                                       +  L+ ll
  gi|242399778|ref|YP_002995203.1| 311 KMELEKLL 318
                                       77666665 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.5      0.22        63      19      54 ..     152     189 ..     141     203 .. 0.73
   2 ?    8.0   0.6     0.014       3.9      31      62 ..     216     245 ..     199     251 .. 0.80
   3 ?    6.4   0.5     0.044        12      12      62 ..     275     311 ..     249     319 .] 0.48

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.22
                           NPV_P10  19 kVdalqqqv..ddvqenlpdvtelnekLdaqsaqLael 54 
                                        ++ ++q v  +++++ + +++ l ++L+a  a+L++ 
  gi|242399778|ref|YP_002995203.1| 152 ELEKMKQTVdlESLEKAIGKIERLRKELEAVKAELEKT 189
                                       45555666544688888889999999999999988865 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.014
                           NPV_P10  31 qenlpdvtelnekLdaqsaqLaeletkvenIq 62 
                                       +e   +v+el+ekL a  ++L  le  v++++
  gi|242399778|ref|YP_002995203.1| 216 EE--TKVKELEEKLKAKEEELSRLERLVDEVT 245
                                       43..5789******************999986 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.044
                           NPV_P10  12 dikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIq 62 
                                        ik++    + l+q+++++++    +++l +              k+e+I+
  gi|242399778|ref|YP_002995203.1| 275 KIKELTRENNELKQRIEELETYKIRFENLRD--------------KIEKIK 311
                                       2333333333333333333333333333333..............333333 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7  20.3    0.0015      0.43      32     144 ..      98     213 ..      81     216 .. 0.87
   2 ?    6.2  21.4    0.0088       2.5     357     462 ..     217     316 ..     213     318 .. 0.95

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0015
                                       HHHHHHHHHHHHHTTTSSS-S---T..T..THHHHHHHHHHHHHHHHHHTHHHHHT-GGGT--S-SHHHHHTTHHHH CS
                              EzrA  32 erkneiknlpvqeelskvkklnltg..e..seekfeewkkkwdeiktkklpeieellfeaeelldkykfkkakkkla 104
                                       e  + ik+ +++e +++++ +++ g  e   +e++e++ ++++++k  + ++++ +l+++++ +d  ++ ka  k++
  gi|242399778|ref|YP_002995203.1|  98 ETYELIKQGKLDELIKTIEMIEKGGlkEviAKEEYEKLMQEYENLKL-EYEKVKAELEKMKQTVDLESLEKAIGKIE 173
                                       445667777777777777777776653233689*************9.9**************************** PP

                                       HHHHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHHHHHHHH CS
                              EzrA 105 eleeeldeveekikkileelkelteseeknreeieklkek 144
                                        l++el+ v+++++k ++e kel++   + r +i +l++k
  gi|242399778|ref|YP_002995203.1| 174 RLRKELEAVKAELEKTRKENKELKKELAEARVKIMELQSK 213
                                       **********************************999876 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0088
                                       HHHHHHHHHHHS-SS---STTGGGTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSS- CS
                              EzrA 357 ekdyeeleekleekkvaYSelqeeleeleekleeieekqeeileslkslrkdEkrAreqldeikkelkeikrkieks 433
                                       e++++eleekl++k+   S+l+  ++e++++  e+e+k+ee++   ++lrk+ ++ +++++e+ +e +e+k++ie+ 
  gi|242399778|ref|YP_002995203.1| 217 ETKVKELEEKLKAKEEELSRLERLVDEVTREKLELEKKVEEFEGLADELRKEKEELEKKIKELTRENNELKQRIEEL 293
                                       57899**********************************************************************98 PP

                                       SS-S-TTTHHHHSTTTSTTTHHHHHHHT- CS
                              EzrA 434 nLPgiPesyleelkeasdeieelakeLek 462
                                             e+y  ++++ +d+ie+++ eLek
  gi|242399778|ref|YP_002995203.1| 294 ------ETYKIRFENLRDKIEKIKMELEK 316
                                       ......79*******************98 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 ?    1.6  21.4       0.9   2.5e+02      65     136 ..     135     210 ..      90     218 .. 0.63
   2 ?   13.1  27.4   0.00028     0.077      64     167 ..     214     316 ..     205     319 .] 0.90

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.9
                           UPF0242  65 l..ekskleekeaklteldeglktkee..aleelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeel 136
                                       l  e ++l+ + +k++++ e++k+  +  +le++  + e+L++el+a + ele+ ++en++L+++l ++   + el
  gi|242399778|ref|YP_002995203.1| 135 LmqEYENLKLEYEKVKAELEKMKQTVDleSLEKAIGKIERLRKELEAVKAELEKTRKENKELKKELAEARVKIMEL 210
                                       1223333333333333333444433223388888888888888888888888888888888888877765554443 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00028
                           UPF0242  64 klekskleekeaklteldeglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelklel 140
                                       ++e+ k++e e+kl++++e+l+  e  + e++ e+ eL++++++ e +  +l++e+++L++k ++  ++++elk+ +
  gi|242399778|ref|YP_002995203.1| 214 RIEETKVKELEEKLKAKEEELSRLERLVDEVTREKLELEKKVEEFEGLADELRKEKEELEKKIKELTRENNELKQRI 290
                                       457788888888999999999999999************************************************** PP

                           UPF0242 141 eeqLaekqellqeyqetieeqrsvlek 167
                                       ee L+  ++++++++ +ie+ + +lek
  gi|242399778|ref|YP_002995203.1| 291 EE-LETYKIRFENLRDKIEKIKMELEK 316
                                       86.9*********************98 PP

>> MscS_porin  Mechanosensitive ion channel porin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9  28.0   0.00044      0.12      11     172 ..     151     314 ..     143     317 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00044
                        MscS_porin  11 deaeqkallqdLeqalnlLdkidkskkkaeelqkaiddaPkelrelqqelealqkkkeeaskeilaklsleeLeqrl 87 
                                       +e e+ ++  dLe+  + + ki++ +k++e+ +  +++  ke +el++el++ + k  e   +++++++ +eLe +l
  gi|242399778|ref|YP_002995203.1| 151 AELEKMKQTVDLESLEKAIGKIERLRKELEAVKAELEKTRKENKELKKELAEARVKIMELQSKRIEETKVKELEEKL 227
                                       66667777778888888899********************************************************* PP

                        MscS_porin  88 lqtssqlqelqeqlaqlnsqlvelqtrperaqqqltearqrlqeirnrLnstaaage..alsqaqrtalqaelaale 162
                                       ++ +++l++l++   +   +  el+   e+      e r++ +e++++++++  +++  + + ++   ++++ + l+
  gi|242399778|ref|YP_002995203.1| 228 KAKEEELSRLERLVDEVTREKLELEKKVEEFEGLADELRKEKEELEKKIKELTRENNelKQRIEELETYKIRFENLR 304
                                       *************************************************7776555546666677777888888888 PP

                        MscS_porin 163 aqieeleqel 172
                                       ++ie  ++el
  gi|242399778|ref|YP_002995203.1| 305 DKIEKIKMEL 314
                                       8887777776 PP

>> MAD  Mitotic checkpoint protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7  54.6    0.0017      0.48      20     258 ..      77     318 ..      61     319 .] 0.78

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0017
                               MAD  20 qkelehkrarielekkasalkrqlee..esdrnqelqkrikllek...reeekeealreqiElarlkkknlealnkk 91 
                                       + e    r  ++ e+ka +l r+  e  ++ +  el k i+ +ek   +e  ++e++++ + +    +k + +  k+
  gi|242399778|ref|YP_002995203.1|  77 RTEQTI-RKHLKGESKAGQLVRETYEliKQGKLDELIKTIEMIEKgglKEVIAKEEYEKLMQEYE-NLKLEYEKVKA 151
                                       555444.4456677777777776554113445678888888888744445445555554444444.45566666788 PP

                               MAD  92 ekekesklaearevisalknelaelkrqiekqelelsekeseleelqerldllkkklseleqli...qqlekkqkel 165
                                       e ek+++  +++ +++a+ +++++l++++e  + el+++++e++el+++l + + k+ el+ ++    + ++ +++l
  gi|242399778|ref|YP_002995203.1| 152 ELEKMKQTVDLESLEKAI-GKIERLRKELEAVKAELEKTRKENKELKKELAEARVKIMELQSKRieeTKVKELEEKL 227
                                       899***********9999.57***************************************99988766677778899 PP

                               MAD 166 aeaeqrikeLefeiqsqeddslivknskselarip.elekelerlreenkklnelkenkelLkEevedlkkkLereE 241
                                       +++e+ +  Le+ + + + ++l++++  +e + ++ el ke+e+l++++k+l   +en+e Lk  +e+l++   r+E
  gi|242399778|ref|YP_002995203.1| 228 KAKEEELSRLERLVDEVTREKLELEKKVEEFEGLAdELRKEKEELEKKIKELT--RENNE-LKQRIEELETYKIRFE 301
                                       9*****************************97776369999999999998875..34444.68899999999999** PP

                               MAD 242 kareelvkLelekekle 258
                                       + r+++ k+++e+ekl 
  gi|242399778|ref|YP_002995203.1| 302 NLRDKIEKIKMELEKLL 318
                                       ******99999999985 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   5.0     0.045        13     139     169 ..     131     161 ..     118     171 .. 0.80
   2 ?    6.4  26.0     0.023       6.5      71     171 ..     136     234 ..     129     236 .. 0.77
   3 ?    5.1  23.6     0.061        17      79     176 ..     220     315 ..     216     318 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.045
                           DUF4201 139 rvPaLlkDYdktkekveekrksvkkLrrkvk 169
                                       ++++L+++Y++ k ++e+ +++++k++++v+
  gi|242399778|ref|YP_002995203.1| 131 EYEKLMQEYENLKLEYEKVKAELEKMKQTVD 161
                                       6889999999999999999999999999764 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.023
                           DUF4201  71 kttktvhalthlkeklhmleselselkkelkekeerlaklrkelykvklerdklrkqneklkqqggllrvPaLlkDY 147
                                       +  ++  +l+ +k k+   ++++    ++l++   ++++lrkel+ vk+e +k rk+n++lk+++++ rv ++++  
  gi|242399778|ref|YP_002995203.1| 136 MQEYENLKLEYEKVKAELEKMKQTVDLESLEKAIGKIERLRKELEAVKAELEKTRKENKELKKELAEARV-KIME-L 210
                                       4455667788888888888888888889999999*********************************665.8888.6 PP

                           DUF4201 148 dktkekveekrksvkkLrrkvkil 171
                                         +  +  + ++  +kL+ k ++l
  gi|242399778|ref|YP_002995203.1| 211 QSKRIEETKVKELEEKLKAKEEEL 234
                                       666666664555555555554444 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.061
                           DUF4201  79 lthlkeklhmleselselkkelkekeerlaklrkelykvklerdklrkqneklkqqggllrvPaLlkDYdktkekve 155
                                       +++l ekl++ e+els+l+   +e ++++ +l+k++++ +   d lrk++e+l+++  +l ++    + +++ e++e
  gi|242399778|ref|YP_002995203.1| 220 VKELEEKLKAKEEELSRLERLVDEVTREKLELEKKVEEFEGLADELRKEKEELEKKIKELTRENN--ELKQRIEELE 294
                                       56778999999999999999999999999999999999999999999999999999999888874..5788999999 PP

                           DUF4201 156 ekrksvkkLrrkvkilemrlk 176
                                         + + ++Lr k+++++m l+
  gi|242399778|ref|YP_002995203.1| 295 TYKIRFENLRDKIEKIKMELE 315
                                       999999999999999988875 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   2.8      0.24        67      56     121 ..     102     173 ..      87     175 .. 0.68
   2 ?    4.9  11.4     0.092        26      50     119 ..     162     229 ..     141     234 .. 0.57
   3 ?   11.4   7.0   0.00088      0.25      49     121 ..     236     311 ..     231     314 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.24
                           DUF1664  56 slaatk.rhLssridrvdk.kldeq..keiskeikeevtevredlseigedvesvkeav..eglesklerie 121
                                        +++ k ++L + i+ ++k  l+e+  ke  +++ +e ++++ + ++++ ++e++k++v  e+le+ + +ie
  gi|242399778|ref|YP_002995203.1| 102 LIKQGKlDELIKTIEMIEKgGLKEViaKEEYEKLMQEYENLKLEYEKVKAELEKMKQTVdlESLEKAIGKIE 173
                                       555555456777777776523444311445567778888999999999999999999985568888888887 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.092
                           DUF1664  50 leqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvke.avegleskler 119
                                       le++ +++ +  ++L ++++ v ++l+++ +  ke+k+e++e+r ++ e+++  + ++e  v++le+kl+ 
  gi|242399778|ref|YP_002995203.1| 162 LESLEKAIGKI-ERLRKELEAVKAELEKTRKENKELKKELAEARVKIMELQS--KRIEEtKVKELEEKLKA 229
                                       33333333333.4577777777777777777777777777777766655544..44443157888888765 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.00088
                           DUF1664  49 qleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvke...aveglesklerie 121
                                       +le++ +++++ k +L++++++ +   de  + ++e++++++e+ ++ +e+++ +e++++    +e+l  k+e+i+
  gi|242399778|ref|YP_002995203.1| 236 RLERLVDEVTREKLELEKKVEEFEGLADELRKEKEELEKKIKELTRENNELKQRIEELETykiRFENLRDKIEKIK 311
                                       699999**************************************99999999888887762226888888888885 PP

>> HALZ  Homeobox associated leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   4.1    0.0003     0.085       6      32 ..     131     157 ..     129     162 .. 0.64
   2 ?   11.7   3.4   0.00084      0.24       9      37 ..     174     202 ..     173     207 .. 0.93
   3 ?    0.3   1.9         3   8.5e+02      21      38 ..     241     258 ..     225     262 .. 0.81
   4 ?    8.3   5.0    0.0093       2.6      14      39 ..     258     280 ..     256     284 .. 0.88
   5 ?    2.6   1.1      0.58   1.6e+02      24      39 ..     279     294 ..     278     297 .. 0.89
   6 ?    2.2   0.2      0.76   2.1e+02      11      31 ..     297     317 ..     294     319 .] 0.60

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.0003
                              HALZ   6 DYdvLKasYdaLksdydsLkkenekLk 32 
                                       +Y+ L + Y++Lk++y+ +k+e ek k
  gi|242399778|ref|YP_002995203.1| 131 EYEKLMQEYENLKLEYEKVKAELEKMK 157
                                       577777777777777777777666544 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00084
                              HALZ   9 vLKasYdaLksdydsLkkenekLkaelqe 37 
                                        L++  +a k++ +  +ken++Lk+el+e
  gi|242399778|ref|YP_002995203.1| 174 RLRKELEAVKAELEKTRKENKELKKELAE 202
                                       79************************986 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 3
                              HALZ  21 ydsLkkenekLkaelqeL 38 
                                       +d + +e+ +L+++++e 
  gi|242399778|ref|YP_002995203.1| 241 VDEVTREKLELEKKVEEF 258
                                       688999999999999885 PP

  == domain 4  score: 8.3 bits;  conditional E-value: 0.0093
                              HALZ  14 YdaLksdydsLkkenekLkaelqeLk 39 
                                       ++ L+   d L+ke+e+L+++++eL+
  gi|242399778|ref|YP_002995203.1| 258 FEGLA---DELRKEKEELEKKIKELT 280
                                       77778...9****************8 PP

  == domain 5  score: 2.6 bits;  conditional E-value: 0.58
                              HALZ  24 LkkenekLkaelqeLk 39 
                                       L +en++Lk+ ++eL 
  gi|242399778|ref|YP_002995203.1| 279 LTRENNELKQRIEELE 294
                                       889**********996 PP

  == domain 6  score: 2.2 bits;  conditional E-value: 0.76
                              HALZ  11 KasYdaLksdydsLkkenekL 31 
                                       K ++++L+ + + +k e ekL
  gi|242399778|ref|YP_002995203.1| 297 KIRFENLRDKIEKIKMELEKL 317
                                       445666666666666666665 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.2       1.9   5.2e+02      32      72 ..      81     120 ..      78     121 .. 0.71
   2 ?    8.8   8.6    0.0071         2      33      93 ..     129     188 ..     126     191 .. 0.69
   3 ?    3.9  13.6      0.23        65      41      96 .]     218     277 ..     181     277 .. 0.49
   4 ?   11.3  12.9    0.0012      0.33      11      92 ..     223     301 ..     213     303 .. 0.89
   5 ?    9.6   6.6     0.004       1.1      29      78 ..     269     318 ..     265     319 .] 0.87

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 1.9
                           BLOC1_2  32 asekykklkdvaaslekkleklnekyeelqpylqqidqiek 72 
                                       +++k  k +++a +l ++  +l + + +l+++++ i+ iek
  gi|242399778|ref|YP_002995203.1|  81 TIRKHLKGESKAGQLVRETYELIK-QGKLDELIKTIEMIEK 120
                                       555666666677777777777665.7899999999999986 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0071
                           BLOC1_2  33 sekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeLEa 93 
                                        e+y+kl ++ ++l+ + ek++++ e++++ ++ ++ +ek + ++e + +eL++   eLE+
  gi|242399778|ref|YP_002995203.1| 129 KEEYEKLMQEYENLKLEYEKVKAELEKMKQTVD-LESLEKAIGKIERLRKELEAVKAELEK 188
                                       577888888888888888888885555444443.567888888888888888877777775 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.23
                           BLOC1_2  41 dvaaslekkleklnekyeelqpylqqid....qiekqvteLeeavseLDeyskeLEakfk 96 
                                       +++++le+kl++ +e+   l+ +++++     ++ek+v+e+e +++eL +   eLE+k+k
  gi|242399778|ref|YP_002995203.1| 218 TKVKELEEKLKAKEEELSRLERLVDEVTreklELEKKVEEFEGLADELRKEKEELEKKIK 277
                                       234444444444444444444444444322225777777888888777777777777775 PP

  == domain 4  score: 11.3 bits;  conditional E-value: 0.0012
                           BLOC1_2  11 leaeleatvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDey 87 
                                       le++l+a  e+++ Le+l  +++++  +l+++++++e  +++l++++eel+   ++i+++ ++ +eL++ ++eL++y
  gi|242399778|ref|YP_002995203.1| 223 LEEKLKAKEEELSRLERLVDEVTREKLELEKKVEEFEGLADELRKEKEELE---KKIKELTRENNELKQRIEELETY 296
                                       7899*****************************************777776...67888889999999999999999 PP

                           BLOC1_2  88 skeLE 92 
                                         + E
  gi|242399778|ref|YP_002995203.1| 297 KIRFE 301
                                       88877 PP

  == domain 5  score: 9.6 bits;  conditional E-value: 0.004
                           BLOC1_2  29 NeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLe 78 
                                        e+ ++k+k+l+++ ++l++ +e+l+  +  ++++ ++i++i+ ++++L 
  gi|242399778|ref|YP_002995203.1| 269 KEELEKKIKELTRENNELKQRIEELETYKIRFENLRDKIEKIKMELEKLL 318
                                       5677899999***************99999************99999985 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   1.9    0.0059       1.7      33      98 ..      90     158 ..      68     161 .. 0.80
   2 ?    3.8  11.3      0.27        76       7      81 ..     164     260 ..     159     277 .. 0.54
   3 ?    7.6   2.5     0.018       4.9       2      46 ..     273     318 ..     272     319 .] 0.92

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0059
                        Syntaxin_2  33 eklhelieeinelikkt..nellkklsqldnsssds.qqklqkekLkkdfkealqeFqkiqrqyaekek 98 
                                       +k+ +l+ e+ elik+    el+k ++ +++ ++++   k + ekL+++++++  e++k+  + ++ ++
  gi|242399778|ref|YP_002995203.1|  90 SKAGQLVRETYELIKQGklDELIKTIEMIEKGGLKEvIAKEEYEKLMQEYENLKLEYEKVKAELEKMKQ 158
                                       6778999999999997654899999999999999777777799****************9988766554 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.27
                        Syntaxin_2   7 kinsnvstleklvkqLgtk........kdteelreklhelieeinel.ikkt.nellkklsqldnsssds....... 66 
                                       ++ + + ++e+l+k L+          k+++el+++l e + +i el +k++ + ++k+l++  + ++ +       
  gi|242399778|ref|YP_002995203.1| 164 SLEKAIGKIERLRKELEAVkaelektrKENKELKKELAEARVKIMELqSKRIeETKVKELEEKLKAKEEElsrlerl 240
                                       56666777777777777662222222345788887777777777776345555556666666544444324444444 PP

                        Syntaxin_2  67 .....qqklqkekLkkdfke 81 
                                            ++kl+ ek +++f+ 
  gi|242399778|ref|YP_002995203.1| 241 vdevtREKLELEKKVEEFEG 260
                                       44444455555555555554 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.018
                        Syntaxin_2   2 ssnlqkinsnvstleklvkqLgtkk.dteelreklhelieeineli 46 
                                       +++++++++ +++l++ ++ L+t k   e+lr+k++++  e+ +l+
  gi|242399778|ref|YP_002995203.1| 273 EKKIKELTRENNELKQRIEELETYKiRFENLRDKIEKIKMELEKLL 318
                                       789*********************978***********99998875 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 ?    8.5  25.7    0.0056       1.6       6     127 ..     118     237 ..     110     240 .. 0.84
   2 ?    5.4  13.2     0.053        15      20      97 ..     241     315 ..     237     319 .] 0.72

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0056
                        Phage_GP20   6 vmkaengkditkakldeveeerdtlkeqlkdrdkqLedLkkkakdneeLqkqieelqaknkkakaeyeakiadlkld 82 
                                       + k   +++i+k++++++ +e ++lk + ++   +Le++k+   d e+L+k+i +++   k+ +a  ++  + +k +
  gi|242399778|ref|YP_002995203.1| 118 IEKGGLKEVIAKEEYEKLMQEYENLKLEYEKVKAELEKMKQT-VDLESLEKAIGKIERLRKELEAVKAELEKTRKEN 193
                                       4466678899*****************************888.9*********999998888766555555667778 PP

                        Phage_GP20  83 naielaLkeakaknekavkalldkdklklkedgelkgLdeqikkL 127
                                       + ++++L ea++k  ++  + ++ +k+k  e+ +lk  +e+++ L
  gi|242399778|ref|YP_002995203.1| 194 KELKKELAEARVKIMELQSKRIEETKVKELEE-KLKAKEEELSRL 237
                                       89*********************999998665.888888888776 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.053
                        Phage_GP20  20 ldeveeerdtlkeqlkdrdkqLedLkkkakdneeLqkqieelqaknkkakaeyea.kiadlkldnaielaLkeakak 95 
                                       +dev+ e+ +l++++++ ++  ++L k+    eeL+k+i+el+ +n++ k+  e+ + +++ ++  ++  ++++k +
  gi|242399778|ref|YP_002995203.1| 241 VDEVTREKLELEKKVEEFEGLADELRKE---KEELEKKIKELTRENNELKQRIEElETYKIRFE-NLRDKIEKIKME 313
                                       6889999999999999999999999777...999999999999999998877765133333333.355556665555 PP

                        Phage_GP20  96 ne 97 
                                        e
  gi|242399778|ref|YP_002995203.1| 314 LE 315
                                       55 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3  27.5     0.022       6.2     289     441 ..      84     232 ..      68     233 .. 0.82
   2 ?    4.8  21.7      0.03       8.5     335     418 ..     215     299 ..     203     317 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.022
                              FapA 289 gkiivngrkgkivggnikalkevkakklGselgtkteiev.gldepelkeklkeleeeleeleeeleklkkkikklp 364
                                       ++++ +++ g++v +++++ k  k+ +l   + t   ie  gl+e  +ke++++l +e+e+l+ e ek+k++++k++
  gi|242399778|ref|YP_002995203.1|  84 KHLKGESKAGQLVRETYELIKQGKLDEL---IKTIEMIEKgGLKEVIAKEEYEKLMQEYENLKLEYEKVKAELEKMK 157
                                       4555455668888888888888887766...334444444488888899999********************99999 PP

                              FapA 365 klkaekqlesekkeqlkklletkeklkeeleeleeelkelkeeleskkeeakikvnkeiypgvkikigkkkliikre 441
                                       +  ++ +  ++   ++++l++++e+ k ele+ ++e kelk+el++  + ++ + +++   ++k+k  ++kl+ k+e
  gi|242399778|ref|YP_002995203.1| 158 Q-TVDLESLEKAIGKIERLRKELEAVKAELEKTRKENKELKKELAEA-RVKIMELQSKRIEETKVKELEEKLKAKEE 232
                                       9.777778899999*********************************.89999999999999999999998888876 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.03
                              FapA 335 lkekl.keleeeleeleeeleklkkkikklpklka.ekqlesekkeqlkklletkeklkeeleeleeelkelkeele 409
                                       + e   kelee+l++ eeel +l++ ++++  +k   ++  +e++   ++l+++ke+l+++++el++e +elk+++e
  gi|242399778|ref|YP_002995203.1| 215 IEETKvKELEEKLKAKEEELSRLERLVDEVTREKLeLEKKVEEFEGLADELRKEKEELEKKIKELTRENNELKQRIE 291
                                       3333359999999999********9999988877767777889999******************************* PP

                              FapA 410 skkeeakik 418
                                       +  e  ki+
  gi|242399778|ref|YP_002995203.1| 292 EL-ETYKIR 299
                                       99.444555 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   9.7     0.031       8.6     130     229 ..     109     217 ..      56     219 .. 0.62
   2 ?    7.4  14.2    0.0087       2.4     115     230 ..     188     308 ..     186     318 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.031
                           DUF4407 130 a..................ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakek 188
                                       +                  +++e+++l ++ ++l+ e+++ +a+l++ +++++ e   +   +           ++ 
  gi|242399778|ref|YP_002995203.1| 109 DeliktiemiekgglkeviAKEEYEKLMQEYENLKLEYEKVKAELEKMKQTVDLESLEKAIGK----------IERL 175
                                       033334444455566666778888888888888888888888888888888887766433222..........3344 PP

                           DUF4407 189 kaqldaaqaelaelkakld.atarlaalraelaeleaerake 229
                                       +++l+a +ael++ +++ +  +++la++r ++ el+++r++e
  gi|242399778|ref|YP_002995203.1| 176 RKELEAVKAELEKTRKENKeLKKELAEARVKIMELQSKRIEE 217
                                       445555555555554444345556677777777776666655 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0087
                           DUF4407 115 eqqeeakelkeqlaaa.....ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtk...gtgttgvaGkgp 183
                                       + ++e+kelk++la+a       +  + +e+++++l+++++a+e++l++l++ ++ e++ +k    ++ +  +G  +
  gi|242399778|ref|YP_002995203.1| 188 KTRKENKELKKELAEArvkimELQSKRIEETKVKELEEKLKAKEEELSRLERLVD-EVTREKlelEKKVEEFEGLAD 263
                                       5667788888888877777763344455566777999999999999999999888.666666577556566677777 PP

                           DUF4407 184 aakekkaqldaaqaelaelkakldatarlaalraelaeleaeraker 230
                                       + ++ k++l+++ +el+  +++   ++r+++l++ + + e+ r+k++
  gi|242399778|ref|YP_002995203.1| 264 ELRKEKEELEKKIKELTRENNE--LKQRIEELETYKIRFENLRDKIE 308
                                       7777777777777777777777..77777777777777666666655 PP

>> DNA_topoisoIV  DNA gyrase/topoisomerase IV, subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3  23.7   2.6e-05    0.0072     273     416 ..      97     243 ..      58     253 .. 0.82
   2 ?   -0.6   4.8       1.7   4.8e+02     395     420 ..     264     289 ..     251     317 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.6e-05
                     DNA_topoisoIV 273 kvleklykktkLessisvnnlvlfdk.kpkyl..slkeilkeflevrlevyerrkeyllekleerleilegllkaln 346
                                       ++  +l+k+ kL + i++  ++   + k+ ++  + +++++e+ +++le+ + + e +  k + +le le+ + +++
  gi|242399778|ref|YP_002995203.1|  97 RETYELIKQGKLDELIKTIEMIEKGGlKEVIAkeEYEKLMQEYENLKLEYEKVKAELEKMKQTVDLESLEKAIGKIE 173
                                       33445889999999999999998888664443227899************999999999999999999999999999 PP

                     DNA_topoisoIV 347 kidevievirkskk.ekkakkeLieelseeqaeyllemrlrrLtkeeveklekeieelekeikelekllak 416
                                        +++ +e ++++++ ++k++keL +el e+   +++e++ +r+ +++v++le++++ +e+e+++le+l+++
  gi|242399778|ref|YP_002995203.1| 174 RLRKELEAVKAELEkTRKENKELKKELAEA-RVKIMELQSKRIEETKVKELEEKLKAKEEELSRLERLVDE 243
                                       ****9*******9999999**********9.778********************************99988 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.7
                     DNA_topoisoIV 395 klekeieelekeikelekllaklkkl 420
                                       +l+ke+eelek+ikel++  ++lk+ 
  gi|242399778|ref|YP_002995203.1| 264 ELRKEKEELEKKIKELTRENNELKQR 289
                                       45555555555555555554443322 PP

>> Retrotrans_gag  Retrotransposon gag protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.9      0.39   1.1e+02      26      79 ..     136     181 ..     123     209 .. 0.57
   2 ?    4.3   0.6      0.18        50      18      88 ..     210     277 ..     201     281 .. 0.70
   3 ?   12.0   2.1   0.00067      0.19      26      86 ..     255     317 ..     234     319 .] 0.80

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.39
                    Retrotrans_gag  26 sesWkdlkkaflktflpserkdqleeelsslrQ..gtesvreYvtrfktladqlde 79 
                                       ++ +++lk +          +++ ++el +++Q  + es+++++ + ++l+ +l+ 
  gi|242399778|ref|YP_002995203.1| 136 MQEYENLKLE----------YEKVKAELEKMKQtvDLESLEKAIGKIERLRKELEA 181
                                       3334444444..........555555566666654456666666666666665554 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.18
                    Retrotrans_gag  18 lvarsidasesWkdlkkaflktflpserkdqleeelsslrQgtesvreYvtrfktladqlde.vlteeakie 88 
                                       l++++i+  +  k+l+++++++ ++    ++le+   +++ ++  +++ v++f+ lad+l++ +++ e+ki+
  gi|242399778|ref|YP_002995203.1| 210 LQSKRIE-ETKVKELEEKLKAKEEE---LSRLERLVDEVTREKLELEKKVEEFEGLADELRKeKEELEKKIK 277
                                       5556666.36677777777777777...55555555588888999999999999999999976555566665 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 0.00067
                    Retrotrans_gag  26 sesWkdlkkaflktflp.serkdqleeelsslrQgtesvreYvtrfktladqlde.vlteeak 86 
                                       +e ++ l ++++k+ ++ +++ ++l++e  +l+Q+ e ++ Y  rf+ l+d++++ +++ e++
  gi|242399778|ref|YP_002995203.1| 255 VEEFEGLADELRKEKEElEKKIKELTRENNELKQRIEELETYKIRFENLRDKIEKiKMELEKL 317
                                       6789999999998877624567899999************************99877776655 PP

>> Bacillus_HBL  Bacillus haemolytic enterotoxin (HBL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   7.1      0.16        43      96     174 ..     128     200 ..      99     209 .. 0.49
   2 ?   11.2   5.9   0.00088      0.25      96     165 ..     226     295 ..     212     311 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.16
                      Bacillus_HBL  96 dkkdkaellellekLqeeiqqnqkevkqlikeLkklklklakdsknFktdv...deltsilagdsgvisqlqneied 169
                                        k++        ekL +e  + + e +++ +eL+k+k+ ++ +s  +++++   + l + l++ ++++++ ++e+++
  gi|242399778|ref|YP_002995203.1| 128 AKEEY-------EKLMQEYENLKLEYEKVKAELEKMKQTVDLES--LEKAIgkiERLRKELEAVKAELEKTRKENKE 195
                                       33333.......44444444444444444444444444333222..2222111244444444444444444444444 PP

                      Bacillus_HBL 170 lqgki 174
                                       l++++
  gi|242399778|ref|YP_002995203.1| 196 LKKEL 200
                                       44443 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00088
                      Bacillus_HBL  96 dkkdkaellellekLqeeiqqnqkevkqlikeLkklklklakdsknFktdvdeltsilagdsgvisqlqn 165
                                       + k+k+e l++le+L +e++  + e +++++e + l+++l k++++++++++elt   +  +  i++l+ 
  gi|242399778|ref|YP_002995203.1| 226 KLKAKEEELSRLERLVDEVTREKLELEKKVEEFEGLADELRKEKEELEKKIKELTRENNELKQRIEELET 295
                                       4589999999999999999999999999999999999999999999999999888776666666666543 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 ?    2.1   0.1      0.83   2.3e+02      53      79 ..     132     158 ..     127     164 .. 0.45
   2 ?    2.8   0.1      0.49   1.4e+02       6      33 ..     162     189 ..     157     213 .. 0.62
   3 ?    7.3   0.2      0.02       5.5      24      85 ..     231     294 ..     217     295 .. 0.69

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.83
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  53 feewkqaaqklvdaLeeisealkqaan 79 
                                       +e+++q+ ++l+ ++e++  +l++ ++
  gi|242399778|ref|YP_002995203.1| 132 YEKLMQEYENLKLEYEKVKAELEKMKQ 158
                                       444444444444444444444433333 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.49
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100   6 peelrqaaarfqkqaeeledelqrlkae 33 
                                        e l++a+ ++ + ++ele++ ++l+++
  gi|242399778|ref|YP_002995203.1| 162 LESLEKAIGKIERLRKELEAVKAELEKT 189
                                       5556666666666666666555555544 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.02
                                       HHHHHHHHHHHHHC.GCGCT.HHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  24 edelqrlkaevdal.qsgWs.GaaadafqaefeewkqaaqklvdaLeeisealkqaanafedaD 85 
                                       e+el+rl++ vd++ +++ +  +  ++f++  +e++++ ++l ++ +e++++ ++ +++ e+ +
  gi|242399778|ref|YP_002995203.1| 231 EEELSRLERLVDEVtREKLElEKKVEEFEGLADELRKEKEELEKKIKELTRENNELKQRIEELE 294
                                       6677777777777777777777777777777777777777777777777777777777666655 PP

>> HTH_40  Helix-turn-helix domain
   [No individual domains that satisfy reporting thresholds (although complete target did)]

>> TelA  Toxic anion resistance protein (TelA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4  23.8      0.23        65      49     188 ..     107     251 ..     104     256 .. 0.74
   2 ?   10.5   5.6   0.00082      0.23      96     149 ..     256     305 ..     251     318 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.23
                              TelA  49 lLseLvkelkeldpdelkee...kklgllplfkkaknkieklfakYekaeeqidkI.....vkeLek...gqdellk 114
                                       +L eL k+++ +++  lke    +        +k+ ++ e+l+ +Yek++++++k      +++Lek   + ++l+k
  gi|242399778|ref|YP_002995203.1| 107 KLDELIKTIEMIEKGGLKEViakE------EYEKLMQEYENLKLEYEKVKAELEKMkqtvdLESLEKaigKIERLRK 177
                                       689999999999999886656421......23456667777777777777777776221112344442212357888 PP

                              TelA 115 dnaaLdqlyeknleyfkeLekyiaaGekkleeldekllpeleakaeasgdpedaqalrdleealdrleqrvqDL 188
                                         +a + + ek+++  keL+k  a ++ k+ el++k ++e + k+ +++ +++ ++l+ le+++d++ +   +L
  gi|242399778|ref|YP_002995203.1| 178 ELEAVKAELEKTRKENKELKKELAEARVKIMELQSKRIEETKVKELEEKLKAKEEELSRLERLVDEVTREKLEL 251
                                       88888889999999999999999999*******************999999*************9998766555 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00082
                              TelA  96 eqidkIvkeLekgqdellkdnaaLdqlyeknleyfkeLekyiaaGekkleelde 149
                                       e+ + +++eL+k+++el k +++L ++ +++++ ++eLe y +  e+    l++
  gi|242399778|ref|YP_002995203.1| 256 EEFEGLADELRKEKEELEKKIKELTRENNELKQRIEELETYKIRFEN----LRD 305
                                       56678899*********************************887766....443 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   5.7     0.032         9      24      54 ..     129     159 ..     127     162 .. 0.85
   2 ?    5.2  18.9       0.1        29       9      66 ..     251     318 ..     250     319 .] 0.50

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.032
                              ZapB  24 qmeieeLkeeneelkeenreleeeneqlkee 54 
                                       ++e+e+L++e e+lk e +++++e+e++k++
  gi|242399778|ref|YP_002995203.1| 129 KEEYEKLMQEYENLKLEYEKVKAELEKMKQT 159
                                       6789999999999999999999999998875 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.1
                              ZapB   9 LEskiqkaidtitlLqmeieeLkeeneelkeenrele..........eeneqlkeereawqerlkkLL 66 
                                       LE+k+++     ++L++e eeL+++ +el++en+el+             e+l++  e+++  l+kLL
  gi|242399778|ref|YP_002995203.1| 251 LEKKVEEFEGLADELRKEKEELEKKIKELTRENNELKqrieeletykIRFENLRDKIEKIKMELEKLL 318
                                       55555555555555555555555555555555555552221111554445555577777777777776 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   9.8       1.6   4.5e+02      59      89 ..     128     158 ..      80     166 .. 0.54
   2 ?   11.0  24.7    0.0016      0.45      12      98 ..     130     214 ..     127     219 .. 0.86
   3 ?    1.8  31.9       1.1   3.1e+02      11      91 ..     220     297 ..     216     319 .] 0.66

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 1.6
                            APG6_N  59 lekeeeelleeLkelekereeleaelaalee 89 
                                        ++e e+l++e ++l+ e e+++ael++ ++
  gi|242399778|ref|YP_002995203.1| 128 AKEEYEKLMQEYENLKLEYEKVKAELEKMKQ 158
                                       3344444444444444444444444444443 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.0016
                            APG6_N  12 eeldkqleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaale 88 
                                       ee++k +++ e+ + +Ye+  ++l+k k++ +   e+le++  ++e+l+ke e+  +eL+++ ke++el++ela+++
  gi|242399778|ref|YP_002995203.1| 130 EEYEKLMQEYENLKLEYEKVKAELEKMKQTVD--LESLEKAIGKIERLRKELEAVKAELEKTRKENKELKKELAEAR 204
                                       67778888888888888888888888877755..6888999999********************************* PP

                            APG6_N  89 eelealeeee 98 
                                        +  +l+ + 
  gi|242399778|ref|YP_002995203.1| 205 VKIMELQSKR 214
                                       **99999875 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 1.1
                            APG6_N  11 leeldkqleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaal 87 
                                       ++el+++l++ e+e   +e+  +++++ek e e   +++ee e   ++l+ke+eel++++kel +e+ el++ +++l
  gi|242399778|ref|YP_002995203.1| 220 VKELEEKLKAKEEELSRLERLVDEVTREKLELE---KKVEEFEGLADELRKEKEELEKKIKELTRENNELKQRIEEL 293
                                       567788888888888888888888888866655...56666666677777777777777777777777777777766 PP

                            APG6_N  88 eeel 91 
                                       e  +
  gi|242399778|ref|YP_002995203.1| 294 ETYK 297
                                       6543 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   4.9      0.18        49      27      58 ..     128     159 ..     104     168 .. 0.74
   2 ?    8.8  12.4     0.009       2.5      10      75 ..     165     239 ..     159     244 .. 0.68
   3 ?    2.5  10.6      0.79   2.2e+02       8      66 ..     218     276 ..     210     279 .. 0.82
   4 ?    6.8  11.4     0.038        11       3      51 ..     248     296 ..     241     319 .] 0.48

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.18
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXX CS
                              YabA  27 lkeelaelleenaeLeleneklrerleeeekk 58 
                                        kee ++l++e ++L+le ek++ +le+ +++
  gi|242399778|ref|YP_002995203.1| 128 AKEEYEKLMQEYENLKLEYEKVKAELEKMKQT 159
                                       3889999****************999655544 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.009
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.........XXXXXXXXXXXXXXXXXXXXXXX CS
                              YabA  10 leeleeqleelleeleelkeelaelleenaeLeleneklrerl.........eeeekkekekkkelsegkenLar 75 
                                       le+   ++e+l +ele++k+el+++ +en+eL+ e  + r ++         e++ k+ +ek k+++e  + L+r
  gi|242399778|ref|YP_002995203.1| 165 LEKAIGKIERLRKELEAVKAELEKTRKENKELKKELAEARVKImelqskrieETKVKELEEKLKAKEEELSRLER 239
                                       4444456788999**********************9999988878877755433333334444444444455555 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.79
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXX CS
                              YabA   8 dkleeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekekkkel 66 
                                       +k++elee+l++  eel++l++ + e++ e  eLe   e++  + +e +k+++e +k++
  gi|242399778|ref|YP_002995203.1| 218 TKVKELEEKLKAKEEELSRLERLVDEVTREKLELEKKVEEFEGLADELRKEKEELEKKI 276
                                       5899******************************9998888877766666666655555 PP

  == domain 4  score: 6.8 bits;  conditional E-value: 0.038
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YabA   3 kkelfdkleeleeqleelleeleelkeelaelleenaeLeleneklrer 51 
                                       k el +k+ee+e   +el +e eel+++++el+ en+eL+   e+l + 
  gi|242399778|ref|YP_002995203.1| 248 KLELEKKVEEFEGLADELRKEKEELEKKIKELTRENNELKQRIEELETY 296
                                       3445555555555555555555555555555555555555544444332 PP

>> Flagellin_N  Bacterial flagellin N-terminal helical region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   1.6     0.029       8.1      49     122 ..     164     237 ..     148     243 .. 0.93
   2 ?    3.6   0.1      0.23        66      84     123 ..     272     311 ..     256     316 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.029
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-TTTS-SHHHHHHHHHHHHHHHHHHH CS
                       Flagellin_N  49 slrsqiaglsqlvrnnslgisrlqtaqgalselsdilqrlkelavaasndsnsdedrqslqaelqqLtdelnri 122
                                       sl+++i +++ l ++ + + + l+ +++  +el++ l + + +++  ++++ ++++ ++l+++l++  +el r+
  gi|242399778|ref|YP_002995203.1| 164 SLEKAIGKIERLRKELEAVKAELEKTRKENKELKKELAEARVKIMELQSKRIEETKVKELEEKLKAKEEELSRL 237
                                       79999*********************************************************999988888765 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.23
                                       HHHHHHHHHHHHT-TTTS-SHHHHHHHHHHHHHHHHHHHH CS
                       Flagellin_N  84 ilqrlkelavaasndsnsdedrqslqaelqqLtdelnria 123
                                         +++kel+  +++ ++  e+ ++++ ++++L+d++++i+
  gi|242399778|ref|YP_002995203.1| 272 LEKKIKELTRENNELKQRIEELETYKIRFENLRDKIEKIK 311
                                       3445999999999999999999999999999999999987 PP

>> Prp19  Prp19/Pso4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.7     0.037        10      13      38 ..     129     154 ..     124     160 .. 0.87
   2 ?   10.5   0.2    0.0017      0.47      10      40 ..     173     203 ..     169     204 .. 0.93
   3 ?    0.4   1.2       2.3   6.6e+02      18      66 ..     243     291 ..     232     293 .. 0.54

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.037
                                       HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             Prp19  13 qnEWDalmletfelrkqleqtrqeLs 38 
                                       ++E+++lm e  +l+ ++e+++ eL 
  gi|242399778|ref|YP_002995203.1| 129 KEEYEKLMQEYENLKLEYEKVKAELE 154
                                       57999999999999999999999985 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0017
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             Prp19  10 stlqnEWDalmletfelrkqleqtrqeLsqa 40 
                                       + l++E +a+  e+ ++rk+++++++eL++a
  gi|242399778|ref|YP_002995203.1| 173 ERLRKELEAVKAELEKTRKENKELKKELAEA 203
                                       689*************************987 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 2.3
                                       HHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHH CS
                             Prp19  18 almletfelrkqleqtrqeLsqaLY.qnDAAvrViArllkerdeareala 66 
                                       ++  e  el k++e+++  L++ L  +++   + i  l++e++e++++++
  gi|242399778|ref|YP_002995203.1| 243 EVTREKLELEKKVEEFE-GLADELRkEKEELEKKIKELTRENNELKQRIE 291
                                       55555555555555553.34444431233444556667777777776665 PP

>> PRKG1_interact  cGMP-dependent protein kinase interacting domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   3.5     0.035       9.8      10      40 ..     129     159 ..     126     169 .. 0.64
   2 ?    5.9  20.1     0.088        25      12      85 ..     171     246 ..     163     255 .. 0.62
   3 ?    6.3   9.5     0.063        18       7      43 ..     263     299 ..     257     316 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.035
                    PRKG1_interact  10 keenerLkreLeelekelselkseleklkqq 40 
                                       kee e+L++e e+l+ e +++k+elek+kq+
  gi|242399778|ref|YP_002995203.1| 129 KEEYEKLMQEYENLKLEYEKVKAELEKMKQT 159
                                       5666777777777777777777777776643 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.088
                    PRKG1_interact  12 enerLkreLeelekelselkseleklkqqrqe..svskrssllelekrerrslerkiseleeelkeleeLraenqr 85 
                                       + erL++eLe ++ el+++++e ++lk++  e      + ++  +e+++ ++le+k++  eeel  le+L  e  r
  gi|242399778|ref|YP_002995203.1| 171 KIERLRKELEAVKAELEKTRKENKELKKELAEarVKIMELQSKRIEETKVKELEEKLKAKEEELSRLERLVDEVTR 246
                                       5567777777777777777766666665522210122333445567777888888888888888888888766554 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.063
                    PRKG1_interact   7 eeekeenerLkreLeelekelselkseleklkqqrqe 43 
                                        e ++e+e+L ++++el++e +elk+++e+l++ + +
  gi|242399778|ref|YP_002995203.1| 263 DELRKEKEELEKKIKELTRENNELKQRIEELETYKIR 299
                                       67899*************************9866333 PP

>> THOC7  Tho complex subunit 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9  15.1   0.00018      0.05      31     102 ..     116     204 ..      67     206 .. 0.75
   2 ?   -0.1  21.3       3.7     1e+03      12     116 ..     216     315 ..     205     319 .] 0.74

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00018
                             THOC7  31 a............esteeeleqlkedllldfaafelsierlqll..akanerereryeaekeeie...seieavree 90 
                                       +            +++ e+l q +e+l+l++++ + ++e+++    +++ e+ + ++e++++e+e   +e+e++r+e
  gi|242399778|ref|YP_002995203.1| 116 EmiekgglkeviaKEEYEKLMQEYENLKLEYEKVKAELEKMKQTvdLESLEKAIGKIERLRKELEavkAELEKTRKE 192
                                       2555666666666677999********************66665115667775555555555555444********* PP

                             THOC7  91 ieelkaqLeear 102
                                       ++elk++L ear
  gi|242399778|ref|YP_002995203.1| 193 NKELKKELAEAR 204
                                       **********98 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 3.7
                             THOC7  12 eerplkrltkrllklltslaesteeeleqlkedllldfaafelsierlqllakanerereryeaekeeieseieavr 88 
                                       ee ++k l ++l +      e++ ++le+l ++++ + +++e  +e ++ la+  ++e+e++e++ +e+ +e  +++
  gi|242399778|ref|YP_002995203.1| 216 EETKVKELEEKLKA-K----EEELSRLERLVDEVTREKLELEKKVEEFEGLADELRKEKEELEKKIKELTRENNELK 287
                                       55555555555555.2....345889999999999999999999999999999999999999988888888888888 PP

                             THOC7  89 eeieelkaqLeearatranrkeydelae 116
                                       + ieel++   +  ++r+  +++  + e
  gi|242399778|ref|YP_002995203.1| 288 QRIEELETYKIRFENLRDKIEKIKMELE 315
                                       8888888777777777776666655555 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   5.8      0.42   1.2e+02     107     178 ..      71     157 ..      66     162 .. 0.50
   2 ?    5.1   9.8     0.066        18     102     147 ..     170     215 ..     161     222 .. 0.84
   3 ?   10.4  18.8    0.0015      0.43     101     178 ..     211     294 ..     206     304 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.42
                            DUF724 107 lleerkklekkieeeesekrkleeeidelekkilelerqlallk................ekkeaadkeiarlksea 167
                                       ++ e+ + e+ i+++ + ++k+ + ++e+ + i++ +  +  +k                e+ e+  +e  +lk e 
  gi|242399778|ref|YP_002995203.1|  71 IAGELGRTEQTIRKHLKGESKAGQLVRETYELIKQGKLDEL-IKtiemiekgglkeviakEEYEKLMQEYENLKLEY 146
                                       55666666777777777777777777766555554444442.22242222222112222255555555555555555 PP

                            DUF724 168 ekleeeledve 178
                                       ek++ ele+++
  gi|242399778|ref|YP_002995203.1| 147 EKVKAELEKMK 157
                                       55555555555 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.066
                            DUF724 102 deqtklleerkklekkieeeesekrkleeeidelekkilelerqla 147
                                        + ++l++e+++++ ++e+ ++e+++l++e++e   ki+el+ ++ 
  gi|242399778|ref|YP_002995203.1| 170 GKIERLRKELEAVKAELEKTRKENKELKKELAEARVKIMELQSKRI 215
                                       57789999**********************************9875 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.0015
                            DUF724 101 kdeqtklleerkklekkieeeesekrkleeeid.......elekkilelerqlallkekkeaadkeiarlkseaekl 170
                                       ++++ + +++ k+le+k++ +e+e ++le  +d       elekk+ e+e  ++ l+++ke+ +k+i++l  e+++l
  gi|242399778|ref|YP_002995203.1| 211 QSKRIE-ETKVKELEEKLKAKEEELSRLERLVDevtreklELEKKVEEFEGLADELRKEKEELEKKIKELTRENNEL 286
                                       444433.567899********************555555555555555555555555******************** PP

                            DUF724 171 eeeledve 178
                                       ++++e+ e
  gi|242399778|ref|YP_002995203.1| 287 KQRIEELE 294
                                       ***99887 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 ?   -0.9  30.3       6.3   1.8e+03      31     141 ..     111     232 ..     105     236 .. 0.67
   2 ?    9.8  24.7    0.0032      0.89      46     128 ..     224     306 ..     217     319 .] 0.77

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 6.3
                     Jnk-SapK_ap_N  31 vVkvLElLeslasrneeeeaeleelreeleqLeteyerekelrkrae........eeleeiedqweeerkelqekve 99 
                                       ++k+ E +e+   ++   ++e e+l +e e+L++eye+ k++ ++ +        e+ + + + +++e +++++++e
  gi|242399778|ref|YP_002995203.1| 111 LIKTIEMIEKGGLKEVIAKEEYEKLMQEYENLKLEYEKVKAELEKMKqtvdleslEKAIGKIERLRKELEAVKAELE 187
                                       57788888888888888899999999999999999999988777777688886775555555566777777777777 PP

                     Jnk-SapK_ap_N 100 qleeenrele.....lkaknaadqlsrleekeaelkkeysklheret 141
                                       ++++en+el+     +++k ++ q +r+ee++ ++ +e+ k+  +e+
  gi|242399778|ref|YP_002995203.1| 188 KTRKENKELKkelaeARVKIMELQSKRIEETKVKELEEKLKA--KEE 232
                                       888888888833333455555555555555555554444333..444 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0032
                     Jnk-SapK_ap_N  46 eeeeaeleelreeleqLeteyerekelrkraeeeleeiedqweeerkelqekveqleeenrelelkaknaadqlsrl 122
                                       ee+    ee    le+L  e +rek + +++ ee+e + d++++e++el++k+++l+ en+el+++++++++   r 
  gi|242399778|ref|YP_002995203.1| 224 EEKLKAKEEELSRLERLVDEVTREKLELEKKVEEFEGLADELRKEKEELEKKIKELTRENNELKQRIEELETYKIRF 300
                                       44444455666789**************************************************8888776655555 PP

                     Jnk-SapK_ap_N 123 eekeae 128
                                       e+  ++
  gi|242399778|ref|YP_002995203.1| 301 ENLRDK 306
                                       544443 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9  22.1     0.075        21     200     382 ..     128     307 ..     123     317 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.075
                          Prominin 200 lvqnyeelekhvsddLddagkhlgldladtlesnvlpaLaelerllenlkeakeqLeqvnklekeLrksgsqLrdgl 276
                                       ++++ye+l  +  ++L+   +++  +l++  +      L++le+ + ++++ +++Le+v++ +++ rk+ ++L++ l
  gi|242399778|ref|YP_002995203.1| 128 AKEEYEKLM-QEYENLKLEYEKVKAELEKMKQTV---DLESLEKAIGKIERLRKELEAVKAELEKTRKENKELKKEL 200
                                       556666666.555667777777777776665555...89999999999999999999999999999999999999** PP

                          Prominin 277 rgvkrdlnqalsnlCqseeCskilssleiekldtskcldqlpnvdevlealeevletnlssivkeglarlneipekv 353
                                        +++ ++ ++ s+ +++++ ++++++l++++ ++s+  + +++v+++  +le+   ++++ ++ e  ++ +e+++k+
  gi|242399778|ref|YP_002995203.1| 201 AEARVKIMELQSKRIEETKVKELEEKLKAKEEELSRLERLVDEVTREKLELEKK-VEEFEGLADELRKEKEELEKKI 276
                                       ****99999999999999999999999998888888889999999999999887.5689999999999999999999 PP

                          Prominin 354 knqtaevvp..dlkkalakgreqikklakki 382
                                       k+ t+e  +  + +++l++ +  +++l  ki
  gi|242399778|ref|YP_002995203.1| 277 KELTRENNElkQRIEELETYKIRFENLRDKI 307
                                       9888765322155555555555555555555 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7  21.6     0.071        20     346     469 ..     106     229 ..      59     238 .. 0.83
   2 ?    5.5  37.7     0.019       5.4     279     466 ..     130     296 ..      99     319 .] 0.41

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.071
                            AAA_13 346 aKrkepfksvelesvkaki.esikklvaeineliakhNekvanleeekeeakkklelhlveeleseldeykkkykkl 421
                                        K +e+ k++e+ +  +   + +k++ +++ +  ++     +++++e e++k+ + l  +e++  +++++ k+++++
  gi|242399778|ref|YP_002995203.1| 106 GKLDELIKTIEMIEKGGLKeVIAKEEYEKLMQEYENLKLEYEKVKAELEKMKQTVDLESLEKAIGKIERLRKELEAV 182
                                       47888888888766665552445667777777777777788899999999*************************** PP

                            AAA_13 422 ekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeeinkeLka 469
                                       ++++ek+ ke ke ++el++++ +i eL+ +   e+  ++e++++Lka
  gi|242399778|ref|YP_002995203.1| 183 KAELEKTRKENKELKKELAEARVKIMELQSKRI-EETKVKELEEKLKA 229
                                       ****************************98865.55679999999997 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.019
                            AAA_13 279 defeekqerLekliekveskkselleklkavsdeasensafeedkeelkaeaealeeq.....LkglqraleaKrke 350
                                       +e+e+ +++ e+                             + ++e++kae+e+++++     L+++  ++e+ rke
  gi|242399778|ref|YP_002995203.1| 130 EEYEKLMQEYEN----------------------------LKLEYEKVKAELEKMKQTvdlesLEKAIGKIERLRKE 178
                                       233333333333............................3333444444444444443322233333344444444 PP

                            AAA_13 351 pfk.svelesvkakiesikklvaeineliakhNekvanleeekeeakkklelhl..veeleseldeykkkykkleka 424
                                       + + ++ele++ ++ +++kk++ae+   i +   k  + e++++e+++kl++ +  +++le  +de ++++ +lek+
  gi|242399778|ref|YP_002995203.1| 179 LEAvKAELEKTRKENKELKKELAEARVKIMELQSKRIE-ETKVKELEEKLKAKEeeLSRLERLVDEVTREKLELEKK 254
                                       44334444444444444444444444444433222111.22333333333333222444444444444444444444 PP

                            AAA_13 425 ieklekelkeeeaelkkleeeikeLekqlrdekpaaeeinke 466
                                       +e+ e  ++e  +e+++le++ikeL ++ ++ k+ +ee++++
  gi|242399778|ref|YP_002995203.1| 255 VEEFEGLADELRKEKEELEKKIKELTRENNELKQRIEELETY 296
                                       444444444444444444444444444444444444444433 PP

>> HemX  HemX, putative uroporphyrinogen-III C-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   7.3     0.053        15      28     100 ..     137     211 ..     118     216 .. 0.55
   2 ?    6.7   5.1     0.014       3.9      35     101 ..     198     260 ..     192     264 .. 0.77
   3 ?    4.4   9.3     0.067        19      33      99 ..     244     310 ..     217     317 .. 0.56

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.053
                              HemX  28 qqvqeltaevaelqqqlaaleqqlaq..veaekeqkqeleerlqqlaeklealekeleqlqkqleelqqqlskvs 100
                                       q+ ++l+ e ++++ +l++++q+++   +e+   + ++l ++l++ + +le+++ke+++l+k+l+e + ++ +++
  gi|242399778|ref|YP_002995203.1| 137 QEYENLKLEYEKVKAELEKMKQTVDLesLEKAIGKIERLRKELEAVKAELEKTRKENKELKKELAEARVKIMELQ 211
                                       333344444455555555555554442233334455555566666666666666666666666666666555555 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.014
                              HemX  35 aevaelqqqlaaleqqlaqveaekeqkqeleerlqqlaeklealekeleqlqkqleelqqqlskvsg 101
                                       +e ae + ++ +l+++    + e+++ +elee+l++++e+l++le+++++ +++  el++++++ +g
  gi|242399778|ref|YP_002995203.1| 198 KELAEARVKIMELQSK----RIEETKVKELEEKLKAKEEELSRLERLVDEVTREKLELEKKVEEFEG 260
                                       3334444444444444....455899999*********************************99877 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.067
                              HemX  33 ltaevaelqqqlaaleqqlaqveaekeqkqeleerlqqlaeklealekeleqlqkqleelqqqlskv 99 
                                        t e+ el++++++ e  ++++++eke+ ++ +++l   +++l+++ +ele+++ + e+l+++++k+
  gi|242399778|ref|YP_002995203.1| 244 VTREKLELEKKVEEFEGLADELRKEKEELEKKIKELTRENNELKQRIEELETYKIRFENLRDKIEKI 310
                                       3333445555555555555555555555555556666666666666666666666666666666665 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   8.3     0.049        14      23      87 ..     133     194 ..     104     197 .. 0.88
   2 ?    4.7  10.2      0.14        40       9      80 ..     173     242 ..     168     251 .. 0.84
   3 ?   12.9   7.5   0.00041      0.12      11      82 ..     251     317 ..     247     319 .] 0.66

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.049
                   Snapin_Pallidin  23 kelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlqklkkRae 87 
                                       ++l q+ e L+ + ++ +++L++++++ +   l+ l++ + K+ +++k++++++  l+k++k  +
  gi|242399778|ref|YP_002995203.1| 133 EKLMQEYENLKLEYEKVKAELEKMKQTVD---LESLEKAIGKIERLRKELEAVKAELEKTRKENK 194
                                       56667777888889999999******999...**************************9998655 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.14
                   Snapin_Pallidin   9 ellepkldeldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlq 80 
                                       e l  +l++++++l+++r++ +eL+++l + + k+ el+        +++ke  +KL++ + ++s+l+  + 
  gi|242399778|ref|YP_002995203.1| 173 ERLRKELEAVKAELEKTRKENKELKKELAEARVKIMELQSKRI--EETKVKELEEKLKAKEEELSRLERLVD 242
                                       568899******************************9999888..447888889999988888888876665 PP

  == domain 3  score: 12.9 bits;  conditional E-value: 0.00041
                   Snapin_Pallidin  11 lepkldeldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlqkl 82 
                                       le k++e++    elr++ eeL +++++l+++ +el++  e     +l++y+ +  n++ ++++++  l+kl
  gi|242399778|ref|YP_002995203.1| 251 LEKKVEEFEGLADELRKEKEELEKKIKELTRENNELKQRIE-----ELETYKIRFENLRDKIEKIKMELEKL 317
                                       56677777777777777777777777777776665555444.....67777777777777776666666554 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 ?    4.6  17.8     0.076        21      36     150 ..      95     214 ..      90     219 .. 0.80
   2 ?    6.6  18.3     0.019       5.2      59     138 ..     213     292 ..     204     319 .] 0.81

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.076
                      HAUS-augmin3  36 LkksGkpiLegeaLeeaLktie...psdlkq.edvellevileeeeesleaLeqelqeLqkekal.klkrlnkLqvq 107
                                       L+++   + +  +L+e  ktie   ++ lk+  + e++e+ ++e e+ + ++e+   eL+k+k+   l+ l+k    
  gi|242399778|ref|YP_002995203.1|  95 LVRETYELIKQGKLDELIKTIEmieKGGLKEvIAKEEYEKLMQEYENLKLEYEKVKAELEKMKQTvDLESLEKAIGK 171
                                       55555556666779999999998865566657888889999999999999999999999999986257889999999 PP

                      HAUS-augmin3 108 aaslqqelrkleeeekeakkklkeaqeelraenaetnavLqql 150
                                       +  l +el+++++e ++++k++ke+++el+++  ++ ++ ++ 
  gi|242399778|ref|YP_002995203.1| 172 IERLRKELEAVKAELEKTRKENKELKKELAEARVKIMELQSKR 214
                                       9999999999999999999999999999999888876665555 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.019
                      HAUS-augmin3  59 sdlkqedvellevileeeeesleaLeqelqeLqkekalklkrlnkLqvqaaslqqelrkleeeekeakkklkeaqee 135
                                       ++ ++ +v++le+ l+++ee l  Le++++e  +ek  ++k+ ++ + +a +l +e+++le++ ke +++++e+++ 
  gi|242399778|ref|YP_002995203.1| 213 KRIEETKVKELEEKLKAKEEELSRLERLVDEVTREKLELEKKVEEFEGLADELRKEKEELEKKIKELTRENNELKQR 289
                                       44445688899999999999999999999999999999999999999999999999999999999988888888877 PP

                      HAUS-augmin3 136 lra 138
                                       +++
  gi|242399778|ref|YP_002995203.1| 290 IEE 292
                                       765 PP

>> Nnf1  Nnf1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   3.6     0.025       6.9      68     105 ..     123     160 ..      60     164 .. 0.88
   2 ?    8.5   4.3    0.0088       2.5      79     109 ..     174     204 ..     171     205 .. 0.92
   3 ?    3.3  16.3      0.38   1.1e+02      33     109 ..     232     294 ..     216     295 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.025
                                       TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              Nnf1  68 PeeliaahlapakkeeqeeLearlqeleaenaelaeev 105
                                        +e+ia   ++++++e e+L+ ++++++ae ++++++v
  gi|242399778|ref|YP_002995203.1| 123 LKEVIAKEEYEKLMQEYENLKLEYEKVKAELEKMKQTV 160
                                       68999999***************************998 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0088
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              Nnf1  79 akkeeqeeLearlqeleaenaelaeeveeqr 109
                                        +++e+e+ +a+l+++++en+el++e++e r
  gi|242399778|ref|YP_002995203.1| 174 RLRKELEAVKAELEKTRKENKELKKELAEAR 204
                                       57899**********************9976 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.38
                                       HHHHHHHHHHHHHHCCHH-T..........TTSSTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              Nnf1  33 ekLneLDdlieeAkerreegeeeasrpevpphtLpPeeliaahlapakkeeqeeLearlqeleaenaelaeeveeqr 109
                                       e+L+ L++l+ e ++++ e e++ ++                 la+++++e+eeLe++++el +en+el++++ee++
  gi|242399778|ref|YP_002995203.1| 232 EELSRLERLVDEVTREKLELEKKVEE--------------FEGLADELRKEKEELEKKIKELTRENNELKQRIEELE 294
                                       45666666666666666654333222..............3469999***************************986 PP

>> TolA_bind_tri  TolA binding protein trimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.9       1.5   4.2e+02      28      53 ..     133     158 ..     108     167 .. 0.73
   2 ?    6.8   0.9     0.025         7      34      66 ..     172     204 ..     162     213 .. 0.73
   3 ?    7.2   3.0     0.018       5.1       3      45 ..     217     259 ..     216     268 .. 0.88
   4 ?    8.0   8.8      0.01       2.9       3      64 ..     231     292 ..     229     295 .. 0.93
   5 ?    3.9   5.3       0.2        57       7      53 ..     270     319 .]     264     319 .] 0.82

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 1.5
                     TolA_bind_tri  28 ealqqelreLRGqiEelqyqleqlee 53 
                                       e+l qe   L+ + E+ + +le++++
  gi|242399778|ref|YP_002995203.1| 133 EKLMQEYENLKLEYEKVKAELEKMKQ 158
                                       55666666666666666666666655 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.025
                     TolA_bind_tri  34 lreLRGqiEelqyqleqleerQrdlYldlDerl 66 
                                       + +LR ++E  + +le++++  ++l ++l e  
  gi|242399778|ref|YP_002995203.1| 172 IERLRKELEAVKAELEKTRKENKELKKELAEAR 204
                                       677888888888888888888888888877654 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.018
                     TolA_bind_tri   3 edrvarLErilearsqlllelqqqlealqqelreLRGqiEelq 45 
                                       e++v++LE++l+a+++ l +l + +++  +e  eL  ++Ee++
  gi|242399778|ref|YP_002995203.1| 217 ETKVKELEEKLKAKEEELSRLERLVDEVTREKLELEKKVEEFE 259
                                       789999*******9999*****999999999999999999876 PP

  == domain 4  score: 8.0 bits;  conditional E-value: 0.01
                     TolA_bind_tri   3 edrvarLErilearsqlllelqqqlealqqelreLRGqiEelqyqleqleerQrdlYldlDe 64 
                                       e+ ++rLEr+++  ++  lel +++e+ +   +eLR + Eel+ ++++l +  ++l + ++e
  gi|242399778|ref|YP_002995203.1| 231 EEELSRLERLVDEVTREKLELEKKVEEFEGLADELRKEKEELEKKIKELTRENNELKQRIEE 292
                                       789***********************************************999999887765 PP

  == domain 5  score: 3.9 bits;  conditional E-value: 0.2
                     TolA_bind_tri   7 arLErilearsqlllelqqqlealqq...elreLRGqiEelqyqleqlee 53 
                                       ++LE++++  ++ + el q++e+l++       LR +iE+ + +le+l+e
  gi|242399778|ref|YP_002995203.1| 270 EELEKKIKELTRENNELKQRIEELETykiRFENLRDKIEKIKMELEKLLE 319
                                       67999999999999999999888876444789999999999999999875 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   2.4      0.28        79      61      93 ..     131     163 ..     124     182 .. 0.71
   2 ?    7.6  18.3     0.014       3.9      49     139 ..     166     254 ..     161     267 .. 0.74
   3 ?    3.3   9.9      0.29        82      73     115 ..     262     304 ..     245     318 .. 0.37

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.28
                              ADIP  61 tirkleaeierlqskierlktqleqlerelalv 93 
                                       + +kl  e+e+l+ ++e++k++le+ ++ ++l 
  gi|242399778|ref|YP_002995203.1| 131 EYEKLMQEYENLKLEYEKVKAELEKMKQTVDLE 163
                                       556777888888888888888888888888753 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.014
                              ADIP  49 drdleqreslnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqrlknal 125
                                       ++ +   e l ++++  +ae+e+ +++ + lk++l++ + ++  +q+k    e+k+k+le+klk + eel+rl++ +
  gi|242399778|ref|YP_002995203.1| 166 EKAIGKIERLRKELEAVKAELEKTRKENKELKKELAEARVKIMELQSKR-IEETKVKELEEKLKAKEEELSRLERLV 241
                                       5555556777888888888999999999999999998888888777764.45789********************99 PP

                              ADIP 126 qqiktqyahelkkk 139
                                       +++    + el kk
  gi|242399778|ref|YP_002995203.1| 242 DEVTR-EKLELEKK 254
                                       98743.23344444 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.29
                              ADIP  73 qskierlktqleqlerelalvqakerqlekklktleqklknek 115
                                         + ++ k++le++ +el+  +++++q   +l+t +    n++
  gi|242399778|ref|YP_002995203.1| 262 ADELRKEKEELEKKIKELTRENNELKQRIEELETYKIRFENLR 304
                                       2222233333333333333333333333333333333333333 PP

>> MbeD_MobD  MbeD/MobD like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.8      0.32        91      12      41 ..     132     161 ..     130     191 .. 0.75
   2 ?    8.2   2.5    0.0097       2.7       7      68 ..     232     293 ..     220     295 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.32
                         MbeD_MobD  12 lEqLQqdYeqrlqeWesafaelqrmfeltq 41 
                                        E+L q+Ye  + e+e   ael +m +   
  gi|242399778|ref|YP_002995203.1| 132 YEKLMQEYENLKLEYEKVKAELEKMKQTVD 161
                                       589999999999999999999999876544 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0097
                         MbeD_MobD   7 qLLsAlEqLQqdYeqrlqeWesafaelqrmfeltqrenaaLseqvtgLsqQVesLseqvrRl 68 
                                       + Ls lE L  + ++ + e e   +e+  + +  ++e+  L++++++L++  ++L ++++ l
  gi|242399778|ref|YP_002995203.1| 232 EELSRLERLVDEVTREKLELEKKVEEFEGLADELRKEKEELEKKIKELTRENNELKQRIEEL 293
                                       55999**************************************************9999866 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1  18.4      0.16        45       3      85 ..     131     237 ..     129     243 .. 0.50
   2 ?    8.3   9.5    0.0044       1.2       2      83 ..     232     315 ..     231     319 .] 0.73

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.16
                             TMPIT   3 eweelekefkeleetakeykqkleelsklq.....skcskeikkqkkrlkelksslkklkksvk............. 61 
                                       e e+l +e+++l+ + +++k++le++++       +k   +i++ +k+l+++k++l+k++k+ k             
  gi|242399778|ref|YP_002995203.1| 131 EYEKLMQEYENLKLEYEKVKAELEKMKQTVdleslEKAIGKIERLRKELEAVKAELEKTRKENKelkkelaearvki 207
                                       55566666666666666666666655544311111344455555666666666666665555443333333333333 PP

                             TMPIT  62 ......eeeeeeveelkeelkerkkvlkev 85 
                                             + ee++v+el+e+lk +++ l+++
  gi|242399778|ref|YP_002995203.1| 208 melqskRIEETKVKELEEKLKAKEEELSRL 237
                                       344444555666666666666666666555 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0044
                             TMPIT   2 eeweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk..eeeeeeveelkeelk 76 
                                       ee+++le+ ++e+  ++ e+++k+ee + l ++++ke ++ +k++kel+++ ++lk++++  e ++ ++e+l+++++
  gi|242399778|ref|YP_002995203.1| 232 EELSRLERLVDEVTREKLELEKKVEEFEGLADELRKEKEELEKKIKELTRENNELKQRIEelETYKIRFENLRDKIE 308
                                       67777777888888888888888888888888888888888888888888888888876644555667788888888 PP

                             TMPIT  77 erkkvlk 83 
                                       ++k+ l+
  gi|242399778|ref|YP_002995203.1| 309 KIKMELE 315
                                       8877665 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 ?   -0.6  26.9         2   5.6e+02      21     138 ..     129     242 ..      80     253 .. 0.65
   2 ?    4.0  20.8     0.076        21      24     109 ..     210     295 ..     208     318 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 2
                             Atg14  21 perlyelrerlaklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkei 97 
                                       +e +++l +++ +lk+e e +k ++ek+ ++ +      + +++   k+e+l+++ +  +++l++ ++  ++lkke+
  gi|242399778|ref|YP_002995203.1| 129 KEEYEKLMQEYENLKLEYEKVKAELEKMKQTVD-----LESLEKAIGKIERLRKELEAVKAELEKTRKENKELKKEL 200
                                       456777777788888888877777776655555.....444444455666666666666666666666666666666 PP

                             Atg14  98 eekkkklaklsdklkkRrsdleslqneleerrk..kqiaklqd 138
                                       +e++ k+ +l++k      + + l+++l+++++  + +++l+d
  gi|242399778|ref|YP_002995203.1| 201 AEARVKIMELQSKRI-EETKVKELEEKLKAKEEelSRLERLVD 242
                                       666666666666542.222234444444443331133444444 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.076
                             Atg14  24 lyelrerlaklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieek 100
                                       l ++r++ +k+k+  e lk k e++   ++ +++ +++   + +k+ee   l  +lr++++el++k+++l++e++e 
  gi|242399778|ref|YP_002995203.1| 210 LQSKRIEETKVKELEEKLKAKEEELSRLERLVDEVTREKLELEKKVEEFEGLADELRKEKEELEKKIKELTRENNEL 286
                                       66788888888888888888888888888888888888899999999999999999999999999999999999999 PP

                             Atg14 101 kkklaklsd 109
                                       k+++++l  
  gi|242399778|ref|YP_002995203.1| 287 KQRIEELET 295
                                       999988754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3838  (0.214067); expected 358.6 (0.02)
Passed bias filter:                      973  (0.0542696); expected 358.6 (0.02)
Passed Vit filter:                       359  (0.0200234); expected 17.9 (0.001)
Passed Fwd filter:                       218  (0.0121591); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              64  [number of targets reported over threshold]
# CPU time: 2.27u 0.43s 00:00:02.70 Elapsed: 00:00:00.69
# Mc/sec: 1391.49
//
Query:       gi|242399779|ref|YP_002995204.1|  [L=247]
Description: KaiC domain protein [Thermococcus sibiricus MM 739]
Scores for complete 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-91  305.9   0.0    1.7e-91  305.7   0.0    1.0  1  ATPase    KaiC
    1.3e-08   34.7   0.0    2.7e-08   33.6   0.0    1.5  1  AAA_25    AAA domain
    5.1e-08   32.0   0.0    7.4e-08   31.4   0.0    1.1  1  GvpD      GvpD gas vesicle protein
     0.0006   19.2   0.5     0.0048   16.2   0.1    2.1  2  Rad51     Rad51
     0.0074   15.4   0.0      0.012   14.7   0.0    1.3  1  T2SSE     Type II/IV secretion system protein
  ------ inclusion threshold ------
      0.019   15.3   0.5      0.042   14.2   0.3    1.8  1  AAA_19    AAA domain
       0.04   13.3   0.0      0.049   13.0   0.0    1.2  1  DnaB_C    DnaB-like helicase C terminal domain
      0.061   13.0   0.4       0.37   10.5   0.6    2.1  2  AAA_24    AAA domain
      0.075   13.4   0.1       0.17   12.3   0.0    1.6  1  AAA_16    AAA ATPase domain
       0.16   11.5   0.0        0.3   10.6   0.0    1.4  1  AAA_7     P-loop containing dynein motor region
       0.22   10.3   0.0       0.37    9.6   0.0    1.2  1  PPV_E1_C  Papillomavirus helicase


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 !  305.7   0.0     1e-94   1.7e-91       1     230 [.       5     237 ..       5     238 .. 0.98

  Alignments for each domain:
  == domain 1  score: 305.7 bits;  conditional E-value: 1e-94
                            ATPase   1 vktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekl 77 
                                       v+tgI+g+Deil+gGipe++vvl++G+pGtGKtif++qFl++g++  gepg++v++ee+++++r+n++++Gwd++ +
  gi|242399779|ref|YP_002995204.1|   5 VETGIPGMDEILHGGIPERNVVLLSGGPGTGKTIFSQQFLWNGLQM-GEPGIYVALEEHPVQVRQNMAQFGWDVKPY 80 
                                       78*****************************************776.****************************** PP

                            ATPase  78 eeegklaiidasesaeesaee......kdkedleelieelaeaikeikakrvviDsitglayeekeavaReilrqlv 148
                                       ee+g++a++da++ ++++++e      +d +d++e+i+ l++aik+i+a+rvv+Ds+t+l y++k+++aR+i+ ql+
  gi|242399779|ref|YP_002995204.1|  81 EEQGMFAMVDAFTAGIGKSKEyekyivHDLTDIREFIDVLRQAIKDINARRVVVDSVTTL-YINKPSLARSIILQLK 156
                                       *****************9999999**99********************************.**************** PP

                            ATPase 149 rvlkklgvTailvsekssseeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeIteegik 225
                                       rvl+++g+T+i+vs++s++e+++gg+gve+  vdg+i+Ldl+ei++el+R+l+++kmRgt+hs+++hpfeIt++gi+
  gi|242399779|ref|YP_002995204.1| 157 RVLAGTGCTSIFVSQISVGERGFGGPGVEH-GVDGIIRLDLDEIDGELKRSLIVWKMRGTSHSMRRHPFEITDKGIT 232
                                       ******************************.********************************************** PP

                            ATPase 226 vleek 230
                                       v+++k
  gi|242399779|ref|YP_002995204.1| 233 VYANK 237
                                       *9875 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.0   1.7e-11   2.7e-08      17     189 ..       7     172 ..       2     176 .. 0.78

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 1.7e-11
                            AAA_25  17 apppprrwlvkgllpagelallaGapgtGKttlaldlalava.tGkpwlgpvapeqgkVlyvsaEdsedelrrRlra 92 
                                       + +p  + +++g +p+  ++ll G pgtGKt +  +     +  G+           + +yv++E+   ++r+ +++
  gi|242399779|ref|YP_002995204.1|   7 TGIPGMDEILHGGIPERNVVLLSGGPGTGKTIFSQQFLWNGLqMGE-----------PGIYVALEEHPVQVRQNMAQ 72 
                                       667888999****************************999883344...........679***************** PP

                            AAA_25  93 vgeal.........rddarllvld......lagveslpLfakdrggtl.ltadvdaleaaieevegvrlvviDplsr 153
                                        g ++         +       +d      +++       + + ++ + + +++d l++ai++++ +r vv+D+++ 
  gi|242399779|ref|YP_002995204.1|  73 FGWDVkpyeeqgmfA------MVDaftagiGKS---KEYEKYIVHDLTdIREFIDVLRQAIKDIN-ARRVVVDSVTT 139
                                       **9987664444331......333444433222...222222333444499************86.*********** PP

                            AAA_25 154 alggdensnsdvgalvealeriarrtgaavllvhHv 189
                                       ++ +   + s +++++ +l+r+ + tg++ ++v + 
  gi|242399779|ref|YP_002995204.1| 140 LYIN---KPSLARSIILQLKRVLAGTGCTSIFVSQI 172
                                       9975...55699******************999876 PP

>> GvpD  GvpD gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.0   4.5e-11   7.4e-08      13     207 ..      26     228 ..      20     239 .. 0.76

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 4.5e-11
                              GvpD  13 llikGaPGtGktlftlrgl.dvlrresdvlyvstrvddetvseay......fsgeaeldktalldllkdpleldldv 82 
                                       +l+ G PGtGkt+f  ++l + l+  ++ +yv+       v +        ++   e    a++d +  +++   + 
  gi|242399779|ref|YP_002995204.1|  26 VLLSGGPGTGKTIFSQQFLwNGLQMGEPGIYVALEEHPVQVRQNMaqfgwdVKPYEEQGMFAMVDAFTAGIGKSKEY 102
                                       7899**************9678***********99888888776645444444444444555556665555555554 PP

                              GvpD  83 dvPiekldlesllefvdeiaaiatkliialdswelvyeylaerydsPed.iktvkndlvvlaresgvrlvlvletaa 158
                                       +  i   dl  + ef+d    +  + i  +++ ++v++ +++ y + ++  + +  +l  +  ++g   + v++   
  gi|242399779|ref|YP_002995204.1| 103 EKYI-VHDLTDIREFID----VLRQAIKDINARRVVVDSVTTLYINKPSlARSIILQLKRVLAGTGCTSIFVSQISV 174
                                       4444.456666667777....56677777888999*****9999555553778888888777788888887777777 PP

                              GvpD 159 nsr......leyivdGvvtlnvkeddrgrlrrdlrleklrGvrignrlqPftlad 207
                                        +r      +e+ vdG++ l++ e   g l+r+l + k+rG +   r +Pf ++d
  gi|242399779|ref|YP_002995204.1| 175 GERgfggpgVEHGVDGIIRLDLDEI-DGELKRSLIVWKMRGTSHSMRRHPFEITD 228
                                       6654444459************987.7************************9988 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1     3e-06    0.0048      18      56 ..       4      42 ..       1      51 [. 0.92
   2 ?    1.1   0.0      0.12   1.9e+02     119     145 ..     115     141 ..      93     159 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3e-06
                                      EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHH CS
                             Rad51 18 qlttGskklDelLgGGietgsiteifGefrsGktqlcht 56
                                      ++ tG   +De+L+GGi+  ++  + G  ++Gkt ++++
  gi|242399779|ref|YP_002995204.1|  4 RVETGIPGMDEILHGGIPERNVVLLSGGPGTGKTIFSQQ 42
                                      689*******************************99987 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.12
                                       HHHHHTHHHHHHS-EEEEEEETTTGGG CS
                             Rad51 119 ellqqaaallaedkfallivDsvtaly 145
                                       e+++ + + +++ + + ++vDsvt+ly
  gi|242399779|ref|YP_002995204.1| 115 EFIDVLRQAIKDINARRVVVDSVTTLY 141
                                       556666666777777889*******99 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   7.4e-06     0.012     117     147 ..      11      41 ..       3      64 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 7.4e-06
                             T2SSE 117 kiaevlrkavrerglilvsGgTgsGKttlly 147
                                        ++e+l+  + er ++l+sGg g+GKt++  
  gi|242399779|ref|YP_002995204.1|  11 GMDEILHGGIPERNVVLLSGGPGTGKTIFSQ 41 
                                       6899***********************9875 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.3   2.6e-05     0.042      10      27 ..      23      40 ..      16     161 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.6e-05
                            AAA_19 10 ekvllvtaGpGtGKTrvl 27
                                      ++v+l+ +GpGtGKT   
  gi|242399779|ref|YP_002995204.1| 23 RNVVLLSGGPGTGKTIFS 40
                                      6899***********765 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 ?   13.0   0.0     3e-05     0.049       2      75 ..       5      78 ..       4     175 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3e-05
                                      BXSSTHHHHHHCT.SBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHHHHHHHHHHHTXX CS
                                      xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C  2 lstgfkdLDklts.GlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeqlvqRllsseaeid 75
                                      ++tg   +D++++ G+ + +++++ + p++Gkt +  ++  n  +    p +++ le +  q+ q +     +++
  gi|242399779|ref|YP_002995204.1|  5 VETGIPGMDEILHgGIPERNVVLLSGGPGTGKTIFSQQFLWNGLQ-MGEPGIYVALEEHPVQVRQNMAQFGWDVK 78
                                      68999999998752688999******************9998775.45577778888888888888776655554 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.6   0.00022      0.37       4      77 ..      25     140 ..      22     144 .. 0.53
   2 ?   -3.3   0.0       3.9   6.4e+03     159     182 ..     183     206 ..     180     217 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00022
                            AAA_24   4 kiliyGpsgiGKTtlakel.......gpkplfidtekGlksldadkfpdie.......................... 47 
                                        +l+ G +g+GKT +  ++       g+  +++ +e+  + +++++    +                          
  gi|242399779|ref|YP_002995204.1|  25 VVLLSGGPGTGKTIFSQQFlwnglqmGEPGIYVALEE--HPVQVRQNMA-Qfgwdvkpyeeqgmfamvdaftagigk 98 
                                       78999**************888888755555554444..3333333322.124444444444333333333333334 PP

                            AAA_24  48 ..........swedfldevvelaaelady..ktlviDtidel 77 
                                                  ++d++++++ l+++ +d+  + +v+D+++ l
  gi|242399779|ref|YP_002995204.1|  99 skeyekyivhDLTDIREFIDVLRQAIKDInaRRVVVDSVTTL 140
                                       444444444455555555555533333331145777777765 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.9
                            AAA_24 159 elkeevDlvlranlkredkvgerv 182
                                        +++ vD ++r++l++ d++ +r 
  gi|242399779|ref|YP_002995204.1| 183 GVEHGVDGIIRLDLDEIDGELKRS 206
                                       577888889999888777555554 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0    0.0001      0.17      24      66 ..      21      69 ..      13     134 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0001
                            AAA_16 24 p..elvllsGesGvGKsslvrellr...alekdggif.lrgkcdqlesa 66
                                      p  ++vllsG +G+GK+   +++l    ++ + g+++ l+++ +q +++
  gi|242399779|ref|YP_002995204.1| 21 PerNVVLLSGGPGTGKTIFSQQFLWnglQMGEPGIYVaLEEHPVQVRQN 69
                                      24499*************9999995455666667777777777777444 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00018       0.3      30      55 ..      20      46 ..      12      55 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00018
                             AAA_7 30 lknkkpvllvGptGtGKtviikd.llk 55
                                      + +++ vll G  GtGKt+  ++ l +
  gi|242399779|ref|YP_002995204.1| 20 IPERNVVLLSGGPGTGKTIFSQQfLWN 46
                                      567788****************95555 PP

>> PPV_E1_C  Papillomavirus helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00023      0.37     254     282 ..      14      43 ..       8      49 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00023
                          PPV_E1_C 254 efLk.gvPkknclvllGppntGkslfamsl 282
                                       e L+ g+P +n+++l G p tGk++f++ +
  gi|242399779|ref|YP_002995204.1|  14 EILHgGIPERNVVLLSGGPGTGKTIFSQQF 43 
                                       5666269*******************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); expected 358.6 (0.02)
Passed bias filter:                      560  (0.0312343); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.65u 0.37s 00:00:01.02 Elapsed: 00:00:00.56
# Mc/sec: 1320.42
//
Query:       gi|242399780|ref|YP_002995205.1|  [L=166]
Description: hypothetical protein TSIB_1805 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.5e-16   60.4   0.1    2.2e-16   59.9   0.1    1.3  1  UPF0113    UPF0113 PUA domain
    1.1e-05   25.9   0.1      2e-05   25.1   0.1    1.5  1  UPF0113_N  UPF0113 Pre-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 !   59.9   0.1   2.4e-20   2.2e-16       2      76 .]      96     164 ..      95     164 .. 0.93

  Alignments for each domain:
  == domain 1  score: 59.9 bits;  conditional E-value: 2.4e-20
                           UPF0113   2 vvvkekaeklFLYGrdvlkesilkitesvkenqvvvVlnengeplGiGkirkdtkaspgkivvknlaDiGeYlRr 76 
                                       +++k+k + lF++G+dv k+++++++   k ++ +v+lne+g +lG+G i+     +++++++kn++DiGe++Rr
  gi|242399780|ref|YP_002995205.1|  96 AILKPKTAFLFTTGKDVPKNGVKEYS--WKGSKKLVILNEEGIILGLGLINP----KSNGKFIKNITDIGEFIRR 164
                                       589***********************..555567****************88....99****************7 PP

>> UPF0113_N  UPF0113 Pre-PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.1   2.2e-09     2e-05       1      82 []       6      83 ..       6      83 .. 0.88

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 2.2e-09
                         UPF0113_N  1 RklseeetrivfekLtkyigdnvkelld..rkdgtycfrlkkkrVyyvseellklaetikpenlisaGtclGkftk... 74
                                      R+ s +e ++++++ +k+ g+  +e++   +++         ++Vy+v+ e+++ +e++k++  + +Gt++G ++    
  gi|242399780|ref|YP_002995205.1|  6 RRASSWEFDLIMKEAEKF-GELKHEFFGivEGK--------FRDVYAVNGEVWRRIESLKIKP-YAFGTFVGTIKVdrn 74
                                      78899*************.99999999944444........*********************9.**********87777 PP

                         UPF0113_N 75 .tkkFrlsi 82
                                        +kF ++i
  gi|242399780|ref|YP_002995205.1| 75 lVEKFYPNI 83
                                      777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.37s 00:00:00.92 Elapsed: 00:00:00.55
# Mc/sec: 911.69
//
Query:       gi|242399781|ref|YP_002995206.1|  [L=171]
Description: hypothetical protein TSIB_1806 [Thermococcus sibiricus MM 739]
Scores for complete 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   54.9   0.2    1.6e-14   54.4   0.2    1.3  1  CxxCxxCC  Putative zinc- or iron-chelating domain
  ------ inclusion threshold ------
      0.033   13.8   0.0      0.043   13.4   0.0    1.2  1  SapC      SapC


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 !   54.4   0.2   1.8e-18   1.6e-14       1      84 [.      15     126 ..      15     127 .. 0.88

  Alignments for each domain:
  == domain 1  score: 54.4 bits;  conditional E-value: 1.8e-18
                          CxxCxxCC   1 eCkeCgaCCkelkvklteedlerlkaaevaeeeeeskkiak...........adgrCvfldeetklCkiYeeRpkic 66 
                                       eCk C +CC+ + ++lt+ d++++ a++ + +++   +++            +d  C+f d+et++Cki++  p+ic
  gi|242399781|ref|YP_002995206.1|  15 ECKFCLDCCRGRFIYLTISDIANIMAHGHDPQDFVLMTAEGgkirfflayreWDLGCIFHDPETGKCKIHSYNPLIC 91 
                                       6****************************99999999998899********************************** PP

                          CxxCxxCC  67 rlfpas.................ekeellaraetC 84 
                                       +++p++                  ++ +l+++e+C
  gi|242399781|ref|YP_002995206.1|  92 KIYPFMvshkplgiegeepfeykGENLWLYYDESC 126
                                       *****988877777777666666556666666666 PP

>> SapC  SapC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   4.8e-06     0.043      73     123 ..      79     139 ..      72     155 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.8e-06
                              SapC  73 gkw.earyiPafvrryPFvlg...........akeeeeelvlciDeesprvseeeGeaLFded 123
                                       gk    +y P++++ yPF+++            + + e+l l+ De++p++   eGe++ +++
  gi|242399781|ref|YP_002995206.1|  79 GKCkIHSYNPLICKIYPFMVShkplgiegeepFEYKGENLWLYYDESCPGI--GEGEKIIKKE 139
                                       5565679*************888888877665455566*************..6899887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       343  (0.019131); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.34s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 961.14
//
Query:       gi|242399782|ref|YP_002995207.1|  [L=593]
Description: Histone acetyltransferase Elp3 like protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-30  106.7   2.0    4.2e-29  102.1   0.1    3.4  3  Radical_SAM      Radical SAM superfamily
    2.9e-28   97.7   0.6    8.1e-28   96.3   0.6    1.8  1  Radical_SAM_C    Radical_SAM C-terminal domain
    2.1e-08   34.4   0.7    5.4e-08   33.1   0.3    2.0  2  Acetyltransf_1   Acetyltransferase (GNAT) family
    0.00016   21.6   0.1    0.00059   19.8   0.1    1.9  2  Acetyltransf_10  Acetyltransferase (GNAT) domain
     0.0093   16.4   0.1      0.019   15.4   0.1    1.6  1  Acetyltransf_7   Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1      0.11     4e+02      78     136 ..      17      72 ..       4      87 .. 0.71
   2 !  102.1   0.1   1.2e-32   4.2e-29       3     158 ..      90     319 ..      88     325 .. 0.96
   3 ?   -2.0   0.0       1.2   4.2e+03     112     112 ..     412     412 ..     353     469 .. 0.60

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.11
                                       EEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  78 iritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealek 136
                                       i  ++++ ++++ +++l r++      ++l+   ++++ +l+ m r++ +e+++e l+k
  gi|242399782|ref|YP_002995207.1|  17 IAKVIISGEIKD-KDQLNRFKVKIARKYHLSKLPTNSD-ILRVM-RKDQREKFKEFLKK 72 
                                       555555555554.7777777776677777777778888.*****.99*****9999986 PP

  == domain 2  score: 102.1 bits;  conditional E-value: 1.2e-32
                                       EESEESS--TTTSCCTT.................HHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGST CS
                                       xxxxxxxxxxxxxxxxx.................xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx RF
                       Radical_SAM   3 vtrgCnlrCsfCarpet.................vrregrgrslsveeileevkelkaekg.vkevilgggepllyp 61 
                                       ++++ ++rC++C+ + +                  ++ ++++ + + +++++ ++++ + + v+++i+gg  p ++ 
  gi|242399782|ref|YP_002995207.1|  90 PFPCPHGRCIYCPGGPSegspqsytgkepsalraLQNVYHPYLIMMNRLKQLYDIGH-DIDkVEVIIQGGTFPAVDL 165
                                       67888899************************************************6.5555*************** PP

                                       THHHHHHHHHHTC.......................................................CCTEEEEEE CS
                                       xxxxxxxxxxxxx.......................................................xxxxxxxxx RF
                       Radical_SAM  62 dfvellerlakla.......................................................vpgiritve 83 
                                       d++e+  ++a +a                                                       ++++r++  
  gi|242399782|ref|YP_002995207.1| 166 DYQEWFIKEAFKAmndfshfkdienleekirnavlfgdidkdplfkaawerthkkpyyyleeeqrkneKAKVRMVGL 242
                                       ***********99**************************************************************** PP

                                       ECSSCHG...HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSH CS
                                       xxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  84 tngtlpd...eeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGend 157
                                       t +t+pd   e++++r+l+lg++rv+lg++++ ++ + ++++rght+e++l+a+++l++ag+k ++++++glpG n+
  gi|242399782|ref|YP_002995207.1| 243 TIETRPDwamEKQIDRMLKLGTTRVELGVQTVFNF-IYERVKRGHTVEDTLRATQLLKDAGLKINYHMMPGLPGSNF 318
                                       ***********************************.****************************************9 PP

                                       H CS
                                       x RF
                       Radical_SAM 158 e 158
                                       e
  gi|242399782|ref|YP_002995207.1| 319 E 319
                                       8 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1.2
                                       S CS
                                       x RF
                       Radical_SAM 112 a 112
                                       +
  gi|242399782|ref|YP_002995207.1| 412 F 412
                                       1 PP

>> Radical_SAM_C  Radical_SAM C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.3   0.6   2.2e-31   8.1e-28       1      80 [.     336     415 ..     336     417 .. 0.98

  Alignments for each domain:
  == domain 1  score: 96.3 bits;  conditional E-value: 2.2e-31
                     Radical_SAM_C   1 pdgvKlypllvikgTeLaelyksgeykplsleeyvdlvadilellppdirvhRltgdipkelliagpwhknlrelie 77 
                                       pd++K yp+lv+k+T L+++yk+g+y+p+++ee+v+l+++++++lp+++rv+R+++dip +l+ ag++h+nl++l+ 
  gi|242399782|ref|YP_002995207.1| 336 PDMLKVYPTLVTKDTILYRWYKEGKYRPYTTEEAVELLVEVYKMLPKWVRVMRIQRDIPVQLVEAGVKHSNLGQLVF 412
                                       8**************************************************************************98 PP

                     Radical_SAM_C  78 krl 80 
                                       ++l
  gi|242399782|ref|YP_002995207.1| 413 NEL 415
                                       887 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       2.4   8.7e+03      82     102 ..     252     272 ..     250     276 .. 0.83
   2 !   33.1   0.3   1.5e-11   5.4e-08      24     117 .]     450     562 ..     404     562 .. 0.72

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.4
                                       HHHHHHHHHHTTESEEEEEEE CS
                    Acetyltransf_1  82 lealeerareegikkivlave 102
                                       +e+ ++r+++ g ++++l v+
  gi|242399782|ref|YP_002995207.1| 252 MEKQIDRMLKLGTTRVELGVQ 272
                                       888899999999999999876 PP

  == domain 2  score: 33.1 bits;  conditional E-value: 1.5e-11
                                       HHHHHHSTTC.EEEE...EEETTEEEEEEEEEEEET.......TSTTEEEEEEEEE.........SGGG..TTSSHH CS
                    Acetyltransf_1  24 feesfsleae.gllv...aeedgeliGfisllkipd.......ekggvayieslaV.........spey..rgkGlG 78 
                                       +e++ +  ++ ++++     +++ liGfi+l++  +       +  + a++++l+V         +p+y  +++G+G
  gi|242399782|ref|YP_002995207.1| 450 REDY-EASEGhEIFLsfeDVKNDILIGFIRLRIPSEkahrkeiNCCPSAIVRELHVygplvpiggKPKYewQHRGYG 525
                                       3333.2223324444233333466************66666663334555557777888888888777777****** PP

                                       HHHHHHHHHHHHHT.TESEEEEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  79 saLlealeeraree.gikkivlaveedndaairlYeklGF 117
                                       ++Ll ++e++a+ee   kk+ +    + ++ +++Y+k+G+
  gi|242399782|ref|YP_002995207.1| 526 RELLAEAERIAFEEfDRKKMLI---ISGVGVREYYRKFGY 562
                                       **************87788533...58999*****88**8 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.6   5.9e+03      31      49 ..     459     480 ..     444     487 .. 0.62
   2 !   19.8   0.1   1.6e-07   0.00059      62     111 ..     518     567 ..     516     572 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.6
                   Acetyltransf_10  31 alllvaeeg...gkivGvielr 49 
                                       + +++ +e+   + ++G+i+lr
  gi|242399782|ref|YP_002995207.1| 459 HEIFLSFEDvknDILIGFIRLR 480
                                       4444444433337788999885 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 1.6e-07
                   Acetyltransf_10  62 eyrgqGigkaLleaveeeaekdgikleltvnaspyavpfYeklGFkavge 111
                                       e++++G+g++Ll ++e+ a ++  ++++ + +    +++Y+k+G+++ g+
  gi|242399782|ref|YP_002995207.1| 518 EWQHRGYGRELLAEAERIAFEEFDRKKMLIISGVGVREYYRKFGYRKDGP 567
                                       79****************87777777********************9886 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   5.4e-06     0.019      35      76 .]     518     564 ..     458     564 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 5.4e-06
                                       GGTTSSHHHHHHHH......TT...SEEEEE.EEEETHHHHHHHHHHTTEEE CS
                    Acetyltransf_7  35 eyrgkGiGraLlea......ae...kgiile.qlelnaekaikfYeklGFee 76 
                                       e++ +G+Gr+Ll+       +e   k++ ++  +       +++Y+k+G+++
  gi|242399782|ref|YP_002995207.1| 518 EWQHRGYGRELLAEaeriafEEfdrKKMLIIsGV-----GVREYYRKFGYRK 564
                                       89**********8534433311322111122122.....3366*******85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (593 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       624  (0.0348039); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.70u 0.33s 00:00:01.03 Elapsed: 00:00:00.51
# Mc/sec: 3510.17
//
Query:       gi|242399783|ref|YP_002995208.1|  [L=252]
Description: hypothetical protein TSIB_1808 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.6e-58  196.7   0.0    5.7e-58  196.4   0.0    1.0  1  NIF3      NIF3 (NGG1p interacting factor 3)


Domain annotation for each model (and alignments):
>> NIF3  NIF3 (NGG1p interacting factor 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  196.4   0.0   3.2e-62   5.7e-58       1     243 [.       6     240 ..       6     242 .. 0.99

  Alignments for each domain:
  == domain 1  score: 196.4 bits;  conditional E-value: 3.2e-62
                              NIF3   1 eivevleelaplelaeswDnvGlqvgdpekevkkvllaldlteevleeAiekgadliithHPlifkplkrlteddyk 77 
                                       eiv++l+e++ ++ +++   +Glqv+  ++ev+k+++a+d++++++ +A + +ad++i+hH+li+++++ +++   +
  gi|242399783|ref|YP_002995208.1|   6 EIVNFLDEYLDINSFPDKSRNGLQVE-GKEEVEKIAFAIDACMDTFIKARAFDADMLIVHHGLIWGGIEYVRGL--V 79 
                                       69***********************6.999********************************************..* PP

                              NIF3  78 krllkkliknnislysaHtnlDaapg.Gvndwlakalglekieplepskeekkeeeeglgrigeleepvsleelakk 153
                                       +++lk l++n+++ly+aH++lD +p+ G+n +l k+lgle  ep+++++      +  +g   e++ep  l  +a+ 
  gi|242399783|ref|YP_002995208.1|  80 QKRLKFLLENELNLYAAHLPLDLHPEvGNNVQLLKLLGLEPKEPFGSYN------GLSIGYTSEFDEPKPLPLVAQI 150
                                       **********************************************998......89******************** PP

                              NIF3 154 lkkklglekvrvagdldkkvkkvaicaGsGaslieeakakgaDlliTGelkhhealdakekgiavidvgHyatErvf 230
                                       l +kl+ ++v++ +   +++k+va+++G G+  i ea++kg+Dl+iTGe+ h+++++ake  ++vi++gHya+E+++
  gi|242399783|ref|YP_002995208.1| 151 LVEKLKTDYVKAYEFGVEEIKRVAVVSGRGGFTIPEAIEKGVDLFITGEFLHDDYHTAKEGRLSVIAAGHYASETLG 227
                                       ***************************************************************************** PP

                              NIF3 231 lealaelLkeklk 243
                                       ++al+  L+ek++
  gi|242399783|ref|YP_002995208.1| 228 VKALMPVLREKFR 240
                                       **********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); 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 0.30s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1610.78
//
Query:       gi|242399784|ref|YP_002995209.1|  [L=450]
Description: hypothetical protein TSIB_1809 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.086   12.5   0.0        1.7    8.3   0.0    2.6  2  CRM1_repeat_2  CRM1 / Exportin repeat 2


Domain annotation for each model (and alignments):
>> CRM1_repeat_2  CRM1 / Exportin repeat 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0     0.021   3.8e+02      16      38 ..      54      74 ..      51      86 .. 0.79
   2 ?    8.3   0.0   9.4e-05       1.7      17      39 ..     145     166 ..     142     169 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.021
                     CRM1_repeat_2 16 lierMakPeEVliveneeGeivr 38
                                      +i+  ++P  V i e  +G  ++
  gi|242399784|ref|YP_002995209.1| 54 IISLNERPTSVTITE--NGTTIK 74
                                      788889*******98..555555 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 9.4e-05
                     CRM1_repeat_2  17 ierMakPeEVliveneeGeivre 39 
                                       i+ M kP+E li + e+G+i  e
  gi|242399784|ref|YP_002995209.1| 145 ITFMTKPKEMLIRT-ENGNILIE 166
                                       677*********77.***99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); 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: 0.63u 0.32s 00:00:00.95 Elapsed: 00:00:00.52
# Mc/sec: 2609.01
//
Query:       gi|242399785|ref|YP_002995210.1|  [L=163]
Description: hypothetical protein TSIB_1810 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); 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: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 985.85
//
Query:       gi|242399786|ref|YP_002995211.1|  [L=117]
Description: hypothetical protein TSIB_1811 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0071   16.5   0.0      0.014   15.5   0.0    1.5  1  MTES_1575  REase_MTES_1575
     0.0074   16.0   0.0     0.0091   15.7   0.0    1.2  1  MmcB-like  DNA repair protein MmcB-like
  ------ inclusion threshold ------
      0.029   13.5   0.2      0.054   12.6   0.1    1.4  2  LAP1C      Lamina-associated polypeptide 1C (LAP1C)


Domain annotation for each model (and alignments):
>> MTES_1575  REase_MTES_1575
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   2.4e-06     0.014      11      46 ..       5      41 ..       2      59 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.4e-06
                         MTES_1575 11 ergyk.vkpqvgvggfriDlvvedpgkyllaIecdgd 46
                                      e g++ vk+   ++g riDl++ ++++++laIe +  
  gi|242399786|ref|YP_002995211.1|  5 EMGFNaVKELSTIDGARIDLAILRENEKILAIEFENS 41
                                      67888566667799*******************9876 PP

>> MmcB-like  DNA repair protein MmcB-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.5e-06    0.0091      24      68 ..       2      46 ..       1      66 [. 0.86

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.5e-06
                         MmcB-like 24 llrelglaalpelsLasGrraDlvalskkgeiwiieikssveDfr 68
                                      +++e+g+ a++els   G r Dl  l ++++i  ie   s + ++
  gi|242399786|ref|YP_002995211.1|  2 MCEEMGFNAVKELSTIDGARIDLAILRENEKILAIEFENSYKWIK 46
                                      6899********************************999876555 PP

>> LAP1C  Lamina-associated polypeptide 1C (LAP1C)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0      0.42   2.5e+03     218     254 ..      34      69 ..      30      75 .. 0.74
   2 ?   12.6   0.1   9.1e-06     0.054     395     410 ..      93     108 ..      81     112 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.42
                                       XXXXXXXXXXXGGGXXBSCHHHHHHHHHHHHHHHHST CS
                             LAP1C 218 lllsvlsyysspaqqveknpAleaFlaqfkqLkdkfq 254
                                       l++++  +y++  q+v  n A++   + f++L   ++
  gi|242399786|ref|YP_002995211.1|  34 LAIEFENSYKWIKQRVLYN-AIKVHRDGFSRLWIVYP 69 
                                       5666667777777888888.89988888888877776 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 9.1e-06
                                       T--HHHHHHHHHHHHH CS
                             LAP1C 395 svglrEiEEkvRDlLk 410
                                        v ++E+EEkvRD+L 
  gi|242399786|ref|YP_002995211.1|  93 VVHPKEVEEKVRDFLA 108
                                       3689**********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.35s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 660.76
//
Query:       gi|242399787|ref|YP_002995212.1|  [L=911]
Description: Alanyl-tRNA synthetase [Thermococcus sibiricus MM 739]
Scores for complete 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-144  481.1   0.0   6.4e-144  480.5   0.0    1.3  1  tRNA-synt_2c  tRNA synthetases class II (A)
    1.8e-19   70.6   9.1    1.8e-19   70.6   9.1    1.9  2  DHHA1         DHHA1 domain
    5.4e-15   55.2   0.3    1.7e-14   53.6   0.3    1.9  1  tRNA_SAD      Threonyl and Alanyl tRNA synthetase second addi
  ------ inclusion threshold ------
       0.07   13.9   0.0       0.38   11.6   0.0    2.2  1  DUF4373       Domain of unknown function (DUF4373)


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 !  480.5   0.0  1.4e-147  6.4e-144       1     552 []      63     601 ..      63     601 .. 0.96

  Alignments for each domain:
  == domain 1  score: 480.5 bits;  conditional E-value: 1.4e-147
                                       HHHHHHHHHHHCTT-EEE----SS-SSSTTCSS--SGGGGGHHHHTTSSCGGSSSEEEEEEEEE-EETTEEGGGGTT CS
                      tRNA-synt_2c   1 eirekFldfFekkgHtvvksssvvpendptllfvnAgmaqfkpiflgkeakpklkravnsQkciRagGkhnDlenVG 77 
                                       e+re+Fl++Fe+k+H +vk+++v+p++++++l+v A++++f+p+++++ea+p+++++++sQ++iR++    D++nVG
  gi|242399787|ref|YP_002995212.1|  63 EMREAFLSYFERKNHGRVKRYPVLPRWRDDVLLVGASIMDFQPWVISGEADPPANPLTISQPSIRFT----DIDNVG 135
                                       89*****************************************************************....****** PP

                                       TSSS--SEEEEEEEEESS.....SS-HHHHHHHHHHHHHTTTT--GGGEEEEEETTEH..HHHHHHHHTTTTEGGGE CS
                      tRNA-synt_2c  78 ktarHhTfFeMlGnfsfg.....dYfkeeaiefawelltkelgldkerlyvtvfeedd..eaveiweklvgvpeeri 147
                                       +t+rH+T+FeM+++++f+     +Y+ +e++e+a+e++tk lg++ e+++++++++++  +a++++e l+++ e ++
  gi|242399787|ref|YP_002995212.1| 136 ITGRHFTIFEMMAHHAFNypgkpIYWMDETVEYAYEFFTKDLGMKGEDITFKENPWAGggNAGPAFEVLYRGLEVAT 212
                                       *********************************************************999***************** PP

                                       EEE-HHHHEEESSSS.............EEEEEEEEEEEECETTSHHCHCCCCTTCTCCHEEEEEEEEEEEEEESTT CS
                      tRNA-synt_2c 148 lrfgekdnfwemgdt.............gpcgpcseiyydrgeeigkrkaaseveadddrvleiwnlvfmqfnreed 211
                                       l+f   ++++ ++               +  +++ ++++++g e+ +++++++++a+d+ + +++  ++++++ + +
  gi|242399787|ref|YP_002995212.1| 213 LVF---MQYKLAPPDadpsqiveikgdkYVPMDTRVVDTGYGLERLVWMSQGTPTAYDAVLGYVVKPLKRMAGID-K 285
                                       ***...8888666555666677777766**********************************************9.9 PP

                                       SHEEEEEEEEEEEEEEHHHHHHHHTTHSSGGGSCCTHHHHHHHHHHHT--TCSTCCHHHHHHHHHHHHHHHHHHHHT CS
                      tRNA-synt_2c 212 gtlkpLpkksidtGmglerlvavLqevrsnydtdlfvpvieaieeisgatyedkdetdealrviaDHvralafalad 288
                                       ++ ++L+++s+ +Gm++++ + +L+ +r+ +++++ +   e+++ +++         +e +++iaDH++al+f+lad
  gi|242399787|ref|YP_002995212.1| 286 IDDRILMENSRLAGMFDIEDMGDLRVLRETVAKNVDMAPDELTRLVRP---------YELIYAIADHTKALTFMLAD 353
                                       *********************************************999.........699***************** PP

                                       T--SSSSHHHHHHHHHHHHHHHHHHHTT-SSTHHHHHHHHHHHHHTTTGCCHHCCHHHHHHHHHHHHHHHHCCHHHH CS
                      tRNA-synt_2c 289 GvvpsnegrgYvlRrllRravrhakkLglkekflaklvavvvevlgdvypelkekeekveeiieeEeerFakTlerG 365
                                       Gvvpsn+++gY++R+l+R+++rh+++Lgl+ + l+++va+++++l++++pe+ke+e+ v ++++ Ee ++a Tl+rG
  gi|242399787|ref|YP_002995212.1| 354 GVVPSNAKAGYLARLLIRKSIRHLRELGLQIP-LSEIVAMHIKELHKTFPEFKEMEDVVIDMVNVEERKYADTLDRG 429
                                       ********************************.******************************************** PP

                                       HHHHHHHHHHCCC..CSEEXHHHHHHHHHCHXXXHHHHHHHHHCTTXEEXHHHHHHHHHHHHHHHCCHHSXSSXXXX CS
                      tRNA-synt_2c 366 lklleelikklkk..kkelsgedafkLydtyGfPvdltkeiaeekglkvdiegfekameeqrerskkekkekklikk 440
                                       ++l++++i++lkk    el++e ++ +y+++G++++++keiae++g++v i++++++++++++++  +++e+k   +
  gi|242399787|ref|YP_002995212.1| 430 NDLVRREIERLKKqgVGELPLERLMLFYESHGLTPEIVKEIAEKEGMTVRIPDNFYSLVAKEAEKGIKEEEEK-KIV 505
                                       *************8889******************************************99999876655555.578 PP

                                       XXXXTTSHCHHCCTSTTTXXXXXXTSXXXXXXSEEEEEEEEEETTEEEESEEXXXXSSSSCSXXXEEEEESSEEEEE CS
                      tRNA-synt_2c 441 dvealkelkkteeflgyeeleaeakvlallkdkefveeveegeevgvvLdrTpfYaesGGqigDeGliekegaefrv 517
                                       d+e +++l++t++ l+yee     +++     kef ++v  + e++vvLd T+fY+e+GGq  D G +++    ++v
  gi|242399787|ref|YP_002995212.1| 506 DFELVQDLPDTRT-LYYEE-----PLM-----KEFDAKVVGIIEDWVVLDATAFYPEGGGQPCDLGELNG----VEV 567
                                       9**********99.9***9.....555.....9**********************************987....56* PP

                                       SEEEEETTEEEEEXSS.XSXXXTTSEEEEEEXHHH CS
                      tRNA-synt_2c 518 kdvqkakgvvlhkgkleegklkvgdkvkaevdeer 552
                                        dvqk+++++lhk+k   +k+k+   v++++++er
  gi|242399787|ref|YP_002995212.1| 568 LDVQKVGKIILHKVKEP-EKFKERGIVHGKINWER 601
                                       ***************97.9************9986 PP

>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       1.9   8.6e+03       9      36 ..     490     515 ..     489     537 .. 0.64
   2 !   70.6   9.1   3.9e-23   1.8e-19       4     138 .]     782     911 .]     779     911 .] 0.92

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.9
                                       HHHHHHHHCHHHHHHHHHHHHHHHTCEE CS
                             DHHA1   9 kelekeleelkealaklkaeellekaee 36 
                                       ke+ek +  ++e+++k+   el++++ +
  gi|242399787|ref|YP_002995212.1| 490 KEAEKGI--KEEEEKKIVDFELVQDLPD 515
                                       7899999..8888888777777665544 PP

  == domain 2  score: 70.6 bits;  conditional E-value: 3.9e-23
                                       HCHHHHHHHHHHHCHHHHHHHHHHHHHHHTCEEECTCEEEEEECHCCHHHHHHHHHHHHHHTHGBTTCEEEEEEEEC CS
                             DHHA1   4 lneerkelekeleelkealaklkaeellekaeevkgvkvlvaevgeewdagalgiaadklksklkkpvivfvakeeg 80 
                                       + ee+k+++ke+e+l+++lakl+  el++++e++ g   ++ +v  e + + l++aa klk+   + +++++++e +
  gi|242399787|ref|YP_002995212.1| 782 FFEEWKQARKEVEKLNKELAKLLVYELENRVEKI-GEIEFIGAV-VEGEIDHLREAALKLKK--SNRIVALISEESN 854
                                       689*******************************.888888888.899**************..9999999999988 PP

                                       TEEEEEEEESSHSS-HHHHHHHHHHHTTCCEEEE.TCEEEEEEEHCHHHHHHHHHHHHH CS
                             DHHA1  81 dkvkvsarskkdgvdagelakeaaaklgggGGGH.dlAaGagipaekleealealeeai 138
                                         v v ++    +++ag+l++ + +  gggGGG+ dlA+G  +++ k++eale+l++a+
  gi|242399787|ref|YP_002995212.1| 855 -AVVVTVGEDL-NYKAGDLIRIITRVAGGGGGGKkDLAQGKIKNILKAKEALEELKKAL 911
                                       .6666666655.*******************************************9985 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 !   53.6   0.3   3.7e-18   1.7e-14       1      43 [.     700     742 ..     700     743 .. 0.98

  Alignments for each domain:
  == domain 1  score: 53.6 bits;  conditional E-value: 3.7e-18
                                       EEEEEETT.EEEEESS---SBGGGC-SEEEECCECCCTCEEEE CS
                          tRNA_SAD   1 vrvvsiGdisvelCgGtHvpnTgeIgafkilseesiakglrRI 43 
                                       +rv  i d++v++CgGtH+p+Tg Ig +kil+ e+i++g+ RI
  gi|242399787|ref|YP_002995212.1| 700 IRVLNIKDWDVQACGGTHLPRTGLIGPIKILRTERIQDGVERI 742
                                       79****************************************9 PP

>> DUF4373  Domain of unknown function (DUF4373)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   8.4e-05      0.38      29      72 ..     463     506 ..     452     514 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.4e-05
                           DUF4373  29 yvkllekiykekgyyiewdeeqlllladkaklevdeeevkeive 72 
                                          ++++i++++g+++++ ++++ l+a++a+ +++eee k+iv+
  gi|242399787|ref|YP_002995212.1| 463 TPEIVKEIAEKEGMTVRIPDNFYSLVAKEAEKGIKEEEEKKIVD 506
                                       55799**************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (911 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       733  (0.0408835); expected 358.6 (0.02)
Passed bias filter:                      592  (0.0330191); 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: 0.84u 0.37s 00:00:01.21 Elapsed: 00:00:00.54
# Mc/sec: 5071.19
//
Query:       gi|242399788|ref|YP_002995213.1|  [L=50]
Description: hypothetical protein TSIB_1813 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.33s 00:00:00.78 Elapsed: 00:00:00.50
# Mc/sec: 298.39
//
Query:       gi|242399789|ref|YP_002995214.1|  [L=406]
Description: hypothetical protein TSIB_1814 [Thermococcus sibiricus MM 739]
Scores for complete 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-09   36.8   0.1      1e-08   35.8   0.1    1.5  1  Peptidase_C39_2  Peptidase_C39 like family
    0.00061   20.2   0.0     0.0014   19.0   0.0    1.7  1  Inhibitor_I69    Spi protease inhibitor
  ------ inclusion threshold ------
      0.032   13.9   0.0       0.07   12.9   0.0    1.5  1  HTH_ABP1_N       Fission yeast centromere protein N-terminal 


Domain annotation for each model (and alignments):
>> Peptidase_C39_2  Peptidase_C39 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8   0.1   1.8e-12     1e-08      11     144 .]     234     380 ..     219     380 .. 0.80

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 1.8e-12
                   Peptidase_C39_2  11 elpngCeptslamvlsyl....gkkvtqnelakelktns.......sgdpntgfvgnit.dksglgvynepivklae 75 
                                       e ++gC+p s +m+++y+      +++++ + + l++++       + +p++  +g    d+ ++++ +e iv+ + 
  gi|242399789|ref|YP_002995214.1| 234 EEWDGCAPISGSMIIAYYelqlQDDWNREAIIDILHHTMgtlngggTLAPQQVTAGIALfDEEYNQLLQEGIVSESI 310
                                       589***************8877668******9999999999999995555665555333577777777777777666 PP

                   Peptidase_C39_2  76 kyglkvsdtrgssieevkkeidagkPvvvsvttfkplndgeikftssgHlvvitGYde.kg..........krvyvn 141
                                       +   ++      s ++v++eid+++P+v+s++          +   +gH+v+++GY+  k+           +++v+
  gi|242399789|ref|YP_002995214.1| 311 SHEFSAYTDFYVSESDVIREIDDNQPFVLSMN----------YHWFNGHAVAVIGYTGwKYndggleyvelSYIIVH 377
                                       66666777789999*****************6..........55589**********96446678999999999999 PP

                   Peptidase_C39_2 142 DPa 144
                                       DP+
  gi|242399789|ref|YP_002995214.1| 378 DPN 380
                                       996 PP

>> Inhibitor_I69  Spi protease inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   2.3e-07    0.0014      44      78 ..      73     107 ..      34     122 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.3e-07
                     Inhibitor_I69  44 asepayYVfnygdgkGFvIVsaddrappiLaYsdt 78 
                                       +s   + Vf++g++ GF++Vsa +++pp+L +s+ 
  gi|242399789|ref|YP_002995214.1|  73 KSVYEFAVFKNGKNVGFILVSARKDMPPVLEFSKA 107
                                       5556688***********************88865 PP

>> HTH_ABP1_N  Fission yeast centromere protein N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.2e-05      0.07      32      55 ..     292     315 ..     283     321 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.2e-05
                        HTH_ABP1_N  32 WFeqeygqkisqstvSeiLSskYa 55 
                                        F +ey+q +++++vSe+ S+ ++
  gi|242399789|ref|YP_002995214.1| 292 LFDEEYNQLLQEGIVSESISHEFS 315
                                       599*******************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 2459.13
//
Query:       gi|242399790|ref|YP_002995215.1|  [L=283]
Description: hypothetical protein TSIB_1815 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.077   12.9   0.5      0.077   12.9   0.5    2.2  2  DUF2721          Protein of unknown function (DUF2721)
        4.2    7.0   7.2         11    5.7   0.3    2.2  2  DUF4131          Domain of unknown function (DUF4131)


Domain annotation for each model (and alignments):
>> DUF2721  Protein of unknown function (DUF2721)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.5   8.5e-06     0.077      47     108 ..       3      57 ..       1      77 [. 0.85
   2 ?   -0.6   0.2      0.13   1.1e+03     100     109 ..     125     134 ..      97     156 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.5e-06
                           DUF2721  47 eelakeiknlrrRarlirrailllvlsallvvlvvlllflsallsldlsllaailfvlalll 108
                                       +++++++++l++R++ +++ ++ll +s++++v v + l          ++l + +f++al++
  gi|242399790|ref|YP_002995215.1|   3 GQVQRQVSSLQQRCKPMKKNFVLLLVSFFFLVGVLFKLSD-------RTILFVPFFIFALVF 57 
                                       5799***************************999887654.......666677777777766 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.13
                           DUF2721 100 ilfvlallll 109
                                        +f++ +l+l
  gi|242399790|ref|YP_002995215.1| 125 TVFIVFVLFL 134
                                       2222222222 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   1.8    0.0035        31       8      46 ..      24      59 ..      18      69 .. 0.59
   2 ?    5.7   0.3    0.0012        11       4      45 ..      96     138 ..      94     154 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.0035
                           DUF4131  8 vllalllllllllllllrrrprrrvllllllllllallg 46
                                      vll++ +++l+  l+       r++l++ +++++l++++
  gi|242399790|ref|YP_002995215.1| 24 VLLLVSFFFLVGVLFK---LSDRTILFVPFFIFALVFSF 59
                                      4444444444444443...56666666666666666554 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0012
                           DUF4131   4 plalvllalllllllllllllrr.rprrrvllllllllllall 45 
                                       ++ ++++++++  +++  ++++  ++++r+ +++++l+l++++
  gi|242399790|ref|YP_002995215.1|  96 GWVAWIIGIFVPSIIFSHFVSKItQKSKRTVFIVFVLFLILTS 138
                                       5778999999999999999988786666666666666655544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       864  (0.0481901); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 1701.32
//
Query:       gi|242399791|ref|YP_002995216.1|  [L=264]
Description: Carbon-nitrogen hydrolase [Thermococcus sibiricus MM 739]
Scores for complete 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-55  188.2   0.0      2e-55  188.0   0.0    1.0  1  CN_hydrolase  Carbon-nitrogen hydrolase
  ------ inclusion threshold ------
        0.1   13.0   0.1       0.22   11.9   0.1    1.5  1  DUF2122       RecB-family nuclease (DUF2122)


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 !  188.0   0.0   2.2e-59     2e-55       2     257 ..       3     243 ..       2     246 .. 0.94

  Alignments for each domain:
  == domain 1  score: 188.0 bits;  conditional E-value: 2.2e-59
                                       EEEEEBB-STTHHHHHHHHHHHHHHHHHHTTESEEEEETTTTTBS..SSHHHHHHHHB.HSSSHHHHHHHHHHHHHT CS
                      CN_hydrolase   2 vAvvQlpqkaadleanlqklleliaeAarkgadLivlPElfitgy..keeahfleaAe.aglgetlallaalarkng 75 
                                       +  +Q+++k  dl anl+k+++li+ Aa+++a+LivlPElf++gy  + ++++ e A+   +get+++l++ a++++
  gi|242399791|ref|YP_002995216.1|   3 IGFIQMEPKLLDLNANLSKAETLIKDAAKQNAKLIVLPELFDVGYnfETKEEVEEIAQqIPDGETTQFLMEQAKEHD 79 
                                       6779*****************************************8855566666666778**************** PP

                                       EEEEEEEEEEECCTTEEEEEEEEEEEETTSEE.EEEEE-SS--EECTTSCECCGHHTSCS-SS.S-EEEETTEEEEE CS
                      CN_hydrolase  76 iavvigliereltngklqayntavlldldgkl.vgkyrKlhLfpgeprpptaverelfepgdg.ipvfdtpvgkiGa 150
                                       + +v+g++e++ ++gkl  yn+av++ + g   +gkyrK+hLf        ++e+  fepg+  + vf   ++k+G+
  gi|242399791|ref|YP_002995216.1|  80 MFIVAGTAEKD-EKGKL--YNSAVIVGPIGGGyIGKYRKIHLF--------YREKLFFEPGNLgFHVFNIGIAKVGI 145
                                       **********6.*****..********977767**********........9************************* PP

                                       EEGGGGGSHHHHHHHHHTT-SEEEEBH.GCCCTCHHHHHHHHHHHHHHHHHHTSEEEEEEBEEEHCETTEEEE--EE CS
                      CN_hydrolase 151 aiCyeigfpellralalkgaeilvnlserapvpksmgppqwellgraralengcfviaanqvggyeqlilwpvghSa 227
                                       +iC + +fpe++r+lalkga+i+         p ++  p+ + ++  r+len +f i an++g   + +l ++g S 
  gi|242399791|ref|YP_002995216.1| 146 MICFDWIFPEAMRTLALKGADIVAH-------PANLVLPYAPKAMPIRSLENRVFSITANRIGE--ERGLRFIGMSQ 213
                                       ***********************88.......558999999***********************..*********** PP

                                       EE-TTS-EEEECCSSSTEEEEEEEEHHHHH CS
                      CN_hydrolase 228 iidpdGrilaglgeeeegvliaeidladvr 257
                                       i +p+ +il +++e++e+v  +ei+ +++r
  gi|242399791|ref|YP_002995216.1| 214 INSPKAEILLRASENKEEVGLVEINVEKAR 243
                                       *************************98776 PP

>> DUF2122  RecB-family nuclease (DUF2122)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   2.5e-05      0.22      12      79 ..      26      95 ..      23     106 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.5e-05
                           DUF2122 12 lklalklgksllvlpdlkDalellk.pekvlllskee.geelleeeeleekgrvllvfsgadegfskkel 79
                                       k a k++++l+vlp+l D+   ++  e+v  + ++    e++++  ++ k++ ++++ g+ e+ +k +l
  gi|242399791|ref|YP_002995216.1| 26 IKDAAKQNAKLIVLPELFDVGYNFEtKEEVEEIAQQIpDGETTQFLMEQAKEHDMFIVAGTAEKDEKGKL 95
                                      57799**************966665156788888877777888888888889999888888777666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       696  (0.0388198); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.53
# Mc/sec: 1511.71
//
Query:       gi|242399792|ref|YP_002995217.1|  [L=39]
Description: hypothetical protein TSIB_1817 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      0.005   16.9  17.1      0.005   16.9  17.1    2.7  2  Ribosomal_L41  Ribosomal protein L41


Domain annotation for each model (and alignments):
>> Ribosomal_L41  Ribosomal protein L41
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.6  13.6         1   1.8e+04       4      11 ..       9      17 ..       3      17 .. 0.87
   2 !   16.9  17.1   2.8e-07     0.005       1      21 [.      16      36 ..      16      37 .. 0.94

  Alignments for each domain:
  == domain 1  score: -4.6 bits;  conditional E-value: 1
                     Ribosomal_L41  4 KWrKK.Rmr 11
                                      KW+KK Rmr
  gi|242399792|ref|YP_002995217.1|  9 KWKKKgRMR 17
                                      9****8887 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 2.8e-07
                     Ribosomal_L41  1 MraKWrKKRmrRLKrKRRKmR 21
                                      Mr KW KKR+rRLKr R K R
  gi|242399792|ref|YP_002995217.1| 16 MRWKWIKKRIRRLKRQRKKER 36
                                      9****************9966 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1233  (0.0687713); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); 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 0.35s 00:00:00.85 Elapsed: 00:00:00.53
# Mc/sec: 223.02
//
Query:       gi|242399793|ref|YP_002995218.1|  [L=219]
Description: Exonuclease SbcD like protein [Thermococcus sibiricus MM 739]
Scores for complete 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-10   39.9   0.1    9.1e-10   39.4   0.1    1.3  1  Metallophos    Calcineurin-like phosphoesterase
     0.0013   18.9   0.0      0.002   18.3   0.0    1.3  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 !   39.4   0.1     1e-13   9.1e-10       2     123 ..      20     129 ..      19     169 .. 0.81

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 1e-13
                                       EEEEEESBTB....TTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHH.HHHHHHH.TSEEEEEC- CS
                       Metallophos   2 rilvigDlHl....algggqlddllkllddllreekpdlvllaGDlvdrgdlekellel.laalvky.pipvylllG 72 
                                       + lv++D+H+    ++g     +++k+l d++++++pdl++++GD+ +  +l  ++ +l ++++ +    + ++++G
  gi|242399793|ref|YP_002995218.1|  20 KTLVLADPHIgfelSRGLRIRTRFEKFLADFIKSKNPDLLIILGDVKEPIGLGAFTKKLlIEFFSEIsEFKTVITKG 96 
                                       78************9999*************9999**************98888888884555555465667***** PP

                                       TTSCHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEEESE CS
                       Metallophos  73 NHegfeeellnkygylgifsepwrsdaevfnnlplaslgsgslkvlllhGg 123
                                       NH+g   ++++               +e f+n+ + ++    + +l+lhG+
  gi|242399793|ref|YP_002995218.1|  97 NHDG---KIEEI--------------TEAFDNIKITDYFLL-DGTLFLHGH 129
                                       ***4...44444..............777888888885554.578888888 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 !   18.3   0.0   2.3e-07     0.002       3     103 ..      21     134 ..      20     163 .. 0.60

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.3e-07
                     Metallophos_2   3 laiiSDlH.........snldaleavlea.lkevgvdaiihaGDleeeep........evleellela...pvlaVr 58 
                                        ++++D H         + + + e++l++ +k+ ++d++i +GD+  +ep        + l e+++     + ++ +
  gi|242399793|ref|YP_002995218.1|  21 TLVLADPHigfelsrglRIRTRFEKFLADfIKSKNPDLLIILGDV--KEPiglgaftkKLLIEFFSEIsefKTVITK 95 
                                       57888888777777666555556666655267899*********8..555444655543333333333555666669 PP

                     Metallophos_2  59 GNnDeevveedvlreaaelgtdlpeeaelelagekvlliHgdpl..g 103
                                       GN+D         +e +e  ++++ ++ + l+g   l++Hg++l  g
  gi|242399793|ref|YP_002995218.1|  96 GNHD------GKIEEITEAFDNIKITDYFLLDG--TLFLHGHQLlpG 134
                                       ****......23333444444444223333345..899999976441 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       283  (0.0157845); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.50
# Mc/sec: 1316.61
//
Query:       gi|242399794|ref|YP_002995219.1|  [L=111]
Description: Transcription regulator, ArsR family [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.2e-11   42.0   1.4    7.2e-11   41.8   0.5    1.6  2  TrmB           Sugar-specific transcriptional regulator TrmB
    9.5e-06   25.6   0.7    9.5e-06   25.6   0.7    1.9  3  HTH_Mga        M protein trans-acting positive regulator (MGA
      2e-05   24.4   0.5      2e-05   24.4   0.5    1.7  2  HTH_11         HTH domain
    8.2e-05   22.1   1.3    0.00013   21.4   0.3    1.9  2  HTH_24         Winged helix-turn-helix DNA-binding
     0.0029   18.0   0.5     0.0053   17.1   0.1    1.7  2  FaeA           FaeA-like protein
     0.0077   16.4   0.0      0.035   14.3   0.0    1.9  2  PaaX           PaaX-like protein
     0.0081   15.9   0.2      0.014   15.2   0.2    1.4  1  HTH_IclR       IclR helix-turn-helix domain
     0.0083   16.2   0.1      0.018   15.1   0.1    1.5  1  HTH_20         Helix-turn-helix domain
     0.0089   15.9   4.1      0.057   13.3   1.7    2.1  2  TFIIE_alpha    TFIIE alpha subunit
     0.0096   15.6   0.3      0.021   14.6   0.3    1.5  1  HTH_DeoR       DeoR-like helix-turn-helix domain
     0.0097   15.7   0.1      0.016   15.0   0.1    1.4  1  HTH_23         Homeodomain-like domain
  ------ inclusion threshold ------
       0.01   15.3   0.9      0.018   14.6   0.0    1.8  2  GerE           Bacterial regulatory proteins, luxR family
      0.029   14.8   0.4      0.047   14.2   0.4    1.5  1  HTH_40         Helix-turn-helix domain
      0.041   13.5   0.5      0.097   12.3   0.5    1.8  1  GntR           Bacterial regulatory proteins, gntR family
      0.042   14.5   0.0      0.083   13.6   0.0    1.5  1  RPA_C          Replication protein A C terminal
      0.048   13.5   1.6      0.061   13.2   0.3    1.8  2  HTH_5          Bacterial regulatory protein, arsR family
      0.075   12.8   0.1       0.15   11.9   0.1    1.5  1  LexA_DNA_bind  LexA DNA binding domain
        1.2    9.2   7.3        4.3    7.4   0.6    3.4  3  HTH_36         Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.8   0.5   7.3e-14   7.2e-11       1      67 [.      12      83 ..       4      84 .. 0.96
   2 ?   -2.2   0.0       3.9   3.8e+03      22      34 ..      95     107 ..      86     109 .. 0.64

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 7.3e-14
                                      HHHCHHHHHCCCHCHHHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST....TTEEEE--H CS
                              TrmB  1 LqklGLseyEakvYlaLl.klgpatadeiaeelgvprskvYevLrsLedkGlVerekgr....pklYravdp 67
                                      L+ lG++++E ++Y+ Ll k+  + ++ei eelg+++ +v e + +L ++G+ +re  +     ++Y+av+p
  gi|242399794|ref|YP_002995219.1| 12 LKNLGFKKNELRIYQLLLeKNSAMHITEIKEELGISERSVREHVLNLYRRGVLKRELIQkgwlGYVYSAVSP 83
                                      789***************999***********************************988899999*****98 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.9
                                       CCHHCHHCCCTTS CS
                              TrmB  22 patadeiaeelgv 34 
                                        ++++e+ +el++
  gi|242399794|ref|YP_002995219.1|  95 VKKINELEKELKR 107
                                       4566677777666 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 !   25.6   0.7   9.5e-09   9.5e-06       5      42 ..      19      56 ..      18      59 .. 0.92
   2 ?   -3.0   0.0       7.8   7.8e+03      14      24 ..      68      77 ..      68      80 .. 0.78
   3 ?   -2.3   0.1       4.8   4.8e+03      24      29 ..      97     104 ..      85     106 .. 0.41

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 9.5e-09
                           HTH_Mga  5 krklkLlelLteneksltldelakeLglseltlqsdis 42
                                      k++l++  lL+e +++++++e+++eLg+se+++++ + 
  gi|242399794|ref|YP_002995219.1| 19 KNELRIYQLLLEKNSAMHITEIKEELGISERSVREHVL 56
                                      799******************************98765 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 7.8
                           HTH_Mga 14 Lteneksltld 24
                                      L++ +++l+++
  gi|242399794|ref|YP_002995219.1| 68 LIQ-KGWLGYV 77
                                      677.9999986 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 4.8
                           HTH_Mga  24 d..elake 29 
                                       +  el ke
  gi|242399794|ref|YP_002995219.1|  97 KinELEKE 104
                                       23355555 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.5     2e-08     2e-05       3      39 ..      22      58 ..      20      71 .. 0.90
   2 ?   -2.5   0.0       5.4   5.3e+03      35      42 ..      97     104 ..      93     108 .. 0.58

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 2e-08
                            HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaL 39
                                      l i++lLle+++ + + e++eeL++S+r vr ++  L
  gi|242399794|ref|YP_002995219.1| 22 LRIYQLLLEKNSAMHITEIKEELGISERSVREHVLNL 58
                                      78*****************************998666 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 5.4
                            HTH_11  35 dIkaLeel 42 
                                        I +Le+ 
  gi|242399794|ref|YP_002995219.1|  97 KINELEKE 104
                                       45555544 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.3   1.3e-07   0.00013       3      48 .]      19      65 ..      17      65 .. 0.91
   2 ?   -1.9   0.0       2.6   2.6e+03      39      46 ..      66      73 ..      66      74 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.3e-07
                            HTH_24  3 etdrkILelLqk.nprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      +++++I++lL + n+ + ++e+ e+lg+S   v++++ +L + G++k
  gi|242399794|ref|YP_002995219.1| 19 KNELRIYQLLLEkNSAMHITEIKEELGISERSVREHVLNLYRRGVLK 65
                                      6899***888886888***************************9986 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.6
                            HTH_24 39 krLeeeGl 46
                                      ++L+++G+
  gi|242399794|ref|YP_002995219.1| 66 RELIQKGW 73
                                      68999998 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   5.4e-06    0.0053      11      57 ..      30      76 ..      17      78 .. 0.86
   2 ?   -2.3   0.1         6     6e+03      41      49 ..      91      99 ..      86     108 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 5.4e-06
                                      H.S----HHHHHHHHTS-HHHHHHHHHHHHHHSSEEEE--SSSSS-E CS
                              FaeA 11 sikapckTreiAdalglsaYQaRyYLeqLekegkikrspvrrGvstl 57
                                      + +++ + +ei + lg+s   +R    +L + g +kr  + +G  ++
  gi|242399794|ref|YP_002995219.1| 30 EKNSAMHITEIKEELGISERSVREHVLNLYRRGVLKRELIQKGWLGY 76
                                      436778899*********************************97665 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 6
                                      HHSSEEEE- CS
                              FaeA 41 kegkikrsp 49
                                      +e ++k+ +
  gi|242399794|ref|YP_002995219.1| 91 RENMVKKIN 99
                                      456666654 PP

>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       1.5   1.5e+03      28      41 ..      10      23 ..       5      25 .. 0.82
   2 !   14.3   0.0   3.5e-05     0.035      27      56 ..      38      67 ..      31      79 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.5
                              PaaX 28 rllaelGiseslvR 41
                                       ll++lG++ + +R
  gi|242399794|ref|YP_002995219.1| 10 GLLKNLGFKKNELR 23
                                      6999****999888 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 3.5e-05
                              PaaX 27 irllaelGiseslvRaalsRlakaGwlvre 56
                                       ++ +elGise++vR  +  l ++G l+re
  gi|242399794|ref|YP_002995219.1| 38 TEIKEELGISERSVREHVLNLYRRGVLKRE 67
                                      57889**********************997 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.2   1.4e-05     0.014       7      50 ..      23      66 ..      21      68 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.4e-05
                                      HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR  7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      +i ++l e + ++ ++e+ +++g++  +v+ ++  L ++G +++
  gi|242399794|ref|YP_002995219.1| 23 RIYQLLLEKNSAMHITEIKEELGISERSVREHVLNLYRRGVLKR 66
                                      566789999*********************************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 !   15.1   0.1   1.8e-05     0.018      13      56 ..      22      66 ..      19      70 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.8e-05
                                      HHHHHHH.STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20 13 rrilraL.araegltaselaerldlskntlsyHLrvLeeagLvev 56
                                      +ri+++L   + ++  +e++e+l++s  +++ H+  L + g +++
  gi|242399794|ref|YP_002995219.1| 22 LRIYQLLlEKNSAMHITEIKEELGISERSVREHVLNLYRRGVLKR 66
                                      7999999999*************************9999999887 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1      0.08        80      31      45 ..       9      23 ..       6      31 .. 0.84
   2 !   13.3   1.7   5.7e-05     0.057      22     102 ..      29     107 ..      24     109 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.08
                                      HHHHHHHTS-HHHHH CS
                       TFIIE_alpha 31 edlakelkidlnelr 45
                                      e l k+l++++nelr
  gi|242399794|ref|YP_002995219.1|  9 EGLLKNLGFKKNELR 23
                                      6799**********9 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 5.7e-05
                                       HHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEE.TTTEEEEEEEE.EECCCHCCCHHHHHHHHHHHH CS
                       TFIIE_alpha  22 LlekgevteedlakelkidlnelrklLnrLyearlvkykrrrd.eekswykyywr.inyeklvdvvkrkleevvkkL 96 
                                       L +++ +   ++++el+i    +r+ + +Ly  ++ k    r+  +k+w  y +  + + +l+  +++ + + + +L
  gi|242399794|ref|YP_002995219.1|  29 LEKNSAMHITEIKEELGISERSVREHVLNLYRRGVLK----RElIQKGWLGYVYSaVSPAELLTKIRENMVKKINEL 101
                                       45678888899***********************986....444789999998853778888888888888888888 PP

                                       HHHHCC CS
                       TFIIE_alpha  97 eeklek 102
                                       e++l+ 
  gi|242399794|ref|YP_002995219.1| 102 EKELKR 107
                                       888765 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.3   2.1e-05     0.021       8      46 ..      28      66 ..      23      68 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.1e-05
                          HTH_DeoR  8 llkqqgklsveelvellgvSeaTiRRDLneLeeqglltR 46
                                      ll++   ++++e+ e+lg+Se  +R    +L   g+l+R
  gi|242399794|ref|YP_002995219.1| 28 LLEKNSAMHITEIKEELGISERSVREHVLNLYRRGVLKR 66
                                      5788889******************99999999999998 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   1.6e-05     0.016      16      43 ..      30      61 ..      18      67 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.6e-05
                            HTH_23 16 e...GlsvreIAreLgvsrrTvy.rwlkryre 43
                                      e    + ++eI +eLg+s+r v+ ++l+ yr+
  gi|242399794|ref|YP_002995219.1| 30 EknsAMHITEIKEELGISERSVReHVLNLYRR 61
                                      334577899**************999999963 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.8e-05     0.018      21      44 ..      38      61 ..      26      61 .. 0.92
   2 ?   -2.5   0.2       3.8   3.8e+03      38      46 ..      91      99 ..      90      99 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.8e-05
                                      HHHHHHHTS-HHHHHHHHHHHHHH CS
                              GerE 21 keIAeelniSekTVkvhksnimkK 44
                                      +eI eel+iSe++V+ h+ n++++
  gi|242399794|ref|YP_002995219.1| 38 TEIKEELGISERSVREHVLNLYRR 61
                                      6999*****************986 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.8
                                      HHHHHHHHT CS
                              GerE 38 ksnimkKLn 46
                                      ++n+ kK+n
  gi|242399794|ref|YP_002995219.1| 91 RENMVKKIN 99
                                      689999987 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.4   4.7e-05     0.047      11      63 ..      33      96 ..      20     110 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.7e-05
                            HTH_40 11 eglsieeIAkerglkesTIegHLaelieeg.............eeidlerlvseeeekeIeeaiek 63
                                      + + i eI +e g++e  + +H+++l++ g             +   ++ + ++e   +I+e + k
  gi|242399794|ref|YP_002995219.1| 33 SAMHITEIKEELGISERSVREHVLNLYRRGvlkreliqkgwlgY--VYSAVSPAELLTKIRENMVK 96
                                      457899***********************854443332222111..11222233555555444433 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.5   9.8e-05     0.097      13      57 ..      24      67 ..       3      73 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9.8e-05
                                      HHTTSS-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              GntR 13 IlsgelrpGdkLPsereLaaefgVsrttvReALrrLeaeglverr 57
                                      I +  l+ ++++    e+ +e+g+s  +vRe   +L ++g++ r+
  gi|242399794|ref|YP_002995219.1| 24 IYQLLLEKNSAM-HITEIKEELGISERSVREHVLNLYRRGVLKRE 67
                                      667778888999.999************************99885 PP

>> RPA_C  Replication protein A C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   8.4e-05     0.083      50      96 ..      20      63 ..       5      64 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.4e-05
                                      HHHHHHHHHHH.SXSTTTEEHHHHHHHSTSXHHHHHHHHHHHHHTTS CS
                             RPA_C 50 laqqvlnlikqspeseeGvhvdeiaqklrlsvndvkqavdeLsneGi 96
                                      ++ ++++l+ +   ++  +h+ ei+++l++s+++v++ v +L   G+
  gi|242399794|ref|YP_002995219.1| 20 NELRIYQLLLE---KNSAMHITEIKEELGISERSVREHVLNLYRRGV 63
                                      55566666655...8899**********************9999997 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.3   6.1e-05     0.061       6      45 ..      23      64 ..      19      66 .. 0.82
   2 ?   -1.8   0.1       2.9   2.9e+03      16      26 ..      96     106 ..      85     106 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.1e-05
                                      HHHHHHTT.SS.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5  6 kILklLae.ge.lcvcelaeelglsqstvShHLkkLreaGLV 45
                                      +I +lL e ++ + ++e+ eelg+s+  v++H   L+  G++
  gi|242399794|ref|YP_002995219.1| 23 RIYQLLLEkNSaMHITEIKEELGISERSVREHVLNLYRRGVL 64
                                      566677776555********************9888888876 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.9
                                       EEHHHHHHHHT CS
                             HTH_5  16 lcvcelaeelg 26 
                                       +++ el +el+
  gi|242399794|ref|YP_002995219.1|  96 KKINELEKELK 106
                                       77888888875 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00015      0.15      28      58 ..      37      66 ..      24      70 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00015
                                      HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE- CS
                     LexA_DNA_bind 28 ireiaralglkSpsaveehLkaLerKGyier 58
                                      i ei ++lg++  ++v eh   L r+G+++r
  gi|242399794|ref|YP_002995219.1| 37 ITEIKEELGIS-ERSVREHVLNLYRRGVLKR 66
                                      78********7.****************987 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1       1.2   1.2e+03      31      51 ..      11      31 ..       7      34 .. 0.75
   2 ?    7.4   0.6    0.0043       4.3      30      53 ..      39      62 ..      36      74 .. 0.81
   3 ?   -1.0   0.1       1.8   1.8e+03      39      51 ..      91     103 ..      84     104 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.2
                            HTH_36 31 lakrlglsknTvsraikeLeq 51
                                      l k+lg +kn  + +  +Le+
  gi|242399794|ref|YP_002995219.1| 11 LLKNLGFKKNELRIYQLLLEK 31
                                      557899999988777777776 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0043
                            HTH_36 30 tlakrlglsknTvsraikeLeqlG 53
                                       + + lg+s+++v+ ++ +L + G
  gi|242399794|ref|YP_002995219.1| 39 EIKEELGISERSVREHVLNLYRRG 62
                                      578889999999999999887777 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 1.8
                            HTH_36  39 knTvsraikeLeq 51 
                                       ++  ++ i+eLe+
  gi|242399794|ref|YP_002995219.1|  91 RENMVKKINELEK 103
                                       5667899999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1020  (0.0568911); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.48u 0.37s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 657.42
//
Query:       gi|242399795|ref|YP_002995220.1|  [L=561]
Description: leucine aminopeptidase [Thermococcus sibiricus MM 739]
Scores for complete 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-19   68.0   0.0    1.7e-18   67.1   0.0    1.5  1  Peptidase_M28  Peptidase family M28
    2.7e-10   39.6   0.0      5e-09   35.4   0.0    2.2  2  DUF4910        Domain of unknown function (DUF4910)
     0.0018   18.3   0.0     0.0043   17.1   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 !   67.1   0.0   2.8e-22   1.7e-18      12     196 ..     226     412 ..     219     414 .. 0.79

  Alignments for each domain:
  == domain 1  score: 67.1 bits;  conditional E-value: 2.8e-22
                                       SEEEEEEEE--B-TTTTCCT---TTTTHHHHHHHHHHHHHCHHGGCCSSEEEEEEEESSCSGSSHHHHHHHHHHC.C CS
                     Peptidase_M28  12 devlllgAHyDsvgvgrgpifvGAdDnAsgvaalLelarvlaasgsrpkrgvrflffdaEEagllGSkafakakp.e 87 
                                       + ++l++AH+ +      p   GA+DnAsg+a+l+elar+l++ +     +  f+f+   E   +G +af+ +++  
  gi|242399795|ref|YP_002995220.1| 226 PPYILFTAHMCHPK----P---GANDNASGAAMLIELARILKE-FYYDSFRFGFAFLWIPE--HYGTQAFI-ENWaR 291
                                       45899999997766....7...********************8.43346666666655556..69******.8888* PP

                                       CTTEEEEEEECS-SSSS--EEE............HHHHHHCHHHHHHHHHHHHHTT-TTSCCEEEEES.STT-STTH CS
                     Peptidase_M28  88 lkkiaavlnlDmvgsggkellf............esgdkssselekelkalakpvgraaaedpfders.grgrsDhs 151
                                       l+++ av+nlDmvg +++   +             + ++  + + + +++  + +g +  +++  ++  + + sDh 
  gi|242399795|ref|YP_002995220.1| 292 LEEYYAVINLDMVGGSEDRSGStimviktplsrfSIISGLLEYFINLANSGGESFGGSPLPKMKMKSYsYEMGSDHD 368
                                       **************99998888888999996555555555555555555666666665555333333247788**** PP

                                       HHHTTT--EEEECTSSS-TTTTSTTSSGGGB-HHHHHHHHHHHHH CS
                     Peptidase_M28 152 pflkagvpvldlaetgfpevyHtprDtldnidkdtlariaelvle 196
                                       +f+  g+p +    t+ ++ yH+++Dt+++i+kd+l+ i+++vl 
  gi|242399795|ref|YP_002995220.1| 369 VFNFFGIPSVMP-ITWPDKFYHSSEDTIEKISKDSLEIIGKAVLS 412
                                       **********99.99************************999986 PP

>> DUF4910  Domain of unknown function (DUF4910)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   0.0   8.4e-13     5e-09      70     147 ..     229     308 ..     218     315 .. 0.85
   2 ?    1.7   0.0     0.016        98     213     231 ..     387     405 ..     352     419 .. 0.73

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 8.4e-13
                                       EEEEEE----S.-TTTTHHHHHHHHHHHHHHTTS..--.SSEEEEEEE-TTHHHHHHHHH-GGGGGGEEEEEE--S- CS
                                       xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DUF4910  70 vllsahvChPs.landnlsGiavatalakalaer..kerrysyrllfvPetiGsitylsrneeklkkikaGlvltcv 143
                                       +l++ah+ChP   andn sG a+++ la+ l+e   ++ r+ + +l++Pe  G+ ++++ n  +l++  a + l +v
  gi|242399795|ref|YP_002995220.1| 229 ILFTAHMCHPKpGANDNASGAAMLIELARILKEFyyDSFRFGFAFLWIPEHYGTQAFIE-NWARLEEYYAVINLDMV 304
                                       99********7369*****************9752256799999************996.67788888888888888 PP

                                       -SSS CS
                                       xxxx RF
                           DUF4910 144 Gdeg 147
                                       G ++
  gi|242399795|ref|YP_002995220.1| 305 GGSE 308
                                       8765 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.016
                                       TTTBTTSSGGG--HHHHHH CS
                                       xxxxxxxxxxxxxxxxxxx RF
                           DUF4910 213 eYhtsaDnldfvkpealee 231
                                        Yh+s+D ++ +++++le 
  gi|242399795|ref|YP_002995220.1| 387 FYHSSEDTIEKISKDSLEI 405
                                       49************99985 PP

>> PA  PA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   7.1e-07    0.0043      17      89 .]     119     190 ..      93     190 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 7.1e-07
                                PA  17 adfegvdvkGkivLvqrtfaeKarnAqaaGAagviivndge...........lgaatgasgnegepdgitiPavgvs 82 
                                       ++   ++ k k+vL+ + + e ++ A ++GA g+i +++g+           +       + + e+    iPav +s
  gi|242399795|ref|YP_002995220.1| 119 DW---EKAKEKVVLIGEKWHENYKKANENGALGFIAYRKGSgkafpyiglflT-------KRDLEW--AKIPAVALS 183
                                       33...37899*****7799******************7666665655533322.......334456..999999999 PP

                                PA  83 redgeal 89 
                                        + ++++
  gi|242399795|ref|YP_002995220.1| 184 EDLANKI 190
                                       9998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (561 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.67u 0.36s 00:00:01.03 Elapsed: 00:00:00.54
# Mc/sec: 3143.59
//
Query:       gi|242399796|ref|YP_002995221.1|  [L=143]
Description: hypothetical protein TSIB_1821 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       770  (0.0429472); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); 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: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 805.96
//
Query:       gi|242399797|ref|YP_002995222.1|  [L=241]
Description: ATPase, RecA superfamily [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.5e-50  169.9   2.4    6.2e-50  169.7   2.4    1.0  1  ATPase     KaiC
    1.1e-06   28.1   0.0    1.3e-05   24.7   0.0    2.1  1  DnaB_C     DnaB-like helicase C terminal domain
    3.6e-06   26.7   0.0    2.5e-05   23.9   0.0    2.0  1  AAA_25     AAA domain
    4.3e-06   26.4   0.1    8.3e-06   25.5   0.1    1.4  1  RecA       recA bacterial DNA recombination protein
    5.4e-06   25.3   1.5      2e-05   23.4   1.5    1.7  1  GvpD       GvpD gas vesicle protein
    0.00024   21.4   0.0    0.00046   20.5   0.0    1.5  1  AAA_22     AAA domain
    0.00049   20.1   0.1     0.0012   18.9   0.1    1.6  1  AAA_14     AAA domain
    0.00059   19.2   0.0    0.00085   18.7   0.0    1.2  1  DUF2075    Uncharacterized conserved protein (DUF2075)
    0.00094   19.2   0.3     0.0014   18.6   0.2    1.3  1  ATPase_2   ATPase domain predominantly from Archaea
    0.00098   19.7   0.1     0.0023   18.4   0.1    1.7  1  AAA_18     AAA domain
      0.001   18.8   0.1     0.0027   17.5   0.0    1.7  1  AAA_24     AAA domain
     0.0018   17.6   0.3     0.0034   16.7   0.3    1.8  1  Rad51      Rad51
     0.0069   16.1   0.0      0.013   15.3   0.0    1.5  1  IstB_IS21  IstB-like ATP binding protein
     0.0088   15.6   0.4      0.011   15.3   0.4    1.5  1  cobW       CobW/HypB/UreG, nucleotide-binding domain
  ------ inclusion threshold ------
      0.013   14.7   3.5      0.033   13.3   0.3    2.3  3  PAXNEB     PAXNEB protein
      0.019   14.9   0.2      0.071   13.0   0.2    1.9  1  NACHT      NACHT domain
      0.067   12.9   0.1       0.12   12.1   0.1    1.4  1  AAA_30     AAA domain
      0.075   13.4   0.4       0.17   12.2   0.4    1.6  1  AAA_19     AAA domain
      0.079   13.3   0.2       0.12   12.7   0.2    1.3  1  AAA_16     AAA ATPase domain
      0.086   13.4   0.3       0.19   12.3   0.2    1.6  1  ABC_tran   ABC transporter
      0.087   13.0   0.3       0.17   12.0   0.2    1.5  1  DUF4760    Domain of unknown function (DUF4760)
       0.09   12.9   0.0       0.12   12.5   0.0    1.3  1  DUF3738    Protein of unknown function (DUF3738)
      0.094   12.9   0.1       0.13   12.5   0.1    1.5  1  AAA_33     AAA domain
       0.11   12.3   0.1       0.22   11.3   0.1    1.5  1  AAA_29     P-loop containing region of AAA domain
       0.11   12.4   1.5       0.14   12.1   0.1    1.8  2  NTPase_1   NTPase
       0.25   11.6   0.3       0.54   10.5   0.3    1.5  1  AAA_28     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 !  169.7   2.4     9e-53   6.2e-50       1     229 [.      17     238 ..      17     240 .. 0.96

  Alignments for each domain:
  == domain 1  score: 169.7 bits;  conditional E-value: 9e-53
                            ATPase   1 vktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekl 77 
                                       v+tg++glD+++ gG+  grv+ +tG pG+GKt+++ qFl++ga++ ge+g+++++  +++ +++++     +l   
  gi|242399797|ref|YP_002995222.1|  17 VSTGVKGLDNLIGGGLIPGRVYVVTGPPGSGKTTLGIQFLVEGAKN-GEKGIYISLVDDSKTIIQDMLYYRFNLLSH 92 
                                       78*******************************************9.****************************** PP

                            ATPase  78 eeegklaiidasesaeesaeekdkedleelieelaeaikeikakrvviDsitgl.ayeekeavaReilrqlvrvlkk 153
                                        ++ k++i d+ +  ++     +k   +e+++e++++i + +akrvviDs t+l    ++++  R+++  l++ l+ 
  gi|242399797|ref|YP_002995222.1|  93 IRSKKIVIYDLGAVLSQG---GKKPTWKEILKEIKRIILHENAKRVVIDSFTPLeFMVQDPENKRKEVVGLIKLLST 166
                                       ***********9997763...468999***************************999******************** PP

                            ATPase 154 lgvTailvsekssseeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeIteegikvlee 229
                                       +++Tai ++e+ +se+ +  y v+     gv+++++   ++++ R l+i+kmRgt+h+++   ++Ite+gi+v++e
  gi|242399797|ref|YP_002995222.1| 167 MEITAIVITEMIESEKYTDDYYVAS----GVVIMHHFMRQYNMIRALQILKMRGTSHDSNLKKIKITENGIEVYNE 238
                                       **********999999999886666....********************************************986 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 !   24.7   0.0   1.9e-08   1.3e-05       2      84 ..      17      98 ..      16     180 .. 0.69

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.9e-08
                                      BXSSTHHHHHHCT.SBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHHHHHHHHHHHTXXHHHH CS
                                      xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C  2 lstgfkdLDklts.GlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeqlvqRllsseaeidskkl 79
                                      +stg k LD+l++ Gl +g ++++ + p+ Gkt+l +++  + a++ +++ +++sl  ++++++q +l  + ++ ++++
  gi|242399797|ref|YP_002995222.1| 17 VSTGVKGLDNLIGgGLIPGRVYVVTGPPGSGKTTLGIQFLVEGAKNGEKG-IYISLVDDSKTIIQDMLYYRFNL-LSHI 93
                                      789*******99637*************************9999876655.56678788888999999866554.3334 PP

                                      HHTTS CS
                                      xxxxx RF
                            DnaB_C 80 rtgkl 84
                                      r+ k+
  gi|242399797|ref|YP_002995222.1| 94 RSKKI 98
                                      44333 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   3.6e-08   2.5e-05      23     163 ..      25     155 ..      14     175 .. 0.64

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 3.6e-08
                            AAA_25  23 rwlvkgllpagelallaGapgtGKttlaldlalava.tGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgeal. 97 
                                       + l++g l+ g + +++G+pg+GKttl ++  ++ a  G+           k +y+s+ d+ +++ + +   + +l 
  gi|242399797|ref|YP_002995222.1|  25 DNLIGGGLIPGRVYVVTGPPGSGKTTLGIQFLVEGAkNGE-----------KGIYISLVDDSKTIIQDMLYYRFNLl 90 
                                       6788876777**************************5555...........66777776665444444433333333 PP

                            AAA_25  98 ..rddarllvldlagveslpLfakdrggtlltadvdaleaaieevegvrlvviDplsralgg...densns 163
                                          + ++  ++dl  v     ++++ + ++ ++ ++++ + i + e+++ vviD+++ +       en+ +
  gi|242399797|ref|YP_002995222.1|  91 shIRSKKIVIYDLGAV-----LSQGGKKPTWKEILKEIKRIILH-ENAKRVVIDSFTPLEFMvqdPENKRK 155
                                       3324566666666444.....33344444456666666666666.78999999988763333331444444 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.1   1.2e-08   8.3e-06      32      87 ..      15      69 ..       4      82 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 1.2e-08
                                      -EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEE CS
                              RecA 32 etissGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaqkkggvaafi 87
                                      + +s+G  +ld+ +G GGl  Gr+  + Gp  sGkttl ++ ++e  k+g    +i
  gi|242399797|ref|YP_002995222.1| 15 SRVSTGVKGLDNLIG-GGLIPGRVYVVTGPPGSGKTTLGIQFLVEGAKNGEKGIYI 69
                                      4689***********.89999***************************99988777 PP

>> GvpD  GvpD gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   1.5   2.9e-08     2e-05       9     201 ..      34     224 ..      33     235 .. 0.72

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 2.9e-08
                              GvpD   9 aGktllikGaPGtGktlftlrgldv.lrresdvlyvstrvddetv.seay...fsgeaeldktalldllkdpleldl 80 
                                       +G+  ++ G PG+Gkt++ +++l    ++ ++ +y+s   d +t+ +++    f+  +++   + + ++  +  l  
  gi|242399797|ref|YP_002995222.1|  34 PGRVYVVTGPPGSGKTTLGIQFLVEgAKNGEKGIYISLVDDSKTIiQDMLyyrFNLLSHIR-SKKIVIYDLGAVLSQ 109
                                       58899*****************96515666778****999988872566534544444444.444445556888898 PP

                              GvpD  81 dvdvPiekldlesllefvdeiaaiatkliialdswelvyeylaerydsPediktvkndlvvlaresgvrlvlvleta 157
                                         + P      + +l+ ++ i    +   + +ds    +  l    ++Pe+ +     l+ l    ++  ++++e  
  gi|242399797|ref|YP_002995222.1| 110 GGKKPT----WKEILKEIKRIILHENAKRVVIDS----FTPLEFMVQDPENKRKEVVGLIKLLSTMEITAIVITEMI 178
                                       888998....555556666665555566677899....666777778898866666678888888888888888887 PP

                              GvpD 158 ansrle...yivdGvvtlnvkeddrgrlrrdlrleklrGvrignrlq 201
                                       + ++     y++ Gvv ++     +  ++r l++ k+rG + ++ l+
  gi|242399797|ref|YP_002995222.1| 179 ESEKYTddyYVASGVVIMHHFMR-QYNMIRALQILKMRGTSHDSNLK 224
                                       777653333999*****954444.36889**********99888776 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   6.6e-07   0.00046       6     100 ..      36     140 ..      34     178 .. 0.68

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 6.6e-07
                            AAA_22   6 gilvvtGesGtGKTtl.lrrlleqldeeakaee....erpevv.......fvtlpsst.sskdllrellralglelk 69 
                                       ++ vvtG++G+GKTtl ++ l+e +++ +k  +     +++++       +++l s   s k +  +l   l +++k
  gi|242399797|ref|YP_002995222.1|  36 RVYVVTGPPGSGKTTLgIQFLVEGAKNGEKGIYislvDDSKTIiqdmlyyRFNLLSHIrSKKIVIYDLGAVLSQGGK 112
                                       6789**********996788889988887777799994444444555522444444443444446666666666666 PP

                            AAA_22  70 aerlsseellealeqalraravielliiDEa 100
                                       +   + +e+l+ + + + +  + + ++iD +
  gi|242399797|ref|YP_002995222.1| 113 K--PTWKEILKEIKRIILHENA-KRVVIDSF 140
                                       6..7888888777777777777.77777754 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   1.7e-06    0.0012       3      70 ..      36     101 ..      34     141 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.7e-06
                            AAA_14   3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklke.ekktylfl 70 
                                       +++v+tG+  +GKTtl  q++ e   + e+ +yi+l d++++ ++d   l+ + +++l++ + k++++ 
  gi|242399797|ref|YP_002995222.1|  36 RVYVVTGPPGSGKTTLGIQFLVEGAKNGEKGIYISLVDDSKTIIQDM--LY-YRFNLLSHiRSKKIVIY 101
                                       799*****************98888899*********9998776654..22.22222222234454444 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   1.2e-06   0.00085       2      49 ..      36      81 ..      35     104 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.2e-06
                           DUF2075  2 avvlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvlvlre 49
                                      +v++VtG +G+GKt +++++l+e    +++++ +y+s   +   +++ 
  gi|242399797|ref|YP_002995222.1| 36 RVYVVTGPPGSGKTTLGIQFLVEG--AKNGEKGIYISLVDDSKTIIQD 81
                                      699*******************99..7777777777765555555555 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 !   18.6   0.2   2.1e-06    0.0014      20      62 ..      35      77 ..      31     175 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.1e-06
                          ATPase_2 20 neiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesi 62
                                       ++y+++Gp gsGKt+L  +++ +  + +++ iy++ + ++++
  gi|242399797|ref|YP_002995222.1| 35 GRVYVVTGPPGSGKTTLGIQFLVEGAKNGEKGIYISLVDDSKT 77
                                      689*******************999999999999876655544 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   3.4e-06    0.0023       2      93 ..      39     151 ..      39     175 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 3.4e-06
                            AAA_18   2 lltGtpGvGKttla.keLskrlgf.........gvnlrdvakenglllevdpealdeskrldedkldklldaleens 68 
                                       ++tG+pG+GKttl+ + L +  ++         ++ ++ ++++ +l++ ++   + +sk++++  l ++l++  + +
  gi|242399797|ref|YP_002995222.1|  39 VVTGPPGSGKTTLGiQFLVEGAKNgekgiyislVDDSKTIIQD-MLYYRFNLLSHIRSKKIVIYDLGAVLSQGGKKP 114
                                       59***********846665555556666788853333333333.444444444777777777777777777777766 PP

                            AAA_18  69 s............aleegknlvidghlaeleseaakd 93 
                                                      e++k +vid++    +  ++ +
  gi|242399797|ref|YP_002995222.1| 115 TwkeilkeikriiLHENAKRVVIDSFTPLEFMVQDPE 151
                                       6777777777777788899999999987776665555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   3.9e-06    0.0027       4      82 ..      37     148 ..      35     157 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.9e-06
                            AAA_24   4 kiliyGpsgiGKTtlakel.......gpkplfidtekGlksldadkfpdie.......................... 47 
                                        ++++Gp+g+GKTtl  ++       g+k ++i + + +           +                          
  gi|242399797|ref|YP_002995222.1|  37 VYVVTGPPGSGKTTLGIQFlvegaknGEKGIYISLVDDS-----------Ktiiqdmlyyrfnllshirskkiviyd 102
                                       679****************77777775555555443323...........222233333335688899999999999 PP

                            AAA_24  48 ............swedfldevvelaaeladyktlviDtideleelcl 82 
                                                   +w+++l+e++ +  +++  k +viD+ + le ++ 
  gi|242399797|ref|YP_002995222.1| 103 lgavlsqggkkpTWKEILKEIKRIILHEN-AKRVVIDSFTPLEFMVQ 148
                                       999999***999***********977766.899*****999876654 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.3   4.9e-06    0.0034      18      59 ..      16      57 ..       3     213 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.9e-06
                                      EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHH CS
                             Rad51 18 qlttGskklDelLgGGietgsiteifGefrsGktqlchtlcv 59
                                      +++tG k lD+l+gGG+  g +  + G  +sGkt l  ++ v
  gi|242399797|ref|YP_002995222.1| 16 RVSTGVKGLDNLIGGGLIPGRVYVVTGPPGSGKTTLGIQFLV 57
                                      599*******************************99988766 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.8e-05     0.013      50      90 ..      38      78 ..      21     127 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.8e-05
                         IstB_IS21 50 ivllGpsGvGKshlaialgveavraglsvlfvrvedLveel 90
                                       v++Gp+G GK+ l i + ve++++g + +++++ d  +++
  gi|242399797|ref|YP_002995222.1| 38 YVVTGPPGSGKTTLGIQFLVEGAKNGEKGIYISLVDDSKTI 78
                                      589****************************9988755554 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 !   15.3   0.4   1.6e-05     0.011       2      22 ..      37      60 ..      36     196 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.6e-05
                                      EEEEEESTTCCHHHHHHHHH...C CS
                              cobW  2 vtvltGflGsGKTtLlnhll...e 22
                                      v+v+tG++GsGKTtL  + l   +
  gi|242399797|ref|YP_002995222.1| 37 VYVVTGPPGSGKTTLGIQFLvegA 60
                                      789************666665543 PP

>> PAXNEB  PAXNEB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.3   4.7e-05     0.033      19      82 ..      17      79 ..      14      83 .. 0.76
   2 ?    2.5   0.0     0.093        64     180     243 ..     112     166 ..      73     179 .. 0.67
   3 ?   -3.8   0.1       7.7   5.3e+03      57      69 ..     187     199 ..     186     204 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.7e-05
                            PAXNEB 19 tStGtpsLDklLgGGLplGsillieEdgttdfakvLlkyFlAeGvvqkhevlvlsldddpeewl 82
                                      +StG++ LD+l+gGGL  G + ++      + +++L   Fl eG  ++ + +++sl dd+++++
  gi|242399797|ref|YP_002995222.1| 17 VSTGVKGLDNLIGGGLIPGRVYVVTGP-PGSGKTTLGIQFLVEGAKNGEKGIYISLVDDSKTII 79
                                      8*******************9999854.444566677777777777777777777766666655 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.093
                            PAXNEB 180 espryssllnqiqqllkkesfsaptkknvlRivipsLlspllydyppeeskpedllkFLhsLra 243
                                       ++p+ +++l++i++++ +    ++      R+vi s+    +  ++p e+k ++++ +++ L  
  gi|242399797|ref|YP_002995222.1| 112 KKPTWKEILKEIKRIILH----EN----AKRVVIDSFTPLEFMVQDP-ENKRKEVVGLIKLLST 166
                                       466688888899888888....34....4599**9998766655444.7777777777776654 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 7.7
                            PAXNEB  57 yFlAeGvvqkhev 69 
                                       y++A Gvv  h+ 
  gi|242399797|ref|YP_002995222.1| 187 YYVASGVVIMHHF 199
                                       99*****999985 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.2    0.0001     0.071       1      31 [.      36      66 ..      36     176 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.0001
                                      SCEEEEC-TTTCHHHHHHHHHHHHCTS-SCC CS
                             NACHT  1 rlvilqGeaGsGKTtLlqklalawaegklpq 31
                                      r+ +++G++GsGKTtL  ++ ++ a++  ++
  gi|242399797|ref|YP_002995222.1| 36 RVYVVTGPPGSGKTTLGIQFLVEGAKNGEKG 66
                                      6889************777766666665454 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00018      0.12      19      34 ..      36      51 ..      32      71 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00018
                            AAA_30 19 rvavltGpAGtGKtta 34
                                      rv v+tGp+G+GKtt+
  gi|242399797|ref|YP_002995222.1| 36 RVYVVTGPPGSGKTTL 51
                                      699***********97 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.4   0.00025      0.17       9      26 ..      34      51 ..      30      72 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00025
                            AAA_19  9 kekvllvtaGpGtGKTrv 26
                                      + +v +vt++pG+GKT++
  gi|242399797|ref|YP_002995222.1| 34 PGRVYVVTGPPGSGKTTL 51
                                      67899***********96 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   0.00018      0.12      25      40 ..      36      51 ..      21      80 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00018
                            AAA_16 25 elvllsGesGvGKssl 40
                                      ++ +++G++G+GK++l
  gi|242399797|ref|YP_002995222.1| 36 RVYVVTGPPGSGKTTL 51
                                      7889***********9 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   0.00027      0.19       8      27 ..      32      51 ..      26      92 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00027
                                      EETTSEEEEEESTTSSHHHH CS
                                      xxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  8 lkegekvaivGenGaGKStL 27
                                      l +g++++++G+ G+GK+tL
  gi|242399797|ref|YP_002995222.1| 32 LIPGRVYVVTGPPGSGKTTL 51
                                      5689***************9 PP

>> DUF4760  Domain of unknown function (DUF4760)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   0.00025      0.17      26     100 ..     112     190 ..     104     219 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00025
                           DUF4760  26 nnakfqealkqlrk.vldsg...kslakftlleekksekgeeeserekiltvlNflEfvavgiesgildEdmikels 98 
                                       + + + e+lk +++  l+++   + + +ft le + ++ +++ +e   ++++l  +E +a+ i + i  E+   ++ 
  gi|242399797|ref|YP_002995222.1| 112 KKPTWKEILKEIKRiILHENakrVVIDSFTPLEFMVQDPENKRKEVVGLIKLLSTMEITAIVITEMIESEKYTDDYY 188
                                       566677777777776544440004568899888888998888999999***********************999987 PP

                           DUF4760  99 vt 100
                                       v 
  gi|242399797|ref|YP_002995222.1| 189 VA 190
                                       63 PP

>> DUF3738  Protein of unknown function (DUF3738)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00018      0.12      41      72 ..      74     105 ..      40     180 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00018
                           DUF3738  41 qlremlqaLLaeRFkLkvhretkelpvYaLvv 72 
                                       + + ++q +L  RF+L  h  +k++ +Y+L +
  gi|242399797|ref|YP_002995222.1|  74 DSKTIIQDMLYYRFNLLSHIRSKKIVIYDLGA 105
                                       56889************************954 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   0.00018      0.13       2      20 ..      38      56 ..      37     175 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00018
                            AAA_33  2 vllvGlpGsGKstlaerll 20
                                       ++ G+pGsGK+tl  + l
  gi|242399797|ref|YP_002995222.1| 38 YVVTGPPGSGKTTLGIQFL 56
                                      6789*********977654 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00032      0.22      24      38 ..      37      51 ..      32      62 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00032
                            AAA_29 24 atlltGpsGsGKSTl 38
                                      ++++tGp GsGK+Tl
  gi|242399797|ref|YP_002995222.1| 37 VYVVTGPPGSGKTTL 51
                                      6899**********8 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1    0.0002      0.14       3      15 ..      39      51 ..      37      77 .. 0.79
   2 ?   -1.8   0.1       3.7   2.5e+03      94     113 ..     130     149 ..     114     184 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0002
                                      EEE--TTSSHHHH CS
                          NTPase_1  3 fiTGppGvGKtTl 15
                                      ++TGppG+GKtTl
  gi|242399797|ref|YP_002995222.1| 39 VVTGPPGSGKTTL 51
                                      79**********9 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.7
                                       HHH-EEEE---STTGGG-HH CS
                          NTPase_1  94 seadviviDEiGkmElkskk 113
                                       ++a  +viD   ++E+ ++ 
  gi|242399797|ref|YP_002995222.1| 130 ENAKRVVIDSFTPLEFMVQD 149
                                       44555667766666666654 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.3   0.00078      0.54       2      15 ..      38      51 ..      37      67 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00078
                            AAA_28  2 ivitGgestGKTtl 15
                                      +v+tG++++GKTtl
  gi|242399797|ref|YP_002995222.1| 38 YVVTGPPGSGKTTL 51
                                      69***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       753  (0.041999); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); 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 0.39s 00:00:01.10 Elapsed: 00:00:00.56
# Mc/sec: 1301.48
//
Query:       gi|242399798|ref|YP_002995223.1|  [L=351]
Description: Dolichol-phosphate mannosyltransferase, fused to membrane-bound GtrA- like domain [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.6e-37  127.4   0.2      7e-37  126.8   0.2    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
      4e-24   85.1   9.5    5.9e-24   84.6   9.5    1.3  1  GtrA             GtrA-like protein
    1.4e-12   48.0   0.0    1.8e-12   47.6   0.0    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    1.2e-06   28.2   0.0    1.8e-06   27.6   0.0    1.2  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
  ------ inclusion threshold ------
      0.016   14.7   0.0      0.028   13.9   0.0    1.4  1  Glyco_transf_21  Glycosyl transferase family 21
      0.064   12.4   0.0       0.11   11.7   0.0    1.3  1  CofC             Guanylyl transferase CofC like


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.8   0.2   2.4e-40     7e-37       1     168 [.       3     168 ..       3     169 .. 0.90

  Alignments for each domain:
  == domain 1  score: 126.8 bits;  conditional E-value: 2.4e-40
                                       EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglra 77 
                                       s++iptyNe ++l+e++e++ +  ++ dfeii+vDD S+D+t+e +e l k   +vrvirr++ +G+++a+ +g+++
  gi|242399798|ref|YP_002995223.1|   3 SIIIPTYNERENLEELFERISRALEDRDFEIIIVDDDSPDKTWEKAEILGK-IYPVRVIRRTNEKGLSSAVIRGFEE 78 
                                       8*********************************************99965.999*******999************ PP

                                       --SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTTC CS
                   Glycos_transf_2  78 atgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnlsfe 154
                                       a+gd+i+++DaD++++p+ ++kl+ea+e+ gad+ +++r++++g+  ++ + ++v  +  +   +    + +n+ + 
  gi|242399798|ref|YP_002995223.1|  79 ANGDIIVVMDADLQHPPEVIPKLIEAIEH-GADISIASRYVKGGKAENWYWWRKVISKGAIMVGRVALPKIRNIKDP 154
                                       *****************************.************99988877766665666666666666666788888 PP

                                       STCCCEEEEHHHHH CS
                   Glycos_transf_2 155 igsaallrrealee 168
                                       ++++++++re++e+
  gi|242399798|ref|YP_002995223.1| 155 VSGFFAFKREVIEN 168
                                       99999999998875 PP

>> GtrA  GtrA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.6   9.5     2e-27   5.9e-24       1     117 []     235     350 ..     235     350 .. 0.97

  Alignments for each domain:
  == domain 1  score: 84.6 bits;  conditional E-value: 2e-27
                              GtrA   1 rFlivGvlgtlvdlallllllellglsyllAnaiafivailfnFilnrrwtFkdrekakllkqflkFvlvsllglll 77 
                                       +F +vG++g+lv+ ++l+ ++e+lg++  lA++ a+++++l+nF++n++wtFkd +++ l  ++l+F++++l+g+l+
  gi|242399798|ref|YP_002995223.1| 235 KFSVVGLSGVLVNEGTLWGFVEFLGWDKRLAVLPATELSVLNNFVWNDIWTFKDLKRKALYLRLLNFHFAALTGALV 311
                                       79*************************************************************************** PP

                              GtrA  78 nllilwllveklgleallaklvgiivalvlnyvlsklfvF 117
                                       +++i+ +l+++ gl++l+a+l+gi++ +++++++++ +++
  gi|242399798|ref|YP_002995223.1| 312 QWAIYLVLLHV-GLHYLVANLIGIGFSFIVRFLFNRNITW 350
                                       ****9988865.88999*******************9998 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 !   47.6   0.0   6.1e-16   1.8e-12       4     119 ..       2     111 ..       1     176 [. 0.85

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 6.1e-16
                   Glyco_tranf_2_3   4 lavlVptfneedvlgevlesllaq.eyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksral 79 
                                       +++++pt+ne + l+e+ e +++  e  ++e+++v+d s ++t e ae l +++p    rv++++++ g    s a+
  gi|242399798|ref|YP_002995223.1|   2 ISIIIPTYNERENLEELFERISRAlEDRDFEIIIVDDDSPDKTWEKAEILGKIYPV---RVIRRTNEKG---LSSAV 72 
                                       79********************6514566******************999999965...8999999766...55567 PP

                   Glyco_tranf_2_3  80 nealravksdlvllvDdDtvvePdtlkrllqffltpkvga 119
                                        ++++ +++d+++++D+D    P+++++l  ++  +++++
  gi|242399798|ref|YP_002995223.1|  73 IRGFEEANGDIIVVMDADLQHPPEVIPKLIEAI-EHGADI 111
                                       7***************************99998.555555 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 !   27.6   0.0   6.1e-10   1.8e-06       1     103 [.       3     102 ..       3     116 .. 0.77

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 6.1e-10
                   Glyco_tranf_2_2   1 svviplraseerhyieervlqkakyy.deeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarNrG 76 
                                       s++ip ++++e+  +ee   ++     d ++e+i+vdd S++k+ e+ + + +      ++ +++k  s   a  rG
  gi|242399798|ref|YP_002995223.1|   3 SIIIPTYNEREN--LEELFERISRALeDRDFEIIIVDDDSPDKTWEKAEILGKIYPVRVIRRTNEKGLS--SAVIRG 75 
                                       79**********..8888855555555****************98776655554444455556566555..55678* PP

                   Glyco_tranf_2_2  77 askaesdlvlFlDaDcfissDkfekil 103
                                       +++a++d+++ +DaD    ++ + k++
  gi|242399798|ref|YP_002995223.1|  76 FEEANGDIIVVMDADLQHPPEVIPKLI 102
                                       ***************877776666655 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 ?   13.9   0.0   9.4e-06     0.028      21     114 ..      71     167 ..      57     174 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9.4e-06
                   Glyco_transf_21  21 nllqaleaakydllvisDsdvrvkpdyLeellaaledpkvglVtslpv..gsdakg..laaaleaaflntlagvlqa 93 
                                       ++++++e+a+ d++v+ D+d   +p+ + +l +a+e+ ++ +  +  +  g +a++  +++++ +    ++ +v+  
  gi|242399798|ref|YP_002995223.1|  71 AVIRGFEEANGDIIVVMDADLQHPPEVIPKLIEAIEH-GADISIASRYvkGGKAENwyWWRKVISKGAIMVGRVALP 146
                                       57899*******************************8.566655555511444444546666655544444444444 PP

                   Glyco_transf_21  94 klsglgfavGksmalrreaLe 114
                                       k   ++  v  + a++re++e
  gi|242399798|ref|YP_002995223.1| 147 KIRNIKDPVSGFFAFKREVIE 167
                                       666666666666666666665 PP

>> CofC  Guanylyl transferase CofC like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   3.6e-05      0.11      24     122 ..      10     115 ..       2     131 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.6e-05
                              CofC  24 eerkellkamlldvidalkrld..vlvvsedeevleyaldel.g....vevvkek.ekdlntavekafeeieekevi 92 
                                       +er++l   ++  ++ al+  d  +++v +d     +++ e  g    v+v++ + ek+l +av + fee + + ++
  gi|242399798|ref|YP_002995223.1|  10 NERENL-EELFERISRALEDRDfeIIIVDDDSPDKTWEKAEIlGkiypVRVIRRTnEKGLSSAVIRGFEEANGDIIV 85 
                                       688887.567889*****986655888877765555554332122333899999889************99999999 PP

                              CofC  93 iipsdiPlikkedvkdllel.ekradvviaP 122
                                       ++ +d+     e++ +l+e  e+ ad+ ia 
  gi|242399798|ref|YP_002995223.1|  86 VMDADLQH-PPEVIPKLIEAiEHGADISIAS 115
                                       99999964.3455555555314556777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); 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: 0.65u 0.35s 00:00:01.00 Elapsed: 00:00:00.55
# Mc/sec: 1922.35
//
Query:       gi|242399799|ref|YP_002995224.1|  [L=209]
Description: hypothetical protein TSIB_1824 [Thermococcus sibiricus MM 739]
Scores for complete 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-46  156.2   0.0      1e-45  155.8   0.0    1.1  1  RNA_Me_trans  Predicted SAM-dependent RNA methyltransferase


Domain annotation for each model (and alignments):
>> RNA_Me_trans  Predicted SAM-dependent RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.8   0.0   5.7e-50     1e-45       3     197 ..       5     187 ..       3     189 .. 0.90

  Alignments for each domain:
  == domain 1  score: 155.8 bits;  conditional E-value: 5.7e-50
                      RNA_Me_trans   3 viEhleeelseWvllEYrhiakevgaenliltslskasleslpeelkslaklelekesveellkelkevkkekvclL 79 
                                        iEhle e+seW+ lEY+h+a+++ +++li+t++++++ e+     ++l   ++ +e+v+++      ++ +k+++L
  gi|242399799|ref|YP_002995224.1|   5 LIEHLE-EISEWLWLEYSHAAQWW-KDKLIFTNVRADEREKF----AKL--GSVLSETVTKFP-----FECSKLIVL 68 
                                       7*****.9****************.89*********755533....322..233445566555.....4569***** PP

                      RNA_Me_trans  80 DpkaekelspedaeefdvflfGGIlGddpprdRTselrkkg...fegRrLGpvqmttDtAvrvtklvvedkvkleei 153
                                       D +ae+el+ped e+  ++++GGIlGd  p++RT+e+ +++   ++ R++G+ q+++D+A  v+kl+++ +++leei
  gi|242399799|ref|YP_002995224.1|  69 DLQAEEELKPEDIEDDTIIVIGGILGDAIPKGRTKEFITSKmkgVKVRHIGKPQYSIDGASIVAKLIAD-GKRLEEI 144
                                       *************************************9988777999********************99.******* PP

                      RNA_Me_trans 154 eyvdepelkfnkkesvempfrYvkdeegkpllpegmlellkkdl 197
                                       eyv++p++++++ ++++++++ +k  +g+pl+++g++el kk+l
  gi|242399799|ref|YP_002995224.1| 145 EYVENPTIRLDNLSEITLHYAVPK-LNGEPLITPGLIELQKKEL 187
                                       ************************.8***************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.35s 00:00:00.93 Elapsed: 00:00:00.54
# Mc/sec: 1155.99
//
Query:       gi|242399800|ref|YP_002995225.1|  [L=119]
Description: hypothetical protein TSIB_1825 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 745.32
//
Query:       gi|242399801|ref|YP_002995226.1|  [L=90]
Description: hypothetical protein TSIB_1826 [Thermococcus sibiricus MM 739]
Scores for complete 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   17.1   0.0     0.0034   17.1   0.0    1.0  1  NTP_transf_5  Uncharacterised nucleotidyltransferase
  ------ inclusion threshold ------
      0.048   13.9   0.0      0.063   13.5   0.0    1.2  1  Fe-S_biosyn   Iron-sulphur cluster biosynthesis


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 !   17.1   0.0   3.8e-07    0.0034      94     144 ..      12      65 ..       8      87 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.8e-07
                      NTP_transf_5  94 mgDiDllvkredldraeelLeelGyeles.d....gsekhevyyrekkgveielhw 144
                                       + D+D+lv+ + ++++ + L+elGy++ + +     ++ +  +    +++ ++l +
  gi|242399801|ref|YP_002995226.1|  12 SVDVDFLVRWDSFKEVYSRLRELGYQSSGfKyfkvVKDGELPFLE--ERINVDLLF 65 
                                       67***********************98773356666666777777..777777755 PP

>> Fe-S_biosyn  Iron-sulphur cluster biosynthesis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   7.1e-06     0.063      70     108 ..      46      84 ..      34      86 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.1e-06
                                       EEEGGGHHHS.TTEEEEEEEETTEEEEEEETCCEEEEEE CS
                       Fe-S_biosyn  70 yvksyslvfldeglvldfvedlgtlgLksdngilddnvg 108
                                       +vk+ +l+fl+e+ ++d   d++ ++L++++++++ +v+
  gi|242399801|ref|YP_002995226.1|  46 VVKDGELPFLEERINVDLLFDRKPSRLSFESPYVKKSVQ 84 
                                       58999******************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); 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:                         2  (0.000111551); expected 0.2 (1e-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 0.35s 00:00:00.81 Elapsed: 00:00:00.51
# Mc/sec: 528.93
//
Query:       gi|242399802|ref|YP_002995227.1|  [L=67]
Description: hypothetical protein TSIB_1827 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       255  (0.0142228); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.36s 00:00:00.87 Elapsed: 00:00:00.54
# Mc/sec: 374.08
//
Query:       gi|242399803|ref|YP_002995228.1|  [L=391]
Description: DEXX-box atpase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-23   83.3   0.0    2.4e-23   82.6   0.0    1.3  1  AAA_14    AAA domain
     0.0029   17.6   0.0     0.0083   16.1   0.0    1.7  1  ATPase_2  ATPase domain predominantly from Archaea
  ------ inclusion threshold ------
      0.099   13.1   0.0       0.22   12.0   0.0    1.5  1  AAA       ATPase family associated with various cellular acti


Domain annotation for each model (and alignments):
>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.6   0.0   4.1e-27   2.4e-23       6     130 ..      48     178 ..      44     179 .. 0.85

  Alignments for each domain:
  == domain 1  score: 82.6 bits;  conditional E-value: 4.1e-27
                            AAA_14   6 vitGaRrvGKTtllkqlikell..vkkesilyinldderdkkladp.ekllelileklkeekktylflDEiqevpew 79 
                                       ++ G+R+vGKTt +k li++ll   ++esilyin++  +d+k      +  ++i+ek    k+ y+flDE+  +++w
  gi|242399803|ref|YP_002995228.1|  48 FVLGPRQVGKTTGIKLLIQKLLkeNPPESILYINVEILPDYKGLSAlIREFQAIREKED-IKTGYIFLDEATSLDGW 123
                                       799**********************************9997744330233466666643.4899************* PP

                            AAA_14  80 ekalkslvdeg..knldvivtGSnskllskeiatsl..agrvaeielyplsfaEf 130
                                       +k +k l+d g  +n  v vtGS+s+  +++i+  +  +g+++++e++plsf E+
  gi|242399803|ref|YP_002995228.1| 124 WKGVKPLIDAGllENNVVTVTGSSSLRVKRDIELFPgrRGKGTTLEVMPLSFGEY 178
                                       *********9999899**************9986653366667***********9 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.4e-06    0.0083      14      57 ..      38      82 ..      25     107 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.4e-06
                          ATPase_2 14 ilerepneiyfiYGpegsGKtaLlkeiienledkdk.yviyyial 57
                                       l+ ep +  f+ Gp+++GKt+ +k +i++l++ +  + i yi++
  gi|242399803|ref|YP_002995228.1| 38 KLSLEPFSLNFVLGPRQVGKTTGIKLLIQKLLKENPpESILYINV 82
                                      3567999***********************966554466666665 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   3.6e-05      0.22       3      70 ..      49     120 ..      48     123 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.6e-05
                                       EESSTTSSHHHHHHHHHHHH...T..HEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS..TSEEEEEETGGGH CS
                               AAA   3 lyGppGtGKTllakavakel...g..vefleisgsellskyvgesekkirelfkeakeka..kpsilfiDEidal 70 
                                       + Gp  +GKT+ +k ++++l   +   ++l i++  l  +y g s   +   f++++ek+  k+  +f+DE+ +l
  gi|242399803|ref|YP_002995228.1|  49 VLGPRQVGKTTGIKLLIQKLlkeNppESILYINVEILP-DYKGLS--ALIREFQAIREKEdiKTGYIFLDEATSL 120
                                       67*****************8654143557777775444.655543..44445667777777888*******9776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); 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: 0.64u 0.35s 00:00:00.99 Elapsed: 00:00:00.53
# Mc/sec: 2216.31
//
Query:       gi|242399804|ref|YP_002995229.1|  [L=43]
Description: hypothetical protein TSIB_1829 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (43 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       248  (0.0138323); expected 358.6 (0.02)
Passed bias filter:                      160  (0.00892409); 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: 0.43u 0.31s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 268.26
//
Query:       gi|242399805|ref|YP_002995230.1|  [L=99]
Description: hypothetical protein TSIB_1830 [Thermococcus sibiricus MM 739]
Scores for complete 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-19   67.9   0.6    6.6e-19   67.7   0.6    1.0  1  DUF2103   Predicted metal-binding protein (DUF2103)


Domain annotation for each model (and alignments):
>> DUF2103  Predicted metal-binding protein (DUF2103)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.7   0.6   3.7e-23   6.6e-19       2      97 ..       5      93 ..       4      94 .. 0.94

  Alignments for each domain:
  == domain 1  score: 67.7 bits;  conditional E-value: 3.7e-23
                           DUF2103  2 pkeklggsHstiiggreGkkllekiakhpevkkviPgvikakgsssggglrvkvtraderGnlrlllrdgssvQevfiv 80
                                      +k+ ++++H+ + g +   k+le+i+  ++vkkviPg+i   +ss+++g+++kv r++ +G l+ll++++ s+Qe+f+v
  gi|242399805|ref|YP_002995230.1|  5 FKRGVKREHHLLKGIE---KALEEISALKGVKKVIPGRI---YSSDSRGFEIKVVRETLTG-LKLLAKSDGSIQEIFLV 76
                                      68899********999...********************...899****************.***************** PP

                           DUF2103 81 ttakdreegeriaeeLn 97
                                      ++++dre  ++ ++ +n
  gi|242399805|ref|YP_002995230.1| 77 VDKADRERIRKEMHRIN 93
                                      ******99988888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); 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: 0.56u 0.35s 00:00:00.91 Elapsed: 00:00:00.54
# Mc/sec: 552.86
//
Query:       gi|242399806|ref|YP_002995231.1|  [L=571]
Description: RNA-binding protein, containing PUA domain [Thermococcus sibiricus MM 739]
Scores for complete 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  171.5   0.9    2.8e-50  170.2   0.2    2.0  2  DUF5591   Domain of unknown function (DUF5591)
    1.3e-09   37.9   1.6    2.9e-09   36.7   1.6    1.5  1  PUA       PUA domain
    5.5e-07   29.6   0.0      1e-06   28.7   0.0    1.5  1  TGT_C2    Patch-forming domain C2 of tRNA-guanine transglycos


Domain annotation for each model (and alignments):
>> DUF5591  Domain of unknown function (DUF5591)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.27   1.6e+03      90     113 ..      94     117 ..      91     139 .. 0.72
   2 !  170.2   0.2   4.7e-54   2.8e-50       1     154 []     265     420 ..     265     420 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.27
                                       HHHHHHHHHHHHHHHT-SEEEE-- CS
                           DUF5591  90 iefvaellakylektkyekviahl 113
                                       +++++e l+++l+++++++v +  
  gi|242399806|ref|YP_002995231.1|  94 LKYINEFLEEVLSRESFDAVYIGN 117
                                       689999999999999998876544 PP

  == domain 2  score: 170.2 bits;  conditional E-value: 4.7e-54
                                       X-HHHHHHHHH---S..SSEEEEEE--SSSSGGGSHHHHHHHHHS---.......SEEEEE-SS-.EEEGGGTT--- CS
                           DUF5591   1 vkrfrervlerYeppeekkvlvLlPcsakkPyseskshrkfaeaikkrk.a...kvheviltsPlGvvPreleevYP 73 
                                       v r+r+rv er++ppe+ + l L+PcsakkPys+s+sh  +++a+k+   +   +vhe+iltsP+GvvPre+e++  
  gi|242399806|ref|YP_002995231.1| 265 VIRWRQRVIERFKPPENVEALFLFPCSAKKPYSHSRSHILYRKALKESLgNgiyRVHELILTSPFGVVPREWEWL-- 339
                                       78*****************************************99998752556*********************.. PP

                                       -------------HHHHHHHHHHHHHHHHHHT-SE.EEE---THHHHHHHHHHTT-SSEEEE--.SS-TTSHHHHHH CS
                           DUF5591  74 aaqYdiavtgewseeeiefvaellakylektkyek.viahleeeyreiveevaeelgleiiytvvedkptskeslkn 149
                                        a+Ydi+vtg+wseeei+ +aellak+lek+ ++  +iahl+e+y e++e+++e  g+ei++t+v++ +tsk+sl++
  gi|242399806|ref|YP_002995231.1| 340 -AKYDIVVTGHWSEEEISSAAELLAKTLEKYPNHIpIIAHLDEAYVEVAERASEISGREIVFTKVKNGTTSKKSLDS 415
                                       .********************************999***************************************** PP

                                       HHHHH CS
                           DUF5591 150 LkeaL 154
                                       Lke++
  gi|242399806|ref|YP_002995231.1| 416 LKETI 420
                                       **986 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   1.6   4.9e-13   2.9e-09      18      72 ..     516     569 ..     509     570 .. 0.95

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 4.9e-13
                                       EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEEE CS
                               PUA  18 sLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksveier 72 
                                       +++a Gv e++ +++++d+V +v   +++v+vG+a +s+ee+ k+ +g++v++++
  gi|242399806|ref|YP_002995231.1| 516 DVFAIGVNEADAKIRPDDIVGVVRD-EKVVGVGKAILSGEEMIKARRGIAVKVRK 569
                                       89*********************99.**************************986 PP

>> TGT_C2  Patch-forming domain C2 of tRNA-guanine transglycosylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.0   1.7e-10     1e-06       2      68 ..     441     502 ..     440     504 .. 0.92

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 1.7e-10
                            TGT_C2   2 rlraiadYqFGagagdaLfpedvtitrsatgrirqvlvdgerlatlraqdgrltLsleGarrlhesl 68 
                                        +r++ d+ FG gagda+ pe ++i+     ++  ++vd+++  t+  qdg+ + +  G +r+ e++
  gi|242399806|ref|YP_002995231.1| 441 NIRKVFDFYFGIGAGDAVLPESAKIK---GSKMLRIQVDNQQTGTY--QDGIISVTPFGMQRIYEAT 502
                                       69************************...66666789********8..***************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (571 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); 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: 0.71u 0.34s 00:00:01.05 Elapsed: 00:00:00.53
# Mc/sec: 3269.92
//
Query:       gi|242399807|ref|YP_002995232.1|  [L=313]
Description: hypothetical protein TSIB_1832 [Thermococcus sibiricus MM 739]
Scores for 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   24.3  43.8     0.0018   17.9  29.2    2.8  3  MscS_porin       Mechanosensitive ion channel porin domain
    2.9e-05   24.1  33.3      0.077   13.0   5.2    3.9  4  DUF1664          Protein of unknown function (DUF1664)
    0.00087   19.5  14.5        2.6    8.4   0.2    4.9  3  WXG100           Proteins of 100 residues with WXG
     0.0034   16.1  46.4      0.064   11.9  28.1    2.1  2  AAA_13           AAA domain
  ------ inclusion threshold ------
      0.014   15.3   5.8      0.014   15.3   5.8    6.7  6  Prefoldin_2      Prefoldin subunit
      0.015   15.5  38.8      0.017   15.4   9.0    3.9  3  DUF5082          Domain of unknown function (DUF5082)
       0.02   15.3   1.5       0.02   15.3   1.5    5.4  5  DUF4140          N-terminal domain of unknown function (DUF41
      0.026   15.1   3.9      0.026   15.1   3.9    4.3  4  Syntaxin-6_N     Syntaxin 6, N-terminal
      0.046   11.9  52.2       0.16   10.1  52.2    1.7  1  EzrA             Septation ring formation regulator, EzrA
      0.053   13.8  52.6      0.037   14.2  13.7    4.2  3  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
      0.055   13.7   0.5       0.19   12.0   0.5    2.1  1  Sterile          Male sterility protein
      0.083   13.3  44.5      0.054   13.9  10.3    4.4  4  Snapin_Pallidin  Snapin/Pallidin
       0.12   12.4  33.3        1.1    9.2  10.6    3.9  4  Laminin_II       Laminin Domain II
       0.14   10.8  49.7      0.054   12.1  20.0    3.1  4  FapA             Flagellar Assembly Protein A
       0.14   11.2  54.9       0.14   11.2  20.1    3.4  4  Atg14            Vacuolar sorting 38 and autophagy-related su
       0.22   11.5  59.8        6.2    6.8  21.4    4.2  3  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
       0.27   10.9  41.1       0.15   11.7  16.4    2.6  2  Laminin_I        Laminin Domain I
       0.34   10.6  59.0       0.52   10.0  20.5    3.7  4  DUF4201          Domain of unknown function (DUF4201)
       0.49   10.6  45.6       0.24   11.6  12.0    2.6  2  ATG16            Autophagy protein 16 (ATG16)
       0.67   10.1  40.1        1.7    8.8  12.3    3.3  3  Fib_alpha        Fibrinogen alpha/beta chain family
       0.98    8.6  46.3      0.039   13.2  15.3    3.1  3  TMPIT            TMPIT-like protein
          1    9.7  16.4        4.5    7.6   1.5    4.2  5  DUF948           Bacterial protein of unknown function (DUF94
          2    8.8  52.5        1.6    9.1   8.2    2.9  1  Fez1             Fez1
        2.8    7.8  28.1          1    9.3   1.2    3.9  4  Sec34            Sec34-like family
        2.9    8.3  51.5      0.045   14.2   4.8    4.1  4  CENP-H           Centromere protein H (CENP-H)
        3.1    7.4  45.3       0.03   14.0  13.2    3.2  3  DUF2968          Protein of unknown function (DUF2968)
        4.3    8.0  43.4        2.5    8.8   7.1    4.2  4  YabA             Initiation control protein YabA
        4.4    7.4  54.1          5    7.2   5.4    4.1  4  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
        4.4    8.1  47.8        3.8    8.3   6.4    4.2  4  Occludin_ELL     Occludin homology domain
        4.7    7.0  54.1       0.69    9.7  23.4    3.1  4  DUF724           Protein of unknown function (DUF724)
        4.8    7.0  16.4        3.2    7.5   1.1    3.2  3  MCPsignal        Methyl-accepting chemotaxis protein (MCP) si
        5.1    7.6  15.9        4.9    7.6   0.4    4.9  5  LPP              Lipoprotein leucine-zipper
        5.2    7.5  25.3        2.1    8.8   8.9    2.9  2  T3SSipB          Type III cell invasion protein SipB
        5.4    7.1  47.9       0.41   10.7  15.2    3.9  1  Mod_r            Modifier of rudimentary (Mod(r)) protein
        5.7    7.5  18.5        6.8    7.2   0.6    4.6  5  NPV_P10          Nucleopolyhedrovirus P10 protein
        9.7    5.2  35.8       0.81    8.7  10.0    2.9  3  FH2              Formin Homology 2 Domain
        9.7    5.6  10.3       0.42   10.0   1.4    2.2  2  Glu_syn_central  Glutamate synthase central domain


Domain annotation for each model (and alignments):
>> MscS_porin  Mechanosensitive ion channel porin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9  29.2   3.7e-06    0.0018      50     227 ..      20     194 ..      14     198 .. 0.88
   2 ?    4.4   8.2      0.05        24      12      68 ..     152     208 ..     147     213 .. 0.85
   3 !   10.6   6.6   0.00061       0.3      17      65 ..     206     254 ..     199     266 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3.7e-06
                        MscS_porin  50 PkelrelqqelealqkkkeeaskeilaklsleeLeqrllqtssqlqelqeqlaqlnsqlvelqtrperaqqqltear 126
                                       P+e++ +++e+e l    e + kei ++  le+L+++l+   ++  e +++ + l ++++e+ t  +++ qq+ e +
  gi|242399807|ref|YP_002995232.1|  20 PEEIKRIKAEIEVL----EREKKEIKER--LEQLQKELNIWVQKRDEKNKEVKHLREKAREYKTKRDEVNQQIQELK 90 
                                       99************....8888888766..69********************************************* PP

                        MscS_porin 127 qrlqeirnrLnstaaage.....alsqaqrtalqaelaaleaqieeleqellsnnnrqeLlklqrdllklriqqleq 198
                                       +  +ei+++Ln + ++       + +  q   l++  + +e +ie le el++n++ +     + ++   +iq l +
  gi|242399807|ref|YP_002995232.1|  91 KNREEINAKLNLLYQEAMeyrakRDEYRQLRRLKMPKEKIEERIEKLEWELQTNPTIT---SEREKQIVDQIQVLAT 164
                                       **********6664444445566888889999999********************865...566666789******* PP

                        MscS_porin 199 elqaLqelln.ekRlaeaekavaqteqlae 227
                                       el+ Lq++    kRl+e+ k ++  +++++
  gi|242399807|ref|YP_002995232.1| 165 ELEILQQADRfHKRLQETRKKIESLKRARR 194
                                       ******997637**********98888766 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.05
                        MscS_porin  12 eaeqkallqdLeqalnlLdkidkskkkaeelqkaiddaPkelrelqqelealqkkke 68 
                                       e++  +++q L   l+ L+++d++ k+++e +k+i++  +  r++  e+++l+++++
  gi|242399807|ref|YP_002995232.1| 152 EKQIVDQIQVLATELEILQQADRFHKRLQETRKKIESLKRARRAMGLEIQKLANQSQ 208
                                       5667788999999***************************************44433 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00061
                        MscS_porin  17 allqdLeqalnlLdkidkskkkaeelqkaiddaPkelrelqqelealqk 65 
                                       + +q  eq l+  +++d+ kk+a+e+++++ +   ++re+++el + +k
  gi|242399807|ref|YP_002995232.1| 206 QSQQFHEQMLKSYQQADEIKKEADEYHQKVIELRDKMREIREELREVEK 254
                                       5667778888889999999999999999999999999999999887733 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   9.2    0.0002     0.097      51     122 ..      27      98 ..      18     100 .. 0.91
   2 !    8.7   3.4    0.0034       1.7      56     121 ..     122     190 ..     117     192 .. 0.74
   3 ?    6.7   2.9     0.014       6.9      56     103 ..     167     214 ..     153     218 .. 0.82
   4 !   13.0   5.2   0.00016     0.077      55     120 ..     201     266 ..     188     270 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.0002
                           DUF1664  51 eqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleriee 122
                                       +   e l++ k+++++r+++++k+l+   +   e ++ev+++re+ +e +++ ++v++ +++l+++ e+i++
  gi|242399807|ref|YP_002995232.1|  27 KAEIEVLEREKKEIKERLEQLQKELNIWVQKRDEKNKEVKHLREKAREYKTKRDEVNQQIQELKKNREEINA 98 
                                       555678999*******************************************************99888876 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0034
                           DUF1664  56 slaatkrhLssridrvdkkldeqkeiskeikeev....tevredlseigedvesvkeaveglesklerie 121
                                        l+  k+++++ri++++++l+ +  i++e ++++    + +  +l ei ++ +  ++  ++  +k+e+++
  gi|242399807|ref|YP_002995232.1| 122 RLKMPKEKIEERIEKLEWELQTNPTITSEREKQIvdqiQVLATEL-EILQQADRFHKRLQETRKKIESLK 190
                                       577889***************998877665555411004444444.466788999999999999999885 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.014
                           DUF1664  56 slaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedv 103
                                       ++ ++ +++ +r+++  kk+++ k++ +++  e++++ ++ ++++e++
  gi|242399807|ref|YP_002995232.1| 167 EILQQADRFHKRLQETRKKIESLKRARRAMGLEIQKLANQSQQFHEQM 214
                                       566788999*******************************99999987 PP

  == domain 4  score: 13.0 bits;  conditional E-value: 0.00016
                           DUF1664  55 eslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleri 120
                                       ++la++ +++ +++ +  ++ de k+ + e +++v e+r++++ei+e++++v++ + ++++k +++
  gi|242399807|ref|YP_002995232.1| 201 QKLANQSQQFHEQMLKSYQQADEIKKEADEYHQKVIELRDKMREIREELREVEKKIFEFDQKHKEL 266
                                       567888888888888888999999999999999999999999999999999999999999997765 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 ?    4.9   0.1     0.064        31       1      34 [.      15      51 ..      15      54 .. 0.62
   2 !    8.4   0.2    0.0053       2.6       8      38 ..      67      97 ..      64     116 .. 0.85
   3 !    8.3   3.7    0.0055       2.7      16      83 ..     189     258 ..     180     261 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.064
                                      CHCSHHHHHHHHHHHHH...HHHHHHHHHHHHHHHHH CS
                            WXG100  1 qikvdpeelrqaaarfq...kqaeeledelqrlkaev 34
                                      q+kvdpee+    a++    ++++e++++l++l++e+
  gi|242399807|ref|YP_002995232.1| 15 QVKVDPEEIKRIKAEIEvleREKKEIKERLEQLQKEL 51
                                      6899999998888877611155555555555555544 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0053
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCG CS
                            WXG100  8 elrqaaarfqkqaeeledelqrlkaevdalq 38
                                       lr++a++++++++e+ +++q+lk+  ++++
  gi|242399807|ref|YP_002995232.1| 67 HLREKAREYKTKRDEVNQQIQELKKNREEIN 97
                                      6899999999999999999999998877765 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0055
                                       HHHHHHHHHHHHHHHHHHHHHC.GCGCT.HHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  16 fqkqaeeledelqrlkaevdal.qsgWs.GaaadafqaefeewkqaaqklvdaLeeisealkqaanafed 83 
                                       +++++  +  e+q+l+++ ++  +++ +  + ad+ ++e +e++q++ +l d++ ei+e+l+++ ++  +
  gi|242399807|ref|YP_002995232.1| 189 LKRARRAMGLEIQKLANQSQQFhEQMLKsYQQADEIKKEADEYHQKVIELRDKMREIREELREVEKKIFE 258
                                       5555555555666666666666444554457788888999999999999999999999999888877655 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5  17.1   0.00035      0.17     386     470 ..       5      89 ..       3      97 .. 0.94
   2 !   11.9  28.1   0.00013     0.064     279     466 ..      80     262 ..      74     270 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00035
                            AAA_13 386 anleeekeeakkklelhlveeleseldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaaee 462
                                       +++ee +e++++k+   +++++++e++ +++++k++++ +e+l+kel+   ++  ++++e+k L+++ r+ k   +e
  gi|242399807|ref|YP_002995232.1|   5 SKIEEGEETMQVKVDPEEIKRIKAEIEVLEREKKEIKERLEQLQKELNIWVQKRDEKNKEVKHLREKAREYKTKRDE 81 
                                       6789999********************************************************************** PP

                            AAA_13 463 inkeLkaf 470
                                       +n+++++ 
  gi|242399807|ref|YP_002995232.1|  82 VNQQIQEL 89 
                                       ****9876 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00013
                            AAA_13 279 defeekqerLekliekveskksellek...lkavsdeasensafeedkeelkaeaealeeqLkglqraleaKrkepf 352
                                       de+++++++L+k  e+++ k + l ++   + a  de+++ ++ +  ke++++++e+le +L+++    +++ k+++
  gi|242399807|ref|YP_002995232.1|  80 DEVNQQIQELKKNREEINAKLNLLYQEameYRAKRDEYRQLRRLKMPKEKIEERIEKLEWELQTNPTITSEREKQIV 156
                                       567778888888888887776544443111333333344444455559***************************** PP

                            AAA_13 353 ksvelesvkakiesikklvaeineliakhNekvanleeekeeakkklelhlveeleseldeykkkykklekaiekle 429
                                        ++++  ++ +i    ++ +++ +  ++  +k+++l+++    + ++ l ++++l ++ +++++++ k  +++ + +
  gi|242399807|ref|YP_002995232.1| 157 DQIQVLATELEIL---QQADRFHKRLQETRKKIESLKRA----RRAMGL-EIQKLANQSQQFHEQMLKSYQQADEIK 225
                                       *766666666555...55666666666655666665554....444444.445566677889999999999999999 PP

                            AAA_13 430 kelkeeeaelkkleeeikeLekqlrdekpaaeeinke 466
                                       ke++e  +++ +l+++++e++++lr++++ + e+ ++
  gi|242399807|ref|YP_002995232.1| 226 KEADEYHQKVIELRDKMREIREELREVEKKIFEFDQK 262
                                       9999999999999999999999999999999888765 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   5.8     3e-05     0.014      69     105 ..      21      57 ..      12      58 .. 0.93
   2 ?    0.1  14.0       1.6   7.6e+02       5      84 ..      63     140 ..      59     144 .. 0.74
   3 ?    0.6   4.0       1.1   5.3e+02      12      45 ..     150     183 ..     140     189 .. 0.78
   4 ?    2.0   0.4       0.4     2e+02       4      28 ..     169     193 ..     167     200 .. 0.74
   5 ?    1.3   4.5      0.65   3.1e+02       1      32 [.     201     232 ..     201     233 .. 0.88
   6 ?    5.2   4.8     0.041        20       8      54 ..     229     275 ..     226     304 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCTS- CS
                       Prefoldin_2  69 erketlekeiktlekqleklekeleelkeelqkklqq 105
                                       e+++++++ei+ le+++++++++le+l++el++ +q+
  gi|242399807|ref|YP_002995232.1|  21 EEIKRIKAEIEVLEREKKEIKERLEQLQKELNIWVQK 57 
                                       57899***************************99887 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.6
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-TT--EEEEETTEEEEE-HHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2   5 nkfqqlqqqlqqlaqqikqletqlkelelvleelelldedtkvyklvGdvlvkqdkeevkeeLeerketlekeiktl 81 
                                       ++ + l+++ ++++++++++++q++el++  ee++     +  y+   +   k+d    + +L+  ke++e++i++l
  gi|242399807|ref|YP_002995232.1|  63 KEVKHLREKAREYKTKRDEVNQQIQELKKNREEINAK--LNLLYQEAMEYRAKRDEYRQLRRLKMPKEKIEERIEKL 137
                                       6778899999999999999999999999999998742..23455555566667777777777888888888888877 PP

                                       HHH CS
                       Prefoldin_2  82 ekq 84 
                                       e +
  gi|242399807|ref|YP_002995232.1| 138 EWE 140
                                       765 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-TT- CS
                       Prefoldin_2  12 qqlqqlaqqikqletqlkelelvleelelldedt 45 
                                       ++ +q++ qi+ l t+l+ l+++    + l e++
  gi|242399807|ref|YP_002995232.1| 150 EREKQIVDQIQVLATELEILQQADRFHKRLQETR 183
                                       6788999999999999999999887766666665 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.4
                                       HHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2   4 inkfqqlqqqlqqlaqqikqletql 28 
                                       + +  + +++lq+  ++i++l++  
  gi|242399807|ref|YP_002995232.1| 169 LQQADRFHKRLQETRKKIESLKRAR 193
                                       6677788888888888888888765 PP

  == domain 5  score: 1.3 bits;  conditional E-value: 0.65
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2   1 qelinkfqqlqqqlqqlaqqikqletqlkele 32 
                                       q+l+n+ qq ++q+ +  qq ++++++ +e +
  gi|242399807|ref|YP_002995232.1| 201 QKLANQSQQFHEQMLKSYQQADEIKKEADEYH 232
                                       78999999999999999999999999999875 PP

  == domain 6  score: 5.2 bits;  conditional E-value: 0.041
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-TT--EEEEETTE CS
                       Prefoldin_2   8 qqlqqqlqqlaqqikqletqlkelelvleelelldedtkvyklvGdv 54 
                                        +++q++ +l  ++++++++l+e+e+ + e+++  ++   yk+v ++
  gi|242399807|ref|YP_002995232.1| 229 DEYHQKVIELRDKMREIREELREVEKKIFEFDQKHKELIAYKMVAKM 275
                                       56788888888888888888888888888888888888888887776 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   1.9    0.0071       3.5      80     119 ..      12      52 ..       3      55 .. 0.78
   2 ?    2.5  12.9      0.34   1.6e+02       7     104 ..      67     166 ..      61     170 .. 0.69
   3 ?   15.4   9.0   3.5e-05     0.017      10      93 ..     170     256 ..     165     259 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0071
                           DUF5082  80 qtyvdkld.elidaieeEIerLenqiseaqgvldtlqsqln 119
                                       +t++ k+d e i++i+ EIe Le +++e +  l++lq++ln
  gi|242399807|ref|YP_002995232.1|  12 ETMQVKVDpEEIKRIKAEIEVLEREKKEIKERLEQLQKELN 52 
                                       55566666455789*********************999987 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.34
                           DUF5082   7 klqaqiaelrseiaaleekIerLkeaktklsdekeslkqkkkklekplnssesWkGk..eennydgirsnlessyqt 81 
                                        l++++ e++ +++ ++++I++Lk+ ++++ ++ + l+q+  + + +  ++  ++     +++ ++  ++le + qt
  gi|242399807|ref|YP_002995232.1|  67 HLREKAREYKTKRDEVNQQIQELKKNREEINAKLNLLYQEAMEYRAKRDEYRQLRRLkmPKEKIEERIEKLEWELQT 143
                                       56777888888899999999999999999999999888888888888777776665432344444444477777777 PP

                           DUF5082  82 yvdkldelidaieeEIerLenqi 104
                                         + + e +++i + I+ L++++
  gi|242399807|ref|YP_002995232.1| 144 NPTITSEREKQIVDQIQVLATEL 166
                                       77777777777777777666665 PP

  == domain 3  score: 15.4 bits;  conditional E-value: 3.5e-05
                           DUF5082  10 aqiaelrseiaaleekIerLkeaktklsdekeslkqkkkklekplnsse...sWkGkeennydgirsnlessyqtyv 83 
                                       +q++   ++++ + +kIe Lk+a++++  e ++l ++ ++  ++ ++s       +ke+++y +++ +l ++++++ 
  gi|242399807|ref|YP_002995232.1| 170 QQADRFHKRLQETRKKIESLKRARRAMGLEIQKLANQSQQFHEQMLKSYqqaDEIKKEADEYHQKVIELRDKMREIR 246
                                       7888999999********************9999999888877777666576667789999999************* PP

                           DUF5082  84 dkldelidai 93 
                                       ++l+e++++i
  gi|242399807|ref|YP_002995232.1| 247 EELREVEKKI 256
                                       ******9998 PP

>> DUF4140  N-terminal domain of unknown function (DUF4140)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   1.5   4.2e-05      0.02      63      98 .]      18      54 ..       3      54 .. 0.81
   2 ?    5.3   5.2     0.057        28      61      95 ..      59      93 ..      55     106 .. 0.60
   3 ?   -0.1   1.1       2.7   1.3e+03      67      80 ..     127     140 ..      92     155 .. 0.57
   4 ?    3.6   7.5      0.19        93      46      95 ..     158     207 ..     129     210 .. 0.71
   5 ?    4.5   3.0     0.095        46      65      88 ..     227     256 ..     207     266 .. 0.58

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.2e-05
                           DUF4140 63 eee.elkalraeleeledelaaledelaaaearlafl 98
                                      +++ e+k+++ae+e le+e+++++++l+ ++++l+++
  gi|242399807|ref|YP_002995232.1| 18 VDPeEIKRIKAEIEVLEREKKEIKERLEQLQKELNIW 54
                                      23335*****************************986 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.057
                           DUF4140 61 eaeeeelkalraeleeledelaaledelaaaearl 95
                                      +++++e+k+lr++ +e ++++++++++++ +++ +
  gi|242399807|ref|YP_002995232.1| 59 DEKNKEVKHLREKAREYKTKRDEVNQQIQELKKNR 93
                                      44444566666666666666666666666666543 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 2.7
                           DUF4140  67 lkalraeleelede 80 
                                        +++++++e+le e
  gi|242399807|ref|YP_002995232.1| 127 KEKIEERIEKLEWE 140
                                       22334444444433 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.19
                           DUF4140  46 aatildvqvervpnreaeeeelkalraeleeledelaaledelaaaearl 95 
                                       ++++l  ++e  ++ + + ++l+++r+++e+l+++++a   e++ + ++ 
  gi|242399807|ref|YP_002995232.1| 158 QIQVLATELEILQQADRFHKRLQETRKKIESLKRARRAMGLEIQKLANQS 207
                                       34555556666666666666899999999999999999999999888775 PP

  == domain 5  score: 4.5 bits;  conditional E-value: 0.095
                           DUF4140  65 e......elkalraeleeledelaaledel 88 
                                       e      ++ +lr++++e+++el+++e+++
  gi|242399807|ref|YP_002995232.1| 227 EadeyhqKVIELRDKMREIREELREVEKKI 256
                                       112234346666666666666666666554 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1       3.3   1.6e+03      73      98 ..      15      40 ..       6      41 .. 0.75
   2 ?    4.8  12.8     0.088        43       7      85 ..      37     121 ..      33     138 .. 0.79
   3 ?   -1.1   6.3       5.9   2.9e+03      39      58 ..     123     142 ..      93     197 .. 0.41
   4 ?   15.1   3.9   5.4e-05     0.026       9      65 ..     199     270 ..     194     309 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 3.3
                      Syntaxin-6_N 73 kfkidekelsrrrafveevreevkem 98
                                      ++k+d++e++r +a +e +++e ke+
  gi|242399807|ref|YP_002995232.1| 15 QVKVDPEEIKRIKAEIEVLEREKKEI 40
                                      58899999999998888888776666 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.088
                      Syntaxin-6_N   7 keeVqkslnkaeslyrrwerlledtsss......tseeldetrteLrkalrsiewdledLeetvriveknpskfkid 77 
                                       k+e+++ l+++++ ++ w + +++++++      +  e++  r+e+++++++++++ e+++   + + ++  +++ +
  gi|242399807|ref|YP_002995232.1|  37 KKEIKERLEQLQKELNIWVQKRDEKNKEvkhlreKAREYKTKRDEVNQQIQELKKNREEINAKLNLLYQEAMEYRAK 113
                                       789***************77667766634678888888888888888888888888888888888888888888888 PP

                      Syntaxin-6_N  78 ekelsrrr 85 
                                        +e ++ r
  gi|242399807|ref|YP_002995232.1| 114 RDEYRQLR 121
                                       88776654 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 5.9
                      Syntaxin-6_N  39 ldetrteLrkalrsiewdle 58 
                                       l+  ++++++ ++++ew+l+
  gi|242399807|ref|YP_002995232.1| 123 LKMPKEKIEERIEKLEWELQ 142
                                       33333333444444444333 PP

  == domain 4  score: 15.1 bits;  conditional E-value: 5.4e-05
                      Syntaxin-6_N   9 eVqkslnkaeslyrrwerlledtss..stseeldetrteLrkalrsiewdledLeetv.............r 65 
                                       e+qk +n+ ++ ++++ +  +++++  ++ +e+++   eLr ++r+i+++l++ e+ +             +
  gi|242399807|ref|YP_002995232.1| 199 EIQKLANQSQQFHEQMLKSYQQADEikKEADEYHQKVIELRDKMREIREELREVEKKIfefdqkhkeliayK 270
                                       8999**********99533333333347899*************************9955555555444442 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1  52.2   0.00032      0.16      79     347 ..       6     270 ..       3     294 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00032
                                       HHHHT-GGGT--S-SHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHHHHHHHHHHHHHHT--TT CS
                              EzrA  79 eieellfeaeelldkykfkkakkklaeleeeldeveekikkileelkelteseeknreeieklkekYrelrkkllan 155
                                       +iee  + ++  +d  ++k++k++++ le e +e++e+++++++el+  +++  ++ +e+++l+ek re ++k  + 
  gi|242399807|ref|YP_002995232.1|   6 KIEEGEETMQVKVDPEEIKRIKAEIEVLEREKKEIKERLEQLQKELNIWVQKRDEKNKEVKHLREKAREYKTKRDEV 82 
                                       56666667777888899***********************************************9977776665555 PP

                                       TTHHHHHHHHHHHHHHHH------.----------HHHHHH...HHHHHHHHHHHHHHHHHHHHHHTTTTTTSHHHH CS
                              EzrA 156 rfsygealeelekqleniekefse.feeltengdyveakei...lkkleeeideleevieeiPelleelkkelpkql 228
                                       +++ +e +++ e+  ++++  ++e +e   +  +y + +++    +k+ee+i++le  +++ P++ +e +k++ +q+
  gi|242399807|ref|YP_002995232.1|  83 NQQIQELKKNREEINAKLNLLYQEaMEYRAKRDEYRQLRRLkmpKEKIEERIEKLEWELQTNPTITSEREKQIVDQI 159
                                       5555555555555555555555441333445555666554422279******************************* PP

                                       HHHHHHHHHSTTS--SGGGSSSSSHHHHHHHHHHHHH..HHHTT--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              EzrA 229 eelkegykemkeegYaleelniekeieelekkieeil..erlkeleledveeelktieeeidsLyddlekEveAkke 303
                                       + l +  + ++++        + k+++e++kkie++    r   le+++ +++ ++ +e++ + y++ ++ ++  +e
  gi|242399807|ref|YP_002995232.1| 160 QVLATELEILQQA------DRFHKRLQETRKKIESLKraRRAMGLEIQKLANQSQQFHEQMLKSYQQADEIKKEADE 230
                                       ****999988876......4788899999999988873233444555555555556666555555555555555555 PP

                                       HTTTSSSSSHHHHT--HHHHTTGGG-TTTS-GGGSSTTTSTTHH CS
                              EzrA 304 veknlkelkeklehlekqnkelkeeldrlkqsYeLseeeleklr 347
                                       +++++ el++k+ +++++++e+++++ + +q    +++el  ++
  gi|242399807|ref|YP_002995232.1| 231 YHQKVIELRDKMREIREELREVEKKIFEFDQ----KHKELIAYK 270
                                       5555555555555555555555555554444....455555555 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   5.4    0.0043       2.1      62      99 ..      16      53 ..       5      57 .. 0.79
   2 ?    4.7  14.8      0.07        34      19      96 ..      60     140 ..      54     162 .. 0.64
   3 ?   14.2  13.7   7.7e-05     0.037       7      98 ..     162     257 ..     155     262 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0043
                                      CCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N 62 akkkkedaeeliaevkelkeelkaleaelkeleaelek 99
                                       k + e++++++ae++ l  e k+++++l++l++el+ 
  gi|242399807|ref|YP_002995232.1| 16 VKVDPEEIKRIKAEIEVLEREKKEIKERLEQLQKELNI 53
                                      44444899999999999999999999999999999986 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.07
                                       CCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT...S-TCCCCCCCHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  19 kkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkk...edaeeliaevkelkeelkaleaelke 92 
                                       +k +e k + ++  e  +kr e++++++el+++r e++++   + ++      + +   + + lk   +++e++ ++
  gi|242399807|ref|YP_002995232.1|  60 EKNKEVKHLREKAREYKTKRDEVNQQIQELKKNREEINAKLNLLYQEAmeyRAKRDEYRQLRRLKMPKEKIEERIEK 136
                                       33335566666677777777777777777777777777777777777644433333333445555555555555555 PP

                                       HHHH CS
                      Seryl_tRNA_N  93 leae 96 
                                       le e
  gi|242399807|ref|YP_002995232.1| 137 LEWE 140
                                       5555 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 7.7e-05
                                       HHH-HHHHHHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT....S-TCCCCCCCHHH CS
                      Seryl_tRNA_N   7 irenpeavkeklkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkk....edaeeliaevkel 79 
                                       + +++e ++++ +  ++ +++ +++ +l ++rr++  e+++l +++ +  +++ k  ++     ++a+e  ++v el
  gi|242399807|ref|YP_002995232.1| 162 LATELEILQQADRFHKRLQETRKKIESLKRARRAMGLEIQKLANQSQQFHEQMLKSYQQAdeikKEADEYHQKVIEL 238
                                       5556666666655555789999***********************99999999999888777778999999999999 PP

                                       HHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  80 keelkaleaelkeleaele 98 
                                        +++ ++ +el+e+e+++ 
  gi|242399807|ref|YP_002995232.1| 239 RDKMREIREELREVEKKIF 257
                                       9999999999999998875 PP

>> Sterile  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.5    0.0004      0.19      20      78 ..     212     269 ..     194     293 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0004
                           Sterile  20 prlvrlykkikklvelleyFtlnewkfdndnlekLldrlseedrkiFnfdvrsidwedY 78 
                                       +++++ y+++ ++ +    +  +  +   d++++++++l+e ++kiF+fd ++ +  +Y
  gi|242399807|ref|YP_002995232.1| 212 EQMLKSYQQADEIKKEADEYHQKVIEL-RDKMREIREELREVEKKIFEFDQKHKELIAY 269
                                       567777777777777777776655444.578*******************987666666 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   1.9    0.0075       3.7      46      90 .]       7      48 ..       2      48 .. 0.82
   2 ?    2.0  10.6      0.59   2.9e+02      14      89 ..      64     137 ..      61     143 .. 0.84
   3 ?    6.6   3.2     0.022        11      29      77 ..     152     191 ..     140     204 .. 0.60
   4 ?   13.9  10.3   0.00011     0.054      13      86 ..     177     256 ..     175     260 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0075
                   Snapin_Pallidin 46 leeaqeaevlpdlkeyakKLvnikkrmsslnerlqklkkRaekLq 90
                                      +ee +e     ++k   + +++ik +++ l+   +++k+R+e+Lq
  gi|242399807|ref|YP_002995232.1|  7 IEEGEE---TMQVKVDPEEIKRIKAEIEVLEREKKEIKERLEQLQ 48
                                      444444...6678888899************************97 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.59
                   Snapin_Pallidin  14 kldeldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlqklkkRaekL 89 
                                       +++ l+ek +e +++ +e+++q+++l+++ +e++   +  + ++++ey++K  + + ++ +l+   +k+++R+ekL
  gi|242399807|ref|YP_002995232.1|  64 EVKHLREKAREYKTKRDEVNQQIQELKKNREEINAKLN-LLYQEAMEYRAKRDEYR-QLRRLKMPKEKIEERIEKL 137
                                       68899999999999999999999999999999999887.88899999999988876.5788888888888888887 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.022
                   Snapin_Pallidin  29 QeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslne 77 
                                        ++  +q++ l+++L+         +l+++++ +k+L++ +k+++sl+ 
  gi|242399807|ref|YP_002995232.1| 152 EKQIVDQIQVLATELE---------ILQQADRFHKRLQETRKKIESLKR 191
                                       4444555555555555.........455555566666666666665554 PP

  == domain 4  score: 13.9 bits;  conditional E-value: 0.00011
                   Snapin_Pallidin  13 pkldeldeklkelrqsQeeLleqldrlnekLke.....leeaqe.aevlpdlkeyakKLvnikkrmsslnerlqklk 83 
                                         l+e+++k+++l++  +++  ++++l+++ ++     l+ +q+ +e+ ++++ey++K+++++ +m ++ e l++++
  gi|242399807|ref|YP_002995232.1| 177 KRLQETRKKIESLKRARRAMGLEIQKLANQSQQfheqmLKSYQQaDEIKKEADEYHQKVIELRDKMREIREELREVE 253
                                       67899999999999999999988888877766611133456788999****************************** PP

                   Snapin_Pallidin  84 kRa 86 
                                       k++
  gi|242399807|ref|YP_002995232.1| 254 KKI 256
                                       997 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  10.6    0.0023       1.1       8      80 ..      33     105 ..      12     110 .. 0.88
   2 ?    6.6   9.4     0.015       7.3       6      87 ..      66     146 ..      60     162 .. 0.71
   3 ?    6.2   4.0      0.02       9.6      13      75 ..     153     214 ..     145     226 .. 0.80
   4 ?    8.7   1.8    0.0035       1.7      11      70 ..     220     281 ..     216     300 .. 0.54

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0023
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHH CS
                        Laminin_II   8 anetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkq 80 
                                        +   ke++e l++l+++l+ + +k  e n++v++  ek++++++  +++++++++L+k+ +++ +kl+ l q
  gi|242399807|ref|YP_002995232.1|  33 LEREKKEIKERLEQLQKELNIWVQKRDEKNKEVKHLREKAREYKTKRDEVNQQIQELKKNREEINAKLNLLYQ 105
                                       55567899999999*********************************************99999999987766 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.015
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHH CS
                        Laminin_II   6 aeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqle 82 
                                       +   e+a e + +  +++q+++++k++ +ein++++   +++ ++ +a rd  r+ + L++  +++++++++l+   
  gi|242399807|ref|YP_002995232.1|  66 KHLREKAREYKTKRDEVNQQIQELKKNREEINAKLNLLYQEAMEY-RAKRDEYRQLRRLKMPKEKIEERIEKLEWEL 141
                                       555677777777777888888888888888888877777777665.4668888999999999*******99999766 PP

                                       HH... CS
                        Laminin_II  83 easss 87 
                                       + + +
  gi|242399807|ref|YP_002995232.1| 142 QTNPT 146
                                       66444 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.02
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGH CS
                        Laminin_II  13 kevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldkl 75 
                                       k++ +q++ l+++le + +++ ++++ ++et +k++++++a r  + +++kL ++ +q  +++
  gi|242399807|ref|YP_002995232.1| 153 KQIVDQIQVLATELE-ILQQADRFHKRLQETRKKIESLKRARRAMGLEIQKLANQSQQFHEQM 214
                                       566677777788875.678899******************************99999999984 PP

  == domain 4  score: 8.7 bits;  conditional E-value: 0.0035
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXX--TTTT CS
                        Laminin_II  11 takevleqlaplsqnlentkeklseinrsveetnekvk..dankairdArrsvkkLeklapq 70 
                                       +a e+++   + +q++ ++++k+ ei+++++e+++k+   d ++    A + v k+  + + 
  gi|242399807|ref|YP_002995232.1| 220 QADEIKKEADEYHQKVIELRDKMREIREELREVEKKIFefDQKHKELIAYKMVAKMRSKKDA 281
                                       44555555555566666666666666666666666555333334444455555555444444 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1  20.0   0.00011     0.054     331     421 ..      22     114 ..       7     125 .. 0.80
   2 ?   10.1   8.8   0.00046      0.22     334     402 ..      74     142 ..      68     145 .. 0.93
   3 ?    5.4  18.7     0.012       5.7     342     443 ..     148     250 ..     118     261 .. 0.75
   4 ?    6.4   2.8    0.0059       2.9     334     391 ..     237     294 ..     227     305 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00011
                              FapA 331 depelkeklkeleeeleeleeeleklkkkikklpklka.ekqlesekkeqlkklletkeklkeeleeleeelkelke 406
                                       + + +k++++ le+e +e++e+le+l+k+++   +++  +++  ++ +e+  ++++++ + +++++el+++++e+++
  gi|242399807|ref|YP_002995232.1|  22 EIKRIKAEIEVLEREKKEIKERLEQLQKELNIWVQKRDeKNKEVKHLREKAREYKTKRDEVNQQIQELKKNREEINA 98 
                                       445677888********************99999977734444455567777777777******************* PP

                              FapA 407 eleskkeea.kikvnk 421
                                       +l+  ++ea ++++++
  gi|242399807|ref|YP_002995232.1|  99 KLNLLYQEAmEYRAKR 114
                                       ****999998888876 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00046
                              FapA 334 elkeklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelk 402
                                       e+k k++e++++++el+++ e++++k+++l +++ e++ + +   ql +l+  kek++e++e+le el+
  gi|242399807|ref|YP_002995232.1|  74 EYKTKRDEVNQQIQELKKNREEINAKLNLLYQEAMEYRAKRDEYRQLRRLKMPKEKIEERIEKLEWELQ 142
                                       688899**************************888*****************************98776 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.012
                              FapA 342 leeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeeleskkeea.ki 417
                                         e+ +++ ++++ l  +++ l++     +  +e ++++++l++++ ++  e+++l ++ ++  e++ +++++a +i
  gi|242399807|ref|YP_002995232.1| 148 TSEREKQIVDQIQVLATELEILQQADRFHKRLQETRKKIESLKRARRAMGLEIQKLANQSQQFHEQMLKSYQQAdEI 224
                                       333444445555555555666666555556677889999999999*********************999999999** PP

                              FapA 418 kvnkeiypgvkikigkkkliikreys 443
                                       k +   y   +i++++k+++i++e  
  gi|242399807|ref|YP_002995232.1| 225 KKEADEYHQKVIELRDKMREIREELR 250
                                       **********************9944 PP

  == domain 4  score: 6.4 bits;  conditional E-value: 0.0059
                              FapA 334 elkeklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklk 391
                                       el++k++e++eel+e+e+++ + ++k k+l + k   ++ s+k  +++++ e++ek+k
  gi|242399807|ref|YP_002995232.1| 237 ELRDKMREIREELREVEKKIFEFDQKHKELIAYKMVAKMRSKKDATFERAVEALEKFK 294
                                       4455556666666666666666666666666655566666666666666666665554 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 ?   11.2  20.1   0.00029      0.14      50     157 ..       9     110 ..       3     114 .. 0.80
   2 ?   -3.1  19.1       6.4   3.1e+03      57     130 ..      60     135 ..      55     171 .. 0.46
   3 ?    1.9  14.1      0.19        94      30     135 ..     119     217 ..     114     220 .. 0.55
   4 ?    8.1  18.3    0.0026       1.2      22     121 ..     177     282 ..     170     301 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00029
                             Atg14  50 egkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklkkRrsdleslqnele 126
                                       eg     ++++++k + + ++++k++i+ l+++++e+k++l+ql+ke+++  +k  ++++++k+ r++++  +++  
  gi|242399807|ref|YP_002995232.1|   9 EG-----EETMQVKVDPEEIKRIKAEIEVLEREKKEIKERLEQLQKELNIWVQKRDEKNKEVKHLREKAREYKTKRD 80 
                                       33.....35889***************************************************99999666666555 PP

                             Atg14 127 errkkqiaklqdaikrieqklsslssktles 157
                                       e  ++qi++l ++  +i  kl+ l ++ +e 
  gi|242399807|ref|YP_002995232.1|  81 EV-NQQIQELKKNREEINAKLNLLYQEAMEY 110
                                       44.5678888887777777777666666665 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 6.4
                             Atg14  57 qledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklk..kRrsdleslqneleerrk 130
                                       ++++++k++++k++e k+++ + ++++qelk+ +++ +++++   ++  ++++k    +  ++l+  ++++eer +
  gi|242399807|ref|YP_002995232.1|  60 EKNKEVKHLREKAREYKTKRDEVNQQIQELKKNREEINAKLNLLYQEAMEYRAKRDeyRQLRRLKMPKEKIEERIE 135
                                       3344444444444444444444444444444444444444443333333333332232111222333444444433 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.19
                             Atg14  30 rlaklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklak 106
                                       +l++lk  ke ++++iek++ + +      ++   ++++ +++  +i+ l  +l e+ ++ ++  k+++e++kk+++
  gi|242399807|ref|YP_002995232.1| 119 QLRRLKMPKEKIEERIEKLEWELQ------TNPTITSEREKQIVDQIQVLATEL-EILQQADRFHKRLQETRKKIES 188
                                       678888888888888887766666......333333333333333333333333.3555666666666666666666 PP

                             Atg14 107 lsdklkkRrsdleslqneleerrkkqiak 135
                                       l+++   +  ++++l n+ ++ +++ +++
  gi|242399807|ref|YP_002995232.1| 189 LKRARRAMGLEIQKLANQSQQFHEQMLKS 217
                                       66665555555555555555555555554 PP

  == domain 4  score: 8.1 bits;  conditional E-value: 0.0026
                             Atg14  22 erlyelrerlaklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeie 98 
                                       +rl e r+++ +lk ++ +++ +i+k+ ++ +   q  ++  ++ ++++e+k++  + ++++ el+dk+++ ++e++
  gi|242399807|ref|YP_002995232.1| 177 KRLQETRKKIESLKRARRAMGLEIQKLANQSQ---QFHEQMLKSYQQADEIKKEADEYHQKVIELRDKMREIREELR 250
                                       599**********************8888888...9999************************************** PP

                             Atg14  99 ekkkklaklsdklk.........kRrsdlesl 121
                                       e  kk+ + ++k k         k+rs+ +++
  gi|242399807|ref|YP_002995232.1| 251 EVEKKIFEFDQKHKeliaykmvaKMRSKKDAT 282
                                       ******99999999888887777444333322 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0  21.0     0.023        11      47     121 ..      23      97 ..       5     101 .. 0.78
   2 ?    0.3  31.6       1.4   6.6e+02       3     123 ..      63     213 ..      59     220 .. 0.80
   3 ?    6.8  21.4     0.013       6.2      19     126 ..     152     265 ..     147     280 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.023
                    CENP-F_leu_zip  47 aEtskaevetlkeeieelaeelreleldLvalrsekeeLekelqkkqervseLeslnsslenlleekEqekvqmk 121
                                           kae+e l+ e++e++e+l++l+ +L+   + ++e +ke+++ +e+  e ++ + +++++++e+ +++ +++
  gi|242399807|ref|YP_002995232.1|  23 IKRIKAEIEVLEREKKEIKERLEQLQKELNIWVQKRDEKNKEVKHLREKAREYKTKRDEVNQQIQELKKNREEIN 97 
                                       344688999999999999999999999999999999999999999999999999999999999998877766655 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.4
                    CENP-F_leu_zip   3 kkklhvlekLKeserkadsLkdkvenLerelemseenqekvileaEtskaevet......lkeeieelaeelrelel 73 
                                       k+ +h++ek +e + k d +++++++L+++ e+++++++ +  ea + +a+  +      lk  +e+++e+ ++le 
  gi|242399807|ref|YP_002995232.1|  63 KEVKHLREKAREYKTKRDEVNQQIQELKKNREEINAKLNLLYQEAMEYRAKRDEyrqlrrLKMPKEKIEERIEKLEW 139
                                       6779***********************************9999998877766555567779**************** PP

                    CENP-F_leu_zip  74 dLvalr........................sekeeLekelqkkqervseLeslnsslenlleekEqekvqmkee 123
                                       +L++                          ++ +  +k lq+ ++++++L++++  +   ++++ ++  q +e+
  gi|242399807|ref|YP_002995232.1| 140 ELQTNPtitserekqivdqiqvlateleilQQADRFHKRLQETRKKIESLKRARRAMGLEIQKLANQSQQFHEQ 213
                                       **986666677777788888888877777777777777888888888888777777777777777777776666 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.013
                    CENP-F_leu_zip  19 adsLkdkvenLerelemseen......qekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLekel 89 
                                       + ++ d+++ L  ele++++       ++++    E+ k +  ++  ei++la++ ++++ ++ +  ++ +e++ke 
  gi|242399807|ref|YP_002995232.1| 152 EKQIVDQIQVLATELEILQQAdrfhkrLQETRKKIESLKRARRAMGLEIQKLANQSQQFHEQMLKSYQQADEIKKEA 228
                                       4467899*********99976111111344444445555555558889***************************** PP

                    CENP-F_leu_zip  90 qkkqervseLeslnsslenlleekEqekvqmkeeska 126
                                        +  ++v eL     ++++ l+e E++  +  +++k+
  gi|242399807|ref|YP_002995232.1| 229 DEYHQKVIELRDKMREIREELREVEKKIFEFDQKHKE 265
                                       ***************************9988888876 PP

>> Laminin_I  Laminin Domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1  14.8     0.017         8      36     115 ..      24     103 ..       2     114 .. 0.76
   2 ?   11.7  16.4   0.00031      0.15      10     138 ..     148     279 ..     141     299 .. 0.63

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.017
                         Laminin_I  36 sakkskieilekelesLaqeteeLqkkatqvlakaqkvnaesertlnnakeLaekikkladnikeilekvatlnene 112
                                       +  k +ie+le+e +++++  e+Lqk+++   +k  + n+e++   ++a e ++k  +++++i+e+ +  +++n + 
  gi|242399807|ref|YP_002995232.1|  24 KRIKAEIEVLEREKKEIKERLEQLQKELNIWVQKRDEKNKEVKHLREKAREYKTKRDEVNQQIQELKKNREEINAKL 100
                                       33456788899999999999999999999999999999999999999999999999999999999988888887765 PP

                         Laminin_I 113 eal 115
                                       + l
  gi|242399807|ref|YP_002995232.1| 101 NLL 103
                                       554 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00031
                         Laminin_I  10 aleapykinanledltkeLqeklskesakkskieilekelesLaqeteeLqkkatqvlakaqkvnaesertlnnake 86 
                                        +e+ ++i  +++ l++eL+   ++ + +k++ e   k++esL+   + +  + ++   + q+  +++ +  ++a e
  gi|242399807|ref|YP_002995232.1| 148 TSEREKQIVDQIQVLATELEILQQADRFHKRLQETR-KKIESLKRARRAMGLEIQKLANQSQQFHEQMLKSYQQADE 223
                                       556666666777777777776666666666665555.6677777777777777777777777777777777777777 PP

                         Laminin_I  87 Laekikkladnikeilekvatlneneealpss..klseelae..aqrlLeelrsRd 138
                                        ++++ + ++++ e+  k+ ++ e+  ++ ++  +++++++e  a ++  ++rs+ 
  gi|242399807|ref|YP_002995232.1| 224 IKKEADEYHQKVIELRDKMREIREELREVEKKifEFDQKHKEliAYKMVAKMRSKK 279
                                       77777777777777777777777766666555334455555544566777777654 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1  23.2     0.002      0.98      47     141 ..      33     126 ..      28     127 .. 0.90
   2 ?   10.0  20.5    0.0011      0.52      56     176 ..     128     250 ..     124     251 .. 0.90
   3 ?    5.5   8.0     0.025        12      74     126 ..     216     268 ..     212     283 .. 0.88
   4 ?   -1.7   0.1       4.1     2e+03      21      50 ..     282     310 ..     269     312 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.002
                           DUF4201  47 lqienqalnkkIeernkeLkrlkkkttktvhalthlkeklhmleselselkkelkekeerlaklrkelykvklerdk 123
                                       l++e ++ ++++e  +keL+   +k   + ++++hl+ek+ +++++  e +++++e++++++++ ++l+ + +e   
  gi|242399807|ref|YP_002995232.1|  33 LEREKKEIKERLEQLQKELNIWVQKRDEKNKEVKHLREKAREYKTKRDEVNQQIQELKKNREEINAKLNLLYQEAME 109
                                       7889999999999999999999999999************************************************* PP

                           DUF4201 124 lrkqneklkqqggllrvP 141
                                       +r+++++ +q   l ++P
  gi|242399807|ref|YP_002995232.1| 110 YRAKRDEYRQLRRL-KMP 126
                                       **999999876554.666 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0011
                           DUF4201  56 kkIeernkeLk.rlkkkttktvhalthlkeklhmleselselkkelkekeerlaklrkelykvklerdklrkqnekl 131
                                       +kIeer ++L+ +l+ + t t+ + +++ +  + l++el+ l++  ++ ++rl++ rk+++++k  r  +  + +kl
  gi|242399807|ref|YP_002995232.1| 128 EKIEERIEKLEwELQTNPTITSEREKQIVDQIQVLATELEILQQ-ADRFHKRLQETRKKIESLKRARRAMGLEIQKL 203
                                       9*********879***************************9975.799***************************** PP

                           DUF4201 132 kqqggllrvPaLlkDY...dktkekveekrksvkkLrrkvkilemrlk 176
                                         q+++++   L   Y   d+ k++ +e +++v +Lr k++++ + l+
  gi|242399807|ref|YP_002995232.1| 204 ANQSQQFHEQMLKS-YqqaDEIKKEADEYHQKVIELRDKMREIREELR 250
                                       ******77666655.8333456889999**************998876 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.025
                           DUF4201  74 ktvhalthlkeklhmleselselkkelkekeerlaklrkelykvklerdklrk 126
                                       k+ ++  ++k+ ++++ +++ el+++++e+ e+l++++k++ +  ++++ l +
  gi|242399807|ref|YP_002995232.1| 216 KSYQQADEIKKEADEYHQKVIELRDKMREIREELREVEKKIFEFDQKHKELIA 268
                                       678999999***************************************99875 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 4.1
                           DUF4201  21 qlakiqeklekkeelgegLtlidFeqlqie 50 
                                       ++++  e lek++  ge+Ltl++ + lq+ 
  gi|242399807|ref|YP_002995232.1| 282 TFERAVEALEKFK-RGEKLTLDELLLLQRY 310
                                       5555556666655.4899999998888875 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7  25.7      0.13        61      72     163 ..      12     120 ..       4     143 .. 0.79
   2 ?   11.6  12.0   0.00049      0.24      26     135 ..     154     266 ..     150     281 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.13
                             ATG16  72 qsakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelre 148
                                       ++ +++ + ++++++++e + l +++ e ++rl +l++el    +k  e+++++++l+++ ++ +tk+++ +++++e
  gi|242399807|ref|YP_002995232.1|  12 ETMQVKVDPEEIKRIKAEIEVLEREKKEIKERLEQLQKELNIWVQKRDEKNKEVKHLREKAREYKTKRDEVNQQIQE 88 
                                       56678888999****************************************************************** PP

                             ATG16 149 keklvq.................dlqDElsaL 163
                                       ++k  +                 + +DE+ +L
  gi|242399807|ref|YP_002995232.1|  89 LKKNREeinaklnllyqeameyrAKRDEYRQL 120
                                       *9998866666666666666666666666554 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00049
                             ATG16  26 rLldrtsaleaenaklekaaasaks.sksskksakekeasasq..snskqsakiqsleqklaqlreelaelyksrge 99 
                                       ++ d+++ l++e + l++a    k  +++ kk ++ k+a+++   + +k ++++q+ ++++++  ++  e  k+  e
  gi|242399807|ref|YP_002995232.1| 154 QIVDQIQVLATELEILQQADRFHKRlQETRKKIESLKRARRAMglEIQKLANQSQQFHEQMLKSYQQADEIKKEADE 230
                                       7899999999999999777665555755555555555555555798888899999999999999999********** PP

                             ATG16 100 laqrllelneelqkleeklkedeerlaeleaeraal 135
                                         q+++el +++++ +e+l+e e+++ e  +++++l
  gi|242399807|ref|YP_002995232.1| 231 YHQKVIELRDKMREIREELREVEKKIFEFDQKHKEL 266
                                       *************************99998888776 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  16.2     0.018       8.7      25     122 ..      32     138 ..      29     144 .. 0.72
   2 ?    2.5   0.9       0.3   1.5e+02      30      63 ..     127     161 ..     121     171 .. 0.72
   3 ?    8.8  12.3    0.0035       1.7      26     129 ..     168     267 ..     163     271 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.018
                                       CCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCH......... CS
                         Fib_alpha  25 lllkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilr......... 92 
                                       +l++ +k++k++le+l++el+   ++  e ++ vk+++++ re +++ ++ ++ i++++k+ e ei+          
  gi|242399807|ref|YP_002995232.1|  32 VLEREKKEIKERLEQLQKELNIWVQKRDEKNKEVKHLREKAREYKTKRDEVNQQIQELKKNRE-EINAklnllyqea 107
                                       68999**************************************99999998999999888877.4432011111111 PP

                                       HHHHHHCCH.HHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  93 lketidaqe.snirvLqnvlesneqkiqkLe 122
                                       ++ + ++ e +++r L+   e+ e++i+kLe
  gi|242399807|ref|YP_002995232.1| 108 MEYRAKRDEyRQLRRLKMPKEKIEERIEKLE 138
                                       3333444445666666666666666666666 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.3
                                       CCCCCHHHCCCCCCCCCCCCHHHHHH.HHHHHHHH CS
                         Fib_alpha  30 ekdvkkdlekleneleeisnstkeae.elvkeikd 63 
                                       ++++++++ekle el+++   t+e e ++v +i+ 
  gi|242399807|ref|YP_002995232.1| 127 KEKIEERIEKLEWELQTNPTITSEREkQIVDQIQV 161
                                       6789999********99988877765145555554 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0035
                                       CCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHH CS
                         Fib_alpha  26 llkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqes 102
                                       +l++   ++k+l++ ++++e++++  + +   ++++ ++ ++  ++  +      + ++e+++e  ++++++++   
  gi|242399807|ref|YP_002995232.1| 168 ILQQADRFHKRLQETRKKIESLKRARRAMGLEIQKLANQSQQFHEQMLK----SYQQADEIKKEADEYHQKVIELRD 240
                                       5678889999999999999999999999988888877776665555553....3344567777888*********** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 103 nirvLqnvlesneqkiqkLeqdidqke 129
                                       ++r++++ l++ e+ki +  q+ ++++
  gi|242399807|ref|YP_002995232.1| 241 KMREIREELREVEKKIFEFDQKHKELI 267
                                       *****************9999987776 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2  15.3     8e-05     0.039       2      83 ..      21     101 ..      20     111 .. 0.92
   2 ?   -2.1   6.2       3.7   1.8e+03      21      73 ..     110     161 ..      94     196 .. 0.47
   3 ?    8.3  11.1    0.0025       1.2       3      83 ..     199     283 ..     197     301 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8e-05
                             TMPIT   2 eeweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelker 78 
                                       ee+++++ e++ le ++ke+k++le+l+k  + ++++ ++++k++k+l+++ +++k++  +e +++++elk++ +e+
  gi|242399807|ref|YP_002995232.1|  21 EEIKRIKAEIEVLEREKKEIKERLEQLQKELNIWVQKRDEKNKEVKHLREKAREYKTKR-DEVNQQIQELKKNREEI 96 
                                       7999****************************************************995.799999******99999 PP

                             TMPIT  79 kkvlk 83 
                                       ++ l+
  gi|242399807|ref|YP_002995232.1|  97 NAKLN 101
                                       88776 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.7
                             TMPIT  21 ykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelke 73 
                                       y++k +e+ +l  +++   +k ++r+++l+ +l++  + ++e+e+++v++++ 
  gi|242399807|ref|YP_002995232.1| 110 YRAKRDEYRQLR-RLKMPKEKIEERIEKLEWELQTNPTITSEREKQIVDQIQV 161
                                       555554444433.3333444445555555555555555444444444444432 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0025
                             TMPIT   3 eweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk....eeeeeeveelkeel 75 
                                       e+++l+++ ++++e+  +  q+ +e++k  ++  +++ + + +++e++++l++++k++     +++e ++ ++ +++
  gi|242399807|ref|YP_002995232.1| 199 EIQKLANQSQQFHEQMLKSYQQADEIKKEADEYHQKVIELRDKMREIREELREVEKKIFefdqKHKELIAYKMVAKM 275
                                       7899****************************************************954333233333445666666 PP

                             TMPIT  76 kerkkvlk 83 
                                       +++k   +
  gi|242399807|ref|YP_002995232.1| 276 RSKKDATF 283
                                       55554443 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 ?    6.5   1.5      0.02       9.7      28      88 ..      23      83 ..      20      84 .. 0.87
   2 ?    4.7   0.5     0.072        35      24      62 ..      68     106 ..      65     124 .. 0.68
   3 ?    0.6   0.1       1.4   6.9e+02      71      74 ..     173     176 ..     117     196 .. 0.56
   4 ?    7.6   1.5    0.0093       4.5      25      87 ..     176     238 ..     164     258 .. 0.80
   5 ?    1.3   0.0      0.86   4.2e+02      22      50 ..     236     264 ..     231     293 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.02
                            DUF948 28 ldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvseln 88
                                      +++++a ie+le++ ++i + +e+l ++ n  ++   ek ++v++l e++++  ++  e+n
  gi|242399807|ref|YP_002995232.1| 23 IKRIKAEIEVLEREKKEIKERLEQLQKELNIWVQKRDEKNKEVKHLREKAREYKTKRDEVN 83
                                      567889999**********************9999999******99999998877666655 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.072
                            DUF948  24 lkktldeaaatieelekqvdpilkevedllakvnelled 62 
                                       l++ ++e ++  +e+++q++++ k+ e++ ak n l ++
  gi|242399807|ref|YP_002995232.1|  68 LREKAREYKTKRDEVNQQIQELKKNREEINAKLNLLYQE 106
                                       555566666666777777777777777777777766554 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 1.4
                            DUF948  71 dplt 74 
                                       d++ 
  gi|242399807|ref|YP_002995232.1| 173 DRFH 176
                                       2222 PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.0093
                            DUF948  25 kktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvsel 87 
                                        k l+e+++ ie+l++  +++  e+++l +++++  e++ +  ++ d++ +++ +  ++v el
  gi|242399807|ref|YP_002995232.1| 176 HKRLQETRKKIESLKRARRAMGLEIQKLANQSQQFHEQMLKSYQQADEIKKEADEYHQKVIEL 238
                                       678899999999999888888888888888888888888888888888877777776666554 PP

  == domain 5  score: 1.3 bits;  conditional E-value: 0.86
                            DUF948  22 lklkktldeaaatieelekqvdpilkeve 50 
                                       ++l++ ++e+++ ++e+ek++ +  ++ +
  gi|242399807|ref|YP_002995232.1| 236 IELRDKMREIREELREVEKKIFEFDQKHK 264
                                       56777788888888888877655555444 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   8.2    0.0033       1.6      17      64 ..     219     266 ..     213     303 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0033
                              Fez1  17 qQLkdsqaevtqklseivalkaqlrelrakleekeeeikeleesleek 64 
                                       qQ  ++++e  +  + +++l+ ++re+r++l+e e++i e++++ +e 
  gi|242399807|ref|YP_002995232.1| 219 QQADEIKKEADEYHQKVIELRDKMREIREELREVEKKIFEFDQKHKEL 266
                                       78999999999***************************9998876543 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   8.6     0.064        31       5      82 ..      23     101 ..      19     113 .. 0.79
   2 ?    2.9   5.8      0.18        89      10      60 ..      63     113 ..      55     160 .. 0.61
   3 ?    5.4   5.2     0.032        15      10      68 ..     170     228 ..     150     235 .. 0.60
   4 ?    9.3   1.2    0.0021         1       3      53 ..     219     269 ..     217     298 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.064
                             Sec34   5 LeskeeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLkyFe.eldpitrk 80 
                                       +++ ++e++ l ++ +e++e Le+l+++ +   +k  + +++ ++l e+ +++++  +e++++++  + + ++i+ k
  gi|242399807|ref|YP_002995232.1|  23 IKRIKAEIEVLEREKKEIKERLEQLQKELNIWVQKRDEKNKEVKHLREKAREYKTKRDEVNQQIQELKkNREEINAK 99 
                                       56667788888888899999999999999999999999999999999999999999999999887664145667777 PP

                             Sec34  81 Ln 82 
                                       Ln
  gi|242399807|ref|YP_002995232.1| 100 LN 101
                                       66 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.18
                             Sec34  10 eecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleel 60 
                                       +e+++l e+++e +++ +e++++ ++ +++ ++++++ + l++e  +++  
  gi|242399807|ref|YP_002995232.1|  63 KEVKHLREKAREYKTKRDEVNQQIQELKKNREEINAKLNLLYQEAMEYRAK 113
                                       444444444444444444444444444444444444444444444443333 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.032
                             Sec34  10 eecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekL 68 
                                       ++ d++ ++++e+ +++e+l+   +++  + ++l ++++q +e+  +  + a+ei+++ 
  gi|242399807|ref|YP_002995232.1| 170 QQADRFHKRLQETRKKIESLKRARRAMGLEIQKLANQSQQFHEQMLKSYQQADEIKKEA 228
                                       44555555555566666666666666666666666666666666666666666665554 PP

  == domain 4  score: 9.3 bits;  conditional E-value: 0.0021
                             Sec34   3 dqLeskeeecdelleqtdealeqLeeleekfksvsektsslheaceqllee 53 
                                       +q ++ ++e de  +++ e+ ++++e++e+ ++v++k  +++++ ++l++ 
  gi|242399807|ref|YP_002995232.1| 219 QQADEIKKEADEYHQKVIELRDKMREIREELREVEKKIFEFDQKHKELIAY 269
                                       566677888999999999999999999999999999999999999999865 PP

>> CENP-H  Centromere protein H (CENP-H)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9  17.3       0.3   1.4e+02       8      77 ..      23      95 ..      12     100 .. 0.81
   2 ?    5.1  14.8      0.06        29       5      74 ..      55     140 ..      51     150 .. 0.76
   3 ?    6.9   8.1     0.017       8.4       9      78 ..     166     231 ..     153     235 .. 0.50
   4 ?   14.2   4.8   9.2e-05     0.045       6      74 ..     226     296 ..     221     309 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.3
                            CENP-H  8 rdelssellklsqelrelqeeltevekenlrlkrknrelaaellelakekesek...eklkeelekleaelkk 77
                                      + ++  e++ l++e +e++e+l++++ke     +k  e+ +e+  l++++++ k   +++++++++l+++ ++
  gi|242399807|ref|YP_002995232.1| 23 IKRIKAEIEVLEREKKEIKERLEQLQKELNIWVQKRDEKNKEVKHLREKAREYKtkrDEVNQQIQELKKNREE 95
                                      566778899999999***************9999999999999777777776665567788888888887665 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.06
                            CENP-H   5 ieqrdelssellklsqelrelqeeltevekenlrlkrknrelaaellelakekesek................eklk 65 
                                       +++rde ++e+++l ++ re + + +ev++++ +lk+  +e+ a+l  l +e+++ +                ek +
  gi|242399807|ref|YP_002995232.1|  55 VQKRDEKNKEVKHLREKAREYKTKRDEVNQQIQELKKNREEINAKLNLLYQEAMEYRakrdeyrqlrrlkmpkEKIE 131
                                       789*******************************************7666666666657666666666555444455 PP

                            CENP-H  66 eelekleae 74 
                                       e++ekle e
  gi|242399807|ref|YP_002995232.1| 132 ERIEKLEWE 140
                                       555555555 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.017
                            CENP-H   9 delssellklsqelrelqeeltevekenlrlkrknrelaaellelakekesekeklkeelekleaelkks 78 
                                        e+ +++ + ++ l+e++++++++++ ++++  + ++la++ + +  e++ ++    ++ +++++e +++
  gi|242399807|ref|YP_002995232.1| 166 LEILQQADRFHKRLQETRKKIESLKRARRAMGLEIQKLANQSQ-QFHEQMLKS---YQQADEIKKEADEY 231
                                       4445555566666666677777777777777777766666663.222222222...23333333333333 PP

  == domain 4  score: 14.2 bits;  conditional E-value: 9.2e-05
                            CENP-H   6 eqrdelssellklsqelrelqeeltevekenlrlkrknrelaael.lelakekesek.eklkeelekleae 74 
                                       ++ de  +++++l  ++re++eel evek++++  +k +el+a     + + k+    e++ e+lek ++ 
  gi|242399807|ref|YP_002995232.1| 226 KEADEYHQKVIELRDKMREIREELREVEKKIFEFDQKHKELIAYKmVAKMRSKKDATfERAVEALEKFKRG 296
                                       6789999**********************************985423333333333357777777777765 PP

>> DUF2968  Protein of unknown function (DUF2968)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0  13.2   6.1e-05      0.03      97     177 ..      21      99 ..      11     102 .. 0.90
   2 ?    3.8   8.3     0.083        40     108     178 ..     127     193 ..     104     195 .. 0.78
   3 ?    1.4   8.7      0.44   2.2e+02     114     177 ..     199     262 ..     192     265 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.1e-05
                           DUF2968  97 veirrikleaqkaqlerqiaasearaerLqadlavarqQeqavaerQkqarkeaaaLeaqreaaqaqlralqrqirq 173
                                        ei+rik  a+ + ler+ ++ ++r+e+Lq++l++  q + + +++ k++r++a+  +++r+++ +q+++l+++ ++
  gi|242399807|ref|YP_002995232.1|  21 EEIKRIK--AEIEVLEREKKEIKERLEQLQKELNIWVQKRDEKNKEVKHLREKAREYKTKRDEVNQQIQELKKNREE 95 
                                       5788876..77899*********************************************************998877 PP

                           DUF2968 174 Lqaq 177
                                       ++a+
  gi|242399807|ref|YP_002995232.1|  96 INAK 99 
                                       7776 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.083
                           DUF2968 108 kaqlerqiaasearaerLqadlavarqQeqavaerQkqarkeaaaLeaqreaaqaqlralqrqirqLqaqq 178
                                       k+++e+ i++ e    +Lq++ +++ + e+++ ++ + + +e + L+ q ++ +++l++++++i++L+++ 
  gi|242399807|ref|YP_002995232.1| 127 KEKIEERIEKLE---WELQTNPTITSEREKQIVDQIQVLATELEILQ-QADRFHKRLQETRKKIESLKRAR 193
                                       444444444443...368999999**********9999*****9997.5678999************9875 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.44
                           DUF2968 114 qiaasearaerLqadlavarqQeqavaerQkqarkeaaaLeaqreaaqaqlralqrqirqLqaq 177
                                       +i++ +++ ++ ++++    qQ  +++++ ++ ++++  L+++ ++++++lr+++++i + +++
  gi|242399807|ref|YP_002995232.1| 199 EIQKLANQSQQFHEQMLKSYQQADEIKKEADEYHQKVIELRDKMREIREELREVEKKIFEFDQK 262
                                       5677777788888888888899999999999999999999999999999999999999887765 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6  14.2    0.0059       2.9       4      79 ..      24     106 ..      21     110 .. 0.76
   2 ?    1.3   6.3       1.1   5.4e+02      12      53 ..      81     128 ..      80     165 .. 0.66
   3 ?    8.8   7.1    0.0051       2.5       5      74 ..     167     236 ..     163     241 .. 0.85
   4 ?    4.8   9.8     0.088        43       4      60 ..     201     257 ..     198     299 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0059
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......XXXXXXXXXXXXXXXXXXXXX CS
                              YabA   4 kelfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerl.......eeeekkekekkkelsegkenL 73 
                                       k + +++e le++ +e++e+le+l++el+  +++ +e + e ++lre+        +e +++ +e kk+ +e + +L
  gi|242399807|ref|YP_002995232.1|  24 KRIKAEIEVLEREKKEIKERLEQLQKELNIWVQKRDEKNKEVKHLREKAreyktkrDEVNQQIQELKKNREEINAKL 100
                                       56788999*****************************************6665443333333344444445555566 PP

                                       XXXXXX CS
                              YabA  74 arlYee 79 
                                       + lY+e
  gi|242399807|ref|YP_002995232.1| 101 NLLYQE 106
                                       666666 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH......X CS
                              YabA  12 eleeqleelleeleelkeelaelleenaeLeleneklrerl......e 53 
                                       e+++q++el+++ ee++++l+ l++e  e ++  ++ r++       e
  gi|242399807|ref|YP_002995232.1|  81 EVNQQIQELKKNREEINAKLNLLYQEAMEYRAKRDEYRQLRrlkmpkE 128
                                       567788888888888888888888888887777776666542223220 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0051
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXXXXXXXXXX CS
                              YabA   5 elfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekekkkelsegkenLa 74 
                                       e++++ ++++++l+e+ +++e+lk++  ++  e ++L  + ++++e++ ++ ++++e kke +e ++++ 
  gi|242399807|ref|YP_002995232.1| 167 EILQQADRFHKRLQETRKKIESLKRARRAMGLEIQKLANQSQQFHEQMLKSYQQADEIKKEADEYHQKVI 236
                                       799999*****************************************97777777777777776666655 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.088
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXX CS
                              YabA   4 kelfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkek 60 
                                       ++l ++ ++++eq+ + +++ +e+k+e  e  ++  eL+   +++re+l+e ekk  
  gi|242399807|ref|YP_002995232.1| 201 QKLANQSQQFHEQMLKSYQQADEIKKEADEYHQKVIELRDKMREIREELREVEKKIF 257
                                       67889999******************************9999999999944443322 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0  21.7     0.051        25       9      89 ..      22     102 ..      15     120 .. 0.59
   2 ?    1.7  15.2      0.51   2.5e+02       9     108 ..     119     217 ..     111     223 .. 0.76
   3 ?    4.2  15.3     0.089        43      12      96 ..     178     258 ..     170     267 .. 0.65
   4 ?    7.2   5.4      0.01         5      57      96 ..     219     258 ..     216     294 .. 0.58

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.051
                        TPR_MLP1_2   9 eikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesaka 85 
                                       eik++k+e+e +e++ ++++e le+ +++++   qk  +   + +   ++ ++++++ +e++++i+elk+++e+ +a
  gi|242399807|ref|YP_002995232.1|  22 EIKRIKAEIEVLEREKKEIKERLEQLQKELNIWVQKRDEKNKEVKHLREKAREYKTKRDEVNQQIQELKKNREEINA 98 
                                       55555555555555555555555555555555555555555555555666666666666666666666666666666 PP

                        TPR_MLP1_2  86 elee 89 
                                       +l+ 
  gi|242399807|ref|YP_002995232.1|  99 KLNL 102
                                       6654 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.51
                        TPR_MLP1_2   9 eikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesaka 85 
                                       ++ +lk  ke+ e++++kl+ +l++   i++e +++   +++  a++++ lq++   +++l+++++++++ +++a+ 
  gi|242399807|ref|YP_002995232.1| 119 QLRRLKMPKEKIEERIEKLEWELQTNPTITSEREKQIVDQIQVLATELEILQQADRFHKRLQETRKKIES-LKRARR 194
                                       57899999****************************************9999987766666666666543.455555 PP

                        TPR_MLP1_2  86 eleeseesweeqkeelekelsel 108
                                       ++  + +++++q +++ +++ ++
  gi|242399807|ref|YP_002995232.1| 195 AMGLEIQKLANQSQQFHEQMLKS 217
                                       55666666666666665555444 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.089
                        TPR_MLP1_2  12 slkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesakaele 88 
                                       +l+e  ++  + l+ +++ +  + + +++  q+++++++k     ++  ++++e++e+ +++ el+++  + ++el 
  gi|242399807|ref|YP_002995232.1| 178 RLQETRKKI-ESLKRARRAMGLEIQKLANQSQQFHEQMLKS---YQQADEIKKEADEYHQKVIELRDKMREIREELR 250
                                       333333333.3344445555555555555555677777765...566777899999999999999999999999999 PP

                        TPR_MLP1_2  89 eseeswee 96 
                                       e e+++ e
  gi|242399807|ref|YP_002995232.1| 251 EVEKKIFE 258
                                       99887654 PP

  == domain 4  score: 7.2 bits;  conditional E-value: 0.01
                        TPR_MLP1_2  57 kelqalreelnelkaeiaelkaeaesakaeleeseeswee 96 
                                       ++  ++++e++e+ +++ el+++  + ++el e e+++ e
  gi|242399807|ref|YP_002995232.1| 219 QQADEIKKEADEYHQKVIELRDKMREIREELREVEKKIFE 258
                                       4445555555555555555555555555555555554433 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4  16.0      0.13        62      27      99 ..      33     110 ..      21     112 .. 0.82
   2 ?    8.3   6.4    0.0078       3.8      12      94 ..     109     191 ..     104     192 .. 0.76
   3 ?    7.5  12.8     0.014       6.9      26      98 ..     174     251 ..     167     261 .. 0.70
   4 ?    3.8  11.4       0.2        97       8      61 ..     205     258 ..     198     303 .. 0.58

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.13
                      Occludin_ELL  27 lhaeleevskkfseLerelkelkegsk....eykkieeeilqeykklkk..dpeyqekkkrceyLkekLshiKklik 97 
                                       l++e +e+++++++L++el+   ++++    e+k++ e+  +eyk ++   +++ qe kk  e++++kL+ + +   
  gi|242399807|ref|YP_002995232.1|  33 LEREKKEIKERLEQLQKELNIWVQKRDeknkEVKHLREK-AREYKTKRDevNQQIQELKKNREEINAKLNLLYQEAM 108
                                       677788999999999998874433332234599999999.9****99888899******************999888 PP

                      Occludin_ELL  98 ey 99 
                                       ey
  gi|242399807|ref|YP_002995232.1| 109 EY 110
                                       88 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0078
                      Occludin_ELL  12 rYkaeFnkeYkeYkelhaeleevskkfseLerelkelkegsk.eykkieeeilqeykklkkdpeyqekkkrceyLke 87 
                                       +Y+a+ ++eY++ ++l+   e++++++++Le el++ ++ ++ ++k+i+++i+    +l+  ++  +  kr+++ ++
  gi|242399807|ref|YP_002995232.1| 109 EYRAK-RDEYRQLRRLKMPKEKIEERIEKLEWELQTNPTITSeREKQIVDQIQVLATELEILQQADRFHKRLQETRK 184
                                       55554.67888888999999***************999877768899999987766666666666666777777777 PP

                      Occludin_ELL  88 kLshiKk 94 
                                       k + +K+
  gi|242399807|ref|YP_002995232.1| 185 KIESLKR 191
                                       7777775 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.014
                      Occludin_ELL  26 elhaeleevskkfseLerelkelkegsk....eykkieeeilqeykklkk.dpeyqekkkrceyLkekLshiKklik 97 
                                       + h++l+e++kk++ L+r  +++  + +    + ++ +e++l++y++  + ++e  e  +++ +L++k++ i++ ++
  gi|242399807|ref|YP_002995232.1| 174 RFHKRLQETRKKIESLKRARRAMGLEIQklanQSQQFHEQMLKSYQQADEiKKEADEYHQKVIELRDKMREIREELR 250
                                       56788888888888888665554444433445788888888888888887777788888888888888888877766 PP

                      Occludin_ELL  98 e 98 
                                       e
  gi|242399807|ref|YP_002995232.1| 251 E 251
                                       5 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.2
                      Occludin_ELL   8 eqrerYkaeFnkeYkeYkelhaeleevskkfseLerelkelkegskeykkieee 61 
                                       +q +++ ++  k Y++  e+++e +e+ +k+ eL+++++e +e+ +e++k + e
  gi|242399807|ref|YP_002995232.1| 205 NQSQQFHEQMLKSYQQADEIKKEADEYHQKVIELRDKMREIREELREVEKKIFE 258
                                       455556666666666666666666666666666666665554444433332222 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7  23.4    0.0014      0.69      48     183 ..       1     143 [.       1     147 [. 0.91
   2 ?    1.8  10.5      0.37   1.8e+02      95     180 ..     118     206 ..     111     214 .. 0.69
   3 ?    3.7  12.0     0.097        47     104     182 ..     165     243 ..     151     245 .. 0.87
   4 ?    6.8  11.4     0.011       5.5      96     173 ..     213     285 ..     211     298 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0014
                            DUF724  48 mvsfagllekvkklsiddsrseleslkeslaeLekhGFdVkalqsrlnkLlslk.deqtklleerkklekkieeees 123
                                       m++++++ e  + ++++++ +e++++k ++  Le++  ++k  +++l+k l++  ++++++ +e k+l +k +e ++
  gi|242399807|ref|YP_002995232.1|   1 MINYSKIEEGEETMQVKVDPEEIKRIKAEIEVLEREKKEIKERLEQLQKELNIWvQKRDEKNKEVKHLREKAREYKT 77 
                                       7889999999999**********************************998888526778899999999999999999 PP

                            DUF724 124 ekrkleeeidelekkilelerqlallk......ekkeaadkeiarlkseaekleeeledveqeFea 183
                                       ++ +++++i+el+k+  e++ +l ll       + k ++ +++ rlk  +ek+ee++e+ e e ++
  gi|242399807|ref|YP_002995232.1|  78 KRDEVNQQIQELKKNREEINAKLNLLYqeameyRAKRDEYRQLRRLKMPKEKIEERIEKLEWELQT 143
                                       9999999999999999999999998888999999999**********************9988775 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.37
                            DUF724  95 nkLlslkdeqtklleerkklekkieeeesekrkleeei.delekkilele..rqlallkekkeaadkeiarlkseae 168
                                       ++L  lk  ++k++e+++kle +++++ +  ++ e++i d+++    ele  +q++++ ++ ++  k+i +lk   +
  gi|242399807|ref|YP_002995232.1| 118 RQLRRLKMPKEKIEERIEKLEWELQTNPTITSEREKQIvDQIQVLATELEilQQADRFHKRLQETRKKIESLKRARR 194
                                       67889999999999999999999988876666555554144554444555225555566888999999999999999 PP

                            DUF724 169 kleeeledveqe 180
                                       ++  e+++  ++
  gi|242399807|ref|YP_002995232.1| 195 AMGLEIQKLANQ 206
                                       988777765544 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.097
                            DUF724 104 qtklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaekleeeledveqe 180
                                         ++l++  +++k+++e +++ ++l+   + +  +i++l +q++++ e++ ++ ++  ++k+ea+++++++ + +++
  gi|242399807|ref|YP_002995232.1| 165 ELEILQQADRFHKRLQETRKKIESLKRARRAMGLEIQKLANQSQQFHEQMLKSYQQADEIKKEADEYHQKVIELRDK 241
                                       567888999999999999999999****************************************9999998877776 PP

                            DUF724 181 Fe 182
                                        +
  gi|242399807|ref|YP_002995232.1| 242 MR 243
                                       55 PP

  == domain 4  score: 6.8 bits;  conditional E-value: 0.011
                            DUF724  96 kLlslkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaeklee 172
                                       ++l+  ++ +++++e  ++++k+ e ++++r++ ee++e+ekki e+ ++ + l      a k +a+++s++++  e
  gi|242399807|ref|YP_002995232.1| 213 QMLKSYQQADEIKKEADEYHQKVIELRDKMREIREELREVEKKIFEFDQKHKEL-----IAYKMVAKMRSKKDATFE 284
                                       577777888999***********************************9998644.....445555555555544433 PP

                            DUF724 173 e 173
                                       +
  gi|242399807|ref|YP_002995232.1| 285 R 285
                                       3 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 ?    5.9   3.1     0.021        10      87     149 ..      36      98 ..      10     108 .. 0.57
   2 ?    3.9   2.6     0.084        41      88     164 ..     156     234 ..     147     239 .. 0.73
   3 ?    7.5   1.1    0.0066       3.2      77     148 ..     200     260 ..     187     274 .. 0.51

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.021
                                       HHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  87 aakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaa 149
                                         kei++ ++++qke n  v+  +e +++v++  e+++e +++  e+ ++++e+++  +ei+a
  gi|242399807|ref|YP_002995232.1|  36 EKKEIKERLEQLQKELNIWVQKRDEKNKEVKHLREKAREYKTKRDEVNQQIQELKKNREEINA 98 
                                       335555555555555555555555555555555555555555555555555555555555543 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.084
                                       HHHHHHHH................HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  88 akeiealii..eiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasieevn 162
                                         +i+ l +  ei ++ ++  + l+etr+++e+     +  g ++++++++ ++  +++    + ++e+ + ++e  
  gi|242399807|ref|YP_002995232.1| 156 VDQIQVLATelEILQQADRFHKRLQETRKKIESLKRARRAMGLEIQKLANQSQQFHEQMLKSYQQADEIKKEADEYH 232
                                       45555554312678999999999999999999998888888999999999999988888777777777777666665 PP

                                       HH CS
                         MCPsignal 163 qa 164
                                       q 
  gi|242399807|ref|YP_002995232.1| 233 QK 234
                                       55 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0066
                                       HHHHHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  77 VrkLAersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeia 148
                                       ++kLA++s+q  ++           + +s +  +e +++++e  ++v e +++++ei e+  ev++ + e  
  gi|242399807|ref|YP_002995232.1| 200 IQKLANQSQQFHEQ-----------MLKSYQQADEIKKEADEYHQKVIELRDKMREIREELREVEKKIFEFD 260
                                       33333333333222...........22233333444555555555555555555555555555555555544 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0         1   4.8e+02       9      36 ..      23      50 ..      20      54 .. 0.62
   2 ?    7.6   0.4      0.01       4.9       3      31 ..      80     108 ..      78     116 .. 0.78
   3 ?    0.0   0.2       2.4   1.2e+03       4      27 ..     154     183 ..     152     196 .. 0.63
   4 ?    3.8   2.1      0.16        76       8      37 ..     199     228 ..     195     230 .. 0.94
   5 ?   -0.6   0.0       3.6   1.8e+03       8      27 ..     234     253 ..     229     259 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 1
                               LPP  9 VsqLkskvdqlssdvnsakaaaqaakeE 36
                                      +++ k++++ l+ + +++k+ +++ ++E
  gi|242399807|ref|YP_002995232.1| 23 IKRIKAEIEVLEREKKEIKERLEQLQKE 50
                                      5556666666666666666666666555 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.01
                               LPP   3 deLssqVsqLkskvdqlssdvnsakaaaq 31 
                                       de+++q+++Lk++ +++++++n + ++a+
  gi|242399807|ref|YP_002995232.1|  80 DEVNQQIQELKKNREEINAKLNLLYQEAM 108
                                       78889999999999999888887776666 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 2.4
                               LPP   4 eLssqVsqLkskvdqlssd......vnsak 27 
                                       ++ +q++ L ++ + l++       +++++
  gi|242399807|ref|YP_002995232.1| 154 QIVDQIQVLATELEILQQAdrfhkrLQETR 183
                                       677888888888877776545544444444 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.16
                               LPP   8 qVsqLkskvdqlssdvnsakaaaqaakeEA 37 
                                       ++++L ++ +q  +++ ++ ++a+++k+EA
  gi|242399807|ref|YP_002995232.1| 199 EIQKLANQSQQFHEQMLKSYQQADEIKKEA 228
                                       79***************************9 PP

  == domain 5  score: -0.6 bits;  conditional E-value: 3.6
                               LPP   8 qVsqLkskvdqlssdvnsak 27 
                                        V +L +k+ ++ +++ +++
  gi|242399807|ref|YP_002995232.1| 234 KVIELRDKMREIREELREVE 253
                                       57788899988888877765 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 ?    3.6   8.5      0.18        86      47     114 ..      22      91 ..       3     165 .. 0.58
   2 ?    8.8   8.9    0.0043       2.1      25      98 ..     177     250 ..     169     300 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.18
                                       THHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---------CHHHHHHHHH....H CS
                           T3SSipB  47 elqtalseakgatddleaaiekadqaksaadaatkkvdeaqkrlkeLaPdePekakleaaeqQagaa..a 114
                                       e+++   e + + ++ ++  e+++q++++ +   +k de  k +k L     e++  + +++Q  +   +
  gi|242399807|ref|YP_002995232.1|  22 EIKRIKAEIEVLEREKKEIKERLEQLQKELNIWVQKRDEKNKEVKHLREKAREYKTKRDEVNQQIQElkK 91 
                                       5555555555555555555555555555555555555555555555555555555444443332211122 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0043
                                       HHHHHHHHHHHHTTTTT----STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT------ CS
                           T3SSipB  25 nrlaawkamskaqqeaasklSdelqtalseakgatddleaaiekadqaksaadaatkkvdeaqkrlkeLaPdeP 98 
                                       +rl+  ++++++ + a  ++  e+q++ ++ ++  +++ ++ ++ad++k++ad+ ++kv e   ++ e+  +  
  gi|242399807|ref|YP_002995232.1| 177 KRLQETRKKIESLKRARRAMGLEIQKLANQSQQFHEQMLKSYQQADEIKKEADEYHQKVIELRDKMREIREELR 250
                                       6677778889999999*************************************************999933322 PP

>> Mod_r  Modifier of rudimentary (Mod(r)) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7  15.2   0.00085      0.41      10      90 ..     167     248 ..     163     305 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00085
                             Mod_r  10 elledeeklealvktl.pevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqeld 85 
                                       e+l++ + ++++++++ +++++lk ++  +  e+++la++  + ++++ +  ++  e  +e++e ++++ e+  ++ 
  gi|242399807|ref|YP_002995232.1| 167 EILQQADRFHKRLQETrKKIESLKRARRAMGLEIQKLANQSQQFHEQMLKSYQQADEIKKEADEYHQKVIELRDKMR 243
                                       7999**********99899********************99999999999999999999999999999999999998 PP

                             Mod_r  86 ellqk 90 
                                       e+ ++
  gi|242399807|ref|YP_002995232.1| 244 EIREE 248
                                       87654 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.3      0.52   2.5e+02      37      65 ..      23      51 ..      12      60 .. 0.50
   2 ?    7.2   0.6     0.014       6.8      10      46 ..      69     102 ..      65     113 .. 0.79
   3 ?    1.6   1.5      0.82     4e+02       8      41 ..     154     190 ..     119     217 .. 0.71
   4 ?    5.5   0.3     0.049        24      14      56 ..     229     254 ..     199     262 .. 0.56
   5 ?    5.4   0.1     0.053        26      13      57 ..     228     255 ..     222     274 .. 0.61

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.52
                           NPV_P10 37 vtelnekLdaqsaqLaeletkvenIqdiL 65
                                      ++ ++++++ +  + +e+++ +e+ q+ L
  gi|242399807|ref|YP_002995232.1| 23 IKRIKAEIEVLEREKKEIKERLEQLQKEL 51
                                      33333333333333333333333333333 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.014
                           NPV_P10  10 radikavddkVdalqqqvddvqenlpdvtelnekLda 46 
                                       r+  ++ ++k d ++qq++++++n ++   +n+kL+ 
  gi|242399807|ref|YP_002995232.1|  69 REKAREYKTKRDEVNQQIQELKKNREE---INAKLNL 102
                                       666677888999999999999998777...8888875 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.82
                           NPV_P10   8 vIradikavddkVdalqqqv...ddvqenlpdvteln 41 
                                       +I + i+ + + ++ lqq+    +++qe  ++++ l+
  gi|242399807|ref|YP_002995232.1| 154 QIVDQIQVLATELEILQQADrfhKRLQETRKKIESLK 190
                                       5667777777777666665333344444444444444 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.049
                           NPV_P10  14 kavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaelet 56 
                                        +                  +++v el +k+ ++ ++L e+e+
  gi|242399807|ref|YP_002995232.1| 229 DEY-----------------HQKVIELRDKMREIREELREVEK 254
                                       222.................33344444444444444444444 PP

  == domain 5  score: 5.4 bits;  conditional E-value: 0.053
                           NPV_P10  13 ikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletk 57 
                                         +  +kV  l +++ +++e+l++v++                 k
  gi|242399807|ref|YP_002995232.1| 228 ADEYHQKVIELRDKMREIREELREVEK-----------------K 255
                                       445555666666666666666655553.................3 PP

>> FH2  Formin Homology 2 Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7  10.0    0.0017      0.81     261     344 ..      14      96 ..       6     114 .. 0.89
   2 ?    0.8   0.6      0.42     2e+02     286     317 ..     128     160 ..     118     188 .. 0.45
   3 ?    4.8  12.9     0.026        12     258     371 ..     180     293 ..     172     295 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0017
                                       GGHHHHTTTHHHCCTS-HHHHHHHHHHHHHHHHHHHHHHHHCCTTSSTT-THHHHHHHHHHHHHHHHHHHHHHHHHH CS
                               FH2 261 ldfsseLknvkkaakvnleslekevkklekglkklekelessekkeepsdkflevlkeflkeaeeklkkleeelkea 337
                                        +++ + +++k+  k ++e le e k+++++l++l+kel+   +k+++++k ++ l+e  +e ++k ++++++ +e+
  gi|242399807|ref|YP_002995232.1|  14 MQVKVDPEEIKR-IKAEIEVLEREKKEIKERLEQLQKELNIWVQKRDEKNKEVKHLREKAREYKTKRDEVNQQIQEL 89 
                                       556667777777.6889************************************************************ PP

                                       HHHHHHH CS
                               FH2 338 kelvkel 344
                                       k++ +e+
  gi|242399807|ref|YP_002995232.1|  90 KKNREEI 96 
                                       *998876 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.42
                                       HHHHHHHHHHHHHHHHCCT.TSSTT-THHHHHH CS
                               FH2 286 kklekglkklekelessek.keepsdkflevlk 317
                                       +k+e++++kle el+++ +  +e +++++++++
  gi|242399807|ref|YP_002995232.1| 128 EKIEERIEKLEWELQTNPTiTSEREKQIVDQIQ 160
                                       566666666666666666653333333333332 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.026
                                       GGGGGHHHHTTTHHHCCTS-HHHHHHHHHHHHHHHHHHHHHHHHCCTTSSTT-THHHHHHHHHHHHHHHHHHHHHHH CS
                               FH2 258 pevldfsseLknvkkaakvnleslekevkklekglkklekelessekkeepsdkflevlkeflkeaeeklkkleeel 334
                                       +e  +  + Lk  ++a  +++++l+++ +++++++ k  +++++ +k++++ ++ +  l++ ++e +e+l+++e++ 
  gi|242399807|ref|YP_002995232.1| 180 QETRKKIESLKRARRAMGLEIQKLANQSQQFHEQMLKSYQQADEIKKEADEYHQKVIELRDKMREIREELREVEKKI 256
                                       55555557889999999******************************88888888889******************* PP

                                       HHHHHHHHHHHHHTT--TTCCHHHHHHHHHHHHHHHH CS
                               FH2 335 keakelvkelveYfgedkkevspeeffkilreFlkef 371
                                        e  ++ kel+ Y   +k + ++++ f+   e l++f
  gi|242399807|ref|YP_002995232.1| 257 FEFDQKHKELIAYKMVAKMRSKKDATFERAVEALEKF 293
                                       *************944444444555444444444444 PP

>> Glu_syn_central  Glutamate synthase central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   2.0      0.86   4.2e+02      79     139 ..      10      88 ..       5     120 .. 0.55
   2 ?   10.0   1.4   0.00087      0.42      59     142 ..     143     247 ..     139     274 .. 0.65

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.86
                                       S----SSS--GGGG-EEEESSSB--HHHH......HHH...........HHSSS-EEEEESEE...........SHH CS
                   Glu_syn_central  79 GkegnlleeeeeqakrlklesPiLteeel......eklkkl.......kekkefkaktlditfeae........ale 134
                                       G+e   ++ ++e+ kr+k e  +L++e+       e   +l        +k++ k k+++ + e++        +++
  gi|242399807|ref|YP_002995232.1|  10 GEETMQVKVDPEEIKRIKAEIEVLEREKKeikerlE---QLqkelniwVQKRDEKNKEVKHLREKAreyktkrdEVN 83 
                                       556666677888999999999999887763332221...11222333422233333444433332233333332233 PP

                                       HHHHH CS
                   Glu_syn_central 135 ealer 139
                                       +++++
  gi|242399807|ref|YP_002995232.1|  84 QQIQE 88 
                                       33333 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00087
                                       SS----TTTTGGG-B--EEES----SSS--GGGG-EEEESSSB--HHHH......HHH........HHSSS-EEEEE CS
                   Glu_syn_central  59 TNPpiDpiREelvmsletllGkegnlleeeeeqakrlklesPiLteeel......eklkkl....kekkefkaktld 125
                                       TNP i + RE+ ++    +l +e ++l++ ++  krl+ ++  +++ +        +   +    +++++f+ ++l+
  gi|242399807|ref|YP_002995232.1| 143 TNPTITSEREKQIVDQIQVLATELEILQQADRFHKRLQETRKKIESLKRarramgLE---IqklaNQSQQFHEQMLK 216
                                       9***************************88877777765444333333223344422...13335556677777777 PP

                                       SEE.................SHHHHHHHHHH CS
                   Glu_syn_central 126 itfeae..............aleealerlce 142
                                          +a+              +l++++++++e
  gi|242399807|ref|YP_002995232.1| 217 SYQQADeikkeadeyhqkviELRDKMREIRE 247
                                       7766554544444444333324444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      4413  (0.246138); expected 358.6 (0.02)
Passed bias filter:                      824  (0.0459591); expected 358.6 (0.02)
Passed Vit filter:                       282  (0.0157287); expected 17.9 (0.001)
Passed Fwd filter:                       167  (0.00931452); 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: 2.39u 0.41s 00:00:02.80 Elapsed: 00:00:00.66
# Mc/sec: 1431.35
//
Query:       gi|242399808|ref|YP_002995233.1|  [L=248]
Description: hypothetical protein TSIB_1833 [Thermococcus sibiricus MM 739]
Scores for complete 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-142  472.6   3.3   3.6e-142  472.5   3.3    1.0  1  SDH_sah          Serine dehydrogenase proteinase
    7.4e-07   29.2   0.2    2.6e-06   27.5   0.1    1.8  2  CLP_protease     Clp protease
      0.003   17.5   0.0     0.0063   16.5   0.0    1.5  1  Peptidase_S49    Peptidase family S49
     0.0067   15.8   0.1       0.02   14.2   0.0    1.8  2  ECH_1            Enoyl-CoA hydratase/isomerase
     0.0094   15.3   0.1      0.013   14.8   0.1    1.2  1  Calmodulin_bind  Calmodulin binding protein-like


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 !  472.5   3.3    1e-145  3.6e-142      35     279 ..       1     245 [.       1     248 [] 0.99

  Alignments for each domain:
  == domain 1  score: 472.5 bits;  conditional E-value: 1e-145
                           SDH_sah  35 larlkvlrkleekrksrvitmihrqesigflGipiykfitiedseevlrairltpkdkpidliihtpGGlvlaatqi 111
                                       +ar+k+l kl +kr+s+vitmihrqesigf+Gip+ykfi+iedsee+lrair++pkdkpidliihtpGGlvlaatqi
  gi|242399808|ref|YP_002995233.1|   1 MARTKLLEKLARKRNSTVITMIHRQESIGFFGIPVYKFISIEDSEEILRAIRMAPKDKPIDLIIHTPGGLVLAATQI 77 
                                       689************************************************************************** PP

                           SDH_sah 112 akalkehkaktrvivphyamsGGtlialaadeiildenavlGpvdpqlgqypaasilkvvekkeakdiddktlilad 188
                                       akalk+h+aktrvi+phyamsGGtlialaadeii+d++avlGpvdpqlgqypa+si+k+ve+k  ++++d+tlilad
  gi|242399808|ref|YP_002995233.1|  78 AKALKDHPAKTRVIIPHYAMSGGTLIALAADEIIMDPHAVLGPVDPQLGQYPAPSIIKAVEQKSIDKVEDQTLILAD 154
                                       ***************************************************************************** PP

                           SDH_sah 189 iakkaikqveefvyellkdkydeekakeiakklteGrwthdypltveelkelGlevntnvpeevyellelyeqplgq 265
                                       +akkai+qv++fvy+llkdky+eekak++a+ lteGrwthdyp+tve+++elGl+vntnvp evy+l+ely+qp++q
  gi|242399808|ref|YP_002995233.1| 155 VAKKAINQVRDFVYHLLKDKYGEEKAKQLAQVLTEGRWTHDYPITVEHARELGLNVNTNVPMEVYTLMELYRQPIKQ 231
                                       ***************************************************************************** PP

                           SDH_sah 266 rpsveyipvpvkkk 279
                                       r++ve++p+pvk++
  gi|242399808|ref|YP_002995233.1| 232 RGTVEFMPYPVKQE 245
                                       ***********954 PP

>> CLP_protease  Clp protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.1   7.2e-10   2.6e-06      36      99 ..      47     110 ..      11     164 .. 0.80
   2 ?   -0.6   0.0      0.29     1e+03     130     174 ..     158     208 ..     151     211 .. 0.68

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 7.2e-10
                                       HHHHHHHH-SSS-EEEEEEE--B-HHHHHHHHHHHHHSSS-EEEEEEEEEETHHHHHHHTS-TT CS
                      CLP_protease  36 qLllLeaedpdkdillyinspGGsvtaglaIydtmqyikpdvsticlGlaaSmgslllaagekg 99 
                                        L ++    +dk+i l+i++pGG v a++ I+ +++ + ++  +i    a+S g+l+++a+++ 
  gi|242399808|ref|YP_002995233.1|  47 ILRAIRMAPKDKPIDLIIHTPGGLVLAATQIAKALKDHPAKTRVIIPHYAMSGGTLIALAADEI 110
                                       34455566899*************************************************9975 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.29
                                       HHHHHHHHHHHHHHHHHHTS-H.HHHHH.....HHCSTEEEEHHHHHHHTS CS
                      CLP_protease 130 eellkikerlneilakhtgqsl.ekiek.....dldrdtflsaeeAveyGL 174
                                       + ++++++ + ++l+++ g++  +++++       + d+ +++e A e GL
  gi|242399808|ref|YP_002995233.1| 158 KAINQVRDFVYHLLKDKYGEEKaKQLAQvltegRWTHDYPITVEHARELGL 208
                                       567777777777777766654314444455456677888888899999887 PP

>> Peptidase_S49  Peptidase family S49
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.7e-06    0.0063       9      40 ..      88     119 ..      80     121 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.7e-06
                                       EEEEEEEEEETHHHHHHTTSSEEEE-TT-EEE CS
                     Peptidase_S49   9 vvasaenvaaSggYylasaadkivanpstivg 40 
                                         +++  +a Sgg ++a aad+i+++p+++ g
  gi|242399808|ref|YP_002995233.1|  88 TRVIIPHYAMSGGTLIALAADEIIMDPHAVLG 119
                                       5577889**********************987 PP

>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   5.5e-06      0.02      98     136 ..      95     133 ..      78     152 .. 0.87
   2 ?   -1.6   0.0      0.36   1.3e+03     180     218 ..     146     184 ..     133     209 .. 0.49

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.5e-06
                                       EEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTC CS
                             ECH_1  98 aaigGGlelalacDiviaadnasfglnelklGlipgagg 136
                                       +a+ GG ++ala+D +i++ +a+ g    +lG +p+  +
  gi|242399808|ref|YP_002995233.1|  95 YAMSGGTLIALAADEIIMDPHAVLGPVDPQLGQYPAPSI 133
                                       899*******************************97544 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.36
                                       HHHHHHHHHHHHHSCHHHHHHHHHHHHHHHH.HHHHHHHH CS
                             ECH_1 180 leealelaeklaekspaalrqlkealnakle.dalaeqle 218
                                       ++++l la  +a+k+++ +r +  +l ++   +++a+ql+
  gi|242399808|ref|YP_002995233.1| 146 EDQTLILA-DVAKKAINQVRDFVYHLLKDKYgEEKAKQLA 184
                                       44444333.3344444444433333222222244443333 PP

>> Calmodulin_bind  Calmodulin binding protein-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1   3.8e-06     0.013     175     228 ..     149     208 ..     141     224 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.8e-06
                   Calmodulin_bind 175 GafhkkLskegIktVqdflkllvkde......ekLrkilgkgmsdkmWektveHAktcdl 228
                                         +  + +k+ I++V+df+ +l kd+      ++L ++l +g  ++++  tveHA++  l
  gi|242399808|ref|YP_002995233.1| 149 TLILADVAKKAINQVRDFVYHLLKDKygeekaKQLAQVLTEGRWTHDYPITVEHARELGL 208
                                       556677899**************99644444478*********************98655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      604  (0.0336884); 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: 0.66u 0.33s 00:00:00.99 Elapsed: 00:00:00.53
# Mc/sec: 1411.65
//
Query:       gi|242399809|ref|YP_002995234.1|  [L=315]
Description: Carbamate kinase [Thermococcus sibiricus MM 739]
Scores for complete 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  100.2   0.1    1.6e-28   99.9   0.1    1.1  1  AA_kinase  Amino acid kinase family
  ------ inclusion threshold ------
       0.19   11.9   0.5        6.1    6.9   0.0    2.7  2  SKI        Shikimate kinase


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 !   99.9   0.1   1.8e-32   1.6e-28       1     240 [.       3     296 ..       3     297 .. 0.87

  Alignments for each domain:
  == domain 1  score: 99.9 bits;  conditional E-value: 1.8e-32
                                       TEEEEEE-TTCCCCTCC........HHHHHHHHHHHHH.HHHTTEEEEEE--HHHHHHHHHH......TCCCCCHHH CS
                         AA_kinase   1 krvVvKlGGssltdkee........aslrrlaeqiaal.kesgnklvvVhGggsftdgllal......ksglssgel 62 
                                       krvV++lGG+++ + ++        +++r+ a+qi ++   +++++v+ hG+g+++ +ll +       +g++    
  gi|242399809|ref|YP_002995234.1|   3 KRVVIALGGNAILQRGQkgtyeeqmENVRKTARQIVDIiLDNEYEVVITHGNGPQVGALLLQqdagehVHGIP---- 75 
                                       79********999666669******************977778*******************86644433333.... PP

                                       C..................E..HHHHHHHHHHHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE.......... CS
                         AA_kinase  63 aa..............glrstleeagevatrdalaslgerlvaallaaglpavglsaaaldateagr.......... 115
                                        a              g   ++++++e+ +r     +++++++ ++++  pa++ ++++++++  +           
  gi|242399809|ref|YP_002995234.1|  76 -AqpmdvcgamsqgqiGYMIQQAIMNELRRRGVERPVATIVTQTIVDKNDPAFQHPSKPVGPFYSEEtakklakekg 151
                                       .24466699999999988899999999999966666666666666666666666666666666655566688***** PP

                                       ...............HHHTTTCEEECCHHHHHHHTT-EEEEESEEEEETTTE.......EEEE-HHHHHHHHHHHCT CS
                         AA_kinase 116 .............degsdgnvesvdaeaieelleagvvpvltgfigldeege.......lgrgssDtiaallAealg 172
                                                     ++s+++  +v+a  i++l+e++++++ +g++g+++ +e        +++++D +   lAe+++
  gi|242399809|ref|YP_002995234.1| 152 wvviedagrgwrrVVPSPDPKGHVEAPIIQDLVEKEFIVISSGGGGIPVVEEngelkgvEAVIDKDLAGERLAEEVN 228
                                       *******************************************998888888778999988**************** PP

                                       SSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHH..CSSS.TTTHHHHCHHHHHHHHHCTT-EEEEE CS
                         AA_kinase 173 AdkliiltdVdGVydadpkkvpdarllpeisvdeaee..saselatgGmkvkhpaalaaarrggipvvIt 240
                                       Ad  +iltdV+G   + ++ +   + l++++  e++   +++++ +g+m +k++aa+++++ gg +++I+
  gi|242399809|ref|YP_002995234.1| 229 ADIFMILTDVNGAAINYGRPN--EKWLEKVTLGEIKRyyEEGHFKKGSMGPKVLAAIRFIEWGGERAIIA 296
                                       ****************99887..699************************************99999996 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1     0.019   1.7e+02      62      77 ..       3      18 ..       1      38 [. 0.84
   2 ?    6.9   0.0   0.00069       6.1      51      80 ..     176     206 ..     174     233 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.019
                                      SSEEEEE-TTGGGSHH CS
                               SKI 62 eglViatGGGavlsee 77
                                      +++Via+GG a+l++ 
  gi|242399809|ref|YP_002995234.1|  3 KRVVIALGGNAILQRG 18
                                      589********99876 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.00069
                                       HHHHHHHHCCCSSEEEEE-TT.GGGSHHHHH CS
                               SKI  51 EsevlkelleeeglViatGGG.avlseenre 80 
                                       E+ ++++l+e+e +Vi+ GGG +++ een e
  gi|242399809|ref|YP_002995234.1| 176 EAPIIQDLVEKEFIVISSGGGgIPVVEENGE 206
                                       77899************98874777777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       655  (0.036533); expected 358.6 (0.02)
Passed bias filter:                      595  (0.0331865); 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: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.51
# Mc/sec: 1841.48
//
Query:       gi|242399810|ref|YP_002995235.1|  [L=428]
Description: oxidoreductase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-11   43.9   0.1    3.8e-11   43.1   0.1    1.5  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    9.1e-10   38.4   0.0    3.2e-09   36.6   0.0    1.9  2  Amino_oxidase  Flavin containing amine oxidoreductase
    2.2e-09   37.0   1.4    0.00015   21.1   0.0    2.8  3  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
     0.0002   21.1   0.1    0.00043   20.0   0.1    1.8  1  DAO            FAD dependent oxidoreductase
     0.0011   18.1   0.1      0.002   17.3   0.1    1.4  1  FAD_binding_2  FAD binding domain
     0.0025   17.1   0.0     0.0046   16.3   0.0    1.3  1  FAD_binding_3  FAD binding domain
     0.0029   18.1   0.6       0.42   11.2   0.1    2.7  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
      0.032   13.0   0.0      0.044   12.6   0.0    1.1  1  MCRA           MCRA family
      0.038   13.3   0.2      0.058   12.7   0.2    1.2  1  FAD_oxidored   FAD dependent oxidoreductase
       0.05   12.3   0.1      0.082   11.6   0.1    1.3  1  HI0933_like    HI0933-like protein


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 !   43.1   0.1   2.1e-14   3.8e-11       2      65 ..      15      78 ..      14      81 .. 0.93

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 2.1e-14
                                      E--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EECETTCEECTS---EEETTHHHHCHHHH CS
                     NAD_binding_8  2 vGaGlsGlvaAylLakagfdvlllekrdrlGGraasyevpgvrvdygahifhgsgyypnvrrll 65
                                      +GaGl+Gl++ ++L k+g+dv++lek++ +GGr + + ++g+ + +ga  + + g++  + +ll
  gi|242399810|ref|YP_002995235.1| 15 IGAGLGGLLTSAFLVKNGYDVTVLEKSPFVGGRFTNIAYKGFQLSTGALHMVPHGENGPLAHLL 78
                                      9**********************************************99998888888888876 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.0   1.8e-12   3.2e-09       2     262 ..      20     251 ..      19     288 .. 0.76
   2 ?   -2.9   0.0       1.8   3.2e+03     321     353 ..     344     376 ..     339     417 .. 0.66

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 1.8e-12
                                       HHHHHHHHHHHTTEEEEEEESSSSSBTTS-EEEETTEEEESS--EEET..TTHHHHHHHHHTTCCCCEEEESCCGCE CS
                     Amino_oxidase   2 aGLaaArqLlsaGfdVtvlEardrvGGRirtvrsdGylielGamwftg..agnpllellkelgledslslpdpgapk 76 
                                        GL +   L  +G+dVtvlE ++ vGGR   +  +G+ + +Ga  + +   + pl +llk l+ + + +   +++pk
  gi|242399810|ref|YP_002995235.1|  20 GGLLTSAFLVKNGYDVTVLEKSPFVGGRFTNIAYKGFQLSTGALHMVPhgENGPLAHLLKLLNANVEIV---NSTPK 93 
                                       6888888899*********************************999999999*********99997766...34466 PP

                                       EEEETTEECCTTEECHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCHHHHHHHHHHH CS
                     Amino_oxidase  77 rvlskggrefpgdlspvpaewealleqgalsaellsleeklrlgleallqktldeldldskslaesleelgrrepgd 153
                                        + + +g+++        ++w+ l  +++  a+ ++l +++++   +         ++++ ++ e+l+e  + ++ +
  gi|242399810|ref|YP_002995235.1|  94 GKFFIDGKIY-----HYREGWKYLSLKEK--AKAMKLLAEIKANKLPKG-------EEAHLNSWEWLSEKIGENEFA 156
                                       7777777776.....33333333322111..123333334444444444.......555555555555555555555 PP

                                       HHHHHHHHHHHHHHHHHHHHHCHTSTTTTCBHHHHTCCCCHHHHHTSCCCEETTHTHHHHHHHHH..TTTTEEEETS CS
                     Amino_oxidase 154 vevwdrliepelfaklefasglfagdpselsaklalpllwelegfggslllprgGlsqlpealae..elrgldirln 228
                                        +    +i      +l++a  l     +e+ +   l ++ + + + g+  l++gG +++ e la+  ++ g++  ++
  gi|242399810|ref|YP_002995235.1| 157 -Y---LFIKS----FLGWAVSL----APEEVSAIELAKEIKATLKWGGPGLIKGGCKAVSEELARivRENGGKMITR 221
                                       .3...55552....22233333....2899999******************************************** PP

                                       EEEEEEEEETTCEEEEETTSTEEEESEEEE-S-H CS
                     Amino_oxidase 229 trVkeikregdgvtvtledgevveaDaVvvTvpl 262
                                       ++  e++      +v + dge++ +D  ++ + +
  gi|242399810|ref|YP_002995235.1| 222 KKAVEVDD----GRVITADGEEYLYDILISNIGI 251
                                       *******9....777788****999998887766 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.8
                                       TEEEEECCECCCSTTTEEEEEEEEECHHHHHHH CS
                     Amino_oxidase 321 geafissdfpsrappgkglvllvyvggdaanel 353
                                       g + +++ fp+ + +g +l++ +y  g+  n++
  gi|242399810|ref|YP_002995235.1| 344 GIEDLYYLFPDLEKNGEVLMVQTYRDGNPVNRV 376
                                       566667777777777777766666555555554 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   8.5e-08   0.00015       1      87 [.      10     105 ..      10     132 .. 0.72
   2 !   13.3   0.1     2e-05     0.036     183     245 ..     201     259 ..     175     275 .. 0.86
   3 ?   -0.4   0.0      0.29   5.3e+02     263     284 ..     381     402 ..     363     407 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 8.5e-08
                                       CSEEEE--SHHHHHHHHHHHHHTS-EEEEE.......TTHCHHHCSHHHHCHHHHHHHHHHHHH......HHHHCHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxx RF
                       Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlve.......legtclnggcllskallgvaedaeias......evvkkln 64 
                                       k+vv iG+G +Gl ++ +l ++g++vt++e       + +++ + g  ls+ +l++  ++e              ln
  gi|242399810|ref|YP_002995235.1|  10 KKVVTIGAGLGGLLTSAFLVKNGYDVTVLEkspfvggRFTNIAYKGFQLSTGALHMVPHGENGPlahllkL----LN 82 
                                       589**************************888887778889999999999999999999887778855540....45 PP

                                       HHCCCCHCCTCEEEEESCEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  65 qgielllgeevvkidpgkkkvkl 87 
                                       +++e ++ +++ k+  + k +++
  gi|242399810|ref|YP_002995235.1|  83 ANVEIVNSTPKGKFFIDGKIYHY 105
                                       55555555554444444444333 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 2e-05
                                       HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S-EEES-HHCS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 183 kelsaaleealekeGvevklgtsvkeidgngeklevvledgeeidadlvvvavGvrpstelle 245
                                       k++s++l++ ++++G ++ ++++++e+d +g+   v++ dgee+ +d ++  +G+r   el++
  gi|242399810|ref|YP_002995235.1| 201 KAVSEELARIVRENGGKMITRKKAVEVD-DGR---VITADGEEYLYDILISNIGIRETVELFG 259
                                       689999*************999999999.444...9********************9999874 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.29
                                       TSBESSTTEEE-GGGCTECCSS CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 263 flrtnvpgiyaiGDvaggkggp 284
                                       + +  ++++y +GD  +g+gg+
  gi|242399810|ref|YP_002995235.1| 381 HVEFPMENVYIVGDANKGEGGI 402
                                       5556789*******98666665 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.1   2.4e-07   0.00043       2     182 ..      12     235 ..      11     384 .. 0.67

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.4e-07
                                       EEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESSSSTHHSTHHHHHHHHHH.HHHH.HHHHHH CS
                               DAO   2 vviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsglrylpeaselarlslea.leel.releee 74 
                                       vv iG+G  Gl t  +L + g  Vt+lek++++g    gr + + + g+     a  +++  + + l++l + l+++
  gi|242399810|ref|YP_002995235.1|  12 VVTIGAGLGGLLTSAFLVKNGydVTVLEKSPFVG----GRFTNIAYKGFQLSTGALHMVPHGENGpLAHLlKLLNAN 84 
                                       888******************************9....888888888884233233555666666444443555554 PP

                                       HSSTTSEEEEEEEEEESS...................................................HHHHHHHH CS
                               DAO  75 lgididyrrtGllslaad...................................................eeeleald 100
                                        +i +   ++G+ ++  +                                                   e+e+++l 
  gi|242399810|ref|YP_002995235.1|  85 VEI-VNSTPKGKFFID-GkiyhyregwkylslkekakamkllaeikanklpkgeeahlnswewlsekigENEFAYL- 158
                                       333.445555555553.22333333555555555555555555555555544444444444444444433444443. PP

                                       HHHHHHHHTTT..TEEEEEH.HHHHHHSTTSTTTSEEEEETTEEEEEHHHHHHHHHHHHHHTT-EEEESECEEEEEE CS
                               DAO 101 kllallleagl..daellda.eevrelepalpgllgalfypdtgqvdpakltaalaraaealGveilegtevtglee 174
                                         +++ l + +    e ++a e+++e++  l ++ g  + ++ g+    ++   lar ++++G++++++ +++++  
  gi|242399810|ref|YP_002995235.1| 159 -FIKSFLGWAVslAPEEVSAiELAKEIKATL-KWGGPGLIKG-GC---KAVSEELARIVRENGGKMITRKKAVEV-- 227
                                       .333332222211222334434444444312.3443344444.33...666666999999999999999888877.. PP

                                       EETCEEEE CS
                               DAO 175 edgkvwgv 182
                                       +dg+v + 
  gi|242399810|ref|YP_002995235.1| 228 DDGRVITA 235
                                       34554444 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   1.1e-06     0.002       2      37 ..      12      48 ..      11      71 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.1e-06
                                      EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS.G CS
                     FAD_binding_2  2 viViGsGlAGLaAAleaaeaGlkvavvekeqefgg.a 37
                                      v+ iG+Gl+GL  ++ + ++G +v+v+ek + +gg  
  gi|242399810|ref|YP_002995235.1| 12 VVTIGAGLGGLLTSAFLVKNGYDVTVLEKSPFVGGrF 48
                                      899****************************999952 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   2.6e-06    0.0046       3      33 ..      11      41 ..      10      43 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.6e-06
                                      EEEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                     FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlvekr 33
                                      +V+ +GaG+ Gl+++ +L + G +v+++ek 
  gi|242399810|ref|YP_002995235.1| 11 KVVTIGAGLGGLLTSAFLVKNGYDVTVLEKS 41
                                      6899*************************95 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.1   0.00024      0.42       1      35 [.      11      45 ..      11      53 .. 0.91
   2 ?    4.3   0.0     0.034        60      41      68 ..     202     229 ..     196     237 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00024
                                      EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                         Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                      kvv +G+G+ gl   ++l + g +Vtv+e s+ + 
  gi|242399810|ref|YP_002995235.1| 11 KVVTIGAGLGGLLTSAFLVKNGYDVTVLEKSPFVG 45
                                      79***************************998766 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.034
                                       HHHHHHHHHHHHTTEEEECSEEEEEEEE CS
                         Pyr_redox  41 easkilqeklekngievllntkveeieg 68 
                                       ++s++l++ +++ng ++++ +k++e++ 
  gi|242399810|ref|YP_002995235.1| 202 AVSEELARIVRENGGKMITRKKAVEVDD 229
                                       689999*******************993 PP

>> MCRA  MCRA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.4e-05     0.044       2      68 ..      10      71 ..       9      90 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.4e-05
                                      -EEEEE--SHHHHHHHHHHHHTT---GGGEEEE-SS-----------------CCC----B.-TT-HH CS
                              MCRA  2 kkaylvGsGiasLaaAvyLirdakvpgenihileelkvaggsldgagdpekGyvlrggrel.eehyec 68
                                      kk+  +G+G+++L + ++L+++    g ++++le+++ +gg ++++    kG+ l +g     +h+e+
  gi|242399810|ref|YP_002995235.1| 10 KKVVTIGAGLGGLLTSAFLVKN----GYDVTVLEKSPFVGGRFTNIA--YKGFQLSTGALHmVPHGEN 71
                                      56778***************97....68**************99875..5789998887654777765 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   3.2e-05     0.058       2      40 ..      12      50 ..      11      62 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.2e-05
                      FAD_oxidored  2 vvVvGGgpaGvaAAiaAaraGakvlLveergvlGGllts 40
                                      vv +G+g++G+       ++G  v ++e+++++GG +t+
  gi|242399810|ref|YP_002995235.1| 12 VVTIGAGLGGLLTSAFLVKNGYDVTVLEKSPFVGGRFTN 50
                                      899*********************************997 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   4.5e-05     0.082       2      38 ..      11      47 ..      10      55 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.5e-05
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HH CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklgrK 38
                                      +v+ iG+G  Gl++++ + k+g +V++lek + +g +
  gi|242399810|ref|YP_002995235.1| 11 KVVTIGAGLGGLLTSAFLVKNGYDVTVLEKSPFVGGR 47
                                      799***************************9988865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); 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: 0.68u 0.34s 00:00:01.02 Elapsed: 00:00:00.51
# Mc/sec: 2507.39
//
Query:       gi|242399811|ref|YP_002995236.1|  [L=165]
Description: Phosphopantetheine adenylyltransferase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-15   56.7   0.0    3.5e-15   56.4   0.0    1.1  1  CTP_transf_like  Cytidylyltransferase-like
    0.00034   20.5   0.1    0.00056   19.8   0.1    1.3  1  FAD_syn          FAD synthetase


Domain annotation for each model (and alignments):
>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.4   0.0   3.9e-19   3.5e-15       1     142 [.      18     154 ..      18     155 .. 0.92

  Alignments for each domain:
  == domain 1  score: 56.4 bits;  conditional E-value: 3.9e-19
                                       EEEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-..SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHH. CS
                   CTP_transf_like   1 lagGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkk..kplasaeeRlemlelakevdevisvdpweltr. 74 
                                       ++gGtFD +HlGH +ll++a++ + + ++vg++sde  k k   +++ +++ Rl+ l ++ ev+     + ++++  
  gi|242399811|ref|YP_002995236.1|  18 VVGGTFDRLHLGHKALLRKAFEVGRY-VYVGITSDEMIKDKPyaEKILPYDIRLRDLLKFFEVNGYSNYRIIKINSa 93 
                                       579***********************.**********9999568****************89998777888888777 PP

                                       .HHHHHTTT.TEEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEEEHTTCEEEEEEECCTTTCSHHHHHH CS
                   CTP_transf_like  75 .evlkklkp.dklylvigadvledfsewkeleeilgnvklvvvsrpekqanvllkaekrtngiSstkire 142
                                         + +k+++ d  ++v+++++++ +   ++ ++  g ++l +v ++       + ++k+ ++iSs+ ir+
  gi|242399811|ref|YP_002995236.1|  94 iGFADKIRSlD--AIVVSEETYKGALLVNKARKEKGLKPLDIVTID-------IVKSKIGSKISSSLIRA 154
                                       76666666669..******************************888.......****************7 PP

>> FAD_syn  FAD synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.1   6.3e-08   0.00056       5      33 ..      13      41 ..       9      48 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 6.3e-08
                           FAD_syn  5 degavvtlGnFDGvHlGHqallkkaveaa 33
                                        ++vv+ G FD +HlGH+all+ka e  
  gi|242399811|ref|YP_002995236.1| 13 RYKKVVVGGTFDRLHLGHKALLRKAFEVG 41
                                      56889999*****************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.53u 0.34s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 963.81
//
Query:       gi|242399812|ref|YP_002995237.1|  [L=448]
Description: Acyl-CoA synthetase, subunit alpha [Thermococcus sibiricus MM 739]
Scores for complete 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-55  185.9   0.3      2e-53  179.9   0.3    2.4  2  Succ_CoA_lig   Succinyl-CoA ligase like flavodoxin domain
    6.9e-17   62.0   0.2    2.4e-16   60.3   0.1    1.9  2  CoA_binding_2  CoA binding domain
    6.3e-06   26.8   5.2    9.6e-06   26.2   1.0    3.1  4  CoA_binding    CoA binding domain
  ------ inclusion threshold ------
      0.032   14.8   0.9       0.18   12.4   0.2    2.4  2  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent


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 !  179.9   0.3   4.4e-57     2e-53       1     138 []     146     283 ..     146     283 .. 0.99
   2 ?    3.4   0.0     0.014        63       3      30 ..     292     319 ..     290     322 .. 0.90

  Alignments for each domain:
  == domain 1  score: 179.9 bits;  conditional E-value: 4.4e-57
                      Succ_CoA_lig   1 pGkialisqSGalalalldwaasrglgfskvvslGneadvdvadlleylaedpetkvillylEsirdgrkflsaarr 77 
                                       +G++alisqSGa++ a l++ +++g+gfs +vs+Gn+ad++++d+l+y+a+d++tkvi+ly+E+++dgrkf++a++ 
  gi|242399812|ref|YP_002995237.1| 146 KGGLALISQSGAFGGAALAMGNEEGIGFSAFVSYGNAADLTESDFLKYFADDKNTKVIALYIEGVKDGRKFIEALKY 222
                                       599************************************************************************** PP

                      Succ_CoA_lig  78 aarkkpvvvlksGrseagaraaashtgalagsdavvdaafrqaGvlrvdsleelfdaaell 138
                                       a+ kkpv+vlk+G+s++g++aa+shtg++ags+++++a f q  +++v+++eelfdaa+++
  gi|242399812|ref|YP_002995237.1| 223 ATSKKPVIVLKAGKSKSGSKAAQSHTGSMAGSYEIYRATFCQFNAIEVEEMEELFDAAKTF 283
                                       **********************************************************986 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.014
                      Succ_CoA_lig   3 kialisqSGalalalldwaasrglgfsk 30 
                                       +ia+i+ SG+ ++   d+a++ gl+++k
  gi|242399812|ref|YP_002995237.1| 292 RIAIITNSGGPGVLATDKAEKLGLEIAK 319
                                       69*******************9998876 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.3   0.1   5.3e-20   2.4e-16       2     113 ..       9     129 ..       8     131 .. 0.93
   2 ?   -2.4   0.0       1.4   6.3e+03      61      75 ..     377     391 ..     350     414 .. 0.55

  Alignments for each domain:
  == domain 1  score: 60.3 bits;  conditional E-value: 5.3e-20
                                       -EEEET--S-TTSHHHHHHHHHHH...HT--EEEESSS-SEETTEES----T.....T--EEEE-S-HHHHGGGHHH CS
                     CoA_binding_2   2 tiaVvGasdnpgkfgykvlrylle...hglpvvpVnpkeeeilgekvyaslaed.pepvdlvdvftppeatpeivke 74 
                                       ++aV+G s ++g  +y +l ++ e   +g +v+pVnpk++e++ ++v  +++++ +++vd++ +++p++ +p++++e
  gi|242399812|ref|YP_002995237.1|   9 SVAVFG-SFKKGAIAYEILGNIIEggfEG-DVTPVNPKGGEVEVANVRLKIEKKlEKNVDVAIIAIPAKFVPPLIDE 83 
                                       79****.9999*************88888.9*********************8679********************* PP

                                       HHHH--SEEEE-TT.......---HHHHHHHHHTT-EEE.ES-HHH CS
                     CoA_binding_2  75 alalgakavwlqpg.......sedeeaaelaeeagirvvgdrCilv 113
                                       ++++   av++ +g         ++e++e+a+++g++v+g++C ++
  gi|242399812|ref|YP_002995237.1|  84 IGDKVKGAVVISAGfsevgnvDLEKELIEKARNKGVKVIGPNCAGI 129
                                       **997777777777*****************************998 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.4
                                       E-S-HHHHGGGHHHH CS
                     CoA_binding_2  61 vftppeatpeivkea 75 
                                       +f+p+e+++  + +a
  gi|242399812|ref|YP_002995237.1| 377 IFIPSEEIARAIIDA 391
                                       334444444433333 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   1.0   2.1e-09   9.6e-06       3      96 .]       7      97 ..       5      97 .. 0.79
   2 ?   -1.6   0.0         1   4.6e+03      77      94 ..     280     297 ..     277     299 .. 0.86
   3 ?   -3.4   0.0       3.6   1.6e+04      40      63 ..     312     334 ..     301     338 .. 0.63
   4 ?   -0.0   0.1      0.32   1.4e+03      68      92 ..     377     399 ..     356     403 .. 0.64

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 2.1e-09
                                      TEEEEEETTTSHHHHHH.HHHHHHHHECEE.EEEEC-TTTTTCEETTEEEESCH.HHHHHHCTTTEEEEES-HHHHHHH CS
                       CoA_binding  3 dtkviviGagglgiagl.yhfkeklkygik.avfgvnprkvgtevlglpvyksv.deleektevdvavitvPaesaqea 78
                                      +++v+v G  ++ +a++     + ++ g++  v +vnp+  g ev+   v  ++ ++le++  vdva+i++Pa+++   
  gi|242399812|ref|YP_002995237.1|  7 PSSVAVFGSFKK-GAIAyEILGNIIEGGFEgDVTPVNPK--GGEVEVANVRLKIeKKLEKN--VDVAIIAIPAKFVPPL 80
                                      578999999888.6777577889999999999*******..65555555553330445555..**************** PP

                                      HHHHHHTT-SEEEEESST CS
                       CoA_binding 79 vdelveagikgiviiteg 96
                                      +de  + ++kg+v+i++g
  gi|242399812|ref|YP_002995237.1| 81 IDEIGD-KVKGAVVISAG 97
                                      ****99.79999999876 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1
                                       HHHHHHHHTT-SEEEEES CS
                       CoA_binding  77 eavdelveagikgiviit 94 
                                       +++ e+ e g k i+iit
  gi|242399812|ref|YP_002995237.1| 280 AKTFEMYESGGKRIAIIT 297
                                       6788999*********99 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 3.6
                                       TTTCEETTEEEESCHHHHHHHCTT CS
                       CoA_binding  40 kvgtevlglpvyksvdeleektev 63 
                                       k+g e+  l  + +++el+e++++
  gi|242399812|ref|YP_002995237.1| 312 KLGLEIAKLSEK-TINELMEFLPP 334
                                       666666666666.77777776655 PP

  == domain 4  score: -0.0 bits;  conditional E-value: 0.32
                                       EES-HHHHHHHHHHHHHTT-SEEEE CS
                       CoA_binding  68 itvPaesaqeavdelveagikgivi 92 
                                       i++P+e+++ a++++  ++ k+iv+
  gi|242399812|ref|YP_002995237.1| 377 IFIPSEEIARAIIDA--KCSKPIVV 399
                                       444666666555543..55666665 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   0.2   4.1e-05      0.18      57      94 ..      60      96 ..      41      98 .. 0.86
   2 ?   -0.2   0.0      0.35   1.6e+03      63      97 .]     368     404 ..     337     404 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.1e-05
                                      HHHHH-SEEEE-S-HHHHHHHHHHCGHHHHTTSEEEEE CS
                     F420_oxidored 57 eaaeeadvvvlavkpedveevlselakdalkgklvisv 94
                                      ++ ++ dv ++a++ + v+ +++e+  d+ kg +vis+
  gi|242399812|ref|YP_002995237.1| 60 KLEKNVDVAIIAIPAKFVPPLIDEI-GDKVKGAVVISA 96
                                      455789*******************.899*******97 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.35
                                       SEEEE-S-HHHHH..HHHHHCGHHHHTTSEEEEESSS CS
                     F420_oxidored  63 dvvvlavkpedve..evlselakdalkgklvisvlag 97 
                                         ++++v+p  ++  e+++++ +++ ++ +v+  +ag
  gi|242399812|ref|YP_002995237.1| 368 SLLIICVPPIFIPseEIARAIIDAKCSKPIVVNFMAG 404
                                       5689999999885226888888888888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (448 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); 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: 0.67u 0.35s 00:00:01.02 Elapsed: 00:00:00.53
# Mc/sec: 2526.26
//
Query:       gi|242399813|ref|YP_002995238.1|  [L=174]
Description: Flavin reductase-related oxidoreductase [Thermococcus sibiricus MM 739]
Scores for complete 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-23   81.8   0.0    6.2e-23   81.6   0.0    1.0  1  Flavin_Reduct  Flavin reductase like domain


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 !   81.6   0.0   3.5e-27   6.2e-23       4     140 ..       9     142 ..       4     156 .. 0.89

  Alignments for each domain:
  == domain 1  score: 81.6 bits;  conditional E-value: 3.5e-27
                                       S-EE-EEEEE.EETTEEEEEEESSEEEEETTTTEEEEEEETTSHHHHHHHHHSEEEEEEEBCCGHHHHHHTCS...S CS
                     Flavin_Reduct   4 vaqpvavvttsvpptsplgatlssftslsldPplvafslrlpsstadalkeagefvinllsesqealadafsqksgp 80 
                                       ++   ++v++  ++++++ + + ++t ls+ P l+++++ ++++t++ + + +efvi++ s +  + ++  ++ksg 
  gi|242399813|ref|YP_002995238.1|   9 YPMRTYLVVS-GQGDEANVMAADWVTVLSHRPSLIGVAISPKRYTHRLISKYQEFVISVPSLEMLEDVWIAGTKSG- 83 
                                       5667789998.8999999*****************************************99988887777777555. PP

                                       CCCCCCCCCCCEEECT.CCCSEEETTCSEEEEEEEEEEECCTTEEEEEEEEEEEEESTTEC CS
                     Flavin_Reduct  81 rtddksifagltwees.ptgapallgalasleCqvvgsvelgdhelfigeVvavkvgddad 140
                                          +k+    +t+ +s + + p +++ala++eC+vv+ +++gdh+ f+ge+v +  ++da 
  gi|242399813|ref|YP_002995238.1|  84 --PSKLREMNMTLVPSkKINTPSIKEALANIECRVVDARDYGDHTWFVGEIVGYTYNEDAF 142
                                       ..4666677888888878999*********************************9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       253  (0.0141112); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); 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: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1045.84
//
Query:       gi|242399814|ref|YP_002995239.1|  [L=324]
Description: O-sialoglycoprotein endopeptidase [Thermococcus sibiricus MM 739]
Scores for complete 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   0.1    1.8e-97  326.3   0.1    1.0  1  Peptidase_M22   Glycoprotease family
    0.00053   19.8   0.0      0.099   12.3   0.0    2.2  2  Carbam_trans_N  Carbamoyltransferase N-terminus
  ------ inclusion threshold ------
      0.028   13.9   0.0       0.34   10.3   0.0    2.2  2  BcrAD_BadFG     BadF/BadG/BcrA/BcrD ATPase 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 !  326.3   0.1  3.1e-101   1.8e-97       1     271 []      22     292 ..      22     292 .. 0.97

  Alignments for each domain:
  == domain 1  score: 326.3 bits;  conditional E-value: 3.1e-101
                                       XCEXEEEEEEEEE....SSSSHHHHHHHHHHHHHHHHHHHHHHHTSTGGGEEEEEEEEESS-HHHHHHHHHHHHHHH CS
                     Peptidase_M22   1 evlanvvasqkelhakyGGvvPelasraHserllplieealaeaglsledldaIavtkgPGlftgLrvGvsfAkgla 77 
                                       +vlanv+++ +   +++GG++P++a+++H++ l pl+++al+ea+++++d+d+Ia+++gPGl+++Lrv++++A++la
  gi|242399814|ref|YP_002995239.1|  22 KVLANVFNTLT---TEKGGIHPKEAAEHHAKLLRPLLKKALQEAKVNIKDVDVIAFSQGPGLGPALRVVATAARALA 95 
                                       58899999887...9************************************************************** PP

                                       HHCT--EEEEEHHHHHHHCCHCTSECSSCEEEEESSSTEEEEEECTTEEEEEEEESSSEHHHHHHHHHHHHT..SSC CS
                     Peptidase_M22  78 lalnkPlvgVnhleahalaarleekeefPvvllvsGghtqvylvkegryeilgetlddaagealdkvarllglpypg 154
                                       l +nkP+vgVnh++ah++ +++  + ++Pv l+vsGg+tq+++ ++gry+++getld+ +g+a+d +ar +gl++pg
  gi|242399814|ref|YP_002995239.1|  96 LRYNKPIVGVNHCIAHVEVTKMF-GIKDPVGLYVSGGNTQILALEGGRYRVFGETLDIGIGNAIDTFAREIGLGFPG 171
                                       *********************99.6799****************99******************************* PP

                                       CHHHHHHHCTC.S.......EETTEEE.CHHHHHHHHHHST.T..HHHHHHHHHHHHHHHHHHHHHHHHHHCTBSEE CS
                     Peptidase_M22 155 gpkieklakeg.kkiefprplkgldfsfsGlktavlkelek.e..vedlaasfqeavvdhlvekteralklpkakel 227
                                       gpkiekla++g k+ie+p+++kg+d+sfsG+ t+++++ ++ +   ed+a+sfqe++++ l+e+tera+++++++e+
  gi|242399814|ref|YP_002995239.1| 172 GPKIEKLAQRGeKYIELPYTVKGMDLSFSGILTEAVRKYKTgKykLEDIAYSFQETAFAALIEVTERAVAHTGKEEV 248
                                       ***********888*************************776477******************************** PP

                                       EEESGGGGXHHHHHCHCCHHHHTTSEEEXXXHHHHSSXCHHHHH CS
                     Peptidase_M22 228 vilGGvaankrLrealeeeaeelglkliiPplkyctdnaamiaw 271
                                       v++GGvaan+rLre+l++++ee+++k+++Pp ++c+dn+amia+
  gi|242399814|ref|YP_002995239.1| 249 VLVGGVAANNRLREMLKTMSEERSIKFFVPPYDLCRDNGAMIAY 292
                                       **********************99******************97 PP

>> Carbam_trans_N  Carbamoyltransferase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.5   0.0     0.002        12       3      70 ..       4      77 ..       2      83 .. 0.69
   2 !   12.3   0.0   1.7e-05     0.099     259     325 ..     211     279 ..     177     291 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.002
                    Carbam_trans_N  3 lGikltlflHDgavalvddgklvaav....eeErltrikrdqk.....lpklkaidyaleeagvelsdiDqivfdei 70
                                      lGi +t   H  ++ +v + k++a v     +E+ + + +++      l +   ++ al+ea v+ +d+D+i+f + 
  gi|242399814|ref|YP_002995239.1|  4 LGIEGT--AHTLGIGIVTEDKVLANVfntlTTEKGGIHPKEAAehhakLLR-PLLKKALQEAKVNIKDVDVIAFSQG 77
                                      799988..8999999999888877662222456655444444333322333.457899***************9875 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 1.7e-05
                    Carbam_trans_N 259 kearekdedlaAsiqvflErlvvevlnivyeklkirnLclaGGvalNiklNsallesglFedv..wvqP 325
                                       k  + k ed+a s+q+     ++ev++ + ++++ +   l GGva+N  l   l   +  +++  +v+P
  gi|242399814|ref|YP_002995239.1| 211 KTGKYKLEDIAYSFQETAFAALIEVTERAVAHTGKEEVVLVGGVAANNRLREMLKTMSEERSIkfFVPP 279
                                       33333446***************************************8887776655544443335555 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 ?    1.1   0.0     0.037   2.2e+02     223     252 ..      35      67 ..      15     102 .. 0.75
   2 ?   10.3   0.0   5.8e-05      0.34     190     249 ..     216     273 ..     198     281 .. 0.65

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.037
                                       ESGGGG-HHH...HHHH.....HHHH-S-EE-- CS
                       BcrAD_BadFG 223 tGGvakneaa...vkelrklvkenygevkinin 252
                                       +GG++ +eaa    k lr+l+k++ +e k+ni+
  gi|242399814|ref|YP_002995239.1|  35 KGGIHPKEAAehhAKLLRPLLKKALQEAKVNIK 67 
                                       566666666522245677777777777777764 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 5.8e-05
                                       -HHHHHHHHHHHHHHHHHHHHHTT---SS...EEEESGGGG-HHHHHHH.....HHHH-S-E CS
                       BcrAD_BadFG 190 kaedIlaglhraialrvialisrsggvtde..vtltGGvakneaavkelrklvkenygevki 249
                                       k edI     +     +i++ +r  + t +  v+l+GGva n    + lr+++k +  e +i
  gi|242399814|ref|YP_002995239.1| 216 KLEDIAYSFQETAFAALIEVTERAVAHTGKeeVVLVGGVAAN----NRLREMLKTMSEERSI 273
                                       55666666666655666666666665555456**********....5555555555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.53
# Mc/sec: 1834.85
//
Query:       gi|242399815|ref|YP_002995240.1|  [L=276]
Description: Inorganic polyphosphate/ATP-NAD kinase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-67  227.7   0.2      3e-67  226.9   0.2    1.4  1  NAD_kinase      ATP-NAD kinase
     0.0019   17.8   0.0     0.0029   17.2   0.0    1.3  1  DAGK_cat        Diacylglycerol kinase catalytic domain
  ------ inclusion threshold ------
      0.079   11.6   0.1       0.12   11.0   0.1    1.1  1  Staph_opine_DH  Staphylopine dehydrogenase


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 !  226.9   0.2     5e-71     3e-67       1     291 [.       2     259 ..       2     260 .. 0.97

  Alignments for each domain:
  == domain 1  score: 226.9 bits;  conditional E-value: 5e-71
                                       .EEEEESSCGGTCSHHHHHHHHHHHCT-..EEEEECCGGCCSSSTT--HHHHTTTT--.......EEECCC-TTTTT CS
                        NAD_kinase   1 kvgivvnpikkeaieraeevarwLldalsrvlevtveeklgeslaeaaefrsevisvlkkvkttddtrkaleafada 77 
                                       k+giv++++++ea+++a +v+++L+ +   ++ev+v+e+   +  +                   +  +++  + ++
  gi|242399815|ref|YP_002995240.1|   2 KFGIVARRDREEALKLAYRVYDFLKVN---NYEVYVDEEAYIHFPH-------------------FSSEDVLSLKKM 56 
                                       78*************************...9*********999776...................8999******** PP

                                       SSSEEEEEE-HHHHHHHHHHHHHCT-EEEEEESSS--SS-SEEGGGHHHHHHHHHHT-SEEEEEEEEEEEEEETTE. CS
                        NAD_kinase  78 gvdliivvGGDGTaldvarllqkaeiPvlgvnaGvkgfltefepeaaaellekllegeirvekrevldavimrskge 154
                                       +vd+ii++GGDGT+l+v + ++k +iP+l+vn+G++gfl+e+ep++++ +++++leg++ +++r+++++++ + +  
  gi|242399815|ref|YP_002995240.1|  57 DVDMIIAIGGDGTVLRVEHNTSK-DIPILAVNMGTLGFLAEIEPAETFFAISRILEGDYFIDERMKIRVFVEDVSI- 131
                                       **********************7.********************************************99988777. PP

                                       .....EEEEEEESSEEEEEESSSSS-EEEEEEETTEEEEEEEESEEEEE-TGGGGTHHHHTT--EE-TT---EEEEE CS
                        NAD_kinase 155 ediadiviensvlnevviirgpgstlielelyvdtelleadqldglivstPtGstayslsaGgplisPgvlailivp 231
                                                + +ln+vvi +  + ++++l++yvd+el+e++++dgli+stPtGstay+lsaGgpl++P++ ail+vp
  gi|242399815|ref|YP_002995240.1| 132 ---------PDALNDVVILTSIPGKVTHLKYYVDGELAEDIRADGLIISTPTGSTAYALSAGGPLVDPRLHAILLVP 199
                                       .........678***************************************************************** PP

                                       ESESSS----EEE-TT-EEEEEE-SS--EEEEETTTEEEEE-TT-EEEEEEESSEEEEEE CS
                        NAD_kinase 232 icPhslssrpiVvssssklrirvasrseallaldGseelelspgdevrvtasdkkfklir 291
                                       + P +l++rp+Vv++ s+++i+v +++e++l +dG+  ++l+ +  +rv +s++k+k++r
  gi|242399815|ref|YP_002995240.1| 200 LAPVALTARPLVVPDCSSIEIEVLTEREIVLTVDGQFYTQLPSNLKIRVEKSPRKTKFVR 259
                                       **********************************************************98 PP

>> DAGK_cat  Diacylglycerol kinase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   4.9e-07    0.0029      48      92 ..      50      90 ..      11      97 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4.9e-07
                                      HHHHHHCC-SEEEEEESHHHHHHHHHHHCTHHCTTSEEEEEE-SS CS
                          DAGK_cat 48 akeakeegvdlivvaGGDGtvsevlnglleelatkpplgiiPlGt 92
                                      + ++k+ +vd+i+++GGDGtv  v +   +    ++p+  + +Gt
  gi|242399815|ref|YP_002995240.1| 50 VLSLKKMDVDMIIAIGGDGTVLRVEHNTSK----DIPILAVNMGT 90
                                      556777789************999887766....77777777777 PP

>> Staph_opine_DH  Staphylopine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   1.9e-05      0.12     331     365 ..      20      54 ..      18      69 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 1.9e-05
                                       ----TT--B----EE-TTS-EE--HHHHHHHHHHH CS
                    Staph_opine_DH 331 ryfDFsavpirkvfideeglldiPRvPkeDyyrlk 365
                                       r +DF  v+  +v++dee++++ P   +eD+  lk
  gi|242399815|ref|YP_002995240.1|  20 RVYDFLKVNNYEVYVDEEAYIHFPHFSSEDVLSLK 54 
                                       67****************************98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); 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:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.54
# Mc/sec: 1532.86
//
Query:       gi|242399816|ref|YP_002995241.1|  [L=339]
Description: Integral membrane protein, putativ [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-53  182.2  25.8      2e-53  181.9  25.8    1.0  1  LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region
  ------ inclusion threshold ------
      0.038   13.7   1.4      0.065   12.9   1.4    1.3  1  RabGAP-TBC       Rab-GTPase-TBC domain


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 !  181.9  25.8   2.2e-57     2e-53       3     301 .]      11     321 ..       8     321 .. 0.86

  Alignments for each domain:
  == domain 1  score: 181.9 bits;  conditional E-value: 2.2e-57
                   LPG_synthase_TM   3 lglalsalllalllrgvdlaalaaalrsldpwwlllalllallsvllralrWrlllrslgarislrrllrayliglf 79 
                                       +g++++++l++++    ++++++++++++d ++lllall+  +++l++  rW ++l+++++ ++  + l a+l+g+f
  gi|242399816|ref|YP_002995241.1|  11 IGIVVILILMWWA----GIEETIELIIRADLRFLLLALLMQVFATLAWVFRWSIFLKRAEVVVRTKDILIATLVGIF 83 
                                       6788889999999....***************************999999*************************** PP

                   LPG_synthase_TM  80 vnnvtPgalg.Gevvrayllkrkegvslskalasvvverlldllalvllgllallllggllaegaa...vllllala 152
                                       +nn+tPga + Ge++r+y+++++++ ++++++a+++++r+ld++ ++l++l+a+ + ++l          l ++al+
  gi|242399816|ref|YP_002995241.1|  84 ANNLTPGARAgGEPARMYVITKRSDSTYGQVFATIMADRILDVIPVLLFTLVAFKYALSLKIKLLLsvlSLSTVALL 160
                                       *********99*******************************************99999988875555444444444 PP

                   LPG_synthase_TM 153 llllavla......lllllllrrrlarlarvlkrlarllarfarklasakr.............klvlasprrllla 210
                                       ++++++l+      l++ ll++ + +  + + +r+a+  +++        +               + ++p  ++ +
  gi|242399816|ref|YP_002995241.1| 161 MIVFVSLLvslnenLAFKLLSKITNLGKRIFPERFAGIESKIE-------ErlkksifefretfLELSKDPVVMGKT 230
                                       4444444444444444444444444444444444444444444.......15566667******999********** PP

                   LPG_synthase_TM 211 fllslliwllealtlylllralgvdvslallllillaltlvgalpplPgGlGvrEaalalllallGvsaaealaaal 287
                                       +++sl+ w++ +l++y+++ ++g+++ ++++l +++a +++g++++lPgG+G+ Ea+  +l+ +l +s+++a++a++
  gi|242399816|ref|YP_002995241.1| 231 LFYSLALWGFMLLRTYFVFESVGYHLEIYKILMVQMAGIALGMISILPGGVGITEAVNSALYLSLRISKSLAVSATV 307
                                       ***************************************************************************** PP

                   LPG_synthase_TM 288 lyrlitlylllllG 301
                                       l+r+i+++l++++G
  gi|242399816|ref|YP_002995241.1| 308 LDRFISFWLPTIIG 321
                                       ************98 PP

>> RabGAP-TBC  Rab-GTPase-TBC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   1.4   7.2e-06     0.065      95     202 ..     161     261 ..     156     271 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.2e-06
                        RabGAP-TBC  95 divaplllvsldeeeaFwcfvsLlekyklrdlytsslpglkrklkvleellkkkdpklykhlkeegldlelfaikwf 171
                                        iv + llvsl+e+ aF++++++   +  + ++ + + g+++k   +ee lkk   ++ + + e++ d+ +     f
  gi|242399816|ref|YP_002995241.1| 161 MIVFVSLLVSLNENLAFKLLSKIT--NLGKRIFPERFAGIESK---IEERLKKSIFEFRETFLELSKDPVVMGKTLF 232
                                       57788889****************..999************99...6899999999999999999999999999999 PP

                        RabGAP-TBC 172 ltlflrefpletvlrlwD.lllegekfvllrv 202
                                         l l  f l  +  +++ + +   +  ++++
  gi|242399816|ref|YP_002995241.1| 233 YSLALWGFMLLRTYFVFEsVGY---HLEIYKI 261
                                       8888888888777777774444...3344544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1007  (0.056166); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); 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: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.54
# Mc/sec: 1891.40
//
Query:       gi|242399817|ref|YP_002995242.1|  [L=383]
Description: Sun/NOL1/NOP nucleolar protein [Thermococcus sibiricus MM 739]
Scores for complete 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-58  195.2   0.0    1.2e-57  194.8   0.0    1.1  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
    1.8e-17   63.0   0.5    3.3e-17   62.2   0.5    1.4  1  PUA              PUA domain
    1.4e-10   41.1   0.0    2.1e-10   40.6   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    7.6e-07   29.5   0.0    7.6e-05   23.1   0.0    2.4  2  Methyltr_RsmF_N  N-terminal domain of 16S rRNA methyltransfer
    4.5e-05   22.9   0.0    7.8e-05   22.1   0.0    1.3  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    9.4e-05   23.1   0.0    0.00021   21.9   0.0    1.6  1  Methyltransf_25  Methyltransferase domain
     0.0012   18.4   0.0     0.0026   17.3   0.0    1.4  1  Methyltransf_5   MraW methylase family
     0.0042   16.6   0.1        0.6    9.6   0.0    2.2  2  Methyltransf_4   Putative methyltransferase
     0.0099   16.0   0.0      0.021   14.9   0.0    1.5  1  FtsJ             FtsJ-like methyltransferase
  ------ inclusion threshold ------
      0.014   15.2   0.0      0.029   14.1   0.0    1.4  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
      0.057   13.7   0.1       0.13   12.5   0.1    1.6  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 !  194.8   0.0   7.2e-61   1.2e-57       3     200 .]     192     380 ..     190     380 .. 0.91

  Alignments for each domain:
  == domain 1  score: 194.8 bits;  conditional E-value: 7.2e-61
                                       HH---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC.. CS
                   Methyltr_RsmB-F   3 lLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlggel 79 
                                       +L+p+e++ i+D+ aaPGgKT+hia+l++n+g+++A+d++k+Rl+++++ l+rLgv+n++++++D r+ ++     +
  gi|242399817|ref|YP_002995242.1| 192 VLDPKEGDLIIDMTAAPGGKTSHIAQLLENRGEILALDKSKNRLSKMKNELERLGVKNVKLIQMDSRNLPELGI--Q 266
                                       89*******************************************************************88655..6 PP

                                       EEEEEEEE--CCGGGTTT-TCHHHH--HHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEES--STTTTHHHHHHHHHH CS
                   Methyltr_RsmB-F  80 fDriLlDaPCsgtgvirrdpdvklrrkekdiaqlaklqkellsaaidllkkgGvlvYsTCsvlveEneevieeaLkk 156
                                        D+iLlDaPC+++gv  +   +  +r++kdi + a+ qk+ ++aai++l+kgGvlvYsTC++  eEne  ++++Lkk
  gi|242399817|ref|YP_002995242.1| 267 ADKILLDAPCTALGVRPK---LWETRTPKDIDATARYQKHFINAAIKSLRKGGVLVYSTCTLSYEENEGNVKYMLKK 340
                                       ***************655...55569*************************************************** PP

                                       -TTEEEESSBSTTSTTSSECEECTSEEE-TTTTSS-SEEEEEEE CS
                   Methyltr_RsmB-F 157 redvelvetelsepkglklgeeagtlrllPhtenkdgffiaklk 200
                                         + e +++ + ++ g+ +++ +   r++Ph+++++gffia+l+
  gi|242399817|ref|YP_002995242.1| 341 GLKLEEQKL-FIGSPGIGINKVQ---RFYPHKHKTQGFFIARLR 380
                                       977777766.4454566666555...9**************996 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.2   0.5     2e-20   3.3e-17       1      70 [.      89     158 ..      89     160 .. 0.98

  Alignments for each domain:
  == domain 1  score: 62.2 bits;  conditional E-value: 2e-20
                                       CEEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEE CS
                               PUA   1 grvvvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksvei 70 
                                       ++vv ++ A + + +ga+L+apGv+++++ ++egd V+i d++g lv++G+a+++++e+  +++g++ve+
  gi|242399817|ref|YP_002995242.1|  89 PKVVANKFASESVYQGAQLYAPGVLKADKGIREGDQVQIRDPKGLLVGIGIARMNAKEMIIATRGVAVEV 158
                                       689*****************************************************************98 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   0.0   1.3e-13   2.1e-10       5     114 ..     199     330 ..     195     368 .. 0.81

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 1.3e-13
                   Methyltransf_31   5 lrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieelekl.ledekfDlils 80 
                                         ++D  ++ G +t  +a++l  ++e+  +D s++ ++++++++++lg++nv++ q d  +l++l ++    D il 
  gi|242399817|ref|YP_002995242.1| 199 DLIIDMTAAPGGKTSHIAQLLENRGEILALDKSKNRLSKMKNELERLGVKNVKLIQMDSRNLPELgIQ---ADKILL 272
                                       5689**************99999*****************************************9888...8***** PP

                   Methyltransf_31  81 nevl...................naladpdkileeiervlkpggilliedpr.....l 114
                                       ++++                   ++   ++ +++ +++ l++gg+l+ +++       
  gi|242399817|ref|YP_002995242.1| 273 DAPCtalgvrpklwetrtpkdidATARYQKHFINAAIKSLRKGGVLVYSTCTlsyeeN 330
                                       *777666777777777777787666666777888*****************9433332 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 !   23.1   0.0   4.7e-08   7.6e-05       2      68 ..       7      76 ..       6      84 .. 0.82
   2 ?    3.9   0.0     0.046        75      75      90 .]     172     187 ..     155     187 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 4.7e-08
                                      -HHHHHHHHHHHGGGHHHHHHHHH--.---EEE--TTS..TTHHHH.HHH.-SS--B-TT-TTEEES--- CS
                   Methyltr_RsmF_N  2 PeeFiekmkellgeeaeaflaaleep.rkkglRvNtlKisveelek.lse.efelepvpwceeGfyleee 68
                                      P e  +++  ++g+eae+++++l+ep  k+ +RvNtlKis+++l + l + + e ++ p+ eeG+y+e+e
  gi|242399817|ref|YP_002995242.1|  7 PVELRRYYYGFFGDEAEELMRTLREPvEKYYIRVNTLKISRDRLIEdLRKeGLEPKRSPYLEEGIYFERE 76
                                      556667788899***********66615779*********9997652555789999**********9986 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.046
                                       HHHHTTS-EE--TTTH CS
                   Methyltr_RsmF_N  75 plheaGlyYiQEpSam 90 
                                         +e+G++Y+Q   +m
  gi|242399817|ref|YP_002995242.1| 172 ESYEKGYFYVQTLPSM 187
                                       579********98888 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   4.8e-08   7.8e-05      42     113 ..     192     263 ..     180     280 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 4.8e-08
                                       H--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS CS
                   Ubie_methyltran  42 lvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfe 113
                                       +  +k+g  ++D+++  g  + ++++ ++++g++  lD ++n L+  ++ l++ g++n++++q ++ +Lp+ 
  gi|242399817|ref|YP_002995242.1| 192 VLDPKEGDLIIDMTAAPGGKTSHIAQLLENRGEILALDKSKNRLSKMKNELERLGVKNVKLIQMDSRNLPEL 263
                                       556899***************************************************************985 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   1.3e-07   0.00021       1      70 [.     201     272 ..     201     287 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.3e-07
                                       EEEET-TTSHHHHHHHCTS.TSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEE CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrl.gkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvs 70 
                                       ++d+ + +G  t ++a+ l ++++++++D s++ l ++++++e+ g+ nv+++q+d ++lp+   + D +++
  gi|242399817|ref|YP_002995242.1| 201 IIDMTAAPGGKTSHIAQLLeNRGEILALDKSKNRLSKMKNELERLGVkNVKLIQMDSRNLPELGIQADKILL 272
                                       78999999**********9769**********************999**************98888887765 PP

>> Methyltransf_5  MraW methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.6e-06    0.0026      14     102 ..     191     281 ..     182     287 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.6e-06
                                       HHT---TT-EEEES--TTSHHHHHHHTT--TT.EEEEEES-HHHHHHHTT.....---.EEEEES-GGGHHHHHHHT CS
                    Methyltransf_5  14 ellepkedgvyiDaTlGaggHsealLeqlsel.rligidrDksalarakerLkefekr.ltlvkgnfkelkealaea 88 
                                       ++l+pke+ + iD+T   gg + ++ + l++  +++++d+ k+ l + k+ L++   + ++l++  +++l e   +a
  gi|242399817|ref|YP_002995242.1| 191 HVLDPKEGDLIIDMTAAPGGKTSHIAQLLENRgEILALDKSKNRLSKMKNELERLGVKnVKLIQMDSRNLPELGIQA 267
                                       6899*************************9999*********************98666***********9998888 PP

                                       TTT-EEEEEEE-S- CS
                    Methyltransf_5  89 nvtkvdgillDLGv 102
                                       +   +d+ +  LGv
  gi|242399817|ref|YP_002995242.1| 268 DKILLDAPCTALGV 281
                                       76677777777776 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0   0.00037       0.6       5      63 ..     201     259 ..     197     267 .. 0.82
   2 ?    4.8   0.0     0.011        17      96     125 ..     301     330 ..     299     348 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00037
                                       EEEET-TTSHHHHHHHHH.STTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCCH CS
                    Methyltransf_4   5 vleiGcGkGeflvalAkk.nPdknflGiEirvkvvakvlkkiealelkNlrilrgdalkv 63 
                                       ++++  + G+ ++++A+  +   ++l+++++++++ k+ ++ e+l++kN+++++ d  + 
  gi|242399817|ref|YP_002995242.1| 201 IIDMTAAPGGKTSHIAQLlENRGEILALDKSKNRLSKMKNELERLGVKNVKLIQMDS-RN 259
                                       6777777777788888752566789*****************************997.44 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.011
                                       SHHHHHHHHHHEEEEEEEEEEESHHHHHHH CS
                    Methyltransf_4  96 qpellkelarvLkkgGvlelaTDveeyaee 125
                                       q+++++++ + L+kgGvl+  T    y e+
  gi|242399817|ref|YP_002995242.1| 301 QKHFINAAIKSLRKGGVLVYSTCTLSYEEN 330
                                       89*******************998888776 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.3e-05     0.021      21     142 ..     197     331 ..     163     346 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.3e-05
                                       TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS.........HHH..TTEEEECS-CCCSSHHHHHCHCHHHS CS
                              FtsJ  21 pgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm.........apl..pgvttiqgditdpetiekikealser 86 
                                       +g+ ++D  aaPGg +  ++q l+++g ++a+D  ++         + l  ++v++iq+d ++      i       
  gi|242399817|ref|YP_002995242.1| 197 EGDLIIDMTAAPGGKTSHIAQLLENRGEILALDKSKNrlskmknelERLgvKNVKLIQMDSRNLPELG-I------- 265
                                       56779******************999********9997865554432224567777777776665544.3....... PP

                                       SEEEEEE--S-..........SS-CHHHHHHHHHCCCCHHHHCCHCCCCECCCEEEECCCH..CCCHH CS
                              FtsJ  87 kvdlvvsDgap..........dvsgvhdldeylqsqLllaalelalkllkpggtfvlkifr..geete 142
                                       ++d ++ D              +   +d+d++ +    +  ++ a+k l++gg++v  +++   ee e
  gi|242399817|ref|YP_002995242.1| 266 QADKILLDAPCtalgvrpklwETRTPKDIDATAR--YQKHFINAAIKSLRKGGVLVYSTCTlsYEENE 331
                                       4777777764334444444445555555555555..57888888888899999999887776544444 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 ?   14.1   0.0   1.8e-05     0.029      59     134 ..     185     258 ..     168     265 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.8e-05
                                       HHHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GG CS
                              PCMT  59 phmvalalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGr 134
                                       p+mva     l+ k+g+ ++++ +  G +t  +a+l++++g +++++++k+  ++ k++l++l+++nv+++  D r
  gi|242399817|ref|YP_002995242.1| 185 PSMVAS--HVLDPKEGDLIIDMTAAPGGKTSHIAQLLENRGEILALDKSKNRLSKMKNELERLGVKNVKLIQMDSR 258
                                       556654..46888999*****************************************************9998865 PP

>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   8.3e-05      0.13       2      63 ..      91     148 ..      90     157 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.3e-05
                           UPF0113   2 vvvkekaeklFLYGrdvlkesilkitesvkenqvvvVlnengeplGiGkirkdtkaspgkiv 63 
                                       vv ++ a++++  G +++  ++lk +++++e+++v + + +g ++GiG++r +     ++++
  gi|242399817|ref|YP_002995242.1|  91 VVANKFASESVYQGAQLYAPGVLKADKGIREGDQVQIRDPKGLLVGIGIARMNA----KEMI 148
                                       666777777777899999999*****************************9954....3333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); expected 358.6 (0.02)
Passed bias filter:                      534  (0.0297841); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.67u 0.33s 00:00:01.00 Elapsed: 00:00:00.52
# Mc/sec: 2219.61
//
Query:       gi|242399818|ref|YP_002995243.1|  [L=170]
Description: hypothetical protein TSIB_1843 [Thermococcus sibiricus MM 739]
Scores for 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-58  194.2   6.5    9.4e-58  194.0   6.5    1.0  1  DUF3201   Protein of unknown function (DUF3201)
  ------ inclusion threshold ------
      0.031   13.8   0.0      0.046   13.2   0.0    1.2  1  Tsp45I    Tsp45I type II restriction enzyme
        0.1   12.8   0.1        0.6   10.3   0.0    2.2  2  Costars   Costars


Domain annotation for each model (and alignments):
>> DUF3201  Protein of unknown function (DUF3201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  194.0   6.5   1.6e-61   9.4e-58       2     150 ..       9     156 ..       8     157 .. 0.96

  Alignments for each domain:
  == domain 1  score: 194.0 bits;  conditional E-value: 1.6e-61
                                       HHHHHHHHHHHHHHHHHHHST..TSEE---EEE-S-EEEETTEEEE--S-EEEEEEETTEEEEEETTEEEEEEEEEG CS
                           DUF3201   2 llnklwedvfelreelkeelkrfgfkveeveevfnaylyldgkweemkyphpafevkpqievgatpesyyfvvavpk 78 
                                        lnk+w+++f ++eelke+l  +gfkve veevfnay+yl+g+w+em yphpafe+kpq+e+gat +s+y+v+ + k
  gi|242399818|ref|YP_002995243.1|   9 HLNKIWGEIFRMNEELKEKLSPMGFKVEPVEEVFNAYIYLEGEWREMIYPHPAFEIKPQGELGATIQSFYIVFGILK 85 
                                       59*************************************************************************** PP

                                       GG--HHHHHHHHHH-SEEEEESS-TTT-EEEE..TTS---HHHHHHHHTSS-SEEEEEEE-T-HHHHHHHHH CS
                           DUF3201  79 eklskefledvleafeklfiygaedfledvynclresplseevidrivesdekviqfevdlddkeklkeelk 150
                                       +k+s+ f+ ++l+ f+k++iyg+e+fled+yn  ++  l +ev+  i+es+e+v+qfev+ ++  ++ e+l+
  gi|242399818|ref|YP_002995243.1|  86 DKISQGFVLEFLKKFPKSYIYGSENFLEDIYN-HKKPKLPDEVYRLITESQEEVLQFEVEEEEASEIEEKLF 156
                                       ********************************.4555577**********************9999999876 PP

>> Tsp45I  Tsp45I type II restriction enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   7.7e-06     0.046     174     220 ..      94     140 ..      79     146 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.7e-06
                            Tsp45I 174 ldliarfnkkyviGeakfltdiGGhqnaqledalkvleaksveavik 220
                                       l+++ +f k y+ G   fl di  h++ +l d +  l ++s+e+v++
  gi|242399818|ref|YP_002995243.1|  94 LEFLKKFPKSYIYGSENFLEDIYNHKKPKLPDEVYRLITESQEEVLQ 140
                                       7999******************************9999999998865 PP

>> Costars  Costars
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.26   1.5e+03      13      38 ..      64      90 ..      62      94 .. 0.71
   2 ?   10.3   0.0    0.0001       0.6      26      56 ..     138     168 ..     112     170 .] 0.80

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.26
                           Costars 13 IkelGekndd.gkvvvtFGeLfekytn 38
                                      Ik +Ge  +  +++++ FG L +k+++
  gi|242399818|ref|YP_002995243.1| 64 IKPQGELGATiQSFYIVFGILKDKISQ 90
                                      666666555546788999999888765 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0001
                           Costars  26 vvtFGeLfekytniseklvGtLlaAkkkklv 56 
                                       v +F +  e+ ++i ekl G ++ Akk++++
  gi|242399818|ref|YP_002995243.1| 138 VLQFEVEEEEASEIEEKLFGFIKLAKKHGVL 168
                                       4566666689999****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); 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: 957.30
//
Query:       gi|242399819|ref|YP_002995244.1|  [L=300]
Description: hypothetical protein TSIB_1844 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-11   44.0   0.0    5.4e-10   39.7   0.0    2.2  2  LEA_2     Late embryogenesis abundant protein


Domain annotation for each model (and alignments):
>> LEA_2  Late embryogenesis abundant protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0     0.018   3.3e+02      54      88 ..     100     133 ..      75     145 .. 0.71
   2 !   39.7   0.0     3e-14   5.4e-10       2      96 ..     188     276 ..     187     281 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.018
                                       EHHHHHHHHHHHH...HCCSEEEEEEEEEEE.EEET CS
                             LEA_2  54 saddlarelrall.agevgleleytlrgrlkvlgkp 88 
                                       +++ ++++l+ ++ +     e+e+++rg +     +
  gi|242399819|ref|YP_002995244.1| 100 NSNEVINALKEHIrS-GERSEVEIKIRGSIF-GLPL 133
                                       556678899999944.466677777777774.3344 PP

  == domain 2  score: 39.7 bits;  conditional E-value: 3e-14
                                       EEEEESSSS-EEEEEEEEEEEESSSEEEEEEECE-EEESSSCEEEEEEEEEEEHHHHHHHHHHHH..HCCSEEEEEE CS
                             LEA_2   2 lrvrNPNsfgvrydgleldlsyngqrlasgtspqgfsqpargtttlevpvsvsaddlarelrallagevgleleytl 78 
                                       ++++NPNsf++++ g+ +++ +n+ ++a+g+  +g+++pa+g  t +++  v+  +l++ ++ ++   +g++ e+tl
  gi|242399819|ref|YP_002995244.1| 188 VKLYNPNSFPLPLFGIKYTIDANNHQIAQGELLEGVTIPANGRATAKIKTLVDTTVLPSVIAEHI--NRGETSELTL 262
                                       899*********************************************************99999..6777777777 PP

                                       EEEEE.EEETTTSCEEEE CS
                             LEA_2  79 rgrlkvlgkpilgsvtvp 96 
                                       +  l v  k   +s++++
  gi|242399819|ref|YP_002995244.1| 263 KFSLGV--KV--FSKEIT 276
                                       777765..33..344444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        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 0.32s 00:00:00.96 Elapsed: 00:00:00.53
# Mc/sec: 1690.94
//
Query:       gi|242399820|ref|YP_002995245.1|  [L=748]
Description: Mfs transporter [Thermococcus sibiricus MM 739]
Scores for complete 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-59  199.2   1.0    4.6e-33  114.6   1.1    2.3  2  MMPL            MMPL family
      2e-14   52.7  27.8    6.2e-09   34.5   4.6    3.4  4  Patched         Patched family
    4.6e-14   52.2  16.4    5.3e-09   35.7   8.3    2.8  2  SecD_SecF       Protein export membrane protein
    8.1e-09   35.5   6.9    0.00086   19.2   0.2    2.6  2  Sterol-sensing  Sterol-sensing domain of SREBP cleavage-activ
    0.00023   21.1   0.1       0.37   10.8   0.0    3.1  2  CorC_HlyC       Transporter associated domain
    0.00057   17.7  24.5     0.0015   16.3  12.0    2.8  2  ACR_tran        AcrB/AcrD/AcrF family
  ------ inclusion threshold ------
       0.43   11.0   5.0        1.6    9.1   0.3    3.5  3  CstA_5TM        5TM C-terminal transporter carbon starvation 


Domain annotation for each model (and alignments):
>> MMPL  MMPL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.6   1.1   1.8e-36   4.6e-33       3     332 ..      44     402 ..      42     403 .. 0.86
   2 !   82.3   0.0   1.1e-26   2.9e-23      82     301 ..     524     737 ..     429     746 .. 0.78

  Alignments for each domain:
  == domain 1  score: 114.6 bits;  conditional E-value: 1.8e-36
                              MMPL   3 spadaesvkamdrleaafpeeadsdkiivvvlaegdealgsaaaeaavdelvdelkkdtkhvgevsdfls....... 72 
                                       +p+d ++vk+   l+++f++ +ds+ iiv v + ++e + +      v + + el+++ ++ + v d++s       
  gi|242399820|ref|YP_002995245.1|  44 LPQDLPAVKDYLTLKNEFQS-GDSALIIVKVNSIEEEGVYD-IRDPEVIRSIHELEERLRVHEYVTDTISiadifiq 118
                                       688999999999999****9.99999999999999999999.6777778889999999999999***9555555555 PP

                              MMPL  73 ...................dpdvaaafvSkDgkaaralvtlegdpgsteadesvaairaaveearpleglkvevtGp 130
                                                           p++ ++f+S+D +++ ++ tl++ +g ++ ++ +++i++ ++e   +++++v  tG+
  gi|242399820|ref|YP_002995245.1| 119 vlgrlpeneeevkfvlntlPPEAVQGFISSDYRTTLVVATLTAGSGAQAVERIYQDIERDINEVNFPKNVEVIQTGT 195
                                       5555556555555666555677******************************************************* PP

                              MMPL 131 aatladlrdasdrdlklievvtlvvilviLlivyrSlvaallplltvvvsllaalglvlilalllglelstfvlgll 207
                                         ++  + ++ ++dl  + +++++ ++++L+  y+S+v a+lpl+  v++++++lg+      llg+ + ++ ++ +
  gi|242399820|ref|YP_002995245.1| 196 IGIAYRILKMLQSDLNRTMAIAFLFVAALLVYFYKSVVRAMLPLIPLVFGVVMTLGF----MGLLGIPIDMV-TTVV 267
                                       ********************************************************9....67788888765.5567 PP

                              MMPL 208 vvlliavGtDYallLvsRyreelaagedreeaviravastgkvvtaaGltvaiamlgLvvarlpvlaqvGvaialGv 284
                                        +++++ G+DY + ++ Ry ee+++g   eea+ +a+a tgk+ ++a+lt ++ + +L+++ lp+l+ +  ++ +G+
  gi|242399820|ref|YP_002995245.1| 268 GAMIVGMGIDYGVHVTNRYYEERKKGMAIEEAAEEAIAETGKALLGAALTTIAGFSALSLSILPSLQRLSGVLIMGL 344
                                       78899************************************************************************ PP

                              MMPL 285 lvdvlivlTllPAllvl........lGraalakprrkrkk...........rwWrrlgrlvvrrPlp 332
                                        ++v  ++ ++P+l+ l         G+                       ++++++g l++  P++
  gi|242399820|ref|YP_002995245.1| 345 SLAVINAVVITPSLVILhedivkkiKGEYE---------VpeirahsgfiaNFFHKMGNLIKNHPKT 402
                                       ***************995555555444443.........0222233335668888888888888875 PP

  == domain 2  score: 82.3 bits;  conditional E-value: 1.1e-26
                              MMPL  82 SkDgkaaralvtlegdpgsteadesvaairaaveear....pleglkvevtGpaatladlrdasdrdlklievvtlv 154
                                       S D     +l++++g+ g t   e++++i++  ee+      + g++++ +G   ++  l  +++++l+ i + + +
  gi|242399820|ref|YP_002995245.1| 524 SGDY--SMTLIQVKGNFGGTNP-ENFREIMQYFEEQAknadFPPGVEIRPAGDLYLTYVLDGLTNQELGRISTYGSI 597
                                       4444..4467777877777665.566666666555555655999********************************* PP

                              MMPL 155 vilviLlivyrSlvaallplltvvvsllaalglvlilalllglelstfvlgllvvlliavGtDYallLvsRyreela 231
                                        +++i ++++r ++  + ++l   ++ l ++g       l+g+  s++ +g  ++ +++ G+DY + L+ R+ eel+
  gi|242399820|ref|YP_002995245.1| 598 FVVIIVVLLFRRPLVSIAMILPMFLGALWTVGY----MGLAGIPFSQTLAGVISM-IVGLGVDYGMHLTHRFLEELR 669
                                       ********************************9....677888998888887665.58******************* PP

                              MMPL 232 agedreeaviravastgkvvtaaGltvaiamlgLvvarlpvlaqvGvaialGvlvdvlivlTllPAllvl 301
                                       +g      +i a+ ++g+ +++ +lt  + +l+L+  +l++++ +G ++a+G++ ++++++T++PAll +
  gi|242399820|ref|YP_002995245.1| 670 EGNPH--PIISALEGVGPGILIGALTTGGGFLALLSGELTAIHDFGKTLAIGIFASMFAAFTVTPALLQV 737
                                       ***99..9***********************************************************965 PP

>> Patched  Patched family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.5   0.1    0.0057        15     450     507 ..      16      72 ..       1     111 [. 0.74
   2 !   34.5   4.6   2.4e-12   6.2e-09     660     773 ..     211     326 ..     165     361 .. 0.82
   3 ?   -3.4   0.0      0.73   1.9e+03     445     504 ..     399     456 ..     383     460 .. 0.69
   4 !   24.9   8.6     2e-09     5e-06     667     809 ..     597     738 ..     588     740 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.0057
                           Patched 450 vlllfvvylaiaiyGcvnikegLepkklvledsplvevlkliekeiwkeglqvevvvn 507
                                         l+ +  l+++iyG+ +++ + +  k + +d p v+ + ++++e ++ g+   ++v+
  gi|242399820|ref|YP_002995245.1|  16 FSLVAMFLLIVSIYGIQQLEFESDLTKQLPQDLPAVKDYLTLKNE-FQSGDSALIIVK 72 
                                       33333445789****************************999555.566666666654 PP

  == domain 2  score: 34.5 bits;  conditional E-value: 2.4e-12
                           Patched 660 iqnivlallcmfvvallfipelitvlvitlsivsidigvi...GflslWgvdLDpismitiimsiGfsvdlsaHiay 733
                                         ++  a++  + va+l+++   +v+ ++l ++ + +gv+   Gf+ l g+ +D ++ +   m +G  +d+  H++ 
  gi|242399820|ref|YP_002995245.1| 211 NRTM--AIAF-LFVAALLVYFYKSVVRAMLPLIPLVFGVVmtlGFMGLLGIPIDMVTTVVGAMIVGMGIDYGVHVTN 284
                                       2333..3332.34677788888888889999999999985555********************************** PP

                           Patched 734 afvrsekd..dakeRvvealealgwPvvqgalSTilgvlvLl 773
                                       ++++++k+   ++e + ea+++ g  ++ +al Ti+g + L 
  gi|242399820|ref|YP_002995245.1| 285 RYYEERKKgmAIEEAAEEAIAETGKALLGAALTTIAGFSALS 326
                                       *******99999************************998775 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 0.73
                           Patched 445 svrlvvlllfvvylaiaiyGcvnikegLepkklvledsplvevlkliekeiwkeglqvev 504
                                         + +  ++f+   ++ +yG  +++++   +k++ e  p +e++k++ ++ +   ++v +
  gi|242399820|ref|YP_002995245.1| 399 HPKTILTVVFIL-TLVFLYGLTQVTTEVRLEKMIPEGIPEIEAMKDV-RYEFGGQDEVDI 456
                                       445555566654.4567899999999999999999998888888877.444445555555 PP

  == domain 4  score: 24.9 bits;  conditional E-value: 2e-09
                           Patched 667 llcmfvvallfipelitvlvitlsivsidigviGflslWgvdLDpismitiimsiGfsvdlsaHiayafvrsekdda 743
                                       ++ ++++ +l+   + ++++++l +    + ++G++ l g+         i m +G  vd+  H +++f ++  +  
  gi|242399820|ref|YP_002995245.1| 597 IF-VVIIVVLLFRRPLVSIAMILPMFLGALWTVGYMGLAGIPFSQTLAGVISMIVGLGVDYGMHLTHRFLEELREGN 672
                                       33.4455566667888888888899999999*************99999999********************99977 PP

                           Patched 744 keRvvealealgwPvvqgalSTilgvlvLlfvdsymvqvFfktvvLvvvigllHgLlilPillslf 809
                                        + +++ale +g  ++ gal T  g l Ll  +  +++ F kt+ + +  +++ ++ + P ll++f
  gi|242399820|ref|YP_002995245.1| 673 PHPIISALEGVGPGILIGALTTGGGFLALLSGELTAIHDFGKTLAIGIFASMFAAFTVTPALLQVF 738
                                       888************************************************************988 PP

>> SecD_SecF  Protein export membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   8.3   2.1e-12   5.3e-09      28     184 ..     205     360 ..     178     364 .. 0.85
   2 !   20.4   1.0     1e-07   0.00027      41     179 ..     596     731 ..     586     741 .. 0.75

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 2.1e-12
                                       HHHHHHHHHHHHHHHHHHHHHHHHT-HHH.HHHHHHHHHHHHHHHHHHHHHTT----HHHHHHHHHHTTSSSHHHHH CS
                         SecD_SecF  28 elaekavlallialvliliyvalrFewrv.alaaiialvhDviitvgvlsllgievdlatvaalLtiiGYSvndtvv 103
                                        l+ +    ++ia+++++  ++  ++  v a+  +i lv+ v++t+g++ llgi++d+ t +   +i+G  ++  v 
  gi|242399820|ref|YP_002995245.1| 205 MLQSDLNRTMAIAFLFVAALLVYFYKSVVrAMLPLIPLVFGVVMTLGFMGLLGIPIDMVTTVVGAMIVGMGIDYGVH 281
                                       5555555677888888887777777765548999999********************8776666789********** PP

                                       HHHHHHHHHHH--SS-HHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHTTTTHHHHHHHHHHTSTTTTTHHHHHH CS
                         SecD_SecF 104 vfdrvrenlrkkkratlkeiinlslnqtLtrtiltslttllvvvallllggdslkdfalallvGlivgtyssifias 180
                                       v++r  e+++  k + ++e++++++ +t +  + + ltt+    al l    sl+ ++ +l++Gl + +++++ i  
  gi|242399820|ref|YP_002995245.1| 282 VTNRYYEERK--KGMAIEEAAEEAIAETGKALLGAALTTIAGFSALSLSILPSLQRLSGVLIMGLSLAVINAVVITP 356
                                       *******954..59****************999999**9999999999999***********************999 PP

                                       HHHH CS
                         SecD_SecF 181 plll 184
                                        l++
  gi|242399820|ref|YP_002995245.1| 357 SLVI 360
                                       8876 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 1e-07
                                       HHHHHHHHHHHT-HHHHHHHHHH.HHHHHHHHHHHHHHTT----HHHHHHHHHHTTSSSHHHHHHHHHHHHHHHH-- CS
                         SecD_SecF  41 lvliliyvalrFewrvalaaiia.lvhDviitvgvlsllgievdlatvaalLtiiGYSvndtvvvfdrvrenlrkkk 116
                                        ++++i v+l F++++ + a+i+ ++  ++ tvg + l gi+++ +  + + +i+G  v+  + ++ r  e+lr+ +
  gi|242399820|ref|YP_002995245.1| 596 SIFVVIIVVLLFRRPLVSIAMILpMFLGALWTVGYMGLAGIPFSQTLAGVISMIVGLGVDYGMHLTHRFLEELREGN 672
                                       478889999999999888887777********************99999999*********************9988 PP

                                       SS-HHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHT.TTTHHHHHHHHHHTSTTTTTHHHHH CS
                         SecD_SecF 117 ratlkeiinlslnqtLtrtiltslttllvvvallllgg.dslkdfalallvGlivgtyssifia 179
                                         ++  +++      L  +++t    +l+   ll  g+  +++df  +l +G+++ ++ +  + 
  gi|242399820|ref|YP_002995245.1| 673 PHPIISALEGVGPGILIGALTTGGG-FLA---LL-SGElTAIHDFGKTLAIGIFASMFAAFTVT 731
                                       8888777665444444433333333.333...32.33346777777777777777666655555 PP

>> Sterol-sensing  Sterol-sensing domain of SREBP cleavage-activation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   1.9   6.2e-07    0.0016      14     119 ..     240     345 ..     230     370 .. 0.85
   2 !   19.2   0.2   3.3e-07   0.00086       5     134 ..     609     736 ..     606     744 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 6.2e-07
                                       HHHHCCHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCHHCCHHCHHHHHHHHTTTCH.HHHHHHHHHHHCCCCHHCC CS
                    Sterol-sensing  14 iivllsvasslgllaylgltltliilevlPflvlavgvdnifvlvkavqrtsrslde.seriaealgevgpsillts 89 
                                       i +++ v+++lg++ +lg+++ ++++ v+  +++ +g+d    +++ + +  ++    +e   ea+ e+g ++l  +
  gi|242399820|ref|YP_002995245.1| 240 IPLVFGVVMTLGFMGLLGIPIDMVTT-VVGAMIVGMGIDYGVHVTNRYYEERKKGMAiEEAAEEAIAETGKALLGAA 315
                                       567789*******************9.************9998888877666655545******************* PP

                                       CHHHHHHH.HHHHCCHHHHHHHHHHHHHHHH CS
                    Sterol-sensing  90 ltellall.lgaltdvpavqeFclfaavavl 119
                                       lt ++ +  l+ l+ +p +q  +   ++++ 
  gi|242399820|ref|YP_002995245.1| 316 LTTIAGFSaLS-LSILPSLQRLSGVLIMGLS 345
                                       *******9677.8899999988777777665 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 3.3e-07
                                       HHHHHHHHHHHHHCCHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCHHCCHHCHHHHHHHHTTTCHHHHHHHHHHHH CS
                    Sterol-sensing   5 kfgLglagviivllsvasslgllaylgltltliilevlPflvlavgvdnifvlvkavqrtsrsldeseriaealgev 81 
                                       + ++++a+++ + l  + ++g + + g++++   + v+  +++  gvd    l++ + +  r+ + ++ i  al+ v
  gi|242399820|ref|YP_002995245.1| 609 RPLVSIAMILPMFLGALWTVGYMGLAGIPFSQTLAGVIS-MIVGLGVDYGMHLTHRFLEELREGN-PHPIISALEGV 683
                                       678999*****************************9998.678**************98777666.899******** PP

                                       CCCCHHCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHH CS
                    Sterol-sensing  82 gpsilltsltellalllgaltdvpavqeFclfaavavlvdFllqitfFvavLs 134
                                       gp il+ +lt    +l  ++ ++ a++ F    a++++ + +   t+  a+L 
  gi|242399820|ref|YP_002995245.1| 684 GPGILIGALTTGGGFLALLSGELTAIHDFGKTLAIGIFASMFAAFTVTPALLQ 736
                                       **********999998666789******************9999999999886 PP

>> CorC_HlyC  Transporter associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   0.00015      0.37      15      56 ..      92     133 ..      90     155 .. 0.88
   2 !    6.7   0.0    0.0029       7.4      32      55 ..     491     515 ..     472     537 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00015
                                       BHHHHHHHHTSTTHHCT-SBHHHHHHHHH-S---TT-EEEEE CS
                         CorC_HlyC  15 pldeleeelglelpeedyeTlgGlllellgriPkegesvevd 56 
                                       +++elee+l ++    d  ++++ +++ lgr+P+++e+v++ 
  gi|242399820|ref|YP_002995245.1|  92 SIHELEERLRVHEYVTDTISIADIFIQVLGRLPENEEEVKFV 133
                                       799********88888999******************77664 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0029
                                       -SBHHHHHHHHH-S---TT-EE.EE CS
                         CorC_HlyC  32 yeTlgGlllellgriPkegesv.ev 55 
                                        +++++ +++++g+iP+ +e++ ++
  gi|242399820|ref|YP_002995245.1| 491 TNSIADIVVQKYGYIPEDKERIkDI 515
                                       468*****************66444 PP

>> ACR_tran  AcrB/AcrD/AcrF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3  12.0   5.8e-07    0.0015     812    1016 ..     151     358 ..     147     363 .. 0.80
   2 !    7.6   2.9   0.00026      0.65     340     497 ..     596     746 ..     530     748 .] 0.71

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 5.8e-07
                                        EEEEEEEEESTTS-HHHHHHHHHHHC...TT..SSTTEEEEEEHHH....HHHHHHHCHHHHHHHHHHHHHHHHH CS
                          ACR_tran  812 rsvvisgnvaegdslseaeeavekia...kkvklpegvtiewtgqa....eqeqeasnsllilvalalllvflvL 879 
                                        r++ + +++ +g     +e + ++i+   ++v++p+ v++  tg+        +  ++ l   +a+a+l+v  +L
  gi|242399820|ref|YP_002995245.1|  151 RTTLVVATLTAGSGAQAVERIYQDIErdiNEVNFPKNVEVIQTGTIgiayRILKMLQSDLNRTMAIAFLFVAALL 225 
                                        56667777777766666666666665111567999999988887651111345678889999************* PP

                                        HHHHTSSSTCHHHHTTHHHHHHHHHHHHHHTT--BSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTCHHHH CS
                          ACR_tran  880 aalyeslsepllilltvPlalvGallalllrglelsviaqvGlilliGlavkNaillvefakelrekegksleea 954 
                                           y+s++ ++l l+ + +++v  l  + l g+++++++ v   +++G+    ++ + + + e+r+ +g+ +eea
  gi|242399820|ref|YP_002995245.1|  226 VYFYKSVVRAMLPLIPLVFGVVMTLGFMGLLGIPIDMVTTVVGAMIVGMGIDYGVHVTNRYYEERK-KGMAIEEA 299 
                                        ************************************98877667899*********9999999999.9999**** PP

                                        HHHHHHHCHHHHHHHHHHHHHHHHHHHCT-STTHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          ACR_tran  955 ileaakeRLrPiLMTalaailGvlPLalstgaGselqqplgivvlgGlvtstvLtLllvPvl 1016
                                        + ea  e  ++ L  al++i G+  L ls      + q l  v++ Gl ++ + ++ ++P l
  gi|242399820|ref|YP_002995245.1|  300 AEEAIAETGKALLGAALTTIAGFSALSLSILP---SLQRLSGVLIMGLSLAVINAVVITPSL 358 
                                        ***********************988888743...444555566667888888888888876 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00026
                                       HHHHHHHHHHHHHSSHHHHHHHHHHHHHHH..HHHHHHHHHTT--BCHHHHHH.HHHHHHHHHHHHHHHHHHHHHHH CS
                          ACR_tran 340 aivLvvlvvflFLqnlratlipaiavPlsl..lgtfavlkalgfslNlltLfg.LvlAiGlvvDdAiVvvEnierkl 413
                                       +i +v++vv+lF + l   + +a+++P+ l  l t+  + + g+     tL g + + +Gl vD  +      +r l
  gi|242399820|ref|YP_002995245.1| 596 SIFVVIIVVLLFRRPL---VSIAMILPMFLgaLWTVGYMGLAGIPFSQ-TLAGvISMIVGLGVDYGM---HLTHRFL 665
                                       5666777777775443...33445555433226666666666655544.333314455688889875...5567777 PP

                                       HHHTS-HHHHHHHHHHHHHHHHHHHHHHHHHHCTGGGGSBHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHS CS
                          ACR_tran 414 eeegekpleaalksmkeiqgalvaialvllavflPilflgGveGklfrqfaltivlaillsvlvaltltPalcallL 490
                                       ee +e + + ++ + + ++  ++ +al+    fl  ++l+G   ++ ++f+ t+++ i +s++ a t+tPal  ++ 
  gi|242399820|ref|YP_002995245.1| 666 EELREGNPHPIISALEGVGPGILIGALTTGGGFL--ALLSGELTAI-HDFGKTLAIGIFASMFAAFTVTPALLQVFY 739
                                       7777788888999999999999999999999996..6778888887.68***********************99887 PP

                                       ---STT- CS
                          ACR_tran 491 kerkeek 497
                                        e+ +++
  gi|242399820|ref|YP_002995245.1| 740 GEKIRGE 746
                                       7766655 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 ?    9.1   0.3   0.00064       1.6      65     114 ..     199     250 ..     143     251 .. 0.77
   2 ?    0.4   0.0      0.32   8.3e+02       5      30 ..     406     431 ..     384     448 .. 0.74
   3 ?    0.4   0.2      0.31     8e+02      74     112 ..     582     626 ..     568     630 .. 0.56

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00064
                          CstA_5TM  65 gintlWplFGaaNQlLAalaLlvvtvwllktgr..kalvtliPmvfmlvvtl 114
                                       ++ +l  l +  N ++A   L+v++++++  +    a++ liP+vf +v+tl
  gi|242399820|ref|YP_002995245.1| 199 AYRILKMLQSDLNRTMAIAFLFVAALLVYFYKSvvRAMLPLIPLVFGVVMTL 250
                                       466677777788999*9999999999998444447999999*********96 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.32
                          CstA_5TM   5 ytfailfvalfalTtlDtatRlaRyi 30 
                                       ++f++ +v l+ lT + t +Rl ++i
  gi|242399820|ref|YP_002995245.1| 406 VVFILTLVFLYGLTQVTTEVRLEKMI 431
                                       45666677777777777777777766 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.31
                          CstA_5TM  74 GaaNQlLAala.....Llvvtvwll.ktgrkalvtliPmvfmlvv 112
                                       G +NQ L  +      ++v+ v+ll ++    +++++Pm++ ++ 
  gi|242399820|ref|YP_002995245.1| 582 GLTNQELGRIStygsiFVVIIVVLLfRRPLVSIAMILPMFLGALW 626
                                       667777765532222133333333324333667777888775555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (748 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       960  (0.0535445); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); 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: 0.86u 0.36s 00:00:01.22 Elapsed: 00:00:00.53
# Mc/sec: 4278.67
//
Query:       gi|242399821|ref|YP_002995246.1|  [L=54]
Description: hypothetical protein TSIB_1848 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.36s 00:00:00.89 Elapsed: 00:00:00.56
# Mc/sec: 290.95
//
Query:       gi|242399822|ref|YP_002995247.1|  [L=39]
Description: hypothetical protein TSIB_1849 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       107  (0.00596798); expected 358.6 (0.02)
Passed bias filter:                       89  (0.00496402); expected 358.6 (0.02)
Passed Vit filter:                         2  (0.000111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.35s 00:00:00.80 Elapsed: 00:00:00.51
# Mc/sec: 228.40
//
Query:       gi|242399823|ref|YP_002995248.1|  [L=65]
Description: 4-oxalocrotonate tautomerase, [Thermococcus sibiricus MM 739]
Scores for 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-10   38.7   0.0    9.3e-10   38.3   0.0    1.2  1  Tautomerase    Tautomerase enzyme
  ------ inclusion threshold ------
      0.033   14.3   0.0      0.038   14.1   0.0    1.1  1  Tautomerase_2  Tautomerase enzyme
       0.13   12.1   0.0       0.21   11.4   0.0    1.3  1  DUF1126        DUF1126 PH-like domain


Domain annotation for each model (and alignments):
>> Tautomerase  Tautomerase enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.3   0.0   1.6e-13   9.3e-10       7      57 ..       8      58 ..       6      61 .. 0.93

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 1.6e-13
                                      ESTCS..-HHHHHHHHHHHHHHHHHHHTS-GGG-EEEEEEE-TTSEEETTEEH CS
                       Tautomerase  7 lvegr..saeqKaeLaervTealvealgaprsaivVvieEvpaenwgvggesv 57
                                      ++eg+  s e+K+eL++r Te+++e++g+  + i+V+i E p+en+g+ ge +
  gi|242399823|ref|YP_002995248.1|  8 IIEGPsiSVEKKRELVKRFTEVASEVYGI--EHITVLIKENPPENVGINGELL 58
                                      5799999*********************9..68*****************976 PP

>> Tautomerase_2  Tautomerase enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   6.3e-06     0.038      41      80 ..      15      52 ..       6      54 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.3e-06
                                      -HHHHHHHHHHHHHHHHHHH---GGGEEEEEEEE-GGGEE CS
                     Tautomerase_2 41 seeqKkaLyralaerlaaklgirpeDvfivlvenpkedWS 80
                                      s+e+K++L+++ +e  ++  gi  e++ + ++enp+e+ +
  gi|242399823|ref|YP_002995248.1| 15 SVEKKRELVKRFTEVASEVYGI--EHITVLIKENPPENVG 52
                                      789******************9..68999********966 PP

>> DUF1126  DUF1126 PH-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   3.5e-05      0.21      42      65 ..      40      63 ..      33      65 .] 0.90

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.5e-05
                           DUF1126 42 tieikEprqrNsGikggkflkRqk 65
                                      t+ ikE +++N Gi+g  +l R++
  gi|242399823|ref|YP_002995248.1| 40 TVLIKENPPENVGINGELLLDRKR 63
                                      899***********9999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); 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:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.52
# Mc/sec: 374.63
//
Query:       gi|242399824|ref|YP_002995249.1|  [L=527]
Description: Fe-S oxidoreductase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.7e-25   88.8   0.2      2e-24   85.9   0.2    2.4  3  B12-binding    B12 binding domain
    4.5e-19   69.4   0.2    9.7e-18   65.1   0.0    2.6  2  Radical_SAM    Radical SAM superfamily
  ------ inclusion threshold ------
      0.046   13.9   0.0       0.25   11.6   0.0    2.3  2  CRISPR_Cas2    CRISPR associated protein Cas2
      0.063   12.6   0.3        6.3    6.0   0.1    2.4  2  PFK            Phosphofructokinase
       0.12   12.8   0.0       0.71   10.3   0.0    2.1  2  Ribosomal_S11  Ribosomal protein S11
       0.19   11.7   2.3        0.3   11.1   0.6    2.1  2  DUF768         Protein of unknown function (DUF768)


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 !   85.9   0.2   6.8e-28     2e-24       7     121 .]      18     132 ..      13     132 .. 0.95
   2 ?   -1.3   0.0      0.72   2.2e+03      20      48 ..     290     318 ..     289     320 .. 0.87
   3 ?   -2.3   0.0       1.5   4.4e+03      43      62 ..     362     380 ..     356     383 .. 0.80

  Alignments for each domain:
  == domain 1  score: 85.9 bits;  conditional E-value: 6.8e-28
                       B12-binding   7 tvggdlhplGlavlaaalrdagfeVqllganven...edivaairaekpdvvglSalltsqleavkelvellkrirp 80 
                                        +g+ +++lGl +la+a++d   eV++++a+++n   e+++++i+ ++pdvvg++++ +++++    +v+  k+++ 
  gi|242399824|ref|YP_002995249.1|  18 AYGYIAPSLGLVSLAGAVKD-IAEVKIIDAEAKNlteEETIEEIATFNPDVVGFTTIASTYVNPSIMIVRKMKERGI 93 
                                       67999***************.78************************************************888888 PP

                       B12-binding  81 rvkvvvGGahpsldpeetleaklgiddvvvgegedaleala 121
                                       + ++v+GG+h+++++ ++l+  +gid+vv+gege+++++++
  gi|242399824|ref|YP_002995249.1|  94 NPIIVFGGHHATFTYPLILR--EGIDFVVIGEGEQTFREII 132
                                       88*****************9..8**************9985 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.72
                       B12-binding  20 laaalrdagfeVqllganvenedivaair 48 
                                       la+ l +ag+++ ++g++   e +++a+r
  gi|242399824|ref|YP_002995249.1| 290 LAEKLAEAGVKIAFMGIESGSEGVLKAMR 318
                                       67889999*********999999999887 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 1.5
                       B12-binding  43 ivaairaekpdvvglSallt 62 
                                       +v+ + ++  dvv +S+ +t
  gi|242399824|ref|YP_002995249.1| 362 FVQMLGDHGLDVVQISI-YT 380
                                       67778888899999998.66 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.11   3.3e+02      47      99 ..      68     137 ..      46     164 .. 0.53
   2 !   65.1   0.0   3.3e-21   9.7e-18       1     167 []     196     363 ..     196     363 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.11
                                       SEEEEEESSTGGGSTTHHHHHHHHHHTC...CCTEEEEEEECSSCHG..............HHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxx..............xxxxxxxxx RF
                       Radical_SAM  47 vkevilgggepllypdfvellerlakla...vpgiritvetngtlpd..............eeklerlle 99 
                                       v++ ++ +  ++    +v++++++  +      g + t++ + +l +              +e++erl+e
  gi|242399824|ref|YP_002995249.1|  68 VGFTTIASTYVNPSIMIVRKMKERGINPiivFGGHHATFTYPLILREgidfvvigegeqtfREIIERLKE 137
                                       4444444444444444444444444443555444444444444442244444444444444566666555 PP

  == domain 2  score: 65.1 bits;  conditional E-value: 3.3e-21
                                       EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                       Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla... 74 
                                       ++++rgC+++C fC+ + +  ++  +r++s e++++e+k + ++ g + v+++ ++  + ++++e +e l  +    
  gi|242399824|ref|YP_002995249.1| 196 IETSRGCPYNCEFCSASAM--WGHAWRFKSNERVVDELKFV-KNLGYNWVFFVDDNFVVPYKYEERIELLNSIIeeg 269
                                       6799*************98..********************.7**********888777777777777777766666 PP

                                       CCTEEEEEEECSSCHG..HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEE CS
                                       xxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  75 vpgiritvetngtlpd..eeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdri 149
                                        ++++  + + +  +   +e +e+l+e+gv    +g+e++++  vlk m++g    ++l+a+++l e  i     +i
  gi|242399824|ref|YP_002995249.1| 270 LNEMNYMIQIRADIIAkhPELAEKLAEAGVKIAFMGIESGSEG-VLKAMRKGLKKNDTLKAIQLLSEQEIITYGGVI 345
                                       5555555555555555669************************.******99*******************9***** PP

                                       EEBTTTSHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 150 vglpGendeeleellell 167
                                       +g p e++++++++++++
  gi|242399824|ref|YP_002995249.1| 346 IGAPYESRKDRKATYKFV 363
                                       ***************996 PP

>> CRISPR_Cas2  CRISPR associated protein Cas2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   8.2e-05      0.25      11      57 ..     354     401 ..     339     416 .. 0.85
   2 ?   -3.4   0.0       3.8   1.1e+04      14      41 ..     483     509 ..     482     514 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.2e-05
                                       CHHHHHHHHHHHHHHTTEEEEETTEEEE.EESHHHHHHHHHHHHHHSH CS
                       CRISPR_Cas2  11 edrkrrrkvakilkkyGfqrvQySVFeg.elseaqleklkkrlkkiid 57 
                                       +drk+  k+ ++l ++G+  vQ S++     s++ +++lk+r    id
  gi|242399824|ref|YP_002995249.1| 354 KDRKATYKFVQMLGDHGLDVVQISIYTPlPGSDSFYRALKNRALLTID 401
                                       79************************9977777778888888776666 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 3.8
                                       HHHHHHHHHHHHTTEEEEETTEEEEEES CS
                       CRISPR_Cas2  14 krrrkvakilkkyGfqrvQySVFegels 41 
                                       +r  + ak l +y  + + + V+ + l+
  gi|242399824|ref|YP_002995249.1| 483 RRILNSAKKLDDY-TIKILEEVYTRHLT 509
                                       5566667888888.77777778877665 PP

>> PFK  Phosphofructokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0    0.0088        26      82     104 ..      83     105 ..      44     123 .. 0.83
   2 ?    6.0   0.1    0.0021       6.3      30      94 ..     301     373 ..     290     378 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.0088
                                       HHHHHHHHHT--EEEEEESHHHH CS
                               PFK  82 kaaenlkklgidaLvviGGdgsl 104
                                        +++++k++gi+ ++v GG  + 
  gi|242399824|ref|YP_002995249.1|  83 MIVRKMKERGINPIIVFGGHHAT 105
                                       6899***************9764 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0021
                                       -EEEEETTHHHHHHTT.........-EEEE-SGGGTT-TT--S-TT-----GGGGSHHHHHHHHHHHHHHT--E CS
                               PFK  30 levygireGfeGliee.........eiekltledvsgilsegGtiLgsaRskefkeregrkkaaenlkklgida 94 
                                       +  +gi+ G eG+++           ++ ++l + ++i++ gG i+g     + k+r+ + k ++ l ++g+d 
  gi|242399824|ref|YP_002995249.1| 301 IAFMGIESGSEGVLKAmrkglkkndTLKAIQLLSEQEIITYGGVIIGAPYESR-KDRKATYKFVQMLGDHGLDV 373
                                       66899********5554434432333335567799************964444.45667899999999999886 PP

>> Ribosomal_S11  Ribosomal protein S11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.72   2.2e+03      54      90 ..     292     302 ..     259     330 .. 0.54
   2 ?   10.3   0.0   0.00024      0.71      48      85 ..     358     395 ..     344     414 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.72
                     Ribosomal_S11  54 ekvldkGikavevkvkgpGpGreaalralaraGlkig 90 
                                       ek                          la+aG+ki+
  gi|242399824|ref|YP_002995249.1| 292 EK--------------------------LAEAGVKIA 302
                                       22..........................333333333 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00024
                     Ribosomal_S11  48 aaekaaekvldkGikavevkvkgpGpGreaalralara 85 
                                       a+ k ++ + d+G++ v++ + +p pG ++  ral++ 
  gi|242399824|ref|YP_002995249.1| 358 ATYKFVQMLGDHGLDVVQISIYTPLPGSDSFYRALKNR 395
                                       5667788999*************************754 PP

>> DUF768  Protein of unknown function (DUF768)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.6    0.0001       0.3      27      56 ..      34      63 ..      32      69 .. 0.89
   2 ?   -1.4   0.0      0.82   2.4e+03      23      46 ..     281     305 ..     278     319 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0001
                            DUF768 27 siaeLteklfadAkaagikseeieeevesv 56
                                      ++++++e  + dA+a+++++ee+ ee+ + 
  gi|242399824|ref|YP_002995249.1| 34 AVKDIAEVKIIDAEAKNLTEEETIEEIATF 63
                                      5899**********************9876 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.82
                            DUF768  23 sDv.vsiaeLteklfadAkaagiks 46 
                                       +D+  +  eL+ekl  +  +  + +
  gi|242399824|ref|YP_002995249.1| 281 ADIiAKHPELAEKLAEAGVKIAFMG 305
                                       7851456799999977665555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (527 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       855  (0.0476881); expected 358.6 (0.02)
Passed bias filter:                      692  (0.0385967); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.71u 0.31s 00:00:01.02 Elapsed: 00:00:00.49
# Mc/sec: 3265.26
//
Query:       gi|242399825|ref|YP_002995250.1|  [L=161]
Description: transcription regulator, MarR family [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-08   33.8   0.0    4.8e-08   32.8   0.0    1.5  1  MarR             MarR family
    4.1e-06   26.6   0.0    8.1e-06   25.6   0.0    1.5  1  MarR_2           MarR family
    6.2e-06   26.0   0.1    1.1e-05   25.2   0.1    1.4  1  TrmB             Sugar-specific transcriptional regulator Trm
    7.6e-06   25.4   0.7    0.00015   21.3   0.0    2.9  4  HTH_24           Winged helix-turn-helix DNA-binding
      1e-05   25.9   0.0    2.7e-05   24.6   0.0    1.7  1  HTH_27           Winged helix DNA-binding domain
    1.5e-05   24.6   0.0    0.00027   20.6   0.0    2.3  3  HTH_IclR         IclR helix-turn-helix domain
    0.00027   20.9   0.0    0.00086   19.3   0.0    1.7  2  HTH_20           Helix-turn-helix domain
    0.00029   20.7   0.1     0.0014   18.5   0.0    2.0  2  HTH_5            Bacterial regulatory protein, arsR family
     0.0017   17.8   0.5      0.011   15.2   0.0    2.0  2  RepL             Firmicute plasmid replication protein (RepL)
     0.0032   17.1   0.0      0.015   14.9   0.0    2.0  2  GntR             Bacterial regulatory proteins, gntR family
     0.0056   16.2   0.1      0.062   12.8   0.0    2.6  3  Sigma70_r4       Sigma-70, region 4
      0.007   16.1   0.8       0.19   11.4   0.0    2.2  2  DUF4423          Domain of unknown function (DUF4423)
     0.0094   15.9   0.0      0.028   14.4   0.0    1.8  1  HTH_36           Helix-turn-helix domain
  ------ inclusion threshold ------
      0.012   16.0   0.0      0.026   14.9   0.0    1.5  1  Rrf2             Transcriptional regulator
      0.013   15.6   0.3       0.84    9.8   0.0    3.0  4  HTH_28           Helix-turn-helix domain
      0.016   15.3   0.0       0.03   14.5   0.0    1.5  1  DprA_WH          DprA winged helix domain
      0.017   15.2   0.0      0.035   14.1   0.0    1.7  1  HTH_29           Winged helix-turn helix
      0.017   15.1   0.2      0.066   13.2   0.0    2.2  3  HTH_11           HTH domain
      0.019   14.9   0.0      0.049   13.6   0.0    1.7  1  HTH_Crp_2        Crp-like helix-turn-helix domain
       0.02   15.0   1.3      0.058   13.5   0.4    2.1  2  DUF2250          Uncharacterized protein conserved in archaea
       0.02   15.0   0.0      0.088   12.9   0.0    1.9  2  HTH_AraC         Bacterial regulatory helix-turn-helix protei
      0.035   14.5   0.1      0.063   13.6   0.1    1.4  1  Penicillinase_R  Penicillinase repressor
      0.046   13.8   0.5      0.069   13.2   0.5    1.2  1  DUF5343          Family of unknown function (DUF5343)
      0.088   12.2   1.1       0.11   11.9   1.1    1.2  1  DNA_primase_lrg  Eukaryotic and archaeal DNA primase, large s
        1.6    9.3   7.8        5.3    7.6   1.3    2.5  2  PNPase           Polyribonucleotide nucleotidyltransferase, R


Domain annotation for each model (and alignments):
>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.0   6.7e-11   4.8e-08      16      58 ..      41      83 ..      38      84 .. 0.95

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 6.7e-11
                                      TTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTSTTS CS
                              MarR 16 gplsvseLakklgvskstvtrvldrLekkGlieRskspeDrRe 58
                                      +pls+ ++a++ g s s+v+++l+ Le  Gl++R k+p+D+R+
  gi|242399825|ref|YP_002995250.1| 41 EPLSLGKIAERTGYSLSHVSTALKLLENIGLVKRIKKPGDKRA 83
                                      799***************************************7 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   1.1e-08   8.1e-06      19      62 .]      41      83 ..      33      83 .. 0.91

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1.1e-08
                                      TSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSSSS CS
                            MarR_2 19 grdltvgelarrlglsksavsrilkrLvaaGLverrpgpeDkRa 62
                                      ++ l+ g +a+r+g+s s vs +lk L+  GLv r + p+DkRa
  gi|242399825|ref|YP_002995250.1| 41 EP-LSLGKIAERTGYSLSHVSTALKLLENIGLVKRIKKPGDKRA 83
                                      32.9***************************************7 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.1   1.6e-08   1.1e-05       3      65 ..      22      88 ..      20      90 .. 0.92

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 1.6e-08
                                      HCHHHHHCCCHCHHHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST...TTEEEE- CS
                              TrmB  3 klGLseyEakvYlaLl.klgpatadeiaeelgvprskvYevLrsLedkGlVerekgr...pklYrav 65
                                       +GLse    +Y +L  + +p++  +iae++g + s v  +L+ Le+ GlV+r+k+    + +Y a+
  gi|242399825|ref|YP_002995250.1| 22 RFGLSELYGYIYGVLFfEDEPLSLGKIAERTGYSLSHVSTALKLLENIGLVKRIKKPgdkRAYYTAI 88
                                      6999999999*****99**************************************888867788877 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       4.5   3.2e+03      22      30 ..      18      26 ..      16      27 .. 0.82
   2 !   21.3   0.0   2.1e-07   0.00015      14      48 .]      39      73 ..      36      73 .. 0.93
   3 ?   -2.2   0.0       4.3   3.1e+03       4      13 ..     110     119 ..     108     124 .. 0.64
   4 ?    0.7   0.2      0.53   3.8e+02       1      15 [.     142     156 ..     142     158 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 4.5
                            HTH_24 22 eLAerlglS 30
                                      + A+r glS
  gi|242399825|ref|YP_002995250.1| 18 DTARRFGLS 26
                                      6799****9 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 2.1e-07
                            HTH_24 14 knprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      ++  +s   +Aer+g S+s v++ lk Le+ Gl+k
  gi|242399825|ref|YP_002995250.1| 39 EDEPLSLGKIAERTGYSLSHVSTALKLLENIGLVK 73
                                      67889999*************************97 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 4.3
                            HTH_24   4 tdrkILelLq 13 
                                       t++++L++L+
  gi|242399825|ref|YP_002995250.1| 110 TRKNLLKALE 119
                                       6666676665 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.53
                            HTH_24   1 ldetdrkILelLqkn 15 
                                       ++ ++ +I+++  kn
  gi|242399825|ref|YP_002995250.1| 142 RNAITERIINIFLKN 156
                                       578999*****9999 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 !   24.6   0.0   3.7e-08   2.7e-05      16      60 ..      40      84 ..      35      88 .. 0.92

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 3.7e-08
                            HTH_27 16 rrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrek 60
                                      +++ +l  +++r+ ++ sh+s +lk L++ GLv+r +++ d+r+ 
  gi|242399825|ref|YP_002995250.1| 40 DEPLSLGKIAERTGYSLSHVSTALKLLENIGLVKRIKKPGDKRAY 84
                                      78889999*******************************999975 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 ?    1.2   0.0      0.46   3.3e+02       9      24 ..      13      28 ..      12      29 .. 0.87
   2 !   20.6   0.0   3.8e-07   0.00027      16      50 ..      40      74 ..      38      76 .. 0.95
   3 ?   -2.8   0.0       7.8   5.6e+03       8      16 ..     117     125 ..     113     134 .. 0.51

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.46
                                      HCT-CTTBSS-BHHHH CS
                          HTH_IclR  9 Ldalaeapqeltlsel 24
                                      ++++a ++++ +lsel
  gi|242399825|ref|YP_002995250.1| 13 MEHFADTARRFGLSEL 28
                                      6899999999999998 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 3.8e-07
                                      BSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR 16 pqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      +++l+l  +A+rtg + S v+  L+ L++ G+v++
  gi|242399825|ref|YP_002995250.1| 40 DEPLSLGKIAERTGYSLSHVSTALKLLENIGLVKR 74
                                      789******************************97 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 7.8
                                       HHCT-CTTB CS
                          HTH_IclR   8 iLdalaeap 16 
                                        L+a++   
  gi|242399825|ref|YP_002995250.1| 117 ALEAIGDDE 125
                                       455555544 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   1.2e-06   0.00086      21      58 ..      39      76 ..      25      78 .. 0.89
   2 ?   -1.7   0.0       4.3   3.1e+03      11      19 ..     110     118 ..     101     133 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.2e-06
                                      TCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                            HTH_20 21 raegltaselaerldlskntlsyHLrvLeeagLvevvr 58
                                      ++e+l+++ +aer + s + +s  L+ Le  gLv++ +
  gi|242399825|ref|YP_002995250.1| 39 EDEPLSLGKIAERTGYSLSHVSTALKLLENIGLVKRIK 76
                                      79********************************9876 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 4.3
                                       HHHHHHHHH CS
                            HTH_20  11 vRrrilraL 19 
                                       +R  +l+aL
  gi|242399825|ref|YP_002995250.1| 110 TRKNLLKAL 118
                                       555556665 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.9e-06    0.0014      11      46 ..      38      73 ..      35      74 .. 0.91
   2 ?   -0.9   0.0       2.1   1.5e+03       2      12 ..     109     119 ..     108     125 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.9e-06
                                      HTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5 11 LaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                       ++++l+ + +ae +g s s vS  Lk L++ GLV+
  gi|242399825|ref|YP_002995250.1| 38 FEDEPLSLGKIAERTGYSLSHVSTALKLLENIGLVK 73
                                      46699******************************7 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.1
                                       HHHHHHHHHHT CS
                             HTH_5   2 ptRlkILklLa 12 
                                       +tR  +Lk+L+
  gi|242399825|ref|YP_002995250.1| 109 QTRKNLLKALE 119
                                       79999999996 PP

>> RepL  Firmicute plasmid replication protein (RepL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.5e-05     0.011      80     109 ..      47      76 ..      43      79 .. 0.93
   2 ?    0.5   0.2       0.5   3.6e+02     126     161 ..     109     143 ..     103     151 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.5e-05
                              RepL  80 elaeetgislktvsetlkileeanilkkka 109
                                       ++ae+tg sl  vs+ lk le+ +++k++ 
  gi|242399825|ref|YP_002995250.1|  47 KIAERTGYSLSHVSTALKLLENIGLVKRIK 76 
                                       79*************************975 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.5
                              RepL 126 kkrlnlLlefeeleqeneelsdeqkikdlegslvek 161
                                       + r+nlL   e ++ ++ e   + k++ +e sl ++
  gi|242399825|ref|YP_002995250.1| 109 QTRKNLLKALEAIGDDESEEAMKIKER-IEFSLQRN 143
                                       678899998888887766555333333.35555555 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   2.2e-05     0.015      22      59 ..      41      77 ..      37      79 .. 0.92
   2 ?   -1.5   0.0       2.9     2e+03       6      17 ..     100     111 ..      96     119 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.2e-05
                                      SB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT CS
                              GntR 22 dkLPsereLaaefgVsrttvReALrrLeaeglverrqg 59
                                      ++L s  ++a++ g s + v  AL+ Le  glv r ++
  gi|242399825|ref|YP_002995250.1| 41 EPL-SLGKIAERTGYSLSHVSTALKLLENIGLVKRIKK 77
                                      789.999***************************9886 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.9
                                       HHHHHHHHHTTS CS
                              GntR   6 yerLredIlsge 17 
                                       y +++ed+++++
  gi|242399825|ref|YP_002995250.1| 100 YKKIEEDVRQTR 111
                                       778888888876 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       1.3   9.4e+02      24      34 ..      17      27 ..      14      28 .. 0.87
   2 !   12.8   0.0   8.6e-05     0.062      16      39 ..      37      61 ..      32      65 .. 0.87
   3 ?   -2.0   0.1       3.8   2.7e+03      35      48 ..     105     118 ..     104     120 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.3
                                      HHHHHHHTS-H CS
                        Sigma70_r4 24 eEIgerlgiSr 34
                                      +++++r+g+S+
  gi|242399825|ref|YP_002995250.1| 17 ADTARRFGLSE 27
                                      7899*****96 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 8.6e-05
                                      HH.TTT--HHHHHHHHTS-HHHHHH CS
                        Sigma70_r4 16 rf.geglTleEIgerlgiSrerVrq 39
                                       f +e+l+l  I+er g S+++V+ 
  gi|242399825|ref|YP_002995250.1| 37 FFeDEPLSLGKIAERTGYSLSHVST 61
                                      4579*******************97 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 3.8
                                       HHHHHHHHHHHHHH CS
                        Sigma70_r4  35 erVrqiekrAlrkL 48 
                                       e Vrq  k+ l+ L
  gi|242399825|ref|YP_002995250.1| 105 EDVRQTRKNLLKAL 118
                                       78999988888877 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   0.00026      0.19      38      76 ..      44      81 ..      28      99 .. 0.80
   2 ?    4.1   0.3     0.048        34     128     150 ..      97     119 ..      76     133 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00026
                           DUF4423 38 dpeelakrlrpkisaeevekalefLlklgllkkded.gky 76
                                      +  ++a+r++   s + v++al++L+++gl+k+ ++ g  
  gi|242399825|ref|YP_002995250.1| 44 SLGKIAERTG--YSLSHVSTALKLLENIGLVKRIKKpGDK 81
                                      56789*****..********************98875555 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.048
                           DUF4423 128 kedyekikkeirefrkkilaiae 150
                                       ++ y+ki++ +r+ rk++l+ +e
  gi|242399825|ref|YP_002995250.1|  97 EAYYKKIEEDVRQTRKNLLKALE 119
                                       466999**********9997665 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   3.9e-05     0.028      27      55 .]      44      72 ..      40      72 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.9e-05
                            HTH_36 27 sqetlakrlglsknTvsraikeLeqlGyi 55
                                      s   +a+r+g s + vs+a+k+Le  G++
  gi|242399825|ref|YP_002995250.1| 44 SLGKIAERTGYSLSHVSTALKLLENIGLV 72
                                      5668*********************9985 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   3.7e-05     0.026      22      57 ..      39      74 ..      33      80 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.7e-05
                                      TCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              Rrf2 22 eeepvsseeiaerqnispsylekilakLrkaglvks 57
                                      e+ep+s+ +iaer++ s s+++  l+ L++ glvk 
  gi|242399825|ref|YP_002995250.1| 39 EDEPLSLGKIAERTGYSLSHVSTALKLLENIGLVKR 74
                                      56789*****************************96 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.29   2.1e+02      14      26 ..      15      27 ..       5      33 .. 0.82
   2 ?    9.8   0.0    0.0012      0.84      14      51 ..      44      78 ..      39      79 .. 0.86
   3 ?   -1.9   0.2       5.3   3.8e+03      27      45 ..      82     100 ..      80     103 .. 0.72
   4 ?   -2.2   0.0       6.8   4.9e+03      30      42 ..     112     124 ..     108     125 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.29
                            HTH_28 14 svreaArelgisr 26
                                        +++Ar++g+s+
  gi|242399825|ref|YP_002995250.1| 15 HFADTARRFGLSE 27
                                      56889******95 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0012
                            HTH_28 14 svreaArelgisrrtvyrWikryeegGiagLvprrrrp 51
                                      s   +A++ g s ++v+  +k +e +G   Lv+r ++p
  gi|242399825|ref|YP_002995250.1| 44 SLGKIAERTGYSLSHVSTALKLLENIG---LVKRIKKP 78
                                      56679********************66...58888877 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 5.3
                            HTH_28  27 rtvyrWikryeegGiagLv 45 
                                       r  y  ik  +e+  ++ +
  gi|242399825|ref|YP_002995250.1|  82 RAYYTAIKNIREWRKEAYY 100
                                       5668888888888877766 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 6.8
                            HTH_28  30 yrWikryeegGia 42 
                                       + ++k++e++G++
  gi|242399825|ref|YP_002995250.1| 112 KNLLKALEAIGDD 124
                                       5688999999975 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   4.1e-05      0.03      22      57 ..      39      74 ..      17      76 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.1e-05
                           DprA_WH 22 gpePvhvDqLvrrtglpaaevsaaLleLELaGlver 57
                                      + eP+++  +++rtg + + vs+aL  LE  Glv+r
  gi|242399825|ref|YP_002995250.1| 39 EDEPLSLGKIAERTGYSLSHVSTALKLLENIGLVKR 74
                                      678**************************8888876 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   4.9e-05     0.035      17      51 ..      47      79 ..      39     109 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.9e-05
                            HTH_29 17 qiAkllglsrrtvyrwlkrfeegGlaalldrrrsg 51
                                       iA+++g+s ++v ++lk+ e+ Gl + ++++  g
  gi|242399825|ref|YP_002995250.1| 47 KIAERTGYSLSHVSTALKLLENIGLVKRIKKP--G 79
                                      79**********************74433333..3 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   9.2e-05     0.066       9      44 ..      36      73 ..      31      86 .. 0.83
   2 ?   -2.2   0.0       5.7   4.1e+03      33      43 ..      85      95 ..      80     104 .. 0.76
   3 ?   -2.6   0.0       7.8   5.6e+03      36      43 ..     115     122 ..     108     127 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9.2e-05
                            HTH_11  9 LleargpisgeeLAeeLnvSrrtvrrdIkaLeelg..v 44
                                      L+ +++p+s  ++Ae+++ S + v   +k Le +g   
  gi|242399825|ref|YP_002995250.1| 36 LFFEDEPLSLGKIAERTGYSLSHVSTALKLLENIGlvK 73
                                      5567889***************************9633 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 5.7
                            HTH_11 33 rrdIkaLeelg 43
                                      +  Ik ++e+ 
  gi|242399825|ref|YP_002995250.1| 85 YTAIKNIREWR 95
                                      77899999885 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 7.8
                            HTH_11  36 IkaLeelg 43 
                                       +kaLe++g
  gi|242399825|ref|YP_002995250.1| 115 LKALEAIG 122
                                       67888877 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   6.9e-05     0.049      21      53 ..      42      74 ..      20      84 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.9e-05
                                      EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEE CS
                         HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglisr 53
                                      pl+   +A++ G + ++vs +l+ L++ gl++r
  gi|242399825|ref|YP_002995250.1| 42 PLSLGKIAERTGYSLSHVSTALKLLENIGLVKR 74
                                      889999************************994 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 ?   13.5   0.4   8.1e-05     0.058      28      80 ..      48     100 ..      46     106 .. 0.75
   2 ?   -0.5   0.1       1.8   1.3e+03      40      61 ..     112     133 ..      96     148 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.1e-05
                           DUF2250  28 iakeleipleevrellkkLeelGLlervegktikrteakl.KkksevhkhHtYY 80 
                                       ia+++  +l++v+ +lk Le++GL++r ++   kr    + K+  e + +  YY
  gi|242399825|ref|YP_002995250.1|  48 IAERTGYSLSHVSTALKLLENIGLVKRIKKPGDKRAYYTAiKNIREWR-KEAYY 100
                                       8999***********************998877765544404334433.34455 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.8
                           DUF2250  40 rellkkLeelGLlervegktik 61 
                                       ++llk+Le +G  e  e+  ik
  gi|242399825|ref|YP_002995250.1| 112 KNLLKALEAIGDDESEEAMKIK 133
                                       3456666666655555555555 PP

>> HTH_AraC  Bacterial regulatory helix-turn-helix proteins, AraC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       3.4   2.5e+03      11      24 ..      16      29 ..      14      29 .. 0.77
   2 ?   12.9   0.0   0.00012     0.088       7      30 ..      41      64 ..      39      69 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 3.4
                                      HHHHHHHTTSSHHH CS
                          HTH_AraC 11 iediAdelgfSrsy 24
                                       +d A  +g+S+ y
  gi|242399825|ref|YP_002995250.1| 16 FADTARRFGLSELY 29
                                      57899999999765 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00012
                                      CT--HHHHHHHTTSSHHHHHHHHH CS
                          HTH_AraC  7 tnltiediAdelgfSrsyFsrlFk 30
                                      ++l+++ iA+  g+S s+ s+++k
  gi|242399825|ref|YP_002995250.1| 41 EPLSLGKIAERTGYSLSHVSTALK 64
                                      689*****************9988 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   8.8e-05     0.063      27     113 ..      48     136 ..      39     137 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.8e-05
                                       --GGG---HHHHHHHHHHHHHTTS-EEEEE..TTEEEEE----XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                   Penicillinase_R  27 leeekelaysTVktllrrLvkKgllsreke..grafiYsplvseeeavasavkqlldklfegsvkelvaafveeekl 101
                                       ++e++  + s V t l+ L++ gl++r k+   ++  Y++  + +e++++a  + +++ + + +k+l+ a+    + 
  gi|242399825|ref|YP_002995250.1|  48 IAERTGYSLSHVSTALKLLENIGLVKRIKKpgDKRAYYTAIKNIREWRKEAYYKKIEEDVRQTRKNLLKALEAIGDD 124
                                       55666777889******************995566667777778999999999999999998888888777665566 PP

                                       XXXXXXXXXXXX CS
                   Penicillinase_R 102 seddleeLrell 113
                                       +++++ +++e +
  gi|242399825|ref|YP_002995250.1| 125 ESEEAMKIKERI 136
                                       666666776665 PP

>> DUF5343  Family of unknown function (DUF5343)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.5   9.7e-05     0.069      30     127 ..      49     155 ..      45     158 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9.7e-05
                           DUF5343  30 lktlglkssnasliiplLkflGfldedGkptel...ykelrn.....edtskkalaeaikeaYsdlFelnedaqnld 98 
                                        ++ g++ s  s++++lL ++G++ +  kp ++   y  ++n     ++++ k ++e ++++ ++l+++ e++ +++
  gi|242399825|ref|YP_002995250.1|  49 AERTGYSLSHVSTALKLLENIGLVKRIKKPGDKrayYTAIKNirewrKEAYYKKIEEDVRQTRKNLLKALEAIGDDE 125
                                       567899999**************9988888765332444444555999999999****************8887777 PP

                           DUF5343  99 keelknlfrtvtgks.dervvkrvantFka 127
                                       +ee ++   ++  +   + +++r++n F++
  gi|242399825|ref|YP_002995250.1| 126 SEEAMKIKERIEFSLqRNAITERIINIFLK 155
                                       766544333333333456788999999986 PP

>> 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 ?   11.9   1.1   0.00015      0.11      25      86 ..      83     142 ..      58     160 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00015
                                       EEEE-HHHHHHHHHHHHHHHHHH..........HHGGGSSS---HHHHHHHCT--....... CS
                   DNA_primase_lrg  25 yaylpkeeleslllekfrkrlekalestkeslpeleeeikederekleellealsesyvaed 86 
                                         y +++++ +  +e++ k++e+++ +t+++l +  e i +de e+ ++++e+++  ++ + 
  gi|242399825|ref|YP_002995250.1|  83 AYYTAIKNIREWRKEAYYKKIEEDVRQTRKNLLKALEAIGDDESEEAMKIKERIE--FSLQR 142
                                       568889999999******************************************9..54444 PP

>> PNPase  Polyribonucleotide nucleotidyltransferase, RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   1.1     0.012       8.8      21      63 ..      79     121 ..      62     125 .. 0.82
   2 ?    7.6   1.3    0.0073       5.3       2      47 ..     114     159 ..     113     161 .] 0.86

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.012
                                       SSHHHHHHHHHHHHHHHHHHHH...HHSTTS-HHHHHHHHHHH CS
                            PNPase  21 teKqeRyaaldeikekvveafaaeleeedeedekeikeifkal 63 
                                        +K + y+a+++i+e  +ea+ +++ee+  +++k++ ++++a+
  gi|242399825|ref|YP_002995250.1|  79 GDKRAYYTAIKNIREWRKEAYYKKIEEDVRQTRKNLLKALEAI 121
                                       689999******************9998888888877777665 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0073
                                       HHHHHHTTTHHHHHHHTTSSSHHHHHHHHHHHHHHHHHHHH...HH CS
                            PNPase   2 leekvaelaeerisealtiteKqeRyaaldeikekvveafaaelee 47 
                                       l ++++++  ++ +ea++i+e+ e + + ++i e +++ f++++ee
  gi|242399825|ref|YP_002995250.1| 114 LLKALEAIGDDESEEAMKIKERIEFSLQRNAITERIINIFLKNEEE 159
                                       56778888889999***************************66555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1450  (0.0808746); expected 358.6 (0.02)
Passed bias filter:                      740  (0.0412739); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.59u 0.34s 00:00:00.93 Elapsed: 00:00:00.50
# Mc/sec: 971.10
//
Query:       gi|242399826|ref|YP_002995251.1|  [L=168]
Description: hypothetical protein TSIB_1853 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      3e-56  190.1   1.3    3.3e-56  190.0   1.3    1.0  1  CarS-like     CDP-archaeol synthase
      2e-10   40.9   1.8      2e-10   40.9   1.8    1.9  2  CTP_transf_1  Cytidylyltransferase family
  ------ inclusion threshold ------
      0.032   13.9   5.4      0.045   13.4   5.4    1.2  1  DUF4203       Domain of unknown function (DUF4203)


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 !  190.0   1.3   5.6e-60   3.3e-56       5     175 .]       4     168 .]       1     168 [] 0.98

  Alignments for each domain:
  == domain 1  score: 190.0 bits;  conditional E-value: 5.6e-60
                         CarS-like   5 ilksiylllpayvanasavlvGGGtpvdlGktlvdGrrliGdGvtyrGtvaGvlvGvlvgliqglleklsilaldss 81 
                                       i ++++++lpay anas v++ G tp+d+Gk++vdGrr+ G+G+t+rG+ +G+++G+l+++iq+ l      + +++
  gi|242399826|ref|YP_002995251.1|   4 IAEALWYILPAYFANASPVVFKGRTPIDFGKKFVDGRRVFGNGKTWRGFFGGLFTGILISIIQYNL------TPHFY 74 
                                       6789*************************************************************9......6799* PP

                         CarS-like  82 gsvlefvilalllafGallGdavGsfikrrlkierGkpalildqldfvlgalllaypvkllpieliilivlitlvlh 158
                                       gs+ + + l++ l+fGallGd++Gsf+krr+++e G pa+ ldq  f+++al+la+p+k l+++ +++++++t+++h
  gi|242399826|ref|YP_002995251.1|  75 GSLSSALKLGFTLSFGALLGDLIGSFVKRRVGMESGYPAVGLDQWGFLIAALILAFPIKTLSTKQVLFLLVVTPFIH 151
                                       ***************************************************************************** PP

                         CarS-like 159 lsaniiayklglkdvwy 175
                                         ani ayk+  k+v++
  gi|242399826|ref|YP_002995251.1| 152 WWANIFAYKMKWKNVPW 168
                                       ****************9 PP

>> CTP_transf_1  Cytidylyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9   1.8   3.3e-14     2e-10     170     231 ..      46     106 ..      41     109 .. 0.96
   2 ?   -0.7   0.5      0.17     1e+03     129     152 ..     137     159 ..     117     163 .. 0.46

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 3.3e-14
                                       --BHHHHHHHHHHHHHHHHHHHHHHHCTS---TTSHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                      CTP_transf_1 170 kKTveGfigGlvaavvvglllalvlskalalsllhllllslllslvavfGDLveSglKRafg 231
                                       +KT+ Gf+gGl++ ++++++ +++++++ + sl ++l l++ ls+ a +GDL+ S +KR++g
  gi|242399826|ref|YP_002995251.1|  46 GKTWRGFFGGLFTGILISIIQYNLTPHF-YGSLSSALKLGFTLSFGALLGDLIGSFVKRRVG 106
                                       6*************************97.7*****************************987 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.17
                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                      CTP_transf_1 129 nikeglllvllllalvvaaDigaY 152
                                       +++  l+l+++  ++ + a i+aY
  gi|242399826|ref|YP_002995251.1| 137 TKQ-VLFLLVVTPFIHWWANIFAY 159
                                       222.22333333344455567777 PP

>> DUF4203  Domain of unknown function (DUF4203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   5.4   7.6e-06     0.045      27     117 ..      52     146 ..      45     162 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.6e-06
                           DUF4203  27 lsgfllgsllvlvlilkvvvlp.sslvqgaslvaalvvGllgGll....a..llfwelglfllga.lgGlllallil 95 
                                       ++g+l++++l+ ++ +++++    sl++ + l+ +l  G+l+G l    +   +  e g  ++g+   G+l+a lil
  gi|242399826|ref|YP_002995251.1|  52 FFGGLFTGILISIIQYNLTPHFyGSLSSALKLGFTLSFGALLGDLigsfVkrRVGMESGYPAVGLdQWGFLIAALIL 128
                                       6788888888888888886544877777777777777777777663333333666778899**************** PP

                           DUF4203  96 sllegglitslpskaiflvivv 117
                                       ++     i++l++k +++++vv
  gi|242399826|ref|YP_002995251.1| 129 AFP----IKTLSTKQVLFLLVV 146
                                       **9....666666666623333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 961.05
//
Query:       gi|242399827|ref|YP_002995252.1|  [L=92]
Description: Molybdopterin converting factor, subunit 1 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-17   62.7   0.0    4.2e-17   62.5   0.0    1.0  1  ThiS      ThiS family
  ------ inclusion threshold ------
      0.094   12.6   0.0       0.21   11.4   0.0    1.5  1  Ub-Mut7C  Mut7-C ubiquitin


Domain annotation for each model (and alignments):
>> ThiS  ThiS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.5   0.0   4.7e-21   4.2e-17       1      77 []       8      92 .]       8      92 .] 0.98

  Alignments for each domain:
  == domain 1  score: 62.5 bits;  conditional E-value: 4.7e-21
                                      EEETTCCHHHHT..CEEEEESSTSBHHHHHHHHHHHTCHHG.........TTTTEEEEETTEEEGCCTTTSB--TTCEE CS
                              ThiS  1 vllfaelrelag..eeelelaegstvaelleaLgerypela.........lerrvavavNgeivprlwldtelkdgDev 68
                                      v++fa+ rel g  ee +el+ gs++++l+e+++  +p  +          e  ++v  Ng+++++   d+elk+gD v
  gi|242399827|ref|YP_002995252.1|  8 VRYFARFRELSGtgEEIIELPKGSKIRDLIEHIKSIHPDFKreafsegynDEVDINVSKNGRYASF---DEELKEGDIV 83
                                      89************************************999********98899************...********** PP

                                      EEEESTTC- CS
                              ThiS 69 ailppVaGG 77
                                      a++pp +GG
  gi|242399827|ref|YP_002995252.1| 84 ALFPPTSGG 92
                                      ********9 PP

>> Ub-Mut7C  Mut7-C ubiquitin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   2.4e-05      0.21      52      75 ..      64      87 ..      58      90 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.4e-05
                          Ub-Mut7C 52 ilvnGesvgfshiledGdrvavyp 75
                                      +  nG++++f++ l++Gd va  p
  gi|242399827|ref|YP_002995252.1| 64 VSKNGRYASFDEELKEGDIVALFP 87
                                      556*****************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.53
# Mc/sec: 520.04
//
Query:       gi|242399828|ref|YP_002995253.1|  [L=236]
Description: Thiamine biosynthesis protein [Thermococcus sibiricus MM 739]
Scores for complete 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-57  195.0   0.0    1.5e-57  194.8   0.0    1.0  1  ThiF             ThiF family
     0.0016   18.5   0.6      0.021   14.9   0.0    2.6  3  Ldh_1_N          lactate/malate dehydrogenase, NAD binding do
     0.0033   16.8   0.7      0.038   13.3   0.0    2.4  3  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
     0.0033   17.0   0.0     0.0058   16.2   0.0    1.4  1  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
     0.0035   17.6   0.1      0.012   15.9   0.1    1.8  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
  ------ inclusion threshold ------
      0.012   15.6   0.1       0.22   11.6   0.0    2.3  2  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
      0.014   15.3   0.0      0.021   14.7   0.0    1.3  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
      0.015   14.9   0.1      0.029   14.0   0.1    1.5  1  ApbA             Ketopantoate reductase PanE/ApbA
       0.16   11.5   0.0        0.4   10.2   0.0    1.7  2  DAO              FAD dependent oxidoreductase


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 !  194.8   0.0   7.3e-61   1.5e-57       1     234 [.      13     234 ..      13     236 .] 0.95

  Alignments for each domain:
  == domain 1  score: 194.8 bits;  conditional E-value: 7.3e-61
                                       THHHHHHHHHHHHHHHHTSEEEEE--SHHHHHHHHHHHHHTTTEEEEEESSB--GGGGGTBTTS-GGGTTSB.HHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx RF
                              ThiF   1 ysrqlallgedgqekLrdskvllvGaGglGsellknLalsGvgkltlvDnDkielsNlnRqflfreediGkp.Kaev 76 
                                       y+rq++++g +gqekL++skv++vG+GglGs+++ +La++Gvg+l l+D  + elsNlnRq+l+ eed  k+ K  +
  gi|242399828|ref|YP_002995253.1|  13 YDRQIRIFGVEGQEKLKKSKVAVVGVGGLGSPVAYYLAAAGVGELLLIDCQTPELSNLNRQILHWEEDLEKNpKPIS 89 
                                       89*******************************************************************7666**** PP

                                       HHHHHHHT-TTSEEEEEES-CCGCCS-HHHHTT-SEEEEESSSHHHHHHHHHHHHHHT-EEEEEEEETTEEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF  77 aaealqeinpdveveavteritdetvleellesvDlVvdalDniearrlvnracvkkgiplieagtlgfegqvvvii 153
                                       a+ +l+++n+d++++++t+ ++ ++  ee+l+++D++vd+lDn+e+r+l++++++kkgipl++++++g++gqv+++i
  gi|242399828|ref|YP_002995253.1|  90 AKWKLERFNSDIKISTFTGILNVKN-IEEVLKDIDVIVDCLDNFETRYLLDEFAHKKGIPLVHGAVEGLYGQVTTVI 165
                                       **********************998.58************************************************* PP

                                       ECCS-ECTSS-TGGS.EECCCCEEHHHHHHCTE-B-HHHHHHHHHHHHHHHHHHHTTBCGGGCCEEEECCTTTTEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF 154 pgktgcyeCldpsstedptekkvplctsiagnipaiatttavvaglaalellkllsgkeklenslltqvdllesrfe 230
                                       pg+t+ +++l+p    +p++k  +++       p++++t +v++ ++++e++kl+ g     +++l  vdl +++fe
  gi|242399828|ref|YP_002995253.1| 166 PGETKGLRDLFP----TPPRK-KENF-------PILGATAGVIGAIQVAEVIKLITGYGAPLANKLLIVDLMHNSFE 230
                                       ***********8....44444.4667.......799*******************999999999999*********9 PP

                                       EECC CS
                                       xxxx RF
                              ThiF 231 nvel 234
                                        v l
  gi|242399828|ref|YP_002995253.1| 231 VVDL 234
                                       8876 PP

>> Ldh_1_N  lactate/malate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0     1e-05     0.021       2      37 ..      32      65 ..      31      92 .. 0.88
   2 ?    0.6   0.0      0.28   5.6e+02      48      74 ..     100     126 ..      94     128 .. 0.79
   3 ?   -1.3   0.1         1   2.1e+03       5      39 ..     195     229 ..     189     235 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1e-05
                                      EEEEETTTSHHHHHHHHHHHHTTSSSEEEEE-SSHH CS
                           Ldh_1_N  2 kvavvGaaGgiGqslalllankkladelaLlDiake 37
                                      kvavvG+ Gg G+++a+ la+ ++++ l L+D ++ 
  gi|242399828|ref|YP_002995253.1| 32 KVAVVGV-GGLGSPVAYYLAAAGVGE-LLLIDCQTP 65
                                      9******.*****************9.9****9865 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.28
                                       HCHCCSTS-EEEEESSGGGGTTESEEE CS
                           Ldh_1_N  48 histflsvkvkvsekeeealkdadvvv 74 
                                       +i++ + + +   ++ ee+lkd+dv+v
  gi|242399828|ref|YP_002995253.1| 100 DIKISTFTGILNVKNIEEVLKDIDVIV 126
                                       5566665666667799*********98 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1
                                       EETTTSHHHHHHHHHHHHT.TSSSEEEEE-SSHHHH CS
                           Ldh_1_N   5 vvGaaGgiGqslalllank.kladelaLlDiakekl 39 
                                       v+Ga  ++++ + l    + +la++l ++D+ ++  
  gi|242399828|ref|YP_002995253.1| 195 VIGA-IQVAEVIKLITGYGaPLANKLLIVDLMHNSF 229
                                       5666.6667777766666778899999999886654 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   1.9e-05     0.038      31      69 ..      25      64 ..       6      83 .. 0.77
   2 ?    1.2   0.0      0.11   2.1e+02      80     111 ..     109     140 ..      94     145 .. 0.74
   3 ?   -2.5   0.0       1.4   2.8e+03      34      54 ..     188     207 ..     180     216 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.9e-05
                                      BS-GTTSEEEEES-SHHHHHHHHHHHHTT-.EEEEESSSH CS
                      2-Hacid_dh_C 31 gkelsgktvGiiGlGrIGqavakrlkafgm.kviaydrsk 69
                                      +++l++++v+++G+G +G+ va +l+a g+ +++ +d + 
  gi|242399828|ref|YP_002995253.1| 25 QEKLKKSKVAVVGVGGLGSPVAYYLAAAGVgELLLIDCQT 64
                                      45899***********************997777777664 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.11
                                       C.EECSHHHHHHH-SEEEE-S--STTTTTSBSH CS
                      2-Hacid_dh_C  80 v.elvsleellaesDivslhlpltpetrhlina 111
                                       + ++ ++ee+l++ D+++ +l  + etr l+++
  gi|242399828|ref|YP_002995253.1| 109 IlNVKNIEEVLKDIDVIVDCLD-NFETRYLLDE 140
                                       4467899********9986555.7778877765 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 1.4
                                       GTTSEEEEES-SHHHHHHHHH CS
                      2-Hacid_dh_C  34 lsgktvGiiGlGrIGqavakr 54 
                                       + g t G+iG+ ++++ v+k+
  gi|242399828|ref|YP_002995253.1| 188 ILGATAGVIGAIQVAE-VIKL 207
                                       5578899999877753.4455 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 !   16.2   0.0   2.9e-06    0.0058       2      53 ..      32      83 ..      31     105 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.9e-06
                                      EEEEE--STTHHHHHHHHHHCT.SEEEEE-S-HHHHHHHCTTS-SS--TTHHH CS
                    UDPG_MGDP_dh_N  2 kisviGlGYvGlvtaavlaeig.hevigvDideekvdklnsgkipiyepgLee 53
                                      k++v+G G +G + a  la++g  e++++D ++   ++ln++ ++  e++Le+
  gi|242399828|ref|YP_002995253.1| 32 KVAVVGVGGLGSPVAYYLAAAGvGELLLIDCQTPELSNLNRQILHW-EEDLEK 83
                                      89********************779***************998875.556665 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   5.8e-06     0.012       1     101 [.      33     154 ..      33     184 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5.8e-06
                                       EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH......................TTTCEEEEE-- CS
                   Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaaka......................lgvrfeaiald 55 
                                       v ++G G+ G++va +la+ +    e+ ++d +  +l +l  ++                       ++++++ +++
  gi|242399828|ref|YP_002995253.1|  33 VAVVGVGGLGSPVAYYLAAAGVG--ELLLIDCQTPELSNLNRQIlhweedleknpkpisakwklerFNSDIKISTFT 107
                                       679****************9976..9999999999999999998999*****************9977888888887 PP

                                       .TTTHHHHHHHHHTTSSEEEE-SSGGGHHHHH.HHHHHHT-EEEESS- CS
                   Sacchrp_dh_NADP  56 .aenyeavLaallkegdlvvnlsppissldvl.kaCietgvhyvdtsi 101
                                        + n++  ++++lk+ d++v+++ +++++ +l ++++++g+  v  ++
  gi|242399828|ref|YP_002995253.1| 108 gILNVKN-IEEVLKDIDVIVDCLDNFETRYLLdEFAHKKGIPLVHGAV 154
                                       4567777.999***************7665543899999998887555 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00011      0.22       8      45 ..      26      63 ..      21      83 .. 0.83
   2 ?    1.3   0.0      0.16   3.3e+02      63      82 ..     109     128 ..      95     140 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00011
                                      S..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESS CS
                      Shikimate_DH  8 eslkekkvlliGaGemaelvakhLlakgvkkvvvaNRt 45
                                      e+lk++kv ++G G +++ va +L+a+gv +++ +  +
  gi|242399828|ref|YP_002995253.1| 26 EKLKKSKVAVVGVGGLGSPVAYYLAAAGVGELLLIDCQ 63
                                      5899*************************999877655 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.16
                                       EEEGCGHHHHHHT-SEEEE- CS
                      Shikimate_DH  63 alkleelkellaeadvvisa 82 
                                       +l++++++e+l+++dv++ +
  gi|242399828|ref|YP_002995253.1| 109 ILNVKNIEEVLKDIDVIVDC 128
                                       6789999*********9976 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   1.1e-05     0.021       1      48 [.      32      83 ..      32     131 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.1e-05
                                      EEEEE--SCCHHHHHHHHHHTT-.EEEEE-S-HHHHHHHHHHHHH...HHHC CS
                           3HCDH_N  1 kvaviGaGtmGagiaavfasagl.eVvlvdiseealekalekiek...slek 48
                                      kvav+G G +G+ +a+ +a+ag+ e  l+d+++  l + +++i +    lek
  gi|242399828|ref|YP_002995253.1| 32 KVAVVGVGGLGSPVAYYLAAAGVgELLLIDCQTPELSNLNRQILHweeDLEK 83
                                      79*******************98689999*9888888777777651113333 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   1.4e-05     0.029       1      47 [.      33      81 ..      33     144 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.4e-05
                                      EEEES-SHHHHHHHHHHHHHTHC.EEEE-SCH.HHHHHHHHCEEEEETT CS
                              ApbA  1 iailGaGaiGsllaakLakagad.vtlilrsr.rlealkknGlrltseg 47
                                      +a++G G++Gs +a++La+ag     li+ +  +l +l+++ l+ +++ 
  gi|242399828|ref|YP_002995253.1| 33 VAVVGVGGLGSPVAYYLAAAGVGeLLLIDCQTpELSNLNRQILHWEEDL 81
                                      69*****************776548888877778888888777777666 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0    0.0002       0.4       1      28 [.      32      62 ..      32      96 .. 0.89
   2 ?   -1.3   0.0      0.62   1.2e+03     152     186 ..     137     169 ..      99     197 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0002
                                      EEEEECTSHHHHHHHHHHHHTT...EEEEES CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg...Vtllek 28
                                      +v+++G G  G+ +Ay+La++g    +l++ 
  gi|242399828|ref|YP_002995253.1| 32 KVAVVGVGGLGSPVAYYLAAAGvgeLLLIDC 62
                                      59******************98778888875 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.62
                                       HHHH.HHHTT-EEEESECEEEEEEEETCEEEEE.EEC CS
                               DAO 152 lara.aealGveilegtevtgleeedgkvwgve.rtt 186
                                       l+++ a ++G+ ++ g  v+gl    g+v++v   +t
  gi|242399828|ref|YP_002995253.1| 137 LLDEfAHKKGIPLVHG-AVEGL---YGQVTTVIpGET 169
                                       4444445555555555.55555...344555543322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); 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 0.35s 00:00:00.96 Elapsed: 00:00:00.54
# Mc/sec: 1313.69
//
Query:       gi|242399829|ref|YP_002995254.1|  [L=147]
Description: Molybdopterin-converting factor subunit 2 [Thermococcus sibiricus MM 739]
Scores for complete 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-36  123.3   0.0    6.6e-36  123.0   0.0    1.1  1  MoaE      MoaE protein


Domain annotation for each model (and alignments):
>> MoaE  MoaE protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.0   0.0   3.7e-40   6.6e-36       4     113 .]      10     119 ..       8     119 .. 0.98

  Alignments for each domain:
  == domain 1  score: 123.0 bits;  conditional E-value: 3.7e-40
                                       S---HHHHHHHH--TT--EEEEEEEE------TS-EEEEEECC-HHHHHHHHHHHHHHHHCCCTTSEEEEEEE-EEE CS
                              MoaE   4 epldvaeiealvaspkaGAvvlFvGtvRdsfdgkkvteLeyeayepmaektleeiaeearerwelervavvHrlGel 80 
                                       e++d++++ +l +s+k G++v+F+G vRd+++g++v++L yeaye+ma +++++i eea er+++ ++ ++Hr+Gel
  gi|242399829|ref|YP_002995254.1|  10 EDFDITNAIKLASSSKSGGLVIFLGEVRDENHGREVKKLIYEAYEEMAIEEMKKIREEALERFPILDMIIWHRYGEL 86 
                                       7899999999999*****************99********************************************* PP

                                       ETTSEEEEEEEEESSHHHHHHHHHHHHHHHHHH CS
                              MoaE  81 evgeasvvvavssahRkeafeaceylidelKkr 113
                                       evge+++++++s++hRkeafeac + +de+Kkr
  gi|242399829|ref|YP_002995254.1|  87 EVGENTILIIASGKHRKEAFEACMWTVDEVKKR 119
                                       *******************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       713  (0.039768); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.35s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 866.46
//
Query:       gi|242399830|ref|YP_002995255.1|  [L=321]
Description: Fe-S oxidoreductase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      6e-07   29.9   0.1    1.7e-06   28.4   0.1    1.7  1  SPASM     Iron-sulfur cluster-binding domain


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 !   28.4   0.1   9.6e-11   1.7e-06       4      68 .]     216     274 ..     215     274 .. 0.84

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 9.6e-11
                             SPASM   4 psrslfInsdGdVvpCcvdkktyveelklGnireesleeIwnseeyqefrkskkfplielCrnCp 68 
                                        s +l+I+ +G V pC +      +++  Gni++++l++I+++ +++ef  +  ++++e+C++Cp
  gi|242399830|ref|YP_002995255.1| 216 LSGTLAITGEGFVLPCPLL-----RNFLKGNIKTMTLKQILRKRKLKEFW-KITKKQFESCNKCP 274
                                       577899**********333.....45899*******************99.455666789****7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       738  (0.0411624); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); 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: 0.62u 0.33s 00:00:00.95 Elapsed: 00:00:00.51
# Mc/sec: 1876.59
//
Query:       gi|242399831|ref|YP_002995256.1|  [L=165]
Description: Adenosine_kin domain containing protein [Thermococcus sibiricus MM 739]
Scores for complete 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-62  207.5   1.5    9.9e-62  207.3   1.5    1.0  1  Adenosine_kin  Adenosine specific kinase


Domain annotation for each model (and alignments):
>> Adenosine_kin  Adenosine specific kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  207.3   1.5   5.5e-66   9.9e-62       1     153 [.      10     162 ..      10     163 .. 0.99

  Alignments for each domain:
  == domain 1  score: 207.3 bits;  conditional E-value: 5.5e-66
                                       EEE---TTEEEEEEEESS.TTHHHHHHHHHHCCSTTSEEEEEEE--STT-EEEEEESSHHHHHHHHHHHHHH--TTE CS
                     Adenosine_kin   1 vkiekpeevnvilgqshf.iktvedlyealvtsvpgikfglafcEasgkrLvrvegndeelvelavknalaigaghv 76 
                                       v++ekpe+v+ i+gq +f i+tv+dl +al+t+vpgikfg+a++Ea+ ++L+r++gnd+el+ela+kna +igaghv
  gi|242399831|ref|YP_002995256.1|  10 VNVEKPEGVECIIGQGNFsIFTVDDLARALLTAVPGIKFGIAMNEAK-PQLTRYTGNDKELEELAAKNAVNIGAGHV 85 
                                       799*******************************************9.9**************************** PP

                                       EEEEEEST-HHHHHHHHHHCTTCEEEEEEESSSEEEEEEEETTEEEEEEEEES---SEE--HHHHHHHHHHHHHTTS CS
                     Adenosine_kin  77 fvillknafPinvlnaiksvpevvkifaAtanplevivaeteqgrgvlgvvDGfspkgveeeedkkerkellrkigY 153
                                       fvi++knafPinvln++k++p vv ++ A+ npl+vi+aete gr+vlg+vDG++++++e++e+kker+el++kigY
  gi|242399831|ref|YP_002995256.1|  86 FVIVMKNAFPINVLNTVKNHPAVVMVYGASENPLQVIIAETELGRAVLGIVDGKAANKIENNEQKKERRELVEKIGY 162
                                       ***************************************************************************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       739  (0.0412181); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.33s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 972.97
//
Query:       gi|242399832|ref|YP_002995257.1|  [L=186]
Description: Nucleoside-triphosphatase [Thermococcus sibiricus MM 739]
Scores for complete 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-51  172.6   0.0    9.4e-51  172.4   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 !  172.4   0.0   5.2e-55   9.4e-51       1     187 []       3     178 ..       3     178 .. 0.86

  Alignments for each domain:
  == domain 1  score: 172.4 bits;  conditional E-value: 5.2e-55
                                       EEEC-S-HHHHHHHHHHTTTECCCE.EECCCCEE----BS.SSHHHHHHHHHHHHHH.HTS-EEEEEEEEEEGGGTT CS
                        Ham1p_like   1 ivfaTgNkgKlrevkeilaeellevkslkelelpeveEtq.gtfeenalkKaraaae.aglpvladDsgLevdaLng 75 
                                       ++f+T+NkgK++e+k +l++ +++v +     + +++E+q +t+ee++   +  + +  + p+++dDsgL+++aLng
  gi|242399832|ref|YP_002995257.1|   3 VLFITSNKGKVKEAKTYLSPLGVKVLQ----RQIDYPEIQaNTLEEVVGFGVMWLKDyLDEPFFIDDSGLFIEALNG 75 
                                       689***************876666653....356777***9*******99998666644778*************** PP

                                       TBGGGTTTTTHTTCHHHHHHHHHHHHCTHTTS--EEEEEEEEEEEETTTTEEEEEEEEEEEEE-SS.--SSSSTTGG CS
                        Ham1p_like  76 lPGvysarfagegaedeenlaklleeleeeeedrsArfvcvlaladpeeeeellfeGeveGeiveeprgeggfGyDp 152
                                       +PGvysa++ ++      +++ +l+ ++e+ ++r+A+f++v++++d+   ++++f+G+++G+i++e+rg+ gfG+Dp
  gi|242399832|ref|YP_002995257.1|  76 FPGVYSAYIYKTL-----GNEGILKLMNEV-KNRRAYFKSVIGYYDG---RIHIFTGITRGHIINEKRGKYGFGFDP 143
                                       *********7644.....445555555422.479**********985...779************************ PP

                                       GEEETT-SSBTTTS.CHHHHHHSHHHHHHHHHHHH CS
                        Ham1p_like 153 iFvpeegektfaelskeeknaiShRgkAlekllef 187
                                       iF pe+++ktfae+++eekn+iShRg+Al++++ +
  gi|242399832|ref|YP_002995257.1| 144 IFLPENSKKTFAEMQTEEKNRISHRGRALAEFARW 178
                                       ****87677**********************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); 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: 0.58u 0.34s 00:00:00.92 Elapsed: 00:00:00.53
# Mc/sec: 1052.94
//
Query:       gi|242399833|ref|YP_002995258.1|  [L=158]
Description: Transcription regulator, Lrp/AsnC family [Thermococcus sibiricus MM 739]
Scores for complete 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-16   58.0   1.2    3.2e-13   49.0   0.5    2.2  2  HTH_24           Winged helix-turn-helix DNA-binding
    3.4e-15   55.7   0.0    5.7e-15   55.0   0.0    1.3  1  AsnC_trans_reg   Lrp/AsnC ligand binding domain
      1e-10   41.3   0.0      3e-10   39.8   0.0    1.8  2  HTH_AsnC-type    AsnC-type helix-turn-helix domain
    1.1e-05   25.2   0.2    2.5e-05   24.1   0.1    1.6  2  TrmB             Sugar-specific transcriptional regulator Trm
    5.6e-05   23.0   0.1    0.00025   20.9   0.1    2.0  2  HTH_11           HTH domain
    0.00018   21.3   0.0    0.00054   19.7   0.0    1.7  2  HTH_IclR         IclR helix-turn-helix domain
    0.00022   21.1   0.0      0.003   17.4   0.0    2.2  2  MarR_2           MarR family
    0.00027   20.8   0.1     0.0014   18.5   0.0    2.1  2  MarR             MarR family
    0.00028   21.3   0.0    0.00066   20.1   0.0    1.6  1  HTH_27           Winged helix DNA-binding domain
    0.00041   20.1   0.1    0.00066   19.4   0.1    1.4  1  HTH_8            Bacterial regulatory protein, Fis family
    0.00073   19.3   0.0      0.045   13.6   0.0    2.3  2  HTH_23           Homeodomain-like domain
    0.00095   19.3   0.3     0.0089   16.2   0.1    2.2  2  B-block_TFIIIC   B-block binding subunit of TFIIIC
      0.004   17.0   0.1     0.0066   16.3   0.1    1.3  1  HTH_5            Bacterial regulatory protein, arsR family
     0.0047   16.7   0.0     0.0083   15.9   0.0    1.4  1  HTH_30           PucR C-terminal helix-turn-helix domain
     0.0098   15.4   0.0        5.4    6.6   0.0    2.6  2  Sigma70_r4       Sigma-70, region 4
  ------ inclusion threshold ------
      0.013   15.5   0.0      0.023   14.7   0.0    1.4  1  HTH_20           Helix-turn-helix domain
      0.022   15.3   0.1      0.037   14.6   0.1    1.4  1  Mga              Mga helix-turn-helix domain
      0.025   14.7   0.2      0.049   13.7   0.2    1.4  1  DUF2250          Uncharacterized protein conserved in archaea
      0.027   14.2   0.1      0.086   12.7   0.0    1.8  2  HTH_10           HTH DNA binding domain
      0.095   12.4   0.0        7.7    6.3   0.0    2.4  2  Sigma70_r4_2     Sigma-70, region 4
       0.11   12.6   0.1         24    5.1   0.0    2.7  2  HTH_3            Helix-turn-helix
       0.12   12.4   0.0       0.17   12.0   0.0    1.3  1  Spore_YhcN_YlaJ  Sporulation lipoprotein YhcN/YlaJ (Spore_Yhc
       0.14   12.3   0.0       0.62   10.2   0.0    1.9  2  HTH_28           Helix-turn-helix domain
       0.14   11.9   0.5        9.4    6.1   0.0    2.8  2  HTH_38           Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.0   0.5   4.3e-16   3.2e-13       2      48 .]      14      60 ..      13      60 .. 0.97
   2 !    7.8   0.0    0.0033       2.5      15      27 ..      86      98 ..      79     100 .. 0.89

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 4.3e-16
                            HTH_24  2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      d  d k+L++L++n+r +++ L+++lg++++tv++r+k+L++eG+I+
  gi|242399833|ref|YP_002995258.1| 14 DAVDMKLLKELKENSRENIATLSKKLGIPRTTVHYRIKKLINEGVIE 60
                                      789*******************************************7 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0033
                            HTH_24 15 nprisqreLAerl 27
                                      +++++qre+A+++
  gi|242399833|ref|YP_002995258.1| 86 DSGLTQREIAKKI 98
                                      789********97 PP

>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.0   0.0   7.6e-18   5.7e-15       1      72 [.      79     150 ..      79     152 .. 0.95

  Alignments for each domain:
  == domain 1  score: 55.0 bits;  conditional E-value: 7.6e-18
                                       EEEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEE CS
                    AsnC_trans_reg   1 vlvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsiv 72 
                                       +lv+ +p++ ++ +e+++++a+++ V e++ ++G++d+l+k+++++ e++ +++++kl++++g+++t t++ 
  gi|242399833|ref|YP_002995258.1|  79 ILVRYNPDSGLTQREIAKKIAQIDGVHEVHIIAGEWDLLIKIRAPSAEDIGKVVVDKLREIKGIGQTVTMVS 150
                                       6788888889999********************************************************986 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.8   0.0     4e-13     3e-10       1      41 [.      13      53 ..      13      54 .. 0.98
   2 ?   -1.8   0.0       3.7   2.8e+03      18      27 ..      89      98 ..      86      99 .. 0.72

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 4e-13
                     HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrL 41
                                      +D++D k+L++L e++R   a L++++G+ ++tv+ R+++L
  gi|242399833|ref|YP_002995258.1| 13 IDAVDMKLLKELKENSRENIATLSKKLGIPRTTVHYRIKKL 53
                                      6***************************************9 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.7
                     HTH_AsnC-type 18 isyaeLAerv 27
                                      ++ +e+A+++
  gi|242399833|ref|YP_002995258.1| 89 LTQREIAKKI 98
                                      5778999875 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.1   3.4e-08   2.5e-05       9      60 ..      16      67 ..      13      72 .. 0.90
   2 ?   -3.0   0.0       9.5   7.1e+03      23      30 ..      89      96 ..      86      98 .. 0.59

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 3.4e-08
                                      HCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTT CS
                              TrmB  9 yEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpk 60
                                       ++k  + L ++ + ++ +++++lg+pr++v   +++L++ G++e+   +p+
  gi|242399833|ref|YP_002995258.1| 16 VDMKLLKELKENSRENIATLSKKLGIPRTTVHYRIKKLINEGVIEKFTIKPN 67
                                      67888899999**********************************9888764 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 9.5
                                      CHHCHHCC CS
                              TrmB 23 atadeiae 30
                                      +t +eia+
  gi|242399833|ref|YP_002995258.1| 89 LTQREIAK 96
                                      55666666 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.1   3.3e-07   0.00025       4      44 ..      19      58 ..      17      66 .. 0.86
   2 ?   -1.3   0.0       2.9   2.1e+03      14      25 ..      87      98 ..      78      99 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 3.3e-07
                            HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                      ++l+ L+e+    ++++L+++L++ r+tv+ +Ik+L   gv
  gi|242399833|ref|YP_002995258.1| 19 KLLKELKENSR-ENIATLSKKLGIPRTTVHYRIKKLINEGV 58
                                      78999966666.6***********************99993 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.9
                            HTH_11 14 gpisgeeLAeeL 25
                                      + ++  e+A+++
  gi|242399833|ref|YP_002995258.1| 87 SGLTQREIAKKI 98
                                      459999999986 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 !   19.7   0.0   7.3e-07   0.00054       8      49 ..      20      60 ..      18      61 .. 0.88
   2 ?   -2.0   0.0       4.3   3.2e+03      17      28 ..      87      98 ..      85      99 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 7.3e-07
                                      HHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR  8 iLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                      +L+ l e  +e +++ l++++g+p++tvh  ++ L+++G +e
  gi|242399833|ref|YP_002995258.1| 20 LLKELKENSRE-NIATLSKKLGIPRTTVHYRIKKLINEGVIE 60
                                      66777788887.9**************************988 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.3
                                      SS-BHHHHHHHH CS
                          HTH_IclR 17 qeltlselArrt 28
                                       +lt +e+A+++
  gi|242399833|ref|YP_002995258.1| 87 SGLTQREIAKKI 98
                                      578999999875 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0     4e-06     0.003      10      53 ..      20      61 ..      13      64 .. 0.86
   2 ?    0.9   0.0      0.56   4.2e+02      16      30 ..      83      97 ..      77     101 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4e-06
                                      HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                            MarR_2 10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53
                                      +L +L  + + + +++ l ++lg+++ +v++++k+L   G +e+
  gi|242399833|ref|YP_002995258.1| 20 LLKELKENSR-E-NIATLSKKLGIPRTTVHYRIKKLINEGVIEK 61
                                      6667777765.3.8999*************************96 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.56
                                      CTTTSEEEHHHHHHH CS
                            MarR_2 16 rrpgrdltvgelarr 30
                                       +p+  lt++e+a++
  gi|242399833|ref|YP_002995258.1| 83 YNPDSGLTQREIAKK 97
                                      5566679*****975 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.9e-06    0.0014       5      50 ..      17      62 ..      13      70 .. 0.91
   2 ?   -0.9   0.0       2.2   1.6e+03      17      27 ..      88      98 ..      80      99 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.9e-06
                                      HHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR  5 qfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRs 50
                                       +++L  l+e+   +++ L kklg+ ++tv   +++L+ +G ie+ 
  gi|242399833|ref|YP_002995258.1| 17 DMKLLKELKENSRENIATLSKKLGIPRTTVHYRIKKLINEGVIEKF 62
                                      6789***************************************986 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.2
                                      TEEHHHHHHHH CS
                              MarR 17 plsvseLakkl 27
                                      +l++ e+akk+
  gi|242399833|ref|YP_002995258.1| 88 GLTQREIAKKI 98
                                      58999***986 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   8.9e-07   0.00066      13      51 ..      25      62 ..      13      70 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 8.9e-07
                            HTH_27 13 rhrrrrkkladlcgrlnvedshisyslkkLtekGLvert 51
                                      + ++ r  +a l+++l +  ++++y +kkL++ G++e+ 
  gi|242399833|ref|YP_002995258.1| 25 K-ENSRENIATLSKKLGIPRTTVHYRIKKLINEGVIEKF 62
                                      4.6788999***************************886 PP

>> HTH_8  Bacterial regulatory protein, Fis family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.1   8.8e-07   0.00066       5      42 .]      16      53 ..      12      53 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 8.8e-07
                                      HHHHHHHHHHHHTTT-HHHHHHHHTS-HHHHHHHHHHT CS
                             HTH_8  5 vEkelIeaALertgGnkskAArlLGisRrtLyrKLkkY 42
                                      v+ +l+++  e ++ n++  ++ LGi R+t+++++kk+
  gi|242399833|ref|YP_002995258.1| 16 VDMKLLKELKENSRENIATLSKKLGIPRTTVHYRIKKL 53
                                      55556666667777799999****************96 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0     6e-05     0.045      10      45 ..      20      57 ..      18      61 .. 0.79
   2 ?    3.4   0.0     0.094        71      15      26 ..      86      97 ..      78      99 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6e-05
                            HTH_23 10 illllae..GlsvreIAreLgvsrrTvy.rwlkryreeG 45
                                       l+ l+e  + ++++ +++Lg++r Tv  r++k   +eG
  gi|242399833|ref|YP_002995258.1| 20 LLKELKEnsRENIATLSKKLGIPRTTVHyRIKKLI-NEG 57
                                      4666776889999***************7777765.465 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.094
                            HTH_23 15 aeGlsvreIAre 26
                                      + Gl++reIA++
  gi|242399833|ref|YP_002995258.1| 86 DSGLTQREIAKK 97
                                      459*******96 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 !   16.2   0.1   1.2e-05    0.0089      24      59 ..      35      69 ..      30      86 .. 0.77
   2 ?    0.9   0.0       0.7   5.2e+02      17      31 ..      87     102 ..      84     108 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.2e-05
                    B-block_TFIIIC 24 LakeskqdprslfyrlksLekkgLIvkqsiidsatk 59
                                      L+k +++    ++yr+k+L + g I+k +i + + k
  gi|242399833|ref|YP_002995258.1| 35 LSKKLGIPRTTVHYRIKKLINEGVIEKFTI-KPNYK 69
                                      77888888999*******************.33333 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.7
                    B-block_TFIIIC  17 sGitqsdLakesk.qd 31 
                                       sG+tq+++ak +  +d
  gi|242399833|ref|YP_002995258.1|  87 SGLTQREIAKKIAqID 102
                                       8********7665355 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   8.9e-06    0.0066       6      47 .]      19      61 ..      18      61 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 8.9e-06
                                      HHHHHHTTSS.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5  6 kILklLaege.lcvcelaeelglsqstvShHLkkLreaGLVek 47
                                      k+Lk L e++   +  l+++lg+++ tv +  kkL ++G++ek
  gi|242399833|ref|YP_002995258.1| 19 KLLKELKENSrENIATLSKKLGIPRTTVHYRIKKLINEGVIEK 61
                                      789999996659*****************************97 PP

>> HTH_30  PucR C-terminal helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.1e-05    0.0083      12      36 ..      29      53 ..      21      55 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.1e-05
                                      TT-HHHHHHHHTS-HHHHHHHHHHH CS
                            HTH_30 12 ggnisatAkaLhvHrnTlryRLrri 36
                                        ni+  +k+L++ r T++yR++++
  gi|242399833|ref|YP_002995258.1| 29 RENIATLSKKLGIPRTTVHYRIKKL 53
                                      5799******************996 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.0    0.0072       5.4      24      44 ..      33      53 ..      28      56 .. 0.84
   2 ?    6.1   0.0     0.011         8      14      29 ..      80      97 ..      75      99 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0072
                                      HHHHHHHTS-HHHHHHHHHHH CS
                        Sigma70_r4 24 eEIgerlgiSrerVrqiekrA 44
                                      + ++++lgi+r +V+ ++k+ 
  gi|242399833|ref|YP_002995258.1| 33 ATLSKKLGIPRTTVHYRIKKL 53
                                      56789**********999986 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.011
                                      HHHH..TTT--HHHHHHH CS
                        Sigma70_r4 14 elrf..geglTleEIger 29
                                        r+  + glT+ EI+++
  gi|242399833|ref|YP_002995258.1| 80 LVRYnpDSGLTQREIAKK 97
                                      45677999********96 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   3.1e-05     0.023      11      55 ..      16      60 ..      12      63 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.1e-05
                                      HHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                            HTH_20 11 vRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLve 55
                                      v +++l++L+++     + l + l+++++t++y++++L   g +e
  gi|242399833|ref|YP_002995258.1| 16 VDMKLLKELKENSRENIATLSKKLGIPRTTVHYRIKKLINEGVIE 60
                                      556777777777777778889999**************9999887 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1     5e-05     0.037      17      63 ..      16      64 ..       9      73 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5e-05
                                      HHHHHHHHHHHHSEEEHHHHHHHCT--HHHHHHHHHHH.HH.HCHCCT- CS
                               Mga 17 lkyqllkflfeeeevsieelaqelyiSestlkrkikel.nk.lLkefdl 63
                                      ++ +llk l e+ + +i+ l+++l i ++t+   ik+l n+ ++++f +
  gi|242399833|ref|YP_002995258.1| 16 VDMKLLKELKENSRENIATLSKKLGIPRTTVHYRIKKLiNEgVIEKFTI 64
                                      6789**************************9777776614434556665 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 ?   13.7   0.2   6.5e-05     0.049       7      56 ..      14      63 ..       9      73 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.5e-05
                           DUF2250  7 delalkvlkhlkkanvdYaksiakeleipleevrellkkLeelGLlerve 56
                                      d +++k+lk lk+   +   +++k+l ip++ v+  +kkL + G +e+ +
  gi|242399833|ref|YP_002995258.1| 14 DAVDMKLLKELKENSRENIATLSKKLGIPRTTVHYRIKKLINEGVIEKFT 63
                                      667899*****************************************976 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00012     0.086      25      48 ..      31      54 ..      26      56 .. 0.88
   2 ?   -2.0   0.0       4.5   3.3e+03      24      33 ..      89      98 ..      83     100 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00012
                            HTH_10 25 tlkeLAkelGIskstlsehLrkae 48
                                      +++ L+k+lGI ++t++++++k +
  gi|242399833|ref|YP_002995258.1| 31 NIATLSKKLGIPRTTVHYRIKKLI 54
                                      7899****************9965 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.5
                            HTH_10 24 vtlkeLAkel 33
                                       t +e+Ak++
  gi|242399833|ref|YP_002995258.1| 89 LTQREIAKKI 98
                                      5567777765 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0      0.01       7.7      33      49 ..      36      52 ..      20      53 .. 0.83
   2 ?    3.8   0.0     0.063        47      26      36 ..      88      98 ..      76     108 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.01
                                      HHHHT--HHHHHHHHHH CS
                      Sigma70_r4_2 33 AellgisegtVksrlsR 49
                                      +++lgi+ +tV +r+++
  gi|242399833|ref|YP_002995258.1| 36 SKKLGIPRTTVHYRIKK 52
                                      6789**********975 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.063
                                      ---HHHHHHHH CS
                      Sigma70_r4_2 26 glsykEIAell 36
                                      gl+++EIA+++
  gi|242399833|ref|YP_002995258.1| 88 GLTQREIAKKI 98
                                      9*******998 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.032        24      14      26 ..      34      46 ..      20      51 .. 0.87
   2 ?    4.6   0.0     0.045        33       9      19 ..      88      98 ..      86      99 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.032
                                      HHHHHHTSSHHHH CS
                             HTH_3 14 eLAeklGvsrsti 26
                                       L++klG++r+t+
  gi|242399833|ref|YP_002995258.1| 34 TLSKKLGIPRTTV 46
                                      699********98 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.045
                                      THHHHHHHHHH CS
                             HTH_3  9 glsqeeLAekl 19
                                      gl+q+e+A+k+
  gi|242399833|ref|YP_002995258.1| 88 GLTQREIAKKI 98
                                      9********97 PP

>> Spore_YhcN_YlaJ  Sporulation lipoprotein YhcN/YlaJ (Spore_YhcN_YlaJ)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00023      0.17      57      94 ..      86     123 ..      66     150 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00023
                   Spore_YhcN_YlaJ  57 ydgetaqniaqrverlegVedarvlvtgndvlVavqtd 94 
                                       + g t  +ia+++++++gV++++ ++ + d+l+ +++ 
  gi|242399833|ref|YP_002995258.1|  86 DSGLTQREIAKKIAQIDGVHEVHIIAGEWDLLIKIRAP 123
                                       4577899*******************999999977766 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00083      0.62       6      40 ..      21      57 ..      18      65 .. 0.75
   2 ?   -0.8   0.0       2.3   1.7e+03      11      21 ..      87      97 ..      80      99 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00083
                            HTH_28  6 ikllaaG.h.svreaArelgisrrtv.yrWikryeegG 40
                                      +k+l++  + +++ ++++lgi r+tv yr  k  +e G
  gi|242399833|ref|YP_002995258.1| 21 LKELKENsReNIATLSKKLGIPRTTVhYRIKKLINE-G 57
                                      566664223488899***********8888777777.5 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.3
                            HTH_28 11 aGhsvreaAre 21
                                      +G ++re+A++
  gi|242399833|ref|YP_002995258.1| 87 SGLTQREIAKK 97
                                      56699999986 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.2      0.11        81      21      42 ..      30      51 ..      21      53 .. 0.70
   2 ?    6.1   0.0     0.013       9.4      19      30 ..      87      98 ..      68      99 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.11
                            HTH_38 21 lslreIArrLgrspsTIsRElk 42
                                      +++++  ++Lg  ++T+++ +k
  gi|242399833|ref|YP_002995258.1| 30 ENIATLSKKLGIPRTTVHYRIK 51
                                      5667777888888888877665 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.013
                            HTH_38 19 eGlslreIArrL 30
                                       Gl++reIA+++
  gi|242399833|ref|YP_002995258.1| 87 SGLTQREIAKKI 98
                                      69*******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       891  (0.049696); expected 358.6 (0.02)
Passed bias filter:                      678  (0.0378158); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.59u 0.35s 00:00:00.94 Elapsed: 00:00:00.53
# Mc/sec: 889.23
//
Query:       gi|242399834|ref|YP_002995259.1|  [L=233]
Description: FwdE-like tungsten formylmethanofuran dehydrogenase, subunit E [Thermococcus sibiricus MM 739]
Scores for complete 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  124.0   0.0    4.9e-36  123.7   0.0    1.1  1  FmdE          FmdE, Molybdenum formylmethanofuran dehydrogena
    1.7e-06   27.8   2.5    3.3e-06   26.9   2.5    1.5  1  zf-dskA_traR  Prokaryotic dksA/traR C4-type zinc finger


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 !  123.7   0.0   5.5e-40   4.9e-36       1     130 [.      23     165 ..      23     167 .. 0.95

  Alignments for each domain:
  == domain 1  score: 123.7 bits;  conditional E-value: 5.5e-40
                                       HHSS--CHHHHHHHHHHHHHHCC....-TT.....SSSEEEEES-STCHHHHHHHHCS--TTTTSEEE--SS-SEEE CS
                              FmdE   1 fHGHlCpglvlGyrmakaalkelgpkeeeg.....deelvaivetdsCldDAiqvltgctlGkgnlivmdygkkalt 72 
                                       fHGH+Cp+++lG+r + +a++el++  + +     +e + aive++sC++D++qv+tgctlG+++li+md+gk alt
  gi|242399834|ref|YP_002995259.1|  23 FHGHVCPYVALGIRTSLIAMNELSVG-RLDysasvNESILAIVEINSCFTDGVQVTTGCTLGNNSLIYMDLGKTALT 98 
                                       9**********************975.4446999******************************************* PP

                                       EEETTT-EEEEEEE-.........CCTHHHHHHHCCT--.GGGS-HHHHHHHHHHHHHHHHHS.HHHH CS
                              FmdE  73 fkkrktgkavrlklk.........eelpelreklakgka.keekeeeeleeeleeaikkilnapeeel 130
                                       ++kr+t ++vr++++         +e++el++k++k+++ ++e e+e l+e++e++++ +l +p ee+
  gi|242399834|ref|YP_002995259.1|  99 LVKRSTWEGVRVYIDaeklekyypPEARELFNKVIKERKgSPE-EREYLKELWEDIARTMLYLPREEF 165
                                       ***************************************6666.8999****************9986 PP

>> zf-dskA_traR  Prokaryotic dksA/traR C4-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   2.5   3.7e-10   3.3e-06       1      36 []     179     216 ..     179     216 .. 0.94

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 3.7e-10
                      zf-dskA_traR   1 giygs..CeeCGEpIpeaRlralPgarlCveCqekaer 36 
                                       +i++s  C+eCGE  +  R++ +   +lC  C++k+++
  gi|242399834|ref|YP_002995259.1| 179 PIFESirCSECGELAMSRRIVYINEEPLCYKCAGKEYH 216
                                       6788899****************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); 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: 0.58u 0.37s 00:00:00.95 Elapsed: 00:00:00.54
# Mc/sec: 1288.92
//
Query:       gi|242399835|ref|YP_002995260.1|  [L=147]
Description: hypothetical protein TSIB_1862 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.4e-34  116.7   0.0    7.7e-34  116.5   0.0    1.1  1  TrmO      tRNA-methyltransferase O


Domain annotation for each model (and alignments):
>> TrmO  tRNA-methyltransferase O
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.5   0.0   4.3e-38   7.7e-34       1     119 []      20     131 ..      20     131 .. 0.89

  Alignments for each domain:
  == domain 1  score: 116.5 bits;  conditional E-value: 4.3e-38
                                       TS-SSGGG--.-EEEEEE-HHH..HGGGTTGGG-SEEEEEEE-TTS...-.SS--E-TT-.SS-E.EGGGS--S-SS CS
                              TrmO   1 giPrqpglaeeaeaeielepeynseealegleefshlwllfvfhenaekklkakvrpprlggnervGvfatRsphRp 77 
                                       ++P q++l+e     +e++pe+  e +l+++e+++hl+ll+++++++ ++   +  pp+ +++e+ GvfatRsphRp
  gi|242399835|ref|YP_002995260.1|  20 ECPSQGRLSE-EIFIVEVFPEF--EGGLKDVETCTHLILLYWLDKAR-RD-VLTAMPPH-DKKEH-GVFATRSPHRP 89 
                                       58******99.7899*******..********************993.33.34555665.54455.*********** PP

                                       S-EEEEEEEEEEEETTEEEEES----TT-EEEEEEE--HHHH CS
                              TrmO  78 npiglsvvklekvegnvlevsgvDlldgtpvlDiKPYvpyaD 119
                                       npig+ vv+l + +g++l v+g+D+ldgtpv+DiKPY + +D
  gi|242399835|ref|YP_002995260.1|  90 NPIGFAVVELIERRGRKLIVKGLDALDGTPVIDIKPYSSAID 131
                                       **************************************9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       191  (0.0106531); expected 358.6 (0.02)
Passed bias filter:                      187  (0.01043); 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 0.32s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 866.38
//
Query:       gi|242399836|ref|YP_002995261.1|  [L=368]
Description: iron ABC transporter ATP-binidng protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-26   93.7   0.0    1.8e-26   93.2   0.0    1.2  1  Peripla_BP_2  Periplasmic binding protein
  ------ inclusion threshold ------
       0.33   11.5   1.8       0.63   10.7   1.8    1.5  1  LPAM_1        Prokaryotic membrane lipoprotein lipid attachme


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.2   0.0     2e-30   1.8e-26       1     234 [.      47     289 ..      47     292 .. 0.93

  Alignments for each domain:
  == domain 1  score: 93.2 bits;  conditional E-value: 2e-30
                                       EEE-SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT............TS-BSBESSSB-HHHHHHH--SEEEE-G CS
                      Peripla_BP_2   1 iaslspsvteillalGatdkvvgvdtttsdpldadklee..........aivevgadgeidvEklaalkPDlvilsk 67 
                                       i++++p+  +i + l atd vvgv+ + + +  + +             +i   g ++ +++E+l+++kPD+++  +
  gi|242399836|ref|YP_002995261.1|  47 IVAVGPGALRIMVYLNATDMVVGVEDCERQWGSGGRPYImahpelkelpSIGPGGPGKLPNLEALINVKPDVIFITY 123
                                       89999*********************99999988665558888888788889999999******************9 PP

                                       GG...GGGHHHHHHHS-EEE----TTS....HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT.-EEE CS
                      Peripla_BP_2  68 glgltdedeellksgiptvivessntg....eslkeqiralgellgledeaeklvaeidsklaaaksaidsekpkpv 140
                                        +   +++++++k gip+v+  +++      ++l ++i+  g++l +ed+a++++++i+s  +++ +++++   + v
  gi|242399836|ref|YP_002995261.1| 124 VD-AKTAQDMQEKTGIPVVVLSYGELTtfedDELFKSIELAGKILKKEDRAKEVINFIKSIQEDLLKRTENVESPSV 199
                                       99.9*******************986699*******************************************99999 PP

                                       EEEEETTE..EEEE-TTSTTTHHHHTS--EESTTT--STT-EEE-HHHHHHH--SEEEEEEHHHHT-S--HHHHT-S CS
                      Peripla_BP_2 141 lvfggadeggyvvagsnsyigdlldalgieniaaeskkseyeeisaEqilasdpdvifvsgraeadnktgleflken 217
                                        v g +++g++ + ++     +++  l ++n+ +e  +++ + i+ E +l +dp++if++       + +l++  ++
  gi|242399836|ref|YP_002995261.1| 200 YVGGIGYKGAHGIESTEAKYPPFVV-LHAKNVVDEL-GEGHKFIDKEKLLDWDPEYIFIDEG---GLSLVLDDYRKS 271
                                       9999999999999999999999999.**********.***********************99...************ PP

                                       HHHHTS.HHHHTT-EEEE CS
                      Peripla_BP_2 218 pllael.pAvkngrVyal 234
                                       p++ e  +Avkng+Vy++
  gi|242399836|ref|YP_002995261.1| 272 PEFYESlKAVKNGNVYGI 289
                                       9876555*********97 PP

>> LPAM_1  Prokaryotic membrane lipoprotein lipid attachment site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.8     7e-05      0.63       1      17 [.       1      17 [.       1      17 [. 1.00

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 7e-05
                            LPAM_1  1 MKKillalgalllLsGC 17
                                      MK+ l+++++l+l sGC
  gi|242399836|ref|YP_002995261.1|  1 MKRALSIIVLLVLISGC 17
                                      ***************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.53
# Mc/sec: 2098.09
//
Query:       gi|242399837|ref|YP_002995262.1|  [L=344]
Description: iron-siderophore ABC transporter permease [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-97  325.6  32.0    3.1e-97  325.3  32.0    1.0  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 !  325.3  32.0  1.8e-101   3.1e-97       2     312 .]      21     339 ..      18     339 .. 0.98

  Alignments for each domain:
  == domain 1  score: 325.3 bits;  conditional E-value: 1.8e-101
                             FecCD   2 lllllllslllgavkispsevfeallgkadsleaeivlelrlprvlaallvGaaLavaGallQtvtrNpLadPsilG 78 
                                       ++++ ++s++ g +++s+ ev+++l+g++d +++++++++r+prvla++lvGa+La++Ga++Q+ +rNpLa+P ++G
  gi|242399837|ref|YP_002995262.1|  21 IFMVSVFSISQGGYNLSIDEVIRVLIGRGDYKSNMVIWNIRFPRVLAGILVGASLAISGAVMQGFLRNPLASPFTMG 97 
                                       5678999********************************************************************** PP

                             FecCD  79 issgaalgavlallll.........lgslslfalplaaflgallalllvlllarkrkgasplkliLaGiavsallsa 146
                                       +s+ga++ga +a+ll+         +   + +a++l+aflga+ a++++llla k kg sp+ +iL+Gia+s+l+ a
  gi|242399837|ref|YP_002995262.1|  98 VSHGAMFGASIAILLGagysessgkIIVNNPYAVVLFAFLGAMSAAAIILLLA-KLKGLSPEAIILSGIAMSSLFVA 173
                                       *********************9998888899**********************.*********************** PP

                             FecCD 147 ltsllllllneealesilfwllGslsgaswskvllllvllllllllllllarkldllalgdetAkslGvnvervrll 223
                                       lt+l++++++e +l+++++w +G+l++ +w++ ++l + +++++ ++++ + +l++ algde+Aks+Gv+ve++r++
  gi|242399837|ref|YP_002995262.1| 174 LTTLIQYFADELQLAAMVYWSFGDLGRTTWREDIMLGISFTAVFTYFIMKRWDLNASALGDEIAKSVGVEVEKTRVI 250
                                       ***************************************************************************** PP

                             FecCD 224 llllvalltavavalvGpigFvGLivPhiarllvgadhrkllplsallGallllladllarlllsptelpvgivtal 300
                                        ++l+++lta++v++vG+igFvGLi+Ph +rll+g d+r l+plsal+Ga+lll ad++arll+sp++lpvg+vt++
  gi|242399837|ref|YP_002995262.1| 251 STFLATFLTAISVSFVGVIGFVGLIAPHAVRLLFGGDYRFLIPLSALMGAFLLLTADTIARLLFSPITLPVGVVTSF 327
                                       ***************************************************************************** PP

                             FecCD 301 iGapffiylllr 312
                                       +Gap+fiyll+r
  gi|242399837|ref|YP_002995262.1| 328 LGAPMFIYLLVR 339
                                       **********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       693  (0.0386525); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); 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: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.52
# Mc/sec: 1978.39
//
Query:       gi|242399838|ref|YP_002995263.1|  [L=251]
Description: iron-siderophore ABC transporter ATPase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.2e-30  105.4   0.0    4.7e-30  104.9   0.0    1.3  1  ABC_tran     ABC transporter
    2.3e-10   40.8   0.1    2.9e-05   24.0   0.0    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
      1e-05   26.1   0.7    2.5e-05   24.9   0.0    1.9  2  AAA_23       AAA domain
    6.5e-05   22.5   0.3      0.014   14.8   0.0    2.1  2  SMC_N        RecF/RecN/SMC N terminal domain
    6.7e-05   22.8   0.2      0.053   13.2   0.0    2.1  2  AAA_15       AAA ATPase domain
    0.00017   21.3   0.1    0.00053   19.7   0.0    1.8  2  AAA_29       P-loop containing region of AAA domain
    0.00073   19.2   0.0     0.0014   18.3   0.0    1.4  1  AAA_27       AAA domain
     0.0063   16.4   0.2          1    9.2   0.0    2.9  3  NTPase_1     NTPase
     0.0066   16.4   0.0      0.015   15.2   0.0    1.5  1  RsgA_GTPase  RsgA GTPase
     0.0084   16.0   0.0      0.016   15.1   0.0    1.7  1  ATPase_2     ATPase domain predominantly from Archaea
  ------ inclusion threshold ------
      0.016   14.1   0.3        2.7    6.7   0.0    2.8  2  ABC_ATPase   Predicted ATPase of the ABC class
      0.016   15.5   0.2       0.36   11.1   0.0    2.1  2  AAA_22       AAA domain
      0.017   14.9   0.0      0.025   14.3   0.0    1.5  1  AAA_30       AAA domain
      0.021   15.3   0.4       0.29   11.5   0.0    2.4  2  AAA          ATPase family associated with various cellular a
      0.026   14.5   0.0        2.4    8.2   0.0    2.3  2  AAA_5        AAA domain (dynein-related subfamily)
       0.03   14.7   0.0       0.07   13.5   0.0    1.5  1  AAA_16       AAA ATPase domain
      0.032   14.2   0.1       0.16   11.9   0.0    1.9  2  Rad17        Rad17 P-loop domain
      0.039   14.0   0.1       0.22   11.6   0.0    2.0  2  MMR_HSR1     50S ribosome-binding GTPase
      0.071   13.0   0.0       0.12   12.3   0.0    1.4  1  NACHT        NACHT domain
      0.093   13.0   0.0       0.17   12.1   0.0    1.4  1  AAA_28       AAA domain
       0.11   13.1   0.1        3.4    8.2   0.0    2.3  2  AAA_18       AAA domain
       0.12   11.5   0.3       0.31   10.2   0.3    1.8  1  NB-ARC       NB-ARC domain
       0.15   11.8   0.0        0.3   10.8   0.0    1.5  2  PRK          Phosphoribulokinase / Uridine kinase 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 !  104.9   0.0     6e-33   4.7e-30       1     137 []      19     163 ..      19     163 .. 0.87

  Alignments for each domain:
  == domain 1  score: 104.9 bits;  conditional E-value: 6e-33
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.....--S-T CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.....pqlfp 72 
                                       l+++sl++++ge+vai+G+nGaGKStL+k++ag  + +e ei   g++l++ ++e+l k ig++pq           
  gi|242399838|ref|YP_002995263.1|  19 LHDISLEVEQGELVAILGPNGAGKSTLMKCIAGIFRCKEVEI--FGEPLHRCSREELAKIIGYVPQSiipgfM---- 89 
                                       789********************************9877666..99*********************443333.... PP

                                       TSBHHHH...............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEES CS
                                       xxxxxxx...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  73 eltvren...............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDE 134
                                         +v ++               e+ e +++ l++l++++l+ +++    ++LSgG+ q+v +aral+++p++ll+DE
  gi|242399838|ref|YP_002995263.1|  90 --RVFDTvllgrrpyigltpsrEDIEIVKQTLKRLKIDHLALKPL----NKLSGGEIQKVNIARALAQEPEILLMDE 160
                                       ..35566666677*****866444444999999999999999999....**************************** PP

                                       TTT CS
                                       xxx RF
                          ABC_tran 135 pta 137
                                       pt+
  gi|242399838|ref|YP_002995263.1| 161 PTN 163
                                       **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 !   24.0   0.0   3.8e-08   2.9e-05       2      27 ..      32      58 ..      31      93 .. 0.77
   2 !   14.9   0.0   2.3e-05     0.018     220     287 ..     118     182 ..      93     197 .. 0.76

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 3.8e-08
                            AAA_21  2 nvliGpNgsGKSnLLdaldllarl.dr 27
                                       ++ GpNg+GKS+L++++ +++r+   
  gi|242399838|ref|YP_002995263.1| 32 VAILGPNGAGKSTLMKCIAGIFRCkEV 58
                                      689******************997633 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 2.3e-05
                            AAA_21 220 gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr 287
                                       ++  l+ ++    p+++lS G  +   ++ al++ +    +ll DEp n+L+ k + +++++ ++ ++
  gi|242399838|ref|YP_002995263.1| 118 TLKRLKIDHLALKPLNKLSGGEIQKVNIARALAQEP---EILLMDEPTNNLDLKSQMEVMKIARKFAE 182
                                       445556666666688899999999999999999988...9*****************99999865555 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   3.2e-08   2.5e-05      14      40 ..      23      50 ..       4      57 .. 0.75
   2 ?   -1.7   0.1       4.4   3.4e+03      29      36 ..     182     189 ..     181     189 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 3.2e-08
                            AAA_23 14 eidF.skgltlItGpNGaGKTTildAik 40
                                      +++     l++I GpNGaGK+T++ +i 
  gi|242399838|ref|YP_002995263.1| 23 SLEVeQGELVAILGPNGAGKSTLMKCIA 50
                                      344433469******************7 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 4.4
                            AAA_23  29 GaGKTTil 36 
                                       ++GKT+i+
  gi|242399838|ref|YP_002995263.1| 182 ESGKTSII 189
                                       79*****7 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   1.9e-05     0.014      24      45 ..      29      50 ..       2      61 .. 0.76
   2 !    6.0   0.0    0.0088       6.9     136     200 ..     134     195 ..     100     213 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.9e-05
                                      SSEEEEEESTTSSHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 24 ksftaivGpNGSGKsnlldAil 45
                                       ++ ai+GpNG+GKs l+  i 
  gi|242399838|ref|YP_002995263.1| 29 GELVAILGPNGAGKSTLMKCIA 50
                                      35789*************9985 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0088
                                       CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                             SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislree 200
                                        LSgGe + v +a  +A    +   + l+De   +LD k   +v ++ ++  ++    i+i ++ +
  gi|242399838|ref|YP_002995263.1| 134 KLSGGEIQKVNIARALA----QEPEILLMDEPTNNLDLKSQMEVMKIARKFAESgKTSIIIMHDVN 195
                                       79999988888877665....3345889*********99888888887766655334455555544 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   6.8e-05     0.053      16      50 ..      21      56 ..      16     128 .. 0.78
   2 !    7.7   0.2    0.0031       2.4     322     361 ..     151     190 ..     139     191 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.8e-05
                            AAA_15 16 dveidlsee.ltvliGkNnsGKSsilealdlFlnnk 50
                                      d++++++   l  + G+N++GKS++++ +  ++  k
  gi|242399838|ref|YP_002995263.1| 21 DISLEVEQGeLVAILGPNGAGKSTLMKCIAGIFRCK 56
                                      55555555569****************998777755 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0031
                            AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandnktQvii 361
                                       +++ ill++EP ++L  + q++++k  ++ a+++kt +ii
  gi|242399838|ref|YP_002995263.1| 151 QEPEILLMDEPTNNLDLKSQMEVMKIARKFAESGKTSIII 190
                                       6789*******************************98887 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   6.8e-07   0.00053      16      46 ..      23      53 ..      13      61 .. 0.76
   2 ?   -2.1   0.1       4.4   3.4e+03      32      39 ..     182     189 ..     181     190 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 6.8e-07
                            AAA_29 16 tieidlkgatlltGpsGsGKSTllDAiqalL 46
                                      ++e+++ + + + Gp+G+GKSTl+  i+ ++
  gi|242399838|ref|YP_002995263.1| 23 SLEVEQGELVAILGPNGAGKSTLMKCIAGIF 53
                                      4556644499*************98777666 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.4
                            AAA_29  32 GsGKSTll 39 
                                       +sGK++++
  gi|242399838|ref|YP_002995263.1| 182 ESGKTSII 189
                                       69***997 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.7e-06    0.0014       2      47 ..       5      50 ..       4      55 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.7e-06
                            AAA_27  2 rlerLdLeryGkftdrsldfsaeeadlhliyGpNEAGKstalrAis 47
                                      r+++L+++  G+   + ++++ e+ +l  i+GpN AGKst+++ i 
  gi|242399838|ref|YP_002995263.1|  5 RVKNLNFSYNGSKILHDISLEVEQGELVAILGPNGAGKSTLMKCIA 50
                                      778888888888777888888899******************9986 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0    0.0013         1       2      32 ..      32      62 ..      31      73 .. 0.89
   2 ?    0.5   0.0      0.62   4.8e+02     112     155 ..      86     129 ..      83     136 .. 0.81
   3 ?    2.9   0.1      0.12        95      89     153 ..     145     213 ..     134     225 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0013
                                      EEEE--TTSSHHHHHHHHHHHH...GGGEEE CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvkvgG 32
                                      v+i Gp G GK+Tl+k ++   + ++v++ G
  gi|242399838|ref|YP_002995263.1| 32 VAILGPNGAGKSTLMKCIAGIFRCKEVEIFG 62
                                      6789***************999999888876 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.62
                                       HHHHHHHHHHHTTTSEEEEE--SS--SHHHHHHHT-TT-EEEE- CS
                          NTPase_1 112 kkfkeaveevLksekpvlavihrrkdlalveeirerkdvkvfev 155
                                       + f +  ++vL   +p ++  + r+d ++v++  +r ++  + +
  gi|242399838|ref|YP_002995263.1|  86 PGFMRVFDTVLLGRRPYIGLTPSREDIEIVKQTLKRLKIDHLAL 129
                                       5688899999999************9999999888866655555 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.12
                                       HHHHH.HHH-EEEE--.-STTGGG-HHHHHHHHHHHT.TTSEEEEE--SS-.-SHHHHHHHT-TT-EEE CS
                          NTPase_1  89 lrkal.seadviviDE.iGkmElkskkfkeaveevLk.sekpvlavihrrk.dlalveeirerkdvkvf 153
                                       + +al +e++++++DE   ++ lks+    ++ + ++ s+k  ++++h  +  l++ +++   k +k++
  gi|242399838|ref|YP_002995263.1| 145 IARALaQEPEILLMDEpTNNLDLKSQMEVMKIARKFAeSGKTSIIIMHDVNlALRFADRFVFMKSGKII 213
                                       3344449999******5568*****98777777766669999999999988788888888777766665 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.9e-05     0.015      85     121 ..      14      51 ..       2      64 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.9e-05
                                       TTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  85 ktkegleelkellkd.ktsvlvGqSGvGKStLinallp 121
                                       + ++ l++++ ++++ ++++++G+ G+GKStL++ +++
  gi|242399838|ref|YP_002995263.1|  14 NGSKILHDISLEVEQgELVAILGPNGAGKSTLMKCIAG 51 
                                       55566677777777779****************99987 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   2.1e-05     0.016      15      70 ..      24      78 ..      17     208 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.1e-05
                          ATPase_2 15 lerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefie 70
                                      le e+ e + i Gp g GK++L+k i+   + k+   i+  +l++ s ++l + i+
  gi|242399838|ref|YP_002995263.1| 24 LEVEQGELVAILGPNGAGKSTLMKCIAGIFRCKE-VEIFGEPLHRCSREELAKIIG 78
                                      677889999*****************99997655.689999999999888877765 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0035       2.7     242     265 ..      26      50 ..      21      54 .. 0.87
   2 ?    3.8   0.1     0.026        20     324     351 ..     136     163 ..     132     215 .. 0.58

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0035
                                       E-SS.EEEEEE-TTSSHHHHHHHHH CS
                        ABC_ATPase 242 ipkG.vtlIvGggfhGKsTLLeAle 265
                                       + +G +++I G++  GKsTL++ ++
  gi|242399838|ref|YP_002995263.1|  26 VEQGeLVAILGPNGAGKSTLMKCIA 50 
                                       6788899***************985 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.026
                                       -HHHHHHHHHHHHHHTT-SEEEEEGGGS CS
                        ABC_ATPase 324 SGStsqAanimealeagakllLiDEDts 351
                                       SG   q +ni++al  + ++lL+DE t 
  gi|242399838|ref|YP_002995263.1| 136 SGGEIQKVNIARALAQEPEILLMDEPTN 163
                                       6777777777788887888888777653 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00046      0.36       4      26 ..      28      50 ..      25      80 .. 0.85
   2 ?    2.7   0.1      0.18   1.4e+02      87     128 ..     147     191 ..      90     200 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00046
                            AAA_22  4 tagilvvtGesGtGKTtllrrll 26
                                      +  ++++ G+ G+GK+tl++ ++
  gi|242399838|ref|YP_002995263.1| 28 QGELVAILGPNGAGKSTLMKCIA 50
                                      567889*************9765 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.18
                            AAA_22  87 rarav...ielliiDEaqh.lr...seealeeLrsllnlsrkgvqliLv 128
                                       ra      +e+l+ DE  + l+   ++e+++  r++++  + ++++i++
  gi|242399838|ref|YP_002995263.1| 147 RA--LaqePEILLMDEPTNnLDlksQMEVMKIARKFAE--SGKTSIIIM 191
                                       22..234678999***9999999755999999999999..888888765 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   3.2e-05     0.025      18      50 ..      29      61 ..      23     190 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.2e-05
                            AAA_30 18 drvavltGpAGtGKttalkalreaweaaggrvi 50
                                        ++++ Gp G+GK+t++k ++ +++ ++ +++
  gi|242399838|ref|YP_002995263.1| 29 GELVAILGPNGAGKSTLMKCIAGIFRCKEVEIF 61
                                      458999***************999887775555 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00038      0.29       3      39 ..      34      77 ..      32      99 .. 0.66
   2 ?    1.5   0.1      0.48   3.8e+02      53      66 ..     146     160 ..     112     204 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00038
                                      EESSTTSSHHHHHHHHHHHH........THEEEEEETTTCSSSST CS
                               AAA  3 lyGppGtGKTllakavakel........gvefleisgsellskyv 39
                                      + Gp G GK++l+k +a  +        g ++ + s  el  k++
  gi|242399838|ref|YP_002995263.1| 34 ILGPNGAGKSTLMKCIAGIFrckeveifGEPLHRCSREELA-KII 77
                                      78***************997222222223445555555544.444 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.48
                                       HHHTS.TSEEEEEET CS
                               AAA  53 akeka.kpsilfiDE 66 
                                       a++ a +p il++DE
  gi|242399838|ref|YP_002995263.1| 146 ARALAqEPEILLMDE 160
                                       333334456666666 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   0.0     0.003       2.4       4      28 ..      34      59 ..      32      79 .. 0.80
   2 ?    4.2   0.0     0.052        41      19      57 ..     145     183 ..     143     228 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.003
                                      EE--SSSSHHHHHHHGGGGB.S--EE CS
                             AAA_5  4 LvGppGtgKselaerlaaal.nreve 28
                                      ++Gp G gKs+l++ +a  + ++eve
  gi|242399838|ref|YP_002995263.1| 34 ILGPNGAGKSTLMKCIAGIFrCKEVE 59
                                      79***************999644444 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.052
                                       GGGGBS--EEEEE--TT--HHHHH--B--.........- CS
                             AAA_5  19 laaalnreveyvqltrdtteedlkgrreikngttslvds 57 
                                       +a+al +e e+ ++ + t+  dlk ++e+++  +++ +s
  gi|242399838|ref|YP_002995263.1| 145 IARALAQEPEILLMDEPTNNLDLKSQMEVMKIARKFAES 183
                                       7999************************98666666554 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   8.9e-05      0.07      20      45 ..      27      50 ..      17      77 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.9e-05
                            AAA_16 20 rsgrpelvllsGesGvGKsslvrell 45
                                       +g  elv + G+ G GKs+l+++++
  gi|242399838|ref|YP_002995263.1| 27 EQG--ELVAILGPNGAGKSTLMKCIA 50
                                      444..89***************9987 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0    0.0002      0.16      35      72 ..      19      56 ..      15      80 .. 0.85
   2 ?   -0.3   0.0       1.1   8.7e+02     133     171 ..     153     191 ..     134     197 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0002
                             Rad17 35 lkadvLesrkkriLLisGPsGCgkstvvkvLskelgik 72
                                      l+  +Le ++ +++ i GP G gkst +k ++ ++  k
  gi|242399838|ref|YP_002995263.1| 19 LHDISLEVEQGELVAILGPNGAGKSTLMKCIAGIFRCK 56
                                      566789999999*****************999887665 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.1
                             Rad17 133 kklilvedlPnkfyrds.dalrevirkylrssealplilv 171
                                        +++l+++  n+    s   + ++ rk+  s+++ ++i++
  gi|242399838|ref|YP_002995263.1| 153 PEILLMDEPTNNLDLKSqMEVMKIARKFAESGKT-SIIIM 191
                                       4556666655777666546777888888888888.65553 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00028      0.22       2      21 ..      32      51 ..      31      80 .. 0.86
   2 ?    0.3   0.0      0.92   7.2e+02      43      82 ..     150     191 ..      85     214 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00028
                                      EEEEESTTSSHHHHHHHHHT CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltg 21
                                      vai+G   +GKStL++ + g
  gi|242399838|ref|YP_002995263.1| 32 VAILGPNGAGKSTLMKCIAG 51
                                      89*************99987 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.92
                                       ETTEEEEEEECGGCSS...HHHHHH.HHHHHHHHHHCTSEEEEE CS
                          MMR_HSR1  43 lkgkeielvDtpGlie...gaseek.glgkaflaleeadlillv 82 
                                        +++ei l+D p   +   +++ e  +++++f++  +   i+++
  gi|242399838|ref|YP_002995263.1| 150 AQEPEILLMDEPT-NNldlKSQMEVmKIARKFAESGK-TSIIIM 191
                                       3345666677666.22222223333466777776666.333333 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00015      0.12       2      24 ..      31      53 ..      30      74 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00015
                                      CEEEEC-TTTCHHHHHHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqklalaw 24
                                      lv++ G++G GK+tL++ +a   
  gi|242399838|ref|YP_002995263.1| 31 LVAILGPNGAGKSTLMKCIAGIF 53
                                      799**************998655 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00022      0.17       2      40 ..      32      74 ..      31      85 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00022
                            AAA_28  2 ivitGgestGKTtlleaLa...ar.gypvvpEaareileekla 40
                                      ++i+G+ ++GK+tl++ +a   +  +++++ E+  +  +e+la
  gi|242399838|ref|YP_002995263.1| 32 VAILGPNGAGKSTLMKCIAgifRCkEVEIFGEPLHRCSREELA 74
                                      89**************999554325888888888887777766 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0    0.0044       3.4       1      18 [.      32      49 ..      32      82 .. 0.87
   2 ?    2.8   0.0      0.21   1.6e+02      27      89 ..     145     201 ..     117     213 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0044
                            AAA_18  1 IlltGtpGvGKttlakeL 18
                                      +++ G+ G+GK+tl k +
  gi|242399838|ref|YP_002995263.1| 32 VAILGPNGAGKSTLMKCI 49
                                      689***********9865 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.21
                            AAA_18  27 nlrdvakenglllevdpealdeskrldedkldklldaleenssaleegknlvidghlaelese 89 
                                       + r +a+e ++ll+++p      + ld + +++++++ ++ ++ +++ + +++ ++   l+++
  gi|242399838|ref|YP_002995263.1| 145 IARALAQEPEILLMDEPT-----NNLDLKSQMEVMKIARKFAE-SGKTSIIIMHDVNLALRFA 201
                                       556667777777777666.....77888888888888888876.7777777877776655544 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.3    0.0004      0.31      19      41 ..      29      50 ..      15     191 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0004
                                      CSEEEEEEESTTSSHHHHHHHHC CS
                            NB-ARC 19 qslvvalvGmgGvGKttlakqil 41
                                      +  +va+ G  G GK+tl+k i 
  gi|242399838|ref|YP_002995263.1| 29 G-ELVAILGPNGAGKSTLMKCIA 50
                                      3.589**************9875 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00039       0.3       2      37 ..      32      64 ..      31      75 .. 0.79
   2 ?   -3.3   0.0       8.1   6.3e+03     147     165 ..     175     193 ..     165     205 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00039
                               PRK  2 IgvagsSGaGkttvarklekifgrekvkaaeiegds 37
                                      +++ g+ GaGk+t+++ +  if+ ++v+   i g  
  gi|242399838|ref|YP_002995263.1| 32 VAILGPNGAGKSTLMKCIAGIFRCKEVE---IFGEP 64
                                      7999*******************66655...55555 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 8.1
                               PRK 147 klqRDiaeRGrsleavlds 165
                                       k+ R  ae G++   +++ 
  gi|242399838|ref|YP_002995263.1| 175 KIARKFAESGKTSIIIMHD 193
                                       5555555555555544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); 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: 0.68u 0.34s 00:00:01.02 Elapsed: 00:00:00.53
# Mc/sec: 1433.32
//
Query:       gi|242399839|ref|YP_002995264.1|  [L=362]
Description: hypothetical protein TSIB_1866 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.8e-47  161.0   5.6    5.1e-47  160.5   5.6    1.2  1  VIT1          VIT family
     0.0011   19.4   3.0     0.0028   18.1   2.5    1.9  1  Rubrerythrin  Rubrerythrin
  ------ inclusion threshold ------
        1.5    9.1   6.5          1    9.7   0.6    3.2  4  DUF1269       Protein of unknown function (DUF1269)


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 !  160.5   5.6   8.5e-51   5.1e-47       1     215 []     146     351 ..     146     351 .. 0.97

  Alignments for each domain:
  == domain 1  score: 160.5 bits;  conditional E-value: 8.5e-51
                              VIT1   1 lrdavlGanDGLvspfalvaGlsaaslgssktvllaGlaellAGaiSMgiGeYlsvkserdlekaerkreeeeleed 77 
                                       +rd+vlG+nDGLv  ++ v Glsa+ ++++k+v ++Gl   +AGa+SMgiG+++sv+s+r++ ++ ++r e  ++ +
  gi|242399839|ref|YP_002995264.1| 146 IRDFVLGMNDGLVELLGAVTGLSAVYVHNPKIVGISGLIVGVAGALSMGIGAFISVRSQRQVNESVKERMEVLFRVS 222
                                       69*************************************************************************** PP

                              VIT1  78 peegeaeelaeilearglseelaqevaaellknpdallelmlreelgpsaseelasplkaAlssalsfliGgliPll 154
                                       p e+ + el e l + g++e+ a+eva++l++n++a+ +l+++ + +        + +++A+ ++l++l+G ++P+l
  gi|242399839|ref|YP_002995264.1| 223 P-ERAKGELMERLLESGMPEDVAREVAEKLSSNESAMINLLVQGGNE--------NEIRSAFYTGLAYLTGIIFPVL 290
                                       *.78889******************************9999996632........6789****************** PP

                              VIT1 155 pylfvesvglalvvsiavtllalllfGavkalltgssklvsalrmlliGalAaaaayligk 215
                                       py++++s  lal +si +++ al+++  v ++l+g s+++++++m++ G++Aa ++yl+gk
  gi|242399839|ref|YP_002995264.1| 291 PYFIASSSLLALPFSIFLAGTALAVVASVISILSGISVRKKIFEMVVTGLGAAFLSYLFGK 351
                                       **********************************************************985 PP

>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   2.5   4.6e-07    0.0028       9     133 ..      14     134 ..       3     138 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 4.6e-07
                                       HHHHHHHHHHHHHHCHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH..B.SSBBS-------TTGGHHHH CS
                      Rubrerythrin   9 gEssarrlYkelaekakegypqiaelFeelAeeEreHakilnklleklepele.levkekvreyaeakpkflttakn 84 
                                        E+++  lY +l++  k    +++  F++l+  E+ Hak+   +l+k+ ++ + +++    + ++++  k l   + 
  gi|242399839|ref|YP_002995264.1|  14 DEYKDSVLYASLSRDEK--DLKLRDEFLRLSHIESNHAKFWHGFLDKRGKKPKkIKIGRLSFFFVKMLRKLLGPGTV 88 
                                       699999*******9999..788****************************999555555555555555555555555 PP

                                       HHHHHHHHHHHHHCHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHHHH CS
                      Rubrerythrin  85 LeeaiegayaeeeemyrfyeelaekegneeakklfkklaeaEkkHeerl 133
                                       ++ ++  ++ e++ + + ++ l +    +e+++++ k++ +E +He ++
  gi|242399839|ref|YP_002995264.1|  89 VS-LL--EMGENSAIQKYFNFLTKYKLSDEEREVISKIIIDELEHEHFF 134
                                       55.33..333333333344444444457889***************999 PP

>> DUF1269  Protein of unknown function (DUF1269)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.1   6.7e+03      77      93 ..      15      31 ..       6      38 .. 0.73
   2 ?   -2.9   0.0       1.4   8.3e+03      75      94 ..     100     119 ..      75     124 .. 0.50
   3 ?    9.7   0.6   0.00017         1      28      74 ..     227     274 ..     160     283 .. 0.88
   4 ?   -3.1   0.2       1.7     1e+04      21      46 ..     310     334 ..     294     343 .. 0.54

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.1
                           DUF1269 77 klggkvlrtslskeeee 93
                                      +++  vl  sls++e++
  gi|242399839|ref|YP_002995264.1| 15 EYKDSVLYASLSRDEKD 31
                                      67788999999987764 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.4
                           DUF1269  75 laklggkvlrtslskeeeek 94 
                                       ++k+   + + +ls+ee+e 
  gi|242399839|ref|YP_002995264.1| 100 IQKYFNFLTKYKLSDEEREV 119
                                       33333334455566665555 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.00017
                           DUF1269  28 aGAlvgalsdvgidddflkelgeklkpgtsalf.llvekatvdkvlea 74 
                                        G l+ +l + g+ +d+ +e++ekl+ ++sa++ llv+  +++++ +a
  gi|242399839|ref|YP_002995264.1| 227 KGELMERLLESGMPEDVAREVAEKLSSNESAMInLLVQGGNENEIRSA 274
                                       57788889999********************98345555666666655 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 1.7
                           DUF1269  21 GaavGAaaGAlvgalsdvgidddflk 46 
                                       G+a+ A + ++ + ls +++++++ +
  gi|242399839|ref|YP_002995264.1| 310 GTAL-AVVASVISILSGISVRKKIFE 334
                                       3332.334445555556666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       894  (0.0498633); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); 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: 0.61u 0.34s 00:00:00.95 Elapsed: 00:00:00.51
# Mc/sec: 2132.55
//
Query:       gi|242399840|ref|YP_002995265.1|  [L=61]
Description: hypothetical protein TSIB_1867 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00059   19.7   0.0    0.00072   19.5   0.0    1.1  1  HTH_11           HTH domain
    0.00075   19.4   0.1     0.0012   18.7   0.1    1.2  1  TBPIP            TBPIP/Hop2 winged helix domain
    0.00088   19.1   0.0    0.00093   19.0   0.0    1.1  1  TrmB             Sugar-specific transcriptional regulator Trm
     0.0018   18.6   0.1     0.0023   18.3   0.1    1.3  1  HARE-HTH         HB1, ASXL, restriction endonuclease HTH doma
     0.0019   18.5   0.0     0.0022   18.3   0.0    1.1  1  Rrf2             Transcriptional regulator
      0.007   16.0   0.0     0.0077   15.9   0.0    1.1  1  SMC_ScpB         Segregation and condensation complex subunit
     0.0089   16.1   0.1     0.0097   15.9   0.1    1.1  1  z-alpha          Adenosine deaminase z-alpha domain
  ------ inclusion threshold ------
      0.015   15.3   0.3      0.018   15.1   0.3    1.2  1  Phage_terminase  Phage terminase small subunit
      0.021   15.2   0.0      0.025   14.9   0.0    1.1  1  FaeA             FaeA-like protein
      0.027   13.8   0.1      0.029   13.8   0.1    1.0  1  RNA_pol_Rpc34    RNA polymerase Rpc34 subunit
      0.051   13.2   0.1      0.068   12.8   0.1    1.3  1  HTH_24           Winged helix-turn-helix DNA-binding
      0.066   13.2   0.1      0.085   12.8   0.1    1.2  1  HTH_36           Helix-turn-helix domain
      0.095   13.0   0.0       0.11   12.9   0.0    1.1  1  TFIIE_beta       TFIIE beta subunit core domain
      0.099   12.1   0.0       0.11   12.0   0.0    1.0  1  DUF2336          Uncharacterised protein conserved in bacteri
       0.11   13.1   0.0       0.13   12.9   0.0    1.2  1  Phage_pRha       Phage regulatory protein Rha (Phage_pRha)
       0.11   12.2   0.0       0.12   12.0   0.0    1.1  1  GntR             Bacterial regulatory proteins, gntR family
       0.13   12.1   0.0       0.17   11.8   0.0    1.2  1  HTH_5            Bacterial regulatory protein, arsR family
       0.15   12.0   0.0       0.17   11.8   0.0    1.1  1  MarR_2           MarR family
       0.16   12.0   0.0       0.19   11.8   0.0    1.2  1  HTH_20           Helix-turn-helix domain
       0.21   11.6   0.0       0.23   11.5   0.0    1.2  1  HTH_Crp_2        Crp-like helix-turn-helix 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 !   19.5   0.0     8e-07   0.00072       7      48 ..      11      51 ..       6      57 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 8e-07
                            HTH_11  7 elLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvpIes 48
                                      + L+e+ +p+ ++e+Ae  ++ ++ v + Ik L++ g +I+s
  gi|242399840|ref|YP_002995265.1| 11 KVLKESGKPLKSAEIAEIAGIDKKEVDKAIKNLKKGG-KIIS 51
                                      679999999****************************.6665 PP

>> TBPIP  TBPIP/Hop2 winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   1.3e-06    0.0012       3      50 ..       6      51 ..       5      53 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.3e-06
                             TBPIP  3 eelvleylqeqnrPfsvqdvvanlqkklgKtavqkaLdeLvdegkiie 50
                                      ee+v++ l+e+ +P+ + ++++    ++ K+ v ka+ +L++ gkii+
  gi|242399840|ref|YP_002995265.1|  6 EEIVFKVLKESGKPLKSAEIAEI--AGIDKKEVDKAIKNLKKGGKIIS 51
                                      89******************986..58*******************96 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0     1e-06   0.00093      13      53 ..       9      50 ..       3      60 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1e-06
                                      HCHHHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEE CS
                              TrmB 13 vYlaLl.klgpatadeiaeelgvprskvYevLrsLedkGlVe 53
                                      v+++L  + +p++  eiae++g+++  v +++++L++ G + 
  gi|242399840|ref|YP_002995265.1|  9 VFKVLKeSGKPLKSAEIAEIAGIDKKEVDKAIKNLKKGGKII 50
                                      5555554456899***********************999765 PP

>> HARE-HTH  HB1, ASXL, restriction endonuclease HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1   2.5e-06    0.0023       5      27 ..       7      29 ..       3      45 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.5e-06
                                      HHHHHHHHHH-S-EEHHHHHHHH CS
                          HARE-HTH  5 eaAkqVLeeegrpltvkeIweki 27
                                      e+ ++VL+e+g+pl+  eI+e++
  gi|242399840|ref|YP_002995265.1|  7 EIVFKVLKESGKPLKSAEIAEIA 29
                                      6789*****************97 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   2.4e-06    0.0022      20      57 ..      14      51 ..       5      53 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.4e-06
                                      SSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              Rrf2 20 eeeeepvsseeiaerqnispsylekilakLrkaglvks 57
                                      +e+++p++s+eiae  +i ++ + k +++L+k g + s
  gi|242399840|ref|YP_002995265.1| 14 KESGKPLKSAEIAEIAGIDKKEVDKAIKNLKKGGKIIS 51
                                      556678**************************998866 PP

>> SMC_ScpB  Segregation and condensation complex subunit ScpB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   8.6e-06    0.0077       6      39 ..      12      45 ..       7      49 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 8.6e-06
                          SMC_ScpB  6 iLfvageplsleeLakilelskeeveealeeLke 39
                                      +L  +g+pl+++e+a+i++++k+ev++a+++Lk+
  gi|242399840|ref|YP_002995265.1| 12 VLKESGKPLKSAEIAEIAGIDKKEVDKAIKNLKK 45
                                      566689**************************97 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 !   15.9   0.1   1.1e-05    0.0097       5      52 ..       5      50 ..       1      54 [. 0.87

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.1e-05
                                      HHHHHHHHHHHC-TTCECCHHHHHHHHCC-HHHHHHHHHHHHHTTSEE CS
                           z-alpha  5 qaekilelLeelgekkaatalalergLstpkreiNrvLydlerkgkvy 52
                                       +e++ ++L+e+g      ++a   g+   k+e+ ++  +l++ gk+ 
  gi|242399840|ref|YP_002995265.1|  5 SEEIVFKVLKESGKPLKSAEIAEIAGID--KKEVDKAIKNLKKGGKII 50
                                      689**********777778888888888..9*************9986 PP

>> Phage_terminase  Phage terminase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.3     2e-05     0.018      13      41 ..      10      38 ..       6      54 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2e-05
                   Phage_terminase 13 yelykEsggtlklkdIAkvLdvsestvrk 41
                                      +++ kEsg+ lk  +IA++ ++ ++ v k
  gi|242399840|ref|YP_002995265.1| 10 FKVLKESGKPLKSAEIAEIAGIDKKEVDK 38
                                      7899********************99974 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   2.8e-05     0.025       1      45 [.       4      49 ..       4      54 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.8e-05
                                      -HHHHH.HHHHH.S----HHHHHHHHTS-HHHHHHHHHHHHHHSSE CS
                              FaeA  1 mkeeIl.eylnsikapckTreiAdalglsaYQaRyYLeqLekegki 45
                                      m+eeI+ + l++ + p k +eiA+ +g+    +   +++L+k gki
  gi|242399840|ref|YP_002995265.1|  4 MSEEIVfKVLKESGKPLKSAEIAEIAGIDKKEVDKAIKNLKKGGKI 49
                                      777775367888899*****************************98 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 ?   13.8   0.1   3.2e-05     0.029      86     136 ..       4      53 ..       1      60 [. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.2e-05
                                       HHHHHHHHHHHHHXSSXEEHHHHHHTTGXXHHHHHHHHHHHHHTTXXEEEE CS
                     RNA_pol_Rpc34  86 edeslVysiIeesGneGIwsrtiksklnLhksvvkkcLksLeskkyiksvk 136
                                        +e++V+++ +esG+    s++i +  ++ k++v+k +k+L + + i s k
  gi|242399840|ref|YP_002995265.1|   4 MSEEIVFKVLKESGKP-LKSAEIAEIAGIDKKEVDKAIKNLKKGGKIISPK 53 
                                       5799**********75.9************************999887755 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   7.5e-05     0.068      12      47 ..      13      49 ..       6      50 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.5e-05
                            HTH_24 12 Lqknpr.isqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      L++ ++ +  +e+Ae  g+ +  v + +k+L++ G I
  gi|242399840|ref|YP_002995265.1| 13 LKESGKpLKSAEIAEIAGIDKKEVDKAIKNLKKGGKI 49
                                      55555557889***********************988 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   9.4e-05     0.085      29      51 ..      23      45 ..      19      49 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.4e-05
                            HTH_36 29 etlakrlglsknTvsraikeLeq 51
                                      + +a+  g++k+ v +aik+L +
  gi|242399840|ref|YP_002995265.1| 23 AEIAEIAGIDKKEVDKAIKNLKK 45
                                      579******************87 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 ?   12.9   0.0   0.00012      0.11      11      52 ..      12      50 ..       8      59 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00012
                        TFIIE_beta 11 ylKkkdgplsleeIlsylslqldlsdknwllleaLknnpkie 52
                                       lK+ ++pl+  eI++   +  d  ++  + ++ Lk+  ki 
  gi|242399840|ref|YP_002995265.1| 12 VLKESGKPLKSAEIAEIAGI--DK-KEVDKAIKNLKKGGKII 50
                                      59*****************9..87.55668899999999985 PP

>> DUF2336  Uncharacterised protein conserved in bacteria (DUF2336)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00012      0.11     159     199 ..       2      42 ..       1      47 [. 0.93

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00012
                           DUF2336 159 grltealllralkagdlaffaaaLaelsglpaervrrilad 199
                                       g ++e+ +++ lk+   ++  a++ae +g++ ++v++++++
  gi|242399840|ref|YP_002995265.1|   2 GTMSEEIVFKVLKESGKPLKSAEIAEIAGIDKKEVDKAIKN 42 
                                       77999*********************************986 PP

>> Phage_pRha  Phage regulatory protein Rha (Phage_pRha)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00014      0.13       2      26 ..      21      45 ..      20      57 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00014
                        Phage_pRha  2 sSleiAelfgkrHknVlrdIrklie 26
                                      +S eiAe  g++ k+V ++I++l++
  gi|242399840|ref|YP_002995265.1| 21 KSAEIAEIAGIDKKEVDKAIKNLKK 45
                                      699*******************955 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00014      0.12      20      56 ..      16      51 ..       5      54 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00014
                                      TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              GntR 20 pGdkLPsereLaaefgVsrttvReALrrLeaeglver 56
                                       G +L +  e+a+  g+++  v +A+++L+  g +++
  gi|242399840|ref|YP_002995265.1| 16 SGKPL-KSAEIAEIAGIDKKEVDKAIKNLKKGGKIIS 51
                                      69999.9***********************9998765 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00019      0.17       8      43 ..       9      47 ..       7      51 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00019
                                      HHHHTT...SSEEHHHHHHHHTS-HHHHHHHHHHHHHTT CS
                             HTH_5  8 LklLae...gelcvcelaeelglsqstvShHLkkLreaG 43
                                      ++ + +   ++l++ e+ae+ g+ +  v+   k L++ G
  gi|242399840|ref|YP_002995265.1|  9 VFKVLKesgKPLKSAEIAEIAGIDKKEVDKAIKNLKKGG 47
                                      55555558789*****************99999998865 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00019      0.17      14      49 ..      13      47 ..       3      51 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00019
                                      HHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTT CS
                            MarR_2 14 LgrrpgrdltvgelarrlglsksavsrilkrLvaaG 49
                                      L  ++ + l  +e+a+  g++k  v +++k L + G
  gi|242399840|ref|YP_002995265.1| 13 LKESGKP-LKSAEIAEIAGIDKKEVDKAIKNLKKGG 47
                                      5555554.999*********************9987 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00022      0.19      20      52 ..      15      47 ..       7      54 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00022
                                      STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCT CS
                            HTH_20 20 araegltaselaerldlskntlsyHLrvLeeag 52
                                       ++++l  +e+ae  +++k+++++ ++ L + g
  gi|242399840|ref|YP_002995265.1| 15 ESGKPLKSAEIAEIAGIDKKEVDKAIKNLKKGG 47
                                      57899999*********************9965 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 ?   11.5   0.0   0.00025      0.23      21      51 ..      19      49 ..       4      57 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00025
                                      EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSE CS
                         HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkregli 51
                                      pl  +e+A++ G+    v ++++ Lk+ g i
  gi|242399840|ref|YP_002995265.1| 19 PLKSAEIAEIAGIDKKEVDKAIKNLKKGGKI 49
                                      88999*********************99866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       980  (0.05466); expected 358.6 (0.02)
Passed bias filter:                      784  (0.043728); expected 358.6 (0.02)
Passed Vit filter:                       107  (0.00596798); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.53u 0.37s 00:00:00.90 Elapsed: 00:00:00.54
# Mc/sec: 340.43
//
Query:       gi|242399841|ref|YP_002995266.1|  [L=506]
Description: non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase (GAPN) [Thermococcus sibiricus MM 739]
Scores for 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-119  396.9   0.0   1.1e-118  396.7   0.0    1.0  1  Aldedh    Aldehyde dehydrogenase family
    0.00067   18.8   0.0     0.0014   17.8   0.0    1.4  1  LuxC      Acyl-CoA reductase (LuxC)


Domain annotation for each model (and alignments):
>> Aldedh  Aldehyde dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  396.7   0.0  1.2e-122  1.1e-118       9     462 .]      39     493 ..      32     493 .. 0.96

  Alignments for each domain:
  == domain 1  score: 396.7 bits;  conditional E-value: 1.2e-122
                                       EEEEETTTCEEEEEEE-B-HHHHHHHHHHHHH.HHHHHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHHHHHH---HH CS
                            Aldedh   9 ievinPatgeviakvpaataedvdaavaaAke.afkawaklpaeeRaeiLrkaadlleerkeelaeletletGkpla 84 
                                        ev +P++g++ia+v++ ++++v++a+a+  e   ++ ++ p e+R + + kaa l++e  e++++++ l++Gkp +
  gi|242399841|ref|YP_002995266.1|  39 SEVKSPIDGRIIARVSRLSRDQVEEALARVYEkGREEIRNYPGEKRVQSFLKAAGLMREAFEDFVNVLILDAGKPKS 115
                                       6899*************************99845669**************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHSEEEEEEC.....TTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHHHHTT-E CS
                            Aldedh  85 earaeveeaidvlryyaelaeklegevlpss.....egklalvrrePlGvvgaItPWNfPlllaawklapalaaGNt 156
                                       +a +e + +i+ l+ ++ + +++ g+ +p +      +++ +v+reP+G ++aI+P+N+Pl+++a k++pal+ GNt
  gi|242399841|ref|YP_002995266.1| 116 NAVGETKATIERLEKTTFESRRMLGDYVPGDwseetLESEGIVKREPYGLILAISPFNYPLFISAAKVVPALLSGNT 192
                                       ***************************999766666677889*********************************** PP

                                       EEEEE-TTSHHHHHHHHHHHHHTTS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHHCTTSEEE CS
                            Aldedh 157 vvlKPaeetplsalllaelfeeaglPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaaknlkrvt 233
                                       v+lKPa+  pl a+++++++e ag+Pk+ + ++t +gs + + +v+++++++++ftGstevg++i ++ +  +k  +
  gi|242399841|ref|YP_002995266.1| 193 VLLKPASADPLAAIMFVRVLELAGFPKESFALLTIPGS-FMDDVVKDRRIRAITFTGSTEVGEHIIRTGG--IKAYH 266
                                       ***********************************886.9999************************999..9**** PP

                                       EEE---EEEEE-TTSHHHHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-T.TSTT-SB- CS
                            Aldedh 234 lElGGknplivledaDldkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdp.ldedtdvG 309
                                       lElGGk+p+ivl+da+l+ a e+ivkg+++++GQ+C a++ +l qe+iy+++ ++++e++k ++  +p +de+  +G
  gi|242399841|ref|YP_002995266.1| 267 LELGGKDPAIVLDDANLELASEKIVKGMVSFSGQRCDAIRLILAQEKIYEDLKARILEKLKGMEPRNPlEDENAVMG 343
                                       ********************************************************************77889**** PP

                                       --SSHHHHHHHHHHHHHHHHTTSEEEE-TTE.SB-SSSTTEE--EEEES-TT...TSHHHHS---SSEEEEEEESSH CS
                            Aldedh 310 PliseaqlekvekyveeakeegaklllGgereeaglekgyfvePtvlanvtp...dmriaqeEiFGPVlsvikfkde 383
                                       Pli+e+++e +e++ ++a+e+ga+ l++       ++kg++v P +l+  ++   d r ++e++FG  + +ik+kde
  gi|242399841|ref|YP_002995266.1| 344 PLIDESSAEYIEEVYKDAVEKGARPLTEF------RRKGNYVWPILLEVSKEkikDLRAFNEDVFGSMALLIKVKDE 414
                                       ***************************87......68**********98875222679******************* PP

                                       HHHHHHHHSSSEESEEEEE-SBHHHHHHHHHHS-SSEEEESSSST--TTTSEB--CGGGEES-BSHHHHHHHTEEEE CS
                            Aldedh 384 eeaieiaNdteyGLaagvftkdleraervaerleaGnvyiNdsttgaaealpfgGvkqSglGreggkegleeytevk 460
                                       +eaieia ++++GL a+vf++ ++ra++va++le+G+v iN++ ++ +   pfgG+k+Sg+Greg  +++e++t++k
  gi|242399841|ref|YP_002995266.1| 415 DEAIEIAKSSRFGLDASVFSECERRARKVARKLEVGSVFINEYPRHGIGYYPFGGMKDSGVGREGIGYSVEQFTTTK 491
                                       ***************************************************************************** PP

                                       EE CS
                            Aldedh 461 tv 462
                                       t+
  gi|242399841|ref|YP_002995266.1| 492 TI 493
                                       96 PP

>> LuxC  Acyl-CoA reductase (LuxC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   1.5e-07    0.0014      57     138 ..     123     212 ..     114     224 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.5e-07
                              LuxC  57 eeLkkvleseLgqpeiLdefl....ktke.....ksyekaqprglvlhvlsgNvpllp.vmsilqglLvknvnllkv 123
                                         ++++ +  ++++++L +++       e     ++  k+ p gl+l + + N pl +    ++ +lL++n  llk+
  gi|242399841|ref|YP_002995266.1| 123 ATIERLEKTTFESRRMLGDYVpgdwS--EetlesEGIVKREPYGLILAISPFNYPLFIsAAKVVPALLSGNTVLLKP 197
                                       56677777788999999888844431..0235568999*****************976156799************* PP

                              LuxC 124 Sssdpflaaallksl 138
                                        s dp +a+ +++ l
  gi|242399841|ref|YP_002995266.1| 198 ASADPLAAIMFVRVL 212
                                       *********999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (506 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.67u 0.33s 00:00:01.00 Elapsed: 00:00:00.52
# Mc/sec: 2925.42
//
Query:       gi|242399842|ref|YP_002995267.1|  [L=372]
Description: Phosphoribosylaminoimidazole carboxylase ATPase subunit [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-51  174.7   0.0    1.9e-51  174.1   0.0    1.3  1  ATP-grasp        ATP-grasp domain
    1.8e-16   59.5   0.5    3.8e-16   58.5   0.1    1.8  2  PurK_C           Phosphoribosylaminoimidazole carboxylase C-t
    1.6e-10   41.3   0.1    2.9e-10   40.4   0.1    1.4  1  ATP-grasp_3      ATP-grasp domain
    1.8e-08   34.2   0.1    1.2e-07   31.5   0.1    2.1  1  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
    1.1e-06   28.3   0.6    3.5e-06   26.7   0.6    1.8  1  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
      2e-05   24.3   0.3    6.5e-05   22.6   0.3    1.8  1  RimK             RimK-like ATP-grasp domain
    0.00069   19.0   0.0      0.083   12.1   0.0    2.2  2  ATPgrasp_ST      Sugar-transfer associated ATP-grasp
  ------ inclusion threshold ------
       0.11   13.1   0.0        0.3   11.6   0.0    1.8  1  XdhC_C           XdhC Rossmann domain
       0.11   12.7   0.1       0.22   11.8   0.1    1.5  1  PRODH            Proline utilization A proline dehydrogenase 
       0.12   12.8   0.1        4.3    7.7   0.0    2.5  2  Radical_SAM      Radical SAM superfamily
       0.12   11.6   0.0       0.27   10.4   0.0    1.5  1  ATPgrasp_YheCD   YheC/D like ATP-grasp
       0.42   11.2   2.5        5.3    7.7   0.1    3.4  4  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas


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 !  174.1   0.0   1.2e-54   1.9e-51       2     171 .]     107     272 ..     106     272 .. 0.95

  Alignments for each domain:
  == domain 1  score: 174.1 bits;  conditional E-value: 1.2e-54
                                       HTTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHCGTTCEEEEE----SEEE CS
                         ATP-grasp   2 eklglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqalealkeekvivEefvpfekEl 78 
                                       +k+g+p+p+f+ ++++ el e a e+g+p+v K+rr+gydGkG  v+r e++l+++l +      ++ efv+ ekE+
  gi|242399842|ref|YP_002995267.1| 107 KKAGVPIPKFIRADRD-ELTEKAIEFGVPLVQKTRRGGYDGKGVAVIRTEKELDKLLPTD----SMLQEFVEIEKEI 178
                                       789*********9988.77777799****************************9998766....899********** PP

                                       EEEEEEETTC-EEE--EEEEE.EETTEEEEEEECEE-SCHHHHHHHHHHHHHHHHHTSSEEEEEEEEEETTCTEEEE CS
                         ATP-grasp  79 svlvvrsaeGetafypvvetv.qedgilrlsvapaevsekaqkkaeeiakkiveeLggvGvfavElFvledgellvn 154
                                       +v+v+r+++G++++ypvve v +e +il   vapa+++e+++++a++ia k+ve+L+gvG+f++E+F+ +dg++l+n
  gi|242399842|ref|YP_002995267.1| 179 AVMVARDQDGNIEVYPVVEMVfNEANILDFLVAPARIDEDIAREAQDIAVKVVEALDGVGIFGIEMFLSKDGTVLLN 255
                                       *******************864789**************************************************** PP

                                       EEESS--GGGGGHHHHB CS
                         ATP-grasp 155 ElapRpHnsGhvtldaa 171
                                       E+apRpHnsGh+t++a+
  gi|242399842|ref|YP_002995267.1| 256 EVAPRPHNSGHYTIEAC 272
                                       ***************98 PP

>> PurK_C  Phosphoribosylaminoimidazole carboxylase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       4.1   6.1e+03      31      41 ..      12      22 ..      11      27 .. 0.83
   2 !   58.5   0.1   2.5e-19   3.8e-16       1      53 [.     298     354 ..     298     357 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 4.1
                            PurK_C 31 KeearpgRKmG 41
                                      K  a++ RK+G
  gi|242399842|ref|YP_002995267.1| 12 KMMAQEARKLG 22
                                      5667889**99 PP

  == domain 2  score: 58.5 bits;  conditional E-value: 2.5e-19
                            PurK_C   1 avMvNlLGedae....ekleellaipgahlHlYgKeearpgRKmGHitvvgdsaeel 53 
                                       avM N+LGe        +++e+l +pg+++H+YgK  +rp RKmGH+tvv ++  ++
  gi|242399842|ref|YP_002995267.1| 298 AVMFNVLGEGYGrpkvLGMKEALRYPGVYVHIYGKPVVRPLRKMGHVTVVNKDLGKA 354
                                       8********998887778888******************************998766 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4   0.1   1.9e-13   2.9e-10       1     159 [.      96     262 ..      96     264 .. 0.78

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 1.9e-13
                                       HTSHHHHHHHHTTT.S---.........-EESS--....SSSEEEEESS-.------B--SS--TTE.......EEE CS
                       ATP-grasp_3   1 asdKlktykkLkeagvkvP.....tkleaeeleee....ekklvvKprdG.aggesvrvveekeeaeaaieevelvq 67 
                                       ++dKl  ++ +k+agv++P     +    +el+e+      +lv K r+G  +g++v v++ ++e+++ +++++++q
  gi|242399842|ref|YP_002995267.1|  96 IQDKLVQMETMKKAGVPIPkfiraD---RDELTEKaiefGVPLVQKTRRGgYDGKGVAVIRTEKELDKLLPTDSMLQ 169
                                       57*****************885552...33333334445889****9886269************************ PP

                                       E---S.EEEEEEEEE.SSSEEEEEEEEEEEET....TEEEEEEES----H..HHHHHHHHHHHHTTSTT--EEEEEE CS
                       ATP-grasp_3  68 efieG.kplSvsllsdgekvlvlavnrqliekaekefvyaGnvtpietel..keevvelaeevvekleglaGyvGvD 141
                                       ef+e  k++ v +  d+  +  +    +++ ++   ++    v+p++ ++  ++e++++a +vve+l + +G++G++
  gi|242399842|ref|YP_002995267.1| 170 EFVEIeKEIAVMVARDQDGNIEVYPVVEMVFNEA--NILDFLVAPARIDEdiAREAQDIAVKVVEAL-DGVGIFGIE 243
                                       ****625788888888887777776666665533..44555566666655559**************.999****** PP

                                       EEESS.SEEEE.EEESS-- CS
                       ATP-grasp_3 142 lvlkdeepyvi.EvNPRlt 159
                                       + l++++ +++ Ev PR+ 
  gi|242399842|ref|YP_002995267.1| 244 MFLSKDGTVLLnEVAPRPH 262
                                       9999977776659****86 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 !   31.5   0.1   7.7e-11   1.2e-07       2     176 ..     106     261 ..     105     266 .. 0.88

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 7.7e-11
                                       HHHTT--B--EEEEETTHHCH-H-HHHHHHHHHC-SSEEEEESSSST.TTTEEEESSGGGHHHHHHHHHTT-SCEEE CS
                   Dala_Dala_lig_C   2 lkaaGlpvvpyvvlekeeakeekkellekveeelgypvfVKpareGS.SvGvskveseeelkeaieeafkydekvlv 77 
                                       +k+aG+p+++++  +++e +e+          e+g p++ K  r G    Gv+ +++e+el + + +  +  e v +
  gi|242399842|ref|YP_002995267.1| 106 MKKAGVPIPKFIRADRDELTEKA--------IEFGVPLVQKTRRGGYdGKGVAVIRTEKELDKLLPTDSMLQEFVEI 174
                                       68999999999999999998888........789********99996268****************99999999999 PP

                                       EE--ESEEEEEEEEE..TSSCEEEEEEEEE-SS.SSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT- CS
                   Dala_Dala_lig_C  78 Eeaiegreievavlg..neklevsevgeivvkk.gfydyeakysddkaqlevpaklekeveekiqelalkaykaldl 151
                                       E+ i      v v    +++ ev +v+e+v ++ ++ d+          l+ pa+++++++++ q++a+k+ +ald+
  gi|242399842|ref|YP_002995267.1| 175 EKEI-----AVMVARdqDGNIEVYPVVEMVFNEaNILDF----------LVAPARIDEDIAREAQDIAVKVVEALDG 236
                                       9755.....555554338889999999999877466665..........689************************* PP

                                       -SEEEEEEEEETTTEEEEEEEESS- CS
                   Dala_Dala_lig_C 152 rGlaRvDfflteegeivlnEvNtlP 176
                                        G+  + +fl+++g+++lnEv + P
  gi|242399842|ref|YP_002995267.1| 237 VGIFGIEMFLSKDGTVLLNEVAPRP 261
                                       *********************8877 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 !   26.7   0.6   2.4e-09   3.5e-06       1     180 [.      98     261 ..      98     290 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 2.4e-09
                                       SHHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCC.TTTTEEEESSHHHHHHHHHHHHHHHHH CS
                       CPSase_L_D2   1 DkesakealkkinvpvvpssaapvetleealaiakeigyPviikaafgl.GGkGmrvarneeelaelvkkalaeaka 76 
                                       Dk    e++kk++vp+ +   a   + +e ++ a e+g+P + k+  g+  GkG  v+r+e+el +l+ +    +  
  gi|242399842|ref|YP_002995267.1|  98 DKLVQMETMKKAGVPIPKFIRA---DRDELTEKAIEFGVPLVQKTRRGGyDGKGVAVIRTEKELDKLLPTD---S-- 166
                                       67778899*******9887777...99**************9998765438**************998643...3.. PP

                                       HHSTS-EEEEE--SSSEEEEEEEEEETTS-EEEEEEEEECCECTCCCCEEEES-SS--HHHHHHHHHHHHHHHHHHT CS
                       CPSase_L_D2  77 afgnkqvlvekslkgpkeiEvevlrDakgnvitvcerenslqlrtqkvievAPsqtLtdeerqalreaavkvvrevg 153
                                              +++++++  kei v v rD++gn+ +    e + +  +     vAP++ ++++  ++ +  avkvv++++
  gi|242399842|ref|YP_002995267.1| 167 -------MLQEFVEIEKEIAVMVARDQDGNIEVYPVVEMVFNEANILDFLVAPAR-IDEDIAREAQDIAVKVVEALD 235
                                       .......467899999***************99999999999988878889**98.67777778899********** PP

                                       -EEEEEEEEEEETTTTEEEEEEEESS- CS
                       CPSase_L_D2 154 vvgagtveflldpkskeyyviEvNtRl 180
                                        vg   +e  l++ ++   + Ev +R 
  gi|242399842|ref|YP_002995267.1| 236 GVGIFGIEMFLSK-DGTVLLNEVAPRP 261
                                       *********9997.9999999999985 PP

>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.3   4.4e-08   6.5e-05       2     164 ..      97     258 ..      96     276 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 4.4e-08
                                       H-HHHHHHHHHHTT-----EEEESS-S-HHHHHHTT-.-SSEEEEE-TT.TT--EEEEE-SHHHHHHHHHHGGG--E CS
                              RimK   2 rdKlkslklLakakikvpntalardeedaekliekiklrfPvvvKsveg.sqGikvvlakkeqklkqvlealkeail 77 
                                       +dKl  ++ + ka++++p++  a  +e +ek ie   +++P+v K+  g   G +v + ++e++l ++   l +  +
  gi|242399842|ref|YP_002995267.1|  97 QDKLVQMETMKKAGVPIPKFIRADRDELTEKAIE---FGVPLVQKTRRGgYDGKGVAVIRTEKELDKL---LPTDSM 167
                                       699999**************99999999999887...789******987256****************...777778 PP

                                       EEEE--SS-SEEEEEEEETT.....EEEEEEEEE--SSS----TTTT-EEEE----HHHHHHHHHHHHHCT.-SEEE CS
                              RimK  78 vqeyieeaenediRvlvvdd.....evvaalrrvskeGdFRsnlhrGgvaeklqlseeekelAikaakame.lvvaG 148
                                       +qe++e +++  i v+v  d     ev   ++ v +e +    l   +  +  ++  e +++A+k+ +a++ + + G
  gi|242399842|ref|YP_002995267.1| 168 LQEFVEIEKE--IAVMVARDqdgniEVYPVVEMVFNEANILDFLVAPARID-EDIAREAQDIAVKVVEALDgVGIFG 241
                                       9*****9876..555666551133347777777777765555555555544.47889999******9998626799* PP

                                       EEEEEETTEEEEE.EEE CS
                              RimK 149 vDllrakrgllvl.Evn 164
                                       ++++ +k+g ++l Ev 
  gi|242399842|ref|YP_002995267.1| 242 IEMFLSKDGTVLLnEVA 258
                                       **888888766542665 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 !   12.1   0.0   5.5e-05     0.083      10      87 ..      87     160 ..      80     205 .. 0.77
   2 !    4.7   0.0      0.01        15     227     265 ..     222     260 ..     218     278 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.5e-05
                       ATPgrasp_ST  10 yNpraefplvddKlkfkelalraglkvpkllgvikeqaeiseleafvkeleegvviKpak.gsgGkGilviteredq 85 
                                       y + + +++++dKl+  e +++ag+++pk        a+++el +  +e+   +v K+ + g  GkG+ vi  +++ 
  gi|242399842|ref|YP_002995267.1|  87 YPSPKILEIIQDKLVQMETMKKAGVPIPK-----FIRADRDELTEKAIEFGVPLVQKTRRgGYDGKGVAVIRTEKEL 158
                                       55677899******999999*********.....345788888888888855589998762689*******775554 PP

                       ATPgrasp_ST  86 dy 87 
                                       d+
  gi|242399842|ref|YP_002995267.1| 159 DK 160
                                       44 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.01
                       ATPgrasp_ST 227 evlelaakaaeklpglgylGwDivldeekgplllElNar 265
                                       e+ ++a+k+ e l g+g++G+ + l +++ +ll E+  r
  gi|242399842|ref|YP_002995267.1| 222 EAQDIAVKVVEALDGVGIFGIEMFLSKDGTVLLNEVAPR 260
                                       66789************************8888887655 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0    0.0002       0.3       3      32 ..       4      33 ..       2      87 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0002
                                      EE--STTHHHHHHHHHHHTEEEEEEES-GG CS
                            XdhC_C  3 ifGaghvaqalarlaaalgfrvtvvdpree 32
                                      i+G+g+ a+ +a+ a++lgf + v+dp+e+
  gi|242399842|ref|YP_002995267.1|  4 IIGGGQLAKMMAQEARKLGFGIAVLDPQEK 33
                                      99*************************986 PP

>> PRODH  Proline utilization A proline dehydrogenase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00015      0.22      14      47 ..     201     234 ..     198     234 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00015
                             PRODH  14 pEaecVapLleaArlpeaeraairalArkLveal 47 
                                        Ea ++  L++ Ar++e+ ++++++ A k veal
  gi|242399842|ref|YP_002995267.1| 201 NEANILDFLVAPARIDEDIAREAQDIAVKVVEAL 234
                                       59999***************************98 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0029       4.3      85     128 ..      45      97 ..      38     134 .. 0.74
   2 ?    2.4   0.0      0.12   1.8e+02      31      96 ..     216     283 ..     210     303 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0029
                                       CSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHH..........H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx..........x RF
                       Radical_SAM  85 ngtlpdeeklerllelgvdrvslgleaaddekvlklmn.rghtf..........e 128
                                        g   d ek++ l+e   d+++ ++e+++ e vlk ++  g+ +          +
  gi|242399842|ref|YP_002995267.1|  45 TGSFMDGEKIRNLAEIS-DVLTYDIEHINVE-VLKELEeEGYPVypspkileiiQ 97 
                                       4555569********99.*************.99988644443355544444444 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.12
                                       HHHHHHHHHHHH.HHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHH CS
                                       xxxxxxxxxxxx.xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  31 veeileevkelk.aekg.vkevilgggepllypdfvellerlaklavpgiritvetngtlpdeekler 96 
                                        e+i++e++ ++ +     ++v ++g e +l +d ++ll + a + ++  + t+e++ t   e ++++
  gi|242399842|ref|YP_002995267.1| 216 DEDIAREAQDIAvKVVEaLDGVGIFGIEMFLSKDGTVLLNEVAPRPHNSGHYTIEACMTSQFEQHIRA 283
                                       5899999999986555569999999**************99999987777777777766644555555 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 ?   10.4   0.0   0.00018      0.27     181     234 ..     214     267 ..     196     284 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00018
                    ATPgrasp_YheCD 181 kileeleelalelaealeesfgrlgElGlDlgidkegkvWllEvNskpgrsifk 234
                                       +i e++ + a+++a  + e++ ++g +G+ + + k+g v l Ev  +p++s   
  gi|242399842|ref|YP_002995267.1| 214 RIDEDIAREAQDIAVKVVEALDGVGIFGIEMFLSKDGTVLLNEVAPRPHNSGHY 267
                                       45555566666666666666668*************************998765 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.1    0.0036       5.3       2      30 ..       2      30 ..       1      40 [. 0.86
   2 ?    1.4   0.0      0.32   4.8e+02      42      70 ..      71      99 ..      57     109 .. 0.78
   3 ?   -3.0   0.0       7.7   1.2e+04      17      33 ..     170     186 ..     167     191 .. 0.78
   4 ?   -3.0   0.0       7.8   1.2e+04      55      65 ..     344     354 ..     331     365 .. 0.48

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0036
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEES CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvver 30
                                      + ++GgG ++ ++A+++++lg  + v++ 
  gi|242399842|ref|YP_002995267.1|  2 IGIIGGGQLAKMMAQEARKLGFGIAVLDP 30
                                      569*****************977777665 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.32
                                      HHHHHHHHHHHTTEEEECSEEEEEEEEET CS
                         Pyr_redox 42 askilqeklekngievllntkveeiegse 70
                                      +  ++ ++le++g  v+ + k+ ei +++
  gi|242399842|ref|YP_002995267.1| 71 INVEVLKELEEEGYPVYPSPKILEIIQDK 99
                                      56678899999999999999999988654 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 7.7
                                       HHHHTTSEEEEEESSSS CS
                         Pyr_redox  17 alaelgkkVtvversdk 33 
                                       ++ e+ k++ v++++d+
  gi|242399842|ref|YP_002995267.1| 170 EFVEIEKEIAVMVARDQ 186
                                       67788899999888887 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 7.8
                                       EEEECSEEEEE CS
                         Pyr_redox  55 ievllntkvee 65 
                                       ++v+ +   ++
  gi|242399842|ref|YP_002995267.1| 344 VTVVNKDLGKA 354
                                       33333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); 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: 0.75u 0.33s 00:00:01.08 Elapsed: 00:00:00.58
# Mc/sec: 1943.82
//
Query:       gi|242399843|ref|YP_002995268.1|  [L=174]
Description: Phosphoribosylaminoimidazole carboxylase catalytic subunit [Thermococcus sibiricus MM 739]
Scores for 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-73  245.8   0.8    1.2e-73  245.6   0.8    1.0  1  AIRC           AIR carboxylase
     0.0045   15.9   0.4      0.015   14.2   0.1    1.8  2  Fe-ADH         Iron-containing alcohol dehydrogenase
  ------ inclusion threshold ------
      0.024   14.2   0.2       0.05   13.2   0.2    1.6  1  PrpR_N         Propionate catabolism activator
      0.027   15.0   0.2        4.1    7.9   0.0    2.2  2  CoA_binding_2  CoA binding domain
       0.03   14.0   0.1      0.038   13.7   0.1    1.3  1  Fe-ADH_2       Iron-containing alcohol dehydrogenase
       0.13   11.9   0.7       0.27   10.9   0.5    1.5  2  DUF4423        Domain of unknown function (DUF4423)


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 !  245.6   0.8     4e-77   1.2e-73       1     147 [.       4     150 ..       4     151 .. 0.99

  Alignments for each domain:
  == domain 1  score: 245.6 bits;  conditional E-value: 4e-77
                                       EEEEEESSGGGHHHHHHHHHHHHHTT-EEEEEE--TTTSHHHHHHHHHHCHTTTEEEEEEEEESS--HHHHHHHHSS CS
                              AIRC   1 kVgiimGSdsDlevmkkaaeilkelgveyevrvvSahrtpeelleyaeeaeerglkviIagAGgaahLpgvvasltt 77 
                                       kVgiimGSdsDl+vmk+aa++l+e+gveye+++vSahrtpe+++eya++a+erg++viIagAGgaahLpg++as+tt
  gi|242399843|ref|YP_002995268.1|   4 KVGIIMGSDSDLPVMKEAAKVLEEFGVEYEITIVSAHRTPERMYEYAKTARERGVEVIIAGAGGAAHLPGMTASITT 80 
                                       69*************************************************************************** PP

                                       S-EEEEEE--STTCCHHHHHHHHT--TTS--EE-SSTHHHHHHHHHHHHHTTT-HHHHHHHHHHHHHHHH CS
                              AIRC  78 lPVigvPvkskalkgldsllSivqmPsgvpvatvaigkaknAallAaqilalkdeelaekleeyreelke 147
                                       lPVigvPvkskal+gldsllSivqmPsgvpvatvai++aknAallA++il++k++e+aekle+yree+++
  gi|242399843|ref|YP_002995268.1|  81 LPVIGVPVKSKALNGLDSLLSIVQMPSGVPVATVAINNAKNAALLALRILSIKYPEIAEKLEKYREEMRK 150
                                       *******************************************************************986 PP

>> Fe-ADH  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.1   4.9e-06     0.015      25      92 ..       4      68 ..       1      70 [. 0.88
   2 ?   -0.4   0.0      0.14   4.1e+02     273     310 ..     121     157 ..     107     168 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.9e-06
                                      EEEEEEEHHHH.HH.THHHHHHHHHCTT-EEEE.EEE-S---HHHHHHHHTTS-TT.--EEEEEESHH CS
                            Fe-ADH 25 ralivtdkgslkksglldkvlesleeagievtvfdgvepnptleeveeaaalareegadvviavGGGs 92
                                      ++ i+ ++ s  ++++++++ + lee g+e+++ + v+ + t e + e a+ are g++v+ia  GG 
  gi|242399843|ref|YP_002995268.1|  4 KVGIIMGSDS--DLPVMKEAAKVLEEFGVEYEI-TIVSAHRTPERMYEYAKTARERGVEVIIAGAGGA 68
                                      6678888884..6899****************6.889*************************976665 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.14
                                       -HHHHHHHHH..........HHHHHHT.......T--H CS
                            Fe-ADH 273 anaillpavlrfnaeaaperlaqlaralggesdeeaae 310
                                         a+l   +l + +++ +e+l+++ +++ ++  ee+a+
  gi|242399843|ref|YP_002995268.1| 121 NAALLALRILSIKYPEIAEKLEKYREEMRKT-VEEKAK 157
                                       4455666667788888888888888888666.333333 PP

>> PrpR_N  Propionate catabolism activator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   1.7e-05      0.05       6      96 ..      35     133 ..      28     159 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.7e-05
                            PrpR_N   6 dievvegdleeavelakeleaegvdviiSrGgtaell....rkhvsvPVveikvs.....gyDilralkqakklgek 73 
                                        i   + + e+  e+ak++ ++gv+vii++ g a+ l     + + +PV+ ++v+     g D l ++ q+      
  gi|242399843|ref|YP_002995268.1|  35 TIVSAHRTPERMYEYAKTARERGVEVIIAGAGGAAHLpgmtASITTLPVIGVPVKskalnGLDSLLSIVQMPSGVP- 110
                                       33344457789999***************999998774433456699*****986111114455555554444444. PP

                            PrpR_N  74 ialvgfeniikglktlselldld 96 
                                       +a v+ +n+ +++    ++l+++
  gi|242399843|ref|YP_002995268.1| 111 VATVAINNAKNAALLALRILSIK 133
                                       66666666666655555555555 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0    0.0014       4.1      53      88 ..      31      66 ..      14      77 .. 0.81
   2 ?    4.9   0.1     0.012        35      28      73 ..      81     126 ..      76     161 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0014
                                      ..T--EEEE-S-HHHHGGGHHHHHHH--SEEEE-TT CS
                     CoA_binding_2 53 pepvdlvdvftppeatpeivkealalgakavwlqpg 88
                                      + ++ +v+  + pe++ e++k a ++g+++++  +g
  gi|242399843|ref|YP_002995268.1| 31 EYEITIVSAHRTPERMYEYAKTARERGVEVIIAGAG 66
                                      67899************************9998766 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.012
                                       --EEEESSS-SEETTEES----T....T--EEEE-S-HHHHGGGHH CS
                     CoA_binding_2  28 lpvvpVnpkeeeilgekvyaslaedpepvdlvdvftppeatpeivk 73 
                                       lpv+ V  k++++ g ++  s+ + p+ v +++v+++ ++ ++++ 
  gi|242399843|ref|YP_002995268.1|  81 LPVIGVPVKSKALNGLDSLLSIVQMPSGVPVATVAINNAKNAALLA 126
                                       7999999999*************74799********9999888775 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 ?   13.7   0.1   1.3e-05     0.038      21     116 ..       4      98 ..       1     126 [. 0.84

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.3e-05
                          Fe-ADH_2  21 kvllvadentkkaagekveeslkeagikvevveeveeeadleeveklvealreketdlvvavGgGtiiDiakyvsak 97 
                                       kv +++++     + ++ ++ l+e g++ e+   v+++++ e +++ ++ +re+++++++a G+G +  +  + ++ 
  gi|242399843|ref|YP_002995268.1|   4 KVGIIMGSDSDLPVMKEAAKVLEEFGVEYEIT-IVSAHRTPERMYEYAKTARERGVEVIIA-GAGGAAHLPGMTASI 78 
                                       78999999999999***************955.5899***********************9.777777788888888 PP

                          Fe-ADH_2  98 lnvpyvsvpT.aaSvDGfas 116
                                       + +p++ vp  + + +G  s
  gi|242399843|ref|YP_002995268.1|  79 TTLPVIGVPVkSKALNGLDS 98 
                                       89999999853556666555 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.3   3.8e+03      85     110 ..      37      62 ..      19      79 .. 0.61
   2 ?   10.9   0.5   8.9e-05      0.27     122     154 ..     125     157 ..     112     162 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.3
                           DUF4423  85 tssevkseavrsyhkqmlelAieale 110
                                       +s++ ++e + +y k   e+++e++ 
  gi|242399843|ref|YP_002995268.1|  37 VSAHRTPERMYEYAKTARERGVEVII 62 
                                       44555566666666666666666665 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 8.9e-05
                           DUF4423 122 ltlaiskedyekikkeirefrkkilaiaeeske 154
                                       l l i   +y++i+++++++r+++++++ee+ +
  gi|242399843|ref|YP_002995268.1| 125 LALRILSIKYPEIAEKLEKYREEMRKTVEEKAK 157
                                       667777889********************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1289  (0.0718947); expected 358.6 (0.02)
Passed bias filter:                      992  (0.0553294); expected 358.6 (0.02)
Passed Vit filter:                       126  (0.00702772); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.66u 0.39s 00:00:01.05 Elapsed: 00:00:00.56
# Mc/sec: 930.54
//
Query:       gi|242399844|ref|YP_002995269.1|  [L=234]
Description: hypothetical protein TSIB_1871 [Thermococcus sibiricus MM 739]
Scores for complete 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-12   46.6  16.1    8.3e-12   45.7  16.1    1.5  1  Rubrerythrin     Rubrerythrin
     0.0051   17.0   5.5      0.024   14.9   0.5    2.2  2  Ferritin_2       Ferritin-like domain
  ------ inclusion threshold ------
      0.013   15.5   2.6      0.021   14.8   0.7    2.3  2  TMF_DNA_bd       TATA element modulatory factor 1 DNA binding
       0.22   11.5   0.8       0.33   11.0   0.1    1.6  2  S-AdoMet_synt_C  S-adenosylmethionine synthetase, C-terminal 


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 !   45.7  16.1   1.9e-15   8.3e-12       1     136 [.      67     207 ..      67     208 .. 0.83

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 1.9e-15
                                       HHHHHHHHHHHHHHHHHHHHHHCHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.......B.SSBBS-- CS
                      Rubrerythrin   1 eiLekAiagEssarrlYkelaekakegypqiaelFeelAeeEreHakilnklleklepele......levkekvrey 71 
                                       e+ e+A+ +E++a + Y+ +a+ +k     i+  ++ lA+eE +H++i++k+ ek+++++       +ev  + +  
  gi|242399844|ref|YP_002995269.1|  67 EVFEIALNAEIKAKEAYEKMASLVK--SDIIRDELLFLAKEEDKHRQIIEKMAEKFKESEGepkkieIEVMGEFKVI 141
                                       67799********************..999*************************9987761100023333444444 PP

                                       -----TTGGHHH.HHHHHHHHHHHHHHCHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Rubrerythrin  72 aeakpkflttak.nLeeaiegayaeeeemyrfyeelaekegneeakklfkklaeaEkkHeerlrkl 136
                                       ae  ++ +++++ nL+e++e+a+++e  +++ y+ela+   ne++k ++k la++E++H ++l+k 
  gi|242399844|ref|YP_002995269.1| 142 AEKMAEAIKKPDfNLDEVYEIAMEAELVSEKLYKELASYGANEKTKFVLKMLADMERQHFNILKKQ 207
                                       4555555555557777**********************************************9985 PP

>> Ferritin_2  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.5   5.3e-06     0.024       1      62 [.      64     118 ..      64     157 .. 0.82
   2 !    4.5   0.5    0.0086        38       6      60 ..     160     207 ..     157     217 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5.3e-06
                        Ferritin_2   1 sdvdiLnfAlnlEyleaafYtaalegaslddkalldaevrevaeeiakheeaHveflkaale 62 
                                       +d +++++Aln+E  + ++Y+++++          ++ +r+ +  +ak+e +H+++++++ e
  gi|242399844|ref|YP_002995269.1|  64 TDKEVFEIALNAEIKAKEAYEKMAS-------LVKSDIIRDELLFLAKEEDKHRQIIEKMAE 118
                                       5899********************8.......567777888888889999999999988865 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0086
                        Ferritin_2   6 LnfAlnlEyleaafYtaalegaslddkalldaevrevaeeiakheeaHveflkaa 60 
                                        ++A+ +E +  + Y++ ++        + +++++ v++ +a+ e++H ++lk+ 
  gi|242399844|ref|YP_002995269.1| 160 YEIAMEAELVSEKLYKELAS-------YGANEKTKFVLKMLADMERQHFNILKKQ 207
                                       56788888888888888876.......7888899999999999999999999985 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 ?   14.8   0.7   4.7e-06     0.021      23      51 ..     101     129 ..      95     135 .. 0.85
   2 ?   -2.5   0.0       1.2   5.3e+03      24      37 ..     193     206 ..     190     206 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.7e-06
                        TMF_DNA_bd  23 kLskkelklnntikkLrkknkelekeike 51 
                                        L+k+e+k++++i k+ +k ke+e e k+
  gi|242399844|ref|YP_002995269.1| 101 FLAKEEDKHRQIIEKMAEKFKESEGEPKK 129
                                       599*********************77555 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.2
                        TMF_DNA_bd  24 Lskkelklnntikk 37 
                                       L++ e+++ n++kk
  gi|242399844|ref|YP_002995269.1| 193 LADMERQHFNILKK 206
                                       78889999999998 PP

>> S-AdoMet_synt_C  S-adenosylmethionine synthetase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       1.6   7.3e+03     110     115 ..      72      77 ..      50      97 .. 0.48
   2 ?   11.0   0.1   7.3e-05      0.33      75     134 ..     126     188 ..     109     192 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.6
                                       HHHHTT CS
                   S-AdoMet_synt_C 110 ieeldL 115
                                         + ++
  gi|242399844|ref|YP_002995269.1|  72 ALNAEI 77 
                                       222222 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 7.3e-05
                                       S-SEEEEEE-S-BSS-HHHHHHHHHH.H---.-HHHHHHHHTT.TSS--TGGGSS-SSS--T- CS
                   S-AdoMet_synt_C  75 epvsisvetfgtekvseeeiaeivke.vfdl.rpaaiieeldL.kkpiykktaayghfgreel 134
                                       ep +i++e +g+ kv  e++ae++k+  f+l ++ +i  e +L +++ yk++a+yg  +++++
  gi|242399844|ref|YP_002995269.1| 126 EPKKIEIEVMGEFKVIAEKMAEAIKKpDFNLdEVYEIAMEAELvSEKLYKELASYGANEKTKF 188
                                       7999******************99863688734788988999945689********8777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1400  (0.0780858); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.51
# Mc/sec: 1368.64
//
Query:       gi|242399845|ref|YP_002995270.1|  [L=180]
Description: N-acetyltransferase, GNAT family [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.4e-14   52.0   0.1    9.7e-14   51.6   0.1    1.1  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    2.4e-09   37.5   0.0    3.7e-09   36.9   0.0    1.3  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
      2e-06   27.9   0.0    3.1e-06   27.3   0.0    1.6  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
    6.6e-06   26.1   0.0    1.3e-05   25.2   0.0    1.5  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
     0.0012   18.8   0.0     0.0019   18.1   0.0    1.3  1  FR47             FR47-like protein
     0.0093   16.1   0.0      0.016   15.3   0.0    1.4  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 !   51.6   0.1   3.3e-17   9.7e-14       8     117 .]      41     164 ..      34     164 .. 0.75

  Alignments for each domain:
  == domain 1  score: 51.6 bits;  conditional E-value: 3.3e-17
                                       HHHHTHHHHHHHHHHHHHHH..HHSTTC..EEEE.EEETTEEEEEEEEEEEET...........TSTTEEEEEEEEE CS
                    Acetyltransf_1   8 lvesffppnedaseeefees..fsleae..gllv.aeedgeliGfisllkipd...........ekggvayieslaV 68 
                                        +  + p + +++ +++e++  f+l  e  +l++   +d+++iG++ l  + +            +++++ ie+++V
  gi|242399845|ref|YP_002995270.1|  41 VENKPSPDDFERFKRVYEPFleFRLGKEfdELYIlKGKDEKIIGTMALVYNLEgkdvwwvpeeiKNEKTGLIEFVMV 117
                                       4444344444444444444455455444448888788889******6666666777777888**899********** PP

                                       SGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  69 speyrgkGlGsaLlealeerareegikkivlaveedndaairlYeklGF 117
                                       +p+yrgkG Gs+Lle + +r+ e g +  ++ ++ ++  a  +Y + GF
  gi|242399845|ref|YP_002995270.1| 118 DPSYRGKGHGSRLLEFAFKRLGELGKDP-YV-ITFPDLEAYSYYLRKGF 164
                                       **************************88.55.346778******99999 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.0   1.2e-12   3.7e-09      11      75 ..      79     165 ..      68     166 .. 0.69

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 1.2e-12
                                       TTEEEEEEEEEEES.................TCTEEEEE-GGGTTSSHHHHHHHH..TTSEEEEE.EEEE..THH.. CS
                    Acetyltransf_7  11 dgkivGfialslld.................aeitrlaVdpeyrgkGiGraLlea..aekgiile.qlel..nae.. 63 
                                       d+ki+G++al+ +                  + i+++ Vdp+yrgkG G++Lle+  ++ g +l    ++    +  
  gi|242399845|ref|YP_002995270.1|  79 DEKIIGTMALVYNLegkdvwwvpeeiknektGLIEFVMVDPSYRGKGHGSRLLEFafKRLG-ELGkDPYVitF-Pdl 153
                                       47888988888888888888888666655533444499****************8342244.32333333321.235 PP

                                       HHHHHHHHTTEE CS
                    Acetyltransf_7  64 kaikfYeklGFe 75 
                                       +a ++Y + GF+
  gi|242399845|ref|YP_002995270.1| 154 EAYSYYLRKGFI 165
                                       89*********7 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0     1e-09   3.1e-06      72     125 ..     108     164 ..      19     167 .. 0.90

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 1e-09
                                       EEEEEEEEEE-CCGTTS-HHHHHHHHHHHHHHHT.T--EEEE--..SSHHHHHTTT- CS
                    Acetyltransf_9  72 kaagvtgVavapehrgrgvlskLlaraleemree.gqplsllfP..ssipiYrrfGy 125
                                       k++ +  V+v+p +rg+g+ s+Ll+ a++++ e  ++p ++ fP   ++++Y r+G+
  gi|242399845|ref|YP_002995270.1| 108 KTGLIEFVMVDPSYRGKGHGSRLLEFAFKRLGELgKDPYVITFPdlEAYSYYLRKGF 164
                                       7899****************************996899******98779*******9 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   4.3e-09   1.3e-05      52     111 ..     108     169 ..      43     174 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 4.3e-09
                   Acetyltransf_10  52 s..hisllfVdpeyrgqGigkaLleaveeeaekdgikleltvnaspyavpfYeklGFkavge 111
                                       +   i+ ++Vdp+yrg+G g++Lle++ +++ + g    +    + +a ++Y + GF +v +
  gi|242399845|ref|YP_002995270.1| 108 KtgLIEFVMVDPSYRGKGHGSRLLEFAFKRLGELGKDPYVITFPDLEAYSYYLRKGFIKVMD 169
                                       255899************************9777666488888888***********98854 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   6.4e-07    0.0019      17      80 ..     105     167 ..      94     174 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 6.4e-07
                                       EE-TTSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EEEEEETT-HHHHHHHHHHT-EEE CS
                              FR47  17 lrkdggelgalqvlpehrrrGlgsrlvkalakeiaergktvllvvvasNtpsirlyeklGfeki 80 
                                        +++ g +  + v+p+ r++G gsrl +   k++ e gk++ +++ + + ++ + y + Gf k 
  gi|242399845|ref|YP_002995270.1| 105 KNEKTGLIEFVMVDPSYRGKGHGSRLLEFAFKRLGELGKDPYVITFP-DLEAYSYYLRKGFIKV 167
                                       45566999*********************************987765.6788888888888886 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   5.4e-06     0.016      27      53 ..     112     138 ..      78     145 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5.4e-06
                   Acetyltransf_CG  27 fthTeVpeelrGkGiAkkLvkaaldda 53 
                                       ++ + V++++rGkG +++L + a++  
  gi|242399845|ref|YP_002995270.1| 112 IEFVMVDPSYRGKGHGSRLLEFAFKRL 138
                                       55578******************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); 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: 0.56u 0.34s 00:00:00.90 Elapsed: 00:00:00.53
# Mc/sec: 1021.33
//
Query:       gi|242399846|ref|YP_002995271.1|  [L=156]
Description: Peroxiredoxin, bacterioferritin comigratory like protein, AhpC/TSA family [Thermococcus sibiricus MM 739]
Scores for 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-35  119.5   0.0    9.7e-35  119.2   0.0    1.1  1  AhpC-TSA       AhpC/TSA family
    3.7e-19   68.9   0.0    4.5e-19   68.6   0.0    1.0  1  Redoxin        Redoxin
    2.8e-08   33.9   0.0    6.5e-08   32.7   0.0    1.6  1  AhpC-TSA_2     AhpC/TSA antioxidant enzyme
    0.00025   21.3   0.0    0.00035   20.8   0.0    1.3  1  Thioredoxin_8  Thioredoxin-like
  ------ inclusion threshold ------
       0.01   15.4   0.0      0.012   15.2   0.0    1.1  1  DUF899         Bacterial protein of unknown function (DUF899)
      0.025   14.6   0.1      0.052   13.6   0.1    1.5  1  HicA_toxin     HicA toxin of bacterial toxin-antitoxin,
      0.053   13.1   0.0      0.081   12.5   0.0    1.3  1  GSHPx          Glutathione peroxidase


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 !  119.2   0.0   3.8e-38   9.7e-35       7     123 ..       5     128 ..       2     129 .. 0.97

  Alignments for each domain:
  == domain 1  score: 119.2 bits;  conditional E-value: 3.8e-38
                                       --EEESTTCEEEECHHH.TTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHHHH-H. CS
                          AhpC-TSA   7 dfelknadgetvslsdy.kgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfiekesl 82 
                                       ++++ ++dg+++ lsd+  gk++vl+fypkd++p+Ctte++++ +l+eef+++g++vigvs+dsp+sh+kf+ek++l
  gi|242399846|ref|YP_002995271.1|   5 NIKVLDEDGNEKPLSDFvLGKWTVLYFYPKDNTPGCTTEAKEFTELIEEFEKLGFQVIGVSCDSPKSHRKFKEKHGL 81 
                                       5677899********************************************************************** PP

                                       SSEEEE-TTSHHHHHTT-EETT......TTECSCEEEEE-TTSBEEE CS
                          AhpC-TSA  83 nfpllsDeegkvakaygvlkee......kglalratfvidkegkiry 123
                                       +++l+sD++ ++ k +g++ ++      +++a+r+tf+++++g i +
  gi|242399846|ref|YP_002995271.1|  82 KIRLISDPNAELHKGLGAWGKKkrygreYEGAIRSTFILSPKGEILW 128
                                       *******************999*********************9965 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.6   0.0   1.8e-22   4.5e-19      14     138 ..       9     137 ..       3     147 .. 0.90

  Alignments for each domain:
  == domain 1  score: 68.6 bits;  conditional E-value: 1.8e-22
                                       ETTCEEEEEHHH.HTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHHHHHHHHHTT-TSEE CS
                           Redoxin  14 aatdgnsvslse.fkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndafvkefwgkeglkfpv 89 
                                       +++dgn+  ls+ + gk +v++f+p   +P C++e+ ++++l e++++ g++v++v++d+    ++f +k+glk+++
  gi|242399846|ref|YP_002995271.1|   9 LDEDGNEKPLSDfVLGKWTVLYFYPKDNTPGCTTEAKEFTELIEEFEKLGFQVIGVSCDSPKSHRKFKEKHGLKIRL 85 
                                       469*********999**9************************9999******************************* PP

                                       EE-TTSHHHHHTT-TTEEE.GGG....EEE-EEEEEEETTEEEEEEESSSCHT CS
                           Redoxin  90 lsDgsaaftkalGlrleedaseg....lrtpryavidedgkvvylevepepet 138
                                       +sD++a++ k lG ++ +++  g     ++++++++  +g + +++  +  ++
  gi|242399846|ref|YP_002995271.1|  86 ISDPNAELHKGLG-AWGKKKRYGreyeGAIRSTFILSPKGEILWKKIKVKAKG 137
                                       *************.66666666679999***************9999887644 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 !   32.7   0.0   2.5e-11   6.5e-08       3      55 ..      48     108 ..      46     149 .. 0.77

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 2.5e-11
                        AhpC-TSA_2   3 srdkpeldaagvklvaigigdp.sakkFvkltgfpfelyvDpsaklyqalglk.......r 55 
                                       +++++e+++ g++++++++++p s +kF +  g ++ l+ Dp+a+l++ lg +       r
  gi|242399846|ref|YP_002995271.1|  48 TELIEEFEKLGFQVIGVSCDSPkSHRKFKEKHGLKIRLISDPNAELHKGLGAWgkkkrygR 108
                                       56789*****************88***************************9855555550 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   1.4e-07   0.00035       1      74 [.      24      93 ..      24     126 .. 0.65

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.4e-07
                                      .SEEEEEE--S.SSHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-SS-HHHHHHHGGGS-TTSEE.EE-TT-HHHH CS
                     Thioredoxin_8  1 gkvvlLyfgas.wcppckaftpklkelyeklkkkkkveivyvsldkkeeefekylkknkkpwlsvpfddkkrnkl 74
                                      gk+++Lyf+ + + p c++  ++ +el e+++ k +++++ vs+d+   + ++ +k+     l ++  ++ + +l
  gi|242399846|ref|YP_002995271.1| 24 GKWTVLYFYPKdNTPGCTTEAKEFTELIEEFE-KLGFQVIGVSCDSP--KSHRKFKEK--HGLKIRLISDPNAEL 93
                                      799*****97626666***************8.7***********74..444444444..444455444445555 PP

>> DUF899  Bacterial protein of unknown function (DUF899)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   4.7e-06     0.012      84     166 ..      36     120 ..      20     140 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.7e-06
                            DUF899  84 gCpgCslladhvdgalahLeardvtlavvsraplekleaykrrmGwtlpwvssaesdfnrdfnvsleeeqaseelpg 160
                                       + pgC++ a+++ + ++++e+ +++++ vs    ++  ++k++ G +++++s+ ++++++ +++  +++++ +e  g
  gi|242399846|ref|YP_002995271.1|  36 NTPGCTTEAKEFTELIEEFEKLGFQVIGVSCDSPKSHRKFKEKHGLKIRLISDPNAELHKGLGAWGKKKRYGREYEG 112
                                       569************************************************************99999998888877 PP

                            DUF899 161 l..svflr 166
                                          s+f+ 
  gi|242399846|ref|YP_002995271.1| 113 AirSTFIL 120
                                       64456655 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 ?   13.6   0.1     2e-05     0.052       2      48 ..      48      97 ..      47      97 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2e-05
                                      HCHHHHHHHTT-EEEEEET....TEEEEE-TTSS-EEEEE.S-SSS--CCC CS
                        HicA_toxin  2 reviklLeklGfevvrqkG....SHvrfkhpdkrgivtvppHpgkelkpgt 48
                                       e+i  +eklGf+v++ +     SH++fk  ++ +i  +   p+ el++g+
  gi|242399846|ref|YP_002995271.1| 48 TELIEEFEKLGFQVIGVSCdspkSHRKFKEKHGLKIRLIS-DPNAELHKGL 97
                                      69999**********65323556*******9999887888.5589999985 PP

>> GSHPx  Glutathione peroxidase
   #    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       5      65 ..       7      70 ..       3      89 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.2e-05
                                      EEEBTTSSEEEGGGGT.TS..EEEEEEEESSSTTHHHHHHHHHHHHHHGGGTEEEEEEEE-TTT CS
                             GSHPx  5 sakdidgekvkleklr.gk..vvlivnvaskCglteqykeleelqkrykdkglvilgfPCnqfg 65
                                      ++ d+dg++ +l+ +  gk  v+ +     + g t++ ke+ el +++++ g+ ++g  C+   
  gi|242399846|ref|YP_002995271.1|  7 KVLDEDGNEKPLSDFVlGKwtVLYFYPKDNTPGCTTEAKEFTELIEEFEKLGFQVIGVSCDSPK 70
                                      5666777777776664344113334455667899**************************8655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 917.60
//
Query:       gi|242399847|ref|YP_002995272.1|  [L=158]
Description: Rubrerythrin-related protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-17   63.2  14.9    3.8e-17   63.0  14.9    1.1  1  Rubrerythrin     Rubrerythrin
    4.5e-07   30.1   4.1     0.0087   16.3   0.2    2.1  2  Ferritin_2       Ferritin-like domain
    5.4e-07   29.9   3.4    0.00038   20.8   0.5    2.2  2  DUF2383          Domain of unknown function (DUF2383)
  ------ inclusion threshold ------
      0.012   14.4   0.9          3    6.6   0.0    2.2  2  FA_desaturase_2  Fatty acid desaturase
      0.019   14.8   2.4      0.026   14.4   2.4    1.2  1  DUF2202          Uncharacterized protein domain (DUF2202)
      0.025   14.4   0.4      0.053   13.3   0.4    1.5  1  SKA2             Spindle and kinetochore-associated protein 2
      0.067   12.8   3.0        2.9    7.5   0.1    2.1  2  DUF3231          Protein of unknown function (DUF3231)
       0.12   12.6   0.5        2.9    8.2   0.1    2.3  2  Coat_F           Coat F domain
       0.14   12.1   1.8        7.7    6.5   0.5    2.5  2  DUF1657          Protein of unknown function (DUF1657)


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 !   63.0  14.9   1.9e-20   3.8e-17       2     136 ..       6     137 ..       5     138 .. 0.86

  Alignments for each domain:
  == domain 1  score: 63.0 bits;  conditional E-value: 1.9e-20
                                       HHHHHHHHHHHHHHHHHHHHHCHHTT-HHHHHHHHHHHHHHHHHHHHHHHHH.HHCSTTHH..B.SSBBS------- CS
                      Rubrerythrin   2 iLekAiagEssarrlYkelaekakegypqiaelFeelAeeEreHakilnkll.eklepele.levkekvreyaeakp 76 
                                        L+ A+  E  + r+Y e+a+kak   +  +++F+ lA eE+eH ++++k++ ekl ++ e  +v+++  +++ +  
  gi|242399847|ref|YP_002995272.1|   6 ALALALEVEKAELRFYIEMAKKAK--DERAKRMFLFLAGEEAEHWDVFEKMFvEKLLQNPEvPQVDKELLQKLTP-- 78 
                                       7999********************..77789*******************8736777777756666666665555.. PP

                                       TTGGHHHHHHHHHHHHHHHHHCHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Rubrerythrin  77 kflttaknLeeaiegayaeeeemyrfyeelaekegneeakklfkklaeaEkkHeerlrkl 136
                                       k++     ++ a+e+++++e+   +fyee+ae++++e+ kk+f++la+ Ek+H+e+l++ 
  gi|242399847|ref|YP_002995272.1|  79 KYEGEISEVK-AVELGMEQEKLTWEFYEEAAEEAEDENLKKIFRELAKVEKSHYELLKAQ 137
                                       4444555666.99********************************************985 PP

>> Ferritin_2  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.2   4.3e-06    0.0087       2      71 ..       3      64 ..       2      78 .. 0.86
   2 !   15.6   0.5   7.1e-06     0.014       3      60 ..      87     137 ..      85     153 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.3e-06
                        Ferritin_2  2 dvdiLnfAlnlEyleaafYtaalegaslddkalldaevrevaeeiakheeaHveflkaaleGaaavakpt 71
                                      +++ L  Al +E  e  fY ++++       ++ d++ ++++  +a +e++H ++++++   ++ +++p+
  gi|242399847|ref|YP_002995272.1|  3 EINALALALEVEKAELRFYIEMAK-------KAKDERAKRMFLFLAGEEAEHWDVFEKMF-VEKLLQNPE 64
                                      5788999***************98.......678999999999***********999998.577666665 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 7.1e-06
                        Ferritin_2   3 vdiLnfAlnlEyleaafYtaalegaslddkalldaevrevaeeiakheeaHveflkaa 60 
                                       v+ ++  +  E l  +fY++a+e       ++ d++ +++++e+ak e++H+e+lka 
  gi|242399847|ref|YP_002995272.1|  87 VKAVELGMEQEKLTWEFYEEAAE-------EAEDENLKKIFRELAKVEKSHYELLKAQ 137
                                       56677788889***********9.......567999*******************986 PP

>> DUF2383  Domain of unknown function (DUF2383)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.1   0.00038      0.75       3      46 ..       4      47 ..       2      64 .. 0.86
   2 !   20.8   0.5   1.9e-07   0.00038      15      53 ..      99     137 ..      86     143 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00038
                                      HHHHHHHHHHHHHHHHHHHHHHHT--SHHHHHHHHHHHHHHHHH CS
                           DUF2383  3 ieaLndLietlkdgeegykeaaekvkdpqlktlleriaeereea 46
                                      i+aL   +e++k   ++y e+a+k+kd++ k ++   a e +e+
  gi|242399847|ref|YP_002995272.1|  4 INALALALEVEKAELRFYIEMAKKAKDERAKRMFLFLAGEEAEH 47
                                      7888889999************************9888887776 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 1.9e-07
                                       HHHHHHHHHHHT--SHHHHHHHHHHHHHHHHHHHHHHHH CS
                           DUF2383  15 dgeegykeaaekvkdpqlktlleriaeereeaaeeLqse 53 
                                          e+y+eaae+++d++lk+++++ a+  + + e L+++
  gi|242399847|ref|YP_002995272.1|  99 LTWEFYEEAAEEAEDENLKKIFRELAKVEKSHYELLKAQ 137
                                       5669***************************99999875 PP

>> FA_desaturase_2  Fatty acid desaturase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0015         3     175     213 ..      24      62 ..      21      76 .. 0.83
   2 ?    6.5   0.2    0.0016       3.2     175     210 ..     107     142 ..      96     153 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0015
                   FA_desaturase_2 175 lakeagdellakicgaiaadEkrHeaaYtrvvekllevd 213
                                       +ak+a+de ++++   +a +E+ H   +++++ + l ++
  gi|242399847|ref|YP_002995272.1|  24 MAKKAKDERAKRMFLFLAGEEAEHWDVFEKMFVEKLLQN 62 
                                       79999*******************999987654444444 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0016
                   FA_desaturase_2 175 lakeagdellakicgaiaadEkrHeaaYtrvvekll 210
                                       +a+ea+de l+ki + +a+ Ek H+   ++  + ++
  gi|242399847|ref|YP_002995272.1| 107 AAEEAEDENLKKIFRELAKVEKSHYELLKAQYDSVM 142
                                       68999*******************865444444433 PP

>> DUF2202  Uncharacterized protein domain (DUF2202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   2.4   1.3e-05     0.026       5     131 ..       7     131 ..       3     155 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.3e-05
                           DUF2202   5 llymreeeklarDvYlelYdrwk....lqiflniakseqthtdavksllekYeledpvkederGkfedeelqelYnk 77 
                                       l    e ek+    Y+e+ ++ k     ++fl +a  e +h d  ++++    l++p       + ++e lq+l  k
  gi|242399847|ref|YP_002995272.1|   7 LALALEVEKAELRFYIEMAKKAKderaKRMFLFLAGEEAEHWDVFEKMFVEKLLQNPEVP----QVDKELLQKLTPK 79 
                                       555566677777777777655442222689************999888876667666555....5688888888777 PP

                           DUF2202  78 LvekgsksledaLkvgatiedldiaDlekalketdnkdikevYenllkGsrnhl 131
                                          +g+ s + a++ g+  e l     e+a +e +++++k+++++l k  + h 
  gi|242399847|ref|YP_002995272.1|  80 Y--EGEISEVKAVELGMEQEKLTWEFYEEAAEEAEDENLKKIFRELAKVEKSHY 131
                                       4..7999999*************************************9999884 PP

>> SKA2  Spindle and kinetochore-associated protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.4   2.7e-05     0.053      20      64 ..      94     141 ..      88     144 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.7e-05
                              SKA2  20 yvqhrLekefqqsypdna..eNpvkLlerlkkv.keelqaLkeqceel 64 
                                       + q++L  ef ++ +++a  eN+ k+ ++l+kv k+ ++ Lk+q + +
  gi|242399847|ref|YP_002995272.1|  94 MEQEKLTWEFYEEAAEEAedENLKKIFRELAKVeKSHYELLKAQYDSV 141
                                       5589*****************************556677888888776 PP

>> DUF3231  Protein of unknown function (DUF3231)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.1    0.0014       2.9      17      80 ..       3      66 ..       1      81 [. 0.88
   2 ?    6.0   0.4    0.0042       8.4      28      66 ..      97     135 ..      83     138 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0014
                           DUF3231 17 EiaslwssyianslgialitgFlqvaedkeikelleralelsnkhikelkelLkeenlpiPsgf 80
                                      Ei  l   ++ + +    +  ++++a+d+  k ++        +h + +++++ e  l+ P+ +
  gi|242399847|ref|YP_002995272.1|  3 EINALALALEVEKAELRFYIEMAKKAKDERAKRMFLFLAGEEAEHWDVFEKMFVEKLLQNPEVP 66
                                      88888888889999999999*********************************99999888766 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0042
                           DUF3231  28 nslgialitgFlqvaedkeikelleralelsnkhikelk 66 
                                       + l+   ++  +++aed+++k+++ +  ++ ++h + lk
  gi|242399847|ref|YP_002995272.1|  97 EKLTWEFYEEAAEEAEDENLKKIFRELAKVEKSHYELLK 135
                                       55566667777899********************99886 PP

>> Coat_F  Coat F domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0       0.1     2e+02       9      55 ..      10      55 ..       5      59 .. 0.76
   2 ?    8.2   0.1    0.0015       2.9      18      48 ..     102     131 ..      94     138 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.1
                            Coat_F  9 lLsteKsaarnyataitEasnpelRqtlkqilneeiemqeelfnlmn 55
                                      +L  eK+  r y  ++  a ++  ++++  ++ ee + ++++f+ m+
  gi|242399847|ref|YP_002995272.1| 10 ALEVEKAELRFYIEMAKKAKDERAKRMFLFLAGEE-AEHWDVFEKMF 55
                                      57778888888888888888888888888776665.56888988886 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0015
                            Coat_F  18 rnyataitEasnpelRqtlkqilneeiemqe 48 
                                         y  a+ Ea +++l+++++++++ e   ++
  gi|242399847|ref|YP_002995272.1| 102 EFYEEAAEEAEDENLKKIFRELAKVEK-SHY 131
                                       56999**************99887554.444 PP

>> DUF1657  Protein of unknown function (DUF1657)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.015        30      19      32 ..      25      38 ..      21      53 .. 0.80
   2 ?    6.5   0.5    0.0039       7.7      16      41 ..     105     130 ..     104     137 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.015
                           DUF1657 19 aLqTedeeAKqmYe 32
                                      a   +de AK+m+ 
  gi|242399847|ref|YP_002995272.1| 25 AKKAKDERAKRMFL 38
                                      55689*******95 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0039
                           DUF1657  16 etFaLqTedeeAKqmYeqaaeqleev 41 
                                       e  a + ede+ K+++ ++a+  +++
  gi|242399847|ref|YP_002995272.1| 105 EEAAEEAEDENLKKIFRELAKVEKSH 130
                                       6678999************9876665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1474  (0.0822132); expected 358.6 (0.02)
Passed bias filter:                      681  (0.0379832); 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: 0.62u 0.35s 00:00:00.97 Elapsed: 00:00:00.55
# Mc/sec: 866.39
//
Query:       gi|242399848|ref|YP_002995273.1|  [L=200]
Description: Phosphate transport system regulator [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-19   69.9   4.1    1.6e-11   44.5   0.4    2.3  2  PhoU      PhoU domain


Domain annotation for each model (and alignments):
>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.3   2.9e-10   5.2e-06       2      85 ..      17      96 ..      16     100 .. 0.81
   2 !   44.5   0.4   8.9e-16   1.6e-11       5      85 ..     116     187 ..     113     191 .. 0.85

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 2.9e-10
                                      HHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHHHH CS
                              PhoU  2 rrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlERigD 80
                                      ++m+ +v+e ++ + ++l  ++    + + ++  ++  l++e+ + + e+l ++qp+a+dlr++ +++++++dl+Ri++
  gi|242399848|ref|YP_002995273.1| 17 QEMGGTVLECVNSLESVL-GGEG---DSIEDNSSKLHILRNELVEIATELLVRYQPMASDLRYIQASIDVSYDLYRISR 91
                                      678888888887555555.3333...566666888888999999998888899************************** PP

                                      HHHHH CS
                              PhoU 81 havni 85
                                      ++ +i
  gi|242399848|ref|YP_002995273.1| 92 YSMEI 96
                                      *9988 PP

  == domain 2  score: 44.5 bits;  conditional E-value: 8.9e-16
                                       HHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHHHHH CS
                              PhoU   5 aeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlERigDh 81 
                                        +iv++m+++al+a+ e+d+  + +++e d+++d+l+ + +++l +  ++ +   + +++      i r+lER++Dh
  gi|242399848|ref|YP_002995273.1| 116 LKIVKKMVELALRAFLEGDETSVGRLLESDEKVDKLYLASIEELNKDSNICK---A-VEA-----LILRHLERMSDH 183
                                       689****************9999****************9999766665433...2.555.....49********** PP

                                       HHHH CS
                              PhoU  82 avni 85 
                                        + i
  gi|242399848|ref|YP_002995273.1| 184 TTYI 187
                                       9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 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:                        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: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1249.49
//
Query:       gi|242399849|ref|YP_002995274.1|  [L=253]
Description: Phosphate import ATP-binding protein pstB [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-33  116.5   0.0    1.5e-33  116.2   0.0    1.1  1  ABC_tran      ABC transporter
    5.6e-09   36.2   0.0    5.4e-05   23.1   0.0    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    1.1e-07   31.5   0.0    2.4e-07   30.5   0.0    1.5  1  SMC_N         RecF/RecN/SMC N terminal domain
    0.00018   21.4   0.0       0.49   10.0   0.0    2.1  2  AAA_15        AAA ATPase domain
    0.00033   20.3   0.0     0.0006   19.5   0.0    1.4  1  AAA_29        P-loop containing region of AAA domain
    0.00044   20.5   0.0     0.0008   19.7   0.0    1.6  1  AAA_22        AAA domain
      0.002   18.5   0.0     0.0025   18.2   0.0    1.4  1  AAA_16        AAA ATPase domain
     0.0064   16.2   0.0      0.012   15.3   0.0    1.5  1  AAA_24        AAA domain
     0.0068   16.2   0.0      0.013   15.2   0.0    1.5  1  PRK           Phosphoribulokinase / Uridine kinase family
      0.009   16.0   0.0      0.019   14.9   0.0    1.5  1  Rad17         Rad17 P-loop domain
     0.0096   15.8   0.0      0.026   14.4   0.0    1.7  2  RsgA_GTPase   RsgA GTPase
     0.0098   16.3   0.0        1.4    9.3   0.0    2.3  2  AAA           ATPase family associated with various cellular 
  ------ inclusion threshold ------
      0.012   16.2   0.0      0.022   15.3   0.0    1.4  1  AAA_23        AAA domain
      0.017   14.9   0.0      0.058   13.1   0.0    1.7  2  AAA_30        AAA domain
      0.027   13.9   0.0       0.93    8.9   0.0    2.1  2  TniB          Bacterial TniB protein
      0.036   14.4   0.0       0.28   11.6   0.0    2.1  2  RNA_helicase  RNA helicase
      0.042   13.7   0.0       0.12   12.3   0.0    1.7  1  ATPase_2      ATPase domain predominantly from Archaea
      0.066   12.8   0.0       0.11   12.1   0.0    1.4  1  AAA_27        AAA domain
      0.082   13.5   0.0        0.2   12.2   0.0    1.6  2  AAA_18        AAA domain
       0.12   11.9   0.0       0.27   10.8   0.0    1.5  1  AAA_25        AAA domain
       0.13   11.4   0.0       0.24   10.6   0.0    1.5  1  NB-ARC        NB-ARC domain
       0.15   12.0   0.0       0.35   10.9   0.0    1.5  1  AAA_5         AAA domain (dynein-related subfamily)


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.2   0.0   1.9e-36   1.5e-33       2     137 .]      21     178 ..      20     178 .. 0.96

  Alignments for each domain:
  == domain 1  score: 116.2 bits;  conditional E-value: 1.9e-36
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--.....SEEEEEETTCEGGG..B-HHHCCHCEEEE-SS--S- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkp.....teGeilldgkdlke..qeleslrkeigvlpqepqlf 71 
                                       k v+lk+ ++++ a++G++G+GKSt+l+++ +ll+       eG++++ g+d+ +   +  ++r+e+g+++q p+ f
  gi|242399849|ref|YP_002995274.1|  21 KGVDLKVPRNTVFAVMGPSGCGKSTMLRAFNRLLELneearVEGKVKIFGRDVYNpeVDPIEVRREVGMVFQYPNPF 97 
                                       789*****************************99988888899***********98766667899************ PP

                                       TTSBHHHH...............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEE CS
                                       xxxxxxxx...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  72 peltvren...............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllD 133
                                       p+lt+++n               e de++e al+k  l +  ++++++ ps+LSgGq+qr++laral+ kpk+ll+D
  gi|242399849|ref|YP_002995274.1|  98 PHLTIYDNvaiglklnglvrskgEIDERVEWALKKAALWDEVKNRLNDYPSNLSGGQRQRLVLARALAMKPKILLMD 174
                                       ***************************************************************************** PP

                                       STTT CS
                                       xxxx RF
                          ABC_tran 134 Epta 137
                                       Epta
  gi|242399849|ref|YP_002995274.1| 175 EPTA 178
                                       **97 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   0.00026      0.21       2      43 ..      33      77 ..      32      93 .. 0.73
   2 !   23.1   0.0   6.6e-08   5.4e-05     225     299 ..     138     208 ..     103     209 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00026
                            AAA_21  2 nvliGpNgsGKSnLLdaldllarl...drdvegltdelsggggir 43
                                       ++ Gp g+GKS+ L+a+  l  l   +r     +++ ++  ++ 
  gi|242399849|ref|YP_002995274.1| 33 FAVMGPSGCGKSTMLRAFNRLLELneeARVEGKVKIFGRDVYNPE 77
                                      5788*****************877766555555555555555554 PP

  == domain 2  score: 23.1 bits;  conditional E-value: 6.6e-08
                            AAA_21 225 engdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHP...kllrrllellkelsrngaQviltTHS 298
                                       e +++ +  +++lS G+++   +l+  l+  +  ++ll DEp ++++P   k +++ll  ++++++    +il+THS
  gi|242399849|ref|YP_002995274.1| 138 EVKNRLNDYPSNLSGGQRQR-LVLARALAMKP--KILLMDEPTANIDPvgtKKIEELL--FELKNE--YTIILVTHS 207
                                       55666677888999999999.55555554444..9*************6666666666..355555..77******* PP

                            AAA_21 299 p 299
                                       p
  gi|242399849|ref|YP_002995274.1| 208 P 208
                                       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 !   30.5   0.0   2.9e-10   2.4e-07      25     207 ..      31     216 ..       5     225 .. 0.76

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 2.9e-10
                                       SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTT..TCHCCCCCC--BTTCSSTTEEEEEEEEEETTEE.SSSSSSCEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                             SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakkl..rseklsdlihkskekasvkkaeveitfdnedkk.lkiekeevs 98 
                                        + a++Gp G+GKs +l A   +L  ++   +  + + + + +++ +  +   + ev ++f+ ++     +  ++v 
  gi|242399849|ref|YP_002995274.1|  31 TVFAVMGPSGCGKSTMLRAFNRLLELNEEARVegKVKIFGRDVYNPEVDPIEVRREVGMVFQYPNPFpHLTIYDNVA 107
                                       56789***************9999876554432245555666666788888889999****9999985456678899 PP

                                       EEEEEETTSEEEEEETTEE...E-HHHHHHHHH.CTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS CS
                                       xxxxxxxxxxxxxxxxxxx...xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  99 isrrvkrkgeseykingke...vtkkevselle.sagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaL 171
                                       i  ++    +s+ +i+++     +k+ + + ++ + + ++++LSgG+++ + la  +A++   p  + l+De  a++
  gi|242399849|ref|YP_002995274.1| 108 IGLKLNGLVRSKGEIDERVewaLKKAALWDEVKnRLNDYPSNLSGGQRQRLVLARALAMK---P-KILLMDEPTANI 180
                                       99888888888888887642213444444444303444789*******987777776654...4.4889******** PP

                                       -HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 172 DeknvkkvaellkeksknaQfivislreemlekadk 207
                                       D   +kk+ ell e +++  +i ++++  + ++++ 
  gi|242399849|ref|YP_002995274.1| 181 DPVGTKKIEELLFELKNEYTIILVTHSPAQAARVSD 216
                                       **************************9888776654 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0    0.0006      0.49      25      54 ..      32      61 ..      20     146 .. 0.83
   2 !    9.8   0.1   0.00072      0.58     323     367 ..     167     209 ..     148     211 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0006
                            AAA_15 25 ltvliGkNnsGKSsilealdlFlnnkekkn 54
                                      +  + G+ ++GKS+ l+a++ +l+ +e+  
  gi|242399849|ref|YP_002995274.1| 32 VFAVMGPSGCGKSTMLRAFNRLLELNEEAR 61
                                      6678899****************9886554 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00072
                            AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSph 367
                                       k++ill++EP a++ p   k + +ll el n+    +i+ THSp 
  gi|242399849|ref|YP_002995274.1| 167 KPKILLMDEPTANIDPVGTKKIEELLFELKNEYT--IILVTHSPA 209
                                       469******************************6..*******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 !   19.5   0.0   7.3e-07    0.0006      14      47 ..      22      55 ..      17      62 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 7.3e-07
                            AAA_29 14 ghtieidlkgatlltGpsGsGKSTllDAiqalLv 47
                                      g ++++ ++ ++ ++GpsG GKST+l A++ lL 
  gi|242399849|ref|YP_002995274.1| 22 GVDLKVPRNTVFAVMGPSGCGKSTMLRAFNRLLE 55
                                      567778777799****************999985 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   9.8e-07    0.0008       6      38 ..      31      82 ..      28     204 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 9.8e-07
                            AAA_22  6 gilvvtGesGtGKTtllrrlleqldeeakaee...................e 38
                                      ++ +v+G+sG+GK+t lr + + l+  ++a+                    e
  gi|242399849|ref|YP_002995274.1| 31 TVFAVMGPSGCGKSTMLRAFNRLLELNEEARVegkvkifgrdvynpevdpiE 82
                                      5779******************998776665566666655555554444441 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   3.1e-06    0.0025      26      52 ..      32      58 ..      23     175 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.1e-06
                            AAA_16 26 lvllsGesGvGKsslvrellralekdg 52
                                      +  + G+sG+GKs+++r++ r le ++
  gi|242399849|ref|YP_002995274.1| 32 VFAVMGPSGCGKSTMLRAFNRLLELNE 58
                                      5689***************99666553 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.5e-05     0.012       2      34 ..      30      61 ..      29      73 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.5e-05
                            AAA_24  2 klkiliyGpsgiGKTtlakelgpkplfidtekG 34
                                      +  ++++Gpsg GK+t+++ + ++ l ++ e+ 
  gi|242399849|ref|YP_002995274.1| 30 NTVFAVMGPSGCGKSTMLRAF-NRLLELNEEAR 61
                                      56789****************.****9998875 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    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       1      36 [.      32      65 ..      32      96 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.6e-05
                               PRK  1 vIgvagsSGaGkttvarklekifgrekvkaaeiegd 36
                                      v +v g+SG+Gk+t+ r+++ +++ ++   a +eg+
  gi|242399849|ref|YP_002995274.1| 32 VFAVMGPSGCGKSTMLRAFNRLLELNEE--ARVEGK 65
                                      5689*****************9994433..344444 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   2.4e-05     0.019      45      69 ..      30      54 ..      18      66 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.4e-05
                             Rad17 45 kriLLisGPsGCgkstvvkvLskel 69
                                      + +  + GPsGCgkst+++   + l
  gi|242399849|ref|YP_002995274.1| 30 NTVFAVMGPSGCGKSTMLRAFNRLL 54
                                      4588899***********9887765 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   3.2e-05     0.026      98     121 ..      29      52 ..      12      67 .. 0.80
   2 ?   -2.2   0.0         4   3.3e+03      87      99 ..     185     197 ..     163     207 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.2e-05
                                       TTSEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallp 121
                                       ++ + +++G+SG GKSt++ a++ 
  gi|242399849|ref|YP_002995274.1|  29 RNTVFAVMGPSGCGKSTMLRAFNR 52 
                                       4578899***********987655 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 4
                                       HTTHHHHHHHCTT CS
                       RsgA_GTPase  87 kegleelkellkd 99 
                                       ++++eel  +lk+
  gi|242399849|ref|YP_002995274.1| 185 TKKIEELLFELKN 197
                                       3455555555555 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0    0.0017       1.4       3      20 ..      35      52 ..      33      93 .. 0.86
   2 ?    4.9   0.0     0.042        34      44      67 ..     152     176 ..     129     213 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0017
                                      EESSTTSSHHHHHHHHHH CS
                               AAA  3 lyGppGtGKTllakavak 20
                                      ++Gp G+GK+++ +a  +
  gi|242399849|ref|YP_002995274.1| 35 VMGPSGCGKSTMLRAFNR 52
                                      78***********99765 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.042
                                       HHHHHHHHHHHHTS.TSEEEEEETG CS
                               AAA  44 kkirelfkeakeka.kpsilfiDEi 67 
                                          r+ +  a++ a kp+il++DE 
  gi|242399849|ref|YP_002995274.1| 152 GGQRQRLVLARALAmKPKILLMDEP 176
                                       4445555555666667*******94 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.0   2.7e-05     0.022      18      43 ..      29      54 ..       8      93 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.7e-05
                            AAA_23 18 skgltlItGpNGaGKTTildAiklaL 43
                                       + ++++ Gp G+GK+T l+A+   L
  gi|242399849|ref|YP_002995274.1| 29 RNTVFAVMGPSGCGKSTMLRAFNRLL 54
                                      67899****************98665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   7.1e-05     0.058      18      49 ..      30      62 ..      25      69 .. 0.82
   2 ?   -1.2   0.0       1.7   1.4e+03     101     122 ..     184     204 ..     138     220 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.1e-05
                            AAA_30 18 drvavltGpAGtGKttalkalreaweaa.ggrv 49
                                      + v ++ Gp G GK+t+l+a ++++e + + rv
  gi|242399849|ref|YP_002995274.1| 30 NTVFAVMGPSGCGKSTMLRAFNRLLELNeEARV 62
                                      568899***************999986644555 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.7
                            AAA_30 101 dtkqlaallkaaekagakvilv 122
                                       +tk++++ll ++++ + ++ilv
  gi|242399849|ref|YP_002995274.1| 184 GTKKIEELLFELKN-EYTIILV 204
                                       66666666666666.4444443 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0    0.0011      0.93      34      64 ..      29      59 ..      23      72 .. 0.78
   2 ?    2.9   0.0     0.075        61     105     158 ..     153     204 ..     131     215 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0011
                              TniB 34 rmpnlllvGdsnnGKtmivekFarlhppekd 64
                                      r     ++G+s +GK+++++ F rl + +++
  gi|242399849|ref|YP_002995274.1| 29 RNTVFAVMGPSGCGKSTMLRAFNRLLELNEE 59
                                      6667899***************998766554 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.075
                              TniB 105 skleqqvlrllrelkvrvLiiDEih.nllagsarkqreflnalksLgnelkipiv 158
                                        + ++ vl+   ++k+++L++DE   n+     +k +   ++l  L+ne+ i +v
  gi|242399849|ref|YP_002995274.1| 153 GQRQRLVLARALAMKPKILLMDEPTaNIDPVGTKKIE---ELLFELKNEYTIILV 204
                                       55666777777899*********65144444444444...445555677777666 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00034      0.28       3      22 ..      35      54 ..      33      75 .. 0.79
   2 ?    0.2   0.0       1.2   9.9e+02      50      88 ..     168     207 ..     163     220 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00034
                      RNA_helicase  3 lyGpsgeGKStlakeLakal 22
                                      + Gpsg+GKSt+ + + + l
  gi|242399849|ref|YP_002995274.1| 35 VMGPSGCGKSTMLRAFNRLL 54
                                      78**********99965544 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.2
                      RNA_helicase  50 qevvvidDfgqvkdee.npsdlaelirlvsstpyplnmas 88 
                                       ++++++d+  ++ d   ++++++ l++l + ++++l + s
  gi|242399849|ref|YP_002995274.1| 168 PKILLMDEPTANIDPVgTKKIEELLFELKNEYTIILVTHS 207
                                       6889999999999999888899999999999999887665 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00014      0.12      20      46 ..      30      56 ..      24      70 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00014
                          ATPase_2 20 neiyfiYGpegsGKtaLlkeiienled 46
                                      n++  + Gp g+GK+++l+ +   le 
  gi|242399849|ref|YP_002995274.1| 30 NTVFAVMGPSGCGKSTMLRAFNRLLEL 56
                                      678889************988666543 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00014      0.11      19      50 ..      23      54 ..       3      56 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00014
                            AAA_27 19 ldfsaeeadlhliyGpNEAGKstalrAisdll 50
                                      +d++  ++ +  ++Gp   GKst+lrA+++ll
  gi|242399849|ref|YP_002995274.1| 23 VDLKVPRNTVFAVMGPSGCGKSTMLRAFNRLL 54
                                      677777899999****************9997 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   0.00025       0.2       3      24 ..      35      56 ..      34      90 .. 0.78
   2 ?   -2.2   0.0       7.2   5.9e+03      35      35 ..     168     168 ..     121     214 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00025
                            AAA_18  3 ltGtpGvGKttlakeLskrlgf 24
                                      ++G++G+GK+t+ ++ +++l++
  gi|242399849|ref|YP_002995274.1| 35 VMGPSGCGKSTMLRAFNRLLEL 56
                                      89**************999744 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 7.2
                            AAA_18  35 n 35 
                                        
  gi|242399849|ref|YP_002995274.1| 168 P 168
                                       2 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00033      0.27      30      50 ..      27      47 ..      17      50 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00033
                            AAA_25 30 lpagelallaGapgtGKttla 50
                                      +p++++ +++G++g+GK+t++
  gi|242399849|ref|YP_002995274.1| 27 VPRNTVFAVMGPSGCGKSTML 47
                                      799****************96 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00029      0.24      20      76 ..      30     143 ..      18     222 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00029
                                       SEEEEEEESTTSSHHHHHHHHCCSHCCCCC.CBTEEEEE...................................... CS
                            NB-ARC  20 slvvalvGmgGvGKttlakqilnksdeveg.rFdsvawv...................................... 57 
                                         v a++G  G+GK+t+++  ++ ++  e+ r ++ + +                                      
  gi|242399849|ref|YP_002995274.1|  30 NTVFAVMGPSGCGKSTMLRAFNRLLELNEEaRVEGKVKIfgrdvynpevdpievrrevgmvfqypnpfphltiydnv 106
                                       46899************987666544333345555555555666666666666666666666666666666666666 PP

                                       ..................EEESXXHHHHHHHXXHHHH CS
                            NB-ARC  58 ..................vvsktdkseeiletilkeL 76 
                                                          v    k+  +++++ ++L
  gi|242399849|ref|YP_002995274.1| 107 aiglklnglvrskgeideRVEWALKKAALWDEVKNRL 143
                                       6666655555555555555555555555555555555 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00043      0.35       4      25 ..      35      58 ..      33      64 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00043
                                      EE--SSSSHHHHHHHGGGGB..S- CS
                             AAA_5  4 LvGppGtgKselaerlaaal..nr 25
                                      + Gp+G+gKs++ + + ++l  n 
  gi|242399849|ref|YP_002995274.1| 35 VMGPSGCGKSTMLRAFNRLLelNE 58
                                      57****************996544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.69u 0.38s 00:00:01.06 Elapsed: 00:00:00.58
# Mc/sec: 1323.61
//
Query:       gi|242399850|ref|YP_002995275.1|  [L=278]
Description: phosphate ABC transporter permease [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.2e-17   61.9  14.6    6.2e-17   61.9  14.6    2.1  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   4.3       0.2   3.6e+03      24      70 ..      21      74 ..       2      84 .. 0.45
   2 !   61.9  14.6   3.4e-21   6.2e-17       1     172 [.      83     268 ..      79     273 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.2
                      BPD_transp_1 24 iivllslPsfvlaillvlvf..........vilsilghlilpviillllsaapyvrl 70
                                        vl+ lP f ++     vf           i  i g+l  ++i  ++l+++++++l
  gi|242399850|ref|YP_002995275.1| 21 LVVLMFLPLFHIVYS---VFkngihvilnrGITFITGTLSEGGIGPAILGTLFLTLL 74
                                      344444444442222...223445555555333333333333333333333333333 PP

  == domain 2  score: 61.9 bits;  conditional E-value: 3.4e-21
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilg.hlilpviillllsaapyvrlirraal 76 
                                       g+++G++a  +++++l ++  +l +++l +P++++++++  ++v+    g ++ l+++++l++ ++pyv + + +a+
  gi|242399850|ref|YP_002995275.1|  83 GFFVGVYAYEYPKSILGRATKFLLQIMLEFPTILVGVFVMQILVV--PMGtYSTLAGALALAIIMIPYVAVYTHEAM 157
                                       567777777*************************88885544333..345266667999999999************ PP

                      BPD_transp_1  77 rslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydysei 153
                                       r++p  ++eaa  lG++r + ++++++P+a++ i+tg+++ ++ + g+++ l+f+    G ++ + ++ +g+++ +i
  gi|242399850|ref|YP_002995275.1| 158 RQIPFAYREAAFSLGVTRVKAVFRILVPMAKRGILTGFLIGIAKVAGETAPLLFTV---GGSYETYQIGIGKPVGAI 231
                                       ********************************************************...667888888888888888 PP

                      BPD_transp_1 154 s..................nggvlalviavlllnlva 172
                                                          +g++l+l+++++ + + +
  gi|242399850|ref|YP_002995275.1| 232 PlliynliqsparehheiaWGASLILLLIFFGIFIPV 268
                                       8888888889999999988777777777777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       689  (0.0384294); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); 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 0.38s 00:00:00.97 Elapsed: 00:00:00.55
# Mc/sec: 1520.30
//
Query:       gi|242399851|ref|YP_002995276.1|  [L=313]
Description: phosphate ABC transporter permease [Thermococcus sibiricus MM 739]
Scores for complete 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-11   42.6  24.1    3.7e-10   39.8  19.4    2.2  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.1   0.4   0.00091        16      35      66 ..      30      95 ..       8     103 .. 0.65
   2 !   39.8  19.4   2.1e-14   3.7e-10      13     182 ..     104     306 ..      97     309 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.00091
                      BPD_transp_1 35 laillvlvf..................................vilsilghlilpviillllsaap 66
                                      l++llv+v                                   +i+++l++++++++++l ls+a 
  gi|242399851|ref|YP_002995276.1| 30 LLMLLVYVYnsmpifhregldiyiknvwkaaeepseeyygvlaAIWGSLYTSVIAILVALPLSLAY 95
                                      333333333777777777777877888888899999999966666666666666666666666554 PP

  == domain 2  score: 39.8 bits;  conditional E-value: 2.1e-14
                      BPD_transp_1  13 nkkldkllrpliivllslPsfvlaillvlvf......................vilsilghlilpviillllsaapy 67 
                                        k+++++l +l++++ +lP+++ +i  v+v+                      +   i g++ +++ +ll ++ +p+
  gi|242399851|ref|YP_002995276.1| 104 PKRIKEWLIILSDIMAGLPTIIYGIWGVFVLvpllkrvvmqplydylsflpifSYPPITGFSYFSAGVLLGIMVTPF 180
                                       68899999**************66666666666799999999999999999998888999***************** PP

                      BPD_transp_1  68 vrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtlllea 144
                                       +  i+r+a + +p  ++ea + lGa+  +   k++l  ++p + +g+ilafg+++g++++++++++++ +++ l  +
  gi|242399851|ref|YP_002995276.1| 181 AAAIIREAYQMIPFTYREAIYSLGATQLE-ATKILLGYIKPAVYSGIILAFGRAIGETAAVSLVIGNT-FNLSLALS 255
                                       *****************************.999********************************776.77777777 PP

                      BPD_transp_1 145 ilgydyseis.............nggvlalviavlllnlvadilqrlldpr 182
                                         gy +s+ +               +++ +++a++++ l +++   +l +r
  gi|242399851|ref|YP_002995276.1| 256 APGYTISSLIanqygnafiyeymTSALFSAGLALFAIGLTVNLAGLYLLRR 306
                                       777777776689999999999998889999999999999999988888777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       684  (0.0381505); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.53
# Mc/sec: 1784.37
//
Query:       gi|242399852|ref|YP_002995277.1|  [L=272]
Description: AP endonuclease [Thermococcus sibiricus MM 739]
Scores for complete 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-20   72.3   0.5      5e-20   71.8   0.5    1.2  1  AP_endonuc_2  Xylose isomerase-like TIM barrel


Domain annotation for each model (and alignments):
>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.8   0.5   2.8e-24     5e-20      39     210 .]      56     216 ..      24     216 .. 0.79

  Alignments for each domain:
  == domain 1  score: 71.8 bits;  conditional E-value: 2.8e-24
                                       HTTSEEEEEEECCCHSTCTHC...HTTCSHHHHHHHHHHHHHHHHHHTBSEEEEEBCCGBCTTTSGHHHHHHHHHHH CS
                      AP_endonuc_2  39 elglriaslslftrfgypded...erearreesvdalkraielaaaLGapllvlhpGtagagpkgseeeawerlaes 112
                                        l+++ +++ ++++  +  +d        +++ ++ +++  e+a+ L+a+++v+h G      k+s+  a+ + ++ 
  gi|242399852|ref|YP_002995277.1|  56 TLDVEFTLHAPTSDGRNIRVDlcvN----SRKNIEIMENVFEIARTLDAKYVVVHGG----DIKDSYHKALVNTRKQ 124
                                       5667777777777777777774333....4566**********************88....99************** PP

                                       HHHHHHHHHHHTSEEEEE--TTTTSSSTCHHHHHHHHHHTTTTEEEEEEHHHHHHHTTTHHHHHHH..HHGGEEEEE CS
                      AP_endonuc_2 113 lneladyaekegvklalEtlagsgvelgdeelarlldavdspnvgvclDtgHlliaeedvddalra..ladrikhvH 187
                                       + el ++ae++gvkl++E+l    +     el  +l++    nv vc+D+gH++i+   +   +++  l + i hvH
  gi|242399852|ref|YP_002995277.1| 125 MMELSAVAEEYGVKLVIENLIDNRIGAFPHELIPFLEE----NVSVCFDIGHAFINSLKYGLGVEEymLLPGIEHVH 197
                                       ***********************975554777777766....599***********5555555555015666***** PP

                                       E.EESSTTTTSSTTEESTTSSSS CS
                      AP_endonuc_2 188 ikDakgdlgagrdrhvpigeGei 210
                                       ++D++g     +d+h+ +geG i
  gi|242399852|ref|YP_002995277.1| 198 LHDNNG----AKDEHRALGEGRI 216
                                       ******....***********87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1648.93
//
Query:       gi|242399853|ref|YP_002995278.1|  [L=377]
Description: phosphate ABC transporter substrate-binding protein [Thermococcus sibiricus MM 739]
Scores for complete 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-56  191.4   0.3    3.4e-56  191.0   0.3    1.0  1  PBP_like_2  PBP superfamily domain
    1.7e-18   67.7   4.2    2.1e-18   67.3   4.2    1.1  1  SBP_bac_1   Bacterial extracellular solute-binding protein
    6.2e-06   25.5   0.0    9.3e-05   21.6   0.0    2.2  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 !  191.0   0.3   5.6e-60   3.4e-56       5     281 ..      40     345 ..      29     346 .. 0.88

  Alignments for each domain:
  == domain 1  score: 191.0 bits;  conditional E-value: 5.6e-60
                        PBP_like_2   5 eatsvge..ifgaGsttpapalrkladafekaapgakvnyastGSgagikalrngdvdfagsdrplteseiaagwaa 79 
                                       ++    +  ++ aG+t+p+  ++k++++++k +p++k++y+++GSg g+ a+++g +d++ +d p++e +  +++  
  gi|242399853|ref|YP_002995278.1|  40 QG----QviMRTAGATFPKYQVQKWIETYQKLNPNVKIEYEGGGSGHGQDAFLKGITDIGRTDPPVKEPTW-NKFLE 111
                                       22....24499********************************************************9933.55555 PP

                        PBP_like_2  80 ngaggliqvpvaigaialvvnkd..nplnlsreaLakIfsgkItnWnd........vlglpadgpIkvvhrsdgsgt 146
                                       +g  ++ q+pv++gaia+v+n++  ++l+lsr++LakIf g+I  W+d         ++lp  + I vvhrsd+sgt
  gi|242399853|ref|YP_002995278.1| 112 TG-DQPLQFPVVVGAIAIVFNVPgvDELRLSRDVLAKIFLGEIEYWDDeaikelnpNANLP-HEKIIVVHRSDSSGT 186
                                       55.******************99788888***********************999655555.999************ PP

                        PBP_like_2 147 tflfstalaeq...............gpwt..asgigasgsegvasav.snngaigyvsvaywlavkgysladvtng 205
                                       t +f+ +l+                 +p +   +gig +g++gv+ ++ ++++ i+y++++y+ ++ ++++a+++n+
  gi|242399853|ref|YP_002995278.1| 187 TAVFTAYLSLIssewaekvgdgkvvdWPVDkmGRGIGGKGNSGVVAVLkQTKYSIAYTELSYAITE-NLPVAAIENK 262
                                       *********8899999888888886633336678999999*******9899*************99.********** PP

                        PBP_like_2 206 agkfvlptaataasalkvakias......nplawslqpveeniadgayPlsrftyiivyqpyayh...gnnaalaka 273
                                       agkfv pt++t+++a+  +k  +      +  +++++ + +++++ +yP+++f++++v q+  ++   +++a ++k+
  gi|242399853|ref|YP_002995278.1| 263 AGKFVKPTEETIKEAVAKVK--AfipdptEGYKEDVKQLLDAPGENSYPIVAFSHFLVWQNRGGKhysPEKASAIKE 337
                                       ************99777755..3448889778888999********************9987655457777****** PP

                        PBP_like_2 274 Fldyllsd 281
                                       Fl ++l++
  gi|242399853|ref|YP_002995278.1| 338 FLRWVLTE 345
                                       *****985 PP

>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.3   4.2   3.5e-22   2.1e-18       7     314 ..      49     348 ..      45     349 .. 0.83

  Alignments for each domain:
  == domain 1  score: 67.3 bits;  conditional E-value: 3.5e-22
                                       HHHHHHHHHHH....HHHHHTTEEEEEEEECHHHHHH...HHHHHHHTTSSSCSEEEE.CGGHHH..HHHHT..TSB CS
                         SBP_bac_1   7 gaalqalvaka....fekehpgikVeiesvgsgslaq...kltlaiaaGdgpaDviav.dndwia..rlaka..gll 71 
                                       ga+++++ +++    ++k++p++k+e+e +gsg +++   k++++i+ +d+p     v +++w +  +  ++  +++
  gi|242399853|ref|YP_002995278.1|  49 GATFPKYQVQKwietYQKLNPNVKIEYEGGGSGHGQDaflKGITDIGRTDPP-----VkEPTWNKflETGDQplQFP 120
                                       6777777777777779**********************************99.....55566666445566689999 PP

                                       ECCHHHHHHTTECTTCCTEEEEHHHHTHHHHCEEEESEEEEEEEEEEEETTTHHCTTGGGSHBHHHHHHHHHHHHHH CS
                         SBP_bac_1  72 lpldpyvkaylapgvkdaadklsssvlpkildskvlyvPlyaargliYNkdlfekagldppwtWdelveaakklkek 148
                                         ++++++  ++pgv+  +++ls +vl+ki+             g i                Wd+ +++  ++ ++
  gi|242399853|ref|YP_002995278.1| 121 VVVGAIAIVFNVPGVD--ELRLSRDVLAKIFL------------GEIE--------------YWDDEAIKELNPNAN 169
                                       9999999999999998..7899999*****99............5555..............*************** PP

                                       CTCT.HCCHCCEEHHHHHHHHHHHHHHHHTGGGEECCCT......................HHCSHHHHS..HHHHH CS
                         SBP_bac_1 149 gkkp.iggarggsasgtayyfalalakslggkvfdkdgg......................gldnpegvt..aatyl 200
                                        + + i+++++++ sgt+++f+ +l++ +   ++ +++g                      g+++   +t  +++y 
  gi|242399853|ref|YP_002995278.1| 170 LPHEkIIVVHRSDSSGTTAVFTAYLSLISS--EWAEKVGdgkvvdwpvdkmgrgiggkgnsGVVAVLKQTkySIAYT 244
                                       ******************************..666666669999************888887777777779999999 PP

                                       HHHHHHHHHHHHHHTTEEECSSHHHHHHHHHTTSCSEEEEEHHHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBET CS
                         SBP_bac_1 201 vklyavanltkelkgkgaenkdgaaalalfeaGeaamaivglwaalaamkvapkvafaadkekpkeelgvaplPagk 277
                                       + +ya+ +   +l+ +  enk g ++++  e+ + a+      +a++ +  ++ + ++++  ++++e  +++++   
  gi|242399853|ref|YP_002995278.1| 245 ELSYAITE---NLPVAAIENKAGKFVKPTEETIKEAV---AKVKAFIPDPTEGYKEDVKQLLDAPGENSYPIVA--- 312
                                       99997777...*****************777555555...5567777778888888888888888888888854... PP

                                       TTTSEEEEEEEEEEBTTCST..HHH...HHHHHHHHTSHHHH CS
                         SBP_bac_1 278 ggkpgilgayglaipkgskn..pea...AkkFldfllspeaq 314
                                             ++   ++ + g k+  pe    +k+Fl+++l+++++
  gi|242399853|ref|YP_002995278.1| 313 ------FSHFLVWQNRGGKHysPEKasaIKEFLRWVLTEGQK 348
                                       ......46666666777777984445789**********997 PP

>> PBP_like  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   1.6e-08   9.3e-05       2     115 ..      62     196 ..      61     212 .. 0.67

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.6e-08
                                       HHHHHH-TTCEEEEEES-HHHHHHHHHTTS-SEEEESS---CCCHHCCCCCEEEEEEEEEEEE-CC-HCHCCCCH.C CS
                          PBP_like   2 eelaeknpgvrvavanvGsggGlkalrageadiagshlldketeeynapalrkaldgievvlvnlarreqglvva.k 77 
                                       e +++ np+v++++ + Gsg G  a+ +g +di+ ++ + ke    ++ ++ +     +    +++  ++ +v++ +
  gi|242399853|ref|YP_002995278.1|  62 ETYQKLNPNVKIEYEGGGSGHGQDAFLKGITDIGRTDPPVKEPTWNKFLETGD-----QPLQFPVVVGAIAIVFNvP 133
                                       7899***********************************88664333332222.....2233333333333333213 PP

                                       CHHHS.........................--BGGGC-S-B-EEEEE-TTSHHHHHHHHHHC- CS
                          PBP_like  78 gnpkk.........................itnwkdladaplrlvnRetGSGtrdlfdellkk 115
                                       g +                           ++  + l+ +++ +v R  +SGt  +f+  l+ 
  gi|242399853|ref|YP_002995278.1| 134 GVDELrlsrdvlakiflgeieywddeaikeLNPNANLPHEKIIVVHRSDSSGTTAVFTAYLSL 196
                                       322212333344445555555555444443555667799******************999864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); 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: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 2388.10
//
Query:       gi|242399854|ref|YP_002995279.1|  [L=432]
Description: transposase ISTsi3 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.2e-31  107.7   0.1    8.2e-31  106.7   0.1    1.5  1  OrfB_IS605      Probable transposase
    1.5e-19   69.6   0.0      3e-19   68.7   0.0    1.5  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
     0.0012   18.2   0.2     0.0031   17.0   0.2    1.8  1  HTH_OrfB_IS605  Helix-turn-helix domain
     0.0023   18.3   0.0     0.0081   16.5   0.0    1.9  1  RuvX            Holliday junction resolvase
  ------ inclusion threshold ------
      0.034   12.9   0.2      0.049   12.3   0.2    1.2  1  MAP65_ASE1      Microtubule associated protein (MAP65/ASE1 fa
       0.11   12.5   0.5        0.3   11.1   0.5    1.7  1  Zn_Tnp_IS1595   Transposase zinc-ribbon domain


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.7   0.1   2.7e-34   8.2e-31       1     119 [.     174     299 ..     174     300 .. 0.97

  Alignments for each domain:
  == domain 1  score: 106.7 bits;  conditional E-value: 2.7e-34
                        OrfB_IS605   1 sipveveve.........lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksk 68 
                                       +i ++ve++         +++pkgn +agiDlG+nnL++v++e+g++fl +gr+lks  +y++++i e qskl+ks+
  gi|242399854|ref|YP_002995279.1| 174 HISYTVEEKlegnswvklPREPKGNLTAGIDLGVNNLMAVYVENGESFLVNGRPLKSIAFYWQERISEYQSKLNKSG 250
                                       6788888889999999999*********************************************************9 PP

                        OrfB_IS605  69 nykkasrklarlhrkrsrrrkhllhklathliktlkevgvetLnvgnmkdi 119
                                          kasrkl+r+h+k + + +h+++ ++++ +++l+++gv+ ++vg++k+i
  gi|242399854|ref|YP_002995279.1| 251 --AKASRKLKRMHEKAKLQARHYINTAVRQTVRRLYDLGVSRIVVGYPKKI 299
                                       ..9*********************************************987 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.7   0.0     1e-22     3e-19       1      69 []     319     388 ..     319     388 .. 0.97

  Alignments for each domain:
  == domain 1  score: 68.7 bits;  conditional E-value: 1e-22
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke.alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       f+ ++++l++ a+eyGi+v +v++ +TS+tC+ Cg+++++ +  + +fkC++ g+++++D+++a+Nilk+
  gi|242399854|ref|YP_002995279.1| 319 FNYVIKRLKEVAEEYGIQVLLVDEDFTSQTCPLCGQRHSNgRIFRGLFKCRREGVVMNADLVGAFNILKK 388
                                       78899***********************************999*************************96 PP

>> HTH_OrfB_IS605  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.2     1e-06    0.0031       1      45 [.       1      44 [.       1      46 [. 0.88

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1e-06
                    HTH_OrfB_IS605  1 MvlkaykyrlyPTpeQeeklartfGcvRfVYNkaLaerkeayeee 45
                                      M +++ ++ l P +eQe  l + + +   ++Nk   er ++ +e 
  gi|242399854|ref|YP_002995279.1|  1 M-KRSVTVKLQPSKEQEKTLFELAQATAIIWNKLNYERLKQFKEF 44
                                      8.******************************9877776666665 PP

>> RuvX  Holliday junction resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   2.7e-06    0.0081      33     101 ..     269     348 ..     244     360 .. 0.56

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.7e-06
                                       ---HHHHHHHHHHHHHHTT--EEEEE------SSS---SS......TTHHH...HHHHHHT....T-EEEEE--S-- CS
                              RuvX  33 rkskekdleelkelvkeeeveeiVvGlPlnldgsegesak......kvrkf...aeeLakrl..kklpvelvDErlt 98 
                                       r+  ++++++  + + +  v++iVvG+P+++  + ++  k      +v +f   +++L++    ++++v lvDE +t
  gi|242399854|ref|YP_002995279.1| 269 RHYINTAVRQTVRRLYDLGVSRIVVGYPKKIAREPEKGKKqnfllsHVWRFnyvIKRLKEVAeeYGIQVLLVDEDFT 345
                                       3322455555555556669*********766433222221011111333331114444443344599********** PP

                                       --X CS
                              RuvX  99 tve 101
                                       + +
  gi|242399854|ref|YP_002995279.1| 346 SQT 348
                                       976 PP

>> MAP65_ASE1  Microtubule associated protein (MAP65/ASE1 family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   1.6e-05     0.049     386     438 ..     210     264 ..     207     284 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.6e-05
                                       HHHHHHHCTS--EETTEEHHHHHHHHHHHHH......HHHHHHHHHHHHHHHHHHH CS
                        MAP65_ASE1 386 veaweeefgrpFlvdGeklleiieeqweeleeky...qererqksarklkkasqte 438
                                       ++a   e+g+ Flv+G +l + i+ +w+e+ + y     ++  k++rklk   ++ 
  gi|242399854|ref|YP_002995279.1| 210 LMAVYVENGESFLVNGRPLKS-IAFYWQERISEYqskLNKSGAKASRKLKRMHEKA 264
                                       5666779***********976.7899999999993433344445555554444333 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 ?   11.1   0.5    0.0001       0.3      19      42 ..     347     370 ..     341     370 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0001
                     Zn_Tnp_IS1595  19 fvCPhCgsr.kayriktrglfqCke 42 
                                       ++CP Cg r +  ri + glf+C++
  gi|242399854|ref|YP_002995279.1| 347 QTCPLCGQRhSNGRIFR-GLFKCRR 370
                                       68*****9966667775.*****85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (432 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       798  (0.0445089); expected 358.6 (0.02)
Passed bias filter:                      602  (0.0335769); 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: 0.69u 0.32s 00:00:01.01 Elapsed: 00:00:00.51
# Mc/sec: 2525.73
//
Query:       gi|242399855|ref|YP_002995280.1|  [L=53]
Description: hypothetical protein TSIB_1882 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.015   15.3   0.3      0.029   14.3   0.3    1.5  1  RHH_1     Ribbon-helix-helix protein, copG family


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.3   1.6e-06     0.029       2      20 ..       6      24 ..       5      25 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.6e-06
                                      EEEEEEHHHHHHHHHHHHH CS
                             RHH_1  2 vsirldeellerLdelarr 20
                                      ++i++d+e+ ++++el+++
  gi|242399855|ref|YP_002995280.1|  6 ITISVDDEVEKKFRELVEK 24
                                      9***************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 351.44
//
Query:       gi|242399856|ref|YP_002995281.1|  [L=40]
Description: hypothetical protein TSIB_1883 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       290  (0.0161749); expected 358.6 (0.02)
Passed bias filter:                      165  (0.00920297); 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: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.50
# Mc/sec: 239.25
//
Query:       gi|242399857|ref|YP_002995282.1|  [L=100]
Description: Linocin_M18 bacteriocin protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.9e-07   30.9   3.7    3.6e-07   30.7   3.7    1.2  1  Rubrerythrin  Rubrerythrin
    1.3e-05   25.5   0.5      2e-05   24.9   0.5    1.5  1  DUF2383       Domain of unknown function (DUF2383)
  ------ inclusion threshold ------
      0.035   14.0   4.1       0.12   12.3   1.8    2.1  2  Ferritin      Ferritin-like domain
       0.13   11.1   0.0       0.14   11.0   0.0    1.0  1  DUF2875       Protein of unknown function (DUF2875)


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 !   30.7   3.7     8e-11   3.6e-07       3      71 ..      24      89 ..       7      99 .. 0.82

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 8e-11
                                      HHHHHHHHHHHHHHHHHHHHCHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSBBS-- CS
                      Rubrerythrin  3 LekAiagEssarrlYkelaekakegypqiaelFeelAeeEreHakilnklleklepelelevkekvrey 71
                                      L  Ai +E +a+++Y+ lae ++   + i+ +F ++A eE+eH + +  +l ++++el  ++ ++ +e+
  gi|242399857|ref|YP_002995282.1| 24 LRWAIEAELDAISFYEQLAELIE--DERIKHIFYDVANEEKEHFGEFLAALFEVDKELA-KYMKDGFEE 89
                                      78899999999999999999999..8899999999999999999999999988888887.444444444 PP

>> DUF2383  Domain of unknown function (DUF2383)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.5   4.4e-09     2e-05       2      53 ..      20      71 ..      19     100 .] 0.89

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 4.4e-09
                                      HHHHHHHHHHHHHHHHHHHHHHHHT--SHHHHHHHHHHHHHHHHHHHHHHHH CS
                           DUF2383  2 vieaLndLietlkdgeegykeaaekvkdpqlktlleriaeereeaaeeLqse 53
                                      +++aL   ie++ d++ +y++ ae ++d+++k+++ ++a+e +e+  e+ + 
  gi|242399857|ref|YP_002995282.1| 20 IAQALRWAIEAELDAISFYEQLAELIEDERIKHIFYDVANEEKEHFGEFLAA 71
                                      56788888*********************************99999887665 PP

>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.8   2.7e-05      0.12      80     130 ..      19      66 ..       4      72 .. 0.59
   2 ?   10.6   4.0   8.7e-05      0.39       2      59 ..      22      76 ..      21      93 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.7e-05
                                       SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHH CS
                          Ferritin  80 sveevleaalehekkvteslrelielaeeegDpatadfledfleeqeehew 130
                                       ++ ++l+ a+e+e ++++ +++l+el e+       +++ d+ +e+ eh  
  gi|242399857|ref|YP_002995282.1|  19 EIAQALRWAIEAELDAISFYEQLAELIED---ERIKHIFYDVANEEKEHFG 66 
                                       55666666666666666666666666663...3556666666666555543 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 8.7e-05
                                      HHHHHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                          Ferritin  2 kaLneqladeltaayqylamawyvkgpgleglaeffdeqaeeerehadklaerilalG 59
                                      +aL+ ++ +el+a+  y ++a  ++++    +++ f++ a ee eh+ +++  + + +
  gi|242399857|ref|YP_002995282.1| 22 QALRWAIEAELDAISFYEQLAELIEDER---IKHIFYDVANEEKEHFGEFLAALFEVD 76
                                      5788889999999999999999999975...556699999999999999987777666 PP

>> DUF2875  Protein of unknown function (DUF2875)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   3.1e-05      0.14     318     377 ..      19      79 ..       7      98 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.1e-05
                           DUF2875 318 engkrlktalqakalkaaweqaldvlpenkkpkrlfydstnskeav.ialnqaladlnkda 377
                                       e  + l+ a++a+    ++ + l+ l e+++ k +fyd +n+++     +  al +++k+ 
  gi|242399857|ref|YP_002995282.1|  19 EIAQALRWAIEAELDAISFYEQLAELIEDERIKHIFYDVANEEKEHfGEFLAALFEVDKEL 79 
                                       668999*******9999999******************99976544045677788877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1009  (0.0562775); expected 358.6 (0.02)
Passed bias filter:                      695  (0.038764); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.35s 00:00:00.91 Elapsed: 00:00:00.52
# Mc/sec: 575.67
//
Query:       gi|242399858|ref|YP_002995283.1|  [L=151]
Description: hypothetical protein TSIB_1885 [Thermococcus sibiricus MM 739]
Scores for complete 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-05   23.4   7.1    9.1e-05   22.9   7.1    1.2  1  Rubrerythrin  Rubrerythrin
     0.0029   17.8   0.6     0.0039   17.4   0.6    1.1  1  Ferritin_2    Ferritin-like domain
     0.0092   16.3   2.2     0.0093   16.3   0.3    2.0  3  DUF2383       Domain of unknown function (DUF2383)


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 !   22.9   7.1   1.5e-08   9.1e-05       3     136 ..      10     145 ..       9     146 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.5e-08
                                       HHHHHHHHHHHHHHHHHHHHCHH.TT..-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSBBS------- CS
                      Rubrerythrin   3 LekAiagEssarrlYkelaekak.eg..ypqiaelFeelAeeEreHakilnklleklepelelevkekvreyaeakp 76 
                                       ++kA+  E +a + Y+    +++ +g  y++++e+  ++A +   H+++++ +l++ ++ ++l  +  + e  e + 
  gi|242399858|ref|YP_002995283.1|  10 VKKAYETEKKAASSYTDGLARIRgQGlrYTKVEEIVGRIAVDTIIHKHLMEAILNAQKELEKLAGEGPIEEIKEIEL 86 
                                       5789999999999999866666666433999***********************99555555655554433333333 PP

                                       TTGGHHHHHHHHHHHHHHHHHCHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Rubrerythrin  77 kflttaknLeeaiegayaeeeemyrfyeelaekegneeakklfkklaeaEkkHeerlrkl 136
                                          + +  ++  +e   + e++m+++y+++ +k++++  k l ++l + E++H ++l++l
  gi|242399858|ref|YP_002995283.1|  87 AP-EQKALVKRFAEMHLEIERDMIETYQKMVDKMTHPLFKGLAEALVKNEQEHHKLLAEL 145
                                       22.33456778889999***************************************9987 PP

>> Ferritin_2  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.6   6.5e-07    0.0039       8     135 ..      12     147 ..       8     148 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 6.5e-07
                        Ferritin_2   8 fAlnlEyleaafYtaalegaslddkalldaevrevaeeiakheeaHveflkaaleGaaavakp..........tfdf 74 
                                        A+  E  +a  Yt +l++++   ++l  ++v e++  ia + + H  +++a l+ ++ ++k+          ++++
  gi|242399858|ref|YP_002995283.1|  12 KAYETEKKAASSYTDGLARIRG--QGLRYTKVEEIVGRIAVDTIIHKHLMEAILNAQKELEKLagegpieeikEIEL 86 
                                       69999*************8754..78888999**********************95555555544444554467888 PP

                        Ferritin_2  75 afdpfadeksflalaavlEdvgvsAYlgaapllsnkelltaaasIlsvEArHaavirtllg 135
                                       a ++ a  k f ++   +E+  ++ Y+  + +++ + ++ +a  ++  E +H  ++++l+ 
  gi|242399858|ref|YP_002995283.1|  87 APEQKALVKRFAEMHLEIERDMIETYQKMVDKMTHPLFKGLAEALVKNEQEHHKLLAELIE 147
                                       9999999*********************************************999998875 PP

>> DUF2383  Domain of unknown function (DUF2383)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.76   4.5e+03      91     107 ..      10      26 ..       7      29 .. 0.76
   2 ?   -3.1   0.0       1.6   9.9e+03      81      98 ..      53      70 ..      46      74 .. 0.54
   3 !   16.3   0.3   1.6e-06    0.0093      10      57 ..     102     149 ..      96     151 .] 0.95

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.76
                                       HHHHHHHHHHHHHHHHH CS
                           DUF2383  91 leeleegEdkaleeyee 107
                                       ++++ e E+ka + y +
  gi|242399858|ref|YP_002995283.1|  10 VKKAYETEKKAASSYTD 26 
                                       67778889999888876 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.6
                                      ------HHHHHHHHHHHH CS
                           DUF2383 81 altsndeeaileeleegE 98
                                      ++ ++  eail++  e E
  gi|242399858|ref|YP_002995283.1| 53 IIHKHLMEAILNAQKELE 70
                                      555555555555544444 PP

  == domain 3  score: 16.3 bits;  conditional E-value: 1.6e-06
                                       HHHHHHHHHHHHHHHHT--SHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                           DUF2383  10 ietlkdgeegykeaaekvkdpqlktlleriaeereeaaeeLqseiral 57 
                                       +e+++d +e+y+++++k  +p +k l+e  +++ +e+ + L++ i+++
  gi|242399858|ref|YP_002995283.1| 102 LEIERDMIETYQKMVDKMTHPLFKGLAEALVKNEQEHHKLLAELIEKY 149
                                       7899***************************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1127  (0.0628591); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); 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: 0.55u 0.33s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 901.17
//
Query:       gi|242399859|ref|YP_002995284.1|  [L=267]
Description: Osmoprotection protein (proX) [Thermococcus sibiricus MM 739]
Scores for complete 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-46  158.3   0.0    3.1e-46  158.1   0.0    1.1  1  OpuAC     Substrate binding domain of ABC-type glycine betain


Domain annotation for each model (and alignments):
>> 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 !  158.1   0.0   1.7e-50   3.1e-46       2     255 ..       2     259 ..       1     261 [. 0.93

  Alignments for each domain:
  == domain 1  score: 158.1 bits;  conditional E-value: 1.7e-50
                                       EEEEEEESSHHHHHHHHHHHHHHHHTTE.EEEEEEEESHHHHHHHHHTTSSSEEEEEEHHHH............... CS
                             OpuAC   2 tivigsknwteqevlaeilkqllekkGy.kveltnlgstavlfaalasGdiDvypeewtgta............... 62 
                                       +ivig k+++eq +la+il++l+e++G+  + +++    ++  +al++G+i vy+ e+tgta               
  gi|242399859|ref|YP_002995284.1|   2 KIVIGAKPFNEQKILAHILGKLFERAGFdYEVRVSEPRLEANLEALEKGEINVYV-EYTGTAynallklppmkewyp 77 
                                       79************************776555555555599**************.********************* PP

                                       ...HHHHHHHHHHHHEEEEEEEESEEECEEEEEEHHHHHHHTTTBHHHHCTHHGGTEEEEEHHCCHSTTSHHCCHHH CS
                             OpuAC  63 ...yeaykkaveekkglevlgplgagnteglavpkyvaekygiksisDLkkpaedlelgakgeflgrpdgwgcekvt 136
                                           +a+ +++  ++++++ ++lg+ n  +lav+k++a+k+ +++isDL+k +++l ++  g +++rpdg++     
  gi|242399859|ref|YP_002995284.1|  78 ekvFNAVVEGFR-EREIQIFARLGFRNDFALAVRKDFAKKNSLETISDLAKISKNLVFACPGPYIERPDGLP----- 148
                                       999999999998.8888889****************************************************..... PP

                                       HHHHHHHT-TTCEEEGSCEEEEHHHHHHHHHTTCSSEEEEETTSTHHHHTTEEE-B-TTSTS-SSEEEEEEEEHHHH CS
                             OpuAC 137 egllkaYgldkvelvegseaamdaelyaaykrgepvvvyawtPdwaikkydlvvLedpkglfppaynvvpvvrkefa 213
                                         l+++Y+l    +++   + m +++y+a+ +ge++v++a+t+d+++  ++l+ L+d+++++pp y++ ++ r e+ 
  gi|242399859|ref|YP_002995284.1| 149 -RLKEVYDL----EFREIKPLMPPQMYEAISKGEVDVITAFTTDARVEVFNLKTLNDDRKALPP-YEAILIGR-ELP 218
                                       .********....77777888888****************************************.88877777.899 PP

                                       HHSCTHHHHHHHHC--HHHHHHHHHHHHTTTT-HHHHHHHHH CS
                             OpuAC 214 ekaPevaafLeklsldtetlnelnaqvdvegkdpeevAkawl 255
                                       ek  e+ ++Le  +++ e ++eln+++d eg+++ee+A++++
  gi|242399859|ref|YP_002995284.1| 219 EKVEEALRLLEG-KITVEMMRELNRKLDFEGRKEEEIAEEFV 259
                                       997777777777.7**************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); 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 0.36s 00:00:00.98 Elapsed: 00:00:00.55
# Mc/sec: 1467.23
//
Query:       gi|242399860|ref|YP_002995285.1|  [L=205]
Description: Osmoprotection protein (proW-1) [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.6e-23   81.6  15.5    7.1e-23   81.3  15.5    1.1  1  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
       0.04   14.4   0.0      0.059   13.8   0.0    1.3  1  MCR_alpha     Methyl-coenzyme M reductase alpha subunit, C-te


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 !   81.3  15.5     8e-27   7.1e-23       2     181 ..      26     199 ..      25     201 .. 0.94

  Alignments for each domain:
  == domain 1  score: 81.3 bits;  conditional E-value: 8e-27
                      BPD_transp_1   2 illGilaa..lnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraal 76 
                                       i++Gi +a    ++k++  +++++ ++++++Psf+++ ++v        lg +++p++++++l a+ +++ +++ +l
  gi|242399860|ref|YP_002995285.1|  26 IVVGIPLAvlSLKSKRVASIIMGFANLVQAIPSFAVVAIVV------PLLGIGFTPAVFAIFLRALLPIVKNTYVGL 96 
                                       7889999998889****************************......99**************************** PP

                      BPD_transp_1  77 rslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydysei 153
                                       +++++  + aar  G+++w+i+r+v++P+a p +++g+ +a++++   a+l+ ++gs+ Glg+l++e + +++++ i
  gi|242399860|ref|YP_002995285.1|  97 NEVNEAMIDAARGIGLTEWEIIRYVRFPHAYPAMFAGIKFAAVLANSIAILTAIIGSG-GLGSLVFEGLASFNTDKI 172
                                       *********************************************9999999999955.7***************99 PP

                      BPD_transp_1 154 snggvlalviavlllnlvadilqrlldp 181
                                       + +g+l ++++ + + l++  + r + p
  gi|242399860|ref|YP_002995285.1| 173 I-AGSLPAILMAVFIDLSFSYMERRFIP 199
                                       9.99999999999999999888877766 PP

>> MCR_alpha  Methyl-coenzyme M reductase alpha subunit, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   6.6e-06     0.059      31     103 ..      81     152 ..      70     167 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.6e-06
                         MCR_alpha  31 fvyygvdyvkdkygglakvka.tlevvkdiatevtlyaleqyekyptlledhfGGsqraavlaaaagistalat 103
                                       f+   + +vk+ y gl++v++  ++  + i+   t + + +y ++p +    f G + aavla + +i ta+  
  gi|242399860|ref|YP_002995285.1|  81 FLRALLPIVKNTYVGLNEVNEaMIDAARGIG--LTEWEIIRYVRFPHAYPAMFAGIKFAAVLANSIAILTAIIG 152
                                       5555567899999999998762456666665..7889999****************************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       702  (0.0391544); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.55
# Mc/sec: 1128.75
//
Query:       gi|242399861|ref|YP_002995286.1|  [L=209]
Description: Osmoprotection protein (proW-2) [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.8e-24   84.8  13.2    7.5e-24   84.5  13.2    1.1  1  BPD_transp_1   Binding-protein-dependent transport system inn
  ------ inclusion threshold ------
       0.09   12.6   0.0       0.17   11.7   0.0    1.5  1  HTH_AsnC-type  AsnC-type helix-turn-helix domain


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.5  13.2   8.4e-28   7.5e-24       2     175 ..      31     194 ..      30     205 .. 0.91

  Alignments for each domain:
  == domain 1  score: 84.5 bits;  conditional E-value: 8.4e-28
                      BPD_transp_1   2 illGilaa..lnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraal 76 
                                       +++G++++  l+++ k+  l  ++ +v+ ++P+++l++l++       ilg +  p i++++l+++ ++ ++++ +l
  gi|242399861|ref|YP_002995286.1|  31 LIIGVFLGfvLYKRPKIAALTFNILNVIETVPTLALLVLFL------PILGLGEKPTIAASVLYSILPIARNTYTGL 101
                                       789******999*****************************......9***************************** PP

                      BPD_transp_1  77 rslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydysei 153
                                        s+++++ e+a+a G+s+++i++kv++P+alp i++g+++a+++ +g  +l  +++++ Glg ++ + i  yd + i
  gi|242399861|ref|YP_002995286.1| 102 TSVERSYLEVAEAIGLSEREILFKVRFPLALPLIAAGVRIAVVFTMGVVTLGGLVAAG-GLGAPIQTGIHLYDRDII 177
                                       ********************************************************66.7***************77 PP

                      BPD_transp_1 154 snggvlalviavlllnlvadil 175
                                        ++g++++++a++l     d +
  gi|242399861|ref|YP_002995286.1| 178 VVTGLWVGILALIL-----DGV 194
                                       76666666666555.....333 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   0.0     2e-05      0.17      18      35 ..     106     123 ..     102     127 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2e-05
                     HTH_AsnC-type  18 isyaeLAervGlSestvl 35 
                                       +sy e+Ae++GlSe ++l
  gi|242399861|ref|YP_002995286.1| 106 RSYLEVAEAIGLSEREIL 123
                                       8*************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       819  (0.0456802); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); 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):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1248.91
//
Query:       gi|242399862|ref|YP_002995287.1|  [L=364]
Description: Osmoprotection protein (proV) [Thermococcus sibiricus MM 739]
Scores for complete 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-35  121.5   0.0      7e-35  120.5   0.0    1.5  1  ABC_tran      ABC transporter
    1.4e-10   41.5   0.6    0.00027   20.9   0.0    2.3  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    2.4e-06   28.1   0.0      5e-06   27.0   0.0    1.6  1  AAA_16        AAA ATPase domain
    1.1e-05   25.8   0.0    0.00021   21.7   0.0    2.7  2  CBS           CBS domain
    3.3e-05   23.4   0.0      0.011   15.2   0.0    2.7  3  SMC_N         RecF/RecN/SMC N terminal domain
    0.00027   20.6   0.0    0.00048   19.8   0.0    1.4  1  AAA_29        P-loop containing region of AAA domain
     0.0005   19.8   0.0     0.0013   18.5   0.0    1.6  1  AAA_30        AAA domain
     0.0006   20.1   0.1     0.0016   18.7   0.1    2.0  1  AAA_22        AAA domain
    0.00095   18.6   0.0     0.0022   17.4   0.0    1.6  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.001   18.8   0.0      0.012   15.4   0.0    2.1  1  DEAD          DEAD/DEAH box helicase
     0.0012   18.8   0.0     0.0027   17.7   0.0    1.6  1  AAA_5         AAA domain (dynein-related subfamily)
     0.0013   18.5   0.0      0.094   12.4   0.0    2.3  2  AAA_24        AAA domain
     0.0017   18.3   0.0     0.0071   16.3   0.0    2.0  2  NACHT         NACHT domain
      0.002   17.9   0.5      0.008   15.9   0.5    1.9  1  AAA_15        AAA ATPase domain
     0.0041   17.3   0.0      0.015   15.4   0.0    2.0  1  AAA_33        AAA domain
     0.0064   16.4   0.1      0.022   14.7   0.0    1.9  2  RsgA_GTPase   RsgA GTPase
  ------ inclusion threshold ------
      0.013   15.5   0.0      0.036   14.0   0.0    1.8  1  Rad17         Rad17 P-loop domain
      0.013   14.7   0.0      0.018   14.2   0.0    1.4  1  G-alpha       G-protein alpha subunit
      0.014   15.9   2.0      0.055   14.0   0.1    2.2  2  AAA_23        AAA domain
      0.015   15.9   0.1      0.049   14.2   0.0    2.0  1  AAA_18        AAA domain
      0.015   14.9   0.0      0.032   13.8   0.0    1.6  1  cobW          CobW/HypB/UreG, nucleotide-binding domain
      0.021   14.4   0.2       0.17   11.5   0.0    2.4  3  AAA_25        AAA domain
      0.021   14.8   0.0       0.16   12.0   0.0    2.1  2  TsaE          Threonylcarbamoyl adenosine biosynthesis protei
      0.022   13.8   0.0      0.045   12.8   0.0    1.4  1  T2SSE         Type II/IV secretion system protein
      0.028   13.7   0.2      0.073   12.3   0.0    1.7  3  TIP49         TIP49 P-loop domain
      0.032   14.7   0.0       0.17   12.3   0.0    2.3  2  AAA           ATPase family associated with various cellular 
      0.035   14.1   0.0      0.069   13.2   0.0    1.5  1  AAA_14        AAA domain
      0.048   13.4   0.1       0.22   11.2   0.1    2.0  2  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
      0.063   13.6   0.0       0.16   12.3   0.0    1.6  1  AAA_19        AAA domain
      0.069   13.0   0.0       0.21   11.5   0.0    1.8  2  DUF4720       Domain of unknown function (DUF4720)
      0.077   12.3   0.0       0.17   11.2   0.0    1.5  1  Zeta_toxin    Zeta toxin
       0.13   12.1   0.1        1.3    8.7   0.0    2.3  3  ATP_bind_1    Conserved hypothetical ATP binding protein
       0.16   11.9   0.0       0.31   10.9   0.0    1.5  1  APS_kinase    Adenylylsulphate kinase
       0.16   11.5   0.0       0.28   10.8   0.0    1.3  1  AAA_27        AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.5   0.0   1.3e-37     7e-35       2     136 ..      25     169 ..      24     170 .. 0.91

  Alignments for each domain:
  == domain 1  score: 120.5 bits;  conditional E-value: 1.3e-37
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       ++v+l++  ge++ ++G++G+GK+tLl+++ +l +p+eGe+ ++g+++++ +  +lr++ig++ q+  lfp++tvr+
  gi|242399862|ref|YP_002995287.1|  25 DHVNLEVIGGELLILIGPSGSGKTTLLRTINRLIEPDEGEVFINGQNIRDFDVVELRRSIGYVIQQIGLFPHMTVRD 101
                                       789************************************************************************** PP

                                       H.........HHHTCHH.HHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x.........xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n.........esdeeie.kalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       n         + +eeie ++ + l+l+ l+++ + + p++LSgGq+qrv laral+ +p+lll+DEp+
  gi|242399862|ref|YP_002995287.1| 102 NiglllklegWVEEEIEeRVKELLRLVALPEEFAVRYPHQLSGGQQQRVGLARALALDPPLLLMDEPF 169
                                       *********9555554413445566777777888899******************************6 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0     5e-07   0.00027       2      34 ..      37      63 ..      36      95 .. 0.72
   2 !   19.0   0.1   1.8e-06   0.00097     232     298 ..     137     201 ..     105     204 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 5e-07
                            AAA_21  2 nvliGpNgsGKSnLLdaldllarldrdvegltd 34
                                       +liGp gsGK++LL+++  l       e++  
  gi|242399862|ref|YP_002995287.1| 37 LILIGPSGSGKTTLLRTINRLI------EPDEG 63
                                      58****************8884......23222 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 1.8e-06
                            AAA_21 232 lparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrll.ellkelsrngaQviltTHS 298
                                       + +++lS G+++  +l+ al+ ++   +lll DEp   L+P l + l  e+++++++ g  ++++TH+
  gi|242399862|ref|YP_002995287.1| 137 RYPHQLSGGQQQRVGLARALALDP---PLLLMDEPFGALDPILRKQLQnEFVRIKEALGKTIVFVTHD 201
                                       568999*****999*******999...**************66666669999999999*********8 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.0   9.4e-09     5e-06      24      64 ..      34      81 ..      28     210 .. 0.64

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 9.4e-09
                            AAA_16 24 pelvllsGesGvGKsslvrellralekdg.giflrgkcdql......e 64
                                      +el++l+G+sG+GK++l+r++ r +e d+  +f++g++ +       +
  gi|242399862|ref|YP_002995287.1| 34 GELLILIGPSGSGKTTLLRTINRLIEPDEgEVFINGQNIRDfdvvelR 81
                                      3899************************73666999988873333333 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0       1.6   8.2e+02      20      52 ..     275     306 ..     274     310 .. 0.71
   2 !   21.7   0.0   3.9e-07   0.00021       7      54 ..     316     362 ..     309     364 .] 0.86

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 1.6
                                       HHHHHHHHHT..SSEEEEEETTTBEEEEEEHHHHH CS
                               CBS  20 ealelmrekg..vsrlPVVdedgklvGivtlrDll 52 
                                       ++l+ m+ek+  + ++ +V e+  l G+  l+ ll
  gi|242399862|ref|YP_002995287.1| 275 KLLKWMKEKNleF-AV-IV-ENTTLKGVTDLKSLL 306
                                       5677798999333.44.68.788899997777776 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 3.9e-07
                                       SSCEEEETTSBHHHHHHHHHHHT..SSEEEEEETTTBEEEEEEHHHHHHH CS
                               CBS   7 rdvvtvppdttleealelmrekg..vsrlPVVdedgklvGivtlrDllra 54 
                                       r++++++p+++l+ al +m++k+  v ++ VV e +k+vG++    +l  
  gi|242399862|ref|YP_002995287.1| 316 REPIVFSPEDSLASALAEMKSKNafV-GI-VV-EKEKPVGVLLANEVLLR 362
                                       7899***************9888988.**.**.7888****998887765 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 ?    5.9   0.1     0.014       7.6      27      44 ..      37      54 ..      25      59 .. 0.86
   2 !   15.2   0.0   2.1e-05     0.011     101     195 ..      56     199 ..      51     219 .. 0.82
   3 ?   -1.6   0.2       2.8   1.5e+03      65     133 ..     242     312 ..     236     314 .. 0.66

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.014
                                      EEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxx RF
                             SMC_N 27 taivGpNGSGKsnlldAi 44
                                       +++Gp GSGK+ ll  i
  gi|242399862|ref|YP_002995287.1| 37 LILIGPSGSGKTTLLRTI 54
                                      679**********99887 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 2.1e-05
                                       EEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT.......................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......................................... RF
                             SMC_N 101 rrvkrkgeseykingkevtkkevsellesagiske.......................................... 135
                                       r ++ + e e++ing++++  +v el +s g  ++                                          
  gi|242399862|ref|YP_002995287.1|  56 RLIEPD-EGEVFINGQNIRDFDVVELRRSIGYVIQqiglfphmtvrdniglllklegwveeeieervkellrlvalp 131
                                       444444.4599********************999999**************************************** PP

                                       .........CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHH...HHHHHCTTSEEEEE CS
                                       .........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxx RF
                             SMC_N 136 .........lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvae...llkeksknaQfivi 195
                                                +LSgG+++ v la  +A+      pl l+De   aLD   +k++ +   ++ke+  ++ ++v+
  gi|242399862|ref|YP_002995287.1| 132 eefavryphQLSGGQQQRVGLARALALD----PPLLLMDEPFGALDPILRKQLQNefvRIKEALGKTIVFVT 199
                                       ************************9985....5*************99988887622234444444444444 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 2.8
                                       C--BTTCSSTTEEEEEEEE.EETTEESSSSSSCEEEEEEEETTSEEEEEETTEEE-H.HHHHHHHHCTT-S CS
                                       xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx RF
                             SMC_N  65 ihkskekasvkkaeveitf.dnedkklkiekeevsisrrvkrkgeseykingkevtk.kevsellesagis 133
                                       +++ k+ ++++  +v+ ++   e+ +++i+++e  ++  ++++ e  + +++++ +  +++++ll+s+ i+
  gi|242399862|ref|YP_002995287.1| 242 VNADKKFKHLDTLRVKDLMiGVENYTVEIKSKEKLLKWMKEKNLEFAVIVENTTLKGvTDLKSLLNSHSIE 312
                                       55555555555556653331445555677777777777888888888888888877668999999988886 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   0.0   9.1e-07   0.00048      23      53 ..      34      66 ..      19      70 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 9.1e-07
                            AAA_29 23 g.atlltGpsGsGKSTllDAiqalLvpak.kvr 53
                                      g   +l+GpsGsGK+Tll  i+ l+ p++ +v 
  gi|242399862|ref|YP_002995287.1| 34 GeLLILIGPSGSGKTTLLRTINRLIEPDEgEVF 66
                                      357889***************999999885555 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   2.4e-06    0.0013      19      51 ..      35      67 ..      27     103 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.4e-06
                            AAA_30 19 rvavltGpAGtGKttalkalreaweaaggrvig 51
                                       + +l Gp G+GKtt+l+++++++e ++g+v++
  gi|242399862|ref|YP_002995287.1| 35 ELLILIGPSGSGKTTLLRTINRLIEPDEGEVFI 67
                                      4899*********************99888876 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1     3e-06    0.0016       6      29 ..      35      58 ..      32     206 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 3e-06
                            AAA_22  6 gilvvtGesGtGKTtllrrlleql 29
                                       +l+++G+sG+GKTtllr++ +  
  gi|242399862|ref|YP_002995287.1| 35 ELLILIGPSGSGKTTLLRTINRLI 58
                                      579***************998865 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   4.1e-06    0.0022       9      53 ..      21      65 ..      13      98 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.1e-06
                      Mg_chelatase  9 eeakraleiaaaGgHnlllvGppGsGKtmlakrlpsllpplseee 53
                                        a   +++ ++Gg  l+l+Gp+GsGKt l + ++ l+ p + e 
  gi|242399862|ref|YP_002995287.1| 21 FIAVDHVNLEVIGGELLILIGPSGSGKTTLLRTINRLIEPDEGEV 65
                                      556667888899***********************9998766555 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   2.3e-05     0.012      12      91 ..      32     270 ..      25     310 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.3e-05
                                       HTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS......................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......................................... RF
                              DEAD  12 lgggdvlvaaeTGsGKTlaflipvlqivyetkgktg......................................... 47 
                                       +gg+ +++ ++ GsGKT+   +  +++++e   ++g                                         
  gi|242399862|ref|YP_002995287.1|  32 IGGELLILIGPSGSGKTTL--LRTINRLIE--PDEGevfingqnirdfdvvelrrsigyviqqiglfphmtvrdnig 104
                                       5677778888888888876..677777776..333346777777788888888888888888888888888888888 PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              DEAD  48 ............................................................................. 47 
                                                                                                                    
  gi|242399862|ref|YP_002995287.1| 105 lllklegwveeeieervkellrlvalpeefavryphqlsggqqqrvglaralaldpplllmdepfgaldpilrkqlq 181
                                       88888888888888888888888888888888888888888888888888888888888888888888888888888 PP

                                       ............................................-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEE. CS
                                       ............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                              DEAD  48 ............................................pkalivePtreLaeqtlnnlkkfkkyidlrvl. 79 
                                                                                   p  l++ P  e + q +n  kkfk+  +lrv+ 
  gi|242399862|ref|YP_002995287.1| 182 nefvrikealgktivfvthdieeafklgdrisimkegrlvqvgyPDELVLNPADEFVAQLVNADKKFKHLDTLRVKd 258
                                       88888888888888888888888888888888999999999999************************976699998 PP

                                       EEETTSSHHHHH CS
                                       xxxxxxxxxxxx RF
                              DEAD  80 liiggvaardql 91 
                                       l+ig ++++ ++
  gi|242399862|ref|YP_002995287.1| 259 LMIGVENYTVEI 270
                                       888854444333 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 !   17.7   0.0     5e-06    0.0027       2      37 ..      37      73 ..      36      90 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 5e-06
                                      EEEE--SSSSHHHHHHHGGGGB.S--EEEEE--TT-- CS
                             AAA_5  2 vlLvGppGtgKselaerlaaal.nreveyvqltrdtt 37
                                      ++L+Gp+G+gK++l + + +++  +e e+  + ++++
  gi|242399862|ref|YP_002995287.1| 37 LILIGPSGSGKTTLLRTINRLIePDEGEVFINGQNIR 73
                                      79********************966666666666555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   0.00018     0.094       6      26 ..      38      57 ..      35      81 .. 0.85
   2 ?    3.5   0.1     0.096        51     111     141 ..     181     211 ..     176     223 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00018
                            AAA_24  6 liyGpsgiGKTtlakelgpkp 26
                                      +++Gpsg+GKTtl++++ ++ 
  gi|242399862|ref|YP_002995287.1| 38 ILIGPSGSGKTTLLRTI-NRL 57
                                      79*************99.554 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.096
                            AAA_24 111 frrllkklqelrknvifiahektrkdedpeg 141
                                        +++++  ++l+k+++f+ h  ++ ++ +++
  gi|242399862|ref|YP_002995287.1| 181 QNEFVRIKEALGKTIVFVTHDIEEAFKLGDR 211
                                       5788888999*************99998754 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.4e-05    0.0071       2      24 ..      36      58 ..      35     110 .. 0.89
   2 ?   -0.4   0.0       1.9   9.8e+02     101     142 ..     268     309 ..     181     332 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.4e-05
                                      CEEEEC-TTTCHHHHHHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqklalaw 24
                                      l+il G++GsGKTtLl+ + +++
  gi|242399862|ref|YP_002995287.1| 36 LLILIGPSGSGKTTLLRTINRLI 58
                                      689***************98776 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.9
                                       ........HHHHHCTTTTT--EEEEEEECCCHHHHCTTSSCE CS
                             NACHT 101 ekqpvrtlLselirkkllpeasllltvrpralrdleeqleea 142
                                        + ++++ L +++++k l  a ++  ++ +++ dl+++l + 
  gi|242399862|ref|YP_002995287.1| 268 VEIKSKEKLLKWMKEKNLEFAVIVENTTLKGVTDLKSLLNSH 309
                                       445556667788888888888888888877777777777665 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.5   1.5e-05     0.008      23      69 ..      35      76 ..      23     340 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.5e-05
                            AAA_15 23 eeltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleife 69
                                      e l +liG+ +sGK+++l+ ++ +++ +    + +++i+ +++++f+
  gi|242399862|ref|YP_002995287.1| 35 E-LLILIGPSGSGKTTLLRTINRLIEPD----EGEVFINGQNIRDFD 76
                                      3.99**********************99....788888888888774 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   2.9e-05     0.015       1      19 [.      36      54 ..      36      96 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.9e-05
                            AAA_33  1 lvllvGlpGsGKstlaerl 19
                                      l++l+G++GsGK+tl++ +
  gi|242399862|ref|YP_002995287.1| 36 LLILIGPSGSGKTTLLRTI 54
                                      789************9865 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   4.2e-05     0.022      95     121 ..      30      56 ..       5      70 .. 0.82
   2 ?   -1.9   0.1       5.2   2.8e+03      44      98 ..     282     307 ..     249     311 .. 0.53

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.2e-05
                                       HHCTTSEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  95 ellkdktsvlvGqSGvGKStLinallp 121
                                       e++ +++ +l+G+SG GK+tL+ +++ 
  gi|242399862|ref|YP_002995287.1|  30 EVIGGELLILIGPSGSGKTTLLRTINR 56 
                                       4566799**************988865 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 5.2
                                       HTT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCT CS
                       RsgA_GTPase  44 ekgiepvivlnKiDlleeeeeleelkeelealgyevllvsaktkegleelkellk 98 
                                       e                            ++l+++v+ v+++t +g+++lk+ll+
  gi|242399862|ref|YP_002995287.1| 282 E----------------------------KNLEFAVI-VENTTLKGVTDLKSLLN 307
                                       2............................22223332.33444566666666665 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   6.9e-05     0.036      42      86 ..      31      76 ..      22     142 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.9e-05
                             Rad17 42 srkkriLLisGPsGCgkstvvkvLskelgiklre.wlnpvslkepd 86
                                          ++L++ GPsG gk+t ++ + +   ++  e ++n+ ++++ d
  gi|242399862|ref|YP_002995287.1| 31 VIGGELLILIGPSGSGKTTLLRTINRLIEPDEGEvFINGQNIRDFD 76
                                      5555799*****************9998887665378999987654 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   3.4e-05     0.018      26      81 ..      37      94 ..      34     329 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.4e-05
                                      EEEEESTTSSHHHHHHHHHHHCS--....--HHHHHCCHHHHHHHHHHHHHHHHHHHHHT CS
                           G-alpha 26 llllGqseSGKsTilkqlkllykkg....fseeelatwraviqlnivrsiktilealesl 81
                                      l+l+G s+SGK+T+l+ + +l ++     f +   +++r++    + rsi  +++++  +
  gi|242399862|ref|YP_002995287.1| 37 LILIGPSGSGKTTLLRTINRLIEPDegevFING--QNIRDFDVVELRRSIGYVIQQIGLF 94
                                      789****************99888766775555..5566666666677777777766654 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1    0.0001     0.055      18      39 ..      33      54 ..      18      58 .. 0.81
   2 ?    1.2   0.2      0.87   4.6e+02     153     175 ..     231     283 ..     172     336 .. 0.49

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 0.0001
                            AAA_23 18 skgltlItGpNGaGKTTildAi 39
                                      +  l +++Gp G+GKTT+l+ i
  gi|242399862|ref|YP_002995287.1| 33 GGELLILIGPSGSGKTTLLRTI 54
                                      5668899************987 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.87
                            AAA_23 153 e..............................rleelekeleeledekkllekl 175
                                                                       +e+++ e++ +e+  k ++++
  gi|242399862|ref|YP_002995287.1| 231 LnpadefvaqlvnadkkfkhldtlrvkdlmiGVENYTVEIKSKEKLLKWMKEK 283
                                       03333333333333333334444433333333333333333333333322222 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   9.3e-05     0.049       2      30 ..      38      74 ..      37     128 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 9.3e-05
                            AAA_18  2 lltGtpGvGKttlakeLskrlgf........gvnlrd 30
                                      +l G++G+GKttl + ++++ +         g+n+rd
  gi|242399862|ref|YP_002995287.1| 38 ILIGPSGSGKTTLLRTINRLIEPdegevfinGQNIRD 74
                                      799**************88743356665667555555 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 ?   13.8   0.0   6.1e-05     0.032       3      30 ..      37      64 ..      35     106 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.1e-05
                                      EEEEESTTCCHHHHHHHHHCT--SS-EE CS
                              cobW  3 tvltGflGsGKTtLlnhllenraglkla 30
                                      ++l G+ GsGKTtLl+++ +  +  +  
  gi|242399862|ref|YP_002995287.1| 37 LILIGPSGSGKTTLLRTINRLIEPDEGE 64
                                      6899************997655555555 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00031      0.17      31      50 ..      32      51 ..      25      54 .. 0.89
   2 ?   -2.7   0.0       7.1   3.7e+03      76     105 ..     106     136 ..      95     155 .. 0.73
   3 ?   -0.8   0.0       1.8   9.5e+02     166     188 ..     178     200 ..     173     201 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00031
                            AAA_25 31 pagelallaGapgtGKttla 50
                                      + gel +l+G++g+GKttl+
  gi|242399862|ref|YP_002995287.1| 32 IGGELLILIGPSGSGKTTLL 51
                                      479***************97 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 7.1
                            AAA_25  76 yvsaEds.edelrrRlravgealrddarllv 105
                                       ++ +E+  e+e+++R++++++ ++++++ +v
  gi|242399862|ref|YP_002995287.1| 106 LLKLEGWvEEEIEERVKELLRLVALPEEFAV 136
                                       5566665567888888888877766666555 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 1.8
                            AAA_25 166 galvealeriarrtgaavllvhH 188
                                       ++l + + ri++++g ++++v H
  gi|242399862|ref|YP_002995287.1| 178 KQLQNEFVRIKEALGKTIVFVTH 200
                                       57889999************999 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0    0.0003      0.16      18      42 ..      29      57 ..      10      65 .. 0.73
   2 ?   -0.0   0.0       1.6   8.4e+02      62      88 ..     244     266 ..     222     300 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0003
                                      H....TEEEEEEESTTSSHHHHHHHHHHH CS
                              TsaE 18 l....gdvilLeGdLGaGKTtlvrglaka 42
                                      l    g++++L G+ G+GKTtl r + + 
  gi|242399862|ref|YP_002995287.1| 29 LevigGELLILIGPSGSGKTTLLRTINRL 57
                                      13345677****************99775 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1.6
                                       ..SSEEEEE-TT-SSTHHHHHCTTCCC CS
                              TsaE  62 ekeglyHfDlYRledeeeleelgleey 88 
                                       +++++ H+D  R++d      +g+e+y
  gi|242399862|ref|YP_002995287.1| 244 ADKKFKHLDTLRVKDL----MIGVENY 266
                                       4455899999999753....3455554 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   8.5e-05     0.045     130     158 ..      35      63 ..      16      69 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.5e-05
                             T2SSE 130 glilvsGgTgsGKttllyallkeinksde 158
                                        l+++ G+ gsGKttll ++   i+ ++ 
  gi|242399862|ref|YP_002995287.1|  35 ELLILIGPSGSGKTTLLRTINRLIEPDEG 63 
                                       578999*************9999987755 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00014     0.073      38      93 ..      22      77 ..      13      93 .. 0.83
   2 ?   -3.0   0.1       5.9   3.1e+03     144     163 ..     194     213 ..     179     278 .. 0.59
   3 ?   -2.8   0.1       5.3   2.8e+03      83     104 ..     260     281 ..     248     313 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00014
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49 38 vivelikekklaGravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslev 93
                                      + v+ ++ + ++G  ++l Gpsg+Gkt l  +i + +  d   v+++g ++   +v
  gi|242399862|ref|YP_002995287.1| 22 IAVDHVNLEVIGGELLILIGPSGSGKTTLLRTINRLIEPDEGEVFINGQNIRDFDV 77
                                      6678888999***************************9999999999988866655 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 5.9
                                       EEEEE-SS-EEEEEE-HHHH CS
                             TIP49 144 kitlktakeekklklgskia 163
                                       +i++ t++ e+ +klg +i 
  gi|242399862|ref|YP_002995287.1| 194 TIVFVTHDIEEAFKLGDRIS 213
                                       45555555555555555543 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 5.3
                                       XXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  83 lsgsevyslevkktevltqalr 104
                                       + g e y++e+k  e l++ ++
  gi|242399862|ref|YP_002995287.1| 260 MIGVENYTVEIKSKEKLLKWMK 281
                                       4566677777777777766654 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   0.00033      0.17       1      22 [.      37      58 ..      37     168 .. 0.77
   2 ?   -1.4   0.0       5.7     3e+03      80     106 ..     267     290 ..     252     310 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00033
                                      EEEESSTTSSHHHHHHHHHHHH CS
                               AAA  1 vllyGppGtGKTllakavakel 22
                                      ++l+Gp G GKT+l + + + +
  gi|242399862|ref|YP_002995287.1| 37 LILIGPSGSGKTTLLRTINRLI 58
                                      589*************998776 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 5.7
                                       HHHHHHHHHHHHHHHHTTTSSSTEEEE CS
                               AAA  80 eeeervvnqLlteldgvkkkeskvivi 106
                                       ++e +  ++Ll+ +++ + +   + vi
  gi|242399862|ref|YP_002995287.1| 267 TVEIKSKEKLLKWMKEKNLE---FAVI 290
                                       34555556666666655552...3333 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   0.00013     0.069       3      54 ..      35      85 ..      33     125 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00013
                            AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpeklle 54
                                      ++l++ G+  +GKTtll+++  +l+ ++e  ++in ++ rd +  + ++ + 
  gi|242399862|ref|YP_002995287.1| 35 ELLILIGPSGSGKTTLLRTIN-RLIEPDEGEVFINGQNIRDFDVVELRRSIG 85
                                      5799************98874.566789999999999999876555444444 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00043      0.22       4      22 ..      37      55 ..      35      59 .. 0.89
   2 ?   -2.1   0.0       5.3   2.8e+03      84     120 ..      94     130 ..      87     138 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00043
                         PduV-EutP  4 illiGkvgsGKttLtqalk 22
                                      ++liG++gsGKttL ++++
  gi|242399862|ref|YP_002995287.1| 37 LILIGPSGSGKTTLLRTIN 55
                                      69************99987 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 5.3
                         PduV-EutP  84 fasvfnkeviGiitkidlaedeenieaveelLksaGa 120
                                       f ++  ++ iG++ k++   +ee  e v+elL+ +  
  gi|242399862|ref|YP_002995287.1|  94 FPHMTVRDNIGLLLKLEGWVEEEIEERVKELLRLVAL 130
                                       5567889999999999998666666678888877655 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    0.0003      0.16      10      34 ..      34      58 ..      27      67 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0003
                            AAA_19 10 ekvllvtaGpGtGKTrvlkhivall 34
                                       ++l+++++ G+GKT++l++i +l+
  gi|242399862|ref|YP_002995287.1| 34 GELLILIGPSGSGKTTLLRTINRLI 58
                                      67899**************998766 PP

>> DUF4720  Domain of unknown function (DUF4720)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       4.4   2.3e+03      21      38 ..     243     260 ..     236     267 .. 0.84
   2 ?   11.5   0.0   0.00039      0.21      19      91 ..     267     340 ..     251     344 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 4.4
                           DUF4720  21 rkeekWkslenPrnrdlf 38 
                                       + ++k+k l+  r +dl+
  gi|242399862|ref|YP_002995287.1| 243 NADKKFKHLDTLRVKDLM 260
                                       568899*****9999996 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00039
                           DUF4720  19 plrkeekWkslenPrnrdlffrtlqayflrrGl.dlekfpaafsiknedprPllfas.dslasafadyeekknsf 91 
                                       +++ + k k l+  ++++l f  +      +G+ dl+ + ++ si+++ ++P++f + dslasa a+ + k n+f
  gi|242399862|ref|YP_002995287.1| 267 TVEIKSKEKLLKWMKEKNLEFAVIVENTTLKGVtDLKSLLNSHSIEEALREPIVFSPeDSLASALAEMKSK-NAF 340
                                       55566677888888888898888887777788669********************97379******98765.465 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   0.00032      0.17      18      57 ..      36      75 ..      34      77 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00032
                        Zeta_toxin 18 lillgGqpGAGKselaellkdelerqgnvvrldpDdlRel 57
                                      l++l G +G+GK++l++ +++ +e++++ v +++ ++R +
  gi|242399862|ref|YP_002995287.1| 36 LLILIGPSGSGKTTLLRTINRLIEPDEGEVFINGQNIRDF 75
                                      5788899**************************9999975 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0    0.0025       1.3       2      21 ..      40      59 ..      39      67 .. 0.86
   2 ?   -0.4   0.1       1.5   7.9e+02     157     234 ..     225     305 ..     188     320 .. 0.60
   3 ?   -0.1   0.1       1.3   6.6e+02     188     232 ..     307     355 ..     251     357 .. 0.61

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0025
                        ATP_bind_1  2 vGpaGsGKttfvgalseile 21
                                      +Gp GsGKtt+ ++++ ++e
  gi|242399862|ref|YP_002995287.1| 40 IGPSGSGKTTLLRTINRLIE 59
                                      8***********99987765 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.5
                        ATP_bind_1 157 lPhvvvlnkfDllkek...lekeleffedvealslllekee.ekykklaeaiaelleefalvlrflplssekeesie 229
                                        P   vln +D +  +   ++k+++++  +   +l++  e+     k++e++ + ++e +l    + +++ + ++++
  gi|242399862|ref|YP_002995287.1| 225 YPDELVLNPADEFVAQlvnADKKFKHLDTLRVKDLMIGVENyTVEIKSKEKLLKWMKEKNLE-FAVIVENTTLKGVT 300
                                       55555556555555443334444444444444444444444544455666666666666666.44445555555555 PP

                        ATP_bind_1 230 dllsl 234
                                       dl sl
  gi|242399862|ref|YP_002995287.1| 301 DLKSL 305
                                       55554 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 1.3
                        ATP_bind_1 188 lllekee.......ekykklaeaiaelleefalvlrflplssekeesiedll 232
                                       +     +         + + + ++a++l e++    f+ + +eke+ + +ll
  gi|242399862|ref|YP_002995287.1| 307 NSH---SieealrePIVFSPEDSLASALAEMKSKNAFVGIVVEKEKPVGVLL 355
                                       222...1222444456667778888888888888888888888888777766 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00059      0.31       4      43 ..      36      74 ..      33      89 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00059
                                      EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTT CS
                        APS_kinase  4 vvwltGlsgsGKstianalekkLvekgisvylLdGdnvRh 43
                                       + l G sgsGK+t+ +++++ + e     + ++G+n+R 
  gi|242399862|ref|YP_002995287.1| 36 LLILIGPSGSGKTTLLRTINRLI-EPDEGEVFINGQNIRD 74
                                      57899**************9655.555566689*****95 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00052      0.28       9      49 ..      16      57 ..       5      58 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00052
                            AAA_27  9 eryGkftd.rsldfsaeeadlhliyGpNEAGKstalrAisdl 49
                                      +ryG f    +++++    +l +++Gp  +GK+t+lr i++l
  gi|242399862|ref|YP_002995287.1| 16 KRYGDFIAvDHVNLEVIGGELLILIGPSGSGKTTLLRTINRL 57
                                      69**9965268999999*********************9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       654  (0.0364772); expected 358.6 (0.02)
Passed bias filter:                      534  (0.0297841); expected 358.6 (0.02)
Passed Vit filter:                       114  (0.00635841); 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: 0.75u 0.35s 00:00:01.10 Elapsed: 00:00:00.52
# Mc/sec: 2125.96
//
Query:       gi|242399863|ref|YP_002995288.1|  [L=300]
Description: Osmoprotection protein (proX) [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-68  231.4   0.6    1.5e-68  231.2   0.6    1.0  1  OpuAC     Substrate binding domain of ABC-type glycine betain


Domain annotation for each model (and alignments):
>> 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 !  231.2   0.6   8.5e-73   1.5e-68       2     256 ..      30     293 ..      29     294 .. 0.98

  Alignments for each domain:
  == domain 1  score: 231.2 bits;  conditional E-value: 8.5e-73
                                       EEEEEEESSHHHHHHHHHHHHHHHHTTE.EEEEEEEESHHHHHHHHHTTSSSEEEEEEHHHH............... CS
                             OpuAC   2 tivigsknwteqevlaeilkqllekkGy.kveltnlgstavlfaalasGdiDvypeewtgta............... 62 
                                       tivigsk+++eq++la++++ lle++Gy ++ + +lg+t v ++al++G+i+vy+ e+tgta               
  gi|242399863|ref|YP_002995288.1|  30 TIVIGSKPFNEQYILAHMIALLLEENGYkAEVKEGLGGTLVNYEALKKGQIHVYV-EYTGTAynnilkleppekwsp 105
                                       9***************************88889999999****************.********************* PP

                                       ...HHHHHHHHHHHHEEEEEEEESEEECEEEEEEHHHHHHHTTTBHHHHCTHHGGTEEEEEHHCCHSTTSHHCCHHH CS
                             OpuAC  63 ...yeaykkaveekkglevlgplgagnteglavpkyvaekygiksisDLkkpaedlelgakgeflgrpdgwgcekvt 136
                                          ye+ k+++ + +g++   +lg+ + + +av+k++aek++++++sDL+ +a +++lg + ef +rpdg++     
  gi|242399863|ref|YP_002995288.1| 106 eyvYEKSKEEMLKRDGVLTIVKLGFRDDYSIAVKKEFAEKNNLEKLSDLAPYAAEMTLGTDPEFATRPDGLP----- 177
                                       *****************9999***************************************************..... PP

                                       HHHHHHHT-TTCEEEGSCEEEEHH.HHHHHHHTTCSSEEEEETTSTHHHHTTEEE-B-TTSTS-SSEEEEEEEEHHH CS
                             OpuAC 137 egllkaYgldkvelvegseaamda.elyaaykrgepvvvyawtPdwaikkydlvvLedpkglfppaynvvpvvrkef 212
                                          +++Yg+     + g++++m + ++y+a+k+g+++++ a+t+d++++ ++l+ Led+kg++pp y++v++v kef
  gi|242399863|ref|YP_002995288.1| 178 -RIKEVYGF----TF-GDVKQMEPtLMYEAIKNGQVDAISAYTTDARVDLFGLKILEDDKGALPP-YDAVILVKKEF 247
                                       .********....55.99***********************************************.*********** PP

                                       HHHSCTHHHHHHHHC..--HHHHHHHHHHHHTTTT-HHHHHHHHHH CS
                             OpuAC 213 aekaPevaafLekls..ldtetlnelnaqvdvegkdpeevAkawla 256
                                       a+k+P v ++L+kl+  +dt+t+++ln++ dve+kd++e+A+++l 
  gi|242399863|ref|YP_002995288.1| 248 ADKYPGVVEALKKLEglIDTDTMRALNYKYDVEKKDAREIAREFLI 293
                                       ****************99**************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 1930.50
//
Query:       gi|242399864|ref|YP_002995289.1|  [L=269]
Description: Heavy-metal cation transporter, ZIP family [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-22   79.7  25.3    4.7e-19   68.8   6.4    2.6  2  Zip             ZIP Zinc transporter


Domain annotation for each model (and alignments):
>> Zip  ZIP Zinc transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6  10.8     4e-07    0.0072      12      96 ..      22     105 ..      13     117 .. 0.58
   2 !   68.8   6.4   2.6e-23   4.7e-19     183     332 ..     124     264 ..     107     265 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4e-07
                               Zip  12 lilsllgllgpllvpkiskl.......lsklllslllafavGvllgtaflhLlPealealeesqleeehthplagll 81 
                                       +++ + ++l+++l+    +l        +++ + + l fa+Gv++  +f +L+ +++e  +         ++ +g+ 
  gi|242399864|ref|YP_002995289.1|  22 MVVAFYAGLFVALMTTFGSLlamfshkMPQWGVDFSLSFAAGVMIVASFTSLILPGIEYSGR--------FLPPGVG 90 
                                       33333333333333333333344444456777777777777777777777777777773333........2666777 PP

                               Zip  82 vllGflllllvekll 96 
                                       ++lG++l++l+++++
  gi|242399864|ref|YP_002995289.1|  91 IMLGIVLIYLIDRFV 105
                                       777777777777776 PP

  == domain 2  score: 68.8 bits;  conditional E-value: 2.6e-23
                               Zip 183 kvraiilllglilHsfidGLAlG..vssssstgislfiAvllHelpeelglgaiLlkaglsrkkavllnllfaltap 257
                                         ++++++l++i+H++++GLA+G  +  + +tg+++ iA+ +  +pe+  + ++L+  + +r + +l+  l++++  
  gi|242399864|ref|YP_002995289.1| 124 LRVVWLIVLAVIIHNLPEGLAVGtsIVFDLKTGLVTAIAIGIQDFPEGTVVSLPLATLQKKRLQPILMGALSGVAEW 200
                                       4569*******************8888899*********************************************** PP

                               Zip 258 lGiliGilvrsisessgaeivsgillalsaGtflYvalvellphEllnekgssslkqsllqllglllGfalmlll 332
                                       + +l+G +       s    + ++ l+l++G +lYv++ e++p E+ + +     +++l+  lg+++Gf +ml+l
  gi|242399864|ref|YP_002995289.1| 201 VMVLFGAF-----FFSVFHGLLPYGLGLAGGAMLYVTVKEMIP-EIYKRE-----ENELYVTLGFFIGFYVMLFL 264
                                       ********.....6666667777889*****************.999999.....69****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.55
# Mc/sec: 1465.59
//
Query:       gi|242399865|ref|YP_002995290.1|  [L=182]
Description: Rubrerythrin-related protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.3e-26   92.0   6.0    5.2e-26   91.7   6.0    1.1  1  Rubrerythrin  Rubrerythrin
    0.00025   20.1   0.4     0.0093   15.0   0.1    2.0  2  Mn_catalase   Manganese containing catalase
     0.0007   19.5   1.8       0.12   12.3   0.3    2.1  2  Ferritin      Ferritin-like domain
     0.0084   16.4   0.4       0.11   12.9   0.1    2.3  2  DUF2383       Domain of unknown function (DUF2383)
     0.0098   16.1   1.7       0.41   10.9   0.2    2.1  2  Ferritin_2    Ferritin-like 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 !   91.7   6.0   1.5e-29   5.2e-26       1     136 [.      30     164 ..      30     165 .. 0.98

  Alignments for each domain:
  == domain 1  score: 91.7 bits;  conditional E-value: 1.5e-29
                                       HHHHHHHHHHHHHHHHHHHHHHCHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH..B.SSBBS------- CS
                      Rubrerythrin   1 eiLekAiagEssarrlYkelaekakegypqiaelFeelAeeEreHakilnklleklepele.levkekvreyaeakp 76 
                                       e+L +Ai++E+ ar++Yk++a++++  ++ +++++e lA eE++H+++l++++ + +p++e +++ke+v +++++ +
  gi|242399865|ref|YP_002995290.1|  30 ELLGMAIKAEIGAREFYKSMASNVD--IETLRNKLEFLAGEEEKHEEFLRNFYAQSFPGEEiVFPKEHVGPELKPVA 104
                                       89***********************..************************************************** PP

                                       TTGGHHHHHHHHHHHHHHHHHCHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Rubrerythrin  77 kflttaknLeeaiegayaeeeemyrfyeelaekegneeakklfkklaeaEkkHeerlrkl 136
                                       + ++  +++ e++++a+++e+ + +fy++l e++ +  +k l+++la +E+ H+ +l+ +
  gi|242399865|ref|YP_002995290.1| 105 EKIKNVQDILELVRWAMEAERIAKQFYSKLEEMTDDNAKKGLLRYLASMENTHYFILKTE 164
                                       ******************************************************998865 PP

>> Mn_catalase  Manganese containing catalase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.7   0.0    0.0071        26     145     184 ..      34      73 ..      28      95 .. 0.87
   2 !   15.0   0.1   2.6e-06    0.0093     133     184 ..     107     158 ..      90     168 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.0071
                       Mn_catalase 145 anlaaEakarlqverlyeltddpgvrdmlsfLlaRelvHq 184
                                       + + aE++ar  ++ +    d   +r+ l+fL   e  H+
  gi|242399865|ref|YP_002995290.1|  34 MAIKAEIGAREFYKSMASNVDIETLRNKLEFLAGEEEKHE 73 
                                       6799****************************99999997 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 2.6e-06
                       Mn_catalase 133 ivasGnliaDlranlaaEakarlqverlyeltddpgvrdmlsfLlaRelvHq 184
                                       i++  +++  +r  + aE  a+  + +l e+tdd   +  l++L   e  H 
  gi|242399865|ref|YP_002995290.1| 107 IKNVQDILELVRWAMEAERIAKQFYSKLEEMTDDNAKKGLLRYLASMENTHY 158
                                       5566666666778899******************************999996 PP

>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.3   3.4e-05      0.12      72     135 ..      20      79 ..       6      83 .. 0.88
   2 !    6.9   0.1    0.0016       5.8      72     118 ..     103     150 ..      88     157 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.4e-05
                                       C-SSSSCSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHH CS
                          Ferritin  72 ieapkefgsveevleaalehekkvteslrelielaeeegDpatadfledfleeqeeheweleal 135
                                       +e+++ef s++e l  a+++e  + e ++ ++  ++ e   ++++ le +  e+e+he++l+++
  gi|242399865|ref|YP_002995290.1|  20 LEKVNEF-SLKELLGMAIKAEIGAREFYKSMASNVDIE---TLRNKLEFLAGEEEKHEEFLRNF 79 
                                       4566777.****************************98...********************986 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0016
                                       C-SSSS.CSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHH CS
                          Ferritin  72 ieapke.fgsveevleaalehekkvteslrelielaeeegDpatadfl 118
                                       ++++ + + +++e ++ a+e+e+ + + + +l e+++++   ++  +l
  gi|242399865|ref|YP_002995290.1| 103 VAEKIKnVQDILELVRWAMEAERIAKQFYSKLEEMTDDNAKKGLLRYL 150
                                       3333334679***************************98776665555 PP

>> DUF2383  Domain of unknown function (DUF2383)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.1     3e-05      0.11      10      52 ..      36      78 ..      23      87 .. 0.88
   2 ?    1.7   0.0     0.088   3.2e+02      11      40 ..     122     151 ..     101     164 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3e-05
                                      HHHHHHHHHHHHHHHHT--SHHHHHHHHHHHHHHHHHHHHHHH CS
                           DUF2383 10 ietlkdgeegykeaaekvkdpqlktlleriaeereeaaeeLqs 52
                                      i++++ ++e+yk++a +v+ + l++ le  a e e++ e L++
  gi|242399865|ref|YP_002995290.1| 36 IKAEIGAREFYKSMASNVDIETLRNKLEFLAGEEEKHEEFLRN 78
                                      89999**************************999998887776 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.088
                                       HHHHHHHHHHHHHHHT--SHHHHHHHHHHH CS
                           DUF2383  11 etlkdgeegykeaaekvkdpqlktlleria 40 
                                       e+++ ++++y++  e  +d++ k ll+  a
  gi|242399865|ref|YP_002995290.1| 122 EAERIAKQFYSKLEEMTDDNAKKGLLRYLA 151
                                       556667777777777777777777766655 PP

>> Ferritin_2  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.2   0.00011      0.41       4      66 ..      30      83 ..      28     117 .. 0.72
   2 !    5.0   0.1    0.0075        27       4      57 ..     115     161 ..     109     166 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00011
                        Ferritin_2  4 diLnfAlnlEyleaafYtaalegaslddkalldaevrevaeeiakheeaHveflkaaleGaaa 66
                                      ++L +A+ +E  + +fY+ ++++          ++ r+ +e +a +ee+H efl++  +  + 
  gi|242399865|ref|YP_002995290.1| 30 ELLGMAIKAEIGAREFYKSMASN-------VDIETLRNKLEFLAGEEEKHEEFLRNFYA--QS 83
                                      57889****************94.......44456788889999999999999998874..33 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0075
                        Ferritin_2   4 diLnfAlnlEyleaafYtaalegaslddkalldaevrevaeeiakheeaHvefl 57 
                                       +++  A+ +E ++ +fY++  e        + d++ + +++ +a+ e +H+ +l
  gi|242399865|ref|YP_002995290.1| 115 ELVRWAMEAERIAKQFYSKLEEM-------TDDNAKKGLLRYLASMENTHYFIL 161
                                       66788************998773.......445555666666666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       790  (0.0440627); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); 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: 0.64u 0.37s 00:00:01.01 Elapsed: 00:00:00.58
# Mc/sec: 946.65
//
Query:       gi|242399866|ref|YP_002995291.1|  [L=207]
Description: hypothetical protein TSIB_1893 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        4.1    7.7   8.5       0.17   12.1   0.7    2.5  3  KleE      Uncharacterized KleE stable inheritance protein


Domain annotation for each model (and alignments):
>> KleE  Uncharacterized KleE stable inheritance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1      0.09   1.6e+03      58      77 ..      12      31 ..       6      60 .. 0.65
   2 ?   12.1   0.7   9.6e-06      0.17      51     100 ..      63     113 ..      49     121 .. 0.86
   3 ?   -1.4   0.1      0.15   2.6e+03      59      89 ..     129     159 ..     118     170 .. 0.69

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.09
                              KleE 58 wvlsidvlfqflrmlyhwnt 77
                                       ++si  l+ f+ ++  wn 
  gi|242399866|ref|YP_002995291.1| 12 ILMSICGLLTFMGIFLTWNI 31
                                      55666666666666666664 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 9.6e-06
                              KleE  51 lvwpvlkwvlsidvlfqflrmlyhwntpg.vhagwtflahfavltlltyfv 100
                                        ++ v + ++s+ +l+  + + y  ++ g v+a+wt+l++  v++  ++fv
  gi|242399866|ref|YP_002995291.1|  63 TMFEVHQAIISFAILLGPVLIAYSLSESGlVKATWTMLLQVGVVAGSAIFV 113
                                       47889999*****************9988689*********9999888887 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.15
                              KleE  59 vlsidvlfqflrmlyhwntpgvhagwtflah 89 
                                       vl i+ +  ++r    ++  +  ++wtf+ +
  gi|242399866|ref|YP_002995291.1| 129 VLLINAISGYVRTPERYKRLAEISSWTFVGF 159
                                       5556666666666666777777778888754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       835  (0.0465726); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.52
# Mc/sec: 1188.06
//
Query:       gi|242399867|ref|YP_002995292.1|  [L=124]
Description: Superoxide reductase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-31  108.5   0.1    2.2e-31  108.3   0.1    1.1  1  Desulfoferrodox  Desulfoferrodoxin


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 !  108.3   0.1   1.2e-35   2.2e-31       2      96 .]       9     120 ..       8     120 .. 0.96

  Alignments for each domain:
  == domain 1  score: 108.3 bits;  conditional E-value: 1.2e-35
                                       SHTTTHTTSEEEEEESEEEETTEEEEEEEESS.SS--BSSSS-EEEEEEEEEETTSS......EEEE-TBS...... CS
                   Desulfoferrodox   2 adekeekHvPvieadevvkagelfevkvkvgk.ipHpneeeHyIewielyleeegek......rvelsaed...... 65 
                                        d+k ekHvPvie+    k+g+l++vkv+vgk ipHpn++eH+I++iely+ +ege+      r++++a++      
  gi|242399867|ref|YP_002995292.1|   9 GDWKGEKHVPVIEY---EKEGDLVKVKVQVGKeIPHPNTTEHHIKYIELYFLPEGENfvyqigRADFTAHGestkgp 82 
                                       689**********5...589**************************************************9****** PP

                                       .......ESEEEEEEEESSSEEEEEEEEETTTEEEEEE CS
                   Desulfoferrodox  66 .......epevtftvklkkekklvalsyCnlHGlWese 96 
                                              ep ++f +k+ k++kl+alsyCn+HGlWe+e
  gi|242399867|ref|YP_002995292.1|  83 nmsdiytEPVAYFVFKTAKKGKLYALSYCNIHGLWENE 120
                                       ******99****************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); 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 0.35s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 691.25
//
Query:       gi|242399868|ref|YP_002995293.1|  [L=54]
Description: Rubredoxin [Thermococcus sibiricus MM 739]
Scores for complete 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   88.9   3.9    1.7e-25   88.7   3.9    1.0  1  Rubredoxin       Rubredoxin
     0.0017   18.1   0.7       0.33   10.7   0.0    2.1  2  zinc_ribbon_10   Predicted integral membrane zinc-ribbon meta
     0.0018   18.3   0.4       0.42   10.7   0.0    2.1  2  zf-Sec23_Sec24   Sec23/Sec24 zinc finger
     0.0031   16.9   1.6       0.32   10.4   0.0    2.1  2  Vps36-NZF-N      Vacuolar protein sorting 36 NZF-N zinc-finge
  ------ inclusion threshold ------
      0.017   14.4   4.5       0.52    9.7   0.3    2.2  2  zf-RanBP         Zn-finger in Ran binding protein and others
      0.025   14.5   0.4       0.63   10.0   0.1    2.0  2  Prok-RING_1      Prokaryotic RING finger family 1
      0.036   14.7   0.8       0.53   10.9   0.1    2.0  2  RbpA             RNA polymerase-binding protein
      0.038   13.5   1.9        3.8    7.1   0.4    2.2  2  TF_Zn_Ribbon     TFIIB zinc-binding
      0.046   13.4   1.1        2.4    8.0   0.0    2.2  2  A2L_zn_ribbon    A2L zinc ribbon domain
      0.068   12.8   1.3       0.37   10.5   0.4    2.1  2  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
      0.081   13.0   2.1       0.21   11.7   2.1    1.7  1  PHD_4            PHD-finger
        0.1   12.4   3.2        1.5    8.6   0.2    2.1  2  zf-MIZ           MIZ/SP-RING zinc finger
        0.1   12.6   1.8        0.9    9.6   1.8    2.0  1  ADK_lid          Adenylate kinase, active site lid
       0.12   12.3   0.1       0.14   12.2   0.1    1.1  1  HypA             Hydrogenase/urease nickel incorporation, met
       0.26   11.8   1.1         24    5.5   0.1    2.1  2  zf-H2C2_2        Zinc-finger double domain
        0.3   10.9   2.3        8.6    6.2   0.4    2.5  2  zinc_ribbon_2    zinc-ribbon domain
       0.41   10.6   3.5        5.1    7.1   0.1    2.1  2  Zn_ribbon_SprT   SprT-like zinc ribbon domain


Domain annotation for each model (and alignments):
>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.7   3.9   1.6e-28   1.7e-25       1      47 []       3      49 ..       3      49 .. 0.99

  Alignments for each domain:
  == domain 1  score: 88.7 bits;  conditional E-value: 1.6e-28
                                      EEEETTT-BEEETTTBBGGGTB-TT--GGGS-TT-BBTTTB-BGGGE CS
                        Rubredoxin  1 kyeCkvCgyvYdpakGdpdegiapgTkFedlPddWvCPdCgvekeqF 47
                                      k++C vCgy+Yd++ Gdp++g+apgT+Fe++PddWvCP Cg++k++F
  gi|242399868|ref|YP_002995293.1|  3 KWKCMVCGYIYDEEAGDPESGVAPGTRFEEIPDDWVCPLCGAPKDMF 49
                                      79*******************************************99 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 ?    5.8   0.7      0.01        11      44      52 ..       3      11 ..       1      13 [. 0.86
   2 !   10.7   0.0   0.00032      0.33      32      52 ..      22      44 ..      19      46 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.01
                    zinc_ribbon_10 44 kyrCpkCga 52
                                      k++C+ Cg 
  gi|242399868|ref|YP_002995293.1|  3 KWKCMVCGY 11
                                      8******97 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00032
                    zinc_ribbon_10 32 nGlapkeeleev..kyrCpkCga 52
                                      +G+ap  ++ee+   ++Cp Cga
  gi|242399868|ref|YP_002995293.1| 22 SGVAPGTRFEEIpdDWVCPLCGA 44
                                      8999*9999999999******97 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 !    6.3   0.1    0.0096        10      23      31 ..       3      11 ..       1      14 [. 0.85
   2 !   10.7   0.0    0.0004      0.42      22      32 ..      35      45 ..      24      49 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0096
                    zf-Sec23_Sec24 23 rwiCnfCnh 31
                                      +w+C  C+ 
  gi|242399868|ref|YP_002995293.1|  3 KWKCMVCGY 11
                                      8******86 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0004
                    zf-Sec23_Sec24 22 krwiCnfCnhk 32
                                        w+C++C+  
  gi|242399868|ref|YP_002995293.1| 35 DDWVCPLCGAP 45
                                      57******975 PP

>> Vps36-NZF-N  Vacuolar protein sorting 36 NZF-N zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.0   0.5    0.0071       7.4       8      17 ..       2      11 ..       1      13 [. 0.86
   2 !   10.4   0.0    0.0003      0.32       5      17 ..      32      44 ..      28      53 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0071
                       Vps36-NZF-N  8 atWvCpICsf 17
                                      a+W C +C +
  gi|242399868|ref|YP_002995293.1|  2 AKWKCMVCGY 11
                                      79******86 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0003
                       Vps36-NZF-N  5 avtatWvCpICsf 17
                                      ++  +WvCp C  
  gi|242399868|ref|YP_002995293.1| 32 EIPDDWVCPLCGA 44
                                      56679******86 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 ?    6.7   0.4    0.0043       4.6       5      12 ..       4      11 ..       3      12 .. 0.84
   2 ?    9.7   0.3   0.00049      0.52       3      11 ..      35      43 ..      34      46 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0043
                                      EE-SSS-- CS
                          zf-RanBP  5 WdCskClv 12
                                      W+C +C++
  gi|242399868|ref|YP_002995293.1|  4 WKCMVCGY 11
                                      99999997 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00049
                                      SSEE-SSS- CS
                          zf-RanBP  3 gdWdCskCl 11
                                      +dW C+ C+
  gi|242399868|ref|YP_002995293.1| 35 DDWVCPLCG 43
                                      699999998 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 ?    3.4   0.0     0.071        75       4      13 ..       3      12 ..       1      20 [. 0.74
   2 ?   10.0   0.1    0.0006      0.63      13      30 ..      29      46 ..      21      49 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.071
                       Prok-RING_1  4 gkkCpvCgke 13
                                      + kC vCg  
  gi|242399868|ref|YP_002995293.1|  3 KWKCMVCGYI 12
                                      5699999865 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0006
                       Prok-RING_1 13 elkeedDiVvCpeCgtpy 30
                                      +++e  D  vCp Cg+p 
  gi|242399868|ref|YP_002995293.1| 29 RFEEIPDDWVCPLCGAPK 46
                                      5666666679******95 PP

>> RbpA  RNA polymerase-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1      0.13   1.4e+02      50      67 ..       3      20 ..       2      28 .. 0.75
   2 ?   10.9   0.1    0.0005      0.53      45      61 ..      31      47 ..      21      54 .] 0.83

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.13
                              RbpA 50 twecrrcGkeakldgeep 67
                                      +w+c  cG     ++ +p
  gi|242399868|ref|YP_002995293.1|  3 KWKCMVCGYIYDEEAGDP 20
                                      7*******8766655555 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0005
                              RbpA 45 aevPetwecrrcGkeak 61
                                       e+P+ w c+ cG++  
  gi|242399868|ref|YP_002995293.1| 31 EEIPDDWVCPLCGAPKD 47
                                      59***********9865 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.4    0.0036       3.8      22      38 ..       6      22 ..       5      23 .. 0.88
   2 ?    6.0   0.0    0.0079       8.4      21      27 ..      38      44 ..      34      53 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0036
                                      ESSSSBEEEECCCCCCC CS
                      TF_Zn_Ribbon 22 CtdCGlVlednsidegp 38
                                      C  CG++ +++  d+++
  gi|242399868|ref|YP_002995293.1|  6 CMVCGYIYDEEAGDPES 22
                                      99999999999999985 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0079
                                      EESSSSB CS
                      TF_Zn_Ribbon 21 vCtdCGl 27
                                      vC+ CG+
  gi|242399868|ref|YP_002995293.1| 38 VCPLCGA 44
                                      6666663 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   0.4     0.027        28       2      10 ..       2      10 ..       1      13 [. 0.81
   2 ?    8.0   0.0    0.0023       2.4      21      29 ..      36      44 ..      34      51 .. 0.66

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.027
                     A2L_zn_ribbon  2 nlkvCsvCg 10
                                        ++C vCg
  gi|242399868|ref|YP_002995293.1|  2 AKWKCMVCG 10
                                      679999997 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0023
                     A2L_zn_ribbon 21 ylvCieCga 29
                                      + vC+ Cga
  gi|242399868|ref|YP_002995293.1| 36 DWVCPLCGA 44
                                      456777775 PP

>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.4   0.00035      0.37       6      15 ..       3      12 ..       1      14 [. 0.85
   2 ?    1.3   0.0      0.25   2.6e+02       9      13 ..      39      43 ..      32      48 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00035
                                      EEE-TTT--E CS
                   Desulfoferrod_N  6 vYkCevCGni 15
                                      ++kC+vCG i
  gi|242399868|ref|YP_002995293.1|  3 KWKCMVCGYI 12
                                      79******87 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.25
                                      -TTT- CS
                   Desulfoferrod_N  9 CevCG 13
                                      C +CG
  gi|242399868|ref|YP_002995293.1| 39 CPLCG 43
                                      88888 PP

>> PHD_4  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   2.1    0.0002      0.21      32      67 ..       5      42 ..       1      43 [. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0002
                             PHD_4 32 eCsvCyeivHpeClkek..egegvvnedlpnsWeCpkC 67
                                       C vC  i   e  + +   ++g+  e++p +W Cp C
  gi|242399868|ref|YP_002995293.1|  5 KCMVCGYIYDEEAGDPEsgVAPGTRFEEIPDDWVCPLC 42
                                      69999999888887766556789999***********9 PP

>> zf-MIZ  MIZ/SP-RING zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.3      0.02        22      41      47 ..       3       9 ..       1      11 [. 0.86
   2 ?    8.6   0.2    0.0015       1.5      41      49 ..      36      44 ..      28      45 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.02
                                      --B-TTT CS
                            zf-MIZ 41 tWnCPvC 47
                                      +W+C vC
  gi|242399868|ref|YP_002995293.1|  3 KWKCMVC 9 
                                      7****** PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0015
                                      --B-TTT-- CS
                            zf-MIZ 41 tWnCPvCsk 49
                                       W CP+C +
  gi|242399868|ref|YP_002995293.1| 36 DWVCPLCGA 44
                                      5******76 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   1.8   0.00086       0.9       2      30 ..       4      45 ..       4      45 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00086
                                      EE-TTT--EEETT.............TB--S...STTB-TTT--. CS
                           ADK_lid  2 rvCpkCGrsYhvv.............fnpPk...veglCDkCGep 30
                                      + C  CG +Y  +             f        + +C  CG p
  gi|242399868|ref|YP_002995293.1|  4 WKCMVCGYIYDEEagdpesgvapgtrF---EeipDDWVCPLCGAP 45
                                      669999999984444444444444433...044489999999976 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00014      0.14      69      96 ..       2      46 ..       1      53 [. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00014
                                      -EEEETTTS-EEECHH.H.HH...............S-TTTSSS- CS
                              HypA 69 vkvrCreCgkefelee.k.al...............rCpkCgsad 96
                                      +k +C +Cg+ +++e+ + +                 Cp Cg+ +
  gi|242399868|ref|YP_002995293.1|  2 AKWKCMVCGYIYDEEAgDpESgvapgtrfeeipddwVCPLCGAPK 46
                                      5789********9776443338999*****************975 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1     0.023        24      15      22 ..       4      11 ..       2      14 .. 0.84
   2 ?    5.4   0.1     0.025        27      15      21 ..      37      43 ..      28      49 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.023
                         zf-H2C2_2 15 yeCplCdk 22
                                      ++C++C++
  gi|242399868|ref|YP_002995293.1|  4 WKCMVCGY 11
                                      79****99 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.025
                         zf-H2C2_2 15 yeCplCd 21
                                      + CplC+
  gi|242399868|ref|YP_002995293.1| 37 WVCPLCG 43
                                      78****7 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1     0.038        40       1       9 [.       5      13 ..       5      17 .. 0.60
   2 ?    6.2   0.4    0.0081       8.6      16      22 ..      39      45 ..      31      46 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.038
                     zinc_ribbon_2  1 fCpnCGael 9 
                                      +C  CG+  
  gi|242399868|ref|YP_002995293.1|  5 KCMVCGYIY 13
                                      577777655 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0081
                     zinc_ribbon_2 16 CpyCGtp 22
                                      Cp CG+p
  gi|242399868|ref|YP_002995293.1| 39 CPLCGAP 45
                                      6666655 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.5     0.028        30       4      14 ..       3      11 ..       3      14 .. 0.81
   2 ?    7.1   0.1    0.0048       5.1       4      11 ..      36      43 ..      34      45 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.028
                    Zn_ribbon_SprT  4 vYrCtgCgrey 14
                                      +++C  Cg  y
  gi|242399868|ref|YP_002995293.1|  3 KWKCMVCG--Y 11
                                      7*******..4 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0048
                    Zn_ribbon_SprT  4 vYrCtgCg 11
                                       ++C+ Cg
  gi|242399868|ref|YP_002995293.1| 36 DWVCPLCG 43
                                      59*****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 338.63
//
Query:       gi|242399869|ref|YP_002995294.1|  [L=171]
Description: Rubrerythrin [Thermococcus sibiricus MM 739]
Scores for complete 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-26   92.3  11.4    3.3e-25   89.1  11.4    2.0  1  Rubrerythrin    Rubrerythrin
     0.0002   21.3   8.7      0.001   19.0   8.7    1.9  1  Ferritin        Ferritin-like domain
  ------ inclusion threshold ------
      0.011   15.6   4.0      0.058   13.2   2.4    2.3  2  Cys_rich_CPCC   Cysteine-rich CPCC
      0.037   14.1   0.2      0.055   13.5   0.2    1.3  1  DZR             Double zinc ribbon
       0.04   13.0   0.0      0.077   12.1   0.0    1.4  1  Exonuc_X-T_C    Exonuclease C-terminal
      0.041   13.6   2.0      0.083   12.6   2.0    1.5  1  zinc_ribbon_2   zinc-ribbon domain
      0.042   13.7   0.2      0.042   13.7   0.2    2.0  2  FdhE            Protein involved in formate dehydrogenase for
      0.047   13.4   1.0      0.069   12.8   1.0    1.2  1  LUC7            LUC7 N_terminus
      0.048   11.8   0.4      0.062   11.5   0.4    1.0  1  HSP70           Hsp70 protein
      0.067   13.1   4.4       0.81    9.6   0.8    2.8  3  zf-FPG_IleRS    Zinc finger found in FPG and IleRS
      0.074   13.3   0.2      0.098   12.9   0.2    1.1  1  CENP-Q          CENP-Q, a CENPA-CAD centromere complex subuni
       0.15   11.6   0.3       0.55    9.9   0.3    2.0  2  RecR            RecR protein
       0.21   11.1   3.2         10    5.7   0.4    2.4  2  TF_Zn_Ribbon    TFIIB zinc-binding
       0.23   11.5   6.0        1.3    9.1   0.6    2.3  2  Rubredoxin      Rubredoxin
        0.3   11.2   7.4        3.8    7.6   0.6    2.5  2  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
       0.37   11.0   3.7        7.7    6.7   3.6    2.4  2  Zn-ribbon_8     Zinc ribbon domain
       0.63   10.2   2.8        7.7    6.8   0.4    2.3  2  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 
          2    8.0   5.2        4.2    6.9   5.2    1.6  1  zf-ribbon_3     zinc-ribbon domain
        6.6    7.3   8.3         16    6.0   0.5    2.9  3  Zn-C2H2_12      Autophagy receptor zinc finger-C2H2 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 !   89.1  11.4   3.5e-28   3.3e-25       1     136 [.      10     124 ..      10     125 .. 0.98

  Alignments for each domain:
  == domain 1  score: 89.1 bits;  conditional E-value: 3.5e-28
                                       HHHHHHHHHHHHHHHHHHHHHHCHH.TT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSBBS------- CS
                      Rubrerythrin   1 eiLekAiagEssarrlYkelaekak.egypqiaelFeelAeeEreHakilnklleklepelelevkekvreyaeakp 76 
                                       ++Le A+agEs+a++ Y+++a+ a+ eg+p+ia+lF+++A +E  Ha++++++l++++ + +               
  gi|242399869|ref|YP_002995294.1|  10 KFLEDAYAGESQAHMKYMIFADFAEkEGFPNIAKLFRAIAFAELVHARNHYQALGNVKDTVN--------------- 71 
                                       69******************************************************999999............... PP

                                       TTGGHHHHHHHHHHHHHHHHHCHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Rubrerythrin  77 kflttaknLeeaiegayaeeeemyrfyeelaekegneeakklfkklaeaEkkHeerlrkl 136
                                              nL++aieg++ e eemy+ y+ +ae +g++ea ++++++ eaEk H+e+++k+
  gi|242399869|ref|YP_002995294.1|  72 -------NLQTAIEGETFEVEEMYPAYKAVAELQGEKEAVRSTHYALEAEKIHAELYKKA 124
                                       .......***************************************************97 PP

>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   8.7   1.1e-06     0.001       3     112 ..      11     134 ..       9     140 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.1e-06
                                       HHHHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS.....SHH.HHHH...... CS
                          Ferritin   3 aLneqladeltaayqylamawyvkgpgleglaeffdeqaeeerehadklaerilalGgtpv.ltra.elee...... 71 
                                        L+++ a e +a+++y+ +a  ++ +g++++a++f+  a  e+ ha   ++ +     t++ l++a e         
  gi|242399869|ref|YP_002995294.1|  11 FLEDAYAGESQAHMKYMIFADFAEKEGFPNIAKLFRAIAFAELVHARNHYQALGNVKDTVNnLQTAiE--Getfeve 85 
                                       689999*****************************************999988777664331333340..2445555 PP

                                       .....C-SSSS...CSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-H CS
                          Ferritin  72 .....ieapke...fgsveevleaalehekkvteslrelielaeeegDp 112
                                            ++a+ e    +++      ale+ek   e ++++ elae+++D 
  gi|242399869|ref|YP_002995294.1|  86 emypaYKAVAElqgEKEAVRSTHYALEAEKIHAELYKKAKELAEQKKDI 134
                                       576664444444423478888889***********************96 PP

>> Cys_rich_CPCC  Cysteine-rich CPCC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.28   2.6e+02      47      64 ..      53      70 ..      48      80 .. 0.81
   2 ?   13.2   2.4   6.1e-05     0.058       1      24 [.     140     160 ..     140     166 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.28
                     Cys_rich_CPCC 47 LreArknfkkfGaceeel 64
                                      L +Ar+ +++ G ++ ++
  gi|242399869|ref|YP_002995294.1| 53 LVHARNHYQALGNVKDTV 70
                                      889*********988765 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 6.1e-05
                     Cys_rich_CPCC   1 yqCpcCgyltleeeegsydiCpvC 24 
                                       y Cp+Cgy+ ++e     + CpvC
  gi|242399869|ref|YP_002995294.1| 140 YICPVCGYTAVDEA---PEKCPVC 160
                                       56***********9...6778888 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.2   5.9e-05     0.055      27      49 .]     135     161 ..     106     161 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.9e-05
                               DZR  27 a...edrCpsCgek.vdpearfCpeCG 49 
                                       +    + Cp Cg+  vd+  + Cp CG
  gi|242399869|ref|YP_002995294.1| 135 EikkVYICPVCGYTaVDEAPEKCPVCG 161
                                       055578999999998999999999998 PP

>> Exonuc_X-T_C  Exonuclease C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   8.2e-05     0.077      62      99 ..     110     145 ..     105     153 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.2e-05
                                       HS-HHHHHHHHTSTTTTT.TSS----EEEEETTS--EE CS
                      Exonuc_X-T_C  62 elsaeelrerlftkkeelaegeerlplklihiNkcPvl 99 
                                        l+ae++++ l+ k++elae+++ + +k + i  cPv+
  gi|242399869|ref|YP_002995294.1| 110 ALEAEKIHAELYKKAKELAEQKKDIEIKKVYI--CPVC 145
                                       6899**************************99..8887 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   2.0   8.8e-05     0.083       2      20 ..     142     161 ..     141     163 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.8e-05
                     zinc_ribbon_2   2 CpnCGaelqdnakF.CpyCG 20 
                                       Cp CG++  d+a+  Cp CG
  gi|242399869|ref|YP_002995294.1| 142 CPVCGYTAVDEAPEkCPVCG 161
                                       ******************** PP

>> FdhE  Protein involved in formate dehydrogenase formation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2   4.4e-05     0.042      89     179 ..      51     150 ..       5     152 .. 0.73
   2 ?    1.3   1.0      0.28   2.6e+02     164     176 ..     150     162 ..     147     169 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.4e-05
                                       HHHHH.T--S-SSHHHHHHHHHHHH-......-HHHHHHHHHHHHTT-GGGS-GGGHHHHHHHHHHHHH..HHHHT- CS
                              FdhE  89 qalle.alkeelpealrealerlrka......daeelealadallageleavdaakavfvaaAlqvvwt..klaaal 156
                                       ++l++ + + ++  ++++++++l++a      + ee+    +a+ + + e+++ +++ +   A +++++  k a++l
  gi|242399869|ref|YP_002995294.1|  51 AELVHaRNHYQALGNVKDTVNNLQTAiegetfEVEEMYPAYKAVAELQGEKEAVRSTHYALEAEKIHAElyKKAKEL 127
                                       4455533444556667777777777744433344777788899999999999999999*99999999753378999* PP

                                       -TTSSS-.-TT-SS-TTT---EE CS
                              FdhE 157 dakalaelaeekglCPvCgsaPv 179
                                        +++     ++  +CPvCg ++v
  gi|242399869|ref|YP_002995294.1| 128 AEQKKDIEIKKVYICPVCGYTAV 150
                                       9888877788899******8776 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.28
                                       .-TT-SS-TTT-- CS
                              FdhE 164 laeekglCPvCgs 176
                                       + e+++ CPvCg 
  gi|242399869|ref|YP_002995294.1| 150 VDEAPEKCPVCGV 162
                                       5677899****95 PP

>> LUC7  LUC7 N_terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   1.0   7.3e-05     0.069     123     200 ..      58     147 ..      46     157 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.3e-05
                                       ..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX................XXXXX CS
                              LUC7 123 kkqeqlkeleekiekllaeaeelgeeGkVdeaqklmkeveelkeekeeleqqyeaaa..............aneese 185
                                       ++ + l ++++++++l + +e  ge+ +V+e     k v el+ eke++++++ a +                e+++
  gi|242399869|ref|YP_002995294.1|  58 NHYQALGNVKDTVNNLQTAIE--GETFEVEEMYPAYKAVAELQGEKEAVRSTHYALEaekihaelykkakeLAEQKK 132
                                       567778888888888888777..88889*******************999888877789999999999887557788 PP

                                       XXXXXXXXXXXXXXX CS
                              LUC7 186 asqekkmkvCeiCGa 200
                                         + kk+ +C +CG 
  gi|242399869|ref|YP_002995294.1| 133 DIEIKKVYICPVCGY 147
                                       88999999*****94 PP

>> HSP70  Hsp70 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.4   6.5e-05     0.062      49     138 ..      57     141 ..      48     150 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.5e-05
                                       HHHHCTTTTGGGEEEXGGGTT.TXBTTSHHHHHHHTTXSSEEEEETTSBEEEEEEETTEEEEHHHHHHHHHHHHHHH CS
                             HSP70  49 aAkrqavtnpkntvfsvKrli.GrkfsdpevqkeikelpykvvkkengkavveveaagekftpeqisamvLkklket 124
                                           qa  n+k+tv ++   i G++f+    ++ ++     v + + +k  v+ +     +++e+i a + kk ke 
  gi|242399869|ref|YP_002995294.1|  57 RNHYQALGNVKDTVNNLQTAIeGETFEV---EEMYPA-YKAVAELQGEKEAVRST--HYALEAEKIHAELYKKAKEL 127
                                       45568999*********98775888885...333332.23455666667777777..459***************** PP

                                       HHHHHTSBEEEEEE CS
                             HSP70 125 aeaylgkkvtdavi 138
                                       ae+  + +++++ i
  gi|242399869|ref|YP_002995294.1| 128 AEQKKDIEIKKVYI 141
                                       ****9999999877 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 ?   -1.3   0.0       2.3   2.1e+03      15      23 ..     101     109 ..      98     109 .. 0.73
   2 ?    3.6   0.0     0.067        63      22      27 ..     140     145 ..     132     146 .. 0.80
   3 ?    9.6   0.8   0.00086      0.81       2      15 ..     155     168 ..     155     169 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2.3
                                       ECTTEEEEE CS
                      zf-FPG_IleRS  15 gqagrstyf 23 
                                       + a rst++
  gi|242399869|ref|YP_002995294.1| 101 KEAVRSTHY 109
                                       4556***98 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.067
                                       EE-TTT CS
                      zf-FPG_IleRS  22 yfCprC 27 
                                       y+Cp+C
  gi|242399869|ref|YP_002995294.1| 140 YICPVC 145
                                       889988 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00086
                                       SB-TTT--BBEEEE CS
                      zf-FPG_IleRS   2 epCpRCwryiervg 15 
                                       e+Cp+C+ + e+ +
  gi|242399869|ref|YP_002995294.1| 155 EKCPVCGVPREKFV 168
                                       8*******999976 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 ?   12.9   0.2    0.0001     0.098      18      89 ..      64     138 ..      38     147 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.0001
                            CENP-Q  18 dggkekeldfeklldekaaleaqLspelhslelLeaeiekeera.le.rdyeaLreLeknakaearerke.klkk 89 
                                       ++ k+++ ++ +++++ + +  +  p+ +++++L+ e+e +  + ++ + ++  +eL k+ak +a++ k+ + kk
  gi|242399869|ref|YP_002995294.1|  64 GNVKDTVNNLQTAIEGETFEVEEMYPAYKAVAELQGEKEAVRSThYAlEAEKIHAELYKKAKELAEQKKDiEIKK 138
                                       6779999********************************87765233134455679**********999876665 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       2.7   2.6e+03       7      16 ..      61      70 ..      60      72 .. 0.84
   2 ?    9.9   0.3   0.00058      0.55      14      37 ..     137     163 ..     124     164 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.7
                                      HHHHHHHHH- CS
                              RecR  7 eaLqeakekv 16
                                      +aL ++k++v
  gi|242399869|ref|YP_002995294.1| 61 QALGNVKDTV 70
                                      7999999998 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00058
                                       HH-EE-TTT--EESSS...S-CCCCST CS
                              RecR  14 ekvrhCsrCgnlteed...lCaICsdp 37 
                                       +kv  C++Cg  + ++    C++C  p
  gi|242399869|ref|YP_002995294.1| 137 KKVYICPVCGYTAVDEapeKCPVCGVP 163
                                       57889*****9987775557****765 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.2     0.012        11       1       8 [.     140     147 ..     140     154 .. 0.68
   2 ?    5.7   0.4     0.011        10       2       9 ..     156     163 ..     155     169 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.012
                                       EEETTTTC CS
                      TF_Zn_Ribbon   1 ykCPnCgs 8  
                                       y+CP+Cg 
  gi|242399869|ref|YP_002995294.1| 140 YICPVCGY 147
                                       67888884 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.011
                                       EETTTTCE CS
                      TF_Zn_Ribbon   2 kCPnCgst 9  
                                       kCP+Cg +
  gi|242399869|ref|YP_002995294.1| 156 KCPVCGVP 163
                                       8*****84 PP

>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.5     0.022        21      35      42 ..     140     147 ..     135     152 .. 0.65
   2 ?    9.1   0.6    0.0014       1.3      36      47 .]     156     167 ..     148     167 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.022
                                       -BBTTTB- CS
                        Rubredoxin  35 WvCPdCgv 42 
                                       ++CP+Cg 
  gi|242399869|ref|YP_002995294.1| 140 YICPVCGY 147
                                       55666654 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0014
                                       BBTTTB-BGGGE CS
                        Rubredoxin  36 vCPdCgvekeqF 47 
                                       +CP+Cgv++e+F
  gi|242399869|ref|YP_002995294.1| 156 KCPVCGVPREKF 167
                                       6*********99 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.6     0.004       3.8       2      11 ..     142     151 ..     142     155 .. 0.82
   2 ?    6.6   1.1    0.0087       8.2       1       6 [.     156     161 ..     156     166 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.004
                    DNA_ligase_ZBD   2 CPvCGsavvR 11 
                                       CPvCG  +v 
  gi|242399869|ref|YP_002995294.1| 142 CPVCGYTAVD 151
                                       *****88885 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0087
                    DNA_ligase_ZBD   1 hCPvCG 6  
                                       +CPvCG
  gi|242399869|ref|YP_002995294.1| 156 KCPVCG 161
                                       6****9 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.1     0.022        21      20      34 ..     131     147 ..     124     151 .. 0.72
   2 ?    6.7   3.6    0.0081       7.7       6      35 ..     140     163 ..     139     168 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.022
                       Zn-ribbon_8  20 sis.daplta.CPeCgs 34 
                                       + + + +++  CP Cg 
  gi|242399869|ref|YP_002995294.1| 131 KKDiEIKKVYiCPVCGY 147
                                       55556667888****96 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0081
                       Zn-ribbon_8   6 YrCeeCghefevlqsisdapltaCPeCgse 35 
                                       Y C  Cg  ++++    d+++++CP Cg +
  gi|242399869|ref|YP_002995294.1| 140 YICPVCG--YTAV----DEAPEKCPVCGVP 163
                                       8899999..5544....455677****964 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 ?    3.5   0.1     0.087        82      32      40 .]     138     146 ..     128     148 .. 0.75
   2 ?    6.8   0.4    0.0081       7.7      16      24 ..     155     163 ..     153     166 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.087
                     Auto_anti-p27  32 gkvyCvaCd 40 
                                       + ++C++C+
  gi|242399869|ref|YP_002995294.1| 138 KVYICPVCG 146
                                       566888885 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0081
                     Auto_anti-p27  16 etCpvCgvP 24 
                                       e CpvCgvP
  gi|242399869|ref|YP_002995294.1| 155 EKCPVCGVP 163
                                       67******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 ?    6.9   5.2    0.0045       4.2       3      24 ..     140     162 ..     138     163 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0045
                       zf-ribbon_3   3 vrCPnCGa.plssddnvCpyCGt 24 
                                       + CP CG   +++   +Cp CG 
  gi|242399869|ref|YP_002995294.1| 140 YICPVCGYtAVDEAPEKCPVCGV 162
                                       67******88************6 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 ?   -2.6   0.0       8.6   8.1e+03       7      18 ..      85      96 ..      85      98 .. 0.67
   2 ?    6.0   0.5     0.017        16       2       9 ..     141     148 ..     141     148 .. 0.85
   3 ?    4.0   1.8     0.073        69       2       7 ..     156     161 ..     155     163 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 8.6
                        Zn-C2H2_12  7 seqFpknvdqde 18
                                      +e++p+  +++e
  gi|242399869|ref|YP_002995294.1| 85 EEMYPAYKAVAE 96
                                      589998655555 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.017
                        Zn-C2H2_12   2 eCPlCseq 9  
                                       +CP+C+++
  gi|242399869|ref|YP_002995294.1| 141 ICPVCGYT 148
                                       6****985 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.073
                        Zn-C2H2_12   2 eCPlCs 7  
                                       +CP+C+
  gi|242399869|ref|YP_002995294.1| 156 KCPVCG 161
                                       7****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1221  (0.068102); expected 358.6 (0.02)
Passed bias filter:                      692  (0.0385967); expected 358.6 (0.02)
Passed Vit filter:                       107  (0.00596798); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.63u 0.32s 00:00:00.95 Elapsed: 00:00:00.54
# Mc/sec: 947.21
//
Query:       gi|242399870|ref|YP_002995295.1|  [L=363]
Description: NAD(P)H:rubredoxin oxidoreductase [Thermococcus sibiricus MM 739]
Scores for complete 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-55  186.2   1.0      1e-54  185.8   1.0    1.1  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    6.6e-22   77.9   1.4    4.3e-15   56.0   0.1    3.2  3  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
      4e-08   32.9   0.0    7.2e-05   22.2   0.0    2.2  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    4.3e-06   26.2   0.5      0.018   14.3   0.1    2.4  2  FAD_binding_3  FAD binding domain
    1.4e-05   24.9   1.0        1.5    8.4   0.0    4.0  4  DAO            FAD dependent oxidoreductase
    0.00089   19.5   0.6       0.11   12.7   0.0    2.8  3  TrkA_N         TrkA-N domain
     0.0031   17.7   0.8       0.62   10.3   0.5    2.6  2  NAD_binding_8  NAD(P)-binding Rossmann-like domain
     0.0035   17.7   0.1       0.41   11.1   0.0    2.5  2  NAD_binding_7  Putative NAD(P)-binding
     0.0039   16.3   1.8        6.7    5.7   0.3    3.3  3  FAD_binding_2  FAD binding domain
      0.004   17.1   0.2      0.013   15.4   0.2    2.0  1  Rubredoxin_C   Rubredoxin NAD+ reductase C-terminal domain
     0.0086   16.4   0.2      0.089   13.1   0.1    2.3  2  DUF3725        Protein of unknown function (DUF3725)
  ------ inclusion threshold ------
       0.01   15.7   0.0       0.14   12.0   0.0    2.2  2  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
      0.015   15.0   1.1       0.32   10.6   0.4    2.4  2  ApbA           Ketopantoate reductase PanE/ApbA
      0.015   14.5   0.0       0.21   10.7   0.0    2.0  2  K_oxygenase    L-lysine 6-monooxygenase (NADPH-requiring)
      0.024   13.7   0.3        3.3    6.7   0.0    2.3  2  Lycopene_cycl  Lycopene cyclase protein
      0.045   12.5   0.6        9.7    4.8   0.0    3.4  4  HI0933_like    HI0933-like protein
       0.12   12.2   0.0       0.43   10.4   0.0    2.0  2  Oxidored_q6    NADH ubiquinone oxidoreductase, 20 Kd subunit


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 !  185.8   1.0   9.6e-58     1e-54       2     292 ..       2     277 ..       1     279 [. 0.92

  Alignments for each domain:
  == domain 1  score: 185.8 bits;  conditional E-value: 9.6e-58
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH......HHHHCHHHHCCCCHC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxx RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias......evvkklnqgielllg 72 
                                       ++v++G Gp+G+++a +l+  ++kvt+ve+e+ +++ +++ls+ ++g+ e+++ +       e     ++gi+l lg
  gi|242399870|ref|YP_002995295.1|   2 RIVIVGNGPGGVELANQLSG-EHKVTIVERENVLHYSKPMLSHYIAGFVEKEKLFPysfswyE-----KKGIDLNLG 72 
                                       89****************98.********************************9997666653.....246****** PP

                                       CTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-T.SEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
                       Pyr_redox_2  73 eevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllp.krivvv 148
                                       +++  id+++k++       +d  +i yd lv+AtG++pr ++ +G  e v++l rtl++ae++k++  + k++++ 
  gi|242399870|ref|YP_002995295.1|  73 VKAEVIDRARKRLIT-----SD-GEIPYDVLVIATGARPRGPTFEGK-EFVQTL-RTLQDAERIKEQIEKyKDALIL 141
                                       **********99999.....23.27**********************.999888.************9999****** PP

                                       S-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 149 GgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgngeklevvledgee 225
                                       GgG+iG+El a lak+g++v lv+++++ll +ld+el++a++e+le  Gve++l ++  ++d+ng     + +d+  
  gi|242399870|ref|YP_002995295.1| 142 GGGFIGLELVANLAKAGYRVRLVHRGSNLL-GLDEELTKAIMEKLEGYGVEFYLDANTLKADENG-----IFTDKGY 212
                                       ******************************.9**************************9999999.....5999999 PP

                                       EEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GGGCTECCSS.--HHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx RF
                       Pyr_redox_2 226 idadlvvvavGvrpstelleeklglelderggivvdeflrtnvpgiyaiGDvaggkggp.elaqaAvq 292
                                       ++ +  + a Gv p++e++  k g+    ++gi++d++ rt+ +++yaiGD+a+  g++  +a+aA++
  gi|242399870|ref|YP_002995295.1| 213 VEGKVKICAFGVIPNKEIA-VKGGIHA--GRGILIDDHFRTSAKDVYAIGDCAEYNGIIgGTAKAAME 277
                                       ******************9.*****98..************************555555145555555 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   1.3e-06    0.0014       1      35 [.       2      35 ..       2      54 .. 0.78
   2 ?   -1.6   0.0       4.1   4.3e+03      51      69 ..      63      81 ..      61      90 .. 0.61
   3 !   56.0   0.1     4e-18   4.3e-15       2      69 ..     138     204 ..     137     211 .. 0.95

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.3e-06
                                      EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                         Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                      ++v+vG G  g+ElA+ l+    kVt+ver++ l 
  gi|242399870|ref|YP_002995295.1|  2 RIVIVGNGPGGVELANQLSGEH-KVTIVERENVLH 35
                                      79*****************976.9******98776 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 4.1
                                      HHTTEEEECSEEEEEEEEE CS
                         Pyr_redox 51 ekngievllntkveeiegs 69
                                      ek+gi++ l+ k+e i+  
  gi|242399870|ref|YP_002995295.1| 63 EKKGIDLNLGVKAEVIDRA 81
                                      5666666666666655533 PP

  == domain 3  score: 56.0 bits;  conditional E-value: 4e-18
                                       EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEE CS
                         Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegs 69 
                                       ++++GgG+iglEl ++la+ g +V +v+r+++ll +lDee+ k+++ekle  g+e++l++++ + +++
  gi|242399870|ref|YP_002995295.1| 138 ALILGGGFIGLELVANLAKAGYRVRLVHRGSNLL-GLDEELTKAIMEKLEGYGVEFYLDANTLKADEN 204
                                       589*******************************.**************************9998876 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 !    8.9   0.1   0.00073      0.77       1      33 [.       4      34 ..       4      46 .. 0.85
   2 !   22.2   0.0   6.8e-08   7.2e-05      80     219 ..      51     186 ..      35     259 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00073
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgnig 33
                                      +I+G GP G++ a +l     ++++i+E++n+ 
  gi|242399870|ref|YP_002995295.1|  4 VIVGNGPGGVELANQLSG--EHKVTIVERENVL 34
                                      7**********9998865..55699****9985 PP

  == domain 2  score: 22.2 bits;  conditional E-value: 6.8e-08
                       Pyr_redox_3  80 rkealeYlrevaksfelpiklfeeVesvkkedegfevetsketyeAkkviiAtGefdkPnklnipGeeklvkhyskv 156
                                       ++++  Y  +  +++ ++ +l  + e +++++   ++ ts +++  + ++iAtG   +P+ + ++G+e  v+  ++ 
  gi|242399870|ref|YP_002995295.1|  51 KEKLFPYSFSWYEKKGIDLNLGVKAEVIDRAR--KRLITSDGEIPYDVLVIATGA--RPRGPTFEGKE-FVQTLRTL 122
                                       55566666677777888888888888888875..4789****************9..**********9.88888888 PP

                       Pyr_redox_3 157 kefhkyagq.....kvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrle 219
                                       ++++ +++q     + ++ Gg+  + +   +l+++g +V++v+rgs++   +     +l   i ++le
  gi|242399870|ref|YP_002995295.1| 123 QDAERIKEQiekykDALILGGGFIGLELVANLAKAGYRVRLVHRGSNLLGLD----EELTKAIMEKLE 186
                                       8777766433323399*****************************9876654....344444555554 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0   0.00034      0.35       4      35 ..       3      33 ..       1      39 [. 0.89
   2 !   14.3   0.1   1.7e-05     0.018       3      79 ..     137     211 ..     135     281 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00034
                                      EEEE--SHHHHHHHHHHHHTTHHEEEEESSSS CS
                     FAD_binding_3  4 VlIVGaGpaGlmlallLseaGvrvvlvekrst 35
                                      ++IVG Gp G+ la+ Ls    +v++ve+ + 
  gi|242399870|ref|YP_002995295.1|  3 IVIVGNGPGGVELANQLSGE-HKVTIVERENV 33
                                      78****************99.9******9876 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 1.7e-05
                                       EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS--EEEHHHHHHHHHTT-HHHHHHHSEECCCCEEEEEEE CS
                     FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpradglnqrtmellrqlGledrilaegapnelmgealyne 79 
                                       d lI G+G  Gl l   L++aG rv+lv + s+   l   + l++  me l+  G+e  + a++ + + +g+++ + 
  gi|242399870|ref|YP_002995295.1| 137 DALILGGGFIGLELVANLAKAGYRVRLVHRGSNLLGLD--EELTKAIMEKLEGYGVEFYLDANTLKADENGIFTDKG 211
                                       789*************************9999887765..7889999*********999999999999999998877 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0    0.0014       1.5       1      31 [.       2      33 ..       2      38 .. 0.86
   2 ?    2.0   0.0      0.11   1.2e+02     149     203 ..      55     104 ..      41     128 .. 0.72
   3 !    7.2   0.4    0.0032       3.3       1      30 [.     137     168 ..     137     172 .. 0.92
   4 ?    2.6   0.0     0.077        81     146     175 ..     175     204 ..     174     237 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0014
                                      EEEEECTSHHHHHHHHHHH.HTTEEEEESSSS CS
                               DAO  1 dvviiGGGiiGlstAyeLa.rrgVtllekgdi 31
                                      ++vi+G G  G+  A +L+ +++Vt++e+++ 
  gi|242399870|ref|YP_002995295.1|  2 RIVIVGNGPGGVELANQLSgEHKVTIVERENV 33
                                      59****************94555******965 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.11
                                       HHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEEEEEEEEEE--GGG CS
                               DAO 149 taalaraaealGveilegtevtgleeedgkvwgverttpgendaadavVnaaGaw 203
                                        ++  +  e++G+++ +g +++ +++ +++   +  t++ge+  +d +V+a+Ga 
  gi|242399870|ref|YP_002995295.1|  55 FPYSFSWYEKKGIDLNLGVKAEVIDRARKR--LI--TSDGEI-PYDVLVIATGAR 104
                                       555556668889999999898888765333..33..444776.6799******86 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0032
                                       EEEEECTSHHHHHHHHHHHHTT..EEEEESSS CS
                               DAO   1 dvviiGGGiiGlstAyeLarrg..Vtllekgd 30 
                                       d +i GGG iGl     La++g  V l+ +g+
  gi|242399870|ref|YP_002995295.1| 137 DALILGGGFIGLELVANLAKAGyrVRLVHRGS 168
                                       789**********************9999985 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.077
                                       HHHHHHHHHHHHHTT-EEEESECEEEEEEE CS
                               DAO 146 akltaalaraaealGveilegtevtgleee 175
                                       ++lt+a+++++e  Gve+++ ++  + +e+
  gi|242399870|ref|YP_002995295.1| 175 EELTKAIMEKLEGYGVEFYLDANTLKADEN 204
                                       679*****************9887776443 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   0.0   0.00011      0.11       1      34 [.       3      34 ..       3      54 .. 0.79
   2 ?    4.2   0.0     0.048        51       2      29 ..     139     166 ..     138     202 .. 0.81
   3 ?   -2.6   0.0       6.1   6.4e+03      74      96 ..     263     285 ..     255     290 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00011
                                      EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHH CS
                            TrkA_N  1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerv 34
                                      i+i+G G  G +la++Ls ++ +v++++++ +++
  gi|242399870|ref|YP_002995295.1|  3 IVIVGNGPGGVELANQLSGEH-KVTIVERE-NVL 34
                                      89*****************99.5*****94.444 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.048
                                       EEES-SHHHHHHHHHHHH.TTEEEEEEES CS
                            TrkA_N   2 iiiGlGrvGrslaeeLse.ggkdvvvidk 29 
                                       +i+G G +G +l+ +L + g+ +v ++ +
  gi|242399870|ref|YP_002995295.1| 139 LILGGGFIGLELVANLAKaGY-RVRLVHR 166
                                       79****************777.4776654 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 6.1
                                       HHHHHHHHHHHHHTSSSEEEEEE CS
                            TrkA_N  74 eanilavllakelnpkkkiiara 96 
                                       e n ++  +ak  ++++++ a +
  gi|242399870|ref|YP_002995295.1| 263 EYNGIIGGTAKAAMEHARVLANI 285
                                       78888888888888888888876 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 ?    4.9   0.0      0.03        32       1      29 [.       5      32 ..       5      35 .. 0.92
   2 !   10.3   0.5   0.00059      0.62       1      30 [.     140     169 ..     140     174 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.03
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrd 29
                                      IvG G +G  +A  L+ + ++v+++e+ +
  gi|242399870|ref|YP_002995295.1|  5 IVGNGPGGVELANQLSGE-HKVTIVEREN 32
                                      9***************97.9******987 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00059
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSSS CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdr 30 
                                       I+G+G+ Gl + + Lakag++v l+ +++ 
  gi|242399870|ref|YP_002995295.1| 140 ILGGGFIGLELVANLAKAGYRVRLVHRGSN 169
                                       89*********************9988766 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 ?    4.6   0.0     0.042        44       9      40 ..       2      32 ..       1     105 [. 0.78
   2 !   11.1   0.0   0.00039      0.41       8      51 ..     136     181 ..     131     292 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.042
                     NAD_binding_7  9 kvlvvGgGevAarkvrklleagakvtvvapev 40
                                      ++++vG G+ + + +++l  +  kvt+v  e 
  gi|242399870|ref|YP_002995295.1|  2 RIVIVGNGPGGVELANQLSGE-HKVTIVEREN 32
                                      789***************999.9****99884 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00039
                     NAD_binding_7   8 kkvlvvGgGevAarkvrklleagakvtvvapev..keeleelvkla 51 
                                       k  l+ GgG ++++ v +l++ag +v +v   +      eel k++
  gi|242399870|ref|YP_002995295.1| 136 KDALILGGGFIGLELVANLAKAGYRVRLVHRGSnlLGLDEELTKAI 181
                                       789*************************988755533333444443 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.044        47       2      33 ..       3      33 ..       2      42 .. 0.84
   2 !    5.7   0.3    0.0063       6.7       1      33 [.     137     169 ..     137     173 .. 0.93
   3 !    5.4   0.1    0.0077       8.1     374     408 ..     240     270 ..     173     275 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.044
                                      EEEE--SHHHHHHHHHHHHTTT-EEEEESSSG CS
                     FAD_binding_2  2 viViGsGlAGLaAAleaaeaGlkvavvekeqe 33
                                      ++++G G +G   A +++ + +kv++ve e++
  gi|242399870|ref|YP_002995295.1|  3 IVIVGNGPGGVELANQLSGE-HKVTIVERENV 33
                                      79*************88554.46*****9987 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0063
                                       SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSG CS
                     FAD_binding_2   1 DviViGsGlAGLaAAleaaeaGlkvavvekeqe 33 
                                       D+++ G+G+ GL   +++a+aG +v +v  +++
  gi|242399870|ref|YP_002995295.1| 137 DALILGGGFIGLELVANLAKAGYRVRLVHRGSN 169
                                       89**************************98875 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.0077
                                       -EEEBETTSBESTTEEESSBTEEE-STCE..ESSSST CS
                     FAD_binding_2 374 gGvetdengrvldadgqpipGLYAaGeva..aggvhg 408
                                        G+ +d+++r+        ++ YA+G +a  +g+++g
  gi|242399870|ref|YP_002995295.1| 240 RGILIDDHFRT------SAKDVYAIGDCAeyNGIIGG 270
                                       599********......************65555555 PP

>> Rubredoxin_C  Rubredoxin NAD+ reductase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.2   1.2e-05     0.013      34      65 ..     326     353 ..     299     358 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.2e-05
                                       -..EEEEEEETTEEEEEEEES-HHHHHHHHHH CS
                      Rubredoxin_C  34 kgkYkklfikngklvGAiliGDtkesaklkkl 65 
                                       +    k+f++ +k++GA++i D+++++ l+k 
  gi|242399870|ref|YP_002995295.1| 326 T----KIFLEGEKVIGAVVIEDVRKAMMLEKK 353
                                       4....9*********************99875 PP

>> DUF3725  Protein of unknown function (DUF3725)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.88   9.3e+02      29      49 ..      67      87 ..      62      96 .. 0.82
   2 !   13.1   0.1   8.4e-05     0.089      23      48 ..     324     349 ..     320     352 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.88
                           DUF3725 29 LEgnrfvRanileivrktlvg 49
                                      +++n +v+a++++  rk l++
  gi|242399870|ref|YP_002995295.1| 67 IDLNLGVKAEVIDRARKRLIT 87
                                      678999***********9985 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 8.4e-05
                           DUF3725  23 eigreFLEgnrfvRanileivrktlv 48 
                                       e ++ FLEg++ + a ++e vrk+++
  gi|242399870|ref|YP_002995295.1| 324 EKTKIFLEGEKVIGAVVIEDVRKAMM 349
                                       67899*******************96 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 ?    1.2   0.0      0.28     3e+02       2      55 ..       3      54 ..       2      65 .. 0.83
   2 ?   12.0   0.0   0.00013      0.14       4      49 ..     140     185 ..     137     202 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.28
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgkl 55
                                      + ++G G  G ++a+++ s +++V++v++ e+ l+ ++ ++++ ++ +vek+kl
  gi|242399870|ref|YP_002995295.1|  3 IVIVGNGPGGVELANQL-SGEHKVTIVER-ENVLHYSKPMLSHYIAGFVEKEKL 54
                                      7899****9***99987.56799**9997.567888888888888888888876 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00013
                                       EE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCC CS
                           3HCDH_N   4 viGaGtmGagiaavfasagleVvlvdiseealekalekiekslekl 49 
                                       ++G G +G ++ a +a+ag++V+lv + ++ l   +e  ++ +ekl
  gi|242399870|ref|YP_002995295.1| 140 ILGGGFIGLELVANLAKAGYRVRLVHRGSNLLGLDEELTKAIMEKL 185
                                       89***********************998877766666666555554 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0      0.09        95       1      48 [.       3      49 ..       3     101 .. 0.80
   2 ?   10.6   0.4    0.0003      0.32       2      31 ..     139     168 ..     138     176 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.09
                                      EEEES-SHHHHHHHHHHHHHTHCEEEE-SCHHHHHHHHHCEEEEETT.C CS
                              ApbA  1 iailGaGaiGsllaakLakagadvtlilrsrrlealkknGlrltseg.g 48
                                      i+i+G G  G  la +L    ++vt++ r++ + + +k  l+ ++ g  
  gi|242399870|ref|YP_002995295.1|  3 IVIVGNGPGGVELANQL-SGEHKVTIVEREN-VLHYSKPMLSHYIAGfV 49
                                      78999999999999999.66899******99.87888877777776653 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0003
                                       EEES-SHHHHHHHHHHHHHTHCEEEE-SCH CS
                              ApbA   2 ailGaGaiGsllaakLakagadvtlilrsr 31 
                                       +ilG G iG  l a+Lakag+ v l+ r+ 
  gi|242399870|ref|YP_002995295.1| 139 LILGGGFIGLELVANLAKAGYRVRLVHRGS 168
                                       79************************9986 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.12   1.3e+02     193     224 ..       2      30 ..       1      42 [. 0.78
   2 ?   10.7   0.0    0.0002      0.21     152     233 ..      97     175 ..      87     197 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.12
                       K_oxygenase 193 riaVvGsGqSaaeifedllrrqkkvelklvtr 224
                                       ri++vG G  + e++++l  + k   +++v r
  gi|242399870|ref|YP_002995295.1|   2 RIVIVGNGPGGVELANQLSGEHK---VTIVER 30 
                                       89999999999999999987765...555555 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0002
                       K_oxygenase 152 lvlgvGtepkiPevleklegkervvHsseylerkeellakkriaVvGsGqSaaeifedllrrqkkvelklvtrseal 228
                                       lv+++G +p  P++  k    +++   +++ + ke+ ++ k+ ++ G+G  + e++ +l++    + ++lv r+++l
  gi|242399870|ref|YP_002995295.1|  97 LVIATGARPRGPTFEGKEF-VQTLRTLQDAERIKEQIEKYKDALILGGGFIGLELVANLAKAG--YRVRLVHRGSNL 170
                                       89**********9866544.47777777777777789999*******************9875..58999***9999 PP

                       K_oxygenase 229 epldd 233
                                         ld+
  gi|242399870|ref|YP_002995295.1| 171 LGLDE 175
                                       98886 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0031       3.3       2      31 ..       3      29 ..       2      38 .. 0.81
   2 ?    4.9   0.1     0.011        11       1      36 [.     137     170 ..     137     178 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0031
                     Lycopene_cycl  2 vvviGaGpAglslAarlteakpglkvvlie 31
                                      +v++G Gp g+ lA++l     + kv+++e
  gi|242399870|ref|YP_002995295.1|  3 IVIVGNGPGGVELANQL---SGEHKVTIVE 29
                                      79***************...4556677776 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.011
                     Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvlieaspsl 36 
                                       D ++ G+G  gl l a+l  ak+g +v l+  + +l
  gi|242399870|ref|YP_002995295.1| 137 DALILGGGFIGLELVANL--AKAGYRVRLVHRGSNL 170
                                       779***************..9999999999877665 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0    0.0092       9.7       2      33 ..       2      32 ..       1      36 [. 0.89
   2 ?    0.5   0.0      0.18   1.9e+02     120     164 ..      63     103 ..      53     110 .. 0.77
   3 ?    2.6   0.1     0.042        45       2      34 ..     137     169 ..     136     172 .. 0.90
   4 ?   -2.2   0.1       1.2   1.3e+03     374     393 ..     251     270 ..     228     271 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0092
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSS CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekak 33
                                      +++++G G+ G+  A ++ + +++V+++e+++
  gi|242399870|ref|YP_002995295.1|  2 RIVIVGNGPGGVELANQL-SGEHKVTIVEREN 32
                                      68***************9.78899***99876 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.18
                                       HHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE---- CS
                       HI0933_like 120 keagvklrletevksvekeedgkfrvktkseeeleadklvlAtGG 164
                                       +++g++l+l  + + +++    + r+ t s++e+  d lv+AtG 
  gi|242399870|ref|YP_002995295.1|  63 EKKGIDLNLGVKAEVIDR---ARKRLIT-SDGEIPYDVLVIATGA 103
                                       667777777777776733...3456777.899***********97 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.042
                                       SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSS CS
                       HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakk 34 
                                       d +++GgG  Gl   +++ak+g rV l+ ++++
  gi|242399870|ref|YP_002995295.1| 137 DALILGGGFIGLELVANLAKAGYRVRLVHRGSN 169
                                       789************************988765 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 1.2
                                       TSTTEEE-GGGBSEEE-TTT CS
                       HI0933_like 374 kvpgLffaGEvlDvegvtGG 393
                                       + ++++ +G + + +g +GG
  gi|242399870|ref|YP_002995295.1| 251 SAKDVYAIGDCAEYNGIIGG 270
                                       5789***************9 PP

>> 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 ?   -1.7   0.0       2.3   2.5e+03      42      65 ..      90     127 ..      68     143 .. 0.58
   2 ?   10.4   0.0   0.00041      0.43      51      95 ..     232     274 ..     174     311 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 2.3
                                       HTTTSEEEEE.ESBE...E.............EEHHHH CS
                       Oxidored_q6  42 kekeadvlvv.eGavtrkp.............kealel 65 
                                       +e   dvlv+ +Ga +r+p              ++ e+
  gi|242399870|ref|YP_002995295.1|  90 GEIPYDVLVIaTGARPRGPtfegkefvqtlrtLQDAER 127
                                       45556666653566666667777444444444344444 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00041
                                       EESBE...EEEHHHHHHHHGGGSSEEEEESHHHHH-TGGGSTT-T CS
                       Oxidored_q6  51 veGavtrkpkealellkelaekakaviavGtCAafGGipaaannp 95 
                                       v+G++  +    + + ++++ +ak v a+G+CA + Gi +   + 
  gi|242399870|ref|YP_002995295.1| 232 VKGGI--HAGRGILIDDHFRTSAKDVYAIGDCAEYNGIIGGTAKA 274
                                       55555..44666666778999****************99655544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); 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: 0.68u 0.33s 00:00:01.01 Elapsed: 00:00:00.53
# Mc/sec: 2048.83
//
Query:       gi|242399871|ref|YP_002995296.1|  [L=179]
Description: rubrerythrin-related protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.6e-20   73.2   4.2    3.3e-20   72.9   4.2    1.1  1  Rubrerythrin  Rubrerythrin
    0.00091   19.1   0.7        1.1    9.1   0.0    2.1  2  DUF2202       Uncharacterized protein domain (DUF2202)
      0.007   16.6   4.9      0.016   15.4   1.2    2.1  2  Ferritin_2    Ferritin-like domain
  ------ inclusion threshold ------
       0.15   12.1   0.0       0.21   11.6   0.0    1.2  1  DDE_Tnp_1_3   Transposase DDE 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 !   72.9   4.2   7.4e-24   3.3e-20       1     135 [.      16     143 ..      16     145 .. 0.97

  Alignments for each domain:
  == domain 1  score: 72.9 bits;  conditional E-value: 7.4e-24
                                       HHHHHHHHHHHHHHHHHHHHHHCHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSBBS-------T CS
                      Rubrerythrin   1 eiLekAiagEssarrlYkelaekakegypqiaelFeelAeeEreHakilnklleklepelelevkekvreyaeakpk 77 
                                       eiL +Aia+E++a  +Y  l e      + i+++F++lA++E+ H+ +l +l++kl+++++ ++  k ++++e ++ 
  gi|242399871|ref|YP_002995296.1|  16 EILGYAIASEEDAKAFYLKLGEGKG---ELIQNFFKDLAKAEEAHKTLLLNLHKKLFGNEN-YITPKGIPFLESTIN 88 
                                       89********************999...*********************************.99************* PP

                                       TGGHHHHHHHHHHHHHHHHHCHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHHHHHH CS
                      Rubrerythrin  78 flttaknLeeaiegayaeeeemyrfyeelaekegneeakklfkklaeaEkkHeerlrk 135
                                       ++t    +e a++ a  +e+ ++r+y+ la+  +++e+k lf++la +E+ H+++ ++
  gi|242399871|ref|YP_002995296.1|  89 VVTLGSMVE-AMKTALMNEKVAERVYKLLAK--RFPEHKALFEFLATQERAHYNSIKA 143
                                       *99999999.*********************..89*******************9887 PP

>> DUF2202  Uncharacterized protein domain (DUF2202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0   0.00025       1.1       2      51 ..      15      67 ..      14      80 .. 0.78
   2 !    8.8   0.2   0.00031       1.4      10      47 ..     104     143 ..      95     170 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00025
                           DUF2202  2 kdsllymreeeklarDvYlelYdrwk...lqiflniakseqthtdavksllek 51
                                      k+ l y    e  a+  Yl+l +  +   ++ f+++ak+e+ h   + +l +k
  gi|242399871|ref|YP_002995296.1| 15 KEILGYAIASEEDAKAFYLKLGEGKGeliQNFFKDLAKAEEAHKTLLLNLHKK 67
                                      66666777778889999**9999766333678***********9988888766 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00031
                           DUF2202  10 eeeklarDvYlelYdrw..klqiflniakseqthtdavks 47 
                                        +ek+a  vY  l +r+  + ++f+ +a  e+ h +++k 
  gi|242399871|ref|YP_002995296.1| 104 MNEKVAERVYKLLAKRFpeHKALFEFLATQERAHYNSIKA 143
                                       589************9843578**************9985 PP

>> Ferritin_2  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   1.2   3.5e-06     0.016       3     107 ..      15     120 ..      13     126 .. 0.80
   2 !    7.7   0.8   0.00087       3.9       3      51 ..      96     146 ..      94     155 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.5e-06
                        Ferritin_2   3 vdiLnfAlnlEyleaafYtaalegaslddkalldaevrevaeeiakheeaHveflkaale...Gaaa......vakp 70 
                                        +iL +A++ E  + afY +  eg          + ++++++++ak eeaH ++l +  +   G++       ++ +
  gi|242399871|ref|YP_002995296.1|  15 KEILGYAIASEEDAKAFYLKLGEG--------KGELIQNFFKDLAKAEEAHKTLLLNLHKklfGNENyitpkgIPFL 83 
                                       689*****************9995........4577899999*********99999988888877773222222333 PP

                        Ferritin_2  71 tfdfafdpfadeksflalaavlEdvgvsAYlgaapll 107
                                       + ++++ ++ +  + +++a + E+v+ + Y+  a+ +
  gi|242399871|ref|YP_002995296.1|  84 ESTINVVTLGSMVEAMKTALMNEKVAERVYKLLAKRF 120
                                       5555889***********************9888876 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00087
                        Ferritin_2   3 vdiLnfAlnlEyleaafYtaalegasldd..kalldaevrevaeeiakhee 51 
                                       v+ ++ Al  E ++   Y+  ++++ +++   ++l +++r+ +++i++hee
  gi|242399871|ref|YP_002995296.1|  96 VEAMKTALMNEKVAERVYKLLAKRFPEHKalFEFLATQERAHYNSIKAHEE 146
                                       678899*****************9999889999999999999999999996 PP

>> DDE_Tnp_1_3  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   4.6e-05      0.21      55     122 ..      39     106 ..      31     130 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.6e-05
                       DDE_Tnp_1_3  55 kGeilavkltpgnvdDrepveelakellgklfaDkgyiskklaeellee.gielitklrknmkkkllsl 122
                                       kGe+++  + +   + +e  ++l  +l+ klf++  yi+ k +  l+++ ++  + ++ + mk+ l++ 
  gi|242399871|ref|YP_002995296.1|  39 KGELIQNFFKDL-AKAEEAHKTLLLNLHKKLFGNENYITPKGIPFLESTiNVVTLGSMVEAMKTALMNE 106
                                       566666544443.33445668899*****************9999977667777778999999999864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.35s 00:00:00.92 Elapsed: 00:00:00.53
# Mc/sec: 1007.62
//
Query:       gi|242399872|ref|YP_002995297.1|  [L=408]
Description: Flavoprotein, [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-07   31.9   0.8    2.5e-07   30.9   0.8    1.6  1  Lactamase_B    Metallo-beta-lactamase superfamily
    4.5e-05   23.1   0.0    7.1e-05   22.4   0.0    1.2  1  Lactamase_B_2  Beta-lactamase superfamily domain
    0.00059   20.1   0.0     0.0012   19.0   0.0    1.6  2  Flavodoxin_1   Flavodoxin
      0.003   17.5   0.0     0.0068   16.3   0.0    1.5  1  Lactamase_B_3  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
       0.13   11.7   0.0       0.21   11.0   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 !   30.9   0.8   6.9e-11   2.5e-07       7     162 ..      41     183 ..      36     241 .. 0.88

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 6.9e-11
                                       EEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCH CS
                       Lactamase_B   7 nsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalf 83 
                                       n+yl+ ++g v+L+D+ +  ++a ++le  ++ ++pk+++++i+ H  +DH G+l+++ ea +++  +   + ++ +
  gi|242399872|ref|YP_002995297.1|  41 NAYLMKTEGAVVLFDA-WKKDYAYQFLETLSRIVDPKEITHIIVHHTEPDHSGALPKVLEANGYNAKIIGTAFAKRL 116
                                       9**************9.88888888999*************************************999999999999 PP

                                       CHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCCC CS
                       Lactamase_B  84 meeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallagetgri 160
                                        e+             ++ + ++ ++e+++++  g+r +  + +  +h ++ ++ ++ ++kv+++ Da+   ++++ 
  gi|242399872|ref|YP_002995297.1| 117 LEAF------------YGIKENVHAVEDGEELKIGSRTLRFISVPWLHWPDTMITYLVEDKVILSCDAGGGYSIPEA 181
                                       9999............455566779999999999999999999999**********************998887776 PP

                                       CC CS
                       Lactamase_B 161 dl 162
                                         
  gi|242399872|ref|YP_002995297.1| 182 ID 183
                                       55 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 !   22.4   0.0     2e-08   7.1e-05       3     130 ..      52     162 ..      51     184 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 2e-08
                                       EEES--TT.HHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHH CS
                     Lactamase_B_2   3 iLiDagpd.lrqqalralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvyla 78 
                                       +L+Da+    + q+l +l   ++  ++++i  +++ h + DH   l+ + e  + ++++++++   + lea      
  gi|242399872|ref|YP_002995297.1|  52 VLFDAWKKdYAYQFLETL---SRIVDPKEITHIIVHHTEPDHSGALPKVLEANGYNAKIIGTAFAKRLLEAFY---- 121
                                       688888876555544444...22347899**********************6666688999999999999884.... PP

                                       CHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEE CS
                     Lactamase_B_2  79 leeepavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlri 130
                                        + +  +nvh ++ ge++++g+  l++  +p  h+  +        ++ +++
  gi|242399872|ref|YP_002995297.1| 122 -GIK--ENVHAVEDGEELKIGSRTLRFISVPWLHWPDT--------MITYLV 162
                                       .344..789************99999999999888776........555555 PP

>> Flavodoxin_1  Flavodoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       3.8   1.4e+04     109     128 ..     103     122 ..      98     130 .. 0.72
   2 !   19.0   0.0   3.5e-07    0.0012       1     140 [.     265     395 ..     265     398 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 3.8
                                       HHHHHHHHTTCEEESSSEEE CS
                      Flavodoxin_1 109 kldekleelGaerllklleg 128
                                       +  ++++ ++a+rll+  +g
  gi|242399872|ref|YP_002995297.1| 103 YNAKIIGTAFAKRLLEAFYG 122
                                       55678888888888876655 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 3.5e-07
                                       EEEETSSSHHHHHHHHHHHHHHHTTTEEEEEEEEGTTSC.....GGGGGTHSEEEEEEEEETTTBEEGGGHHHHHHH CS
                      Flavodoxin_1   1 ilYgSetGnteklAkqlaeelgehgfnadvvslsdydes.....lseieeealllvvtsTfgnGdppengesffqdl 72 
                                       ++Y+S++G  e   +   +el++ gf++ v+++ d +       l e+++ + l++++sT+     p      ++ l
  gi|242399872|ref|YP_002995297.1| 265 VIYDSMYGFVERSVRIAIDELQKLGFEPVVYKFTDKEAPavsdiLGEVPDSEALIIGASTYEANVHP-R---IRYTL 337
                                       89********************************9997788999999*************9988888.2...33555 PP

                                       HHHHCHHGCCSTTTTEEEEEEEEECTTSSSTTHHHHHHHHHHHHTTCEEESSSEEEETTSTHGHHHHH CS
                      Flavodoxin_1  73 lelkgdeledgdlsgvrfavfglGdsayenFcaagkkldekleelGaerllkllegdednqegqeeaf 140
                                       +el        d  + +  v+ lG  ++ +   ag+++++++++  ++ + + +e+   ++++ e+ +
  gi|242399872|ref|YP_002995297.1| 338 YELL-------DKANYEKPVLILGTFGWAG--VAGREIETLIKRSRFDHVDT-VEVRGRPTDEDEAKI 395
                                       5555.......3468888999999999999..99999999999988888887.777777765555555 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.9e-06    0.0068       7      82 ..      40     147 ..      38     181 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.9e-06
                     Lactamase_B_3   7 hnsflletagarilvDPfkanlgyeppa........eeaDlvlisqaledHahletlkql................. 58 
                                       +n++l++t+ga++l D +k+   y+  +        +e+  +++ +  +dH    +l+++                 
  gi|242399872|ref|YP_002995297.1|  40 YNAYLMKTEGAVVLFDAWKKDYAYQFLEtlsrivdpKEITHIIVHHTEPDHSG--ALPKVleangynakiigtafak 114
                                       79****************85555554448888888899999***999999964..344444557************* PP

                     Lactamase_B_3  59 .........aenvkvleegeslevggleirava 82 
                                                +env+ +e+ge+l++g+  +r ++
  gi|242399872|ref|YP_002995297.1| 115 rlleafygiKENVHAVEDGEELKIGSRTLRFIS 147
                                       ************************966555444 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 ?   11.0   0.0     6e-05      0.21       1      58 [.      44     100 ..      44     120 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6e-05
                     Lactamase_B_6   1 lLeldnvkiLlDvGwdeskvslesalkelekvi..ptvdliLLshatlehlGayallyak 58 
                                       l++ +++ +L D   +++     + l+ l++++  +++ +i++ h +++h Ga++ ++ +
  gi|242399872|ref|YP_002995297.1|  44 LMKTEGAVVLFDAWKKDY--A-YQFLETLSRIVdpKEITHIIVHHTEPDHSGALPKVLEA 100
                                       577888999999654554..3.479*******9878*****************9877654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       587  (0.0327403); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); 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: 0.64u 0.33s 00:00:00.97 Elapsed: 00:00:00.52
# Mc/sec: 2375.74
//
Query:       gi|242399873|ref|YP_002995298.1|  [L=152]
Description: Thioredoxin peroxidase [Thermococcus sibiricus MM 739]
Scores for complete 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-34  117.3   0.0    4.4e-34  117.1   0.0    1.0  1  AhpC-TSA       AhpC/TSA family
    1.2e-21   77.0   0.0    1.4e-21   76.7   0.0    1.0  1  Redoxin        Redoxin
    3.1e-05   23.9   0.0    4.6e-05   23.3   0.0    1.2  1  SCO1-SenC      SCO1/SenC
  ------ inclusion threshold ------
       0.02   15.2   0.0      0.035   14.4   0.0    1.4  1  Thioredoxin_8  Thioredoxin-like
      0.054   13.1   0.0       0.08   12.5   0.0    1.3  1  GSHPx          Glutathione peroxidase


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 !  117.1   0.0   1.2e-37   4.4e-34       1     121 [.       6     129 ..       6     132 .. 0.97

  Alignments for each domain:
  == domain 1  score: 117.1 bits;  conditional E-value: 1.2e-37
                                       TTSB----EEESTTCEEEECHHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHH CS
                          AhpC-TSA   1 vgdkapdfelknadgetvslsdykgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfi 77 
                                       vg+kapdf lk++dg++++ls ++gk+v+l f+p +w+ vC+++++al+++ye+f++++v  +g+svd+  + k+++
  gi|242399873|ref|YP_002995298.1|   6 VGEKAPDFVLKDQDGKEFRLSGFRGKKVLLSFHPLAWTSVCEKQMRALEENYEKFESLNVVPVGISVDPIPTKKAWA 82 
                                       79*************************************************************************** PP

                                       HH-H..SSEEEE-..TTSHHHHHTT-EETTTTECSCEEEEE-TTSBE CS
                          AhpC-TSA  78 ekes.lnfpllsD..eegkvakaygvlkeekglalratfvidkegki 121
                                       e+++  ++++lsD  ++g+vak yg+++e++g+  ra +++d+egk 
  gi|242399873|ref|YP_002995298.1|  83 EDIGlKKLRILSDfwPHGEVAKLYGIFREKEGFSERANILVDEEGKM 129
                                       ****4479*************************************96 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.7   0.0   3.9e-25   1.4e-21       1     131 [.       5     133 ..       5     146 .. 0.86

  Alignments for each domain:
  == domain 1  score: 76.7 bits;  conditional E-value: 3.9e-25
                                       -TTSBB---ECCEETTCEEEEEHHHHTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHHHH CS
                           Redoxin   1 kagdkaPdftlplaatdgnsvslsefkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndafvk 77 
                                       k+g+kaPdf+l++  +dg+++ ls f+gkkv++ f p a++ +C +++++le+ +e++++ +v  v++++d  +  k
  gi|242399873|ref|YP_002995298.1|   5 KVGEKAPDFVLKD--QDGKEFRLSGFRGKKVLLSFHPLAWTSVCEKQMRALEENYEKFESLNVVPVGISVDPIPTKK 79 
                                       69*********88..**************************************************999988777655 PP

                                       HHHHH.TT-TSEEEE-..TTSHHHHHTT-TTEEE.GGGEEE-EEEEEEETTEEEEEE CS
                           Redoxin  78 efwgk.eglkfpvlsD..gsaaftkalGlrleedaseglrtpryavidedgkvvyle 131
                                       +++++   +k ++lsD  + ++++k +G  +    +eg+  ++ +++de+gk +  +
  gi|242399873|ref|YP_002995298.1|  80 AWAEDiGLKKLRILSDfwPHGEVAKLYG--IFRE-KEGFSERANILVDEEGKMIFFK 133
                                       5555585558899*****9*********..5543.4668************988665 PP

>> SCO1-SenC  SCO1/SenC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   1.3e-08   4.6e-05       2      67 ..      11      74 ..      10      80 .. 0.96

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 1.3e-08
                         SCO1-SenC  2 gpFelvdqdgeavteedlegkpslvffgFthCpdvCpttlanmaevldalgeeaekvqplfiTvDP 67
                                       +F l dqdg++++ + ++gk +l+ f     ++vC +++  ++e +++++    +v p+ i+vDP
  gi|242399873|ref|YP_002995298.1| 11 PDFVLKDQDGKEFRLSGFRGKKVLLSFHPLAWTSVCEKQMRALEENYEKFESL--NVVPVGISVDP 74
                                      58************************************************998..9*********9 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   9.6e-06     0.035       2      57 ..      31      88 ..      30     110 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 9.6e-06
                                      SEEEEEE--S.SSHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-S..S-HHHHHHHGGGS CS
                     Thioredoxin_8  2 kvvlLyfgas.wcppckaftpklkelyeklkkkkkveivyvsld..kkeeefekylkkn 57
                                      k vlL f+   w + c++ ++ l e yek++ + +v+ v +s+d   +++++ + +   
  gi|242399873|ref|YP_002995298.1| 31 KKVLLSFHPLaWTSVCEKQMRALEENYEKFE-SLNVVPVGISVDpiPTKKAWAEDIGLK 88
                                      77888888755999****************8.8***********665788888777655 PP

>> GSHPx  Glutathione peroxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.2e-05      0.08       3      59 ..      12      70 ..      11     101 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.2e-05
                                      GBEEEBTTSSEEEGGGGTTSEEEEE..EEESSSTTHHHHHHHHHHHHHHGGGTEEEEEE CS
                             GSHPx  3 elsakdidgekvkleklrgkvvliv..nvaskCglteqykeleelqkrykdkglvilgf 59
                                      ++  kd+dg+++ l+ +rgk vl+     a +    +q + lee ++++++  +v +g 
  gi|242399873|ref|YP_002995298.1| 12 DFVLKDQDGKEFRLSGFRGKKVLLSfhPLAWTSVCEKQMRALEENYEKFESLNVVPVGI 70
                                      57889*****************9752256766666779999999999999887776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.36s 00:00:00.91 Elapsed: 00:00:00.54
# Mc/sec: 848.43
//
Query:       gi|242399874|ref|YP_002995299.1|  [L=290]
Description: 2-oxoacid:ferredoxin oxidoreductase, subunit beta [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-31  109.6   0.2    2.3e-31  108.6   0.2    1.5  2  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
    3.6e-25   87.9   1.1    6.3e-25   87.1   0.5    1.7  2  PFO_beta_C    Pyruvate ferredoxin oxidoreductase beta subunit
     0.0059   17.1   2.1       0.56   10.8   0.3    2.3  2  Pet100        Pet100


Domain annotation for each model (and alignments):
>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.6   0.2   3.9e-35   2.3e-31      16     153 .]      56     199 ..      48     199 .. 0.95
   2 ?   -3.6   0.0       1.4   8.3e+03     131     145 ..     226     240 ..     221     242 .. 0.78

  Alignments for each domain:
  == domain 1  score: 108.6 bits;  conditional E-value: 3.9e-35
                                       SSSSEEEC.ETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEEEEEEE-SBCCCHHH CS
                      TPP_enzyme_C  16 krprsylt.sgglgtmGyglpaAiGaklakpdrevvaivGDGgflmi.lqelatavrrnlpitvvvlnNegygmtgg 90 
                                       +++++y++ +g+++ +G+++p+A+++k+a+p+ +v+a  GDG+++   +++l++a+rrn +itv+v++N++yg+t+g
  gi|242399874|ref|YP_002995299.1|  56 AKMPHYINvNGYHTLHGRAIPIATAVKAANPSLTVIAEGGDGDMYAEgGNHLIHAIRRNPDITVLVHDNQIYGLTKG 132
                                       457899999******************************************************************** PP

                                       H...HHHHTCCTTTTSBB.BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHHHHCSSSEEEEEE CS
                      TPP_enzyme_C  91 q...qepfggkrksgpagkdlkpvdfaklaealGak.garvekadveeleealkealekkgpaliev 153
                                       q   +++ g k+ ++p g  ++p+++ +la al a+ +ar    + +e  e+lk+a+++kg a++++
  gi|242399874|ref|YP_002995299.1| 133 QaspTTMPGVKTPTQPWGVFEEPFNPIALAIALDASfVARTFMGYFKESVEILKKAIQHKGLAIVDI 199
                                       *9998999999999999999****************999989999********************97 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 1.4
                                       .HHHHHHHHHHHHCS CS
                      TPP_enzyme_C 131 dveeleealkealek 145
                                       d+ + eea+k+a+e+
  gi|242399874|ref|YP_002995299.1| 226 DPYDREEAFKRAIES 240
                                       556789999999976 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 ?   -3.3   0.0       1.7     1e+04      11      22 ..     176     187 ..     172     191 .. 0.70
   2 !   87.1   0.5     1e-28   6.3e-25       1      65 [.     203     264 ..     203     265 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.7
                                       XXXXX-EEEGGG CS
                        PFO_beta_C  11 dwYkervyklee 22 
                                        ++ke v  l++
  gi|242399874|ref|YP_002995299.1| 176 GYFKESVEILKK 187
                                       588888877766 PP

  == domain 2  score: 87.1 bits;  conditional E-value: 1e-28
                                       XTTTXSSSXSXXXXX-EEEGGGST---EEHHHHHHHHT-----EEEEEEEETTS--HHHHHHT.. CS
                        PFO_beta_C   1 CvtFNkvnTfdwYkervykleedgyDpsdlekAlekalewgdkiplGifYkeekptyeerleelk 65 
                                       Cv+FNkvnT++wY+e++y ++   +Dp d+e+A+++a e  d++plGifY  ekpt+ee+++++k
  gi|242399874|ref|YP_002995299.1| 203 CVSFNKVNTYEWYREHTYWMKG--HDPYDREEAFKRAIE-SDPLPLGIFYIHEKPTFEEQVPAYK 264
                                       *********************6..***************.**********************998 PP

>> Pet100  Pet100
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.7   0.1    0.0035        21      15      40 ..     199     224 ..     196     240 .. 0.74
   2 !   10.8   0.3   9.3e-05      0.56      17      58 ..     243     284 ..     242     289 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0035
                            Pet100  15 vffPvgvfyyfnqpeyfeefvvktkr 40 
                                       +f P + f  +n+ e+++e++  +k 
  gi|242399874|ref|YP_002995299.1| 199 IFHPCVSFNKVNTYEWYREHTYWMKG 224
                                       78899**************9988775 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 9.3e-05
                            Pet100  17 fPvgvfyyfnqpeyfeefvvktkreffppeeke.lreeleelk 58 
                                       +P+g+fy+  +p  fee v  +k++  p  +++   ee++++ 
  gi|242399874|ref|YP_002995299.1| 243 LPLGIFYIHEKP-TFEEQVPAYKKDKTPLWQRKpKIEEIKKIL 284
                                       6***********.9**********9999444432334443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); 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:                         3  (0.000167327); expected 0.2 (1e-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 0.37s 00:00:00.90 Elapsed: 00:00:00.53
# Mc/sec: 1651.89
//
Query:       gi|242399875|ref|YP_002995300.1|  [L=570]
Description: 2-oxoacid:ferredoxin oxidoreductase, subunit alpha [Thermococcus sibiricus MM 739]
Scores for complete 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-56  189.7   0.0    9.1e-56  189.2   0.0    1.2  1  POR_N         Pyruvate flavodoxin/ferredoxin oxidoreductase, 
    6.8e-31  107.7   0.1    1.8e-30  106.3   0.1    1.7  1  POR           Pyruvate ferredoxin/flavodoxin oxidoreductase
    0.00051   20.3   0.0     0.0015   18.8   0.0    1.9  1  PFOR_II       Pyruvate:ferredoxin oxidoreductase core domain 
    0.00054   19.6   0.2     0.0014   18.3   0.2    1.6  1  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP b


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 !  189.2   0.0     2e-59   9.1e-56       2     221 ..     213     438 ..     212     447 .. 0.92

  Alignments for each domain:
  == domain 1  score: 189.2 bits;  conditional E-value: 2e-59
                                       HHHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCC CS
                             POR_N   2 aaiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmien 78 
                                       +a+a+g+++++ YP++Ps+ +a   a++++++e+    v q+e+Ei+ai+++iGA +aGar++++TSg G++Lm+e+
  gi|242399875|ref|YP_002995300.1| 213 GAVAGGMNFLSFYPMSPSTGVAVFSAQHAEDFEI---IVEQVEDEISAINMAIGAWFAGARGMVTTSGGGFALMSEA 286
                                       78999****************************7...9*************************************** PP

                                       HHHHHHTT--EEEEEEEEE-STTBEEEEE--TTCHHHH.....S---EEEE-SSHHHHHHHHHHHHHHHHHCTSEEE CS
                             POR_N  79 lglaageelPvvivvvaRalpstglsirtdqsDlmaar.....dtglivlasenvqeafdlalvAfnlAekvrvPvi 150
                                       l la+++e Pvvi++++R +p+tgl++rt q+Dl+ a+     +++ i+la+++++eaf l+++AfnlA + +vPvi
  gi|242399875|ref|YP_002995300.1| 287 LSLAGMAENPVVIHLAQRPGPATGLPTRTMQGDLNLALysghgEFPRIILAPGSIEEAFYLTAEAFNLADRDQVPVI 363
                                       ***************************************************************************** PP

                                       EEEEHHHH.HEEEEEEC-SGG...GS-----SBXXXXXXXX...SXXXBXXTXXTSSXXEEESBXBXTTSXBXXXX CS
                             POR_N 151 vlfDgfllshevekvelpdee..delklikekleeyerkey...aldpekpiargtaanpdtglehrekgneaeda 221
                                       +l+D++++ +++ +++  d    +  k+i e+ ++y+r++    +++p+  + +g     ++g eh+e g ++ed+
  gi|242399875|ref|YP_002995300.1| 364 ILTDQYFV-DTYYNLPDVDLGkiKVEKHIVETDKDYKRYKLtedGISPRGIPGYGEGVLIANGNEHDEWGDITEDE 438
                                       ********.99999888888744445666666667777666888**************************999983 PP

>> POR  Pyruvate ferredoxin/flavodoxin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.3   0.1     4e-34   1.8e-30       1     177 []      16     177 ..      14     177 .. 0.94

  Alignments for each domain:
  == domain 1  score: 106.3 bits;  conditional E-value: 4e-34
                                       CTSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHHHHGGGEE CS
                               POR   1 GGqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetlsehldglk 77 
                                       +GqG++t+ +il++++  +Gy+v+an+ey+s+ rGg  ++++ris++ +v++    + d+l+ +    l  + ++l+
  gi|242399875|ref|YP_002995300.1|  16 AGQGIQTVEEILTRVLKLSGYNVYANKEYMSRVRGGINTTEIRISSK-KVRAFV-KRIDILIPFKRGVLPWVEKRLT 90 
                                       4**********************************************.999999.**************888888** PP

                                       EEEEEEEECTCGTT-CCHHHCTS-HHHHHHHT-EEEEE-HHHHHHHCCC.CCHHHHHHHHHHHHHHTS-HHHHHHHH CS
                               POR  78 pggiiiynseelkpdelkkakeeerelkerlgvrvygvdatkiakeiggneraaNtvmlGalaallglplealeeai 154
                                       ++++++   e ++++ l k              ++++v+++++ak+ g  ++++Nt++ G +++l+  ++e l+e +
  gi|242399875|ref|YP_002995300.1|  91 ENTVVLGERENVEEEYLSKI-------------NFVEVPLNDMAKDVGS-SLYLNTIAAGLVVGLFHGDFEVLKEYL 153
                                       *******9987666666554.............4689*********998.*************************** PP

                                       HCCS-CH..HHHHHHHHHHHHHHH CS
                               POR 155 kkrfpkkk.eviekNlkafragye 177
                                       +krf+ k+ ev+ kN++a+++gy+
  gi|242399875|ref|YP_002995300.1| 154 RKRFGSKGeEVVSKNIEAAKKGYD 177
                                       *****999***************7 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 !   18.8   0.0   3.4e-07    0.0015       1     101 [.     471     560 ..     471     565 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 3.4e-07
                                       -SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHHHHHHH CS
                           PFOR_II   1 AevvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlveevkaa 77 
                                       A+++iva Gs+  ++++a ++l +e  +v ++  ++++P Pe ++kell + k ++++++n++  ++    e  k+ 
  gi|242399875|ref|YP_002995300.1| 471 AKYMIVAWGSTYHVIREALETLGRE--DVAFMHFKWVYPLPE-KVKELL-EGKFLIDIEQNVTAQFA----ELLKKE 539
                                       89********************998..89************7.599999.78999*******64443....333333 PP

                                       TGGGTSEEEEEE--GGG----HHH CS
                           PFOR_II  78 lkkskvkvvnfvaglgGrditved 101
                                       l    v++ + v +  Gr ++ve+
  gi|242399875|ref|YP_002995300.1| 540 L---GVEIHHRVLKYDGRPFSVEE 560
                                       3...23455556666666666555 PP

>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.2   3.1e-07    0.0014      30     157 ..     235     364 ..     224     371 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.1e-07
                                       HHCCHHCT..TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHCHHHHHHHHHHT--EEEEEEE--CCCH CS
                      TPP_enzyme_N  30 lldalseeq.girvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatnaltalaeAkvdriPllvlsgdrptslr 105
                                       ++ a ++e+ +i v ++ +E +a+++A g   a g +g+v + sg G++ +  al  A  +  P+++  ++rp   +
  gi|242399875|ref|YP_002995300.1| 235 VFSAQHAEDfEIIVEQVEDEISAINMAIGAWFA-GARGMVTT-SGGGFALMSEALSLAGMAENPVVIHLAQRPGPAT 309
                                       6666667765666667899**********9888.67999987.555***************************9999 PP

                                       H..S..TC--T-CCHHHCCCSSEEEE-SSGGGHHHHHH...HHHHHHHSSS--EEEE CS
                      TPP_enzyme_N 106 g..qgvlqqeldqlalfrpvtkyaervtspeelpealr...rAirtalsgrpgPvyl 157
                                       g  + ++q    +lal+  + ++ + +  p +++ea+    +A+  a  + + Pv +
  gi|242399875|ref|YP_002995300.1| 310 GlpTRTMQ-GDLNLALYSGHGEFPRIILAPGSIEEAFYltaEAFNLA-DRDQVPVII 364
                                       98888888.44477888877777777777777777765555888888.777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (570 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); 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: 0.69u 0.32s 00:00:01.01 Elapsed: 00:00:00.51
# Mc/sec: 3381.22
//
Query:       gi|242399876|ref|YP_002995301.1|  [L=216]
Description: Probable peroxiredoxin [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.4e-31  108.2   0.0    3.5e-31  107.7   0.0    1.2  1  AhpC-TSA    AhpC/TSA family
    2.5e-14   53.2   0.0    3.2e-14   52.9   0.0    1.1  1  Redoxin     Redoxin
    1.1e-09   37.9   0.2      2e-09   37.2   0.2    1.4  1  1-cysPrx_C  C-terminal domain of 1-Cys peroxiredoxin


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 !  107.7   0.0   5.9e-35   3.5e-31       1     123 [.       4     134 ..       4     135 .. 0.98

  Alignments for each domain:
  == domain 1  score: 107.7 bits;  conditional E-value: 5.9e-35
                                       TTSB----EEESTTCEEEECHHH...TTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHH CS
                          AhpC-TSA   1 vgdkapdfelknadgetvslsdy...kgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshk 74 
                                       +g+k+p++e+k+++ + ++l +y   kgk+ +lf +p+d++pvCtte  al+k++++f+e+gve ig+svd+++sh 
  gi|242399876|ref|YP_002995301.1|   4 IGEKFPEVEVKTTH-GAIKLPEYfaeKGKWFLLFSHPADFTPVCTTEFYALQKRVDKFRELGVEPIGLSVDQVFSHI 79 
                                       89*********999.99********999************************************************* PP

                                       HHHHH-H.......SSEEEE-TTSHHHHHTT-EETTTTECSCEEEEE-TTSBEEE CS
                          AhpC-TSA  75 kfiekes......lnfpllsDeegkvakaygvlkeekglalratfvidkegkiry 123
                                       k++e ++      ++fp+++D  g++a+++g++ + ++++ ra+fv+d++g+ir+
  gi|242399876|ref|YP_002995301.1|  80 KWMEWIKenlgeeITFPVIADDRGELADRLGMIPSGATTTARAVFVVDDRGIIRA 134
                                       *********************************999*****************97 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.9   0.0   5.4e-18   3.2e-14       3     136 ..       5     141 ..       3     151 .. 0.84

  Alignments for each domain:
  == domain 1  score: 52.9 bits;  conditional E-value: 5.4e-18
                                       TSBB---ECCEETTCEEEEEHHH...HTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHH. CS
                           Redoxin   3 gdkaPdftlplaatdgnsvslse...fkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndaf. 75 
                                       g+k+P+++    +t   +++l e    kgk  ++++ p+ f+P+C++e  +l+k  ++++e gv+ +++++d+    
  gi|242399876|ref|YP_002995301.1|   5 GEKFPEVEV---KTTHGAIKLPEyfaEKGKWFLLFSHPADFTPVCTTEFYALQKRVDKFRELGVEPIGLSVDQVFSh 78 
                                       889999994...46666777777733567779***********************9999***********9998778 PP

                                       ..HHHHHHH...TT-TSEEEE-TTSHHHHHTT-TTEEE.GGGEEE-EEEEEEETTEEEEEEESSSC CS
                           Redoxin  76 ..vkefwgk...eglkfpvlsDgsaaftkalGlrleedaseglrtpryavidedgkvvylevepep 136
                                          +e++++   e+++fpv++D  ++++  lG+    + +++  +++++v+d+ g ++++ + p +
  gi|242399876|ref|YP_002995301.1|  79 ikWMEWIKEnlgEEITFPVIADDRGELADRLGMI---PSGATTTARAVFVVDDRGIIRAIVYYPAE 141
                                       889999999999999*****************44...4555569*************998776655 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 !   37.2   0.2   3.3e-13     2e-09       1      37 [.     155     195 ..     155     198 .. 0.94

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 3.3e-13
                                       HHHHHHHHT-BB-TTT.T.....BT-EEE---SSHHHHHHHH CS
                        1-cysPrx_C   1 ALQladkhgvatPAnWkp.....GdkvivpPpateedavkry 37 
                                       AL+ ++++gva P+ W p     GdkvivpP++t ++++kr 
  gi|242399876|ref|YP_002995301.1| 155 ALKISTEKGVALPHKW-PnneliGDKVIVPPASTVDQVKKRE 195
                                       8999************.99********************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); 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:                         3  (0.000167327); expected 0.2 (1e-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: 1372.61
//
Query:       gi|242399877|ref|YP_002995302.1|  [L=251]
Description: N-glycosylase/DNA lyase (AGOG) (8-oxoguanine DNA glycosylase) [Thermococcus sibiricus MM 739]
Scores for complete 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-83  278.9   0.4    4.7e-83  278.3   0.4    1.2  1  AGOG      N-glycosylase/DNA lyase


Domain annotation for each model (and alignments):
>> AGOG  N-glycosylase/DNA lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  278.3   0.4   2.6e-87   4.7e-83       2     238 ..      12     234 ..      11     243 .. 0.95

  Alignments for each domain:
  == domain 1  score: 278.3 bits;  conditional E-value: 2.6e-87
                                       HHHCCCHHHHHHHHHCCTSHHHHHHHHHHCCC-H.HHHHHHHHHHHHT-SS-TT-HHHHHHHHHHHHCTS-.-SSHH CS
                              AGOG   2 ellkelgieevlkleekvDpQykaveelveklgedelfvklvilNaLvSYqLsgrGEewWkefskyfseke.iknil 77 
                                       ++lkelgie+++++eekvD+Q+ a+e l ++l++delf+klvi+N++vSYqLsg+GE+wW+efs+yfs+k  i++i+
  gi|242399877|ref|YP_002995302.1|  12 SILKELGIECARTIEEKVDLQFSALESLHKNLNDDELFLKLVIANSIVSYQLSGKGENWWWEFSNYFSKKPpIESIV 88 
                                       69*****************************************************************87762667** PP

                                       HHHHHHHHH-TTS-TTHHHHHHHHHHHCCHHHTTTHHHHHHHHHTHHHHHHHHHHHHTS-TTSHHHHHHHHHHHHHH CS
                              AGOG  78 eefikflekskgnrrlreakikRiekivefledleleelksylenleelleelakilgskkesKTvvFavKmlyYal 154
                                       +++ +fl++sk+n+rl++ k++R++k+++fl++l++e+l++y++n+ ++++ lak++++k+++KT+vFavKm++Ya+
  gi|242399877|ref|YP_002995302.1|  89 KAYSEFLPRSKSNKRLIQLKLNRLKKLEPFLNSLAIEDLRKYYQNMLRFRDRLAKVMNAKEDAKTIVFAVKMFGYAS 165
                                       ***************************************************************************** PP

                                       HHHHTS-----TTS-----HHHHHHHHHTTS-SS-HHHHHHTHCCHCS.HHHHHHHHHHHHT--HHHHHHHHH.HHC CS
                              AGOG 155 rialgeeiplpfeipiPvDvRiakltktsglielknekklarkelvqeevieaWkevsreseiPplhlDsllW.vlg 230
                                       ria+g +ip+p+ei+iP+D Ri+ +t                 ++++ + +++W+evs+e +iPplh+Ds+lW vlg
  gi|242399877|ref|YP_002995302.1| 166 RIAFGDFIPYPMEIDIPKDFRIENYTR----------------RFTDRNSTTFWREVSKEVGIPPLHIDSILWpVLG 226
                                       ***************************................8999999*************************99 PP

                                       CHHHCCS- CS
                              AGOG 231 ksaleled 238
                                       + ++  e+
  gi|242399877|ref|YP_002995302.1| 227 RDTRVAER 234
                                       98865554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       838  (0.0467399); expected 358.6 (0.02)
Passed bias filter:                      593  (0.0330749); 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: 0.63u 0.34s 00:00:00.97 Elapsed: 00:00:00.54
# Mc/sec: 1402.87
//
Query:       gi|242399878|ref|YP_002995303.1|  [L=202]
Description: Membrane-bound NADP+-reducing complex MBX, subunit MbxN (dehydrogenase subunit) [Thermococcus sibiricus MM 739]
Scores for complete 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   50.8  10.6      6e-08   32.2   2.0    2.2  2  Fer4      4Fe-4S binding domain
    1.7e-11   44.5  10.4    2.9e-11   43.8  10.4    1.4  1  Fer4_7    4Fe-4S dicluster domain
    1.6e-10   41.0  18.7    6.5e-08   32.6   9.1    1.8  2  Fer4_21   4Fe-4S dicluster domain
    2.7e-08   33.8   9.3    4.5e-08   33.1   9.3    1.4  1  Fer4_9    4Fe-4S dicluster domain
      3e-08   33.7  19.6    2.5e-06   27.5  11.2    2.0  2  Fer4_10   4Fe-4S dicluster domain
    4.9e-08   33.8   7.4    0.00095   20.1   0.0    2.7  2  Fer4_16   4Fe-4S double cluster binding domain
    3.6e-05   24.2   9.0      0.025   15.1   1.7    2.4  3  Fer4_17   4Fe-4S dicluster domain
      4e-05   23.4  12.9     0.0055   16.7   3.4    2.3  2  Fer4_2    4Fe-4S binding domain
     0.0001   22.2  14.0     0.0017   18.3   1.5    2.2  2  Fer4_6    4Fe-4S binding domain
    0.00013   22.6   4.2        0.3   11.9   0.1    2.5  2  Fer4_15   4Fe-4S single cluster domain
    0.00055   20.1   8.2      0.015   15.5   0.9    2.3  2  Fer4_18   4Fe-4S dicluster domain
     0.0015   19.3  17.8      0.019   15.9   4.5    2.2  2  Fer4_3    4Fe-4S binding domain
     0.0019   19.0   3.1       0.35   11.8   0.4    2.3  2  Fer4_22   4Fe-4S dicluster domain
     0.0067   16.9  11.8       0.35   11.3  12.4    2.4  2  Fer4_8    4Fe-4S dicluster domain
     0.0084   16.6  10.3       0.12   12.9   2.1    2.6  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
  ------ inclusion threshold ------
      0.036   14.6  14.5       0.37   11.4   4.0    2.3  2  Fer4_4    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 !   23.7   1.6   2.5e-08   2.8e-05       3      24 .]      56      77 ..      54      77 .. 0.91
   2 !   32.2   2.0   5.3e-11     6e-08       1      23 [.      89     111 ..      89     112 .. 0.95

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 2.5e-08
                                      EETTTSSS-THHHHHSTTTEEE CS
                              Fer4  3 ideekCigCGaCvevCPvgAIt 24
                                       ++  CigC+ C ++CP  AI+
  gi|242399878|ref|YP_002995303.1| 56 LNWKTCIGCNMCGQICPARAIE 77
                                      68889***************96 PP

  == domain 2  score: 32.2 bits;  conditional E-value: 5.3e-11
                                       EEEETTTSSS-THHHHHSTTTEE CS
                              Fer4   1 vvideekCigCGaCvevCPvgAI 23 
                                       ++id+ +C++C  Cv+vCP+gA+
  gi|242399878|ref|YP_002995303.1|  89 PKIDYGRCTFCQFCVDVCPTGAL 111
                                       68********************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 !   43.8  10.4   2.6e-14   2.9e-11       1      52 []      60     110 ..      60     110 .. 0.94

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 2.6e-14
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                       +CigC+ C + Cp++aie++  e ek+ ++++id+ +C++C+ Cv+vCPtga
  gi|242399878|ref|YP_002995303.1|  60 TCIGCNMCGQICPARAIEMTWIEGEKR-AHPKIDYGRCTFCQFCVDVCPTGA 110
                                       6*******************9877776.99********************98 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   2.0   2.8e-07   0.00032      34      59 .]      54      78 ..      44      78 .. 0.81
   2 !   32.6   9.1   5.8e-11   6.5e-08       4      55 ..      57     109 ..      54     112 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.8e-07
                           Fer4_21 34 lkvvedeCvGCnlCssvCPvedciem 59
                                      +++  ++C+GCn+C ++CP   +iem
  gi|242399878|ref|YP_002995303.1| 54 HTLNWKTCIGCNMCGQICPA-RAIEM 78
                                      5566789************5.99998 PP

  == domain 2  score: 32.6 bits;  conditional E-value: 5.8e-11
                           Fer4_21   4 dedkCigCgkCliaCedtshqai..eidaktvlkvvedeCvGCnlCssvCPved 55 
                                       + ++CigC+ C + C+  +++    e++++++ k+   +C+ C+ C++vCP+ +
  gi|242399878|ref|YP_002995303.1|  57 NWKTCIGCNMCGQICPARAIEMTwiEGEKRAHPKIDYGRCTFCQFCVDVCPT-G 109
                                       5679************9998875225555566677789*************6.4 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   9.3     4e-11   4.5e-08       2      50 ..      61     110 ..      60     111 .. 0.91

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 4e-11
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraase.eaCigCgaCveaCpkga 50 
                                       C+gC+ C + Cpa ++++ + e++ r + + +  +C++C+ Cv++Cp+ga
  gi|242399878|ref|YP_002995303.1|  61 CIGCNMCGQICPARAIEMTWIEGEKRAHPKIDyGRCTFCQFCVDVCPTGA 110
                                       ******************99999988877666799*************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 !   27.5  11.2   2.2e-09   2.5e-06       6      56 .]      58     107 ..      54     107 .. 0.74
   2 !   18.1   1.2   1.9e-06    0.0021       1      23 [.      88     110 ..      88     132 .. 0.79

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 2.2e-09
                           Fer4_10   6 ddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                        +tCi+C+ C + CPa      +  e ++ ++ ++++++Ct+c  Cv++CP
  gi|242399878|ref|YP_002995303.1|  58 WKTCIGCNMCGQICPA-RAIEMTWIEGEKRAHPKIDYGRCTFCQFCVDVCP 107
                                       589*************.2222222333444555669**************9 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 1.9e-06
                           Fer4_10   1 kvvidddtCirCgkCvkaCPadl 23 
                                       +++id  +C+ C+ Cv++CP+ +
  gi|242399878|ref|YP_002995303.1|  88 HPKIDYGRCTFCQFCVDVCPTGA 110
                                       5689999*************955 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.9   5.8e-06    0.0065       1      20 [.      60      79 ..      60      94 .. 0.77
   2 !   20.1   0.0   8.5e-07   0.00095       1      22 [.      95     116 ..      95     147 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 5.8e-06
                           Fer4_16  1 rCgtCgkCaevCPtnaikek 20
                                      +C++C+ C ++CP++ai+++
  gi|242399878|ref|YP_002995303.1| 60 TCIGCNMCGQICPARAIEMT 79
                                      5****************987 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 8.5e-07
                           Fer4_16   1 rCgtCgkCaevCPtnaikekke 22 
                                       rC+ C+ C++vCPt+a+ + ++
  gi|242399878|ref|YP_002995303.1|  95 RCTFCQFCVDVCPTGALGHVEH 116
                                       6****************98844 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   1.7   2.2e-05     0.025      41      58 ..      56      73 ..      28      76 .. 0.76
   2 !   12.8   1.3   0.00012      0.13      28      59 ..      75     109 ..      73     111 .. 0.58
   3 !   12.3   1.2   0.00017      0.19       1      17 [.      95     111 ..      95     144 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.2e-05
                           Fer4_17 41 ekaslCieCgeCerkCPq 58
                                       ++++Ci+C++C + CP+
  gi|242399878|ref|YP_002995303.1| 56 LNWKTCIGCNMCGQICPA 73
                                      489**************7 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00012
                           Fer4_17  28 aaklglleeaeke...ekaslCieCgeCerkCPqg 59 
                                       a++++ +e++++       ++C+ C+ C+ +CP g
  gi|242399878|ref|YP_002995303.1|  75 AIEMTWIEGEKRAhpkIDYGRCTFCQFCVDVCPTG 109
                                       55555555554442212567777788887777764 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 0.00017
                           Fer4_17   1 rCiqCgyClpeCpsyea 17 
                                       rC+ C++C+++Cp+++ 
  gi|242399878|ref|YP_002995303.1|  95 RCTFCQFCVDVCPTGAL 111
                                       7************8665 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   2.0   0.00015      0.17       7      22 .]      58      73 ..      54      73 .. 0.88
   2 !   16.7   3.4   4.9e-06    0.0055       1      22 []      87     108 ..      87     108 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00015
                            Fer4_2  7 tdrCigCgaCvsaCPa 22
                                        +CigC+ C + CPa
  gi|242399878|ref|YP_002995303.1| 58 WKTCIGCNMCGQICPA 73
                                      568************8 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 4.9e-06
                            Fer4_2   1 apvvvdtdrCigCgaCvsaCPa 22 
                                       a++++d  rC+ C  Cv++CP+
  gi|242399878|ref|YP_002995303.1|  87 AHPKIDYGRCTFCQFCVDVCPT 108
                                       689******************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 !    9.2   5.2    0.0012       1.3       8      24 .]      60      76 ..      59      76 .. 0.94
   2 !   18.3   1.5   1.5e-06    0.0017       2      24 .]      89     111 ..      88     111 .. 0.94

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0012
                            Fer4_6  8 kCigCgdCvrvCPegai 24
                                       CigC+ C  +CP+ ai
  gi|242399878|ref|YP_002995303.1| 60 TCIGCNMCGQICPARAI 76
                                      5*************998 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 1.5e-06
                            Fer4_6   2 veidpdkCigCgdCvrvCPegai 24 
                                       + id+ +C+ C  Cv+vCP+ga+
  gi|242399878|ref|YP_002995303.1|  89 PKIDYGRCTFCQFCVDVCPTGAL 111
                                       789******************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 !   11.7   0.7    0.0003      0.33       3      20 ..      56      73 ..      55      79 .. 0.88
   2 !   11.9   0.1   0.00026       0.3       2      20 ..      90     108 ..      90     145 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0003
                           Fer4_15  3 vDrdaCigcglCvaeape 20
                                      +++++Cigc++C + +p 
  gi|242399878|ref|YP_002995303.1| 56 LNWKTCIGCNMCGQICPA 73
                                      789*************96 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00026
                           Fer4_15   2 vvDrdaCigcglCvaeape 20 
                                       ++D  +C+ c  Cv+++p+
  gi|242399878|ref|YP_002995303.1|  90 KIDYGRCTFCQFCVDVCPT 108
                                       59999************96 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   1.0    0.0016       1.8      57      73 ..      57      73 ..      38      80 .. 0.81
   2 !   15.5   0.9   1.3e-05     0.015      53      74 ..      88     109 ..      74     111 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0016
                           Fer4_18 57 gagdcidcescvkvcPt 73
                                      +   ci c++c ++cP 
  gi|242399878|ref|YP_002995303.1| 57 NWKTCIGCNMCGQICPA 73
                                      5568************7 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.3e-05
                           Fer4_18  53 rkekgagdcidcescvkvcPtg 74 
                                       + + + g c+ c++cv+vcPtg
  gi|242399878|ref|YP_002995303.1|  88 HPKIDYGRCTFCQFCVDVCPTG 109
                                       44556799************98 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   5.4    0.0019       2.2       1      15 []      61      75 ..      61      75 .. 0.92
   2 !   15.9   4.5   1.7e-05     0.019       1      15 []      96     110 ..      96     110 .. 0.97

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0019
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+gC+ C + CP +A
  gi|242399878|ref|YP_002995303.1| 61 CIGCNMCGQICPARA 75
                                      ************776 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1.7e-05
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       Ct C+ Cv+vCP+gA
  gi|242399878|ref|YP_002995303.1|  96 CTFCQFCVDVCPTGA 110
                                       ****99********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 !   11.8   0.4   0.00031      0.35      76      94 ..      55      73 ..      38      75 .. 0.78
   2 !    7.6   0.1    0.0063       7.1       1      19 [.      95     113 ..      88     132 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00031
                           Fer4_22 76 kfgesgCvGCgRCieacpv 94
                                      + + ++C+GC+ C + cp+
  gi|242399878|ref|YP_002995303.1| 55 TLNWKTCIGCNMCGQICPA 73
                                      457889***********97 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0063
                           Fer4_22   1 rClsCgaCtlvCptCsCfd 19 
                                       rC  C+ C  vCpt    +
  gi|242399878|ref|YP_002995303.1|  95 RCTFCQFCVDVCPTGALGH 113
                                       7999999999999976555 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   3.9     0.005       5.6      49      62 ..      59      72 ..      35      75 .. 0.72
   2 !   11.3  12.4   0.00031      0.35       3      64 ..      59     109 ..      57     110 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.005
                            Fer4_8 49 wsCttcgaCtevCp 62
                                      ++C +c++C + Cp
  gi|242399878|ref|YP_002995303.1| 59 KTCIGCNMCGQICP 72
                                      45555555555555 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00031
                            Fer4_8   3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                       + Ci+C +C + Cp+   +  +  + +++a     + +        ++Ct c+ C++vCp+g
  gi|242399878|ref|YP_002995303.1|  59 KTCIGCNMCGQICPARAIEMTW-IEGEKRAHP---KID-------YGRCTFCQFCVDVCPTG 109
                                       57************55555444.333333222...233.......489************87 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   2.1   0.00011      0.12       4      18 ..      59      73 ..      56      74 .. 0.90
   2 !    8.0   1.3    0.0038       4.3       1      17 [.      91     107 ..      91     109 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
                           Fer4_13  4 dtCiacgaCvelaPd 18
                                      +tCi+c+ C++++P 
  gi|242399878|ref|YP_002995303.1| 59 KTCIGCNMCGQICPA 73
                                      69************5 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0038
                           Fer4_13   1 VDrdtCiacgaCvelaP 17 
                                       +D  +C+ c+ Cv+++P
  gi|242399878|ref|YP_002995303.1|  91 IDYGRCTFCQFCVDVCP 107
                                       68889************ PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   2.9    0.0029       3.2       2      16 ..      59      73 ..      58      75 .. 0.90
   2 ?   11.4   4.0   0.00033      0.37       3      17 .]      95     109 ..      93     109 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0029
                            Fer4_4  2 erCigCgsCvaaCPq 16
                                      ++CigC  C  +CP 
  gi|242399878|ref|YP_002995303.1| 59 KTCIGCNMCGQICPA 73
                                      68***********96 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00033
                            Fer4_4   3 rCigCgsCvaaCPqg 17 
                                       rC+ C  Cv++CP+g
  gi|242399878|ref|YP_002995303.1|  95 RCTFCQFCVDVCPTG 109
                                       9************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       686  (0.038262); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.53
# Mc/sec: 1144.97
//
Query:       gi|242399879|ref|YP_002995304.1|  [L=391]
Description: Membrane-bound NADP+-reducing complex MBX, subunit MbxL (dehydrogenase subunit) [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.7e-71  239.4   0.0      2e-69  233.7   0.0    2.1  1  Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd s
  ------ inclusion threshold ------
        0.2   10.5   0.0       0.33    9.8   0.0    1.3  1  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 !  233.7   0.0   2.3e-73     2e-69       2     271 .]     139     391 .]     138     391 .] 0.96

  Alignments for each domain:
  == domain 1  score: 233.7 bits;  conditional E-value: 2.3e-73
                                       TT-HHHHHHHHHHHHHHHHHHHHHHSSSSS-TTBESSBBSS---.TTHHHHHHHHHHHHHHHHHHHHHHHHSSSSHH CS
                    Complex1_49kDa   2 lGaltvflyafreRekildlleevtGaRltasyiriGGvarDlp.egllekikeflkelekkldeleklltknrifk 77 
                                       lG  t   +a + Re+++ l+e++tGaR+ + y+++GGv+rD+p +++l+++k+++++l++kl++++++l +n i+ 
  gi|242399879|ref|YP_002995304.1| 139 LGVYTAGQWAAAYRERFMALFEQLTGARVYHIYTIPGGVRRDIPgDKWLRQLKDTVEYLKDKLKDFDNILFQNYITY 215
                                       69999**************************************9569****************************** PP

                                       HHHSSSS-BSHHHHHHHTT-SSSSGGGT-TTTHHHHSS-SSGGGS-------SSBSHHHHHHHHHHHHHHHHHHHHH CS
                    Complex1_49kDa  78 kRtkgvgvlskeealelgltGpvlRasGvkyDlRkaepYeaYdeldfdvpvgeegDvydRylvrveEmrqSlkIieq 154
                                       +R++g+gv++k+ al+ g+tGp+lRa+Gvk D+R+ +pY  Y eldf+vpv +egD+++R lvr  E++q l I+eq
  gi|242399879|ref|YP_002995304.1| 216 NRLEGIGVMDKKFALAEGVTGPNLRATGVKADVRRLDPYLLYPELDFEVPVLKEGDSLARALVRRFEIEQDLYILEQ 292
                                       ***************************************************************************** PP

                                       HHHT--..S-SB---TTTS---GGGGGT-HHHHHHHHHHHHS-----SEEEEEEEEETTEEEEEEEEEESSSS-SEE CS
                    Complex1_49kDa 155 aleklpe.gpvlaedkkvalpkkeevkksmealihhfklvtegfkvpkgevyaavEapkGelgvylvsdgsskpyrl 230
                                       +le  p  gp+++ed+k +  +                     fkvp+g++ya+vEa+ G +g y+vsdg++kpyr+
  gi|242399879|ref|YP_002995304.1| 293 LLEMGPPdGPYKVEDPKLKALP--------------------RFKVPAGDAYAHVEATGGDFGAYVVSDGGNKPYRV 349
                                       ***99644*****999875444....................467******************************** PP

                                       EEE-HHHHT.TTTHHHHTTTS-SGGGTHHHHTT---HHHHH- CS
                    Complex1_49kDa 231 kirapsfvn.lqaleellkgellaDvvailgsldivlgevDR 271
                                       +ir ps  + ++++e+ll g+++aDv++il +l  + +++DR
  gi|242399879|ref|YP_002995304.1| 350 QIRGPSISHgIRVIEQLLVGARIADVPVILMTLGNCPPDIDR 391
                                       *******997899****************************9 PP

>> NiFeSe_Hases  Nickel-dependent hydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   3.7e-05      0.33       1      69 [.      63     131 ..      63     136 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 3.7e-05
                                       --HHHHTTTS-GGGHHHHHHTT-SSSTTHHHHHHHHHHHHHHT----HHHHHHHHHHHHHHHHHHHHHH CS
                      NiFeSe_Hases   1 RGlElilkgrdprdawalvqRiCGVCttvHalasvravedAlgikipknarlirnliaaalllhdhivh 69 
                                       RG+E++ + r      al  R+C   + v      +av++ +g ++p+ a+ ir+++  +  + +++ +
  gi|242399879|ref|YP_002995304.1|  63 RGFEKLAELRPWYTNIALLLRVCVPEPDVPEAVYSMAVDELVGWEVPERAQWIRTVVLEMARVTSYLFW 131
                                       89999999999999999999999999999999999***********************99999988866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.37s 00:00:01.03 Elapsed: 00:00:00.58
# Mc/sec: 2029.11
//
Query:       gi|242399880|ref|YP_002995305.1|  [L=175]
Description: Membrane-bound NADP+-reducing complex MBX, subunit MbxK (dehydrogenase subunit) [Thermococcus sibiricus MM 739]
Scores for complete 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-23   81.6   0.7    8.6e-23   81.3   0.7    1.1  1  Complex1_30kDa  Respiratory-chain NADH dehydrogenase, 30 Kd s
  ------ inclusion threshold ------
       0.11   12.5   0.2       0.15   12.0   0.2    1.3  1  Autophagy_N     Autophagocytosis associated protein (Atg3), N


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 !   81.3   0.7   9.6e-27   8.6e-23       2     119 ..      33     153 ..      32     156 .. 0.90

  Alignments for each domain:
  == domain 1  score: 81.3 bits;  conditional E-value: 9.6e-27
                                       E--HHHHHHHHHHHHH...TT--EEEEEEEEETT.SSSEEEEEEEE--S-.-EEEEEE....-..S-BEE--TTT-S CS
                    Complex1_30kDa   2 vvepedllevakflkdeeelgfdvlsdltavDek.eerfevvyhllsleknerirvkvevdee..epevpSvtdlfp 75 
                                       ++++e+++e++++lk+    +f+ ++++tavD+  ++++e+vy++ s+++ ++ +vk++++++  + +vpSv d++p
  gi|242399880|ref|YP_002995305.1|  33 HIPAERIREFLTLLKE---SNFETMMQITAVDWIkDGEIELVYQMWSYTHAVHAFVKTRIPRDvdKARVPSVRDIYP 106
                                       6899***********9...89***********99899***********************99555999********* PP

                                       THHHHHHHHHHHSHHBCTTSSTSS.-SSS.STT.SSS-TTSTTS--- CS
                    Complex1_30kDa  76 gadwyEREayDmfGivfeghpdlr.rill.ped.feghPLRkdfpls 119
                                        a+ yER+a++++ ++feg+ +l+  ++l +ed   g   Rkdf++ 
  gi|242399880|ref|YP_002995305.1| 107 VAETYERDAHEFYKVTFEGNDKLKmPWILeDEDkEAGVSHRKDFDML 153
                                       **********************9766666466645899******986 PP

>> Autophagy_N  Autophagocytosis associated protein (Atg3), N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   1.6e-05      0.15       8      81 ..      39     107 ..      33     172 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.6e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       Autophagy_N   8 vreyltpvlkeSkFretGvitpeeFvaAGDy.LvhkfptWsWasaeeskrksyLPkdKqfLvtrnVpcykRakql 81 
                                       +re lt  lkeS+F++  +it  ++++ G+  Lv++   Ws ++a ++ +k+ +P+d       +Vp+ + +  +
  gi|242399880|ref|YP_002995305.1|  39 IREFLT-LLKESNFETMMQITAVDWIKDGEIeLVYQ--MWSYTHAVHAFVKTRIPRDVD---KARVPSVRDIYPV 107
                                       566555.789*******************9548876..699999999999999998844...4556666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.34s 00:00:00.90 Elapsed: 00:00:00.53
# Mc/sec: 994.20
//
Query:       gi|242399881|ref|YP_002995306.1|  [L=193]
Description: Membrane-bound NADP+-reducing complex MBX, subunit MbxJ (dehydrogenase subunit) [Thermococcus sibiricus MM 739]
Scores for complete 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-19   67.7   0.0    1.2e-18   67.1   0.0    1.3  1  Oxidored_q6  NADH ubiquinone oxidoreductase, 20 Kd subunit
  ------ inclusion threshold ------
      0.052   12.9   0.0      0.073   12.4   0.0    1.2  1  RE_NgoFVII   NgoFVII restriction endonuclease


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 !   67.1   0.0   1.4e-22   1.2e-18       1     130 [.      25     136 ..      25     137 .. 0.91

  Alignments for each domain:
  == domain 1  score: 67.1 bits;  conditional E-value: 1.4e-22
                                       -SHH.HHHHT-TTTTHHHHHHTEEEEEETTT-S--HHHHHHTHTTTSEEEEEESBE...EEEHHHHHHHHGGGSSEE CS
                       Oxidored_q6   1 CtGc.sisllaleedlldllelielryhetlladskeeeieakekeadvlvveGavtrkpkealellkelaekakav 76 
                                       CtGc  i++  l+++ +dl     +r+++    +++          ad+++++G vt k+ +++ +++e+ +++k+v
  gi|242399881|ref|YP_002995306.1|  25 CTGCgGIEMPPLMTSRYDL-----ERFGMMPNPAPR---------MADLFLITGYVTPKTLKRIIITYEMQPDPKYV 87 
                                       99**7799999********.....999887777777.........8******************************* PP

                                       EEESHHHHH-TGGGSTT-TEE-HHHHHHHC.S-E.EEE-SSS--HHHHHHHHHH CS
                       Oxidored_q6  77 iavGtCAafGGipaaannpsvgeevgellevvpvdinipGCPphpeailetlla 130
                                        a G+C  +GGi+  ++ ++    +++l++++pvd+ i+GC p+pea+++++++
  gi|242399881|ref|YP_002995306.1|  88 LAHGSCPLNGGIY--WDGYNA---IKHLDKYLPVDVAIAGCMPRPEAVMDGIKK 136
                                       *************..553333...568***********************9986 PP

>> RE_NgoFVII  NgoFVII restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   8.1e-06     0.073       9      64 ..      58     114 ..      51     122 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.1e-06
                                       EEEEEESXXXHHHHHHHHHHHHXXXXSEEEEEEXSHHHH.XXXHHHHHHHHHHHHHH CS
                        RE_NgoFVII   9 elliisGYvspaslselikllkeqsdikitlivGMyple.glskrlheallklnkkl 64 
                                        l++i+GYv+p++l++ i + + q+d k  l  G +pl+ g+  + ++a+++l+k+l
  gi|242399881|ref|YP_002995306.1|  58 DLFLITGYVTPKTLKRIIITYEMQPDPKYVLAHGSCPLNgGIYWDGYNAIKHLDKYL 114
                                       799**********************************6637999*******999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); 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: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 1112.62
//
Query:       gi|242399882|ref|YP_002995307.1|  [L=309]
Description: Membrane-bound NADP+-reducing complex MBX, subunit MbxM (dehydrogenase subunit) [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.4e-51  173.2  27.0    8.7e-51  173.0  27.0    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 !  173.0  27.0   4.8e-55   8.7e-51       3     297 ..       8     306 ..       6     308 .. 0.92

  Alignments for each domain:
  == domain 1  score: 173.0 bits;  conditional E-value: 4.8e-55
                                       HHHHHHHHHHHHH.HHHHHHHHHHHHHTTS--S-SSTTTTTTHHHHHHHHHCCS-----TTS-HHHHHHHHHHHHHH CS
                            NADHdh   3 lllllvvlllvva.lltlleRkvlAriqdRlGPnrvGplGllqplaDalKlllKediipkkadkllfllapvlalil 78 
                                       +l++l+ ++++v  +++++ R v+Ari++R+GP      ++ qp+ D++Kll K++ i ++   l++ ++ + al +
  gi|242399882|ref|YP_002995307.1|   8 ALFILI-YATFVGfMFMGIIRIVTARIHRRVGP------PIYQPILDTIKLLSKKSNITHG---LIYDFGVIYALGA 74 
                                       555664.5555554999****************......9****************99976...5************ PP

                                       HHCTTTTS-SSS.SSS--TTHHHHHHHHHHHCHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            NADHdh  79 allafaviPfge.vladlnvglllilalsslgvygillaGwasnskYallGalRsaaqmisyEvalglsllavvlla 154
                                       ++la+++iP+g+  +     +l+li  l+ + ++gi++a+++s+++Ya +Ga R++  m+++ v+lg++++a++ ++
  gi|242399882|ref|YP_002995307.1|  75 TILAIMFIPLGNiGVLRAYGDLVLITFLLEIPMLGIMFAAMSSGNPYAGIGAQRALLTMLAIQVPLGFAIVALAEYY 151
                                       ***********7645555579******************************************************** PP

                                       -SS-HHHHHHCCCTT.-C...CCCHHHHHHHHHHHHHHCCTCTTBTTTTSTTSSSSCCCTT-HCHHHHHHHHHHHHH CS
                            NADHdh 155 gslslseiveaqeei.wf...illqllafiifliallaetnraPFDlpeaesELvaGfhtEYsgmkfalfflaeyan 227
                                       g++s+ eiv aq+++ w    ++l l+a+i++ ++l a  ++ PFD++ a  E+  G+++E++g +++++ +++ ++
  gi|242399882|ref|YP_002995307.1| 152 GTFSTYEIVMAQQSMgWSitaLPL-LFAAIAYDLVLQAMFGKEPFDIMIAPGEISLGPMVEFGGKHMGILQIQHAIA 227
                                       **********99888786565665.889999999******************************************* PP

                                       HHHHHHHHHHHCT.SS-HCCS.........HHHHHHHHHHHHHHHHHHHHHC----TCHHHHHHHCCTCHHHHHHHH CS
                            NADHdh 228 mvlvsalavllFlgGwllpfs.........gllwfllKvllllflfiwiratlpRlRydqlmklgwkvllplalanl 295
                                       ++   ++++ +FlgG  + +          +l ++l+K +++l++++++ a++pR+ +dq+ +++wk+ + +a +  
  gi|242399882|ref|YP_002995307.1| 228 LFGETLFFSNIFLGGAVITIFgssilntiaTLAVLLIKQIAVLLVATFMGAIFPRFTIDQAARFYWKWPTIIAALGA 304
                                       ***************9877768999999999999**********************************999998776 PP

                                       HH CS
                            NADHdh 296 ll 297
                                       +l
  gi|242399882|ref|YP_002995307.1| 305 IL 306
                                       65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       716  (0.0399353); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); 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: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.54
# Mc/sec: 1737.13
//
Query:       gi|242399883|ref|YP_002995308.1|  [L=617]
Description: Membrane-bound NADP+-reducing complex MBX, subunit MbxH' (dehydrogenase subunit) [Thermococcus sibiricus MM 739]
Scores for complete 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-62  210.0  31.6    4.1e-62  210.0  31.6    1.8  2  Proton_antipo_M  Proton-conducting membrane transporter
  ------ inclusion threshold ------
        4.4    7.3   4.9        2.3    8.2   0.9    2.6  2  SLATT_fungal     SMODS and SLOG-associating 2TM effector doma


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.6      0.33     3e+03     249     286 ..      66     105 ..      43     112 .. 0.51
   2 !  210.0  31.6   4.6e-66   4.1e-62       1     292 [.     116     423 ..     116     424 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.33
                   Proton_antipo_M 249 llvlllsla..GlPptagFlskfliLeaavavslillvla 286
                                       +++++l     G+  + gF + +++ +   + + +l++l+
  gi|242399883|ref|YP_002995308.1|  66 FALNTLNWFflGIGALVGFAAILALVSTGRDSYEWLFALM 105
                                       3333322222255555555555555555555555555544 PP

  == domain 2  score: 210.0 bits;  conditional E-value: 4.6e-66
                   Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskal..... 72 
                                       andL+++++++E++  ++++++  + ++     Aslk+fll+ +g  ++Ll++ ++y+  gt +f ++ +a+     
  gi|242399883|ref|YP_002995308.1| 116 ANDLMTFFIFWEIMTFASFMMVLHYNRS-----ASLKYFLLSVFGAYAMLLALGIIYAKLGTFDFGAIQQAMyqday 187
                                       89********************999666.....**************************************9***** PP

                   Proton_antipo_M  73 ......elglnslelllllllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirllllla... 140
                                             e+ ++++e  l++ll+l+++ vK++++plh+W pday e   + +a+++++l+kagv+++i l +l+    
  gi|242399883|ref|YP_002995308.1| 188 asafggETLISKNESALIYLLFLIAFGVKAGMFPLHVWAPDAYSETNQSYTAMFSGVLSKAGVYGFILLYVLMGtrl 264
                                       *****999*********************************************************998888875444 PP

                   Proton_antipo_M 141 .......vssneisqlllilaiismllgslvalaqtdiKrllAySsishlGymlialavatqygveaaiihllthal 210
                                               s+ +  +++++l+ +++++g+l+a  q di++l AySsis+lGy+l++++v+t+ +++aa++h+l+hal
  gi|242399883|ref|YP_002995308.1| 265 alefgafRSATKFGYIIAFLGGLTIIVGGLLAALQEDIRKLFAYSSISQLGYILVGIGVGTALSIQAAMFHVLSHAL 341
                                       444555557888999************************************************************** PP

                   Proton_antipo_M 211 fkallFllagsviyerektrdirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavslillvla. 286
                                       fk l Fl++  ++y++   ++++++ggLa+kmP+++++ +v++lslaG+Pp+ gF sk+ ++ea+++ +l +l  + 
  gi|242399883|ref|YP_002995308.1| 342 FKGLFFLIVATIVYRT-GKTTFADMGGLAEKMPFTFAMAFVAILSLAGIPPLVGFASKWVLFEAVISQNLPILGGMv 417
                                       *********8887777.7889*********************************************99998887765 PP

                   Proton_antipo_M 287 vvasvl 292
                                       +++s++
  gi|242399883|ref|YP_002995308.1| 418 FFGSAI 423
                                       677666 PP

>> SLATT_fungal  SMODS and SLOG-associating 2TM effector domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.9   0.00026       2.3      20      66 ..     250     298 ..     230     301 .. 0.75
   2 ?   -1.9   0.2      0.36   3.2e+03      17      41 ..     504     528 ..     501     534 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00026
                      SLATT_fungal  20 lnlaiglQvllgAllt.aLgalssgr.tqvaitvLGalnTviAglLArl 66 
                                       ++ +i+l vl+g  l+   ga+ s      +i+ LG+l+ ++ glLA l
  gi|242399883|ref|YP_002995308.1| 250 VYGFILLYVLMGTRLAlEFGAFRSATkFGYIIAFLGGLTIIVGGLLAAL 298
                                       566777778887766524799988777999*****************87 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.36
                      SLATT_fungal  17 slalnlaiglQvllgAlltaLgals 41 
                                       +la+++ +++ ++++ ++  Lga  
  gi|242399883|ref|YP_002995308.1| 504 ALAVTIYLVVGIIIAGIIYFLGAKV 528
                                       5677888999999999999999964 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (617 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       915  (0.0510346); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.78u 0.34s 00:00:01.12 Elapsed: 00:00:00.52
# Mc/sec: 3561.78
//
Query:       gi|242399884|ref|YP_002995309.1|  [L=494]
Description: Membrane-bound NADP+-reducing complex MBX, subunit MbxH (dehydrogenase subunit) [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-62  211.4  25.1    1.6e-62  211.4  25.1    2.5  3  Proton_antipo_M  Proton-conducting membrane transporter
    1.1e-05   24.9  12.8    1.1e-05   24.9  12.8    2.7  3  NADHdeh_related  NADH dehydrogenase I, subunit N related prot
     0.0053   16.3   0.5     0.0053   16.3   0.5    3.5  4  PIRT             Phosphoinositide-interacting protein family


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 ?   -3.1   0.7      0.59   3.6e+03     124     138 ..      86     100 ..      75     126 .. 0.46
   2 !  211.4  25.1   2.7e-66   1.6e-62       3     291 ..     129     417 ..     127     419 .. 0.94
   3 ?   -0.5   0.1     0.097   5.8e+02      74     104 ..     437     467 ..     420     473 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.59
                   Proton_antipo_M 124 lvkagvlllirllll 138
                                       +v+++ +l++++++ 
  gi|242399884|ref|YP_002995309.1|  86 VVTLASFLMTVFSMR 100
                                       333333333333332 PP

  == domain 2  score: 211.4 bits;  conditional E-value: 2.7e-66
                   Proton_antipo_M   3 dLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskalelglnsl 79 
                                       d++ l++++E++ ++ y L +++k+  +s+eA+lk+++l+ +gs+++L+gi+l+y+  gtl++  + +    ++n  
  gi|242399884|ref|YP_002995309.1| 129 DIFNLFVFMEITAISAYALTAYNKTG-ESSEAALKYVVLGGIGSSFFLVGIALIYGSLGTLNMAHIGQL-ASMINPT 203
                                       8899*******************887.*****************************************9.9999*** PP

                   Proton_antipo_M  80 elllllllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirlllllavssneis..qlllila 154
                                       ++ ++l ll++gl+v + q+pl+ W pday+eaP pv+a+++a +vka+++++ r++ +l+ ++++ s   ll++l+
  gi|242399884|ref|YP_002995309.1| 204 AAKIGLALLIFGLAVEAEQFPLNAWAPDAYQEAPHPVTAMFSAFVVKASLYAIGRIIYILSAAEGWSSvlRLLIVLG 280
                                       *************************************************************666665411468899* PP

                   Proton_antipo_M 155 iismllgslvalaqtdiKrllAySsishlGymlialavatqygveaaiihllthalfkallFllagsviyerektrd 231
                                       ++++++g + al+q+++Kr+ AySsi+++G++ ++la++t+ gv+a+++h++ ha++kal+Fl++g v  e     +
  gi|242399884|ref|YP_002995309.1| 281 TLTVIVGEMSALRQNNVKRMFAYSSIAQVGLIAMGLALGTESGVSASVFHMFNHAIVKALMFLAVGYVAIEL-GGVE 356
                                       *****************************************************************9996665.7789 PP

                   Proton_antipo_M 232 irayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavslillvla.vvasv 291
                                       + + +gL k+mPi+a +++v+++s+ G+P++  F+sk+ ++ aa++++  ++v++ + as+
  gi|242399884|ref|YP_002995309.1| 357 MSKFEGLGKRMPITAFAITVGAISIIGIPLFNVFWSKIQLILAALNAEYTWVVALiLGASL 417
                                       ***************************************9999999999988888466655 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.097
                   Proton_antipo_M  74 lglnslelllllllllvgllvKsaqvplhlW 104
                                         ++++ +l+l++lllv++++ ++ +p  +W
  gi|242399884|ref|YP_002995309.1| 437 EKVKENSVLALIMLLLVAFIIVIGIYPEPFW 467
                                       4567888899999999999999988887777 PP

>> NADHdeh_related  NADH dehydrogenase I, subunit N related protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9  12.8   1.9e-09   1.1e-05      60     191 ..      99     234 ..      72     266 .. 0.77
   2 ?   -6.5   6.8         3   1.8e+04      99     149 ..     307     355 ..     272     430 .. 0.49
   3 ?   -3.4   0.0      0.86   5.2e+03      26      39 ..     446     459 ..     436     475 .. 0.54

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1.9e-09
                   NADHdeh_related  60 lkvvsldelkirrllaivcglatlgavvtgdvfnftlflaliGianiGivaavkkefvleaafnyGlvaliatlplf 136
                                       ++ v+++     ++l ++  l ++g + tgd+fn  +f+ +  i+   + a  k  +  eaa +y ++  i++ +++
  gi|242399884|ref|YP_002995309.1|  99 MRAVNVEPKDKYAMLFLLLMLGATGMIATGDIFNLFVFMEITAISAYALTAYNKTGESSEAALKYVVLGGIGSSFFL 175
                                       4555665555667888888999***************************99999*********************** PP

                   NADHdeh_related 137 ggaalilastGtlsifelaklagd.vlliakl...llvlGvvGetGvaPfyaakaeifr 191
                                        g ali +s Gtl +  + +la    +++ak+   ll+ G++ e+   P+ a   + ++
  gi|242399884|ref|YP_002995309.1| 176 VGIALIYGSLGTLNMAHIGQLASMiNPTAAKIglaLLIFGLAVEAEQFPLNAWAPDAYQ 234
                                       ***************99998876545777775333778888888777777665555544 PP

  == domain 2  score: -6.5 bits;  conditional E-value: 3
                   NADHdeh_related  99 aliGianiGivaavkkefvleaafnyGlvaliatlplfggaalilastGtl 149
                                       a +G+  +G+  + ++     + f+    a++ +  +f + + ++ + G +
  gi|242399884|ref|YP_002995309.1| 307 AQVGLIAMGLALGTESGVS-ASVFHMFNHAIVKA-LMFLAVGYVAIELGGV 355
                                       3344444444333222211.11122211222222.2333333333344443 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 0.86
                   NADHdeh_related  26 tlilfvvalifvil 39 
                                       +li+++++++++++
  gi|242399884|ref|YP_002995309.1| 446 ALIMLLLVAFIIVI 459
                                       33333333333333 PP

>> PIRT  Phosphoinositide-interacting protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       1.4   8.3e+03      99     114 ..      13      28 ..       6      38 .. 0.71
   2 ?   -1.8   1.5      0.35   2.1e+03      48      56 ..      57      65 ..      42     126 .. 0.60
   3 !   16.3   0.5   8.9e-07    0.0053      48     102 ..     162     216 ..     141     219 .. 0.89
   4 ?   -1.5   0.5       0.3   1.8e+03      76     104 ..     322     349 ..     269     352 .. 0.62

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 1.4
                              PIRT  99 vcGlvwvpiikkkrkq 114
                                       ++   ++pi+k+ +k 
  gi|242399884|ref|YP_002995309.1|  13 LFSAFFIPILKRLNKS 28 
                                       5667789999886664 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.35
                              PIRT 48 kpiivlsvG 56
                                      kpii+++ G
  gi|242399884|ref|YP_002995309.1| 57 KPIIIMAGG 65
                                      555555433 PP

  == domain 3  score: 16.3 bits;  conditional E-value: 8.9e-07
                              PIRT  48 kpiivlsvGgavfllGvvittlsrnstlknkdkevfklsGpaflslGlmllvcGl 102
                                       k +++  +G++ fl+G+++   s  +    +  ++  ++ p++  +Gl ll++Gl
  gi|242399884|ref|YP_002995309.1| 162 KYVVLGGIGSSFFLVGIALIYGSLGTLNMAHIGQLASMINPTAAKIGLALLIFGL 216
                                       7788999***********999988999999999999******************9 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 0.3
                              PIRT  76 knkdkevfklsGpaflslGlmllvcGlvw 104
                                          +++vf+++  a++   lm+l +G v 
  gi|242399884|ref|YP_002995309.1| 322 SGVSASVFHMFNHAIVK-ALMFLAVGYVA 349
                                       33455666676666544.57777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (494 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       995  (0.0554967); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.71u 0.34s 00:00:01.05 Elapsed: 00:00:00.54
# Mc/sec: 2775.18
//
Query:       gi|242399885|ref|YP_002995310.1|  [L=113]
Description: Membrane-bound NADP+-reducing complex MBX, subunit MbxG (Na+/H+ transporter subunit) [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.5e-33  112.0   3.2    1.1e-32  111.7   3.2    1.0  1  Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase cha
     0.0011   18.9   2.3     0.0011   18.9   2.3    1.8  2  DUF2108      Predicted membrane protein (DUF2108)
  ------ inclusion threshold ------
       0.43   10.8   5.0       0.28   11.4   0.9    2.0  2  DUF4418      Domain of unknown function (DUF4418)


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 !  111.7   3.2   1.9e-36   1.1e-32       2     105 .]       4     110 ..       3     111 .. 0.97

  Alignments for each domain:
  == domain 1  score: 111.7 bits;  conditional E-value: 1.9e-36
                                       HHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHHHHHHHHC................TTSCGGHHHHHHHH CS
                       Oxidored_q2   2 lllliallfliGlygvllrrnllkvliglelisnavnlllvlagvftegtlvi...tnpatefadplpqalvLtaiv 75 
                                       +++ +++l+liGly +l++rn+lk+l+gl++++++vnlll+ +g+ +++ ++i    ++ ++++dp+pqalvLtaiv
  gi|242399885|ref|YP_002995310.1|   4 YYFASIALILIGLYAILVKRNVLKMLVGLSIMETGVNLLLISVGYVSGRSAPIlseGITPDKAVDPIPQALVLTAIV 80 
                                       7899**********************************************999**99999***************** PP

                                       HHHHHHHHHHHHHHHHHHHSSS-BCCG--X CS
                       Oxidored_q2  76 igaaetavgLallvrlyreygtddvqelrr 105
                                       ig+a+ta++L+++++ly++y+t++v+e+rr
  gi|242399885|ref|YP_002995310.1|  81 IGVATTAMALSVVINLYEKYKTLNVEEIRR 110
                                       ***************************975 PP

>> DUF2108  Predicted membrane protein (DUF2108)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   2.3   1.8e-07    0.0011       6      47 ..       8      49 ..       5      58 .. 0.95
   2 ?   -1.0   0.4      0.29   1.7e+03      10      18 ..      79      87 ..      72      97 .. 0.49

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.8e-07
                           DUF2108  6 alalaliGaigvillkkpldKlimlalleaGlillivakgYL 47
                                      ++al+liG  ++++ ++ l+ l+ l+++e+G+ ll+++ gY+
  gi|242399885|ref|YP_002995310.1|  8 SIALILIGLYAILVKRNVLKMLVGLSIMETGVNLLLISVGYV 49
                                      789**************************************7 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.29
                           DUF2108 10 aliGaigvi 18
                                      ++iG + ++
  gi|242399885|ref|YP_002995310.1| 79 IVIGVATTA 87
                                      333333332 PP

>> DUF4418  Domain of unknown function (DUF4418)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.9   4.8e-05      0.28      40      79 ..       6      45 ..       2      52 .. 0.90
   2 ?    1.2   0.2     0.066   3.9e+02      37      49 ..      79      91 ..      69     105 .. 0.49

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.8e-05
                           DUF4418 40 gvGivllvlgllalfvkkkklrrglsiavillgvlvilip 79
                                        +i+l+++gl a++vk++ l++++ ++++ +gv ++li 
  gi|242399885|ref|YP_002995310.1|  6 FASIALILIGLYAILVKRNVLKMLVGLSIMETGVNLLLIS 45
                                      56899***************************99999986 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.066
                           DUF4418 37 aelgvGivllvlg 49
                                      +++gv++  ++l+
  gi|242399885|ref|YP_002995310.1| 79 IVIGVATTAMALS 91
                                      2222222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       694  (0.0387082); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); 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: 0.48u 0.32s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 700.00
//
Query:       gi|242399886|ref|YP_002995311.1|  [L=241]
Description: Membrane-bound NADP+-reducing complex MBX, subunit MbxF (Na+/H+ transporter subunit) [Thermococcus sibiricus MM 739]
Scores for complete 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   82.0  14.1    4.2e-23   82.0  14.1    2.2  2  MnhB      Domain related to MnhB subunit of Na+/H+ antiporter
  ------ inclusion threshold ------
      0.022   14.7   2.6       0.11   12.3   0.8    2.2  2  DUF5134   Domain of unknown function (DUF5134)
       0.18   11.6   0.0        0.3   10.9   0.0    1.4  1  OPA3      Optic atrophy 3 protein (OPA3)


Domain annotation for each model (and alignments):
>> MnhB  Domain related to MnhB subunit of Na+/H+ antiporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.8      0.22   1.3e+03      63      84 ..      62      86 ..       9      96 .. 0.62
   2 !   82.0  14.1   7.1e-27   4.2e-23       1     122 [.     102     225 ..     102     227 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.22
                              MnhB 63 a...prileglglllavltgllgll 84
                                      +   + +l  + +l+++ tg+++ll
  gi|242399886|ref|YP_002995311.1| 62 NyrgFDTLGEVTVLFIASTGVAALL 86
                                      2333334445556666666666655 PP

  == domain 2  score: 82.0 bits;  conditional E-value: 7.1e-27
                              MnhB   1 ilrtvarllvplillvslylllrGhnsPGGGFqgGlilaaalillylafgleelekllrvklaprileglglllavl 77 
                                       +l t a+ll+p+++l+++y++++Gh++PGGGF gG+++a+a++lly+af + e   + ++ ++   legl+ + +v 
  gi|242399886|ref|YP_002995311.1| 102 VLTTGAKLLLPFVMLFGAYIFIHGHLTPGGGFPGGATIATAFLLLYVAFTVYE---IDHKIFE--PLEGLAGVGYVT 173
                                       57899*********************************************999...5555544..899********* PP

                              MnhB  78 tgllglllg..fltslflel.el...llgeve..lgtallfdlgVylvVvggl 122
                                       +gl+gl++g  fl  ++++  +l    +g  +  +g+++++ ++++l+V++ l
  gi|242399886|ref|YP_002995311.1| 174 VGLIGLAVGgyFLFDWIWQSwGLgkeNIGR-LfsAGFIPIIYILIGLKVGTEL 225
                                       ********99*9999988874557764443.235***************9876 PP

>> DUF5134  Domain of unknown function (DUF5134)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1     0.031   1.9e+02     104     126 ..       6      36 ..       3      62 .. 0.66
   2 ?   12.3   0.8   1.9e-05      0.11      33     115 ..      72     151 ..      53     182 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.031
                           DUF5134 104 vtgvlavyFaaaalvwlarllp........a 126
                                       v+ +la++F+++  +w+a+ l+        +
  gi|242399886|ref|YP_002995311.1|   6 VKRILAIVFILIIGLWMAKGLDqvpfgedrM 36 
                                       6778999**9999999998887554544430 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 1.9e-05
                           DUF5134  33 lavvfalaalwflvlavvrrrataarrlahlyhavmmlAMvyMaaamalaaggghsghaaagasmpggvplvtgvla 109
                                       ++v+f + + ++++l++++r    +++ + +  ++   A +    +m  +a    +gh ++g   pgg +++t++l+
  gi|242399886|ref|YP_002995311.1|  72 VTVLFIASTGVAALLWRKKR---KRTAKKEGSVVLTTGAKLLLPFVMLFGAYIFIHGHLTPGGGFPGGATIATAFLL 145
                                       69**************9766...456666778888888888888888888888899999999999999888877777 PP

                           DUF5134 110 vyFaaa 115
                                       +y a  
  gi|242399886|ref|YP_002995311.1| 146 LYVAFT 151
                                       776554 PP

>> OPA3  Optic atrophy 3 protein (OPA3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   5.1e-05       0.3      76     109 ..      65      98 ..      34     105 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 5.1e-05
                              OPA3  76 GAellgEafifsvagglilyEywrssrkeakkee 109
                                       G ++lgE++++++a++ + +  wr++rk ++k+e
  gi|242399886|ref|YP_002995311.1|  65 GFDTLGEVTVLFIASTGVAALLWRKKRKRTAKKE 98 
                                       889**************************88876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       643  (0.0358637); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.54
# Mc/sec: 1343.21
//
Query:       gi|242399887|ref|YP_002995312.1|  [L=91]
Description: Membrane-bound NADP+-reducing complex MBX, subunit MbxD (Na+/H+ transporter subunit) [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-16   60.8  10.4    1.3e-16   60.5  10.4    1.1  1  DUF4040   Domain of unknown function (DUF4040)
  ------ inclusion threshold ------
       0.01   15.9   6.4      0.013   15.5   6.4    1.1  1  TspO_MBR  TspO/MBR family
      0.094   12.7   1.2      0.094   12.7   1.2    1.5  2  DUF3084   Protein of unknown function (DUF3084)
        1.6    6.9   5.2        1.8    6.8   5.2    1.0  1  DUF2070   Predicted membrane protein (DUF2070)
        2.3    8.1  10.9       0.43   10.5   7.0    1.7  2  DUF2721   Protein of unknown function (DUF2721)
        3.8    7.7   8.0       0.46   10.7   2.2    1.9  2  DUF4418   Domain of unknown function (DUF4418)


Domain annotation for each model (and alignments):
>> DUF4040  Domain of unknown function (DUF4040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.5  10.4   4.4e-20   1.3e-16       1      67 []      11      77 ..      11      77 .. 0.98

  Alignments for each domain:
  == domain 1  score: 60.5 bits;  conditional E-value: 4.4e-20
                           DUF4040  1 lllvlaalaavlardrlaavillgvvGllvallfvllgAPDvAlTqaavveglttvllllalrrlpr 67
                                      +l++++a++av   d+laav+ +++v+l+++++f++l+APDvA+ +aa++++l+ ++++++++r++r
  gi|242399887|ref|YP_002995312.1| 11 ALMIISAIFAVEWGDLLAAVVGMAAVSLFASIAFFFLQAPDVAMVEAAIGAALSAAVFIFTIKRTER 77
                                      69**************************************************************986 PP

>> TspO_MBR  TspO/MBR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   6.4   4.4e-06     0.013      42     108 ..       5      75 ..       2      80 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.4e-06
                                       HHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHTSGGCTTTTTSGGGHHHHHHHHHHHHHHHH.HHCCCC CS
                          TspO_MBR  42 vWtvlyilmgvaaylvwka...lalyavqlvlnllwsplffglkspvlalvdivallglvvali.lafskv 108
                                       v +++ +lm ++a+ +++    la+ +   ++ l+ s++ff l+ p +a+v+ ++ ++l++a++ ++++++
  gi|242399887|ref|YP_002995312.1|   5 VAIFIAALMIISAIFAVEWgdlLAAVVGMAAVSLFASIAFFFLQAPDVAMVEAAIGAALSAAVFiFTIKRT 75 
                                       566778899999988777788866777788999999******************96666665551444444 PP

>> DUF3084  Protein of unknown function (DUF3084)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.2   3.2e-05     0.094       3      34 ..       7      39 ..       5      41 .. 0.92
   2 ?   -1.9   0.0       1.2   3.4e+03      54      61 ..      61      68 ..      49      76 .. 0.52

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.2e-05
                           DUF3084  3 llilallvlggliAy.lgDrlGtkvGkkrlslF 34
                                      ++i+al++++++ A+  gD l+  vG + +slF
  gi|242399887|ref|YP_002995312.1|  7 IFIAALMIISAIFAVeWGDLLAAVVGMAAVSLF 39
                                      799***********857***************9 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.2
                           DUF3084 54 aaltlavl 61
                                      aal+ av+
  gi|242399887|ref|YP_002995312.1| 61 AALSAAVF 68
                                      33333333 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   5.2    0.0006       1.8     107     174 ..       6      74 ..       1      82 [. 0.48

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0006
                           DUF2070 107 slalvfalrllvlvavsdesllkavlpaliqpllailllvly.fspesfllllllslifalavylfivv 174
                                       ++++++ + +  ++av   +ll av+  ++ +l+a ++++++  ++  ++ +++  ++ a+++++ i+ 
  gi|242399887|ref|YP_002995312.1|   6 AIFIAALMIISAIFAVEWGDLLAAVVGMAAVSLFASIAFFFLqAPDVAMVEAAIGAALSAAVFIFTIKR 74 
                                       344444444444444444455555555555555554444444144444455555555555555554444 PP

>> DUF2721  Protein of unknown function (DUF2721)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   7.0   0.00014      0.43      77     118 ..       6      47 ..       1      50 [. 0.86
   2 ?   -0.8   0.1      0.45   1.4e+03      67      81 ..      59      69 ..      52      78 .. 0.46

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00014
                           DUF2721  77 vvlvvlllflsallsldlsllaailfvlalllllvslllflr 118
                                       ++++ +l+++sa++++++  l+a++ ++a ++l++s+++f++
  gi|242399887|ref|YP_002995312.1|   6 AIFIAALMIISAIFAVEWGDLLAAVVGMAAVSLFASIAFFFL 47 
                                       45566777778999*************************987 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.45
                           DUF2721 67 illlvlsallvvlvv 81
                                      i     +al +++ +
  gi|242399887|ref|YP_002995312.1| 59 IG----AALSAAVFI 69
                                      22....222222222 PP

>> DUF4418  Domain of unknown function (DUF4418)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.3      0.24   7.2e+02      99     113 ..       4      18 ..       1      22 [. 0.52
   2 ?   10.7   2.2   0.00015      0.46      36      79 ..      28      71 ..      25      75 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.24
                           DUF4418  99 pvlivlgillillal 113
                                       +v+i++++l+i+ a+
  gi|242399887|ref|YP_002995312.1|   4 WVAIFIAALMIISAI 18 
                                       455555555554333 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00015
                           DUF4418 36 qaelgvGivllvlgllalfvkkkklrrglsiavillgvlvilip 79
                                       a++g+++v l+++++ +f+++ ++ ++ + + ++l+++v++++
  gi|242399887|ref|YP_002995312.1| 28 AAVVGMAAVSLFASIAFFFLQAPDVAMVEAAIGAALSAAVFIFT 71
                                      5899************************9999999999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1035  (0.0577277); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.35s 00:00:00.88 Elapsed: 00:00:00.54
# Mc/sec: 507.84
//
Query:       gi|242399888|ref|YP_002995313.1|  [L=137]
Description: Membrane-bound NADP+-reducing complex MBX, subunit MbxC (Na+/H+ transporter subunit) [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.4e-25   87.2   4.9    8.1e-25   86.9   4.9    1.1  1  PhaG_MnhG_YufB  Na+/H+ antiporter subunit
  ------ inclusion threshold ------
       0.32   10.9   0.7       0.52   10.2   0.7    1.5  1  TarH            Tar ligand binding domain homologue


Domain annotation for each model (and alignments):
>> PhaG_MnhG_YufB  Na+/H+ antiporter subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.9   4.9   9.1e-29   8.1e-25       1      79 []      11      94 ..      11      94 .. 0.95

  Alignments for each domain:
  == domain 1  score: 86.9 bits;  conditional E-value: 9.1e-29
                    PhaG_MnhG_YufB  1 llllGalfvllgaigllrlpdvytRlhaatkadtlGlllillGlllrf.slaa....slkllliilfllltaPvaahli 74
                                      l+l+G++f +++++gl+r+pdvy+R+++atk++tlG+l +++G+ + +  +      + k l+i++flllt+P+aah++
  gi|242399888|ref|YP_002995313.1| 11 LVLFGTFFYVVSSLGLIRMPDVYNRMQTATKSATLGSLGVIIGVGIWAiGEVGsyswIPKTLIIAVFLLLTNPIAAHAL 89
                                      799*******************************************77555559************************* PP

                    PhaG_MnhG_YufB 75 araay 79
                                       raay
  gi|242399888|ref|YP_002995313.1| 90 IRAAY 94
                                      ****8 PP

>> TarH  Tar ligand binding domain homologue
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.7   5.8e-05      0.52       5      46 ..       1      42 [.       1      63 [. 0.91

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 5.8e-05
                                      XXXXXXXXXXXXXXXXXXXXXXSSSSSSHHHHHHHCHHHHHH CS
                              TarH  5 isIrtrLllvlallgvLllvsgglglsglsrsndalrevytn 46
                                      +sI + +  vl+l+g ++ v++ lgl+ + +  ++++++ ++
  gi|242399888|ref|YP_002995313.1|  1 MSIASIIGQVLVLFGTFFYVVSSLGLIRMPDVYNRMQTATKS 42
                                      68999999***********************99999998665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); 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: 0.53u 0.36s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 789.95
//
Query:       gi|242399889|ref|YP_002995314.1|  [L=82]
Description: Membrane-bound NADP+-reducing complex MBX, subunit MbxB (Na+/H+ transporter subunit) [Thermococcus sibiricus MM 739]
Scores for complete 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   72.3  11.4    3.1e-20   72.3  11.4    1.9  2  MrpF_PhaF  Multiple resistance and pH regulation protein F (M
  ------ inclusion threshold ------
      0.064   13.0   4.5      0.076   12.8   4.3    1.3  1  IncD       Inclusion membrane protein D
       0.28   10.6   3.9       0.33   10.3   3.9    1.0  1  DUF2417    Region of unknown function (DUF2417)


Domain annotation for each model (and alignments):
>> MrpF_PhaF  Multiple resistance and pH regulation protein F (MrpF / PhaF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.9      0.15   8.9e+02      13      23 ..       7      17 ..       4      21 .. 0.56
   2 !   72.3  11.4   5.2e-24   3.1e-20       1      53 []      27      79 ..      27      79 .. 0.98

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.15
                         MrpF_PhaF 13 llvallallai 23
                                       l+a+ ++l++
  gi|242399889|ref|YP_002995314.1|  7 FLIAVAVILSM 17
                                      45555555555 PP

  == domain 2  score: 72.3 bits;  conditional E-value: 5.2e-24
                         MrpF_PhaF  1 aDRvvAlDllgtllvallallailtgrpayldvalvlAllgFvgtvafarfle 53
                                      aDR+vA+D ++tl+++l++l+a+ ++r+++ldvalv+A+l+Fvg++afar++e
  gi|242399889|ref|YP_002995314.1| 27 ADRIVAVDIMTTLTTGLMVLFALHYRRAIFLDVALVYAVLAFVGVIAFARYME 79
                                      7**************************************************86 PP

>> IncD  Inclusion membrane protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   4.3   1.3e-05     0.076      32      81 ..      25      75 ..      10      82 .] 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.3e-05
                              IncD 32 ptakrlvavavatilavallvvagllfsgvlcspvsvlaasl.ffgvgafl 81
                                       ta r+vav + t l+  l+v+  l +   +   v+++ a l f+gv af 
  gi|242399889|ref|YP_002995314.1| 25 TTADRIVAVDIMTTLTTGLMVLFALHYRRAIFLDVALVYAVLaFVGVIAFA 75
                                      589************************999999888776665377999984 PP

>> DUF2417  Region of unknown function (DUF2417)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   3.9   5.6e-05      0.33      82     159 ..       4      78 ..       2      81 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 5.6e-05
                           DUF2417  82 lalillslianllnllffglpSkldrvlnivlavLllvnllllllvkytReregfvgiasvlWaaltfllgilldry 158
                                       + l l++++  l  + ff  p ++dr++ + ++  l   l++l++ +y R    f+++a+ ++a+l f+  i++ ry
  gi|242399889|ref|YP_002995314.1|   4 IYLFLIAVAVILSMYRFFRGPTTADRIVAVDIMTTLTTGLMVLFALHYRRA--IFLDVAL-VYAVLAFVGVIAFARY 77 
                                       6788999999999999**************99999999*******999765..6677665.5777777777776666 PP

                           DUF2417 159 v 159
                                       +
  gi|242399889|ref|YP_002995314.1|  78 M 78 
                                       5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1008  (0.0562218); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 536.27
//
Query:       gi|242399890|ref|YP_002995315.1|  [L=168]
Description: Membrane-bound NADP+-reducing complex MBX, subunit MbxA (Na+/H+ transporter subunit) [Thermococcus sibiricus MM 739]
Scores for complete 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-46  157.7   0.3    1.8e-46  157.5   0.3    1.0  1  MNHE      Na+/H+ ion antiporter subunit
  ------ inclusion threshold ------
      0.027   14.5   2.6       0.04   14.0   2.6    1.2  1  TspO_MBR  TspO/MBR 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 !  157.5   0.3   2.1e-50   1.8e-46       2     144 ..      15     164 ..      14     166 .. 0.92

  Alignments for each domain:
  == domain 1  score: 157.5 bits;  conditional E-value: 2.1e-50
                              MNHE   2 lllflvWllltgs..lgelllGlllallvalllrrll.....lplrrv.llrllayllvflweivkanldVakrvlr 70 
                                       l+lf++W++lt s   +e+ +G++++l++ +l+++++      +l+++ +++++ay+++flw +++anldVa+rvl+
  gi|242399890|ref|YP_002995315.1|  15 LILFIIWMFLTSSfdSQEITIGAVFSLIIGALTYEVFterglENLNPKrMAYAIAYIPYFLWAMIMANLDVAYRVLH 91 
                                       89*******************************9999999984444446677************************* PP

                              MNHE  71 pklpirpgivkvplrlksdlaltllansitltPGTltvdvdedrrvlyvHvldvede.eeeareeikgrlErrll 144
                                       pk+pi+pgiv++++ l+++++ ++lansitltPGT+t+dv+ d+  +++H++dv+d+  e a+e+i++ +E+ l+
  gi|242399890|ref|YP_002995315.1|  92 PKRPINPGIVECKTILTNNTGKLALANSITLTPGTITLDVKGDH--YFIHWIDVKDKsIEGASEHITKPFEKFLK 164
                                       ***************************************88666..********6655999***********987 PP

>> TspO_MBR  TspO/MBR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   2.6   4.4e-06      0.04      63     130 ..      11      84 ..       3      88 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.4e-06
                                       HHHHHHHHHHTSGGCT..TTTTSGGGHHHHHHHHHHHHHHHHH.....HCCCC-HHHHHHHCHHHHHHHHHHHHH CS
                          TspO_MBR  63 lyavqlvlnllwsplf..fglkspvlalvdivallglvvalil.....afskvdklaallllpyllWllfatyln 130
                                       ly+v l+l ++w++l   f  +++++++v  +++ +l++ ++      +  + + + a+  +py+lW ++++ l 
  gi|242399890|ref|YP_002995315.1|  11 LYTV-LILFIIWMFLTssFDSQEITIGAVFSLIIGALTYEVFTergleNLNPKRMAYAIAYIPYFLWAMIMANLD 84 
                                       6666.777777777652266688888888888777666666654444333666668899********99987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       843  (0.0470188); expected 358.6 (0.02)
Passed bias filter:                      550  (0.0306766); 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: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 1010.59
//
Query:       gi|242399891|ref|YP_002995316.1|  [L=166]
Description: Regulator of amino acid metabolism, , containing act domain [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-07   30.8   0.1    3.5e-07   29.9   0.1    1.5  1  ACT              ACT domain
  ------ inclusion threshold ------
      0.021   14.6   0.1      0.037   13.8   0.1    1.4  1  ACT_7            ACT domain
      0.048   13.8   0.0       0.11   12.7   0.0    1.6  1  HU-CCDC81_euk_2  CCDC81 eukaryotic HU domain 2


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 !   29.9   0.1   5.8e-11   3.5e-07      12      66 ..     106     158 ..     104     159 .. 0.97

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 5.8e-11
                                       THHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHTTC CS
                               ACT  12 GlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealkkle 66 
                                       G+La+v++ +adrgiNi+ +     e    ++++++i+++   + e++++l kle
  gi|242399891|ref|YP_002995316.1| 106 GILAKVASKIADRGINIIQVVAEDPEL--YPEATLTIITEKPIPGELINELSKLE 158
                                       9**************************..8***********************98 PP

>> ACT_7  ACT domain
   #    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      20      41 ..     104     125 ..      95     129 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.2e-06
                                       S--HHHHHHHHHHTTT---EEE CS
                             ACT_7  20 vtGivaklaspLaeagIsifqi 41 
                                       ++Gi+ak+as+ a+ gI+i q+
  gi|242399891|ref|YP_002995316.1| 104 AIGILAKVASKIADRGINIIQV 125
                                       68*****************987 PP

>> HU-CCDC81_euk_2  CCDC81 eukaryotic HU domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.8e-05      0.11       4      29 ..      41      66 ..      40      68 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.8e-05
                   HU-CCDC81_euk_2  4 plnytelaaaaglsrdvVescvqetf 29
                                      ++ yt++a+a+ ++r+vV+ +v  ++
  gi|242399891|ref|YP_002995316.1| 41 EVPYTKIAKALDVDRRVVKETVTMIL 66
                                      578******************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       624  (0.0348039); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); 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: 0.58u 0.36s 00:00:00.94 Elapsed: 00:00:00.56
# Mc/sec: 896.64
//
Query:       gi|242399892|ref|YP_002995317.1|  [L=419]
Description: MooA-like molybdenum cofactor biosynthesis protein A related [Thermococcus sibiricus MM 739]
Scores for complete 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-25   88.8   0.1    1.4e-24   87.3   0.0    1.7  3  Radical_SAM  Radical SAM superfamily
     0.0051   16.9   0.0      0.013   15.6   0.0    1.7  1  Fer4_14      4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.027   14.8   0.5       0.42   11.0   0.2    2.5  2  S1           S1 RNA binding domain
      0.091   12.8   1.7       0.21   11.6   1.7    1.7  1  TRAM         TRAM domain
       0.15   11.3   0.1       0.95    8.7   0.0    2.0  2  WD-3         WD-repeat region


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 ?   -3.6   0.0       3.4   1.2e+04      59      79 ..      26      44 ..      16      64 .. 0.59
   2 !   87.3   0.0     4e-28   1.4e-24       5     166 ..     123     287 ..     120     288 .. 0.94
   3 ?   -3.1   0.0       2.5   9.1e+03      74     115 ..     356     401 ..     321     410 .. 0.61

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 3.4
                                      GSTTHHHHHHHHHHTCCCTEE CS
                                      xxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 59 lypdfvellerlaklavpgir 79
                                      ly+df++ l++ a ++  +++
  gi|242399892|ref|YP_002995317.1| 26 LYADFEKNLLEKAIKR--KFK 44
                                      5555555555555442..222 PP

  == domain 2  score: 87.3 bits;  conditional E-value: 4e-28
                                       SEESS--TTTSCCTT..HHHHHHHHHHHHHHHHHHHHHHHHHTT..SEEEEEESSTGGGSTTHHHHHHHHHHTCCCT CS
                                       xxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   5 rgCnlrCsfCarpet..vrregrgrslsveeileevkelkaekg..vkevilgggepllypdfvellerlaklavpg 77 
                                        gCn  C+fC++ e   +r++   ++++v+++l+ + e+++ kg   +  + g gepl+yp +vel+  l+++  + 
  gi|242399892|ref|YP_002995317.1| 123 TGCNVSCIFCSVDEGpySRTRILDYVVDVDYLLKWFNEVAQFKGkrLEAHLDGQGEPLVYPFIVELVQGLRENP-NV 198
                                       7***************************************55555899*************************4.66 PP

                                       EEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEEEBT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  78 iritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvdrivglp 153
                                         i++ +ng l++++ +e+l+e+g+drv+l+++++d+ek + lm+ + +++ +vle  e+l +agi+ v +  v++ 
  gi|242399892|ref|YP_002995317.1| 199 SVISMQSNGALLNDKLIEELAEAGLDRVNLSIHSFDPEKAKMLMGmKDYDLNHVLEMAEALINAGID-VLFAPVIIF 274
                                       6689**********************************9999999999*******************.9******** PP

                                       TTSHHHHHHHHHH CS
                                       xxxxxxxxxxxxx RF
                       Radical_SAM 154 Gendeeleellel 166
                                       G nd e e ++e+
  gi|242399892|ref|YP_002995317.1| 275 GINDMEAESFIEF 287
                                       *****99999988 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 2.5
                                       C.....CCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHH CS
                                       x.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  74 a.....vpgiritvetngtlpdeeklerllelgvdrvslgleaadde 115
                                              + +++ ++ +g     e+l+  +++ + +++ +++ +d+ 
  gi|242399892|ref|YP_002995317.1| 356 PlefhvGEVVKVKIILPGRIE-GEMLAVARNRLIEVINTNAKVGDEI 401
                                       144444556666666666665.6666666666666666666666665 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 !   15.6   0.0   3.6e-06     0.013       6      92 ..     123     210 ..     119     230 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.6e-06
                           Fer4_14   6 sgCnlsCkgCd.....nketwks..elgkpqteelleqilkdlkkseikiqglvltG.GePLhyenkkellklvkrl 74 
                                        gCn+sC +C           +    l  + + + l + ++++ + + k+ +  l G GePL y   + +++lv+ l
  gi|242399892|ref|YP_002995317.1| 123 TGCNVSCIFCSvdegpY----SRtrILDYVVDVDYLLKWFNEVAQFKGKRLEAHLDGqGEPLVY---PFIVELVQGL 192
                                       59********9643321....222123333344444555656666666666777********99...********** PP

                           Fer4_14  75 keeypekkiwletngtle 92 
                                       +e+ +   i +++ng l 
  gi|242399892|ref|YP_002995317.1| 193 RENPNVSVISMQSNGALL 210
                                       ***988999999999875 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.14   5.1e+02      49      61 ..     358     370 ..     338     371 .. 0.84
   2 ?   11.0   0.2   0.00012      0.42      40      64 ..     385     409 ..     381     412 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.14
                                       CEETTEEEEEEEE CS
                                S1  49 vlkvGdevkvkvl 61 
                                       +++vG+ vkvk++
  gi|242399892|ref|YP_002995317.1| 358 EFHVGEVVKVKII 370
                                       6789999999996 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00012
                                       SCEESCHHHCEETTEEEEEEEEEEE CS
                                S1  40 darvedpdevlkvGdevkvkvlkvd 64 
                                       +  +e++++  kvGde+kvk+ +++
  gi|242399892|ref|YP_002995317.1| 385 NRLIEVINTNAKVGDEIKVKIVRTR 409
                                       457899***************9976 PP

>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.7   5.7e-05      0.21       4      54 ..     361     410 ..     358     418 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.7e-05
                                       XXXEEEEEEEEE-.TTSEEEEEET.TEEEEETT--T..TEEEEEEEEEE-S CS
                              TRAM   4 vGstqeVlveglsksegegiGrtdngkvvfvpgdlpgIGdfVeVkItkvkr 54 
                                       vG+++ V++  +++ ege+++    ++ + v ++++++Gd+ +VkI +++ 
  gi|242399892|ref|YP_002995317.1| 361 VGEVVKVKIILPGRIEGEMLAVAR-NRLIEVINTNAKVGDEIKVKIVRTRH 410
                                       9********************999.999999999999*********98875 PP

>> WD-3  WD-repeat region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.13   4.8e+02      72     143 ..     183     255 ..     167     261 .. 0.73
   2 ?    8.7   0.0   0.00026      0.95     188     226 ..     320     361 ..     316     376 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.13
                                       HHHHHHHHHS-----------.-G.GG--HHHHHHHHHS-SS-E......EEE-GGG-EEEEEEETTE.EEEEEEE CS
                              WD-3  72 dFlqelkellesekalkskkeseslpsakyyarlleeleklgwekl....lqidedlksiklkakdssgreHllel 143
                                        F++el++ l ++ + +  +  ++ + a + ++l+eel + g +++     ++d++  ++ + +kd    +H+le+
  gi|242399892|ref|YP_002995317.1| 183 PFIVELVQGLRENPNVSVIS--MQSNGALLNDKLIEELAEAGLDRVnlsiHSFDPEKAKMLMGMKDYD-LNHVLEM 255
                                       69999999999666655555..5557999999999999999999885555566666666655555555.6666665 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00026
                                       HTHHHHHHHHHHHHHS-....--BSSS--TT--EEEEEEETTE CS
                              WD-3 188 slqeFwdvldeldektw....VLePekptrkdtsrrialkenv 226
                                       s+++F++ l el+ekt     VL+Pe+   ++++r i+l+ +v
  gi|242399892|ref|YP_002995317.1| 320 SFKKFYNWLRELEEKTDmrplVLKPEHFG-MHKRRFIPLEFHV 361
                                       79**************555559*****87.5788899988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (419 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       685  (0.0382063); expected 358.6 (0.02)
Passed bias filter:                      606  (0.0338); 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: 0.62u 0.33s 00:00:00.95 Elapsed: 00:00:00.49
# Mc/sec: 2572.46
//
Query:       gi|242399893|ref|YP_002995318.1|  [L=377]
Description: UDP-N-acetylglucosamine 2-epimerase [Thermococcus sibiricus MM 739]
Scores for complete 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-119  398.8   0.0   1.9e-119  398.6   0.0    1.0  1  Epimerase_2      UDP-N-acetylglucosamine 2-epimerase
     0.0026   17.3   0.0       0.35   10.4   0.0    2.2  2  AIRC             AIR carboxylase
  ------ inclusion threshold ------
      0.014   16.0   0.1         16    6.2   0.0    3.3  3  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
      0.027   14.5   0.0      0.081   12.9   0.0    1.8  2  Glyco_transf_4   Glycosyltransferase Family 4
      0.043   13.8   0.0       0.11   12.5   0.0    1.7  2  Glyco_trans_4_2  Glycosyl transferase 4-like
      0.045   13.3   0.1       0.13   11.8   0.1    1.8  1  Glycos_transf_1  Glycosyl transferases group 1
        0.1   12.7   0.1       0.35   10.9   0.0    1.8  2  Glyco_transf_28  Glycosyltransferase family 28 N-terminal dom


Domain annotation for each model (and alignments):
>> Epimerase_2  UDP-N-acetylglucosamine 2-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  398.6   0.0  7.5e-123  1.9e-119       7     346 ..      26     360 ..      21     361 .. 0.96

  Alignments for each domain:
  == domain 1  score: 398.6 bits;  conditional E-value: 7.5e-123
                                       -..EEEEEEE-S--SGGGTHHHHHHTT----SEEE---S--HHHHHHHHHHHHHHHHHHH--SEEEEESSSHHHHHH CS
                       Epimerase_2   7 selelqlvvtGqHldremgdtvfeeleiekpdydlnsdsqslakstgrvligleevleeekpDlvlvlGDtnetlag 83 
                                       + l+  l++tGqH+d+em+++++eele++ ++y+l+++s++ a +tg ++i++eevl++e+pD+ lv+GDtn++lag
  gi|242399893|ref|YP_002995318.1|  26 RGLKPLLIHTGQHYDYEMSKVFLEELELRGINYHLEVGSGTQAYQTGIAMIKIEEVLMKEDPDVTLVQGDTNTVLAG 102
                                       478899*********************************************************************** PP

                                       HHHHHHTT-EEEEET-----S-TT..SHHHHHHHHHHHT-SEEEESSHHHHHHHHHTT--GGGEEE---HHHHHHHH CS
                       Epimerase_2  84 alaAfklripvaHveAGlRsfdltegmpeEinRhlidklsdlhfapteearenLlkegeeeerifvvGntviDalll 160
                                       ala +kl+ipvaHveAGlRsfd+t  mpeEinR+l+d+ s+++fapteear+nL +eg+  e ++vvGnt++Da+++
  gi|242399893|ref|YP_002995318.1| 103 ALASVKLKIPVAHVEAGLRSFDRT--MPEEINRILADHASEVLFAPTEEARKNLEREGI-IEGVYVVGNTIVDAVFQ 176
                                       ************************..*********************************.679************** PP

                                       HHHHHH...T-HHHHHH..--SS-EEEEE---HHHHTSHHHHHHHHHHHHHHHHHH--EEEEE--..HHHHHHH... CS
                       Epimerase_2 161 skeeieeklkaseilke..lkekkyvlvtlHrrenedeperlkeilealkalakekdvevvvpvhnnprtrkrl... 232
                                       ++e +e+   +s+il++  lk k+y+++t+Hr+en+d+ e+lk+++e++++l      +vv+pvh  prt+krl   
  gi|242399893|ref|YP_002995318.1| 177 NSEIAER---KSKILEKfgLKPKEYAVLTAHRAENTDSAENLKKLVEIIESLPI----PVVYPVH--PRTEKRLkdl 244
                                       *999994...56999999*********************999999999999987....59*****..*******999 PP

                                       ..HHHHHH-TTEEEE----HHHHHHHHHC-SEEEES-HHHHHHHHHCT--EEESSSS-S-THHHHTTSEEE-TT-HH CS
                       Epimerase_2 233 ..leeleelenvtlieplgyldflsllknaklvltdSgGiqeEapslgvpvvnlReeteRpegveagtnvlvgtdke 307
                                         +e+l++ ++v+l++plgyldfl+l+knak+vltdSgGiqeE+++l vp+++lR +teRpe+++ag nvlvg +ke
  gi|242399893|ref|YP_002995318.1| 245 glWERLKAKDHVILTKPLGYLDFLKLQKNAKIVLTDSGGIQEESIILSVPCLTLRYNTERPETIKAGGNVLVGLEKE 321
                                       9988898889******************************************************************* PP

                                       HHHHHHHHHCT-..--......--TT-SS-HHHHHHHHH CS
                       Epimerase_2 308 eIvaaleklledkkelekmanaknpYgdGkaseriveil 346
                                       ++++ +e+ll+d++ +++mana+np+gdG++ er+v+il
  gi|242399893|ref|YP_002995318.1| 322 RVIHYVERLLNDEEFYSRMANAENPFGDGRSGERMVDIL 360
                                       *************************************98 PP

>> AIRC  AIR carboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0   0.00014      0.35       4      83 ..      33     116 ..      31     126 .. 0.90
   2 !    4.7   0.0    0.0083        21      12      41 ..     178     208 ..     169     223 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00014
                                       EEESSGGGHHHHHHHHHHHHHTT-EEEEEE--...TTTSHHHHHHHHHHCHTTTEEEEEEEEESS--HHHHHHHHS. CS
                              AIRC   4 iimGSdsDlevmkkaaeilkelgveyevrvvS...ahrtpeelleyaeeaeerglkviIagAGgaahLpgvvaslt. 76 
                                       i +G + D+e+ k   e l+  g++y+++v S   a++t   ++++ e   +++ +v ++    +  L+g++as+  
  gi|242399893|ref|YP_002995318.1|  33 IHTGQHYDYEMSKVFLEELELRGINYHLEVGSgtqAYQTGIAMIKIEEVLMKEDPDVTLVQGDTNTVLAGALASVKl 109
                                       6678999***********************886668899999*******************999**********987 PP

                                       SS-EEEE CS
                              AIRC  77 tlPVigv 83 
                                       ++PV  v
  gi|242399893|ref|YP_002995318.1| 110 KIPVAHV 116
                                       9999766 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0083
                                       HHHHHHHHHHHHHTT-EE.EEEE--TTTSHH CS
                              AIRC  12 levmkkaaeilkelgvey.evrvvSahrtpe 41 
                                        e++++  +il+++g++  e+ v+ ahr  +
  gi|242399893|ref|YP_002995318.1| 178 SEIAERKSKILEKFGLKPkEYAVLTAHRAEN 208
                                       67889999********7659********865 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0    0.0094        24      36      60 ..      37      61 ..      21      66 .. 0.86
   2 ?    6.2   0.0    0.0061        16       8      54 ..      94     139 ..      93     150 .. 0.79
   3 ?   -1.0   0.0         1   2.7e+03      40      70 ..     148     178 ..     140     189 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0094
                                      TTSSHHHHHHHHHHHHHTTEEEECS CS
                         Pyr_redox 36 rllDeeaskilqeklekngievlln 60
                                      + +D e+sk++ e+le +gi+ +l+
  gi|242399893|ref|YP_002995318.1| 37 QHYDYEMSKVFLEELELRGINYHLE 61
                                      6799*****************9986 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0061
                                       SHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTT CS
                         Pyr_redox   8 GyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekng 54 
                                       G+++  lAgala  + k+ v + +  l+  +D+++ +++ + l ++ 
  gi|242399893|ref|YP_002995318.1|  94 GDTNTVLAGALASVKLKIPVAHVEAGLR-SFDRTMPEEINRILADHA 139
                                       889999******************9999.666666666666665554 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 1
                                       HHHHHHHHHHHHHTTEEEECSEEEEEEEEET CS
                         Pyr_redox  40 eeaskilqeklekngievllntkveeiegse 70 
                                       eea+k+l+++   +g+ v+ nt v ++ +++
  gi|242399893|ref|YP_002995318.1| 148 EEARKNLEREGIIEGVYVVGNTIVDAVFQNS 178
                                       6777888888888899999999998887665 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   3.1e-05     0.081      51     166 ..      65     170 ..      19     173 .. 0.71
   2 ?   -2.6   0.0       1.9   4.8e+03      95     108 ..     225     238 ..     209     258 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.1e-05
                    Glyco_transf_4  51 lkrllrslaflrrlrrllkrekpDvvHahspaal.gaallalrrrlgiplVltvHglyekrllkarlkplsrllral 126
                                         +++++  ++ ++ ++l +e+pDv  +++     +a++la+  +l+ip+ +   gl          ++ + + +++
  gi|242399893|ref|YP_002995318.1|  65 GTQAYQTGIAMIKIEEVLMKEDPDVTLVQGDTNTvLAGALASV-KLKIPVAHVEAGLR---------SFDRTMPEEI 131
                                       4556777788999*************99976555055555555.5*****99988888.........3444444444 PP

                    Glyco_transf_4 127 errl.lrradrviavSeatadelrerygvppekitVipnGv 166
                                        r l  +++  ++a++e+++++l++  g+  e ++V+ n +
  gi|242399893|ref|YP_002995318.1| 132 NRILaDHASEVLFAPTEEARKNLER-EGII-EGVYVVGNTI 170
                                       4445234577899************.9998.7899999866 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.9
                    Glyco_transf_4  95 lgiplVltvHglye 108
                                       l ip+V+ vH   e
  gi|242399893|ref|YP_002995318.1| 225 LPIPVVYPVHPRTE 238
                                       67788888887665 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 ?   12.5   0.0   4.5e-05      0.11      60     123 ..      72     134 ..      41     145 .. 0.78
   2 ?   -3.3   0.0       3.4   8.6e+03      79     105 ..     255     279 ..     255     282 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.5e-05
                   Glyco_trans_4_2  60 ylkafklkklikkikPDvvhahyakpygllgslaarlsgvipvvlsvwGldvlkfpkksklkkl 123
                                        ++++k+ +++ k+ PDv  ++  +  +l+g+la+ +++ ipv+    Gl  ++   + ++ ++
  gi|242399893|ref|YP_002995318.1|  72 GIAMIKIEEVLMKEDPDVTLVQGDTNTVLAGALASVKLK-IPVAHVEAGLRSFDRTMPEEINRI 134
                                       46789********************99999999988887.***988888888877766665555 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.4
                   Glyco_trans_4_2  79 hahyakpygllgslaarlsgvipvvls 105
                                       h++ +kp+g+l  ++ +l +  ++vl+
  gi|242399893|ref|YP_002995318.1| 255 HVILTKPLGYLD-FL-KLQKNAKIVLT 279
                                       777788888877.55.55555888876 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 ?   11.8   0.1   5.1e-05      0.13       4     168 ..     186     343 ..     183     345 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.1e-05
                                       HHHHHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHH..HHHHCTTCGGGEE CS
                   Glycos_transf_1   4 kkrkklgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkkl..aeelelsdnvifl 78 
                                       k+ +k g++ k++ +l+ +r e++   ++l k+++ ++     +v++ +      ek+lk+l   e l+ +d+vi++
  gi|242399893|ref|YP_002995318.1| 186 KILEKFGLKPKEYAVLTAHRAENTDSAENLKKLVEIIESL-PIPVVYPVH--PRTEKRLKDLglWERLKAKDHVILT 259
                                       5566777788888888888888888888888888877543.444444444..4556666654225888889999999 PP

                                       ECCHSSSHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEET.TTTHCHHCHTTTSEEEE-TT-HHHHHHHHHH CS
                   Glycos_transf_1  79 gevsredleellknadifvlpsisEgfGivllEAmaaglpviasn.aggpaevvkdgetGllvkpnnaealaeairk 154
                                       + + + d  +l kna+i++      + Gi   E++ + +p+++   +   +e++k g + l+  +   e  + ++++
  gi|242399893|ref|YP_002995318.1| 260 KPLGYLDFLKLQKNAKIVLTD----SGGIQ-EESIILSVPCLTLRyNTERPETIKAGGNVLVGLE--KERVIHYVER 329
                                       999988888888889988877....66765.6*************99***********7444444..6********* PP

                                       HHHSHHHHHHHHHH CS
                   Glycos_transf_1 155 lledeelrerlgen 168
                                       ll+dee + r+ ++
  gi|242399893|ref|YP_002995318.1| 330 LLNDEEFYSRMANA 343
                                       ********999875 PP

>> Glyco_transf_28  Glycosyltransferase family 28 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00014      0.35       7     119 ..       8     118 ..       5     135 .. 0.82
   2 ?   -1.9   0.0       1.2   3.1e+03      17      51 ..     245     277 ..     244     290 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00014
                                       SSHHHHHHHHHHHHHHHCTT-EEEEEEETCCCHHHHHHCCT-EEEE---GHCTT..CHHHHCCHHHHHHHHHHHHHH CS
                   Glyco_transf_28   7 GTgGhvfPalAlakeLkkegheVrylgtkrgleerlveeaglefepiageklrrklspknlkeilkvlkavvkakki 83 
                                       GT+  ++  + ++++++k+g +   l  + g      e +++ +e++++++ +  l ++  +++ + + a++k+ ++
  gi|242399893|ref|YP_002995318.1|   8 GTRPEIIKLVPVIRAFEKRGLKP--LLIHTGQHYDY-EMSKVFLEELELRGINYHLEVGSGTQAYQTGIAMIKIEEV 81 
                                       77777777778888888888554..55566666666.779************************************* PP

                                       HHHHHHCCCCCCCCCCC.HCCCCCHCCCTTHCCCCCH CS
                   Glyco_transf_28  84 lkeakpdavvgtggyvs.lpaviaaplaripviihEq 119
                                       l ++ pd+++  g     l+  +a+ +++ipv   E+
  gi|242399893|ref|YP_002995318.1|  82 LMKEDPDVTLVQGDTNTvLAGALASVKLKIPVAHVEA 118
                                       *********999976551566799*******987666 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.2
                                       HHHHHHHCTT-EEEEEEETCCCHHHHHHCCT-EEE CS
                   Glyco_transf_28  17 AlakeLkkegheVrylgtkrgleerlveeaglefe 51 
                                        l ++Lk+++ +V  l ++ g+ ++l+ +++ +++
  gi|242399893|ref|YP_002995318.1| 245 GLWERLKAKD-HVI-LTKPLGYLDFLKLQKNAKIV 277
                                       5778999999.676.88888888888888777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.70u 0.37s 00:00:01.06 Elapsed: 00:00:00.59
# Mc/sec: 1915.68
//
Query:       gi|242399894|ref|YP_002995319.1|  [L=458]
Description: UDP-N-acetyl-D-mannosaminuronate dehydrogenase [Thermococcus sibiricus MM 739]
Scores for complete 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-52  175.8   0.1    1.2e-51  174.9   0.1    1.3  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
    2.7e-26   91.6   0.0    6.3e-26   90.4   0.0    1.7  1  UDPG_MGDP_dh    UDP-glucose/GDP-mannose dehydrogenase family,
    6.3e-26   90.8   0.0    2.3e-25   89.1   0.0    2.0  1  UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family,
    2.5e-07   31.0   0.0    8.8e-07   29.2   0.0    1.9  1  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
    3.2e-05   23.9   0.0    8.2e-05   22.6   0.0    1.8  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
    0.00028   20.3   0.0    0.00062   19.1   0.0    1.5  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
     0.0013   18.1   0.0     0.0053   16.1   0.0    1.9  2  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
     0.0019   18.7   0.1        1.5    9.4   0.0    2.9  2  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
     0.0042   17.1   0.0       0.15   12.0   0.0    2.5  2  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
  ------ inclusion threshold ------
       0.01   15.1   0.0      0.021   14.1   0.0    1.4  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
      0.072   12.7   0.0       0.27   10.9   0.0    1.9  2  ApbA            Ketopantoate reductase PanE/ApbA
        0.1   13.1   0.1       0.46   11.1   0.1    2.2  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
       0.17   12.2   0.1       0.36   11.1   0.1    1.5  1  NAD_binding_11  NAD-binding of NADP-dependent 3-hydroxyisobut


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 !  174.9   0.1   8.9e-55   1.2e-51       2     181 ..      41     218 ..      40     223 .. 0.95

  Alignments for each domain:
  == domain 1  score: 174.9 bits;  conditional E-value: 8.9e-55
                                       EEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS--TTHHHHHHHHCHTTTEEEES-HHHHHHC-S CS
                    UDPG_MGDP_dh_N   2 kisviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipiyepgLeelvkkavesgrlsfttdvekaveead 78 
                                       +i+viGlGY+Gl+ta+++a++g++vig  i +e v+klnsg+++i+ep++++l++ka++ grl++t++ +  ++  d
  gi|242399894|ref|YP_002995319.1|  41 EIAVIGLGYIGLPTAIMFANAGFNVIGYEIRKEVVEKLNSGNSHIIEPEIDDLLHKAIDRGRLKATSNKDD-IRGKD 116
                                       79***************************************************************998776.***** PP

                                       EEEE-----B-TTTTCB-THHHHHHHHHHHHHHHCEEEEEE-S---TTHHHHCHHHHHHHHCSS-TTCEEEEE---- CS
                    UDPG_MGDP_dh_N  79 vifiaVgTPskkkgkaaDlkyvesaarsiaealkkgkvvvvkSTvpvgtaeelvkkileeaskkkgvdfdvvsnPEf 155
                                       v +i+V TP ++ +k++Dl+y+e+a+r++ae++kkg++vv++ST+p+ t+ ++ + i e +  k gvdf++v+ PE+
  gi|242399894|ref|YP_002995319.1| 117 VYLICVQTPLRD-DKTPDLTYLEEAVRTVAETMKKGSLVVIESTIPPMTTLKMGRLIEEIRGFKAGVDFYMVHAPER 192
                                       ************.**************************************87777777777777************ PP

                                       --TTSHHHHHHS-S-EEEEESSCHHH CS
                    UDPG_MGDP_dh_N 156 lregsavkdllnpdrvviGveekkae 181
                                       + +g + k+l+ + r+++Gv+e++ae
  gi|242399894|ref|YP_002995319.1| 193 VMPGRIFKELVYNSRIIGGVTEESAE 218
                                       ***********************998 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 !   90.4   0.0   4.6e-29   6.3e-26       2      93 ..     239     325 ..     238     326 .. 0.97

  Alignments for each domain:
  == domain 1  score: 90.4 bits;  conditional E-value: 4.6e-29
                      UDPG_MGDP_dh   2 tAEliKlaaNaflatkIsfiNelanlcealgidveeVieavgldprigpkflkpglGvGGsclpkDvkaLvalaeel 78 
                                       t+E++Kl++N+f++++I+++Ne+a l++++g+++ e ie ++++pr   k+++pg+GvGG+clpkD++ L++ a+e 
  gi|242399894|ref|YP_002995319.1| 239 TSEMVKLMENTFRDVNIALANEFALLAHQYGVNIFEAIELANTHPR--VKIHTPGIGVGGHCLPKDPYLLLSSAKE- 312
                                       89********************************************..5*************************98. PP

                      UDPG_MGDP_dh  79 gleaelleavrevNe 93 
                                         ++ l++++re+Ne
  gi|242399894|ref|YP_002995319.1| 313 --DFGLIQKAREINE 325
                                       ..6***********8 PP

>> UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.1   0.0   1.6e-28   2.3e-25       2     104 ..     353     442 ..     352     443 .. 0.95

  Alignments for each domain:
  == domain 1  score: 89.1 bits;  conditional E-value: 1.6e-28
                                       EE-SSSSTT-S--TT-HHHHHHHHHHHCTSEEEEE-SSTHHCCCCHHGGBTCCEEES-CHHHHTT-SEEEE-S--GG CS
                    UDPG_MGDP_dh_C   2 ilGlafKkdtdDlReSpaldiieeLleegaevkiyDPkvkeeaveaeleekgvevvdsleealkgadaiviltehde 78 
                                       +lGla+K d+dD+R+Spal+ +e ++e+ +ev+ yDP+vk  ++             +leealkgada+vi+t+h++
  gi|242399894|ref|YP_002995319.1| 353 VLGLAYKGDSDDIRNSPALAFVEGIKEDVKEVRSYDPYVKGTHE-------------TLEEALKGADAAVIATDHSQ 416
                                       9***************************************9664.............569***************** PP

                                       GGGS-HHHHHHCCSS-EEEESSS-CC CS
                    UDPG_MGDP_dh_C  79 fkeldlaklkelmkpavvfDgrnvld 104
                                       fk+ld++k+ +lm++++++Dgr +++
  gi|242399894|ref|YP_002995319.1| 417 FKNLDWEKIGSLMRNKILIDGRYIVK 442
                                       **********************9987 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.0   6.4e-10   8.8e-07       1     105 [.      41     173 ..      41     182 .. 0.77

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 6.4e-10
                                       EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT...................EEE-SSHHHHHHHCSE CS
                     NAD_binding_2   1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg...................akaaesieelvasldv 58 
                                       +i++iGlG +G + a  +++ag++v++y+ +ke ve+l + +                      a+s ++ +++ dv
  gi|242399894|ref|YP_002995319.1|  41 EIAVIGLGYIGLPTAIMFANAGFNVIGYEIRKEVVEKLNSGNshiiepeiddllhkaidrgRLKATSNKDDIRGKDV 117
                                       59************************************999876666666666666666654445555555555588 PP

                                       EEE-SS....SHHHHHHHHHS.....HCCC--TT-EEEE-S---HHHHHHHHHHHH CS
                     NAD_binding_2  59 vitmvk....agkavdevieg.....llealkkgdilidgstsspedtrelakelk 105
                                        +++v+    ++k  d ++ +     ++e++kkg++++  st+ p +t ++ + ++
  gi|242399894|ref|YP_002995319.1| 118 YLICVQtplrDDKTPDLTYLEeavrtVAETMKKGSLVVIESTIPPMTTLKMGRLIE 173
                                       88888722214444444454478888*******************99998877665 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   5.9e-08   8.2e-05       2      47 ..      42      87 ..      41     165 .. 0.79
   2 ?   -3.0   0.0       4.2   5.8e+03     105     126 ..     228     249 ..     217     256 .. 0.68

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 5.9e-08
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHH CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseealekalekieksle 47
                                      +aviG G +G   a +fa+ag++V  ++i++e +ek ++  ++ +e
  gi|242399894|ref|YP_002995319.1| 42 IAVIGLGYIGLPTAIMFANAGFNVIGYEIRKEVVEKLNSGNSHIIE 87
                                      9*****************************9999987766555333 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4.2
                                       -TTSEEEE--SSS-HHHHCCCS CS
                           3HCDH_N 105 kpdailasnTSslsiselaeal 126
                                        +  i+ +n+ + ++ +l+e++
  gi|242399894|ref|YP_002995319.1| 228 AKGQIFRTNSTTSEMVKLMENT 249
                                       5566777777777777777665 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 !   19.1   0.0   4.5e-07   0.00062      27     125 ..      38     155 ..      31     158 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 4.5e-07
                                       ---EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEE............HCHHHHHHHHHHHH CS
                       AlaDh_PNT_C  27 epakvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvev............lksqeellaeavke 91 
                                       + a++ viG G  Gl  + + ++ g +V  +++r+++ e+l+s +++++e              + ++ + ++ ++ 
  gi|242399894|ref|YP_002995319.1|  38 KSAEIAVIGLGYIGLPTAIMFANAGFNVIGYEIRKEVVEKLNSGNSHIIEPeiddllhkaidrGRLKATSNKDDIRG 114
                                       5799***************************************9999999999*****9999856666677889999 PP

                                       -SEEEE---BT..TSS---SC-.....HHHHHTS-TTEEEE CS
                       AlaDh_PNT_C  92 advvigtvlip..GkkaPkLvt.....eemvksMkpgsViv 125
                                        dv   +v+ p    k+P L       +++ ++Mk+gs +v
  gi|242399894|ref|YP_002995319.1| 115 KDVYLICVQTPlrDDKTPDLTYleeavRTVAETMKKGSLVV 155
                                       99998889988335689999642111144557899999987 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 !   16.1   0.0   3.9e-06    0.0053      35      76 ..      38      79 ..      21      97 .. 0.76
   2 ?   -1.5   0.0         1   1.4e+03      82     100 ..     395     413 ..     381     435 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.9e-06
                                      TTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHH CS
                      2-Hacid_dh_C 35 sgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeee 76
                                      +  ++++iGlG IG  +a +++  g++vi+y+ +k+  e+ +
  gi|242399894|ref|YP_002995319.1| 38 KSAEIAVIGLGYIGLPTAIMFANAGFNVIGYEIRKEVVEKLN 79
                                      56789****************************988766444 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1
                                       ECSHHHHHHH-SEEEE-S- CS
                      2-Hacid_dh_C  82 lvsleellaesDivslhlp 100
                                       +++lee+l+ +D  ++++ 
  gi|242399894|ref|YP_002995319.1| 395 HETLEEALKGADAAVIATD 413
                                       4566666666666665543 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0    0.0011       1.5       2      71 ..      42     124 ..      41     155 .. 0.89
   2 ?    6.3   0.0      0.01        14      39      93 ..     374     436 ..     349     437 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0011
                                       EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC.................-EEECECHHHHHHH CS
                     F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg.................vkvtavdneeaaee 61 
                                       i++iG G +g   a  +++ag    +++ + +  +e +e+l +  +                  +++a++n++ ++ 
  gi|242399894|ref|YP_002995319.1|  42 IAVIGLGYIGLPTAIMFANAG---FNVI-GYEIRKEVVEKLNSGNShiiepeiddllhkaidrGRLKATSNKDDIRG 114
                                       9********************...9999.9999999999998877789999999*****99996677777******* PP

                                       -SEEEE-S-H CS
                     F420_oxidored  62 advvvlavkp 71 
                                        dv++++v++
  gi|242399894|ref|YP_002995319.1| 115 KDVYLICVQT 124
                                       *******986 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.01
                                       HHHHHHHHC........-EEECECHHHHHHH-SEEEE-S-HHHHHHHHHHCGHHHHTTSEEEE CS
                     F420_oxidored  39 aeelaeelg........vkvtavdneeaaeeadvvvlavkpedveevlselakdalkgklvis 93 
                                       +e ++e+++        vk t+ + eea++ ad  v+a   ++++++  e   ++ ++k++i+
  gi|242399894|ref|YP_002995319.1| 374 VEGIKEDVKevrsydpyVKGTHETLEEALKGADAAVIATDHSQFKNLDWEKIGSLMRNKILID 436
                                       555555555555666778889999******************999997666688888899887 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   0.00011      0.15       1      42 [.      41      82 ..      41     120 .. 0.94
   2 ?    2.4   0.0       0.1   1.4e+02      61      85 ..     396     420 ..     386     455 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
                                      -EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHHS CS
                    NAD_Gly3P_dh_N  1 kiavlGaGswGtalAkvlaenghevrlwvreeelieeineeh 42
                                      +iav+G G  G   A+++a++g +v  +  ++e++e++n+ +
  gi|242399894|ref|YP_002995319.1| 41 EIAVIGLGYIGLPTAIMFANAGFNVIGYEIRKEVVEKLNSGN 82
                                      59************************************9865 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.1
                                       S-HHHHHTT--EEEE---HHHHHHH CS
                    NAD_Gly3P_dh_N  61 tdlaealkgadiivlvvPsqalrev 85 
                                       + l+ealkgad  v++  ++ +++ 
  gi|242399894|ref|YP_002995319.1| 396 ETLEEALKGADAAVIATDHSQFKNL 420
                                       5699*************99999876 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 ?   14.1   0.0   1.5e-05     0.021     142     190 ..      37      87 ..      15      97 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.5e-05
                                       T..SEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHH CS
                                       x..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 142 p..krivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaale 190
                                       +  + i+v+G GyiG+ +A+++a++g +v   e r++++++l++  s ++e
  gi|242399894|ref|YP_002995319.1|  37 NksAEIAVIGLGYIGLPTAIMFANAGFNVIGYEIRKEVVEKLNSGNSHIIE 87 
                                       244789***********************9999999999888887777665 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0    0.0002      0.27       1      78 [.      42     124 ..      42     147 .. 0.80
   2 ?   -1.4   0.0       1.2   1.7e+03     111     133 ..     199     221 ..     196     242 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0002
                                       EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHCEEEEETT.....CEEEEEECEEECCH.SCCCCS-ES CS
                              ApbA   1 iailGaGaiGsllaakLakagadvtlilrsr.rlealkknGlrltseg.....geeilrppealsae.ekselepid 70 
                                       ia++G+G iG   a + a+ag +v+ +  ++  +e+l++ ++++ +++     ++ i r + ++  + +k +++  d
  gi|242399894|ref|YP_002995319.1|  42 IAVIGLGYIGLPTAIMFANAGFNVIGYEIRKeVVEKLNSGNSHIIEPEiddllHKAIDRGRLKA--TsNKDDIRGKD 116
                                       89*************************999999999****999999997553333333333333..35578888888 PP

                                       EEEE-SSG CS
                              ApbA  71 lvivtvKa 78 
                                       + +++v +
  gi|242399894|ref|YP_002995319.1| 117 VYLICVQT 124
                                       88888865 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.2
                                       HTTTSTTSEEEEEEEE-EEEEEE CS
                              ApbA 111 lrealpkprvlggvtthgatreg 133
                                       ++e + ++r++ggvt+ +a+  +
  gi|242399894|ref|YP_002995319.1| 199 FKELVYNSRIIGGVTEESAELAE 221
                                       566677789******99998776 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00034      0.46       2      39 ..      42      79 ..      41      96 .. 0.81
   2 ?   -2.2   0.0       4.6   6.4e+03      40      56 ..     240     256 ..     217     271 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00034
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllD 39
                                      ++v+G Gyigl  A ++a+ g +V   e ++++  +l+
  gi|242399894|ref|YP_002995319.1| 42 IAVIGLGYIGLPTAIMFANAGFNVIGYEIRKEVVEKLN 79
                                      89******************988887777777776655 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 4.6
                                       HHHHHHHHHHHHHTTEE CS
                         Pyr_redox  40 eeaskilqeklekngie 56 
                                        e+ k++++ +++ +i 
  gi|242399894|ref|YP_002995319.1| 240 SEMVKLMENTFRDVNIA 256
                                       35555555555555554 PP

>> NAD_binding_11  NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00026      0.36       4      43 ..     241     280 ..     239     283 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00026
                    NAD_binding_11   4 qavKlvnnlllainlaaasEalvlaekaGldpekvlevin 43 
                                       + vKl+ n+   +n+a a E  +la+++G+++ +++e  n
  gi|242399894|ref|YP_002995319.1| 241 EMVKLMENTFRDVNIALANEFALLAHQYGVNIFEAIELAN 280
                                       579****************************999888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (458 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.73u 0.40s 00:00:01.12 Elapsed: 00:00:00.59
# Mc/sec: 2344.77
//
Query:       gi|242399895|ref|YP_002995320.1|  [L=365]
Description: hypothetical protein TSIB_1922 [Thermococcus sibiricus MM 739]
Scores for 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-89  297.8   0.1    1.1e-88  297.5   0.1    1.1  1  DUF354           Protein of unknown function (DUF354)
    0.00033   20.7   0.0    0.00076   19.5   0.0    1.7  1  Glyco_transf_4   Glycosyltransferase Family 4
      0.001   18.0   0.1      0.047   12.5   0.0    2.3  2  LpxB             Lipid-A-disaccharide synthetase
     0.0078   16.2   0.0      0.016   15.2   0.0    1.5  1  Glyco_trans_4_2  Glycosyl transferase 4-like
  ------ inclusion threshold ------
      0.017   14.0   0.0      0.031   13.2   0.0    1.4  1  Epimerase_2      UDP-N-acetylglucosamine 2-epimerase
      0.023   14.4   0.0       0.04   13.6   0.0    1.3  1  Hydrolase_3      haloacid dehalogenase-like hydrolase


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 !  297.5   0.1   3.8e-92   1.1e-88       2     323 ..       5     325 ..       4     347 .. 0.94

  Alignments for each domain:
  == domain 1  score: 297.5 bits;  conditional E-value: 3.8e-92
                            DUF354   2 dvwidltnaphvryfrdlikkfekeGievlltardsGdlaklvklynfvfksiGkhG.vtlkekliesakrvinlsk 77 
                                       ++w+d+ naph ++f+ +i+++ek G evl+t r++  l+ ++++ ++ +  +GkhG  tl+ kli s +r  +l+k
  gi|242399895|ref|YP_002995320.1|   5 KIWVDIVNAPHAHFFKGIIRELEKRGHEVLVTTREFDGLTEILDMLGIDYYIVGKHGgSTLEGKLIASVERQHKLAK 81 
                                       8*******************************************************6489***************** PP

                            DUF354  78 liaevkpdvalakhsvelprvafGlnipvvyvldnehaeaankltlpladeiikpividendlkktGadpnrirrye 154
                                       li e kpd++l k s e prvafGl+ip++   dn+ a a nkl +p+++ +i p++id ++l k Gad n ++  +
  gi|242399895|ref|YP_002995320.1|  82 LIIEEKPDISLYKNSPEAPRVAFGLGIPTIGFADNDTATAVNKLMMPFTQRLIYPKAIDAYELIKCGADVNSLKPLN 158
                                       ***************************************************************************** PP

                            DUF354 155 Gtsevinvqsyeideeilkdlnlkledektilmrpepslasyldadchkdvltkiveklkdridilviprdeeqkei 231
                                       G  e++++  +   ++ lk+l+  l     i+mr ep +a y ++d+ k++l +i+  l d + i+++pr e q++ 
  gi|242399895|ref|YP_002995320.1| 159 GIPELAHLYGFIPTKKPLKELG--LTAYSYIVMRTEPIKANYFNGDAEKSILENIIPLLPD-VPIVLFPRTETQAKR 232
                                       **********************..677899**************************99987.78************* PP

                            DUF354 232 yeevdnviviketvdalsllkrsdlviGaGGtmnreaallGipvvscypqkllsvdkyliekdlmirstdvdeivnt 308
                                       +e ++nv+++ +  d+lsll+ + l+iGaGGtmnrea  lG+p++s yp+kll++ k+li+    ++std  e+ + 
  gi|242399895|ref|YP_002995320.1| 233 FEHFENVMIPDHVTDSLSLLYYAKLMIGAGGTMNREALALGTPTISTYPGKLLAITKWLINLRIKFHSTDPIEVSEK 309
                                       ****************************************************************************9 PP

                            DUF354 309 alrllvdklekkk.li 323
                                       a  l+ ++   +k ++
  gi|242399895|ref|YP_002995320.1| 310 AWELMRKNGAFRKhVR 325
                                       9999998865554333 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   2.5e-07   0.00076      11     101 ..      22     112 ..      15     145 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 2.5e-07
                    Glyco_transf_4  11 LaraLarrGheVtvvtpgddgpleeev....elvvrvprvplpllkrllrslaflrrlrrllkrekpDvvHahspaa 83 
                                       ++r+L +rGheV v t++ dg +e  +    ++++ ++     l ++l  s+    +l++l+ +ekpD+  + +++ 
  gi|242399895|ref|YP_002995320.1|  22 IIRELEKRGHEVLVTTREFDGLTEILDmlgiDYYIVGKHGGSTLEGKLIASVERQHKLAKLIIEEKPDISLYKNSPE 98 
                                       689*********************9999996333444444446777888899999**************87776555 PP

                    Glyco_transf_4  84 lgaallalrrrlgiplVl 101
                                       +  +  a    lgip++ 
  gi|242399895|ref|YP_002995320.1|  99 APRV--AFG--LGIPTIG 112
                                       5333..334..6788775 PP

>> LpxB  Lipid-A-disaccharide synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.013        38      27      65 ..      15      51 ..       9      59 .. 0.81
   2 !   12.5   0.0   1.6e-05     0.047     248     304 ..     243     299 ..     204     316 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.013
                                      T-EEE.EEE-HHHHHTT-EEEEEGGGH------------H CS
                              LpxB 27 elefv.GvggekmeaeglealaemeeisvvGlievlkkll 65
                                       ++f+ G+   ++e+ g e+l++++e+   Gl+e+l  l 
  gi|242399895|ref|YP_002995320.1| 15 HAHFFkGII-RELEKRGHEVLVTTREFD--GLTEILDMLG 51
                                      455443888.89**************98..9****99875 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 1.6e-05
                                       -EEEES-HHHHHHH-SEEEESSTTHHHHHHHTT--EEE--..---HHHHHHHHHHHHHS CS
                              LpxB 248 llllsgealealaaadlaliksGTaaLEaalaktPmvvay..rvkpltfflakrlvkik 304
                                        ++   ++l +l +a+l + + GT++ Ea +++tP++ +y  ++  +t +l+ + +k++
  gi|242399895|ref|YP_002995320.1| 243 DHV--TDSLSLLYYAKLMIGAGGTMNREALALGTPTISTYpgKLLAITKWLINLRIKFH 299
                                       333..358999*****************************5556667777777777765 PP

>> Glyco_trans_4_2  Glycosyl transferase 4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   5.3e-06     0.016       6      77 ..      11      90 ..       8      95 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.3e-06
                   Glyco_trans_4_2  6 anlssvhtlr.lakeLakrgyeVhvitp.kkgakdeleaegihvhrlkvd..rkgpleylka....fklkklikkikPD 76
                                      +n++  h  + +++eL krg+eV v t+  +g  ++l + gi  + + +   +    ++++      kl+kli ++kPD
  gi|242399895|ref|YP_002995320.1| 11 VNAPHAHFFKgIIRELEKRGHEVLVTTReFDGLTEILDMLGIDYYIVGKHggSTLEGKLIASverqHKLAKLIIEEKPD 89
                                      577777766548****************77777**********999954433333667775336645************ PP

                   Glyco_trans_4_2 77 v 77
                                      +
  gi|242399895|ref|YP_002995320.1| 90 I 90
                                      8 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 ?   13.2   0.0     1e-05     0.031     221     283 ..     219     278 ..     191     281 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1e-05
                                       E--..HHHHHHHHHHHHH-TTEEEE----HHHHHHHHHC-SEEEES-HHHHHHHHHCT--EEE CS
                       Epimerase_2 221 pvhnnprtrkrlleeleelenvtlieplgyldflsllknaklvltdSgGiqeEapslgvpvvn 283
                                       p+ + prt+ +++ ++e++env++ +   ++d lsll  akl+++  g++ +Ea +lg+p++ 
  gi|242399895|ref|YP_002995320.1| 219 PIVLFPRTETQAK-RFEHFENVMIPD--HVTDSLSLLYYAKLMIGAGGTMNREALALGTPTIS 278
                                       4444577777775.688888888866..56899***************************995 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.3e-05      0.04      21      89 ..      20      85 ..      15      96 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.3e-05
                                      HHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEEEEGGGTEEECTTTEEEEE--B-HHHHHHHHH CS
                       Hydrolase_3 21 keaikklkekgikvviATGRslravlpvleelgldlpvialNGaliddekgkilykstiskedvkeiik 89
                                      k +i++l+++g++v   T R++ ++ ++l+ lg+d ++++ +G+ +   +gk++++ + +++ +k ii+
  gi|242399895|ref|YP_002995320.1| 20 KGIIRELEKRGHEVL-VTTREFDGLTEILDMLGIDYYIVGKHGGST--LEGKLIASVERQHKLAKLIIE 85
                                      6689*********86.566***********************9999..778888766666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         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: 00:00:00.54
# Mc/sec: 2017.07
//
Query:       gi|242399896|ref|YP_002995321.1|  [L=188]
Description: SpoIIM-like stage II sporulation protein M related [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-31  108.5  19.4    3.7e-31  108.3  19.4    1.0  1  SpoIIM    Stage II sporulation protein M


Domain annotation for each model (and alignments):
>> SpoIIM  Stage II sporulation protein M
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.3  19.4   2.1e-35   3.7e-31       2     156 .]      13     182 ..      12     182 .. 0.83

  Alignments for each domain:
  == domain 1  score: 108.3 bits;  conditional E-value: 2.1e-35
                            SpoIIM   2 lllflvgillgallaa......snfa..eqis.....seskensalslflaifanNlrvalllfllGllllgiptil 65 
                                       + lfl+g llg+l++       +  a  ++++      + ++ +++slf++if+nN+rva++  ++Gl l+g++++ 
  gi|242399896|ref|YP_002995321.1|  13 IGLFLLGCLLGILFTGvspesaE--AlfSNLKsffggTIGENIDKFSLFTFIFFNNTRVAIISAFGGL-LFGVVPAG 86 
                                       679*************6655441..13334447777878899999**********************6.******** PP

                            SpoIIM  66 vllinGfvlGav.aalvaefgglllflllilPhgilelpaiiiagaaglrlgkal.rsrrkalkeakrellklllll 140
                                       +l++nGfv+G+v +++ ++  ++l +ll+i+Phg+le+pa+ +ag  g++   ++ r r+  ++++ + ++k + +l
  gi|242399896|ref|YP_002995321.1|  87 ILFFNGFVVGIVlGYFHSQGESFLRLLLAIVPHGVLEIPAFAVAGLGGVEWYFEVvRGRGTLKERFMNGFVKSMRML 163
                                       **********885666666699*****************************99999777777777666665555555 PP

                            SpoIIM 141 vp...llliAaliEafvtp 156
                                       ++   +lliAa++Ea++tp
  gi|242399896|ref|YP_002995321.1| 164 ALallMLLIAAFVEAYITP 182
                                       55555*************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       708  (0.0394891); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.33s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1168.41
//
Query:       gi|242399897|ref|YP_002995322.1|  [L=96]
Description: Lipoate-protein ligase A, C-terminal section, partial [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-06   27.6   0.7    2.9e-06   27.2   0.6    1.3  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 !   27.2   0.6   1.6e-10   2.9e-06      10      61 ..       7      58 ..       3      85 .. 0.79

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 1.6e-10
                                      EEETTEEEEEEEEEETTEEEEEEEEESBS..SSSHCHHHHHHHTTSBSSHHHHH CS
                    Lip_prot_lig_C 10 krfdwGtvevrldvekgiIkdikiyGDff..gpkdieeleekLigvkyekeaie 61
                                      ++ + G + ++++ ++++  d+ki+GDff   ++ i+elee L+g  +e+  +e
  gi|242399897|ref|YP_002995322.1|  7 HKAKKGLIRFEIEEKDNVAIDVKITGDFFvyPEETIAELEETLKGRNLEE--LE 58
                                      67889************************6559999*********99986..33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); 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 0.33s 00:00:00.88 Elapsed: 00:00:00.55
# Mc/sec: 527.94
//
Query:       gi|242399898|ref|YP_002995323.1|  [L=644]
Description: Arginyl-tRNA synthetase [Thermococcus sibiricus MM 739]
Scores for complete 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-39  134.5   4.6    1.2e-24   86.9   2.3    2.3  2  tRNA-synt_1d     tRNA synthetases class I (R)
    8.6e-35  119.5   0.4    3.3e-34  117.6   0.4    2.1  1  DALR_1           DALR anticodon binding domain
    1.5e-22   80.0   0.8    4.8e-22   78.3   0.1    2.3  2  Arg_tRNA_synt_N  Arginyl tRNA synthetase N terminal domain
    2.2e-05   23.9   0.0    4.6e-05   22.9   0.0    1.6  1  tRNA-synt_1e     tRNA synthetases class I (C) catalytic domai
     0.0019   16.6   0.1     0.0035   15.6   0.1    1.5  1  tRNA-synt_1      tRNA synthetases class I (I, L, M and V)
  ------ inclusion threshold ------
      0.065   12.0   0.3        0.5    9.1   0.1    2.5  3  tRNA-synt_1g     tRNA synthetases class I (M)
      0.087   12.5   0.1       0.17   11.5   0.1    1.5  1  DMSP_lyase       Dimethlysulfonioproprionate lyase
        2.6    7.6   8.2        4.3    6.9   4.4    2.3  2  DUF4795          Domain of unknown function (DUF4795)


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 !   86.9   2.3   5.4e-28   1.2e-24       2     239 ..     106     367 ..     105     379 .. 0.75
   2 !   47.5   0.0   5.2e-16   1.2e-12     230     337 ..     390     496 ..     382     508 .. 0.89

  Alignments for each domain:
  == domain 1  score: 86.9 bits;  conditional E-value: 5.4e-28
                                       HHHHHCCTTTT..---SST-EEEEE----BTTS--BHHHHHHHHHHHHHHHHHHHCT-EEEEEE--B-SSTCHH.HH CS
                      tRNA-synt_1d   2 vssiLvqkrkl.qkksrekkkvvvdfssPniakemhvGhLrstiiGdavsrlleflGydvirlnhvGDWGtqfG.lL 76 
                                       v++iL +++++ + k +e kkv+v+++s n  k++h+Gh r +++Gd+v+r++ +lGy+v   n++ D G qf  +L
  gi|242399898|ref|YP_002995323.1| 106 VKEILQKGEHFgESKIGEGKKVIVEHTSVNPTKPLHMGHARNAVLGDTVARIMRALGYNVEVQNYIDDLGVQFAqVL 182
                                       889999999988899**********************************************************7234 PP

                                       HHHHH.........HHTTTTTTS-----S..CCCHHHHHHHHCCCSHCCCHHHHHHHHHHHCT-HHHHHHHHH.HHH CS
                      tRNA-synt_1d  77 iayle.........kkqdekllqeqelqd..LeafykeakkdydeeeifaerarnyvvkLqsgdedirklwkl.lvd 141
                                         yl+         k+ +ek l+++++ d  L  +y+e++k+++e  +++++ r+++++L+++d++i +  ++   d
  gi|242399898|ref|YP_002995323.1| 183 WGYLNmreefesiiKELKEKGLSKEDILDhaLGLLYVEVHKKMEEYPEVEREIRSIMKELEKEDNEISEKGRKlAED 259
                                       44443111111222334566666777755457889*****************************9977665552678 PP

                                       HHHHHHHHHHHHCT---EC.--CC..CCCCCHHHHHHHHHCTT...-EEE..CTTCEEEEECCC...TSSCCEECC- CS
                      tRNA-synt_1d 142 itrtelqklydrldvtlie.rGes..lykeslneivkelkkkg...lvke..sdGalvvfldef...gkrlgvvvqk 207
                                       +++ +++ +y rl ++      es  +    ++e  k +++++    ++e    Ga ++ l +     ++   v+ +
  gi|242399898|ref|YP_002995323.1| 260 VVKAQMKTTY-RLSISYDLlSWESdiVRSGIFEESYKRIQENShfeWAQEgkYKGAFIMKLGDLfpdLENPDTVLIR 335
                                       8888766655.56665433334555455556666666666654111455522579999999988564344456999* PP

                                       TTS-B-HHHHHHHHHHHHHHTT--SEEEEEEE CS
                      tRNA-synt_1d 208 sDGgylytttDiaaakerkeelkadkvlyvid 239
                                       sDG+ +yt +Dia    +  +  ad+   v d
  gi|242399898|ref|YP_002995323.1| 336 SDGTATYTGKDIAYHLWKFGKVSADMRYKVWD 367
                                       *************9999998888888766655 PP

  == domain 2  score: 47.5 bits;  conditional E-value: 5.2e-16
                                       --SEEEEEEECCCHHHHHHHHHHHHCTTSSTTTSEEEEEEE--EE-TTSSBSBCSSSTC-..BHHHHHHHHHHHHHH CS
                      tRNA-synt_1d 230 kadkvlyvidsrqslhlqqiflilkkigyvpeskdlehanfGmvlgkdkkkfktrkGetv..kLadlLdealeralq 304
                                       +a+ v+ v+ s+q    + +  +lk +gy+ e  + +h  +  v+ + + kf+ rkG  +   ++++Ldea++ra++
  gi|242399898|ref|YP_002995323.1| 390 NAEIVINVVGSEQRYEQMAVAYALKLLGYEEEYHNFHHLAYEHVV-RPEGKFSGRKGTWIgfTVDEVLDEAVKRAKE 465
                                       5778999******9999999999*******************995.55567******98733679************ PP

                                       HHCCCCCCTS-CCCCHCHHHHHHHHHHHHCCCC CS
                      tRNA-synt_1d 305 likeknkdkvlqadelekvaeavgvgaikyaDl 337
                                       l++ekn+   l+ +e+ek+ae vgvga++y+ +
  gi|242399898|ref|YP_002995323.1| 466 LVEEKNPS--LSGEEKEKIAEIVGVGAVRYNLV 496
                                       ********..*******************9755 PP

>> DALR_1  DALR anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.6   0.4   1.5e-37   3.3e-34       1     119 []     522     644 .]     522     644 .] 0.98

  Alignments for each domain:
  == domain 1  score: 117.6 bits;  conditional E-value: 1.5e-37
                                       HHHHHHHHHHHHHHTTCTTCCCCHCCHCC.....S-SHHHHHHHHHHHTHHHHHHHHHHHT-THHHHHHHHHHHHHH CS
                            DALR_1   1 vqyahaRiksilrkaeeegekleeealal.....leeeeekeLlkalaqfpevleeaaeelephklaeylyeLaatf 72 
                                       +qyahaR++sil+ka eeg++ +++al+        +++ekeL+k + +fpe++++a ++ +ph la+y+ eLa+ f
  gi|242399898|ref|YP_002995323.1| 522 IQYAHARCASILKKAMEEGINIDKDALLKnadfsKLDNKEKELIKIISKFPEIVKTAGRDIKPHLLATYANELAMVF 598
                                       7***********************999999**988899*************************************** PP

                                       HHHHHHCTSTTSCTHHH.HHHHHHHHHHHHHHHHHHHHTT----S-- CS
                            DALR_1  73 hkfYnkervlkeeeeelaaaRLaLvkavrqvLangLdlLGieapekm 119
                                       ++fY + +vlk+ee ++ + RL Lv a++qvL+n+L l+Gieape m
  gi|242399898|ref|YP_002995323.1| 599 NSFYMALPVLKAEEGVR-ELRLLLVIATKQVLKNTLGLMGIEAPEVM 644
                                       ***************99.***************************98 PP

>> Arg_tRNA_synt_N  Arginyl tRNA synthetase N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.3   0.1   2.2e-25   4.8e-22       3      85 .]      14      96 ..      12      96 .. 0.93
   2 ?   -3.2   0.0         6   1.4e+04      51      62 ..     251     262 ..     236     268 .. 0.62

  Alignments for each domain:
  == domain 1  score: 78.3 bits;  conditional E-value: 2.2e-25
                                      HHHHHHHHHHHHHSS-HHHHGGG-E-.SSGGG-SEEEEGGGG--TT-..-HHHHHHHHHHT---TTT..EEEEEEETT. CS
                   Arg_tRNA_synt_N  3 lkeaiaealkkaagadleeeeiviekpknpkfGDyatnvamqlakklkknPreiAeeiaekleksei..iekvevagpG 79
                                      lk++i+e l+k    ++ e ei  ++++n +fGD+at va+ lak +kk+Pr iA+eia++le++    i+kvevag+G
  gi|242399898|ref|YP_002995323.1| 14 LKTIISEMLEKE--GKTWEGEILFDETPNMEFGDFATTVAFLLAKVFKKAPRIIAQEIASNLEDKLPeyIAKVEVAGAG 90
                                      789999999999..5788889****9**************************************95556********** PP

                                      EEEEEE CS
                   Arg_tRNA_synt_N 80 FiNffL 85
                                      +iNffL
  gi|242399898|ref|YP_002995323.1| 91 YINFFL 96
                                      *****8 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 6
                                       .-HHHHHHHHHH CS
                   Arg_tRNA_synt_N  51 knPreiAeeiae 62 
                                       ++ r++Ae++++
  gi|242399898|ref|YP_002995323.1| 251 EKGRKLAEDVVK 262
                                       356777777776 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 !   22.9   0.0   2.1e-08   4.6e-05      23      58 ..     140     172 ..     122     260 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 2.1e-08
                                       -BHHHHHHHHHHHHHHHHHHHTT-EEEEEEEBB--S CS
                      tRNA-synt_1e  23 shlGhaRslvafDilrrilqalgYdvqfvqnvtDid 58 
                                        h+GhaR++v  D ++ri++algY+v+ vqn    d
  gi|242399898|ref|YP_002995323.1| 140 LHMGHARNAVLGDTVARIMRALGYNVE-VQNYI--D 172
                                       7*************************9.67753..3 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 !   15.6   0.1   1.6e-06    0.0035      33      80 ..     135     182 ..     111     247 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.6e-06
                       tRNA-synt_1  33 yvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaieakv 80 
                                       + t  lH+Gha + +l d+v r+ r  G++v+ +  +D  G+   +++
  gi|242399898|ref|YP_002995323.1| 135 NPTKPLHMGHARNAVLGDTVARIMRALGYNVEVQNYIDDLGVQFAQVL 182
                                       556779********************************9999877766 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 ?    9.1   0.1   0.00022       0.5      11      49 ..     137     175 ..     128     181 .. 0.84
   2 ?   -0.9   0.1      0.24   5.3e+02      63     120 ..     253     313 ..     240     327 .. 0.77
   3 ?   -3.1   0.0       1.1   2.5e+03     340     372 ..     481     512 ..     478     513 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00022
                                       SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---S CS
                      tRNA-synt_1g  11 ngklHlGhllevisaDifaRykrlrgeevlfvcgtDehG 49 
                                       + +lH+Gh+++++ +D +aR  r+ g++v      D  G
  gi|242399898|ref|YP_002995323.1| 137 TKPLHMGHARNAVLGDTVARIMRALGYNVEVQNYIDDLG 175
                                       5689***********************997666666555 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.24
                                       HHHHHHHHHHHHHHHHHHTT---SEEEETTSHHHHHHHHHHHHHHHHTT-EE...EEEEEE CS
                      tRNA-synt_1g  63 peelvekvheeikelfkklnisfdkygrttseehkelvqeifkklkekgliy...ekeieq 120
                                        ++l+e+v +++ ++  +l+is+d  +  ++   + + +e +k+++e+ +++   e+++++
  gi|242399898|ref|YP_002995323.1| 253 GRKLAEDVVKAQMKTTYRLSISYDLLSWESDIVRSGIFEESYKRIQENSHFEwaqEGKYKG 313
                                       568899999999999999*******999999999999999999999999985221444444 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 1.1
                                       HHHHHH-HHHHHHHHHHHS-TTS-EEE-HHHHH CS
                      tRNA-synt_1g 340 ealerldadllRYylaaeapekkDldfswedfv 372
                                       +++e + + ++RY l++ +pek  + f+wed+ 
  gi|242399898|ref|YP_002995323.1| 481 KIAEIVGVGAVRYNLVKYSPEK-IITFRWEDVL 512
                                       5667788999*****9998875.5899999875 PP

>> DMSP_lyase  Dimethlysulfonioproprionate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   7.7e-05      0.17      54     156 ..     368     468 ..     359     475 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.7e-05
                        DMSP_lyase  54 alepaLeweqsyseadasadfldkyayaeivGprglekrddvalGlvllaPkvrYPdHhhaaeelYlvlsggaefrq 130
                                       +++++ +w++ + ++ ++  f+++     +vG +   ++  va  l ll+ + +Y + hh a e   v  +g  f+ 
  gi|242399898|ref|YP_002995323.1| 368 KINDHKTWTTAKDGERMPGRFANAEIVINVVGSEQRYEQMAVAYALKLLGYEEEYHNFHHLAYEHV-VRPEG-KFSG 442
                                       6778889*****************************************************998864.44455.7999 PP

                        DMSP_lyase 131 geaewlsrgiGevifnepgikhamrs 156
                                        ++ w+ + ++ev+ ++ +    +  
  gi|242399898|ref|YP_002995323.1| 443 RKGTWIGFTVDEVLDEAVKRAKELVE 468
                                       ********999998666665555555 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   4.4    0.0019       4.3      89     155 ..     188     259 ..     185     272 .. 0.79
   2 ?    1.4   0.1     0.089     2e+02      65     112 ..     536     583 ..     532     595 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0019
                           DUF4795  89 akkeLekmleellekleeqeealkkaldtLqeelkekld.....rlelepLkeqleerlkelqkelqeamek 155
                                       + +e+e +++el ek  ++e+ l+ al  L  e+ +k++     + e+ ++ ++le++ +e++++ ++ +e 
  gi|242399898|ref|YP_002995323.1| 188 MREEFESIIKELKEKGLSKEDILDHALGLLYVEVHKKMEeypevEREIRSIMKELEKEDNEISEKGRKLAED 259
                                       334555555666666669************************9999**********9999999887766554 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.089
                           DUF4795  65 eeelaekadkeaLatkvsrdqfDeakkeLekmleellekleeqeealk 112
                                       ++e+ +  dk+aL + ++ +++D++ keL k++++  e ++ + +++k
  gi|242399898|ref|YP_002995323.1| 536 AMEEGINIDKDALLKNADFSKLDNKEKELIKIISKFPEIVKTAGRDIK 583
                                       57777888999999999999***********99998888887777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (644 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1230  (0.0686039); expected 358.6 (0.02)
Passed bias filter:                      808  (0.0450667); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); 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: 0.87u 0.35s 00:00:01.22 Elapsed: 00:00:00.57
# Mc/sec: 3396.97
//
Query:       gi|242399899|ref|YP_002995324.1|  [L=295]
Description: Dihydrodipicolinate synthase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      2e-62  210.5   0.0    2.2e-62  210.4   0.0    1.0  1  DHDPS        Dihydrodipicolinate synthetase family
  ------ inclusion threshold ------
       0.01   16.1   0.0      0.018   15.3   0.0    1.4  1  DHquinase_I  Type I 3-dehydroquinase


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 !  210.4   0.0   2.5e-66   2.2e-62       3     287 ..       2     289 ..       1     291 [. 0.94

  Alignments for each domain:
  == domain 1  score: 210.4 bits;  conditional E-value: 2.5e-66
                                       SEEEEE----B-TTSSB-HHHHHHHHHHHHHCT-SEEEESSCCCTGGGS-HHHHHHHHHHHHHHHTTSSEEEEE--- CS
                             DHDPS   3 sgiitalvtpfdedgkldkealrklieflinkgvdglvvaGttGEsatlsteekeqlveiaveaakgripviagvGs 79 
                                       +g++++lvtpf+ed  +d+ al++ i++l + gv g+++  ttGE+ +l+ ee++ l+e+ +e++      + g+ s
  gi|242399899|ref|YP_002995324.1|   2 RGVVVPLVTPFNEDYSIDFPALEEHINYLQKIGVHGIFINATTGEFTSLNNEERKLLAEKGRELVSSAFY-LVGTAS 77 
                                       799**************************************************************98776.568899 PP

                                       SSHHHHHHHHHCCCCCT-SEEEEE---SS---HHHHHHHHHHHHHCHSS-EEEEE-HHHHSHHHHHHHHHHHHT.ST CS
                             DHDPS  80 nstseaiklakkaeeaGadgvlavtPYYnkpsqeglyqhfkaiieatdlpvilYnvpsrtgadlspetvkrLae.le 155
                                        +t e i+l+k+a+e Gad v++ +PYY + +   l +h+  ++e+t+ p+ilYn+ps     +s+  +krLa  ++
  gi|242399899|ref|YP_002995324.1|  78 TNTFEVIELTKHAQEIGADYVVIAPPYYCPLNDDALFKHYSMVAEKTEIPIILYNIPSC-ANPMSVSLIKRLALeYS 153
                                       9********************************************************65.568**********88** PP

                                       TEEEEEE-SS-CTHHHHHHCCC...STTSEEEES-GGGHHHHHHTT-SEEEESCHHCHHHHHHHHHHHHHTT-HHHH CS
                             DHDPS 156 nivgvKeavgdleevikikkev...gkdlviysGddelllsalslGadGvisvtsniagermrqlikalkeGdlaea 229
                                       ni+g+Ke+++++++v +++ ev   +kd+ ++ G d+++l++l lG+dG i + +n+a+e+  +l+ka +e +++ a
  gi|242399899|ref|YP_002995324.1| 154 NIAGIKETIDSINHVRNVIFEVkreRKDFKVFTGLDQHFLNTLLLGGDGGIMACANFAPELHLELYKAFEEKNFEMA 230
                                       ************888877655422279************************************************** PP

                                       HHHHHHHHHHHHHCCCC.SCCHHHHHHHHCTTSSSBB.--TTS--S-HHHHHHHHHHHH CS
                             DHDPS 230 aelnekllplikilfae.pnvilvktalellGlvveatlrkPltpleeeekeeleallk 287
                                        e+ +kl ++ k +  + ++ + +k a+++ G+  +++lr+P+     e ke++++ll+
  gi|242399899|ref|YP_002995324.1| 231 MEYAQKLAKVSKVYELAsSFGSAIKIAMNIRGFSIKPVLRPPYIMDRGEVKERIKQLLT 289
                                       *************98886899***********************999999999998886 PP

>> DHquinase_I  Type I 3-dehydroquinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.0     2e-06     0.018     107     185 ..      53     132 ..      23     135 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2e-06
                                       HHHHHHHHTT-EEEEEEEESS----HH..HHHHHHHHHHHTT-SEEEEEE--SSHHHHHHHHHHHHHHHHHT-SS-E CS
                       DHquinase_I 107 rlieekreggtkvIvSyhdfegtpsae..elkallekmqalgaDivKiavmaksieDvlrllsltseakeekdeapl 181
                                       + ++   e+g  ++ S     gt s +  e+++l++++q++gaD v ia +  +  + ++l++ +s + +ek+e+p+
  gi|242399899|ref|YP_002995324.1|  53 EERKLLAEKGRELVSSAFYLVGTASTNtfEVIELTKHAQEIGADYVVIAPPYYCPLNDDALFKHYS-MVAEKTEIPI 128
                                       4455556779999999999*******999***********************************96.5555789*** PP

                                       EEEE CS
                       DHquinase_I 182 Iama 185
                                       I ++
  gi|242399899|ref|YP_002995324.1| 129 ILYN 132
                                       *998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); 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 0.33s 00:00:00.93 Elapsed: 00:00:00.53
# Mc/sec: 1669.49
//
Query:       gi|242399900|ref|YP_002995325.1|  [L=415]
Description: Peptide chain release factor subunit 1 [Thermococcus sibiricus MM 739]
Scores for complete 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-47  159.2   0.0    1.2e-46  158.3   0.0    1.5  1  eRF1_2          eRF1 domain 2
      2e-34  118.4   1.8    2.9e-34  117.9   0.6    1.9  2  eRF1_3          eRF1 domain 3
    1.9e-15   57.4   0.2      6e-15   55.7   0.0    2.0  2  baeRF_family10  Bacterial archaeo-eukaryotic release factor f
    6.6e-15   55.6   0.0    2.2e-14   53.9   0.0    1.9  2  acVLRF1         Actinobacteria/chloroflexi VLRF1 release fact
    1.9e-10   40.9   0.0    3.1e-10   40.1   0.0    1.4  1  eRF1_1          eRF1 domain 1
     0.0055   16.9   1.6       0.81    9.9   0.1    2.4  2  MCM6_C          MCM6 C-terminal winged-helix domain
     0.0055   16.7   0.1      0.012   15.7   0.1    1.6  1  HypA            Hydrogenase/urease nickel incorporation, meta
  ------ inclusion threshold ------
      0.026   14.6   0.3      0.054   13.6   0.3    1.5  1  zf-RRPl_C4      Putative ribonucleoprotein zinc-finger pf C4 
      0.027   15.0   0.0      0.076   13.6   0.0    1.8  1  baeRF_family12  Bacterial archaeo-eukaryotic release factor f
      0.028   13.7   0.0         19    4.6   0.0    3.4  3  SeqA_N          SeqA protein N-terminal domain
      0.048   13.8   1.0       0.11   12.7   0.3    1.9  2  Zn-ribbon_8     Zinc ribbon domain
       0.11   12.6   0.4       0.19   11.8   0.4    1.3  1  DZR             Double zinc ribbon
       0.59    9.6   2.8        7.2    6.2   0.3    2.3  2  zf-ribbon_3     zinc-ribbon domain


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 !  158.3   0.0   8.9e-50   1.2e-46       2     132 ..     140     271 ..     139     272 .. 0.99

  Alignments for each domain:
  == domain 1  score: 158.3 bits;  conditional E-value: 8.9e-50
                                       EEEEEEETTEEEEEEEESSCEEEEEEEE------BSTTBSCCCCHHHHHHHHHHHHHHHHHHHHHHHHH.HCHTTTE CS
                            eRF1_2   2 vglivldegeAtigllkgsrtevlkkievsvPkKhkrGgqsarrfeRlreekleeflkkvaeaankafl.lvdkdkl 77 
                                       +gli ++++eAtig+l+g+++ev++ ++++vP+K+++Ggqsarr+eR+re++++ef+k+++e+a++ fl l++kd+l
  gi|242399900|ref|YP_002995325.1| 140 YGLITVEKNEATIGILRGKKIEVIEDLTSNVPGKTRAGGQSARRYERIREQEAHEFMKRIGEHASSVFLpLLEKDEL 216
                                       8**************************************************************************** PP

                                       SEEEEEESSTHHHHHHHHHHHHHHHHTCCEEEEE-S-TSCHHHHHHHHCCHHHHC CS
                            eRF1_2  78 kgiilagpgfvkeefldkdlldaelkkkviklvdvsyggesglnevlekaaevlk 132
                                       kgii++gpg++keef+++++l++el+k+++ +vd+sy+ge+gl+e++eka++ l 
  gi|242399900|ref|YP_002995325.1| 217 KGIIIGGPGPTKEEFVEGEYLHHELRKRILGVVDISYHGEYGLRELVEKASDILR 271
                                       ***************************************************9986 PP

>> eRF1_3  eRF1 domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       9.1   1.3e+04      12      36 ..      43      67 ..      35      80 .. 0.49
   2 !  117.9   0.6   2.1e-37   2.9e-34       2     113 .]     276     414 ..     275     414 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 9.1
                                      HHHHHCTCSSEEESHHHHHHHHHTT CS
                            eRF1_3 12 leelakdtgkavYGveevlkalemg 36
                                      +++l+++ g+a   + ++ + + +g
  gi|242399900|ref|YP_002995325.1| 43 MQQLREEYGTAQNIKSKTTRKNVLG 67
                                      4444444333333333333333333 PP

  == domain 2  score: 117.9 bits;  conditional E-value: 2.1e-37
                                       HHHHHHHHHHHHHHHCTCSSEEESHHHHHHHHHTT-EEEEEEEHCHHTSSSH.HHHHS................... CS
                            eRF1_3   2 iqekklleefleelakdtgkavYGveevlkalemgAvetLLvseelersrdt.lkekv................... 58 
                                       ++e+kl+++f+++l kdtg+++YG++ev+kale+gAv+ LL+se ++r r++ l++++                   
  gi|242399900|ref|YP_002995325.1| 276 VKERKLVQQFFKHLVKDTGLITYGEKEVRKALELGAVDILLLSEGYDRVRVKaLCNNCgweelktmteaefelykkn 352
                                       79**************************************************999999******************* PP

                                       ....-HHH-HHHHHH...HHHHHHHHHHHTT-EEEEE-TTSHHHHHHHHHTTTEEEEESS-- CS
                            eRF1_3  59 ....ketgeelelve...lieelvenveesgakveiisseseeGeqlvkafgGiaaiLRykv 113
                                           +++++++  ve   ++eel++ +ee ga+veiis ++eeG+q++kafgGiaaiLRyk+
  gi|242399900|ref|YP_002995325.1| 353 lkacPKCNSQNISVEkwdVAEELIKIAEEGGAEVEIISLDTEEGQQFYKAFGGIAAILRYKL 414
                                       ****88888888888888******************************************96 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 !   55.7   0.0   4.3e-18     6e-15       4     138 ..     128     269 ..     126     278 .. 0.86
   2 ?   -2.9   0.0       5.2   7.1e+03      75     104 ..     370     399 ..     370     403 .. 0.73

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 4.3e-18
                    baeRF_family10   4 apLlealdeyerygvvlvdreraRlfevylgeleeveevegevpgrtktggwksqdrfqrreeeqaerhlkevAell 80 
                                       +pL e l+  + yg++ v++++a +   ++ ++e  e+++++vpg+t++gg+ s +r++r +e+ a++++k+++e++
  gi|242399900|ref|YP_002995325.1| 128 EPLEEMLRVKDAYGLITVEKNEATIGILRGKKIEVIEDLTSNVPGKTRAGGQ-SARRYERIREQEAHEFMKRIGEHA 203
                                       79**************************************************.************************ PP

                    baeRF_family10  81 akll....eergverlvlgGdeeetaall..drlpkalrarvvgtlplpv.da.saaaVlekaeea 138
                                        +++    e+++++ +++gG+   +++++  + l+ +lr+r+ g ++++  ++   ++++eka ++
  gi|242399900|ref|YP_002995325.1| 204 SSVFlpllEKDELKGIIIGGPGPTKEEFVegEYLHHELRKRILGVVDISYhGEyGLRELVEKASDI 269
                                       *97533327788*********777777762357***********9866664445777777777665 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5.2
                    baeRF_family10  75 evAellaklleergverlvlgGdeeetaal 104
                                       +vAe l k++ee g+e  +++ d+ee +++
  gi|242399900|ref|YP_002995325.1| 370 DVAEELIKIAEEGGAEVEIISLDTEEGQQF 399
                                       589999999999998877766666666555 PP

>> acVLRF1  Actinobacteria/chloroflexi VLRF1 release factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.9   0.0   1.6e-17   2.2e-14       3     104 ..     140     243 ..     138     272 .. 0.80
   2 ?   -1.2   0.0       1.7   2.3e+03      59      89 ..     263     307 ..     254     314 .. 0.58

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 1.6e-17
                           acVLRF1   3 lgvllvrrggfavgvveggelvaskvgtrdvqgrtaaGGwSqqRfaRrrenqadalleavaeaaarllaeesae... 76 
                                       +g++ v +   ++g+++g++++  +  t++v g+t+aGG+S +R++R re++a + ++++ e+a  ++ +  ++   
  gi|242399900|ref|YP_002995325.1| 140 YGLITVEKNEATIGILRGKKIEVIEDLTSNVPGKTRAGGQSARRYERIREQEAHEFMKRIGEHASSVFLPLLEKdel 216
                                       788999999999********************************************************554444456 PP

                           acVLRF1  77 ..vvlgGdrslvaevledarlaplatlare 104
                                         +++gG+  + +e+ e + l   ++  r+
  gi|242399900|ref|YP_002995325.1| 217 kgIIIGGPGPTKEEFVEGEYL---HHELRK 243
                                       67*************999663...333333 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.7
                           acVLRF1  59 leavaeaaarllaeesae..................vvlgGdrslvaev 89 
                                       +e++ + ++++ a                       +++ G++++++++
  gi|242399900|ref|YP_002995325.1| 263 VEKASDILREHEA----VkerklvqqffkhlvkdtgLITYGEKEVRKAL 307
                                       4444444444431....11123445555555556778888888888876 PP

>> eRF1_1  eRF1 domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.1   0.0   2.3e-13   3.1e-10       5     128 ..      16     133 ..      12     134 .. 0.94

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 2.3e-13
                                       EE..CTBTTSCCEEEEEE-SCHHHHHHHHHCHTTHEEEEEEEECHHH.......--CEEEEEEEEEEEEEEECTT.. CS
                            eRF1_1   5 kr..dlekdgsgsvtLipeddedlwhlynliapgdsvrastvrkvqresstgsreservklkLtikvekvdfdkd.. 77 
                                       ++  +++++ +++v+L+++ d dl ++++ ++++++++ ++++k +r         ++v+ +L+  ++ ++++ +  
  gi|242399900|ref|YP_002995325.1|  16 EElkKIRGRATELVSLYIPADYDLNKVMQQLREEYGTAQNIKSKTTR---------KNVLGALERAMQHLKLYRQtp 83 
                                       4455999**************************************99.........9****************9988 PP

                                       .SSEEEEEEEEEEGGGG--TTSEEEEEE-TTSEEEEEECE.ESHHHHHHHHHH CS
                            eRF1_1  78 .agvlrisGkvieenehvklgafhtldlelkrpftiikee.wdsfalerLkea 128
                                        +g+  + G v e+++   +     + +++++p++++ ++ ++ f +e+L+e+
  gi|242399900|ref|YP_002995325.1|  84 eTGLALFVGNVSEQEG---VSDIRVFAIVPPEPLNVRLYRcDQTFVTEPLEEM 133
                                       88************99...99*****************999999*******98 PP

>> MCM6_C  MCM6 C-terminal winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.1     0.011        15      29      85 ..      19      75 ..       6     112 .. 0.77
   2 !    9.9   0.1   0.00059      0.81      45      83 ..     264     302 ..     261     331 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.011
                            MCM6_C 29 eeegiekeeLvewYleqieeeleseeeleeekklvekvlkrLvkdkvLlevreeaee 85
                                      ++   +++eLv+ Y+ +  +  + +++l+ee  +++++ ++  + +vL +++++ ++
  gi|242399900|ref|YP_002995325.1| 19 KKIRGRATELVSLYIPADYDLNKVMQQLREEYGTAQNIKSKTTRKNVLGALERAMQH 75
                                      44555789*********9999999***************999999999999887776 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00059
                            MCM6_C  45 qieeeleseeeleeekklvekvlkrLvkdkvLlevreea 83 
                                       ++++++  e+e  +e+klv++  k+Lvkd  L+   e++
  gi|242399900|ref|YP_002995325.1| 264 EKASDILREHEAVKERKLVQQFFKHLVKDTGLITYGEKE 302
                                       567889999***********************9987766 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 !   15.7   0.1   8.4e-06     0.012      64     100 ..     321     367 ..     261     379 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 8.4e-06
                                       EEEE--EEEETTTS-EEECHH.HHH..........S-TTTSSS-EEEE CS
                              HypA  64 ieevpvkvrCreCgkefelee.kal..........rCpkCgsadveiv 100
                                       +++v+vk+ C++Cg e  ++  + +           CpkC+s+++++ 
  gi|242399900|ref|YP_002995325.1| 321 YDRVRVKALCNNCGWEELKTMtE-AefelykknlkACPKCNSQNISVE 367
                                       67899*********433222222.24588999999********99886 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 ?   13.6   0.3   3.9e-05     0.054      51      94 ..     326     367 ..     303     378 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.9e-05
                        zf-RRPl_C4  51 rdkLCtkCkeknekekeircetfeeylkklklCkeCkervekvl 94 
                                        + LC++C  ++ k  +++  +fe y k lk C +C +++ +v 
  gi|242399900|ref|YP_002995325.1| 326 VKALCNNCGWEELK--TMTEAEFELYKKNLKACPKCNSQNISVE 367
                                       478*****977665..566666****************998765 PP

>> baeRF_family12  Bacterial archaeo-eukaryotic release factor family 12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   5.5e-05     0.076      42     127 ..     165     254 ..     162     265 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.5e-05
                    baeRF_family12  42 egssdrpGrsssggagrsameetdfkeqeeerFakeladeLkk....rakegkferlvlvappetlgelrkh..lhk 112
                                       +++s+ pG+++ gg++  a   +  +eqe ++F+k++ +         +++++ + +++ +p +t +e+ +   lh 
  gi|242399900|ref|YP_002995325.1| 165 DLTSNVPGKTRAGGQS--ARRYERIREQEAHEFMKRIGEHASSvflpLLEKDELKGIIIGGPGPTKEEFVEGeyLHH 239
                                       7788999997777777..22344444458999****99999884444689*******************86444*** PP

                    baeRF_family12 113 evkkrlvgeiaknlt 127
                                       e++kr+ g ++  + 
  gi|242399900|ref|YP_002995325.1| 240 ELRKRILGVVDISYH 254
                                       ******999988776 PP

>> SeqA_N  SeqA protein N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.014        19       2      25 ..     158     181 ..     157     183 .. 0.94
   2 ?    1.4   0.0      0.14     2e+02      19      28 ..     197     206 ..     195     212 .. 0.83
   3 ?    3.0   0.1     0.045        63      23      30 ..     264     271 ..     259     272 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.014
                            SeqA_N   2 KtIevDeeLYrYIasntqaiGESa 25 
                                       K+Iev e+L + + ++t+a G Sa
  gi|242399900|ref|YP_002995325.1| 158 KKIEVIEDLTSNVPGKTRAGGQSA 181
                                       99****************999998 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.14
                            SeqA_N  19 qaiGESaSdI 28 
                                       ++iGE aS +
  gi|242399900|ref|YP_002995325.1| 197 KRIGEHASSV 206
                                       79******86 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.045
                            SeqA_N  23 ESaSdILR 30 
                                       E aSdILR
  gi|242399900|ref|YP_002995325.1| 264 EKASDILR 271
                                       89*****9 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       6.1   8.4e+03       6      12 ..     119     124 ..     119     134 .. 0.62
   2 ?   12.7   0.3   7.8e-05      0.11       8      35 ..     330     363 ..     324     365 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 6.1
                       Zn-ribbon_8   6 YrCeeCg 12 
                                       YrC++  
  gi|242399900|ref|YP_002995325.1| 119 YRCDQ-T 124
                                       88887.3 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 7.8e-05
                       Zn-ribbon_8   8 CeeCghefevlqsisdap.......ltaCPeCgs.e 35 
                                       C++Cg   e+l ++++a+       l+aCP+C+s +
  gi|242399900|ref|YP_002995325.1| 330 CNNCG--WEELKTMTEAEfelykknLKACPKCNSqN 363
                                       *****..999999999999999998888****9955 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.4   0.00014      0.19      13      39 ..     328     364 ..     322     369 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00014
                               DZR  13 rfCseCgtk.lkavaa.........edrCpsCgekvd 39 
                                         C++Cg + lk +++          ++Cp+C++++ 
  gi|242399900|ref|YP_002995325.1| 328 ALCNNCGWEeLKTMTEaefelykknLKACPKCNSQNI 364
                                       58*****98798888799***************9965 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.1     0.038        53       5      10 ..     330     335 ..     327     340 .. 0.82
   2 ?    6.2   0.3    0.0052       7.2       3      13 ..     354     365 ..     352     367 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.038
                       zf-ribbon_3   5 CPnCGa 10 
                                       C+nCG+
  gi|242399900|ref|YP_002995325.1| 330 CNNCGW 335
                                       999998 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0052
                       zf-ribbon_3   3 vrCPnCGa.pls 13 
                                       + CP+C++ ++s
  gi|242399900|ref|YP_002995325.1| 354 KACPKCNSqNIS 365
                                       67*****97776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1235  (0.0688828); expected 358.6 (0.02)
Passed bias filter:                      948  (0.0528752); expected 358.6 (0.02)
Passed Vit filter:                       114  (0.00635841); 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: 0.74u 0.34s 00:00:01.08 Elapsed: 00:00:00.53
# Mc/sec: 2363.75
//
Query:       gi|242399901|ref|YP_002995326.1|  [L=78]
Description: hypothetical protein TSIB_1928 [Thermococcus sibiricus MM 739]
Scores for complete 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   29.3  23.2    9.6e-07   28.9  23.2    1.2  1  BofA            SigmaK-factor processing regulatory protein B


Domain annotation for each model (and alignments):
>> BofA  SigmaK-factor processing regulatory protein BofA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9  23.2   5.4e-11   9.6e-07       2      74 ..       8      77 ..       4      78 .] 0.86

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 5.4e-11
                              BofA  2 gilllllvikllkkplkillkllinavlGlvlLflvNllgavfglhipiNlitaliagflGipGvilLillkl 74
                                      ++ll ++++ +lk  + +l ++++na++Gl+lL ++N+lg+    h+ ++li+ li++++Gi Gv+lL++l++
  gi|242399901|ref|YP_002995326.1|  8 IVLLTIAAAIVLKLTFSVLKWMAMNAIVGLILLGILNYLGI---AHVEMSLINFLIVAVGGILGVFLLLFLSY 77
                                      4566666677777888889999***************6666...48*************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1339  (0.0746835); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.33s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 459.98
//
Query:       gi|242399902|ref|YP_002995327.1|  [L=192]
Description: hypothetical protein TSIB_1929 [Thermococcus sibiricus MM 739]
Scores for 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-07   29.2   0.0     0.0057   17.0   0.0    2.4  2  HEAT_2        HEAT repeats
    0.00032   20.8   0.0    0.00077   19.6   0.0    1.7  1  RTP1_C1       Required for nuclear transport of RNA pol II C-
     0.0031   16.1   0.0       0.77    8.2   0.0    2.0  2  Adaptin_N     Adaptin N terminal region
  ------ inclusion threshold ------
      0.015   15.4   0.2          5    7.1   0.1    2.1  2  Cnd1          non-SMC mitotic condensation complex subunit 1
      0.053   12.8   0.1       0.13   11.5   0.0    1.6  2  Rcd1          Cell differentiation family, Rcd1-like
      0.075   12.4   0.1        1.9    7.8   0.0    2.7  3  DUF1186       Protein of unknown function (DUF1186)
      0.089   12.9   0.1        1.5    9.0   0.0    2.6  3  V-ATPase_H_C  V-ATPase subunit H
       0.11   13.1   0.1        1.2    9.8   0.0    2.6  3  HEAT_EZ       HEAT-like repeat
       0.16   12.3   0.1        3.6    8.1   0.0    3.0  4  HEAT          HEAT repeat


Domain annotation for each model (and alignments):
>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0   0.00052         1      25      58 ..      28      61 ..      21      71 .. 0.88
   2 !   17.0   0.0   2.9e-06    0.0057       7      74 ..      83     160 ..      77     164 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00052
                            HEAT_2 25 grignpealpaLvellededpavRraaaeaLgai 58
                                        ++++++++a++ell+ ++p  R  a   Lg++
  gi|242399902|ref|YP_002995327.1| 28 SAMKDKKYVDAIIELLDEHKPGLRGDALLLLGEL 61
                                      56899************************99986 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 2.9e-06
                            HEAT_2   7 alendpdpevrraairaLg..........rignp...ealpaLvellededpavRraaaeaLgaigdpealpaLkel 70 
                                       +l++dpdp+v+ +a ++            +       e++p+L ++l++ d++  + a   L +++ +ealp+ +el
  gi|242399902|ref|YP_002995327.1|  83 LLVEDPDPYVKENAMQTFElmlrffpwaeE---MfrnEIVPLLMDILKNGDRNRKAFAMLMLKKLKVKEALPLIAEL 156
                                       6889************99988888765543...15559*************************************99 PP

                            HEAT_2  71 lddd 74 
                                       ++ +
  gi|242399902|ref|YP_002995327.1| 157 VNVE 160
                                       8754 PP

>> RTP1_C1  Required for nuclear transport of RNA pol II C-terminus 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   3.9e-07   0.00077       4     102 ..      39     150 ..      36     159 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 3.9e-07
                           RTP1_C1   4 alkdlqdpllpvrahglvlLrkliekkskeavldiekilkl.lleaLkdedsYvYLnaikgLvaLadvfp....... 72 
                                       +++ l +  + +r+ +l+lL +l+++++   ++ ie  l + +l  ++d+d+Yv  na+++++ +  +fp       
  gi|242399902|ref|YP_002995327.1|  39 IIELLDEHKPGLRGDALLLLGELVSRHKDLMMEYIEDGLPVrVLLLVEDPDPYVKENAMQTFELMLRFFPwaeemfr 115
                                       67888999999**************9998888888877766266699******************976543322222 PP

                           RTP1_C1  73 eevlklLleeyeeeneke.....slderlkvGEaL 102
                                       +e+++lL++  ++ ++++      + ++lkv EaL
  gi|242399902|ref|YP_002995327.1| 116 NEIVPLLMDILKNGDRNRkafamLMLKKLKVKEAL 150
                                       78888888888444433322332344555666665 PP

>> Adaptin_N  Adaptin N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0   0.00039      0.77     149     186 ..      30      69 ..      25      78 .. 0.78
   2 !    5.7   0.0    0.0023       4.6     122     163 ..      84     124 ..      77     164 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00039
                                       CCCC.HHHHHHHCTT-SSHHHHHHHHHHHHHH.HCCCCCC CS
                         Adaptin_N 149 lrkq.lveeikellsdkdpgvvlaAvalleei.kkndrll 186
                                       ++++ +v+ i+ell++++pg+ + A+ ll e+  ++++l+
  gi|242399902|ref|YP_002995327.1|  30 MKDKkYVDAIIELLDEHKPGLRGDALLLLGELvSRHKDLM 69 
                                       4566689***********************9974444443 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0023
                                       HHT-SSHHHHHHHHHHHHHCCCCCHHCCCCCHHHHHHHCTT- CS
                         Adaptin_N 122 llkdrspyvrkkAalailklykkdpdllrkqlveeikellsd 163
                                       l++d++pyv+ +A +++  +++  p++ ++ + +ei+ ll d
  gi|242399902|ref|YP_002995327.1|  84 LVEDPDPYVKENAMQTFELMLRFFPWAEEM-FRNEIVPLLMD 124
                                       788999999999999988888887777444.47777666644 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 ?    6.4   0.0    0.0043       8.6      49      96 ..      25      72 ..      13      79 .. 0.87
   2 ?    7.1   0.1    0.0025         5      30      49 ..      85     109 ..      67     160 .. 0.57

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0043
                              Cnd1 49 ilndmvkekgflselaklleDenprVvanalaalteiseksenaiynl 96
                                      il   +k+k+ ++ + +ll++++p  +  al++l e+ ++ ++++++ 
  gi|242399902|ref|YP_002995327.1| 25 ILISAMKDKKYVDAIIELLDEHKPGLRGDALLLLGELVSRHKDLMMEY 72
                                      5667899********************************988887765 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0025
                              Cnd1  30 LkDedpyVRktaaivvakL.....i 49 
                                       ++D+dpyV+++a+ ++  +      
  gi|242399902|ref|YP_002995327.1|  85 VEDPDPYVKENAMQTFELMlrffpW 109
                                       4677777777777655444343333 PP

>> Rcd1  Cell differentiation family, Rcd1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       0.8   1.6e+03     114     114 ..      53      53 ..      12      84 .. 0.58
   2 ?   11.5   0.0   6.5e-05      0.13     134     165 ..     113     144 ..     109     163 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.8
                              Rcd1 114 t 114
                                        
  gi|242399902|ref|YP_002995327.1|  53 D 53 
                                       2 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 6.5e-05
                              Rcd1 134 lldteivplclrimesGselsktvAtfIlqki 165
                                       + ++eivpl++ i+++G+   k  A+  l+k+
  gi|242399902|ref|YP_002995327.1| 113 MFRNEIVPLLMDILKNGDRNRKAFAMLMLKKL 144
                                       6789*************************996 PP

>> DUF1186  Protein of unknown function (DUF1186)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.22   4.4e+02     103     130 ..      12      37 ..       7      66 .. 0.67
   2 ?    0.4   0.0      0.17   3.4e+02     115     141 ..      78     104 ..      50     120 .. 0.73
   3 ?    7.8   0.0   0.00094       1.9      48      90 ..     123     165 ..     110     170 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.22
                           DUF1186 103 rilasvsdGnvepikeLieneevneyvr 130
                                       +++  +s+G++e i  Li   +  +yv 
  gi|242399902|ref|YP_002995327.1|  12 KVIKMISQGDLEEI--LISAMKDKKYVD 37 
                                       56666666666665..555555555554 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.17
                           DUF1186 115 pikeLieneevneyvrgaalksllvLl 141
                                       p++ L+  e+ + yv+  a++++  +l
  gi|242399902|ref|YP_002995327.1|  78 PVRVLLLVEDPDPYVKENAMQTFELML 104
                                       677777777889999999999987654 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.00094
                           DUF1186  48 eelleeedyilhiyalyLLaqfreekaypliiklfslpgdial 90 
                                        ++l++ d     +a+ +L + + ++a+pli +l+++++ + l
  gi|242399902|ref|YP_002995327.1| 123 MDILKNGDRNRKAFAMLMLKKLKVKEALPLIAELVNVEEAVIL 165
                                       6888899999999************************998865 PP

>> V-ATPase_H_C  V-ATPase subunit H
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.078   1.5e+02      81     114 ..      30      63 ..       8      66 .. 0.68
   2 ?    9.0   0.0   0.00074       1.5      42     113 ..      34     104 ..      29     107 .. 0.70
   3 ?   -1.3   0.0       1.1   2.3e+03      90     112 ..     122     144 ..     114     151 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.078
                      V-ATPase_H_C  81 leklkaKekimellehedeevkyeALkavqkllv 114
                                       +++ k  + i+ell+++ + ++  AL+ + +l++
  gi|242399902|ref|YP_002995327.1|  30 MKDKKYVDAIIELLDEHKPGLRGDALLLLGELVS 63 
                                       2333444689999999999999999998888876 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00074
                      V-ATPase_H_C  42 kllkkLiklleeskdktvlavalnDigelvkllpegkkvleklkaKekimellehedeevkyeALkavqkll 113
                                       k + ++i+ll+ ++++     al  +gelv+ +++      + +   +++ l+e++d+ vk +A+++ + +l
  gi|242399902|ref|YP_002995327.1|  34 KYVDAIIELLD-EHKPGLRGDALLLLGELVSRHKDLMMEYIEDGLPVRVLLLVEDPDPYVKENAMQTFELML 104
                                       55666666663.444544455555577777766655555556678899*******************98776 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.1
                      V-ATPase_H_C  90 imellehedeevkyeALkavqkl 112
                                       +m++l++ d++ k  A++ ++kl
  gi|242399902|ref|YP_002995327.1| 122 LMDILKNGDRNRKAFAMLMLKKL 144
                                       67777777777777777766665 PP

>> HEAT_EZ  HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1      0.46   9.2e+02      23      54 ..      33      60 ..      30      61 .. 0.75
   2 ?    9.8   0.0   0.00058       1.2       3      53 ..      50     101 ..      48     103 .. 0.88
   3 ?   -0.4   0.0      0.91   1.8e+03      28      39 ..     117     128 ..     113     141 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.46
                           HEAT_EZ 23 qplvpeilpaLlalLnddsd.eVRaaAagaLgn 54
                                      +++v++i+ +L      +++   R+ A+  Lg 
  gi|242399902|ref|YP_002995327.1| 33 KKYVDAIIELLD-----EHKpGLRGDALLLLGE 60
                                      568888888888.....7776668888888886 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00058
                           HEAT_EZ   3 vRraAawaLGrlaggepellqplvpeilpaLlalL.nddsdeVRaaAagaLg 53 
                                       +R  A++ LG+l +  ++l+  ++++ lp  + lL +d+++ V+++A  +++
  gi|242399902|ref|YP_002995327.1|  50 LRGDALLLLGELVSRHKDLMMEYIEDGLPVRVLLLvEDPDPYVKENAMQTFE 101
                                       67789999999999999999999999999999999899999******99986 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.91
                           HEAT_EZ  28 eilpaLlalLnd 39 
                                       ei+p+L+  L++
  gi|242399902|ref|YP_002995327.1| 117 EIVPLLMDILKN 128
                                       799999977765 PP

>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.54   1.1e+03       4      29 ..      38      63 ..      36      65 .. 0.73
   2 ?    8.1   0.0    0.0018       3.6       5      25 ..      81     101 ..      77     107 .. 0.79
   3 ?   -3.3   0.0       8.1   1.6e+04       1       9 [.     118     126 ..     118     130 .. 0.67
   4 ?   -2.6   0.0       5.1     1e+04       2      10 ..     150     158 ..     149     162 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.54
                                      HHHHHHT-SSHHHHHHHHHHHHHHHH CS
                              HEAT  4 lllkllsDpspeVReaAakaLgalae 29
                                      ++++ll    p  R  A++ Lg+l++
  gi|242399902|ref|YP_002995327.1| 38 AIIELLDEHKPGLRGDALLLLGELVS 63
                                      56777766666677789999999987 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0018
                                       HHHHHT-SSHHHHHHHHHHHH CS
                              HEAT   5 llkllsDpspeVReaAakaLg 25 
                                       +l l +Dp+p V e+A +++ 
  gi|242399902|ref|YP_002995327.1|  81 VLLLVEDPDPYVKENAMQTFE 101
                                       555679**********99986 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 8.1
                                       HHHHHHHHH CS
                              HEAT   1 llPlllkll 9  
                                       ++Pll+  l
  gi|242399902|ref|YP_002995327.1| 118 IVPLLMDIL 126
                                       678877655 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 5.1
                                       HHHHHHHHT CS
                              HEAT   2 lPlllklls 10 
                                       lPl+ +l +
  gi|242399902|ref|YP_002995327.1| 150 LPLIAELVN 158
                                       899998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.35s 00:00:00.98 Elapsed: 00:00:00.54
# Mc/sec: 1065.67
//
Query:       gi|242399903|ref|YP_002995328.1|  [L=96]
Description: beta-lactamase regulatory-like protein, mazg protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.7e-13   50.6   0.2    3.3e-13   49.6   0.0    1.6  2  MazG       MazG nucleotide pyrophosphohydrolase domain
    2.6e-06   27.6   0.3    3.7e-06   27.1   0.3    1.3  1  MazG-like  MazG-like family
     0.0022   18.4   1.2      0.003   18.0   1.2    1.3  1  PRA-PH     Phosphoribosyl-ATP pyrophosphohydrolase
  ------ inclusion threshold ------
        0.1   13.2   0.3       0.13   12.9   0.3    1.1  1  ECM11      Extracellular mutant protein 11


Domain annotation for each model (and alignments):
>> MazG  MazG nucleotide pyrophosphohydrolase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.78   3.5e+03      12      20 ..       4      12 ..       2      19 .. 0.60
   2 !   49.6   0.0   7.4e-17   3.3e-13       3      69 ..      23      82 ..      21      87 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.78
                                      HHHHHHHHH CS
                              MazG 12 eEvgEvaea 20
                                      +E +E++ +
  gi|242399903|ref|YP_002995328.1|  4 KEFQELIKE 12
                                      455555443 PP

  == domain 2  score: 49.6 bits;  conditional E-value: 7.4e-17
                                      HHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHH CS
                              MazG  3 petllaylleEvgEvaeaIkkedrdeleeELGDvLlqvlflaniaeeeggidledvaetileKlerR 69
                                      +e + ++  eE+gE+aea++k+dr++++eE +DvL ++++lani     g+d+e++a    +K+   
  gi|242399903|ref|YP_002995328.1| 23 LEKTFLWFSEEIGELAEALRKNDREAMDEEFADVLAWLVSLANI----VGVDVEEAA---KKKYPGV 82
                                      67888999************************************....********9...5566555 PP

>> MazG-like  MazG-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.3   8.3e-10   3.7e-06      12      59 ..      25      75 ..      17      79 .. 0.88

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 8.3e-10
                         MazG-like 12 kaell..ksveelfkallkgseeeildeLAdviiylylLAdrlGidfee.i 59
                                      k++l+  ++++el +al k+++e++ +e Adv++ l+ LA+ +G+d+ee  
  gi|242399903|ref|YP_002995328.1| 25 KTFLWfsEEIGELAEALRKNDREAMDEEFADVLAWLVSLANIVGVDVEEaA 75
                                      78888555789************************************9933 PP

>> PRA-PH  Phosphoribosyl-ATP pyrophosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   1.2   6.6e-07     0.003      26      74 ..      25      73 ..       3      77 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 6.6e-07
                                      HHHHHHHHHHHHHHHHT-SCHHHHHHHHHHHHHHHHHHHHHHCT--CHH CS
                            PRA-PH 26 lraaligEEavElleaasegdlaeladelaDllYvtygllvllGidlda 74
                                      +   ++ EE+ El ea  ++d++ + +e aD+l  +  l+   G+d ++
  gi|242399903|ref|YP_002995328.1| 25 KTFLWFSEEIGELAEALRKNDREAMDEEFADVLAWLVSLANIVGVDVEE 73
                                      4566899**************************9999999999999887 PP

>> ECM11  Extracellular mutant protein 11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.3   2.8e-05      0.13      76     120 ..       3      51 ..       1      57 [. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.8e-05
                             ECM11  76 ldqfsellkklkeaRrakr...ktaaefeaeierReeavrkkgee.ldr 120
                                       +++f+el+k+l   R +kr   kt+  f +ei + +ea+rk+ +e +d+
  gi|242399903|ref|YP_002995328.1|   3 IKEFQELIKELYFHRDEKRgleKTFLWFSEEIGELAEALRKNDREaMDE 51 
                                       789**************99666789999************986541555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1009  (0.0562775); expected 358.6 (0.02)
Passed bias filter:                      720  (0.0401584); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 614.56
//
Query:       gi|242399904|ref|YP_002995329.1|  [L=142]
Description: nucleic acid-binding protein, contains PIN domain [Thermococcus sibiricus MM 739]
Scores for 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   0.1    1.2e-14   54.9   0.1    1.0  1  PIN       PIN domain
    0.00092   19.7   1.1     0.0013   19.3   1.1    1.3  1  PIN_12    PIN domain
  ------ inclusion threshold ------
      0.021   14.1   0.2      0.022   14.1   0.2    1.1  1  Pox_A11   Poxvirus A11 Protein


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 !   54.9   0.1     2e-18   1.2e-14       1     121 [.      10     138 ..      10     139 .. 0.94

  Alignments for each domain:
  == domain 1  score: 54.9 bits;  conditional E-value: 2e-18
                                       EEE-HHHHHHHH.TTSHHHHHHHHHHHTS....SEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEE CS
                               PIN   1 ivlDTsvliall.rgeekaeaarklleel....eelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilp 72 
                                       i+ DTs++ial  r  +++++a++ +e+      + v+   vl E+l+++++ + ++  a +l +++   + + i +
  gi|242399904|ref|YP_002995329.1|  10 IYMDTSAMIALAsRTYKNHKKAKEFFEKSiksgINFVVGRPVLGEFLNGVSK-RVNKRTAVQLYKSYTNSRVVIIEK 85 
                                       799**********999999999***99999999*******************.888888888888888888888888 PP

                                       BCHHHHHHHHHHHHHHH....SBHHHHHHHHHHHHHT-EEE.ESSTHHHHHHH CS
                               PIN  73 idaeiaeeaaeialkyg....llpnDaliaAtAkehgikliatfDedfrrvak 121
                                         +e++e+a++i+++y+     +++D+l  + +++ +i+  +tfD+df+ +++
  gi|242399904|ref|YP_002995329.1|  86 EIEEDWEKAWKIFKQYEdqkgMDVIDCLSFVIMERLKIREAFTFDRDFETYGF 138
                                       ***************************************999******98776 PP

>> PIN_12  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   1.1   2.1e-07    0.0013       1     104 [.      10     110 ..      10     134 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 2.1e-07
                            PIN_12   1 ifiDTnifld...effrlseeealkklleliesgkiklivpdivldEflknrekkieeskklekalkslsklksakk 74 
                                       i++DT+ ++      +++   ++ k+++e   + +i+ +v   vl Efl+ ++k++++      a++ ++ +++ + 
  gi|242399904|ref|YP_002995329.1|  10 IYMDTSAMIAlasRTYKNH--KKAKEFFEKSIKSGINFVVGRPVLGEFLNGVSKRVNKR----TAVQLYKSYTNSRV 80 
                                       89*******8433444444..45666655555557*********************977....45555777777777 PP

                            PIN_12  75 klnekkkllslkeikkkieekveeslkkll 104
                                        + ek+ +++ ++  k+++++ +++   ++
  gi|242399904|ref|YP_002995329.1|  81 VIIEKEIEEDWEKAWKIFKQYEDQKGMDVI 110
                                       777777777777777777777666555544 PP

>> Pox_A11  Poxvirus A11 Protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.2   3.7e-06     0.022     187     239 ..      60     110 ..      26     134 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.7e-06
                           Pox_A11 187 ssevnkrvaivnyaslnksdlsledlevcseeeidkiykvvkqynesrkkkil 239
                                       s+ vnkr a+  y s ++s + +  +e+  ee+ +k +k+ kqy++++   ++
  gi|242399904|ref|YP_002995329.1|  60 SKRVNKRTAVQLYKSYTNSRVVI--IEKEIEEDWEKAWKIFKQYEDQKGMDVI 110
                                       789*****************998..56667999*************9877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       851  (0.047465); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); 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: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 821.35
//
Query:       gi|242399905|ref|YP_002995330.1|  [L=107]
Description: hypothetical protein TSIB_1932 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
       0.01   15.6   0.1      0.012   15.4   0.1    1.1  1  Cwf_Cwc_15  Cwf15/Cwc15 cell cycle control protein
      0.066   13.6   0.5        0.1   13.0   0.5    1.3  1  ParD        Antitoxin ParD
       0.14   12.4   0.6       0.19   11.9   0.6    1.3  1  TAF         TATA box binding protein associated factor (TAF)


Domain annotation for each model (and alignments):
>> Cwf_Cwc_15  Cwf15/Cwc15 cell cycle control protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.1     2e-06     0.012     142     191 ..      13      62 ..       4      83 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2e-06
                                       -------------------------------------------------- CS
                        Cwf_Cwc_15 142 dedetaeLlrELekikreraeekerkerekaeeeekereeeiatgNpLln 191
                                        +det+e l+ L+ ++  r +e +r++ ek ++e+k+  e+++++ p+ +
  gi|242399905|ref|YP_002995330.1|  13 VDDETHEVLKMLAILRGKRLKEIAREALEKYAKEHKKEVEKLIQKDPIWD 62 
                                       59******************************************999977 PP

>> ParD  Antitoxin ParD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.5   1.7e-05       0.1       6      41 ..      11      45 ..       7      58 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.7e-05
                              ParD  6 IditpeqhqrlkAvAAlqGksikeYvLerlleepke 41
                                       ++ +e h  lk +A l+Gk +ke + e l  + ++
  gi|242399905|ref|YP_002995330.1| 11 TEVDDETHEVLKMLAILRGKRLKEIAREALE-KYAK 45
                                      6999********************8866553.2222 PP

>> TAF  TATA box binding protein associated factor (TAF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.6   3.2e-05      0.19      23      52 ..      18      48 ..      11      58 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.2e-05
                                      HHHHHHHHHHHHHHHHHHHHHHH.HHHHHTT CS
                               TAF 23 deaaalLaedveyrlkeivqeaa.kfmrhsk 52
                                       e++++La     rlkei++ea+ k+ +  k
  gi|242399905|ref|YP_002995330.1| 18 HEVLKMLAILRGKRLKEIAREALeKYAKEHK 48
                                      6999******************856666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1283  (0.07156); expected 358.6 (0.02)
Passed bias filter:                      760  (0.0423894); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.37s 00:00:00.96 Elapsed: 00:00:00.55
# Mc/sec: 581.69
//
Query:       gi|242399906|ref|YP_002995331.1|  [L=72]
Description: hypothetical protein TSIB_1933 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-18   65.6   4.6    4.7e-18   65.1   4.6    1.2  1  DUF2283   Protein of unknown function (DUF2283)
  ------ inclusion threshold ------
      0.013   15.3   0.0       0.14   12.0   0.0    2.0  2  KTSC      KTSC domain


Domain annotation for each model (and alignments):
>> DUF2283  Protein of unknown function (DUF2283)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.1   4.6   5.3e-22   4.7e-18       1      48 [.       2      49 ..       2      49 .. 0.99

  Alignments for each domain:
  == domain 1  score: 65.1 bits;  conditional E-value: 5.3e-22
                           DUF2283  1 kitYDpeaDalYIylsegpveeseevdddiilDfDedGrlvGIEiLnA 48
                                      ki+YDp+aD+lYI ++eg++ +++evd+d+ +++De+Gr+ GIEi+nA
  gi|242399906|ref|YP_002995331.1|  2 KIRYDPKADILYILIKEGEIFDTDEVDEDVWIEYDENGRIMGIEIWNA 49
                                      8**********************************************9 PP

>> KTSC  KTSC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.6e-05      0.14       7      38 ..       2      33 ..       1      34 [. 0.93
   2 ?    2.4   0.0     0.016   1.4e+02       8      21 ..      33      46 ..      32      52 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.6e-05
                                      EEEEETTTTEEEEEETTTEEEEEES--HHHHH CS
                              KTSC  7 sigYdpetqtLeieFkngsvyqYsgVpeevye 38
                                      +i Ydp+  +L+i  k g++ +  +V e+v+ 
  gi|242399906|ref|YP_002995331.1|  2 KIRYDPKADILYILIKEGEIFDTDEVDEDVWI 33
                                      589************************99996 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.016
                                      EEEETTTTEEEEEE CS
                              KTSC  8 igYdpetqtLeieF 21
                                      i+Yd++ +++ ie 
  gi|242399906|ref|YP_002995331.1| 33 IEYDENGRIMGIEI 46
                                      78********9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.33s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 440.56
//
Query:       gi|242399907|ref|YP_002995332.1|  [L=93]
Description: hypothetical protein TSIB_1934 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.6e-12   46.1   0.8    6.3e-12   45.7   0.8    1.3  1  DUF4258      Domain of unknown function (DUF4258)
     0.0059   16.9   0.5     0.0092   16.3   0.5    1.3  1  BrnT_toxin   Ribonuclease toxin, BrnT, of type II toxin-antit
     0.0074   16.2   1.5     0.0087   16.0   1.5    1.1  1  PBECR3       phage-Barnase-EndoU-ColicinE5/D-RelE like nuclea
  ------ inclusion threshold ------
       0.17   12.1   0.3        2.5    8.3   0.1    2.1  2  Fe-S_biosyn  Iron-sulphur cluster biosynthesis


Domain annotation for each model (and alignments):
>> DUF4258  Domain of unknown function (DUF4258)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.7   0.8   1.4e-15   6.3e-12       1      57 [.       4      79 ..       4      91 .. 0.76

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 1.4e-15
                           DUF4258  1 fsaHArermaeRgIseedieevlenG..........eiieeys............lvlgktsegrplhvvvapdedpv. 56
                                      f++HAr+r++eR+I e++ie+vl+++                +            l+  +++eg+ ++vv+++d +   
  gi|242399907|ref|YP_002995332.1|  4 FTEHARQRLKERKIEEDEIEKVLKKPkwkfydlknaH-----QiaigerrkeghyLIIAYDREGESIKVVTVIDVSRNl 77
                                      8*************************88777555550.....2444444456777788888888888888887776665 PP

                           DUF4258 57 .v 57
                                       +
  gi|242399907|ref|YP_002995332.1| 78 eK 79
                                      54 PP

>> BrnT_toxin  Ribonuclease toxin, BrnT, of type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.5   2.1e-06    0.0092       6      72 ..       8      71 ..       5      76 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.1e-06
                        BrnT_toxin  6 aasnlkkHgvsfeeaeevfedplalevedrredegEeRfiaiG..tidgrllvvvftereekiRiISaR 72
                                      a++ lk++++  +e+e+v+++p+   ++d +    +   iaiG   ++g++l++++  ++e i+++++ 
  gi|242399907|ref|YP_002995332.1|  8 ARQRLKERKIEEDEIEKVLKKPKWK-FYDLK----NAHQIAIGerRKEGHYLIIAYDREGESIKVVTVI 71
                                      67889*************9888875.66652....7899****977888999999999999***99875 PP

>> PBECR3  phage-Barnase-EndoU-ColicinE5/D-RelE like nuclease3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   1.5     2e-06    0.0087      42     111 ..      11      76 ..       3      82 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2e-06
                            PBECR3  42 stekdrgqidianipdiiknPDkviyggknkkeksieyvKkinngylvvvevdkkknelyvktmykikek 111
                                          k+r+++  + i++++k+P   +y+ kn    +i +  + ++g++++++ d+++++++v+t  + + +
  gi|242399907|ref|YP_002995332.1|  11 RL-KERKIE-EDEIEKVLKKPKWKFYDLKNAH--QIAIGERRKEGHYLIIAYDREGESIKVVTVIDVSRN 76 
                                       22.444444.68*****************999..799999999********************9887755 PP

>> Fe-S_biosyn  Iron-sulphur cluster biosynthesis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.1   0.00056       2.5       3      22 ..       2      21 ..       1      27 [. 0.86
   2 ?    2.2   0.0     0.043   1.9e+02      20      33 ..      49      63 ..      36      89 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00056
                                      EEE-HHHHHHHHHHHHCTTE CS
                       Fe-S_biosyn  3 itlteaAaeklkkllaedkk 22
                                      it+te A ++lk+ + e+++
  gi|242399907|ref|YP_002995332.1|  2 ITFTEHARQRLKERKIEEDE 21
                                      9***********99887765 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.043
                                      TTEC...EEEEEECCTS CS
                       Fe-S_biosyn 20 dkke...lrLdvddggg 33
                                      +  e   l++++d +g 
  gi|242399907|ref|YP_002995332.1| 49 K--EghyLIIAYDREGE 63
                                      2..223699****9983 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1055  (0.0588432); 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:                         4  (0.000223102); expected 0.2 (1e-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 0.36s 00:00:00.90 Elapsed: 00:00:00.54
# Mc/sec: 520.64
//
Query:       gi|242399908|ref|YP_002995333.1|  [L=435]
Description: transposase ISTsi3 [Thermococcus sibiricus MM 739]
Scores for complete 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  103.6   0.7    1.5e-29  102.7   0.0    1.9  2  OrfB_IS605      Probable transposase
    3.2e-22   78.2   0.0    5.7e-22   77.4   0.0    1.4  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
     0.0021   16.8   0.0     0.0033   16.2   0.0    1.2  1  MAP65_ASE1      Microtubule associated protein (MAP65/ASE1 fa
     0.0065   16.9   0.1      0.017   15.5   0.1    1.7  1  RuvX            Holliday junction resolvase


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       1.2   5.3e+03      68      89 ..      13      34 ..       4      40 .. 0.56
   2 !  102.7   0.0   3.3e-33   1.5e-29       1     119 [.     173     298 ..     173     299 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.2
                        OrfB_IS605 68 knykkasrklarlhrkrsrrrk 89
                                      k  +++ ++la ++ k+ +r++
  gi|242399908|ref|YP_002995333.1| 13 KETERTLKELAQISSKVWNRVN 34
                                      3345555555555555555554 PP

  == domain 2  score: 102.7 bits;  conditional E-value: 3.3e-33
                        OrfB_IS605   1 sipveveve.........lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksk 68 
                                       +i v ve++         +++p gn  agiDlG+nnL++v++e+g++fl +gr+lks  +y++k+iae qsk++ks+
  gi|242399908|ref|YP_002995333.1| 173 HISVSVEKKlqgeewvelPREPLGNLPAGIDLGVNNLIAVYVENGESFLVNGRPLKSIAFYWQKRIAEYQSKINKSG 249
                                       567777777888889998999*******************************************************9 PP

                        OrfB_IS605  69 nykkasrklarlhrkrsrrrkhllhklathliktlkevgvetLnvgnmkdi 119
                                          k s+kl+r+h+k + + +h+++ ++++ +++l+++gv+ ++vg++k+i
  gi|242399908|ref|YP_002995333.1| 250 --AKKSKKLTRMHQKAKLQARHYINTTVRQTVERLYHLGVSRIVVGYPKEI 298
                                       ..9*********************************************987 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.4   0.0   1.3e-25   5.7e-22       1      69 []     318     387 ..     318     387 .. 0.98

  Alignments for each domain:
  == domain 1  score: 77.4 bits;  conditional E-value: 1.3e-25
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke.alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       f++++++l++ a+eyGi+v +vn+a+TSktC++Cg+ ++  +  + +fkCp+ g+++++D+++a+Nilkr
  gi|242399908|ref|YP_002995333.1| 318 FNTVIQRLKEVAEEYGIQVLVVNEAFTSKTCPVCGKPHEGaRFVRGLFKCPATGLVFNADLVGAFNILKR 387
                                       7899************************************99**************************97 PP

>> MAP65_ASE1  Microtubule associated protein (MAP65/ASE1 family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   7.4e-07    0.0033     388     444 ..     211     266 ..     196     282 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.4e-07
                                       HHHHHCTS--EETTEEHHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHCX CS
                        MAP65_ASE1 388 aweeefgrpFlvdGeklleiieeqweeleekyqererqksarklkkasqteeeilkg 444
                                       a   e+g+ Flv+G +l + i+ +w+++ + yq +  ++ a+k kk ++ ++++  +
  gi|242399908|ref|YP_002995333.1| 211 AVYVENGESFLVNGRPLKS-IAFYWQKRIAEYQSKINKSGAKKSKKLTRMHQKAKLQ 266
                                       555699**********976.799**********************999999887654 PP

>> RuvX  Holliday junction resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   3.8e-06     0.017      19     101 ..     254     347 ..     245     350 .. 0.57

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.8e-06
                                       -S--SS---EEEEE---HHHHHHHHHHHHHHTT--EEEEE--......----SSS---SSTTHHH...HHHHHHT.. CS
                              RuvX  19 dplgilaspletierkskekdleelkelvkeeeveeiVvGlP......lnldgsegesakkvrkf...aeeLakrl. 85 
                                       ++l+++ ++ +  +r+  ++++++  e + +  v++iVvG+P       n  ++++    +v +f   +++L++   
  gi|242399908|ref|YP_002995333.1| 254 KKLTRMHQKAKLQARHYINTTVRQTVERLYHLGVSRIVVGYPkeiarnSNKGKKQNYLLSHVWRFntvIQRLKEVAe 330
                                       444444444444445544677777777777779*********55443211112222222333333111444444335 PP

                                       ..T-EEEEE--S----X CS
                              RuvX  86 .kklpvelvDErlttve 101
                                        ++++v +v+E +t+++
  gi|242399908|ref|YP_002995333.1| 331 eYGIQVLVVNEAFTSKT 347
                                       5699***********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (435 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       924  (0.0515366); expected 358.6 (0.02)
Passed bias filter:                      664  (0.037035); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.35s 00:00:01.03 Elapsed: 00:00:00.53
# Mc/sec: 2468.33
//
Query:       gi|242399909|ref|YP_002995334.1|  [L=51]
Description: hypothetical protein TSIB_1936 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.053   13.5   0.2      0.098   12.6   0.2    1.4  1  RHH_1     Ribbon-helix-helix protein, copG family


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   5.5e-06     0.098       2      20 ..       4      22 ..       3      23 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.5e-06
                                      EEEEEEHHHHHHHHHHHHH CS
                             RHH_1  2 vsirldeellerLdelarr 20
                                      +++++d+e+ ++++el+++
  gi|242399909|ref|YP_002995334.1|  4 INVSVDDEVEKKFRELVEK 22
                                      89**************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 317.86
//
Query:       gi|242399910|ref|YP_002995335.1|  [L=37]
Description: hypothetical protein TSIB_1937 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.073   13.5   0.1      0.089   13.2   0.1    1.1  1  NblA      Phycobilisome degradation protein nblA


Domain annotation for each model (and alignments):
>> NblA  Phycobilisome degradation protein nblA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   4.9e-06     0.089      25      49 ..      12      36 ..       9      37 .] 0.92

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.9e-06
                                      HHHHHHHHHHHHHHHHHHHHHHHTT CS
                              NblA 25 aqelLlelyrqmmvkenlirellKh 49
                                      + e L++l r  + ke li ++lK+
  gi|242399910|ref|YP_002995335.1| 12 VDETLIQLIRRTVRKEILIDSMLKK 36
                                      6799********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.34s 00:00:00.78 Elapsed: 00:00:00.50
# Mc/sec: 221.53
//
Query:       gi|242399911|ref|YP_002995336.1|  [L=66]
Description: hypothetical protein TSIB_1938 [Thermococcus sibiricus MM 739]
Scores for 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   32.2   0.0    1.1e-07   32.1   0.0    1.0  1  PIN_2     PIN domain


Domain annotation for each model (and alignments):
>> PIN_2  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.0   6.1e-12   1.1e-07      28      78 ..       2      53 ..       1      61 [. 0.87

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 6.1e-12
                             PIN_2 28 eliapeeaveeiekhkealvkksklseeeleelle.lletkikiveeslyes 78
                                      +l++pe+a++e++k+k++++kksk+s+e++ee+ + +l + + +++es+y +
  gi|242399911|ref|YP_002995336.1|  2 DLYTPEYAYDELQKYKSEIIKKSKFSPERFEEIDFgILSHIVIPIPESEYIN 53
                                      79*******************************9966677777799998864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 428.88
//
Query:       gi|242399912|ref|YP_002995337.1|  [L=129]
Description: hypothetical protein TSIB_1939 [Thermococcus sibiricus MM 739]
Scores for complete 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   24.2   0.5    3.6e-05   23.6   0.5    1.3  1  Class_IIIsignal  Class III signal peptide


Domain annotation for each model (and alignments):
>> Class_IIIsignal  Class III signal peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.5     2e-09   3.6e-05       1      24 [.       6      29 ..       6      32 .. 0.94

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 2e-09
                   Class_IIIsignal  1 kKGQiSlEyiLLilavlviaiiai 24
                                      kK+Q+SlEy+ +++ +lvi++i+ 
  gi|242399912|ref|YP_002995337.1|  6 KKAQGSLEYSAMVALALVIILITV 29
                                      8*********************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1317  (0.0734564); expected 358.6 (0.02)
Passed bias filter:                      768  (0.0428356); 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 0.31s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 775.29
//
Query:       gi|242399913|ref|YP_002995338.1|  [L=142]
Description: hypothetical protein TSIB_1940 [Thermococcus sibiricus MM 739]
Scores for complete 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   34.4   3.3    2.6e-08   33.6   3.3    1.4  1  Class_IIIsignal  Class III signal peptide
  ------ inclusion threshold ------
       0.13   12.4   0.2       0.16   12.0   0.2    1.4  1  DUF2275          Predicted integral membrane protein (DUF2275


Domain annotation for each model (and alignments):
>> Class_IIIsignal  Class III signal peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   3.3   2.9e-12   2.6e-08       1      27 []      11      37 ..      11      37 .. 0.97

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 2.9e-12
                   Class_IIIsignal  1 kKGQiSlEyiLLilavlviaiiaiyyy 27
                                      kKGQ++lEy+++i+a+l+i+ ++ +y+
  gi|242399913|ref|YP_002995338.1| 11 KKGQGALEYLFMIAAALIIIFVVVRYI 37
                                      8************************96 PP

>> DUF2275  Predicted integral membrane protein (DUF2275)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   1.8e-05      0.16      26      80 ..       4      59 ..       2     112 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.8e-05
                           DUF2275 26 lvrlflrlkrklalaglivlilAavgf.gvvsyatiskmdvvrvlkkaglslkaee 80
                                      l++lf r k ++al+ l ++++A++++  vv y   ++ ++   +  a l+ +ae 
  gi|242399913|ref|YP_002995338.1|  4 LRKLFKRKKGQGALEYLFMIAAALIIIfVVVRYISGAGQQATGTSDIAALQSQAEL 59
                                      689***************99999876515566655555555555555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       916  (0.0510904); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1006.65
//
Query:       gi|242399914|ref|YP_002995339.1|  [L=182]
Description: hypothetical protein TSIB_1941 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.2e-05   23.4   0.1    0.00024   21.0   0.0    2.3  3  HTH_11           HTH domain
     0.0048   17.1   0.2       0.02   15.1   0.0    2.0  2  UPF0122          Putative helix-turn-helix protein, YlxM / p1
  ------ inclusion threshold ------
      0.015   15.4   0.0      0.044   13.9   0.0    1.8  1  HTH_7            Helix-turn-helix domain of resolvase
      0.015   15.3   0.0          3    8.0   0.0    2.4  2  SpoIIID          Stage III sporulation protein D
      0.023   14.5   0.2       0.27   11.0   0.2    2.3  1  HTH_38           Helix-turn-helix domain
      0.027   14.5   0.0      0.054   13.5   0.0    1.5  1  HTH_29           Winged helix-turn helix
      0.028   14.2   0.0       0.11   12.4   0.0    2.0  1  HTH_23           Homeodomain-like domain
      0.031   14.3   0.3       0.16   12.1   0.0    2.3  3  HTH_22           HTH domain
       0.04   14.0   0.0      0.079   13.1   0.0    1.6  1  HTH_28           Helix-turn-helix domain
      0.051   13.7   0.1        2.7    8.2   0.0    2.8  3  HU-CCDC81_euk_2  CCDC81 eukaryotic HU domain 2
      0.073   13.3   0.0      0.099   12.8   0.0    1.2  1  Tubulin          Tubulin/FtsZ family, GTPase 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 ?   -2.5   0.0       3.1     5e+03      36      51 ..      20      35 ..      13      36 .. 0.72
   2 ?   -1.5   0.0       1.5   2.4e+03      17      25 ..      74      82 ..      70      91 .. 0.70
   3 !   21.0   0.0   1.5e-07   0.00024      13      39 ..     151     177 ..     142     182 .] 0.83

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 3.1
                            HTH_11 36 IkaLeelgvpIesepg 51
                                      +k+L+e+   +es pg
  gi|242399914|ref|YP_002995339.1| 20 LKELREKAKILESMPG 35
                                      6778877777777665 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.5
                            HTH_11 17 sgeeLAeeL 25
                                      sg+++ e+L
  gi|242399914|ref|YP_002995339.1| 74 SGKDIIERL 82
                                      666666665 PP

  == domain 3  score: 21.0 bits;  conditional E-value: 1.5e-07
                            HTH_11  13 rgpisgeeLAeeLnvSrrtvrrdIkaL 39 
                                        + ++++e+A+ +nvSr  +++dI+++
  gi|242399914|ref|YP_002995339.1| 151 PKALNISEIARLFNVSRDSIYNDIEQI 177
                                       456999******************988 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 ?   -1.2   0.1       1.4   2.4e+03      76      91 ..      74      89 ..      64      98 .. 0.58
   2 !   15.1   0.0   1.2e-05      0.02      33      57 ..     153     177 ..     143     180 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.4
                           UPF0122 76 kreellekikdkllkq 91
                                        ++++e++++k  k+
  gi|242399914|ref|YP_002995339.1| 74 SGKDIIERLQEKIRKK 89
                                      5566666666665553 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 1.2e-05
                           UPF0122  33 DlSlsEiAeefnvsrqavydnikrt 57 
                                        l +sEiA  fnvsr ++y+ i+++
  gi|242399914|ref|YP_002995339.1| 153 ALNISEIARLFNVSRDSIYNDIEQI 177
                                       5789*****************9875 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.7e-05     0.044      24      39 ..     156     171 ..     153     172 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.7e-05
                                       STTTSSSS---SSSS- CS
                             HTH_7  24 iskIAkevnisRsTvY 39 
                                       is+IA+ +n+sR ++Y
  gi|242399914|ref|YP_002995339.1| 156 ISEIARLFNVSRDSIY 171
                                       99*************9 PP

>> SpoIIID  Stage III sporulation protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1     0.016        26      24      51 ..      62      90 ..      52      97 .. 0.81
   2 ?    8.0   0.0    0.0018         3      22      46 ..     156     180 ..     134     181 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.016
                           SpoIIID 24 kaakvfgvskstvhkDvterLk.kinkkl 51
                                      k a ++ v+  t  kD+ erL+ ki kk+
  gi|242399914|ref|YP_002995339.1| 62 KKADKYIVAEHTSGKDIIERLQeKIRKKI 90
                                      5789999*************972455555 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0018
                           SpoIIID  22 vRkaakvfgvskstvhkDvterLkk 46 
                                       + ++a+ f+vs+  +++D+ ++Lk+
  gi|242399914|ref|YP_002995339.1| 156 ISEIARLFNVSRDSIYNDIEQILKE 180
                                       7789****************99985 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.2   0.00016      0.27      17      40 ..     149     173 ..     129     176 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00016
                            HTH_38  17 la.eGlslreIArrLgrspsTIsRE 40 
                                       ++ + l+++eIAr+ ++s+ +I++ 
  gi|242399914|ref|YP_002995339.1| 149 WNpKALNISEIARLFNVSRDSIYND 173
                                       663448999*************985 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   3.3e-05     0.054      12      32 ..     154     173 ..     142     181 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.3e-05
                            HTH_29  12 vstvsqiAkllglsrrtvyrw 32 
                                       + ++s+iA+l ++sr+++y+ 
  gi|242399914|ref|YP_002995339.1| 154 L-NISEIARLFNVSRDSIYND 173
                                       4.9****************85 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   6.6e-05      0.11       5      36 ..     134     172 ..     130     181 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.6e-05
                            HTH_23   5 reRlrillllae.......GlsvreIAreLgvsrrTvyr 36 
                                       +eR  il  ++e        l+++eIAr+++vsr  +y+
  gi|242399914|ref|YP_002995339.1| 134 EERRAILGKALElfgwnpkALNISEIARLFNVSRDSIYN 172
                                       55556666666555555556789**************95 PP

>> HTH_22  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1       3.6   5.9e+03      27      35 ..      77      85 ..      75      91 .. 0.78
   2 ?   -2.1   0.0       2.6   4.2e+03      17      29 ..     128     140 ..     118     143 .. 0.79
   3 ?   12.1   0.0   9.7e-05      0.16      44      62 ..     156     174 ..     154     175 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3.6
                            HTH_22 27 eivraLdek 35
                                      +i+++L+ek
  gi|242399914|ref|YP_002995339.1| 77 DIIERLQEK 85
                                      678888876 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.6
                            HTH_22  17 verltkeekieiv 29 
                                       +e+l+ ee+++i 
  gi|242399914|ref|YP_002995339.1| 128 LENLSIEERRAIL 140
                                       6789999999986 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 9.7e-05
                            HTH_22  44 vekvAekLgiSraTvYryL 62 
                                       ++++A+ +++Sr ++Y+ +
  gi|242399914|ref|YP_002995339.1| 156 ISEIARLFNVSRDSIYNDI 174
                                       679**************87 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   4.8e-05     0.079      14      30 ..     155     171 ..     135     176 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.8e-05
                            HTH_28  14 svreaArelgisrrtvy 30 
                                       +++e+Ar++++sr+++y
  gi|242399914|ref|YP_002995339.1| 155 NISEIARLFNVSRDSIY 171
                                       7899************9 PP

>> HU-CCDC81_euk_2  CCDC81 eukaryotic HU domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       1.3     2e+03      20      29 ..      15      24 ..      12      30 .. 0.84
   2 ?    1.7   0.0      0.18   2.9e+02      24      46 ..      78     100 ..      76     105 .. 0.77
   3 ?    8.2   0.0    0.0017       2.7       3      30 ..     152     179 ..     150     181 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.3
                   HU-CCDC81_euk_2 20 vVescvqetf 29
                                       Ve+c++e+ 
  gi|242399914|ref|YP_002995339.1| 15 SVEGCLKELR 24
                                      69*****986 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.18
                   HU-CCDC81_euk_2  24 cvqetfqalgdllrngknvelef 46 
                                        ++++  ++ + ++n + v+++f
  gi|242399914|ref|YP_002995339.1|  78 IIERLQEKIRKKIKNTEIVDFTF 100
                                       56777778888888999999999 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0017
                   HU-CCDC81_euk_2   3 vplnytelaaaaglsrdvVescvqetfq 30 
                                       + ln +e+a+  ++srd + + ++++++
  gi|242399914|ref|YP_002995339.1| 152 KALNISEIARLFNVSRDSIYNDIEQILK 179
                                       579****************999998875 PP

>> Tubulin  Tubulin/FtsZ family, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     6e-05     0.099      64     117 ..      40      97 ..      22     105 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6e-05
                                       S-GS........EEEE--CCC..CTTC--TT-HHHHHHHHHHTHHHHHHHHTT-SE.S CS
                           Tubulin  64 ikags..elfnpnklllgkeg..agnngaggypevgkeaaeeileeirkevekcdslq 117
                                        k++     f + k+ l+ +    + +++ ++++ gk ++e ++e+irk++++++ ++
  gi|242399914|ref|YP_002995339.1|  40 AKIELsfGAFMEIKIALSIDPtkKADKYIVAEHTSGKDIIERLQEKIRKKIKNTEIVD 97 
                                       55555555555555555444423899**************************998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       818  (0.0456244); expected 358.6 (0.02)
Passed bias filter:                      612  (0.0341346); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        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: 00:00:00.49
# Mc/sec: 1110.24
//
Query:       gi|242399915|ref|YP_002995340.1|  [L=412]
Description: Metalloprotease [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-09   37.0   9.9    1.7e-06   27.5   0.3    2.7  2  Peptidase_M50   Peptidase family M50
    0.00014   21.9   0.7    0.00022   21.3   0.7    1.3  1  Zn-ribbon_8     Zinc ribbon domain
  ------ inclusion threshold ------
      0.045   14.1   2.1        0.1   13.0   0.4    2.3  2  zf-IS66         zinc-finger binding domain of transposase IS6
      0.089   12.9   0.4       0.16   12.1   0.4    1.3  1  DUF1272         Protein of unknown function (DUF1272)
      0.097   12.5   0.3       0.18   11.6   0.3    1.5  1  zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
       0.11   11.9   0.1       0.22   10.9   0.1    1.4  1  zf_Rg           Reverse gyrase zinc finger
       0.11   12.5   0.2        0.2   11.7   0.2    1.3  1  HypA            Hydrogenase/urease nickel incorporation, meta
       0.14   12.4   0.1       0.22   11.8   0.1    1.2  1  DUF2072         Zn-ribbon containing protein
       0.33   10.8   1.4         12    5.8   0.1    2.2  2  TFIIS_C         Transcription factor S-II (TFIIS)
       0.53   10.1   2.4        5.3    6.9   2.2    2.1  2  A2L_zn_ribbon   A2L zinc ribbon domain


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 !   11.1   5.1   9.5e-05      0.17       2     108 ..     175     253 ..     174     294 .. 0.85
   2 !   27.5   0.3   9.2e-10   1.7e-06     190     226 ..     300     336 ..     263     344 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9.5e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50   2 filllgilvvvHElGHflvAklcgvkveefsigfGpkllsfkkgeteYaiallp....LGGyVkmageepeeelsee 74 
                                       f + ++ ++  HE+ H ++A  +gvk                    +Y+i++      LG++++++   p+++    
  gi|242399915|ref|YP_002995340.1| 175 FSISVLAILGTHEMSHKIAATFHGVKS-----------------TFPYFIPFPNilgtLGAVIRVKYPIPTRN---- 230
                                       8899999******************99.................347888777677779******99999988.... PP

                                       ....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50  75 eakaflkkspwqrllivlAGplanfilailvfvv 108
                                                  + +    +Gp+a+fi+ai v+++
  gi|242399915|ref|YP_002995340.1| 231 -----------AAIDLGSSGPIAGFIVAIPVLLI 253
                                       ...........89999999999999999999876 PP

  == domain 2  score: 27.5 bits;  conditional E-value: 9.2e-10
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50 190 sflqllalisvnLgilNLlPipvLDGghllfalleai 226
                                       ++++++ ++++ +++lNL+P  +LDGgh+++a+l + 
  gi|242399915|ref|YP_002995340.1| 300 HPVAIAGWVGILVTFLNLVPAAQLDGGHIARAFLGEK 336
                                       88999***************************99765 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.7   1.2e-07   0.00022       5      36 ..       9      39 ..       5      42 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.2e-07
                       Zn-ribbon_8  5 eYrCeeCghefevlqsisdaplta.CPeCgsev 36
                                       Y+C +Cg   ev+ s +da l++ CP+Cg+++
  gi|242399915|ref|YP_002995340.1|  9 VYECIDCG-HREVMES-NDALLEKaCPKCGGDM 39
                                      6*******.7799985.55665666*****965 PP

>> zf-IS66  zinc-finger binding domain of transposase IS66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1         1   1.8e+03       4      10 ..      12      19 ..       9      23 .. 0.67
   2 ?   13.0   0.4   5.8e-05       0.1       1      29 [.      29      56 ..      29      56 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1
                           zf-IS66  4 CpcCGg.l 10
                                      C +CG+ +
  gi|242399915|ref|YP_002995340.1| 12 CIDCGHrE 19
                                      77888744 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 5.8e-05
                           zf-IS66  1 prtCpcCGgllkpigedrvreeldipPak 29
                                      +++Cp+CGg+++ +g + ++ +++  Pak
  gi|242399915|ref|YP_002995340.1| 29 EKACPKCGGDMVIVGFE-ITPVVEEEPAK 56
                                      689**************.99888877775 PP

>> DUF1272  Protein of unknown function (DUF1272)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.4   8.9e-05      0.16      27      52 ..      10      40 ..       8      42 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.9e-05
                           DUF1272 27 yEctFC.....aeCaeevlenvCPncgGelv 52
                                      yEc  C      e  +++le+ CP cgG++v
  gi|242399915|ref|YP_002995340.1| 10 YECIDCghrevMESNDALLEKACPKCGGDMV 40
                                      6666663322224568899**********97 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.3    0.0001      0.18       3      13 ..      31      41 ..      29      43 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0001
                                      E-SSS--EEEE CS
                    zf-C4_Topoisom  3 kCPkCggdLvl 13
                                       CPkCggd+v+
  gi|242399915|ref|YP_002995340.1| 31 ACPKCGGDMVI 41
                                      7********97 PP

>> zf_Rg  Reverse gyrase zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00012      0.22       4      17 ..      26      39 ..      24      41 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00012
                             zf_Rg  4 avfeklCPNCgGdi 17
                                      a++ek CP CgGd+
  gi|242399915|ref|YP_002995340.1| 26 ALLEKACPKCGGDM 39
                                      899*********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 ?   11.7   0.2   0.00011       0.2      68      97 ..       7      40 ..       2      47 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00011
                                      --EEEETTTS-EEECHH.H...HHS-TTTSSS-E CS
                              HypA 68 pvkvrCreCgkefelee.k...alrCpkCgsadv 97
                                      + +++C +Cg++  +e+ +   +  CpkCg+  v
  gi|242399915|ref|YP_002995340.1|  7 KGVYECIDCGHREVMESnDallEKACPKCGGDMV 40
                                      67889*****988866633355669*****9765 PP

>> DUF2072  Zn-ribbon containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00012      0.22       3      30 ..      11      40 ..      10     101 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00012
                           DUF2072  3 kCtkCek..vfedgskeilkGCpsCGgkkF 30
                                      +C +C++  v+e+ ++ + k Cp+CGg + 
  gi|242399915|ref|YP_002995340.1| 11 ECIDCGHreVMESNDALLEKACPKCGGDMV 40
                                      699**85438999999999*******9874 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.1    0.0068        12      29      37 ..      10      18 ..       7      20 .. 0.88
   2 ?    3.9   0.1     0.027        49       2      11 ..      31      40 ..      30      42 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0068
                           TFIIS_C 29 ykCtkCghr 37
                                      y+C++Cghr
  gi|242399915|ref|YP_002995340.1| 10 YECIDCGHR 18
                                      99****998 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.027
                           TFIIS_C  2 kCpkCgsrea 11
                                       CpkCg++ +
  gi|242399915|ref|YP_002995340.1| 31 ACPKCGGDMV 40
                                      6*****9865 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   2.2     0.003       5.3       4      28 ..      10      36 ..       8      37 .. 0.91
   2 ?    5.3   0.2     0.009        16       4      15 ..      30      41 ..      28      42 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.003
                     A2L_zn_ribbon  4 kvCsvCggngilnseqgyl..vCieCg 28
                                      ++C+ Cg+  ++ s+++ l   C++Cg
  gi|242399915|ref|YP_002995340.1| 10 YECIDCGHREVMESNDALLekACPKCG 36
                                      78***************98667****8 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.009
                     A2L_zn_ribbon  4 kvCsvCggngil 15
                                      k C +Cgg++++
  gi|242399915|ref|YP_002995340.1| 30 KACPKCGGDMVI 41
                                      6799******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       806  (0.0449551); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 2837.16
//
Query:       gi|242399916|ref|YP_002995341.1|  [L=130]
Description: hypothetical protein TSIB_1943 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-35  120.6   0.4    1.8e-35  120.6   0.4    1.7  3  DUF126         Aconitase X swivel domain
     0.0085   16.1   1.0     0.0099   15.9   1.0    1.1  1  DDR_swiveling  DD-reactivating factor swiveling domain
  ------ inclusion threshold ------
      0.069   11.8   0.1      0.081   11.6   0.1    1.1  1  GATase_2       Glutamine amidotransferases class-II


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 ?   -3.0   0.0       1.1   6.6e+03      20      33 ..       7      20 ..       4      22 .. 0.70
   2 !  120.6   0.4     3e-39   1.8e-35       1      80 []      24     103 ..      24     103 .. 0.99
   3 ?   -3.4   0.0       1.4   8.6e+03       5      14 ..     117     126 ..     114     128 .. 0.73

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.1
                                      SSTT-B-TTSEEEE CS
                            DUF126 20 plegqsiagkiLvl 33
                                      ++ g ++ g+ Lv 
  gi|242399916|ref|YP_002995341.1|  7 KIFGGKVRGTALVS 20
                                      67788888888875 PP

  == domain 2  score: 120.6 bits;  conditional E-value: 3e-39
                                       --TTS-B-TTT-BB-S.-SSSTT-B-TTSEEEES--S--SS-TTHHHHHHHHT-S-SEEEESS--HHHHHHHHHHT- CS
                            DUF126   1 lSflggvdpetGkvidkghplegqsiagkiLvlpsgkGStvgsyvllelakngtaPaAlilreadpilalGaivadi 77 
                                       lSflggvdp+tG++id +++++g+++++kiLv+p+gkGStvgsy++++l+kng+aP+A++++ea++i+a+Gai+a+i
  gi|242399916|ref|YP_002995341.1|  24 LSFLGGVDPNTGVIIDVESDIRGENVKDKILVFPRGKGSTVGSYIVYQLKKNGVAPKAIVVEEAETIVATGAIIAGI 100
                                       8**************************************************************************** PP

                                       -EE CS
                            DUF126  78 Plv 80 
                                       P+v
  gi|242399916|ref|YP_002995341.1| 101 PMV 103
                                       *98 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 1.4
                                       S-B-TTT-BB CS
                            DUF126   5 ggvdpetGkv 14 
                                        +vd+++G+v
  gi|242399916|ref|YP_002995341.1| 117 IEVDADKGEV 126
                                       4688888887 PP

>> DDR_swiveling  DD-reactivating factor swiveling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   1.0   1.7e-06    0.0099      15     100 ..      28     112 ..      15     128 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.7e-06
                     DDR_swiveling  15 gGlGlgvGetvkleelekakkeeevivvvpkevdfeeaaklinealekgvkikgailqkddgvlvenrlekkiPivd 91 
                                       gG+   +G+++++e+  + ++ ++ i+v p+    +  + ++ +  ++gv  k++++++ ++++ +  +   iP+vd
  gi|242399916|ref|YP_002995341.1|  28 GGVDPNTGVIIDVESDIRGENVKDKILVFPRGKGSTVGSYIVYQLKKNGVAPKAIVVEEAETIVATGAIIAGIPMVD 104
                                       8999999*******99999999999**************************************************** PP

                     DDR_swiveling  92 evslidkvP 100
                                        + +  k+ 
  gi|242399916|ref|YP_002995341.1| 105 KIDT-SKIR 112
                                       9865.4454 PP

>> GATase_2  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   1.4e-05     0.081     337     402 ..      63     127 ..      57     130 .] 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.4e-05
                                       E-SSEEEEEE-TT--S--EEEEETT--EEEESSTTSS---GGGEEEEEE--TT-EEEEETTTTEEE CS
                          GATase_2 337 tdGkvvgavLDRnGLRPaRylvtkddlvvlasEvGvldleeeevvekgrlqPGrmllvdleegril 402
                                       t G ++  +L +nG+ P  ++v + +  ++a  + +  ++  + +  ++++ G+++ vd ++g++ 
  gi|242399916|ref|YP_002995341.1|  63 TVGSYIVYQLKKNGVAPKAIVVEEAE-TIVATGAIIAGIPMVDKIDTSKIRSGQIIEVDADKGEVN 127
                                       56899999*********987776665.567888899999999999*****************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.55
# Mc/sec: 716.26
//
Query:       gi|242399917|ref|YP_002995342.1|  [L=386]
Description: hypothetical protein TSIB_1944 [Thermococcus sibiricus MM 739]
Scores for 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-146  487.3   0.0   3.4e-146  487.1   0.0    1.0  1  DUF521    Protein of unknown function (DUF521)
  ------ inclusion threshold ------
       0.22   12.0   2.1       0.59   10.6   0.1    2.7  4  HTH_40    Helix-turn-helix domain


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 !  487.1   0.0  3.8e-150  3.4e-146       1     400 [.       1     382 [.       1     383 [. 0.98

  Alignments for each domain:
  == domain 1  score: 487.1 bits;  conditional E-value: 3.8e-150
                            DUF521   1 mkLtkeeeamlnGeeGealqkameilvalGeilgAerLvpvtsahvsgvsyktigdaglefleelaekgakvrvptt 77 
                                       m+Ltkeee +l Ge+G  lqkameilvalGei+gA+rL+p++sa+++gvsyk+igdag+efl++++++gakv+v+tt
  gi|242399917|ref|YP_002995342.1|   1 MYLTKEEELILVGEYGYSLQKAMEILVALGEIYGADRLIPIKSAQIAGVSYKNIGDAGIEFLQDFVNAGAKVTVYTT 77 
                                       9**************************************************************************** PP

                            DUF521  78 lnpigvdlerweelgvdeefaekqeriieayeklGveltftCtpyllgnapkkGehlawsESsavvyaNSvlGarTn 154
                                       lnp+g+          de f+ekq++i+e y+++G+e+t tCtpy+  n pk+G+h+awsESsav++aNS++GarTn
  gi|242399917|ref|YP_002995342.1|  78 LNPAGIG---------DETFMEKQRKILELYRDMGIEITSTCTPYYGANLPKFGDHIAWSESSAVSFANSIIGARTN 145
                                       ***9887.........899********************************************************** PP

                            DUF521 155 reggpsalaaAitGrtpeyGlhldenRkptvlveveaesedeadygalGylvGkkvgeriPvlkglekpsedelKal 231
                                       reggps laaAi+G+tp+yGlhldenRk+tvlve+ a+ +d +dy++lGy++Gk +++++P++kgl+++++d lK+l
  gi|242399917|ref|YP_002995342.1| 146 REGGPSSLAAAIVGKTPNYGLHLDENRKATVLVEIIAKIKDFVDYSFLGYYLGKALKNDVPYFKGLKPEKNDYLKEL 222
                                       ***********************************999*************************************** PP

                            DUF521 232 gAalaasgavalfhiegvTPeaetleealgekekaekititkedleevleelskakeekvdlvalGcPhlsleElre 308
                                       gA++aa+g++al+h+eg TPe   ++ea+   +k eki++ +e+l+ev e++ +a+ +++d++++GcPh+s++E++e
  gi|242399917|ref|YP_002995342.1| 223 GASMAATGSIALYHVEGETPE---YKEAI--TDKIEKIQVGEEELKEVKEKF-NADWSEIDAIVIGCPHASIQEIKE 293
                                       *********************...77777..4779*****************.999999****************** PP

                            DUF521 309 laellkgkkkkvkvelwvttsrevkeeaerlglveklekaGvkvlsdtCmvvsplikkkevkkvatnSgKaahYlpg 385
                                       +aell+ ++k  k +l++t+sr vk+  ++lg++e +e+ ++k++ d+C++vsp+ k+  ++ +atnSgKa +Y+++
  gi|242399917|ref|YP_002995342.1| 294 IAELLRMREKPLKAPLLITASRVVKSLSDALGYTEVIERYNGKIIVDSCLIVSPVKKW--YNGIATNSGKASFYFSS 368
                                       *******************************************************985..9**************88 PP

                            DUF521 386 ltgvkvalgsleecv 400
                                         g kv+l ++++++
  gi|242399917|ref|YP_002995342.1| 369 G-GLKVRLDNTDKLI 382
                                       7.5*****9999887 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.36   3.2e+03      52      85 ..      20      54 ..       5      54 .. 0.74
   2 ?   -3.1   0.0       1.3   1.2e+04      51      66 ..      89     104 ..      73     113 .. 0.77
   3 ?   10.6   0.1   6.6e-05      0.59      50      83 ..     241     274 ..     224     280 .. 0.76
   4 ?   -3.2   0.0       1.3   1.2e+04      14      21 ..     290     297 ..     285     305 .. 0.62

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.36
                            HTH_40 52 eeekeIeeaiek.vgseklkpikealpeevsydeI 85
                                      +++ eI  a+ + +g ++l pik a    vsy  I
  gi|242399917|ref|YP_002995342.1| 20 QKAMEILVALGEiYGADRLIPIKSAQIAGVSYKNI 54
                                      55666777777656688899999999888888876 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.3
                            HTH_40  51 eeeekeIeeaiekvgs 66 
                                        e++++I e ++++g 
  gi|242399917|ref|YP_002995342.1|  89 MEKQRKILELYRDMGI 104
                                       5888899988888764 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 6.6e-05
                            HTH_40  50 seeeekeIeeaiek..vgseklkpikealpeevsyd 83 
                                       ++e +++I++ iek  vg+e+lk++ke+++ +  ++
  gi|242399917|ref|YP_002995342.1| 241 TPEYKEAITDKIEKiqVGEEELKEVKEKFNAD--WS 274
                                       4589999******95566999********764..44 PP

  == domain 4  score: -3.2 bits;  conditional E-value: 1.3
                            HTH_40  14 sieeIAke 21 
                                       +i+eIA+ 
  gi|242399917|ref|YP_002995342.1| 290 EIKEIAEL 297
                                       45666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      573  (0.0319594); 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: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.50
# Mc/sec: 2327.57
//
Query:       gi|242399918|ref|YP_002995343.1|  [L=53]
Description: hypothetical protein TSIB_1945 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       125  (0.00697194); expected 358.6 (0.02)
Passed bias filter:                      122  (0.00680462); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.32s 00:00:00.76 Elapsed: 00:00:00.49
# Mc/sec: 324.95
//
Query:       gi|242399919|ref|YP_002995344.1|  [L=313]
Description: Intein/rRNA intron-related DNA endonuclease [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-24   85.5   0.5    7.1e-13   48.7   0.1    2.5  2  LAGLIDADG_3     LAGLIDADG-like domain
      3e-06   27.2   0.1     0.0003   20.8   0.0    2.9  3  LAGLIDADG_WhiA  WhiA LAGLIDADG-like domain
     0.0025   18.0   0.0       0.25   11.5   0.0    2.5  2  Hom_end         Homing endonuclease
     0.0049   16.9   0.3      0.017   15.2   0.3    1.9  1  HTH_7           Helix-turn-helix domain of resolvase
  ------ inclusion threshold ------
      0.034   14.2   0.6        1.1    9.2   0.0    2.6  3  LAGLIDADG_2     LAGLIDADG DNA endonuclease family
      0.052   13.2   0.0       0.24   11.1   0.0    2.1  2  HTH_33          Winged helix-turn helix
      0.055   13.6   0.0       0.33   11.1   0.0    2.3  2  HTH_28          Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> LAGLIDADG_3  LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   0.1   5.8e-12   1.5e-08       4      54 ..      74     124 ..      71     146 .. 0.88
   2 !   48.7   0.1   2.8e-16   7.1e-13       3      83 .]     163     258 ..     161     258 .. 0.92

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 5.8e-12
                                       HHHHHHHHHHCCECCECSTTTTSEEEEES-HHHHHHHHHHHHHCT.HSCEE CS
                       LAGLIDADG_3   4 aafLrGlfdaDGsvskskkkgvsisltssskelledvqrlLlrlGIestiy 54 
                                       +a++ G f +DGs sk+k+++ +i+l+  +k+++e +q+ L+ lGI++t+ 
  gi|242399919|ref|YP_002995344.1|  74 LAYIIGVFLGDGSTSKRKDGKYRIKLKVIDKDFAERFQKTLEDLGIKATLG 124
                                       79*****************9999*************************986 PP

  == domain 2  score: 48.7 bits;  conditional E-value: 2.8e-16
                                       HHHHHHHHHHHCCECCECSTTTTS..EEEEES-HHHHHHHHHHHH.HCT.HSCEEEEEEE-SCCCC........... CS
                       LAGLIDADG_3   3 kaafLrGlfdaDGsvskskkkgvs..isltssskelledvqrlLl.rlGIestiyekkkakgrgvy........... 65 
                                        ++fL+Glfd++G  + s k++ +  + l++s++ell    +lLl ++GI +++ +++k++ + v            
  gi|242399919|ref|YP_002995344.1| 163 PREFLQGLFDSEGFPVISAKNTFRvqVALANSDLELLSFTEKLLLeKFGISTRLVQTHKKNTPIVIrgveykynvdm 239
                                       699***********999999998899*****************999***********6666666669********** PP

                                       .ECCCHCHCTTCGGGTTTX CS
                       LAGLIDADG_3  66 .rlliisgenlkrFlekig 83 
                                         l+i++ + +++F+++ig
  gi|242399919|ref|YP_002995344.1| 240 yLLWIYRLSHVQKFAKEIG 258
                                       9999**************8 PP

>> LAGLIDADG_WhiA  WhiA LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   1.2e-07    0.0003       3      55 ..      75     128 ..      73     144 .. 0.89
   2 ?    2.8   0.0     0.049   1.2e+02       3      60 ..     165     227 ..     163     233 .. 0.62
   3 ?   -0.8   0.0      0.65   1.7e+03      34      60 ..     247     273 ..     227     283 .. 0.66

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.2e-07
                    LAGLIDADG_WhiA   3 aflrGaflasGsindpekk.yhLEivspdeelaeqlqkllnefeleakilerrk 55 
                                       a++ G+fl+ Gs ++ + + y + + + d+++ae+ qk l+ ++++a +     
  gi|242399919|ref|YP_002995344.1|  75 AYIIGVFLGDGSTSKRKDGkYRIKLKVIDKDFAERFQKTLEDLGIKATLGFEHD 128
                                       799************98888************************9998765555 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.049
                    LAGLIDADG_WhiA   3 aflrGaflasGsindpekk.yhLEivspde..elaeqlqklln.efeleakiler.rkkyvvy 60 
                                        fl+G+f ++G+    +k+ +   +++ ++  el++   kll  +f++++++++  +k++ ++
  gi|242399919|ref|YP_002995344.1| 165 EFLQGLFDSEGFPVISAKNtFRVQVALANSdlELLSFTEKLLLeKFGISTRLVQThKKNTPIV 227
                                       799999999997444444447777666554115566666655448999999876504444455 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.65
                    LAGLIDADG_WhiA  34 aeqlqkllnefeleakilerrkkyvvy 60 
                                       ++ +qk ++e++++a+ ++++ +  + 
  gi|242399919|ref|YP_002995344.1| 247 LSHVQKFAKEIGFTARRKQKKLEDALH 273
                                       566777777777777777666555544 PP

>> Hom_end  Homing endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   9.7e-05      0.25      14      65 ..      74     126 ..      63     143 .. 0.85
   2 ?    3.9   0.0     0.023        59      16      42 ..     165     191 ..     161     240 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 9.7e-05
                           Hom_end  14 REaFlaGLvdsdgyvkkeked..satvktedksvmegivklarsLGikasvktk 65 
                                       + a++ G   +dg+++k+k +   + +k +dk   e+  k  + LGika+   +
  gi|242399919|ref|YP_002995344.1|  74 L-AYIIGVFLGDGSTSKRKDGkyRIKLKVIDKDFAERFQKTLEDLGIKATLGFE 126
                                       5.89*************99888999999*********************97654 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.023
                           Hom_end  16 aFlaGLvdsdgyvkkekedsatvkted 42 
                                        Fl GL ds+g      ++++ v+   
  gi|242399919|ref|YP_002995344.1| 165 EFLQGLFDSEGFPVISAKNTFRVQVAL 191
                                       6**********9777666666666554 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.3   6.6e-06     0.017      10      38 ..      15      49 ..       5      53 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 6.6e-06
                                      HHGGGGSSTTTT--STTTSSS......S---SSSS CS
                             HTH_7 10 dinrvvkLleeGisiskIAke......vnisRsTv 38
                                       ++r+++L+e+G+s s+IA +      v+isR Tv
  gi|242399919|ref|YP_002995344.1| 15 IMERAKELREQGTSYSQIASIigeefnVKISRPTV 49
                                      499****************9744444445777776 PP

>> LAGLIDADG_2  LAGLIDADG DNA endonuclease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   0.00043       1.1       4      50 ..      77     120 ..      74     151 .. 0.70
   2 ?    2.4   0.0     0.055   1.4e+02     128     162 ..     194     229 ..     173     236 .. 0.73
   3 ?   -1.8   0.0       1.1   2.7e+03      36      75 ..     240     280 ..     220     296 .. 0.55

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00043
                                       HHHHHHTT-EEE-SSTTS-BEEEEEE..S-HHHHHHHHHHTGGG--S CS
                       LAGLIDADG_2   4 liGlLLGDgslekrkkrknvrfefkqskkhkeYllyvfellkeylls 50 
                                       +iG+ LGDgs  +++k+ ++r+++k   ++k++++   + l++++++
  gi|242399919|ref|YP_002995344.1|  77 IIGVFLGDGST-SKRKDGKYRIKLKV--IDKDFAERFQKTLEDLGIK 120
                                       89999999999.55555566666654..7777777777777777665 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.055
                                       S-HHHHHHHHHHHHHHH---EEEEEETTE.EEEEE- CS
                       LAGLIDADG_2 128 fseeevellvkaLkdkfnlkcrvkkkgkk.yviyik 162
                                          e + +  k L +kf++  r+ +++kk   i i+
  gi|242399919|ref|YP_002995344.1| 194 SDLELLSFTEKLLLEKFGISTRLVQTHKKnTPIVIR 229
                                       4455555556899**********9999987556655 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 1.1
                                       HHHHHHHHTG.GG--S--EEEEEE-TTSEEEEEEEE---BG CS
                       LAGLIDADG_2  36 Yllyvfellk.eyllsnpkivkrktrrksetklrfqtrslp 75 
                                       Yll+++ l + +  +++  +  r++++k e +l+++ +++ 
  gi|242399919|ref|YP_002995344.1| 240 YLLWIYRLSHvQKFAKEIGFTARRKQKKLEDALHLSEMPVI 280
                                       55666554331222333334444444456666666666554 PP

>> HTH_33  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   9.2e-05      0.24       8      33 ..      30      55 ..      25      56 .. 0.91
   2 ?   -3.1   0.0       2.5   6.4e+03      22      39 ..     245     262 ..     245     263 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9.2e-05
                            HTH_33  8 arlaqlieerfgvsysvsgvyrlLkr 33
                                      +++a  i e+f+v++s+ +v r+ k 
  gi|242399919|ref|YP_002995344.1| 30 SQIASIIGEEFNVKISRPTVMRWCKG 55
                                      689********************986 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.5
                            HTH_33  22 ysvsgvyrlLkrlGfsyq 39 
                                       y  s+v +  k++Gf+ +
  gi|242399919|ref|YP_002995344.1| 245 YRLSHVQKFAKEIGFTAR 262
                                       566778888888999865 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00013      0.33       8      35 ..      21      55 ..      14      58 .. 0.81
   2 ?   -1.4   0.0         1   2.7e+03      20      30 ..     208     218 ..     204     222 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00013
                            HTH_28  8 lla.aGhsvre....aArelgi..srrtvyrWikr 35
                                      +l  +G s+++    + +e+++  sr tv rW+k 
  gi|242399919|ref|YP_002995344.1| 21 ELReQGTSYSQiasiIGEEFNVkiSRPTVMRWCKG 55
                                      45524669999999999****************95 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1
                            HTH_28  20 relgisrrtvy 30 
                                       +++gis r v+
  gi|242399919|ref|YP_002995344.1| 208 EKFGISTRLVQ 218
                                       89***999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       729  (0.0406604); expected 358.6 (0.02)
Passed bias filter:                      599  (0.0334096); 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: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.50
# Mc/sec: 1884.41
//
Query:       gi|242399920|ref|YP_002995345.1|  [L=44]
Description: hypothetical protein TSIB_1947 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       240  (0.0133861); expected 358.6 (0.02)
Passed bias filter:                      200  (0.0111551); 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: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 284.35
//
Query:       gi|242399921|ref|YP_002995346.1|  [L=415]
Description: Phosphohydrolase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-14   53.8   0.0    3.3e-14   53.0   0.0    1.4  1  2_5_RNA_ligase2  2'-5' RNA ligase superfamily
    5.9e-07   30.2   3.1    1.4e-06   29.0   3.1    1.6  1  Metallophos      Calcineurin-like phosphoesterase
    2.6e-06   27.7   0.0    4.9e-06   26.8   0.0    1.4  1  Metallophos_2    Calcineurin-like phosphoesterase superfamily
  ------ inclusion threshold ------
       0.37   11.0   3.7       0.98    9.7   1.0    2.8  2  DapH_N           Tetrahydrodipicolinate succinyltransferase N


Domain annotation for each model (and alignments):
>> 2_5_RNA_ligase2  2'-5' RNA ligase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.0   0.0   7.4e-18   3.3e-14      14     141 ..      41     182 ..      25     210 .. 0.81

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 7.4e-18
                   2_5_RNA_ligase2  14 rslydkayprwp..pHitLlypfvededl..adlaellsrlaketepfevrldgfgvFeh.kksvvylsvsdsealq 85 
                                       ++  + ++ rw   pHitL+y f  ++     d+a+ ++++a+ ++ +++  dgf v  + k++v   +++ s++l+
  gi|242399921|ref|YP_002995346.1|  41 THIKSTHTGRWHkvPHITLIYNFRLKKGItdRDIAKIIQNVASKYTFVKFYYDGFEVKKGdKGYVFAFKIKASDKLK 117
                                       55566678888889*************9999***************************995555************* PP

                   2_5_RNA_ligase2  86 alraallealpeagdkeds.........geftPHlTiaqsadstsaaelleklaqalpplefevd 141
                                       +lr+++++++++  + + +         ++f +H+Ti+++ +++sa  l+++ + + ++l++   
  gi|242399921|ref|YP_002995346.1| 118 KLRRDIYNKIKPFIEERPDvikfndadeDKFWFHATIGYQLSEKSANILIKETQTEYEYLPAFAL 182
                                       ************9777766788999999******************7777766444443333333 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   3.1   3.1e-10   1.4e-06       2     123 ..     241     374 ..     240     411 .. 0.65

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 3.1e-10
                                       EEEEEESBTB......TTCCTHHHHHHHHHHHHHHH.....TTESEEEEESTSSSSSHHHHHHHHHHHHHHHHTSEE CS
                       Metallophos   2 rilvigDlHl......algggqlddllkllddllre.....ekpdlvllaGDlvdrgdlekellellaalvkypipv 67 
                                       +i++i+D+H+      +++  ++ d++++ + ll++     +++d+v ++GD +  g  + +  ++l++l     ++
  gi|242399921|ref|YP_002995346.1| 241 KIWLISDTHFdhaniiKYCARPFVDIKEMNRVLLKNwnntvKRNDIVYFLGD-ISFGKHSRSPRYWLSKLNG---KI 313
                                       8***************9999999999999988877766677788999999**.8888777755555555565...99 PP

                                       EEEC-TTS....CHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTE..EEEEEEESE CS
                       Metallophos  68 ylllGNHe....gfeeellnkygylgifsepwrsdaevfnnlplaslgsgs..lkvlllhGg 123
                                       + ++GNHe    g ++e+ n  g++        +d++ f+++ + ++  ++  +++ +++ +
  gi|242399921|ref|YP_002995346.1| 314 IYIKGNHEktnlGKHYEIVNYKGHKFF-LVHDPKDVDSFDGWIIHGHKHNNdlINYPFVNKE 374
                                       ********7755323333333333222.2223333556666666655555455455444444 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 !   26.8   0.0   1.1e-09   4.9e-06       2     103 ..     241     357 ..     241     381 .. 0.76

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 1.1e-09
                     Metallophos_2   2 klaiiSDlH...................snldaleavlealkevgvdaiihaGDl..eeeepevleellela.pvla 56 
                                       k+ +iSD+H                    n+ +l+++ + +k+   d ++++GD+  ++ + +  ++l +l+ ++++
  gi|242399921|ref|YP_002995346.1| 241 KIWLISDTHfdhaniikycarpfvdikeMNRVLLKNWNNTVKRN--DIVYFLGDIsfGKHSRSPRYWLSKLNgKIIY 315
                                       6889*****************9999999899999999*******..********997666666899999999***** PP

                     Metallophos_2  57 VrGNnDeevveedvlreaaelgtdlpeeaelelagekvlliHgdpl.........g 103
                                       ++GN++           ++ lg++   ++ ++ +g k++l+H+ ++         +
  gi|242399921|ref|YP_002995346.1| 316 IKGNHE-----------KTNLGKH---YEIVNYKGHKFFLVHDPKDvdsfdgwiiH 357
                                       ******...........4444444...47777778888888877433333333332 PP

>> DapH_N  Tetrahydrodipicolinate succinyltransferase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   1.0   0.00022      0.98       4      68 ..      72     139 ..      69     147 .. 0.72
   2 ?    0.3   0.1      0.18   8.3e+02      21      48 ..     314     340 ..     312     352 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00022
                                       HHHHHHHHH.---B-EEEEEEEE-.C.TC----.TTSEEEE-SSEEEEEEE.HHHHHHHHHHTTTTEE CS
                            DapH_N   4 eeIikyIke.akKkTpvkvYvkgelkeeelefp.eevkvfgsedsgvvfGd.wkeieevleenkdkie 68 
                                       ++I+k+I++ a K T vk+Y++g + ++  +     +k+  s++ + +  d +++i++++ee+ d i+
  gi|242399921|ref|YP_002995346.1|  72 RDIAKIIQNvASKYTFVKFYYDGFEVKKGDKGYvFAFKIKASDKLKKLRRDiYNKIKPFIEERPDVIK 139
                                       689****99789**********9765444433335677777777777777745677777777777665 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.18
                                       EEEEE-.C.TC----TTSEEEE-SSEEE CS
                            DapH_N  21 vYvkgelkeeelefpeevkvfgsedsgv 48 
                                       +Y+kg+ ++ +l  + e+  + ++++  
  gi|242399921|ref|YP_002995346.1| 314 IYIKGNHEKTNLGKHYEIVNYKGHKF-F 340
                                       7*****87666644444444444333.3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       834  (0.0465168); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); 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: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 2579.05
//
Query:       gi|242399922|ref|YP_002995347.1|  [L=276]
Description: Carbohydrate/pyrimidine kinase, PfkB family [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.9e-43  147.6   0.0    5.9e-43  147.3   0.0    1.1  1  PfkB          pfkB family carbohydrate kinase
      1e-09   38.2   0.0    2.1e-09   37.2   0.0    1.4  1  Phos_pyr_kin  Phosphomethylpyrimidine kinase


Domain annotation for each model (and alignments):
>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.3   0.0   6.6e-47   5.9e-43       4     295 ..       3     271 ..       1     275 [. 0.88

  Alignments for each domain:
  == domain 1  score: 147.3 bits;  conditional E-value: 6.6e-47
                                       EEEEEEEEEEEEEECSSHTTSEEEESEEEEEEESHHHHHHHHHHHTT-EEEEEEEEESSHHHHHHHHHHHHTTEEET CS
                              PfkB   4 vvviGealidliavseklegelvevktveksaGGagaNvAvalarlgadvafigavGdDnfGeflleelkkegvdtd 80 
                                       +vv+G++ id + + +k         +    +GGa+  vA+ +a  ga+v ++++vG+D+  e l+++  +e +d++
  gi|242399922|ref|YP_002995347.1|   3 LVVLGHVAIDHVIFPDK---------REIILPGGAATAVATSAALSGAKVGLVTKVGKDFPKEWLKKL--EEILDIK 68 
                                       67778888888877777.........666779****************************66666666..788**** PP

                                       TEEEESSSEEEEEEEEETTTSEEEEEEEEGGGGGHHHHHHHHHHHHHGCTSEEEEESEECTTSHHHHHHHHHHHHHH CS
                              PfkB  81 yvkidedtrtglalivvdedgertivfnrgaaadltkeeleededlleeadllyisgllsselpeavleelaeaakn 157
                                       +v++ e+    +++i  + dg  +  ++ g a  + +++     ++  +a++++i+  +++e   ++ ++l+  + +
  gi|242399922|ref|YP_002995347.1|  69 GVHVLEGNTIHIYMIYHE-DGTVDAPVDMGVAQRMGETKI---PEEYLSAKIFHIAP-IPPEEQLKAINRLRGKRIS 140
                                       *******999***99999.688899999998888888765...666689*******8.6665555555555555555 PP

                                       TTEEEEEECESSSHHHHHHHHHHHCTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTSSEEEEEEGGGEEEE CS
                              PfkB 158 ggtfdpnlldplgaqfkeallellaladllkpneeElealtgekledieealaalhklkakgaktvvvtlGkeGalv 234
                                        + f p + +      ke ++e+++ a +++pne+E+  +tgek  +ieea+++lh+    g k++v+t+G++G+l 
  gi|242399922|ref|YP_002995347.1| 141 LD-FNPTYIEEYKT-KKELMREIISRAEIIFPNEREALTITGEK--SIEEAAKKLHE---WGSKLIVITMGERGVLM 210
                                       55.99999999998.69***************************..**********9...899************** PP

                                       EETTEEEEEEE.SSSS-SBGTTHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHTSSSS CS
                              PfkB 235 vekdgelkvpavpkvkvvDttGAGDsfvggflaallegksleealrfanavAalvvqkkga 295
                                       ++++   +++a+p  ++vD+tGAGD+f+ggfla +++gk+lee+++ +   A  v++kkg+
  gi|242399922|ref|YP_002995347.1| 211 YDGERFTRFEALPISEIVDPTGAGDAFAGGFLAYYVKGKPLEECIKQGLLRAREVLKKKGS 271
                                       ********************************************************99996 PP

>> Phos_pyr_kin  Phosphomethylpyrimidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.2   0.0   2.3e-13   2.1e-09     109     224 ..     154     258 ..     147     271 .. 0.88

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 2.3e-13
                                       HHHHHHHTGGG-SEEE-BHHHHHHHHT---SSHHHHHHHHHHHHHTT-SEEEEEEGGS-SSSEEEEEEEETSSEEEE CS
                      Phos_pyr_kin 109 vealkeeLlplatvitPNlpEaeaLlgekikteedmkeaakkllklgakaVlikGghlegeeavvtdvlydgeevee 185
                                        + l +e++ +a++i PN  Ea  ++g     e++++eaakkl++ g+k ++i+ g+    + v   ++ydge++++
  gi|242399922|ref|YP_002995347.1| 154 KKELMREIISRAEIIFPNEREALTITG-----EKSIEEAAKKLHEWGSKLIVITMGE----RGV---LMYDGERFTR 218
                                       4566677*******************9.....89********************998....355...788******* PP

                                       EEEE----.S--BTHHHHHHHHHHHHHHCTSSHHHHHHHH CS
                      Phos_pyr_kin 186 leaeriet.knthGtGCtlssaiaaelakgesleeAvkkA 224
                                       +ea  i++  +  G+G++++    a+  kg++lee +k++
  gi|242399922|ref|YP_002995347.1| 219 FEALPISEiVDPTGAGDAFAGGFLAYYVKGKPLEECIKQG 258
                                       **97765427889************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.49
# Mc/sec: 1705.46
//
Query:       gi|242399923|ref|YP_002995348.1|  [L=39]
Description: hypothetical protein TSIB_1950 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       714  (0.0398237); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 296.52
//
Query:       gi|242399924|ref|YP_002995349.1|  [L=164]
Description: hypothetical protein TSIB_1951 [Thermococcus sibiricus MM 739]
Scores for 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-46  155.5   2.4    1.1e-45  155.3   2.4    1.0  1  DUF2118        Uncharacterized protein conserved in archaea (
  ------ inclusion threshold ------
      0.037   13.8   0.1       0.98    9.3   0.0    2.3  2  Biotin_lipoyl  Biotin-requiring enzyme
       0.15   12.4   0.1       0.84   10.0   0.0    2.1  2  YjzC           YjzC-like protein


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 !  155.3   2.4   1.8e-49   1.1e-45       1     151 []       2     163 ..       2     163 .. 0.99

  Alignments for each domain:
  == domain 1  score: 155.3 bits;  conditional E-value: 1.8e-49
                           DUF2118   1 yklPrlYvEgkese...............eevevileeeeevekfadkveekklkgkvvYeelldeivdvleekvtr 62 
                                       +k+P+l+vE + +e               +++ev ++++e++++f+d+ ++k++k k+vY++ ++ +vd+ e+k+  
  gi|242399924|ref|YP_002995349.1|   2 EKIPQLFVESNLEEcvdgekarvdcriiqDNIEVKVKKGEKIPEFIDPKRAKFMK-KEVYDR-FHFYVDKYEHKMMC 76 
                                       59***************************************************98.******.************** PP

                           DUF2118  63 dviivlpderklillkkGdklklipvegvkvtlivdvGdrveegdtlaavttrkgevrylrapvegvVvfikeepag 139
                                       + ii lpd+r+ i l kGd+l+l+pveg++ ++i+ vG+rv++ d++aa+tt+kgev+yl++p++gvVv+i+e ++ 
  gi|242399924|ref|YP_002995349.1|  77 NAIIILPDRRTEIRLYKGDELMLLPVEGYVSSIIAGVGNRVRKSDAFAAITTKKGEVHYLKPPKTGVVVYIDEFTN- 152
                                       ****************************************************************************. PP

                           DUF2118 140 krpnyiyyilpe 151
                                        rp+y+yyilpe
  gi|242399924|ref|YP_002995349.1| 153 -RPHYVYYILPE 163
                                       .**********8 PP

>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.029   1.7e+02      17      28 ..      33      44 ..      27      46 .. 0.81
   2 ?    9.3   0.0   0.00016      0.98      14      56 ..     103     147 ..      99     150 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.029
                                      CSESSSTTCEE- CS
                     Biotin_lipoyl 17 vevlvkvGdkVk 28
                                      +ev+vk+G+k+ 
  gi|242399924|ref|YP_002995349.1| 33 IEVKVKKGEKIP 44
                                      689999999985 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00016
                                       E..ECSESSSTTCEE-TTSEEEEEECTTEEEE.EEBSSSEEEEEE CS
                     Biotin_lipoyl  14 eg.vvevlvkvGdkVkagqvlaeveamKmeme.ieapkaGvvkei 56 
                                       eg v +++  vG  V + +  a + + K e++ ++ pk+Gvv++i
  gi|242399924|ref|YP_002995349.1| 103 EGyVSSIIAGVGNRVRKSDAFAAITTKKGEVHyLKPPKTGVVVYI 147
                                       5778889999999*************9999864888999999987 PP

>> YjzC  YjzC-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00014      0.84      29      45 ..      29      45 ..      19      55 .. 0.86
   2 ?   -1.0   0.0      0.39   2.3e+03      33      42 ..      87      96 ..      84      97 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00014
                              YjzC 29 vkdpkevkLekGdrFPe 45
                                      ++d+ evk++kG++ Pe
  gi|242399924|ref|YP_002995349.1| 29 IQDNIEVKVKKGEKIPE 45
                                      89**************9 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.39
                              YjzC 33 kevkLekGdr 42
                                      +e++L kGd+
  gi|242399924|ref|YP_002995349.1| 87 TEIRLYKGDE 96
                                      689*****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       641  (0.0357521); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1159.42
//
Query:       gi|242399925|ref|YP_002995350.1|  [L=95]
Description: hypothetical protein TSIB_1952 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       401  (0.022366); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 617.61
//
Query:       gi|242399926|ref|YP_002995351.1|  [L=44]
Description: hypothetical protein TSIB_1953 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       138  (0.00769703); expected 358.6 (0.02)
Passed bias filter:                      116  (0.00646996); 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 0.22s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 341.24
//
Query:       gi|242399927|ref|YP_002995352.1|  [L=163]
Description: FKBP-type PPIase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-22   78.4   0.0    6.3e-22   77.7   0.0    1.4  1  FKBP_C    FKBP-type peptidyl-prolyl cis-trans isomerase


Domain annotation for each model (and alignments):
>> FKBP_C  FKBP-type peptidyl-prolyl cis-trans isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.7   0.0   3.5e-26   6.3e-22       4      93 ..       5     150 ..       2     151 .. 0.83

  Alignments for each domain:
  == domain 1  score: 77.7 bits;  conditional E-value: 3.5e-26
                                       BB-TTCEEEEEEEEEETTSSEEEEH...........CC..HTSEEEEETTSSSSCHHHHHHHTTSBTT-EEEEEEEG CS
                            FKBP_C   4 eakegdtVtvhykgkledgkvfdss...........rs..rakplefkvGsgqvikGfeealegmkvGekrtltipp 67 
                                       ++++gd+V ++y gk+e+g+vfd++           ++   + pl  +vG g++i+G++e+l gm+vGek+t+tipp
  gi|242399927|ref|YP_002995352.1|   5 KVEKGDFVVFNYIGKFENGEVFDTTyediakeagiyMEdrTYGPLGANVGVGELIPGMDEGLIGMEVGEKKTITIPP 81 
                                       4799*********************7777777777621669************************************ PP

                                       GGTTTT......................................TTBCTTT.....B.TTSEEEEEEEE CS
                            FKBP_C  68 elaYge......................................kglaggv.....ippnatLvFeveL 93 
                                       e +Yg                                        g+++ +       +++tLvFeve+
  gi|242399927|ref|YP_002995352.1|  82 EKGYGIprddliidvptsefekagiepiegayimtdsgiaritaVGEENVTldfnhPLAGKTLVFEVEI 150
                                       ******9*********99999988888888888877777777763332222344445566********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.46
# Mc/sec: 1062.29
//
Query:       gi|242399928|ref|YP_002995353.1|  [L=308]
Description: Bacterial type II secretion system protein F domain, [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.3e-16   59.0   1.5    4.3e-16   59.0   1.5    3.0  3  T2SSF           Type II secretion system (T2SS), protein F
  ------ inclusion threshold ------
      0.065   12.9   0.0        0.1   12.3   0.0    1.2  1  DHFR_1          Dihydrofolate reductase
        1.1    8.8  14.0        1.9    8.1   1.4    2.4  2  Peptidase_M50B  Peptidase M50B-like


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 ?   -5.0   4.4         3   1.8e+04     108     124 ..      44      60 ..      35      61 .. 0.58
   2 !   59.0   1.5   7.1e-20   4.3e-16       4     123 ..     104     227 ..     102     229 .. 0.91
   3 ?    1.9   0.2     0.035   2.1e+02      97     118 ..     275     296 ..     270     299 .. 0.84

  Alignments for each domain:
  == domain 1  score: -5.0 bits;  conditional E-value: 3
                                       XXXXXXXXXXXXXXXXX CS
                             T2SSF 108 llvvallvllillaill 124
                                       l+ ++l +l +++++l+
  gi|242399928|ref|YP_002995353.1|  44 LVSMLLGILTAIVVFLI 60 
                                       44555555555555555 PP

  == domain 2  score: 59.0 bits;  conditional E-value: 7.1e-20
                                       HHHHHHHTT--HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTSSHHHHHC....T-TT.TS.-HHHHHHHHHHHHHT CS
                             T2SSF   4 qlatllsaGvplveaLellaeeaengplaeelkriarrlraGgslseale....rtpssef.pelvvqlirageegg 75 
                                       ++a+ l+aGv++ eaLe ++    +g+l++e+kr++ +++ G s  eal+    r+ +s +  +  + +++a e+g 
  gi|242399928|ref|YP_002995353.1| 104 YIASSLRAGVSFSEALEEASTAR-FGALTDEFKRTVSEIKRGRSTYEALKafalRNRRSIIiYRSTMIILEAYERGA 179
                                       57999***************999.****************************9955555666*************** PP

                                       -HHHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXXXX CS
                             T2SSF  76 nLaevLerlaeyleeerelrrkllaallepllllvvallvllillail 123
                                       ++a+vL ++a +++e ++++++++a++   ++++++a+ +l++ ++ +
  gi|242399928|ref|YP_002995353.1| 180 PMADVLVAVANDVREILRIKKERKASTGMQAMFFIIASGFLGPAILGI 227
                                       *************************99999999988888887776544 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.035
                                       HHHHHHHTTXXXXXXXXXXXXX CS
                             T2SSF  97 kllaallepllllvvallvlli 118
                                       k  a + + ++l++++l+++l+
  gi|242399928|ref|YP_002995353.1| 275 KFSAGFKYSAMLAIMGLVIFLV 296
                                       6778899999*******99987 PP

>> DHFR_1  Dihydrofolate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.7e-05       0.1      43      84 ..     144     185 ..     132     209 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.7e-05
                                       EHHHHHCC-.S--TTCEEEEE-S-TT---TTEEEESSHHHHC CS
                            DHFR_1  43 GrkTfeslgkrpLpnrkniVltrnedlkvegvevvssleeal 84 
                                       Gr T+e+l+  +L nr++i++ r++ +  e  e  + ++++l
  gi|242399928|ref|YP_002995353.1| 144 GRSTYEALKAFALRNRRSIIIYRSTMIILEAYERGAPMADVL 185
                                       9********99**********999885554444444444443 PP

>> Peptidase_M50B  Peptidase M50B-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   1.4   0.00032       1.9     117     162 ..      43      88 ..      25     101 .. 0.78
   2 ?    5.5   5.3    0.0019        11      63     108 ..     208     254 ..     202     303 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00032
                    Peptidase_M50B 117 lvlllllgallllvlllaedelleflllflgvflllgsvrdiddli 162
                                       l++ +llg+l+++v++l ++  l +l +f++vfl ++ v++ ++l 
  gi|242399928|ref|YP_002995353.1|  43 LLVSMLLGILTAIVVFLIPSVKLYALPVFFIVFLGIAWVYPYWKLA 88 
                                       5677788888888888898999999999999999999999988885 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0019
                    Peptidase_M50B  63 glgqiltllaGYlgpallGlllillsasgkarlllvllv.llllvll 108
                                          ++++++ G+lgpa+lG++  l+++ +++++ l l v +++ vll
  gi|242399928|ref|YP_002995353.1| 208 MQAMFFIIASGFLGPAILGIVSQLIGSMNTPEIGLNLPVdAIYNVLL 254
                                       55699*****************9999999988877655523333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       948  (0.0528752); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 1881.13
//
Query:       gi|242399929|ref|YP_002995354.1|  [L=353]
Description: Bacterial type II secretion system protein F domain protein [Thermococcus sibiricus MM 739]
Scores for 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-23   80.6   1.0      9e-23   80.6   1.0    3.1  4  T2SSF     Type II secretion system (T2SS), protein F
    6.6e-05   21.9   4.6      0.017   13.9   0.3    2.0  2  DUF2207   Predicted membrane protein (DUF2207)
  ------ inclusion threshold ------
       0.31   11.4   9.4        1.5    9.2   8.7    2.0  2  Cgr1      Cgr1 family
       0.43   10.1   3.3         19    4.8   2.3    2.1  2  RED_N     RED-like protein N-terminal region


Domain annotation for each model (and alignments):
>> T2SSF  Type II secretion system (T2SS), protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1         1   4.6e+03      82      97 ..      43      58 ..      37      98 .. 0.58
   2 ?   -0.3   1.9      0.21   9.5e+02     100     117 ..     120     137 ..     104     156 .. 0.54
   3 !   80.6   1.0     2e-26     9e-23       2     123 ..     185     309 ..     184     311 .. 0.97
   4 ?   -4.5   3.2         4   1.8e+04     102     124 ..     322     344 ..     314     345 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1
                                      HHHHHHHHHHHHHHHH CS
                             T2SSF 82 erlaeyleeerelrrk 97
                                      ++l++++ ee e + +
  gi|242399929|ref|YP_002995354.1| 43 KKLQREITEEKEKKEE 58
                                      3444444444333332 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.21
                                       HHHHTTXXXXXXXXXXXX CS
                             T2SSF 100 aallepllllvvallvll 117
                                       a ++++ ++ ++ +++l+
  gi|242399929|ref|YP_002995354.1| 120 ALMIGVSIFTAIFAFILG 137
                                       223333333333333333 PP

  == domain 3  score: 80.6 bits;  conditional E-value: 2e-26
                                       HHHHHHHHHTT--HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTSSHHHHHC....T-TT.TS-HHHHHHHHHHHHH CS
                             T2SSF   2 lrqlatllsaGvplveaLellaeeaengplaeelkriarrlraGgslseale....rtpssefpelvvqlirageeg 74 
                                       lr++a+llsaGv+++ea+ ++a+ + +gp++ee++ ++r++  G+s+++al     r+ s+  +++v q++ra + g
  gi|242399929|ref|YP_002995354.1| 185 LRHMASLLSAGVGIAEAMVSVANAD-YGPISEEFELMIRDMHGGTSFEDALTrfeeRMASENVSRVVKQILRATRFG 260
                                       89***********************.**************************999999999**************** PP

                                       T-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXXXX CS
                             T2SSF  75 gnLaevLerlaeyleeerelrrkllaallepllllvvallvllillail 123
                                       gnLa++L +lae++  e++++  +  ++   ++++++ + ++++ l+++
  gi|242399929|ref|YP_002995354.1| 261 GNLADILYKLAEDFSFEYRMKLVEYIQKVNGIAFVYMFITIIMPTLFVV 309
                                       ********************************************99887 PP

  == domain 4  score: -4.5 bits;  conditional E-value: 4
                                       HHTTXXXXXXXXXXXXXXXXXXX CS
                             T2SSF 102 llepllllvvallvllillaill 124
                                        + p +l+v++l+ ++++ ++++
  gi|242399929|ref|YP_002995354.1| 322 VMPPSALAVILLFAFPAISSMVV 344
                                       56677888888888888888876 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.3   3.8e-06     0.017     321     431 ..      40     162 ..      15     178 .. 0.62
   2 !   10.0   0.5   5.7e-05      0.26     351     432 ..     257     349 ..     211     353 .] 0.53

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.8e-06
                           DUF2207 321 alldlLfdkseeg.ks.............lkeikkyakkskk..kakkfkkalkkwksavkkkergyfdkkgkkklk 381
                                       +ll+ L+++++e+  +             +ke++k +++  +    ++f++ ++++++++k   + +++++ k  + 
  gi|242399929|ref|YP_002995354.1|  40 QLLKKLQREITEEkEKkeeeeieeliewrKKELEKSFSHRFSefILRRFRRPVESFTRSIKGLDYDLLRANIKMSKE 116
                                       34444444444442223444444443333344444444433357889999999999999999999999999999999 PP

                           DUF2207 382 klsalglgliilglilillallllvlllvfllilllillliaiivlllfs 431
                                        + al +g+ i+  i+++++ +ll    ++   ++++l+l+++i  +l+ 
  gi|242399929|ref|YP_002995354.1| 117 QYVALMIGVSIFTAIFAFILGVLL----ILPIDISIMLGLLGFIGGFLYM 162
                                       999999999888888887776664....4444444444444444444433 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 5.7e-05
                           DUF2207 351 kkfkkalkkwksavkk....kergyfdkkgkkklk.klsalglgliilglilillallllvll.............. 408
                                       ++f  +l+++  ++ +    +         + kl  +++ ++ ++++ ++i i++  l++v +              
  gi|242399929|ref|YP_002995354.1| 257 TRFGGNLADILYKLAEdfsfE--------YRMKLVeYIQKVNGIAFVYMFITIIMPTLFVV-Ailaasmmsrtvvmp 324
                                       444444444444444422221........22222202222222222222222222222222.123556677888899 PP

                           DUF2207 409 .lvfllilllillliaiivlllfsr 432
                                        + +++ill++++ i+++v+++++r
  gi|242399929|ref|YP_002995354.1| 325 pSALAVILLFAFPAISSMVVFMIKR 349
                                       9999999999999999999888754 PP

>> Cgr1  Cgr1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   8.7   0.00034       1.5      41      79 ..      37      75 ..      31      87 .. 0.90
   2 ?    0.3   0.0       0.2   9.1e+02      29      49 ..     233     253 ..     222     257 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00034
                              Cgr1 41 kkakaiKklekeLkdekeaerqrrieaikerrkakeEke 79
                                      ++ + +Kkl++e+ +eke+++++ ie++ e rk++ Ek 
  gi|242399929|ref|YP_002995354.1| 37 ERLQLLKKLQREITEEKEKKEEEEIEELIEWRKKELEKS 75
                                      677899*****************************9995 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.2
                              Cgr1  29 kkkswekrqekrkkakaiKkl 49 
                                         +++e+r++ ++ ++ +K+ 
  gi|242399929|ref|YP_002995354.1| 233 ALTRFEERMASENVSRVVKQI 253
                                       57899****999999999986 PP

>> RED_N  RED-like protein N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   2.3    0.0042        19      94     124 ..      40      71 ..      39      85 .. 0.69
   2 ?    4.0   0.0     0.007        31      84      97 ..      95     108 ..      93     119 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0042
                                       XXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXX CS
                             RED_N  94 aLLqkvrseikkkeeeeeeee.ekelekkaee 124
                                        LL+k ++ei++++e++eeee e+ +e +++e
  gi|242399929|ref|YP_002995354.1|  40 QLLKKLQREITEEKEKKEEEEiEELIEWRKKE 71 
                                       59********9988777666635555544433 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.007
                                       XXXXXXXXXXXXXX CS
                             RED_N  84 hThLvKGLDyaLLq 97 
                                        T  +KGLDy LL+
  gi|242399929|ref|YP_002995354.1|  95 FTRSIKGLDYDLLR 108
                                       57889*******95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2033  (0.113392); expected 358.6 (0.02)
Passed bias filter:                      877  (0.0489152); expected 358.6 (0.02)
Passed Vit filter:                       135  (0.0075297); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.70u 0.32s 00:00:01.02 Elapsed: 00:00:00.49
# Mc/sec: 2145.37
//
Query:       gi|242399930|ref|YP_002995355.1|  [L=1113]
Description: Type II secretion system protein [Thermococcus sibiricus MM 739]
Scores for complete 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-55  186.2   0.0    1.2e-51  175.4   0.0    2.4  2  T2SSE            Type II/IV secretion system protein
    1.3e-22   80.2   0.0    4.7e-22   78.4   0.0    2.0  1  Intein_splicing  Intein splicing domain
      1e-19   70.6   0.1    1.8e-16   60.2   0.0    2.8  2  LAGLIDADG_3      LAGLIDADG-like domain
    3.4e-06   27.2   0.0    3.5e-05   23.9   0.0    2.4  2  Hom_end          Homing endonuclease
    0.00011   21.7   1.0    0.00031   20.2   0.2    2.1  2  FtsK_SpoIIIE     FtsK/SpoIIIE family
    0.00087   19.1   0.1        1.8    8.3   0.0    2.4  2  DEAD             DEAD/DEAH box helicase
     0.0014   18.9   0.6     0.0063   16.8   0.3    2.3  2  HTH_31           Helix-turn-helix domain
     0.0024   17.2   0.0     0.0057   16.0   0.0    1.5  1  Zeta_toxin       Zeta toxin
     0.0054   16.5   0.1      0.013   15.2   0.1    1.6  1  AAA_29           P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.015   15.8   0.0      0.049   14.2   0.0    1.8  1  ABC_tran         ABC transporter
      0.016   15.5   0.1       0.79   10.0   0.0    2.4  2  PT-HINT          Pretoxin HINT domain
      0.026   14.6   0.1        8.5    6.5   0.0    2.8  2  LAGLIDADG_WhiA   WhiA LAGLIDADG-like domain
      0.026   14.5   0.2       0.74    9.9   0.1    2.6  2  HTH_19           Helix-turn-helix domain
      0.078   13.4   0.0       0.21   11.9   0.0    1.7  1  AAA_16           AAA ATPase domain
      0.084   13.2   0.2       0.23   11.8   0.2    1.7  1  AAA_19           AAA domain
       0.12   12.6   0.1       0.27   11.5   0.1    1.6  1  AAA_28           AAA domain
       0.13   11.2   0.0       0.22   10.4   0.0    1.2  1  DUF5427          Family of unknown function (DUF5427)


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 !  175.4   0.0   1.1e-54   1.2e-51       6     228 ..     196     428 ..     192     430 .. 0.95
   2 !    8.3   0.0     0.001       1.1     226     262 ..     950     983 ..     946     994 .. 0.70

  Alignments for each domain:
  == domain 1  score: 175.4 bits;  conditional E-value: 1.1e-54
                             T2SSE   6 eallddekvsdihvekper.vkvrervdgielreveelekaalerlisriaalakldiseerplqdarlpekgvrlr 81 
                                       ++l++d++  +++v    + v v  r+  +   ++++ +++++  +i+ria  ++++i+++ pl+darlp +g r++
  gi|242399930|ref|YP_002995355.1| 196 DPLVRDDNLEEVMVVGTRKpVYVWHRKFYMCKTNINFDDEREILNIIERIARQVGRRIDQQTPLLDARLP-DGSRVN 271
                                       67889999***************99999999***************************************.****** PP

                             T2SSE  82 vvllPvvag.ealviRkksakeltlddlgaeealkekiaevlrkavr....erglilvsGgTgsGKttllyallkei 153
                                       + + Pv+ + ++l+iRk ++  lt+ dl + ++++ +ia++l   v     +  ++lv+GgTgsGKtt+l+al  +i
  gi|242399930|ref|YP_002995355.1| 272 ATIRPVSLEgPTLTIRKFKKDPLTIIDLLKYGTFNLEIASLLWIFVDglgvKPANVLVAGGTGSGKTTTLNALAMFI 348
                                       *******999*****************************9998888533336789********************** PP

                             T2SSE 154 nksderivtvEDpvEiqleganqvqlnak......kakvtfadllraaLRlrPDrimvGEiRdketleilkAvnTGH 224
                                       + s er++ +ED++E+ql  ++ v+l+++      ++++t+ dl++++LR+rPDri+vGE+R+ e+ ++  A+nTGH
  gi|242399930|ref|YP_002995355.1| 349 PPS-ERVISIEDTAELQLPIEHWVRLETRppniegRGEITMDDLVKNTLRMRPDRIIVGEVRGPEARTMFTAMNTGH 424
                                       ***.************************************************************************* PP

                             T2SSE 225 lgsl 228
                                        g+l
  gi|242399930|ref|YP_002995355.1| 425 NGAL 428
                                       *965 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.001
                             T2SSE 226 gslsTlHansaagalerLeqlgaeveaaelkssilav 262
                                       + ++T+H+nsa +++ rLe   ++v+   +    l+v
  gi|242399930|ref|YP_002995355.1| 950 C-MGTIHSNSARETIVRLESPPMNVP--RIMIPALDV 983
                                       4.99**************98774444..333344444 PP

>> Intein_splicing  Intein splicing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.4   0.0   4.5e-25   4.7e-22      18     134 .]     473     949 ..     434     949 .. 0.93

  Alignments for each domain:
  == domain 1  score: 78.4 bits;  conditional E-value: 4.5e-25
                                       ECTTEEEEEETTTTEEEEEEEEEEEEEEEE...EEEEEEETTS-EEEEETT-EEEECCTTEEEEEECCC--TT-EEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Intein_splicing  18 kegeevlslnledlklevksvkkliklklk...elyeiklesgrkikaTpeHkllvvrdegivEkradeLkegdlia 91 
                                       k+ +ev+s+   dlk  +  v+k+++ k++   +l++ik++ g+++++T++H+++v+++++++ ++a++L++gd +a
  gi|242399930|ref|YP_002995355.1| 473 KDRFEVVSVG-PDLKAGKHVVSKVWRRKVRkdeKLMRIKTRTGNEVILTKNHPFFVFSNGDVMRTEAEKLRVGDRVA 548
                                       3333444443.345555555999**99998899******************************************** PP

                                       EE........................................................................... CS
                                       xx........................................................................... RF
                   Intein_splicing  92 vp........................................................................... 93 
                                       v                                                                            
  gi|242399930|ref|YP_002995355.1| 549 VMmrppkapqrrafvdpkvyagvsdyylvpngngmlkvpnngippkkaqfllsvnsnlvklirevddnlaylagvll 625
                                       99*************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                   Intein_splicing  94 ............................................................................. 93 
                                                                                                                    
  gi|242399930|ref|YP_002995355.1| 626 gdgyiasngyyisatfddeaymeaflnvtskflpnytpqikfngksavvtvsskifaevlsrmfnipkgkkseiwgv 702
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                   Intein_splicing  94 ............................................................................. 93 
                                                                                                                    
  gi|242399930|ref|YP_002995355.1| 703 pdvvlsnddlmryfiaglfdadgyvdesgpsvilttksenaarkiwyalqrlgiistvsrvknrgfkdgeifritis 779
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                   Intein_splicing  94 ............................................................................. 93 
                                                                                                                    
  gi|242399930|ref|YP_002995355.1| 780 gvedlkkfakliplhhsrkrsklesilkskktyrgrrtyrvpisagmirplrqrlsltiaelsklashhagekises 856
                                       ***************************************************************************** PP

                                       ................................................HSCEEEEEEEEEEEEECE....EEEEEEE CS
                                       ................................................xxxxxxxxxxxxxxxxxx....xxxxxxx RF
                   Intein_splicing  94 ................................................dadvvwdkvksievedee....eyVYdlt 118
                                                                                       ++ v+wd+v+s+e+   e    ey Ydlt
  gi|242399930|ref|YP_002995355.1| 857 lirhvekgrvseirrsalkgialafqqvaedigdeeawtmakrlqlvaEGGVYWDEVVSVEEVRPEelgiEYLYDLT 933
                                       ***********************************************9999*********98766523447****** PP

                                       ETTT-EEEECTTEEE- CS
                                       xxxxxxxxxxxxxxxx RF
                   Intein_splicing 119 vednhNFvangiivHN 134
                                       v d hN+vangi+v N
  gi|242399930|ref|YP_002995355.1| 934 VDDDHNYVANGILVSN 949
                                       ************9866 PP

>> LAGLIDADG_3  LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0045       4.7       4      47 ..     617     657 ..     614     688 .. 0.82
   2 !   60.2   0.0   1.7e-19   1.8e-16       2      82 ..     712     791 ..     711     792 .. 0.93

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0045
                                       HHHHHHHHHHCCECCECSTTTTSEEEEES-HHHHHHHHHHHHHC CS
                       LAGLIDADG_3   4 aafLrGlfdaDGsvskskkkgvsisltssskelledvqrlLlrl 47 
                                       +a+L+G   +DG++  ++ +   is t  ++ ++e + ++ +++
  gi|242399930|ref|YP_002995355.1| 617 LAYLAGVLLGDGYIASNGYY---ISATFDDEAYMEAFLNVTSKF 657
                                       79****************88...****99999999988887777 PP

  == domain 2  score: 60.2 bits;  conditional E-value: 1.7e-19
                                       HHHHHHHHHHHHCCECCECSTTTTSEEEEES-HHHHHHHHHHHHHCT.HSCEEEEEEE-SCCCC..ECCCHCHCTTC CS
                       LAGLIDADG_3   2 vkaafLrGlfdaDGsvskskkkgvsisltssskelledvqrlLlrlGIestiyekkkakgrgvy..rlliisgenlk 76 
                                        ++ f++GlfdaDG+v++s+     + lt++s++ ++++ + L+rlGI+st+ + k+++ ++    r++i++ e+lk
  gi|242399930|ref|YP_002995355.1| 712 LMRYFIAGLFDADGYVDESGPS---VILTTKSENAARKIWYALQRLGIISTVSRVKNRGFKDGEifRITISGVEDLK 785
                                       6799****************88...******************************77777777778*********** PP

                                       GGGTTT CS
                       LAGLIDADG_3  77 rFleki 82 
                                       +F++ i
  gi|242399930|ref|YP_002995355.1| 786 KFAKLI 791
                                       ***998 PP

>> Hom_end  Homing endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0         1   1.1e+03      16      35 ..     618     638 ..     609     652 .. 0.81
   2 !   23.9   0.0   3.3e-08   3.5e-05       2     104 ..     702     798 ..     701     805 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1
                           Hom_end  16 aFlaGLvdsdgyvkkeked.s 35 
                                       a+laG   +dgy  ++ +  s
  gi|242399930|ref|YP_002995355.1| 618 AYLAGVLLGDGYIASNGYYiS 638
                                       7***********998855444 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 3.3e-08
                           Hom_end   2 ipsflaseaievREaFlaGLvdsdgyvkkekedsatvktedksvmegivklarsLGikasvktkeekidakgvkhqf 78 
                                       +p  + s++  +R +F+aGL d+dgyv++    s+ ++t +++  ++i    + LGi  +v+     ++++g k   
  gi|242399930|ref|YP_002995355.1| 702 VPDVVLSNDDLMR-YFIAGLFDADGYVDES-GPSVILTTKSENAARKIWYALQRLGIISTVSR----VKNRGFKDGE 772
                                       5666777777789.9*************99.66****************************99....5788999999 PP

                           Hom_end  79 cyaitlsggdalksvlskcalakkrv 104
                                        ++it+sg + lk+  +  +l + r+
  gi|242399930|ref|YP_002995355.1| 773 IFRITISGVEDLKKFAKLIPLHHSRK 798
                                       9******9999998887777777666 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.2     3e-07   0.00031      38      59 ..     323     344 ..     315     348 .. 0.88
   2 ?   -1.6   0.0       1.3   1.4e+03     108     139 ..    1050    1084 ..    1044    1111 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 3e-07
                                       S-.SEEEE--TTSSHHHHHHHH CS
                      FtsK_SpoIIIE  38 mashllvaGatgsGKStalntL 59 
                                        ++++lvaG+tgsGK+t+ln+L
  gi|242399930|ref|YP_002995355.1| 323 KPANVLVAGGTGSGKTTTLNAL 344
                                       467******************9 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.3
                                        HHHHHHHHHHHHH...HHHHHTT-SSHHHHHHHHH CS
                      FtsK_SpoIIIE  108 aleeLvkemeery...alfreagvrsiaaydgeia 139 
                                        + eeL++e+ +r+   + + e+g+rsi+ +   i 
  gi|242399930|ref|YP_002995355.1| 1050 TTEELLEERLKREvvlQWMVEKGIRSIEEVGHYIR 1084
                                        5689999*999999999999*******99655554 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0017       1.8      15      31 ..     325     341 ..     314     372 .. 0.73
   2 !    8.2   0.0    0.0019         2     106     144 ..     449     487 ..     418     507 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0017
                                       CEEEEEESTTSSHHHHH CS
                                       xxxxxxxxxxxxxxxxx RF
                              DEAD  15 gdvlvaaeTGsGKTlaf 31 
                                        +vlva+ TGsGKT+  
  gi|242399930|ref|YP_002995355.1| 325 ANVLVAGGTGSGKTTTL 341
                                       69************974 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0019
                                       HHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 106 grlddllstgklnlsqvrflVlDEadrlldqgfsdfinr 144
                                       grl++  s++  ++++++++VlDE dr+   + ++++++
  gi|242399930|ref|YP_002995355.1| 449 GRLFEKYSDRVEKYKDLEYIVLDEKDRFEVVSVGPDLKA 487
                                       67777665555569**************99988888876 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.3     6e-06    0.0063       6      51 ..     827     878 ..     824     887 .. 0.92
   2 ?   -2.2   0.0       5.3   5.6e+03      45      61 ..    1038    1054 ..    1033    1056 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 6e-06
                            HTH_31   6 LralReraGLsqeevAerlg......vsestlsrlEqGrrgrpspavleala 51 
                                        r lR+r  L+ +e+ +++       +ses ++++E Gr  + ++++l  +a
  gi|242399930|ref|YP_002995355.1| 827 IRPLRQRLSLTIAELSKLAShhagekISESLIRHVEKGRVSEIRRSALKGIA 878
                                       688******************************************9998777 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 5.3
                            HTH_31   45 avlealaralgldpaer 61  
                                        +v ++la+  gl+ +e+
  gi|242399930|ref|YP_002995355.1| 1038 RVMNQLAEHTGLTTEEL 1054
                                        67788888888877765 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   5.4e-06    0.0057      15      50 ..     323     358 ..     320     362 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 5.4e-06
                        Zeta_toxin  15 rPklillgGqpGAGKselaellkdelerqgnvvrld 50 
                                       +P+ +l++G++G+GK++++++l+  + + ++v+ ++
  gi|242399930|ref|YP_002995355.1| 323 KPANVLVAGGTGSGKTTTLNALAMFIPPSERVISIE 358
                                       799*******************99888888888875 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 !   15.2   0.1   1.3e-05     0.013      20      50 ..     323     352 ..     309     356 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.3e-05
                            AAA_29  20 dlkgatlltGpsGsGKSTllDAiqalLvpak 50 
                                       +++ ++l++G +GsGK+T l A+++ + p++
  gi|242399930|ref|YP_002995355.1| 323 KPA-NVLVAGGTGSGKTTTLNALAMFIPPSE 352
                                       444.49*****************99888776 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   4.6e-05     0.049      14      50 ..     327     364 ..     321     388 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.6e-05
                                       EEEEESTTSSHHHHHHHHTTSS--SEEEEEET.TCEGG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx RF
                          ABC_tran  14 vaivGenGaGKStLlkllagllkpteGeilld.gkdlk 50 
                                       v + G +G+GK+t l++la    p e  i ++  ++l+
  gi|242399930|ref|YP_002995355.1| 327 VLVAGGTGSGKTTTLNALAMFIPPSERVISIEdTAELQ 364
                                       6789********************99999998334443 PP

>> PT-HINT  Pretoxin HINT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00075      0.79      24      87 ..     484     547 ..     472     551 .. 0.75
   2 ?    2.6   0.0      0.14   1.5e+02      97     124 ..     916     944 ..     890     956 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00075
                           PT-HINT  24 deasgkvaekpvlarygneyqelvylkisdgignsevlisnkihPfys..k..gkfieakelkvGdkl 87 
                                       d+++gk     v  r +++ + l+ +k     gn+ v i +k hPf++  +  +   ea++l+vGd++
  gi|242399930|ref|YP_002995355.1| 484 DLKAGKHVVSKVWRRKVRKDEKLMRIKTRT--GNE-V-ILTKNHPFFVfsNgdVMRTEAEKLRVGDRV 547
                                       667777777888888899999998888887..554.4.45688**98633422455689*******96 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.14
                           PT-HINT  97 veeiklkdePl.kaynlkvadfhtyfvkg 124
                                       vee++ ++  +   y+l+v+d h y  +g
  gi|242399930|ref|YP_002995355.1| 916 VEEVRPEELGIeYLYDLTVDDDHNYVANG 944
                                       33333333222146***********8775 PP

>> LAGLIDADG_WhiA  WhiA LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0     0.008       8.5       3      61 ..     618     676 ..     616     690 .. 0.78
   2 ?    5.1   0.0     0.023        24       2      56 ..     714     766 ..     713     809 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.008
                    LAGLIDADG_WhiA   3 aflrGaflasGsindpekkyhLEivspdeelaeqlqkllnef..eleakilerrkkyvvyl 61 
                                       a+l+G++l+ G i++  ++y +   ++de ++e+  ++ ++f  + + +i+   k+ vv++
  gi|242399930|ref|YP_002995355.1| 618 AYLAGVLLGDGYIAS--NGYYISATFDDEAYMEAFLNVTSKFlpNYTPQIKFNGKSAVVTV 676
                                       79***********99..67********************9997555555555555555544 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.023
                    LAGLIDADG_WhiA   2 kaflrGaflasGsindpekkyhLEivspdeelaeqlqkllnefeleakilerrkk 56 
                                       ++f++G+f a G + +   +    + +++e++a+++  +l+++++ + +++++++
  gi|242399930|ref|YP_002995355.1| 714 RYFIAGLFDADGYVDESGPS--VILTTKSENAARKIWYALQRLGIISTVSRVKNR 766
                                       68999*********996555..567999*********************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 ?    9.9   0.1    0.0007      0.74       3      53 ..     826     882 ..     824     893 .. 0.85
   2 ?    1.7   0.0      0.26   2.7e+02      41      60 ..    1036    1055 ..     995    1058 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0007
                            HTH_19   3 rLkeaReelgltqeelae......rlgisrskisaiEngkkdvpsaelllkiaealg 53 
                                       +++ +R  l lt++el++        +is s i++ E+g+  ++ ++ l+ ia a+ 
  gi|242399930|ref|YP_002995355.1| 826 MIRPLRQRLSLTIAELSKlashhaGEKISESLIRHVEKGRVSEIRRSALKGIALAFQ 882
                                       68899*************88887777777**********777999999998888875 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.26
                            HTH_19   41 saelllkiaealgidleyll 60  
                                        ++++++++ae  g+++e+ll
  gi|242399930|ref|YP_002995355.1| 1036 PSRVMNQLAEHTGLTTEELL 1055
                                        26788*************98 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    0.0002      0.21      23      74 ..     323     372 ..     307     419 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0002
                            AAA_16  23 rpelvllsGesGvGKsslvrellralekdg.giflrgkcdqlesaipysalaq 74 
                                        p +vl+ G  G+GK++ +++l+  +  ++ +i ++ +++     +p  ++++
  gi|242399930|ref|YP_002995355.1| 323 KPANVLVAGGTGSGKTTTLNALAMFIPPSErVISIEDTAELQ---LPIEHWVR 372
                                       5689******************99998886455577777666...66655555 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   0.00022      0.23       9      30 ..     323     344 ..     318     354 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00022
                            AAA_19   9 kekvllvtaGpGtGKTrvlkhi 30 
                                       k  ++lv +G G+GKT++l++ 
  gi|242399930|ref|YP_002995355.1| 323 KPANVLVAGGTGSGKTTTLNAL 344
                                       56789**************975 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00025      0.27       2      20 ..     327     345 ..     326     362 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00025
                            AAA_28   2 ivitGgestGKTtlleaLa 20 
                                       + + Gg ++GKTt+l+aLa
  gi|242399930|ref|YP_002995355.1| 327 VLVAGGTGSGKTTTLNALA 345
                                       7899**************9 PP

>> DUF5427  Family of unknown function (DUF5427)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00021      0.22     194     239 ..     160     208 ..     142     212 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00021
                           DUF5427 194 ptltellktlappi..sshEvLqIhithDlvnypsLdplvy.ekFsrvm 239
                                       +++++++k+lap +     E+L  +++  +++y +Ldplv+ +++++vm
  gi|242399930|ref|YP_002995355.1| 160 RAVKNIMKELAPNVseGRMEILINLVVQNMIGYGKLDPLVRdDNLEEVM 208
                                       5689**********66678***99****************725788888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); 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: 0.86u 0.34s 00:00:01.20 Elapsed: 00:00:00.50
# Mc/sec: 6635.76
//
Query:       gi|242399931|ref|YP_002995356.1|  [L=301]
Description: hypothetical protein TSIB_1958 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.54
# Mc/sec: 1683.10
//
Query:       gi|242399932|ref|YP_002995357.1|  [L=473]
Description: hypothetical protein TSIB_1959 [Thermococcus sibiricus MM 739]
Scores for complete 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-132  441.0  25.0   4.2e-132  440.8  25.0    1.0  1  DUF515         Protein of unknown function (DUF515)
  ------ inclusion threshold ------
      0.027   14.5   0.3      0.084   13.0   0.3    1.8  1  Insulin_TMD    Insulin receptor trans-membrane segment
      0.034   14.3   1.0      0.034   14.3   1.0    2.4  3  DUF4330        Domain of unknown function (DUF4330)
       0.35   10.9   8.5      0.047   13.7   1.4    2.9  3  RcpC           Flp pilus assembly protein RcpC/CpaB
       0.79    9.7   8.6       0.97    9.4   0.1    3.7  3  GA-like        GA-like domain
        2.8    8.3  12.5        3.1    8.1   2.2    3.2  3  GA             GA module
        4.8    7.1   7.9      0.087   12.8   0.5    1.9  2  Ferlin_C       Ferlin C-terminus
        5.9    7.0   7.2       0.75    9.9   0.7    2.3  2  NAD_binding_6  Ferric reductase NAD binding domain


Domain annotation for each model (and alignments):
>> DUF515  Protein of unknown function (DUF515)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  440.8  25.0  1.9e-135  4.2e-132      12     447 ..      43     471 ..      30     473 .] 0.98

  Alignments for each domain:
  == domain 1  score: 440.8 bits;  conditional E-value: 1.9e-135
                            DUF515  12 kksrrssrisslrekerrkrliiGasvlvvivillvfaiYsyienkeleeLENakaakieeinklFaseyaNdpqKl 88 
                                        + r++s+++ lre+err r+iiGas+l +i+i++v+++Y + +n++ ++LE ak ak++e+nk+F++e+aNd+ K 
  gi|242399932|ref|YP_002995357.1|  43 APARKPSKLGRLRERERRRRIIIGASILAIIIIAVVVGVYITYQNRAAKQLEEAKLAKVAEVNKYFTGELANDTLKT 119
                                       589************************************************************************** PP

                            DUF515  89 llinKiqaansiEelekidvrtifeqakkeleeeiieleqakkekelkqlKqeainqikaafgellslsladelkkK 165
                                       +lin+i+ a+siEelekidv+++ +q+k        ++eq++++kel++ K  +  +++  f+ lls  l+ e+k  
  gi|242399932|ref|YP_002995357.1| 120 QLINQINRAQSIEELEKIDVKSLADQRKA-------QIEQERLQKELQDAKMLKLSEVEHSFELLLSQPLSAEMKSE 189
                                       **************************986.......588999*********************************** PP

                            DUF515 166 ivaeleeLlkqvdsaktieevleikvdkyllsldkkyYllkldkiptsdvilekngekslitkdevkkiiksvgsls 242
                                       ++++l++L ++++sakt++evl i+ + yll l++kyY + +d  pt++vil+k+ eks++tk e+k + + v+++ 
  gi|242399932|ref|YP_002995357.1| 190 VIQTLNQLKEKINSAKTKDEVLLIDANPYLLDLWRKYYYYLIDGTPTQKVILKKGTEKSIYTKAEAKYVLSKVTDFA 266
                                       ***************************************************************************** PP

                            DUF515 243 eLkeykvtpVelvevvlvlvrekqvGkliapGDevkvYaKdeatiayeivdssYvillllsveagsisvSEsqsqss 319
                                       eL++y +++ e+v+++lvl re+++G+++ +GD+vk++a+ ++t++++i d++Y+ ++ll  ++g isvSEsq  s+
  gi|242399932|ref|YP_002995357.1| 267 ELIQYTIEKAEMVQIALVLPRENVNGAFLSSGDKVKIFAQVNSTTIQKIADEGYISTVLLLKDSGVISVSESQTESN 343
                                       ***************************************************************************** PP

                            DUF515 320 svseesstsssessstsespGdvsisdsssasdsssvsqstseslsssisYsvNLaeiLkAiaadkldasdevkaql 396
                                        +s++++t +s+  s s++pGd sis  +  ++s+s++qs+s++ s+s++Y v L eiLkAiaa+k+ a+devk+ql
  gi|242399932|ref|YP_002995357.1| 344 DISSSTETAYSDQYSESYAPGDQSISYEQAKDESHSTTQSSSQTISASYTYNVALNEILKAIAANKIAAPDEVKEQL 420
                                       ***************************************************************************** PP

                            DUF515 397 gnYGkellelEdntqllaldEnvkllvivevPsekvpdilevedeivvikv 447
                                       + Y +++l lE++t+l+a d + k+lvivevP e+v di++  ++  v k+
  gi|242399932|ref|YP_002995357.1| 421 ERYKWKVLGLEQETGLMATDPTAKVLVIVEVPAEFVEDIIKYRNALYVTKI 471
                                       ********************************************9998886 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 ?   13.0   0.3   3.7e-05     0.084      16      39 ..      62      85 ..      56      90 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.7e-05
                       Insulin_TMD 16 kIvigPviciillllvigavfvvv 39
                                       I+ig  i++i+++ v+++v++  
  gi|242399932|ref|YP_002995357.1| 62 RIIIGASILAIIIIAVVVGVYITY 85
                                      69*******************965 PP

>> DUF4330  Domain of unknown function (DUF4330)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   1.0   1.5e-05     0.034      20     101 ..      69     148 ..      64     177 .. 0.60
   2 ?   -0.7   0.2      0.65   1.4e+03      52      98 ..     278     319 ..     239     347 .. 0.57
   3 ?   -2.2   0.1       1.8   4.1e+03      52      78 ..     389     417 ..     370     460 .. 0.51

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.5e-05
                           DUF4330  20 lailvilavivgiflkpgtsgsvaqaeaaa.tkpvevdvvvrglevpeelakvkegektniiirnqPagdv...eik 92 
                                       +++++i+av+vg+++ + ++ +++q e+a+ +k  ev+ ++ g+ +++    + + +  n i+r q   ++   ++k
  gi|242399932|ref|YP_002995357.1|  69 ILAIIIIAVVVGVYITYQNR-AAKQLEEAKlAKVAEVNKYFTGELAND----TLKTQLINQINRAQSIEELekiDVK 140
                                       45669999999999999999.556655534355555666666555544....3444555555555555554222666 PP

                           DUF4330  93 dvkvlprkv 101
                                       +   +++  
  gi|242399932|ref|YP_002995357.1| 141 SLADQRK-A 148
                                       6555333.3 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.65
                           DUF4330  52 pvevdvvvrglevpeelakvkegektniiirnqPagdveikdvkvlp 98 
                                        v++ +v+  ++v+ ++++   g+k++i+++     +++i ++  + 
  gi|242399932|ref|YP_002995357.1| 278 MVQIALVLPRENVNGAFLS--SGDKVKIFAQV---NSTTIQKIADEG 319
                                       3333333333344443333..77777777755...555555555444 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1.8
                           DUF4330  52 pvevdvvvrglevpeelak..vkegektn 78 
                                       + ++++ v   e+ +++a+  + + ++++
  gi|242399932|ref|YP_002995357.1| 389 SASYTYNVALNEILKAIAAnkIAAPDEVK 417
                                       33366666666663333331223333333 PP

>> RcpC  Flp pilus assembly protein RcpC/CpaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.2      0.45     1e+03      33      68 ..     136     177 ..     124     212 .. 0.70
   2 ?   13.7   1.4   2.1e-05     0.047       9      68 ..     276     349 ..     272     411 .. 0.77
   3 ?   -1.8   0.0       1.4   3.1e+03      78     103 ..     435     460 ..     415     465 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.45
                              RcpC  33 rVDVlltesekedsesektvaelllqnvrVLavgq.......e 68 
                                        +DV    +++++++ e++  +  lq+++ L++ +        
  gi|242399932|ref|YP_002995357.1| 136 KIDVKSL-ADQRKAQIEQERLQKELQDAKMLKLSEvehsfelL 177
                                       5777777.78888888999999999999999887755555540 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 2.1e-05
                              RcpC   9 pgkrAvaievdevtgvaglirpGdrVDVllt...esekedsesektvaelllqnvrVLavgq...........e 68 
                                       + ++ +a+    ++ ++ +++ Gd V +++     + ++ +++   ++ lll++  V++v +           +
  gi|242399932|ref|YP_002995357.1| 276 AEMVQIALVLPRENVNGAFLSSGDKVKIFAQvnsTTIQKIADEGYISTVLLLKDSGVISVSEsqtesndisssT 349
                                       67899999999********************986566666666777788899**********333222222220 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 1.4
                              RcpC  78 eekkkeaetastvtLevtpeqaekLa 103
                                       +  +++++++  v++ev+ e +e+++
  gi|242399932|ref|YP_002995357.1| 435 GLMATDPTAKVLVIVEVPAEFVEDII 460
                                       44455566667899999999998886 PP

>> GA-like  GA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   1.6       1.4   3.1e+03       5      21 ..      90     106 ..      87     107 .. 0.79
   2 ?    3.2   0.1     0.038        84      29      45 ..     121     137 ..     111     140 .. 0.88
   3 ?    9.4   0.1   0.00043      0.97      29      42 ..     197     210 ..     185     213 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.4
                           GA-like   5 keaLkeAKeaAkaeLka 21 
                                       +++L+eAK a +ae ++
  gi|242399932|ref|YP_002995357.1|  90 AKQLEEAKLAKVAEVNK 106
                                       6899****988888766 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.038
                           GA-like  29 yiekIdkAkTvEgVkaL 45 
                                        i++I+ A+++E+ +++
  gi|242399932|ref|YP_002995357.1| 121 LINQINRAQSIEELEKI 137
                                       589*********98875 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.00043
                           GA-like  29 yiekIdkAkTvEgV 42 
                                         ekI++AkT+++V
  gi|242399932|ref|YP_002995357.1| 197 LKEKINSAKTKDEV 210
                                       579*********99 PP

>> GA  GA module
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   2.2    0.0014       3.1      32      55 ..     114     137 ..      87     140 .. 0.78
   2 ?   -3.6   0.3       6.6   1.5e+04      11      21 ..     152     162 ..     146     163 .. 0.53
   3 ?    6.5   0.1    0.0047        10      37      52 ..     195     210 ..     192     215 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0014
                                GA  32 NnaQkqalkdqinqattraeVaqi 55 
                                       N+  k++l++qin a++++e+++i
  gi|242399932|ref|YP_002995357.1| 114 NDTLKTQLINQINRAQSIEELEKI 137
                                       77779****************987 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 6.6
                                GA  11 dqkLaqaKqnA 21 
                                       +++L+++ q+A
  gi|242399932|ref|YP_002995357.1| 152 QERLQKELQDA 162
                                       44555555555 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.0047
                                GA  37 qalkdqinqattraeV 52 
                                       ++lk++in+a+t +eV
  gi|242399932|ref|YP_002995357.1| 195 NQLKEKINSAKTKDEV 210
                                       689************9 PP

>> Ferlin_C  Ferlin C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.7   1.7         8   1.8e+04     127     135 ..      71      79 ..      61      85 .. 0.44
   2 ?   12.8   0.5   3.9e-05     0.087      38     127 ..     142     231 ..     118     233 .. 0.80

  Alignments for each domain:
  == domain 1  score: -4.7 bits;  conditional E-value: 8
                          Ferlin_C 127 iallilall 135
                                        +++i +++
  gi|242399932|ref|YP_002995357.1|  71 AIIIIAVVV 79 
                                       222222233 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 3.9e-05
                          Ferlin_C  38 KkkkkrsekkpedlefkdssgntflllgkveaelelltkeeAekepvGkgrkepepl.ekpnrpktsfswlvnrlKt 113
                                          +++ ++++e l+ k+   + +l l++ve  +ell ++   +e   +  +  ++l ek n  kt  ++l+  + +
  gi|242399932|ref|YP_002995357.1| 142 LADQRKAQIEQERLQ-KELQDAKMLKLSEVEHSFELLLSQPLSAEMKSEVIQTLNQLkEKINSAKTKDEVLLIDANP 217
                                       334455677788888.7888899999***********999999999999888888854899**************** PP

                          Ferlin_C 114 fiffiWkkykkyii 127
                                        +  +W+ky  y+i
  gi|242399932|ref|YP_002995357.1| 218 YLLDLWRKYYYYLI 231
                                       ***********998 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 ?    9.9   0.7   0.00033      0.75      58     110 ..      92     144 ..      84     173 .. 0.79
   2 ?   -0.1   0.5       0.4   8.9e+02      41      96 ..     325     379 ..     297     435 .. 0.53

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00033
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     NAD_binding_6  58 eleeeksegnieihiYlTseyeaedasdqlissiegenseslkqgvdavsgtr 110
                                       +lee k  +  e++ Y+T+e   ++ + qli++i+  +s ++ +++d+ s   
  gi|242399932|ref|YP_002995357.1|  92 QLEEAKLAKVAEVNKYFTGELANDTLKTQLINQINRAQSIEELEKIDVKSLAD 144
                                       56666666799*************************99999999999988666 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.4
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxx RF
                     NAD_binding_6  41 wvvressslewfkdvLneleeeksegnieihiYlTseyea....edasdqlissiegens 96 
                                        + ++s+ +++ +   ++ e+++  ++ ++++ ++ +y++    +d+s ++++++++ +s
  gi|242399932|ref|YP_002995357.1| 325 LLLKDSGVISVSE---SQTESND--ISSSTETAYSDQYSEsyapGDQSISYEQAKDESHS 379
                                       5555555555555...3222222..22333333333333322222222222222222211 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (473 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2208  (0.123152); expected 358.6 (0.02)
Passed bias filter:                      707  (0.0394333); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.72u 0.31s 00:00:01.03 Elapsed: 00:00:00.48
# Mc/sec: 2993.42
//
Query:       gi|242399933|ref|YP_002995358.1|  [L=107]
Description: hypothetical protein TSIB_1960 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       216  (0.0120475); expected 358.6 (0.02)
Passed bias filter:                      201  (0.0112109); 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 0.30s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 689.95
//
Query:       gi|242399934|ref|YP_002995359.1|  [L=357]
Description: GTPase, MMR1/HSR1 family [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.3e-16   58.7   0.6    9.2e-13   48.3   0.0    2.6  2  MMR_HSR1       50S ribosome-binding GTPase
    2.7e-11   43.2   0.8    1.6e-06   27.7   0.1    2.4  2  FeoB_N         Ferrous iron transport protein B
    9.3e-11   41.9   0.3    3.2e-10   40.2   0.3    1.8  1  RsgA_GTPase    RsgA GTPase
    3.6e-06   26.7   0.6      9e-05   22.1   0.5    2.8  3  GTP_EFTU       Elongation factor Tu GTP binding domain
    1.8e-05   24.9   0.7       0.46   10.5   0.1    3.2  3  Dynamin_N      Dynamin family
    0.00011   21.7   1.5     0.0039   16.7   0.1    2.4  2  Arf            ADP-ribosylation factor family
  ------ inclusion threshold ------
      0.016   15.4   2.1       0.41   10.9   0.2    3.0  3  Roc            Ras of Complex, Roc, domain of DAPkinase
      0.017   15.1   0.1       0.05   13.6   0.1    1.7  1  MMR_HSR1_Xtn   C-terminal region of MMR_HSR1 domain
      0.033   14.1   0.2      0.083   12.8   0.1    1.8  2  Thioredoxin_6  Thioredoxin-like domain
      0.056   12.8   0.1       0.14   11.4   0.1    1.7  1  AIG1           AIG1 family
       0.07   12.7   1.4        3.4    7.2   0.3    2.3  2  Ras            Ras family
      0.082   13.5   0.3       0.31   11.6   0.0    2.2  2  AAA_18         AAA domain
       0.12   12.0   2.0       0.97    9.0   0.2    2.5  2  cobW           CobW/HypB/UreG, nucleotide-binding 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 !    8.4   0.2    0.0016       2.2      72     114 .]      13      54 ..       1      54 [. 0.80
   2 !   48.3   0.0   6.7e-16   9.2e-13       1      58 [.     109     164 ..     109     230 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0016
                                       HHHCTSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                          MMR_HSR1  72 aleeadlillvvdaseeklkpldeeleelleeakkplilvlnk 114
                                       a++e d+il vvda+ + +   + ++e++ ++++k+l++v+nk
  gi|242399934|ref|YP_002995359.1|  13 AIREGDIILEVVDAR-DPIGTRNLKVEKIAQKEGKKLLIVMNK 54 
                                       35567********88.77888999999**999**********8 PP

  == domain 2  score: 48.3 bits;  conditional E-value: 6.7e-16
                                       EEEEEESTTSSHHHHHHHHHTS.TEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSS CS
                          MMR_HSR1   1 evaivGrpNvGKStLinaltge.kaivsdkpgtTrdinegrvklkgkeielvDtpGlie 58 
                                       +v++vG+pNvGKSt+in l g+ ++ ++ +pg T+  + +r++   k+i +vD pG++ 
  gi|242399934|ref|YP_002995359.1| 109 KVVLVGYPNVGKSTIINVLKGKhAVGTAPIPGYTKGKQLIRLS---KKIWVVDSPGVVP 164
                                       699******************9667*****************9...69********853 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 !   13.8   0.1   2.3e-05     0.032      78     155 ..      16      92 ..       4      93 .. 0.83
   2 !   27.7   0.1   1.2e-09   1.6e-06       2      61 ..     109     166 ..     108     177 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.3e-05
                                       SSSEEEEEEEGGGH..HHHHHHHHHHHHTTSSEEEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTTTBTHHHH CS
                            FeoB_N  78 epdvvvnvvdatnl..ernLyLtlqllelgvpvvlalnmideaekkgieidlkkLsekLgvpvvktsakkkegieel 152
                                       e d++++vvda      rnL +       g+++++++n+ d + kk  e   +  +++ ++p+v +sa++++g+  l
  gi|242399934|ref|YP_002995359.1|  16 EGDIILEVVDARDPigTRNLKVEKIAQKEGKKLLIVMNKADLVPKKWAE---EYKQKNKDIPIVFISARERKGTGIL 89 
                                       679********9864579999999999999*************998765...334566799***********99888 PP

                                       HHH CS
                            FeoB_N 153 lka 155
                                       +++
  gi|242399934|ref|YP_002995359.1|  90 REE 92 
                                       776 PP

  == domain 2  score: 27.7 bits;  conditional E-value: 1.2e-09
                                       EEEEEESTTSSHHHHHHHHHTTS.EEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSS CS
                            FeoB_N   2 tvalvGnpnvGkttlfnaltgak.qkvgNwpGvtvekkegklklkgkeveivDlPGiYsls 61 
                                       +v+lvG pnvGk+t++n l g++    +  pG t  k+  +l+   k++ +vD PG+  ++
  gi|242399934|ref|YP_002995359.1| 109 KVVLVGYPNVGKSTIINVLKGKHaVGTAPIPGYTKGKQLIRLS---KKIWVVDSPGVVPID 166
                                       79******************98724567789999999999988...99********97665 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   0.3   2.3e-13   3.2e-10      42     162 ..      41     163 ..      32     167 .. 0.77

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 2.3e-13
                                       HHHTT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTH.......TTHHHHHHHC....TTS.EEEEEC CS
                       RsgA_GTPase  42 aeekgiepvivlnKiDlleeeeeleelkeelealgyevllvsaktk.......egleelkell....kdk.tsvlvG 106
                                       a+++g +++iv+nK+Dl+ ++  +ee+k++ +++  +++++sa+++       e++++l++++    kdk  +vlvG
  gi|242399934|ref|YP_002995359.1|  41 AQKEGKKLLIVMNKADLVPKKW-AEEYKQKNKDI--PIVFISARERkgtgilrEEIKKLAKEFfeqgKDKvKVVLVG 114
                                       6788899*************99.99999988888..777777776611222223444555444222233324799** PP

                                       STTSSHHHHHHHHCTT-----S--------------SEEEEEETTTEEEESS-SSS CS
                       RsgA_GTPase 107 qSGvGKStLinallpelelktgevseklgrGkhTTtavellelaegglliDtPGfr 162
                                          vGKSt+in+l++++ + t+ +          T+  +l++l+++ +++D+PG+ 
  gi|242399934|ref|YP_002995359.1| 115 YPNVGKSTIINVLKGKHAVGTAPIPGY-------TKGKQLIRLSKKIWVVDSPGVV 163
                                       ************************985.......56679***************85 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.5   6.5e-08     9e-05      88     171 ..      11     111 ..       8     127 .. 0.77
   2 ?   -0.3   0.0      0.49   6.7e+02       4      23 ..     108     127 ..     105     133 .. 0.83
   3 ?    1.0   0.0      0.19   2.6e+02      69      95 ..     151     180 ..     141     182 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 6.5e-08
                                       HHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGST....HHHHHHHHHHHHHHHHHH....... CS
                          GTP_EFTU  88 irglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrl....kaelkeiveevkqklsrk....... 153
                                         ++r  D+ + vvda++ + ++  +v ++a+keg ++ +++NK+D +     +e+k+  +++   +          
  gi|242399934|ref|YP_002995359.1|  11 NDAIREGDIILEVVDARDPIGTRNLKVEKIAQKEGKKLLIVMNKADLVpkkwAEEYKQKNKDIPIVF--Isarerkg 85 
                                       5678899*****************************************5555555555555555555..14578888 PP

                                       ........HHHHHHHHHTTTTTEEEE CS
                          GTP_EFTU 154 ........eeklekygekgekevpvv 171
                                               ++  +++ e+g+++v+vv
  gi|242399934|ref|YP_002995359.1|  86 tgilreeiKKLAKEFFEQGKDKVKVV 111
                                       88887776666666677776777766 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.49
                                       EEEEEEESTTSSHHHHHHHH CS
                          GTP_EFTU   4 rnigiighvDhGKtTLtdrL 23 
                                       ++++++g  + GK+T++  L
  gi|242399934|ref|YP_002995359.1| 108 VKVVLVGYPNVGKSTIINVL 127
                                       678999999******99866 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.19
                                       SEEEEEEEESSSG...GGHHHHHHHHHT-S CS
                          GTP_EFTU  69 kylinliDtPGHv...dFskevirglrvlD 95 
                                       +++i ++D+PG v   dF + virg   +D
  gi|242399934|ref|YP_002995359.1| 151 SKKIWVVDSPGVVpidDFEELVIRGGFPAD 180
                                       578999*****9755579999999976666 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.1   0.00033      0.46     120     167 ..       8      54 ..       1      55 [. 0.90
   2 !   10.2   0.1   0.00042      0.58       1      30 [.     110     139 ..     110     143 .. 0.89
   3 ?    0.5   0.0       0.4   5.5e+02     100     117 ..     151     168 ..     141     206 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00033
                                       HHHHHHHSTTEEEEEEEETTS-CCC-CHHHHHHHHSTTBTTEEEEEE- CS
                         Dynamin_N 120 elvkeyikkadiilavtsanhdlsnsealflarevdpkgkrtivvltk 167
                                       ++v+ +i++ diil v++a   +  +++l++++ ++++gk+ ++v++k
  gi|242399934|ref|YP_002995359.1|   8 RVVNDAIREGDIILEVVDARDPIG-TRNLKVEKIAQKEGKKLLIVMNK 54 
                                       78999*****************99.999******************99 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00042
                                       EEEEEBTTTTHHHHHHHHHTS--S---SSS CS
                         Dynamin_N   1 iavvGsqSsGKSSvlnaLlgedilprgpnp 30 
                                       +++vG  + GKS+++n L g++   + p+p
  gi|242399934|ref|YP_002995359.1| 110 VVLVGYPNVGKSTIINVLKGKHAVGTAPIP 139
                                       799******************988777765 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.4
                                       S-SEEEEE---B-SSSGT CS
                         Dynamin_N 100 vkgltlvDlPGldsvnkr 117
                                        k++ +vD+PG+  +++ 
  gi|242399934|ref|YP_002995359.1| 151 SKKIWVVDSPGVVPIDDF 168
                                       678899*****9876655 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.3     0.022        30      83     139 ..      18      69 ..       2      99 .. 0.68
   2 !   16.7   0.1   2.8e-06    0.0039      10      49 ..     103     142 ..      93     158 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.022
                                       SEEEEEEETT-CTTHHHHHHHHHHHCTSGCCTTSEEEEEEE-TTSTTSS-HHHHHHH CS
                               Arf  83 davifvvDsadreRleeakeeLkalleeeelkevallvlaNKqDlpealseeelrel 139
                                       d ++ vvD+ d   + + + +++++ ++   +  +ll++ NK Dl     +ee +++
  gi|242399934|ref|YP_002995359.1|  18 DIILEVVDARDP--IGTRNLKVEKIAQK---EGKKLLIVMNKADLVPKKWAEEYKQK 69 
                                       555556665554..33334444455444...45679********9988877777664 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 2.8e-06
                                       T.TTEEEEEEEESTTSSHHHHHHHHHHSSCEECSSSSSEE CS
                               Arf  10 lkkkelrilllGLDnaGKtTilkklkleelvttvPTigfn 49 
                                       + k +++++l+G  n GK+Ti++ lk ++ v t P  g++
  gi|242399934|ref|YP_002995359.1| 103 QGKDKVKVVLVGYPNVGKSTIINVLKGKHAVGTAPIPGYT 142
                                       336789***************************9988776 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 ?    0.8   0.0       0.4   5.5e+02     102     119 ..      37      56 ..      14      58 .. 0.65
   2 ?    2.1   0.1      0.16   2.2e+02      94     114 ..      58      78 ..      44      82 .. 0.74
   3 ?   10.9   0.2   0.00029      0.41       1      22 [.     109     130 ..     109     153 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.4
                                       HHHHCSSS..-EEEEEE-TT CS
                               Roc 102 lkkvagks..pvilvgnkiD 119
                                       ++k a+k+  ++++v+nk+D
  gi|242399934|ref|YP_002995359.1|  37 VEKIAQKEgkKLLIVMNKAD 56 
                                       44444433227899****99 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.16
                                       CHHHHHHHHHHHCSSS-EEEE CS
                               Roc  94 nlkeWlkelkkvagkspvilv 114
                                         k+W +e k++++++p++++
  gi|242399934|ref|YP_002995359.1|  58 VPKKWAEEYKQKNKDIPIVFI 78 
                                       3479*******9999999987 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00029
                                       EEEEESSTTSSHHHHHHCHCT- CS
                               Roc   1 KvvlvGdsgvGKtsllkrfved 22 
                                       KvvlvG  +vGK+++++ +  +
  gi|242399934|ref|YP_002995359.1| 109 KVVLVGYPNVGKSTIINVLKGK 130
                                       9***************987655 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 ?   13.6   0.1   3.6e-05      0.05      57     100 ..      47      93 ..      24      98 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.6e-05
                      MMR_HSR1_Xtn  57 pclyvlNKiDlisleeldelare...pnsvviSaekelnldeLkeki 100
                                       + l+v+NK+Dl+ ++  +e +++     +v+iSa+++++   L e+i
  gi|242399934|ref|YP_002995359.1|  47 KLLIVMNKADLVPKKWAEEYKQKnkdIPIVFISARERKGTGILREEI 93 
                                       789********99999999888633236788*****99998888887 PP

>> Thioredoxin_6  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1     6e-05     0.083      85     133 ..      61     113 ..      37     130 .. 0.89
   2 ?   -3.3   0.0       5.4   7.4e+03      73      91 ..     202     220 ..     201     222 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6e-05
                                       HHHHHHHTSS--EEEEEEE-TTSTTHHHHHHHHHHHHHHT....TTT-EEEEE CS
                     Thioredoxin_6  85 enaeelfeeglppllllflkkddeeteklkkaiekvakef....kdkinfala 133
                                       + aee+ ++++ + +++++  ++++t  l+++i+k+akef    kdk++++l+
  gi|242399934|ref|YP_002995359.1|  61 KWAEEYKQKNKDIPIVFISARERKGTGILREEIKKLAKEFfeqgKDKVKVVLV 113
                                       56899999999999**************************9999999999887 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 5.4
                                       HH---SEEE-SHHHHHHHH CS
                     Thioredoxin_6  73 knslplvreltpenaeelf 91 
                                       +++++ ++ +++en e++ 
  gi|242399934|ref|YP_002995359.1| 202 EAIIEKYGIIDFENEEQIL 220
                                       5678899999999999986 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1    0.0001      0.14       2      63 ..     109     166 ..     108     174 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0001
                                       EEEEESSTTSSHHHHHHHHHTS--SS--TTTS---SS-EEEEEEETTEEEEEEE--SCCCTT CS
                              AIG1   2 tivlvGktgnGkSaTgNsilgkkaFesklsaqsvtkkcqkksrtwdgkkinViDTPglfdls 63 
                                       ++vlvG   +GkS+ +N + gk+a  +     ++    + k+  +  kki V+D Pg++ ++
  gi|242399934|ref|YP_002995359.1| 109 KVVLVGYPNVGKSTIINVLKGKHAVGTA----PIPGYTKGKQLIRLSKKIWVVDSPGVVPID 166
                                       79********************998887....6777777777799999*********87655 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.022        31     100     148 ..      40      85 ..      15     101 .. 0.71
   2 ?    7.2   0.3    0.0025       3.4       1      18 [.     109     126 ..     109     134 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.022
                                       HST.TTSEEEEEEETTTGGGG-SS-HHHHHHHHHHHT.SEEEEEBTTTTCT CS
                               Ras 100 vae.envpivLvGnKvDleekravsteegeelakelg.lkfletSAktnen 148
                                       +a+ e  ++++v nK+Dl       ++ +ee+ ++++ ++ + +SA+++++
  gi|242399934|ref|YP_002995359.1|  40 IAQkEGKKLLIVMNKADLV-----PKKWAEEYKQKNKdIPIVFISARERKG 85 
                                       3333445889999999996.....566666666666668888888888776 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0025
                                       EEEEEESTTSSHHHHHHH CS
                               Ras   1 KlvlvGdsavGKtslllr 18 
                                       K+vlvG  +vGK+++++ 
  gi|242399934|ref|YP_002995359.1| 109 KVVLVGYPNVGKSTIINV 126
                                       9*************9975 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00023      0.31       1      23 [.     110     132 ..     110     174 .. 0.82
   2 ?   -1.6   0.1       2.7   3.7e+03      51      77 ..     210     236 ..     189     300 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00023
                            AAA_18   1 IlltGtpGvGKttlakeLskrlg 23 
                                       ++l G+p vGK+t+ + L+ +++
  gi|242399934|ref|YP_002995359.1| 110 VVLVGYPNVGKSTIINVLKGKHA 132
                                       789**************976654 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.7
                            AAA_18  51 rldedkldklldaleenssaleegknl 77 
                                       ++d ++ +++l+a+ e    l +g+ +
  gi|242399934|ref|YP_002995359.1| 210 IIDFENEEQILKAIGEKKGLLKKGGKV 236
                                       444444444444444444433333333 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 ?    9.0   0.2   0.00071      0.97     113     166 ..      18      70 ..       3      76 .. 0.74
   2 ?    1.8   0.1      0.11   1.6e+02       3      20 ..     110     127 ..     108     138 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00071
                                       CEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HHHHCHC..HHHHHHHH CS
                              cobW 113 davvavvDaknleaeeekieekaedqlaaadllvlnKtDlldeeallekleerl 166
                                       d+++ vvDa+     ++ + ek+ ++  +  l+v+nK+Dl++++   e+ +++ 
  gi|242399934|ref|YP_002995359.1|  18 DIILEVVDARDPIGTRNLKVEKIAQKEGKKLLIVMNKADLVPKKWA-EEYKQKN 70 
                                       77889999988866677777777777788889**********9933.4555444 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.11
                                       EEEEESTTCCHHHHHHHH CS
                              cobW   3 tvltGflGsGKTtLlnhl 20 
                                       +vl+G++  GK+t++n l
  gi|242399934|ref|YP_002995359.1| 110 VVLVGYPNVGKSTIINVL 127
                                       799***********9966 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       665  (0.0370907); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); 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: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.47
# Mc/sec: 2265.92
//
Query:       gi|242399935|ref|YP_002995360.1|  [L=365]
Description: N6-adenine-specific DNA methylase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-40  138.5   0.0    4.4e-39  134.2   0.0    2.3  2  UPF0020          Putative RNA methylase family UPF0020
    1.2e-24   87.1   1.8    1.2e-24   87.1   1.8    1.5  2  THUMP            THUMP domain
    7.4e-09   35.6   0.0    2.1e-08   34.1   0.0    1.7  1  Methyltransf_31  Methyltransferase domain
    1.1e-08   35.7   0.0    4.4e-08   33.7   0.0    2.1  2  Methyltransf_25  Methyltransferase domain
    2.3e-07   30.6   0.1    5.2e-07   29.4   0.0    1.6  2  Methyltransf_15  RNA cap guanine-N2 methyltransferase
    1.6e-06   27.6   0.0    2.7e-06   26.9   0.0    1.3  1  N6_Mtase         N-6 DNA Methylase
    5.7e-06   26.9   0.0    1.8e-05   25.3   0.0    1.9  1  Methyltransf_11  Methyltransferase domain
      1e-05   25.3   0.0    4.8e-05   23.2   0.0    1.8  2  N6_N4_Mtase      DNA methylase
    0.00021   20.8   0.0    0.00041   19.9   0.0    1.5  1  Methyltransf_4   Putative methyltransferase
    0.00043   19.9   0.0    0.00071   19.2   0.0    1.3  1  MTS              Methyltransferase small domain
    0.00077   19.1   0.0     0.0015   18.2   0.0    1.4  1  Cons_hypoth95    Conserved hypothetical protein 95
     0.0032   16.9   0.1      0.017   14.4   0.0    1.9  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family
     0.0041   16.6   0.0       0.18   11.3   0.0    2.3  2  AviRa            RRNA methyltransferase AviRa
  ------ inclusion threshold ------
      0.013   14.3   0.0      0.025   13.4   0.0    1.6  1  MtmB             Monomethylamine methyltransferase MtmB
      0.053   13.4   0.0        1.9    8.3   0.0    2.4  2  Methyltransf_23  Methyltransferase 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 ?   -3.0   0.0       4.1   4.8e+03     135     156 ..      93     114 ..      78     140 .. 0.66
   2 !  134.2   0.0   3.6e-42   4.4e-39       1     195 [.     191     358 ..     191     360 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 4.1
                                       ---HHHHHHHHHHHHHHHHHH- CS
                           UPF0020 135 lgskkalekLYseflrelkrvl 156
                                       l+++kal+++Y+ ++++l +++
  gi|242399935|ref|YP_002995360.1|  93 LEKEKALQEIYDFVSNSLIENY 114
                                       4556666666666555554444 PP

  == domain 2  score: 134.2 bits;  conditional E-value: 3.6e-42
                                       -SSS-SS---SS-HHHHHHHHHHTT--TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH- CS
                           UPF0020   1 RgyRefngpapLketLAaalvrlagwkpgepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearael 77 
                                       R +R++++pa+Lk+++A a+++la++++g+  lDPmCGsGtilIE al g +                         
  gi|242399935|ref|YP_002995360.1| 191 RPWRVYDHPAHLKASIANAMIELAELDEGS-VLDPMCGSGTILIELALRGYEGK----------------------- 243
                                       78***********************98876.67***************999888....................... PP

                                       -EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE----------HHHHHHHHHHHHHHHHH CS
                           UPF0020  78 klygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnpPYGerlgskkalekLYseflrelkr 154
                                        ++g+++ +++++ga  Na +agv d+i++ q da+ L +  ++vd +++n+PYG ++g+kk + +LY +f  el++
  gi|242399935|ref|YP_002995360.1| 244 -IIGIEKYKKHLKGAMMNALAAGVLDKIDLIQGDATRLSHYLDSVDFVISNLPYGLKIGKKKLIPELYMKFFAELSK 319
                                       .9*************************************77779********************************* PP

                                       H-TT..-EEEEEESSHHHHHCC---ESEEEEEEETTEEEEE CS
                           UPF0020 155 vlrgggrlvlltsenkalekaleeralrkvkeknvklglll 195
                                       +l +  r v+lt+e+ka+eka+ee+ ++ ++ + v +g+l+
  gi|242399935|ref|YP_002995360.1| 320 ILGK--RGVFLTTEKKAIEKAFEENGFKIIHHRLVGHGGLM 358
                                       ****..*****************************999987 PP

>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.1   1.8   9.7e-28   1.2e-24      11     144 .]      32     182 ..      20     182 .. 0.93
   2 ?   -3.6   0.0       9.2   1.1e+04      18      38 ..     320     340 ..     315     346 .. 0.63

  Alignments for each domain:
  == domain 1  score: 87.1 bits;  conditional E-value: 9.7e-28
                                       T.H-SEEEEETTEEEEECTEEEEEETHHHHHHHHHTST.......TECEEEEE.......EEEEESSHHHHHHHHHH CS
                             THUMP  11 kvnverveagkgrivvelkgekpeedeellkealekar.......giqrvipv.......cevceadledileaake 73 
                                       k++ve++++g +++++ + +e+++ de+  k+ +e+a        +++rvi++         ++e++l++i++++++
  gi|242399935|ref|YP_002995360.1|  32 KGKVEEKPSGVEGRILAEIEESYYLDEKGKKREFEIASflnensrLLHRVIFQlsstklsNLEKEKALQEIYDFVSN 108
                                       34678889999999999999***************9999999999*************9999*************** PP

                                       HHHHHHHHCT-EEEEEEEESSSTSSSHHHHHHHHHHHHHHCCTT....-EE-SSS-SEEEEEEEETTEEEEEEEC CS
                             THUMP  74 ivkkkfeeeketFaVrvkrrgkhfeftsreinrevGkaivektg....lkVdlenPdivvrveiikdkayisidr 144
                                          +++ + +e+FaVr +r+g+h efts +++++vG ai +k++    +kV+l++P +++r+e+i+d ++++id+
  gi|242399935|ref|YP_002995360.1| 109 SLIENYVKISESFAVRGFRKGEH-EFTSIDVAKTVGSAIYDKLSkfgtPKVNLDHPSVIFRAEVINDVFFLGIDT 182
                                       ********99*************.*************************************************96 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 9.2
                                       EEETTEEEEECTEEEEEETHH CS
                             THUMP  18 eagkgrivvelkgekpeedee 38 
                                       + gk+++++ + ++ +e++ e
  gi|242399935|ref|YP_002995360.1| 320 ILGKRGVFLTTEKKAIEKAFE 340
                                       456666666666665555544 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.0   1.8e-11   2.1e-08       5     113 ..     219     333 ..     216     352 .. 0.77

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 1.8e-11
                   Methyltransf_31   5 lrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdieeleklledekfDlils 80 
                                        +vlD+ CG+G++++ela + g +++++Gi+  ++ ++ A  na   g+   + + qgd++ l+     +++D+++s
  gi|242399935|ref|YP_002995360.1| 219 GSVLDPMCGSGTILIELA-LRGYEGKIIGIEKYKKHLKGAMMNALAAGVLdKIDLIQGDATRLS--HYLDSVDFVIS 292
                                       579***************.77889******************998888644***********99..3458******* PP

                   Methyltransf_31  81 nevl.naladpdkile.......eiervlkpggilliedpr 113
                                       n +    +  ++ i e       e+++ l + g++l+++ +
  gi|242399935|ref|YP_002995360.1| 293 NLPYgLKIGKKKLIPElymkffaELSKILGKRGVFLTTEKK 333
                                       *6666333333333334444444888888888888777665 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       7.9   9.5e+03      77      91 ..      90     104 ..      68     107 .. 0.68
   2 !   33.7   0.0   3.7e-11   4.4e-08       1      74 [.     221     296 ..     221     325 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 7.9
                                       SSHHHHHHHHHHHHH CS
                   Methyltransf_25  77 lsdedlekalkeiar 91 
                                       ls+ + ekal+ei++
  gi|242399935|ref|YP_002995360.1|  90 LSNLEKEKALQEIYD 104
                                       455667889999886 PP

  == domain 2  score: 33.7 bits;  conditional E-value: 3.7e-11
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEEESTG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvssgal 74 
                                       vLd  cG+G+++++la r+ ++k++g++  ++ l+ a  +a ++g+  +++++qgda++l+   +s+D+v+s+  +
  gi|242399935|ref|YP_002995360.1| 221 VLDPMCGSGTILIELALRGYEGKIIGIEKYKKHLKGAMMNALAAGVldKIDLIQGDATRLSHYLDSVDFVISNLPY 296
                                       89**************99649*****************************************999*******5333 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 ?   -2.9   0.0       3.7   4.4e+03     115     131 ..      87     103 ..      55     120 .. 0.49
   2 !   29.4   0.0   4.3e-10   5.2e-07       3      82 ..     220     297 ..     218     304 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 3.7
                   Methyltransf_15 115 kniilfLPrnsdlnqla 131
                                          +  L ++  l++++
  gi|242399935|ref|YP_002995360.1|  87 STKLSNLEKEKALQEIY 103
                                       22223333333333333 PP

  == domain 2  score: 29.4 bits;  conditional E-value: 4.3e-10
                   Methyltransf_15   3 vilDlfsGaGGnviqfalv..fekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklklekikvdlvfl 77 
                                        +lD+++G+G   i++al     k+i+ie+ +++l+ a  Na + gv dki+l++gd + l +   l+++  d+v+ 
  gi|242399935|ref|YP_002995360.1| 220 SVLDPMCGSGTILIELALRgyEGKIIGIEKYKKHLKGAMMNALAAGVLDKIDLIQGDATRLSHY--LDSV--DFVIS 292
                                       58***************9964349*********************************9876554..3344..67777 PP

                   Methyltransf_15  78 SpPwG 82 
                                         P G
  gi|242399935|ref|YP_002995360.1| 293 NLPYG 297
                                       77766 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0   2.3e-09   2.7e-06      33     143 ..     205     303 ..     202     319 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 2.3e-09
                          N6_Mtase  33 evsklivellepksgesvyDpacGsggllvqaekvlkeedgktkelsiyGqeknettyrLakmNlllhgieykkvki 109
                                       ++ + ++el+e  +g sv+Dp cGsg +l++ +           e +i G ek ++  + a mN l  g+  k ++ 
  gi|242399935|ref|YP_002995360.1| 205 SIANAMIELAELDEG-SVLDPMCGSGTILIELALR-------GYEGKIIGIEKYKKHLKGAMMNALAAGVLDK-IDL 272
                                       678899999999999.5*************98763.......4567899********************9988.776 PP

                          N6_Mtase 110 rlgdtlekpkfekdkkfdvvvaNppfnqkewkek 143
                                        +gd+    +     ++d+v++N p++ k   +k
  gi|242399935|ref|YP_002995360.1| 273 IQGDATRLSHY--LDSVDFVISNLPYGLK-IGKK 303
                                       66665443333..479***********98.4444 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   1.5e-08   1.8e-05       1      94 [.     222     327 ..     222     329 .. 0.82

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 1.5e-08
                                       EEET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCT.SS-TT-EEEEEEES... CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg..arvvgvDlskemlklakekaseegl..kvefvvadaekl.pfednsfDlvvsse... 69 
                                       Ld  cG+G ++ +la rg  ++++g++  k+ lk a ++a  +g+  k++++++da++l  + d s+D+v+s+    
  gi|242399935|ref|YP_002995360.1| 222 LDPMCGSGTILIELALRGyeGKIIGIEKYKKHLKGAMMNALAAGVldKIDLIQGDATRLsHYLD-SVDFVISNLpyg 297
                                       6888***********88889****************99999999999************55666.*******98654 PP

                                       ....-CCC-....CCHHHHHHHHHHHEEEEEEE CS
                   Methyltransf_11  70 ....vlhhv....edpekalkeiaRvLkpgGll 94 
                                                    e  +k+++e+ ++L + G++
  gi|242399935|ref|YP_002995360.1| 298 lkigK---KklipELYMKFFAELSKILGKRGVF 327
                                       43321...1334556788888888888888876 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0     4e-08   4.8e-05     171     227 ..     197     255 ..     168     259 .. 0.84
   2 ?   -2.5   0.0       2.9   3.4e+03      36      55 ..     311     330 ..     287     350 .. 0.50

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 4e-08
                                       --SS---HHHHHHHHHHHS-TT-EEEETT-TTTHHHHHHHHTT-E..EEEEESSHHHHH CS
                       N6_N4_Mtase 171 kHpaqkPvallerlIklstkkgdivlDpFaGSGtTavaakelgrk..fiGieieeeyve 227
                                        Hpa   + ++  +I+l   ++++vlDp +GSGt++++ +  g +   iGie+++++++
  gi|242399935|ref|YP_002995360.1| 197 DHPAHLKASIANAMIELAELDEGSVLDPMCGSGTILIELALRGYEgkIIGIEKYKKHLK 255
                                       489999999999************************98877765555********9987 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.9
                                       HHHHHHHHHHEEEEEEEEEE CS
                       N6_N4_Mtase  36 ekvlkevrrvLkddgsifin 55 
                                        k+++e+ ++L + g+++  
  gi|242399935|ref|YP_002995360.1| 311 MKFFAELSKILGKRGVFLTT 330
                                       34455555555555555544 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   3.4e-07   0.00041       5      69 ..     221     285 ..     217     331 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 3.4e-07
                                       EEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHC.TTSSEEEEES-CCCHHHHCS- CS
                    Methyltransf_4   5 vleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkieal.elkNlrilrgdalkvllelle 69 
                                       vl+  cG+G++l++lA +  + +++GiE+++k ++ ++ ++ a   l  + +++gda + l+++l 
  gi|242399935|ref|YP_002995360.1| 221 VLDPMCGSGTILIELALRGYEGKIIGIEKYKKHLKGAMMNALAAgVLDKIDLIQGDA-TRLSHYLD 285
                                       56667***************************99877665555528899********.88999986 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   5.9e-07   0.00071      28     138 ..     214     330 ..     205     345 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 5.9e-07
                                       HCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTTTST.TS-EEEE CS
                               MTS  28 pkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..vevvasdvleeve.ekkfdli 101
                                        +  +g+vlD  cG G + ++la +  e ++  +++ ++ l+ a  n+ a ++   +++++ d++   +  +++d++
  gi|242399935|ref|YP_002995360.1| 214 AELDEGSVLDPMCGSGTILIELALRGYEGKIIGIEKYKKHLKGAMMNALAAGVLdkIDLIQGDATRLSHyLDSVDFV 290
                                       4446799****************************************999888669*******986555359***** PP

                                       EE---S..TTTC.HCHHHHHHHHHHHHHHHEEEEEEEEEE CS
                               MTS 102 vsNPPf..hagk.atelavaeeliaeAkeaLkegGeLliV 138
                                       +sN P+  + gk +   ++ ++++ae  ++L + G +l  
  gi|242399935|ref|YP_002995360.1| 291 ISNLPYglKIGKkKLIPELYMKFFAELSKILGKRGVFLTT 330
                                       *****83244443667899999********9999988765 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   1.3e-06    0.0015      38     175 ..     214     354 ..     200     362 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.3e-06
                                       CCHCC-EEEETT-TTSHHHHHHHHTT-S.EEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-E CS
                     Cons_hypoth95  38 aeiegarvLDlfaGsGalglEAlSRgak.kavlvekdkeavkilkenleelkleeetaelkedaleallklakkkee 113
                                       ae+++ +vLD  +GsG++ +E + Rg + k++ +ek k+ +k    n  + ++ ++++ ++ da++  + l     +
  gi|242399935|ref|YP_002995360.1| 214 AELDEGSVLDPMCGSGTILIELALRGYEgKIIGIEKYKKHLKGAMMNALAAGVLDKIDLIQGDATRLSHYL----DS 286
                                       3489999*******************9835667*********99999999999999*******99999988....57 PP

                                       EEEEEE--SSSTTCH.........HHHHHHHHHTT-EEEEEEEEEEEECCSSS--.-TTEEEEEEEEETT CS
                     Cons_hypoth95 114 fdivflDPPyakell........ieevlelleekkllkenalvvvetekekelpespenlelvkekkyge 175
                                       +d+v  + Py  +          + + +++l   k+l ++++ ++ ++k+ e   + +++++++++ +g+
  gi|242399935|ref|YP_002995360.1| 287 VDFVISNLPYGLKIGkkklipelYMKFFAELS--KILGKRGVFLTTEKKAIEKAFEENGFKIIHHRLVGH 354
                                       8*********8664422222333333334443..778777766665556655555566677777776665 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   1.4e-05     0.017      45     126 ..     215     298 ..     200     305 .. 0.85
   2 ?   -1.3   0.0       0.9   1.1e+03     201     230 ..     332     361 ..     325     363 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.4e-05
                                       S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSS.TEEEEE--TTT-TTS-T-EEEE CS
                   Ubie_methyltran  45 vkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegki.nieflqanaeeLpfeddsfDvv 120
                                       ++   +vlD  +G+g + ++l+   g +gk+++++  ++ Lk +   +   g+  +i+++q++a +L    ds D+v
  gi|242399935|ref|YP_002995360.1| 215 ELDEGSVLDPMCGSGTILIELAL-RGYEGKIIGIEKYKKHLKGAMMNALAAGVLdKIDLIQGDATRLSHYLDSVDFV 290
                                       4455689*************985.6899*********************9999989*****************9987 PP

                                       E..EES-G CS
                   Ubie_methyltran 121 t..vsfGl 126
                                          + +Gl
  gi|242399935|ref|YP_002995360.1| 291 IsnLPYGL 298
                                       41245665 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.9
                                       HHHHHHHHHHTTEEEEEEEEEGGGTEEEEE CS
                   Ubie_methyltran 201 qetlkeliedaGfksveyesltgGvvaihi 230
                                       ++ +++ +e+ Gfk ++++ ++ G + +h+
  gi|242399935|ref|YP_002995360.1| 332 KKAIEKAFEENGFKIIHHRLVGHGGLMVHL 361
                                       67889999*******999999988888875 PP

>> AviRa  RRNA methyltransferase AviRa
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.049        58      55      73 ..     219     237 ..     196     261 .. 0.74
   2 !   11.3   0.0   0.00015      0.18     145     229 ..     266     350 ..     247     354 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.049
                             AviRa  55 ltlyDpCCGgayLltvlgl 73 
                                        ++ Dp CG++ +l  l+l
  gi|242399935|ref|YP_002995360.1| 219 GSVLDPMCGSGTILIELAL 237
                                       4899*******99987765 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00015
                             AviRa 145 eekeievfkaditekeeeaekevdivitDlPYGelvswqgeseepvkqlleslaavldpeesvvaviadkk..kkie 219
                                          +i++++ d t+ + +   +vd vi  lPYG     ++   e   +++++l+++l  +++v   + +k   k  e
  gi|242399935|ref|YP_002995360.1| 266 VLDKIDLIQGDATRLS-HYLDSVDFVISNLPYGLKIGKKKLIPELYMKFFAELSKIL-GKRGVFLTTEKKAieKAFE 340
                                       4567788888888554.44556************999999999999***********.7788877666653214455 PP

                             AviRa 220 herfrrlerl 229
                                       +++f+ +++ 
  gi|242399935|ref|YP_002995360.1| 341 ENGFKIIHHR 350
                                       6666666655 PP

>> MtmB  Monomethylamine methyltransferase MtmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.1e-05     0.025     337     386 ..       3      53 ..       1     129 [. 0.69

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.1e-05
                              MtmB 337 emclletaaqaiadtas.GrellsGvaaakGvvkdkttGlearlmgevaia 386
                                       +m ++ t+ q i d a    e+l+ +a+ kG v++k  G+e r+++e+  +
  gi|242399935|ref|YP_002995360.1|   3 KMKFVLTTPQGIEDLAKrEVEMLIKSAGLKGKVEEKPSGVEGRILAEIEES 53 
                                       688999999*****98624689*************************9765 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0    0.0016       1.9      21      54 ..     216     251 ..     197     293 .. 0.84
   2 ?    2.5   0.0     0.099   1.2e+02     148     164 ..     332     348 ..     321     349 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0016
                   Methyltransf_23  21 raggrvLdiGcGtGillevlrengf..svtgvDlsp 54 
                                          g+vLd  cG+G+ l +l+ +g+  +++g++ + 
  gi|242399935|ref|YP_002995360.1| 216 LDEGSVLDPMCGSGTILIELALRGYegKIIGIEKYK 251
                                       56789********************99999999764 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.099
                   Methyltransf_23 148 arslkelleeaGlevve 164
                                        +++++++ee+G+++++
  gi|242399935|ref|YP_002995360.1| 332 KKAIEKAFEENGFKIIH 348
                                       5799***********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.49
# Mc/sec: 2233.83
//
Query:       gi|242399936|ref|YP_002995361.1|  [L=225]
Description: 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase, FAA hydrolase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-68  230.9   0.0    1.5e-68  230.7   0.0    1.0  1  FAA_hydrolase  Fumarylacetoacetate (FAA) hydrolase family
  ------ inclusion threshold ------
      0.062   13.1   0.1       0.15   11.9   0.1    1.6  1  KH_2           KH domain


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 !  230.7   0.0   1.7e-72   1.5e-68       1     217 [.      17     217 ..      17     218 .. 0.96

  Alignments for each domain:
  == domain 1  score: 230.7 bits;  conditional E-value: 1.7e-72
                                       .EEEEEEE--SHHHHHTTT.-SS-EEEEEEGGGE.EETTE..EE-TTSSSS-EE......EEEEEEEESS-B--T-- CS
                     FAA_hydrolase   1 kivcdglnyaehvreagkaaeeppdrhiplepvfflkrasslvgpgdpirrPagsekldyEvELavvigkplrevls 77 
                                       ki+c g+nyaeh++e+g   +e p+     epv+flk++s+l+gp+++i +P++s+++d+EvELav+igk+ +++ +
  gi|242399936|ref|YP_002995361.1|  17 KIICLGRNYAEHAKELG---HEIPK-----EPVIFLKPPSALIGPNQTIILPRKSNHVDHEVELAVIIGKRGKNI-P 84 
                                       69**************8...67777.....999******************************************.9 PP

                                       HHHHHTTEEEEEEEEEEE-SBGGG---..HHHHHHTGGGEEEEEE-B--B-.STT---SS-EEEEEETTEEEEEEEG CS
                     FAA_hydrolase  78 veeAedaiaGytllnDvsaRdlqaeek.aplgwflgksfdtftpiGpwivtpdeledpedlelrlrvngeevqdsnt 153
                                        ++A d+++Gyt+l D++aRdlq+e+k + l+w+  k+fdtf+piGp +v + e+   +dle+ l vnge +q s+t
  gi|242399936|ref|YP_002995361.1|  85 KAKALDYVLGYTILMDLTARDLQWEAKkKGLPWTVVKGFDTFAPIGPRVVDKREIN-VDDLEIGLKVNGEIRQLSRT 160
                                       **************************97777************************6.68****************** PP

                                       GGTTTSHHHHHHHHHHHH-B-TT-EEEEEES.......S--EE--TT-EEEEEETTTEEEEEEE CS
                     FAA_hydrolase 154 kdmifspaeliahlsagltLepGdliltGTpsgvgaeeeslkflkdgDeveveieglGelrnrV 217
                                       ++mif++ e+i+++s+++tLe Gd+i+tGTp+gvg        l++gD+ve+ ieg+G+l+ +V
  gi|242399936|ref|YP_002995361.1| 161 SKMIFKIDEIIEYVSSIMTLEKGDIIATGTPEGVG-------PLRHGDVVEAWIEGIGTLKEEV 217
                                       *********************************98.......5*****************9988 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   1.7e-05      0.15      24      51 ..      60      87 ..      49      89 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.7e-05
                                      SCEEEEEEEESCHHHHHTGGGHHHHHHH CS
                              KH_2 24 anrviiviresqpgivIGkgGsnikkig 51
                                      +++ + v +e + +++IGk+G+ni k +
  gi|242399936|ref|YP_002995361.1| 60 PRKSNHVDHEVELAVIIGKRGKNIPKAK 87
                                      467889999***************8876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); 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 0.32s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 1326.54
//
Query:       gi|242399937|ref|YP_002995362.1|  [L=384]
Description: Tryptophanyl-tRNA synthetase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.8e-24   84.9   0.0      8e-24   84.5   0.0    1.2  1  tRNA-synt_1b     tRNA synthetases class I (W and Y)
  ------ inclusion threshold ------
      0.059   13.5   0.1       0.12   12.5   0.1    1.5  1  ssDBP_DBD        Single stranded DNA-binding protein ss DNA b
      0.062   12.8   0.0       0.17   11.4   0.0    1.7  2  Aromatic_hydrox  Homotrimeric ring hydroxylase


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 !   84.5   0.0   1.3e-27     8e-24       7     293 .]      74     347 ..      68     347 .. 0.89

  Alignments for each domain:
  == domain 1  score: 84.5 bits;  conditional E-value: 1.3e-27
                                       EEEEEEETSSS-BGGGHHHHHHHHHHHH.TTSEEEEEEEHHHHHTTTTT-SSHHHHHHHHHHHHHHHHHHHHHTCHT CS
                      tRNA-synt_1b   7 rvysGidPTgklHlGylvplkklvelqk.aghevffliaDlhAiigdpskaeerklrkreevlenaikaqlakgldp 82 
                                        +y+G  P+g++H+G+++p+    +lq+  g+++++ i D + ++ +p+   +    +++  +en+   ++a+g+dp
  gi|242399937|ref|YP_002995362.1|  74 FLYTGRGPSGPMHIGHIIPFFATKWLQEnFGVNLYVQITDDEKFLFKPQ---LTFEGTKRWAYENI-LDIIAVGFDP 146
                                       68*************************9779******************...44444455555555.779******* PP

                                       TTEEEEETHHHHTTHHHHHHHHHHHTTCBHHHHHHHHHCCHHCSSSC--BHHHHHHHHHHHHHHHHTCHS.EEEEEG CS
                      tRNA-synt_1b  83 ekaevvlqsewlehlelaellrdlgklgslnrmlqfksvkkrleegegislgeftYplLqaaDilllkad.lvpgGs 158
                                       +k+ ++  se  +  e+a  +++ ++    + +  f +     ++    ++g + +p  qaa  ++ +++ l p   
  gi|242399937|ref|YP_002995362.1| 147 DKTFIFQDSEFTKIYEMAIPIAKKVTYSMAKAVFGFNE-----QS----KIGMIFFPAIQAAPTFFEEKRsLIPAAI 214
                                       ******************99999999777788888888.....33....5889*********999988888****** PP

                                       GGHHHHHHHHHHHHHHHHHSTTSS-EEEEET-BBSTTSSS.BTTCETTCGC-BTTCCHHHHHHHH.HHCHCSTTC.. CS
                      tRNA-synt_1b 159 DQkqnielgrdlarrfnkkevfkkpegltvplltgldGek.KmSKSagnsaIfLddekesvkkki.qkavtdsde.. 231
                                       DQ+   ++ rd a+++++     k  +l  ++++gl G   KmS S++++aI+L+d++e++ kki ++a+t  ++  
  gi|242399937|ref|YP_002995362.1| 215 DQDPYWRIQRDFAESLGYY----KTAALHSKFVPGLMGLGgKMSASKPETAIYLTDDPEEAGKKIwKYALTGGRAta 287
                                       ******************9....**************9877********************9999466777777699 PP

                                       SHHHHHHHHHTHHHCHHHHHHHHCCSEEESSHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH CS
                      tRNA-synt_1b 232 evekllklktelsnelierleavsgkkpkreaeellaeevtklvhggdlkkalaealnelle 293
                                       + ++ l + +  +  +++ le + + ++ +++ e + +++++++ +g++k+ l e+++++l+
  gi|242399937|ref|YP_002995362.1| 288 KEQRELGGEPDKCV-VFKWLEIFFEPDE-KKLLERYIACKNGEILCGQCKRYLIEKVQNFLK 347
                                       99999*********.**********999.67777778899******************9985 PP

>> ssDBP_DBD  Single stranded DNA-binding protein ss DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1     2e-05      0.12      13      93 ..      62     137 ..      51     153 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2e-05
                         ssDBP_DBD  13 lvlirwntgktsagrlfgrygpggrpeffkllfgavagslreqfgpdgenifnrirdsekfretsrelfdglkkwff 89 
                                       lvl  +++gk     l+   gp g   + +++    +  l+e+fg    n++ +i d ekf    +  f+g k+w +
  gi|242399937|ref|YP_002995362.1|  62 LVLKDYEAGKGF--FLYTGRGPSGPMHIGHIIPFFATKWLQENFG---VNLYVQITDDEKFLFKPQLTFEGTKRWAY 133
                                       666666666643..4666678888777777666666678999996...69*************************** PP

                         ssDBP_DBD  90 eeav 93 
                                       e+ +
  gi|242399937|ref|YP_002995362.1| 134 ENIL 137
                                       9865 PP

>> Aromatic_hydrox  Homotrimeric ring hydroxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   2.8e-05      0.17      21      82 ..     121     182 ..     105     202 .. 0.76
   2 ?   -2.7   0.0      0.57   3.4e+03      51      71 ..     214     234 ..     212     243 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.8e-05
                   Aromatic_hydrox  21 ddivvlgkrrvikanWrlavengfdPghvlihkdsqlviesdlalplGfkPvgeratevkvv 82 
                                       ++++  g +r    n    +  gfdP   +i +ds++ +  ++a+p+  k +   a+ v  +
  gi|242399937|ref|YP_002995362.1| 121 PQLTFEGTKRWAYENILDIIAVGFDPDKTFIFQDSEFTKIYEMAIPIAKKVTYSMAKAVFGF 182
                                       5555556666666666666677************************9988777666665555 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.57
                   Aromatic_hydrox  51 ihkdsqlviesdlalplGfkP 71 
                                       i +d  + i++d+a +lG+  
  gi|242399937|ref|YP_002995362.1| 214 IDQDPYWRIQRDFAESLGYYK 234
                                       67788899999*******954 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1167  (0.0650901); expected 358.6 (0.02)
Passed bias filter:                      827  (0.0461264); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.29s 00:00:00.96 Elapsed: 00:00:00.48
# Mc/sec: 2402.58
//
Query:       gi|242399938|ref|YP_002995363.1|  [L=462]
Description: Succinyl-coa synthetase alpha subunit related protein [Thermococcus sibiricus MM 739]
Scores for complete 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-60  200.8   4.5    3.2e-58  195.4   0.9    3.7  4  Succ_CoA_lig   Succinyl-CoA ligase like flavodoxin domain
    5.6e-27   94.5   1.1    6.9e-25   87.8   0.2    2.9  3  CoA_binding_2  CoA binding domain
    1.2e-17   64.3   2.3    1.1e-16   61.3   0.9    2.5  2  CoA_binding    CoA binding domain
     0.0085   16.2   0.0       0.95    9.6   0.0    3.0  3  Hydrolase_6    Haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.058   14.0   0.6      0.058   14.0   0.6    3.2  4  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
      0.079   12.2   0.1       0.95    8.7   0.0    2.2  2  DUF4849        Putative glycoside hydrolase Family 18, chitin
      0.082   12.7   0.0       0.27   11.0   0.1    1.8  2  GTP_CH_N       GTP cyclohydrolase N terminal
       0.13   12.3   0.0          1    9.4   0.0    2.4  3  Hpr_kinase_N   HPr Serine kinase N terminus


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 ?    1.7   0.0     0.091     2e+02       3      36 ..      68     101 ..      66     125 .. 0.88
   2 !  195.4   0.9   1.4e-61   3.2e-58       2     138 .]     155     291 ..     154     291 .. 0.99
   3 ?   -1.4   0.0       0.8   1.8e+03       3      29 ..     301     327 ..     299     335 .. 0.85
   4 ?    2.1   0.0     0.067   1.5e+02      41      91 ..     366     419 ..     358     447 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.091
                      Succ_CoA_lig   3 kialisqSGalalalldwaasrglgfskvvslGn 36 
                                       ++a+is  G ++ ++l+ + ++g++ + v+s+G 
  gi|242399938|ref|YP_002995363.1|  68 DVAVISIPGRFVPQILEECGQKGVKGAVVISAGF 101
                                       6999***************************995 PP

  == domain 2  score: 195.4 bits;  conditional E-value: 1.4e-61
                      Succ_CoA_lig   2 GkialisqSGalalalldwaasrglgfskvvslGneadvdvadlleylaedpetkvillylEsirdgrkflsaarra 78 
                                       G+ia++sqSGa+++a+ldwaa++++g+sk++slGn+ad+d++d++eyl++d++tkvi++ylE+++dg+kfl+aar a
  gi|242399938|ref|YP_002995363.1| 155 GGIAFMSQSGAFGAAILDWAARHEVGMSKFISLGNMADLDESDFMEYLKDDKATKVITAYLEGVKDGKKFLKAARDA 231
                                       89*************************************************************************** PP

                      Succ_CoA_lig  79 arkkpvvvlksGrseagaraaashtgalagsdavvdaafrqaGvlrvdsleelfdaaell 138
                                       ++kkpvv+lksGr+eaga+aaashtg+lags+a+++aaf+q+Gvl+++s+++lf++a++l
  gi|242399938|ref|YP_002995363.1| 232 TKKKPVVILKSGRTEAGAKAAASHTGSLAGSYAIYQAAFEQTGVLEARSMRQLFNYAKAL 291
                                       *********************************************************986 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.8
                      Succ_CoA_lig   3 kialisqSGalalalldwaasrglgfs 29 
                                       ++a+++  G+ ++++ d + + gl+++
  gi|242399938|ref|YP_002995363.1| 301 RVAIVTNGGGAGVMMSDGLLEVGLKIA 327
                                       699************999998888776 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.067
                      Succ_CoA_lig  41 dvadlleylaedpetkvilly..lEsirdgrkflsaarraark.kpvvvlksGr 91 
                                        ++  ++y  ed++++v+++   + s    +  ++a+ ++++  kpv+ + +G 
  gi|242399938|ref|YP_002995363.1| 366 RYETAMRYALEDENVDVLAVIalFQSPALDDGIVDAVGKMQEYgKPVIFIAPGG 419
                                       56678899999999987655311455555789999999999999****999986 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.8   0.2   3.1e-28   6.9e-25       2     114 ..      11     133 ..      10     135 .. 0.97
   2 ?   -2.7   0.0       3.6   8.1e+03      11      27 ..     162     178 ..     157     181 .. 0.57
   3 ?    4.3   0.0     0.025        56      52     106 ..     379     437 ..     362     440 .. 0.76

  Alignments for each domain:
  == domain 1  score: 87.8 bits;  conditional E-value: 3.1e-28
                                       -EEEET--S-TTSHHHHHHHHHHH...HT--EEEESSS-SEETTEES----T....T--EEEE-S-HHHHGGGHHHH CS
                     CoA_binding_2   2 tiaVvGasdnpgkfgykvlrylle...hglpvvpVnpkeeeilgekvyaslaedpepvdlvdvftppeatpeivkea 75 
                                       ++aV+Gas+++gk g+ ++++l +   +g +++pVn kee++lg k+y+s+ e p  vd++++ +p   +p+i++e+
  gi|242399938|ref|YP_002995363.1|  11 SVAVIGASNKEGKIGNAIMKNLINfgfKG-RIYPVNVKEEKVLGIKAYKSVLEIPDSVDVAVISIPGRFVPQILEEC 86 
                                       79**********************99999.**********************968********************** PP

                                       HHH--SEEEE-TT........---HHHHHHHHHTT-EEE.ES-HHHH CS
                     CoA_binding_2  76 lalgakavwlqpg........sedeeaaelaeeagirvvgdrCilve 114
                                       +++g+k++++ ++        + +++++e+a++ +ir+vg++C++v 
  gi|242399938|ref|YP_002995363.1|  87 GQKGVKGAVVISAgfkeagnvELENKLLEVARKWNIRIVGPNCLGVT 133
                                       *******9999999*******************************96 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.6
                                       -TTSHHHHHHHHHHHHT CS
                     CoA_binding_2  11 npgkfgykvlryllehg 27 
                                       ++g fg  +l++  +h+
  gi|242399938|ref|YP_002995363.1| 162 QSGAFGAAILDWAARHE 178
                                       44556666666665554 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.025
                                       ...T--EEEE-S-HHHHGGGHHHHHHH...--SEEEE-TT.---HHHHHHHHHTT-EEE CS
                     CoA_binding_2  52 dpepvdlvdvftppeatpeivkealal...gakavwlqpg.sedeeaaelaeeagirvv 106
                                       ++ ++ ++ +f  p+    iv++++++   g +++ + pg ++ e++a++ e+ g++v 
  gi|242399938|ref|YP_002995363.1| 379 NVDVLAVIALFQSPALDDGIVDAVGKMqeyGKPVIFIAPGgAYPEKMARRIEKTGVPVF 437
                                       34555699999999999999999988866655555555555**************9986 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.3   0.9   4.9e-20   1.1e-16       3      96 .]       9     100 ..       7     100 .. 0.97
   2 ?    1.7   0.0       0.2   4.4e+02      35      60 ..     419     446 ..     404     453 .. 0.80

  Alignments for each domain:
  == domain 1  score: 61.3 bits;  conditional E-value: 4.9e-20
                                       TEEEEEETTTSHHHHHH.HHHHHHHHECEE.EEEEC-TTTTTCEETTEEEESCHHHHHHHCTTTEEEEES-HHHHHH CS
                       CoA_binding   3 dtkviviGagglgiagl.yhfkeklkygik.avfgvnprkvgtevlglpvyksvdeleektevdvavitvPaesaqe 77 
                                       + +v+viGa++++++++   +k+ +++g+k  +++vn +   ++vlg+++yksv e++++  vdvavi +P +++ +
  gi|242399938|ref|YP_002995363.1|   9 PQSVAVIGASNKEGKIGnAIMKNLINFGFKgRIYPVNVK--EEKVLGIKAYKSVLEIPDS--VDVAVISIPGRFVPQ 81 
                                       679***************************9********..*******************..*************** PP

                                       HHHHHHHTT-SEEEEESST CS
                       CoA_binding  78 avdelveagikgiviiteg 96 
                                       + +e+ ++g+kg+v+i++g
  gi|242399938|ref|YP_002995363.1|  82 ILEECGQKGVKGAVVISAG 100
                                       ****************976 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.2
                                       EC-TTTTTCEET..TEEEESCHHHHHHH CS
                       CoA_binding  35 gvnprkvgtevl..glpvyksvdeleek 60 
                                       g  p+k+++ ++  g+pv+++v++ ++ 
  gi|242399938|ref|YP_002995363.1| 419 GAYPEKMARRIEktGVPVFETVEDGVDA 446
                                       66677778777666********998776 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0         2   4.5e+03      20      36 ..     222     240 ..     212     259 .. 0.61
   2 ?    2.7   0.0     0.059   1.3e+02       5      41 ..     272     310 ..     268     343 .. 0.71
   3 !    9.6   0.0   0.00042      0.95      17      74 ..     396     454 ..     386     459 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2
                                       HHHHHHHHHTT..-EEEEE CS
                       Hydrolase_6  20 aealnalraag..kpvvll 36 
                                       +++l+a r+a   kpvv+l
  gi|242399938|ref|YP_002995363.1| 222 KKFLKAARDATkkKPVVIL 240
                                       5566666666433666665 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.059
                                       STTTSEE..TTEE-TTHHHHHHHHHHTT-EEEEEE---S CS
                       Hydrolase_6   5 idGvLwr..gdkaipgaaealnalraagkpvvllTNnss 41 
                                         GvL     +++++ a+ +  +  a+g +v+++TN+++
  gi|242399938|ref|YP_002995363.1| 272 QTGVLEArsMRQLFNYAKALTMQKPANGDRVAIVTNGGG 310
                                       5566653223445555555555666889********987 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00042
                                       TTHHHHHHHHHHTT-EEEEEE---SS-HHHHHHHHHHTT----G..GGEEEHHHHHHHHH CS
                       Hydrolase_6  17 pgaaealnalraagkpvvllTNnsskseeeyakkleklgvdite..eqvvtsataaaeyl 74 
                                       +g ++a+  +++ gkpv+++  ++  + e++a ++ek gv++ e  e+ v + +a+++y 
  gi|242399938|ref|YP_002995363.1| 396 DGIVDAVGKMQEYGKPVIFIAPGGAYP-EKMARRIEKTGVPVFEtvEDGVDAVYALVKYG 454
                                       68899*****************99998.99***********6443488888888888875 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.6   2.6e-05     0.058       2      94 ..      12      99 ..      11     101 .. 0.82
   2 ?   -1.5   0.0       1.7   3.9e+03       8      32 ..     164     189 ..     157     243 .. 0.57
   3 ?   -2.0   0.0       2.4   5.4e+03      27      47 ..     237     257 ..     221     292 .. 0.59
   4 ?   -0.7   0.0      0.96   2.2e+03       2      46 ..     302     344 ..     301     365 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.6e-05
                                      EEEETT....SHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHH CS
                     F420_oxidored  2 igiiGa....Gnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedvee 76
                                      +++iGa    G++g a++++l++ g  +  i+ + + ++ek+       g+k+ + +  e  ++ dv v++++ + v++
  gi|242399938|ref|YP_002995363.1| 12 VAVIGAsnkeGKIGNAIMKNLINFG-FKGRIYPV-NVKEEKVL------GIKAYK-SVLEIPDSVDVAVISIPGRFVPQ 81
                                      677776566699*************.77788856.66777774......555555.677788999************** PP

                                      HHHHCGHHHHTTSEEEEE CS
                     F420_oxidored 77 vlselakdalkgklvisv 94
                                      +l+e  ++  kg +vis+
  gi|242399938|ref|YP_002995363.1| 82 ILEECGQKGVKGAVVISA 99
                                      ****************97 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.7
                                       SHHHHHHHHHHHHTTS.-GGCEEEEE CS
                     F420_oxidored   8 Gnmgealasgllaaga.qpheivvan 32 
                                       G +g+a++  ++++ +   + i ++n
  gi|242399938|ref|YP_002995363.1| 164 GAFGAAILDWAARHEVgMSKFISLGN 189
                                       56666666555555444444443333 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 2.4
                                       CEEEEEESSCCCHHHHHHHHC CS
                     F420_oxidored  27 eivvansrnpekaeelaeelg 47 
                                        +++ + r++  a+++a++ g
  gi|242399938|ref|YP_002995363.1| 237 VVILKSGRTEAGAKAAASHTG 257
                                       233344555666666665555 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 0.96
                                       EEEE.TTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHH CS
                     F420_oxidored   2 igii.GaGnmgealasgllaagaqpheivvansrnpekaeelaeel 46 
                                       ++i+  +G  g  +  gll+ g    +i   + r++ek +++ ee 
  gi|242399938|ref|YP_002995363.1| 302 VAIVtNGGGAGVMMSDGLLEVG---LKIAELSGRTNEKFAKAIEEG 344
                                       6777667778888999999999...777777789999988877764 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 ?    8.7   0.0   0.00043      0.95      47      96 ..      50      96 ..      40     112 .. 0.78
   2 ?    0.8   0.0      0.11   2.4e+02     236     267 ..     175     205 ..     162     234 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00043
                           DUF4849 47 ekvpssqaqslsalPDSvDfvsltnpeelseaeleeikkvkeKGtkvlys 96
                                      +  + +  +s+ ++PDSvD+ ++  p     + lee     +KG+k  + 
  gi|242399938|ref|YP_002995363.1| 50 KVLGIKAYKSVLEIPDSVDVAVISIPGRFVPQILEECG---QKGVKGAVV 96
                                      5667888899****************999999888875...455554443 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.11
                           DUF4849 236 lvnevpadrfivavsleslddtdkktgyvdtk 267
                                       +  ev   +fi + +++ ld++d  + y + +
  gi|242399938|ref|YP_002995363.1| 175 ARHEVGMSKFISLGNMADLDESDFME-YLKDD 205
                                       567888999************99999.55443 PP

>> GTP_CH_N  GTP cyclohydrolase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00012      0.27      21      85 ..     226     294 ..     208     317 .. 0.68
   2 ?   -1.6   0.0      0.86   1.9e+03      67     126 ..     329     388 ..     319     401 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00012
                          GTP_CH_N  21 WgakdakeRGpvvasrkksslkkrna....iGahsGsYsvYralavasgkldaehkpdltntepavkig 85 
                                        +a+da+++ pvv  ++ ++ +   a     G+ +GsY++Y+a    +g l+a+ + +l n + a +++
  gi|242399938|ref|YP_002995363.1| 226 KAARDATKKKPVVILKSGRTEAGAKAaashTGSLAGSYAIYQAAFEQTGVLEARSMRQLFNYAKALTMQ 294
                                       467888888898876654443333221122688899*******99999999998888887777666654 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.86
                          GTP_CH_N  67 ldaehkpdltntepavkigpqpsWsdpkkivslDpfghlvaevfkeelekgldirPtiav 126
                                       l+ + + ++ ++    k++++ s+++p +i+   p +   + +     ++++d+   ia+
  gi|242399938|ref|YP_002995363.1| 329 LSGRTNEKFAKAIEEGKLPEHMSYKNPIDIIGDAPSSRYETAMRYALEDENVDVLAVIAL 388
                                       555666677777788889999999999999998888877777666677778998888876 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 ?   -1.1   0.0       0.8   1.8e+03      89     108 ..     106     125 ..      94     128 .. 0.76
   2 ?   -2.6   0.0       2.4   5.4e+03      58      77 ..     196     215 ..     194     245 .. 0.58
   3 ?    9.4   0.0   0.00046         1      72     122 ..     401     451 ..     395     453 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.8
                                       TT---HHHHHHHHHH---EE CS
                      Hpr_kinase_N  89 gleppeellelaeeygvpll 108
                                       ++e +++lle+a++ ++ ++
  gi|242399938|ref|YP_002995363.1| 106 NVELENKLLEVARKWNIRIV 125
                                       4558999********99885 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.4
                                       HHHHHT-HHHHH..HHHHHH CS
                      Hpr_kinase_N  58 lsYleklseeerkerleklf 77 
                                       ++++e l++++  +++  ++
  gi|242399938|ref|YP_002995363.1| 196 SDFMEYLKDDKATKVITAYL 215
                                       55555555555555555444 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.00046
                                       HHHHHHTT--S-EEEETTT---HHHHHHHHHH---EEEESS-HHHHHTTHH CS
                      Hpr_kinase_N  72 rleklfskkipciiltrgleppeellelaeeygvpllrtklstsefiaeli 122
                                       ++ k+ +++ p+i ++ g   pe++++  e++gvp++ t +   + + +l 
  gi|242399938|ref|YP_002995363.1| 401 AVGKMQEYGKPVIFIAPGGAYPEKMARRIEKTGVPVFETVEDGVDAVYALV 451
                                       56789999*******************************988777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (462 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.64u 0.33s 00:00:00.97 Elapsed: 00:00:00.52
# Mc/sec: 2698.20
//
Query:       gi|242399939|ref|YP_002995364.1|  [L=196]
Description: Transcriptional regulatory protein, arsR family [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-15   56.1   0.2    7.2e-15   54.6   0.2    1.9  1  HTH_5           Bacterial regulatory protein, arsR family
    3.8e-15   55.7   0.0    1.7e-14   53.6   0.1    2.0  2  HTH_20          Helix-turn-helix domain
    4.3e-08   32.6   0.3    1.1e-07   31.3   0.3    1.7  1  HTH_24          Winged helix-turn-helix DNA-binding
      3e-07   30.3   0.3    7.9e-07   28.9   0.3    1.8  1  HTH_11          HTH domain
    3.5e-06   26.8   0.0    1.6e-05   24.7   0.0    2.0  2  MarR_2          MarR family
      6e-06   26.1   0.2    1.4e-05   24.9   0.2    1.6  1  TrmB            Sugar-specific transcriptional regulator TrmB
    3.2e-05   23.6   1.9    0.00017   21.2   1.1    2.3  1  ArsR            ArsR transcriptional regulator
    4.2e-05   23.2   0.0    9.2e-05   22.1   0.0    1.5  1  HTH_23          Homeodomain-like domain
    6.1e-05   23.0   0.0    0.00012   22.1   0.0    1.5  1  HTH_29          Winged helix-turn helix
    0.00017   21.3   0.1    0.00049   19.8   0.1    1.8  1  HTH_38          Helix-turn-helix domain
     0.0005   20.0   0.4     0.0019   18.1   0.2    2.0  2  HTH_Crp_2       Crp-like helix-turn-helix domain
     0.0011   19.2   2.3      0.046   14.0   0.1    2.2  2  DUF2513         Hypothetical protein (DUF2513)
     0.0015   18.3   0.0      0.004   16.9   0.0    1.7  1  HTH_IclR        IclR helix-turn-helix domain
      0.002   17.8   0.1     0.0054   16.4   0.1    1.8  1  Sigma70_r4_2    Sigma-70, region 4
     0.0037   16.8   0.1      0.011   15.2   0.1    1.9  1  Sigma70_r4      Sigma-70, region 4
     0.0071   16.5   0.5      0.027   14.7   0.1    2.1  2  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
  ------ inclusion threshold ------
      0.011   15.8   0.0      0.023   14.8   0.0    1.5  1  HTH_28          Helix-turn-helix domain
      0.015   15.7   1.2      0.058   13.9   1.2    2.2  1  HTH_40          Helix-turn-helix domain
      0.016   15.0   1.6      0.016   15.0   1.6    2.3  2  TFIIE_alpha     TFIIE alpha subunit
      0.019   15.4   0.2      0.059   13.9   0.2    1.8  1  HTH_27          Winged helix DNA-binding domain
      0.021   14.4   2.8      0.025   14.1   2.8    1.1  1  Isy1            Isy1-like splicing family
      0.021   14.7   0.9       0.59   10.1   0.2    2.3  2  MarR            MarR family
      0.032   14.4   0.1       0.45   10.7   0.0    2.4  2  HTH_17          Helix-turn-helix domain
      0.048   13.8   0.2       0.17   12.1   0.1    2.0  1  HTH_34          Winged helix DNA-binding domain
      0.062   13.4   0.0       0.13   12.3   0.0    1.6  1  HTH_7           Helix-turn-helix domain of resolvase
       0.16   11.8   1.9       0.21   11.4   0.4    2.0  2  HTH_DeoR        DeoR-like helix-turn-helix domain
       0.31   11.3   5.0         22    5.4   0.0    3.2  3  DUF4099         Protein of unknown function (DUF4099)


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 !   54.6   0.2   1.1e-17   7.2e-15       2      46 ..      23      67 ..      22      68 .. 0.97

  Alignments for each domain:
  == domain 1  score: 54.6 bits;  conditional E-value: 1.1e-17
                                      HHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  2 ptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                       tR++ILklL+++e+++++l+++lg+++ tv hH  kL+e GLVe
  gi|242399939|ref|YP_002995364.1| 23 DTRRQILKLLRNREMTISQLSDILGKTPQTVYHHIEKLKEVGLVE 67
                                      59******************************************8 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.6   0.1   2.6e-17   1.7e-14       2      59 ..      15      71 ..      14      72 .. 0.96
   2 ?   -0.9   0.0       2.6   1.7e+03      12      28 ..     111     125 ..     109     157 .. 0.59

  Alignments for each domain:
  == domain 1  score: 53.6 bits;  conditional E-value: 2.6e-17
                                      HHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECT CS
                            HTH_20  2 qiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvre 59
                                      ++++++++ +Rr il++L r++++t s+l + l+ +++t+++H+++L e+gLvev r+
  gi|242399939|ref|YP_002995364.1| 15 EVIKLMLEDTRRQILKLL-RNREMTISQLSDILGKTPQTVYHHIEKLKEVGLVEVKRT 71
                                      6899**************.************************************986 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.6
                                       HHHHHHHHSTCTTB-HH CS
                            HTH_20  12 RrrilraLaraegltas 28 
                                        ++i++aL  +  +  +
  gi|242399939|ref|YP_002995364.1| 111 KLDIFKAL--GYRFDEE 125
                                       56777777..3333333 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 !   31.3   0.3   1.6e-10   1.1e-07       1      48 []      21      67 ..      21      67 .. 0.94

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 1.6e-10
                            HTH_24  1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      l +t+r+IL+lL+    +++++L++ lg +p+tv  ++++L+e Gl++
  gi|242399939|ref|YP_002995364.1| 21 LEDTRRQILKLLRN-REMTISQLSDILGKTPQTVYHHIEKLKEVGLVE 67
                                      5789******9998.99**************************99986 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.3   1.2e-09   7.9e-07       2      45 ..      25      67 ..      24      75 .. 0.89

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 1.2e-09
                            HTH_11  2 llqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg.vp 45
                                      ++qil+lL ++r+ +++++L++ L+ + +tv+ +I++L+e g v+
  gi|242399939|ref|YP_002995364.1| 25 RRQILKLL-RNRE-MTISQLSDILGKTPQTVYHHIEKLKEVGlVE 67
                                      79******.8888.9*************************99544 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   2.3e-08   1.6e-05       4      55 ..      22      70 ..      20      75 .. 0.92
   2 ?   -1.5   0.0       3.7   2.5e+03      34      47 ..     138     151 ..     133     153 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 2.3e-08
                                      -HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2  4 tpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                      + + +++L  L++r+   +t+++l + lg ++++v  ++++L + GLve ++
  gi|242399939|ref|YP_002995364.1| 22 EDTRRQILKLLRNRE---MTISQLSDILGKTPQTVYHHIEKLKEVGLVEVKR 70
                                      66899*********9...9*****************************9876 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.7
                                       SHHHHHHHHHHHHH CS
                            MarR_2  34 sksavsrilkrLva 47 
                                       ++s++++i k+L+ 
  gi|242399939|ref|YP_002995364.1| 138 EHSYTTKISKELEG 151
                                       6899****999986 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.2   2.1e-08   1.4e-05      15      58 ..      29      72 ..      27      86 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 2.1e-08
                                      HHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB 15 laLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                      l+Ll++ ++t+++++ +lg   ++vY  +++L++ GlVe+++ +
  gi|242399939|ref|YP_002995364.1| 29 LKLLRNREMTISQLSDILGKTPQTVYHHIEKLKEVGLVEVKRTE 72
                                      68*************************************99866 PP

>> ArsR  ArsR transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   1.1   2.6e-07   0.00017      13      93 ..      19     101 ..      15     168 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 2.6e-07
                              ArsR  13 vfdsetkkkvyeelskeWlteeeleeklgee...veealklLkkikliEsqWrmpepgekpekeYhtsYskvqanfq 86 
                                       ++ ++t +++++ l ++ +t ++l++ lg+    v + ++ Lk+++l+E + +  + g+  ek Y  + + + +n++
  gi|242399939|ref|YP_002995364.1|  19 LMLEDTRRQILKLLRNREMTISQLSDILGKTpqtVYHHIEKLKEVGLVEVKRTEMK-GNLVEKYYGRTADVFYINLY 94 
                                       5667899**********************987678899*************88888.*******************9 PP

                              ArsR  87 csledls 93 
                                       +  ++l 
  gi|242399939|ref|YP_002995364.1|  95 LGDKELR 101
                                       9887775 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   1.4e-07   9.2e-05       4      43 ..      22      62 ..      20      67 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.4e-07
                            HTH_23  4 ereRlrillllae.GlsvreIAreLgvsrrTvyrwlkryre 43
                                      e+ R +il+ll++  +++++ +++Lg +++Tvy+ +++ +e
  gi|242399939|ref|YP_002995364.1| 22 EDTRRQILKLLRNrEMTISQLSDILGKTPQTVYHHIEKLKE 62
                                      67899*******99*******************88887665 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   1.8e-07   0.00012       1      45 [.      25      69 ..      25      80 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.8e-07
                            HTH_29  1 RaqallllaeGvstvsqiAkllglsrrtvyrwlkrfeegGlaall 45
                                      R q+l ll+  ++t+sq+  +lg +++tvy++++   e Gl   +
  gi|242399939|ref|YP_002995364.1| 25 RRQILKLLRNREMTISQLSDILGKTPQTVYHHIEKLKEVGLVEVK 69
                                      8899999999999*************************9976555 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.1   7.4e-07   0.00049      10      41 ..      25      57 ..      19      59 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 7.4e-07
                            HTH_38 10 ReeIerll.aeGlslreIArrLgrspsTIsREl 41
                                      R++I +ll ++ +++++   +Lg+ p+T++ ++
  gi|242399939|ref|YP_002995364.1| 25 RRQILKLLrNREMTISQLSDILGKTPQTVYHHI 57
                                      8999999549********************988 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.2   2.9e-06    0.0019      18      54 ..      33      70 ..      16      77 .. 0.76
   2 ?   -1.8   0.0       4.7   3.1e+03      42      52 ..     156     166 ..     154     178 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.9e-06
                                      EEEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ET CS
                         HTH_Crp_2 18 ielpltqeelAsmlGltretvsrilseLkreglis.rg 54
                                       +  +t  +l+++lG t++tv   + +Lk+ gl++ ++
  gi|242399939|ref|YP_002995364.1| 33 RNREMTISQLSDILGKTPQTVYHHIEKLKEVGLVEvKR 70
                                      3458999****************************544 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.7
                                       HHHHHHTTSEE CS
                         HTH_Crp_2  42 lseLkreglis 52 
                                       l+e+++e +i 
  gi|242399939|ref|YP_002995364.1| 156 LKEFSNEDIIH 166
                                       89999999997 PP

>> DUF2513  Hypothetical protein (DUF2513)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.1   6.9e-05     0.046      12      65 ..      22      76 ..      12      94 .. 0.73
   2 ?    5.1   0.3     0.041        27      19      54 ..     136     176 ..     122     184 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.9e-05
                           DUF2513 12 ltle.eletkeeslddeeeklsaidgyskeeiiyhlkllaeagLieaekkkakss 65
                                       + + ++ +  ++ + ++++ls+i g + ++++ h+++l e gL+e++ ++ k +
  gi|242399939|ref|YP_002995364.1| 22 EDTRrQILKLLRNREMTISQLSDILGKTPQTVYHHIEKLKEVGLVEVKRTEMKGN 76
                                      44443344444555555666778************************99988877 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.041
                           DUF2513  19 tkeeslddeeekls.....aidgyskeeiiyhlkllaeagL 54 
                                       +ke+s++++++k+      +++++s+e+ii ++++l  a+L
  gi|242399939|ref|YP_002995364.1| 136 EKEHSYTTKISKELegkeeSLKEFSNEDIIHAVEWLSMAEL 176
                                       3333333333333344456****************999887 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0     6e-06     0.004      15      49 ..      33      67 ..      27      70 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 6e-06
                                      TBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR 15 apqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                      +++e+t+s+l++ +g ++ tv++++  L e G+ve
  gi|242399939|ref|YP_002995364.1| 33 RNREMTISQLSDILGKTPQTVYHHIEKLKEVGLVE 67
                                      46889*****************************8 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   8.1e-06    0.0054      10      49 ..      20      59 ..      16      62 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 8.1e-06
                                      TS-HHHHHHHHHHHTS---HHHHHHHHT--HHHHHHHHHH CS
                      Sigma70_r4_2 10 eLperqreifllryleglsykEIAellgisegtVksrlsR 49
                                      +L   +r+i+ l +  ++++ + + +lg +++tV++++ +
  gi|242399939|ref|YP_002995364.1| 20 MLEDTRRQILKLLRNREMTISQLSDILGKTPQTVYHHIEK 59
                                      78999********************************976 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   1.7e-05     0.011       5      37 ..      21      53 ..      20      60 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.7e-05
                                      S-HHHHHHHHHHHTTT--HHHHHHHHTS-HHHH CS
                        Sigma70_r4  5 LpererevlelrfgeglTleEIgerlgiSrerV 37
                                      L++  r++l+l + +++T ++++++lg +  +V
  gi|242399939|ref|YP_002995364.1| 21 LEDTRRQILKLLRNREMTISQLSDILGKTPQTV 53
                                      78889***********************99998 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 !   14.7   0.1   4.1e-05     0.027      22      56 ..      36      70 ..      21      72 .. 0.82
   2 ?   -1.0   0.1       3.1     2e+03      19      33 ..     136     150 ..     124     158 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.1e-05
                                      SB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                    Fe_dep_repress 22 vvktkdlaerLnvspssVsemlkkLekdGyveyek 56
                                        + ++l+ +L+  p +V   ++kL++ G+ve++ 
  gi|242399939|ref|YP_002995364.1| 36 EMTISQLSDILGKTPQTVYHHIEKLKEVGLVEVKR 70
                                      45779***************************985 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3.1
                                       HHSSB-HHHHHHHHT CS
                    Fe_dep_repress  19 ekkvvktkdlaerLn 33 
                                       ek+   t++++++L+
  gi|242399939|ref|YP_002995364.1| 136 EKEHSYTTKISKELE 150
                                       445556899999996 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   3.4e-05     0.023       2      38 ..      25      62 ..      24      70 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.4e-05
                            HTH_28  2 RleiikllaaGh.svreaArelgisrrtvyrWikryee 38
                                      R++i+kll + + ++++++ +lg +++tvy  i ++ e
  gi|242399939|ref|YP_002995364.1| 25 RRQILKLLRNREmTISQLSDILGKTPQTVYHHIEKLKE 62
                                      99*******6555********************99887 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   1.2   8.7e-05     0.058       4      46 ..      27      69 ..      24     193 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 8.7e-05
                            HTH_40  4 etlell.eeglsieeIAkerglkesTIegHLaelieegeeidle 46
                                      + l+ll +  ++i + +++ g +++T++ H+ +l e g  ++++
  gi|242399939|ref|YP_002995364.1| 27 QILKLLrNREMTISQLSDILGKTPQTVYHHIEKLKEVGL-VEVK 69
                                      5678887999************************99986.5554 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   1.6   2.4e-05     0.016       5      75 ..      15      84 ..      14     116 .. 0.89
   2 ?    1.4   0.1      0.42   2.8e+02       9      41 ..     121     153 ..     113     162 .. 0.57

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.4e-05
                                      HHHHHCS-HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTEEEEEEEE CS
                       TFIIE_alpha  5 evvrkfygeeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrdeekswykyywr 75
                                      ev++ + ++   ++l+ L  + e+t  +l+  l+  ++ + + + +L+e +lv++kr    +  ++kyy r
  gi|242399939|ref|YP_002995364.1| 15 EVIKLMLEDTRRQILKLLR-NREMTISQLSDILGKTPQTVYHHIEKLKEVGLVEVKRTEMKGNLVEKYYGR 84
                                      7999999999999999776.*************************************99999999999955 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.42
                                       HCS-HHHHHHHHHHHCTTSEBHHHHHHHHTS-H CS
                       TFIIE_alpha   9 kfygeeavlvldvLlekgevteedlakelkidl 41 
                                       +f +e+   v+d + ek       ++kel+ + 
  gi|242399939|ref|YP_002995364.1| 121 RFDEEQLLDVMDRITEKEHSYTTKISKELEGKE 153
                                       344455555555555555555555555555444 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 ?   13.9   0.2   8.8e-05     0.059       7      54 ..      27      72 ..      23      79 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 8.8e-05
                            HTH_27  7 lvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgde 54
                                      ++L l+r  +r++++++l++ l  + +++   ++kL e GLve ++ e
  gi|242399939|ref|YP_002995364.1| 27 QILKLLR--NREMTISQLSDILGKTPQTVYHHIEKLKEVGLVEVKRTE 72
                                      7899999..*********************************766655 PP

>> Isy1  Isy1-like splicing family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   2.8   3.8e-05     0.025      55     191 ..       3     144 ..       1     189 [. 0.65

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.8e-05
                              Isy1  55 EIsrkvakIqdaglgeyqiRdlNDeiNkLlrekrhWekrIkeLgGpdykr...kapkmldeegkev.......pgkk 121
                                         ++kv+ I d+++    + d   +i kLlr++++  ++++++ G++ +    + +k+ +     v       +g+ 
  gi|242399939|ref|YP_002995364.1|   3 AMKKKVMVITDPEVIKLMLEDTRRQILKLLRNREMTISQLSDILGKTPQTvyhHIEKLKEVGL--VevkrtemKGNL 77 
                                       5789**************************************888776663332233322221..123444449999 PP

                              Isy1 122 gyrYFGrAkeLPgVkelfekek..kkeekkkkeraelfknidadYYGyrdeedgvlleleaeaekeareeav 191
                                         +Y+Gr  +   +   +  ++    ++++ k++ ++fk ++      r +e++ l  +++  eke   ++ 
  gi|242399939|ref|YP_002995364.1|  78 VEKYYGRTADVFYINLYLGDKElrYLARSRLKTKLDIFKALGY-----RFDEEQLLDVMDRITEKEHSYTTK 144
                                       9**********99999998888432233555566667777544.....445554444444444444333332 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.2   0.00088      0.59      12      51 ..      31      70 ..      22      72 .. 0.87
   2 ?    2.7   0.0      0.19   1.2e+02      32      45 ..     140     153 ..     136     153 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00088
                                      HHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                              MarR 12 lyeqgplsvseLakklgvskstvtrvldrLekkGlieRsk 51
                                      l ++ ++++s+L + lg ++ tv   + +L + Gl+e ++
  gi|242399939|ref|YP_002995364.1| 31 LLRNREMTISQLSDILGKTPQTVYHHIEKLKEVGLVEVKR 70
                                      455678******************************9876 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.19
                                       HHHHHHHHHHHHTT CS
                              MarR  32 stvtrvldrLekkG 45 
                                       s++t+++++Le k+
  gi|242399939|ref|YP_002995364.1| 140 SYTTKISKELEGKE 153
                                       899********986 PP

>> HTH_17  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   0.00068      0.45       2      23 ..      37      58 ..      36      66 .. 0.92
   2 ?    0.8   0.1      0.84   5.6e+02      30      47 ..     115     131 ..      94     134 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00068
                            HTH_17  2 ltveEaAelLgvsrstvyrlir 23
                                      +t+++++++Lg  ++tvy  i 
  gi|242399939|ref|YP_002995364.1| 37 MTISQLSDILGKTPQTVYHHIE 58
                                      9*****************9885 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.84
                            HTH_17  30 ak..iGrrwriprsdleewl 47 
                                       +k      +r++++ l + +
  gi|242399939|ref|YP_002995364.1| 115 FKalG---YRFDEEQLLDVM 131
                                       45433...99**99998766 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00025      0.17       9      50 ..      31      72 ..      25      80 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00025
                            HTH_34  9 LasvdeadfvelkealeatdgnLsvhlkkLekagYievdkef 50
                                      L+ ++e++ ++l++ l+ t    + h++kL++ g +ev+ + 
  gi|242399939|ref|YP_002995364.1| 31 LLRNREMTISQLSDILGKTPQTVYHHIEKLKEVGLVEVKRTE 72
                                      7789*********************************99865 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0    0.0002      0.13      12      39 ..      26      54 ..      18      59 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0002
                                      GGGGSSTTTT.--STTTSSSS---SSSS- CS
                             HTH_7 12 nrvvkLleeG.isiskIAkevnisRsTvY 39
                                       +++kLl++  ++is++ ++++ +++TvY
  gi|242399939|ref|YP_002995364.1| 26 RQILKLLRNReMTISQLSDILGKTPQTVY 54
                                      58999**9999****************** PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.4   0.00032      0.21       3      44 ..      26      66 ..      25      71 .. 0.88
   2 ?   -1.9   0.0       4.3   2.8e+03       1      14 [.     178     191 ..     178     193 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00032
                          HTH_DeoR  3 eqilellkqqgklsveelvellgvSeaTiRRDLneLeeqgll 44
                                       qil+ll++ + +++ +l++ lg +++T+   +++L+e gl+
  gi|242399939|ref|YP_002995364.1| 26 RQILKLLRN-REMTISQLSDILGKTPQTVYHHIEKLKEVGLV 66
                                      589999987.579************************99985 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.3
                          HTH_DeoR   1 Rieqilellkqqgk 14 
                                       R+++ lellk+ g 
  gi|242399939|ref|YP_002995364.1| 178 RDKEALELLKKLGE 191
                                       78888999999886 PP

>> DUF4099  Protein of unknown function (DUF4099)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.033        22       9      62 ..      58     111 ..      56     114 .. 0.86
   2 ?    1.5   0.1      0.55   3.7e+02      24      50 ..     128     153 ..     115     157 .. 0.77
   3 ?    4.8   0.4     0.052        35       5      32 ..     167     194 ..     165     196 .] 0.90

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.033
                           DUF4099   9 eeLeklGiskedlek.sgdldkLlkgrktpllpvsieleggekieldarlslvrd 62 
                                       e+L+++G+ + +  + +g+l +  +gr  +++ +++ l g+++++  ar +l+++
  gi|242399939|ref|YP_002995364.1|  58 EKLKEVGLVEVKRTEmKGNLVEKYYGRTADVFYINLYL-GDKELRYLARSRLKTK 111
                                       689999987765555599****99**************.*****99999988876 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.55
                           DUF4099  24 sgdldkLlkgrktpllpvsieleggek 50 
                                        +++d++ + +++ + ++s ele g++
  gi|242399939|ref|YP_002995364.1| 128 LDVMDRITEKEHSYTTKISKELE-GKE 153
                                       4599*****************95.444 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.052
                           DUF4099   5 kidweeLeklGiskedleksgdldkLlk 32 
                                        + w ++++lG +ke le  ++l ++lk
  gi|242399939|ref|YP_002995364.1| 167 AVEWLSMAELGRDKEALELLKKLGEILK 194
                                       699****************999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1225  (0.0683251); expected 358.6 (0.02)
Passed bias filter:                      692  (0.0385967); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              27  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1236.60
//
Query:       gi|242399940|ref|YP_002995365.1|  [L=83]
Description: hypothetical protein TSIB_1967 [Thermococcus sibiricus MM 739]
Scores for complete 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  100.3   5.2    5.6e-29  100.1   5.2    1.0  1  DUF211          Uncharacterized ArCR, COG1888
  ------ inclusion threshold ------
      0.014   15.8   0.4      0.031   14.7   0.4    1.6  1  HMA             Heavy-metal-associated domain
      0.018   15.4   0.6      0.025   15.0   0.2    1.5  2  Streptin-Immun  Lantibiotic streptin immunity protein
      0.028   14.8   0.0      0.036   14.4   0.0    1.2  1  BRCT            BRCA1 C Terminus (BRCT) domain


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 !  100.1   5.2   1.2e-32   5.6e-29      17      88 ..       2      73 ..       1      74 [. 0.97

  Alignments for each domain:
  == domain 1  score: 100.1 bits;  conditional E-value: 1.2e-32
                                      HHHHHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHHCTT-EEEEEEEEEEESS----- CS
                            DUF211 17 ivelakklaelegvdgvnitvkevDketenlkitieGenidyeeieeaieelggvihSiDevvaGkkiveev 88
                                      ++ela  l+el+gvdgvnit++e+Dketen+kiti G+n+dyeei ++iee+ggv+hSiD v+aGkki+ee+
  gi|242399940|ref|YP_002995365.1|  2 VTELALGLSELKGVDGVNITLVEIDKETENVKITIVGDNLDYEEIVRTIEEFGGVVHSIDMVAAGKKIIEES 73
                                      689*******************************************************************86 PP

>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.4     7e-06     0.031      21      60 ..      10      54 ..       8      55 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 7e-06
                               HMA 21 selpgV.....esvkvdlatktvtVegdaestklrkiieaiekag 60
                                      sel+gV     + v++d +t  v ++ + + +++++i+++ie+ g
  gi|242399940|ref|YP_002995365.1| 10 SELKGVdgvniTLVEIDKETENVKITIVGDNLDYEEIVRTIEEFG 54
                                      55555555599999****************************976 PP

>> Streptin-Immun  Lantibiotic streptin immunity protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.2   5.6e-06     0.025      51      90 ..      19      58 ..      10      61 .. 0.90
   2 ?   -2.3   0.0       1.4   6.3e+03      71      85 ..      69      83 .]      66      83 .] 0.59

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 5.6e-06
                    Streptin-Immun 51 svtleqiekeieklqnelskkideyeelvrkldkfvkvln 90
                                      ++tl +i+ke e+++  +  +  +yee+vr +++f+ v+ 
  gi|242399940|ref|YP_002995365.1| 19 NITLVEIDKETENVKITIVGDNLDYEEIVRTIEEFGGVVH 58
                                      799999*******99999888889***********99975 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.4
                    Streptin-Immun 71 kideyeelvrkldkf 85
                                       i+e e    +l++f
  gi|242399940|ref|YP_002995365.1| 69 IIEESETPQDRLEEF 83
                                      456666666666665 PP

>> BRCT  BRCA1 C Terminus (BRCT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   8.1e-06     0.036       7      37 ..      30      58 ..      27      81 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 8.1e-06
                                      TTEEEEEEESTSSHHHHHHHHHHHHTTCEEE CS
                              BRCT  7 hgckfvitgvldnftrdeleelikehGGkvt 37
                                      +++k+ i  v dn + +e+ ++i+e+GG v+
  gi|242399940|ref|YP_002995365.1| 30 ENVKITI--VGDNLDYEEIVRTIEEFGGVVH 58
                                      6899999..********************93 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); 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: 0.48u 0.32s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 502.98
//
Query:       gi|242399941|ref|YP_002995366.1|  [L=186]
Description: ArsR family transcriptional regulator [Thermococcus sibiricus MM 739]
Scores for complete 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-13   49.0   0.1    8.1e-13   48.0   0.1    1.6  1  HTH_5     Bacterial regulatory protein, arsR family
      1e-10   41.5   0.0      3e-10   40.0   0.0    1.7  2  HTH_20    Helix-turn-helix domain
    1.7e-06   27.8   0.0    6.9e-06   25.9   0.0    1.9  2  MarR_2    MarR family
    1.9e-05   24.5   0.8     0.0017   18.2   0.1    2.8  3  MarR      MarR family
      4e-05   23.3   0.0    7.5e-05   22.4   0.0    1.5  1  HTH_IclR  IclR helix-turn-helix domain
      8e-05   22.5   0.2    0.00032   20.6   0.0    2.1  2  HTH_11    HTH domain
    0.00014   22.3   0.5    0.00093   19.6   0.1    2.4  3  HTH_27    Winged helix DNA-binding domain
    0.00017   21.1   0.0     0.0004   19.9   0.0    1.8  1  HTH_24    Winged helix-turn-helix DNA-binding
    0.00069   19.3   0.3     0.0012   18.5   0.3    1.4  1  HTH_38    Helix-turn-helix domain
     0.0011   18.8   0.0     0.0026   17.6   0.0    1.6  1  TrmB      Sugar-specific transcriptional regulator TrmB
     0.0082   16.5   0.0      0.021   15.2   0.0    1.8  1  Rrf2      Transcriptional regulator
  ------ inclusion threshold ------
      0.017   15.4   0.1       0.34   11.2   0.0    2.3  2  DUF2513   Hypothetical protein (DUF2513)
      0.038   13.8   0.3      0.064   13.1   0.3    1.5  1  RB_A      Retinoblastoma-associated protein A 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 !   48.0   0.1   5.9e-16   8.1e-13       2      46 ..      19      63 ..      18      64 .. 0.97

  Alignments for each domain:
  == domain 1  score: 48.0 bits;  conditional E-value: 5.9e-16
                                      HHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  2 ptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      +tRl IL+lL++++++++el+  l++ +st+ +H   L+eaG+Ve
  gi|242399941|ref|YP_002995366.1| 19 KTRLYILSLLRDRPMTISELSMLLNKDPSTIHRHITLLKEAGFVE 63
                                      79******************************************8 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   0.0   2.2e-13     3e-10       4      57 ..      13      65 ..      10      68 .. 0.95
   2 ?   -3.4   0.0       7.9   1.1e+04      40      49 ..     137     147 ..     130     150 .. 0.68

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 2.2e-13
                                      HHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                            HTH_20  4 aeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevv 57
                                      +++La+++R+ il++L r++++t sel  +l  +++t+++H+  L eag+ve  
  gi|242399941|ref|YP_002995366.1| 13 IKILAEKTRLYILSLL-RDRPMTISELSMLLNKDPSTIHRHITLLKEAGFVEEI 65
                                      589*************.**********************************976 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 7.9
                                       HHHHHH.HHHH CS
                            HTH_20  40 tlsyHL.rvLe 49 
                                       tls+ + ++Le
  gi|242399941|ref|YP_002995366.1| 137 TLSRDMiKKLE 147
                                       36766668887 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0     5e-09   6.9e-06       7      53 ..      21      64 ..      18      71 .. 0.92
   2 ?   -1.1   0.0       1.3   1.7e+03       6      33 ..     157     184 ..     153     186 .] 0.74

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 5e-09
                                      HHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                            MarR_2  7 qarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53
                                       + +L  L++rp   +t++el   l+ ++s+++r++  L +aG+ve+
  gi|242399941|ref|YP_002995366.1| 21 RLYILSLLRDRP---MTISELSMLLNKDPSTIHRHITLLKEAGFVEE 64
                                      567999999**9...9*****************************97 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.3
                                       HHHHHHHHHHCTTTSEE..EHHHHHHHHTS CS
                            MarR_2   6 aqarvLaaLgrrpgrdl..tvgelarrlgl 33 
                                          ++L+ L ++p   l   ++ + + lgl
  gi|242399941|ref|YP_002995366.1| 157 IRIMALMTLINSPK--LqeEAKKIRELLGL 184
                                       56789999999998..66677777777776 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   1.3e-06    0.0017       9      49 ..      25      64 ..      18      73 .. 0.82
   2 ?    3.8   0.0      0.04        55       4      25 ..      91     112 ..      89     118 .. 0.87
   3 ?   -3.1   0.0       5.6   7.7e+03      37      43 ..     142     148 ..     141     150 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.3e-06
                                      HHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              MarR  9 LrilyeqgplsvseLakklgvskstvtrvldrLekkGlieR 49
                                      L +l +  p+++seL + l+ ++st+ r ++ L ++G++e 
  gi|242399941|ref|YP_002995366.1| 25 LSLL-RDRPMTISELSMLLNKDPSTIHRHITLLKEAGFVEE 64
                                      4444.4568******************************85 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.04
                                       HHHHHHHHHHHSTTEEHHHHHH CS
                              MarR   4 tqfviLrilyeqgplsvseLak 25 
                                       + +v+++++++++++++ eL  
  gi|242399941|ref|YP_002995366.1|  91 NAWVAMEKIHTEEAIRLYELLT 112
                                       6799**************9976 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 5.6
                                       HHHHHHH CS
                              MarR  37 vldrLek 43 
                                       ++++Le 
  gi|242399941|ref|YP_002995366.1| 142 MIKKLEG 148
                                       899**95 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   5.5e-08   7.5e-05      16      50 ..      30      64 ..      22      66 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 5.5e-08
                                      BSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR 16 pqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      ++++t+sel+  +   +St hR++  L e G+ve 
  gi|242399941|ref|YP_002995366.1| 30 DRPMTISELSMLLNKDPSTIHRHITLLKEAGFVEE 64
                                      789******************************96 PP

>> HTH_11  HTH 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   0.00032       2      44 ..      21      61 ..      20      70 .. 0.87
   2 ?   -2.4   0.0       3.5   4.9e+03      38      48 ..     110     120 ..     109     123 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.3e-07
                            HTH_11  2 llqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                      +l il lL + r+ ++++eL+  Ln   +t++r+I  L+e+g+
  gi|242399941|ref|YP_002995366.1| 21 RLYILSLL-RDRP-MTISELSMLLNKDPSTIHRHITLLKEAGF 61
                                      56789999.6665.***************************94 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.5
                            HTH_11  38 aLeelgvpIes 48 
                                        L+e+g++I  
  gi|242399941|ref|YP_002995366.1| 110 LLTEAGFKIRN 120
                                       68999999965 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1   6.8e-07   0.00093       8      58 ..      24      70 ..      17      79 .. 0.87
   2 ?   -0.3   0.0       1.2   1.6e+03      27      40 ..      93     106 ..      91     124 .. 0.79
   3 ?   -2.8   0.0       6.6   9.2e+03      31      43 ..     134     147 ..     117     148 .. 0.65

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 6.8e-07
                            HTH_27  8 vLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrr 58
                                      +L l+r  +r++++++l+  ln + s+i+  +  L e+G+ve+ g+e  + 
  gi|242399941|ref|YP_002995366.1| 24 ILSLLR--DRPMTISELSMLLNKDPSTIHRHITLLKEAGFVEEIGKE--GN 70
                                      466666..************************************999..44 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.2
                            HTH_27  27 rlnvedshisyslk 40 
                                       ++ +e++h+ ++++
  gi|242399941|ref|YP_002995366.1|  93 WVAMEKIHTEEAIR 106
                                       78899999999998 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 6.6
                            HTH_27  31 edshis.yslkkLt 43 
                                       +  + s  ++kkL+
  gi|242399941|ref|YP_002995366.1| 134 QFETLSrDMIKKLE 147
                                       55566777888886 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 !   19.9   0.0   2.9e-07    0.0004      10      48 .]      26      63 ..       9      63 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2.9e-07
                            HTH_24 10 elLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      + L ++  ++++eL+  l+  pst++r++  L+e+G+++
  gi|242399941|ref|YP_002995366.1| 26 S-LLRDRPMTISELSMLLNKDPSTIHRHITLLKEAGFVE 63
                                      4.556699****************************996 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.3   8.9e-07    0.0012       3      41 ..      14      53 ..      12      54 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 8.9e-07
                            HTH_38  3 khLsleeReeIerll.aeGlslreIArrLgrspsTIsREl 41
                                      k L    R  I  ll ++ ++++e   +L+++psTI+R++
  gi|242399941|ref|YP_002995366.1| 14 KILAEKTRLYILSLLrDRPMTISELSMLLNKDPSTIHRHI 53
                                      6778888999999972577*******************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 !   17.6   0.0   1.9e-06    0.0026      15      62 ..      25      74 ..      19      79 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.9e-06
                                      HHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST..TTEE CS
                              TrmB 15 laLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr..pklY 62
                                      l Ll+  p+t++e++  l+ + s++ + +  L+++G+Ve + ++   klY
  gi|242399941|ref|YP_002995366.1| 25 LSLLRDRPMTISELSMLLNKDPSTIHRHITLLKEAGFVEEIGKEgnEKLY 74
                                      5799***********************************98644446666 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.5e-05     0.021      15      67 ..      23      73 ..      15      88 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.5e-05
                                      HHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT-TCEEE CS
                              Rrf2 15 lyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvrGkgGGyrL 67
                                      ++L++ ++ +p++++e++   n  ps + + ++ L++ag+v+ + Gk+G  +L
  gi|242399941|ref|YP_002995366.1| 23 YILSLLRD-RPMTISELSMLLNKDPSTIHRHITLLKEAGFVEEI-GKEGNEKL 73
                                      44555555.67******************************965.77776666 PP

>> DUF2513  Hypothetical protein (DUF2513)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00025      0.34      34      65 ..      41      72 ..      23      84 .. 0.80
   2 ?    1.8   0.0      0.21   2.9e+02      32      59 ..      91     121 ..      77     137 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00025
                           DUF2513 34 idgyskeeiiyhlkllaeagLieaekkkakss 65
                                      + + +  +i  h++ll eag++e   k+ +++
  gi|242399941|ref|YP_002995366.1| 41 LLNKDPSTIHRHITLLKEAGFVEEIGKEGNEK 72
                                      55667779***************998887776 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.21
                           DUF2513  32 s...aidgyskeeiiyhlkllaeagLieaek 59 
                                       +   a+++   ee i  ++ll eag+   +k
  gi|242399941|ref|YP_002995366.1|  91 NawvAMEKIHTEEAIRLYELLTEAGFKIRNK 121
                                       234589999999999999******9954444 PP

>> RB_A  Retinoblastoma-associated protein A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.3   4.6e-05     0.064     151     183 ..     123     155 ..      92     158 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.6e-05
                              RB_A 151 dfykviEsfvkaedkLprdlvkhLnsieeqiLe 183
                                       +f+ +i  f+ + ++L+rd++k L+ +e + Le
  gi|242399941|ref|YP_002995366.1| 123 EFISIIKRFISQFETLSRDMIKKLEGVEMNRLE 155
                                       799*************************98887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       745  (0.0415528); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); 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: 0.53u 0.33s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1133.39
//
Query:       gi|242399942|ref|YP_002995367.1|  [L=485]
Description: YjeF-ralted probable carbohydrate kinase [Thermococcus sibiricus MM 739]
Scores for complete 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-52  178.7   0.0    1.9e-52  178.2   0.0    1.2  1  Carb_kinase   Carbohydrate kinase
      1e-33  116.6   0.0    3.4e-33  115.0   0.0    1.8  2  YjeF_N        YjeF-related protein N-terminus
    0.00064   19.2   0.0     0.0013   18.2   0.0    1.4  1  HK            Hydroxyethylthiazole kinase family
     0.0048   16.3   0.0     0.0087   15.5   0.0    1.3  1  Phos_pyr_kin  Phosphomethylpyrimidine kinase
  ------ inclusion threshold ------
       0.13   11.7   0.0       0.28   10.6   0.0    1.5  1  PcrB          PcrB family


Domain annotation for each model (and alignments):
>> Carb_kinase  Carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.2   0.0   5.4e-56   1.9e-52       1     241 [.     232     474 ..     232     476 .. 0.89

  Alignments for each domain:
  == domain 1  score: 178.2 bits;  conditional E-value: 5.4e-56
                                       EEEEE-BTTCHHHHHHHHHHHHCTT-SEEEEEESSTT...TCCCCTTTTTCEECCTTHTTTS....--SSS-SEEEE CS
                       Carb_kinase   1 vlvigGsedytGAallaalaalrlgaglvsvatesea...iavlksylpevivhplledeqa.kileklerldavvi 73 
                                       +l+igGse+y GA++laa+aa+ + ++lv  a+ +     i+ ++ +l    +++++ +e++  +l++++ +davv+
  gi|242399942|ref|YP_002995367.1| 232 LLIIGGSEEYFGAPYLAAKAASYI-VDLVYLAMPEYSarrINDPNIILRPFEGKNFT-KEDVeDVLSIADGVDAVVL 306
                                       58******************9876.79999999765501144455566666666776.6777799************ PP

                                       -TT-SSSHCHHH.HCHHHCCCCS-EEEEGGGGGSGGGG...TTTTSSEEEE--HHHHHHHCTTTCH.HCCSHHHHHH CS
                       Carb_kinase  74 GpGLgrdekikk.lleevlekdeplviDAdgLnllaqknelserkaeviLTPhkkEfkrLlkaivk.keddrlelar 148
                                       GpG g++ ++k  ++e+v+  ++p+viDAd+L+ +a++     + +e +LTPh++Efk L++   + + ++++el+ 
  gi|242399942|ref|YP_002995367.1| 307 GPGIGEKAETKDfVIEFVRWCEKPMVIDADALKAIAEDL-DVLKGKEFVLTPHPGEFKILFGKKPEgSLEEKAELVM 382
                                       *******99999889**********************95.5667889**************99887799******** PP

                                       HHHHHHTTEEEEESTTSEEEECTTEEEEE----GGG-STTHHHHHHHHHHHHHHCTSSHHHHHHHHHHHHHHHHHHH CS
                       Carb_kinase 149 elaqklnavvllkgekdvivspegevlinstgssalakGGsGDvLaGligalLaqneasyeaaiaaawlhgaasdea 225
                                       + aq +n+++llkg +d+i + + + + n+tg+ ++++GG+GDvL+Gl+galLa +++++ aa ++a+l+g a+d +
  gi|242399942|ref|YP_002995367.1| 383 KKAQDINGTILLKGRHDIISN-GIAWKYNKTGNNGMTTGGTGDVLSGLVGALLALENKPLRAASVGAFLNGLAGDMV 458
                                       *****************9988.999999************************************************* PP

                                       CCCT-TS-HCHHHHHH CS
                       Carb_kinase 226 aekkgvgmlatelski 241
                                       +e+ g   +a +++++
  gi|242399942|ref|YP_002995367.1| 459 KEEMGENFTALDVAEK 474
                                       ***9998887777665 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 !  115.0   0.0   9.4e-37   3.4e-33       3     169 ..      27     187 ..      25     188 .. 0.91
   2 ?   -1.7   0.0      0.63   2.2e+03      53     131 ..     253     329 ..     210     339 .. 0.64

  Alignments for each domain:
  == domain 1  score: 115.0 bits;  conditional E-value: 9.4e-37
                            YjeF_N   3 eLmenagravaevlrallgnspaekkvlvlvGsgnnGgdglaaArhLaqegakVtvllleeee.kldedaeralell 78 
                                       +Lmenag++va+++++++    ++ k+ v+ G gnnGgdg++aArhL + + +Vt++l+ +e+  ++e+a+ ++e+l
  gi|242399942|ref|YP_002995367.1|  27 QLMENAGAGVAKIIEERV---GEGLKIAVFSGTGNNGGDGFVAARHL-SFENNVTLFLVGDEAkIGSEEARHNWEIL 99 
                                       8*****************...8*************************.99999***8888777699*********** PP

                            YjeF_N  79 kkag.gkvveekpeedleeklsapvdlviDAllGiglrgelreelaeliewlnss..eapvlavDiPSGldadtGav 152
                                       +k+  +k++  k++ + +    +  d+++DAllG g+rge re++ ++ie++n+   + ++++vD+PSG+ +d   v
  gi|242399942|ref|YP_002995367.1| 100 RKLDfVKIIVLKDSTYIKPLDLSGFDVIVDALLGAGTRGEPREPIRSAIEKINKYagRVKIVSVDLPSGYPSD---V 173
                                       ***8457888888888876666*********************************98889**********666...5 PP

                            YjeF_N 153 sgtavkadvtvtfgapk 169
                                           vk+d+ vtf++ k
  gi|242399942|ref|YP_002995367.1| 174 R---VKCDFAVTFQWDK 187
                                       5...9999999999977 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.63
                            YjeF_N  53 gakVtvllleeeekldedaeralellkkaggkvveekpeedleeklsapvdlviDAllGiglrgelreelaeliewl 129
                                       ++ V+++ l+ +e   + +++   +l+ ++gk ++++++ed    +   vd v+ +  Gig + e ++ + e+++w+
  gi|242399942|ref|YP_002995367.1| 253 SYIVDLVYLAMPEYSARRINDPNIILRPFEGKNFTKEDVEDVL-SIADGVDAVVLG-PGIGEKAETKDFVIEFVRWC 327
                                       4556666666666666666666666666666666666666543.222334433333.36677777777777777777 PP

                            YjeF_N 130 ns 131
                                        +
  gi|242399942|ref|YP_002995367.1| 328 EK 329
                                       65 PP

>> HK  Hydroxyethylthiazole kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   3.7e-07    0.0013     141     225 ..     378     461 ..     366     472 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.7e-07
                                       HHHHHHHHHHHTSEEEEESSSEEEEESSEEEEEE-S-GGGGGSTTHHHHHHHHHHHHHTTBSSHHHHHHHHHHHHHH CS
                                HK 141 vaavqkvAqklrvvvvvtGevDvvsdgkkvyklknGtellgkitasGCllgsvvaaflavkkdkllaaveavllykv 217
                                        + v k Aq ++ ++++ G+ D++s+g      k G++ ++   ++G +l+  v+a la+++++l aa  +  l  +
  gi|242399942|ref|YP_002995367.1| 378 AELVMKKAQDINGTILLKGRHDIISNGIAWKYNKTGNNGMTT-GGTGDVLSGLVGALLALENKPLRAASVGAFLNGL 453
                                       5678899**********************99999****9986.89**********************9666677788 PP

                                       HH.HHHHH CS
                                HK 218 Agkeaaar 225
                                       Ag+ ++++
  gi|242399942|ref|YP_002995367.1| 454 AGDMVKEE 461
                                       88655554 PP

>> Phos_pyr_kin  Phosphomethylpyrimidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   2.4e-06    0.0087     105     221 ..     334     444 ..     313     455 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.4e-06
                                       SHHHHHHHHHHT...GGG-SEEE-BHHHHHHHHT---S.SHHHHHHHHHHHHHTT-SEEEEEEGGS-SSSEEEEEEE CS
                      Phos_pyr_kin 105 eeeavealkeeL...lplatvitPNlpEaeaLlgekik.teedmkeaakkllklgakaVlikGghlegeeavvtdvl 177
                                       +++a++a++e+L     +  v+tP   E + L g+k + ++e+  e   k ++    ++l+kG h         d++
  gi|242399942|ref|YP_002995367.1| 334 DADALKAIAEDLdvlKGKEFVLTPHPGEFKILFGKKPEgSLEEKAELVMKKAQDINGTILLKGRH---------DII 401
                                       555666665554211456789*************777766665555555555556899*******.........444 PP

                                       ETSSEEEEEEEE----S--BTHHHHHHHHHHHHHHCTSSHHHHH CS
                      Phos_pyr_kin 178 ydgeeveeleaerietknthGtGCtlssaiaaelakgesleeAv 221
                                        +++   ++++   +  +t GtG++ls  + a la ++++  A 
  gi|242399942|ref|YP_002995367.1| 402 -SNGIAWKYNKTGNNGMTTGGTGDVLSGLVGALLALENKPLRAA 444
                                       .5566677777777888999***************999988876 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   7.9e-05      0.28      17      78 ..     285     348 ..     278     354 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 7.9e-05
                                       S-CHHHHHHH..HCTT-SEEEEECSTCHHHHHHHHHHHHHCTSSS-EEEEESSGGG--TTSSEE CS
                              PcrB  17 enpdEiveiv..iesgtDavmigGsqsvtldntvrllkkvsriklPivlepsnvegvvryaDal 78 
                                       + + E ve v  i +g Dav++g  ++ + +    +++ v+ ++ P+v+   + +++++++D+l
  gi|242399942|ref|YP_002995367.1| 285 NFTKEDVEDVlsIADGVDAVVLGPGIGEKAETKDFVIEFVRWCEKPMVIDADALKAIAEDLDVL 348
                                       55778888887889*********99999999999999***99*******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (485 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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: 00:00:00.49
# Mc/sec: 2971.92
//
Query:       gi|242399943|ref|YP_002995368.1|  [L=464]
Description: hypothetical protein TSIB_1970 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-24   86.6   0.0    2.8e-24   86.2   0.0    1.1  1  Amino_oxidase  Flavin containing amine oxidoreductase
    1.2e-19   70.2   0.0    4.5e-19   68.3   0.0    1.8  1  GDI            GDP dissociation inhibitor
      1e-13   51.3   0.1    2.1e-13   50.3   0.1    1.5  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
      1e-10   41.8   0.3    0.00012   21.8   0.0    2.7  3  DAO            FAD dependent oxidoreductase
    4.8e-08   32.6   0.1     0.0013   18.1   0.0    2.9  3  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    5.2e-08   32.4   0.1     0.0003   20.0   0.0    3.0  3  FAD_binding_2  FAD binding domain
    5.7e-08   31.9   0.1     0.0055   15.5   0.2    2.1  2  HI0933_like    HI0933-like protein
    3.3e-07   30.8   0.9      0.007   16.9   0.1    2.4  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    6.8e-06   25.7   0.1    0.00085   18.8   0.0    2.1  2  FAD_oxidored   FAD dependent oxidoreductase
      3e-05   23.4   0.1    5.2e-05   22.6   0.1    1.4  1  FAD_binding_3  FAD binding domain
    5.8e-05   22.5   0.2    0.00011   21.5   0.2    1.4  1  Thi4           Thi4 family
     0.0046   17.0   0.1      0.011   15.7   0.0    1.7  2  NAD_binding_9  FAD-NAD(P)-binding
  ------ inclusion threshold ------
       0.12   12.2   0.0       0.23   11.3   0.0    1.4  1  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
       0.15   11.3   0.4        8.3    5.6   0.1    2.2  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
       0.21   10.6   0.8       0.55    9.2   0.2    1.8  2  GIDA           Glucose inhibited division protein A


Domain annotation for each model (and alignments):
>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.2   0.0   2.3e-27   2.8e-24       1     450 [.      11     449 ..      11     451 .. 0.76

  Alignments for each domain:
  == domain 1  score: 86.2 bits;  conditional E-value: 2.3e-27
                                       HHHHHHHHHHHHTTEEEEEEESSSSSBTTS-EEEET........TEEEESS--EEETTTHHHHHHHHHTTCCCCEEE CS
                     Amino_oxidase   1 laGLaaArqLlsaGfdVtvlEardrvGGRirtvrsd........GylielGamwftgagnpllellkelgledslsl 69 
                                       ++GL a + L+  G++V v+E ++ vGGR++t+  +        +y ++ G ++f   ++ l  +l+++g + + ++
  gi|242399943|ref|YP_002995368.1|  11 FTGLLAGSLLAKEGYRVAVFERNSFVGGRAATRTPKewgwaereDYRVDFGHHVFAT-NSYLEFILDRVGAKRHFKF 86 
                                       58**********************************9*8888888**********99.999***************7 PP

                                       ESCCGCEEEEETTEECC...TTEECHH.HHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHCCCCHH.HHHHHHH CS
                     Amino_oxidase  70 pdpgapkrvlskggref...pgdlspv.paewealleqgalsaellsleeklrlgleallqktldeldl.dskslae 141
                                          ++   + +k+gr +    g l+++   +w  l ++ +l +++ls+ ek+++g   ++++ +  ++l d++ ++e
  gi|242399943|ref|YP_002995368.1|  87 VPLNM--PYFYKNGRLHkppVGFLEQLrAYPWIPLRSKLRL-RKFLSYVEKVSFGEVMEKWAYRPLEELyDEFGFDE 160
                                       77674..5555778887666444444424446666664444.59999999999999999966665444327788888 PP

                                       CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHTSTTTTCBHHHHTCCCCHHHHHTSCCCEETTHTHHHHHHHHH CS
                     Amino_oxidase 142 sleelgrrepgdvevwdrliepelfaklefasglfagdpselsaklalpllwelegfggslllprgGlsqlpealae 218
                                         +el+ +++ +    + ++++        +s+  ++ +     +     l+  + ++ +l+ ++gG ++++eal +
  gi|242399943|ref|YP_002995368.1| 161 NARELFTDGFVA-GYQTIIDTE-------RNSAGDLILC-----MK--AYLRGIKRYKTPLFSAEGGVGAIAEALRK 222
                                       888888888888.444444444.......6777755444.....33..3345566666666667899********** PP

                                       ..TTTTEEEETSEEEEEEEEETTCEEEEETTSTEEEESEEEE-S-HHHHHSSEEES.CCSH.HHHHHHHHS.EEEEE CS
                     Amino_oxidase 219 ..elrgldirlntrVkeikregdgvtvtledgevveaDaVvvTvplgvlkailfsP.plpd.ekaeairnl.gfgsv 290
                                         e+ g++++l+t V+ei  e+++ +   +  ++++a++V+ ++p++ l   l +   lp+ ++ + i+   +++++
  gi|242399943|ref|YP_002995368.1| 223 tiEENGGEVHLGTNVTEIIVENGEAKGLKVGEKTIQAKRVLFAAPVYYLL-RLIKEgNLPEeFAERLIEGEkEATNL 298
                                       ********************888877766677888***************.77777799774777777766899999 PP

                                       EEEEEEESSGGSGCSTSECE......CECCCEEETTTEEEEECCECCCSTTTEEEEEEEEECHHHHHHHTTS-HHHH CS
                     Amino_oxidase 291 nkvilefdrkfwednalgqg......vlvseltttlgeafissdfpsrappgkglvllvyvggdaaneleslsdeel 361
                                       + +i   +r+  e+     g       ++  + ++    +  s+   +ap+g+ ++ ++ +++      e++ ++el
  gi|242399943|ref|YP_002995368.1| 299 FLIIGGAKRPLTEKP---IGtwimapRSEVKNVDSYYLIYEVSPELKQAPEGNYPLSIAVLAD------EKTNKKEL 366
                                       999999999995543...345444333333333333333333334568899999977777775......34488*** PP

                                       HHHHHHHHHHHHTGTSSTCSEEEEEECCTETTTSSSEEE.BTTHHHHHHHHHHCHHCSTTEEE.SGGGCTTTTTSHH CS
                     Amino_oxidase 362 vqavlrdLrklfgeevpepkatlvtrWhtdplargsysyvsvgpghedydplakpegdprlffAGehtsreypgtve 438
                                       +++ + dL+ lf+    +    +  +W+++ ++  +    ++    ++++   ++ ++++l++AG++ ++e+ ++v+
  gi|242399943|ref|YP_002995368.1| 367 AKKMVADLEALFP----NFDFENDWDWKAEVMFPIVDGIGRTIDWYWERRLGPET-PIKNLYVAGDS-AQELSSGVD 437
                                       *************....777777999**999997777666777677777777777.***********.7788888** PP

                                       HHHHHHHHHHHH CS
                     Amino_oxidase 439 gAilSGlraAar 450
                                       g+ +S+l a ++
  gi|242399943|ref|YP_002995368.1| 438 GCASSALFAIEA 449
                                       *****9977555 PP

>> GDI  GDP dissociation inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.3   0.0   3.8e-22   4.5e-19       5     292 ..       2     275 ..       1     285 [. 0.87

  Alignments for each domain:
  == domain 1  score: 68.3 bits;  conditional E-value: 3.8e-22
                                       ECEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSSCGGG-EE-HHHHHHHH-TTHHHHHHH--GGG--EESS--BEE CS
                               GDI   5 ydvivlGtGlkecilsGllsvdgkkvlhldrndyyGgesasltleqlyerfkleekpeeklGkdrdwnvdlipkfll 81 
                                       ydv ++G+G++  +   ll+ +g +v +++rn++ Gg +a+ t +            e  + +  d+ vd+    + 
  gi|242399943|ref|YP_002995368.1|   2 YDVAIVGAGFTGLLAGSLLAKEGYRVAVFERNSFVGGRAATRTPK------------EWGWAEREDYRVDFGHHVFA 66 
                                       9***********99999*********************9975432............233556679*********** PP

                                       TTSHHHHHHHHTTGGGCS-EEE-SEEEEEETCEEEE--SSHHHHHC-.TTS-HHHHHHHHHHHHHHHH-BTTBGGGS CS
                               GDI  82 anGelvkiliktdvtrylefkaveGsyvykegkiakvpanelealas.pllglfekrrakkfleyvseyeeddpkty 157
                                       +n  l  il +    r+++f  ++  y yk+g+++k p+  le l + p + l  k r++kfl yv++ +  +    
  gi|242399943|ref|YP_002995368.1|  67 TNSYLEFILDRVGAKRHFKFVPLNMPYFYKNGRLHKPPVGFLEQLRAyPWIPLRSKLRLRKFLSYVEKVSFGEV--M 141
                                       *********************************************76489****************98765443..2 PP

                                       TT--TTTSBHHHHHHHCT--HHHHH.HHHHHTS--SSS.GGGGSBCHHHHHHHHHHHHHHCCCSS-SEEEETT-TTH CS
                               GDI 158 edldlkkatmkevykkfdlsedtkd.fiGhalalyrdd.dylkqpaletleriklyaeslarygkspylyplyGlGe 232
                                       e+       ++e+y++f+++e++++ f+   +a y++  d  ++ a + +  +k y   + ry k+p +    G+G 
  gi|242399943|ref|YP_002995368.1| 142 EK--WAYRPLEELYDEFGFDENARElFTDGFVAGYQTIiDTERNSAGDLILCMKAYLRGIKRY-KTPLFSAEGGVGA 215
                                       22..2446789************99466667888887525667789999**************.68999******** PP

                                       HHHHHHHHHHHTT-EEETS--ECEEEE-TTS-EEEEEETTEEEEECEEE.E-GGG-CCCEE CS
                               GDI 233 lpqgfarlsaiyGGtymlnkpvdevvldedgkvvGvkseeevakakkvi.cdpsylpekvr 292
                                       + +++ +    +GG   l ++v+e+++ e+g + G+k +e++++ak+v+ + p y   ++ 
  gi|242399943|ref|YP_002995368.1| 216 IAEALRKTIEENGGEVHLGTNVTEIIV-ENGEAKGLKVGEKTIQAKRVLfAAPVYYLLRLI 275
                                       ***************************.9*****************986378988765555 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 !   50.3   0.1   1.8e-16   2.1e-13       1      56 [.       6      69 ..       6      76 .. 0.88

  Alignments for each domain:
  == domain 1  score: 50.3 bits;  conditional E-value: 1.8e-16
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EECE..TT......CEECTS---EEETT CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasyev..pg......vrvdygahifhgsg 56
                                      IvGaG++Gl+a +lLak+g++v ++e+++ +GGraa+++    g      +rvd g h+f++ +
  gi|242399943|ref|YP_002995368.1|  6 IVGAGFTGLLAGSLLAKEGYRVAVFERNSFVGGRAATRTPkeWGwaeredYRVDFGHHVFATNS 69
                                      9*************************************996612555667**********9965 PP

>> DAO  FAD dependent oxidoreductase
   #    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       1      37 [.       3      41 ..       3     102 .. 0.86
   2 ?   -1.2   0.0      0.96   1.1e+03     287     319 ..     127     159 ..     117     200 .. 0.70
   3 !   16.6   0.3   3.7e-06    0.0045     147     203 ..     215     269 ..     192     285 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1e-07
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGG CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaS 37
                                      dv+i+G+G +Gl +   La++g  V+++e+++++g  a 
  gi|242399943|ref|YP_002995368.1|  3 DVAIVGAGFTGLLAGSLLAKEGyrVAVFERNSFVGGRAA 41
                                      8********************************995433 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.96
                                       HHHHHHHHHSGGGCGEEEEEEEEEEE...TTSSEEE CS
                               DAO 287 ellealrklfPqlgdvlrkwaGlrpl...pdglpli 319
                                       ++l++++k++  +g+v +kwa +rpl    d++ + 
  gi|242399943|ref|YP_002995368.1| 127 KFLSYVEKVS--FGEVMEKWA-YRPLeelYDEFGFD 159
                                       4445555555..789999999.99943335665443 PP

  == domain 3  score: 16.6 bits;  conditional E-value: 3.7e-06
                                       HHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEE.EEEEEEEE--GGG CS
                               DAO 147 kltaalaraaealGveilegtevtgleeedgkvwgverttpgen.daadavVnaaGaw 203
                                       + + al++++e++G+e+++gt+vt++  e+g ++g+++   ge+  +a+ v  aa ++
  gi|242399943|ref|YP_002995368.1| 215 AIAEALRKTIEENGGEVHLGTNVTEIIVENGEAKGLKV---GEKtIQAKRVLFAAPVY 269
                                       67899********************9788888888832...66533456699998655 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.1e-06    0.0013       1      70 [.       2      74 ..       2      87 .. 0.68
   2 !   10.7   0.0   0.00019      0.23     184     234 ..     215     265 ..     172     268 .. 0.86
   3 ?   -0.4   0.0      0.46   5.5e+02     265     278 ..     416     429 ..     411     441 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.1e-06
                                      CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHH.HCHHHHHHHHHHHHH...HHHHCHHHHCCCC CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx...xxxxxxxxxxxxx RF
                       Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcll.skallgvaedaeias...evvkklnqgiell 70
                                      +dv+++G+G+ Gl a   la+ g++v+++ +++ +++g+    +++ +g+ae+++ +     +v   n+ +e++
  gi|242399943|ref|YP_002995368.1|  2 YDVAIVGAGFTGLLAGSLLAKEGYRVAVF-ERNSFVGGRAATrTPKEWGWAEREDYRVdfgHHVFATNSYLEFI 74
                                      68999999999999999999999999999.77778887766643344444444444334465555555555555 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00019
                                       HHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 184 elsaaleealekeGvevklgtsvkeidgngeklevvledgeeidadlvvva 234
                                       ++++al++ +e++G ev+lgt+v+ei+ ++ +++     +++i+a+ v++a
  gi|242399943|ref|YP_002995368.1| 215 AIAEALRKTIEENGGEVHLGTNVTEIIVENGEAKGLKVGEKTIQAKRVLFA 265
                                       578999999999************999999988855555666999999887 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.46
                                       BESSTTEEE-GGGC CS
                                       xxxxxxxxxxxxxx RF
                       Pyr_redox_2 265 rtnvpgiyaiGDva 278
                                       +t ++++y++GD a
  gi|242399943|ref|YP_002995368.1| 416 ETPIKNLYVAGDSA 429
                                       6889********99 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   2.5e-07    0.0003       1      39 [.       3      41 ..       3      66 .. 0.91
   2 !    8.1   0.0     0.001       1.2     139     199 ..     212     266 ..     180     306 .. 0.82
   3 ?    0.3   0.0      0.25     3e+02     389     409 ..     416     439 ..     402     443 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.5e-07
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGG CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggata 39
                                      Dv ++G+G+ GL A+  +a++G +vav e  + +gg +a
  gi|242399943|ref|YP_002995368.1|  3 DVAIVGAGFTGLLAGSLLAKEGYRVAVFERNSFVGGRAA 41
                                      9******************************99999766 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.001
                                       HHHHHHHHHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-- CS
                     FAD_binding_2 139 tghallarlvesarkagvdfqerteadeLivedgrvtGavvenpesgrevrirakavvlat 199
                                          a++++l ++++++g +++  t+++e+ive+g++ G  v       e +i+ak+v+ a+
  gi|242399943|ref|YP_002995368.1| 212 GVGAIAEALRKTIEENGGEVHLGTNVTEIIVENGEAKGLKVG------EKTIQAKRVLFAA 266
                                       556899*********************************999......5566677777665 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.25
                                       EESSBTEEE-STCE...ESSSSTT CS
                     FAD_binding_2 389 gqpipGLYAaGeva...aggvhga 409
                                       ++pi++LY aG  a   ++gv+g 
  gi|242399943|ref|YP_002995368.1| 416 ETPIKNLYVAGDSAqelSSGVDGC 439
                                       68**********996666777665 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.2   4.6e-06    0.0055       1      36 [.       2      37 ..       2      41 .. 0.93
   2 !   14.2   0.0   1.1e-05     0.013     101     161 ..     206     265 ..     193     267 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.6e-06
                                      -SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                       HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllekakklg 36
                                      +dv+++G+G  Gl+a   +ak+g rV+++e+++ +g
  gi|242399943|ref|YP_002995368.1|  2 YDVAIVGAGFTGLLAGSLLAKEGYRVAVFERNSFVG 37
                                      59*****************************98776 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 1.1e-05
                                       EEETT.-CHHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE- CS
                       HI0933_like 101 lFpvsdkaedivdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlA 161
                                       lF ++     i +al k+++e+g +++l t+v+++  e++++  +k+ +e++++a+++++A
  gi|242399943|ref|YP_002995368.1| 206 LFSAEGGVGAIAEALRKTIEENGGEVHLGTNVTEIIVENGEAKGLKV-GEKTIQAKRVLFA 265
                                       67777778899************************************.**********998 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   5.9e-06     0.007       2      35 ..       4      37 ..       3      47 .. 0.90
   2 !   12.1   0.1   0.00019      0.22      41      78 ..     215     252 ..     196     255 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 5.9e-06
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                      v++vG+G++gl +++ la+ g +V v+er++ + 
  gi|242399943|ref|YP_002995368.1|  4 VAIVGAGFTGLLAGSLLAKEGYRVAVFERNSFVG 37
                                      89***************************98766 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00019
                                       HHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEEE CS
                         Pyr_redox  41 easkilqeklekngievllntkveeiegsedgvesvkl 78 
                                       +++++l++ +e+ng ev+l+t+v+ei  ++ + +++k+
  gi|242399943|ref|YP_002995368.1| 215 AIAEALRKTIEENGGEVHLGTNVTEIIVENGEAKGLKV 252
                                       68999*********************977766777665 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   7.1e-07   0.00085       1      40 [.       3      42 ..       3      82 .. 0.92
   2 ?    4.9   0.0     0.012        14      89     139 ..     216     262 ..     174     267 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 7.1e-07
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGllts 40
                                      Dv +vG+g  G+ A    a++G +v++ e++ ++GG ++ 
  gi|242399943|ref|YP_002995368.1|  3 DVAIVGAGFTGLLAGSLLAKEGYRVAVFERNSFVGGRAAT 42
                                      9***********************************8865 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.012
                      FAD_oxidored  89 akavleemlaeagvtvllntrlvevekegkriesvtveskegrktirAkvf 139
                                        +++l + ++e+g +v l+t ++e+++e+++ ++++v    g+kti+Ak++
  gi|242399943|ref|YP_002995368.1| 216 IAEALRKTIEENGGEVHLGTNVTEIIVENGEAKGLKV----GEKTIQAKRV 262
                                       455666777*******************999******....5889999877 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.1   4.4e-08   5.2e-05       2      34 ..       2      34 ..       1      45 [. 0.91

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 4.4e-08
                                      EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSS CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrs 34
                                      +dV+IVGaG +Gl++++lL++ G rv + e+ s
  gi|242399943|ref|YP_002995368.1|  2 YDVAIVGAGFTGLLAGSLLAKEGYRVAVFERNS 34
                                      69***************************9975 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.2   9.3e-08   0.00011      19      55 ..       3      38 ..       1      42 [. 0.92

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 9.3e-08
                                      EEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--T CS
                              Thi4 19 DvvivGaGssGLtaayylakkpdlkvailersvspGG 55
                                      Dv+ivGaG +GL a+  lak+ + +va++er+  +GG
  gi|242399943|ref|YP_002995368.1|  3 DVAIVGAGFTGLLAGSLLAKE-GYRVAVFERNSFVGG 38
                                      9********************.*********988887 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 !   15.7   0.0   9.5e-06     0.011       1      48 [.       5      47 ..       5      60 .. 0.82
   2 ?   -2.3   0.0       3.4     4e+03     107     152 ..     220     265 ..     215     266 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 9.5e-06
                     NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsep.gagrvwrtdqse 48
                                      aivGaG++Gl++   L+++       ++ +f+++++ g gr++ ++ +e
  gi|242399943|ref|YP_002995368.1|  5 AIVGAGFTGLLAGSLLAKE-----GYRVAVFERNSFvG-GRAATRTPKE 47
                                      8********9887766666.....7***********55.8888777555 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.4
                     NAD_binding_9 107 llarlpegvtvevhraevvdleeradgqavlladgaslaadaVvLA 152
                                       l ++ +e+    ++ ++v+++  ++++++ l+ ++++++a++V  A
  gi|242399943|ref|YP_002995368.1| 220 LRKTIEENGGEVHLGTNVTEIIVENGEAKGLKVGEKTIQAKRVLFA 265
                                       4444444444455688999998888888888888899999999776 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00019      0.23       2      33 ..       4      35 ..       3      56 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00019
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HH CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdisee 33
                                      va++GaG  G    +++a++g++V ++++++ 
  gi|242399943|ref|YP_002995368.1|  4 VAIVGAGFTGLLAGSLLAKEGYRVAVFERNSF 35
                                      9**************************99865 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 ?    5.6   0.1    0.0069       8.3       2      33 ..       6      36 ..       5      41 .. 0.92
   2 ?    3.5   0.0     0.029        34      84     135 ..     217     269 ..     200     305 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0069
                       Pyr_redox_3  2 IiGaGPaGlaaaielkkagledylilEkgnig 33
                                      I+GaG  Gl a+  l k g  ++ + E+++ +
  gi|242399943|ref|YP_002995368.1|  6 IVGAGFTGLLAGSLLAKEGY-RVAVFERNSFV 36
                                      9*******************.79****99765 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.029
                       Pyr_redox_3  84 leYlrevaksfelpiklfeeVesvkk.edegfevetsketyeAkkviiAtGef 135
                                       +e lr+  +++  +++l ++V+++   ++e   ++  ++t++Ak+v+ A+  +
  gi|242399943|ref|YP_002995368.1| 217 AEALRKTIEENGGEVHLGTNVTEIIVeNGEAKGLKVGEKTIQAKRVLFAAPVY 269
                                       6678889999999999*****999883456688999999*******9998666 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.2   0.00046      0.55       1      30 [.       3      32 ..       3      46 .. 0.89
   2 ?   -1.0   0.0      0.61   7.3e+02      54     105 ..     222     272 ..     210     312 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00046
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEEES CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLith 30
                                      dv ++G+G  G+ A   +a+ G++v+ +  
  gi|242399943|ref|YP_002995368.1|  3 DVAIVGAGFTGLLAGSLLAKEGYRVAVFER 32
                                      799***********************9844 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.61
                                       HHHHHHT-SHHHHHHHHEEEEEEESTTS-CCC-EEEEEE-HHHHHHHHHHHH CS
                              GIDA  54 rEidalggliikaadkagiqfrilNrskGpavralraqvdrelyskevtekl 105
                                       + i++ gg++   ++ ++i +    + kG  v++  +q+ r l+++ v   l
  gi|242399943|ref|YP_002995368.1| 222 KTIEENGGEVHLGTNVTEI-IVENGEAKGLKVGEKTIQAKRVLFAAPVYYLL 272
                                       4455555555555555555.22233556666666666666665555554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (464 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); 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: 0.73u 0.37s 00:00:01.10 Elapsed: 00:00:00.58
# Mc/sec: 2422.90
//
Query:       gi|242399944|ref|YP_002995369.1|  [L=82]
Description: hypothetical protein TSIB_1971 [Thermococcus sibiricus MM 739]
Scores for complete 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   16.6   1.7     0.0063   16.6   1.7    1.5  2  DUF1206   Domain of Unknown Function (DUF1206)
  ------ inclusion threshold ------
       0.04   13.8   1.1        2.9    7.9   0.2    2.1  2  SAYSvFN   Uncharacterized conserved domain (SAYSvFN)
       0.16   10.7   0.2       0.16   10.7   0.2    1.0  1  DUF2207   Predicted membrane protein (DUF2207)


Domain annotation for each model (and alignments):
>> DUF1206  Domain of Unknown Function (DUF1206)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   1.7     1e-06    0.0063      43      65 ..      10      32 ..       2      33 .. 0.85
   2 ?   -2.2   0.0      0.79   4.7e+03      17      20 ..      55      58 ..      50      72 .. 0.54

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1e-06
                           DUF1206 43 pfGrvllglvglgllgyglwqlv 65
                                       fG vl++++g++++gyg+ ql+
  gi|242399944|ref|YP_002995369.1| 10 IFGVVLVIVIGFAIIGYGILQLL 32
                                      49*****************9985 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.79
                           DUF1206 17 alqa 20
                                      ++++
  gi|242399944|ref|YP_002995369.1| 55 LVSV 58
                                      2222 PP

>> SAYSvFN  Uncharacterized conserved domain (SAYSvFN)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.2   0.00049       2.9      13      34 ..       7      28 ..       2      34 .. 0.87
   2 ?    5.0   0.0    0.0038        23      22      43 ..      54      75 ..      44      77 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00049
                           SAYSvFN 13 aelefgavfvilsllvliftnl 34
                                       el fg+v vi+ ++++i + +
  gi|242399944|ref|YP_002995369.1|  7 RELIFGVVLVIVIGFAIIGYGI 28
                                      6788**************9975 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0038
                           SAYSvFN 22 vilsllvliftnlrsgerkege 43
                                       ++s+l++i++ l s++r ++e
  gi|242399944|ref|YP_002995369.1| 54 YLVSVLFIIIMELLSSSRPKEE 75
                                      4567777777777776776665 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.2   2.7e-05      0.16     381     427 ..       7      64 ..       2      82 .] 0.66

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 2.7e-05
                           DUF2207 381 kklsalglgliilglilillallllvll.............lvfllilllillliaiivl 427
                                        +l++  +++i++g+++i +++l+l ++                 l+ ++++ +++ii++
  gi|242399944|ref|YP_002995369.1|   7 RELIFGVVLVIVIGFAIIGYGILQLLPHsvathavppaekfR--NLLAIYLVSVLFIIIM 64 
                                       5678889999999999999999999999**********8542..2222222233333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1013  (0.0565006); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.34s 00:00:00.84 Elapsed: 00:00:00.53
# Mc/sec: 469.35
//
Query:       gi|242399945|ref|YP_002995370.1|  [L=113]
Description: hypothetical protein TSIB_1972 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.52   10.0   4.8       0.63    9.7   4.8    1.0  1  Tetraspanin  Tetraspanin family


Domain annotation for each model (and alignments):
>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   4.8   3.5e-05      0.63       9      98 ..      11     106 ..       5     110 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 3.5e-05
                                       XXXXXXXXXXXXXXXXXXXX.XXX.....................XXXXXX..XXXXXXXXX..XXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxx..xxxxxxxxxxxxx RF
                       Tetraspanin   9 nllfwligivllavGvwlrl.khaeaalacllsesaedpailaillivvGv..llfllgflG..cigalkenkclll 80 
                                       ++ +++++++l++ G + ++   + ++++  l + +++p+  ++ li  G+  ll++ +++G  ++g  k ++  l 
  gi|242399945|ref|YP_002995370.1|  11 AVPLFIFSVILVITG-YGIVsPRTISTFTFGLVSYQNAPTLHSYRLIRYGFtvLLLVHSYAGfeIFGLKKIRNQRLR 86 
                                       455667777777777.444443344455555566666677777777777776588999****887886665555555 PP

                                       XXX..XXXXXXXXXXXXXXX CS
                                       xxx..xxxxxxxxxxxxxxx RF
                       Tetraspanin  81 tfs..llllvlfllelaagi 98 
                                       +f+  lll++++ ++ +a+i
  gi|242399945|ref|YP_002995370.1|  87 LFLgyLLLFIVIYALWVATI 106
                                       55534677777777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); 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 0.28s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 776.38
//
Query:       gi|242399946|ref|YP_002995371.1|  [L=206]
Description: oxidoreductase molybdopterin binding [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-26   93.3   0.0    2.4e-26   92.4   0.0    1.4  1  Oxidored_molyb  Oxidoreductase molybdopterin binding domain


Domain annotation for each model (and alignments):
>> Oxidored_molyb  Oxidoreductase molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.4   0.0   1.3e-30   2.4e-26       8     168 ..      54     187 ..      45     191 .. 0.90

  Alignments for each domain:
  == domain 1  score: 92.4 bits;  conditional E-value: 1.3e-30
                                       GCCC-EEEEESTCSSEEEEEHHHHHHC-EEEEEEEEE-TTTTHHHHCHH--SS----TTSEEEEEEEEEEHHHHHHH CS
                    Oxidored_molyb   8 dpekwrlevdglvekplslslddLkalpavevtatlqCagnrrkelnkkkvkglqwgagavsnaeWtGvrlrdvLek 84 
                                         e+w +ev+glvekp++++l++Lk++p++ v + l C+                   +a  +  W+Gv+l+ +Le+
  gi|242399946|ref|YP_002995371.1|  54 ASEEWVIEVTGLVEKPMNITLSQLKEMPQTAVFSELYCVA---------------YPGKARKQGLWKGVKLSYILEQ 115
                                       4679************************************...............344677899************* PP

                                       TTB-ETT..EEEEEEEEE-TCCTEEEEEEEHHHHCTT.T-EEEEEETTEE--CCCTTT-EEE-TTB-GGGSBTTEEE CS
                    Oxidored_molyb  85 agvkkpearhvvfegadeeleeskygasiplekaled.dvlLAyemngepLppdhGyPlRlvvpglvgarsvKwlkr 160
                                       agvk + a  v f++ d      ++++ + le+al++ + ++Aye n++p++p      Rl+ pg++g++++K+l +
  gi|242399946|ref|YP_002995371.1| 116 AGVK-DGAIKVAFYARD------GFTTDLTLEEALTNdELIIAYEFNNKPIEP------RLIAPGMWGYKWIKYLVK 179
                                       ***7.9*********99......5***********66379************9......9***************** PP

                                       EEEESS-- CS
                    Oxidored_molyb 161 ievsdees 168
                                       iev+d + 
  gi|242399946|ref|YP_002995371.1| 180 IEVVDYNF 187
                                       ***99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); 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: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1322.36
//
Query:       gi|242399947|ref|YP_002995372.1|  [L=77]
Description: hypothetical protein TSIB_1974 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.32s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 496.99
//
Query:       gi|242399948|ref|YP_002995373.1|  [L=106]
Description: hypothetical protein TSIB_1975 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.038   14.5   1.5        8.2    7.0   0.1    2.1  2  PAP2_C    PAP2 superfamily C-terminal


Domain annotation for each model (and alignments):
>> PAP2_C  PAP2 superfamily C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1   0.00047       8.4      31      70 ..      25      65 ..       4      69 .. 0.81
   2 ?    7.0   0.1   0.00046       8.2      34      55 ..      81     102 ..      71     103 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.00047
                            PAP2_C 31 ilkvillllallglfliiasrkHYtvDVllglyittlvf.l 70
                                      i  +ill+ al  ++++i+ +  + v  l++++i+ lvf l
  gi|242399948|ref|YP_002995373.1| 25 IPGYILLMGALEVYLIMILRKGFFPVKLLFAYFIMALVFeL 65
                                      4566777778888999999999****************955 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.00046
                            PAP2_C  34 villllallglfliiasrkHYt 55 
                                       v+ ++l+++  f++++++ H +
  gi|242399948|ref|YP_002995373.1|  81 VLPWYLSAVVGFILVLKHVHNS 102
                                       788*****************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      139  (0.0077528); 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 0.31s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 705.50
//
Query:       gi|242399949|ref|YP_002995374.1|  [L=43]
Description: hypothetical protein TSIB_1976 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      147  (0.00819901); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 287.17
//
Query:       gi|242399950|ref|YP_002995375.1|  [L=88]
Description: hypothetical protein TSIB_1977 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score 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   15.5   0.3      0.017   15.3   0.3    1.1  1  ThiW      Thiamine-precursor transporter protein (ThiW)


Domain annotation for each model (and alignments):
>> ThiW  Thiamine-precursor transporter protein (ThiW)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.3   9.2e-07     0.017      79     144 ..      18      84 ..       9      87 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 9.2e-07
                              ThiW  79 agllyrltr.klllaalgEvlGtgiiGallaypvaklllgkeaallvlvisFilstliGsviallvl 144
                                       +gll++l + +l l  l   +Gt+ +      p+  ll+g    ++++v+++ ls+l+G vi+l +l
  gi|242399950|ref|YP_002995375.1|  18 VGLLWTLRKeNLPLKSLLVYFGTATVLEFPYAPFKGLLTGYFDGIFLFVLPWYLSALAGLVISLKLL 84 
                                       577777766345678889999***99999999******************************99877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      181  (0.0100954); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.30s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 578.61
//
Query:       gi|242399951|ref|YP_002995376.1|  [L=56]
Description: hypothetical protein TSIB_1978 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       245  (0.013665); expected 358.6 (0.02)
Passed bias filter:                      201  (0.0112109); 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: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 362.28
//
Query:       gi|242399952|ref|YP_002995377.1|  [L=190]
Description: hypothetical protein TSIB_1979 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-35  122.2   0.1    1.4e-35  121.8   0.1    1.1  1  Macro     Macro domain
     0.0031   16.8   0.0     0.0043   16.4   0.0    1.1  1  GRDB      Glycine/sarcosine/betaine reductase selenoprotein B


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 !  121.8   0.1   1.6e-39   1.4e-35       1     117 [.      30     155 ..      30     156 .. 0.97

  Alignments for each domain:
  == domain 1  score: 121.8 bits;  conditional E-value: 1.6e-39
                                       EEEEETTSS-CSHHHHHHHHHHHHHHHHHHHHHHHHHHS......--TTSEEEEE-TTSS...SSEEEEEESE-TTT CS
                             Macro   1 VnAaNsrllggggvagaihraagkalkeeckelekkqgg......cllGeavvtpaynlp...akyvihtvgplfts 68 
                                       VnAaN++l++gggva+ai++aa  +++e+++  ++++++      +++Ge+vvtpa++++   ++yvihtvgp++  
  gi|242399952|ref|YP_002995377.1|  30 VNAANKYLEHGGGVAYAIAKAASGDVREYIRISKEAMREqigrgwIEHGEVVVTPAMKMEqygIRYVIHTVGPYCGG 106
                                       9*****************************99998877788899****************9**************** PP

                                       STSTTHHHHHHHHHHHHHHHHHHTT-SEEEEE-TTSSTTSBTHHHHHHH CS
                             Macro  69 skskeeeellakayknalelaeekgiksvafPaistGifgvpweeaarv 117
                                       +++++++e+l+ka+  al++aee g+ks+afPais+Gi+g+p+ee++++
  gi|242399952|ref|YP_002995377.1| 107 KWDEDKKEKLKKAILGALKKAEELGVKSIAFPAISAGIYGCPFEEVVKT 155
                                       *********************************************9876 PP

>> 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 !   16.4   0.0   4.8e-07    0.0043      30     107 ..      80     159 ..      72     164 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 4.8e-07
                              GRDB  30 gavGpglalkkalkdeaevvati..iCGDnyfaenleeaveeilelvkklepdll..iaGPafnaGRYGvacgevak 102
                                        +v p++++++       v++t+   CG ++  +++e+ ++ il ++kk e   +  ia Pa  aG YG+   ev+k
  gi|242399952|ref|YP_002995377.1|  80 VVVTPAMKMEQYG--IRYVIHTVgpYCGGKWDEDKKEKLKKAILGALKKAEELGVksIAFPAISAGIYGCPFEEVVK 154
                                       4667777777665..47899999778**********************9997655459************9999999 PP

                              GRDB 103 avkee 107
                                       + +e 
  gi|242399952|ref|YP_002995377.1| 155 TFREV 159
                                       87765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); 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: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1273.04
//
Query:       gi|242399953|ref|YP_002995378.1|  [L=424]
Description: 5-methylthioadenosine/S-adenosylhomocysteine deaminase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.7e-82  276.9   1.0    3.1e-82  276.7   1.0    1.0  1  Amidohydro_1  Amidohydrolase family
    9.9e-21   74.7   0.4    1.1e-13   51.5   0.0    2.2  2  Amidohydro_3  Amidohydrolase family
     0.0077   15.6   0.0      0.013   14.8   0.0    1.3  1  A_deaminase   Adenosine/AMP deaminase
  ------ inclusion threshold ------
      0.048   14.0   0.6       0.17   12.2   0.6    2.0  1  Urease_alpha  Urease alpha-subunit, N-terminal domain
        9.4    6.1   8.4        1.3    9.0   1.0    2.8  3  DUF5424       Family of unknown function (DUF5424)


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 !  276.7   1.0   8.6e-86   3.1e-82       1     344 []      51     398 ..      51     398 .. 0.95

  Alignments for each domain:
  == domain 1  score: 276.7 bits;  conditional E-value: 8.6e-86
                                       EEEE-EEEEEEECETTECSSS....GHHHHH..........STTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTHHH CS
                      Amidohydro_1   1 ivlPGlIDaHvHleqsllrga....tledwl..........vppetaaealesgiktalksGtttvadmgattstgi 63 
                                       ++ PG+I+aH+H ++ llrg      l++wl          ++   +++++  g+ +++k Gttt+ dm++    ++
  gi|242399953|ref|YP_002995378.1|  51 VISPGFINAHTHSPMVLLRGLaddiSLMEWLqnyvwpvekkLKRVHIYWGALLGTLEMIKTGTTTFVDMYF----HM 123
                                       589**************************************9999**************************....9* PP

                                       HHHHHHHHTSSSEEEEEEESSEGGSGCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHHHHHHHHH CS
                      Amidohydro_1  64 ealleaaeelplglrilggkvsldrgsaetskasreklkagaaetikgkadgvvkvalapheapafsdeelkealke 140
                                       e +++a+ee+  glr++++++++d g++e +  ++++ ++   ++i   ++ +v+  ++ph+++++s+ +l ++ ++
  gi|242399953|ref|YP_002995378.1| 124 EEVAKAVEEI--GLRAYLSYGMVDLGDEEKRSIEIRETLKL-LKFIESLSSPRVEFLFGPHAPYTCSPKLLTWVREK 197
                                       *********8..*************6666666666666677.48********************************* PP

                                       HHHHTTEEEEEETSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEEHHHHHHHHHHHHHHCEEH CS
                      Amidohydro_1 141 akkrdlpvaiHaletkgevedaeaafgetiehgthlevaeslglldeiklilahgvhltpteaellkerlkeagvah 217
                                       a++ +++++iH++etk ev+++++++g     +t++e +++lg+l+   +i+ahgv+lt++e+e+l++r  ++ ++h
  gi|242399953|ref|YP_002995378.1| 198 ADETGKMITIHLSETKDEVKQIKEKYG-----KTPVELLDELGFLKN-DVIAAHGVWLTDKEIEILAKR--DVTIVH 266
                                       ***************************.....78*************.*********************..****** PP

                                       HHHHHHHSEHHHHHHHHHHHHTSCEEEEEECTTSSCCGGHHHHHHHHHHHHHHCCTTTTHCHCHHHHHHHHHTHHHH CS
                      Amidohydro_1 218 cpfsnsilrsgrealrkaldeGvkvglgtDgaasgnslnlleelrlalklqrgllyedeegglslkealrmaTingA 294
                                        p+sn++l+sg++ l+k+l++Gv+v+lgtDgaas+n+l+++ee++la++l++ ++  +++   ++k +++maT+ngA
  gi|242399953|ref|YP_002995378.1| 267 NPASNMKLGSGVMSLEKLLKAGVNVALGTDGAASNNNLDMIEEMKLAALLHK-VHTLNPTL-ADAKTVFKMATQNGA 341
                                       ************************************************9999.44447777.99************* PP

                                       HHTT-TTTSSSS-TTSB--EEEECC.CT........CGGGTTTCTSEEEEEEEETTEEE CS
                      Amidohydro_1 295 kalglddkvGsievGkdADlvvvdl.di........laafvglkkdgnvkkvivkGklv 344
                                       kal+l  ++G i++G  AD +v+d  ++        ++++v++++ + v ++iv+Gk+v
  gi|242399953|ref|YP_002995378.1| 342 KALRL--NAGVIKEGALADVIVIDFnKPhlrpitniISHIVYSANGNDVETTIVDGKVV 398
                                       *****..******************84456777888*********************98 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.1   3.6e-08   0.00013       2      23 ..      44      63 ..      43      80 .. 0.82
   2 !   51.5   0.0   3.1e-17   1.1e-13     258     472 ..     184     398 ..     102     399 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 3.6e-08
                      Amidohydro_3  2 viDakGrlvlPGFvDsHtHlag 23
                                      viDakGr+  PGF+ +HtH  +
  gi|242399953|ref|YP_002995378.1| 44 VIDAKGRVISPGFINAHTH--S 63
                                      9******************..3 PP

  == domain 2  score: 51.5 bits;  conditional E-value: 3.1e-17
                      Amidohydro_3 258 pdfedealaelvaaadergldvaihaigdaavd.dvldafeaa....aekngnqdrr.rlehaegvtesqiervaal 328
                                        +++ + l+++ ++ade g  + ih  ++++   ++ + + ++     +++g+      ++h+ ++t+++ie +a+ 
  gi|242399953|ref|YP_002995378.1| 184 YTCSPKLLTWVREKADETGKMITIHLSETKDEVkQIKEKYGKTpvelLDELGFLKNDvIAAHGVWLTDKEIEILAKR 260
                                       3366666999999************99999988788888888887775556655442367777777**********9 PP

                      Amidohydro_3 329 qvaagvqpvfnfedelldsrlgperargstpvkellnagvkvalgsD..apvgpfdpwprigaavmrktrrggevlr 403
                                        v++   p++n            + ++g+  +  ll+agv+valg+D  a  + +d + ++  a  + ++   + l+
  gi|242399953|ref|YP_002995378.1| 261 DVTIVHNPASNM-----------KLGSGVMSLEKLLKAGVNVALGTDgaASNNNLDMIEEMKLAALLHKV---HTLN 323
                                       999999999999...........778999******************99888999999999877777776...5555 PP

                      Amidohydro_3 404 pdeelsleealalyTrgpAkalgledrkGtLevGadADlvvldadpldvdppelaear..............vrltv 466
                                       p    +  +++++ T+++Akal+l    G +++Ga AD++v+d     + +p+l+ ++              v+ t+
  gi|242399953|ref|YP_002995378.1| 324 PT-LADAKTVFKMATQNGAKALRLNA--GVIKEGALADVIVID-----FNKPHLRPITniishivysangndVETTI 392
                                       55.99*********************..**************9.....445555555555566789999******** PP

                      Amidohydro_3 467 vdGrvv 472
                                       vdG+vv
  gi|242399953|ref|YP_002995378.1| 393 VDGKVV 398
                                       *****9 PP

>> A_deaminase  Adenosine/AMP deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   3.7e-06     0.013     220     298 ..     245     318 ..     228     326 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.7e-06
                                       E-GGGGGSHHHHHHHHHCT-EEEE-HHHHCCCSST-TTTT-CHHHHHHTT-EEEE--BSCCCCT.-SHHHHHHHHHH CS
                       A_deaminase 220 HGvrlrkdpvLqyllalaqiplevcPlSNvalgafleyaenPlkeflerglnvslntDDPlqfg.ttLieeYaiaaq 295
                                       HGv l + +   + la++ +++   P+SN++l          l+++l++g+nv+l+tD  +  + +++iee++ aa 
  gi|242399953|ref|YP_002995378.1| 245 HGVWLTDKE--IEILAKRDVTIVHNPASNMKL----GSGVMSLEKLLKAGVNVALGTDGAASNNnLDMIEEMKLAAL 315
                                       777665544..36789999*************....455667999*************998765156*******998 PP

                                       HHT CS
                       A_deaminase 296 vfk 298
                                        +k
  gi|242399953|ref|YP_002995378.1| 316 LHK 318
                                       776 PP

>> Urease_alpha  Urease alpha-subunit, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.6   4.8e-05      0.17      69     100 ..       4      37 ..       1      54 [. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.8e-05
                      Urease_alpha  69 vitnavil..DatgivkadigikdgrivaiGkag 100
                                       +i n  ++  D   i+kadi i + +i++iGk  
  gi|242399953|ref|YP_002995378.1|   4 LIKNGYVIygDSLKIIKADIYIENNKISKIGKDL 37 
                                       5666666555889******************965 PP

>> DUF5424  Family of unknown function (DUF5424)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   1.0   0.00036       1.3      65     111 ..       4      48 ..       1      57 [. 0.84
   2 ?    0.2   0.0      0.18   6.5e+02     102     155 ..     279     327 ..     270     348 .. 0.71
   3 ?   -1.3   0.5      0.49   1.8e+03      74     107 ..     387     423 ..     345     424 .] 0.59

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00036
                           DUF5424  65 ivknGviiyevvetlikasnaitkdkklvdkilddGinavdklieaa 111
                                       ++knG++iy  +  +ika   i+ +++ ++ki +d   + d +i+a 
  gi|242399953|ref|YP_002995378.1|   4 LIKNGYVIYGDSLKIIKAD--IYIENNKISKIGKDLTKSADHVIDAK 48 
                                       79***************96..66777779999999999988888775 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.18
                           DUF5424 102 navdklieaaiylssvgepivedvtssfglvdqykelkheallfelyipnstsa 155
                                        +++kl +a + ++     + +d ++s    d  +e+k  all ++++ n t a
  gi|242399953|ref|YP_002995378.1| 279 MSLEKLLKAGVNVA-----LGTDGAASNNNLDMIEEMKLAALLHKVHTLNPTLA 327
                                       55566666665555.....45666666778899999999999999999999877 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.49
                           DUF5424  74 evvetlikasnaitkdkklv....dkilddGinavdkl 107
                                       +v +t+++    ++ d++++    +kild  +  vdkl
  gi|242399953|ref|YP_002995378.1| 387 DVETTIVDG-KVVMLDREVLtideEKILDKVQKIVDKL 423
                                       455555544.4444555544234358888888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (424 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       892  (0.0497518); expected 358.6 (0.02)
Passed bias filter:                      659  (0.0367561); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 3091.27
//
Query:       gi|242399954|ref|YP_002995379.1|  [L=257]
Description: Purine-nucleoside phosphorylase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    8.9e-49  165.9   0.0    1.1e-48  165.5   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 !  165.5   0.0   6.2e-53   1.1e-48       1     231 [.       3     235 ..       3     237 .. 0.95

  Alignments for each domain:
  == domain 1  score: 165.5 bits;  conditional E-value: 6.2e-53
                                       CEEEEESSH..HHHHHHHHHEEEEEEEEEE.TTEEEEEEEETTEEE.EEEE--....SSHHHHHHHHHHHHHHHC-- CS
                         PNP_UDP_1   1 kiaiivgsp..gevellaespleetpfgregrgfkfvtGtlkgkpv.vivstG....iGkpnaavvaeirllkefgv 70 
                                       +i+ii+gs+  g +e+        tp+gr+  +  + +G+++g++v +i ++G      ++ + ++a+i++lke gv
  gi|242399954|ref|YP_002995379.1|   3 RIGIIGGSGvyGVFEPKETV-KVHTPYGRP--SAPVEIGEIEGVEVaFIPRHGknheFPPHEVPYRANIWALKEVGV 76 
                                       69*******96555555555.99*******..*********8877769********77777777************* PP

                                       SEEEEEEEEEESSTTT-TT-EEEEEEEEESSSCCGCCTHHCCTCCCCTTSSEE--HHHHHHHHHCHHTTTTTEEE.E CS
                         PNP_UDP_1  71 kaiiriGtaGglnpdlkvGDvvipddainfdgrsplygpkeegqyfpdsydapadpelrallkeaaealgikvhr.G 146
                                       ++ii i ++G+l++++k+GD+vi+d++i+f+  +++++++ + + +  ++d+ ++pe+r++  e a++l+i+vh+ G
  gi|242399954|ref|YP_002995379.1|  77 ERIIGITAVGSLKEEYKPGDIVITDQFIDFTKKRDYTFYNGPRVAHFSMADP-FCPEMRKIFYETAKELNIPVHEkG 152
                                       ******************************************9999999999.************************ PP

                                       EEEEESESS-CHHHHHHHHHHTC-CEEESSHHHHHHHHHHTT--EEEEEEEEETTTBETTCTCH.HCCCHHHHHHHH CS
                         PNP_UDP_1 147 vvatadgfyaeteaelrllrrlgadaveMEtaavaqlArelgipfaairvvsdlaaggadaeatheeveefaqeaak 223
                                       ++++ +g++++t+ae+ ++r++   +++M+ +++++lArelg+++  i++v+d ++ +a+++ + +ev +++qe+ +
  gi|242399954|ref|YP_002995379.1| 153 TYVCIEGPRFSTRAESMMFRQFA-HIIGMTLVPEVVLARELGMCYTNIAAVTD-YDVWAEKPVDAQEVIKVMQENNE 227
                                       **********************9.*****************************.899******************** PP

                                       HHHHHHHH CS
                         PNP_UDP_1 224 naaallla 231
                                       ++ +ll+a
  gi|242399954|ref|YP_002995379.1| 228 KVRKLLKA 235
                                       *****997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      583  (0.0325172); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1729.77
//
Query:       gi|242399955|ref|YP_002995380.1|  [L=249]
Description: daunorubicin ABC transporter [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.5e-18   64.9  25.0      1e-17   64.3  25.0    1.2  1  ABC2_membrane    ABC-2 type transporter
    0.00011   22.3   7.1      0.018   15.2   0.1    2.4  2  YbjM             Putative inner membrane protein of Enterobac
  ------ inclusion threshold ------
       0.51    9.4  36.4      0.033   13.3  26.9    2.0  2  ABC2_membrane_3  ABC-2 family transporter protein
        8.6    6.9   7.6       0.62   10.6   1.7    2.1  3  IBV_3C           IBV 3C 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 !   64.3  25.0   2.3e-21     1e-17      16     210 .]      15     216 ..       4     216 .. 0.88

  Alignments for each domain:
  == domain 1  score: 64.3 bits;  conditional E-value: 2.3e-21
                     ABC2_membrane  16 rdpslgllwrliqplllalvfgtvfgnlg..nsedglnr............pgllffsvlflafsaltsvapvfere 78 
                                       +    g+++++++p+l++l+f +  +++   +      +            pg++++ +++     + s+ ++ +++
  gi|242399955|ref|YP_002995380.1|  15 KEAIGGFISQFLTPILYFLFFAFSLSRTVnfE------YhgktisyllyvlPGIIAIQIFYSY--PVVSSTTFNDVR 83 
                                       5555688*******************844341......1333334466699999998888888..6666669***** PP

                     ABC2_membrane  79 rgvlerelvsplyslsayvlakvlvelpvsllqalifllivyflvgldls..rfflflllllltalaasslgllisa 153
                                        g++   l  +  sls y+lakvlve +v +l++l ++++ +++++l+ls    + f+l+ll+++++ +s+g++i++
  gi|242399955|ref|YP_002995380.1|  84 FGIIRTSLLGGG-SLSGYILAKVLVESTVVILVSLFLVFVGVLFLNLYLSsaTLLQFVLYLLVSTVFWISMGIIIGV 159
                                       ************.*************9999999999999999999*****8666*********************** PP

                     ABC2_membrane 154 lapsfedasqlaslvllpllllsGffipidsmpkwlqwiaylnPltyavealrsnlf 210
                                        ++ + + ++l  l+ lp+++++++f+ + s p+w+ ++ ++nPlty v +lr +l+
  gi|242399955|ref|YP_002995380.1| 160 KMRGELTRNMLFALLNLPTIFTAPVFYLKGSAPMWIEFLGKINPLTYHVVGLREILL 216
                                       *****************************************************9975 PP

>> YbjM  Putative inner membrane protein of Enterobacteriaceae
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1     4e-06     0.018       7      55 ..      20      68 ..      14      80 .. 0.83
   2 !    8.9   2.8   0.00035       1.6      66     107 ..     115     156 ..      96     167 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4e-06
                              YbjM  7 gvvlcfllftlvflsqklevsgasaaeglrgelgLLlfllPGivaalls 55
                                      g ++ fl  +l fl+   ++s +   e ++  +  Ll++lPGi+a  + 
  gi|242399955|ref|YP_002995380.1| 20 GFISQFLTPILYFLFFAFSLSRTVNFEYHGKTISYLLYVLPGIIAIQIF 68
                                      6778888889999999999999999999999*************97665 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00035
                              YbjM  66 Gallaapvcllvlklvlaseeslwqelay.llSavFWcalGal 107
                                        +l  + v +l l+l+l+ + +l+q + y l+S vFW ++G +
  gi|242399955|ref|YP_002995380.1| 115 VSLFLVFVGVLFLNLYLS-SATLLQFVLYlLVSTVFWISMGII 156
                                       344445566677777555.5556665555268********976 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   1.8     0.012        54       4      28 ..      21      46 ..      18      55 .. 0.77
   2 ?   13.3  26.9   7.4e-06     0.033     158     336 ..      53     235 ..      40     243 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.012
                   ABC2_membrane_3  4 liitlllPiilvlllglifsnsve.d 28
                                      +i+++l Pi+++l++++ +s +v+ +
  gi|242399955|ref|YP_002995380.1| 21 FISQFLTPILYFLFFAFSLSRTVNfE 46
                                      45999999999999999988777654 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 7.4e-06
                   ABC2_membrane_3 158 nvasflvg.liliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilll.afglg 232
                                       ++  ++++ +i+i +++ +++ +++   ++ + +i+   l+ g s + y+l+k+l   +v +l++l+++++ ++   
  gi|242399955|ref|YP_002995380.1|  53 SYLLYVLPgIIAIQIFYSYPV-VSSTTFNDVRFGIIRTSLLGGGSLSGYILAKVLVESTVVILVSLFLVFVgVLF-- 126
                                       333344443777777777777.666788888889999999*****************************998888.. PP

                   ABC2_membrane_3 233 ipfgnlglllllfllfglayialgyllsslfknseta....qilifivilllsgffgglfp.ledlpsalkwifsii 304
                                       ++ + + ++ll f+l++l+++++   ++ ++     +    + l  +++l + +f +++f    + p ++  ++ i+
  gi|242399955|ref|YP_002995380.1| 127 LNLYLSSATLLQFVLYLLVSTVFWISMGIIIGVKMRGeltrNMLFALLNL-PTIFTAPVFYlKGSAPMWIEFLGKIN 202
                                       99999999**********************99995553333555555555.8888888877366799********** PP

                   ABC2_membrane_3 305 Pffapglgllrli.tgdplweillsliilalfa 336
                                       P+++  +gl  ++  g  ++e+++  ++l   +
  gi|242399955|ref|YP_002995380.1| 203 PLTYHVVGLREILlLGGAPVEFWIISLLLGMGS 235
                                       ************76888899*995544444333 PP

>> IBV_3C  IBV 3C protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1       1.3   5.6e+03      49      62 ..      54      67 ..      22      76 .. 0.65
   2 ?   10.6   1.7   0.00014      0.62       6      59 ..     104     161 ..     100     182 .. 0.75
   3 ?   -2.6   0.0       1.8     8e+03      18      33 ..     205     220 ..     197     225 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.3
                            IBV_3C 49 ytwvvipgakgtaf 62
                                      y   v+pg     +
  gi|242399955|ref|YP_002995380.1| 54 YLLYVLPGIIAIQI 67
                                      33344444444444 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00014
                            IBV_3C   6 ksleeng.sfltalyii...vgflalyllgralqafvqaadacclfwytwvvipgakg 59 
                                       k l e    +l +l+++   v fl lyl   +l  fv       +fw +  +i g k 
  gi|242399955|ref|YP_002995380.1| 104 KVLVESTvVILVSLFLVfvgVLFLNLYLSSATLLQFVLYLLVSTVFWISMGIIIGVKM 161
                                       5554443145666664432256999****************************99985 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 1.8
                            IBV_3C  18 lyiivgflalyllgra 33 
                                        y +vg+  + llg a
  gi|242399955|ref|YP_002995380.1| 205 TYHVVGLREILLLGGA 220
                                       5889999999999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1007  (0.056166); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 1464.20
//
Query:       gi|242399956|ref|YP_002995381.1|  [L=311]
Description: daunorubicin ABC transporter ATP-binding protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.3e-23   82.3   0.0    8.7e-23   81.4   0.0    1.5  2  ABC_tran     ABC transporter
    2.7e-07   30.7   1.6      0.002   18.0   0.0    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    6.5e-05   23.5   2.2    0.00013   22.6   1.5    1.7  2  AAA_23       AAA domain
     0.0032   16.9   0.1      0.059   12.8   0.1    2.2  1  SMC_N        RecF/RecN/SMC N terminal domain
     0.0036   17.0   0.0      0.065   12.9   0.1    2.1  2  AAA_15       AAA ATPase domain
     0.0037   17.0   0.5      0.008   15.9   0.5    1.5  1  AAA_29       P-loop containing region of AAA domain
     0.0095   16.3   0.0      0.019   15.3   0.0    1.6  1  AAA_16       AAA ATPase domain
  ------ inclusion threshold ------
      0.011   16.2   0.2      0.065   13.6   0.2    2.3  1  AAA          ATPase family associated with various cellular a
      0.011   16.0   0.1      0.033   14.4   0.1    1.9  1  AAA_22       AAA domain
      0.012   15.5   0.1      0.026   14.4   0.1    1.6  1  RsgA_GTPase  RsgA GTPase
       0.04   13.8   0.4       0.61    9.9   0.0    2.5  3  ATPase_2     ATPase domain predominantly from Archaea
      0.042   13.0   0.4       0.13   11.5   0.4    1.9  1  NB-ARC       NB-ARC domain
      0.048   13.5   0.0      0.082   12.7   0.0    1.4  1  ATP_bind_1   Conserved hypothetical ATP binding protein
      0.061   13.5   0.0       0.12   12.6   0.0    1.4  1  Roc          Ras of Complex, Roc, domain of DAPkinase
      0.069   12.7   0.1       0.63    9.5   0.1    2.2  2  AAA_7        P-loop containing dynein motor region
      0.091   12.3   0.1       0.29   10.7   0.1    1.8  2  cobW         CobW/HypB/UreG, nucleotide-binding domain
      0.097   12.3   0.1       0.15   11.6   0.1    1.3  1  SRP54        SRP54-type protein, GTPase domain
       0.11   12.4   0.0       0.23   11.4   0.0    1.6  1  Rad17        Rad17 P-loop domain
       0.16   12.2   0.0       0.34   11.1   0.0    1.5  1  AAA_28       AAA domain
       0.24   11.1   0.1        0.4   10.4   0.1    1.6  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 !   81.4   0.0   9.7e-26   8.7e-23       5     136 ..      26     165 ..      20     166 .. 0.93
   2 ?   -2.6   0.0       8.3   7.5e+03      59      80 ..     230     263 ..     203     293 .. 0.57

  Alignments for each domain:
  == domain 1  score: 81.4 bits;  conditional E-value: 9.7e-26
                                       EEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                          ABC_tran   5 slklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.. 79 
                                       s +++ g ++ i+G+nGaGK+tL+++l+   kp++G  ++ g d+ + ++++ r+ i+ + q+ +l+  l+vr+n  
  gi|242399956|ref|YP_002995381.1|  26 STDISSG-ILSILGPNGAGKTTLVNILTTTFKPQKGMAKIFGLDVVK-DKKKIREMISLCAQDLELDVLLSVRTNlk 100
                                       4455544.789*********************************999.99*************************** PP

                                       ...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHH.TSSEEEEESTT CS
                                       ...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                          ABC_tran  80 ...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallk.kpkllllDEpt 136
                                                  e +++++++++ +gl+e ++++v     +LSgG ++r +lara+l  ++kl+++DEpt
  gi|242399956|ref|YP_002995381.1| 101 fygiirgipknELEKRLDDIVEMFGLTEHQHKRV----LELSGGLRRRTQLARAFLDpRSKLIFIDEPT 165
                                       **********9999**************999999....*****************98467999*****9 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 8.3
                                       HCEEEE-SS--S-TTSB.HHHH............H CS
                                       xxxxxxxxxxxxxxxxx.xxxx............x RF
                          ABC_tran  59 keigvlpqepqlfpelt.vren............e 80 
                                        ++ v +++ +lfp+l  + +n            +
  gi|242399956|ref|YP_002995381.1| 230 GKVMVTFKK-ELFPQLMgMLSNylkrnnlgkiigK 263
                                       344444444.5555554444444444444444443 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.5   0.00016      0.14       4      19 ..      36      51 ..      33      76 .. 0.85
   2 !   18.0   0.0   2.3e-06     0.002     234     298 ..     134     196 ..      63     201 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00016
                            AAA_21  4 liGpNgsGKSnLLdal 19
                                      + GpNg+GK++L  +l
  gi|242399956|ref|YP_002995381.1| 36 ILGPNGAGKTTLVNIL 51
                                      89**********9998 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 2.3e-06
                            AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrll.ellkelsrngaQviltTHS 298
                                       + elS G +r   l+ a+l+ ++  +l++iDEp +gL+P + +++  +l++e s++g  ++ltT +
  gi|242399956|ref|YP_002995381.1| 134 VLELSGGLRRRTQLARAFLDPRS--KLIFIDEPTLGLDP-IGKKITwDLIREMSKEGYYFVLTTND 196
                                       44679999999666666666665..8*************.44555567777778878888888866 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   1.5   1.4e-07   0.00013      15      41 ..      23      53 ..      10      78 .. 0.84
   2 ?   -1.5   0.1       3.4     3e+03     127     148 ..      72      93 ..      50     148 .. 0.54

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.4e-07
                            AAA_23 15 idF....skgltlItGpNGaGKTTildAikl 41
                                      i++    s+g+  I GpNGaGKTT+++ ++ 
  gi|242399956|ref|YP_002995381.1| 23 INLstdiSSGILSILGPNGAGKTTLVNILTT 53
                                      55555559******************99986 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.4
                            AAA_23 127 skkiilnlilflgqerfeefel 148
                                        kk+i ++i++++q+ +   +l
  gi|242399956|ref|YP_002995381.1|  72 DKKKIREMISLCAQDLELDVLL 93 
                                       3344445555555544322222 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.1   6.6e-05     0.059      18      44 ..      25      51 ..      16     214 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.6e-05
                                      EEEETTSSEEEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 18 vilpfsksftaivGpNGSGKsnlldAi 44
                                       ++++s+++ +i+GpNG+GK+ l++ +
  gi|242399956|ref|YP_002995381.1| 25 LSTDISSGILSILGPNGAGKTTLVNIL 51
                                      567899999************998765 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.1   7.2e-05     0.065      19      55 ..      23      73 ..      16     138 .. 0.69
   2 ?    2.0   0.0      0.15   1.3e+02     322     355 ..     154     187 ..     140     194 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.2e-05
                            AAA_15 19 idlsee....ltvliGkNnsGKSsilealdlFlnnkekkn.............k 55
                                      i+ls +    +  + G+N++GK++++++l   ++ +   +             k
  gi|242399956|ref|YP_002995381.1| 23 INLSTDissgILSILGPNGAGKTTLVNILTTTFKPQ---KgmakifgldvvkdK 73
                                      55555545559999***************8877766...233455555444332 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.15
                            AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandn 355
                                        ++++++i+EP + L p  +k+ ++l++e+++++
  gi|242399956|ref|YP_002995381.1| 154 PRSKLIFIDEPTLGLDPIGKKITWDLIREMSKEG 187
                                       56899*************************9987 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.5     9e-06     0.008      19      50 ..      29      59 ..      20      63 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 9e-06
                            AAA_29 19 idlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                      i+ +g+  + Gp+G+GK+Tl+  +++ + p+k
  gi|242399956|ref|YP_002995381.1| 29 IS-SGILSILGPNGAGKTTLVNILTTTFKPQK 59
                                      44.56899*************99998888876 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   2.2e-05     0.019      24      55 ..      31      62 ..      14     163 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.2e-05
                            AAA_16 24 pelvllsGesGvGKsslvrellralekdggif 55
                                      ++++ + G+ G GK++lv+ l + ++ ++g +
  gi|242399956|ref|YP_002995381.1| 31 SGILSILGPNGAGKTTLVNILTTTFKPQKGMA 62
                                      27999**************9999999885444 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2   7.3e-05     0.065       3      55 ..      36      85 ..      34     209 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.3e-05
                                      EESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCSSSSTTHHHHHHHHHHHHHHH CS
                               AAA  3 lyGppGtGKTllakavakelg..vefleisgsellskyvgesekkirelfkeake 55
                                      + Gp G GKT+l++ + ++++    + +i g +++     + +kkire+++ + +
  gi|242399956|ref|YP_002995381.1| 36 ILGPNGAGKTTLVNILTTTFKpqKGMAKIFGLDVV-----KDKKKIREMISLCAQ 85
                                      67*****************9743446777777777.....666777777665443 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   3.7e-05     0.033       5      37 ..      31      63 ..      28     184 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.7e-05
                            AAA_22  5 agilvvtGesGtGKTtllrrlleqldeeakaee 37
                                       gil + G+ G+GKTtl++ l+ +++ ++  ++
  gi|242399956|ref|YP_002995381.1| 31 SGILSILGPNGAGKTTLVNILTTTFKPQKGMAK 63
                                      5899*****************999976655544 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   2.9e-05     0.026      93     122 ..      25      54 ..      15      82 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.9e-05
                                       HHHHCTTSEEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase  93 lkellkdktsvlvGqSGvGKStLinallpe 122
                                       l++ +++ +  ++G+ G+GK+tL+n l+ +
  gi|242399956|ref|YP_002995381.1|  25 LSTDISSGILSILGPNGAGKTTLVNILTTT 54 
                                       66778889999***************9876 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 ?    9.9   0.0   0.00068      0.61      20      61 ..      31      73 ..      15     140 .. 0.72
   2 ?    0.2   0.0      0.67     6e+02     189     219 ..     168     200 ..     162     205 .. 0.78
   3 ?    0.1   0.1      0.68   6.1e+02      45     121 ..     201     292 ..     194     306 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00068
                          ATPase_2 20 neiyfiYGpegsGKtaLlkeiienl.edkdkyviyyialrees 61
                                      + i+ i Gp g GKt+L++ + +    +k+  +i+  ++ +++
  gi|242399956|ref|YP_002995381.1| 31 SGILSILGPNGAGKTTLVNILTTTFkPQKGMAKIFGLDVVKDK 73
                                      56889*************9998888456677888877776544 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.67
                          ATPase_2 189 vddldketalnflkegfkeleel..skedfeei 219
                                       +d++ k+ ++++++e++ke + +  + +d+ e+
  gi|242399956|ref|YP_002995381.1| 168 LDPIGKKITWDLIREMSKEGYYFvlTTNDMAEV 200
                                       78999999**********997666766666655 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.68
                          ATPase_2  45 edkdkyviyyialreesiskldefie......eeeekkklekal...........giavpkaeleeilk.....eks 99 
                                       e+++++++++ + r +  ++l+ef +                 +           ++ +++++l +i+       + 
  gi|242399956|ref|YP_002995381.1| 201 ESLSDEIVFIHKGRIILHTTLREFKHvyagkvM-------VTFKkelfpqlmgmlSNYLKRNNLGKIIGkdtveLED 270
                                       456677888888888888888888334432220.......2222333455566664555555555554432222455 PP

                          ATPase_2 100 klvfkaielllekikkkgkkii 121
                                       kl+f  + l+l++i  + ++i+
  gi|242399956|ref|YP_002995381.1| 271 KLAFYELLLFLRDIGFDITQIV 292
                                       6666666666666666666655 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.4   0.00014      0.13      16      76 ..      27      87 ..      19     217 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00014
                                      TTSCSEEEEEEESTTSSHHHHHHHHCCSHCCCCCCBTEEEEEEEESXXHHHHHHHXXHHHH CS
                            NB-ARC 16 delqslvvalvGmgGvGKttlakqilnksdevegrFdsvawvvvsktdkseeiletilkeL 76
                                       ++ s ++++ G  G GKttl++     ++  +g   ++   vv ++ k++e++   +++L
  gi|242399956|ref|YP_002995381.1| 27 TDISSGILSILGPNGAGKTTLVNILTTTFKPQKGMAKIFGLDVVKDKKKIREMISLCAQDL 87
                                      567777***************9877777666665555555555555555555555555555 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   9.2e-05     0.082       1      52 [.      36      81 ..      36      92 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.2e-05
                        ATP_bind_1  1 vvGpaGsGKttfvgalseilelrgrsvavvNLDPAaeelpYeaavdirelit 52
                                      ++Gp G+GKtt+v+ l+ +++ ++   ++  LD   +      +  ire+i+
  gi|242399956|ref|YP_002995381.1| 36 ILGPNGAGKTTLVNILTTTFKPQKGMAKIFGLDVVKD------KKKIREMIS 81
                                      68*******************9999999999997776......444666665 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 ?   12.6   0.0   0.00013      0.12       3      45 ..      35      77 ..      34      91 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00013
                                      EEESSTTSSHHHHHHCHCT-CCC-E..EETTTTEEEEEEECGGSG CS
                               Roc  3 vlvGdsgvGKtsllkrfvedkfsek..ekstigvdfltkevtkik 45
                                       ++G +g+GKt+l++ ++  +f+++    +++g+d+++ +  ki+
  gi|242399956|ref|YP_002995381.1| 35 SILGPNGAGKTTLVNILT-TTFKPQkgMAKIFGLDVVKDKK-KIR 77
                                      589***********9888.6666551256788999987653.444 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   0.1   0.00071      0.63      38      83 ..      36      81 ..      23      87 .. 0.90
   2 ?    0.8   0.0      0.33   2.9e+02     103     147 ..     158     201 ..     137     262 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00071
                             AAA_7 38 lvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdiie 83
                                      + Gp G GKt++++ l+++++++k + +++ +    + ++++++i 
  gi|242399956|ref|YP_002995381.1| 36 ILGPNGAGKTTLVNILTTTFKPQKGMAKIFGLDVVKDKKKIREMIS 81
                                      68**********************9999999999999999888885 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.33
                             AAA_7 103 vvFvDDlnmpakekygaqppiellRqlldyggwYdrkklefkeik 147
                                       ++F+D+      +  g++ +  l+R +  +g+++ +++ ++ e++
  gi|242399956|ref|YP_002995381.1| 158 LIFIDEPT-LGLDPIGKKITWDLIREMSKEGYYFVLTTNDMAEVE 201
                                       56777654.357889999999999999999999888766666655 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00033      0.29       4      26 ..      35      58 ..      32      81 .. 0.79
   2 ?   -1.6   0.0       1.9   1.7e+03      33      78 ..     194     249 ..     179     266 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00033
                                      EEEESTTCCHHHHHHHHH.CT--S CS
                              cobW  4 vltGflGsGKTtLlnhll.enrag 26
                                       + G+ G+GKTtL+n l+ + + +
  gi|242399956|ref|YP_002995381.1| 35 SILGPNGAGKTTLVNILTtTFKPQ 58
                                      6889**********9988533444 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.9
                                       ESS-SSCHC.CCCCC.........HCCCT.EEEETTTTECCHCTT-HHHHHHHHHH CS
                              cobW  33 vNefgevsi.Daell.........retgveivelenGciCctlredllkelealee 78 
                                       +N++ ev+    e++         ++t  e  ++  G++  t +++l ++l  +++
  gi|242399956|ref|YP_002995381.1| 194 TNDMAEVESlSDEIVfihkgriilHTTLREFKHVYAGKVMVTFKKELFPQLMGMLS 249
                                       55555543212222233333333333444477777788888888877777766655 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00017      0.15       4      39 ..      34      69 ..      31      87 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00017
                                      EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEEST CS
                             SRP54  4 illvGlqGaGKTttlaKLaallkkegkkvllvaaDt 39
                                      + ++G++GaGKTt +  L   +k ++  + +  +D+
  gi|242399956|ref|YP_002995381.1| 34 LSILGPNGAGKTTLVNILTTTFKPQKGMAKIFGLDV 69
                                      5689******************99988888877776 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00025      0.23      46      72 ..      32      58 ..      19     104 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00025
                             Rad17 46 riLLisGPsGCgkstvvkvLskelgik 72
                                       iL i GP G gk+t v++L+  + ++
  gi|242399956|ref|YP_002995381.1| 32 GILSILGPNGAGKTTLVNILTTTFKPQ 58
                                      4999****************9877665 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00038      0.34       4      22 ..      36      54 ..      34      87 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00038
                            AAA_28  4 itGgestGKTtlleaLaar 22
                                      i+G+ ++GKTtl++ L+ +
  gi|242399956|ref|YP_002995381.1| 36 ILGPNGAGKTTLVNILTTT 54
                                      89**************966 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   0.00045       0.4      20      46 ..      33      60 ..      26     187 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00045
                            AAA_30 20 vavltGpAGtGKttalkalreaweaa.g 46
                                      +  + Gp G+GKtt+++ l+ +++ + g
  gi|242399956|ref|YP_002995381.1| 33 ILSILGPNGAGKTTLVNILTTTFKPQkG 60
                                      56789**************988877744 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       652  (0.0363657); expected 358.6 (0.02)
Passed bias filter:                      579  (0.032294); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 2420.17
//
Query:       gi|242399957|ref|YP_002995382.1|  [L=489]
Description: hypothetical protein TSIB_1984 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      2e-16   60.8   0.0    4.3e-16   59.7   0.0    1.6  1  Radical_SAM  Radical SAM superfamily
    6.2e-11   42.7   2.4    1.6e-10   41.3   0.4    2.5  3  SPASM        Iron-sulfur cluster-binding domain
    1.8e-09   37.7   0.1    6.8e-09   35.9   0.0    2.0  2  PqqD         Coenzyme PQQ synthesis protein D (PqqD)
     0.0084   16.4   0.0       0.23   11.7   0.0    2.5  2  Fer4_12      4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.017   15.4   0.1      0.038   14.2   0.1    1.5  1  DUF4777      Domain of unknown function (DUF4777)


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 !   59.7   0.0   1.2e-19   4.3e-16       3     152 ..     140     285 ..     138     304 .. 0.89

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 1.2e-19
                                       EESEESS--TTTSCCTT.HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTE CS
                                       xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   3 vtrgCnlrCsfCarpet.vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgi 78 
                                        t+ C+l Cs+C+     + + +++ ++ + + l++++e++   g+k + ++gge ++y+d+ + ++++  +     
  gi|242399957|ref|YP_002995382.1| 140 LTERCSLECSYCNMALEaKFKPDDEVIMATGDALRLLDEAR-ALGAKILGISGGEITAYSDIFKVIRHAFDI--GYQ 213
                                       6899**********999888899999999***********6.889*******************99999999..9** PP

                                       EEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  79 ritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivgl 152
                                       ++ + t ++ ++++++erl   g  r++++++++d+e+++kl+  ++t+e  l+++ +l +ag+k   +r ++ 
  gi|242399957|ref|YP_002995382.1| 214 HVIFGTKAVGITKKFAERLYGSGARRIQISIDTLDPETYQKLI-LNGTLESALRGIYNLIDAGFKI-HVRSTIT 285
                                       *******************************************.*********************5.4444433 PP

>> SPASM  Iron-sulfur cluster-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       3.7   1.3e+04      37      45 ..      55      63 ..      53      74 .. 0.83
   2 ?   -0.4   0.0      0.48   1.7e+03      29      39 ..      97     107 ..      86     151 .. 0.65
   3 !   41.3   0.4   4.5e-14   1.6e-10       1      67 [.     360     427 ..     360     433 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 3.7
                             SPASM 37 eesleeIwn 45
                                      e+sle+I n
  gi|242399957|ref|YP_002995382.1| 55 ENSLEDIVN 63
                                      7899**987 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.48
                             SPASM  29 elklGnirees 39 
                                       + klGni++ +
  gi|242399957|ref|YP_002995382.1|  97 KRKLGNITKSK 107
                                       46778885432 PP

  == domain 3  score: 41.3 bits;  conditional E-value: 4.5e-14
                             SPASM   1 CfapsrslfInsdGdVvpCcvd.....kktyveelklGnireesleeIw.nseeyqefrkskkfplielCrnC 67 
                                       C a+  s++  ++G+V++C  d       +y +++++Gn + +sl+eIw ns+ +++fr   k +  ++C++C
  gi|242399957|ref|YP_002995382.1| 360 CSAGILSIAAYPNGNVTLC--DsgrtlMTKYPKKYVFGNFKYQSLKEIWeNSKTLNKFR---KSKFLPPCSEC 427
                                       555566677789*******..6667664567778***************77779*****...44455569999 PP

>> PqqD  Coenzyme PQQ synthesis protein D (PqqD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   0.0   1.9e-12   6.8e-09      22      67 .]      48      93 ..      46      93 .. 0.95
   2 ?   -2.3   0.0       1.7   5.9e+03      39      65 ..     155     183 ..     154     184 .. 0.65

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 1.9e-12
                                      HHHH-SSSS-HHHHHHHHHHHCT--HHHHHHHHHHHHHHHHCTT-- CS
                              PqqD 22 iWklldgersveeivaalaeeydvdeeeaeadvlafldqLrekgli 67
                                      +++l+ ge+s+e+iv  ++++y+v++e+++ dv++f++ +++++++
  gi|242399957|ref|YP_002995382.1| 48 VLRLCTGENSLEDIVNLISQKYEVSKERVKHDVQNFISFMHKNDVL 93
                                      89***************************************99875 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.7
                                       HHHHC.T--HHH..HHHHHHHHHHHHHCTT CS
                              PqqD  39 laeey.dvdeee..aeadvlafldqLrekg 65 
                                       l +++  +d e+  a  d l++ld+ r+ g
  gi|242399957|ref|YP_002995382.1| 155 LEAKFkPDD-EVimATGDALRLLDEARALG 183
                                       677774444.33338889999999887765 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 ?    1.7   0.0     0.082   2.9e+02      56     127 ..       2      77 ..       1      82 [. 0.60
   2 !   11.7   0.0   6.3e-05      0.23      10      87 ..     139     215 ..     132     233 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.082
                           Fer4_12  56 ltllGGEPllpenaeallelvkevkeekp....ekdiwlytgytleelskkekeellkeidvlvdGkfeesledes 127
                                       + +lGG+ +++   +  ++l++    + +    e++ +  t ++++ l+    e+ l+ i  l++ k+e s+e+ +
  gi|242399957|ref|YP_002995382.1|   2 IAILGGDTMEYPILRPDVDLIETNAGAIInkarENKFMFVTYTQFDVLRLCTGENSLEDIVNLISQKYEVSKERVK 77 
                                       5677888777555444445555444433311113344445555555555447888999999999999999998865 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 6.3e-05
                           Fer4_12  10 lfvsgCnlsCkgCfnketwsfksgkef..tkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekp 84 
                                       +++++C+l+C++C      +fk  +e+   +  + ++++++     + l ++GGE  +   ++++ +++++    ++
  gi|242399957|ref|YP_002995382.1| 139 ILTERCSLECSYCNMALEAKFKPDDEVimATGDALRLLDEARALGAKILGISGGEITA---YSDIFKVIRHAFDIGY 212
                                       56899********888777888777772245556678888888888*********998...7888888888777776 PP

                           Fer4_12  85 ekd 87 
                                       + +
  gi|242399957|ref|YP_002995382.1| 213 QHV 215
                                       544 PP

>> DUF4777  Domain of unknown function (DUF4777)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   1.1e-05     0.038      21      48 ..      57      84 ..      55      86 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.1e-05
                           DUF4777 21 TldEivervaerydlseeelkkvVkntL 48
                                      +l+ iv+ ++++y++s+e++k++V+n+ 
  gi|242399957|ref|YP_002995382.1| 57 SLEDIVNLISQKYEVSKERVKHDVQNFI 84
                                      7899*********************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (489 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       872  (0.0486363); expected 358.6 (0.02)
Passed bias filter:                      584  (0.0325729); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.48
# Mc/sec: 3092.49
//
Query:       gi|242399958|ref|YP_002995383.1|  [L=37]
Description: hypothetical protein TSIB_1985 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.44
# Mc/sec: 254.39
//
Query:       gi|242399959|ref|YP_002995384.1|  [L=608]
Description: hypothetical protein TSIB_1988 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.3e-11   45.0   1.1    2.9e-11   43.8   0.1    2.0  2  S_layer_C   S-layer like family, C-terminal region
     0.0079   15.5   0.0      0.014   14.7   0.0    1.3  1  PurA        PurA ssDNA and RNA-binding protein
  ------ inclusion threshold ------
      0.015   15.1   2.3      0.015   15.1   2.3    3.3  3  Beta_helix  Right handed beta helix region
       0.18   11.6   0.1       0.49   10.2   0.1    1.6  1  BRX_N       Transcription factor BRX N-terminal domain


Domain annotation for each model (and alignments):
>> S_layer_C  S-layer like family, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1      0.59   2.6e+03      42      75 ..      57      90 ..      36     117 .. 0.57
   2 !   43.8   0.1   6.5e-15   2.9e-11     152     216 ..     519     582 ..     511     585 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.59
                         S_layer_C 42 leykdeekledkvvglalkykgdkladikdkdkv 75
                                      ++++ +  + + +  l   y++++ + +kd  + 
  gi|242399959|ref|YP_002995384.1| 57 IQNSGKLVIRNATLELLQDYHNNYGIVVKDTSEL 90
                                      4444444445555555555555555555555444 PP

  == domain 2  score: 43.8 bits;  conditional E-value: 6.5e-15
                         S_layer_C 152 i.LvGGPvvNkvtkeLedklkvaityeednksaatiavienaangndvlvvAGsDRegTkaAalal 216
                                       + L+GGPv+N++t+e      v++t+e+++k +++i+       g   l+vAGsDR+gTka ++ l
  gi|242399959|ref|YP_002995384.1| 519 VaLIGGPVANSITNEYMSRFPVEVTNEYPGKGKGVIEAT--IIDGKIYLLVAGSDRWGTKAGVEIL 582
                                       449*******************************98643..345777789***********99977 PP

>> PurA  PurA ssDNA and RNA-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   3.1e-06     0.014     122     191 ..      51     122 ..      38     134 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.1e-06
                              PurA 122 qrqqialPaqGlielrdalteliedygegde..ddeeaelpeeksltvdnkrfyfdvGsnkyGvflrisevk 191
                                       q+ +i++   G + +r+a  el++dy ++     ++++el  e s+   + +f+ +  sn+ Gvf  +s  k
  gi|242399959|ref|YP_002995384.1|  51 QEGNIIIQNSGKLVIRNATLELLQDYHNNYGivVKDTSELVVEDSVITSDYQFHINFHSNSKGVFTGLSSTK 122
                                       678899********************9987666788889998888889999**************9999877 PP

>> Beta_helix  Right handed beta helix region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   2.3   3.4e-06     0.015      12     111 ..      43     144 ..      31     165 .. 0.51
   2 ?    6.7   2.6    0.0013       5.8      13      65 ..     171     225 ..     151     333 .. 0.70
   3 ?    0.4   0.6      0.11   5.1e+02      35      44 ..     320     332 ..     261     455 .. 0.55

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.4e-06
                                       EEESEEEES-SS-SEEE-SSS-.EEES-EEES....-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S--EEES CS
                        Beta_helix  12 tiknntisnsggyGiylrgssnvvienneian....nsgsGiyilgssnntisnntisdnngggialfgasnnlien 84 
                                       +i+++t+       i +++s++ vi+n +++      + +Gi ++ +s+ ++++++i+  ++++i++  +s+ ++ +
  gi|242399959|ref|YP_002995384.1|  43 KIEDMTFLQ--EGNIIIQNSGKLVIRNATLELlqdyHNNYGIVVKDTSELVVEDSVITSDYQFHINFHSNSKGVFTG 117
                                       444444444..444555555555555544443444445555555555555555555555555555555555555555 PP

                                       -EEES-SS-SEE-T.T-S--EEES-EEE CS
                        Beta_helix  85 neitdnggsGiyln.yssnntienNiid 111
                                          t+++   i+l+ +s+ ++i+n+ +d
  gi|242399959|ref|YP_002995384.1| 118 LSSTKRAP-IISLStGSPVLQISNSSFD 144
                                       55555543.3444433444444444444 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0013
                                       EESEEEES-SS-SEEE-SSS-.EEES...-EEES-SS-SEEE-TT..-S-EEES-EEE CS
                        Beta_helix  13 iknntisnsggyGiylrgssnvvien...neiannsgsGiyilgs..snntisnntis 65 
                                       +   +++n  + G+ ++++s   i++    +i++++ +Gi++  +  +++ti+n++i 
  gi|242399959|ref|YP_002995384.1| 171 VGQINVTN-LHEGVNIGNASV--ISDkyvVRIQDSTLDGIWMWTQkdAEVTIKNSYIG 225
                                       44556666.599999999997..55524455666999***999999999999999994 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.11
                                       EEES-EEES...- CS
                        Beta_helix  35 vienneian...n 44 
                                        i+++ei++    
  gi|242399959|ref|YP_002995384.1| 320 FIKDSEISWleiK 332
                                       2223333332220 PP

>> BRX_N  Transcription factor BRX N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00011      0.49      13      23 ..     242     252 ..     241     256 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00011
                             BRX_N  13 IKSLTaQLKdM 23 
                                       +KSLT QLKd+
  gi|242399959|ref|YP_002995384.1| 242 VKSLTPQLKDI 252
                                       9*********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (608 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); 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: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 4144.30
//
Query:       gi|242399960|ref|YP_002995385.1|  [L=240]
Description: 3-isopropylmalate dehydratase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.7e-41  140.9   0.0    6.6e-41  140.7   0.0    1.0  1  PAC2         PAC2 family
  ------ inclusion threshold ------
      0.028   14.3   0.1       0.04   13.8   0.1    1.2  1  EMP24_GP25L  emp24/gp25L/p24 family/GOLD


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 !  140.7   0.0   7.3e-45   6.6e-41       1     212 [.      17     220 ..      17     221 .. 0.94

  Alignments for each domain:
  == domain 1  score: 140.7 bits;  conditional E-value: 7.3e-45
                                       EEEESSCGGGHHHHHHHHHHHHTTEEEEEEEEHCCHSBCCCC.SEEEEETTEEE-SEEEEEETTT.SEEEEEEE... CS
                              PAC2   1 LilGfpgiGnVgqlavdlLiesleaekvgeidsdyllpfvgprpvvlveegrelepprlyakdsgsrdllvlqg... 74 
                                       +i+G+pgiG+Vg++a+++L+ +l++e +g+++s++ lp     p+ l+ eg++ +p r+y k+    +l+v +    
  gi|242399960|ref|YP_002995385.1|  17 FIEGYPGIGLVGHIAANFLAKELNMEMIGYVESPF-LP-----PMSLILEGKPNPPLRFYGKS----NLIVAVAdiy 83 
                                       69*********************************.9*.....9*9**************886....5888888899 PP

                                       E-HSCHHHHHHHHHHHHHHHTTESEEEEEEEEEESS-ES..TTS-.EEEEEESSHHHHHHHHCT.....-CEEEEHH CS
                              PAC2  75 repilqyeefakalldwaeelgvkevvvLggldageradvphtrpekvtgaatdeelleelees.....eyggivgi 146
                                       + p l +e +ak+l++++++++ ++v+ Lgg++ g+      +++ +v+g++ +ee  ++l++      +yg i g+
  gi|242399960|ref|YP_002995385.1|  84 IPPTLVNE-IAKELTSYLKQNNAEKVISLGGMGIGFF-----KEHMEVWGVGGSEEENKDLKNLgvkilKYGSIMGM 154
                                       99999999.************************7776.....5788************99974445668******** PP

                                       HHHHHHHHHHTT-EEEEEEEEEECCC--HHHHHHHHHHHHHHHT---HCHHHHHHHHHHHHHHHHH CS
                              PAC2 147 tglLlsaakergipavgllaevphylpdPkaaaalleflskllglevdtedLeedaeeleeqleel 212
                                       +g Ll +a++++++++ ll+e+ +  pdP aaa ++e+l+kl+ +ev+ e+L ++a+ +eeql ++
  gi|242399960|ref|YP_002995385.1| 155 SGKLLWEASKENLKVYTLLGETFGDRPDPGAAANVIEVLKKLAPIEVSIEPLLKEAQIIEEQLRKM 220
                                       ***************************************************************986 PP

>> EMP24_GP25L  emp24/gp25L/p24 family/GOLD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   4.5e-06      0.04     110     146 ..     200     236 ..     163     238 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.5e-06
                       EMP24_GP25L 110 kekletleselkkleekldsikreqkylrereerlrd 146
                                       + ++e+l +e + +ee+l+++++++++ r+r e+ ++
  gi|242399960|ref|YP_002995385.1| 200 EVSIEPLLKEAQIIEEQLRKMHEQMEFARKRAEKEYE 236
                                       66899999************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       900  (0.050198); expected 358.6 (0.02)
Passed bias filter:                      673  (0.037537); 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: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 1417.87
//
Query:       gi|242399961|ref|YP_002995386.1|  [L=126]
Description: hypothetical protein TSIB_1990 [Thermococcus sibiricus MM 739]
Scores for complete 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  120.8   0.5    3.1e-35  120.6   0.5    1.1  1  DUF473    Protein of unknown function (DUF473)


Domain annotation for each model (and alignments):
>> DUF473  Protein of unknown function (DUF473)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.6   0.5   1.7e-39   3.1e-35       1     114 [.       1     111 [.       1     115 [. 0.96

  Alignments for each domain:
  == domain 1  score: 120.6 bits;  conditional E-value: 1.7e-39
                            DUF473   1 MkvvaLtGiseevieeLkknklrtielrsahNvitllklevgdlvFlTsvsleDltkGteGiiaevlsveistkrvv 77 
                                       M +++L+Gis++++++L++n +rtie+rsa+Nvi++++l+ g+ vFlT+  l+D+t+GteGiiaevl++e +++r+ 
  gi|242399961|ref|YP_002995386.1|   1 MDLLVLAGISRKTLDQLLRNPYRTIEIRSARNVIAIQSLKLGERVFLTYETLQDITQGTEGIIAEVLKIERMEQRIP 77 
                                       899************************************************************************** PP

                            DUF473  78 essesfieErEttvarvqlkllglgrvrevkeeellk 114
                                       ++++   +ErE t++r+ql+l+glg+v e+++e+ + 
  gi|242399961|ref|YP_002995386.1|  78 WEES---DEREQTICRLQLRLKGLGKVIEISTEGEVV 111
                                       ****...***********************9987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); 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: 00:00:00.44
# Mc/sec: 859.40
//
Query:       gi|242399962|ref|YP_002995387.1|  [L=250]
Description: hypothetical protein TSIB_1991 [Thermococcus sibiricus MM 739]
Scores for complete 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-85  285.7   0.1    2.5e-85  285.5   0.1    1.0  1  NucS            Endonuclease NucS
  ------ inclusion threshold ------
      0.016   15.5   0.1       0.15   12.3   0.1    2.1  1  DUF4263         Domain of unknown function (DUF4263)
       0.06   13.3   1.5        0.2   11.6   0.1    2.5  3  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an


Domain annotation for each model (and alignments):
>> NucS  Endonuclease NucS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  285.5   0.1   4.2e-89   2.5e-85       3     223 ..      26     244 ..      24     249 .. 0.97

  Alignments for each domain:
  == domain 1  score: 285.5 bits;  conditional E-value: 4.2e-89
                              NucS   3 avlvvlarCkvsyeGraksrLeegerlivikpdGaflvhkdrkvePvnWqppkssltaevedgslilksirrkpeee 79 
                                       a++ ++arC+vsy Graks+L  g+r+i+ikpdG+fl+h+  k+ePvnWqpp+ss+  ++ +++lil+s+rrkp+e 
  gi|242399962|ref|YP_002995387.1|  26 AIVTIFARCNVSYDGRAKSELGLGDRVIIIKPDGSFLIHQKEKREPVNWQPPGSSVSLKIGEDKLILRSVRRKPKEI 102
                                       7899************************************************************************* PP

                              NucS  80 LkveieevehasayeledveelvldGseaelaeliiehpdLieeGfkpvareyavaiGivdiLgkdeegklvivelk 156
                                       L+v + +v++ s++++ed+e l l Gseae+a+l++e+p+Lie Gfkp+ +e  +  Gi+diLgkd++g++v++e+k
  gi|242399962|ref|YP_002995387.1| 103 LEVGLIDVYLLSYFQAEDYESLALMGSEAEMADLVFENPELIEPGFKPIFKEKSIRHGIIDILGKDKDGNIVVLEFK 179
                                       ***************************************************************************** PP

                              NucS 157 rrkaevdaveqLkryvellkedsvldkvrGvlvapsittdaekllkeeglefkeldppkdskrnids 223
                                       rr+a+++av+qLkryve ++e++   +vrG+lvaps+t++a++ll++eglefk+l ppk+ k+  + 
  gi|242399962|ref|YP_002995387.1| 180 RRRADLHAVSQLKRYVETMREEYK--NVRGILVAPSLTSGAKRLLEKEGLEFKKLTPPKKEKSRKGR 244
                                       ***********************9..*********************************99776555 PP

>> DUF4263  Domain of unknown function (DUF4263)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   2.5e-05      0.15       3      63 ..     129     190 ..     127     220 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.5e-05
                           DUF4263   3 sEkkwqkffeknpwll....ypiisefpik.evdfksDfllidslngnivlvEikkpdknlltkek 63 
                                       sE+++ ++  +np l+    +pi++e +i+  +    D+l +d+ +gniv+ E+k+   +l   ++
  gi|242399962|ref|YP_002995387.1| 129 SEAEMADLVFENPELIepgfKPIFKEKSIRhGI---IDILGKDK-DGNIVVLEFKRRRADLHAVSQ 190
                                       566777777788999999999999999997533...5*******.**********99888766555 PP

>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1      0.11   6.7e+02      24      38 ..      49      62 ..      44      71 .. 0.56
   2 ?   11.6   0.1   3.4e-05       0.2      16      46 .]      69     100 ..      66     100 .. 0.92
   3 ?   -3.6   0.0         2   1.2e+04      24      41 ..     171     179 ..     169     183 .. 0.51

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.11
                                      TCEEEEEECTTCCCC CS
                    MazE_antitoxin 24 Gdevelevdgdkiil 38
                                      Gd+v++ +++d++ l
  gi|242399962|ref|YP_002995387.1| 49 GDRVII-IKPDGSFL 62
                                      666666.66663333 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 3.4e-05
                                       HHHCCEEC.TCEEEEEECTTCCCCCCCHHSXS CS
                    MazE_antitoxin  16 rfelgire.Gdevelevdgdkiilrplkslpk 46 
                                       r++ ++++ G++v l + +dk+ilr ++++pk
  gi|242399962|ref|YP_002995387.1|  69 REPVNWQPpGSSVSLKIGEDKLILRSVRRKPK 100
                                       8999***********************99875 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 2
                                       TCEEEEEECTTCCCCCCC CS
                    MazE_antitoxin  24 Gdevelevdgdkiilrpl 41 
                                       G+         + +l+++
  gi|242399962|ref|YP_002995387.1| 171 GN---------IVVLEFK 179
                                       34.........4555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); 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: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1726.28
//
Query:       gi|242399963|ref|YP_002995388.1|  [L=526]
Description: DNA repair and recombination protein radA [Thermococcus sibiricus MM 739]
Scores for complete 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-86  287.9   0.2    1.2e-70  237.7   0.0    2.1  2  Rad51            Rad51
    7.9e-24   84.1   3.9    1.2e-23   83.6   2.6    2.0  2  Intein_splicing  Intein splicing domain
    1.2e-10   41.8   1.4    1.2e-10   41.8   1.4    2.1  1  HHH_5            Helix-hairpin-helix domain
      3e-07   30.2   0.1      0.011   15.2   0.0    2.4  2  RecA             recA bacterial DNA recombination protein
    6.8e-06   25.6   0.2      0.059   12.7   0.3    2.4  2  ATPase           KaiC
    1.4e-05   25.3   0.0    3.7e-05   23.9   0.0    1.7  1  Cdd1             Pathogenicity locus
    1.4e-05   24.7   2.1     0.0062   16.4   0.1    2.7  2  HHH              Helix-hairpin-helix motif
    0.00043   20.3   3.5     0.0014   18.7   0.1    3.0  3  HHH_2            Helix-hairpin-helix motif
    0.00074   19.8   0.6     0.0017   18.6   0.6    1.6  1  PT-HINT          Pretoxin HINT domain
      0.002   17.9   0.0     0.0078   16.0   0.0    2.1  1  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
     0.0029   17.8   0.0      0.015   15.6   0.0    2.3  1  IMS_HHH          IMS family HHH motif
     0.0069   16.0   0.1      0.041   13.5   0.1    2.0  2  AAA_25           AAA domain
  ------ inclusion threshold ------
      0.022   15.2   0.1      0.083   13.3   0.0    2.0  1  BAF              Barrier to autointegration factor
      0.024   15.0   0.6       0.31   11.5   0.1    2.7  2  HHH_8            Helix-hairpin-helix domain
       0.22   10.6   0.8        4.2    6.4   0.3    2.1  2  PAXNEB           PAXNEB 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 !   47.9   0.4   8.5e-16     1e-12       3      51 ..     106     154 ..     104     161 .. 0.95
   2 !  237.7   0.0     1e-73   1.2e-70      51     254 ..     322     526 .]     319     526 .] 0.96

  Alignments for each domain:
  == domain 1  score: 47.9 bits;  conditional E-value: 8.5e-16
                                       -EBHHHHHHHHHSS-EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHH CS
                             Rad51   3 fvsavellekrsellqlttGskklDelLgGGietgsiteifGefrsGkt 51 
                                       f+ a e+ +kr  + ++ttGsk+lD+lLgGGiet++++e+fGef+sGk 
  gi|242399963|ref|YP_002995388.1| 106 FMRADEYFQKRAVVGKITTGSKSLDKLLGGGIETQAVSEVFGEFGSGKC 154
                                       89999******************************************96 PP

  == domain 2  score: 237.7 bits;  conditional E-value: 1e-73
                                       HHHHHHHHHHTTS-TTTS--SSEEEEEESSS---GGGGHHHHHHTT--HHHHGGGEEEEE--STTHHHHHHHHTHHH CS
                             Rad51  51 tqlchtlcvtvqlplelgGgegkavyidtegtfrperlveiaerykldkeevlenvayaRaytiehqeellqqaaal 127
                                       tql+htl+v+vq p e gG +g +v+idte tfrper+ +iae  ++d++evl+n+ +aRa++++hq+ l+++a + 
  gi|242399963|ref|YP_002995388.1| 322 TQLAHTLAVIVQKPPEEGGLNGSVVWIDTENTFRPERIKQIAESRGMDPDEVLKNIYVARAFNSNHQMLLVEKAEEI 398
                                       9**********************************************************************998877 PP

                                       H.....HHS-EEEEEEETTTGGGCH-------THHHHHHHHHHHHHHHHHHHHH--EEEEEEE-------.------ CS
                             Rad51 128 l.....aedkfallivDsvtalyRtdfsgrgelakRqqklgkllrtLrkladefevavvitnqvvaqvdgqaalfsa 199
                                       +     +e+ ++ll+vDs+t ++R+++ grg la+Rqqkl+k+l  L++la+ +++av++tnqv+a++d+    f +
  gi|242399963|ref|YP_002995388.1| 399 IkeklpSEKPVKLLVVDSLTGHFRSEYVGRGTLAERQQKLAKHLADLHRLANLYDIAVFVTNQVQARPDA----FFG 471
                                       62222245789***********************************************************....99* PP

                                       ------HHHHHHHH-SEEEEEEE-STTEEEEEEES-SSS-S-EEEEEEETTEEE- CS
                             Rad51 200 dpkkPigGlvlahasttRlalrkgkgeeRivkvvdsPnlpeleavfaigeeGied 254
                                       dp++PigG++lah++t+R++lrkgk  +R+++++dsP+lpe ea fai+e+G+ed
  gi|242399963|ref|YP_002995388.1| 472 DPTRPIGGHILAHSATVRVYLRKGKAGKRVARLIDSPHLPEGEAAFAITEKGVED 526
                                       *****************************************************87 PP

>> Intein_splicing  Intein splicing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.6   2.6   9.7e-27   1.2e-23      10     134 .]     172     321 ..     161     321 .. 0.87
   2 ?   -2.7   0.0       4.3   5.1e+03      64      79 ..     385     401 ..     375     414 .. 0.77

  Alignments for each domain:
  == domain 1  score: 83.6 bits;  conditional E-value: 9.7e-27
                                       EEHHHHCC..................ECTTEEEEEETTTTEEEEEEEEEEEEEEEEEEEEEEETTS-EEEEETT-EE CS
                                       xxxxxxxx..................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Intein_splicing  10 vkieelve..................kegeevlslnledlklevksvkkliklklkelyeiklesgrkikaTpeHkl 68 
                                        +iee+++                   e  +v   n+++ k+e+ +v+ + k k+++l+++kl+ g ++k+T+ H++
  gi|242399963|ref|YP_002995388.1| 172 ESIEEMYNkyatkngeipfdngfavpLEVVSVYTFNIKTRKVEKTKVSYIYKEKVSTLVKLKLSTGIELKVTQSHPV 248
                                       4677777777777777777666665555566788899**************************************** PP

                                       EECCT.TEEEEEECCC--TT-EEEEE.......HSCEEEEEEEEEEEEECEEEEEEEEETTT-EEEE.CTTEEE- CS
                                       xxxxx.xxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx RF
                   Intein_splicing  69 lvvrd.egivEkradeLkegdliavp.......dadvvwdkvksievedeeeyVYdltvednhNFva.ngiivHN 134
                                       lv++d  ++   +a+e++ gd ++         + ++ +++v+s+e  d+++yVYdl v+++hNF+a ng+i+HN
  gi|242399963|ref|YP_002995388.1| 249 LVFKDgLKW--IKASEVQIGDRVVGIgevppksEVNLRFHQVESVEIFDYNDYVYDLVVPETHNFIApNGLILHN 321
                                       *********..8***********977888898788899************************************9 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4.3
                                       TT-EEEECCT.TEEEEE CS
                                       xxxxxxxxxx.xxxxxx RF
                   Intein_splicing  64 peHkllvvrd.egivEk 79 
                                       ++H++l v++ e+i+  
  gi|242399963|ref|YP_002995388.1| 385 SNHQMLLVEKaEEIIKE 401
                                       78999999777777644 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.8   1.4   9.9e-14   1.2e-10       3      57 .]      45      99 ..      43      99 .. 0.95

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 9.9e-14
                                      HHHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHHHH CS
                             HHH_5  3 eLlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriilelkd 57
                                      ++ +++G+Gp+tA +l +aG++s+e++a a++ eL ++ G+++  A +ii+++++
  gi|242399963|ref|YP_002995388.1| 45 SIEDLPGVGPATAEKLREAGYDSLEAIAVASPLELKELAGVSEGAALKIIQAARE 99
                                      56799************************************************96 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0     6e-05     0.071      26      68 ..     114     155 ..      89     191 .. 0.76
   2 !   15.2   0.0   9.2e-06     0.011     117     226 ..     393     499 ..     324     507 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6e-05
                                       -.-----EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHH CS
                              RecA  26 keklkvetissGslaldialGiGGlpkGriieiyGpessGktt 68 
                                       +++  v  i++Gs +ld  lG GG+    + e++G   sGk  
  gi|242399963|ref|YP_002995388.1| 114 QKRAVVGKITTGSKSLDKLLG-GGIETQAVSEVFGEFGSGKCF 155
                                       33456889*************.******************964 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 9.2e-06
                                       HHHHHHH.HHHHTTT--SEEEEE-TTT---STT-----------HHHHHHHHHHHHHHHHHTTT--EEEEEEE---- CS
                              RecA 117 eqaleia.dalvrsgaidlivvdsvaalvpkaeieGemgdskvglqarlmsqalrkltgaisksntvvifinqirek 192
                                       e+a ei+ ++l     + l+vvds++    ++e  G     +++ + + +++ l  l    +  +++v   nq++ +
  gi|242399963|ref|YP_002995388.1| 393 EKAEEIIkEKLPSEKPVKLLVVDSLTGHF-RSEYVG---RGTLAERQQKLAKHLADLHRLANLYDIAVFVTNQVQAR 465
                                       66777652556666789******998765.555444...33444444556788888888888888999999****** PP

                                       -------------HHHHHHH-SEEEEEEEES--- CS
                              RecA 193 iGvmfgnpetttGGralkfyasvrldvrrieeik 226
                                           fg+p    GG+ l   a+vr+ +r+ ++ k
  gi|242399963|ref|YP_002995388.1| 466 PDAFFGDPTRPIGGHILAHSATVRVYLRKGKAGK 499
                                       ****************************987655 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.3   4.9e-05     0.059       2      33 ..     123     154 ..     122     162 .. 0.93
   2 !   10.4   0.0   0.00025       0.3      51     200 ..     345     505 ..     338     525 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.9e-05
                            ATPase   2 ktgIeglDeilkgGipegrvvlitGepGtGKt 33 
                                        tg + lD++l gGi  ++v  + Ge G+GK 
  gi|242399963|ref|YP_002995388.1| 123 TTGSKSLDKLLGGGIETQAVSEVFGEFGSGKC 154
                                       7999***************************7 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00025
                            ATPase  51 gvfvtveepa..edlrenakslGwdlekleeegklaiidasesaeesaeekdkedleelieela.eaikeikakrvv 124
                                       +v + +e +   e +++ a+s G+d +++ ++  +++  a++s+++         +e+  e ++ +  +e+ +k +v
  gi|242399963|ref|YP_002995388.1| 345 VVWIDTENTFrpERIKQIAESRGMDPDEVLKN--IYVARAFNSNHQM------LLVEKAEEIIKeKLPSEKPVKLLV 413
                                       56677776545599******************..9999999998773......33444444444044568889**** PP

                            ATPase 125 iDsitgl..aye.......ekeavaReilrqlvrvlkklgvTailvsekss.........seeaaggygveefivdg 183
                                       +Ds+tg+  +++       e+++++ + l  l r l++l+  a++v+++ +           + +gg+ +++ +++ 
  gi|242399963|ref|YP_002995388.1| 414 VDSLTGHfrSEYvgrgtlaERQQKLAKHLADLHR-LANLYDIAVFVTNQVQarpdaffgdPTRPIGGHILAH-SATV 488
                                       *****99422221111111233333333444433.3334444444444333477777766567777777777.7777 PP

                            ATPase 184 vivLdlkeieeelvRtl 200
                                        + L++ ++ +++ R +
  gi|242399963|ref|YP_002995388.1| 489 RVYLRKGKAGKRVARLI 505
                                       77777777777777766 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   3.1e-08   3.7e-05       2      43 ..      40      81 ..      39      90 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 3.1e-08
                              Cdd1  2 rkalkelqdiPniGkalaedlvelGirsveelkgedpeelye 43
                                      +k++k+++d+P++G+a+ae+l+e G+ s+e ++  +p el e
  gi|242399963|ref|YP_002995388.1| 40 KKEIKSIEDLPGVGPATAEKLREAGYDSLEAIAVASPLELKE 81
                                      67899********************************99965 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   5.2e-06    0.0062      11      29 ..      44      62 ..      37      63 .. 0.87
   2 !    7.3   0.4     0.004       4.7       1      28 [.      67      94 ..      67      96 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 5.2e-06
                                      HHHHTSTT-SHHHHHHHHH CS
                               HHH 11 eeLlalPGVGpktAeaIls 29
                                      + +++lPGVGp+tAe+ ++
  gi|242399963|ref|YP_002995388.1| 44 KSIEDLPGVGPATAEKLRE 62
                                      67899**********9875 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.004
                                      SHHHHHTSSHHHHHTSTT-SHHHHHHHH CS
                               HHH  1 sleglipasreeLlalPGVGpktAeaIl 28
                                      sle++  as+ eL++l GV +  A +I+
  gi|242399963|ref|YP_002995388.1| 67 SLEAIAVASPLELKELAGVSEGAALKII 94
                                      7999*****************9998887 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.43   5.1e+02      22      36 ..      19      33 ..      16      36 .. 0.89
   2 !   18.7   0.1   1.2e-06    0.0014       9      60 ..      50     102 ..      48     105 .. 0.91
   3 ?   -1.8   0.1       2.9   3.5e+03      17      31 ..     436     450 ..     433     455 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.43
                             HHH_2 22 rFksldaLkkaslee 36
                                      +F++ldaL + s+ee
  gi|242399963|ref|YP_002995388.1| 19 EFEELDALDELSVEE 33
                                      89********99998 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 1.2e-06
                             HHH_2   9 rhVGektAklLakr.FksldaLkkasleeLlevddiGeeiAqsivefFenekn 60 
                                       + VG +tA++L ++ ++sl+a++ as  eL e+ ++ e  A +i++  ++ +n
  gi|242399963|ref|YP_002995388.1|  50 PGVGPATAEKLREAgYDSLEAIAVASPLELKELAGVSEGAALKIIQAAREAAN 102
                                       78*********9866*****************************998887776 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 2.9
                             HHH_2  17 klLakrFksldaLkk 31 
                                       ++Lak+  +l +L++
  gi|242399963|ref|YP_002995388.1| 436 QKLAKHLADLHRLAN 450
                                       679999999998875 PP

>> PT-HINT  Pretoxin HINT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.6   1.4e-06    0.0017      21      94 ..     204     275 ..     201     322 .. 0.66

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.4e-06
                           PT-HINT  21 lakdeasgkvaekpvlarygneyqelvylkisdgignsevlisnkihPfys..k.gkfieakelkvGdklldesGkv 94 
                                        + + ++ kv +  v   y ++   lv lk+s gi     l+ ++ hP  +  +  k+i+a e++ Gd+++   G+v
  gi|242399963|ref|YP_002995388.1| 204 YTFNIKTRKVEKTKVSYIYKEKVSTLVKLKLSTGIE----LKVTQSHPVLVfkDgLKWIKASEVQIGDRVVG-IGEV 275
                                       56688899999999*******************985....7888889864421458*************974.2333 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 !   16.0   0.0   6.5e-06    0.0078       8      29 ..      51      72 ..      41      82 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 6.5e-06
                   DNA_pol_lambd_f  8 GVGpktAkkwyakGirtledlr 29
                                      GVGp+tA+k+ ++G+ +le + 
  gi|242399963|ref|YP_002995388.1| 51 GVGPATAEKLREAGYDSLEAIA 72
                                      9******************885 PP

>> IMS_HHH  IMS family HHH motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.2e-05     0.015      12      31 ..      45      64 ..      41      65 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.2e-05
                           IMS_HHH 12 pitkipGiGgklgekLeklG 31
                                      +i ++pG+G+ ++ekL+  G
  gi|242399963|ref|YP_002995388.1| 45 SIEDLPGVGPATAEKLREAG 64
                                      799*************9887 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.66   7.9e+02      12      48 ..     119     155 ..     110     158 .. 0.85
   2 !   13.5   0.1   3.4e-05     0.041      70     188 ..     341     461 ..     322     465 .. 0.67

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.66
                            AAA_25  12 vadlaapppprrwlvkgllpagelallaGapgtGKtt 48 
                                       v+++ +  +++++l++g +  ++++ ++G  g+GK +
  gi|242399963|ref|YP_002995388.1| 119 VGKITTGSKSLDKLLGGGIETQAVSEVFGEFGSGKCF 155
                                       5667777888999**********************87 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 3.4e-05
                            AAA_25  70 eqgkVlyvsaEdsedelrrRlravgeal..rddarllvldlagveslpLfakdrggtlltadvdaleaaieevegvr 144
                                        +g V+++++E++    ++R++++ e +  ++d+ l  +++a+      f + +++ l++ + + + +++ + + v+
  gi|242399963|ref|YP_002995388.1| 341 LNGSVVWIDTENTF--RPERIKQIAESRgmDPDEVLKNIYVARA-----FNSNHQMLLVEKAEEIIKEKLPSEKPVK 410
                                       489**********8..7899999995554499999999998886.....44444555565554445556666455** PP

                            AAA_25 145 lvviDplsralgg.......densnsdvgalvealeriarrtgaavllvhH 188
                                       l+v+D+l+  ++          +++ + ++ +++l r+a  +++av+++ +
  gi|242399963|ref|YP_002995388.1| 411 LLVVDSLTGHFRSeyvgrgtLAERQQKLAKHLADLHRLANLYDIAVFVTNQ 461
                                       *******98766644433222233333577778888888888888887765 PP

>> BAF  Barrier to autointegration factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   6.9e-05     0.083      18      41 ..      44      67 ..      38      74 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.9e-05
                               BAF 18 KevtalaGigevlgkkLeekGfdk 41
                                      K++++l+G+g+  ++kL+e+G+d 
  gi|242399963|ref|YP_002995388.1| 44 KSIEDLPGVGPATAEKLREAGYDS 67
                                      99********************96 PP

>> HHH_8  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00026      0.31      40      65 ..      41      62 ..      12      63 .. 0.78
   2 ?    0.7   0.1      0.57   6.8e+02      41      66 ..      72      96 ..      66      98 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00026
                                      S-HHHHTTHCTTSTT--HHHHHHHHH CS
                             HHH_8 40 eeitsleeeltklpgiGkkiaakiee 65
                                      +ei+    ++++lpg+G+++a+k++e
  gi|242399963|ref|YP_002995388.1| 41 KEIK----SIEDLPGVGPATAEKLRE 62
                                      2344....4799************99 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.57
                                      -HHHHTTHCTTSTT--HHHHHHHHHH CS
                             HHH_8 41 eitsleeeltklpgiGkkiaakieei 66
                                      +++s  e l++l g+ ++ a ki + 
  gi|242399963|ref|YP_002995388.1| 72 AVASPLE-LKELAGVSEGAALKIIQA 96
                                      4556555.9**************875 PP

>> PAXNEB  PAXNEB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.3    0.0035       4.2      20      34 ..     123     137 ..     120     143 .. 0.90
   2 ?    2.2   0.0     0.067        80      42      87 ..     362     405 ..     358     411 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0035
                            PAXNEB  20 StGtpsLDklLgGGL 34 
                                        tG++sLDklLgGG+
  gi|242399963|ref|YP_002995388.1| 123 TTGSKSLDKLLGGGI 137
                                       69************8 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.067
                            PAXNEB  42 ieEdgttdfakvLlkyFlAeGvvqkhevlvlsldddpeewlreLPg 87 
                                       i E++ +d  +vL  +++A    ++h++l++     +e + ++LP+
  gi|242399963|ref|YP_002995388.1| 362 IAESRGMDPDEVLKNIYVARAFNSNHQMLLVEK--AEEIIKEKLPS 405
                                       889999*********************999987..67777788997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (526 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       805  (0.0448993); expected 358.6 (0.02)
Passed bias filter:                      631  (0.0351944); 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):              15  [number of targets reported over threshold]
# CPU time: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.49
# Mc/sec: 3255.43
//
Query:       gi|242399964|ref|YP_002995389.1|  [L=333]
Description: Calcium-gated potassium channel protein [Thermococcus sibiricus MM 739]
Scores for complete 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-18   65.3   0.6    8.7e-18   64.7   0.6    1.4  1  TrkA_N           TrkA-N domain
    1.6e-16   60.0  12.1    3.4e-16   59.0  12.1    1.5  1  Ion_trans_2      Ion channel
    0.00043   19.6  10.3    0.00088   18.6  10.3    1.5  1  Ion_trans        Ion transport protein
     0.0085   16.1   4.5       0.01   15.8   3.8    1.5  1  ABC2_membrane_4  ABC-2 family transporter protein
  ------ inclusion threshold ------
      0.018   14.9   0.1      0.027   14.4   0.1    1.2  1  NAD_binding_10   NAD(P)H-binding
      0.024   14.6   0.0       0.28   11.2   0.0    2.2  2  Castor_Poll_mid  Castor and Pollux, part of voltage-gated ion


Domain annotation for each model (and alignments):
>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.7   0.6   2.9e-21   8.7e-18      15     115 ..     134     241 ..     120     242 .. 0.84

  Alignments for each domain:
  == domain 1  score: 64.7 bits;  conditional E-value: 2.9e-21
                                       HHHHHTT.......EEEEEEESSHHHHHHHH.HTTSEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHHHHHHHH CS
                            TrkA_N  15 eeLsegg.......kdvvvidkdeerveelr.eeglevvvgdatdeevLeeagiekadaviaatgddeanilavlla 83 
                                        eL+++        k+++v+  de+  ++l+ +e++e+++g+ t++e+Le+a+i++a++v+ a+gdd ++++++l++
  gi|242399964|ref|YP_002995389.1| 134 LELRDAIsngqaenKPIIVVLPDENERKKLTlAEEIEIIIGEFTNKETLERANIKDASYVLLALGDDSESVFVTLMI 210
                                       5554432345567778********99999975888****************************************** PP

                                       HHHTSSSEEEEEESSGGGHHHHHHHTTSEEEE CS
                            TrkA_N  84 kelnpkkkiiaraqdpehaellkklgadvvis 115
                                       k+l + +k+ ++a + e + llk++gad+vi+
  gi|242399964|ref|YP_002995389.1| 211 KQLSN-AKVFVEALKHESVSLLKQAGADRVIT 241
                                       *9888.79**********************96 PP

>> Ion_trans_2  Ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.0  12.1   1.1e-19   3.4e-16       4      77 ..      30     100 ..      24     102 .. 0.85

  Alignments for each domain:
  == domain 1  score: 59.0 bits;  conditional E-value: 1.1e-19
                                       HHTCHHHHHHHHT....T---HHHHHHHHHHHHTTS----SSTT-----HHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Ion_trans_2   4 llvlifgaviysleegwekwsfldalYfsfvtltTiGYGdivpetdagrlftivyillGlalfalflavlgkvl 77 
                                       +l+ ++ a++y++    e+  f++alY++++t+ TiGYGdi+p t +gr+++i+  + G+a+f++f+++l++++
  gi|242399964|ref|YP_002995389.1|  30 VLLALVLALLYMY---AENVGFFTALYWAVITMATIGYGDITPSTLLGRIIAIFASIAGIATFTAFVSILAEYF 100
                                       3444444455555...5677**************************************************9987 PP

>> Ion_trans  Ion transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6  10.3   2.9e-07   0.00088     178     237 ..      47     100 ..       4     106 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.9e-07
                                       SHHHHHHHHHHHHTTSSHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Ion_trans 178 nfftallwlfrlmttegwgdilyatldekskvaliyfvifiilgsflllNlliaviadnf 237
                                        fftal+w++ +m t+g+gdi++ tl ++      + +if  ++++ ++  ++ + a++f
  gi|242399964|ref|YP_002995389.1|  47 GFFTALYWAVITMATIGYGDITPSTLLGR------IIAIFASIAGIATFTAFVSILAEYF 100
                                       49***************************......******************9999998 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 !   15.8   3.8   3.5e-06      0.01       8      70 ..      16      83 ..      14      90 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.5e-06
                   ABC2_membrane_4  8 Klkrskivwllvlaallvpllallyfnllgktgldpaefys...lsvfgftll...lllplilgiiasy 70
                                      Klkrsk++ l+++++ll+ +lally+ ++++ g+++a +     ++++g++ +   +ll  i++i+as+
  gi|242399964|ref|YP_002995389.1| 16 KLKRSKLFALALAVVLLALVLALLYM-YAENVGFFTALYWAvitMATIGYGDItpsTLLGRIIAIFASI 83
                                      *************************7.6899**999877552223455555445557888888888875 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1     9e-06     0.027      28      96 ..     156     242 ..     137     257 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 9e-06
                                       THHHCHHHHCTTTCEEEE--TT-CCHHHHH.HTT-SEEEES---TCC.........HHHH..........HHHHHHH CS
                    NAD_binding_10  28 npeklaeleaeeglevvegdvtdvedlaea.lkgadaVvsalggggk.........deeg..........aknivda 84 
                                       ++++ ++l  +e++e++ g++t++e+l++a +k+a+ V+ alg +++         +                 v  
  gi|242399964|ref|YP_002995389.1| 156 DENERKKLTLAEEIEIIIGEFTNKETLERAnIKDASYVLLALGDDSEsvfvtlmikQ--LsnakvfvealKHESVSL 230
                                       555555666679***************99868**********988877766555431..155334444444444666 PP

                                       HHHCT--EEEEE CS
                    NAD_binding_10  85 akeagvkRfvlv 96 
                                       +k+ag  R+++ 
  gi|242399964|ref|YP_002995389.1| 231 LKQAGADRVITS 242
                                       777777777765 PP

>> Castor_Poll_mid  Castor and Pollux, part of voltage-gated ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.13   3.8e+02      24      92 ..     108     178 ..     101     189 .. 0.68
   2 ?   11.2   0.0   9.4e-05      0.28      32      88 ..     275     330 ..     244     333 .] 0.77

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.13
                   Castor_Poll_mid  24 lLnfeknefylkelpelegkkyedvllafqeavviGikvassgkiylnPeddev..lqegdkl.lviaeddd 92 
                                       +++ +k +f  + +    g + e++ll++ +a+  G    ++  i++ P+++e   l+  +++ ++i+e ++
  gi|242399964|ref|YP_002995389.1| 108 MMGMHKVKFKGHYVIMGRGESIESALLELRDAISNGQ-AENKPIIVVLPDENERkkLTLAEEIeIIIGEFTN 178
                                       5666666666666666678888999999999999998.5555888899988764226666666455566555 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 9.4e-05
                   Castor_Poll_mid  32 fylkelpelegkkyedvllafqeavviGikvassgkiylnPeddevlqegdkllvia 88 
                                       +   ++pe+eg+k++++   + +     i  ++  +i+l P  d+++ ++ kllvi 
  gi|242399964|ref|YP_002995389.1| 275 ITSMRIPEVEGMKFGEAFNILYNRGLFLI-GYATDEIHLMPPLDTIIPNNAKLLVIK 330
                                       556789*********99877666554445.345589*******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1221  (0.068102); expected 358.6 (0.02)
Passed bias filter:                      654  (0.0364772); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 2106.42
//
Query:       gi|242399965|ref|YP_002995390.1|  [L=202]
Description: hypothetical protein TSIB_1994 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      513  (0.0286129); 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: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 1169.99
//
Query:       gi|242399966|ref|YP_002995391.1|  [L=335]
Description: hypothetical protein TSIB_1995 [Thermococcus sibiricus MM 739]
Scores for complete 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-07   30.2   0.5    7.5e-07   29.5   0.5    1.3  1  PIN_4     PIN 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 !   29.5   0.5   4.2e-11   7.5e-07       4     126 ..     112     248 ..     109     253 .. 0.68

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 4.2e-11
                             PIN_4   4 DTnvlLhdpe.alksfkeehdvviPitVleELdklKkgsse.......relarlarqanrlldellekesgrlkvqt 72 
                                       DTn l h +   +k + e  ++ i   V +E+++  + +          ++ ++    +++ +  ++k+ +   +  
  gi|242399966|ref|YP_002995391.1| 112 DTNLLYHAFLsKIKGI-EGVQIAIVDLVKKEVENAMNFKYSpahlrelGRILHNSHLLQEFSNRRMKKSRKATYIAL 187
                                       9**9999864157888.9***************99888886655633323333333333333333444332222222 PP

                             PIN_4  73 s.aeelpeee.......seseknDnrIlavalelkeekpdrkvvLvskDinlrikAkalgie 126
                                       +  e+l+++        ++ ++nD+ I+++  e+++++  + vvL++ Di +   A+++g+e
  gi|242399966|ref|YP_002995391.1| 188 ReYEKLKDKIievksidEKTNTNDELIIKTLKEFDKNT-PSLVVLLTADIAMTDIARIEGVE 248
                                       234444432134555544478***************99.69*******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1069  (0.0596241); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); 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 0.35s 00:00:00.94 Elapsed: 00:00:00.51
# Mc/sec: 1962.19
//
Query:       gi|242399967|ref|YP_002995392.1|  [L=159]
Description: hypothetical protein TSIB_1996 [Thermococcus sibiricus MM 739]
Scores for complete 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   27.6   0.0    1.4e-06   27.4   0.0    1.1  1  Cas_Cas02710  CRISPR-associated protein (Cas_Cas02710)
     0.0045   16.6   0.2     0.0055   16.3   0.2    1.1  1  Cas_DxTHG     CRISPR-associated (Cas) DxTHG family
      0.009   14.7   0.0       0.01   14.5   0.0    1.1  1  DUF1887       Domain of unknown function (DUF1887)


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 !   27.4   0.0   2.4e-10   1.4e-06       6      91 ..      23     115 ..      19     134 .. 0.79

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 2.4e-10
                                       HHHHH--SEEEEEE-TGGGGGHHHHH.......HHH-S-...EEEEE--TT-HHHHHHHHHHHHHHS..TTS-EEEE CS
                      Cas_Cas02710   6 sIaelrPerVvflasekSekkleevk.......ealgkklkqevlldedandllelykkikevleka.leeeevivD 74 
                                        ++++rP+++++++ +  e kl++ +       ea+g ++k+++++ ++ +++le+ +ki ++l+    ++ e+++D
  gi|242399967|ref|YP_002995392.1|  23 VMNGYRPDKIYIFLENTHEGKLPQTVealkiisEAYGFSPKIYWEI-IEEDNFLEADEKIGTLLKTLkENKYEIAMD 98 
                                       57899********998888888776622223335555555556665.55689*************9977889***** PP

                                       -SSS-HHHHHHHHHHHH CS
                      Cas_Cas02710  75 lTgGtkeMtaglalagi 91 
                                       +T+G+k+  +g+a+ + 
  gi|242399967|ref|YP_002995392.1|  99 ITSGKKALVVGAAIHAL 115
                                       ************99775 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 !   16.3   0.2   9.1e-07    0.0055      43     172 ..      27     156 ..      10     158 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 9.1e-07
                         Cas_DxTHG  43 edpdkvvilltdtladkeaeekeeaaklkeeleelle......iekvd.veiipgggteeelwe...ifekllekle 109
                                       + pdk++i+l         e k     l + +e l++      ++++   eii     e++++e    + +ll+ l+
  gi|242399967|ref|YP_002995392.1|  27 YRPDKIYIFLEN-----THEGK-----LPQTVEALKIiseaygFSPKIyWEIIE----EDNFLEadeKIGTLLKTLK 89 
                                       455677777777.....44444.....333333333333333333333233333....3444445666667888888 PP

                         Cas_DxTHG 110 en.deiilDiThGfrylPvlallalaylrnvknltikgiyYgaf..keeeedPil.......dlteflelsdw 172
                                       en  ei +DiT+G   l v+ ++++a       l+i++++Y ++   e ++ P++       +l++f+e + w
  gi|242399967|ref|YP_002995392.1|  90 ENkYEIAMDITSGKKAL-VVGAAIHALP-----LEIEHLFYLSLqdIEHSNRPYMmiplhvqRLKDFMEGRRW 156
                                       88799************.6666665555.....8889999999999999999999888888888888776655 PP

>> DUF1887  Domain of unknown function (DUF1887)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   1.7e-06      0.01      21     102 ..      24     110 ..       3     130 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.7e-06
                           DUF1887  21 ldkelkpehl.vlivteaq...kekanrlekvlkekgidvei.feledevdleeleeslkglleelka.aeevvlNv 91 
                                       + ++ +p+++ ++++++++    ++++ l+ + +  g + +i  e+ +e+++ e +e++  ll+ lk  + e+++ +
  gi|242399967|ref|YP_002995392.1|  24 M-NGYRPDKIyIFLENTHEgklPQTVEALKIISEAYGFSPKIyWEIIEEDNFLEADEKIGTLLKTLKEnKYEIAMDI 99 
                                       3.4889999746777766666667788899999999999887359**********************9889****** PP

                           DUF1887  92 tgGtklmalga 102
                                       t G+k   +ga
  gi|242399967|ref|YP_002995392.1| 100 TSGKKALVVGA 110
                                       *****999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1147.67
//
Query:       gi|242399968|ref|YP_002995393.1|  [L=153]
Description: hypothetical protein TSIB_1997 [Thermococcus sibiricus MM 739]
Scores for 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  108.4   0.7    3.6e-31  108.1   0.7    1.0  1  DUF2284   Predicted metal-binding protein (DUF2284)
  ------ inclusion threshold ------
      0.058   13.3   0.2       0.32   10.9   0.0    1.9  2  ADH_N     Alcohol dehydrogenase GroES-like domain


Domain annotation for each model (and alignments):
>> DUF2284  Predicted metal-binding protein (DUF2284)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.1   0.7     4e-35   3.6e-31       3     139 ..       9     137 ..       7     145 .. 0.95

  Alignments for each domain:
  == domain 1  score: 108.1 bits;  conditional E-value: 4e-35
                           DUF2284   3 idaedivveervrlkCekgCknYgknlsCPPavptveefrkilkeYkkallvqtkaeledeeddkeemkevkeelek 79 
                                       i a+di++++r ++kC+  C+ Y kn sCPP++p+ +e+++ +k+Y+k ll+++++++e+ +d+       k+e+ +
  gi|242399968|ref|YP_002995393.1|   9 ILAKDIKISPRPIWKCR-SCPAYAKNPSCPPYTPSWKETKELMKHYEKTLLIKFEVDPEKFDDE-------KREVLT 77 
                                       7799*************.**************************************99877776.......999*** PP

                           DUF2284  80 illelekeafeagypkalalsagsCtlCetCayeegepCrhpekarpsmealGidvfkta 139
                                        ll+ e+e+f++g   ala+++g C++C++C+ +++++C+ p+k+r s+ ++Gi++++++
  gi|242399968|ref|YP_002995393.1|  78 YLLNREQELFKNGNFYALAFFPGDCNYCKECEFKKTKKCKIPTKVRFSIDGVGIELSSIV 137
                                       *************99****************************************99887 PP

>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0     0.073   6.6e+02      59      75 ..      16      32 ..       7      52 .. 0.81
   2 ?   10.9   0.0   3.6e-05      0.32      65      94 ..     100     129 ..      80     141 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.073
                                      EEE-SEEE-SSSHHHHT CS
                             ADH_N 59 VvvepliscgeCaaCke 75
                                      +   p+++c +C+a  +
  gi|242399968|ref|YP_002995393.1| 16 ISPRPIWKCRSCPAYAK 32
                                      55678899999998765 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 3.6e-05
                                       EE-SSSHHHHTT-GGG-TTBEETTTSS-SS CS
                             ADH_N  65 iscgeCaaCkegeenlCeeakllgvsldGg 94 
                                         c+ C++C+ ++++ C+  + + +s+dG 
  gi|242399968|ref|YP_002995393.1| 100 GDCNYCKECEFKKTKKCKIPTKVRFSIDGV 129
                                       45**********************999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       909  (0.0507); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1166.05
//
Query:       gi|242399969|ref|YP_002995394.1|  [L=242]
Description: Short-chain alcohol dehydrogenase [Thermococcus sibiricus MM 739]
Scores for complete 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-56  189.2   0.8    9.5e-56  189.0   0.8    1.0  1  adh_short_C2   Enoyl-(Acyl carrier protein) reductase
    2.2e-54  183.9   0.9    2.7e-54  183.6   0.9    1.1  1  adh_short      short chain dehydrogenase
    2.8e-14   53.5   0.5      9e-14   51.8   0.2    1.7  2  KR             KR domain
    4.8e-05   22.9   0.4    0.00049   19.6   0.1    2.1  2  Epimerase      NAD dependent epimerase/dehydratase family
     0.0007   18.9   0.4     0.0013   18.1   0.4    1.5  1  THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase,
  ------ inclusion threshold ------
      0.024   14.0   0.0      0.035   13.5   0.0    1.2  1  PALP           Pyridoxal-phosphate dependent enzyme
      0.071   12.5   2.3       0.11   11.9   0.2    2.2  3  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,


Domain annotation for each model (and alignments):
>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.0   0.8   3.7e-59   9.5e-56       1     232 [.      12     238 ..      12     239 .. 0.95

  Alignments for each domain:
  == domain 1  score: 189.0 bits;  conditional E-value: 3.7e-59
                                       TTTTSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSE..EEE--TTSHHHHHHHHHHHHHHHSSEEEEE CS
                      adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgae..vlecDVtdeeqvealveevvekfgklDilv 74 
                                       Ga +gIGraiA +l ++G++v++ + ++ + +k++eel +++g e  v+++DV+++++v+++ e++  kfg++Dilv
  gi|242399969|ref|YP_002995394.1|  12 GASRGIGRAIAVSLSQKGCNVAINYSKDVEgAKKTEELCKAHGVEtlVVKADVSNRSEVRNMLEKIITKFGRIDILV 88 
                                       999***************************9************77666***************************** PP

                                       E-----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSCCEEEEEEEGGGTSB.STTTT.HHHHHHHHHH CS
                      adh_short_C2  75 nnagiapklkgpfletsreefdraldvnlyslfllakaalplmkeggsivnlssvgaerv.vpnyn.aygaaKaale 149
                                       nnagi  k  ++ +e++++++dr+l+vnl+++f +++++l++mk+ g+i+n++s++++    p+   +y+a+K++l+
  gi|242399969|ref|YP_002995394.1|  89 NNAGILGK-ASNPMEITDDDWDRVLNVNLKGAFIVSQEVLKYMKR-GKIINIASIAGKGEiSPHVGaHYSASKGGLI 163
                                       ********.8888******************************86.89*******887653677778********** PP

                                       HHHHHHHHHHGGGTEEEEEEEE--BHCTGGGGSTTHHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEE CS
                      adh_short_C2 150 altrylAvelgpkgiRvNavspgpikTlaasgikgfdelleelearaplgrlgtpeevaeaalfLasdeasyitGqt 226
                                       alt +lA++l+p  i vNav+pg ++T++ ++++     +e l++ +  g++++pe++a+a++fL+ ++   itG++
  gi|242399969|ref|YP_002995394.1| 164 ALTFNLARHLAP-HILVNAVAPGSVETELIEDAD-----KESLKKLTLTGKIANPEDIAHAVIFLLEND--QITGEI 232
                                       ************.9***************98887.....67889999*******************987..8***** PP

                                       EEESTT CS
                      adh_short_C2 227 lvvDgG 232
                                       + v+gG
  gi|242399969|ref|YP_002995394.1| 233 IDVNGG 238
                                       *****9 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.6   0.9   1.1e-57   2.7e-54       1     192 [.       6     197 ..       6     200 .. 0.94

  Alignments for each domain:
  == domain 1  score: 183.6 bits;  conditional E-value: 1.1e-57
                                       SEEEEESTTSHHHHHHHHHHHHTT-EEEE.EESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHS CS
                         adh_short   1 kvvlvtGassGIGraiakelakeGakvvv.vdrseekleevakelkeegakalaiqvDvtdreevealvekavkklg 76 
                                       kv+lvtGas+GIGraia  l ++G++v++ +++  e ++++ + +k++g + l++++Dv++r+ev++++ek++ k+g
  gi|242399969|ref|YP_002995394.1|   6 KVALVTGASRGIGRAIAVSLSQKGCNVAInYSKDVEGAKKTEELCKAHGVETLVVKADVSNRSEVRNMLEKIITKFG 82 
                                       89***************************99999999*9999999*99***************************** PP

                                       SESEEEE---S.S--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGG..TSB-TTBHHHH CS
                         adh_short  77 kldvLvnNAGi.tgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvag..kvpvagvaaYs 150
                                       ++d+LvnNAGi  + ++  e+++++w+rv++vNl+g+f ++++vl++m+   +G+I+n++S+ag  + +  ++a Ys
  gi|242399969|ref|YP_002995394.1|  83 RIDILVNNAGIlGKASNPMEITDDDWDRVLNVNLKGAFIVSQEVLKYMK---RGKIINIASIAGkgEISPHVGAHYS 156
                                       ***********87788888****************************98...9**********943455678899** PP

                                       HHHHHHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHHCT CS
                         adh_short 151 AsKaavagltrslakelaptgirvnavaPGlvdTdmakelre 192
                                       AsK+++++lt +la+ lap+ i vnavaPG v+T++ +++ +
  gi|242399969|ref|YP_002995394.1| 157 ASKGGLIALTFNLARHLAPH-ILVNAVAPGSVETELIEDADK 197
                                       *******************9.**************9887665 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.8   0.2   3.5e-17     9e-14       3     139 ..       8     143 ..       6     159 .. 0.84
   2 ?   -0.4   0.0      0.37   9.6e+02       7      32 ..     160     185 ..     152     232 .. 0.57

  Alignments for each domain:
  == domain 1  score: 51.8 bits;  conditional E-value: 3.5e-17
                                       EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHS CS
                                KR   3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaee 79 
                                        l+tG+  g+G+++a  l +kg +  +  s++ +    +k++ + ++a+g+e  vv+aDvs++++v+++le+i +++
  gi|242399969|ref|YP_002995394.1|   8 ALVTGASRGIGRAIAVSLSQKGCNVAINYSKDVE---GAKKTEELCKAHGVETLVVKADVSNRSEVRNMLEKIITKF 81 
                                       59*****************************933...333344555678**************************** PP

                                       S---EEEE--------.-TTT--HHHHHHHHTTTTHHHHHHHHHTTT.S--SEEEEEEEHHH CS
                                KR  80 ppikGvihaAgvlrdk.lleemtaedleqvlapKvkGawnLhelled.esldffvlfSSiag 139
                                       ++i   ++ Ag+l ++   +e t++d+++vl+  +kGa  + + + +  +   ++ ++Siag
  gi|242399969|ref|YP_002995394.1|  82 GRIDILVNNAGILGKAsNPMEITDDDWDRVLNVNLKGAFIVSQEVLKyMKRGKIINIASIAG 143
                                       *************86516799*****************999764444377777888888876 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.37
                                       TTTSHHHHHHHHHHHHHHS-EEEEE- CS
                                KR   7 GGlGgLGlelarwlaekgarhlvlls 32 
                                       GGl +L   lar+la +   + v  +
  gi|242399969|ref|YP_002995394.1| 160 GGLIALTFNLARHLAPHILVNAVAPG 185
                                       66666666666666655433333333 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1   1.9e-07   0.00049       1     115 [.       8     140 ..       8     157 .. 0.69
   2 ?    1.7   0.0     0.059   1.5e+02     215     238 ..     212     233 ..     150     236 .. 0.60

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.9e-07
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC........EEEE--TT-HH....HHHHHHHHH.T CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl........elveldltdrs....alerlfkee.q 64 
                                       +lVtGa+  iG+a++  l +kg +v    ++  +++++ +e l         +v++d+ +rs     le+++ ++ +
  gi|242399969|ref|YP_002995394.1|   8 ALVTGASRGIGRAIAVSLSQKGCNVAINYSKDVEGAKKTEE-LckahgvetLVVKADVSNRSevrnMLEKIITKFgR 83 
                                       59********************9976666664444444433.458999*99999********444445667777889 PP

                                       -SEEEE--S.---HHHHHHSHHHHHH....HHTHHHHHHHHHHHHHTCT.EEEEEEE CS
                         Epimerase  65 pdavihlAa.vggvaassedpadfie....knlqgtlnlleaarkagvk.rllflsS 115
                                       +d+ ++ A+  g  ++ +e   d ++     nl+g+  + +++ k+  + +++++ S
  gi|242399969|ref|YP_002995394.1|  84 IDILVNNAGiLGKASNPMEITDDDWDrvlnVNLKGAFIVSQEVLKYMKRgKIINIAS 140
                                       999999999666666666655554431111666666666666666644445565555 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.059
                                       HHHHHHHHHHHHHHHTT-STTEEE CS
                         Epimerase 215 veDvaeaillvlehvdagdkgeiy 238
                                        eD+a a++++le+ d+  +gei+
  gi|242399969|ref|YP_002995394.1| 212 PEDIAHAVIFLLEN-DQ-ITGEII 233
                                       68999999999999.43.466665 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 !   18.1   0.4     5e-07    0.0013      33     100 ..       2      66 ..       1      93 [. 0.85

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 5e-07
                                       --TT-EEEEE---TTTHHHHHHHHHCTT-EEEEE-TTSCCHHHHHCCSSEEEE-SS-TT-B-GGGS-T CS
                     THF_DHG_CYH_C  33 elegkkvvvvGrsnivgkplallLleknatVtvchsktkdlaeitreadivvvavGkpelikaemvke 100
                                       el+gk ++v G+s+ +g+++a+ L++k++ V +  sk  + a++t   + ++ a G+  l+ +  v++
  gi|242399969|ref|YP_002995394.1|   2 ELKGKVALVTGASRGIGRAIAVSLSQKGCNVAINYSKDVEGAKKT---EELCKAHGVETLVVKADVSN 66 
                                       799*****************************9888775555544...44888888888887777765 PP

>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.4e-05     0.035      56     155 ..       7     109 ..       2     123 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.4e-05
                                       SEEEEEBSSHHHHHHHHHHHHHT-EEEEEEETTS-..HHHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHH.STTCE CS
                              PALP  56 ktvveassGNhgralAaaaallGlkvtivvpadas..pekvallrllGaevvevggdydeavaaaaelaae.gegay 129
                                         +v++ s   gra+A   +  G+ v i  ++d+   +   +l++++G e  +v+ d+ ++ ++ ++++++ ++++ 
  gi|242399969|ref|YP_002995394.1|   7 VALVTGASRGIGRAIAVSLSQKGCNVAINYSKDVEgaKKTEELCKAHGVETLVVKADVSNRSEV-RNMLEKiITKFG 82 
                                       55666666669************************5557779************9999999998.444444488888 PP

                                       E--TTTSHHHHHHHHTHHHHHH.HHTT CS
                              PALP 130 lvsqfdnptviegygtiglEil.eqlg 155
                                        ++   n ++i+g ++  +Ei  ++++
  gi|242399969|ref|YP_002995394.1|  83 RIDILVNNAGILGKASNPMEITdDDWD 109
                                       888888999999999999999656665 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   4.2e-05      0.11      33      94 ..       2      64 ..       1      80 [. 0.89
   2 ?   -0.7   0.0      0.31   7.9e+02     108     127 ..     121     139 ..     112     141 .. 0.71
   3 ?   -3.7   0.0       2.6   6.5e+03     136     153 ..     218     235 ..     216     236 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.2e-05
                                      -GTTSEEEEES-SH.HHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-SE CS
                      2-Hacid_dh_C 33 elsgktvGiiGlGr.IGqavakrlkafgmkviaydrskkkeeeeeelgvelvsleellaesDi 94
                                      el+gk   + G+ r IG+a+a  l++ g++v +   +  + +++ e+ ++ + +e+l+ ++D+
  gi|242399969|ref|YP_002995394.1|  2 ELKGKVALVTGASRgIGRAIAVSLSQKGCNVAINYSKDVEGAKKTEELCKAHGVETLVVKADV 64
                                      7999999****9988****************98777777666777778899********9997 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.31
                                       SBSHHHHHCSTTTEEEEESS CS
                      2-Hacid_dh_C 108 linaeelakmkkgailiNta 127
                                       ++++e l+ mk+g  +iN+a
  gi|242399969|ref|YP_002995394.1| 121 IVSQEVLKYMKRGK-IINIA 139
                                       67778888888776.56665 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 2.6
                                       HHHHHHHTTSCCEEEES- CS
                      2-Hacid_dh_C 136 aLleaLksgkiagaalDv 153
                                       a++  L++ +i g  +Dv
  gi|242399969|ref|YP_002995394.1| 218 AVIFLLENDQITGEIIDV 235
                                       778889999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); 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: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 1608.95
//
Query:       gi|242399970|ref|YP_002995395.1|  [L=178]
Description: Phospholipid-binding protein, PBP family [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.9e-32  110.0   0.0    1.2e-31  109.7   0.0    1.0  1  PBP       Phosphatidylethanolamine-binding protein


Domain annotation for each model (and alignments):
>> PBP  Phosphatidylethanolamine-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.7   0.0   6.8e-36   1.2e-31       2     132 .]      38     175 ..      37     175 .. 0.96

  Alignments for each domain:
  == domain 1  score: 109.7 bits;  conditional E-value: 6.8e-36
                                       --GGG..CSBGGS-EEEEES--TTSSEEEEEEEETTSCCTCTTEEEEEEEEEETTSSEE-TTC............EE CS
                               PBP   2 lpkky..egentsPplswsdvpegtksyalvviDpDapkvsetflHwvvtnipasvtslpega............vq 64 
                                       +p+ky  eg ++sPpl++ ++ +++ +  ++v DpDap v++ f+Hwv++nip  ++++peg             vq
  gi|242399970|ref|YP_002995395.1|  38 IPSKYacEGADISPPLKLGGLSDEAVTIGIIVDDPDAP-VGT-FTHWVAWNIP-PTSEIPEGVpkekvvetpikmVQ 111
                                       78999999******************************.888.*********9.7889***9999************ PP

                                       -B-TTSSCCCCS---B--STTS..EEEEEEEEEESSSG--BGSS-SHHHHHHHHCTTEEEEEEEEEEE CS
                               PBP  65 gknslgeesesgYlgpcPpkgdgkHrYvfllyaldvealdlkagftraelgaaiaghvlakatlagnY 132
                                       g+n++g+   +gY gpcPp g+g H+Y+f++y +d++ l+lk+g+t+++l++a++gh+++  +l+g Y
  gi|242399970|ref|YP_002995395.1| 112 GRNDFGR---IGYNGPCPPRGHGVHHYHFKVYVIDTT-LNLKPGATKKDLERAMKGHIIQFGELVGLY 175
                                       *******...***********************9999.589**********************99988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        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 0.30s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1092.13
//
Query:       gi|242399971|ref|YP_002995396.1|  [L=157]
Description: hypothetical protein TSIB_2000 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00063   20.0   0.8        1.4    9.3   0.1    3.7  4  TPR_12           Tetratricopeptide repeat
     0.0019   18.2   1.6        1.5    9.1   0.1    3.7  4  TPR_2            Tetratricopeptide repeat
     0.0025   17.6   3.3       0.15   11.9   0.1    3.7  4  TPR_1            Tetratricopeptide repeat
     0.0096   15.6   0.4      0.013   15.3   0.4    1.1  1  TPR_21           Tetratricopeptide repeat-like domain
  ------ inclusion threshold ------
      0.011   16.0   0.1          3    8.1   0.3    3.0  3  ANAPC3           Anaphase-promoting complex, cyclosome, subun
      0.012   16.3   0.5          5    8.2   0.0    3.3  3  TPR_14           Tetratricopeptide repeat
      0.026   14.5   0.1       0.23   11.5   0.0    2.3  2  TPR_3            Tetratricopeptide repeat
      0.029   14.9   0.5        2.2    8.9   0.1    2.7  3  TPR_19           Tetratricopeptide repeat
      0.035   14.1   0.5       0.11   12.5   0.2    1.8  1  SRP_TPR_like     Putative TPR-like repeat
      0.062   13.6   0.0        1.1    9.6   0.0    2.9  3  PPR              PPR repeat
      0.091   12.7   0.1        5.7    6.9   0.0    3.2  4  Clathrin_H_link  Clathrin-H-link


Domain annotation for each model (and alignments):
>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.21   3.4e+02      18      36 ..       3      21 ..       1      38 [. 0.52
   2 ?    3.5   0.0     0.052        85      26      65 ..      23      61 ..      20      62 .. 0.68
   3 !    9.3   0.1   0.00084       1.4      13      67 ..      51     100 ..      47     102 .. 0.80
   4 ?    3.9   0.0      0.04        66       6      30 ..     114     138 ..     109     140 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.21
                            TPR_12 18 rydeAlellekaleiarrl 36
                                      ++ ++++l+e++  +++r 
  gi|242399971|ref|YP_002995396.1|  3 EWYQSRALYETVSKLINRG 21
                                      5666666666665555443 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.052
                            TPR_12 26 lekaleiarrllGpdhpltattlrnLgrly.ralgryeeAl 65
                                      l  aleia+++  pd+   a ++        r++ +y+eAl
  gi|242399971|ref|YP_002995396.1| 23 LTNALEIAQSI--PDKGIRAKSMSMVTVEMaRKRMNYKEAL 61
                                      67899999999..8888888877766555324444666665 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.00084
                            TPR_12  13 lrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlel 67 
                                        r++ +y eAle   ka+  +     ++++++  +l  L+  +++l+ry+eAl++
  gi|242399971|ref|YP_002995396.1|  51 ARKRMNYKEALEKTIKAILDI-----ENYENVTKALMSLAFEFLELKRYDEALKI 100
                                       566777888877777776666.....77788999******************976 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.04
                            TPR_12   6 lnnlaavlrrlgrydeAlellekal 30 
                                       + +++++l+r g+ +eA+++ +  l
  gi|242399971|ref|YP_002995396.1| 114 QAEVGLALAREGKIQEAFKIINDIL 138
                                       5458999999999999999876655 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       3.5   5.7e+03      13      22 ..      19      28 ..      15      31 .. 0.67
   2 ?    1.2   0.1      0.31   5.1e+02      16      27 ..      56      67 ..      51      69 .. 0.79
   3 !    9.1   0.1   0.00093       1.5       2      22 ..      79      99 ..      78     101 .. 0.91
   4 ?    4.4   0.0     0.029        47       6      22 ..     116     132 ..     111     139 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3.5
                             TPR_2 13 klgdyeeAle 22
                                      ++gd+  Ale
  gi|242399971|ref|YP_002995396.1| 19 NRGDLTNALE 28
                                      6677777765 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.31
                             TPR_2 16 dyeeAleafekA 27
                                      +y+eAle   kA
  gi|242399971|ref|YP_002995396.1| 56 NYKEALEKTIKA 67
                                      799999876666 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.00093
                             TPR_2  2 ealynlGlayyklgdyeeAle 22
                                      +al+ l+   ++l++y+eAl+
  gi|242399971|ref|YP_002995396.1| 79 KALMSLAFEFLELKRYDEALK 99
                                      68999**************97 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.029
                             TPR_2   6 nlGlayyklgdyeeAle 22 
                                       + Gla+++ g+ +eA +
  gi|242399971|ref|YP_002995396.1| 116 EVGLALAREGKIQEAFK 132
                                       579************76 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       2.5   4.1e+03      16      29 ..      22      28 ..      18      31 .. 0.57
   2 ?    2.2   0.1      0.11   1.8e+02      12      22 ..      52      62 ..      50      68 .. 0.77
   3 !   11.9   0.1   9.1e-05      0.15       2      22 ..      79      99 ..      78      99 .. 0.94
   4 ?    1.3   0.1      0.21   3.5e+02       8      20 ..     118     130 ..     112     132 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.5
                                      -HHHHHHHHHHHHH CS
                             TPR_1 16 kydeAleyyekALe 29
                                      ++         ALe
  gi|242399971|ref|YP_002995396.1| 22 DLTN-------ALE 28
                                      4444.......555 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.11
                                      HHTT-HHHHHH CS
                             TPR_1 12 fklgkydeAle 22
                                      +k  +y+eAle
  gi|242399971|ref|YP_002995396.1| 52 RKRMNYKEALE 62
                                      57789999998 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 9.1e-05
                                      HHHHHHHHHHHHTT-HHHHHH CS
                             TPR_1  2 kalynlGnayfklgkydeAle 22
                                      kal  l+  +++l++ydeAl+
  gi|242399971|ref|YP_002995396.1| 79 KALMSLAFEFLELKRYDEALK 99
                                      799****************97 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 0.21
                                       HHHHHHTT-HHHH CS
                             TPR_1   8 GnayfklgkydeA 20 
                                       G+a+ + gk +eA
  gi|242399971|ref|YP_002995396.1| 118 GLALAREGKIQEA 130
                                       999*********9 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.4   7.7e-06     0.013      38     165 ..       6     130 ..       2     145 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 7.7e-06
                            TPR_21  38 eAsalYqqlqeaveakdaakakeaaeeladeyggtaYaalaaLllAkaaveagdlaaA.kaqLewvlekakdeelka 113
                                       +  alY+++ +  +++d ++a e a+++ d+  + +  ++ +   A++ ++ +   +A +++++++l+ ++ e++++
  gi|242399971|ref|YP_002995396.1|   6 QSRALYETVSKLINRGDLTNALEIAQSIPDKGIRAKSMSMVTVEMARKRMNYK---EAlEKTIKAILDIENYENVTK 79 
                                       6789***************************9999888888888888877655...441566666677666666555 PP

                            TPR_21 114 larlRLarvllaekkydeAlktLeakkeeafaalvaelrGDilvaqgkldeA 165
                                        a + La   l+ k ydeAlk     k+ + +++++   G +l+++gk++eA
  gi|242399971|ref|YP_002995396.1|  80 -ALMSLAFEFLELKRYDEALKIAGFIKDISNRSKIQAEVGLALAREGKIQEA 130
                                       .8899*****************999999999999999999999999999999 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.17   2.8e+02      33      76 ..      17      61 ..       5      63 .. 0.75
   2 ?    8.1   0.3    0.0018         3      48      78 ..      70     100 ..      50     104 .. 0.67
   3 ?    3.1   0.0     0.068   1.1e+02      30      52 ..     118     141 ..     105     154 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.17
                                      HHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHH CS
                            ANAPC3 33 lylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAi 76
                                      l ++g+ + A+e++++  ++  + +   +++ + + k  +y+eA+
  gi|242399971|ref|YP_002995396.1| 17 LINRGDLTNALEIAQSIpDKGIRAKSMSMVTVEMARKRMNYKEAL 61
                                      678899999999999997777777777777777777777777776 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0018
                                       CTSHHHC-HHHHHHHHHHHHHTT-HHHHHHH CS
                            ANAPC3  48 kaklnskslgcrylfAqcllkLkkyeeAiaa 78 
                                       + + +++  ++++ +A   l+Lk+y+eA+++
  gi|242399971|ref|YP_002995396.1|  70 DIENYENVTKALMSLAFEFLELKRYDEALKI 100
                                       2233455559999999999*********987 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.068
                                       HHHHHHTT-HHHHHHHHHCT.SHH CS
                            ANAPC3  30 AlclylngqykrAyellrka.kln 52 
                                       +l+l + g+ ++A++++++  + +
  gi|242399971|ref|YP_002995396.1| 118 GLALAREGKIQEAFKIINDIlDDD 141
                                       78999***********99885555 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0       0.4   6.4e+02       3      27 ..       9      33 ..       7      52 .. 0.79
   2 ?    2.9   0.1      0.16   2.6e+02       3      23 ..      80     100 ..      78     101 .. 0.84
   3 ?    8.2   0.0     0.003         5       5      36 ..     115     146 ..     112     154 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.4
                            TPR_14  3 allalaeallalGdpdeAiallrra 27
                                      al++ ++ l ++Gd+  A+++++ +
  gi|242399971|ref|YP_002995396.1|  9 ALYETVSKLINRGDLTNALEIAQSI 33
                                      666667778999****999998765 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.16
                            TPR_14   3 allalaeallalGdpdeAial 23 
                                       al+ la  +l+l ++deA+++
  gi|242399971|ref|YP_002995396.1|  80 ALMSLAFEFLELKRYDEALKI 100
                                       6778888899********986 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.003
                            TPR_14   5 lalaeallalGdpdeAiallrralalaPddae 36 
                                       ++ + al++ G+ +eA ++ +++l+++ + ++
  gi|242399971|ref|YP_002995396.1| 115 AEVGLALAREGKIQEAFKIINDILDDDVKTWA 146
                                       566889******************99877665 PP

>> TPR_3  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00014      0.23       3      21 ..      80      98 ..      78     100 .. 0.91
   2 ?   -0.1   0.0      0.62     1e+03       9      20 ..     119     130 ..     117     132 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00014
                                      HHHHHHHHHHHTT-HHHHH CS
                             TPR_3  3 ylysyAaefynkkkyqeAr 21
                                       l+s+A+ef   k+y+eA+
  gi|242399971|ref|YP_002995396.1| 80 ALMSLAFEFLELKRYDEAL 98
                                      59****************7 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.62
                                       HHHHHTT-HHHH CS
                             TPR_3   9 aefynkkkyqeA 20 
                                        ++   +k+qeA
  gi|242399971|ref|YP_002995396.1| 119 LALAREGKIQEA 130
                                       5667789****9 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.072   1.2e+02      35      52 ..      17      34 ..       6      39 .. 0.64
   2 ?    3.1   0.1     0.084   1.4e+02      27      47 ..      80     100 ..      53     102 .. 0.68
   3 ?    8.9   0.1    0.0013       2.2       2      57 ..      89     143 ..      88     152 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.072
                            TPR_19 35 llalgqldeAealLdalp 52
                                      l++ g+l+ A ++ + +p
  gi|242399971|ref|YP_002995396.1| 17 LINRGDLTNALEIAQSIP 34
                                      445555555555555555 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.084
                            TPR_19  27 arllLAeallalgqldeAeal 47 
                                       a++ LA   l+l+++deA ++
  gi|242399971|ref|YP_002995396.1|  80 ALMSLAFEFLELKRYDEALKI 100
                                       555556667888999999876 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0013
                            TPR_19   2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                       l+ ++y+eAl++   + ++  + + +++    al   g ++eA +++++++++d +
  gi|242399971|ref|YP_002995396.1|  89 LELKRYDEALKIAGFI-KDISNRSKIQAEVGLALAREGKIQEAFKIINDILDDDVK 143
                                       677899***9999996.888889999999999999****************99987 PP

>> SRP_TPR_like  Putative TPR-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   6.9e-05      0.11      22      75 ..      86     141 ..      62     154 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.9e-05
                      SRP_TPR_like  22 valiklekyeeaLkllkkgsa..lsedvrfEkaYvlYklkkykkalkilkkveaee 75 
                                         +++l +y+eaLk++   +     ++++ E   +l +  k ++a ki++ + +++
  gi|242399971|ref|YP_002995396.1|  86 FEFLELKRYDEALKIAGFIKDisNRSKIQAEVGLALAREGKIQEAFKIINDILDDD 141
                                       4578999******976555440045678899999**************99887664 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       2.1   3.4e+03      12      30 ..      19      37 ..      14      38 .. 0.74
   2 ?   -0.6   0.0       1.2     2e+03      14      22 ..      92     100 ..      86     101 .. 0.82
   3 ?    9.6   0.0   0.00069       1.1       9      29 ..     120     140 ..     119     142 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2.1
                               PPR 12 knGkleeAlelfkeMkekG 30
                                        G+l  Ale+ + + +kG
  gi|242399971|ref|YP_002995396.1| 19 NRGDLTNALEIAQSIPDKG 37
                                      6799999999877776666 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.2
                               PPR  14 GkleeAlel 22 
                                        +++eAl++
  gi|242399971|ref|YP_002995396.1|  92 KRYDEALKI 100
                                       789***986 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00069
                               PPR   9 gycknGkleeAlelfkeMkek 29 
                                       +++++Gk++eA++++++++++
  gi|242399971|ref|YP_002995396.1| 120 ALAREGKIQEAFKIINDILDD 140
                                       799************998876 PP

>> Clathrin_H_link  Clathrin-H-link
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0    0.0035       5.7      14      40 ..      15      41 ..       9      43 .. 0.88
   2 ?   -0.9   0.0      0.95   1.5e+03      18      27 ..      53      62 ..      40      67 .. 0.76
   3 ?    0.8   0.0      0.29   4.7e+02      16      29 ..      88     101 ..      78     106 .. 0.84
   4 ?   -0.9   0.0      0.98   1.6e+03      18      28 ..     123     133 ..     120     137 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0035
                   Clathrin_H_link 14 eqllaqgnykeAakvAaespqgiLRtp 40
                                      ++l+++g+  +A ++A + p + +R +
  gi|242399971|ref|YP_002995396.1| 15 SKLINRGDLTNALEIAQSIPDKGIRAK 41
                                      689*****************9999975 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.95
                   Clathrin_H_link 18 aqgnykeAak 27
                                      +++nykeA +
  gi|242399971|ref|YP_002995396.1| 53 KRMNYKEALE 62
                                      6789*99975 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.29
                   Clathrin_H_link  16 llaqgnykeAakvA 29 
                                       +l+ ++y eA k+A
  gi|242399971|ref|YP_002995396.1|  88 FLELKRYDEALKIA 101
                                       566789*******9 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 0.98
                   Clathrin_H_link  18 aqgnykeAakv 28 
                                       ++g+++eA+k+
  gi|242399971|ref|YP_002995396.1| 123 REGKIQEAFKI 133
                                       68999***998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1080  (0.0602376); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1170.24
//
Query:       gi|242399972|ref|YP_002995397.1|  [L=42]
Description: hypothetical protein TSIB_2001 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       132  (0.00736237); expected 358.6 (0.02)
Passed bias filter:                      121  (0.00674884); 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: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 314.53
//
Query:       gi|242399973|ref|YP_002995398.1|  [L=188]
Description: Transmembrane electron transport protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.041   13.3  14.7       0.05   13.1  14.7    1.1  1  LysE         LysE type translocator


Domain annotation for each model (and alignments):
>> LysE  LysE type translocator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1  14.7   2.8e-06      0.05      15     191 ..       4     186 ..       1     188 [] 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.8e-06
                              LysE  15 lkqgikrgfkggilvalgvligdavlillgllGlalLlkaapivlsilrllGgayLlwlgvlalrdakekkveae.k 90 
                                       ++ ++k+ + +  + a+g++ + a++i   +lG+ l++      +  ++++G++  ++ g+  +   +ek+     k
  gi|242399973|ref|YP_002995398.1|   4 IALSLKENISKRKIYAVGLAFVAAIYISYYILGVGLVIL---TKTIPIWIAGAVAIAFGGYTFITGYLEKSRIVGkK 77 
                                       556777777777888999999999999999999999888...44667888888888888888888887776554414 PP

                              LysE  91 sve.......aslvkpflkglllsls....NPkailfwlsvisallakaeqygdagrlilaaglvvasliwfsllaf 156
                                       +v+       a++   f+ g+l+s++       ++l ++ +is ++    + + + + ++ +++++  li ++ ++ 
  gi|242399973|ref|YP_002995398.1|  78 EVRrnifrkeATIFGAFSLGVLISFTllpcSAGTYLAYAILISKVGR---TLTLILLALYNIIFILPLLIILFTMGS 151
                                       444667778899************96433345566666667777766...7888888888888888888******** PP

                              LysE 157 laarlsrrlsskkvlriinvvvgvlligfavklll 191
                                       +++  s +++  +++r +++ +g++li++++++++
  gi|242399973|ref|YP_002995398.1| 152 ITESKSISQKIVQRSRELSMAAGAILIALGIYIII 186
                                       *******************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       960  (0.0535445); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); 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):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1351.50
//
Query:       gi|242399974|ref|YP_002995399.1|  [L=111]
Description: Glutaredoxin-related protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 741.67
//
Query:       gi|242399975|ref|YP_002995400.1|  [L=48]
Description: hypothetical protein TSIB_2004 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 360.44
//
Query:       gi|242399976|ref|YP_002995401.1|  [L=176]
Description: hypothetical protein TSIB_2005 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-14   53.8   5.2    5.4e-08   33.2   0.2    2.3  2  CBS       CBS domain
  ------ inclusion threshold ------
        0.1   11.7   0.0       0.11   11.5   0.0    1.1  1  DHC_N2    Dynein heavy chain, N-terminal region 2


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 !   22.6   1.0   1.2e-08   0.00011       3      52 ..      18      69 ..      16      73 .. 0.78
   2 !   33.2   0.2     6e-12   5.4e-08       2      52 ..     100     150 ..      99     155 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.2e-08
                                      HHSBSSCE....EEETTSBHHHHHHHHHHHTSSEEEEE.ETTT.BEEEEEEHHHHH CS
                               CBS  3 dimtrdvv....tvppdttleealelmrekgvsrlPVV.dedg.klvGivtlrDll 52
                                      dim  ++v     v+ d+++ ++l+l+ +++ +++ VV d++  kl G++   D++
  gi|242399976|ref|YP_002995401.1| 18 DIM--PPVismpIVTLDSPIVDVLKLL-RTR-HHVWVVsDKESmKLEGVIRYLDVI 69
                                      776..443355599*************.777.7*****7444469*****988886 PP

  == domain 2  score: 33.2 bits;  conditional E-value: 6e-12
                                       HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEE.EEEETTTBEEEEEEHHHHH CS
                               CBS   2 gdimtrdvvtvppdttleealelmrekgvsrl.PVVdedgklvGivtlrDll 52 
                                       +d+m ++++t+++++t+ +al +mr+++v ++  ++de g l G ++lr l+
  gi|242399976|ref|YP_002995401.1| 100 ADVMEHNIMTIDENATVLDALIKMRRYKV-QIlAIIDEKGTLKGEISLRLLI 150
                                       79************************999.66379************99665 PP

>> DHC_N2  Dynein heavy chain, N-terminal region 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   1.3e-05      0.11     211     284 ..      39     120 ..       6     134 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 1.3e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHT.THH.HHHHTHHHHH..HHHHHHHHHHHHHHHHHTTSGGGG........STT CS
                            DHC_N2 211 lsrlqeildewlkvQrkWlyLepifssed.irkqlpeeak..rFksvdkewkkimkevskdpnvle.....atskpg 279
                                       l+ l++  ++w+   ++ + Le++    d i+  lp e +  rF +++  +k+i+  ++k  +v+e     + ++  
  gi|242399976|ref|YP_002995401.1|  39 LKLLRTRHHVWVVSDKESMKLEGVIRYLDvICILLPPENTkaRFGNISAIFKSILGGAEKAADVMEhnimtIDENAT 115
                                       777888889999999**********99666*****9988767**************999987666611100333333 PP

                                       HHHHH CS
                            DHC_N2 280 llekl 284
                                       +l+ l
  gi|242399976|ref|YP_002995401.1| 116 VLDAL 120
                                       44444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1147.78
//
Query:       gi|242399977|ref|YP_002995402.1|  [L=422]
Description: NapA-2 Na+/H+ antiporter [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.5e-50  170.9  39.5    4.7e-50  170.5  39.5    1.0  1  Na_H_Exchanger  Sodium/hydrogen exchanger family
  ------ inclusion threshold ------
       0.01   16.1  10.5       0.01   16.1  10.5    3.8  6  DUF308          Short repeat of unknown function (DUF308)
       0.52    8.7   1.3        3.2    6.0   0.0    2.1  2  CBP_BcsG        Cellulose biosynthesis protein BcsG
        6.9    6.2   9.2        0.6    9.7   3.7    2.0  2  PepSY_TM        PepSY-associated TM 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 !  170.5  39.5     1e-53   4.7e-50       3     381 .]       9     384 ..       7     387 .. 0.91

  Alignments for each domain:
  == domain 1  score: 170.5 bits;  conditional E-value: 1e-53
                                       HHHHHHHHHHH..H.HHHTTSXHHHHHHHHHHHHTTTTTS............HHHCHCCHHHHCHHCCHHHHCTCGC CS
                    Na_H_Exchanger   3 llillallvgl..l.arrlklpeivgliiaGlllGpsglg.lieps......eedlevlselglilllFlaGleldl 69 
                                       +l++++++++l  + ++r+ lp ++g+i++G++lG+ +   +i+p       +e +e+l++lg+i+llFl Gl +d 
  gi|242399977|ref|YP_002995402.1|   9 TLGVALIFGKLgdHiMERFELPGVLGEILMGIVLGNLIYFgIIKPEylvmhsNEAFELLARLGIIFLLFLGGLDTDV 85 
                                       567778888889*77********************977655788888888888************************ PP

                                       CTGCCTHHHHHHHHHHHHHHHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC.CCCTSTCCCCCCHHH CS
                    Na_H_Exchanger  70 relrknlksilllallgvlitvvliGlllylllilgiplleallfgailsatdpvvvlailkeegrvperlgtlllg 146
                                       ++l+k +  +++  + gv+++++l G++     +l++p  ea+++g++l+at+++++++++ ++g +++++g   l+
  gi|242399977|ref|YP_002995402.1|  86 EMLKKTGAVATVSTIMGVFVPLLL-GYFGLK--LLDYPSREAFAAGVLLTATSIGITVRVMMDLGVLRSDVGAASLS 159
                                       ************************.998774..79****************************************** PP

                                       HHHHHHHHCCCCCHHHHHHTXXXXXTSSSTSXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS..CTHHHHHHHHHHH CS
                    Na_H_Exchanger 147 esvlnDavavvllavllalakeeaggetslllllliflvvavgglllglvigwllrlitrft..dddrelevllvll 221
                                       +sv++D +++ l+ ++++             ++l+ +  +a++++++glv ++  ++ +rf+   + ++  + +vl+
  gi|242399977|ref|YP_002995402.1| 160 ASVMDDFLGIALIIFAVGTG-----------SVLGLIGKMAIFFIITGLVAWYTIEKYIRFSewLHVEKGVLGMVLA 225
                                       ************99977665...........889999999999999999999999999999996677777778899* PP

                                       HHHHHHHHHHTSXXXHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHSXHHHHHXXHHHHHHHHH CS
                    Na_H_Exchanger 222 lallaallaellgvsgilgaflaGlvlseyefsnklseklesfreglfnplfFvlvGlsldlkvlnnhlsvlilvll 298
                                       l++l ++lae++   +i gaf+aGlvls+ ++++++  +++++++g+++p+fFv++G+ ldl v+ ++++ l l+ +
  gi|242399977|ref|YP_002995402.1| 226 LMFLFSALAEHWFDAAIEGAFMAGLVLSKLPEGKRIMDDIRAIAYGFLVPVFFVYTGAMLDLRVF-TSFDALSLAGV 301
                                       *****************************************************************.58888888888 PP

                                       HHHHHHTHHHHHHHHHTTTXSSXHHHHHHCCCCSS.BHHHHHHHHHHHHHHXHHHHTTSSTTTCSTSXHHHHHHHHH CS
                    Na_H_Exchanger 299 ilvaillgrilavflllrllglslrealiigfgglqrgavalalaalgpalgllarelyallivvvlftvlvqGlsl 375
                                       ++v+ ++g++l+  + +  +g++ + al +g++ ++r +val+ + ++ + g+++++  + +i+++l+ + +  +++
  gi|242399977|ref|YP_002995402.1| 302 LTVIAVIGKVLGRGVGAMTMGWNGKKALQMGISSIPRTEVALVDLMVAIQGGAIPQNDAPKFIAATLIFITISVIIT 378
                                       8888889**********99************************9999999998888666666666666666667778 PP

                                       HHHHHC CS
                    Na_H_Exchanger 376 kpllkk 381
                                       +pllk+
  gi|242399977|ref|YP_002995402.1| 379 PPLLKW 384
                                       888776 PP

>> DUF308  Short repeat of unknown function (DUF308)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   1.2         1   4.6e+03      32      41 ..       7      16 ..       3      48 .. 0.57
   2 ?   -1.8   0.4      0.89     4e+03      60      64 ..      70      74 ..      27      80 .. 0.52
   3 ?   -3.0   0.3       2.2   9.7e+03      24      31 ..      97     104 ..      91     116 .. 0.52
   4 ?   16.1  10.5   2.3e-06      0.01       8      73 .]     166     230 ..     160     230 .. 0.91
   5 ?   -3.6   0.3       3.2   1.5e+04      56      70 ..     270     284 ..     265     285 .. 0.67
   6 ?   -2.8   0.3       1.9   8.3e+03      22      29 ..     299     306 ..     289     319 .. 0.58

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1
                            DUF308 32 llvsGivqii 41
                                      l+  G++ i+
  gi|242399977|ref|YP_002995402.1|  7 LFTLGVALIF 16
                                      2333333333 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.89
                            DUF308 60 lGily 64
                                      lGi++
  gi|242399977|ref|YP_002995402.1| 70 LGIIF 74
                                      23333 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 2.2
                            DUF308  24 lvllfGil 31 
                                       +++++G++
  gi|242399977|ref|YP_002995402.1|  97 VSTIMGVF 104
                                       22222222 PP

  == domain 4  score: 16.1 bits;  conditional E-value: 2.3e-06
                            DUF308   8 vlGilalllPvaallalvllf..GilllvsGivqiiaafaarkknrggrwlglllGilyliaGllllf 73 
                                        lGi+++++ v ++++l l+   +i++++ G+v ++   + +k+ r + wl++  G+l ++++l++lf
  gi|242399977|ref|YP_002995402.1| 166 FLGIALIIFAVGTGSVLGLIGkmAIFFIITGLVAWY---TIEKYIRFSEWLHVEKGVLGMVLALMFLF 230
                                       59***********9999999555************6...569************************98 PP

  == domain 5  score: -3.6 bits;  conditional E-value: 3.2
                            DUF308  56 lglllGilyliaGll 70 
                                       +g+l+ ++++  G++
  gi|242399977|ref|YP_002995402.1| 270 YGFLVPVFFVYTGAM 284
                                       667777777777766 PP

  == domain 6  score: -2.8 bits;  conditional E-value: 1.9
                            DUF308  22 lalvllfG 29 
                                       + + ++++
  gi|242399977|ref|YP_002995402.1| 299 AGVLTVIA 306
                                       22222222 PP

>> CBP_BcsG  Cellulose biosynthesis protein BcsG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.3     0.021        94      91     120 ..     185     214 ..     176     241 .. 0.81
   2 ?    6.0   0.0   0.00071       3.2     415     479 ..     327     391 ..     321     413 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.021
                          CBP_BcsG  91 inlkmllalivllivylllsqwirvttlvl 120
                                       i    ++ +i+ l++++ ++++ir++ +  
  gi|242399977|ref|YP_002995402.1| 185 IGKMAIFFIITGLVAWYTIEKYIRFSEWLH 214
                                       5556778889999***********997765 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.00071
                          CBP_BcsG 415 kmqiaglreiPspsithvpvgvkliglkaekegkpveitqptSylalselvsrlleknifaeeev 479
                                       k    g+  iP  ++  v  +v + g  ++++++p  i ++  ++ +s +++  l k  f+ee  
  gi|242399977|ref|YP_002995402.1| 327 KALQMGISSIPRTEVALVDLMVAIQGGAIPQNDAPKFIAATLIFITISVIITPPLLKWAFKEEIE 391
                                       555568899******************************************98888777776444 PP

>> PepSY_TM  PepSY-associated TM region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   3.7   0.00013       0.6     127     193 ..     181     236 ..     171     265 .. 0.81
   2 ?   -2.0   0.3      0.51   2.3e+03     179     193 ..     272     286 ..     266     328 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00013
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          PepSY_TM 127 lvglaallllvllvsGlilwwprrkkkrfftfrpkkgrrfwldlHnvlGvwllpfllllalTGlvws 193
                                       ++gl + + ++ +++Gl+ w  + k             rf   lH   Gv++++++l++ ++ l+  
  gi|242399977|ref|YP_002995402.1| 181 VLGLIGKMAIFFIITGLVAWYTIEKY-----------IRFSEWLHVEKGVLGMVLALMFLFSALAEH 236
                                       57999999************887764...........3555556******************99864 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.51
                                       xxxxxxxxxxxxxxx RF
                          PepSY_TM 179 lpfllllalTGlvws 193
                                       +++ +++++TG+++ 
  gi|242399977|ref|YP_002995402.1| 272 FLVPVFFVYTGAMLD 286
                                       555567777777763 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       947  (0.0528195); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 2960.91
//
Query:       gi|242399978|ref|YP_002995403.1|  [L=443]
Description: 4-aminobutyrate aminotransferase [Thermococcus sibiricus MM 739]
Scores for complete 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-113  378.9   0.0   2.8e-113  378.6   0.0    1.0  1  Aminotran_3      Aminotransferase class-III
     0.0013   17.9   0.0     0.0024   17.1   0.0    1.3  1  Methyltransf_33  Histidine-specific methyltransferase, SAM-de
  ------ inclusion threshold ------
      0.095   11.9   0.0       0.46    9.6   0.0    1.9  2  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 !  378.6   0.0  4.7e-117  2.8e-113       7     406 .]      21     424 ..      15     424 .. 0.97

  Alignments for each domain:
  == domain 1  score: 378.6 bits;  conditional E-value: 4.7e-117
                                       --SCEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHC CS
                       Aminotran_3   7 dnlllvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllkla 83 
                                       + +++v+ ka++++++dv+g++y+D++s  av n+Gh++++vvka+keq ++l h  f   ++ + l laekl ++ 
  gi|242399978|ref|YP_002995403.1|  21 TYAPIVAIKAQNARVWDVEGREYIDFLSDAAVQNVGHNNERVVKAIKEQTDNLLHFTFIYGFTIEPLLLAEKLGEIS 97 
                                       44569999**************************************************9999999999********* PP

                                       T-..SEEEEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEEEE CS
                       Aminotran_3  84 pkgldkvflansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevvrl 160
                                       p +  kv++  sGs+A+ +A+K+ r+      +t++  i+++ +++ G t+ga s+tg  + + + +   l +v+++
  gi|242399978|ref|YP_002995403.1|  98 PVDNPKVVFGLSGSDANDGAIKFVRA------YTKRRTILSYLKSYYGATYGASSITGL-DFHVRALVGELSDVHYI 167
                                       **888*********************......9**************************.666666666789***** PP

                                       -TTBGGGTB-HHHHHHHHHHHHHHHH.....CHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEEE CS
                       Aminotran_3 161 kypdeevlkeneeeeaalleeleale.....kkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvllivD 232
                                       +ypd++++++ +e++a+ +e++e ++     ++ +d vaA+  Epiqg++G++v++++++++++++ ++h++ll+vD
  gi|242399978|ref|YP_002995403.1| 168 PYPDCYRCPFGKEKNACKMECIEYIKakfegEVYADGVAALFAEPIQGDAGMIVPPDDYFKRVKKILDEHGILLVVD 244
                                       ***********************999989999999****************************************** PP

                                       -TTTTTTTTSSSSGGGGCTS--SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTSB--TTTT-HHHHHHHHHHHHHHH CS
                       Aminotran_3 233 EvqtGfGrTGklfAlehagvspDlmtlaKaltgGlplsavlataevmqalapgshgsTfgGnplacavalavleiie 309
                                       Evq+G+GrTGk+fA+eh+g+ pD++t+aK l+gGlp+sav+++a++m+ l p +h  T +Gnp+  ++a+av+e ie
  gi|242399978|ref|YP_002995403.1| 245 EVQSGLGRTGKWFAVEHFGIRPDIITIAKPLGGGLPISAVIGRADIMDSLPPLGHTFTLSGNPVTSRAAMAVIEEIE 321
                                       ***************************************************************************** PP

                                       HTTHHHHHHHHHHHHHHHHHHHCTT-TTEEEEEEETTEEEEEEBCCCETTC......HHHHHHHHHCTEE-EEETTT CS
                       Aminotran_3 310 eekllenaqelgaalkegLeelqkkyevikevRgkGlmiaielkeeaevke......keilkkakekGvlilsaGdn 380
                                       e++ll++a++lg++  ++Le+++k++e i++vRgkGlmi+++l++++e+ke      k+++ +a e G++i  +  n
  gi|242399978|ref|YP_002995403.1| 322 EKNLLKRAEKLGNYAMKKLEKMKKEHELIGDVRGKGLMIGVDLVKDKETKErayneaKKVVWRAYELGLIIAFLQGN 398
                                       ************************************************999******99*************9999* PP

                                       EEEE---TT--HHHHHHHHHHHHHHH CS
                       Aminotran_3 381 virllppliitdeeidelleilkkal 406
                                       v+r+ ppl+i+ e ++e+l++l++a+
  gi|242399978|ref|YP_002995403.1| 399 VLRIQPPLTIEGELLEEGLNRLEQAI 424
                                       ***********************997 PP

>> Methyltransf_33  Histidine-specific methyltransferase, SAM-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0     4e-07    0.0024     158     203 ..     338     385 ..     319     393 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4e-07
                   Methyltransf_33 158 eeaaafLrklraal.....gpgdllLlGvDlvkdeekleaAYndsagv.taa 203
                                       ++ ++    ++++       +g+ l++GvDlvkd+e+ e+AYn++++v ++a
  gi|242399978|ref|YP_002995403.1| 338 KKLEK----MKKEHeligdVRGKGLMIGVDLVKDKETKERAYNEAKKVvWRA 385
                                       44333....33332224444599********************998751555 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 ?    0.1   0.0      0.06   3.6e+02      64      98 ..      98     132 ..      61     145 .. 0.80
   2 ?    9.6   0.0   7.7e-05      0.46     171     327 ..     228     377 ..     164     420 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.06
                                       HTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEE CS
                     Aminotran_1_2  64 klkreaavvvgsGagaliealifllklnpgdeilv 98 
                                       ++++ + v  +sG++a++ a++f+  + + + il+
  gi|242399978|ref|YP_002995403.1|  98 PVDNPKVVFGLSGSDANDGAIKFVRAYTKRRTILS 132
                                       44455467788************997777777776 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 7.7e-05
                                       HHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHHHHHHH CS
                     Aminotran_1_2 171 eklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilgnaavvsqlrkls 247
                                       + + ++ +++++ll+vDe+ +g+  + + ++  ++++ +++      + +K +G  G+ + +++g a++ + l  l 
  gi|242399978|ref|YP_002995403.1| 228 KRVKKILDEHGILLVVDEVQSGLGRTGKWFAVEHFGIRPDII-----TIAKPLG-GGLPISAVIGRADIMDSLPPLG 298
                                       555566********************8866555999888876.....8999997.4777899999999999999998 PP

                                       HHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSSEEEEEETHHCHHHHHH CS
                     Aminotran_1_2 248 rpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgmflltdlsaetakelsk 322
                                        +f+     ++++a++a+++  ++k  +l +++++l + +++  +++ +++ + ++   g  l+ +++  ++ke  +
  gi|242399978|ref|YP_002995403.1| 299 HTFTLsgNPVTSRAAMAVIEEIEEK--NLLKRAEKLGNYAMKKLEKM-KKEHELIGDVRGKGLMIGVDLVKDKETKE 372
                                       8888867778888999888888876..77777777777776666666.33555555555555555555555555555 PP

                                       HHHHT CS
                     Aminotran_1_2 323 kLlee 327
                                          +e
  gi|242399978|ref|YP_002995403.1| 373 RAYNE 377
                                       55555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (443 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); 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: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 3126.52
//
Query:       gi|242399979|ref|YP_002995404.1|  [L=441]
Description: permease, major facilitator superfamily [Thermococcus sibiricus MM 739]
Scores for complete 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   80.5  58.6    8.4e-19   67.7  30.8    2.0  2  MFS_1       Major Facilitator Superfamily
    1.3e-07   30.9  20.5    2.1e-07   30.1  20.5    1.3  1  MFS_1_like  MFS_1 like family
    0.00048   18.8   6.1    0.00048   18.8   6.1    2.9  3  MFS_2       MFS/sugar transport protein


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.7  30.8   1.4e-22   8.4e-19      16     346 ..      44     380 ..      32     380 .. 0.76
   2 !   26.7  19.8   4.1e-10   2.5e-06       2     177 ..     247     423 ..     246     437 .. 0.83

  Alignments for each domain:
  == domain 1  score: 67.7 bits;  conditional E-value: 1.4e-22
                             MFS_1  16 gpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalg.lllllfasslwlllvl 91 
                                       + ++p ++a + g+ + e+gll+++ +l++ ++++++G lsd++  r+v++++ +l++++ l++l++++++w ll++
  gi|242399979|ref|YP_002995404.1|  44 SQIVP-LYAMQMGAGAGEVGLLTSISTLTSTIGTVFWGKLSDKLLKRKVFIIMGFLSVSFfLAVLSMVNNFWELLIV 119
                                       55667.4445788999***************************8788877777777777735555577********* PP

                             MFS_1  92 rvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlf 168
                                         l +++ g+ +++ ++l+ + + k++   ++g ++   + + ++g llg +l+  l +r + +++a++ + af+++
  gi|242399979|ref|YP_002995404.1| 120 NSLYSFFLGSTVSIPIVLLFRNVRKTRWEEGVGKFNKIGGWAWVVGLLLGFVLVRFLTFRELLLLFALLNIPAFIIA 196
                                       ****************************************************************************9 PP

                             MFS_1 169 llllpeepperkrkspkeeekgtgpaplvp...........awkallkdpvlwillialllfffgfsglltllplyl 234
                                       +  ++e p+  +r++ k+     +++ + +           + ++  +++ +  l +++++f++   +++t lp++ 
  gi|242399979|ref|YP_002995404.1| 197 WKTIREAPVYLHRSNIKPF----VNQVIQKgrylpnflvhlPTRLKISPK-FRGLYLSSFFFWVSSGMYSTQLPVF- 267
                                       9999999999999999998....555555566555566664444444444.43466666666667777*******9. PP

                             MFS_1 235 qevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavt.....ssavllllv 306
                                           g+++  ++ ++  l + ++   all  r+ ++l +r + l  + + +  ++g+ ll ++     s  +l++++
  gi|242399979|ref|YP_002995404.1| 268 LIKNGFTN-QEVFGMALLNSSIS---ALLYQRVGRKLESRSAVLALMQGYFSRTVGISLLLLPlavpnSLLFLSIAS 340
                                       99999993.33333333333333...445555555555555554444444433333333332222434555555559 PP

                             MFS_1 307 lvliGfglgfvfpsllalasdlappeeagtasglfntags 346
                                       +vl+G  ++ +++sl++l+ ++  p+e+g a++  n+++s
  gi|242399979|ref|YP_002995404.1| 341 YVLWGYSWSYISVSLTSLIGRMSTPREQGNALATSNLVNS 380
                                       999*****************************99998875 PP

  == domain 2  score: 26.7 bits;  conditional E-value: 4.1e-10
                             MFS_1   2 llaaflsalarsilgpalpl.alaedlgispseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllf..al 74 
                                       +l+ f+   +++++++ lp  ++++ ++   +e   ++++  l +++++l++ r++ ++ +r+ vl l+   f   +
  gi|242399979|ref|YP_002995404.1| 247 YLSSFFFWVSSGMYSTQLPVfLIKNGFT--NQE---VFGMALLNSSISALLYQRVGRKLESRSaVLALMQGYFsrTV 318
                                       6889999999999999999966666666..443...77889999999************999977777555441145 PP

                             MFS_1  75 g.lllll.fa..sslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllas 146
                                       g +llll +a  +sl  l +++ vl G   + +  +  +li ++++++e+g a++  ++ +s G+ilg l+gg++as
  gi|242399979|ref|YP_002995404.1| 319 GiSLLLLpLAvpNSLLfLSIASYVLWGYSWSYISVSLTSLIGRMSTPREQGNALATSNLVNSSGFILGSLIGGVVAS 395
                                       5333333445777777799********************************************************** PP

                             MFS_1 147 slgWravfyilaivsllafvlfllllpeepp 177
                                        +g+ + f  + ++s+la++    llp  +p
  gi|242399979|ref|YP_002995404.1| 396 KIGFDLNFASASVLSFLAII---PLLPLMRP 423
                                       ******************99...66666665 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 !   30.1  20.5   3.6e-11   2.1e-07      25     374 ..      50     394 ..      40     404 .. 0.78

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 3.6e-11
                        MFS_1_like  25 ylkskglkaseigiitlilpltsilsppiwgvlaDrfgkrkkvvilslllsavlflsllfippskerqeesklevsv 101
                                       y  + g  a e+g++t+i  lts ++  +wg l+D++ krk  +i++ l    +++ +l                  
  gi|242399979|ref|YP_002995404.1|  50 YAMQMGAGAGEVGLLTSISTLTSTIGTVFWGKLSDKLLKRKVFIIMGFLSVSFFLA-VLS----------------- 108
                                       6667788899******************************9999998766555555.553................. PP

                        MFS_1_like 102 aqdvdaektfwilfllvvlasfflaailvlldaatlkelgedrkd..yGrqrlfGsvGyaifafitGilidhysvnl 176
                                              ++fw l+++ +l+sffl +++ +  ++ +++++++r +   G+    G  G+a    ++G+l+ ++ v +
  gi|242399979|ref|YP_002995404.1| 109 -----MVNNFWELLIVNSLYSFFLGSTVSIPIVLLFRNVRKTRWEegVGKFNKIG--GWA---WVVGLLLGFVLVRF 175
                                       .....569*******************************7776652355544444..343...34566666666777 PP

                        MFS_1_like 177 lpysallyvlaallvisllvvlil..netekesklkvtksl..................qvllnilknpeviifllv 233
                                       l ++ ll+++a+l + +++++ +   +   + +  ++   +                  +  +++   p+  ++ l 
  gi|242399979|ref|YP_002995404.1| 176 LTFRELLLLFALLNIPAFIIAWKTirEAPVYLHRSNI---KpfvnqviqkgrylpnflvHLPTRLKISPKFRGLYLS 249
                                       7778899999999988888843321122222333333...246678***********97445567779********* PP

                        MFS_1_like 234 alilgmswgiienFlflYLkelgasn.tllGslvalgvvaeiplfffaeklleklGhvklliiall.ayilrfllya 308
                                        ++  +s+g++ + l ++L + g++n ++ G+++    ++ +    ++ kl  +  +  l+   ++ ++ + +ll+ 
  gi|242399979|ref|YP_002995404.1| 250 SFFFWVSSGMYSTQLPVFLIKNGFTNqEVFGMALLNSSISALLYQRVGRKLESRSAVLALMQGYFSrTVGISLLLLP 326
                                       *******************77777652799*9999999999999999999999888888876555422344555554 PP

                        MFS_1_like 309 ii...enawlvlpievLhgisfgllwaaaveyvskiapksleatgqgllsglyfglGralGsliGGllw 374
                                       +    + + l +   vL g+s   + +++++ + ++ +++ ++   +    l  + G  lGsliGG++ 
  gi|242399979|ref|YP_002995404.1| 327 LAvpnSLLFLSIASYVLWGYSWSYISVSLTSLIGRMSTPREQGNALATS-NLVNSSGFILGSLIGGVVA 394
                                       4455555556667789****************************99965.566899**********985 PP

>> MFS_2  MFS/sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   6.1     8e-08   0.00048     245     340 ..      45     139 ..      27     154 .. 0.81
   2 ?   -0.9   0.7     0.075   4.5e+02     172     200 ..     179     209 ..     154     323 .. 0.61
   3 !    9.4   2.9   5.6e-05      0.33      80     162 ..     318     402 ..     309     440 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 8e-08
                             MFS_2 245 glllYyltyvlgngsaasvfllvvtisallgiplwqplakrlgkkntyllgalltivllvlvlllqpsnlllflvll 321
                                        ++ +y+  +   + ++ +++ + t+ +++g+++w +l  +l k+++++++  l +++++ vl +  +n + +l++ 
  gi|242399979|ref|YP_002995404.1|  45 QIVPLYAMQMGAGAGEVGLLTSISTLTSTIGTVFWGKLSDKLLKRKVFIIMGFLSVSFFLAVLSM-VNNFWELLIVN 120
                                       45555554444466677777777899999************************************.*********** PP

                             MFS_2 322 viagfgvgvaallpwsmla 340
                                        +++f++g+ +++p  +l 
  gi|242399979|ref|YP_002995404.1| 121 SLYSFFLGSTVSIPIVLLF 139
                                       ***********99988875 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.075
                             MFS_2 172 lifaliialLmllgviivvlgtkervem..r 200
                                       + ++l++alL + ++ii++ + +e   +  r
  gi|242399979|ref|YP_002995404.1| 179 RELLLLFALLNIPAFIIAWKTIREAPVYlhR 209
                                       4556666666666666666666666555433 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 5.6e-05
                             MFS_2  80 vsiillftppelsqsakfiwllvtyillrilytlfeipyvslvpvltkdydeRtsltsvrsfls...vlggvlaail 153
                                       v+i ll +p+ + + +++ + +++y+l+   ++ ++++ +sl+  +++ +++ + l++   + s   +lg++++ ++
  gi|242399979|ref|YP_002995404.1| 318 VGISLLLLPLAVPN-SLLFLSIASYVLWGYSWSYISVSLTSLIGRMSTPREQGNALATSNLVNSsgfILGSLIGGVV 393
                                       56667777777544.8888999************************9999999999886554441114555555555 PP

                             MFS_2 154 afllvlilg 162
                                       a+ + + l+
  gi|242399979|ref|YP_002995404.1| 394 ASKIGFDLN 402
                                       555554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.49
# Mc/sec: 2698.92
//
Query:       gi|242399980|ref|YP_002995405.1|  [L=716]
Description: DNA helicase, UvrD/REP family [Thermococcus sibiricus MM 739]
Scores for complete 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-58  196.5   0.0    6.3e-58  195.7   0.0    1.4  1  AAA_12           AAA domain
      4e-57  194.0   0.1    1.9e-56  191.8   0.2    1.9  2  AAA_11           AAA domain
    3.6e-12   46.4   0.1    4.4e-07   29.8   0.0    2.8  3  AAA_30           AAA domain
    6.5e-08   33.0   0.0    4.8e-07   30.2   0.0    2.4  2  AAA_19           AAA domain
    1.3e-05   25.1   0.0        0.1   12.3   0.0    3.2  3  Viral_helicase1  Viral (Superfamily 1) RNA helicase
     0.0001   21.9   2.3    0.00083   19.0   0.0    2.3  2  UvrD-helicase    UvrD/REP helicase N-terminal domain
     0.0015   17.7   0.2     0.0046   16.1   0.0    1.9  2  T2SSE            Type II/IV secretion system protein
     0.0039   16.7   0.1        0.3   10.5   0.0    3.1  4  PhoH             PhoH-like protein
      0.005   16.7   0.2       0.86    9.4   0.0    2.5  2  Helicase_RecD    Helicase
     0.0052   16.0   0.0      0.042   13.0   0.0    2.2  2  PIF1             PIF1-like helicase
  ------ inclusion threshold ------
      0.011   16.1   0.7       0.16   12.2   0.0    3.1  4  AAA_22           AAA domain
      0.022   14.7   0.4       0.18   11.8   0.4    2.2  1  ResIII           Type III restriction enzyme, res subunit
        0.1   12.3   0.0       0.42   10.3   0.0    1.9  1  DEAD             DEAD/DEAH box helicase
       0.12   12.2   0.0       0.35   10.7   0.0    1.8  1  UvrD_C_2         UvrD-like helicase C-terminal domain
       0.13   12.6   0.1       0.59   10.6   0.0    2.2  1  AAA              ATPase family associated with various cellul
       0.58    9.5   3.6         18    4.6   0.1    3.2  3  UvrD_C           UvrD-like helicase C-terminal domain


Domain annotation for each model (and alignments):
>> AAA_12  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.7   0.0   5.7e-61   6.3e-58       2     198 ..     484     685 ..     483     686 .. 0.94

  Alignments for each domain:
  == domain 1  score: 195.7 bits;  conditional E-value: 5.7e-61
                            AAA_12   2 erSlferllkkekekvvlLdtqYRmhpeIsrfpsklfYkgkLkdaesvkkrele...........aqealeeplepl 67 
                                       +++lfe+l++ ++ k ++L++qYRm++ +++fps++fY+gk+k++ svk+ +l             ++ + +  epl
  gi|242399980|ref|YP_002995405.1| 484 SETLFEKLIELYPFKAKMLEIQYRMNQLLMEFPSREFYNGKIKADGSVKDITLAdlkvrepffgePWDSILKREEPL 560
                                       79********************************************999999999999******9889999999*** PP

                            AAA_12  68 vfidvekseeekekke...ksyiNeeEaelvvklvekllkkgseeerkkigvitpYraqvellkkklkekeeeksek 141
                                       +f+d+++ +++ e+++   +s  N+ Ea lv ++ve+ll+ g ++  + ig+itpY +qv+ +++ +++   ++   
  gi|242399980|ref|YP_002995405.1| 561 IFVDTSNRTDKWERQRkgsTSRENPLEALLVREIVERLLRMGIKK--EWIGIITPYDDQVDSIRSIIQD---DE--- 629
                                       *****87776666555667**************************..9********************4...33... PP

                            AAA_12 142 eievntvdgfQGrekdviilslVRsnekkeigflkderrlNValTRAkskliivGnk 198
                                        ie++tvdg+QGrek++iilslVRsn+k+e+gfl d rrlNV++TRAk+kl+++G++
  gi|242399980|ref|YP_002995405.1| 630 -IEIHTVDGYQGREKEIIILSLVRSNKKGELGFLMDLRRLNVSITRAKRKLVVIGDS 685
                                       .99****************************************************97 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.8   0.2   1.7e-59   1.9e-56       1     261 []     229     478 ..     229     478 .. 0.91
   2 ?   -0.7   0.0      0.87   9.8e+02       4      76 ..     615     699 ..     613     709 .. 0.68

  Alignments for each domain:
  == domain 1  score: 191.8 bits;  conditional E-value: 1.7e-59
                            AAA_11   1 klndsqreaiksalseseitliqGPPGtgKTktivellsqllsrrkseeeksakpriLvCapSNaAvDellerllrg 77 
                                       +ln+sq+ea++ al +++++li+GP GtgKT+t+vel+ q           +++++iL++a+SN+AvD+l+erl+  
  gi|242399980|ref|YP_002995405.1| 229 NLNQSQKEAVSYALGSEDFFLIHGPFGTGKTRTLVELIVQE---------VKRGNKILATAESNVAVDNLVERLWG- 295
                                       59***************************************.........789***********************. PP

                            AAA_11  78 lldsegekykpkivRvgneeeriseavksvsleekvekrlekeekaqlakeiskeleklakelrafeeeeek..... 149
                                                k+k+vR+g+++ r+s ++k+ +l  +ve++ +     ++++e++++ e+la + ++ ++   +     
  gi|242399980|ref|YP_002995405.1| 296 ---------KVKLVRLGHPS-RVSVHLKESTLAFQVESHERY----RKVRELRNKAERLAVMRDQYKKPTPQmrrgl 358
                                       .........9**********.9**************999955....4556666666666665555555555566699 PP

                            AAA_11 150 ...........eklkkskekskskleqerrklkkerkelskeleeaeesleeevldeaeivltTlsgagskllekla 215
                                                   +  +    +  k+ ++  +l++++++l k  e++e+++ +e+++++++vl+T+s+a+ + ++++ 
  gi|242399980|ref|YP_002995405.1| 359 tnnqilklayrGRGSRGVPAKDIKQMAQWITLNEQIQKLYKFAEKIESEIIQEIIEDVDVVLSTNSSAALEFIKDA- 434
                                       99*9999*98878888888888999999************************************************. PP

                            AAA_11 216 kkfdvviIDEAaqavEpstliPlrlgakkvvLvGDpkQLpatvisk 261
                                        +fdv iIDEA+qa+ ps+liP+ ++ +++vL+GD+kQLp+t++s+
  gi|242399980|ref|YP_002995405.1| 435 -EFDVAIIDEASQATIPSVLIPIAKA-RRFVLAGDHKQLPPTILSE 478
                                       .9*********************999.*****************96 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.87
                            AAA_11   4 dsqreaiksalsese..itliqGPPGtgKTktivellsqllsr.........rk.seeeksakpriLvCapSNaAvD 68 
                                       d+q ++i+s+++ +e  i  + G  G  K   i++l+++   +         r+ ++   +ak+++ v + S++ v+
  gi|242399980|ref|YP_002995405.1| 615 DDQVDSIRSIIQDDEieIHTVDGYQGREKEIIILSLVRSNK-KgelgflmdlRRlNVSITRAKRKLVVIGDSETLVN 690
                                       56777888888887777777888888888888888888874.33666665552247777888888888888888887 PP

                            AAA_11  69 e.llerllr 76 
                                       + + +rl+ 
  gi|242399980|ref|YP_002995405.1| 691 HeTYKRLIH 699
                                       424555555 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.0     4e-10   4.4e-07       2      66 ..     230     293 ..     229     343 .. 0.86
   2 !   13.4   0.0   4.3e-05     0.048      81     130 ..     389     473 ..     354     495 .. 0.70
   3 ?   -1.7   0.0       1.8     2e+03     105     126 ..     665     686 ..     660     713 .. 0.69

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 4e-10
                            AAA_30   2 lnaeQaaavealltsgdrvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeel 66 
                                       ln++Q++av  +l+s+d + +++Gp GtGKt +l +l     ++g ++++ A ++ a ++L e l
  gi|242399980|ref|YP_002995405.1| 230 LNQSQKEAVSYALGSED-FFLIHGPFGTGKTRTLVELIVQEVKRGNKILATAESNVAVDNLVERL 293
                                       89**************9.*************999999777777899**************98754 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 4.3e-05
                            AAA_30  81 k..........................................grarlepg.tllivDEagmvdtkqlaallkaaek 114
                                       +                                          +    +++ ++ i+DEa+ + + ++   +++a++
  gi|242399980|ref|YP_002995405.1| 389 TlneqiqklykfaekieseiiqeiiedvdvvlstnssaalefiK----DAEfDVAIIDEASQATIPSVLIPIAKARR 461
                                       44444444444444555555555555555777777777653321....44569**********99998666666655 PP

                            AAA_30 115 agakvilvGDerQlas 130
                                            +l+GD++Ql++
  gi|242399980|ref|YP_002995405.1| 462 ----FVLAGDHKQLPP 473
                                       ....**********97 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 1.8
                            AAA_30 105 laallkaaekagakvilvGDer 126
                                       l++l  ++++a+ k++++GD +
  gi|242399980|ref|YP_002995405.1| 665 LRRLNVSITRAKRKLVVIGDSE 686
                                       5566666666677777777754 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0   4.2e-10   4.8e-07       1     143 [.     234     473 ..     234     475 .. 0.76
   2 ?   -1.7   0.0       3.1   3.4e+03     125     139 ..     672     686 ..     590     695 .. 0.76

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 4.2e-10
                            AAA_19   1 qreave.alkekvllvtaGp.GtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae....... 68 
                                       q+eav+ al ++ ++++ Gp GtGKTr+l++ +   v++g    ++il+ a  + A+++l erl +   +       
  gi|242399980|ref|YP_002995405.1| 234 QKEAVSyALGSEDFFLIHGPfGTGKTRTLVELIVQEVKRG----NKILATAESNVAVDNLVERLWGKV-Klvrlghp 305
                                       899998888777666666666**********998888888....89*****************93333.24555555 PP

                            AAA_19  69 ...atTiHrlal................................................................. 77 
                                                  +                                                                 
  gi|242399980|ref|YP_002995405.1| 306 srvS-------Vhlkestlafqvesheryrkvrelrnkaerlavmrdqykkptpqmrrgltnnqilklayrgrgsrg 375
                                       5440.......144445556666778888888888888888888999999999999999999999999999999999 PP

                            AAA_19  78 ..........................................ldfddlltealelleeaeeekklqeee.llivDEf 111
                                                                                 + + +  + ale++++        +e+ + i+DE+
  gi|242399980|ref|YP_002995405.1| 376 vpakdikqmaqwitlneqiqklykfaekieseiiqeiiedvdVVLSTNSSAALEFIKD--------AEFdVAIIDEA 444
                                       99999999999*9999999999999888888888777766553344444445555553........2334999**** PP

                            AAA_19 112 qdvdelqyrLlkallgekkklllvGDpdQliy 143
                                       ++ +  + ++l  ++ ++ +++l GD++Ql++
  gi|242399980|ref|YP_002995405.1| 445 SQAT--IPSVLIPIA-KARRFVLAGDHKQLPP 473
                                       *876..456677777.5566**********97 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.1
                            AAA_19 125 llgekkklllvGDpd 139
                                       ++  k kl+++GD +
  gi|242399980|ref|YP_002995405.1| 672 ITRAKRKLVVIGDSE 686
                                       343445688888865 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 ?    2.2   0.0      0.11   1.3e+02       2      30 ..     249     273 ..     248     298 .. 0.72
   2 !   12.3   0.0     9e-05       0.1      55     102 ..     428     473 ..     394     523 .. 0.83
   3 !    6.7   0.0    0.0049       5.4     178     233 ..     626     682 ..     571     683 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.11
                   Viral_helicase1   2 vvhGvpGcGKStlirkllrtsliltvnrp 30 
                                       ++hG  G GK++ +++l+ ++    v r 
  gi|242399980|ref|YP_002995405.1| 249 LIHGPFGTGKTRTLVELIVQE----VKRG 273
                                       799999***********9983....2222 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 9e-05
                   Viral_helicase1  55 malvkstkgkililDEylllhaGyilllaalskaklvilfGDplQipf 102
                                         ++k+ ++++ i+DE+ +++  +  +l+ ++ka+ ++l GD++Q p 
  gi|242399980|ref|YP_002995405.1| 428 LEFIKDAEFDVAIIDEASQAT--IPSVLIPIAKARRFVLAGDHKQLPP 473
                                       344455689********9998..6777******************885 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0049
                   Viral_helicase1 178 ealgvrevttvhevqGltfdkVtlvllketdlelis..esrenllvAlTRhrkslvil 233
                                       ++   + ++tv + qG + +  +l l +++++ ++    +   l v +TR++++lv++
  gi|242399980|ref|YP_002995405.1| 626 QDDEIE-IHTVDGYQGREKEIIILSLVRSNKKGELGflMDLRRLNVSITRAKRKLVVI 682
                                       444445.9********9999887655555554443355889**************986 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 !   19.0   0.0   7.4e-07   0.00083       1      71 [.     230     299 ..     230     342 .. 0.77
   2 ?    1.6   1.5      0.14   1.6e+02     204     294 ..     378     470 ..     310     471 .. 0.60

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 7.4e-07
                                       SSHHHHHHHHS...-SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSHHHHHHHHHHHHHHHHH CS
                     UvrD-helicase   1 lnpeqreaias...lggpilveAsAGsGKTfvlaerilrlikeeeiepdrilvvTFTnkAaeElkeRieealkk 71 
                                       ln++q+ea+     ++  +l+    G+GKT++l+e+i++ +k +    ++il+    n A + l eR+  ++k 
  gi|242399980|ref|YP_002995405.1| 230 LNQSQKEAVSYalgSEDFFLIHGPFGTGKTRTLVELIVQEVKRG----NKILATAESNVAVDNLVERLWGKVKL 299
                                       6889999998875444556777777*******************....99****************99885444 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.14
                                       TSCSHHHHHHHHHHHHHHHHHHHHTCEEHHHHHHHHHH.....HHHHCHHHHHHHH.HHSSEEEESSGGG-BHHHHH CS
                     UvrD-helicase 204 ekasdlqkkiaeflkeyqeqkkeenalDfsdllhalle.....lleeneelaealr.erykeiliDEyQDTnkiQyr 274
                                        k+ ++  +++++ +++q+  k+ + ++ s+++ +++e     l+++ + ++e+++  +++++ iDE+     +Q++
  gi|242399980|ref|YP_002995405.1| 378 AKDIKQMAQWITLNEQIQKLYKFAEKIE-SEIIQEIIEdvdvvLSTNSSAALEFIKdAEFDVAIIDEA-----SQAT 448
                                       3444455566666666666666666666.344555555688867777888999997358********7.....3444 PP

                                       HHHHHHTTTTT..EEEEE-GGG CS
                     UvrD-helicase 275 ilkllasghee..lfmvGDpkQ 294
                                       i + l+   +   +++ GD kQ
  gi|242399980|ref|YP_002995405.1| 449 IPSVLIPIAKArrFVLAGDHKQ 470
                                       4444333222222888888888 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 !   16.1   0.0   4.1e-06    0.0046     112     166 ..     228     283 ..     151     291 .. 0.83
   2 ?   -2.6   0.1         2   2.2e+03      37      91 ..     399     460 ..     384     471 .. 0.53

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.1e-06
                             T2SSE 112 ealkekiaevlrkavrerglilvsGgTgsGKttll.yallkeinksderivtvEDp 166
                                       ++l++ ++e++++a+ ++  +l+ G+ g+GKt +l   +++e++  ++ + t+E  
  gi|242399980|ref|YP_002995405.1| 228 RNLNQSQKEAVSYALGSEDFFLIHGPFGTGKTRTLvELIVQEVKRGNKILATAESN 283
                                       45558999999*********************77658999****999999999865 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2
                             T2SSE  37 reveelekaalerlisriaalakldis.eerplqdarlp......ekgvrlrvvllPvvage 91 
                                       + +e++e++ ++ +i+ + ++ + + s   + + da++        +++ +  vl+P++++ 
  gi|242399980|ref|YP_002995405.1| 399 KFAEKIESEIIQEIIEDVDVVLSTNSSaALEFIKDAEFDvaiideASQATIPSVLIPIAKAR 460
                                       34455555666666666655444433303345555555555555444555555555555555 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0   0.00027       0.3       5      47 ..     230     273 ..     228     324 .. 0.88
   2 ?   -2.5   0.0       2.6   2.9e+03     135     182 ..     362     408 ..     358     432 .. 0.65
   3 ?    2.4   0.0      0.08        90     123     159 ..     439     472 ..     426     500 .. 0.82
   4 ?   -4.0   0.0       7.4   8.2e+03      94     116 ..     619     641 ..     614     648 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00027
                                       -SHHHHHHHH.HHHH-SEEEEE--TTSSTTHHHHHHHHHHHHTT CS
                              PhoH   5 ktkeQkeyle.alkkndivfaiGpaGtGKtylavalavealkkk 47 
                                        +++Qke+++ al ++d+  + Gp GtGKt   v l v+ +k++
  gi|242399980|ref|YP_002995405.1| 230 LNQSQKEAVSyALGSEDFFLIHGPFGTGKTRTLVELIVQEVKRG 273
                                       57788887762566****************99999999888875 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.6
                                       HHHHHHTTB-TT-EEEEEE--------------THHHHHHTTT-TTEE CS
                              PhoH 135 qmkmfltRlGenskvvvtGdvtqidlpkgkksGlaealevlknvegie 182
                                       q+  +  R G++s+ v + d++q+ +  + ++ ++++ + ++++e+  
  gi|242399980|ref|YP_002995405.1| 362 QILKLAYR-GRGSRGVPAKDIKQMAQWITLNEQIQKLYKFAEKIESEI 408
                                       55555555.889999999999998888777777777777777755333 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.08
                                       EEE-SGGG--HHHHHHHHTTB-TT-EEEEEE------ CS
                              PhoH 123 vilDEAQnttkeqmkmfltRlGenskvvvtGdvtqid 159
                                        i+DEA   +++++  +l+ + +  ++v++Gd +q  
  gi|242399980|ref|YP_002995405.1| 439 AIIDEA---SQATIPSVLIPIAKARRFVLAGDHKQLP 472
                                       588998...56678899*****************975 PP

  == domain 4  score: -4.0 bits;  conditional E-value: 7.4
                                       TCHHHHHHTTSEEEEEGGGGTT- CS
                              PhoH  94 ekvekllekgkievaplaymRGr 116
                                       +++++++++++ie+  +    Gr
  gi|242399980|ref|YP_002995405.1| 619 DSIRSIIQDDEIEIHTVDGYQGR 641
                                       56788899999999988888777 PP

>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0   0.00077      0.86       3      57 ..     251     304 ..     249     352 .. 0.72
   2 ?    4.9   0.1     0.019        22      77     120 ..     429     465 ..     366     470 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00077
                     Helicase_RecD   3 tAdRGRGKSaalGlalaaliaegksnilvtapskenvktlfeflakglealglke 57 
                                        +  G+GK+ +l  ++ + +++g+ +il ta s+ +v++l+e+l  +++ ++l +
  gi|242399980|ref|YP_002995405.1| 251 HGPFGTGKTRTLVELIVQEVKRGN-KILATAESNVAVDNLVERLWGKVKLVRLGH 304
                                       5667****************9987.9****************9977776655544 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.019
                     Helicase_RecD  77 eyiapdellklkeqadllvvDEAAaiplpllkkllekfkrvvla 120
                                       e      ++k   + d+ ++DEA++  +p +   + k +r+vla
  gi|242399980|ref|YP_002995405.1| 429 E------FIKDA-EFDVAIIDEASQATIPSVLIPIAKARRFVLA 465
                                       2......23322.45999******99999988877788888877 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   3.7e-05     0.042       2      66 ..     230     289 ..     229     339 .. 0.84
   2 ?    0.1   0.0      0.31   3.5e+02     144     158 ..     462     476 ..     459     510 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.7e-05
                                       --HHHHHHHHHH......HCTS-EEEEESTTSSCHHHHHHHHHHCHCTCCCEEEEESSHHHHHCC CS
                              PIF1   2 LneeQkkvfdaiieavlnekgklfFvtGsgGtgKtflwkallkklrsegkivlavAssGvAalll 66 
                                       Ln++Qk+++  ++      +  +f ++G  GtgKt  + +l+ +  ++g+++la+A s vA  +l
  gi|242399980|ref|YP_002995405.1| 230 LNQSQKEAVSYAL-----GSEDFFLIHGPFGTGKTRTLVELIVQEVKRGNKILATAESNVAVDNL 289
                                       6777777777663.....45678999*********99999999888999***********98766 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.31
                                       EEEE--TTS-----S CS
                              PIF1 144 vvlgGDfrQilPvie 158
                                        vl+GD +Q++P i 
  gi|242399980|ref|YP_002995405.1| 462 FVLAGDHKQLPPTIL 476
                                       69**********884 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00014      0.16       5      32 ..     245     272 ..     241     346 .. 0.76
   2 ?   -2.9   0.1       6.5   7.3e+03      84     100 ..     429     444 ..     402     454 .. 0.68
   3 ?   -2.6   0.0       5.4   6.1e+03      92     117 ..     472     496 ..     456     505 .. 0.77
   4 ?   -0.2   0.0      0.98   1.1e+03      79     117 ..     665     702 ..     646     708 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00014
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldee 32 
                                       + + +++G+ GtGKT++l +l  q +++
  gi|242399980|ref|YP_002995405.1| 245 EDFFLIHGPFGTGKTRTLVELIVQEVKR 272
                                       67899************99998887643 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 6.5
                            AAA_22  84 qalraravielliiDEa 100
                                       + ++++    + iiDEa
  gi|242399980|ref|YP_002995405.1| 429 EFIKDAEF-DVAIIDEA 444
                                       44444555.67788887 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 5.4
                            AAA_22  92 ielliiDEaqhlrseealeeLrslln 117
                                       ++ ++ +Ea  l se+++e+L +l+ 
  gi|242399980|ref|YP_002995405.1| 472 PPTILSEEARAL-SETLFEKLIELYP 496
                                       567778899999.9999999988875 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 0.98
                            AAA_22  79 lealeqalraravielliiDEaqhlrseealeeLrslln 117
                                       l++l+  + ++++ +l++i + + l ++e ++ L ++++
  gi|242399980|ref|YP_002995405.1| 665 LRRLNVSITRAKR-KLVVIGDSETLVNHETYKRLIHFVK 702
                                       5677777888888.9********9867999988888876 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   0.00016      0.18       4      75 ..     230     341 ..     227     451 .. 0.52

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00016
                                       E-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHG...... CS
                            ResIII   4 lreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleef...... 74 
                                       l++ Q+ea+   l       +  +li+ + GtGKT+++++li +  k g+  k+l  + ++  ++ + e++      
  gi|242399980|ref|YP_002995405.1| 230 LNQSQKEAVSYAL-----GSEDFFLIHGPFGTGKTRTLVELIVQEVKRGN--KILATAESNVAVDNLVERLwgkvkl 299
                                       5556666666655.....4566889*****************99999766..8888888875555555444444466 PP

                                       .........................................G CS
                            ResIII  75 .........................................k 75 
                                                                                +
  gi|242399980|ref|YP_002995405.1| 300 vrlghpsrvsvhlkestlafqvesheryrkvrelrnkaerlA 341
                                       666666666666666666665555555555555555544441 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00038      0.42       3      54 ..     233     280 ..     231     494 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00038
                                       HHHHHHHHHHTTCEEE.EEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEE CS
                                       xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   3 iQaeaiplilgggdvl.vaaeTGsGKTlaflipvlqivyetkgktgpkalive 54 
                                        Q+ea+  +lg +d++ ++++ G+GKT   +  ++q+v     k+g+k+l  +
  gi|242399980|ref|YP_002995405.1| 233 SQKEAVSYALGSEDFFlIHGPFGTGKTRTLVELIVQEV-----KRGNKILATA 280
                                       69********999875499****************999.....4444444444 PP

>> UvrD_C_2  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00032      0.35       6      52 .]     634     682 ..     630     682 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00032
                          UvrD_C_2   6 tihkaQGsefpaVivfdpdlaaarmgel....rrrlLYtavTRAreklilv 52 
                                       t+   QG e +++i+      + + gel      r L + +TRA++kl+++
  gi|242399980|ref|YP_002995405.1| 634 TVDGYQGREKEIIIL--SLVRSNKKGELgflmDLRRLNVSITRAKRKLVVI 682
                                       788889999888888..444444446667888999*************996 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   0.00052      0.59       2      27 ..     249     277 ..     248     343 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00052
                                       EEESSTTSSHH.HHHHHHHHHHT..HEEE CS
                               AAA   2 llyGppGtGKT.llakavakelg..vefl 27 
                                       l++Gp GtGKT +l++ +++e++   ++l
  gi|242399980|ref|YP_002995405.1| 249 LIHGPFGTGKTrTLVELIVQEVKrgNKIL 277
                                       89*********889999999985333333 PP

>> UvrD_C  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1     0.016        18     177     277 ..     226     422 ..      44     483 .. 0.67
   2 ?    0.4   0.0       0.3   3.4e+02      53     106 ..     586     639 ..     563     647 .. 0.88
   3 ?    3.5   0.1     0.034        38     331     346 ..     668     683 ..     662     686 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.016
                                       xxxxxxxxxxxxx................................................................ RF
                            UvrD_C 177 Fieliraleeknl................................................................ 189
                                       F +++++ +++++                                                                
  gi|242399980|ref|YP_002995405.1| 226 FDRNLNQSQKEAVsyalgsedfflihgpfgtgktrtlvelivqevkrgnkilataesnvavdnlverlwgkvklvrl 302
                                       33333333333337777777777777777777777777777777777777777777777777777777777777777 PP

                                       ..........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........ RF
                            UvrD_C 190 ..........................elllkkiektaeerqalvskyadlfkelaeklaelkekseskr........ 232
                                                                 +  +++++++ae+   ++ +y++   ++++ l++ +  +   r        
  gi|242399980|ref|YP_002995405.1| 303 ghpsrvsvhlkestlafqvesheryrK--VRELRNKAERLAVMRDQYKKPTPQMRRGLTNNQILKLAYRgrgsrgvp 377
                                       777777777777666666666443221..333444444445556667777777777776666555555577888887 PP

                                       .....xxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C 233 .....kkee....klenlreLysllkelekkeeeeeveeklneileiatLsese 277
                                            +  +      e++++Ly++++++e        e  ++ei+e+     s+
  gi|242399980|ref|YP_002995405.1| 378 akdikQ-MAqwitLNEQIQKLYKFAEKIES-------EI-IQEIIEDVDVVLST 422
                                       644421.11234444555555555555555.......44.66666665444333 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.3
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C  53 eEaekiaatikallekneklediavLvRsnkdadkiskaLkkegipfnvvdeek 106
                                        Ea  + +++++ll + +k+e i +++    + d+i   ++  +i++ +vd+++
  gi|242399980|ref|YP_002995405.1| 586 LEALLVREIVERLLRMGIKKEWIGIITPYDDQVDSIRSIIQDDEIEIHTVDGYQ 639
                                       5778888999999999*********************************99875 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.034
                                       xxxxxxxxxxxxxxxx RF
                            UvrD_C 331 fYVaiTRAkkrLfisy 346
                                       + V iTRAk++L+++ 
  gi|242399980|ref|YP_002995405.1| 668 LNVSITRAKRKLVVIG 683
                                       5699*********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (716 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       805  (0.0448993); expected 358.6 (0.02)
Passed bias filter:                      591  (0.0329634); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); 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: 0.81u 0.33s 00:00:01.14 Elapsed: 00:00:00.53
# Mc/sec: 4101.13
//
Query:       gi|242399981|ref|YP_002995406.1|  [L=72]
Description: hypothetical protein TSIB_2010 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      204  (0.0113782); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 495.14
//
Query:       gi|242399982|ref|YP_002995407.1|  [L=102]
Description: hypothetical protein TSIB_2011 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.2e-05   23.5  30.0     0.0056   16.6   3.6    2.6  2  Gly-zipper_Omp   Glycine zipper
     0.0027   17.7   5.3     0.0029   17.6   5.3    1.0  1  DUF441           Protein of unknown function (DUF441)
  ------ inclusion threshold ------
       0.22   11.3  37.7        1.6    8.6  21.0    3.0  3  Gly-zipper_YMGG  YMGG-like Gly-zipper
        1.6    8.7   5.4        1.5    8.8   0.3    2.1  2  RseC_MucC        Positive regulator of sigma(E), RseC/MucC
        2.2    8.2   8.0       0.19   11.6   2.5    2.0  2  MtrG             Tetrahydromethanopterin S-methyltransferase,
        4.6    7.6   8.5        2.1    8.7   0.2    2.3  2  MscL             Large-conductance mechanosensitive channel, 
        8.2    6.7  19.9          9    6.6  11.6    2.2  2  DUF456           Protein of unknown function (DUF456)


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 !   16.6   3.6   2.2e-06    0.0056       9      43 ..      15      62 ..      13      63 .. 0.72
   2 !   12.3  18.5   5.1e-05      0.13       1      31 [.      72     101 ..      66     102 .] 0.93

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.2e-06
                    Gly-zipper_Omp  9 aGaliGgavg.............grgtGaliGAavGaavGgliGaamd 43
                                       G ++Gg+               ++ + a++G+a+G a+G + G+a+d
  gi|242399982|ref|YP_002995407.1| 15 FGVVVGGIFEnsnltyrltkkytNPEKAAIVGGAAGTALGWVGGKAID 62
                                      45555554221123677777777779*******************998 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 5.1e-05
                    Gly-zipper_Omp   1 iGaaiGAaaGaliGgavggrgtGaliGAavG 31 
                                       iGa +GA +Ga++Gg vg  ++G ++GAavG
  gi|242399982|ref|YP_002995407.1|  72 IGARVGARVGAAFGGLVGV-AIGLVVGAAVG 101
                                       899***************5.7********99 PP

>> DUF441  Protein of unknown function (DUF441)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   5.3   1.1e-06    0.0029      42     134 ..       3     100 ..       1     102 [] 0.82

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.1e-06
                            DUF441  42 kkglelGviiltiavLvP.iatgkislkellealkslkg..liallvgilvavlsgkGvellkeqpevvvalvlGti 115
                                       +k+l lG++++  +v+v  i +++  + +l+++ ++++   ++  ++g +  +++gk +++l+ ++   ++  +G+ 
  gi|242399982|ref|YP_002995407.1|   3 RKALALGLVLMAFGVVVGgIFENSNLTYRLTKKYTNPEKaaIVGGAAGTALGWVGGKAIDYLSGRAAAYIGARVGAR 79 
                                       68999*********99963777777777899998877641144446777888999999******************* PP

                            DUF441 116 lgvvf..lkGvpvGPliaaGi 134
                                       +g +f  l Gv++G +++a++
  gi|242399982|ref|YP_002995407.1|  80 VGAAFggLVGVAIGLVVGAAV 100
                                       *****7778********9987 PP

>> Gly-zipper_YMGG  YMGG-like Gly-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9  10.7     0.017        44      12      45 ..      14      59 ..       7      60 .. 0.75
   2 ?    6.4  27.8    0.0029       7.4       2      44 ..      42      89 ..      41      93 .. 0.68
   3 ?    8.6  21.0   0.00061       1.6       6      41 ..      69     102 .]      65     102 .] 0.85

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.017
                                      XXXXXXXXXXXXXXXXX.............XXXXXXXXXXXXXXXX- CS
                   Gly-zipper_YMGG 12 aaGAvvGaliGsgggkG.............AaiGAaaGalaGgaiGa 45
                                      a G vvG+++  +                 A++G+aaG + G + G+
  gi|242399982|ref|YP_002995407.1| 14 AFGVVVGGIFE-NSNLTyrltkkytnpekaAIVGGAAGTALGWVGGK 59
                                      56888888888.22222566777777888799999999999988886 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0029
                                      ...XXXXXXXXXXXXXXXXXX.....XXXXX...XXXXXXXXXXXXXXXXX CS
                   Gly-zipper_YMGG  2 gavrGAaiGAaaGAvvGaliG.....sgggk...GAaiGAaaGalaGgaiG 44
                                      +a+ G+a+G+a+G v+G +i      +       GA +GA +Ga++Gg++G
  gi|242399982|ref|YP_002995407.1| 42 AAIVGGAAGTALGWVGGKAIDylsgrA---AayiGARVGARVGAAFGGLVG 89
                                      67889*****************85442...233366666666666666655 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.00061
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                   Gly-zipper_YMGG   6 GAaiGAaaGAvvGaliGsgggkGAaiGAaaGalaGg 41 
                                        A iGA +GA vGa++G  g  G aiG ++Ga++G+
  gi|242399982|ref|YP_002995407.1|  69 AAYIGARVGARVGAAFG--GLVGVAIGLVVGAAVGY 102
                                       6889*************..98888888888888885 PP

>> RseC_MucC  Positive regulator of sigma(E), RseC/MucC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.3   0.00058       1.5      75     115 ..      10      62 ..       5      72 .. 0.84
   2 ?    2.1   1.3     0.067   1.7e+02      85     110 ..      73      96 ..      63     101 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00058
                         RseC_MucC  75 llllilgallgsall............gssellaalgallglvlgflivrlls 115
                                       l+l+ +g+++g ++             ++ e +a++g+ +g++lg++  + ++
  gi|242399982|ref|YP_002995407.1|  10 LVLMAFGVVVGGIFEnsnltyrltkkyTNPEKAAIVGGAAGTALGWVGGKAID 62 
                                       7788888888888888888999999999******************9988776 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.067
                         RseC_MucC  85 gsallgssellaalgallglvlgfli 110
                                       g    ++  + aa+g+l+g+++g+++
  gi|242399982|ref|YP_002995407.1|  73 GAR--VGARVGAAFGGLVGVAIGLVV 96 
                                       333..367788999999999999876 PP

>> MtrG  Tetrahydromethanopterin S-methyltransferase, subunit G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       0.9   2.3e+03      48      56 ..      14      22 ..       8      30 .. 0.78
   2 ?   11.6   2.5   7.3e-05      0.19      25      61 ..      60      96 ..      58      99 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.9
                              MtrG 48 lYGlviGli 56
                                      ++G+v+G i
  gi|242399982|ref|YP_002995407.1| 14 AFGVVVGGI 22
                                      678888755 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 7.3e-05
                              MtrG 25 kvefvnsEiaqriGkkvGRdiGilYGlviGliillvy 61
                                       +++ ++  a  iG +vG  +G ++G ++G+ i lv 
  gi|242399982|ref|YP_002995407.1| 60 AIDYLSGRAAAYIGARVGARVGAAFGGLVGVAIGLVV 96
                                      689999999999******************9998875 PP

>> MscL  Large-conductance mechanosensitive channel, MscL
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.2    0.0008       2.1      15      50 ..      11      48 ..       4      84 .. 0.78
   2 ?    1.0   4.5      0.19   4.8e+02      12      28 ..      85     101 ..      77     102 .] 0.86

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0008
                              MscL 15 idLAvgviiGaaft..kiVtslvkdiimpliglllggv 50
                                      + +A gv++G+ f+  ++   l+k+  +p  ++++gg+
  gi|242399982|ref|YP_002995407.1| 11 VLMAFGVVVGGIFEnsNLTYRLTKKYTNPEKAAIVGGA 48
                                      679**********6225888888888888888888764 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.19
                              MscL  12 GnvidLAvgviiGaaft 28 
                                       G ++ +A+g+++Gaa++
  gi|242399982|ref|YP_002995407.1|  85 GGLVGVAIGLVVGAAVG 101
                                       778999********975 PP

>> DUF456  Protein of unknown function (DUF456)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   2.1     0.012        30      28      78 ..       7      54 ..       2      62 .. 0.68
   2 ?    6.6  11.6    0.0035         9      58      94 ..      65     101 ..      55     102 .] 0.67

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.012
                            DUF456 28 gwlflavllvlallglvldylapalgakraGaskrgligaivGaivGffll 78
                                       ++++++++ +++ g++ +  ++++ +k++  ++++   aivG+ +G+ l+
  gi|242399982|ref|YP_002995407.1|  7 ALGLVLMAFGVVVGGIFENSNLTYRLTKKYTNPEKA---AIVGGAAGTALG 54
                                      456677777777788888888899999999887766...555555554332 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0035
                            DUF456  58 GaskrgligaivGaivGffllpplGlllgpflgaflg 94 
                                        +  ++ iga vGa vG+ +++ +G+ +g ++ga +g
  gi|242399982|ref|YP_002995407.1|  65 SGRAAAYIGARVGARVGAAFGGLVGVAIGLVVGAAVG 101
                                       4556677777777777777777777777777777664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       792  (0.0441742); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 672.80
//
Query:       gi|242399983|ref|YP_002995408.1|  [L=169]
Description: hypothetical protein TSIB_2012 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-30  105.8  13.9    2.6e-30  105.5  13.9    1.0  1  SpoIIM    Stage II sporulation protein M


Domain annotation for each model (and alignments):
>> SpoIIM  Stage II sporulation protein M
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.5  13.9   1.4e-34   2.6e-30       1     155 [.       3     162 ..       3     163 .. 0.86

  Alignments for each domain:
  == domain 1  score: 105.5 bits;  conditional E-value: 1.4e-34
                            SpoIIM   1 alllflvgillgallaasnfaeqis...seskensalslflaifanNlrvalllfllGllllgiptilvllinGfvl 74 
                                       ++++fl+g+++g+++a  n+    s   + +  ++++  +l++f++N++va+ll+ + + +lg++t++ l+ nGf+l
  gi|242399983|ref|YP_002995408.1|   3 SVFFFLLGLIFGVFSALFNDY---SayfGFDPFDNSNPGVLFFFKHNIKVAFLLWCGAV-TLGVITLVNLFSNGFIL 75 
                                       5799*************3333...22333333334445799**************9996.***************** PP

                            SpoIIM  75 GavaalvaefgglllflllilPhgilelpaiiiagaaglrlgkal......rsrrkalkeakrellklllllvplll 145
                                       G+   +++++ g++  lll+lPhgi+e+p +iiag+ag+++ ++l      +++   ++e ++e++kl+ +++ l+l
  gi|242399983|ref|YP_002995408.1|  76 GSAVRTTSTQIGVFRTLLLVLPHGIFEIPGLIIAGSAGFKIPYELlrfalgKKEEMITEEDAKEFFKLVGVSIALIL 152
                                       *66666666656*********************************999998777778888***************** PP

                            SpoIIM 146 iAaliEafvt 155
                                       iAa+iE+ +t
  gi|242399983|ref|YP_002995408.1| 153 IAAIIESKIT 162
                                       ******9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1177.58
//
Query:       gi|242399984|ref|YP_002995409.1|  [L=429]
Description: ATPase, AAA superfamily [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.6e-38  131.0   0.2      1e-37  129.1   0.1    2.0  2  AAA_14        AAA domain
    8.2e-13   48.6   0.1    1.4e-12   47.8   0.1    1.5  1  DUF4143       Domain of unknown function (DUF4143)
    0.00057   19.9   0.3      0.027   14.4   0.1    2.7  3  ATPase_2      ATPase domain predominantly from Archaea
     0.0013   19.1   0.0     0.0098   16.3   0.0    2.2  2  RNA_helicase  RNA helicase
     0.0063   16.8   0.0      0.059   13.6   0.0    2.5  2  AAA_22        AAA domain
  ------ inclusion threshold ------
      0.011   15.8   0.0       0.02   14.9   0.0    1.4  1  ResIII        Type III restriction enzyme, res subunit
      0.018   13.9   0.0      0.041   12.7   0.0    1.6  1  AAA_35        AAA-like domain
      0.033   13.9   0.0       0.19   11.4   0.0    2.2  3  AAA_24        AAA domain
       0.11   13.0   0.0         17    6.0   0.0    2.5  2  AAA_18        AAA domain
       0.15   11.9   0.0       0.29   10.9   0.0    1.4  1  DNA_pack_N    Probable DNA packing protein, N-terminus
        0.2   11.6   0.1        1.2    9.0   0.0    2.1  2  BBS2_N        Ciliary BBSome complex subunit 2, N-terminal


Domain annotation for each model (and alignments):
>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.1   0.1   6.4e-41     1e-37       3     131 .]      35     168 ..      33     168 .. 0.91
   2 ?   -1.7   0.0       1.7   2.7e+03      13      22 ..     267     276 ..     263     296 .. 0.78

  Alignments for each domain:
  == domain 1  score: 129.1 bits;  conditional E-value: 6.4e-41
                            AAA_14   3 kilvitGaRrvGKTtllkqlikell...vkkesilyinldderdkkladpe..kllelileklke..ekktylflDE 72 
                                       ++lvi G+Rr+GKT++++q+ikell   v+ke+++yinl+d+r  + +  +   ll+++ +++ e  ++++y+flDE
  gi|242399984|ref|YP_002995409.1|  35 RALVIIGPRRAGKTYFMFQIIKELLkqgVRKEETIYINLEDPRIIDTTLDDllGLLDVYYSQFPEnvKGHNYFFLDE 111
                                       789*****************************************8877554556667777774335799******** PP

                            AAA_14  73 iqevpewekalkslvdegknldvivtGSnskllskeiatslagrvaeielyplsfaEfl 131
                                       iq v++wek+++ l+d++   +viv+GS+s llskeiat+l+gr   i++yp+sf+E+l
  gi|242399984|ref|YP_002995409.1| 112 IQTVKNWEKFVRFLLDKN--QRVIVSGSSSRLLSKEIATELRGRSVPIRVYPFSFREIL 168
                                       ****************77..58***********************************96 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.7
                            AAA_14  13 vGKTtllkql 22 
                                       vGKTt+++ l
  gi|242399984|ref|YP_002995409.1| 267 VGKTTVANYL 276
                                       8****97644 PP

>> DUF4143  Domain of unknown function (DUF4143)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.8   0.1   8.7e-16   1.4e-12      21     120 ..     285     372 ..     179     374 .. 0.80

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 8.7e-16
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DUF4143  21 verlppwsespnskkrlrkspKlyfvDtGLlvallgldkeelledsenkGallEnlVaqeLlkysekegaklyyyrd 97 
                                       ++ l++    +  k +    +K y+vD GLl++ lg++         ++G+llEnlV+ eLlk+  + + +++yyr+
  gi|242399984|ref|YP_002995409.1| 285 FYPLRAL--IKSYKLQELYGFKPYLVDNGLLTS-LGVQ---------DEGRLLENLVFTELLKFDLEPNRDVFYYRT 349
                                       5555555..666666777789*********999.4444.........369**************8888********* PP

                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                           DUF4143  98 kngaEvDfvielkggkivpiEvK 120
                                       ++g+EvDfvi +kg+   +i+v 
  gi|242399984|ref|YP_002995409.1| 350 RDGKEVDFVILEKGRIKQAIQVT 372
                                       **********8778777888875 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   1.7e-05     0.027      21      57 ..      35      73 ..      26      85 .. 0.79
   2 ?    2.4   0.0     0.076   1.2e+02     152     197 ..     124     167 ..     108     207 .. 0.79
   3 ?   -3.3   0.0       4.1   6.6e+03      29      39 ..     265     275 ..     262     294 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.7e-05
                          ATPase_2 21 eiyfiYGpegsGKtaLlkeiienledkdk..yviyyial 57
                                      + ++i Gp++ GKt ++ +ii++l++++   +   yi+l
  gi|242399984|ref|YP_002995409.1| 35 RALVIIGPRRAGKTYFMFQIIKELLKQGVrkEETIYINL 73
                                      5689********************876654444444555 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.076
                          ATPase_2 152 ltkekhlcvviclsSeglfiervyneselegrhkyilvddldketa 197
                                        + +k+ +v++ +sS  l+ +  +   el+gr+  i v ++ + ++
  gi|242399984|ref|YP_002995409.1| 124 FLLDKNQRVIVSGSSSRLLSK--EIATELRGRSVPIRVYPFSFREI 167
                                       556789999999999999998..56678999999999999977665 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 4.1
                          ATPase_2  29 egsGKtaLlke 39 
                                       +++GKt++ + 
  gi|242399984|ref|YP_002995409.1| 265 INVGKTTVANY 275
                                       58999987654 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0     6e-06    0.0098       2      46 ..      38      81 ..      37     124 .. 0.72
   2 ?   -0.4   0.0      0.91   1.5e+03       8      18 ..     266     276 ..     261     295 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 6e-06
                      RNA_helicase  2 wlyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdg 46
                                      ++ Gp++ GK++++ +++k+llk+    k++++y++  +  + d 
  gi|242399984|ref|YP_002995409.1| 38 VIIGPRRAGKTYFMFQIIKELLKQG-VRKEETIYINLEDPRIIDT 81
                                      799*******************988.7777999997766666554 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.91
                      RNA_helicase   8 geGKStlakeL 18 
                                       ++GK+t+a++L
  gi|242399984|ref|YP_002995409.1| 266 NVGKTTVANYL 276
                                       68*******95 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   3.6e-05     0.059       5      66 ..      34      92 ..      30     156 .. 0.75
   2 ?   -1.1   0.0       1.3     2e+03      16      26 ..     267     277 ..     266     298 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.6e-05
                            AAA_22  5 agilvvtGesGtGKTtllrrlleqldeeakaee..erpevvfvtlpsstsskdllrellralgl 66
                                      ++ lv++G+  +GKT+ + ++ ++l      ++  ++ e+++++l  +   ++ l +ll  l++
  gi|242399984|ref|YP_002995409.1| 34 QRALVIIGPRRAGKTYFMFQIIKELL-----KQgvRKEETIYINLEDPRIIDTTLDDLLGLLDV 92
                                      789***************99999994.....3346999******99999777777777777774 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.3
                            AAA_22  16 tGKTtllrrll 26 
                                       +GKTt+++ l 
  gi|242399984|ref|YP_002995409.1| 267 VGKTTVANYLE 277
                                       7****998764 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 ?   14.9   0.0   1.2e-05      0.02      22      96 ..      32     108 ..       9     143 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.2e-05
                                       .TTSEEEEEESTTSTHHHHHHHHHHHH-S.......-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B-- CS
                            ResIII  22 krdkrglikmaTGtGKTlvaaklierllkkgkee..kflflvprkslleqtleefkkflseaykeigkkvsgdkkka 96 
                                       k ++ ++i  +  +GKT+ ++++i++llk+g ++   + +      +++ tl+++  +l+ +y++  ++v+g ++ +
  gi|242399984|ref|YP_002995409.1|  32 KVQRALVIIGPRRAGKTYFMFQIIKELLKQGVRKeeTIYINLEDPRIIDTTLDDLLGLLDVYYSQFPENVKGHNYFF 108
                                       55666667777779***************98776657777788899**************99999999999999887 PP

>> AAA_35  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.5e-05     0.041      18      69 ..      21      75 ..      12     134 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.5e-05
                            AAA_35 18 pieekcyeeiekpGalirikapkkmGKtSLlarilakakqq...gyktvsldlql 69
                                       +e++++ +i k    + i +p++ GKt ++ +i+++  +q   + +t++++l+ 
  gi|242399984|ref|YP_002995409.1| 21 LVERNINYSIPKVQRALVIIGPRRAGKTYFMFQIIKELLKQgvrKEETIYINLED 75
                                      688999999999999999*******************999933334577888764 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00012      0.19       5      44 ..      37      84 ..      34     132 .. 0.74
   2 ?   -1.2   0.0      0.89   1.5e+03      13      23 ..     267     279 ..     265     287 .. 0.75
   3 ?   -3.1   0.0       3.2   5.3e+03     107     142 ..     380     416 ..     378     420 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00012
                            AAA_24  5 iliyGpsgiGKTtlakel..........gpkplfidtekGlksldadkfp 44
                                      ++i+Gp  +GKT+++ ++          ++++++i++e+   ++ ++ ++
  gi|242399984|ref|YP_002995409.1| 37 LVIIGPRRAGKTYFMFQIikellkqgvrKEETIYINLED--PRIIDTTLD 84
                                      79****************9999****9999999999998..445554444 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.89
                            AAA_24  13 iGKTtlakel..g 23 
                                       +GKTt+a+ l   
  gi|242399984|ref|YP_002995409.1| 267 VGKTTVANYLefL 279
                                       8******988553 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 3.2
                            AAA_24 107 laeefrrllkklqelrk.nvifiahektrkdedpege 142
                                       +++e++ l+ + +el+  +  +i + ++++++++ +e
  gi|242399984|ref|YP_002995409.1| 380 YEREISALVGASKELNCrDLLLITWDQEETIKKKGKE 416
                                       6778888888999999999999999999999988766 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0      0.03        48       2      86 ..      38     141 ..      37     149 .. 0.70
   2 ?    6.0   0.0      0.01        17       8      22 ..     266     280 ..     265     357 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.03
                            AAA_18   2 lltGtpGvGKttlakeLskrl.gf..................gvnlrdvakenglllevdpealdeskrldedkldk 59 
                                       ++ G+ ++GKt +   + k+l +                    + l d++   + +++++pe ++ ++ +  d   +
  gi|242399984|ref|YP_002995409.1|  38 VIIGPRRAGKTYFMFQIIKELlKQgvrkeetiyinledpriiDTTLDDLLGLLDVYYSQFPENVKGHNYFFLDE-IQ 113
                                       68999******988888554423355667777899999999999999**************9555555555555.22 PP

                            AAA_18  60 lldaleenss.aleegknlvidghlael 86 
                                        ++++e+  +  l++++ ++++g  + l
  gi|242399984|ref|YP_002995409.1| 114 TVKNWEKFVRfLLDKNQRVIVSGSSSRL 141
                                       3333333333567777888887766655 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.01
                            AAA_18   8 GvGKttlakeLskrl 22 
                                        vGKtt+a++L+ ++
  gi|242399984|ref|YP_002995409.1| 266 NVGKTTVANYLEFLE 280
                                       69*********6554 PP

>> DNA_pack_N  Probable DNA packing protein, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00018      0.29     182     208 ..      34      60 ..      18      66 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00018
                        DNA_pack_N 182 qkasvfLvPRRHGKTWilvalisllla 208
                                       q+a v + PRR GKT+++  +i  ll+
  gi|242399984|ref|YP_002995409.1|  34 QRALVIIGPRRAGKTYFMFQIIKELLK 60 
                                       99********************87765 PP

>> BBS2_N  Ciliary BBSome complex subunit 2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0   0.00076       1.2      77     100 ..     331     354 ..     322     359 .. 0.91
   2 ?   -0.8   0.0      0.84   1.4e+03      42      74 ..     372     403 ..     360     407 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00076
                            BBS2_N  77 tnllaYdveeNsdlFykevpDGvn 100
                                       t+ll +d e N d+Fy  + DG +
  gi|242399984|ref|YP_002995409.1| 331 TELLKFDLEPNRDVFYYRTRDGKE 354
                                       789******************976 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.84
                            BBS2_N  42 esevslLninkevtalaagklkekqekdiLlig 74 
                                       + e++  n ++e++al  ++ ke + +d+Lli 
  gi|242399984|ref|YP_002995409.1| 372 TYELNESNYEREISALVGAS-KELNCRDLLLIT 403
                                       55677778899999997655.555588999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.49
# Mc/sec: 2632.19
//
Query:       gi|242399985|ref|YP_002995410.1|  [L=317]
Description: UDP-or dTTP-glucose 4-epimerase or 4-6-dehydratase [Thermococcus sibiricus MM 739]
Scores for complete 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-56  190.5   0.0    4.1e-56  190.2   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    1.4e-51  175.9   0.0    3.9e-51  174.4   0.0    1.6  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    1.1e-22   80.4   0.0    1.4e-22   80.1   0.0    1.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    1.6e-16   60.2   0.0    2.1e-16   59.9   0.0    1.1  1  RmlD_sub_bind    RmlD substrate binding domain
    9.8e-16   57.7   0.0    7.2e-15   54.9   0.0    1.9  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    1.3e-13   51.3   0.0    1.8e-13   50.8   0.0    1.2  1  NAD_binding_10   NAD(P)H-binding
    1.9e-12   46.9   0.1      3e-10   39.7   0.1    2.6  1  NAD_binding_4    Male sterility protein
    2.3e-10   40.4   0.0    1.2e-07   31.5   0.0    2.2  2  NmrA             NmrA-like family
    5.6e-07   29.2   0.1    8.3e-06   25.4   0.0    2.4  3  adh_short        short chain dehydrogenase
  ------ inclusion threshold ------
      0.011   15.6   0.3       0.13   12.2   0.3    2.2  1  KR               KR domain
      0.058   13.7   0.0       0.11   12.8   0.0    1.5  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 !  190.2   0.0   2.5e-59   4.1e-56       1     241 []       3     241 ..       3     241 .. 0.94

  Alignments for each domain:
  == domain 1  score: 190.2 bits;  conditional E-value: 2.5e-59
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC......EEEE--TT-HHHHHHHHHHHT-SEEEE- CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl......elveldltdrsalerlfkeeqpdavihl 71 
                                       +lVtG++GfiGs+lv++l+e g+ev +ld ls +s ++++         e++++dl+ r+ +e+++k  ++dav+hl
  gi|242399985|ref|YP_002995410.1|   3 VLVTGGAGFIGSHLVDRLMEDGHEVRVLDDLSAGSLENLK-GWidherfEFMHGDLRRRDICEKAVK--GVDAVFHL 76 
                                       79*****************************555554444.445999********************..9******* PP

                                       -S---HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHH CS
                         Epimerase  72 AavggvaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKla 148
                                       Aa   v+   ++p+ ++e+n+ +t+nllea+rk +vk l f sSs+vYG+ +++p+ e+   gpl+p s Y+ aKla
  gi|242399985|ref|YP_002995410.1|  77 AANPEVRIGTQSPELLYETNVLITYNLLEAMRKEDVKALAFTSSSTVYGEAKTIPTPEDY--GPLEPISVYGGAKLA 151
                                       *****************************************************9977777..8************** PP

                                       HHHHHHHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHH CS
                         Epimerase 149 geklveayaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillv 225
                                       +e l+  ya++++++a+++rl n++G+r    ++++vi  +i+k++++ + + +lgdgt++  +l+v+D +ea+l++
  gi|242399985|ref|YP_002995410.1| 152 AEALISGYAHTFDVKAVVFRLANIIGKR----SNHGVIYDFINKLKKNPNRLEILGDGTQRKSYLHVSDTVEAMLYL 224
                                       ****************************....***************999*************************** PP

                                       HHHHTT-ST.TEEEEES CS
                         Epimerase 226 lehvdagdk.geiyniG 241
                                        ++  + dk  ++yniG
  gi|242399985|ref|YP_002995410.1| 225 FKEFLKEDKiYDAYNIG 241
                                       *9976655557799998 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 !  174.4   0.0   2.4e-54   3.9e-51       1     331 [.       4     308 ..       4     309 .. 0.87

  Alignments for each domain:
  == domain 1  score: 174.4 bits;  conditional E-value: 2.4e-54
                                       EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-S CS
                     GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpd 77 
                                       L+TG+aGfiGs+l+++L+e g+ev +++++s+  ++++++ + +      +e++++++gDl+ ++  e++++ v  d
  gi|242399985|ref|YP_002995410.1|   4 LVTGGAGFIGSHLVDRLMEDGHEVRVLDDLSA-GSLENLKGWID------HERFEFMHGDLRRRDICEKAVKGV--D 71 
                                       9***********************98876544.46666666654......469********************9..9 PP

                                       EEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TT.S-----SHH CS
                     GDP_Man_Dehyd  78 evynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEt.tpfyPrsPY 153
                                       +v++LAA   V+   ++Pe  +e+nvl t++LLea+r+  ++    + ++S+s+vYG+++ +p  E+  p++P s Y
  gi|242399985|ref|YP_002995410.1|  72 AVFHLAANPEVRIGTQSPELLYETNVLITYNLLEAMRKEDVK---ALAFTSSSTVYGEAKTIPTPEDyGPLEPISVY 145
                                       **************************************8764...6889**************988768******** PP

                                       HHHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHH CS
                     GDP_Man_Dehyd 154 aaaKlyadwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwghvkDyv 230
                                       + aKl+a+ ++  y +++++ av+ +l n  + r  ++     i +++ + +++ +   +lG++ ++++++hv+D+v
  gi|242399985|ref|YP_002995410.1| 146 GGAKLAAEALISGYAHTFDVKAVVFRLANIIGKRS-NH---GVIYDFINKLKKNPNRLEILGDGTQRKSYLHVSDTV 218
                                       *********************************95.44...569**********9999999**************** PP

                                       HHHHHHHHC....SS-.--EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS- CS
                     GDP_Man_Dehyd 231 eamwlmlqq....dkp.edyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpge 302
                                       eam  ++++    dk  + y+i++ +  +v+e++e+   e+g + e+  +                 vd  +  +g+
  gi|242399985|ref|YP_002995410.1| 219 EAMLYLFKEflkeDKIyDAYNIGSEDWITVKEIAEIVSREMGLNPEFYFT---------------GGVDGGRGWKGD 280
                                       **9765443222266547799*********************99888643...............346777777899 PP

                                       -SB--B-THHHHHHH----SS-HHHHHHH CS
                     GDP_Man_Dehyd 303 vdlllgdaskakeeLgWkpkvsfeelvre 331
                                       v+ +l +++kak + gWkpk++  + v++
  gi|242399985|ref|YP_002995410.1| 281 VKVMLLNIEKAKAK-GWKPKMNSYQAVEK 308
                                       99999999999966.99999988887776 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 !   80.1   0.0   8.3e-26   1.4e-22       1     226 [.       4     222 ..       4     247 .. 0.83

  Alignments for each domain:
  == domain 1  score: 80.1 bits;  conditional E-value: 8.3e-26
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkk..viegDvtdkdkleealegvdvvihlas 75 
                                       +vtGgaGF+G++lv +L++ +  +evrvlD     +l +    ++ +   +++gD++  d  e+a++gvd+v+hla+
  gi|242399985|ref|YP_002995410.1|   4 LVTGGAGFIGSHLVDRLMEDG--HEVRVLDDLSAGSLENLKGWIDHERfeFMHGDLRRRDICEKAVKGVDAVFHLAA 78 
                                       69****************999..6******66655554433333333355*************************** PP

                         3Beta_HSD  76 lvdva.gkltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKa 151
                                         +v+ g+++ + +++ nv  T n+lea +k +v++l +tSs  v g+   ++ i     e + +  + ++y   K 
  gi|242399985|ref|YP_002995410.1|  79 NPEVRiGTQSPELLYETNVLITYNLLEAMRKEDVKALAFTSSSTVYGE---AKTIPT--PEDYGPLEPISVYGGAKL 150
                                       *999735999**************************************...888883..3445677799******** PP

                         3Beta_HSD 152 laEklvlkaNgrtlknggrlyTcaLRpagiyGegdk..llvpllkqlaklglalfkigdeevlsdrvYvgNvawahi 226
                                        aE+l+            ++  +  R a i G +++  ++  ++++l+k+ + l  +gd  + +++  v   + a +
  gi|242399985|ref|YP_002995410.1| 151 AAEALISGYAH-----TFDVKAVVFRLANIIGKRSNhgVIYDFINKLKKNPNRLEILGDGTQRKSYLHVSDTVEAML 222
                                       *****976555.....44778999********998733577999******999999999999999998877666655 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 !   59.9   0.0   1.3e-19   2.1e-16       1     234 [.       1     262 [.       1     268 [. 0.89

  Alignments for each domain:
  == domain 1  score: 59.9 bits;  conditional E-value: 1.3e-19
                                       EEEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT....................T--TTSHHHHHHHHHHH--SEEEE CS
                     RmlD_sub_bind   1 mkilvtGanGqlGseLakqlaeeglevlaltre....................eldltdaeavaellkeakpdvvvn 57 
                                       mk+lvtG+ G +Gs+L+++l e+g+ev  l+                      + dl++++  ++++k    d+v +
  gi|242399985|ref|YP_002995410.1|   1 MKVLVTGGAGFIGSHLVDRLMEDGHEVRVLDDLsagslenlkgwidherfefmHGDLRRRDICEKAVKG--VDAVFH 75 
                                       89****************************766799*******************************99..789*** PP

                                       ------HHHHHHSHHHHHHHHTHHHHHHHHHHHHCT-E.EEEEEEGGGS-S-TTS-B-TT.S----SSHHHHHHHHH CS
                     RmlD_sub_bind  58 aAAytavDkaEseeeaayavnaeavealAeaaaavgal.LihvStDyVFdGekkrpYeed.detsPlnvYGrtKlaG 132
                                       +AA  +v    + +e+ y+ n+  + +l ea ++ +++ L + S+  V+  +k+ p  ed  + +P++vYG +Kla 
  gi|242399985|ref|YP_002995410.1|  76 LAANPEVRIGTQSPELLYETNVLITYNLLEAMRKEDVKaLAFTSSSTVYGEAKTIPTPEDyGPLEPISVYGGAKLAA 152
                                       ***********************************9954999*******999999966652688************* PP

                                       HHHHHH....H-SSEEEEEE-SEESSSSS-.HH.HHHHHHHHH-SEEEEESS..-EE--EEHHHHHHHHHHHHHHCH CS
                     RmlD_sub_bind 133 Eqavla....agkkalivRtswvygekgkn.fv.ktmlrlakereelkvvaD..qlgsPTsardlAevllqllekaa 201
                                       E  +         ka+++R + + g++ +   +   + +l k+ ++l++  D  q  s  ++ d  e++l+l ++ +
  gi|242399985|ref|YP_002995410.1| 153 EALISGyahtFDVKAVVFRLANIIGKRSNHgVIyDFINKLKKNPNRLEILGDgtQRKSYLHVSDTVEAMLYLFKEFL 229
                                       ****98433234589*********995554144145666779999*****995566667789*************** PP

                                       H.GGG-EEEE---BS-EEHHHHHHHHHHHHCHT CS
                     RmlD_sub_bind 202 eekelagvyHlanegetswlefArailkeagad 234
                                       +e +++  y +++e+ ++  e+A+ + +e+g +
  gi|242399985|ref|YP_002995410.1| 230 KEDKIYDAYNIGSEDWITVKEIAEIVSREMGLN 262
                                       **************************9998875 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.9   0.0   4.4e-18   7.2e-15       1     194 [.       3     201 ..       3     267 .. 0.78

  Alignments for each domain:
  == domain 1  score: 54.9 bits;  conditional E-value: 4.4e-18
                                       EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T CS
                   Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelk 77 
                                       vlvtG++G iGs+lv+++++   +  +l + +  +l +++  +    +++++++      gd+r ++ +eka++  +
  gi|242399985|ref|YP_002995410.1|   3 VLVTGGAGFIGSHLVDRLMEDGHEVRVLDDLSAGSLENLKGWI----DHERFEFM----HGDLRRRDICEKAVK--G 69 
                                       8*****************9987665555566667777777665....56667555....8**************..* PP

                                       -SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEE......GGGS.........S--SHHH CS
                   Polysacc_synt_2  78 vdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliSt......DKAv.........nPtnvmG 139
                                       vd+vfh AA  +V +  + p    +tNvl t n++ea  + +vk++ + S+       K +         +P++v+G
  gi|242399985|ref|YP_002995410.1|  70 VDAVFHLAANPEVRIGTQSPELLYETNVLITYNLLEAMRKEDVKALAFTSSstvygeAKTIptpedygplEPISVYG 146
                                       *********************************************99988722333324433333333338****** PP

                                       HHHHHHHHHHHHGGG--SSS--EEEEEEE-EETT..GTTSSHHHHHHHHHTT.SSEEE CS
                   Polysacc_synt_2 140 atKrlaekllqalakeseekktkfvvvRfGNVlg..SrGSviplFkkqikeg.gpvtv 194
                                        +K++ae l+  +a++    + k vv R  N++g  S+  vi  F +++k++ + + +
  gi|242399985|ref|YP_002995410.1| 147 GAKLAAEALISGYAHTF---DVKAVVFRLANIIGkrSNHGVIYDFINKLKKNpNRLEI 201
                                       ***********999998...89999********9556678999999999887566665 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 !   50.8   0.0   1.1e-16   1.8e-13       1     131 [.       7     156 ..       7     175 .. 0.76

  Alignments for each domain:
  == domain 1  score: 50.8 bits;  conditional E-value: 1.1e-16
                                       TTTSHHHHHHHHHHHHC-T-EEEEEET.THHHCHHHH...CTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCC CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvR.npeklaele...aeeglevvegdvtdvedlaealkgadaVvsalggggk 73 
                                       G+ G +G++lv++l ++ ghev++l   ++ +l++l+   ++e+ e ++gd+   +  ++a+kg+daV+  +++ + 
  gi|242399985|ref|YP_002995410.1|   7 GGAGFIGSHLVDRLMED-GHEVRVLDDlSAGSLENLKgwiDHERFEFMHGDLRRRDICEKAVKGVDAVFHLAANPEV 82 
                                       99***************.5***9984423445555555559***************************999977666 PP

                                       .....HHHH..........HHHHHHHHHHCT--EEEEEEETTTTSGCGCH...HHHHHHHCCHHHHHHHHHHHHHH CS
                    NAD_binding_10  74 .....deeg..........aknivdaakeagvkRfvlvsaigvgdevpge...fgewnkellkaylaakraaeell 131
                                                          + n+++a+++++vk + + s+  v+ e+++     +    e ++ y  ak aae+l+
  gi|242399985|ref|YP_002995410.1|  83 rigtqS--PellyetnvliTYNLLEAMRKEDVKALAFTSSSTVYGEAKTIptpEDYGPLEPISVYGGAKLAAEALI 156
                                       565441..14456666799************************987554210022222245566667777777765 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.7   0.1   1.9e-13     3e-10       1     215 [.       5     185 ..       5     214 .. 0.81

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 1.9e-13
                                       EE-TTSHHHHHHHHHHHHHS-.TEEEEEE-SSSHHHHHHHHHHHT-SS-HHHHHHHHHTTTEEEEE--TTSGGGG-- CS
                     NAD_binding_4   1 lTGaTGFLGkvLlekLLrttpevkiyllvRaksgesaeeRleeelekkelfsallkelaerikvveGDlseprlGLs 77 
                                       +TG+ GF+G++L+ +L+++  ev++   + a s     e       + + +        er ++++GDl + +    
  gi|242399985|ref|YP_002995410.1|   5 VTGGAGFIGSHLVDRLMEDGHEVRVLDDLSAGSL----E-------NLKGWI-----DHERFEFMHGDLRRRD---- 61 
                                       7******************996433333333322....2.......222332.....26899********998.... PP

                                       HHHHHHHHHH--EEEE--SS..-S.STTSSE.EHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS CS
                     NAD_binding_4  78 eedlqelaeevdviihsaAt..vnfdepyke.llrvNveGtrevlelakklkklkvllhvSTayvngeregeveekv 151
                                           ++ ++ vd+++h aA+  v++  + +e l+++Nv+ t ++le  +k   + +l + S+++v+ge ++      
  gi|242399985|ref|YP_002995410.1|  62 --ICEKAVKGVDAVFHLAANpeVRIGTQSPElLYETNVLITYNLLEAMRKEDVK-ALAFTSSSTVYGEAKT------ 129
                                       ..467888999********844666666555589************99988777.**************94...... PP

                                       -H......HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE-.-SSST-- CS
                     NAD_binding_4 152 yeegekeekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitg.esktGwi 215
                                                  + e     +    Y   K +aE l+  +++  ++++v++R+ +i+g +s  G+i
  gi|242399985|ref|YP_002995410.1| 130 ---------IPTPEDYGPLEPISVYGGAKLAAEALISGYAHTFDVKAVVFRLANIIGkRSNHGVI 185
                                       .........45677777777888*****************999************9966666766 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.0   7.5e-11   1.2e-07       1      83 [.       3      86 ..       3     120 .. 0.87
   2 !    6.9   0.0    0.0026       4.2     159     228 ..     191     262 ..     180     284 .. 0.79

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 7.5e-11
                                      EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHH....HSTTEEEES-TT-HHHHHHHHTT-SEEEE---GG CS
                              NmrA  1 IlviGaTGrqGksvvrallkaghkvralvRdtkselakslk....eaGvelvkgdlddkeslvealkgvdvvfsvtgfy 75
                                      +lv+G++G +G+++v+ l+++gh+vr+l  d++   +++lk    ++  e+++gdl  +++ ++a+kgvd+vf   +  
  gi|242399985|ref|YP_002995410.1|  3 VLVTGGAGFIGSHLVDRLMEDGHEVRVL-DDLSAGSLENLKgwidHERFEFMHGDLRRRDICEKAVKGVDAVFHLAA-- 78
                                      79************************98.57766666665522227899*************************999.. PP

                                      S-HHHHHH CS
                              NmrA 76 skeiedgk 83
                                      + e+++g+
  gi|242399985|ref|YP_002995410.1| 79 NPEVRIGT 86
                                      78888776 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0026
                                       EE-TTS.-EEEEESS-TTS-EE-HHHHHHHHHHHHHHH...HHHHTTEEEEE-SEEE-HHHHHHHHHHHHTS- CS
                              NmrA 159 dtappedkvtllgpgnpkavlldaeeDiGafvikilkd...prklkgkriklagntlsgneivelfekkigkt 228
                                       +++++ + +++lg+g     +l ++ D+ ++++ ++k+   ++k+   +   +++ ++++ei+e+ ++++g +
  gi|242399985|ref|YP_002995410.1| 191 KLKKNPNRLEILGDGTQRKSYL-HVSDTVEAMLYLFKEflkEDKIYDAYNIGSEDWITVKEIAEIVSREMGLN 262
                                       3444444899******999999.8999999888888885324444556777899***************9976 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0   5.1e-09   8.3e-06       3      73 ..       3      72 ..       1      77 [. 0.85
   2 ?    1.0   0.0      0.16   2.6e+02     146     170 ..     142     166 ..     136     174 .. 0.83
   3 ?   -3.7   0.0       4.2   6.9e+03      48      70 ..     290     312 ..     284     314 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 5.1e-09
                                      EEEESTTSHHHHHHHHHHHHTT-EEEE.EESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHH CS
                         adh_short  3 vlvtGassGIGraiakelakeGakvvv.vdrseekleevakelkeegakalaiqvDvtdreevealvekavk 73
                                      vlvtG+++ IG  ++++l+++G +v v  d s+  le+++  +    +++ ++++D++ r+ +e++v+ + +
  gi|242399985|ref|YP_002995410.1|  3 VLVTGGAGFIGSHLVDRLMEDGHEVRVlDDLSAGSLENLKGWIDH--ERFEFMHGDLRRRDICEKAVKGVDA 72
                                      9**************************445566666666666665..68******************99865 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.16
                                       BHHHHHHHHHHHHHHHHHHHHHGGG CS
                         adh_short 146 vaaYsAsKaavagltrslakelapt 170
                                        ++Y+ +K a ++l++  a+ +  +
  gi|242399985|ref|YP_002995410.1| 142 ISVYGGAKLAAEALISGYAHTFDVK 166
                                       799************9999877665 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 4.2
                                       TSEEEEEE-TTTSHHHHHHHHHH CS
                         adh_short  48 gakalaiqvDvtdreevealvek 70 
                                       +aka  ++  ++++++ve++v++
  gi|242399985|ref|YP_002995410.1| 290 KAKAKGWKPKMNSYQAVEKTVRE 312
                                       56788888889999999988876 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.3   7.9e-05      0.13       3      29 ..       3      29 ..       2     130 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.9e-05
                                      EEEETTTSHHHHHHHHHHHHHHS-EEE CS
                                KR  3 ylitGGlGgLGlelarwlaekgarhlv 29
                                      +l+tGG+G +G +l++ l+e+g +  v
  gi|242399985|ref|YP_002995410.1|  3 VLVTGGAGFIGSHLVDRLMEDGHEVRV 29
                                      69********************76544 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   6.8e-05      0.11       5      75 ..       8      82 ..       4     120 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.8e-05
                                      S-SHHHHHHHHHHHH.TTEEEEEEESSH....HHHHHHHHTT.SEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHH CS
                            TrkA_N  5 GlGrvGrslaeeLse.ggkdvvvidkde....erveelreeg.levvvgdatdeevLeeagiekadaviaatgddea 75
                                      G+G +G++l+++L+e g+ +v v d+      e+++   +++ +e+++gd  ++++ e+a ++ +dav  ++ + e+
  gi|242399985|ref|YP_002995410.1|  8 GAGFIGSHLVDRLMEdGH-EVRVLDDLSagslENLKGWIDHErFEFMHGDLRRRDICEKA-VKGVDAVFHLAANPEV 82
                                      89*************556.6****9987544455666677778*************9998.6666766666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.64u 0.38s 00:00:01.02 Elapsed: 00:00:00.52
# Mc/sec: 1848.91
//
Query:       gi|242399986|ref|YP_002995411.1|  [L=134]
Description: Nucleotidyltransferase [Thermococcus sibiricus MM 739]
Scores for complete 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   61.6   0.0    7.2e-17   61.3   0.0    1.1  1  Polbeta       Polymerase beta, Nucleotidyltransferase
     0.0024   18.1   0.1     0.0037   17.5   0.1    1.4  1  NTP_transf_2  Nucleotidyltransferase domain
  ------ inclusion threshold ------
       0.17   11.7   0.0       0.21   11.4   0.0    1.1  1  NTP_transf_6  Nucleotidyltransferase


Domain annotation for each model (and alignments):
>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.3   0.0   1.2e-20   7.2e-17       1      92 [.      16     103 ..      16     104 .. 0.96

  Alignments for each domain:
  == domain 1  score: 61.3 bits;  conditional E-value: 1.2e-20
                                       -STTTTHHHHHHHHSTTEEEEEE-S------EEEEEEEESS---HHHHHHHHHHHHHH.SSSEEEEEETTTS-HHHH CS
                           Polbeta   1 ekikeilekekeielaylFGSrakgkareeSDiDlavllkekldleeelelaaelediklgkkvDlvdlneapplll 77 
                                       ++i+++l ++ke+ +ay++GS+ +++  +  DiD+a++++ ++dl +ele+++el     g  vD+ ++n+ap +++
  gi|242399986|ref|YP_002995411.1|  16 KRITDFLINRKEVLFAYIHGSFIENRPFR--DIDVAIYVDGDHDLAYELEMEEELTWF-VGFPVDVRVINDAPVTFR 89 
                                       57999******************988887..*************************99.9***************** PP

                                       HHHHHS-EEEES-SH CS
                           Polbeta  78 yeilkegkllyskde 92 
                                       +++l+ g+ll+s+d+
  gi|242399986|ref|YP_002995411.1|  90 FKALE-GELLFSRDD 103
                                       *****.*******97 PP

>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   6.2e-07    0.0037      11      80 ..      25      85 ..      11     101 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 6.2e-07
                                      HTTTSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEEEEECEEECC CS
                      NTP_transf_2 11 lepvakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleellglevdlvtrekle 80
                                      +  v  ++++GS+  +   +  DiD++++++ +++       l +  e++++l ++ g +vd+++++  +
  gi|242399986|ref|YP_002995411.1| 25 RKEVLFAYIHGSFIENR--PFRDIDVAIYVDGDHD-------LAYELEMEEELTWFVGFPVDVRVINDAP 85
                                      44477788899998776..999***********76.......688999999************9887766 PP

>> NTP_transf_6  Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   3.6e-05      0.21      31      82 ..      39      91 ..      27     108 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.6e-05
                      NTP_transf_6 31 setginDiDviYFdpsdlseeaekaleaklkelfp.elpwevkNqarmhlwne 82
                                      ++++ +DiDv+ + + d + + e+++e++l+  +  ++++ v N a +  +++
  gi|242399986|ref|YP_002995411.1| 39 ENRPFRDIDVAIYVDGDHDLAYELEMEEELTWFVGfPVDVRVINDAPVTFRFK 91
                                      678999****999999999***********99998888889999999887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); 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 0.35s 00:00:00.91 Elapsed: 00:00:00.56
# Mc/sec: 722.97
//
Query:       gi|242399987|ref|YP_002995412.1|  [L=145]
Description: hypothetical protein TSIB_2016 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-32  111.8   1.9      2e-32  111.6   1.9    1.1  1  DUF86           Protein of unknown function DUF86
    0.00038   20.4   1.5    0.00068   19.6   1.5    1.5  1  NTase_sub_bind  Nucleotidyltransferase substrate binding prot


Domain annotation for each model (and alignments):
>> DUF86  Protein of unknown function DUF86
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.6   1.9   2.2e-36     2e-32       4     119 .]      23     139 ..      20     139 .. 0.95

  Alignments for each domain:
  == domain 1  score: 111.6 bits;  conditional E-value: 2.2e-36
                                       HHHHHCCHH...TSTSCCGSHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----SSC..HHHHHHHTTSS-HHHHHH CS
                             DUF86   4 aleklkefteeldeeeflsdeleydavernlqvigEaaidiakhlakklgikkpgdy..ifeilaekgviaeepeep 78 
                                       al+ l+e+  + +ee+fl+++++  ++++nl v++Ea+idia hl++k++++ p+dy  +f++l+e+g+i+e+  ++
  gi|242399987|ref|YP_002995412.1|  23 ALQNLRELS-SFSEEDFLKNKHYISSAKYNLLVAIEACIDIAYHLISKNRMRLPQDYadTFRVLVENGIISEHLGKR 98 
                                       666777776.778**************************************************************** PP

                                       HHHHHCCHHHHHT-CCCTTHHHHHHHHHHTCHHHHHHHHHH CS
                             DUF86  79 wrkmiglRNrLvHgYlgidpeivwsiikenlpdleeflesi 119
                                       +  m+++RNrLvH Y++i+++++++ +k++++d+eefl++i
  gi|242399987|ref|YP_002995412.1|  99 LMLMVRFRNRLVHIYWEINDKKIYHYLKDDVRDVEEFLNKI 139
                                       *************************************9876 PP

>> NTase_sub_bind  Nucleotidyltransferase substrate binding protein like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   1.5   7.6e-08   0.00068       2     124 ..      16     139 ..      15     141 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 7.6e-08
                                       -HHHHHHHHHHHHHHHHHHH-.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTSSSCCTTTHHHHHHHHHTTS- CS
                    NTase_sub_bind   2 rlsnlekAlasLeeavelsrd.dplsdlerdgvIqrFEftyElawkllkryleeegisaeavsprdliReaaeagli 77 
                                       r+s+ e+Al++L+e  + s++   +++++++++  +  ++ E ++ +   ++ ++ +     +  d++R  +e+g+i
  gi|242399987|ref|YP_002995412.1|  16 RVSEAENALQNLRELSSFSEEdFLKNKHYISSAKYNLLVAIEACIDIAYHLISKNRMR-LPQDYADTFRVLVENGII 91 
                                       6788889999999888875442334455555555566666777777777777776664.333559************ PP

                                       S-..HHHHHHHHHHHGCGGGTTSHHHHHHHHHTHH.HHHHHHHHHHHHH CS
                    NTase_sub_bind  78 ed..gevwlemledRnltshtYdeetaeevveaiaeeylpelkallekl 124
                                       ++  g++ + m++ Rn+  h+Y e + +++++ ++ + + +++++l+k+
  gi|242399987|ref|YP_002995412.1|  92 SEhlGKRLMLMVRFRNRLVHIYWEINDKKIYHYLK-DDVRDVEEFLNKI 139
                                       6634788*************************999.7788888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1038  (0.057895); expected 358.6 (0.02)
Passed bias filter:                      575  (0.0320709); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.34s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 877.38
//
Query:       gi|242399988|ref|YP_002995413.1|  [L=331]
Description: Sugar-phosphate nucleotydyltransferase [Thermococcus sibiricus MM 739]
Scores for complete 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-40  136.9   0.0    9.9e-40  136.7   0.0    1.1  1  NTP_transferase  Nucleotidyl transferase
    9.8e-10   39.0   0.0    1.3e-09   38.7   0.0    1.2  1  NTP_transf_3     MobA-like NTP transferase domain
    6.4e-05   22.5   4.7    0.00093   18.8   1.6    3.3  3  Hexapep          Bacterial transferase hexapeptide (six repea
     0.0077   15.2   0.0       0.03   13.3   0.0    1.9  2  Fucokinase       L-fucokinase
  ------ inclusion threshold ------
      0.055   13.6   2.1       0.14   12.2   0.3    2.3  2  Trans_coact      Phage late-transcription coactivator


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 !  136.7   0.0   2.8e-43   9.9e-40       2     247 ..       3     234 ..       2     235 .. 0.93

  Alignments for each domain:
  == domain 1  score: 136.7 bits;  conditional E-value: 2.8e-43
                                       EEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGT.SEEEE CS
                   NTP_transferase   2 avILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfg.vevli 77 
                                        +I+aGG+ tRLwP+t+  +k+l+pv++k  +i++ l++  + g e    v+t++  +   ++++e++++g + ++ 
  gi|242399988|ref|YP_002995413.1|   3 VLIMAGGYATRLWPITKGKPKPLLPVGDK-YIIDYILEKTKDLGLEV--HVSTNKFFEKHFKNWAEKNNIGlIVEET 76 
                                       68***************************.9**********988876..8999999999999999999999877888 PP

                                       EEESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEEC CS
                   NTP_transferase  78 alepegkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGviead 154
                                       + e+e+ gt +A++ a+  l+ ++    +l+++gD l++  + e++k+   +    ++++ + + e a++yGv+ ++
  gi|242399988|ref|YP_002995413.1|  77 ISEEEKLGTIGAIKYAVSELGVDD----YLIVAGDNLFSFSLGEFLKHYSGRPL--IAVYDVGDFELAKRYGVVLVE 147
                                       8899999**************999....7*******************999988..999***************999 PP

                                       TTSBEEEEECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEE CS
                   NTP_transferase 155 eegrverfvEKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWsD 231
                                       + +rv++f+EKP ++k s+l+s+G+Y f ++v+++  ++lee +r ++  + +++ +l+++ + +a+ f+d  yW D
  gi|242399988|ref|YP_002995413.1| 148 G-DRVIDFQEKPLQPK-STLISTGVYAFPKDVIEKVGEYLEEGNRDSP--GYFIEWLLKKDVEIYAYKFDD--YWYD 218
                                       8.6*************.*******************669999966555..779******************..9*** PP

                                       XSSHHHHHHHHHHHHH CS
                   NTP_transferase 232 vGtldslleaneklae 247
                                       +G+ ds+lea++ l++
  gi|242399988|ref|YP_002995413.1| 219 IGSADSYLEAMKTLLK 234
                                       **********998876 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 !   38.7   0.0   3.5e-13   1.3e-09       1      98 [.       3     110 ..       3     191 .. 0.83

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 3.5e-13
                                       EEEEEESS-TTT.....TTTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH...CHHHHHHTTCTS-EEE-.... CS
                      NTP_transf_3   1 aviLAGGrSsRm.....ggdKallplggkpllervldalraagvdevvvvggd...eevlaalarlgvrvved.... 65 
                                       ++i+AGG ++R+     g++K+llp+g+k +++++l++ +++g+ ev v+++    ++ ++ +++ ++ ++++    
  gi|242399988|ref|YP_002995413.1|   3 VLIMAGGYATRLwpitkGKPKPLLPVGDKYIIDYILEKTKDLGL-EVHVSTNKffeKHFKNWAEKNNIGLIVEetis 78 
                                       58**********9999888***********************97.9******9886667777777765543332333 PP

                                       TTSS-SHHHHHHHHHHHH.SSSCEEEEETT-TT CS
                      NTP_transf_3  66 edpgkgplaslaaalraaadadavlvlacDmPl 98 
                                       e++  g++++++ a++++ + d +l++a+D  +
  gi|242399988|ref|YP_002995413.1|  79 EEEKLGTIGAIKYAVSEL-GVDDYLIVAGDNLF 110
                                       77789************9.9**********977 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   1.6   2.6e-07   0.00093       6      35 ..     251     280 ..     246     281 .. 0.73
   2 ?   -1.9   0.0      0.92   3.3e+03       8      18 ..     287     297 ..     285     300 .. 0.52
   3 ?    2.8   0.0     0.029     1e+02       2      24 ..     303     329 ..     302     330 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.6e-07
                                       TTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                           Hexapep   6 snvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                       + v+I ++a i+g  ++G++++Ig+++vi 
  gi|242399988|ref|YP_002995413.1| 251 NPVVIKKGARILGRSIVGPYAYIGENCVIE 280
                                       557788888888888888888888888875 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.92
                                       EEE-TTEEEET CS
                           Hexapep   8 vlIgpfavigg 18 
                                       ++I  ++vi+g
  gi|242399988|ref|YP_002995413.1| 287 SIIFGNTVIRG 297
                                       45555566655 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.029
                                       EEEETTEEE-T....TEEEETTEEE-T CS
                           Hexapep   2 tvIGsnvlIgp....faviggnVkIGd 24 
                                       ++I +++ I++     + +gg++kI +
  gi|242399988|ref|YP_002995413.1| 303 SIIDEKCEIRNlelkKSLVGGHAKIQR 329
                                       578899*****9999999999999976 PP

>> Fucokinase  L-fucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.24   8.7e+02     132     155 ..     162     185 ..     138     189 .. 0.80
   2 !   13.3   0.0   8.4e-06      0.03     230     315 ..     216     300 ..     196     322 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.24
                        Fucokinase 132 ekvlldsGvvffdhktaekLlkly 155
                                       + +l+ +Gv++f ++++ek  +++
  gi|242399988|ref|YP_002995413.1| 162 KSTLISTGVYAFPKDVIEKVGEYL 185
                                       778999******999999876665 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 8.4e-06
                        Fucokinase 230 FyHlgttaeylehltkdaslkeelsltstafsaiknkkekkkesavvinSvlessvsvgegsviehsslkgnvsigs 306
                                       +y +g   +yle +    ++ +  +++ + +s+i n    kk   +   S++ +++ +ge++vie+s++++++    
  gi|242399988|ref|YP_002995413.1| 216 WYDIGSADSYLEAMKTLLKESQIEEIQISSYSKIINPVVIKKGARILGRSIVGPYAYIGENCVIENSDVSDSII-FG 291
                                       3458999999999888888777778888888888555544455555558********************98774.44 PP

                        Fucokinase 307 nsivsglel 315
                                       n+++ g  +
  gi|242399988|ref|YP_002995413.1| 292 NTVIRGSTI 300
                                       455555544 PP

>> Trans_coact  Phage late-transcription coactivator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1      0.31   1.1e+03       1      23 [.      66      89 ..      66      99 .. 0.75
   2 ?   12.2   0.3     4e-05      0.14      16      48 ..     222     257 ..     219     257 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.31
                       Trans_coact  1 kqkfsleIEelvae.eglsYlEAv 23
                                      k++++l +Ee  +e e+l  + A+
  gi|242399988|ref|YP_002995413.1| 66 KNNIGLIVEETISEeEKLGTIGAI 89
                                      6789999*9999884557777666 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 4e-05
                       Trans_coact  16 glsYlEAvlewceendiee...eqvpklIskpLkeK 48 
                                         sYlEA+ + + e++iee   ++++k I++ ++ K
  gi|242399988|ref|YP_002995413.1| 222 ADSYLEAMKTLLKESQIEEiqiSSYSKIINPVVIKK 257
                                       579************999722256678888877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2106.19
//
Query:       gi|242399989|ref|YP_002995414.1|  [L=414]
Description: Capsular polysaccharide biosynthesis protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-28   99.6  17.5    1.9e-28   99.6  17.5    2.1  2  Polysacc_synt    Polysaccharide biosynthesis protein
    9.9e-17   61.3   6.7    9.9e-17   61.3   6.7    4.9  5  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai
    5.2e-14   52.2  10.2    5.2e-14   52.2  10.2    2.0  2  Polysacc_synt_3  Polysaccharide biosynthesis protein
    6.9e-06   24.9  11.1    6.9e-06   24.9  11.1    2.2  2  MurJ             Lipid II flippase MurJ
     0.0001   22.0   8.8     0.0001   22.0   8.8    3.0  3  MatE             MatE


Domain annotation for each model (and alignments):
>> Polysacc_synt  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.6  17.5   5.4e-32   1.9e-28       1     274 []       9     279 ..       9     279 .. 0.89
   2 ?    1.1   3.9     0.059   2.1e+02     174     240 ..     298     368 ..     284     405 .. 0.67

  Alignments for each domain:
  == domain 1  score: 99.6 bits;  conditional E-value: 5.4e-32
                     Polysacc_synt   1 llkgvivlllsqlitkllafvtlvylarilgpegfGlvalalaivtllviltdlGlnaalvreiakyrekkelvsli 77 
                                       l k++ +l+ + +i+klla+ ++v+l+r+lgpeg G++++++  v+ll i++dlG++ +l re+a+ re  +l  l+
  gi|242399989|ref|YP_002995414.1|   9 LIKNAGWLFGAEVISKLLAYGVVVLLSRTLGPEGLGQYSFIFYYVGLLGIFSDLGVGYYLMREVARDRE--KLNELL 83 
                                       579*****************************************************************9..455555 PP

                     Polysacc_synt  78 llnvllvllvlvllfllllliaaflglpelavlylilalmllllvgvasfrrglfqglermkyaavsqvveqlsrvi 154
                                         ++ l ++++++ fl++  i  fl +pe   +++ila + ++l+ ++ +++ +  + e  ky a+  ++e+   + 
  gi|242399989|ref|YP_002995414.1|  84 PGALGLKIILAIVNFLVIVGITLFLPKPEWMKILIILAGAEAILTWISYLFVRIMYAYEITKYEALAITIERFWAFF 160
                                       55555555555556666666655*****************************************************9 PP

                     Polysacc_synt 155 lvliavflfld....ivaavlgavlaalvggivslavlrkkfrprfvilslklvrellsfsapltisslaillytyi 227
                                         ++++++f++    iv +++g++l  l+++  +l ++       +  ++ ++++ ll+ s p+ +  l++l+y + 
  gi|242399989|ref|YP_002995414.1| 161 VGGAVLYTFKSlslfIVMLLAGYTLRELLRIKWGLQFVD----ELKIRFRPEMWKGLLKKSYPFWLIGLFTLIYYRT 233
                                       999999999999999999999999999999999999888....444444488************************* PP

                     Polysacc_synt 228 dsillglllgaeavGiYnaayqllvaisgllapivtaalfPvfselq 274
                                       d+++l ll g+++ GiY+aay+l  + s ++ +iv +++ P +++l+
  gi|242399989|ref|YP_002995414.1| 234 DMVMLNLLKGDYETGIYRAAYTLIEV-SLFVPSIVVSTTMPSMARLW 279
                                       *********************99886.6677777777*****99986 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.059
                     Polysacc_synt 174 vlaalvggivslavlrkkfr....prfvilslklvrellsfsaplti..sslaillytyidsillglllgaea 240
                                       v+  +vg+ +++++ r  ++    + + +l    v ++l f++p+++  s l+++ +++   + +++++g +a
  gi|242399989|ref|YP_002995414.1| 298 VFLGVVGLAGYYIFAR--LGilivFGEEFLPSVPVLKILAFAVPFMFlnSLLGSYMNATGKELAFTKITGFTA 368
                                       4445555444444444..4246777777777999999999999999844455566666666666665555554 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   3.8     0.029     1e+02      91     139 ..      87     134 ..      58     136 .. 0.64
   2 ?   -4.7  14.6         5   1.8e+04      35     105 ..      94     174 ..      91     191 .. 0.68
   3 ?    2.5   0.3      0.04   1.4e+02      64      86 ..     172     196 ..     170     243 .. 0.88
   4 ?    0.4   0.6      0.17   6.2e+02      83     109 ..     286     311 ..     235     322 .. 0.60
   5 !   61.3   6.7   2.8e-20   9.9e-17       1      76 [.     330     405 ..     330     410 .. 0.95

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.029
                   Polysacc_synt_C  91 llkpllaalvmgivvylllllllgllllaalalllavlvgalvYlllll 139
                                       l   +++a+v ++v+++++l+l++  ++  + ++la++ ++l ++  l+
  gi|242399989|ref|YP_002995414.1|  87 LGLKIILAIVNFLVIVGITLFLPKPEWMK-ILIILAGAEAILTWISYLF 134
                                       33668888999999888999998888877.7777777766666665554 PP

  == domain 2  score: -4.7 bits;  conditional E-value: 5
                   Polysacc_synt_C  35 lvigalvklilnllli.plf.gi....vGa.aiatvlallvvavlnlyalrrllgiklellrrllkpllaalvmgiv 104
                                       +++ +lv ++++l+l  p++  i     Ga ai t +++l+v ++  y + ++  + +  + r++  ++ ++v++  
  gi|242399989|ref|YP_002995414.1|  94 AIVNFLVIVGITLFLPkPEWmKIliilAGAeAILTWISYLFVRIMYAYEITKYEALAI-TIERFWAFFVGGAVLYTF 169
                                       5556666666666666644424455557744899999999999999999999999999.699999999999999998 PP

                   Polysacc_synt_C 105 ....v 105
                                           +
  gi|242399989|ref|YP_002995414.1| 170 kslsL 174
                                       44321 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.04
                   Polysacc_synt_C  64 lallvvavlnlyalrrllgikl..e 86 
                                       l+l++v++l  y lr ll+ik+  +
  gi|242399989|ref|YP_002995414.1| 172 LSLFIVMLLAGYTLRELLRIKWglQ 196
                                       799******************9654 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 0.17
                   Polysacc_synt_C  83 iklellrrllkpllaalvmgivvylll 109
                                       +++ l+++   +l++  v+g++ y+++
  gi|242399989|ref|YP_002995414.1| 286 LNV-LFKKSSQMLVFLGVVGLAGYYIF 311
                                       222.34444444555555555544333 PP

  == domain 5  score: 61.3 bits;  conditional E-value: 2.8e-20
                   Polysacc_synt_C   1 vLailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplfgivGaaiatvlallvvavlnlya 76 
                                       vL ila++++f++l+++l+s+++++g++ +++k++ ++al++++ln++li  fg+ Gaaiatv+++ +++vl   +
  gi|242399989|ref|YP_002995414.1| 330 VLKILAFAVPFMFLNSLLGSYMNATGKELAFTKITGFTALLNVALNYFLIINFGAEGAAIATVISQGLASVLSSKI 405
                                       799******************************************************************9997655 PP

>> Polysacc_synt_3  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.2  10.2   1.4e-17   5.2e-14       1     293 []      33     329 ..      33     329 .. 0.80
   2 ?    1.5   0.8      0.04   1.4e+02      82     156 ..     328     401 ..     326     413 .. 0.54

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 1.4e-17
                   Polysacc_synt_3   1 vLARLLspedFGvvaialvvislanlfvdmGlssaliqkedlteedlstvftfnlvlgllialvlfllapliasfyn 77 
                                       +L+R L pe  G +++++  ++l+ +f+d+G++  l ++  +++e+l+ +    l l +++a+v fl+   i  f+ 
  gi|242399989|ref|YP_002995414.1|  33 LLSRTLGPEGLGQYSFIFYYVGLLGIFSDLGVGYYLMREVARDREKLNELLPGALGLKIILAIVNFLVIVGITLFLP 109
                                       699************************************************************************** PP

                   Polysacc_synt_3  78 qpelvtvlrvlalvlilsglssvqeallrrelkFkklfkitlvssvvg....vivaivlAllglgvwALvigtllss 150
                                       +pe  ++l +la    +       + l+ r +   +++k++ +++++     ++v+ ++ ++ +++  ++++ l+  
  gi|242399989|ref|YP_002995414.1| 110 KPEWMKILIILAGAEAI---LTWISYLFVRIMYAYEITKYEALAITIErfwaFFVGGAVLYTFKSLSLFIVMLLAGY 183
                                       *******9999854333...222333333333333344444333333311115555555566666666666666665 PP

                   Polysacc_synt_3 151 llslvl.lwlaskwr..prlkfslkslkelfsfglklllsnllnylarnldnlliGkvlssaaLGlYsvakrlaslp 224
                                       +l+ +l + + +++   ++++f+ +  k l++ +  + l +l   ++ ++d ++   + ++++ G+Y  a++l+++ 
  gi|242399989|ref|YP_002995414.1| 184 TLRELLrIKWGLQFVdeLKIRFRPEMWKGLLKKSYPFWLIGLFTLIYYRTDMVMLNLLKGDYETGIYRAAYTLIEVS 260
                                       5543331333333323399999999*************************************************987 PP

                   Polysacc_synt_3 225 vaeitsviakVlfPalSrl.qddkkklrelylkvlrlialivlPiavglavvaellvkvllGsqWleavp 293
                                       +  + s++ + ++P+++rl ++dk  l+ l++k+ +++ ++ +  ++g +++a+l + +++G+++l++vp
  gi|242399989|ref|YP_002995414.1| 261 L-FVPSIVVSTTMPSMARLwREDKTTLNVLFKKSSQMLVFLGVVGLAGYYIFARLGILIVFGEEFLPSVP 329
                                       6.6677777788888888648999*******************************************997 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.04
                   Polysacc_synt_3  82 vtvlrvlalvlilsglssvqeallr...relkFkklfkitlvssvvgvivaivlAllglgvwALvigtllssllslv 155
                                       v+vl++la+ + +  l+s+  ++++   +el F+k++ +t + +v+   + i    + +g+   +i t++s+ l +v
  gi|242399989|ref|YP_002995414.1| 328 VPVLKILAFAVPFMFLNSLLGSYMNatgKELAFTKITGFTALLNVALNYFLI----INFGAEGAAIATVISQGLASV 400
                                       6889999998876666666665554222677777766665554444433333....334444444444444444444 PP

                   Polysacc_synt_3 156 l 156
                                       l
  gi|242399989|ref|YP_002995414.1| 401 L 401
                                       3 PP

>> MurJ  Lipid II flippase MurJ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   7.3      0.98   3.5e+03     358     446 ..      94     180 ..      88     186 .. 0.67
   2 !   24.9  11.1   1.9e-09   6.9e-06     241     392 ..     253     398 ..     188     411 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 0.98
                              MurJ 358 slislvlnillsllll.pplgvvglalatslsaliglvllyvllrkrlklteargiktflaklvvllalaavvilll 433
                                       +++++ + +++ l+l  p +  + + la + + l  + +l+v++  + ++t+ +++++++++   ++++ ++v++ +
  gi|242399989|ref|YP_002995414.1|  94 AIVNFLVIVGITLFLPkPEWMKILIILAGAEAILTWISYLFVRIMYAYEITKYEALAITIER-FWAFFVGGAVLYTF 169
                                       44444444444544441456667777777777777888888888888899999999999999.66666666666666 PP

                              MurJ 434 ssltqaewvvgsl 446
                                       +sl+   ++v+ l
  gi|242399989|ref|YP_002995414.1| 170 KSLSL--FIVMLL 180
                                       66666..777765 PP

  == domain 2  score: 24.9 bits;  conditional E-value: 1.9e-09
                              MurJ 241 rilqlPlglfgvsis.tvlLPrlSrsakekdedevrdllsqairltllllipvsfgllvlskpivsllferGnFsee 316
                                       ++  + ++lf+ si+ ++ +P+++r   e+    ++ l +++ +++++l ++  +g  ++++  + ++f       e
  gi|242399989|ref|YP_002995414.1| 253 AYTLIEVSLFVPSIVvSTTMPSMARLWREDK-TTLNVLFKKSSQMLVFLGVVGLAGYYIFARLGILIVF------GE 322
                                       4555667788777642578*****8876655.55***********************************......68 PP

                              MurJ 317 dveataevLaayalgLipyalvklllrvfYAredtktPvkislislvlnillsllllpplgvvglalatslsalig 392
                                       ++     vL++ a++++++ l+ ll ++  A +   + +ki+ +++ ln++l+++l++++g+ g a+at++s  + 
  gi|242399989|ref|YP_002995414.1| 323 EFLPSVPVLKILAFAVPFMFLNSLLGSYMNATGKELAFTKITGFTALLNVALNYFLIINFGAEGAAIATVISQGLA 398
                                       9999*******************************************************************98444 PP

>> MatE  MatE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1      0.87   3.1e+03      16      40 ..      31      55 ..      19      66 .. 0.46
   2 ?   -1.8   2.8      0.61   2.2e+03      75     128 ..     116     170 ..     109     177 .. 0.66
   3 !   22.0   8.8   2.9e-08    0.0001       5     161 .]     223     377 ..     219     377 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.87
                              MatE 16 dtllvgrlgskalAavsialsilsl 40
                                      ++ll   lg++ l+ +s+ +  + l
  gi|242399989|ref|YP_002995414.1| 31 VVLLSRTLGPEGLGQYSFIFYYVGL 55
                                      2222222244444444444433333 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.61
                              MatE  75 glilllllsliiallvllfseq.ilslftqdeevlelakrylrililgipalalq 128
                                       +li+l++  +i++ + +lf ++  ++ +t+ e+++  ++r+  + + g++++ + 
  gi|242399989|ref|YP_002995414.1| 116 ILIILAGAEAILTWISYLFVRImYAYEITKYEALAITIERFWAFFVGGAVLYTFK 170
                                       4455555555555555555554145557777778888888888888888888775 PP

  == domain 3  score: 22.0 bits;  conditional E-value: 2.9e-08
                              MatE   5 enllesllslidtllvgrl.gskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqglilll 80 
                                         l+  +++ +d+++++ l g+ + + + +a +++++  +++  + + + + +++ + + + + +++ + ++  +l+
  gi|242399989|ref|YP_002995414.1| 223 IGLFTLIYYRTDMVMLNLLkGDYETGIYRAAYTLIEVSLFVPSIVVSTTMPSMARLWREDK-TTLNVLFKKSSQMLV 298
                                       5577889999******************************999999999999999997666.778888887777766 PP

                              MatE  81 llsliiallvl.lfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislislllni 156
                                       +l+++  + ++ + +  il +f+ +      +   l+il++ +p+++l+ +l ++++++gk  + + i+ +++lln+
  gi|242399989|ref|YP_002995414.1| 299 FLGVVGLAGYYiFARLGILIVFGEE---FLPSVPVLKILAFAVPFMFLNSLLGSYMNATGKELAFTKITGFTALLNV 372
                                       6666655555505555566666433...457899******************************************* PP

                              MatE 157 plnyl 161
                                        lny+
  gi|242399989|ref|YP_002995414.1| 373 ALNYF 377
                                       ***95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       788  (0.0439511); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.65u 0.33s 00:00:00.98 Elapsed: 00:00:00.50
# Mc/sec: 2514.60
//
Query:       gi|242399990|ref|YP_002995415.1|  [L=472]
Description: Pyrophosphorylase [Thermococcus sibiricus MM 739]
Scores for complete 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-50  169.6   0.0    1.2e-49  169.1   0.0    1.2  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
    3.5e-27   95.2   1.7    1.4e-23   83.3   0.1    2.2  2  adh_short        short chain dehydrogenase
    5.3e-22   78.5   0.0    9.2e-22   77.7   0.0    1.3  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
      2e-10   41.2   0.0    4.7e-10   40.1   0.0    1.6  1  NTP_transf_3     MobA-like NTP transferase domain
    1.4e-05   25.1   0.0    0.00033   20.6   0.0    2.3  2  KR               KR domain
    0.00032   20.3   0.0    0.00055   19.6   0.0    1.4  1  NTP_transferase  Nucleotidyl transferase
  ------ inclusion threshold ------
      0.013   14.6   0.0      0.021   14.0   0.0    1.2  1  RmlD_sub_bind    RmlD substrate binding domain
      0.089   12.1   0.8       0.36   10.2   0.0    2.2  3  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas


Domain annotation for each model (and alignments):
>> 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 !  169.1   0.0   5.3e-53   1.2e-49       2     213 ..       6     221 ..       5     228 .. 0.92

  Alignments for each domain:
  == domain 1  score: 169.1 bits;  conditional E-value: 5.3e-53
                                       EEEEECTTSSCTT-SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHHHHHGG..CCE.EEEE--S CS
                              IspD   2 vvvipAAGsGkRmkaglpKqflelkgqtllehtvdallaskavdkivvvvseddteefeqllld..ksi.qlvaGGd 75 
                                       v++i A G+G+R++ ++pKqf++++g+ ++eht+d++  ++ vd++ vv++++  ++f +  l+  k+i ++++GG+
  gi|242399990|ref|YP_002995415.1|   6 VAIILAGGVGSRLGWETPKQFVKIAGKKVIEHTLDVFETHPLVDEVYVVINPYYYDYFLETILPkyKKItKVLKGGS 82 
                                       689*****************************************************99765555485552689**** PP

                                       SHHHHHHHHHHTTSSTT.SEEEE--TT-TT--HHHHHHHHHHHHTTCSEEEEEEE-SSEEEEEETTTBEEEEETGTT CS
                              IspD  76 eRaesVlnglkalegea.kfVLvHDaARpllkaadiaellaaaeqstqgailalpvkDtikrveadglvaetedReg 151
                                       +R+es + g+ a++++  + VL+HDa Rpl++++ i ++++a++  + ++ +++p  Dti   +   +++  ++R+ 
  gi|242399990|ref|YP_002995415.1|  83 TRQESSKIGVYAIDDNSvEKVLIHDAVRPLITKDIITNVIKALDV-HCAVDVVIPAIDTIVVSD-GRTILRIPNRKF 157
                                       **************9999**************************8.55667799*******999.89********** PP

                                       EEEEEEEEEEEHHHHHHHHHHHHHCT--.-SSHHHHHHHT.T--EEEEE--TTG----SHHHHH CS
                              IspD 152 LwaaqtPqgFrvdlllaahakgeqegae.itDdaslveki.GlsvkvVeGeednlKittpeDla 213
                                       L++ qtPqgFr++++l+ah+ +e eg++ +tDd slv +     v+vV G+ +n+K t++ D  
  gi|242399990|ref|YP_002995415.1| 158 LYQGQTPQGFRREVILKAHKLAEDEGFNqATDDCSLVLRYnLCDVHVVSGSVTNVKFTYNVDYY 221
                                       **************************86379****986663789****************9975 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.3   7.1e-05      0.16       1      33 [.     254     286 ..     254     288 .. 0.92
   2 !   83.3   0.1   6.4e-27   1.4e-23      56     189 ..     289     420 ..     285     426 .. 0.96

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7.1e-05
                                       SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESC CS
                         adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrs 33 
                                       kv++v G++sGIG +i++     Ga++++++r+
  gi|242399990|ref|YP_002995415.1| 254 KVIVVFGGTSGIGEKIVEIAKHYGARTYAFSRK 286
                                       89************************9998875 PP

  == domain 2  score: 83.3 bits;  conditional E-value: 6.4e-27
                                       -TTTSHHHHHHHHHHHHHHHSSESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEE CS
                         adh_short  56 vDvtdreevealvekavkklgkldvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIv 132
                                       vDv++ ++++++++ + +k g++d +vn AG  ++g+ ++ + +++ + +++N+ g + +t++ l++ + +++G+I+
  gi|242399990|ref|YP_002995415.1| 289 VDVSNPDSIDEALKSVYEKEGTIDYIVNTAGTLKMGSLESREITDIVEEVNINFLGSVFVTKLGLKY-I-RNGGSII 363
                                       8******************************************************************.4.7****** PP

                                       EEEEGGGTSB-TTBHHHHHHHHHHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHH CS
                         adh_short 133 nvsSvagkvpvagvaaYsAsKaavagltrslakelaptgirvnavaPGlvdTdmake 189
                                         +S     +  +++ YsA+Ka+++ +++++++e+++++i++++++P  ++T+m+ +
  gi|242399990|ref|YP_002995415.1| 364 LFGSSSYTRGRMNYSIYSATKAGLVNFVQAVSDEVSDREIKISIIVPERTKTPMRLK 420
                                       ******************************************************866 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 !   77.7   0.0   4.1e-25   9.2e-22      31     181 ..     266     421 ..     250     439 .. 0.90

  Alignments for each domain:
  == domain 1  score: 77.7 bits;  conditional E-value: 4.1e-25
                                       HHHHHHHHHHTTSE..E....EE--TTSHHHHHHHHHHHHHHHSSEEEEEE-----EGCSS-GGGH-HHHHHHHHHH CS
                      adh_short_C2  31 kkrveelaeelgae..v....lecDVtdeeqvealveevvekfgklDilvnnagiapklkgpfletsreefdraldv 101
                                        +++ e+a+ +ga+  +      +DV+++++++++ + v ek g++D++vn ag  +   g++++ +  ++ + +++
  gi|242399990|ref|YP_002995415.1| 266 GEKIVEIAKHYGARtyAfsrkTGVDVSNPDSIDEALKSVYEKEGTIDYIVNTAGTLKM--GSLESREITDIVEEVNI 340
                                       57788899999977542678889***********************************..***************** PP

                                       HTHHHHHHHHHHHHHCTSCCEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHHHHHHHGGGTEEEEEEEE--BHCTG CS
                      adh_short_C2 102 nlyslfllakaalplmkeggsivnlssvgaervvpnynaygaaKaalealtrylAvelgpkgiRvNavspgpikTla 178
                                       n+ + + ++k  l+++++ggsi+   s + +r+  ny++y+a+Ka+l+++++++  e+ +++i++  + p  +kT++
  gi|242399990|ref|YP_002995415.1| 341 NFLGSVFVTKLGLKYIRNGGSIILFGSSSYTRGRMNYSIYSATKAGLVNFVQAVSDEVSDREIKISIIVPERTKTPM 417
                                       ****************************************************************************9 PP

                                       .GGG CS
                      adh_short_C2 179 .asg 181
                                         ++
  gi|242399990|ref|YP_002995415.1| 418 rLKN 421
                                       4444 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 !   40.1   0.0   2.1e-13   4.7e-10       1     124 [.       7     139 ..       7     189 .. 0.64

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 2.1e-13
                                       EEEEEESS-TTTT..TTHHHHCCCCCCHHHHHHHHHCTT..-CEEEEECSH...CHHHH.HHTTCT.S-EEE-TTS. CS
                      NTP_transf_3   1 aviLAGGrSsRmg..gdKallplggkpllervldalraag.vdevvvvggd...eevla.alarlg.vrvvededp. 68 
                                       a+iLAGG +sR+g  ++K++++++gk ++e++ld ++ ++ vdev+vv ++   +  l+  l++++ ++ v    + 
  gi|242399990|ref|YP_002995415.1|   7 AIILAGGVGSRLGweTPKQFVKIAGKKVIEHTLDVFETHPlVDEVYVVINPyyyDYFLEtILPKYKkITKVLKGGSt 83 
                                       79***********744**********************9868*******9955433332133333334434443330 PP

                                       .S-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTS.SEEEEESS CS
                      NTP_transf_3  69 .gkgplaslaaalraaadadavlvlacDmPlltpelverllaaaaasga.dvvvptye 124
                                        ++    +++a  +  ++ + vl+  +  Pl+t++++  +++a++ + a dvv+p+ +
  gi|242399990|ref|YP_002995415.1|  84 rQESSKIGVYAIDD--NSVEKVLIHDAVRPLITKDIITNVIKALDVHCAvDVVIPAID 139
                                       12333334444333..378999999999999999999999999976654366666655 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1     0.081   1.8e+02       3      28 ..     256     281 ..     255     288 .. 0.76
   2 !   20.6   0.0   1.5e-07   0.00033      60     161 ..     289     392 ..     285     403 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.081
                                       EEEETTTSHHHHHHHHHHHHHHS-EE CS
                                KR   3 ylitGGlGgLGlelarwlaekgarhl 28 
                                        ++ GG+ g+G ++++   + gar+ 
  gi|242399990|ref|YP_002995415.1| 256 IVVFGGTSGIGEKIVEIAKHYGARTY 281
                                       5899**********987777777764 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 1.5e-07
                                       --TT-HHHHHHHHHHHHHHSS---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTT..S--SEEEEE CS
                                KR  60 aDvsdkdavealleeikaeeppikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelled..esldffvlf 134
                                       +Dvs++d++ ++l+++ ++e++i  ++++Ag+l+ + le+ +  d+ + ++  + G+  + +l  +  ++   ++lf
  gi|242399990|ref|YP_002995415.1| 289 VDVSNPDSIDEALKSVYEKEGTIDYIVNTAGTLKMGSLESREITDIVEEVNINFLGSVFVTKLGLKyiRNGGSIILF 365
                                       8**************************************************************999999******** PP

                                       EEHHHHH--TT-HHHHHHHHHHHHHHH CS
                                KR 135 SSiagllgsagqanYaaaNaflDalae 161
                                        S + + g +  + Y+a+ a l  +++
  gi|242399990|ref|YP_002995415.1| 366 GSSSYTRGRMNYSIYSATKAGLVNFVQ 392
                                       ****************99887766666 PP

>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   2.5e-07   0.00055       2      66 ..       7      68 ..       6      91 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.5e-07
                                      EEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHH.TT-SEEEEEEETTTHHHHHHHHT CS
                   NTP_transferase  2 avILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlan.sgieeiivvltqehsflveeqlk 66
                                      a+ILaGG G+RL     +++k+ v ++gk ++i++tl        ++e++vv++++    + e + 
  gi|242399990|ref|YP_002995415.1|  7 AIILAGGVGSRL---GWETPKQFVKIAGK-KVIEHTLDVFEThPLVDEVYVVINPYYYDYFLETIL 68
                                      8**********8...57999999999999.*********9986799**********9998888765 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   9.2e-06     0.021       3      71 ..     256     330 ..     254     355 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 9.2e-06
                                       EEEESTTSHHHHHHHHHCTTTSEEEEEE-TT.T--TTSHHHHHHHH.....HHH--SEEEE------HHHHHHSH CS
                     RmlD_sub_bind   3 ilvtGanGqlGseLakqlaeeglevlaltre.eldltdaeavaell.....keakpdvvvnaAAytavDkaEsee 71 
                                       i+v+G++  +G ++++ +++ g+ ++a++r+  +d++++++++e+l     ke   d +vn+A   ++   Es e
  gi|242399990|ref|YP_002995415.1| 256 IVVFGGTSGIGEKIVEIAKHYGARTYAFSRKtGVDVSNPDSIDEALksvyeKEGTIDYIVNTAGTLKMGSLESRE 330
                                       89**************************77648*************66666666788999999887777777764 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 ?   -2.9   0.0       1.7   3.7e+03      36      51 ..       3      18 ..       2      30 .. 0.89
   2 ?   -1.1   0.0      0.45     1e+03     146     161 ..      34      49 ..      22      57 .. 0.76
   3 ?   10.2   0.0   0.00016      0.36      28      72 ..     245     290 ..     225     318 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.7
                                      TSEEEEES-SHHHHHH CS
                      2-Hacid_dh_C 36 gktvGiiGlGrIGqav 51
                                      +ktv+ii +G +G+++
  gi|242399990|ref|YP_002995415.1|  3 DKTVAIILAGGVGSRL 18
                                      69**********9986 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.45
                                       CCEEEES--SSSSSGT CS
                      2-Hacid_dh_C 146 iagaalDvfeeeplpe 161
                                       +    lDvfe+ pl +
  gi|242399990|ref|YP_002995415.1|  34 VIEHTLDVFETHPLVD 49 
                                       444689******9985 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.00016
                                       CGSBS-GTTSEEEEE.S-SHHHHHHHHHHHHTT-EEEEESSSHHHH CS
                      2-Hacid_dh_C  28 allgkelsgktvGii.GlGrIGqavakrlkafgmkviaydrskkke 72 
                                       + + ++l++k + ++ G+  IG+++ +++k  g++ +a++r+   +
  gi|242399990|ref|YP_002995415.1| 245 ESKLSNLKDKVIVVFgGTSGIGEKIVEIAKHYGARTYAFSRKTGVD 290
                                       45556788888888736999********************996633 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (472 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.49
# Mc/sec: 2919.20
//
Query:       gi|242399991|ref|YP_002995416.1|  [L=385]
Description: CDP-glycerol:poly(glycerophosphate) glycerophosphotransferase [Thermococcus sibiricus MM 739]
Scores for complete 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-84  281.6   0.1    1.1e-83  281.2   0.1    1.1  1  Glyphos_transf  CDP-Glycerol:Poly(glycerophosphate) glyceroph
  ------ inclusion threshold ------
       0.17   12.3   0.0       0.35   11.2   0.0    1.4  1  Pas_Saposin     Pas factor saposin fold


Domain annotation for each model (and alignments):
>> Glyphos_transf  CDP-Glycerol:Poly(glycerophosphate) glycerophosphotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  281.2   0.1   1.2e-87   1.1e-83       2     366 ..      15     378 ..      14     379 .. 0.91

  Alignments for each domain:
  == domain 1  score: 281.2 bits;  conditional E-value: 1.2e-87
                                       ........G-EEEEEEEEBTTTTBS-HHHHHHHHHHHHH-TTSEEEEEESSGGG..----SS-EEEETTSHHHHHHH CS
                    Glyphos_transf   2 lyrlqlrlpldkklvlfesfegkkvsdnpkalfeylrelapkvkivwvvkkdsk..arlkkgakvvkrnslryllll 76 
                                       ++++++  p+d  +++f+s   +++sdnp++l+e+++el +++k+vwvv+++ k  +++++++ +v++++++yl  +
  gi|242399991|ref|YP_002995416.1|  15 FAKINRLIPKDGRVIMFIST--PDFSDNPRYLYEKAKELLEGYKFVWVVNDKTKfqNLDNESTVFVQYRTFEYLKWI 89 
                                       678899999***********..*****************************999*9999999*************** PP

                                       HHEEEEEESS---TTS---TTSEEEE--SS--SB--GGG-S---TS-HHHHHHHHHTT-SEEEESSHHHHHHHHHHT CS
                    Glyphos_transf  77 lrakylvsnsnfplyvrkrknqvylqtwhGtpLkkmGldeeekkaaatkqellrevsswdylisaneestsifaraf 153
                                        +akyl+ +  +   + k+ nq  + +whG p+k+ G+ ++++            +   d+l++++++   i+ + f
  gi|242399991|ref|YP_002995416.1|  90 IKAKYLILS--HGVPYWKSGNQIAILLWHGLPIKRDGVWIKNYW-----------HILPDFLTVPSRFVGVIYSSLF 153
                                       *********..4446779*****************888886555...........5568****************** PP

                                       T--GGGEEES--GGGHHHHHSTT-H..HHHHHHHTT--SS-EEEEEE----GGG--.GSS----TT-HHHHH.HHHT CS
                    Glyphos_transf 154 nikkeeiletGyPrnDvlvkaesed..vkrireelgipkdkkvilyaPTwRddevg.esyrfelkldlerla.kalg 226
                                       ++  + ile G+Pr+Dvl+ +++++  + +++e+l++p dkkv+lyaPTwR+++ + ++  f   ++ ++l+   + 
  gi|242399991|ref|YP_002995416.1| 154 GVPPQDILELGIPRTDVLFLNKNNEklKVELKEKLNLPLDKKVVLYAPTWREWNPTfQFKLFLELATNKELQkVLKI 230
                                       ******************85555554899*************************99767777777888889856677 PP

                                       TTEEEEE--SHHHHTT---TT-TTTEEE-TT-S......-HHHHHHT-SEEEESS-THHHHHGGGT--EEEE-TTTT CS
                    Glyphos_transf 227 edyvillklHpliqekikikeksdyvvdvsdee......dvedlllasDiLiTDYSSvmFDyavldrPiifyayDle 297
                                       +++++++k+Hp  + +i  +e   ++  +++++        ++lll+sD+LiTDYSS+++Dy++ldrP+ify++D++
  gi|242399991|ref|YP_002995416.1| 231 NNAMLVFKPHPQEEANILSYEFPKNFHIITSNNmlkkglTTNELLLVSDLLITDYSSIFWDYLILDRPMIFYVPDID 307
                                       9****************998877777777777769999999************************************ PP

                                       TTTTTSSBSS-.TTTSSSS-EESSHHHHHHHHTTHHHHHHH.THHHHHHHHHHHSTT--S-HHHHHHHHHH CS
                    Glyphos_transf 298 eYsekrgfyld.yekelPGpvveteeelieelksidkedee.yeekrrafrdkfckydDgrsservvrlif 366
                                       +Y+++rg++l+ +e+++PG+++++ ++l++ ++ + +e ++  e kr+  r+ ++k++Dg+sser++r+ f
  gi|242399991|ref|YP_002995416.1| 308 DYRAHRGLILEpFEEWVPGKIAYSVDALVKTISGVLEEGKDgFEYKRKWLRNIMYKHQDGKSSERIIRYFF 378
                                       **********************************998876526889999******************9866 PP

>> Pas_Saposin  Pas factor saposin fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   3.9e-05      0.35      22      43 ..     179     200 ..     175     208 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.9e-05
                       Pas_Saposin  22 kiRqnLYeqLdLsfdkqlaLYs 43 
                                       k++ +L e+L+L++dk++ LY+
  gi|242399991|ref|YP_002995416.1| 179 KLKVELKEKLNLPLDKKVVLYA 200
                                       5677899**************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.49
# Mc/sec: 2364.36
//
Query:       gi|242399992|ref|YP_002995417.1|  [L=386]
Description: Glycosyl transferase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-37  128.7   0.0    2.5e-37  128.1   0.0    1.3  1  Glycos_transf_1  Glycosyl transferases group 1
    3.8e-27   95.3   0.0    7.3e-27   94.4   0.0    1.5  1  Glyco_trans_1_4  Glycosyl transferases group 1
    1.6e-21   77.0   0.0    2.3e-21   76.5   0.0    1.2  1  Glyco_transf_4   Glycosyltransferase Family 4
    1.9e-12   47.9   0.0    2.6e-12   47.5   0.0    1.2  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    1.2e-09   38.3   0.0    2.7e-09   37.2   0.0    1.5  1  Glyco_trans_4_2  Glycosyl transferase 4-like
    3.5e-06   27.3   0.0    1.1e-05   25.7   0.0    1.8  2  Glyco_trans_1_2  Glycosyl transferases group 1
  ------ inclusion threshold ------
      0.017   14.9   0.1      0.054   13.2   0.1    1.8  1  Glyco_transf_5   Starch synthase catalytic domain
       0.11   12.2   0.0       0.36   10.5   0.0    1.8  2  DUF3492          Domain of unknown function (DUF3492)


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 !  128.1   0.0   1.1e-40   2.5e-37       6     169 ..     200     362 ..     195     365 .. 0.97

  Alignments for each domain:
  == domain 1  score: 128.1 bits;  conditional E-value: 1.1e-40
                                       HHHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCH CS
                   Glycos_transf_1   6 rkklgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevs 82 
                                       r++l+++ +kkiil v++l+++Kg+++li+a++++    +++v l+i+G+g+ +kel+ ++++l+l++ v + g ++
  gi|242399992|ref|YP_002995417.1| 200 REQLNLPRDKKIILNVANLVPVKGQSYLIEAMEKVVSH-RKDVMLIIVGDGPLKKELEIQIKKLNLENYVMLAGAKP 275
                                       78999******************************998.************************************** PP

                                       SSSHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSH CS
                   Glycos_transf_1  83 redleellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairkllede 159
                                       ++++  ++++ad+fvlps sEg ++v  EA+ +glp + +++gg++e++++++ Gll++p++++ lae+i  +le+e
  gi|242399992|ref|YP_002995417.1| 276 HSEILLWMNAADLFVLPSLSEGNPTVMFEALGVGLPFVGTAVGGVPEIITSEDYGLLCPPKDPKCLAEKILIALEKE 352
                                       ***************************************************************************** PP

                                       HHHHHHHHHH CS
                   Glycos_transf_1 160 elrerlgena 169
                                         re++ ++a
  gi|242399992|ref|YP_002995417.1| 353 WNREKIMNYA 362
                                       8888888877 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.4   0.0   3.3e-30   7.3e-27       2     132 ..     210     349 ..     209     351 .. 0.89

  Alignments for each domain:
  == domain 1  score: 94.4 bits;  conditional E-value: 3.3e-30
                                       EEEEEES---GG.GTHHHHHHHHHHHH.H..HEEEEEES---...HHHHHHHT..T-T.TEEEE---..THHHHHHH CS
                   Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkk..dvrlvivGdgp.rpeeleelaa..gleerveftGfv..edlaella 71 
                                       ++il v +l  +vkg+ +l+ea++++ ++  dv l+ivGdgp + +ele +++  +le+ v ++G    +++  +++
  gi|242399992|ref|YP_002995417.1| 210 KIILNVANL-VPVKGQSYLIEAMEKVVSHrkDVMLIIVGDGPlK-KELEIQIKklNLENYVMLAGAKphSEILLWMN 284
                                       78999****.578**********777744345**********65.699988866899999*****998778****** PP

                                       H-SEEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHHH CS
                   Glyco_trans_1_4  72 aadvfvaPs..egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailrLl 132
                                       aad+fv+Ps  eg + ++ Ea+ +glp V t+vgg++e++  ++ gll+pp+dp+ lae+il  l
  gi|242399992|ref|YP_002995417.1| 285 AADLFVLPSlsEGNPTVMFEALGVGLPFVGTAVGGVPEIItsEDYGLLCPPKDPKCLAEKILIAL 349
                                       ****************************************977889***************9776 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.5   0.0     1e-24   2.3e-21       6     167 ..      22     187 ..      20     190 .. 0.78

  Alignments for each domain:
  == domain 1  score: 76.5 bits;  conditional E-value: 1e-24
                    Glyco_transf_4   6 rhvleLaraLarrGheVtvvtpgddgpleeev...elvvrvprvplpllk....rllrslaflrrlrrllkre..kp 73 
                                       ++v e +r+L     +V+v++p++ g  ++ +   ++ vrv ++++++ +    r ++  +f++++ r++kre  ++
  gi|242399992|ref|YP_002995417.1|  22 VFVKEQVRYLENYFENVYVISPQPWGSNRNLRdyeYDNVRVYYPRFFHAPveffRKRLGDSFFKAALRIIKREklEF 98 
                                       667777777777766899999888777777667665555555555444332211333445677899999*9999*** PP

                    Glyco_transf_4  74 DvvHahspaalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrllrradrviavSeatadelre 150
                                       D++Hah+ ++ g+a+++l ++  +plV+t Hg +     +    +++ ++++  +++l++ad++++vS++    l +
  gi|242399992|ref|YP_002995417.1|  99 DLIHAHFTWPSGYAAAKLSKEFSVPLVITGHGYD----IYELPFRGREWFKK-VKFALDSADHIVTVSKSNFTILTT 170
                                       ***************99999**************....45555555566655.78889******************* PP

                    Glyco_transf_4 151 rygvppekitVipnGvD 167
                                       ++++p++ki VipnG +
  gi|242399992|ref|YP_002995417.1| 171 KLDIPEDKISVIPNGFN 187
                                       ***************87 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.5   0.0   1.2e-15   2.6e-12      15     160 .]      32     185 ..      20     185 .. 0.76

  Alignments for each domain:
  == domain 1  score: 47.5 bits;  conditional E-value: 1.2e-15
                   Glyco_trans_4_4  15 aarGheVtvltpapapg...apeleedgvrvhrlpvprrp....spladlaalralrrllrqrrerpdvvhahs.pt 83 
                                       +     V v+ p+p ++    +++e d vrv+  ++ ++p    + +   ++  a+ r++++++  +d++hah  ++
  gi|242399992|ref|YP_002995417.1|  32 ENYFENVYVISPQPWGSnrnLRDYEYDNVRVYYPRFFHAPveffRKRLGDSFFKAALRIIKREKLEFDLIHAHFtWP 108
                                       55555566777777666333334789999999877777774322122223566777777788***********98** PP

                   Glyco_trans_4_4  84 aglaarlarrrrgiplvvtlhglllrrgsgavrrlyralerrllrradavlvvseaeaeelra.lgvpadrvvvvpn 159
                                       +g+aa+ ++   ++plv+t hg +  +  ++++r +    +++l +ad++++vs +    l+  l +p d++ v+pn
  gi|242399992|ref|YP_002995417.1| 109 SGYAAAKLSKEFSVPLVITGHGYDIYEL-PFRGREWFKKVKFALDSADHIVTVSKSNFTILTTkLDIPEDKISVIPN 184
                                       **9999998899**********999877.555554445569*********************9999*********** PP

                   Glyco_trans_4_4 160 g 160
                                       g
  gi|242399992|ref|YP_002995417.1| 185 G 185
                                       8 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 !   37.2   0.0   1.2e-12   2.7e-09       8     137 ..      19     159 ..      16     161 .. 0.75

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 1.2e-12
                   Glyco_trans_4_2   8 lssvhtlrlakeLakrgyeVhvitpkkga.kdeleaegihvhrlkvdrkg..pleyl.k.a....f.klkklik..k 72 
                                       ++ v++++ +++L +   +V+vi+p++    ++l+++ +   r+  +r +  p+e++ k +    f +  ++ik  k
  gi|242399992|ref|YP_002995417.1|  19 HGGVFVKEQVRYLENYFENVYVISPQPWGsNRNLRDYEYDNVRVYYPRFFhaPVEFFrKrLgdsfFkAALRIIKreK 95 
                                       6778999999999998899******5544499999999999999767444446666632235555435577776225 PP

                   Glyco_trans_4_2  73 ikPDvvhahyakpygllgslaar.lsgvipvvlsvwGldvlkfpkksk.lkklllklalkkatkvis 137
                                       +++D++hah ++p g++++ +++ +s  +p+v++ +G d+++ p++++ ++k+ +k+al +a+ + +
  gi|242399992|ref|YP_002995417.1|  96 LEFDLIHAHFTWPSGYAAAKLSKeFS--VPLVITGHGYDIYELPFRGReWFKK-VKFALDSADHIVT 159
                                       67************998876666344..8******************975554.7999999998865 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       4.4   9.9e+03      49      65 ..     140     156 ..     128     163 .. 0.76
   2 !   25.7   0.0   5.1e-09   1.1e-05       3      91 ..     290     375 ..     286     376 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 4.4
                   Glyco_trans_1_2  49 leelaekiryllanpee 65 
                                         e+ +k++++l++ + 
  gi|242399992|ref|YP_002995417.1| 140 GREWFKKVKFALDSADH 156
                                       57888999999988765 PP

  == domain 2  score: 25.7 bits;  conditional E-value: 5.1e-09
                   Glyco_trans_1_2   3 LnpsrsespnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraiaeaarerv 77 
                                       + ps se++ +++fEa++ G + + ++  g++e++t ++ ++l    d++ laeki  +l+ +  r++i   ++++ 
  gi|242399992|ref|YP_002995417.1| 290 VLPSLSEGNPTVMFEALGVGLPFVGTAVGGVPEIITSEDYGLLCPpkDPKCLAEKILIALEKEWNREKIM--NYAD- 363
                                       569999********************99****************99**********88776666666555..5555. PP

                   Glyco_trans_1_2  78 laehtydhraeqll 91 
                                         ++t+ + ++q+l
  gi|242399992|ref|YP_002995417.1| 364 --QYTWGNVVNQIL 375
                                       ..778888888887 PP

>> Glyco_transf_5  Starch synthase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   2.4e-05     0.054     100     224 ..      62     163 ..      10     172 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.4e-05
                    Glyco_transf_5 100 lYgdk..gedyednaerfa.lfsraalelleklgwkpdvihah.DWhtalvpallkelykerglfkkiktvftiHNl 172
                                       +Y +   + ++e   +r+   f +aal+++++ + ++d+ihah  W ++ ++a l +          +++v+t H  
  gi|242399992|ref|YP_002995417.1|  62 VYYPRffHAPVEFFRKRLGdSFFKAALRIIKREKLEFDLIHAHfTWPSGYAAAKLSKEF-------SVPLVITGHG- 130
                                       33333333444444555557788999******5558*******88******99998874.......2********4. PP

                    Glyco_transf_5 173 ayqgrfpkdelaalglpaedfekldglefygkvnflkagivyadavttVSpt 224
                                        y+         + +lp         ++  + ++ +k ++  ad+++tVS++
  gi|242399992|ref|YP_002995417.1| 131 -YD---------IYELP---------FRGREWFKKVKFALDSADHIVTVSKS 163
                                       .33.........22344.........22223455677788888888888875 PP

>> DUF3492  Domain of unknown function (DUF3492)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00016      0.36     158     205 ..      83     130 ..      80     150 .. 0.90
   2 ?   -2.4   0.0       1.4   3.2e+03     236     256 ..     145     164 ..     141     167 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00016
                           DUF3492 158 llspllkllaeelpkadvyHavstGyAgllgallkerkgtpllltEHG 205
                                       ++++ l ++++e  + d++Ha+ t   g+ +a l+++ ++pl++t HG
  gi|242399992|ref|YP_002995417.1|  83 FFKAALRIIKREKLEFDLIHAHFTWPSGYAAAKLSKEFSVPLVITGHG 130
                                       5677788899999**********************************9 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.4
                           DUF3492 236 eslgrlvYeaadkiitlyekn 256
                                       + +  ++ ++ad+i+t++++n
  gi|242399992|ref|YP_002995417.1| 145 KKVK-FALDSADHIVTVSKSN 164
                                       5444.88899********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 2493.03
//
Query:       gi|242399993|ref|YP_002995418.1|  [L=75]
Description: glycosyltransferase, family 1 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00019   21.4   0.0     0.0002   21.4   0.0    1.0  1  Glyco_trans_4_2  Glycosyl transferase 4-like
  ------ inclusion threshold ------
      0.031   14.7   0.0      0.033   14.6   0.0    1.0  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain


Domain annotation for each model (and alignments):
>> 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 !   21.4   0.0   2.3e-08    0.0002       7      59 ..       4      65 ..       1      71 [. 0.75

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 2.3e-08
                   Glyco_trans_4_2  7 nlssvhtlrl...akeLakrgyeVhvitp..kkga.kdeleaegihvhrlkvdrkg....ple 59
                                      n +++h+ r+   a++L k+gy+V+vi    kk +   ++  +g++v+r+++++ +    p+e
  gi|242399993|ref|YP_002995418.1|  4 NNGYTHDPRVtaeAESLVKHGYKVKVIAWdrKK-EyPSYETINGVEVIRIRIPSIIdkllPFE 65
                                      5678998887666888***********995334.35999************995443234555 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   3.6e-06     0.033       6      49 ..      12      56 ..       9      68 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.6e-06
                   Glyco_trans_4_4  6 yvaelaraLaarGheVtvlt..papapgapeleedgvrvhrlpvpr 49
                                      +v + a++L+++G+ V v++  +++ ++++ ++ +gv+v+r+++p 
  gi|242399993|ref|YP_002995418.1| 12 RVTAEAESLVKHGYKVKVIAwdRKKEYPSY-ETINGVEVIRIRIPS 56
                                      677779**************8555555555.89*********9885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); 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: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 472.27
//
Query:       gi|242399994|ref|YP_002995419.1|  [L=566]
Description: asparagine synthetase [Thermococcus sibiricus MM 739]
Scores for complete 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-74  250.1   0.0    7.2e-74  249.6   0.0    1.2  1  Asn_synthase  Asparagine synthase
    6.7e-47  158.4   0.0      1e-46  157.9   0.0    1.3  1  GATase_7      Glutamine amidotransferase domain
    9.2e-44  148.9   0.0    1.4e-43  148.3   0.0    1.3  1  GATase_6      Glutamine amidotransferase domain
    0.00034   20.1   0.1     0.0012   18.4   0.1    1.8  1  DUF3700       Aluminium induced protein
  ------ inclusion threshold ------
      0.064   12.4   0.0      0.098   11.8   0.0    1.2  1  NAD_synthase  NAD synthase


Domain annotation for each model (and alignments):
>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  249.6   0.0     2e-77   7.2e-74       2     298 ..     239     549 ..     238     565 .. 0.82

  Alignments for each domain:
  == domain 1  score: 249.6 bits;  conditional E-value: 2e-77
                      Asn_synthase   2 lrelLedaVkrrlradvpvGalLSGGlDSSliaalaarqsk.splktFsigfeekgsdeakyakevaehlgtehtel 77 
                                       +r+ +++aV+rrl advpvG++LSGGlDSS+i++++++ +k  ++ktFs+ f   + de+ky++ v+++++++ ++ 
  gi|242399994|ref|YP_002995419.1| 239 FRDIFKKAVQRRLIADVPVGSCLSGGLDSSSIVCMMREINKnLEIKTFSLVFPGFKLDESKYQESVVRECNVKRYTT 315
                                       6899***********************************99889********7799********************* PP

                      Asn_synthase  78 vlteeelldalpdviyhleepfadrsaiplyllsrlakrkgvkvvLsGeGaDElfgGYpyfykaals.rsrefeklp 153
                                        +t+ ++l+ ++d++y  eepf   s + +y +++lak++g+kv+L G+G+DE+ gGY+ f+        r f++++
  gi|242399994|ref|YP_002995419.1| 316 TFTVGDILRDIDDLVYSQEEPFFTLSIYGQYRVMKLAKEHGMKVLLDGQGSDEILGGYHHFFEYYFAeLFRSFRWIK 392
                                       ***********************************************************765544220335566666 PP

                      Asn_synthase 154 .........................larslrasllarklrklaellelaeardleelaelyrlkasdsae....... 198
                                                                 ++ +++ l +r++  la                          +       
  gi|242399994|ref|YP_002995419.1| 393 liseiiayyktykswspisnmifylSPKFVKRLLWKRRFPYLA--------------------------Ddfveryk 443
                                       9777776666555554444433332222222222222222222..........................22222333 PP

                      Asn_synthase 199 .....aelegedelhrelyldlktllpgdllrk.DrasmahglEaRvPflDhrlvevalrlppelklrggieKyiLR 269
                                            +   g++ l+++l+l  +++   +llr  D+ sm++++E RvPf+Dh+lve++l+lp+e k+++gi+K iLR
  gi|242399994|ref|YP_002995419.1| 444 drgskEPQWGAKSLKEALILAETYYSLPHLLRFeDKNSMRWSIESRVPFCDHELVEYVLSLPAEAKIDKGITKKILR 520
                                       333337788****************999999999******************************************* PP

                      Asn_synthase 270 ealegylPeeileRp.Kegfsapvgewklk 298
                                       eal+g+lPe+i +R+ K gf  p ++  l+
  gi|242399994|ref|YP_002995419.1| 521 EALRGILPEDIRTRTsKIGFATPDEDI-LR 549
                                       *********************999887.65 PP

>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.9   0.0   2.8e-50     1e-46       1     122 [.      42     163 ..      42     164 .. 0.95

  Alignments for each domain:
  == domain 1  score: 157.9 bits;  conditional E-value: 2.8e-50
                          GATase_7   1 hrrlsi.idseagaQPmvs.sedgrlvivfnGeiyNykelreeLeakghrfrtksDtevllalleaewgeealerln 75 
                                       h rl+i ++s++g+QPm   +++++++iv+nGe+yN+ elr+eLe++g++f++++Dtev+la++ + wg ++++++n
  gi|242399994|ref|YP_002995419.1|  42 HVRLAIiDLSPKGHQPMRYeKDGREIWIVYNGEVYNFMELRKELEERGYTFNSNTDTEVILAAYLE-WGFDCIKKFN 117
                                       7899997889********9666777***************************************97.********** PP

                          GATase_7  76 GmfAfaiwdeeekrlllaRDrlGikPLyygedkgdallfaSelkall 122
                                       Gm+Afai+d+ ++ l+l RDr+GikPLyy++d g++++f+Se+ka+l
  gi|242399994|ref|YP_002995419.1| 118 GMWAFAIYDKGKNLLFLSRDRFGIKPLYYYYD-GQNIIFSSEIKAIL 163
                                       ********************************.89**********97 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.3   0.0   3.9e-47   1.4e-43       1     134 []      27     158 ..      27     158 .. 0.97

  Alignments for each domain:
  == domain 1  score: 148.3 bits;  conditional E-value: 3.9e-47
                          GATase_6   1 pdasglaslvedevalaHvRlaivglaeeegaqPf.psedgr.lllvhNGeiynykelreelpalkglafrsrsDte 75 
                                       pd++++  +v+++v l+HvRlai++l+  +g+qP+ +++dgr +++v+NGe+yn+ elr+el++ +g++f+s++Dte
  gi|242399994|ref|YP_002995419.1|  27 PDDEDI--YVDENVSLGHVRLAIIDLS-PKGHQPMrYEKDGReIWIVYNGEVYNFMELRKELEE-RGYTFNSNTDTE 99 
                                       789999..******************9.*******86666666*********************.************ PP

                          GATase_6  76 vllalleelGeevlerlrGmfafaiwdkrentlilardrlgvkplyyavdesglafase 134
                                       v+la++ e+G +++++++Gm afai+dk +n l+l rdr+g+kplyy +d+++++f+se
  gi|242399994|ref|YP_002995419.1| 100 VILAAYLEWGFDCIKKFNGMWAFAIYDKGKNLLFLSRDRFGIKPLYYYYDGQNIIFSSE 158
                                       **********************************************************8 PP

>> DUF3700  Aluminium induced protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   3.3e-07    0.0012      76     175 ..      66     161 ..      45     169 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 3.3e-07
                           DUF3700  76 difClfqGslenlasLkkq...yGLskta.nevllvieayrtLrdrgPypadqvvkdleGkfafvlydskaktvfva 148
                                       +i+ +++G++ n ++L+k+    G + ++ ++  +++ ay              +k+++G +af +yd+ ++ +f++
  gi|242399994|ref|YP_002995419.1|  66 EIWIVYNGEVYNFMELRKEleeRGYTFNSnTDTEVILAAYLEW-------GFDCIKKFNGMWAFAIYDKGKNLLFLS 135
                                       5666666777776666654222233322202344455566432.......23579********************** PP

                           DUF3700 149 ldadgsvplyWGiaadgsvvisddlel 175
                                       +d+ g  ply+  +++  +++s +++ 
  gi|242399994|ref|YP_002995419.1| 136 RDRFGIKPLYYYYDGQN-IIFSSEIKA 161
                                       ***********998875.666666554 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   2.7e-05     0.098       7      96 ..     241     334 ..     237     374 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.7e-05
                                       HHHHHHHHHCTTSEEEEE..E-SSHHHHHHHHHHHHHHT..CGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE- CS
                      NAD_synthase   7 dflkeyvkkagakgvvlG..lSGGvDSslvaalavkalg..kenvlalllPssvsseedvedalalaenlgievkti 79 
                                       d+ k+ v+++    v +G  lSGG+DSs + ++ +++    + + ++l++P+ + +e+ +++++    n++  ++t+
  gi|242399994|ref|YP_002995419.1| 241 DIFKKAVQRRLIADVPVGscLSGGLDSSSIVCMMREINKnlEIKTFSLVFPGFKLDESKYQESVVRECNVKRYTTTF 317
                                       567788888888888888779*******999999887641145778999********99999988877888888899 PP

                                       --HHHHHHHHHHHHHHH CS
                      NAD_synthase  80 dikpivrafeqelkeak 96 
                                        + +i+r +++ + +++
  gi|242399994|ref|YP_002995419.1| 318 TVGDILRDIDDLVYSQE 334
                                       99999998888655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (566 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.66u 0.32s 00:00:00.98 Elapsed: 00:00:00.50
# Mc/sec: 3423.93
//
Query:       gi|242399995|ref|YP_002995420.1|  [L=344]
Description: UDP-n-acetylglucosamine 2-epimerase [Thermococcus sibiricus MM 739]
Scores for complete 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-118  395.8   0.0   1.6e-118  395.6   0.0    1.0  1  Epimerase_2      UDP-N-acetylglucosamine 2-epimerase
  ------ inclusion threshold ------
      0.012   15.7   0.0      0.022   14.8   0.0    1.5  1  Glyco_trans_4_2  Glycosyl transferase 4-like


Domain annotation for each model (and alignments):
>> Epimerase_2  UDP-N-acetylglucosamine 2-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  395.6   0.0  1.8e-122  1.6e-118       4     346 ..       9     339 ..       6     340 .. 0.94

  Alignments for each domain:
  == domain 1  score: 395.6 bits;  conditional E-value: 1.8e-122
                                       TTS-..EEEEEEE-S--SGGGTHHHHHHTT----SEEE---S--HHHHHHHHHHHHHHHHHHH--SEEEEESSSHHH CS
                       Epimerase_2   4 kaeselelqlvvtGqHldremgdtvfeeleiekpdydlnsdsqslakstgrvligleevleeekpDlvlvlGDtnet 80 
                                       ++ + l++++++tGqH+d+em++++f++l+i++pdy+l+++s+s++ +tg++l+++e vl++ekpDlvlv+GDtn+t
  gi|242399995|ref|YP_002995420.1|   9 EK-KGLDEVIIHTGQHYDYEMNKIFFDQLGIREPDYNLGVGSGSHGYQTGEMLKRIEGVLMKEKPDLVLVYGDTNST 84 
                                       44.589*********************************************************************** PP

                                       HHHHHHHHHTT-EEEEET-----S-TT..SHHHHHHHHHHHT-SEEEESSHHHHHHHHHTT--GGGEEE---HHHHH CS
                       Epimerase_2  81 lagalaAfklripvaHveAGlRsfdltegmpeEinRhlidklsdlhfapteearenLlkegeeeerifvvGntviDa 157
                                       lagalaA+kl+i+vaHveAGlRsfd++  mpeE+nR+l+d++sd++fapte+a +nL +eg+ +e ++ +G++++Da
  gi|242399995|ref|YP_002995420.1|  85 LAGALAAVKLHIKVAHVEAGLRSFDKR--MPEEVNRVLTDHISDYLFAPTETAVKNLHNEGI-KEGVYLTGDVMYDA 158
                                       ***************************..*********************************.779*********** PP

                                       HHHHHHHHH...T-HHHHHH..--SS-EEEEE---HHHHTSHHHHHHHHHHHHHHHHHH--EEEEE--..HHHHHHH CS
                       Epimerase_2 158 lllskeeieeklkaseilke..lkekkyvlvtlHrrenedeperlkeilealkalakekdvevvvpvhnnprtrkrl 232
                                       ll++ + +e   ++s+il+e  l+ kky+l+t+Hr+en+d++++l++i++a+ +  +     +v+p+h  prtr+ l
  gi|242399995|ref|YP_002995420.1| 159 LLYNIKVAE---RESKILDElgLRPKKYILATVHRAENTDNKKNLENIVNAFIESGEL----IVFPAH--PRTRRYL 226
                                       ****99998...4569999999********************9999999999999987....9*****..*****99 PP

                                       .....HHHHHH-TTEEEE----HHHHHHHHHC-SEEEES-HHHHHHHHHCT--EEESSSS-S-THHHHTTSEEE-TT CS
                       Epimerase_2 233 .....leeleelenvtlieplgyldflsllknaklvltdSgGiqeEapslgvpvvnlReeteRpegveagtnvlvgt 304
                                            +e++++ +n+ l++p+gy d+l l +nak +ltdSgG+q+Ea++l+vp+++lRe+te++e+v+ g+n+lvg+
  gi|242399995|ref|YP_002995420.1| 227 elynlIEKIKNSNNLLLVDPVGYFDMLVLEENAKKILTDSGGVQKEAYFLKVPCITLRERTEWVETVKDGWNILVGA 303
                                       9976666666667**************************************************************** PP

                                       -HHHHHHHHHHHCT-..--......--TT-SS-HHHHHHHHH CS
                       Epimerase_2 305 dkeeIvaaleklledkkelekmanaknpYgdGkaseriveil 346
                                       dke+I+ a++++  + ++       +  +gdGkas+ri+eil
  gi|242399995|ref|YP_002995420.1| 304 DKEKILWAIAEFEPSGET------YTYKFGDGKASKRIAEIL 339
                                       *************77333......3457************98 PP

>> Glyco_trans_4_2  Glycosyl transferase 4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   2.4e-06     0.022      17     119 ..       5     115 ..       1     135 [. 0.69

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.4e-06
                   Glyco_trans_4_2  17 akeLakrgyeVhvitpkkgakdeleaegihvhrl..kvd......rkgpleyl..kaf.klkklikkikPDvvhahy 82 
                                        +eL k+g++ ++i  +++++ e  +++i + +l  + +       +g+ +y    ++ ++  ++ k+kPD+v ++ 
  gi|242399995|ref|YP_002995420.1|   5 SRELEKKGLDEVIIHTGQHYDYE--MNKIFFDQLgiREPdynlgvGSGSHGYQtgEMLkRIEGVLMKEKPDLVLVYG 79 
                                       56777777776666666554333..3334344442233345555545588888543544999*************** PP

                   Glyco_trans_4_2  83 akpygllgslaarlsgvipvvlsvwGldvlkfpkksk 119
                                        +   l+g+laa ++  i+v+    Gl  +++  + +
  gi|242399995|ref|YP_002995420.1|  80 DTNSTLAGALAAVKLH-IKVAHVEAGLRSFDKRMPEE 115
                                       99999*****999997.99988888887777765555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2265.95
//
Query:       gi|242399996|ref|YP_002995421.1|  [L=355]
Description: glycosyltransferase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-17   64.5   0.0    1.6e-17   64.0   0.0    1.2  1  Glyco_transf_4   Glycosyltransferase Family 4
      4e-14   53.3   0.0      6e-14   52.8   0.0    1.2  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    4.7e-12   46.1   0.1    1.1e-11   44.9   0.1    1.6  1  Glyco_trans_4_2  Glycosyl transferase 4-like
      4e-05   24.1   0.0    7.8e-05   23.1   0.0    1.5  1  Glyco_trans_1_4  Glycosyl transferases group 1
    0.00016   21.4   0.3     0.0032   17.2   0.3    2.5  1  Glyco_transf_5   Starch synthase catalytic domain
     0.0039   17.5   0.0       0.01   16.2   0.0    1.7  2  Glyco_trans_1_2  Glycosyl transferases group 1
  ------ inclusion threshold ------
      0.039   13.5   0.1       0.11   12.0   0.1    1.8  1  Glycos_transf_1  Glycosyl transferases group 1
      0.073   12.6   0.1       0.12   11.9   0.1    1.3  1  Ssu72            Ssu72-like protein


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 !   64.0   0.0   7.3e-21   1.6e-17       8     166 ..      17     174 ..      15     176 .. 0.86

  Alignments for each domain:
  == domain 1  score: 64.0 bits;  conditional E-value: 7.3e-21
                    Glyco_transf_4   8 vleLaraLarrGheVtvvtpgddgpleeev....elvvrvprvplpllkrllrslaflrrlrrllkrekpDvvHahs 80 
                                       v+  a+ La++GheV++++ +++g+ ++e+     +v+rv+ +   ++  +l+ + f++ + r++ + kpD +H+h+
  gi|242399996|ref|YP_002995421.1|  17 VYKEAKSLAKHGHEVYIIAWDREGKYPKEEviegFRVIRVGPKAGYGPLMALKLPLFYLNAFRVILKLKPDAIHTHD 93 
                                       78889*************9999999999999888666777777777778888899999999999999********** PP

                    Glyco_transf_4  81 paalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrllrradrviavSeatadelrerygvppe 157
                                       + +++++ +  ++++++  V+ vH+lye      r+++ s l+++l   ++ +ad vi+v +++ + l+er +  p+
  gi|242399996|ref|YP_002995421.1|  94 FDTAVLGFFFKKLKKKVMWVYDVHDLYE---SFVRNNRVSSLIKRLDSIIMGKADIVITVNQEMMKILLERAR--PN 165
                                       ****999988888999999********7...67899999*******************************444..55 PP

                    Glyco_transf_4 158 kitVipnGv 166
                                         ++i n +
  gi|242399996|ref|YP_002995421.1| 166 MTVIIMNTI 174
                                       666666655 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 !   52.8   0.0   2.7e-17     6e-14       6     157 ..      16     169 ..      14     172 .. 0.78

  Alignments for each domain:
  == domain 1  score: 52.8 bits;  conditional E-value: 2.7e-17
                   Glyco_trans_4_4   6 yvaelaraLaarGheVtvltpapapgap.eleedgvrvhrlpvprrpspladla....alralrrllrqrrerpdvv 77 
                                       +v+  a++La++GheV +++ +  ++ p e++ +g rv+r+   ++ +pl  l+    +l a+r +l   + +pd +
  gi|242399996|ref|YP_002995421.1|  16 RVYKEAKSLAKHGHEVYIIAWDREGKYPkEEVIEGFRVIRVGPKAGYGPLMALKlplfYLNAFRVIL---KLKPDAI 89 
                                       6777799*************65555544258899******974444444444443333445666666...******* PP

                   Glyco_trans_4_4  78 hahsptaglaarlar.rrrgiplvvtlhgll..lrrgsgavrrlyralerrllrradavlvvseaeaeelralgvpa 151
                                       h+h++ ++ ++ + + +++++ +v+++h+l   ++r + +v +l+++l++ ++  ad v++v +++++ l ++ +p 
  gi|242399996|ref|YP_002995421.1|  90 HTHDFDTAVLGFFFKkLKKKVMWVYDVHDLYesFVR-NNRVSSLIKRLDSIIMGKADIVITVNQEMMKILLERARP- 164
                                       *****98888988884667*********96544554.57899******************************9998. PP

                   Glyco_trans_4_4 152 drvvvv 157
                                        +++v+
  gi|242399996|ref|YP_002995421.1| 165 -NMTVI 169
                                       .55554 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 !   44.9   0.1   4.8e-15   1.1e-11      14     136 ..      18     148 ..       3     151 .. 0.74

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 4.8e-15
                   Glyco_trans_4_2  14 lrlakeLakrgyeVhvitp.kkga.kdeleaegihvhrlkvdrkg..pleylka..fkl..kklikkikPDvvhahy 82 
                                       ++ ak+Lak+g+eV++i   ++g+  +e++ eg++v+r+  + +g  pl  lk+  f l  +++i k+kPD +h+h 
  gi|242399996|ref|YP_002995421.1|  18 YKEAKSLAKHGHEVYIIAWdREGKyPKEEVIEGFRVIRVG-PKAGygPLMALKLplFYLnaFRVILKLKPDAIHTHD 93 
                                       566999************9766667999***********5.333335888887444555459*************** PP

                   Glyco_trans_4_2  83 akpygllgslaarlsgvipvvlsvwGldvlkfpkksk....lkklllklalkkatkvi 136
                                           ++lg ++++l++++ +v++v+  d +++  +++    l k l  + + ka+ vi
  gi|242399996|ref|YP_002995421.1|  94 FDT-AVLGFFFKKLKKKVMWVYDVH--DLYESFVRNNrvssLIKRLDSIIMGKADIVI 148
                                       766.789******************..5544433332222355555555555666666 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 !   23.1   0.0   3.5e-08   7.8e-05      20     131 ..     200     315 ..     193     318 .. 0.72

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 3.5e-08
                                       HHHHHHHHH.H.HEEEEEES---...HHHHHHHTT-T.TEEEE---..THHHHHHHH-SEEEE...--...-..--S CS
                   Glyco_trans_1_4  20 lleavpllrkk.dvrlvivGdgp.rpeeleelaagleerveftGfv..edlaellaaadvfva...Ps...e..gfg 84 
                                       +++++  + +  dv + i+G+g+ + +e++      +++ +++G+v  e   e l++a+v+ +   Ps        +
  gi|242399996|ref|YP_002995421.1| 200 FVKEIVDISSTlDVSIRIAGSGTlK-DEIK------SSSAVYLGHVphERALEELSRAHVTFIlydPSvlnNkiASP 269
                                       6777777776767*******99744.3665......36799*****865566666666666553777788624678* PP

                                       HHHHHHHHTT-EEEE-TGGGTTT--TTSSEE--TT-.HHHHHHHHHHH CS
                   Glyco_trans_1_4  85 lkllEamaaglpvVatdvggiaevvgengllvppgd.pealaeailrL 131
                                       +kl Eam  g+pv + +   ++e +  + +++p +   +a  +a+ ++
  gi|242399996|ref|YP_002995421.1| 270 NKLFEAMWTGTPVLVVKG-TLPEKL-AEKFVIPVDYsKSAVKKALKEI 315
                                       ***************997.778844.2348887654355666666655 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 !   17.2   0.3   1.4e-06    0.0032     120     173 ..      75     120 ..      17     162 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.4e-06
                    Glyco_transf_5 120 raalelleklgwkpdvihahDWhtalvpallkelykerglfkkiktvftiHNla 173
                                         a +++ k   kpd ih+hD  ta+++++ k+l+k      k+  v+ +H l 
  gi|242399996|ref|YP_002995421.1|  75 LNAFRVILK--LKPDAIHTHDFDTAVLGFFFKKLKK------KVMWVYDVHDLY 120
                                       444555555..49********************984......599999999875 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 ?   -3.4   0.0       6.1   1.4e+04      41      56 ..     108     123 ..     103     127 .. 0.76
   2 !   16.2   0.0   4.6e-06      0.01      13      84 ..     270     340 ..     244     347 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 6.1
                   Glyco_trans_1_2  41 kevilfedleelaeki 56 
                                       k+v+++ d+++l e +
  gi|242399996|ref|YP_002995421.1| 108 KKVMWVYDVHDLYESF 123
                                       6788888888887765 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 4.6e-06
                   Glyco_trans_1_2  13 lrlfEaaacGafaltddaegleelftpgkevilfe.dleelaekiryllanpeerraiaeaarervlaehtyd 84 
                                        +lfEa+  G+++l+ + + +e+l   +k vi ++ +   + +++++ ++ p+ +++ a+ +r+ +l+++t+d
  gi|242399996|ref|YP_002995421.1| 270 NKLFEAMWTGTPVLVVKGTLPEKLA--EKFVIPVDySKSAVKKALKEIIETPKVIKKKAHFGRKIFLKKYTWD 340
                                       59**************666666665..44699999999**********************************7 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 ?   12.0   0.1     5e-05      0.11      75     167 ..     232     330 ..     199     334 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5e-05
                                       GGEEECCHSSSHHHHHHCESEEEEEESS......BSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT.- CS
                   Glycos_transf_1  75 viflgevsredleellknadifvlpsis......EgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpn.n 144
                                         +lg+v++e+  e l++a+++++           + +  l EAm  g+pv++++   p ++ ++ +    ++   +
  gi|242399996|ref|YP_002995421.1| 232 AVYLGHVPHERALEELSRAHVTFILYDPsvlnnkIASPNKLFEAMWTGTPVLVVKGTLPEKLAEKFV----IPVDyS 304
                                       45778888777777777777777763336778777788899*************9988888887776....555559 PP

                                       HHHHHHHHHHHHHSH...HHHHHHHH CS
                   Glycos_transf_1 145 aealaeairkllede...elrerlge 167
                                         a ++a+++++e +   ++ +++g+
  gi|242399996|ref|YP_002995421.1| 305 KSAVKKALKEIIETPkviKKKAHFGR 330
                                       99999******999977777666665 PP

>> Ssu72  Ssu72-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   5.5e-05      0.12      59     119 ..     102     162 ..      84     177 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.5e-05
                                       HHHHHHHHHHHHHHHTSHHHHHHHHHHH-SS--BGGG---.--SEEEESSHHHHHHHHHHH CS
                             Ssu72  59 iyedLkskdkelyeanGllkmldrnrkiKkaPerwqeaeekkfdvvitceervfdavvedl 119
                                        +++Lk+k   +y  + l +   rn+++ +  +r  ++  +k d+vit+++ +++ ++e  
  gi|242399996|ref|YP_002995421.1| 102 FFKKLKKKVMWVYDVHDLYESFVRNNRVSSLIKRLDSIIMGKADIVITVNQEMMKILLERA 162
                                       57899***********************************************999988865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.31s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2180.83
//
Query:       gi|242399997|ref|YP_002995422.1|  [L=324]
Description: Glycosyl transferase 2 [Thermococcus sibiricus MM 739]
Scores for complete 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   88.4   0.0    6.2e-25   88.0   0.0    1.3  1  Glycos_transf_2  Glycosyl transferase family 2
    1.6e-17   64.2   0.0    3.3e-17   63.1   0.0    1.5  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    9.6e-09   35.1   0.2    3.1e-08   33.5   0.2    1.7  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
    2.1e-08   34.3   1.0    4.3e-08   33.3   0.7    1.5  2  Glyco_trans_2_3  Glycosyl transferase family group 2
  ------ inclusion threshold ------
       0.01   16.3   0.0      0.018   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 !   88.0   0.0   1.7e-28   6.2e-25       1     107 [.       7     114 ..       7     180 .. 0.88

  Alignments for each domain:
  == domain 1  score: 88.0 bits;  conditional E-value: 1.7e-28
                                       EEEEEESS-TTTHHHHHHHHHHH.GGCCEEEEEEEEES-SSCHHHHHGGGCH.C-TTEEEEEESSS-HHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaq.dpypdfeiivvDDgStDetveileelak.edprvrvirreenvGkagalnagl 75 
                                       sv+ip+yNeek++ ++le  ++q +p++++ei++ D  StD+t+ei++++ + +++ v++ +++++  +  a+n g+
  gi|242399997|ref|YP_002995422.1|   7 SVIIPAYNEEKYIGKCLEEWVNQdYPKDRYEILLYDGMSTDKTAEIVRDFERrYPELVKYRKNPKR-RQVYAFNIGI 82 
                                       8***************************************************77777888888877.********** PP

                                       HH--SSEEEEEESSEEE-TTHHHHHHHHHHH. CS
                   Glycos_transf_2  76 raatgdyilflDaDdepdpdwleklvealekd 107
                                       ++a+gd+++++ a+ +p++d+l+k ve + + 
  gi|242399997|ref|YP_002995422.1|  83 QEARGDFFIIFGAHAYPERDFLRKSVETFLEI 114
                                       ***************************99875 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.1   0.0   9.3e-21   3.3e-17       1     224 [.       4     228 ..       4     232 .. 0.82

  Alignments for each domain:
  == domain 1  score: 63.1 bits;  conditional E-value: 9.3e-21
                   Glyco_tranf_2_3   1 prdlavlVptfneedvlgevlesllaqey..prvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgk 75 
                                       p+ ++v++p++nee+++g++le+ ++q+y  +r+e+ + + +s+++t+e ++ +++++p   v++    +n+  +  
  gi|242399997|ref|YP_002995422.1|   4 PF-VSVIIPAYNEEKYIGKCLEEWVNQDYpkDRYEILLYDGMSTDKTAEIVRDFERRYPEL-VKYR---KNPK-RRQ 74 
                                       67.9*************************5555**************************95.6753...4454.467 PP

                   Glyco_tranf_2_3  76 sralnealravksdlvllvDdDtvvePdtlkrllqff.....ltpkvgavgtpvfllnrstlvsalgalefaerhlr 147
                                       ++a n +++ +++d+ +++ + +  e d+l++++ +f     + pk + vg++   l++s+l     al +      
  gi|242399997|ref|YP_002995422.1|  75 VYAFNIGIQEARGDFFIIFGAHAYPERDFLRKSVETFleikeKEPKLAGVGGKIIKLYESRLAK-FVALIYSSPLSG 150
                                       7899*********************************999444445555555554445665533.333333444444 PP

                   Glyco_tranf_2_3 148 flaarralgvltlnG.sgslirrevlkelegldplflltdDyelglrlrragfrtayvpgaavrevfpsslkayikq 223
                                        + ++++ +  +  + ++ l++ ++ +e++g+d+  l++ D+e  lr+ ++ ++  + p+ + +   +s++k + kq
  gi|242399997|ref|YP_002995422.1| 151 ASTFWYEEKPHFAKTvAFALYDKKIAEEIGGFDEDMLTGNDFEFNLRINKRDYKLFFNPEIVSYYFARSTWKGFLKQ 227
                                       4557766665444555789***************99999**********************999999*********9 PP

                   Glyco_tranf_2_3 224 r 224
                                        
  gi|242399997|ref|YP_002995422.1| 228 S 228
                                       6 PP

>> Glyco_tranf_2_2  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.2   8.5e-12   3.1e-08       1     215 [.       7     214 ..       7     236 .. 0.79

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 8.5e-12
                   Glyco_tranf_2_2   1 svviplraseerhyieerv..lqkakyy.deeielivvddgSsekfleevssiidln.llvylkdeddkayslaaar 73 
                                       sv+ip +++e+  yi   +    ++  y  +  e+++ d+ S++k++e v+ +      lv +++++++   +  a 
  gi|242399997|ref|YP_002995422.1|   7 SVIIPAYNEEK--YIGKCLeeWVNQD-YpKDRYEILLYDGMSTDKTAEIVRDFERRYpELVKYRKNPKR--RQVYAF 78 
                                       89****99876..5988884322333.34899*********************8765155566777665..577899 PP

                   Glyco_tranf_2_2  74 NrGaskaesdlvlFlDaDcfissDkfekilklitikklrenidaavvlpvvdlnkedsevlkdvedltassrvledl 150
                                       N G+++a +d+ +   a  +   D + k ++  t ++++e     ++    +++k     l +   l+ ss +   +
  gi|242399997|ref|YP_002995422.1|  79 NIGIQEARGDFFIIFGAHAYPERDFLRKSVE--TFLEIKEKE-PKLAGVGGKIIKLYESRLAKFVALIYSSPLS-GA 151
                                       ****************************999..899998864.4555555677777777888888888888887.77 PP

                   Glyco_tranf_2_2 151 laakstlvkffapssssilinrraflevGGyDErfrGhgaEDfdlllRlakaikslekmpvelly 215
                                        ++       fa+    +l  ++   e+GG+DE +   + +Df++ lR+ k+  +l   p  ++y
  gi|242399997|ref|YP_002995422.1| 152 STFWYEEKPHFAKTVAFALYDKKIAEEIGGFDEDM--LTGNDFEFNLRINKRDYKLFFNPEIVSY 214
                                       7776666679*************************..8899*********986666344444444 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   0.0       2.7   9.6e+03      56      85 ..      76     105 ..      71     111 .. 0.70
   2 !   33.3   0.7   1.2e-11   4.3e-08      77     194 ..     169     279 ..     164     280 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 2.7
                   Glyco_trans_2_3  56 hgkdilvrealgrvvpsvGsgaflrrsalq 85 
                                       +++ i  +ea g+++ ++G+ a   r+ l+
  gi|242399997|ref|YP_002995422.1|  76 YAFNIGIQEARGDFFIIFGAHAYPERDFLR 105
                                       556666678888888888888876666655 PP

  == domain 2  score: 33.3 bits;  conditional E-value: 1.2e-11
                   Glyco_trans_2_3  77 aflrrsalqevggwdgdessvsEDfdmglrlqrkGyrvrfvpeslvkekspltlraalrQrkRwayGceleklillv 153
                                       a+ + + ++e+gg+d  +  ++ Df++ lr+ ++ y+++f pe + + + ++t++ +l+Q   +        + +++
  gi|242399997|ref|YP_002995422.1| 169 ALYDKKIAEEIGGFD-EDMLTGNDFEFNLRINKRDYKLFFNPEIVSYYFARSTWKGFLKQSFNYGAV-----KSMAI 239
                                       67788999*******.6689****************************************9888888.....56555 PP

                   Glyco_trans_2_3 154 rllgylgsllw.salplhlallllfsllalalvlllllllaa 194
                                         ++ ++s+lw +++ ++ + +l+  +++l++ ++l++ll++
  gi|242399997|ref|YP_002995422.1| 240 --RKGYFSPLWiFPIGFLGFEMLIPFWSILMWPFILYWLLLF 279
                                       ..4555555553778888888888888999999988888865 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   4.9e-06     0.018       2      50 ..      14      68 ..      13      95 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.9e-06
                   Glyco_tranf_2_4  2 neadiLpeflahhlalgf....drilvydndstDgtrailkelpe..vkllhvdk 50
                                      ne+++++++l+   + ++     +il+yd +stD+t++i++  ++   +l++ +k
  gi|242399997|ref|YP_002995422.1| 14 NEEKYIGKCLEEWVNQDYpkdrYEILLYDGMSTDKTAEIVRDFERryPELVKYRK 68
                                      788888777777666665442156****************886543333444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); 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: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2190.01
//
Query:       gi|242399998|ref|YP_002995423.1|  [L=201]
Description: CysE serine O-acetyltransferase [Thermococcus sibiricus MM 739]
Scores for complete 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   81.4  16.5      3e-08   33.1   1.6    4.6  5  Hexapep          Bacterial transferase hexapeptide (six repea
    2.4e-16   59.2  16.6    2.6e-10   39.9   5.0    4.0  4  Hexapep_2        Hexapeptide repeat of succinyl-transferase
     0.0082   16.0   1.9      0.011   15.6   0.5    1.9  2  DUF951           Bacterial protein of unknown function (DUF95
  ------ inclusion threshold ------
       0.03   13.9   0.5       0.03   13.9   0.5    2.2  2  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
       0.12   12.2   3.4       0.42   10.4   0.2    2.9  3  zinc_ribbon_2    zinc-ribbon domain
       0.13   12.7   0.0       0.23   11.9   0.0    1.3  1  Acetyltransf_11  Udp N-acetylglucosamine O-acyltransferase; D
       0.29   10.7   0.2       0.29   10.7   0.2    1.9  2  Sgf11            Sgf11 (transcriptional regulation protein)
       0.36   11.0   3.2        0.6   10.3   3.2    1.3  1  DUF2613          Protein of unknown function (DUF2613)
        4.4    7.7   7.8        4.9    7.5   4.7    2.5  2  DUF1922          Domain of unknown function (DUF1922)


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 !   22.9   0.0   2.5e-08   4.9e-05       9      36 .]       6      33 ..       3      33 .. 0.92
   2 !   33.1   1.6   1.5e-11     3e-08       1      34 [.      16      49 ..      16      51 .. 0.93
   3 !   27.0   0.2   1.2e-09   2.5e-06       2      31 ..      53      82 ..      52      85 .. 0.95
   4 !   26.7   1.3   1.5e-09     3e-06       2      36 .]     103     137 ..     102     137 .. 0.92
   5 ?   -3.2   0.0         4     8e+03      23      30 ..     182     189 ..     182     189 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 2.5e-08
                                      EE-TTEEEETTEEE-TTEEEETTEEEES CS
                           Hexapep  9 lIgpfaviggnVkIGdnvkIgagvvigg 36
                                      +++p av+ +nV+IG++++I++++ i++
  gi|242399998|ref|YP_002995423.1|  6 FVHPLAVVEENVEIGEGTRIWHFAHIRK 33
                                      799*********************9985 PP

  == domain 2  score: 33.1 bits;  conditional E-value: 1.5e-11
                                      TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEE CS
                           Hexapep  1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvi 34
                                      ++ IG+++ I++fa+i+ ++kIG+n+ Ig  v+i
  gi|242399998|ref|YP_002995423.1| 16 NVEIGEGTRIWHFAHIRKGAKIGKNCNIGKDVYI 49
                                      589**************************88877 PP

  == domain 3  score: 27.0 bits;  conditional E-value: 1.2e-09
                                      EEEETTEEE-TTEEEETTEEE-TTEEEETT CS
                           Hexapep  2 tvIGsnvlIgpfaviggnVkIGdnvkIgag 31
                                      + IG+nv+I +++ ++ +Vk+ ++v +g++
  gi|242399998|ref|YP_002995423.1| 53 VEIGNNVKIQNGVSVYRGVKVEEDVFLGPH 82
                                      78**************************95 PP

  == domain 4  score: 26.7 bits;  conditional E-value: 1.5e-09
                                       EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEES CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvigg 36 
                                       t + +++ Ig+ a+i  +V+IG+++ +gag+v+++
  gi|242399998|ref|YP_002995423.1| 103 TLVKKGASIGAHATIVCGVTIGEYAMVGAGAVVTK 137
                                       6677899**************************86 PP

  == domain 5  score: -3.2 bits;  conditional E-value: 4
                                       -TTEEEET CS
                           Hexapep  23 GdnvkIga 30 
                                       G+ vkI +
  gi|242399998|ref|YP_002995423.1| 182 GREVKIKR 189
                                       78899865 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 ?   -0.4   0.0      0.51     1e+03      17      22 ..      16      21 ..       6      25 .. 0.50
   2 !   39.9   5.0   1.3e-13   2.6e-10       3      34 .]      36      69 ..      34      69 .. 0.94
   3 ?    4.3   0.0     0.017        34       2      12 ..      71      81 ..      70      82 .. 0.91
   4 !   19.4   1.8   3.3e-07   0.00065      10      34 .]     111     137 ..     107     137 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.51
                                      SEEE-T CS
                         Hexapep_2 17 GvslGd 22
                                       v++G+
  gi|242399998|ref|YP_002995423.1| 16 NVEIGE 21
                                      233333 PP

  == domain 2  score: 39.9 bits;  conditional E-value: 1.3e-13
                                      EE-TT-EE-TT-EE..SEEE-TT-EE-TT-EE-S CS
                         Hexapep_2  3 iIGdnCliGanagi..GvslGdncvvgaGvvita 34
                                      +IG+nC+iG++ +i  Gv++G+n+++++Gv +++
  gi|242399998|ref|YP_002995423.1| 36 KIGKNCNIGKDVYIdvGVEIGNNVKIQNGVSVYR 69
                                      8************888***************995 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.017
                                      EEE-TT-EE-T CS
                         Hexapep_2  2 viIGdnCliGa 12
                                      v++++++++G+
  gi|242399998|ref|YP_002995423.1| 71 VKVEEDVFLGP 81
                                      89********7 PP

  == domain 4  score: 19.4 bits;  conditional E-value: 3.3e-07
                                       E-TT-EE..SEEE-TT-EE-TT-EE-S CS
                         Hexapep_2  10 iGanagi..GvslGdncvvgaGvvita 34 
                                       iGa a+i  Gv++G+ + vgaG v+t+
  gi|242399998|ref|YP_002995423.1| 111 IGAHATIvcGVTIGEYAMVGAGAVVTK 137
                                       9*****778*****************7 PP

>> DUF951  Bacterial protein of unknown function (DUF951)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       2.8   5.7e+03      23      34 ..      31      42 ..      27      48 .. 0.77
   2 !   15.6   0.5   5.7e-06     0.011      31      53 ..     176     198 ..     173     199 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.8
                            DUF951 23 lRvGadiklkCl 34
                                      +R Ga+i  +C+
  gi|242399998|ref|YP_002995423.1| 31 IRKGAKIGKNCN 42
                                      788999887775 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 5.7e-06
                            DUF951  31 lkClgcgrevmlpRskfekkikk 53 
                                       +kC++cgrev ++R++ ek +k+
  gi|242399998|ref|YP_002995423.1| 176 FKCSHCGREVKIKREDYEKYLKE 198
                                       69*****************9996 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   0.1       7.1   1.4e+04      11      13 ..     118     120 ..     116     124 .. 0.70
   2 ?   13.9   0.5   1.5e-05      0.03       6      18 ..     175     187 ..     170     190 .. 0.86

  Alignments for each domain:
  == domain 1  score: -4.2 bits;  conditional E-value: 7.1
                                       TT- CS
                   Desulfoferrod_N  11 vCG 13 
                                       vCG
  gi|242399998|ref|YP_002995423.1| 118 VCG 120
                                       566 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 1.5e-05
                                       EEE-TTT--EEEE CS
                   Desulfoferrod_N   6 vYkCevCGniVeV 18 
                                       ++kC +CG +V++
  gi|242399998|ref|YP_002995423.1| 175 IFKCSHCGREVKI 187
                                       8**********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 ?   -3.6   0.0       5.2     1e+04       5      10 ..     119     124 ..     119     127 .. 0.66
   2 ?    1.4   0.1      0.14   2.8e+02       5      11 ..     159     165 ..     158     166 .. 0.69
   3 ?   10.4   0.2   0.00021      0.42       1       9 [.     177     185 ..     169     190 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 5.2
                     zinc_ribbon_2   5 CGaelq 10 
                                       CG ++ 
  gi|242399998|ref|YP_002995423.1| 119 CGVTIG 124
                                       887765 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.14
                     zinc_ribbon_2   5 CGaelqd 11 
                                       CG++l++
  gi|242399998|ref|YP_002995423.1| 159 CGRKLKE 165
                                       8888765 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00021
                     zinc_ribbon_2   1 fCpnCGael 9  
                                       +C++CG+e+
  gi|242399998|ref|YP_002995423.1| 177 KCSHCGREV 185
                                       688888887 PP

>> Acetyltransf_11  Udp N-acetylglucosamine O-acyltransferase; Domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00012      0.23       1      17 [.     138     154 ..     138     155 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00012
                                       BB-TTEEEETTTTEEEE CS
                   Acetyltransf_11   1 DVpPfvlvagnparlrg 17 
                                       DVpPf lv gnparl+g
  gi|242399998|ref|YP_002995423.1| 138 DVPPFGLVFGNPARLKG 154
                                       9*************998 PP

>> Sgf11  Sgf11 (transcriptional regulation protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       1.2   2.4e+03       9      14 ..     158     163 ..     155     165 .. 0.76
   2 ?   10.7   0.2   0.00015      0.29       2      18 ..     173     189 ..     172     189 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.2
                                       TTSSEE CS
                             Sgf11   9 nCgRqi 14 
                                       +CgR+ 
  gi|242399998|ref|YP_002995423.1| 158 YCGRKL 163
                                       699986 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00015
                                       C-EEE-TTTSSEEEGGG CS
                             Sgf11   2 seyvtCpnCgRqiaasR 18 
                                       ++ ++C  CgR+++  R
  gi|242399998|ref|YP_002995423.1| 173 NVIFKCSHCGREVKIKR 189
                                       678**********8765 PP

>> DUF2613  Protein of unknown function (DUF2613)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   3.2    0.0003       0.6       4      33 ..     111     140 ..     108     150 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0003
                           DUF2613   4 gPaaaSaVaGivlGvvavfgvtavvqqdsr 33 
                                       ++a a +V G+++G  a +g++avv++d  
  gi|242399998|ref|YP_002995423.1| 111 IGAHATIVCGVTIGEYAMVGAGAVVTKDVP 140
                                       567799*******************98754 PP

>> DUF1922  Domain of unknown function (DUF1922)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.8   3.5e+03      21      30 ..      39      48 ..      32      55 .. 0.68
   2 ?    7.5   4.7    0.0024       4.9       4      33 ..     155     189 ..     154     192 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.8
                                      EEETTTEEEE CS
                           DUF1922 21 rkCvCGktik 30
                                      ++C  Gk + 
  gi|242399998|ref|YP_002995423.1| 39 KNCNIGKDVY 48
                                      6677777654 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0024
                                       EEETTS--EEEE....TT-SEEEET.TTEEEE--S CS
                           DUF1922   4 fRCdCGRvlYak....egaktrkCv.CGktikvke 33 
                                       f C CGR l  k    eg+   kC  CG+++k+k+
  gi|242399998|ref|YP_002995423.1| 155 FVCYCGRKLKEKigenEGNVIFKCShCGREVKIKR 189
                                       789****9987633336677778855******997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       723  (0.0403257); expected 358.6 (0.02)
Passed bias filter:                      564  (0.0314574); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1305.50
//
Query:       gi|242399999|ref|YP_002995424.1|  [L=366]
Description: Pleiotropic regulatory protein degT [Thermococcus sibiricus MM 739]
Scores for complete 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-142  472.9   0.0   8.3e-142  472.8   0.0    1.0  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    1.7e-09   37.4   0.1    2.7e-09   36.7   0.1    1.2  1  Beta_elim_lyase  Beta-eliminating lyase
    4.2e-08   32.7   0.1    7.5e-08   31.9   0.1    1.3  1  Aminotran_1_2    Aminotransferase class I and II
    5.5e-08   32.1   0.1    9.9e-08   31.3   0.0    1.4  2  Aminotran_5      Aminotransferase class-V
    0.00079   18.1   0.1     0.0011   17.5   0.1    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
     0.0015   17.4   0.0     0.0021   16.9   0.0    1.2  1  OKR_DC_1         Orn/Lys/Arg decarboxylase, major domain
  ------ inclusion threshold ------
      0.066   11.8   0.0      0.085   11.4   0.0    1.3  1  SHMT             Serine hydroxymethyltransferase
       0.12   12.6   0.0       0.52   10.6   0.0    2.0  1  DUF2795          Protein of unknown function (DUF2795)


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 !  472.8   0.0  3.7e-145  8.3e-142       2     360 ..       9     360 ..       8     361 .. 0.98

  Alignments for each domain:
  == domain 1  score: 472.8 bits;  conditional E-value: 3.7e-145
                                       HHHHHHHHHHHHHTSS-SSSSHHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHH CS
                   DegT_DnrJ_EryC1   2 ikeeeleaveevlksgwltsgpeveeFEkafaaylgvkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatan 78 
                                       i+eee++av+evlksg+l sg+ev+eFEk+fa+ylg+kh iav +GtaAl +aLral++gpgde+I++++tF+a+an
  gi|242399999|ref|YP_002995424.1|   9 IGEEEINAVTEVLKSGMLASGKEVKEFEKEFAQYLGAKHGIAVVNGTAALDVALRALKIGPGDEIITTPFTFIASAN 85 
                                       689************************************************************************** PP

                                       HHHHTT-EEEEE-B-TTTSSB-GGGCGGG--TTEEEEEEB-GGGB---HHHHHHHHHHCT-EEEEE-TT-TT-EETT CS
                   DegT_DnrJ_EryC1  79 avlelgakpvfvDvdpdtynidpaaieaaitertkaIlpVhlyGqvadmdalkaiaakhglkvieDaAhAlGatykg 155
                                       a+l  ga+pvf+D+d++tyn+dp+++ ++it +tkaI++VhlyGq+adm+a k+ia++++l+++eD+A+A+Ga+++g
  gi|242399999|ref|YP_002995424.1|  86 AILFQGARPVFADIDEKTYNLDPNDVLEKITDKTKAIVVVHLYGQPADMKAFKEIAEDYKLYLVEDCAQAHGAEFEG 162
                                       ***************************************************************************** PP

                                       EECCCSSSEEEEE-BTTSSS-SSS-EEEEESTHHHHHHHHHHHBTTCECCTCSSCECCSS---B-B-BHHHHHHHHH CS
                   DegT_DnrJ_EryC1 156 kkvGalgdaavfSFyptKnlttGeGGavvtndeelaekarvlrnhGlkrkaekryvgevelGynyrlteiqAAigla 232
                                       +kvG++gd+a+fSFyptKn+ttGeGG+vvtn++ela++a ++rnhG++    ++y +   lGyn+r+t+i+AAig+a
  gi|242399999|ref|YP_002995424.1| 163 QKVGTFGDIAAFSFYPTKNMTTGEGGMVVTNEDELAKRADLIRNHGQA----EKYLHVE-LGYNLRMTNINAAIGRA 234
                                       **********************************************99....7999999.***************** PP

                                       HHCTHHHHHHHHHHHHHHHHHHHHTCCCCEESCGGTTSSSEEESCEEEEEHCCHHHCHHHHHHHHHHCCEE-B-SGS CS
                   DegT_DnrJ_EryC1 233 qLerldelvarRreiaelykeeLaelegtaelttpketkkhawhlyavlveeeaevkrdelvealkeegigtrvhyp 309
                                       qL++ld ++++R e+a+l++e++++++g +++ ++++ k h++h+y+++ve+++ ++rdel+++l+e+gig+ vhyp
  gi|242399999|ref|YP_002995424.1| 235 QLRKLDAWNEKRIENAKLLSEGISKIDGLTPPYVDERVK-HVFHQYVIRVEDDFPLSRDELMAKLREKGIGSAVHYP 310
                                       ****************************99999999888.*************99********************** PP

                                       CHGGGSCCHHHHHHCCCHC-HHHHHHHHHEEEEEGGTTGSHHHHHHHHHHH CS
                   DegT_DnrJ_EryC1 310 nplhrqpvyaerkeeasgdlpnaerlaervlsLplypelteedvdrVveal 360
                                       +p+h qp+y++   + ++ +pna ++++rvlsLp++p+++eed+ ++v++l
  gi|242399999|ref|YP_002995424.1| 311 IPVHHQPFYQKLG-YPKDICPNAIEASKRVLSLPVHPAVSEEDIAYIVSTL 360
                                       ************7.55678*****************************987 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.1   1.2e-12   2.7e-09      30     279 ..      28     266 ..      21     278 .. 0.79

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 1.2e-12
                                       --HHHHHHHHHHHHHTT-SEEEEES-HHHHHHHHHHHH-.-TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBT CS
                   Beta_elim_lyase  30 edktvnrLedavaelfgkeaalfvpqGtaAnsillkill.qrgeevivtepahihfdetgaiaelagvklrdlknke 105
                                         k+v+++e+++a+++g+++++ v++GtaA  ++l++l   +g+e+i t    + f    ++  ++g++++ ++++e
  gi|242399999|ref|YP_002995424.1|  28 SGKEVKEFEKEFAQYLGAKHGIAVVNGTAALDVALRALKiGPGDEIITT---PFTFIASANAILFQGARPVFADIDE 101
                                       568899*****************************99987999*99765...5788888999999******999999 PP

                                       T.TBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHHTS- CS
                   Beta_elim_lyase 106 a.GkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaakslgei 181
                                       +  ++d++++ ++i++      k+k+i++   + +  Gq+  ++     ++ia++y++ l+ D A    a      +
  gi|242399999|ref|YP_002995424.1| 102 KtYNLDPNDVLEKITD------KTKAIVVV--HLY--GQPADMKA---FKEIAEDYKLYLVEDCAQAHGAE----FE 161
                                       8789**********99......35566553..556..89877665...566799*********99866654....55 PP

                                       CHHHHTTSSEEEEES..SSTT--SS-EEEEE-HH.......HHHHHHHH....HHHHT---SSTHHHHH..HHHHHH CS
                   Beta_elim_lyase 182 vkemfsyvDsvtmsl..kKdllanvGgvlafrddel...edylaerveq....rkylggglrqagvlaaleagiral 249
                                        +++    D+  +s+  +K++++  Gg++++++del    d +++  +     +  lg +lr   + aa   g   l
  gi|242399999|ref|YP_002995424.1| 162 GQKVGTFGDIAAFSFypTKNMTTGEGGMVVTNEDELakrADLIRNHGQAekylHVELGYNLRMTNINAA--IGRAQL 236
                                       556666677666665449****************99999555555554411115557999999999999..888888 PP

                                       HHSSTTHHHHHHHHHHHHHHHHHCT--EEE CS
                   Beta_elim_lyase 250 eeglaslerdhktaeqlaeklelvrlaipr 279
                                        + +a  e+  ++a+ l e+++++++ +p 
  gi|242399999|ref|YP_002995424.1| 237 RKLDAWNEKRIENAKLLSEGISKIDGLTPP 266
                                       888888899999999999999999886554 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 !   31.9   0.1   3.3e-11   7.5e-08      47     193 ..      33     157 ..      20     176 .. 0.91

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 3.3e-11
                                       HHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBE CS
                     Aminotran_1_2  47 peleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasyknilrlsggevvryply 123
                                       +e+e++ a++lg        ++  + v +G+ al++al +l  + pgdei+    t+    n++   g+  v   ++
  gi|242399999|ref|YP_002995424.1|  33 KEFEKEFAQYLG--------AKHGIAVVNGTAALDVALRALK-IGPGDEIITTPFTFIASANAILFQGARPVFADID 100
                                       89**********........888***********99999999.********************************66 PP

                                       ETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTC CS
                     Aminotran_1_2 124 seedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagf 193
                                        e++++ld ++++e++++      ktk i+v       G+ a+ +  +++   a+ y+l+l+ D a a++
  gi|242399999|ref|YP_002995424.1| 101 -EKTYNLDPNDVLEKITD------KTKAIVVVHL---YGQPADMKAFKEI---AEDYKLYLVEDCAQAHG 157
                                       .*****************......9999998755...5999999999999...99999999988776665 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.0   4.4e-11   9.9e-08      42     182 ..      29     158 ..      12     177 .. 0.87
   2 ?   -2.9   0.0       1.1   2.5e+03     270     295 ..     226     251 ..     178     276 .. 0.60

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 4.4e-11
                                       HHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEE CS
                       Aminotran_5  42 tkaveearekvaelinaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkv 118
                                        k v+e ++++a+ ++a+  + i ++ Gt+ a+ +++++l  ++ pgdei++t     a      ++  ++ga+ ++
  gi|242399999|ref|YP_002995424.1|  29 GKEVKEFEKEFAQYLGAK--HGIAVVNGTA-ALDVALRAL--KIGPGDEIITTPFTFIASA----NAILFQGARPVF 96 
                                       578999************..5888888877.*********..69**********9888877....455599****** PP

                                       EEBETT.SCBEGGGHHHH--TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTTT CS
                       Aminotran_5 119 ipldee.geldldelekllnektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqavgh 182
                                       + +de+  +ld++++ +++++ktk++ + h     G   ++++++++a +++ +++ D aqa g 
  gi|242399999|ref|YP_002995424.1|  97 ADIDEKtYNLDPNDVLEKITDKTKAIVVVHL---YGQPADMKAFKEIAEDYKLYLVEDCAQAHGA 158
                                       ***9862699******************996...8**************************9775 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.1
                                       CHHHHHHHHHHHHHHHHHHHHHCTST CS
                       Aminotran_5 270 eigleaiekhekelaeyllerlkslp 295
                                       +i+++  +++ ++l ++ ++r+++ +
  gi|242399999|ref|YP_002995424.1| 226 NINAAIGRAQLRKLDAWNEKRIENAK 251
                                       44444444444444444444444433 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 !   17.5   0.1     5e-07    0.0011      55     222 ..      33     200 ..      29     216 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 5e-07
                                       HHHHHHHHHHHT-SEEEEESSHHHHHHHHHHTT.S-TTEEEEEESTSSHHHHHHHHHTHHH...TTCEEEEESTTSH CS
                   Cys_Met_Meta_PP  55 svleeriaaLeggeaalavssGmaAiaaailal.lkaGdeivvsddlYggtqrllkkvlkk...lgievkfvdtsdl 127
                                       + +e++ a+  g+++++av  G+aA+++a++al +  Gdei+++   +  + + +     +     i+ k ++  d+
  gi|242399999|ref|YP_002995424.1|  33 KEFEKEFAQYLGAKHGIAVVNGTAALDVALRALkIGPGDEIITTPFTFIASANAILFQGARpvfADIDEKTYNL-DP 108
                                       6799**************************9995678**********999888766655554445677777776.88 PP

                                       HHHHHHCCTTEEEEEEESS-TTTT----HHHHHHHHHHTT-EEEEEGTTTHTTTS-GGGGT..-SEEEEET..TTTT CS
                   Cys_Met_Meta_PP 128 eelekaikentklvylEtptnpllkvvDiekiaklakkagvlvvvDntfaspllqrplklg..aDivvhSa..TKyl 200
                                       +++ ++i+++tk++ +        + +D+++  ++a + ++ +v D + a ++ ++  k g   Di   S   TK +
  gi|242399999|ref|YP_002995424.1| 109 NDVLEKITDKTKAIVVVH---LYGQPADMKAFKEIAEDYKLYLVEDCAQAHGAEFEGQKVGtfGDIAAFSFypTKNM 182
                                       999999999999986543...33445688888888888888888888777777777777774446666664335544 PP

                                       TCSSS--EEEEEESSCHHHHHH CS
                   Cys_Met_Meta_PP 201 gGhsdvvaGvivvkgkeelkke 222
                                           +  +G++v+++ +el+k+
  gi|242399999|ref|YP_002995424.1| 183 T---TGEGGMVVTNE-DELAKR 200
                                       2...33456666555.566665 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 !   16.9   0.0   9.4e-07    0.0021      67     141 ..      31     105 ..      12     160 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 9.4e-07
                                       HHHHHHHHHHHHCT-SEEEEESSHHHHHHHHHHHHH--TTEEEEEESS--HHHHHHHHHS-EEEEEE--EB-TTS CS
                          OKR_DC_1  67 aikeaqkyaarvfgadksyfvvnGTsssnkvvlnavltpgdlvlvdRNcHKSiehalvlsgatPvylepernalg 141
                                        +ke +k  a+  ga +   vvnGT++   ++    + pgd ++    +  + ++a+++ ga Pv+   ++  + 
  gi|242399999|ref|YP_002995424.1|  31 EVKEFEKEFAQYLGAKHGIAVVNGTAALDVALRALKIGPGDEIITTPFTFIASANAILFQGARPVFADIDEKTYN 105
                                       468889999*****************9999999999******************************988877775 PP

>> SHMT  Serine hydroxymethyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   3.8e-05     0.085     147     211 ..      97     159 ..      75     259 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.8e-05
                                       E-B-TTTSSB-HHHHHHHHHHH--SEEEEE-SST-S---HHHHHHHHHHTT-EEEEE-GGGHHHH CS
                              SHMT 147 ykvdketglidydelekkakefkPklivaGtsaysrlidyarlreiadevgayllvdmahiaGlv 211
                                         +d++t  +d +++ +k ++   k iv     y +  d + ++eia++ + yl+ d a   G  
  gi|242399999|ref|YP_002995424.1|  97 ADIDEKTYNLDPNDVLEKITDKT-KAIVV-VHLYGQPADMKAFKEIAEDYKLYLVEDCAQAHGAE 159
                                       56888999999887766655543.43433.468*************************9888755 PP

>> DUF2795  Protein of unknown function (DUF2795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00023      0.52       5      25 ..     286     306 ..     286     310 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00023
                           DUF2795   5 dyPatKdeLveyArrngApde 25 
                                       d+P ++deL+ ++r++g + +
  gi|242399999|ref|YP_002995424.1| 286 DFPLSRDELMAKLREKGIGSA 306
                                       8***************97665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.30s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 2277.24
//
Query:       gi|242400000|ref|YP_002995425.1|  [L=145]
Description: HEPN domain protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-32  112.2   1.3    1.9e-32  111.9   1.3    1.0  1  HEPN      HEPN domain


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 !  111.9   1.3   1.1e-36   1.9e-32       1     117 [.      11     133 ..      11     134 .. 0.98

  Alignments for each domain:
  == domain 1  score: 111.9 bits;  conditional E-value: 1.1e-36
                                       HHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHTT--.SSCCHHHHHHCCHHHT....-HHHHHH CS
                              HEPN   1 aeewlrrAeedleaAellleegdydlacfhaqqaaekalKAlllkkggeppkthdlreLleelkkelke.seelree 76 
                                       +e+w+r+A+++l++A  +le+ +y++a f+aqqaae+a+KA+l   g   p +h++++Ll+el +++++ ++e+  +
  gi|242400000|ref|YP_002995425.1|  11 YERWMREAKRTLSSAYSDLEHAYYEWASFKAQQAAELAVKAILRGIGLA-PIGHSITKLLRELNTLGIDvPKEILYY 86 
                                       699*********************************************9.*************************** PP

                                       HHHHHCCCHHCCCTSS--S......--HHHHHHHHHHHHHHHHHHHH CS
                              HEPN  77 leeLekayiesrYpdakee......yteedaeealkdaeevlelvee 117
                                       + eL++ yi  rYpda++e      y+ee a+e+++++e+++++ve 
  gi|242400000|ref|YP_002995425.1|  87 AMELDRNYIAPRYPDAYSEgapfeyYSEEIAKELISYVEKIIKFVEG 133
                                       ********************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      585  (0.0326287); 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: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 885.25
//
Query:       gi|242400001|ref|YP_002995426.1|  [L=133]
Description: DNA polymerase, beta domain protein region [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-11   44.0   0.0    3.3e-11   43.3   0.0    1.3  1  NTP_transf_2    Nucleotidyltransferase domain
    4.9e-07   29.7   0.0    8.2e-07   29.0   0.0    1.4  1  Polbeta         Polymerase beta, Nucleotidyltransferase
    0.00029   21.0   0.0    0.00041   20.5   0.0    1.4  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 !   43.3   0.0   5.4e-15   3.3e-11       6      74 ..      12      95 ..       4     129 .. 0.77

  Alignments for each domain:
  == domain 1  score: 43.3 bits;  conditional E-value: 5.4e-15
                                      HHHHHHTTTSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHH...............HHHEHHHHHHHHCCCEEECTTE CS
                      NTP_transf_2  6 eelkelepvakvvlfGSyarGtalkgSDiDllvvlpeevsre...............kkeegleklaeiikfleellgl 69
                                      ++ + le++a ++lfGSyarG ++  SD D++v++++ +  +               +++ +++ ++e+ k+le l + 
  gi|242400001|ref|YP_002995426.1| 12 RIARHLEGKATIILFGSYARGNYNLASDFDIIVISDKLKGNPlertrglymlneeflPVDIIAYTRKEFLKALENLSPS 90
                                      56677888******************************87668888888888888888888888888888888888877 PP

                                      EEEEE CS
                      NTP_transf_2 70 evdlv 74
                                        d +
  gi|242400001|ref|YP_002995426.1| 91 ALDAM 95
                                      77777 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.0   1.4e-10   8.2e-07      11      70 ..      18      76 ..       8     104 .. 0.71

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 1.4e-10
                                      HHHHSTTEEEEEE-S------EEEEEEEESS-..--HHHHHHHHHHHHHH.SSSEEEEEETT CS
                           Polbeta 11 keielaylFGSrakgkareeSDiDlavllkek..ldleeelelaaelediklgkkvDlvdln 70
                                      ++ + ++lFGS+a+g+++  SD+D+ v+ ++   + le+   l++  e+      vD++ + 
  gi|242400001|ref|YP_002995426.1| 18 EGKATIILFGSYARGNYNLASDFDIIVISDKLkgNPLERTRGLYMLNEEF---LPVDIIAYT 76
                                      444889***********************999775555555555555554...355555544 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 !   20.5   0.0   6.8e-08   0.00041       8      55 ..       4      52 ..       2     115 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 6.8e-08
                                      HHHHHHHHHHHHHH-TT-EEEE-HHHHTT-SE.ESSEEEEEEBTTBSTT CS
                    DNA_pol_B_palm  8 ealealvkkaakeldpevevivcGSYRRgaes.sGDvDvlitkkdakse 55
                                      e+l+a+v++ a++l+ ++++i  GSY Rg+ + + D D+++  ++ k +
  gi|242400001|ref|YP_002995426.1|  4 EKLKAFVERIARHLEGKATIILFGSYARGNYNlASDFDIIVISDKLKGN 52
                                      7899************************9865389******99887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 886.25
//
Query:       gi|242400002|ref|YP_002995427.1|  [L=319]
Description: NADH dependent dehydrogenase like protein [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-30  105.9   0.9    3.7e-30  105.2   0.9    1.4  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
    2.7e-06   27.4   0.0    1.7e-05   24.8   0.0    2.1  1  GFO_IDH_MocA_C   Oxidoreductase family, C-terminal alpha/beta
    1.4e-05   25.6   0.5    3.6e-05   24.3   0.2    1.8  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    4.2e-05   24.2   0.8    0.00011   22.8   0.8    1.8  1  NAD_binding_3    Homoserine dehydrogenase, NAD binding domain
    0.00071   20.2   0.4      0.002   18.8   0.4    1.7  1  CoA_binding      CoA binding domain
      0.007   16.6   3.3      0.026   14.7   0.3    2.5  3  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
  ------ inclusion threshold ------
      0.018   14.9   1.9       0.07   13.0   1.8    2.0  2  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
       0.02   15.0   0.4       0.02   15.0   0.4    2.6  3  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
       0.02   13.8   0.5       0.04   12.8   0.3    1.6  2  OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin famil
      0.033   14.6   0.4      0.071   13.6   0.4    1.5  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
      0.079   13.3   0.1       0.16   12.4   0.1    1.5  1  DrsE             DsrE/DsrF-like family


Domain annotation for each model (and alignments):
>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.2   0.9   2.3e-33   3.7e-30       1     120 []       5     125 ..       5     125 .. 0.96

  Alignments for each domain:
  == domain 1  score: 105.2 bits;  conditional E-value: 2.3e-33
                                       EEEEEETTSHHHHHHHHHHHHTTTTE..EEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTTESEEEE-S-GGGH CS
                      GFO_IDH_MocA   1 lrvaiiGaGkigskhlrplnesqrle..evvalldpdaeraeavaesfgveaysdleelladpeidavivatpngth 75 
                                       lrv+++G+G++g++h+r + e  r+   e+v++ d + era++va +f+ +a+ d++el++ +  dav++a+p+++h
  gi|242400002|ref|YP_002995427.1|   5 LRVGVVGVGNMGYHHARIYSEMAREGkvELVGVADANLERAKEVASQFKTKAFGDYKELVK-EGLDAVSIAVPTSLH 80 
                                       69**************888888665588*********************************.66************* PP

                                       HHHHHHHHHTT-EEEEESSS-SSHHHHHHHHHHHHHHTS-EEEE- CS
                      GFO_IDH_MocA  76 eelakaaleagkhvllEKPlattveeakelvelaekkgklvsvgy 120
                                       +++a++++e+g++vl+EKP+a ++e a+e++++a+k++++++vg+
  gi|242400002|ref|YP_002995427.1|  81 KQVALEFIENGVNVLVEKPIAESIENAQEIMRAAKKNNVTLMVGH 125
                                       *******************************************97 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 !   24.8   0.0     1e-08   1.7e-05       1      95 [.     137     218 ..     137     237 .. 0.73

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 1e-08
                                       HHHHHTTTTSSEEEEEEEEECBEEECHHHHCCGGSHHCSTSHHHHTCHHHHHHHHHHHTSEEEEEEEEE.SEEESCT CS
                    GFO_IDH_MocA_C   1 KelIengklGevvsvdvwtldtragaeakkrwkrrkkksgGvlgdlgiHdiDllqwLfGqppsvvaalgrmrqnaea 77 
                                       Ke+I +g lGe+v+ +        +++  ++  r    + Gv +dl++HdiD++ +L+ +   +v+a    r++ + 
  gi|242400002|ref|YP_002995427.1| 137 KEAISQGLLGEIVTMN--------AKRVGPMVVRI--ADVGVIIDLAVHDIDVMSFLADSRVKEVYAKA--RNVKHP 201
                                       7888888888888885........44444444434..588***************************98..899999 PP

                                       CCSCSEEEEEEEEEEETT CS
                    GFO_IDH_MocA_C  78 aededaavmsvlnlekgs 95 
                                       a+++d+a +++l + kg 
  gi|242400002|ref|YP_002995427.1| 202 AKVDDYA-LILLGFDKGM 218
                                       9999999.4554444443 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 !   24.3   0.2   2.2e-08   3.6e-05       1      81 [.       6      87 ..       6      97 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 2.2e-08
                                      EEEEETTSHHH...HHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHH.H-SEEEE-S-HHHHH CS
                     F420_oxidored  1 kigiiGaGnmg...ealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaae.eadvvvlavkpedve 75
                                      ++g++G Gnmg   + + s ++++g + + + va + n e+a+e a++++ k+++ d++e+++   d v +av+++ ++
  gi|242400002|ref|YP_002995427.1|  6 RVGVVGVGNMGyhhARIYSEMAREG-KVELVGVA-DANLERAKEVASQFKTKAFG-DYKELVKeGLDAVSIAVPTSLHK 81
                                      69*********44345667888888.77777766.********************.9999999678**********999 PP

                                      HHHHHC CS
                     F420_oxidored 76 evlsel 81
                                      +v+ e 
  gi|242400002|ref|YP_002995427.1| 82 QVALEF 87
                                      998765 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 !   22.8   0.8     7e-08   0.00011       1     116 [.      11     123 ..      11     124 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 7e-08
                                       --SHHHHHHHHHHHH---SSEEEEEEEEESSEEE-TTHHHHHT--CB---HHHHHHHHS.-EEEEE-S--.HHHHTT CS
                     NAD_binding_3   1 GlGaiGsavleqlkrqqseielelvavadrdsllskdrkallasealtldlddliahld.pdvvVEcass.eavael 75 
                                       G+G+ G   +++  ++++e ++elv+vad++ l++++  a   +++   d ++l++  +  d  V  a + +  +++
  gi|242400002|ref|YP_002995427.1|  11 GVGNMGYHHARIYSEMAREGKVELVGVADAN-LERAKEVASQFKTKAFGDYKELVK--EgLDA-VSIAVPtSLHKQV 83 
                                       99*****************************.777777777788889999*****9..43444.3444440455667 PP

                                       HHHHHHTTEEEE-S--CGGG-HHHHHHHTSSSTTS--.EE- CS
                     NAD_binding_3  76 vlkaLkagkdvvtankgaladealyeeLreaaeangakiyv 116
                                       +l+++++g++v++    a +  +  +e++ aa++n+++++v
  gi|242400002|ref|YP_002995427.1|  84 ALEFIENGVNVLVEKPIAES-IENAQEIMRAAKKNNVTLMV 123
                                       79***********9888887.89999**********98865 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.4   1.2e-06     0.002       3      91 ..       4      96 ..       2      97 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.2e-06
                                      TEEEEEETTTSHHHHHHHHHHHHHHECEEEEEEC-TTTTTCEET.....TEEEESCHHHHHHHCTTTEEEEES-HHHHH CS
                       CoA_binding  3 dtkviviGagglgiaglyhfkeklkygikavfgvnprkvgtevl.....glpvyksvdeleektevdvavitvPaesaq 76
                                      + +v+v+G+g++g   +   +e+ + g ++++gv +  + +  +       +++ + +el+++ + d+  i+vP    +
  gi|242400002|ref|YP_002995427.1|  4 MLRVGVVGVGNMGYHHARIYSEMAREGKVELVGVADANLERAKEvasqfKTKAFGDYKELVKE-GLDAVSIAVPTSLHK 81
                                      568***********9999999999999999999999877766666699999************.*************** PP

                                      HHHHHHHHTT-SEEE CS
                       CoA_binding 77 eavdelveagikgiv 91
                                      ++++e +e+g+++ v
  gi|242400002|ref|YP_002995427.1| 82 QVALEFIENGVNVLV 96
                                      ***********9876 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.3   1.6e-05     0.026       1      68 [.       6      80 ..       6      93 .. 0.75
   2 ?    1.9   0.1      0.14   2.3e+02      42      83 ..      99     143 ..      81     151 .. 0.69
   3 ?   -2.4   0.0       2.9   4.7e+03      48      48 ..     197     197 ..     157     246 .. 0.53

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.6e-05
                                      EEEEE--SHHHHHHHHHH...HHTT-..EEEEE-SSHHHHHHHHHTT.EEE-SSHHHHHHHC.SEEEE-SSSHHH CS
                     NAD_binding_2  1 kigfiGlGvMGsnmalnl...lkagy..kvavynrtkekveelvaeg.akaaesieelvasl.dvvitmvkagka 68
                                      ++g++G+G+MG + a+     +++g    v v + + e+++e++++   ka+ + +elv++  d+v + v+ + +
  gi|242400002|ref|YP_002995427.1|  6 RVGVVGVGNMGYHHARIYsemAREGKveLVGVADANLERAKEVASQFkTKAFGDYKELVKEGlDAVSIAVPTSLH 80
                                      58*********998875533255543114667788888888888884599*********9866*****9998755 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.14
                                       T.EEE-SSHHHHHHHC..SEEEE-SSSHHHHHHHHHSHCCC--TT CS
                     NAD_binding_2  42 g.akaaesieelvasl..dvvitmvkagkavdeviegllealkkg 83 
                                         a+ +e+++e+++++  + v +mv + +  +  + +l+ea+++g
  gi|242400002|ref|YP_002995427.1|  99 PiAESIENAQEIMRAAkkNNVTLMVGHVERFNPAVLKLKEAISQG 143
                                       244445555555555555889999999999999999988888776 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 2.9
                                       S CS
                     NAD_binding_2  48 s 48 
                                       +
  gi|242400002|ref|YP_002995427.1| 197 N 197
                                       2 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   1.8   4.3e-05      0.07       2      65 ..       7      69 ..       6     117 .. 0.70
   2 ?   -0.3   0.0      0.51   8.2e+02      13      47 ..      82     116 ..      78     132 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.3e-05
                                      EEEE--SCCHHHHHHHHHHT..T-EEEEE-S-HHHHHHHHHHHHH.HHHCCTTTTSS-HHHHCCCHH CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasa..gleVvlvdiseealekalekiek.sleklvekgklkeeeveaala 65
                                      v+v+G G mG   a +  +   + +V lv ++++ le+a+e +++ +++ +   g +k e v++ l+
  gi|242400002|ref|YP_002995427.1|  7 VGVVGVGNMGYHHARIYSEMarEGKVELVGVADANLERAKEVASQfKTKAF---GDYK-ELVKEGLD 69
                                      9*********999988765433789**************999987333333...3333.33333333 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.51
                                       HHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHH CS
                           3HCDH_N  13 giaavfasagleVvlvdiseealekalekieksle 47 
                                       ++a  f+++g++V +    +e++e+a+e +++  +
  gi|242400002|ref|YP_002995427.1|  82 QVALEFIENGVNVLVEKPIAESIENAQEIMRAAKK 116
                                       67888999999999999988888888877666433 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.4   1.2e-05      0.02      12      74 ..       4      65 ..       1      86 [. 0.73
   2 ?    1.7   0.1      0.15   2.5e+02      29      99 ..      61     130 ..      57     138 .. 0.82
   3 ?   -2.2   0.1       2.5     4e+03     108     118 ..     169     178 ..     149     204 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.2e-05
                                      T-EEEEES-SHHHHHHHH...HHHCC.T-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHH CS
                      Shikimate_DH 12 ekkvlliGaGemaelvak...hLlak.gvkkvvvaNRtlerakelaeelkgeeiealkleelkella 74
                                        +v ++G G+m+   a+    ++++ +v+ v va  +lerake+a+++k++     ++ ++kel++
  gi|242400002|ref|YP_002995427.1|  4 MLRVGVVGVGNMGYHHARiysEMAREgKVELVGVADANLERAKEVASQFKTK-----AFGDYKELVK 65
                                      56899*******976654111566664788899****************777.....4444444444 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.15
                                       HHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SSSSS-SB-HHHHHCCH CS
                      Shikimate_DH  29 khLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisataseepilekeeveeal 99 
                                       k L+++g+++v +a  t  + k++a e+ ++ +++l  + + e +++a  ++ a + +++ l  ++ve+ +
  gi|242400002|ref|YP_002995427.1|  61 KELVKEGLDAVSIAVPTSLH-KQVALEFIENGVNVLVEKPIAESIENAQEIMRAAKKNNVTLMVGHVERFN 130
                                       67888888888888877665.67788887888888888999999999999999999999999999998865 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 2.5
                                       EEE--SS-SB- CS
                      Shikimate_DH 108 lvDiavPRdve 118
                                       ++D+av  d++
  gi|242400002|ref|YP_002995427.1| 169 IIDLAVH-DID 178
                                       5555553.433 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 ?   12.8   0.3   2.5e-05      0.04     132     239 ..       7     117 ..       3     151 .. 0.83
   2 ?   -2.0   0.0      0.79   1.3e+03      50     136 ..     219     239 ..     172     287 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.5e-05
                                       EEEE--SHHHHHHHHHHCCCS--SEEEEE-SSHHHHHHHHHHCCS.CTT-EEECSCHHHHT.TSSEE.EE----SS- CS
                   OCD_Mu_crystall 132 laiiGaGvqaetqlealkavldikevriydrdeeaaekfaenlqefefevsackseeeave.gadiv.vtvTaakap 206
                                       ++++G G + + ++++ ++++   +v + ++ + + e++ e +++  f+ +a ++ +e v+ g d v ++v ++ + 
  gi|242400002|ref|YP_002995427.1|   7 VGVVGVGNMGYHHARIYSEMAREGKVELVGVADANLERAKEVASQ--FKTKAFGDYKELVKeGLDAVsIAVPTSLHK 81 
                                       79************************************9999995..99*********9963788664788888889 PP

                                       SB-GGGS-TT-EEEE...-S--STT--SB-HHHHHC CS
                   OCD_Mu_crystall 207 ilkaewvkpGahina...vgadapgkteLdddilkr 239
                                        +  e++++G+ ++    ++ + ++ +e+ +++ k+
  gi|242400002|ref|YP_002995427.1|  82 QVALEFIENGVNVLVekpIAESIENAQEIMRAAKKN 117
                                       9999******98864333666667777777766654 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.79
                                       TEEEEEEEEEETTTTEEEEEEEEEETTTCCCTSSSEEEEEEEE-TTT--EEEEEE-HHHHHHHHHHHHHHHHHHHS- CS
                   OCD_Mu_crystall  50 rgelevmpaylagrellgvKlvnshpenkksglptvtalvvLndpetGvplalmdatlltalRTaAvsavaakyLar 126
                                       +g++e                                                                  +  L +
  gi|242400002|ref|YP_002995427.1| 219 DGVIE------------------------------------------------------------------TNRLTP 229
                                       44443..................................................................222333 PP

                                       TT--EEEEE- CS
                   OCD_Mu_crystall 127 kdasvlaiiG 136
                                       +  ++l i+G
  gi|242400002|ref|YP_002995427.1| 230 HKTRTLNIVG 239
                                       3333333333 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.4   4.3e-05     0.071       1      93 [.       6      94 ..       6      97 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.3e-05
                                      EEEEETTTSHHHHHHHHHHHC...TSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEEGGGGGCTT-SEEEE-SCH CS
                    Semialdhyde_dh  1 kvaivGatGyvGqellrlLee...hpevelvvllsssrsaGkklaeavkaleegkdlkvedvdeeelkevdivflalpa 76
                                      +v++vG  G++G   +r+ +e   + +velv ++  + +  k++a+        k+  + d++e   +++d v  a+p 
  gi|242400002|ref|YP_002995427.1|  6 RVGVVG-VGNMGYHHARIYSEmarEGKVELVGVADANLERAKEVASQ------FKTKAFGDYKELVKEGLDAVSIAVPT 77
                                      699999.7888877777766642266666666555555555555555......668888888888889*********** PP

                                      HHHHHHHHHHHHTTSEE CS
                    Semialdhyde_dh 77 gvskelapklaeagvkv 93
                                      + +k++a +++e+gv v
  gi|242400002|ref|YP_002995427.1| 78 SLHKQVALEFIENGVNV 94
                                      **************987 PP

>> DrsE  DsrE/DsrF-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   9.7e-05      0.16      18      76 ..      65     123 ..      52     125 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9.7e-05
                                       HHHHHHHHHH..HTTT-EEEEEE-GGGGGGGBS---TGGGTS---GGGGGGCGGGT-EEEE CS
                              DrsE  18 realelalaa..aalghevsvffygdGvllllkgqtanpadeknlaellkalkeygvklyv 76 
                                       +e+l++  +a   +l+ +v++ f+ +Gv++l++  ++ +++ +n +e ++a+k+++v+l+v
  gi|242400002|ref|YP_002995427.1|  65 KEGLDAVSIAvpTSLHKQVALEFIENGVNVLVE--KPIAESIENAQEIMRAAKKNNVTLMV 123
                                       66777777775566779999*************..99999*******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       840  (0.0468515); expected 358.6 (0.02)
Passed bias filter:                      577  (0.0321825); 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: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2099.03
//
Query:       gi|242400003|ref|YP_002995428.1|  [L=449]
Description: NDP-sugar dehydrogenase [Thermococcus sibiricus MM 739]
Scores for complete 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-41  139.8   0.3    1.3e-40  138.9   0.3    1.4  1  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
    2.4e-25   89.0   0.1    1.2e-24   86.7   0.0    2.1  2  UDPG_MGDP_dh_C   UDP-glucose/GDP-mannose dehydrogenase family
    1.5e-21   76.4   0.0    3.4e-21   75.3   0.0    1.6  1  UDPG_MGDP_dh     UDP-glucose/GDP-mannose dehydrogenase family
    3.7e-10   40.2   0.7    4.8e-09   36.6   0.3    2.8  2  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
    3.8e-08   33.5   0.2    6.1e-06   26.3   0.1    2.5  2  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
    5.1e-06   26.5   0.5    1.5e-05   25.0   0.2    1.9  2  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
    1.2e-05   24.8   0.0      0.029   13.7   0.0    2.7  3  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
    0.00019   21.7   0.3     0.0076   16.5   0.1    3.0  2  TrkA_N           TrkA-N domain
     0.0015   18.5   0.0     0.0042   17.1   0.0    1.7  1  SRR1             SRR1
     0.0032   17.1   0.2     0.0081   15.8   0.1    1.7  2  ApbA             Ketopantoate reductase PanE/ApbA
     0.0057   16.0   0.2      0.014   14.7   0.2    1.6  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
  ------ inclusion threshold ------
      0.019   15.1   0.1        6.5    6.9   0.0    3.5  2  DpaA_N           Dipicolinate synthase subunit A N-terminal d
      0.043   14.4   2.1       0.14   12.8   0.8    2.6  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
      0.068   12.8   0.0       0.12   12.1   0.0    1.3  1  TPMT             Thiopurine S-methyltransferase (TPMT)
      0.093   12.3   0.2       0.34   10.4   0.0    1.9  2  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
       0.13   12.1   0.1       0.31   10.9   0.1    1.6  1  DFP              DNA / pantothenate metabolism flavoprotein
       0.17   12.6   0.0       0.41   11.4   0.0    1.7  1  Methyltransf_25  Methyltransferase domain


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 !  138.9   0.3   1.3e-43   1.3e-40       2     182 ..      21     199 ..      20     204 .. 0.91

  Alignments for each domain:
  == domain 1  score: 138.9 bits;  conditional E-value: 1.3e-43
                                       EEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS-.-TTHHHHHHHHCHTTTEEEES-HHHHHHC- CS
                    UDPG_MGDP_dh_N   2 kisviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipiy.epgLeelvkkavesgrlsfttdvekaveea 77 
                                       +++v GlG +Gl+ aa++ae+g +vigvDi+e+ v+++nsg  +i  epgL+elv+++v++g+l++ttd   a+++a
  gi|242400003|ref|YP_002995428.1|  21 TVAVYGLGKMGLPLAAAFAEHGANVIGVDINEKVVESINSGTNHINeEPGLSELVERNVKAGKLKATTDGVWAAKQA 97 
                                       699******************************************6279**************************** PP

                                       SEEEE-----B-TTTTCB-THHHHHHHHHHHHHHHCEEEEEE-S---TTHHHHCHHHHHHHHCSS-TTCEEEEE--- CS
                    UDPG_MGDP_dh_N  78 dvifiaVgTPskkkgkaaDlkyvesaarsiaealkkgkvvvvkSTvpvgtaeelvkkileeaskkkgvdfdvvsnPE 154
                                       dv++i V+T ++++g+   l+ v ++a++ia+ l+kg++v+++ T+p+gt+e ++ +ilee   k   +f++++ PE
  gi|242400003|ref|YP_002995428.1|  98 DVMIIIVPTLTDDRGNL-KLDPVYDVAHKIAKGLEKGDIVITEATMPPGTTE-SLIPILEESGLKL-GEFGLAHAPE 171
                                       *************5555.*********************************9.7779999999875.89******** PP

                                       ---TTSHHHHHHS-S-EEEEESSCHHHH CS
                    UDPG_MGDP_dh_N 155 flregsavkdllnpdrvviGveekkaea 182
                                       +   g+a++d+  +   ++G++++k+ +
  gi|242400003|ref|YP_002995428.1| 172 RTMSGTAIRDITGQYPKIVGASDEKTLE 199
                                       **********997766666666666543 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 ?   -0.7   0.0       1.8   1.9e+03      27      74 ..      39     104 ..      32     113 .. 0.60
   2 !   86.7   0.0   1.2e-27   1.2e-24       1     104 [.     335     430 ..     335     431 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.8
                                       HHCTSEEEEE-SSTHHCCCCHHGG..................BTCCEEES-CHHHHTT-SEEEE-S CS
                    UDPG_MGDP_dh_C  27 leegaevkiyDPkvkeeaveaele..................ekgvevvdsleealkgadaivilt 74 
                                       +e+ga+v  +D + k  ++ ++++                  + +++ +++   a+k+ad+++i++
  gi|242400003|ref|YP_002995428.1|  39 AEHGANVIGVDINEKVVESINSGTnhineepglselvernvkAGKLKATTDGVWAAKQADVMIIIV 104
                                       555555555555444444444443445555555555555555556666677777888888888876 PP

  == domain 2  score: 86.7 bits;  conditional E-value: 1.2e-27
                                       EEE-SSSSTT-S--TT-HHHHHHHHHHHCTSEEEEE-SSTHHCCCCHHGGBTCCEEES-CHHHHTT-SEEEE-S--G CS
                    UDPG_MGDP_dh_C   1 ailGlafKkdtdDlReSpaldiieeLleegaevkiyDPkvkeeaveaeleekgvevvdsleealkgadaiviltehd 77 
                                       ++lGl+f+ ++ ++ +Spa+ ii+eL+e ga+v +yDP++++e++e+           +++e +k++dai+i+t+h+
  gi|242400003|ref|YP_002995428.1| 335 LVLGLTFRGGVREFTKSPAILIIKELKEWGAKVYAYDPVCTPEDAERF--------GVEWKEDFKDIDAIIIVTDHK 403
                                       69******************************************9983........34679**************** PP

                                       GGGGS-HHHHHHCCSS-EEEESSS-CC CS
                    UDPG_MGDP_dh_C  78 efkeldlaklkelmkpavvfDgrnvld 104
                                       ef++ldl+ ++++++++v++Dgrnvld
  gi|242400003|ref|YP_002995428.1| 404 EFRDLDLEGIAKQVRNKVIIDGRNVLD 430
                                       *************************98 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 !   75.3   0.0   3.2e-24   3.4e-21       2      93 ..     221     308 ..     220     309 .. 0.97

  Alignments for each domain:
  == domain 1  score: 75.3 bits;  conditional E-value: 3.2e-24
                      UDPG_MGDP_dh   2 tAEliKlaaNaflatkIsfiNelanlcealgidveeVieavgldprigpkflkpglGvGGsclpkDvkaLvalaeel 78 
                                       +AE++K+++ ++++++I+++Nela  ce++g+d+ e+++a++++p    +++ pg+GvGG+c+p  +++ ++l+++ 
  gi|242400003|ref|YP_002995428.1| 221 AAEAVKVFEGVYRDVNIALANELALWCEEHGLDALEIFKAANTQPY--CHLHMPGAGVGGHCIPIYPWFVINLVKK- 294
                                       7*********************************************..6*************************88. PP

                      UDPG_MGDP_dh  79 gleaelleavrevNe 93 
                                        ++++l++++re+N+
  gi|242400003|ref|YP_002995428.1| 295 -TNPRLIKTAREIND 308
                                       .59***********7 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.3   4.6e-12   4.8e-09       2     114 ..      22     164 ..      21     199 .. 0.82
   2 ?    0.3   0.0      0.68   7.1e+02      17      92 ..     359     428 ..     355     435 .. 0.55

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 4.6e-12
                                       EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT.....................EEE-SSHHHHHHHCS CS
                     NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg.....................akaaesieelvasld 57 
                                       +++ GlG+MG ++a  ++++g +v++++ +++ ve++ +                       +ka+++   +++++d
  gi|242400003|ref|YP_002995428.1|  22 VAVYGLGKMGLPLAAAFAEHGANVIGVDINEKVVESINSGTnhineepglselvernvkagkLKATTDGVWAAKQAD 98 
                                       899***************************88888877765899999********999987777777777788888* PP

                                       EEEE-SSSHHHHHHHHHS.........HCCC--TT-EEEE-S---HHHHHHHHHHHHHTT-EEEEE CS
                     NAD_binding_2  58 vvitmvkagkavdevieg.........llealkkgdilidgstsspedtrelakelkekglkflda 114
                                       v+i++v+  ++ +  ++          +++ l+kgdi+i  +t+ p +t+ l   l+e+glk+ + 
  gi|242400003|ref|YP_002995428.1|  99 VMIIIVPTLTDDRGNLKLdpvydvahkIAKGLEKGDIVITEATMPPGTTESLIPILEESGLKLGEF 164
                                       ******976543333332333333444******************************999987555 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.68
                                       HHHHTT-EEEEE-..SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHS.HCCC--TT-EEEE-S CS
                     NAD_binding_2  17 nllkagykvavyn..rtkekveelvaegakaaesieelvasldvvitmvkagkavdevieg.llealkkgdilidgs 90 
                                       +l++ g kv++y+   t+e +e++   g+++     e ++++d++i+ v++ k+ +++  + +++++ +++++idg 
  gi|242400003|ref|YP_002995428.1| 359 ELKEWGAKVYAYDpvCTPEDAERF---GVEWK----EDFKDIDAIII-VTDHKEFRDLDLEgIAKQV-RNKVIIDGR 426
                                       566667777777732333333333...33333....33445666654.5555666555444266666.677888876 PP

                                       -- CS
                     NAD_binding_2  91 ts 92 
                                       ++
  gi|242400003|ref|YP_002995428.1| 427 NV 428
                                       65 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 !   26.3   0.1   5.8e-09   6.1e-06       2     108 ..      22     132 ..      21     148 .. 0.76
   2 ?    4.4   0.0     0.031        33      37      78 ..     299     340 ..     287     358 .. 0.88

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 5.8e-09
                                       EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHH..HHSSBTT.....TBTT----TTEEEES-HHHHHTT-- CS
                    NAD_Gly3P_dh_N   2 iavlGaGswGtalAkvlaenghevrlwvreeelieein..eehenvk.....yLpgiklpenlvattdlaealkgad 71 
                                       +av G G+ G  lA+++ae+g +v     +e+++e+in  ++h n++      ++      +l+attd   a+k+ad
  gi|242400003|ref|YP_002995428.1|  22 VAVYGLGKMGLPLAAAFAEHGANVIGVDINEKVVESINsgTNHINEEpglseLVERNVKAGKLKATTDGVWAAKQAD 98 
                                       9*********************************9999444666654211113333444557899************ PP

                                       EEEE---HHHHHHHHHHHCCC--TT-EEEE---SEET CS
                    NAD_Gly3P_dh_N  72 iivlvvPsqalrevlkklkgllkkkailvsliKGiee 108
                                       ++++ vP+ +  +   kl+++ +   ++  ++KG+e+
  gi|242400003|ref|YP_002995428.1|  99 VMIIIVPTLTDDRGNLKLDPVYD---VAHKIAKGLEK 132
                                       *******9877766666666553...33345566665 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.031
                                       HHHHHSSBTTTBTT----TTEEEES-HHHHHTT--EEEE--- CS
                    NAD_Gly3P_dh_N  37 eineehenvkyLpgiklpenlvattdlaealkgadiivlvvP 78 
                                        i++++e ++++p++ ++ +++  +++ ++lkg++++vl ++
  gi|242400003|ref|YP_002995428.1| 299 LIKTAREINDFMPHHVVELSIKGLNEVGKSLKGSNVLVLGLT 340
                                       68999*********************************9875 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 !   25.0   0.2   1.4e-08   1.5e-05       1      81 [.      21      99 ..      21     109 .. 0.67
   2 ?   -2.2   0.0         3   3.2e+03     155     175 ..     193     213 ..     191     216 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1.4e-08
                                      EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEEES-HHHHH.C CS
                           3HCDH_N  1 kvaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklkeeeveaalarisfttdleeav.d 78
                                      +vav G G mG  +aa+fa++g +V  vdi+e+ +e+ ++  ++ +++    g  +  e++  + ++++ttd   a+ +
  gi|242400003|ref|YP_002995428.1| 21 TVAVYGLGKMGLPLAAAFAEHGANVIGVDINEKVVESINSGTNH-INEE--PGLSELVERNVKAGKLKATTDGVWAAkQ 96
                                      69******************************999877766665.2222..2222222333344455555444444445 PP

                                      -SE CS
                           3HCDH_N 79 adl 81
                                      ad+
  gi|242400003|ref|YP_002995428.1| 97 ADV 99
                                      555 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3
                                       --HHHHHHHHHHHHHTT-EEE CS
                           3HCDH_N 155 Tseetvatvvelakkigktpv 175
                                       ++e+t+++v  +++ i+k+ v
  gi|242400003|ref|YP_002995428.1| 193 SDEKTLEAVIGIYETINKKGV 213
                                       7899************99877 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   2.7e-05     0.029      37      73 ..      20      56 ..       7      78 .. 0.83
   2 ?   -3.7   0.0       6.2   6.6e+03      89     104 ..      94     109 ..      88     114 .. 0.76
   3 !    8.1   0.0    0.0015       1.5      51      99 ..     356     400 ..     299     405 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.7e-05
                                      SEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH CS
                      2-Hacid_dh_C 37 ktvGiiGlGrIGqavakrlkafgmkviaydrskkkee 73
                                       tv++ GlG++G  +a  +++ g++vi++d ++k  e
  gi|242400003|ref|YP_002995428.1| 20 FTVAVYGLGKMGLPLAAAFAEHGANVIGVDINEKVVE 56
                                      69*****************************998666 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 6.2
                                       HHH-SEEEE-S--STT CS
                      2-Hacid_dh_C  89 laesDivslhlpltpe 104
                                        +++D+ ++ +p   +
  gi|242400003|ref|YP_002995428.1|  94 AKQADVMIIIVPTLTD 109
                                       5899999999995444 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0015
                                       HHHHHHHTT-EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-SEEEE-S CS
                      2-Hacid_dh_C  51 vakrlkafgmkviaydrskkkeeeeeelgvelvsleellaesDivslhl 99 
                                       ++k lk++g+kv+ayd+  ++e+ +e+ gv   + +e +++ D +++++
  gi|242400003|ref|YP_002995428.1| 356 IIKELKEWGAKVYAYDPVCTPED-AERFGV---EWKEDFKDIDAIIIVT 400
                                       67899*************99988.777776...7777778778777765 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   7.2e-06    0.0076       1      43 [.      22      63 ..      22     116 .. 0.89
   2 ?    1.8   0.0      0.26   2.7e+02      58      76 ..     388     406 ..     357     441 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 7.2e-06
                                      EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSE CS
                            TrkA_N  1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreegle 43
                                      +++ GlG++G  la  + e+g +v+++d +e++ve++   g++
  gi|242400003|ref|YP_002995428.1| 22 VAVYGLGKMGLPLAAAFAEHGANVIGVDINEKVVESIN-SGTN 63
                                      6899***************6657***********9975.5555 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.26
                                       TTGGGESEEEE-SSSHHHH CS
                            TrkA_N  58 agiekadaviaatgddean 76 
                                        + +++da+i++t+++e+ 
  gi|242400003|ref|YP_002995428.1| 388 EDFKDIDAIIIVTDHKEFR 406
                                       5678999******999764 PP

>> SRR1  SRR1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0     4e-06    0.0042      23      50 ..     354     380 ..     352     382 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4e-06
                              SRR1  23 lelveelkiessrsvyaqDPvftevDka 50 
                                       +++++elk++ ++ vya+DPv+t++D++
  gi|242400003|ref|YP_002995428.1| 354 ILIIKELKEWGAK-VYAYDPVCTPEDAE 380
                                       6899999999998.************86 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   7.6e-06    0.0081       1      82 [.      22     110 ..      22     126 .. 0.82
   2 ?   -2.2   0.0       2.6   2.8e+03      61      77 ..     383     401 ..     357     436 .. 0.56

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 7.6e-06
                                       EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHCEEEEETTCEEEEEECEEECCH......SCCCCS-ES CS
                              ApbA   1 iailGaGaiGsllaakLakagadvtlilrsr.rlealkknGlrltseggeeilrppealsae......ekselepid 70 
                                       +a+ G+G +G  laa  a++ga+v+ ++ ++  +e++++   ++++e g   l ++++ + +          ++++d
  gi|242400003|ref|YP_002995428.1|  22 VAVYGLGKMGLPLAAAFAEHGANVIGVDINEkVVESINSGTNHINEEPGLSELVERNVKAGKlkattdGVWAAKQAD 98 
                                       689****************************99999************55555555555444466677566778999 PP

                                       EEEE-SSGGGHH CS
                              ApbA  71 lvivtvKayqte 82 
                                       ++i+ v+++ ++
  gi|242400003|ref|YP_002995428.1|  99 VMIIIVPTLTDD 110
                                       999999998766 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.6
                                       H..SCCCCS-ESEEEE-SS CS
                              ApbA  61 e..ekselepidlvivtvK 77 
                                           k++ ++id +i+ + 
  gi|242400003|ref|YP_002995428.1| 383 GveWKEDFKDIDAIIIVTD 401
                                       2655667889999988873 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.2   1.3e-05     0.014      30     110 ..      21     151 ..      16     154 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.3e-05
                                       EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEE............................. CS
                       AlaDh_PNT_C  30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvev............................. 77 
                                       +v v G G  Gl  +a+ ++ ga+V  +D+++++ e ++s  ++ ++                              
  gi|242400003|ref|YP_002995428.1|  21 TVAVYGLGKMGLPLAAAFAEHGANVIGVDINEKVVESINSGTNH-INEepglselvernvkagklkattdgvwaakq 96 
                                       5899********999999999*******************7777.66668999************************ PP

                                       ......................HCHHHHHHHHHHHH-SEEEE---BTTSS---SC CS
                       AlaDh_PNT_C  78 ......................lksqeellaeavkeadvvigtvlipGkkaPkLv 110
                                                             ++  ++++a+ +++ d+vi+ + +p  ++  L+
  gi|242400003|ref|YP_002995428.1|  97 advmiiivptltddrgnlkldpVYDVAHKIAKGLEKGDIVITEATMPPGTTESLI 151
                                       **********************9********************999987777766 PP

>> DpaA_N  Dipicolinate synthase subunit A N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.059        62      36      92 ..      81     136 ..       9     147 .. 0.68
   2 ?    6.9   0.0    0.0062       6.5      13      56 ..     355     397 ..     353     404 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.059
                                       BTTEEEE-GGGS-GGG-SEEE--TT.-BETTTEE-BSS-SS-EE-.HHHHHTS-TT-EE CS
                            DpaA_N  36 iegvekaesleealedadviilPvp.gtkdggeintpfseeklsl.eelleklkkgqll 92 
                                         +++ +++   a ++adv+i  vp +t+d+g+++    +    +  ++++ l+kg ++
  gi|242400003|ref|YP_002995428.1|  81 AGKLKATTDGVWAAKQADVMIIIVPtLTDDRGNLKL---DPVYDVaHKIAKGLEKGDIV 136
                                       444455555555567777776666657899999887...44444555666666666655 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0062
                                       HHHHHHHHTT-EEEEES-TSSS-BTTEEEE-GGGS-GGG-SEEE CS
                            DpaA_N  13 ylarkLaekgakvslygleleekiegvekaesleealedadvii 56 
                                        ++++L+e gakv++y     +  +  +   + +e+++d d+ii
  gi|242400003|ref|YP_002995428.1| 355 LIIKELKEWGAKVYAYDP-VCTPEDAERFGVEWKEDFKDIDAII 397
                                       689*************87.4444444455556777888888888 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 ?   12.8   0.8   0.00013      0.14       2      71 ..      22     106 ..      21     141 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00013
                                       EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC....................-EEECECHHHH CS
                     F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg....................vkvtavdneea 58 
                                       +++ G G+mg  la  ++++g    +++ + + n++ +e++ +  +                     k+t+ d   a
  gi|242400003|ref|YP_002995428.1|  22 VAVYGLGKMGLPLAAAFAEHG---ANVI-GVDINEKVVESINSGTNhineepglselvernvkagkLKATT-DGVWA 93 
                                       7899*****************...8988.778888888888777778889999********9999989999.9999* PP

                                       HHH-SEEEE-S-H CS
                     F420_oxidored  59 aeeadvvvlavkp 71 
                                       a++adv ++ v++
  gi|242400003|ref|YP_002995428.1|  94 AKQADVMIIIVPT 106
                                       ********99985 PP

>> TPMT  Thiopurine S-methyltransferase (TPMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00011      0.12      53     114 ..      36      99 ..      32     104 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00011
                                       HHH-BTTEEEEEE-S-HHHHHHHHHHHTT...SGGGGGEEEE--...........-TTT---SS- CS
                              TPMT  53 vwlAeqgrevvGvelselAvekffeeanl...epkvkelsgvkeysageiellcgdvFtlraeel 114
                                       +++Ae+g +v+Gv++ e+ ve+ ++ +n    ep ++el ++++ +ag+++  +  v++++++++
  gi|242400003|ref|YP_002995428.1|  36 AAFAEHGANVIGVDINEKVVESINSGTNHineEPGLSELVERNV-KAGKLKATTDGVWAAKQADV 99 
                                       689*******************9987776555666777766666.88888877777777766665 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 ?   10.4   0.0   0.00032      0.34       6      36 ..      30      60 ..      27      90 .. 0.82
   2 ?   -1.5   0.0       1.4   1.5e+03      39      74 ..     361     397 ..     356     422 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00032
                                      HHHHHHHHHHHTT-EEEEEESSGGHHHHHHH CS
                      adh_short_C2  6 IGraiAkalaeeGaevvltdlneeakkrvee 36
                                      +G  +A a+ae+Ga+v+ +d+ne+  +++++
  gi|242400003|ref|YP_002995428.1| 30 MGLPLAAAFAEHGANVIGVDINEKVVESINS 60
                                      57789******************99555544 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.4
                                       HHTTSEEEE--.TTSHHHHHHHHHHHHHHHSSEEEEE CS
                      adh_short_C2  39 eelgaevlecD.VtdeeqvealveevvekfgklDilv 74 
                                       +e ga+v++ D V  +e+ e++  e +e+f+ +D ++
  gi|242400003|ref|YP_002995428.1| 361 KEWGAKVYAYDpVCTPEDAERFGVEWKEDFKDIDAII 397
                                       4567777777778888888888888899999988776 PP

>> DFP  DNA / pantothenate metabolism flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00029      0.31      29      68 ..      28      67 ..      25     138 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00029
                                      -HHHHHHHHHHHHTT-EEEEEE-S-SS---TT-EEEE--S CS
                               DFP 29 GkmGyalAeaaaarGaeVtlvsgpvsletpegvevvkves 68
                                      GkmG+ lA+a+a+ Ga+V  v  + ++ +  +  + ++++
  gi|242400003|ref|YP_002995428.1| 28 GKMGLPLAAAFAEHGANVIGVDINEKVVESINSGTNHINE 67
                                      9******************998886544433333444444 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00039      0.41       7      54 ..      26      78 ..      23     105 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00039
                                      TTSHHHHHHHCTS..TSSEEEEEESSHHHHHHHHHHHHH..TTT.TEEEEESB CS
                   Methyltransf_25  7 GtGrltlalakrl..gkakvtgvDiseemleaareraee..egl.nvefvqgd 54
                                      G G++ l la+++  + a+v+gvDi+e+ +e +++  ++  e++   e+v+ +
  gi|242400003|ref|YP_002995428.1| 26 GLGKMGLPLAAAFaeHGANVIGVDINEKVVESINSGTNHinEEPgLSELVERN 78
                                      56777777777776525*************99885544332333344455554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (449 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2835.46
//
Query:       gi|242400004|ref|YP_002995429.1|  [L=72]
Description: hypothetical protein TSIB_2033 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       232  (0.0129399); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 482.27
//
Query:       gi|242400005|ref|YP_002995430.1|  [L=421]
Description: Archaeal ATPase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-06   27.5   0.1    5.5e-06   26.4   0.1    1.6  1  AAA_14           AAA domain
  ------ inclusion threshold ------
      0.021   15.1   0.2        1.5    9.1   0.1    2.5  2  AAA_22           AAA domain
      0.025   14.7   0.1      0.055   13.6   0.1    1.5  1  AsiA             Anti-Sigma Factor A
       0.04   13.9   0.1      0.098   12.7   0.0    1.6  2  ResIII           Type III restriction enzyme, res subunit
      0.079   13.4   5.0        1.2    9.6   5.0    2.6  1  DUF234           Archaea bacterial proteins of unknown functi
       0.13   12.7   0.6       0.32   11.4   0.0    2.0  3  AAA              ATPase family associated with various cellul
       0.16   11.7   0.1       0.38   10.4   0.0    1.7  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase


Domain annotation for each model (and alignments):
>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.1   2.1e-09   5.5e-06       2      90 ..      25     111 ..      24     125 .. 0.78

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 2.1e-09
                            AAA_14   2 rkilvitGaRrvGKTtllkqlikell..vkkesilyinldderdkkladpekllelileklkeekktylflDEiqev 76 
                                       +k l+i G R++GKT+++++ ++ +   +  +s   i+l++ ++ +++++++ll l+le       + +++DE +++
  gi|242400005|ref|YP_002995430.1|  25 SKWLLIYGRRKTGKTFYIREKARYNKyfIVTKSKTVIELQSGEELNQEEFRRLLPLLLETE-----ERIIIDEFHRL 96 
                                       6889***************999888889667777778888888877788877888888852.....45********9 PP

                            AAA_14  77 pe.wekalkslvdeg 90 
                                       +e ++++l+++  +g
  gi|242400005|ref|YP_002995430.1|  97 NEpFFSMLQGMSGRG 111
                                       875777777666655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1     0.022        57       7      29 ..      27      49 ..      23      83 .. 0.74
   2 ?    9.1   0.1   0.00057       1.5      72     135 ..      68     125 ..      53     127 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.022
                            AAA_22  7 ilvvtGesGtGKTtllrrlleql 29
                                       l+++G   tGKT+ +r+ ++ +
  gi|242400005|ref|YP_002995430.1| 27 WLLIYGRRKTGKTFYIREKARYN 49
                                      589************99977654 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00057
                            AAA_22  72 rlsseellealeqalraravielliiDEaqhlrseealeeLrsllnlsrkgvqliLvGtpelrk 135
                                       +l++ee++++l   l++  +   +iiDE+++l +e  ++ L  ++   r +++li   ++ +r+
  gi|242400005|ref|YP_002995430.1|  68 ELNQEEFRRLLPLLLETEER---IIIDEFHRL-NEPFFSMLQGMSG--RGKMTLITSTMHYFRR 125
                                       45555555555555555555...*********.8999988888887..8888887777777766 PP

>> AsiA  Anti-Sigma Factor A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   2.1e-05     0.055      30      77 ..      50      97 ..      42     102 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.1e-05
                                      HHHHHHHHHHT-.ESSSSE--HHHHHHHHHTS-HHHHHHHHHHSHHHH CS
                              AsiA 30 klfvellneiGvrtteGkkltqnsfrkivarLtqedkkelreefseGf 77
                                      k f+       +  + G +l+q  fr+++  L   + + +++ef   +
  gi|242400005|ref|YP_002995430.1| 50 KYFIVTKSKTVIELQSGEELNQEEFRRLLPLLLETEERIIIDEFHRLN 97
                                      5666666667777899****************************8755 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.8e-05     0.098      94     147 ..      45      99 ..       9     135 .. 0.56
   2 ?   -2.9   0.0       2.3     6e+03      14      60 ..     377     394 ..     363     401 .. 0.53

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.8e-05
                                       B--........-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS. CS
                            ResIII  94 kka.kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgak 147
                                       k + +++++ +k+ +v++ qs  + ++ee +    ll ++++ iiiDE Hrl++ 
  gi|242400005|ref|YP_002995430.1|  45 KARyNKYFIVTKSKTVIELQSGEELNQEEFRRLLPLLLETEERIIIDEFHRLNEP 99 
                                       222123333334444444444444443335555566666777**********994 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.3
                                       HHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEE CS
                            ResIII  14 nlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflfl 60 
                                       +++ek                             l++ ++ ek+l++
  gi|242400005|ref|YP_002995430.1| 377 KIEEK-----------------------------LHEFENAEKILIV 394
                                       33333.............................3333333344433 PP

>> DUF234  Archaea bacterial proteins of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   5.0   0.00049       1.2      65      98 ..     343     377 ..     290     378 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00049
                            DUF234  65 kkeeeiDivaldeeekkalfgEvKwkn..sekeakk 98 
                                       k + e+D+  +d+++   +++EvKwk+  +++e++k
  gi|242400005|ref|YP_002995430.1| 343 KPQLEVDVALVDHKKV-KVVAEVKWKDsvKKEEIRK 377
                                       4678***999988886.889*******766666666 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 ?   11.4   0.0   0.00013      0.32       1      71 [.      28      97 ..      28     124 .. 0.67
   2 ?   -2.3   0.0       2.2   5.8e+03       2      21 ..     103     122 ..     102     145 .. 0.77
   3 ?   -3.2   0.1       4.2   1.1e+04      41      68 ..     373     398 ..     355     401 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00013
                                      EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS..TSEEEEEETGGGHH CS
                               AAA  1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakeka..kpsilfiDEidala 71
                                      +l+yG   tGKT  ++  a+    +f+ ++ ++++   ++ +e+  +e f+++      +   ++iDE+++l+
  gi|242400005|ref|YP_002995430.1| 28 LLIYGRRKTGKTFYIREKARYN-KYFIVTKSKTVI--ELQSGEELNQEEFRRLLPLLleTEERIIIDEFHRLN 97
                                      699*****************94.445555555555..2333333333333333222232236699*****996 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.2
                                       EEESSTTSSHHHHHHHHHHH CS
                               AAA   2 llyGppGtGKTllakavake 21 
                                       +l G  G GK +l+ + ++ 
  gi|242400005|ref|YP_002995430.1| 103 MLQGMSGRGKMTLITSTMHY 122
                                       57899999999998877765 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 4.2
                                       HHHHHHHHHHHHHHHTSTSEEEEEETGG CS
                               AAA  41 esekkirelfkeakekakpsilfiDEid 68 
                                       e  +ki+e + e ++ a  +il++ E +
  gi|242400005|ref|YP_002995430.1| 373 EEIRKIEEKLHEFEN-A-EKILIVPERE 398
                                       333444444444332.2.4777777755 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   0.00015      0.38      10      77 ..      37      99 ..      36     119 .. 0.75
   2 ?   -2.4   0.1       1.2   3.2e+03      31      68 ..     359     394 ..     339     401 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00015
                   Viral_helicase1 10 GKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEylllhaG 77
                                      GK+  ir+ +r + + +++ ++t++ l  g      l+ + ++ +l+ l+++   +++i+DE+ +l+  
  gi|242400005|ref|YP_002995430.1| 37 GKTFYIREKARYNkYFIVTKSKTVIELQSGE----ELNQEEFRRLLPLLLET--EERIIIDEFHRLNEP 99
                                      ************9866666666566666664....55566677788888876..99*******998755 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.2
                   Viral_helicase1  31 taelltegkpklpnlsvrtvdsflmalvkstkgkilil 68 
                                        +++  ++k+ ++++++r +++ l+ + +    kili+
  gi|242400005|ref|YP_002995430.1| 359 KVVAEVKWKDSVKKEEIRKIEEKLHEFENA--EKILIV 394
                                       355666777888888888888777766654..677766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1156  (0.0644765); expected 358.6 (0.02)
Passed bias filter:                      800  (0.0446204); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.64u 0.34s 00:00:00.98 Elapsed: 00:00:00.48
# Mc/sec: 2628.84
//
Query:       gi|242400006|ref|YP_002995431.1|  [L=431]
Description: ATPase, AAA superfamily [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.6e-38  131.0   0.2    4.9e-38  130.1   0.2    1.5  1  AAA_14        AAA domain
    2.8e-08   34.0   0.1    5.6e-08   33.0   0.1    1.5  1  DUF4143       Domain of unknown function (DUF4143)
    0.00016   22.0   0.0      0.024   14.9   0.0    2.4  1  AAA_22        AAA domain
    0.00018   21.5   0.5     0.0014   18.6   0.2    2.2  2  ATPase_2      ATPase domain predominantly from Archaea
     0.0086   16.5   0.0      0.015   15.8   0.0    1.4  1  AAA           ATPase family associated with various cellular 
     0.0087   16.1   0.1        0.1   12.6   0.1    2.5  1  DUF2487       Protein of unknown function (DUF2487)
  ------ inclusion threshold ------
      0.033   14.2   0.1      0.087   12.8   0.1    1.7  1  ResIII        Type III restriction enzyme, res subunit
      0.039   14.2   0.3        1.4    9.1   0.1    2.7  2  Roc           Ras of Complex, Roc, domain of DAPkinase
        0.1   13.0   0.0       0.25   11.8   0.0    1.7  2  RNA_helicase  RNA helicase


Domain annotation for each model (and alignments):
>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.1   0.2   2.5e-41   4.9e-38       2     131 .]      35     167 ..      34     167 .. 0.94

  Alignments for each domain:
  == domain 1  score: 130.1 bits;  conditional E-value: 2.5e-41
                            AAA_14   2 rkilvitGaRrvGKTtllkqlikell..vkkesilyinldderdkkla.dpekllelileklkeekktylflDEiqe 75 
                                       +k+++  G+Rr+GKT+l++ql++el   ++kesi+yin++der++k+  + ++l+  i e++ ++k+ ylflDEiq+
  gi|242400006|ref|YP_002995431.1|  35 NKVVTFAGCRRTGKTYLMFQLMRELSkhADKESIFYINFEDERLEKSIkTLTELIPTIEELYGKKKMLYLFLDEIQN 111
                                       68999*******************99******************7754155688899999876689*********** PP

                            AAA_14  76 vpewekalkslvdegknldvivtGSnskllskeiatslagrvaeielyplsfaEfl 131
                                       + +w ++++++ d+++n++++++GS+skl s+ei tsl+gr+ ++e++plsf+Efl
  gi|242400006|ref|YP_002995431.1| 112 IANWDSWVRRVNDSRRNVKLFLSGSSSKLSSREIPTSLRGRAITFEVFPLSFHEFL 167
                                       *******************************************************7 PP

>> DUF4143  Domain of unknown function (DUF4143)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.1   2.8e-11   5.6e-08       3     109 ..     230     364 ..     182     372 .. 0.83

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 2.8e-11
                                       xxxxxxxxxxxxxxxx..........................................xxxxxxxxxxxxxxxxxxx RF
                           DUF4143   3 Dirklagvrdpeelrk..........................................glverlppwsespnskkrl 37 
                                       Di +  +vr+p elr+                                          + ++ ++ +  sp+ k r+
  gi|242400006|ref|YP_002995431.1| 230 DIVERYNVRNPGELRTfirlllnseyfslskmertiksmgysiskatlsnyldylrecYFMFPVEIY--SPKVKLRI 304
                                       5555566666666666777777777777777777888888888888899999988777777777777..******** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DUF4143  38 rkspKlyfvDtGLlvallgldkeelledsenkGallEnlVaqeLlkysekegaklyyyrdkngaEvDfviel 109
                                       +   K+yfvDt+ l+    l++++    +en G+l+En+V+ eLl+    +g+++ y    +g EvDfv+ +
  gi|242400006|ref|YP_002995431.1| 305 QYPKKIYFVDTAFLTF---LSTKF----DENIGKLMENAVFIELLR----RGKEINYALG-EGWEVDFVVPE 364
                                       ***********99776...45555....5689**************....7999998887.5*******953 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   1.2e-05     0.024      11     131 ..      41     137 ..      34     143 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.2e-05
                            AAA_22  11 tGesGtGKTtllrrlleqldeeakaeeerpevv.fvtlpsstsskdllrellralglelkaerlsseellealeqal 86 
                                        G+  tGKT+l+ +l+++l ++a     ++e + +++   +         l + +        +++ el+ ++e+  
  gi|242400006|ref|YP_002995431.1|  41 AGCRRTGKTYLMFQLMRELSKHA-----DKESIfYINFEDER--------LEKSI--------KTLTELIPTIEELY 96 
                                       56666666666666666664432.....33333133333333........22222........478899999***** PP

                            AAA_22  87 raravielliiDEaqhlrseealeeLrsllnlsrkgvqliLvGtp 131
                                        ++++   l +DE+q++   +++  +++++n+sr +v+l+L G  
  gi|242400006|ref|YP_002995431.1|  97 GKKKM-LYLFLDEIQNI---ANWDSWVRRVNDSRRNVKLFLSGSS 137
                                       *****.***********...666666678888*********9987 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 !   18.6   0.2   7.2e-07    0.0014      22      76 ..      37      99 ..      29     129 .. 0.75
   2 ?    1.0   0.1      0.16   3.3e+02     155     221 ..     126     192 ..      91     205 .. 0.62

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 7.2e-07
                          ATPase_2 22 iyfiYGpegsGKtaLlkeiienl.edkdkyviyyialreesiskldefie.......eeeekk 76
                                      ++   G ++ GKt L+ +++ +l ++ dk+ i+yi++++e+++k  +++        e + kk
  gi|242400006|ref|YP_002995431.1| 37 VVTFAGCRRTGKTYLMFQLMRELsKHADKESIFYINFEDERLEKSIKTLTeliptieELYGKK 99
                                      5555699*************999889999*********9999987777554555444334444 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.16
                          ATPase_2 155 ekhlcvviclsSeglfiervyneselegrhkyilvddldketalnflkegfkel.eel.skedfeeiyr 221
                                       ++++ + + +sS  l+ +  +    l+gr+ + +v +l +++ l f  +   ++ ++l  +e + ei r
  gi|242400006|ref|YP_002995431.1| 126 RRNVKLFLSGSSSKLSSR--EIPTSLRGRAITFEVFPLSFHEFLHFKGFSLPDNiKKLaFSEKKTEILR 192
                                       445555566777777777..4455688888888888888888888888777777444464455555555 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 !   15.8   0.0   7.3e-06     0.015       2      74 ..      39     116 ..      38     143 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 7.3e-06
                                       EEESSTTSSHHHHHHHHHHHH.....THEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS...TSEEEEEETGGGH CS
                               AAA   2 llyGppGtGKTllakavakel.....gvefleisgsellskyvgesekkirelfkeakeka...kpsilfiDEidal 70 
                                        + G   tGKT+l+ ++++el     + +++ i+  + +   +++s k + el+ +++e     k   lf+DEi ++
  gi|242400006|ref|YP_002995431.1|  39 TFAGCRRTGKTYLMFQLMRELskhadKESIFYINFEDER---LEKSIKTLTELIPTIEELYgkkKMLYLFLDEIQNI 112
                                       5778889*************9544444668888888888...66677777777777766666634599********* PP

                                       HHHH CS
                               AAA  71 aksr 74 
                                       a+ +
  gi|242400006|ref|YP_002995431.1| 113 ANWD 116
                                       9877 PP

>> DUF2487  Protein of unknown function (DUF2487)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.1   5.2e-05       0.1       2      95 ..     305     407 ..     304     425 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.2e-05
                           DUF2487   2 tylqekeyvDTaliPlipvdfaeemkkaasqaefiallaeelErqlk...GRv..lllPa.....ftYlkeeekeee 68 
                                       +y ++  +vDTa +  ++ +f+e++ k +++a fi+ll +  E ++    G    +++P+     ++Y  ++ ++ e
  gi|242400006|ref|YP_002995431.1| 305 QYPKKIYFVDTAFLTFLSTKFDENIGKLMENAVFIELLRRGKEINYAlgeGWEvdFVVPEeeliqVSYDVNDPETLE 381
                                       5778889*******************************998888884322532236777522222566666666554 PP

                           DUF2487  69 verlkeweeelkeegfkhvvfitsdee 95 
                                        ++lk +++++++ g ++v++it d e
  gi|242400006|ref|YP_002995431.1| 382 -RELKGLKKAANTFGYEKVTLITWDIE 407
                                       .59999999999999999999999975 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   4.4e-05     0.087      35      80 ..      46      91 ..      12     128 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.4e-05
                                      STHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG CS
                            ResIII 35 tGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflse 80
                                      tGKT+++++l+++l+k++++e ++ +  + + le+ ++++++++++
  gi|242400006|ref|YP_002995431.1| 46 TGKTYLMFQLMRELSKHADKESIFYINFEDERLEKSIKTLTELIPT 91
                                      8****************99999888888888888888777777765 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 ?    9.1   0.1   0.00073       1.4       4     113 ..      40     133 ..      36     139 .. 0.73
   2 ?   -2.0   0.0         2   3.9e+03      44      63 ..     387     406 ..     371     417 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00073
                                       EESSTTSSHHHHHHCHCT-CCC.-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SGGCTTTT-HHHHCT CS
                               Roc   4 lvGdsgvGKtsllkrfvedkfs.ekekstigvdfltkevtkikgvendkkvkkvklniWDtaGqerfrslhplylre 79 
                                       + G  ++GKt l+ +++++  +  +++s++ ++f +++++        k++k++          e + ++++ly ++
  gi|242400006|ref|YP_002995431.1|  40 FAGCRRTGKTYLMFQLMRELSKhADKESIFYINFEDERLE--------KSIKTL---------TELIPTIEELYGKK 99 
                                       5677888999999888887655144566677777766552........223322.........47888899999999 PP

                                       SCEEEEEEEGHHHHCHHHHHHHHHHHCSSS-EEE CS
                               Roc  80 aalailvydsrssenlkeWlkelkkvagkspvil 113
                                       + l++++ + ++ +n ++W++ +++ +++ +++l
  gi|242400006|ref|YP_002995431.1| 100 KMLYLFLDEIQNIANWDSWVRRVNDSRRNVKLFL 133
                                       9999988889999999999999999988887776 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2
                                       SGGCTTBTTTTCEEEEEEEE CS
                               Roc  44 ikgvendkkvkkvklniWDt 63 
                                       +k+  n+   +kv+l  WD+
  gi|242400006|ref|YP_002995431.1| 387 LKKAANTFGYEKVTLITWDI 406
                                       44445555567788888887 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00012      0.25       2      41 ..      39      75 ..      38     114 .. 0.84
   2 ?   -3.4   0.0       6.4   1.3e+04      58      82 ..     231     255 ..     225     262 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00012
                      RNA_helicase  2 wlyGpsgeGKStlakeLakallkklklkkkdsvysrnped 41
                                       + G +++GK++l+ +L+++l+k+     k+s+++ n ed
  gi|242400006|ref|YP_002995431.1| 39 TFAGCRRTGKTYLMFQLMRELSKHA---DKESIFYINFED 75
                                      5789999***************888...445666555555 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 6.4
                      RNA_helicase  58 fgqvkdeenpsdlaelirlvsstpy 82 
                                       + ++ +  np +l ++irl  + +y
  gi|242400006|ref|YP_002995431.1| 231 IVERYNVRNPGELRTFIRLLLNSEY 255
                                       5554444478899999999877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); 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: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.48
# Mc/sec: 2697.98
//
Query:       gi|242400007|ref|YP_002995432.1|  [L=413]
Description: hypothetical protein TSIB_2036 [Thermococcus sibiricus MM 739]
Scores for complete 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  105.3   0.0    4.8e-30  104.3   0.0    1.6  1  AAA_14    AAA domain
    1.6e-13   50.9   0.2    6.1e-13   49.0   0.2    1.8  1  DUF4143   Domain of unknown function (DUF4143)
  ------ inclusion threshold ------
       0.14   11.2   0.0       0.23   10.5   0.0    1.2  1  T2SSE     Type II/IV secretion system protein


Domain annotation for each model (and alignments):
>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.3   0.0   8.1e-34   4.8e-30       3     131 .]      40     158 ..      38     158 .. 0.93

  Alignments for each domain:
  == domain 1  score: 104.3 bits;  conditional E-value: 8.1e-34
                            AAA_14   3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqevpew 79 
                                        i+vi+G+Rr+GK++l+ + +k ++       y+n+dde ++k +d++++l+l  e  ++ + + lflDE+q+v++w
  gi|242400007|ref|YP_002995432.1|  40 LIKVISGPRRAGKSFLAARTLKGYF------GYVNFDDEVLAKTEDFNEILKLTHEV-YG-DFKTLFLDEVQNVEGW 108
                                       589**************99998777......**************998888888885.56.5677************ PP

                            AAA_14  80 ekalkslvdegknldvivtGSnskllskeiatslagrvaeielyplsfaEfl 131
                                       e ++ ++ + g  ++v++tGSnsklls+e+at+l+gr+ e+++ p+sf+Efl
  gi|242400007|ref|YP_002995432.1| 109 ELFVDRMRRLG--YNVVLTGSNSKLLSSELATHLTGRYWEVKVLPFSFREFL 158
                                       *********99..89************************************7 PP

>> DUF4143  Domain of unknown function (DUF4143)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.0   0.2     1e-16   6.1e-13      18     118 ..     251     354 ..     212     358 .. 0.79

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 1e-16
                                       x..................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DUF4143  18 k..................glverlppwsespnskkrlrkspKlyfvDtGLlvallgldkeelledsenkGallEnl 76 
                                                          +++ +++++  s ++++ l++  K+y+vD++Ll a  g+ +      s+n+G+ +En+
  gi|242400007|ref|YP_002995432.1| 251 LdigsvhtvknyvdyleesFIILKAERF--SYKLRESLKSPKKVYVVDPALLSA--GFIS------SPNLGRKMENA 317
                                       0444455556666677789*********..*********************999..4442......469******** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DUF4143  77 VaqeLlkysekegaklyyyrdkngaEvDfvielkggkivpiE 118
                                       Va eLl+    +g++l+y+rd  ++EvDfv++++ + + +i+
  gi|242400007|ref|YP_002995432.1| 318 VAVELLR----RGYELWYWRDV-RREVDFVLKKGLKIVELIQ 354
                                       *******....8********95.9*******96555555555 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   3.8e-05      0.23     100     169 ..      10      83 ..       2      93 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 3.8e-05
                             T2SSE 100 akeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallk....einksderivtvEDpvEi 169
                                       +++++l+ l +e+ +k + +e l++ +++  + ++sG+   GK+ l+   lk    ++n +de +   ED  Ei
  gi|242400007|ref|YP_002995432.1|  10 TQKYELERLKKEPYVKREAEEKLKQGLQTDLIKVISGPRRAGKSFLAARTLKgyfgYVNFDDEVLAKTEDFNEI 83 
                                       678899**************************************987555432222888889999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       690  (0.0384851); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); 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: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 2695.88
//
Query:       gi|242400008|ref|YP_002995433.1|  [L=51]
Description: adenylyl-sulfate kinase [Thermococcus sibiricus MM 739]
Scores for complete 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   27.9   0.1    2.5e-06   27.5   0.1    1.2  1  APS_kinase  Adenylylsulphate kinase


Domain annotation for each model (and alignments):
>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.1   1.4e-10   2.5e-06     128     155 ..       2      29 ..       1      32 [. 0.93

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 1.4e-10
                                       TTSSSSHTTTSS-----SS-SEEEETTT CS
                        APS_kinase 128 eGeikeftGidspYeaPenpelvvdtdk 155
                                       +Geik++tG d  Ye+Penpe++vd++k
  gi|242400008|ref|YP_002995433.1|   2 RGEIKGVTGYDGVYEEPENPEVKVDSSK 29 
                                       7************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 333.96
//
Query:       gi|242400009|ref|YP_002995434.1|  [L=46]
Description: hypothetical protein TSIB_2038 [Thermococcus sibiricus MM 739]
Scores for 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-06   26.7   0.6    4.2e-06   26.6   0.6    1.0  1  TauE      Sulfite exporter TauE/SafE
  ------ inclusion threshold ------
      0.044   14.0   0.5      0.056   13.7   0.2    1.4  1  DUF3784   Domain of unknown function (DUF3784)


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 !   26.6   0.6   4.7e-10   4.2e-06     196     236 .]       3      43 ..       1      45 [. 0.84

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 4.7e-10
                              TauE 196 llllpgallGallGarlarrlsertlrrlfallllvlgvkl 236
                                       l+l++ga+ G++lG++++++ ++++l++++ +++l++gv +
  gi|242400009|ref|YP_002995434.1|   3 LFLALGAVPGVYLGSHANTKADKERLKKIINVVILIIGVLM 43 
                                       56889999999999999999999999999999999999876 PP

>> DUF3784  Domain of unknown function (DUF3784)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2   6.2e-06     0.056      35      59 ..      21      45 ..      14      46 .] 0.92

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.2e-06
                           DUF3784 35 ekydekklsrfmgivllligilfll 59
                                      +k d+++l + + +v+l+ig+l+l+
  gi|242400009|ref|YP_002995434.1| 21 TKADKERLKKIINVVILIIGVLMLV 45
                                      799******************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       893  (0.0498076); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); 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: 0.36u 0.29s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 329.84
//
Query:       gi|242400010|ref|YP_002995435.1|  [L=262]
Description: hypothetical protein TSIB_2039 [Thermococcus sibiricus MM 739]
Scores for complete 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   30.7   0.0    2.7e-06   27.8   0.0    2.3  3  AbiEi_1          AbiEi antitoxin C-terminal domain
    0.00075   19.6   0.0     0.0019   18.3   0.0    1.8  1  AbiEi_4          Transcriptional regulator, AbiEi antitoxin
  ------ inclusion threshold ------
      0.027   13.9   0.0      0.041   13.3   0.0    1.2  1  DUF4348          Domain of unknown function (DUF4348)
      0.076   12.7   0.1       0.26   11.0   0.0    1.8  2  CUE              CUE domain
        0.1   13.0   0.0       0.21   12.0   0.0    1.5  1  Penicillinase_R  Penicillinase repressor


Domain annotation for each model (and alignments):
>> AbiEi_1  AbiEi antitoxin C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.58   2.1e+03     103     142 ..      26      65 ..      17      66 .. 0.69
   2 !   27.8   0.0   7.5e-10   2.7e-06      20     142 ..      87     204 ..      77     205 .. 0.83
   3 ?   -1.2   0.0      0.65   2.3e+03      99     126 ..     224     251 ..     217     259 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.58
                           AbiEi_1 103 ldnvlevLdelaeevkpeeLeellsgrpasvlqRlgyLLe 142
                                        +++    +el +++ ++ L +l++      l+R  yL++
  gi|242400010|ref|YP_002995435.1|  26 VQEIKGLFPELSDDMIKKVLSSLARKGYLYRLKRGIYLVN 65 
                                       5566666778888888888888887777777777777766 PP

  == domain 2  score: 27.8 bits;  conditional E-value: 7.5e-10
                           AbiEi_1  20 yagllsAawlhGaahrqpqriqvlvpkpakkipkglarvefvvrinvaalptkdvaaeaggvpvssPeatavdlatr 96 
                                       y+  +sA +l+G+ + +p +i v+ p    k++ g    + +   + +a+      a ++gv +s+ + t +d  ++
  gi|242400010|ref|YP_002995435.1|  87 YVAFSSALRLYGLIEYEPFTIFVATPEKSGKREIGEYTIKAI-ALGEKAIG----MALKDGVYTSTLAKTFFDCFYK 158
                                       77899*************999999996555566565555555.33333333....4999****************** PP

                           AbiEi_1  97 psavggldnvlevLdelaeevkpeeLeellsgrp.asvlqRlgyLLe 142
                                       p+++gg++++ ++L e ae+++ ee  +  +     s  qR+gy+Le
  gi|242400010|ref|YP_002995435.1| 159 PAYCGGYSEITKALYE-AEKIDWEEFLSYFKRFAsDSLCQRTGYILE 204
                                       ***************9.9****9998888877776***********8 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.65
                           AbiEi_1  99 avggldnvlevLdelaeevkpeeLeell 126
                                        v+ +++++++L+   e v++ +L + l
  gi|242400010|ref|YP_002995435.1| 224 RVRAWSKLVPTLPSRGEGVREWKLIDNL 251
                                       6899*******99888888887777665 PP

>> AbiEi_4  Transcriptional regulator, AbiEi antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   5.4e-07    0.0019      29      48 ..      45      64 ..      19      65 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 5.4e-07
                           AbiEi_4 29 lrrLvrkGwLvrlrrGvYal 48
                                      l+ L rkG L rl+rG+Y++
  gi|242400010|ref|YP_002995435.1| 45 LSSLARKGYLYRLKRGIYLV 64
                                      99****************86 PP

>> DUF4348  Domain of unknown function (DUF4348)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.2e-05     0.041     121     181 ..     177     237 ..     166     239 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.2e-05
                                       -SS---HHHHHHHHHH-HHHHHH.TEEEEEEEEEE-.SSSTT-EEEEEE-HHHHHHHS----S CS
                           DUF4348 121 enenedFlkFyerFatDsvfqke.slkeplkfvtad.pdddfsilegtldveqWeafkPelpk 181
                                       + + e+Fl++++rFa+Ds+ q++  + e +k  +++ p++ ++ + g ++   W+++ P+lp+
  gi|242400010|ref|YP_002995435.1| 177 KIDWEEFLSYFKRFASDSLCQRTgYILELVKSLGVNvPEEVIEYFRGRVR--AWSKLVPTLPS 237
                                       445689***************87368888888888735666788888764..69999999986 PP

>> CUE  CUE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   7.3e-05      0.26       5      25 ..      26      46 ..      24      48 .. 0.92
   2 ?   -1.6   0.0      0.64   2.3e+03      14      22 ..     212     220 ..     212     221 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 7.3e-05
                                      HHHHHHHSTTS-HHHHHHHHH CS
                               CUE  5 letLkemFPdldeevIravLr 25
                                      ++++k +FP+l+++ I++vL+
  gi|242400010|ref|YP_002995435.1| 26 VQEIKGLFPELSDDMIKKVLS 46
                                      899*****************5 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.64
                                       TS-HHHHHH CS
                               CUE  14 dldeevIra 22 
                                       +++eevI++
  gi|242400010|ref|YP_002995435.1| 212 NVPEEVIEY 220
                                       689****97 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   5.7e-05      0.21       1      57 [.       7      60 ..       7      64 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.7e-05
                                      ---S-SHHHHHHHHHS-EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEET CS
                   Penicillinase_R  1 lgelEaevmeilwekgeatvkevveeleeekelaysTVktllrrLvkKgllsrekeg 57
                                      l++ E+ v+ ++  ++ +tv+e+   ++e    ++  +k +l+ L +Kg+l r k g
  gi|242400010|ref|YP_002995435.1|  7 LTKTEQGVISVIKGADIVTVQEIKGLFPEL---SDDMIKKVLSSLARKGYLYRLKRG 60
                                      6899*******************9999987...******************998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); 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: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1850.20
//
Query:       gi|242400011|ref|YP_002995436.1|  [L=136]
Description: hypothetical protein TSIB_2040 [Thermococcus sibiricus MM 739]
Scores for complete 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-08   33.3   0.0    5.7e-08   33.0   0.0    1.1  1  AbiEii    Nucleotidyl transferase AbiEii toxin, Type IV TA sy
  ------ inclusion threshold ------
       0.11   12.5   0.0       0.15   12.0   0.0    1.2  1  LktC      Actinobacillus actinomycetemcomitans leukotoxin act


Domain annotation for each model (and alignments):
>> AbiEii  Nucleotidyl transferase AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.0   6.4e-12   5.7e-08       8     110 ..      34     128 ..      28     134 .. 0.79

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 6.4e-12
                            AbiEii   8 lsaladklvFkGGTaLslayg...lipRfSeDIDlsllrgdrkellealkealeeiaaalaeeglkvklaasigege 81 
                                        + +++k ++kGGT L+ +y       RfSeD+D+ +  gd +++ +++ e ++ i +++++   +           
  gi|242400011|ref|YP_002995436.1|  34 WEIFGEKAILKGGTGLNRVYLariGTVRFSEDMDIDYFNGDVETSAQEIVEGMKGIEGFNVKGSRI----------- 99 
                                       56789***************999999***********99*********************996666........... PP

                            AbiEii  82 dyeglrl..rypaefggyarqkikieigfre 110
                                        ++++r+   y++    + r+++k+e+ +  
  gi|242400011|ref|YP_002995436.1| 100 LHRTFRFdcYYTN--TLGNRDRVKVEFYLSR 128
                                       3333444114444..5666678999987665 PP

>> LktC  Actinobacillus actinomycetemcomitans leukotoxin activator LktC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.7e-05      0.15      32      64 ..      18      50 ..       9      62 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.7e-05
                              LktC 32 nsvkkvrkitvilaqivgilsekaiwkyqstfn 64
                                      n+v+k +ki++ l+q+  i++ekai k  + +n
  gi|242400011|ref|YP_002995436.1| 18 NYVDKEEKISLLLSQLWEIFGEKAILKGGTGLN 50
                                      99************************9877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       261  (0.0145574); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.46
# Mc/sec: 881.73
//
Query:       gi|242400012|ref|YP_002995437.1|  [L=393]
Description: IS element ISTsi1 orfB, transposase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-25   89.0   0.3    3.9e-25   87.6   0.0    2.0  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    3.1e-08   33.9   0.2    3.1e-08   33.9   0.2    2.1  2  OrfB_IS605      Probable transposase
  ------ inclusion threshold ------
       0.02   14.2   0.0      0.037   13.3   0.0    1.4  1  Baculo_ME53     Baculoviridae ME53
      0.034   14.0   0.1      0.066   13.1   0.1    1.4  1  C1_1            Phorbol esters/diacylglycerol binding domain 
      0.047   13.7   0.3      0.084   12.9   0.3    1.3  1  DZR             Double zinc ribbon
      0.092   12.2   0.8       0.32   10.4   0.8    1.9  1  Vps36-NZF-N     Vacuolar protein sorting 36 NZF-N zinc-finger
       0.16   11.4   1.5        7.8    6.1   0.2    2.3  2  zf-ribbon_3     zinc-ribbon 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 ?   -3.2   0.1       3.3   8.5e+03       1      16 [.     246     261 ..     246     263 .. 0.87
   2 !   87.6   0.0   1.5e-28   3.9e-25       1      69 []     290     357 ..     290     357 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 3.3
                    OrfB_Zn_ribbon   1 frklkeqleykakeyG 16 
                                       ++kl +++ + a++yG
  gi|242400012|ref|YP_002995437.1| 246 YYKLANKIVELAEKYG 261
                                       6799999999999998 PP

  == domain 2  score: 87.6 bits;  conditional E-value: 1.5e-28
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       f+kl+ ++eykak +G+kv+ v+payTS+ C+ Cg k+++ + +r++kC+nCgfeadrDv++++Ni  r
  gi|242400012|ref|YP_002995437.1| 290 FHKLQSIIEYKAKLKGVKVVFVDPAYTSSLCPICGGKLSP-NGHRVLKCSNCGFEADRDVVGSWNIRLR 357
                                       89**************************************.*************************875 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.7      0.32   8.1e+02      25      87 ..      32      90 ..      32      93 .. 0.68
   2 !   33.9   0.2   1.2e-11   3.1e-08       8     105 ..     167     259 ..     160     269 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.32
                        OrfB_IS605 25 innLatvvtedgtwflykgrrlks.dykylakeiaelqsklkksknykkasrklarlhrkrsrr 87
                                      +n L+t++ e+    +++ +rlk+ +y++l+k   el s ++ +    +  + + + +rkr+rr
  gi|242400012|ref|YP_002995437.1| 32 VNSLITYAFEN---NITSFKRLKKeKYEELRKDYPELPSHYHYTA--CQMASSIYKNYRKRKRR 90
                                      57788888888...7777777764267788888888888777776..56666666666666665 PP

  == domain 2  score: 33.9 bits;  conditional E-value: 1.2e-11
                        OrfB_IS605   8 velpkpkgnkaagiDlGinnL.atvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlhrk 83 
                                       +e ++++++  +g+Dl+ nn+ +++++++   f+    + ++    +  +++++q+k+k     kk++r l ++ ++
  gi|242400012|ref|YP_002995437.1| 167 KEVEVKEPEDFVGVDLNENNItLSLSDGE---FVQIITHEREIRTGYFVKRRKIQKKVKVG---KKRQRLLEKYGER 237
                                       5568899**********998636888888...9999999999999999*************...69*********** PP

                        OrfB_IS605  84 rsrrrkhllhklathliktlke 105
                                        ++r+++l+ kla+++++   +
  gi|242400012|ref|YP_002995437.1| 238 ERNRLDDLYYKLANKIVELAEK 259
                                       ***************9986544 PP

>> Baculo_ME53  Baculoviridae ME53
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.4e-05     0.037     248     293 ..     297     343 ..     280     354 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.4e-05
                       Baculo_ME53 248 kkfekvldga.vvfylkkedkeycklckktkly.tknPvlscskcGft 293
                                        +++  l+g+ vvf     +   c +c  +kl   ++ vl cs cGf 
  gi|242400012|ref|YP_002995437.1| 297 IEYKAKLKGVkVVFVDPAYTSSLCPICG-GKLSpNGHRVLKCSNCGFE 343
                                       4666666665277777788999******.****99***********96 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 ?   13.1   0.1   2.6e-05     0.066       9      38 ..     315     344 ..     309     347 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.6e-05
                                       SS--B-TTT-SB--SSSS-EEEETTT--EE CS
                              C1_1   9 kqptfCkhCgeflwgkekqglkCswCkllv 38 
                                       + ++ C  Cg  l+  +++ lkCs+C++ +
  gi|242400012|ref|YP_002995437.1| 315 YTSSLCPICGGKLSPNGHRVLKCSNCGFEA 344
                                       56789********88***********9875 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.3   3.3e-05     0.084      12      39 ..     317     345 ..     312     348 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.3e-05
                               DZR  12 arfCseCgtklkavaa.edrCpsCgekvd 39 
                                       +  C+ Cg kl++  +   +C++Cg ++d
  gi|242400012|ref|YP_002995437.1| 317 SSLCPICGGKLSPNGHrVLKCSNCGFEAD 345
                                       568*********99889999****98876 PP

>> Vps36-NZF-N  Vacuolar protein sorting 36 NZF-N zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.8   0.00012      0.32      12      48 ..     320     349 ..     313     357 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00012
                       Vps36-NZF-N  12 CpICsfsNevpsnfdpnastplPpClaCGvkpdleli 48 
                                       CpIC       ++++p + + + +C +CG ++d++++
  gi|242400012|ref|YP_002995437.1| 320 CPICG------GKLSP-NGHRVLKCSNCGFEADRDVV 349
                                       77776......66776.689999***********988 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.2    0.0031       7.8      17      26 .]     318     327 ..     316     327 .. 0.84
   2 ?    4.1   0.1     0.013        33       4      23 ..     336     341 ..     332     347 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0031
                       zf-ribbon_3  17 nvCpyCGtkl 26 
                                       + Cp CG+kl
  gi|242400012|ref|YP_002995437.1| 318 SLCPICGGKL 327
                                       57*****997 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.013
                       zf-ribbon_3   4 rCPnCGaplssddnvCpyCG 23 
                                       +C+nC              G
  gi|242400012|ref|YP_002995437.1| 336 KCSNC--------------G 341
                                       45555..............5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1060  (0.0591221); expected 358.6 (0.02)
Passed bias filter:                      788  (0.0439511); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); 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 0.35s 00:00:01.04 Elapsed: 00:00:00.55
# Mc/sec: 2133.44
//
Query:       gi|242400013|ref|YP_002995438.1|  [L=202]
Description: IS element ISTsi1 orfA, resolvase [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.4e-26   92.6   0.2    3.2e-26   92.2   0.2    1.1  1  Resolvase      Resolvase, N terminal domain
    7.6e-15   54.8   0.4    1.8e-14   53.7   0.4    1.7  1  HTH_17         Helix-turn-helix domain
    0.00012   22.1   0.1    0.00026   21.0   0.1    1.6  1  MerR_1         MerR HTH family regulatory protein
    0.00082   19.1   0.1     0.0032   17.2   0.1    2.0  2  HTH_23         Homeodomain-like domain
    0.00099   18.8   0.1     0.0017   18.1   0.1    1.4  1  MerR           MerR family regulatory protein
  ------ inclusion threshold ------
      0.021   14.7   0.3      0.026   14.4   0.3    1.4  1  DUF2797        Protein of unknown function (DUF2797)
      0.025   14.9   1.1         13    6.2   0.0    3.3  3  Ish1           Putative stress-responsive nuclear envelope pr
      0.027   14.6   0.1        0.1   12.8   0.1    1.9  2  AbiEi_4        Transcriptional regulator, AbiEi antitoxin
      0.029   13.5   0.2      0.055   12.6   0.1    1.3  1  CRM1_C         CRM1 C terminal
      0.057   13.4   0.2        1.6    8.8   0.1    2.5  2  DNA_pol3_a_NI  DNA polymerase III polC-type N-terminus I
      0.085   12.9   0.0       0.27   11.3   0.0    1.8  2  B12-binding    B12 binding domain
       0.11   12.0   0.1         16    5.1   0.1    2.5  2  Sigma70_r4     Sigma-70, region 4


Domain annotation for each model (and alignments):
>> Resolvase  Resolvase, N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.2   0.2   2.1e-29   3.2e-26       1     137 [.      57     189 ..      57     197 .. 0.94

  Alignments for each domain:
  == domain 1  score: 92.2 bits;  conditional E-value: 2.1e-29
                                       EEEEEEES-----THHHHHHHHHHHH-S--..SE...EEEE.S-TT-TT-HHHHHHHHHHTT-EE.EEEESSCCCC- CS
                         Resolvase   1 aigYaRvSteeqddslerQkealrayakenglkivkefeDkgvSGakleRpglkrllaalregkgdvlvvekldRLa 77 
                                       +++YaRvS+++q+++lerQ e l++y+ ++g+++vk+ +D   SG +++R+glk+l +++++g++  +v++  dRL+
  gi|242400013|ref|YP_002995438.1|  57 VVIYARVSSQDQKEDLERQAEYLKNYCSSKGYQVVKILTDI-SSGLNENRKGLKQLFKLVENGEITKVVITYKDRLT 132
                                       699**************************************.***********************9*********** PP

                                       S...S-HHHHHHHHHTT-EEEESS..SS----HHHHHHHHHHHHHHHHHHHHHCT-TTHH CS
                         Resolvase  78 Rsvrdlltlleelrekgvslvsldegidtstpmgrlllqilaalaeferelirertkegl 137
                                       R  +++l+  + ++++gv++ ++ +  +++tp+++l+ ++la++  f  +l  +r+++ +
  gi|242400013|ref|YP_002995438.1| 133 RFGFKYLK--QYFNSHGVEIEVIFD-DEEKTPEKELVEDLLAIVTSFAGKLYGMRSHKKK 189
                                       *9999885..589999999999998.8899*********************999998764 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.7   0.4   1.2e-17   1.8e-14       1      50 [.       3      52 ..       3      53 .. 0.96

  Alignments for each domain:
  == domain 1  score: 53.7 bits;  conditional E-value: 1.2e-17
                            HTH_17  1 lltveEaAelLgvsrstvyrlirrgelpaakiGrrwriprsdleewlekr 50
                                      l+ + EaA+ Lgvs+ t+ r+i++g+l+a++iG+ +r+p+s++ + le++
  gi|242400013|ref|YP_002995438.1|  3 LYRTGEAAKKLGVSKMTILRWIQSGKLKAHRIGKEYRVPESEIKRLLEGK 52
                                      699********************************************985 PP

>> MerR_1  MerR HTH family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.1   1.8e-07   0.00026       1      36 [.       4      39 ..       4      56 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.8e-07
                                      EEHHHHHHHHTS-HHHHHHHHHHTT-S-EE-TTS-E CS
                            MerR_1  1 ysigevakilgvtthtlrywekegllkpkrteggrr 36
                                      y+ ge+ak+lgv++ t+  w + g+lk  r ++ +r
  gi|242400013|ref|YP_002995438.1|  4 YRTGEAAKKLGVSKMTILRWIQSGKLKAHRIGKEYR 39
                                      899***************************777755 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   2.2e-06    0.0032      18      39 ..       4      25 ..       2      26 .. 0.89
   2 ?   -2.2   0.0       2.7     4e+03      22      32 ..      33      43 ..      29      53 .. 0.64

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.2e-06
                            HTH_23 18 lsvreIAreLgvsrrTvyrwlk 39
                                      +++ e+A++Lgvs++T+ rw++
  gi|242400013|ref|YP_002995438.1|  4 YRTGEAAKKLGVSKMTILRWIQ 25
                                      56779***************97 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.7
                            HTH_23 22 eIAreLgvsrr 32
                                      +I +e+ v+++
  gi|242400013|ref|YP_002995438.1| 33 RIGKEYRVPES 43
                                      66677766665 PP

>> MerR  MerR family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1   1.1e-06    0.0017       1      36 [.       5      39 ..       5      40 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.1e-06
                                      EHHHHHHHHTTTHHHHHHHHHTTSSTSEEETTTSSE CS
                              MerR  1 tIgevAeltGvsprtLRyYEreGLipppeRtegGyR 36
                                      ++ge+A+++Gvs  t+ ++ + G++ +++R    yR
  gi|242400013|ref|YP_002995438.1|  5 RTGEAAKKLGVSKMTILRWIQSGKL-KAHRIGKEYR 39
                                      58***********************.8888777777 PP

>> DUF2797  Protein of unknown function (DUF2797)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.3   1.7e-05     0.026      78     160 ..       7      87 ..       2     186 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.7e-05
                           DUF2797  78 nssevKVGiTrkeqvptRwidQGAvqaiplaevanRrlaglvevalketvaDktnwrkmlksevedvdlsaeaeela 154
                                        +++ K G+++ +    Rwi  G  +a  + + + R  + +++  l+ ++ Dk+  ++  +s+ ++ dl+++ae l+
  gi|242400013|ref|YP_002995438.1|   7 GEAAKKLGVSKMT--ILRWIQSGKLKAHRIGK-EYRVPESEIKRLLEGKTLDKVVIYARVSSQDQKEDLERQAEYLK 80 
                                       5667899999965..56*************98.567777777778888888************************** PP

                           DUF2797 155 eliae.e 160
                                       +++++  
  gi|242400013|ref|YP_002995438.1|  81 NYCSSkG 87 
                                       ***9931 PP

>> Ish1  Putative stress-responsive nuclear envelope protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0    0.0089        13       7      20 ..      77      90 ..      69      95 .. 0.89
   2 ?    5.4   0.0     0.015        23       8      18 ..     138     148 ..     137     151 .. 0.89
   3 ?   -0.7   0.1       1.2   1.9e+03      26      36 ..     187     197 ..     179     198 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0089
                              Ish1  7 sdLkkWLdshGipv 20
                                      ++Lk++++s G++v
  gi|242400013|ref|YP_002995438.1| 77 EYLKNYCSSKGYQV 90
                                      79*********875 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.015
                              Ish1   8 dLkkWLdshGi 18 
                                       +Lk++ +shG+
  gi|242400013|ref|YP_002995438.1| 138 YLKQYFNSHGV 148
                                       7*********8 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.2
                              Ish1  26 tRdeLlklard 36 
                                       ++  L++++++
  gi|242400013|ref|YP_002995438.1| 187 KKKRLVEAVKN 197
                                       78999999996 PP

>> AbiEi_4  Transcriptional regulator, AbiEi antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   6.7e-05       0.1      15      38 ..       5      29 ..       2      30 .. 0.95
   2 ?   -2.7   0.0       4.5   6.7e+03      31      41 ..     113     123 ..     110     123 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.7e-05
                           AbiEi_4 15 ttrelea.aGispsalrrLvrkGwL 38
                                      +t e+++ +G+s +++ r++++G+L
  gi|242400013|ref|YP_002995438.1|  5 RTGEAAKkLGVSKMTILRWIQSGKL 29
                                      899********************98 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4.5
                           AbiEi_4  31 rLvrkGwLvrl 41 
                                       +Lv+ G+++++
  gi|242400013|ref|YP_002995438.1| 113 KLVENGEITKV 123
                                       69999*99875 PP

>> CRM1_C  CRM1 C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   3.7e-05     0.055     198     258 ..      69     127 ..      57     153 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.7e-05
                            CRM1_C 198 ekkkeaanqFyknyylsllkevlkvltDtdhksgfklqaelLaklirlvesgsikvpllee 258
                                       +++ e   +++kny  s   +v+k+ltD    sg++++ + L++l++lve+g+i++ +++ 
  gi|242400013|ref|YP_002995438.1|  69 KEDLERQAEYLKNYCSSKGYQVVKILTDI--SSGLNENRKGLKQLFKLVENGEITKVVITY 127
                                       45678889999****************96..69*********************9988772 PP

>> DNA_pol3_a_NI  DNA polymerase III polC-type N-terminus I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.16   2.4e+02       8      30 ..      37      60 ..      33      62 .. 0.86
   2 ?    8.8   0.1    0.0011       1.6      15      41 ..     111     137 ..     104     143 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.16
                     DNA_pol3_a_NI  8 qlklp.delkslfedaeiekvvvh 30
                                      ++ +p  e+k l+e  +++kvv++
  gi|242400013|ref|YP_002995438.1| 37 EYRVPeSEIKRLLEGKTLDKVVIY 60
                                      567788999************997 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0011
                     DNA_pol3_a_NI  15 lkslfedaeiekvvvhkkskkwefyis 41 
                                       l +l e++ei+kvv++ k +  +f ++
  gi|242400013|ref|YP_002995438.1| 111 LFKLVENGEITKVVITYKDRLTRFGFK 137
                                       67889*****************99886 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       2.2   3.3e+03      17      33 ..      76      92 ..      72     110 .. 0.79
   2 ?   11.3   0.0   0.00018      0.27       3      51 ..     122     177 ..     120     200 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.2
                       B12-binding 17 lavlaaalrdagfeVql 33
                                      + +l+++++ +g++V+ 
  gi|242400013|ref|YP_002995438.1| 76 AEYLKNYCSSKGYQVVK 92
                                      57899999999999873 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00018
                       B12-binding   3 vllatvggdlhplGlavlaaalrdagfeVqllganven.......edivaairaek 51 
                                        +++t++ +l  +G+++l++++  +g+e++++  + e+       ed++a + +++
  gi|242400013|ref|YP_002995438.1| 122 KVVITYKDRLTRFGFKYLKQYFNSHGVEIEVIFDDEEKtpekelvEDLLAIVTSFA 177
                                       68999*************************99777777789778888777777765 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.013        20      25      37 ..       8      20 ..       4      30 .. 0.91
   2 ?    5.1   0.1      0.01        16      24      41 ..      32      49 ..      20      57 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.013
                                      HHHHHHTS-HHHH CS
                        Sigma70_r4 25 EIgerlgiSrerV 37
                                      E +++lg+S++++
  gi|242400013|ref|YP_002995438.1|  8 EAAKKLGVSKMTI 20
                                      89*********98 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.01
                                      HHHHHHHTS-HHHHHHHH CS
                        Sigma70_r4 24 eEIgerlgiSrerVrqie 41
                                      + Ig+++ ++++ +++++
  gi|242400013|ref|YP_002995438.1| 32 HRIGKEYRVPESEIKRLL 49
                                      68*************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1193  (0.0665402); expected 358.6 (0.02)
Passed bias filter:                      793  (0.04423); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); 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 0.35s 00:00:00.94 Elapsed: 00:00:00.51
# Mc/sec: 1193.80
//
Query:       gi|242400014|ref|YP_002995439.1|  [L=147]
Description: hypothetical protein TSIB_2043 [Thermococcus sibiricus MM 739]
Scores for complete 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-12   46.3   0.1    6.3e-12   46.0   0.1    1.1  1  AbiEii    Nucleotidyl transferase AbiEii toxin, Type IV TA sy


Domain annotation for each model (and alignments):
>> AbiEii  Nucleotidyl transferase AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.0   0.1   3.5e-16   6.3e-12     124     223 ..      31     136 ..      13     143 .. 0.75

  Alignments for each domain:
  == domain 1  score: 46.0 bits;  conditional E-value: 3.5e-16
                            AbiEii 124 leelggpafevpvysleellaeKllalldrgrdrsraRDlyDlalLleaeldaealaeallaylasrgr........ 192
                                       l   ++ +++++vysle+lla+K++al+     r +++D+yD+ + l+ +l+ +++ +al++ l++++         
  gi|242400014|ref|YP_002995439.1|  31 L---DSYPTMFRVYSLEDLLAKKVVALY----SRMEGKDIYDVFHALNLDLEVDKFLKALELNLRFYRIegdfwsel 100
                                       3...446999******************....***********************9988888888888856666666 PP

                            AbiEii 193 .....pgelrlaplellreaeadealradwkaflam 223
                                            +   + +++++ ++  + ++lr +w++ +++
  gi|242400014|ref|YP_002995439.1| 101 idklaQAKENARQIGNSTNHFIPKTLRPNWEELIES 136
                                       666664444444455666666666667777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 1070.91
//
Query:       gi|242400015|ref|YP_002995440.1|  [L=352]
Description: Glucose-1-phosphate thymidylyltransferase [Thermococcus sibiricus MM 739]
Scores for complete 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  172.4   0.0    1.5e-50  172.1   0.0    1.1  1  NTP_transferase  Nucleotidyl transferase
    6.5e-09   36.3   0.0    9.6e-09   35.8   0.0    1.2  1  NTP_transf_3     MobA-like NTP transferase domain
    9.9e-09   34.6  13.9    1.9e-05   24.2   1.3    4.4  4  Hexapep          Bacterial transferase hexapeptide (six repea
    0.00045   19.3   0.2    0.00065   18.8   0.2    1.1  1  Fucokinase       L-fucokinase
    0.00053   19.7   2.9    0.00053   19.7   2.9    3.3  4  Hexapep_2        Hexapeptide repeat of succinyl-transferase
    0.00088   17.5   0.7     0.0069   14.6   0.6    1.9  1  DUF4954          Domain of unknown function (DUF4954)
  ------ inclusion threshold ------
      0.031   14.2   0.0      0.045   13.7   0.0    1.2  1  CTP_transf_3     Cytidylyltransferase
      0.083   12.5   0.0       0.19   11.4   0.0    1.5  1  GGA_N-GAT        GGA N-GAT 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 !  172.1   0.0   6.8e-54   1.5e-50       1     245 [.       2     234 ..       2     237 .. 0.91

  Alignments for each domain:
  == domain 1  score: 172.1 bits;  conditional E-value: 6.8e-54
                                       EEEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEE CS
                   NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevli 77 
                                       ka+IL+GG GtRL+PLt +++k+l+pv++k +++ + ++ ++++gi++i +++ + +++ + e +k+ + ++ e+++
  gi|242400015|ref|YP_002995440.1|   2 KALILSGGHGTRLRPLTYSQQKQLIPVANK-PVLFYAIEDVIEAGIHDIGIIVGPSKEQVI-ETVKSVD-WDAEIEF 75 
                                       799***************************.*****************7777776666555.5566564.7788*** PP

                                       EEESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEEC CS
                   NTP_transferase  78 alepegkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGviead 154
                                       +++ e+kg+A+A+++a ++l+d++    v++Lg+++l ++ + + +++++e++   ++++++++v +++++Gv+e +
  gi|242400015|ref|YP_002995440.1|  76 IYQGEPKGLAHAIKVASDYLGDDDF---VMYLGDNIL-REGIVRHLEHFKEENF--DASILLQEVPNPQQFGVAELS 146
                                       ************************6...888877765.559999******9999..9******************** PP

                                       TTS.BEEEEECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EE CS
                   NTP_transferase 155 eeg.rverfvEKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWs 230
                                       e+g +++r++EKPk ++ s+la  G+Y+f++ v++   +++++++r e eitd+++ ++++g++   +  +++  W+
  gi|242400015|ref|YP_002995440.1| 147 EDGrTIKRLIEKPKVPP-SNLALVGVYFFKPIVHEAV-RNIKPSWRDELEITDAIQWLIDHGYRVGWTKVTGW--WK 219
                                       77769************.*************999888.89***************************999996..** PP

                                       EXSSHHHHHHHHHHH CS
                   NTP_transferase 231 DvGtldslleanekl 245
                                       D+G+++++lean+ +
  gi|242400015|ref|YP_002995440.1| 220 DTGKPEDILEANRLI 234
                                       ***********9876 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 !   35.8   0.0   4.3e-12   9.6e-09       1     111 [.       3     120 ..       3     147 .. 0.78

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 4.3e-12
                                       EEEEEESS-TTTT.....TTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHHTTC....TS-EEE-T CS
                      NTP_transf_3   1 aviLAGGrSsRmg.....gdKallplggkpllervldalraagvdevvvvggd..eevlaalarl....gvrvvede 66 
                                       a+iL GG+++R+      + K+l+p+++kp+l ++++ + +ag++++ +++g+  e+v + +++     +++++++ 
  gi|242400015|ref|YP_002995440.1|   3 ALILSGGHGTRLRpltysQQKQLIPVANKPVLFYAIEDVIEAGIHDIGIIVGPskEQVIETVKSVdwdaEIEFIYQG 79 
                                       79**********6554436****************************999888566777777655221135556665 PP

                                       TSS-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCH CS
                      NTP_transf_3  67 dpgkgplaslaaalraaadadavlvlacDmPlltpelverllaaa 111
                                       +  kg +++++ a + + ++d +++ ++D +l ++ +v++l + +
  gi|242400015|ref|YP_002995440.1|  80 E-PKGLAHAIKVASDYL-GDDDFVMYLGDNIL-REGIVRHLEH-F 120
                                       4.588888888888888.999999******76.8888877754.3 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   1.3   8.3e-09   1.9e-05       2      30 ..     254     282 ..     253     283 .. 0.95
   2 !   14.2   0.3   1.2e-05     0.028       7      29 ..     282     298 ..     281     315 .. 0.67
   3 ?    2.6   0.2     0.054   1.2e+02      22      31 ..     324     333 ..     322     334 .. 0.85
   4 ?    0.7   0.0      0.21   4.8e+02      21      28 ..     343     350 ..     338     350 .. 0.70

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 8.3e-09
                                       EEEETTEEE-TTEEEETTEEE-TTEEEET CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIga 30 
                                       +vI+++++I+  +vi g+V+IG+nv+I +
  gi|242400015|ref|YP_002995440.1| 254 VVIEEGAQIDESTVIKGPVVIGRNVVIKN 282
                                       79*************************86 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 1.2e-05
                                       TEEE-TTEEEETTEEE-TTEEEE CS
                           Hexapep   7 nvlIgpfaviggnVkIGdnvkIg 29 
                                       n++Igp++ ig+n++I      +
  gi|242400015|ref|YP_002995440.1| 282 NSYIGPYTSIGNNCVI------E 298
                                       4445555555555554......3 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.054
                                       E-TTEEEETT CS
                           Hexapep  22 IGdnvkIgag 31 
                                       IG++vkI +g
  gi|242400015|ref|YP_002995440.1| 324 IGRGVKIVRG 333
                                       9999999886 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.21
                                       EE-TTEEE CS
                           Hexapep  21 kIGdnvkI 28 
                                       +IGdn++I
  gi|242400015|ref|YP_002995440.1| 343 VIGDNSRI 350
                                       67777776 PP

>> Fucokinase  L-fucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.2   2.9e-07   0.00065     271     326 ..     257     310 ..     225     321 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.9e-07
                        Fucokinase 271 kesavvinS.vlessvsvgegsviehsslkgnvsigsnsivsglelesseeslelpd 326
                                       +e+a + +S v+++ v +g++ vi++s +++ +sig+n+++ + e+e s   + lpd
  gi|242400015|ref|YP_002995440.1| 257 EEGAQIDEStVIKGPVVIGRNVVIKNSYIGPYTSIGNNCVIENTEVEDS---IILPD 310
                                       55666655428899*******************************9975...66776 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.6       2.4   5.4e+03      14      21 ..      44      54 ..      42      54 .. 0.66
   2 ?   -2.5   0.0         2   4.5e+03      10      20 ..     250     262 ..     248     270 .. 0.66
   3 !   19.7   2.9   2.4e-07   0.00053       1      28 [.     271     299 ..     271     299 .. 0.97
   4 ?   -0.2   0.1      0.39   8.8e+02       4      10 ..     344     350 ..     342     350 .. 0.60

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.4
                                      -EE...SEEE- CS
                         Hexapep_2 14 agi...GvslG 21
                                      agi   G+++G
  gi|242400015|ref|YP_002995440.1| 44 AGIhdiGIIVG 54
                                      56444499998 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2
                                       E-TT-EE..SEEE CS
                         Hexapep_2  10 iGanagi..Gvsl 20 
                                       i+ + +i  G ++
  gi|242400015|ref|YP_002995440.1| 250 IHGRVVIeeGAQI 262
                                       6666665556555 PP

  == domain 3  score: 19.7 bits;  conditional E-value: 2.4e-07
                                       .EEE-TT-EE-TT-EES..EEE-TT-EE-T CS
                         Hexapep_2   1 pviIGdnCliGanagiG..vslGdncvvga 28 
                                       pv IG n++i +n++iG  +s+G+ncv+++
  gi|242400015|ref|YP_002995440.1| 271 PVVIGRNVVI-KNSYIGpyTSIGNNCVIEN 299
                                       89********.*****99**********97 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 0.39
                                       E-TT-EE CS
                         Hexapep_2   4 IGdnCli 10 
                                       IGdn+ i
  gi|242400015|ref|YP_002995440.1| 344 IGDNSRI 350
                                       6666654 PP

>> DUF4954  Domain of unknown function (DUF4954)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.6   3.1e-06    0.0069     191     255 ..     260     331 ..     243     350 .. 0.46

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.1e-06
                           DUF4954 191 vkigdyatiegaskl.engtinSskeap.veiGegVi.....ledfiissGskikdgavisrcfvGqavklk 255
                                       ++i++ ++i+g   + +n  i+ s   p ++iG++ +     +ed+ii   s+i d+  i+++++G++vk+ 
  gi|242400015|ref|YP_002995440.1| 260 AQIDESTVIKGPVVIgRNVVIKNSYIGPyTSIGNNCVienteVEDSIILPDSEIRDAGRIVESLIGRGVKIV 331
                                       344444444444444233333333333313344433211111334555555555555555555555555554 PP

>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0     2e-05     0.045      15     119 ..      22     124 ..      20     148 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2e-05
                                       TGGGSEETTEEHHHHHHHHHHHTTTTSE.EEEEES-HHHHHHHHHTT..SEEEE--TTCSSHHHHHHHHHHHHTTT. CS
                      CTP_transf_3  15 gKnlldlggkpliayvleaalkskafek.vivaTDseeiknvakefg..asvlvtrsslesdterflevvkaflmse 88 
                                       +K l++ ++kp ++y +e +++++  +  +iv  ++e++ +++k+    a++ ++ + ++++++   +v +++l + 
  gi|242400015|ref|YP_002995440.1|  22 QKQLIPVANKPVLFYAIEDVIEAGIHDIgIIVGPSKEQVIETVKSVDwdAEIEFIYQGEPKGLAHAIKVASDYLGD- 97 
                                       79********************9997769*****************999*************************99. PP

                                       TTSEEEEE-TT-TT--HHHHHHHHHHHHHST CS
                      CTP_transf_3  89 neeiivnlqGdnPllqeevikkaietlkenq 119
                                        ++  v + Gdn l   e i + +e+ ke++
  gi|242400015|ref|YP_002995440.1|  98 -DD-FVMYLGDNIL--REGIVRHLEHFKEEN 124
                                       .33.3344567755..334666666666665 PP

>> GGA_N-GAT  GGA N-GAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   8.5e-05      0.19      17      29 ..     222     234 ..     221     241 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8.5e-05
                         GGA_N-GAT  17 knpeDLqaANrLI 29 
                                       ++peD+ +ANrLI
  gi|242400015|ref|YP_002995440.1| 222 GKPEDILEANRLI 234
                                       58**********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); 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:                         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 0.31s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2219.88
//
Query:       gi|242400016|ref|YP_002995441.1|  [L=333]
Description: RfbB dTDP-glucose 4,6-dehydratase [Thermococcus sibiricus MM 739]
Scores for complete 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-83  278.5   0.0    1.1e-82  278.2   0.0    1.1  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    5.2e-63  212.7   0.0    6.3e-63  212.5   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    1.1e-20   73.8   0.0    1.4e-20   73.5   0.0    1.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    4.9e-18   65.2   0.0    1.1e-17   64.1   0.0    1.5  1  RmlD_sub_bind    RmlD substrate binding domain
    1.9e-12   46.9   0.0    1.1e-10   41.2   0.0    2.6  1  NAD_binding_4    Male sterility protein
      1e-11   44.5   0.0    1.7e-10   40.5   0.0    2.0  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    5.4e-07   29.7   0.0    8.9e-07   29.0   0.0    1.3  1  NAD_binding_10   NAD(P)H-binding
     0.0044   17.3   0.0     0.0077   16.5   0.0    1.4  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
     0.0063   16.0   0.0      0.025   14.0   0.0    1.8  1  adh_short        short chain dehydrogenase
     0.0066   16.0   0.0      0.011   15.3   0.0    1.3  1  NmrA             NmrA-like family


Domain annotation for each model (and alignments):
>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  278.2   0.0   5.9e-86   1.1e-82       1     332 []       4     304 ..       4     304 .. 0.94

  Alignments for each domain:
  == domain 1  score: 278.2 bits;  conditional E-value: 5.9e-86
                                       EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-S CS
                     GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpd 77 
                                       L+TG+ GfiGs+++++ l+k+ + + +++++++ + ++ ++l++   +e +e+++++kgD++D + + +l++ev  d
  gi|242400016|ref|YP_002995441.1|   4 LVTGGMGFIGSNFIRYVLDKHDD-WEVINLDKLGYGSNPANLKD---FEGDERYTFVKGDINDFELVSKLIKEV--D 74 
                                       9*******************665.57789999999999999986...55689*********************9..9 PP

                                       EEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHH CS
                     GDP_Man_Dehyd  78 evynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYa 154
                                       +v+n+AA+shVd+s+++P +++e nvlG++++Leair+++  ++vr++++S++Ev G+  +  +tE+ ++ P sPY+
  gi|242400016|ref|YP_002995441.1|  75 AVVNFAAESHVDRSISTPYAFIESNVLGVYTILEAIRKVN--PEVRLVHISSDEVHGDIMKGSFTEEDRLMPSSPYS 149
                                       **************************************87..78********************************* PP

                                       HHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHH CS
                     GDP_Man_Dehyd 155 aaKlyadwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwghvkDyve 231
                                       a+K++ d++v  + ++y+l a+++++ n+++p++   f++++i++++ r+ +g+ +++++G ++++Rdw +v+D+v+
  gi|242400016|ref|YP_002995441.1| 150 ASKAAGDTLVLGWARTYNLNASITRCTNNYGPYQ---FPEKLIPKTIIRASMGL-KIPIYGTGQNVRDWIYVEDHVR 222
                                       *********************************6...****************9.78889***************** PP

                                       HHHHHHHCSS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--SB--B CS
                     GDP_Man_Dehyd 232 amwlmlqqdkpedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevdlllg 308
                                       a+ ++l +++p        e +++    e+++le++kti +              gk++  ++++ +rpg++ ++  
  gi|242400016|ref|YP_002995441.1| 223 AVEAVLLKGEP-------REIYNISAGEERTNLEVVKTILKL------------MGKDEDLIEFVEDRPGHDLRYSL 280
                                       **********8.......688889999999999999988754............3556668999************* PP

                                       -THHHHHHH----SS-HHHHHHHH CS
                     GDP_Man_Dehyd 309 daskakeeLgWkpkvsfeelvrem 332
                                       d  k+ ++L W+pkvsfee+++++
  gi|242400016|ref|YP_002995441.1| 281 DSWKIMRDLKWRPKVSFEEGIKKT 304
                                       *********************986 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  212.5   0.0   3.5e-66   6.3e-63       2     240 ..       4     239 ..       3     240 .. 0.97

  Alignments for each domain:
  == domain 1  score: 212.5 bits;  conditional E-value: 3.5e-66
                                       EEETTTSHHHHHHHHHHHHCT..SEEEEEES-STTTTCHHCHHC......EEEE--TT-HHHHHHHHHHHT-SEEEE CS
                         Epimerase   2 lVtGatGfiGsalvkallekg..yevigldrlssasntarledl......elveldltdrsalerlfkeeqpdavih 70 
                                       lVtG+ GfiGs++++++l+k+  +evi+ld+l ++sn a+l+d       ++v++d+ d + + +l+k  ++dav++
  gi|242400016|ref|YP_002995441.1|   4 LVTGGMGFIGSNFIRYVLDKHddWEVINLDKLGYGSNPANLKDFegderyTFVKGDINDFELVSKLIK--EVDAVVN 78 
                                       9*******************99999******************9************************..89***** PP

                                       --S---HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCT.EEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHH CS
                         Epimerase  71 lAavggvaassedpadfieknlqgtlnlleaarkagvk.rllflsSsevYGkdaeqpkeettltgplkpnspYaaaK 146
                                       +Aa+++v++s+++p +fie+n+ g++++lea+rk +++ rl+++sS+ev G+  +    + t+++ l p+spY+a+K
  gi|242400016|ref|YP_002995441.1|  79 FAAESHVDRSISTPYAFIESNVLGVYTILEAIRKVNPEvRLVHISSDEVHGDIMK---GSFTEEDRLMPSSPYSASK 152
                                       ************************************999************8777...455555599********** PP

                                       HHHHHHHHHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHH CS
                         Epimerase 147 lageklveayaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeail 223
                                       +ag+ lv  +a++y+lna i+r++n+yGp+   ++++++ip+ i ++  g  ++ ++g+g+++Rd++yveD+++a+ 
  gi|242400016|ref|YP_002995441.1| 153 AAGDTLVLGWARTYNLNASITRCTNNYGPY---QFPEKLIPKTIIRASMGL-KIPIYGTGQNVRDWIYVEDHVRAVE 225
                                       ******************************...9*****************.************************* PP

                                       HHHHHHTT-STTEEEEE CS
                         Epimerase 224 lvlehvdagdkgeiyni 240
                                       +vl +   g+++eiyni
  gi|242400016|ref|YP_002995441.1| 226 AVLLK---GEPREIYNI 239
                                       *****...999*****9 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.5   0.0   7.9e-24   1.4e-20       1     222 [.       4     221 ..       4     235 .. 0.87

  Alignments for each domain:
  == domain 1  score: 73.5 bits;  conditional E-value: 7.9e-24
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlD...lrespelleelskvnvkkviegDvtdkdkleealegvdvvihla 74 
                                       +vtGg+GF+G++ ++ +++ ++ +ev  lD      +p  l++++  ++ ++++gD++d + +++ +++vd+v+  a
  gi|242400016|ref|YP_002995441.1|   4 LVTGGMGFIGSNFIRYVLDKHDDWEVINLDklgYGSNPANLKDFEGDERYTFVKGDINDFELVSKLIKEVDAVVNFA 80 
                                       69****************************555456777777888888888************************** PP

                         3Beta_HSD  75 slvdvag.kltedeimkvnvkGTrnvleacvkagvr.vlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypes 149
                                       + + v     t   + + nv G  ++lea +k + + +lv+ Ss ev g+      i++g  ++e   +++++y+ s
  gi|242400016|ref|YP_002995441.1|  81 AESHVDRsISTPYAFIESNVLGVYTILEAIRKVNPEvRLVHISSDEVHGD------IMKGSFTEEDRLMPSSPYSAS 151
                                       ****988466778899**************998755259*********99......7778888999999******** PP

                         3Beta_HSD 150 KalaEklvlkaNgrtlknggrlyTcaLRpagiyGegd..kllvpllkqlaklglalfkigdeevlsdrvYvgNva 222
                                       Ka  + lvl           +l+    R +  yG+++  ++l p     a +gl++  +g  +++ d++Yv+  +
  gi|242400016|ref|YP_002995441.1| 152 KAAGDTLVLGWAR-----TYNLNASITRCTNNYGPYQfpEKLIPKTIIRASMGLKIPIYGTGQNVRDWIYVEDHV 221
                                       *********7666.....447888999********97556778888888899*******************9754 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 !   64.1   0.0     6e-21   1.1e-17       1     234 [.       1     261 [.       1     273 [. 0.77

  Alignments for each domain:
  == domain 1  score: 64.1 bits;  conditional E-value: 6e-21
                                       EEEEEESTTSHHHHHHHHHCTT..TSEEEEEE-TT.....................T--TTSHHHHHHHHHHH--SE CS
                     RmlD_sub_bind   1 mkilvtGanGqlGseLakqlae..eglevlaltre.....................eldltdaeavaellkeakpdv 54 
                                       m++lvtG+ G +Gs+ ++ +    +++ev+ l++                      + d++d e v +l+ke   d+
  gi|242400016|ref|YP_002995441.1|   1 MRLLVTGGMGFIGSNFIRYVLDkhDDWEVINLDKLgygsnpanlkdfegderytfvKGDINDFELVSKLIKE--VDA 75 
                                       89**************998754237899**999889***********************************9..789 PP

                                       EEE------HHHHHHSHHHHHHHHTHHHHHHHHHHHHCT..-EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHH CS
                     RmlD_sub_bind  55 vvnaAAytavDkaEseeeaayavnaeavealAeaaaavg..alLihvStDyVFdGekkrpYeeddetsPlnvYGrtK 129
                                       vvn AA   vD+  s + a  + n+ +v ++ ea ++v+  + L+h+S+D V     k  ++e+d+  P + Y ++K
  gi|242400016|ref|YP_002995441.1|  76 VVNFAAESHVDRSISTPYAFIESNVLGVYTILEAIRKVNpeVRLVHISSDEVHGDIMKGSFTEEDRLMPSSPYSASK 152
                                       ************************************9954499*********98889999***************** PP

                                       HHHHHHHHH....H-SSEEEEEE-SEESSSSS-HHHHHHHHHHH-SEEEEESS-EE--EEHHHHHHH..HHHHHHHC CS
                     RmlD_sub_bind 130 laGEqavla....agkkalivRtswvygekgknfvktmlrlakereelkvvaDqlgsPTsardlAev..llqlleka 200
                                       +aG   vl     ++ +a i R +  yg +  +f ++++ +   r ++ +    +g+   +rd   v   + ++e+ 
  gi|242400016|ref|YP_002995441.1| 153 AAGDTLVLGwartYNLNASITRCTNNYGPY--QFPEKLIPKTIIRASMGLKIPIYGTGQNVRDWIYVedHVRAVEAV 227
                                       ******986655588899999999999885..344444444444444444434444444444432221123333333 PP

                                       HH.GGG-EEEE---BS-EEHHHHHHHHHHHHCHT CS
                     RmlD_sub_bind 201 aeekelagvyHlanegetswlefArailkeagad 234
                                       + + e  ++y +++ +e + le+ + ilk +g+d
  gi|242400016|ref|YP_002995441.1| 228 LLKGEPREIYNISAGEERTNLEVVKTILKLMGKD 261
                                       3334446666666666666666666666666655 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.2   0.0     6e-14   1.1e-10       1     205 [.       5     177 ..       5     223 .. 0.83

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 6e-14
                                       EE-TTSHHHHHHHHHHHHHS-.TEEEEEE-SSSHHHHHHHHHHHT-SS-HHHHHHHHHTTTEEEEE--TTSGGGG-- CS
                     NAD_binding_4   1 lTGaTGFLGkvLlekLLrttpevkiyllvRaksgesaeeRleeelekkelfsallkelaerikvveGDlseprlGLs 77 
                                       +TG+ GF+G+ +++  L+++++ +++ l +   g++++  l         + ++  e  er ++v+GD+++ +l   
  gi|242400016|ref|YP_002995441.1|   5 VTGGMGFIGSNFIRYVLDKHDDWEVINLDKLGYGSNPA-NL---------K-DF--EGDERYTFVKGDINDFEL--- 65 
                                       79*****************9998998887777663332.23.........1.11..347899*******98765... PP

                                       HHHHHHHHHH--EEEE--SS-S.STTSSE...EHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS CS
                     NAD_binding_4  78 eedlqelaeevdviihsaAtvnfdepyke...llrvNveGtrevlelakklkklkvllhvSTayvngeregeveekv 151
                                          + +l++evd++++ aA  ++d+++++   +++ Nv+G+  +le  +k++    l+h+S+  v+g+  +      
  gi|242400016|ref|YP_002995441.1|  66 ---VSKLIKEVDAVVNFAAESHVDRSISTpyaFIESNVLGVYTILEAIRKVNPEVRLVHISSDEVHGDIMKG----- 134
                                       ...899********************9996667899****************999*******7777777743..... PP

                                       -H......HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-E CS
                     NAD_binding_4 152 yeegekeekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsi 205
                                                  + ++++    +  Y+ sKa+++ lv  ++r  +l+++i R+++
  gi|242400016|ref|YP_002995441.1| 135 -----------SFTEEDRLMPSSPYSASKAAGDTLVLGWARTYNLNASITRCTN 177
                                       ...........3455556667789***************************976 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.5   0.0   9.5e-14   1.7e-10       1     267 [.       3     273 ..       3     282 .. 0.71

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 9.5e-14
                                       EEEETTTSHHHHHHHHHHHHH.B-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT.. CS
                   Polysacc_synt_2   1 vlvtGagGsiGselvrqilkk.kpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleel 76 
                                       +lvtG+ G iGs+++r +l+k +  ++i l++  +     + +      ++++    + v gd++d e ++k+++  
  gi|242400016|ref|YP_002995441.1|   3 LLVTGGMGFIGSNFIRYVLDKhDDWEVINLDKLGYGSNPANLKD--FEGDERY----TFVKGDINDFELVSKLIK-- 71 
                                       59*****************9856678888887777666555543..2333334....3468**************.. PP

                                       T-SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-S.EEEEEEEGGG..............SS--SHH CS
                   Polysacc_synt_2  77 kvdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvk.kvvliStDKA..............vnPtnvm 138
                                       +vd+v++ AA  hV    + p+  i+ Nvlg  +++ea  + + + ++v iS+D                  P + +
  gi|242400016|ref|YP_002995441.1|  72 EVDAVVNFAAESHVDRSISTPYAFIESNVLGVYTILEAIRKVNPEvRLVHISSDEVhgdimkgsfteedrLMPSSPY 148
                                       ***************************************999876489******75222222222222223577777 PP

                                       HHHHHHHHHHHHHGGG--SSS--EEEEEEE-EETTG...TTSSHHHHHHHHHTTSSEEES-T.T-EEEEE-HHHHHH CS
                   Polysacc_synt_2 139 GatKrlaekllqalakeseekktkfvvvRfGNVlgS...rGSviplFkkqikeggpvtvTdp.emtRyfmtieeavq 211
                                        a+K++ + l+   a++    + + +++R  N  g       +ip+   + + g ++++  + + +R ++ +e+ v+
  gi|242400016|ref|YP_002995441.1| 149 SASKAAGDTLVLGWARTY---NLNASITRCTNNYGPyqfPEKLIPKTIIRASMGLKIPIYGTgQNVRDWIYVEDHVR 222
                                       777777777777666655...34555555555544411134678877777777777777432145677888888888 PP

                                       HHHHHHHH--SS-EEEE--.-EEEHHHHHHHH..........SSSS-EEE----TT CS
                   Polysacc_synt_2 212 LvlqalalakggeifvldmGepvkivdlakalielsgleekkeedieikitGlRpG 267
                                        v   l +++  ei+   +Ge  + ++++k++++l+g++e+      i+++  RpG
  gi|242400016|ref|YP_002995441.1| 223 AVEAVLLKGEPREIYNISAGEERTNLEVVKTILKLMGKDED-----LIEFVEDRPG 273
                                       88888888888888888888888888888888888875444.....3566666666 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 !   29.0   0.0     5e-10   8.9e-07       1     129 [.       7     157 ..       7     175 .. 0.77

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 5e-10
                                       TTTSHHHHHHHHHHHHC-.T-EEEEE.....ETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---T CS
                    NAD_binding_10   1 GAtGkvGrllvkellarg.ghevtal.....vRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsalggg 71 
                                       G+ G +G+  ++  l+++ ++ev  l       np+ l+++e +e+ + v+gd++d e + + +k +daVv  ++ +
  gi|242400016|ref|YP_002995441.1|   7 GGMGFIGSNFIRYVLDKHdDWEVINLdklgyGSNPANLKDFEGDERYTFVKGDINDFELVSKLIKEVDAVVNFAAES 83 
                                       8889999999999999998788764421112579***********************************99988887 PP

                                       CCHHHH.............HHHHHHHHHHCT--.EEEEEEETTTTSGCG.CHHHHHHHHCCHHHH.HHHHHHHH CS
                    NAD_binding_10  72 gkdeeg.............aknivdaakeagvk.Rfvlvsaigvgdevp.gefgewnkellkayl.aakraaee 129
                                       + d+ +             + +i++a ++ + + R+v +s+  v  +++ g+f e ++ + ++ + a k+a + 
  gi|242400016|ref|YP_002995441.1|  84 HVDRSIstpyafiesnvlgVYTILEAIRKVNPEvRLVHISSDEVHGDIMkGSFTEEDRLMPSSPYsASKAAGDT 157
                                       776666777888888889999********985339******999876551555555555655545045555554 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   4.3e-06    0.0077       3      78 ..       5      81 ..       3     100 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4.3e-06
                                      EE--.SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH....TTTCEEEEE--TTTHHHHHHHHHTTSSEEEE- CS
                   Sacchrp_dh_NADP  3 iiGa.GsvGqavaellarhfdvdaeitvadrskeklealaaka....lgvrfeaialdaenyeavLaallkegdlvvnl 76
                                      + G+ G++G+ +++++++++d    + v+  +k +     a++      +r ++++ d+++ e  +++l+ke d+vvn 
  gi|242400016|ref|YP_002995441.1|  5 VTGGmGFIGSNFIRYVLDKHDD---WEVINLDKLGYGSNPANLkdfeGDERYTFVKGDINDFEL-VSKLIKEVDAVVNF 79
                                      55666**********9999985...777777777666666666666699**************9.*************8 PP

                                      SS CS
                   Sacchrp_dh_NADP 77 sp 78
                                      + 
  gi|242400016|ref|YP_002995441.1| 80 AA 81
                                      76 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   1.4e-05     0.025       4     167 ..       4     166 ..       2     175 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.4e-05
                                       EEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT..TSEEEEEE-TTTSHHHHHHHHHHHHHHHSSE CS
                         adh_short   4 lvtGassGIGraiakelakeGakvvvvdrseekleevakelkee..gakalaiqvDvtdreevealvekavkklgkl 78 
                                       lvtG+++ IG ++ + ++ +  +  v++  +       ++lk+    ++++++++D++d e v++l++++       
  gi|242400016|ref|YP_002995441.1|   4 LVTGGMGFIGSNFIRYVLDKHDDWEVINLDKLGYGSNPANLKDFegDERYTFVKGDINDFELVSKLIKEV------- 73 
                                       899999999999999998876666665555556666777777666567899*******999999888876....... PP

                                       SEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHH...HHHHHH......HCTTEEEEEEEEGGGTSB-TTB CS
                         adh_short  79 dvLvnNAGitgsgpfselseeewervievNltgvflltra...vlpaml......kqssGrIvnvsSvagkvpvagv 146
                                       d++vn A+ +      + s ++  + ie N+ gv+ + +a   v p+        ++  G+I   +S + + ++   
  gi|242400016|ref|YP_002995441.1|  74 DAVVNFAAES----HVDRSISTPYAFIESNVLGVYTILEAirkVNPEVRlvhissDEVHGDIMK-GSFTEEDRLMPS 145
                                       *******993....44556666788899999998776655000555533557777778888766.778888899999 PP

                                       HHHHHHHHHHHHHHHHHHHHH CS
                         adh_short 147 aaYsAsKaavagltrslakel 167
                                       ++YsAsKaa + l+  +a+ +
  gi|242400016|ref|YP_002995441.1| 146 SPYSASKAAGDTLVLGWARTY 166
                                       *************99999876 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   6.1e-06     0.011       2      72 ..       4      80 ..       3      94 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 6.1e-06
                                      EESSTTSHHHHHHHHHHHH..HT-EEEEEES-S...-SHHHHHHH.HSTTEEEES-TT-HHHHHHHHTT-SEEEE-- CS
                              NmrA  2 lviGaTGrqGksvvrallk..aghkvralvRdt...kselakslk.eaGvelvkgdlddkeslvealkgvdvvfsvt 72
                                      lv+G+ G +G+ ++r++l+  ++++v  l +     +  ++k ++ ++  ++vkgd++d e++++++k+vd+v    
  gi|242400016|ref|YP_002995441.1|  4 LVTGGMGFIGSNFIRYVLDkhDDWEVINLDKLGygsNPANLKDFEgDERYTFVKGDINDFELVSKLIKEVDAVVNFA 80
                                      8*****************96677777776655566566777777634567899******************997554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.70u 0.34s 00:00:01.04 Elapsed: 00:00:00.55
# Mc/sec: 1815.63
//
Query:       gi|242400017|ref|YP_002995442.1|  [L=74]
Description: hypothetical protein TSIB_2046 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.2e-19   70.5   4.4    1.3e-19   70.4   3.0    1.6  2  DUF104      Protein of unknown function DUF104
  ------ inclusion threshold ------
      0.035   13.8   0.1      0.039   13.7   0.1    1.1  1  Cactin_mid  Conserved mid region of cactin
       0.04   13.9   0.1      0.074   13.0   0.1    1.5  1  DUF1967     Domain of unknown function (DUF1967)


Domain annotation for each model (and alignments):
>> DUF104  Protein of unknown function DUF104
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.4   3.0   2.1e-23   1.3e-19       1      59 []       1      56 [.       1      56 [. 0.96
   2 ?   -0.0   0.0      0.21   1.3e+03      26      39 ..      56      69 ..      55      73 .. 0.71

  Alignments for each domain:
  == domain 1  score: 70.4 bits;  conditional E-value: 2.1e-23
                            DUF104  1 MskvIeavYEnGvLKPLekvdLkEGeevkikIeeakeilkklkgilkeadeeeleelle 59
                                      M+ ++eavYEnGvLKPL+k++Lk+G++v+ik+e     + +++g++++a+++el+el+e
  gi|242400017|ref|YP_002995442.1|  1 MPIIVEAVYENGVLKPLKKLNLKDGQKVRIKVEL---DVSEYYGVFGKASSKELKELEE 56
                                      999*******************************...788899*************876 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.21
                            DUF104 26 eevkikIeeakeil 39
                                      eevki ++  k+ l
  gi|242400017|ref|YP_002995442.1| 56 EEVKIFLKGDKDAL 69
                                      78999988855544 PP

>> Cactin_mid  Conserved mid region of cactin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   6.5e-06     0.039      60      97 ..      30      67 ..      13      73 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.5e-06
                        Cactin_mid 60 adleieleePykileglsleeleeleediksyleleks 97
                                       ++e+++ e y ++ + s++el+elee++k +l+ +k+
  gi|242400017|ref|YP_002995442.1| 30 IKVELDVSEYYGVFGKASSKELKELEEEVKIFLKGDKD 67
                                      6789999999***********************99986 PP

>> DUF1967  Domain of unknown function (DUF1967)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   1.2e-05     0.074      43      64 ..      10      31 ..       6      38 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.2e-05
                                      HTTHHHHHHTTT--TT-EEEET CS
                           DUF1967 43 klGvedaLrkaGakeGdtVrIg 64
                                      ++Gv + L+k+  k+G++VrI 
  gi|242400017|ref|YP_002995442.1| 10 ENGVLKPLKKLNLKDGQKVRIK 31
                                      68*******************4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       760  (0.0423894); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); 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: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 447.63
//
Query:       gi|242400018|ref|YP_002995443.1|  [L=185]
Description: RfbC dTDP-4-dehydrorhamnose 3,5-epimerase [Thermococcus sibiricus MM 739]
Scores for complete 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-77  258.2   0.0    3.1e-77  258.0   0.0    1.0  1  dTDP_sugar_isom  dTDP-4-dehydrorhamnose 3,5-epimerase


Domain annotation for each model (and alignments):
>> dTDP_sugar_isom  dTDP-4-dehydrorhamnose 3,5-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  258.0   0.0   1.8e-81   3.1e-77       2     169 .]       8     177 ..       7     177 .. 0.99

  Alignments for each domain:
  == domain 1  score: 258.0 bits;  conditional E-value: 1.8e-81
                                       -SSTTCEEEEE-EEEETTEEEEEEEEHHHHHHHTS-----EEEEEEEETTBEEEEEEESSCS---EEEEEEESEEEE CS
                   dTDP_sugar_isom   2 teiegvlliepkvfgDeRGfflesfneeefaeagleaefvqdnlsvskkgvlRGlHfqkepkaqaklvrvvrGevld 78 
                                       +ei++v+li+pkvf+DeRGff+e++++ +f++ag++ +f+qdn+s+sk gvlRGlHfq+ep+aqak+vr++rG ++d
  gi|242400018|ref|YP_002995443.1|   8 LEIPDVILIKPKVFEDERGFFMETYKKPDFEKAGIKGDFIQDNHSKSKYGVLRGLHFQREPYAQAKIVRCIRGVIYD 84 
                                       68*************************************************************************** PP

                                       EEEE-BTTSTTTT-EEEEEEETTT--EEEE-TTEEEEEEE-SSEEEEEEEESS---GGGEEEE-TT-TTTT---..S CS
                   dTDP_sugar_isom  79 vaVDlRkgSptfgkwvgveLsaenkrqlyipegfahGflvlsdeaevlYkvteyyapesergirwnDpelgidw..e 153
                                       vaVDlRk+Sptfgkwvgv Ls++nk qlyip+gfahGflvlsd aev+Ykv+++yap++e+gi wnDp++gidw  +
  gi|242400018|ref|YP_002995443.1|  85 VAVDLRKDSPTFGKWVGVILSEHNKWQLYIPKGFAHGFLVLSDVAEVVYKVDNVYAPNYEGGIIWNDPDIGIDWpvD 161
                                       ****************************************************************************9 PP

                                       S.B--HHHHT-B-HHH CS
                   dTDP_sugar_isom 154 elilSekDkaapslae 169
                                       ++++SekD ++p+l+e
  gi|242400018|ref|YP_002995443.1| 162 KPTVSEKDMKWPTLRE 177
                                       9************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       269  (0.0150036); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); 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: 00:00:00.49
# Mc/sec: 1146.86
//
Query:       gi|242400019|ref|YP_002995444.1|  [L=287]
Description: dTDP 4-dehydrorhamnose reductase [Thermococcus sibiricus MM 739]
Scores for complete 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-87  292.0   0.0    4.7e-87  291.7   0.0    1.0  1  RmlD_sub_bind    RmlD substrate binding domain
    8.5e-24   84.3   0.0    1.1e-23   84.0   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    4.4e-15   55.9   0.2    1.7e-14   54.0   0.0    1.8  2  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
      1e-10   41.2   2.3    8.8e-10   38.2   0.9    2.5  2  Polysacc_synt_2  Polysaccharide biosynthesis protein
    4.2e-07   29.4   0.1    1.5e-06   27.5   0.1    2.1  2  NAD_binding_4    Male sterility protein
    0.00033   20.8   0.1     0.0029   17.7   0.0    2.2  2  DapB_N           Dihydrodipicolinate reductase, N-terminus
     0.0025   18.2   0.1       0.01   16.3   0.0    2.1  2  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
  ------ inclusion threshold ------
       0.14   12.1   0.0       0.18   11.7   0.0    1.2  1  EB_dh            Ethylbenzene dehydrogenase
       0.16   11.8   0.1       0.29   11.0   0.1    1.3  1  FadR_C           FadR C-terminal domain


Domain annotation for each model (and alignments):
>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  291.7   0.0   2.3e-90   4.7e-87       1     284 [.       1     283 [.       1     285 [. 0.97

  Alignments for each domain:
  == domain 1  score: 291.7 bits;  conditional E-value: 2.3e-90
                                       EEEEEESTTSHHHHHHHHHCTT.TSEEEEEE-TTT--TTSHHHHHHHHHHH--SEEEE------HHHHHHSHHHHHH CS
                     RmlD_sub_bind   1 mkilvtGanGqlGseLakqlae.eglevlaltreeldltdaeavaellkeakpdvvvnaAAytavDkaEseeeaaya 76 
                                       m++ ++GanGqlGs+L++ + + + +ev++lt ++ld+t  ++++ +lk+ kpdv++n+AAy +vD aE  +e+a++
  gi|242400019|ref|YP_002995444.1|   1 MRVAIIGANGQLGSDLVEVFGSdSSFEVVPLTHSDLDVTILDTLE-VLKKLKPDVIINTAAYVRVDDAELYPEKAFQ 76 
                                       89****************98764899***************9985.88999************************** PP

                                       HHTHHHHHHHHHHHHCT-EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHHHH-SSEEEEEE-SEES CS
                     RmlD_sub_bind  77 vnaeavealAeaaaavgalLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqavlaagkkalivRtswvyg 153
                                       vna ++ ++A++a++++a+ +++StDyVFdG+k +pY+e+d ++P+nvYG +K+aGE   ++++ k++i+R++ +yg
  gi|242400019|ref|YP_002995444.1|  77 VNAIGALNVARVAEEIDAVNVYISTDYVFDGSKGEPYTEEDIPNPINVYGLSKYAGEIFTKNYSRKHYIIRVASLYG 153
                                       ****************************************************************************9 PP

                                       S.....SSS-HHHHHHHHHHH-SEEEEESS-EE--EEHHHHHHHHHHHHHHCHH.GGG-EEEE---BS-EEHHHHHH CS
                     RmlD_sub_bind 154 e.....kgknfvktmlrlakereelkvvaDqlgsPTsardlAevllqllekaaeekelagvyHlanegetswlefAr 225
                                       +     kg nfv+ m+++ak+ ee++vv+Dq+ sPT+++d+A+ l +lle + e    +gvyH++n+g +sw+ef +
  gi|242400019|ref|YP_002995444.1| 154 KagasgKGGNFVEFMVQKAKRGEEIRVVDDQFMSPTYTKDVARTLKKLLELKPE----FGVYHMVNDGFCSWYEFTK 226
                                       988988999*****************************************9998....******************* PP

                                       HHHHHHCHTTSEEEEE-CCCS--SS---SBE-B--HHHHHCCT----BHHHHHHHHHHH CS
                     RmlD_sub_bind 226 ailkeagadseevkpistaeyptpAkRPanSvLdtekleatfgiklrewrealkevlke 284
                                       ai++ +g +  +v+pi+++e  + AkRP+ S+L++++le   g+k+r+wr+alke+l+e
  gi|242400019|ref|YP_002995444.1| 227 AIFEILGWEV-DVRPIKSDELKRLAKRPRFSALRNKRLEGL-GLKMRPWRSALKEYLRE 283
                                       ********76.****************************99.9************9986 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.0   0.0   5.4e-27   1.1e-23       2     228 ..       4     204 ..       3     215 .. 0.91

  Alignments for each domain:
  == domain 1  score: 84.0 bits;  conditional E-value: 5.4e-27
                                       EEETTTSHHHHHHHHHHHHCT.SEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---H CS
                         Epimerase   2 lVtGatGfiGsalvkallekg.yevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggv 77 
                                        ++Ga+G++Gs lv+ + +    ev+ l++                +ld+t  + le ++k+ +pd++i+ Aa+  v
  gi|242400019|ref|YP_002995444.1|   4 AIIGANGQLGSDLVEVFGSDSsFEVVPLTHS---------------DLDVTILDTLE-VLKKLKPDVIINTAAYVRV 64 
                                       69***************9999899*******...............99999988665.66778************** PP

                                       HHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSS.BSTCSTTS----SSHHHHHHHHHHHHH CS
                         Epimerase  78 aassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqp.keettltgplkpnspYaaaKlageklv 153
                                       ++   +p++ ++ n++g+ln++ +a + ++   +++s++ v+  ++  p +ee++     +p + Y+++K+age  +
  gi|242400019|ref|YP_002995444.1|  65 DDAELYPEKAFQVNAIGALNVARVAEEIDA-VNVYISTDYVFDGSKGEPyTEEDI----PNPINVYGLSKYAGEIFT 136
                                       ****************************99.99*********9888888455555....69**************** PP

                                       HHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHH CS
                         Epimerase 154 eayaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvleh 228
                                       ++y +++     i+r+ +lyG+    g+  +++  +++k+++g+ e+ +++  ++ +   y +Dva+ +  +le 
  gi|242400019|ref|YP_002995444.1| 137 KNYSRKH----YIIRVASLYGKAGASGKGGNFVEFMVQKAKRGE-EIRVVD--DQFMSPTYTKDVARTLKKLLEL 204
                                       ******9....799*********88888****************.*****9..899999********99999986 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 ?   -0.3   0.0      0.27   5.4e+02       2      19 ..       5      22 ..       5      44 .. 0.77
   2 !   54.0   0.0   8.5e-18   1.7e-14      69     271 ..      45     237 ..      31     262 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.27
                                      EETTTSHHHHHHHHHHHH CS
                     GDP_Man_Dehyd  2 iTGiaGfiGsylaelLle 19
                                      i G +G+ Gs l+e + +
  gi|242400019|ref|YP_002995444.1|  5 IIGANGQLGSDLVEVFGS 22
                                      779**********98765 PP

  == domain 2  score: 54.0 bits;  conditional E-value: 8.5e-18
                                       HHHHHHT-SEEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS CS
                     GDP_Man_Dehyd  69 rllaevqpdevynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEtt 145
                                       ++l++ +pd ++n AA   Vd     Pe+ ++vn++G+l++  ++ ++     v  + +St+ v+   +  p+tE+ 
  gi|242400019|ref|YP_002995444.1|  45 EVLKKLKPDVIINTAAYVRVDDAELYPEKAFQVNAIGALNVARVAEEIDA---VN-VYISTDYVFDGSKGEPYTEED 117
                                       799*************************************9999998753...44.679******999999****** PP

                                       -----SHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEE CS
                     GDP_Man_Dehyd 146 pfyPrsPYaaaKlyadwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRd 222
                                         +P + Y+ +K + + +++ny +++ +  v + +       +g +fv+     +v+++++g++  + +   d+  +
  gi|242400019|ref|YP_002995444.1| 118 IPNPINVYGLSKYAGEIFTKNYSRKHYIIRVASLYGKAGASGKGGNFVEF----MVQKAKRGEEIRV-V--DDQFMS 187
                                       *************************9999999999888888888898864....4566677764443.2..344556 PP

                                       EEEHHHHHHHHHHHHHC.SS---EEE-TT-EEECHHCHHCCHHCCCHHHH CS
                     GDP_Man_Dehyd 223 wghvkDyveamwlmlqq.dkpedyviatgethsvrefvelaflelgktie 271
                                        ++ kD+++ + ++l+   +   y + +    s  ef ++ f+ lg +++
  gi|242400019|ref|YP_002995444.1| 188 PTYTKDVARTLKKLLELkPEFGVYHMVNDGFCSWYEFTKAIFEILGWEVD 237
                                       66667777777777663133445555555555666666665555555555 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.17   3.4e+02       1      32 [.       3      34 ..       3      43 .. 0.78
   2 !   38.2   0.9   4.4e-13   8.8e-10      71     198 ..      45     184 ..      36     187 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.17
                                      EEEETTTSHHHHHHHHHHHHHB-SEEEEEES- CS
                   Polysacc_synt_2  1 vlvtGagGsiGselvrqilkkkpkkiillerd 32
                                      v + Ga G +Gs lv+ + + +  +++ l ++
  gi|242400019|ref|YP_002995444.1|  3 VAIIGANGQLGSDLVEVFGSDSSFEVVPLTHS 34
                                      6799***********99888777777666665 PP

  == domain 2  score: 38.2 bits;  conditional E-value: 4.4e-13
                                       HHTT..T-SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEGGGS..............S CS
                   Polysacc_synt_2  71 kaleelkvdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliStDKAv..............n 133
                                       ++l++lk+dv++++AA+ +V  +e +p +a++ N +g+ nv+++a e +  + v+iStD                 n
  gi|242400019|ref|YP_002995444.1|  45 EVLKKLKPDVIINTAAYVRVDDAELYPEKAFQVNAIGALNVARVAEEIDAVN-VYISTDYVFdgskgepyteedipN 120
                                       68899*****************************************999876.79****764333333334444448 PP

                                       --SHHHHHHHHHHHHHHHGGG--SSS--EEEEEEE-EETTG..TTSSHHHHHHHHHTTSSEEES-TT CS
                   Polysacc_synt_2 134 PtnvmGatKrlaekllqalakeseekktkfvvvRfGNVlgS..rGSviplFkkqikeggpvtvTdpe 198
                                       P+nv+G++K + e ++ ++++++       v+  +G   +S   G  + +  ++ k+g+++ v d +
  gi|242400019|ref|YP_002995444.1| 121 PINVYGLSKYAGEIFTKNYSRKH---YIIRVASLYGKAGASgkGGNFVEFMVQKAKRGEEIRVVDDQ 184
                                       ***************99999998...44555566776654422689999999999999999998875 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.1   7.7e-10   1.5e-06      88     208 ..      52     153 ..      31     195 .. 0.79
   2 ?   -1.8   0.0      0.68   1.4e+03     170     184 ..     216     230 ..     168     235 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 7.7e-10
                                       --EEEE--SS-S.ST..TS.SEEHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H......HH CS
                     NAD_binding_4  88 vdviihsaAtvnfde..py.kellrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyeegekeekl 161
                                        dvii+ aA v++d+   y +++++vN  G+ +v + a+++ +    +++ST yv + ++ge               
  gi|242400019|ref|YP_002995444.1|  52 PDVIINTAAYVRVDDaeLYpEKAFQVNAIGALNVARVAEEIDAV--NVYISTDYVFDGSKGEP-------------- 112
                                       59***********985434256*****************99665..89****88888888653.............. PP

                                       H--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE- CS
                     NAD_binding_4 162 dederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitg 208
                                          ++++  +  n Y  sK+++E   ++++r+      i+R+  ++g
  gi|242400019|ref|YP_002995444.1| 113 --YTEEDIPNPINVYGLSKYAGEIFTKNYSRK----HYIIRVASLYG 153
                                       ..4567788899*****************966....56888888877 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.68
                                       TTCCCHHHHHHHHHH CS
                     NAD_binding_4 170 kglpntYeqsKalaE 184
                                       +g+   Ye++Ka+ E
  gi|242400019|ref|YP_002995444.1| 216 DGFCSWYEFTKAIFE 230
                                       566677888888766 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   1.5e-06    0.0029       1      57 [.       1      56 [.       1      69 [. 0.77
   2 ?    0.4   0.0      0.34   6.7e+02       6      44 ..     155     194 ..     153     212 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.5e-06
                                      EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BE CS
                            DapB_N  1 ikvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglgklgvav 57
                                      ++va++Ga+G +G+ +v++  +++++e+v   +++  ++   d  e+l++ k +v +
  gi|242400019|ref|YP_002995444.1|  1 MRVAIIGANGQLGSDLVEVFGSDSSFEVVPLTHSDL-DVTILDTLEVLKKLKPDVII 56
                                      89***************************9988765.55555555555555555544 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.34
                                       ETTTSHHHHHHHHHHHHSTTEEEEEEEETTC.STTTTTBH CS
                            DapB_N   6 vGasGrmGkevvkaveeaedlelvaavdrke.selegkda 44 
                                       +GasG+ G+ v  +v++a++ e   +vd +  s++  kd+
  gi|242400019|ref|YP_002995444.1| 155 AGASGKGGNFVEFMVQKAKRGEEIRVVDDQFmSPTYTKDV 194
                                       699*****99999999998887777777654355555555 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   5.1e-06      0.01       1      34 [.       2      35 ..       2      99 .. 0.92
   2 ?   -0.8   0.0      0.98     2e+03      35      58 ..     156     182 ..     122     212 .. 0.61

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 5.1e-06
                                      EEEEETTTSHHHHHHHHHHHCTSSEEEEEEEEST CS
                    Semialdhyde_dh  1 kvaivGatGyvGqellrlLeehpevelvvllsss 34
                                      +vai+Ga G  G++l+++  ++ ++e+v l+ s+
  gi|242400019|ref|YP_002995444.1|  2 RVAIIGANGQLGSDLVEVFGSDSSFEVVPLTHSD 35
                                      7***************************999876 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.98
                                       T...TTTSBHHHHSGGGTTTECEBEEE CS
                    Semialdhyde_dh  35 r...saGkklaeavkaleegkdlkved 58 
                                           + G+ ++++v++ + g++++v d
  gi|242400019|ref|YP_002995444.1| 156 GasgKGGNFVEFMVQKAKRGEEIRVVD 182
                                       322223444444444555555555544 PP

>> EB_dh  Ethylbenzene dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   9.2e-05      0.18      89     150 ..     136     197 ..     102     220 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.2e-05
                                       ....STT--GGG.......................T-BTTB-EEEEEEETT-SS-EEEEESSTTSEE-GGGGG.. CS
                             EB_dh  89 chegarglpgapakeeatgsky.............mgtagsfvdlwqWkagrseplglvddgyvleerqndkgkt 150
                                       +++             + +++y              g++g+fv+ +  ka+r+e+  +vdd+++++ +++d  +t
  gi|242400019|ref|YP_002995444.1| 136 TKN-------------YSRKHYiirvaslygkagaSGKGGNFVEFMVQKAKRGEEIRVVDDQFMSPTYTKDVART 197
                                       333.............444444555555555555599****************************9998886655 PP

>> FadR_C  FadR C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00014      0.29       9      75 ..      38     103 ..      32     107 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00014
                            FadR_C   9 lniletlirldedkvpelvedllsaRtnisaiyireavknnpekslevlaevkeledkaeafaefDY 75 
                                       + il+tl  l + k   +++    +R++ ++ y ++a++ n+  +l+v + ++e+ d  + + + DY
  gi|242400019|ref|YP_002995444.1|  38 VTILDTLEVLKKLKPDVIINTAAYVRVDDAELYPEKAFQVNAIGALNVARVAEEI-DAVNVYISTDY 103
                                       679*******************************************998777776.56678888888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 1925.99
//
Query:       gi|242400020|ref|YP_002995445.1|  [L=473]
Description: Lipopolysaccharide O-side chain biosynthesis protein (O-antigen transpoter) [Thermococcus sibiricus MM 739]
Scores for complete 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-42  143.6  33.4    7.5e-42  143.6  33.4    3.0  3  Polysacc_synt    Polysaccharide biosynthesis protein
    3.4e-23   82.3  22.4    3.4e-23   82.3  22.4    2.6  2  Polysacc_synt_3  Polysaccharide biosynthesis protein
    3.3e-16   59.6  24.5    3.3e-16   59.6  24.5    4.2  4  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai
    0.00014   20.6  49.2    0.00014   20.6  49.2    2.0  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 !  143.6  33.4   1.7e-45   7.5e-42       2     273 ..       8     276 ..       7     277 .. 0.93
   2 ?    2.3  17.1      0.02        92      77     193 ..     292     408 ..     285     416 .. 0.84
   3 ?   -0.3   5.9      0.13   5.8e+02     154     194 ..     417     455 ..     412     472 .. 0.53

  Alignments for each domain:
  == domain 1  score: 143.6 bits;  conditional E-value: 1.7e-45
                     Polysacc_synt   2 lkgvivlllsqlitkllafvtlvylarilgpegfGlvalalaivtllviltdlGlnaalvreiakyrekkelvslil 78 
                                       +k+++vl++++++++ll+f ++ y+ar+lgp+++G++++ala+++++ +++++Gl+   vre+a+ ++   l +++l
  gi|242400020|ref|YP_002995445.1|   8 AKNMAVLFVARVVSMLLGFFYVMYTARYLGPANYGILSFALALTGIFGVIANFGLDPLTVREVARDKS---LARKYL 81 
                                       79*****************************************************************8...****** PP

                     Polysacc_synt  79 lnvllvllvlvllfllllliaa.flglpelavlylilalmllllvgvasfrrglfqglermkyaavsqvveqlsrvi 154
                                        n ++++l++ +l++l+  + + +lg pe ++ +++++ +  ++ g++ ++++++q++erm+  ++ q++++  +++
  gi|242400020|ref|YP_002995445.1|  82 ANGIVLKLLFGTLTFLIVSLVVnLLGYPEITIKVVYIITISIIIGGINNLFSSIYQAFERMEFMSIGQILQSALFLA 158
                                       **************99988866799999999999988888889********************************** PP

                     Polysacc_synt 155 lvliavflfldivaavlgavlaalvggivslavlrkkfrprfvilslklvrellsfsapltisslaillytyidsil 231
                                       + + a+ l+l +v+ ++++++ +l+ + +  ++   kf + +   +l  ++  +++++p+ +  +ai +y++ d+i+
  gi|242400020|ref|YP_002995445.1| 159 FAITAIKLGLNVVHFAMIYLIVNLIVLGYHVVITALKFLRLKIEVDLGFWKSVVREAWPFLGMNVAIMIYFRTDTIM 235
                                       ***********99999999999999977777777777756666666******************************* PP

                     Polysacc_synt 232 lglllgaeavGiYnaayqllvaisgllapivtaalfPvfsel 273
                                       l++l g++avGiYnaay+++ + s l+ +i  +++fPvfs++
  gi|242400020|ref|YP_002995445.1| 236 LSKLVGDTAVGIYNAAYKIADL-SLLVPSIGVSVVFPVFSRS 276
                                       *******************997.5566666666*******97 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.02
                     Polysacc_synt  77 illnvllvllvlvllfllll.liaaflglpelavlylilalmll.llvgvasfrrglfqglermkyaavsqvveqls 151
                                       i+++ +++l ++++++l++   i +++g+ +l+++ ++ +l+ +  + +v+ f++++    +++k ++  +v+  + 
  gi|242400020|ref|YP_002995445.1| 292 IKSACYIALPMAIIVTLFSNkIILVIFGQDYLNSISVLEILIWTsAVKYVSMFQGNIMVVINKQKFTFKVTVIMAIL 368
                                       5556677777888888888624556**************9999999*********************9999999999 PP

                     Polysacc_synt 152 rvilvliavflfldivaavlgavlaalvggivslavlrkkfr 193
                                        +il l+++   + +v+a++++++  ++g+ ++++++  +++
  gi|242400020|ref|YP_002995445.1| 369 NIILNLVLISRYS-YVGAAFATLITEITGLTIGFVFMS-RWG 408
                                       9999999999999.999999999999999988887766.564 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.13
                     Polysacc_synt 154 ilvliavflfldivaavlgavlaalvggivslavlrkkfrp 194
                                         v+ia++++ +i++ + + v+ a++ +++ ++v+   +  
  gi|242400020|ref|YP_002995445.1| 417 LIVAIATLIMTAILVKITSNVFKAVLLIFIIYLVVV--YLA 455
                                       456666666666666666666655555544444444..322 PP

>> Polysacc_synt_3  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.3  22.4   7.7e-27   3.4e-23       3     292 ..      33     326 ..      31     327 .. 0.90
   2 ?   -5.9  10.8         4   1.8e+04     112     177 ..     356     417 ..     326     459 .. 0.52

  Alignments for each domain:
  == domain 1  score: 82.3 bits;  conditional E-value: 7.7e-27
                   Polysacc_synt_3   3 ARLLspedFGvvaialvvislanlfvdmGlssaliqkedlteedlstvftfnlvlgllialvlfllapliasfynqp 79 
                                       AR L p+++G++++al++++++ +++++Gl+  ++++  ++++ +++     +vl ll+ +++fl+  l+ ++++ p
  gi|242400020|ref|YP_002995445.1|  33 ARYLGPANYGILSFALALTGIFGVIANFGLDPLTVREVARDKSLARKYLANGIVLKLLFGTLTFLIVSLVVNLLGYP 109
                                       9******************************************999999999************************* PP

                   Polysacc_synt_3  80 el.vtvlrvlalvlilsglssvqeallrrelkFkklfkitlvssvvgvivaivlAllglgvwALvigtllssllslv 155
                                       e+ ++v+ ++ +++i+ g++++ +++++   + + +++ +++ s++ +++ai++  lgl+v  +++  l+ +l+ l 
  gi|242400020|ref|YP_002995445.1| 110 EItIKVVYIITISIIIGGINNLFSSIYQAFERMEFMSIGQILQSALFLAFAITAIKLGLNVVHFAMIYLIVNLIVLG 186
                                       973689**********************9999999999***********************9888888888877765 PP

                   Polysacc_synt_3 156 ..llwlaskw.rprlkfslkslkelfsfglklllsnllnylarnldnlliGkvlssaaLGlYsvakrlaslpvaeit 229
                                         ++++a+k+ r++++++l   k++++  + +l+ n++ +++ ++d+++  k+++++a+G+Y+ a+++a+l +  + 
  gi|242400020|ref|YP_002995445.1| 187 yhVVITALKFlRLKIEVDLGFWKSVVREAWPFLGMNVAIMIYFRTDTIMLSKLVGDTAVGIYNAAYKIADLSL-LVP 262
                                       11344444433699999****************************************************9865.566 PP

                   Polysacc_synt_3 230 sviakVlfPalSrlqddkkklrely.lkvlrlialivlPiavglavvaellvkvllGsqWleav 292
                                       s+  +V+fP++Sr  +++  + + + + ++++  +i+lP+a+++ ++++ ++ v++G+ +l+++
  gi|242400020|ref|YP_002995445.1| 263 SIGVSVVFPVFSRSFKNNLTYFKFLsNLLIKSACYIALPMAIIVTLFSNKIILVIFGQDYLNSI 326
                                       77789*******97666666666550556788899*************************9886 PP

  == domain 2  score: -5.9 bits;  conditional E-value: 4
                   Polysacc_synt_3 112 kklfkitlvssvvgvivaivlAllglgvwALvigtllssllslvllwlaskwrprlkfslkslkel 177
                                       k +fk     +v+++i+ i+l l++ + ++ v    ++ ++ +  l++   +  r+  +++  + l
  gi|242400020|ref|YP_002995445.1| 356 KFTFK----VTVIMAILNIILNLVLISRYSYVGAAFATLITEITGLTIGFVFMSRWGYNFDLPRLL 417
                                       33333....445555555555555555555555554444444444444444444444444333333 PP

>> Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   6.7       0.4   1.8e+03      60     141 ..      16     103 ..      11     105 .. 0.63
   2 ?   -2.4  17.1         1   4.6e+03       2     112 ..     116     230 ..     115     270 .. 0.76
   3 ?   -0.5   0.7      0.26   1.1e+03      79     114 ..     280     315 ..     260     325 .. 0.62
   4 !   59.6  24.5   7.4e-20   3.3e-16       1     136 [.     328     455 ..     328     459 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.4
                   Polysacc_synt_C  60 iatvlallvvavlnlyalrrllgiklellrrllkpllaalvmgivvylllllllglllla............al.al 123
                                       +a v+++l+++++ +y +r l   ++     +l  +la  ++++v   ++++ l  l+              +   +
  gi|242400020|ref|YP_002995445.1|  16 VARVVSMLLGFFYVMYTARYLGPANY----GILSFALALTGIFGV---IANFGLDPLTVRevardkslarkyLAnGI 85 
                                       46667777777776666665555555....444556666666666...44444444443346788888887633688 PP

                   Polysacc_synt_C 124 llavlvgalvYlllllll 141
                                       +l++l+g l +l++ l+ 
  gi|242400020|ref|YP_002995445.1|  86 VLKLLFGTLTFLIVSLVV 103
                                       888888888888888765 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1
                   Polysacc_synt_C   2 LailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllli.plfgivGaaiatvlallvvavln.lya 76 
                                       + i+++sii+ ++++++ssi q+  r  ++ +  ++  ++ l++ +  i   +++v  a+  ++  l+v+ ++ ++ 
  gi|242400020|ref|YP_002995445.1| 116 VYIITISIIIGGINNLFSSIYQAFERMEFMSIGQILQSALFLAFAITAIkLGLNVVHFAMIYLIVNLIVLGYHvVIT 192
                                       57999********************************************5566678888888888888888886667 PP

                   Polysacc_synt_C  77 lrrllgikl....ellrrllkpllaalvmgivvyllllll 112
                                       + + l++k+     +++++++ +   l+m ++++   ++ 
  gi|242400020|ref|YP_002995445.1| 193 ALKFLRLKIevdlGFWKSVVREAWPFLGMNVAIM--IYFR 230
                                       7778888887777666666666666666666622..3333 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.26
                   Polysacc_synt_C  79 rllgiklellrrll.kpllaalvmgivvylllllllg 114
                                       +l+ +k+ l + l+   + +al m+i+v+l+ + ++ 
  gi|242400020|ref|YP_002995445.1| 280 NLTYFKF-LSNLLIkSACYIALPMAIIVTLFSNKIIL 315
                                       3455555.34444456677777888887755555554 PP

  == domain 4  score: 59.6 bits;  conditional E-value: 7.4e-20
                   Polysacc_synt_C   1 vLailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplfgivGaaiatvlallvvavlnlyal 77 
                                       vL il+++  + ++s++ ++i+  +++qk+++k++vi a++++ilnl+li ++++vGaa+at++++++++ + ++++
  gi|242400020|ref|YP_002995445.1| 328 VLEILIWTSAVKYVSMFQGNIMVVINKQKFTFKVTVIMAILNIILNLVLISRYSYVGAAFATLITEITGLTIGFVFM 404
                                       799**********************************************************************9998 PP

                   Polysacc_synt_C  78 rrllgiklellrrllkpllaalvmgivvylllllllgllllaalalllavlvgalvYll 136
                                       +r  g++++ l rll +++a+l+m ++   l++++ +++     +ll+ ++  ++vYl+
  gi|242400020|ref|YP_002995445.1| 405 SR-WGYNFD-LPRLLIVAIATLIMTAI---LVKITSNVFKA---VLLIFIIYLVVVYLA 455
                                       88.889996.6777789**********...66666666552...344444466667665 PP

>> MurJ  Lipid II flippase MurJ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6  49.2   3.1e-08   0.00014      52     438 ..      73     439 ..      65     459 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 3.1e-08
                              MurJ  52 aaefvrkvltllilvlllvtligilaapllirllatgfdeetlelavsllrillpylllvslsavfgavLnarkkFf 128
                                        ++++rk l   i++ ll+ +++ l   l+++ll ++       +++++++i+  ++++ ++  +f+++ +a ++  
  gi|242400020|ref|YP_002995445.1|  73 DKSLARKYLANGIVLKLLFGTLTFLIVSLVVNLLGYPE------ITIKVVYIITISIIIGGINNLFSSIYQAFERME 143
                                       56677777777788888888899999999999999987......********************************* PP

                              MurJ 129 apafsPvllNvsvIltllllanklgeeailaLaiGvliGgvlqllvqlpalkkagll.lkprfafrdeglkkflkll 204
                                        +++ ++l +  +  + ++ a klg + +       +i +++ l+v  ++++ + l+ l+++++      k +++ +
  gi|242400020|ref|YP_002995445.1| 144 FMSIGQILQSALFL-AFAITAIKLGLNVVHF----AMIYLIVNLIVLGYHVVITALKfLRLKIEVDLGFWKSVVREA 215
                                       ********996554.4455555666222222....234445555555555555555533444443444445666666 PP

                              MurJ 205 lptllgvsvsqlnllvdta.lAsflaegsvsilayadrilqlPlglfgvsistvlLPrlSrsakekdedevrdllsq 280
                                        p l  + + ++ + +dt+ l++ +  ++v i++ a  i+ l l + ++ +s v++P +Srs+k++ +  ++ l + 
  gi|242400020|ref|YP_002995445.1| 216 WPFLGMNVAIMIYFRTDTImLSKLVGDTAVGIYNAAYKIADLSLLVPSIGVS-VVFPVFSRSFKNNLTY-FKFLSNL 290
                                       6666666666677777765267779999999999999*****9999999987.789********99888.******* PP

                              MurJ 281 airltllllipvsfgllvlskpivsllferGnFseedveataevLaayalgLipyalvklllrvfYAredtktPvki 357
                                        i+    +++p++++++++s++i+ ++f  G+   +++  +  ++  +a+  +++   ++++      + +k  +k+
  gi|242400020|ref|YP_002995445.1| 291 LIKSACYIALPMAIIVTLFSNKIILVIF--GQDYLNSISVLEILIWTSAVKYVSMFQGNIMVV----INKQKFTFKV 361
                                       ****************************..877777777777777777777777766666665....6999****** PP

                              MurJ 358 slislvlnillsllllpplgvvglalatslsaliglvllyvllrkrlk.lteargiktflaklvvllalaavvilll 433
                                       ++i+++lni+l+l+l++++++vg a+at +  + gl++ +v++ +    ++  r++++ +a  ++++a++  +   +
  gi|242400020|ref|YP_002995445.1| 362 TVIMAILNIILNLVLISRYSYVGAAFATLITEITGLTIGFVFMSRWGYnFDLPRLLIVAIAT-LIMTAILVKI---T 434
                                       *******************************************9986635555555555555.4444433333...3 PP

                              MurJ 434 ssltq 438
                                       s++++
  gi|242400020|ref|YP_002995445.1| 435 SNVFK 439
                                       33333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (473 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1271  (0.0708907); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.71u 0.32s 00:00:01.03 Elapsed: 00:00:00.49
# Mc/sec: 2887.54
//
Query:       gi|242400021|ref|YP_002995446.1|  [L=306]
Description: Glycosyl transferase, family 2 [Thermococcus sibiricus MM 739]
Scores for 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-37  126.4   0.0    1.4e-36  125.8   0.0    1.4  1  Glycos_transf_2  Glycosyl transferase family 2
    8.3e-13   48.4   3.1    4.6e-12   46.0   3.1    1.9  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
      1e-12   48.5   0.0    1.4e-12   48.0   0.0    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
  ------ inclusion threshold ------
      0.012   16.1   0.0      0.023   15.2   0.0    1.5  1  Glyco_tranf_2_4  Glycosyl transferase family 2
      0.036   13.6   0.2       0.14   11.7   0.0    1.8  2  NTP_transferase  Nucleotidyl transferase
       0.09   11.7   0.3       0.12   11.2   0.3    1.1  1  Branch_AA_trans  Branched-chain amino acid transport protein
        0.1   11.9   0.0       0.17   11.2   0.0    1.5  1  Rhamno_transf    Putative rhamnosyl transferase


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 !  125.8   0.0   5.6e-40   1.4e-36       4     128 ..       1     124 [.       1     167 [. 0.83

  Alignments for each domain:
  == domain 1  score: 125.8 bits;  conditional E-value: 5.6e-40
                                       EEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--S CS
                   Glycos_transf_2   4 iptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraatg 80 
                                       +p+yN ek++++++es+l+q + pdfe+i++DDgS+D+++ei++++ k+d+r+r i +++n+G a+ +n+glr+a+g
  gi|242400021|ref|YP_002995446.1|   1 MPSYNHEKYIAQAIESVLNQ-TFPDFELIIIDDGSKDRSKEIIKAYEKKDKRIRAIFHKNNKGIARTMNEGLRKAKG 76 
                                       7*******************.******************************************************** PP

                                       SEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCH CS
                   Glycos_transf_2  81 dyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeier 128
                                       ++i+++ +Dd++ +d+lek ++++ek+++ vv+    +i+   ++   
  gi|242400021|ref|YP_002995446.1|  77 KFIALFSSDDVWVKDKLEKQLKFFEKNDDLVVWSEGLVIDAQGNPTGG 124
                                       **************************7777776665555555555554 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 !   46.0   3.1   1.8e-15   4.6e-12       7     233 ..       4     217 ..       1     236 [. 0.76

  Alignments for each domain:
  == domain 1  score: 46.0 bits;  conditional E-value: 1.8e-15
                   Glyco_tranf_2_2   7 raseerhyieerv...lqkakyydeeielivvddgSsekfleevssiidlnllv.ylkdeddkayslaaarNrGask 79 
                                       +++e+  yi + +   l++++   +++eli++ddgS +   e +++  ++ +++  + +++    + a++ N G  k
  gi|242400021|ref|YP_002995446.1|   4 YNHEK--YIAQAIesvLNQTF---PDFELIIIDDGSKDRSKEIIKAYEKKDKRIrAIFHKN--NKGIARTMNEGLRK 73 
                                       55554..68887744245444...7*********************999999886555664..4599********** PP

                   Glyco_tranf_2_2  80 aesdlvlFlDaDcfissDkfekilklitikklrenidaavvlpvvdlnkedsevlk.dvedltassrvledllaaks 155
                                       a++ ++    +D+ +  Dk+ek+lk      + e  d +vv++    ++++ +       +++  s+   +     +
  gi|242400021|ref|YP_002995446.1|  74 AKGKFIALFSSDDVWVKDKLEKQLK------FFEKNDDLVVWSEGLVIDAQGNPTGgTFTQMYGASKKK-KSGNLFE 143
                                       *************************......66677889999988888888775431223333333332.3333333 PP

                   Glyco_tranf_2_2 156 tlvkffapssssilinrraflevGGyDErfrGhgaEDfdlllRlakaikslekmpvellykarakslsnykGfrrfl 232
                                        l k     + s++++++ +  +  yDEr+  +  +D+ +++ la  +++   + +  +y+ + k+    +  r +l
  gi|242400021|ref|YP_002995446.1| 144 ELLKGNYIFGQSVILKKKNIKDI-TYDERL--KYLNDYKFMVDLAYNYEFYYIPEPLAMYRIHGKNSI-LSDRREWL 216
                                       44444444566666677766665.7*****..999***************988888889999999876.77778887 PP

                   Glyco_tranf_2_2 233 e 233
                                        
  gi|242400021|ref|YP_002995446.1| 217 R 217
                                       5 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 !   48.0   0.0   5.5e-16   1.4e-12       9     113 ..       2     102 ..       1     111 [. 0.89

  Alignments for each domain:
  == domain 1  score: 48.0 bits;  conditional E-value: 5.5e-16
                   Glyco_tranf_2_3   9 ptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralnealra 85 
                                       p++n e+++   +es+l+q+ p++e+++++d+s++   e +++   + +d r+r ++ ++n g    +r +ne+lr 
  gi|242400021|ref|YP_002995446.1|   2 PSYNHEKYIAQAIESVLNQTFPDFELIIIDDGSKDRSKEIIKAY--EKKDKRIRAIFHKNNKG---IARTMNEGLRK 73 
                                       89**********************************99999974..3345699**99988755...5889******* PP

                   Glyco_tranf_2_3  86 vksdlvllvDdDtvvePdtlkrllqff.l 113
                                       +k+++++l+ +D+v+ +d l+++l ff +
  gi|242400021|ref|YP_002995446.1|  74 AKGKFIALFSSDDVWVKDKLEKQLKFFeK 102
                                       **************************942 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 ?   15.2   0.0   8.9e-06     0.023       1      58 [.       4      62 ..       4     100 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 8.9e-06
                   Glyco_tranf_2_4  1 rneadiLpeflahhlalgf.d.rilvydndstDgtrailkelpevkllhvdksyederrq 58
                                      +n ++++ + ++  l+  f d +++++d++s+D++ +i+k++++ +  +++  +++ + +
  gi|242400021|ref|YP_002995446.1|  4 YNHEKYIAQAIESVLNQTFpDfELIIIDDGSKDRSKEIIKAYEKKD-KRIRAIFHKNNKG 62
                                      58999*********999995446****************9964422.2233333333333 PP

>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   5.5e-05      0.14      26     131 ..       2     105 ..       1     122 [. 0.84
   2 ?   -0.5   0.1       0.3   7.6e+02     175     197 ..     145     166 ..     134     181 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.5e-05
                                       EETTETETTHHHHHHHHHTT-SEE.EEEEETTTHHHHHHHHTTSGGGTSEEEEEEESS--BGGHHHHHTHHHHTTSS CS
                   NTP_transferase  26 pvlgkerliqatlsrlansgieei.ivvltqehsflveeqlkegskfgvevlialepegkgtAdAvalaaelledek 101
                                       p ++ e+ i + ++ ++n+ + +  ++++ +  + + +e +k+ +k + ++ +++ +++kg+A  +  +++ ++ ++
  gi|242400021|ref|YP_002995446.1|   2 PSYNHEKYIAQAIESVLNQTFPDFeLIIIDDGSKDRSKEIIKAYEKKDKRIRAIFHKNNKGIARTMNEGLRKAKGKF 78 
                                       66777788888999999988877626667777778888888888888899***********************9999 PP

                                       E..EEEEETTEEEESTTHHHHHHHHHTHSS CS
                   NTP_transferase 102 sdelvlvLggDhlikdayeeavkkaiekaa 131
                                          ++l+ ++D+++kd++e+ +k++++++ 
  gi|242400021|ref|YP_002995446.1|  79 ---IALFSSDDVWVKDKLEKQLKFFEKNDD 105
                                       ...79999****************998876 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.3
                                       ECCSEEEEETTHHHHHHHCCHHH CS
                   NTP_transferase 175 assGiYvfnsevllflakdleel 197
                                       + +G+Y+f ++v+l++ k++++ 
  gi|242400021|ref|YP_002995446.1| 145 LLKGNYIFGQSVILKK-KNIKDI 166
                                       5689********9999.666654 PP

>> Branch_AA_trans  Branched-chain amino acid transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.3   4.7e-05      0.12     299     359 ..     222     284 ..     220     302 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.7e-05
                   Branch_AA_trans 299 vseyFskllp.klsYkklvviftlisfllanlGltkiiavsvPvLvllYPlaia.livlslle 359
                                       vs yF ++   ++s k  +++   i+ + a+lG  ki+   +PvLv + P+++  li+l l+ 
  gi|242400021|ref|YP_002995446.1| 222 VSTYFLERYGdRISKKLRAMLYHRIASAYAQLGERKIVLSYLPVLVKIDPISLYpLILLGLVA 284
                                       678998877669***************************************996477776665 PP

>> Rhamno_transf  Putative rhamnosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   6.8e-05      0.17      48     123 ..      14      86 ..       8     185 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6.8e-05
                     Rhamno_transf  48 LpslraQtdqdFtllvligdtlPekfrerladlladlpqvrlivvppmehrealrevlreareaseaevlqfRlDd 123
                                       + s+ +Qt +dF+l++ i+d + ++ +e +++ +++ +++r i++++ + ++ +++  ++ r+a+ ++++ f  Dd
  gi|242400021|ref|YP_002995446.1|  14 IESVLNQTFPDFELII-IDDGSKDRSKEIIKAYEKKDKRIRAIFHKNNKGIARTMN--EGLRKAKGKFIALFSSDD 86 
                                       689**********976.799999*******************99988774443333..366777777777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       740  (0.0412739); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 2024.53
//
Query:       gi|242400022|ref|YP_002995447.1|  [L=365]
Description: pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Thermoanaerobacter [Thermococcus sibiricus MM 739]
Scores for complete 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-139  462.9   0.0   9.4e-139  462.7   0.0    1.0  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
      1e-12   47.9   0.0    2.2e-12   46.9   0.0    1.4  1  Aminotran_1_2    Aminotransferase class I and II
    2.9e-06   26.1   0.0    3.7e-06   25.7   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    8.7e-05   21.9   0.0     0.0002   20.7   0.0    1.6  1  Beta_elim_lyase  Beta-eliminating lyase
    0.00012   21.2   0.0    0.00018   20.6   0.0    1.2  1  Aminotran_5      Aminotransferase class-V


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 !  462.7   0.0  2.6e-142  9.4e-139       2     360 ..      14     359 ..      13     360 .. 0.97

  Alignments for each domain:
  == domain 1  score: 462.7 bits;  conditional E-value: 2.6e-142
                                       HHHHHHHHHHHHHTSS-SSSSHHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHH CS
                   DegT_DnrJ_EryC1   2 ikeeeleaveevlksgwltsgpeveeFEkafaaylgvkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatan 78 
                                       ikee+ +av++vl+sgw++ g+e ++FE++fa+ylg+++ai+v+sG++Al l+ +alg+g+gdeVI++s+tF++t+ 
  gi|242400022|ref|YP_002995447.1|  14 IKEEIDNAVQRVLESGWFILGEELKKFEEEFAKYLGANYAIGVNSGSDALYLSVKALGIGRGDEVITVSHTFISTVD 90 
                                       7899************************************************************************* PP

                                       HHHHTT-EEEEE-B-TTTSSB-GGGCGGG--TTEEEEEEB-GGGB---HHHHHHHHHHCT-EEEEE-TT-TT-EETT CS
                   DegT_DnrJ_EryC1  79 avlelgakpvfvDvdpdtynidpaaieaaitertkaIlpVhlyGqvadmdalkaiaakhglkvieDaAhAlGatykg 155
                                       a++++ga+pvfvD+dp+ty+id+++ie++it++tkaI+pVhlyG++admd + +ia+khgl+vieDa++A+Ga+ykg
  gi|242400022|ref|YP_002995447.1|  91 AIVRNGARPVFVDIDPETYTIDVNQIEEKITKKTKAIIPVHLYGHPADMDPIMEIAEKHGLYVIEDASQAHGAEYKG 167
                                       ***************************************************************************** PP

                                       EECCCSSSEEEEE-BTTSSS.-SSS-EEEEESTHHHHHHHHHHHBTTCECCTCSSCECCSS---B-B-BHHHHHHHH CS
                   DegT_DnrJ_EryC1 156 kkvGalgdaavfSFyptKnl.ttGeGGavvtndeelaekarvlrnhGlkrkaekryvgevelGynyrlteiqAAigl 231
                                       kkvG++g +a+fSFyptKnl ++G++Ga+vtnd+elae++r++rn+G+     k+y++++ +G+n+rl+eiqAAi++
  gi|242400022|ref|YP_002995447.1| 168 KKVGSIGHVACFSFYPTKNLgAYGDAGAIVTNDNELAERLRMMRNYGSP----KKYYHDF-IGVNSRLDEIQAAILR 239
                                       ***********************************************99....8******.**************** PP

                                       HHHCTHHHHHHHHHHHHHHHHHHHHTCCCCEESCGGTTSSSEEESCEEEEEHCCHHHCHHHHHHHHHHCCEE-B-SG CS
                   DegT_DnrJ_EryC1 232 aqLerldelvarRreiaelykeeLaelegtaelttpketkkhawhlyavlveeeaevkrdelvealkeegigtrvhy 308
                                       ++L++l+++++rRreia+ly+e L++ +  +++ +++++k h++hly+++ +     +rdel++ l ++gi+t++hy
  gi|242400022|ref|YP_002995447.1| 240 VKLKYLNRWNERRREIAKLYNEFLKDTGV-ITPVEKEWAK-HVYHLYVIRHK-----ERDELQQYLLRNGIKTQIHY 309
                                       **************************885.4556666666.**********9.....68****************** PP

                                       SCHGGGSCCHHHHHHCCCHC-HHHHHHHHHEEEEEGGTTGSHHHHHHHHHHH CS
                   DegT_DnrJ_EryC1 309 pnplhrqpvyaerkeeasgdlpnaerlaervlsLplypelteedvdrVveal 360
                                       p+p+h+q++y +   +   +lp++e++++++lsLp+ p+l++ +v+++++ +
  gi|242400022|ref|YP_002995447.1| 310 PVPVHLQKAYLDLGVK--VRLPVTEQISQEILSLPMFPHLSDTEVEKIARVV 359
                                       *************644..57****************************9877 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 !   46.9   0.0     6e-16   2.2e-12      46     330 ..      37     303 ..      28     311 .. 0.84

  Alignments for each domain:
  == domain 1  score: 46.9 bits;  conditional E-value: 6e-16
                                       HHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEB CS
                     Aminotran_1_2  46 lpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasyknilrlsggevvrypl 122
                                       l+++ee+ ak+lg        ++ a+ v sG++al   +++l  + +gde++  + t+ s  +++  +g+  v + +
  gi|242400022|ref|YP_002995447.1|  37 LKKFEEEFAKYLG--------ANYAIGVNSGSDALYLSVKALG-IGRGDEVITVSHTFISTVDAIVRNGARPVFVDI 104
                                       689**********........888*******************.********************************6 PP

                                       EETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSH CS
                     Aminotran_1_2 123 yseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsld 199
                                       + +e++++d++++ee++++      ktk i+   p +  G  a+ + + ++   a+k++l+++ D   a+++  + +
  gi|242400022|ref|YP_002995447.1| 105 D-PETYTIDVNQIEEKITK------KTKAII---PVHLYGHPADMDPIMEI---AEKHGLYVIEDASQAHGAEYKGK 168
                                       6.9****************......9****9...88889999999999999...***********887777766321 PP

                                       THHHHGGSTTSTTEEEEEES..SSTTSSGGG-EEEEEE.EHHHHHHHHHHHHHHTS..........SHHHHHHHHHH CS
                     Aminotran_1_2 200 avatranveeepnllivgsl..sKafGlaGeRvGyilg.naavvsqlrklsrpfls..........ssllqaavaaa 263
                                            ++   +   + + s+   K++G++G   G+i+  + ++++ lr + + +             s l ++ aa+
  gi|242400022|ref|YP_002995447.1| 169 ----KVGSIGH---VACFSFypTKNLGAYG-DAGAIVTnDNELAERLRMMRNYGSPkkyyhdfigvNSRLDEIQAAI 237
                                       ....2333333...445555557*******.788888835588888887776432233335777789********** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCS..CSSEEEEEETHHCHHHHHHHHHHTCTE CS
                     Aminotran_1_2 264 lsdallkqseleemrqrlqkrrkelrdeLaelglkvlasq..sgmflltdlsaetakelskkLleevgv 330
                                       l+ +l++ ++ +e+r++++k+  e+ +      ++ ++++   ++++l ++++++ +el++ Ll + g+
  gi|242400022|ref|YP_002995447.1| 238 LRVKLKYLNRWNERRREIAKLYNEFLKDTGV--ITPVEKEwaKHVYHLYVIRHKERDELQQYLLRN-GI 303
                                       ********************99999888644..44444444689**********99******9877.55 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0     1e-09   3.7e-06      56     231 ..      39     214 ..      36     303 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 1e-09
                                       HHHHHHHHHHT-SEEEEESSHHHHHHHHHHTT.S-TTEEEEEESTSSHHHHHHHHHTHHH.TTCEEEEES.TTSHHH CS
                   Cys_Met_Meta_PP  56 vleeriaaLeggeaalavssGmaAiaaailal.lkaGdeivvsddlYggtqrllkkvlkk.lgievkfvd.tsdlee 129
                                        +ee+ a+  g++ a+ v+sG  A+ +++ al +  Gde+++ ++ + +t + + +   + + ++++    t d+++
  gi|242400022|ref|YP_002995447.1|  39 KFEEEFAKYLGANYAIGVNSGSDALYLSVKALgIGRGDEVITVSHTFISTVDAIVRNGARpVFVDIDPETyTIDVNQ 115
                                       6899**************************996788************998766544444366666643314699** PP

                                       HHHHCCTTEEEEEEESS-TTTT----HHHHHHHHHHTT-EEEEEGTTTHTTTS-GGGGT..-SEEEEET..TTTTTC CS
                   Cys_Met_Meta_PP 130 lekaikentklvylEtptnpllkvvDiekiaklakkagvlvvvDntfaspllqrplklg..aDivvhSa..TKylgG 202
                                       +e++i+++tk++    p     + +D+  i+++a k+g+ v+ D++ a ++  +  k g    + + S   TK lg 
  gi|242400022|ref|YP_002995447.1| 116 IEEKITKKTKAII---PVHLYGHPADMDPIMEIAEKHGLYVIEDASQAHGAEYKGKKVGsiGHVACFSFypTKNLGA 189
                                       ***********96...777788889*************************9999999997556777775559****9 PP

                                       SSS--EEEEEESSCHHHHHHHHHHHHHHT CS
                   Cys_Met_Meta_PP 203 hsdvvaGvivvkgkeelkkelkflqnalG 231
                                        +d  aG+iv+++ +el+++l+++  + G
  gi|242400022|ref|YP_002995447.1| 190 YGD--AGAIVTND-NELAERLRMMR-NYG 214
                                       999..69999999.99999999875.333 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   5.7e-08    0.0002      34     242 ..      37     233 ..      34     286 .. 0.68

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 5.7e-08
                                       HHHHHHHHHHHTT-SEEEEES-HHHHHHHHHHHH-.-TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTT.TB CS
                   Beta_elim_lyase  34 vnrLedavaelfgkeaalfvpqGtaAnsillkill.qrgeevivtepahihfdetgaiaelagvklrdlknkea.Gk 108
                                        +++e+++a+++g+++a+ v +G  A  +++k+l   rg+evi    +h++  +  ai + +g++++ ++++ +  +
  gi|242400022|ref|YP_002995447.1|  37 LKKFEEEFAKYLGANYAIGVNSGSDALYLSVKALGiGRGDEVIT--VSHTFISTVDAI-VRNGARPVFVDIDPEtYT 110
                                       57899****************************9889*999975..69*******999.567888888886655499 PP

                                       E-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHHTS-CHHH CS
                   Beta_elim_lyase 109 mdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaakslgeivkem 185
                                       +d++++e++i+++ +      +i+    + +  G +  ++    + +ia+k+g+ ++ D+     a    g +v ++
  gi|242400022|ref|YP_002995447.1| 111 IDVNQIEEKITKKTK------AIIPV--HLY--GHPADMDP---IMEIAEKHGLYVIEDASQAHGAE-YKGKKVGSI 173
                                       ************444......44322..344..77776665...5667899***9999998655544.555555555 PP

                                       HTTSSEEEEESSSTT--SS-.EEEEE-HH....HHHHHHHHHHHHT-.--SSTHHHHH....... CS
                   Beta_elim_lyase 186 fsyvDsvtmslkKdllanvG.gvlafrddeledylaerveqrkylgg.glrqagvlaa......l 242
                                          v  +++  +K+l+a  + g ++++d+     laer ++++ +g+ + + ++++++       
  gi|242400022|ref|YP_002995447.1| 174 GH-VACFSFYPTKNLGAYGDaGAIVTNDN----ELAERLRMMRNYGSpKKYYHDFIGVnsrldeI 233
                                       43.33666667888888433555555555....47777777555554133345555555555554 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   4.9e-08   0.00018      43     181 ..      35     162 ..       7     169 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 4.9e-08
                                       HHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEE CS
                       Aminotran_5  43 kaveearekvaelinaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvi 119
                                       + +++ +e++a+ ++a+     i + ++++a+ l +++l+  + +gde+++++    +++    ++  r ga+ +++
  gi|242400022|ref|YP_002995447.1|  35 EELKKFEEEFAKYLGANY---AIGVNSGSDALYLSVKALG--IGRGDEVITVSHTFISTV----DAIVRNGARPVFV 102
                                       567788999999999997...6788888899999999994..9********998888877....5555899**99** PP

                                       EBETT.SCBEGGGHHHH--TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTT CS
                       Aminotran_5 120 pldee.geldldelekllnektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqavg 181
                                        +d+e  ++d++++e+++++ktk+++  h     G   +++ i ++a k+g +v+ Da+qa g
  gi|242400022|ref|YP_002995447.1| 103 DIDPEtYTIDVNQIEEKITKKTKAIIPVHL---YGHPADMDPIMEIAEKHGLYVIEDASQAHG 162
                                       *99762699*****************9996...79999999999999*************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       735  (0.040995); expected 358.6 (0.02)
Passed bias filter:                      595  (0.0331865); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.67u 0.30s 00:00:00.97 Elapsed: 00:00:00.51
# Mc/sec: 2144.94
//
Query:       gi|242400023|ref|YP_002995448.1|  [L=333]
Description: hypothetical protein TSIB_2052 [Thermococcus sibiricus MM 739]
Scores for complete 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   0.0    1.9e-08   34.6   0.0    1.3  1  Acetyltransf_6  Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_6  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   0.0   1.1e-12   1.9e-08       8     138 ..     172     298 ..     166     313 .. 0.86

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 1.1e-12
                    Acetyltransf_6   8 rrkrrkleelgevrfrvatdpedleallelfraqwarrpdvfadpltraflrdllaalaargalrlyvlrldgrpvA 84 
                                       rr+++++ ++g     v+ + +d+++ +  +++  +++  +  + +t + ++ l++++  ++ + l++++ +g+ vA
  gi|242400023|ref|YP_002995448.1| 172 RRSIKNAKSHG----LVIKQTDDFDTYMSIVEENLRKK-YGVKPTHTADEIKLLASRF--PEHIKLFAVYYKGEMVA 241
                                       66666677766....36688999******999888888.555699*************..***************** PP

                    Acetyltransf_6  85 valglrsgd.rlyywlggydpelaklspgllllweliedaaee..Glrrfdlgggde 138
                                       ++++++s++ ++++++++ ++  ++l + ++l+ +li ++  +   +++fd+g+++e
  gi|242400023|ref|YP_002995448.1| 242 GVIMYESNKkVAHAQYIASNEIGKELYALDYLFDYLINEYYSRinPRKYFDFGISTE 298
                                       ******9987899*****************************743699******987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2118.72
//
Query:       gi|242400024|ref|YP_002995449.1|  [L=308]
Description: hypothetical protein TSIB_2053 [Thermococcus sibiricus MM 739]
Scores for complete 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   34.3   0.9    4.8e-07   29.0   0.4    2.4  2  Glyco_hydro_130  beta-1,4-mannooligosaccharide phosphorylase
    8.5e-07   28.8   0.1      0.032   13.8   0.0    2.2  2  Glyco_hydro_32N  Glycosyl hydrolases family 32 N-terminal dom


Domain annotation for each model (and alignments):
>> Glyco_hydro_130  beta-1,4-mannooligosaccharide phosphorylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.4   5.3e-11   4.8e-07      66     120 ..     180     232 ..     171     240 .. 0.88
   2 !    3.2   0.0     0.004        35      70     119 ..     243     294 ..     233     301 .. 0.76

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 5.3e-11
                                       E.EEEEEEESSSSS-EE-SS---EE-TTS-B--EEEEEEEEETTEEEEEEE.EES CS
                   Glyco_hydro_130  66 slrigledlkdGikktlepeevvlpedkqellgveDPRvvkinskyyltYtgrdl 120
                                       s++i + ++kdGi ++++p  +v p+ ++e + +  PRv+k n+kyy+ Yt +++
  gi|242400024|ref|YP_002995449.1| 180 SYDIRYIESKDGITFERKPGTIVIPNNNTE-YRIGRPRVYKFNEKYYMFYT-KGV 232
                                       6789999********************999.78999***************.554 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.004
                                       EEEEESSSSS-EE-SS--.-E..E-TTS-B--EEEEEEEEETTEEEEEEE.EE CS
                   Glyco_hydro_130  70 gledlkdGikktlepeev.vl..pedkqellgveDPRvvkinskyyltYtgrd 119
                                       g++++ dGi++ ++  e+ +   p+ ++  + ++ P +++ ++k y+ Y g++
  gi|242400024|ref|YP_002995449.1| 243 GFAESFDGIHWVRKDHEIgITpsPRGWDSEMLCY-PSLIQYEDKIYMFYNGNG 294
                                       7999****99998887763331145555555555.9*************9876 PP

>> Glyco_hydro_32N  Glycosyl hydrolases family 32 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   3.5e-06     0.032      63     177 ..      80     197 ..      73     206 .. 0.84
   2 !   12.7   0.3   7.6e-06     0.069      16      88 ..     218     293 ..     215     300 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.5e-06
                                       GGCTTEEEEEEEEE-TT-EEEEEEEE-T...CS.EEEEEEEEESSTTSSEEE-TT--SB-.-TTTSTTSEEEEEEEE CS
                   Glyco_hydro_32N  63 efdsngafSGsavvdddklvllYTgnvk...ee.eqvQnlayskdkgreftkyeenpviaekpeentkhfRDPkvaw 135
                                        fd+ng+  G +v  ++k+ ++Y g +     +      la+skd+g++f+++++ p++++   + +  +R  + + 
  gi|242400024|ref|YP_002995449.1|  80 AFDDNGMILGDVVKYKNKIRMYYVGFQLvkkAKfLAFSGLAISKDEGYTFRRISNAPILDR--IDRELYIRAIHSVL 154
                                       5899*********************865655445778899*******************97..45677888888889 PP

                                       ETTTEEEEEEEECCT.TCCEEEEEEESSSSSEEEECCESEECC CS
                   Glyco_hydro_32N 136 kedgkwvmvvgaqdk.kkgkillYkskdlkewelaselleskk 177
                                        e+gkw++  +a++k +    + Y s d++  e ++ ++ ++k
  gi|242400024|ref|YP_002995449.1| 155 FENGKWRIWYAAGNKwEYIGGKPYPSYDIRYIESKDGITFERK 197
                                       999**********998888889999999988877777766655 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 7.6e-06
                                       EECTTEEEEEEEEETTSSSS-SBEEEEEEESSSSSB..EEEEEEE-SS.SGGCTTEEEEEEEEE-TT-EEEEEEEE CS
                   Glyco_hydro_32N  16 vyykgeYhlFYqynpkgavwgnisWghavSkDlvhW..eelpvalapd.eefdsngafSGsavvdddklvllYTgn 88 
                                        +++++Y++FY    k  ++ +   g a+S D +hW  +++++ ++p+ +  ds+     s ++ +dk++++Y gn
  gi|242400024|ref|YP_002995449.1| 218 YKFNEKYYMFYTKGVKRGNHFDYLPGFAESFDGIHWvrKDHEIGITPSpRGWDSEMLCYPSLIQYEDKIYMFYNGN 293
                                       469**********9999999999*************444567778887433455554457999**********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 1991.61
//
Query:       gi|242400025|ref|YP_002995450.1|  [L=247]
Description: hypothetical protein TSIB_2054 [Thermococcus sibiricus MM 739]
Scores for complete 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   53.4  17.4      4e-06   26.3   3.6    3.8  4  Hexapep     Bacterial transferase hexapeptide (six repeats)
    2.3e-06   27.2   9.3       0.37   10.6   0.1    4.6  4  Hexapep_2   Hexapeptide repeat of succinyl-transferase
     0.0011   19.6   0.0     0.0038   17.8   0.0    2.0  2  PglD_N      PglD N-terminal domain
  ------ inclusion threshold ------
       0.18   10.7   0.5        5.4    5.8   0.2    1.9  2  Fucokinase  L-fucokinase


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 !   15.4   0.1   2.5e-06     0.011       8      28 ..     115     135 ..     114     138 .. 0.95
   2 !   26.3   3.6   8.9e-10     4e-06       2      36 .]     145     179 ..     144     179 .. 0.96
   3 !   20.3   0.7   7.4e-08   0.00033       2      34 ..     181     213 ..     180     215 .. 0.95
   4 ?   -3.0   0.1       1.6   7.3e+03      19      24 ..     222     227 ..     220     228 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.5e-06
                                       EEE-TTEEEETTEEE-TTEEE CS
                           Hexapep   8 vlIgpfaviggnVkIGdnvkI 28 
                                       ++I+p + ig +V+IGdn+ I
  gi|242400025|ref|YP_002995450.1| 115 TFIHPTVFIGRDVEIGDNCFI 135
                                       68*****************98 PP

  == domain 2  score: 26.3 bits;  conditional E-value: 8.9e-10
                                       EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEES CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvigg 36 
                                       ++IG+nv+I++  +ig+  +I d++++++gv i g
  gi|242400025|ref|YP_002995450.1| 145 VKIGNNVVIWAKNHIGHRSVIKDHCYLASGVIISG 179
                                       79******************************976 PP

  == domain 3  score: 20.3 bits;  conditional E-value: 7.4e-08
                                       EEEETTEEE-TTEEEETTEEE-TTEEEETTEEE CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvi 34 
                                       + IG+ +++g ++ + + +kI ++++Ig+g+ +
  gi|242400025|ref|YP_002995450.1| 181 CEIGEYSFLGVNCSLNDRIKIAKDTIIGNGAIV 213
                                       78****************************987 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 1.6
                                       TEEE-T CS
                           Hexapep  19 nVkIGd 24 
                                       +V +G+
  gi|242400025|ref|YP_002995450.1| 222 GVYVGN 227
                                       566664 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 !   10.6   0.1   8.2e-05      0.37       9      25 ..     116     134 ..     115     135 .. 0.73
   2 !    5.4   0.1    0.0033        15      20      32 ..     141     153 ..     140     155 .. 0.74
   3 ?    3.5   0.0     0.014        62      20      32 ..     165     177 ..     157     178 .. 0.89
   4 !    9.8   1.0   0.00015      0.66       4      32 ..     183     213 ..     182     215 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 8.2e-05
                                       EE-TT-EES..EEE-TT-E CS
                         Hexapep_2   9 liGanagiG..vslGdncv 25 
                                       +i++   iG  v++Gdnc 
  gi|242400025|ref|YP_002995450.1| 116 FIHPTVFIGrdVEIGDNCF 134
                                       7888888866688888885 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0033
                                       E-TT-EE-TT-EE CS
                         Hexapep_2  20 lGdncvvgaGvvi 32 
                                       + +++++g++vvi
  gi|242400025|ref|YP_002995450.1| 141 IQRKVKIGNNVVI 153
                                       5677888888887 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.014
                                       E-TT-EE-TT-EE CS
                         Hexapep_2  20 lGdncvvgaGvvi 32 
                                       + d c +++Gv+i
  gi|242400025|ref|YP_002995450.1| 165 IKDHCYLASGVII 177
                                       6799*******98 PP

  == domain 4  score: 9.8 bits;  conditional E-value: 0.00015
                                       E-TT-EE-TT-EE.S.EEE-TT-EE-TT-EE CS
                         Hexapep_2   4 IGdnCliGanagi.G.vslGdncvvgaGvvi 32 
                                       IG+ +++G+n+     +++ ++ ++g+G ++
  gi|242400025|ref|YP_002995450.1| 183 IGEYSFLGVNCSLnDrIKIAKDTIIGNGAIV 213
                                       99**********6534666666666665544 PP

>> PglD_N  PglD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   8.4e-07    0.0038       1      77 [.      24     105 ..      24     106 .. 0.83
   2 ?   -2.3   0.0       1.6   7.1e+03       4       6 ..     206     208 ..     173     224 .. 0.60

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 8.4e-07
                            PglD_N   1 kivIiGaGGhgkvvadiieangeyeiigflDdnk...ktevegypvlgkaiellkslseeeyevviAIG...nnkvR 71 
                                       k+vIiG G  +   ++   +   ye+++f  +++   kt++ g+pv++     ++ + +e+y++++A+     n+vR
  gi|242400025|ref|YP_002995450.1|  24 KLVIIGTGETAEIAYEYFTDYSPYEVVAFAVEREyldKTKLFGLPVVPF-ENVEEIYPPEKYKAFVAVSytkLNRVR 99 
                                       79**************************999885344678889****95.455566678*********966667799 PP

                            PglD_N  72 kkiaek 77 
                                        +++++
  gi|242400025|ref|YP_002995450.1| 100 ARLYHE 105
                                       888875 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.6
                            PglD_N   4 IiG 6  
                                       IiG
  gi|242400025|ref|YP_002995450.1| 206 IIG 208
                                       333 PP

>> Fucokinase  L-fucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0    0.0046        21     299     331 ..     124     154 ..     117     157 .. 0.73
   2 ?    5.8   0.2    0.0012       5.4     281     337 ..     153     214 ..     150     238 .. 0.69

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.0046
                        Fucokinase 299 kgnvsigsnsivsglelesseeslelpddtilq 331
                                       + +v+ig n+++ + +  +   ++++ ++++++
  gi|242400025|ref|YP_002995450.1| 124 GRDVEIGDNCFIFEYNNIQR--KVKIGNNVVIW 154
                                       46778888888877777765..57788887776 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0012
                        Fucokinase 281 lessvsvgegsvie.hsslk......gnvsigsnsivsglelesseeslelpddtilqtlslkl 337
                                       +  + ++g +svi+ h+ l       g ++ig+ s++ g++ + ++ ++++ +dti+ + +++ 
  gi|242400025|ref|YP_002995450.1| 153 IWAKNHIGHRSVIKdHCYLAsgviisGFCEIGEYSFL-GVNCSLND-RIKIAKDTIIGNGAIVV 214
                                       5666778888888778888733333333457777777.66666553.58999999987666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); 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: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1738.59
//
Query:       gi|242400026|ref|YP_002995451.1|  [L=98]
Description: transcription regulator, SpoVT/AbrB family [Thermococcus sibiricus MM 739]
Scores for complete 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   37.4   0.3    3.6e-07   30.0   0.0    2.2  2  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
    2.9e-09   36.9   0.0      2e-05   24.6   0.0    2.1  2  AbrB-like       AbrB-like transcriptional regulator
    0.00012   22.0   0.3       0.45   10.6   0.1    2.2  2  TRAM            TRAM domain
    0.00051   20.1   0.2     0.0015   18.6   0.1    1.7  2  CSD2            Cold shock domain
     0.0013   18.5   0.1        0.1   12.4   0.1    2.2  2  eIF-1a          Translation initiation factor 1A / IF-1
  ------ inclusion threshold ------
       0.04   13.6   0.0       0.14   11.9   0.0    1.8  2  OB_RNB          Ribonuclease B OB domain
      0.078   13.2   0.1        4.2    7.6   0.0    2.1  2  CDC48_N         Cell division protein 48 (CDC48), N-terminal 


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 !    5.7   0.1    0.0055        14       7      29 ..      15      37 ..      11      41 .. 0.89
   2 !   30.0   0.0   1.4e-10   3.6e-07       2      30 ..      56      84 ..      55      96 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0055
                                      EEEEE-CCCHHHCCEECTCEEEE CS
                    MazE_antitoxin  7 gavriPkevrfelgireGdevel 29
                                      g++ iP+  r+  gi+eGd ve+
  gi|242400026|ref|YP_002995451.1| 15 GRIIIPAGTRKFYGINEGDFVEV 37
                                      7899******999******8887 PP

  == domain 2  score: 30.0 bits;  conditional E-value: 1.4e-10
                                      EETTEEEEEE-CCCHHHCCEECTCEEEEE CS
                    MazE_antitoxin  2 kvGnsgavriPkevrfelgireGdevele 30
                                      +vG+ ga +iPk++r+ ++i++Gd +e+ 
  gi|242400026|ref|YP_002995451.1| 56 RVGEQGALVIPKALREVMNIKPGDVLEVL 84
                                      89*************************96 PP

>> AbrB-like  AbrB-like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0   0.00013      0.33      29      64 ..       5      40 ..       4      44 .. 0.90
   2 !   24.6   0.0   7.9e-09     2e-05      21      63 ..      43      85 ..      40      91 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00013
                         AbrB-like 29 asYrvsVqknGnLliGsaYTkklgLkpGdefeIklg 64
                                      a+++v V+k G+++i +   k  g++ Gd  e+k+ 
  gi|242400026|ref|YP_002995451.1|  5 AKFHVVVHKIGRIIIPAGTRKFYGINEGDFVEVKII 40
                                      789************99988889*********9985 PP

  == domain 2  score: 24.6 bits;  conditional E-value: 7.9e-09
                         AbrB-like 21 skkkrGrkasYrvsVqknGnLliGsaYTkklgLkpGdefeIkl 63
                                      +++++ r+ +++++V + G L+i +a  + +++kpGd +e+ l
  gi|242400026|ref|YP_002995451.1| 43 ENNEKAREGTFTARVGEQGALVIPKALREVMNIKPGDVLEVLL 85
                                      567889********************************99976 PP

>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.1   0.00017      0.45      38      54 ..      30      44 ..      14      46 .. 0.79
   2 !   10.2   0.0   0.00022      0.57      15      48 ..      47      84 ..      43      90 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00017
                                      -T..TEEEEEEEEEE-S CS
                              TRAM 38 lpgIGdfVeVkItkvkr 54
                                      ++  GdfVeVkI k ++
  gi|242400026|ref|YP_002995451.1| 30 NE--GDFVEVKIIKYEN 44
                                      88..********99765 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00022
                                      E-.TTSEEEEEET.TEEEEETT-.......-T..TEEEEEE CS
                              TRAM 15 lsksegegiGrtdngkvvfvpgd.......lpgIGdfVeVk 48
                                      ++ +eg++++r+ ++ ++++p++       +p  Gd++eV 
  gi|242400026|ref|YP_002995451.1| 47 KA-REGTFTARVGEQGALVIPKAlrevmniKP--GDVLEVL 84
                                      44.9****************************..****996 PP

>> CSD2  Cold shock domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.1   5.9e-07    0.0015      12      54 ..      16      61 ..       9      65 .. 0.81
   2 ?   -0.9   0.0      0.73   1.9e+03      19      35 ..      71      87 ..      62      95 .. 0.62

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 5.9e-07
                              CSD2 12 difipkeklk..gakdGdkVvveiteypdk.knpeGevievLGkkg 54
                                      +i+ip+  +k  g ++Gd V v+i++y+++ k  eG+ +   G++g
  gi|242400026|ref|YP_002995451.1| 16 RIIIPAGTRKfyGINEGDFVEVKIIKYENNeKAREGTFTARVGEQG 61
                                      6999977655559**************95525599*9999999987 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.73
                              CSD2 19 klkgakdGdkVvveite 35
                                      + ++ k Gd+  v ++ 
  gi|242400026|ref|YP_002995451.1| 71 EVMNIKPGDVLEVLLLA 87
                                      44567778877766555 PP

>> eIF-1a  Translation initiation factor 1A / IF-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.1   4.1e-05       0.1      31      59 ..      19      48 ..      16      57 .. 0.84
   2 ?    4.3   0.0     0.014        36      30      51 ..      64      85 ..      51      93 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.1e-05
                                      E-HHHHCT----TT-EEEEEE-TT-TT.EE CS
                            eIF-1a 31 ipgkfRnkiwikrGdyVlVelspydlt.kG 59
                                      ip+  R++  i++Gd+V V++++y+ + k+
  gi|242400026|ref|YP_002995451.1| 19 IPAGTRKFYGINEGDFVEVKIIKYENNeKA 48
                                      5666788889**************977665 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.014
                                      EE-HHHHCT----TT-EEEEEE CS
                            eIF-1a 30 eipgkfRnkiwikrGdyVlVel 51
                                       ip+ +R  + ik+Gd+  V l
  gi|242400026|ref|YP_002995451.1| 64 VIPKALREVMNIKPGDVLEVLL 85
                                      589999999*******987765 PP

>> OB_RNB  Ribonuclease B OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   5.4e-05      0.14      34      55 ..      31      53 ..      22      55 .. 0.89
   2 ?   -1.2   0.0      0.63   1.6e+03      24      34 ..      64      74 ..      58      94 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.4e-05
                                      TT-EEEEEEEE.SSSEEEEEEEE CS
                            OB_RNB 34 hGDrVlvritk.gdrrgrregrv 55
                                       GD+V+v+i k   ++++reg++
  gi|242400026|ref|YP_002995451.1| 31 EGDFVEVKIIKyENNEKAREGTF 53
                                      6**********9999****9975 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.63
                                      E-HHHHTTS-T CS
                            OB_RNB 24 ippeqmkkamh 34
                                      + p+ ++++m+
  gi|242400026|ref|YP_002995451.1| 64 VIPKALREVMN 74
                                      55677888887 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 ?    7.6   0.0    0.0016       4.2      58      82 ..      15      39 ..       7      42 .. 0.81
   2 ?    3.6   0.0     0.029        73      15      37 ..      61      83 ..      49      85 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0016
                                      TEEEE-HHHHHHHT--TTEEEEEEE CS
                           CDC48_N 58 giIrmdgvtRknagvsiGdkVtVrk 82
                                      g I + + tRk  g++ Gd V+V+ 
  gi|242400026|ref|YP_002995451.1| 15 GRIIIPAGTRKFYGINEGDFVEVKI 39
                                      6677788899999999999999986 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.029
                                      TEEEE-HHHHHHHTS-TTSEEEE CS
                           CDC48_N 15 givridpedmeelglepgdvvei 37
                                      g  +i ++  e ++++pgdv+e+
  gi|242400026|ref|YP_002995451.1| 61 GALVIPKALREVMNIKPGDVLEV 83
                                      44456667777789999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 635.42
//
Query:       gi|242400027|ref|YP_002995452.1|  [L=73]
Description: hypothetical protein TSIB_2056 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1238  (0.0690501); expected 358.6 (0.02)
Passed bias filter:                      680  (0.0379274); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 531.05
//
Query:       gi|242400028|ref|YP_002995453.1|  [L=105]
Description: hypothetical protein TSIB_2057 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.25s 00:00:00.58 Elapsed: 00:00:00.39
# Mc/sec: 813.94
//
Query:       gi|242400029|ref|YP_002995454.1|  [L=273]
Description: hypothetical protein TSIB_2058 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-05   24.5  13.2     0.0007   19.6   7.5    2.7  2  bZIP_1          bZIP transcription factor
    9.4e-05   21.8   6.0    0.00013   21.3   6.0    1.2  1  HAP1_N          HAP1 N-terminal conserved region
     0.0014   18.1   9.1     0.0023   17.3   9.1    1.3  1  GAS             Growth-arrest specific micro-tubule binding
     0.0025   17.9   6.6     0.0025   17.9   6.6    2.8  2  bZIP_2          Basic region leucine zipper
  ------ inclusion threshold ------
      0.013   15.4   5.8      0.021   14.7   5.8    1.4  1  Wtap            WTAP/Mum2p family
      0.048   14.3   2.9       0.19   12.4   1.0    2.4  2  EST1            Telomerase activating protein Est1
      0.048   14.0  12.6       0.36   11.2   5.8    3.7  3  TSC22           TSC-22/dip/bun family
      0.054   12.3   2.3      0.074   11.8   2.3    1.1  1  UPF0061         Uncharacterized ACR, YdiU/UPF0061 family
      0.065   13.4   0.2       0.29   11.3   0.1    2.1  2  FYRC            F/Y rich C-terminus
      0.072   12.8   0.5       0.11   12.1   0.5    1.3  1  DUF4988         Domain of unknown function
      0.083   13.4   5.8       0.21   12.1   5.8    1.8  1  DUF16           Protein of unknown function DUF16
      0.093   12.8   0.1       0.55   10.3   0.0    2.3  2  HTH_20          Helix-turn-helix domain
       0.12   12.2   0.9       0.45   10.4   0.3    2.0  2  Colicin         Colicin pore forming domain
       0.13   12.5   2.3       0.23   11.6   2.0    1.5  1  STN1_2          CST, Suppressor of cdc thirteen homolog, comp
       0.16   10.2   0.5       0.25    9.6   0.5    1.2  1  SpecificRecomb  Site-specific recombinase
       0.19   12.0   6.8       0.17   12.1   5.1    1.7  1  Med30           Mediator complex subunit 30
       0.19   11.0   3.3       0.57    9.5   1.8    2.1  2  DctP            Bacterial extracellular solute-binding protei
       0.22   10.4   1.4       0.22   10.4   1.4    1.1  1  LMBR1           LMBR1-like membrane protein
       0.23   11.4   1.8       0.39   10.7   1.8    1.8  1  RUN             RUN domain
       0.24   11.3   3.9       0.57   10.1   0.0    3.0  2  HxlR            HxlR-like helix-turn-helix
       0.46    8.2   8.1       0.58    7.9   8.1    1.1  1  Nup88           Nuclear pore component
        0.5   11.5   3.8       0.64   11.1   0.6    2.3  2  DUF5320         Family of unknown function (DUF5320)
       0.57   10.1   7.6       0.18   11.7   3.5    2.1  2  Prefoldin       Prefoldin subunit
       0.58   10.2   3.4        1.1    9.3   3.1    1.6  1  ATG11           Autophagy-related protein 11
       0.66   10.3  10.6       0.54   10.6   9.1    1.6  2  OmpH            Outer membrane protein (OmpH-like)
        0.7   10.4  15.7        2.1    8.8  15.7    1.9  1  ZapB            Cell division protein ZapB
       0.72   10.0   6.5        1.6    8.9   6.5    1.6  1  Herpes_BLRF2    Herpesvirus BLRF2 protein
        1.2    9.6   3.5        0.4   11.1   0.5    1.8  1  DUF4140         N-terminal domain of unknown function (DUF414
        1.4    9.7   3.1        7.4    7.3   2.8    2.2  2  FliD_N          Flagellar hook-associated protein 2 N-terminu
        1.6    9.1  10.4          2    8.8   8.8    1.9  2  Uso1_p115_C     Uso1 / p115 like vesicle tethering protein, C
        1.6    8.5   8.8        9.8    5.9   5.5    2.6  3  FTO_CTD         FTO C-terminal domain
        1.6    9.0   8.4       0.95    9.7   5.6    2.1  2  XhlA            Haemolysin XhlA
        1.9    9.2  11.4         51    4.6  11.5    2.8  2  YabA            Initiation control protein YabA
        1.9    9.0  14.0        4.5    7.8  14.0    1.6  1  APG6_N          Apg6 coiled-coil region
        3.3    6.2   9.6        4.9    5.7   9.6    1.1  1  FapA            Flagellar Assembly Protein A
        4.1    7.0  11.5         11    5.7  11.5    1.6  1  GrpE            GrpE
        6.9    5.7   8.0         14    4.6   7.0    1.8  2  Atg14           Vacuolar sorting 38 and autophagy-related sub


Domain annotation for each model (and alignments):
>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   7.5   1.4e-06    0.0007      25      58 ..     184     217 ..     183     225 .. 0.85
   2 !    7.4   0.3    0.0096       4.6      33      59 ..     241     267 ..     229     268 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.4e-06
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  25 qaeieeLerrvkaLekeNksLkseleelkkevek 58 
                                        ++i+ Le+rvkaLe+eNk+L++++ +l+ e   
  gi|242400029|ref|YP_002995454.1| 184 DKRIKSLEERVKALEEENKELREKIRKLEMEKTA 217
                                       589************************9876554 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0096
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  33 rrvkaLekeNksLkseleelkkevekL 59 
                                       ++++ +++eN+ +++ +++ +k  ++L
  gi|242400029|ref|YP_002995454.1| 241 EKAEHFKEENERYREIVKRVNKVFAEL 267
                                       5899***************99987765 PP

>> HAP1_N  HAP1 N-terminal conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   6.0   2.6e-07   0.00013     164     237 ..     186     255 ..     141     268 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 2.6e-07
                            HAP1_N 164 qldlLqeklreLeeeNekLreeasqLktetdtlEekEqqLvldcveqlseanqqiaelseelarkleelerqqe 237
                                       ++  L e+++ LeeeN++Lre+  +L++e +++    ++L+l ++e ++ +++ +++     ++ +ee+er++e
  gi|242400029|ref|YP_002995454.1| 186 RIKSLEERVKALEEENKELREKIRKLEMEKTAYKTLNEKLLLMLTEIMELTDRALEK----AEHFKEENERYRE 255
                                       56789*******************************999999888877777665543....3333444444444 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 !   17.3   9.1   4.7e-06    0.0023      54     135 ..     185     266 ..     174     271 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.7e-06
                               GAS  54 qenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleqrfekvekerdelykkfe 130
                                       ++ k+l+e +k++eee++eLr+++++ e +k ++k l+++l  +  e+ +l+  +  + ++f++  + + e+ k+ +
  gi|242400029|ref|YP_002995454.1| 185 KRIKSLEERVKALEEENKELREKIRKLEMEKTAYKTLNEKLLLMLTEIMELTDRALEKAEHFKEENERYREIVKRVN 261
                                       6889************************************************************9999999999999 PP

                               GAS 131 aaiqe 135
                                       +++ e
  gi|242400029|ref|YP_002995454.1| 262 KVFAE 266
                                       88766 PP

>> bZIP_2  Basic region leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   6.6   5.2e-06    0.0025      26      54 .]     186     214 ..     183     214 .. 0.94
   2 ?    0.3   0.4       1.6   7.7e+02      32      51 ..     241     260 ..     234     262 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 5.2e-06
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_2  26 keeeleervkeLeeeNaqLrqkveqLeke 54 
                                       + ++leervk LeeeN +Lr+k+++Le e
  gi|242400029|ref|YP_002995454.1| 186 RIKSLEERVKALEEENKELREKIRKLEME 214
                                       7789**********************987 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.6
                                       HHHHHHHHHHHHHHHHHHHH CS
                            bZIP_2  32 ervkeLeeeNaqLrqkveqL 51 
                                       e++++ +eeN++ r+ v+ +
  gi|242400029|ref|YP_002995454.1| 241 EKAEHFKEENERYREIVKRV 260
                                       67888999999999888876 PP

>> Wtap  WTAP/Mum2p family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   5.8   4.4e-05     0.021      87     153 ..     186     247 ..     140     249 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.4e-05
                              Wtap  87 tGkrLmakcrvLeqENeELgkvleegrvakLeselalqkkfveelkkaleeleelleeleeevevlq 153
                                       + k+L ++++ Le+EN+EL      +++ kLe+e+ + k+++e+l   l+e+ el + + e +e ++
  gi|242400029|ref|YP_002995454.1| 186 RIKSLEERVKALEEENKEL-----REKIRKLEMEKTAYKTLNEKLLLMLTEIMELTDRALEKAEHFK 247
                                       568999*************.....78999*************************9999999998876 PP

>> EST1  Telomerase activating protein Est1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   1.0   0.00039      0.19      39     117 ..     154     229 ..     141     232 .. 0.76
   2 ?    1.1   0.0       1.2   5.9e+02      44      68 ..     241     265 ..     229     271 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00039
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH-B-HTT............-.....-----.----TTB--TTSHHH.HHH CS
                              EST1  39 rklklklvkflksaigfYqsliqrllsefelelssvlkvilksktklpekessekse.teseeeksslssseqksav 114
                                       +k ++ +++f +s  +f+ + ++r+ ++f+   ++ +k++++ +  l+e+ ++   e  ++ e+++ ++++ +++ +
  gi|242400029|ref|YP_002995454.1| 154 MKDRKGFRRFSTSQMAFWDKVLERITEIFR---DKRIKSLEERVKALEEENKE-LREkIRKLEMEKTAYKTLNEKLL 226
                                       444489**********************88...45566666566665555544.55558888888888888887888 PP

                                       HHH CS
                              EST1 115 lkl 117
                                       l+l
  gi|242400029|ref|YP_002995454.1| 227 LML 229
                                       777 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHHHHHHHHHHHHH-B CS
                              EST1  44 klvkflksaigfYqsliqrllsefe 68 
                                       +  +++k++ + Y+++++r  + f 
  gi|242400029|ref|YP_002995454.1| 241 EKAEHFKEENERYREIVKRVNKVFA 265
                                       4468999999999999999998886 PP

>> TSC22  TSC-22/dip/bun family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0       1.3   6.3e+02      10      25 ..      25      40 ..      24      64 .. 0.87
   2 ?   11.2   5.8   0.00075      0.36      22      50 ..     186     214 ..     178     233 .. 0.80
   3 ?    2.7   1.0      0.33   1.6e+02      22      44 ..     231     257 ..     220     263 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 1.3
                             TSC22 10 fAVrEeVevLkekIke 25
                                      f+ rE  + L+e I +
  gi|242400029|ref|YP_002995454.1| 25 FTARELSDRLREAISN 40
                                      7889999*****9986 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00075
                             TSC22  22 kIkeLeernseleeENslLkalaspeqle 50 
                                       +Ik Leer+++leeEN+ L++ + +  +e
  gi|242400029|ref|YP_002995454.1| 186 RIKSLEERVKALEEENKELREKIRKLEME 214
                                       69999999999999999999887665554 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.33
                             TSC22  22 kIkeLe....ernseleeENslLkala 44 
                                       +I eL+    e+ ++ +eEN+ +++++
  gi|242400029|ref|YP_002995454.1| 231 EIMELTdralEKAEHFKEENERYREIV 257
                                       67777611114678999*******876 PP

>> UPF0061  Uncharacterized ACR, YdiU/UPF0061 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   2.3   0.00015     0.074     321     437 ..     141     264 ..     122     271 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00015
                           UPF0061 321 eykevyttkYaqlmlkkLGleklsekekefdselleellelLqetqvdYneffveLaeskskkwrdeaesi.leese 396
                                       e ++++ + Y++ m+ + G+++ s+++  f +++le++ e++++++++  e  v+  e+++k+ r++ +++ +e+++
  gi|242400029|ref|YP_002995454.1| 141 EIRDILWEFYETQMKDRKGFRRFSTSQMAFWDKVLERITEIFRDKRIKSLEERVKALEEENKELREKIRKLeMEKTA 217
                                       566777788*************************************9765555554455566666666555033333 PP

                           UPF0061 397 .kelee......ekleeWrelYkklleele..edeleeraerlkkvNpkt 437
                                        k+l+e      +   e +el  ++le++e  ++e+e+ +e++k+vN  +
  gi|242400029|ref|YP_002995454.1| 218 yKTLNEklllmlT---EIMELTDRALEKAEhfKEENERYREIVKRVNKVF 264
                                       5445554554442...3333333444333311345555566666666555 PP

>> FYRC  F/Y rich C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1    0.0006      0.29       6      43 ..     152     190 ..     149     212 .. 0.83
   2 ?   -1.7   0.0       6.8   3.3e+03      23      38 ..     251     266 ..     243     269 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0006
                              FYRC   6 vtveedpdlsfeassatevWqkvlervqelrkeaglk.l 43 
                                        +++++++++  ++s  + W+kvler++e  +++++k l
  gi|242400029|ref|YP_002995454.1| 152 TQMKDRKGFRRFSTSQMAFWDKVLERITEIFRDKRIKsL 190
                                       678999999999*****************8888887633 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 6.8
                              FYRC  23 evWqkvlervqelrke 38 
                                       e ++++++rv++  +e
  gi|242400029|ref|YP_002995454.1| 251 ERYREIVKRVNKVFAE 266
                                       56899999*9997665 PP

>> DUF4988  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.5   0.00023      0.11       3      30 ..     185     212 ..     183     233 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00023
                           DUF4988   3 ddvndlkdrvaaleeqvkelndniealk 30 
                                       +++ +l++rv+alee+ kel ++i +l+
  gi|242400029|ref|YP_002995454.1| 185 KRIKSLEERVKALEEENKELREKIRKLE 212
                                       689*********************9996 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   5.8   0.00043      0.21      34      98 ..     176     238 ..     150     268 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00043
                                       HHHHHH..HHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHHHHHHH CS
                             DUF16  34 qrLkki..eakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetleliletLqkinkR 98 
                                       +r+++i  ++++++l+e++++le++ +++ eki++l+ e  a +     ++e l l+l  + ++ +R
  gi|242400029|ref|YP_002995454.1| 176 ERITEIfrDKRIKSLEERVKALEEENKELREKIRKLEMEKTAYKT----LNEKLLLMLTEIMELTDR 238
                                       445554446788999999999999999999999999999999888....444444444444444444 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0    0.0011      0.55      15      61 .]      16      81 ..      15      81 .. 0.90
   2 ?   -0.9   0.1       3.7   1.8e+03      45      56 ..     187     199 ..     177     212 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0011
                                      HHHHHSTCTTB-HHHHHHHHT....................S-HHHHHHHHHHHHHCTTEEEECTEE CS
                            HTH_20 15 ilraLaraegltaselaerld....................lskntlsyHLrvLeeagLvevvregr 61
                                      i+ ++ + +++ta el +rl+                    +sk+ +s+ Lr L   g+++++r++r
  gi|242400029|ref|YP_002995454.1| 16 IYEHF-GTGEFTARELSDRLReaisnpalianpaflkvyrrVSKKMISNDLRRLYAMGFLKRRRVKR 81
                                      66777.7889**********778888999999999999999***********************976 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 3.7
                                       HHHHHH.CTTEEE CS
                            HTH_20  45 LrvLee.agLvev 56 
                                       ++ Lee + ++e 
  gi|242400029|ref|YP_002995454.1| 187 IKSLEErVKALEE 199
                                       4444444444443 PP

>> Colicin  Colicin pore forming domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       1.6   7.5e+02      75      96 ..      48      69 ..      41      90 .. 0.81
   2 ?   10.4   0.3   0.00093      0.45      36      72 ..     176     212 ..     144     249 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.6
                           Colicin 75 aiakalesvdkkilaenlekls 96
                                      a  k  + v kk+++++l +l 
  gi|242400029|ref|YP_002995454.1| 48 AFLKVYRRVSKKMISNDLRRLY 69
                                      5678889999*******99984 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00093
                           Colicin  36 relaedarGkkirslsdalksfekikrnlnkkikakd 72 
                                       +++ e  r k+i+sl++ +k++e  +++l +ki++ +
  gi|242400029|ref|YP_002995454.1| 176 ERITEIFRDKRIKSLEERVKALEEENKELREKIRKLE 212
                                       67889999*************************8754 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 ?   11.6   2.0   0.00048      0.23      35     112 ..     188     266 ..     168     270 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00048
                                       HHHHSCGGSHHHHHHHHHHHHHHHHHHCT.-SEEEHHHHHT-HHHHHHHSSHHCH-SS---SS----SCHHHHHHHH CS
                            STN1_2  35 esssdasellkslvsllsekikefllekk.vqtfyqqeletveslvslaskpvkessaaeevevagesaskqirslf 110
                                       +s ++  ++l+++ + l eki+++ +ek+  +t++ + l +++++++l++++++++++ +e++ + +   k+++++f
  gi|242400029|ref|YP_002995454.1| 188 KSLEERVKALEEENKELREKIRKLEMEKTaYKTLNEKLLLMLTEIMELTDRALEKAEHFKEENERYREIVKRVNKVF 264
                                       4555555668999999********97765168899999********************9999999999********9 PP

                                       HH CS
                            STN1_2 111 ke 112
                                        e
  gi|242400029|ref|YP_002995454.1| 265 AE 266
                                       87 PP

>> SpecificRecomb  Site-specific recombinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.5   0.00051      0.25     151     233 ..     188     268 ..     165     269 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00051
                    SpecificRecomb 151 evlsvqiaalgle.pelrrrlpeleeeespFlalqrelealleayeaaledeeeaeedlkhlrvlldqcreavdrvr 226
                                       + l  +++al+ e +elr++ ++le+e++++ +l+++l  +l+++ +    +++a e+++h++   +  re+v+rv 
  gi|242400029|ref|YP_002995454.1| 188 KSLEERVKALEEEnKELREKIRKLEMEKTAYKTLNEKLLLMLTEIME---LTDRALEKAEHFKEENERYREIVKRVN 261
                                       5667788887654279*************************999998...778889999999999999999999999 PP

                    SpecificRecomb 227 khleenG 233
                                       k ++e G
  gi|242400029|ref|YP_002995454.1| 262 KVFAELG 268
                                       8777665 PP

>> Med30  Mediator complex subunit 30
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   5.1   0.00036      0.17      42     127 ..     182     267 ..     172     272 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00036
                             Med30  42 qaqdrkkklqeqlrqlkvlfkkLrliYekckencqgleevpiesLipyvdeekskreerkkseevkqlkeerkelle 118
                                       +  +r+k l+e++++l++  k+Lr    k++ + ++ + ++ + L+++++  +    + +k+e+ k+ +e+ +e+++
  gi|242400029|ref|YP_002995454.1| 182 FRDKRIKSLEERVKALEEENKELREKIRKLEMEKTAYKTLNEKLLLMLTEIMELTDRALEKAEHFKEENERYREIVK 258
                                       567899*******************9999999999999999888888888778888888999*************** PP

                             Med30 119 klkeknkqL 127
                                       +++++ ++L
  gi|242400029|ref|YP_002995454.1| 259 RVNKVFAEL 267
                                       **9998887 PP

>> DctP  Bacterial extracellular solute-binding protein, family 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.95   4.6e+02      98     118 ..      96     116 ..      80     120 .. 0.84
   2 ?    9.5   1.8    0.0012      0.57     214     260 ..     169     215 ..     162     234 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.95
                                       HHHHHHHHHTEEEEEEEEEEE CS
                              DctP  98 kllkslekkglkvLafwenGf 118
                                       +++ sl ++glk+La++ +G+
  gi|242400029|ref|YP_002995454.1|  96 EYRYSLSSQGLKYLAYMASGG 116
                                       6778999*********98886 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0012
                                       HHHHHS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSEE CS
                              DctP 214 ktwdsLpedlqaileeaakeatelqrklveeleeealqklkeagvev 260
                                       ++wd+  e++ +i+++   ++ e   k++ee+++e+++k+++  +e 
  gi|242400029|ref|YP_002995454.1| 169 AFWDKVLERITEIFRDKRIKSLEERVKALEEENKELREKIRKLEMEK 215
                                       79****************************************77765 PP

>> LMBR1  LMBR1-like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   1.4   0.00045      0.22     243     330 ..     167     258 ..      22     267 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00045
                             LMBR1 243 lrkyleeilkkvPeeiaeklksnenkteeslaklekqlikalqkrertekqwkrlleka.lelediik...nksske 315
                                            +++l+ + e +++k  ++ ++  ++l +++k+l ++++k e +++ +k+l ek  l l +i++    + +k 
  gi|242400029|ref|YP_002995454.1| 167 QMAFWDKVLERITEIFRDKRIKSLEERVKALEEENKELREKIRKLEMEKTAYKTLNEKLlLMLTEIMEltdRALEKA 243
                                       22444555556666666666668888999****************************99645555554100445555 PP

                             LMBR1 316 kefkssessrrgefa 330
                                       ++fk++ +++r+ ++
  gi|242400029|ref|YP_002995454.1| 244 EHFKEENERYREIVK 258
                                       555554445555444 PP

>> RUN  RUN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.8   0.00081      0.39      12      69 ..     158     220 ..      30     262 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00081
                               RUN  12 hGLrrsses........llralglkkessfwallekvakllteaesllsavqelealhsskkrsad 69 
                                        G+rr s+s        l+r  ++++ +++ +l e+v+ l +e ++l +++++le  ++++k   +
  gi|242400029|ref|YP_002995454.1| 158 KGFRRFSTSqmafwdkvLERITEIFRDKRIKSLEERVKALEEENKELREKIRKLEMEKTAYK---T 220
                                       57777777799999999999***************************************986...3 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0    0.0012      0.57      29      56 ..      54      81 ..      48     110 .. 0.83
   2 ?    0.2   1.3       1.4   6.6e+02      18      47 ..     184     215 ..     171     250 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0012
                                      TTS-HHHHHHHHHHHHHTTSEEEEEESS CS
                              HxlR 29 pkisqkmLaqrLreLeqdglierevype 56
                                        +s+km+++ Lr+L + g+++r+ +++
  gi|242400029|ref|YP_002995454.1| 54 RRVSKKMISNDLRRLYAMGFLKRRRVKR 81
                                      579******************9987765 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.4
                                       -EEHHHHHHHSTTS-..HHHHHHHHHHHHHTT CS
                              HxlR  18 kkRfselkralpkis..qkmLaqrLreLeqdg 47 
                                        kR + l++++  +   +k L +++r+Le ++
  gi|242400029|ref|YP_002995454.1| 184 DKRIKSLEERVKALEeeNKELREKIRKLEMEK 215
                                       45666666665555411355666666666543 PP

>> Nup88  Nuclear pore component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   8.1    0.0012      0.58     532     615 ..     173     266 ..     119     269 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0012
                             Nup88 532 qllsratqvlReeylkkqe.lv......reeiekrvkllkkqke...qqleelqsleeerkslseraeklAekyeei 598
                                       ++l+r t+++R++ +k  e  v      ++e+  +++ l+ +k+      e l  +  e  +l++ra ++Ae++ e 
  gi|242400029|ref|YP_002995454.1| 173 KVLERITEIFRDKRIKSLEeRVkaleeeNKELREKIRKLEMEKTaykTLNEKLLLMLTEIMELTDRALEKAEHFKEE 249
                                       57999999999998875431221111114678889999999886221344567778889999*************** PP

                             Nup88 599 kdkQeklvrrvkkvlkr 615
                                       +++  ++v+rv+kv+ +
  gi|242400029|ref|YP_002995454.1| 250 NERYREIVKRVNKVFAE 266
                                       *************9876 PP

>> DUF5320  Family of unknown function (DUF5320)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1       2.3   1.1e+03      37      63 ..      79     110 ..      59     128 .. 0.57
   2 ?   11.1   0.6    0.0013      0.64      43      99 .]     157     211 ..     136     211 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 2.3
                           DUF5320  37 fGr...grggrglgrgfgrrrraggarla..a 63 
                                       + r   +  g  + rg+ +r+  ++ +l   a
  gi|242400029|ref|YP_002995454.1|  79 VKRkvmTKSGKVCHRGYEYRYSLSSQGLKylA 110
                                       33333233388899999987776666665542 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0013
                           DUF5320  43 grglgrgfgrrrraggarlaaaetaeaskeeekelLeeqaeaLeeeleaikkrlkel 99 
                                       + g++r f  +++a++ ++  ++ +e   +++++ Lee+ +aLeee +++++++++l
  gi|242400029|ref|YP_002995454.1| 157 RKGFRR-FSTSQMAFWDKVL-ERITEIFRDKRIKSLEERVKALEEENKELREKIRKL 211
                                       345555.5555555555555.79999999**********************999875 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   3.5   0.00037      0.18      83     113 ..     184     214 ..     178     220 .. 0.92
   2 ?   -0.3   0.2         2   9.7e+02      12      26 ..     240     254 ..     215     268 .. 0.50

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00037
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  83 kkkleelekqlekleeeleklkdqittlean 113
                                       +k++++le+ ++ leee ++l+++i +le++
  gi|242400029|ref|YP_002995454.1| 184 DKRIKSLEERVKALEEENKELREKIRKLEME 214
                                       8*************************99986 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 2
                                       HHHHHHHHHHHHHHH CS
                         Prefoldin  12 laqlkeaieelektl 26 
                                       l++ +  +ee+e+ +
  gi|242400029|ref|YP_002995454.1| 240 LEKAEHFKEENERYR 254
                                       223333333333333 PP

>> ATG11  Autophagy-related protein 11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   3.1    0.0024       1.1       6      48 ..     185     224 ..     183     253 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0024
                             ATG11   6 krfkdveelakkltkenkskkekleklqseskekitlknfkvg 48 
                                       kr+k++ee +k l++enk  +ek++kl++   ek ++k++++ 
  gi|242400029|ref|YP_002995454.1| 185 KRIKSLEERVKALEEENKELREKIRKLEM---EKTAYKTLNEK 224
                                       799**************************...77777776654 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       4.4   2.1e+03      59     106 ..     136     182 ..     118     189 .. 0.49
   2 ?   10.6   9.1    0.0011      0.54      28     104 ..     186     266 ..     165     269 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 4.4
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              OmpH  59 eekeqelqkkeqelqqkqqqkaqelqkkqqellkpildkinkaikeva 106
                                       +++ +e+++   e+ + q ++++ +++ +   ++ + dk+ + i+e+ 
  gi|242400029|ref|YP_002995454.1| 136 KKAPEEIRDILWEFYETQMKDRKGFRRFSTSQMA-FWDKVLERITEIF 182
                                       4444456666666666333333444444444444.4455555554444 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0011
                                       H....HHHHHHHHHHHHHHHHHHHHHHHHTTTS..-HHHHHHHHHHHHHHHHHHHHHH..HHHHHHHHHHHHHHHHH CS
                              OmpH  28 f....kklqaeleakekelqklqeelqkkakkl.ekeekeqelqkkeqelqqkqqqka..qelqkkqqellkpildk 97 
                                       +    +++ ++le+++kel++++++l+   +++ + ++  ++l  + +e++++ +++    e  k+++e +++i+++
  gi|242400029|ref|YP_002995454.1| 186 RikslEERVKALEEENKELREKIRKLE---MEKtAYKTLNEKLLLMLTEIMELTDRALekAEHFKEENERYREIVKR 259
                                       143337888889999999999999997...3333388999999999999999666666778899999999999**** PP

                                       HHHHHHH CS
                              OmpH  98 inkaike 104
                                       +nk+ +e
  gi|242400029|ref|YP_002995454.1| 260 VNKVFAE 266
                                       **99876 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8  15.7    0.0044       2.1       7      60 ..     188     255 ..     184     268 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0044
                              ZapB   7 eqLEskiqkaidtitlLqmeieeLkeeneelkeenrele..............eeneqlkeereawqe 60 
                                       + LE++++++ ++ ++L+++i++L++e+ ++k  n++l               e+ e++kee e  +e
  gi|242400029|ref|YP_002995454.1| 188 KSLEERVKALEEENKELREKIRKLEMEKTAYKTLNEKLLlmlteimeltdralEKAEHFKEENERYRE 255
                                       679**************************999999999999*99999999999777777777776654 PP

>> Herpes_BLRF2  Herpesvirus BLRF2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   6.5    0.0032       1.6       5      61 ..     188     244 ..     184     263 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0032
                      Herpes_BLRF2   5 EdlaaelakLkvENkaLkkklkssvspkdeeLTaaekeavltstvgrlsskaakkie 61 
                                         l+++++ L+ ENk+L++k+++   +k    T +ek +++     +l+ +a +k e
  gi|242400029|ref|YP_002995454.1| 188 KSLEERVKALEEENKELREKIRKLEMEKTAYKTLNEKLLLMLTEIMELTDRALEKAE 244
                                       6799*********************************9988888899****999976 PP

>> DUF4140  N-terminal domain of unknown function (DUF4140)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.5   0.00083       0.4      60      95 ..     179     215 ..     134     220 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00083
                           DUF4140  60 reaeeee.lkalraeleeledelaaledelaaaearl 95 
                                       +e+++++ +k+l++++++le+e ++l+++++ +e ++
  gi|242400029|ref|YP_002995454.1| 179 TEIFRDKrIKSLEERVKALEEENKELREKIRKLEMEK 215
                                       4556665588888888888888888888888877654 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 ?    7.3   2.8     0.015       7.4      15      51 ..     196     232 ..     183     251 .. 0.70
   2 ?    1.5   0.0         1   5.1e+02       9      46 ..     229     266 ..     227     268 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.015
                                       XXXXXXXXXXXXXXXXXXXHHHHHHHHHHHHHHHHHH CS
                            FliD_N  15 aerakldkleqkktklewkqsayrelnsklsnlksal 51 
                                       a + + ++l +k  kle +++ay++ln kl  + +++
  gi|242400029|ref|YP_002995454.1| 196 ALEEENKELREKIRKLEMEKTAYKTLNEKLLLMLTEI 232
                                       3334445699*******************98888866 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 1
                                       XXXXXXXXXXXXXXXXXXXXXXXXXHHHHHHHHHHHHH CS
                            FliD_N   9 vkqlmkaerakldkleqkktklewkqsayrelnsklsn 46 
                                       ++++m+   + l+k e  k+++e  +++++ +n+ +++
  gi|242400029|ref|YP_002995454.1| 229 LTEIMELTDRALEKAEHFKEENERYREIVKRVNKVFAE 266
                                       56778888888888888888888888888888876665 PP

>> Uso1_p115_C  Uso1 / p115 like vesicle tethering protein, C terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   8.8    0.0041         2      46      91 ..     186     231 ..     179     244 .. 0.89
   2 ?    2.8   2.4       0.3   1.4e+02       6      59 ..     211     262 ..     210     267 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0041
                       Uso1_p115_C  46 qakeleaenkklekeleklraelkeekekekekqkEldDLLlllgD 91 
                                       + k+le+++k+le+e ++lr+++++ + ++ + ++  + LLl+l+ 
  gi|242400029|ref|YP_002995454.1| 186 RIKSLEERVKALEEENKELREKIRKLEMEKTAYKTLNEKLLLMLTE 231
                                       56899********************99999888999999****997 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.3
                       Uso1_p115_C   6 leseaaslkdeneklkaelqslskalesleqkeakkaaesqakeleaenkklek 59 
                                       le e++ +k++nekl   l +  + +  + +k   ++ +++++++++ +k+++k
  gi|242400029|ref|YP_002995454.1| 211 LEMEKTAYKTLNEKLLLMLTEIMELTDRALEK--AEHFKEENERYREIVKRVNK 262
                                       78889999999999998888888877777777..33344445555555554444 PP

>> FTO_CTD  FTO C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1      0.15        71     103     135 ..     136     168 ..     118     174 .. 0.89
   2 ?    5.9   5.5      0.02       9.8      66     125 ..     177     237 ..     167     254 .. 0.88
   3 ?    0.1   0.1       1.2   5.9e+02      88     118 ..     235     265 ..     231     267 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.15
                           FTO_CTD 103 leteeeildvllelLeerqelReewaartrska 135
                                       ++++eei d l e+ e++ + R+++++++ s++
  gi|242400029|ref|YP_002995454.1| 136 KKAPEEIRDILWEFYETQMKDRKGFRRFSTSQM 168
                                       567899*********************999876 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.02
                           FTO_CTD  66 klhd.yWkrkieeLeeawkkmElltrlvLdalrkasetleteeeildvllelLeerqelRe 125
                                       ++++ +  ++i++Lee  k++E   + + +++rk + ++ + +++ ++ll +L+e+ el +
  gi|242400029|ref|YP_002995454.1| 177 RITEiFRDKRIKSLEERVKALEEENKELREKIRKLEMEKTAYKTLNEKLLLMLTEIMELTD 237
                                       566668889****************999999*****999999*************999865 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 1.2
                           FTO_CTD  88 ltrlvLdalrkasetleteeeildvllelLe 118
                                       lt  +L+++++ +e++e+ +ei++ + +++ 
  gi|242400029|ref|YP_002995454.1| 235 LTDRALEKAEHFKEENERYREIVKRVNKVFA 265
                                       3566888899999999999999988888776 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   5.6     0.002      0.95       2      38 ..     174     212 ..     173     225 .. 0.86
   2 ?   -1.2   0.1       5.1   2.5e+03      30      39 ..     228     237 ..     214     262 .. 0.57

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.002
                              XhlA   2 ikerleri..etkldnleervdkleekaaeaeekiknle 38 
                                       ++er+++i  ++++++leerv+ lee + e +eki  le
  gi|242400029|ref|YP_002995454.1| 174 VLERITEIfrDKRIKSLEERVKALEEENKELREKIRKLE 212
                                       677888877789999999999999999999999998876 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 5.1
                              XhlA  30 aeekiknlee 39 
                                       ++++i++l++
  gi|242400029|ref|YP_002995454.1| 228 MLTEIMELTD 237
                                       4444444433 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       4.4   2.1e+03      67      81 ..      59      73 ..      29      74 .. 0.79
   2 ?    4.6  11.5      0.11        51       8      64 ..     185     251 ..     165     267 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 4.4
                                      XXXXXXXXXXXXXXX CS
                              YabA 67 segkenLarlYeeGF 81
                                      +   + L+rlY  GF
  gi|242400029|ref|YP_002995454.1| 59 KMISNDLRRLYAMGF 73
                                      445678999**9999 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.11
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH..........XXXXXXXXXXXX CS
                              YabA   8 dkleeleeqleelleeleelkeelaelleenaeLeleneklrerl..........eeeekkekekkk 64 
                                       +++++lee++++l ee +el+e++ +l  e ++ ++ nekl  +l           e+ ++ ke+++
  gi|242400029|ref|YP_002995454.1| 185 KRIKSLEERVKALEEENKELREKIRKLEMEKTAYKTLNEKLLLMLteimeltdraLEKAEHFKEENE 251
                                       4688889999999999999999999998888888888998888877776665443222222222223 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8  14.0    0.0093       4.5      44     112 ..     162     250 ..     117     264 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0093
                            APG6_N  44 k....................qdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeer 100
                                       +                     d+ +++lee++++le+e +el e++++le e+ + +   ++l   l ++ e  +r
  gi|242400029|ref|YP_002995454.1| 162 RfstsqmafwdkvleriteifRDKRIKSLEERVKALEEENKELREKIRKLEMEKTAYKTLNEKLLLMLTEIMELTDR 238
                                       04444444444445555555579999999999999999999999999999999998877777776666666666666 PP

                            APG6_N 101 fwreynelqlel 112
                                        +++   ++ e 
  gi|242400029|ref|YP_002995454.1| 239 ALEKAEHFKEEN 250
                                       665555555444 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   9.6      0.01       4.9     336     411 ..     184     260 ..     177     267 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.01
                              FapA 336 keklkeleeeleeleeeleklkkkikklpklka.ekqlesekkeqlkklletkeklkeeleeleeelkelkeelesk 411
                                       ++++k lee++++leee ++l++ki+kl+++k   k l+++ + +l ++ e   +  e+ e+ +ee ++  e +++ 
  gi|242400029|ref|YP_002995454.1| 184 DKRIKSLEERVKALEEENKELREKIRKLEMEKTaYKTLNEKLLLMLTEIMELTDRALEKAEHFKEENERYREIVKRV 260
                                       57889*************************88755556666667777777777777777777777766666655554 PP

>> GrpE  GrpE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7  11.5     0.022        11      25      99 ..     184     264 ..     167     271 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.022
                                       HHCTTSCCCCCCTTTTTTTTHHHHHHH..HHHHHHHHHHHHHHHHHHHHHHHHHHHHHC......HHH-HHHHHHHH CS
                              GrpE  25 ekevkelkekllrllaefenlrkrtek..ekeeakkfaiekfakdLLpvlDnleralksak....eneeekslleGv 95 
                                       +k++k+l+e+++ l++e ++lr++ +k    + a+k+ +ek++  L ++++  +ral+ a+    ene+  ++++ v
  gi|242400029|ref|YP_002995454.1| 184 DKRIKSLEERVKALEEENKELREKIRKleMEKTAYKTLNEKLLLMLTEIMELTDRALEKAEhfkeENERYREIVKRV 260
                                       35788888888888888888888776521344678888899999999999888888887766433444444666655 PP

                                       HHHH CS
                              GrpE  96 emtl 99 
                                       + + 
  gi|242400029|ref|YP_002995454.1| 261 NKVF 264
                                       5544 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 ?   -0.4   0.0         1     5e+02     229     278 ..       4     111 ..       1     113 [. 0.64
   2 ?    4.6   7.0     0.029        14      22      93 ..     185     256 ..     172     265 .. 0.66

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1
                             Atg14 229 shyLsirLPaeltlphscqpi........................................................ 249
                                       s++L+ r +  +++ h+ +                                                          
  gi|242400029|ref|YP_002995454.1|   4 SEILDFRTLLTIIYEHFGTGEftarelsdrlreaisnpalianpaflkvyrrvskkmisndlrrlyamgflkrrrvk 80 
                                       67888888888888888886677777777777777777777777777777777666666666666666666655554 PP

                             Atg14 250 rplfiekslpkls..peteseflegvalLay 278
                                       r+ + ++    +   +  +s +++g+++Lay
  gi|242400029|ref|YP_002995454.1|  81 RKVMTKSGKVCHRgyEYRYSLSSQGLKYLAY 111
                                       4443333333333567777777777777776 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.029
                             Atg14  22 erlyelrerlaklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsql 93 
                                       +r+ +l er++ l +e+++l++ki k++ +k++ ++l++k+    + + el  +  ++ e+ +e +++ ++ 
  gi|242400029|ref|YP_002995454.1| 185 KRIKSLEERVKALEEENKELREKIRKLEMEKTAYKTLNEKLLLMLTEIMELTDRALEKAEHFKEENERYREI 256
                                       478888999999999999999999988888885555555554444444444444444444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2004  (0.111774); expected 358.6 (0.02)
Passed bias filter:                      839  (0.0467957); expected 358.6 (0.02)
Passed Vit filter:                       188  (0.0104858); 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: 0.76u 0.37s 00:00:01.12 Elapsed: 00:00:00.53
# Mc/sec: 1542.35
//
Query:       gi|242400030|ref|YP_002995455.1|  [L=330]
Description: Glycosyl transferase 2 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-21   76.2   1.8    4.6e-10   39.6   0.3    2.2  2  Glycos_transf_2  Glycosyl transferase family 2
      4e-14   53.1   0.0    9.8e-07   28.9   0.0    2.3  2  Glyco_tranf_2_3  Glycosyltransferase like family 2
    1.8e-06   28.0   0.0    2.8e-06   27.4   0.0    1.3  1  Glyco_trans_2_3  Glycosyl transferase family group 2
    0.00089   19.0   0.2     0.0023   17.6   0.2    1.7  1  Glyco_tranf_2_5  Glycosyltransferase like family
  ------ inclusion threshold ------
      0.015   14.8   0.0       0.14   11.7   0.0    2.1  1  Glyco_transf_21  Glycosyl transferase family 21


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   0.3   1.3e-13   4.6e-10       1      57 [.       7      62 ..       7      75 .. 0.89
   2 !   36.1   0.1   1.5e-12   5.3e-09      52     129 ..     100     181 ..      83     229 .. 0.79

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 1.3e-13
                                      EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEE CS
                   Glycos_transf_2  1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvr 57
                                      s++i   N +    e+les+ ++ +yp+++++vvD+gS+D++v+ ++e+a+++ rv 
  gi|242400030|ref|YP_002995455.1|  7 SIIILNWNGWRDTIECLESVYRI-TYPNYDVVVVDNGSQDDSVQKIKEYAEGKVRVN 62
                                      89*********************.**************************8666555 PP

  == domain 2  score: 36.1 bits;  conditional E-value: 1.5e-12
                                       C-TTEEEEEESSS-HHHHHHHHHHHH--SS....EEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCC CS
                   Glycos_transf_2  52 edprvrvirreenvGkagalnaglraatgd....yilflDaDdepdpdwleklvealekdgadvvlgqrprifgetd 124
                                        d r ++i+++ n G+ag+ n g++ a +     yil+l+ D+++dp++l +lv+ +e d++ +++g   ++ + ++
  gi|242400030|ref|YP_002995455.1| 100 VDRRMILIKNKDNYGFAGGNNIGIKFALSVlnpeYILLLNNDTVVDPKFLDELVKVAESDEKIGIVGPKIYYYDYKG 176
                                       478999*********************9999999*************************999888887776666655 PP

                                       CCCHC CS
                   Glycos_transf_2 125 eiern 129
                                       +    
  gi|242400030|ref|YP_002995455.1| 177 RSDVI 181
                                       55544 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   3.3e-08   0.00012       1      57 [.       4      57 ..       4      67 .. 0.88
   2 !   28.9   0.0   2.7e-10   9.8e-07      79     212 ..     123     264 ..      68     282 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 3.3e-08
                   Glyco_tranf_2_3  1 prdlavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalp 57
                                      pr +++++ ++n  ++  e+les+ +++yp+++vvvv+++s+++ ++ ++e a+  +
  gi|242400030|ref|YP_002995455.1|  4 PR-VSIIILNWNGWRDTIECLESVYRITYPNYDVVVVDNGSQDDSVQKIKEYAE--G 57
                                      67.****************************************99999999543..3 PP

  == domain 2  score: 28.9 bits;  conditional E-value: 2.7e-10
                   Glyco_tranf_2_3  79 lnealravksdlvllvDdDtvvePdtlkrllqff.ltpkvgavgtpvfll.n.rs...........tlvsalgalef 141
                                       ++ al+  +++++ll++ Dtvv+P +l+ l+ ++  ++k+g+vg + + + + ++           +++  + +   
  gi|242400030|ref|YP_002995455.1| 123 IKFALSVLNPEYILLLNNDTVVDPKFLDELVKVAeSDEKIGIVGPKIYYYdYkGRsdviwfdggriHWWWLWAYS-- 197
                                       4455667889************************9999******8887752433345555555555557777663.. PP

                   Glyco_tranf_2_3 142 aerhlrflaarralgvltlnGsgslirrevlkelegldplflltdDyelglrlrragfrtayvpgaavrev 212
                                            +  + ++  +v  ++G+ +++ ++++k l  +   f   +D+elg  + r g r+  vp + v++ 
  gi|242400030|ref|YP_002995455.1| 198 --SSKDSERDTHPRNVEWITGAALMMNTKYFKTL-NSKY-FFGNEDVELGIKANRKGLRVICVPSSKVWHK 264
                                       ..455566667778888889**************.4444.6777*************************98 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 !   27.4   0.0   7.8e-10   2.8e-06       1     135 [.     134     275 ..     134     324 .. 0.69

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 7.8e-10
                   Glyco_trans_2_3   1 iilllDaDtvlppdclreiaaela.spevaivqgpvlvm....nvanwleelaalffaedhgkdilvrealgr.vvp 71 
                                       +illl  Dtv++p +l e++   + + +++iv  +++++    ++  ++     +++  +++ + ++++ + r + p
  gi|242400030|ref|YP_002995455.1| 134 YILLLNNDTVVDPKFLDELVKVAEsDEKIGIVGPKIYYYdykgRSDVIWFDGGRIHW--WWLWAYSSSKDSERdTHP 208
                                       79**********************558999999999985576434444555555555..555555555544442777 PP

                   Glyco_trans_2_3  72 .....svGsgaflrrsalqevggwdgdessvsEDfdmglrlqrkGyrvrfvpeslvkek.spltlraalr 135
                                            ++G+  + + + ++ +   +++ ++  ED ++g+++ rkG+rv+ vp+s v+ k + ++ +a ++
  gi|242400030|ref|YP_002995455.1| 209 rnvewITGAALMMNTKYFKTL---NSKYFFGNEDVELGIKANRKGLRVICVPSSKVWHKvGVSRKKAKVN 275
                                       8888899************99...44557789**********************7755515555555444 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 !   17.6   0.2   6.4e-07    0.0023      53     195 ..     131     269 ..      93     282 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 6.4e-07
                   Glyco_tranf_2_5  53 dakykvYlhqDvliinkdfikdlleiFkkdkkiGmiG..vvGakslpesgvww.eskk.kvgkvietskeeakelra 125
                                       + +y + l++D++ + ++f+ +l+++ ++d+kiG++G  +   ++  +s v+w ++ + +   ++ +     +  ++
  gi|242400030|ref|YP_002995455.1| 131 NPEYILLLNNDTV-VDPKFLDELVKVAESDEKIGIVGpkIYYYDYKGRSDVIWfDGGRiHWWWLWAY-----SSSKD 201
                                       5689999999986.799********************776777888888899944332233344444.....44444 PP

                   Glyco_tranf_2_5 126 eeeeseyeeVeaidGllmatqydv..pwredlftgfhfYdvsqslefekagykvvVpnqekpWvihdsgfkk 195
                                       +e+++++++Ve i G  +++ +    + +++ f  f   dv+  ++ +++g +v+    +k+W  h+ g ++
  gi|242400030|ref|YP_002995455.1| 202 SERDTHPRNVEWITGAALMMNTKYfkTLNSKYF--FGNEDVELGIKANRKGLRVICVPSSKVW--HKVGVSR 269
                                       67899**********766654433226666644..4456****************99999***..7766444 PP

>> Glyco_transf_21  Glycosyl transferase family 21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   3.8e-05      0.14      30     157 ..     131     267 ..     123     277 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.8e-05
                   Glyco_transf_21  30 kydllvisDsdvrvkpdyLeellaaled.pkvglVtslpvgsdakg....laaaleaaflntlagvlqa.kls.... 96 
                                       + ++++++  d++v+p++L+el++  e+ +k+g+V   ++++d kg    ++ +  + +   l+++ ++ + +    
  gi|242400030|ref|YP_002995455.1| 131 NPEYILLLNNDTVVDPKFLDELVKVAESdEKIGIVGPKIYYYDYKGrsdvIWFDGGRIHWWWLWAYSSSkDSErdth 207
                                       568999999**************96654499****998888888883344333333333222233333231112233 PP

                   Glyco_transf_21  97 ..glgfavGksmalrreaLeaiGGfealadeLAeDyalgkllraaGlkvvlspapiaqtsvpr 157
                                          ++ ++G++++++++ ++ +     ++    eD +lg   +++Gl+v+++p   ++++v+ 
  gi|242400030|ref|YP_002995455.1| 208 prNVEWITGAALMMNTKYFKTLNSKYFFGN---EDVELGIKANRKGLRVICVPSSKVWHKVGV 267
                                       448899999999999999999976666665...899999999999999999999888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); 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: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2153.06
//
Query:       gi|242400031|ref|YP_002995456.1|  [L=564]
Description: hypothetical protein TSIB_2060 [Thermococcus sibiricus MM 739]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (564 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       884  (0.0493056); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); 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):               0  [number of targets reported over threshold]
# CPU time: 0.67u 0.29s 00:00:00.96 Elapsed: 00:00:00.48
# Mc/sec: 3519.51
//
Query:       gi|242400032|ref|YP_002995457.1|  [L=402]
Description: Glycosyl transferase, group 1 [Thermococcus sibiricus MM 739]
Scores for complete 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  134.7   0.0    3.7e-39  134.0   0.0    1.3  1  Glycos_transf_1  Glycosyl transferases group 1
    8.1e-28   97.5   0.1    1.6e-27   96.6   0.1    1.5  1  Glyco_trans_1_4  Glycosyl transferases group 1
    9.5e-18   64.8   0.0    1.5e-17   64.1   0.0    1.4  1  Glyco_transf_4   Glycosyltransferase Family 4
    2.5e-10   41.0   0.0    3.7e-10   40.5   0.0    1.3  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
      5e-08   33.2   0.0    1.4e-07   31.8   0.0    1.7  2  Glyco_trans_1_2  Glycosyl transferases group 1
    5.3e-08   33.0   0.0    1.4e-07   31.7   0.0    1.7  1  Glyco_trans_4_2  Glycosyl transferase 4-like


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.0   0.0   1.2e-42   3.7e-39       6     171 ..     219     383 ..     214     384 .. 0.98

  Alignments for each domain:
  == domain 1  score: 134.0 bits;  conditional E-value: 1.2e-42
                                       HHHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCH CS
                   Glycos_transf_1   6 rkklgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevs 82 
                                       r++l+++ +kkiil v++l+++Kg+++li+a++++    +++v l+i+G+g+ +kel+ ++++l+l++ v + g ++
  gi|242400032|ref|YP_002995457.1| 219 REQLNLPRDKKIILNVANLVPVKGQSYLIEAMEKVVSH-RKDVMLIIVGDGPLKKELEIQIKKLNLENYVMLAGAKP 294
                                       78999******************************998.************************************** PP

                                       SSSHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSH CS
                   Glycos_transf_1  83 redleellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairkllede 159
                                       ++++  ++++ad+fvlps sEg ++v  EA+ +glp + +++gg++e++++++ Gll++p ++e lae+i k+le+e
  gi|242400032|ref|YP_002995457.1| 295 HSEILLWMNAADLFVLPSLSEGNPTVMFEALGVGLPFVGTAVGGVPEIIVSEDYGLLCPPADPECLAEKILKALEKE 371
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHH CS
                   Glycos_transf_1 160 elrerlgenark 171
                                        +re+++++a++
  gi|242400032|ref|YP_002995457.1| 372 WDREKIRKYAEQ 383
                                       *********986 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 !   96.6   0.1   5.2e-31   1.6e-27       2     133 ..     229     369 ..     228     370 .. 0.90

  Alignments for each domain:
  == domain 1  score: 96.6 bits;  conditional E-value: 5.2e-31
                                       EEEEEES---GG.GTHHHHHHHHHHHH.H..HEEEEEES---...HHHHHHHT..T-T.TEEEE---..THHHHHHH CS
                   Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkk..dvrlvivGdgp.rpeeleelaa..gleerveftGfv..edlaella 71 
                                       ++il v +l  +vkg+ +l+ea++++ ++  dv l+ivGdgp + +ele +++  +le+ v ++G    +++  +++
  gi|242400032|ref|YP_002995457.1| 229 KIILNVANL-VPVKGQSYLIEAMEKVVSHrkDVMLIIVGDGPlK-KELEIQIKklNLENYVMLAGAKphSEILLWMN 303
                                       78999****.578**********777744345**********65.699988866899999*****998778****** PP

                                       H-SEEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHHHH CS
                   Glyco_trans_1_4  72 aadvfvaPs..egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailrLle 133
                                       aad+fv+Ps  eg + ++ Ea+ +glp V t+vgg++e++  ++ gll+pp dpe lae+il+ le
  gi|242400032|ref|YP_002995457.1| 304 AADLFVLPSlsEGNPTVMFEALGVGLPFVGTAVGGVPEIIvsEDYGLLCPPADPECLAEKILKALE 369
                                       **************************************99977889****************9987 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.1   0.0   5.1e-21   1.5e-17      54     167 ..      97     206 ..      60     209 .. 0.77

  Alignments for each domain:
  == domain 1  score: 64.1 bits;  conditional E-value: 5.1e-21
                    Glyco_transf_4  54 llrslaflrrlrrllkre.kpDvvHahspaalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerr 129
                                        l +  f+r+   + ++  ++D++Hah+ ++ g+a+++l ++  +plV+t Hg +     +    +++ ++++  ++
  gi|242400032|ref|YP_002995457.1|  97 GLGDKLFRRYSIFIQQNKiEFDLIHAHFTWPSGYAAAKLSKEFSVPLVITGHGYD----IYELPFRGREWFKK-VKF 168
                                       4444444444444443336*****************99999**************....45555555566655.788 PP

                    Glyco_transf_4 130 llrradrviavSeatadelrerygvppekitVipnGvD 167
                                       +l++ad++++vS++    l +++++p++ki VipnG +
  gi|242400032|ref|YP_002995457.1| 169 ALDSADHIVTVSKSNFTILTTKLDIPEDKISVIPNGFN 206
                                       89**********************************87 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.5   0.0   1.2e-13   3.7e-10      68     160 .]     111     204 ..      73     204 .. 0.85

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 1.2e-13
                   Glyco_trans_4_4  68 rqrrerpdvvhahs.ptaglaarlarrrrgiplvvtlhglllrrgsgavrrlyralerrllrradavlvvseaeaee 143
                                       +q +  +d++hah  +++g+aa+ ++   ++plv+t hg +  +  ++++r +    +++l +ad++++vs +    
  gi|242400032|ref|YP_002995457.1| 111 QQNKIEFDLIHAHFtWPSGYAAAKLSKEFSVPLVITGHGYDIYEL-PFRGREWFKKVKFALDSADHIVTVSKSNFTI 186
                                       667788*******98****9999998899**********999877.555554445569******************* PP

                   Glyco_trans_4_4 144 lra.lgvpadrvvvvpng 160
                                       l+  l +p d++ v+png
  gi|242400032|ref|YP_002995457.1| 187 LTTkLDIPEDKISVIPNG 204
                                       **9999***********8 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 ?   -3.1   0.0       3.5     1e+04      49      65 ..     159     175 ..     147     182 .. 0.76
   2 !   31.8   0.0   4.8e-11   1.4e-07       3      80 ..     309     388 ..     305     395 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3.5
                   Glyco_trans_1_2  49 leelaekiryllanpee 65 
                                         e+ +k++++l++ + 
  gi|242400032|ref|YP_002995457.1| 159 GREWFKKVKFALDSADH 175
                                       57888999999988765 PP

  == domain 2  score: 31.8 bits;  conditional E-value: 4.8e-11
                   Glyco_trans_1_2   3 LnpsrsespnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraiaeaarerv 77 
                                       + ps se++ +++fEa++ G + + ++  g++e++  ++ ++l    d+e laeki ++l+ + +r++i++ a +++
  gi|242400032|ref|YP_002995457.1| 309 VLPSLSEGNPTVMFEALGVGLPFVGTAVGGVPEIIVSEDYGLLCPpaDPECLAEKILKALEKEWDREKIRKYAEQFT 385
                                       569999********************99***************999**********************999999887 PP

                   Glyco_trans_1_2  78 lae 80 
                                       +++
  gi|242400032|ref|YP_002995457.1| 386 WEN 388
                                       665 PP

>> Glyco_trans_4_2  Glycosyl transferase 4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.0   4.5e-11   1.4e-07      71     137 ..     113     178 ..     103     180 .. 0.85

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 4.5e-11
                   Glyco_trans_4_2  71 kkikPDvvhahyakpygllgslaar.lsgvipvvlsvwGldvlkfpkksk.lkklllklalkkatkvis 137
                                       +ki++D++hah ++p g++++ +++ +s  +p+v++ +G d+++ p++++ ++k+ +k+al +a+ + +
  gi|242400032|ref|YP_002995457.1| 113 NKIEFDLIHAHFTWPSGYAAAKLSKeFS--VPLVITGHGYDIYELPFRGReWFKK-VKFALDSADHIVT 178
                                       699*************998876666344..8******************975554.7999999998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.62u 0.26s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 2610.06
//
[ok]
